@article {pmid42599548, year = {2026}, author = {Medeiros, WB and Hidalgo-Martinez, KJ and Penna, DDPS and Oliveira, VM}, title = {Environmental filtering shapes biosynthetic potential and resistome of antarctic microbiomes.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {9}, pages = {}, pmid = {42599548}, issn = {1573-0972}, mesh = {Antarctic Regions ; *Microbiota/genetics ; Multigene Family ; Metagenome ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics ; Phylogeny ; Ecosystem ; Drug Resistance, Bacterial/genetics ; }, abstract = {Environmental filtering is a major driver of microbial community assembly in Antarctic ecosystems, yet its influence on biosynthetic potential and antimicrobial resistance remains poorly understood. Here, we analyzed 319 medium- to high-quality metagenome-assembled genomes (MAGs) recovered from four Antarctic sites (Whalers Bay, Crater Lake, Fumarole Bay, and Hannah Point) to investigate the relationship between geochemical gradients, biosynthetic gene clusters (BGCs), and antimicrobial resistance genes (ARGs). Integrating genome-resolved metagenomics, biosynthetic mining, resistome profiling, and environmental analyses, we identified 1,197 BGCs, with terpene clusters representing more than 25% of the total. Several biosynthetic hotspots were detected, including an Acidobacteriota MAG harboring 62 BGCs. Resistome composition exhibited strong site-specific structuring and was significantly associated with geochemical variables, particularly cobalt, iron, organic carbon, and thermal variation. Network analyses revealed highly connected MAGs affiliated with Pseudomonadota and Actinomycetota, linking diverse BGC and ARG classes. At the same time, genomic co-localization of biosynthetic and resistance determinants suggests potential adaptive associations between secondary metabolism and self-resistance mechanisms. Together, these findings demonstrate that environmental filtering shapes both the taxonomic and functional organization of Antarctic microbiomes and highlight polar ecosystems as reservoirs of unexplored biosynthetic diversity with potential biotechnological relevance.}, } @article {pmid42599752, year = {2026}, author = {Zhou, Y and Shao, Q and Liu, C and Tian, J and Guan, X and Zhang, X and Lu, J}, title = {Seasonal Dynamics of Community and Function of Gut Microbiome in Taihangshan Macaque (Macaca mulatta tcheliensis): Inferred From Metagenomic Data.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.70163}, pmid = {42599752}, issn = {1749-4877}, support = {No.31672302;No.32070446//National Natural Science Foundation of China/ ; }, abstract = {The gut microbiome is a key regulator of host nutritional intake, growth, and health, playing an essential role in mediating host adaptation to environmental changes. The northernmost population of rhesus macaque, Taihangshan macaque (Macaca mulatta tcheliensis), faces severe survival challenges, such as food shortages and harsh temperatures during winter and early spring. Previous studies have shown that they cope with seasonal changes through behavioral adaptations, such as adjusting food resources and flexibly regulating macronutrient intake. However, the role of the gut microbiome in supporting the seasonal adaptation of Taihangshan macaques remains unclear. Herein, we investigated seasonal variations in gut microbiome alpha diversity, composition, and functions from fecal samples of Taihangshan macaques using metagenomic analysis. The results showed that: (1) totally 435 non-redundant metagenome assembled genomes (MAGs) were generated; (2) alpha diversity was significantly higher in spring and winter than in summer and autumn; and (3) in winter, pathways of fatty acid biosynthesis and essential amino acid (EAA) biosynthesis, as well as CAZymes (GH3 and GH5) involved in cellulose and hemicellulose degradation, were significantly enriched. In contrast, pathways related to carbohydrate, energy, and glycan biosynthesis and metabolism, along with CAZymes (GT8 and GH23) potentially facilitating fat synthesis and storage, were enriched in summer. These functional adjustments likely help the host cope with seasonal variations in food availability and environmental conditions. Overall, this study provides new insights into how the gut microbiome responds to seasonal changes in diet and environmental factors in mammals inhabiting temperate forests.}, } @article {pmid42600417, year = {2026}, author = {Kasaiyan, S and Mateo, J and Buzzanca, D and Chiarini, E and Alessandria, V and Caro, I}, title = {Technological and microbial changes in cooked sausages incorporating cooked chickpea as a meat replacer and powdered banana pseudostem.}, journal = {Meat science}, volume = {242}, number = {}, pages = {110204}, doi = {10.1016/j.meatsci.2026.110204}, pmid = {42600417}, issn = {1873-4138}, abstract = {This study investigated the quality and microbial dynamics of vacuum-packaged cooked pork sausages reformulated by partially replacing meat protein (13%) with cooked chickpea paste and incorporating powdered banana pseudostem (BPS; 0%-0.4%) as a fibre source. Four sausages: Control (CON), CCP without BPS (CCP-0), and CCP with low (0.2%) or high (0.4%) BPS (CCP-BL and CCP-BH) were analysed over 20 days of refrigerated vacuum storage (3-7 °C). Composition, liquid retention, texture profile, colour, and microbial counts were evaluated. High-resolution shotgun metagenomics was applied to characterize bacterial and fungal dynamics. Composition and cooking yield remained unaffected by the reformulations (p > 0.05). However, substituting meat with cooked chickpea increased centrifugation loss (2 percentage points) and decreased hardness (2-3N), chewiness (∼3 N), and elasticity (0.04-0.05 units). Incorporating BPS increased initial product pH (up to 0.1 units), while decreasing lightness (up to 4 units). Initial total mesophilic bacterial counts were about 1 Log CFU/g higher in sausages with BPS and reached levels near 7 Log CFU/g across all batches by day 10. Adding chickpea supported the growth and survival of Enterobacteriaceae during storage. Shotgun metagenomics revealed that Brochothrix thermosphacta dominated the spoilage microbiota in CON and CCP-0 batches, exceeding 80% relative abundance by day 20. Conversely, BPS inclusion introduces plant-associated taxa (Klebsiella michiganensis and Pantoea rwandensis), significantly elevating alpha diversity and reducing B. thermosphacta percentage (< 20% relative abundance). While cooked chickpeas alter sausage textural characteristics, BPS serves as a functional fibre that modulates vacuum-packaged spoilage ecology.}, } @article {pmid42600516, year = {2026}, author = {Hu, Q and Wan, T and Liu, Y and Zhong, H and Chen, Y and Ao, Z and Jin, X and Guo, S}, title = {A real-world retrospective cohort study reveals the clinical utility of metagenomic next-generation sequencing in lower respiratory tract infections.}, journal = {Journal of infection and public health}, volume = {19}, number = {10}, pages = {103332}, doi = {10.1016/j.jiph.2026.103332}, pmid = {42600516}, issn = {1876-035X}, abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) are complicated by diverse pathogens, posing challenges to traditional diagnostics. However, robust evidence on LRTI pathogen spectra and metagenomic next-generation sequencing (mNGS) clinical utility remains limited.

METHODS: A retrospective analysis was conducted among 815 patients with suspected LRTIs who underwent mNGS and conventional microbiological testing(CMT) of bronchoalveolar lavage fluid. We evaluated the pathogen spectrum, the diagnostic value of mNGS across different infection categories, and its utility in guiding antibiotic therapy.

RESULT: Following exclusions, 754 patients demonstrated 84.5% mNGS positivity. mNGS detected DNA viruses (33.85%, EBV predominating), bacteria (30.83%), fungi (23.30%), mycobacteria (9.43%), and special pathogens (2.59%). Confirmed pathogens included Mycobacterium tuberculosis (n = 124), Candida albicans (n = 118), Pseudomonas aeruginosa (n = 87), Pneumocystis jirovecii (n = 65), Haemophilus influenzae (n = 50) and Aspergillus fumigatus (n = 48). mNGS showed higher positivity than CMT (84.5% vs 53.6%, P < 0.05), with sensitivities of 90.6% (LRTIs), 73.3% (bacterial), 74.7% (fungal), and 81.9% (tuberculosis); specificities were 22.6%, 56.5%, 73.5%, and 96.4%. Its high sensitivity but modest specificity necessitates cautious interpretation. mNGS guided treatment adjustments in 48.4% of patients, with higher rates in critically ill patients (60.1% vs 45.7%, P < 0.05), though clinical improvement was lower in this group (54.7% vs 79.2%, P < 0.05).

CONCLUSIONS: mNGS comprehensively detects pathogens in LRTIs, including bacteria, fungi, mycobacteria, DNA viruses, and special pathogens. While its broad diagnostic value and treatment guidance utility are significant, integration with clinical context is essential to distinguish true pathogens from colonization.}, } @article {pmid42600761, year = {2026}, author = {Hong, Z and Lu, Z and Shi, R and Zheng, S and Luo, J and Chen, J and Xie, Z and Zheng, JS and Chen, YM and Zhang, Z}, title = {Prospective associations of tea consumption with skeletal muscle mass and strength: Insights from the gut microbiome and proteomics.}, journal = {Pharmacological research}, volume = {231}, number = {}, pages = {108398}, doi = {10.1016/j.phrs.2026.108398}, pmid = {42600761}, issn = {1096-1186}, abstract = {Tea consumption may be associated with skeletal muscle health, but longitudinal evidence based on repeated assessments remains limited. We examined the associations of tea intake and serum biomarkers with repeated skeletal muscle measures and explored whether these associations might be partly explained by multi-omics features. In this prospective cohort, 3408 adults were followed for approximately 12 years. Skeletal muscle mass was measured by dual-energy X-ray absorptiometry, handgrip strength by digital dynamometry, gut microbial taxonomic and functional profiles by shotgun metagenomic sequencing, serum proteins by data-independent acquisition mass spectrometry, and fecal metabolites by targeted UPLC-MS/MS metabolomics. Linear mixed-effects models examined longitudinal associations, and mediation analyses estimated indirect effects. In longitudinal analyses, higher tea consumption frequency was associated with greater appendicular skeletal muscle mass, appendicular skeletal muscle index, and handgrip strength (β: 0.037-0.140; 95% CI: 0.002-0.205). Higher circulating flavan-3-ols showed similar associations with these muscle-related outcomes (β: 0.085-0.174; 95% CI: 0.007-0.254), whereas no significant associations were observed with walking speed. Exploratory multi-omics analyses identified tea-related differences in gut microbial species and functional pathways, fecal metabolites, and circulating proteins, including Gemmiger formicilis, amino acid biosynthesis pathways, fructose 1,6-bisphosphate, VTN, CFI, CNDP1, and ITIH4. Exploratory mediation analyses identified statistical indirect associations involving multi-omics features, with estimated proportions mediated ranging from 4.5% to 19.0%. Overall, higher tea consumption and circulating biomarkers were associated with greater skeletal muscle mass and strength, accompanied by distinct multi-omics features that may provide potential biological links between tea exposure and muscle-related outcomes.}, } @article {pmid42600856, year = {2026}, author = {Li, Y and Chen, L and Zhang, J and Zhang, Y and Wang, M and Zhang, R and Fang, W and Zhang, P and Zhang, G}, title = {Metagenomics reveals rumen residues as a superior inoculum for volatile fatty acid production in vitro.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135627}, doi = {10.1016/j.biortech.2026.135627}, pmid = {42600856}, issn = {1873-2976}, abstract = {Rumen microbiome is widely recognized as an efficient system for lignocellulose degradation. Rumen fluid (RF) has been often used as the inoculum in previous study of bioprocesses, however, the potential of rumen solids (RS) to enhance volatile fatty acid (VFA) production remains underexplored. The anaerobic fermentation performance of RS, RF, and RF + RS mixture as inocula was compared using corn stover as substrate, with RS addition at 5%, 10%, or 20% (w/w) to corn stover and RF addition at 1:2 (v/v) to buffer solution. At a corn stover content of 2.5% (w/v, based on final working volume), the highest VFA concentration of 10.05 g/L was achieved with 20% RS as inoculum, outperforming those with both RF and RF + RS. Metagenomic analysis revealed significant differences in bacterial, fungal, and archaeal community structures with 20% RS and RF. With 20% RS, hydrolytic bacteria (e.g., Enterobacter) dominated the ecological niche, microbial co-occurrence network analysis of the 2,000 most abundant genera revealed a simpler network with fewer negative associations, and functional analysis demonstrated a notable increase in relative abundance of glycosyltransferase (GT) families within carbohydrate-active enzymes (CAZymes). With 20% RS, enrichment in glycolysis-related genes was observed, indicating a preference for carbohydrate degradation, while acid-producing pathways were enriched such as pyruvate metabolism with RF. Rumen solids, as a superior inoculum for VFA production, effectively enhanced lignocellulose bioconversion by enriching specific low-abundance microbial taxa, forming a microbial network with fewer negative associations, increasing the relative abundance of GT families, and strengthening the systemic hydrolysis capacity.}, } @article {pmid42601406, year = {2026}, author = {Antman, T and Lewin-Epstein, O and Yerushalmi, T and Broder, YS and Zeevi, D}, title = {Global microbial DNA signatures of temperature and nutrient limitation across ecosystems.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42601406}, issn = {2058-5276}, abstract = {Microbial genomes continuously adapt to environmental conditions, but identifying universal signatures of adaptation remains challenging. Here we show that environmental temperature can be accurately predicted across ecosystems from DNA composition alone (R[2] = 0.75), using tetranucleotide frequencies from 1,235 marine and soil metagenomes and a machine learning approach. This predictive signal was also apparent within individual taxa, consistent with a fundamental temperature-associated signature. By contrast, GC content exhibited opposite correlations with temperature in soil (positive) and marine (negative) environments. This phenomenon was probably driven by differences in nutrient availability, as GC content increases with nutrients while nutrients decrease with temperature in marine samples. By integrating these observations, we identified specific tetranucleotides, with 50% GC, that displayed consistent and robust temperature correlations across environments and may have contributed to the stability of predictions. This work highlights metagenome-wide DNA-temperature associations, relevant for understanding microbial community responses to global changes.}, } @article {pmid42601613, year = {2026}, author = {Lotfi, M and Jalal, D and Sayed, AA}, title = {plsMD: a plasmid reconstruction tool from short-read assemblies.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {42601613}, issn = {1471-2105}, mesh = {*Plasmids/genetics ; *Software ; *Sequence Analysis, DNA/methods ; Genome, Bacterial ; Whole Genome Sequencing/methods ; }, abstract = {BACKGROUND: While whole genome sequencing has become a cornerstone of antimicrobial resistance surveillance, the reconstruction of plasmid sequences from short-read data remains a challenge due to repetitive sequences and assembly fragmentation. Current computational tools for plasmid identification and binning have limitations in reconstructing full plasmid sequences, hindering downstream analyses like phylogenetic studies and antimicrobial resistance gene tracking.

RESULTS: We present plsMD, a tool designed for full plasmid reconstruction from short-read assemblies. plsMD integrates Unicycler assemblies with replicon and full plasmid sequence databases to guide plasmid reconstruction through a series of contig manipulations. Using two datasets - an established benchmark dataset used in previous benchmarking studies and a novel dataset consisting of newly sequenced bacterial isolates - plsMD outperformed existing tools in both. In the benchmark dataset, it achieved excellent recall, precision, and F1 scores of 91.3%, 95.5%, and 92.0%, respectively. In the novel dataset, it achieved recall, precision, and F1 scores of 77.6, 88.9 and 74.5%, respectively. plsMD supports two usage modalities: single-sample analysis for plasmid reconstruction and gene annotation, and batch-sample analysis for phylogenetic investigations of plasmid transmission.

CONCLUSIONS: plsMD represents a significant advancement in plasmid analysis, offering a robust solution for utilizing existing short-read whole genome sequencing data to study plasmid-mediated antimicrobial resistance spread and evolution.}, } @article {pmid42601633, year = {2026}, author = {Albastaki, A and Naji, M and Moussa, M and Smith, J}, title = {Soil Microbiomes Across Depth and Ecosystems in Dubai, UAE: Potential Environmental Signatures for Forensic Geolocation.}, journal = {Environmental microbiology reports}, volume = {18}, number = {4}, pages = {e70403}, doi = {10.1111/1758-2229.70403}, pmid = {42601633}, issn = {1758-2229}, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Ecosystem ; Soil/chemistry ; Metagenomics ; Forensic Sciences ; Phylogeny ; }, abstract = {Soil microbial communities exhibit strong sensitivity to environmental gradients, yet their distribution across depth and land-use types in hyper-arid environments remains poorly characterised. Using whole-genome shotgun metagenomics via Oxford Nanopore Technologies long-read sequencing, we profiled soil microbial communities across six contrasting land-use sites in Dubai, UAE: urban, industrial (two locations), marine, desert and agricultural, where each sampled at three depth intervals (0-25 cm, 25-50 cm and 50-100 cm). Marine soils exhibited extreme salinity (EC 23.7-30.7 dS m[-1]) and the highest organic matter content (1.19%-1.76%), while desert soils were nutrient-poor with minimal salinity. Actinomycetota and Pseudomonadota co-dominated across all sites, collectively accounting for 77%-96% of classified sequences. Actinomycetota prevailed in undisturbed desert horizons (up to 53.4%), while Pseudomonadota dominated nutrient-enriched environments, reaching 69.4% at industrial sites. A notable compositional reversal was observed in the desert deep horizon (50-100 cm), where Pseudomonadota increased to 56.8%, departing from the expected oligotrophic depth gradient. PERMANOVA confirmed land use as the primary driver of community composition (p = 0.001), with depth exerting a secondary but significant effect (p ≤ 0.01). NMDS ordination revealed strong site-specific clustering, with each environment harbouring a distinctive microbial fingerprint with promising forensic geolocation potential.}, } @article {pmid42602060, year = {2026}, author = {Sahu, K and Yao, Q}, title = {metaIVP: an integrative metavirome focused metagenomic processing pipeline.}, journal = {BMC methods}, volume = {3}, number = {1}, pages = {37}, pmid = {42602060}, issn = {3004-8729}, abstract = {BACKGROUND: Metagenomic studies increasingly rely on complex, multi-tool pipelines to recover and characterize viral and non-viral genomes from mixed microbial communities. While these pipelines enable high-resolution genome recovery, limited functionality in downstream post-processing workflows and insufficient logging structures often hinder reproducibility, error tracing, and selective re-analysis. These challenges are particularly critical in metaviral analyses, where viral and non-viral genomes must be processed using distinct methodologies. To address these limitations, we introduce metaIVP, a modular, integrative, and flexible framework designed to systematically manage genome content purification, re-binning, quality assessment, and downstream analyses of viral and non-viral metagenomic contexts.

METHODS: The metaIVP framework is organized into hierarchical modules, each governed by dedicated log files that explicitly control execution state and re-runnability. Contig-level and bin-level analytical and purification steps are implemented as essential modules to isolate genome contents, followed by separate viral and non-viral post-processing workflows. Viral workflows incorporate contamination detection, genome quality evaluation, host prediction, and virus-specific binning. Non-viral analyses include genome binning, alignment and mapping statistics, genome quality assessment, and replication rate estimation. Checkpoints are explicitly defined such that deletion of selected module- or sub-module-level logs enables targeted re-execution of specific analytical steps without rerunning the full pipeline. All analyses are integrated to depict a comprehensive system in the metagenomic samples, with focus on the metaviromic information.

RESULTS: The usage of metaIVP was demonstrated using both a well-controlled human gut virome dataset and a geographically structured environmental metavirome dataset, showing its broad applicability across host-associated and environmental systems. The pipeline effectively separates viral and non-viral genomic content, improves viral bin purity, and preserves sample-specific functional, taxonomic, and host-association features after virome enrichment. Compared with recent state-of-the-art approaches, metaIVP achieves comparable performance, particularly when optional re-binning with vRhyme is applied, while maintaining a higher fraction of high-confidence viral bins.

DISCUSSION: The metaIVP addresses a key gap in metavirome analysis by jointly characterizing viral and non-viral genomic components and supporting integrative downstream analyses within a single framework. Its user-friendly, modular, and controllable design allows flexible execution and provides a foundation for incorporating additional downstream analytical tools as metavirome methodologies continue to evolve.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s44330-026-00090-7.}, } @article {pmid42602126, year = {2026}, author = {Ortúzar, M and Formariz, V and Suescún-Sepúlveda, JA and González-Hernández, M and Riesco, R and Garrido-Oter, R and Trujillo, ME}, title = {From natural assemblages to synthetic communities in the Lupinus microbiome.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1891479}, pmid = {42602126}, issn = {1664-462X}, abstract = {INTRODUCTION: Plant roots harbour complex microbial communities that enhance nutrient acquisition, stress tolerance, and pathogen defence, yet their assembly and functional dynamics remain incompletely understood.

RESULTS: In this work, we isolated over 700 bacterial strains from wild Lupinus angustifolius across multiple compartments and soil types, capturing both dominant and rare bacterial taxa. Using co-occurrence network analysis, we selected representative strains to assemble synthetic communities (SynComs) of varying complexity, which were inoculated under sterile and non-sterile conditions. Plants were inoculated with SynComs of increasing complexity under both non-sterile soil and gnotobiotic conditions. SynCom inoculation reshaped root-associated microbiota, moderately influenced the rhizosphere, and had limited impact on bulk soil communities. Increasing SynCom complexity enhanced plant growth and triggered host transcriptional responses involving hormone signaling, defence pathways, and metabolic reprogramming.

DISCUSSION: These findings indicate that soil-driven filtering and microbial interactions govern microbiome assembly and plant responses. Incorporating taxa with distinct ecological roles, including low-abundance members, improves SynCom functionality and advances understanding of plant-microbe interactions in natural and agricultural systems.}, } @article {pmid42602195, year = {2026}, author = {Maitray, A and Rishi, P and Conrady, CD and Binkley, E and Williams, BK and Yeh, S and Nicola, MD and Finger, PT}, title = {Vitreoretinal Lymphoma: A Comprehensive Clinical Review and Current Standards in Management.}, journal = {Journal of vitreoretinal diseases}, volume = {}, number = {}, pages = {24741264261474159}, pmid = {42602195}, issn = {2474-1272}, abstract = {PURPOSE: To summarize current evidence on clinical features, multimodal imaging findings, diagnostic techniques, and management strategies for vitreoretinal lymphoma.

METHODS: A literature review was performed to provide updated information on available treatment options for vitreoretinal lymphoma.

RESULTS: Diagnosis of vitreoretinal lymphoma requires vitreous biopsy, with or without retinal/subretinal tissue, for cytology and immunohistochemistry, along with ancillary tests such as flow cytometry, cytokine profiling (interleukin-10/interleukin-6 ratio >1), immunoglobulin heavy chain gene rearrangement analysis, and detection of the MYD88 L265P mutation. Optical coherence tomography and other multimodal imaging techniques have become increasingly useful in raising suspicion, guiding biopsy, and monitoring treatment response. No standardized treatment protocol exists for isolated vitreoretinal lymphoma. Management options include intravitreal chemotherapy (methotrexate and/or rituximab), radiation therapy, and systemic chemotherapy, often showing a good initial response, but relapse and subsequent central nervous system (CNS) involvement are common, resulting in poor overall prognosis and survival. For vitreoretinal lymphoma with CNS disease, current strategies favor high-dose methotrexate-based systemic chemotherapy, with or without intrathecal chemotherapy; whole-brain radiation is generally reserved as rescue therapy. Emerging directions for earlier diagnosis include metagenomic deep sequencing, and chimeric antigen receptor T-cell (CAR-T) therapy has shown promise for treatment of selected relapsed/refractory cases of primary CNS lymphoma with a potential to prolong survival.

CONCLUSIONS: Treatment of vitreoretinal lymphoma requires a multidisciplinary, individualized approach that integrates multimodal imaging, cytologic and molecular diagnostics, CNS evaluation, and tailored local or systemic therapy. Prospective multicenter studies are needed to refine diagnostic algorithms and standardize management.}, } @article {pmid42594461, year = {2026}, author = {Lu, D and Chen, B and Nie, E and Lian, S and Li, R and Guo, R and Fu, S}, title = {Indole inhibits anaerobic digestion by disrupting AHLs-mediated quorum sensing.}, journal = {Journal of hazardous materials}, volume = {516}, number = {}, pages = {143267}, doi = {10.1016/j.jhazmat.2026.143267}, pmid = {42594461}, issn = {1873-3336}, abstract = {The emerging understanding highlights indole as a disruptive factor to quorum sensing (QS) mechanisms, prompting further investigation into its role in anaerobic digestion (AD) system inhibition. However, relevant studies are still scarce and the potential mechanism linking indole and AD inhibition remains unclear. This study showed that indole (1, 2, and 3 mM) significantly reduced cumulative methane production by 8.47-51.89% and extended the lag phase by 1.34-6.68 days. Time-series AHLs quantification, metagenomics, and circular clustering heatmaps analysis revealed that indole might disrupt microbial communication between hydrolysis-acidification bacteria and acetoclastic methanogens by reducing the AHLs level (C6-HSL, 3-oxo-C8-HSL, C10-HSL, C12-HSL, 3-oxo-C10-HSL, and C18-HSL). Notably, indole degradation alleviated the inhibition of C10-HSL, C18-HSL, and 3-oxo-C10-HSL, which might restore hydrolysis and acidification and mitigate AD inhibition. Exogenous AHLs (1 and 5 µM) restored methane production by 48.44-55.59% in 3 mM indole-inhibited reactors (p < 0.05), while the quorum quenching agent vanillin further reduced methane production by 72.55%, suggesting that AHLs play an important role in helping microorganisms resist indole stress. These findings highlight the importance of AHLs-mediated inter-microbial communication in counteracting indole-inhibited methanogenesis inhibition, suggesting potential practical strategies to enhance AD stability and efficiency in challenging conditions.}, } @article {pmid42595035, year = {2026}, author = {Mao, H and Deng, Y and Wang, X and Yu, Q and Zhao, Z and Zhang, Y}, title = {Two-phase anaerobic digestion with sub-thermophilic hydrolysis: Regulating metabolites to accelerate electron transfer and enhance methanogenesis.}, journal = {Environmental research}, volume = {307}, number = {}, pages = {125448}, doi = {10.1016/j.envres.2026.125448}, pmid = {42595035}, issn = {1096-0953}, abstract = {Sub-thermophilic anaerobic digestion accelerates the hydrolysis and acidogenesis of complex substrates to improve methane production, but methanogens may be inhibited under such condition. Two-phase anaerobic digestion (TPAD) system can decouple the hydrolytic-acidogenic and methanogenic phases to optimize microbial activity in each phase. Therefore, in this study, a novel temperature-phased strategy combining a 45°C hydrolytic-acidogenic phase with a 37°C methanogenic phase (TPAD45°C/37°C) was developed to accelerate the degradation of agricultural waste and avoid the sub-thermophilic temperature-induced inhibition of methanogenesis. Results showed that 45°C hydrolytic phase increased ethanol and acetate production, and decreased propionate production compared to the 37°C control. Consequently, at a solid retention time of 20 days, the methane yield in the TPAD45°C/37°C group was 31.8% and 13.0% higher than that in the TPAD37°C/37°C and TPAD45°C/45°C groups, respectively. Mechanistically, the TPAD45°C/37°C group exhibited the highest McrA activity and coenzyme F420 content, indicating superior methanogenic activity. Furthermore, Tafel polarization and temperature-dependent conductivity analyses revealed that the higher levels of ethanol from 45°C hydrolysate provided a stronger thermodynamic driving force to minimize the energy barrier and improve intrinsic electron transfer rates, thereby enhancing methanogenesis. Additionally, the TPAD45°C/37°C group exhibited the highest overall metabolic potential. Microbial community analysis revealed that this system enriched the methanogens, which in turn promoted the degradation of complex substrates and increased methane production. This study provided an economically viable, energy-positive, and highly resilient technological strategy for the sustainable valorization of agricultural waste.}, } @article {pmid42595117, year = {2026}, author = {Hashimoto, M and Oki, H and Kawahara, K and Fujii, KK and Koide, T}, title = {Molecular basis of collagen triple helix recognition by VWF A-like domain 2 of collagen VII: Implications for interlaced anchoring fibril formation.}, journal = {The Journal of biological chemistry}, volume = {}, number = {}, pages = {113448}, doi = {10.1016/j.jbc.2026.113448}, pmid = {42595117}, issn = {1083-351X}, abstract = {Anchoring fibrils formed by collagen VII play a critical role in stabilizing the dermal-epidermal junction. The N-terminal non-collagenous (NC1) domain of collagen VII binds firmly to basement membrane components including collagen IV and has also been reported to interact with mesenchymal fibrillar collagens via its von Willebrand factor A-like domain 2 (A2 domain). To elucidate how collagen VII recognizes fibrillar collagen, we performed yeast two-hybrid screening using a triple-helical random peptide library, which resulted in the identification of a Met-Gly-Φ (Φ; aromatic amino acid residue) motif. Biochemical analysis with synthetic triple-helical peptides revealed a binding preference of Trp > Phe as the Φ residue by the A2 domain despite Trp being absent in native collagens. The crystal structure of the A2 domain in complex with the Nle (Met surrogate)-Gly-Trp-containing peptide revealed a unique mechanism by which two distinct hydrophobic pockets of the A2 domain accommodate the Nle and Trp residues corresponding to the Met-Gly-Φ motif, engaging all three chains of the triple helix. Subsequent molecular dynamics simulations demonstrated that the A2 domain recognizes the corresponding native Met-Gly-Phe motif in a similar manner, but with lower affinity, implying a transient interaction with mesenchymal collagens. The findings obtained in this work suggest models in which transient A2-triple helix interaction promotes the recruitment of collagen I and III fibrils into the arc-shaped structure of anchoring fibrils. This also provides a foundation for linking structural understanding to skin fragility diseases caused by collagen VII dysfunction.}, } @article {pmid42595349, year = {2026}, author = {Yang, Z and Ramakrishnan, M and Wang, B and Wei, Q and Ahmad, Z}, title = {Optimized Controlled-Release Fertilization Improves Productivity and Reshapes the Rhizosphere Microbiome in Lei Bamboo: A Metagenomic Assessment.}, journal = {Environmental microbiology}, volume = {28}, number = {8}, pages = {e70401}, pmid = {42595349}, issn = {1462-2920}, support = {2018YFD060010403//National Key Research and Development Program of China/ ; 2021F1065-10//Special Project of Zhejiang Provincial Scientific Research Institutes/ ; }, mesh = {*Fertilizers/analysis ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Poaceae/microbiology/growth & development ; Nitrogen/metabolism ; Metagenomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; Soil/chemistry ; Urea/metabolism ; }, abstract = {Intensive nitrogen fertilization in Lei bamboo (Phyllostachys praecox) plantations has increased productivity but has also reduced nitrogen-use efficiency (NUE), accelerated nutrient losses, and contributed to soil degradation. How nutrient-release strategies influence rhizosphere microbiome assembly and ecosystem functioning remains poorly understood. Here, we developed a bamboo shoot-specific controlled-release fertilizer (CRF) and evaluated different urea-CRF blending ratios to identify sustainable fertilization strategy for Lei bamboo production. Mixed CRF-urea treatments outperformed both sole-fertilizer applications and the unfertilized control. T2 (30% urea + 70% CRF) achieved the highest shoot yield, whereas T3 (50% urea + 50% CRF) enhanced NUE. Optimized fertilization improved soil nutrient availability and organic matter accumulation without significantly affecting soil pH. Metagenomic analysis revealed the enrichment of taxa associated with nutrient transformation, organic matter turnover, and plant growth. However, pathway-level analysis revealed shifts in carbon, nitrogen, and sulfur cycling activities under optimized nutrient-release regimes. Our results demonstrate that synchronizing nitrogen release with plant and microbial demand enhances rhizosphere function, productivity and NUE. T2 delivered the strongest overall agronomic performance by maximizing shoot yield while maintaining improved nutrient retention and ecological stability. These findings provide a mechanistic link between fertilization strategy, rhizosphere microbial dynamics, and ecosystem function, supporting sustainable Lei bamboo production.}, } @article {pmid42595408, year = {2026}, author = {McQueen, AD and Calomeni-Eck, AJ and Cicerrella, AS and Chung, SH and Malmfeldt, MP and Lindsay, DL and Gong, P}, title = {Enhancing early-season detection of harmful algal blooms caused by sediment-borne overwintering cyanobacteria using metagenomic and qPCR tools.}, journal = {Harmful algae}, volume = {158}, number = {}, pages = {103160}, doi = {10.1016/j.hal.2026.103160}, pmid = {42595408}, issn = {1878-1470}, mesh = {*Harmful Algal Bloom ; *Cyanobacteria/genetics/classification/physiology ; *Geologic Sediments/microbiology ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics/analysis ; Seasons ; Lakes/microbiology ; Real-Time Polymerase Chain Reaction/methods ; Polymerase Chain Reaction ; }, abstract = {To better inform adaptive management strategies for harmful algal blooms (HABs), there is a critical need to improve detection capabilities of bloom risks earlier in the growing season. Emerging molecular tools such as metagenomic Next-Generation Sequencing (NGS) and amplification-based quantitative polymerase chain reaction (qPCR) can accurately identify the taxonomy of cyanobacteria and akinetes of which the latter are particularly challenging to distinguish morphologically and estimate their abundance. This study aimed to evaluate the contribution of these advanced molecular tools to assessing the presence, density, and planktonic growth potential of overwintering cyanobacterial cells in sediments from historically HAB-impacted waterbodies in the USA. We conducted 14-day incubation experiments using field-collected lake sediments and characterized cyanobacterial taxonomy and abundance in the sediments (pre-incubation) and overlying water (post-incubation) using light microscopy, genus-specific qPCR, and 16S rRNA amplicon sequencing. By analyzing qualitative and quantitative results, we not only identified the prevailing cyanobacterial genera that moved from sediment to water column over the incubation but also determined their relative abundance and the cyanobacterial genera consistent between sediment and water column. This study demonstrated that metagenomic and qPCR tools provided additional lines of evidence to augment traditional microscopy and improved taxonomic identification and quantification. Our approach can better inform planktonic growth potential of problematic cyanobacteria to enhance early detection capabilities, and guide targeted countermeasures taken to improve preventative or remedial HAB management, reducing environmental and public health impacts.}, } @article {pmid42595551, year = {2026}, author = {Wang, L and Yang, J and Li, D and Zhang, F and Yan, JA and Wang, YY and Sun, J and Cao, H}, title = {[Tremella fuciformispolysaccharide retards the progression of colorectal cancer by regulating the gut microbiota-metabolome axis].}, journal = {Zhonghua zhong liu za zhi [Chinese journal of oncology]}, volume = {48}, number = {8}, pages = {975-982}, doi = {10.3760/cma.j.cn112152-20250925-00485}, pmid = {42595551}, issn = {0253-3766}, support = {MS2024064//Jiangsu Province Science and Technology Development Program of Traditional Chinese Medicine (General Project)/ ; YJZ202305//the Jiangnan University Affiliated Hospital Research-Oriented Hospital Medical Research Project (General Project)/ ; KX-25-C166//Wuxi City 2025 Soft Science Research Project/ ; }, mesh = {Animals ; *Colorectal Neoplasms/pathology/metabolism/microbiology/drug therapy/chemically induced ; Humans ; Mice ; HT29 Cells ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Polysaccharides/pharmacology ; NF-kappa B/metabolism ; Male ; *Basidiomycota/chemistry ; *Metabolome/drug effects ; Azoxymethane ; Apoptosis/drug effects ; Dextran Sulfate ; Cell Proliferation/drug effects ; Feces/chemistry/microbiology ; Disease Progression ; Colon/pathology/metabolism ; }, abstract = {Objective: To investigate the anti-colorectal cancer effect of tremella fuciformis polysaccharides (TFP) via the gut microbiota-metabolite axis. Methods: Colorectal cancer was induced in C57BL/6J mice using azoxymethane/dextran sulfate sodium. TFP or distilled water was administered by gavage for 3 weeks. Disease activity index (DAI), colon length, tumor burden, histopathology, gut microbiota (metagenomics), fecal metabolites (untargeted metabolomics), and colonic protein expression (Western blot) were assessed. Pyridoxic acid's effect on HT-29 cells was tested in vitro. Results: TFP significantly reduced DAI [2.0(1.8, 3.3) vs. 3.5(2.8, 4.5), P＜0.01], increased colon length [(7.2±1.1) vs. (5.5±0.5) cm, P＜0.05], lowered pathological score [6(3, 8) vs. 9(8, 10), P＜0.05], and decreased tumor number [2(1, 3) vs. 4(3, 4), P＜0.05] and volume [(11.02±7.88) vs. (24.99±3.38), P＜0.01]. Metagenomics revealed that TFP significantly reshaped gut microbiota (R[2]=0.173, P=0.027), enriching Candidatus Amulumruptor, Helicobacter, and Akkermansia. Metabolomics showed distinct profiles (R[2]=0.159, P=0.004), with pyridoxic acid elevated 1.20 fold (P＜0.001). Pyridoxic acid suppressed HT-29 cell viability and migration, and correlated positively with several upregulated bacteria, suggesting a microbiota-metabolite axis underlying its anti-tumor effect. TFP downregulated nuclear factor-κB (NF-κB) (P＜0.01) and upregulated phosphorylated AMP-activated protein kinase alpha (p-AMPKα) (P＜0.001), BAX (P＜0.001), and cleaved caspase-3 (P＜0.05). Conclusion: TFP inhibits colorectal cancer progression by modulating gut microbiota, elevating pyridoxic acid, suppressing NF-κB, and activating AMPK-mediated apoptosis.}, } @article {pmid42595815, year = {2026}, author = {Vasquez, YM and Nardi, T and Terasaki, GM and Byl, P and Brůna, T and Villada, JC and Romero-Gutiérrez, MF and Mock, T and James, TY and , and Woyke, T and Schulz, F}, title = {Genomic catalogue of giant viruses reveals expanded diversity and functional potential.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42595815}, issn = {2058-5276}, support = {Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, abstract = {Nucleocytoplasmic large DNA and Mirusviricota viruses exhibit taxonomic richness which continually expands due to metagenomic sequencing. Here we curate a database of giant virus metagenome-assembled genomes (GVMAGs V2), comprising 8,508 species-level representatives from 18,727 GVMAGs, a sixfold increase from the previous giant virus phylogenetic frameworks. Phylogenomics revealed 712 previously undescribed genera, 13 previously unknown viral families and an order we propose named Mycodnavirales. By accounting for alternative and custom genetic codes, we improved gene calling in over 1,300 GVMAGs, enabling more accurate identification of protein-coding genes. Database mining uncovered putative endogenous viral elements in hosts spanning algae, fungi and parasitic protists, highlighting that giant virus integration is widespread and evolutionarily persistent. Protein-level analysis revealed enriched genes for pollutant degradation in Algavirales and widespread biosynthetic gene clusters linked to antimicrobial-like and antibiotic resistance gene-like activity. This public resource will serve as a foundation for expanding giant virus diversity, uncovering virus-host interactions and exploring viral evolution.}, } @article {pmid42595818, year = {2026}, author = {Cumbo, F and Blankenberg, D}, title = {Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {42595818}, issn = {1546-1696}, support = {U24HG006620//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; U24CA231877//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; }, abstract = {Accurately characterizing metagenome-assembled genomes remains a substantial challenge due to the presence of sequencing errors, incomplete assembly and contamination. Here, we present MetaSBT, a tool for organizing, indexing and characterizing microbial reference genomes and metagenome-assembled genomes, demonstrated in this study using viruses. MetaSBT identifies clusters of genomes across all seven taxonomic levels using the Sequence Bloom Tree data structure, which relies on Bloom filters to index large amounts of genomes based on their k-mer composition. We built an initial set of databases composed of over 190,000 viral genomes from public sources, grouped into sequence-consistent clusters at different taxonomic levels. We defined over 40,000 candidate species, ~80% of which, to our knowledge, do not match viral species in reference databases to date. Furthermore, we showed that our databases are useful to existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. The open-source framework and databases are fully integrated into the Galaxy platform.}, } @article {pmid42595876, year = {2026}, author = {Knuth, D and Mäder, P and Boekhorst, J and Poll, C and Kandeler, E and Alaoui, A and Pasković, I and Polić Pasković, M and Baldi, I and Bureau, M and Alcon, F and Contreras, J and Glavan, M and Abrantes, N and Campos, I and Norgaard, T and Huerta Lwanga, E and Geissen, V and Harkes, P}, title = {Beneath the surface: non-target effects of multiple pesticides on the soil microbiome in organic and conventional agricultural European fields.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {42595876}, issn = {1614-7499}, support = {862568//HORIZON EUROPE Framework Programme/ ; }, abstract = {Previous studies have shown that diverse cocktails of pesticide mixtures are omnipresent in agricultural soils yet miss a clear link to the effects on the soil microbiome. In this study, we linked the occurrence of pesticides in conventional and organic agricultural soils of the SPRINT (Sustainable plant protection transition) projects' Case Study Sites to the composition and function of soil microbial communities. Metagenomic sequencing, phospholipid fatty acids analysis and enzyme activity measurements were used to characterize the soil microbiome and effects of site-specific parameters such as pH and SOC, and pesticide residues. Differences in the soil microbiome were strongly influenced by the geographic origin of the samples, with the pH value as dominant driver. Against our hypothesis, effects of the investigated management systems were limited, yet significant at the European level. Notably, an association between some pesticides could still be observed after accounting for the variation explained by the environmental factors. Among these, especially fungicides, with modes of action that aim to interfere with processes in microorganisms, seemed to affect the soil microbiome. This might occur either by directly affecting these processes in non-target organisms or by changing co-dependencies between fungi and bacteria. Next to fungicides, aminomethylphosphonic acid showed a significant effect on the soil microbial composition and an interactive, possibly synergistic effect with the persistent pesticide hexachlorobenzene. The latter raises concerns about a possible interaction of recently applied pesticides and persistent "legacy" pesticides. This work highlights that even though environmental parameters can overshadow the effects of pesticides, especially the identity of the pesticides present, can have an influence on the soil microbiome.}, } @article {pmid42597171, year = {2026}, author = {Wang, T and Liang, H and Wu, Y and Zhang, X and Zhang, S and Wei, Z and Li, W and Song, W and Luo, Z and Al-Dalali, S}, title = {Multi-omics profiling of microbial ecology and non-volatile compounds across fermentation stages of spontaneous litchi (Litchi chinensis Sonn.) fermented vinegar-like beverage.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1908193}, pmid = {42597171}, issn = {2296-861X}, abstract = {INTRODUCTION: Litchi fruit vinegar-like beverages (LVBs) are notable processed products derived from litchi fruit, yet few studies have focused on the systematic characterization of microbial and metabolic dynamics during their natural fermentation process.

METHODS: This work employed a comprehensive methodology integrating metagenomics and untargeted metabolomics based on UHPLC-MS/MS (Orbitrap Q Exactive HF-X) to elucidate the dynamic profiles of the microbial community and non-volatile metabolites, as well as their interrelations, across the various spontaneous fermentation stages of LVBs.

RESULTS: Metagenomic analysis indicated reduced microbial diversity and substantial structural changes within the community. Bacteria dominated the fermentation, accounting for 69.16 - 99.04% of the microbial community based on the taxonomically classified reads at the kingdom level. During the preliminary stage, Leuconostoc, Enterobacter, and Klebsiella were the prevalent genera. During the mid-fermentation stage, Komagataeibacter and Lactiplantibacillus emerged as the predominant genera in acid production. In the final stage, the microbial community was dominated primarily by Zymomonas and the Acetobacteriaceae family, including Acetobacter and Komagataeibacter. The non-targeted metabolomics study identified 2,382 metabolites through comprehensive database matching (in-house library, HMDB, KEGG, and metDNA algorithm) and stringent quality filtering (identification score > 0.5 and QC CV < 0.5), which were categorized into 20 distinct groups. Thirty seven metabolites, including amino acids, organic acids, and benzene derivatives, were identified as probable distinct differential metabolites based on a p-value threshold of p < 0.05, VIP > 1.0, and a fold change (FC ≥ 2 or ≤ 0.5) between consecutive fermentation stages in pairwise OPLS-DA of litchi vinegar-like beverage fermentation. Spearman correlation analysis revealed a highly organized ecological interaction network among dominant bacteria, physicochemical parameters, and non-volatile taste metabolites in the LVB fermentation system. Zymomonas mobilis, Acetobacter pasteurianus, Leuconostoc suionicum, and Lactiplantibacillus plantarum facilitated fermentation through metabolic synergy. Meanwhile, stage-specific enrichment of distinct Enterobacteriaceae species (Enterobacter hormaechei, and Enterobacter quasiroggenkampii) reflected species-level niche differentiation and resource competition, rather than a unified family-wide competitive behavior.

DISCUSSION: These findings provide a theoretical framework for engineering synthetic consortia and bioaugmentation approaches, informing the selection of starters and co-cultures to enhance LVB sensory and bioactive properties, alongside facilitating sfruit valorization.}, } @article {pmid42597276, year = {2026}, author = {Ding, Y and Li, Q and He, F and Zheng, Q and Zhao, G and Wan, J and Fang, Y and Yang, T and Zou, L and Yu, W and Dai, J}, title = {The Impact of Human Immunodeficiency Virus Co‑Infection on the Pathogen Spectrum and Outcomes of Severe Community‑Acquired Pneumonia: Insights from Metagenomic Next‑Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {599541}, pmid = {42597276}, issn = {1178-6973}, abstract = {PURPOSE: Severe community-acquired pneumonia (SCAP) causes high morbidity and mortality. Metagenomic next-generation sequencing (mNGS) data comparing pathogen profiles in SCAP between people living with human immunodeficiency virus (HIV) (PLWH) and HIV-uninfected individuals remain scarce.

PATIENTS AND METHODS: We retrospectively enrolled 72 SCAP patients at Kunming Third People's Hospital. We compared alpha diversity of respiratory microbiota, pathogen spectrum and healthcare resource utilization (HRU) between the two groups. We also assessed whether HIV infection was an independent risk factor for 30-day mortality.

RESULTS: mNGS detected pathogens in 70 of 72 patients (97.2%). PLWH showed higher detection rates of Pneumocystis jirovecii (p < 0.001), Human gammaherpesvirus 4 (EBV) (p = 0.013), and Human betaherpesvirus 5 (CMV) (p < 0.001). Among the 54 SCAP patients who survived 30 days, HRU metrics did not differ between groups. Elevated D-dimer level was an independent risk factor for 30-day mortality in SCAP patients (hazard ratio [HR]: 1.02, 95% confidence interval [CI]: 1.004-1.030; p = 0.0127).

CONCLUSION: HIV co‑infection in SCAP patients is associated with a distinct pathogen spectrum but does not affect HRU or 30‑day mortality. Elevated D‑dimer level is an independent risk factor for 30‑day mortality in SCAP patients.}, } @article {pmid42597328, year = {2026}, author = {Wu, B and Lu, S and Liu, H}, title = {Precision diagnostics in bronchiectasis: current advances in imaging, microbiology, biomarkers, and digital health.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1907636}, pmid = {42597328}, issn = {2296-858X}, abstract = {Bronchiectasis is a complex, chronic airway syndrome driven by a vicious cycle of irreversible bronchial dilatation, impaired mucociliary clearance, recurrent infection, and tissue-destructive inflammation. Reflecting its profound clinical heterogeneity, patients with identical structural damage on high-resolution computed tomography (HRCT) often exhibit divergent profiles in airway microbiology, inflammatory endotypes, exacerbation frequencies, and therapeutic responses, indicating that static anatomical classification fails to capture disease complexity. Sole reliance on visual CT inspection, standard sputum cultures, and subjective symptom tracking misses the driving mechanisms of individual disease progression. Emerging modalities-artificial intelligence (AI)-driven quantitative imaging, molecular microbiology, high-throughput biomarker profiling, and digital remote monitoring-aim to address these gaps. Our analysis shows that while these tools cannot substitute for bedside clinical acumen, they clarify obscure phenotypes, expose actionable treatable traits, and enable earlier, preemptive strategies. This review evaluates these contemporary diagnostic frameworks in non-cystic fibrosis bronchiectasis, dissecting their clinical utility, evidentiary maturity, and the economic and logistical barriers to routine adoption. Given that current evidence remains fragmented, advancing the field demands standardized imaging protocols, transparent algorithmic pipelines, clinically actionable metagenomic reporting, and robust validation in underrepresented Asian and Chinese cohorts. The real challenge lies not in generating more data, but in integrating these heterogeneous, high-dimensional datasets into pragmatic, point-of-care decision pathways that improve patient outcomes without widening disparities in global healthcare delivery.}, } @article {pmid42597565, year = {2026}, author = {Okonta, EO and Nnadi, CO and Paul-Chima, UO}, title = {The gut microbiome as a plausible but unproven moderator of cinnamon trial outcomes in type 2 diabetes: toward phytochemical standardization and precision nutraceuticals.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1874182}, pmid = {42597565}, issn = {2296-861X}, abstract = {Cinnamon (Cinnamomum spp.) has been widely investigated as an adjunctive nutraceutical for glycemic management in type 2 diabetes mellitus, yet clinical findings remain inconsistent. This variability is commonly attributed to differences in cinnamon species, dosage, intervention duration, baseline glycemic status and phytochemical standardization, alongside methodological factors such as trial quality, dietary patterns, medication use, adherence and endpoint selection. One potential contributor that has received limited attention is the gut microbiome. We propose a testable hypothesis that a substantial proportion of the marked inter-trial heterogeneity observed in cinnamon meta-analyses (I[2] > 75%) may reflect underlying gut-microbial metabotypes differing in their ability to convert cinnamon polyphenols and procyanidins into bioactive metabolites. Type 2 diabetes is associated with altered microbial composition, reduced butyrate-producing taxa and disrupted metabolic pathways. Cinnamon phytochemicals, including polyphenols, cinnamaldehyde, procyanidins and coumarin, undergo microbial biotransformation that may influence their bioavailability and metabolic effects. Because cinnamaldehyde is rapidly absorbed in the proximal gastrointestinal tract, colon-targeted delivery systems may be required to rigorously evaluate microbiome-mediated mechanisms. No randomized controlled trial has directly examined whether microbiome composition modifies cinnamon's glycemic effects in type 2 diabetes. Future studies should therefore incorporate microbiome-informed designs, including phytochemical fingerprinting, safety monitoring and, where feasible, metagenomic and metabolomic profiling, to distinguish true biological non-response from intervention heterogeneity and advance precision nutraceutical approaches for diabetes management.}, } @article {pmid42597686, year = {2026}, author = {Annaswamy, V and Mikesh, M and Dinkeloo, K}, title = {The Microbiome of Nurdles: Life on the Primary Microplastics of the Texas Gulf Coast.}, journal = {microPublication biology}, volume = {2026}, number = {}, pages = {}, pmid = {42597686}, issn = {2578-9430}, abstract = {Nurdles are small, pre-production plastic pellets. Globally, nurdles are the second largest source of microplastic pollution due to release during manufacture and transport. As these nurdles persist in the environment, they undergo weathering-a process that significantly increases surface area and colonization by microbes. To gain an understanding of the composition of the microbiome found on nurdles, full-length 16S targeted metagenomic sequencing was performed on DNA extracted from nurdles collected from the Texas Gulf Coast. Sequencing data showed a greater amount and diversity of microbes found to be associated with nurdles than with the sand from which the nurdles were collected.}, } @article {pmid42597889, year = {2026}, author = {Ren, S and Ren, S and Chen, H and Zhang, W and Zhang, T and Chong, H and Wang, Z and Cao, W and Yong, X and Zhou, J}, title = {SuSha: A multi-model ensemble learning framework for predicting microbial salinity adaptation.}, journal = {Engineering microbiology}, volume = {6}, number = {3}, pages = {100292}, pmid = {42597889}, issn = {2667-3703}, abstract = {Current research on microbial salinity adaptation faces substantial challenges, including the limited predictive accuracy of traditional single-gene models and difficulty in dissecting systemic biological responses to salinity stress in complex natural habitats. To overcome these bottlenecks, the multi-model ensemble learning tool SuSha, which leverages genome-wide amino acid composition features, was developed. By extracting features from the whole-genome data of 123 bacterial and archaeal species with well-defined salinity adaptations, a 24-dimensional feature vector was constructed, comprising the frequencies of 20 standard amino acids and four aggregated functional categories. Based on this, an ensemble model was developed by integrating algorithms such as random forest, bagging, and extra trees. Five-fold cross-validation demonstrated that this 24-dimensional feature-based ensemble model achieved a global accuracy of 0.765 and an area under the curve of 0.941, significantly outperforming individual baseline models. Furthermore, the model was externally validated using 2678 metagenomic samples from six global regions, encompassing freshwater, marine, and hypersaline habitats. SuSha exhibited high robustness, ecological consistency across diverse salinity gradients, and a classification accuracy of over 90% for extreme halophiles, particularly within the extreme halophilic range. By enabling high-precision genotype-to-phenotype predictions using a habitat-adaptive algorithm-switching strategy, SuSha provides a robust computational framework for inferring the physiological potential of uncultivated microorganisms and mining microbial resources in extreme environments.}, } @article {pmid42598143, year = {2026}, author = {Mollick, SA and Khual, GK and Ghosh, A and Patel, SK and Bhattacharyya, S and Roy, CS and Maile, A and Nagarajaram, HA and Longkumer, M and Babu, MN and Kundapur, AR and Uniyal, S and Chattterjee, A and Mitra, M and Sikdar, M and Urade, BP and Pulamaghatta, VN}, title = {Gut microbial diversity and candidate keystone taxa in Indian tribes: Insights across lifestyle-ecological continuum and health associations.}, journal = {Current research in microbial sciences}, volume = {11}, number = {}, pages = {100650}, pmid = {42598143}, issn = {2666-5174}, abstract = {Despite the critical role of the gut microbiome in host physiology and health, it remains poorly characterized in Indigenous populations undergoing rapid acculturation. This study presents high-resolution, whole-genome metagenomic profiling of gut microbiota from five Particularly Vulnerable Tribal Groups (PVTGs) of Southern India, Irula, Jenu Kuruba, Kurumba, Chenchu, and Konda Savara, spanning distinct ecological zones and cultural transitions. Using an ecology-lifestyle continuum framework, we investigated taxonomic and functional diversity with a focus on identifying computationally inferred candidate keystone taxa, defined by their association with variation in community ordination structure. A leave-one-taxon-out ordination framework identified 121 candidate keystone taxa, many of which were population-specific and have not been widely reported. Functional analyses revealed a conserved core of metabolic pathways, including glycolysis and folate biosynthesis, alongside group-specific enrichment in xenobiotic degradation, amino acid biosynthesis, mucin metabolism, and lipid processing, associated with differences in dietary and environmental exposures across populations. Large-scale disease-association mapping (n = 5,625) linked 50 candidate keystone taxa to 14 conditions, with 44 associated with health and 6 with disease. While Fusicatenibacter saccharivorans and Alistipes shahii were enriched in healthy states, Ruminococcus gnavus, Bifidobacterium longum, Flavonifractor plautii, and Blautia wexlerae were enriched in disease-associated profiles. Cross-cohort validation against an independent set of traditional metagenomes (n = 119) further showed that a subset of Indian tribal core candidate keystone taxa was consistently identified across geographically distinct populations, with partial conservation of community associations and health associations, indicating reproducible context-dependent microbial association patterns across traditional populations. Alpha diversity was highest in minimally acculturated groups, with higher degrees of acculturation associated with reduced microbial diversity and greater enrichment of disease-associated taxa. Overall, this study provides a context-aware framework for understanding gut microbiome dynamics in culturally transitioning populations, emphasizing the conservation of microbial heritage and informing population-specific microbiome-based interventions.}, } @article {pmid42598172, year = {2026}, author = {Udahemuka, JC and Cassidy, H and Schuele, L and Uwibambe, E and Ngabo, MG and Masirika, LM and Sindayiheba, R and Otani, S and Gashegu, M and Twizere, JC and Aarestrup, F and Ndayisenga, F and Oude Munnink, BB and Koopmans, MPG and Ndishimye, P}, title = {Persistent circulation of Rift Valley fever virus lineage C in Rwanda, 2022-2025.}, journal = {One health (Amsterdam, Netherlands)}, volume = {23}, number = {}, pages = {101529}, pmid = {42598172}, issn = {2352-7714}, abstract = {Rwanda has experienced recurrent Rift Valley fever virus outbreaks in the last decade. In this study, we investigated whether these outbreaks resulted from repeated introductions or sustained local circulation. We generated RVFV whole-genome sequences from livestock samples collected between 2022 and 2025 using Nanopore sequencing. Genomic analyses indicated the outbreaks resulted from sustained local circulation of lineage C rather than repeated introductions, suggesting ongoing transmission likely driven by sporadic spillover. This study underscores the importance of continuous genomic One Health surveillance in endemic settings.}, } @article {pmid42598412, year = {2026}, author = {Wang, X and Chen, W and Zhang, H and Cao, D and Sun, J and Hu, H}, title = {Gut microbial biomarkers for major depressive disorder: a cross-sectional study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1690285}, pmid = {42598412}, issn = {2235-2988}, mesh = {Humans ; *Major Depressive Disorder/microbiology/diagnosis/virology ; *Biomarkers/analysis/blood ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Female ; Adult ; Male ; Metagenomics ; Bacteria/genetics/classification/isolation & purification ; Middle Aged ; Viruses/genetics/classification/isolation & purification ; Feces/microbiology/virology ; }, abstract = {BACKGROUND: Alterations in the gut microbiota have been associated with a variety of psychiatric disorders, including major depressive disorder (MDD). However, the relationship between MDD and gut microbial communities remains incompletely understood. Most previous studies have primarily focused on gut bacteria, with relatively limited attention to other microbial components.

METHODS: In this study, we analyzed gut microbial profiles from 36 patients with MDD and 36 healthy controls using metagenomic sequencing data. The MaAsLin2 algorithm was applied to identify potential microbial biomarkers associated with MDD.

RESULTS: A total of 6 bacterial biomarkers and 7 viral biomarkers were identified. The models based on these features demonstrated strong predictive performance, with area under the curve (AUC) values of 0.891 for bacteria and 0.878 for viruses. Notably, the combined bacterial-viral model achieved an AUC of 0.946. These findings were further evaluated through external testing in two unrelated research cohorts. In the Shanxi cohort, the AUC values were 0.825 (bacteria), 0.803 (viruses), and 0.972 (combined model). In the Wuhan cohort, the AUC values were 0.683 (bacteria), 0.693 (viruses), and 0.784 (combined model).

CONCLUSION: In summary, our results highlight the potential of gut bacterial and viral biomarkers as candidate biomarkers and potential auxiliary tools for MDD assessment and suggest that integrating multi-domain microbial features may improve prediction accuracy.}, } @article {pmid42598558, year = {2026}, author = {Abbasi, H and Hawn, SE and Javanbakht, A and Seedat, S and Bourassa, K and Sinnott, SM and Seligowski, AV and Hemmings, S and Kimbrel, NA and Wolf, E and Smith, AK and Brick, L and Mehta, D}, title = {From molecules to minds: Integrative multi-omics in psychiatry.}, journal = {Journal of mood and anxiety disorders}, volume = {15}, number = {}, pages = {100194}, pmid = {42598558}, issn = {2950-0044}, abstract = {Psychiatric disorders are biologically complex conditions arising from interactions across genomic, epigenomic, transcriptomic, proteomic, metabolomic, and metagenomic layers. Single-omics approaches rarely capture more than a fraction of the variance in complex conditions, underscoring the importance of integrative multi-omics frameworks. This mini-review summarizes key methodologies and their application in psychiatric research, with a focus on systems-level integration of genomic risk scores, transcriptomic networks, and neuroimaging data to advance biological understanding of disorders such as depression, schizophrenia, and Alzheimer's disease. We also outline the infrastructural requirements for effective multi-omics research, including standardized biobanking, Laboratory Information Management Systems, adherence to FAIR data principles, and federated learning approaches for privacy-preserving analysis. Importantly, we highlight the need for greater global inclusivity in psychiatric genomics. Current datasets are heavily biased toward relatively high-resourced and predominantly White, non-Hispanic populations, limiting generalizability. Initiatives such as the Psychiatric Genomics Consortium-Africa and H3ABioNet demonstrate how locally led efforts can strengthen capacity, promote data sovereignty, and support equitable research practices. Advancing multi-omics psychiatry will require coordinated investment in infrastructure, training, and inclusive international collaboration. This mini-review serves primarily as a conceptual roadmap, highlighting what integrative approaches have demonstrated so far and future directions for the field.}, } @article {pmid42598885, year = {2026}, author = {Baidya, AK and Aich, P}, title = {Serum-Cecal Metabolome Integration Predicts Gut Microbial Communities and Reveals Pathway-Level Host-Microbe Crosstalk Under Disease-Induced Dysbiosis.}, journal = {Omics : a journal of integrative biology}, volume = {}, number = {}, pages = {15578100261479266}, doi = {10.1177/15578100261479266}, pmid = {42598885}, issn = {1557-8100}, abstract = {The gut microbiome shapes systemic physiology through metabolites that enter circulation, yet most computational approaches focus on predicting metabolite profiles from microbial features rather than inferring microbial composition from host metabolomes. Here, we investigate whether host-derived metabolomic profiles can be leveraged to predict gut microbial community structure and to determine how disease-associated dysbiosis reshapes metabolite-microbe interactions and gut-to-systemic metabolic communication. We developed an integrative multi-omics framework combining serum and cecal metabolomics with 16S rRNA-based microbiome profiling. Supervised learning models demonstrated that cecal metabolites carry predictive signals for microbial abundances across conditions. Regularized canonical correlation analysis (rCCA) revealed cross-compartment metabolite-microbe networks. These analyses showed both conserved and condition-specific interaction patterns, indicating substantial network reorganization under disease-associated dysbiosis. Pathway-level integration further identified metabolic pathways linking the gut microbiome, the cecal environment, and the systemic circulation, representing coordinated gut-to-systemic communication axes. Together, our results establish a multi-omics strategy for predictive inference of gut microbial composition from host metabolomes and provide a framework for identifying pathway-level mechanisms underlying host-microbe metabolic crosstalk.}, } @article {pmid42599000, year = {2026}, author = {Wang, W and Jiang, L and Niu, T and Zhang, M and Chen, L and Jia, X and Yuan, L and Tian, K and Li, X}, title = {Resolving the Phylogenetic Placement of the FSfaCV/PCV5-Related Viruses Within the Genus Macochavirus.}, journal = {Transboundary and emerging diseases}, volume = {2026}, number = {1}, pages = {e8481347}, doi = {10.1155/tbed/8481347}, pmid = {42599000}, issn = {1865-1682}, support = {2023YFD1800500//National Key Research and Development Program of China/ ; 32500538//National Natural Science Foundation of China/ ; D18007//111 Project/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, mesh = {Animals ; *Phylogeny ; Genome, Viral ; Swine ; *Swine Diseases/virology/epidemiology ; China/epidemiology ; *DNA Viruses/genetics/classification ; Circovirus/genetics ; }, abstract = {Metagenomic analysis of fecal samples from diarrheic pigs in China identified 10 complete circular single-stranded DNA viral genomes previously designated as putative porcine circovirus 5 (PCV5)-like viruses. Genome characterization revealed a typical cressdnavirus organization with bidirectionally oriented Rep and Cap genes. Phylogenetic analyses based on complete genomes and encoded proteins showed that these viruses do not cluster with members of Circoviridae but instead form a distinct lineage within the family Pecoviridae, closely related to the genus Macochavirus. Sequence identity, genetic distance, and nucleotide diversity analyses supported their classification as a coherent viral group. Comparative analyses indicated greater sequence divergence in the Rep region than in the Cap region. These findings support reclassification of putative PCV5 as a porcine-associated lineage within the genus Macochavirus, designated porcine Macochavirus (PMV), thereby resolving their long-standing taxonomic ambiguity and expanding the recognized diversity of cressdnaviruses within the family Pecoviridae.}, } @article {pmid42599081, year = {2026}, author = {Buddhasiri, S and Singhla, T and Pengpanun, S and Eiamsam-Ang, T and Thiennimitr, P}, title = {Shotgun metagenomic sequence data from milk and fecal samples of dairy cattle in Thailand.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0056426}, doi = {10.1128/mra.00564-26}, pmid = {42599081}, issn = {2576-098X}, abstract = {We report shotgun metagenomic sequence data from milk and fecal samples of dairy cattle in Thailand. This data set captures microbial genetic profiles from mammary- and gut-associated sample types and provides a resource for future comparative microbiome, functional, and antimicrobial resistance gene analyses in dairy cattle.}, } @article {pmid42599332, year = {2026}, author = {Lee, SY and Hwang, S and Cho, I and Lee, H and Lee, J and Koo, D and Kim, JW and Cho, KS}, title = {Functional dynamics and interactions within the bacterial community responsible for biodegradable plastic degradation during aerobic composting.}, journal = {Biodegradation}, volume = {37}, number = {4}, pages = {}, pmid = {42599332}, issn = {1572-9729}, support = {RS-2025-02311604 & RS-2025-07902968//Ministry of Trade, Industry and Energy/ ; }, mesh = {*Composting ; Biodegradation, Environmental ; Aerobiosis ; *Bacteria/metabolism/genetics/classification ; *Biodegradable Plastics/metabolism ; Polyesters/metabolism ; Polyhydroxybutyrates ; Sewage/microbiology ; *Plastics/metabolism ; }, abstract = {Though biodegradable plastics have been widely developed as sustainable alternatives to petroleum-based plastics, their degradation behavior and microbial interactions in composting environments remain insufficiently understood. In this study, the degradation characteristics of polyhydroxybutyrate (PHB), polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), and polybutylene succinate (PBS), and the interactions between bacterial communities and functional genes, were evaluated in a 41-day aerobic composting system using anaerobically digested sewage sludge as substrate. Composting parameters were similarly affected by all biodegradable plastics, and the final compost reached a Solvita compost maturity index of 8.0 with no detectable pathogenic bacteria and a CO2 index of 7.83, indicating stable composting. After 41 days of composting, microcracks and microbial attachment were observed on all biodegradable plastic surfaces, with PHB and PBAT showing the most pronounced structural damage and biofilm formation, whereas microbial attachment to PLA was limited. Although biodegradable plastic addition did not greatly alter the overall bacterial community structure, it selectively promoted specific bacterial genera (Symbiobacterium, Paenibacillus, and Psychrobacillus). PICRUSt2-based functional gene prediction revealed that PHB degradation-related genes exhibited the highest predicted abundance, whereas PLA- and PBS-related genes showed low abundance, indicating differences in functional degradation potential among plastic types. Positive correlations among esterase- and hydrolase-related genes under biodegradable plastic-amended conditions suggest that coordinated microbial functional responses to biodegradable plastic addition. Network analysis further indicated that biodegradable plastic addition influenced interactions between specific bacterial genera and degradation-related functional genes. Overall, this study provides insights into bacterial functional adaptation during biodegradable plastic degradation under aerobic composting conditions.}, } @article {pmid42586034, year = {2026}, author = {Ibarbalz, FM and Pierella Karlusich, JJ}, title = {Genes from the deep: Evolution's untapped biotechnology.}, journal = {Cell host & microbe}, volume = {34}, number = {8}, pages = {1486-1488}, doi = {10.1016/j.chom.2026.07.004}, pmid = {42586034}, issn = {1934-6069}, mesh = {*Biotechnology ; Metagenomics/methods ; Evolution, Molecular ; *Bacteria/genetics ; }, abstract = {The deep sea, Earth's largest yet least-explored biome, harbors vast microbial diversity. In this issue of Cell Host & Microbe, Guo et al. uncover its hidden functional potential through metagenomics guided by AI-predicted protein folds, while Eriksson et al. reveal how microbial diversity is structured across latitude and depth.}, } @article {pmid42586263, year = {2026}, author = {Zhou, Y and Guo, Q and Zhao, X and Zhang, W and Zhang, H and Huang, S and He, Z and Xie, Y and Zhang, W and Gu, J and Pan, S and Li, W}, title = {Blood and gut virome remodeling in gastric cancer: Anellovirus expansion and novel virus discovery.}, journal = {Virologica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.virs.2026.08.010}, pmid = {42586263}, issn = {1995-820X}, abstract = {Gastric cancer (GC) is a prevalent malignancy worldwide, yet effective early diagnostic tools remain lacking, and the role of the virome, a key component of the tumor microenvironment, in GC progression is largely unknown. This study aimed to characterize the virome landscapes in peripheral blood and feces of GC patients versus healthy controls, and to identify viral signatures associated with GC onset and metastasis. We performed viral metagenomic sequencing on pooled libraries from 100 GC patients (45 non-metastatic, 55 metastatic) and 50 healthy controls, followed by taxonomic annotation, diversity assessment, LEfSe differential abundance testing, and co-occurrence network analysis. In blood, the GC virome shifted from a bacteriophage-dominated profile in controls to one overwhelmingly dominated by Anelloviridae (> 80%), with significantly decreased alpha diversity. In contrast, the gut virome of GC patients showed increased alpha diversity and coexistence of diverse bacteriophages. LEfSe identified betatorquevirus in blood as a key discriminatory taxon for GC. Network analysis revealed negative correlations between Anelloviridae and multiple bacteriophage families, suggesting niche competition. We also discovered 67 provisional novel anellovirus species and one novel gemykibivirus in GC patient blood. Collectively, our findings indicate that GC is associated with compartment-specific virome remodeling in blood and gut, and that expansion of blood anelloviruses holds promise as a non-invasive biomarker. This study provides a foundational resource for understanding the virome's role in GC.}, } @article {pmid42586379, year = {2026}, author = {Zhuo, Q and Wei, R and Su, Y and Shao, H and Han, L and Huang, G}, title = {Responses of biogeochemical cycles to polyethylene microplastics exposure during aerobic fermentation of dairy manure.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135605}, doi = {10.1016/j.biortech.2026.135605}, pmid = {42586379}, issn = {1873-2976}, abstract = {Microplastics (MPs) are emerging contaminants that may disrupt Earth's biogeochemical cycles of elements, yet their effects on multi-element cycling during aerobic fermentation of livestock manure remain unclear. This study evaluated how polyethylene (PE) MPs and fermentation strategy affected multi-element functional potential during aerobic fermentation of dairy manure solids by integrating metagenomic functional profiling, co-occurrence networks, and other complementary approaches. Fermentation time dominated functional gene succession, with treatment separation becoming most evident on day 30. Biomarkers were confined to the C cycling and detected only in the low concentration treatments, with none at the higher concentration. Network analysis revealed predominantly positive associations among genes involved in different elemental cycles. The membrane-covered treatment at the lower concentration formed the most connected network. The pathway profiles and network topology in the membrane-covered treatment at the higher concentration were similar to those of the blank control. This suggests that, under high MPs exposure, the membrane-covered treatment retained a functional profile similar to the blank control, likely in association with the more stable fermentation conditions in the membrane-covered treatment. Physicochemical properties, process variables, and gas emissions jointly explained 78% of functional gene variation. Mantel tests and structural equation modelling further linked fermentation conditions, gas emissions, and multi-element functional potential. Overall, multi-element functional responses to MP exposure varied with fermentation stage, strategy, and PE MP concentration. These findings highlight the importance of fermentation management when assessing multi-element functional responses to MP exposure during manure valorization.}, } @article {pmid42586589, year = {2026}, author = {Carsello, EA and Liston, K and Maust, B and Deutsch, G and Wright, J and Wong, S and Morgan, L and Vora, S}, title = {Balamuthia mandrillaris presenting as central nervous system vasculitis in a young child.}, journal = {BMJ case reports}, volume = {19}, number = {8}, pages = {}, doi = {10.1136/bcr-2026-275051}, pmid = {42586589}, issn = {1757-790X}, mesh = {Humans ; *Vasculitis, Central Nervous System/parasitology/diagnosis ; Male ; *Balamuthia mandrillaris/isolation & purification/genetics ; *Amebiasis/diagnosis/parasitology/complications/drug therapy ; Brain/pathology/parasitology ; Diagnosis, Differential ; }, abstract = {Balamuthia mandrillaris is a rare and difficult-to-diagnose infection with high mortality. We present the case of an immunocompetent toddler presenting with central nervous system (CNS) vasculitis. He was initially diagnosed with Takayasu arteritis and had an initial period of improvement following immunosuppressive therapy. Subsequently, he had rapid decompensation with diffuse intracranial lesions progressing to severe neurological injury and compassionate extubation. Metagenomic sequencing of the CSF and pathology and PCR from brain biopsy were positive for B. mandrillaris To our knowledge, this is the first case of Balamuthia presenting as a mixed vessel CNS vasculitis and highlights the importance of consideration of this infection in cases of vasculitis, particularly in mixed vessel disease. It further demonstrates the potential use of newer diagnostics, namely CSF metagenomic testing and amoeba PCR, in earlier diagnosis and treatment.}, } @article {pmid42586639, year = {2026}, author = {Humayun, S and Justine, EE and Rjabovs, V and Lee, HJ and Darko, CNS and Reile, I and Kim, YJ and Tuvikene, R}, title = {Gut-protective efficacy of red algal galactans: The role of structure and molecular weight.}, journal = {Carbohydrate polymers}, volume = {389}, number = {}, pages = {125609}, doi = {10.1016/j.carbpol.2026.125609}, pmid = {42586639}, issn = {1879-1344}, mesh = {Molecular Weight ; Humans ; *Galactans/chemistry/pharmacology/isolation & purification ; *Rhodophyta/chemistry ; Animals ; Caco-2 Cells ; Oxidative Stress/drug effects ; Rheology ; Mice ; }, abstract = {Linking structure, rheology, and bioactivity, this study demonstrates how red algal galactans can be tailored as functional food ingredients with gut-protective potential. Funoran and furcellaran were isolated from Gloiopeltis furcata and Furcellaria lumbricalis, respectively, and characterized using chromatographic and NMR spectroscopic techniques. Funoran was identified as a highly sulfated, methoxylated agaran (22.7% sulfate), whereas furcellaran exhibited a hybrid κ-/β-carrageenan structure (17.4% sulfate). High molecular weights (3955 and 2966 kDa) were observed and reduced via controlled autohydrolysis without sulfate loss. Structural variations governed rheological behavior, with furcellaran showing ion-dependent gelation and funoran forming weaker networks. Both native and depolymerized galactans were non-cytotoxic to Caco-2 cells, maintained tight junction integrity, and reduced oxidative stress. In a DSS-induced colitis model, treatments alleviated clinical symptoms, decreased pro-inflammatory cytokines and MPO activity, and restored barrier-related proteins. Metagenomic analysis revealed partial correction of dysbiosis, including enrichment of short-chain fatty acid producing taxa, particularly in depolymerized funoran. Overall, structural features and molecular weight critically determine both rheological and biological functions. Depolymerization enhances fermentability while preserving bioactivity, highlighting red-algal galactans as promising multifunctional hydrocolloids for food and gut health applications.}, } @article {pmid42586789, year = {2026}, author = {Deas, G and Macgregor, K and Kite, D and Ward, H and May, A and Powell, M and Jenkins, M}, title = {HIV-associated CD8 encephalitis: role of metagenomics in complex CNS presentations.}, journal = {Practical neurology}, volume = {}, number = {}, pages = {}, doi = {10.1136/pn-2026-005308}, pmid = {42586789}, issn = {1474-7766}, abstract = {We describe a 54-year-old woman living with HIV who presented with a tonic-clonic seizure and rapidly progressive encephalitis. Despite an undetectable plasma viral load while taking Biktarvy, initial investigations revealed cerebrospinal fluid escape with an HIV viral load of 474 copies/mL. Extensive testing for opportunistic infections and autoantibodies was negative. Brain biopsy and metagenomic next-generation sequencing identified frequent CD8+ T-cell infiltration and human pegivirus, though the latter was deemed a bystander. The patient's condition improved significantly, notably without the high-dose corticosteroids typically required for CD8+ encephalitis. This recovery suggests a moderate, self-limiting phenotype of the disease. The case highlights the diagnostic utility of metagenomics in complex presentations while cautioning against the misinterpretation of non-pathogenic commensals.}, } @article {pmid42587158, year = {2026}, author = {Sinha, T and Brushett, S and Fernández-Pato, A and Garmaeva, S and Andreu-Sánchez, S and Spreckels, JE and Mallon, CA and Kuzub, N and Gois, MB and Wu, J and Kruk, M and Jankipersadsing, SA and Dekens, JAM and Gacesa, R and Vila, AV and Bang, C and Perenboom, C and Franke, A and Tytgat, HLP and Mottaz, SC and Peters, L and de Jonge, A and Verkade, HJ and Swertz, MA and Wijmenga, C and Kuipers, F and Scherjon, S and Sikkema, J and Sprikkelman, AB and de Kroon, MLA and Prins, JR and Gordijn, SJ and Koppelman, GH and Reijneveld, SA and , and Fu, J and Yassour, M and Kurilshikov, A and Zhernakova, A}, title = {Maternal influences on infant gut microbiome and health.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {42587158}, issn = {1476-4687}, abstract = {The establishment of the infant gut microbiome is critical for later health[1,2], yet how it is shaped by maternal and early-life factors remains unclear. Here we metagenomically sequenced 4,526 longitudinal faecal samples from 714 mother-infant pairs in the Dutch birth cohort Lifelines NEXT, spanning 12 weeks of pregnancy to 1 year postpartum. We integrated these data with 474 clinical and exposure variables, and with ultra-deep sequencing of breast milk and vaginal microbiomes. We observe that the maternal gut microbiome undergoes only subtle changes during pregnancy and postpartum, influenced by diet, infections and pre-pregnancy smoking. The maternal gut microbiome is a major reservoir for infant gut strains, with only occasional transmission from vaginal and breast milk microbiomes. Mother-infant gut strain sharing is time dependent, and higher maternal gut species abundance increases the likelihood of strain transmission. We find that the maternal gut microbiome is a predictor of infant eczema. Mode of delivery and feeding mode primarily shaped the infant gut microbiome and its functional profiles, with maternal exposures also having a role. Of 585 vaginally delivered infants, 155 were born at home, but home delivery was only moderately associated with infant gut microbiome composition, similar to other birth parameters such as duration of pushing and ruptured membranes. Overall, we highlight the central role of the mother and her microbiome in shaping the infant gut ecosystem and early health outcomes.}, } @article {pmid42587419, year = {2026}, author = {Chang, H and Yang, Y and Zhang, P and Lei, Z and Zhang, Y and Li, S and Wang, L and Wang, Y and Jiang, J and Li, L and Shi, H and Shi, A}, title = {Disrupted Gut Viral-Bacterial Ecology of Patients With Liver Cirrhosis.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {46}, number = {9}, pages = {e70836}, doi = {10.1111/liv.70836}, pmid = {42587419}, issn = {1478-3231}, support = {2025JC-YBQN-1179//Natural Science Basic Research Program of Shaanxi Province/ ; 2025SCIPT-63//Scientific Research Supporting Fund of the Second Affiliated Hospital of Xi'an Jiaotong University/ ; }, mesh = {Humans ; *Liver Cirrhosis/microbiology/virology ; *Virome ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Bacteria/genetics ; Case-Control Studies ; Metagenome ; Metagenomics ; Male ; }, abstract = {BACKGROUND: The gut microbiota contributes to liver cirrhosis (LC), yet the gut virome and its cross-kingdom ecology with bacteria are less well defined.

METHODS: To characterize LC-associated virome alterations and assess their clinical relevance, we reanalyzed publicly available faecal metagenomes from patients with LC and healthy controls. After quality control and removal of human reads, sequences were mapped to the Chinese Gut Viral Catalogue at 95% nucleotide similarity, viral operational taxonomic units (vOTUs) were annotated using the latest ICTV framework, and viral functions were inferred by KEGG annotation. Differential vOTUs and bacterial species, virus-bacteria networks and random forest classifiers were constructed with internal and external validation.

RESULTS: LC showed reduced viral richness and Shannon diversity, and a distinct Bray-Curtis separation from controls. Ten viral families and 473 vOTUs differed between groups (59 LC-enriched). KEGG-based profiling highlighted functional shifts in LC-enriched viruses, including increased K01185 (lysozyme) and K02172 (blaR1). Virus-bacteria networks were markedly sparser in LC than in controls (130 vs. 509 significant correlations). A virome-based random forest model distinguished patients from controls with high accuracy in internal (optimal AUC = 0.911) and external (optimal AUC = 0.773) validation cohorts, and the model combining viral and bacterial features achieved similarly robust performance.

CONCLUSIONS: LC is associated with disrupted gut viral-bacterial ecology, and virome features show promise as non-invasive biomarkers, warranting longitudinal and mechanistic follow-up.}, } @article {pmid42587714, year = {2026}, author = {Becherucci, V and Romano, F and Russo, E}, title = {Artificial Intelligence for Integrated Analysis of Non-Blood Biological Fluids: From Biomarker Discovery to Clinical Decision-Support Systems.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {15}, pages = {}, doi = {10.3390/diagnostics16152478}, pmid = {42587714}, issn = {2075-4418}, abstract = {The analysis of non-blood biological fluids, including cerebrospinal fluid (CSF), serous effusions, and synovial fluid, plays a central role in laboratory medicine by providing essential diagnostic and prognostic information for neurological, infectious, inflammatory, and neoplastic diseases. However, the interpretation of these specimens remains challenging because it requires the integration of heterogeneous biochemical, cytological, microbiological, molecular, and clinical data, often in the absence of standardized analytical workflows. Artificial intelligence (AI), particularly Machine Learning (ML) and Deep Learning (DL), is emerging as a powerful approach for extracting clinically relevant information from complex multidimensional datasets beyond the capabilities of conventional analytical methods. AI-driven Clinical Decision-Support Systems (CDSSs) can integrate laboratory findings with clinical, demographic, imaging, and multi-omics data, supporting diagnostic interpretation, patient stratification, and personalized clinical decision-making. At the same time, the convergence of AI with proteomics, metabolomics, metagenomics, and other omics technologies is accelerating biomarker discovery and advancing precision laboratory medicine. Current evidence indicates different levels of maturity across biological fluids. AI-assisted interpretation of CSF biomarkers and digital cytology of serous effusions currently show the strongest clinical evidence, whereas applications involving synovial fluid and integrated multi-omics remain largely exploratory. Although important technical, methodological, and regulatory challenges still limit widespread clinical implementation, AI has the potential to improve diagnostic accuracy, reduce interpretative variability, and support more integrated diagnostic workflows. This mini-review summarizes current and emerging AI applications in non-blood biological fluid analysis, with particular emphasis on biomarker discovery, CDSS, multi-omics integration, current evidence, existing limitations, and future perspectives for precision laboratory medicine.}, } @article {pmid42587989, year = {2026}, author = {Zhang, X and Sun, L and Yang, L and Li, X and Cao, Z and Pan, C}, title = {Identification of Key Microorganisms and Metabolic Pathways Associated with the Formation of Off-Flavour Compounds in the Pit Mud of Strong-Flavour Baijiu.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {15}, pages = {}, doi = {10.3390/foods15152731}, pmid = {42587989}, issn = {2304-8158}, support = {231111112000//Henan Province/ ; }, abstract = {Off-flavours represent one of the most prevalent and severe causes of deteriorating pit mud quality in Strong-Flavour Baijiu production. However, the key compounds responsible for these off-flavours and their formation mechanisms remain poorly understood, thereby limiting quality control in the production process of Strong-Flavour Baijiu pit mud. To investigate the origin of off-flavours in pit mud, this study employed gas chromatography-mass spectrometry coupled with metagenomic methods to compare samples from normal and off-flavoured pit mud. The results show that the main cause of off-flavours in pit mud is the abnormal accumulation of acids such as heptanoic acid and hexanoic acid due to imbalanced nutrient ratios, along with insufficient synthesis of key esters including ethyl hexanoate, ethyl butyrate, and ethyl lactate; microorganisms such as Fermentimonas, Methanoculleus, Hortaea and Proteiniphilum, which are non-strictly anaerobic and acid-sensitive in the pit mud, are key microbes associated with these odour compounds. Furthermore, based on the annotation from the KEGG database, this study further inferred the possible microbial metabolic pathways that could lead to the formation of these off-flavour compounds, including starch and cellulose degradation pathways, biosynthesis pathways of valine, leucine, and isoleucine, pyruvate metabolism pathways, and butyric acid metabolism pathways. In summary, the study systematically analysed the key substances related to the odour of the pit mud of strong-flavour Chinese Baijiu and its microbial sources, providing a theoretical basis for the quality regulation of the pit mud during production and developing high-quality artificial pit mud.}, } @article {pmid42587998, year = {2026}, author = {Lefèvre, H and Fadhlaoui, K and Guez, JS and Lainé, E and Beyssac, E}, title = {Resistance of Bamboo Fibers to Gastrointestinal Digestion and Their Nutrient-Dependent Fermentation by Human Gut Microbiota.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {15}, pages = {}, doi = {10.3390/foods15152740}, pmid = {42587998}, issn = {2304-8158}, abstract = {Bamboo fibers are increasingly incorporated into food products as sustainable dietary fiber ingredients, yet their gastrointestinal digestion resistance and fermentative behavior by human gut microbiota remain insufficiently characterized. This study combined an INFOGEST-based in vitro digestion protocol with colonic fermentation using fecal microbiota from three healthy donors as an exploratory donor panel. Bamboo fibers were resistant to salivary, gastric, and intestinal enzymatic hydrolysis, as demonstrated by the absence of structural modifications in FTIR spectra, preserved morphology observed by scanning electron microscopy, and negligible release of reducing sugars (<0.1 g/L across all digestive phases), in contrast to extensively hydrolyzed wheat starch used as a positive control. During in vitro colonic fermentation, microbial responses were strongly dependent on substrate availability. In nutrient-limited minimal medium, bamboo fiber supplementation increased gas production, acidification, and SCFA formation compared with control conditions. Concomitantly, SCFA concentrations increased under minimal-medium conditions, although the magnitude of the response varied among donors, with the strongest changes observed for donor 1 (acetate reaching 5.4 vs. 3.3 g/L and propionate 1.48 vs. 0.76 g/L). These effects were markedly attenuated in nutrient-rich medium, indicating competition with readily fermentable substrates. Beta-diversity analyses and metagenomic profiling revealed that microbial community composition clustered primarily according to donor identity rather than experimental conditions. SEM further showed surface erosion and microbial attachment on fermented fibers, supporting partial structural alteration. Overall, bamboo fibers are resistant to upper gastrointestinal digestion but display context-dependent fermentative activity by human gut microbiota under carbohydrate-limited conditions, highlighting the importance of inter-individual variability, dietary context and substrate availability in determining their fermentative potential.}, } @article {pmid42588064, year = {2026}, author = {De Sales-Millan, A and Reyes-Ferreira, P and González-Cervantes, RM and Luna-Álvarez, M and Guillén-López, S and Cobo-Díaz, JF and Ramos, S and Aguirre-Garrido, JF and Velázquez-Aragón, JA}, title = {Clinical Improvement and Taxonomic-Functional Gut Microbiome Remodeling After Six Months of Multi-Strain Synbiotic Supplementation in Mexican Children with Autism Spectrum Disorder.}, journal = {Nutrients}, volume = {18}, number = {15}, pages = {}, doi = {10.3390/nu18152441}, pmid = {42588064}, issn = {2072-6643}, support = {E022 Program Recursos Fiscales para la Investigación//Instituto Nacional de Pediatria/ ; }, mesh = {Humans ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Mexico ; Longitudinal Studies ; *Synbiotics/administration & dosage ; Child ; Feces/microbiology ; Child, Preschool ; Probiotics/administration & dosage ; Dietary Supplements ; Treatment Outcome ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; }, abstract = {Background/Objectives: Gut dysbiosis in children with autism spectrum disorder (ASD) has been associated with alterations in microbial ecology and metabolic function that may contribute to gastrointestinal dysfunction and the severity of clinical manifestations. Synbiotic and probiotic supplementation has emerged as a promising microbiome-targeted strategy for ASD; however, its effects on gut microbiome composition, functional potential, and clinical outcomes remain incompletely understood. We conducted a longitudinal study of Mexican children diagnosed with ASD to analyze changes in the composition, diversity, and functional potential of the gut microbiome during six months of multi-strain synbiotic supplementation. Methods: Stool samples were collected from 25 children with ASD at baseline and after 3 and 6 months of multi-strain synbiotic supplementation. Gut microbiome composition and diversity were analyzed by 16S rRNA gene sequencing, whereas whole metagenome sequencing (WMS) was performed in a subset of samples to evaluate the functional potential of the fecal microbiome. Gastrointestinal symptoms were assessed using the Rome IV criteria, and ASD severity was evaluated with the Childhood Autism Rating Scale (CARS). Results: Twenty-five children with ASD completed the 6 months of synbiotic supplementation. Overall, ASD severity decreased, reflected by a reduction in total CARS score, and improvements in several CARS domains. Gastrointestinal symptoms also decreased significantly. Longitudinal microbiome profiling revealed significant taxonomic and diversity changes over the supplementation period, while WMS identified changes in microbial metabolic potential, including enrichment of tryptophan biosynthesis pathways and reduced L-rhamnose degradation. Conclusions: This exploratory research provides proof-of-concept evidence supporting multi-strain synbiotic supplementation in children with ASD. Larger controlled studies are needed to confirm these findings and clarify their relevance to microbiota-gut-brain axis interactions. The observed concordance between clinical improvements and microbiome remodeling supports further investigation of microbiome-targeted interventions according to ASD severity and duration of supplementation.}, } @article {pmid42588960, year = {2026}, author = {Kiss, J and Libisch, B and Ozoaduche, CL and Fébel, H and Rasschaert, G and Lambrecht, E and Heyndrickx, M and Szabó, M and Keresztény, T and Posta, K and Olasz, F}, title = {Genetic Elements Associated with the Acquired Resistome of the Gut Microbiota in a Broiler Rooster Flock in Hungary.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {15}, pages = {}, doi = {10.3390/ani16152322}, pmid = {42588960}, issn = {2076-2615}, support = {TKP2020-NKA-24//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00007//National Research, Development and Innovation Office/ ; 2019-2.1.11-TÉT-2020-00141//National Research, Development and Innovation Office/ ; GINOP_PLUSZ-2.1.1-21-2022-00221//National Research, Development and Innovation Office/ ; }, abstract = {Antibiotic resistance in Gram-negative bacteria poses a global health threat, and poultry farming provides an important reservoir for multidrug-resistant pathogens. Our study aimed to characterize the faecal microbiota and acquired resistome of Ross-308 roosters in Hungary. Amplicon and shotgun metagenomics revealed a faecal microbiota dominated by the Firmicutes, Bacteroidota, and Proteobacteria and a diverse faecal resistome, including qnrB and an aadA1-bearing integron. Culture-based screening of an antibiotic-free rooster yielded the MDR Escherichia coli strain K1G, displaying resistance also to third-generation cephalosporins and fluoroquinolones. Whole-genome sequencing classified K1G as a serotype O23:H16-ST453 avian pathogenic E. coli (APEC) strain featuring a set of chromosomal virulence factors (including astA, hlyE, lpfA, and iss) and three plasmids: a phage-like plasmid, a mosaic virulence plasmid (carrying blaTEM-1b, hlyF, iutA, ompT, iucD, and cvaC), and an IncC type 1 resistance plasmid harbouring blaCMY-2. The detection of identical or closely related ST453 E. coli strains also in broiler meat in Hungary highlights a potential risk of transmission to humans through the food chain. Moreover, the carriage of multiple acquired antibiotic resistance genes in E. coli K1G indicates that individual chickens can harbour or transmit antibiotic resistance even in the absence of direct antibiotic exposure.}, } @article {pmid42589241, year = {2026}, author = {Wang, Q and Wang, BY and Wilus, D and Xie, H}, title = {Effects of Non-Surgical Periodontal Therapy on Dental Plaque Microbiome.}, journal = {International journal of molecular sciences}, volume = {27}, number = {15}, pages = {}, doi = {10.3390/ijms27156584}, pmid = {42589241}, issn = {1422-0067}, support = {R16GM149359/GM/NIGMS NIH HHS/United States ; U54MD007586/MD/NIMHD NIH HHS/United States ; }, mesh = {Humans ; *Dental Plaque/microbiology ; *Microbiota/genetics ; Female ; Male ; Adult ; Middle Aged ; *Periodontitis/microbiology/therapy ; Metagenome ; Dental Scaling ; Root Planing ; Metagenomics/methods ; }, abstract = {Periodontitis, a chronic inflammatory disease affecting approximately 40% of U.S. adults aged 30 years and older, is characterized by dysbiosis of the dental plaque microbiome. However, although scaling and root planing (SRP) is the cornerstone of periodontal treatment, its effects on the taxonomic composition and functional potential of the dental plaque microbiome remain incompletely understood. In this study, we used whole-metagenome shotgun sequencing to characterize taxonomic composition and functional potential in dental plaque microbiomes collected from 39 patients with Stage II or III generalized periodontitis before and 3-4 months after SRP. Consistent with clinical improvement, periodontal therapy significantly reduced probing depth, clinical attachment level, bleeding on probing, and plaque index. Whole-metagenome shotgun sequencing identified 3.18 million non-redundant genes and 12,353 microbial species across 78 samples, revealing increased gene and species richness after treatment, along with a significant restructuring of the microbial community. Established periodontal pathogens, including Porphyromonas gingivalis, as well as the emerging pathogens Escherichia coli and Burkholderia multivorans, decreased following treatment. Tannerella forsythia also showed a marked reduction after treatment, although this decrease was not significant after false discovery rate (FDR) correction. In contrast, health-associated early colonizers, including multiple Actinomyces species and Streptococcus cristatus, increased. Functional annotation using the Carbohydrate-Active Enzymes (CAZy) database identified significant treatment-associated differences in carbohydrate-active enzymes, including multiple glycosyltransferases, indicating remodeling of the predicted functional potential of the dental plaque microbiome. These findings demonstrate that successful SRP promotes coordinated taxonomic and predicted functional remodeling of the dental plaque microbiome and highlight the value of shotgun metagenomic sequencing for characterizing both taxonomic and functional recovery following periodontal therapy.}, } @article {pmid42589351, year = {2026}, author = {Shen, H and Huang, S and Wang, Z and Zhou, S and Huang, L and Zhang, H and Han, Y and Jiang, J and Guo, H}, title = {Glycyrrhizic Acid Alleviates Atherosclerosis in ApoE[-/-] Mice via Microbial Indole-3-Lactic Acid-Mediated AhR-p65 Interaction in the Endothelium.}, journal = {International journal of molecular sciences}, volume = {27}, number = {15}, pages = {}, doi = {10.3390/ijms27156694}, pmid = {42589351}, issn = {1422-0067}, support = {No. 3332025150//Fundamental Research Funds for the Central Universities/ ; No. 2025-I2M-KJ-016//CAMS Innovation Fund for Medical Sciences/ ; }, mesh = {Animals ; *Atherosclerosis/drug therapy/metabolism/microbiology/etiology/pathology ; Mice ; *Glycyrrhizic Acid/pharmacology/therapeutic use ; *Receptors, Aryl Hydrocarbon/metabolism ; *Indoles/metabolism ; Male ; *Transcription Factor RelA/metabolism ; *Apolipoproteins E/deficiency/genetics ; Gastrointestinal Microbiome/drug effects ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; Humans ; Fecal Microbiota Transplantation ; Endothelium, Vascular/metabolism/drug effects ; Mice, Knockout ; }, abstract = {Glycyrrhizic acid (GL), a natural triterpenoid glycoside extracted from the "medicine food homology" herb Glycyrrhiza glabra L., exhibits potent anti-atherosclerotic effects; yet its underlying mechanisms remain unclear due to its poor oral bioavailability. The gut microbiota plays a pivotal role in the development of atherosclerosis (AS). In this study, the microbiota-dependent anti-AS effects of GL were evaluated in high-fat diet (HFD)-fed ApoE[-/-] mice using antibiotic depletion and fecal microbiota transplantation (FMT). Integrated metagenomic and metabolomic analyses were performed to identify the key bioactive microbial metabolite. Further in vivo and in vitro experiments, including co-immunoprecipitation and dual-luciferase reporter assays, were utilized to elucidate the underlying molecular mechanisms. It was demonstrated that oral administration of GL alleviated AS in a microbiota-dependent manner by reversing gut dysbiosis, improving intestinal barrier function, and reducing pro-inflammatory lipopolysaccharide (LPS) levels. GL shifted intestinal tryptophan metabolism toward bacterial-derived indole-3-lactic acid (ILA) production, suppressing LPS-induced vascular endothelial adhesion dysfunction by activating the aryl hydrocarbon receptor (AhR). Mechanistically, ILA-activated AhR interacted with the NF-κB subunit p65 in the cytoplasm, effectively preventing the nuclear translocation of p65 and suppressing the promoter activities of adhesion molecules (VCAM1 and ICAM1), resulting in the amelioration of HFD-induced AS. These findings elucidate the microbiota-dependent mechanism of orally administered GL against AS, and highlight the therapeutic potential of targeting the ILA-AhR-p65 axis in the vascular endothelium as a strategy for AS.}, } @article {pmid42589520, year = {2026}, author = {Dima, V and Calomfirescu Avramescu, A and Mirea, A and Toma, AI and Bohiltea, RE and Bivoleanu, A and Stewart, DL}, title = {Ureaplasma Species in Perinatal Disease: From the Age of Innocence to the Missing Villain.}, journal = {International journal of molecular sciences}, volume = {27}, number = {15}, pages = {}, doi = {10.3390/ijms27156865}, pmid = {42589520}, issn = {1422-0067}, mesh = {Humans ; *Ureaplasma Infections/microbiology ; *Ureaplasma/pathogenicity/physiology ; Female ; Pregnancy ; Infant, Newborn ; Chorioamnionitis/microbiology ; Animals ; }, abstract = {Ureaplasma urealyticum and Ureaplasma parvum occupy an odd place in perinatal medicine: dismissed for decades as harmless residents of the female genital tract, they are now recognized as pathogens with real consequences for preterm newborns. This review traces that paradigm shift, from organisms once dismissed as harmless colonizers to pathogens now implicated in chorioamnionitis, preterm birth, and a range of serious neonatal morbidities, and describes the molecular mechanisms that underlie their pathogenicity: Toll-like receptor (TLR1/2/6/9)-mediated NF-κB and MyD88/IRAK4/TRAF6 signaling, NLRP3 inflammasome activation and pyroptosis, and blood-brain barrier disruption via claudin-5/occludin downregulation and MMP-mediated tight junction cleavage. We also review the evidence for biofilm-conferred antibiotic tolerance and the clinical associations between Ureaplasma colonization and intraventricular hemorrhage (pooled OR 1.62, 95% CI 1.23-2.13), bronchopulmonary dysplasia (pooled OR 2.30, 95% CI 1.65-3.20), late-onset sepsis, and neurodevelopmental impairment. Diagnosis remains a weak point: culture sensitivity is below 10% compared with polymerase chain reaction (PCR) testing, and no randomized trial has yet shown that microbiological eradication translates into better clinical outcomes-a gap we examine critically. Whether these organisms cause disease seems to depend on gestational age, bacterial load, serovar-specific virulence, and host immune competence. We argue that this conditionality calls for risk stratification rather than dismissal whenever Ureaplasma is identified in clinical specimens, and that the field needs a paradigm shift toward Ureaplasma screening in high-risk pregnancies and targeted neonatal PCR testing, backed by adequately powered interventional trials.}, } @article {pmid42589527, year = {2026}, author = {Coppini, M and Mauceri, R and Vacca, D and Bertolazzi, G and Caponio, VCA and Rodolico, V and Belmonte, B and Campisi, G}, title = {Longitudinal Exploratory Analysis of Salivary Microbiota Profiles in Patients with Oral Squamous Cell Carcinoma Before and After Surgery: A Pilot Study.}, journal = {International journal of molecular sciences}, volume = {27}, number = {15}, pages = {}, doi = {10.3390/ijms27156873}, pmid = {42589527}, issn = {1422-0067}, mesh = {Humans ; *Saliva/microbiology ; Pilot Projects ; *Mouth Neoplasms/microbiology/surgery ; Female ; Male ; *Microbiota ; *Carcinoma, Squamous Cell/surgery/microbiology ; Middle Aged ; Aged ; Longitudinal Studies ; Metagenomics/methods ; Bacteria/genetics/classification ; Adult ; Metagenome ; }, abstract = {Salivary microbiome profiling may represent a promising non-invasive approach for characterizing OSCC-associated microbial patterns and longitudinal microbiome dynamics during patient management. This exploratory pilot study aimed to longitudinally assess salivary microbiota profiles in patients with oral squamous cell carcinoma (OSCC) before and after tumor resection using Oxford Nanopore Technology. Unstimulated saliva samples were collected from 16 patients with OSCC at two time points (before and after tumor resection) and from 10 OSCC-free reference subjects. Microbial DNA was extracted using the QIAamp DNA Blood Kit (QIAGEN GmbH, Hilden, Germany) and subjected to long read metagenomic sequencing using the Oxford Nanopore MinION platform (v. 20.06.4, Oxford Nanopore Technologies, Oxford, UK). Taxonomic profiling was performed to longitudinally characterize salivary microbiota composition within patients and to provide descriptive comparisons with the OSCC-free reference cohort. Longitudinal analysis identified differences in salivary microbiota profiles between pre- and post-resection samples. Before surgery, an increased relative abundance of Neisseria subflava and Leptotrichia buccalis was observed. Post-surgical samples showed higher levels of Glaesserella parasuis, Streptomyces anulatus, and Lactobacillus species. Distinct microbial patterns were also descriptively observed between OSCC patients and OSCC-free controls, suggesting disease-associated dysbiosis. This exploratory longitudinal pilot study suggests differences in salivary microbiota profiles between samples collected before and after tumor resection in patients with OSCC, including changes in taxonomic composition and reduced alpha diversity. Given the limited sample size and the potential influence of unmeasured perioperative factors, these findings should be considered hypothesis-generating. Larger, well-controlled longitudinal studies incorporating standardized oral health assessment and detailed perioperative metadata are required to clarify the biological and clinical relevance of these observations.}, } @article {pmid42589560, year = {2026}, author = {Valenzuela, B and Navarrete-Diaz, I and Cayo, M and Solís-Cornejo, F and Zamorano, P}, title = {Genome-Resolved Metagenomics Reveals Thermophilic Microbial Diversity and Putative Hydrolase-Encoding Genes in the El Tatio Geothermal Field.}, journal = {International journal of molecular sciences}, volume = {27}, number = {15}, pages = {}, doi = {10.3390/ijms27156905}, pmid = {42589560}, issn = {1422-0067}, support = {Fondo para el Desarrollo en Investigación: en artes, ciencias y/o tecnología para actividades de titulación de pregrado": "Bioprospección de Genes de Enzimas Hidrolíticas mediante Análisis Metagenómico en el Campo Geotermal El Tatio"//University of Antofagasta/ ; }, mesh = {*Metagenomics/methods ; *Metagenome ; Phylogeny ; *Archaea/genetics/classification/enzymology ; *Hydrolases/genetics ; *Hot Springs/microbiology ; *Bacteria/genetics/classification/enzymology ; Chile ; }, abstract = {Geothermal ecosystems constitute important reservoirs of thermophilic microorganisms and their associated metabolic functions; however, the genome-resolved diversity and enzymatic potential of high-altitude geothermal systems remain poorly characterized. Here, we applied shotgun metagenomics and genome-resolved approaches to investigate thermophilic microbial communities inhabiting geothermal sediments from the El Tatio geothermal field, a polyextreme hydrothermal system located at ~4300 m above sea level in the Andean Altiplano of northern Chile. Genome reconstruction yielded 657 metagenome-assembled genomes (MAGs), including 190 near-complete and 273 high-quality genomes, providing a comprehensive genome-resolved view of microbial diversity in this environment. Taxonomic analyses revealed diverse archaeal and bacterial communities dominated by members of Thermoproteota, Methanobacteriota, Deinococcota, and Actinomycetota . Functional screening identified 612 high-confidence putative hydrolase-encoding genes distributed across multiple thermophilic lineages, including genes associated with esterases, lipases, proteases, and glycoside hydrolases. Notably, several candidates were recovered from archaeal MAGs affiliated with Thermoproteus, Sulfolobales, Pyrobaculum, and Acidilobaceae, expanding the genomic repertoire of putative hydrolytic functions in thermophilic archaea. Sequence-based thermostability prediction identified proteins with estimated melting temperatures exceeding 80 °C, with the highest predicted value reaching 87.6 °C. Collectively, these results expand current knowledge of microbial diversity and functional potential in high-altitude geothermal ecosystems and identify El Tatio as a rich source of putative hydrolase-encoding genes for future biochemical and biotechnological exploration.}, } @article {pmid42589672, year = {2026}, author = {Zeng, C and Chen, J and Yong, X and Xie, Y}, title = {Convergent Gut Microbiome Remodeling Across Ischemic Stroke, Myocardial Infarction, and Longevity Reveals a Shared Ecological Signature of Aging and Disease.}, journal = {International journal of molecular sciences}, volume = {27}, number = {15}, pages = {}, doi = {10.3390/ijms27157020}, pmid = {42589672}, issn = {1422-0067}, support = {cstc2021jcyj-msxmx0848//Natural Science Foundation of Chongqing/ ; BSKJ2022006//Bishan District Science and Technology Bureau/ ; 81773954//National Natural Science Foundation of China (NSFC)/ ; 202310617015//National College Student Innovation and Entrepreneurship Program/ ; X2024160170123, X2026106170029//Chongqing College Students' Innovation and Entrepreneurship Project/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Aging ; *Myocardial Infarction/microbiology ; *Longevity ; *Ischemic Stroke/microbiology ; Male ; Female ; Aged ; Dysbiosis/microbiology ; }, abstract = {Gut microbiota dysbiosis has been associated with ischemic stroke (IS), myocardial infarction (MI), and aging, but whether these contexts share reproducible microbial features remains unclear. We conducted an exploratory and hypothesis-generating descriptive study of genus-level microbiota patterns across an internal IS cohort and publicly available external IS, MI, and age-stratified or longevity-associated datasets. Analyses were performed within predefined age strata and interpreted cautiously because of the small internal cohort, cross-cohort heterogeneity, and the absence of direct metabolite, intestinal barrier, inflammatory, or microbial activity measurements. No taxon in the internal cohort remained statistically significant after false-discovery-rate correction; therefore, all taxonomic observations were treated as descriptive. Candidate overlapping features included repeated detection of Escherichia-Shigella and Klebsiella and non-uniform patterns among genera previously associated with short-chain fatty acid metabolism, including Faecalibacterium, Blautia, and Roseburia. Lachnoclostridium and Bacteroides showed opposite abundance gradients in selected cross-dataset comparisons. These observations suggest possible ecological overlap across ischemic disease and age-associated microbiome contexts, but they do not establish causality, disease-specific biomarkers, or shared microbial function. The mechanistic models discussed in this manuscript are literature-informed hypotheses based on exploratory compositional data and require future validation in larger, harmonized longitudinal cohorts using metagenomic, metabolomic, clinical, and experimental measurements.}, } @article {pmid42590140, year = {2026}, author = {Guo, F and Zhang, L and Liu, Z and Zhou, B and Fan, H and Zhang, D and Yang, Q and Li, T and Ge, Y}, title = {Clinical Utility of Metagenomic Next-Generation Sequencing in Adult Patients with Fever of Unknown Origin: A Retrospective Real-World Study.}, journal = {Journal of clinical medicine}, volume = {15}, number = {15}, pages = {}, doi = {10.3390/jcm15156038}, pmid = {42590140}, issn = {2077-0383}, support = {2022-PUMCH-B-043.//Peking Union Medical College Hospital/ ; }, abstract = {Background: Fever of unknown origin (FUO) remains a major diagnostic challenge due to its heterogeneous etiologies and nonspecific clinical manifestations. Although metagenomic next-generation sequencing (mNGS) represents a promising diagnostic tool, its clinical utility in adult patients with FUO remains incompletely characterized. Methods: In this study, we retrospectively analyzed adult FUO patients who underwent mNGS testing at Peking Union Medical College Hospital between March 2022 and April 2024. Clinically meaningful diagnostic contribution was determined according to the final clinical diagnosis following multidisciplinary adjudication. Diagnostic performance, pathogen spectrum, therapeutic impact, specimen type, and predictors of clinically meaningful mNGS results were evaluated. Results: A total of 127 FUO patients were included in the study. Infectious diseases accounted for 53.5% of final diagnoses, followed by noninfectious inflammatory diseases (11.0%), malignancies (10.2%), and undiagnosed conditions (19.7%). mNGS made a clinically meaningful diagnostic contribution in 31.5% (40/127) of patients, despite an overall positivity rate of 56.7% (72/127), and showed a higher sensitivity than conventional culture for infectious etiologies (69.1% vs. 16.9%), though with a lower specificity (57.6% vs. 96.0%). Diagnostic contribution varied significantly by specimen type, with drainage fluid/abscess samples showing the highest diagnostic yield (90.9%). Lower white blood cell count was independently associated with clinically meaningful mNGS results (OR 0.87, 95% CI 0.77-0.98). Conclusions: mNGS provides clinically meaningful diagnostic value in adult patients with FUO, particularly for identifying occult infectious etiologies. Lesion-directed sampling, whenever feasible, and careful interpretation of sequencing results in the clinical context are essential to maximize the diagnostic utility of this approach. A lower white blood cell count was independently associated with clinically meaningful mNGS results, although this finding requires validation in larger prospective studies.}, } @article {pmid42591141, year = {2026}, author = {Szeitz, A and Pinto, J and Pieters, A}, title = {Editorial: Advances in mass spectrometry: transforming analytical chemistry in molecular and spatial biology, multimodal omics, and bioanalysis.}, journal = {Frontiers in molecular biosciences}, volume = {13}, number = {}, pages = {1926838}, pmid = {42591141}, issn = {2296-889X}, } @article {pmid42591156, year = {2026}, author = {Kütahya, C and Pániker, CC and Ly, F and Jerath, A and Little, E and Gali, R and Haimi, MZBD and Malek, AHBA and Muhamad, KB and Supian, SB and Young, TB and Lawrence, S and Bell, T and Nee, TY and Jiménez, JI and Huynh, F}, title = {Masterbatch-enabled acceleration of polyolefin biodegradation under open air terrestrial environmental conditions.}, journal = {Npj Materials degradation}, volume = {10}, number = {1}, pages = {90}, pmid = {42591156}, issn = {2397-2106}, abstract = {Polyolefins, commonly used in packaging and single-use products, are notoriously persistent in the environment, contributing significantly to environmental pollution. In scientific literature to date, polyolefins have not been reported to fully biodegrade. This study examines the biodegradation potential of polyolefin materials, specifically polyethylene (PE) and polypropylene (PP), enhanced through the incorporation of Biotransformation Masterbatch technology. The inclusion of the Biotransformation Masterbatch accelerated and enabled the full biodegradation of PE and PP, as demonstrated by laboratory weathering, and biodegradation studies in soil at mesophilic temperatures. Ecotoxicity tests revealed no adverse effects on test organisms in both soil and water environments, while metagenomics analysis demonstrated that biodegradation of these polyolefins did not significantly change the soil microbiota composition, which showed higher metabolic activity compared to virgin plastic controls. These findings demonstrate that Biotransformation technology provides an effective solution for delivering polyolefin-based materials with reduced environmental impact. It offers a sustainable alternative to conventional plastics, preserving the performance characteristics of traditional polyolefins while addressing the problem with fugitive plastic waste in the environment.}, } @article {pmid42591585, year = {2026}, author = {Chen, G and Pan, Y and Bai, Z and Zheng, Y and Wei, Y}, title = {Synergistic algae-bacteria interactions in a novel membrane aeration biofilm system: performance and microbial function.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1900925}, pmid = {42591585}, issn = {1664-302X}, abstract = {Low carbon-to-nitrogen (C/N) ratio wastewater poses a major challenge to biological nitrogen removal due to insufficient electron donors for denitrification. In this study, an algae-bacteria membrane-aerated biofilm reactor (AB-MABR) was established to enhance nitrogen removal under carbon-limited conditions, and its performance was compared with that of a conventional bacterial MABR (B-MABR). The results showed that the AB-MABR achieved superior pollutant removal performance, with COD, NH4 [+]-N, and TN removal efficiencies being 4.0, 21.9, and 12.3% higher, respectively, than those of the B-MABR. Overall, AB-MABR outperformed B-MABR in pollutant removal. The removal efficiencies of COD, NH4 [+]-N, and TN were 92.3, 77.2, and 66.6%, respectively, which were markedly higher than those achieved by B-MABR (88.8, 55.3, and 54.3%). The incorporation of microalgae significantly enhanced microbial metabolic activity, as evidenced by higher ATP content, electron transport system activity (ETSA), and cytochrome c (Cyt-c) levels. Meanwhile, EPS production increased by 25% in the AB-MABR, accompanied by greater accumulation of protein-like and humic-like substances. SEM and CLSM analyses revealed that microalgae promoted the formation of a denser and more stratified biofilm with higher biomass and stronger structural stability. Metagenomic analysis further demonstrated that pathways associated with microbial metabolism, secondary metabolite biosynthesis, and environmental adaptation were enriched in the AB-MABR system, indicating enhanced metabolic potential and ecological resilience. Overall, microalgal incorporation strengthened electron transfer, stimulated EPS secretion, improved biofilm development, and enhanced microbial metabolic functions, thereby promoting nitrogen transformation and removal under low C/N conditions. These findings provide new insights into the synergistic mechanisms of algae-bacteria biofilms and demonstrate the potential of AB-MABR technology for sustainable nitrogen removal from carbon-limited wastewater.}, } @article {pmid42591617, year = {2026}, author = {Mukhedkar, D and Stosic, MS and Székely, AJ and Avershina, E and Arroyo Mühr, LS}, title = {Strong catchment-specific structuring of Swedish wastewater microbiomes in a paired two-timepoint metagenomic survey.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1907599}, pmid = {42591617}, issn = {1664-302X}, abstract = {INTRODUCTION: Wastewater microbial communities integrate signals from human populations, environmental inputs, and sewer infrastructure, but the extent to which these communities vary between wastewater catchments compared with individual sampling occasions remains incompletely understood.

METHODS: We analyzed influent wastewater from 16 wastewater treatment plant sites across Sweden, collected at two paired within-year timepoints, Week 3 and Week 21, using shotgun metagenomic sequencing and compositional data analysis.

RESULTS: Classified genus-level profiles were dominated by bacteria (96.54%), with smaller contributions from viruses (2.03%), eukaryota (1.05%) and archaea (0.40%). Genus-level alpha diversity increased between the two sampled timepoints, with median within-site changes of +10 genera in richness and +0.21 in Shannon diversity (p < 0.003). In contrast, overall community composition was primarily structured by wastewater treatment plant site: site explained 58.3% of total variance (p = 0.0003), whereas sampling timepoint explained 3.7% and was not significant (p = 0.106). Within-site compositional change between the two timepoints was nevertheless evident (p = 4.8 × 10[-4]), but the magnitude and direction of change varied across sites, indicating heterogeneous local shifts rather than a synchronized national temporal pattern. Genera detected in at least 75% of sites at both sampled timepoints accounted for most classified community abundance, whereas most measured within-site Aitchison turnover was accounted for by genera outside the high-prevalence shared fraction. Geographic distance and the number of connected inhabitants showed no significant association with genus-level community composition.

DISCUSSION: These findings indicate that Swedish influent wastewater microbiomes are strongly catchment-specific across paired sampling timepoints and support the use of site-specific reference profiles when interpreting wastewater metagenomic data. Denser temporal sampling and additional catchment metadata will be needed to assess seasonality, long-term stability, and the local drivers of wastewater microbiome variation.}, } @article {pmid42591668, year = {2026}, author = {Dell'Alma, M and Cesana, M and Kenny, P and Peron, G and Cafarella, C and Rigano, F and Mondello, L and Mangieri, N and Pizzi, S and Russo, P and Mora, D and Gargari, G}, title = {Multi-omic characterization of microbial dynamics during spontaneous fermentation of sweet wine Picolit variety.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1857803}, pmid = {42591668}, issn = {1664-302X}, abstract = {INTRODUCTION: Spontaneous wine fermentation is driven by the ecological succession of vineyard-derived microorganisms, yet little is known about how this process unfolds in Picolit, a grape variety characterized by acinellatura (berry millerandage) and elevated sugar concentration. This study aimed to characterize the microbial and metabolic dynamics of spontaneous Picolit fermentation and to identify the ecological and functional transitions occurring throughout the process.

METHODS: An integrated multi-omic approach combining shotgun metagenomics and untargeted metabolomics was applied to spontaneous fermentations of Picolit grapes produced at Aquila del Torre, an organic and biodynamic winery located in Savorgnano del Torre (Friuli-Venezia Giulia, Italy), within the newly established "Friuli Colli Orientali Sottozona Savorgnano D.O.C." Five fermentation stages were sampled and analyzed to investigate microbial succession, functional pathways and metabolomic changes.

RESULTS: The initial must displayed high microbial richness dominated by non-Saccharomyces yeasts, oxidative bacteria and Botrytis cinerea. An atypical persistence and increasing abundance of B. cinerea suggested a strong interaction between grape physiology and fungal activity. Early fermentation stages were characterized by diverse non-Saccharomyces taxa, including Lachancea, Pichia, Torulaspora and Schizosaccharomyces, which were associated with acid modulation, aromatic precursor release and phenolic turnover. From mid-fermentation onward, a multi-species Saccharomyces consortium established functional dominance, coinciding with a marked reduction in bacterial diversity and a transition from aroma-related metabolic pathways to stress adaptation functions. Multi-omic network analyses revealed a progressive loss of modularity as fermentation progressed and the system became more stable.

DISCUSSION: These findings demonstrate that spontaneous Picolit fermentation follows a distinctive ecological trajectory shaped by grape physiology, terroir and native microbial diversity. The persistence of B. cinerea, together with the succession of non-Saccharomyces and Saccharomyces populations, highlights unique microbial interactions that may contribute to wine identity. Overall, the results support the enological value of spontaneous fermentation and provide a microbial and functional framework for understanding and valorizing wines produced under the Savorgnano Bianco D.O.C.}, } @article {pmid42591980, year = {2026}, author = {Zhao, X and Ming, X and Shang, Z and Zhou, M and Xiao, Y}, title = {Epstein-Barr Virus-Positive B-Cell Lymphoproliferative Disorder Complicated by Septic Shock in Activated PI3Kδ Syndrome: A Pediatric Case Report and Literature Review.}, journal = {Case reports in hematology}, volume = {2026}, number = {}, pages = {3644513}, pmid = {42591980}, issn = {2090-6560}, abstract = {Activated phosphoinositide 3-kinase delta syndrome (APDS) is a rare inborn error of immunity caused by gain-of-function variants in PIK3CD and characterized by recurrent infections, lymphoproliferation, and impaired viral control. We report a 17-year-old male with a heterozygous PIK3CD c.3061G > A (p.E1021K) variant who presented with progressive edema, extensive hypermetabolic lymphadenopathy, splenomegaly, and Epstein-Barr virus (EBV) DNAemia. A core needle biopsy of the right inguinal lymph node demonstrated an immunodeficiency-associated EBV-positive B-cell lymphoproliferative disorder with extensive monotypic plasmacytoid differentiation. Because the biopsy contained limited mature B-cell tissue, the pathological findings favored a polymorphic B-LPD although EBV-positive diffuse large B-cell lymphoma with plasmacytic differentiation could not be excluded. The patient received anti-B-cell-directed therapy and supportive treatment. He was subsequently readmitted with septic shock and acute respiratory distress syndrome. Blood metagenomic next-generation sequencing detected Escherichia coli and Klebsiella pneumoniae, together with antimicrobial-resistance genes including blaNDM. Despite intensive antimicrobial and organ-supportive treatment, the patient remained critically ill and was discharged at his family's request for transfer to a local hospital; his subsequent outcome was unavailable. This case highlights the diagnostic difficulty of classifying EBV-positive B-cell proliferations using limited biopsy tissue in APDS and the competing risks of lymphoproliferative disease and severe infection. Adequate tissue sampling and pathological characterization, close microbiological surveillance, and individualized multidisciplinary management are essential in this setting.}, } @article {pmid42592599, year = {2026}, author = {Tao, G and Tang, W and Zhao, Y and Ma, Y and Xu, Y}, title = {A case report of ocular infection caused by Aspergillus fumigatus.}, journal = {AME case reports}, volume = {10}, number = {}, pages = {154}, pmid = {42592599}, issn = {2523-1995}, abstract = {BACKGROUND: Aspergillus fumigatus (A. fumigatus) can cause invasive infections in various sites of the body, including invasive pulmonary, hematogenous disseminated, and intracranial infections, posing substantial challenges for diagnosis and treatment. The methods of identification in this laboratory are worthy of study.

CASE DESCRIPTION: A 44-year-old male was admitted to our hospital with a 1.5-month history of bilateral scleral icterus accompanied by progressive visual deterioration. The patient was previously diagnosed with acute liver failure [hepatitis B e-antigen (HBeAg)-negative chronic hepatitis B] at another hospital. During hospitalization, his vision in the left eye decreased. Slit-lamp examination during ophthalmologic consultation suggested left endophthalmitis, with concurrent suspicion of retinal detachment. Examinations at admission confirmed the presence of hepatitis B virus (HBV) DNA, acute liver failure (Child-Pugh Class C), moderate anemia. The levels of the inflammatory markers were significantly elevated, including interleukin (IL-6, IL-8, IL-1β), and interferon-gamma (IFN-γ). After obtaining informed consent, emergency vitrectomy of the left eye was performed, retinal detachment repositioning and laser photocoagulation for retinal lesions, cryotherapy for retinal lesions, and vitreous silicone oil implantation in the left eye. The vitreous was cultured, then identified using next-generation metagenomic sequencing (mNGS) technology, enabling the detection of Aspergillus within a short period of time. This enabled a rapid diagnosis of Aspergillus endophthalmitis, guiding subsequent clinical management. After undergoing anti-infection and liver-protective treatment, the patient's condition stabilized and he was discharged from the hospital.

CONCLUSIONS: mNGS is a technology that can directly perform high-throughput sequencing of all the genetic material (DNA and/or RNA) of microorganisms in clinical samples (such as blood, bronchoalveolar lavage fluid, cerebrospinal fluid, etc.). The combination of mNGS and conventional detection methods effectively improves the detection rate of fungi.}, } @article {pmid42592806, year = {2026}, author = {Saavedra-Lozano, J and Agüera, M and Velasco-Arnaiz, E}, title = {Evolving paradigms in pediatric osteomyelitis: modern insights into an old disease.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1097/QCO.0000000000001231}, pmid = {42592806}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: Acute hematogenous osteomyelitis (AHO) remains a potentially devastating infection in children, in which delayed diagnosis or inadequate therapy can result in significant long-term sequelae. This review provides an update of the epidemiology, diagnosis and management of pediatric AHO, with particular emphasis on emerging diagnostic tools and evolving therapeutic strategies aimed at preventing complications.

RECENT FINDINGS: Improved recognition by clinical and laboratory algorithms of age-specific pathogens, like Kingella kingae in young children or highly virulent organisms including methicillin-resistant Staphylococcus aureus (MRSA), may allow for individualized therapy. Novel molecular techniques, such as metagenomic next-generation sequencing (mNGS), offer the potential for broader and faster microbiological diagnosis. Multidisciplinary protocols that integrate early MRI may enhance anatomic delineation of infection and lead to faster detection of complications. Antibiotic stewardship programs based on local epidemiology support optimized empiric and targeted therapy, while early transition to oral antibiotics has been shown to improve quality of life and reduce healthcare resource utilization without compromising clinical outcomes.

SUMMARY: Although AHO continues to pose diagnostic and therapeutic challenges, its management is shifting toward individualized, evidence-based care driven by advances in diagnostics, risk stratification and antimicrobial stewardship. Future research should focus on developing and validating multidisciplinary protocols to further improve the accuracy of diagnosis.}, } @article {pmid42593076, year = {2026}, author = {Ramos Romano, AL and Coutouné, N and Rego-Costa, A and Desai, MM and Carazzolle, MF and Gombert, AK}, title = {Dynamics of contaminant microbes in bioethanol production from sugarcane.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jimb/kuag020}, pmid = {42593076}, issn = {1476-5535}, abstract = {The dynamics and impact of microbial contaminants in industrial sugarcane bioethanol production in Brazil were investigated through a two-year metagenomic study across two biorefineries. Shotgun metagenomic sequencing revealed that temporal shifts in the contaminant microbiome dynamics within production seasons were more pronounced than inter-annual or inter-mill variations. While Saccharomyces spp. dominated, bacterial communities, primarily within the Firmicutes phylum and dominated by the genera Lactobacillus, Limosilactobacillus, and Bacillus, exhibited dynamic changes. Correlation analyses with industrial process parameters revealed a complex interplay: lower Lactobacillus levels in one mill were associated with increased ethanol yield, whereas higher levels in another mill correlated with reduced yeast viability and increased flocculation. The presence of Limosilactobacillus was linked to decreased yeast viability, whereas Bacillus showed potential for inhibiting both Lactobacillus and Limosilactobacillus. These findings highlight the nuanced and species-specific impacts of bacterial contaminants on bioethanol production, underscoring the need for strain-level functional studies and targeted interventions to optimize fermentation efficiency and stability in industrial settings.}, } @article {pmid42593705, year = {2026}, author = {Wei, W and Zhou, L and Huang, Y and Lu, Z and Zhang, R and Zeng, M and Wang, X}, title = {Association Between Gut Microbiota Dysbiosis and Bilirubin Metabolism Dysregulation in Children with Heart Failure.}, journal = {Journal of cardiovascular translational research}, volume = {19}, number = {1}, pages = {}, pmid = {42593705}, issn = {1937-5395}, mesh = {Humans ; *Heart Failure/microbiology/diagnosis/blood ; *Bilirubin/blood ; *Dysbiosis ; *Gastrointestinal Microbiome ; Female ; Child, Preschool ; Male ; Child ; Case-Control Studies ; Biomarkers/blood ; Feces/microbiology ; Age Factors ; Metabolomics ; Infant ; Ribotyping ; Clostridium/genetics ; Adolescent ; Eubacteriales ; }, abstract = {Patients with heart failure (HF) demonstrate dysregulation in bilirubin metabolism. The specific characteristics of intestinal bilirubin metabolism in HF remain unclear. This study involved metagenomic sequencing and metabolomic profiling of fecal samples from 45 children with HF and 32 healthy children. Serum total bilirubin levels were 11.3umol/L, 19.4umol/L and 5.0umol/L in HF New York Heart Association (NYHA) I-II, NYHA III-IV and control group (p < 0.001), and the median gut microbiome health index (GMHI) were - 0.78, -1.53 and 0.09 in each (p < 0.001). The abundance of 2 bacteria species containing bilirubin reductase, Ruminococcus gnavus (p = 0.028) and Clostridium sp.M62/1 (p = 0.002) significantly decreased in NYHA III-IV group. The gut downstream bilirubin products, urobilinogen and stercobilin were decreased in the HF group; while the upstream bilirubin products, unconjugated and conjugated bilirubin increased. Dysbiosis of the gut microbiome and the decrease of bilirubin reductase containing bacteria in pediatric HF patients related to a reduction in gut bilirubin metabolism.}, } @article {pmid42594431, year = {2026}, author = {Huo, P and Li, Y and Han, T and Zhang, T and Gao, P}, title = {Labile carbon supply modulates H2O2-mediated N2O emissions during sediment denitrification: Insights from metagenomics.}, journal = {Journal of environmental management}, volume = {415}, number = {}, pages = {130690}, doi = {10.1016/j.jenvman.2026.130690}, pmid = {42594431}, issn = {1095-8630}, abstract = {Reactive oxygen species (ROS), particularly hydrogen peroxide (H2O2), are critical yet complex regulators of the nitrogen cycle. While H2O2 is known to modulate nitrous oxide (N2O) emissions during heterotrophic denitrification, how this regulation interacts with labile carbon supplies remains poorly understood. Here, we investigated the response of N2O emissions to exogenous H2O2 gradients under varying carbon-to-nitrogen (C/N) ratios in riverine sediments. We found that labile carbon addition (glucose) significantly broadened the tolerance window of denitrification to H2O2 stress and altered the dose-response relationship of N2O emissions across H2O2 concentrations ranging from 49 to 1960 μmol kg[-1] dry soil. Under carbon-limited conditions (NC), H2O2 reduced cumulative N2O emissions by 36.98% during the initial 6 h, coinciding with decreased relative genomic representation of Class I complete-repertoire genera and Class II nosZ-bearing genera lacking at least one upstream module. Conversely, under high-carbon conditions, H2O2 addition resulted in a 20.74% increase in cumulative N2O emissions compared to the control. Metagenomic analysis revealed a concurrent enrichment of denitrification and antioxidant genes (e.g., katG, trxB). This enriched genetic potential, contrasted with the observed N2O accumulation, highlights an apparent uncoupling between genomic capacity and phenotypic activity. This suggests that while the microbial community retains the genetic potential for denitrification, acute oxidative stress likely constrains terminal N2O reduction. These findings indicate that the convergence of labile carbon supply and ROS generation represents an important trigger for transient N2O pulses. This study deepens the understanding of the role of H2O2 in regulating denitrification-derived N2O emissions.}, } @article {pmid42594433, year = {2026}, author = {Fan, Y and Wei, Q and Zhang, P and Zou, L and Aisikaier, A and Ma, X and Dai, Z and Tian, Y and Li, Y and Wang, F and Yang, S and Cao, W}, title = {Hydrological regime modulates nitrogen retention-removal shifts in a glacier-oasis alpine river by restructuring multi-trophic interactions and microbial assembly.}, journal = {Journal of environmental management}, volume = {415}, number = {}, pages = {130604}, doi = {10.1016/j.jenvman.2026.130604}, pmid = {42594433}, issn = {1095-8630}, abstract = {Nitrogen (N) cycling in glacier-oasis alpine rivers exhibits distinct spatiotemporal patterns driven by multi-trophic community interactions. This study integrated 16S/18S rRNA sequencing with metagenomic analysis to investigate N-transformation dynamics across trophic levels and their response to varying hydrological regimes. The α-diversity of multi-trophic communities exhibited trophic-level-specific longitudinal patterns, with bacteria and algae generally showing higher diversity in the oasis reach (OR), whereas protozoans and metazoans were more diverse in the glacial reach (GR). In the OR, the species turnover of microeukaryotes exceeded 40%, and the pooled OR-irrigation channel reach (ICR) group exhibited 9.1-22.6-fold greater network complexity than the GR. The abundances of functional genes associated with nitrification and denitrification were 12.3-13.8 and 4.7-9.6 times higher in the OR than in the GR, respectively; N fixation potential was 2.4-14.1 times greater and bacterial α-diversity was 0.94-1.42 times higher in the OR than in the GR. Notably, only during the dry season did the GR exhibit 63-84% higher nitrate assimilation than the OR. Path analysis revealed that algae-protozoan symbiosis promoted N assimilation and retention (β = 0.87), whereas bacterial communities enhanced dissimilatory nitrate reduction and denitrification, facilitating N removal (β > 0.66). In contrast, metazoan predation (β = -0.78) and dissolved oxygen (β = -0.24) suppressed denitrification. The differentiation of N-cycling functions was governed by high α- and β-diversity within microbial communities. Heterogeneous selection and dispersal limitation during community assembly, acting through cross-trophic cascading effects, collectively balanced N retention against removal and ultimately determined the fate of N in the river ecosystem. Climate change may redistribute N-cycling hotspots along alpine rivers by altering hydrological regimes and riverine gradients, potentially increasing eutrophication risk by reducing N removal and enhancing N retention.}, } @article {pmid42580113, year = {2026}, author = {Zhang, Y and Xu, Z and Chu, W and He, H and Ma, L and Zhang, J and Ye, C}, title = {Underappreciated role of polluted storm sewer discharge in the accumulation of antibiotic resistance genes in downstream sediments.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143253}, doi = {10.1016/j.jhazmat.2026.143253}, pmid = {42580113}, issn = {1873-3336}, abstract = {Polluted storm sewers (PSSs) are important pathways for contaminant transport to receiving waters, yet the association between PSS discharge and antimicrobial resistance in downstream sediments remains poorly understood. We investigated antibiotic resistance gene (ARG) distributions in paired upstream-downstream stream water and sediments around six PSS outfalls, together with PSS outfall samples, using metagenomic sequencing and binning. Downstream sediments exhibited transitional ARG profiles between upstream and PSS sediments, indicating a compositional linkage with PSS sediments. Acquired ARGs (sulfonamide and tetracycline resistance genes) were enriched in downstream sediments, while the intrinsic chromosomal resistance determinant mexB showed a similar pattern, consistent with their higher abundances in PSS discharges. SourceTracker indicated that sediment sources (87%) from upstream and PSSs contributed more to downstream sediment ARG profiles than water sources. The intermediate suspended solid levels in downstream water between PSS water and upstream water further supported particle-associated transport. Sulfonamide resistance genes were associated with putative plasmid contigs and co-occurred with qacEdelta1 and IS91, suggesting potential mobility. Azonexus was the dominant potential host of sulfonamide and tetracycline resistance genes, whereas Pseudomonas_E was associated with mexB enrichment. Collectively, these findings highlighted PSS discharge as an important anthropogenic pathway associated with ARGs in downstream sediments.}, } @article {pmid42580122, year = {2026}, author = {Gao, Z and Xue, L and Ma, Y and Chen, C and Ling, H and Wang, L and Zhang, W and Qian, J and Yang, Z and Hua, M and Pan, B}, title = {Mechanistic insights into low-dose nZVI-enhanced process stability under variable industrial loads in field-scale anaerobic treatment: Interfacial evolution and strain-resolved adaptation.}, journal = {Water research}, volume = {307}, number = {}, pages = {126665}, doi = {10.1016/j.watres.2026.126665}, pmid = {42580122}, issn = {1879-2448}, abstract = {Anaerobic treatment of industrial wastewater is limited by high variability and low biodegradability, which compromise process stability under varying industrial loads. A low-dose nanoscale zero-valent iron (nZVI)-augmented continuous-flow strategy was proposed and evaluated long-term in an on-site 3000 L reactor coupled to a full-scale expanded circulating granular sludge bed (ECSB). nZVI increased the mean chemical oxygen demand (COD) removal efficiency from 12.96% to 25.94% and reduced effluent fluctuation by 49%. Concurrently, sludge aggregation intensified, accompanied by protein enrichment in tightly bound extracellular polymeric substances (T-EPS) and a shift in dissolved organic matter (DOM) fluorescence toward humic-like hydrolytic intermediates. Metagenome-assembled genomes indicated a stable community core without structural replacement, alongside enriched iron-metabolism pathways. Incomplete electron-output pathways in key populations further suggest a possible contribution of nZVI-derived iron phases to conductive-material-mediated direct interspecies electron transfer (cDIET). Nonsynonymous single-nucleotide variant (SNV) trajectories and strain deconvolution further identified population-level selection in genes for iron homeostasis, oxidative stress, and electron transfer. These findings reposition nZVI from a reactive supplement to an interfacial stability regulator. More broadly, they provide field-scale evidence that refined nanomaterial dosing strategies can stabilize anaerobic treatment under real industrial loads by coupling interfacial reorganization with within-population adaptation.}, } @article {pmid42580131, year = {2026}, author = {Liu, C and Zhang, H and Guo, Z and Jiang, L and Yu, L and Zhu, C and Zhu, G}, title = {Electron flow boosted highly selective ammonium production from microbial nitrate reduction.}, journal = {Water research}, volume = {307}, number = {}, pages = {126656}, doi = {10.1016/j.watres.2026.126656}, pmid = {42580131}, issn = {1879-2448}, abstract = {Microbial dissimilatory nitrate reduction to ammonium (DNRA) process is considered as a bridge connecting nitrification and denitrification processes, which helps to improve the removal efficiency of nitrate wastewater. However, the competitiveness of DNRA was weaker than the denitrification, resulting in over 60-70% of nitrogen loss each year as N2 or N2O via denitrification. Here, we report a strategy of employing electron flow to rapidly initiate DNRA process (e-DNRA) with no external energy input. This e-DNRA strategy lies in establishing a high carbon-to-nitrogen ratio habitat to create favorable conditions for the growth and reproduction of DNRA bacteria. Subsequently, DNRA functional bacteria are enriched under reducing microenvironment induced by electron flow, ultimately forming a stable biofilm with high DNRA activity. By controlling extracellular electron flow, a nitrate reduction efficiency, conversion efficiency of nitrate to ammonium, and yield rate of 93.2%, 92.7%, and 1.23 µmmol N d[-1] g[-1] (MLSS) m[-3] were achieved, respectively. Transcriptome analysis and [15]N isotope tracing technology demonstrated that electron flow promoted the expression of nrfA gene by an order of magnitude. Genus-level microbial community structure revealed species Lentimicrobium, Geobacter, and Thauera are the primary determinants for the high DNRA efficiency. Moreover, metagenome-assembled genomes found that the electron flow increased the expression of cyt b and cyt c1 subunits in complex III by 1-2 orders of magnitude which sustained the high-rate DNRA. The proposed e-DNRA strategy provides a new solution for the synergistic treatment of nitrate wastewater and ammonium recovery.}, } @article {pmid42580322, year = {2026}, author = {Yang, L and Xiang, L and Rilong, J and Yihe, H}, title = {Tuberculous Arthritis Diagnosed by Metagenomic Sequencing after Negative Microbiology Studies and a 4-Year Delay.}, journal = {The American journal of tropical medicine and hygiene}, volume = {}, number = {}, pages = {}, doi = {10.4269/ajtmh.26-0309}, pmid = {42580322}, issn = {1476-1645}, abstract = {Tuberculous arthritis of the knee is a rare form of extrapulmonary tuberculosis that often presents with nonspecific symptoms, leading to delayed or missed diagnosis, particularly in elderly patients with comorbidities. We report the case of a 70-year-old man with a 2-year history of left knee pain and recurrent swelling. The patient was under therapy for lung cancer. He underwent two arthroscopic procedures for both diagnostic and therapeutic purposes. Repeated standard tests for tuberculosis were negative before metagenomic next-generation sequencing (mNGS) identified Mycobacterium tuberculosis nearly 2 years later. After 1-year triple-antituberculous therapy, he remained asymptomatic at the 2-year follow-up. This case highlights a high index of suspicion for indolent infection in culture-negative chronic arthropathy. The use of mNGS-increasingly accessible and cost effective-enables rapid and sensitive diagnosis of paucibacillary extrapulmonary tuberculosis.}, } @article {pmid42580423, year = {2026}, author = {Song, W and Shang, H and Yang, H}, title = {Performance stability and adaptability of embedded phosphorus removal biofillers: insights from microbial community responses and regulatory mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135602}, doi = {10.1016/j.biortech.2026.135602}, pmid = {42580423}, issn = {1873-2976}, abstract = {Given the typically low phosphorus (P) concentrations in municipal wastewater, this study established a reactor employing embedded P removal biofillers (EBPAOs). The P removal performance of the system was systematically evaluated under three aerobic-phase operating modes: high-P batch feeding (Experiment S), low-P batch feeding (Experiments T10-T2), and low-P continuous feeding (Phases A-E). The results exhibited that, under the low-P batch feeding mode, the aerobic P uptake rate (Pup-rate) of the EBPAOs followed the Michaelis-Menten equation (R[2] = 0.940). Under the continuous feeding mode, the Pup-rate remained stable throughout the aerobic phase. When the influent PO4[3-]-P concentrations were sequentially adjusted to 10, 8, 6, 4, and 2 mg/L, with corresponding hydraulic retention times (HRTs) of 60, 50, 40, 30, and 25 min, respectively, the aerobic effluent PO4[3-]-P concentration remained below 0.3 mg/L in all cases. The volumes of wastewater treated per cycle were 2.5, 3, 3.75, 5, and 6 times the nominal reactor volume, respectively. Microbial community analysis revealed that Candidatus_Accumulibacter (48.59-58.82%) was the dominant genus in the EBPAOs. Metagenomic analysis further showed that, as the influent PO4[3-]-P concentration decreased, polyphosphate-accumulating organisms (PAOs) consumed more COD to synthesize additional polyhydroxyalkanoates (PHA), thereby providing the energy required for efficient P uptake under aerobic low-P conditions. Concurrently, the abundances of the PstS gene and genes associated with the Embden-Meyerhof-Parnas (EMP) pathway, the tricarboxylic acid (TCA) cycle, and PHA synthesis were significantly upregulated. In conclusion, EBPAOs enable efficient and stable P removal from low-P wastewater.}, } @article {pmid42580547, year = {2026}, author = {Wei, Y and Zhu, L and Jin, X and Yao, H and He, S and Feng, P and Yu, F and Xiang, Y and Li, Z and He, S}, title = {Metagenomic indications of potential pathogen-associated and antibiotic resistance risks following UV-chlorine disinfection in sprout production.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128943}, doi = {10.1016/j.envpol.2026.128943}, pmid = {42580547}, issn = {1873-6424}, abstract = {Hydroponic agriculture commonly relies on low-pressure UV combined with chlorination (LPUV-chlorine) disinfection for water reuse, yet its impacts on non-coliform pathogens and associated resistance risks remain insufficiently understood. Here, metagenomic analysis of a commercial sprout production system revealed that LPUV-chlorine treatment did not completely remove pathogen-associated DNA signals and was associated with an increased relative abundance of Pseudomonas aeruginosa, accompanied by increased abundance of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). The relative abundances of VFGs related to biofilm formation and exoenzyme activity increased by 16∼18-fold compared to source water (SW), while β-lactam resistance genes showed marked increases in relative abundance. Network analysis revealed statistical associations between several pathogen-associated taxa and ARG profiles but did not establish their genomic hosts or transfer pathways. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further revealed higher relative representation of genes associated with two-component systems and flagellar assembly, suggesting potential stress-adaptive functions and preferential persistence. In contrast, medium-pressure UV (MPUV) achieved ≥ 4-log reductions of P. aeruginosa, Escherichia coli, and Salmonella enterica within seconds, with 40.24%, 2.29%, and 26.44% lower fluence than LPUV, respectively. Transcriptomic analysis revealed decreased expression of selected virulence-associated genes and increased expression of phage-associated genes, suggesting potential effects on virulence-related functions and prophage responses. These findings highlight a potential pathogen-selection risk under LPUV-chlorine disinfection and indicate MPUV as a promising chlorine-free microbial risk control strategy in hydroponic water reuse systems.}, } @article {pmid42581103, year = {2026}, author = {Wang, R and Tabrizian, T and Wang, D and English, J and Ayer, A and Gal, M and Yang, WL and Wu, Z and Mao, K and Novaj, A and Zhang, X and Basu, I and Brodin, NP and Koba, W and Saxena, D and Choi, J and Augenlicht, LH and Ericsson, A and Gavathiotis, E and Guha, C and Huffman, DM}, title = {TNFR1 signaling connects inflammation to impaired fatty acid oxidation to drive intestinal stem cell aging.}, journal = {Nature aging}, volume = {}, number = {}, pages = {}, pmid = {42581103}, issn = {2662-8465}, support = {P30CA013330//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; 1210OD023591-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30DK020541//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; T32AG23475//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R56AG052981//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; P30AG038072//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; T32AG23475//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; }, abstract = {Aging is characterized by a decline in function of intestinal stem cells (ISCs), but the extent to which this is shaped by systemic factors is unclear. Here we show that the ISC aging phenotype can be propagated from old to young mice utilizing heterochronic parabiosis, and implicate a role for inflammation in these effects, as anti-inflammatory drugs, including TNF antibodies, restored function. Parabiotic rescue experiments demonstrate that TNFR1 knockout protected young ISCs from the old environment. In young organoids, TNF downregulated crypt budding, while impairing mitochondrial pathways and fatty acid oxidation (FAO). However, aged ISC function was enhanced by boosting mitochondrial fusion, whereas FAO in aged crypts was improved by countering inflammation with salicylate treatment. Thus, these data identify the old environment through the progeronic factor TNF, as a driver of ISC aging phenotypes through intestinal epithelial cell TNF receptor 1 signaling to downregulate FAO, proliferation and regenerative capacity in these cells.}, } @article {pmid42581991, year = {2026}, author = {Song, X and Liu, X and Lou, M and Xu, J and Gong, X and Yang, Q and Chen, G and Mei, J}, title = {Atypical cat-scratch disease with acute high-grade fever and neuropsychiatric symptoms: a case report.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1810698}, pmid = {42581991}, issn = {2297-1769}, abstract = {OBJECTIVE: To report an atypical case of neurological cat-scratch disease (NCSD) presenting with acute-onset fever and prominent neuropsychiatric manifestations in an older adult.

PATIENT: An 85-year-old East Asian man with a history of hypertension and coronary artery disease.

RESULTS: Three months after a cat scratch, the patient developed abrupt high-grade fever, followed by nocturnal delirium with visual hallucinations and a witnessed seizure-like episode, and later complained of occipital headache. Physical examination revealed mild bilateral axillary and left supraclavicular lymphadenopathy without focal neurologic deficits. Cerebrospinal fluid cultures and stains were negative for bacteria and fungi. Serum metagenomic next-generation sequencing (mNGS) detected Bartonella henselae. After antibiotic therapy, the fever and headache resolved.

CONCLUSION: Cat-scratch disease should be considered as a rare but important infectious etiology in patients presenting with febrile illness accompanied by delirium or other neuropsychiatric symptoms. Clinicians should carefully inquire about recent cat exposure or scratch history and consider early pathogen-directed empiric antibiotic therapy to minimize diagnostic delay and improve outcomes.}, } @article {pmid42582033, year = {2026}, author = {Shi, P and Liu, Z and Wu, X and Zhao, F and Xu, J and Li, Q and Ye, M and Nian, D}, title = {Clinical utility of CSF metagenomic next-generation sequencing in suspected CNS infection: performance against a composite reference standard and read-count stratification.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1905481}, pmid = {42582033}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Retrospective Studies ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/virology ; Male ; Reference Standards ; Adult ; Middle Aged ; Sensitivity and Specificity ; Aged ; *Cerebrospinal Fluid/virology ; Meningitis/diagnosis/cerebrospinal fluid ; Young Adult ; Adolescent ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) is increasingly used to identify pathogens in suspected central nervous system (CNS) infections. However, integrating these results into real-world clinical decision-making remains problematic, particularly given the lack of standardized quantitative metrics beyond raw read counts.

METHODS: We retrospectively analyzed 46 patients with suspected encephalitis, meningitis, or meningoencephalitis who underwent CSF mNGS testing. Etiologic certainty was classified using a composite clinical reference standard as Definite, Probable, or Unlikely. We assessed concordance between mNGS findings and the Likely etiology category (Definite or Probable), calculated diagnostic performance metrics, characterized the detected pathogens, and explored a tiered interpretation framework based on maximum read counts per patient (<10, 10-49, and >=50). Trends across read-count strata were evaluated using the Cochran-Armitage test, and exact binomial 95% confidence intervals (CIs) were calculated.

RESULTS: CSF mNGS detected pathogens in 13 of 46 patients (28.3%). Positivity increased with greater adjudicated diagnostic certainty, from 0% in Unlikely cases to 11.8% in Probable cases and 73.3% in Definite cases. Within the composite reference framework, mNGS showed 40.6% sensitivity, 100% specificity, 100% positive predictive value, and 42.4% negative predictive value, indicating stronger rule-in than rule-out performance. Viral detections predominated, with herpes simplex virus type 1 and varicella-zoster virus as the most frequent pathogens; all findings should be interpreted in the context of DNA-only testing. Among mNGS-positive patients with Likely etiologies, the proportion classified as Definite increased across higher max-read strata, but these tier-specific estimates were imprecise and should be viewed as exploratory.

CONCLUSION: In this real-world cohort, positive CSF mNGS results supported an infectious etiology more strongly than negative results excluded it. Max-read-based stratification may have exploratory interpretive value for positive findings, but it should not be considered a validated clinical decision rule and requires confirmation in larger multicenter studies with standardized reference standards.}, } @article {pmid42582222, year = {2026}, author = {Zhang, Q and Zhang, Z and Zhang, Z and Qin, G and Jin, M and Chen, B and Yu, Y and Wang, T and Wang, M and Lu, T and Zhu, D and Cui, L and Qian, H and Rillig, MC and Zhu, YG}, title = {Potential plastic biodegradation in lakes worldwide.}, journal = {Innovation (Cambridge (Mass.))}, volume = {7}, number = {8}, pages = {101338}, pmid = {42582222}, issn = {2666-6758}, abstract = {Plastic pollution is ubiquitous, yet the biodegradation of plastic waste remains poorly understood due to limited knowledge of microbial plastic degradation potential. Here, we demonstrate that plastic waste shapes the global distribution of plastic-degrading potential across 182,661 lakes worldwide using integrated metagenomic and machine learning analyses and identify a tipping point (≥7.44 particles/m[3]) for effective in situ bioremediation. We constructed, for the first time, a catalog of candidate plastic-degrading bacteria, including 15,715 nonredundant enzyme homologs and 4,856 metagenome-assembled genomes. To facilitate future applications, we developed a computational approach to categorizing candidate plastic-degrading bacteria according to their degradation potential, ecological risk, environmental adaptation, and competition capacity. Furthermore, we customized eight template culture media based on the growth factor biosynthesis profiles of high-priority candidate plastic-degrading bacteria. Using these media, we successfully enriched the plastic-degrading microbial communities and isolated a high-priority strain, Serratia ficaria HfyG-1, from Xiazhu Lake, which harbors a wide variety of previously uncharacterized putative degrading enzymes that effectively degrade polylactic acid and polyethylene terephthalate. Our study provides a molecular resource for the bioremediation of plastic-polluted environments worldwide and highlights a proof-of-concept framework for identifying, investigating, and exploiting unknown functional microorganisms for practical applications.}, } @article {pmid42582600, year = {2026}, author = {Chen, J and Fan, W and Chen, X and Zhang, H and Feng, M and He, S and Song, C and Wang, J}, title = {Domestication shapes the gut microbial structure and metabolic function in felids: a metagenomic study of wild and domestic cats.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1828152}, pmid = {42582600}, issn = {1664-302X}, abstract = {INTRODUCTION: The domestication process has profoundly altered the dietary patterns and living conditions of cats, with corresponding effects on their gut microbiome.

METHODS: This study compared the gut microbiota composition and metabolic functions between wild felids (Otocolobus manul and Felis bieti) and domestic cats using metagenomic sequencing.

RESULTS: Taxonomic analysis revealed significantly higher microbial alpha diversity and distinct community structure in wild felids compared to domestic cats. The gut microbiota of domestic cats was characterized by a higher relative abundance of Bacteroidota (when compared to F. bieti) and of Pseudomonadota, Uroviricota, and Cyanobacteriota, as well as an enrichment of carbohydrate-associated genera such as Segatella. In contrast, wild felids exhibited enrichment of potential pathogens (e.g., Clostridium perfringens, Escherichia coli) and genera including Clostridium and Fusobacterium, alongside a higher abundance of microbial genes linked to protein degradation and fermentation. Functional metagenomic analysis further identified consistent differences in microbial metabolic potential across both wild species comparisons. Wild felids showed higher abundances of genes involved in butyrate production, lysine degradation, and de novo synthesis of vitamins and cofactors. Domestic cats, in contrast, exhibited enrichment of genes for plant polysaccharide hydrolysis, ketone body formation, aromatic amino acid biosynthesis, and salvage of folate derivatives.

DISCUSSION: These results suggest that domestication is associated with a shift in the gut microbial functional repertoire - from a butyrogenic, protein-catabolic, and de novo-synthesizing profile in wild felids toward a more carbohydrate-hydrolyzing, ketogenic, and salvage-oriented profile in domestic cats, reflecting dietary and environmental adaptations.}, } @article {pmid42582632, year = {2026}, author = {Tshisekedi, KA and Van Den Bossche, T and Martens, L and De Maayer, P and Botes, A}, title = {Temporal and Functional Profiling of the Microbiome of High and Low Nitrogen Content Barley Seed in Silo Storage.}, journal = {Food science & nutrition}, volume = {14}, number = {8}, pages = {e72179}, pmid = {42582632}, issn = {2048-7177}, abstract = {Barley grain quality is influenced by nitrogen content and storage conditions; however, their impact on the composition and function of the grain microbiome is not well understood. This study combined metataxonomic (16S rRNA and ITS) profiling, metagenome sequencing, and metaproteome analyses to characterize the structure and function of the barley grain microbiome. Grains with high (> 1.5%) and low (< 1.5%) nitrogen content from a single barley cultivar (Kadie) were sampled at harvest and after 3, 6, and 9 months of storage. Amplicon sequencing revealed a community dominated by Proteobacteria, Firmicutes, and Ascomycota, while metagenomics confirmed the abundance of genera such as Erwinia, Pantoea, and Pseudomonas, aligning with previous reports of barley endophytes. While a consistent set of core microbial genera was identified, their relative abundances varied throughout storage. Metagenomic analysis revealed the high-nitrogen grain microbiome had potential for rapid metabolic activity that declined post-harvest, whereas the low nitrogen grain community sustained prolonged metabolic potential. Metaproteomics confirmed that these functional shifts revealed a temporal transition from active growth to stress tolerance. Findings from this work contribute to a better understanding of the barley grain microbiome during prolonged storage, offering insights that could help optimize storage for malting and brewing.}, } @article {pmid42583033, year = {2026}, author = {Bi, D and Yu, S and Zhang, M and Huang, Y and Dou, Z and Tian, B and Lu, J}, title = {The gut virome and regulatory T cell axis in health and systemic disease.}, journal = {Microbiome research reports}, volume = {5}, number = {2}, pages = {14}, pmid = {42583033}, issn = {2771-5965}, abstract = {The gut virome, comprising bacteriophages and eukaryotic viruses, represents a complex and dynamic component of the intestinal microbiome whose functional significance has long been underestimated. Emerging evidence highlights the gut virome as a pivotal modulator of the host immune system, particularly in regulating the balance and function of regulatory T cells (Tregs), which are essential for maintaining immune homeostasis. This review distinguishes two mechanistic axes by which the virome influences Tregs: (i) an indirect 'virome-bacteriome-metabolite-Treg axis', and (ii) a direct 'viral pathogen-associated molecular patterns (PAMPs)-pattern recognition receptors (PRRs)-Treg' signaling axis. This review comprehensively examines the dualistic role of the gut virome in preserving intestinal equilibrium and its involvement in the pathogenesis or amelioration of intestinal inflammatory disorders such as inflammatory bowel disease (IBD). Furthermore, the influence of the gut virome extends beyond the gut, potentially impacting systemic immune-related diseases. By integrating recent advances in metagenomics, viromics, and immunology, we elucidate the molecular mechanisms through which the gut virome orchestrates immune regulation. This synthesis aims to provide a comprehensive understanding of the gut virome as a critical immune regulator and to explore its potential as a biomarker for disease diagnosis and a novel target for therapeutic intervention.}, } @article {pmid42583788, year = {2026}, author = {Han, L and Wu, X and Gong, B and Li, X and Li, X and Wang, Z}, title = {A Two-Sample Mendelian Randomisation Analysis of the Oral Microbiome and Oral/Oropharyngeal/Tongue Cancers.}, journal = {Oral health & preventive dentistry}, volume = {24}, number = {}, pages = {613-621}, doi = {10.3290/j.ohpd.c_2778}, pmid = {42583788}, issn = {1757-9996}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Microbiota/genetics ; *Tongue Neoplasms/microbiology ; *Oropharyngeal Neoplasms/microbiology ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; *Mouth Neoplasms/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Tongue/microbiology ; }, abstract = {OBJECTIVE: To assess the potential causal relationships of the oral microbiome with the risks of oral cancer, oropharyngeal cancer, and tongue cancer using two-sample Mendelian randomisation (MR) analysis, while distinguishing these from reverse causal effects of the cancers on microbial abundance.

METHODS AND MATERIALS: Using single-nucleotide polymorphisms as instrumental variables, we applied the MR inverse-variance-weighted approach to evaluate the effects of the dorsal-tongue and salivary microbiomes on oral, oropharyngeal, and tongue cancers. Analyses were conducted with the R package TwoSampleMR, leveraging genome-wide association study (GWAS) summary statistics from CNGBdb, the FinnGen consortium, and other sources. Sensitivity, heterogeneity, and pleiotropy assessments were performed. Additionally, reverse MR sensitivity analyses were conducted to explore the possible causal influence of cancers on the oral microbiota.

RESULTS: Using a single nucleotide polymorphism (SNP) significance threshold of p 5 × 10-6, our large-scale MR study revealed genetically supported causal relationships between microbial taxa derived from saliva and the tongue and the risk of oral, oropharyngeal, and tongue cancers. Integrating these results, we found that both 's Veillonella_rogosae_mgs_2008' and 's unclassified_mgs_1048' conferred a reduced risk of oropharyngeal and tongue cancers. Sensitivity analyses based on heterogeneity tests and pleiotropy evaluations further corroborated the robustness of our findings, lending additional credibility to the conclusions.

CONCLUSION: This study leveraged large-scale publicly available genetic data and identified significant causal relationships between the oral microbiota and cancers of the oral cavity, oropharynx, and tongue. Reverse MR analyses indicated that oral and tongue cancers may in turn alter the abundance of specific oral microbes, suggesting a potential bidirectional causal loop. Future work should integrate metagenomic data to further validate these microbiota-cancer associations.}, } @article {pmid42583799, year = {2026}, author = {Lee, I and Suk, KT and Park, JY and Yong, D and Kim, DJ and Kim, BS and Lee, SS}, title = {Fecal microbiota transplantation accelerates clearance of carbapenemase-producing Enterobacterales intestinal carriage: influence of recipient gut microbiome ecology.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag414}, pmid = {42583799}, issn = {1537-6613}, abstract = {BACKGROUND: Persistent intestinal carbapenemase-producing Enterobacterales (CPE) carriage challenges infection prevention and antimicrobial stewardship. We evaluated fecal microbiota transplantation (FMT) for decolonization and response-associated recipient microbiome features.

METHODS: This prospective cohort study assessed intestinal CPE clearance in 131 adult carriers (68 receiving FMT; 63 under observation). Responders achieved clearance, defined as three consecutive negative rectal surveillance cultures for CPE, obtained at 3-day intervals within 1 month after FMT. Following least absolute shrinkage and selection operator (LASSO)-based covariate selection, Cox proportional hazards models estimated associations between FMT and time to successful decolonization within prespecified 0-30-day and 0-90-day windows. A longitudinal metagenomic subcohort of 21 FMT recipients (102 fecal samples) underwent shotgun sequencing to characterize taxonomic composition, microbial network organization, functional pathways, antimicrobial resistance genes (ARGs), and donor engraftment.

RESULTS: After LASSO-based covariate selection, FMT was associated with faster CPE clearance than observation at 1 month (hazard ratio, 4.02; 95% confidence interval, 1.84-8.79), with effects sustained at 3 months. Responders showed relatively preserved baseline microbial network organization and enrichment of taxa annotated with arginine-related pathway features, suggesting metabolic relevance to microbial niche competition. After FMT, responders had greater engraftment of donor-associated taxa and donor-like ecological reassembly, with reduced Klebsiella pneumoniae dominance and ARG abundance.

CONCLUSIONS: FMT may accelerate intestinal decolonization in CPE carriers; response variability was associated with recipient gut-microbiome ecology, suggesting microbiome-guided patient selection could optimize microbiota-based strategies.}, } @article {pmid42584065, year = {2026}, author = {Roush, C and Whiteley, M}, title = {Dental wastewater reveals a hidden reservoir of oral bacteriophage diversity.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0182026}, doi = {10.1128/spectrum.01820-26}, pmid = {42584065}, issn = {2165-0497}, abstract = {Bacteriophages (phages) are being explored as alternatives or complements to antibiotics because of their ability to selectively kill bacterial pathogens. However, phages that infect many oral bacteria remain undiscovered. Here, we discovered that dental wastewater harbors previously underexplored phage diversity. Viral particles concentrated from dental wastewater displayed diverse morphologies, including abundant filamentous phage-like particles. Deep long-read metagenomic sequencing of concentrated viral particles generated 7.4 billion bases of sequence data and yielded 255 medium- to high-quality viral operational taxonomic units (vOTUs), including 46 predicted complete genomes. Comparison with large phage databases revealed that 63 of these 255 vOTUs had no detectable match, indicating that extensive sequencing of dental wastewater substantially expands the number of potential bacteriophages associated with the human oral microbiome. Host prediction linked many vOTUs to oral-associated bacterial taxa, including species with few or no previously reported phages, such as Porphyromonas gingivalis, Tannerella forsythia, and Candidatus Saccharibacteria. Functional annotation identified diverse genes associated with antiphage defense systems within a subset of vOTUs, suggesting that oral phages may contribute to the movement of genes encoding bacterial immune functions within the oral microbiome. Together, these findings expand the known oral phageome and show that dental wastewater contains a largely untapped diversity of phages.IMPORTANCEThe human oral cavity contains a diverse microbial community, but the bacteriophages (phages) that infect many oral bacteria remain poorly characterized. This gap limits our understanding of how phages shape oral microbial communities. Here, we show that dental wastewater is an underexplored source of oral phage diversity. Deep long-read metagenomic sequencing revealed 255 medium- to high-quality phage operational taxonomic units, many of which are not present in existing oral phage databases. These genomes include predicted phages of periodontal disease-associated bacteria and other oral taxa with few or no known phages. Dental wastewater therefore expands the known human oral phageome and reveals candidate phages linked to bacteria associated with oral health and disease.}, } @article {pmid42584072, year = {2026}, author = {Eiler, A}, title = {Rethinking evolutionary inference in metagenomic time series.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0069326}, doi = {10.1128/msystems.00693-26}, pmid = {42584072}, issn = {2379-5077}, abstract = {As ecologists increasingly use metagenomic time series to track evolution in the wild, there is a risk of misinterpreting ecological dynamics as rapid adaptation. This Perspective identifies methodological limitations that generate misleading signatures of microbial evolution. A primary issue is confusing evolutionary change (driven by de novo mutation or horizontal gene transfer) with ecological lineage turnover, such as seasonal oscillations or the reactivation of dormant lineages. Current metagenome-assembled genomes can collapse micro-diverse lineages and decouple adaptive mobile elements, creating inaccurate genomic signatures of sweeps or stasis. To address these issues, I propose a framework integrating long-read sequencing, pangenome graph theory, and forward-time simulations to model populations as temporal genetic networks and better resolve microbial evolutionary dynamics.}, } @article {pmid42584101, year = {2026}, author = {Yu, D and Zhang, L and Agu, D and Gao, N and Xiao, Y and Zhang, M and Zhang, J and Yan, J}, title = {Temporal succession of microbiomes and resistomes during buried rat carcass decomposition.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0043726}, doi = {10.1128/msphere.00437-26}, pmid = {42584101}, issn = {2379-5042}, abstract = {Burial is a prevalent approach for disposing of human and animal carcass. Carcass decomposition is a key natural disturbance that reshapes microbial communities and modulates biogeochemical cycles. Animal intestines serve as critical natural reservoirs of antibiotic resistance genes (ARGs), and carcass decomposition concurrently remodels intestinal bacterial assemblages and resistome profiles. Most previous studies have characterized microbial succession in surface-exposed carcasses, yet the coordinated temporal shifts of intestinal microbiota, resistomes, and horizontal gene transfer (HGT) signatures within buried carcasses remain underexplored. We established a buried rat carcass model and performed metagenomic sequencing to characterize temporal dynamics of intestinal bacteria, ARGs, mobile genetic elements (MGEs), and HGT events. Bacterial communities underwent directional succession accompanied by reduced α-diversity and stage-specific β-diversity. Proteobacteria gradually outcompeted Firmicutes and Bacteroidetes to become dominant taxa. The resistome followed regular temporal changes: tetracycline and macrolide-lincosamide-streptogramin (MLS) ARGs prevailed in early decomposition, while multidrug, β-lactam, polymyxin, and quinolone ARGs accumulated in mid-late stages, with ARG richness peaking on day 28. Approximately 83% of temporally dynamic ARG subtypes were positively correlated with decomposition duration. Procrustes analysis (R[2] = 0.859) revealed strong correlations between bacterial succession and resistome dynamics, with Proteobacteria as potential multidrug-resistant hosts and major HGT donors. This study identifies a correlative cascade of microbial succession that drives MGE functional shift, which in turn increased HGT potential and ultimately leads to resistome accumulation in buried carcass intestinal habitats. These findings expand the theoretical framework of disturbance-driven microbial-resistome co-succession and offer insights into drivers of antibiotic resistance propagation in terrestrial cadaver systems.IMPORTANCEAnimal carcass burial is a ubiquitous natural terrestrial disturbance, and carcass intestinal contents represent a major endogenous reservoir of environmental antibiotic resistance genes (ARGs). Although extensive research has characterized microbial succession of exposed carcasses, the co-occurrence patterns of gut microbiome and resistome together with associated horizontal gene transfer (HGT) under buried conditions remain underexplored. Using metagenomic profiling of decomposing rat intestinal feces, this study explores a potential correlative cascade spanning bacterial succession, mobile genetic element (MGE) functional shifts, increased HGT potential, and gradual ARG enrichment. Our findings expand the ecological data set focused on subsurface buried carcass habitats and advance mechanistic knowledge of coupled microbiome-resistome succession driven by postmortem decomposition.}, } @article {pmid42584108, year = {2026}, author = {Vaziri, GJ and Pritchard, JC and Howard, JI and Stamm, GE and O'Connor, DH and Newman, CM and Aliota, MT and Dzikwi-Emennaa, A}, title = {Metagenomic sequencing detects viruses and bacteria in a cross-sectional clinical cohort of undifferentiated febrile illness in Nigeria.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0015726}, doi = {10.1128/msphere.00157-26}, pmid = {42584108}, issn = {2379-5042}, abstract = {UNLABELLED: Molecular and microscopy-based diagnostic capacity is often insufficient or unavailable in places where infectious disease burdens are highest, such as in West Africa. Rapid diagnostic testing (RDT) can provide quick and affordable diagnoses of common infections but is an imperfect solution due to limitations around detecting and dealing with false-negative and false-positive results. An alternative to RDT is unbiased metagenomic sequencing for pathogen surveillance. Here, we present data from unbiased metagenomic sequencing used to identify causes of undiagnosed febrile illness in Jos, Plateau State, Nigeria. Proof of concept for this approach has been demonstrated by several groups who have identified epidemic and endemic viral diseases like Lassa fever, yellow fever, and chikungunya. We show that unbiased deep sequencing and metagenomic analysis can be used to identify RNA viruses in clinical samples. We sequenced RNA from sera of patients (n = 343), many of whom were acutely febrile (76%), in a survey of clinics in Jos. We detected five human-infecting viruses in 39 (11 %) specimens. Among these were hepatitis B virus, human pegivirus, and several anelloviruses. While most of the viruses identified are unlikely to cause clinical symptoms in the patients we sampled, their presence demonstrates the validity of our approach. Additionally, our sequencing data allowed us to identify genetic material from potentially pathogenic bacteria, another possible etiological agent of febrile illness.

IMPORTANCE: In low-resource areas, fevers due to infectious pathogens are a major source of illness, but tools for detecting and identifying such pathogens are often limited. Unbiased approaches for identifying genetic material from all potentially infectious organisms in a sample represent an opportunity for discovering sources of fever. Metagenomic sequencing can improve insight into pathogen landscapes in low-resource settings, potentially providing early detection of disease outbreaks. However, unbiased metagenomic sequencing (mNGS) is no panacea; it is susceptible to contamination and false positives. We used mNGS to evaluate serum from >300 Nigerian clinic-goers in Jos, Nigeria, most of whom (>70%) had fevers of unknown origin. Our goal was to understand arbovirus prevalence in Jos, Nigeria, and identify the sources of infection not routinely monitored for at clinics. We detected hepatitis B virus, as well as nonpathogenic anelloviruses. Our study provides insight into the utility and limitations of mNGS for pathogen surveillance.}, } @article {pmid42584675, year = {2026}, author = {Tozluyurt, A and Acar, A}, title = {Postoperative Nocardia cyriacigeorgica infection after glioblastoma resection: correlating metagenomic next-generation sequencing with conventional microbiology.}, journal = {Naunyn-Schmiedeberg's archives of pharmacology}, volume = {}, number = {}, pages = {}, pmid = {42584675}, issn = {1432-1912}, abstract = {Postoperative nocardial infection after cranial surgery is rare and difficult to diagnose because Nocardia spp. grow slowly in conventional culture. Metagenomic next-generation sequencing (mNGS) can shorten the interval to microbial detection, but read abundance is influenced by commensal DNA and by contamination during sampling, laboratory processing, and sequencing. mNGS findings therefore require correlation with conventional microbiology and with the clinical context. An 84-year-old woman developed purulent surgical wound discharge with epidural empyema approximately 2 weeks after resection of a World Health Organization grade 4 glioblastoma and postoperative corticosteroid exposure. Revision surgery comprised extensive debridement, removal of the infected bone flap and fixation screw, and evacuation of the empyemas. Direct Gram and modified acid-fast stains of the operative specimen showed branching, acid-fast filamentous organisms on day 1. mNGS of abscess fluid reported 196,785 reads assigned to Nocardia cyriacigeorgica on day 7, and culture on buffered charcoal yeast extract agar yielded N. cyriacigeorgica on day 18, confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. More than 20 million reads were assigned to Corynebacterium tuberculostearicum, yet no corresponding coryneform predominance was seen microscopically; its significance was therefore interpreted cautiously as a possible skin-derived or background contribution, although a true polymicrobial contribution could not be excluded. Surgical source control with intravenous meropenem and amikacin was followed by resolution of the infection. Additionally, three multimodal artificial intelligence systems were each queried five times with the same prompt. mNGS enabled earlier species-level recognition of N. cyriacigeorgica than culture, but direct microscopy gave the earliest diagnostic clue and culture remained essential for confirmation and isolate recovery. Taxonomic read abundance must not be equated with causality. The artificial intelligence outputs were discordant between systems and, in one system, incorrect in a stable and reproducible way; this illustrates current limitations rather than clinical readiness and supports the need for prespecified, blinded, multi-case validation before clinical deployment.}, } @article {pmid42584818, year = {2026}, author = {Sharma, S and Sharma, PK and Gupta, E and Dash, PK and Srivastava, A}, title = {Simplified Inhouse Nanoweb Membrane Enrichment Coupled Viral Whole Genome Shotgun Metagenomics Approach for Waste Water Surveillance.}, journal = {Food and environmental virology}, volume = {18}, number = {3}, pages = {}, pmid = {42584818}, issn = {1867-0342}, mesh = {*Genome, Viral ; *Wastewater/virology ; *Metagenomics/methods ; *Sewage/virology ; SARS-CoV-2/genetics/isolation & purification ; India ; *Viruses/genetics/isolation & purification/classification ; *Environmental Monitoring/methods ; COVID-19/virology ; Shotgun Sequencing ; Animals ; }, abstract = {Wastewater/sewage represents a highly complex environmental matrix and harbors various viruses including viruses of epidemic and pandemic potential like Influenza A and, SARS-CoV-2. The limitations of available methods for sample concentration are cost, efficiency and time. NGS- metagenomics offer sample to virus genomic characterization for even non-cultivable viruses at highest resolution. In this study, we have collected samples from sewage treatment plants located in Gwalior region of Central India (December 2023 to March 2025). In this study a novel in house nanoweb membrane-based sample enrichment followed by magnetic bead based nucleic acid extraction was optimized in conjunction to shotgun whole genome metagenomics on Nanopore and ion torrent NGS. Both the methods were found comparable with commercially available methods by virus specific TaqMan qPCR. Both the methods were found successful in virus recovery at two log through 10[2]GC/50 ml feline calicivirus, Influenza A virus, Zika virus, SARS-CoV-2 spiked in sewage matrix alone or in mixture), suggesting the optimized protocol found working for virus characterization at strain level. Here, we have standardized a simple field amenable waste water sample enrichment followed by nucleic acid extraction protocol, that can easily be integrated with latest onsite downstream molecular diagnostic platforms. The developed method is very simple, cost effective and field deployable. This will help to develop a suitable strategic plan for sewage surveillance towards early warning/microbial forensics and future decisions for prevention and therapeutic interventions.}, } @article {pmid42584931, year = {2026}, author = {Kaszecki, E and Azimychetabi, Z and Emery, RJN and Saville, BJ}, title = {Integrated transcriptomic and hormonomic insights into cadmium tolerance of a Euglena mutabilis fungal-algal-bacterial consortium.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {8}, pages = {}, doi = {10.1099/mic.0.001750}, pmid = {42584931}, issn = {1465-2080}, mesh = {*Cadmium/metabolism/toxicity ; *Transcriptome ; *Euglena/genetics/metabolism/drug effects ; *Microbial Consortia/genetics ; *Fungi/genetics/metabolism ; Gene Expression Profiling ; *Bacteria/genetics/metabolism/classification ; Chloroplasts/metabolism ; }, abstract = {Acidic, metal-contaminated environments harbour specialized microbial consortia adapted to extreme stress. We examined an environmental Euglena mutabilis culture naturally associated with Talaromyces and Acidiphilium acidophilum and exposed it to cadmium (Cd). Integrated transcriptomic, hormonal, structural and taxonomic analyses revealed a coordinated Cd-tolerance strategy. RNA sequencing showed differential regulation of metal transporters consistent with a shift from Cd uptake to intracellular sequestration. Transmission electron microscopy confirmed Cd compartmentalization within chloroplasts and increased paramylon granules. Cd exposure suppressed light-harvesting complex genes and formate/nitrite transporters while maintaining core photosynthetic function. Hormone profiling indicated strong repression of bioactive auxin and cytokinin (CK) free bases, alongside accumulation of CK nucleotides and downregulation of CK biosynthetic and activation genes. Metagenomics revealed Cd-driven enrichment of Talaromyces and Acidiphilium, implicating them in detoxification and stress support. Together, these responses highlight early Cd uptake followed by chloroplast-based detoxification, metabolic buffering via paramylon, hormonal downregulation of growth and community-mediated resilience.}, } @article {pmid42585057, year = {2026}, author = {de Oliveira, FF and A C Fernandes, M}, title = {BIKE: A Binary $K$-mer Exact Counter with Alphabet-Independent Memory and Deterministic Parallelism.}, journal = {IEEE transactions on computational biology and bioinformatics}, volume = {PP}, number = {}, pages = {}, doi = {10.1109/TCBBIO.2026.3723002}, pmid = {42585057}, issn = {2998-4165}, abstract = {K-mer counting is a fundamental computational task in bioinformatics, underpinning genome assembly, metagenomic classification, error correction, and similarity analysis. Existing exact-counting methods rely on hash tables or static allocation strategies whose memory requirements grow exponentially with the alphabet size and substring length, rendering them impractical for amino acid sequences at moderate-to-large values of $k$. We propose BIKE (Binary K-mer Exact Counter), a novel exact k-mer counting algorithm whose memory footprint depends exclusively on the input sequence length $n$, independently of the alphabet size m or the $k$-mer length $k$. BIKE decomposes the counting problem into $n-1$ mutually independent pivot-based comparison blocks operating entirely on binary matrices, requiring only one bit per entry, and employs a union-find aggregation mechanism that guarantees exact counts for $k$-mers of arbitrary multiplicity. This structural regularity yields a fully deterministic degree of parallelism, enabling closed-form analytical models that provide accurate execution-time predictions under ideal parallel execution assumptions. Experimental results on real biological sequences confirm functional correctness and demonstrate memory reductions of up to three orders of magnitude over classical exact methods for amino acid alphabets. Analytical performance projections, derived from the closed-form parallel model, indicate that an FPGA realisation of BIKE would be expected to outperform CPU-based dynamic allocation at moderate sequence lengths; however, these remain theoretical estimates pending hardware implementation. BIKE is therefore presented as a theoretical and data-structural contribution, establishing a new algorithmic foundation for alphabet-independent, exactly-counted, and deterministically parallel $k$-mer analysis.}, } @article {pmid42585229, year = {2026}, author = {Fellows Yates, JA and Hübner, A and Borry, M and , and Warinner, C}, title = {De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.}, journal = {PLoS computational biology}, volume = {22}, number = {8}, pages = {e1014591}, doi = {10.1371/journal.pcbi.1014591}, pmid = {42585229}, issn = {1553-7358}, mesh = {*DNA, Ancient/analysis ; *Metagenomics/methods ; *Metagenome/genetics ; *Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Humans ; }, abstract = {Ancient DNA provides a direct window into the evolutionary processes that have shaped living microbial species today, as well as their now extinct relatives. Advances in both sequencing methods and de novo assembly techniques have not only resulted in a flood of modern metagenomic sequencing data, but they have also allowed palaeogenomicists to retrieve vast amounts of ancient DNA from past microorganisms, including species and strains without modern reference genomes. However, the degraded nature of ancient DNA means that the standard techniques of genome assembly developed for modern DNA are unlikely to perform effectively, unless heavily modified. This hinders the incorporation of ancient data into broader metagenomic studies that would otherwise benefit from having deep time information on the evolution of different microbial species. In this primer and protocol paper, we provide guidance on ways to adapt existing metagenomic de novo assembly processes, including data input, tools, and settings, in order to perform more robustly and effectively on ancient DNA. After assembly, we then further describe how ancient DNA contigs can be identified and validated. The key steps of ancient metagenomic assembly are now integrated in a dedicated ancient DNA mode in the established pipeline nf-core/mag. By introducing support for ancient DNA data in nf-core/mag, we aim to improve the ability of researchers to more regularly integrate de novo assembled ancient microbial data into broader metagenomics studies of microbial ecology and evolution.}, } @article {pmid42585836, year = {2026}, author = {Cao, Y and Du, P and Zhai, R and Guo, Y and Lin, M and Wang, Z}, title = {Drought stress adaptation in Ficus carica L.: Modulation of ROS scavenging, nitrogen uptake, and rhizosphere bacterial community assembly and functions.}, journal = {Microbiological research}, volume = {313}, number = {}, pages = {128678}, doi = {10.1016/j.micres.2026.128678}, pmid = {42585836}, issn = {1618-0623}, abstract = {Rhizosphere microorganisms are crucial for plant drought resistance; however, their response to drought stress in fig plants remains poorly understood. In this study, potted 'BoJi Red' fig plants were utilized to systematically investigate drought-induced changes in the structure, assembly processes, and functional potential of rhizosphere bacterial communities. The results showed that drought significantly inhibited fig growth, photosynthesis, and nitrogen uptake, while increasing reactive oxygen species (ROS) content and antioxidant enzyme activities, although these enzyme activities declined under severe drought conditions. Bacterial community richness and diversity significantly increased under moderate and severe drought, shifting toward drought-resistant groups, notably Actinomycetota and Bacillota. The number of nodes, links, and key species in the microbial co-occurrence network decreased as drought intensified, with stochastic processes dominating community assembly. Moreover, ecological niche breadth and the proportion of generalist species increased with drought severity. Notably, Nocardioidaceae was significantly enriched under drought, and metagenomic profiling indicated this taxon is strongly associated with carbohydrate metabolism pathways, with predicted genetic potential to participate in soil carbon turnover and nutrient transformation. Additionally, drought significantly reduced the abundance of nitrogen-fixing genes (nifD, nifK) and weakened the relative contribution of Rhizobiaceae to nitrogen fixation; correlative functional profiling suggests Nocardioidaceae may possess alternative nitrogen cycling pathways that could partially offset suppressed rhizosphere nitrogen fixation capacity. Overall, these findings indicate that the fig plant response to drought stress involves both physiological adjustments in the host and functional reconfiguration of the rhizosphere microbial community, with Nocardioidaceae playing a key role in maintaining rhizosphere functions and enhancing drought tolerance.}, } @article {pmid42585873, year = {2026}, author = {Wang, H and Liang, Z and Guo, W and Ni, L and Lv, X}, title = {Mechanized Qu-making may contribute to lactic acid bacteria overproliferation in Hongqu rice wine brewing: Insights into microbial dysbiosis and flavor quality deterioration.}, journal = {International journal of food microbiology}, volume = {461}, number = {}, pages = {112013}, doi = {10.1016/j.ijfoodmicro.2026.112013}, pmid = {42585873}, issn = {1879-3460}, abstract = {Hongqu (HQ) serves as the core saccharification and fermentation starter (commonly referred to as "Qu") for Hongqu rice wine (HQW), a traditional Chinese fermented alcoholic beverage celebrated for its unique sensory characteristics and potential health-promoting properties. Driven by industrialization, mechanized Qu production has been progressively implemented to enhance process reproducibility, scalability, and operational efficiency. However, the implications of this technological transition on microbial community assembly, metabolic function and flavor formation during HQW brewing remain insufficiently characterized. To address this gap, this study employed an integrated metagenomic and metabolomic approach to comparatively analyze the taxonomic composition and functional metabolic profiles of mechanized Hongqu (MHQ) and traditional Hongqu (THQ), and further monitored their dynamic succession throughout HQW brewing process. Results demonstrated that MHQ exhibited significantly higher saccharification capacity and markedly enriched abundance of Saccharomyces cerevisiae, yet displayed a substantial reduction in Aspergillus niger compared with THQ (1.06% versus 43.41%). Paradoxically, despite these favorable starter attributes, HQW fermentation inoculated with MHQ induced an uncontrollable proliferation of lactic acid bacteria (LAB), predominantly represented by Pediococcus acidilactici, Lactiplantibacillus plantarum and Weissella paramesenteroides. This LAB-dominant consortium proliferated markedly during HQW fermentation, resulting in a community compositional shift toward bacterial dominance, evidenced by a fungi-to-bacteria ratio of 1.00:5.88 in MHQW, whereas THQW retained fungal dominance, with a corresponding ratio of 1.00:0.26. This structural shift coincided with significant declines in the relative abundances of functional fungi, including Saccharomyces cerevisiae and Monascus purpureus, possibly involving changes in niche occupation and acidification. These microbial community changes were associated with a metabolic shift characterized by excessive accumulation of organic acids, dysregulated biogenic amine profiles, depletion of free amino acids, and diminished synthesis of key volatile flavor compounds. Quantitatively, MHQW exhibited significantly higher final titratable acidity (12.67 g/L vs. 5.76 g/L), lower ethanol yield (17.29% v/v vs. 20.39% v/v), elevated total organic acid content (16.62 g/L vs. 6.28 g/L), and reduced total free amino acid concentration (3366.23 mg/L vs. 4303.93 mg/L) relative to THQW. Collectively, these findings indicate that mechanized Qu-making may disrupt the delicate "fungi-bacteria" ecological equilibrium essential for robust and balanced HQW fermentation, potentially favoring LAB proliferation. This study highlights the potential value of rational microbiome design to control LAB proliferation while maintaining functional fungi, which is important for optimizing mechanized Qu-making processes and improving flavor quality and fermentation robustness in HQW production. Collectively, our work provides a mechanism-informed framework for advancing Huangjiu modernization through rational microbiome engineering.}, } @article {pmid42585927, year = {2026}, author = {Ma, J and Qin, K and Qiao, Z and Ren, Z and Yang, X and Liu, Y}, title = {Integrative multi-omics reveals comprehensive gut-liver-adipose metabolic changes in peak laying hens with high or low egg production.}, journal = {Poultry science}, volume = {105}, number = {11}, pages = {107493}, doi = {10.1016/j.psj.2026.107493}, pmid = {42585927}, issn = {1525-3171}, abstract = {Eggs serve as an indispensable global nutritional resource, sustaining the economic foundation of the commercial poultry industry. To meet this continuous demand, egg formation involves an exceptionally energy-intensive biological process requiring continuous yolk precursor synthesis, which imposes a massive metabolic burden on laying hens. However, the comprehensive metabolic differences across the gut-liver-adipose axis between peak laying hens with high or low egg production remain incompletely characterized. A total of 180 healthy Hy-Line Brown laying hens (45-week-old) were continuously fed and monitored for production performance over a 6-week period. Following the exclusion of individuals with extremely low egg production (≤10 eggs during the 6-week monitoring period; n = 5) and candidate hens that repeatedly produced unqualified eggs over multiple weeks (n = 20), the remaining hens were ranked by 6-week average laying rate and allocated into FH (high-production hens at 50 weeks of age, n = 15) and FL (low-production hens at 50 weeks of age, n = 14) groups. Initial body weight did not differ significantly between groups (FH: 1936 ± 29.0 g; FL: 1894 ± 48.2 g; P-value = 0.446). We integrated transcriptomic, untargeted metabolomic, targeted bile acid metabolomics, and microbiome (16S rRNA and metagenomic) profiles to characterize comprehensive metabolic changes across the gut-liver-adipose axis associated with divergent egg-production phenotypes. The results showed that: (1) FH hens exhibited higher serum APOB and lower conjugated bile acids (TCDCA, TCA, and THDCA), with hepatic upregulation of FASN, PPARA, CPT1A, and VTG1 along with downregulation of CYP7A1, CYP7B1, CYP8B1, and CYP27A1; (2) intersecting module hub genes (MHGs) with differentially expressed genes (DEGs) identified 354 upregulated and 299 downregulated core genes, with EEF2 identified as the primary hepatic downregulated hub gene; (3) in abdominal fat, GSEA revealed significant enrichment in fatty acid transport (NES = 1.54), long-chain fatty acid metabolic process (NES = 1.39), and steroid hormone biosynthesis (NES = 1.85), accompanied by significant downregulation of ANGPTL4 and upregulation of HSD3B1, VTG1, VTG2, and VTG3; (4) ileal mucosal transcriptomics identified 619 DEGs (502 upregulated), with GSEA highlighting enrichment in cell junction organization (NES = 1.52) and tube morphogenesis (NES = 1.39), which were further categorized into functional modules including enteric synaptic signaling, epithelial adhesion, mucosal vascularization, and tissue renewal; (5) the functional profile of the ileal microbiota in FH hens showed enrichment of functions related to complex carbohydrate degradation and carbohydrate-binding modules, with keystone taxa including Blautia and Bifidobacterium associated with production and lipid markers. Collectively, these findings suggest that high egg production during the peak laying period is associated with coordinated metabolic differences across the liver, abdominal fat tissue, and intestine. The observed profiles included reduced hepatic translation-related and primary bile acid synthesis-related signatures, adipose endocrine-related changes and microbial functional potential related to carbohydrate utilization and antioxidant-related functional potential. These findings provide candidate multi-omics features for precision nutritional strategies and genetic improvement in commercial poultry.}, } @article {pmid42585954, year = {2026}, author = {Yang, S and Zhang, X and Wang, K and Zhao, X and Li, X}, title = {Pyrite fuels electron fluxes to accelerate hydrocarbon removal in coastal wetland soil.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143275}, doi = {10.1016/j.jhazmat.2026.143275}, pmid = {42585954}, issn = {1873-3336}, abstract = {Natural sulfide minerals drive subsurface electron flow, but their role in hydrocarbon turnover is poorly understood. Here, we investigated whether pyrite (FeS2) can sustain electron transfer and accelerate petroleum hydrocarbon degradation in coastal wetland soils using a microbial electrochemical system (MES). High-dose pyrite amendment markedly enhanced long-term voltage output and increased cumulative charge by 34% over 120 days, indicating persistent subsurface electron release. Since pyrite improved soil conductivity and stimulated extracellular electron transfer, as reflected by elevated cytochrome c, extracellular polymeric substances production, and electroactive protein-like components. These electron transfer processes nearly doubled total petroleum hydrocarbon removal and promoted dissolved organic matter transformation from recalcitrant lignin-like compounds toward more bioavailable lipid- and protein-like components. Meanwhile, pyrite oxidation intensified Fe[2 +]/Fe[3+] cycling, secondary iron mineral formation, and coupled carbon-iron-sulfur transformations. Metagenomic analysis further revealed enrichment of hydrocarbon degraders, electroactive microorganisms, sulfate reducers, and methanogens, together with upregulation of genes involved in carbon metabolism, nitrogen cycling, iron-sulfur transformation, conductive pili assembly, and ubiquinone biosynthesis. These findings identify pyrite as a geological energy node that fuels persistent subsurface electron fluxes to enhance hydrocarbon removal in coastal wetland soils, highlighting the potential of activating natural iron-sulfur minerals for in situ bioremediation in anoxic coastal zones.}, } @article {pmid42585955, year = {2026}, author = {Han, X and Gao, Y and Chen, J and Yang, P and Liang, X and Wang, L and Ge, Y and Gui, H and He, Y and Zhan, F and Zhang, X and Kuzyakov, Y}, title = {Microplastics disrupt bacterial defense within the plant-AMF-bacteria continuum to amplify Cd bioavailability.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143257}, doi = {10.1016/j.jhazmat.2026.143257}, pmid = {42585955}, issn = {1873-3336}, abstract = {The plant-arbuscular mycorrhizal fungi (AMF)-bacteria continuum provides a critical barrier against heavy-metal toxicity, but how microplastics (MPs) disrupt rhizosphere functions and exacerbate phytotoxicity remains unresolved. Using a maize-AMF-bacteria system in cadmium (Cd)-contaminated soil, we investigated two MP fractions differing in size and morphology added at increasing Cd contents. Although AMF colonization remained resilient, MPs induced fraction-dependent bacterial functional decoupling. Small MPs shifted the microbiome from extracellular Cd-immobilizing taxa (Sphingomonadaceae and Rhizobiaceae) toward intracellular stress-tolerant lineages. Large MPs restricted bacterial contacts, suppressing density-dependent cooperation. Metagenomic profiling and analysis of metagenome-assembled genomes (MAGs) revealed reduced potential for quorum sensing, ABC transporters, and alpha-linolenic acid metabolism under large MP exposure, compromising biofilm formation and extracellular Cd sequestration. Partial least squares path modeling indicated that bulk-soil chemistry did not define Cd uptake by plants. Instead, depletion of available Cd in soil reflected a biological sink associated with enhanced plant uptake. Enhanced Cd accumulation was associated with loss of rhizosphere defense mechanisms: potential root-barrier disruption by large MPs and weakened microbial buffering. Consequently, large MPs increased the Cd bioconcentration factor by 57.5%, compared with 32.1% for small MPs. These findings show that MPs amplify legacy Cd risks without increasing bulk-soil Cd availability, through disruption of root-interface integrity and microbial protection.}, } @article {pmid42585962, year = {2026}, author = {Xian, ZN and Hu, J and Wang, Z and Gong, H and Dai, X and Zhu, N}, title = {Process-resolved effects of dibutyl phthalate on sludge anaerobic fermentation: Enzyme inhibition and metabolic disruption underlie the suppression of acidogenesis.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143232}, doi = {10.1016/j.jhazmat.2026.143232}, pmid = {42585962}, issn = {1873-3336}, abstract = {Growing evidence suggests that leaching of plasticizers such as dibutyl phthalate (DBP) from microplastics inhibits methanogenesis in anaerobic digesters treating waste activated sludge. However, how DBP influences upstream anaerobic fermentation (AF) remains unclear. This study evaluated the effects of DBP on overall sludge AF and separately on solubilization, hydrolysis, and acidogenesis processes. Volatile fatty acid (VFA) production showed a V-shaped response to environmentally relevant DBP concentrations. A reduction of 45.3% was observed at 0.5 mg/L DBP, whereas reductions exceeded 95% at 1-2 mg/L. The inhibition then weakened with increasing DBP, with a 60.5% reduction at 200 mg/L, an upper-bound level selected to bracket the maximum concentration reported in sludge. Stage-specific effects intensified with DBP concentration and peaked at 200 mg/L, where solubilization increased by 34.6%, whereas hydrolysis and acidogenesis decreased by 30.8% and 11.2%, respectively. The combined influence of these processes explained the nonmonotonic VFA response. Notably, enzyme assays and molecular simulations indicated that DBP inhibited ACK in a competitive-like manner and reduced its activity. Metagenomic analysis further indicated that DBP reduced genetic potential for downstream pathways converting pyruvate and acetyl-CoA to fermentation products. Collectively, these results reveal a DBP-induced fluctuating AF response and provide mechanistic insights into optimizing anaerobic treatment of plasticizer-laden sludge.}, } @article {pmid42585964, year = {2026}, author = {Wang, X and Liao, H and Wang, X and Wang, Y and Li, D and Ma, H and Yang, J and Qian, X and Wang, H and Li, Q and Xiu, Z and Yang, Y}, title = {Cobalamin-autonomous Trichlorobacter facilitates robust In situ bioremediation of halogenated solvents.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143046}, doi = {10.1016/j.jhazmat.2026.143046}, pmid = {42585964}, issn = {1873-3336}, abstract = {Organohalide-respiring bacteria (OHRB) are key mediators of chlorinated solvent detoxification in anoxic groundwater, yet their practical application is often constrained by vitamin B12 (cobalamin) auxotrophy and the requirement for strictly controlled anoxic and nutrient conditions. Here, we report the enrichment and characterization of a Trichlorobacter-dominated consortium (NB-12) that sustains efficient dihaloelimination of halogenated alkanes under minimal nutrient and relaxed anoxic constraints. The NB-12 enrichment completely transformed 1,2-dichloroethane (1,2-DCA) to ethene within 40 h (≥3.3 μmol h[-1]) and also dechlorinated 1,2-dichloropropane and 1,1,2-trichloroethane, as well as debrominated 1,2-dibromoethane and 1,2-dibromopropane. Exogenous vitamin B12 supplementation did not enhance dechlorination kinetics or product yields. Amplicon sequencing and metagenomic analyses identified Trichlorobacter lovleyi as the dominant population (>60% relative abundance) and revealed a complete anaerobic cobalamin biosynthesis pathway in the corresponding metagenome-assembled genome, indicating corrinoid autonomy at the community level. Notably, the NB-12 consortium retained sustained dehalogenation activity in non-sterile, unbuffered, and oxygen-leaky mesocosms prepared using only tap water, trace elements, and lactate-conditions mimicking challenging in situ environments. Field bioaugmentation using this "low-input" inoculant resulted in successful aquifer colonization and a reduction in 1,2-DCA concentrations in contaminated groundwater. Together, these results demonstrate that corrinoid-autonomous, Trichlorobacter-dominated enrichments can relax key physiological and operational constraints of OHR-based remediation, expanding the applicability of low-input, cost-effective strategies for in situ treatment of halogenated alkane-contaminated groundwater.}, } @article {pmid42586007, year = {2026}, author = {López-Cañizares, J and Truchado, P and Macrì, M and Cobo-Díaz, JF and Álvarez-Ordóñez, A and Bonetta, S and Allende, A}, title = {Water reuse within a circular economy: Long-read metagenomics reveals distinct residual resistome profiles across full-scale wastewater-reclamation systems in Murcia, Spain.}, journal = {Chemosphere}, volume = {411}, number = {}, pages = {145063}, doi = {10.1016/j.chemosphere.2026.145063}, pmid = {42586007}, issn = {1879-1298}, abstract = {Water reuse is a key pillar of circular economy strategies, particularly in water-scarce regions, by preserving freshwater resources and supporting agricultural production. Current regulations promote the use of reclaimed water for irrigation, placing wastewater treatment plants (WWTPs) at the center of this transition. However, emerging risks related to antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) challenge the safety of reuse as these determinants may persist after treatment. This study evaluated the effectiveness of ozonation, sodium hypochlorite, UV-C irradiation, and membrane bioreactor (MBR) systems in reducing ARGs in effluents from the Region of Murcia (Spain) across five sampling campaigns between 2023 and 2024. Metagenomic sequencing identified ARGs associated with 17 antibiotic classes, with macrolide-, β-lactam-, and tetracycline-ARGs dominating. Total ARG abundance was lower in treated effluents than in influents, with the greatest percentage reduction in MBR system, although based on only two effluent samples. Selected macrolide-, sulfonamide-, tetracycline- and β-lactam-ARGs nevertheless remained detectable after treatment, with distinct gene-specific profiles among the wastewater-reclamation systems. Effluent samples differed in the taxonomic composition of ARG-carrying reads and in the detection of ARGs putatively co-localized on mobilome associated contigs. These findings show that total ARG reduction alone does not fully characterize wastewater-reclamation performance because substantial decreases in total ARG burden were accompanied by different residual resistome profiles. Combining ARG abundance, identity, potential hosts, and genomic context enables a fuller assessment of reclaimed-water treatment. These metagenomic associations indicate potential persistence and mobility but do not constitute direct evidence of horizontal gene transfer or quantitative environmental risk.}, } @article {pmid42575184, year = {2026}, author = {Zha, Y and Wang, Z and Sun, W and Meng, J and Liu, Y and Wang, B}, title = {Metagenomic insights into biogeochemical functional potential and resistome dynamics of PM2.5 microbial communities.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125444}, doi = {10.1016/j.envres.2026.125444}, pmid = {42575184}, issn = {1096-0953}, abstract = {Atmospheric particulate matter harbors diverse microorganisms, yet their functional potential in biogeochemical cycling and the associated risks of resistome remain poorly understood. Here, we performed metagenomic sequencing on PM2.5 samples collected across four months to unravel the microbial genetic repertoire involved in methane, nitrogen, phosphorus, and sulfur cycling, as well as the resistome, and pathogen composition. A broad range of functional genes was detected for each biogeochemical cycle, with more than 65% of gene subtypes shared across all months, indicating conserved functional signatures. In contrast, more than 80% of the resistome showed temporal variation in abundance, with the lowest richness observed in March. Temporal shifts were also observed in resistome composition, with several resistance determinants reaching higher abundances in April and May. Network analysis indicated frequent co-occurrence among several pathogenic and opportunistic taxa. Contig-based profiling identified 51 potential pathogenic taxa, including 32 human- or animal-associated taxa. In addition, both PM10 and PM2.5 concentrations were associated with pathogen abundance and functional gene richness (e.g., antibiotic resistance genes and virulence factors). Together, this metagenomic survey suggests contrasting temporal patterns between conserved biogeochemical functional potential and more variable resistome-related traits in PM2.5 microbial communities. While constrained by limited temporal coverage and sample size, this study provides preliminary insights into the ecological and potential public health relevance of airborne microbial communities in urban environments.}, } @article {pmid42575312, year = {2026}, author = {Benmazouz, I and Kövér, L and Laczkó, L and Gyure, P and Kardos, G}, title = {Carriage of ESBL-Producing Enterobacterales in Urban and Rural Hooded Crows in Hungary.}, journal = {Journal of global antimicrobial resistance}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgar.2026.08.004}, pmid = {42575312}, issn = {2213-7173}, abstract = {BACKGROUND: Considering the increasing reports of antimicrobial resistance (AMR) in wildlife, highlighting its complexity, importance, and spread. We investigated the prevalence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales in the hooded crow.

METHODS: Faecal samples were collected from 52 rural and 212 urban wild crows in Hungary, caught using ladder traps, and tested for ESBL presence. Bacterial species were identified using MALDI-TOF. Antibiotic susceptibility was tested using the disc diffusion method, and ESBL producers were detected based on double-disc synergy. ESBL-encoding genes were identified using PCR, and WGS was performed on isolated ESBL-producing E. coli (197/221 isolated ESBLs).

RESULTS: Four of the sampled rural hooded crows and 130 urban ones (7.7% vs. 61%, chi-square p < 0.0001) yielded ESBL producers with the overwhelming dominance of E. coli. The blaCTX-M-1 group was predominant in both groups. In addition to CTX-M genes, genes encoding resistance to other antibiotic classes, such as APHs, sul genes, tet genes, etc, various virulence factors, and several incompatible plasmids were also detected. Most isolates belonged to the B1 and A phylogenetic groups. Overall, 22 sequence types (STs) and 33 distinct cgSTs were defined. The most prevalent ST was ST58, followed by ST10, S38, ST155, ST442, and more.

CONCLUSIONS: The much higher carrier frequency among urban crows points to the role of anthropogenic sources in the emergence of ESBL producers. Hooded crows, due to their increasing presence in cities and proximity to humans, likely facilitate the dissemination of ESBL producers between the environment and humans.}, } @article {pmid42575416, year = {2026}, author = {Li, W and Yu, Z and Zhang, J and Yang, W and Yang, R and Li, X and Wang, S and Wu, P}, title = {Biodegradable and conventional microplastics differentially affected greenhouse gas emissions from a flooded paddy soil: Insight into metagenomic analysis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128934}, doi = {10.1016/j.envpol.2026.128934}, pmid = {42575416}, issn = {1873-6424}, abstract = {Paddy soils are important sources of greenhouse gases (GHGs), and microplastics (MPs) are increasingly widespread in paddies. However, the type-dependent effects of biodegradable and conventional MPs on methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) emissions remain unclear. Here, an incubation experiment was conducted to evaluate the effects of polyethylene (PE), polyethylene terephthalate (PET), Polybutylene succinate (PBS), and polylactic acid (PLA) on GHG emissions and the involved mechanism was clarified. PLA significantly increased cumulative CH4 and CO2 emissions by 264% and 27.3%, respectively, whereas PE and PET inhibited CH4 and CO2 emissions. In contrast, PE significantly enhanced N2O emissions by 93.1%, while PLA had no significant effect. Mechanistically, PLA increased dissolved organic carbon (DOC), soil pH, HCl-extractable Fe(II), and soluble/exchangeable Mn contents, but decreased soil redox potential (Eh) and sulfate content, creating favorable conditions for microbial anaerobic metabolism. PLA increased the relative abundances of methanogenic taxa and genes (fwdA, fdhA, acsC, cdhC, mttB, and mtbC), but decreased those associated with anaerobic methane oxidation (mcrA, mtrH, and mer), indicating greater CH4-production potential. PLA also increased fermentation (ldh, pfl, ackA, adhE, and por), sulfate-reduction (sat, aprA, aprB, dsrA, and dsrB), and iron-reduction (feR) gene abundances, suggesting greater anaerobic carbon-transformation potential. PE and PET increased denitrifiers and related genes (narH, narI, nirK, and norB), indicating greater N2O-production potential, whereas increased nosZ abundance under PLA treatment suggested greater N2O-reduction potential. Overall, MPs differentially affected paddy GHG emissions in a type-dependent manner, and biodegradable PLA exacerbated short-term GHG emission risks from paddy soils.}, } @article {pmid42575708, year = {2026}, author = {de Oliveira, AFB and Carneiro, BS and de Carvalho, JB and de Oliveira, AR and da Costa da Silva, AL and de Oliveira Veras, AA and Baraúna, RA and das Graças, DA}, title = {Nanopore Long-Read Metagenomics Reveals Pollution-Driven Antibiotic Resistance and Xenobiotic Degradation in Urban Beach Microbiomes.}, journal = {Environmental microbiology reports}, volume = {18}, number = {4}, pages = {e70396}, doi = {10.1111/1758-2229.70396}, pmid = {42575708}, issn = {1758-2229}, support = {445350/2024-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {*Metagenomics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism/drug effects ; *Xenobiotics/metabolism ; Brazil ; *Bathing Beaches ; *Drug Resistance, Bacterial ; Biodiversity ; *Drug Resistance, Microbial ; Phylogeny ; Biodegradation, Environmental ; Cities ; }, abstract = {Coastal ecosystems are vital for biodiversity but are increasingly threatened by urbanisation and pollution, which significantly alter local microbial communities. This study assessed bacterial diversity and functional profiles in urban and island beaches in Belém, Brazil. Urban beaches showed significantly higher microbial diversity and evenness, alongside functional plasticity due to pollutant input, while island beaches hosted more specialised and stable communities. Taxonomic analysis revealed the significant enrichment of opportunistic genera such as Comamonas, Clostridium and Paenibacillus in urban areas, and the massive dominance of Prochlorococcus and Candidatus Pelagibacter in island sites. Furthermore, shotgun metagenomics identified a robust genomic potential for xenobiotic degradation and antibiotic resistance in urban microbiomes, whereas island microbiomes were significantly enriched in genes for energy production and biosynthesis. These results underscore the ecological divergence between anthropogenically impacted and natural coastal environments, highlighting the importance of microbiome monitoring for sustainable coastal management.}, } @article {pmid42575975, year = {2026}, author = {Pust, MM and Mohamed, AMT and Stražar, M and Arias-Rojas, A and Cunningham-Oakes, E and Brown, EM and Bumber, A and Pishchany, G and Li, C and Ananthakrishnan, AN and Darby, AC and Vlamakis, H and Plichta, DR and Xavier, RJ}, title = {Antisense transcription reveals disease-associated adaptations in the human gut microbiome.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42575975}, issn = {2058-5276}, support = {P30 DK043351//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 DK127171//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 AI172147//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 530694780//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {The gut microbiome is a dynamic ecosystem in which microorganisms constantly adjust their transcriptional programmes. Here we developed metastrand, a framework that integrates strand-aware metatranscriptomics and metagenomics to quantify mRNAs and antisense RNAs (asRNAs) in complex microbial communities at gene-level resolution. In inflammatory bowel disease (IBD), microbial asRNA programmes converged across patients during active disease, correlated with faecal metabolites and calprotectin levels and remained stable during persistent inflammation, highlighting their potential as biomarkers of inflammatory activity in the gut. These programmes involved antisense-to-sense transcriptional shifts at insertion sequence elements with functionally diverse passenger genes and preceded their detection at new genomic locations, linking asRNA dynamics to structural genome rearrangements and redistribution of adaptive functions under selective pressure. Similar dynamics were observed in a mouse model of colitis, oxidative stress in vitro and in patients with pathogen-confirmed gastroenteritis, establishing asRNAs as an important dimension of microbial adaptation in health and disease.}, } @article {pmid42576026, year = {2026}, author = {Shiba, S and Yachida, S and Mizutani, S and Totoki, Y and Nakamura, H and Hama, N and Miyoshi, N and Arai, Y and Saito-Adachi, M and Kimura, H and Hayashi, Y and Takamaru, H and Tanaka, K and Hayashi, R and Rokutan, H and Ikuta, S and Kanemitsu, Y and Doki, Y and Eguchi, H and Hattori, S and Saito, Y and Yamada, T and Shibata, T}, title = {Prevalence and chronology of colibactin-associated mutational processes and their microbiome spectra in Japanese colorectal cancer.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {42576026}, issn = {1546-1718}, support = {JP25ck0106800//Japan Agency for Medical Research and Development (AMED)/ ; JP26ck0106162//Japan Agency for Medical Research and Development (AMED)/ ; JP23jk0210009//Japan Agency for Medical Research and Development (AMED)/ ; JP21cm0106477//Japan Agency for Medical Research and Development (AMED)/ ; JP25gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106800//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106800//Japan Agency for Medical Research and Development (AMED)/ ; JP22ck0106546//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106799//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106874//Japan Agency for Medical Research and Development (AMED)/ ; JP26ck0106162//Japan Agency for Medical Research and Development (AMED)/ ; JP21cm0106477//Japan Agency for Medical Research and Development (AMED)/ ; JP25ama221430//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP26jf0126022//Japan Agency for Medical Research and Development (AMED)/ ; JP23jk0210009//Japan Agency for Medical Research and Development (AMED)/ ; JP26jf0126022//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP22ck0106546//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106799//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106874//Japan Agency for Medical Research and Development (AMED)/ ; JP25ama221430//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP22ck0106546//Japan Agency for Medical Research and Development (AMED)/ ; JP21cm0106477//Japan Agency for Medical Research and Development (AMED)/ ; JP25ama221430//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP16H06279, 22K16336//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20H03662, 23H02892, 25K21771//MEXT | Japan Science and Technology Agency (JST)/ ; }, abstract = {The incidence of colorectal cancer (CRC) has risen in recent decades, with a disproportionate increase observed among younger individuals in Japan and other countries. The etiological contribution of the gut microbiota to CRC pathogenesis is recognized, yet the mechanisms involved remain to be fully clarified. Here we integrated whole-genome sequencing (WGS) and transcriptome profiling of CRC with whole-genome metagenomic sequencing of fecal samples to interrogate host-microbiome interactions at high resolution. Application of interpretable artificial intelligence enabled the stratification of CRC into four distinct microbiome-informed subtypes. WGS analysis identified mutational signatures SBS88 and ID18, linked to colibactin exposure, as early clonal events detected in 44.8% of non-hypermutated patients. Notably, these signatures were significantly more frequent among patients born after the 1960s. Microbiome-based subclassification revealed subtype-specific clinical and molecular features. Collectively, our findings indicate that colibactin exposure constitutes a prevalent and potentially modifiable risk factor for CRC in the Japanese population.}, } @article {pmid42576510, year = {2026}, author = {Nio, SA and Mantilen Ludong, DP}, title = {Water Deficit During the Vegetative Stage Alters the Structure of Root-Associated Microbial Communities in Local North Sulawesi Rice.}, journal = {Pakistan journal of biological sciences : PJBS}, volume = {29}, number = {5}, pages = {243-250}, doi = {10.3923/pjbs.2026.243.250}, pmid = {42576510}, issn = {1812-5735}, mesh = {*Oryza/microbiology/growth & development/metabolism ; *Plant Roots/microbiology ; Droughts ; Water/metabolism ; *Microbiota/physiology ; Indonesia ; Rhizosphere ; }, abstract = {Background and Objective: Changes in rhizosphere microbial populations have been reported in response to drought, temperature fluctuations, CO2 levels and other environmental factors. However, the structure of the root-associated microbes in local North Sulawesi rice using a metagenomic approach has not yet been investigated. This study examined the microbial community structure in local North Sulawesi rice (cv. Superwin) under drought (water deficit) conditions compared to well-watered conditions at the vegetative phase. Materials and Methods: Rice plants were grown in polybags filled with a 5:1:1 mixture of garden soil, compost and rice husks and were allowed to grow until the four-fully-expanded leaf stage. They were then subjected to two treatments for 14 days: well-watered conditions (irrigated to 100% field capacity) and water deficit conditions (0% field capacity). Root samples were collected for next-generation sequencing analysis to assess molecular response of Superwin rice to water deficit. Results: During drought, several root-associated microbes were more prevalent, including Nitrospirota at the phylum level, Rubrobacteria at the class level, Micrococcales at the order level, Gaiellaceae at the family level, Gaiella at the genus level and Gaiella occulta at the species level. Conclusion: Root-associated microbes, including taxa Nitrospirota, Rubrobacteria, Micrococcales, Gaiellaceae, Gaiella and Gaiella occulta, have a higher relative abundance in rice plants under water deficit. Gaiella occulta serves as sensitive indicator of water deficit in North Sulawesi local rice, i.e. Superwin.}, } @article {pmid42576818, year = {2025}, author = {Pearce, DA and Crown, M and Nelson, A and Jabeen, K and Thompson, JR and Argyraki, A and Hursthouse, AS and Bashton, M and Entwistle, JA}, title = {House dust-a Pandora's box of antimicrobial resistance (AMR) activity?.}, journal = {Sustainable microbiology}, volume = {2}, number = {4}, pages = {qvaf022}, pmid = {42576818}, issn = {2755-1970}, abstract = {The presence and spread of Antibiotic Resistant Bacteria (ARB) and Antibiotic Resistant Genes (ARGs) in the environment is now recognised as one of the top ten global public health threats to humanity. In a previous study, we used citizen science and MiSeq to target 16S rRNA gene amplicons to investigate house dust microbiomes across diverse households and found a core microbiome. In this study, we used shotgun metagenomics to target antimicrobial resistance (AMR) genes in order to investigate the potential for functional differences and to test the hypothesis that there was a core resistome associated with this core microbiome, including any patterns in a core resistome in terms of likely origin and mechanisms of action. In this study we did not find a core resistome, but found that the predominant and most diverse mechanisms of Anti-Microbial Resistance (AMR) in the dust samples were antibiotic target alteration and antibiotic efflux, accounting for ∼70% of cumulative RPKMs detected, potentially representing a compromise between the certainty of working and energy investment required. Despite the core home microbiome previously detected in diverse house dust samples, there was only limited evidence for a core resistome, with only two AMR genes present in all samples.}, } @article {pmid42576826, year = {2025}, author = {Shatara, FJ and Kothari, A and Hou, L and Yokota, K and Majumder, EL}, title = {Microplastic characteristics differentially influence cyanobacterial harmful algal bloom microbial community membership, growth, and toxin production.}, journal = {Sustainable microbiology}, volume = {2}, number = {1}, pages = {qvaf003}, pmid = {42576826}, issn = {2755-1970}, abstract = {Terrestrial runoffs contribute to cyanobacterial harmful algal blooms (cHABs) by providing nutrients and other pollutants that may facilitate cyanobacterial growth. Microplastics (MPs) are being detected at increasing concentrations in various aquatic systems worldwide, including freshwater, yet the MP effects on cHAB formation, toxin production, and transport are largely unknown. We used the statistical design of experiments to elucidate microbe-plastic interactions with freshwater algal bloom communities obtained from a HAB event in the Great Lakes. These experiments measured the impact of differing sizes, concentrations, and UV aging times of polyethylene, polypropylene, and cellulose fibers on the chlorophyll-a content of Trichormus (previously Anabaena variabilis) and Microcystis aeruginosa and microcystin-LR content in M. aeruginosa. Additionally, we conducted metagenomic sequencing on the total community and 16S rRNA microbial community sequencing on members of the total community bound to plastics after 4 weeks of culturing. The results indicate that M. aeruginosa growth rate was inhibited in the presence of polymers, while production of microcystin-LR generally increased in the presence of MPs. Changes to growth of T. variabilis varied with polymer type, size, and UV aging time. These results suggest that specific MP characteristics, not just their presence, may influence the toxicity, growth, and dispersal of cHABs across aquatic systems.}, } @article {pmid42576858, year = {2024}, author = {Alfahl, Z and Chueiri, A and Carolan, S and Darcy, G and Hussain, N and Cahill, N and O'Connor, L}, title = {Antimicrobial resistance detection methods in water environments: a scoping review.}, journal = {Sustainable microbiology}, volume = {1}, number = {1}, pages = {qvae034}, pmid = {42576858}, issn = {2755-1970}, abstract = {Antimicrobial resistance (AMR) in water environments poses a significant threat to public health, ecosystem stability, and the effectiveness of antimicrobial treatments. This review aims to provide a comprehensive overview of the methods used to detect AMR in various water environments. A literature search was conducted following the PRISMA guidelines. Original articles published in English relating to AMR in water environments were included. Reviews, protocols, and abstracts were excluded. A total of 115 publications were selected for full-text evaluation. Overall, river water samples were the most commonly assessed samples across all of the reviewed studies (49/115 studies, 42%). The top 3 countries investigating AMR genes in water samples were the USA (19 studies, 17%), China (11 studies, 10%), and Brazil (10 studies, 9%). The review revealed that polymerase chain reaction and metagenomic methods are increasingly preferred for their high sensitivity, specificity, and comprehensive detection capabilities, appearing in 65/115 (57%) and 31/115 (27%) studies, respectively. Despite higher costs and technical complexity, these methods provide valuable insights into the resistome of water environments. Culture-dependent methods, while most cost effective and straightforward, are limited by their time-consuming nature and inability to detect non-viable resistant organisms, reducing their effectiveness in comprehensive AMR surveillance. The review addresses the challenges and limitations of current detection methods and proposes directions for future research to develop more robust, cost-effective, and user-friendly detection methods. The review highlights the urgent need for integrated approaches to monitor and mitigate AMR in water environments, ensuring better public health and environmental protection.}, } @article {pmid42576874, year = {2024}, author = {Cowan, DA and Babenko, D and Bird, R and Botha, A and Breecker, DO and Clarke, CE and Francis, ML and Gallagher, T and Lebre, PH and Nel, T and Potts, AJ and Trindade, M and Van Zyl, L}, title = {Oxalate and oxalotrophy: an environmental perspective.}, journal = {Sustainable microbiology}, volume = {1}, number = {1}, pages = {qvad004}, pmid = {42576874}, issn = {2755-1970}, abstract = {Oxalic acid is one of the most abundant organic acids produced by plants. Much of the global production of oxalic acid is deposited on soil surfaces in leaf litter to be oxidized by microorganisms, resulting in a pH increase and shifting the carbonate equilibria. In what is known as the oxalate-carbonate pathway, calcium oxalate metabolism results in CO2 being sequestered into soils as insoluble calcite (CaCO3). There is a growing appreciation that the global scale of this process is sufficiently large to be an important contribution to global carbon turnover budgets. The microbiomics, genetics, and enzymology of oxalotrophy are all soundly established, although a more detailed understanding of the landscape-scale kinetics of the process would be needed to incorporate oxalotrophy as an element of process models informing the relevant Sustainable Development Goals. Here, we review the current state of knowledge of oxalotrophs and oxalotrophy and the role they play in terrestrial ecosystem services and functions in terms of carbon sequestration and nutrient cycling. We emphasize the relevance of these to the Sustainability Development Goals (SDGs) and highlight the importance of recognizing oxalotrophy, when accounting for the natural capital value of an ecosystem.}, } @article {pmid42576880, year = {2024}, author = {Provencher, J and George, PBL and Thaler, M and Vincent, WF and Duchaine, C and Culley, AI and Girard, C}, title = {Microbial antibiotic resistance genes across an anthropogenic gradient in a Canadian High Arctic watershed.}, journal = {Sustainable microbiology}, volume = {1}, number = {1}, pages = {qvae021}, pmid = {42576880}, issn = {2755-1970}, abstract = {Antibiotic resistance is one of the biggest challenges to public health. While the discovery of antibiotics has decreased pathogen-caused mortality, the overuse of these drugs has resulted in the increased transfer and evolution of antibiotic resistance genes (ARGs) in bacteria. ARGs naturally occur in wild bacterial communities, but are also found in increased concentrations in environments contaminated by wastewater effluent. Although such ARGs are relatively well described in temperate environments, little is known about the distribution and dissemination of these genes in the Arctic. We characterized the ARGs in microbial communities from aerosols, lakes and microbial mats around a remote Arctic hamlet using metagenomic approaches. Specific objectives were to (i) compare ARGs across habitats, (ii) to characterize ARG populations along a continuum of anthropogenically influenced environments, and (iii) to identify ARGs of viral origin. We identified ARGs in all habitats throughout the watershed, and found that microbial mats in the most impacted area had the highest diversity of ARGs relative to uncontaminated sites, which may be a remnant signal of wastewater effluent inputs in the area during the 20th century. Although we identified ARGs predominantly in bacterial genomes, our data suggests that mimiviruses may also harbor ARGs.}, } @article {pmid42577134, year = {2026}, author = {Wang, H and Jiang, L and Zhong, L and Zhang, H and Li, Y and Zhai, Z and Liu, W and Ma, M and Chen, Q and Tang, X}, title = {Responses of host energy status, intestinal structure and gut microbiota during post-hibernation recovery in high- and low-altitude populations of the plateau frog Rana kukunoris.}, journal = {Frontiers in physiology}, volume = {17}, number = {}, pages = {1891419}, pmid = {42577134}, issn = {1664-042X}, abstract = {BACKGROUND: Hibernation is an important seasonal strategy that enables amphibians to cope with low temperature and food scarcity. However, how high- and low-altitude amphibian populations differ in host energy status, digestive system structure and gut microbiota during post-hibernation recovery remains insufficiently understood.

OBJECTIVE: This study aimed to evaluate post-hibernation changes in host energy status, intestinal structure and gut microbial composition and functional potential in high- and low-altitude populations of the plateau frog Rana kukunoris.

METHODS: We compared high-altitude and low-altitude populations of R. kukunoris before and after hibernation by integrating morphological traits, whole-animal metabolic rate, digestive tract length, small-intestinal histology and shotgun metagenomic profiles of small-intestinal contents.

RESULTS: After hibernation, both populations showed significant decreases in body mass, liver mass and hepatosomatic index, together with increased whole-animal metabolic rate, indicating a transition from energy reserve depletion to metabolic recovery. The hepatosomatic index showed a significant altitude × stage interaction, suggesting stronger relative liver energy depletion in the low-altitude population. Digestive system analysis showed that the low-altitude population exhibited more pronounced structural remodeling, including shortened digestive tract length, increased muscularis thickness and reduced epithelial thickness after hibernation, whereas the high-altitude population showed a relatively conservative response. Metagenomic analysis showed that alpha diversity remained relatively stable, whereas beta diversity, dominant microbial taxa and functional potential shifted among groups. Microbial functional profiles were mainly associated with metabolism, nutrient transformation and carbohydrate utilization.

CONCLUSION: Post-hibernation recovery in R. kukunoris involves cross-level parallel responses in host energy status, digestive system structure and gut microbiota. High- and low-altitude populations may adopt different physiological recovery strategies after hibernation, providing new evidence for understanding seasonal adaptation in amphibians inhabiting cold environments.}, } @article {pmid42577254, year = {2026}, author = {Ouedraogo, FJ and Poulain, AJ and Aris-Brosou, S}, title = {Glacial meltwater is associated with gene-specific diversification of metal resistance genes in high Arctic soil microbiomes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1903619}, pmid = {42577254}, issn = {1664-302X}, abstract = {Climate warming accelerates glacial meltwater delivery to Arctic lakes, mobilizing metals from thawing catchments and reshaping the selective landscape experienced by resident microbes. Whether these gradients leave detectable signatures of diversification in environmental resistance genes remains unclear. We investigated four metal resistance genes (merA, arsC, cadA, and chrR) in metagenomic datasets from Lake Hazen (Nunavut, Canada), the largest High Arctic freshwater lake, sampled across a natural hydrological gradient of Control, Low-runoff, and High-runoff regimes. Using a space-for-time substitution design, we combined population-genetic and codon-based approaches to quantify diversity and candidate selection signals, including nucleotide diversity, Tajima's D, non-synonymous-to-synonymous diversity ratios, McDonald-Kreitman tests with outgroup-sensitivity analysis, site-level episodic selection (MEME with false-discovery-rate correction), and gene-wide tests (BUSTED and BUSTED-E) and complemented these with ortholog clustering, within-clade re-analysis, taxonomic profiling, rarefaction, and phylogenetic beta-diversity. Marked heterogeneity emerged among genes: merA showed increasing diversity and patterns consistent with diversification along the runoff gradient, and these signals were preserved within the largest orthologous cluster (90% of haplotypes), supporting an interpretation of within-orthogroup diversification; cadA displayed the strongest McDonald-Kreitman signal under low and high runoff, but its gene-wide BUSTED-E signal collapsed within a single ortholog cluster, suggesting that part of the apparent diversifying signal at the gene-family level reflects inter-subfamily heterogeneity; chrR exhibited the strongest regime structure but its largest orthologous cluster was dominated by Control sequences and 93% of High-regime haplotypes were affiliated with a single bacterial order (Hyphomicrobiales), indicating that the regime contrast for this gene reflects compositional turnover rather than within-lineage evolution; arsC remained largely consistent with neutral or purifying evolution across regimes. Because these inferences derive from metagenomic gene pools sampled across only three hydrological regimes and aggregate variants across taxa, we interpret them as exploratory, hypothesis-generating patterns rather than as demonstrations of population-level adaptation. Our findings highlight environmental resistance genes as candidate indicators of changing biogeochemical conditions in rapidly warming polar ecosystems, while underscoring the importance of orthology and community-composition controls when inferring selection from metagenomic data.}, } @article {pmid42577359, year = {2026}, author = {Wu, H and Song, DC and Yao, Z and Wang, Q and Yan, ZZ and He, FL and Guo, SJ and Wang, LD}, title = {Microbial carbon fixation pathways shifts during artificial Haloxylon ammodendron restoration with clay sand barriers in arid deserts: a metagenomic analysis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1884493}, pmid = {42577359}, issn = {1664-302X}, abstract = {Soil microbial carbon fixation is influenced by the combined effects of microbial community composition, functional gene distribution, and environmental factors, and is closely associated with vegetation restoration processes. However, the soil carbon fixation process and its coupling mechanisms mediated by microorganisms at different vegetation restoration stages in arid regions remain unclear. In this study, we applied metagenomic sequencing to investigate soil from a clay sand barrier Haloxylon ammodendron sand-fixing restoration area at the southeastern edge of the Badain Jaran Desert, spanning a 60-year vegetation restoration time sequence (1, 5, 10, 20, 40, and 60 years) and shifting sand as a control. We explored the impacts of vegetation restoration and its long-term sequence on soil properties, microbial community structure, carbon fixation genes, and carbon fixation pathways. The results showed that vegetation restoration improved regional soil nutrient levels and organic carbon accumulation, with these positive effects progressively amplified over the restoration time sequence. Additionally, vegetation restoration not only reshaped microbial community composition but also induced changes in carbon fixation-related genes and pathways. A 10-year restoration period served as a critical time point, with microbial community diversity and carbon fixation gene abundance exhibiting pronounced fluctuations during the first 10 years, followed by relative stabilization thereafter. This threshold likely reflects a transition from intense plant-microbe competition to a more balanced coexistence as vegetation succession progresses and soil conditions stabilize. Among the six major microbial carbon fixation pathways, the rTCA cycle had the highest relative gene abundance, making it the dominant carbon fixation pathway in the region. Soil properties, particularly soil water content (SWC) and total phosphorus (TP), were identified as critical factors influencing both microbial community composition and carbon fixation-related genes. These findings suggest that clay sand barrier Haloxylon restoration not only fulfills its role in sand stabilization but also alters the soil environment, driving a functional shift in the microbial community from autotrophic to heterotrophic processes. This study deepens our understanding of soil carbon fixation processes in arid desert ecosystems and provides theoretical guidance for carbon management in similar arid regions.}, } @article {pmid42577398, year = {2026}, author = {Zhang, J and Chen, J and Hu, M and Wang, J and Ning, S and Zhang, W and Sun, R}, title = {Viral metagenomic analysis of human bocavirus in pediatric pneumonia: detection pattern and genetic characterization.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1868618}, pmid = {42577398}, issn = {2235-2988}, mesh = {Humans ; *Human bocavirus/genetics/isolation & purification/classification ; *Metagenomics ; Retrospective Studies ; Female ; Infant ; Bronchoalveolar Lavage Fluid/virology ; Phylogeny ; Male ; Child, Preschool ; *Parvoviridae Infections/virology/epidemiology ; Child ; Genotype ; China/epidemiology ; High-Throughput Nucleotide Sequencing ; *Pneumonia, Viral/virology ; Genome, Viral ; }, abstract = {BACKGROUND: Human bocavirus (HBoV) is frequently detected in pediatric respiratory samples, but its clinical role remains difficult to interpret because of asymptomatic shedding and frequent co-detection with other pathogens. Data from bronchoalveolar lavage fluid (BALF), which more directly reflects the lower respiratory tract, remain limited.

METHODS: This retrospective study analyzed 179 BALF samples collected from pneumonia patients in the Jiangnan region of China between July and December 2025. Metagenomic next-generation sequencing (mNGS) was used for HBoV detection, mNGS-derived abundance estimation, genotype assignment, and genome coverage analysis. VP1 and NS1 gene fragments were used for phylogenetic analysis, and recombination screening was performed using RDP4.

RESULTS: Using the predefined ≥10-read mNGS screening threshold, HBoV signals were detected in 22 of 30 pediatric samples (73.3%; 95% CI, 54.1-87.7%) and in none of the 149 adult samples (0%; 95% CI, 0-2.45%), showing an age-related detection pattern in this cohort (Fisher's exact test, P = 6.91 × 10[-]²²). HBoV1 was assigned as the dominant genotype in all HBoV mNGS signal-positive samples. RPM values varied among these samples, but they should be interpreted as mNGS-derived relative abundance rather than absolute viral load. Genome coverage analysis and partial VP1/NS1 phylogenetic placement provided additional support for HBoV1 read-based detection and genotype assignment. RDP4 analysis did not detect recombination events involving the study-derived VP1 or NS1 fragments.

CONCLUSIONS: HBoV1 was frequently detected in pediatric BALF samples in this retrospective cohort, suggesting that HBoV1 signals may be relevant to the interpretation of some pediatric lower respiratory tract samples. However, because qPCR validation, healthy controls, and a comprehensive multi-pathogen co-infection assessment were not included, these data do not establish HBoV1 as the direct causative agent of pneumonia. Larger studies with quantitative validation and more complete clinical data are needed.}, } @article {pmid42577453, year = {2026}, author = {Rakhmankulova, A and Kozhakhmetov, S and Kovenskiy, A and Mukhanbetzhanov, N and Katkenov, N and Jarmukhanov, Z and Terzic, M and Bapayeva, G and Ukybassova, T and Aimagambetova, G and Kim, Y and Primbetov, B and Imankulova, B and Kongrtay, K and Kadroldinova, N and Galym, M and Makhambetova, S and Nurgaliyeva, K and Abdiyeva, Z and Zhumakanova, Z and Smagulova, B and Vinogradova, E and Kamzayeva, N and Kushugulova, A}, title = {Multi-kingdom cervical microbiome structure in health and dysbiosis: a cross-sectional study from Kazakhstan.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1836889}, pmid = {42577453}, issn = {1664-302X}, abstract = {INTRODUCTION: The cervicovaginal microbiome is a key determinant of reproductive health. Its multi-kingdom structure and ecological interactions remain insufficiently characterized across diverse populations. This study aimed to define the composition and cross-kingdom dynamics of the cervical microbiome in women without HPV infection and with normal cytology in a Kazakhstani population.

METHODS: In this cross-sectional study, cervical samples from 92 reproductive-age women were analyzed using whole-genome metagenomic sequencing to characterize bacterial, viral, fungal, and archaeal communities, together with predicted functional pathways. Microbial communities were stratified into community state types based on dominant bacterial species.

RESULTS: Bacterial composition differed markedly across community states, with Lactobacillus-dominated profiles associated with low diversity and anaerobe-rich communities associated with higher diversity. In contrast, viral, fungal, and archaeal diversity remained relatively stable, although descriptive compositional shifts indicated variation in bacteriophages, methanogenic archaea, and opportunistic fungi in non-Lactobacillus communities. Functional analyses indicated CST-associated pathway differences, suggesting greater metabolic flexibility in dysbiotic states, and exploratory network analysis revealed CST-associated restructuring of bacterial and cross-kingdom co-variation patterns. Notably, more than half of participants exhibited non-Lactobacillus-dominated communities despite the absence of infection or cytological abnormalities, indicating population-specific microbiome configurations.

DISCUSSION: Study demonstrates that the cervical microbiome is accompanied by exploratory cross-kingdom compositional variation and ecological states traditionally considered dysbiotic may represent stable, population-specific configurations, highlighting the need for context-dependent definitions of microbial health.}, } @article {pmid42577546, year = {2026}, author = {Zhan, M and Chen, H and Li, Z and Liu, S and Lu, B and Wang, Z and Wang, H}, title = {Lower Respiratory Microbiome Dysbiosis Is Associated With Poor Prognosis in Acute Severe Lower Respiratory Tract Infection.}, journal = {MedComm}, volume = {7}, number = {8}, pages = {e70907}, pmid = {42577546}, issn = {2688-2663}, abstract = {Acute severe lower respiratory tract infections (asLRTIs) pose a significant clinical challenge, especially in critically ill patients, but the role of the lower respiratory tract microbiome (LRTM) remains unclear. This study aimed to characterize LRTM composition and host immune factors to identify prognostic features of clinical outcomes. The study included 53 asLRTI patients and 35 controls. Metagenomics, metabolomics, proteomics, and RNA sequencing were conducted, while analysis of similarities (ANOSIM) and Cox regression were performed for statistics. Clinical data, including pneumonia severity scores, were collected on BALF sampling, with a 100-day follow-up. LRTM samples were grouped into five clusters (C1-C5). Cluster C5 resembled controls, while others showed significantly lower diversity. LRTM composition correlated with prognosis, with higher pathogenic bacteria abundance linked to poorer outcomes. Cluster C3 was associated with poor prognosis and reduced survival. Metabolite analysis revealed elevated α-ketoisocaproic acid in asLRTIs and higher 10-nitrolinoleate in poor-prognosis patients. Immune responses varied across clusters, with distinct gene and cytokine expression patterns. Cluster C1, associated with Acinetobacter baumannii, exhibited heightened IL17 pathway activation. LRTM composition in asLRTIs is linked to clinical outcomes, with no single gradient of difference but distinct community states characterized by varying pathogens, metabolites, and immune responses.}, } @article {pmid42577578, year = {2026}, author = {Song, Y and Zhang, X and Wang, H and Wang, Y and Zhang, S and Li, Y and Cui, X and Li, X and Li, Y and Wang, J and Su, J and Zheng, Y and Gai, W and Liu, W}, title = {Clinical value of radial endobronchial ultrasound combined with metagenomic next-generation sequencing in the malignant tumors patients with pulmonary infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1799148}, pmid = {42577578}, issn = {2235-2988}, mesh = {Humans ; Female ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Retrospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Aged ; Microbiota ; *Endosonography/methods ; *Respiratory Tract Infections/diagnosis/microbiology ; *Neoplasms/complications/drug therapy ; Bacteria/classification/genetics/isolation & purification ; Bronchoscopy ; Aged, 80 and over ; Adult ; Sepsis ; }, abstract = {INTRODUCTION: Patients treated with systemic anti-tumor therapies are more likely to develop pulmonary infections due to weakened immune systems. This study aims to evaluate the clinical application of radial endobronchial ultrasound (R-EBUS) combined with metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of pulmonary infections among patients undergoing systemic anti-tumor therapy.

METHODS: This study is a single-center retrospective analysis that includes 84 patients with pulmonary infections following systemic anti-tumor therapy. Patients were stratified into sepsis (SOFA score ≥2, n=32) and non-sepsis (SOFA score <2, n=52) groups based on Sepsis-3.0 criteria. BALF samples were subjected to both mNGS and conventional microbiological tests (CMT). Pathogen profiles, diagnostic performance, clinical impact on antimicrobial therapy, and microbiome diversity were analyzed.

RESULTS: mNGS demonstrated a significantly higher positive detection rate than CMT (95.24% vs. 30.95%, P < 0.001). mNGS identified a broader spectrum of pathogens, including bacteria, fungi, and viruses, and detected mixed infections more frequently than CMT. The clinical impact of mNGS was positive in 84.52% of cases, primarily by initiating targeted therapy or confirming empirical treatment. Microbiome analysis revealed significantly lower alpha diversity (Shannon, ACE, Chao1 indices) in the severe group compared to the non-severe group.

DISCUSSION: EBUS-guided mNGS of BALF was associated with improved pathogen detection in malignancy patients with pulmonary infections, leading to a high rate of beneficial antimicrobial adjustments. Distinct microbial signatures are associated with infection severity, suggesting potential diagnostic and therapeutic implications.}, } @article {pmid42577588, year = {2026}, author = {Brock, R and Schaupp, L and Schütte, A and Zhou-Suckow, Z and Butz, S and Schatterny, J and Mayer, S and Frank, A and Mengel, JP and Weigel, M and Hain, T and Dalpke, A and Boutin, S and Mall, MA}, title = {Preventive intrapulmonary treatment with Ligilactobacillus murinus reduces airway inflammation and mucus plugging in mice with cystic fibrosis-like lung disease.}, journal = {ERJ open research}, volume = {12}, number = {4}, pages = {}, pmid = {42577588}, issn = {2312-0541}, abstract = {BACKGROUND: Chronic airway dysbiosis plays an important role in the pathogenesis of cystic fibrosis (CF) lung disease and may serve as a therapeutic target. However, studies investigating the effects of direct therapeutic targeting of the airway microbiome are lacking. In this study, we therefore used βENaC-overexpressing (βENaC-Tg) mice and determined the evolution of abnormal lung microbiota and effects of re-balancing bacterial communities on chronic airway inflammation and mucus plugging in this model of CF lung disease.

METHODS: The development of the respiratory microbiome was determined by 16S rRNA gene sequencing and the effects of preventive intranasal instillation of endogenous probiotic bacteria on the lung phenotype were determined in βENaC-Tg mice and wild-type littermates.

RESULTS: Neonatal βENaC-Tg mice developed severe respiratory dysbiosis characterised by an increase in the relative abundance of Streptococcus and a decrease in Ligilactobacillus compared to wild-type littermates. Ligilactobacillus murinus SMH17 was identified as the dominant Ligilactobacillus species in the lungs of neonatal wild-type mice. Preventive treatment by intranasal instillation of L. murinus SMH17 was well tolerated and reduced age-specific markers of airway inflammation including inflammatory cell counts and proinflammatory cytokines in neonatal and juvenile βENaC-Tg mice. In addition, preventive treatment with L. murinus SMH17 reduced airway mucus plugging in βENaC-Tg mice by ∼40%.

CONCLUSION: Preventive intrapulmonary application of the endogenous probiotic L. murinus SMH17 reduces airway inflammation and mucus plugging in mice with CF-like lung disease. These data support further elucidation of inhaled probiotics as a strategy to treat chronic airway dysbiosis in patients with CF.}, } @article {pmid42577598, year = {2026}, author = {Zhang, Q and Lei, M and Li, H and Yi, G and Li, D}, title = {Case Report: Pediatric Rickettsia felis encephalitis-a rare case and literature review.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1867339}, pmid = {42577598}, issn = {2296-2360}, abstract = {BACKGROUND: Rickettsia felis (R. felis), an obligate intracellular bacterium, has been reported to cause human encephalitis. Clinical reports of R. felis encephalitis remain rare, particularly in children. Herein, we present a pediatric case and review the relevant literature.

CASE REPORT: A previously healthy 9-year-old boy initially presented with fever and headache. Following admission, he developed hyperpyrexia and somnolence. Cranial magnetic resonance imaging revealed a left temporal lobe lesion with ipsilateral temporoparietal meningeal enhancement, and electroencephalography showed background slowing. Metagenomic next-generation sequencing of cerebrospinal fluid detected a high abundance of R. felis sequences, whereas autoantibody testing for central nervous system autoimmune diseases was negative. Based on these findings, a diagnosis of R. felis encephalitis was established. The child fully recovered and was discharged after receiving doxycycline-based antimicrobial therapy combined with glucocorticoids, intravenous immunoglobulin, and intracranial pressure management.

CONCLUSION: This rare case highlights that R. felis infection should be included in the differential diagnosis of encephalitis. Metagenomic next-generation sequencing is recommended for early etiological diagnosis to facilitate timely and effective clinical intervention.}, } @article {pmid42577830, year = {2026}, author = {Martínez-Cuesta, R and Hoess, R and Geist, J and Schloter, M and Schulz, S}, title = {The larval gut as a mirror: bacterial community composition and functional potential of mayfly larvae reflect site and seasonality differences.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag192}, pmid = {42577830}, issn = {2730-6151}, abstract = {Land use intensification is a major driver of biodiversity loss across ecosystems, yet its consequences for host-associated microbiomes in freshwater food webs remain poorly understood. In this case study, we used the gut microbiome of mayfly larvae (Ephemera danica) as a sensitive biological interface to assess how site-specific adjacent land use types shape microbial community composition and functions in stream ecosystems. Larvae were sampled in summer and autumn from sites adjacent to forest, extensive grassland, and intensive agriculture along the Otterbach stream (Bavarian Forest, Germany). Combining 16S ribosomal RNA (rRNA) amplicon sequencing with long-read metagenomics, we show that site-specific land use, in interaction with seasonality, significantly restructures larval gut bacterial communities without affecting alpha diversity. Rather than introducing distinct agriculturally derived taxa, agricultural land use acted as a selective environmental filter, enriching bacterial groups with specific functional traits. Taxa enriched in the sites adjacent to agricultural sites harboured genes involved in complex carbon and xenobiotic degradation, short-chain fatty acid production, efflux pumps, and stress response. These functional signatures were further supported by 14 metagenome-assembled genomes linked to these enriched taxa. Together, our results reveal that site in combination with seasonality not only reshaped bacterial community composition without affecting alpha diversity but also triggered shifts in the abundance of genes involved in microbial-host interactions and degradation pathways in E. danica larvae. This study also highlights the larval gut microbiome as a sensitive indicator of environmental change, suggesting that environmental microbial shifts may have cascading consequences for freshwater trophic interactions and ecosystem functioning.}, } @article {pmid42577885, year = {2026}, author = {Li, J and Jiang, Z and Li, X and Fang, W and Jiang, Y and Hu, Y and Dong, Y and Xie, X and Shi, L and Kappler, A and Wang, Y}, title = {Dissimilatory iodate-reducing microorganisms inhabit marine oxygen minimum zones.}, journal = {National science review}, volume = {13}, number = {15}, pages = {nwag397}, pmid = {42577885}, issn = {2053-714X}, abstract = {Based on theoretical thermodynamic calculations, microbial IO3 [-] reduction precedes NO3 [-] reduction, and it was previously proposed that dissimilatory iodate-reducing microorganisms (DIRMs) inhabit a unique niche above marine oxygen minimum zones (OMZs). Here we demonstrate that dissimilatory IO3 [-] reduction lags behind NO3 [-] reduction in two representative strains Azonexus hydrophilus NCP973 and Denitromonas iodatirespirans IR-12. Correspondingly, the functional genes idrABP1P2 for DIRMs were found to be exclusively distributed across depth profiles of global OMZs where NO3 [-] reduction is active. Combined with widespread detection and heterologous expression of the idrABP1P2 of metagenome-assembled genomes (MAGs) from the OMZs, these findings suggest that DIRMs inhabit marine OMZs and contribute to I[-] production and accumulation. As OMZs expand under global warming, DIRMs could enhance volatile iodine fluxes to the atmosphere by producing the precursor I[-]. Given the environmental health importance of atmospheric iodine, integrating this pathway into marine iodine biogeochemical models will improve our capability of understanding and predicting the future changes in oceanic iodine emissions.}, } @article {pmid42577916, year = {2026}, author = {Demmer, RT and Pope, ZC and Avenido, FRR and Mitchell, NR and Richmond Hubbard, PF and Johnson, S and Sharma, S and McDonough, DJ and Rydell, SA and Johnson, A and Pereira, MA}, title = {The Effect of Physical Activity on the Gut Microbiome in Prediabetes: Results from a Randomized Controlled Trial.}, journal = {Diabetes, obesity, and cardiometabolic CARE}, volume = {1}, number = {2}, pages = {219-229}, pmid = {42577916}, issn = {3067-3534}, abstract = {OBJECTIVE: To test the effect of physical activity on the gut microbiome and circulating short chain fatty acids among sedentary adults with prediabetes and overweight/obesity.

RESEARCH DESIGN AND METHODS: In a pilot and feasibility trial, we randomized 77 adults with prediabetes and a sedentary lifestyle into one of two groups: 1) Intervention: Invited to engage in home-based moderate intensity walking 3x/week for 30 minutes/session in weeks 1-4 and for 45 minutes/session during weeks 5-8 of the 8-week intervention; or 2) Control: Maintained habitual physical activity levels. We performed metagenomic sequencing from stool collected at baseline, week 4, and week 8, with short-chain fatty acids (SCFA) measured from serum collected at baseline and week 8. Taxonomic and functional profiling were performed on the metagenomic reads; alpha diversity metrics were subsequently derived. Linear regression assessed the difference in change between the intervention and control groups for alpha-diversity and SCFA levels.

RESULTS: We screened 1,533 participants for eligibility and consented 132. Of these, 87 entered the run-in phase and 77 were randomized. Participants were 51.4±8.9 years old, 87.7% female, and 74% non-Hispanic White. Mean fasting glucose was 103.3±13.2 while mean BMI was 34.4±5.7. In comparison to control, the intervention group experienced decreased alpha diversity as characterized by Shannon, Richness, and Faith's diversity indices by intervention week 8 (P<0.05). Changes in SCFA levels were not statistically significant different in intervention vs. control.

CONCLUSIONS: Randomization to a walking intervention resulted in modest gut microbiome changes among adults with overweight/obesity and prediabetes.}, } @article {pmid42577946, year = {2026}, author = {Du, X and Meng, Q and Wang, L and Zhang, Z}, title = {Exploratory Evaluation of Chlorhexidine Decolonization and Skin Colonization Dynamics of Candida auris in ICU Patients: A Prospective Pilot Study.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {619168}, pmid = {42577946}, issn = {1178-6973}, abstract = {OBJECTIVE: Candida auris has emerged as a nosocomial pathogen in intensive care units (ICUs), and evidence for chlorhexidine-based decolonization remains limited. We report an exploratory pilot study describing skin colonization dynamics in four ICU patients with C. auris infection or colonization who received chlorhexidine decolonization alongside standard infection control measures.

METHODS: Four consecutive C. auris-positive patients admitted to the ICU of a tertiary teaching hospital in Inner Mongolia, China, between January 31 and March 12, 2026, were enrolled. Two patients (intervention group) received twice-daily 2% chlorhexidine gluconate whole-body skin decolonization; two (non-intervention group) did not, based on family consent. All patients received identical baseline infection control measures. Skin swabs from the nares, axillae, groin, and external ear canals, together with environmental samples, were cultured serially. All isolates were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). For one patient, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BAL) fluid was performed as part of routine clinical workup.

RESULTS: Skin colonization burden declined progressively in both intervention patients: Case A fell from 34 colony-forming units (CFU)/swab at baseline to 4 CFU/swab by Day 12, and Case B from 10 CFU/swab (Day 4) to 5 CFU/swab by Day 6 (discharged on Day 10). Colonization burden did not decline in the non-intervention group (Case C: 24-30 CFU/swab in groin across Day 0-12). Clinical outcomes differed between groups, but the non-randomized design, baseline imbalance in infection status, and universal co-infection with multidrug-resistant organisms preclude any causal inference. C. auris was recovered from 1 of 93 environmental surveillance samples (a suction bottle) and was eliminated by targeted disinfection; no healthcare worker hand cultures were positive.

CONCLUSION: In this four-patient pilot study, twice-daily chlorhexidine decolonization was accompanied by a reduction in skin colonization burden, but the findings are hypothesis-generating only. The small sample size, non-randomized design, baseline differences, and lack of molecular typing limit interpretation. Adequately powered, preferably randomized, studies with whole-genome sequencing are needed.}, } @article {pmid42577950, year = {2026}, author = {Davis, HE and Torres, J and Adler, MJ and Parker, BJ}, title = {A Wolbachia coinfection in the common bed bug.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag197}, pmid = {42577950}, issn = {2730-6151}, abstract = {The common bed bug (Cimex lectularius) relies on an obligate mutualism with the Wolbachia strain wCle to supplement B vitamins deficient in human blood. Using metatranscriptomic and metagenomic sequencing of hospital-collected bed bugs, we found that some individuals also harbor a second strain of Wolbachia (wChem). Using publicly available data we showed that wChem is distributed in bed bugs worldwide at intermediate frequencies and may have moved recently between C. lectularius and Cimex hemipterus, the tropical bed bug, which also feeds on human hosts. We found that wChem encodes a highly expressed cifA/B operon in males and females, consistent with cytoplasmic incompatibility, a reproductive manipulation strategy used by Wolbachia to increase in frequency in host populations. Together, these results demonstrate that some bed bugs harbor a Wolbachia coinfection of a nutritional mutualist and a potentially manipulative facultative symbiont. This discovery identifies a previously hidden aspect of bed bug biology with significant implications for its evolution, spread, and potential control.}, } @article {pmid42577959, year = {2026}, author = {Sun, Z and He, C and Ma, X and Wu, P and Wang, T and Yuan, J and Pu, Y and Zhou, X and Mei, Z and Song, H and Wang, Y and Yue, H and Fu, Y and Zheng, J and Pan, A and Chen, D and Hong, S and Pan, XF and Zheng, Y}, title = {A gut microbiome-lipid axis in early pregnancy is associated with metabolic dysregulation and diabetes risk.}, journal = {iMeta}, volume = {}, number = {}, pages = {e70166}, pmid = {42577959}, issn = {2770-596X}, abstract = {Gestational diabetes mellitus (GDM) reflects metabolic dysregulation that becomes clinically apparent during pregnancy and shares key pathophysiological features with broader forms of diabetes. Gut microbiome-host metabolic interactions may contribute to this process, yet their role in early pregnancy remains incompletely understood. In this prospective nested case-control study within the Tongji-Huaxi-Shuangliu Birth Cohort, 784 pregnant women, including 222 who developed GDM, underwent first-trimester gut metagenomic and plasma lipidomic profiling. Cross-omics analyses were performed to identify microbiome-lipid associations and potential mediation patterns. Women who later developed GDM showed reduced gut microbial diversity and altered microbial profiles in early pregnancy. We identified 26 microbial species associated with GDM risk, with seven species, including Ruminococcus bicirculans (R. bicirculans), showing concordant associations in external type 2 diabetes populations. Microbial pathways related to fatty acid and lipid biosynthesis were enriched in women at higher risk. Plasma lipidomics revealed widespread alterations, particularly among glycosphingolipid-related metabolites. Integrated analyses suggested that lipidomic variation statistically accounted for part of the microbiome-GDM association. A class-level dihexosylceramide feature, DHC 24:1, consistent with lactosylceramide-related metabolites, emerged as a potential mediator and was prioritized for exploratory follow-up. Experimental analyses provided functional support for a microbiome-lipid-host interaction axis. R. bicirculans promoted lactosylceramide 24:1 production in vitro, bacterial colonization and metabolite administration improved insulin tolerance in vivo, and lactosylceramide 24:1 modulated insulin-stimulated AKT signaling dynamics in hepatocytes. These findings identify a gut microbiome-lipid axis associated with metabolic dysregulation in pregnancy and suggest a potential mechanism linking microbial metabolism to host insulin signaling.}, } @article {pmid42578670, year = {2026}, author = {Li, Z and Sun, J and Yang, J and Han, P and Min, L and Cheng, Y and Zou, Y and Liu, Z}, title = {Exploring the hypothetical role of Bacteroides species in depression progression: insights from metagenomic analysis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0315324}, doi = {10.1128/spectrum.03153-24}, pmid = {42578670}, issn = {2165-0497}, abstract = {Depression, a psychiatric disorder with significant morbidity and mortality, has a complex etiology. Recent advances in microbiome research have highlighted the potential role of fecal microbiota in depression pathogenesis. This study utilized shotgun metagenomic sequencing to compare the fecal microbiota of 28 depression patients and 26 healthy individuals. Significant differences in fecal microbiota composition were observed between the two groups. We generated 350 non-redundant high-quality metagenome-assembled genomes (MAGs) by binning and conducted comparisons between the depression and control groups. Notably, we found that the MAGs enriched in people with depression mostly belonged to Bacteroides, indicating a close link between Bacteroides abundance and the development of depression, suggesting that Bacteroides might be a potential culprit for depression. In the depression group, we found that the module of nitric oxide synthesis was remarkably enriched, and all Bacteroides MAGs contained genes annotated as nitric oxide synthase, suggesting that increased levels of Bacteroides may contribute to elevated nitric oxide synthesis. A distinct microbial signature consisting of Arthrobacter sp._U41, Bacillus cereus, Campylobacter rectus, and Pasteurella dagmatis accurately discriminates between depressed individuals and healthy controls, achieving an average area under the receiver operating characteristic curve of 0.950. This research sheds light on the potential role of fecal microbiota in depression and highlights specific metabolic pathways and microbial markers for further investigation.IMPORTANCEThis research highlighted significant differences in the composition and function of fecal microbiota between individuals with depression and healthy individuals, particularly the enrichment of Bacteroides metagenome-assembled genomes (MAGs) in depression patients. The upregulation of the nitric oxide synthesis pathway associated with these MAGs belonging to Bacteroides in the gut of depression patients had also been observed. The selected bacterial biomarkers reliably differentiate depression cases from healthy controls with high diagnostic accuracy (mean area under the receiver operating characteristic curve = 0.950). Our results suggest the importance of exploring microbial markers as potential diagnostic and therapeutic targets in managing depression.}, } @article {pmid42578673, year = {2026}, author = {Mirăuță, B and Riza, A-L and Streata, I and Pirvu, A and Dorobantu, S and Dragos, A and Surleac, M and Netea, MG}, title = {Resistome and microbiome-immune interactions in an Eastern European population with high antibiotic use.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0052826}, doi = {10.1128/spectrum.00528-26}, pmid = {42578673}, issn = {2165-0497}, abstract = {The gut microbiome influences host health, affecting gastrointestinal, metabolic, immune, cardiovascular, and neurological functions. A balanced microbiome is associated with favorable health outcomes. However, excessive antibiotic use and dietary habits can disrupt this ecosystem, leading to dysbiosis and affecting body homeostasis. This first comprehensive metagenomic analysis of the gut microbiome in a healthy Romanian cohort, a population underrepresented in microbiome studies and characterized by high antibiotic consumption, addresses a gap in current microbiome research. We report an enrichment of Enterobacteriaceae although overall composition is more comparable to other European than non-European cohorts. Community configurations align with established enterotype patterns, and our analysis provides insight into their relationship with within-phylum diversity. The analysis of antimicrobial resistance provides insight into the prevalence of resistance genes within this reservoir. We specifically report the presence of cfr(E), a Clostridioides difficile gene, and tet(X5), a variant from the ubiquitous tet family, genes not previously reported in healthy European populations. Integration with data from the European Centre for Disease Prevention and Control links the overall prevalence of resistance genes in this reservoir to antibiotic classes with higher community consumption in this population, notably beta-lactams and quinolones, highlighting potential targets for antibiotic stewardship programs. Finally, we investigate the relationship between the microbial profile and the systemic immune responses, inferred from correlations with in vitro cytokine production. Notably, we identify potential immune-priming roles for Collinsella, Flavonifractor, and Bifidobacterium species.IMPORTANCEThis first comprehensive study of the healthy gut microbiome in a Romanian cohort addresses a gap in current microbiome research, dominated by data sets from a limited number of regions. It sets a baseline for the microbiome and resistome composition of this population, and, while definitions of "healthy" microbiomes, or baseline resistomes, remain lacking, such study helps contextualize future studies and support the monitoring of dynamics. The Enterobacteriaceae abundance suggests a microbiome composition potentially influenced by antimicrobial consumption, a relevant pattern in a region with a high burden of nosocomial infections. In addition, the prevalence of antimicrobial resistance genes and the concordance with commonly used antibiotics in the community reinforce the need to address antibiotic use in public health strategies. Although gut microbiome-immunity relationships remain incompletely understood, our findings support a role for microbiome composition in immune-related traits and provide a valuable resource for future studies.}, } @article {pmid42578999, year = {2026}, author = {Conway Morris, A and Edgeworth, JD and Povoa, P}, title = {Clinical metagenomics: a call to action.}, journal = {Intensive care medicine}, volume = {}, number = {}, pages = {}, pmid = {42578999}, issn = {1432-1238}, support = {MR/V006118/1/MRC_/Medical Research Council/United Kingdom ; }, } @article {pmid42579079, year = {2026}, author = {Yu, J and Xiong, Q and Li, X}, title = {Synergistic degradation of sulfamethoxazole by Enterococcus wangshanyuanii F4 and black soldier fly larvae.}, journal = {Biodegradation}, volume = {37}, number = {4}, pages = {}, pmid = {42579079}, issn = {1572-9729}, support = {39829117//Nanjing Tech University/ ; }, mesh = {Animals ; Larva/microbiology/metabolism/growth & development ; *Sulfamethoxazole/metabolism ; *Enterococcus/metabolism ; Biodegradation, Environmental ; *Simuliidae/microbiology/metabolism ; *Diptera/microbiology ; }, abstract = {This study demonstrates that inoculation with the Enterococcus wangshanyuanii strain F4 in a germ-free black soldier fly larval (BSFL) system enhances sulfamethoxazole (SMX) degradation, larval growth, and substrate conversion. Following inoculation with strain F4, the net SMX degradation rate reached 37.08%, and the net substrate consumption rate reached 46.12%, both representing significant improvements compared to the control group. Metagenomic analysis revealed that strain F4 modulated the BSFL gut microbial community structure and enriched functional genes associated with organic pollutant degradation. Accordingly, the activities of key degradation enzymes in the larval gut, including catechol-1,2-dioxygenase (C12O), catechol-2,3-dioxygenase (C23O), and peroxidase (POD), were significantly elevated following inoculation. Taken together, these findings suggest a synergistic effect between Enterococcus wangshanyuanii F4 and the host during the degradation process, which significantly enhances the removal of SMX by black soldier fly larvae. This provides a theoretical basis for the use of symbiotic microbial augmentation strategies in antibiotic bioremediation.}, } @article {pmid42579339, year = {2026}, author = {Douwes, H and Dutkiewicz, Z and Rinke, C}, title = {Predicting the plastic biodegradation potential within microbial lineages and across global ecosystems.}, journal = {Microbial genomics}, volume = {12}, number = {8}, pages = {}, doi = {10.1099/mgen.0.001814}, pmid = {42579339}, issn = {2057-5858}, mesh = {*Plastics/metabolism ; *Biodegradation, Environmental ; *Bacteria/genetics/classification/metabolism/enzymology ; Metagenome ; *Archaea/genetics/classification/metabolism/enzymology ; Ecosystem ; Phylogeny ; Metagenomics ; Genome, Bacterial ; Hidden Markov Models ; }, abstract = {Plastic waste pollution is a global issue that threatens biodiversity and human health. Current plastic waste management practices are not sufficient to keep up with increasing plastic production rates. Microorganisms have the capacity to degrade different types of bio-based and synthetic plastics through enzymatic reactions, offering an alternative solution to traditional plastic recycling techniques. A limited number of plastic-degrading enzymes have been identified, sequenced and characterized; however, studies exploring the distribution of homologues of these enzymes across habitats and microbial taxa have remained scarce. Here, we applied analytical techniques to search for genes encoding potential plastic-degrading enzymes in environmental metagenome datasets and genomes of the Genome Taxonomy Database (GTDB) to explore the geographic and taxonomic distribution patterns of plastic-degrading microorganisms. Hidden Markov Models (HMMs) were constructed from amino acid sequences of known, experimentally verified and putative plastic-degrading enzymes. The HMMs were applied to landfill, soil, river, lake and ocean metagenomes and all archaeal and bacterial genomes in the GTDB. An abundance of hits was discovered across aquatic and terrestrial metagenomes with the majority occurring in polluted rivers, polar oceans and deep ocean samples. GTDB hits were mainly consistent with known plastic-degrading microbial lineages, while also revealing potential plastic-degrading archaeal taxa. The results of this study may be able to assist in the discovery of novel plastic-degrading enzymes for application in plastic waste biodegradation solutions.}, } @article {pmid42579903, year = {2026}, author = {Zhang, W and Wei, Z and Liu, Y and Xiao, Y}, title = {Rupture and dissemination of a mycotic aneurysm caused by the Aspergillus fumigatus complex: A diagnostic challenge posed by a non‑sporulating isolate.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {4}, pages = {117595}, doi = {10.1016/j.diagmicrobio.2026.117595}, pmid = {42579903}, issn = {1879-0070}, abstract = {A 45-year-old male with a history of lumbar tuberculosis presented with a ruptured mycotic iliac artery aneurysm as the initial manifestation. Imaging demonstrated aneurysm rupture with pseudoaneurysm formation and concurrent disseminated lesions involving the vertebrae and soft tissues. Intraoperative specimens grew an Aspergillus fumigatus strain that exhibited highly atypical morphology: the colonies were albino‑like, slow‑growing, and non‑sporulating, differing markedly from the classic A. fumigatus phenotype. Peripheral blood metagenomic sequencing detected A. fumigatus, and the serum galactomannan antigen was markedly elevated. Molecular sequencing confirmed the isolate as A. fumigatus sequence type ST26 and identified the multidrug resistance‑associated gene ABCA. The final diagnosis was disseminated aspergillosis presenting as a ruptured mycotic iliac artery aneurysm, complicated by prosthetic graft infection and multiorgan dissemination. The patient received systemic antifungal therapy with voriconazole, along with adequate surgical drainage and debridement. Subsequently, his inflammatory markers declined gradually, and he was discharged on hospital day 58.}, } @article {pmid42580006, year = {2026}, author = {Zhang, L and Xu, W and Wang, Y and Liu, Y and Feng, X and Liu, Q}, title = {Metagenomic profiling of tick-borne viromes across four ecologically diverse provinces in China.}, journal = {Ticks and tick-borne diseases}, volume = {17}, number = {5}, pages = {102693}, doi = {10.1016/j.ttbdis.2026.102693}, pmid = {42580006}, issn = {1877-9603}, abstract = {Ticks are important vectors of emerging viruses, and China's ecological landscapes may influence the transmission dynamics of tick-borne viruses (TBV). In 2021, a total of 2867 ticks collected from Inner Mongolia, Hebei, Hunan, and Hainan provinces were subjected to metagenomic sequencing to characterize TBV diversity. A total of eleven TBVs were identified, comprising three members of the family Phenuiviridae (severe fever with thrombocytopenia syndrome virus, Lihan tick virus, Dabieshan tick virus), three belonging to Nairoviridae (Huangpi tick virus 1, Shanxi tick virus 2, Henan tick virus), one in Chuviridae (Wuhan tick virus 2), one in Rhabdoviridaes (Wuhan tick virus 1), and three unclassified viruses (Hubei tick virus 2, Bole tick virus 4, and Tacheng tick virus 7). Viral composition varied significantly across tick species and geographic regions, with phylogenetic analysis revealing distinct regional clustering patterns. Notably, Lihan tick virus was detected for the first time in Hunan Province, Bole tick virus 4 was identified in argasid ticks from Inner Mongolia for the first time, and a novel lineage of severe fever with thrombocytopenia syndrome virus was discovered in Shijiazhuang, Hubei Province. These findings underscore substantial TBV diversity shaped by tick species and geographic origin, emphasizing the necessity for ongoing surveillance to guide the development of targeted prevention and control strategies.}, } @article {pmid42580037, year = {2026}, author = {Kearney, A and Chau, K and Kotay, S and Martin, J and Kirby, A and Mathers, AJ and Stoesser, N}, title = {Hospital sinks and healthcare-associated infection: ecology, transmission, surveillance and mitigation.}, journal = {EBioMedicine}, volume = {131}, number = {}, pages = {106415}, doi = {10.1016/j.ebiom.2026.106415}, pmid = {42580037}, issn = {2352-3964}, abstract = {Hospital sinks are recognised polymicrobial reservoirs for multi-drug resistant organisms and have been implicated in patient transmission and outbreaks. Earlier studies on sink-associated microbes predominantly focused on specific species or resistance mechanisms (e.g. carbapenemases) using targeted microbiological methods. More recently, less selective approaches (e.g. metagenomic sequencing) have enabled broader characterisation of these microbial communities. This review summarises current evidence describing hospital sink-trap microbiomes, examining ecological determinants, surveillance strategies and interventions aiming to mitigate transmission from these reservoirs. We discuss biotic and abiotic factors that shape microbial selection/persistence, assess approaches to managing these reservoirs to reduce patient risk, and highlight priorities for future research to inform evidence-based practice in healthcare settings.}, } @article {pmid42571590, year = {2026}, author = {Tinta, T and Fadeev, E and Celussi, M and Balestra, C and Klun, K and Mozetič, P and Herndl, GJ}, title = {Microbial degradation of jellyfish detritus promotes phytoplankton growth in coastal marine ecosystems.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag185}, pmid = {42571590}, issn = {2730-6151}, abstract = {Gelatinous zooplankton (hereinafter cnidarian Medusozoa and ctenophores or "jellyfish") are widespread in marine ecosystems and can form blooms, releasing large amounts of labile, protein-rich organic matter (jelly-OM) upon decay. This material fuels intense bacterial activity, yet its ecological consequences remain poorly understood. We conducted a two-stage microcosm experiment simulating a bloom decay of the invasive ctenophore Mnemiopsis leidyi to examine microbial processing of jelly-OM and its effect on primary production (PP). In the first stage, over the course of 3 days, we observed jelly-OM stimulating rapid growth of opportunistic bacterial community. The community was dominated by Pseudoalteromonadaceae-key degraders of diverse jellyfish, which exhibited enhanced metabolism of amino acids, lipids, and carbohydrates and elevated extracellular enzymatic activities, including leucine aminopeptidase, lipase, chitinase, and alkaline phosphatase. These processes led to marked ammonium accumulation. In the second stage, exposure of a fresh microbial assemblage to residues from jelly-OM degradation resulted in a significant increase of PP and phytoplankton biomass over a period of five days. This was dominated by diatoms and was fueled by accumulated ammonium. Concurrently, the bacterial community shifted toward taxa typically associated with phytoplankton blooms. Together, these results, further supported by in situ observations, reveal a likely coupling between jellyfish decay and phytoplankton growth, suggesting that jellyfish blooms act as transient but powerful nutrient sources capable of triggering ecosystem shifts. As jellyfish are projected to thrive under future ocean conditions, our findings underscore the need to re-evaluate their role in biogeochemical cycles-particularly as overlooked drivers of phytoplankton dynamics.}, } @article {pmid42571770, year = {2026}, author = {Qian, D and Xu, Z and Yuan, M and Li, Z and Zhu, Q and Peng, M and Gong, J and Yang, J and Hu, J and Hou, H}, title = {Unlocking the hidden carbon pool: Refractory organic matter drives superior chain elongation in sludge alkaline fermentation liquid.}, journal = {Water research}, volume = {306}, number = {}, pages = {126422}, doi = {10.1016/j.watres.2026.126422}, pmid = {42571770}, issn = {1879-2448}, abstract = {Converting waste activated sludge (WAS) into medium-chain fatty acids (MCFAs) via chain elongation (CE) offers a promising route for sludge valorization. In two-stage sludge CE systems, primary fermentation is typically optimized to maximize the short-chain fatty acid (SCFA) pool for downstream MCFA production; however, whether retained refractory dissolved and undissolved organic matter (rDOM and rUOM) also contributes to CE remains unclear. Here, we evaluated the roles of rDOM and rUOM in ethanol-driven CE using sludge alkaline fermentation liquid (SAFL) and thermal-alkaline pretreatment fermentation liquid (STAPFL) as feedstocks. Although SAFL contained fewer SCFAs after primary fermentation than STAPFL (3.25 vs. 3.60 g COD/L), it yielded 44% more MCFAs during CE (11.56 vs. 8.03 g COD/L). Integrated physicochemical and molecular analyses indicated that this advantage arose from greater retention of refractory organics during primary alkaline fermentation and their continued mobilization during downstream CE. Filtration experiments and COD-based estimation indicated a much greater total apparent COD contribution from retained rUOM and rDOM in SAFL than in STAPFL (2.16 vs. 0.15 g COD/L). FT-ICR-MS and metagenomic analyses further suggested compositional transformation of retained refractory organics and stronger functional potential for coordinated hydrolysis, acidogenesis, and CE in SAFL, which together supported continued precursor supply and higher MCFA production. These results indicate that downstream MCFA production in real sludge fermentation liquids depends not only on the initial soluble SCFA pool, but also on the continued mobilization of retained refractory carbon during CE. This study advances understanding of retained refractory carbon utilization during ethanol-driven CE in two-stage sludge fermentation for MCFA production.}, } @article {pmid42571814, year = {2026}, author = {Ge, S and Sun, M and He, J and Pan, Y and Xu, Y and Wang, L and Luo, R and Zhong, Y and Wang, Y and Huang, J and Hu, M and Huang, Z and Wu, G and Wan, Y and Mo, L and Wu, F and Nie, C and Zhou, H and He, Y and Ma, Z and He, X and Gao, J}, title = {Gut microbial DL-endopeptidase protects against alcohol-associated liver disease via hepatocyte NOD2 signaling.}, journal = {Free radical biology & medicine}, volume = {255}, number = {}, pages = {712-729}, doi = {10.1016/j.freeradbiomed.2026.08.020}, pmid = {42571814}, issn = {1873-4596}, abstract = {Chronic alcohol consumption disrupts gut-liver homeostasis not only by inducing direct hepatotoxic injury, but also by perturbing host-microbial defense mechanisms that normally protect the liver from metabolic and inflammatory stress. We show that hepatocyte-specific deletion of Nod2 exacerbates ethanol-induced steatosis, oxidative stress, and mitochondrial dysfunction, establishing NOD2 as a critical protective factor in alcohol-associated liver disease (ALD). Importantly, beyond its direct hepatotoxic effects, ethanol exposure simultaneously diminishes this protective NOD2 pathway by limiting microbiota-derived ligand availability. Guided by this functional deficit, clinical metagenomic analysis (n = 1516) revealed that alcohol consumption is associated with a selective depletion of gut microbial DL-endopeptidase, a rate-limiting enzyme for NOD2 ligand generation, which inversely correlated with liver injury severity. Mice receiving fecal microbiota from donors with low DL-endopeptidase activity showed increased susceptibility to ALD. Importantly, supplementation with a NOD2 ligand or its clinical analogue, mifamurtide, restored mitochondrial homeostasis and alleviated liver injury. Together, these findings identify the gut microbial DL-endopeptidase-NOD2 axis as a key protective mechanism against ethanol-induced liver injury and a promising therapeutic target in alcohol-associated liver disease.}, } @article {pmid42571819, year = {2026}, author = {Li, S and Cai, M and Chen, L and Liang, J and Luo, X and Meng, J and Cao, Y and Liu, G and Hu, Y and Cai, S and Zou, M}, title = {Serine synergizes with lipopolysaccharide to induce macrophage pyroptosis through extracellular Hsp90α and early skin immune microenvironment disruption in diabetic foot.}, journal = {Metabolism: clinical and experimental}, volume = {}, number = {}, pages = {156732}, doi = {10.1016/j.metabol.2026.156732}, pmid = {42571819}, issn = {1532-8600}, abstract = {BACKGROUND: The pathogenesis of early-stage skin lesions in diabetic foot (DF) remains poorly understood, and cannot be fully explained by conventional theories. Skin microbiota dysbiosis has recently emerged as a critical factor, but the underlying mechanisms remain unclear.

METHODS: In this study, we integrated metabolomics and metagenomics analyses of skin samples to investigate metabolic dysregulation driven by microbial dysbiosis.

RESULTS: We identified elevated serine as a key metabolic alteration strongly correlated with a dysbiotic microbiota structure. Functionally, we demonstrate that abnormal serine accumulation contributes to the dysregulation of the early skin immune microenvironment in the diabetic foot. Mechanistically, our results reveal that excess serine synergizes with lipopolysaccharide (LPS) to stimulate the release of eHsp90α from keratinocytes, which was strictly dependent on the Akt/mTOR/HIF-1α pathway. This released eHsp90α then acts as a damage-associated molecular pattern, promoting both the migration and subsequent pyroptotic cell death of macrophages.

CONCLUSIONS: Collectively, our findings suggest a novel pathogenic axis where a microbiota-host derived metabolite collaborates with a bacterial endotoxin to promote inflammatory cell death, which is closely associated with early skin lesions in DF. This work not only elucidates a new mechanism for DF pathogenesis but also suggests that the serine-eHsp90α-pyroptosis axis may serve as a potential candidate for future therapeutic exploration.}, } @article {pmid42571835, year = {2026}, author = {Wang, G and Li, J and Wang, D and Chen, SS and Zheng, G and Zhou, S and Wang, T and Zhou, Y}, title = {Microbial community structure, function and environmental drivers of the urban soil plastisphere in a typical megacity, China.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125432}, doi = {10.1016/j.envres.2026.125432}, pmid = {42571835}, issn = {1096-0953}, abstract = {The plastisphere in urban soils remains poorly understood despite its potential ecological significance. Here, 42 samples, including 21 soil samples and 21 plastisphere samples, were collected from seven functional zones in Nanjing, and metagenomic sequencing, bioinformatics, and quantitative modeling with multisource geographic and soil data were employed to investigate the community structure, function and environmental drivers of the soil plastisphere in this typical megacity, China. Fungi, particularly Ascomycota and the genus Fusarium (LDA score=4.73), exhibited stronger selective enrichment in the plastisphere than bacteria did, with this pattern being consistent across all functional zones, suggesting that the intrinsic properties of microplastics (MPs) govern taxonomic assembly. Plastisphere co-occurrence networks were simpler, more modular, and less robust than soil networks were, indicating that the structurally vulnerable microbial community was shaped predominantly by stochastic assembly (R[2]>0.2). Functional analysis further revealed significant alterations in the characteristics of denitrification genes (napA, norB, and narH/narY/nxrB), suggesting modified nitrogen cycling potential. Critically, pollutants, especially MPs themselves, partially overrode geospatial and edaphic factors as direct drivers of plastisphere communities, representing fundamental decoupling from the natural environmental matrix governing bulk soil. Pollutants strongly negatively affected fungal compositions and networks in the plastisphere, amplifying the ecological hazards of coexisting contaminants. These findings revealed that MP pollution modified microbial community assembly in urban soils, creating a decoupled, pollutant-driven microbial system. Integrating these effects into urban environmental risk assessments is therefore urgently needed.}, } @article {pmid42571869, year = {2026}, author = {Manzoor, M and Leskelä, J and Könönen, E and Lahti, L and Putaala, J and Pussinen, PJ and Paju, S}, title = {Shotgun Metagenomic Analysis Reveals Taxonomic and Functional Transitions in the Salivary Microbiome During Periodontal Disease Progression.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.70184}, pmid = {42571869}, issn = {1600-051X}, support = {296541//Research Council of Finland/ ; 316777//Research Council of Finland/ ; 355532//Research Council of Finland/ ; 340750//Research Council of Finland/ ; 369310//Research Council of Finland/ ; 286246//Research Council of Finland/ ; 318075//Research Council of Finland/ ; 322656//Research Council of Finland/ ; //Finnish Dental Society Apollonia/ ; //Sigrid Juselius Foundation/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; }, abstract = {AIM: To characterise multi-kingdom salivary microbiome profiles across clinically defined periodontal states and identify stage-specific taxonomic and functional alterations using shotgun metagenomic sequencing.

MATERIALS AND METHODS: In this cross-sectional study, 204 adults (mean age 40.3 ± 7.6 years) from the SECRETO study (NCT01934725) underwent clinical and radiographic oral examinations and were classified into six periodontal groups: periodontal health, localised gingivitis, generalised gingivitis, gingivitis with pockets, mild periodontitis (Stages I-II) and severe periodontitis (Stages III-IV). Saliva samples were analysed using shotgun metagenomic sequencing to evaluate microbial diversity, taxonomic composition and functional pathways.

RESULTS: Beta diversity differed between periodontal health and the different disease states (Bray-Curtis: p = 0.049; Jaccard: p = 0.043). Gingivitis with pockets and severe periodontitis showed a significant enrichment of disease-associated species Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Porphyromonas endodontalis, Fusobacterium nucleatum and Parvimonas micra. Among non-bacterial taxa, Candida, Moineauvirus, Pyricularia and Roseolovirus were the predominant genera. A composite metagenomic classifier showed high discriminative performance for gingivitis with pockets (AUC = 0.90; 95% CI: 0.770-1.000) and severe periodontitis (AUC = 0.865; 95% CI: 0.762-0.968).

CONCLUSION: Salivary multi-kingdom microbiome transitions closely reflect the progression of periodontal disease and provide promising biomarkers for identifying at-risk individuals.}, } @article {pmid42572222, year = {2026}, author = {Kirilina, IV and Roumiantsev, SA and Gaponov, AM and Savchyk, DV and Khusnutdinova, DR and Grigoryeva, TV and Teplyakova, ED and Shestopalov, AV}, title = {[The contribution of the intestinal microbiome to the formation of the general profile of bacterial DNA in the blood of obese children].}, journal = {Voprosy pitaniia}, volume = {95}, number = {3}, pages = {107-116}, doi = {10.33029/0042-8833-2026-95-3-107-116}, pmid = {42572222}, issn = {0042-8833}, support = {//The research was carried out under the contract no. 0373100122119000041 within the project "Creation of a bank of biosamples of blood serum and feces from healthy donors and patients with obesity, metabolic syndrome, type 2 diabetes mellitus, and impaired mucosal barrier of the gastrointestinal tract, in order to identify candidate species nonspecific mediators of the quorum sensing microbiota systems of human, which modulate the endocrine and metabolic function of adipose tissue"/ ; }, mesh = {Humans ; Child ; *DNA, Bacterial/blood ; Cross-Sectional Studies ; Feces/microbiology ; Adolescent ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; *Pediatric Obesity/microbiology/blood ; Lipid Metabolism ; Carbohydrate Metabolism ; Obesity/microbiology/blood ; *Gastrointestinal Microbiome ; }, abstract = {UNLABELLED: Obesity is a multifactorial disease. The gut microbiome disturbances play a significant role in the development of obesity, but emerging data point to a blood microbiome and its association with obesity and other pathologies. Bacterial DNA in the blood represents a pathogen-associated molecular pattern capable of activating the immune system and thereby triggering a cascade of inflammatory responses. The question remains open as to where the bacterial DNA originates, which biotopes shape it, and what role the gut microbiome plays in forming the pool of bacterial DNA in blood. The aim of the study was to compare the bacterial DNA profiles of feces and blood in obese children, to establish relationships between bacterial DNA in blood and feces, and with carbohydrate and lipid metabolism parameters.

MATERIAL AND METHODS: This single-center, cross-sectional study included children and adolescents aged 10 to 18 years with varying degrees of alimentary-constitutional obesity (n=79) and without obesity (n=84). The taxonomic profile of bacterial DNA in blood and feces was analyzed using metagenomic sequencing. Bacterial DNA was isolated from blood and stool samples, and the v3-v4 variable region of the 16S rRNA gene was sequenced. To identify the relationship between bacterial DNA in blood and feces and lipid and carbohydrate metabolism parameters [glucose, total cholesterol, high-density lipoprotein and low-density lipoprotein (LDL)], Spearman's correlation coefficients were calculated.

RESULTS: When comparing bacterial DNA from blood and feces, obese children more often isolated DNA from the families Lactobacillaceae (p=0.043), Porphyromonadaceae (p=0.022), Ruminococcaceae (p=0.065) and less often from Prevotellaceae (p=0.028) and Coriobacteriaceae (p=0.085) compared to children and adolescents without obesity. In obese children, the contribution of intestinal taxa (Lachnospiraceae, Ruminococcaceae, Bacteroidaceae) to the formation of the bacterial DNA profile of the blood was significantly reduced, but the contribution of extraintestinal biotopes (skin, soil and water) was more diverse. Positive associations were found between bacterial DNA of fecal Ruminococcaceae taxa and the level of total cholesterol (ρ=0.347, p=0.002) and LDL (ρ=0.313, p=0.005) and of fecal Coriobacteriaceae and these lipid metabolism parameters (ρ=0.304, p=0.007 and ρ=0.317, p=0.005) in obese children. No positive associations were found between fecal and blood taxa and glucose level.

CONCLUSION: In obese and non-obese children and adolescents, the general profile of bacterial blood DNA is formed by both intestinal and extra-intestinal biotopes. However, in obese children, taxa from extra-intestinal biotopes predominate in the formation of the blood microbiome, which is confirmed by analyzing the proximity of the taxonomic composition of bacterial DNA in blood and feces based on beta diversity indices. The relationship of taxa with blood cholesterol and LDL levels can be considered as a target for microbiota modification and thus reducing the risks of metabolic complications in obesity.}, } @article {pmid42572739, year = {2026}, author = {Lin, H and Deng, Y and Chen, Z and Huang, A and Yuan, K}, title = {Clinical Insights into Strongyloides stercoralis Pulmonary Hyperinfection Syndrome.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {628404}, pmid = {42572739}, issn = {1178-6973}, abstract = {BACKGROUND: Strongyloides stercoralis pulmonary hyperinfection syndrome (SPHS) is a rare, frequently fatal complication of strongyloidiasis that is difficult to recognize because of its nonspecific multisystem manifestations. Diagnosis requires a high index of suspicion.

METHODS: This retrospective study identified 29 hospitalized patients with strongyloidiasis at Chaozhou Central Hospital between November 2018 and January 2026. We compared the clinical data of five patients with SPHS (SPHS group) and 21 patients with uncomplicated/chronic strongyloidiasis (non-SPHS group) and described the detailed clinical profiles of the five patients with SPHS.

RESULTS: All five SPHS patients (median age, 67; 4/5 were male) had diabetes mellitus, glucocorticoid exposure, rural soil contact, fever, and nonspecific pulmonary computed tomography (CT) abnormalities; four (4/5, 80%) had gastrointestinal and/or neurological manifestations and intestinal obstruction. All five patients had multisystem laboratory abnormalities without eosinophilia. S. stercoralis was detected in respiratory specimens from all patients, and three (3/5, 60%) were confirmed by bronchoalveolar lavage fluid metagenomic next-generation sequencing (mNGS) or targeted next-generation sequencing (tNGS) within 2-5 days. All patients had bacterial coinfections. Adequate antimicrobial coverage was achieved in four (4/5, 80%) patients; one patient (1/5, 20%) received both ivermectin and albendazole, and three (3/5, 60%) received albendazole monotherapy. Three patients (3/5, 60%) died of severe complications. Compared with the non-SPHS group, the SPHS group had a significantly lower median eosinophil count (0.01 × 10[9]/L); higher rates of corticosteroid exposure, diabetes mellitus, neurological and gastrointestinal symptoms, intestinal obstruction, severe complications, and mortality; and a longer time to laboratory confirmation (all P < 0.05).

CONCLUSION: In high-risk patients, normal or low eosinophil counts do not exclude SPHS. Early examination of respiratory specimens using microscopy and, when available, mNGS/tNGS may shorten the time to diagnosis. For these patients, early recognition of SPHS, antiparasitic therapy, and the management of bacterial coinfections are essential.}, } @article {pmid42572760, year = {2026}, author = {Zhong, L and Yuan, K}, title = {First Case of Concurrent Cytomegalovirus and Aspergillus tamarii Pulmonary Infections in a Mantle Cell Lymphoma Patient: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {623986}, pmid = {42572760}, issn = {1178-6973}, abstract = {Patients with mantle cell lymphoma (MCL) who undergo chemotherapy are at high risk of developing opportunistic pulmonary infections. Concurrent infection with cytomegalovirus (CMV) and the rare pathogen Aspergillus tamarii (A. tamarii) has never previously been reported in MCL patients. In this case report, we present the first documented instance of concurrent CMV and A. tamarii pneumonia in a MCL patient. A 69-year-old man with MCL developed a cough, chills, exertional dyspnoea, and hypoxemia after five cycles of rituximab-bendamustine (R-Benda) chemotherapy. Chest computed tomography (CT) showed bilateral ground-glass opacities. Metagenomic next-generation sequencing (mNGS) of the blood and bronchoalveolar lavage fluid (BALF) simultaneously revealed CMV and A. tamarii infections. The patient initially achieved rapid clinical improvement with ganciclovir and voriconazole. However, the infection relapsed following unauthorised premature discontinuation of ganciclovir and voriconazole without medical advice. Long-term oral voriconazole with regular TDM and close monitoring of ganciclovir-related myelosuppression resulted in sustained remission. This is the first reported case of concurrent CMV and A. tamarii pulmonary coinfection in a MCL patient, and mNGS enables the rapid and accurate diagnosis of mixed rare infections. Voriconazole is effective against A. tamarii; TDM and full-course treatment are essential for preventing relapse. We present a practical workflow for managing immunocompromised patients with rare mixed pulmonary infections to improve outcomes.}, } @article {pmid42573887, year = {2026}, author = {Yang, L and Zhao, J and Han, T and Qi, H and Zhao, F and Sun, Z}, title = {Modulating the gut-joint axis: Bifidobacterium longum subsp. infantis B8762 is associated with selective gut microbial and metabolic alterations in knee osteoarthritis.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {8}, pages = {}, pmid = {42573887}, issn = {1573-0972}, support = {U25A20733//National Natural Science Foundation of China/ ; 2022YFD2100702//National Key Research and Development Program of China/ ; YLXKZX-NND-006//Inner Mongolia Agricultural University First-Class Discipline Scientific Research Special Program/ ; CARS36//Earmarked Fund for China Agriculture Research System/ ; }, mesh = {Humans ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Osteoarthritis, Knee/microbiology/metabolism/therapy ; *Probiotics/administration & dosage ; Metabolome ; *Bifidobacterium/physiology ; Metabolomics ; Male ; Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenomics ; Female ; Knee Joint/microbiology/metabolism ; *Bifidobacterium longum ; }, abstract = {Knee osteoarthritis (KOA) is a debilitating degenerative joint disorder characterized by chronic low-grade inflammation and metabolic dysregulation. The gut microbiota has emerged as an important regulator of systemic inflammatory responses. Building upon our previous clinical findings that Bifidobacterium longum subsp. infantis B8762 (B8762) improved clinical symptoms and inflammatory markers in patients with KOA, the present study investigated the associated alterations in the gut microbiome and fecal metabolome. Fecal samples were collected from probiotic (n = 20) and placebo (n = 20) groups at baseline (0 M) and after a 1-month intervention (1 M). Integrated metagenomic and untargeted metabolomic analyses were performed to characterize changes in gut microbial composition, functional potential, and metabolic profiles. Metagenomic reads mapped to the B8762 reference genome showed a greater increase in B8762-associated mapping rates in the probiotic group than in the placebo group, supporting an association between B8762 supplementation and longitudinal changes in the gut microbiome. Longitudinal analysis further demonstrated greater increases in microbial alpha diversity in the probiotic group. Species-level analyses suggested selective alterations in gut microbial composition, with nominally higher relative abundances of Bifidobacterium pseudocatenulatum and Anaerostipes caccae and lower relative abundances of Holdemania filiformis and Lachnospira SGB5077 (nominal P < 0.05). HUMAnN3-based functional profiling identified enrichment of microbial pathways related to carbon utilization and amino acid biosynthesis, including the bifidobacterial shunt and branched-chain amino acid biosynthesis pathways. Untargeted metabolomics identified nominal between-group differences in metabolites primarily related to lipid metabolism, including lower relative abundances of aldosterone and 7α-hydroxy-4-cholesten-3-one in the probiotic group (nominal P < 0.05). Correlation analysis further revealed associations between differential taxa and selected metabolites, suggesting potential links between gut microbial alterations and steroid-related metabolic pathways. Overall, B8762 supplementation was associated with longitudinal changes in B8762-associated genomic signals, gut microbial diversity and composition, microbial functional potential, and fecal metabolic profiles. These findings provide exploratory multi-omics evidence supporting an association between B8762 supplementation and gut microbial-metabolic remodeling in KOA and generate hypotheses for future mechanistic studies of the gut-joint axis.}, } @article {pmid42574061, year = {2026}, author = {Parks, DH and Chaumeil, PA and Chuvochina, M and Hugenholtz, P}, title = {Stop codon reassignment to tryptophan in members of the bacterial phylum Actinomycetota.}, journal = {Microbial genomics}, volume = {12}, number = {8}, pages = {}, doi = {10.1099/mgen.0.001767}, pmid = {42574061}, issn = {2057-5858}, mesh = {*Tryptophan/genetics ; *Codon, Terminator/genetics ; Phylogeny ; Genome, Bacterial ; Evolution, Molecular ; Animals ; Metagenome ; *Actinobacteria/genetics/classification ; }, abstract = {Reassignment of stop codons is a significant evolutionary event with recoding of UGA to tryptophan being previously identified in only three bacterial phyla, the Bacillota, Pseudomonadota and Verrucomicrobiota. Here, we present genomic evidence of this reassignment in a fourth bacterial phylum, the Actinomycetota, specifically in the family Eggerthellaceae. We identify the UGA stop-to-tryptophan reassignment in 34 metagenome-assembled genomes recovered from the stool samples of diverse mammalian hosts, including equids and primates. Canonical markers for this reassignment are consistently observed including conserved UGA codons aligning to tryptophan, loss of release factor 2 (prfB) and presence of a tRNA[Trp](UCA) gene. We infer that this reassignment occurred at least twice as the lineages containing reassigned genomes are paraphyletic, forming two distinct groups separated by a third lineage with strains that use UGA as a stop codon. These lineages represent three new Eggerthellaceae genera for which we propose the type species Equivita altericodex, Gorillivita intestinalis and Tapirivita inops reflecting isolation source and genomic properties. Organisms representing these genera have reduced genomes and complete or partial loss of biosynthetic pathways, suggesting increasing host dependency and a transition to obligate symbiosis. This likely facilitated stop codon reassignment in Equivita and Gorillivita and suggests Tapirivita is primed for reassignment. This work expands the known phylogenetic diversity of UGA stop-to-tryptophan reassignment in the bacterial domain and establishes the Eggerthellaceae as a new focal point for understanding the evolutionary drivers of genetic code plasticity.}, } @article {pmid42575094, year = {2026}, author = {Zhai, J and Li, Y and Liu, J and Su, X and Cui, R and Zheng, D and Sun, Y and Yu, J and Dai, C}, title = {Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102974}, doi = {10.1016/j.xcrm.2026.102974}, pmid = {42575094}, issn = {2666-3791}, abstract = {The global rise of inflammatory bowel disease (IBD) reflects environmental shifts, yet how these changes are embedded in the gut microbial ecology remains unclear. We construct a microbiome atlas comprising 245,627 profiles. By classifying countries into three epidemiologic stages, we establish a framework. As the IBD burden increases, the gut microbial alpha diversity declines, and community structures form distinct clusters. This transition is characterized by a gradient of core genera. Integrating six shotgun metagenomic cohorts, we identify the depletion of anabolic pathways in IBD patients. Strain-level analysis reveals that epidemiologic staging shapes genetic architecture within species, identifying an IBD-enriched subclade of Eisenbergiella associated with elevated fecal cholic acid. We develop a microbial inflammatory risk score (MIRS), based on 19 genera, that discriminates IBD from controls (area under the curve [AUC] = 0.92). MIRS correlates with IBD prevalence. Our study provides an atlas linking epidemiology to microbiome ecology and strain evolution, offering a foundation for population-level surveillance and interventions in IBD.}, } @article {pmid42575174, year = {2026}, author = {Zhang, J and Zhang, B and Lu, X and Li, S and Wang, X and Kong, F and Diao, M and Shi, J}, title = {Heavy-metal stress shapes habitat-specific microbial survival strategies in estuarine environments.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125434}, doi = {10.1016/j.envres.2026.125434}, pmid = {42575174}, issn = {1096-0953}, abstract = {Estuarine ecosystems face increasing heavy metal pollution from rapid urbanization and industrialization, yet the microbial adaptive strategies to multiple metal stressors across different habitats remain poorly understood. This study investigated the diversity and composition of bacterial and fungal communities across free-living (FL), particle-attached (PA), and sediment (SE) fractions from three estuaries with varying heavy metal contamination, and further investigated functional adaptations of bacterial communities. High-throughput amplicon sequencing revealed habitat-specific communities, with SE hosting the highest alpha diversity and enrichment of metal-resistant genera such as Woeseia and Sva1033. Environmental filtering, particularly by Zn, was the dominant driver shaping bacterial assemblages across all habitats, whereas fungal communities displayed greater stochastic assembly patterns. Analysis of 44 high-quality bacterial metagenome-assembled genomes (MAGs) revealed diverse metal resistance genes (cusA, znuB, and zntA), along with enriched metabolic pathways for carbon, nitrogen, and sulfur cycling. Notably, both active efflux/oxidative stress defense and indirect immobilization mechanisms were observed across all habitats, but their relative importance differed: FL and PA communities exhibited a greater reliance on active metal efflux (czcAB) and oxidative stress defense (trxAB) to maintain intracellular homeostasis, whereas SE communities displayed a stronger genomic potential for sulfate reduction (dsrAB) that may contribute to metal immobilization through sulfide precipitation. This metabolic partitioning highlights the complementary roles of different habitats in mediating metal toxicity and biogeochemical cycling, providing new insights into microbial resilience in polluted estuaries and underscoring the urgency of addressing heavy-metal contamination in these critical ecosystems.}, } @article {pmid42570316, year = {2026}, author = {Tilves, C and Holingue, C and Wanigatunga, SK and Chia, CW and Zhao, N and Wu, MN and Schrack, JA and Simonsick, EM and Ferrucci, L and Tanaka, T and Spira, AP and Mueller, NT}, title = {Associations of self-reported and actigraphic sleep with gut microbiome composition and diversity among older adults.}, journal = {Sleep}, volume = {}, number = {}, pages = {}, doi = {10.1093/sleep/zsag217}, pmid = {42570316}, issn = {1550-9109}, abstract = {STUDY OBJECTIVES: Poor sleep is linked to adverse health outcomes. Animal studies suggest the gut microbiome may influence sleep, but human findings remain inconsistent. We examined associations of self-reported insomnia symptoms, daytime sleepiness, and actigraphy-measured sleep with gut microbiome diversity and composition in older adults.

METHODS: We studied 869 Baltimore Longitudinal Study of Aging participants with self-reported sleep and shotgun metagenomic sequencing; 332 also had actigraphy. We tested associations of sleep with alpha diversity, beta diversity, and species composition using regression, PERMANOVA, and ANCOM-BC2, adjusting for age, sex, BMI, physical activity, education, and depressive symptoms.

RESULTS: Participants had mean age 70.7 years; 54.8% were female and 66.9% White. Trouble falling asleep ≥5 times/week was associated with higher Shannon diversity (β=0.41 SD; 95% CI: 0.09, 0.73) and Pielou's evenness, but not richness metrics. No actigraphy-measured sleep variables were associated with alpha or beta diversity. Beta diversity analyses suggested excessive sleepiness (1-2 o 3-4 times/week) was associated with different microbial composition, though variance explained was small. In species-level analyses, frequent insomnia symptoms or excessive sleepiness were associated with depleted or undetected Eubacterium sp. CAG:251. In exploratory actigraphy models, each doubling of sleep efficiency was associated with higher Eubacterium sp. CAG:251 prevalence (PR=2.15; 95% CI: 1.47, 3.14), while each 30-minute increase in wake after sleep onset was associated with lower prevalence (PR=0.49; 95% CI: 0.29, 0.81).

CONCLUSIONS: Global diversity findings were limited and inconsistent, whereas subjective and objective sleep disturbances converged on Eubacterium sp. CAG:251. Findings are exploratory and require longitudinal replication.}, } @article {pmid42570388, year = {2026}, author = {Malik, K and Iqbal, A and Du, M and Chen, T and Li, C}, title = {Impact of Epichloë endophyte on rhizosphere resistome dynamics in wild barley and bluegrass.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143115}, doi = {10.1016/j.jhazmat.2026.143115}, pmid = {42570388}, issn = {1873-3336}, abstract = {Fungal endophytes are universally present in plant tissues to enhance stress resilience and growth of plants. They can change the microbial communities and functional characteristics of the rhizosphere without harming the host. However, the effect of their colonization on the distribution of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in rhizosphere soil remains largely unexplored. In the present study, the impact of the Epichloë bromicola fungal endophyte on the rhizosphere resistome structure and environmental factors in wild barley (Hordeum brevisubulatum) and bluegrass (Poa pratensis) plants was investigated. The rhizosphere ARGs and MGEs communities were characterized through metagenome analysis. Simultaneously, their relationship with key rhizosphere environmental variables was evaluated using redundancy analysis (RDA) and Mantel tests. The results revealed that infection altered the taxonomic distribution of ARGs and MGEs-carrying bacteria. Besides, it reduced the prevalence of the predominant genera Sphingomonas and Nocardioides, while increasing the contribution of the less prevalent genera Bradyrhizobium and Rubrivivax to multidrug efflux and macrolide resistance mechanisms. Co-occurrence network analysis showed decreased modularity, indicating a less compartmentalized resistome-mobilome under infection. The findings revealed that endophyte infection fundamentally restructured the rhizosphere resistome by changing environmental pressures and favoring stress-response mechanisms. The study provides novel insights into how fungal endophytes influence microbial resistome assembly and HGT processes, their role in environmental antibiotic resistance dissemination, and One Health resistome dynamics in the rhizosphere.}, } @article {pmid42570600, year = {2026}, author = {Gao, Q and Lu, J and Hou, J and Ding, W and Xu, D and Zhou, C and You, G}, title = {Multi-omics reveals niche partitioning of nitrogen and phosphorus cycling between free-living and particle-attached fractions across an N:P gradient in eutrophic Lake Taihu.}, journal = {Water research}, volume = {306}, number = {}, pages = {126615}, doi = {10.1016/j.watres.2026.126615}, pmid = {42570600}, issn = {1879-2448}, abstract = {Cyanobacterial blooms in hyper-eutrophic lakes are managed through nitrogen-to-phosphorus (N:P) control, yet single-axis nutrient reduction has often been insufficient to achieve sustained bloom suppression in shallow systems such as Lake Taihu, China. We hypothesised that the missing management dimension is spatial: free-living (FL, 0.22-3 µm) and particle-attached (PA, >3 µm) fractions may deploy distinct nutrient-acquisition machineries under the same bulk N:P. Native Lake Taihu assemblages were cultured at four N:P molar ratios (5, 16, 23, 40; TN fixed at 2.0 mg N L[-1]; TP adjusted to 0.886, 0.277, 0.192, and 0.111 mg P L[-1], respectively) for 28 days, then sequentially filtered and analysed by 16S amplicon sequencing, shotgun metagenomics and 15-T Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) of dissolved organic matter (24 paired-fraction biomass samples + 8 DOM samples). Three key findings emerged. First, FL and PA carry the genetic potential for chemically distinct phosphorus-acquisition strategies (hereafter termed the P-currency split): FL is enriched in the high-affinity inorganic-Pi transporter genes pstSCAB (dominated by Synechococcus), whereas PA carries the genetic potential to mobilise organic P via phoD and ugpQ (dominated by Bacteroidota); the PstS + Ppk1 dual-wheel hypothesis was not supported under fraction-resolved testing. Second, PA harbours the genetic potential for a consistent nitrogen-cycle hotspot across all N:P levels, with nifH enriched 1.8-5.0-fold in PA and 87% attributable to the heterotroph Porphyrobacter. Third, Synechococcus shows an apparent stoichiometric niche-shift from FL dominance at N:P = 23 (43.8%) to PA dominance at N:P = 40 (54.1%). Together, the joint N:P × fraction model explained 95.8% of community variance (Mantel r = 0.963 within PA). These findings identify the phoD-anchored Bacteroidota guild and PA-aggregate disruption as candidate fraction-resolved management levers that complement conventional nutrient reduction in shallow eutrophic lakes.}, } @article {pmid42570687, year = {2026}, author = {Xu, X and Fan, K and Ling, N and Li, J and Yang, T and Gao, GF and Ma, Y and Nie, L and Zhang, J and Chu, H}, title = {Soil pH regulates organic carbon pool by changing microbial life-history strategy.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.08.028}, pmid = {42570687}, issn = {2090-1224}, abstract = {INTRODUCTION: The stability of the vast soil carbon pool, crucial for climate regulation, depends on microbial processes that govern carbon loss as CO2 or its stabilization in soil. Microbial life-history strategies, representing tradeoffs between resource acquisition (A-strategy) and growth yield (Y-strategy), are central to soil organic carbon (SOC) dynamics. However, how abiotic factors modulate these strategies and, in turn SOC fate remains unclear.

OBJECTIVES: Using the black soil region of Northeast China, which harbors substantial yet vulnerable SOC reserves, this study aimed to identify the dominant abiotic driver shaping microbial life-history strategies and to elucidate how this driver influences SOC stabilization pathways.

METHODS: We conducted a field survey combining metagenomic profiling of microbial attributes (diversity, functional potential, and inferred life-history strategy) with measurements of soil properties including extracellular enzyme activities and SOC fractions. This integrative approach traced the pathway from abiotic drivers to microbial traits and ultimately to carbon allocation.

RESULTS: Soil pH emerged as the key environmental gradient, with a threshold at pH 6.43 marking a systemic shift in microbial ecology and carbon processing. Acidic soils (pH 4.60-6.43) favored A-strategists, characterized by large genomes, enriched carbohydrate-active enzymes, and high extracellular enzyme activity, enabling polymer degradation and humification but limiting mineral-associated organic carbon (MAOC) formation. In contrast, neutral soils (pH 6.43-8.87) supported Y-strategists with streamlined genomes and biosynthetic metabolism, promoting microbial necromass accumulation and MAOC stabilization. Distinct functional guilds underpinned the A- and Y-strategies and frequent horizontal gene transfer in acidic soils further reinforced the A-strategy dominance under low pH.

CONCLUSION: Our findings reveal a mechanistic link between microbial life-history strategies and SOC stabilization, demonstrating that pH may shape the balance between A- and Y-strategists and their contrasting carbon pathways. This insight enhances predictive models of SOC dynamics and highlights pH management as a key lever for agroecosystems carbon retention.}, } @article {pmid42570745, year = {2026}, author = {Xia, H and Xie, J and Wang, XY and Wang, Y}, title = {Detection, occurrence, development, diagnosis and treatment of vaginal microbiome in gynecological cancers.}, journal = {Critical reviews in oncology/hematology}, volume = {}, number = {}, pages = {105531}, doi = {10.1016/j.critrevonc.2026.105531}, pmid = {42570745}, issn = {1879-0461}, abstract = {Gynecological cancers, including cervical, endometrial, and ovarian cancers, represent a growing global health burden with increasing incidence and mortality. The vaginal microbiome has emerged as a promising target for early cancer diagnosis and therapeutic intervention. Therefore, this review summarizes the composition and dynamics of the vaginal microbiome, emphasizing its association with the pathogenesis of gynecological cancers through chronic inflammation, immune modulation, and hormonal interactions. Advances in technologies such as 16S rRNA sequencing, metagenomics, and multi-omics have enabled the identification of potential microbial biomarkers. Probiotics, antibiotics, and vaginal microbiota transplantation are treatment technologies of gynecological cancers demonstrating considerable potential in restoring microbial balance and improving clinical outcomes. Furthermore, significant challenges persist in standardizing microbial biomarkers and translating research findings into precision therapies. Future studies should prioritize large-scale clinical validation and develop integrative strategies to harness the potential of the vaginal microbiome for cancer prevention and personalized treatment.}, } @article {pmid42570953, year = {2026}, author = {Ladyhina, V and Sternberg-Lewerin, S and Sannö, A and Bongcam-Rudloff, E and Dicksved, J and Rajala, E}, title = {Longitudinal investigation of the resistomes in Swedish pig farms.}, journal = {npj antimicrobials and resistance}, volume = {4}, number = {1}, pages = {}, pmid = {42570953}, issn = {2731-8745}, abstract = {We conducted a longitudinal profiling of environmental resistomes and microbiomes from ten Swedish pig farms in a low-antimicrobial usage context. Samples were collected from pig pen environments and analysed using shotgun metagenomic sequencing. Resistome and microbiome profiles showed stronger temporal than farm-specific variation, with several age-associated trends. Age-related trajectories diverged between microbiome and resistome, indicating that resistance dynamics are shaped by factors beyond microbial succession. The highest relative abundance of resistance determinants was observed for tetracyclines, followed by aminoglycosides, macrolide-lincosamide-streptogramin antibiotics, beta-lactams, and folic acid synthesis inhibitors-drug classes commonly used in Swedish pig production. Resistome patterns were partially associated with phenotypic resistance profiles from previous studies, while analysis of antimicrobial usage alone could not fully explain the observed resistome. Overall, these findings suggest that additional factors beyond antimicrobial usage contribute to the persistence and dissemination of antibiotic resistance genes in pig farm environments.}, } @article {pmid42571392, year = {2026}, author = {Sirimongkol, D and Wongluechai, P and Chamsai, T and Weluwanarak, T and Chaipromkhieo, N and Sangkachai, N and Tonchiangsai, K and Pabutta, C and Kerdsiri, P and Sariya, L}, title = {Metagenomic analysis of commensal small mammal samples from an international cargo shipping area, Bangkok Port, reveals potential zoonotic pathogens and implications for One Health surveillance.}, journal = {One health (Amsterdam, Netherlands)}, volume = {23}, number = {}, pages = {101534}, pmid = {42571392}, issn = {2352-7714}, abstract = {Commensal small mammals, such as rats and shrews, are recognized reservoirs for numerous zoonotic pathogens; however, their role in pathogen circulation at transport hubs remains underexplored. This study employs shotgun metagenomic sequencing to characterize microbial communities and assess zoonotic potential in tissue samples from commensal small mammals captured at Bangkok Port, an international cargo shipping hub in Thailand between June and August 2025. Following host read depletion, taxonomic profiling was performed to identify bacterial taxa of public health relevance, including sequences assigned to Bordetella spp., Yersinia pestis, Bartonella elizabethae, and Acinetobacter baumannii. The virulence factor and antibiotic resistance gene profiles revealed that some of these pathogens have pathogenic potential and are related to drug-resistant bacteria. In addition, Y. pestis was identified as a shared taxon among rats, shrews, and their associated fleas. The findings support the ecological roles of mammalian hosts and their ectoparasites as reservoirs for pathogens of public health concern. These results emphasize the need to strengthen surveillance programs for commensal small mammals to monitor and mitigate the spread of transboundary pathogens at international maritime gateways.}, } @article {pmid42566961, year = {2026}, author = {Seeholzer, A and Pfaff, F and Wunderlich, A and Meier, D and Zyla, A and Lueders, T and Einsiedl, F}, title = {In situ treatment of nitrate polluted groundwater by methane-dependent denitrification: meso‑scale flume proof-of-concept.}, journal = {Water research}, volume = {306}, number = {}, pages = {126593}, doi = {10.1016/j.watres.2026.126593}, pmid = {42566961}, issn = {1879-2448}, abstract = {Nitrate concentrations in groundwater frequently exceed the EU drinking water limit of 50 mgL[-1], threatening drinking water quality. This study evaluates a novel in situ nitrate removal strategy based on methane injection to stimulate autochthonous denitrifiers. Methane was injected into a meso‑scale artificial aquifer equipped with horizontal injection wells and a comprehensive monitoring system. We hypothesized that methane injection promotes methanotrophic denitrification and enhances microbial nitrate removal in groundwater. Following methane injection over four months, nitrate concentrations declined from ∼55 mg L[-1] (0.89 mM) to 36 mg L[-1] (0.58 mM). Concurrent isotopic shifts of up to 11‰ in both δ[15]N of dissolved nitrate and δ[13]C of dissolved methane provided strong evidence for enhanced microbial nitrate reduction coupled to methane oxidation. Spatio-temporal analyses of sediment microbiomes revealed successive enrichment of canonical aerobic methano- and methylotrophs (Methylomonandaceae and Methylophilaceae). While only the first hosted metagenomic methane oxidation capacities, the second was associated with complete denitrification. Likely, they thus interacted synergistically under oxygen-limited conditions, suggesting an indirect coupling between oxygen limited methane oxidation and denitrification. Only towards the distal, anoxic end of the flume, true anaerobic methanotrophs affiliated with the Methylomirabilaceae also were enriched. Spatial analyses indicated that sediment heterogeneity influenced methane distribution and, therefore, microbial nitrate removal in the flume. Overall, methane injection effectively stimulated microbial nitrate degradation, providing meso‑scale proof of concept for future pilot-scale remediation of nitrate-contaminated groundwater.}, } @article {pmid42567235, year = {2026}, author = {Ma, HC and Wang, DJ and Yuan, ZJ and Shi, B and Chen, ZH and Zhuo, M and Zeng, JY and Aqib, AI}, title = {Systematic approach for revealing biomarkers of diarrheal microbiome of yaks through Metagenomics sequencings.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108700}, doi = {10.1016/j.micpath.2026.108700}, pmid = {42567235}, issn = {1096-1208}, abstract = {Yaks are important food ruminants on the Plateau, but the presence of a diarrhea disease is seriously threatening the yak sector. To detect bacterial biomarkers of diarrhea in this animal, metagenomics sequencing of fecal samples from diarrhea (group D) and normal (group H) yaks was performed. The results showed 61963 936 432 and 63 972 070 354 clean samples in the diarrheal and normal yaks, respectively. Genotyping in group D (20 000) was statistically lower than that in group H (80 000) (p<0.05). Firmicutes and bacteroides levels in diarrheal yaks (1.03) were lower than in normal animals. There were 23 phyla and 696 species significantly different between the two yak groups including species of pathogenic Bacteroides fragilis, Alloprevotella tannerae, Parabacteroides merdae, Anaerococcus marasmi, and beneficial Methanobrevibacter millerae, Elusimicrobium minutum, Adlercreutzia equolifaciens. Our results may contribute to the prevention and treatment of diarrheal in yaks in the cold plains areas.}, } @article {pmid42567289, year = {2026}, author = {Ma, J and Xia, Q and Xiong, J and Zhou, J and Zhang, Q}, title = {Impact mechanism of cigarette butt leachate in runoff on the nutrient removal capacity of bioretention cells: metagenomic insights.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135553}, doi = {10.1016/j.biortech.2026.135553}, pmid = {42567289}, issn = {1873-2976}, abstract = {Discarded cigarette butts become soaked in surface runoff during rainfall, causing various pollutants within them to leach. The extent to which discarded cigarette butts impair bioretention cell nutrient removal efficiency remains understudied. In this study, three bioretention cells were constructed, exposed to simulated runoff containing non-cigarette-tip, low-concentration cigarette-tip, and high-concentration cigarette butt leachate. The effectiveness of nitrogen, phosphorus, and carbon purification was then determined; metagenomic sequencing was also performed to examine the microorganisms within the filler to propose a mechanism of how cigarette butt leachate input influences bioretention cell nutrient purification. The input of cigarette butt leachate limited filler adsorption capacity, but had little effect on the effluent NH4[+]-N concentration (1.08-1.14 mg/L). Cigarette butt leachate inhibited the nitrification potential in the upper layer of the cells as well as the denitrification potential in the lower layer; effluent NO3[-]-N increased from 0.51 to 1.93 to 0.57-5.47 mg/L. The inflow of cigarette butt leachate had little effect on phosphorus removal, with efficiencies consistently ranging from 50.60% to 73.69%. Cigarette butt leachate enhanced the carbon release potential of slow-release carbon sources within the filler and impeded potential electron donor production. This study demonstrated that cigarette butt disposal significantly impaired the nitrogen removal capacity of bioretention cells.}, } @article {pmid42567290, year = {2026}, author = {Wang, K and Wang, D and Li, D and Yu, P and Li, Y and Zeng, H and Ding, F and Zhang, J}, title = {Hydrodynamic control of oxygen intrusion and shear stabilizes functional zonation for nitrogen removal in an integrated UASB.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135585}, doi = {10.1016/j.biortech.2026.135585}, pmid = {42567290}, issn = {1873-2976}, abstract = {Aeration-reflux coupling can establish functional zonation in integrated upflow anaerobic sludge blanket (UASB) reactors, but the hydrodynamic basis remains insufficiently quantified. This study integrated computational fluid dynamics (CFD) with metagenome-derived KO-genus profiling based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) from vertically resolved samples to link hydrodynamic characteristics with microbial functions. CFD analysis showed that aeration established an oxygen-exposed zone in the upper reactor, whereas internal reflux regulated downward bubble entrainment and generated shear hotspots. These hydrodynamic features shaped mixing patterns, maintained stable functional zoning, and preserved a micro-oxic niche for simultaneous anammox and denitrification (SAD) granules. Metagenomic and gene-network analyses revealed distinct vertical stratification of ammonia-oxidizing bacteria (AOB) and anaerobic ammonium-oxidizing bacteria (AnAOB) along the reactor height. They also identified a coupled NO2[-] supply-sink loop involving Nitrosomonas, Ca. Kuenenia, and denitrifying bacterium, supporting functional partitioning within the UASB. Operationally, a reflux ratio of 15 achieved the highest and most stable total nitrogen removal efficiency 90% within the optimal aeration, corresponding to a dissolved oxygen concentration of approximately 2 mg/L. In addition to nitrogen-transformation pathways, the vertically resolved metagenomes revealed cofactor-related functional potential, including molybdenum-cofactor and folate-associated metabolism, within the spatially structured microbial community. Together, these results demonstrate that aeration-reflux design can mechanistically sustain functional partitioning, granulation, and efficient nitrogen removal in integrated UASB systems by jointly regulating the oxygen and shear threshold. This strategy provides practical guidance for treating low-carbon, ammonia-rich side streams.}, } @article {pmid42567813, year = {2026}, author = {Gosai, HB and Panseriya, HZ and Patel, PG and Patel, AC and Shankar, A and Varjani, S and Dave, BP}, title = {Retraction notice to "Exploring bacterial communities through metagenomics during bioremediation of polycyclic aromatic hydrocarbons from contaminated sediments" [Sci. Total Environ. 842 (2022) 156794].}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {182131}, doi = {10.1016/j.scitotenv.2026.182131}, pmid = {42567813}, issn = {1879-1026}, } @article {pmid42568080, year = {2026}, author = {Ma, S and Zhang, C and Yao, Y and Zhou, M and Chen, A and Chen, Y and Chen, Y and Wang, J and Abudushalamu, G and Cai, S and Zhao, F and Chen, D and Li, X and Zheng, Y and Fan, J and Gao, X and Liu, Y and Fan, W and Zhu, F and Yang, J and Miao, M and Fan, X and Wu, G}, title = {A three-metabolite microbiota-associated signature for early risk stratification of gestational diabetes mellitus.}, journal = {Cardiovascular diabetology}, volume = {25}, number = {1}, pages = {}, pmid = {42568080}, issn = {1475-2840}, support = {82302609//National Natural Science Foundation of China/ ; 82373781//National Natural Science Foundation of China/ ; BK20230840//Natural Science Foundation of Jiangsu Province/ ; JSKLCCM202202015//Jiangsu Provincial Key Laboratory of Critical Care Medicine/ ; }, mesh = {Humans ; Female ; *Diabetes, Gestational/diagnosis/microbiology/blood ; Pregnancy ; *Metabolomics ; Risk Assessment ; Prospective Studies ; Risk Factors ; Biomarkers/blood ; Case-Control Studies ; *Gastrointestinal Microbiome ; Adult ; Metagenomics ; Predictive Value of Tests ; Gestational Age ; *Propionates/blood ; Prognosis ; *Bacteria/metabolism/classification ; Multiomics ; }, abstract = {BACKGROUND: Gestational diabetes mellitus (GDM) is associated with adverse pregnancy outcomes and long-term metabolic and cardiovascular risk. However, oral glucose tolerance testing at 24-28 gestational weeks limits early risk stratification. Gut microbiota-associated metabolites may reflect early metabolic abnormalities, including those relevant to cardiometabolic health, but robust early-pregnancy biomarkers remain limited.

METHODS: We conducted a multicenter nested case-control and prospective study involving 2,693 pregnant women. Untargeted metabolomics and metagenomics were integrated to identify GDM-associated metabolites and gut microbial alterations. Three consistently dysregulated metabolites, 3-hydroxydecanoic acid, γ-Glu-Leu, and propionic acid, were quantified by targeted LC-MS/MS. Candidate algorithms were compared using repeated 10-fold cross-validation, and a final generalized linear model was externally and prospectively validated.

RESULTS: Women who later developed GDM showed an adverse early-pregnancy metabolic profile, including higher BMI, triglycerides, and platelet count. Untargeted metabolomics identified 14 persistently altered metabolites enriched in energy, oxidative stress, and amino acid metabolism pathways. Metagenomics revealed taxonomic restructuring and coordinated microbiota-metabolite associations. The three-metabolite model achieved AUCs of 0.838 (95% CI, 0.791-0.885) in training, 0.840 (95% CI, 0.769-0.911) in internal validation, 0.955 (95% CI, 0.925-0.985) and 0.917 (95% CI, 0.875-0.958) in two external cohorts, and 0.969 (95% CI, 0.937-1.000) in the prospective cohort.

CONCLUSION: Early microbiota-associated metabolic dysregulation is detectable before routine GDM diagnosis. This compact three-metabolite panel may support early GDM risk stratification and provides metabolic evidence relevant to broader cardiometabolic risk assessment in pregnancy.}, } @article {pmid42568342, year = {2026}, author = {Tedersoo, L and Prous, M and Chen, M and Anslan, S and Saar, I and Dubois, B and Mikryukov, V}, title = {Benchmarking Full-Length ITS Metabarcoding Across Illumina 2 × 500, PacBio, and Oxford Nanopore Sequencing Using Mock and Soil Communities.}, journal = {Molecular ecology resources}, volume = {26}, number = {6}, pages = {e70189}, doi = {10.1111/1755-0998.70189}, pmid = {42568342}, issn = {1755-0998}, support = {101200758//HORIZON EUROPE European Research Council/ ; TK200//Estonian Ministry of Education and Research/ ; 362828//Research Council of Finland/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods/standards ; *Soil Microbiology ; *Metagenomics/methods ; Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; DNA, Ribosomal Spacer/genetics/chemistry ; Benchmarking ; Biodiversity ; }, abstract = {Metabarcoding is a powerful tool for biodiversity comparisons, where standard-size DNA barcodes (> 500 bases) offer better taxonomic resolution than shorter ones. Still, the choice of sequencing platforms and bioinformatics pipelines may strongly affect inferred diversity due to various technical biases. We assessed the relative performance of Illumina MiSeq i100 (2 × 500 paired-end), PacBio Revio and Oxford Nanopore MinION sequencing and bioinformatics pipelines, using full-length ITS amplicon sequencing datasets from a 103-species mock community and 45 composite soil samples. Despite numerous low-quality reads, PacBio yielded the lowest overall error rate and highest number of taxa. Illumina revealed the highest proportion of chimeric and index-switched reads, along with a strong bias towards shorter amplicons. MinION data analysed using PRONAME and Minovar-a bioinformatics pipeline presented here-had the largest proportion of low-quality data, and rare taxa were lost during data filtering and read polishing steps. Although Minovar enabled amplicon sequence variant (ASV) level precision for common taxa, we recommend clustering ASVs into OTUs. For PacBio, standard filtering approaches outperformed the ASV approach because they retained rare taxa. For Illumina, a stringent ASV approach or removal of rare OTUs would limit artefacts. Across all platforms, excess PCR cycles promoted chimeric and low-quality reads and lost quantitativity in biodiversity assessments. With moderate differences in effect sizes, all analytical approaches supported the conclusion that sampling design determines how we see soil biodiversity responses to land use. For biodiversity surveys based on the full-length ITS metabarcoding, we recommend using PacBio sequencing with standard, non-ASV pipelines.}, } @article {pmid42568732, year = {2026}, author = {Saikia, D and Basumatary, P and Nath, A and Kalita, JJ and Neog, K and Purkait, MK and Bora, U}, title = {Metagenomic and Metatranscriptomic Insights into the Structure and Function of the Gut Microbial Community of Antheraea assamensis Helfer.}, journal = {Indian journal of microbiology}, volume = {66}, number = {4}, pages = {982-1001}, pmid = {42568732}, issn = {0046-8991}, abstract = {UNLABELLED: Antheraea assamensis Helfer is an economically important, endemic, lepidopteran insect native to Northeast India that produces a lustrous golden-coloured silk of distinct quality and durability. To date, the gut microbiota of A. assamensis has remained largely unexplored. The present work aimed to comprehensively identify and characterize the gut microbial community of A. assamensis through culture-independent approach. The gene expression analysis of the gut microbial community was studied through metatranscriptomic analysis. The influence of the host leaf-associated microbiota on larval gut microbial composition and its variation to changes in host plant was also investigated. The results have identified over 30 bacterial and archaeal phyla indicating a highly diverse gut microbial community of A. assamensis dominated by Proteobacteria (25.78%), Patescibacteria (12.77%), Planctomycetota (12.66%), Chloroflexi (8.63%), Acidobacteria (6.85%) and Actinobacteria (3.39%). Functional analysis of A. assamensis gut microbiota through shotgun metagenomic and metatranscriptomic investigation revealed key associations between the insect and its gut microbial community including host leaf digestion, metabolite detoxification, chitinase production and fat body metabolism. The host leaf-associated microbiota was found to occupy a major portion of the total larval gut microbiota. However, the diversity of the larval gut microbiota was greater than the host leaf-associated microbiota. The findings of this study will illustrate the structure of the gut microbial community of A. assamensis, their key interactions with the host organism and the role of host leaf-associated microbiota on the holobiont.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01525-5.}, } @article {pmid42568769, year = {2026}, author = {Liu, L and Liu, J and He, J and Xing, Y and Zhang, D and Zhang, X and Ma, C and Xu, M and Li, R and Peng, M and Mei, S}, title = {Correction: Multi-kingdom gut microbiota analysis identifies bacterial-viral association in multiple myeloma.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1927101}, doi = {10.3389/fmicb.2026.1927101}, pmid = {42568769}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1798330.].}, } @article {pmid42568840, year = {2026}, author = {Liang, W and Tingting, L and Ying, L and Sa, W and Yuanyuan, Z and Hongxin, Z}, title = {Comprehensive Pathogen Spectrum Analysis Using mNGS in AIDS Patients With Pulmonary Infections: Diagnostic Value and Clinical Implications.}, journal = {Open forum infectious diseases}, volume = {13}, number = {8}, pages = {ofag395}, pmid = {42568840}, issn = {2328-8957}, abstract = {BACKGROUND: This study evaluated the diagnostic value of metagenomic next-generation sequencing (mNGS) in identifying pathogens causing pulmonary infections in 64 acquired immunodeficiency syndrome (AIDS) patients at Beijing Ditan Hospital.

METHODS: Bronchoalveolar lavage fluid (BALF) samples were analyzed using mNGS and conventional microbiological tests (CMT). Diagnostic performance was compared, and random forest analysis was used to assess pathogenicity.

RESULTS: mNGS detected 45 pathogens, including 14 viruses, 3 fungi, and 28 bacteria. Compared with CMT, mNGS showed higher sensitivity for detecting bacteria (75.0% vs 29.17%), fungi (45.0% vs 16.67%), and viruses (80.0% vs 20.83%). Mixed infections were identified in 55.2% of cases, predominantly Pneumocystis pneumonia (PCP) with bacterial coinfections. However, mNGS had lower concordance with CMT for viruses (24.1% for cytomegalovirus) and Mycobacterium tuberculosis (75.0%). Random forest analysis highlighted Candida albicans and Stenotrophomonas maltophilia as highly pathogenic.

CONCLUSIONS: While mNGS demonstrated superior broad-spectrum detection, its limitations in viral and TB diagnosis underscore the need for optimized protocols. The study supports mNGS as a complementary tool for diagnosing complex pulmonary infections in AIDS patients, enhancing precision medicine but requiring further refinement for widespread clinical adoption.}, } @article {pmid42568886, year = {2026}, author = {Muigano, MN}, title = {Functional genetic signatures of the gut microbiome in cardiometabolic diseases: mechanisms and translational opportunities.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1847345}, pmid = {42568886}, issn = {2813-4338}, abstract = {The human gut microbiome plays a very important role in the regulation of host metabolism and overall physiological homeostasis. Disruptions in microbial community function have been increasingly implicated in cardiometabolic diseases, including obesity, type 2 diabetes, cardiovascular disease, and metabolic dysfunction-associated liver disease. Advances in metagenomic sequencing have identified functional genetic signatures within the gut microbiome for short-chain fatty acid biosynthesis, bile acid metabolism, lipopolysaccharide (LPS) production, amino acid metabolism, trimethylamine N-oxide (TMAO) generation, and carbohydrate-active enzymes (CAZymes). Across cardiometabolic conditions, a consistent pattern emerges of depletion of beneficial metabolic functions and enrichment of pro-inflammatory and metabolically disruptive pathways. These findings point to the importance of microbial functional capacity, rather than taxonomic composition alone, in shaping disease risk and progression. This review explores the functional genetic signatures for cardiometabolic diseases and translational potential of these signatures including their potential roles as diagnostic biomarkers, therapeutic targets, and tools for precision therapy. This understanding of microbiome-derived functional pathways may inform the development of targeted strategies aimed at restoring metabolic balance and improving cardiometabolic health.}, } @article {pmid42569238, year = {2026}, author = {Dolkar, P and Themchuirin, L and Sonia, N and Atri, A and Yadav, P and Siwach, S and Modeel, S and Negi, RK}, title = {Fish gut-water interface as a hotspot for the dissemination of antibiotic resistance genes across natural and aquaculture systems.}, journal = {Current research in microbial sciences}, volume = {11}, number = {}, pages = {100646}, doi = {10.1016/j.crmicr.2026.100646}, pmid = {42569238}, issn = {2666-5174}, abstract = {Freshwater ecosystems are important reservoirs and transmission pathways for antibiotic resistance genes (ARGs), yet host-mediated microbial selection and anthropogenic pressure on fish gut resistome remain poorly characterised, especially in major South Asian river systems. We performed shotgun metagenomics and genome-resolved binning from 194 fish representing four species, along with host-associated water samples, collected from six geographically distinct sites spanning two major river systems (the Yamuna and the Indus) and two aquaculture farms. The fish gut nurtures distinct microbial communities from the surrounding water, revealing strong host-mediated filtering of environmental microbiota. Across all samples, 1108 ARG subtypes conferring resistance to 14 antibiotic classes were detected, including extended-spectrum β-lactamases (blaTEM and blaCTX-M) and WHO critical-priority carbapenemases (blaIMP and blaOXA). Fish from the Indus River maintained diverse but comparatively stable resistomes dominated by intrinsic chromosomal efflux mechanisms, whereas fish from the urbanized Yamuna River, particularly Labeo boggut, exhibited noticeable enrichment of clinically important ARGs. The prevalence of mobile genetic elements (MGEs) and virulence factors (VFs) were consistently more abundant in the fish gut microbiome than in the host's surrounding water, indicating an increased potential for horizontal gene transfer and microbial persistence. A total of 19 metagenome-assembled genomes (MAGs) carrying multiple ARGs, VFs, and plasmid-associated markers were detected, identifying bacterial populations capable of maintaining and disseminating antimicrobial resistance. These outcomes confirm that fish inhabiting anthropogenically influenced river systems can serve as important reservoirs of clinically relevant resistance determinants, highlighting potential risks for environmental dissemination, aquaculture and human exposure through aquatic ecosystems.}, } @article {pmid42569267, year = {2026}, author = {Shi, Q and Song, Q and Liu, X and Mei, G and Gao, C and Du, H and Xia, Z and Liu, M and Song, J and Zhang, L and Zhu, R and Cheng, Z and Cao, J and Rao, D and Zhang, Y and Wang, Z and Han, J}, title = {Macrogenomic analysis showcases the diversity of tick RNA viruses in Mentougou, Beijing, China.}, journal = {New microbes and new infections}, volume = {73}, number = {}, pages = {101819}, doi = {10.1016/j.nmni.2026.101819}, pmid = {42569267}, issn = {2052-2975}, abstract = {BACKGROUND: Ticks are the second most significant vector of human pathogens worldwide, with 911 documented species globally and a broad distributed across China. Currently, over 160 tick-borne viruses (TBVs) have been identified, several of which pose substantial threats to human health, such as Dabie bandavirus, Jingmen tick virus, Alongshan virus, Songling virus, Beiji nairovirus, and Langya henipavirus, raising increasing global attention. Despite their significance, the diversity of TBVs in Beijing remains poorly characterized.

METHODS: In this study, we conducted metagenomic sequencing on tick samples collected from Mentougou District, Beijing. The obtained reads were subjected to quality control, de novo assembly, and viral sequence identification, followed by phylogenetic and evolutionary analyses.

RESULTS: Our results identified 19 distinct viral species spanning 12 families, including Hepelivirales, Solemoviridae,Mymonaviridae, Nodaviridae,Permutotetraviridae, Phenuiviridae,Rhabdoviridae, Tombusviridae,Totiviridae, Peribunyaviridae,Flaviviridae, Nodaviridae,Tymoviridae, Tombusviridae. Among these, six novel viruses from five virus families were discovered. A potential pathogen, Tick jingmen-like virus, was also detected in the selected pathogens. These findings underscore the remarkable diversity of RNA viruses harbored by ticks in Mentougou District.

CONCLUSIONS: Our research findings reveal a previously unrecognized diversity of tick-borne viruses in the Mentougou District, Beijing, and provide essential baseline data for informing future surveillance strategies and guiding prevention and control of tick-borne diseases in the Beijing metropolitan area.}, } @article {pmid42569308, year = {2026}, author = {Fan, G and Wang, K and Qi, X and Shi, Y and Li, J and Zhang, Y and Yang, B and Wang, K and Lv, J}, title = {Integrative multi-omics analysis identifies microbial dysbiosis and functional metabolic reprogramming in acute kidney injury.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1781145}, doi = {10.3389/fmed.2026.1781145}, pmid = {42569308}, issn = {2296-858X}, abstract = {BACKGROUND: Acute kidney injury (AKI) is a life-threatening syndrome with high morbidity and mortality, yet its early diagnosis and underlying mechanisms remain poorly defined. Emerging evidence implicates gut dysbiosis and microbial metabolic dysfunction in AKI pathogenesis via the gut-kidney axis, yet a comprehensive, multi-omics characterization of microbial functional alterations in general AKI populations remains lacking.

METHODS: We conducted a prospective multi-omics study including 16 patients with acute kidney injury (AKI) and 16 age- and sex-matched healthy controls (HCs). Plasma metabolomic profiling was performed using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS). Gut microbiome composition and function were characterized through whole-metagenome sequencing of stool samples. Differential taxonomic and metabolite features were identified using multivariate and univariate statistical analyses. Microbial functional potential was assessed across four hierarchical layers: Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthologs (KOs) genes, pathways, gut-metabolite modules (GMMs), and gut-brain modules (GBMs), to achieve high-resolution mapping of metabolic pathways and taxon-specific functional contributions. Integrated microbe-metabolite-phenotype relationships were evaluated using Spearman correlation analysis.

RESULTS: Metabolomic profiling identified 65 differentially abundant metabolites between AKI patients and healthy controls (HCs), including 53 upregulated and 12 downregulated metabolites. These metabolites were mainly enriched in carbohydrate metabolism (e.g., starch and sucrose metabolism, fructose and mannose metabolism) and amino acid metabolism pathways. Among them, Maltol (C11918, AUC = 0.961), D-Quinovose (C02522, AUC = 0.926), and L-fucose (CO1019, AUC = 0.926) demonstrated the most robust diagnostic potential. Further feature selection using a random forest model identified an optimal panel of three metabolites, which achieved good discriminative performance (AUC = 0.859, 95% CI: 0.7073-1). Metagenomic analysis revealed significant gut microbiota dysbiosis in AKI, characterized by reduced α-diversity and distinct β-diversity compared to HCs. Taxonomic profiling showed depletion of key short-chain fatty acid-producing bacteria, including Faecalibacterium prausnitzii, along with enrichment of taxa such as Phocaeicola and Bifidobacterium pseudocatenulatum, as well as Phocaeicola vulgatus at the species level. Functional analysis indicated that AKI was associated with enhanced amino acid and carbohydrate metabolism, increased xenobiotic degradation, and alterations in neuroactive metabolic pathways. Integrated analysis further revealed significant correlations between altered microbial taxa, metabolic pathways, and clinical indicators. Specifically, health-associated taxa were negatively correlated with systemic inflammation markers (IL-6, IL-8) and renal injury markers (SCr, BUN), whereas Bacteroides uniformis showed positive associations with metabolic alterations in AKI.

CONCLUSION: This multi-omics study reveals coordinated gut microbial dysbiosis and systemic metabolic reprogramming in AKI. The depletion of key commensals, rather than pathogen overgrowth, appears central to AKI-associated functional disruption. These findings highlight potential microbial and metabolic biomarkers and offer mechanistic insights into AKI pathogenesis.}, } @article {pmid42569339, year = {2026}, author = {Xue, K and Hu, C and Lin, Z and Mao, X and Zhu, H and Xie, Y and Luo, Q and Zhu, F}, title = {Multi-omics profiling of oral microbial functional signatures and systemic immune-metabolic features in perinatal depression.}, journal = {Brain, behavior, & immunity - health}, volume = {56}, number = {}, pages = {101300}, doi = {10.1016/j.bbih.2026.101300}, pmid = {42569339}, issn = {2666-3546}, abstract = {BACKGROUND: Perinatal depression (PND) occurs during a period marked by profound endocrine, metabolic, and immune adaptation. Although alterations in immune-metabolic regulation have been reported in PND, how such changes manifest across distinct biological compartments remains unclear. The oral mucosal ecosystem represents an immunologically active interface with direct connections to systemic circulation, yet its functional characteristics in PND have been insufficiently explored. In this study, we examined whether PND is characterized by differences in oral microbial functional profiles alongside systemic immune-metabolic features.

METHODS: We performed an integrated multi-omics analysis combining salivary shotgun metagenomics and untargeted serum metabolomics in 31 women with PND and 32 healthy controls. Oral microbial taxonomic composition and inferred functional profiles were analyzed together with circulating metabolites related to endocrine and immune processes. Cross-omics analyses were used to evaluate overall concordance as well as pathway- and feature-level associations between microbial functional signals and host metabolic features.

FINDINGS: The oral microbiome of women with PND showed largely preserved community structure and diversity, while differences were observed at the level of inferred functional pathways, including enrichment of lipopolysaccharide biosynthesis and virulence-associated functional categories. Concurrently, the serum metabolome exhibited differences in steroid-related metabolites, bile acid profiles, and lipid mediator-associated features involved in immune modulation, including putatively annotated resolvin D5. Global concordance between oral microbial functional profiles and systemic metabolomic patterns was limited; however, reproducible associations were observed at the pathway and feature levels, such as an inverse association between the relative abundance of the genus Abiotrophia and the bile acid taurochenodeoxycholate-7-sulfate.

INTERPRETATION: Together, these findings describe concurrent differences in oral microbial functional signatures and systemic immune-metabolic features in women with PND, occurring in the context of minimal changes in microbial community composition. The limited global concordance and selective pathway-level correspondence across omic layers are consistent with asynchronous patterns of biological variation during the perinatal period. These observations support the potential relevance of the oral-systemic axis as a non-invasive perspective for characterizing biological heterogeneity associated with perinatal depression.}, } @article {pmid42569915, year = {2026}, author = {Lin, CP and Geroldi, A and Selem, N and Liti, G and Tsai, IJ}, title = {A Global Synthesis of Yeast in Microbiomes.}, journal = {Yeast (Chichester, England)}, volume = {}, number = {}, pages = {}, doi = {10.1002/yea.70039}, pmid = {42569915}, issn = {1097-0061}, support = {Impulscience 2024 - SMIC//Fondation Bettencourt Schueller/ ; AS-IA-113-L04//Academia Sinica/ ; 114-2628-B-001-014-//National Science and Technology Council, R.O.C/ ; }, abstract = {Yeasts are widespread members of microbial communities across terrestrial, aquatic, and host-associated environments, yet they remain underrepresented in microbiome studies due to low abundance and methodological biases. By combining a literature review with a meta-analysis of ~44,000 fungal metabarcoding samples from the GlobalFungi database, we show that yeasts occur in over 90% of samples, confirming their global ubiquity. Basidiomycetous lineages-especially Agaricomycotina-were most frequently detected, whereas Saccharomycotina showed stronger signals in anthropogenic, aquatic, host-associated, and food-related settings depending on the dataset. Although yeasts typically comprised only ~0.1% of fungal reads, their distributions were structured rather than uniform and reflected distinct habitat associations across environments. In ~3% of samples, yeasts exceeded 25% of reads, with genera such as Aureobasidium, Hanseniaspora, and Saccharomyces episodically dominating nutrient-rich or human-influenced environments. Cosmopolitan genera including Vishniacozyma, Solicoccozyma and Rhodotorula were broadly distributed but remain underreported in microbiome surveys. Shotgun metagenomic data further confirmed yeast presence across diverse microbiomes, with yeast-derived reads being a small fraction of total metagenomic sequences, reflecting the 'curse of low abundance'. Despite their rarity, yeasts are likely to contribute to nutrient cycling, plant growth, and host interactions. We recommend inclusive multi-kingdom approaches-improved primer design, optimised fungal DNA recovery, long-read sequencing, and quantitative tools-to better integrate yeasts into microbiome research.}, } @article {pmid42562512, year = {2026}, author = {Murthy, N and Nayak, KN and Tanu, and Priya, S and Priyadarshini, P}, title = {Dual-stage assessment of Salmonella-specific bacteriophage formulation: Antibiofilm activity on food matrices and in vivo efficacy against the murine salmonellosis model.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119738}, doi = {10.1016/j.foodres.2026.119738}, pmid = {42562512}, issn = {1873-7145}, mesh = {Animals ; *Biofilms/growth & development ; *Salmonella Phages/physiology ; Mice ; Disease Models, Animal ; Humans ; *Salmonella Infections/microbiology/therapy/prevention & control ; *Food Microbiology ; Chickens/microbiology ; *Salmonella/virology ; *Salmonella Food Poisoning/prevention & control/microbiology ; HT29 Cells ; Meat/microbiology ; Female ; Fruit/microbiology ; }, abstract = {Foodborne infections caused by Salmonella infection remain a major global concern due to increasing multidrug resistance and biofilm formation, resulting in significant morbidity and mortality. Thus, the development of potential alternatives, including bacteriophage cocktail formulations, is emerging as a promising strategy. In this direction, we developed a Salmonella-specific phage formulation (BPF-Sal) and evaluated its stability, biocontrol efficacy, in vitro safety, antibiofilm activity and protective potential in an in vivo model. Interestingly, BPF-Sal remained stable across a wide range of pH values and temperatures while maintaining significant lytic activity. Further, it effectively reduced Salmonella contamination on chicken breast and mixed fruit matrices to below detection limits (<1 CFU/100 μL) within 6 h and 10 h, respectively, compared to conventional preservatives. In HT-29 cells, BPF-Sal (10[2]-10[1][0] PFU/mL) exhibited no cytotoxicity, preserved cellular morphology, and showed efficient phage internalization. It also displayed antibiofilm activity, reducing preformed Salmonella biofilms by 90-92% at MOI 100 and up to 98% at MOI 1000, as confirmed by crystal violet assay, scanning electron and fluorescence microscopy. In a murine salmonellosis model, oral administration of BPF-Sal conferred significant protection, preventing weight loss and reducing bacterial loads along with improved health status and histopathological outcomes. Metagenomic analysis revealed infection-induced gut dysbiosis, characterized by enrichment of Proteobacteria and depletion of beneficial taxa. BPF-Sal partially restored microbial balance, while combination therapy further improved microbiota normalization. Thus, our findings establish BPF-Sal as a safe, effective, multifunctional phage-based strategy for Salmonella biocontrol and other phage-based applications.}, } @article {pmid42562513, year = {2026}, author = {Liu, QJ and Mei, JL and Wen, X and Lu, YH and Zeng, Y and Liu, ZY and Xu, HY and Wang, ST and Jiang, F and Yang, CB and Chi, YL and Xu, ZH}, title = {Cellar age reshapes Huangshui micro-ecosystem and metabolism to drive flavor formation in strong-aroma baijiu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119740}, doi = {10.1016/j.foodres.2026.119740}, pmid = {42562513}, issn = {1873-7145}, mesh = {Fermentation ; Metabolomics ; *Odorants/analysis ; *Taste ; Bacteria/metabolism/genetics ; *Wine/analysis/microbiology ; *Alcoholic Beverages/analysis/microbiology ; Metagenomics ; *Microbiota ; Flavoring Agents ; }, abstract = {Huangshui, a slurry-like liquid exuded during strong-aroma Baijiu fermentation, serves as the core medium for material exchange between pit mud and fermented grains. However, how its micro-ecosystem evolves with cellar age and drives flavor formation remains unclear. Using Huangshui as a dynamic window, this study integrated metagenomics, metabolomics, and flavoromics to compare its temporal dynamics in new and old cellars over a complete fermentation cycle, systematically characterizing how cellar age is associated with the restructuring of the microbial community and metabolic functions of Huangshui, and how these changes are consistent with the flavor profiles observed in the final base liquor. The results showed that Huangshui from old cellars harbored a more diverse and stable microbial community, forming a syntrophic consortium of caproic acid-producing bacteria (Caproicibacterium, Caproiciproducens), syntrophic bacteria (Syntrophomonas), and methanogenic archaea (Methanosarcina), whereas new cellars were dominated by lactic acid bacteria (Acetilactobacillus). Metabolically, the old-cellar community exhibited a clear phase-dependent division. During the acid-producing phase, the TCA cycle, arginine biosynthesis, and pyruvate metabolism were preferentially activated to generate core precursors; during esterification, butanoate metabolism and acyl-CoA supply pathways were enhanced. This orderly shift was associated with higher concentrations of ethyl caproate and ethyl octanoate in old-cellar base liquor. Functional gene analysis revealed coordinated upregulation of chain-elongation, methanogenic, and acetate-activating pathways in old cellars. Network analysis revealed a tightly coupled caproic acid-producing co-occurrence module in old cellars, which was not observed in new ones. Together, these findings suggest that Huangshui may serve as a rapid proxy for assessing both the fermentation status and the maturity level of the cellar. This work identifies potential bioaugmentation targets to accelerate flavor development in new cellars and provides a theoretical basis for the precise micro-ecological management of strong-aroma Baijiu quality.}, } @article {pmid42562527, year = {2026}, author = {Sun, Y and Guo, S and Kwok, LY and Guo, Y and Jiao, Y and He, Q and Zhang, H and Wang, J}, title = {Fermented milk derived from a novel probiotic strain enhances digestive function and attenuates dextran sulfate sodium-induced colitis via the microbiota-metabolite-immune axis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119757}, doi = {10.1016/j.foodres.2026.119757}, pmid = {42562527}, issn = {1873-7145}, mesh = {Animals ; *Colitis/chemically induced/prevention & control/metabolism ; *Probiotics/pharmacology ; Dextran Sulfate ; Male ; Rats ; *Gastrointestinal Microbiome/physiology ; *Cultured Milk Products/microbiology ; Bifidobacterium animalis/metabolism ; *Digestion ; Rats, Sprague-Dawley ; Cytokines/metabolism ; Colon/pathology/metabolism ; Disease Models, Animal ; Fatty Acids, Volatile/metabolism ; }, abstract = {Probiotic-fermented dairy products are increasingly recognized for their dual role in nutrient optimization and disease prevention. This study investigated the mechanisms by which Bifidobacterium animalis subsp. lactis Probio-M8 fermented milk enhances digestive efficiency and protects against dextran sulfate sodium-induced colitis in rats. FM8 supplementation promoted weight gain without excessive adipogenesis, elevated leptin levels, and amplified sucrase, lactase, aminopeptidase, and lipase activities, outperforming conventional fermented milk. Metagenomic analysis revealed microbial restructuring with Corynebacterium glutamicum and Bifidobacterium animalis enrichment, and increased short-chain fatty acids.Untargeted metabolomics identified FM8-responsive metabolites, including p-hydroxybenzaldehyde and indole-3-carboxaldehyde, linked to anti-inflammatory pathways. In dextran sulfate sodium-challenged rats, FM8 pre-administration attenuated colitis severity by reducing disease activity index scores, normalizing colon histology, and suppressing interleukin (IL)-6 and IL-17 while elevating IL-10 and IL-22. Mechanistically, FM8 enriched Bifidobacterium animalis and butyrate levels, which inversely correlated with mucosal injury and pro-inflammatory cytokines. These findings demonstrate that FM8 enhances gastrointestinal health through tripartite microbiota-metabolite-immune interactions, highlighting its functional potential for metabolic optimization and colitis prevention.}, } @article {pmid42562693, year = {2026}, author = {Zhang, Y and Yang, S and Yang, J and Wu, Z and Liu, H and Nie, Z and Qu, J and Hu, Y and Shao, Y and Liu, J and Liu, F and Hua, D}, title = {Retraction notice to "Temporal hormetic response of soil microbes to cadmium: A metagenomic perspective" [Sci. Total Environ. 891 (2023) 164190].}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {182119}, doi = {10.1016/j.scitotenv.2026.182119}, pmid = {42562693}, issn = {1879-1026}, } @article {pmid42562842, year = {2026}, author = {Lechleiter, N and Wedemeyer, J and Junker, J and Wilczek, M and Klich, D and Olech, W and Anusz, K and Homeier-Bachmann, T and Didkowska, A}, title = {Microbiome and resistome of the European bison (Bison bonasus).}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42562842}, issn = {2045-2322}, mesh = {Animals ; *Bison/microbiology ; *Microbiota/genetics ; Feces/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Archaea/genetics/classification/isolation & purification ; Phylogeny ; }, abstract = {After facing extinction in the early 20th century, populations of the two remnant genetic lines of European bison are now under continuous health monitoring. Faecal samples were taken from five Polish and one German herd of European bison over the course of several years. Through metagenomic sequencing, the bacterial and archaeal microbiome as well as the resistome of these samples could be characterized. Significant differences were mainly found between the bacterial microbiome of samples taken from droppings as opposed to rectal samples. Apart from this, the microbiome and resistome had low differentiation, showing no significant influence of individual factors or location. Oscillospiraceae, Lachnospiraceae and Bacteroidaceae were the dominant bacterial families, the archaeome was mostly made up by Methanobacteriaceae. Genes from resistance classes like Aminoglycosides and Macrolide, Lincosamide and Streptogramine were present. This study characterises the microbiome and resistome of the European bison with the help of metagenomics, providing novel insights into its biology.}, } @article {pmid42563165, year = {2026}, author = {Richie, TG and Wiechman, H and Vogt, B and Ingold, C and Heeren, L and Kamke, A and Pogranichniy, S and Monk, K and Summers, T and Ran, Q and Sarkar, S and Plattner, BL and Sidebottom, AM and Chang, EB and Lee, STM}, title = {Microbially derived glutathione from Eubacterium rectale alleviates oxidative stress and promotes intestinal epithelial recovery.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42563165}, issn = {2049-2618}, mesh = {*Oxidative Stress/drug effects ; Animals ; *Glutathione/metabolism/pharmacology ; Reactive Oxygen Species/metabolism ; Mice ; Colon/microbiology/metabolism ; *Intestinal Mucosa/metabolism/microbiology/drug effects ; Nitric Oxide/metabolism ; Intestinal Barrier Function ; Gastrointestinal Microbiome ; Metagenomics ; Mice, Knockout ; Interleukin-10/genetics ; }, abstract = {BACKGROUND: Certain microbes inhabiting the gut have been implicated in maintaining gut homeostasis and promoting gut damage repair. Lachnospiraceae members were highly detected in dysbiotic IL-10 KO mice that displayed similar physiological outcomes as control mice. Lachnospiraceae is a highly diverse family of microbes that have been shown to display both commensal and pathogenic characteristics in the colon environment.

RESULTS: We investigated the impact of genetic variation in five Lachnospiraceae strains on lowering cellular inflammation and reactive oxygen species (ROS) levels. Cell-free spent media (CFSM) from Eubacterium rectale resulted in lowered ROS, and nitric oxide levels in stressed colon cells and colon organoids. CFSM-treated organoids showed reduced ROS accumulation, improved epithelial integrity, and partial recovery of barrier function compared to oxidatively stressed controls. We demonstrated through shotgun metagenomics, metabolomics, host RNA sequencing, and molecular techniques that glutathione (GSH) biosynthesized by E. rectale alleviated host ROS damage. We showed downregulation of cell stress and immune response genes, indicating recovery from ROS stress. Chemical depletion of GSH in CFSM confirmed the role of microbial derived GSH in alleviation of ROS in colon cells.

CONCLUSIONS: In this study, we identify E. rectale as a potential probiotic by lowering colon inflammation and ROS damage through production of reduced glutathione. Microbially derived GSH has not been well established in the Lachnospiraceae family which are a large member of the overall gut microbiota. Understanding more about the impacts of microbial functions including GSH on lowering inflammation is needed to develop potential probiotics or therapies for chronic inflammatory conditions. Video Abstract.}, } @article {pmid42563841, year = {2023}, author = {Grose, C and Bonthius, DJ}, title = {Meningitis caused by the varicella vaccine virus in 17 immunized children and adolescents from the United States, Europe, and Japan.}, journal = {Annals of the Child Neurology Society}, volume = {1}, number = {2}, pages = {96-101}, pmid = {42563841}, issn = {2831-3267}, abstract = {The varicella vaccination program has an excellent safety record. The vaccine virus, like its wild-type counterpart, can enter latency and later reactivate as herpes zoster. A lesser known but serious adverse event following reactivation is varicella vaccine meningitis. We investigate that adverse event. We performed a literature search using the PubMed and Google Scholar search engines to locate all published cases of varicella vaccine meningitis. We continued the search through January 2023. We found 17 cases of varicella vaccine meningitis. The first case was published in 2003, and the last case was published in 2023. The children lived in the United States, Greece, Germany, Switzerland, and Japan. Among the 17 cases, 14 were immunocompetent; nine of the 17 were adolescents. One potential risk factor was the administration of corticosteroids three to four weeks before the onset of meningitis. Varicella vaccine meningitis is a rare but one of the more serious adverse events that occurs several years following varicella vaccination. In immunocompetent children, this complication is treatable with a single course of intravenous acyclovir after hospitalization.}, } @article {pmid42564172, year = {2026}, author = {Rojas, L and Zuluaga, J and Cardona, AF}, title = {Microbiome as a prediction of immunotherapy response in lung cancer.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1849553}, pmid = {42564172}, issn = {1664-3224}, mesh = {Humans ; *Lung Neoplasms/immunology/drug therapy/microbiology/therapy ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects ; *Immunotherapy/methods ; *Gastrointestinal Microbiome/immunology/drug effects ; Treatment Outcome ; Animals ; *Microbiota/immunology ; }, abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of lung cancer (LC), offering durable responses in non-small cell lung cancer (NSCLC) and, to a lesser extent, small cell lung cancer (SCLC). Nevertheless, clinical outcomes remain highly heterogeneous, with many patients experiencing primary or acquired resistance and/or immune-related adverse events (irAEs) that impair their quality of life and treatment adherence. The human microbiome, particularly in the gut and oral compartments, has emerged as a critical modulator of systemic antitumor immunity and a promising noninvasive predictive biomarker for ICI efficacy and toxicity. This narrative review synthesizes the current evidence on microbiome composition, diversity, and function in patients with LC receiving ICIs as monotherapy, dual blockade, or in combination regimens, as well as clinically relevant biomarkers associated with treatment response and toxicity. Higher gut microbial alpha diversity and enrichment of beneficial taxa (e.g., Akkermansia muciniphila, Faecalibacterium prausnitzii, and certain Firmicutes) are consistently linked to improved progression-free survival (PFS) and overall survival (OS), mediated by microbial metabolites such as short-chain fatty acids and inosine, which enhance T-cell priming, tumor microenvironment remodeling, and gut-lung axis communication. Microbiome-disruptive exposures, particularly antibiotics and proton pump inhibitors (PPIs), induce dysbiosis and are strongly associated with poorer survival outcomes. Mechanistic insights from preclinical models and clinical cohorts, alongside clinical confounders, underscore the complementary role of the microbiome relative to established markers such as programmed death-ligand 1 (PD-L1) and tumor mutational burden. Prospective standardization of metagenomic profiling and microbiome-modulating interventions represents a key next step in translating these findings into personalized immunotherapy strategies for LC.}, } @article {pmid42564198, year = {2026}, author = {Martínez-Álvaro, M and Greenacre, M and Blasco, A}, title = {Omics data in relative values are almost subcompositionally coherent.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809364}, pmid = {42564198}, issn = {1664-302X}, abstract = {INTRODUCTION: Omics data are compositional and often expressed as relative abundances after total sum scaling normalization. An important statistical issue with compositional data is the lack of subcompositional coherence, meaning that relative abundances change when data are re-normalized after removing or adding features. While this problem is well documented for small compositions, it has not been investigated in large Omics datasets, which typically contain hundreds or thousands of features and where subcompositions are ubiquitous. Subcompositions arise, for example, when using different reference datasets, sequencing depths or when filtering low-abundant features from the database. In such cases, the most abundant features are preferentially retained, whereas variation between original or full compositions and subcompositions is mainly driven by less abundant features. The standard solution to this problem is the use of logratio transformations, but these complicate interpretations and require handling zeros, which are frequent in Omics data and whose imputation introduces spurious variability.

METHODS: Here, we evaluated subcompositional coherence in five representative Omics datasets: fecal 16S metagenomics, rumen metagenomics (taxonomic and functional levels), liver transcriptomics, and plasma metabolomics, considering both unsupervised and supervised learning contexts. We generated 100 random subcompositions comprising one-third of the original features under an abundance-weighted subcomposition scheme and compared their statistical outputs with those from the full composition.

RESULTS AND DISCUSSION: Raw Omics data showed near-perfect coherence: relative abundances, pairwise correlations and sample distances all exhibited very high (scaled) concordances (≥0.98-0.99). Outputs from commonly used supervised models (linear regression, PLS, random forest, and linear mixed models with a Gaussian kernel) were also highly subcompositionally coherent. We conclude that large Omics datasets expressed as relative abundances are almost subcompositionally coherent when considering a weighted subcomposition scheme, thereby challenging one of the criticisms of using relative data in the Omics field over logratio transformations.}, } @article {pmid42564309, year = {2026}, author = {Akther, SM and Krakko, D and Shi, W}, title = {Rhizosphere microbiomes in drought-tolerant and drought-sensitive bermudagrass genotypes: root exudate association.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1868900}, pmid = {42564309}, issn = {1664-302X}, abstract = {INTRODUCTION: Plant-microbiome interactions in the rhizosphere are critical for plant adaptation to environmental stress; however, the coordinated roles of root exudates and microbiome dynamics remain poorly understood.

METHODS: Integrating untargeted metabolomics and shotgun metagenomics, we analyzed drought responses in drought-tolerant and drought-sensitive bermudagrass genotypes.

RESULTS: Drought stress shaped the root exudate chemistry, which likely reprogrammed microbiome functions, such as TccC toxins and the Type VI secretion system, without considerable broad taxonomic shifts. A few metabolites, including riboflavin and 1-carboxy-6-hydroxy-3,4-dihydro-beta-carboline, were associated with Massilia putida, particularly in the rhizosphere of the drought-tolerant genotype.

DISCUSSION: Our data suggest a potential explanation for a genotype-driven strategy of microbiome modulation via metabolite signaling.}, } @article {pmid42564713, year = {2026}, author = {Lizhu, Y and Chen, Y and Zhang, X and Luo, Y and Zhuo, Z and Wang, J and Duan, Y and Chai, L and Qiu, J and Gao, Z and Wang, T and Yan, H and Liang, X and Wang, Y and Su, Y and Guan, L and Liu, Y}, title = {Oral microbiota dysbiosis related to the cortical thinning and cognitive impairment in cerebral small vessel disease.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2705667}, pmid = {42564713}, issn = {2000-2297}, abstract = {BACKGROUND: Prior studies have linked the microbiota to brain diseases, whereas the longitudinal effects of the oral microbiota on cortical thinning and cognitive impairments in cerebral small vessel disease (CSVD) remain unexplored.

METHODS: We recruited 120 CSVD patients and 40 healthy controls (HCs). The subgingival plaque microbiota was sequenced by a metagenomic approach. Cortical thickness was assessed using GM-centile, an age- and sex-normalized MRI metric. Differential microbial taxa and KEGG orthologs (KOs) between groups were identified using MaAsLin2. Associations between key differential taxa with CSVD-specific cortical thinning were examined using the Spearman test, and those with MoCA score and plasma inflammatory markers (CRP and lymphocyte counts) were examined by linear regression models. Mediation models evaluated the indirect role of cortical thinning in the relationship between microbial abundance and cognitive function. Generalized estimation equations validated the longitudinal effects of the microbiota on cortical thinning progression.

RESULT: We identified distinct oral microbiota dysbiosis in CSVD, including depletion of g_Selenomonas and g_Leptotrichia and enrichment of g_Treponema. The abundance of these microbes was correlated with longitudinal cortical thinning in the frontal gyrus, insular lobes, and inferotemporal gyrus. Enrichment analysis revealed that CSVD-enriched KOs were linked to the upregulation of LPS-mediated pro-inflammatory pathways, while those depleted were associated with the reduced biosynthesis of neuroprotective short-chain fatty acids (SCFAs). g_Leptotrichia abundance showed negatively correlation with CRP (p = 0.045). Mediation analyses indicated that the association between g_Leptotrichia depletion and baseline cognitive impairment was mediated by bilateral insular cortical thinning (both p < 0.05). Additionally, the association between g_Leptotrichia depletion and one-year cognitive decline was mediated by superior frontal cortical thinning (p = 0.033).

CONCLUSIONS: Oral microbiota dysbiosis in CSVD patients reflects a pro-inflammatory state, characterized by enhanced LPS synthesis and reduced SCFAs production. This dysbiosis is associated with CSVD-specific cortical thinning in regions vulnerable to neuroinflammation, which in turn mediates cognitive impairment.}, } @article {pmid42564864, year = {2026}, author = {Yan, Z and Qian, X and Liu, Y and Tian, L}, title = {Pediatric pyopneumothorax caused by Prevotella oris successfully diagnosed via mNGS: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1888298}, pmid = {42564864}, issn = {2296-858X}, abstract = {BACKGROUND: Empyema and pyopneumothorax are severe complications of pediatric community-acquired pneumonia. While typically caused by aerobic bacteria, anaerobic infections, particularly those involving Prevotella oris (P. oris), are exceedingly rare in children. This study aims to explore the clinical characteristics, diagnostic challenges, and therapeutic strategies for pediatric pyopneumothorax caused by P. oris, thereby enhancing clinical awareness of this uncommon opportunistic pathogen.

CASE PRESENTATION: We retrospectively analyzed the clinical data of a 10-year-old male admitted to the Hebei Children's Hospital in October 2025, presenting with acute chest pain and a history of tooth extraction 1 week prior to symptom onset. Radiological imaging revealed bilateral pneumonia with bilateral pleural effusions (predominantly on the left side). Pleural fluid analysis was consistent with an empyema. Traditional bacterial cultures of blood and pleural fluid yielded negative results. However, probe-based targeted metagenomic next-generation sequencing (mNGS) of the pleural fluid identified P. oris with a high relative abundance (81.86%), alongside other minor oral commensals. Based on the molecular diagnosis and the patient's ongoing clinical deterioration, cefoperazone-sulbactam was selected to strengthen coverage against anaerobic Gram-negative organisms, while linezolid was temporarily added to cover potential Gram-positive pleural co-infection during the acute deterioration phase. This was combined with closed thoracic drainage and intrapleural urokinase instillation for fibrinolysis, leading to a complete clinical recovery.

CONCLUSION: Prevotella oris is a rare but significant pathogen in pediatric empyema. A high index of suspicion should be maintained for anaerobic infections in children presenting with a history of dental procedures, abnormal immune parameters or possible immunological vulnerability, or poor response to empirical antibiotics. Traditional cultures are often inadequate; therefore, mNGS serves as a crucial tool for the early detection and precise treatment of difficult-to-culture anaerobes.}, } @article {pmid42565114, year = {2026}, author = {Russell, AL and Olthoff, B and Zhang, C and Lutz, C and Franklin, CL and Ericsson, AC}, title = {Gut microbiota and pathobiont exposure influences disease incidence in non-obese diabetic mice.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1844128}, pmid = {42565114}, issn = {1664-302X}, abstract = {While the non-obese diabetic (NOD) mouse is the most widely used animal model of type 1 diabetes (T1D), it suffers from poor reproducibility in disease incidence often attributed to variables in the environment, including the gut microbiota (GM). Prior research suggests a protective effect of segmented filamentous bacteria (SFB) on disease incidence, but it is unclear whether other pathobiont organisms or resident GM affect disease incidence. The objectives of the current study were to determine the effect of supplier-origin GMs and three different microbial challenges (SFB, Helicobacter hepaticus, and Mouse Hepatitis Virus [MHV]) on early-stage insulitis and lifelong disease incidence in NOD mice. The fecal microbiome was assessed pre- and post-disease onset to identify shifts in composition and predicted function of the GM. Results show that all three microbes influence T1D incidence and insulitis severity. Overall, SFB, MHV, and a high-richness microbiome were associated with lower disease incidence, while H. hepaticus and a low-richness microbiome were associated with higher disease incidence. H. hepaticus, but not SFB or MHV, was associated with significant changes in beta-diversity of the GM. While immune outcomes were not included, these findings provide guidance on microbes affecting disease incidence in NOD mice and evidence that such microbes may contribute to poor reproducibility in NOD mice or other mouse models.}, } @article {pmid42565123, year = {2026}, author = {Luo, J and Fan, J and Liu, H and Lv, X and Tang, Z and Wang, X and An, F and Chen, Y}, title = {Loofah sponge carriers: Uncovering the mechanisms of enhanced anammox performance in low-nitrogen wastewater treatment.}, journal = {iScience}, volume = {29}, number = {8}, pages = {116070}, pmid = {42565123}, issn = {2589-0042}, abstract = {This study investigated eco-friendly immobilization carriers for AnAOB to enhance nitrogen removal from low-nitrogen domestic wastewater. Natural loofah sponge was evaluated as a novel biofilm carrier, with polyurethane sponge and polyethylene carrier as references. Microbial morphology, community structure, and nitrogen metabolism-related functional genes were systematically analyzed. Although the loofah sponge biofilm possessed the lowest abundances of Planctomycetota (39.38%) and Candidatus Brocadia (38.35%), it achieved over 90% TNRE and a maximum TNRR of 0.067 kgN/(m[3]·d). The loofah sponge biofilm carrier also exhibited a denser, more uniform biofilm structure by SEM and higher relative abundances of key functional enzyme genes (hdh, hzs, nirS, and nirK) and ammonium transporter genes (amt and FNT) via metagenomic analysis. Long-term operation and typical cycle experiments validated its superior and stable anammox performance, providing a promising, sustainable, and easily applicable carrier strategy for practical anammox wastewater treatment systems.}, } @article {pmid42565581, year = {2026}, author = {Jin, Q and Wu, Z and Yang, Z and Li, Z}, title = {[Pulmonary disease caused by Mycobacterium abscessus in an infant: A case report and literature review].}, journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences}, volume = {51}, number = {5}, pages = {1070-1076}, doi = {10.11817/j.issn.1672-7347.2026.250083}, pmid = {42565581}, issn = {1672-7347}, mesh = {Humans ; Female ; *Mycobacterium abscessus/isolation & purification ; Infant ; *Mycobacterium Infections, Nontuberculous/drug therapy/diagnosis/microbiology ; Amikacin/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; Linezolid/therapeutic use ; *Lung Diseases/microbiology/drug therapy ; Azithromycin/therapeutic use ; Cefoxitin/therapeutic use ; }, abstract = {Pulmonary infection caused by Mycobacterium abscessus is rare in children without underlying pulmonary disease, especially in infants. A 3-month-old female infant was admitted to the Third Xiangya Hospital of Central South University on July 29, 2023. Cough was her only clinical manifestation, and chest computed tomography revealed multiple patchy and mass-like high-density opacities in both lungs. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid confirmed the diagnosis of Mycobacterium abscessus pulmonary disease. Further evaluation for immunodeficiency and whole-exome sequencing revealed no abnormalities. The patient improved after combination therapy with amikacin, cefoxitin, linezolid, and azithromycin, without adverse reactions. For rare pulmonary infections in infants with atypical clinical manifestations and a low positivity rate of conventional etiological tests, metagenomic next-generation sequencing may facilitate early diagnosis.}, } @article {pmid42565866, year = {2026}, author = {Priti, K and Chandra, H and Sagar, K}, title = {Microbial lipases: advances in metagenomics and artificial intelligence for enzyme discovery and engineering.}, journal = {Archives of microbiology}, volume = {208}, number = {11}, pages = {}, pmid = {42565866}, issn = {1432-072X}, mesh = {*Metagenomics/methods ; *Lipase/genetics/metabolism/chemistry ; *Protein Engineering/methods ; *Artificial Intelligence ; *Bacteria/enzymology/genetics ; Biotechnology ; Substrate Specificity ; }, abstract = {Microbial lipases are versatile biocatalysts with high catalytic efficiency, substrate specificity, stability, and ability to catalyze a wide range of processes under mild environmental conditions, which make them highly valuable in various industrial and biotechnological applications. However, traditional methods of enzyme discovery and engineering rely on cultured microorganisms and labor-intensive experimental processes. This study highlights recent developments in metagenomics and AI technologies for microbial lipase discovery and engineering and providing a brief overview of the sources, structural features, physicochemical properties, and industrial applications of lipases. Recent breakthroughs in metagenomics have provided new access to novel enzymes from non-cultivable microbial communities, and the rising significance of artificial intelligence in enzyme discovery, structure prediction, protein engineering, and bioprocess optimization is presented. This study also highlights the important synergy between metagenomics and artificial intelligence technologies for the identification and rational design of enzymes, integrating extensive sequence databases with predictive computational modeling tools. In addition, there are still various challenges, such as low heterologous expression levels, a lack of quality information, and limited industrial-scale validation. We anticipate that future advances in protein language models, generative artificial intelligence, synthetic biology, and multi-omics integration will accelerate enzyme discovery, engineering, and large-scale industrial implementation. Overall, the use of metagenomics, artificial intelligence, and experimental approaches has tremendous potential for developing efficient and economically viable lipases for sustainable biotechnological applications.}, } @article {pmid42565999, year = {2026}, author = {Islam, SMS and Chowdhury, MN and Supty, SI and Tanoy, NM and Yadav, DN and Roy, S and Riea, ATM and Obaydullah, M and Tasnim, Z and Zaman, MS and Rahman, MA and Sabuj, MSS and Islam, MS and Hossain, MA and Islam, MS and Akanda, MR}, title = {Molecular and environmental drivers of antimicrobial resistance: global epidemiology, resistome dynamics, and one health strategies.}, journal = {Archives of microbiology}, volume = {208}, number = {11}, pages = {}, pmid = {42565999}, issn = {1432-072X}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; Global Health ; *Bacteria/drug effects/genetics ; *One Health ; *Drug Resistance, Multiple, Bacterial/genetics ; *Drug Resistance, Bacterial ; *Bacterial Infections/microbiology/epidemiology/drug therapy ; Environmental Microbiology ; Interspersed Repetitive Sequences ; }, abstract = {Antimicrobial resistance (AMR) has evolved into a critical global health security challenge, threatening the effectiveness of modern medicine and increasing morbidity and mortality worldwide. This review integrates current evidence on the molecular and environmental drivers of AMR, alongside global epidemiological patterns, resistome dynamics, and one health-based intervention strategy. Recent surveillance data indicate that AMR contributes to approximately 4.7 million deaths annually, with the highest burden concentrated in low- and middle-income countries, where resistance rates in key pathogens such as Escherichia coli, Klebsiella pneumoniae, and methicillin-resistant Staphylococcus aureus remain alarmingly high. At the molecular level, AMR is driven primarily by horizontal gene transfer mediated by mobile genetic elements, including plasmids, integrons, and transposons, enabling rapid dissemination of multidrug resistance among clinically important pathogens, including critical high-risk threats and critical multidrug-resistant organisms. Environmental reservoirs, including wastewater effluents, agricultural runoff, soil, and hospital discharge systems, serve as major hotspots for the selection and amplification of resistance genes. These environments facilitate the evolution of environmental resistomes, in which subinhibitory antibiotic concentrations, heavy metals, and other pollutants exert strong coselective pressures. Additionally, biofilm formation, metabolic adaptation, and climate-related stressors further increase the persistence and spread of resistance determinants. The integration of genomic surveillance and metagenomic approaches have improved the understanding of resistome structure and transmission pathways, yet significant gaps remain in linking environmental and clinical datasets. To address these challenges, emerging One Health strategies emphasize coordinated interventions across the human, animal, and environmental sectors. Novel approaches such as antimicrobial stewardship, phage therapy, CRISPR-based antimicrobials, and AI-driven drug discovery are being explored alongside improved diagnostics and environmental control measures. Collectively, a cross-sectoral, integrated One Health framework is essential to mitigate the emergence of AMR and sustain antimicrobial efficacy globally.}, } @article {pmid42566284, year = {2026}, author = {Oláh, ÁA and Dudás-Györki, Z and Dunay, IR and Dunay, MP}, title = {Alterations in the feline oral microbiome in common oral diseases - A comprehensive review.}, journal = {European journal of microbiology & immunology}, volume = {}, number = {}, pages = {}, doi = {10.1556/1886.2026.00040}, pmid = {42566284}, issn = {2062-509X}, abstract = {The most prevalent diagnostic conditions in domestic cats (Felis catus) are oral diseases, affecting up to 90% of older cats. Periodontal disease (PD), feline chronic gingivostomatitis (FCGS), and tooth resorption (TR) are the principal clinically relevant entities, each with distinct histopathological and microbiological features. Certain molecular techniques, including 16S rRNA sequencing, shotgun metagenomics, and metatranscriptomics, have substantially advanced our understanding of the feline oral microbiome alterations. This review summarizes the findings of the healthy oral microbiome and its disease-associated shifts in PD, FCGS, TR, and feline immunodeficiency virus (FIV)-associated pathology. The healthy oral cavity is dominated by Proteobacteria, Bacteroidota, Bacillota, Fusobacteria, and Actinobacteria, notably Porphyromonas, Moraxella, Capnocytophaga, and Fusobacterium. Dental disease is characterised by expansion of Bacteroidota and Spirochaetota, enrichment of Treponema, Peptostreptococcus, Filifactor, and Fusobacterium nucleatum, and depletion of commensals. The contributions of fungi, viruses, and host immunity are critically evaluated, alongside the development of microbiome-based diagnostics and therapeutics. We argue that dysbiosis is a unifying (albeit not monocausal) feature of feline oral pathology and identify gaps in current knowledge that require further investigation.}, } @article {pmid42566318, year = {2026}, author = {Beaton, ADM and Croxford, JT and Díaz de Aguinaga, AC and Horsburgh, E and Mark, DR and McQueary, LS and Murray-Clelland, KR and Tucker, SK and Roe, AJ and McHugh, RE}, title = {Interactions at the Streptomyces - animal interface: ecology, defence and disease.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {8}, pages = {}, doi = {10.1099/mic.0.001747}, pmid = {42566318}, issn = {1465-2080}, mesh = {*Streptomyces/physiology/genetics/metabolism ; Animals ; Humans ; Soil Microbiology ; Microbiota ; Insecta/microbiology ; Nematoda/microbiology ; }, abstract = {Streptomyces are filamentous, spore-forming members of the Actinomycetota, renowned for their capacity to produce chemically diverse, specialized metabolites with medically important properties. Traditionally, Streptomyces have been viewed as soil-dwelling microbes, and their roles in soil ecology, plant health and plant disease have been extensively studied. However, advances in metagenomic sequencing and molecular approaches have greatly expanded our ability to investigate interkingdom interactions between Streptomyces and more complex organisms, including animals. In recent years, a growing body of work has revealed diverse and often intimate associations between Streptomyces and members of the Animalia. These include interactions with microfauna such as nematodes (Nematoda), insects (Insecta), including bees and ants, mammals such as bats (Chiroptera) and humans (Homo sapiens). This review consolidates our current knowledge of Streptomyces - animal interactions, with a particular focus on chemical ecology and the roles of specialized metabolites in shaping these relationships. This work highlights the emerging body of work investigating the role of Streptomyces ecology beyond soil ecosystems and draws attention to the importance of exploring non-traditional niches, including animal-associated microbiomes, to deepen our understanding of microbial-animal interactions and to expand opportunities for natural product discovery.}, } @article {pmid42566872, year = {2026}, author = {Pei, Y and Xu, Z and Xie, L and Wang, H}, title = {Enrichment of bile salt hydrolase-producing bacteria mediated by tetracycline resistance genes is associated with intestinal barrier damage in Rana chensinensis tadpoles.}, journal = {Ecotoxicology and environmental safety}, volume = {323}, number = {}, pages = {120624}, doi = {10.1016/j.ecoenv.2026.120624}, pmid = {42566872}, issn = {1090-2414}, abstract = {Tetracycline (TET) is a pervasive contaminant in aquatic environments, yet how it reshapes gut microbiota composition and function to influence bile acid (BA) profiles and intestinal health remains poorly understood. In this study, Rana chensinensis tadpoles at Gosner stage 26 (Gs26) were exposed to environmentally relevant concentrations of tetracycline hydrochloride (10 and 100 μg/L) until metamorphic climax Gs38 and examined using a multi-pronged approach integrating histological analysis, intestinal targeted BA metabolomics, and fecal metagenomic sequencing. Our results showed that TET exposure disrupted intestinal barrier integrity in a dose-dependent manner, as evidenced by reduced enterocyte height, widened intercellular spaces, and irregular nuclear morphology. Metagenomic profiling revealed that TET treatment significantly enriched tetracycline resistance genes (e.g., tet(Q), tet(T), tetA(46), tetA(60)), which was accompanied by an increased abundance of bile salt hydrolase (BSH)-producing bacteria, including Bacteroides, Parabacteroides, and Vibrio. This microbial shift was accompanied by enhanced BA deconjugation, as reflected by a significantly increased ratio of unconjugated to conjugated BAs (p < 0.01). Notably, the enhanced deconjugation activity was paralleled by a marked accumulation of the hydrophobic and cytotoxic BA, chenodeoxycholic acid (CDCA) (p < 0.001), which was accompanied by a 73.9% reduction in total BA levels - a pattern that may reflect Farnesoid X Receptor (FXR)-mediated negative feedback regulation of hepatic BA synthesis, although this pathway was not directly examined. Furthermore, elevated CDCA levels were associated with intestinal histopathological damage. Collectively, these findings suggest a potential mechanistic cascade in which TET-induced enrichment of antibiotic resistance genes is associated with the expansion of BSH-active microbiota, together with disrupted BA homeostasis and compromised intestinal barrier function in amphibians. Causal relationships within this cascade await functional validation. Our study highlights the hidden ecological risks of antibiotic contamination in aquatic ecosystems and underscores the need for further molecular investigations into the signaling pathways involved.}, } @article {pmid42566873, year = {2026}, author = {Wang, Z and Mi, X and Li, W and Niu, Y and Zhao, Y and Fu, A}, title = {Integrated metagenomic and phosphorus fractionation analyses elucidate the mechanism driving soil phosphorus immobilization under erythromycin stress.}, journal = {Ecotoxicology and environmental safety}, volume = {323}, number = {}, pages = {120630}, doi = {10.1016/j.ecoenv.2026.120630}, pmid = {42566873}, issn = {1090-2414}, abstract = {Erythromycin (EM) is widely detected in agroecosystems, yet its mechanistic impact on microbially driven soil phosphorus (P) cycling remains limited. Here, we integrated Hedley P fractionation with metagenomic sequencing in soil microcosms exposed to EM (0, 10, and 50 mg/kg) to track changes in P fractions, microbial community, and functional genetic potential. Our results revealed that EM caused significant P immobilization, reducing bioavailable P by 34.7-46.2% and active organic P by 22.8-24.3%, respectively, compared to the treatment without EM. This immobilization was also accompanied by a 12.14-20.61% decrease in acid and alkaline phosphatase activities. Concurrently, EM restructured the microbial community, specifically reducing key P-cycling genera such as Solirubrobacter, Gemmatimonas, Gaiella, and Blastococcus, while enriching Steroidobacter and Bacteroidota. Crucially, metagenomic analysis revealed that EM suppressed the core genes central to purine metabolism (purB, purH, purF, and purL), pyrimidine metabolism (phyH and nrdB/F), and pyruvate metabolism (pckG and ppdK), as well as the two-component regulatory system (SenX3 and RegX3). These suppression genes are significantly correlated with labile P pools, indicating a direct link between genetic perturbation and P bioavailability. Although EM increased alternative P-acquisition genes, such as gcd and phnA, this response appeared insufficient to compensate for the suppression of core P-cycling functions. Collectively, our findings indicate that EM exposure impairs soil P cycling by reducing core P-cycling genes and taxa, suppressing enzymatic P mineralization, and triggering compensatory responses. This link between suppressed microbial genes and impaired soil P cycling contributes to understanding how antibiotics may induce functional degradation.}, } @article {pmid42566926, year = {2026}, author = {Carvalho, LB and da Silva, GR and de Oliveira Franzote, VH and Larcerda-Júnior, GV and Fernandes-Júnior, PI and Oliveira, VM and Matteoli, FP}, title = {Marked dominance of Actinomycetota and compositional shifts in bacterial communities in Brazilian dryland soils under land-use change.}, journal = {Microbiological research}, volume = {313}, number = {}, pages = {128660}, doi = {10.1016/j.micres.2026.128660}, pmid = {42566926}, issn = {1618-0623}, abstract = {Tropical dry forests are among the most threatened and least studied tropical forest ecosystems worldwide. The Caatinga, the largest tropical dry forest in South America, comprises preserved and agriculturally impacted areas, providing a valuable model system to investigate how semiarid soil bacterial communities respond to natural seasonality and land-use change. Here, we evaluated how land-use and seasonality shape microbial community structure and ecological strategies in soils from conserved forest (CEF) and agriculture-influenced areas (BEF) across rainy and dry seasons using a contig-based taxonomy approach combined with ANCOM-BC2 differential abundance analysis and co-occurrence networks inference. A total of 74 phyla and 1015 genera were identified, with marked predominance of Actinomycetota (61.4%). Seasonal responses were mainly detected in BEF, where Trebonia and Mycobacterium were enriched during the dry season, while Solirubrobacter was more abundant in the rainy season. Taxa putatively associated with plant growth promotion and biological soil crust formation were consistently detected in both areas, whereas oligotrophic and methanotrophic groups were more enriched in CEF and taxa related to biocontrol potential were more represented in BEF. The proportion of seasonal generalists was higher in CEF than in BEF, representing 86.0% and 46.6% of the detected taxa, respectively, suggesting greater temporal stability in conserved soils. Co-occurrence networks revealed that CEF exhibited a sparser and more modular structure, whereas BEF displayed a highly interconnected network. Notably, all module hubs belonged to Actinomycetota. Together, these findings demonstrate that land-use intensification reshapes bacterial ecological strategies and network organization, reducing community heterogeneity under agricultural management.}, } @article {pmid42566957, year = {2026}, author = {Qi, S and Wu, Z and Ni, P and Hou, J and Chen, S and He, R}, title = {Pulsed oxygen supplementation for toluene biodegradation in groundwater with coexisting nitrate: Kinetics and metabolic pathway.}, journal = {Water research}, volume = {306}, number = {}, pages = {126631}, doi = {10.1016/j.watres.2026.126631}, pmid = {42566957}, issn = {1879-2448}, abstract = {Pulsed air sparging can supplement oxygen to effectively stimulate biodegradation of toluene in groundwater. However, nitrate, commonly coexisting with toluene, can compete with oxygen for electron donors, while this specific influence on toluene degradation kinetics and metabolic pathway is still unclear. In this study, the influence of nitrate on toluene degradation during pulsed oxygen supplementation was investigated at different pulsed levels with the initial headspace concentration of 5% (O5), 10% (O10) and 21% (O21). Results showed that the average first-order toluene biodegradation rate coefficients in O5, O10 and O21 were 0.14, 0.50 and 0.73 h[-1], respectively, suggesting that oxygen greatly enhanced toluene biodegradation. Nitrite was initially accumulated in O10, which was further consumed after toluene supplementation. A numerical model was developed to simulate the degradation kinetics of toluene, demonstrating that the degradation rate coefficient of toluene by oxygen was >10 times higher than nitrate. Additionally, when the supplemented oxygen was insufficient (O5), nitrate and nitrite acted as important electron acceptors. Under such conditions, toluene might be anaerobically oxidized to benzoyl-CoA, which underwent ring-opening reactions by the regulation of badDEFG, bamBC and boxAB. When the supplemented oxygen was sufficient (O10 and O21), toluene might be degraded aerobically into catechol and dihydroxybenzoic acid, which further underwent ring-opening reactions associated with dmpB, catAE, pcaGH, chqB and ligAB. The proposed degradation pathway was supported by the detection of selected intermediates including o-cresol, benzoic acid and hydroxybenzoic acid. These findings provide insights into the toluene degradation pathway and mechanism during pulsed oxygen supplementation.}, } @article {pmid42554585, year = {2026}, author = {Yang, Y and Olah, P and Salava, A and Barker, J and Lauerma, A and Andersson, B and Fyhrquist, N and Homey, B and Alenius, H}, title = {Multi-omics analyses reveal host-microbe interactions in atopic dermatitis and psoriasis.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {}, number = {}, pages = {}, doi = {10.1111/jdv.70654}, pmid = {42554585}, issn = {1468-3083}, support = {261366//FP7 Health/ ; 821511//Innovative Medicines Initiative 2 Joint Undertaking/ ; }, abstract = {BACKGROUND: Atopic dermatitis (AD) and psoriasis (PSO) are chronic inflammatory skin diseases that impose substantial physical and psychological burdens. Although fungal-bacterial balance is important for skin immune homeostasis, the role of the skin mycobiome and its interaction with bacterial communities and host immunity in these diseases remains poorly understood.

OBJECTIVES: To characterize alterations in the skin mycobiome and its interactions with bacterial communities and host immune responses in AD and PSO.

METHODS: Adult patients with chronic AD, plaque-type PSO and healthy volunteers were included in this study. Skin microbiota samples and biopsies were collected from lesional and non-lesional skin areas, including the posterior thigh for AD and the lower back for PSO. Whole-metagenome shotgun sequencing was used to profile microbial communities. SparCC was used to construct fungal-bacterial co-occurrence networks, and integration of host transcriptomic and microbial features was performed using O2PLS.

RESULTS: Both AD and PSO showed disease-associated restructuring of Malassezia species and reduced fungal-bacterial ecological connectivity in lesional skin. In AD, Malassezia arunalokei was inversely associated with Staphylococcus aureus and linked to antimicrobial peptide-centred host gene modules enriched for IL-17 signalling. Its abundance decreased with increasing disease severity and inversely correlated with inflammatory immune cell signatures. In PSO, altered Malassezia composition was associated with IL-17-driven transcriptional programmes and lipid metabolic pathways, suggesting interactions between fungal imbalance and inflammatory-metabolic processes.

CONCLUSIONS: Our findings expand current models of skin dysbiosis beyond bacteria and suggest that disrupted fungal-bacterial interactions are linked to immune activation in AD and PSO and, in AD, to disease severity. Although further validation is required, skin microbiome features may provide clinically relevant information for disease monitoring, patient stratification and future microbiome-informed therapeutic strategies. Our study lays the groundwork for microbiome modulation as a potential therapeutic strategy for AD and PSO.}, } @article {pmid42554630, year = {2026}, author = {Tandon, A and Bais, AK and Shrinet, J and Tripathi, V and Gupta, D}, title = {Effect of alcohol and smoking on methamphetamine users' oral microbiome and metabolome.}, journal = {The American journal of drug and alcohol abuse}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/00952990.2026.2697752}, pmid = {42554630}, issn = {1097-9891}, abstract = {Background: The oral microbiome comprises the microbial communities inhabiting the oral cavity, whereas the oral metabolome reflects the small molecules generated by host and microbial metabolic activity. These systems may provide insight into substance-related physiological disruption, including altered inflammation, immune signaling, and host - microbial interactions. Although the individual effects of methamphetamine, alcohol, and smoking have been explored, their combined impact on these systems remains largely unexplored.Objectives: To investigate the metabolic and microbiome alterations associated with chronic methamphetamine use in individuals with alcohol and tobacco use.Methods: High-throughput metabolomic and microbiome datasets from methamphetamine users (Males:168, Females: 50), stratified by self-reported tobacco smoking and alcohol use, were analyzed using integrative bioinformatics approaches, including multivariate and pathway enrichment analyses, to identify dysregulated metabolic pathways and microbial alterations across defined subgroups.Results: The study revealed significant upregulation in metabolites like prostaglandin E2 (log-2-fold-change: 2.63, Cohen's D: |~0.881|, p-val: 7.1 × 10[-10]) and glutamylisoleucine (log-2-fold-change: 1.42, Cohen's D: |~0.88|, p-val: 2.5 × 10[-2]). Microbes such as Bacteroides (log-2-fold-change: -4.91, Cohen's D: |~1.95|, p-val: 1.3 × 10[-4]) and Brachymonas (log-2-fold-change: -2.47, Cohen's D: |~1.09|, p-val: 5.8 × 10[-3]) were significantly downregulated. This suggests that long-term concurrent methamphetamine use, alcohol consumption, and smoking are associated with alterations in microbial and metabolic pathways related to oxidative stress, glutathione metabolism, and neuroactive signaling.Conclusions: The oral microbiome and metabolomic profiles may serve as accessible indicators of substance-related biological disruption. They may also help identify clinically relevant targets for monitoring risk, guiding personalized interventions, and developing informed strategies to support recovery.}, } @article {pmid42555106, year = {2026}, author = {Luo, Z and Liu, Y and Wu, H and Xiao, Y and Li, Y and Liu, M and Li, C and Zhu, D and Jin, LN and Dong, T and Yan, W}, title = {Zoo gut plastispheres enable pathogen escape and adaptation.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag207}, pmid = {42555106}, issn = {1751-7370}, abstract = {In zoos, intensive human contact and artificial feeding may create pathways for microplastic (MP) ingestion and gut colonization. We hypothesized that ingested MPs form intestinal plastispheres with elevated pathogenic potential and enhanced environmental persistence. To test this, we surveyed feces from 15 zoo-dwelling species and coupled particle characterization, feces-derived intestinal simulations, metagenomic sequencing, and a subsequent water-exposure experiment. Zoo feces contained more abundant MPs than reported for wild counterparts, with fragments predominating and polyethylene terephthalate (PET)/polystyrene (PS) dominating polymer profiles. MP burdens tracked human-animal interaction patterns, with human-fed species (e.g., Tiger, Elephant) carrying the highest loads (88-212 items/g). MPs supported dense biofilms whose composition diverged from bulk gut communities, exhibiting greater compositional variability and substrate-specific assembly. Metagenomic analyses revealed coordinated enrichment of potentially pathogenic taxa, virulence factor genes (VFGs), and antibiotic resistance genes (ARGs), with ARG profiles dominated by efflux- and inactivation-related mechanisms and tightly associated with mobile genetic elements. Elevated Type II/III/IV/VI secretion systems and effector delivery-related VFGs occurred within extracellular polymeric substance-rich biofilms, suggesting enhanced potential for ARG retention and horizontal gene transfer. During the 35-day aquatic exposure, MP-associated communities persisted longer than non-plastic particle-associated communities and free gut microbiota, suggesting that plastic-specific properties promote microbial persistence. PET/PS plastispheres showed the slowest declines in bacterial activity and favored the persistence of Enterococcus, Enterobacter, and Clostridium. Overall, intestinal MPs in zoo animals may select, enrich, and export high-risk microbiomes, highlighting the need for MP mitigation and evidence-based management of zoos and adjacent ecosystems.}, } @article {pmid42555404, year = {2026}, author = {Hosen, MA and Rahman, T and Rahatuzzaman, and Kabir, RB and Ahsan, CR and Rahman, M and Yasmin, M and Jubair, M}, title = {Uncovering the Hidden Diversity and Antimicrobial Resistance of Uropathogens in a Tertiary-Care Hospital in Bangladesh.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {8327078}, pmid = {42555404}, issn = {1687-918X}, abstract = {Urinary tract infections (UTIs) are among the most common bacterial infections worldwide; however, their diagnosis in low- and middle-income countries often relies on conventional culture and biochemical methods with limited sensitivity. This study evaluated the limitations of routine diagnostic approaches and explored the microbial diversity and antimicrobial resistance (AMR) profiles of uropathogens in a tertiary-care hospital in Bangladesh using integrated culture-based and molecular methods. Among 30 patient urine samples collected in 2025, 10 were selected for detailed analysis due to funding and resource limitations; therefore, the findings should be interpreted as exploratory and may be subject to selection bias. Of these 10 samples, routine hospital diagnostics identified only eight isolates, whereas extended biochemical analysis detected 29 isolates, indicating substantial underestimation of microbial diversity in standard practice. Antibiotic susceptibility testing revealed a high prevalence of multidrug resistance, with 83% and 80% of isolates resistant to ampicillin and clindamycin, respectively. In contrast, nitrofurantoin and fosfomycin retained effectiveness against most isolates, supporting their continued clinical utility. 16S rRNA gene sequencing further revealed complex and heterogeneous microbial communities, with several samples dominated by Escherichia-Shigella, whereas others exhibited polymicrobial profiles including commensal and opportunistic genera. Despite taxonomic variability, microbial diversity did not differ significantly between inpatient and outpatient groups. Functional pathway prediction demonstrated a largely conserved metabolic profile across samples, including pathways associated with virulence, iron acquisition, and AMR. Overall, this study demonstrates that conventional diagnostic methods substantially underestimate uropathogen diversity and may contribute to misdiagnosis and inappropriate antibiotic use. Integrating molecular approaches into routine clinical workflows could improve pathogen detection, enhance AMR surveillance, and support more effective management of UTIs in Bangladesh and similar resource-limited settings.}, } @article {pmid42555569, year = {2026}, author = {Vitry, G and Angdisen, J and Arriaga, P and Irgen-Gioro, S and Sawant, MA and Vuong, DC and Ilhardt, P and Fehr, J and Cwikla, B and Ponnaiya, B and Inman, JL and Mao, JH and Snijders, AM and Hamid, S and Caballero-Lima, D and Garty, G and Apfeldorf, K and Laiakis, EC}, title = {Monitoring radiation exposure through skin swab multi-omic profiling.}, journal = {PloS one}, volume = {21}, number = {8}, pages = {e0354734}, pmid = {42555569}, issn = {1932-6203}, mesh = {Humans ; *Skin/radiation effects/metabolism/microbiology ; Animals ; Multiomics ; Mice ; Metabolomics/methods ; *Radiation Exposure/analysis ; Metabolome/radiation effects ; Lipidomics ; Skin Microbiome ; }, abstract = {Exposure to ionizing radiation poses major health risks across medical, occupational, and spaceflight settings, driving the need for rapid, non-invasive biodosimetry tools. As the body's most accessible organ and the most frequent site of radiation injury, the skin represents a promising interface for monitoring exposure. Using colonized human skin equivalents (coHSE; 0 Gy n = 8, 1 Gy n = 6, 4 Gy n = 6) and mice (n = 6/group) models, we performed multi-omic profiling, integrating metabolomics, lipidomics, and metagenomics, on skin swab samples collected after exposure to 0, 1, or 4 Gy of x-rays. We identified two distinct metabolite panels: one discriminating irradiated from non-irradiated skin, and another distinguishing dose-specific response. These panels included conserved radiation-responsive metabolites (e.g., uric acid, xanthine, taurine) and skin-specific markers associated with barrier integrity (e.g., proline, arginine). Diacylglycerol network enrichment and shifts in radioprotective microbial taxa, including Lachnospiraceae and Lactobacillales, further supported a repair-driven molecular response. These data support the feasibility of skin swab signatures for non-invasive exposure classification, providing a molecular and microbial framework for skin based monitoring measure development and motivating validation in human cohorts for real-world biodosimetry.}, } @article {pmid42556262, year = {2026}, author = {Dai, W and Yang, F and Chen, W and Liu, C and Henawy, AR and Liu, X and Huang, F and Cai, M and Zheng, L and Yu, Z and Gong, Y and van Huis, A and Zhang, J and Cheng, W}, title = {Paenibacillus polymyxa drives root fatty acyl metabolites-rhizosphere Pseudomonas abundance interaction to suppress root-knot nematode disease in tomato.}, journal = {Microbiological research}, volume = {312}, number = {}, pages = {128662}, doi = {10.1016/j.micres.2026.128662}, pmid = {42556262}, issn = {1618-0623}, abstract = {Root-knot nematodes (RKNs) pose a severe threat to global agricultural production, highlighting the urgent need for effective biocontrol agents. However, the mechanisms by which biocontrol agents suppress RKNs in complex soil environments remain poorly understood, which hinders the development and practical application of these agents. In the present study, the application of Paenibacillus polymyxa KM2501-1 significantly reduced RKN disease, with a control efficacy of 69.89%. Metabolomics analysis revealed that the biocontrol agent P. polymyxa altered the composition of tomato root exudates, leading to the identification of a key fatty acyl metabolite 8-methylnon-6-enoic acid. Specifically, P. polymyxa increased the abundance of 8-methylnon-6-enoic acid, which exhibited repellent activity against RKNs in vitro and suppressed RKN infection in situ. Metagenomic analysis further demonstrated that P. polymyxa reshaped the tomato rhizosphere microbial community and promoted the enrichment of Pseudomonas putida, particularly its representative strains PR035 and PR036. Both strains exhibited significant biocontrol efficacy against Meloidogyne incognita. A significant positive correlation was observed between the levels of key metabolite 8-methylnon-6-enoic acid and the abundance of P. putida, and their combined application exhibited effective control against M. incognita. Overall, this study demonstrates that the suppression of RKNs by P. polymyxa is associated with triggering the exudation of fatty acyl metabolites from tomato roots and enriching rhizosphere Pseudomonas populations. These findings provide valuable insights into the interplay between root metabolites and the rhizosphere microbiome in mediating synergistic plant disease control, offering a theoretical basis for the development of next-generation microbial nematicides.}, } @article {pmid42556698, year = {2026}, author = {Li, E and Xie, X and Zhang, Y and Yan, L and Wang, Y}, title = {Sediment heterogeneity drives divergent arsenic transformation pathways through organic matter-microbial coupling in aquifers.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {408}, number = {}, pages = {128911}, doi = {10.1016/j.envpol.2026.128911}, pmid = {42556698}, issn = {1873-6424}, abstract = {Arsenic (As) speciation in groundwater is controlled not only by aqueous redox chemistry but also by sedimentary matrices that preserve organic matter, structure metabolism, and regulate Fe-S-As coupling. However, how sedimentary organic matter (SOM) and microbial functional differentiation jointly direct arsenic toward thioarsenate formation and methylation remains insufficiently constrained. This study combined sedimentological characterization, X-ray diffraction mineralogical analysis, Fe/As sequential extraction, excitation-emission matrix fluorescence spectroscopy, FT-ICR-MS molecular characterization of SOM, and metagenomic sequencing across three hydrogeochemical zones. Sediments shifted from coarse-grained alluvial deposits in the low-As recharge zone (ALZ) to fine-grained, organic-rich lacustrine sediments in the thioarsenate-enriched zone (HGD) and the methylation zone (SHX), with clay enrichment in HGD and carbonate enrichment in SHX. Along this gradient, ALZ showed open recharge conditions with labile SOM and dynamic redox environments, whereas As in HGD and SHX shifted from surface-bound forms to poorly crystalline and crystalline Fe-associated fractions, alongside SOM evolution toward humified, aromatic, highly unsaturated, and sulfur-containing molecules. The HGD exhibited enrichment of polyphenols and CHOS/CHONS compounds, providing substrates and redox-active ligands for Fe-S-As coupling. Metagenomics revealed zone-specific functional differentiation. The ALZ was dominated by Proteobacteria supporting heterotrophic metabolism, sulfur oxidation, and arsenic resistance. The HGD showed enhanced sat-aprAB-dsrAB pathways and weakened soxABCDXYZ-mediated sulfur oxidation, favoring reduced sulfur accumulation, Fe-As mineral sulfidation, and thioarsenate formation. The SHX displayed enrichment of arsC and arsenic resistance/efflux genes, supporting As(V) reduction and methylated As transformation. These results demonstrate that sediment heterogeneity governs As speciation and migration through coupled SOM evolution and microbial functional reorganization.}, } @article {pmid42557068, year = {2026}, author = {, and , }, title = {[Chinese expert consensus on the diagnosis and treatment of pneumoconiosis complicated with tuberculosis].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {49}, number = {8}, pages = {821-833}, doi = {10.3760/cma.j.cn112147-20260512-00273}, pmid = {42557068}, issn = {1001-0939}, support = {NHC202309//Open Project of NHC Key Laboratory of Pneumoconiosis/ ; 2022YFC2302900//National Key Research and Development Program/ ; }, mesh = {Humans ; *Pneumoconiosis/diagnosis/complications/therapy ; *Tuberculosis, Pulmonary/diagnosis/complications/therapy ; China ; }, abstract = {Pneumoconiosis complicated with pulmonary tuberculosis is characterized by high prevalence and disability rates, as well as difficulty in early diagnosis, constituting a serious public health problem. The Chinese Society of Tuberculosis (Chinese Medical Association) and the Society of Labor Hygiene and Occupational Diseases (Chinese Preventive Medicine Association) organized multidisciplinary experts in respiratory diseases, occupational diseases, tuberculosis and other related fields to formulate the Chinese expert consensus on the diagnosis and treatment of pneumoconiosis complicated with tuberculosis. This consensus aims to enhance professional practitioners' understanding of the disease, improve the capacity for early clinical diagnosis, and further advance the prevention and treatment of pneumoconiosis complicated with pulmonary tuberculosis in China. It summarizes 12 key clinical issues and proposes 13 targeted recommendations to address difficulties and misconceptions in clinical practice. This consensus was registered on the International Practice Guidelines Registry Platform (PREPARE-2024CN271). It aims to enhance the standardized diagnosis and treatment of pneumoconiosis complicated by pulmonary tuberculosis, improve patient outcomes, and provide practical guidance for the prevention and control of occupational and infectious diseases in China. The main recommendations are as follows.Recommendation 1: Clinicians and pathologists are advised to pay attention to the mixed pathological features of pneumoconiosis complicated with pulmonary tuberculosis. For patients with pneumoconiosis presenting atypical imaging manifestations or poor response to conventional treatment, pathological specimens should be actively obtained to confirm the diagnosis. Combined use of acid-fast staining, Mycobacterium tuberculosis culture or molecular pathological detection is recommended to increase the detection rate (2C).Recommendation 2: When performing chest CT examinations and dynamic follow-up for pneumoconiosis patients, clinicians and radiologists should focus on multifocal and polymorphic lesions, as well as short-term imaging changes suggestive of active tuberculosis (2C).Recommendation 3: For patients with suspected pulmonary tuberculosis complicated with pneumoconiosis: (1) Be aware that sputum bacteriological tests may yield false-negative results due to dust interference. Repeated sampling or combined detection methods are recommended, including bacteriological and molecular tests on bronchoalveolar lavage fluid (BALF) obtained via bronchoscopy. Results of immunological assays such as the interferon-γ release assay (IGRA) and tuberculin skin test (TST)shall also be combined for comprehensive judgment. (2) In cases with atypical imaging findings and clinical symptoms, bronchoscopy-guided pathological sampling (e.g., EBUS-GS [endobronchial ultrasound with guide sheath], ENB [electromagnetic navigation bronchoscopy]) is prioritized. When microbiological evidence is insufficient, percutaneous lung biopsy or pleural biopsy (for patients with pleural effusion) is suggested to clarify the diagnosis (2B).Recommendation 4: The diagnosis of pneumoconiosis complicated with pulmonary tuberculosis shall follow the integrated diagnostic principle. Provided that patients meet the national diagnostic criteria for pneumoconiosis and pulmonary tuberculosis respectively, a comprehensive assessment shall be conducted combining occupational exposure history, dynamic imaging changes and laboratory results. Patients shall be stratified for managementaccording to the activity of tuberculosis (2C).Recommendation 5: For differential diagnosis between pneumoconiosis complicated with pulmonary tuberculosis and non-tuberculous mycobacterial (NTM) lung disease: (1) NTM lung disease commonly involves the apical and anterior segments of the upper lobes, the right middle lobe and the lingular segment of the left upper lobe. Typical imaging manifestations include a combination of centrilobular nodules and bronchiectasis. (2) Multiple thin-walled cavities are frequently seen in silicosis complicated with NTM lung disease. (3) Pathologically, NTM lesions are dominated by epithelioid granulomas with inconspicuous caseous necrosis. (4) Definitive diagnosis relies on mycobacterial culture and species identification, complying with combined clinical, imaging and microbiological criteria (2C).Recommendation 6: For patients with pneumoconiosis complicated with pulmonary tuberculosis who present progressively enlarged cavities or newly developed cavities accompanied by aggravated symptoms after anti-tuberculosis treatment, radiologists shall evaluate imaging signs of pulmonary aspergillosis, such as the early halo sign and the late air crescent sign within cavities (2C).Recommendation 7: For patients with suspected pneumoconiosis complicated with pulmonary aspergillosis: (1) Bronchoscopy is performed to collect BALF or tissue specimens for fungal culture and pathological examination (gold standard). (2) Conduct BALF galactomannan (GM) test, metagenomic next-generation sequencing (mNGS) or other DNA detection assays. (3) Detect serum specific antibodies against Aspergillus fumigatus (e.g., IgE-m3, IgM) (1A).Recommendation 8: For patients with pneumoconiosis complicated with drug-susceptible pulmonary tuberculosis: (1) Adopt the standard first-line four-drug anti-tuberculosis regimen. (2) Ensure a sufficient treatment course (generally ≥6-8 months). (3) Extend the treatment course to≥9-12 months for patients with severe lesions or concomitant tracheal, pleural or extrapulmonary tuberculosis, so as to improve clinical outcomes and reduce recurrence (2A).Recommendation 9: For patients receiving concurrent treatment for pneumoconiosis (including tetrandrine, nintedanib, pirfenidone, glucocorticoids, bronchodilators, etc.) and rifampicin-containing anti-tuberculosis regimens: (1) Be aware that rifampicin, a potent hepatic enzyme inducer, may accelerate the metabolism of concomitant drugs such as glucocorticoids and nintedanib and reduce their efficacy. (2) Adjust the dose of affected drugs accordingly when rifampicin is initiated or discontinued (1B).Recommendation 10: Extracorporeal membrane oxygenation (ECMO) may be used as a bridge to lung transplantation only for end-stage pneumoconiosis patients complicated with pulmonary tuberculosis awaiting transplantation (2D).Recommendation 11: For end-stage patients with pneumoconiosis complicated with pulmonary tuberculosis who have received adequate and standard anti-tuberculosis therapy, the feasibility of lung transplantation shall be evaluated. Pre-transplant precautions: (1) Ensure complete control of active tuberculosis. (2) Optimize the anti-tuberculosis regimen (e.g., replace rifampicin with rifabutin) to maintain the effective concentration of immunosuppressants (2D).Recommendation 12: For patients with severe, end-stage pneumoconiosis complicated with pulmonary tuberculosis who no longer benefit from active treatment, palliative care and hospice care shall be initiated. Clinicians and medical teams shall communicate fully with patients and their families about the condition, prognosis, treatment options and medical burden. The core goals are to relieve symptoms, alleviate suffering and improve quality of life (2D).Recommendation 13: For patients with pneumoconiosis complicated with tuberculosis who meet the indications for surgical or interventional therapy, a multidisciplinary team shall conduct joint decision-making and implement treatment in a timely manner after full assessment of pulmonary function, nutritional status and surgical risks. Surgical treatment is mainly indicated for patients with drug-resistant tuberculosis with localized lesions, persistent cavitary lesions with ongoing mycobacterial excretion, destroyed lung, massive hemoptysis unresponsive to medical treatment, tuberculous empyema and other critical conditions. Interventional therapy can be applied for emergency treatment of massive hemoptysis, as well as palliative treatment for pulmonary artery stenosis secondary to tuberculosis or pneumoconiosis (2C).}, } @article {pmid42557256, year = {2026}, author = {Gicquel, M and Planillo, A and Heitlinger, E and Forslund-Startceva, SK and Kramer-Schadt, S and Ferreira, SCM and Jarquín-Díaz, VH}, title = {Farming practices exert selection pressures on the resistome of natural populations of house mice.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42557256}, issn = {2041-1723}, support = {FO1279/6-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; HE7320/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KR4266/4-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; F01KI1909A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 01KI2404B//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, mesh = {Animals ; Mice/microbiology ; *Selection, Genetic ; Anti-Bacterial Agents/pharmacology ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Livestock/microbiology ; Genes, Bacterial ; *Agriculture ; Germany ; Swine ; }, abstract = {The factors maintaining antimicrobial resistance genes (ARGs) in non-domesticated animal microbiomes remain unclear for species inhabiting human-dominated or less human-impacted landscapes. We analysed 875 gut metagenomes from natural populations of house mice (Mus musculus) on German farms between 2016 and 2022 to identify environmental and host determinants of ARG occurrence. Using joint species distribution models, we quantified the influence of landscape, climate and mouse associated characteristics on the occurrence of individual ARGs and on trait dependence among genes. Environmental variables and livestock farming intensity explained 27% of ARG variation, whereas host characteristics accounted for 8%. Analysis of ARG traits revealed that agricultural land use and exposure to livestock increased the occurrence of potentially mobile ARGs. Pig density was strongly associated with an integron-encoded sulfonamide resistance gene (sul1) and genes conferring tetracycline (tet) and beta-lactam resistance (cblA-1) (posterior probability 0.75). Consistently, mouse resistomes have a distinctive resistome, but share more than 50% of ARGs with livestock manure, including widespread genes and those promoted in livestock. Here, we show that landscape conditions, particularly farming intensity, shape the distribution of specific ARGs and potentially mobile ARGs in house mice microbiomes.}, } @article {pmid42557544, year = {2026}, author = {Martínez-Cuesta, R and Craighero, A and Walch, S and Helmreich, B and Schloter, M and Schulz, S}, title = {Urban green roofs host intrinsic resistomes shaped by management but not dominated by pathogenic resistance.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42557544}, issn = {1471-2180}, mesh = {Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Cities ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Metagenomics/methods ; Plasmids/genetics ; Biodiversity ; }, abstract = {BACKGROUND: Urban green roofs are increasingly introduced to enhance urban biodiversity and ecosystem services, yet their role in shaping antimicrobial resistance in cities remains unclear. Using long-read metagenomic sequencing, we characterized antimicrobial resistance genes (ARGs) across an experimental extensive green roof system with plots under four different management regimes specifically designed to test the influence of vegetation and organic amendments, as green waste, which although widely used to improve substrate quality, has been flagged as a potential ARG source.

RESULTS: We detected 62 ARGs across the four management regimes, which were dominated by target-modification and mixed mechanisms conferring resistance to naturally occurring antibiotics such as bacitracin (bacA) and rifamycin (arr, rox, rph), rather than efflux-based multidrug resistance, which is typically co-selected by anthropogenic pollutants. The ARGs were mainly chromosomally encoded, with only two ARGs located on plasmids, and associated with non-pathogenic environmental taxa. The management regime had a significant effect on ARG richness, ARG composition and plasmid abundance, but not on average genome size-normalized ARG abundance. We also detected aph3-II and tlmA as enriched in the unamended samples, which were carried by oligotrophic bacteria, pointing towards microbial competition in a nutrient-limited environment.

CONCLUSIONS: Overall, our findings indicate that green roof management supports a substrate resistome driven by ecological constraints rather than clinical threats. However, further research is required to evaluate potential risks and support the safe integration of green roofs within a One Health framework.}, } @article {pmid42557545, year = {2026}, author = {Rodríguez Del Río, Á and Cui, Y and Mansour, I and Rillig, MC}, title = {Genomic characteristics and geographical distribution of uncultivated soil prokaryotes.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {42557545}, issn = {1471-2164}, mesh = {*Soil Microbiology ; Metagenomics ; Metagenome ; *Bacteria/genetics/classification ; *Genome, Bacterial ; *Genomics ; Phylogeography ; Phylogeny ; *Prokaryotic Cells ; *Archaea/genetics/classification ; }, abstract = {Most soil prokaryotic species remain uncultivated, limiting our understanding of the terrestrial microbiome. Metagenomic sequencing, and particularly the study of metagenome-assembled genomes (MAGs), represents an unprecedented opportunity to characterize the genomic features and biogeography of uncultivated prokaryotic taxa at the large scale. Here, we analyze 40,039 genomic bins from cultivated and uncultivated soil taxa within the SMAG catalog, and examine the occurrence of uncultivated prokaryotes in 9,012 metagenomic samples from the Sandpiper resource. Compared to genera with cultivated representatives, uncultivated soil prokaryotes show smaller genomes, lower G + C content, tendency to acidophilic, non-alkaline, thermophilic and host-associated lifestyles, and slower growth rates, with the latter having the highest predictive power for cultivation status. Uncultivated soil microbes also show unique gene repertoires, characterized by a depletion of biosynthetic and motility genes. We also show that completely uncultivated genera are more abundant in tropical and arctic soils, indicating substantial hidden diversity in these regions. Our work emphasizes that current cultivation efforts systematically fail to capture a particular fraction of soil prokaryotic diversity, and provides guidelines for future cultivation strategies.}, } @article {pmid42557906, year = {2026}, author = {Teklay, YT}, title = {Integrative Bioinformatics Approaches in Environmental Biotechnology: A Review.}, journal = {TheScientificWorldJournal}, volume = {2026}, number = {1}, pages = {e3495506}, pmid = {42557906}, issn = {1537-744X}, mesh = {*Computational Biology/methods ; *Biotechnology/methods ; Multiomics ; Genomics ; Biodegradation, Environmental ; }, abstract = {Environmental biotechnology increasingly relies on bioinformatics to address global challenges in pollution control or degradation, biodiversity conservation, and sustainable resource management. By integrating genomics, computational tools, and artificial intelligence, bioinformatics enables the analysis of complex biological datasets, such as metagenomes and environmental DNA (deoxyribonucleic acid), to uncover microbial diversity, pollutant degradation pathways, and ecological resilience. High-throughput sequencing technologies and multiomics integration provide novel insights into microbial communities and their functional roles in bioremediation and ecosystem monitoring. Predictive modeling further enhances our ability to simulate microbial behavior in contaminated environments and assess the long-term impacts of biotechnological interventions. Despite increased progress, challenges remain in managing large-scale data, fostering interdisciplinary collaboration, and developing user-friendly bioinformatics platforms. Future directions emphasize the application of machine learning, sustainable resource management, and collaborative frameworks to bridge bioinformatics and environmental sciences. Unlike traditional descriptive reviews, this work provides a critical evaluation of the functional gaps between genomic potential and in situ microbial activity. It offers a novel synthesis of how multiomics integration and predictive modeling can move beyond species cataloging toward a more robust, evidence-based framework for environmental sustainability.}, } @article {pmid42558149, year = {2026}, author = {Ding, R and Qi, F and Dai, Q and Li, K and Zhang, Y}, title = {Multi-omics analysis identifies a hepatocyte-associated signature in alcohol-related liver injury.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1844110}, pmid = {42558149}, issn = {1664-3224}, mesh = {Animals ; *Hepatocytes/metabolism ; Multiomics ; Humans ; *Liver Diseases, Alcoholic/metabolism/genetics/etiology ; Mice ; Male ; Ethanol/adverse effects ; Metabolomics/methods ; Transcriptome ; Feces/chemistry/microbiology ; Gene Expression Profiling ; Gastrointestinal Microbiome ; Disease Models, Animal ; Liver/metabolism ; Metabolome ; Mice, Inbred C57BL ; Metagenomics ; }, abstract = {Alcohol-related liver disease (ALD) is a major cause of liver-related morbidity and mortality worldwide, yet the associations linking alcohol-induced gut microbial alterations to metabolic remodeling and hepatocyte dysfunction remain incompletely understood. Here, we applied an integrative multi-omics strategy combining untargeted fecal metabolomics, shotgun metagenomics, mouse liver bulk RNA sequencing, and reanalysis of publicly available human hepatic single-cell and bulk transcriptomic datasets to characterize alcohol exposure-associated gut-liver immunometabolic features. In a mouse model of acute ethanol-induced liver injury, fecal metabolomic and metagenomic profiling revealed marked alterations in microbial functional potential and fecal metabolic composition, identifying six convergent metabolic pathways across fecal multi-omics layers, including nucleotide metabolism, the pentose phosphate pathway, histidine metabolism, glycerophospholipid metabolism, glycine/serine/threonine metabolism, and the phosphotransferase system. Reanalysis of human ALD single-cell transcriptomes showed hepatocyte-enriched activity patterns for several corresponding pathways, suggesting potential pathway-level associations between fecal metabolic alterations and hepatic transcriptional responses. Integrative transcriptomic analysis further identified a ten-gene hepatocyte-associated signature, comprising LRG1, ORM1, ORM2, TAT, HP, FGB, FGG, ITIH3, NNMT, and AGT, which was associated with pathway activity and showed consistent upregulation across acute ethanol-induced liver injury and human ALD/AH transcriptomic datasets. In an external human cohort, this signature stratified patients into exploratory molecular subgroups with distinct metabolic pathway activities and clinical outcome distributions. Collectively, these findings provide a hypothesis-generating multi-omics framework for investigating alcohol-related liver injury and support further validation in chronic ethanol exposure models and functional studies.}, } @article {pmid42558191, year = {2026}, author = {Wu, D and Wang, X and Li, T and Wang, X}, title = {Persistent CD4[+] lymphopenia is associated with recurrent Nocardia farcinica infection and acquired resistance in an AIDS patient: a case report with immunological warning.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1894622}, pmid = {42558191}, issn = {1664-3224}, mesh = {Humans ; Male ; *Nocardia Infections/immunology/drug therapy/diagnosis/microbiology ; Adult ; *Nocardia/drug effects/immunology ; Recurrence ; Anti-Bacterial Agents/therapeutic use ; *Acquired Immunodeficiency Syndrome/immunology/complications/drug therapy ; CD4 Lymphocyte Count ; *Drug Resistance, Bacterial ; *AIDS-Related Opportunistic Infections/immunology/drug therapy/microbiology ; *CD4-Positive T-Lymphocytes/immunology ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; }, abstract = {After severe depletion of CD4 T cells in AIDS patients, they are not only prone to a first-time Nocardia infection, but also, even if cured, unable to form protective immune memory, leaving them susceptible to reinfection with the same pathogen. More seriously, in the absence of immune surveillance, irregular drug use can accelerate the selection of drug-resistant strains. A 32-year-old man with AIDS and persistent CD4+ count below 100 cells/μL for over three years (nadir 2 cells/μL) developed right lower lobe pneumonia caused by Nocardia farcinica four years before the current admission, which was cured with a TMP-SMX-containing regimen. The isolate was sensitive to trimethoprim-sulfamethoxazole (TMP-SMX), and the lesion nearly resolved after treatment. He was prescribed long-term TMP-SMX prophylaxis at discharge but stopped taking it on his own. One year before the current admission, he received sulfadiazine plus pyrimethamine for clinically diagnosed cerebral toxoplasmosis, but his adherence was poor and irregular. On current admission (day 1), he was readmitted with high fever and sepsis. Chest CT showed multiple cavities in the left lower lobe. Blood cultures flagged positive at 25 hours and were identified as Nocardia farcinica. The microbiologist reviewed his old records, found the previous nocardial history, and recommended bronchoalveolar lavage (BAL). BAL metagenomic next-generation sequencing again identified Nocardia farcinica, but susceptibility testing now showed resistance to TMP-SMX (MIC ≥8/152). He improved after switching to imipenem plus amikacin. He received intravenous imipenem plus amikacin for 14 days, followed by oral linezolid for 6 weeks. At the last follow-up (approximately one year after discharge), his CD4[+] had risen to only 11 cells/μL, and he had no further nocardial infection. This case shows that when CD4[+] stays below 100 for a long time, even a first nocardial infection can be cured but may leave insufficient immune memory, rendering the patient susceptible to subsequent infection. The distinction between true reinfection and late relapse could not be definitively established in the absence of strain-level homology data. Irregular, sub-therapeutic sulfonamide exposure, combined with a non-functional immune system, can select for resistant strains.}, } @article {pmid42558207, year = {2026}, author = {Yang, Y and Ren, L and Zhang, Y and Wang, X and Shang, J and Zhang, L}, title = {Microbiota in cholestatic diseases: crosstalk among bile composition, the biliary microbiome, and host immunity.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1884030}, pmid = {42558207}, issn = {1664-3224}, mesh = {Humans ; Animals ; *Microbiota/immunology ; Bile Acids and Salts/metabolism ; *Cholestasis/microbiology/immunology/metabolism ; *Bile/metabolism/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; }, abstract = {Cholestatic liver diseases are a heterogeneous group of hepatobiliary disorders caused by impaired bile formation, secretion, or excretion, leading to hepatocyte injury, biliary inflammation, fibrosis, and eventually cirrhosis. Traditional studies have largely focused on isolated mechanisms, including bile acid toxicity, immune dysregulation, and genetic susceptibility. However, recent advances in metagenomics, metabolomics, and immunology have highlighted the critical role of the gut and biliary microbiota in disease pathogenesis. This review proposes the core concept of a "tripartite interplay among bile composition, biliary microbiome, and host immunity," integrating the dynamic crosstalk among these three axes in cholestatic liver diseases. Bile composition shapes microbial communities and modulates immune responses through receptors such as FXR and TGR5. In turn, the biliary microbiome regulates bile acid metabolism and immune activity through microbial metabolites. Meanwhile, the host immune system senses microbial signals via pattern-recognition receptors, triggering inflammatory pathways and influencing microbial colonization and metabolism. These reciprocal interactions form complex feedback loops that drive disease progression from early inflammation to chronic fibrosis and cirrhosis. Based on this framework, emerging diagnostic approaches combine microbial signatures, bile acid profiles, and immune markers into multidimensional biomarker systems. Therapeutically, integrated strategies targeting the microbiome, bile acid metabolism, and immune pathways may offer synergistic benefits. Despite challenges including sampling difficulty, interindividual variability, and limitations of current models, future technologies such as single-cell sequencing, spatial transcriptomics, and multi-omics integration may enable precision diagnosis and targeted therapy.}, } @article {pmid42558343, year = {2026}, author = {Liu, L and Lin, J and Sang, K and Lai, J and Huang, N and Zhong, P and Liu, Y and Chen, S}, title = {Bile acid signaling at the gut-vascular interface: a novel modulator of hantavirus endothelial barrier dysfunction.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1883162}, pmid = {42558343}, issn = {2235-2988}, mesh = {Animals ; Humans ; *Orthohantavirus/pathogenicity/physiology ; *Bile Acids and Salts/metabolism ; *Signal Transduction ; Receptor, Farnesoid X-Activated ; Rats ; *Endothelial Cells/virology/metabolism ; Gastrointestinal Microbiome ; *Hantavirus Infections/virology/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; NF-kappa B/metabolism ; Lung/virology/microbiology ; Vascular Cell Adhesion Molecule-1/metabolism/genetics ; }, abstract = {Hantavirus infection triggers life-threatening hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS), driven by severe endothelial barrier breakdown and systemic capillary leakage. Clinical severity varies widely with undefined host regulators, and no targeted endothelial-protective treatments exist. Recent data link hantaviruses to gut microbiome remodeling, while bile acid (BA) receptors FXR and TGR5 potently inhibit NF-κB-mediated endothelial inflammation. We synthesize four core lines of evidence. First, metagenomic reports confirm hantavirus reshapes gut/lung microbiota in rodent reservoirs. Second, we re-analyzed three public GEO datasets via standardized RNA-seq/microarray pipelines: (i) GSE245916: SEOV-infected human/rat lung ECs show conserved VCAM1/ICAM1 upregulation (human VCAM1 log2FC=+1.17, P = 0.023; rat Icam1 log2FC=+0.32, padj=0.016) with unaltered FXR; (ii) GSE7271: SEOV-infected rat lung displays sustained Nfkb1 suppression (all timepoints, P<0.05) and day-15 Slc10a2 downregulation (P = 0.028); (iii) GSE270172: PUUV 3D vessel chips feature robust IL6 elevation (log2FC=+1.22, P = 3.1×10[-8]) and disrupted BA transporters (ABCC3 log2FC=-1.44, P = 7.4×10[-][12]). TGR5 (GPBAR1) was undetectable in endothelial cells across all datasets. Third, FXR/TGR5 agonists repress NF-κB inflammation and mitigate lung vascular injury. Fourth, HTNV upregulates CH25H to block HMGCR-dependent cholesterol synthesis, depleting BA precursor substrates. We propose a unified pathogenic model: hantavirus-triggered gut dysbiosis plus virus-impaired cholesterol metabolism deplete circulating FXR/TGR5 agonistic BAs, relieving constitutive inhibition of endothelial NF-κB and monocyte NLRP3 inflammasomes to exacerbate capillary leakage. We define tiered testable predictions covering clinical multi-omics cohorts, in vitro receptor modulation assays and in vivo pharmacological interventions. This gut microbiota-BA-FXR/TGR5 axis represents a repurposable therapeutic target for hantavirus diseases, though direct causal evidence connecting BA signaling to viral vascular damage remains absent; our framework offers a rigorous testable roadmap for subsequent validation.}, } @article {pmid42559032, year = {2026}, author = {Sun, Y and Li, X and Zheng, X and Sun, X and Liu, J and Zhang, S and Zhang, G and He, W and Huo, W and Zuo, J}, title = {Habitat environment is associated with the microbiota of the human terminal airway.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1887778}, pmid = {42559032}, issn = {1664-302X}, abstract = {While environmental exposures are closely associated with the human microbiome, the microbial landscape of the terminal airways remains largely uncharacterized due to the ethical challenges of tissue sampling. To address this gap, we analyzed surgically resected idiopathic lung bullae (localized developmental anomalies surrounded by otherwise normal tissue) to establish a baseline microbiome atlas. We performed ultra-deep metagenomic sequencing on terminal airway tissues from 60 subjects residing in two climatically distinct Chinese cities: Zhuhai (a subtropical coastal region) and Yinchuan (an arid, high-altitude industrial area on the Qinghai-Tibet Plateau). Our analysis revealed that the high-altitude Yinchuan cohort exhibited significantly higher microbial loads and alpha diversity compared to the coastal Zhuhai cohort. Functionally, the Yinchuan microbiome was enriched in taxa associated with fatty acid beta-oxidation, alongside a markedly higher burden of virulence factors and antibiotic resistance genes. These compositional and functional differences may be associated with regional variation in climate, altitude, and local antibiotic usage patterns, whereas the Zhuhai cohort exhibited greater fungal diversity. Ultimately, this study provides the tissue-resolved microbial atlas of the human terminal respiratory tract and reveals substantial differences in microbial composition and function across distinct habitat environments. Furthermore, these findings suggest a potential association between environmental conditions and variation in resident microbiota, providing a basis for future investigations into how environmental change may influence respiratory microecology and human health.}, } @article {pmid42559092, year = {2026}, author = {Wang, H and Han, X and Zeng, H and Liu, B and Chen, C and Wu, G}, title = {Lumbar postoperative Aspergillus flavus infection after lumbar spondylolisthesis fusion: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1879141}, pmid = {42559092}, issn = {2296-858X}, abstract = {Surgical site infection following lumbar internal fixation and fusion is predominantly bacterial. Aflatoxin-associated discitis is extremely rare in immunocompetent patients and often results in delayed diagnosis and inadequate empirical antimicrobial treatment. This report presents a 74-year-old immunocompetent male patient who underwent elective posterior lumbar interbody fusion for grade II degenerative lumbar spondylolisthesis and developed intractable low back pain 3 months postoperatively. Despite multiple courses of broad-spectrum antibiotic therapy administered at two external hospitals, his symptoms did not resolve. Conventional bacterial, mycobacterial, and fungal cultures, as well as histopathological examination of percutaneous biopsy and intraoperative specimens, yielded negative microbial results. Metagenomic next-generation sequencing (mNGS) specifically identified Aspergillus flavus in all tissue samples, confirming the etiological diagnosis of fungal discitis. The patient received staged combined antifungal and surgical management. Intravenous voriconazole was used for induction therapy, followed by radical debridement of infected spinal tissue, internal fixation revision, and bone graft reconstruction. Oral voriconazole was prescribed for 3 months of postoperative maintenance therapy. A 12-month follow-up showed marked pain relief, and serial imaging and laboratory tests confirmed complete eradication of the infection with no recurrence. This case is systematically compared with previously reported Aspergillus spinal infections in immunocompetent hosts. mNGS serves as a valuable adjunctive diagnostic tool for clinically suspected atypical infections when conventional examinations are negative. Although limited by a single-case, single-center design without statistical generalizability, this report expands clinical recognition of post-fusion fungal discitis in immunocompetent patients and provides practical evidence for precise diagnosis and individualized management of refractory spinal surgical site infections.}, } @article {pmid42559169, year = {2026}, author = {Wang, B and Zhao, M and Chen, Q and Zhang, F and Fan, M and Lian, X}, title = {Severe fever with thrombocytopenia syndrome complicated by invasive pulmonary aspergillosis and septic shock: a case report highlighting the role of mNGS.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1888410}, pmid = {42559169}, issn = {2296-858X}, abstract = {BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne viral hemorrhagic fever associated with high mortality, and no specific antiviral therapy is currently available. Patients with SFTS often develop immune dysfunction, rendering them susceptible to secondary opportunistic infections, particularly invasive pulmonary aspergillosis (IPA). Early diagnosis of this co-infection is critical but remains challenging due to nonspecific clinical manifestations and radiological findings.

CASE PRESENTATION: A 61-year-old male farmer from a hilly region presented in July 2024 with fever, dyspnea, and altered consciousness. On admission, he exhibited septic shock and multiple-organ dysfunction, including severe thrombocytopenia, leukopenia, liver injury, and acute kidney injury. Metagenomic next-generation sequencing (mNGS) of blood and bronchoalveolar lavage fluid rapidly identified SFTS virus, Aspergillus fumigatus, Aspergillus flavus, and multiple Gram-negative bacteria. Chest imaging revealed bilateral nodules distributed along the bronchovascular bundles, suggestive of angioinvasive IPA. Treatment consisted of imipenem/cilastatin, isavuconazonium sulfate, continuous renal replacement therapy, and mechanical ventilation. The patient gradually improved and was discharged after 30 days, with complete clinical recovery documented at the 3-month and 9-month follow-up visits.

CONCLUSION: This case highlights the diagnostic value of mNGS in critically ill patients with SFTS and suspected co-infections, as it enables early pathogen identification and targeted therapy. Clinicians in endemic areas should maintain a high index of suspicion for SFTS and IPA in patients presenting with unexplained fever, thrombocytopenia, and organ dysfunction. However, the favorable outcome cannot be attributed solely to mNGS, as multiple supportive interventions were administered concurrently; the clinical improvement likely reflects a synergistic effect of timely targeted therapy and comprehensive intensive care.}, } @article {pmid42559206, year = {2026}, author = {Viver, T and Gago, JF and Bustos-Caparros, E and Aldeguer-Riquelme, B and Rodriguez Rojas, LM and Ramírez, AS and Albuquerque, L and Amiour, S and Oren, A and Mutlu, MB and Venter, SN and Baxter, BK and Llames, ME and González, B and Rodríguez-Valdecantos, G and Banciu, HL and Stott, MB and Santos, F and Hedlund, BP and Antón, J and Amann, R and Konstantinidis, KT and Rossello-Mora, R}, title = {Metagenomics reveal unrestricted dispersal of extreme halophiles and higher connectivity among coastal vs. inland solar salterns and hypersaline lakes.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag165}, pmid = {42559206}, issn = {2730-6151}, abstract = {Hypersaline environments constitute ideal systems for studying evolutionary processes and microbial diversification due to their relatively low (and thus tractable) diversity and geographically isolated nature. Based on metagenomic sequencing of samples from 25 hypersaline sites in 11 countries taken within a single year, we explored the relationships between environmental factors, geographic distance, and microbial community structure and diversification. Our results revealed that microbial communities of coastal sites were more similar to each other than those of the inland sites, reflecting higher connectivity due to ocean currents and nearly unrestricted dispersal. Conversely, inland hypersaline environments showed less connectivity and higher genetic and taxonomic dissimilarities that did not correlate with the distance between the sampled sites. The latter results reflect reduced species migration characterizing inland sites as well as site-specific environmental factors selecting for divergent taxa. The 484 MAGs recovered, representing 284 distinct species, revealed a striking global ubiquity, with 62.5% of the species showing cosmopolitanism, defined as being present at both coastal and inland sites. Most cosmopolitan species showed allopatric differentiation, reflected by an increased frequency of non-synonymous substitutions between MAGs of the same species recovered from more distant sites. However, a few cases of truly cosmopolitan genomovars (average nucleotide identity, or ANI > 99.8%), were also observed. Our results suggest that extreme halophiles have nearly unrestricted global dispersal among ocean-connected sites, and to a lesser extent, among geographically isolated inland sites, although cases of allopatric diversification were also observed.}, } @article {pmid42559331, year = {2026}, author = {Hajjaji, O and Al-Soudy, AS and Daoud, R and Benhida, R and Mokhtar, MM}, title = {Calibrating tetranucleotide-frequency distances for metagenomic binning with right-skewed distribution models.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag207}, pmid = {42559331}, issn = {2635-0041}, abstract = {SUMMARY: Metagenomic binning is a pivotal step in reconstructing metagenome-assembled genomes (MAGs) from complex microbial communities, and it critically depends on reliable measures of similarity between contigs. In many workflows, tetranucleotide-frequency (TNF) distances are translated into probabilistic evidence of a shared genome of origin. Despite their central role, these distances are often modeled with convenient but poorly matched assumptions, even though they are intrinsically non-negative and frequently exhibit pronounced right-skewness-features that can distort tail behavior and weaken downstream thresholding decisions. In this work, we introduce a likelihood-based framework for characterizing intra- and inter-genomic TNF distance distributions with flexible right-skewed parametric models and for converting fitted distributions into calibrated distance-to-probability scores within a MaxBin-style scheme. Our approach provides a principled statistical basis for distributional assessment, probability calibration, and transparent operating-point selection, with the goal of improving robustness and interpretability in TNF-driven binning.

All codes related to the article are available through a public GitHub repository at https://github.com/omar-hajjaji/Calibrating-TNF-Distances-for-Metagenomic-Binning-with-Right-Skewed-Distribution-Models.}, } @article {pmid42560056, year = {2026}, author = {Bernate, E and Shi, Y and Franck, E and Crofts, TS}, title = {A functionally selected Acinetobacter sp. phosphoethanolamine transferase gene from the goose fecal microbiome confers colistin resistance in E. coli.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0246825}, doi = {10.1128/aem.02468-25}, pmid = {42560056}, issn = {1098-5336}, abstract = {Polymyxins are last-resort antibiotics for infections caused by multidrug-resistant gram-negative bacteria such as Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii. This makes the rise of bacteria exhibiting polymyxin E (colistin) resistance, largely through modification of lipid A moieties, concerning and suggests that it is important to document the potential sources of the corresponding resistance genes. This study searched for potential emerging colistin resistance genes from the environment by investigating a previously performed functional metagenomic selection for colistin resistance of a goose fecal microbiome. We found that the selection captured Acinetobacter sp. DNA fragments that all contained eptA genes. We confirmed their ability to confer significant colistin resistance in Escherichia coli via modification of lipid A in the outer membrane. Furthermore, we found evidence for mobilization of closely related eptA genes in Acinetobacter genomes, marking them as potential mcr genes or their precursors. This study highlights the potential for functional metagenomic selections for colistin resistance to capture genes from unexpected environmental sources such as the goose fecal microbiome.IMPORTANCEColistin is an important antibiotic of last resort, and increasing resistance to this drug via mobile phosphoethanolamine transferase genes, such as mcr-1, threatens its clinical utility. Given the discovery of mcr-1 in pigs, the ability of animals to act as vectors in the spread of colistin resistance is alarming. We show here that functionally selected Acinetobacter phosphoethanolamine transferase genes from the goose microbiome have the ability to confer clinical levels of colistin resistance when transferred into E. coli. While the genes are annotated as eptA homologs, closer study of these genes suggests that they may be mobilized within the Acinetobacter genus, suggesting that they may be mcr genes of concern instead.}, } @article {pmid42560070, year = {2026}, author = {Lambisia, AW and Nyawa, OK and Maina, G and Katama, EN and Mutunga, M and Agoti, CN}, title = {Near-complete genomes from six human coronavirus HKU1-positive samples recovered by metagenomics in coastal Kenya, 2024-2025.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0064226}, doi = {10.1128/mra.00642-26}, pmid = {42560070}, issn = {2576-098X}, abstract = {Human coronavirus HKU1 is globally endemic but genomically understudied. We present six near-complete HKU1 genomes from samples collected in coastal Kenya (2024-2025) that fell into genotypes A (n = 3) and B (n = 3). The data expand the global HKU1 genomic database and will support molecular assay development and phylogeography studies.}, } @article {pmid42560299, year = {2026}, author = {Liang, F and Li, J and Yue, Y and Pan, J and Liu, C and Cheng, D and Zhang, N and Li, K and Chu, F and Wu, H}, title = {Distinct Gut Microbiome and Metabolome Profiles Associate with Differential Responses to Immunotherapy in Colorectal Cancer.}, journal = {Polish journal of microbiology}, volume = {75}, number = {2}, pages = {168-194}, doi = {10.33073/pjm-2026-016}, pmid = {42560299}, issn = {2544-4646}, mesh = {Humans ; *Colorectal Neoplasms/therapy/microbiology/metabolism ; *Metabolome ; *Immunotherapy ; *Gastrointestinal Microbiome ; Female ; Feces/microbiology ; Male ; Middle Aged ; Aged ; Metabolomics ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {The composition of the intestinal microbiome has been identified as a key factor influencing the efficacy of immune checkpoint inhibitors. This study aimed to systematically evaluate the potential associations among gut microbiota, metabolic profiles, and clinical outcomes in patients with MSI-H advanced colorectal cancer (CRC) treated with immunotherapy. Twenty advanced CRC patients receiving immunotherapy were enrolled and categorized into clinical benefit response (CBR) and non-benefit (NCB) groups based on treatment efficacy. Fecal samples were analyzed using metagenomic sequencing and untargeted metabolomics. The results revealed significant enrichments of s_Clostridium unclassified and metabolites such as guanosine, 3-carboxy-4-methyl-5-propyl-2-furanpropionic acid, and quercetin 3-(6"-malonyl-glucoside) in the CBR group, suggesting their potential positive predictive value for immunotherapy response. Conversely, the NCB group showed significant enrichments of s_Roseburia hominis, s_Marseilla massiliensis, and metabolites including pyrophosphate, riboflavin, and PC(22:5(4Z,7Z,10Z,13Z,16Z)/14:0), indicating a possible association with treatment resistance. By integrating fecal metagenomics and metabolomics, this study reveals distinctive "flora-metabolite" interactions linked to therapeutic response in advanced CRC patients undergoing immunotherapy. Specific microbial and metabolic profiles were positively or negatively correlated with immunotherapy outcomes, highlighting their potential not only as predictive biomarkers but also as a theoretical foundation for developing individualized immunotherapy strategies based on microecological modulation.}, } @article {pmid42560300, year = {2026}, author = {He, X and Ma, S and Zhou, Y and Wei, J and Zhuo, Z and Ma, L}, title = {In Vitro Antibacterial Activity of Sulbactam-Durlobactam and Eravacycline Against Carbapenem-Resistant Acinetobacter baumannii in China and Analysis of Sulbactam-Durlobactam Resistance Mechanisms.}, journal = {Polish journal of microbiology}, volume = {75}, number = {2}, pages = {210-219}, doi = {10.33073/pjm-2026-019}, pmid = {42560300}, issn = {2544-4646}, mesh = {*Acinetobacter baumannii/drug effects/genetics ; *Sulbactam/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Carbapenems/pharmacology ; China ; Microbial Sensitivity Tests ; *Tetracyclines/pharmacology ; *Azabicyclo Compounds/pharmacology ; Humans ; Acinetobacter Infections/microbiology ; *Drug Resistance, Multiple, Bacterial ; Drug Resistance, Bacterial ; }, abstract = {The management of carbapenem-resistant Acinetobacter baumannii (CRAB) infections remains a formidable clinical challenge. This study evaluated the in vitro antimicrobial activities of sulbactam-durlobactam (SUL-DUR) and eravacycline (ERV) against CRAB isolates and elucidated the genomic landscapes of resistance and virulence determinants in SUL-DUR-resistant strains to inform therapeutic decision-making. A total of 233 clinical CRAB isolates were collected and screened for susceptibility to SUL-DUR and ERV using the Kirby-Bauer (K-B) disk diffusion assay. Isolates exhibiting resistance to SUL-DUR were further characterized via metagenomic next-generation sequencing (mNGS) to identify key resistance and virulence factors. SUL-DUR and ERV demonstrated robust in vitro activity, with susceptibility rates of 92.3% and 91.4%, respectively. Notably, no isolates exhibited concurrent non-susceptibility to both agents. Genomic analysis of 14 SUL-DUR-resistant strains revealed a complex and heterogeneous distribution of genetic determinants. The presence of bla NDM-1 was identified as a critical driver of SUL-DUR resistance. Additionally, reduced susceptibility was potentially associated with specific mutations in bla OXA-23, bla OXA-66, and bla TEM-1, while hyperactive efflux systems and altered membrane permeability further synergized to enhance the resistance phenotype. Despite the extensive-drug-resistant (XDR) nature of current CRAB isolates, they maintain high sensitivity to SUL-DUR and ERV. Our findings underscore that SUL-DUR and ERV represent highly promising therapeutic options with significant development potential and broad clinical application prospects for the management of CRAB-related infections.}, } @article {pmid42560417, year = {2026}, author = {Gautham, M and Koteswari, P}, title = {Granulomatous amoebic encephalitis: pathogenesis, diagnostic advances, therapeutic challenges, and emerging treatment strategies.}, journal = {Medical microbiology and immunology}, volume = {215}, number = {1}, pages = {}, pmid = {42560417}, issn = {1432-1831}, mesh = {Humans ; *Acanthamoeba/pathogenicity ; *Amebiasis/diagnosis/therapy/drug therapy ; *Balamuthia mandrillaris/pathogenicity ; Blood-Brain Barrier ; *Infectious Encephalitis/diagnosis/therapy ; Animals ; *Central Nervous System Protozoal Infections/diagnosis/therapy ; Antiprotozoal Agents/therapeutic use ; }, abstract = {Granulomatous amoebic encephalitis (GAE) is a rare but highly fatal central nervous system infection caused primarily by Acanthamoeba spp. and Balamuthia mandrillaris. Delayed diagnosis and the absence of standardized treatment protocols contribute to mortality exceeding 90%. This review summarizes current knowledge regarding GAE pathogenesis, diagnosis, therapeutic challenges, and emerging treatment strategies. The pathogenesis involves amoebic adhesion, secretion of proteases and phospholipases, host inflammatory responses, and blood-brain barrier disruption. Recent advances in molecular diagnostics improve early pathogen detection, while drug repurposing, nanotechnology-based delivery systems, and cyst-targeted approaches represent promising therapeutic strategies. Nevertheless, treatment remains challenging because of poor blood-brain barrier penetration, cyst-associated resistance, and limited clinical evidence. Continued integration of molecular diagnostics, mechanistic studies, translational research, and multicentre clinical investigations is essential for improving outcomes in this devastating disease.}, } @article {pmid42560632, year = {2026}, author = {Peng, M and Xu, Y and Cao, X and Xue, Y and Pang, J and Zhou, S and Xu, P and Yang, Y and Zhang, X and Qian, J and Wang, Y and Lu, X and Wan, Y and Sun, Y and Hua, X and Xu, Y and Chen, B and Ouyang, J}, title = {Clinical Research on Microecological Landscape for Infection Risk Stratification in Newly Diagnosed Patients with Hematological Conditions.}, journal = {Infectious diseases and therapy}, volume = {}, number = {}, pages = {}, pmid = {42560632}, issn = {2193-8229}, support = {BE2023656//Jiangsu Provincial Key Research and Development Program/ ; QNX25036//Nanjing Municipal Health Science and Technology Development Special Fund/ ; 2021-LCYJ-MS-19//Clinical Trials from the Affiliated Drum Tower Hospital/ ; 2022-LCYJ-PY-46//Center for Clinical Trials, Japan Medical Association/ ; }, abstract = {INTRODUCTION: Infection is a common and potentially fatal complication during the treatment of hematological diseases, particularly in the context of chemotherapy-induced immunosuppression. The nonselective use of antibiotic prophylaxis in patients with neutropenia in China has persistently accelerated antimicrobial resistance. Early identification of patients at high risk for infection before clinical symptom onset could enable targeted preventive strategies; however, reliable and biologically informed screening approaches remain limited.

METHODS: We developed a prediction model for infection risk stratification in newly diagnosed patients with hematological conditions. Plasma metagenomic next-generation sequencing was performed in a prospective cohort of 230 patients. Among them, 116 patients provided prechemotherapy, non-neutropenic plasma samples (cohort A), and 114 patients provided postchemotherapy, neutropenic samples (cohort B). Microbial community profiles were analyzed, and machine learning approaches were applied to construct classifiers for neutropenia status and subsequent infection risk.

RESULTS: Plasma metagenomic profiling revealed a complex microecological landscape in patients with hematological conditions and identified distinct microbial features associated with neutropenia. A trained random forest classifier successfully distinguished patients without neutropenia from patients with neutropenia, achieving an area under the receiver operating characteristic curve of 0.8324. Importantly, a microorganism-based random forest model was established to predict patients at high risk of infection, yielding an area under the curve of 0.942. Nested cross-validation demonstrated high classification accuracy, correctly identifying 99.1% of patients who subsequently developed infections and 72.7% of patients who remained infection-free. Furthermore, integration of microbial features with clinical metrics improved predictive performance, resulting in an area under the curve of 0.953.

CONCLUSIONS: This microorganism-based prediction model provides an effective tool for infection risk stratification in patients with hematological conditions. By enabling early identification of high-risk individuals, the model has potential clinical utility for guiding precise preventive interventions and optimizing infection management strategies, which can significantly reduce the use of prophylactic antibiotics, thereby mitigating the development of resistance.

REGISTRATION NUMBER: ChiCTR2100042992.}, } @article {pmid42561044, year = {2026}, author = {Du, P and Zhou, M and Wang, L and Zhang, X}, title = {Pharmacist-Led Management of Elizabethkingia Keratitis: Precision Therapy Guided by Culture and mNGS to Improve Clinical Outcomes and Efficiency.}, journal = {Cornea}, volume = {}, number = {}, pages = {}, pmid = {42561044}, issn = {1536-4798}, abstract = {PURPOSE: This study evaluated the clinical efficacy of a pharmacist-led antimicrobial stewardship program augmented by metagenomic next-generation sequencing (mNGS) for managing rare, multidrug-resistant Elizabethkingia keratitis.

METHODS: We conducted a retrospective case series of 5 male patients (mean age 56.4 years) diagnosed with Elizabethkingia keratitis (3 E. meningoseptica, 2 Elizabethkingia anophelis) between 2020 and 2025. Initial microbiological identification relied on corneal scraping culture and MALDI-TOF MS, while mNGS was strategically used in 1 complex case to identify potential copathogens. Clinical pharmacists provided interventions including minimum inhibitory concentration-guided therapy and the extemporaneous preparation of fortified antibiotic eye drops, such as 2% amikacin and 10% piperacillin/tazobactam. We assessed clinical outcomes, visual acuity (LogMAR), and the length of hospital stay.

RESULTS: Although conventional culture confirmed Elizabethkingia species in all cases, mNGS offered critical genomic insights in 1 complex case by detecting culture-negative co-pathogens Nocardia pneumoniae and Fusarium proliferatum, which directly guided the addition of targeted antifungal and antibacterial therapy. All Elizabethkingia isolates demonstrated extensive resistance to carbapenems and cephalosporins. After pharmacist-led interventions, mean visual acuity improved significantly from 1.56 ± 0.77 to 0.90 ± 0.25 LogMAR. Furthermore, the length of hospital stay decreased markedly from 40 days in the index case to an average of 10.7 ± 4.9 days in the final 3 cases as diagnostic and therapeutic protocols were refined.

CONCLUSIONS: Integrating clinical pharmacists within a multidisciplinary team, supported by mNGS for comprehensive polymicrobial detection, enables precision pharmacotherapy for multidrug-resistant Elizabethkingia keratitis. This approach promotes successful ocular salvage and visual recovery while substantially improving clinical efficiency through shortened hospitalization.}, } @article {pmid42561698, year = {2026}, author = {Cai, Y and Zhai, J and Lin, M and Huang, W and Zhang, R and Zheng, CW and Luo, YH and Rittmann, BE}, title = {Biodegradation of potassium amyl xanthate from mining flotation wastewater with minimal CS2 emission.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143195}, doi = {10.1016/j.jhazmat.2026.143195}, pmid = {42561698}, issn = {1873-3336}, abstract = {The mining industry produces significant volumes of flotation wastewater that contains xanthates, such as potassium amyl xanthate (PAX, C6H11OS2K), that pose toxicity risks to ecosystems and humans. In this study, an oxygen-based membrane biofilm reactor (O2-MBfR) was applied to biodegrade high concentrations (75∼200 mg/L) of PAX; the MBfR achieved > 99% removal of PAX with minimal carbon disulfide (CS2) emission at a PAX surface loading rate of 770 mg/m2-d. The microbial community adapted to changing PAX loading and O2 pressure, and it consistently gave efficient removals of PAX and soluble COD, as well as negligible CS2 emission. Metagenomic sequencing revealed that Mesorhizobium, Zoogloea, Sediminibacterium, Afipia, and Devosia were important genera that contributed in different ways to oxidation of PAX, PAX metabolites, and CS2. PAX degradation began with cleavage of C-O or C-S bonds, which was followed by oxidation of sulfur-containing intermediates. Also, the efficient biodegradation of xanthates offers a potential strategy to avoid flotation tailings caused by flotation wastewater reuse.}, } @article {pmid42561992, year = {2026}, author = {Mourik, K and Sidorov, I and Meijers, E and van den Brink, S and Bos, S and Aarts, L and Veetil, NK and Boers, SA and Eggink, D and Meijer, A and de Vries, JJC}, title = {Probe-based metagenomic sentinel surveillance of viral respiratory infections in primary care: a prospective, national, pilot study.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101473}, doi = {10.1016/j.lanmic.2026.101473}, pmid = {42561992}, issn = {2666-5247}, abstract = {BACKGROUND: With the introduction of metagenomics in clinical diagnostics unfolding and the expanding role of pathogen genomics in national surveillance, conditions are favourable for the further maturation of these approaches in public health surveillance. In this study, we aimed to pilot the use of probe-based metagenomics for nationwide sentinel surveillance through general practitioner (GP) networks and for the genomic characterisation of both anticipated and emerging respiratory viruses in primary care.

METHODS: This prospective, pilot study included patients with acute respiratory illness attending GP practices participating in nationwide sentinel virological surveillance in the Netherlands, from Jan 10, 2025, to April 25, 2025. On predefined selection days, 90-100 combined nasopharyngeal and oropharyngeal swab specimens were analysed through parallel metagenomic testing using probes targeting 15 488 strains of human and animal viruses. Results were compared with a standard two-tiered surveillance strategy comprising PCR targeting 17 viruses, followed by amplicon-based nanopore whole-genome sequencing of influenza viruses, SARS-CoV-2, and respiratory syncytial virus (RSV). The primary outcome was detection and in-depth genomic characterisation of viruses within and beyond the scope of standard screening. Sensitivity, specificity, positive and negative predictive values, and genome coverage were analysed.

FINDINGS: 93 patients were included, with a median age of 51 years (IQR 33-67); 55 (59%) were women and 38 (41%) were men. Overall, 74 (80%) specimens tested positive through standard PCR-based screening. Metagenomic surveillance detected viruses in 88 (95%) specimens, including DNA viruses known to establish latent infections. For viruses targeted by routine PCR, metagenomics showed a pooled sensitivity of 93·8% (95% CI 88·1-98·7), specificity of 99·8% (95% CI 99·5-100·0), positive predictive value of 96·2% (95% CI 91·8-100·0), and negative predictive value of 99·7% (95% CI 91·8-100·0), with a median genome coverage of 99·4% (IQR 96·9-99·9%). Metagenomic data enabled simultaneous full genomic characterisation of circulating viruses targeted by current amplicon-based surveillance, including influenza viruses (success rate 30 [86%] of 35 detections) and RSV (six [86%] of seven), and of viruses that were post hoc characterised by whole-genome sequencing in response to epidemiological findings during the study period (human metapneumoviruses [hMPV], five [50·0%] of ten), and non-targeted viruses such as adenoviruses. The data facilitated characterisation of a reassortant A(H3N2) influenza virus, potential vaccine escape mutants, markers of susceptibility to influenza antiviral drugs and RSV monoclonal antibodies, and a human A(H1N2)v influenza virus infection.

INTERPRETATION: The technically robust and comprehensive performance across heterogeneous circulating viruses shown here supports evaluation in larger prospective studies in high-prevalence settings, where implementation might be most cost-efficient. Further optimisation of probe-based enrichment strategies could reduce turnaround time and facilitate integration into routine public health surveillance.

FUNDING: The Netherlands Organisation for Health Research and Development (ZonMw), and the Ministry of Health, Welfare and Sport (VWS).}, } @article {pmid42562314, year = {2026}, author = {Qian, Z and Qian, W and Si-Wei, W and Pei, Z and Yi, L and Shan-Ling, X and Chen, C}, title = {Metagenomic Next-Generation Sequencing (mNGS) for Detecting Pathogens and Antimicrobial Resistance Genes (ARGs), and Guiding Antimicrobial Therapy in Cancer Patients from Southwest China.}, journal = {Journal of global antimicrobial resistance}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgar.2026.07.026}, pmid = {42562314}, issn = {2213-7173}, abstract = {BACKGROUND: Cancer patients often face etiological diagnosis challenges due to repeated hospitalizations, antibiotic exposure, and conventional microbiology tests (CMTs) limitations (low positivity, long turnaround). Metagenomic next-generation sequencing (mNGS) enables rapid and accurate pathogen detection, however, its clinical utility in cancer patients requires further investigation.

METHODS: Two years of mNGS results and clinical data of cancer patients in Sichuan Cancer Hospital were collected. The pathogens and antimicrobial resistance genes (ARGs) were analyzed. The diagnostic performance was evaluated via sensitivity, specificity, accuracy, positive and negative predictive value. The clinical significance in guiding antimicrobial therapy was assessed by comparing outcomes between mNGS-guided and empirical therapy groups. Multivariable logistic regression analysis was performed to explore risk factors for multidrug-resistant organisms (MDROs) and opportunistic pathogens infections in cancer population.

RESULTS: The study included 340 mNGS results from 267 cancer patients. Streptococcus pneumoniae, Pseudomonas aeruginosa, Candida albicans and Epstein-Barr virus were the most common Gram-positive and Gram-negative bacteria, fungus and virus, respectively. The main ARGs were ESBLs and aminoglycoside resistance genes. mNGS showed high pathogen diagnostic sensitivity (97.50%) and moderate ARGs diagnostic sensitivity (64.29%). The mNGS-guided group had lower mortality (29.5% vs. 34.1%, p=0.65) and shorter duration of mechanical ventilation (39.34 ± 81.15 vs. 42.30 ±102.39 hours, p= 0.88). Age (p=0.028) and prior 90-day antibiotic use (p=0.047) independently predicted MDROs infections; immunodeficiency predicted Pneumocystis jirovecii (p=0.005) and Aspergillus spp. (p=0.010) infections.

CONCLUSION: mNGS was reliable for pathogen diagnosis in cancer patients. However, its clinical significance on guiding antimicrobial therapy requires more prospective multicenter studies to confirm.}, } @article {pmid42562454, year = {2026}, author = {Zheng, X and Sun, P and He, C and Liu, M and Qiu, J and Ding, Z and Zhang, Y and Zhou, S and Zhou, J and Sun, J and Feng, W and Zhang, L and Cheng, N and Xu, Q and Li, X and Yang, L and Liang, A}, title = {Royal jelly enhances ovarian function by modulating taurocholic acid metabolism and attenuating oxidative stress in D-galactose-induced POI mice.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119500}, doi = {10.1016/j.foodres.2026.119500}, pmid = {42562454}, issn = {1873-7145}, mesh = {Animals ; Female ; *Oxidative Stress/drug effects ; Royal Jelly ; Galactose ; Mice ; *Fatty Acids/pharmacology ; *Ovary/drug effects/metabolism ; *Taurocholic Acid/metabolism ; Disease Models, Animal ; *Primary Ovarian Insufficiency/chemically induced/drug therapy/metabolism ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Estradiol/blood ; }, abstract = {Premature ovarian insufficiency (POI) is a complex endocrine and metabolic disorder frequently associated with oxidative stress. Royal jelly (RJ) is a well-recognized natural functional food with multiple health benefits; however, its potential effects on POI remain unexplored. This study aimed to investigate the therapeutic potential and underlying mechanisms of RJ in a D-galactose (D-gal)-induced POI mouse model. The results showed that RJ increased serum estradiol (E2) levels, enhanced ovarian reserve and oocyte maturation, reduced ovarian oxidative stress, and ultimately improved the fertility of D-gal-treated mice. Integrated metagenomic and metabolomic analyses revealed that RJ alleviated D-gal-induced gut microbiota dysbiosis, notably increasing the abundance of Muribaculaceae bacterium, and restored levels of taurocholic acid (TCA), which positively correlated with both Muribaculaceae bacterium abundance and serum E2 levels. Importantly, TCA supplementation alone recapitulated the protective effects of RJ by reversing D-gal-induced reductions in E2 and anti-Müllerian hormone (AMH) levels, restoring follicle numbers, and alleviating oxidative stress. Mechanistically, TCA activated the nuclear factor erythroid 2-related factor 2 (NRF2) antioxidant pathway in ovarian tissue, while simultaneously enhancing intestinal β-glucuronidase activity to modulate systemic E2 metabolism. In conclusion, RJ alleviates D-gal-induced POI in mice by modulating the gut microbiota-bile acid-ovarian axis, providing novel insights into its potential application for POI prevention and treatment.}, } @article {pmid42562478, year = {2026}, author = {Zhang, HY and Huang, TC and Chai, LJ and Shi, W and He, YX and Lu, ZM and Zhang, XJ and Wang, ST and Shen, CH and Shi, JS and Xu, ZH}, title = {Integrating ecological networks and metagenomics to decipher core microbial drivers of organic acid metabolism during heaped fermentation of sauce-flavor Baijiu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119702}, doi = {10.1016/j.foodres.2026.119702}, pmid = {42562478}, issn = {1873-7145}, mesh = {*Fermentation ; *Metagenomics/methods ; *Food Microbiology ; *Bacteria/metabolism/genetics/classification ; Volatile Organic Compounds/metabolism/analysis ; Acetic Acid/metabolism/analysis ; Caproates/analysis ; Taste ; Lactic Acid/metabolism/analysis ; *Fermented Foods/microbiology ; *Microbiota ; Pentanoic Acids ; Hemiterpenes ; }, abstract = {Organic acids play crucial roles in both flavor quality and microbial succession of sauce-flavor Baijiu; however, the core microbial drivers responsible for their metabolism remain poorly understood. This study systematically investigated the microbial drivers of organic acid metabolism across six sequential rounds (R1-R6) of heaped fermentation. A total of 24 organic acids were identified, including nine non-volatile organic acids (NVOAs) and 15 volatile organic acids (VOAs). HPLC analysis revealed that the total content of acetic acid and nine NVOAs increased significantly across rounds, rising from 29.35 g/kg in R1 to 66.40 g/kg in R6. Lactic acid was the most abundant NVOA, while acetic acid, isovaleric acid, and hexanoic acid were the primary volatile contributors. Co-occurrence network analysis identified 488 consistently correlated bacterial pairs that clustered into two distinct guilds. Guild 2, mainly comprising Virgibacillus, Kroppenstedtia, Oceanobacillus, and Bacillus, exhibited high abundance (47%-78%) across all rounds and was defined as the core bacterial guild. Spearman correlation analysis revealed that guild 2 was positively correlated with NVOAs (69.41%) but negatively correlated with VOAs (63.02%). Metagenomic analysis reconstructed seven key pathways involved in organic acid biosynthesis. Kroppenstedtia, Lentibacillus, Desmospora, and Oceanobacillus were identified the taxa harboring the genetic potential most frequently detected across multiple pathways, with Kroppenstedtia and Lentibacillus exhibiting the highest gene abundances. These findings provide a theoretical foundation for targeted regulation of organic acid content in sauce-flavor Baijiu production.}, } @article {pmid42562481, year = {2026}, author = {Tan, G and Qi, S and Hu, M and Wang, D and Lin, K and Wang, Y and Chen, S and Zhang, Q and Zhao, L}, title = {Understanding phage dynamics and their potential roles during soy sauce fermentation using metagenome-assembled genomes.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119707}, doi = {10.1016/j.foodres.2026.119707}, pmid = {42562481}, issn = {1873-7145}, mesh = {*Fermentation ; *Bacteriophages/genetics/classification/physiology ; *Soy Foods/microbiology/virology ; *Metagenome ; Genome, Viral ; *Food Microbiology ; Metagenomics ; }, abstract = {The composition and functional roles of phages in fermented foods have been gaining increasing attention. However, their ecological functions and underlying mechanisms in high-salt soy sauce fermentation remain largely unexplored. In this study, we investigated phage communities, their potential functions, phage-host interactions, and host defense mechanisms in two different soy sauce fermentation processes (Cantonese-type process, CP; Japanese-type process, JP) using shotgun metagenomics. A total of 823 phage species (viral operational taxonomic units, vOTUs) were identified, with the majority exhibiting a temperate lifestyle (89.19%). The most abundant family was Straboviridae (CP, 9.95%-11.39%; JP, 12.04%-13.73%), followed by Salasmaviridae (CP, 6.92%-7.94%; JP, 5.70%-7.02%). Although the phage composition differed between the two processes, the number of vOTUs was positively correlated with prokaryotic species richness, total acidity, and amino acid nitrogen content, and negatively correlated with pH. A comparative genomic analysis revealed that 91 phages were associated with 26 bacterial genomes (metagenome-assembled genomes, MAGs), with Lactococcus petauri (MAG16) and Halomonas elongata (MAG51) hosting the most phage species. An analysis of host defense mechanisms showed that all 45 bacterial MAGs harbored CRISPR-Cas type I systems, and 95.6% encoded restriction-modification systems. Functional annotation using the KEGG and CAZymes databases indicated that the phages predominantly encoded genes related to cell growth, replication, and metabolism of amino acids, carbohydrates, and nucleotides, with more genes enriched in the JP than in the CP. Additionally, auxiliary metabolic genes (e.g., pfkA, ldh, adhP, ilvE, and arcA) were identified in 29 phages. These genes are potentially involved in metabolic pathways that may be linked to flavor compound production. Together, these findings provide novel insights into the ecological and potential functional roles of phages during soy sauce fermentation.}, } @article {pmid42562486, year = {2026}, author = {Sehar, H and Chen, Z and Zhang, J and Wu, K and Li, BS and Yan, H}, title = {Microbial composition, dynamics, and functional roles in jinhua ham fermentation: integrating starter cultures and multi-omics for quality and safety.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119711}, doi = {10.1016/j.foodres.2026.119711}, pmid = {42562486}, issn = {1873-7145}, mesh = {*Fermentation ; *Meat Products/microbiology/analysis ; Multiomics ; *Food Microbiology ; Animals ; Bacteria/metabolism/classification ; *Microbiota ; Food Safety ; Swine ; Fungi/metabolism ; }, abstract = {Jinhua ham, a traditional Chinese dry-cured meat product with nearly a millennium of production history, derives its characteristic colour, layered aroma, and umami-rich taste from the coordinated biochemical activity of a dynamic microbial ecosystem across an eight-to-ten-month fermentation timeline. This review provides a critical synthesis of research between 2018 and 2025 on microbial composition, community dynamics, functional roles, safety risks, starter culture applications, and multi-omics characterisation of Jinhua ham fermentation, unified by precision fermentation as an organising framework. High-throughput sequencing has established that halotolerant bacterial genera, Staphylococcus, Psychrobacter, Halomonas, and Lactobacillus, and fungal communities comprising Aspergillus, Debaryomyces, Meyerozyma, and Penicillium undergo deterministic, physicochemically driven succession, with their enzymatic activities governing proteolysis, lipolysis, volatile compound formation, colour stabilisation, and the accumulation of biogenic amines, mycotoxins, and antimicrobial resistance genes (ARGs). Autochthonous starter cultures, including Staphylococcus xylosus, Lactiplantibacillus plantarum, and Penicillium aethiopicum, improve process controllability, safety, and sensory consistency, yet their mechanistic basis and validation remain incompletely established. Genomic and metabolomic approaches have generated datasets, but integrated metagenomics-metabolomics coupling, capable of linking microbial gene networks to flavour compound production, and metatranscriptomic characterisation of gene expression remain the unmet methodological needs. Five research directions are proposed: achieving species-level microbial resolution through long-read sequencing and longitudinal sampling; validating flavour-forming pathways through isotopic tracing and controlled inoculation; standardising analytical protocols for cross-study comparability; conducting starter culture and ARG safety validation; and developing low-salt fermentation strategies. Together, these directions define the research investment required to advance Jinhua ham production from empirical tradition to precision-engineered consistency.}, } @article {pmid42562511, year = {2026}, author = {Lee, JW and Kim, YM and Kim, YJ and Jeong, KC and Kim, SA}, title = {Wastewater irrigation reshapes the microbiome and resistome of radish sprouts: Insights from 16S rRNA and shotgun metagenomic sequencing.}, journal = {Food research international (Ottawa, Ont.)}, volume = {241}, number = {}, pages = {119739}, doi = {10.1016/j.foodres.2026.119739}, pmid = {42562511}, issn = {1873-7145}, mesh = {*Raphanus/microbiology/growth & development ; *Wastewater/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Agricultural Irrigation/methods ; Animals ; Metagenomics/methods ; Shotgun Sequencing ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Swine ; }, abstract = {Water scarcity is increasing the reliance on treated wastewater in fresh produce production, yet its effects on the microbial and hygienic quality of fresh produce remain unclear. This study evaluated the influence of wastewater irrigation on the microbiome and antibiotic resistance gene (ARG) profiles of radish sprouts grown under commercially relevant conditions. Using culture-dependent methods and integrated sequencing (16S rRNA and shotgun metagenomics), we tracked microbial and resistome dynamics across the sprout production process under three irrigation regimes: swine wastewater, treated wastewater, and sterile distilled water. Wastewater irrigation markedly increased microbial loads, with aerobic plate counts exceeding 8.0 log CFU/g in final radish sprouts. Both wastewater treatments were dominated by Pseudomonas and Acinetobacter. Resistome profiling showed persistent multidrug, bacitracin, and polymyxin resistance genes in wastewater-irrigated sprouts, while sulfonamide resistance genes occurred exclusively under wastewater irrigation, suggesting wastewater-associated environmental transmission. Higher ARG subtype richness in wastewater treatments suggested that conventional wastewater treatment processes do not completely eliminate diverse ARGs. ARG-host linkage analysis suggested an elevated potential for horizontal gene transfer within edible plant tissues. Overall, wastewater irrigation altered the microbiological quality of radish sprouts and facilitated ARG persistence, underscoring the need for improved post-treatment and preventive water management to safeguard fresh produce safety.}, } @article {pmid42551498, year = {2026}, author = {Da Costa, A and Groussin, P and Barengo, A and Yvorel, C and Mohammed, R and Romeyer, C and Boukhris, M and Benali, K}, title = {Cardiac Implantable Electronic Device Infections: Emerging Paradigms in Precision Prevention and Personalized Management.}, journal = {Trends in cardiovascular medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tcm.2026.08.002}, pmid = {42551498}, issn = {1873-2615}, abstract = {Cardiac implantable electronic device (CIED) infections remain a major source of morbidity, mortality, and healthcare expenditure despite continuing advances in device technology. Increasing procedural complexity, repeat interventions, and an aging population with multiple comorbidities have shifted the focus from treatment alone toward comprehensive infection prevention. Biofilm formation is now recognized as the central pathogenic mechanism underlying CIED infection, explaining both the limited efficacy of antimicrobial therapy in the presence of retained hardware and the need for complete system extraction in established infection. This narrative review summarizes contemporary evidence supporting a multimodal approach to CIED infection prevention and personalized management. Prevention extends beyond perioperative antibiotic prophylaxis and skin antisepsis to encompass structured patient optimization, procedural contamination control, hematoma prevention, targeted Staphylococcus aureus decolonization, antibacterial envelopes, taurolidine-based pocket antisepsis, emerging antibiofilm technologies, and novel device platforms such as leadless pacemakers and extravascular implantable cardioverter-defibrillators. Risk stratification using PADIT, BLISTER, and complementary prediction models enables individualized allocation of preventive interventions according to estimated infection risk rather than uniform prophylaxis. Advances in diagnosis now combine multimodality imaging with biofilm-oriented microbiology, including device sonication, molecular diagnostics, and metagenomic sequencing, supporting pathogen-directed antimicrobial therapy and individualized clinical decision-making. Contemporary management likewise requires multidisciplinary expertise integrating extraction-risk assessment, complete hardware removal when indicated, optimized antimicrobial stewardship, and carefully planned reimplantation strategies. Rather than using the term precision medicine in its traditional genomic sense, this review emphasizes precision prevention and personalized management, whereby preventive and therapeutic interventions are tailored to each patient's quantified infection risk by integrating procedural, microbiological, host-related, and biofilm-associated determinants. Future improvements in clinical outcomes will depend on implementing integrated, risk-guided prevention strategies supported by multidisciplinary expert teams and emerging diagnostic and preventive technologies.}, } @article {pmid42551604, year = {2026}, author = {Liu, J and Ni, Y and Chen, M and Zhang, Y and Zhang, H and Kong, Q}, title = {Iron-carbon enhanced constructed wetland microbial fuel cells for sulfamethoxazole wastewater treatment: Performance evaluation and mechanistic insights.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135565}, doi = {10.1016/j.biortech.2026.135565}, pmid = {42551604}, issn = {1873-2976}, abstract = {Sulfamethoxazole (SMX) is frequently found in aquatic environments, causing ecological toxicity and accelerating the spread of antibiotic resistance genes (ARGs). The conventional constructed wetlands (CWs) face challenges in removing antibiotics and recovering energy. Constructed wetland-microbial fuel cells (CW-MFCs) are a combination of constructed wetlands and bio-electrochemical technology, enhancing pollutant removal and bioelectricity production. In this study, an iron-carbon particle-enhanced CW-MFC (FCCW) was constructed for SMX removal. The decontamination performance, electrochemical properties, metagenomic profiles, ARG distribution, and transformation products of SMX were analyzed. The results showed that the FCCW displayed superiority in power generation performance with an average voltage of 286.16 mV, a peak power density of 5.40 mW·m[-2], a peak current density of 32.48 mW·m[2], and a low internal resistance of 382.10 Ω. The FCCW achieved the highest removal rates of TN (51.66±1.63%), NH4[+]-N (65.49±1.96%), TP (96.69±2.46%), COD (80.90±2.98%), and SMX (96.49±2.77%). Metagenomic analysis revealed that Proteobacteria and Actinobacteria dominated in the three systems and the iron-carbon particles increased the relative abundance of genes associated with energy metabolism and pollutant transformation. Additionally, the FCCW showed a more diffuse distribution of ARGs and no localized accumulation. The analysis of transformation intermediates showed that the FCCW may rely on a glutathione (GSH)-related conjugation pathway associated with lower accumulation of certain toxic intermediates. Overall, the enhanced performance of the FCCW was attributed to improved redox conditions, more efficient electron transfer, and changes in microbial functional composition. Therefore, the FCCW system offers a promising approach for in-situ electricity generation and stable pollutant treatment performance.}, } @article {pmid42551623, year = {2026}, author = {Shahid, M and Raj, A and Shafi, Z and Ali, S}, title = {Nanopesticides-rhizo-microbiome interactions: Biochemical mechanisms, ecotoxicological effects and implications for pesticide fate and transformation.}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {}, number = {}, pages = {110651}, doi = {10.1016/j.cbpc.2026.110651}, pmid = {42551623}, issn = {1532-0456}, abstract = {Nano-enabled pesticides (NanoPs) formulations have emerged as promising alternative to conventional pesticides by improving ingredient stability, delivery, and controlled release. However, their unique physicochemical properties also influence interactions with soil microorganisms, raising concerns regarding ecological safety and long-term impacts on soil ecosystem functions. This review has critically synthesized the current knowledge about NanoPs-microbiome interactions with a focus on biochemical mechanisms underlying microbial responses and implications for pesticide fate and transformation. We review how the properties of NPs (e.g., particle size, surface charge, coatings, dissolution, and eco-corona formation) influence mobility, bioavailability, and microbial exposure. Mechanistic evidence of oxidative stress, membrane damage, enzyme inhibition, metal-ion-mediated toxicity and quorum sensing interference is critically synthesized to elucidate biochemical basis of NanoPs-induced microbial responses. Recent advances in high throughput sequencing and multi-omics technologies are also used to assess changes in microbial diversity, community composition, functional redundancy, microbial interaction networks and ecosystem resilience. The review further compares conventional and nano-formulated pesticides, highlighting differences in microbial toxicity, degradation kinetics, transformation pathways, and metabolite profiles. Current challenges associated with environmental fate assessment, standardized ecotoxicological testing, and microbiome-informed risk evaluation are critically discussed. Emerging opportunities for integrating metagenomics, artificial intelligence, and predictive modelling into environmental risk assessment are also highlighted. Finally, we propose a future research framework centered on microbiome-informed safe-by-design NanoPs, standardized testing protocols, and long-term field validation to support development of environmentally responsible nano-enabled crop protection technologies while preserving soil biodiversity and ecosystem functions.}, } @article {pmid42551913, year = {2026}, author = {Liao, T and Ding, SC and Yu, J and Gu, W}, title = {Enriching Microbial Cell-Free DNA in Clinical Metagenomics Using Epigenetic Filters.}, journal = {Clinical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/clinchem/hvag089}, pmid = {42551913}, issn = {1530-8561}, support = {CA230156//NIH K08/ ; //Burroughs-Wellcome CAMS Award/ ; }, abstract = {INTRODUCTION: Noninvasive cell-free DNA (cfDNA) metagenomic sequencing enables hypothesis-free detection of microbial pathogens in patients with suspected infections. However, its clinical sensitivity is often limited by the overwhelming background of host-derived cfDNA, which can obscure low-abundance microbial signals. We developed an epigenetically guided enrichment strategy, termed Epigenetically filtered Metagenomic Sequencing (EpiMeta-seq), to selectively enrich microbial cfDNA based on fundamental differences in DNA methylation between microbial and human genomes.

METHODS: EpiMeta-seq uses the methylation-sensitive restriction enzyme HpaII to selectively digest unmethylated CCGG sites, which are prevalent in microbial genomes but largely methylated in human DNA. Only fragments cleaved once at unmethylated sites are incorporated into sequencing libraries, thereby enriching microbial cfDNA prior to sequencing. We assessed plasma samples from patients with microbiologically confirmed infections. Metagenomics informatics involved alignment, removal of host DNA, and taxonomic classification of sequencing reads to a curated reference database.

RESULTS: In spike-in experiments at a 1:1000 dilution, EpiMeta-seq achieved a mean enrichment of 24.5-fold for fungal species and 11.4-fold for bacterial species compared with unenriched whole-genome sequencing. In 23 clinical plasma samples representing 12 pathogens, EpiMeta-seq produced an average 10.0-fold increase in microbial reads per million. Viral DNA showed the highest enrichment (mean 11.5-fold), while bacterial enrichment varied across species (1.2- to 30.8-fold).

CONCLUSIONS: By leveraging genome-wide methylation differences between host and microbial DNA, EpiMeta-seq is a proof-of-concept, orthogonal enrichment strategy for improving microbial cfDNA signal-to-background ratio across diverse pathogen types in metagenomic sequencing.}, } @article {pmid42552309, year = {2026}, author = {Lal, A and Riopelle, JC and Villarin, K and Mathur, M and Enriquez, L and Xiao, R and Phemister-Jimenez, N and Gilbert, K and Cole, SD and Tilyou, M and Kennedy, KP and Vaca, E and Castillo, W and Weisberg, M and Mattei, LM and Beiting, DP}, title = {Human wastewater contamination drives the emergence of multidrug-resistant bacteria in the Galápagos marine ecosystem.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42552309}, issn = {2041-1723}, support = {STS-1557138//National Science Foundation (NSF)/ ; }, mesh = {*Wastewater/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; Humans ; Ecuador ; Ecosystem ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics/drug effects/isolation & purification ; *Bacteria/genetics/drug effects/isolation & purification ; Seawater/microbiology ; Plasmids/genetics ; Sewage/microbiology ; Metagenomics ; Enterobacteriaceae/genetics/isolation & purification/drug effects ; }, abstract = {Antimicrobial resistance poses a global threat to public health. Mobile microbiological laboratories can enable environmental monitoring of antimicrobial resistance, particularly in geographically remote and resource-limited locations, such as the Galápagos archipelago. Here, we report the development of a mobile laboratory for antimicrobial resistance surveillance of marine sites surrounding San Cristóbal, the archipelago's second most populated island, which has experienced rapid urbanization and intense international tourism pressure. On-site metagenomic sequencing of wastewater-contaminated marine sites reveals a stark shift in microbial genera and a higher count of antimicrobial resistance genes compared to uncontaminated marine sites, mirroring metagenomic results of local untreated sewage. Over 40% of lactose-fermenting Enterobacteriaceae isolates collected directly from sewage or marine environments near sites of wastewater outfall exhibit multidrug resistance. Long-read sequencing and de novo assembly of bacterial genomes and plasmids from multidrug-resistant Escherichia coli reveal frequent and rapid reassortment of antimicrobial resistance genes on plasmids, generating a diverse and functional resistome on the island. This study not only provides a framework for conducting antimicrobial resistance research in low-resource settings but also underscores the impact of wastewater contamination on the environmental antimicrobial resistance landscape and highlights potential threats to human and animal health.}, } @article {pmid42552346, year = {2026}, author = {Wu, YL and Fairweather, JH and Campbell, M and Hergt, J and Yusiharni, E and Smirk, M and Dodd, A and Sun, X and Clode, P and Hubbard, A and Allentoft, ME and McDonald, J}, title = {Biological contributions to manganese oxides in rock varnish at Murujuga (Western Australia).}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42552346}, issn = {2045-2322}, support = {LP190100724//Australian Research Council/ ; }, mesh = {*Oxides/chemistry/metabolism/analysis ; *Manganese Compounds/chemistry/metabolism/analysis ; Western Australia ; X-Ray Diffraction ; *Paint/analysis ; Metagenome ; Manganese ; }, abstract = {Rock varnish is a ubiquitous Mn-rich coating on exposed rock surfaces in arid environments, yet the mechanisms underlying its formation remain debated. Here, we investigate rock varnish from Murujuga, Western Australia, to assess the role of microbial processes in manganese (Mn) accumulation. Bulk compositional and mineralogical analyses confirm high concentrations of Mn, Fe, Al, and Si; however, the Mn matrix is predominantly composed of amorphous to poorly crystalline phases that fall below the indexing or detection thresholds of X-ray diffraction (XRD) and electron backscatter diffraction (EBSD). Nanoscale characterization reveals a Mn-rich matrix encasing discrete Fe and Al-Si grains, featuring nanometre scale laminations and particle size distribution characteristic of biogenic Mn oxides. High-quality metagenome-assembled genomes (MAGs) reveal a pronounced dominance of Chroococcidiopsidaceae and Rubrobacter_F, pioneer taxa known to accumulate intracellular Mn for defence mechanisms. Furthermore, targeted functional annotation using Hidden Markov Models (HMMs) confirms a widespread, community-level genomic potential for biologically influenced Mn accumulation and utilization. Because this biomineralisation is an ongoing process governed by local environmental stressors, these rock coatings have high potential as long-term paleoenvironmental and climate proxies. This is the first microbiomic characterisation of the rock varnish from the Murujuga Cultural Landscape, and an important step in unlocking the potential of this deposit as a chronological marker for this region's petroglyphs.}, } @article {pmid42553031, year = {2026}, author = {Wang, Y and Lei, J and Cui, S and Zhou, P and Wu, Y}, title = {Beyond detection: quantitative interpretation of Aspergillus-positive bronchoalveolar lavage fluid metagenomic next-generation sequencing for diagnostic stratification and prediction of respiratory deterioration.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1897649}, pmid = {42553031}, issn = {2235-2988}, mesh = {Humans ; *Aspergillus/genetics/isolation & purification ; *Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology/drug therapy ; Female ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Male ; Middle Aged ; Aged ; Prognosis ; ROC Curve ; Antifungal Agents/therapeutic use ; }, abstract = {BACKGROUND: The increasing use of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) has substantially improved the detection of Aspergillus species in patients with suspected pulmonary infections. However, positive mNGS results frequently present a clinical dilemma because Aspergillus may represent invasive pulmonary aspergillosis (IPA), airway colonization, or transient fungal detection. The clinical value of quantitative fungal burden assessment remains insufficiently defined, particularly regarding risk stratification among untreated patients.

METHODS: We conducted a retrospective real-world cohort study including 114 hospitalized patients with BALF mNGS-positive Aspergillus detected between April 2024 and November 2025. Patients were classified according to clinical IPA diagnosis, antifungal treatment status, and occurrence of respiratory deterioration during a 3-month follow-up period. Quantitative fungal burden was expressed as reads per ten million (RPTM). Receiver operating characteristic (ROC) analysis, logistic regression, integrated discrimination improvement (IDI), and category-free net reclassification improvement (NRI) were used to evaluate diagnostic and prognostic performance.

RESULTS: Among 114 patients, 31 met clinical diagnostic criteria for IPA and 83 were classified as non-IPA. Aspergillus burden was significantly higher in IPA patients than in non-IPA patients (logarithmic scale median RPTM 2.46 vs. 0.30, P < 0.001). ROC analysis identified an exploratory cohort-derived diagnostic threshold of 75 RPTM for IPA discrimination (AUC = 0.853, 95% CI 0.745-0.960). Among 77 patients who did not receive antifungal therapy, 31 experienced respiratory deterioration during follow-up. Higher RPTM values were independently associated with deterioration (adjusted OR = 5.27, 95% CI 1.78-17.06, P = 0.001). An exploratory RPTM threshold of 2.5 showed modest discriminatory ability for subsequent respiratory deterioration, with an AUC of 0.682. Incorporation of quantitative fungal burden significantly improved discrimination and reclassification performance beyond conventional clinical variables. In contrast, baseline RPTM showed no significant association with respiratory deterioration among patients receiving antifungal therapy.

CONCLUSIONS: Quantitative interpretation of Aspergillus-positive BALF mNGS results may provide additional information beyond simple pathogen detection. Two exploratory cohort-derived thresholds were identified: a higher threshold associated with clinical IPA adjudication and a lower threshold associated with subsequent respiratory deterioration among untreated patients. These findings are hypothesis-generating and require external validation before clinical application. RPTM should be interpreted as an adjunctive marker within the overall clinical context rather than as a standalone diagnostic or prognostic threshold.}, } @article {pmid42553092, year = {2026}, author = {Guo, N and Chen, S and Guo, L and Qiu, X and Li, Z}, title = {Metagenomic next-generation sequencing: new horizons in microbiology.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1824160}, pmid = {42553092}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Animals ; COVID-19/diagnosis ; Computational Biology/methods ; Pandemics ; SARS-CoV-2/genetics ; Public Health ; One Health ; }, abstract = {The COVID-19 pandemic has exposed vulnerabilities in global health systems while accelerating the adoption of metagenomic next-generation sequencing (mNGS) as a transformative tool for culture-independent, unbiased microbial detection. In clinical diagnostics, mNGS enables simultaneous detection of diverse pathogens without prior hypothesis, though its yield depends heavily on specimen type and clinical context. In public health, mNGS has demonstrated remarkable utility in outbreak tracing, novel pathogen discovery, antimicrobial resistance (AMR) surveillance, and One Health initiatives. However, massive data volumes pose persistent challenges in bioinformatics, standardization, and computational demands. Future integration of artificial intelligence, automated platforms, and multi-omics approaches will enhance the conversion of raw data into actionable insights. Collectively, mNGS is poised to drive a paradigm shift from reactive responses to proactive, system-level microbial surveillance across human, animal, and environmental health.}, } @article {pmid42553304, year = {2026}, author = {Geng, Q and Wang, Y and Fan, Y and Liu, N and Zhao, X}, title = {First reported survival of anthrax meningoencephalitis in a low-incidence region: successful management with mNGS-guided combination therapy.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1792720}, pmid = {42553304}, issn = {2235-2988}, mesh = {Humans ; Male ; *Meningoencephalitis/drug therapy/microbiology/diagnosis ; *Anti-Bacterial Agents/therapeutic use ; Middle Aged ; *Anthrax/drug therapy/diagnosis/microbiology ; Drug Therapy, Combination/methods ; *Bacillus anthracis/genetics/isolation & purification/drug effects ; Ciprofloxacin/therapeutic use ; High-Throughput Nucleotide Sequencing ; Amikacin/therapeutic use ; Treatment Outcome ; Animals ; Penicillin G/therapeutic use ; Linezolid/therapeutic use ; Levofloxacin/therapeutic use ; Cerebrospinal Fluid/microbiology ; }, abstract = {We report a rare survival case of anthrax meningoencephalitis in a 56-year-old male from a low-incidence region. The patient presented with nasal discharge, fever, headache, and rapid onset of coma following the slaughter of a diseased cow. Physical examination revealed a characteristic ulcerative eschar on the right index finger, while laboratory investigations showed significant leukocytosis and hemorrhagic cerebrospinal fluid (CSF) characterized by elevated protein and decreased glucose levels. Although initial microscopy misidentified the pathogen as Bacillus cereus, metagenomic next-generation sequencing (mNGS) of the CSF confirmed Bacillus anthracis within 48 hours. This rapid molecular diagnosis enabled a timely switch to a CDC-recommended combination regimen, initially with quadruple therapy (penicillin G, ciprofloxacin, amikacin, and linezolid) followed by optimization to triple therapy (penicillin G, levofloxacin, and linezolid) during the ICU stay, ultimately leading to the patient's full neurological recovery. This case underscores that the synergistic use of rapid mNGS-based diagnosis and appropriate combination therapy is critical for achieving survival in anthrax meningoencephalitis.}, } @article {pmid42553918, year = {2026}, author = {Chen, H and Zhang, B and Zhu, B and Zhou, P and Xu, C and Li, Q and Chen, W}, title = {Comparison of the effects of stent-based diversion technique versus prophylactic double-lumen ileostomy on intestinal flora in postoperative patients with rectal cancer.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1791364}, pmid = {42553918}, issn = {1664-302X}, abstract = {BACKGROUND: The stent-based diversion technique (SDT), as a novel surgical approach for reducing anastomotic leakage (AL) following low anterior resection (LAR), achieving effective intestinal diversion while avoiding ileostomy and subsequent stoma reversal surgery. Although multicenter randomized controlled trials have demonstrated the safety of SDT, the alterations in postoperative intestinal microbiota following SDT remain inadequately characterized.

METHODS: This study enrolled 40 patients with mid-low rectal cancer (21 SDT, 19 PDI). Rectal swab samples were collected preoperatively and at 3 weeks and 3 months postoperatively (n = 120) for metagenomic sequencing. α- and β-diversity analyses were performed to compare microbial community characteristics. LEfSe was used for differential analysis of species and KEGG functional pathways. Postoperative clinical outcomes including AL and anastomotic stricture (AS) were assessed.

RESULTS: The SDT group showed a significantly lower incidence of AS compared with the PDI group (4.76% vs. 31.58%, p < 0.05). Preoperative α- and β-diversity were comparable between groups. Postoperatively, the SDT group exhibited higher microbial richness at both 3 weeks and 3 months (both p < 0.05). In the PDI group, the α-diversity showed a continuous decline from 3 weeks to 3 months postoperatively compared with the preoperative baseline (p < 0.05). However, the SDT group demonstrated no significant decrease in α-diversity at 3 weeks (p > 0.05), but did at 3 months (p < 0.05). Significant intergroup β-diversity divergence emerged from 3 weeks onward (both p < 0.05). The SDT group showed significant structural changes from 3 weeks to 3 months (p < 0.05), whereas the PDI group remained stable. At 3 weeks, opportunistic pathogens (e.g., Parvimonas micra) were enriched in the PDI group, while the SDT group enriched beneficial taxa (e.g., Akkermansia). By 3 months, the PDI group exhibited enrichment of oral/genitourinary-derived bacteria (Prevotellaceae, Porphyromonas, Fusobacterium), whereas the SDT group showed higher abundance of beneficial Bacteroidota (e.g., Phocaeicola vulgatus). Functionally, the SDT group enriched amino acid and carbohydrate metabolism pathways, while the PDI group enriched translation and energy metabolism pathways.

CONCLUSION: We found that SDT better preserves postoperative gut microbiota diversity, promotes the restoration of beneficial bacteria, and influences microbial functional pathways, thereby establishing a more favorable microbiome environment for patients.}, } @article {pmid42554318, year = {2026}, author = {Lin, H and Wu, W and Fang, H and Chen, Y and Wu, H and Lai, X and Li, L}, title = {Integrated Metabolomic and Metagenomic Profiling Reveals Distinct Microbial-Metabolic Signatures in the Adenoma-Carcinoma Sequence of Colorectal Cancer.}, journal = {Biomedical chromatography : BMC}, volume = {40}, number = {9}, pages = {e70588}, doi = {10.1002/bmc.70588}, pmid = {42554318}, issn = {1099-0801}, support = {3502Z202374067//Natural Science Foundation of Xiamen, China/ ; }, mesh = {Humans ; *Colorectal Neoplasms/metabolism/microbiology ; *Metabolomics/methods ; *Adenoma/metabolism/microbiology ; *Metabolome/physiology ; Feces/microbiology ; *Metagenomics/methods ; Male ; Female ; Multiomics ; Middle Aged ; *Gastrointestinal Microbiome/physiology/genetics ; Biomarkers, Tumor/metabolism/analysis ; Aged ; }, abstract = {Colorectal cancer (CRC) arises via the stepwise adenoma-carcinoma sequence (ACS). Gut microbial dysbiosis and host metabolic reprogramming jointly correlate with CRC onset and advancement, yet their stage-specific crosstalk across ACS remains largely unclear. Limited multi-omics research on microbial-metabolic interactions throughout ACS hinders the development of early diagnostic biomarkers and preventive strategies. Here, we combined untargeted mucosal metabolomics and fecal shotgun metagenomic sequencing in 36 participants, covering healthy controls, ACS, and CRC patients. We systematically analyzed microbial composition, functions, differential metabolites, and enriched pathways and integrated multi-omics data to screen stage-specific signatures. Distinct gut microbial profiles and progressive functional shifts toward pathogenicity and abnormal carbohydrate metabolism were observed along ACS. Mucosal metabolism was continuously disrupted, with prominent alterations in taurine-hypotaurine, sphingolipid, and bile acid pathways. Core differential metabolites showed excellent diagnostic performance. Microbe-metabolite interactions were progressively enhanced to form a concerted pro-tumor axis. This study characterizes unique ACS-stage microbial-metabolic features. Dysregulated metabolic pathways and key microbe-metabolite crosstalk are closely associated with CRC progression, offering novel non-invasive biomarkers and premalignant intervention targets.}, } @article {pmid42554471, year = {2026}, author = {Olivo, D and Collins, D and de Koch, M and Revekant, C and Kraberger, S and Varsani, A}, title = {Metagenome-assembled genomes of papillomaviruses from mallard and northern pintail cloacal swabs.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0072626}, doi = {10.1128/mra.00726-26}, pmid = {42554471}, issn = {2576-098X}, abstract = {There is little known about papillomavirus diversity in waterfowl. From cloacal swabs of one mallard and three northern pintails sampled in New Mexico (USA), we identified four papillomavirus genomes. These papillomaviruses share >92.7% genome-wide nucleotide pairwise identity with Anas platyrhynchos papillomavirus 3 (AplaPV3) identified from a mallard in Missouri (USA).}, } @article {pmid42546224, year = {2026}, author = {Pavlovic, NR and Malings, CA and Huang, M and He, Y and Diez, S and Bratburd, J and Mahmoud, H and Schnell, J and Hang, Y and Anderson, L and Grodzinsky, G and deSouza, P and Mead, MI and Rao, Y and Velho, R and Davignon, D and Munde, S and Sayeed, A and Aekakkararungroj, A and Joshi, A and Olayinka, O and Rondouba, HD and Pant, P}, title = {Satellite-derived air quality data can effectively support health needs when use cases, Earth observing capabilities, and capacities align.}, journal = {Journal of the Air & Waste Management Association (1995)}, volume = {}, number = {}, pages = {1-27}, doi = {10.1080/10962247.2026.2698602}, pmid = {42546224}, issn = {2162-2906}, abstract = {Advances in Earth observation (EO) remote sensing technologies have delivered a range of aerosol and trace gas pollution data with ever-improving spatial and temporal resolution, significantly benefitting assessments of global air quality (AQ). Furthermore, the application of data synthesis techniques incorporating satellite EO with other information sources has improved the availability of satellite-derived estimates of pollutant exposure at local to global scales. These data have been applied to address a diversity of use cases in AQ monitoring and public health, from long-term trend tracking, exposure assessment, and epidemiological analysis to short-term emissions identification and early warning. Successful application of satellite EO to address AQ and AQ-related health problems requires an alignment between (1) the technical capabilities of satellite data to provide relevant information, (2) a defined case for using this information to address a particular need, and (3) the human capacity, computational resources, operational plans, and policy and governance frameworks to implement a solution and take action, and to sustain the solution for as long as the need remains. Only when there is substantial alignment across all these factors can satellite EO information be effectively translated into public health benefits. This paper surveys applications of satellite EO to AQ assessment and AQ-related health management globally, synthesizing key commonalities into recommendations for how satellite EO can effectively support health needs. We also identify gaps in current satellite EO capabilities, use-case applications, and feasibility factors where future research and investment could reduce barriers to increased application of satellite EO to address pressing public health concerns related to AQ worldwide.Implications: This paper summarizes insights collected through the Group on Earth Observations (GEO) Health Community of Practice Air Quality and Respiratory Health Work Group on the current state and gaps in the use of satellite EO to support air quality and related health decision-making globally. We synthesize these insights into general recommendations for how satellite EO capabilities, use cases, and feasibility considerations can be aligned towards effective use of satellite EO data for air quality and related health effects. We also identify barriers and gaps in current capabilities, uses, and capacities, making recommendations for how these might be addressed.}, } @article {pmid42546623, year = {2026}, author = {Chen, J and Zhang, X and Liu, N and Chen, X and Wang, Y and Lin, Q and Bao, Y}, title = {Multi-omics analysis provides mechanistic insights into tanninase-assisted flavor evolution in Phyllanthus emblica L. wine.}, journal = {Food chemistry}, volume = {525}, number = {Pt 3}, pages = {150651}, doi = {10.1016/j.foodchem.2026.150651}, pmid = {42546623}, issn = {1873-7072}, abstract = {Winemaking from Phyllanthus emblica L. is limited by astringency and tannin-associated instability. This study evaluated tanninase pretreatment followed by Saccharomyces cerevisiae fermentation for improving tannin-rich P. emblica L. wine. Metagenomics, LC-MS, and HS-SPME-GC-MS were used to characterize microbial succession and metabolite profiles. A total of 231 non-volatile metabolite features and 183 volatile flavor compounds were putatively annotated. Tanninase pretreatment reduced tannin content from 0.23% to 0.15% before inoculation and was associated with increased ellagic acid, suggesting partial hydrolysis of hydrolysable tannins. The NF group showed higher S. cerevisiae abundance, reaching 77.64%, and altered phenolic, organic acid, fatty acid, amino acid-related, and aroma-related metabolite profiles. Microbial-metabolite analysis suggested that aromatic amino acid metabolism may contribute to floral and fruity ester formation through the Ehrlich pathway. Sensory evaluation showed reduced bitterness/astringency, clearer appearance, and improved overall quality in NF wine.}, } @article {pmid42546643, year = {2026}, author = {Liu, S and Li, Y and Du, C and Zhu, X and Wang, S and Zeng, X and Jia, Y}, title = {Metal(loid) contamination shifts microbial carbon and nitrogen cycling potential in paddy soils.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143137}, doi = {10.1016/j.jhazmat.2026.143137}, pmid = {42546643}, issn = {1873-3336}, abstract = {Trace metal(loid) contamination in paddy soils derived from either geogenic sources or mining activities is widely occurring in mid-south to south China and south to south east Asia. Due to their toxicities, these trace metal(loid)s may influence microbial community assembly and carbon/nitrogen (C/N) cycling. However, how metal(loid) contamination reshapes community composition, functional potential, and genomic traits of key functional microorganisms remains unclear. Here, we collected paddy soil samples from mid-south to south China and classified them into low- and high-contamination groups based on the Nemerow index. The associations among contamination level, microbial community composition, C/N-cycling potential, and genomic traits of key functional microorganisms were examined by combining soil physicochemical characterization, 16S rRNA gene amplicon sequencing, metagenomics, and metagenome-assembled genome (MAG) reconstruction. Bacterial and archaeal richness did not differ significantly between contamination levels, whereas community composition varied markedly. Methane oxidation genes were enriched in high-contamination soils, whereas methanogenesis genes were more abundant in low-contamination soils. Denitrification- and dissimilatory nitrate reduction to ammonium (DNRA)-related genes increased under heavy contamination, whereas several nitrogen fixation genes declined. Environmental association analyses identified As, Cd, Pb, Cr, and Zn as key variables associated with C/N cycling genes. Several MAGs carried both elemental cycling genes and metal(loid)-response or transformation genes, suggesting potential multifunctionality in contaminated paddy soils. Overall, metal(loid) contamination, together with associated edaphic variation, reorganized microbial communities and redistributed C/N cycling potential. This work provides a genomic basis for identifying microorganisms that could serve as bioindicators or functional targets in contaminated paddy soils.}, } @article {pmid42546794, year = {2026}, author = {Li, S and Chen, T and Liu, J and Lu, K and Chen, X and Lin, L and Lin, Y}, title = {Enriched microplastic-associated biofilms exacerbate gut microbial dysbiosis and metabolic disruption in mice.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128873}, doi = {10.1016/j.envpol.2026.128873}, pmid = {42546794}, issn = {1873-6424}, abstract = {Microplastics (MPs) and opportunistic pathogens are recognized as emerging environmental hazards, yet the health risks associated with mammalian exposure to biofilms enriched on MP surfaces remain poorly characterized. This study evaluated the characteristics of microbial biofilms enriched on MPs from aquatic and sediment matrices over 12 weeks and assessed their potential health impacts using a murine mammalian model. Metagenomic profiling showed that the enriched biofilms exhibited alterations in community composition, accompanied by an overrepresentation of genes associated with antibiotic resistance, iron acquisition, and virulence traits. In the murine model, dietary exposure to the MP-associated biofilms coincided with changes in host intestinal inflammatory markers and a distinct shift in the gut microbiota profile. Metabolomic analysis further revealed synchronous alterations in extracellular and fecal metabolite profiles, including profiles linked to secondary bile acid pathways, alongside a downregulation of intestinal barrier tight junction markers. These parallel taxonomic and metabolic shifts indicate that environmental biofilms enriched on microplastics can provoke complex physiological responses in a mammalian host. This study provides a valuable framework for assessing the potential mammalian health risks posed by plastisphere-associated microbial complexes.}, } @article {pmid42548291, year = {2026}, author = {Nicolas, P and Beigneux, Y and Guennoc, AM and Destras, G and Mossad, M and Bal, A and Talagrand-Reboul, E and Rodriguez, C and Cappy, P and Gubavu, C and Marignier, R and Vukusic, S and Jarraud, S and Maillart, E and Josset, L and Pourcher, V}, title = {Borrelia miyamotoi meningoradiculitis complicating ocrelizumab treatment for multiple sclerosis: A report of three cases.}, journal = {Multiple sclerosis (Houndmills, Basingstoke, England)}, volume = {}, number = {}, pages = {13524585261473068}, doi = {10.1177/13524585261473068}, pmid = {42548291}, issn = {1477-0970}, abstract = {Ocrelizumab is an anti-CD20 monoclonal antibody that is highly effective in multiple sclerosis (MS) but is associated with an increased risk of opportunistic infections that may be difficult to diagnose. We report three MS patients treated with ocrelizumab who developed severe meningoradiculitis. Routine investigations failed to identify any pathogen, whereas metatranscriptomic analysis of cerebrospinal fluid (CSF) detected Borrelia miyamotoi RNA. All patients improved after appropriate antibiotic therapy. B. miyamotoi should be considered in anti-CD20-treated MS patients presenting with meningoradiculitis, and CSF metatranscriptomics should be used to investigate undiagnosed central or peripheral nervous system infections, particularly in immunocompromised individuals. Ocrelizumab is a highly effective treatment widely used in MS but has been associated with an increased risk of infection. We report three cases of B. miyamotoi infections in patients receiving ocrelizumab in which routine laboratory tests failed to detect the pathogen.}, } @article {pmid42548466, year = {2026}, author = {Yang, L and Tao, Y and He, Y and Liu, S and Gan, L and Dai, A and Ni, Q and Wang, Y and Li, F and Liu, Q and Hu, Y and Wang, Y and Lu, W}, title = {Metagenomic and metabolomic profiling in primary aldosteronism with coexisting obstructive sleep apnea.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1858100}, pmid = {42548466}, issn = {1664-2392}, mesh = {Humans ; *Sleep Apnea, Obstructive/metabolism/complications/microbiology/genetics ; Female ; *Hyperaldosteronism/metabolism/complications/genetics/microbiology ; Male ; *Metagenomics/methods ; *Metabolomics/methods ; Prospective Studies ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; *Metabolome ; Adult ; Feces/microbiology ; Polysomnography ; }, abstract = {BACKGROUND: Primary aldosteronism (PA) frequently coexists with obstructive sleep apnea (OSA), and this comorbidity is associated with increased cardiometabolic risk. Although both PA and OSA have been individually linked to gut microbiome alterations, it remains unclear which layer of gut microbiome-associated variation best reflects clinical heterogeneity in PA with coexisting OSA.

METHODS: In this prospective observational study, we performed shotgun metagenomic sequencing and untargeted fecal metabolomic profiling in 29 adults with clinically confirmed PA, who were stratified according to OSA severity (G1-G4) based on overnight polysomnography. Microbial gene richness, taxonomic composition, functional potential based on KEGG annotation, and antibiotic resistance gene profiles were analyzed using standardized bioinformatic workflows. Metabolomic variation was assessed using multivariate analysis, pathway enrichment, and additional exploratory analyses incorporating apnea-hypopnea index (AHI) as a continuous variable. Multiple-testing correction was applied to metabolite-level comparisons.

RESULTS: Global gut microbial gene richness, alpha diversity, beta diversity, and broad functional profiles did not show strong group-level separation across OSA severity strata. Additional analyses using AHI as a continuous variable similarly showed no significant association between AHI and overall gene richness or alpha diversity indices. Nevertheless, selective genera showed exploratory associations with AHI, suggesting that localized taxonomic signals may occur despite relative stability of global community structure. Antibiotic resistance gene profiles showed marked inter-individual variability without clear group-level separation, although ARO richness showed an exploratory inverse association with AHI. In contrast, fecal metabolomic profiling revealed nominal phenotype-associated differences, including trehalose-related metabolites and FAHFA species that showed inverse exploratory associations with AHI. However, no individual metabolite remained significant after global Benjamini-Hochberg false discovery rate correction.

CONCLUSIONS: In PA with coexisting OSA, gut microbiome-associated heterogeneity appears to be more readily reflected by selected taxonomic and metabolic signals than by global microbial diversity or broad functional potential. However, given the small sample size, limited control of clinical and lifestyle confounders, and lack of metabolite-level significance after global FDR correction, these findings should be interpreted as exploratory and hypothesis-generating. Larger controlled cohorts incorporating PA subtype, medication exposure, dietary assessment, and longitudinal validation are needed.}, } @article {pmid42548546, year = {2026}, author = {Cao, L and Zhao, Y and Wang, R and Liu, Y and Luo, L and Yan, H and Li, N}, title = {The value of mNGS in the diagnosis of central nervous system infections in immunodeficient hosts with decompensated cirrhosis complicated by Listeria encephalitis: Case Report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1857949}, pmid = {42548546}, issn = {2296-858X}, abstract = {INTRODUCTION: The incidence of central nervous system (CNS) infections caused by Listeria monocytogenes is rising, yet it remains rarely reported and frequently misdiagnosed in patients with decompensated cirrhosis. This report evaluates the diagnostic utility of metagenomic next-generation sequencing (mNGS) in this specific population.

CASE PRESENTATION: A 62-year-old male with a 7-year history of cirrhosis presented with fever, headache, and loss of consciousness. At admission, the patient was in a decompensated state with a Child-Pugh score of 9 (Grade B) and a Model for End-Stage Liver Disease (MELD) score of 12, characterized by hypoalbuminemia and mild ascites.

DIAGNOSIS AND INTERVENTION: To avoid delayed treatment, broad-spectrum antibiotics were used before the results of blood and cerebrospinal fluid cultures were available. Preliminary cerebrospinal fluid (CSF) analysis showed an atypical inflammatory response in the context of cirrhosis-associated immune dysfunction. Although conventional CSF cultures remained negative, mNGS detected Listeria monocytogenes sequences within 16 h. Early mNGS-guided targeted therapy, followed by multidisciplinary management under real-world drug availability constraints, was associated with significant clinical improvement and successful discharge.

CONCLUSION: Cirrhosis-associated immune dysfunction (CAID) and hypersplenism can mask typical CSF diagnostic markers. mNGS provides a rapid, unbiased diagnostic paradigm that is crucial for shortening diagnostic duration and guiding precision therapy in immunocompromised hosts.}, } @article {pmid42548723, year = {2026}, author = {Zhang, L and Huang, D and Song, J and Zhao, T and Yang, F and Li, C and Zheng, F}, title = {Case Report: Intestinal mycobacterium abscessus infection in a child.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1815227}, pmid = {42548723}, issn = {2296-2360}, abstract = {The diagnosis and treatment of Mycobacterium abscessus infections present significant challenges, especially in the rare cases of extrapulmonary involvement in pediatric patients. These cases are characterized by diagnostic difficulties, limited therapeutic options, scarce clinical experience, and a lack of evidence-based treatment guidelines. This article reports on a 6-year-old child who experienced fever and abdominal pain. Metagenomic next-generation sequencing (mNGS) facilitated the rapid and accurate identification of Mycobacterium abscessus as the causative pathogen. Under a standardized full-course protocol, an individualized therapy regimen (that includes Imipenem, Azithromycin, and Linezolid) led to favorable clinical outcomes. Through the analysis of this successfully treated case, we aim to derive clinical insights and identify potential limitations, with the goal of exploring effective diagnostic and therapeutic approaches for pediatric patients with non-tuberculous mycobacterial (NTM) infections in the future.}, } @article {pmid42548731, year = {2026}, author = {Xu, X and Yu, T and Wu, H and Guo, Y and Li, M and Han, Y and Zhao, L and Yu, X}, title = {The composition alteration of gut microbiota in lung cancer: a systematic review and meta-analysis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1873706}, pmid = {42548731}, issn = {1664-302X}, abstract = {BACKGROUND: The association between the gut microbiota and lung cancer remains understudied. In this study, we conducted a comprehensive systematic review and meta-analysis to quantitatively synthesize evidence from multiple cohorts to identify robust and consistent alterations in gut microbial diversity and taxonomy associated with lung cancer.

METHODS: A systematic literature search was performed across PubMed, Cochrane Library, Embase, and Web of Science databases up to June 5, 2025. The analysis summarized key microbiota characteristics from the selected studies, including alpha diversity, beta diversity, and relative taxonomic abundance. This meta-analysis was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines.

RESULTS: Our systematic search identified 12,810 articles, out of which 27 studies comprising 2,263 individuals, involving 1,234 lung cancer patients and 1,029 non-cancer controls, were included for qualitative synthesis. Meta-analysis revealed a significant reduction in microbial alpha diversity of 25 studies in lung cancer patients. Significant decreases were indicated in the ACE index (SMD = -0.64, 95% CI: -1.14 to -0.13), Chao1 index (SMD = -0.31, 95% CI: -0.60 to -0.02), and Shannon index (SMD = -0.25, 95% CI: -0.57 to 0.08). Chinese cohorts showed significantly lower Chao1and Shannon by subgroup analysis. Twenty-seven studies assessed beta diversity, in which 20 studies (74.0%) reported a significant difference in overall microbial community structure between lung cancer patients and non-cancer controls. Quantitative meta-analysis by forest plot revealed, compared to non-cancer controls, lung cancer patients exhibited decreased relative abundances of phylum Firmicutes (SMD = -0.47, 95% CI: -0.91 to -0.02), and increased abundances of phylum Bacteroidetes (SMD = 0.53, 95% CI: 0.24 to 0.82). Furthermore, we observed a marked depletion of beneficial short-chain fatty acid producers of genus Lachnospira (SMD = -1.01, 95% CI: -1.29 to -0.73).

CONCLUSION: This meta-analysis demonstrates that lung cancer is consistently associated with gut microbiota dysbiosis characterized by reduced microbial diversity and reproducible taxonomic alterations. Clinically, these findings suggest that gut microbiota may serve as non-invasive biomarkers for lung cancer detection and patient stratification, and may also help predict immunotherapy response and inform future microbiota-targeted therapeutic strategies.

https://www.crd.york.ac.uk/PROSPERO/view/CRD42024537463, CRD42024537463.}, } @article {pmid42549413, year = {2026}, author = {Feng, S and Si, X and Lu, C and Gao, Z and Wang, J and Yang, Q and Lu, S and Su, T and Yang, J and He, X and Wu, L}, title = {Washed microbiota transplantation improves clinical symptoms, gut microbiota, and metabolic profiles in autism spectrum disorder in a twin cohort.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1885281}, pmid = {42549413}, issn = {1664-302X}, abstract = {OBJECTIVE: Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition characterized by impaired social communication, repetitive behaviors, and restricted interests. Dysregulation of the microbiota-gut-brain axis is closely associated with the pathogenesis of ASD. Washed microbiota transplantation (WMT) has emerged as a promising intervention for ASD, but existing cohort studies lack genetically identical controls, making it difficult to distinguish intervention-related changes from genetic and environmental confounding factors. This twin-paired controlled study adopted a study design that minimizes the influence of genetics and shared environment, to explore the associations of WMT with clinical symptoms, gut microbiota, and metabolic profiles in children with ASD.

METHODS: Three pairs of age- and environment-matched twins (one ASD-affected, one typically developing sibling) were enrolled. WMT was administered to the ASD participant in each pair. Fecal samples were collected at baseline and post-intervention. Gut microbiota and metabolic profiles were analyzed using metagenomic sequencing and targeted metabolomics, respectively. Clinical outcomes were evaluated using the Childhood Autism Rating Scale (CARS), Autism Behavior Checklist (ABC), Sleep Disturbance Scale for Children (SDSC), and Bristol Stool Form Scale (BSFS). Relevant observations were carried out to explore potential changing trends.

RESULTS: After WMT, CARS, ABC, SDSC, and BSFS exhibited small numerical directional shifts toward healthier values, but none reached statistical significance. Gut microbial structure and function presented a shifting trend toward the profile of their typically developing twin siblings. Abnormal lipid and energy metabolism indicators showed partial ameliorative trends, and the number of differential metabolites between ASD patients and healthy siblings was markedly reduced. Tyrosine and phenylalanine metabolic pathways, together with Segatella, Negativibacillus, and Sangeribacter, may be associated with incomplete phenotypic changes in this cohort.

LIMITATIONS: Although the twin-pair design has high internal validity and can provide strong causal inference evidence for the effect of microbiota transplantation in treating ASD, this study has limitations such as a small sample size, a single-center non-randomized observational design. All findings in this pilot study are merely descriptive trends, and the relevant mechanism analysis only provides correlational clues. A single session of microbiota transplantation failed to fully adjust aromatic amino acid metabolism in ASD children. No definitive causal relationship can be concluded based on the findings of this small-sample pilot study.

CONCLUSION: Under tightly controlled genetic and environmental conditions, gut microbial dysbiosis presents correlational characteristics with ASD-related phenotypes. WMT was associated with consistent remodeling of gut microbial ecology and partial resolution of metabolic dysregulation in ASD children, with multi-omic signatures converging toward healthy twins. Clinical rating scales only displayed non-significant minor numerical shifts, which cannot be interpreted as evidence of clinical symptom improvement. These initial findings provide exploratory mechanistic clues and phenotypic data supporting WMT as a targeted microbiome intervention approach for ASD, and await further validation through large-scale randomized controlled trials.

CLINICAL TRIAL REGISTRATION: Identifier ChiCTR2400091105.}, } @article {pmid42549419, year = {2026}, author = {Li, X and Jiang, J and Li, X and Jian, G and Li, F}, title = {Effects of diarrhea and antibiotic-induced microbial elimination on dynamic changes in fecal microbial communities and antibiotic resistance of Hu sheep lambs (Ovis aries).}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21574}, pmid = {42549419}, issn = {2167-8359}, mesh = {Animals ; *Diarrhea/microbiology/veterinary/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Sheep/microbiology ; *Feces/microbiology ; *Sheep Diseases/microbiology/drug therapy ; *Gastrointestinal Microbiome/drug effects/genetics ; Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; *Drug Resistance, Microbial/genetics ; }, abstract = {BACKGROUND: As a highly reproductive meat sheep breed in China, Hu sheep is an important economic group in ruminant animal breeding. However, research on its intestinal microbiomes under the background of diarrhea and antibiotic treatment remains relatively limited.

METHODS: This study investigated the intestinal microbiota of Hu sheep lambs in the preliminary stage of diarrhea (group DM), the late recovery stage of diarrhea (group DL), and the healthy stage (group H). Diseased individuals (groups DM and DL) were treated with a combination of Shuanghuanglian, Cefazolin, Lincomycin, and Dexamethasone (0.2 mL dosage). To characterize the intestinal microbiota, fecal samples were collected from all groups, and metagenomic sequencing was performed. Using metagenomic binning tools and co-assembly methods, we reconstructed 482 high-quality non-redundant metagenome assembled genomes (MAGs).

RESULTS: Among these MAGs, 70% belong to the phyla Bacillota, Bacteroidota, and Pseudomonadota, highly consistent with the typical structure of intestinal microbiota in ruminants. Functional annotation revealed that the genes encoding carbohydrate-active enzymes (CAZymes) are more abundant in Bacillota and Bacteroidota, which supports the degradation and energy metabolism functions of Hu sheep on fibrous feed. During the preliminary stage of diarrhea, the virulence genes carried by symbiotic bacteria such as Lachnospiraceae, Acutalibacteraceae and Bacteroidaceae were enriched. Although diarrhea symptoms alleviated during the late recovery stage of diarrhea, the combined use of multiple antibiotics led to the continuous enrichment of antibiotic resistance genes (ARGs) related to lincosamides and cephalosporins. The average abundance of cephalosporin-related ARGs in group DL was significantly higher than that in group DM and H, indicating a risk of residual ARGs. Microbial diversity analysis showed that there was no significant overall difference in MAGs between group DM and H, but both groups showed significant differences compared to group DL, suggesting that antibiotic driven clearance of sensitive bacteria is the core driving force. Moreover, our study shows that the abundance of the zoonotic pathogens Barnesiella and Campylobacter significantly increased in the diarrhea group (p <  0.05), and they carry 567 and 382 virulence genes, respectively. Their pathogenicity is regulated by the dynamic changes in the host intestinal microbiota.

CONCLUSIONS: This study not only expands the genomic database of ruminant intestinal microorganisms but also provides a key theoretical basis for formulating intestinal microecological regulation strategies and optimizing diarrhea treatment regimens for Hu sheep.}, } @article {pmid42549425, year = {2026}, author = {Maynez-Perez, AO and Cahyo, HN and Niu, P and Aho, VTE and Pope, PB and Schwarm, A}, title = {Intricate microbiome differences observed in lactating cows across methane intensity phenotypes.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag155}, pmid = {42549425}, issn = {2730-6151}, abstract = {Methane emissions from ruminants can be expressed through several metrics as total production, yield, or intensity, each reflecting distinct aspects of energy utilisation. Among these, methane intensity defined as grams of methane emitted per kilograms of energy-corrected milk, directly links emissions to productive efficiency; however, the microbial mechanisms underlying variation in this trait remain unclear. Here, we applied genome-resolved metagenomics and metatranscriptomics to characterise rumen microbial identity, functional potential, and transcriptional activity in lactating cows differing in methane intensity while sharing breed and diet. Microbial community composition and diversity were comparable across phenotypes. However, rumen microbial gene expression revealed marked functional divergence. The rumen content of low-methane-intensity cows showed enriched transcription of fructan-degrading carbohydrate-active enzymes and butyrate-forming pathways, primarily encoded by RUG440 (Atopobiaceae) metagenome-assembled genomes. These functions suggest a fructan-butyrate metabolic axis supported by potential cross-feeding between primary degraders and butyrate producers. Conversely, the high-methane intensity rumen exhibited greater transcription of pectin-degrading carbohydrate-active enzymes, mainly carried by Prevotella metagenome-assembled genomes, suggesting methyl-ester hydrolysis and methanol release. Despite higher methanogenesis transcript levels in high-methane intensity cows, total methane production did not differ between groups. Together, these findings reveal two contrasting functional configurations of the rumen microbiome in Norwegian Red dairy cattle: a fructan-butyrate-oriented metabolism in low-methane-intensity cows and a pectin-methanol-oriented metabolism in high-methane-intensity counterparts. This study provides genome-resolved, multi-omic evidence that microbial carbohydrate specialization and fermentation routing contribute to methane intensity phenotypes in dairy cows, offering mechanistic insights for improving ruminant climate efficiency.}, } @article {pmid42549478, year = {2026}, author = {Armstrong, E and Pinto, R and Kulikova, M and Yee, NR and Rishu, A and Muscedere, J and Sibley, S and Maslove, DM and Boyd, JG and Evans, GA and Detsky, M and Marshall, JC and Taggart, LR and Friedrich, JO and Tsang, JLY and Duan, E and Ali, KF and McCullagh, D and Findlater, A and Daley, P and Ramendra, R and Lother, S and Lamontagne, F and Fowler, R and Daneman, N and Coburn, B}, title = {Association of anti-anaerobic antibiotics with mortality and the gut microbiome: a sub-study of the BALANCE randomized clinical trial.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciag460}, pmid = {42549478}, issn = {1537-6591}, abstract = {BACKGROUND: Patients with suspected bloodstream infection often receive broad-spectrum antibiotics with anaerobic activity in the absence of clinical indication for anaerobic coverage. Anti-anaerobic antibiotics have been linked to adverse clinical outcomes in other populations, potentially by depleting intestinal anaerobes.

METHODS: We conducted a planned sub-study of the multisite BALANCE randomized controlled trial of antibiotic duration for bloodstream infection to assess the impact of anti-anaerobic antibiotics (receipt from three days pre-index culture to seven days post-index) on mortality and gut microbiome composition with metagenomic sequencing in patients without clinical indication for anaerobic coverage who survived to seven days post-index culture. The primary exposure was receipt of anti-anaerobic antibiotics from three days prior to the index culture to seven days post-index culture.

RESULTS: Among the 2851 eligible patients included in our primary analysis, 2106 (74%) received anti-anaerobic antibiotics and 745 (26%) did not. After balancing measured potential confounders through inverse probability of treatment weighting, anti-anaerobic antibiotics were associated with higher 90-day mortality (OR = 1.41, 95% CI 1.03 to 1.92, p = 0.03) and depletion of gut anaerobe relative abundance (fixed effect estimate = -16.59, 95% CI -30.67 to -2.52, p = 0.02). Increased duration of anti-anaerobic antibiotics was associated with greater mortality risk and additional gut anaerobe depletion.

CONCLUSIONS: Anti-anaerobic antibiotics are associated with increased mortality and gut microbiome disruption in patients with bloodstream infection. Minimizing exposure to anti-anaerobic antibiotics for bloodstream infection should be further explored in clinical trials as a potential treatment strategy to improve patient outcomes.}, } @article {pmid42549897, year = {2026}, author = {Schultz, J and Altalhi, S and Camargo, AP and Kyrpides, NC and Rosado, AS}, title = {Catalog of metagenome-assembled genomes of prokaryotic communities from the Red Sea hydrothermal vents.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0048226}, doi = {10.1128/mra.00482-26}, pmid = {42549897}, issn = {2576-098X}, abstract = {This study presents medium- and high-quality prokaryotic metagenome-assembled genomes (MAGs) from microbial mats and sediments at Hatiba Mons, a Red Sea hydrothermal system. We recovered 1,217 bacterial and archaeal MAGs across 75 phyla, dominated by Planctomycetota and Thermoproteota. Approximately 70% of these genomes likely represent previously uncharacterized taxa.}, } @article {pmid42549916, year = {2026}, author = {Liu, X and Fan, X and Wu, W and Ni, W and Hu, Y and Yang, Q and Wei, J and Yan, F and Chen, X and Yang, J and Hu, B and Yu, X and Li, W}, title = {Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical sample types, with analysis of paired bronchoalveolar lavage fluid and blood samples.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0405725}, doi = {10.1128/spectrum.04057-25}, pmid = {42549916}, issn = {2165-0497}, abstract = {Conventional metagenomic next-generation sequencing (mNGS) suffers from host nucleic acid interference and poor performance in low-biomass samples. Probe-capture metagenomic sequencing (PC-mNGS), which enriches microbial targets via hybridization probes, shows superior sensitivity but lacks systematic multi-sample evaluations. This study compared PC-mNGS and mNGS across diverse clinical specimens (bronchoalveolar lavage fluid [BALF], blood, cerebrospinal fluid [CSF]) and assessed the clinical utility of pathogen co-detection in paired BALF-blood samples from sepsis patients. A total of 282 samples (81 BALF, 141 blood, 25 CSF, 35 others) sequenced by both PC-mNGS and mNGS were analyzed. Additionally, 621 paired BALF-blood samples from sepsis patients with pulmonary infections were evaluated. PC-mNGS achieved higher pathogen detection rates (66.67% vs 57.10%, P = 0.000198) than mNGS, particularly in blood (66.67% vs 47.52%, P = 2.5 × 10[-5]). PC-mNGS detected more bacteria (19 species exclusive) and fungi (11 species exclusive) than mNGS. Viruses showed comparable detection. BALF and CSF exhibited high overall agreement (OPA: 96.30% and 88%, respectively), while blood had lower concordance (NPA: 54.05%, OPA: 70.92%). A total of 60.55% of BALF-positive samples (PC-mNGS) had co-detected pathogens in blood. Gram-negative bacteria (e.g., Klebsiella pneumoniae) and fungi (e.g., Candida albicans) showed higher blood co-detection rates than viruses. In this study, PC-mNGS detected more pathogens and showed a higher positivity rate than mNGS in blood samples. BALF sequencing data, particularly bacterial reads per million (RPM), may predict bloodstream co-detection, aiding in sepsis management. However, clinical validation and integration with traditional diagnostics are needed to confirm utility. This study highlights PC-mNGS as a promising tool for complex infections but underscores the need for rigorous multi-context validation.IMPORTANCEAccurate and rapid identification of pathogens is critical for effective treatment of severe infectious diseases, such as sepsis. This study demonstrates that probe-capture metagenomic sequencing (PC-mNGS) detected more pathogens in blood samples compared to conventional metagenomic sequencing, especially for bacterial and fungal infections. By analyzing paired lung and blood samples, we show that high pathogen levels in lung fluid may predict bloodstream infection, offering a potential early warning for clinicians. These findings support the use of PC-mNGS as a more sensitive diagnostic tool, which could lead to faster, more targeted therapies and better outcomes for patients with complex infections.}, } @article {pmid42550599, year = {2026}, author = {Miozzi, L and Rotunno, S and Frascati, F and Marra, M and Nugnes, F and Bernardo, U and Marian, D and Bertacca, S and Ballardini, M and Accotto, GP and Vaira, AM and Noris, E}, title = {Vector-enabled metagenomics reveals the first detection of the geminivirus beet curly top Iran virus in Europe.}, journal = {The Journal of general virology}, volume = {107}, number = {8}, pages = {}, doi = {10.1099/jgv.0.002271}, pmid = {42550599}, issn = {1465-2099}, mesh = {*Geminiviridae/genetics/isolation & purification/classification ; *Metagenomics/methods ; Animals ; *Plant Diseases/virology ; *Insect Vectors/virology ; Europe ; Citrullus/virology ; Cucurbita/virology ; *Hemiptera/virology ; DNA, Viral/genetics ; Phylogeny ; Genome, Viral ; }, abstract = {Geminiviruses are among the most threatening emerging insect-borne viruses and are responsible for serious outbreaks worldwide. Climate change (i.e. higher temperatures) could further exacerbate their impact on crops, highlighting the need for new diagnostic approaches to manage potentially dangerous situations. vector-enabled metagenomics (VEM) exploits the natural ability of highly mobile insects to accumulate viruses acquired from plants over time and space within an ecosystem; this approach is effective for monitoring the presence of new invasive or indigenous viruses in large areas. Geminiviruses have circular ssDNA genomes that can be readily targeted by rolling circle amplification (RCA). The combination of RCA and VEM largely increases the chances of detecting geminiviruses. This approach enabled us to identify the becurtovirus beet curly top Iran virus (BCTIV, Becurtovirus betae) in insects collected in Europe. BCTIV is a major pathogen of sugar beet but can also infect plants of other families; it is transmitted by cicadellids and has so far been detected only in Iran and Anatolia (Turkey). We also show that two cucurbit species, watermelon (Citrullus lanatus) and zucchini (Cucurbita pepo) are both natural and experimental hosts for BCTIV.}, } @article {pmid42551151, year = {2026}, author = {Deng, WQ and Lu, ZM and Li, XB and Fan, ZY and Li, T and Zhang, XJ and Chai, LJ and Xu, HY and Zhang, QS and Shi, JS and Chen, G and Xu, ZH}, title = {Decoding the thermocyclic solar-driven fermentation: Multi-omics insights into microbial and metabolic dynamics of traditional Chishui river basin soy sauce.}, journal = {Food chemistry}, volume = {525}, number = {Pt 4}, pages = {150595}, doi = {10.1016/j.foodchem.2026.150595}, pmid = {42551151}, issn = {1873-7072}, abstract = {Traditional Chishui River Basin soy sauce is produced through prolonged solar-cycle fermentation under diurnal temperature fluctuations and moisture absorption. Here, we employed integrated metagenomic and metabolomic analyses to investigate microbial and metabolic dynamics throughout fermentation. Results revealed a three-phase microbial succession: initial fungal-hydrolytic phase dominated by Aspergillus oryzae (82.28%), marked by proteolysis and amino acid accumulation; transitional phase enriched with Weissella (23.45%) and Zygosaccharomyces rouxii (5.85%), producing organic acids, esters, and maillard intermediates; maturation phase dominated by Bacillus (86.48%), associated with sharp increases in umami-enhancing peptides, pyrazines (e.g., tetramethylpyrazine), and phenolic compounds (e.g., 4-ethylguaiacol). Extended sun exposure selects for Bacillus dominance, allows sufficient time for slow chemical reactions, and enriches the volatile profile with stable pyrazines and phenolic compounds. These findings validate the flavor and mechanisms of traditional Chishui River Basin soy sauce and offer strategies for fermentation optimization via environmental and microbial regulation while maintaining product authenticity.}, } @article {pmid42551230, year = {2026}, author = {Zhuang, T and Wang, X and Zheng, W and Lu, W and Hao, L and Wang, X and Huang, C and Wang, R and Hu, Y and Wang, Z and Chen, K and Li, T and Yang, Q and Yang, L and Ding, L}, title = {Enrichment of Akkermansia muciniphila by red ginseng promotes GDF15 secretion and suppresses obesity in mice.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {160}, number = {}, pages = {158600}, doi = {10.1016/j.phymed.2026.158600}, pmid = {42551230}, issn = {1618-095X}, abstract = {BACKGROUND: Obesity is a growing global health burden with rising incidence. Red ginseng (RGS), a traditional processed ginseng product, shows potential for improving metabolic parameters, though its anti-obesity mechanism remains incompletely understood.

PURPOSE: This study investigated the therapeutic effects of short-term RGS administration on obesity and sought to elucidate the underlying mechanism.

METHODS: A high-fat diet (HFD)-induced obese mouse model was used to assess short-term RGS effects. Antibiotic treatment and fecal microbiota transplantation were performed to evaluate gut microbiota involvement. 16S rRNA sequencing and metagenomic analysis identified key bacterial species, and mass spectrometry-based proteomics identified A. muciniphila-derived proteins. The growth differentiation factor 15 (GDF15)-GFRAL axis was interrogated using Gfral[‒/‒] mice.

RESULTS: Short-term RGS treatment suppressed appetite, reduced body weight, and elevated circulating GDF15 in diet-induced obese (DIO) mice. RGS enriched A. muciniphila, and its depletion abrogated RGS-mediated weight loss and appetite suppression. The A. muciniphila-derived protein Amuc_1631 was identified as a key effector promoting GDF15 secretion. Mechanistically, RGS upregulated colonic Gdf15 transcription via the PERK-eIF2α-ATF4-CHOP axis and activated the brainstem GDF15-GFRAL pathway. The RGS 50% ethanol eluate (RGS/50) fraction was identified as the potential active component responsible for A. muciniphila enrichment and GDF15 elevation.

CONCLUSIONS: This study identifies a gut microbiota-dependent mechanism underlying the anti-obesity effects of RGS, centered on A. muciniphila enrichment and its derived protein Amuc_1631, which promotes GDF15 secretion to suppress food intake via the GDF15-GFRAL axis.}, } @article {pmid42551280, year = {2026}, author = {Filker, S and Katzenmeier, S and Breiner, HW and Brandt, MI and Hestetun, JT and Dahlgren, TG and Kupczok, A and Stoeck, T}, title = {Response of marine benthic viral communities to anthropogenic disturbances.}, journal = {The Science of the total environment}, volume = {1049}, number = {}, pages = {182106}, doi = {10.1016/j.scitotenv.2026.182106}, pmid = {42551280}, issn = {1879-1026}, abstract = {Viruses are key regulators of microbial mortality, gene flow, and metabolic functioning in marine sediments, yet their responses to different forms of anthropogenic disturbance remain poorly understood. Here, we present the first comparative viral metagenomic analysis of benthic viral communities across two major but contrasting disturbance regimes: organic enrichment beneath salmon aquaculture farms and crude-oil contamination near offshore oil installations. Using 123 sediment metagenomes from Scotland and Norway, we assessed how virus diversity, taxonomic composition, and community structure vary between high- and low-impact sites within each disturbance type and across regions. Virus alpha-diversity increased consistently under high-impact conditions in all environments, suggesting enhanced microbial turnover or productivity in disturbed sediments. Viral taxonomic profiles revealed strong habitat specificity. Beta-diversity analyses showed that viral community composition differed clearly between disturbance regimes, although these patterns were expressed within the context of region-specific environmental settings and sedimentary processes that also influence benthic microbial dynamics. Only a very small core set of vOTUs occurred in all samples with peak abundances throughout all low-impact categories suggesting strong environmental filtering. Together, these findings reveal that benthic viral communities are highly sensitive to environmental perturbation and reflect the contrasting microbial and geochemical processes associated with organic enrichment and hydrocarbon contamination. Our results advance the understanding of viral ecology in industrially impacted marine sediments and highlight the potential of virus-based indicators in next-generation biomonitoring tools that capture the full complexity of benthic microbial dynamics in anthropogenically impacted coastal and offshore ecosystems.}, } @article {pmid42551374, year = {2026}, author = {Wu, Y and Liu, K and Ding, Y and Yan, Q and Guo, F and Zhang, H and Wu, X}, title = {Glycitein-mediated rhizosphere signaling recruitment and CobB deacetylation synergistically enhance fomesafen bioremediation by Klebsiella variicola W28.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143171}, doi = {10.1016/j.jhazmat.2026.143171}, pmid = {42551374}, issn = {1873-3336}, abstract = {Fomesafen, a persistent diphenyl ether herbicide, causes carry-over phytotoxicity and threatens agricultural soil ecosystems. Here, the previously isolated fomesafen-degrading strain Klebsiella variicola W28 was used to elucidate a cross-kingdom rhizosphere signaling mechanism linking soybean root exudates to bacterial colonization and fomesafen degradation. Untargeted metabolomics showed that fomesafen stress selectively enriched glycitein in soybean root exudates. Glycitein enhanced W28 chemotaxis, motility, biofilm formation, and root-surface colonization, while metagenomic and random forest analyses revealed the assembly of a cooperative rhizosphere consortium enriched in Azotobacter, Klebsiella, cobB, and pcaG/H. Mechanistically, glycitein activated purine metabolism and the NAD[+] salvage pathway, thereby supporting the NAD[+]-dependent deacetylase CobB. GST pull-down, BiFC, and LCA confirmed direct CobB-LysR-pca interaction. EMSA showed that LysR-pca repressed the pcaGH promoter, whereas CobB-mediated deacetylation weakened DNA binding and relieved transcriptional repression. Molecular docking and product profiling demonstrated that heterologously expressed PcaGH directly transformed fomesafen, producing benzoic acid. Pot experiments confirmed that glycitein enhanced W28-mediated fomesafen degradation in soil. These findings define a root exudate-NAD[+] homeostasis-lysine deacetylation-pcaGH activation circuit, reveal how plant signals coordinate rhizosphere recruitment with intracellular catabolic activation, and provide a mechanistic basis for precision in situ bioremediation of diphenyl ether-contaminated soils.}, } @article {pmid42551380, year = {2026}, author = {Zhang, H and Chen, C and Wei, G and Zhang, B and Yang, X and Zhang, Y and Wu, H and Qiu, G and Zhu, S and Wei, C}, title = {Process architecture governs nitrate fate by controlling dissimilatory nitrate reduction to ammonium (DNRA)-denitrification competition in industrial wastewater systems.}, journal = {Water research}, volume = {306}, number = {}, pages = {126590}, doi = {10.1016/j.watres.2026.126590}, pmid = {42551380}, issn = {1879-2448}, abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) is increasingly recognized as an alternative nitrate reduction pathway, yet its quantitative importance and regulatory mechanisms in engineered wastewater treatment systems remain poorly resolved. Here, DNRA and denitrification were systematically quantified across four full-scale coking wastewater treatment plants operated under contrasting recirculation and non-recirculation modes. Long-term performance monitoring combined with [15]N stable isotope tracing showed that DNRA accounted for 8.0-29.5% of total nitrate reduction, with substantially higher contributions under recirculation-based operation. Although denitrification remained the dominant pathway for nitrate removal, enhanced DNRA promoted ammonium accumulation and significantly impaired total nitrogen removal efficiency. Process configuration was associated with contrasting nitrate-reduction outcomes by reshaping local substrate stoichiometry and toxicity exposure: high COD/NO3[-] ratios and persistent nitrogenous toxicants in recirculation systems were associated with greater DNRA contribution, whereas spatially decoupled non-recirculation configurations maintained more balanced conditions that favored denitrification and supported anaerobic ammonium oxidation. Integrated analyses of microbial community assembly, ecological networks, and metagenome-resolved functions revealed that non-recirculation systems maintained higher microbial diversity, functional redundancy, and network robustness, while recirculation systems exhibited undominated assembly and enrichment of DNRA-associated taxa and genes. Collectively, these results demonstrate that nitrate reduction pathways are not solely determined by microbial functional potential, but instead emerge from the coupled interactions among process configuration, material composition, and microbial functionality. This study highlights that controlling the fate of nitrogen in engineered wastewater systems relies heavily on designing environmental conditions that selectively favor the utilization of existing metabolic potential.}, } @article {pmid42542144, year = {2026}, author = {Li, X and Wang, B and Zeng, W and Zhang, L and Peng, Y}, title = {Robust nitrogen removal through simultaneous denitrification and anammox driven by alkaline sludge fermentation liquid at varying nitrification levels.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135552}, doi = {10.1016/j.biortech.2026.135552}, pmid = {42542144}, issn = {1873-2976}, abstract = {Operational instability of partial nitrification (PN) remains a major barrier to mainstream energy-efficient wastewater treatment. Here, a stable simultaneous denitrification-anammox system driven by alkaline sludge fermentation liquor (ASFL) under varying nitrification levels (PN, complete nitrification, and their coexistence) has been presented. Through a 240-day continuous operation treating municipal wastewater, this system achieved high nitrogen removal efficiency, ranging from 96.9 ± 2.0% under PN to 95.7 ± 2.4% under coexistence of PN and complete nitrification. Isotope tracing and microbial analyses indicated that ASFL-supported heterotrophic denitrification was the dominant nitrogen removal pathway, whereas anammox activity remained detectable but contributed only to a limited extent under the investigated conditions. Metagenomic analysis revealed functional shifts in nitrogen metabolism while the core carbon metabolic potential remained largely conserved. Combined with an optimized iron-assisted strategy for effluent polishing, this ASFL-driven simultaneous denitrification-anammox framework provides a sustainable, circular pathway for energy-efficient nitrogen removal, addressing the inherent vulnerability of mainstream PN applications.}, } @article {pmid42542146, year = {2026}, author = {McKnight, MM and Lakshminarasimman, N and Parker, W and Neufeld, JD}, title = {Microbiology of a membrane aerated biofilm reactor upgrade in a municipal wastewater treatment facility.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135550}, doi = {10.1016/j.biortech.2026.135550}, pmid = {42542146}, issn = {1873-2976}, abstract = {Novel wastewater treatment biotechnologies, including membrane aerated biofilm reactors (MABR), aim to reduce energy consumption, and improve nitrogen removal and nitrification in cold weather conditions. A municipal wastewater treatment plant (WWTP) in southern Ontario was upgraded with a large-scale MABR system in 2022, which was installed upstream of the existing conventional activated sludge (CAS) system. Here we evaluated how the MABR upgrade impacted mixed liquor and MABR biofilm microbial communities spatially and temporally, which previously has not been done in large-scale hybrid MABR-CAS systems. Microbial communities were characterized using 16S rRNA gene amplicon sequencing, with selected MABR biofilm samples analyzed with metagenomics to evaluate the functional potential of the biofilm for nitrification and denitrification. The CAS mixed liquor before the upgrade included ammonia-oxidizing bacteria (AOB; Nitrosomonas) and nitrite-oxidizing bacteria (NOB; Nitrotoga), which exhibited seasonal abundance and activity patterns. Following the upgrade, seeding from the MABR biofilm increased diversity of the mixed liquor, including nitrifiers. Along with AOB, Nitrospira NOB and comammox Nitrospira were present in the MABR biofilm, representing upwards of 10 % of microbial community profiles. Metagenomic sequencing showed that biofilm microbial communities were equipped to perform nitrification and denitrification in the system. Overall, characterization of microbial communities in the WWTP showed that the MABR installation increased microbial diversity, concomitant with increased representation of nitrifier groups and coinciding with reductions in plant effluent nitrogen concentrations.}, } @article {pmid42542148, year = {2026}, author = {Zhong, Y and Su, Q and Pan, X and Zou, X and Zhang, J and He, J and Ng, HY}, title = {Long-term stability of anaerobic digestion of thermally hydrolyzed waste activated sludge driven by N-doped Biochar-Supported Magnetite: Metagenomic insights into direct interspecies electron transfer.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135546}, doi = {10.1016/j.biortech.2026.135546}, pmid = {42542148}, issn = {1873-2976}, abstract = {Fluctuations in organic loading often destabilize anaerobic digestion (AD) performance, thereby limiting methane (CH4) production. This study evaluated effects of hybrid conductive material, N-doped biochar-supported magnetite (Fe3O4@N-BC), on long-term stability of AD of thermally hydrolyzed waste activated sludge in up-flow anaerobic sludge blanket (UASB) reactors under decreasing hydraulic retention times (18-6 days). Fe3O4@N-BC-amended reactor maintained superior and stable performance, achieving 22-122% higher CH4 yields than the Control reactor over the 150-day operational period. Enhanced stability was associated with improved hydrolysis and the establishment of direct interspecies electron transfer (DIET) between Clostridium and Methanosarcina. Electron transfer was facilitated through multiple pathways, including conductive materials, e-pili, and extracellular polymeric substances. The CH4/CO2 ratio is proposed as a rapid and practical indicator of DIET under comparable conditions. The results provide metagenomic insights into the mechanism of Fe3O4@N-BC-mediated DIET during AD and highlight its potential application in reactors under dynamic operational conditions.}, } @article {pmid42543104, year = {2026}, author = {Fan, J and Cao, S and Du, R and Peng, Y}, title = {Synergistic operational optimizations and microbial responses stabilize filamentous-dominated continuous-flow partial denitrification-anammox at low-temperature.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135549}, doi = {10.1016/j.biortech.2026.135549}, pmid = {42543104}, issn = {1873-2976}, abstract = {The operational stability of continuous-flow partial denitrification-anammox (PD/A) systems is frequently constrained by insufficient nitrite supply and temperature sensitivity of anammox bacteria, particularly under low-temperature stress. In such conditions, filamentous bacteria often proliferate excessively, and their overgrowth has long been associated with reactor instability and performance deterioration. Here, we demonstrate stable nitrogen removal in a filamentous-dominated continuous-flow PD/A reactor at an average temperature of 16.7 °C through operational optimizations and microbial responses. The reactor achieved 89.8 % total nitrogen removal, with ammonium and nitrate removal efficiencies of 97.2 % and 91.5 %, respectively, with anammox contributing up to 98.3 % of nitrogen removal. Metagenomic analyses revealed that the filamentous genus Sphaerotilus dominated the microbial community (29.3-41.5 %) but sustained the genomic potential for nitrite availability to support anammox. Genome-centric reconstruction confirmed that a Sphaerotilus-affiliated MAG5 possessed adaptive features under low temperature. Additional heterotrophs, including Leptothrix, Rubrivivax, and Thauera, harbored genomic potential for auxiliary nitrate-to-nitrite conversion. Crucially, the synergy between this genomic potential for nitrite provision and engineered biomass retention (specifically mesh filtration and regular sludge return) facilitated the enrichment of Ca. Brocadia, increasing its relative abundance from 2.4 % to 5.4 %. Concurrently, Ca. Brocadia reinforced low-temperature adaptability by expanding the genetic potential of energy-generating carbon metabolic pathways and increasing its contribution to the cold shock protein gene cspA from 6.6 % to 21.0 %. Collectively, this study reveals that integrating strategic biomass retention with microbial responses provides a viable pathway to sustain stable nitrogen removal in filamentous-dominated continuous-flow PD/A systems.}, } @article {pmid42543651, year = {2026}, author = {Nannya, Y}, title = {[Hematopoietic cell transplantation in the era of genome analysis].}, journal = {[Rinsho ketsueki] The Japanese journal of clinical hematology}, volume = {67}, number = {7}, pages = {794-801}, doi = {10.11406/rinketsu.67.794}, pmid = {42543651}, issn = {0485-1439}, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/methods ; Myelodysplastic Syndromes/genetics/therapy ; *Genomics ; Neoplasm, Residual ; Polymorphism, Single Nucleotide ; *Hematologic Neoplasms/genetics/therapy ; Leukemia, Myeloid, Acute/genetics/therapy ; Graft vs Host Disease ; }, abstract = {Genomic information for hematologic malignancies is now routinely available in clinical practice, supporting the adaptation of hematopoietic cell transplantation, selection of conditioning intensity, and implementation of post-transplant maintenance therapy through refinement of disease risk assessment and minimal residual disease (MRD) measurement. This review presents the current evidence on the effective utilization of genomic information for acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and myeloproliferative neoplasms (MPN). It also presents an up-to-date framework for optimal donor selection based on donor genome information, addressing both donor clonal hematopoiesis of indetermined significance and the risk that related donor candidates may carry the same hereditary predisposition. Finally, it discusses research showing that patient and donor genetic polymorphisms (SNPs) can predict transplant complications such as GVHD, and that reduced gut microbiota diversity, as detected by metagenomic analysis, impacts GVHD severity and survival. These examples illustrate the multifaceted role of genomic information in research efforts to improve hematopoietic cell transplantation outcomes.}, } @article {pmid42543873, year = {2026}, author = {Wang, J and Peng, Q}, title = {Innovations, Applications, and Future Trends in Veterinary Diagnostic Technologies.}, journal = {Transboundary and emerging diseases}, volume = {2026}, number = {1}, pages = {e6973879}, doi = {10.1155/tbed/6973879}, pmid = {42543873}, issn = {1865-1682}, support = {32470195//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Veterinary Medicine/trends/methods ; *Animal Diseases/diagnosis ; High-Throughput Nucleotide Sequencing/veterinary ; }, abstract = {Veterinary diagnostics is undergoing a significant transformation driven by technological advancements, extending its scope from the traditional confirmation of specific pathogens to the continuous, dynamic surveillance of animal population's health. This paradigm shift has the potential to enable more timely disease control, precise intervention, and enhanced public health security. Traditional clinical and laboratory diagnostic methods, such as microbial culture, serological assays, and nucleic acid-based polymerase chain reaction, form the cornerstone of the current diagnostic framework and are widely applied based on varying detection needs and practical environments. Nonetheless, the field is experiencing profound innovation. Firstly, novel detection technologies are emerging, such as digital PCR (dPCR), CRISPR-Cas-based molecular diagnostic tools, next-generation sequencing (NGS), and metagenomic sequencing. These technologies have not only achieved breakthroughs in sensitivity and specificity but, more importantly, enable the unbiased discovery of novel pathogens. Secondly, the deep integration of artificial intelligence (AI) and big data is reshaping the diagnostic pipeline. By consolidating and analyzing multimodal information streams from imaging, genomics, wearable devices, and production data, AI algorithms can provide objective, quantitative decision support, facilitating a transition from post-symptomatic diagnosis towards predictive and preventive health management. This scoping review systematically summarizes both mainstream and emerging veterinary diagnostic technologies, elaborates and discusses their advantages and limitations as well as future developmental directions, while highlighting that the combined application of multiple methods represents an optimal diagnostic strategy.}, } @article {pmid42545016, year = {2026}, author = {Seo, Y and Kim, J and Yeom, M and Park, S-Y and Lee, S and Ahn, S and Hahm, D-H and Kim, K and Kwon, S-K and Park, H-J}, title = {Gut microbiota contributes to the therapeutic effect of acupuncture in atopic dermatitis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0391225}, doi = {10.1128/spectrum.03912-25}, pmid = {42545016}, issn = {2165-0497}, abstract = {UNLABELLED: The gut microbiome is increasingly recognized as a central regulator of immune homeostasis, metabolic balance, and therapeutic outcomes. Atopic dermatitis (AD), a chronic inflammatory skin disease, is closely linked to gut microbial dysbiosis. Traditionally regarded as a neurostimulatory therapy, acupuncture (Acu) has demonstrated increasing efficacy in alleviating AD symptoms and improving gastrointestinal function. These observations suggest that the therapeutic effects of Acu in AD may be mediated, in part, by modulation of the gut microbiome. In this study, AD patients were stratified into responder (R) and non-responder (NR) groups based on clinical improvement. Gut microbiome profiling revealed that R patients exhibited greater microbial diversity and compositional stability, indicative of a more balanced gut ecosystem. Specific taxa, including Alistipes ihumii and Odoribacter splanchnicus, were enriched in R individuals and may serve as microbial predictors of treatment responsiveness. Importantly, fecal microbiota transplantation (FMT) from R donors restored Acu efficacy in a mouse model of AD, whereas FMT from NR donors did not. These findings support the gut-skin axis and highlight the integral role of the gut microbiome in mediating the therapeutic effects of Acu for AD, suggesting potential for microbiome-based personalized treatment.

IMPORTANCE: Increasing evidence supports the gut microbiome's role in modulating treatment responses in atopic dermatitis (AD), but direct evidence linking acupuncture efficacy with microbiome composition has been lacking. Previous studies did not assess causal relationships via fecal microbiota transplantation (FMT) or functional metagenomics. This study identifies specific gut microbes associated with acupuncture response in AD and confirms their causal role using FMT. It also links functional metabolic pathways to therapeutic efficacy, offering a mechanism-based insight. Our findings support microbiome-informed personalized acupuncture approaches for AD and suggest gut microbiota as a therapeutic modulator in neuroimmune regulation.

CLINICAL TRIALS: This study was registered in the Korean Clinical Trial Registry (CRIS, registration number: KCT0005422).}, } @article {pmid42545024, year = {2026}, author = {Carlson-Jones, JAP and Goddard, TR and Papudeshi, B and Mallawaarachchi, V and Whiteson, KL and Warner, MS and Morton, JM and Jersmann, HPA and Edwards, RA}, title = {DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.}, journal = {Clinical microbiology reviews}, volume = {}, number = {}, pages = {e0035225}, doi = {10.1128/cmr.00352-25}, pmid = {42545024}, issn = {1098-6618}, abstract = {SUMMARYDNA sequencing has revolutionized microbial surveillance in cystic fibrosis (CF), transforming pathogen identification from culture-dependent to total microbial community identification using molecular-based approaches. Techniques such as 16S rRNA gene sequencing have uncovered the complexity of the CF airway microbiome, while shotgun metagenomics, metatranscriptomics, and viromics now provide strain-level, functional, and viral insights beyond bacterial identification. Despite these advances, key technical and logistical challenges remain, including the processing of high-viscosity sputum samples, overwhelming host DNA contamination, managing large data sets, and the integration of complex bioinformatic outputs into clinical workflows. Emerging innovations such as host DNA depletion protocols, targeted enrichment panels, and adaptive sampling on Oxford Nanopore platforms are helping to overcome these barriers, improving microbial recovery and sequencing efficiency. As cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies are changing the lives of people with cystic fibrosis (pwCF), sequencing offers an unprecedented opportunity to track potential microbial adaptation in response. This review investigates current advances, limitations, and translational opportunities in DNA sequencing for CF airway microbiome surveillance, highlighting how these technologies can help reshape research and clinical microbiology in the post-modulator era.}, } @article {pmid42545805, year = {2026}, author = {}, title = {Correction to: Ghost-rocks' microbiota: metagenomic insights into their influence on the biogeochemistry of karstic cave and groundwater.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {8}, pages = {}, doi = {10.1093/femsec/fiag088}, pmid = {42545805}, issn = {1574-6941}, } @article {pmid42546031, year = {2026}, author = {Kawagishi, T and Sakai, Y and Oki, H and Nouda, R and Kanai, Y and Kawahara, K and Nakamura, S and Shimojima, M and Saijo, M and Matsuura, Y and Kobayashi, T}, title = {Nelson Bay Orthoreovirus cell attachment protein σC determines strain-specific differences in infectivity and pathogenesis.}, journal = {PLoS pathogens}, volume = {22}, number = {8}, pages = {e1014409}, doi = {10.1371/journal.ppat.1014409}, pmid = {42546031}, issn = {1553-7374}, mesh = {Animals ; *Orthoreovirus/pathogenicity/genetics/metabolism ; Virulence ; *Reoviridae Infections/virology/metabolism ; Chiroptera/virology ; Mice ; Humans ; *Sigma Factor/metabolism/genetics ; }, abstract = {Nelson Bay orthoreovirus (NBV) was initially discovered in a bat sample but has since been isolated from patients with acute respiratory tract diseases. Accumulating reports of NBV isolation from patients with respiratory tract viral infections suggest that NBV is able to transmit and cause disease in humans. However, the underlying molecular mechanisms remain unclear. We previously established a reverse genetics system for NBV Miyazaki-Bali/2007 (MB) strain isolated from a patient with an acute respiratory tract disease. We found that the fusion-associated small transmembrane protein (FAST)-which is necessary for syncytium formation-and cell attachment protein σC play crucial roles in MB virulence; however, whether these gene products determine the strain-specific difference in NBV virulence remains unclear. Therefore, here, we compared the virulence of the MB strain with that of the NBV strain isolated from a bat sample (NelB strain). We found that the NelB strain did not cause a virulent phenotype in the mouse model. Using reverse genetics, we found that the S1 gene segment correlates with the virulent phenotypes of NBV strains. Moreover, among the three proteins encoded by the S1 gene segment, structural protein σC, but not nonstructural proteins FAST or p17, contributed to the difference in virulence in vivo. Further analysis using a panel of σC mutant viruses showed that the middle body domain in σC was involved in the different virulent phenotypes, rather than the C-terminal head domain, which contains a putative receptor-binding domain. These results provide new insights into the mechanisms underlying NBV transmission and pathogenesis.}, } @article {pmid42542141, year = {2026}, author = {Liu, W and Zhang, Y and Yue, C and Wang, J and Li, J and Lu, H and He, S and Peng, Y}, title = {Impacts of carbon source type on metabolic pathways and microbial synergy in the simultaneous anammox and endogenous denitrification process.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135540}, doi = {10.1016/j.biortech.2026.135540}, pmid = {42542141}, issn = {1873-2976}, abstract = {Simultaneous anammox and endogenous denitrification (SAED) process enables efficient nitrogen removal from low carbon-to-nitrogen wastewater, yet how carbon source type influences microbial synergy and system robustness remains unclear. This study evaluated the sludge characteristics, performance, and ecological traits of three SAED systems fed with acetate (HAc), propionate (HPr), and glucose (Glc) over 476 days. Results showed that the Glc-fed system achieved the highest and most stable nitrogen removal performance (95.0 % ± 2.4 %), significantly outperforming the HAc-fed (93.3 % ± 2.7 %) and HPr-fed (87.6 % ± 2.5 %) systems. Glucose promoted the formation of large (∼870 μm), dense granules with a high organic fraction (0.904), effectively mitigating the sludge washout and inorganic mineral precipitation observed in HAc-fed and HPr-fed systems. Microbial ecological network analysis reveals that different types of carbon sources reconfigured heterotrophic communities by mediating distinct microbial interactions. The Glc-fed system exhibited the highest proportion of positive correlations (90.9 %), particularly between Denitratisoma (13.5 %) and Candidatus Brocadia (22.2 %), bolstering system robustness. Furthermore, metagenomic analysis further confirms that nitrate reductase genes (nar/nap at 674.8 RPKM in total) were significantly more enriched than nitrite reductase genes (nir at 210.6 RPKM in total) in the Glc-fed system, facilitating an efficient nitrate-to-nitrite shunt for anammox bacteria while bypassing the competitive pathways (e.g., full denitrification in HAc-fed; DNRA in HPr-fed). Therefore, leveraging glucose-driven metabolic flux optimizes both sludge characteristics and microbial interactions in SAED process, providing a robust treatment for low-carbon wastewater.}, } @article {pmid42537279, year = {2026}, author = {Sohrab, A and Stancheva, R and Mansoor, F and Wei, B and Stubler, S and Boyer, GL and Shriver, R and Blaszczak, J and Goel, R}, title = {Cyanobacterium Microcoleus in toxic benthic mats on different streambed substrates: Ecophysiology and important metabolic pathways.}, journal = {Water research}, volume = {306}, number = {}, pages = {126515}, doi = {10.1016/j.watres.2026.126515}, pmid = {42537279}, issn = {1879-2448}, abstract = {Benthic cyanobacteria, notably the genus Microcoleus, are a common contributor to benthic harmful algal blooms globally and can produce neurotoxins. Microcoleus can thrive in nutrient-limited freshwater environments, which present significant environmental and public health challenges. In May 2023, we observed Microcoleus mat growing in a small tributary of the Virgin River in Zion National Park near the Temple of Sinawava and collected benthic mats from three rock and three sandy substrate (strata) sites in the Virgin River. The overall objective of this study was to evaluate the effect of the bottom substrate (sand versus rock) on the ecophysiology of cyanobacteria, primarily Microcoleus, and other coexisting bacteria. Toxin measurements revealed that all the benthic mat samples contained anatoxin-a (ATX377.13±18.05 µg/g of wet mat) and dihydroanatoxin-a (15±0.3 µg/g of wet mat), and anatoxin-A was also present in the water column (0.377 µg/L). Low chlorophyll-a levels and microscopy results indicate that the toxins in the water flowing into the Virgin River presumably originated from benthic sources rather than from planktonic algae. Community analysis showed strong cyanobacterial dominance (>60%) in mats. Biofilms, especially those formed on sand as compared to those formed on rocks, supported greater heterotrophic bacterial diversity. A single dominant toxigenic Microcoleus genotype occurred across both strata (rock and sand) at all sampled sites, and it is closely related to the Microcoleus anatoxicus previously found in the Russian River, CA. Bottom strata type effects were most prominent in phosphorus acquisition: rock-associated heterotrophic communities showed higher expression of phosphonate utilization genes (C-P lyase) and glycerophosphodiester utilization (ugp). Samples from both substrates showed strong expression of pst/pho regulators, indicating organic phosphorus uptake. Active nitrogen fixation genes were also found in some metagenomic-assembled genomes (MAGs), suggesting internal nitrogen cycling in Microcoleus mats. Despite producing dihydroanatoxin-a, Microcoleus MAGs from this study lack the anaK gene, which is hypothesized to convert anatoxin-a to dihydroanatoxin-a. Toxic Microcoleus genomes recovered from Zion National Park encoded a complete thiamine biosynthesis pathway, including thiD. This contrasts with previous studies, which reported thiD loss in toxic Microcoleus. Overall, our results show a stable toxic Microcoleus genotype that dominates across substrates, while substrate-linked community functions between rock and sand habitats vary, especially in phosphorus acquisition.}, } @article {pmid42537940, year = {2026}, author = {Jiang, Q and Xu, Y and Xu, P and Kang, Y and Ou, R and Wu, X and Peng, X and Li, L}, title = {Untangling how thermal pretreatment and distiller's grains enhance humification and reduce emissions in food waste residue composting.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135527}, doi = {10.1016/j.biortech.2026.135527}, pmid = {42537940}, issn = {1873-2976}, abstract = {To address the challenges of slow start-up, poor humification efficiency, and elevated gaseous pollutant emissions during food waste residue composting, this study employed a synergistic strategy combining high-temperature pretreatment (HTP) with the addition of distiller's grains (DG). By monitoring the composting process, humification, gas emissions, and conducting metagenomic analysis, the enhancement potential and underlying mechanisms of this strategy were elucidated. The results indicated that, compared to conventional composting, the synergistic enhancement of HTP and DG significantly shortened the maturity period by 35.7 %, increased the humification index by over 55.0 %, and elevated the total nitrogen, total phosphorus, and total potassium contents of the final product by 28.1 %, 14.3 %, and 17.1 %, respectively, while achieving the highest levels of available nutrients and synergistic reductions in greenhouse gas and odor emissions. Mechanistically, HTP rapidly improved the physical structure of the feedstock, establishing a favorable foundation for microbial activity; DG selectively enriched core functional genera, including Pseudomonas and Marinobacter, and upregulated functional genes associated with N2O reduction (nosZ), sulfur oxidation, and lignocellulose degradation, thereby enhancing humus synthesis and pollutant gas mitigation at the metabolic level. This study elucidates the synergistic mechanism of physical pretreatment and bioaugmentation from a microbial functional perspective, providing not only a feasible 'waste-treats-waste' technical pathway for the resource utilization of food waste residue but also a theoretical basis for the targeted design of efficient and low-emission composting processes.}, } @article {pmid42538237, year = {2026}, author = {Szentiványi, T and Vásárhelyi, Z and Garamszegi, LZ}, title = {Emerging methods in noninvasive parasite surveillance in wildlife disease ecology.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2026.07.006}, pmid = {42538237}, issn = {1471-5007}, abstract = {Noninvasive approaches are increasingly reshaping parasite and disease surveillance by reducing stress and harm to hosts while expanding opportunities for ecological and epidemiological research. In this opinion article, we discuss these emerging approaches, which rely on molecular, citizen-science, and computational methods, for monitoring parasites, vectors, and hosts. These tools can improve spatial and temporal coverage, support the surveillance of rare or threatened hosts and parasites, and contribute to the understanding of transmission pathways and disease dynamics. However, their reliability depends on careful validation, standardized protocols, and awareness of methodological limitations. While not direct substitutes for invasive methods, these approaches lift a considerable burden from wildlife. Integrating noninvasive approaches thus provides a strong basis for advancing disease ecology, wildlife health monitoring, and biodiversity conservation.}, } @article {pmid42538347, year = {2026}, author = {Rath, C and Fursule, A and Wong, F and Rao, S and Patole, S}, title = {Influence of probiotics on faecal antibiotic resistome in neonates: a systematic review.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {42538347}, issn = {1530-0447}, abstract = {BACKGROUND: Antimicrobial resistance (AMR) and its associated complications represent a major global health threat. Probiotics, among the limited available preventive strategies, may play an important role in reducing the risk of AMR.

METHODS: A systematic review of studies assessing faecal antibiotic resistome in neonates who did versus did not receive probiotic supplementation. Databases were searched in October 2025.

RESULTS: Eighteen studies (n = 3496) were included, comprising eight randomized controlled trials (RCTs) and ten observational studies (non-RCTs). Ten of the eighteen studies (RCTs: 5, non-RCTs: 5) reported significant reduction in the prevalence of faecal antibiotic resistome among probiotic supplemented infants. Five of the eight studies that reported no reduction relied on culture or polymerase-chain reaction-based methods rather than metagenomic analyses. No consistent associations were observed between probiotic dose and strain, or type of milk feeding and resistome colonization. Most included studies were assessed as having a low risk of bias. The certainty of evidence was rated as low to very low.

CONCLUSION: Probiotic supplementation may reduce faecal AMR gene colonization in neonates. Future RCTs should employ standardized study designs and include quantitative assessment of AMR gene abundance, along with clinically relevant outcomes such as sepsis and its associated complications.

IMPACT: The first comprehensive systematic review focused on the effect of probiotics on neonatal fecal resistome and mobile genetic elements, incorporating evidence from 18 studies involving 3496 neonates. Suggests a potential role for targeted probiotic strategies as an intervention for reducing early neonatal antimicrobial resistance colonization, particularly in preterm infants at high risk of multi-drug resistance sepsis. Positions microbiome modulation as a strategy complementary to antibiotic stewardship in tackling global neonatal antimicrobial resistance.}, } @article {pmid42538924, year = {2026}, author = {Bechara, NR and Garcia, M and Bland, MJ and Raymann, K}, title = {Parallel and Divergent Evolution in Pseudomonas aeruginosa Under Constant and Fluctuating Predator-Mediated Selection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.07.22.739916}, pmid = {42538924}, issn = {2692-8205}, abstract = {UNLABELLED: Environmental predation is a major driver of bacterial evolution and may indirectly influence virulence through coincidental selection. However, how sustained versus fluctuating predator pressure shapes long-term evolutionary trajectories remains poorly understood. Here, we used experimental evolution to investigate the genetic and phenotypic responses of Pseudomonas aeruginosa to continuous, absent, or fluctuating exposure to the protozoan predator Tetrahymena thermophila over 180 days. Whole-population and isolate-level shotgun metagenomic sequencing revealed fewer mutations over time but increasing frequencies of surviving mutations, consistent with selection, extensive gene-level parallel evolution, and signatures of both positive and purifying selection. Recurrently mutated genes encompassed diverse functional pathways, reflecting both shared and treatment-specific adaptive responses. Despite this parallelism, historical contingency was evident, with starting conditions influencing subsequent evolutionary trajectories. We also observed the emergence of hypermutator lineages, which are frequently recovered from chronic lung infections, suggesting that repeatedly evolving elevated mutation rates may represent a common adaptive strategy of P. aeruginosa across environmental and host-associated settings. Fluctuating predation repeatedly reshaped the adaptive landscape, leading to greater temporal turnover of mutations and a higher accumulation of mutations that ultimately reached fixation than in constant environments. Phenotypic assays revealed widespread divergence in fitness, motility, biofilm formation, siderophore production, protease activity, hemolysis, and cell size, whereas virulence in an invertebrate host model varied among treatments but did not differ significantly. Together, these findings demonstrate that variation in predator-mediated selection reshapes the dynamics and genetic targets of bacterial adaptation, highlighting the roles of ecological context, historical contingency, and hypermutability in driving the evolutionary trajectories of opportunistic pathogens.

SIGNIFICANCE STATEMENT: Environmental predators are drivers of bacterial evolution, yet their effects on adaptation remain poorly understood. We used experimental evolution to show that constant and fluctuating protozoan predation produce evolutionary trajectories in Pseudomonas aeruginosa, altering tempo, predictability, and targets of adaptation. Adaptation to predator-present or predator-absent environments shaped evolutionary trajectories, demonstrating importance of historical contingency. Fluctuating predation promoted turnover of mutations as populations adapted to selective pressures. We also observed repeated emergence of hypermutator lineages, a hallmark of chronic infections, suggesting that elevated mutation rates represent a favored adaptive strategy across environmental and host-associated settings. These findings provide insight into the environmental origins of genetic changes commonly associated with opportunistic pathogens, while showing that these changes do not necessarily increase virulence.}, } @article {pmid42539019, year = {2026}, author = {Paulson, JN and Whalen, AJ and Tindimwebwa, S and Hansen, J and Natukwatsa, D and Steven, K and Ochora, M and Mulondo, R and Kabachelor, EM and Ramelmeier, K and Nsubuga, BK and Omadi, PO and Magombe, J and Cohen, C and Muzahura, N and Onen, J and Ssenyonga, P and Broach, JR and Morton, SU and Osman, M and Joloba, M and Kigozi, E and Katabalwa, A and Apako, J and Amutuhaire, H and Tumuhairwe, JB and Kayemba, A and Namyalo, J and Masengere, H and Nambuya, H and Namutosi, A and Kasuswa, S and Omo, E and Tibenkana, I and Yayi, A and Muvawala, J and Nadiope, W and Muwanguzi, A and Kumbakumba, E and Ericson, JE and Schiff, SJ}, title = {Village-level surveillance of neonatal disease with integrated real-time dashboards and quality-control in Uganda.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.07.21.26358401}, pmid = {42539019}, abstract = {INTRODUCTION: Neonatal mortality remains disproportionately high in sub-Saharan Africa, where an estimated 27 neonatal deaths per 1,000 live births occur annually. Infections, including sepsis and meningitis, account for a substantial proportion of these deaths, while neural tube defects (NTDs) contribute significantly to both neonatal mortality and long-term disability. Existing surveillance systems in the region are predominantly facility-based, missing the substantial proportion of births and deaths that occur in the community. Population-based surveillance platforms that capture community-level data are urgently needed to generate accurate incidence estimates, identify modifiable risk factors, and guide evidence-based interventions.

COHORT DESCRIPTION: The Consortium to Reduce Infant Mortality (CONRIM) is a multi-institutional partnership among Ugandan physicians and scientists, Yale University, Penn State University, Boston Children's Hospital/Harvard Medical School, and Uganda's National Planning Authority. CONRIM conducts prospective, community-based neonatal surveillance within the Busoga Kingdom in eastern Uganda. A network of 813 trained Village Health Team members conducts household-level visits using a structured Open Data Kit (ODK)-based mobile questionnaire to capture every birth, assess for danger signs of possible serious bacterial infection (pSBI), screen for NTDs, and record maternal nutrition and folic acid use, water, sanitation and hygiene (WASH) conditions, and health care utilization.

FINDINGS TO DATE: Since surveillance began in June 2025, the platform has registered approximately 22,200 household submissions and over 5,700 newborn encounters across the Jinja District (population 660,000). Early data have identified higher than expected rates of infants with NTDs including encephalocele and spina bifida; documented folic acid non-use in before and during most pregnancies; characterized WASH conditions in birthplaces; and mapped geospatial hotspots of neonatal infection risk in northeastern rural subcounties. Prospective 28-day follow-up of all live births has demonstrated a neonatal mortality rate of 21.5 per 1000 live births. A real-time data quality monitoring system with 21 automated quality control flags maintains a 99% clean-record rate.

FUTURE PLANS: Ongoing and planned activities include laboratory-based confirmation of neonatal sepsis via blood culture and cerebrospinal fluid analysis with polymerase chain reaction capacity, portable neuroimaging for NTDs, environmental sampling, genomic studies of folate metabolism pathway genes, linkage with facility-based records at Jinja Regional Referral Hospital and Mulago National Referral Hospital, and community-level interventions informed by surveillance findings.

KEY MESSAGES: What is already known on this topic: Neonatal mortality remains disproportionately high in sub-Saharan Africa, with sepsis and neural tube defects (NTDs) among the leading preventable causes. Existing surveillance systems are predominantly facility-based and fail to capture births, deaths, and environmental exposures occurring at the community level. Emerging approaches in digital health, geospatial analytics, and pathogen genomics have demonstrated potential to enhance infectious disease surveillance, but these have rarely been integrated into population-based neonatal monitoring systems in low-resource settings.What this study adds: The Consortium to Reduce Infant Mortality (CONRIM) is a multidisciplinary initiative designed to develop scalable, population-based systems for understanding and reducing neonatal mortality through integrated epidemiologic, environmental, and biologic data. This paper describes one implementation of the CONRIM framework in the Busoga Kingdom of eastern Uganda, where a network of 813 trained Village Health Team members conducts longitudinal, community-based surveillance of births, neonatal outcomes, NTDs, maternal nutrition (including folic acid use), water, sanitation and hygiene (WASH) conditions, and care-seeking behaviour. This implementation integrates: real-time digital data capture with automated quality control,geospatial information systems (GIS) and remote sensing to characterize environmental risk factors,population-level genomic and metagenomic sampling to investigate host and pathogen factors, anda One Health framework linking human, animal, and environmental exposures. Early findings highlight high data completeness, geospatial clustering of neonatal infection risk, low preconception folic acid use, and identification of NTD cases not captured by facility-based systems.How this study might affect research, practice, or policy: This study demonstrates the feasibility of implementing a community-based, real-time neonatal surveillance system within an existing community health worker network in a low-resource setting. By integrating geospatial, genomic, and environmental data within a unified platform, the CONRIM framework enables more precise identification of drivers of neonatal morbidity and mortality.The approach supports targeted public health interventions, including geographically informed infection control strategies, improved referral pathways, and evidence generation for folic acid fortification policies. More broadly, CONRIM provides a scalable infrastructure for future interventional studies and precision public health strategies aimed at reducing neonatal mortality.}, } @article {pmid42539242, year = {2026}, author = {De Santiago, A and Bik, H}, title = {MeioBIOME: A snakemake workflow for the parallel analysis of meiofaunal genomes and host-associated bacteria/archaea.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.07.23.740139}, pmid = {42539242}, issn = {2692-8205}, abstract = {Microbes closely interact with every living organism, including meiofauna (i.e., microbial eukaryotes 38 μm - 1 mm in length), and influence the development, life cycle, and evolution of diverse metazoans. Together, meiofauna and their microbiomes, collectively referred to as the holobiont, underpin biogeochemical cycles and drive decomposition of organic matter. However, our understanding of the ecological and evolutionary dynamics of meiofauna microbiomes are limited, typically owed to low-resolution 16S rRNA surveys, which cannot accurately delineate bacterial taxa. Single-specimen holobiont sequencing can help overcome the limitations of metabarcoding approaches by 1) generating metagenome-assembled genomes (MAGs) of the host microbiome and 2) recovering host single-copy genes (SCGs) to phylogenetically confirm the identity of the host organism. However, most bioinformatics pipelines for the assembly of metagenomic datasets have been developed for the assembly of high-complexity microbial communities of bulk sediment or soil samples (and cannot be used for the assembly of host genomes), rely on co-assembly approaches (which collapses strain-level genomic information of bacterial taxa), and focus on binning either prokaryotic or eukaryotic taxa. Therefore, there is a tremendous need for a computational workflow for the dual analysis of host genomes and their microbiomes. Here, we developed MeioBIOME, a modular Snakemake pipeline for the reproducible analysis of holobiont metagenomes obtained from individually sequenced microbial metazoa. We analyze publicly available single-specimen metagenomics datasets to show the utility of MeioBIOME and recover host-associated symbiont MAGs and host SCGs. Additionally, we integrate state-of-the-art binning algorithms which generate more MAGs than the DOE Joint Genome Institute metagenomic pipeline. We anticipate that MeioBIOME will facilitate studies of phylosymbiosis by generating high-quality host genome skims (to build well-supported host phylogenetic trees) and host-associated prokaryotic MAGs obtained from single specimens.}, } @article {pmid42539626, year = {2026}, author = {Han, J and Zhao, W and Deng, R and Wang, Y and Gong, W and Wang, Z and Sun, G and Liu, H and Geng, M and Zhang, Y}, title = {Sodium oligomannate reduces cerebral infarction and improves neurological function through microbiota remodeling in MCAO/R rats.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1880590}, doi = {10.3389/fphar.2026.1880590}, pmid = {42539626}, issn = {1663-9812}, abstract = {BACKGROUND: Ischemic stroke is the second leading cause of death worldwide, characterized by high mortality and a narrow therapeutic window for thrombolysis. Gut microbiota dysbiosis and gliosis following ischemic stroke are key drivers of post-stroke neurological impairment. Sodium oligomannate (GV-971) is a low-molecular-weight acidic oligosaccharide that targets the gut-brain axis. It alleviates gliosis and improves cognitive dysfunction by remodeling gut microbiota in Alzheimer's disease. However, it is still unknown whether GV-971 has pharmacological activity against ischemic stroke.

METHODS: Here, we explore the efficacy of GV-971 on infarct volume, gliosis, blood-brain barrier integrity, gut microbiota composition, and post-stroke cognitive impairment (PSCI) using a middle cerebral artery occlusion/reperfusion (MCAO/R) model in male Sprague-Dawley rats.

RESULTS: Administer medication before surgery for 4 consecutive days and once after surgery, after stroke 24-hour triphenyltetrazolium chloride (TTC) staining revealed that 0.3 mg/kg GV-971 significantly reduced infarct volume in ischemic brain tissue from 37.81±2.391% to 13.30±4.801% and neurological impairment score of GV-971 treatment significantly decreased from 11.50±0.54 to 7.29±1.47. After stroke 24-hour immunofluorescence analysis of glial activation confirmed that GV-971 significantly reduced central inflammatory responses. Western blot combined with Evans blue staining collectively demonstrated that after stroke 24-hour, GV-971 exerts a significant protective effect on the blood-brain barrier. In the gut, GV-971 reversed microbial dysbiosis, as revealed by shotgun metagenomics, enhanced intestinal barrier integrity, and suppressed colonic inflammation. Antibiotic depletion abolished GV-971's neuroprotective effect, while fecal microbiota transplantation from GV-971-treated donors restored protection, supporting a microbiota-dependent contribution. Furthermore, GV-971-treated rats subjected to MCAO/R exhibited significant improvements in motor and cognitive function. For example, on day 35, Y-maze test results indicated that GV-971 administered either before MCAO/R (pre-treatment) or during the perioperative period (co-treatment) increased spontaneous alternation rate from 60.95±4.91% to 85.60±6.32% and 85.64±5.027%. On day 32, novel object recognition assay results indicated that GV-971 treatment increased new-object exploration from 0.2039±0.03752 to 0.3991±0.1122 (pre-treatment) and 0.5066±0.06982 (co-treatment). On day 42, Barnes maze test results indicated that GV-971 treatment reduced the time required to locate the target hole from 76.45±17.41s to 31.03±20.75 s and 33.37±19.30 s for pre- and co-treatment, respectively.

CONCLUSION: Taken together, GV-971 demonstrated neuroprotective potential in experimental ischemic stroke.}, } @article {pmid42539687, year = {2026}, author = {Wang, Z and Yang, H and Liu, J and Li, X}, title = {Diagnostic value of metagenomic next-generation sequencing in deep neck space infections: a retrospective study of 32 patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1874210}, doi = {10.3389/fcimb.2026.1874210}, pmid = {42539687}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; *Neck/microbiology ; Female ; Male ; *Bacteria/genetics/classification/isolation & purification ; Middle Aged ; Aged ; *Bacterial Infections/diagnosis/microbiology ; Adult ; Aged, 80 and over ; DNA, Bacterial/genetics ; }, abstract = {INTRODUCTION: Deep neck space infections (DNSI) are rapidly progressive suppurative conditions in which early identification of causative pathogens is critical for clinical decision-making. This study evaluated the diagnostic performance and clinical utility of metagenomic next-generation sequencing (mNGS) in patients with DNSI.

METHODS: In this retrospective observational study, 32 patients with radiologically confirmed DNSI who underwent surgical drainage between October 2023 and August 2025 were included. Intraoperative purulent specimens were analyzed using both conventional bacterial culture and mNGS. A composite clinical reference standard integrating clinical presentation, imaging findings, surgical observations, inflammatory markers, and expert assessment was used to evaluate the clinical relevance of detected microorganisms.

RESULTS: mNGS detected microbial DNA in 84.4% of patients and demonstrated a broader pathogen detection spectrum and shorter reporting time than conventional culture, particularly for anaerobic and fastidious organisms. Frequently detected organisms included Prevotella spp. and Streptococcus constellatus. Interpretation of these findings required careful consideration of anatomical involvement, organism abundance, and prior antimicrobial exposure to distinguish clinically relevant pathogens from colonizing organisms or residual nonviable DNA. Discordant findings between culture and mNGS, including culture-positive/mNGS-negative and dual-negative cases, were observed and likely reflected differences in sampling adequacy, organism viability, sequencing depth, and methodological limitations. Antimicrobial therapy was adjusted in selected patients following mNGS reporting.

DISCUSSION: mNGS may serve as a valuable adjunct to conventional microbiological diagnostics by expanding pathogen detection in selected DNSI cases, particularly when fastidious or anaerobic organisms are involved. However, its results should be interpreted cautiously in the context of clinical and microbiological findings. Prospective controlled studies are needed to further define the clinical role of mNGS in the management of DNSI.}, } @article {pmid42539859, year = {2026}, author = {Vuth, H and Wang, W and Qin, W and Yang, M and Li, Y and Zhou, Q and Xu, X and Zhang, J and Zhao, H}, title = {Application of metagenomic next-generation sequencing as an adjunct to conventional microbiological testing for the diagnosis of infection in kidney transplant recipients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1713707}, doi = {10.3389/fcimb.2026.1713707}, pmid = {42539859}, issn = {2235-2988}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Retrospective Studies ; Female ; Male ; *Transplant Recipients ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Adult ; Sputum/microbiology ; Bacteria/genetics/isolation & purification ; *Microbiological Techniques/methods ; Aged ; }, abstract = {BACKGROUND: Kidney transplant recipients are highly susceptible to opportunistic and nosocomial infections that demand rapid and accurate diagnosis due to the broad and complex spectrum of pathogens. Conventional microbiological testing (CMT) is often limited, particularly when patients are already receiving antimicrobial therapy at the time of sampling. This study aimed to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) as a complementary diagnostic approach to CMT, with a focus on concordance and discrepancies between the two methods across peripheral blood, sputum, bronchoalveolar lavage fluid (BALF), and urine samples.

METHODS: We conducted a retrospective study of kidney transplant recipients with suspected infections who underwent simultaneous mNGS and CMT testing between March 2022 and May 2024. The impact of prior antibiotic exposure on diagnostic yield was assessed. Detection of antimicrobial resistance (AMR) genes by mNGS and subsequent modifications in anti-infective management were also analyzed.

RESULTS: A total of 243 samples (57 blood, 96 sputum, 71 BALF, 19 urine) were included. Across all sample types, mNGS demonstrated significantly higher positive rates than CMT (blood: 78.95% vs 21.05%; BALF: 90.14% vs 19.72%; sputum: 92.71% vs 20.83%; urine: 89.47% vs 36.84%; all P<0.001). Prior antibiotic exposure markedly reduced CMT positivity but had minimal impact on mNGS detection. Concordance analysis showed 40.35% of samples were positive by both methods, while 60.1% were negative by CMT but positive by mNGS. In addition to pathogens identified by CMT, mNGS detected a broader range of microorganisms, including viruses (e.g., cytomegalovirus, Epstein-Barr virus, SARS-CoV-2), fungi (Pneumocystis jirovecii), and parasites (Strongyloides stercoralis, Toxoplasma gondii). Overall, mNGS-guided results refined antibiotic treatment strategies in 110 cases (60.11%).

CONCLUSION: mNGS serves as a valuable adjunct to CMT in kidney transplant recipients, providing rapid and comprehensive pathogen identification. However, from a health economics perspective, mNGS should be applied selectively according to clinical needs, rather than as a universal first-line diagnostic method.}, } @article {pmid42540632, year = {2026}, author = {Li, Y and He, J and He, X and Peng, Y and Luo, X and Xie, X and Fu, Y and Long, H}, title = {Clinical Characteristics of Patients With AIDS and Talaromyces marneffei Infection of the Central Nervous System: A Retrospective Observation Study.}, journal = {AIDS research and treatment}, volume = {2026}, number = {}, pages = {9954449}, doi = {10.1155/arat/9954449}, pmid = {42540632}, issn = {2090-1240}, abstract = {OBJECTIVE: To analyze the clinical characteristics of patients with acute immunodeficiency syndrome (AIDS) combined with Talaromyces marneffei (TM) infection of the central nervous system (CNS), thereby improving awareness toward early diagnosis and treatment.

METHODS: The clinical data of eight patients with AIDS who were treated for CNS TM infection in the Guiyang Public Health Treatment Center from May 2021 to November 2022 were retrospectively analyzed.

RESULTS: The median age of the patients was 43.50 (range: 35.00-58.00) years, and all eight were male. TM infection was confirmed via metagenomic next-generation sequencing (mNGS) in three cases, positive cerebrospinal fluid (CSF) cultures of TM in four cases, and both in one case. CSF and blood cultures were both positive for one patient, whereas multiple blood cultures were negative for the other seven. The number of nucleated cells and the protein level in the CSF were elevated in five and six patients, respectively, and the CSF levels of glucose and chloride were low in four patients each. Seven patients had intracranial lesions upon head imaging, and all eight were discharged from the hospital with improvement after antifungal treatment. The median CD4+ T-cell count was 58.50/μL (range: 39.00-73.00/μL), indicating severe immunosuppression.

CONCLUSION: The clinical characteristics and CSF-related examinations of patients with AIDS combined with CNS TM infection are not distinct, complicating diagnosis and increasing the likelihood of misdiagnosis. Early diagnosis and systemic antifungal therapy can improve patients' prognosis.}, } @article {pmid42540776, year = {2026}, author = {Ren, C and Zhuo, X and Yang, X and Yao, X and Gong, S and Xiong, H and Fang, F and Zhang, W}, title = {Copy number variation analysis of cerebrospinal fluid metagenomic next-generation sequencing data in assisting the diagnosis of pediatric brain tumors.}, journal = {Pediatric investigation}, volume = {}, number = {}, pages = {}, doi = {10.1002/ped4.70076}, pmid = {42540776}, issn = {2574-2272}, } @article {pmid42541130, year = {2026}, author = {Verhoeven, JTP and Shapiro, JT and Holm Jensen, R and McCleery, RA and Monadjem, A and Hansen, AJ and Pénzes, JJ and Canuti, M}, title = {Characterizing the parvovirome of Swazi bats: novel species, highly divergent lineages, endogenous viral elements, and taxonomic challenges.}, journal = {Virus evolution}, volume = {12}, number = {1}, pages = {veag042}, doi = {10.1093/ve/veag042}, pmid = {42541130}, issn = {2057-1577}, abstract = {Parvoviridae (small, nonenveloped ssDNA viruses) currently includes 281 species in two vertebrate- and four invertebrate-infecting subfamilies. While parvovirus-derived sequences are frequently identified in viromes, their taxonomy and host affiliation can be challenging due to high host and genetic diversity. We investigated the faecal parvovirome of 46 bats (7 insectivorous and 1 frugivorous species) from Eswatini and identified 28 novel viral species in 29 individuals (63.0%). The majority of these (22/28, 78.6%) belonged to nine genera (including two that are previously undescribed) within the invertebrate-infecting subfamily Densovirinae. A novel virus in the genus Brevipenbrevirus (arthropod-infecting subfamily Penbrevirinae) was found in 19.6% of the animals, including several frugivorous Epomophorus wahlbergi bats. A novel bat protoparvovirus (vertebrate-infecting subfamily Parvovirnae) was found both in the faeces and blood of one Afronycteris nanus bat. A highly divergent virus (Swazi bat-associated megaparvovirus 1, SwaBA-MePV-1) was found in the faeces, but not in the blood, of two insectivorous bats (Mops pumilus and Scotophilus viridis). Compared to other parvoviruses, SwaBA-MePV-1 presented two additional coding cassettes, significantly increasing its genome size. Homology modelling showed capsid protein C-terminal elongation, a previously undescribed strategy of parvoviral particle size expansion. Exploring public repositories identified 10 related uncharacterized viruses with similar genome organization and complete endogenous viral elements (EVEs) in eight beetle species, suggesting a coleopteran host affiliation. The complete genome of another highly divergent virus (SwaBA microparvovirus 1), without any detectable exogenous or endogenous relatives, was found in the faeces, but not in the blood, of one insectivorous Mops condylurus bat. Importantly, when comparing our sequences to references in Genbank, we observed that taxonomic mislabelling in sequence repositories can seriously misguide automatic taxonomy assignments (~75% of sequences initially identified as parvoviruses were discarded as false positives). These errors are amplified as new mislabelled sequences become dominant, highlighting the importance of prioritizing taxonomy validation and correct annotations in repositories. This study demonstrates that faecal samples from insectivorous chiropterans are rich in (novel) parvoviruses from various hosts. The discovery of highly divergent lineages (outside current sub-families) and EVEs helps clarify parvovirus evolutionary history and emphasizes how much of the parvoviral world remains unexplored.}, } @article {pmid42541871, year = {2026}, author = {Mo, H and Meng, G and Wei, Y and Liu, J and Chai, B}, title = {Low-dose heavy metals reprogram microbial carbon metabolism and decouple genomic potential from carbon fluxes in riverine wetlands.}, journal = {Journal of environmental management}, volume = {415}, number = {}, pages = {130618}, doi = {10.1016/j.jenvman.2026.130618}, pmid = {42541871}, issn = {1095-8630}, abstract = {River wetland sediments represented an important global carbon sink. Low-dose heavy metal pollution was widespread in aquatic ecosystems, yet its impacts on microbial carbon cycling remained poorly understood. Here, we demonstrated that even when metal concentrations remained within current environmental quality standards, heavy metals could fundamentally reprogram microbial carbon metabolism in riverine wetlands under long-term low-dose heavy metal stress. In the Fen River Basin, microbial communities associated with carbon cycling were significantly restructured: α-diversity (Shannon index) was significantly higher in polluted sites (p < 0.05), and the abundance of core carbon-degradation and carbon-fixation genes (e.g., GAPDH, sucC, accC) was significantly elevated, while methanogenesis genes (e.g., hdrB2) were suppressed, leading to a pronounced functional trade-off. Notably, we inferred a potential decoupling between microbial functional potential and actual ecosystem processes in laboratory microcosms, where CO2 and CH4 emissions were suppressed despite elevated genetic potential, exhibiting a non-monotonic dose-response pattern. Together, these findings revealed a cascading mechanism linking environmental filtering, community restructuring, functional differentiation, and carbon flux regulation, highlighting a stress-induced metabolic state characterized by high maintenance costs and low efficiency. These results challenge current environmental standards and underscore the hidden ecological risks of low-dose pollution to wetland carbon sinks.}, } @article {pmid42541893, year = {2026}, author = {Akhtar, MS and Zaman, W}, title = {Portable metagenomics for preventive surveillance and outbreak control in livestock and poultry: Pathogen detection, resistome profiling, and antimicrobial stewardship.}, journal = {Research in veterinary science}, volume = {210}, number = {}, pages = {106352}, doi = {10.1016/j.rvsc.2026.106352}, pmid = {42541893}, issn = {1532-2661}, abstract = {Conventional diagnostics for livestock and poultry outbreaks commonly rely on culture or targeted PCR panels, which may be too slow or too narrow to guide early control decisions. Portable metagenomics, particularly real-time nanopore sequencing, offers a route to broad pathogen detection, antimicrobial-resistance gene profiling, and outbreak investigation within an integrated workflow. This implementation-focused review evaluates how near-point-of-care metagenomics may support preventive veterinary medicine through earlier detection, surveillance, cohorting, biosecurity decisions, and antimicrobial stewardship. We synthesize sample-to-answer workflows for enteric and respiratory disease in food-producing animals, including sampling, nucleic-acid extraction, host depletion or target enrichment, library preparation, sequencing, bioinformatics, quality control, and interpretation. Applications in calf diarrhea, bovine respiratory disease, poultry outbreaks, mastitis, and resistome monitoring are considered alongside the central limitation that detection alone does not establish causation. Pathogen and resistance-gene signals must therefore be interpreted with clinical signs, lesions, epidemiology, controls, and confirmatory testing. We also propose a minimum reporting checklist, intended as a practical framework rather than a validated consensus standard. Portable metagenomics is not a replacement for conventional diagnostics, but appropriately validated workflows can reduce uncertainty during time-sensitive outbreaks and support more judicious antimicrobial use.}, } @article {pmid42542139, year = {2026}, author = {Xu, JJ and Xu, ZQ and Yu, J and Wang, MH and Li, WH and Jin, RC}, title = {Biochar-driven regulation of anammox systems under varying nitrogen loads: performance, microbial community and metabolic mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135542}, doi = {10.1016/j.biortech.2026.135542}, pmid = {42542139}, issn = {1873-2976}, abstract = {This study examined the effects of wheat straw biochar on the anaerobic ammonium oxidation (anammox) process during stepwise decrease in influent substrate concentrations. Biochar exerted a dual role depending on nitrogen load. During phase I (300 mg·L[-1] NH4[+]-N and NO2[-]-N), the biochar group exhibited 1-4% higher relative abundances of selected anammox related genes, including hzs and hdh, than the control group. At the end of phases III and IV, the electron transport system activity in the biochar-amended reactor was 10% and 46% above the corresponding control values, respectively, whereas improvement in specific anammox activity (SAA) and total nitrogen removal efficiency (TNRE) was observed after stabilization in phase IV. At 50 mg·L[-1] NH4[+]-N and 50 mg·L[-1] NO2[-]-N, the SAA reached 12.5 mg N·(g volatile suspended solids (VSS)·d) [-1], 7% higher than that of the control group, while the TNRE was approximately 6% higher. Metagenomic analysis revealed phase-dependent differences in functional-gene relative abundance. The biochar group showed higher relative abundances of denitrification genes (nirS, norB, and nosZ) and genes related to dissimilatory nitrate reduction to ammonium (DNRA), including nrfA, together with lower relative abundances of nitrification genes (amoA, amoB, and amoC). These differences were consistent with reduced substrate competition and potential coupling between anammox and denitrification. These findings provided a mechanistic basis for applying wheat straw biochar to anammox systems operated under changing nitrogen loading conditions.}, } @article {pmid42531833, year = {2026}, author = {Wang, Y and Liu, Z and Hou, Q and Xu, Y and Chen, W and Chen, M and Liu, J and Tang, J and Wang, Y and Zhou, M and Wu, X and Wang, X}, title = {Poricoic acid a ameliorates ulcerative colitis via AMPK/PPARγ pathway-dependent cellular senescence inhibition and concomitant gut microbiota-metabolome modulation.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {160}, number = {}, pages = {158628}, doi = {10.1016/j.phymed.2026.158628}, pmid = {42531833}, issn = {1618-095X}, abstract = {BACKGROUND: Ulcerative colitis (UC) is an intractable inflammatory bowel disorder characterized by persistent intestinal inflammation and impaired gut barrier integrity. Its pathogenesis is multifactorial, involving gut microbiota dysbiosis, metabolic dysfunction, and cellular senescence. Current therapeutic regimens remain limited, underscoring an urgent need for innovative agents that target these interrelated pathological cascades.

PURPOSE: This study aimed to evaluate the pharmacological effects of poricoic acid A (PAA) on DSS-induced senescence in intestinal epithelial cells and in a murine model of ulcerative colitis (UC), as well as the underlying molecular mechanisms.

METHODS: We established a DSS-stimulated senescent intestinal epithelial cell model and a DSS-induced UC mouse model. Multi-omics and bioinformatics strategies, including network pharmacology, transcriptome profiling, gut metagenomics, and intestinal targeted metabolomics, were combined with molecular docking to predict candidate signaling axes. Subsequent pharmacological inhibition and siRNA-mediated silencing assays were performed to validate core pathways functionally.

RESULTS: PAA robustly suppressed DSS-induced senescence and inflammatory responses in intestinal epithelial cells. In vivo assays verified that PAA alleviated UC-related manifestations, including body weight loss, rectal hemorrhage, and colonic histological injury. Joint network pharmacology and transcriptomic screening identified the AMPK/PPARγ as the core pathway mediating PAA's bioactivity. Mechanistic experiments confirmed that PAA directly bound and activated PPAR, further functionally triggering downstream AMPK/SirT1/PGC1α signaling. Blockade of AMPK via pharmaceutical antagonists or siRNA largely abolished PAA's anti-senescence and anti-inflammatory capacities; PPARγ suppression, in turn, secondary deactivated the AMPK and its downstream functional effectors. In mouse models, AMPK inhibition drastically compromised PAA's protective effects against UC. Moreover, PAA treatment of UC is closely associated with remodeling of the gut microbiome-metabolome axis and restoration of intestinal homeostasis.

CONCLUSION: PAA exerts potent anti-senescence, anti-inflammatory, and colon-protective effects in UC via activating the AMPK/PPARγ signaling pathway. Such beneficial activity may be associated with the normalization of gut microbiota-metabolome homeostasis. This work identifies novel molecular targets and a promising lead compound for the intervention of ulcerative colitis.}, } @article {pmid42531877, year = {2026}, author = {Zhu, X and Zhang, X and Zhang, X and Al-Dhabi, NA and Tang, W and Wu, P and Wang, A}, title = {Decoding the metabolic synergy and extracellular electron transfer bottleneck in manganese-driven nitrogen removal: Mechanisms underlying the dominance of comammox bacteria.}, journal = {Water research}, volume = {306}, number = {}, pages = {126584}, doi = {10.1016/j.watres.2026.126584}, pmid = {42531877}, issn = {1879-2448}, abstract = {Manganese-redox-driven autotrophic nitrogen removal holds immense potential for low-carbon wastewater treatment, yet practical operations suffer from oxygen intrusion that triggers complete ammonia oxidation (comammox). This study employed a step-wise Mn acclimation strategy (10 to 20 mg/L Mn[2+]) over 180 days to decipher the metabolic synergy among manganese-dependent anaerobic ammonium oxidation (Mnammox), comammox, and manganese-autotrophic denitrification (MnAD) consortia. Results revealed that comammox enrichment elevated ammonia removal to 41.1 % but shifted nitrate removal from 95.5 % to net accumulation (negative values). Metagenomics confirmed that comammox Nitrospira secured niche dominance (abundance surging to 7.7 %) due to high substrate affinity and robust genomic flexibility (encoding 17 manganese oxidases). Furthermore, Nitrospira exhibited dual "deoxygenation" and "ammonia oxidation synergy" functions, alleviating the over-reduction of solid-phase biogenic manganese oxides (BioMnOx). Mineralogical characterization suggested that this mechanism stabilized the Mn[4+] proportion, sustaining the material basis of Mn transformation. However, activity tests demonstrated that the nitrate generation rate of comammox (1.6 mg/L/h) significantly outpaced the reduction rate of MnAD (0.8 mg/L/h). This bottleneck stems from the low inorganic electron donor utilization and solid-liquid interfacial mass transfer resistance, which suppress extracellular electron transfer (EET) efficiency. In conclusion, this study unveils a novel coupled metabolic pathway between comammox and Mn transformation, while clarifying the existence of an EET bottleneck within the system. These findings theoretically highlight the necessity of interfacial regulation strategies (e.g., incorporating conductive media) in future studies, thereby balancing comammox activity and MnAD capacity for optimized nitrogen removal.}, } @article {pmid42532286, year = {2026}, author = {Zhang, Y and Hu, L and Ding, X and Liu, L and Xue, L and Miao, L}, title = {Investigating Gut Microbiota and their metabolites as Biomarkers for Tacrolimus Pharmacokinetic Variability.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {}, number = {}, pages = {107626}, doi = {10.1016/j.ejps.2026.107626}, pmid = {42532286}, issn = {1879-0720}, abstract = {Tacrolimus (TAC), a cornerstone immunosuppressant in transplantation, presents a clinical challenge due to its narrow therapeutic index and substantial interindividual pharmacokinetic (PK) variability. This exploratory study investigated the association between gut microbiota composition, short-chain fatty acid (SCFA) metabolites, and TAC PK variability during the early post-kidney transplantation period. Based on prediction errors derived from a previously established population PK model, 36 transplant recipients were stratified into positive (n=17) and negative (n=19) deviation groups. Metagenomic sequencing and targeted SCFA metabolomic analysis of fecal samples revealed that the negative deviation group exhibited significantly reduced gut microbial diversity and altered community structure. Among 142 differentially abundant taxa, 10 microbial features, including Enterococcaceae - associated taxa, showed discriminative potential between the two PK phenotypes (AUC > 0.7), with three Enterococcus species (E. durans, E. faecium, and E. hirae) showing particularly robust signals (Cohen's d > 1.0 and power > 80%). Functional analysis suggested downregulation of butyrate biosynthesis pathways in the negative deviation group, which was consistent with significantly lower fecal butyrate and total SCFA concentrations. These hypothesis-generating findings suggest that gut microbiota and SCFAs are associated with TAC PK phenotypes, but independent validation in larger cohorts is required before clinical translation.}, } @article {pmid42532775, year = {2026}, author = {Nealon, NJ}, title = {Next-Generation Sequencing in Companion Animal Practice for Infectious Disease Diagnostics and Characterizing Normal Microbiomes.}, journal = {The Veterinary clinics of North America. Small animal practice}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cvsm.2026.06.005}, pmid = {42532775}, issn = {1878-1306}, abstract = {The purpose of this article is to review and compare the most common and emergent next-generation sequencing methodologies used in small animal veterinary practice, with a focus on their applications to bacterial diagnostics and assessment of the healthy gut microbiome. These methodologies include whole genome sequencing, amplicon sequencing, shotgun metagenomic sequencing, and transcriptomics. Understanding the benefits and limitations of each methodology will help small animal practitioners to make informed decisions for their patients and maximize the utility of each test as part of a complete patient health assessment.}, } @article {pmid42533345, year = {2026}, author = {Devasahayam, BRF and McNeil, T and Wubet, T and Schmutzer, T}, title = {Nanopore sequencing reveals coordinated host and microbiome responses across barley genotypes.}, journal = {BMC biology}, volume = {24}, number = {1}, pages = {}, pmid = {42533345}, issn = {1741-7007}, mesh = {*Hordeum/genetics/microbiology ; *Microbiota/genetics ; *Genotype ; Nanopore Sequencing ; Rhizosphere ; Plant Roots/microbiology/genetics ; Metagenome ; Metagenomics ; Transcriptome ; }, abstract = {BACKGROUND: Barley (Hordeum vulgare L.) provides a suitable model for studying domestication-driven plant-microbiome interactions. Although wild, landrace, and modern genotypes host distinct rhizosphere communities, the extent to which roots and microbes reciprocally influence each other remains unclear. Here, we applied an integrated multi-omics approach combining long-read metagenomics, root transcriptomics, and plant genomics to understand genotype-specific host-microbiome coordination.

RESULTS: Oxford Nanopore whole metagenome sequencing (WMS) revealed genotype-associated shifts in rhizosphere communities across seasons. Functional profiling showed a conserved metabolic backbone including amino acid metabolism, energy production, and secondary metabolite biosynthesis, alongside genotype-dependent variation in carbohydrate metabolism and transport-associated pathways. Genome-resolved analysis through metagenome-assembled genomes (MAGs) further detailed the taxonomic and functional architecture of key rhizosphere lineages. Root transcriptome profiling identified extensive differential expression associated with microbial perception, signaling, defense, and metabolic processes. Integration of host and microbiome data revealed coordinated molecular patterns, indicating that barley genotypes are associated with distinct microbial assemblages and corresponding transcriptional responses.

CONCLUSIONS: These findings indicate that domestication has shaped coordinated associations between barley genotypes and their rhizosphere microbiomes, reflected in both microbial community composition and host transcriptional regulation. This work provides new insights into the evolutionary tuning of plant-microbiome relationships and highlights opportunities for microbiome-informed strategies in barley improvement.}, } @article {pmid42533554, year = {2026}, author = {Yang, K and Yang, M and Yu, Q and Liong, MT and Chen, D and Cai, M}, title = {The Effect of a Probiotic on Gut Microbiota Stability and Systemic Well-Being during Short-Term Travel.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2510037}, doi = {10.4014/jmb.2510.10037}, pmid = {42533554}, issn = {1738-8872}, mesh = {Humans ; *Probiotics/administration & dosage ; *Bifidobacterium/physiology ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; Adult ; *Travel ; Male ; China ; Female ; Feces/microbiology ; Young Adult ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Short-term travel, particularly to new environments, can disrupt gut microbiota homeostasis and induce a range of physical and psychological symptoms. While probiotics are proposed to mitigate these effects, evidence from well-controlled trials during domestic travel, especially along unique routes like China's Silk Road, remains limited. This study investigated the efficacy of a multi-strain Bifidobacterium probiotic in maintaining gut microbiota stability and alleviating travel-related symptoms. In a randomized, double-blind, placebo-controlled trial, 74 healthy adults traveling to Xinjiang were assigned to receive either a probiotic (n = 39; B. longum subsp. infantis M-63, B. breve M-16V, and B. longum BB536, 1.5 × 10[9] CFU/day) or a placebo (n = 35) for five days during travel. Gut microbiota was profiled via metagenomic sequencing (pre- and post-travel), and symptoms were recorded daily. Primary outcomes were changes in gut microbiota composition and function (KEGG pathways). Secondary outcomes included respiratory, gastrointestinal, and systemic symptom scores. Data were analyzed on an intention-to-treat basis. While alpha and beta diversity remained stable in both groups, the probiotic group exhibited a distinct post-travel microbiota enriched with beneficial taxa, including Bifidobacterium breve and Intestinibacillus at the genus level, and Lacticaseibacillus rhamnosus, Lacticaseibacillus paracasei, and other Lacticaseibacillus species. qPCR confirmed significant increases in administered strains B. longum subsp. infantis (p < 0.001) and B. breve (p < 0.001). KEGG analysis revealed that the probiotic group maintained a metabolically focused profile (e.g., peptidoglycan biosynthesis, histidine metabolism), whereas the placebo group showed increased abundance of microbial pathways associated with host disease-related signaling (e.g., Huntington disease, various cancers) and inflammatory signaling (e.g., PI3K-Akt signaling pathway). Symptomatically, the probiotic group demonstrated a significantly greater reduction than the placebo in irritability (-92% vs. -31%; p = 0.033) and fatigue (-24% vs. +43%; p = 0.024) post-travel, and reported less dizziness (-100% vs. -35%; p = 0.024). Supplementation with a multi-strain Bifidobacterium probiotic during short-term travel promoted the colonization of beneficial bacteria, stabilized gut microbial function against travel-induced dysregulation, and may contribute to supporting systemic well-being during travel.}, } @article {pmid42533584, year = {2026}, author = {He, LW and Tang, RX and Liu, SY and Zhang, ZJ and Li, Y and Wang, XM and Yue, BS and Fan, ZX}, title = {Host phylogeny and diet shape gut microbiome and virome in wild small mammals of Gongga Mountain, China.}, journal = {Zoological research}, volume = {47}, number = {4}, pages = {1332-1352}, doi = {10.24272/j.issn.2095-8137.2025.448}, pmid = {42533584}, issn = {2095-8137}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Phylogeny ; *Virome ; *Diet/veterinary ; China ; *Rodentia ; *Mammals/virology ; }, abstract = {Gut microbiotas play pivotal roles in host adaptation, yet their composition and function in high-altitude small mammals remain poorly characterized. This study investigated how host phylogeny (order-level) and dietary habits shape the gut microbiome and virome of three mammalian orders (Eulipotyphla, Rodentia, Lagomorpha) in Gongga Mountain, a biodiversity hotspot on the Qinghai-Xizang Plateau. Metagenomic sequencing of 219 samples from 22 species revealed order-specific microbial signatures: Eulipotyphla (carnivorous) harbored higher abundances of potential pathogens (e.g., Helicobacter, Hafnia) and Retroviridae; Lagomorpha (herbivorous) was enriched in cellulolytic bacteria (e.g., Lachnospiraceae, Prevotella) and carbohydrate-active enzymes (CAZymes); Rodentia (omnivorous) showed intermediate traits. We reconstructed 1 385 high-quality metagenome-assembled genomes (MAGs), 1 328 representing novel species, and identified 749 viral operational taxonomic units (vOTUs), >80% being Caudoviricetes. Crucially, Retroviridae abundance in Eulipotyphla suggests zoonotic risk. Phage-host network analysis indicated Caudoviricetes regulates cellulolytic bacteria in Lagomorpha. Host phylogeny and diet jointly drive gut microbiome divergence in small mammals. We establish the first gut microbiome and virome resource of small mammals in the high-altitude area of Gongga Mountain, highlighting Eulipotyphla as a potential vector for zoonotic pathogens.}, } @article {pmid42533623, year = {2026}, author = {Kerns, KA and Naumann, AA and Soon, LY and Hendrickson, EL and Barbour, A and Chen, D and Trivedi, HM and Glogauer, M and McLean, JS}, title = {Zinc-stabilized stannous fluoride modulates the periodontal microbiome, reducing Fusobacteria, key Gram-negative species, and overall inflammation within an experimental gingivitis clinical trial.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jper.70168}, pmid = {42533623}, issn = {1943-3670}, abstract = {BACKGROUND: This study aimed to evaluate the effects of a dentifrice containing stannous fluoride stabilized with zinc phosphate on subgingival microbiome composition and clinical inflammation during experimental gingivitis, compared with a sodium fluoride control.

METHODS: This investigation was conducted as a secondary analysis of a randomized, parallel-arm, double-blind, controlled clinical trial. Clinical resolution of experimental gingivitis was assessed using bleeding on probing, gingival index, and plaque index. Deeply sequenced subgingival plaque metagenomic data were analyzed to compare microbial composition and functional potential between a stannous fluoride stabilized with zinc phosphate dentifrice (test) and a sodium fluoride dentifrice (control) over a 21-day experimental gingivitis period.

RESULTS: Use of the stannous fluoride stabilized with zinc phosphate dentifrice was associated with depletion of periodontal disease-associated Gram-negative bacteria, including Fusobacterium nucleatum and multiple Porphyromonas and Prevotella species. This reduction in Gram-negative taxa corresponded with shifts in microbial community metabolic functions and was associated with significantly reduced clinical inflammation compared with the control over the 21-day period.

CONCLUSIONS: Short-term use of stannous fluoride stabilized with zinc phosphate may provide additional protection against gingival inflammation by limiting the outgrowth of key periodontal pathogens, including the bridging organism Fusobacterium nucleatum, and by altering plaque functional capacity. These effects were associated with improved periodontal health outcomes compared with a standard sodium fluoride dentifrice.

PLAIN LANGUAGE SUMMARY: In this study, we analyzed bacteria within the periodontal pocket using deep metagenomic sequencing to better resolve bacterial species and their functions. Results from this study show that using a toothpaste containing stannous fluoride stabilized with zinc phosphate was associated with the reduction of several important Gram-negative bacteria associated with periodontal disease, including Fusobacterium nucleatum and species of Porphyromonas and Prevotella compared with a control toothpaste. These bacteria are well‑known contributors to gingival inflammation and biofilm maturation. When levels of these specific bacteria decreased within the stannous fluoride treatment group, the overall subgingival microbiome shifted which notably persisted during the subsequent 21-day oral hygiene abstention period in this experimental gingivitis model - resulting in significantly lower clinical inflammation. Our findings suggest that even short‑term use of stannous fluoride stabilized with zinc phosphate may provide added protection against early gingival inflammation. Notably, stannous fluoride stabilized with zinc phosphate appears to limit the growth of key periodontal pathogens-particularly Fusobacterium nucleatum, an important bridging organism in subgingival biofilms-and may alter the functional activity of dental plaque in ways that support improved periodontal health when compared with a standard sodium fluoride toothpaste.}, } @article {pmid42534147, year = {2026}, author = {Somtha, B and Visedthorn, S and Saejew, T and Pavatung, P and Wathanavasin, W and Kanjanabuch, T and Payungporn, S}, title = {Bacterial metagenomic analysis of patients with chronic kidney disease undergoing hemodialysis based on 16S rDNA amplicon sequencing.}, journal = {Biomedical reports}, volume = {25}, number = {3}, pages = {105}, pmid = {42534147}, issn = {2049-9442}, abstract = {Chronic kidney disease (CKD) is a medical condition affecting >800 million patients globally, with end-stage kidney disease representing the most severe stage, usually requiring dialysis as a form of renal replacement therapy. As these patients have an increased risk of sepsis-associated mortality, and due to the limitations that arise from the use of traditional methods, prompt and accurate approaches in pathogen identification are required to ensure appropriate clinical management. The present study aimed to identify and analyze the bacterial profile of hemodialysis (HD) catheters obtained from patients with CKD who were undergoing hemodialysis using 16S ribosomal DNA (rDNA) amplicon sequencing. The present study proposed the use of the metagenomic approach in clinical laboratory settings. The results obtained in the present study revealed that the bacterial profile between site A (from the patient to the dialysis machine) and site V (from the machine back into the patient) had notable differences, with α- and β-diversity indices suggesting an increased diversity at site V. In addition, analyses of the relative abundance and linear discriminant analysis effect size revealed the presence of known pathogens, including Klebsiella pneumoniae, Gardnerella vaginalis, Escherichia coli, Staphylococcus epidermidis, Acinetobacter baumannii, Corynebacterium striatum and Stenotrophomonas maltophilia. In summary, the findings of the present study highlighted the potential use of 16S rDNA amplicon sequencing as a culture-independent alternative for determining pathogens in patients undergoing HD.}, } @article {pmid42534357, year = {2026}, author = {Tania, MNT and Sabrin, MS and Mannan, MA and Islam, MM and Hossain, MT and Rahman, MH and Islam, MR and Sultana, S and Hossain, MS and Islam, M}, title = {Comparative 16S rRNA Gene Amplicon Sequencing of the Fecal Microbiome in Pet Dogs and Cats of Different Breeds in Dhaka City, Bangladesh: With Preliminary Insights Into Zoonotic Relevance.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {8738439}, pmid = {42534357}, issn = {1687-918X}, abstract = {Dogs and cats are the most commonly kept pets, and the popularity of different breeds of them continues to increase in Dhaka City, Bangladesh. Pets naturally harbor a diverse gut microbiome that plays a significant role in digestion, immunity, and overall health. Although pets provide valuable companionship, their feces may occasionally harbor bacteria with zoonotic potential. However, little is known about the fecal microbial diversity and its zoonotic relevance in Bangladesh. This study investigated the diversity of pets' fecal microbiome using 16S rRNA metagenomics and explored the zoonotic bacterial taxa. Fecal samples were collected from 24 apparently healthy pets, including 12 dogs and 12 cats, from randomly selected households in Dhaka City. High-throughput sequencing revealed a diverse microbial community comprising 1,148 amplicon sequence variants (ASVs) distributed across 20 phyla and 258 genera. Although cats showed slightly higher microbial richness and diversity, both species shared common bacterial phyla such as Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. Relative abundance of bacterial taxa varied between pet species and among breeds rather than the presence of distinct microbial groups. Furthermore, Enterococcus cecorum, Schaalia canis, Campylobacter helveticus, and Sutterella wadsworthensis were the explored bacterial taxa with zoonotic relevance rather than a direct assessment of zoonotic risk; however, they were very low in number than the dominating bacteria. This study provides the first 16S rRNA-based metagenomic snapshot of the fecal microbiome of 24 urban pets in Bangladesh and highlights the need for routine microbial surveillance and public awareness about zoonoses.}, } @article {pmid42534735, year = {2026}, author = {Berríos-Farías, V and Guajardo-Leiva, S and Gallardo-Cerda, J and Galbán-Malagón, C and Egas, C and Molina-Montenegro, MA and Castro-Nallar, E}, title = {Metagenomic insights into potential PET hydrolases from Antarctic soils and rhizospheres.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1749101}, pmid = {42534735}, issn = {1664-302X}, abstract = {Polyethylene terephthalate (PET) is a persistent synthetic polymer that is increasingly detected in terrestrial environments, where it influences soil microbial activity and carbon cycling. Microorganisms capable of hydrolyzing PET and related polyesters constitute a valuable enzymatic resource for developing low-temperature biocatalysts and for advancing the understanding of soil functional adaptation to plastic pollution. Here, we conducted a metagenomic analysis of soil and rhizosphere samples from the Antarctic vascular plants Deschampsia antarctica and Colobanthus quitensis, as sources of microbial enzymes with potential PET-hydrolytic activity. Hidden Markov Models constructed from experimentally validated PET hydrolases identified 152 putative PET hydrolases (pPETHs) spanning multiple protein families. Four candidates exhibited amino acid motifs characteristic of Ideonella sakaiensis PETase, including the conserved alpha/beta hydrolase fold and the Ser-His-Asp catalytic triad. One candidate from a Duganella genome also contained a tryptophan residue associated with efficient product release during PET hydrolysis. Molecular docking and molecular dynamics analyses revealed that candidates retain the core catalytic architecture of established PET hydrolases, while simultaneously displaying structural signatures of cold adaptation. These findings demonstrate the diversity of PET-hydrolase-like genes within Antarctic rhizosphere and soil microbiomes, broadening the current understanding of microbial enzymatic potential under cold, oligotrophic conditions. The identified sequences highlight the rhizosphere as a reservoir of functional diversity relevant to soil biotechnology, cold-adapted catalysis, and microbial strategies for transforming recalcitrant carbon substrates.}, } @article {pmid42534880, year = {2026}, author = {Gao, Y and Huang, Y and Li, W and Huang, Y and Zhao, X and Chu, C and Zhang, X and Chen, J and Wang, Y and Li, Y and Geng, H}, title = {Clinical utility of metagenomic next-generation sequencing in infants with severe infections.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1842600}, pmid = {42534880}, issn = {1664-302X}, abstract = {OBJECTIVE: This study aimed to compare pathogen detection rates between metagenomic next-generation sequencing (mNGS) and conventional microbiological culture in critically ill infants younger than 1 year of age, and to investigate the associations between mNGS positivity and clinical laboratory parameters.

METHODS: We conducted a single-centre retrospective study including infants with severe infections admitted to the Children's Hospital of Soochow University between 1 January 2023 and 31 December 2025, who underwent both mNGS and conventional culture testing. Patients were classified into mNGS-positive and mNGS-negative groups, and clinical characteristics and laboratory findings were compared between groups. Candidate predictors of mNGS positivity were identified using least absolute shrinkage and selection operator (LASSO) regression, followed by multivariable logistic regression analysis. The predictive performance of key variables was evaluated using receiver operating characteristic (ROC) curve analysis.

RESULTS: A total of 105 infants and 153 biological specimens were included. The overall mNGS positivity rate, as well as positivity rates across all specimen types except cerebrospinal fluid, were significantly higher than those of conventional culture (p < 0.05). LASSO regression identified eosinophil percentage, mean corpuscular haemoglobin (MCH), procalcitonin (PCT), cholinesterase, and serum calcium as candidate predictors of mNGS positivity. Multivariable logistic regression revealed that MCH (OR = 0.755, 95%CI: 0.657-0.869), cholinesterase (OR = 0.999, 95%CI: 0.999-1.000), and PCT (OR = 1.180, 95%CI: 1.050-1.320) were independently associated with mNGS positivity. ROC analysis demonstrated that MCH, cholinesterase, and PCT individually showed moderate discriminatory performance, whereas a combined model incorporating all three variables achieved substantially improved predictive performance (AUC = 0.842, 95%CI: 0.758-0.912), with a sensitivity of 87.2% and specificity of 81.6%.

CONCLUSION: mNGS demonstrated superior pathogen detection compared with conventional culture in critically ill infants. MCH, cholinesterase, and PCT were independently associated with mNGS positivity, and a combined multi-marker model substantially improved the prediction of mNGS-positive cases.}, } @article {pmid42534899, year = {2026}, author = {Guitart-Matas, J and Bravo, M and Tort-Miró, C and Giler-Baquerizo, N and Fraile, L and Caldas-Ramayo, Y and Ballester, M and Migura-Garcia, L}, title = {Dynamics of archaeal diversity and functionality in the piglet gut microbiome under common antimicrobial treatments.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1833734}, pmid = {42534899}, issn = {2235-2988}, mesh = {Animals ; *Archaea/classification/genetics/drug effects ; Swine ; Metagenomics ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Metagenome ; Weaning ; *Biodiversity ; *Anti-Infective Agents/administration & dosage/pharmacology ; Gene Expression Profiling ; Phylogeny ; Diarrhea/drug therapy/veterinary ; Anti-Bacterial Agents ; }, abstract = {INTRODUCTION: The gut microbiota comprises a diverse and dynamic community of microorganisms that collectively enhance host metabolism, physiology, and overall functionality. In this context, the swine archaeome remains largely underexplored despite growing evidence that archaea may greatly influence host health. Advances in high-throughput approaches provide new opportunities to reveal the dynamics and composition of archaea. Herein, we uncover the taxonomic and functional landscape of the piglet archaeome during the weaning transition under multiple experimental conditions, integrating shotgun metagenomic and metatranscriptomic analyses to elucidate its contribution to gut microbial ecology.

METHODS: The seven experimental conditions included four antibiotic treatments for post-weaning diarrhoea (trimethoprim/sulfamethoxazole, colistin, gentamicin, amoxicillin), an oral vaccine, acidifiers in drinking water, and a no-intervention group. A total of 280 faecal samples were collected longitudinally one day before weaning (ST1), three days (ST2), two weeks (ST3), and four weeks (ST4) after the start of the treatment. Treatment was initiated eleven days after arrival at the experimental farm following the onset of clinical signs. Shotgun metagenomics was used to assess archaeal taxonomic diversity and recover archaeal metagenome-assembled genomes (aMAGs), while metatranscriptomics was integrated to assess differentially expressed genes at ST1, ST2, and ST4.

RESULTS: The results revealed archaea as the second most abundant microorganism, exhibiting a longitudinal increase in diversity over the experimental time. The most predominant genus was Methanobrevibacter, including Methanobrevibacter smithii. Eleven high-quality aMAGs were recovered, belonging to the Methanobacteriota and Thermoplasmatota phyla. Genome-inferred functional analyses revealed that the predominant metabolic processes included the biosynthesis of nucleic acids, amino acids, organic anions, and vitamins. Additional functional traits suggested potential roles in the degradation of sugars, amino acids, and antibiotics were also observed. Moreover, significant differences were detected on the archaeal metatranscriptome between the experimental groups treated with antibiotics and the rest of the groups, underscoring their response to changes in microbial interactions, substrate availability and, in some cases, direct effect of the antimicrobials on metabolic pathways.

DISCUSSION: Altogether, this study highlights the biological significance of archaeal dynamics during initial life stages and demonstrates how combining metagenomics and metatranscriptomics uncovers their functional potential and the pathways actively expressed in the piglets' gut.}, } @article {pmid42535091, year = {2026}, author = {Xiao, Y and Lu, Y and Hu, Y and Shi, R and Mai, D and Lv, R and Pan, J and Pan, Y and Tan, J and Hao, Z and Wang, J}, title = {Metagenomic analysis of the gut microbiota in Cygnus cygnus and isolation, identification, and safety assessment of Bacillus.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1898323}, pmid = {42535091}, issn = {1664-302X}, abstract = {INTRODUCTION: As a national second-class protected wild animal, the intestinal microbial community of Cygnus cygnus is highly important for health status and ecological balance. The potential application value of probiotics in animal health and disease prevention has attracted much attention, but few studies have investigated probiotics derived from wild animals.

METHODS: We initially collected fecal samples before and after the migration of the C. cygnus for macrogenomic sequencing. We subsequently isolated Bacillus spp. from C. cygnus feces and determined their hemolytic properties and tolerance to acid and bile salts to identify potential candidates. We subsequently studied the position of a candidate in phylogenetic trees using 16S rRNA sequences, as well as its susceptibility to antibiotics, toxicity, and effects on animal health.

RESULTS: Metagenomic analysis revealed that the abundance of the Firmicutes phylum tended to decrease after the migration of C. cygnus, whereas the relative abundance of the Fusobacteria phylum increased. Although the diversity and abundance of the gut microbiota of C. cygnus remained relatively balanced before and after migration, the microbial community structure changed significantly after migration. These changes were related to reductions in carbohydrate metabolism and energy metabolism, as well as a decrease in the abundance of genes encoding glycoside hydrolases. Twelve strains were isolated and screened, and two strains, Bacillus subtilis S07a and N1B, without hemolytic activity were found to have good tolerance to acid and bile salts. It was sensitive to 14 kinds of antibiotics, but B. subtilis S07a inhibited on three common pathogenic bacteria. Animal studies have shown that B. subtilis S07a (1 × 10[9] CFU/mL) is safe for use in mice. It also has anti-inflammatory potential and enhances intestinal barrier function to meet the probiotic and safety requirements of probiotics.

CONCLUSION: Metagenomic analysis revealed reduced abundance of carbohydrate-degrading microbes in the gut of C. cygnus post migration. The isolated B. subtilis S07a exhibits desirable in vitro probiotic potential and satisfactory in vivo safety.}, } @article {pmid42535839, year = {2026}, author = {Bolino, MJ and Frese, SA}, title = {CAMEO: a CAZyme mapping engine optimized for HUMAnN.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0070726}, doi = {10.1128/mra.00707-26}, pmid = {42535839}, issn = {2576-098X}, abstract = {There are technical barriers to creating functional mapping databases and a dearth of validated databases that can be easily implemented by users. We present CAMEO, a precomputed and validated mapping file for carbohydrate-active enzymes, as well as an approach to building new CAZyme mapping files, for use with HUMAnN.}, } @article {pmid42535840, year = {2026}, author = {Kim, J and Kim, H and Goh, J and Nam, SW and Chung, EJ and Shin, S and Park, Y and Han, Y and Kim, J-E and Kwak, W}, title = {Complete genomes from a xenic Dolichospermum flosaquae FBCC-A233 culture reveal genome-inferred metabolic asymmetry with associated bacteria.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0101426}, doi = {10.1128/spectrum.01014-26}, pmid = {42535840}, issn = {2165-0497}, abstract = {Cyanobacteria form phycosphere communities with associated bacteria, but genome-resolved resources are needed to formulate testable hypotheses about their metabolic interactions. Here, we reconstructed three complete circular genomes from a unialgal xenic culture, including Dolichospermum flosaquae FBCC-A233 and two associated alphaproteobacterial genomes assigned to Sphingorhabdus sp. and Brevundimonas sp. Genome-wide read mapping and genome-quality assessment supported the three recovered genomes as high-quality circular reconstructions. Comparative genome analysis placed the cyanobacterial genome within the Dolichospermum flosaquae species cluster under the GTDB framework, while the associated bacterial genomes represented Sphingorhabdus sp. and a putative undescribed Brevundimonas species-level lineage. Genome architecture analysis indicated reduced genome size and gene content in Brevundimonas relative to genus-level references although additional metrics did not support a strong conclusion of classical genome streamlining. Selected KEGG module and KO-level reconstructions indicated genome-inferred metabolic asymmetries across the consortium. FBCC-A233 encoded photosynthesis- and nitrogen-related modules and a BioU-mediated de novo biotin biosynthesis route, whereas the associated bacteria lacked complete de novo biotin biosynthesis but retained biotin-dependent carboxylase genes. FBCC-A233 also encoded extensive anaerobic corrinoid biosynthesis potential; however, canonical DMB-containing cobalamin completion, cobamide identity, and complete transporter systems were not resolved. Together, these complete genomes provide a genome-resolved resource for investigating genome-inferred metabolic differentiation and ecological interactions in cyanobacteria-associated bacterial consortia.IMPORTANCEPhycosphere interactions between cyanobacteria and associated bacteria can shape aquatic microbial communities, but many proposed interactions remain difficult to evaluate without genome-resolved resources. This study provides three complete circular genomes from a unialgal xenic Dolichospermum flosaquae culture, capturing the cyanobacterium and two co-maintained bacterial associates. Our analysis identifies genome-inferred metabolic asymmetries, particularly in biotin- and cobamide-related pathways. D. flosaquae FBCC-A233 encoded candidate de novo biotin and corrinoid biosynthesis capacity, whereas the associated bacteria lacked complete de novo pathways but retained cofactor-dependent enzymes. These findings nominate cofactor-related dependencies as experimentally testable hypotheses while emphasizing unresolved uptake, export, cobamide identity, and growth-dependence mechanisms. The complete genomes and KO-level reconstructions generated here provide a resource for future studies of cyanobacteria-associated consortia.}, } @article {pmid42535843, year = {2026}, author = {Luan, L and Song, X and Zeng, Y and Xie, Y and Hong, Y and Tang, J and Ma, C and Gu, B and Wang, L}, title = {Differential pro-tumorigenic effects of Helicobacter pylori and Streptococcus anginosus on AGS cells: contact-dependent versus metabolite-driven mechanisms.}, journal = {mBio}, volume = {}, number = {}, pages = {e0158926}, doi = {10.1128/mbio.01589-26}, pmid = {42535843}, issn = {2150-7511}, abstract = {Gastric cancer remains a major global health burden, ranking fifth worldwide in both incidence and mortality. While Helicobacter pylori is a well-established Group I carcinogen, increasing evidence suggests that non-H. pylori bacteria, including Streptococcus anginosus, may also contribute to gastric carcinogenesis. However, their comparative pathogenic roles and interactions remain poorly defined. In this study, public databases showed stage-dependent abundance changes of H. pylori and S. anginosus but no significant correlation during gastric cancer progression. We further quantified both bacteria in gastric fluid samples collected from 500 individuals using a non-invasive gastric string test and in fecal samples from an independent cohort of 500 individuals by qPCR. In the two cohorts, no significant correlations were observed between the two bacterial pathogens, suggesting distinct colonization and pathogenic patterns. To evaluate functional differences, AGS cell co-culture models were established to explore their pro-tumorigenic effects. H. pylori predominantly exerted tumor-promoting effects through bacterial cell-associated mechanisms, whereas S. anginosus exerted stronger pro-tumorigenic effects via its metabolites. In particular, transcriptomic analysis revealed that proliferation-associated genes, including DEK and RTF1, were significantly upregulated by 21.9-fold and 19.2-fold, respectively, in cells treated with Streptococcus anginosus metabolite (SAM). Metabolomic profiling of SAM identified increased levels of spermidine and polyamine-related metabolites. Among these, N-acetylcadaverine, N-acetyltyrosine, N-acetyltryptophan, and urocanic acid were experimentally validated to significantly promote AGS cell proliferation. Collectively, these findings demonstrate that H. pylori and S. anginosus drive gastric tumorigenesis through contact-dependent and metabolite-mediated mechanisms, respectively, highlighting bacterial metabolites as emerging contributors to gastric cancer progression.IMPORTANCEThe gastric microbiota plays a critical role in gastrointestinal health and disease. However, the ecological interactions between Helicobacter pylori and non-H. pylori bacteria remain poorly understood. Among established bacterial pathogens linked to gastric carcinogenesis, H. pylori and Streptococcus anginosus are recognized as major contributors. In this study, we systematically evaluated infection patterns and potential associations between these two pathogens using public metagenomic data sets and qPCR analysis of clinical samples (feces and gastric fluid) from multicenter cohorts. We found no significant association between their infection statuses (P > 0.05), indicating independent colonization patterns and likely differences in their pathogenic mechanisms within the human host. Complementary in vitro and cellular analyses further showed that H. pylori primarily acts through direct mucosal colonization and virulence factors, whereas S. anginosus influences host responses mainly via its metabolic products. These findings demonstrate that H. pylori and S. anginosus operate through distinct colonization strategies and pathogenic pathways. They underscore the importance of accounting for mechanistic heterogeneity in gastric microbiome research and provide a conceptual framework for future investigations into microbe-driven pathogenesis of gastric disease.}, } @article {pmid42535886, year = {2026}, author = {Eckles, AE and Poelstra, JW and Toth, HN and McKenzie, ZA and Jacobs, JM and Peduto Hand, F}, title = {Transmission of Xanthomonas campestris pv. incanae and Associated Microbiome in Matthiola incana Seed.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-03-26-0074-FI}, pmid = {42535886}, issn = {0031-949X}, abstract = {Xanthomonas campestris pv. incanae (Xci) is known to cause systemic infections in the stem of Matthiola incana. Prior research observed that the pathogen can invade the vascular system and extend into the seed peduncles of infected plants, suggesting a likely mean for internal contamination of the seeds. However, this and other potential pathways of seed infection and seed-to-seed transmission, have not been sufficiently investigated. Using both culture-based and metagenomic approaches, we evaluated the potential for and efficiency of seed infection by Xci after vascular and floral inoculation of the mother plants, as well as the possibility for seed-to-seed transmission. We also explored the diversity of the M. incana seed microbiome in response to inoculation with Xci. Results showed that the vascular system was a viable and highly efficient pathway of seed infection by Xci, unlike the floral organs, and that seed infection by the vascular pathway negatively impacted seed germination. We also demonstrated that seed-to-seed transmission of Xci occurred at an epidemiologically significant degree. The primary difference among microbiomes of seeds harvested from inoculated and non-inoculated plants was the presence of Xci, which had extremely high relative and absolute abundance in infested seeds. Additionally, minor effects of inoculation treatment, seed infection pathway, and the interaction between the two were observed for overall seed microbial community composition and diversity. These findings pave the way to future exploration of the seed microbiome in M. incana.}, } @article {pmid42535896, year = {2026}, author = {Pongchaikul, P and Warintaksa, P and Jenjaroenpun, P and Opasawatchai, A and Settacomkul, R and Vivithanaporn, P and Hadratchai, S and Singsnaeh, A and Thaipisuttikul, I and Wongsurawat, T and Chaemsaithong, P}, title = {Intra-amniotic infection: diagnosis, nomenclature, clinical significance, management, and microbiologic tools used for the diagnosis.}, journal = {Clinical microbiology reviews}, volume = {}, number = {}, pages = {e0007026}, doi = {10.1128/cmr.00070-26}, pmid = {42535896}, issn = {1098-6618}, abstract = {SUMMARYIntra-amniotic infection is the main cause of spontaneous preterm birth and adverse maternal-fetal outcomes; therefore, rapid, robust, and accurate diagnosis remains a clinical priority. Conventional microbiological techniques, especially culture-based methods, are limited by long turnaround times and the inability to detect fastidious or unculturable organisms. This review summarizes the diagnosis, nomenclature, clinical significance, management, and laboratory approaches for diagnosing intra-amniotic infection. Targeted nucleic acid amplification methods, including species-specific polymerase chain reaction and broad-range 16S rRNA gene sequencing, have improved the detection of bacterial DNA and enabled the identification of organisms that evade routine culture in intra-amniotic infection. More recently, whole-genome sequencing and metagenomic next-generation sequencing have provided culture-independent strategies for comprehensive pathogen profiling, allowing simultaneous detection of bacteria, viruses, and fungi, as well as characterization of antimicrobial resistance determinants and virulence-associated genes. However, challenges remain, particularly in low-biomass samples such as amniotic fluid, where contamination, host DNA background, and data interpretation can compromise specificity. This review critically evaluates the advantages and limitations of each molecular modality and discusses pre-analytical, analytical, and bioinformatic considerations essential for reliable implementation. Integration of molecular diagnostics into clinical workflows holds promise for improving etiological diagnosis and guiding targeted therapy in intra-amniotic infection, thereby improving maternal and fetal outcomes.}, } @article {pmid42535958, year = {2026}, author = {Atallah, C and Richardson, L and Beracochea, M and Finn, RD}, title = {PIMENTO: A primer inference toolkit to facilitate large-scale calling of amplicon sequence variants.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giag083}, pmid = {42535958}, issn = {2047-217X}, abstract = {The identification of amplicon sequence variants from DNA metabarcoding data is a common method for revealing the taxonomic makeup of environmental samples, and for allowing comparative studies between similar datasets. A significant hurdle to the large-scale calling of amplicon sequence variants from publicly available nucleotide datasets is the heterogeneous presence of primer sequences in reads, the removal of which is a necessary pre-processing step for this form of analysis. Furthermore, as the details of the experimental primers are rarely captured in the metadata associated with the sequence records, there is a need for a method that can automatically infer the presence and identity of primers in sequencing data. In this work, we introduce the PrIMER infereNce TOolkit (PIMENTO), a Python package which uses a dual-strategy approach for identifying primers that are present in sequencing reads to enable their removal, and therefore facilitate amplicon sequence variant calling at scale.}, } @article {pmid42536401, year = {2026}, author = {Walker, JR and Varona, NS and Wallace, BA and Aguilar, A and O'Beirne, MD and Werne, JP and Luque, A and Gilhooly, WP and Bosco-Santos, A and Silveira, CB}, title = {Abundance-activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag197}, pmid = {42536401}, issn = {1751-7370}, abstract = {Meromictic lakes serve as analogs of redox-stratified ancient oceans with well-mixed surface waters and anoxic bottoms. In sulfide-rich lakes, purple and green sulfur bacteria (PSB, GSB) dominate the anoxic zones where light penetrates, and their biosignatures can guide interpretations of geologic records. Although PSB and GSB biosignatures indicate presence, they do not directly reflect the community composition of modern analog lakes, posing a challenge for interpretation. Here, we investigate this decoupling by integrating metagenomics, metatranscriptomics, and metaHi-C virus-host linkages with the geochemical profiles of three meromictic lakes. In the phototrophic microbial plates, PSB transcriptional activity far exceeded their abundance (73% of total microbial community activity versus 30% of abundance), whereas GSBs displayed the opposite pattern. Concurrently, PSBs were exclusively associated with temperate viruses, however, GSBs were targeted by lytic infections. Sulfate-reducing bacteria and viruses encoding genes for sulfate reduction were most active where sulfide concentration was lowest. These results reveal that viral replication strategies are associated with the decoupling between abundance and activity in anoxygenic phototrophs and sulfate reducers. These relationships could accelerate sulfur regeneration, contribute to sustaining phototrophy, and ultimately reflect in the lake's bulk biosignatures.}, } @article {pmid42537275, year = {2026}, author = {Yan, G and Jiang, ZX and Wu, JL and Wang, T and Hu, JT and Qiu, LW and Zhou, C and Ren, H}, title = {Precise H2 supply enables quantitative control of on-demand deep nitrate removal while preserving denitrification completeness.}, journal = {Water research}, volume = {306}, number = {}, pages = {126571}, doi = {10.1016/j.watres.2026.126571}, pmid = {42537275}, issn = {1879-2448}, abstract = {Precise control of deep nitrate (NO3[-]) removal is increasingly required for industrial water reuse, yet different reuse scenarios demand different target NO3[-] concentrations that cannot be readily achieved by conventional heterotrophic denitrification processes. Here, we demonstrate that membrane-mediated H2 supply enables on-demand deep hydrogenotrophic denitrification by quantitatively matching H2 supply with targeted NO3[-] removal. During 180 days of continuous operation in an H2-based membrane biofilm reactor (H2-MBfR), effluent NO3[-] concentrations were predictably tuned from 0.1 to 4.5 mg-N/L by progressively reducing H2 transfer flux, closely matching stoichiometric expectations. Crucially, partial NO3[-] removal under H2-limited conditions preserved denitrification completeness while avoiding accumulation of NO2[-], NO, N2O, or NH4[+]. Metagenomic analysis further revealed that complete hydrogenotrophic denitrifiers possessing the full enzymatic repertoire for NO3[-] to N2 reduction dominated the biofilm community (92-97% of MAG abundance). Under H2 over-supply conditions, excess electrons were channeled into biofilm-derived organic matter production via extracellular protein secretion pathways, consequently elevating effluent COD concentrations-a risk that can be avoided through precise H2 regulation. These findings establish that membrane-mediated H2 supply achieved quantitative control of deep denitrification without compromising denitrification completeness, providing a mechanistic basis for balancing desired NO3[-] removal, water quality protection, and operational costs in applications requiring deep yet tailored nitrogen control.}, } @article {pmid42526577, year = {2026}, author = {Yang, W and Teng, Y and Yang, Z and Song, X and He, L and Liu, Y and Tan, W and An, H and Shi, P and Hu, C and Ao, L and Guo, H}, title = {Chronic paternal exposure to low-dose OBS reprograms progeny's intestinal cholesterol metabolism and increases IBD susceptibility.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128846}, doi = {10.1016/j.envpol.2026.128846}, pmid = {42526577}, issn = {1873-6424}, abstract = {Sodium p-perfluorous nonenoxybenzenesulfonate (OBS) as a novel alternative to perfluorooctane sulfonate (PFOS) has been extensively used in numerous manufacturing processes, contributing to increasingly grim environmental contamination. Abundant evidence has highlighted the endocrine and metabolic-disrupting properties of OBS, establishing it as an unsafe surrogate for PFOS. However, the intergenerational toxicity of OBS, particularly the impact of paternal exposure on offspring, remains unexplored. Using a murine model, we demonstrated that chronic paternal exposure to low-dose OBS led to gut barrier disruption and heightened susceptibility to dextran sodium sulfate (DSS)-induced colitis in offspring. Through integrated multi-omics analyses including DNA methylome, transcriptome, metagenome, ChIP-seq and metabolome, we uncovered that OBS exposure induced hypermethylation of the Clock promoter in paternal sperm. This epigenetic modification was identified as the causal factor underlying the downregulation of the CLOCK-ABCA1 axis and consequent impairment of cholesterol efflux in offspring colon. Validation using multicolor immunohistochemistry and single-cell transcriptomics in clinical cohorts further substantiated the involvement of the CLOCK-ABCA1 pathway, not only in the disruption of intestinal homeostasis but also in inflammatory bowel disease (IBD) pathogenesis. Collectively, our study provides insight into the intergenerational toxicity of emerging PFAS, which also facilitates the identification of potential targets for the early warning and therapeutic intervention of IBD.}, } @article {pmid42526667, year = {2026}, author = {Cui, P and Zhang, H and Hu, T and Huang, Q and Hu, X and Wang, Q and Diwan, AD and Wang, T and Zhao, X and Lu, S and Chen, X}, title = {The Metabolite indole-3-acetic acid of Bacteroides ovatus ameliorates ovariectomy-induced bone loss by activating AhR and inhibiting oxidative stress.}, journal = {Free radical biology & medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.freeradbiomed.2026.07.050}, pmid = {42526667}, issn = {1873-4596}, abstract = {Postmenopausal osteoporosis represents a systemic skeletal condition distinguished by diminished bone mass and heightened skeletal fragility. Emerging evidence has highlighted a significant relationship between bone metabolism and disturbances in gut microbiota (GM) homeostasis. However, the exact mechanisms by which GM dysbiosis contributes to postmenopausal osteoporosis remain insufficiently understood. Herein, integrating weighted gene co-expression network analysis with machine learning, a notable depletion of Bacteroides ovatus (B. ovatus) was identified in the GM of women with postmenopausal osteoporosis. Metagenomic sequencing further validated the reduced abundance of B. ovatus in ovariectomized (OVX) mice. Notably, live B. ovatus (LBO), but not heat-killed B. ovatus (KBO), effectively mitigated bone loss in OVX mice and restored intestinal mucosal barrier integrity. Both untargeted and targeted metabolomic profiling revealed substantial alterations in tryptophan metabolism in OVX mice, particularly a significant reduction in indole-3-acetic acid (IAA). Oral supplementation with IAA notably alleviated bone loss in OVX mice. Mechanistically, IAA stimulated AhR, enhancing NQO1 expression, reducing intracellular ROS buildup, and ultimately suppressing osteoclast differentiation and bone resorption. This investigation demonstrates, for the first time, the protective effects of B. ovatus and its metabolite IAA in counteracting estrogen deficiency-induced bone loss and may present a promising microbial-targeted strategy for osteoporosis prevention.}, } @article {pmid42526894, year = {2026}, author = {O'Halloran, DM}, title = {STRONGYLID COINFECTIONS IN SYMPATRIC CHIMPANZEES AND GORILLAS FROM THE REPUBLIC OF THE CONGO REVEALED BY FECAL METAGENOMICS.}, journal = {The Journal of parasitology}, volume = {112}, number = {4}, pages = {443-450}, doi = {10.1645/25-102}, pmid = {42526894}, issn = {1937-2345}, mesh = {Animals ; *Gorilla gorilla/parasitology ; *Feces/parasitology ; Congo/epidemiology ; *Pan troglodytes/parasitology ; *Ape Diseases/parasitology/epidemiology ; Metagenomics ; *Coinfection/veterinary/parasitology/epidemiology ; Female ; Sympatry ; *Nematode Infections/veterinary/parasitology/epidemiology ; *Strongylida/genetics/classification/isolation & purification ; Male ; *Intestinal Diseases, Parasitic/parasitology/veterinary/epidemiology ; Metagenome ; }, abstract = {Soil-transmitted strongylid nematodes are common intestinal parasites of African great apes, yet most surveys have relied on microscopy or targeted PCR assays that are limited in taxonomic breadth and comparability across hosts. I reanalyzed 46 publicly available shotgun fecal metagenomes from sympatric central chimpanzees (Pan troglodytes troglodytes; n = 18) and western lowland gorillas (Gorilla gorilla gorilla; n = 28) in the Goualougo Triangle, Nouabalé-Ndoki National Park, Republic of the Congo, to test whether host species structures genus-level strongylid community composition and relative read signal. Non-host reads were classified against a custom strongylid-focused database targeting 4 genera repeatedly reported from African apes: Ancylostoma, Necator, Oesophagostomum, and Trichostrongylus. All 4 focal genera were detected in every library under baseline filtering, and multi-genus detection remained robust under increasingly stringent read-count thresholds. However, host species differed strongly in community composition. Chimpanzee libraries had relatively even genus-level profiles, whereas gorilla libraries were consistently Necator-dominated. Gorillas also had substantially higher relative strongylid read abundance. The results show that shotgun metagenomic reanalysis can recover host-structured strongylid community signals from wildlife samples and can complement targeted parasitological surveys in conservation and One Health surveillance.}, } @article {pmid42527912, year = {2026}, author = {Tiefensee, M and Weng, N and Ohlsson, JA and Westerholm, M}, title = {Metagenomic and cultivation-based description of a syntrophic butyrate-oxidizing bacterium from a thermophilic and high-ammonia biogas process.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42527912}, issn = {1471-2180}, mesh = {Oxidation-Reduction ; Phylogeny ; *Ammonia/metabolism ; *Butyrates/metabolism ; *Metagenomics/methods ; *Biofuels/microbiology ; Metagenome ; Methane/metabolism ; Acetates/metabolism ; Anaerobiosis ; *Bacteria/genetics/metabolism/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Ammonia inhibition in anaerobic digestion can lead to butyrate accumulation and reduced methane yield. Despite the importance of syntrophic butyrate oxidation in mitigating this effect, the microorganisms and interactions involved under high-ammonia conditions remain poorly understood. Here, we combine metagenomics and cultivation studies to describe a novel ammonia-tolerant syntrophic butyrate-oxidizing bacterium and its interactions with acetate-oxidizing bacteria and hydrogenotrophic methanogens enriched from a high-ammonia, thermophilic biogas process.

RESULTS: The enrichment culture degraded butyrate at rates of 0.12-0.47 mmol/day. Amplicon sequencing and phylogenetic analyses of a retrieved metagenome-assembled genome (MAG) assigned the putative syntrophic butyrate-oxidizing bacterium (SBOB) to the genus Syntrophothermus, for which we propose the provisional species name 'Candidatus Syntrophothermus ammoniitolerans'. Metagenomic analyses revealed the genomic potential for β-oxidation and essential electron transfer pathways associated with syntrophic energy conservation. Furthermore, one additional MAG (MAG9) possessed a complete β-oxidation pathway but lacked key genes associated with reverse electron transfer, making its role as a SBOB uncertain. Acetate produced during butyrate oxidation was further oxidized by syntrophic acetate-oxidizing bacteria and ultimately converted to methane by hydrogenotrophic methanogens, illustrating a tightly coupled metabolic network that supports butyrate degradation under high-ammonia conditions. Three methanogenic MAGs, affiliated with the genera Methanoculleus and Methanothermobacter, were identified as potential hydrogen- or formate-consuming partners.

CONCLUSIONS: Together, these results identify a novel syntrophic butyrate-oxidizing candidate that enables butyrate degradation under high-ammonia conditions via tightly coupled interactions with acetate-oxidizing bacteria and hydrogenotrophic methanogens, sustaining methane production under ammonia stress.}, } @article {pmid42528583, year = {2026}, author = {Aili, A and Deng, H and Zhang, H and Wang, W and Pan, L}, title = {Amiodarone-induced granulomatous lung injury mimicking organizing pneumonia: a case report.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1848041}, pmid = {42528583}, issn = {1663-9812}, abstract = {BACKGROUND: Amiodarone-induced pulmonary toxicity (APT) has a broad clinical spectrum, and its radiologic and histopathologic appearances vary considerably. Granulomatous lung injury, however, is rarely described and may be confused with organizing pneumonia (OP) or infection.

CASE PRESENTATION: An elderly man who had been receiving 5-month amiodarone therapy developed a 3-week history of pleuritic chest pain and progressive dyspnea. Chest computed tomography (CT) demonstrated bilateral ground-glass opacities and subpleural-predominant consolidations, with scattered reversed halo signs raising the possibility of an OP-like pattern. A positive serum Cryptococcal antigen (CrAg) result obtained at an outside hospital led to empiric antifungal therapy, but the patient did not improve. After admission, bronchoalveolar lavage (BAL) revealed lymphocytosis, and metagenomic testing did not detect Cryptococcus or other pathogens; fungal stains on biopsy specimens were also negative. Percutaneous lung biopsy showed focal non-necrotizing granulomas with prominent eosinophilic inflammation. After discontinuation of amiodarone and initiation of systemic corticosteroid therapy, his symptoms improved rapidly and follow-up imaging demonstrated interval regression.

CONCLUSION: This case illustrates that an OP-like CT pattern may mask an uncommon granulomatous phenotype of amiodarone-related lung injury. A positive fungal biomarker should therefore be weighed against the microbiological work-up, tissue findings, medication history, and treatment response before infection is accepted as the final diagnosis.}, } @article {pmid42528818, year = {2026}, author = {Chen, M and Wang, X and Peng, G and Jiang, L and Liang, H and Cui, P}, title = {Gut microbiota induces immune-related alterations in gene expression, RNA methylation, and metabolism in glioblastoma revealed by single-cell and spatial multi-omics.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1899954}, pmid = {42528818}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology/drug effects ; RNA Methylation ; *Brain Neoplasms/metabolism/genetics/immunology/microbiology ; Mice ; Multiomics ; *Glioblastoma/metabolism/genetics/immunology/microbiology ; Humans ; *Gene Expression Regulation, Neoplastic ; Epitranscriptome ; Single-Cell Analysis ; Spatial Transcriptomics ; Epigenesis, Genetic ; Tumor Microenvironment/immunology ; Single-Cell Gene Expression Analysis ; Gene Expression Profiling ; }, abstract = {Glioblastoma (GBM) is a highly malignant tumor with poor prognosis and limited effective treatment options. Emerging studies have suggested that gut microbiota may influence glioma progression through the gut-brain axis, though the precise mechanisms remain largely unclear. In this study, we employed a comprehensive multi-omics approach-encompassing single-cell transcriptomics, spatial transcriptomics, metagenomics, metabolomics, and m6A-seq-to investigate how antibiotic-induced gut microbiota disruption impacts glioma progression in a mouse model. Gene expression analysis revealed significant alterations in antibiotics-treated mice (ABX-treated mice), including reduced expression of Epha6 and upregulated expression of Tead1, key genes associated with glioma progression and immune modulation. Spatial transcriptomics and metabolomic profiling identified reduced methionine levels in gliomas of ABX-treated mice, linking gut-derived metabolite changes to epigenetic regulation via m6A methylation. Single-cell RNA sequencing further demonstrated an increased proportion of AC-like cells, disrupted intercellular communication, and aberrations in the EPHA and NRXN signaling pathways. These findings highlight the interplay between gut microbiota, immune signaling, and epigenetic modifications in shaping the glioma microenvironment. This study advances our understanding of the gut-brain axis in glioma biology and proposes the EPHA pathway as a promising biomarker for the immune-mediated modulation of tumor progression, thereby providing new insights into the role of the gut-brain axis in glioma regulation.}, } @article {pmid42528820, year = {2026}, author = {Cui, B and Li, H and Cui, R and Jiang, X and Jin, X}, title = {Metabolic dysfunction-associated steatotic liver disease with alcohol- and iron overload-related cholestatic liver injury: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1805756}, pmid = {42528820}, issn = {2296-858X}, abstract = {A 38-year-old woman with a >10-year history of heavy alcohol consumption presented with acute-onset jaundice and massive hepatomegaly. Laboratory tests revealed a cholestatic-pre-dominant liver injury pattern with extreme γ-glutamyl transferase elevation (>1,000 U/L) and marked hyperferritinemia (>1,500 ng/ml). Imaging excluded extrahepatic biliary obstruction. Liver biopsy demonstrated steatohepatitis with ductular reaction and stage F2 fibrosis. Metagenomic next-generation sequencing (mNGS) was negative for infectious pathogens. After alcohol abstinence, metabolic intervention, a short empiric corticosteroid course, and supportive therapy, liver function gradually improved. This case highlights a reversible cholestatic phenotype in alcohol-associated steatotic liver injury with metabolic dysfunction and suspected secondary iron overload.}, } @article {pmid42528906, year = {2026}, author = {Zhang, M and Wang, S and Gao, J and Jie, J and Yu, Q and Li, D and Song, L and Fan, X}, title = {Type VI secretion system completeness shapes evolutionary trade-offs in the Acinetobacter baumannii resistome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1867466}, pmid = {42528906}, issn = {1664-302X}, abstract = {The rapid global dissemination of multidrug-resistant Acinetobacter baumannii poses a critical threat to public health, yet the role of the Type VI Secretion System (T6SS)-a contact-dependent interbacterial weapon-in shaping the antimicrobial resistome remains poorly understood. Here, we integrated clinical metagenomics and large-scale comparative genomics to investigate the association between T6SS completeness and resistome organization. T6SS status was not independently associated with overall antimicrobial resistance genes (ARGs) burden or alpha diversity after controlling for shared evolutionary history and genomic background. However, T6SS completeness was associated with distinct resistome composition across multiple lineages. T6SS-complete genomes were preferentially enriched in chromosomally associated resistance determinants, including intrinsic β-lactamases and multidrug efflux systems, alongside tighter genomic co-localization between ARGs and mobile genetic elements (MGEs), consistent with localized chromosomal integration of resistance-associated mobile elements. This foundational prerequisite was supported by experimental validation of efficient T6SS-dependent interbacterial killing in a hyper-resistant lineage. Conversely, T6SS-incomplete genomes were significantly enriched in highly potent exogenously acquired ARGs, including blaNDM-1 and blaCTX-M, frequently alongside structurally uncoupled MGEs. Together, these findings are consistent with an evolutionary trade-off model in which T6SS-complete and T6SS-incomplete A. baumannii populations exhibit distinct resistance acquisition strategies and contrasting genomic contexts of horizontal gene transfer, thereby contributing to divergent resistome organization.}, } @article {pmid42528952, year = {2026}, author = {Liu, X and Cheng, W and Li, C and Dessie, W and Qi, C and Ayaz, M and Xu, X}, title = {Integrated metagenomic and metabolomic insights into microbial metabolic reprogramming in the rhizosphere of the invasive plant Praxelis clematidea under low-temperature stress.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1852122}, pmid = {42528952}, issn = {1664-302X}, abstract = {A primary factor preventing the spread of the invasive plant Praxelis clematidea to higher latitudes and altitudes is the low-temperature stress induced by global climate change. The present study investigated the impact of low-temperature stress on the rhizosphere soil micro-ecosystem of P. clematidea, with the aim of examining its adaptive micro-ecological mechanisms via a comprehensive multi-omics approach. The rhizosphere soils of plants were compared under low-temperature (LT, 5 °C) or normal-temperature (HT, 25 °C) treatments. Using soil physicochemical analysis, enzyme activity assay, metagenomics, and non-targeted metabolomics, we observed that LT stress did not significantly alter microbial alpha diversity but strongly shifted the community structure. This change enriched cold-tolerant bacterial taxa, including Nocardiopsis, Sphingobium and Azoarcus. The LT stress was associated with altered carbon and nitrogen cycling, as indicated by increased soil urease activity but decreased alkaline phosphatase and catalase activities. The nitrate-N and ammonium-N levels increased, but total nitrogen, total organic carbon, and organic matter were reduced. Additionally, metagenomic study revealed overexpression of major microbial carbon metabolism genes (e.g., TCA cycle and glycolysis) and downregulation of nitrogen assimilation genes (e.g., glnA and NasA). Furthermore, metabolomics indicated a rise in carbohydrates and vitamins, along with a notable accumulation of stress-resistant secondary metabolites such as phenolic acids, flavonoids, and terpenes in the rhizosphere soils under LT stress. Correlation analysis indicated strong positive associations between the enriched cold-tolerant genera and these stress-resistant metabolites (e.g., costunolide and choline sulfate). Functional enrichment analysis suggested a metabolic reprogramming signature coupled with low-temperature treatment. Finally, this integrated multi-omics study reveals that P. clematidea is associated with an altered rhizosphere microbiome, differential functional gene abundance, and reorganized metabolic networks under low-temperature conditions. These findings offer a vital micro-ecological elucidation for P. clematidea effective colonization and propagation in novel, colder habitats.}, } @article {pmid42529042, year = {2026}, author = {Ma, X and Guo, S and Feng, Y and Su, M and Wei, F and Liu, X}, title = {Rapid clinical validation of an RNA/DNA hybrid tagmentation-based metagenomic workflow for respiratory RNA virus detection.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1849991}, pmid = {42529042}, issn = {1664-302X}, abstract = {BACKGROUND: In the post-pandemic era, co-circulation of multiple respiratory RNA viruses has increased the need for timely diagnosis and reliable recognition of mixed infections. Although reverse transcription quantitative polymerase chain reaction (RT-qPCR) remains the clinical standard for respiratory virus detection, its target-restricted design limits the detection of unexpected or coinfecting pathogens. Conventional metagenomic next-generation sequencing (mNGS) provides hypothesis-free pathogen detection, but routine clinical use is still limited by long turnaround times and complex library preparation. Therefore, a sequencing-based strategy that preserves broad, unbiased detection while offering a simplified workflow and clinically acceptable turnaround time is needed.

METHODS: We optimized and clinically validated CATCH, a rapid RNA/DNA hybrid tagmentation-based mNGS workflow, for respiratory RNA virus detection. Analytical performance was assessed using standardized reference materials, including SARS-CoV-2 and influenza A virus, with evaluations of sensitivity, reproducibility, short-term stability, and host-background interference. Clinical validation was performed in retrospective and prospective respiratory infection cohorts, and assay performance was benchmarked against RT-qPCR and multiplex PCR. The same sequencing data were further examined for semiquantitative viral assessment, coinfection detection, and exploratory respiratory microbial profiling.

RESULTS: The optimized CATCH workflow shortened library preparation to approximately 3 h, with about 35 min of hands-on time, enabling same-day sequencing-based diagnostics. Broad detection was achieved across seven clinically relevant respiratory RNA viruses. Sequencing-derived viral abundance showed a significant overall correlation with viral input concentration, supporting semiquantitative interpretation, although virus- and subtype-specific variability highlighted biological constraints on absolute quantification. Using SARS-CoV-2 and influenza A virus as representative targets, CATCH achieved clinically actionable limits of detection with high reproducibility and stability. In clinical cohorts, CATCH showed high concordance with routine molecular assays and identified mixed respiratory infections missed by targeted testing. Exploratory analyses also demonstrated the feasibility of respiratory microbial community profiling from the same sequencing dataset.

CONCLUSION: CATCH is a rapid and clinically deployable RNA virus mNGS workflow that helps bridge targeted molecular diagnostics and conventional metagenomic sequencing. By combining broad pathogen detection, coinfection identification, and semiquantitative assessment within a streamlined workflow, CATCH provides a practical framework for comprehensive respiratory RNA virus diagnosis and syndromic surveillance.}, } @article {pmid42529077, year = {2026}, author = {Zhao, X and McCarter, SJ and Gupta, VK and Grant, KM and St Louis, EK and Kantarci, K and Savica, R and Hill, M and Vuong, HE and Staley, C and Boeve, BF and Ross, OA and Teigen, LM and Sung, J}, title = {Shotgun metagenomic analysis reveals taxonomic and functional alterations in the gut microbiome across prodromal and symptomatic Lewy body disease.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1834726}, pmid = {42529077}, issn = {2813-4338}, abstract = {BACKGROUND: Lewy body disease (LBD) is a progressive neurodegenerative a-synucleinopathy, whereas isolated REM sleep behavior disorder (iRBD) is recognized as a prodromal stage of LBD. Although growing evidence implicates the gut-brain axis in neurodegeneration, the taxonomic and functional roles of the gut microbiome across the prodromal-to-symptomatic LBD continuum remain poorly defined.

METHODS: Here, we performed shotgun metagenomic sequencing on stool samples from 25 patients with LBD (10 mild cognitive impairment due to LBD [MCI-LB] and 15 dementia with Lewy bodies [DLB]), 10 individuals with iRBD, and their household matched cohabitant controls to characterize disease-associated microbial alterations while minimizing environmental confounding.

RESULTS: Despite no significant differences in global microbial diversity, we identified convergent shifts in microbial taxa, metabolic pathways, and gene families across disease stages. Both LBD and iRBD showed increased abundance of microbial taxa potentially associated with gut barrier disruption, as well as higher abundance of functional pathways related to lipopolysaccharide biosynthesis. LBD showed lower abundance of pathways related to complex carbohydrate fermentation, and both groups showed lower abundance of pathways associated with neurotransmitter-related metabolism. In particular, pathways and gene families associated with starch degradation were reduced in LBD, and those associated with histidine-to-glutamate/ GABA metabolism were reduced in both groups.

DISCUSSION: These exploratory findings represent the first high-resolution, shotgun metagenomic characterization of gut microbiome alterations across the LBD continuum, highlighting functional patterns that may serve as candidate markers of disease progression in future longitudinal and mechanistic studies.}, } @article {pmid42529131, year = {2026}, author = {Huang, B and Chen, Z and Xue, W and Pu, Z and Zhou, Y and Koay, SSN and Kong, P and Zhao, Y and Tai, L and Lan, Z and Xian, Y and Chen, AJ}, title = {Synergistic Anti-Obesity Effect of Akkermansia muciniphila AKM Lab-01 and Garcinia cambogia Extract via Gut Microbiota Remodeling in Diet-Induced Obese Mice.}, journal = {Food science & nutrition}, volume = {14}, number = {8}, pages = {e72140}, pmid = {42529131}, issn = {2048-7177}, abstract = {Obesity is a global health crisis driven by complex metabolic dysregulation. Although Akkermansia muciniphila (AKK) has emerged as a promising next-generation probiotic for metabolic health, its synergistic potential with natural anti-obesity compounds remains largely unexplored. Here, we evaluated the combined administration of pasteurized A. muciniphila (AKM Lab-01) and Garcinia cambogia extract (GCE) in a mouse model of high-fat diet-induced obesity. The combination treatment significantly ameliorated obesity-related phenotypes, including reduced body weight, decreased fat mass, improved serum metabolic parameters, and attenuated adipose tissue inflammation. Adipose tissue transcriptomic profiling revealed enhanced lipid catabolism and downregulation of pro-inflammatory pathways. Metagenomic sequencing showed marked gut microbiota remodeling, characterized by increased abundance of Lactococcus and decreased levels of Clostridium and Eisenbergiella. Integrated correlation analysis linked these microbial shifts to transcriptional reprogramming in adipose tissue. Using a 3 T3-L1 adipocyte model, we further confirmed that Lactococcus plays a potential role in regulating lipid metabolism and inflammation. Collectively, these findings strongly suggest that the AKM Lab-01 and GCE combination may exert synergistic anti-obesity effects via a gut microbiota-host metabolic axis, supporting its potential as a novel synbiotic strategy for obesity management.}, } @article {pmid42529303, year = {2026}, author = {Wang, W and Cen, C and Yang, J}, title = {Dominant Role of Habitat Transformation in Driving the Divergence of Health-Risk Related Microbial Functional Genes in Karst Mountain Parks: A Metagenomic Study.}, journal = {Ecology and evolution}, volume = {16}, number = {8}, pages = {e74112}, pmid = {42529303}, issn = {2045-7758}, abstract = {The transformation of natural forests into urban parks has had a profound impact on subterranean ecosystems. Nevertheless, the underlying mechanisms by which this land use change affects human health through alterations in soil microbial functional genes remain to be elucidated. Focusing on a karst mountain park in Guiyang, China, we used metagenomic sequencing to compare the abundance and composition of antibiotic resistance genes (ARGs), pathogen-host interaction genes (PHIs), and virulence factor genes (VFs) between remnant forests and artificial green spaces, and examined how plant diversity and soil chemometrics drove their variation. Habitat type emerged as the strongest driver of gene composition. PHIs and VFs were more abundant in remnant forests and positively correlated with native plant diversity, while ARGs were enriched in artificial green spaces. All three gene categories showed positive correlations with soil nitrogen content in artificial green spaces. Remnant forests harbored microbial functions linked to complex plant-microbe interactions, whereas intensive management in artificial green spaces selects for antibiotic resistance and nutrient-adaptive genes. These findings reveal distinct health risks across habitats, suggesting that differentiated park management strategies are needed to mitigate public health risks while maintaining ecological sustainability.}, } @article {pmid42529392, year = {2026}, author = {Cambara, JCO and Cuber, P and Khattak, F and Lebre, PH and Galgano, S and Houdijk, J and Smallman, D and Estridge, P and Allen, MJ and Short, F and Sutcliffe, M and Mkrtchyan, HV}, title = {Long-reads metagenomics reveals the effects of dulse supplementation on the poultry caecal bacteriome and its associated genetic repertoire.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1868730}, pmid = {42529392}, issn = {1664-302X}, abstract = {INTRODUCTION: Dulse (Palmaria palmata) is a macroalgal feed ingredient rich in polysaccharides and bioactive compounds that offers a sustainable strategy to enhance animal health and productivity through modulation of gut microbiota. However, the impact of dulse supplementation on the taxonomic composition and genetic repertoire of the broiler chicken caecal microbiota remains poorly characterised.

METHODS: We applied long-read shotgun metagenomic sequencing on 18 caecal samples collected from 27-day-old male Ross 308 broilers following a 7-day feeding trial with three dietary treatments - a reference diet, a soyabean meal-supplemented diet, and a diet supplemented with 30% dulse - to investigate the effects of dulse inclusion on microbial community composition, genetic diversity, and antimicrobial resistance (AMR) and virulence determinants.

RESULTS: Across all dietary treatments, the Clostridia class predominated (71%), whereas primary fermenters (L. phocaeense), lactic acid bacteria (L. salivarius), and hydrogenotrophic cross-feeders (B. hydrogenotrophica) were enriched in the reference diet, dulse-supplemented and soyabean meal-supplemented groups, respectively (KW p < 0.05), contributing to potential improvements in caecal function, immune resilience, and nutrient utilisation while reducing pathogen load. The overall resistome profiles were comparable across dietary treatments and were dominated by genes conferring resistance to tetracyclines, lincosamides, and aminoglycosides. In contrast, the virulome displayed diet-associated shifts: Enterobacteriaceae were enriched in the dulse and reference diets relative to the soyabean meal diet, with an expanded functional repertoire of virulence-associated genes, particularly those involved in adhesion, iron acquisition, and secretion systems. Multidrug resistance genes, virulence determinants, and Col/IncF-type plasmid replicons were associated with E. coli reads, highlighting its potential resistance and virulence arsenal within the caecal microbiota.

DISCUSSION: Our findings suggest that the benefits of dulse extend beyond its nutritional value, residing in its ability to foster ecosystem resilience; by promoting a diverse, niche-stabilised microbiota, dulse minimises the risk of opportunistic pathogen proliferation, supporting its use as a sustainable, functional feed ingredient.}, } @article {pmid42529424, year = {2026}, author = {McCammon, SD and Chen See, JR and Wright, JR and Anderson, SLC and Russell, TJ and Lamendella, RM and Firneno, TJ}, title = {Spatial organization of cutaneous microbiomes reveals putative microbial contributions to host chemical defenses in the American toad.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1860796}, pmid = {42529424}, issn = {1664-302X}, abstract = {Chemical defenses are widely evolved throughout the tree of life. Animals can exploit mutualisms with toxin-producing symbionts as a mechanism of chemical defense. However, this has only begun to be explored in depth, and how these mutualisms may relate to how animals synthesize or acquire their toxins has been even less studied. True toads synthesize their own toxins and offer a novel system to study the interplay between the cutaneous skin microbiome and how it may contribute to toxin synthesis or biotransformation. In this study, we investigated whether the cutaneous microbiome of the American toad (Anaxyrus americanus) was spatially structured across body surfaces in relation to toxin storage and secretion and assessed whether microbial communities exhibit distinctive bacterial taxa involved in toxin-related biochemical pathways. To do this, we used 16S rRNA gene sequencing, diversity metrics, differential abundance comparisons, functional pathway predictions, and ecological interaction networks. Our results indicate that the dorsal and ventral cutaneous surfaces harbor distinct bacterial assemblages, with the dorsal surface being enriched for bacterial taxa associated with the predicted potential to degrade or transform structurally complex organic compounds. This study provides insights into how the toad skin microbiome may contribute to the chemical defenses of toads and could reveal novel aspects of host-microbiome interactions in amphibians.}, } @article {pmid42529500, year = {2026}, author = {Li, L and Wang, D and Huang, C}, title = {Enterococcus faecium pneumonia diagnosed by metagenomic next-generation sequencing in a patient with chronic obstructive pulmonary disease.}, journal = {IDCases}, volume = {45}, number = {}, pages = {e02695}, pmid = {42529500}, issn = {2214-2509}, abstract = {Enterococcus faecium is a rare pathogen in community-acquired pneumonia (CAP), and its diagnosis is challenging, particularly when prior antibiotic therapy hampers isolation by conventional culture. We report a 72-year-old man with a 6-year history of chronic obstructive pulmonary disease (COPD) who presented with fever, cough, and progressive dyspnea. Despite empirical broad-spectrum antibiotics (piperacillin-tazobactam followed by imipenem-cilastatin), his condition deteriorated into acute respiratory distress syndrome (ARDS) requiring invasive mechanical ventilation. All routine cultures of blood, sputum, and throat swabs were negative, and extensive atypical pathogen screening was unrevealing. Metagenomic next-generation sequencing (mNGS) of sputum and subsequently bronchoalveolar lavage (BAL) fluid, performed at the ISO 15189-accredited central laboratory of Qujing Central Hospital of Yunnan Province, detected high read counts of E. faecium (sputum: 22,710 reads; BAL: 7921 reads; opportunistic pathogen, classification B), with simultaneous routine screening for 31 resistance genes, 4 resistance loci, and virulence genes, all negative. Additionally, sputum mNGS detected Epstein-Barr virus (Human gammaherpesvirus 4, 6715 reads, normal microbiota, classification C), and BAL fluid mNGS detected HSV-1 (Human alphaherpesvirus 1, 407 reads, normal microbiota, classification C). Both herpesviruses had classification C and were interpreted as non-pathogenic "bystanders"; no antiviral therapy was administered. The patient gradually improved on imipenem-cilastatin plus moxifloxacin and was successfully extubated and discharged. This case suggests that E. faecium can cause severe CAP in COPD patients, and mNGS is a valuable diagnostic tool when conventional cultures are negative; herpesviruses with classification C detected by mNGS should not be overinterpreted.}, } @article {pmid42530375, year = {2026}, author = {Wang, Z and Gao, Q and Li, S and Fang, Z and Hu, L and Li, R and Zeng, Z and Liu, Y and Li, C and Chen, H}, title = {Epigallocatechin gallate inhibits high-fat/choline diet-induced trimethylamine production via regulation of intestinal Serratia and Lactobacillus communities.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo02528e}, pmid = {42530375}, issn = {2042-650X}, abstract = {High-fat/choline diets can induce the production of the enterogenous metabolite trimethylamine-N-oxide (TMAO). TMAO is synthesized from its precursor trimethylamine (TMA), which is generated via choline cleavage catalyzed by choline trimethylamine-lyase/choline TMA-lyase-activating enzyme (CutC/D) expressed by gut microbes; subsequently, TMA is oxidized to TMAO by flavin-containing monooxygenase 3 (FMO3) in the liver. While epigallocatechin gallate (EGCG) is well recognized for its gut microbiota-remodeling capacity, how it modulates TMA/TMAO metabolism through this pathway, along with the time-dependent effectiveness of EGCG intervention, remains to be elucidated. We conducted animal experiments to evaluate the inhibitory effect of time-dependent EGCG intervention on TMA/TMAO production induced by high-fat/choline diets in mice. We further identified gut bacterial strains associated with TMA levels using metagenomics and machine learning techniques, and verified the underlying mechanisms through in vitro anaerobic culture and molecular simulations. Results demonstrated EGCG significantly reduced TMA/TMAO levels in mice by regulating the choline-CutC/D-FMO3 axis. Specifically, Serratia exhibited a positive correlation with CutC enzyme activity, while Lactobacillus showed a negative correlation with TMA levels. Mechanistically, EGCG exerted a direct bacteriostatic effect on Serratia marcescens by disrupting its cell membrane structure and inhibiting its CutC enzyme activity. Meanwhile, EGCG significantly enriched Lactobacillus johnsonii, with the abundance of this strain peaking after long-term intervention. Although Lactobacillus johnsonii does not directly degrade TMA, it indirectly reduces TMA levels by inhibiting the growth of Serratia marcescens. Long-term continuous supplementation with EGCG yielded the optimal inhibitory effect on TMA/TMAO production. Hence, EGCG exerts its function primarily through a dual mechanism: directly inhibiting the growth and CutC enzyme activity of the TMA-producing bacterium Serratia marcescens, and indirectly antagonizing Serratia marcescens by promoting the proliferation of the beneficial bacterium Lactobacillus johnsonii. This study provides novel theoretical insights into the mechanism by which EGCG alleviates TMA/TMAO metabolic disorders induced by high-fat/choline diets via gut microbiota modulation.}, } @article {pmid42530605, year = {2026}, author = {Yasuda, K and Iida, N and Takeshita, Y and Masuo, Y and Honda, M and Takamura, T and Yamashita, T}, title = {Tofogliflozin alters amino acid metabolism in gut microbiota linked to hepatic transcriptomic signatures in MASLD.}, journal = {Journal of gastroenterology}, volume = {}, number = {}, pages = {}, pmid = {42530605}, issn = {1435-5922}, abstract = {BACKGROUND: A deeper understanding of the relationship between dysbiotic gut microbiota and liver tissue-level molecular and histopathological phenotypes in metabolic dysfunction-associated steatotic liver disease (MASLD) remains needed. We aimed to characterize the associations between gut microbial metabolic functions and treatment responses in participants with MASLD.

METHODS: We performed a prespecified sub-analysis of a randomized controlled trial comparing the sodium-glucose cotransporter 2 inhibitor (SGLT2i) tofogliflozin and the sulfonylurea (SU) glimepiride in participants with MASLD and type 2 diabetes (ClinicalTrials.gov NCT02649465). Fecal whole-genome shotgun metagenomics, liver RNA sequencing, serum profiling, and histopathological assessments were integrated to investigate microbiota-host interactions.

RESULTS: Microbial metabolic pathways, rather than taxonomic composition, differed significantly between participants with MASLD and healthy controls. Among the altered microbial pathways, amino acid metabolism emerged as a prominent functional category and was selected for further investigation. Pathways related to amino acid metabolism, particularly phenylalanine metabolism, exhibited opposing patterns: phenylalanine degradation was enriched in MASLD and positively correlated with liver fibrosis scores, whereas phenylalanine biosynthesis inversely correlated with fibrosis severity. Microbial phenylalanine degradation was positively associated with 28 hepatic pathways, including the non-alcoholic fatty liver disease (NAFLD) pathway, in which mitochondria-associated genes were core-enriched. Both SGLT2i and SU treatments improved NAFLD activity scores and altered microbial metabolic pathways without significantly changing microbial species composition. Notably, SGLT2i increased phenylalanine biosynthesis pathways, which were inversely associated with liver fibrosis.

CONCLUSIONS: Gut microbial amino acid metabolism, particularly phenylalanine metabolism, is closely linked to liver fibrosis and molecular pathways in MASLD. Modulation of microbial metabolic functions may represent a promising therapeutic strategy beyond changes in microbial composition.}, } @article {pmid42530606, year = {2026}, author = {Cui, C and Shi, H and Naito, Y and Otani, K and Chan, FKL}, title = {Clinical applications of gut microbiome for non-invasive diagnosis of colorectal neoplasia.}, journal = {Journal of gastroenterology}, volume = {}, number = {}, pages = {}, pmid = {42530606}, issn = {1435-5922}, abstract = {Colorectal cancer (CRC) is the third most common malignancy and the second leading cause of cancer-related death worldwide. While screening programs have reduced mortality, current stool-based tests such as the faecal immunochemical test (FIT) and tumour marker assays, remain limited in sensitivity for adenoma detection and rely on relatively later-stage biological signals in the carcinogenic process. False positives lead to unnecessary invasive procedures, whilst missed adenomas continue to progress, highlighting the need for alternative strategies. Accumulating evidence implicates the gut microbiome in CRC pathogenesis, which involves tumour-associated dysbiosis and microbial ecosystem shifts. Multinational metagenomic studies have consistently identified reproducible microbial signatures that can serve as biomarkers of disease and may predate the biological signals used in conventional screening. PCR-based microbial markers have emerged as practical tools for clinical application, enabling sensitive and specific detection of adenomas and CRC. A recent microbial panel incorporating Fusobacterium nucleatum, Hungatella hathewayi, Christensenella hongkongensis, and a novel bacterial gene marker m3 from Lachnoclostridium demonstrated improved sensitivity for adenomas whilst maintaining comparable accuracy for CRC. International guidelines have begun to recommend combining microbiome-based assays with FIT into integrated screening programs that target multiple biologic processes across the pathogenesis. Microbiome-based stool testing represents a promising non-invasive approach that improves detection of adenomas in early-stage disease, often missed by FIT alone and could enable more refined risk stratification. Further validation across diverse populations, assessment of cost-effectiveness, and integration into established screening infrastructures will be critical for broad clinical adoption.}, } @article {pmid42530881, year = {2026}, author = {Lakamp, A and Aluthge, ND and Kuehn, LA and Snelling, WM and Wells, J and Hales, K and Neville, B and Fernando, SC and Spangler, ML}, title = {Impact of reducing metagenomic sequencing depth on phenotypic prediction accuracy of feed intake and average daily gain in beef cattle.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skag236}, pmid = {42530881}, issn = {1525-3163}, abstract = {Metagenomic information can aid in both genomic and phenotypic predictions of economically relevant traits. Financial restraints often result in a trade-off between the number of samples sequenced and the depth of sequencing. Therefore, it is critical to understand how changes in sequencing depth impact phenotypic prediction accuracy to make optimal use of resources. This study utilized host genomic and rumen metagenomic information of 717 beef cattle to make phenotypic predictions for average daily dry matter intake (ADDMI) and average daily gain (ADG). Metagenomic samples were sequenced at an average depth of 20 million reads (20M set) and were downsampled to 50% (10M set), 25% (5M set), and 10% of the reads (2M set). Rumen microbial open reading frames (ORF) were predicted from each set of reads and used to define a random metagenomic effect in a mixed model framework. Variance components were estimated for each model using all available data, i.e., no masking of phenotypes. Cross-validation schemes were utilized to determine prediction accuracy. Models which incorporated host genomic and metagenomic information explained more variation and generally had greater prediction accuracies than models with either effect alone. Models using the 2M or 5M set resulted in smaller microbiability estimates and lower prediction accuracy for both ADDMI and ADG compared to models using the 10M or 20M sets, though these differences were often not large when measures of uncertainty were considered. For ADDMI, there were only slight differences in microbiability and prediction accuracy between different downsampled sets in most scenarios. For ADG, the 20M set had roughly equivalent microbiability estimates as the other sets but also had a notably greater prediction accuracy, dependent on cross-validation scheme. Spearman correlations of metagenomic effect solutions, termed the estimated metagenomic value (EMV), between all sets for all models were always >0.90. However, the correlations between the EMV for models with the 5M, 10M, and 20M sets were always higher than those with the EMV from the 2M set. The 10M and 20M EMV always had correlations >0.98. Thus, dependent on trait and reference population composition, metagenomic predictions from data sequenced at a depth of 2-10 million reads per sample may yield results approximately equivalent to those from data sequenced at 20 million reads per sample in terms of variance explained and phenotypic prediction accuracy.}, } @article {pmid42531280, year = {2026}, author = {Arjomand Fard, N and Githaka, JM and Veniamin, S and Guan, LL and Aujla, H and Kaur, A and Lerner, EP and Zaidi, D and Armet, AM and Andrews, J and Han, X and Vallance, BA and Madsen, K and Perry, T and Wine, E}, title = {Host-microbe Interactions in the Appendix of Children with Inflammatory Bowel Diseases.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpgi.00080.2026}, pmid = {42531280}, issn = {1522-1547}, support = {//Women and Children's Health Research Institute (WCHRI)/ ; 166218//Canadian Institutes of Health Research (CIHR)/ ; MT2-168050//Canadian Institutes of Health Research (CIHR)/ ; }, abstract = {The human appendix is traditionally considered a vestigial organ; however, clinical observations link it to inflammatory bowel diseases (IBD), including Crohn disease and ulcerative colitis (UC), as suggested by peri-appendicular inflammation and reported protective effect of appendectomy in UC. Despite these associations, its functional contribution remains poorly defined. Here, we performed a multi-omics analysis of appendix tissue from pediatric IBD patients and non-IBD surgical controls (n = 15) to characterize microbial composition and host molecular landscape. Metagenomic sequencing revealed Proteobacteria enrichment and reduced microbial diversity in IBD appendices. Correlations between host transcriptomes and mucus-associated microbial pathways indicated associations consistent with host-microbe interactions linked to immune activation. Fluorescence in situ hybridization confirmed bacterial localization, and functional assays of appendix-derived Klebsiella variicola isolates demonstrated invasive capacity in vitro. Our findings suggest that the appendix represents a distinct microbial niche in pediatric IBD and may contribute to host-microbe perturbations associated with disease.}, } @article {pmid42531353, year = {2026}, author = {Riddell V, J and Shatadru, RN and Smith, GJ and McGivern, BB and Ellenbogen, JB and Jurgensen, SK and Fofana, A and Tfaily, MM and Wrighton, KC and Sullivan, MB}, title = {Viruses help shape microbiome response to polyphenol rewiring of methane-suppressed peat microcosms.}, journal = {PLoS biology}, volume = {24}, number = {7}, pages = {e3003925}, doi = {10.1371/journal.pbio.3003925}, pmid = {42531353}, issn = {1545-7885}, abstract = {Human activities are accelerating permafrost thaw and subsequent methane emissions from increased microbial activity, prompting microbiome engineering efforts as an emissions mitigation strategy. We recently demonstrated that catechin amendment could drastically reduce methane emissions (>80%) in peat microcosms by enriching catechin-degrading prokaryotes that outcompeted methanogens for hydrogen. However, viral contributions to such microbiome-level responses remain unexplored and we hypothesized that viral dynamics could help shape the microbiome response as nutrient amendments may alter cellular physiology in ways that could induce lytic viral activity. Here, we performed virus eco-genomics analyses of the previously-studied time-resolved multi-omics data collected from catechin-amended peat microcosms. We conservatively identified 900 putatively lytic viral operational taxonomic units (vOTUs), with 41% predicted to infect active host genomes including the most transcriptionally active vOTUs predicted to infect key catechin-degrading genera (Clostridium and undescribed Bacillota JAGFXR01). Notably, a single JAGFXR01-targeting vOTU dominating the viral response (>40% of community viral transcription; 20-156-fold more abundant than its host), which we interpreted as induction resulting in intense lytic activity that could release catechin degradation intermediates to other community members. Consistent with this, gene expression analysis revealed elevated catechin-intermediate degradation and hydrogenase signals in 34 additional polyphenol-degrading metagenome-assembled genomes. These findings support a model consistent with a viral shunt-like process that extends our previous prokaryote-centric model: viral lysis of fast-growing catechin degraders redistributes phenolic intermediates to diverse phenol-degrading taxa that sustain methane suppression via hydrogen consumption. Beyond carbon cycling importance in this system, elucidating unintended virus-mediated responses to nutrient and prebiotic interventions will enable more predictable and effective microbiome engineering strategies across soil, ocean, and human ecosystems.}, } @article {pmid42531517, year = {2026}, author = {Cheng, C and Wang, L and Li, R and Lai, W and Sun, C and Cui, J and Zhu, B and Zhang, J}, title = {Association Characteristics and Potential Mechanisms of Aging, Gut Microbiota, and Hearing Loss.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.70156}, pmid = {42531517}, issn = {1749-4877}, support = {32370536//National Natural Science Foundation of China/ ; QNTS202304//CIB Youth Exploration Project/ ; //Tianchi Talents Fund of Xinjiang/ ; }, abstract = {Age-related hearing loss (ARHL) is the leading sensory disability among the global elderly, yet its pathogenesis remains unclear. The "gut-ear axis" hypothesis offers a novel perspective. Using young, middle-aged, and aging C57BL/6 mice, we systematically investigated the interplay between aging, gut microbiota, and hearing loss through auditory function tests, cochlear histology, microbiome, and metabolome profiling. Results showed that aging induced a gradient hearing decline starting at high frequencies, progressing to severe pan-frequency loss in old age. Histology confirmed the degeneration of inner hair cells and synaptic connections, alongside hair cell loss in the basal cochlea. While gut microbiota α-diversity remained stable, β-diversity shifted significantly, marked by increased Bacteroidota and decreased Bacillota. Furthermore, 22 genera, 67 species, and 207 functional pathways were identified as being commonly associated with both aging and hearing loss. Metabolomic profiling further screened out 285 metabolites significantly associated with aging, 16 of which were also correlated with hearing loss. KEGG enrichment analysis suggested that chronic inflammation mediated by arachidonic acid metabolism, energy metabolic dysfunction regulated by the PPAR signaling pathway, and actin cytoskeleton homeostasis imbalance may represent a potential axis linking systemic metabolic dysregulation to cochlear‑specific damage. Moreover, these metabolites exhibited significant correlations with gut microbiota abundance. In conclusion, aging is associated with ARHL progression alongside gut microbiota remodeling and metabolic dysregulation. These findings supported a potential relationship between gut microbial-metabolic alterations and ARHL, which suggested that the gut microbiota may represent a candidate target for future mechanistic investigation.}, } @article {pmid42531759, year = {2026}, author = {Pacholak, A and Musielok, Ł and Smułek, W}, title = {Effect of pyrethrins and permethrin insecticides on soil bacterial biodiversity.}, journal = {Ecotoxicology and environmental safety}, volume = {322}, number = {}, pages = {120564}, doi = {10.1016/j.ecoenv.2026.120564}, pmid = {42531759}, issn = {1090-2414}, abstract = {Soil microorganisms play a key role in maintaining ecosystem stability, yet they are frequently exposed to insecticides used in agriculture and pest control. This study investigated the effects of natural pyrethrins and synthetic permethrin on soil bacterial metabolic activity, functional diversity, community structure, and biodegradation potential. Soil samples collected from a long-term protected, non-agricultural forest area were incubated with commercial formulations containing pyrethrins (Afizol AE) or permethrin (Afanisep® 25 WP) for 7 and 15 days. Microbial metabolic activity was assessed using the Alamar Blue assay and Biolog EcoPlate™ system, while bacterial community composition was analyzed through 16S rRNA gene sequencing. Additionally, the degradation of insecticide active compounds was quantified using UHPLC-QTOF-MS. Permethrin-treated soils exhibited the highest and most sustained microbial metabolic activity, whereas pyrethrin-treated soils showed an initial stimulation followed by a decline over time. Functional diversity indices revealed that permethrin initially promoted metabolic diversity, but prolonged exposure led to a reduction in substrate utilization breadth. Metagenomic analysis demonstrated pronounced shifts in bacterial community composition under both treatments, with strong selection toward Firmicutes-dominated assemblages. Biodegradation assays confirmed substantial degradation of both pyrethrins and permethrin, although incomplete removal and partial accumulation of selected compounds were observed. The obtained results highlight that both natural and synthetic pyrethroids significantly alter soil bacterial communities, emphasizing the need to consider their short-term ecological effects on soil health.}, } @article {pmid42520923, year = {2026}, author = {Khan, AR}, title = {Letter to the Editor regarding Neluvhola et al, Histopathological assessment of granulomatous hepatitis: a retrospective study.}, journal = {Clinics and research in hepatology and gastroenterology}, volume = {}, number = {}, pages = {102894}, doi = {10.1016/j.clinre.2026.102894}, pmid = {42520923}, issn = {2210-741X}, } @article {pmid42521068, year = {2026}, author = {Pavon, JAR and Neves, NADS and Martins, AP and Pinho, JB and de Souza, VJ and Nunes, MRT and Slhessarenko, RD}, title = {RNA viruses in sylvatic mosquitoes and phlebotomine sand flies from Alto Pantanal, Mato Grosso, Brazil 2019.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {108258}, doi = {10.1016/j.actatropica.2026.108258}, pmid = {42521068}, issn = {1873-6254}, abstract = {The Pantanal biome harbors exceptional biodiversity but has been increasingly impacted by climate change and human activities. This region is considered a high-risk zone for zoonotic spillover, making viral studies in sylvatic mosquitoes and other invertebrates indispensable, as these vectors are involved in the transmission of pathogens of public health concern. This study aimed to describe viral genomes identified in Aedes spp., Ochlerotatus sp., Mansonia sp., Phlebotomus sp., Psorophora spp., and Anopheles spp. dipterans collected in March and June 2019, in Pirizal and Porto São Luiz, Alto Pantanal, Mato Grosso State, Brazil. Diptera specimens were pooled by genera, and nucleic acids were extracted, followed by library preparation and sequencing on the Illumina NextSeq 500/550 platform. A total of 39 putative viral sequences were recovered, including 23 potentially novel viruses. Coding-complete genomes were identified from Virgaviridae (n=1), Rhabdoviridae (n=1), and Metaviridae (n=1), as well as seven coding-complete segments from Partitiviridae (n=4) and Solemoviridae (n=3). Additionally, 29 partial genomes were recovered from Partitiviridae (n=7), Metaviridae (n=6), Chuviridae (n=2), Sedoreoviridae (n=1), Nodaviridae (n=3), Tombusviridae (n=2), Phasmaviridae (n=2), Flaviviridae (n=3), Virgaviridae (n=1), and Solemoviridae (n=2). Viral characterization in Diptera specimens has gained increasing importance with the advancement of metagenomic approaches, which contribute to global One Health initiatives by providing data that may support the prediction and prevention of future viral spillover events.}, } @article {pmid42521693, year = {2026}, author = {Rodríguez-Ramos, JA and Zimmerman, AE and Wu, R and Bell, SL and Alfaro, TD and Reichart, NJ and Hofmockel, KS and Nelson, WC}, title = {Preparation method shapes the recovery and ecological interpretation of DNA and RNA soil viral communities.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42521693}, issn = {2041-1723}, support = {FWP 70880//DOE | SC | Biological and Environmental Research (BER)/ ; FWP 70880//DOE | SC | Biological and Environmental Research (BER)/ ; }, mesh = {*Soil Microbiology ; Metagenomics/methods ; *RNA, Viral/isolation & purification/genetics ; *RNA Viruses/genetics/isolation & purification ; *DNA, Viral/isolation & purification/genetics ; Soil/chemistry ; *DNA Viruses/genetics/isolation & purification ; Metagenome ; *Virome/genetics ; Genome, Viral ; Bacteria/genetics ; }, abstract = {Deciphering viral ecology in soils is challenging due to soil's high physicochemical and microbial community complexity. To enhance detection of DNA and RNA viruses, we applied different preparation methods to soils collected from a grassland field experiment. Analyses included metagenomics and metatranscriptomics of size-fractionated extracellular viruses, total soil metagenomics and metatranscriptomics, total soil metatranscriptomics with polyadenylation enrichment, and metagenomics of bacteria/archaea as well as eukaryote-enriched samples. DNA viromes outperformed total soil metagenomes in viral detection and quality. Contrastingly, RNA viromes and total soil metatranscriptomes performed similarly for viral recovery, though RNA viromes yielded higher-quality genomes. Together, our results highlight how different preparation methods can influence the recovery and quality of DNA and RNA vOTUs. Further, we demonstrate the power of different methods in identifying distinct viral communities with unique host predictions, which in turn can have significant implications for ecological investigations related to interkingdom interactions.}, } @article {pmid42521984, year = {2026}, author = {Bogovič, P and Slunečko, J and Kodre, M and Kogoj, R and Jakob, MB and Korva, M and Ružić-Sabljić, E and Strle, F}, title = {Human Cases of Borrelia miyamotoi Disease, Slovenia, 2025.}, journal = {Emerging infectious diseases}, volume = {32}, number = {8}, pages = {1319-1322}, doi = {10.3201/eid3208.260326}, pmid = {42521984}, issn = {1080-6059}, mesh = {Humans ; *Borrelia/genetics/classification/isolation & purification ; Slovenia/epidemiology ; *Borrelia Infections/epidemiology/diagnosis/microbiology ; Female ; Male ; Animals ; Adult ; Middle Aged ; }, abstract = {We identified human Borrelia miyamotoi infections in Slovenia in 2 of 337 adults with undifferentiated fever tested positive by metagenomic sequencing and PCR. Both patients reported recent local tick bites. The illness was mild and self-limited. Our findings underscore the need to consider this pathogen in evaluating fever after tick bite.}, } @article {pmid42523101, year = {2026}, author = {Zhou, X and Wei, G and Song, T and Yu, Y and Chen, J and Long, J and Tao, X and Zhang, J and Jiang, L}, title = {Metagenomic next-generation sequencing for tuberculosis diagnosis: enhanced performance and cost-effectiveness.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0097026}, doi = {10.1128/spectrum.00970-26}, pmid = {42523101}, issn = {2165-0497}, abstract = {UNLABELLED: Metagenomic next-generation sequencing (mNGS) is a promising tool for diagnosing challenging infections like tuberculosis (TB). However, previous studies largely focused on case-specific application of mNGS in TB diagnosis. Thus, we conducted a retrospective observational study to first systematically evaluate the diagnostic performance and cost-effectiveness of mNGS for TB diagnosis. We retrieved a total of 16,776 results of the seven TB diagnostic assays, including mNGS, tuberculosis IgG antibody, TB interferon-γ release assay (TB-IGRA), TB-DNA, Xpert MTB/RIF (Xpert), culture, and acid-fast bacilli staining (AFS) from 3,757 participants with suspected TB infection at Sichuan Provincial People's Hospital from September 2021 to July 2024. Diagnostic metrics were compared against a composite reference standard. Microbial composition and a cost-utility analysis were performed. Among seven TB assays studied, the World Health Organization (WHO)-recommended assays AFS, culture, and Xpert, as well as TB-IGRA, were requested most frequently for TB diagnosis, whereas mNGS ranked last. mNGS demonstrated the highest specificity (100%), accuracy (72.3%), and area under the curve (AUC) (0.795). Its sensitivity in bronchoalveolar lavage fluid and tissue was 71.0% and 72.7%, respectively. Sequential use of mNGS after initial WHO-recommended tests (Xpert/Culture/AFS) significantly improved diagnostic performance (sensitivity, 70.4%; AUC, 0.823). Microbial analysis associated Candida albicans with TB. Cost-utility analysis showed sequential mNGS became cost-effective at higher willingness-to-pay thresholds (>200,000 RMB per correct diagnosis). mNGS offers superior specificity for TB diagnosis. A sequential strategy applying mNGS to conventional-test-negative cases provides enhanced diagnostic performance and is cost-effective at higher healthcare investment values, supporting its utility for diagnostically challenging TB.

IMPORTANCE: This study systematically assesses the diagnostic performance and cost utility of metagenomic next-generation sequencing (mNGS) for tuberculosis (TB) in a large real-world cohort of 3,757 suspected patients, comparing it against six conventional assays (tuberculosis IgG antibody, TB interferon-γ release assay, TB-DNA, Xpert, culture, and acid-fast bacilli staining). mNGS demonstrated the highest specificity (100%), accuracy (72.3%), and area under the curve (AUC) (0.795), with sensitivities of 71.0% in bronchoalveolar lavage fluid and 72.7% in tissue. Notably, sequential use of mNGS after the World Health Organization-recommended tests significantly improved sensitivity to 70.4% and AUC to 0.823. Candida albicans showed significant differences among the three groups. The sequential mNGS strategy was cost-effective compared with no mNGS, and its cost-effectiveness increased with a rising willingness-to-pay threshold. Overall, these results highlight mNGS as a valuable supplementary tool for challenging TB cases, especially when conventional tests are inconclusive, and provide strong evidence for integrating it into diagnostic algorithms to optimize clinical decision-making and resource allocation.}, } @article {pmid42523106, year = {2026}, author = {Xu, S and Yang, L and Gao, J and Shi, Y and Tang, X and Cai, H and Yang, L and Han, Y and Lin, L and Meng, R and Sun, J and Guan, W-j and Tang, T and Shu, W and Cao, C and Zheng, X-y and Wang, Z and Yi, X}, title = {The associations of human genetic variations with airway microbiome, environmental exposures, and respiratory health.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0044226}, doi = {10.1128/msystems.00442-26}, pmid = {42523106}, issn = {2379-5077}, abstract = {UNLABELLED: The intricate interactions between environmental exposures, the respiratory microbiome, and host genetic variations remain inadequately understood in the context of respiratory health. This study utilized sputum metagenomic data from 1,651 individuals in our previous cohort to elucidate these associations. Mendelian randomization indicated that air pollutants (e.g., SO2, CO, and PM2.5) were associated with lung function, which is potentially mediated by microbes, such as Actinomyces, Haemophilus influenzae, and Veillonella spp. Several genetic loci associated with respiratory microbiome variation were found to be linked to genotype-dependent associations between environmental exposures and lung function. For bacteria, the MEOX1 locus (rs1973191819) was associated with lower Filifactor alocis abundance under air pollutant exposure. The FAM110D (1:26157175) and USP36 (rs1343834070) loci showed associations with higher levels of certain pathogenic taxa (e.g., Ralstonia pickettii, Neisseria) and lower levels of the commensal Oribacterium, increasing chronic obstructive pulmonary disease (COPD) risk. For fungi, DNAJC18 and CCDC57 loci exhibited associations with Candida and Penicillium abundance, respectively. These genotype-dependent associations between the microbiome and environmental exposures provide insights into airway dysbiosis and susceptibility to respiratory diseases.

IMPORTANCE: This study reveals why individuals exposed to identical air pollution exhibit varying degrees of respiratory severity, pointing to a critical missing link: our genetics. While pollution is a known disease trigger, our findings demonstrate that host genetic variation actively regulates and shapes the respiratory microbiome under environmental stress. By mapping specific genetic loci to pollutant-driven bacterial shifts, this work elucidates how host genetics filters environmental risks to govern microbial homeostasis. These results underscore the necessity of incorporating host-microbiome genetic regulation into environmental health research. Ultimately, this study shifts the paradigm toward personalized medicine, enabling the early identification of at-risk individuals and the development of targeted, microbiome-informed interventions.}, } @article {pmid42523201, year = {2026}, author = {Kananen, K and Tran, N and Bradley, PH}, title = {Phylogenize2: robust phylogenetic methods link genes to phenotypes across host-associated and environmental microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.07.15.738685}, pmid = {42523201}, issn = {2692-8205}, abstract = {UNLABELLED: In microbiome studies, associations between microbial functions and the environment are often confounded by phylogeny. While some methods explicitly account for this confounder, they require information about genome content, limiting their use in biomes where few genomes have been available. To make these methods more universally accessible, we have developed Phylogenize2, a redesigned phylogeny-aware tool for linking microbial gene families to abundance phenotypes. Phylogenize2 integrates large metagenome-assembled genome collections, including both biome-specific collections from MGnify and a broadly sampled general purpose database, GlobDB, to substantially expand species coverage, allowing its application in environments like the mouse gut and ocean. In addition, by default, Phylogenize2 uses a new robust phylogenetic testing framework that has been optimized for microbial abundance data, while also allowing the use of other comparative methods such as POMS. In an experimental mouse study, Phylogenize2 identifies that Muribaculaceae with higher abundance on a high-fat diet are enriched for proteins in the thioredoxin family, with likely roles in oxidative stress. When we apply Phylogenize2 to a polar ocean study, we find that a molybdenum-dependent PaoABC/YagTSR-like aldehyde oxidoreductase system differentiates mesopelagic from surface-dwelling Flavobacteriaceae , suggesting that aldehyde detoxification may be important for organisms that degrade marine snow. Together, these results show that Phylogenize2 expands phylogeny-aware microbiome analysis beyond the human gut and can provide insight into the genetic basis of microbiome-encoded traits in diverse environments.

IMPORTANCE: Microbiome studies often set out to identify which microbes are more or less abundant across environments, but these patterns can be difficult to interpret. Phylogenize2 is an open-source software package that allows researchers to ask whether individual microbial gene families are associated with the environment across independent branches of the microbial tree of life. By incorporating large collections of genomes from uncultivated microbes, as well as modern statistical methods designed for microbial abundance data, Phylogenize2 makes this approach practical for microbiomes beyond the human gut, including in model organisms like lab mice and free-living environments like the ocean. We also provide a pipeline that allows the use of new genome collections. In two case studies, we demonstrate that Phylogenize2 effectively prioritizes specific genes and pathways from metagenomic data, thereby leading researchers from changes in microbial abundance to more biologically interpretable explanations.}, } @article {pmid42523339, year = {2026}, author = {Tran, N and Kananen, K and Bradley, PH}, title = {A robust, sensitive phylogenetic method enables gene-level metagenomic analyses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.07.15.738679}, pmid = {42523339}, issn = {2692-8205}, abstract = {UNLABELLED: A key goal in the microbiome field is to move from taxonomic associations towards mechanistic hypotheses about microbial gene function. However, most methods for linking microbiome changes to specific genes are biased towards finding marker genes, with weak evidence for functional relevance. Phylogenetic regression can address this issue and has been previously applied to changes in microbial prevalence, but many environments (such as the gut in health vs. disease) are characterized more by changes in abundance, which presents unique statistical challenges. We show that when applied to real differential abundances from metagenomes, phylogenetic regression has an anti-conservative bias, indicating inflated false positives. We develop an alternative non-parametric method called "robust permutration," designed specifically for differential abundance data, and evaluate its performance against phylogenetic regression as well as several other phylogenetic comparative methods in realistic simulations of metagenomic data. These results show that robust permutration is the most powerful method that appropriately controls the false positive rate. We further apply robust permutration to a human case-control study of liver cirrhosis, revealing that Lachnospiraceae abundance in disease is linked to a previously uncharacterized iron- sulfur transcription factor encoded near homologs of the butyryl-CoA oxygen oxidoreductase system, a recently discovered system for oxygen detoxification. This illustrates how robust, sensitive phylogenetic methods can enable the generation of new molecular hypotheses directly from metagenomic case-control data.

IMPORTANCE: Previously, we showed that phylogenetic regression can effectively detect genes associated with microbial presence or absence while correcting for evolutionary relationships. Unexpectedly, however, we here observe that this method can lead to high false positive rates when applied to microbial abundance data. In realistic simulations, other methods we test either have similar problems with false positives, or display very low power. We outline a new statistical test that better accounts for measurement uncertainty, outliers, and model violations, achieving more balanced sensitivity and accuracy than competing methods. Applying this test to a cirrhosis study reveals an uncharacterized transcription factor enriched in disease, with an apparent role in oxidative stress based on its sequence and gene neighborhood. This suggests a functional explanation for the observed taxonomic shifts, and demonstrates how improved phylogenetic methods could help inform future microbiome-targeted treatments.}, } @article {pmid42523359, year = {2026}, author = {Uwamanzu-Nna, A and Olagoke, O and Shi, CX and Mengistie, HD and Asfaha, K and Read, TD and Dean, D}, title = {Ocular community state types reveal distinct microbial compositions among microbiomes with implications for trachoma control.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42523359}, issn = {2692-8205}, abstract = {Trachoma, a chronic ocular disease caused by Chlamydia trachomatis (Ct), is the leading infectious cause of blindness worldwide. Despite WHO's SAFE (Surgery, Antibiotics, Facial cleanliness, Environmental improvement) strategy, ~100M are at risk of blindness. Using metagenomic shotgun sequencing, we characterized the ocular microbiome of 680 villagers in Amhara Ethiopia, identifying 10 Community State Types (CSTs) associated with different population characteristics. Children with the highest prevalence of inflammatory trachoma and Ct were in CST10, dominated by Haemophilus influenzae and four other Haemophilus spp. Adults with the highest prevalence of scarring trachoma were in CST3 and CST6, dominated by Corynebacterium macginleyi. CST5, dominated by Mesomycoplasma hyorhinis and Staphylococcus aureus, had the lowest prevalence of Ct and trachoma, and was the only CST without zoonotic Chlamydia spp. Both M. hyorhinis, a zoonotic porcine bacterium, and S. aureus are capable of forming biofilms, which may competitively prevent/down-regulate chlamydial infections. Other CSTs were dominated by environmental species like Vibrio. This is the first microbiome study to develop CSTs for trachoma. Pathogenic and potentially protective microbes showed distinct associations with demographic, clinical, and chlamydial characteristics, which will guide the design of microbial therapeutics as alternatives to antibiotics and strategies for WHO's global elimination of blinding trachoma.}, } @article {pmid42523540, year = {2026}, author = {Danner, R and Cho, J and Detwiler, Z and Williams, J and Han, JA and Yang, C and Diebold, X and Maeder, K and Van Vranken, JG and Walker, AS and Lesser, C and Chaudhari, SN}, title = {Gut microbiome derived folate metabolite suppresses colorectal cancer progression.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.07.14.738490}, pmid = {42523540}, issn = {2692-8205}, abstract = {The gut microbiota influences colorectal cancer (CRC) progression, primarily through the secretion of small molecule metabolites. While numerous microbial products are known to drive CRC, endogenous protective mechanisms remain largely uncharacterized. Utilizing a folate metabolomics platform, we demonstrate that the healthy gut microbiota produces folinic acid (FA), a known chemotherapeutic adjuvant also known as leucovorin. This microbially derived folinic acid is progressively depleted in mouse models of colitis-associated CRC and in human clinical metagenomic cohorts with advancing disease severity. Mechanistically, folinic acid acts as a signaling molecule that directly binds and inhibits the intracellular protease calpain-2. This interaction stabilizes epithelial E-cadherin protein expression and suppresses CRC epithelial-to-mesenchymal transition driving metastasis. Genetically manipulating gut microbial production of FA is sufficient to modulate CRC in vivo , even in the presence of chronic inflammation. This study reframes folinic acid from a chemotherapeutic enhancer to an endogenous microbial metabolite that actively suppresses CRC progression.}, } @article {pmid42523736, year = {2026}, author = {Togaev, U and Mathur, V and Rakhmonkulova, A and Agarwal, S and Mathur, A and Turageldiyev, S and Ruzmetov, R and Turaev, AS and Tillyabaev, Z and Matchanov, A and Sillam-Dussès, D}, title = {Comparative metagenomic analysis of gut microbiota in Anacanthotermes turkestanicus and A. ahngerianus reveals diet- and habitat-driven functional divergence.}, journal = {Frontiers in insect science}, volume = {6}, number = {}, pages = {1807673}, pmid = {42523736}, issn = {2673-8600}, abstract = {The gut microbiome of termites plays a crucial role in lignocellulose degradation and nutrient recycling. This study presents the first metagenomic characterization of the gut microbiota in two lower termite species, Anacanthotermes ahngerianus and Anacanthotermes turkestanicus, collected from distinct ecological habitats. In Uzbekistan, the first lives in building a mound in nature in the West part while the second mainly lives in contact with human constructions in the East part without building a proper mound. Both species showed similar bacterial dominance (~53%) in their guts but A. ahngerianus exhibited higher overall microbial diversity (Shannon index: 4.046 vs. 3.363; Simpson's index: 0.927 vs. 0.776). Moreover, both termite species showed differences in microbial profiles, including bacterial taxa and eukaryotic groups relevant to lower-termite gut symbiosis. Protist-associated eukaryotic reads were retained because flagellated protists are essential symbionts of lower termites, whereas unexpected non-protist eukaryotic assignments were interpreted cautiously and were not used as evidence of functional gut symbionts or host adaptation. Functional profiling revealed enrichment of pathways related to carbohydrate metabolism, amino acid transport, and energy production in both species. However, A. turkestanicus exhibited stronger bacterial dominance associated with lignocellulose degradation and nitrogen cycling, while A. ahngerianus maintained a more balanced representation of bacteria, fungi, and viruses. These findings suggest that species identity and ecological habits may be associated with differences in gut microbiome structure and predicted functional potential.}, } @article {pmid42523741, year = {2026}, author = {Hong, X and Cai, Z and Yu, Z and Fu, H and Cai, J and Wu, Z and Wu, X and Kuang, Z}, title = {Omadacycline for peritoneal dialysis-associated peritonitis caused by Coxiella burnetii: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1829483}, pmid = {42523741}, issn = {2296-858X}, abstract = {INTRODUCTION: Peritoneal dialysis-associated peritonitis (PDAP) is a serious complication of peritoneal dialysis (PD), contributing significantly to hospitalization rates and mortality. In recent years, infections caused by uncommon pathogens such as Coxiella burnetii have increasingly been identified, posing significant challenges to managing PDAP.

CASE PRESENTATION: We report a 62-year-old male hospitalized for recurrent PDAP unresponsive to empirical antibiotics (meropenem, later meropenem/vancomycin). Metagenomic next-generation sequencing (mNGS) of peritoneal fluid identified C. burnetii. Intravenous omadacycline was initiated as part of a multi-agent regimen (100 mg daily after 200 mg loading dose). Within 48 h, hemodynamic stability was achieved, and inflammatory markers (procalcitonin, C-reactive protein, effluent white blood cell count) normalized progressively over the subsequent week. The patient recovered fully and was discharged, and remained relapse-free during 3 months of follow-up.

CONCLUSION: This case highlights the critical importance of identifying pathogens in patients with PDAP. Despite significant confounders (concurrent broad-spectrum antibiotics, ICU support, and polymicrobial infection) that limit definitive attribution, the use of omadacycline was associated with clinical recovery and suggests a potential role as an alternative therapeutic option for Coxiella burnetii infection. Further studies are warranted to validate its efficacy.}, } @article {pmid42523840, year = {2026}, author = {Bankar, VR and Chapadgaonkar, SS and Bhattacharyya, K and K, P}, title = {From diversity to function: microbiome-mediated plant growth promotion, secondary metabolism, and antimicrobial resistance in Rauwolfia serpentina.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1796770}, pmid = {42523840}, issn = {2673-7647}, abstract = {INTRODUCTION: This study presents the first metagenomic analysis of the root and rhizosphere microbiomes of Rauvolfia serpentina, an endangered medicinal plant. Metagenomic sequencing and bioinformatics analysis were used to characterize the diverse microbial communities and their functional attributes to assess the ecological and biotechnological potential of this plant-associated microbiome.

METHODS: High-throughput Illumina sequencing and bioinformatics analysis were used to profile the microbial communities. Functional annotation was performed to identify plant growth-promoting traits using PLABASE, to predict pathways for the biosynthesis of novel bioactive compounds using antiSMASH, and to identify antimicrobial resistance genes using ResFinder.

RESULTS: The analysis revealed highly diverse microbial communities in both habitats, predominantly composed of Pseudomonadota, Bacillota, and Actinomycetota, with minor but consistent contributions from archaea and eukaryotes. Functional annotation identified extensive PGPTs, including genes associated with phosphate solubilization, nitrogen fixation, siderophore-mediated iron acquisition, and stress tolerance. The rhizosphere microbiome exhibited greater metabolic versatility and stress tolerance, characterized by a higher copy number of heavy metal efflux pumps, whereas the root microbiome was enriched in genes involved in plant hormone regulation and plant-microbe interactions. A diverse array of non-ribosomal peptide synthase, polyketide synthase, and lasso peptide pathways were predicted, underscoring the potential to produce novel bioactive compounds. These distinct functional profiles demonstrates that the protected root endomicrobiome specializes in plant signalling and nutrient assimilation, while the rhizosphere microbiome, facing higher competition, specializes in nutrient acquisition and stress resilience.

CONCLUSION: These findings provide novel insights into the ecological specialization and biotechnological potential of the R. serpentina microbiome, offering significant implications for the sustainable utilization and conservation of this endangered medicinal plant.}, } @article {pmid42523956, year = {2026}, author = {Zhou, M and Zhao, Y and Sun, X and Mou, W and Liu, Y and Shi, C and Li, Z and Cheng, Y and Tian, X and Fan, J and Wang, J}, title = {Chronic granulomatous disease secondary to a rare compound heterozygote mutation in an adolescent cured by hematopoietic stem cell transplantation: a case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1780075}, pmid = {42523956}, issn = {2296-2360}, abstract = {BACKGROUND: Chronic granulomatous disease (CGD) is a rare inherited primary immunodeficiency characterized by recurrent infections and aberrant inflammation due to defects in the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase complex.

CASE PRESENTATION: We report a case of recurrent pneumonia and significantly elevated IgE levels in an adolescent. Metagenomic next-generation (mNGS) sequencing contributed to the identification of Burkholderia multivorans in bronchoalveolar lavage fluid and the initiation of appropriate treatment. Whole exome sequencing (WES) revealed two point mutations in the CYBA gene. The patient was cured by hematopoietic stem cell transplantation.

CONCLUSIONS: Application of mNGS contributed to the early identification of B. multivorans and the initiation of appropriate treatment. Timely screening by WES contributed to the diagnosis of the patient.}, } @article {pmid42524013, year = {2026}, author = {Li, J and Lian, S and Liu, Y and Yang, X and Liu, D and Chen, J and Xiong, H}, title = {From serum inflammatory markers to fluid, tissue, and molecular assays: current advances in the laboratory diagnosis of bone and joint infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1865643}, pmid = {42524013}, issn = {2235-2988}, mesh = {Humans ; *Biomarkers/blood/analysis ; Prosthesis-Related Infections/diagnosis ; *Osteomyelitis/diagnosis ; *Molecular Diagnostic Techniques/methods ; *Arthritis, Infectious/diagnosis ; Synovial Fluid/chemistry ; *Clinical Laboratory Techniques/methods ; }, abstract = {Bone and joint infections (BJIs), including periprosthetic joint infection (PJI), fracture-related infection (FRI), and osteomyelitis, present persistent diagnostic challenges driven by biofilm formation and a high incidence of culture-negative cases. Traditional diagnostic modalities relying on peripheral serum markers and conventional cultures are often limited by insufficient specificity or prolonged turnaround times. This narrative review critically evaluates recent advances in laboratory diagnosis for bone and joint infections, with particular attention to disease-specific applicability across periprosthetic joint infection, fracture-related infection, native vertebral osteomyelitis, diabetic foot osteomyelitis, and other osteomyelitis-related conditions. Current evidence indicates that while traditional serum inflammatory markers are valuable for initial screening, their susceptibility to aseptic inflammatory confounders precludes standalone diagnostic confirmation. In contrast, localized sampling demonstrates significant superiority: novel synovial fluid biomarkers, notably calprotectin and alpha-defensin, accurately reflect the infection microenvironment and offer exceptional diagnostic specificity. At the tissue level, the integration of multiple deep-tissue sampling with preprocessing techniques like sonication has substantially enhanced the recovery of occult biofilm-encased pathogens. Furthermore, targeted and untargeted molecular assays, including multiplex PCR panels, broad-range bacterial PCR, amplicon-based sequencing, and untargeted shotgun metagenomic sequencing, have expanded the diagnostic toolkit for culture-negative, low-virulence, and polymicrobial infections. The diagnostic framework for BJIs has decisively shifted from the pursuit of a solitary "silver bullet" marker toward multimodal, culture-independent assay panels and artificial intelligence-assisted risk stratification algorithms. Future clinical breakthroughs will depend heavily on the global standardization of disease definitions, robust external validation of predictive models, and the seamless integration of advanced laboratory techniques into multidisciplinary team (MDT) workflows.}, } @article {pmid42524415, year = {2026}, author = {Allaart, MT and Tyakht, AV and Ley, RE and Pabst, M and Stouten, GR and Angenent, LT}, title = {D- and L-lactate consumers are taxonomically, biochemically, and energetically different.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag180}, pmid = {42524415}, issn = {2730-6151}, abstract = {D- and L-lactate are routinely produced as intermediates in fermentative ecosystems. However, the microbial fate of these stereoisomers remains poorly understood. Given that D-lactate is an unavoidable byproduct of digestion and a neurotoxin, understanding its microbial turnover not only holds ecological pertinence but also the potential to uncover new links between gut microbiota metabolism and host health. Here, we used chemostat bioreactors (pH 7.0, 37°C, and a solids retention time of 4 days) to enrich for lactate-consuming communities. DL-lactate-consuming consortia were enriched, characterized, and used as inoculum for duplicate bioreactors fed exclusively with D- or L-lactate. After steady-state was reached, the fed lactate stereoisomers were switched to assess community resilience. Regardless of the fed stereoisomer, the fermentation product spectra were consistent and dominated by acetate, propionate, and CO2. However, microbial communities and biomass yields diverged sharply, with a high relative abundance of Anaerotignum in D-lactate enrichments and Acidipropionibacterium and Propionibacterium in L-lactate enrichments. Notably, the biomass yield for D-lactate feeding was less than half that for L-lactate feeding, suggesting that the two isomers are metabolized through distinct biochemical pathways despite similar product spectra. Metagenomic and metaproteomic analyses confirmed divergence in D- and L-lactate conversion at both the phylogenetic and pathway levels. Our findings reveal how the stereoisomer identity of microbes shapes their niche specialization, with implications for understanding the ecology and clinical impact of lactate metabolism.}, } @article {pmid42524456, year = {2026}, author = {Shao, L and Lv, G and Yuan, Y and Xu, C and Tai, H and Li, Y}, title = {Antimicrobial Management of Severe Chlamydia psittaci Pneumonia in Adults: A Narrative Review.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {625008}, pmid = {42524456}, issn = {1178-6973}, abstract = {Chlamydia psittaci is an obligate intracellular bacterium and an increasingly recognized cause of severe community-acquired pneumonia (CAP) in adults, with contemporary multicenter Chinese cohorts reporting severe-stratum in-hospital mortality clustering around 8-9% and higher figures in acute respiratory distress syndrome (ARDS)-enriched series. β-Lactam therapy lacks reliable activity against this pathogen, yet considerable practice variation persists in the selection, sequencing, and de-escalation of intracellularly active agents in the era of routine metagenomic and targeted next-generation sequencing (mNGS, tNGS). The aim of this review is to provide a phase- and severity-stratified, bedside antimicrobial framework for severe psittacosis in adults-clarifying when to select, continue, switch, or combine intracellularly active agents at the 48- to 72-hour ICU decision points. This narrative review, reported in accordance with the SANRA framework, synthesizes the post-2015 antimicrobial evidence for severe C. psittaci pneumonia in adults and integrates treatment phase (empirical versus targeted), severity context, organ support, and antimicrobial stewardship at the 48- to 72-hour ICU decision points. Drawing on six multicenter cohorts and the largest dedicated multicenter dataset to date (Fang 2026, n = 186; severe-stratum mortality 7/81 = 8.6%), phase-by-severity stratification reconciles apparently discordant tetracycline- and fluoroquinolone-favoring cohort signals. Doxycycline is the preferred targeted backbone in confirmed non-pregnant disease; reflex class-switching is not required when severely ill patients are already improving on an empirical fluoroquinolone at NGS confirmation. Omadacycline is a renal-sparing alternative when acute kidney injury, anticipated continuous renal replacement therapy, or unreliable doxycycline access alters the standard pathway; high-dose tigecycline is reserved for salvage; azithromycin retains its clearest targeted role in pregnancy. Apparent nonresponse at 72 hours should trigger structured reassessment for coinfection, secondary organizing pneumonia, pulmonary embolism, and inadequate antimicrobial exposure before any salvage escalation. Adjunctive corticosteroid use should follow contemporary severe-CAP guidance pending pathogen-specific data from the NCT07352865 adaptive trial. Recommendations are calibrated using GRADE-adapted certainty and strength, with explicit acknowledgment that the comparative evidence base remains overwhelmingly retrospective and geographically concentrated in Chinese tertiary hospitals.}, } @article {pmid42524580, year = {2026}, author = {Ji, BC and Aung, T and Smart, C and Khan, Y}, title = {A Complex Case of Behçet's Disease With Severe Genital Ulceration: Diagnostic Challenges.}, journal = {Cureus}, volume = {18}, number = {6}, pages = {e111658}, pmid = {42524580}, issn = {2168-8184}, abstract = {Behçet's syndrome (BS) is a chronic, multisystem variable vessel vasculitis defined by recurrent oral and genital ulcers, diverse mucocutaneous lesions, and potential involvement of the eyes, joints, vasculature, central nervous system, and gastrointestinal tract. Diagnosis remains a clinical challenge given the absence of pathognomonic laboratory or histological findings. We present a case of a 36-year-old Caucasian male patient with hypothyroidism who developed a severe, rapidly progressive first episode of BS characterized by hemorrhagic vesicular and bullous skin lesions, oral ulceration, and necrotic genital ulceration requiring surgical debridement. Extensive infectious evaluation, including plasma cell-free metagenomic next-generation sequencing (cf-mNGS), was entirely negative. Serologic workup was unremarkable; HLA-B51 was negative, and pathergy was equivocal. Skin punch biopsy demonstrated pan-dermal neutrophilic inflammation with acute vasculitis and focal epidermal necrosis - a critical histopathological feature distinguishing BS from Sweet syndrome, in which true vasculitis is characteristically absent. Under the International Criteria for Behçet's Disease (ICBD), the patient scored ≥4 points (oral ulcers: 2 points; genital ulcers: 2 points; skin lesions: 1 point). He responded to high-dose corticosteroids (prednisone 50 mg daily) and colchicine, achieving full remission within nine weeks with no recurrence. This case illustrates the diagnostic complexity of BS in the absence of classic genetic markers, emphasizes histopathology as the critical discriminator from neutrophilic dermatosis mimics, and underscores the importance of systematic multidisciplinary evaluation before initiating immunosuppressive therapy.}, } @article {pmid42524765, year = {2026}, author = {Littlejohn, C and Chang, YC and Teles, F and Korostoff, JM and Redding, LE}, title = {Evolution of the fecal and oral microbiota after prophylactic antibiotics administered for dental surgeries.}, journal = {Journal of the American Dental Association (1939)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.adaj.2026.04.020}, pmid = {42524765}, issn = {1943-4723}, abstract = {BACKGROUND: The human oral and gut microbiomes play critical roles in maintaining overall health. Although systemic antibiotics are frequently prescribed perioperatively in dental procedures, their impact on microbiota composition and diversity remains inadequately understood. The authors' objective was to characterize the evolution of the gut and oral microbiomes after a course of antibiotics administered for dental surgeries. The authors hypothesized that the microbiome would experience disruption but eventually recover to baseline levels and that patient-related factors would influence the extent of disruption and recovery.

METHODS: Saliva and stool samples were collected from patients undergoing dental surgeries and receiving prophylactic antibiotics (n = 64) at baseline and then at 3, 10, 30, and 90 days after surgery. Microbial diversity and composition were assessed using 16S ribosomal RNA sequencing. Shotgun metagenomics sequencing was applied to a subset of samples to evaluate changes in antimicrobial resistance genes.

RESULTS: Significant (P < .01) declines in alpha diversity were observed in both oral and fecal microbiomes, most notably at days 3 and 10, with near recovery at day 90. The oral microbiome exhibited greater disruption than the gut microbiome, suggesting higher susceptibility to postoperative disturbance. Patient-level factors including sex, race, gastroesophageal reflux disease, and antibiotic type influenced baseline diversity, disruption, and recovery. Results of taxonomic analyses revealed that key health-associated genera were substantially altered postsurgery. Some antimicrobial resistance genes increased in relative abundance over time, consistent with potential long-term ecological consequences of antibiotic use.

CONCLUSIONS: The findings highlight the dynamic response of the human microbiome to antibiotic exposure and oral surgery and underscore the importance of antibiotic stewardship in practice. Further research on functional outcomes and host-microbiome interactions is warranted to optimize perioperative care in dentistry.

PRACTICAL IMPLICATIONS: Consideration of patient factors is essential to minimize unnecessary disruption of the microbiome and mitigate the risk of developing resistance.}, } @article {pmid42524914, year = {2026}, author = {Calixto, SL and Macedo, ACLP and Aguiar, JAK}, title = {GUT MICROBIOTA ALTERATIONS IN RODENT MODELS OF CHOLESTASIS INDUCED BY BILE DUCT LIGATION: A SYSTEMATIC REVIEW.}, journal = {Arquivos de gastroenterologia}, volume = {63}, number = {}, pages = {e25159}, doi = {10.1590/S0004-2803.24612025-159}, pmid = {42524914}, issn = {1678-4219}, mesh = {Animals ; *Cholestasis/microbiology ; *Gastrointestinal Microbiome/physiology ; Disease Models, Animal ; Ligation ; Bile Ducts/surgery ; Mice ; *Dysbiosis/microbiology ; Rats ; }, abstract = {BACKGROUND AND OBJECTIVE: Cholestatic liver diseases are a major public health issue, marked by impaired bile flow and significant disruptions in liver and systemic physiology. Growing evidence points to the gut microbiota as a key player in cholestasis pathogenesis through gut-liver axis interactions. This systematic review aimed to synthesize and evaluate current findings on intestinal microbiota changes in rodents (rats and mice) subjected to bile duct ligation (BDL)-induced cholestasis, focusing on microbial diversity, taxonomic shifts, and potential pathophysiological implications.

METHODS: A comprehensive literature search was conducted in PubMed, Scopus, and Embase for studies published from January 2020 to February 2025, following PRISMA guidelines. Eligible studies included original research using BDL in rodents without therapeutic intervention and reporting gut microbiota profiles. Data were qualitatively analyzed, emphasizing experimental conditions and microbiome outcomes.

RESULTS: Twenty-two studies met inclusion criteria. Most used 16S rRNA sequencing; two used shotgun metagenomics. BDL consistently induced gut dysbiosis, with reductions in alpha diversity (in most studies), altered beta diversity, and shifts in dominant phyla such as Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Verrucomicrobiota. At finer taxonomic levels, increases in Prevotella, Enterococcus, Escherichia coli, and Alistipes were common, while Lactobacillus and Ruminococcus often decreased. Elevated levels of Akkermansia muciniphila and Bifidobacterium pseudolongum may represent compensatory microbial responses.

CONCLUSION: Bile duct ligation (BDL)-induced cholestasis leads to complex changes in the microbiota that can worsen intestinal barrier integrity, increase bacterial translocation, and intensify liver inflammation. These findings reinforce the central role of the gut-liver axis and corroborate the potential of microbiota-targeted therapies in the management of cholestatic liver diseases. However, as most of the available evidence derives from experimental models, further well-designed clinical studies are needed to validate the safety, efficacy, and translational applicability of these strategies in human diseases.}, } @article {pmid42525193, year = {2026}, author = {Feng, WJ and Qin, C and Zhang, MS and Luo, ZY and Chen, BW and Wu, L and Zhang, FG and Deng, JJ and Luo, XC}, title = {Seeking soil microbial degraders and enzymatic genes for efficient biomass recycling.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {42525193}, issn = {1559-0291}, support = {2022-440000-4301030404-9580//The Dedicated Fund for Rural Revitalization in Guangdong Province/ ; 202206010137//Science and Technology Program of Guangzhou/ ; 2022A1515010568//Natural Science Foundation of Guangdong Province/ ; }, abstract = {Biodegradation is the most sustainable biomass recycling strategy, yet the absence of efficient microbial degraders remains a critical bottleneck. While soil microorganisms can decompose diverse biomass, their functional specificity for distinct agricultural by-products remains inadequately characterized. To address this, five agricultural by-products, including fish skin, soybean meal, shrimp shell, corn straw and chicken feather, were individually or combinatorially incubated in soil. Comparative analysis of 16 S rRNA amplicons and metagenomics from actively degrading microbial communities versus native soil identified key functional degraders. Declines in Chao1 and Shannon indices within biomass-amended soil groups indicated community simplification, driven by the dominance of novel utilizers over indigenous taxa. Genera enriched in native soil were replaced by divergent taxa across biomass types, revealing substrate-dependent community succession. LEfSe analysis identified biomass-specific utilizers at multiple taxonomic levels. Co-occurrence network analysis showed strong positive co-occurrence patterns between significantly enriched operational taxonomic units (OTUs), suggesting potential co-occurrence patterns and shared responses to biomass amendment. FAPROTAX revealed enhanced C/N/S metabolism during biomass utilization. Metagenomic screening identified markedly higher numbers of biomass-degradation genes encoding hydrolases (e.g., proteases, cellulases, chitinases), consistent with significantly elevated enzyme activities in amended soils compared to undetectable levels in controls. Among six candidate OTUs substantially enriched in chicken feather-amended soil, three species demonstrated efficient feather degradation, with some exhibiting multi-substrate capability. This study elucidates substrate-dependent biomass cycling in soil and provides candidate degraders, including Vicinamibacterales-related OTUs, unclassified Enterobacteriaceae, Sphingobacterium paludis, Sphingobacterium griseoflavum, and Lysinibacillus mangiferihumi, as well as enzymatic gene resources for engineered biomass recycling.}, } @article {pmid42525291, year = {2026}, author = {Gutiérrez-Ávila, JL and Gutiérrez-Rebolledo, GA and Avila-Bonilla, RG and Pardo, MES}, title = {Functional Equivalence and Conserved Sexual Dimorphism in the Gut Microbiome: A Cross-Species Meta-analysis.}, journal = {Journal of molecular evolution}, volume = {}, number = {}, pages = {}, pmid = {42525291}, issn = {1432-1432}, abstract = {The murine model is a standard system in translational microbiome research, yet its functional equivalence to the human microbiome remains debated. To evaluate its translational validity, we conducted a comparative whole-genome shotgun (WGS) metagenomic meta-analysis, integrating an initial retrieval of 520 datasets from 5 independent cohorts (BioProjects) across Homo sapiens (n = 202), Mus musculus (n = 75), and Drosophila melanogaster (n = 243) samples. Taxonomic and functional profiles were evaluated using strict bioinformatic quality control and batch-effect mitigation. Taxonomic profiling revealed pronounced divergence driven by host-specific ecological constraints and filtering. However, metabolic reconstruction demonstrated substantial functional equivalence, supporting the functional redundancy hypothesis for core mammalian metabolic circuits. We also noted a methodological vulnerability in our dataset: a low-depth murine sample clustered with invertebrate profiles, suggesting that technical noise or insufficient depth might artificially compress mammalian functional diversity. Comparative analysis identified sex-biased metabolic pathways conserved across mammalian hosts. Specifically, we observed a consistent enrichment of steroid metabolism in females and mineralocorticoid regulation in males. These findings indicate that functional conservation between humans and mice is modular rather than global. Consequently, the translational value of the murine model lies in domain-specific functional equivalence rather than taxonomic imitation. Moreover, the conservation of sex-specific metabolic signatures suggests that biological sex is a fundamental organising principle of microbiome function. This study highlights the necessity of mapping conserved metabolic modules and rigorously controlling inter-study variance to effectively deploy murine models in biomedical research.}, } @article {pmid42526286, year = {2026}, author = {Tito Tadeo, RY}, title = {Comment on: "Glucose metabolism's impact on Blastocystis presence in the human gut".}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {64}, number = {}, pages = {106736}, doi = {10.1016/j.clnu.2026.106736}, pmid = {42526286}, issn = {1532-1983}, } @article {pmid42526571, year = {2026}, author = {Ji, Q and Liu, S and Wang, C and Liang, G and Hou, G and Liu, X and Yu, Z and Wang, Z and Liu, R}, title = {Heavy metal (Cu(II)) Stress Alters Lysogeny-Lysis Balance and Drives Phage-mediated Transfer of Co-resistance in the Activated Sludge Process.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128858}, doi = {10.1016/j.envpol.2026.128858}, pmid = {42526571}, issn = {1873-6424}, abstract = {The co-selection of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) by heavy metals poses significant ecological risks. However, the contribution of bacteriophages (phages), particularly temperate phages, to this process via horizontal gene transfer (HGT) remains poorly understood. Here, we integrated metagenomics, metaviromics, and metatranscriptomics to investigate the impact of escalating Cu(II) concentrations (0.05-20.00 mg/L) on phage lifestyle dynamics and the dissemination of resistance genes in an activated sludge reactor. Our results revealed that phage-mediated HGT events of resistance genes were strongly threshold-dependent, predominantly occurring at high Cu(II) levels (10.00-20.00 mg/L). While the general temperate phage community shifted toward lysogeny to cope with stress, specific phages that mediated HGT of resistance genes exhibited higher lytic activity. Metatranscriptomic analysis further indicated upregulated transcriptional activity of HGT-associated MRGs under high Cu(II) stress, potentially conferring an adaptive advantage to hosts against metal toxicity. Notably, nearly all HGT events were associated with temperate phages, among which approximately 40% of the identified viral clusters (VCs) simultaneously harbored multiple resistance types, even in the absence of antibiotic selective pressure. Collectively, our findings highlight the important role of temperate phages in mediating resistance gene dissemination under Cu(II) stress and underscore the need to incorporate viral dynamics into resistance risk assessment in activated sludge systems.}, } @article {pmid42166402, year = {2026}, author = {Peta Martinez, NA and Reinoso Arnaldi, M and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA}, title = {Microbiota-Based Interventions Differentially Rescue Gut and Social Behavior Phenotypes in <italic>Drosophila</italic> with Kdm5 Deficiency.}, journal = {Developmental neuroscience}, volume = {}, number = {}, pages = {1-21}, doi = {10.1159/000552681}, pmid = {42166402}, issn = {1421-9859}, abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a lifelong neurological and developmental disorder that is often accompanied by gastrointestinal (GI) issues. The bidirectional communication system known as the gut microbiota-brain axis may help explain how GI dysfunction contributes to neurological symptoms. Loss-of-function mutations in the histone demethylases KDM5A, KDM5B, or KDM5C are found in patients with intellectual disability and ASD. Here, we use a genetically tractable Drosophila model of loss-of-function of the ASD-associated chromatin regulator Kdm5 to investigate how host genetic disruption influences gut microbial composition and social behavior. Previous studies using a Drosophila Kdm5 loss-of-function (Kdm5LOF) revealed gut microbial dysbiosis, reduced abundance of Lactiplantibacillus plantarum, and impaired social behavior. While L. plantarum supplementation rescued intestinal abnormalities, it did not restore social behavior.

METHODS: We evaluated multiple microbiota-based interventions, including probiotic supplementation with L. plantarum, Lactobacillus helveticus, their combination, and fecal microbiota transplantation (FMT), to determine their capacity to modulate gut microbial composition and behavior in adult Kdm5LOF flies. Gut bacterial abundance was quantified using colony-forming unit assays and full-length 16S rRNA gene sequencing. Social behavior was assessed using the social distance assay, while anxiety-like behavior and locomotion were evaluated using the open field test. Gut-specific Kdm5 knockdown was used to assess tissue-specific contributions to microbiota and behavioral phenotypes.

RESULTS: Kdm5 deficiency resulted in reduced abundance of culturable Lactobacillus, Acetobacter, and Enterobacter species, accompanied by impaired social behavior. L. plantarum supplementation restored gut microbial abundance in both whole-body Kdm5LOF and gut-specific Kdm5 knockdown models but did not significantly rescue social behavior. In contrast, L. helveticus significantly improved social interaction in Kdm5LOF flies despite minimal effects on gut bacterial abundance, revealing a dissociation between microbial restoration and behavioral outcomes. Gut-specific Kdm5 knockdown phenocopied both microbial and social defects observed in Kdm5LOF mutants. Notably, FMT from healthy donors partially restored Lactobacillus abundance, reshaped gut microbial community structure, and partially improved social behavior in Kdm5LOF recipient flies.

CONCLUSION: Together, these findings identify Kdm5 as a key regulator of gut microbial viability and social behavior and demonstrate that microbiota-based interventions exert strain- and phenotype-specific effects. Our results reveal that restoration of microbial abundance alone is insufficient to rescue social behavior and highlight the importance of functional host-microbe interactions in gut-brain communication. This work establishes Drosophila as a tractable platform for dissecting epigenetic regulation of microbiota-behavior relationships in the context of disruption of an ASD-associated gene and for studying microbiota-based modulation of host physiology and behavior. All experiments were conducted in adult flies, and thus, these findings reflect post-developmental effects of Kdm5 disruption.}, } @article {pmid42508343, year = {2026}, author = {Singh, CK and Sodhi, KK and Seth, R and Seth, RK}, title = {Gamma radiation-induced changes in the male adult gut bacterial community composition of a serious pest, Spodoptera litura (Noctuidae: Lepidoptera) and its F1 progeny.}, journal = {Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine}, volume = {237}, number = {}, pages = {112830}, doi = {10.1016/j.apradiso.2026.112830}, pmid = {42508343}, issn = {1872-9800}, abstract = {Spodoptera litura (Fabr), a noctuid Lepidopteran pest, can be effectively controlled using Inherited Sterility Technique (IS), a modified version of the Sterile Insect Technique (SIT). To ensure its operational success, the role of the gut microbiome in irradiation-induced fitness effects needs to be characterized. The role of gut bacteriome of the irradiated (130Gy) male adult moth and their F1 progeny was systematically examined. The current study aims to assess the effect of irradiation on bacterial diversity and relate with the reproductive performance of radio-sterilized moths. A culture-independent, high-throughput amplicon sequencing approach targeting bacterial 16S rRNA gene regions was employed to profile microbiome composition and diversity. Three experimental regimens were established: (i) unirradiated control males (N), (ii) partially sterilized males exposed to 130Gy (130Gy P1), and (iii) male F1 progeny derived from irradiated male parent (130Gy F1). Bacterial diversity and richness were reduced in gut of both the irradiated male parent and its F1 progeny compared with control (N). The Proteobacteria abundance was increased in the gut of 130 Gy P as compared to the control, whereas in the 130Gy F1 gut, its abundance was decreased significantly. The Firmicutes dominated the gut microbiome of the 130Gy F1 male moths. Further, the principal component analysis plot showed that the normal male moths were more closely related to 130 Gy P male moths in terms of gut bacterial diversity than to 130Gy F1 male moths. The functional pathways involved in the chitin and chloramphenicol were enriched in the guts of irradiated parent moths, whereas lignin degradation was enriched in 130Gy F1 progeny with respect to the control. This study might indicate the relevance of microbiome in reproductive fitness of irradiated moths and help in the optimization of this radio-genetic technique by validating the proposed gamma dose of 130Gy, towards pest control operations.}, } @article {pmid42508663, year = {2026}, author = {Wang, Z and Gu, Z and Yan, C and Zhou, J and Dai, B and Luo, L and Wang, X and Shi, P and Xia, S}, title = {Sulfur vacancies enhance pyrite-driven autotrophic denitrification: mechanistic insights into electron-supplying pathways.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135508}, doi = {10.1016/j.biortech.2026.135508}, pmid = {42508663}, issn = {1873-2976}, abstract = {Pyrite-driven autotrophic denitrification (PAD) is a promising carbon-free strategy for nitrate-contaminated wastewater treatment, yet the role of sulfur vacancies (SVs) remains poorly understood. Herein, we investigated the effects of SVs on denitrification activity, interfacial reactivity, and microbial mechanisms in PAD. Electrochemical characterization and batch tests indicated that SVs introduction boosted electron release from pyrite, achieving 98.1% nitrate removal, 1.59-fold higher than pristine pyrite. By integrating X-ray photoelectron spectroscopy, density functional theory calculations, and metagenomic results, we propose a mechanistic framework in which SVs enhance the electron-supplying capacity of pyrite via two routes: (i) SVs strengthen interactions between pyrite and microbial electron shuttles (e.g., riboflavin and methyl-naphthoquinone), supporting the potential involvement of extracellular electron transfer in enhancing electron availability to denitrifiers; and (ii) SVs are expected to weaken local Fe-S bonding and promote Fe(III)-mediated pyrite oxidation, thereby favoring Fe(II) mobilization and the potential involvement of sulfur intermediates (S[0], S2O3[2-]) during PAD. These changes were accompanied by altered surface Fe/S speciation and enrichment of sulfur-oxidizing denitrifiers, particularly Thiobacillus. Additionally, SV-enriched PAD system also exhibited superior resistance to antibiotic and metal stress and achieved continuous nitrogen polishing from real secondary effluent, confirming its strong potential for engineering scalability and practical implementation.}, } @article {pmid42509323, year = {2026}, author = {Spazzapan, M and Raison, N and Steves, C and Sahai, A}, title = {The urinary microbiome, overactive bladder and bladder pain syndrome/interstitial cystitis - mechanisms, diagnostics and therapeutic opportunities.}, journal = {Nature reviews. Urology}, volume = {}, number = {}, pages = {}, pmid = {42509323}, issn = {1759-4820}, abstract = {Overactive bladder and bladder pain syndrome/interstitial cystitis are prevalent, multifactorial disorders with poorly understood pathophysiology. The discovery of the urinary microbiome has overturned the sterile urine paradigm and created new opportunities for mechanistic and translational research. Increasing evidence suggests that bladder microbial communities are associated with urothelial signalling, immune tone and neural pathways that influence urgency, pain and treatment response. In overactive bladder, Lactobacillus-predominant profiles are associated with lower symptom burden and improved response to pharmacotherapy, whereas Gardnerella-enriched and Pseudomonadota-enriched communities positively correlate with refractory disease. In bladder pain syndrome/interstitial cystitis, microbial alterations are not based on a single pathogenic signature but converge on metabolic and immune dysregulation. Multi-omics studies integrating metagenomics, metabolomics and host immune data are beginning to define functional pathways linking microbial metabolites, epithelial barrier function and nociceptor sensitization. Results from emerging clinical trials suggest that urinary microbiome profiling might enable patient stratification and inform treatment selection, whereas interventions, such as probiotics, oestrogen therapy or dietary modulation, hold potential as adjunctive strategies. Together, these advances position the urinary microbiome as a promising contributor to lower urinary tract health and a potential target for precision urology, although the functional importance and causal role of the low-biomass urinary microbiome in disease remain crucial unresolved questions.}, } @article {pmid42509522, year = {2026}, author = {Chen, PY and Hsu, TW and Chiang, TY and Huang, CL}, title = {Comparative analysis of root microbiomes in four Swertia species from Taiwan.}, journal = {Journal of plant research}, volume = {}, number = {}, pages = {}, pmid = {42509522}, issn = {1618-0860}, support = {NSTC 103-2621-B-006-002-//National Science and Technology Council/ ; }, abstract = {Swertia (Gentianaceae) comprises four species endemic to Taiwan that possess significant medicinal potential. While root microbiomes are known to promote plant adaptation, the microbial ecology of Taiwanese Swertia remains largely unexplored. We investigated the rhizosphere and root endosphere microbiomes of these species using 16S rRNA gene sequencing and predictive functional profiling, integrated with host phylogenetic data. Our results revealed that rhizosphere bacterial communities were significantly more diverse than those in the root endosphere. PERMANOVA indicated that host species and plant compartment significantly influenced bacterial communities, but the high residual variance suggests that much of the community variation remains unexplained by the variables measured in this study. Phylogenetic analysis indicated that the root endosphere is more strongly influenced by host phylogeny, with closely related species harboring more similar communities. Functional profiling further demonstrated that the rhizosphere is predicted to be enriched in pathways related to nitrogen fixation and organic matter degradation, whereas the endosphere harbors bacterial taxa potentially associated with pathogen suppression. These findings underscore the multifaceted roles of the root microbiome in supporting the development, stress adaptation, and ecosystem sustainability of Swertia species in Taiwan's unique altitudinal gradients.}, } @article {pmid42509999, year = {2026}, author = {Hazan, S and Spradling-Reeves, KD and Papoutsis, A and Walker, SJ}, title = {Correction: Hazan et al. Shotgun Metagenomic Sequencing of Gut Microbiota in Triplet Sibling with ASD and Gastrointestinal Symptoms: A Descriptive Case Report. Children 2020, 7, 255.}, journal = {Children (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/children13070863}, pmid = {42509999}, issn = {2227-9067}, abstract = {The title of this publication [...].}, } @article {pmid42510718, year = {2026}, author = {Liu, J and Liu, S and Zhou, X and Zhong, Z and Hu, Q and Li, Q and Lin, Z and Huang, X and Zheng, B}, title = {Protective Effects of Fructus mume Extract Against Deoxynivalenol-Induced Intestinal and Liver Injury in Mice.}, journal = {Biology}, volume = {15}, number = {14}, pages = {}, doi = {10.3390/biology15141172}, pmid = {42510718}, issn = {2079-7737}, support = {JZ230013//the Key Project of Fujian Provincial Education and Scientific Research Program for Young and Middle-aged Teachers/ ; KLY24109XA//Fujian Provincial Department of Finance/ ; }, abstract = {Deoxynivalenol (DON), a prevalent mycotoxin, induces intestinal and hepatic injury. Fructus mume extract (FME) possesses bioactive properties, yet its protective role against DON remains unclear. This study aimed to investigate the protective mechanisms of FME in DON-challenged mice. Male C57BL/6 mice were divided into control, DON (3 mg/kg), and DON with low-, medium-, or high-dose FME groups for 4 weeks. Analyses included histopathology, UPLC-Q-TOF-MS, network pharmacology, biochemistry, qRT-PCR, immunohistochemistry, a TUNEL assay, metagenomics, and metabolomics. FME significantly alleviated growth inhibition and tissue damage. Among the 38 components identified by UPLC-Q-TOF-MS, all 38 acted on 156 genes, including IL-1β, caspase3, and BAX, to alleviate DON-induced intestinal and hepatic injury. FME enhanced hepatic antioxidant capacity and reduced inflammation by suppressing NF-κB signaling. FME upregulated tight junction proteins, inhibited apoptosis, and restored microbial diversity by enriching beneficial bacteria. Metabolomics revealed FME reversed DON-induced metabolic disruptions in the liver. Correlation analysis indicated FME remodeled the microbiota-liver metabolite network. In conclusion, FME attenuates DON-induced intestinal injury by modulating the gut-liver axis through antioxidant, anti-inflammatory, and anti-apoptotic activities.}, } @article {pmid42510727, year = {2026}, author = {Meng, X and Xue, Y and Shen, M and Shen, Y}, title = {UV Aging Strengthens the Effects of Polyvinyl Chloride Microplastics on Soil Bacterial Community Structure and Predicted Functional Profiles.}, journal = {Biology}, volume = {15}, number = {14}, pages = {}, doi = {10.3390/biology15141181}, pmid = {42510727}, issn = {2079-7737}, support = {42507354//National Natural Science Foundation of China/ ; 24KJB610005//Jiangsu Provincial Fundamental Science Research Program for Higher Education Institutions/ ; }, abstract = {Soil microplastics undergo aging, but how aging modifies their effects on soil bacterial communities remains unclear. Here, we conducted a 180-day incubation experiment with no PVC (CK), pristine PVC microplastics (IP), and UV-aged PVC microplastics (AP, 0.5%, w/w). UV aging markedly altered PVC surface properties: roughness increased from approximately 12.9 to 21.8 nm, water contact angle decreased from 91.44° to 82.38°, and the O/C ratio increased from 0.37 to 0.43. Bacterial richness indices were largely unchanged, whereas Shannon diversity decreased under AP, indicating reduced community evenness. Bray-Curtis analysis showed significant community separation among treatments (PERMANOVA: R[2] = 0.364, p = 0.003), with UV aging further altering the trajectory of PVC-induced community reorganization. At the genus level, AP was associated with enrichment of Methylobacillus and lower robustness in exploratory co-occurrence network analysis, suggesting a distinct bulk-soil bacterial response compared with IP. Functional prediction further suggested that AP and IP were associated with different predicted pathway profiles, with AP showing higher predicted representation of pathways related to carbon metabolism, respiratory energy metabolism, potential prokaryotic carbon fixation, environmental sensing, cellular maintenance, and antimicrobial-resistance-associated categories, whereas IP was mainly associated with transport- and communication-related predicted functions. These predicted functional patterns require further validation using metagenomic, qPCR, transcriptomic, biochemical, or chemical approaches. Overall, these findings highlight the need to consider the UV aging status of PVC microplastics when evaluating their effects on soil bacterial communities.}, } @article {pmid42510739, year = {2026}, author = {Liu, X and Zhao, X and Li, H and Wu, Y and Yao, Y and Wang, Z}, title = {Comparative Study on Blood Gas Indicators, Antioxidant Capacity, Intestinal Metabolome, and Microbiome in High- and Low-Performance Tumbler Pigeons.}, journal = {Biology}, volume = {15}, number = {14}, pages = {}, doi = {10.3390/biology15141193}, pmid = {42510739}, issn = {2079-7737}, support = {2023B02036//The Xinjiang Uygur Autonomous Region Key Research and Development Project/ ; }, abstract = {The purpose of this experiment is to investigate the differences in blood gas indicators, antioxidant indicators, and lactate content between high- and low-performance tumbler pigeons after exercise, and to use metabolomics and metagenomics techniques to screen for differential metabolites and bacteria related to tumbler pigeon exercise. This experiment selected 12 high-performing (HP) and 12 low-performing (LP) tumbler pigeons, half male and half female, and all pigeons were raised under the same conditions. Three experimental pigeons were grouped for exercise training, with a 20 min training session. The results showed significant differences (p < 0.05) in multiple blood gas parameters related to acid-base balance and gas exchange between the HP and LP groups after tumbler pigeon exercise. In addition, the content of glutathione peroxidase (GSH Px), superoxide dismutase (SOD), and catalase (CAT) in the liver of the HP group of tumbler pigeons was significantly lower than that of the LP group (p < 0.05). In comparison, the content of malondialdehyde (MDA) was significantly higher than that of the LP group (p < 0.05). The content of lactate (Lac) was significantly higher than that of the LP group (p < 0.05). Non-targeted metabolomics analysis revealed that differential metabolites were mainly enriched in pathways such as biosynthesis of unsaturated fatty acids, starch and sucrose metabolism, and fatty acid synthesis. Intestinal metagenomics analysis revealed that the Corynebacteriaceae, Bacillus, Pseudomonad phylum and Corynebacterium were significant biomarkers with significant differences in the gut microbiota of the HP group of tumbler pigeons (p < 0.05). In summary, there are significant differences in blood physiological parameters, antioxidant capacity, lactate content, intestinal metabolites, and gut microbiota between high- and low-performance tumbler pigeons after exercise. This result provides theoretical guidance and data support for cultivating high-performance tumbler pigeons.}, } @article {pmid42511030, year = {2026}, author = {Chen, P and Liu, C and Wang, S and Zhang, H and Li, J and Karrow, NA and Mao, Y and Yang, Z and Li, M}, title = {Integrated Rumen Metabolomics and Metagenomics Reveal Microbe-Metabolite Signatures Associated with Heat Tolerance in Dairy Cows.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {14}, pages = {}, doi = {10.3390/ani16142152}, pmid = {42511030}, issn = {2076-2615}, support = {BK20241934//Natural Science Foundation of Jiangsu Province/ ; 2022YFF1001200//National Key Research and Development Program of China/ ; }, abstract = {Heat stress impairs dairy cow productivity and rumen function, but rumen metabolic features associated with natural heat tolerance remain unclear. This study generated rumen fluid metabolomic data and integrated them with previously generated metagenomic abundance data from the same heat-tolerant (HT) and heat-sensitive (HS) Holstein cows selected from a cohort of 120 cows using an entropy-weighted TOPSIS model. Untargeted LC-MS identified 116 differential metabolites, including 66 enriched in HS cows and 50 enriched in HT cows. The HS cows showed higher levels of nucleotide-related metabolites, whereas HT cows were enriched in thiamine, L-malate, and argininosuccinic acid. Pathway enrichment mainly involved nucleotide metabolism, pyrimidine metabolism, pyruvate metabolism, and thiamine metabolism. Reanalysis of metagenomic data identified 12 differential microbial taxa, including HT-enriched Prevotella and Ruminococcus flavefaciens. Spearman correlation analysis revealed phenotype-associated microbe-metabolite associations, and ROC analysis based on the discovery dataset suggested that uridine 5'-monophosphate, thiamine, L-malate, and argininosuccinic acid had exploratory potential to distinguish HT and HS cows. These findings provide exploratory evidence that rumen microbe-metabolite associations are related to natural heat tolerance in dairy cows.}, } @article {pmid42511119, year = {2026}, author = {Zhang, B and Ma, X and He, Z and Liu, J and Chen, P and Wang, F and Xie, J and Lv, C and Pan, F}, title = {Effects of Perilla Seed Extract Dietary Supplementation on Meat Quality, Rumen Fermentation, and Rumen Microbiome-Metabolome of Tan Lambs.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {14}, pages = {}, doi = {10.3390/ani16142242}, pmid = {42511119}, issn = {2076-2615}, support = {2023GAAS42//Gansu Academy of Agricultural Sciences/ ; }, abstract = {Perilla seed extract (PSE), a natural resource rich in α-linolenic acid and flavonoids, represents a promising dietary strategy to sustainably optimize rumen fermentation and improve the nutritional profile of ruminant meat. This study evaluated the effects of dietary PSE supplementation on rumen fermentation, microbiome-metabolome profiles, and subsequent meat quality in Tan lambs. Sixty 3-month-old male Tan lambs were randomly assigned to four dietary treatments (n = 15 per treatment) containing 0% (CON), 0.01% (LPSE), 0.03% (MPSE), or 0.05% (HPSE) PSE on a dry matter (DM) basis. In the rumen, the 0.03% PSE inclusion increased the propionate proportion from 20.50% to 23.80% (P-linear = 0.004) and carboxymethyl cellulase activity from 12.45 to 14.85 U/mL (P-linear = 0.007; P-quadratic = 0.045). Exploratory metagenomics showed that 0.03% PSE enriched Prevotella (18.67% to 21.06%) and Ruminococcus_E (1.20% to 2.13%), while decreasing the biohydrogenating genus Butyrivibrio compared with CON (LDA > 2, p < 0.05). These microbial shifts were accompanied by the accumulation of beneficial metabolites (e.g., small peptides and itaconic acid) and up-regulation of the pantothenate and CoA biosynthesis pathway. Consequently, the 0.03% PSE diet optimized meat quality, decreasing shear force by 12.7% (from 45.65 to 39.85 N; P-linear = 0.005, P-quadratic = 0.018) and drip loss (from 4.82% to 3.85%; P-linear = 0.022, P-quadratic = 0.015), while increasing redness (P-linear = 0.012, P-quadratic = 0.045). Furthermore, it increased meat C18:3n-3 (from 0.62% to 0.91%) and total n-3 PUFA (from 1.12% to 1.52%), while decreasing the n-6/n-3 ratio from 6.76 to 5.13 (P-linear ≤ 0.005 for all). Flavor amino acids also increased (P-linear = 0.008). These findings suggest that 0.03% PSE supplementation potentially improves lamb meat quality by favorably modulating rumen fermentation and microbe-metabolite interactions, highlighting its promise as a natural feed additive, though further validation is warranted.}, } @article {pmid42511143, year = {2026}, author = {Di Martino, B and Carnevale, M and Corsi, L and Sarchese, V and Pellegrini, F and Smoglica, C and Petrini, A and Martella, V and Marsilio, F and Di Profio, F}, title = {Emerging Mammarenaviruses in Wildlife: Expanding Host Range and Implications.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {14}, pages = {}, doi = {10.3390/ani16142263}, pmid = {42511143}, issn = {2076-2615}, abstract = {Mammarenaviruses are enveloped, ambisense, single-stranded RNA viruses capable of causing fatal hemorrhagic fevers and severe neurological disorders in humans. Although muroid rodents have historically been recognized as the primary reservoirs for major pathogens like Lassa virus, recent surveillance has revealed a significant expansion of their host range. This review aims to synthesize current global data regarding the epidemiology of mammarenaviruses in conventional reservoirs and the emergence of novel arenaviruses in non-traditional mammalian hosts. To achieve this, we comprehensively analyzed recent molecular and metagenomic surveillance data, evolutionary studies, and epidemiological reports published worldwide. Key discoveries include Wenzhou virus in Asian house shrews, Plateau Pika virus in plateau pikas, and an independent, geographically clustered of hedgehog-associated arenaviruses across Europe. Ultimately, this review underscores the global distribution of these pathogens and the critical need for continued, multi-host surveillance worldwide.}, } @article {pmid42511188, year = {2026}, author = {Meanti, F and Bellassi, P and Fontana, A and Dall'Asta, M and Rebecchi, A}, title = {Unveiling Microbial Dynamics in the Spontaneous Fermentation of Oat and Rice Okara Sourdoughs.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {14}, pages = {}, doi = {10.3390/foods15142442}, pmid = {42511188}, issn = {2304-8158}, support = {F/310136/01-05/X56//Ministry of Enterprises and Made in Italy/ ; }, abstract = {Sourdough fermentation is increasingly explored as a sustainable strategy for the valorisation of cereal-based by-products, although okara from oat- and rice-based beverage production remains largely underexplored. This study investigates the microbial evolution and nutritional characteristics of oat and rice okara sourdoughs obtained by spontaneous fermentation using the back-slopping technique. High-throughput sequencing revealed dynamic but matrix-dependent microbial composition. At the beginning of fermentation, oat okara was dominated by the Bacillus genus, while the Streptococcus genus was the most abundant in rice okara. After 30 days of back-slopping, the bacterial communities of both matrices were dominated by Lactobacillus, accounting for 80.1% and 73.3% of the relative abundance in oat and rice okara sourdoughs, respectively. Secondary bacterial taxa differed between matrices, with Weissella prevailing in oat okara (7.0%) and Acetobacter in rice okara (11.2%). Yeast communities showed a substrate-dependent temporal succession, being initially dominated by Pichia in both oat and rice okara sourdoughs (96.6% and 97.1%, respectively), whereas Saccharomyces became predominant at later fermentation stages, reaching 54.8% in oat okara and 83.5% in rice okara. From a nutritional perspective, okara sourdoughs exhibited promising characteristics, being rich in proteins and free amino acids, particularly glutamic acid, aspartic acid and leucine. The fatty acid profile was marked by oleic, linoleic and stearic acids, while nutritionally important minerals associated with musculoskeletal and immune function, such as calcium, zinc and selenium, were present in relevant quantities in the sourdoughs. These findings provide new insights into oat and rice okara sourdoughs and support the use of fermented okara as a sustainable ingredient with potential functional relevance.}, } @article {pmid42511198, year = {2026}, author = {Zhang, S and Wu, Y and Wang, F and Li, H and Zheng, N and Chen, H and Zhao, Y}, title = {Camel Milk Alleviates Chronic Fatigue Syndrome-like Symptoms in Mice by Modulating the Small Intestinal Microbiota and Inflammation.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {14}, pages = {}, doi = {10.3390/foods15142451}, pmid = {42511198}, issn = {2304-8158}, support = {2025D01B138//Science and Technology Department of Xinjiang Uyghur Autonomous Region/ ; }, abstract = {This study aimed to investigate the therapeutic effects of camel milk (CM) on chronic fatigue syndrome (CFS) and elucidate the mechanisms underlying the microbiota-gut-brain axis. Using a murine model of CFS induced by chronic restraint and forced swimming stress, we administered lyophilized CM (1500 mg/kg/day, equivalent to approximately 121.5 mg/kg/day in humans based on body surface area conversion using the standard allometric scaling formula) orally. CM supplementation was significantly associated with ameliorated fatigue-like behaviors, as evidenced by prolonged swimming endurance and reduced immobility time. Metagenomic analysis revealed that CM was associated with reshaping of the small intestinal microbiota, including enrichment of beneficial Lactococcus lactis and suppression of pathobionts (H. hepaticus and H. typhlonius). These microbial shifts correlated with increased luminal lactic acid, improved intestinal barrier integrity (increased villus height, reduced crypt depth), and attenuated local inflammation (reduced TNF-α and IL-6, elevated IL-10). Consequently, CM was associated with reduced bacterial translocation and systemic inflammation, and normalization of hypothalamic-pituitary-adrenal (HPA) axis hyperactivity. We conclude that CM is associated with prevention of CFS-like symptoms through modulation of the gut ecosystem and strengthening of the intestinal barrier, potentially breaking the vicious cycle of gut inflammation and HPA axis dysfunction, although causality remains to be established through fecal microbiota transplantation or similar mechanistic studies.}, } @article {pmid42511274, year = {2026}, author = {Huang, H and Li, X and Zhang, K and Liang, B and Bai, S and Dong, X and Yan, D}, title = {Dietary Green Alfalfa Supplementation Reduces Backfat Thickness and Improves Muscle Water-Holding Capacity in Diqing Tibetan Pigs.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {14}, pages = {}, doi = {10.3390/foods15142528}, pmid = {42511274}, issn = {2304-8158}, support = {XDYC-QNRC-2023-0394//Young Talent Project of the Yunnan Province Xing Dian Ying Talent Support Program/ ; 202305AF150128//Yunnan Provincial Academician Expert Workstation Project/ ; 202202AE090005, 202302AE090015//Major Science and Technology Special Projects of Yunnan Province/ ; }, abstract = {Feed scarcity constrains livestock production, particularly on the Qinghai-Tibet Plateau. The effects of green alfalfa (GA) on Diqing Tibetan pig performance remain unclear. This study aimed to evaluate GA effects on Diqing Tibetan pig performance and to explore the potential underlying mechanisms through integrated metagenomic, transcriptomic, and metabolomic analyses. Thirty-six Diqing Tibetan pigs were randomly assigned to two groups and fed either a basal diet or a diet containing 90% basal diet and 10% GA. GA did not adversely affect growth performance but reduced 6-7 rib backfat thickness and muscle water loss rate by 19.79% (FDR = 0.027) and 17.80% (FDR = 0.036), while increasing muscle moisture content by 3.51% (FDR = 0.036). GA increased cecal microbial alpha diversity, Bacteroidota-related taxa, and functional genes related to lipid and vitamin metabolism, while decreasing Bacillota and Lactobacillus johnsonii. In the longissimus dorsi, TNNI1, MYL2 and MYL3 were upregulated, whereas FOS and FOSB were downregulated; GA increased vanillyl alcohol, L-histidine, LPE (0:0/22:5), and licochalcone B, but decreased glyceryl monostearate, benzaldehyde, cortisol, tryptamine, 4-ethyloctanoic acid, 8-methylnonanoic acid, and purine. Overall, 10% GA reshaped gut microbial, muscle transcriptomic, metabolomic profiles and collectively influenced 6-7 rib backfat thickness and muscle water-holding capacity in Diqing Tibetan pigs.}, } @article {pmid42511774, year = {2026}, author = {Nappo, A and Abbasi, AM and Berno, G and Rueca, M and Smoquina, F and Gruber, CEM and Fabeni, L and Spezia, PG and Carletti, F and Pietrucci, D and Petricciuolo, M and Carnevali, A and Sanna, N and Talarico, C and Federici, E and Chillemi, G and Maggi, F}, title = {Comparative Analysis of Viral Communities in Hospital, University and Urban Wastewater by Shotgun Metagenomic Sequencing.}, journal = {International journal of molecular sciences}, volume = {27}, number = {14}, pages = {}, doi = {10.3390/ijms27146430}, pmid = {42511774}, issn = {1422-0067}, support = {CUP F53C24001620001//European Union Next-GenerationEU/ ; Ricerca Corrente-Linea 1 on emerging and re-emerging infections//Ministry of Health/ ; }, abstract = {Wastewater-based surveillance has emerged as a powerful approach for population-level monitoring of pathogen circulation in a timely and non-invasive manner. In this study, shotgun metagenomic sequencing was applied to wastewater samples collected from a hospital (HP), a university campus (UN), and a wastewater treatment plant (WTP). Viral sequences were taxonomically classified using Kraken2. Specifically, HP samples showed the highest viral richness, followed by WTP and UN samples (HP vs. UN, p = 0.0003; WTP vs. UN, p = 0.0018). Using Jaccard distance, significant differences were observed between WTP and UN (R[2] = 0.181, p < 0.001), WTP and HP (R[2] = 0.159, p < 0.001), and UN and HP (R[2] = 0.223, p < 0.001), and similarly, for Sørensen-Dice dissimilarity: WTP vs. UN (R[2] = 0.238, p < 0.001), WTP vs. HP (R[2] = 0.212, p < 0.001), and UN vs. HP (R[2] = 0.307, p < 0.001). Human-associated viral families were detected across all sources, predominantly Poxviridae, Orthoherpesviridae, Polyomaviridae and Circoviridae. Furthermore, the taxonomic composition of indirectly associated viruses, mainly Anelloviridae and Crassvirales, was examined. Overall, these findings support the potential of wastewater metagenomics as a reliable tool for monitoring viral diversity within environmental and public health contexts, although further research is needed to establish its operational utility for routine surveillance applications within a One Health framework.}, } @article {pmid42511982, year = {2026}, author = {Xu, Y and Li, C and Zhao, Y and Lei, S and Yang, W and Yao, S and Wu, K and Huang, J and Yu, Z and Chen, S}, title = {Tracking Gut Homeostasis: Key Taxa Transitions and Core Network Hyper-Connectivity as Early Signals of Dysbiosis.}, journal = {Biomedicines}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/biomedicines14071508}, pmid = {42511982}, issn = {2227-9059}, support = {2022JJ30916//Hunan Provincial Natural Science Foundation/ ; 82270564//National Natural Science Foundation of China/ ; 82470564//National Natural Science Foundation of China/ ; 2022M713521//China Postdoctoral Science Foundation/ ; }, abstract = {Background: Although the gut microbiota is generally recognized to remain relatively stable in healthy individuals, its taxonomic composition still undergoes subtle temporal fluctuations. To systematically characterize these dynamic variations, we adopted "enterotypes" as a macroscopic and practical metric to evaluate the structural dynamics of the intestinal microbial community. Methods: We longitudinally recruited a cohort of healthy adults and collected a total of 72 shotgun metagenomic fecal samples across approximately 40 days. All samples underwent metagenomic sequencing, and subjects were grouped by their predominant enterotypes and longitudinal fluctuation patterns. We evaluated the microbial markers and the longitudinal co-occurrence network topologies of different groups to clarify the potential factors causing gut microbial fluctuations. Results: Longitudinal tracking revealed that those undergoing persistent alterations in microbial communities exhibited diarrhea symptoms, accompanied by markedly greater variability in gut microbiota. The reduction in Alistipes shahii is a potential predictive marker for community instability, exhibiting a cross-validated AUC of 0.824 (95% CI: 0.760-0.888). Furthermore, the co-occurrence network and correlation analysis indicated that fluctuating communities exhibited significantly higher clustering coefficients and denser connectivity among core taxa. Rather than indicating robustness, this dense architecture reflected an increased degree of microbial interdependence within the unstable gut microbial community. Conclusions: This preliminary study discovered candidate bacteria taxa that may serve as indicators of disturbances in the gut microbiota. Furthermore, the hyper-connectivity during continuous fluctuations suggested that increased interdependent microbial relationships meant diminished gut resilience. These results offer a new perspective for detecting early signals of dysbiosis and understanding mechanisms underlying stability of gut microbiota.}, } @article {pmid42512542, year = {2026}, author = {Liu, L and Zhang, J and Ma, Q and Wang, J}, title = {Herpesvirus-Associated Visual Impairment: Clinical Features, Etiological Spectrum, and Treatment Outcomes in Consecutive Patients from a Tertiary Neurological Clinic.}, journal = {Brain sciences}, volume = {16}, number = {7}, pages = {}, doi = {10.3390/brainsci16070768}, pmid = {42512542}, issn = {2076-3425}, abstract = {[Background] Herpesvirus infections can induce diverse visual impairments with permanent sequelae, yet systematic data on their clinical spectrum and outcomes remain scarce. [Methods] We conducted a single-center retrospective cohort study at the Department of Neurology, Beijing Tongren Hospital, Capital Medical University. Thirteen consecutive patients (19 affected eyes) with herpesvirus-related visual impairment admitted between January 2016 and January 2025 were enrolled. Demographic data, clinical manifestations, etiological tests (polymerase chain reaction [PCR], metagenomic next-generation sequencing [mNGS], serology), neuroimaging, treatment regimens, and visual outcomes were analyzed. [Results] The cohort had a mean age of 50.4 years (range 31-66), with male predominance (84.6%, 11/13). Varicella zoster virus (VZV) was the leading pathogen (76.9%, 10/13), followed by herpes simplex virus type 1 (HSV-1), Epstein-Barr virus (EBV), and pseudorabies virus (PRV). Eight patients (61.5%) developed optic neuritis (ON) secondary to VZV infection, and five patients (38.5%) suffered from acute retinal necrosis (ARN), which was caused by VZV (n = 2), HSV-1 (n = 2), and PRV (n = 1). Bilateral involvement occurred in 46.2% (6/13) of patients. ARN was associated with the most severe visual loss. At the disease nadir, 46.2% of patients (6/13) presented with no light perception (NLP). Notably, five of these six NLP cases were diagnosed with ARN. Etiological confirmation was achieved in only 38.5% (5/13) of cases. mNGS of cerebrospinal and vitreous fluid, alongside aqueous humor PCR, are pivotal for diagnosing HSV-1/EBV mixed infections and rare PRV infection. All patients received antiviral therapy, 11 of whom (84.6%) were treated with intravenous antiviral agents. Glucocorticoids were administered as combination therapy to all patients. However, only one of eight VZV-ON eyes showed genuine visual improvement. In VZV-ARN, the initially involved eyes stayed NLP at final follow-up, while the fellow eyes recovered vision. Still, all non-VZV ARN patients had persistent bilateral NLP during follow-up. [Conclusions] Herpesvirus-associated visual impairment is dominated by VZV, manifests as ON or ARN, and carries a high risk of severe permanent vision loss-particularly in ARN. The emergence of zoonotic PRV underscores the need for heightened clinical vigilance. Diagnostic delays and insufficient interdisciplinary collaboration contribute substantially to poor outcomes.}, } @article {pmid42513364, year = {2026}, author = {Zheng, L and Wang, X and Li, J and He, H and Chen, X}, title = {Metagenomic Next-Generation Sequencing Versus Conventional Microbiological Tests for Pathogen Identification and Prognostic Evaluation in Pediatric Patients with Post-Cardiac Surgery Infections: A Retrospective Cohort Study.}, journal = {Journal of clinical medicine}, volume = {15}, number = {14}, pages = {}, doi = {10.3390/jcm15145450}, pmid = {42513364}, issn = {2077-0383}, support = {Chinese Academy of Medical Sciences Fuwai Hospital high-level Hospital Research Fund（2025-GSP-QN-40,2025-GSP-QN-7 and 2025-GSP-GG-19）//Fu Wai Hospital/ ; }, abstract = {Object: Postoperative infection is a severe complication after pediatric cardiac surgery, which is closely associated with sepsis, multiple organ dysfunction, prolonged mechanical ventilation, extended ICU stay and increased mortality. Conventional microbiological tests (CMT) are limited by low sensitivity, long turnaround time, and poor capacity for detecting viruses and polymicrobial infections. This study aimed to compare the diagnostic efficacy of mNGS with that of CMT, and to explore the impact of polymicrobial infection on clinical outcomes in this high-risk pediatric population. Methods: A retrospective cohort study was conducted on 4889 pediatric patients admitted to the PICU after cardiac surgery from January 2025 to March 2026. A total of 510 patients were diagnosed with postoperative infections, including 879 CMT specimens and 86 mNGS specimens enrolled for analysis. Pathogen detection rates, pathogen spectrum and antimicrobial resistance profiles were compared between the two detection methods. Clinical prognostic indicators including mechanical ventilation duration, PICU length of stay and the requirement for continuous renal replacement therapy (CRRT) were further compared between patients with polymicrobial infection and monomicrobial infection. Results: Respiratory tract infection accounted for 87.8% of all postoperative infections, and Gram-negative bacteria were the predominant pathogens, accounting for 65.9%. The overall pathogen detection rate of mNGS was significantly higher than that of CMT (79.1% vs. 56.5%, p < 0.001). Notably, mNGS exhibited significantly better performance in detecting viruses (37.2% vs. 5.8%, p < 0.001), anaerobic pathogens and polymicrobial infections (38.2% vs. 5.4%, p < 0.001). Patients with polymicrobial infections had significantly longer mechanical ventilation time, longer PICU stay, and higher CRRT utilization rate (all p < 0.05), indicating a poorer clinical prognosis. Gram-negative bacteria showed high resistance to penicillins and early-generation cephalosporins, but remained susceptible to carbapenems and β-lactamase inhibitor combination agents. Gram-positive bacteria showed a high resistance rate to penicillin, while maintaining 100% susceptibility to vancomycin and linezolid. Conclusions: mNGS serves as a more sensitive and comprehensive tool for pathogen detection in children with post-cardiac surgery infections, especially for viral and polymicrobial infections. Polymicrobial infection is an independent risk factor for adverse clinical outcomes. Routine application of mNGS in critically ill children may help guide targeted antimicrobial therapy and improve prognosis.}, } @article {pmid42513896, year = {2026}, author = {Ma, P and Ma, F and Hu, Q and Zhang, W and Gu, H and Wei, D and An, Z}, title = {Study on Gut Microbiota Adaptation of Plateau Zokor (Eospalax baileyi) to High-Altitude Environments.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071390}, pmid = {42513896}, issn = {2076-2607}, abstract = {To further investigate altitude-associated variations in gut microbiota and serum metabolites of plateau zokors (Eospalax baileyi) and elucidate their adaptive mechanisms to high-altitude environments, we performed fecal metagenomic sequencing and serum metabolomic profiling (Q200 platform) on individuals from high (3700 m, n = 6) and low (2700 m, n = 6) elevations, followed by integrated analysis of microbial and metabolomic datasets. Results indicated that in high-altitude plateau zokors, the relative abundance of Firmicutes decreased, while that of Bacteroidota increased. The dominant genera within this group were identified as Bacteroides and unclassified members of the Lachnospiraceae family. Moreover, the abundances of Bacteroides and unclassified members of the Muribaculaceae family increased with elevation. At the species level, seven fully annotated differentially abundant taxa were identified: Candidatus Amulumruptor caecigallinarius, Schaedlerella arabinosiphila, Muribaculum gordoncarteri, Heminiphilus faecis, Prevotellamassilia timonensis, Staphylococcus aureus, and Bacteroides graminisolvens. KEGG enrichment analysis indicated significant upregulation (p < 0.05) of energy supply pathways, such as oxidative phosphorylation, and antioxidant-related pathways, including β-alanine and lysine metabolism, in the high-altitude group. Conversely, cysteine and methionine metabolism pathways were markedly downregulated (p < 0.05). Serum levels of ursodeoxycholic acid and tauroursodeoxycholic acid (TUDCA) were significantly elevated (p < 0.05), while deoxycholic acid (DCA) levels decreased (p < 0.05). In conclusion, the composition and function of gut microbiota, along with serum metabolite profiles, differ significantly (p < 0.05) between plateau zokors from different altitudes. Through synergistic interactions between gut microbiota and host metabolites, plateau zokors develop adaptive mechanisms that integrate energy metabolism, oxidative stress response, intestinal barrier integrity, and mucosal immunity. This ultimately facilitates their acclimatization to high-altitude extreme environments characterized by hypoxia and low temperatures.}, } @article {pmid42513908, year = {2026}, author = {Carvalho, APA and Almada, MS and Leal, CD and Fernandes, J and Costa, MC and Fonseca, VS and Giovanetti, M and Alcantara, LCJ and Araújo, JC}, title = {International Airport Wastewater as a Sentinel Site for Genomic Surveillance of Human Viruses and Bacteriophages.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071402}, pmid = {42513908}, issn = {2076-2607}, support = {424004/2021-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 01779-23//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 306899/2022-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 0000000-X//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; }, abstract = {Airports are strategic targets for wastewater-based epidemiology because they concentrate highly mobile populations and may provide early signals of pathogen circulation. However, metagenomic investigations of airport wastewater remain limited, particularly in South America. Here, we present one of the first hybrid-capture target-enriched metagenomic investigations of airport wastewater in Brazil, integrating the detection of human-associated viruses and bacteriophage-derived host signatures to evaluate airports as sentinel surveillance sites. Seven untreated wastewater samples collected from a major Brazilian airport between December 2021 and March 2023 were concentrated, subjected to nucleic acid extraction, and analyzed using hybrid-capture target-enriched next-generation sequencing. Taxonomic analysis identified 615 viral and bacteriophage-associated taxa, including 440 viruses and 175 bacteriophages. Among the viral fraction, 21 human-associated viral taxa representing eight viral families were selected for detailed analysis. Norovirus GII was detected in all samples, while Mamastrovirus 1 and JC polyomavirus were detected in six of seven samples. SARS-CoV-2 and dengue virus type 1 were simultaneously detected in the March, 2023 sample. The bacteriophage fraction comprised 47 host-associated phage groups, with Streptococcus-associated phages predominating across samples. These findings demonstrate that airport wastewater can capture diverse human viral and bacteriophage-derived signatures associated with population mobility, supporting its application in environmental genomic surveillance and early-warning systems for emerging and circulating pathogens.}, } @article {pmid42513909, year = {2026}, author = {Luo, D and Ponsero, AJ and Wright, K and Baker, DJ and Telatin, A and Townsley, C and Giotis, ES}, title = {Microbiome Stability in Wild and Rehabilitated Insectivorous Bats Revealed by Shotgun Metagenomics.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071403}, pmid = {42513909}, issn = {2076-2607}, support = {MR/Z506242/1/MRC_/Medical Research Council/United Kingdom ; RGS\R2\242527//Royal Society/ ; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG2260/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Wildlife rehabilitation can alter host-associated microbial communities, yet the effects of temporary managed care on the gut microbiome of insectivorous bats remain poorly understood. We used shotgun metagenomic sequencing to investigate gut microbiome composition in wild and rehabilitated bats from Yorkshire, United Kingdom. A total of 25 faecal metagenomes were analysed from four bat species (Myotis daubentonii, Pipistrellus pipistrellus, Nyctalus noctula, and Nyctalus leisleri), including wild baseline individuals and bats undergoing temporary managed care for 1-49 days. Microbial community structure clustered primarily according to host species and roost location, with no significant separation associated with rehabilitation status. Among bats in managed care, bacterial alpha diversity did not differ significantly with time in care (H = 2.30, p = 0.32). Archaeal communities displayed markedly lower interindividual variation than bacterial communities (coefficient of variation: 12.2% vs. 41.8%), indicating a highly conserved archaeal microbiome across hosts. Rehabilitated bats exhibited modest compositional shifts in bacterial communities, including increased relative abundances of Yersiniaceae and Lactobacillaceae and reduced abundances of environmentally associated taxa such as Pseudomonadaceae and Erwiniaceae. These changes may reflect controlled dietary provision and reduced environmental exposure during care. Overall, no marked rehabilitation-associated differences in gut microbiome diversity or community structure were detected under the current sampling design. These findings are consistent with microbiome stability during temporary managed care, although longitudinal studies are required to confirm microbiome dynamics within individual bats. Nonetheless, this study provides an initial baseline for future microbiome-informed wildlife rehabilitation studies.}, } @article {pmid42513924, year = {2026}, author = {Li, F and Suo, L and Bian, K and Sun, K and Yang, C and Tang, J}, title = {First Report of Bergeyella zoohelcum Associated with Hemorrhagic Pneumonia in Forest Musk Deer (Moschus berezovskii): Evidence from Bacterial Culture, 16S rRNA Sequencing, and Metagenomic Analysis.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071418}, pmid = {42513924}, issn = {2076-2607}, support = {2025NC-YBXM-120//Shaanxi Key Research and Development Program/ ; 2024k-08//Science and Technology Projects of Shaanxi Academy of Science/ ; 2025k-26//Science and Technology Projects of Shaanxi Academy of Science/ ; }, abstract = {Hemorrhagic pneumonia is a severe and often fatal disease in captive forest musk deer (Moschus berezovskii), but the pathogen remains incompletely understood. Based on incomplete statistics, the estimated incidence in captive populations ranges from 20% to 80%, with the disease occurring mainly in autumn, winter, and early spring. The disease has an acute onset and rapid progression. Due to the species' strong stress response, affected animals rarely show behavioral changes, making early detection difficult. In this study, we investigated a mortality case presenting with oral bleeding and hematemesis on a forest musk deer farm. Postmortem examination revealed diffuse hemorrhagic pneumonia, and lung tissue samples were collected for histopathology, bacterial isolation, full-length 16S rRNA gene sequencing, and DNA/RNA virome sequencing. Histological examination showed extensive alveolar hemorrhage, fibrinous exudate, and macrophage infiltration. Bacterial culture and 16S rRNA gene sequencing identified Bergeyella zoohelcum as the predominant bacterium, accounting for 100% of the bacterial community in the lung tissue. Virome analysis revealed predominantly DNA bacteriophages (e.g., Cirlivirales, Cremevirales, Microviridae) and no known pathogenic RNA viruses; only seven low-abundance, unclassified RNA viral contigs of low completeness were detected. These results indicate that B. zoohelcum is the likely causative agent of hemorrhagic pneumonia in this case, with no evidence of viral involvement. This study provides the first direct association of B. zoohelcum with hemorrhagic pneumonia in forest musk deer, highlighting its pathogenic potential and the importance of monitoring this bacterium in captive populations.}, } @article {pmid42513986, year = {2026}, author = {Gan, L and Fang, S and Wu, H and Yao, T and Chen, W and Li, Y and Han, Y and Zhou, L}, title = {Metagenomic Insights into the Seasonal Distribution and Dissemination Risks of Biocide and Metal Resistance Genes in a Subtropical Coastal Ecosystem.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071480}, pmid = {42513986}, issn = {2076-2607}, support = {No. GXKEYLA-2023-01-1//Ministry of Agriculture and Rural Affairs/ ; }, abstract = {The widespread use of antimicrobial biocides and metals has led to the continuous accumulation of biocide and metal resistance genes (BMRGs) in the environment. The issue is of growing concern, as it reduces the efficacy of these agents and poses a potential threat to coastal ecological security. However, the extent of coastal BMRG pollution, its transmission mechanisms, and the influence of seasonal variations on its assembly remain poorly understood. In this study, metagenomic sequencing was employed to investigate BMRGs, microbiomes, and mobile genetic elements (MGEs) within the subtropical nearshore ecosystem of the Beibu Gulf during the autumn and winter seasons. A total of 33 BMRG types and 457 subtypes were detected, with higher subtype diversity in winter than in autumn (440 vs. 326 subtypes). Notably, genes resistant to multi-biocides exhibited the highest diversity, whereas those resistant to both biocides and metals were the most abundant. Co-occurrence network analysis showed that 22 of the 23 detected BMRGs in the winter network were associated with MGEs, especially transposase-related elements such as tnpA. Path modeling indicated that BMRG abundance was more strongly associated with bacterial community composition in autumn, whereas MGE-related variables showed stronger associations in winter. These findings suggest a pronounced seasonal shift in the underlying mechanisms shaping BMRG dynamics, with bacterial communities playing a dominant role in autumn and MGEs playing a more critical role in winter. This seasonal shift highlights the need for season-specific monitoring of BMRGs, coastal pollution control, and resistance-risk management in subtropical coastal ecosystems.}, } @article {pmid42513994, year = {2026}, author = {Duan, C and Wang, D and Tan, L and Wang, Q and Tan, Z and Cheng, Y}, title = {Habitat-Dependent Ecological Differentiation of Soil and Water Microbiomes in High-Altitude Alpine Meadow Ecosystems on the Qinghai-Tibetan Plateau.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071489}, pmid = {42513994}, issn = {2076-2607}, support = {2023-NK-147//Science and Technology Department of Qinghai Province/ ; }, abstract = {High-altitude ecosystems are characterized by extreme environmental conditions that strongly influence microbial community structure and function. However, whether soil and water microbiomes exhibit similar ecological responses to environmental variation in alpine meadow ecosystems on the Qinghai-Tibetan Plateau remains poorly understood. Here, we combined 16S rRNA gene amplicon sequencing and metagenomic sequencing to compare soil and water microbiomes across two regions (LZ and NQ) with distinct physicochemical profiles. Environmental heterogeneity was more pronounced in water habitats, where all measured parameters (pH, total nitrogen, total organic carbon, and chemical oxygen demand) varied significantly between sites (p < 0.001). Correspondingly, water microbiomes exhibited greater regional differentiation than soil microbiomes, evidenced by stronger beta-diversity separation (PERMANOVA, R[2] = 0.667 vs. 0.376) and a lower proportion of shared ASVs (65.3% vs. 97.2%). Ecological assembly analysis revealed a sharp contrast: water communities were primarily governed by deterministic processes (accounting for >80% of assembly, with heterogeneous selection as the dominant driver), whereas soil microbiomes were dominated by stochastic processes (>50%). Furthermore, water microbiomes underwent more intense network restructuring, with interaction complexity increasing significantly from 70 nodes and 268 edges in the LZ region to 130 nodes and 577 edges in the NQ region, whereas soil networks remained relatively stable (146 nodes/368 edges to 128 nodes/391 edges). Functional profiling further indicated broader regional redistribution in water compared to the relatively conserved functional framework of soil communities. Resistome analysis identified distinct ARG structures between habitats while revealing 25 overlapping categories, suggesting potential ecological connectivity. Collectively, our findings demonstrate that water microbiomes are more sensitive to regional environmental variation than soil microbiomes, with aquatic communities responding through deterministic restructuring and heightened interaction complexity. These results provide quantitative evidence that high-altitude soil and water microbiomes adopt distinct ecological strategies, offering new insights into the mechanisms governing microbial adaptation and antibiotic resistance distribution.}, } @article {pmid42514009, year = {2026}, author = {Zheng, H and Zhang, Y and Wang, Z and Li, D}, title = {Bacterial Diversity, Structure, and Function in Rhizosphere and Bulk Soils of Grapevines: Comparing Gravelly, Calcareous, and Aeolian Sandy Textures.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071504}, pmid = {42514009}, issn = {2076-2607}, support = {U20A2042//Key Project of the National Natural Science Foundation of China Regional Innovation and Devel-opment Joint Fund/ ; 2025QN03197//National Natural Science Foundation of Inner Mongolia Autonomous Region/ ; CARS-29-zp-03//Water Physiology and Water-saving Cultivation in the National Grape Industry Technology System/ ; }, abstract = {Soil texture is a key determinant shaping bacterial communities in vineyard ecosystems, yet how different soil textures modulate bacterial characteristics in rhizosphere versus bulk soils during grapevine growth remains poorly understood. This study collected rhizosphere and bulk soil samples from five commercial Vitis vinifera cv. Cabernet Sauvignon vineyards in the eastern piedmont of Helan Mountain, Ningxia, China, spanning three distinct textures (gravelly, calcareous, and aeolian sandy soils). Shotgun metagenomic sequencing, soil physicochemical analysis, and four soil enzyme activity (alkaline phosphatase, urease, catalase, and invertase) measurements were conducted, using PERMANOVA and RDA to identify dominant driving factors. The results showed that bacteria accounted for 97.6% of all annotated sequences, representing the dominant group in soil microbial communities. Significant differences in bacterial abundance and alpha diversity (Chao1, ACE, Shannon, and Simpson) were observed in bulk soils across textures, whereas rhizosphere soils showed significant abundance differences but similar diversity levels. However, the 50 cm bulk soil sampling distance may have attenuated the true rhizosphere effect, and these findings should be interpreted with this methodological constraint in mind. Notably, bacterial community structure differed significantly between soils of the same pedogenic type but different textures, confirming that soil texture, rather than pedogenic classification, is the primary driver. Thirteen dominant bacterial phyla (>1% relative abundance) were identified, with Proteobacteria (47.7%), Actinobacteriota (22.9%), and Acidobacteriota (6.5%) as the main taxa. Mantel tests revealed significant correlations between nitrogen, phosphorus, organic matter contents and enzyme activities in rhizosphere soils (r ≥ 0.4, p < 0.01). RDA indicated that total phosphorus (TP), organic matter (OM), alkali-hydrolyzable nitrogen (AN), Mg, pH, available K (AK), and enzyme activities were key drivers of bacterial community structure (p < 0.05). Annotated metabolic functions based on KEGG orthology indicated lower overall metabolic pathway abundances in gravelly soils compared to calcareous and aeolian sandy soils. In conclusion, soil texture, rather than broad pedogenic classification, primarily shapes vineyard bacterial communities, providing a theoretical basis for precision viticulture and sustainable soil management.}, } @article {pmid42514018, year = {2026}, author = {Yin, Y and Zhao, B and Li, R and Wang, R and Peng, J and Xia, B and Tian, J}, title = {Identification of Leptotrichia hofstadii as a Post-Treatment Recurrence Biomarker in Severe Early Childhood Caries.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071513}, pmid = {42514018}, issn = {2076-2607}, support = {82301078//National Natural Science Foundation of China/ ; L232110//Beijing Natural Science Foundation/ ; }, abstract = {Recurrence remains a significant challenge following the treatment of Severe Early Childhood Caries (S-ECC). This study aimed to identify candidate recurrence-related biomarkers for S-ECC and elucidate their potential pathogenic mechanisms. Through metagenomic sequencing of supragingival plaque from 32 children at one month post-treatment, we identified Leptotrichia hofstadii as one of the potential biomarkers for S-ECC recurrence (AUC = 0.8438 for the sequencing set and AUC = 0.75 for the validation set). In vitro dual-species biofilm assays using crystal violet staining and Confocal Laser Scanning Microscopy (CLSM) demonstrated that L. hofstadii promotes early-stage S. mutans colonization and extracellular polysaccharide (EPS) formation through contact-dependent synergistic interactions. Scanning electron microscopy revealed that L. hofstadii may function as a spatial scaffold within dual-species biofilm. Furthermore, this synergy significantly accelerates environmental acidification, leading to earlier attainment of the critical demineralization threshold (pH 5.5). At the transcriptional level, carbohydrate metabolism-related pathways were upregulated in dual-species biofilm, including starch and sucrose metabolism, PTS and ABC transporters. Additionally, the fruA gene, which degrades fructan in EPS was downregulated in the dual-species biofilm compared with S. mutans monoculture. These findings suggest that L. hofstadii facilitates a cariogenic microenvironment by enhancing the metabolic activity of S. mutans biofilms. Collectively, this study identifies L. hofstadii as a potential biomarker for S-ECC recurrence prediction and provides preliminary insights into possible interspecies mechanisms, offering valuable clues for future research into targeted preventive strategies.}, } @article {pmid42514045, year = {2026}, author = {Wang, M and He, Q and Qiu, Y and Huang, L and Zhang, Y and Ye, D and He, Z and Wen, C}, title = {High Humidity Exacerbates Rheumatoid Arthritis in Mice via Prevotella stercorea-Mediated Chondroitin Sulfate Degradation.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071540}, pmid = {42514045}, issn = {2076-2607}, support = {82405212//National Natural Science Foundation of China/ ; 82274382//National Natural Science Foundation of China/ ; 82474147//National Natural Science Foundation of China/ ; }, abstract = {Background: Rheumatoid arthritis (RA) is influenced by environmental exposures. High humidity has been clinically associated with worsened joint symptoms, but the microbial and metabolic mechanisms remain unclear. We investigated whether a gut microbiota-metabolism axis contributes to humidity-associated aggravation of collagen-induced arthritis (CIA). Methods: CIA mice were maintained under normal or high relative humidity. We integrated 16S rRNA and metagenomic sequencing, liquid chromatography-tandem mass spectrometry metabolomics, and intestinal barrier assessments. Fecal microbiota transplantation (FMT) was performed to evaluate microbiota dependency. Based on multi-omics findings, we quantified chondroitin sulfate (CS) and conducted functional experiments involving Prevotella stercorea (P. stercorea) supplementation, CS administration, and in vitro degradation assays. Results: High humidity aggravated arthritis severity and systemic inflammation, including increased interleukin-6, interleukin-17A, and granulocyte colony-stimulating factor, and was accompanied by impaired intestinal barrier integrity. FMT supported a microbiota-dependent contribution. Metagenomic analysis identified enrichment of P. stercorea and glycosaminoglycan degradation pathways under high humidity. CS abundance was reduced in articular cartilage, P. stercorea degraded CS in vitro and was associated with cartilage CS loss in vivo, and CS supplementation attenuated arthritis under high humidity and reduced the arthritis-promoting effects associated with P. stercorea. Conclusions: High humidity is associated with microbiota-dependent functional remodeling, enhanced CS degradation, and aggravated arthritis in CIA mice. These findings suggest that humidity-associated alterations in microbial CS metabolism may link environmental exposure to cartilage disruption and joint inflammation.}, } @article {pmid42514066, year = {2026}, author = {Nawaz, MA and Nawaz, MZ and Haider, SZ and Alghamdi, HA and Yan, W}, title = {Small Regulatory RNAs in Prokaryotes: Key Features, Identification, Environmental Roles, and Applications.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071561}, pmid = {42514066}, issn = {2076-2607}, support = {RGP2/665/46//King Khalid University/ ; }, abstract = {Small non-coding RNAs (sRNAs) are ubiquitous post-transcriptional regulators that enable rapid bacterial adaptation to fluctuating environments. Previous reviews have largely focused on sRNA mechanisms in model organisms. This review integrates computational prediction, meta-omics-based discovery, and synthetic biology applications of small regulatory RNAs in marine and environmental prokaryotes, providing a multi-layered perspective from identification to functional and engineering applications. The current landscape of sRNA identification tools is critically evaluated, with emphasis on strategies to overcome challenges such as false-positive predictions. Recent advances in mapping the RNA interactome and emerging evidence of previously underappreciated roles of sRNAs in environmental adaptation are discussed. Additionally, metagenomic and metatranscriptomic studies revealing the diversity of environmental sRNAs in uncultured microbial communities are summarized, highlighting their ecological significance. Finally, a curated overview of synthetic sRNA applications in metabolic engineering, including target genes and enhanced product yields, is provided as a resource for strain engineering. Collectively, this review provides a holistic view of prokaryotic sRNA biology, distinguishing it from more narrowly focused studies. Overall, sRNAs are highlighted as key regulatory elements linking microbial environmental adaptation with emerging biotechnological applications through advances in meta-omics guided discovery and synthetic RNA engineering.}, } @article {pmid42514075, year = {2026}, author = {Ferreira, NE and Mendes-Correa, MC and Costa, ACD}, title = {Editorial for the Special Issue "Advances in Viral Metagenomics".}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071570}, pmid = {42514075}, issn = {2076-2607}, abstract = {Viral metagenomics has fundamentally transformed how we investigate the virosphere [...].}, } @article {pmid42514080, year = {2026}, author = {Chang, Y and Liu, X and Song, L and Xu, F and Zhang, Z and Yu, M and Wu, G and Zhang, D and Xu, C}, title = {Cold Exposure Shifts Gut Microbial Butyrate Synthesis Toward the Lysine-Dependent and But-Mediated Terminal Pathways to Enhance Cold Tolerance in Min Pigs.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071575}, pmid = {42514080}, issn = {2076-2607}, support = {32302709//National Natural Science Foundation of China/ ; ZL2024C012//Heilongjiang Provincial Natural Science Foundation/ ; LH2023C013//Heilongjiang Provincial Natural Science Foundation/ ; }, abstract = {This study combined seasonal observation in Min pigs and acute cold challenge experiments in Min pigs and Large White pigs to analyze changes in gut butyrate synthesis under cold exposure and its association with thermogenesis. Compared with summer, Min pigs in winter showed significantly higher Bacteroidota abundance (p = 0.006), lysine-pathway genes (p < 0.05), and relative gene abundance of the but terminal pathway (p < 0.05). Fecal (47.96 vs. 40.24 µmol/L, p = 0.020) and serum (4.64 vs. 2.17 µmol/L, p = 0.046) butyrate were also elevated and correlated with 10 thermogenesis-related genes (p < 0.05). Acute cold challenge increased serum butyrate (p = 0.017) and SLC16A1 expression (adjusted p = 0.027) only in Min pigs. Min pigs exhibited higher lysine pathway abundance and greater but terminal contribution than Large White pigs. Metagenomic binning recovered 40 lysine-pathway MAGs (27 unique to Min pigs) and 15 dual-pathway MAGs (11 unique to Min pigs), with Bacteroidota MAGs harboring complete lysine and dual terminal pathways. Collectively, cold exposure correlates with enrichment of lysine-dependent and but terminal butyrate synthesis pathways, highlighting butyrate-producing bacteria as candidate taxa for further investigation of cold-induced gut metabolic remodeling in pigs.}, } @article {pmid42514086, year = {2026}, author = {Zheng, Y and Ma, N and Zhao, B and Li, Y and Tian, Y and Liu, J and Quan, Y}, title = {Wastewater Metagenomics for Antimicrobial Resistance and Pathogen Surveillance: A Bibliometric Analysis.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071583}, pmid = {42514086}, issn = {2076-2607}, support = {YDZJ202601ZYTS183//Jilin Province Science and Technology Department/ ; }, abstract = {Wastewater systems are critical reservoirs where antibiotic resistance genes, antibiotic-resistant bacteria, and pathogens converge and disseminate into receiving waters, posing risks to ecosystems and public health. Metagenomics enables culture-independent surveillance of resistome and pathogens in wastewater. After the COVID-19 pandemic, the rapid expansion of wastewater-based epidemiological surveillance, together with growing emphasis on the One Health framework, has further promoted the integration of wastewater metagenomic monitoring with public-health surveillance strategies. However, no bibliometric study has systematically mapped the global research landscape at the intersection of metagenomics, wastewater systems, antimicrobial resistance, and pathogen surveillance. This study retrieved 1161 publications from the Web of Science Core Collection and used CiteSpace to conduct bibliometric analyses. From 2010 to 2025, annual publications increased from 1 to 219, with 72.7% of the total output concentrated between 2021 and 2025. China led in publication output but showed low betweenness centrality, whereas Australia and Sweden served as key intermediaries. Keyword analysis revealed a gradual thematic evolution from the basic detection of antibiotic resistance genes in activated sludge, through studies of dissemination mechanisms, to recent work on One Health and wastewater surveillance. Literature co-citation analysis showed that integration between environmental monitoring and public health literature remains limited, suggesting that the translation of metagenomic surveillance data into health risk assessment frameworks is still at an early stage. By mapping the field's knowledge structure and gaps, this review highlights priorities for advancing wastewater-based Antimicrobial Resistance surveillance, including standardizing analytical methods, developing artificial intelligence-assisted resistome analysis, promoting equitable participation from underrepresented regions, and operationalizing One Health surveillance, thereby supporting the translation of wastewater monitoring into actionable public-health solutions.}, } @article {pmid42514091, year = {2026}, author = {Valiakhmetov, EE and Frolov, M and Sukhanov, AY and Miftakhov, AK and Validov, SZ}, title = {Strain-Specific Loci in Bacterial Genomes: Whole-Genome Discovery, Genomic Context, and Application for Multi-Strain qPCR Monitoring.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071587}, pmid = {42514091}, issn = {2076-2607}, support = {FMEG-2027-0007//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Monitoring individual strains in complex microbial communities remains a fundamental challenge in microbial ecology and biotechnology. Here, we present an integrated pipeline for identifying and validating strain-specific loci (SSL) in four biotechnologically relevant plant growth promoting strains from three genera (Stenotrophomonas, Bacillus, and Pseudomonas). The pipeline applies a two-round specificity-filtering strategy combining whole-genome comparison and high-sensitivity BLASTn validation of revealed strain-specific loci (SSL) against the NCBI nucleotide database. SSL count decreased with increasing Average nucleotide identity (ANIb) of the strains used for the analysis, ranging from one locus in B. halotolerans (ANIb = 98.91%) to 15 loci in S. rhizophila (ANIb = 86.49%). All 25 SSL were universally AT-rich, mainly accessory-genome-associated, with flanking regions enriched in genes of unknown function (34.6%) and mobile genetic elements (19.2%). TaqMan qPCR assays targeting SSL demonstrated high specificity-no target sequences were detected across ten geographically distinct soil samples, nor in a native rhizosphere metagenome-and sensitivity, with limits of detection of 0.01-0.1 pg of genomic DNA. Spike-in experiments in soil yielded method detection limits (MDL) of 850-15,000 CFU/g. All four strains were detected in the wheat rhizosphere seven days after consortium application in a field experiment, validating the pipeline for multi-strain field monitoring.}, } @article {pmid42514099, year = {2026}, author = {Flores-Fernández, CN and Hiron, TK and Dobrijevic, D and Zavaleta, AI and Jeffries, JWE and O'Callaghan, CA and Lye, GJ and Ward, JM and Cárdenas-Fernández, M}, title = {Taxonomic and Functional Comparative Metagenomics of Peruvian Salterns: Insights into Microbial Communities and Aminotransferase Potential.}, journal = {Microorganisms}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/microorganisms14071595}, pmid = {42514099}, issn = {2076-2607}, support = {BB/M027864/1//UK Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/R021627/1//BBSRC ERA CoBioTech/ ; EP/S024883/1//Engineering and Physical Sciences Research Council/ ; 007-2014-FONDECYT//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; EP/S01778X/1//Future Biomanufacturing Research Hub/ ; }, abstract = {Metagenomic analysis of extreme environments is essential in biotechnological research. This work aimed to determine and compare the microbial diversity of two Peruvian saline environments and characterise their functional profiles. Soil metagenomic DNA (mDNA) was analysed from Maras and Pilluana salterns, both with a thalassohaline origin but with different geographical and environmental conditions. Maras samples exhibited more diversity and a remarkably higher abundance of archaea (phylum Euryarchaeota). The most dominant bacterial phyla across all the samples were Pseudomonadota and Actinomycetota. Multiple pathways specific to archaea were more abundant in Maras, as were pathway-related synthesis and degradation of compatible osmolytes such as glycine betaine and ectoine. The most abundant pathways in Pilluana were associated with fatty acid biosynthesis and oxidation. A total of 49 and 47 metagenomic-assembled genomes (MAGs) were retrieved from Maras and Pilluana samples, respectively. Bacterial MAGs were mainly classified within the phyla Psudomonadota, Actinomycetota, Planctomycetota, and Gemmatimonadota. Additionally, a total of 20 putative aminotransferases class III (ATs, PF00202) from Maras3 were cloned and expressed in E. coli Rosetta, and their substrate scoping was assayed against several aldehyde and ketone substrates; AT pQR3082 and pQR3090 showed unique broad substrate acceptance for aromatic and aliphatic substrates. Our study provides new insights into the microorganisms and metabolic pathways of these unique extreme environments, highlighting the promising biotechnological potential of metagenomic ATs.}, } @article {pmid42514486, year = {2026}, author = {Chen, X and Wang, J and Tang, L and Zeng, Z and Gao, D and Yi, Y and Qin, L and Xiao, Y and Yang, H and Yang, B}, title = {From Traditional to Omics-Driven: Emerging Strategies for Isolation, Cultivation, and Identification of Plant Endophytes.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {14}, pages = {}, doi = {10.3390/plants15142118}, pmid = {42514486}, issn = {2223-7747}, support = {Grant No. YLS-2025-ZY02030//Yuelushan Laboratory Breeding Program/ ; No. 22A0151//the Scientific Research Fund of Hunan Provincial Education Department/ ; No. CX20251060//the Hunan Province Graduate Student Scientific Research Innovation Project/ ; No. 31800076//the National Natural Science Foundation of China/ ; No. 2019JJ50245//Natural Science Foundation of Hunan province, China/ ; 2024RC2052//Joint Talent Introduction Program of Yuelushan Laboratory/ ; }, abstract = {Plant endophytes can regulate host plant growth, improve stress resistance, and facilitate the biosynthesis of secondary metabolites, with great research value and application potential. However, traditional approaches for the isolation, cultivation and identification of plant endophytes are constrained by low culturability, limited species diversity, and loss of their original ecological functions inside host tissues. In recent years, integrated multi-omics strategies combining metagenomics, metatranscriptomics, and metaproteomics have exhibited the greatest potential to mitigate culturability limitations by enabling genome-guided targeted strain isolation and in situ functional activity profiling, among which the cultivation and targeted isolation of endophytes benefit most from omics integration. These approaches drive a paradigm shift from conventional blind screening to precise targeted isolation, and from generic medium culture to omics-guided rational cultivation, greatly improving the accuracy of strain identification and functional characterization. Nevertheless, current omics-based strategies still face inherent limitations including high experimental costs, complex operational procedures, and challenging data interpretation. The most critical future direction lies in establishing standardized experimental protocols and shared resource databases, combined with microfluidic platforms and artificial intelligence-assisted bioinformatics analysis, to address the core bottlenecks restricting endophyte isolation, cultivation and identification. This review is the first to systematically summarize research progress on traditional approaches, omics technologies and emerging strategies for plant endophyte isolation, cultivation and identification, highlights prevailing challenges and developmental trends in this field, and provides methodological references for the efficient exploitation and sustainable utilization of plant endophyte resources.}, } @article {pmid42514595, year = {2026}, author = {Wang, LJ and Ji, F and Qi, SY and Li, QF and Zhao, M and Xu, CJ and Li, YT and Zhang, AL}, title = {Pine-Extracted Volatile Oils Suppress Root Rot in Psammosilene tunicoides Through Direct Antifungal Activity and Rhizosphere Microbiome Modulation.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {14}, pages = {}, doi = {10.3390/plants15142228}, pmid = {42514595}, issn = {2223-7747}, support = {No.20254916CE340047//Yunnan Key Laboratory of Chinese Medicine Processing/ ; }, abstract = {Frequent outbreaks of root rot in Psammosilene tunicoides W. C. Wu & C. Y. Wu severely compromise the quality of its medicinal materials and hinder its large-scale cultivation. Interestingly, wild P. tunicoides growing under pine trees rarely experience this disease. To explore the potential basis of root rot suppression, we evaluated the direct antifungal activity of pine-derived volatile oils and the associated changes in the rhizosphere microbiome. GC-MS showed that pine turpentine was dominated by α-pinene (45.50%) and longifolene (28.20%). In vitro assays confirmed its highly efficient inhibition (81.65-94.71%) against major root rot pathogens in P. tunicoides. Beyond direct antifungal effects, metagenomic analysis indicated that volatile oil (SYR) treatment was associated with shifts in the rhizosphere microbiome, including increased relative abundances of potentially beneficial taxa, such as Paenibacillus, Trichoderma, and Geosiphon. Pine volatiles might be associated with shifts in the rhizosphere microbial community of P. tunicoides, potentially involving plant-mediated changes in root exudation and the enrichment of certain beneficial microbes. However, it remains to be further elucidated regarding the specific mechanisms underlying these community changes. Functional prediction of the microbial community suggested a predominance of metabolic pathways, secondary metabolite biosynthesis, and flagellar assembly in the SYR group. Conclusively, pine volatiles may contribute to root rot suppression through two potential processes: direct pathogen inhibition and beneficial microbiome enrichment. This study provides a theoretical basis for establishing sustainable agroforestry co-planting systems for P. tunicoides.}, } @article {pmid42514670, year = {2026}, author = {Ericsson, AC}, title = {A Comprehensive Review of the Equine Gut Microbiome in Health and Disease.}, journal = {Veterinary sciences}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/vetsci13070659}, pmid = {42514670}, issn = {2306-7381}, abstract = {Molecular microbiology has revolutionized our understanding of the complex host-associated microbiomes required for normative development and physiology. Horses and other members of the family Equidae are particularly reliant on the early maturation and lifelong maintenance of an unusually rich hindgut microbiome for optimal digestion and overall health and performance. Research on the equine gut microbiome has accelerated in the past several years, necessitating a renewed appraisal of the field. The present work is a comprehensive and critical review of the literature regarding the bacterial gastrointestinal microbiome of horses. First, the developmental trajectory of the foal gut microbiome is discussed, followed by descriptions of the taxonomic membership of the core equine gut microbiome, its primary functions and effects on host physiology, and intrinsic and extrinsic factors that shape the equine microbiome during health, with a focus on diet and supplements. Next, evidence supporting adverse effects on the equine gut microbiome of gastrointestinal conditions including colic and colitis, extraintestinal conditions including obesity and laminitis, and pharmacological interventions including antibiotics and non-steroidal anti-inflammatory drugs is summarized. Lastly, clinical and experimental research investigating the effects of treatments targeting the gut microbiome of horses, including probiotics, prebiotics, and fecal microbiome transfer, is critically examined. Conclusions summarize the connection between natural (i.e., wild) equine behavior and the health of the equine gut microbiome and the impacts of human management.}, } @article {pmid42514689, year = {2026}, author = {Abi, K and Xia, Z and Gou, L and Zhang, W and Ji'e, K and Li, S and Gao, T and Banma, W and Yang, F}, title = {Integrated 16S rRNA and Metagenomic Analysis of Pulmonary Microbiota in Sheep with Pneumonia.}, journal = {Veterinary sciences}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/vetsci13070679}, pmid = {42514689}, issn = {2306-7381}, support = {SCCXTD-2024-14//Innovation Team Development Funds for Sichuan Mutton Goat & Sheep/ ; 2024CXTD08//Scientific and Technological Innovation Team for Qinghai-Tibetan Plateau Research in Southwest Minzu University/ ; }, abstract = {Sheep are a major livestock species in China, yet pneumonia-related mortality poses a significant obstacle to intensive farming. In this study, 115 sheep lung samples were collected and classified into different pneumonia severity groups based on lung lesion scoring. Subsequently, this study employed 16S rRNA sequencing to systematically investigate the structure and diversity of the pulmonary microbiota in sheep, including alpha diversity, beta diversity, and LEfSe analyses. Metagenomic techniques were also applied to analyze the abundance of metabolic pathways, exploring the associations between functional gene differences and pneumonia severity, as well as putative antibiotic resistance genes, virulence factors, and the species contributions of functional genes in severe pneumonia cases. Microbial richness and diversity were significantly higher in the severe pneumonia group than in the healthy/mild lesion group (p < 0.05). While the dominant microbial structures were similar across the groups, notable differences were observed in the abundance of respiratory disease-associated genera, with Pasteurella, Mannheimia, Mycoplasma, Bibersteinia, and Moraxella identified as significantly enriched in severe cases. Moreover, several genera originating from the gut and oral cavity were also associated with pneumonia, suggesting a potential gut-lung axis. Carbohydrate metabolism was the most prevalent pathway in all groups, whereas amino acid metabolism was significantly enriched in the severe pneumonia group. Putative antibiotic resistance genes were differentially enriched; the severe pneumonia group showed significant enrichment of genes conferring resistance to aminoglycosides, tetracyclines, and polymyxins. Virulence factor analysis identified nutritional/metabolic factors and adhesion as the predominant virulence mechanisms. Species contribution analysis further revealed that Mannheimia, Mycoplasma, Pasteurella, and Moraxella were the predominant species associated with functional gene enrichment. In conclusion, the current study reveals associations between changes in the pulmonary microbiota structure and function and the severity of pneumonia in sheep, aiming to provide a foundation for future hypothesis-driven research on the role of the pulmonary microbiota in pneumonia progression.}, } @article {pmid42514698, year = {2026}, author = {Sun, Y and Xu, S and Luo, Z and Fan, T and Zhou, X}, title = {Analysis of Bacterial Diversity in Fresh Milk from Commercial Dairy Farms in Xinjiang Based on Metagenomic Sequencing.}, journal = {Veterinary sciences}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/vetsci13070688}, pmid = {42514698}, issn = {2306-7381}, support = {2023NY03-1//Xinjiang Production and Construction Corps/ ; 2024AB035//Xinjiang Production and Construction Corps/ ; }, abstract = {To investigate the biological characteristics of microbes in fresh milk, this study gathered fresh milk from seven large-scale dairy farms in the southern and northern regions of Xinjiang, analyzing the composition and abundance of bacterial communities in these samples through metagenomic sequencing technology. Firmicutes, Proteobacteria, and Actinobacteria were consistently identified as the dominant phyla across all samples, with stable relative abundance patterns across regions. At the genus level, the genera with the highest relative abundances were Sporosarcina, Streptococcus, and Escherichia, with relative abundances of 2.51-2.58%, 2.23-2.27%, and 1.93-1.97%, respectively. While exploring species richness, it was observed that the XN group had the most OTUs, the DR group had the fewest, and there were significant differences in community structure between the ND group and the other six groups. Further Alpha diversity analysis revealed no significant variation in Chao1 indices across the seven sample groups, highlighting a significant difference in Shannon index for ND samples, and no significant differences in Shannon indices between the CJ, JY, KT, DR, and TR samples. Shifting focus to functional potential, the top three relative abundances in the microbial metagenome KEGG functional library are biological systems, human diseases, and environmental information processing; additionally, within the CAZy (Carbohydrate-Active enZymes) database, the three most abundant categories are glycosyltransferases (GT), glycoside hydrolases (GH), and carbohydrate-binding modules (CBM). By delineating these patterns, this study demonstrates the microbial spectrum characteristics of fresh milk from southern and northern Xinjiang, China, offering a theoretical foundation for enhancing the quality of fresh milk in the area.}, } @article {pmid42514990, year = {2026}, author = {Kumar, M and Suleimenova, S and Nuralibekov, S and Kasymbekov, Y and Sabyrzhan, T and Isbekov, K and Assylbekova, S and Fefelov, V and Pangereyev, B and Karamendin, K and Kydyrmanov, A}, title = {Metagenomic Characterization and Molecular Screening of Pathogens in Freshwater Amphipods (Gammarus lacustris) from Kazakhstan: Implications for Aquaculture Biosecurity.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/pathogens15070663}, pmid = {42514990}, issn = {2076-0817}, support = {BR23591095//Ministry of Agriculture of the Republic of Kazakhstan/ ; }, abstract = {Freshwater amphipods of the genus Gammarus are important trophic components of aquatic ecosystems and are increasingly considered a potential bioresource for aquaculture. However, their role in the maintenance and transmission of infectious agents remains poorly understood. This study evaluated the presence of major crustacean and fish pathogens in Gammarus lacustris populations from Kazakhstan and characterized associated viral communities using metagenomic sequencing. Six pooled samples collected from freshwater ecosystems across Kazakhstan were screened using PCR and RT-PCR assays targeting World Organisation for Animal Health (WOAH)-listed pathogens, including White Spot Syndrome Virus, Taura Syndrome Virus, Infectious Myonecrosis Virus, Aphanomyces astaci, and Aphanomyces invadans. In parallel, high-throughput sequencing (Illumina NovaSeq) was performed to assess virome composition and structure. No WOAH-listed pathogens were detected, suggesting a low detectable occurrence of major notifiable agents under the conditions of the present study. Metagenomic analysis revealed a virome dominated by RNA viruses, particularly picorna-like viruses (Picornaviridae), Dicistroviridae, and Marnaviridae. Phylogenetic and genome organization analyses identified potentially novel or highly divergent viral lineages within Picornavirales. Collectively, these findings suggest a favorable epizootiological profile of G. lacustris populations while highlighting freshwater amphipods as hosts of diverse and partially uncharacterized viral communities relevant to aquatic disease surveillance and aquaculture biosecurity.}, } @article {pmid42515020, year = {2026}, author = {Dalle Carbonare, L and Vareschi, A and Dervishi, K and Deiana, M and Locatelli, E and Minoia, A and Piritore, FC and Ruggiero, A and Barbu, IC and Zipeto, D and Piubelli, C and Valenti, MT}, title = {High-Touch, High-Risk: An Exploratory Microbiome Analysis of Hospital Wheelchairs.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/pathogens15070693}, pmid = {42515020}, issn = {2076-0817}, support = {FUR LDC//University of Verona/ ; FUR MTV//University of Verona/ ; Fondi Ricerca Corrente" - L3P6//Ministry of Health/ ; }, abstract = {In this exploratory pilot study, quantitative analyses were performed on seven leather wheelchairs and the protective barrier was evaluated on three leather wheelchairs, while shotgun metagenomic sequencing (Illumina and Oxford Nanopore) was conducted on pooled samples obtained from seven leather and three fabric wheelchairs to characterize microbial DNA recovered from wheelchair surfaces under routine clinical conditions. Microbial DNA and biomass were detected on all sampled surfaces, with median DNA concentrations of approximately 0.015 ng/µL, median cell counts of approximately 4.8 × 10[5] cells/mL, and median OD600 values of approximately 0.038, although variability among wheelchairs was observed. NGS analysis revealed heterogeneous microbial communities composed mainly of taxa associated with human skin microbiota and environmental sources. Opportunistic taxa including Escherichia coli, Staphylococcus haemolyticus, Achromobacter xylosoxidans, and Clostridioides difficile DNA were detected. Differences in microbial composition were observed between the pooled fabric and leather samples, with fabric samples characterized by the dominance of specific taxa and leather samples exhibiting a more heterogeneous microbial profile. In addition, median DNA concentration, cell counts, and OD600 values were reduced by approximately 98-100% on the protective barrier compared with uncovered wheelchair surfaces, with statistically significant differences between conditions. Overall, these findings suggest that hospital wheelchairs may harbor measurable levels of microbial biomass and microbial DNA despite routine sanitation procedures. Lower contamination levels were observed on the protective barrier under the conditions tested. Due to the exploratory nature of the study, the small sample size, and the use of pooled samples for metagenomic analyses, these observations should be interpreted with caution and require confirmation in larger studies.}, } @article {pmid42515023, year = {2026}, author = {Montoya, JG and Cho, SM and Smith, S and Gomez, CA and Contopoulos-Ioannidis, DG}, title = {The Hidden Risk of Toxoplasmosis in the Expanding Immunomodulated Host Population: A Call for Guidelines and Registries in Patients on Biologics, Small Molecules, and Cellular Therapies.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/pathogens15070696}, pmid = {42515023}, issn = {2076-0817}, abstract = {Targeted immunotherapies with biologics, small molecules, and CAR T-cell therapies have revolutionized treatment across autoimmune, chronic inflammatory, oncologic, and transplant-related conditions. However, they have also expanded the population of patients susceptible to opportunistic infections. Toxoplasma gondii (T. gondii), a globally prevalent parasite, has emerged as an underrecognized pathogen in this immunomodulated host population. Toxoplasmosis, in such patients, can occur either through reactivation of a chronic/latent/past infection or from an acute/primary infection and may be severe and even fatal. We present here the recommendations for such patients from the Remington Lab, the National Reference Center for Toxoplasmosis in the US. Screening for Toxoplasma infections is needed at baseline prior to starting targeted immunotherapy to identify seropositive patients who would benefit from prophylaxis or pre-emptive strategies and seronegative patients who would benefit from measures to prevent primary/acute infections. Prompt diagnosis of Toxoplasma disease (toxoplasmosis) with molecular tools (T. gondii PCR and/or agnostic metagenomics next-generation sequencing), and prompt initiation of anti-Toxoplasma therapy, can be lifesaving and prevent permanent neurocognitive sequelae and vision loss. The immunomodulatory effects of these therapies persist for several months after discontinuation, thereby extending the window of vulnerability. T. gondii-seropositive women are at increased risk of vertical transmission, even if targeted immunotherapy was discontinued several months before conception. We make a call for education, guidelines, prospective registries, targeted research, and addition of toxoplasmosis risk in the Warnings section of drug leaflets (and particularly so for T. gondii-seropositive women who intend to conceive after having been on targeted immunotherapies).}, } @article {pmid42515101, year = {2026}, author = {Weng, M and Zhou, G and Wu, Q and Chen, Q and Li, J and Wang, Z and Li, W}, title = {Mycobacterium tuberculosis and Mycobacterium avium Complex Cutaneous Co-Infection: Diagnostic and Therapeutic Challenges.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/pathogens15070774}, pmid = {42515101}, issn = {2076-0817}, abstract = {Cutaneous co-infection with Mycobacterium tuberculosis (MTB) and Mycobacterium avium complex (MAC) is extremely rare and easily missed due to overlapping histopathological features. We report a previously healthy, HIV-negative middle-aged woman who presented with a progressive destructive mass in the left inguinal-perineal region. Imaging revealed sinus tract formation, osteolytic bone lesions, and chronic inflammation in the right middle lobe of the lung. Initial metagenomic next-generation sequencing (mNGS) detected 3756 reads of the Mycobacterium tuberculosis complex (MTBC) and 111 reads of Mycobacterium intracellulare (M. intracellulare); the latter was interpreted as possible colonization or contamination because of its low abundance. Empirical anti-tuberculosis therapy produced only transient partial improvement, followed by paradoxical worsening, local recurrence, and new bone destruction. After a high suspicion of mixed infection, a MAC-directed combination regimen (including azithromycin and a short course of amikacin) was added, leading to complete clinical cure; subsequent repeat cultures confirmed the presence of MAC. This is the first report of cutaneous MTB-MAC co-infection in the inguinal-perineal region of an adult without overt immune abnormalities, accompanied by disseminated bone lesions. This case highlights that in regions where nontuberculous mycobacteria (NTM) are co-endemic, atypical destructive skin lesions with paradoxical worsening despite initial response to anti-tuberculosis therapy should raise suspicion of MAC co-infection. The combination of mNGS and conventional culture facilitates identification of mixed infections and guides precision therapy, but mNGS results must be interpreted cautiously in the clinical context.}, } @article {pmid42515556, year = {2026}, author = {Martino, F and Panmei, K and Duchen, D and Thomas, DL and Kandathil, AJ and Clipman, SJ}, title = {Read-Level Error Characterization of Rolling-Circle Amplification-Based Nanopore Sequencing of the Circular DNA Virome.}, journal = {Viruses}, volume = {18}, number = {7}, pages = {}, doi = {10.3390/v18070704}, pmid = {42515556}, issn = {1999-4915}, support = {1DP2DA056130-01/NH/NIH HHS/United States ; R01DA058567/NH/NIH HHS/United States ; }, abstract = {Oxford Nanopore technology enables cost-effective, portable, long-read analyses of pathogen genomes. Accurate detection and interpretation of small circular viral genomes, including Anelloviridae, remain challenging due to limited base-level error quantification in rolling-circle amplification (RCA)-derived datasets. Here, we characterized read-level sequencing error profiles using M13mp18, a 7.2 kb circular phage genome, subjected to 1X and 3X shearing during library preparation. M13mp18 DNA was serially diluted into pooled anellovirus-positive plasma DNA extracts. Using custom error-analysis pipelines, we quantified mismatch, insertion, and deletion rates and evaluated consensus reconstruction accuracy across simulated sequencing depths. Since metagenomic viromes contain mixtures of related genomes and uneven coverage across taxa, depth-normalized subsampling was used to assess the precision of read-level error estimates under heterogeneous coverage. Across four benchmarked datasets, per-base error rates ranged from 0.018 to 0.022 errors per aligned base. Complete M13mp18 reference reconstruction was achieved at input levels ≥ 4.6 log10 copies, and consensus sequences reached 100% identity at depths ≥ 15X when sufficient reads were available. Below 4.6 log10 input copies, recovery was inconsistent. These findings provide a controlled empirical characterization of read-level error behavior in RCA-derived nanopore sequencing and support the interpretation of circular DNA virome data generated in complex metagenomic backgrounds.}, } @article {pmid42515578, year = {2026}, author = {Meyer, C and Jackson, VLN and de Haan, F and Bolhuis, H and Allen, MJ and Monier, A and Brussaard, CPD}, title = {Infection Dynamics and Coexistence of Two Novel Arctic Phytoplankton Viruses.}, journal = {Viruses}, volume = {18}, number = {7}, pages = {}, doi = {10.3390/v18070726}, pmid = {42515578}, issn = {1999-4915}, support = {na//University of Amsterdam/ ; na//Royal Netherlands Institute for Sea Research/ ; }, abstract = {Marine algal viruses exhibit a high level of diversity, and closely related viruses targeting the same algal host species can stably coexist. Here we report an example of a single virus-host system concealing hidden complexity. We discovered two double stranded (ds) DNA viruses infecting the Arctic picophytoplankter Micromonas polaris coexisting in culture for over a decade. Genomic sequencing of the lysate originally characterized as MpoV-44T revealed that it comprises two distinct prasinoviruses with ~203-204 kb genomes (MpoV-44T.A and MpoV-44T.B), of which conserved regions only accounted for 36% (the nucleotide level). The viruses were subsequently separated and compared at both genomic and phenotypic levels. In dual infection studies using a single host strain under nutrient-replete conditions, MpoV-44T.A outcompeted MpoV-44T.B. Yet MpoV-44T.B-like viruses were more abundant than MpoV-44T.A-like ones in natural Arctic metagenomes. This apparent paradox may be explained by differences in host strain specificity and/or possible resilience to nutrient stress by MpoV-44T.B, which we hypothesize based on genomic data. This work unveils hidden virus diversity, illustrating that the dynamics of viral coexistence are not always easily predictable, and underscores the importance of studying the underlying mechanisms at play.}, } @article {pmid42515580, year = {2026}, author = {Yin, L and Huang, P and Xu, Y and Peng, O and Zhu, K and Xie, E and Yang, S and Liu, J and Li, X and Yan, Z and Qin, J and Lin, W}, title = {Avian Orthoreovirus in China: Molecular Evolution, Transmission Ecology, Immune Modulation, and Integrated Control in the Genomic Era.}, journal = {Viruses}, volume = {18}, number = {7}, pages = {}, doi = {10.3390/v18070728}, pmid = {42515580}, issn = {1999-4915}, support = {2023YFD1301800//the National Key R&D Program of China/ ; 2024090301, YF2025NYRC03 and 2024020101//the Science and Technology Plan Program of Yunfu city/ ; 2024CXTD15//the Fourth Round of Guangdong Provincial Modern Agricultural Industry Technology System Innovation Team Construction Project/ ; 2023B1212070018//the Science and Technology Plan Program of Guangdong Province/ ; }, abstract = {Avian orthoreovirus (ARV) has re-emerged as one of the most important viral pathogens affecting modern poultry production worldwide. In China, the epidemiological landscape of ARV has undergone a substantial transformation over the past decade, characterized by increasing genotypic diversity, frequent genome reassortment, an expanding host range, and recurrent vaccine-breakthrough outbreaks. Growing evidence indicates that contemporary ARV populations evolve within a dynamic multispecies transmission network shaped by intensive poultry production, host adaptation, and vaccine-associated selective pressures. Recent molecular studies have revealed extensive genetic heterogeneity among circulating strains and highlighted the limitations of conventional σC-based classification systems for accurately describing viral evolution, pathogenicity, and antigenic diversity. Whole-genome analyses further demonstrate that reassortment among chicken-origin, duck-origin, and goose-origin orthoreoviruses plays a pivotal role in generating novel viral variants with altered biological properties. In parallel, accumulating evidence suggests that ARV exerts broad immunomodulatory effects through the disruption of innate antiviral signaling, impairment of lymphoid organ function, interference with vaccine responsiveness, and the enhancement of susceptibility to secondary infections. These findings indicate that ARV should be regarded not only as an arthrotropic pathogen but also as an important immunopathological agent influencing flock health and productivity. This review summarizes current knowledge of ARV in China, with an emphasis on molecular epidemiology, genomic evolution, reassortment mechanisms, transmission ecology, immune interference, vaccine escape, and integrated prevention strategies. Particular attention is given to the increasing importance of whole-genome surveillance, phylodynamic analysis, and multispecies epidemiological monitoring for understanding contemporary ARV evolution. Future perspectives involving structural vaccinology, precision immunization, metagenomics-assisted surveillance, and predictive evolutionary modeling are also discussed. Collectively, sustainable ARV control will likely require genome-informed and adaptive prevention frameworks integrating virology, immunology, epidemiology, and precision poultry management.}, } @article {pmid42515587, year = {2026}, author = {Yuan, L and Zhang, N and Yuan, M and Xu, J and Liu, Z and Li, Z}, title = {Novel Species Diversity in China's Northeastern Border Region.}, journal = {Viruses}, volume = {18}, number = {7}, pages = {}, doi = {10.3390/v18070735}, pmid = {42515587}, issn = {1999-4915}, support = {No. 2025ZD01900100//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project/ ; }, abstract = {The northeastern region of China is characterized by complex ecosystems, including forests and wetlands, and borders North Korea, Russia, and Mongolia. It serves not only as a natural reservoir for various microorganisms but also as a critical geographical and ecological hub for cross-border exchanges in Northeast Asia. Based on metagenomics and meta-transcriptomics investigations, this study systematically reviews the current research status of novel pathogens in the northeastern border region of China. It systematically organizes the newly discovered species, their classifications, and geographical distributions, with a focus on analyzing novel viruses that have potential pathogenicity to humans. The novel viruses identified in the northeastern border region belong to 11 viral families, including 9 from the Nairoviridae, 4 from the Rhabdoviridae, 3 each from the Astroviridae, Picornaviridae, and Parvoviridae, and 1-2 from other viral families, indicating a broad diversity of newly discovered viruses. These novel viruses are found in a wide range of hosts, including humans, ticks, minks, Marmota sibirica, and Myodes rufocanus, underscoring the significant public health risks these viruses pose. Geographically, the novel viruses discovered in the northeastern border region show a clustering pattern, with new species primarily concentrated in areas bordering Russia and North Korea. This highlights the unique role of the region as a hotspot for cross-border pathogen transmission and risk. The findings provide a systematic scientific reference for understanding the spectrum of unknown novel pathogens and their geographical distribution in the northeastern border region, assessing the risk of emerging infectious diseases, and optimizing active surveillance systems.}, } @article {pmid42515641, year = {2026}, author = {Liu, W and Wang, Y and Ma, J and Liang, X and Yang, L}, title = {Composting Restructures Chicken Manure Viral Communities and Attenuates Virus-Associated Antibiotic Resistance Signals: Paired Metagenome and Virome Analyses.}, journal = {Viruses}, volume = {18}, number = {7}, pages = {}, doi = {10.3390/v18070789}, pmid = {42515641}, issn = {1999-4915}, support = {42407182//National Natural Science Foundation of China/ ; }, abstract = {Composting is widely used to reduce biological risks during manure recycling, but changes in viral communities and virus-associated antibiotic resistance genes (ARGs) remain poorly resolved. This study aimed to assess changes in DNA viral communities, eukaryotic viral protein signals, virus-associated ARGs, and predicted virus-host linkages during chicken manure composting using paired analyses of total-community metagenomes and viral-particle-enriched viromes. Both approaches recovered viral assemblages dominated by Uroviricota and lytic viruses but produced distinct profiles. Viromes yielded more taxonomically assigned viral operational taxonomic units and a higher proportion of relatively complete viral genomes, whereas metagenomes produced a larger predicted virus-host network. Composting restructured viral communities, reducing manure-associated genera and enriching stage-specific groups. Eukaryotic viral protein signals declined during composting. Virus-associated ARGs accounted for 24.83-38.76% of ARG abundance in metagenomes and 5.38-45.09% in viromes, with lower abundance and richness in viromes. Selected virus-associated ARGs showed transient early enrichment, particularly in the virome. By maturity, both overall virus-associated ARG signals and higher-risk ARG signals had declined. Predicted virus-host associations included bacterial groups containing potential opportunistic pathogens. These results show that composting restructures viral communities and attenuates virus-associated ARG signals, while metagenomes and viromes provide complementary but non-interchangeable views of viral ecology and ARG risk.}, } @article {pmid42515794, year = {2026}, author = {Frăsinariu, OE and Ștreangă, V and Rugină, AL and Mîndru, DE and Vintilă, TC and Bădulescu, OV and Bararu-Bojan, I and Lupu, VV and Lupu, A and Mihai, A and Loghin, II and Popescu, DE and Teșoi, DF}, title = {Gut Microbiota and Metabolic Dysfunction-Associated Steatotic Liver Disease: From Dysbiosis to Metagenomic Insights and Therapeutic Perspectives.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {19}, number = {7}, pages = {}, doi = {10.3390/ph19071113}, pmid = {42515794}, issn = {1424-8247}, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) has emerged as the most common chronic liver disorder in the pediatric population, closely paralleling the global rise in childhood obesity. Increasing evidence highlights the gut-liver axis as a key contributor to MASLD pathogenesis, with gut microbiota dysbiosis influencing hepatic steatosis through multiple interconnected mechanisms, including increased intestinal permeability, endotoxemia, altered bile acid metabolism, and modulation of host energy homeostasis. In children, the characterization of microbiota signatures associated with MASLD remains challenging due to heterogeneity across studies, age-related microbial dynamics, and methodological variability. This review synthesizes current evidence regarding the role of the gut microbiota in pediatric MASLD, focusing on pathogenetic pathways, reported microbial patterns, and microbiota-targeted therapeutic strategies, while incorporating relevant mechanistic evidence from adult studies where pediatric data remain limited. Although several taxa have been repeatedly associated with pediatric MASLD, findings are not yet sufficiently consistent for clinical application. Interventions such as probiotics, prebiotics, and dietary modulation show promising but still preliminary results, with limited high-quality pediatric trials available. A deeper mechanistic understanding and standardized study designs are needed to clarify causality and to support microbiota-based precision approaches in pediatric MASLD management.}, } @article {pmid42515825, year = {2026}, author = {Kean, K and Mayne, RM and Reid, K and Secret, S and Singleton, BK and Rockett, R and Rajendra, P and Harvala, H and Breuer, J and Azim Ansari, M and Lythgoe, K and Simmonds, P and Golubchik, T}, title = {A Snapshot of the UK Blood Donor Plasma Virome: A Retrospective Cross-Sectional Cohort Study.}, journal = {Journal of medical virology}, volume = {98}, number = {8}, pages = {e71081}, doi = {10.1002/jmv.71081}, pmid = {42515825}, issn = {1096-9071}, support = {NIHR203338//National Institute for Health and Care Research/ ; }, abstract = {Estimates of population prevalence and genetic diversity of bloodborne viruses in healthy humans are essential to support population-scale monitoring for transfusion transmission risk. In the UK and globally, blood donations are routinely screened for a limited number of high-consequence pathogens, but the full composition of the plasma virome remains to be characterized. Using a novel quantitative targeted metagenomics sequencing approach, we analyzed previously unscreened plasma donations collected by NHS Blood and Transplant in England for all major pathogenic and known commensal human bloodborne viruses, and quantified their viral burden. Here we show that in a representative sample of 5064 UK blood donors in pools of 24 collected over a 1-month period, the virome was dominated by a small number of largely persistent species, representing < 10% (10/106) of previously identified human bloodborne viruses. The principal genera of human anelloviruses (TTV, TTMV and TTMDV) were detected in 89% of pools, albeit at low read count, inconsistent with measured anellovirus viral loads. In contrast, human pegivirus type 1 (HPgV-1), had an estimated population prevalence of 3.7% (95% CI 3.0%-4.4%), with high read count and complete genome recovery in around one half of positive pools, consistent with high titer in plasma. Less common detections included one species of gemykibovirus in five separate plasma pools, one hepatitis C virus (genotype 1a), and polyomaviruses and herpesviruses with prevalences between 0.04% (parvovirus 4, BK polyomavirus) to 0.41% (human herpesvirus 6). Phylogenetic analyses revealed mixed TTV, TTMV, and TTMDV populations and almost exclusively genotype 2 HPgV-1, consistent with known genotype distributions in Europe. Our results provide a baseline for describing the healthy plasma virome in UK blood donors.}, } @article {pmid42515960, year = {2026}, author = {Kopp, AR and Uhlemann, AC}, title = {Gut dysbiosis and multidrug-resistant colonization in solid organ transplantation.}, journal = {Current opinion in organ transplantation}, volume = {}, number = {}, pages = {}, doi = {10.1097/MOT.0000000000001303}, pmid = {42515960}, issn = {1531-7013}, abstract = {PURPOSE OF REVIEW: The purpose of this review is to summarize recent advances in the understanding of the interplay between gut dysbiosis and MDRO colonization and infection in SOT patients.

RECENT FINDINGS: Recent studies have added complementary metagenomics, internal transcribed spacer sequencing, metabolomics, and pathway analysis to descriptive microbiome profiling. Enhanced ecologic frameworks have identified microbial, functional, and clinical signatures associated with MDRO colonization and infection. Microbiome-targeting interventions are emerging as strategies to reduce morbidity associated with MDRO infection.

SUMMARY: MDRO infection is a significant cause of post-transplant mortality. Persistent gut dysbiosis peri-transplant reduces colonization resistance and predisposes patients to adverse clinical outcomes. Understanding the dynamics of this process will aid in the care of these high-risk patients.}, } @article {pmid42516269, year = {2026}, author = {López-Martínez, KP and Hereira-Pacheco, S and Hernández-Oaxaca, D and López-Ruiz, F and Vázquez-Rosas-Landa, M}, title = {rbims: an R package for integrative functional profiling and pathway-level discrimination in metagenome-assembled genomes.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1831383}, pmid = {42516269}, issn = {2673-7647}, abstract = {Metagenomics enables the recovery of metagenome-assembled genomes (MAGs), providing access to the metabolic potential of uncultured microbial communities that drive ecosystem function and biogeochemical cycles. However, as MAGs datasets increase in size and complexity, comparing functional repertoires and identifying ecologically meaningful traits across experimental gradients becomes increasingly difficult. Here, we present rbims, a modular R package for integrative functional profiling of MAGs and metagenomic datasets. rbims supports annotations from KEGG, dbCAN, InterProScan, MEROPS, and PICRUSt2, and enables the calculation of gene presence/absence, raw abundance, and pathway coverage, as well as metadata-informed comparative analyses and publication-ready visualizations. Beyond descriptive profiling, rbims implements an exploratory discriminant framework that combines compositional differential analysis (ALDEx2) with random forest-based feature ranking to prioritize candidate metabolic traits associated with environmental factors. Importantly, it extends gene-level analysis to pathway-level directional bias testing, allowing users to evaluate whether the majority of genes within a metabolic route are consistently enriched toward a given condition. We applied rbims to 42 MAGs recovered from a hydrocarbon enrichment experiment in the North Atlantic Ocean. The workflow identified widespread hexadecane and phenanthrene degradation potential, detected enriched oxidoreductase-related protein families, and revealed a strong pathway-level directional bias toward deep-water MAGs for phenanthrene, naphthalene, and hexadecane degradation pathways. By integrating annotation parsing, quantitative trait analysis, statistical discrimination, and visualization in a reproducible framework, rbims provides a user-friendly platform for functional interpretation in genome-resolved metagenomics.}, } @article {pmid42516368, year = {2026}, author = {Zhang, Y and Wang, S and Chang, S and Li, Y and Dang, Y and Wang, Z}, title = {Navigating the gut-metabolite-immune axis: enhancing efficacy and mitigating toxicity of immune checkpoint inhibitors.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1803970}, pmid = {42516368}, issn = {1664-3224}, abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized the oncological landscape by disrupting inhibitory pathways, notably programmed cell death protein-1/programmed death-ligand 1 (PD-1/PD-L1) and cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4) pathways, thereby reinvigorating host antitumor immunity. Although these agents have emerged as frontline standard therapies for malignancies, their clinical utility remains limited. Interpatient therapeutic variability is inextricably linked to the composition and functional capacity of the gut microbiome. The underlying mechanisms appear to involve a complex dialogue between the microbiota and host immune system, where microbial metabolites serve as critical mediators in remodeling the tumor microenvironment. Despite these insights, progression in the field remains constrained due to heterogeneity in study cohorts and sample-processing methodologies, hindering the establishment of reproducible individualized predictive models and clinical intervention strategies. Consequently, there is an urgent need to systematically delineate the microbiome-metabolite-immune axis to optimize the balance between ICI efficacy and systemic toxicity. By synthesizing the latest evidence, this review aimed to highlight the pivotal roles of specific taxa, including Bacteroides, Bifidobacterium, and Akkermansia muciniphila, in ICI efficacy. These microbes and their metabolic byproducts potentiate therapeutic responses by enhancing dendritic cell cross-presentation and promoting CD[8+] T-cell infiltration, often via activation of the cyclic GMP-AMP synthase-stimulator of interferon genes or nucleotide-binding oligomerization domain-containing protein 2 signaling pathways. Furthermore, these microbial components demonstrate the ability to protect the heart and colon against inflammation and barrier disruption, thereby mitigating immune-related adverse events. Although the feasibility and safety of interventions such as fecal microbiota transplantation and supplementation with next-generation encapsulated probiotics, postbiotics, or dietary fiber have been demonstrated in preclinical and Phase I trials, substantial hurdles remain. Future progress requires large-scale, multicenter, standardized, longitudinal studies integrating metagenomics and metabolomics to construct robust cross-cancer and cross-population predictive models. Such rigorous validation would enable the development of precise microbial interventions that maximize therapeutic gains while minimizing the incidence of adverse reactions.}, } @article {pmid42516434, year = {2026}, author = {Pan, M and Wei, Y and Luo, C and Lin, H and Lu, W and Lin, Y and Mai, Z and Deng, J and Huang, Y and Yu, H and Huang, J and Zhang, J}, title = {Tracheobronchial invasion by nontuberculous mycobacteria: a rare but overlooked clinical manifestation-a multicenter retrospective analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1872833}, pmid = {42516434}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis/epidemiology/pathology ; Female ; *Nontuberculous Mycobacteria/pathogenicity/isolation & purification ; Male ; Aged ; Bronchoscopy ; Middle Aged ; *Bronchi/microbiology/pathology ; Aged, 80 and over ; Tomography, X-Ray Computed ; }, abstract = {BACKGROUND: Nontuberculous mycobacteria (NTM) can disseminate and infect various organs throughout the body. However, whether NTM can infect tracheobronchial tissue is rarely reported. This study aimed to address the knowledge gap regarding the epidemiological, demographic, and clinical characteristics of patients with tracheobronchial NTM infection.

METHODS: In this multicenter retrospective cohort study, clinical, demographic, microbiological, and radiological data from hospitalized patients with tracheobronchial NTM infections from January 2015 to May 2025 were collected and analyzed descriptively.

RESULTS: Twenty-nine patients (2.3%) were included, and all the patients presented with disseminated NTM infection. Seventeen patients had comorbidities, including 5 with acquired immunodeficiency syndrome and 1 with anti-interferon-γ autoantibody syndrome. Median diagnostic delay was 130 days, and 89.7% of the patients were initially misdiagnosed with tuberculosis or malignancy. The most common symptoms were cough, expectoration, anemia, fever, weight loss, skin lesions, and bone pain. Chest CT revealed nodules, patchy opacities, mass-like shadows, and bronchial stenosis, with or without hilar/mediastinal lymphadenopathy, whereas osteolytic bone destruction was evident in 11 patients. The most common features of bronchoscopy were intraluminal masses/neoplasms/nodules. Metagenomic next-generation sequencing (mNGS) of BALF (n=12) demonstrated 100% positivity, outperforming BALF culture (46.2%, 12/26) and sputum culture (39.3%, 11/28). Mycobacterium colombiense accounted for 24.1% of cases. With respect to therapeutic management, 27 patients received systemic antimicrobial therapy, while 2 did not receive specific anti-N™ treatment. One patient underwent combined endoscopic resection. Overall, 23 patients (79.3%) achieved improvement or cure, 5 showed disease progression, 1 experienced relapse, and 1 died.

CONCLUSIONS: Tracheobronchial NTM infection is rare but clinically significant, often occurring in the context of disseminated disease with pulmonary involvement. Immunocompromised hosts, particularly those with AIDS or anti-IFN-γ autoantibody syndrome, are highly susceptible. Bronchoscopy typically reveals mass lesions causing luminal stenosis or occlusion. In this cohort, M. colombiense was the most frequently isolated NTM species. Early bronchoscopy, mNGS-based pathogen detection, and timely systemic or endoscopic intervention should be considered to prevent irreversible airway stenosis. Further studies are needed to validate optimal treatment strategies.

CLINICAL TRIAL REGISTRATION: https://www.ClinicalTrials.gov, identifier NCT07377864.}, } @article {pmid42516567, year = {2026}, author = {Figueroa-Pratts, PG and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA}, title = {Optimized Field Collection and Gut Dissection Workflows for Microbiome Studies of the Citrus Root Weevil, Diaprepes abbreviatus.}, journal = {Bio-protocol}, volume = {16}, number = {14}, pages = {e5761}, pmid = {42516567}, issn = {2331-8325}, abstract = {Careful dissection of insect gut tissues is essential for microbiome studies to ensure accurate characterization of internal microbial communities and preservation of DNA integrity. Because insect-associated microbiomes are highly sensitive to contamination, effective removal of external microbes prior to dissection is critical to minimize bias in downstream analyses. While ethanol- and bleach-based surface sterilization methods are commonly used, standardized workflows integrating field collection, sterilization, and dissection remain limited. Here, we present a step-by-step protocol for the field collection, surface sterilization, and dissection of gut tissues from the agricultural pest Diaprepes abbreviatus (Coleoptera: Curculionidae), optimized for genomic DNA extraction and microbiome analyses. Using wild-caught specimens, this workflow incorporates a rigorous surface sterilization and dissection strategy that minimizes external contamination while preserving biologically relevant microbial signatures and DNA integrity for downstream microbiome analyses. The protocol provides a standardized framework for insect gut microbiome studies and can be broadly adapted to other wild-caught insect species requiring careful collection, disinfection, and sterile dissection prior to molecular analysis. The protocol integrates field collection and laboratory processing steps into a streamlined workflow that minimizes contamination while preserving tissue integrity for downstream applications. Key features • Designed for wild-caught Diaprepes abbreviatus collected directly from agricultural host trees, this protocol can also be adapted for other insect species. • Integrates field collection, surface sterilization, and sterile gut dissection into a single workflow to minimize contamination. • Sequential ethanol and diluted bleach treatment effectively removes external microbes prior to dissection. • Enables isolation of intact gut tissues suitable for high-quality DNA extraction and downstream microbiome sequencing.}, } @article {pmid42517159, year = {2026}, author = {Xie, T and Xu, JY and Lin, D and Liu, Y and Wang, YF and Yang, ZG and Lee, PKH and Zhu, D}, title = {Cigarette Butts as an Emerging Urban Habitat Driving Microbial Niche Differentiation.}, journal = {Research (Washington, D.C.)}, volume = {9}, number = {}, pages = {1380}, pmid = {42517159}, issn = {2639-5274}, abstract = {Cigarette butts are common yet overlooked pollutants in urban environments. How this anthropogenic niche shapes microbial life-history strategies and evolutionary mechanisms remains poorly understood, limiting assessments of microbial adaption and urban ecosystem health. However, systematic and multiscale evidence on the ecological effects of cigarette butts on microbial communities remains scarce. Here, we collected cigarette butts, litter, and soil samples from urban parks in 35 Chinese cities and integrated third-generation 16S ribosomal RNA sequencing, metagenomics, and transcriptomics to resolve microbial community composition, functional potential, and evolutionary patterns. The results revealed that microbial communities in cigarette butts were shaped by strong deterministic processes, showed low spatial heterogeneity, and were taxonomically distinct from those in natural niche (i.e., litter) and surrounding soil, with notable enrichment of Proteobacteria, particularly the family Pseudomonadaceae. Functional trait analysis showed that butt-associated communities favored environmental responsiveness and fast-growth strategies, contrasting with metabolism- and resource acquisition-oriented strategies in the litter. Population genomic analysis suggested stronger positive selection in cigarette butt-associated Pseudomonadaceae, while the pure culture experiment provided strain-level evidence that cigarette butt exposure induced the up-regulation of key functional genes in Pseudomonas aeruginosa PAO1. This study demonstrates that cigarette butts, as an emerging ecological niche, reshape microbial community assembly, life-history strategies, and adaptive evolution, offering new insights into microbe-driven evolution on artificial surfaces.}, } @article {pmid42517538, year = {2026}, author = {Fehr, D and Flack, N and Masenga, G and Mosha, N and Li, N and White, A and Semango, G and Distler, M and Lang, C and Grimm, F and Scharl, M and Mavura, D and Masenga, JE and Schmid-Grendelmeier, P and Brüggen, MC}, title = {Dietary Habits and Atopic Dermatitis Significantly Influence the Fecal Microbiome.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.70459}, pmid = {42517538}, issn = {1398-9995}, support = {LF-OC-20-000418//LEO Fondet/ ; 0456/2024//Vontobel-Stiftung/ ; //Bruno Bloch Stiftung/ ; }, abstract = {BACKGROUND: Atopic dermatitis (AD) has been associated with microbial gut dysbiosis in children. Data in adults is scarce.

OBJECTIVE: We sought to explore the fecal microbiome composition in AD patients versus healthy controls (HC) and investigate the impact of environmental aspects such as the geographical location and dietary habits.

METHODS: In this case control study, a total of 140 fecal samples from 69 AD patients and 71 HC from Tanzania (TZ) and Switzerland (CH) were analyzed. Illumina shotgun metagenomics sequencing was performed followed by taxonomic profiling, calculation of alpha/beta diversity, and permutational multivariate analysis of variance. Differentially abundant species and genera between AD and HC were evaluated.

RESULTS: Alpha diversity (Shannon Index) did not significantly differ between AD and HC. The presence of AD was identified as a significant source of fecal microbiome variation (Bray-Curtis beta diversity). On the species level, Faecalibacterium taiwanense was more abundant in AD, and Vescimonas sp000435555 in HC. On the genus level, CAG-302 (NCBI: Clostridium) was more abundant in HC. Geographical location was associated with distinct dietary habits. Prevotella was significantly more abundant in TZ, whereas Alistipes and Bacteroides were significantly more abundant in CH.

CONCLUSIONS: The presence of AD significantly impacted the fecal microbiome variation and was associated with a particular microbial composition. The impact of geographical location on the fecal microbiome may be related to nutritional differences. Our data support the rationale of a gut-skin axis and pave the way towards therapeutic approaches modulating the microbiome.}, } @article {pmid42517626, year = {2026}, author = {Price, DC and Bezhani, FL and Meng, Z and Porfirio-LaStrapes, M and Wagner, NE and Javanmard, M and Han, T and Barnes, MM}, title = {Metaviromic profiling of mosquito excreta using superhydrophobic collection devices expands the known RNA virome of North America.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0093826}, doi = {10.1128/spectrum.00938-26}, pmid = {42517626}, issn = {2165-0497}, abstract = {Nearly 30% of emerging infectious disease events worldwide are transmitted by arthropod vectors, and this proportion continues to rise. Rapid and accurate detection is critical for directing vector control interventions, thereby reducing the likelihood of widespread transmission. Surveillance of infected mosquitoes can provide an early warning of impending human infection; however, conventional virus testing relies on processing large pools of mosquitoes and requires labor-intensive pre-processing. During rapidly developing epidemic or panzootic events, these delays may limit the effectiveness of public health responses. Mosquito excreta has recently emerged as a promising alternative substrate for pathogen detection. Sugar-fed mosquitoes regularly excrete gut contents, offering a rich source of nucleic acids. In this study, we developed and applied custom superhydrophobic excreta-collection funnels that efficiently aggregate excreta produced by field-collected Culex mosquitoes into attached microcentrifuge tubes. Shotgun metagenomic sequencing of this material revealed a diverse RNA virome, including both globally distributed viruses and those reported here for the first time from the Americas. Beyond virus detection, additional analyses enabled confirmation of host mosquito species and identification of trypanosomatid parasites, demonstrating the broader utility of mosquito excreta for integrated surveillance. We anticipate that methods and devices of this type will become valuable components of vector surveillance programs, particularly in remote or resource-limited settings where repeated collections are challenging. Overall, our findings highlight the potential of excreta-based monitoring to improve early detection of emerging or unknown pathogens of One Health importance, refine our understanding of mosquito virome biogeography, and facilitate the discovery of previously undescribed viruses.IMPORTANCEMany infectious diseases that affect people and animals are spread by mosquitoes and other biting insects, and the number of these outbreaks is increasing. Detecting pathogens in mosquito populations early can provide a critical warning before human cases begin, allowing health officials to act quickly. However, traditional surveillance requires collecting and processing large numbers of mosquitoes, which can be slow and labor-intensive during fast-moving outbreaks. Here we demonstrate a simpler approach: testing mosquito waste. When mosquitoes feed on sugar, they excrete material that contains genetic traces of viruses and other organisms. Using specially designed collection devices and modern genetic sequencing, we show that mosquito excreta can reveal a wide range of viruses and parasites while also identifying the mosquito species present. This method could make disease surveillance faster and more practical in remote or resource-limited settings, improving our ability to detect emerging pathogens that threaten human, animal, and environmental health.}, } @article {pmid42518002, year = {2026}, author = {Gao, Y and Dong, J and Peng, O and Yan, Z and Chen, M and Yin, Y and Sun, M and Zhang, J and Huang, Y and Xiang, Y and Qi, Z and Ge, J and Qin, L and Li, L and Zhang, Y}, title = {A novel Chaphamaparvovirus detected in breeding Muscovy Ducks with hepatitis.}, journal = {Veterinary research communications}, volume = {50}, number = {5}, pages = {}, pmid = {42518002}, issn = {1573-7446}, support = {202110TD, R2020PY-JX014, R2020QD-049, R2020PY-JC001//Special Fund for Scientific Innovation Strategy-Construction of High Level Academy of Agriculture Scienc/ ; 2023B1212060040//Guangdong Province Key Laboratory of Livestock Disease Prevention/ ; }, abstract = {Since 2022, a decrease in egg production and hatchability, along with hepatitis-like symptoms, has been frequently reported in Muscovy duck farms in southern China. Using metagenomic sequencing, a novel Chaphamaparvovirus (ChPV), designated MuChPV-GD2022, was detected in the livers of the diseased ducks. Phylogenetic analysis revealed that the MuChPV-GD2022 strain shares 61.8-77.4% genome identity with duck-origin Chaphamaparvoviruses, and 44.3-77.4% with avian-origin Chaphamaparvoviruses. The NS1 protein amino acid sequence showed a 29.3-71.5% similarity to those of other known Chaphamaparvoviruses. These findings support the classification of MuChPV-GD2022 as a new species in the genus Chaphamaparvovirus, family Parvoviridae. Since virus isolation was not achieved due to technical constraints, the evidence suggests MuChPV may be associated with the hepatitis-like disease. Furthermore, a TaqMan qPCR assay targeting NS1 gene of the virus was developed and validated for specificity, sensitivity, and repeatability, which provides a sensitive tool not only for virus detection but also for epidemiological surveillance of MuChPV infections.}, } @article {pmid42518032, year = {2026}, author = {Li, F and Zhao, H and Lei, Y and Luo, J and Chen, B and Li, C and Zhao, X and Jiang, H}, title = {Fufangteng Yixin Formula alleviates myocardial ischemia-reperfusion injury by modulating gut microbiota and resultant metabolites in rats.}, journal = {Journal of natural medicines}, volume = {}, number = {}, pages = {}, pmid = {42518032}, issn = {1861-0293}, support = {2024GXNSFBA010207//Guangxi Natural Science Foundation Joint Special Project/ ; }, abstract = {This study aimed to explore whether Fufangteng Yixin Formula (FFTYXF) can ameliorate myocardial ischemia-reperfusion injury (MIRI) by regulating the gut microbiota and resultant metabolites. Wistar rats were given FFTYXF by gavage for 7 days, and MIRI rat model was established. Serum level of inflammatory markers was determined by ELISA, and heart function was evaluated by echocardiography. Myocardial histological changes and infarct size were examined by hematoxylin-eosin and triphenyltetrazolium chloride staining, respectively. 16S rRNA gene and metagenomics analyses were employed to explore gut microbiota, while untargeted metabolomics analysis was used to explore serum metabolites. FFTYXF pretreatment could significantly improve cardiac function, reduce infarct size, decrease level of inflammatory factors (TNF-α and IL-6) and inflammatory cells infiltration. At genus level, g__Oscillibacter and g__Rikenellaceae_RC9_gut_group were identified as key microbial bacteria in MIRI rat response to FFTYXF pretreatment. After FFTYXF pretreatment, the functional categories of gut microbiota were participated in fatty acid (FA) biosynthesis/metabolism, glycolysis _ gluconeogenesis and sphingolipid metabolism. Genes response to FFTYXF pretreatment in MIRI rats included K00023 (phbB), K00281 (GLDC, gcvP), K03879 (ND2), K07827 (KRAS) and K15192 (BTAF1), and they were mainly participated in carbon, butanoate, glyoxylate and dicarboxylate metabolism. Differential metabolites were also mainly participated in FA biosynthesis/metabolism, such as alpha-Linolenic acid, omega-3/omega-6 FA, and flavan-3-ol metabolic pathway. Abundance of g__Rikenellaceae_RC9_gut_group positively correlated with differential metabolites FAHFA 34:0, FAHFA 16:1/18:3, and FA 24:5. FFTYXF could alleviate MIRI by modulating gut microbial bacteria alteration and resultant metabolites, particularly short-chain FAs.}, } @article {pmid42518220, year = {2026}, author = {Di, D and Wang, S and Qiu, W and Gai, X and Xiao, J and Wang, S and Zhuo, R and Chen, G}, title = {Multi-omics analysis reveals the mechanisms on biochar-mediated cadmium transport in Salix: insight into rhizosphere phosphorus-iron coupling and transporter expression.}, journal = {Tree physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/treephys/tpag104}, pmid = {42518220}, issn = {1758-4469}, abstract = {Biochar addition promoted cadmium (Cd) phytoremediation of woody plants, especially phosphors (P)-modified biochar. However, the underlying mechanism on the uptake and transport of Cd mediated by biochar remains unclear. Here, we integrated the physiological, metagenomics, transcriptomics, and in situ laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) imaging analysis to investigate how bamboo biochar (BBC) and phytic acid modified biochar (PABC) impact Cd accumulation and transport in Salix J1010 through root-soil interface. Our results showed that PABC significantly increased Cd translocation from roots to aboveground by 77.9% and total Cd accumulation in plan by 203%, respectively. Iron plaque emerged as a key factor, with PABC-mediated inhibition of iron plaque (-44.6%) accelerating Cd uptake. This iron plaque decrease is closely accompanied by the decreased soil redox potential (Eh), enriched resin-P and inorganic P fractions, and potential coupling of P mineralization and Fe(III)-reducing processes in the rhizosphere soil. Transcriptomics analysis further revealed that PABC influenced root metal transporter expression, downregulating vacuolar sequestration-related ABC, CAX, MTP gene families, while upregulating most ZIP, HMA, and YSL genes families involved in xylem loading. LA-ICP-MS imaging corroborated the enhanced Cd transport in xylem tissue. PABC enhanced leaf cell-wall Cd binding and antioxidant defenses, thereby promoting Cd detoxification and accumulation. Collectively, the enhanced phytoremediation capacity of willow was driven by coordinating trade-offs across multiple levels, including the rhizosphere, subcellular scales, and whole-plant. The results provide a mechanistic basis for biochar-assisted phytoremediation strategies in Cd-contaminated soils.}, } @article {pmid42518254, year = {2026}, author = {Van Etten, J and Johnson, MD}, title = {Beyond adaptive gene transfers: a primer on horizontal gene transfer across scales.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icag125}, pmid = {42518254}, issn = {1557-7023}, abstract = {Horizontal gene transfer (HGT) is a fundamental ecological and evolutionary process involving the movement of genetic material across taxa within a single generation. While traditionally studied at the level of individual genes with encoded adaptive functions, recent advances in genomics and metagenomics highlight the need for a broader, integrative framework. Here, we expand the concept of the "ecology of DNA transfer," which conceptualizes HGT as a multi-layered process spanning the genome, cell, and ecological context. We further explore how the fate and expression of transferred DNA vary over evolutionary timescales, from recently acquired, transcriptionally silenced sequences to ancient, fully integrated genes. Together, this framework underscores HGT as a dynamic, context-dependent process shaped by interactions across biological scales.}, } @article {pmid42518807, year = {2026}, author = {Hamiyeh, R and Salhab, Z and Bahmad, HF and Abou Fayad, AG and Abou-Kheir, W}, title = {Anticancer natural products from the Middle East and North Africa: biodiversity, mechanisms, and translational challenges.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1846357}, doi = {10.3389/fonc.2026.1846357}, pmid = {42518807}, issn = {2234-943X}, abstract = {Cancer remains one of the leading causes of morbidity and mortality worldwide, imposing substantial clinical, societal, and economic burdens. Despite major advances in surgical oncology, systemic chemotherapy, radiation therapy, molecularly targeted therapeutics, and immune checkpoint inhibition, contemporary cancer treatment remains constrained by dose-limiting toxicities, intratumoral and intertumoral heterogeneity, and the inexorable emergence of multifaceted drug resistance mechanisms. These persistent therapeutic challenges have reinstated interest in natural products (NPs) as evolutionarily refined sources of anticancer agents characterized by structurally diverse molecular targets and pleiotropic mechanisms of action. Indeed, a substantial proportion of currently approved anticancer drugs are either directly derived from or structurally inspired by natural compounds. This comprehensive review examines the role of NPs as anticancer agents, with particular emphasis on bioactive compounds isolated from plants, fungi, marine organisms, and environmental bacteria indigenous to the Middle East and North Africa (MENA) region. We summarize exemplary MENA-derived NPs demonstrating cytotoxic, antiproliferative, pro-apoptotic, anti-angiogenic, anti-metastatic, and immunomodulatory activities across a wide range of preclinical cancer models. Mechanistically, these compounds converge on critical oncogenic signaling networks, including p53-caspase apoptotic cascades, NF-κB transcriptional inhibition, reactive oxygen species modulation, cell-cycle arrest, epigenetic reprogramming, and suppression of tumor invasion and chronic inflammation. In parallel, we highlight transformative technological innovations-including high-throughput phenotypic and biochemical screening platforms, metagenomics, genome mining algorithms, biosynthetic gene cluster activation, and synthetic biology approaches-that are fundamentally reshaping NP discovery and enabling access to previously cryptic or unculturable microbial biosynthetic pathways. These methodological advances, coupled with multi-omics integration, artificial intelligence-driven compound prediction, and heterologous expression systems, are accelerating the identification and characterization of structurally novel anticancer agents. Collectively, the evidence presented underscores the MENA region as a significantly underexplored yet exceptionally promising biodiverse reservoir of anticancer NPs with substantial therapeutic potential. Strategic harnessing of this biodiversity through interdisciplinary collaborative research, ethically governed bioprospecting frameworks, and translational development pipelines may yield structurally innovative, mechanistically distinct, and potentially safer therapeutic modalities to complement existing cancer treatments and address critical unmet clinical needs in precision oncology.}, } @article {pmid42519007, year = {2026}, author = {Zhao, Z and Zhao, F and Zhang, M and Sun, J and Wang, X and Lou, J and She, R and Kwok, LY and Sun, Z and Huangfu, W and Menghe, B}, title = {Multi-omics profiling reveals gut microbiome signatures associated with cognitive decline in Alzheimer's disease.}, journal = {iScience}, volume = {29}, number = {8}, pages = {116622}, doi = {10.1016/j.isci.2026.116622}, pmid = {42519007}, issn = {2589-0042}, abstract = {Alzheimer's disease (AD) is increasingly being linked to gut microbial dysbiosis via the gut-brain axis. We applied integrated metagenomics and metabolomics to characterize gut microecology in 28 patients with AD and 33 controls. Metagenomic analysis revealed distinct microbial community structures, with increased abundance of Akkermansia massiliensis, Alistipes onderdonkii, and Barnesiella intestinihominis in AD. Phageome analysis revealed increased richness and altered composition, with more Podoviridae and fewer Microviridae. Functional profiling identified shifts in microbial metabolic pathways involving tryptophan and short-chain fatty acid metabolism. Untargeted metabolomics revealed elevated fecal spermidine, taurocholate, and glycerophosphocholine levels in patients with AD. A random forest model combining metabolites, gut metabolic modules, and bacteriophages achieved good within-cohort classification (AUC = 0.83) but lacked external validation due to unavailable matched fecal metabolomic data. Overall, these findings link AD to coordinated disruptions across bacterial, viral, and metabolic gut layers, highlighting the need for external validation and mechanistic studies.}, } @article {pmid42519018, year = {2026}, author = {Zhang, Z and Shu, Y and Liu, X and Xu, B and Chen, J and Zhang, Z and Wang, K and Hua, Y}, title = {Multi-omics reveals functional recovery of the gut microbiome in rescued Sunda pangolins (Manis javanica).}, journal = {iScience}, volume = {29}, number = {8}, pages = {116754}, doi = {10.1016/j.isci.2026.116754}, pmid = {42519018}, issn = {2589-0042}, abstract = {The Sunda pangolin (Manis javanica), a critically endangered myrmecophage, often develops severe gastrointestinal disturbance after trafficking, creating major challenges for post-rescue rehabilitation. We integrated 16S rRNA gene sequencing, shotgun metagenomics, untargeted metabolomics, and gas chromatography-mass spectrometry (GC-MS) quantification of short-chain fatty acids to investigate gut ecosystem recovery in rescued pangolins across the first abnormal fecal stage, 1 week post-rescue, and 1 month post-rescue. Fecal consistency improved during rehabilitation, accompanied by a shift from facultative taxa enriched in Streptococcus and Lactobacillus to a more anaerobic community containing Clostridium, Romboutsia, Bacteroides, and related taxa. Metagenomic and metabolomic profiles indicated recovery of functions associated with chitin degradation, short-chain fatty acid production, amino acid metabolism, and cofactor biosynthesis. Increased fecal butyrate and multi-omics associations supported recovery of microbial metabolic function. These findings provide insight into the microbial and metabolic dynamics of gut ecosystem recovery in rescued pangolins and may help assess rehabilitation progress in this critically endangered species.}, } @article {pmid42519058, year = {2026}, author = {Pi, N and He, X and Zhu, L and Hou, X and Wu, X and Zhang, J and Yang, L and Shen, D and Zou, Z and Xiang, R and Wu, X}, title = {City-scale resistome-mobilome architecture and mobility-associated ARG backbones across a megacity watershed.}, journal = {iScience}, volume = {29}, number = {8}, pages = {116841}, doi = {10.1016/j.isci.2026.116841}, pmid = {42519058}, issn = {2589-0042}, abstract = {Antimicrobial resistance (AMR) in urban watersheds is shaped by diverse anthropogenic inputs, and linking reads-level resistome-mobilome associations to local antibiotic resistance gene (ARG) genetic contexts can strengthen environmental surveillance. Here, we analyzed 63 deeply sequenced shotgun metagenomes from a Chongqing megacity watershed spanning surface water, river sediments, wastewater treatment activated sludge, livestock wastewater, and hospital wastewater. Reads-based profiling revealed strong habitat structuring of ARG subtypes and MobileElementFinder-derived mobilome families, and total ARG loads co-varied with mobile genetic element (MGE), biocide resistance, and metal resistance axes. To add sequence-resolved context, we surveyed 8,043 ARG-carrying contigs and integrated element-level MGE calls with open reading frame (ORF)-level mobility functions to define putative mobility tiers. Wastewater-impacted habitats showed higher representation of contigs carrying conjugation-related mobility signals, whereas sediments exhibited high ARG and MGE loads but weaker ARG-MGE coupling. This megacity-scale framework prioritizes mobility-associated and co-selection genetic contexts for environmental AMR monitoring and mitigation.}, } @article {pmid42519143, year = {2026}, author = {Tan, X and Liao, J and Xu, Z}, title = {Misdiagnosed acute Q fever due to Coxiella burnetii in Guangxi China: A case report and literature review.}, journal = {IDCases}, volume = {45}, number = {}, pages = {e02661}, doi = {10.1016/j.idcr.2026.e02661}, pmid = {42519143}, issn = {2214-2509}, abstract = {Coxiella burnetii (C. burnetii), a Gram-negative obligate intracellular bacterium, is the etiological agent of Q fever. Timely diagnosis and initiation of appropriate therapy are critical for favorable clinical outcomes, particularly in cases of acute Q fever. This report describes a case of C. burnetii infection in a 35-year-old male electrical grid engineer who presented with a 4-day history of febrile illness, peaking at 40.0 °C. Associated symptoms included night sweats, chills, anorexia, nausea, non-productive cough, and chest tightness. During hospitalization, the patient also developed headache and vomiting. Metagenomic next-generation sequencing (mNGS) of peripheral blood identified C. burnetii as the causative pathogen. The patient was treated with oral doxycycline (100 mg twice daily) for 14 days and levofloxacin (500 mg once daily) for 5 days. Following antimicrobial therapy, the patient's symptoms resolved rapidly, with no clinical evidence of relapse or progression to chronic Q fever during follow-up. This report describes a case of Q fever diagnosed by mNGS. The case highlights the diagnostic value of mNGS in patients presenting with febrile illness of unknown origin. It also serves as a reminder to clinicians that, even in regions where Q fever is enzootic in animals but no human cases have been reported, the possibility of human infection should not be overlooked.}, } @article {pmid42519144, year = {2026}, author = {Asai, N and Igarashi, Y and Miyazaki, N and Shiota, A and Yamagishi, Y and Nakamura, A and Osugi, A and Matsumoto, Y and Nakamura, S and Murakami, S and Takami, A and Mitarai, S and Mikamo, H}, title = {First reported recovery and genomic characterization of a previously uncharacterized Mycobacterium species from human blood cultures in an immunocompromised patient: A case report.}, journal = {IDCases}, volume = {45}, number = {}, pages = {e02667}, doi = {10.1016/j.idcr.2026.e02667}, pmid = {42519144}, issn = {2214-2509}, abstract = {Mycobacteremia is an uncommon opportunistic infection in immunocompromised hosts. We report the recovery of a previously uncharacterized Mycobacterium species from two independent blood culture sets obtained from an immunocompromised patient with persistent fever. She presented with persistent fever, and two independent blood culture sets yielded a Mycobacterium species. No focal source of infection was identified. Initial identification by MALDI-TOF mass spectrometry suggested Mycobacterium diernhoferi; however, species-level identification could not be confirmed by molecular methods. Whole-genome sequencing demonstrated that the isolate could not be assigned to any currently recognized Mycobacterium species. Average nucleotide identity analysis showed 90.5% similarity to M. diernhoferi and 84.4% to Mycobacterium frederiksbergense, suggesting a previously uncharacterized species. Combination antimicrobial therapy was followed by resolution of fever and no recurrent positive blood cultures during treatment. Although the patient ultimately died because of progression of the underlying hematological malignancy, the patient showed sustained clinical improvement without recurrent positive blood cultures during therapy. To our knowledge, this is the first reported recovery of this genomically distinct Mycobacterium species from human blood cultures. This case highlights the value of whole-genome sequencing in recognizing previously uncharacterized Mycobacterium species recovered from human blood cultures. The pathogenic role of this organism requires further investigation.}, } @article {pmid42519489, year = {2026}, author = {Al Khafaji, A and Vallejo-España, D and Gómez-Llorente, C and Camacho, J}, title = {A realistic simulation-based benchmark of microbiome normalization in sample stratification and taxa-level analysis.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1863340}, doi = {10.3389/fbinf.2026.1863340}, pmid = {42519489}, issn = {2673-7647}, abstract = {MOTIVATION: Normalization is a critical step in microbiome studies because sequencing depth and sparsity can strongly affect downstream analyses. In real datasets, however, the underlying biological signal is unknown, making it difficult to determine whether a normalization method preserves true group differences or introduces distortions. To address this problem in a way that remains relevant to real applications, we developed a simulation-based evaluation framework informed by real microbiome data. The framework generates realistic datasets with known ground truth and enables quantitative comparison of normalization methods at both the sample and taxa levels.

RESULTS: Method performance depended on taxonomic resolution and on whether sequencing depth was confounded with group structure. In our case study, model-based normalization-factor methods, particularly edgeR-TMM and, in some settings, DESeq2, gave the closest match to the simulated biological contrast, indicating better recovery of taxa-level differences while preserving sample-level separation. TSS and rarefaction were often the next-best performers. Shannon diversity analyses further showed that sequencing-depth differences alone could create false-positive group differences for several methods, whereas rarefaction remained closest to nominal Type I error control. These results also showed that visual or statistical sample separation alone was not sufficient to judge normalization performance, because apparent group differences did not always correspond to correct taxa-level recovery. Rather than identifying a universally best method, the proposed framework provides a coherent strategy for evaluating existing and new normalization approaches under realistic, data-dependent scenarios.}, } @article {pmid42519695, year = {2026}, author = {Wang, X and Wang, J and Chen, W and Sun, J and Li, J and Hu, H}, title = {Metagenome analysis reveals multi-kingdom gut microbiota as diagnostic markers for colorectal cancer.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1805055}, doi = {10.3389/fmicb.2026.1805055}, pmid = {42519695}, issn = {1664-302X}, abstract = {BACKGROUND: Colorectal cancer (CRC) is a major contributor to cancer-related morbidity and mortality globally. Emerging evidence suggests that gut microbiota plays a pivotal role in CRC development. However, the precise link between CRC and gut microbial dysbiosis remains poorly understood.

METHODS: In this study, we analyzed metagenomic datasets from 578 samples, sourced from five geographically distinct cohorts, including CRC patients and healthy controls from China, Austria, and Spain. This diverse cohort enabled us to investigate changes in the gut microbiome-bacteria, viruses, fungi, and archaea-in CRC patients across varying genetic and environmental contexts.

RESULTS: Our analysis led to the identification of 12 bacterial, 18 viral, and 1 fungal marker using a diagnostic model based on the gut microbiome. Notably, the multi-kingdom model, incorporating these markers, outperformed single-domain models in diagnostic accuracy. Integrating 24 microbial markers-comprising 9 bacterial, 14 viral, and 1 fungal marker-yielded an impressive AUROC of 0.911 for CRC diagnosis.

CONCLUSION: This model demonstrated robust performance across four independent cohorts, confirming its potential as a highly accurate, non-invasive diagnostic tool for CRC.}, } @article {pmid42519699, year = {2026}, author = {Akbar, A and Rahmeh, R and Kishk, M and Almutairi, B and Al-Mutairi, S and Al-Waalan, T and Shajan, A}, title = {Microbial diversity and bioremediation potential in mangrove sediments-a metagenomic analysis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1826301}, doi = {10.3389/fmicb.2026.1826301}, pmid = {42519699}, issn = {1664-302X}, abstract = {Mangroves in Kuwait are exposed to increasing levels of polycyclic aromatic hydrocarbons (PAHs) originating from industrial activities and urban runoff. However, the potential of native mangrove microbial communities for PAH bioremediation has not yet been explored. Sediment samples were collected from three locations (Shuwaikh, Al Khiran, and Sulaibikhat) at varying distances from Avicennia marina roots. The concentration of PAHs was determined using GC-MS. To assess microbial diversity, a metagenomic approach was used to evaluate diversity metrics. The statistical analysis included the non-parametric Kruskal-Wallis test (p < 0.05) to compare the median values of different groups and the non-parametric PERMANOVA test (p-values 0.001-0.009) to assess the differences among groups. The results of the study showed the presence of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and chrysene PAHs at varying concentrations across the studied sites. Naphthalene concentrations reached a maximum of 89.64 μg/kg at the Sulaibikhat site and a minimum of 12 μg/kg at the Shuwaikh site. Metagenomic analysis revealed significant differences in microbial diversity between root distances and sites. The rhizosphere samples had higher alpha diversity and richness than the other sediment samples. Beta diversity analysis clustered the samples into groups of sample types and sites. The pairwise comparison between rhizosphere and sediment samples revealed significant differences in microbial communities between rhizosphere and sediment samples in Shuwaikh (p = 0.012) and Al Khiran (p = 0.007) sites. The heatmap of gene presence/absence revealed the enrichment of genes involved in hydrocarbon degradation (alkB, nahA, nahB, phnABC) and plant growth promotion. Functional analysis using KEGG revealed the metabolic capabilities of the isolates, including the presence of peptide/nickel transporters. All bacterial strains were identified by 16S rRNA gene sequencing, and the major groups of bacteria identified were Pseudomonas, Burkholderia, and Rhodococcus, which are known to have the ability to degrade PAHs and promote plant growth. Microorganisms of different species at various sites of Kuwait mangroves showed higher diversity in rhizosphere areas. Microorganisms living in such zones possess the necessary genes to degrade oil as well as for plant growth and thus have the potential for bioremediation of polluted sites by oil. The high level of PAH contamination in the sediment close to the roots of mangroves indicates localized pollution.}, } @article {pmid42519700, year = {2026}, author = {Pellegrinetti, TA and Molligan, J and Mendes, LW and Pedrinho, A and Pérez-López, E}, title = {Rethinking metagenome-assembled genome completeness: are we truly recovering complete genomes?.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1884628}, doi = {10.3389/fmicb.2026.1884628}, pmid = {42519700}, issn = {1664-302X}, } @article {pmid42519702, year = {2026}, author = {Xiong, W and Yan, X and Guo, H and Yu, B and Qi, J and Li, H and Zeng, Z and Dai, Y and Yu, Z and Tang, D}, title = {Day-21 gut microbiota community state types are associated with bronchopulmonary dysplasia classification in preterm infants: a pilot shotgun metagenomic study.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1835952}, doi = {10.3389/fmicb.2026.1835952}, pmid = {42519702}, issn = {1664-302X}, abstract = {INTRODUCTION: Bronchopulmonary dysplasia (BPD) is a major complication in preterm infants, and its clinical classification remains strongly influenced by gestational maturity and the evolving respiratory course. In this exploratory study, we investigated whether early-life gut microbiota configurations at postnatal day 21 are associated with subsequent formal BPD classification at 36 weeks postmenstrual age and whether they provide ecological information relevant to preterm infant microbiome development.

METHODS: In a prospective cohort of 23 preterm infants with gestational age <32 weeks or birth weight <1,500 g, shotgun metagenomic sequencing of day-21 fecal samples was performed. Community state types (CSTs) were identified using unsupervised clustering, and their taxonomic, functional, and exploratory discrimination patterns were assessed in relation to subsequent BPD classification.

RESULTS: Two CSTs were identified. CST1 was dominated by commensal taxa and exhibited functional enrichment in metabolic homeostasis pathways. CST2 was characterized by pathobionts, fragmented taxon-pathway association networks, and enrichment in virulence-related pathways. BPD was observed in 1 of 11 CST1 infants and 7 of 12 CST2 infants (9.1% vs. 58.3%; two-sided Fisher's exact test, p = 0.027), although this association was based on very small cell counts. In exploratory discrimination analysis, a model combining CST status with gestational age showed an apparent AUC of 0.892; however, leave-one-out cross-validation yielded a lower AUC of 0.800, indicating likely optimism in the apparent model performance.

DISCUSSION: These preliminary, observational findings suggest that day-21 gut microbiota profiles and CST classification may provide ecological information associated with formal BPD classification. However, this analysis should be interpreted as exploratory discrimination rather than validation of a clinically useful prediction model. Establishing causality or clinical utility requires validation in larger cohorts that systematically track longitudinal confounders such as gestational age, feeding mode, antibiotics, and probiotics.}, } @article {pmid42519731, year = {2026}, author = {Yi, M and Dai, Y and Liu, C and Lang, H and Jiang, X and Yuan, X}, title = {Case Report: Pediatric mediastinal actinomycosis mimicking lymphoma diagnosed by tissue metagenomic next-generation sequencing.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1882250}, doi = {10.3389/fped.2026.1882250}, pmid = {42519731}, issn = {2296-2360}, abstract = {Mediastinal actinomycosis is rare in children, and when it presents as a mass-like lesion, its clinical and imaging features overlap substantially with lymphoma, making differential diagnosis extremely challenging. We report a 2-year-1-month-old girl admitted with fever and cough. Contrast-enhanced chest computed tomography (CT) showed multiple enlarged mediastinal and bilateral hilar lymph nodes coalescing into a mass-like lesion with heterogeneous enhancement and small hypoenhancing foci, encasement of adjacent mediastinal vessels, and compression of the left main bronchus and the origin of the lingular bronchus. Magnetic resonance imaging (MRI) demonstrated heterogeneous signal intensity and enhancement; the radiologic differential included lymphoproliferative and granulomatous disease. Bone marrow biopsy, leukemia immunophenotyping, and tumor markers did not support malignancy. Ultrasound-guided biopsy of the mediastinal lesion revealed necrotizing granulomatous inflammation. Metagenomic next-generation sequencing (mNGS) of unstained tissue sections detected Actinomyces oris with mixed oropharyngeal flora, while Mycobacterium tuberculosis complex, fungi, viruses, and atypical pathogens were not detected. Pulmonary inflammation improved with antimicrobial therapy; however, repeat CT on January 28, 2026 showed little change in the mediastinal-hilar lesions. Because lymphoma could not be excluded, thoracoscopic partial resection was performed at another hospital, and postoperative pathology again showed granulomatous inflammation with caseous necrosis and negative acid-fast staining. Oral amoxicillin-clavulanate was continued postoperatively, in line with the principle of 2-6 weeks of intravenous therapy followed by 6-12 months of oral antibiotics for thoracic actinomycosis, with duration individualized to residual disease, imaging response, and drug tolerance. Follow-up ultrasonography on April 13, 2026 demonstrated reduction of the residual lesion, and the patient remained asymptomatic. This case highlights that pediatric mediastinal actinomycosis can mimic lymphoma and that integrated assessment of deep-tissue pathology, mNGS, serial imaging, and treatment response can guide diagnostic and therapeutic decision-making, preventing misdiagnosis and mistreatment.}, } @article {pmid42519736, year = {2026}, author = {Zhao, L and Ming, Y and Zeng, L and Yi, M and Tao, X and Yuan, W}, title = {Neonatal varicella complicated by Staphylococcus aureus lung abscess in a preterm infant: a case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1845229}, doi = {10.3389/fped.2026.1845229}, pmid = {42519736}, issn = {2296-2360}, abstract = {BACKGROUND: Neonatal varicella is a rare but potentially life-threatening condition, particularly in preterm infants. Although secondary bacterial infections are common complications, deep organ involvement such as lung abscess formation is exceedingly rare. Reports describing neonatal varicella complicated by Staphylococcus aureus lung abscess are scarce.

CASE PRESENTATION: We report a 26-day-old preterm infant (32 weeks' gestation, birth weight 1.94 kg) who developed a progressive vesiculopustular skin lesions and respiratory deterioration following exposure to maternal varicella. Despite initial topical treatment, the rash rapidly worsened and was accompanied by poor responsiveness, apnea, cyanosis, and hypothermia. On admission, the infant presented with extensive skin lesions, respiratory distress requiring non-invasive ventilation, coagulopathy, and thrombocytopenia. Intravenous acyclovir and immunoglobulin were initiated. Although the skin lesions gradually crusted and resolved, respiratory abnormalities persisted and oxygen supplementation remained necessary. Chest imaging subsequently revealed a right upper lobe abscess. Blood cultures remained negative; however, respiratory metagenomic next-generation sequencing (mNGS) identified Staphylococcus aureus, confirming secondary bacterial infection. Initial antibiotic therapy with vancomycin was selected because of severe pulmonary infection and the local prevalence of oxacillin-resistant Staphylococcus aureus. However, subtherapeutic trough concentrations and limited clinical response prompted a switch to linezolid. Following treatment adjustment, the infant showed gradual clinical and radiographic improvement and was discharged in stable condition. Follow-up imaging confirmed complete resolution of the lung abscess.

CONCLUSIONS: This case represents a rare presentation of neonatal varicella complicated by Staphylococcus aureus lung abscess in a preterm infant. It highlights that apparent resolution of cutaneous lesions does not exclude ongoing deep-seated bacterial infection and that persistent respiratory abnormalities should prompt early imaging evaluation, even in the absence of typical respiratory signs. In culture-negative cases, mNGS may facilitate pathogen identification and guide targeted antimicrobial therapy. Early recognition, individualized antimicrobial management, and therapeutic drug monitoring are important for optimizing outcomes in high-risk neonates. This case also underscores the importance of timely post-exposure prophylaxis and the limited availability of varicella-zoster immune globulin (VZIG) in some regions.}, } @article {pmid42519816, year = {2026}, author = {Wang, B and Xu, Z and Dong, B}, title = {Migration and biotransformation mechanisms of risk-priority antibiotics in wastewater biotreatment: An integrated multi-omics and molecular dynamics perspective.}, journal = {Eco-Environment & Health}, volume = {5}, number = {3}, pages = {100260}, doi = {10.1016/j.eehl.2026.100260}, pmid = {42519816}, issn = {2772-9850}, abstract = {Understanding the fate and transformation of antibiotics is essential for controlling antibiotic pollution in wastewater treatment plants (WWTPs). This study integrated metagenomics, metaproteomics, molecular dynamics (MD) simulations, and pathway analysis to elucidate the behavior of ciprofloxacin (CIP), sulfamethoxazole (SMX), and roxithromycin (ROX) under single- and mixed-antibiotic exposures in an activated sludge system. Fate analysis revealed divergent pathways: SMX was predominantly biodegraded (>70%), whereas CIP and ROX were mainly adsorbed onto sludge, showing poor removal and high effluent residuals (CIP > 50%, ROX > 60%). Under mixed-antibiotic stress, microorganisms favored lower-energy degradation pathways, leading to simplified (skip-step) transformations. MD simulations unveiled that within the extracellular polymeric substances (EPS) matrix, the protein fraction exhibited the strongest binding. Docking and MD simulations on a proteomics-derived interface-associated protein (OmpA) revealed a co-adsorption behavior under mixed-antibiotic exposure, where CIP strongly anchored through multipoint hydrogen bonding/electrostatic interactions and facilitated SMX stabilization in the same pocket via aromatic stacking. Multi-omics analyses revealed a microbial "survival-first" strategy dominated by resistance and repair. Notably, transporter-related stress responses were prominent under mixed stress, and several ABC transporter-associated components (e.g., K02003/K02004 and K02033) were negatively correlated with removal efficiency, coinciding with reduced degradation by key genera such as Micropruina and Ottowia. Under mixed-antibiotic stress, a confluence of reinforced resistance (e.g., Type IV secretion system K03205), altered EPS binding, and skewed energy allocation (e.g., downregulation of cofactor synthesis ko01240) led to incomplete degradation and widespread persistence. This study provides a multiscale theoretical framework for optimizing WWTPs to control antibiotic pollution.}, } @article {pmid42519835, year = {2026}, author = {Baertschi, I and Jordi, SBU and Gardaz, LJ and Bigi, FV and Sokollik, C and Juillerat, P and Yilmaz, B}, title = {Strain-level ecological filtering governs microbial colonization of the human gut.}, journal = {Cell reports}, volume = {45}, number = {8}, pages = {117775}, doi = {10.1016/j.celrep.2026.117775}, pmid = {42519835}, issn = {2211-1247}, abstract = {Microbial colonization of the human gut is typically inferred from species-level profiling, yet durable establishment operates at the strain level. Here, using longitudinal shotgun metagenomics across multiple donor-recipient pairs undergoing fecal microbiota transplantation, we show that colonization is governed by lineage-dependent strain-level ecological filtering. Strain-resolved analyses reveal that gut colonization imposes reproducible population-genetic bottlenecks, characterized by reduced nucleotide diversity and selective strain capture. Lineage identity is the primary determinant of strain fate: certain taxa exhibit high donor-strain fidelity, whereas dominant gut lineages, most notably Lachnospiraceae, display broad species-level engraftment but limited capture of donor-identical strains. Repeated transplantation progressively increases species-level retention, building ecological memory, yet fails to overcome intrinsic barriers to consensus-level donor-strain capture. Clinical remission aligned specifically with directional donor-strain replacement rather than taxonomic remodeling alone, identifying strain-level lineage compatibility as a candidate determinant of therapeutic success. Collectively, these findings establish that gut colonization is constrained by strain-level ecological filtering and reframe microbiota transplantation as a selective evolutionary process in which lineage identity, not inoculum diversity, gates therapeutic integration.}, } @article {pmid42520232, year = {2026}, author = {Bhuta, R and Kuntz, T and DeNardo, B and Morgan, X and Shapiro, J}, title = {Shotgun Metagenomics Identify Unique Changes of the Intestinal Microbiome in Pediatric Survivors of Acute Lymphoblastic Leukemia.}, journal = {Rhode Island medical journal (2013)}, volume = {109}, number = {8}, pages = {32-37}, pmid = {42520232}, issn = {2327-2228}, abstract = {BACKGROUND: Intestinal microbiota plays an important role in human health and metabolism. Microbial dysbiosis has been observed in various chronic conditions, many of which are late effects of leukemia treatment. We previously observed significant differences in the gut microbiome of pediatric ALL survivors compared to healthy sibling controls. Shotgun metagenomic analyses were completed to better characterize the durability and metabolic implication of these changes.

PROCEDURE: Shotgun metagenomic sequencing was completed on DNA extracted from stool samples obtained from nine survivors of childhood acute lymphoblastic leukemia (ALL) and 10 healthy sibling controls.

RESULTS: Beta diversity (dissimilarity between samples) was significant with survivors' microbiomes becoming more similar to siblings further from treatment. The functional potential of gluconate-5-dehydrogenase enzyme (Ga5DH) decreased significantly with time from treatment. Relative abundance of Faecalibacterium prausnitzii was identified as the major contributor to differential Ga5DH expression within subjects.

CONCLUSIONS: Time from treatment has a significant effect on functional microbial recovery in ALL. Increased time from chemotherapy corresponds to microbiomes becoming more similar to sibling controls in select dyads. More significant differences were noted in patients closer to treatment. Additional, prospective studies will focus on deeper characterization of these findings and further investigate the functional role of Ga5DH in ALL survivors.}, } @article {pmid42520323, year = {2026}, author = {Huang, Z and Li, Z and Wu, F and Zhou, D}, title = {Gut microbiota metabolites and microbiota-targeted interventions in bone metabolism: from SCFAs and TMAO to probiotics and FMT.}, journal = {Postgraduate medical journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/postmj/qgag099}, pmid = {42520323}, issn = {1469-0756}, abstract = {BACKGROUND: Accumulating evidence supports a microbiota-gut-bone axis in which intestinal microbes influence skeletal remodeling through barrier integrity, immune signaling, and metabolite production.

METHODS: This review emphasizes specific metabolites, strain-level intervention data, and translational limitations.

RESULTS: Preclinical studies consistently show that dysbiosis, barrier disruption, and altered microbial metabolites promote osteoclastogenesis and suppress osteoblast function. Among short-chain fatty acids, propionate and butyrate have the strongest direct anti-osteoclast evidence, whereas acetate a bone-relevant systemic substrate/signaling molecule with context-dependent skeletal effects. Trimethylamine N-oxide has been linked mechanistically to impaired osteogenic commitment of bone marrow stromal cells and inflammatory signaling, although human epidemiologic findings are not uniform. These mechanisms appear particularly relevant in postmenopausal osteoporosis and glucocorticoid-induced osteoporosis, where estrogen deficiency or glucocorticoid exposure amplifies intestinal permeability, inflammatory tone, and microbial dysbiosis. In humans, the clinical signal is promising but heterogeneous. Fecal microbiota transplantation remains largely preclinical in bone disease and faces major challenges in donor selection, protocol standardization, timing, and long-term safety.

CONCLUSIONS: Overall, the field is moving from associative observations toward causal and precision-oriented models, but large, well-phenotyped human studies integrating metagenomics, metabolomics, proteomics, and host clinical data are still needed before microbiota-targeted therapies can be routinely incorporated into osteoporosis care.}, } @article {pmid42520350, year = {2026}, author = {Chen, Q and Niu, X and Wu, W and Shi, H and Liu, G and Chen, L and Wang, H and Zhang, Y}, title = {Composted cattle manure enhances microbial nitrogen retention and increased seed watermelon yield in saline-alkali soil.}, journal = {Microbiological research}, volume = {312}, number = {}, pages = {128647}, doi = {10.1016/j.micres.2026.128647}, pmid = {42520350}, issn = {1618-0623}, abstract = {Soil salinity and alkalinity represent a global environmental challenge that severely hampers agricultural productivity. While composted manure amendment represents a sustainable strategy relates to nutrient supplementation and soil health improvement. However, the influence of composted manure on microbial nitrogen cycles in a saline-alkali soil remains obscure. Saline-alkali soil amendment with cattle manure (CM) and composted CM (CCM) were conducted to systematically evaluate their efficacy in ameliorating soil physicochemical properties and enhancing crop productivity under saline-alkaline stress conditions. Physicochemical properties of saline-alkali soils under different amendments were investigated. The changes in microbial communities and nitrogen metabolism were analyzed using metagenomic sequencing and qPCR. Furthermore, the correlations between microbial nitrogen cycle and soil physicochemical factors were assessed. Compared to control (CK), soil salinity was significantly mitigated by 43.0%% and 51.9% in CM and CCM treatments. The organic matter, humus and nitrogen contents were also significantly increased in CM and CCM treatments. CCM significantly improved abundance of nrf in dissimilatory nitrate reduction to ammonium (DNRA), while reducing amoA abundance in nitrification. These findings suggest a potential redirection of microbial nitrogen fluxes toward retention rather than loss pathways, thereby enhances soil fertility. And the seed yield in CCM treatment was significantly higher than those of CM and CK. Our results provided mechanistic evidence for the use of composted manure as a sustainable strategy for enhancing soil fertility, mitigating salinization, and increasing crop yield of saline-alkali soils.}, } @article {pmid42520695, year = {2026}, author = {Zhou, HZ and He, T and Song, Z and Li, Z and Huang, JW and Min, J and Xu, ZM and Ma, K}, title = {Microplastics (PET and PVC) disrupt palygorskite-mediated cadmium stabilization in paddy soil: Polymer-specific rhizosphere mechanisms and ecological consequences.}, journal = {Journal of environmental management}, volume = {415}, number = {}, pages = {130590}, doi = {10.1016/j.jenvman.2026.130590}, pmid = {42520695}, issn = {1095-8630}, abstract = {Microplastics (MPs) are emerging disruptors to soil heavy metal remediation, yet how different polymer types undermine mineral-mediated in-situ immobilization remains unclear. Using a multi-omics approach (16S rRNA gene sequencing, metagenomics, transcriptomics and metabolomics), we aimed to elucidate the polymer-specific mechanisms by which polyethylene terephthalate (PET) and polyvinyl chloride (PVC) residues destabilize palygorskite-immobilized cadmium (Cd) in paddy soil, at both the soil and microbial levels. PET and PVC differentially induced the remobilization of palygorskite-immobilized Cd (F1: +132.43% and 85.52%) via distinct rhizosphere pathways. At the soil/plant level, PET enriched PETase-carrying Acidobacteriota and suppressed the ammonium transporter gene OsNRT2.3, lowering rhizosphere pH from 7.05 to 6.30. This acidification was associated with the remobilization of mineral-bound Cd and increased brown rice Cd from 0.03 to 0.06 mg/kg. PVC, in contrast, did not acidify the rhizosphere but instead induced severe root oxidative stress (MDA +78%, POD +60%), likely impairing root-barrier integrity and enhancing Cd uptake. At the microbial level, PET enriched keystone taxon Gaiella via homogeneous selection (HoS), supporting stress adaptation through branched-chain amino acid metabolism, whereas PVC redirected microbial carbon flux toward the pentose phosphate pathway and increased the genetic potential for acetate-dependent methanogenesis (acs +22.67%). These findings demonstrate that MPs compromise the durability of Cd immobilization through polymer-specific rhizosphere processes, with distinct ecological trade-offs, providing critical insights for heavy metal remediation in microplastic-polluted paddy soils.}, } @article {pmid42520702, year = {2026}, author = {Huang, J and Chen, F and Zhang, Z and Zu, Y and Cao, D and Huang, T and Li, Z and Wang, A}, title = {Electrode-Triggered niche differentiation and endogenous electron cycling boost bioremediation of mixed aromatic contaminants in oligotrophic groundwater.}, journal = {Water research}, volume = {306}, number = {}, pages = {126537}, doi = {10.1016/j.watres.2026.126537}, pmid = {42520702}, issn = {1879-2448}, abstract = {Chlorinated and non-chlorinated aromatic contaminants frequently co-occur in groundwater, but their synergistic bioremediation is often hindered by conflicting redox requirements, microbial niche competition, and the need for external organic carbon sources. Here, we present an electro-stimulated bio-circulation well (ES-BCW) that couples electrode-mediated redox regulation with internal hydraulic recirculation, enabling the simultaneous continuous reductive dechlorination and oxidative aromatic degradation without exogenous organic carbon supplementation. Under continuous operation (120 d), the ES-BCW system achieved average removal rates of 53.2 µmol L[-1] d[-1] for 1,2,4-trichlorobenzene (1,2,4-TCB) and 169.5 µmol L[-1] d[-1] for toluene, respectively, demonstrating competitive performance for anaerobic co-treatment of mixed aromatic contaminants. Optimal weak electrical stimulation (1.2 V) with a controlled reflux (50%) promoted spatial niche differentiation between cathodic reductive and anodic oxidative zones. Microbial analysis revealed selective enrichment of dechlorinating (Dechloromonas and Sphingobium), toluene-degrading (Azoarcus and Thauera), and electroactive (Geobacter and Sulfurospirillum) genera. Integrated metagenomic and metabolomic analyses revealed coordinated enrichment of dechlorination (pcpB, pcpC) and toluene oxidation (bssABC, bbsG) genes, coupled with increased abundances of energy carriers and key electron transfer components (i.e. cytochromes). These shifts collectively supported enhanced electron flux redistribution, metabolic synergy, and sustained acetate cycling, establishing a self-amplifying loop of endogenous carbon reuse that enabled redox partitioning between cathodic reductive and anodic oxidative niches. The ES-BCW system offers an endogenous carbon-driven strategy for synergistic bioremediation of mixed aromatic contaminated oligotrophic groundwater.}, } @article {pmid42520798, year = {2026}, author = {Zhang, WJ and Hu, A and Wu, Z and Liu, L and Li, C and Wang, Y and Wei, Z and Lu, R and Li, J and He, Y and Zhang, T and Liu, S and Wang, J and Meng, L and Xiao, X and Zhao, W}, title = {Unveiling active microbial processes in Earth's deepest seawater.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.07.001}, pmid = {42520798}, issn = {1934-6069}, abstract = {Microorganisms dominate life in the hadal zone, yet extreme sampling difficulty and low biomass have precluded characterization of their in situ activities. Here, we analyze microbiome samples collected from hadal seawaters via in situ filtration during 12 human-occupied vehicle dives. DNA-protein co-extraction and metagenome-guided metaproteomic analysis identify 135,073 non-redundant active proteins, with over 95% being hadal-specific. Metaproteomic quantification distinguishes highly active and less active taxa that differ in biogeographic origins and genomic traits. Hadal microorganisms operate a metabolic regime fundamentally distinct from the upper ocean, preferentially utilizing refractory organic matter (aromatics, halogenated compounds, and D-amino acids) and expanded electron acceptors (thiosulfate and heavy metals), collectively shaping hadal element cycling. Active viruses extend beyond "Piggyback-the-Winner" dynamics, enhancing host adaptation through auxiliary metabolic genes. These findings provide proteome-level evidence of hadal microbial activities and reveal biogeochemical cycling distinct from that of the upper ocean, highlighting the underappreciated significance of hadal microbiomes within global ocean ecosystems.}, } @article {pmid42520901, year = {2026}, author = {Zhang, L and Zhao, B and Zhang, X and Li, Y and Li, H and Yuan, S and Ning, H and Lv, B and Li, L and Fan, X and Yue, X}, title = {Fe[2+] Alters Carbon and Nitrogen Metabolic Networks in a Composite Microbial Consortium: Metagenomic Insights into the Shift from Denitrification to DNRA.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125349}, doi = {10.1016/j.envres.2026.125349}, pmid = {42520901}, issn = {1096-0953}, abstract = {Conventional biological nitrogen removal processes are constrained by lengthy treatment trains and dependence on organic carbon sources, necessitating the development of novel enhanced nitrogen removal strategies that integrate multiple functions and ensure operational stability. In this study, a synthetic bacterial consortium was constructed, comprising the aerobic denitrifier Pseudomonas stutzeri, the facultative anaerobic denitrifier Klebsiella sp., and the heterotrophic nitrifying-aerobic denitrifying bacterium Alcaligenes sp. The effects of five iron species as well as their combined effects with polyacrylamide (PAM), on nitrogen removal performance and oxidative stress responses of the consortium were investigated, and metagenomic sequencing was employed to elucidate the regulatory mechanisms of Fe[2+] on metabolic processes. The results showed that, compared with the other iron species, the Fe[2+] group achieved a 20-30% increase in nitrate-N removal efficiency. The addition of PAM attenuated the specific regulatory effects of different iron species through physical mass-transfer limitation. Metagenomic analysis revealed that Fe[2+] modulated the carbon and nitrogen metabolic networks: in the carbon metabolic network, enrichment of the por gene in the glycolytic pathway generated substantial reducing power in the form of reduced ferredoxin; concomitantly, the transcript abundance of the dissimilatory nitrate reduction to ammonium pathway increased from 775 to 802, whereas that of the denitrification pathway decreased from 1259 to 1222. This study elucidates the intrinsic mechanism by which Fe[2+] promotes synergistic carbon and nitrogen removal, providing a theoretical foundation for the development of a multi-process coupled deep nitrogen removal system integrating bioaugmentation, chemical regulation, and physical sedimentation.}, } @article {pmid42501817, year = {2026}, author = {Gaye, A and Vaidya, V and Toure, M and Ndiaye, IM and Gallon, S and Yade, MS and Ngom, B and Sow, D and Diop, NC and Kebe, O and Ndiaye, YD and Diallo, MA and Sene, A and Tine, A and Deme, AB and Diedhiou, Y and Dia, AK and Badiane, AS and Sy, M and Ndiaye, D and Herrera, BB}, title = {A tiered molecular surveillance framework linking rapid dengue detection to genomic epidemiology in Senegal.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {109009}, doi = {10.1016/j.ijid.2026.109009}, pmid = {42501817}, issn = {1878-3511}, abstract = {BACKGROUND: Arboviral surveillance in Africa is limited by fragmented diagnostic capacity and insufficient integration of molecular detection with genomic epidemiology, particularly in settings where dengue (DENV), Zika (ZIKV), and chikungunya (CHIKV) viruses co-circulate and present with overlapping clinical syndromes.

METHODS: We conducted a molecular surveillance study across multiple regions in Senegal, including samples collected from 367 individuals with febrile or non-febrile illness. A tiered workflow was implemented using multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) screening for DENV, ZIKV, and CHIKV, performed on a combination of individually tested samples (n=43) and pooled samples (three individuals per pool). DENV RT-qPCR-positive samples were further characterized by reverse transcription recombinase polymerase amplification (RT-RPA) serotyping and genomic sequencing.

FINDINGS: Multiplex RT-qPCR revealed concurrent circulation of multiple arboviruses. Among individually tested samples, positivity rates were 20·9% (9/43) for DENV, 9·3% (4/43) for ZIKV, and 11·6% (5/43) for CHIKV. In pooled screening across all sites (108 pools), positivity rates were 18·5% for DENV (20/108), 5·6% for ZIKV (6/108), and 10·2% for CHIKV (11/108), indicating widespread arboviral transmission. DENV-1-4 serotyping by RT-RPA demonstrated complete concordance with RT-qPCR and identified exclusive circulation of DENV-2, enabling triage of samples for downstream genomic sequencing. Amplicon-based sequencing substantially improved genome recovery compared with metagenomic sequencing, yielding near-complete genomes in 77·8% (14/18) of RT-RPA-positive samples. Phylogenetic analyses demonstrated that all sequences clustered within the DENV-2 cosmopolitan genotype (genotype II), lineage II-F.1.1, closely related to recent strains from West Africa and Asia. Time-resolved reconstruction suggested recent emergence (∼2022-2023) and rapid expansion, consistent with ongoing transmission and regional dissemination.

INTERPRETATION: These findings demonstrate co-circulation of DENV, ZIKV, and CHIKV in Senegal and provide evidence of recent expansion of DENV-2 within a globally connected transmission network. A tiered strategy integrating pooled molecular screening with RT-RPA triage and genomic sequencing offers a scalable framework for arboviral surveillance in resource-limited settings.}, } @article {pmid42501920, year = {2026}, author = {Kim, JE and Cho, H and Lee, J and Park, JI and Koh, JH and Park, S and Kang, E and Kim, YC and Kim, DK and Kim, YS and Min, S and Song, EY and Moon, KC and Kim, BS and Lee, H}, title = {Pretransplant Gut Microbiome Signatures Predict Early Acute Rejection After Kidney Transplantation.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajt.2026.07.023}, pmid = {42501920}, issn = {1600-6143}, abstract = {Early identification of rejection remains a critical unmet need in kidney transplantation, as conventional tools detect rejection only after irreversible allograft injury. The pre-transplant gut microbiome may provide novel predictive signals by modulating immune homeostasis. Pre-transplant stool samples underwent shotgun metagenomic sequencing. Composition, functional profiles, and networks were compared between rejection and non-rejection (protocol biopsy ≤ 2 weeks). A pre-specified SCFA biosynthetic KO panel was tested with FDR correction. Stepwise Random Forest models were developed with subgroup analyses and tested in a temporal validation cohort. Of 78 recipients, 26 (33.3%) developed biopsy-proven early acute rejection. Three taxa including Phascolarctobacterium faecium were FDR-significantly reduced. At the gene level, mcmB (a key propionate-biosynthetic enzyme) was the only KO reaching FDR significance in the pre-specified SCFA panel (q = 0.018). Network analysis revealed selective microstructural reorganization. AUC improved stepwise (0.565 → 0.681 → 0.765), was preserved across rejection subtypes (TCMR-spectrum 0.74; ABMR 0.85), and reached 0.721 in temporal validation with improved reclassification (NRI 0.11; IDI 0.055) and clinical net benefit at thresholds 0.2-0.5. Pre-transplant gut microbiome signatures were independently associated with early acute rejection. Microbiome-augmented models outperformed clinical-only models and remained robust in temporal validation, supporting microbiome-based pre-transplant risk stratification.}, } @article {pmid42502253, year = {2026}, author = {Niles, DT and Moulton, EA and Bocchini, CE}, title = {Metagenomic Next-Generation Sequencing for Diagnosis of Infectious Diseases in Pediatric Transplant Patients.}, journal = {Transplant infectious disease : an official journal of the Transplantation Society}, volume = {}, number = {}, pages = {e70272}, doi = {10.1111/tid.70272}, pmid = {42502253}, issn = {1399-3062}, abstract = {Metagenomic next-generation sequencing (mNGS) is a significant advancement in the diagnostic evaluation of infectious diseases, especially in immunocompromised patients at risk for complex, atypical, and opportunistic infections. In pediatric solid organ transplant (SOT) and hematopoietic stem cell transplant (HSCT) recipients, mNGS can augment a diagnostic evaluation when conventional microbiological testing (CMT) fails to identify the infectious etiology. Current evidence supports the use of mNGS for specific syndromes, including complicated pneumonia, central nervous system infections, and febrile neutropenia, due to greater sensitivity. While it is considered a second-line test, early application for high-risk infections, such as diagnosis of invasive fungal disease, has been shown to be impactful. Furthermore, mNGS can detect donor-derived infections (DDIs), where the breadth of the assay can identify unexpected pathogens transmitted via the graft that are often omitted from routine screening protocols. Despite the potential, interpretation remains challenging due to the detection of DNA from commensal organisms, latent viral reactivation, and low-level detection of pathogens that do not correlate with disease. Establishing diagnostic stewardship is key to directing testing to maximize diagnostic yield and improve clinical outcomes.}, } @article {pmid42502975, year = {2026}, author = {Taldaev, A and Smutin, D and Danilov, L and Kashchenko, G and Ryabova, A and Adonin, L}, title = {Brain Transcriptomic Reprogramming and Comb-Associated Microbiome Variation During the Larva-To-Pupa Transition in Apis Mellifera.}, journal = {Archives of insect biochemistry and physiology}, volume = {122}, number = {4}, pages = {e70196}, pmid = {42502975}, issn = {1520-6327}, support = {25-26-00381//Russian Science Foundation/ ; }, mesh = {Animals ; Bees/microbiology/growth & development/genetics/metabolism ; *Brain/metabolism/growth & development ; Larva/growth & development/microbiology/genetics/metabolism ; *Transcriptome ; *Microbiota ; Pupa/growth & development/microbiology/genetics/metabolism ; Metamorphosis, Biological ; }, abstract = {The larva-to-pupa transition in honey bees (Apis mellifera) involves extensive neural remodeling, yet the molecular dynamics of brain development and their relationship with the surrounding microbial environment remain poorly characterized. This study integrated brain transcriptomic profiling with comb-associated metagenomic analysis to characterize stage-specific molecular signatures during metamorphosis. RNA sequencing of larval and pupal brains was combined with honeycomb shotgun metagenomics from the same sample. Brain transcriptomes exhibited marked stage-specific divergence. Pupae displayed downregulation of transcriptional regulators, ecdysone and insulin signaling, and growth-related pathways, alongside upregulation of cuticular proteins, glutathione metabolism, and odorant-binding proteins. Notably, numerous poorly annotated, lineage-specific loci showed extreme stage-specific regulation. In contrast, comb-associated microbial communities remained globally stable across developmental stages, though supervised ordination identified stage-discriminatory taxa, including core symbionts and opportunistic pathogens. Integrative network analysis revealed significant correlations between comb potential bee pathogens' abundances and brain transcripts involved in translation, stress response, and metabolic regulation. Our data suggest that honey bee neural maturation is primarily driven by intrinsic transcriptional reprogramming, while structured variation in the external microbial milieu correlates with host neural gene expression. Honeycomb microbiome shift should be the consequence of the environmental conditions changes and host developmental shifts. Their roles in that process, as well as the brood immune system-comb microbiome interactions, may be part of future research.}, } @article {pmid42503761, year = {2026}, author = {Li, Z and Wang, L and Huang, F and Han, S and Zhang, Y}, title = {Root Metabolic Shifts Drive Genome-Resolved Cometabolism of Phthalates and Coupled Humification in Mollisols.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c05506}, pmid = {42503761}, issn = {1520-5851}, abstract = {Extensive import of mixed phthalate esters (PAEs) threatens Mollisol ecosystems. Nevertheless, mechanisms through which plant roots orchestrate the cometabolic degradation of PAEs and couple this with soil humification remain unclear. This study integrated plant physiology, untargeted metabolomics, and genome-resolved metagenomics to decipher response trajectories of the Pak Choi-Mollisol root-microbe system across a mixed PAEs gradient. The findings indicated that under mild stress (5 mg/kg), plants sustained a "growth-driven" homeostasis alongside a stable rhizospheric microbiome. In contrast, acute toxicity (20 mg/kg) initiated pronounced metabolic shifts, characterized by a "survival-overgrowth" strategy. Specifically, carbon fluxes shifted from primary assimilation to secondary defense hubs. This physiological tradeoff reversed the root exudate profile, shifting from basic carbohydrates to massive efflux of specific organic acids and phenolics. Critically, these allelochemicals functioned as exogenous elicitors, selectively recruiting specific metagenome-assembled genomes (MAGs). Genomic evidence confirmed that single keystone MAGs (Pseudomonas and Burkholderia) coharbored pcaG/H and extracellular laccase genes, establishing a self-contained cometabolic module for concurrent PAEs degradation and carbon stabilization. Consequently, based on correlative multiomics evidence, extensive carbon efflux was associated with a putative coupling between PAEs detoxification and stable humic carbon accumulation, as indicated by a 48.7% increase in the humification index (HIX). Ultimately, this multiomics framework elucidates the plant-driven enhancement of carbon sinks within contaminated soils.}, } @article {pmid42505077, year = {2026}, author = {Zhang, Q and Li, D and Liu, B and Zhang, Y and Li, M and Guo, R and Ni, Y and Chen, S and Ni, B and Qiu, L and Xing, G and Dong, H and Yan, Q and Li, S and Zou, X and Cao, B}, title = {A Comprehensive Microbial Gene Catalog of the Human Airway Microbiome Across Anatomical Sites and Geographic Regions.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e76589}, doi = {10.1002/advs.76589}, pmid = {42505077}, issn = {2198-3844}, support = {BRWEP2024W114060104//Beijing Research Ward Excellence Program/ ; 82341113//National Natural Science Foundation of China/ ; 025-NHLHCRF-JBGS-B-WZ-06//National High Level Hospital Clinical Research Funding/ ; 2022YFA1304303//National Key R&D Program of China/ ; }, abstract = {The respiratory microbiota is a critical determinant of airway health, yet functional characterization remains challenging due to the lack of a high-resolution reference catalog. To address this gap and enable systematic investigation at both species and gene levels, we constructed the integrated Human Airway Microbiome Gene Catalog (iHAMGC) through high-throughput metagenomic analysis of 12,273 airway samples. This catalog comprises 24,185,985 non-redundant microbial genes and provides extensive taxonomic and functional annotations, with a particular focus on clinically relevant elements, including antibiotic resistance genes, virulence factors, and antimicrobial peptides. We further resolved the bacterial hosts of resistance genes and virulence factor genes, as well as taxa contributing to antimicrobial peptide activity. The iHAMGC captures site-specific microbial and functional variations across distinct airway niches and reveals regional differences in functional potential. By offering a comprehensive, publicly accessible reference for airway microbial genes, the iHAMGC serves as a foundational resource for advancing our understanding of the airway microbiota in respiratory health and disease.}, } @article {pmid42505127, year = {2026}, author = {Díaz-Rúa, R and Drautz-Moses, DI and Zhao, X and Perumal, S and Esau, L and Angelov, A and Putra, A and Driguez, P and Cheung, MS and Palescandolo, E}, title = {Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0001326}, doi = {10.1128/spectrum.00013-26}, pmid = {42505127}, issn = {2165-0497}, abstract = {UNLABELLED: Metagenomics enables comprehensive exploration of microbial communities but is influenced by library preparation and sequencing technologies, affecting recovery of microbial genomes and proteins. Here, we benchmarked six Illumina-compatible short-read library preparation conditions in triplicate at 2 × 150 bp and 2 × 250 bp read lengths alongside PacBio HiFi long-read sequencing using a composite environmental sample of marine mangrove sediment and terrestrial palm tree soil. Longer short reads (2 × 250 bp) combined with optimal library preparation approaches improved assembly quality, protein detection, and metagenome-assembled genome (MAG) recovery, achieving results approaching those of long-read sequencing. TruSeq libraries at 2 × 250 bp recovered more than sevenfold more unique proteins than the same kit at 2 × 150 bp (811,701 vs 110,108) using the same number of sequencing reads, while recovering a comparable number of high-quality MAGs to PacBio HiFi long-read sequencing (11 vs 18) and surpassing it in protein discovery by almost 10-fold (811,701 vs 87,745) at less than half of the sequencing cost. Furthermore, biosynthetic gene cluster analysis identified 46 biosynthetic gene clusters in TruSeq-250PE assemblies compared to 38 in PacBio HiFi, with several showing no close match in the MIBiG database. Although long reads yield more contiguity and complete genomes, longer short reads offer a cost-effective, scalable alternative for uncovering microbial and functional diversity. These findings provide critical guidance for metagenomic experimental design, demonstrating that strategic selection of library preparation chemistry and sequencing parameters can reveal more unknown microbial information in complex biomes without requiring additional sequencing depth.

IMPORTANCE: Metagenomic outcomes are strongly influenced by library preparation and sequencing strategies, yet their combined effects in complex environmental samples remain poorly defined. Here, we provide the first direct comparison of Illumina NovaSeq short-read metagenomic sequencing at 2 × 150 bp and 2 × 250 bp across multiple library preparation kits, alongside PacBio HiFi long-read sequencing. We show that sequencing read length and library preparation critically shape assembly quality, protein recovery, and metagenome-assembled genome (MAG) reconstruction. These findings demonstrate that short-read sequencing at 2 × 250 bp, with appropriate library preparation, can match long-read technologies in MAG recovery while substantially surpassing them in protein discovery. With less than half of the sequencing price and a 3.5-fold reduction in cost per gigabase of usable data, this method facilitates more accessible large-scale metagenomic analysis within complex environmental systems.}, } @article {pmid42505598, year = {2026}, author = {Fortaleza, JAG and Cabuhat, KSP and Lagunzad, HC and Panizales, WB and Cruz, JTP and Matamis, JG and Mamaat, JER and Libres, AC and Dulay, RMR and Nuevo, JJM}, title = {Artificial Intelligence in Bacteriophage Science: A Comprehensive Narrative Review of Applications, Challenges, and Translational Opportunities.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/antibiotics15070635}, pmid = {42505598}, issn = {2079-6382}, abstract = {Antimicrobial resistance and persistent biofilm-associated infections have renewed interest in bacteriophages as alternatives or complements to conventional antibiotics. However, broader therapeutic adoption remains constrained by slow phage discovery, incomplete genome characterization, narrow host range, complex therapeutic matching, and manufacturing variability. Artificial intelligence (AI) offers computational approaches that may help address several of these limitations. This comprehensive narrative review discusses current AI applications across the bacteriophage pipeline, including metagenomic phage discovery, genome annotation, phage-host interaction prediction, personalized phage selection, cocktail optimization, and phage-antibiotic combination design. The review also examines AI-assisted synthetic biology approaches, including receptor-binding protein redesign, CRISPR-enabled engineering, generative genome design, and biosafety screening, as well as emerging applications in bioprocess optimization, yield prediction, purification analytics, quality assurance, and supply-chain management. Current evidence suggests that AI may accelerate phage identification, improve host-range prediction, support therapeutic optimization, and strengthen manufacturing consistency, potentially facilitating the transition of phage therapy from individualized rescue interventions toward more scalable antimicrobial platforms. Nevertheless, major limitations remain, including fragmented, taxonomically biased datasets; limited external validation; restricted interpretability; privacy concerns; biosafety oversight; and evolving regulatory frameworks. Future progress will depend on standardized datasets, multimodal validation, scalable manufacturing systems, experimental and clinical verification, and coordinated regulatory development.}, } @article {pmid42505622, year = {2026}, author = {Braunstein, R and Rimon, A and Teitelbaum, R and Coppenhagen-Glazer, S and Molho-Pessach, V and Hazan, R}, title = {Isolation and Characterization of ΦCA1NRNZ, a Lytic Bacteriophage Targeting the Emerging Device-Associated Pathogen Cutibacterium avidum.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/antibiotics15070659}, pmid = {42505622}, issn = {2079-6382}, support = {3015005777//Milgrom Family Support Program/ ; ISF1349/20//Israel Science Foundation/ ; A2232//Rosetrees Trust/ ; }, abstract = {Background: Cutibacterium avidum is an emerging opportunistic pathogen responsible for device-associated infections, including prosthetic joint and breast implant infections. Unlike its relative C. acnes, for which phage therapy has been explored, C. avidum infections are recalcitrant to antibiotics, and no infecting bacteriophages have been described to date. Here, we report the isolation and characterization of ΦCA1NRNZ, to the best of our knowledge, the first lytic phage described against C. avidum. Methods: ΦCA1NRNZ was obtained from wastewater sampling at the Sorek Treatment Facility in Jerusalem. Wastewater metagenomics, transmission electron microscopy, genome sequencing, host-range testing, efficiency of plating (EOP), aerobic and anaerobic lysis assays, and antibiofilm assays against mature C. avidum biofilms were performed. Results: Metagenomic analysis indicated low and transient detection of C. avidum-classified reads in wastewater. ΦCA1NRNZ was identified as a long-tailed Caudoviricetes with a ~320 nm virion. Its 33,712 bp dsDNA genome (GenBank PV441878.1) encodes 46 predicted proteins, shares 76.5% nucleotide identity with C. acnes phage ΦFD1, and contains divergent tail-fiber and host-recognition genes. No known bacterial virulence, toxin, human pathogenicity-associated, or antibiotic-resistance genes were identified. ΦCA1NRNZ lysed all 11 clinical C. avidum isolates tested under aerobic and anaerobic conditions, with EOP values of 0.11-5.55, mean 1.87, and showed no lytic activity against 25 C. acnes isolates. Against mature biofilms, ΦCA1NRNZ reduced total biomass by 28.4% (p = 0.014), reduced viable cell counts by approximately two logs, and increased extracellular ATP release (p < 0.001). Conclusions: The strict species specificity and significant in vitro antibiofilm activity of ΦCA1NRNZ support its potential for phage therapy of device-associated C. avidum infections.}, } @article {pmid42505651, year = {2026}, author = {Niculescu, AG and Iacob, CM and Brătilă, E and Tocariu, R and Coroleucă, CA and Corcionivoschi, N and Vrancianu, CO and Popescu, DL and Popa, GL and Popa, MI and Cristian, RE and Grigore, GA}, title = {Antibiotic-Driven Gut Microbiome Dysbiosis: Resistome Dynamics, Metabolic Disruption, and Paths to Restoration.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/antibiotics15070688}, pmid = {42505651}, issn = {2079-6382}, support = {PN-IV-P2-2.1-TE-2023-1449//Executive Unit for Financing Higher Education, Research, Development and Innovation/ ; Component C9/Investment no. 8 (I8), PNRR-III-C9-2023-I8, contract no 760231, ID proiect - CF 53/28.12.2023//Ministry of Research and Innovation/ ; }, abstract = {The gut microbiome is a dynamic ecosystem that plays essential roles in host metabolism, immune regulation, colonization resistance, and maintenance of intestinal homeostasis. Antibiotic exposure profoundly disrupts this ecosystem by reducing microbial diversity, depleting beneficial commensals, reshaping microbial metabolic functions, and remodeling the gut resistome through the selection and dissemination of antibiotic resistance genes (ARGs). Increasing evidence from longitudinal metagenomic, multi-omics, and experimental studies indicates that these perturbations may persist long after antibiotic withdrawal due to incomplete ecological recovery, sustained mobile genetic element-mediated ARG dissemination, and altered microbiome resilience. Beyond antimicrobial resistance, antibiotic-induced dysbiosis has been associated with reduced short-chain fatty acid production, altered bile acid metabolism, impaired epithelial barrier function, and broader disturbances in host metabolic homeostasis, although many of these relationships remain associative rather than causal. This review provides an integrated overview of antibiotic-driven gut microbiome dysbiosis, emphasizing the ecological, functional, metabolic, and resistome-level consequences of antibiotic exposure together with the mechanisms governing microbiome recovery. Current microbiome-targeted restoration strategies, including probiotics, phage therapy, fecal microbiota transplantation, and next-generation microbiome therapeutics, are critically evaluated with particular attention to their evidence maturity, limitations, and translational potential. Finally, key knowledge gaps and future research priorities are discussed to support the development of more effective microbiome-preserving antimicrobial strategies and to limit the long-term dissemination of antimicrobial resistance.}, } @article {pmid42505659, year = {2026}, author = {Espinoza-Culupú, A and Vasquez, SR and Toribio, IV and Farfán-López, M and Ramos, BM and Távara, MC and Palacios-Rodriguez, AP and da Silva Junior, PI and Ramirez, P}, title = {Integrated Genome Mining, Bacterial Co-Culture Activation, and Peptidomic Analyses Identify Antimicrobial Peptide Candidates from South American Bacteria.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/antibiotics15070696}, pmid = {42505659}, issn = {2079-6382}, support = {PE501084176-2023-PROCIENCIA//PROCIENCIA/ ; }, abstract = {Background/Objectives: Antimicrobial resistance (AMR) is a major global health threat that requires the discovery of new antimicrobial agents. Environmental microbiomes from understudied regions represent a valuable source of antimicrobial peptide (AMP) candidates. This study aimed to identify and prioritize AMP candidates from South American genomic and metagenomic datasets and to investigate the antimicrobial potential of bioactive secretomes obtained through bacterial co-culture. Methods: A total of 853 genomes and 360 metagenomes were analyzed using a reproducible genome- and metagenome-mining pipeline combined with machine learning-based AMP prediction. Predicted AMP candidates were further characterized using complementary bioinformatic tools to assess physicochemical, structural, hemolytic, toxicological, anti-inflammatory, and anticancer properties. Selected environmental isolates were subjected to bacterial co-culture, followed by SPE-C18 and HPLC fractionation. Antimicrobial activity, antioxidant activity, hemolysis, minimum inhibitory concentration (MIC), and LC-MS/MS peptidomic analyses were performed on bioactive secretome fractions. Results: Genome and metagenome mining identified diverse AMP candidate sequences associated with bacterial genera including Streptomyces, Bacillus, Burkholderia, and Shewanella. Structural predictions revealed a predominance of α-helical conformations among prioritized candidates. Several secretome fractions obtained from co-cultures displayed antimicrobial activity against Gram-positive and Gram-negative bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Active fractions showed no detectable hemolytic activity and exhibited antioxidant activity in DPPH assays. MIC analyses indicated broad-spectrum activity against Escherichia coli ATCC 11229, Pseudomonas aeruginosa ATCC 27853, Klebsiella pneumoniae, carbapenem-resistant Acinetobacter baumannii, and MRSA, with an apparent MIC of 10,000 mg/L. LC-MS/MS analysis of bioactive fractions identified peptide sequences by de novo sequencing, including KTESHHK, KRVGPRR, GLFPRLGVSPR, and HHAEHLVHFR. Conclusions: Integrated genome mining, bacterial co-culture activation, and peptidomic analyses provide a useful framework for prioritizing antimicrobial peptide candidates from environmental microbiomes. The identification of peptide-containing bioactive fractions with antimicrobial and antioxidant activities highlights the potential of South American bacterial resources for the discovery of novel antimicrobial compounds. Further purification, peptide synthesis, and biological validation will be required to determine the contribution of individual peptides to the observed activities.}, } @article {pmid42505669, year = {2026}, author = {Kim, D and Lee, WS and Lee, KH and Choi, MH and Hong, JS and Park, YJ and Yoon, JG and Lee, K and Jeong, SH}, title = {Changes in the Gut Microbiome Following Perioperative Prophylactic Cefazolin Administration in Patients Undergoing Orthopedic Surgery: A Longitudinal Prospective Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/antibiotics15070706}, pmid = {42505669}, issn = {2079-6382}, support = {2022-ER2106-00//Korea Disease Control and Prevention Agency/ ; 2023-ER-2106-020//Korea Disease Control and Prevention Agency/ ; }, abstract = {INTRODUCTION: Cefazolin is a first-generation cephalosporin with a moderate antimicrobial spectrum and the ability to induce the production of beta-lactamases by bacterial hosts. We investigated the effect of prophylactic cefazolin administration on the gut microbiome in patients undergoing orthopedic surgery.

METHODS: A total of 42 patients were included in this study, and fecal samples were collected before cefazolin administration, within 3 days after administration, and 1 month after surgery. Shotgun whole-metagenome sequencing was performed with DNA extracted from fecal samples to assess the taxonomic composition and antimicrobial resistance genes (ARGs).

RESULTS: Within 3 days after perioperative prophylactic cefazolin administration, both the diversity indices and the Gut Microbiome Health Index were significantly decreased. Furthermore, a decrease in two beneficial anaerobic Gram-positive taxa, Ruminococcus and Fusicatenibacter, and an increase in Enterobacterales was observed. The relative abundances of ARGs related to fluoroquinolone and beta-lactam antimicrobials including penicillin, cephalosporin, carbapenem, and monobactam, were also significantly increased. The changes in the taxonomic composition and resistome related to perioperative cefazolin administration partially reverted after one month.

CONCLUSIONS: Our findings suggest that even perioperative administration of a single-class antimicrobial agent could be related to the decrease of the gut microbiome diversity with potentially unfavorable taxonomic changes and lead to an increase in ARGs.}, } @article {pmid42505832, year = {2026}, author = {Mancini, P and Brandtner, D and Cordeschi, G and Iaconelli, M and Mastrantonio, V and Porretta, D and La Rosa, G}, title = {Evaluating the Effect of Sampling Scale on Mosquito Virome Characterization Using PacBio HiFi Long-Read Metagenomics.}, journal = {Insects}, volume = {17}, number = {7}, pages = {}, doi = {10.3390/insects17070721}, pmid = {42505832}, issn = {2075-4450}, abstract = {Characterizing the mosquito virome is essential for understanding host-microbiota interactions and vector competence, but it can be influenced by sample scale, sequencing strategy, and host depletion. This study evaluated the effect of sampling scale on mosquito virome characterization using a third-generation sequencing (TGS) metagenomics approach based on PacBio HiFi long reads, applied to L4 larvae and adults of Aedes mariae, analyzing single individuals and pools of increasing size before and after host genome removal. The results showed that sequencing yield did not increase with pool size, indicating that the total number of reads is not proportional to the number of individuals. Host genome removal reduced the overall number of reads but altered their composition, increasing the relative proportion of assigned viral reads and reducing unclassified sequences. Despite a similar total read output, virome diversity increased with pool size, with larger pools showing greater taxonomic richness driven by the contribution of each individual. However, the high proportion of unassigned reads suggests the presence of uncharacterized viruses. This methodological workflow was technically feasible for both single-individual and pooled samples. Single-individual analyses may provide complementary information on individual-level virome composition and on low-abundance viral taxa that could be less apparent in pooled samples, whereas pooled samples may facilitate the detection of a broader range of viral taxa and may better capture the shared component of viral diversity within the analyzed population.}, } @article {pmid42505983, year = {2026}, author = {Li, D and Wu, X and Yuan, F and Zhou, F and Cai, B and Wei, K and Huang, W}, title = {Microbial Community Differentiation and Predicted Chemical-Defense-Related Functional Potential Across Distinct Microhabitats of Cultured Hemicentrotus pulcherrimus.}, journal = {Marine drugs}, volume = {24}, number = {7}, pages = {}, doi = {10.3390/md24070243}, pmid = {42505983}, issn = {1660-3397}, support = {2025Y01//Ningde Normal University/ ; }, mesh = {Animals ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Sea Urchins/microbiology ; Aquaculture ; Quorum Sensing ; Ecosystem ; }, abstract = {Sea urchins harbor diverse microbial communities that may contribute to host-associated ecological interactions, microbial competition, and chemical defense. However, the compartment-specific organization of sea urchin-associated microbiota and their predicted chemical-defense-related functional potential remain poorly understood under aquaculture conditions. In this study, 16S rRNA gene amplicon sequencing was used to characterize microbial communities in rearing water, coelomic fluid, intestine, stomach contents, and surface mucus of Hemicentrotus pulcherrimus (H. pulcherrimus). KEGG Orthology (KO)-based functional prediction was further performed to evaluate predicted chemical-defense-related functional potential, including predicted chemical-defense-related pathways, siderophore-related functions, quorum sensing-related functions, and bacterial competition- and secretion system-related functions. Rarefaction curves and Coverage values indicated sufficient sequencing depth. Alpha diversity and Nonmetric multidimensional scaling (NMDS) analyses revealed clear microbial differentiation among the five sample types, with rearing water showing higher microbial richness. Taxonomic analysis identified Pseudomonadota, Bacteroidota, Campylobacterota, Bacillota, Planctomycetota, and Spirochaetota as dominant phyla, with several discriminative taxa across compartments. KO prediction showed that total predicted abundance of predicted chemical-defense-related KOs differed significantly among sample types. Among host-associated compartments, surface mucus showed relatively higher predicted siderophore-related KO potential, whereas stomach contents showed higher predicted quorum sensing-related KO potential among host-associated compartments. These findings suggest compartment-specific microbial communities and predicted chemical-defense-related functional potential in cultured H. pulcherrimus under aquaculture conditions. Because these functions were inferred from 16S-based KO prediction, they should be interpreted as preliminary hypotheses for future metagenomic, metabolomic, and culture-dependent validation.}, } @article {pmid42506218, year = {2026}, author = {Abán, CL and Larama, G and Ducci, A and Fallard, A and Ortiz, J and Vargas-Gil, S and Pérez-Brandan, C}, title = {Legacy Effects of Urochloa brizantha Cover Cropping on Rhizosphere Fungal Communities and Soil Properties in a Degraded Common Bean System.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, doi = {10.3390/jof12070456}, pmid = {42506218}, issn = {2309-608X}, support = {2023-705 PD-I093-INTA, FONCyT-PICT 2019-00896, PIP 2022-2024 112202101 00162CO, ANID project, ATE220038.//National Institute of Agricultural Technology (INTA), The National Scientific and Technical Research Council (CONICET) and by the Concurso Anillos de Investigación en Áreas Temáticas,/ ; }, abstract = {Intensive agricultural practices based on continuous monocropping and prolonged bare-soil fallows have contributed to soil degradation and loss of biological functioning. Replacing fallows with cover crops (CCs) is a promising strategy to restore soil quality, yet their legacy effects on rhizosphere fungal communities remain poorly understood. This study evaluated the legacy effects of Urochloa (syn. Brachiaria) brizantha cover cropping on rhizosphere fungal communities, as well as soil physicochemical and biological properties, in a degraded common bean system. A field experiment with a randomized complete block design included: bare fallow (BM), one (B1) or two (B2) CC cycles before bean, a perennial pasture (PB), and a pristine soil reference (PS). High-throughput sequencing showed that Urochloa-based treatments significantly shifted fungal community composition compared to BM, increasing saprotrophic and beneficial taxa (e.g., Mortierella, Penicillium, Coprinellus) and reducing potential pathogens such as Fusarium. These changes were associated with higher soil organic carbon, aggregate stability, microbial biomass, and enzyme activities, especially in B2 and PB. Indicator taxa identified by LEfSe were linked to organic matter decomposition and nutrient cycling. Multivariate analyses revealed strong associations between fungal community structure and soil properties. Overall, U. brizantha cover cropping induced measurable legacy effects, promoting soil biological recovery even after short-term implementation.}, } @article {pmid42506289, year = {2026}, author = {Cruz, GMD and Fraga, AS and Garcia, MT and Junqueira, JC}, title = {Oral Mycobiome: Composition, Functionality and Clinical Implication.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, doi = {10.3390/jof12070528}, pmid = {42506289}, issn = {2309-608X}, support = {310265/2022-3//National Council for Scientific and Technological Development/ ; 88887.149515/2025-00//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; }, abstract = {Historically, the study of oral fungal species was limited by the inability to cultivate most of them. However, advances in metagenomic techniques have enabled the direct identification of microbial genomes from human samples, markedly broadening our understanding of the oral mycobiome. This narrative review aims to analyze the available scientific evidence on the composition and dynamics of the oral mycobiome, as well as its influence on the development of local pathological conditions. The oral mycobiome is highly diverse, with emphasis on genus Candida, followed by Cladosporium, Aureobasidium and Saccharomyces. Candida albicans remains the most frequently identified species in both health and diseases state. However, individuals with oral candidiasis present a higher detection of Candida dubliniensis, Candida parapsilosis, Pichia kudriavzevii, Antrodiella micra and Cladosporium sphaerospermum. In dental caries, C. albicans and C. dubliniensis are associated with advanced lesions, whereas Debaryomyces and Rhodotorula may exert protective effects against Streptococcus mutans, a cariogenic bacterium. In periodontitis, an increase in yeast-bacteria interactions is observed. Additionally, C. albicans has been implicated in oral carcinogenesis through multiple mechanisms. These findings highlight the need for a deeper understanding of the oral mycobiome to enable early detection of oral diseases and the development of therapeutic approaches.}, } @article {pmid42506302, year = {2026}, author = {Chen, J and Wu, M and Deng, Z and Ying, Y and Lu, M}, title = {Oxygenation-Based Severity Stratification and a Proposed Clinical Diagnostic Workflow for Non-HIV Pneumocystis jirovecii Pneumonia: A Single-Center Observational Study.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, doi = {10.3390/jof12070541}, pmid = {42506302}, issn = {2309-608X}, support = {Z-2017-24-2202//the Specialized Research Fund for Pathogenic Metagenomics of the Bacterial Infection and Drug Resistance Prevention of the Chinese Medical Association/ ; LCYX-2026-11//Beijing Pharmaceutical Association Clinical Pharmacy Research Project/ ; }, abstract = {Non-HIV Pneumocystis jirovecii pneumonia (PJP) is a life-threatening opportunistic fungal pneumonia that may progress rapidly in immunocompromised hosts. Broad bronchoalveolar lavage fluid (BALF) molecular testing supports microbiologic recognition, but additional organisms often require bedside adjudication. We conducted a single-center observational study of 49 HIV-negative adults with clinically confirmed PJP, routine BALF metagenomic next-generation sequencing support, and complete 30-day follow-up. Diagnosis required compatible symptoms and chest computed tomography findings, microbiologic support for P. jirovecii, and infectious disease specialist exclusion of isolated colonization. The primary endpoint was ICU-level care requirement, defined as ICU admission, invasive mechanical ventilation, or 30-day all-cause mortality. Recent immunosuppressive exposure was present in 48 patients (98.0%). ICU-level care was required in 15 patients (30.6%); all ventilation and death events occurred in this group, and 30-day mortality was 10.2%. Baseline PaO2/FiO2 < 200 mmHg was associated with higher proportions of ICU admission, mechanical ventilation, and death. Chronic kidney disease, lower creatinine clearance, higher lactate dehydrogenase, and bacterial co-pathogen context showed exploratory signals, whereas overall co-pathogen positivity was heterogeneous. These findings support integrating oxygenation status, host vulnerability, and conservative co-pathogen adjudication to guide escalation and antimicrobial decisions after BALF testing.}, } @article {pmid42506410, year = {2026}, author = {Han, M and Liu, X and Guo, Y and Xu, Q and Wei, L and Wei, J and Khan, MZ and Wang, C and Zhang, Z}, title = {Managing Anti-Nutritional Factors in Plant-Based Feeds: Implications for Herbivore Nutrition and Production.}, journal = {Metabolites}, volume = {16}, number = {7}, pages = {}, doi = {10.3390/metabo16070456}, pmid = {42506410}, issn = {2218-1989}, support = {2023YFD1302004//National Key R&D Program of China/ ; }, abstract = {Anti-nutritional factors (ANFs) in terrestrial plant feeds constrain efficient herbivore production, an issue intensified by rising feed costs and growing demand for animal products. Unlike previous reviews that focus on single ANFs or feed types, this review provides an integrated, cross-species framework linking ANF chemistry, rumen microbial interactions, and mitigation strategies. It examines major ANF classes-tannins, phytates, saponins, oxalates, protease inhibitors, lectins, glucosinolates, and gossypol-and their distribution and biochemical modes of action. Mechanistic pathways are grouped into digestive effects (reduced palatability and enzyme inhibition), microbial effects (altered rumen microbiota and fermentation), metabolic effects (impaired absorption), and mineral interactions (nutrient complexation and chelation). Species-specific responses are evaluated, emphasizing the partial detoxification capacity of the rumen microbiome and the dose-dependent nature of ANF effects. Mitigation strategies-physical, chemical, microbial, enzymatic, probiotic, and genetic-are critically assessed for efficacy, scalability, and sustainability. Emerging metabolomic and metagenomic evidence shows that certain ANFs confer functional benefits at controlled doses; for example, tannins improve nitrogen retention, saponins reduce methane, and phytic acid scavenges free radicals. This synthesis supports strategic management rather than complete elimination, informing safe and sustainable use of terrestrial feeds under evolving food-security and environmental challenges.}, } @article {pmid42506444, year = {2026}, author = {Lu, Q and Zhao, H and RuKeye, K and Geng, Y and Du, J and Chen, L and Zhu, Q and Xi, C and Li, J}, title = {Impact of Ear Stage Drought Stress on Yield and Rhizosphere Metagenomic Profiles in Maize Cultivars with Contrasting Drought Tolerance.}, journal = {Metabolites}, volume = {16}, number = {7}, pages = {}, doi = {10.3390/metabo16070493}, pmid = {42506444}, issn = {2218-1989}, support = {32460482//Yunnan Agricultural University/ ; }, abstract = {Background/Objectives: Drought stress is a primary constraint on maize productivity, yet the role of rhizosphere microbial communities in modulating cultivar-specific drought resilience remains poorly understood. This study aimed to investigate the physiological and microbiome-mediated responses underlying differences in drought tolerance between contrasting cultivars to better understand drought tolerance mechanisms. Methods: Two maize cultivars with contrasting drought tolerance-NK718 (tolerant) and Zhongdan 808 (sensitive)-were subjected to drought stress at the V12 stage. We assessed yield components, oxidative stress indicators (Malondialdehyde (MDA)), and antioxidant enzyme activities (Superoxide Dismutase (SOD), Peroxidase (POD), Catalase (CAT)). Metagenomic sequencing was employed to analyze structural and functional shifts in the rhizosphere microbiota. Results: Drought significantly suppressed yield and physiological performance in both cultivars. However, the sensitive cultivar suffered more pronounced yield losses and severe oxidative stress, indicated by elevated Malondialdehyde (MDA) and decreased antioxidant enzyme activities. Conversely, the tolerant cultivar maintained superior physiological homeostasis. Metagenomic sequencing revealed drought-induced microbial shifts, including decreased Proteobacteria and Ascomycota, alongside increased Actinobacteriota and Mucoromycota. Notably, the drought-tolerant cultivar exhibited enhanced microbial community stability and more complex co-occurrence networks. Furthermore, it enriched specific functional pathways, such as phenylpropanoid biosynthesis, which positively correlated with yield stability and antioxidant capacity. Conclusions: Maize drought tolerance is underpinned by the coordinated regulation of plant physiological adaptation and the structural and functional stabilization of the rhizosphere microbiome. These findings offer a theoretical framework for developing breeding strategies that leverage root-microbe interactions to optimize maize yields under water-limited conditions.}, } @article {pmid42506453, year = {2026}, author = {Munzone, M and Marmo, GM and Polizzi, A and Jovanova, E and Angjelova, A and Lupi, SM and Isola, G}, title = {Metagenomics in the Interplay Among Oral and Gut Dysbiosis.}, journal = {Metabolites}, volume = {16}, number = {7}, pages = {}, doi = {10.3390/metabo16070502}, pmid = {42506453}, issn = {2218-1989}, support = {PNRR-POC-2023-12 377 354//Ministero della Salute/ ; }, abstract = {Periodontitis is a chronic inflammatory disease increasingly recognized as a manifestation of complex microbial dysbiosis extending beyond the oral cavity. Recent advances in spatial metagenomics provide unprecedented resolution to investigate microbial community structure, function, and localization within periodontal niches and along the oral-gut axis. This review aims to explore how spatially resolved metagenomic approaches refine our understanding of the ecological and functional shifts in bacterial populations associated with periodontitis and their systemic implications. By integrating spatial mapping with shotgun metagenomics, we highlight distinct microenvironmental signatures within periodontal pockets, characterized by anaerobic pathobionts, metabolic reprogramming, and localized inflammatory gradients. Furthermore, we examine evidence supporting bidirectional interactions between oral and gut microbiota, suggesting that oral-derived taxa may contribute to gut dysbiosis through translocation and ecological disruption. From a basic science perspective, spatial metagenomics reveals niche-specific microbial functions and interspecies interactions that are not captured by bulk sequencing. Clinically, these insights open avenues for precision diagnostics and targeted therapeutics, including microbiome modulation strategies tailored to spatial microbial organization. Overall, this work underscores the importance of spatial context in metagenomic analyses and advances the conceptual framework linking periodontal disease to systemic microbial dysbiosis.}, } @article {pmid42506917, year = {2026}, author = {Han, Z and Zang, C and Zhang, C and Di, W and Zeng, Q}, title = {Genetically predicted gut microbiota and risk of pediatric asthma and food allergy in East Asian populations: a two-sample Mendelian randomization study.}, journal = {The Journal of asthma : official journal of the Association for the Care of Asthma}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/02770903.2026.2706359}, pmid = {42506917}, issn = {1532-4303}, abstract = {OBJECTIVE: To investigate the genetically predicted associations between gut microbiota composition and the risk of pediatric asthma and food allergy in East Asian populations using a bidirectional two-sample Mendelian randomization (MR) approach.

METHODS: We performed bidirectional two-sample MR analyses using summary-level genome-wide association study (GWAS) data. Genetic instruments for 500 gut microbial taxa were obtained from the 4D-SZ cohort, which included 3,432 Chinese individuals who underwent whole-metagenome shotgun sequencing. Outcome GWAS summary statistics for pediatric asthma (547 cases and 161,803 controls; GCST90018675) and food allergy (3,777 cases and 165,939 controls; GCST90018625) were derived from the Biobank Japan project. All participants were of East Asian ancestry. The primary MR analysis was conducted using the inverse-variance weighted (IVW) method, with MR-Egger, weighted median, and weighted mode analyses used as complementary approaches. Sensitivity analyses included Cochran's Q test for heterogeneity, the MR-Egger intercept test for horizontal pleiotropy, and MR-PRESSO for outlier detection.

RESULTS: The IVW analysis identified nine gut microbial taxa with nominally significant associations with pediatric asthma risk (p < 0.05). Among them, Subdoligranulum showed a suggestive protective association (OR = 0.91, 95% CI: 0.83-0.99), whereas Solobacterium showed a suggestive risk association (OR = 1.08, 95% CI: 1.00-1.16). For food allergy, eighteen taxa were nominally associated with disease risk (p < 0.05). Bacteroides helcogenes showed a suggestive protective association (OR = 0.96, 95% CI: 0.94-0.98), whereas Alistipes shahii showed a suggestive risk association (OR = 1.03, 95% CI: 1.00-1.05). Sensitivity analyses yielded generally consistent results. Reverse MR analyses did not identify significant genetically predicted effects of pediatric asthma or food allergy on gut microbiota composition.

CONCLUSION: This exploratory MR study provides suggestive evidence that specific gut microbial taxa may be associated with pediatric asthma and food allergy in East Asian populations. These findings offer preliminary support for the role of the gut microbiota in allergic diseases and underscore the importance of population-specific research. Further large-scale studies with stricter multiple-testing correction are needed to validate these associations.}, } @article {pmid42507748, year = {2026}, author = {Curtis, A and Fitzpatrick, DA and Harrison, F and Kavanagh, K}, title = {Aspergillus fumigatus coinfection facilitates Pseudomonas aeruginosa chronicity within an ex-vivo pig lung model.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {7}, pages = {}, doi = {10.1099/mic.0.001745}, pmid = {42507748}, issn = {1465-2080}, mesh = {Animals ; *Aspergillus fumigatus/pathogenicity/physiology/genetics ; *Pseudomonas aeruginosa/pathogenicity/genetics/growth & development/physiology ; *Coinfection/microbiology ; *Lung/microbiology/pathology/immunology ; Swine ; *Pseudomonas Infections/microbiology/immunology ; Disease Models, Animal ; Virulence ; Proteomics ; *Aspergillosis/microbiology ; Proteome ; }, abstract = {Pseudomonas aeruginosa and Aspergillus fumigatus represent the dominant bacterial and fungal pathogens in the lungs of adults with cystic fibrosis. Understanding how these species interact with each other and the host may provide insight into pathology and microbial succession in the lung. The ex vivo pig lung model is suitable for studying host responses to pathogens in an ethical and cost-effective manner due to its rich cell complexity and anatomical and immunological similarities to humans. Metagenomic analysis demonstrated that A. fumigatus promoted the proliferation of Pseudomonadota and P. aeruginosa in coinfected explants. Proteomic analysis of coinfected alveolar lung explants identified reduced virulence of A. fumigatus in competition with P. aeruginosa with reductions in abundance of dipeptidyl-peptidase 5 (-10.30-fold) and thioredoxin reductase gliT (-11.72-fold) and a reduction in amide biosynthetic processes. P. aeruginosa flourished in coinfected tissue and increased protein translation and amino acid biosynthesis and cellular nitrogen utilization. Examination of changes in the porcine proteome indicated specific nutritional utilization with A. fumigatus inducing greater complement activation and utilization of amino acids, while P. aeruginosa infection induced greater natural killer cell toxicity and potential butanoate metabolism from the host. Increased abundance of proteins associated with inflammation and immune activation was observed in coinfected samples relative to the mono-infected tissues. Coinfection also resulted in the reduction in abundance of ferritin and lactotransferrin, which may indicate elevated bioavailability of iron that could facilitate P. aeruginosa virulence.}, } @article {pmid42508029, year = {2026}, author = {Poshvina, DV and Balkin, AS and Vasilchenko, AS}, title = {Metagenome-Assembled Genomes from Northern West Siberia: Insights into Microbial Diversity in Permafrost and Contemporary Soils.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag182}, pmid = {42508029}, issn = {1365-2672}, abstract = {AIMS: Permafrost thawing due to global warming threatens to release long-preserved microbial communities, including potentially novel bacterial lineages. Despite the importance of West Siberian permafrost for climate models, genome-resolved studies of its microbial diversity remain limited. This study aimed to recover and characterize metagenome-assembled genomes (MAGs) from permafrost and contemporary soils of northern West Siberia, and to assess their biosynthetic and antibiotic resistance potential.

METHODS AND RESULTS: We reconstructed 117 MAGs from soil samples collected from northern West Siberia, including ancient permafrost deposits (~10 000 and ~ 39 000 years old) and contemporary soils. Permafrost deposits exhibited significantly higher biosynthetic gene cluster (BGC) diversity compared to contemporary soils (Shannon H' = 4.15 vs. 3.36-3.59) with terpenes, RiPP-like and NRPS-like clusters being the most abundant. Notably, Vulcanimicrobiota and Verrucomicrobiota were recovered exclusively from permafrost in this dataset. A total of 14 unique antibiotic resistance genes conferring resistance to eight drug classes were detected. The RND efflux pump gene, adeF, dominated the resistome across all biomes, while Van family genes were largely restricted to permafrost at the phylum level. Verrucomiocota showed the highest adeF load followed by Planctomicrobiota and Pseudomonodota. A strong correlation was observed between bacterial genes and antibiotic resistance genes across biomes (Spearman's ρ = 0.893, p = 0.007).

CONCLUSIONS: This genome-resolved study reveals a high level of undiscovered bacterial diversity in West Siberian permafrost including habitat-specific lineages. Our findings highlight permafrost as a rich repository of novel biosynthetic potential and emphasize the importance of metagenomic exploration of Arctic ecosystems under climate change.}, } @article {pmid42508263, year = {2026}, author = {Yang, P and Liu, H and Xu, J and Liu, Y and Ren, C and Cheng, D and Wang, Y and Zhang, L and Cao, X and Häggblom, MM and Zhang, J}, title = {Microbial cleavage and mineralization of acesulfame by Shinella sp. strain KJ01.}, journal = {Water research}, volume = {306}, number = {}, pages = {126561}, doi = {10.1016/j.watres.2026.126561}, pmid = {42508263}, issn = {1879-2448}, abstract = {Acesulfame (ACE), a widely used artificial sweetener, has long been regarded as a persistent marker compound in wastewater treatment systems. Although emerging evidence indicates that ACE can be microbially degraded, the mechanisms governing its initial cleavage and ultimate environmental fate remain poorly resolved. Here, we isolated an ACE-degrading bacterium, Shinella sp. strain KJ01, from activated sludge using D2O-probed Raman-activated cell sorting. Integrated evidence from total organic carbon removal, CO2 production, and transient accumulation of transformation products (TPS) indicates substantial mineralization of ACE by strain KJ01. Comprehensive TP profiling further revealed that hydrolysis was the major initial transformation route of ACE in strain KJ01, while trace and transient intermediates suggested the possible occurrence of minor monooxygenation- and deoxygenation-related side reactions. Multi-omics analyses identified a formylglycine-dependent arylsulfonase (AtsA) as a key enzyme associated with the initial cleavage of ACE, which was further validated through in vivo heterologous expression and in vitro enzymatic assays. AtsA catalyzes the conversion of ACE to acetoacetamide-N-sulfonic acid, initiating structural destabilization and enabling downstream metabolism. A metagenomic survey of wastewater treatment plants revealed widespread occurrence of atsA, with its abundance positively associated with regional ACE loads, suggesting pollutant-driven functional enrichment. Together, these findings link enzyme-level mechanisms to system-scale microbial processes and provide a mechanistic framework for understanding the environmental fate of persistent anthropogenic contaminants in wastewater treatment systems.}, } @article {pmid42508264, year = {2026}, author = {Huang, Z and Wang, C and Liu, H and Wang, J and Tian, C and Shen, J and Feng, J and Wang, X}, title = {Seasonal bloom alternation drives periodic shifts in carbon sink function via differential dissolved organic matter processing in a plateau lake.}, journal = {Water research}, volume = {306}, number = {}, pages = {126568}, doi = {10.1016/j.watres.2026.126568}, pmid = {42508264}, issn = {1879-2448}, abstract = {Frequent algal blooms alter dissolved organic matter (DOM) dynamics and carbon sink functions in eutrophic lakes, yet how bloom type governs DOM molecular transformation and microbial carbon pump (MCP) direction remains unresolved. Integrating Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), metagenomics, Biolog EcoPlate, and incubation experiments, we investigated DOM composition, microbial functions, and refractory dissolved organic carbon (RDOC) formation during cyanobacterial (Pseudanabaena sp.) and dinoflagellate (Peridinium sp.) blooms in Lake Erhai. Cyanobacterial blooms released CHON-enriched, high-molecular-weight (HMW) DOM with elevated carboxyl-rich alicyclic molecules (CRAMs, 39.53 %) accumulation, exhibiting expanded synthesis-dominated meta-metabolome networks and intracellular carbon storage modules (GT35, GH13) with progressively broadening substrate utilization. Conversely, dinoflagellate blooms produced low-molecular-weight (LMW), oxidized, and sulfur-rich DOM with elevated polycyclic aromatic hydrocarbons (PAHs, 14 %), characterized by removal-dominated networks and extracellular degradation modules including polysaccharide lyases and peptidoglycan-degrading enzymes (GH24, CBM50) with specialized catabolic activity. Summer warming promoted cyanobacterial biomass and DOM accumulation, yet enhanced microbial activity functioned as a carbon turnover engine that suppressed net RDOC accumulation. In contrast, lower temperatures in autumn and winter suppressed dinoflagellate biomass, but substrate-specific enzymatic catalysis sustained efficient RDOC formation via activated carbohydrate-active enzymes (CAZymes). These findings suggest that seasonal alternation between cyanobacterial and dinoflagellate blooms modulates MCP direction, driving periodic shifts in Lake Erhai's carbon sink function and indicating that plateau lake carbon management should integrate seasonal temperature variations and algal community composition.}, } @article {pmid42508265, year = {2026}, author = {Li, Z and Gao, J and Wang, P and Fan, Y and He, Y}, title = {Sulfate-driven organic phosphorus mineralization stimulates endogenous phosphorus release in the effluent-receiving river.}, journal = {Water research}, volume = {306}, number = {}, pages = {126557}, doi = {10.1016/j.watres.2026.126557}, pmid = {42508265}, issn = {1879-2448}, abstract = {Seasonal algal blooms in effluent-receiving rivers are being exacerbated by often-overlooked sulfate discharge from wastewater treatment plants. Sulfate inputs can alter sulfur-iron-phosphorus (S:Fe:P) ratios, regulating the contributions of dissimilatory sulfate reduction (DSR) and dissimilatory iron reduction (DIR) to P release. However, how and to what extent DSR and DIR participate in P release under sulfate input remains unknown. Diffusive gradients in thin films (DGT), pathway-specific inhibitors, and microbiological analyses were combined to investigate P release pathways under different S:Fe:P ratios and to quantitatively differentiate the relative contributions of DSR and DIR to P release. It was found that elevated S:Fe:P ratios shifted the primary labile P release from the DIR-driven zone (20-80 mm) to the DSR-driven zone (80-120 mm). Inhibitor experiments further confirmed that sulfate-mediated P release was dominated by DSR (95.4%) in the actual effluent-receiving river. P fractions and metagenomic analyses identified that DSR-driven P release was governed by organic P (OP) mineralization, as evidenced by decreased OP fractions (e.g., NaOHNRP) and increased abundance of OP-mineralizing genes (e.g., phoD). These findings underscored that DSR-driven OP pools in deep sediments (80-120 mm) served as key sources of sulfate-mediated P release in effluent-receiving rivers and highlighted the importance of controlling sulfate discharge to mitigate eutrophication.}, } @article {pmid42508331, year = {2026}, author = {Zhang, J and Cao, W and Xiong, W and Yao, Y and Jiang, D and Liang, W and Wang, L}, title = {Revealing the correlation between microbial community and flavor compounds in traditional Chinese sourdough by integrating flavoromics and metagenomics.}, journal = {International journal of food microbiology}, volume = {460}, number = {}, pages = {111927}, doi = {10.1016/j.ijfoodmicro.2026.111927}, pmid = {42508331}, issn = {1879-3460}, abstract = {Traditional Chinese sourdough (CTS) is mainly used for the fermentation of steamed pastries, providing a unique natural fluffiness and distinctive flavor, and thus holds important culinary value. However, the microbial mechanisms underlying the diversity of its regional characteristic flavors remain poorly understood. In this study, we integrated metagenomic sequencing with multi-platform flavor profiling-including high-performance liquid chromatography (HPLC), electronic nose, gas chromatography-mass spectrometry (GC-MS), and gas chromatography-ion mobility spectrometry (GC-IMS)-to characterize the physicochemical properties, microbial composition, and flavor compounds of 10 CTS samples collected from five provinces across China. A total of 1231 genera and 3358 species were identified, with Fructilactobacillus sanfranciscensis, Saccharomyces cerevisiae and Lactiplantibacillus plantarum being the dominant species. Flavor profiling analysis revealed 109 volatile organic compounds (VOCs), of which 11 key aroma-active compounds (e.g., 1-nonanol, phenethyl alcohol) were identified based on odor activity values (OAV ≥ 1). Using orthogonal partial least squares (O2PLS) modeling, we established associations between 25 potential flavor-producing microorganisms and specific metabolites. Notably, S. cerevisiae exhibited a significant positive correlation with acetic acid, 1-nonanol and glutamic acid, while L. plantarum showed a strong positive correlation with phenethyl alcohol. This study reveals the correlation patterns between microbial communities and flavor compounds in CTS, offering foundational insights for starter culture design, flavor standardization, and industrial application of traditional fermented doughs.}, } @article {pmid42501710, year = {2026}, author = {Coves, M and Midoux, C and Lossouarn, J and Mariadassou, M and Ngo, VQH and Jardillier, L and Krupovic, M and Chapleur, O and Mazéas, L and Bize, A}, title = {Host-virus dynamics in anaerobic digesters facing abiotic inhibition.}, journal = {Water research}, volume = {305}, number = {}, pages = {126521}, doi = {10.1016/j.watres.2026.126521}, pmid = {42501710}, issn = {1879-2448}, abstract = {Viruses play a major role in controlling the structure and dynamics of microbial communities in anaerobic digesters, ecosystems sensitive to disturbances that inhibit methane production. Here, we studied the interplay between abiotic disturbances, microbiome and virome composition, and process performance, to assess whether provirus induction can be triggered by abiotic stresses known to inhibit anaerobic digestion (ammonium, phenol and sodium chloride). We monitored viral dynamics in batch mesophilic anaerobic digesters fed with biowaste through shotgun metavirome sequencing. The diversity of both prokaryotes and viruses was high, with Clostridiales dominating the prokaryotic community and Caudoviricetes dominating the viromes. We identified 132 viral contigs and 19 host genera that were differentially abundant under disturbed conditions. No significant impact of the tested abiotic stresses on provirus induction was observed under the current experimental and analytical framework. The results were consistent with viruses exerting steady, background-level predation through a putative combination of kill-the-winner dynamics at the sub-genus level and piggyback-the-winner dynamics, rather than stress-triggered, synchronous lytic bursts. A few auxiliary metabolic genes were detected, potentially targeting carbon, sulfur and cofactor metabolism in anaerobic digestion. Temperate viruses were dominant, representing up to 71% of the viral genomes confirmed as complete across all conditions. Electron microscopy analysis revealed diverse virus-like particles, including head-tailed particles typical of Caudoviricetes, but also spherical, rod-shaped and spindle-shaped particles typical of archaeal viruses. Notably, we present a new virus family, Eurekaviridae, of spindle-shaped viruses associated with methanogenic archaea.}, } @article {pmid42501789, year = {2026}, author = {Sun, J and Meng, L and Gao, Z and Wang, X and Jin, Y and Yang, H and Sang, H and Zhai, J and Song, Y and Wen, S}, title = {First report and molecular characterization of bovine kobuvirus in beef cattle from eastern Inner Mongolia, China.}, journal = {Veterinary journal (London, England : 1997)}, volume = {}, number = {}, pages = {106794}, doi = {10.1016/j.tvjl.2026.106794}, pmid = {42501789}, issn = {1532-2971}, abstract = {This study presents the first molecular epidemiological investigation and genomic characterization of bovine kobuvirus (BKoV) in eastern Inner Mongolia, China. A total of 162 clinical samples were collected in July 2023 and tested for BKoV using nested PCR, yielding an overall detection rate of 18.52%. Differences in BKoV detection rates were observed among sample types, with a significantly higher detection rate in faecal samples than in blood samples. Metagenomic sequencing generated a near-complete genome sequence of strain NM21, which has been submitted to the GenBank database under accession number PV797393. Phylogenetic analyses based on the partial 3D gene sequences and the near-complete genome sequence of strain NM21 showed that all BKoV sequences detected in this study clustered within Clade 1. Amino acid sequence alignment revealed 21 clade-associated amino acid differences that were relatively conserved within each clade; among them, position 66 of the VP0 protein showed a consistent difference between the two clades, with the corresponding amino acid absent in Clade 2 sequences. Bioinformatic analysis of the major capsid protein VP1 predicted three candidate linear B-cell epitopes. Selection pressure analysis showed that the VP1 gene was generally under purifying selection. Recombination analysis suggested that strain NM21 may contain a potential recombination signal in the 2B non-structural protein region. These findings provide baseline data for elucidating the epidemiological characteristics, genetic evolution, and potential antigenic features of BKoV in eastern Inner Mongolia. They may serve as a reference for subsequent molecular surveillance and evolutionary studies.}, } @article {pmid42498022, year = {2026}, author = {Li, X and Zhu, Z and Wang, Y and Zhang, Y and Dang, X and Zhao, C and Hou, S and Li, B and Ma, F and Hao, L and Zhu, T}, title = {Genome-resolved characterization of candidate thermotolerance traits and predicted protein conformational behavior in Calditerricola during hyperthermophilic composting of organic wastes.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135501}, doi = {10.1016/j.biortech.2026.135501}, pmid = {42498022}, issn = {1873-2976}, abstract = {Hyperthermophilic composting (HC) can generate temperatures above 80 °C without external heating, thereby accelerating organic-waste stabilization; however, how dominant heat-adapted microorganisms maintain cellular function under such extreme conditions remains unclear. Here, we integrated metagenomics, metagenome-assembled genome reconstruction, Calditerricola-resolved functional profiling, partial least squares path modeling, and molecular dynamics simulations to investigate candidate thermotolerance-related traits associated with Calditerricola enrichment during HC. The pile temperature reached 82.6 °C on day 2 and peaked at 86.6 °C on day 4, accompanied by progressive humification, with humic substances increasing from 40.45 to 51.28 mg/g and HA/FA reaching 3.45. Microbial communities differed significantly among composting phases (R[2] = 0.975, P = 0.004), and Calditerricola increased from 0.02% in the initial phase to 6.1% in the thermophilic phase before declining to 0.7% in maturation. Community-level profiles showed comparatively modest variation in selected thermotolerance-related pathways, whereas the independently normalized Calditerricola profile displayed clearer phase-associated increases in functions linked to polyamine metabolism, membrane/envelope homeostasis, proteostasis, and DNA maintenance. Path modeling revealed consistent positive associations between Calditerricola enrichment and polyamine synthesis, membrane stability, and proteostasis. qPCR further revealed phase-associated increases in the community-level copy numbers of representative target genes, particularly polA and speE. During 100-ns simulations at 360 K, the predicted apo structures of PolA, AtpD, SpeE, and FabH retained their overall folds and comparatively stable catalytic-residue geometries. Together, these results define an association-based multi-module framework of candidate traits linked to Calditerricola persistence during HC, providing a genome-resolved basis for prioritizing testable thermotolerance targets in engineered high-temperature waste-treatment systems.}, } @article {pmid42498043, year = {2026}, author = {Kaki, D and Kore, U and Talari, A and Komati, A and Garlapati, C and Dondra, T and De, S and Mandava, K}, title = {Modern approaches to gut microbiome investigation: Sequencing, culturomics, metabolomics, and beyond.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107636}, doi = {10.1016/j.mimet.2026.107636}, pmid = {42498043}, issn = {1872-8359}, abstract = {The human gut microbiome is a complex and constantly evolving community of trillions of microorganisms that are crucial to various aspects of health and disease. It impacts digestion, metabolism, immune function, neurological processes, and vulnerability to illnesses. Recent technological advancements in biology and engineering have transformed microbiome research, allowing for more detailed analysis of microbial composition, functions, and interactions with the host. This review offers a thorough overview of both current and emerging methods for studying the gut microbiome, including sample collection techniques, culture-based approaches like culturomics and microfluidics, as well as culture-independent methods such as 16S rRNA sequencing, shotgun metagenomics, and the integration of multi-omics approaches like metabolomics, proteomics, and transcriptomics. It also discusses innovative tools including single-cell genomics, spatial transcriptomics, and microbiome-on-a-chip platforms, which hold promise for revealing host-microbe interactions at unprecedented levels of detail. The review underscores the importance of combining biological insights with engineering innovations particularly microfluidics and organ-on-a-chip models to recreate gut environments that mimic physiological conditions. Additionally, it explores the potential of artificial intelligence and machine learning in analyzing data and developing predictive models for personalized microbiome-based diagnostics and therapies. Acknowledging challenges such as microbial diversity, environmental sensitivity, and technical hurdles, this review aims to guide researchers in choosing optimal tools to study the gut microbiota, deepen mechanistic understanding, and translate findings into clinical applications that enhance human health.}, } @article {pmid42498369, year = {2026}, author = {Zhu, X and Qian, M and Li, J and Zhu, W and Bi, Z}, title = {Reevaluating glycogen-accumulating organisms as ecological flexors: Mechanistic insights into glycogen-accumulating organisms-mediated enhancement of phosphorus enrichment.}, journal = {Journal of environmental sciences (China)}, volume = {167}, number = {}, pages = {344-352}, doi = {10.1016/j.jes.2025.11.006}, pmid = {42498369}, issn = {1001-0742}, mesh = {*Glycogen/metabolism ; *Phosphorus/metabolism/analysis ; *Waste Disposal, Fluid/methods ; Bioreactors/microbiology ; Biofilms ; *Water Pollutants, Chemical/metabolism ; Wastewater ; Polyphosphates ; }, abstract = {This study challenges the view that glycogen-accumulating organisms (GAOs) solely hinder phosphorus removal in wastewater treatment. We investigated how GAOs influence phosphorus recovery in biofilm sequencing batch reactors (BSBRs) under varying carbon-to-phosphorus (C/P) ratios (20-40 mg-COD/mg-P) and dissolved oxygen (DO) levels (4-6 mg/L). By adjusting C/P and DO, we established systems with GAOs abundances ranging from 21.02 % to 2.49 % and polyphosphate-accumulating organisms (PAOs) abundances from 8.21 % to 25.73 %. Surprisingly, high GAOs abundance (21.02 %) correlated with superior phosphorus recovery (> 80 mg/L) and >95 % removal efficiency, contradicting conventional EBPR models. Metagenomic analysis revealed GAOs enhanced glycogen degradation and PHA synthesis, supporting energy-intensive phosphorus accumulation. Reduced GAOs abundance impaired acetate uptake and PHB polymerization, lowering system performance. GAOs also maintained microbial diversity and stabilized functional gene expression. We conclude that GAOs play a beneficial metabolic role in biofilm systems by optimizing carbon use for phosphorus enrichment, enabling stable recovery even when GAOs outnumber PAOs.}, } @article {pmid42498374, year = {2026}, author = {Sun, X and Zhang, Q and Wang, J and Zhang, B and Guo, J and Zhang, K and Li, M and Lu, Z and Shi, J and Kang, S}, title = {Emerging proglacial lake constraints on mercury transport and transform patterns in glacial meltwater runoff on China's Tibetan plateau.}, journal = {Journal of environmental sciences (China)}, volume = {167}, number = {}, pages = {389-399}, doi = {10.1016/j.jes.2025.10.009}, pmid = {42498374}, issn = {1001-0742}, mesh = {*Mercury/analysis ; *Lakes/chemistry ; Tibet ; *Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; *Ice Cover/chemistry ; Geologic Sediments/chemistry ; Methylmercury Compounds/analysis ; }, abstract = {The rapid expansion of proglacial lakes on the Tibetan Plateau introduces uncertainties in mercury (Hg) cycling following glacial retreat. This study investigated Hg dynamics in a glacierized watershed by combining comprehensive sampling of glaciers and proglacial lakes to assess their role in Hg transport and methylation. The total Hg (THg) and methylmercury (MeHg) concentrations in aquatic systems ranged from 0.71 to 3.35 ng/L and 0.01-0.11 ng/L, respectively. Compared with glacial meltwater, glacial lake water contained lower THg concentrations (1.20 ng/L) but higher MeHg concentrations (0.09 ng/L), indicating active Hg methylation. Sediment THg (4.34-69.15 ng/g) exhibited spatial heterogeneity, reflecting divergent Hg inputs from supraglacial and subglacial sources. Elevated THg and MeHg in central lake sediments suggest substantial Hg deposition and transformation, likely driven by meltwater-derived organic carbon. Hg isotopic signatures analyses further revealed that Hg speciation is governed by meltwater inputs, atmospheric deposition, bedrock weathering. Additionally, metagenomic analysis has revealed that sediments in periglacial regions, particularly those in proglacial lakes, exhibit a high potential for Hg methylation, indicating that microbial activity may also be a significant factor influencing regional Hg cycling. As proglacial lakes expand, their capacity to modulate Hg fluxes may intensify, with potential glacial lake outburst floods (GLOFs) further altering Hg transport pathways. These findings highlight growing risks to hydrochemical stability in alpine watersheds and the broader Third Pole region under climate-driven glacier loss.}, } @article {pmid42499546, year = {2026}, author = {Jiang, Z and Li, L and Long, Q and Guo, W and Wang, M and Li, X and Li, J and Yi, Y}, title = {Cross-sectional gut microbiota and serum metabolite differences across clinically defined groups in colorectal cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1815707}, pmid = {42499546}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/blood/microbiology/pathology ; Cross-Sectional Studies ; Female ; Feces/microbiology ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Aged ; Metabolomics ; *Serum/chemistry ; *Metabolome ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Colorectal cancer (CRC) is a prevalent malignancy associated with alterations in the gut microbiota and host metabolic profiles. This cross-sectional study aimed to characterize gut microbiota and serum metabolite differences among healthy controls (HC), patients with non-metastatic colorectal cancer (CRC-nm), and patients with metastatic colorectal cancer (CRC-m). Stool metagenomic sequencing and untargeted serum metabolomics were performed in 107 participants, followed by exploratory differential analyses and internally cross-validated modeling to identify candidate microbial and metabolic features and evaluate their discriminatory performance. Differential analyses identified two CRC-m-enriched species-level features (Enterocloster clostridioformis and Lactobacillus crispatus) and two CRC-m-depleted features (Megamonas rupellensis and Phocaeicola plebeius) across comparisons with both CRC-nm and HC groups. Metabolomic analysis identified eight pathway-mapped metabolites, mainly involved in amino acid-related metabolic pathways. In modeling analyses, metabolite-only models provided the primary discriminatory signal, whereas adding bacterial features did not improve predictive performance. Integrated microbiota-metabolite models showed lower internal performance than metabolite-only models in some comparisons, including CRC-m versus CRC-nm. Overall, these findings suggest that observed discriminatory performance was primarily driven by serum metabolite features rather than additional bacterial features, and highlight candidate microbial and metabolic markers for future validation. Because all CRC-m cases were stage IV and all CRC-nm cases were stages I-III, these results should be interpreted as exploratory cross-sectional group differences that may reflect disease stage, tumor burden, or broader progression-related changes rather than metastasis-specific biology.}, } @article {pmid42499661, year = {2026}, author = {Dai, L and Kong, FL}, title = {Effect of programmed cell death protein-1 inhibitor combined with platinum-containing dual-agent chemotherapy regimen on gut microbiota in Lewis lung cancer model mice.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1885048}, pmid = {42499661}, issn = {1664-302X}, abstract = {PURPOSE: To explore the effects of programmed cell death protein-1 (PD-1) combined with pemetrexed (PEM) and carboplatin (CARB) chemotherapy regimen on the gut microbiota in the Lewis lung cancer model mice compared to chemotherapy alone.

MATERIALS AND METHODS: C57BL/6 J male mice aged 10-12 weeks were selected to establish the Lewis lung cancer model by planting tumors in the right forelimb, and were randomly divided into negative control group (NC group), chemotherapy group (PEM-CARB group), and chemotherapy combined with immunotherapy group (PEM-CARB-PD-1 group), with eight mice in each group. The total RNA of fecal bacteria was collected from the feces of mice in each group after two cycles of drug administration. 16S rRNA gene amplification and high-throughput sequencing were performed to analyze the Alpha diversity, Beta diversity, composition, and function in the gut microbiota.

RESULTS: The Alpha diversity was not statistically different between the PEM-CARB-PD-1 group and the PEM-CARB group (Shannon index: p = 0.645; Simpson index: p = 0.879). The Beta diversity between the PEM-CARB-PD-1 group and PEM-CARB group was statistically different [weighted Unifrac Principal Co-ordinate Analysis (PCoA), p = 0.001; unweighted Unifrac PCoA, p < 0.001]. However, the Beta diversity between the PEM-CARB-PD-1 group and the NC group did not reveal statistical differences (weighted Unifrac PCoA, p = 0.690; unweighted Unifrac PCoA, p = 0.135). Compared to the PEM-CARB group, the combination of the PD-1-inhibitor affects both the "response-favorable taxa" and "response-unfavorable taxa" for immunotherapy. Notably, the PEM-CARB-PD-1 group had an increased abundance of Gram-positive bacterial phenotypes relative to the PEM-CARB group (p = 0.038). Nearly no statistically significant differences in metabolic pathways were seen between the PEM-CARB-PD-1 group and the PEM-CARB group.

CONCLUSION: Combination therapy affects both "response-favorable taxa "and "response-unfavorable taxa associated with immunotherapy, and the ultimate impact remains dependent on the ratio of the two types of flora. Predicted metabolic pathway analysis using PICRUSt2 suggested that the combination regimen may not further reduce predicted functional pathway abundance beyond that observed with chemotherapy alone. However, these predictions require validation through direct metagenomic or metabolomic approaches.}, } @article {pmid42499785, year = {2026}, author = {Lin, JY and Gontijo, JB and McMillan, CK and Fudyma, JD and Wang, D and Yao, EH and Sayre, JM and Emerson, JB and Lipson, DA and Lazcano, C and Scow, KM and Mazza Rodrigues, JL}, title = {Multi-omics resolved integration reveals microbial niche separation in soil aggregates.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag161}, pmid = {42499785}, issn = {2730-6151}, abstract = {The soil matrix is a heterogeneous mixture composed of aggregates-three-dimensional complexes composed of organic materials and mineral particles. Soil aggregates vary considerably in physical and chemical properties by size, making them unique habitats for distinct microbial communities and metabolic pathways. Yet, this microscale spatial variability is often overlooked in studies that use homogenized soil cores. We investigated the microbial taxonomy, functional gene composition, and metabolic products observed in four aggregate size fractions ranging from 8 mm to free particles (below 53 μm) collected from agricultural soils under two different management practices. The functional gene composition differed significantly among aggregate sizes, with higher abundances of genes for the degradation of plant-derived compounds in the macroaggregates and for biomass recycling in the two smallest size fractions. These differences were corroborated by significant differences in the composition of the metabolome but not in specific enzyme activities. Both taxonomic profiling and reconstruction of genomes from metagenomes revealed a higher abundance of ammonia-oxidizing archaea in the macroaggregates in comparison to other aggregate sizes, and analysis of their genomes revealed complementary metabolisms potentially enabling them to colonize different niches within the same habitat. Together, our results show that soil microbial communities and their functions are shaped by the size of soil aggregates, likely driven by differences in resource availability between macro- and microaggregates.}, } @article {pmid42500245, year = {2026}, author = {Chen, AS and Nguyen, LH and Gray, B and Williams, K and Gurung, J and Canha, L and McGoldrick, J and Hubbard, J and Khalili, H}, title = {Specific carbohydrate diet versus Mediterranean diet in adult patients with mild to moderate ulcerative colitis: a randomized controlled-feeding trial.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1838160}, pmid = {42500245}, issn = {2296-861X}, abstract = {BACKGROUND AND AIMS: This pilot randomized controlled-feeding trial compared the effect of Specific Carbohydrate Diet (SCD) and Mediterranean diet (MeD) in mild to moderate ulcerative colitis (UC).

METHODS: Seventeen adults were randomized to a 6-week SCD (n = 8) or MeD (n = 9) intervention. Primary outcome was change in partial Mayo Clinic score (pMCS).

RESULTS: The study was discontinued early due to significant dropout (n = 9, 52.9%). There was no significant between-group differences observed for pMCS change (SCD, -0.8; MeD, -1.3; p = 0.499) or secondary outcomes. Exploratory metagenomic analysis revealed enrichment of Parasutterella excrementihominis in SCD at week 10.

CONCLUSION: In this pilot trial, SCD and MeD showed no difference in therapeutic effects for patients with mild to moderate UC. However, the study was limited by a significant drop out in both arms.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier NCT04398550.}, } @article {pmid42500469, year = {2026}, author = {Lu, M and Qi, D and Wang, Q and Sun, X and Shi, Y and Zhang, X and Feng, Y and Yang, X and Song, L and Dong, C and Yuan, C}, title = {Metagenomic insights into rhizosphere microbial communities and functional gene profiles associated with the responses of tea yield and quality to nitrogen-zinc co-fertilization.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1852312}, pmid = {42500469}, issn = {1664-462X}, abstract = {Optimal co-fertilization of nitrogen (N) and zinc (Zn) offers a promising approach for promoting the growth of tea plant (Camellia sinensis (L.) O. Kuntze), sustaining stable yield, and improving tea quality. However, the specific roles of rhizosphere microorganisms in mediating the tea yield and quality after N-Zn co-fertilization remain unclear. Here, a field experiment was carried out to assess the influence of N-Zn co-fertilization on the growth of tea plant, as well as the structure and functions of rhizosphere microbial communities in tea plantations. Results showed that N application contributed more to the increment of tea yield than Zn fertilization, whereas Zn supply significantly promoted the synthesis of free amino acids and reduced tea polyphenol contents as well as TP/AA at moderate N level. Zn addition decreased the level of soil NO3 [-]-N but increased NH4 [+]-N concentrations at both moderate and high N levels. Soil metagenomic sequencing indicated that Zn supply significantly increased the relative abundances of microbial taxa involved in denitrification, such as Arthrobacter, Bacillus, Terrabacter and Burkholderia, as well as up-regulated the relative abundances of narH, nasA, nasB, napB, nirB, nirD and norB genes at high N level, which are related to some metabolic potential pathways like denitrification and nitrate reductase. Partial least squares path models showed that fertilization initially altered soil properties and enzyme activities, thereby affecting rhizosphere microbial communities and functional gene profiles, which sequentially contributed to the nutrient accumulation in tea plants and ultimately influenced tea yield. Random forest analysis further identified soil properties such as pH, OM, AP, NH4 [+]-N, NO3 [-]-N and AZn as the most influential factors affecting tea yield and quality. Overall, our results highlight the relationship between tea yield and quality with rhizosphere microbial communities and functional gene profiles under different N-Zn co-fertilizations. All these findings provide new perspective for nutrient use and management in tea plantations.}, } @article {pmid42500599, year = {2026}, author = {Ai, X and Liu, R and Lv, Y and Chen, L and Duan, R and Ma, X and Li, L and Ding, H and Shen, H and Hu, Y and Zhu, X and Zhang, Y}, title = {Functional signatures of the gut microbiome in middle-aged regular runners: insights from a metagenomic study.}, journal = {Frontiers in physiology}, volume = {17}, number = {}, pages = {1826138}, pmid = {42500599}, issn = {1664-042X}, abstract = {INTRODUCTION: Exercise influences host metabolism and inflammation, but its functional effects on the gut microbiome in middle-aged populations remain unclear. This study used shotgun metagenomics to investigate the associations between long-term endurance running and the gut microbial ecosystem and its functional potential in middle-aged adults.

METHODS: We conducted a cross-sectional analysis comparing 33 middle-aged regular runners with 33 sedentary controls. No significant differences in age, BMI, dietary intake between groups. Fecal samples underwent metagenomic sequencing at an average depth of 10.97 Gb per sample. Following stringent quality control, taxonomic profiling, diversity analyses, and differential abundance testing were performed. Functional potential was annotated using GO, eggNOG, KEGG, CARD, VFDB, and CAZy databases.

RESULTS AND DISCUSSION: The gut microbiota of middle-aged regular runners (RG, n = 33) and sedentary controls (CG, n = 33) was compared using metagenomic sequencing. No significant differences were observed between the two groups in terms of age, BMI, or self-reported dietary patterns. Although no significant differences in α-diversity or β-diversity were found, taxonomic profiling revealed differences in microbial community composition between the groups. Runners exhibited an increased relative abundance of carbohydrate-fermenting and short-chain fatty acid (SCFA)-producing species, including Prevotella copri, Lachnospira eligens, and Collinsella intestinalis. KEGG functional analysis revealed enrichment of genes associated with antibiotic biosynthesis pathways in runners, whereas the control group was enriched in genes related to lipid metabolism and xenobiotic degradation. The total abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs) was significantly lower in runners. Carbohydrate-active enzyme (CAZy) profiling further indicated that runners harbored higher abundances of carbohydrate-binding modules and glycosyltransferase families, while controls were enriched in complex polysaccharide-degrading enzymes. Nonetheless, the cross-sectional design, qualitative dietary assessment, residual sex imbalance, and lack of metabolomic validation limit causal inference. Longitudinal intervention studies incorporating metabolomic analyses are warranted to confirm these associations and elucidate the directional adaptation of the gut microbiota to long-term regular exercise.}, } @article {pmid42501556, year = {2026}, author = {Bhuyan, B}, title = {Enhancing crop productivity under stress through plant growth-promoting bacterial consortia: Relevance to sustainable development goals.}, journal = {Microbiological research}, volume = {312}, number = {}, pages = {128641}, doi = {10.1016/j.micres.2026.128641}, pmid = {42501556}, issn = {1618-0623}, abstract = {Abiotic and biotic stresses significantly threaten global food security and agricultural sustainability. Achieving the United Nations Sustainable Development Goals (SDGs), particularly SDG 2 (Zero Hunger), SDG 6 (Clean Water and Sanitation), SDG 12 (Responsible Consumption and Production), SDG 13 (Climate Action), and SDG 15 (Life on Land), requires sustainable agricultural approaches. Recently, plant growth-promoting bacterial (PGPB) consortia have emerged as an effective strategy for enhancing crop productivity under stress conditions. These microbial communities improve plant growth through mechanisms such as nitrogen fixation, phosphate solubilization, phytohormone production, siderophore secretion, ACC deaminase activity, induction of systemic resistance, while enhancing nutrient uptake, antioxidant activity, osmotic regulation, and stress-responsive signalling pathways, thus improving plant health and productivity. Compared with single-strain inoculants, consortia provide synergistic effects that enhance rhizosphere colonization, microbial survival, and plant-microbe interactions, thus contributing to the achievement of the SDGs. Recent advances in modern tools such as metagenomics, metatranscriptomics, metabolomics, and machine learning for predictive microbiome modelling, as well as field-level engineering approaches such as encapsulation technologies, biochar-based carriers, seed coating, and root microbiome editing, have accelerated the development of efficient microbial formulations for sustainable agriculture. This review discusses the potential of PGPB consortia as a sustainable solution for boosting crop productivity under stress. The integration of consortia into modern agricultural practices can play a crucial role in supporting resilient farming systems and advancing the global SDG agenda. This review highlights the key limitations, challenges, and research gaps associated with PGPB consortia, as well as future prospects for enhancing crop productivity.}, } @article {pmid42492779, year = {2026}, author = {Yeni, DK and Güven, D and Büyük, F and Gökmen, MC}, title = {Artificial intelligence-based methods and applications in clinical and diagnostic microbiology: Current challenges and future perspectives.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107638}, doi = {10.1016/j.mimet.2026.107638}, pmid = {42492779}, issn = {1872-8359}, abstract = {Microbiology laboratories play a critical role in the diagnosis and management of infectious diseases. However, recent advancements aimed at reducing human workload and minimizing time loss are gaining popularity. Artificial intelligence (AI) technologies, particularly machine learning (ML) and deep learning (DL), have been reported to contribute significantly to microbial laboratory diagnostics. Through this approach, molecular methods, genetic sequencing, microbiological meta-analyses, and related fields benefit from faster and more accurate analytic capabilities. In addition to diagnostic applications, AI is increasingly used in genomics, metagenomics, antimicrobial resistance (AMR) prediction, and drug and vaccine discovery, enabling more comprehensive and data-driven microbiological analysis. This review comprehensively evaluates current AI applications in microbiology, highlighting their advantages, limitations, and implementation challenges. It further examines the suitability of different AI methodologies for specific laboratory tasks and compares AI-driven approaches with conventional expert-based practices. Finally, the study emphasizes the complementary roles of AI systems and human expertise, underscoring their synergistic potential to improve diagnostic accuracy, efficiency, and clinical decision-making.}, } @article {pmid42492921, year = {2026}, author = {Lu, Z and Zhang, S and Song, N and Feng, X and Zhou, Z and Liu, Y and Li, M}, title = {Archaeal Diversity Sheds New Light on the Origin of the Eukaryotic Endomembrane System.}, journal = {Annual review of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-micro-042524-032136}, pmid = {42492921}, issn = {1545-3251}, abstract = {The emergence of the endomembrane system marks a pivotal milestone in eukaryogenesis, transforming a primitive prokaryotic cell into a highly intracellular, compartmentalized eukaryotic cell. The molecular machinery underlying the endomembrane system has been considered a defining feature of eukaryotes. Yet its evolutionary origin remains elusive. Over the past decade, the rapid expansion of archaeal diversity, coupled with advancements in metagenomic technologies and cell biological characterization, has revealed that many key protein components of the endomembrane system likely originated from the archaeal ancestors of eukaryotes, a specific archaeal lineage that underwent a symbiotic fusion with the mitochondrial ancestor. This review summarizes and discusses the remarkable progress made in these research fields, offering a refined perspective on the origin of the eukaryotic endomembrane system within an updated tree of life.}, } @article {pmid42493609, year = {2026}, author = {Yang, Y and Li, N and Zhou, L and Gong, S and He, Z and Tang, S and Ni, J and Liu, Y and Chan, JWY and Or, BPN and Lam, SP and Zhang, J and Chan, PKS and Chen, Z and Wong, SH and Mok, VCT and Chan, NY and Chau, SWH and Lai, CKC and Scheperjans, F and Wang, J and Huang, B and Wing, YK}, title = {Gut Microbiome in Depression with and without REM Sleep Behavior Disorder.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {42493609}, issn = {1476-5578}, support = {18190221//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; 05162876//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; C4044-21G//Research Grants Council, University Grants Committee (RGC, UGC)/ ; }, abstract = {Major depressive disorder (MDD) is a risk factor for neurodegeneration, yet its heterogeneity makes identifying at-risk subtype challenging. Notably, MDD frequently co-occurs with REM sleep behavior disorder (RBD), a specific prodrome of α-synucleinopathy. It remains unclear whether comorbid MDD + RBD reflects a benign antidepressant effect, or higher neurodegenerative risk. Given growing recognition of gut-brain axis in neuropsychiatry, we aimed to delineate microbial signatures of MDD + RBD. We employed a four-group case-control design (N = 420) comprising 124 healthy controls (HC); 80 MDD without RBD features (MDD-only); 82 MDD + RBD; and 134 iRBD without psychiatric disease. All participants underwent clinical evaluation and provided fecal samples for metagenomic sequencing. Random Forest model was used to distinguish MDD + RBD, and further assessed in a validation dataset of 65 participants with MDD + RBD (n = 31) and MDD-only (n = 34). MDD + RBD exhibited prodromal neurodegenerative features, including elevated total likelihood ratio of prodromal Parkinson's Disease, olfactory deficits, and subtle motor signs. The microbial composition in MDD + RBD differed from HC and MDD-only, while resembling iRBD. Taxonomically, MDD + RBD exhibited an iRBD-like dysbiosis (e.g., enriched Akkermansia muciniphila, Ruthenibacterium lactatiformans; depleted Faecalibacterium prausnitzii), alongside depression-associated shifts (e.g., Streptococcus parasanguinis and Actinomyces oris). Functionally, MDD + RBD showed attenuated capacity of B‑vitamin biosynthesis and polysaccharides degradation, mirroring iRBD. The Random Forest machine-learning model distinguished MDD + RBD in older adults from MDD-only with an AUC of 0.73 in cross-validation and 0.79 in the validation dataset. MDD + RBD may represent a biologically distinct depression subtype associated with potential neurodegenerative risk. Gut microbiome provides a candidate approach for potential risk stratification in psychiatric populations.}, } @article {pmid42493771, year = {2026}, author = {Yi, Y and Xie, F and Xia, C and Li, J and Zhao, P and Liu, M and Ma, X and Chen, J}, title = {Hypertension and gut microbial hydrogenases: a comparison of hydrogen metabolism and etiology.}, journal = {Medical gas research}, volume = {16}, number = {4}, pages = {352-358}, doi = {10.4103/mgr.MEDGASRES-D-25-00128}, pmid = {42493771}, issn = {2045-9912}, mesh = {*Hydrogenase/metabolism/genetics ; *Hydrogen/metabolism ; *Hypertension/microbiology/etiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; }, abstract = {JOURNAL/mgres/04.03/01612956-202612000-00006/figure1/v/2026-07-23T200825Z/r/image-tiff Hypertension is a prevalent chronic condition and serves as a significant risk factor for numerous cardiovascular and cerebrovascular disorders. Gut microbiota dysbiosis has been considered to contribute to the pathogenesis of hypertension. It has been reported that a large majority of gut microbiota possess genes encoding hydrogenases. These hydrogenases are involved in the alteration of gut microbiota in non-infectious colitis, suggesting a potential link between microbial hydrogen metabolism and disease onset. This study aims to explore the relationship between hydrogenase expression patterns in the gut microbiome and the incidence of hypertension. In this study, publicly available gut microbiome metagenomic data were used to comprehensively analyze the expression patterns of hydrogenases in the gut microbiota of hypertensive patients. Compared with the control group, a 2.3-fold increase in electron bifurcating [FeFe] group A3 hydrogenases (P = 0.0299), a 55.6% decrease in [NiFe] group 1d hydrogenases (P = 0.0097), increased hydrogen-sensing hydrogenases and decreased hydrogen-uptake hydrogenases in the hypertension group. The main difference between the two groups is reflected in the abundance of [NiFe] hydrogenase subtypes. After eliminating the effects of factors such as age, sex, and lifestyle, significant differences in the abundance of [FeFe] group A3, [NiFe] group 1d, and [NiFe] group 1c were observed between the two groups, suggesting that these three indicators could serve as potential biomarkers for diagnosing the onset of hypertension. Additionally, Mendelian randomization analysis showed a protective effect of hydrogen metabolism against hypertension (odds ratio = 0.72, 95% confidence interval: 0.61-0.85, P < 0.001). Our study advances the understanding of microbiome-mediated mechanisms in hypertension by demonstrating an association between hydrogenase expression dynamics and blood pressure regulation, providing a foundation for future microbiome-based diagnostic and therapeutic strategies.}, } @article {pmid42493801, year = {2026}, author = {Van Den Bossche, T and Grenga, L and Alves, G and Arntzen, MØ and Benndorf, D and Brauer, M and Figeys, D and Henry, C and Hettich, RL and Heyer, R and Jagtap, PD and Jehmlich, N and Kleiner, M and Li, L and Mesuere, B and Pabst, M and Pandhal, J and Pope, PB and Seifert, J and Trautwein-Schult, A and Verschaffelt, P and Wilmes, P and Armengaud, J and Kunath, BJ}, title = {The Metaproteomics Initiative: five years of community-driven progress.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42493801}, issn = {2049-2618}, mesh = {*Proteomics/methods ; *Microbiota ; Humans ; Metagenomics ; }, abstract = {The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community. Over the past 5 years, the Initiative has developed into a structured, global network of researchers. It has launched community-driven benchmark studies, helped shape emerging metadata and reporting standards, developed practical guidance and training materials, organized international symposia, and fostered connections across the microbiome research landscape (https://metaproteomics.org/). We outline the Initiative's organization, activities, achievements, and ongoing efforts, and reflect on how sustained, community-led coordination has shaped the development of metaproteomics as a field. We further position the Grand Metaproteome Challenges as a next step toward coordinated, community-scale biological research, aimed at advancing functional microbiome studies across clinical, industrial, and environmental application domains, and invite engagement from the wider microbiome and omics communities. Video Abstract.}, } @article {pmid42494748, year = {2026}, author = {Wang, X and Wang, C and Gao, J and Li, L}, title = {Bilateral Encephalitozoon hellem Keratoconjunctivitis With Microsporidial Spores in Parrot Feces.}, journal = {Cureus}, volume = {18}, number = {7}, pages = {e113157}, pmid = {42494748}, issn = {2168-8184}, abstract = {We describe bilateral Encephalitozoon hellem keratoconjunctivitis in a 39-year-old immunocompetent woman with two years of daily close contact with a pet parrot. She presented with a three-week history of bilateral ocular redness, itching, foreign-body sensation, and blurred vision that had not improved with topical fluorometholone, lubricants, and levofloxacin prescribed for presumed dry eye disease. Slit-lamp examination showed bilateral conjunctival inflammation and diffuse superficial punctate corneal infiltrates. Giemsa staining of a left-eye corneal scraping demonstrated oval spore-like structures, while bacterial and fungal cultures were negative. Metagenomic next-generation sequencing (mNGS) of the same specimen detected 9,684 reads assigned to E. hellem, with a relative abundance of approximately 98% and genome coverage of 63%, supporting the diagnosis. Fluorescence microscopy of a fecal specimen from the pet parrot revealed a small number of spore-like structures morphologically compatible with microsporidia, but no molecular typing was performed. The symptoms and corneal lesions resolved over six weeks during treatment with topical 0.02% polyhexamethylene biguanide, topical 0.5% gatifloxacin administered as post-scraping antibacterial prophylaxis, and a short course of oral albendazole, with no recurrence during four months of follow-up. This case highlights the diagnostic value of combining corneal-scraping microscopy with mNGS in treatment-refractory keratoconjunctivitis and the importance of obtaining a detailed avian-exposure history. It also illustrates that microscopic findings in avian feces alone cannot establish zoonotic transmission.}, } @article {pmid42494846, year = {2026}, author = {Mthembu, TP and Hlongwane, NL and Salawu-Rotimi, A and Hadebe, K and Pierneef, R}, title = {Metagenomic analysis of fecal and environmental microbiota in rural mixed livestock farming systems in South Africa.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1828785}, pmid = {42494846}, issn = {2235-2988}, mesh = {Animals ; South Africa ; *Feces/microbiology ; *Metagenomics ; *Livestock/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Environmental Microbiology ; *Microbiota ; Cattle ; Soil Microbiology ; Phylogeny ; Metagenome ; Swine ; Sheep ; Biodiversity ; Water Microbiology ; Rural Population ; }, abstract = {In South African rural areas, farmers often practice mixed extensive livestock farming, facilitating microbial exchange among and between animal species and their environment. The composition and transmission potential of microbiomes between animals and their environments in these smallholder livestock systems remain largely unexplored, creating a gap in understanding how mixed-livestock farming affects gut and environmental microbiomes. Shotgun metagenomics was used to uncover the fecal and environmental microbiota in smallholder mixed livestock systems, aiming to understand microbiome transfer within these systems. A total of 111 samples were collected in KwaZulu-Natal and Eastern Cape provinces of South Africa, including 76 fecal samples from cattle, goats, sheep, pigs, and chickens; 18 soil samples; and 17 water samples. Taxonomic analysis of the sequencing data identified Proteobacteria as the dominant phylum across most hosts, except that pigs were dominated by Firmicutes. Moraxellaceae and Pseudomonadaceae were the differentiating families between monogastrics and ruminants. Although microbial diversity differences were significantly attributed to the host, genera such as Acinetobacter, Chryseobacterium, Flavobacterium, Pedobacter, and Pseudomonas were consistently found across all animal and environmental hosts. Cattle shared more genera with the environment than other animal species. Opportunistic pathogens, including Enterococcus spp., Escherichia coli, and Clostridium spp., were found across all the livestock species, and were highest in chickens. Additionally, some pathogens were detected in water but none in soil, suggesting water as a potential medium for pathogen transmission. The microbial exchange between livestock and their surroundings highlights the permeability of host-environment boundaries in smallholder systems.}, } @article {pmid42494847, year = {2026}, author = {Zhang, L and Yan, K and Xu, P and Xiao, Y and Guo, C and Dai, G and Lin, J and Liu, D and Rao, M and Lin, Z and Zhao, P and Zheng, M and Zhou, Y and Lu, H}, title = {Phage-antibiotic synergy attenuates Acinetobacter baumannii resistance in refractory pneumonia: a precision therapeutic case.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1851410}, pmid = {42494847}, issn = {2235-2988}, mesh = {*Acinetobacter baumannii/drug effects/virology ; Humans ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; *Acinetobacter Infections/therapy/microbiology ; *Phage Therapy/methods ; *Bacteriophages/physiology/isolation & purification ; Drug Resistance, Multiple, Bacterial ; Fosfomycin/administration & dosage/therapeutic use ; Polymyxin B/therapeutic use/administration & dosage ; Amikacin/administration & dosage/therapeutic use ; *Pneumonia, Bacterial/therapy/microbiology ; Microbial Sensitivity Tests ; }, abstract = {Extensively drug-resistant (XDR) Acinetobacter baumannii pneumonia carries severe pneumonia, respiratory failure and high mortality, showing limited therapeutic options in critically ill patients. Although bacteriophage (phage) therapy represents a promising alternative against drug-resistant infections, its clinical use remains largely empirical. Here, we reported a systematically planned phage-antibiotic combination strategy in a critically ill patient with refractory XDR A. baumannii pneumonia. A virulent phage targeting the patient-derived strain was isolated from hospital wastewater and classified within the class Caudoviricetes, with no virulence, toxin, or antibiotic resistance genes. In vitro time-kill assays showed that phage monotherapy failed to persistently suppress bacteria proliferation, whereas phage-antibiotic therapy achieved synergistic inhibition of A. baumannii growth for over 48 h. The patient received nebulized phage therapy (5 × 10[9] PFU/mL twice daily) combined with intravenous fosfomycin (8 g, every 8 hours), amikacin (0.2 g, every 12 hours), and polymyxin B (500, 000 U, every 12 hours). Clinically, treatment was associated with rapid normalization of arterial carbon dioxide tension (PaCO2), clearance of A. baumannii sputum cultures by day 4, declining inflammatory markers, and no treatment-related toxicity.Longitudinal metagenomic sequencing further revealed approximately 52-fold reduction in pathogen abundance and significant decrease of A. baumannii-associated antimicrobial resistance genes (ARGs) in the lung, highlighting the potential of precision phage-antibiotic therapy for recalcitrant XDR bacterial infections.}, } @article {pmid42494985, year = {2026}, author = {McKindles, K and Seto, K and Ahrendt, S and Salamov, A and Chovatia, M and Wang, M and Barry, K and Grigoriev, IV and McKay, RM and James, TY}, title = {Single-cell genomics, metagenomics, and transcriptomics of Rhizophydium megarrhizum, an obligate fungal parasite of Planktothrix agardhii.}, journal = {Aquatic ecology}, volume = {60}, number = {3}, pages = {92}, pmid = {42494985}, issn = {1386-2588}, abstract = {UNLABELLED: Chytrids (phylum Chytridiomycota) are zoosporic fungi that play key roles as parasites of aquatic microorganisms, yet they are understudied and genomic resources for algal-infecting chytrids remain scarce. Here, we present the first comparative genomic analysis of multiple isolates of a single chytrid species (order Rhizophydiales) infecting the cyanobacterium Planktothrix agardhii. Isolates were collected from Sandusky Bay, Lake Erie, across two bloom years (2018 and 2019). Using single cell sequencing and metagenomic assembly, we generated individual genomes averaging 15.36 ± 0.12 Mbp in size with ~ 75% completeness, and a pangenome. Gene ontology analyses highlighted the presence of categories related to cellular structure, biosynthetic regulation, and interspecies interactions. As a preliminary exploration of gene expression during infection, we also performed RNA sequencing on a subset of size-sorted samples. These data suggest that chytrids consistently express high levels of cytoskeletal genes, alongside numerous hypothetical proteins, and that zoospores may upregulate carbohydrate-binding proteins implicated in host recognition. On the host side, P. agardhii showed transcriptional shifts in pathways associated with buoyancy and nutrient acquisition, patterns that could represent defensive adjustments or parasite-driven manipulation. Together, this study generates reference genomes for Planktothrix-infective chytrids, identifies conserved gene content across isolates from different bloom years, and provides preliminary transcriptomic insights into parasite and host responses. These resources lay the foundation for deeper investigations into chytrid genome evolution, infection biology, and their ecological roles in shaping cyanobacterial bloom dynamics.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10452-026-10329-8.}, } @article {pmid42495136, year = {2026}, author = {Gewirtz, MA and Zhang, Y and Vaidy, N and Redekar, NR and Minerva, N and Haddad, JA and Oringher, JL and Afruza, R and Chakraborty, M and Menkart, MG and Gopalakrishna, H and Hercun, J and Lack, J and Kleiner, DE and Lionakis, MS and Koh, C and Heller, T}, title = {Chronic hepatitis D infection is associated with distinguishing microbial and functional features in the gut microbiome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1851892}, pmid = {42495136}, issn = {1664-302X}, abstract = {BACKGROUND: The microbiome of patients with hepatitis D virus (HDV) has yet to be characterized. This study aims to (1) characterize gut microbial composition in HDV, (2) determine its functional profile, (3) identify microbial species that contribute to changes in pathway expression, and (4) correlate the changes in the gut microbiome with clinical markers of disease severity.

METHODS: Cross-sectional analyses of 35 HDV-infected patients and 32 healthy controls (HCs) were performed. DNA and RNA were isolated from stool and sequenced by shotgun-sequencing. Microbial and functional profiles were compared between the HDV-cohort and HCs to identify disease-specific alterations to the gut microbiome. Clinical metadata were used to identify correlations with disease severity.

RESULTS: There were significant changes in the composition of the gut microbiome in HDV-infected patients as compared with HCs, spanning multiple bacterial phyla. Expression of 194 pathways was significantly increased in the HDV group. Pathways that were upregulated in the HDV cohort were related to amino acid and carbohydrate biosynthesis or involved important metabolic cofactors and carriers. Several microbial species, including Bacteroides fragilis, Cateibacterium mitsuokai, and Faecalibacterium prausnitzii, were identified as contributing to the differentially expressed pathways. Four genera correlated with hepatic venous pressure gradient (HVPG).

CONCLUSION: There are significant differences in microbial composition between HDV and HCs, several of which are found to be altered in other liver diseases. Upregulated pathways suggest a broader dysregulation of energy metabolism, even in early disease. These findings provide insight into pathways that may lead to liver disease progression in HDV.}, } @article {pmid42495138, year = {2026}, author = {Pang, Y and Chen, Y and Huang, Q and You, F and Fang, R and Geng, M and Ke, X and Tang, J and Ling, J and Cheng, Y and Zhao, C and Deng, X and Guo, J and Miao, C}, title = {Temperature regulation mechanisms of diapause in Coridius chinensis revealed by multi-omics integration: coordinated responses of Brain-Gut-Fat Body.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1810191}, pmid = {42495138}, issn = {1664-302X}, abstract = {Diapause in Coridius chinensis is a complex survival strategy that enables them to survive under prolonged cold stress. To elucidate the mechanisms of temperature regulation during diapause, we conducted multi-omics analyses, including gut metagenomics, brain transcriptomics, and fat body metabolomics, under both normal (25 °C) and diapause conditions (4 °C). Gut microbiome analysis revealed an extreme polarization during diapause, dominated by the endosymbionts Pantoea endophytica (52%) and Rickettsia bellii (47.4%), while functional microbiota such as Pantoea and Dietzia were significantly reduced. This shift suggests a trade-off where microbial metabolic diversity is sacrificed in favor of intracellular symbionts that may regulate host mitochondrial activity and suppress energy consumption. Brain transcriptomic analysis indicated a downregulation of neural signaling pathways related to feeding suppression, stress resistance, and circadian rhythm regulation. Fat body metabolomics identified the coordinated activation of 13 core pathways that link energy storage with stress adaptation, with dynamic changes ranging from rapid stress responses (0-300 AU) to energy storage dominance (300-500 AU), and finally to a state of homeostasis (>500 AU). Notably, dysregulated choline metabolism was significantly correlated with necrotic features (r = 0.78, p < 0.001), while catecholamine biosynthesis derived from tyrosine emerged as a corrective pathway, revealing the mechanistic link between metabolic flexibility and survival. Adults primarily utilize plants within the Cucurbitaceae, Fabaceae, and Solanaceae families as hosts, underpinned by long-standing folk traditions in specific localities regarding their dietary consumption or therapeutic application.}, } @article {pmid42495148, year = {2026}, author = {Cagle, R and Proll, S and Minot, SS and Purcell, H and Zhu, W and Djukovic, D and Liu, C and Fiedler, T and DeMeules, M and Mielcarek, M and Srinivasan, S and Raftery, D and Wu, M and Pergam, SA and Fredricks, DN}, title = {Acute gastrointestinal graft-versus-host disease is associated with reductions of secondary bile acids following allogeneic hematopoietic cell transplantation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1818647}, pmid = {42495148}, issn = {1664-302X}, abstract = {INTRODUCTION: Allogeneic hematopoietic cell transplantation (HCT) can cure hematologic malignancies, but 30-70% of recipients experience acute graft-versus-host disease (GvHD). GvHD is associated with perturbations in the gut microbiome. Bile acids are host derived compounds that are transformed by gut bacteria and bind to specific host cell receptors, informing our hypothesis that changes in bile acid-metabolizing gut bacteria alter bile acid levels to affect gut physiology and immunity during GvHD.

METHODS: In a longitudinal case-control study of patients with and without acute gut GvHD, we characterized bile acid concentrations and the gut microbiome in stool.

RESULTS: Primary and conjugated bile acid levels were similar regardless of gut GvHD status, but endogenous secondary bile acid concentrations were associated with gut GvHD (p = 0.009). We observed 4.4-fold lower levels of endogenous secondary bile acids in GvHD, particularly lithocholic acid and derivatives (p = 0.004/padjusted = 0.02, fold change (FC) = 0.23). There was a 100-fold lower median abundance (p = 0.002 and FC < 0.01) and 20-fold lower median diversity of bacterial bile acid 7α-dehydroxylation (bai) genes (p = 0.0007 and FC < 0.05) in patients with GvHD.

DISCUSSION: This provides evidence that acute gut GvHD patients are deficient in microbial bai genes that make secondary bile acids.}, } @article {pmid42495540, year = {2026}, author = {Chen, Y and Lai, Y and Liu, Z and Zhang, K and Zheng, J and Lu, S and Huang, Z}, title = {The adaptation of the gut microbiome to social environmental changes in an Asian langur.}, journal = {iScience}, volume = {29}, number = {8}, pages = {116779}, pmid = {42495540}, issn = {2589-0042}, abstract = {Social environments profoundly impact social animals' gut microbiome. Understanding such effects is critical for evaluating population fitness and conservation. Employing 16S rRNA and metagenomic sequencing, we investigated the gut microbiome of the endangered white-headed langur (Trachypithecus leucocephalus) to clarify its potential adaptive strategies to social environmental changes. Distinct differences were observed among social groups: the all-male group was enriched in Bacillota and showed stronger cellulose degradation potential, which might be associated with greater cellulose intake and higher cortisol and T3 levels; mixed-sex group was enriched in Actinomycetota, Pseudomonadota, and non-carbohydrate metabolism genes, possibly due to more young leaves consumption and reproductive needs. Alpha male replacement also shaped gut microbiome: the third alpha male period had highest Bacteroidota and lowest metabolic genes abundance, potentially related to improved food quality during this period. These preliminary findings highlight gut microbial adaptation to social environments in the studied population, providing implications for the conservation of this endangered species.}, } @article {pmid42496113, year = {2026}, author = {Piperni, E and Blanco-Míguez, A and Mengoni, C and Piccinno, G and Punčochář, M and Ren, J and Segata, N and Asnicar, F and Poole, AC}, title = {Resistant starch types 2 and 4 induce distinct and reversible changes in the human gut microbiome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0076326}, doi = {10.1128/spectrum.00763-26}, pmid = {42496113}, issn = {2165-0497}, abstract = {Resistant starch (RS) can confer benefits for the gut microbiome and host cardiometabolic health. However, different types of resistant starch can differentially affect gut microbiome composition and functional capacity, especially given interindividual variability in responses, thus limiting the application of resistant starch in dietary strategies. We used shotgun metagenomics to perform a secondary analysis of samples collected during a previously reported randomized clinical trial to determine the effects of dietary supplementation with two types of resistant starch (RS2 and RS4) and a digestible starch (control) on the gut microbiome. Both resistant starch types induced distinct but transient alterations in the gut microbial community. RS2 enriched the keystone degrader, Ruminococcus bromii, and Blautia glucerasea, whereas RS4 favored Parabacteroides distasonis and known but uncharacterized microbial species such as a Lachnospiraceae bacterium. Moreover, we detected strain-level differences in the response of Bifidobacterium adolescentis to resistant starch. Microbial functional profiling revealed an enhanced capacity for complex carbohydrate utilization following resistant starch intake, including increased abundance of specific α-amylases, glycoside hydrolases, starch utilization systems, and other currently uncharacterized genes. Identifying the bacterial strains and genes that respond to different RS types will help to more accurately predict who will benefit from a given RS type. Our findings demonstrate that RS2 and RS4 differentially shape microbial ecology and metabolic capacity and provide a foundation for microbiome-informed personalization of resistant starch-based dietary interventions.IMPORTANCEDietary intake influences human health by modulating metabolism, partly by shaping the microbiota inhabiting the gut. Resistant starch (RS), a dietary fiber, is associated with metabolic improvements. While previous research has explored how RS alters the gut microbiome, RS comprises five types with differing physical and chemical characteristics, and the distinct impacts of each type on the microbiome and host health have not been fully characterized, particularly using high-resolution approaches such as shotgun metagenomics. In this secondary analysis of samples from a longitudinal crossover intervention study, we link dietary supplementation with RS2 and RS4 with distinct and transient changes in the composition and functional potential of the human gut microbiome. Specifically, we identify species that increase in abundance with each RS type, accompanied by increases in genes and pathways involved in complex carbohydrate utilization. The findings support the development of precision nutrition strategies utilizing RS supplementation to improve metabolic health.This study is registered with ClinicalTrials.gov as NCT05743790.}, } @article {pmid42496142, year = {2026}, author = {Hosayn, A and Wollants, E and Bloemen, M and André, E and Van Ranst, M and Karatas, M and Matthijnssens, J}, title = {Human rotavirus C strain detected in wastewater in Leuven, Belgium.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0066526}, doi = {10.1128/mra.00665-26}, pmid = {42496142}, issn = {2576-098X}, abstract = {Surveillance of urban wastewater in Leuven, Belgium, detected human rotavirus C (RVC) in April 2025. Our analyses revealed a G4P[2] strain closely related to RVC strains detected in feces of schoolchildren in China in March 2025.}, } @article {pmid42496154, year = {2026}, author = {Zhang, J and Cai, L and Wang, L and Zhang, L and Meng, N and Chen, A and Ma, Q}, title = {Marine antifouling biocide 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one disrupts sediment microbiome structure and function: insights from absolute quantification and enzyme activity dynamics.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0081926}, doi = {10.1128/aem.00819-26}, pmid = {42496154}, issn = {1098-5336}, abstract = {The organic booster biocide DCOIT (4,5-dichloro-2-n-octyl-4-isothiazolin-3-one) is widely used in marine antifouling systems, yet its ecological impacts on sediment microbiomes remain poorly understood. Here, we integrated absolute quantitative 16S rRNA gene sequencing, metagenomics, and enzyme activity assays to examine microbial responses to DCOIT exposure (0-50 μg/g sediment) over 30 days. DCOIT induced oxidative stress and bioenergetic impairment, accompanied by reduced microbial activity and inhibition of key enzyme-mediated processes involved in organic matter turnover and nitrogen transformation. Absolute quantification revealed a compensatory increase in total microbial abundance by Day 30, despite persistent diversity loss and community restructuring. Metagenomic analysis showed that DCOIT disturbed functional potentials related to carbon and nitrogen cycling. Kordiimonas, Aliikangiella, and Neptuniibacter emerged as potential contributors to nitrogen transformation, whereas Marinobacter was more closely associated with potential DCOIT transformation. DCOIT exposure also enriched adaptive traits, including chemotaxis, motility, quorum sensing, and biofilm regulation, and was accompanied by increased multidrug efflux systems and heavy metal resistance determinants. Our findings provide novel insights into the ecotoxicological risks of isothiazolinone biocides and highlight the potential for DCOIT to undermine sediment ecosystem functions and microbial habitat health. Given its extensive application, this study emphasizes the need to consider the microbial ecological consequences of DCOIT accumulation in seafloor environments.IMPORTANCEDCOIT is widely used in marine antifouling coatings and can accumulate in benthic sediments, yet its effects on sediment microbiomes remain poorly defined. This study shows that DCOIT disrupts microbial energy status, enzyme activities, community structure, and nitrogen-cycling functions while selecting for adaptive traits and resistance-related determinants. By integrating absolute quantification, metagenomics, and enzyme assays, our work demonstrates that DCOIT poses microbial ecological risks beyond toxicity to macroorganisms and should be considered in assessments of antifouling biocides.}, } @article {pmid42496932, year = {2026}, author = {Kumar, A and Dakal, TC and Parveen, K and Bhushan, R and Dhabhai, B and Parveen, A and Yadav, P and Tandon, R}, title = {Revisiting Algorithms, Tools, and Applications for Sequence and Phylogenetic Analyses in the NGS-Based Omics Era.}, journal = {Biochemical genetics}, volume = {}, number = {}, pages = {}, pmid = {42496932}, issn = {1573-4927}, support = {BT/RLF/Re-entry/38/2017//Department of Biotechnology, India Department of Biotechnology (DBT), Government of India/ ; }, abstract = {Integrating high-throughput sequencing with phylogenetic analysis now spans everything from single genes to long-read pangenomes and metagenomes, yet practitioners still face fragmented, tool-centric guidance. This review revisits algorithms, tools, and workflows for sequence and phylogenetic analysis in the NGS-based omics era, with a focus on comparative performance and scenario-driven decision-making. We first organise classical approaches to tree reconstruction - distance methods, maximum parsimony, maximum likelihood, and Bayesian inference - around core criteria of consistency, efficiency, robustness, and computational cost. We then examine multiple sequence alignment strategies, contrasting progressive, consistency-based, and structure-aware algorithms (such as MAFFT variants and T-Coffee family tools) with segment-based and incremental approaches (for example DIALIGN, anchored domains, and local updates) and alignment-free representations based on k-mers, absent words, and related statistics. For inference, we compare heuristic engines optimised for ultra-large alignments (FastTree, VeryFastTree, online tree optimisation) with full ML frameworks (IQ-TREE, RAxML-NG) and Bayesian platforms for time-scaled phylogenies and phylodynamics (MrBayes, BEAST family). We explicitly discuss trade-offs in accuracy, memory, scalability, and uncertainty support, and show how GPU-enabled implementations change the feasible design space. Beyond these core components, we address current trends that strongly influence method choice: long-read assemblies and pangenomes; data quality issues, contamination, recombination, and horizontal gene transfer; phylogenetic placement and alignment-free screening in metagenomics; and real-time pathogen surveillance using Nextstrain-style workflows. A dedicated section covers workflow management and containerisation (Snakemake, Nextflow, Docker/Singularity) together with benchmarking datasets and FAIR reporting, positioning reproducible pipelines as a first-class requirement rather than an afterthought. To make the review directly actionable, we provide a methodological checklist, a decision framework figure mapping input data to recommended strategies, and a large comparative table summarising algorithmic principles, best use cases, strengths, limitations, scalability, uncertainty support, and reproducibility notes for widely used tools. Applications in infectious disease genomics, oncology, and microbiome research illustrate how these choices translate into biological and clinical insight in practice.}, } @article {pmid42497006, year = {2026}, author = {Arjunan, S and Pemberton, I and Li, XS and Sangwan, N and Akino, L and Opoku, E and Verbovetskiy, D and Nemet, I and Kim, HS and Masumiya, H and Wang, Z and Lupica, JA and Tian, MY and Mao, K and Mallela, DP and Mohan, M and Schumacher, S and Rennison, JH and Prasad, S and Laurita, KR and Chodisetty, V and Chung, MK and Van Wagoner, DR and Barnard, J and Smith, JD and Wazni, O and Hazen, SL and Koeth, RA}, title = {Gut microbial trimethylamine N-oxide generation promotes risk of atrial fibrillation via muscarinic receptor-mediated autonomic dysfunction.}, journal = {The Journal of clinical investigation}, volume = {}, number = {}, pages = {}, doi = {10.1172/JCI201684}, pmid = {42497006}, issn = {1558-8238}, abstract = {Gut microbiota-derived trimethylamine N-oxide (TMAO) plays a role in the pathogenesis of cardiovascular disease. The role of TMAO in the pathogenesis of atrial fibrillation (AF) remains uncertain. TMAO levels were quantified in plasma from serial subjects undergoing elective cardiac catheterizations (N=5090) and shown to independently associate with prevalent AF following adjustment for risk factors (TMAO adjusted odds ratio 1.7 [95% confidence interval 1.3-2.1]; P<0.01). Human cAMP response element modulator isoform IbΔC-X transgenic mice (CREM-IbΔC-X), a spontaneous mouse model of AF, supplemented with a TMAO diet developed AF sooner. C57BL/6J mice on and off a TMAO had more inducible AF via a transesophageal pacing study compared to chow controls. Dietary choline supplementation increased circulating TMAO levels and significantly accelerated AF onset in CREM-IbΔC-X mice (P<0.01). Iodomethylcholine (IMC), the gut microbial CutC/D inhibitor that suppresses choline→TMA(O) metabolic transformation, reduced circulating TMAO levels (P<0.0001) and choline induced AF onset (P<0.01). Cecal metagenomic analyses showed that choline supplementation induced changes in microbial communities associated with AF, while many of these changes were attenuated by IMC. Choline supplementation promoted overall adverse atrial remodeling with left atrial dilation. Optical mapping studies showed that mice supplemented with choline exhibited reduced conduction velocity, shortened action potential duration at 80% repolarization, and decreased wavelength. TMAO inhibits muscarinic receptor 2 resulting in autonomic dysfunction that promotes AF. In summary, the gut microbial metabolite TMAO, independently associated with AF risk in subjects, enhances AF in multiple AF mouse models via autonomic dysfunction, and is a therapeutic target for prevention of AF.}, } @article {pmid42497560, year = {2026}, author = {Wu, H and Chen, Y and Chen, S and Li, M and Zhang, Y and Zhao, M and Han, G and Chen, N}, title = {Hydrological inundation threshold regulates the carbon source-sink transition in unvegetated tidal flats.}, journal = {Water research}, volume = {305}, number = {}, pages = {126544}, doi = {10.1016/j.watres.2026.126544}, pmid = {42497560}, issn = {1879-2448}, abstract = {Unvegetated tidal flats cover extensive areas of global coastlines, but their role in atmospheric CO2 exchange remains poorly understood. Here we investigate how hydrological regimes regulate carbon uptake in these ecosystems through a marsh organ experiment in the subtropical Zhangjiang Estuary, China that integrated sediment-atmosphere CO2 and CH4 flux measurements, porewater geochemistry, and metagenomic sequencing. We identified a site-specific hydrological transition in which sediment-atmosphere CO2 exchange shifted from a weak source to sustained net uptake under more frequent inundation, with the transition occurring around an annual inundation frequency of approximately 10-30% in this experimental system. This transition coincided with declining porewater NO3[-]/Cl[-] and SO4[2-]/Cl[-] ratios and increasing pH, dissolved CO2 concentration, and carbonate system derived estimated alkalinity, consistent with enhanced anaerobic redox processes and alkalinity-associated CO2 dissolution and retention. Although CH4 emissions increased under frequent inundation, incorporating CH4 into global warming potential did not substantially offset the CO2 sink transition. Metagenomic analyses further showed an enrichment of rTCA-related carbon-fixation taxa under frequent inundation, indicating greater microbial autotrophic carbon-fixation potential. This functional potential was associated with porewater geochemical changes and increased microbial biomass carbon, supporting the possibility of hydrologically modulated geochemical-microbial coupling during the CO2 source-sink transition. Together, our results unveil a previously unrecognized mechanism in which a hydrologically-modulated geochemical-microbial coupling drives CO2 uptake in frequently inundated sediments. These findings extend current blue carbon frameworks by highlighting the previously overlooked role of unvegetated tidal flats in coastal carbon cycling and climate regulation.}, } @article {pmid42497710, year = {2026}, author = {Sadok, I and Jonik, I and Rachwał, K and Iwaniak, P and Wicha-Komsta, K}, title = {Boosting kynurenic acid in kombucha via substrate selection: metagenomic and biochemical insights.}, journal = {Food chemistry}, volume = {525}, number = {Pt 2}, pages = {150517}, doi = {10.1016/j.foodchem.2026.150517}, pmid = {42497710}, issn = {1873-7072}, abstract = {Kombucha is gaining global popularity for its health benefits. This study explored the use of chestnut honey, a rich source of kynurenic acid (KYNA), to produce kombucha enriched with this metabolite. Five variants were prepared using different green/black tea blends and carbon sources: white sugar or acacia honey (controls) versus chestnut honey. Samples were analyzed for tryptophan metabolites, physicochemical properties, and microbial diversity. Komagataeibacter and Enterobacter were predominant bacterial genera in SCOBY. Candida and Aspergillus were predominated in the single sample analyzed for fungi. During fermentation, tryptophan decreased, while kynurenine increased. KYNA levels remained largely stable during fermentation and were mainly influenced by the fermentation substrate. No melatonin pathway derivatives were detected. On day 7, chestnut honey yielded kombucha with 381.680-739.915 μmol/L KYNA and elevated myricetin. Overall, chestnut honey-based kombucha represents a system in which substrate composition appears to be the main factor influencing KYNA levels in the final beverage.}, } @article {pmid42497724, year = {2026}, author = {Jiang, G and Yin, Y and Tian, L and Lu, JN and Cai, X and Deng, T and Cao, Y and Wang, S and Tang, YT and Morel, JL and Qiu, R and Ruan, Z and Chao, Y}, title = {Keystone and potentiator taxa in hyperaccumulator rhizospheres: A new perspective for microbiome-assisted phytoremediation.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143053}, doi = {10.1016/j.jhazmat.2026.143053}, pmid = {42497724}, issn = {1873-3336}, abstract = {Soil heavy-metal contamination threatens agroecosystem functioning, and hyperaccumulators, together with their rhizosphere microbiomes, offer promise for the phytoremediation of contaminated soils. Most rhizosphere microbiome studies have emphasized keystone taxa, but abundant and stable non-keystone members may also contribute to community functioning. Here, we examined the rhizosphere microbiome of the Ni hyperaccumulator Odontarrhena chalcidica using a combination of amplicon and metagenomic sequencing. Keystone taxa were identified as taxa supported by multiple ecological inference approaches, whereas potentiator taxa were defined as abundant and stable taxa that were not identified as keystones. We then compared their taxonomic composition, functional potential, and model-predicted metabolic interactions. Keystone and potentiator taxa were taxonomically distinct. Potentiator taxa showed broader functional potential than keystone taxa, suggesting that these stable non-keystone members may contribute functions that are overlooked by keystone-focused analyses alone. Genome-scale metabolic modeling further predicted greater metabolite exchange in mixed keystone-potentiator assemblages than in single-role assemblages, with model-predicted metabolic support directed mainly from potentiator taxa to keystone taxa. These findings indicate that abundant and stable non-keystone taxa can complement keystone taxa in the rhizosphere microbiome of a Ni hyperaccumulator. More broadly, this study provides an analytical strategy for identifying candidate microbial combinations that may support microbiome-assisted phytoremediation of metal-contaminated soils.}, } @article {pmid42484632, year = {2026}, author = {Vernon, JJ and Lynch, J and Yu, X and Do, T}, title = {Clostridioides difficile in the oral microbiome: an in silico analysis.}, journal = {Journal of medical microbiology}, volume = {75}, number = {7}, pages = {}, doi = {10.1099/jmm.0.002188}, pmid = {42484632}, issn = {1473-5644}, mesh = {Humans ; *Clostridioides difficile/genetics/isolation & purification/classification ; Saliva/microbiology ; *Dental Plaque/microbiology ; *Microbiota ; *Clostridium Infections/microbiology/epidemiology ; Periodontitis/microbiology ; *Mouth/microbiology ; Computer Simulation ; Computational Biology ; Metagenomics ; Female ; Male ; }, abstract = {Introduction. High rates of recurrent Clostridioides difficile infection (CDI) and environmental contamination are attributed to its ability to form spores. Periodontal diseases are characterized by gingival inflammation, caused by dental plaque accumulation.Hypothesis. Periodontal plaque could harbour C. difficile spores, acting as a reservoir for reinfection.Aim. Compare the prevalence and abundance of C. difficile in metagenomic sequences of saliva and dental plaque from healthy and periodontal disease patients.Methodology. Publicly available metagenomic reads from oral samples of healthy (n=80) and periodontitis (n=204) patients were analysed for C. difficile presence through an in-house bioinformatic pipeline. Briefly, reads underwent quality control (cutadapt/fastQC) prior to subsampling of 3 million reads (seqtk). Reads and MEGAHIT-assembled contigs were aligned to a C. difficile reference genome (ASM1888508v1) or a full non-redundant protein DIAMOND database. Outputs were filtered, annotated (Entrez Direct) and top hits identified via National Center for Biotechnology Information blast. Abundance and prevalence were compared between cohorts.Results. Low levels of C. difficile sequences were observed, with significantly higher prevalence in periodontitis (7.4%, n=15/204) vs. healthy cohorts (5.0%, n=4/80) (P=0.0087) with reference genome alignment. Using the full non-redundant database, prevalence was also higher in periodontitis (14.2% vs. 3.8%; P=0.012), along with significantly greater average C. difficile sequence counts (0.608 vs. 0.075; P=0.018) and relative abundance (0.00029% vs. 0.0000003%; P=0.009).Conclusion. Sequences pertaining to C. difficile were detected in oral samples, with significantly more observed in periodontal disease compared to healthy cohorts. This highlights the possibility for dental plaque to act as a reservoir, potentially contributing to reinfection in CDI patients.}, } @article {pmid42484695, year = {2026}, author = {Vieira, CS and Lemos, LN and Morais, DK and Rosado, AS and Pylro, VS}, title = {Uneven global coverage of halophilic metagenomes limits comparative analyses of microbial adaptation to saline environments.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {42484695}, issn = {1678-4405}, mesh = {Metagenomics ; *Metagenome ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Ecosystem ; Salinity ; *Adaptation, Physiological ; Biodiversity ; }, abstract = {Halophilic microorganisms are central to biotechnology, bioremediation, and astrobiology because they persist under extreme and polyextreme conditions analogous to extraterrestrial environments. Although metagenomics has transformed the study of halophilic biodiversity, available datasets remain fragmented and unevenly documented. To assess how halophilic metagenomic research reflects the global exploration of hypersaline environments, we analyzed PubMed-indexed studies and associated sequencing metadata deposited at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using a curation workflow. Our quantitative analysis reveals a severe geographic bias linked to uneven global research investment (Gini coefficient = 0.736), with a small number of countries contributing to many publicly available datasets. In contrast, the environmental distribution of these samples showed moderate ecological uniformity (Pielou's Evenness = 0.818), though we identified pervasive gaps in metadata completeness that hinder dataset interoperability. Our curated dataset highlights a strong research focus on polyextremophilic habitats, positioning these ecosystems as prime targets for biotechnological and astrobiological bioprospecting. Additionally, the geographical bias highlights the need for interoperable global data frameworks and more equitable investment in data generation and analysis, especially in underrepresented regions of the Global South.}, } @article {pmid42485280, year = {2026}, author = {K V, S and Thaha, N and Dehury, B}, title = {In silico identification and biophysical characterization of candidate antimicrobial peptides from the Indian marine microbiome targeting multidrug-resistant ESKAPE pathogens.}, journal = {PloS one}, volume = {21}, number = {7}, pages = {e0353985}, pmid = {42485280}, issn = {1932-6203}, mesh = {*Antimicrobial Peptides/pharmacology/chemistry ; Molecular Dynamics Simulation ; *Microbiota ; *Drug Resistance, Multiple, Bacterial/drug effects ; Acinetobacter baumannii/drug effects ; India ; Computer Simulation ; *Anti-Bacterial Agents/pharmacology/chemistry ; Klebsiella pneumoniae/drug effects ; Pseudomonas aeruginosa/drug effects ; Machine Learning ; }, abstract = {The global health crisis of antimicrobial resistance necessitates the discovery of new antibacterial agents. Underexplored marine microbiomes, particularly from the biodiverse Indian coast, represent a rich potential source of antimicrobial peptides (AMPs). Targeting the urgent threat of multidrug-resistant ESKAPE pathogens, the present study aimed to computationally identify novel, membrane-active AMPs from these unique metagenomic datasets, with a focus on inhibiting Gram-negative bacteria. In this study, we computationally mined Indian marine high-resolution shotgun metagenomic datasets through quality filtering, de novo assembly, and small open reading frame prediction. An ensemble of six machine learning-based AMP prediction tools identified over 51,000 high-confidence candidate AMPs. Subsequent filtering based on physicochemical properties and AlphaFold3-predicted structures prioritized ten peptides with favourable membrane-active characteristics. Two lead candidates, c_AMP_1 and c_AMP_2, were subjected to all-atom molecular dynamics simulations within Gram-negative membrane mimetic models of Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. Our simulations indicated distinct membrane interaction modes: c_AMP_1 adopted a stable, surface-associated α-helical orientation, while c_AMP_2 displayed a more flexible, membrane-inserting orientation in the simulations. Analysis of the MD simulations revealed distinct predicted peptide-membrane interaction profiles, characterized by specific hydrogen bonding patterns, peptide tilt angles, and membrane thinning, which collectively suggest differing biophysical interaction modes. Taken together, our work suggests the Indian marine microbiome as a promising reservoir for novel AMP candidates and suggests that an integrated computational pipeline - combining machine learning, structural biology, and biophysical simulation - may help prioritize candidate peptides for future experimental validation against critical pathogens.}, } @article {pmid42485562, year = {2026}, author = {Dalal, R and Barot, J and Binsuwaidan, R and Alshammari, N and Adnan, M and Patel, M and Patel, K}, title = {Substrate-Driven Microbiome Assembly in Water Hyacinth Vermicompost: Combined 16S rRNA and Shotgun Metagenomics for Sustainable Agriculture.}, journal = {Journal of basic microbiology}, volume = {66}, number = {7}, pages = {e70185}, pmid = {42485562}, issn = {1521-4028}, support = {PNURSP2026R304//Princess Nourah bint Abdulrahman University/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Eichhornia/microbiology ; Metagenomics ; Biomass ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; Animals ; *Soil Microbiology ; Archaea/classification/genetics/isolation & purification/metabolism ; Composting ; Agriculture ; Fungi/classification/genetics/isolation & purification/metabolism ; Shotgun Sequencing ; Phylogeny ; }, abstract = {Substrate composition is a primary determinant of microbial succession and functional dynamics in vermicomposting systems. However, comparative insights into how biomass pre-treatment influences microbial architecture and how different sequencing approaches capture these changes remain limited. In this study, evaluation was carried out on microbial community structure and metabolic potential in vermicompost derived from three forms of Eichhornia crassipes (water hyacinth) biomass, burnt biomass (BB), composted biomass (CB) and dry biomass (DB) using both 16S rRNA gene amplicon sequencing and shotgun metagenomics. All treatments were dominated by bacterial communities (> 97%), with Proteobacteria (Pseudomonadota), Firmicutes (Bacillota), Actinobacteria and Bacteroidota representing core phyla across substrates. However, metagenomics revealed broader domain-level coverage, detecting Archaea and Fungi that were underrepresented in 16S datasets. Substrate-specific signatures were evident such as, composted biomass exhibited enrichment of lignin degradation and carbon cycling pathways; dry biomass showed methanogenesis, fermentation and phosphate solubilization signatures; and burnt biomass was associated with nitrogen fixation and sulphur metabolism. Shannon diversity was highest in composted biomass (H' = 5.21), reflecting enhanced niche diversification during substrate maturation. Comparative analysis demonstrated that 16S rRNA sequencing effectively captured dominant bacterial structure, whereas shotgun metagenomics provided superior taxonomic resolution and direct functional inference, particularly for low-abundance and non-bacterial taxa. Notably, functional differentiation among treatments was more pronounced than broad taxonomic shifts, indicating that biomass pre-treatment exerts stronger influence on ecological function than on core community composition. These findings demonstrate that integrating taxonomic and functional metagenomics enables substrate-specific optimization of vermicompost formulations and provides a framework for designing microbiome-informed strategies for sustainable agriculture and invasive biomass valorization.}, } @article {pmid42485926, year = {2026}, author = {de Bruijn, DGJ and Gusinac, A and Ederveen, THA and Le, ND and Kulkarni, P and Meijer, RI and Janssen, MCH and Zweers, HEE}, title = {Gut microbiota alterations in individuals with mitochondrial disease caused by the m.3243A >G mutation.}, journal = {Molecular genetics and metabolism}, volume = {149}, number = {1-2}, pages = {110208}, doi = {10.1016/j.ymgme.2026.110208}, pmid = {42485926}, issn = {1096-7206}, abstract = {People with mitochondrial disease (MD) associated with the m.3243 A > G mutation often experience gastrointestinal complaints and dysmotility, suggesting dysbiosis of the gut microbiome. A common phenotype of the m.3243 A > G mutation is Maternally Inherited Diabetes and Deafness (MIDD). Previous studies have shown that other forms of diabetes are associated with an altered gut microbiome. Therefore, our study aimed to investigate the gut microbiota of people with MD caused by the m.3243 A > G mutation compared to healthy controls (Lifelines®) and people with type 1 diabetes (T1D). Fecal samples of 30 people with the m.3243 A > G mutation were used for shotgun metagenomic sequencing. The MD group was compared with 60 healthy controls and 60 people with T1D from different datasets, and were matched for age, sex, and BMI. We found that the Bray-Curtis β-diversity of the gut microbiota differed significantly between MD compared to healthy controls and T1D, while there was a non-significant reduction in Shannon α-diversity in the MD group. The gut microbiota of the MD group was characterized by reduced Faecalibacterium prausnitzii, and increased Escherichia coli, Ruminococcus gnavus, and Ruminococcus torques levels compared to healthy controls and T1D. This pattern aligns with microbial signatures reported in inflammatory bowel disease, which is associated with mitochondrial dysfunction in intestinal epithelial cells. Overall, our explorative study suggest that people with the m.3243 A > G mutation exhibit a dysbiotic gut microbiota, which may pave the way for future research aimed at developing new therapies, dietary adjustments and their potentials to improve quality of life.}, } @article {pmid42486223, year = {2026}, author = {Leena, DA and Chaudhary, S and Mehdi, MM}, title = {Pesticide-driven microbial resistance: Ecological impact and mitigation strategies development of multiple drug resistance due to pesticide exposure.}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {}, number = {}, pages = {110630}, doi = {10.1016/j.cbpc.2026.110630}, pmid = {42486223}, issn = {1532-0456}, abstract = {The persistent use of agricultural pesticides is increasingly recognized as an important driver of antimicrobial resistance (AMR) and multidrug resistance (MDR) in environmental microorganisms. This review synthesizes current knowledge on the molecular mechanisms underlying pesticide-induced MDR, its ecological and evolutionary consequences, advances in resistance surveillance, and emerging mitigation strategies. Chronic pesticide exposure promotes MDR through interconnected genetic mechanisms (mutations and horizontal gene transfer), biochemical mechanisms (detoxification enzymes), physiological adaptations (stress responses and biofilm-associated tolerance), and molecular regulatory processes (efflux pump activation and altered gene expression), resulting in cross-resistance to clinically relevant antimicrobial agents. These mechanisms alter microbial community structure, facilitate the dissemination of antibiotic resistance genes, and impair essential ecosystem functions. Recent advances in PCR, whole-genome sequencing, metagenomics, and other omics technologies have improved resistance detection, although important knowledge gaps remain regarding the long-term effects of sub-lethal pesticide exposure and resistance dynamics in environmental microbiomes. By integrating mechanistic, ecological, evolutionary, and surveillance perspectives within a One Health framework, this review provides a comprehensive synthesis of pesticide-induced MDR and identifies key research priorities for developing sustainable resistance mitigation strategies.}, } @article {pmid42486447, year = {2026}, author = {Lv, Z and You, H and Leng, H and Sheng, H and Li, W and Liu, F and Li, Z and Zhu, J and Zhang, G}, title = {Recycling sludge carbon sources via different iron-based activated PDS into denitrification systems for nitrogen removal: focusing on efficacy, community structure and molecular mechanism.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135481}, doi = {10.1016/j.biortech.2026.135481}, pmid = {42486447}, issn = {1873-2976}, abstract = {Advanced oxidation processes (AOPs) effectively solubilized organic matter from sludge, generating a liquid phase with substantial recovery potential. Because organic composition and concentration were governed by oxidation intensity, elucidating this relationship was essential for optimizing downstream resource recovery. This study systematically compared the cracking solution generated from sewage sludge utilizing different AOPs (US/Fe(II)/PDS vs US/Fe1/PDS vs US/Fe-C/PDS). The SCOD were 673 mg/L, 556.8 mg/L, and 676 mg/L in US/Fe(II)/PDS, US/Fe1/PDS and US/Fe-C/PDS systems, respectively, including high concentrations of short-chain volatile fatty acid, proteins and polysaccharides (PS). Correspondingly, there demonstrated superior NO3[-]-N, NH4[+]-N and total nitrogen removal efficiencies of 13.6%, 50%, and 50%, respectively, primarily attributed to the optimal oxidation capacity and abundant organic carbon in US/Fe-C/PDS system. Additionally, no significant difference was observed between US/Fe-C/PDS system and control group (CH3COONa) during denitrification, suggesting cracking solution in sludge had strong application potential as a carbon source. Sequencing results revealed stable bacterial communities across all systems, implying that the cracking solution had negligible influence on the structure of core denitrifying taxa. A robust nitrogen-cycling function was maintained, accompanied by up-regulate of genes (napAB, nirS/K, norBC and nosZ) associated with PS-sustained-release carbon source metabolism and denitrification in US/Fe-C/PDS system. These results suggested that PS-sustained-release carbon source driving efficient nitrogen removal and promoting sludge resource recycling in US/Fe-C/PDS system.}, } @article {pmid42486450, year = {2026}, author = {Wu, Y and Sun, Y and Yu, R and Cui, Y and Yang, F and Li, J and Zhang, Z}, title = {In situ sludge reduction induced by graphene oxide: Mechanistic insights into metabolic uncoupling, maintenance energy and cryptic growth.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135479}, doi = {10.1016/j.biortech.2026.135479}, pmid = {42486450}, issn = {1873-2976}, abstract = {Nanomaterials are increasingly recognized as stressors in biological wastewater treatment systems, yet the effects on biomass yield remain poorly understood. This study systematically evaluated the effects of low-dose graphene oxide (GO; 0.1 and 1 mg/L) on pollutant removal and sludge yield in activated sludge systems. At day 40, sludge yields were 0.356, 0.298, and 0.237 g VSS/g COD in the Control, 0.1 and 1 mg/L GO systems, respectively, corresponding to reductions of 16.29% (p = 0.055) and 33.43% (p < 0.05) without compromising nitrogen removal. GO exposure also loosened floc structure and increased mean intrafloc dissolved oxygen concentrations by 23.88% and 32.84%, respectively (both p < 0.01). Activities of isocitrate dehydrogenase, α-ketoglutarate dehydrogenase, and the electron transport system increased, indicating intensified endogenous oxidative metabolism. Despite enhanced respiration, ATP production decreased by 19.48% (p < 0.05) and 27.95% (p < 0.01), suggesting uncoupling between oxidation and phosphorylation. Intracellular reactive oxygen species increased by 65.46% and 145.60% (both p < 0.01), respectively. The resulting oxidative stress increased maintenance energy demand and promoted cell death and cryptic growth. Metagenomic analysis further revealed enrichment of genes related to oxidative stress responses, macromolecular repair, and extracellular polymeric substance secretion, together with decrease of genes involved in cell replication and division. Collectively, enhanced intrafloc oxygen transfer and endogenous respiration, oxidation-phosphorylation uncoupling, increased maintenance energy demand, and cryptic growth jointly drove GO-induced sludge reduction.}, } @article {pmid42486470, year = {2026}, author = {Delebecque, CJ and La Monica, MB and Keller, D and Shannon, W and Ziegenfuss, TN and Zimmerman, NP}, title = {The effects of a postbiotic supplement on biomarkers of microbiome, gastrointestinal, cardiometabolic, and immunometabolic health.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-14}, doi = {10.1163/18762891-bja00129}, pmid = {42486470}, issn = {1876-2891}, abstract = {The gut microbiome is increasingly recognised as a modifiable contributor to metabolic, immune, and stress-related physiology, yet many nutritional interventions produce broad microbial shifts that may be poorly tolerated. We investigated the effects of a fermented and pasteurised oat-based preparation (Keystone) on microbiome composition and selected biomarkers in a 4-week randomised, double-blind, placebo-controlled trial in generally healthy adults. Seventy-six participants completed the intervention (38 placebo, 38 Keystone). Stool samples collected at baseline and week 4 underwent shotgun metagenomic sequencing, and serum butyrate, IL-8, morning cortisol, albumin/globulin ratio, routine clinical chemistries, DASS-21, and SF-36 were assessed. The intervention did not affect alpha or beta diversity. In contrast, species-level analysis showed a distinct compositional signature, with enrichment of taxa including Akkermansia spp., Bacteroides intestinalis, Bifidobacterium pseudocatenulatum, and Anaerostipes caccae in the Keystone group, alongside lower abundance of several Haemophilus, Megasphaera, and Prevotella taxa relative to placebo (FDR < 0.001). Nominally significant baseline-by-treatment interactions were observed for morning cortisol (P = 0.03), IL-8 (P = 0.04), and albumin/globulin ratio (P = 0.03), while serum butyrate showed a near-significant trend (P = 0.053). SF-36 emotional well-being improved within the Keystone group. No adverse events were reported. These results indicate that Keystone was safe and well tolerated and selectively modulates the gut microbiome, with exploratory associations for host stress and inflammatory markers that offer key insights for future follow-up studies. Trial registration: The trial was IRB approved and registered with ClinicalTrials.gov NCT07527286.}, } @article {pmid42486576, year = {2026}, author = {Venugopal, DC and Srinivas, KS}, title = {Challenges and future directions in head and neck microbiome research.}, journal = {Advances in immunology}, volume = {170}, number = {}, pages = {189-227}, doi = {10.1016/bs.ai.2026.03.010}, pmid = {42486576}, issn = {1557-8445}, mesh = {Humans ; *Head and Neck Neoplasms/microbiology/therapy/immunology ; *Microbiota/immunology ; Animals ; *Dysbiosis/microbiology/immunology/therapy ; Fecal Microbiota Transplantation ; Metabolomics ; Metagenomics ; Probiotics/therapeutic use ; }, abstract = {The microbial imbalance in head and neck cancer (HNC) is a promising area of research for developing targeted therapies. Maintenance of microbial diversity and balance through prebiotics, probiotics and faecal microbial transplantation (FMT) holds a potential approach in reestablishing the gut health. Preclinical studies and early clinical trials have shown positive results in restoring the favourable microbial environment, thereby minimizing the inflammation and maximizing the positive immune response. However, the link between microbial flora associated with oral dysbiosis, the associated biomarkers and HNC tumorigenesis needs to be further explored. Future research focusses on developing standardised strategies for maintaining the microbial environment, to serve as an adjunct to the standard treatment protocols for HNC. Biomarkers predicting immune response, synthetic genetically engineered beneficial bacteria, integration of metagenomics, metabolomics and meta transcriptomics for intra-tumoral microbial evaluation are the focus areas of emerging research.}, } @article {pmid42486580, year = {2026}, author = {Perera, ML and Perera, IR}, title = {Microbiome based diagnostic approaches.}, journal = {Advances in immunology}, volume = {170}, number = {}, pages = {93-125}, doi = {10.1016/bs.ai.2026.03.004}, pmid = {42486580}, issn = {1557-8445}, mesh = {Humans ; *Microbiota/immunology ; *Head and Neck Neoplasms/diagnosis/microbiology ; Dysbiosis ; Animals ; Early Detection of Cancer ; }, abstract = {Cancers of the Head and Neck (HNC) ranks seventh most abundant cancer category according to global incidence. thus posing a pertinent health hallenge. Shift in the homeostatic relationship of head and neck microbiome, causes microbial metabolic dysbiosis. Consequently, there is an increase in the pathobiome and pathogenic functions potentiating initiation and progression of carcinogenesis. Infection, inflammation and immune mediation trigger the pathogenic mechanisms. Accordingly, periodontitis perpetrated by unsatisfactory oral hygiene is connected to initiation and progression of HNC supported by substantial evidence. Further, mechanistic evidence is emerging on pathogenesis of bacteria-mediated carcinogenesis via toxins, carcinogenic metabolites and inflammatory cytokines with a view to possible treatments to halt progression of cancers. Advancements in surgical management techniques and adjuvant radiotherapy treatment, chemotherapy and emerging therapies such as immunotherapy, have not significantly increased overall disease free survival rates of most of HNCs. Early detection of cancers therefore, facilitates favorable outcomes such as better survival rates. Nevertheless, traditional invasive diagnostic approaches such as tissue biopsy gives rise to pain and discomfort to the patient In contrast, microbiome based diagnostic approaches, underpinned by salivary and mouth rinse microbiome analyses offers promising non-invasive, screening tools for early detection of HNC. This is augmented by advances in next generation sequencing, third generation sequencing, bioinformatics and machine learning technologies. Current developments in metagenomics, transcriptomics along with metabolomics enhanced harnessing the immense potential saliva possesses as a valuable screening and diagnostic tool, not only for cancer detection but for a range of diseases such as gastrointestinal diseases, autoimmune and metabolic disorders. Microbiome signatures in risk assessment of HNC is emerging as a new dimension in personalized risk assessment, risk stratification and care based pathways. Salivary microbiome analyses provides a promising approach for risk stratification, early stratification, through to assessment of prognosis, treatment success and survival of HNC patients suggested by accumulating evidence. Against this backdrop, we aim to provide an overview of microbiome based diagnostic approaches exploring new dimensions of detection and identification of HNC specific microbial biomarkers, microbial signatures, screening tools, primary diagnostic biomarkers, prognostic markers and interpersonal microbiome in the arena of personalized medicine.}, } @article {pmid42487113, year = {2026}, author = {Ma, Y and Sun, J and Guo, C and Cao, J and Zhang, L and Zhu, F and Yu, X and Yang, L and Fang, J}, title = {Exploring brain-gut interaction mechanisms in Transcutaneous auricular Vagus Nerve stimulation for Major Depressive Disorder.}, journal = {BMC psychiatry}, volume = {26}, number = {1}, pages = {}, pmid = {42487113}, issn = {1471-244X}, support = {82474663//National Natural Science Foundation of China/ ; HLCMHPP2023072//High Level Chinese Medical Hospital Promotion Projec/ ; }, mesh = {Humans ; Magnetic Resonance Imaging ; *Major Depressive Disorder/therapy/physiopathology/diagnostic imaging ; Female ; *Vagus Nerve Stimulation/methods ; Male ; Adult ; *Transcutaneous Electric Nerve Stimulation/methods ; *Brain/physiopathology/diagnostic imaging ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Brain-Gut Axis/physiology ; Treatment Outcome ; }, abstract = {BACKGROUND: The gut microbiota is intricately implicated in the pathogenesis of Major Depressive Disorder (MDD), with the vagus nerve serving as a key regulatory bridge. Transcutaneous Auricular Vagus Nerve Stimulation (taVNS) has emerged as a promising non-invasive therapeutic strategy for MDD by modulating the gut-brain axis, yet the precise brain-gut interaction mechanisms underlying its antidepressant effects remain poorly characterized. This study is a registered clinical trial (ChiCTR2200059591; Registered 4 May 2022; https://www.chictr.org.cn).

OBJECTIVE/HYPOTHESIS: This study aimed to verify the clinical efficacy of taVNS for MDD and elucidate the underlying brain-gut crosstalk mechanisms, by integrating comprehensive clinical assessments, resting-state functional magnetic resonance imaging (rs-fMRI) neuroimaging data and gut metagenomic profiling.

METHODS: Ninety-five patients diagnosed with MDD were randomly allocated at a 1:1 ratio to either the active taVNS group (auricular concha stimulation) or the sham taVNS group (superior concha of mid-helix stimulation). Eighty patients (40 per group) completed the entire intervention course and were included in the final statistical analysis. All participants underwent 30-minute stimulation twice daily (4/20 Hz, 3-8 mA) for 8 consecutive weeks (5 days per week). Standardized clinical assessments were administered at baseline and post-intervention, including the 17-item Hamilton Depression Rating Scale (HAMD-17), 14-item Hamilton Anxiety Rating Scale (HAMA-14), and Gastrointestinal Symptom Rating Scale (GSRS). Rs-fMRI was performed to quantify core neural activity metrics, including amplitude of low-frequency fluctuation (ALFF), fractional ALFF (fALFF), regional homogeneity (ReHo), and degree centrality (DC); fecal samples were collected for high-throughput metagenomic analysis. Spearman correlation analysis and mediation analysis were further conducted to dissect the interactive relationships between brain neural activity and gut microbiota.

RESULTS: The active taVNS group achieved significantly superior clinical efficacy relative to the sham group, with a HAMD-17 response rate of 62.50% and remission rate of 35.00%, versus 30.00% and 2.50% in the sham group (all P < 0.05). Rs-fMRI analyses revealed significant group×time interaction effects on neural activity: decreased ALFF in the right calcarine sulcus; altered fALFF in the right inferior temporal gyrus, left cuneus, right superior frontal gyrus (SFG) and right angular gyrus; reduced ReHo in the right calcarine sulcus and bilateral insula; and increased DC in the right caudate nucleus and left anterior cingulate gyrus. Gut microbiota profiling identified anaerobic butyrate-producing bacteria and Faecalibacterium prausnitzii as potential biomarkers linked to taVNS therapeutic effects. HAMD-17 scores were negatively correlated with Faecalibacterium prausnitzii abundance (r=-0.566, P < 0.01) and positively correlated with anaerobic butyrate-producing bacteria abundance (r = 0.406, P < 0.01). Mediation analysis suggested that fALFF values in the right SFG may indirectly modulate depressive symptoms via regulating Faecalibacterium prausnitzii abundance (indirect effect 95% CI: 0.3039-2.4466), with a significant partial mediation effect observed, though future studies controlling for dietary and other confounding variables are needed to confirm this relationship.

CONCLUSION: taVNS effectively alleviates depressive symptoms in MDD patients via dual complementary pathways: directly modulating neural activity in the right SFG to regulate depression-related brain function, and indirectly maintaining gut microbiota homeostasis by enriching beneficial taxa such as Faecalibacterium prausnitzii. These findings provide novel mechanistic insights into the brain-gut interaction underlying the antidepressant effects of taVNS, laying a theoretical foundation for its clinical application in MDD management.}, } @article {pmid42487141, year = {2026}, author = {Kedia, S and Rani, PS and Nyambero, M and Bandsode, V and Peddireddy, V and Ahmed, N}, title = {Comparative genomics of Bifidobacterium crudilactis NASR_001 - unveiling the tapestry of a putative probiotic.}, journal = {Gut pathogens}, volume = {18}, number = {1}, pages = {}, pmid = {42487141}, issn = {1757-4749}, abstract = {BACKGROUND: Bifidobacteria are the initial colonizers of the human gastrointestinal tract. Due to an obligate anaerobic character, the isolation and culture of Bifidobacterium spp. is challenging. This bottleneck has led to studies being focused on metagenomic analysis rather than genome sequencing of Bifidobacterium spp. from pure cultures. Our metadata analysis revealed paucity of Bifidobacterium genomes reported from the Indian subcontinent. In this report, we describe the selective isolation and whole genome sequencing (WGS) of Bifidobacterium crudilactis from a pure culture of dairy origin from India.

RESULTS: The WGS by Oxford Nanopore long-read sequencing of genomic DNA of B. crudilactis isolate NASR_001 revealed a single circular chromosome of 2,347,652 bp with a GC content of 57.5%. Genome annotation predicted 1923 coding sequences, 6 rRNAs, 46 tRNAs with no CRISPR arrays. Moreover, average nucleotide identity (ANI) analysis with B. crudilactis LMG 23 609 (RefSeq accession GCF_000738005.1) and B. crudilactis MAG UW_FK_BIF1_1 (RefSeq accession GCF_047836735.1) showed 98.8% and 97.3% similarity, respectively, revealing thereby a closest identity and functional similarity to B. crudilactis. The presence of genetic attributes for carbohydrate metabolism, stress response genes and absence of antimicrobial resistance (AMR) encoding genes, as well as paucity of virulence genes signify B. crudilactis NASR_001 to be a putative probiotic organism.

CONCLUSION: The genome sequence of B. crudilactis NASR_001 represents a high-quality genome, representative of the species. It offers valuable insights for further exploration of its promising probiotic potential and functional characteristics.}, } @article {pmid42487569, year = {2026}, author = {Allen, XJ and Cowger, C and Brown-Guedira, G and Hawkes, CV}, title = {Mycobiome Simplification in Wheat Is Associated With the Pathogen Parastagonospora nodorum.}, journal = {Molecular ecology}, volume = {35}, number = {14}, pages = {e70485}, doi = {10.1111/mec.70485}, pmid = {42487569}, issn = {1365-294X}, support = {NNF19SA0059348//Novo Nordisk Fonden/ ; 7005451//U.S. Department of Agriculture (HATCH Project)/ ; }, mesh = {*Triticum/microbiology/genetics ; *Ascomycota/pathogenicity/genetics ; *Plant Diseases/microbiology/genetics ; *Mycobiome/genetics ; Host-Pathogen Interactions/genetics ; North Carolina ; Plant Leaves/microbiology ; Metagenomics ; }, abstract = {Plant mycobiomes are essential to plant health, yet their assembly under biotic stressors such as pathogen infection remains poorly understood. Plant pathogens can influence microbial community composition through direct antagonism and suppression of host immune responses, potentially altering mycobiome composition in ways that could affect plant performance. We investigated how the wheat (Triticum aestivum L.) foliar mycobiome was associated with inoculation with the fungal pathogen Parastagonospora nodorum (Berk.) Quaedvlieg, Verkley & Crous, which can cause substantial loss of yield and grain density throughout its range. To address this, we studied inoculation effects in four wheat cultivars planted in a randomized block design at two North Carolina field sites. We used ITS amplicon metagenomics to characterize wheat mycobiome richness, composition, and structure. We found that P. nodorum inoculation reduced fungal richness by up to 38.5%. We also found simplified foliar fungal networks for plants inoculated with P. nodorum, with up to 13.1% fewer taxa present and up to 41.2% fewer associations among those taxa. As part of these changes, increasing P. nodorum absolute abundance was correlated with increasing proportional representation of pathogens in wheat leaves due to loss of non-pathogenic taxa. Fewer fungal taxa and reduced network connectivity were particularly evident in reportedly susceptible cultivars and at one of the two sites where conditions favoured pathogen success. Based on these results, we suggest that pathogen infection plays a significant role in mycobiome assembly and has implications for disease management and mycobiome-based interventions in agricultural systems.}, } @article {pmid42487618, year = {2026}, author = {Atara, S and Antaliya, K and Vaghamshi, N and Vansia, A and Ghelani, A and Patel, R and Dudhagara, P}, title = {Environmental emergence and dissemination of clinically relevant multidrug-resistant bacteria and resistance genes in sewage and aquatic ecosystems.}, journal = {Osong public health and research perspectives}, volume = {}, number = {}, pages = {}, doi = {10.24171/j.phrp.2026.0186}, pmid = {42487618}, issn = {2210-9099}, abstract = {OBJECTIVES: This study characterized multidrug-resistant (MDR) bacteria in sewage, river, and marine ecosystems in South Gujarat, India.

METHODS: Water samples were collected from 25 hospital drainage, sewage treatment/pumping, Tapi River, and coastal marine sites at multiple time points. From 270 screened colonies, 166 morphologically and biochemically distinct nonduplicate isolates were retained. Antimicrobial susceptibility was assessed, and isolates were classified as MDR, extensively drug-resistant (XDR), or pan-drug-resistant (PDR). Biofilm formation, metabolic activity, extracellular polymeric substance protein, heavy metal tolerance, extended-spectrum β-lactamase production, carbapenemase production, and metallo-β-lactamase activity were assessed phenotypically. Tapi River estuary water was used for taxonomic profiling and antibiotic resistance gene (ARG) detection.

RESULTS: The 166 isolates comprised 45 bacterial species, with clinically significant Gram-negative pathogens predominating, including Pseudomonas aeruginosa (n=24, 14.5%), Ochrobactrum intermedium (n=16, 9.6%), Stenotrophomonas maltophilia (n=15, 9.0%), and Escherichia coli (n=12, 7.2%). MDR phenotypes were detected in 80.1% of isolates; 18.1% were XDR, and 1.8% were PDR, with PDR isolates confined to river water samples. Biofilm formation was observed in 86.1% (n=143) of isolates, including 28.3% (n=47) strong, 24.7% (n=41) moderate, and 32.5% (n=54) weak producers. Extended-spectrum β-lactamase production was confirmed in 13.4% of Gram-negative isolates, and carbapenemase activity was detected in 11 isolates. Zinc and copper tolerance were significantly higher in XDR than in MDR isolates (p<0.05). Metagenomics identified efflux pumps as the dominant ARG class (36.2%), followed by target-site mutations (21.3%) and β-lactamases (14.9%), and detected blaCTX-M-15, blaTEM-207, gyrA, and parC.

CONCLUSION: These interconnected aquatic systems represent important reservoirs for community-level antimicrobial resistance transmission.}, } @article {pmid42487706, year = {2026}, author = {He, Z and Hua, R and Wu, T and Qu, H and Yang, G and Wang, S and Gao, F and Jing, Y}, title = {Microbial functional gene assembly is associated with soil carbon and nitrogen dynamics during grassland degradation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1878594}, pmid = {42487706}, issn = {1664-302X}, abstract = {INTRODUCTION: Grassland degradation is often accompanied by changes in the structure and function of soil microbial communities. However, the mechanisms by which the assembly of microbial functional communities is associated with alterations in soil carbon and nitrogen pools remain unclear.

METHODS: This study was conducted along a degradation gradient in a typical steppe of Inner Mongolia. Metagenomics, community null models, and structural equation modeling were used to examine microbial functional gene assembly, carbon and nitrogen cycling genes, and their associations with soil carbon and nitrogen pools.

RESULTS: The assembly of microbial functions shifted from being predominantly influenced by stochastic processes to deterministic processes, with the strongest deterministic filtering observed during the moderate degradation stage. The abundance of the aerobic oxidation gene porA decreased with increasing degradation, whereas fermentation genes, including ldh and atoB, increased significantly during moderate degradation. Denitrification genes, including narG, nirK, norB, and nosZ, reached their highest abundance during the heavy degradation stage. Mineral-associated organic carbon exhibited a nonlinear pattern characterized by an initial increase followed by a decrease. Structural equation modeling revealed that microbial biomass carbon was the central variable linking microbial functional differentiation with changes in soil carbon and nitrogen pools. During the heavy degradation stage, soil ammonium nitrogen showed a numerical increase, suggesting that nitrogen released from mineral-associated organic carbon decomposition may be predominantly converted into inorganic forms.

DISCUSSION: These findings indicate that the threshold-like decline of microbial biomass carbon, rather than specific restructuring of functional gene profiles, was closely associated with the collapse of stable carbon-nitrogen pool stability during grassland degradation. Changes in functional genes may therefore represent responsive signals accompanying microbial biomass carbon attenuation. The continuous decrease in microbial biomass carbon and associated shifts in functional gene ratios may serve as potential indicators of declining carbon-nitrogen stability in grassland soils.}, } @article {pmid42487710, year = {2026}, author = {Zhili, G and Jie, L and Yuyue, X and Fang, Y and Dianqun, R and Qin, Z and Xiaojun, L}, title = {Fecal metagenomic profiling in patients with colorectal adenomas to characterize gut microbial composition and functional potential.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1842365}, pmid = {42487710}, issn = {1664-302X}, abstract = {OBJECTIVE: To investigate differences in gut microbiota between patients with colorectal adenoma (CRA) and healthy individuals using metagenomic sequencing, and to analyze the correlation between microbial abundance and polyp diameter and number.

METHODS: Metagenomic sequencing was performed on fecal samples from 60 patients with CRA and 30 healthy controls. Species-level and functional analyses of the gut microbiome were conducted.

RESULTS: Metagenomic profiling revealed a distinct microbial signature in CRA. Statistical analysis identified significant differences in taxonomic composition between the two groups. Overall, 487 genes showed significant abundance differences. Among these, approximately 55.37% were significantly enriched in the adenoma group, suggesting specificity for CRA, while 175 genes were significantly reduced. Alpha diversity analysis indicated similar microbial richness and evenness between the groups, whereas beta diversity confirmed significant structural differences in the microbial community. KEGG enrichment analysis of the top 20 differentially abundant species showed that these microbes were primarily associated with metabolic pathways. The greater number of increased versus decreased genes implied a more pronounced expansion of pathogenic bacteria relative to the loss of beneficial bacteria. Linear discriminant analysis effect size (LEfSe) analysis indicated that Fusobacterium nucleatum, Alistipes, and Bacteroides fragilis could serve as diagnostic microbial biomarkers for CRA. LEfSe further identified 38 differentially abundant bacterial clades, with genera such as Bacteroides, Peptostreptococcus, and Parabacteroides enriched in patients. Finally, correlation analysis linked the abundance of specific microbial taxa with polyp number and diameter.

CONCLUSION: This study confirms distinct gut microbiota profiles in patients with CRA compared with healthy individuals, highlights significant microbiome alterations associated with CRA, and reveals novel correlations between specific microorganisms and polyp characteristics, suggesting that microbial changes may contribute to adenoma development.}, } @article {pmid42487713, year = {2026}, author = {Chen, M and Zhang, S and Lu, M and Zhu, D and Xiao, M and Liao, Y and Li, Y and Zhou, T and Wang, M and Song, Q}, title = {Age-associated gut microbiome succession, colonization resistance, and relative resistome patterns in an antibiotic-restricted infant cohort.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1862116}, pmid = {42487713}, issn = {1664-302X}, abstract = {BACKGROUND: Early infancy is critical for gut microbiome assembly and the establishment of colonization resistance against pathobionts. Whether age-associated microbiome maturation is accompanied by changes in colonization-resistance proxies and relative antimicrobial resistance gene profiles under low infant antibiotic exposure remains unclear.

METHODS: We analyzed shotgun metagenomes from 82 fecal samples collected from 54 healthy infants (54 at 1 month and 28 at 6 months). Taxonomic and functional profiles were generated using MetaPhlAn 4 and HUMAnN3, and AMR genes were annotated using RGI/CARD. Age-associated taxa were screened by LEfSe and tested using MaAsLin2 with adjustment for key perinatal covariates.

RESULTS: Age group was associated with modest but statistically significant differences in community structure (Bray-Curtis PERMANOVA R [2] = 0.03, p = 0.005) and higher species richness at 6 months (p < 0.001), with no statistically significant difference in Shannon or Simpson indices. In adjusted models, skin-associated pioneer taxa, including Staphylococcus epidermidis, were lower at 6 months, whereas several anaerobic or oral-associated taxa were higher, including Flavonifractor plautii. Enterobacteriaceae relative abundance was lower at 6 months than at 1 month (median 16.64 vs. 1.86%, p < 0.001), and Bifidobacterium-Enterobacteriaceae antagonism indices were higher. However, Escherichia coli and Klebsiella spp. did not show significant genus-level reductions. Copies per million (CPM)-normalized β-lactamase (bla) relative abundance showed no statistically significant timepoint difference and was positively correlated with selected Bifidobacterium species.

CONCLUSIONS: In this infant antibiotic-restricted cohort, microbiome profiles at 6 months were associated with lower relative abundance of potential pathobionts and higher colonization-resistance proxy indices. CPM-normalized bla relative abundance showed no statistically significant timepoint difference. These observational findings do not establish the genomic host or mobility of bla genes. Quantitative and host-resolved studies are needed to distinguish compositional shifts from absolute resistome trajectories.}, } @article {pmid42487715, year = {2026}, author = {Zlatnar, M and Alves, RP and Toledo, GV and Wicaksono, WA and Berg, G}, title = {Metagenomic analysis reveals functional potential and storage-driven dynamics of the Kalamata olive microbiome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1890405}, pmid = {42487715}, issn = {1664-302X}, abstract = {BACKGROUND: Fermented olives are a staple of the Mediterranean diet due to their nutritional value. Despite advances in olive microbiome research, published research on the functional contributions of fermented food-associated microbiota and the impact of storage on these microbial communities remains limited.

METHODS: We studied the bacterial communities of ready-to-eat Kalamata olives, stored in glass jars or vacuum-sealed bags at various temperatures (4°C, 8°C and 15°C) for 55-day period. The bacterial abundance, taxonomical composition and functional potential were analyzed by quantitative PCR and amplicon sequencing of 16 rRNA gene, and metagenome sequencing.

RESULTS: The microbiota was dominated by Lactobacillaceae (94.6%), a family of lactic acid bacteria (LAB), with dominant genera such as Pediococcus, Lactiplantibacillus and Secundilactobacillus. At the functional level, bacterial genes involved in the biosynthesis of vitamins B1, B2, B5, B7, B9, B12, and vitamin K, as well as short-chain fatty acid metabolism, were observed. Importantly, those functions were not restricted to LAB, underscoring the potential functional contribution of non-LAB taxa to the olive microbiome. Despite conservation, post-fermentation storage, especially the incubation time, temperature, and packaging, influenced the bacterial communities. Lactic acid bacteria were enriched in olives stored at 15°C, whereas non-LAB taxa proliferated more at lower temperatures.

CONCLUSION: Our study showed that Kalamata olives contain a highly abundant and diverse microbiota that responds to storage practices and carries genes encoding functions that may contribute to the characteristics and quality of the fermented product.}, } @article {pmid42487717, year = {2026}, author = {Li, X and Ke, L and Wang, T and Lei, Z and Tian, F and Zhang, Y and Liu, X}, title = {Shared and condition-associated gut microbiota alterations in older adults with depression and constipation: evidence from the American Gut Project.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1891231}, pmid = {42487717}, issn = {1664-302X}, abstract = {BACKGROUND: Constipation and depression frequently co-occur in older adults, and growing evidence suggests that gut microbiota dysbiosis may be a shared feature of both conditions. The microbiota has well-established roles in gastrointestinal motility and gut-brain axis signaling, and compositional alterations have been independently reported in each condition. However, whether older adults with constipation and those with depression share common microbiota characteristics have not been systematically investigated.

AIM: This study aimed to characterize gut microbiota alterations in older adults with depression or constipation using 16S rRNA amplicon sequencing data from the American Gut Project, focusing on microbial features shared by, or specific to, the two conditions.

METHODS: We retrieved fecal 16S rRNA sequencing data from 513 older adults in the publicly available American Gut Project database, including HC (n = 277), DP (n = 78), and CP (n = 158). We compared alpha and beta diversity, taxonomic composition, and genus-level differential abundance among groups, used random forest models to explore features contributing to group discrimination, and performed covariate-adjusted and sensitivity analyses to assess robustness.

RESULTS: Alpha diversity was comparable among groups, whereas beta diversity revealed detectable differences in community composition. After adjustment for age, sex, and BMI, Bray-Curtis-based differences remained evident, with the most consistent pairwise difference between CP and HC. At the genus level, CP showed depletion of health-associated butyrate-producing taxa and enrichment of selected mucin- or inflammation-associated taxa, whereas DP was characterized by enrichment of Erysipelatoclostridium and [Ruminococcus]_gnavus_group and depletion of UCG-002 and selected health-associated genera. Random forest analyses further identified key microbial contributors to group discrimination.

CONCLUSION: We identified subtle and partially overlapping genus-level microbiota alterations in older adults with constipation and depression, with constipation showing the most consistent differences from healthy controls. These findings provide exploratory evidence that selected microbiota alterations may be relevant to the clinical overlap between the two conditions, although their functional roles require validation in longitudinal studies integrating metagenomic and metabolomic profiling.}, } @article {pmid42487961, year = {2026}, author = {Li, X and Wang, J and Wang, J and Yang, J and Li, Y and Li, Y and Liu, B}, title = {Pulmonary function impairment patterns and their clinical correlates in patients with pulmonary tuberculosis complicated by pulmonary infection: a single-center retrospective cross-sectional study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1870280}, pmid = {42487961}, issn = {2296-858X}, abstract = {BACKGROUND AND OBJECTIVE: Pulmonary tuberculosis is a major cause of respiratory morbidity worldwide, and pulmonary function impairment is increasingly recognized as an important consequence of the disease. However, the functional patterns of pulmonary impairment in patients with pulmonary tuberculosis complicated by pulmonary infection, especially in hospitalized populations, remain insufficiently characterized. This study aimed to describe pulmonary function impairment patterns in such patients and to explore their clinical correlates.

METHODS: This single-center retrospective cross-sectional study included hospitalized patients with pulmonary tuberculosis complicated by pulmonary infection who were admitted between November 2024 and October 2025, underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing, and had interpretable pulmonary function results. The analysis was retrospective because all study variables were extracted from pre-existing hospitalization records and database entries rather than being prospectively collected for the present pulmonary function study. Although the parent project is an ongoing prospective study with follow-up, no longitudinal follow-up data were used in the present analysis. Clinical, laboratory, immunologic, gas-exchange, microbiological, and pulmonary function data were extracted from the institutional database and electronic medical records.

RESULTS: A total of 72 patients were included. Pulmonary function abnormalities were common. Diffusion impairment was the most frequent phenotype, occurring in 37 patients (51.4%), followed by reduced respiratory reserve in 36 (50.0%) and obstructive ventilatory impairment in 30 (41.7%). Restrictive ventilatory impairment, mixed ventilatory impairment, and small airway dysfunction were less common. Patients with diffusion impairment were more likely to be male than those without diffusion impairment (73.0% vs. 42.9%, P = 0.019), and smoking history showed a borderline between-group difference. Patients with reduced respiratory reserve had significantly higher IL-6 levels than those without reduced respiratory reserve [13.18 (5.52-38.00) vs. 4.53 (1.94-12.28) pg/ml, P = 0.005]. In exploratory multivariable analysis, no variable was independently associated with diffusion impairment or reduced respiratory reserve after adjustment, although lymphocyte count showed a non-significant positive trend for diffusion impairment.

CONCLUSION: Pulmonary function impairment was highly prevalent in patients with pulmonary tuberculosis complicated by pulmonary infection, with diffusion impairment and reduced respiratory reserve as the predominant phenotypes. These findings suggest that pulmonary dysfunction in this population extends beyond conventional ventilatory defects and may involve substantial abnormalities in gas transfer and respiratory capacity. Comprehensive pulmonary function assessment may provide clinically relevant information for functional evaluation and individualized management in this patient group.}, } @article {pmid42488200, year = {2026}, author = {Nayak, SK and Bhattacharyya, P and Pradhan, C and Tripathy, PS and Padhy, SR and Parida, SP and Moharana, A and Rath, M and Nayak, A and Dash, SS and Das, SK and Priya, H}, title = {Identification of key carbon-fixation pathways and underlying genes for higher CO2 fixation of mangrove-associated microalgae.}, journal = {3 Biotech}, volume = {16}, number = {8}, pages = {350}, pmid = {42488200}, issn = {2190-572X}, abstract = {UNLABELLED: Mangrove systems are major blue-carbon reservoirs, storing 4.4 to 11.7 petagrams of organic carbon globally and supporting diverse microalgal communities that drive primary productivity and coastal carbon cycling. The Sundarban, one of the world's largest (3,629.57 km[2]) mangrove-dominated coastal systems, holds a substantial carbon stock (26.62 Tg). Rising salinity and anthropogenic pressure are altering the diversity of microalgal communities, highlighting the importance of identifying resilient taxa capable of sustaining carbon fixation. To address this need, we conducted whole-genome metagenomic profiling of degraded mangrove soils. The data revealed six dominant microalgal taxa adapted to prevailing salinity and nutrient stress. These six taxa were subsequently isolated from the same habitats, and a 16-day ambient CO2 (420 ppm) screening was undertaken to evaluate the specific growth rate and biomass gain of the algae. Among them, three physiologically resilient strains Chlorella sp., Limnospira platensis, and Leptolyngbya boryana were selected for controlled CO2-enrichment concentrations (0.04%, 0.05%, 0.20%, 10%) to mimic future climate change scenarios. Among those microalgae, the Leptolyngbya boryana showed the highest biomass yield (1.31 g L[-1]), carbon content (0.52 g C g[-1] dry weight), and CO2-fixation rate (up to 149 mg CO2 L[-1] d[-1]). Metagenomic analysis further identified that L. boryana possessed the strongest representation of carbon-fixation pathways like Calvin-Benson-Bassham (CBB) cycle and the reductive TCA (rTCA) cycle, regulated by enriched key genes such as cbbL, cbbS, gap2, zwf, and accC. Therefore, this result positions L. boryana as a promising microalgal candidate for carbon sequestration in future CO2-rich environments under saline coastal ecology.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04986-7.}, } @article {pmid42488424, year = {2026}, author = {Ni, Y and Wu, W and Liu, J and Feng, C and Jin, B and Zhao, T and Gu, Y and Su, X and Li, C and Yuan, X}, title = {Clinical diagnostic value of targeted next generation sequencing for lower respiratory tract infection: a retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1713445}, pmid = {42488424}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Respiratory Tract Infections/diagnosis/microbiology/virology ; Female ; Male ; Bacteria/genetics/classification/isolation & purification ; Middle Aged ; Aged ; Metagenomics/methods ; Sensitivity and Specificity ; Fungi/genetics/classification/isolation & purification ; Viruses/classification/genetics/isolation & purification ; }, abstract = {OBJECTIVE: Lower respiratory tract infections (LRTIs) progress swiftly and require timely, accurate pathogen detection to enhance patient outcomes. This study aims to utilize the targeted metagenomic next-generation sequencing (tNGS) technology as a novel approach to investigate the types of pathogens involved in infections following different structural lung diseases.

METHODS: This retrospective cohort study enrolled 329 patients with suspected LRTIs admitted to three medical centers from June 2023 and June 2024. The study analyzed the pathogenic spectrum of lung infections and compared the diagnostic outcomes of tNGS with those of conventional microbiological techniques (CMTs).

RESULTS: tNGS demonstrated significantly higher sensitivity (97.8% vs. 28.9%, p<0.05) and accuracy (96.6% vs. 30.3%, p<0.05) than CMTs, along with a high concordance rate (87.8%) with clinically confirmed pathogens. Pathogen profiling revealed that Mycoplasma pneumoniae (21.88%), Aspergillus fumigatus (5.17%), and influenza A virus subtype H3N2 (13.07%) were the predominant bacterial, fungal, and viral pathogens, respectively. Several key pathogens, including Pseudomonas aeruginosa, Haemophilus influenzae, Nocardia abscessus, Aspergillus fumigatus, Influenza A virus H3N2, and Influenza B virus, were detected more frequently in the SLD group than in the non-SLD group. Among 193 patients whose treatment was adjusted based on tNGS results, 35.2% initiated new treatment regimens, 25.4% continued their original treatment, and 7.3% required treatment escalation, with 90.2% of these patients showing clinical improvement.

CONCLUSION: These findings showed that tNGS demonstrates significant promise for the etiological diagnosis and tailored management of LRTIs.}, } @article {pmid42488460, year = {2026}, author = {Gangwar, P and Xu, Q and Seangmany, J and Katte, P and Turakhia, Y}, title = {metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.}, journal = {NAR genomics and bioinformatics}, volume = {8}, number = {3}, pages = {lqag080}, pmid = {42488460}, issn = {2631-9268}, mesh = {*Metagenomics/methods ; *Phylogeny ; *Haplotypes ; Humans ; *Software ; Biological Specimen Banks ; }, abstract = {Metagenomic sequencing is transforming diverse areas of health and biological sciences, including pathogen surveillance, clinical diagnostics, and microbiome research. However, the inherent complexity of metagenomic data limits most computational tools to species-level classification and abundance estimation, overlooking within-species genetic diversity that drives key phenotypes. We present metaWEPP, a novel computational pipeline that achieves near-haplotype resolution in metagenomic analysis for species with adequate representation in reference genome biobanks and having sufficient sequencing depth and genome coverage. Specifically, metaWEPP assigns sequencing reads to species using standard taxonomic classifiers, phylogenetically places them onto species-specific mutation-annotated trees of publicly available sequences, and selects the haplotypes that best explain the sample. It also reports unaccounted alleles indicative of novel variants and provides an interactive dashboard for read-level visualization. Applied to diverse metagenomic and mixed-genome samples from prior studies, metaWEPP produced concordant species-level results, while revealing finer lineage- and haplotype-level insights not captured by existing tools. On various clinical samples, metaWEPP identified infecting pathogens and additionally provided credible lineage- and haplotype-level information that can support clinical decision-making. On wastewater samples, metaWEPP uncovered previously undetected haplotype clusters of epidemiological relevance. These findings demonstrate metaWEPP's ability to advance various clinical, epidemiological, and research applications with deeper, actionable insights.}, } @article {pmid42488632, year = {2026}, author = {Long, T and Song, J and Li, SG}, title = {Case Report: Hemophagocytic lymphohistiocytosis after SARS-CoV-2 infection revealing clinically diagnosed stage IVB diffuse large B-cell lymphoma in quiescent adult-onset Still's disease.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1879628}, pmid = {42488632}, issn = {1664-3224}, mesh = {Humans ; Male ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/etiology/drug therapy ; Aged ; *COVID-19/complications ; SARS-CoV-2 ; *Lymphoma, Large B-Cell, Diffuse/diagnosis/drug therapy/complications/pathology ; *Still's Disease, Adult-Onset/complications/drug therapy/diagnosis ; Rituximab/therapeutic use ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; }, abstract = {BACKGROUND: Adult hemophagocytic lymphohistiocytosis (HLH) may be triggered by infection, malignancy, or systemic inflammatory disease. Attribution is challenging when recent SARS-CoV-2 infection, quiescent adult-onset Still's disease (AOSD), and an occult B-cell clonal disorder coexist.

CASE REPORT: A 71-year-old man with AOSD controlled for 14 years on low-dose methotrexate developed persistent fever and fatigue after mild SARS-CoV-2 infection. He subsequently developed cytopenias, hyperferritinemia, markedly elevated lactate dehydrogenase, diffuse FDG-avid lymphadenopathy, hepatosplenomegaly, elevated soluble interleukin-2 receptor, reduced natural killer-cell activity, and bone marrow hemophagocytosis, fulfilling HLH criteria. Broad pathogen evaluation, including blood and bone marrow metagenomic next-generation sequencing, did not identify an alternative infectious trigger. Bone marrow histopathology did not show definite tumor cells; however, flow cytometry identified monoclonal mature B cells, and peripheral-blood smear high-throughput sequencing detected lymphoma-associated mutations including MYD88, CD79B, IGLL5, PRDM1, DTX1, DUSP2, and BTG1. Multidisciplinary consultation favored probable lymphoma-associated HLH with clinically diagnosed stage IVB diffuse large B-cell lymphoma. HLH-directed therapy followed by rituximab-based lymphoma-directed chemotherapy led to transient clinical improvement, but the patient later died from infectious complications.

CONCLUSION: Mild SARS-CoV-2 infection may act as a co-trigger or unmasking event rather than the sole cause of HLH. Persistent high lactate dehydrogenase and soluble interleukin-2 receptor, diffuse lymphadenopathy, clonal mature B cells, lymphoma-associated mutations, and negative broad pathogen testing should prompt evaluation for occult lymphoma-associated HLH.}, } @article {pmid42488664, year = {2026}, author = {Chen, M and Zhou, H and Zhou, Z and He, Y and Jiang, Y}, title = {Clinical features of Q fever confirmed by plasma metagenomic next-generation sequencing.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1847365}, pmid = {42488664}, issn = {1664-3224}, mesh = {Humans ; *Q Fever/immunology/blood/diagnosis/microbiology/genetics ; Male ; Middle Aged ; Female ; Retrospective Studies ; *Coxiella burnetii/immunology ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Adult ; Autoantibodies/blood/immunology ; Fever ; Aged ; Antibodies, Antiphospholipid/blood ; }, abstract = {BACKGROUND: The clinical features of acute Q fever and their link to transient autoantibodies remain poorly defined. We characterized 44 plasma mNGS-confirmed cases and identified predictors of prolonged fever.

METHODS: Retrospective study (2021-2026) of 44 patients with confirmed Q fever (mNGS + clinical + exposure criteria). Patients were grouped by post-treatment fever duration (>7 days vs. ≤7 days).

RESULTS: Cohort was predominantly middle-aged (median 52.5 years) and male (95.5%). Common presentations: fever (95.5%), headache (45.5%), pulmonary involvement (51.2%). Elevated CRP (97.7%) and ESR (90.9%) were universal. Transient antiphospholipid antibodies (78.9%, all negative at 12 weeks) and ANA (23.5%) were frequent. Prolonged fever (>7 days) was associated with higher WBC, CRP, ESR, lower CD8+ and B cells, and aPL positivity (all p<0.05).

CONCLUSIONS: Acute Q fever frequently induces transient autoantibodies. Prolonged fever correlates with an inflammatory and lymphopenic phenotype, underscoring immune dysregulation in recovery.}, } @article {pmid42488891, year = {2026}, author = {Slullitel, PA and Lohmann, FA and Albani-Forneris, AF and Buljubasich, M and García-Mansilla, AM and Salagoity, F and Lucero, CM and Comba, F and Zanotti, G and Piñero, TA and Buttaro, MA}, title = {The Gut-Joint Axis in Hip Osteoarthritis: Distinct Articular Microbial Profiles and Metabolic Potential Compared With Nonarthritic Controls.}, journal = {JB & JS open access}, volume = {11}, number = {3}, pages = {}, pmid = {42488891}, issn = {2472-7245}, abstract = {BACKGROUND: Intestinal dysbiosis and systemic microbial translocation potentially contribute to chronic joint inflammation. However, the role of the gut-joint axis in the genesis of osteoarthritis still needs to be elucidated. This investigation characterized taxonomic signatures and proinflammatory metabolic pathways within the hip joint to define their contribution to the pathophysiology of osteoarthritis relative to nonarthritic controls.

METHODS: A prospective cohort of 48 patients undergoing hip arthroplasty was enrolled. Specimens including synovial fluid, articular cartilage, and acetabular fossa tissue were collected from patients with primary hip osteoarthritis (n = 20) and femoral neck fracture (n = 20). Metagenomic profiling was performed using 16S-rRNA gene sequencing (V3-V4 region). Alpha and beta diversity, taxonomic composition, and predicted functional pathways (PICRUSt2) were compared based on diagnosis (arthritis vs. fracture) and sample location.

RESULTS: Osteoarthritic samples demonstrated reduced alpha diversity evenness compared with fracture controls (p = 0.031). While beta diversity was primarily driven by specimen type rather than diagnosis, significant taxonomic differences were observed at the genus level. Pseudomonas, Atopostipes, and Staphylococcus showed significant differential abundance between groups, both by specimen location and diagnosis. Functional predictive analysis revealed a marked enrichment of the KDO2-lipid A biosynthesis pathway in osteoarthritic specimens, specifically within the genus Pseudomonas. Key genes involved in lipopolysaccharide biosynthesis and export, including lpxB, lpxL, and lpxM, exhibited significantly higher median abundances in osteoarthritic joints compared with controls (p < 0.00000001).

CONCLUSIONS: Patients with hip osteoarthritis exhibited specific taxonomic and predicted lipopolysaccharide-related pathways differences compared with nonarthritic controls, consistent with microbial molecular signatures in a noninfectious inflammatory joint environment, despite the absence of major diagnosis-driven community-level differences.

LEVEL OF EVIDENCE: Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.}, } @article {pmid42488935, year = {2026}, author = {Whelan, FJ}, title = {How the social lives of bacteria affect their pangenome.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20250039}, pmid = {42488935}, issn = {1744-1358}, support = {MR/Y016343/1//UK Research and Innovation (UKRI)/ ; SBF009\1062//Academy of Medical Sciences (The Academy of Medical Sciences)/ ; }, abstract = {Although the study of microbes started with type strains and reference genomes, advances in sequencing technology and new interest in mixed microbial communities have made us aware that a single genome cannot and does not reflect the diversity of a given bacterial species. Bacteria rarely occupy an environmental or host niche alone and quickly diversify into strains upon colonization of a new niche. The genetic diversity present within a phylogenetically related set of bacterial strains (the 'pangenome') is influenced by the niche that they occupy and how they interact with the other microorganisms that they share that niche with. In this review, I examine how the social lives of bacteria can affect their genetic diversity and the bioinformatic techniques that we use to detect that diversity.}, } @article {pmid42488938, year = {2026}, author = {Kraft, TS and Venkataraman, VV and Gurven, M and Suratman, MN and Goldberg, TL}, title = {Ethno-etiology meets virology: land leeches (family: Haemadipsidae) as potential disease vectors.}, journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume = {}, number = {}, pages = {}, doi = {10.1093/trstmh/trag077}, pmid = {42488938}, issn = {1878-3503}, support = {//American Association of Biological Anthropologists/ ; //University of Wisconsin-Madison/ ; //John D. MacArthur Professorship Chair/ ; }, abstract = {OBJECTIVES: Hematophagous terrestrial leeches are common in rainforest habitats and widely regarded as pests. Despite limited research, circumstantial evidence raises the possibility that, beyond being an annoyance, terrestrial leeches could potentially transmit diseases.

METHODS: We explored this possibility using multiple approaches. First, we reviewed published literature to synthesize knowledge related to disease transmission by leeches. Second, we collected terrestrial leeches (genus Haemadipsa) from human-occupied rainforests in Peninsular Malaysia and applied metagenomic methods for virus discovery to their anterior segments. Finally, we conducted interviews to probe local knowledge and behavior related to leeches, testing whether cultures may encode information that recognizes and helps to prevent vector-borne disease transmission.

RESULTS: Results indicate that terrestrial leeches are potential disease vectors, particularly via mechanical vector-borne transmission stimulated by human removal techniques. Supporting this, we identified four novel viruses within leeches, three of which are distantly related to medically important animal and human viruses which could potentially be transmitted among animal species, including humans. However, ethno-etiological evidence suggests that local Indigenous cultures do not recognize land leeches as disease vectors or promote behaviors likely to reduce transmission, suggesting knowledge may not encompass difficult-to-observe vectors.

CONCLUSION: We conclude that disease transmission by terrestrial leeches is plausible and merits experimental study. Accession numbers: PX094876, PX118495, PX118496, PX118497, PX118498, PX118499.}, } @article {pmid42489029, year = {2026}, author = {Ma, R and Guo, G and Liu, C and Deng, P and Dong, X and Mu, L and Qu, Q and Hu, X}, title = {Microplastic Pollution Is Associated with Fragmentation and Environmental Sensitivity of Marine Planktonic Microbial Communities.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c06158}, pmid = {42489029}, issn = {1520-5851}, abstract = {The effects of increasing marine microplastic (MP) pollution on the microbial community structure and function remain uncertain, particularly under natural conditions. Specifically, our study focuses on free-living marine microbial communities (0.8-5 μm) rather than plastisphere biofilms. Here, we systematically evaluated differences in microbial community responses to environmental gradients across MP concentration regimes on the basis of a response modulation analysis framework (RMAF). In this framework, co-occurrence network analysis, random forest modeling, and SHapley Additive exPlanations (SHAP) and partial dependence-based interpretation methods are integrated to quantify changes in microbial sensitivity and ecological interactions. Through the use of Tara Oceans metagenomic data, we analyzed seven functional gene categories and species diversity across MP concentration gradients. High-MP environments (with concentrations exceeding 5,500 items·km[-2]) were characterized by a notable decrease in nondominant taxa (from 17-21% to 6.53-9.45%) alongside increased dominance of abundant species. The functional profiles showed higher abundance levels of genes involved in carbon, nitrogen, and sulfur cycling. The results of network analysis indicated reduced connectivity and increased fragmentation, suggesting weakened ecological interactions and decreased system stability. Microbial communities in high-MP environments exhibited increased sensitivity to environmental drivers, characterized by response centralization and niche compression, suggesting a narrower range of environmental responses. MPs were associated with high microbial functional activity and potential indications of low ecosystem resilience.}, } @article {pmid42489451, year = {2026}, author = {Roques, S and Tournayre, J and Dou, PS and Yanibada, B and Boudra, H and Popova, M and Morgavi, DP}, title = {Integrative analysis of rumen microbiota activity and host metabolism following methanogenesis inhibition in dairy cattle.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0026926}, doi = {10.1128/spectrum.00269-26}, pmid = {42489451}, issn = {2165-0497}, abstract = {Enteric methane emission from dairy cattle is an environmental challenge. The most efficient mitigation strategies nowadays include the use of methanogenesis inhibitors that specifically target the rumen methanogens. Specific inhibitors, such as 3-nitrooxypropanol (3-NOP), reduce methane emissions without negative effects on the products of fermentation that serve as energy metabolites for the host. However, the concomitant effects of methanogenesis inhibition on rumen microbiota and host metabolism are poorly characterized. Thus, the objective of this study was to explore the association between rumen microbiota and host metabolism when methanogenesis is inhibited. Thirteen dairy cows were used as controls, and 12 were supplemented with 3-NOP for 6 weeks. Rumen microbiota composition and activity were characterized using metagenomics and metatranscriptomics. The host metabolism was assessed in a previous publication by a metabolomic analysis of the plasma. Microbiota data were used as explanatory variables of the metabolome data in a multiblock sparse partial least squares analysis. Overall, the association between rumen microbiota and host metabolism was moderate. Notwithstanding this, a few downregulated transcripts related to glycolysis, hydrogen transfer, and protein synthesis, together with a decrease in the proportion of taxa of the Oscillospirales order, showed a correlation with host one-carbon metabolites (|r| > 0.6). These associations raised novel hypotheses that remain to be elucidated, especially with regard to the effects of dihydrogen on the accumulation of microbial glycolysis and methanogenesis metabolite intermediates.IMPORTANCEDairy cattle produce a substantial amount of methane, a potent greenhouse gas. Several strategies have been designed to reduce methane production by targeting the rumen microbiota. One such strategy specifically inhibits methanogens with a molecule called 3-nitrooxypropanol. This study uses an integrative data analysis approach, combining rumen microbiota and host metabolome information, to explore the consequences of inhibiting methanogenesis on the holobiont. This provides additional holistic insight into the effect of methane mitigation strategies on dairy cattle.}, } @article {pmid42489455, year = {2026}, author = {Aguilar-Rangel, EJ and Lüneberg, K and Medina, DA and Siebe, C and Alcántara-Hernández, RJ and Servín-Garcidueñas, LE}, title = {Metagenomes from untreated wastewater and the soil irrigated with it for 50 years in the Mezquital Valley, Mexico.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0129925}, doi = {10.1128/mra.01299-25}, pmid = {42489455}, issn = {2576-098X}, abstract = {The Mezquital Valley is a unique site for studying the gradual effects of wastewater irrigation on agricultural soils. We report metagenomes from soils irrigated for 50 years and their corresponding irrigation water. Potentially pathogenic bacteria dominated the wastewater, while the soil harbored a diverse community mainly involved in biogeochemical cycling.}, } @article {pmid42489464, year = {2026}, author = {Mori, K and Nishimura, Y and Ijichi, M and Iwahashi, Y and Sudo, S and Yoshizawa, S}, title = {Metagenome-assembled genomes from time-series samples of artificial seawater aquarium water.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0069526}, doi = {10.1128/mra.00695-26}, pmid = {42489464}, issn = {2576-098X}, abstract = {We report 804 metagenome-assembled genomes (MAGs) reconstructed from a water conditioning tank during the establishment of an artificial seawater aquarium at SEA LIFE Nagoya. These MAGs were assigned to 27 phyla (26 bacterial phyla and 1 archaeal phylum), providing a genome-resolved resource for investigating the microbial diversity of artificially managed marine environments.}, } @article {pmid42489979, year = {2026}, author = {Zhao, Z and Zhao, Y and Sun, Y and Bao, Y and Feng, J and Jiang, T and Lin, A}, title = {Metagenomic screening of antimicrobial peptide candidates and isolation of two active peptides from bat gut bacteria.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {8}, pages = {}, pmid = {42489979}, issn = {1573-0972}, support = {32430066, 32271558, 32571749//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Antimicrobial Peptides/pharmacology/isolation & purification/genetics/chemistry ; Microbial Sensitivity Tests ; Metagenomics/methods ; *Chiroptera/microbiology ; Anti-Bacterial Agents/pharmacology/isolation & purification ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/drug effects ; Bacteriocins/pharmacology/isolation & purification/genetics ; Amino Acid Sequence ; Tandem Mass Spectrometry ; Metagenome ; }, abstract = {Bacterial antibiotic resistance has intensified the need to identify new antimicrobial molecules from underexplored microbial systems. Wild mammalian gut microbiota may harbor antimicrobial peptide (AMP) candidates and candidate bacteriocins, but these systems remain poorly investigated as sources for antimicrobial discovery. Here, we used parallel metagenomic and culture-dependent approaches to explore candidate AMP sequences and candidate bacteriocins from the gut bacteria of the Asian particolored bat Vespertilio sinensis. Machine-learning screening of 553,401 short non-redundant ORF protein sequences identified 12,907 candidate AMP sequences. Of these, 31 were prioritized after in silico safety and structural filtering. In parallel, culture-dependent screening yielded two antagonistic bacterial isolates, CQJ and LYS. Activity-guided purification followed by LC-MS/MS identified two active peptides, CQJ01 and LYS01, with no exact matches in public databases. Both peptides exhibited broad in vitro antibacterial activity against 16 pathogenic strains, with minimum inhibitory concentration (MIC) values as low as 8 µg/mL against selected Gram-positive and Gram-negative bacteria. CQJ01 retained activity across pH 2-9 and after heat treatment up to 80 °C, whereas LYS01 retained activity from - 20 °C to 100 °C. Both peptides remained active after catalase, trypsin, papain, and proteinase K treatments but were sensitive to pepsin. They showed low hemolytic activity and limited cytotoxicity in preliminary assays. These findings support bat gut bacteria as an underexplored source of AMP candidates and candidate bacteriocins.}, } @article {pmid42490446, year = {2026}, author = {Löwe, J and von Kügelgen, A and Planelles-Herrero, VJ and McAndrew, MBL and Oliva, MA and Vosseberg, J and Köstlbacher, S and Dharamshi, JE and Appler, KE and MacLeod, FI and Nobs, SJ and Jørgensen, SL and Burns, BP and Baker, BJ and Bharat, TAM and Derivery, E and Tamarit, D and Ettema, TJG}, title = {Eukaryotic-like microtubules and dynamic instability of Asgard archaeal tubulins.}, journal = {Science advances}, volume = {12}, number = {30}, pages = {eaeh1082}, doi = {10.1126/sciadv.aeh1082}, pmid = {42490446}, issn = {2375-2548}, mesh = {*Tubulin/metabolism/chemistry/genetics ; *Microtubules/metabolism/chemistry ; *Archaea/metabolism/genetics ; Phylogeny ; *Archaeal Proteins/chemistry/metabolism/genetics ; Models, Molecular ; Eukaryota/metabolism ; }, abstract = {Eukaryotic cells change their shapes, actively segregate their DNA, and contain membrane networks, facilitated by a complex cytoskeleton containing actin filaments, microtubules made from tubulin, and other components. These filaments have ancient evolutionary origins because actin- and tubulin-like proteins form prokaryotic cytoskeletons in archaea and bacteria. Bona fide eukaryotic F-actin can be traced back to crenarchaea and Asgard archaea, which are the closest known relatives of eukaryotes. A possible Asgard archaeal origin of microtubules was suggested recently with the discovery of a lokiarchaeon containing AtubAB mini microtubules that share architectural features with their eukaryotic counterparts. Using phylogenetic analyses of metagenomic data, here we report the broad occurrence of tubulins in Asgard archaea. Biochemical and structural analyses showed that one of our previously unidentified heimdallarchaeial AtubAB tubulin pairs forms four-protofilament mini microtubules that show dynamic instability and are inhibited by the tubulin drug maytansine. Our work raises the possibility that microtubule architecture and dynamics evolved in Asgard archaea prior to eukaryogenesis.}, } @article {pmid42490589, year = {2026}, author = {Torgerson, EG and Adams, M and Lock, LR and Simonis, MC and Dyer, KE and Vicente-Santos, A and Fenton, MB and Simmons, NB and Becker, DJ and Achee, NL}, title = {Neotropical bats as sentinels for emerging zoonoses in Central America: A case study identifying Trypanosoma cruzi in bats from Belize using metagenomic next-generation sequencing.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {7}, pages = {e0013851}, doi = {10.1371/journal.pntd.0013851}, pmid = {42490589}, issn = {1935-2735}, mesh = {Animals ; *Chiroptera/parasitology ; High-Throughput Nucleotide Sequencing ; *Trypanosoma cruzi/isolation & purification/genetics ; Metagenomics ; *Zoonoses/parasitology/epidemiology ; Belize/epidemiology ; *Chagas Disease/veterinary/epidemiology/parasitology ; *Communicable Diseases, Emerging/epidemiology/parasitology/veterinary ; Disease Reservoirs/parasitology ; Humans ; }, abstract = {Emerging zoonoses remain a global public health concern. Surveillance of infectious and vector-borne diseases is vital for predicting and mitigating detrimental effects of zoonotic spillover events. Beyond assessing what microorganisms are circulating in specific environments, it is important to understand how potential reservoir hosts, especially animals such as bats, participate in pathogen transmission. Bats can host and potentially spread infections caused by bacteria, viruses, fungi, and protozoa. However, bats can also act as sentinels that test positive for pathogenic microorganisms without necessarily contributing to the pathogen replication cycle. Metagenomic next-generation sequencing (mNGS) provides an efficient means to broadly screen for pathogens, although microorganism selectivity can sometimes be lower than targeted approaches. Pairing mNGS results with higher-sensitivity tests such as quantitative PCR (qPCR) can validate results and together these tools provide a relatively fast and reliable method for conducting surveillance. To test this approach, we conducted an exploratory study surveying the types of microorganisms circulating in Belize by collecting 263 blood samples from 20 different bat species captured in the Orange Walk District in 2019, 2022, and 2023. We used mNGS to initially characterize the microbial communities and qPCR to confirm presence and intensity of human pathogens of interest. We detected 1,430 different microorganisms with some relevance to human or animal health, including the protozoan Trypanosoma cruzi, which was detected in the phyllostomid bats Desmodus rotundus and Artibeus jamaicensis. qPCR confirmed the presence and intensity of Trypanosoma cruzi in mNGS-positive bat samples. We documented the types of pathogenic microorganisms circulating throughout the bat community in northern Belize to demonstrate the capacity for bats to serve as sentinels.}, } @article {pmid42490944, year = {2026}, author = {Song, Y and Wang, H and Lin, L and Cheng, Y and Shen, Y}, title = {Clinical characteristics and outcomes of severe Legionella pneumophila pneumonia diagnosed by metagenomic next-generation sequencing in children: a case series of 8 patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1865333}, doi = {10.3389/fcimb.2026.1865333}, pmid = {42490944}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; *Legionella pneumophila/genetics/isolation & purification ; *Legionnaires' Disease/diagnosis/drug therapy/microbiology ; Infant ; Child, Preschool ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; *Metagenomics ; Infant, Newborn ; Anti-Bacterial Agents/therapeutic use ; Child ; Community-Acquired Pneumonia ; Treatment Outcome ; China ; }, abstract = {INTRODUCTION: Severe Legionella pneumophila (LP) pneumonia is exceedingly rare in children, and clinical data remain scarce.

METHODS: We retrospectively analyzed the clinical data of 8 children with severe LP pneumonia diagnosed by metagenomic next-generation sequencing (mNGS) at Henan Children's Hospital between January 2020 and January 2026.

RESULTS: The cohort comprised 3 males and 5 females with a median age of 74 days (range, 8 days to 9 years); neonates accounted for 50.0% (4/8), and 75.0% (6/8) had no underlying diseases. Six cases were community-acquired and 2 were hospital-acquired. The predominant manifestations were tachypnea/dyspnea (100.0%) and fever (87.5%); neonates presented with lethargy and poor feeding. Complications included respiratory failure (87.5%), multiple organ dysfunction (62.5%), and septic shock (37.5%). Procalcitonin, interleukin-6, and LDH were elevated in all cases, while ALB was uniformly decreased. Bilateral pulmonary involvement was seen in 87.5% on chest imaging. mNGS detected LP in all 8 cases (100%), whereas conventional sputum and blood cultures failed to identify LP in any case; LP was isolated from a surgical pus specimen in only 1 case. Co-infections were identified in 50.0%. All initial empirical regimens failed to cover LP. After mNGS-guided targeted therapy, the fluoroquinolone-rifampin combination (2 cases) achieved complete recovery, while macrolide-based regimens yielded variable outcomes. Overall, 50.0% were cured or improved, while 50.0% died or had treatment withdrawn. LP bacteremia and septic shock were uniformly associated with poor outcomes.

DISCUSSION: Severe LP pneumonia in children predominantly affects neonates and can occur without recognized immunodeficiency. mNGS detected LP in all cases where conventional culture failed. In this small cohort, fluoroquinolone-containing combination regimens were associated with favorable outcomes.}, } @article {pmid42490978, year = {2026}, author = {Balkrishna, A and Chaudhary, P and Singh, S and Saini, A and Kumari, A and Mahato, KI and Arya, V}, title = {Artificial intelligence in soil microbiome-driven agriculture: from practical limits to a translational roadmap.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1860559}, doi = {10.3389/frmbi.2026.1860559}, pmid = {42490978}, issn = {2813-4338}, abstract = {BACKGROUND: Soil microbiome research has been revolutionized by advances in high-throughput sequencing and multi-omics technologies, generating massive datasets that capture the taxonomic, functional, and metabolic diversity of microbial communities in agricultural soils; however, interpreting these complex datasets and translating them into practical agronomic insights remains challenging.

OBJECTIVES: To critically assess the role of artificial intelligence (AI) in soil microbiome-driven agriculture, focusing on methodological developments, prediction performance, existing limitations, and translational opportunities.

METHODS: A narrative review was conducted to evaluate commonly used AI approaches, including random forest, gradient boosting, support vector machines, and deep learning architectures, alongside key microbiome data types such as amplicon sequencing, metagenomics, and functional gene profiling, with integration of environmental, agronomic, and meteorological datasets.

RESULTS: The prediction of crop productivity, disease risk, nutrient cycling dynamics, and soil health indicators may be enhanced by AI-assisted integration of microbiome, soil physicochemical, and meteorological data, according to several studies. However, broad generalizations about predictive robustness and generalizability are limited by significant diversity in datasets, validation methods, and model architectures.

DISCUSSION: To address these limitations, a five-phase implementation framework integrating centralized data systems, AI-driven analytics, multi-omics profiling, standardized soil sampling, and feedback-based model retraining within precision agriculture systems is proposed, providing a pathway for translating microbiome insights into field-scale decision support.

CONCLUSION: AI-enabled soil microbiome applications hold significant potential for sustainable agriculture, but future advancements will require large, multisite datasets, improved validation strategies, interpretable modeling approaches, and integration with digital agriculture technologies, highlighting both opportunities and practical constraints.}, } @article {pmid42491000, year = {2026}, author = {Duman, M and Armwood, A and Ajmi, N and Taşçı, G and Speare, D and Yavaş, Ö and Saticioglu, IB}, title = {Capsulated Lactococcus garvieae caused devastating mortality in Atlantic bluefin tuna, Thunnus thynnus: genomic and histopathologic characterization.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1831351}, doi = {10.3389/fcimb.2026.1831351}, pmid = {42491000}, issn = {2235-2988}, mesh = {Animals ; *Tuna/microbiology ; *Lactococcus/genetics/isolation & purification/classification/pathogenicity ; *Gram-Positive Bacterial Infections/veterinary/microbiology/mortality/pathology ; *Fish Diseases/microbiology/mortality/pathology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Genome, Bacterial ; Whole Genome Sequencing ; Genomics ; Microscopy, Electron, Transmission ; }, abstract = {Atlantic bluefin tuna (ABFT; Thunnus thynnus) is among the most valuable commodities in Mediterranean mariculture, and recent increases in seawater temperatures have coincided with the re-emergence of bacterial diseases causing catastrophic losses. During the summer 2025 mortality event, we investigated stranded and moribund ABFT using bacteriological isolation and identification, high-throughput 16S amplicon profiling of tissue-associated bacterial communities, whole-genome sequencing to resolve a complete genome of the etiologic agent, transmission electron microscopy, and gross and histopathological examinations. Across multiple organs, the metagenomic profiles were overwhelmingly dominated by Lactococcus garvieae, supporting a primary systemic bacterial etiology. The isolate displayed a capsulated phenotype, and genome analysis identified a capsule-associated gene cluster consistent with a capsulated lineage. Capsule expression was further confirmed ultrastructurally by transmission electron microscopy. Pathology indicated fulminant septicemia with prominent hemorrhagic lesions and severe cardioperitoneal involvement, including fibrinous epicarditis with abundant Gram-positive cocci, alongside marked hepatic and splenic pathology. Collectively, these data document, for the first time in two decades, the detection of a capsulated L. garvieae serotype or lineage associated with ABFT mass mortality. Rapid etiologic confirmation, mitigation of temperature-related and husbandry-associated stress, and targeted prevention strategies (including vaccination and biosecurity) are recommended to reduce recurrence in warming coastal waters.}, } @article {pmid42491023, year = {2026}, author = {Xu, Z and Xu, L and Liu, J and Pang, L and Xia, L}, title = {Clinical characteristics of lung abscess by red complex bacteria infection: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1861751}, doi = {10.3389/fmed.2026.1861751}, pmid = {42491023}, issn = {2296-858X}, abstract = {BACKGROUND: Treponema denticola, Porphyromonas gingivalis and Tannerella forsythia are common oral pathogens collectively referred to as the "red complex bacteria", serve as crucial periodontopathic agents. Owing to the challenges associated with anaerobic culture, their contribution to lower respiratory tract infections, especially lung abscess, is often undervalued. Metagenomic next-generation sequencing (mNGS) has evolved as a potent instrument for the identification of fastidious organisms.

CASE PRESENTATION: A 63-year-old male with chronic cough and hemoptysis was admitted to our hospital. Chest computed tomography showed an indeterminate space-occupying lesion in the right upper lobe, and repeated sputum cultures were negative. Lung cancer was the primary consideration, so a CT-guided percutaneous core needle biopsy of the lung lesion was performed. Nevertheless, the pathology favored inflammation over lung cancer, leading us to continue investigating the causative pathogen. Following mNGS analysis of the puncture biopsy tissue, Treponema denticola and Porphyromonas gingivalis were detected. Both organisms belong to the red complex bacteria, closely associated with periodontitis that the patient had. Intravenous piperacillin-tazobactam followed by oral amoxicillin-clavulanate was prescribed. The patient recovered and subsequent chest computed tomography confirmed the improvement.

CONCLUSIONS: This case highlights the role of oral red complex bacteria in culture-negative chronic lung abscesses. mNGS is a crucial diagnostic tool for identifying these fastidious anaerobes, enabling targeted therapy and improving clinical outcomes.}, } @article {pmid42491029, year = {2026}, author = {DeSalle, AJ and Agbajelola, VI and Ericsson, AC and Shyu, CR and Palaniappan, K and Shacham, E and Raghavan, RK}, title = {Seasonal variation in the bacterial microbiome of questing nymphal ticks in Missouri, United States.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1863755}, doi = {10.3389/fmicb.2026.1863755}, pmid = {42491029}, issn = {1664-302X}, abstract = {BACKGROUND: Seasonal environmental variation may influence the composition of tick-associated bacterial communities. This study assessed seasonal differences in the microbiome of questing nymphal ticks collected from Missouri, United States.

METHODS: Questing ticks were collected during early and late seasonal periods at a livestock-associated site in central Missouri. To minimize confounding by developmental stage, microbiome analyses were restricted to nymphal ticks. Bacterial communities were characterized using 16S rRNA gene sequencing. Alpha diversity (richness, Shannon, and Simpson indices), beta diversity (Jaccard and Bray-Curtis dissimilarities), and differential abundance analyses were performed. Community differences were evaluated using permutational multivariate analysis of variance (PERMANOVA).

RESULTS: Sequencing generated 984-101,293 reads per sample. Sequencing depth was strongly correlated with observed richness (R [2] = 0.808, p = 2 × 10[-7]). Comparisons of non-rarefied and rarefied datasets revealed no significant differences between early- and late-season nymphal ticks in observed richness, Shannon diversity, or Simpson diversity (all p > 0.05). In contrast, beta-diversity analyses identified significant differences in bacterial community membership between seasonal groups based on Jaccard dissimilarity (PERMANOVA: F = 1.5, R [2] = 0.066, p = 0.0102), whereas Bray-Curtis dissimilarity showed a non-significant trend toward seasonal separation (F = 2.2, R [2] = 0.090, p = 0.0834). Differential abundance analysis identified 18 amplicon sequence variants (ASVs) with raw p-values < 0.05, of which one Rickettsia-associated ASV remained significant following false discovery rate correction.

CONCLUSION: Seasonal differences in bacterial community composition were detected among nymphal ticks despite similar levels of microbial richness and alpha diversity. The enrichment of a Rickettsia-associated ASV in early-season ticks suggests that season may influence the occurrence of specific bacterial taxa within tick microbiomes. Further studies using higher-resolution sequencing and pathogen-specific approaches are needed to clarify the ecological significance of these seasonal patterns.}, } @article {pmid42491347, year = {2026}, author = {Jin, Y and Clasen, F and Garcia-Guevara, F and Arif, S and Schierwagen, R and Bidkhori, G and Praktiknjo, M and Brol, MJ and Uschner, FE and Castelli, FA and Pons, N and Quinquis, B and Galleron, N and Da Silva, K and Junot, C and Shawcross, DL and Moyes, DL and Jalan, R and Ehrlich, SD and Patel, VC and Trebicka, J and Shoaie, S}, title = {Integrative host-microbiome modeling uncovers the implication of oral-gut translocation in advanced cirrhosis.}, journal = {iMeta}, volume = {5}, number = {3}, pages = {e70131}, doi = {10.1002/imt2.70131}, pmid = {42491347}, issn = {2770-596X}, abstract = {Liver cirrhosis is associated with profound disruption of host-microbiome metabolic interactions. Using paired oral and fecal metagenomics combined with genome-scale metabolic modeling, we investigated how microbial translocation along the oral-gut axis influences microbial metabolism at different cirrhosis severities. Reactobiome-based functional profiling revealed progressive metabolic convergence between oral and gut microbiomes, quantified by a decrease in oral-gut metabolic distance. Translocation-associated microbial species enriched in patients with cirrhosis were predicted to have elevated capacities for ammonia and acetate production. Microbial-community and host metabolic modeling further suggested that these microbial metabolic shifts may influence host energy metabolism and redox balance across the liver, brain, and skeletal muscle. Together, these findings suggest a potential acetate-ammonia metabolic axis linking oral-gut microbial translocation with systemic metabolic stress in advanced cirrhosis.}, } @article {pmid42491466, year = {2026}, author = {Zhang, J and Lu, T and Tang, Q and Chen, SC and Garza, DR and Liu, B and Cui, Y and Wei, Y and Richnow, HH}, title = {Antiviral defense systems drive persistence of antimicrobial-resistant bacteria but limit the transfer of antimicrobial resistance genes in anaerobic digestion.}, journal = {iMeta}, volume = {5}, number = {3}, pages = {e70145}, doi = {10.1002/imt2.70145}, pmid = {42491466}, issn = {2770-596X}, abstract = {Phage-host interactions critically shape environmental antimicrobial resistance (AMR). Using swine manure anaerobic digestion and multi-omics (metagenomics, meta-transcriptomics, and Hi-C), we mapped the phage-bacteria arms race and its impact on AMR dynamics. We revealed that phage-mediated lysis overwhelmingly dominates transduction, while phages rarely carry antimicrobial resistance genes (ARGs), and phage-borne ARGs showed no expression, challenging the paradigm of phages as primary vectors of ARGs. Crucially, the intense on-going phage-host arms race drives the widespread presence and expression of antiviral defense systems (ADSs) in antimicrobial-resistant bacteria (ARB). These ADSs exhibit a vital ecological dual role: they protect ARBs from phage lysis promoting persistence while simultaneously suppressing horizontal gene transfer (HGT, e.g., conjugation), as validated by in vitro conjugation assays. Our findings elucidate this duality, offering a novel framework to harness phage lytic pressure and ADS-mediated HGT suppression for environmental AMR mitigation.}, } @article {pmid42491572, year = {2026}, author = {Tian, L and Qin, J and Deng, Y and Liu, L and Wang, S and Zhang, M and Guan, T and Xu, Y}, title = {Ecological and functional succession of the microbial community during pit mud maturation in Nongxiangxing Baijiu.}, journal = {Current research in microbial sciences}, volume = {11}, number = {}, pages = {100640}, doi = {10.1016/j.crmicr.2026.100640}, pmid = {42491572}, issn = {2666-5174}, abstract = {Pit mud (PM) microbiota play a vital role in Baijiu flavor formation, yet its ecological and functional succession during maturation remains incompletely elucidated. Here, physicochemical profiling, amplicon sequencing, and metagenomics were integrated to investigate 5-, 15-, and 30-year PM of Sichuan Tang Dynasty Laojiao cellars. Bacteria dominated the community (82.59%), followed by Archaea (16.99%), with Lactobacillus acetotolerans, Ruminococcaceae CPB6, and Methanobacterium paludis as major species. Discrepancies between sequencing methods were reflected in fungal taxa which had low-abundance. The 15-year PM exhibited distinct community and functional features, indicating a critical transitional stage. Functional analysis revealed that fermentation-relevant functions were mainly contributed by 7 key genera and 5 species. Physicochemical properties changed with pit age, characterized by increased moisture as well as decreased acidity and humic substance levels. Moisture, ammonium nitrogen (NH4[+]-N), available phosphorus, and age were identified as key drivers shaping microbial composition and function. Moisture was identified as the most central mediator, establishing a three-tier cascade causal chain from microorganisms to nutrient accumulation. Functionally, 5-year PM sustained a simple, Lactobacillus-dominated, growth-oriented community; 15-year PM shifted toward aromatic compound degradation, nitrogen utilization, flavor-precursor synthesis; and 30-year PM developed into a stable, flavor-optimized ecosystem enriched in caproic-acid-producing Ruminococcaceae CPB6. Overall, PM maturation is driven by microbiome functional evolution, and the 15-year represented a pivotal period. This study provides a theoretical foundation for scientific PM management and targeted microbial regulation in Baijiu production.}, } @article {pmid42491666, year = {2026}, author = {Liu, C and Li, X and Mansoldo, FRP and Chen, T and Meng, F and Tang, R and Zhou, S and Yang, Q and Shao, R and Yao, M}, title = {microeco 2: A comprehensive R package for downstream analysis of microbiome omics data.}, journal = {iMeta}, volume = {5}, number = {3}, pages = {e70132}, doi = {10.1002/imt2.70132}, pmid = {42491666}, issn = {2770-596X}, abstract = {Efficient downstream analysis of microbiome data remains a major challenge for researchers. Since its initial release in late 2020, the R microeco package has been widely used for downstream statistical analysis and visualization of omics data, such as amplicon sequencing. Compared with its initial release, the current second version of the microeco package has undergone extensive updates and enhancements. The key upgrades include: (1) The addition of classes for data normalization and machine learning, respectively; (2) The incorporation of additional analytical methods and the addition of functions across various classes; (3) Optimization of the parameter system to expand the applicable scenarios of relevant methods; (4) Code restructuring to enhance the connectivity between statistical analysis and visualization within each class; (5) Extension of certain functions to enable the analysis of abundance data in complex formats generated from bioinformatic analyses of metagenomic/metatranscriptomic data; (6) Incorporation of several analytical methods commonly used in transcriptomic and metabolomic data analyses. Overall, the microeco package 2.0 offers broader method coverage and a wider range of application scenarios compared to the previous version and other existing R packages. The steady growth in user downloads demonstrates that the microeco package, which is built on R6 (a class-based object-oriented programming system for R), has established a broad and active user base. The second version of the microeco R package is open-source and available on the Comprehensive R Archive Network and GitHub (https://github.com/ChiLiubio/microeco).}, } @article {pmid42491728, year = {2026}, author = {Suzuki, D and Yang, J and Obana, N and Yachida, S and Shiba, S and Mizutani, S and Takamaru, H and Saito, Y and Fukuda, S and Yamada, T}, title = {Clinical strains isolated from early-stage colorectal cancer patients promote tumorigenesis.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21488}, doi = {10.7717/peerj.21488}, pmid = {42491728}, issn = {2167-8359}, mesh = {*Colorectal Neoplasms/microbiology/pathology ; Humans ; Animals ; Mice ; *Carcinogenesis ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; Metagenome ; Male ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is prevalent worldwide and is associated with gut commensals. Recent studies have highlighted the effects of gut microbes on CRC development driven by their strain diversity. Nevertheless, the impact of the gut microbial community on tumorigenesis in early-stage (ES) CRC remains unexplored.

METHODS: To assess the potential gut microbial community, which is critical to tumorigenesis in early-stage CRC, we collected publicly available shotgun metagenomes from CRC patient faecal samples from a Japanese population. Correlation analysis of the microbial profiles derived from the metagenomes revealed an ES CRC-associated community. To elucidate the strain diversity of the targeted community, we isolated strains from ES CRC patient faecal samples and employed comparative genomics. To evaluate the strain-specific effects of the community on tumorigenesis, we introduced an isolated strain cocktail into a CRC mouse model.

RESULTS: Among the most significant ES CRC-associated species, we identified Lancefieldella parvula (Lp), as reported in a previous study. The 20 species were identified as positively correlated with Lp. Seven of the 20 species were associated with ES CRC, including Actinomyces and Solobacterium. Schaalia odontolytica (So) (formerly known as Actinomyces odontolyticus) and Solobacterium moorei (Sm) were previously reported as potential species that promote CRC. Thus, we isolated clinical strains of Lp, So, and Sm from faecal samples as potential members of the ES CRC-associated community. Comparative genomics revealed that iron-related genes were shared among clinical strains. In the oral challenge with clinical strains, namely, Lp, So, and Sm, the mice exhibited shorter survival and significantly increased tumorigenesis, suggesting that the cocktail of clinical strains is more pathogenic to the CRC mouse model than the type strain is. In summary, we inferred that the ES CRC-associated community could promote CRC, and the effects depend on the strains involved.}, } @article {pmid42491748, year = {2026}, author = {Taurino, G and Mancabelli, L and Milani, C and Longhi, G and Lugli, GA and Ughini, C and Bianchi, MG and Chiu, M and Kayali, S and Gaiani, F and Aloe, R and Turroni, F and Bussolati, O and Ventura, M}, title = {Fecal calprotectin and gut microbiome in a cohort without intestinal pathologies from northern Italy.}, journal = {iScience}, volume = {29}, number = {7}, pages = {116578}, doi = {10.1016/j.isci.2026.116578}, pmid = {42491748}, issn = {2589-0042}, abstract = {Fecal calprotectin is a biomarker for intestinal inflammatory conditions, while specific taxa of gut microbiota are proposed as biomarkers for inflammatory bowel disease. However, the relationship between microbiota and calprotectin levels is still largely unexplored. Using shallow shotgun metagenomics, we investigate microbial taxonomic and functional patterns correlated with calprotectin levels in fecal samples of 515 adult individuals without known intestinal pathologies, enrolled within the Parma Microbiota Project. The median value of calprotectin was 23.6 μg/g, but levels higher than the normal threshold of 50 μg/g were measured in 20% of participants. While no changes were detected in alpha- and beta-diversities, calprotectin levels were negatively associated with butyrate-producing bacteria, while positively correlated with several opportunistic pathogens. Functional analysis showed significant correlations between calprotectin levels and the predicted microbial enzymatic functions. If confirmed in longitudinal studies, these findings could indicate early microbial biomarkers of gut inflammatory conditions.}, } @article {pmid42492212, year = {2026}, author = {Kong, Y and Jimenez, K and Osborn, K and Zhang, Y and Low, S and Sytko, C and Tran, T and Choi, YSA and Ho, SJ and Nguyen, J and Astilla, T and Aziz, S and Low, O and Chowdhry, R and Henning, L and Dickerson, C and Jones, A and Mahendra, S and Jay, JA}, title = {Integrating multi-method approach reveals extensive antibiotic resistance dissemination from concentrated animal feeding operations to surface waters.}, journal = {Water research}, volume = {305}, number = {}, pages = {126548}, doi = {10.1016/j.watres.2026.126548}, pmid = {42492212}, issn = {1879-2448}, abstract = {Concentrated animal feeding operations (CAFOs) are important sources of antimicrobial resistance (AMR), but how mixed livestock inputs and seasonality shape antibiotic resistance profiles in receiving surface waters remains uncertain. We integrated culture-based screening, qPCR, and shotgun metagenomics to assess AMR in surface waters influenced by dairy and mixed swine and dairy operations across seasonal campaigns. CAFO-impacted sites, which were shown to have much greater levels of multidrug resistance among purified Escherichia coli isolates in our previous study, had higher culturable E. coli than reference sites, and extended-spectrum beta-lactamase (ESBL)-producing E. coli were detected only at CAFO sites during spring. qPCR analysis showed significantly higher relative abundances of tetracycline (tetW) and macrolide (ermF) resistance genes at CAFO-impacted sites, with strong co-occurrence between the cattle fecal marker CowM3 and these antibiotic resistance genes (ARGs) (adjusted p < 0.05). Metagenomic profiling identified 619 unique ARG subtypes. CAFO-impacted sites contributed substantially greater resistance diversity, with 198 unique subtypes detected compared to 15 unique subtypes at reference sites. Seasonal shifts in metagenomic data were pronounced at dairy sites, including spring increases in tetracycline-, rifamycin-, and florfenicol-associated resistance. ESKAPE pathogens were detected only at CAFO-impacted sites, while Pseudomonas aeruginosa and Klebsiella pneumoniae were identified as putative ARG hosts. Across methods, culture and molecular approaches provided complementary information, with ESBL total coliforms correlating better with qPCR and metagenomic results (p < 0.005) then ESBL E. coli. By integrating phenotypic and molecular evidence, this study highlights seasonal windows of enhanced detectability and supports integrated One Health surveillance of AMR at agricultural-environment interfaces.}, } @article {pmid42492447, year = {2026}, author = {Li, L and Gad, M and Adyari, B and Hou, L and Wang, Y and Rizk, NM and Marouf, MA and Claude, NJ and Al-Herrawy, AZ and Abdelfadiel, A and Hu, A}, title = {Cross-regional metagenomic insights into clinical and stable resistomes in urban wastewater systems.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {143012}, doi = {10.1016/j.jhazmat.2026.143012}, pmid = {42492447}, issn = {1873-3336}, abstract = {Antimicrobial resistance (AMR) is a growing global threat, with elevating risks in low- and middle-income countries due to inadequate infrastructure and limited regulation. However, comprehensive analyses on AMR profiles in these regions remain scarce. We compared AMR risks across full-scale wastewater treatment plants (WWTPs) in Egypt (Cairo) and China (Xiamen), utilizing shotgun metagenomic sequencing, bioinformatics, and multivariate analysis. Our results indicated that while influent samples exhibited comparable AMR risk levels, the activated sludge and effluent from Egyptian WWTPs showed significantly higher risks, characterized by greater clinical ARG abundance, enhanced mobility potential, and more diverse pathogenic hosts. We identified 51 stable ARGs that persisted across WWTPs, seasons and treatment units. These stable ARGs showed strong association with pathogen community and were detected across a broader range of pathogenic hosts, and were predominantly plasmids-borne. Plasmids were the primary vectors of horizontal gene transfer (HGT) of clinical ARGs, whereas viruses showed selective associations with stable ARGs. Key pathogens facilitating HGT of both clinical and stable ARGs included Alcaligenes faecalis and Shigella spp., with cross-domain putative HGT events also being detected. These findings address a critical knowledge gap in underrepresented regions and provide risk-based strategies to mitigate ARG dissemination in urban wastewater systems.}, } @article {pmid42492757, year = {2026}, author = {Demirci, M}, title = {Metabolic Reprogramming and Taxonomic Drivers in Bacterial Vaginosis: A Large-Scale Metagenomic Meta-Analysis.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {103067}, doi = {10.1016/j.anaerobe.2026.103067}, pmid = {42492757}, issn = {1095-8274}, abstract = {OBJECTIVE: Bacterial vaginosis (BV) represents a profound ecological shift from a Lactobacillus-dominated microbiota to a diverse polymicrobial biofilm associated with adverse outcomes. While taxonomic signatures are well-documented, the functional mechanisms driving this transition remain obscured. This study elucidates the genomic potential for metabolic reprogramming and the putative "functional handover" underpinning the stability of the dysbiotic state.

METHODS: A computational meta-analysis of 3,557 vaginal microbiomes from diverse global cohorts was performed using the standardized MGnify pipeline. A high-resolution subset of 187 whole-genome shotgun (WGS) metagenomes was stratified to compare functional potential across demographic groups. Taxon-function interaction networks were constructed, utilizing a dual-filter statistical approach (p < 0.05 and effect size ranking), to map the shift from homeostatic maintenance to dysbiotic metabolic potential.

RESULTS: BV was characterized by a fundamental shift from "maintenance" pathways to high-turnover "growth-oriented" genomic repertoires. While ABC transporter-like domains were present in healthy communities, dysbiosis was marked by a quantitative expansion and diversification of these systems alongside P-loop NTPases. Network analysis revealed a putative "functional handover": while Gardnerella serves as the adherent structural scaffold, the metabolic burden appears to be associated with secondary anaerobes, specifically BVAB1 and Sneathia, which exhibit strong genomic correlations with nutrient transport and stress response pathways. Crucially, microbiomes from women of African ancestry (Black cohort) exhibited a distinct functional profile with genomic signatures consistent with functions previously associated with resistome expansion (e.g., tetracycline/macrolide resistance), contrasting with Asian cohorts.

CONCLUSION: BV is a state of metabolic reprogramming where genomic functional dominance is transferred from Lactobacillus to a cooperative network of anaerobic opportunists. Identifying BVAB1 and Sneathia as candidate metabolic engines, supported by a Gardnerella scaffold, challenges current therapeutic paradigms and highlights the potential for precision medicine targeting specific functional drivers and resistome profiles across diverse populations.}, } @article {pmid42479457, year = {2026}, author = {You, J and Khan, RM and Reji, N}, title = {Gut microbiome profiles as predictors of response to chemoradiotherapy in locally advanced rectal cancer.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {}, doi = {10.1556/030.2026.02874}, pmid = {42479457}, issn = {1588-2640}, abstract = {This prospective cohort study investigates the predictive role of gut microbiota composition in determining the therapeutic response to neoadjuvant chemoradiotherapy (CRT) in patients with locally advanced rectal cancer (LARC) at Qiqihar Jianhua Hospital. A total of 178 patients underwent standardized CRT protocols and were stratified into responders and non-responders based on pathological tumor regression grades. Gut microbiome profiling was conducted via 16S rRNA amplicon sequencing and shotgun metagenomics at three treatment stages (pre-, mid-, and post-CRT). Responders exhibited significantly higher alpha diversity (Shannon, Chao1) at baseline and maintained greater microbial richness throughout treatment. Taxonomic analysis identified Faecalibacterium, Akkermansia, and Bifidobacterium as enriched in responders, while non-responders showed elevated Clostridium, Escherichia, and Streptococcus. Multivariate regression confirmed Faecalibacterium (OR = 1.16, P = 0.0002) and Akkermansia (OR = 1.27, P = 0.0146) as independent predictors of CRT response. Functional profiling revealed enrichment of anti-inflammatory pathways (butyrate synthesis, tryptophan metabolism) in responders and pro-inflammatory, stress-related functions (lipopolysaccharide biosynthesis, oxidative stress) in non-responders. Exploratory microbiome modulation using probiotics or fecal microbiota transplantation (FMT) targeting Faecalibacterium and Akkermansia demonstrated increased responder rates by 12.5 and 18.2%, respectively. These findings highlight the potential of gut microbiome signatures as non-invasive biomarkers for CRT response prediction and as targets for adjunctive therapeutic strategies. Personalized microbiome-informed treatment may enhance CRT efficacy and reduce unnecessary exposure in non-responders, paving the way for precision oncology in rectal cancer.}, } @article {pmid42479737, year = {2026}, author = {Wang, H and Zhang, Q and Sun, B and Shen, D and Lu, L and Li, H and Fang, K and Li, H and Yan, H and Chen, F and Zhao, T and Chen, L and Rong, M and Liu, W and Hu, Z and Ai, J and Zhang, W}, title = {Artificial intelligence risk prediction model for common respiratory pathogens in China based on heterogeneous multi-source clinical and geographic data: A modeling study.}, journal = {PLOS digital health}, volume = {5}, number = {7}, pages = {e0001553}, pmid = {42479737}, issn = {2767-3170}, abstract = {Most respiratory pathogens exhibit distinct seasonal and periodic outbreak patterns driven by climatic factors. However, predictive models that jointly consider climate, air quality index (AQI), and socioeconomic variables are lacking. We retrospectively analyzed targeted or metagenomic next-generation sequencing data from 153,544 respiratory samples collected from 1,880 centers across 30 provinces in China between September 2022 and September 2024. Monthly positivity rates were matched with geographic, climatic, AQI, and GDP data. CO(0.098 ± 0.016), HCHO(0.096 ± 0.021), O3(0.102 ± 0.019), sunshine hours(0.103 ± 0.028), wind speed(0.114 ± 0.024), and GDP(0.095 ± 0.019). were identified as the key geographical factors for the positivity across most respiratory pathogens via mean Gini index reduction, and a gradient boosting decision tree(GBDT) model was trained and benchmarked against other AI methods using the DISO metric. This model accurately simulated the epidemiological trends from September 2022 to September 2024 and outperformed alternative models with the lowest DISO metric of 0.12 in influenza A, 0.21 in SARS-CoV-2, 0.25 in RSV. The GBDT model was used to predict the short-term epidemic of 10 respiratory pathogens between October and December 2024. The predictions showed consistent trends with the external validation cohort for RNA viruses including SARS-CoV-2 and influenza A virus, but differed for bacterial pathogens. Integrating air quality, climatic, and socioeconomic data yields robust predictions of respiratory infection dynamics in the short-term by the GBDT model, bolstering public health surveillance and offering a framework potentially applicable to other infectious diseases.}, } @article {pmid42479812, year = {2026}, author = {Jia, Y and Yan, Y and Chen, B and Shu, WS and Lu, H}, title = {Revealing Dual Synergistic Strategies in Sulfate-Reducing Microbiomes for Sulfamethoxazole Biodegradation via DNA-SIP and Metagenomics.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c05921}, pmid = {42479812}, issn = {1520-5851}, abstract = {Sulfate-reducing microbiomes (SRMs) have shown strong potential for antibiotic remediation, yet the active microorganisms and community-level strategies associated with sulfamethoxazole (SMX) biotransformation remain poorly understood. In this study, long-term bioreactor operation (269 days; 500-1500 μg/L SMX), DNA-stable isotope probing (DNA-SIP), and metagenomic analyses were integrated to investigate the microbial contributors and functional organization underlying SRM-driven SMX biotransformation. Desulfobacterium, a key SRM member, was co-enriched with Geobacter and Leptolinea in the [13]C-labeled heavy fraction, suggesting potential metabolic complementarity during community-level SMX biotransformation. Genome-resolved analyses further revealed structured patterns of inferred horizontal gene transfer (HGT) and predicted metabolite exchange among keystone taxa. The transferred genes were mainly associated with energy conservation, transport, sulfur-associated metabolism, and stress-response functions, whereas the predicted exchanged metabolites included carbon metabolites, amino acid-related sulfur compounds, purine-related intermediates, and cofactor-associated metabolites. Together, these findings suggest that HGT-associated functional redistribution and metabolic complementarity may contribute to the persistence and coordinated activity of sulfate-reducing microbiomes under high SMX stress. This study links SIP-identified active populations with genome-inferred interaction patterns in a sulfate-reducing system and provides new insight into microbiome-based anaerobic strategies for antibiotic-containing wastewater treatment.}, } @article {pmid42480186, year = {2026}, author = {Xiang, Y and Cui, K and Zhou, H and Tian, Y and Liu, X and Yao, H and Li, X}, title = {Perfluorooctane sulfonate drives the synergistic dissemination of antimicrobial resistance and pathogenicity during sludge anaerobic digestion.}, journal = {Water research}, volume = {305}, number = {}, pages = {126541}, doi = {10.1016/j.watres.2026.126541}, pmid = {42480186}, issn = {1879-2448}, abstract = {Per- and polyfluoroalkyl substances, one of the most prevalent and persistent emerging contaminants in sludge, may drive the dissemination of antimicrobial resistance and pathogenicity during sludge treatment. However, the mechanisms underlying perfluorooctane sulfonate (PFOS)-mediated propagation of antibiotic resistance genes (ARGs) and virulence factors (VFs) remain poorly understood. This study investigated the effects of PFOS (1 and 10 μg/g-dw) on ARGs dynamics and virulence risks. Quantitative PCR and metagenomic analysis revealed that PFOS stress led to the widespread enrichment of ARGs, the total abundance of mobile genetic elements (MGEs) and VFs also increased by 33.22-37.62% and 6.71-8.41%, respectively. Metagenomic binning results demonstrated that most metagenome-assembled genomes carrying ARGs or VFs simultaneously harbored MGEs. Mechanistically, excessive reactive oxygen species production and enhanced substrate-level phosphorylation for ATP generation may contribute to the increased horizontal transfer potential of ARGs under PFOS stress, which further facilitated the convergence of antimicrobial resistance and virulence traits within pathogens. Furthermore, PFOS may have hindered the negative regulation of the RhlI/RhlR quorum sensing system on the Type III secretion system, stimulating the secretion of VFs. This study elucidates the mechanisms by which PFOS promotes the dissemination of ARGs and pathogenicity during anaerobic digestion, highlighting the potentially overlooked environmental health risks of PFOS during sludge disposal.}, } @article {pmid42480452, year = {2026}, author = {Shan, X and Shi, L and Zhu, T and Liang, X and Yang, J and Zhou, G and He, L and Mei, B and Wang, S and Li, F}, title = {Microbial tryptophan-IPA axis mediates 6:2 chlorinated polyfluorinated ether sulfonate (6:2Cl-PFESA)-induced gut-brain dysfunction and neurobehavioral impairments.}, journal = {Environment international}, volume = {214}, number = {}, pages = {110422}, doi = {10.1016/j.envint.2026.110422}, pmid = {42480452}, issn = {1873-6750}, abstract = {Chlorinated polyfluoroalkyl ether sulfonic acids (Cl-PFESAs) are widely used substitutes for perfluorooctane sulfonate (PFOS) and are increasingly detected in environmental and human matrices, yet their neurobehavioral risks during early life remain poorly defined. Here, male C57BL/6J mice were orally exposed to F-53B (6:2Cl-PFESA; 0.1 or 1 mg/kg/day) during juvenility for four weeks. F-53B selectively impaired recognition memory and social novelty preference, whereas locomotor activity, anxiety-like behavior, and Y-maze working memory were largely preserved. Mechanistically, F-53B compromised intestinal barrier integrity, as evidenced by reduced occludin expression and disrupted ZO-1 continuity, accompanied by elevated circulating lipopolysaccharide (LPS) and a systemic pro-inflammatory cytokine shift. In parallel, the hippocampus exhibited microglial activation, enhanced inflammatory signaling, and reduced PSD95 expression, consistent with neuroinflammatory stress and synaptic vulnerability. Shotgun metagenomics revealed pronounced microbiome restructuring and network rewiring, while widely targeted metabolomics converged on a marked disruption of tryptophan metabolism, characterized by depletion of microbiota-derived indole metabolites, including indole-3-propionic acid (IPA), together with altered serotonin-related signatures. Notably, oral IPA supplementation rescued behavioral deficits and attenuated gut-brain inflammatory alterations, restoring intestinal aryl hydrocarbon receptor (AhR) nuclear translocation, reducing LPS and cytokine levels, and ameliorating hippocampal inflammatory phenotypes. Collectively, these findings provide mechanistic evidence that a microbiota-tryptophan metabolite-gut barrier-inflammation axis links exposure to substitute PFAS with selective neurobehavioral dysfunction, highlighting microbiota-derived metabolites as potential modulators of PFAS-associated neurotoxicity.}, } @article {pmid42480622, year = {2026}, author = {Ren, X and Ma, J and Zhao, Y and Yang, M and Li, Y and Song, W and Wang, N}, title = {Microbiome Remodeling During Aging: Integrative Multi-Omics and Spatiotemporal Perspectives on Immune and Metabolic Regulation.}, journal = {Ageing research reviews}, volume = {}, number = {}, pages = {103269}, doi = {10.1016/j.arr.2026.103269}, pmid = {42480622}, issn = {1872-9649}, abstract = {Changes in the gut microbiota occur throughout the human lifespan, and maintaining microbial homeostasis plays a critical role in promoting healthy aging. In recent years, substantial progress has been made in elucidating the mechanistic links between aging and microbiota remodeling, highlighting the central role of microbiota-host interactions in regulating immune responses and maintaining metabolic homeostasis. These findings provide new potential targets for the precision prevention and treatment of age-related diseases. This review systematically summarizes the patterns of gut microbiota succession across different stages of the human life cycle, including infancy, adolescence, adulthood, and old age, as well as the mechanisms through which the microbiota regulates immune and metabolic functions. Furthermore, the role of the gut microbiota as a key mediator linking aging with an increased risk of chronic inflammation, cardiovascular disease, cognitive impairment, neurodegenerative disorders, and cancer was explored. In addition, this review evaluates the therapeutic potential of microbiota-targeted interventions, such as dietary modification, probiotic and prebiotic supplementation, fecal microbiota transplantation (FMT), and lifestyle interventions-in maintaining microbiome homeostasis and mitigating age-related diseases. The feasibility of personalized microbiota-based intervention strategies is also discussed. Finally, we highlight the current challenges and limitations in this field and outline future research directions. In particular, integrating multi-omics approaches with metagenomic sequencing, including emerging spatial and spatiotemporal multi-omics technologies, is crucial for advancing our understanding of the complex interactions within the gut microbiome. These insights provide a theoretical framework for optimizing anti-aging therapeutic strategies and promoting healthy lifespan extension.}, } @article {pmid42480833, year = {2026}, author = {Bai, M and Wang, L and Wang, B and Liao, X and Sun, M and Zeng, W and Peng, Y}, title = {Carbon Conversion in Sludge Fermentation Liquid Drives Exogenous-to-Endogenous Transition of Partial Denitrification for Integration with Anammox.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125290}, doi = {10.1016/j.envres.2026.125290}, pmid = {42480833}, issn = {1096-0953}, abstract = {Traditional biological nitrogen removal processes for wastewater characterized by a low carbon-to-nitrogen (C/N) ratio often rely heavily on external carbon sources, resulting in excessively high operational costs. This study investigated the feasibility of using sludge fermentation liquid (SFL) as an alternative carbon source to drive the endogenous partial denitrification-anammox (EnPDA) process for efficient nitrogen removal. A sequencing batch reactor (SBR) was operated for 285 days, consisting of a partial denitrification (PD) phase (183 days) and a subsequent EnPDA phase (102 days). During the PD phase, exogenous PD (ExPD) shifted to endogenous PD (EnPD). After integrating anammox, the single-stage EnPDA system achieved a total inorganic nitrogen removal efficiency of 95.1 ± 1.2%, and maintained 93.8 ± 1.8% efficiency even under elevated ammonium loading. The batch tests revealed the robustness of EnPDA system and its preference for nitrate as the electron acceptor. Microbial community analysis showed a functional shift from Thauera to the endogenous denitrifier Ca. Competibacter, with Ca. Brocadia (1.04%) as the dominant anammox bacterium. Metagenomic analysis revealed 68.6% increased abundance of denitrification-related (narGHI) genes and 7.8-fold enhancement of anammox-related (hzs/hdh) genes. Furthermore, the genes related to carbon metabolism were also upregulated to sustain endogenous electron supply. This work clarifies the microbial and metabolic mechanisms underlying the transition of ExPD to EnPD. The study validates that SFL-driven EnPDA is a cost-effective strategy for advanced nitrogen removal from low C/N wastewater.}, } @article {pmid42480835, year = {2026}, author = {Wang, J and Chen, JY and He, YZ and Wu, JJ and Li, ZH}, title = {Functional instability and community-level compensatory mechanisms in the anammox system under long-term acetamiprid stress.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125298}, doi = {10.1016/j.envres.2026.125298}, pmid = {42480835}, issn = {1096-0953}, abstract = {Acetamiprid is a frequently detected neonicotinoid insecticide that is widely present in water bodies and may disrupt the stability of the anaerobic ammonium oxidation (anammox) process. This study investigated the response threshold and mechanistic transition of the anammox system under long-term acetamiprid stress. The system remained stable at 0-2.5 mg/L acetamiprid, and nitrogen removal efficiency (NRE) did not change significantly. At 5-15 mg/L acetamiprid, NRE was maintained at approximately 80%, whereas the NO3[-]-N/NH4[+]-N ratio increased to 0.40, and specific anammox activity (SAA) declined. This apparent maintenance of reactor performance was likely sustained by community-level functional compensation. At 50 mg/L acetamiprid, reactive oxygen species (ROS) levels increased by 74%, the protective effect of extracellular polymeric substances (EPS) weakened, and NRE decreased by 9.11%, indicating that the compensatory capacity of the microbial community had been exceeded and that the reactor had entered an unstable state. Overall, the reactor exhibited a stage-dependent transition from apparent stability to latent functional impairment and ultimately to overt instability. Community and metagenomic analyses further suggested that acetamiprid exposure reduced the ecological dominance and functional contributions of Candidatus Kuenenia and Candidatus Jettenia, while increasing the relative importance of Candidatus Brocadia and associated populations such as Ignavibacterium, and enhancing their stress response and xenobiotic-related functions. This transition indicates that the system shifted from a mode dominated by core anammox bacteria to a more distributed, multispecies compensatory state. These findings provide new insights into the stability boundaries and failure transitions of the anammox system under pesticide stress.}, } @article {pmid42480947, year = {2026}, author = {Zhang, J and Li, L and Yang, X and Chen, S and Li, Z and Li, R and Wang, C and Tian, Y}, title = {Efficient sludge reduction and phosphorus recovery in innovative coupled sequencing batch and worm reactor Process: Performance, mass balance and metagenomic mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135478}, doi = {10.1016/j.biortech.2026.135478}, pmid = {42480947}, issn = {1873-2976}, abstract = {The efficient release and phosphorus recovery (PR) are core to enhancing the sustainable operation of municipal wastewater treatment systems. To address this issue, this study constructed an innovative coupled sequencing batch reactor (SBR)-worm reactor (WR)-PR process. By leveraging the synergistic regulation between worm predation and microbial activity, the process achieved the dual objectives of sludge reduction and the efficient release and targeted recovery of phosphorus from the solid phase to the liquid phase. By subjecting only approximately 6% of the influent flow to chemical phosphorus recovery, an efficient recovery of 45% of the influent total phosphorus (TP) was achieved. During 160 days of continuous operation, the coupled process exhibited excellent stability in pollutant removal, with removal rates of chemical oxygen demand (COD), total nitrogen (TN), and TP reaching 95%, 71%, and 97%, respectively. Sludge reduction of 49% was achieved through worm predation, with direct worm predation contributing 69%. Sludge characteristics were significantly improved, with the sludge volume index (SVI) decreasing by 46% and dewaterability increasing by 20%. Extracellular polymeric substance (EPS) analysis revealed that side‑stream predation reduced total EPS content, increased the protein/polysaccharide (PN/PS) ratio. Metagenomic analysis confirmed that side-stream biological predation significantly enriched key functional microbial groups and intensified the expression of genes related to phosphorus transport and metabolism. This work elucidates the microbial synergistic mechanisms within the coupled process, providing a novel pathway for the simultaneous achievement of efficient sludge reduction and PR in municipal wastewater treatment.}, } @article {pmid42481505, year = {2026}, author = {Song, W and Wang, Z and Liu, Y and Wang, Q and Li, M and Shi, W and Gao, Z and Chen, Y}, title = {Kocuria rosea LAT6 enhances wheat salt tolerance via modulation of rhizosphere microbial function and nitrogen cycling.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01103-7}, pmid = {42481505}, issn = {2055-5008}, support = {ZR2025QC186//Natural Science Foundation of Shandong Province/ ; SYS202206, ZR2021MC190//Natural Science Foundation of Shandong Province/ ; 2021YFF1000403//National Key R&D Program of China/ ; SKL81103//Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; No. 2022KJ333//Youth Innovation Team of Shandong Provincial Department of Science and Technology/ ; tsqn202103162//Taishan Scholars Program/ ; 2024CXPT072//Key R&D Program of Shandong Province, China/ ; }, abstract = {Pioneer plants in saline-alkali soils support unique rhizosphere microbial communities. Some of these microbes promote plant salt tolerance and growth, although the underlying mechanisms are not yet fully understood. In this study, we isolated Kocuria rosea LAT6 from the rhizosphere of pioneer plants in saline-alkali soils. Genome sequencing revealed genes associated with plant growth promotion and stress adaptation. Inoculation with LAT6 markedly reshaped the rhizosphere microbiota, and metagenomic analysis indicated that specific microbial taxa contributed to enhanced nitrogen-cycling functions. Transcriptome profiling further demonstrated that LAT6 promotes nitrate transport and stimulates phenylpropanoid biosynthesis in wheat. It reveals how microbial reorganization and plant-microbiome interactions enhance nitrogen use under salt stress, highlighting the potential of salt-tolerant consortia for saline-alkaline crops.}, } @article {pmid42481656, year = {2026}, author = {Stallhofer, J and Leonhardt, J and Semmler, J and Neugebauer, S and Kiehntopf, M and Löhden, W and Homeister, L and Ungelenk, M and Hübner, CA and Steube, A and Waschina, S and Stallmach, A}, title = {Loss of TGR5-activating bile acids is associated with disease activity in inflammatory bowel disease.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42481656}, issn = {2045-2322}, mesh = {Humans ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Bile Acids and Salts/metabolism/blood ; *Inflammatory Bowel Diseases/metabolism/microbiology/pathology ; Female ; Feces/chemistry/microbiology ; Male ; Gastrointestinal Microbiome ; Adult ; Middle Aged ; }, abstract = {The gut microbiota communicates extensively with its host through small metabolites, such as bile acids. Primary bile acids are synthesized by the host and secreted into the intestine, where they are actively converted by the microbiota into secondary bile acids. Depending on the resulting bile acid composition, the host's bile acid receptor, Takeda G protein-coupled receptor 5 (TGR5), is activated and mediates immune tolerance. It has been suggested that a disturbed bile acid profile in inflammatory bowel disease (IBD) might lead to inflammation via reduced activation of TGR5. Our study is the first to investigate whether bile acid-induced TGR5 activation differs between healthy individuals and patients with IBD. Bile acid profiles in stool and plasma were quantified by mass spectrometry, and TGR5 bioactivity was assessed from these profiles. In parallel, metagenomic sequencing was performed on fecal samples. We demonstrate that reduced alpha diversity in IBD is associated with a loss of microbial capacity for bile acid transformation, resulting in a significantly decreased secondary-to-primary bile acid ratio (sBA/pBA) in both stool and circulation. TGR5 bioactivity induced by bile acid profiles was substantially reduced in IBD patients, and a lower TGR5 bioactivity correlated with increased inflammatory activity.}, } @article {pmid42481973, year = {2026}, author = {Wang, Y and Fu, X and Liu, Y and Li, R and Zhu, G and Chen, Z}, title = {Household cluster of psittacosis caused by Chlamydia psittaci ST388 in China: a case report and genomic analysis.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13940-0}, pmid = {42481973}, issn = {1471-2334}, support = {2026JKP-07//Disease Prevention and Control Innovation Team of Zhejiang Province/ ; 2026JKY035//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; 2025JK104//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; }, abstract = {In March 2025, a married couple in Jiaxing City, Zhejiang Province, China, presented with fever and pneumonia. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid confirmed Chlamydia psittaci (C. psittaci) infection. Epidemiological investigation revealed exposure to a pet budgerigar purchased one month prior. Environmental sampling detected C. psittaci in the bird's feces and the patients' living spaces. Phylogenetic analysis of the ompA gene identified the strains as genotype A, and multilocus sequence typing (MLST) determined the sequence type (ST) as ST388. Two cohabiting elderly parents without bird exposure remained asymptomatic and PCR-negative. Phylogenetic analysis showed the avian and environmental isolates formed a distinct clonal cluster. This report highlights the risk of zoonotic transmission from asymptomatic avian carriers and the utility of genomic surveillance in outbreak investigation. Clinicians should consider psittacosis in atypical pneumonia cases with bird exposure.}, } @article {pmid42482126, year = {2026}, author = {Zhai, Y and Kim, Y and Ban, GH and Kim, YM and Kim, SC and Bae, D and Jeong, KC and Kim, SA}, title = {Environmental reservoirs and transmission pathways of antimicrobial resistance across the pork production continuum.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02444-3}, pmid = {42482126}, issn = {2049-2618}, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a major One Health challenge linking human, animal, and environmental health, yet the contribution of food production environments to resistance transmission remains poorly understood.

RESULTS: We conducted a longitudinal shotgun metagenomic study across the pork production continuum from farm to retail to identify environmental AMR reservoirs and transmission pathways of antimicrobial resistance genes (ARGs). Assembly-based, genome-resolved, and source-tracking analyses were integrated to characterize resistomes, microbial communities, and horizontal gene transfer dynamics. ARG abundance and diversity were highest at farms, slaughterhouses, and processing plants and declined toward retail, although clinically relevant resistance determinants persisted throughout processing. Slaughterhouse environments emerged as major contributors to ARG contamination on carcasses, highlighting the importance of environmental exposure at intermediate stages. Resistome structure was closely linked to microbial community composition, with persistent taxa such as Acinetobacter and Pseudomonas serving as key ARG carriers, including genes conferring resistance to tetracycline, aminoglycosides, macrolide-lincosamide-streptogramin, and β-lactams, multidrug efflux. Co-localization of ARGs with mobile genetic elements demonstrated ongoing potential for horizontal transfer across production stages, and genome-resolved metagenome-assembled genome analyses revealed overlapping resistance and virulence profiles between slaughterhouse- and processing plant-associated bacteria, indicating adaptive persistence within pork production environments.

CONCLUSIONS: Resistome composition across the pork production chain is largely shaped by stage-specific environmental sources, highlighting potential intervention points to mitigate AMR transmission. Video Abstract.}, } @article {pmid42482889, year = {2026}, author = {Zhang, XY and Huang, J and Gao, YE and Li, J and Wen, Y}, title = {Sympathetic ophthalmia induced by vitrectomy for endogenous fungal endophthalmitis: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1863685}, pmid = {42482889}, issn = {2296-858X}, abstract = {INTRODUCTION: Sympathetic ophthalmia (SO) is a rare but serious inflammatory ocular disorder. We report a case of endogenous fungal endophthalmitis caused by Aspergillus flavus infection, which resulted in SO in the contralateral eye after two vitrectomy procedures.

CASE REPORT: A 22-year-old man presented to our hospital with a 2-week history of redness and blurred vision in his right eye. Three months earlier, he had undergone two vitrectomy procedures for fungal endophthalmitis in his left eye, with culture results positive for Aspergillus flavus. Upon admission, antifungal therapy was administered; however, his health condition did not improve and progressively deteriorated. Metagenomic sequencing and microbial culture of intraocular fluid from the right eye revealed no fungi. Multimodal imaging, including optical coherence tomography (OCT), ocular B-scan ultrasonography, fundus examination, and indocyanine green angiography (ICGA), supported a definitive diagnosis of sympathetic ophthalmia. Treatment with prednisone and adalimumab stabilized the patient's condition. During the 13-month follow-up period, the patient's best-corrected visual acuity (BCVA) was 1.0 in the right eye and 0.04 in the left eye, with no observed recurrences.

CONCLUSION: Sympathetic ophthalmia is a complex ocular disorder characterized by diverse clinical and imaging features, making early diagnosis and treatment challenging. This case underscores the importance of timely intervention and aggressive therapeutic strategies for managing this condition.}, } @article {pmid42482921, year = {2026}, author = {Kumari, BSS and Golla, N}, title = {Bacterial ligninolytic enzymes and their applications in bioremediation.}, journal = {3 Biotech}, volume = {16}, number = {8}, pages = {342}, pmid = {42482921}, issn = {2190-572X}, abstract = {UNLABELLED: Bacterial ligninolytic enzymes demonstrate high stability and catalytic efficiency across a wide range of environmental conditions, with production strongly influenced by strain-specific and process parameters. Enzyme yields vary significantly depending on the fermentation strategy, with solid-state fermentation (SSF) consistently producing higher activities than submerged fermentation (SmF) due to enhanced substrate-microbe interactions and stronger induction by lignocellulosic materials. In contrast, SmF provides improved control over pH, temperature, and aeration, enabling greater process reproducibility and scalability despite comparatively lower enzyme yields. Comparative analysis further indicates that enzyme production is highly strain-dependent and influenced by environmental parameters, including pH, temperature, substrate type, and incubation time. Among bacterial genera, Bacillus, Streptomyces, Acinetobacter, and Micrococcus exhibit consistently high enzyme production, with certain strains showing significantly elevated manganese peroxidase (MnP) and lignin peroxidase (LiP) activities under optimized conditions. Xenobiotic compounds, including synthetic dyes, pesticides, and Maillard reaction products, act as both substrates and inducers, stimulating enzyme production through oxidative stress-mediated pathways. Reactive oxygen species generated during pollutant exposure enhance the expression of bacterial ligninolytic enzymes, while structural similarities between xenobiotics and lignin-derived compounds facilitate their degradation. Sequential enzyme activity is observed, with MnP initiating early-stage oxidation followed by laccase-mediated transformation, indicating synergistic degradation mechanisms. Bacterial ligninolytic enzymes achieve degradation efficiencies exceeding 90% for a wide range of pollutants, including dyes, pesticides, and plastic-associated compounds. Spectroscopic and chromatographic analyses (UV-Vis, FT-IR, GC-MS, and LC-MS) confirm the conversion of complex aromatic compounds into simpler, less toxic intermediates. The integration of advanced omics-based approaches, including metagenomics, metatranscriptomics, and metaproteomics, is increasingly recognized as a powerful strategy for the discovery and functional characterization of novel ligninolytic bacteria and their enzymes. These findings demonstrate that bacterial ligninolytic enzymes are efficient and robust systems for pollutant degradation and lignin valorization, with strong potential for large-scale biotechnological applications.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04859-z.}, } @article {pmid42482932, year = {2026}, author = {Yan, Z and Zhou, F and Lin, D and Ruan, D and Liu, Y and Yang, M and Meng, F and Huang, S and Liu, L and Zheng, E and Cai, G and Yang, J and Zhang, Z}, title = {Domestication reshapes the swine gut microbiome: metagenomic insights into taxonomic and functional divergence across wild and domestic populations.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1854568}, pmid = {42482932}, issn = {1664-302X}, abstract = {BACKGROUND: The gut microbiota constitutes a highly diverse, complex, and dynamically evolving ecosystem within the host. However, the domestication process may alter microbial community composition and function. Here, we investigate these shifts using metagenomic analysis.

METHODS: Microbial diversity was evaluated using alpha and beta-diversity analysis. Furthermore, LEfSe and Functional analyses were employed to delineate significant disparities in microbial abundance and functional potential between wild boars (WB), Chinese domestic pigs (CDP), and Western domestic pigs (WDP).

RESULTS: Our analysis revealed distinct microbial signatures across populations. WB exhibit greater diversity differentiation from WDP, while showing higher similarity to CDP. WB were significantly enriched in the genera Treponema, Oscillibacter, and Pseudoflavonifractor. In contrast, Chinese domestic breeds were characterized by Lactobacillus, Prevotella and Ruminococcus, while WDP retained high abundances of Alistipes, Bacteroides and Clostridium. Functionally, the wild boar microbiome showed significantly higher activity in pathways related to plant secondary metabolite degradation and nutrient biosynthesis. Conversely, domestic pig microbiomes showed significant enrichment in antimicrobial resistance genes and DNA damage repair pathways.

CONCLUSIONS: These findings indicate that domestication has influenced the swine gut microbiota, contributing to distinct compositional and functional divergences. Future research may explore the potential of reintroducing wild-derived probiotics to enhance domestic pig health.}, } @article {pmid42483398, year = {2026}, author = {Zhao, Y and Liu, Z and Chen, X and Huang, Y and Li, S and Mao, X and Zheng, X and Yao, X and Hu, B and Zhu, L and Zhang, T}, title = {Environmental effectiveness of the National Action Plan to Contain Antimicrobial Resistance: evidence from Chinese soil.}, journal = {National science review}, volume = {13}, number = {14}, pages = {nwag387}, pmid = {42483398}, issn = {2053-714X}, abstract = {Soil antibiotic resistance genes (ARGs) represent an emerging planetary health threat. However, the environmental impacts of antimicrobial resistance (AMR) control policies remain unclear. Based on 2243 Chinese metagenomes, we generated a 14-year (2009-2022) spatiotemporal profile of Chinese soil ARGs and developed an open-access platform based on the interactive map. Relative to pre-2015 samples, the relative abundance of total ARGs (52.6%) and Rank I ARGs (77.0%) in croplands decreased markedly after 2016, coinciding with the national AMR control policy period (2016-2020). Comparing soil resistomes globally (2556 metagenomes) revealed homogenization in croplands, reflecting convergent ARG profiles under similar agricultural pressures across regions. This underscores the need for a shift from national to global intervention. Our findings highlight the importance of coordinated strategies that combined chemical pollution control with agricultural best practices to curb ARGs' dissemination under the One Health framework.}, } @article {pmid42483952, year = {2026}, author = {Oyama, LB}, title = {From sequence space to ecological function: microbiome-derived antimicrobial peptides as community effectors and therapeutic leads.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20250036}, pmid = {42483952}, issn = {1744-1358}, support = {BB/X012794/1//UKRI | Biotechnology and Biological Sciences Research Council (AFRC)/ ; BB/Z515346/1//UK Research and Innovation (UKRI)/ ; }, abstract = {Antimicrobial peptide research has long centred on host defence molecules, yet microbiomes themselves encode a diverse and increasingly important repertoire of peptide-based antimicrobials. These microbiome-derived antimicrobial peptides include bacteriocins, ribosomally synthesised and post-translationally modified peptides, cryptic short open reading frame-encoded peptides, embedded antimicrobial regions within larger proteins, and selected peptide antibiotics recovered from human, animal, plant and environmental microbiomes. Recent advances in genome mining, metagenomics, and machine learning have greatly expanded the scale of discovery, moving the field from a handful of landmark exemplars to large candidate catalogues spanning the global microbiome. In the clearest cases, these molecules are not only anti-infective leads but ecological effectors: they mediate microbial competition, enforce colonisation resistance, and influence community structure within densely occupied niches. The present review synthesises the field across discovery classes, microbiome sources, ecological roles, and translational bottlenecks, emphasizing a central limitation of the field: candidate catalogues are expanding at extraordinary scale, while evidence for native expression, producer assignment, ecological function, and in vivo relevance remains limited for the vast majority of predicted molecules. Progress will depend on workflows that connect sequence level prediction to biological context through expression support, producer assignment, community level validation, and perturbation-based approaches that distinguish ecological association from causal function. Microbiome-derived antimicrobial peptides are best understood not only as promising therapeutic leads, but also as molecular mediators of microbial social life whose ecological origins are central to their interpretation and future application.}, } @article {pmid42484256, year = {2026}, author = {Chavarría, KJS and Gomes, EO and Chaves, BA and Sampaio, VS and Silva-Neto, AV and Brito, D and Silva, LFAD and Dias, MYO and Sacchetto, L and Bernardi, V and Marques, BC and Buenemann, M and Vasilakis, N and Nogueira, ML and Lacerda, MVG and Mourão, MPG and Baía-da-Silva, DC}, title = {Integrated surveillance of arboviruses in febrile patients from the Brazilian Amazon reveals complex co-circulation dynamics and hidden viral diversity.}, journal = {Revista da Sociedade Brasileira de Medicina Tropical}, volume = {59}, number = {suppl 1}, pages = {e00422026}, doi = {10.1590/0037-8682-0042-2026}, pmid = {42484256}, issn = {1678-9849}, mesh = {Humans ; Brazil/epidemiology ; Cross-Sectional Studies ; Male ; Female ; *Arboviruses/genetics/classification/isolation & purification ; *Arbovirus Infections/epidemiology/virology/diagnosis ; Child, Preschool ; Adult ; Phylogeny ; Middle Aged ; Adolescent ; Enzyme-Linked Immunosorbent Assay ; Child ; *Fever/virology ; Coinfection/virology ; Young Adult ; Aged ; }, abstract = {BACKGROUND: Arboviral infections continue to be a significant public health challenge in the Brazilian Amazon. Overlapping symptoms, limited laboratory access, and the circulation of multiple arboviruses hamper clinical diagnosis. This study aimed to characterize the epidemiological, clinical, laboratory and genomic profiles of arboviral infections in febrile patients in Manaus, Brazil, and explore additional viral agents using metagenomic sequencing.

METHODS: A cross-sectional study was conducted between February 2021 and February 2023 at a tertiary reference center in Manaus, Brazil. Patients aged ≥ 5 years of age presenting with a rash and either a fever or a history of fever lasting <7 days and a negative thick blood smear for malaria were enrolled. Serum samples were tested for dengue virus (DENV), Zika virus (ZIKV), Chikungunya virus (CHIKV), yellow fever virus (YF), Oropouche virus (OROV), and Mayaro virus (MAYV) using ELISA and RT-qPCR. Positive samples were subjected to amplicon-based genome sequencing for phylogenetic analysis. A subset of RT-qPCR negative samples was analyzed using de novo shotgun metagenomic sequencing.

RESULTS: Among the 708 enrolled participants, 243 (34.3%) had a laboratory-confirmed arboviral infection: 92 (37.9%) DENV, 64 (26.3%) CHIKV, and 4 (1.6%) ZIKV, while 83 (34.2%) laboratory profiles were compatible with coinfection, predominantly DENV+CHIKV (55/83; 66.3%). Circulation of DENV-1 genotype V and DENV-2 genotypes III (Asian American) and II (Cosmopolitan) was identified. Metagenomic analysis of 35 samples detected Pegivirus hominis and Erythroparvovirus primate 1.

CONCLUSIONS: These findings demonstrate complex arbovirus co-circulation in Manaus and support integrated surveillance strategies combining molecular, serological, and genomic approaches.}, } @article {pmid42484341, year = {2026}, author = {Sato, Y and Uda, Y and Nagao, Y}, title = {Maternal contact and age-dependent succession influence the assembly of the calf rumen microbiome and virome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0167726}, doi = {10.1128/spectrum.01677-26}, pmid = {42484341}, issn = {2165-0497}, abstract = {Early-life colonization of the rumen is particularly important; however, the processes by which microbial and viral communities are transmitted and developed remain poorly understood. Here, we present a genome-resolved investigation of the effects of maternal contact and age-dependent succession on the calf rumen microbiome and DNA virome by comparing calves raised with or without maternal contact across early life using the metagenome-assembled genomes (MAGs) and viral operational taxonomic units (vOTUs) reconstructed from whole- and virus-like particle metagenomes. Across longitudinal samples from calves and their mothers, we identified 694 MAGs and 30,479 vOTUs, substantially expanding current genome databases and revealing extensive microbial and viral novelty. Our analyses demonstrated that both prokaryotes and DNA viruses are shared between dams and calves, with greater sharing observed in calves raised with maternal contact than in calves raised without maternal contact. Notably, viral sharing between cow-calf pairs was markedly lower compared to prokaryotes, suggesting high turnover and rapid viral diversification. Age-associated analyses further revealed coordinated shifts in prokaryotes and their viruses, with dominant genera such as Prevotella, Ruminococcus, and Fibrobacter, and their corresponding viruses increasing after day 40. These findings indicate that the early-life rumen microbiome and DNA virome undergo substantial age-dependent succession and are associated with maternal contact, providing new insights into host-microbe-virus interactions during rumen development.IMPORTANCEThis study provides one of the first genome-resolved views of DNA viral community development during early rumen colonization in calves (from 1 week to 70 days of age) and reveals how maternal contact and age influence the establishment of the calf rumen microbiome and virome. By analyzing longitudinal samples from calves raised with or without their mothers, we show that prokaryotes and their viruses undergo coordinated, age-dependent succession. Our results demonstrate that maternal separation alters the assembly of the calf rumen microbiome, highlighting the influence of maternal contact during early-life rumen development. These findings underscore the high plasticity of the early-life rumen ecosystem and suggest that early management practices, such as maternal separation, can have lasting effects on rumen development. This work provides fundamental insights into the establishment and succession of the calf rumen microbiome and DNA virome during early life and may contribute to future microbiome manipulation studies.}, } @article {pmid42484489, year = {2026}, author = {Xu, C and Ling, W and Xiao, X and Wang, M and Lu, J and Tang, J}, title = {Integrating Cerebrospinal Fluid Metagenomic Next-Generation Sequencing and Immune Profiling in Recurrent HSV-1 Encephalitis: A Case Report and Narrative Review.}, journal = {Journal of child neurology}, volume = {}, number = {}, pages = {8830738261465526}, doi = {10.1177/08830738261465526}, pmid = {42484489}, issn = {1708-8283}, abstract = {BackgroundRecurrent herpes simplex virus type 1 (HSV-1) encephalitis in children is rare, and its pathophysiology remains incompletely understood. Both viral reactivation and host immune dysregulation have been implicated. Advances in metagenomic next-generation sequencing (mNGS) and immune profiling provide new opportunities to elucidate disease mechanisms.Case Presentation: We detail a 13-year-old boy of Qiang ethnicity who experienced 3 neurologic episodes, including 2 virologically confirmed HSV-1 encephalitis events over 7 years. The third recurrence involved fever, seizures, and progressive bilateral temporal lobe lesions visible on magnetic resonance imaging. Cerebrospinal fluid (CSF) mNGS confirmed HSV-1 reactivation, and viral genomic sequencing demonstrated a highly conserved viral genome without high-confidence nonsynonymous mutations. Immune profiling showed compartmentalized central nervous system inflammation with elevated CSF cytokines (interleukin [IL]-6, IL-8, IL-10, interferon [IFN]-α, IFN-γ) and altered lymphocyte subsets, despite normal serum results. The patient was treated with acyclovir, intravenous immunoglobulin, and low-dose corticosteroids, which controlled seizures but left persistent neurocognitive deficits. Multidisciplinary follow-up is crucial to mitigate long-term neurocognitive sequelae.Literature Review: We reviewed 10 previously published pediatric cases of recurrent HSV-1 encephalitis, which demonstrated heterogeneous recurrence intervals, contralateral or novel lesion involvement, and frequent cognitive sequelae. Few studies integrated viral genomics or immune profiling.ConclusionsThe findings suggest that recurrent pediatric HSV-1 encephalitis may be driven by viral reactivation in the context of CNS-restricted immune dysregulation, rather than reinfection or viral evolution.}, } @article {pmid42477351, year = {2026}, author = {Hu, L and Hou, B and Yan, S and Tai, W and Xia, Y and Wu, J and Li, D and Shi, B}, title = {Lacticaseibacillus rhamnosus OF44 alleviates allergic rhinitis by rebalancing host immunity and gut microbial function.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00974-6}, pmid = {42477351}, issn = {2396-8370}, abstract = {Allergic rhinitis (AR) involves a maladaptive type 2 inflammatory response driven by systemic immune imbalance and gut dysbiosis. Here, we identify a probiotic strain, Lacticaseibacillus rhamnosus OF44, with significant probiotic potential that alleviates allergic pathology and is associated with coordinated immunological and microbial reprogramming. In an ovalbumin-induced AR rat model, OF44 administration markedly reduced nasal allergic symptoms, normalized serum and nasal immunoglobulin and cytokine levels, and restored the balance of Th1/Th2/Th17/Treg cell populations. Metagenomic profiling revealed that OF44 reshaped the gut microbial structure by enriching beneficial commensals (Rikenellaceae, Alistipes) and suppressing the proinflammatory family Enterobacteriaceae. Functional profiling further demonstrated that OF44 reversed the AR-associated enrichment of pro-inflammatory pathways, including biofilm formation, flagellar assembly, and multidrug resistance, while restoring metabolic pathways related to amino acid metabolism, energy metabolism, and short-chain fatty acid production. Integrated taxonomic-functional correlation analysis suggested that butanoate and lipoic acid metabolic pathways were microbial functions potentially associated with enhanced immune regulation. Collectively, these findings demonstrate that OF44 attenuates AR by reprogramming gut microbial composition and functional capacity, providing mechanistic support for its application as a functional probiotic for the management of allergic disease.}, } @article {pmid42477402, year = {2026}, author = {Guo, F and Li, B and Song, P and Zhang, M and Hu, T and Lin, Z and Gao, H and Liang, C and Zhang, T and Cai, Z}, title = {Gut microbiota mediates dietary adaptation across spatially varying diets in the endangered Przewalski's gazelle (Procapra przewalskii).}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10717-8}, pmid = {42477402}, issn = {2399-3642}, support = {2024-SF-146//QingHai Department of Science and Technology (Bureau of Science and Technology of Qinghai Province)/ ; 32570609//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {The extreme and heterogeneous Qinghai-Tibet Plateau challenges wildlife survival. Przewalski's gazelle (Procapra przewalskii) is confined to the northeastern Plateau around Qinghai Lake, where habitat fragmentation exposes isolated populations to distinct plant resources. How this species adapts to dietary heterogeneity via internal physiology remains unclear. Here, we integrated dietary analysis, shotgun metagenomics, and untargeted metabolomics to examine relationships among diet, gut microbiome function, and metabolic outputs across three regions. We observed population-specific differences in plant consumption, gut microbial composition, and functional potential, notably in carbohydrate degradation, plant secondary metabolite transformation, and energy metabolism. Metabolomics revealed shifts in short-chain fatty acids and lipid- and energy-related pathways. Co-occurrence networks and partial least squares path modeling (PLS-PM) indicated diet influences metabolites indirectly via the gut microbiome as a key mediator. Our findings establish a "diet-gut microbiome-metabolic output" framework, highlighting microbial mechanisms underpinning local adaptation and informing conservation of endangered plateau species.}, } @article {pmid42477662, year = {2026}, author = {Chao-Chao, Q and Zhi-Ruo, L and Xiao-Qing, L and Yan-Hong, M and Yue-Ying, Z and Ning, P and Ji-Chan, S and Xian-Gao, J}, title = {Exploring differences in alveolar microbiome between pulmonary tuberculosis patients with different treatment outcomes: a metagenomic study from China.}, journal = {BMC pulmonary medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12890-026-04500-y}, pmid = {42477662}, issn = {1471-2466}, abstract = {This study aimed to investigate differences in the composition and functional characteristics of alveolar microbiota in patients with pulmonary tuberculosis (PTB) exhibiting differential therapeutic responses. Thirty-two patients with drug-sensitive PTB who had completed standard anti-tuberculosis therapy were enrolled and classified into good-response (n = 16) and poor-response (n = 16) groups. Bronchoalveolar lavage fluid (BALF) samples were collected and analysed using metagenomic sequencing to characterize microbial community and functional pathways. No significant differences were observed in α-diversity between the two groups; however, β-diversity analysis demonstrated moderate but significant in microbial community structure (ANOSIM, R = 0.381, P < 0.001). The good efficacy group was characterized by enrichment of Prevotella, Staphylococcus, and oral commensal bacteria including Fusobacterium and Rothia, together with significantly increased pathways related to peptidoglycan biosynthesis, glutathione metabolism, energy production, and DNA repair. In contrast, the poor efficacy group was characterised by enrichment of Microbacterium and activation of functional pathways associated with biofilm formation. These findings suggest that both the taxonomic composition and functional activity of the pulmonary microbiome are closely associated with anti-tuberculosis treatment outcomes.}, } @article {pmid42477714, year = {2026}, author = {Zhang, Y and Chang, ZH and Gan, S and Wang, SH and Luo, JX and Jin, L and Zhai, XF and Sun, YB}, title = {Hologenomic rewiring facilitates dietary adaptation to chitin-rich marine resources in the crab-eating frog.}, journal = {Frontiers in zoology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12983-026-00626-1}, pmid = {42477714}, issn = {1742-9994}, support = {XNYB24-07//Foundation of Key Laboratory of Southwest China Wildlife Rsources Conservation (Ministry of Education)/ ; 2022YFF0802300//National Key Research Development Program of China/ ; 202401BC070011//Yunnan Fundamental Research Projects/ ; }, abstract = {BACKGROUND: Secondary adaptation of amphibians to marine environments is exceptionally rare. The crab-eating frog, Fejervarya cancrivora, is the only known amphibian capable of completing its life cycle in intertidal zones, where it faces dual challenges: high salinity stress and a diet rich in chitinous crab exoskeletons. While osmoregulatory adaptations have been well documented, the synergistic roles of the host's digestive system and its gut microbiota in this dietary specialization remain unclear.

RESULTS: Here, we integrated histological analysis, comparative transcriptomics, chitinase activity assays, and gut metagenomics to compare F. cancrivora with its freshwater congener, F. multistriata. We found that F. cancrivora has evolved a thicker gastric muscularis and longer gastric villi, consistent with enhanced processing of hard prey. Comparative transcriptomic analysis revealed an expanded repertoire of putative chitinase encoding transcripts (15 vs. 8 non-redundant transcripts), and both gastric and intestinal tissues exhibit significantly higher and more pH-tolerant chitinase activity. In contrast, the gut microbiota of F. cancrivora is not enriched for microbial chitin degradation genes, but instead is functionally specialized for lipid metabolism and DNA repair pathways. A controlled feeding experiment confirmed that the microbial enrichment in lipid metabolism is diet-driven, while the DNA repair pathways is largely independent of diet and likely reflects microbiome-intrinsic adaptation to chronic saline stress.

CONCLUSIONS: Together, these findings suggest a partially partitioned host-microbiome strategy in which host manages chitin breakdown, while the microbiota optimizes energy harvest and intrinsic stress tolerance. Our findings provide a new paradigm for amphibian marine adaptation, and highlights host-microbiome functional differentiation during niche expansion.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid42477746, year = {2026}, author = {Jiang, P and Zhou, M and Wen, Y and Hu, Z and Hu, Y and Liu, M}, title = {Genome-resolved gut microbial guild and fecal metabolic signatures associated with post-weaning estrus return in sows.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00601-5}, pmid = {42477746}, issn = {2524-4671}, support = {2022YFA1304204//National Key R&D Program of China/ ; }, abstract = {Post-weaning estrus return is critical for sow reproductive efficiency. The gut microbiota is associated with post-weaning estrus of sows, potentially through effects on nutrient utilization and metabolic regulation. However, current microbial signatures associated with estrus return remain poorly resolved at the strain-level. Here, we explored the relationship between the gut microbiome and post-weaning estrus in sows using metagenomics and metabolomics profiling of 85 fecal samples. From 2,704 non-redundant metagenome-assembled genomes (MAGs), 608 estrus-associated MAGs were identified by LEfSe analysis. Among these, 48 high-quality MAGs were selected for co-abundance network analysis, which revealed two competing microbial functional guilds. Guild 1 was significantly enriched in the normal group, harboring more β-glucosidase and folate biosynthesis genes, but fewer antibiotic resistance genes and virulence factors than Guild 2. A random forest model based on these 48 MAGs demonstrated excellent performance in distinguishing between the normal and non-return sows (AUROC = 0.946) and was validated in an independent dataset (n = 29, AUROC = 0.818). Additionally, the guild-level microbiome index (GMI) derived from abundance differences between the two guilds also showed good discriminatory power (AUROC = 0.799). Integrated multi-omics analysis revealed alterations in fecal bile acid metabolism in non-return sows, characterized by a significantly increased ratio of secondary to primary bile acids and the accumulation of specific secondary bile acids. Notably, the enrichment of the Clostridia strain SFHK01 sp016296675, a member of Guild 2, and its encoded 12α-HSDH gene was positively associated with specific secondary bile acids, suggesting that this specific strain is involved in the distinct metabolic alterations observed in non-return sows. These findings provide the genome-resolved and guild-based insights into the gut microbial signatures associated with post-weaning estrus return, offering a basis for potential microbiota-targeted interventions to improve sow reproductive performance.}, } @article {pmid42477864, year = {2026}, author = {Lakamp, AD and Adams, S and Kuehn, LA and Snelling, WM and Wells, J and Hales, K and Neville, B and Fernando, SC and Spangler, ML}, title = {Influence of host genetics on the functional composition of the rumen metagenome in beef cattle1.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skag224}, pmid = {42477864}, issn = {1525-3163}, abstract = {Cattle rely on the microorganisms in their rumen to break down plant matter into useable nutrients. Studies have demonstrated that the rumen microbiome plays a critical role in economically important traits. One factor that impacts rumen microbial community assembly is the host genome. Previous studies have demonstrated host genetics affect rumen microbial community composition and the association of microbiome features with production traits. However, gaps exist relative to the underlying host genetic influence on functional features of the rumen metagenome. Here we elucidated the relationship between host genetics and functional composition of the rumen metagenome while identifying metagenomic features which may provide targets for genetic selection. Rumen samples were collected via esophageal tubing from 717 beef cattle on four diets and were subjected to shotgun sequencing from which open reading frames (ORFs) were predicted. Animal genotypes were generated from imputation based on low-pass sequencing and array data. The log-transformed relative abundance of 16,350 ORFs were used as phenotypes in linear mixed models with the random effect of host genotype. In this population of 717 animals, approximately 4% of the ORFs had heritability estimates larger than twice their standard error and more than 10% of the ORFs had estimates greater than 0.20. Functions of highly heritable ORFs included aromatic amino acid biosynthesis and genome regulation. Additionally, some ORFs were genetically correlated with production traits. Eleven host genes were associated with more than one ORF. The functionality of these candidate host genes can be generally classified as either immune-related, metabolism-related, or possibly involved in host-microbiome crosstalk. Host genetics influence the rumen microbiome function making genetic selection of the host an avenue to alter rumen microbiome functionality. Associations between host genes and rumen metagenome composition indicate multiple potential biological mechanisms underlie these associations. Moreover, a portion of the highly heritable ORFs are genetically correlated with feed efficiency traits making them potential selection targets to increase productivity. The functions of the candidate host genes show the rumen metagenome is influenced by multiple complex biological systems of the host.}, } @article {pmid42477955, year = {2026}, author = {Fariba, E and Rosanna, V and Domenico, C and Gaetano, S and Mauro, L and Lucio, LR}, title = {Oral and Pancreatobiliary Microbiota in Cancer: A Systematic Review of Compositional Alterations and Their Clinical Implications.}, journal = {Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jop.70172}, pmid = {42477955}, issn = {1600-0714}, abstract = {BACKGROUND: Associations between microbial dysbiosis and malignancies of the pancreatobiliary system have been described in recent studies. As a result of the limited number of studies that have been done specifically on the malignancies of the biliary tract, information regarding oral, biliary and tumour-related microbial alterations was combined to provide an overview of the microbial changes that may occur.

METHODS: Studies that involved observations on the composition or presence of dysbiosis of the microbiota from oral (saliva, oral rinse, dental plaque) or other non-oral specimens (bile, pancreatic tissue, duodenal tissue and bacteria-derived extracellular vesicles from plasma) in patients with pancreatobiliary malignancies were considered. The risk of bias was evaluated using the Newcastle-Ottawa Scale (NOS) for case-control study designs and the JBI Checklist for cross-sectional studies.

RESULTS: There were a total of 16 studies involving 1426 participants that were conducted using both case-control and cross-sectional study designs. Samples were collected from saliva, oral wash, bile, pancreatic and duodenal tissues and bacterial extracellular vesicles isolated from plasma samples. The most common method used was 16S rRNA sequencing, and two used shotgun metagenomics. In all the studies, patients with pancreatobiliary cancers, especially PDAC, had a significantly higher abundance of opportunistic microbes like Streptococcus, Veillonella, Fusobacterium, Prevotella and a lower abundance of commensal bacteria like Neisseria and Corynebacterium. There was overlap of microbial profile in the oral cavity and tumour/bile compartments in a few studies.

CONCLUSIONS: Although the current data is preliminary and observational in nature, there are consistent findings linking microbiota dysbiosis with cancers of the pancreatobiliary region within both oral and non-oral body sites. Causality has not been established yet. The use of microbial signatures as a basis for biomarker development is a promising research direction.}, } @article {pmid42478129, year = {2026}, author = {Zhou, Y and Xu, J and Zhou, W and Wu, P and Yang, S and Ji, L and Shen, Q and Wang, X and Liu, Y and Zhou, C and Zhang, W and Xu, M}, title = {Genetic Diversity and Genomic Characteristics of the Respiratory Virome in Patients With Severe Fungal Infections.}, journal = {Journal of medical virology}, volume = {98}, number = {7}, pages = {e71063}, doi = {10.1002/jmv.71063}, pmid = {42478129}, issn = {1096-9071}, support = {2023YFD1801300//National Key Research and Development Programs of China/ ; 82550118//National Natural Science Foundation of China/ ; 82341106//National Natural Science Foundation of China/ ; BK20241926//Natural Science Foundation of Jiangsu Province/ ; }, mesh = {Humans ; *Genetic Variation ; *Virome/genetics ; *Genome, Viral ; *Respiratory Tract Infections/virology/microbiology ; Sputum/virology ; Metagenomics ; Phylogeny ; *Mycoses/virology/microbiology ; *Viruses/genetics/classification/isolation & purification ; Female ; Male ; Middle Aged ; Adult ; Sequence Analysis, DNA ; }, abstract = {Respiratory tract infections represent a leading cause of morbidity and mortality globally, with viral pathogens accounting for a substantial proportion of these cases. However, research on the human respiratory virome is still in its infancy, and our understanding of this field remains relatively limited. In the present study, viral metagenomic sequencing was conducted on 65 sputum samples obtained from patients with severe fungal infections. We successfully assembled viral genome sequences belonging to four distinct viral families: Anelloviridae, Genomoviridae, Microviridae, and Inoviridae. Through systematic analysis of the virome composition, this study characterized the structural features of the respiratory virome in patients with severe fungal infections. The findings provide a foundational description of viral diversity in this specific clinical context. These findings lay a theoretical foundation for clinical pathogen detection, targeted interventions, and the development of future prevention strategies.}, } @article {pmid42478355, year = {2026}, author = {Mu, M and Mu, C and Liu, H and Song, J and Du, X and Ge, Y and Lei, P and Mo, X and Wei, Y and Zhang, C and Zhao, C}, title = {Microbial Reduction of Methane Emissions from High-Altitude Thermokarst Lakes.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c17973}, pmid = {42478355}, issn = {1520-5851}, abstract = {Thermokarst lakes, a typical landscape resulting from abrupt permafrost thaw, are expected to be a substantial CH4 source. Climate change perturbs CH4 dynamics in these systems, particularly through increasingly frequent wet-dry cycles in small thermokarst lakes. However, how wet-dry alternation alters microbial communities remains poorly understood, and quantifying the effects of microbial shifts on CH4 emissions from these lakes represents a key challenge. Here, by integrating field observations, laboratory incubation experiments, and amplicon sequencing, we show that seasonal thermokarst lakes with wet-dry alternation exhibit a 41-70% decrease in diffusive CH4 emissions compared with perennial lakes. Alternating wet-dry cycles lead to a 33-37% decrease in the relative abundances of methanogens and a 39-59% decline in syntrophic partners in lake sediments, while the anaerobic methanotrophic archaea Candidatus Methanoperedens increased from 0.2% to 20.8%. Functional gene analyses indicate acetoclastic methanogenesis, dominated by Methanosaeta, is the primary pathway of CH4 production. The reduction in CH4 emissions is associated with changes in sediment properties, as well as decreased abundances of methylotrophic Methanomassiliicoccaceae and syntrophs. Moreover, denitrifying anaerobic CH4 oxidation processes mediated by Candidatus Methanoperedens lead to a further decline in CH4 emissions. This study provides novel insights into the microbial changes and pathways regulating diffusive CH4 emissions from seasonal thermokarst lakes, which is crucial for assessing permafrost carbon-climate feedback and prioritizing CH4 mitigation strategies.}, } @article {pmid42478812, year = {2026}, author = {Henige, M and Anklam, K and Yoon, I and Wheeler, J and Dawson, G and Döpfer, D}, title = {Effect of Saccharomyces cerevisiae fermentation postbiotic supplementation on metagenomics of digital dermatitis lesions in lactating Holstein cows.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0030426}, doi = {10.1128/spectrum.00304-26}, pmid = {42478812}, issn = {2165-0497}, abstract = {Digital dermatitis (DD) is the leading cause of lameness in cattle, posing major animal welfare and economic concerns. Effective prevention strategies are increasingly important given emerging antimicrobial resistance associated with common DD treatments. Supplementation with Saccharomyces cerevisiae fermentation postbiotics (SCFP) has been shown to enhance innate immunity and reduce DD lesion development. This study evaluated the effect of a commercial SCFP supplement on the microbial composition of DD lesions using shotgun metagenomic sequencing to characterize microbial communities and associated antimicrobial resistance genes. Beta diversity analysis revealed that stage M4 DD lesions from SCFP-supplemented cows had a trend for different microbial compositions compared with controls (P = 0.051). At the genus level, M2 lesions were found to have statistically significant lower abundance of the genera Desulfovibrio, Pseudomonas, Staphylococcus, Anaerotignum, Caproicibacterium, and Bacteroides in the SCFP treatment group compared with the control (P < 0.05). M2 lesions from the SCFP treatment group were also found to have statistically significant higher abundance of the genera Fusobacterium, Citricoccus, Listeria, and Fundicoccus as compared with the control (P < 0.05). M4 lesions were found to have statistically significant lower abundance of the genera Blautia and Petrimonas in the SCFP treatment group compared with the control (P < 0.05). At the species level, M2 lesions were found to have statistically significant lower abundance of the species Desulfovibrio sp. G11, Anaerotignum sp. MB30-C6, Caproicibacterium argilliputei, and Prevotella intermedia in the SCFP treatment group compared with the control (P < 0.05). M2 lesions from the SCFP treatment group were also found to have statistically significant higher abundance of the species Fundicoccus culcitae and Helcococcus ovis as compared with the control (P < 0.05). Metagenomic analysis identified antimicrobial resistance genes associated with multiple antibiotics commonly used for DD treatment, including tetracyclines, lincosamides, and pleuromutilins. These findings demonstrate the potential for SCFP supplementation to alter the microbial composition of DD lesions while highlighting the ongoing concerns regarding antimicrobial resistance in DD management.IMPORTANCEDigital dermatitis (DD) causes substantial economic loss and welfare concerns in cattle production systems worldwide. Our findings show that dietary supplementation with Saccharomyces cerevisiae fermentation postbiotics (SCFP) has the potential to alter the microbial ecology of DD lesions. Importantly, this work identifies antimicrobial resistance genes within DD lesions, underscoring the limitations of antibiotic-based control strategies. By linking nutritional supplementation to changes in microbial communities and resistance gene profiles, this study advances understanding of non-antibiotic approaches to disease mitigation and supports the development of sustainable, microbiome-informed management practices in food animal production.}, } @article {pmid42478878, year = {2026}, author = {Davis, EC and Jackson, CM and Diaz, NS and Susana, J and Nelson, A and Insel, R and Seppo, AE and Järvinen, KM}, title = {Maternal Perinatal Gut Microbiome Is Shaped by Traditional Farming Lifestyle and Associated With Early Childhood Atopic Disease.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.70446}, pmid = {42478878}, issn = {1398-9995}, support = {U01 AI131344/AI/NIAID NIH HHS/United States ; //University of Rochester University Research Award/ ; NIFA 67012-35010//U.S. Department of Agriculture/ ; T32 ES007026/ES/NIEHS NIH HHS/United States ; P30 ES001247/ES/NIEHS NIH HHS/United States ; T32 HL066988/HL/NHLBI NIH HHS/United States ; }, abstract = {Maternal exposure to a traditional farming lifestyle during pregnancy is associated with protection against allergic disease in childhood; however, the mechanism remains unclear. Pre-clinical work has demonstrated a role for the maternal gut microbiome in fetal immune programming. Given the diverse microbial exposure on farms, we sought to assess whether the maternal gut microbiome may mediate the relationship between maternal farm exposure and protection against offspring allergic disease. Deep shotgun metagenomic analysis of the perinatal fecal microbiome showed that women from an Old Order Mennonite traditional farming community (OOM, n = 68) harbored a more diverse gut microbiome relative to women from urban/suburban Rochester, NY (ROC, n = 55). We identified several bacterial species differentially abundant between lifestyle groups, including those from Dorea, Anaerobutyricum, Bifidobacterium, and Bacteroides genera, which translated to marked differences in microbiome functional capacity. These differences in the gut microbiome composition were accompanied by targeted metabolite findings indicating higher serum acetate and isobutyrate levels in OOM women that were positively correlated with cord plasma levels and infant systemic IgA concentrations. Among urban women, maternal microbiome composition was associated with early childhood atopic disease outcomes. Specifically, Dorea longicatena and Segatella copri were least abundant in urban mothers whose infants developed atopic disease (atopic dermatitis) or IgE-mediated food allergy alone, respectively, and were most abundant in the OOM mothers. Together, these findings highlight the maternal gut microbiome and metabolites as potential contributors to prenatal farming lifestyle protection against early childhood allergic disease.}, } @article {pmid42471440, year = {2026}, author = {Xiang, ZF and Wang, H and Yang, F and Chen, SJ and Huang, TS and Wang, SQ and Jiang, ZH and Hu, YY and Xiang, M and Wang, KX and Wang, YZ and Huang, YL and Li, YR and Shi, M and Hou, W and Chen, LJ}, title = {Metatranscriptomics reveals urbanization-driven divergence in rodent viromes and zoonotic risks in Chinese megacities.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10711-0}, pmid = {42471440}, issn = {2399-3642}, support = {2023KF003//State Key Laboratory of Virology (SKLV)/ ; U20A20396//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Metagenomic sequencing has advanced our understanding of wildlife-associated viruses and enabled identification of potential zoonotic pathogens. However, most studies remain geographically limited, with few systematic comparisons of virome compositions across urbanization gradients. To address this gap, we conducted large-scale sampling in two densely populated Chinese megacities-Wuhan and Shenzhen-with distinct climates. We collected 1,072 rodents from four species that frequently interact with humans, enabling comparative analysis of urban rectal virome dynamics and zoonotic risks in rodents. We identified 35 vertebrate-associated viruses. Among them, 9 were potentially novel species, including Norovirus and Orthopicobirnavirus species, and 3 had zoonotic potential, namely Orthohantavirus seoulense and human coronavirus OC43 (HCoV_OC43). We also discovered two viruses previously unreported in rodents, Erinaceus hedgehog Seoul orthohantavirus and Canine astrovirus, which revealed cross-order transmission risk. Additionally, 22 high-risk viruses were identified, with Wuhan and Shenzhen showing distinct prevalence patterns. Our analysis shows that inter-city rectal virome divergence is structured by meteorological variables, independently explaining 5.0% of the variation in viral community composition. Our findings highlight the importance of spatial distance in shaping the distribution and transmission of rodent-borne viruses. These insights are essential for proactive surveillance and mitigation of emerging zoonotic threats in high-density urban environments.}, } @article {pmid42472228, year = {2026}, author = {Li, X and Fan, M and Yue, J and Xie, J and Zhang, Y and Lu, X and Liu, L and Li, X and Huang, Y}, title = {Metagenomic Next-Generation Sequencing for Brain Abscess: Improved Pathogen Detection, Targeted Antimicrobial Therapy, and Association with Fewer Surgical Interventions.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {617362}, pmid = {42472228}, issn = {1178-6973}, abstract = {BACKGROUND: Brain abscesses demand prompt, accurate pathogen identification; however, identification using conventional culture is limited, especially for anaerobic and polymicrobial infections. We compared the diagnostic and clinical utility of metagenomic next-generation sequencing (mNGS) with that of conventional culture in patients with brain abscess.

METHODS: We retrospectively included 115 patients with confirmed brain abscess pathogens. Seventy-two patients underwent both mNGS and conventional culture, and 43 underwent culture alone. We evaluated diagnostic performance, pathogen profiles, adjustments to antimicrobial regimens, and clinical outcomes.

RESULTS: mNGS detected pathogens in 86.1% of patients versus 44.4% for culture (Cohen's kappa test p=0.004; McNemar's test p=0.0001). It identified mixed infections in 53.2% of cases, whereas culture predominantly revealed single pathogens. mNGS produced substantially higher detection rates than culture for anaerobic bacteria (50.0% vs 16.7%) and oral-derived bacteria (77.6% vs 61.1%). Antimicrobial regimens were adjusted in 54.2% of patients based on mNGS results; 61.5% of these adjustments involved de-escalation, and vancomycin was discontinued in 77.8% of patients. mNGS use was associated with a lower surgical intervention rate (47.2% vs 65.1%, P = 0.002). There were no differences in length of hospital stay, fever duration, Glasgow Outcome Scale score, or hospitalization costs. In eight patients without reported dental history, mNGS revealed occult odontogenic foci, enabling source control and potentially reducing recurrence risk.

CONCLUSION: mNGS outperformed conventional culture for detecting mixed infections, anaerobes, and pathogens of d origin. It may inform targeted antimicrobial therapy and assist in identifying the infection source. In this single‑center retrospective study, which is subject to potential selection bias, mNGS use was associated with a lower rate of surgical intervention; however, this finding should be interpreted as an association rather than causation, and prospective studies are needed to confirm this observation. These findings support the integration of mNGS into diagnostic algorithms for brain abscess.}, } @article {pmid42472698, year = {2026}, author = {Zhong, Y and Peng, L}, title = {Immune-guided calibration of metagenomic next-generation sequencing (mNGS) results in a pregnant patient with Listeria infection: a case report.}, journal = {The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {39}, number = {1}, pages = {2698915}, doi = {10.1080/14767058.2026.2698915}, pmid = {42472698}, issn = {1476-4954}, mesh = {Humans ; Female ; Pregnancy ; *Listeriosis/diagnosis/immunology/drug therapy ; Adult ; *Pregnancy Complications, Infectious/diagnosis/immunology/drug therapy/microbiology ; High-Throughput Nucleotide Sequencing ; Listeria monocytogenes/genetics/isolation & purification ; Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: Listeriosis during pregnancy is a rare but life-threatening infection that often presents with nonspecific symptoms, making timely diagnosis difficult. This article reports a case in which the clinical presentation and immune profile were highly consistent with Listeria monocytogenes infection, leading to a presumptive clinical diagnosis. The patient was successfully treated following a diagnostic approach that integrated host immune profiling with AI-assisted decision-making, despite dual interference from Ureaplasma urealyticum detected by metagenomic next-generation sequencing (mNGS) and Staphylococcus capitis detected by blood culture.

CASE PRESENTATION: A 25-year-old female patient, at 37[+6 ]weeks of gestation, presented with persistent high fever following induced labor due to intrauterine fetal death. External hospital blood culture and our hospital's reproductive tract mNGS suggested Staphylococcus capitis and Ureaplasma urealyticum, respectively. However, intensified treatment targeting these pathogens was ineffective.

DIAGNOSTIC PROCESS: Further investigation revealed a characteristic immune imbalance in the patient: a concurrent significant elevation of IFN-γ and IL-10, accompanied by activated CD8+ T cells. With AI-assisted analysis, this immune profile was found to be highly consistent with Listeria monocytogenes infection.

TREATMENT AND OUTCOME: After switching to ampicillin combined with gentamicin, the patient's body temperature rapidly normalized, and she recovered and was discharged.

CONCLUSION: When etiological diagnosis reaches an impasse, integrating host immune characteristics with AI-assisted decision-making can provide crucial diagnostic clues for infections caused by rare pathogens when microbiological confirmation is unavailable.}, } @article {pmid42472835, year = {2026}, author = {Contreras-Martinez, H and la Hoz, DE and López, Y and López, Y and Hoyos, R and Romero, L and Alemán, M and Martínez, C and Gastelbondo, B and Álvarez, K and Borja, G and Galeano, K and García, A and Fragoso, P and Arrieta, G and Mattar, S}, title = {First molecular detection of the genus Almendravirus in Johnbelkinia ulopus and Anopheles apicimacula mosquitoes from the Colombian Caribbean.}, journal = {Parasites & vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-026-07432-y}, pmid = {42472835}, issn = {1756-3305}, abstract = {BACKGROUND: Rhabdoviridae includes many viruses, among which rabies virus is notable. Other genera in this family can infect mammals, birds, reptiles, fish, and plants.

METHODS: Between October 2022 and July 2023, mosquitoes were collected from some municipalities in the Córdoba and Cesar departments, Colombian Caribbean. Pools were formed according to taxonomic identification and geographic area. RNA was extracted, and sequencing was performed using MGI-G50 platform. Bioinformatics analyses were performed using the Galaxy platform and the Diamond-MEGAN program. The MAFFT program was used for sequence alignment. The Prokka program was used for genome annotation, IQ-TREE was used for phylogenetic reconstruction, and iTOL was used to visualize and edit the tree. The Clustal Omega program of the European Molecular Biology Laboratory (EMBL-EBI) was used to construct a percent similarity matrix, and Unipro UGENE was used to align the amino acids of the L protein with the conserved consensus sequence (GDNQ).

RESULTS: Two new genomes showing high similarity to Almendravirus arboretum (ABTV), and Almendravirus chico (RCHV) were identified in a single pool of Johnbelkinia ulopus mosquitoes collected in Córdoba. Additionally, a third genome with a low similarity percentage to the L segment of the Almendravirus menghai (MRV) from China was detected in Anopheles apicimacula from Cesar.

CONCLUSIONS: This is the first study in Colombia that reports the ABTV and RCHV in Jb. ulopus mosquitoes and the first report of a phylogenetically similar sequence to the MRV, which could be a new virus of the Rhabdoviridae family.}, } @article {pmid42473456, year = {2026}, author = {Nwaiwu, O and Onyeaka, H and Ibekwe, VI and Okorondu, SI and Nnokwe, JC and Edward, KC and Chikezie, PC and Offor-Emenike, IU and Ewelike, NC and Anyanwu, NJ and Nwachukwu, IN and Chinakwe, EC and Okorondu, MM}, title = {Molecular phylogeny of 16S rRNA sequences from Ugba (Pentaclethra macrophylla) seeds.}, journal = {Access microbiology}, volume = {8}, number = {7}, pages = {}, pmid = {42473456}, issn = {2516-8290}, abstract = {The evolutionary analysis of bacterial species harbouring 16S rRNA sequences detected in the oil bean seeds of Ugba (Pentaclethra macrophylla) was carried out. The food product has a high socio-economic relevance to communities where it is consumed. Species such as Kurthia gibsonii, Stenotrophomonas geniculata and Alcaligenes nematophilus found in Ugba may have occurred in the environment and entered the sample in the field during or before harvest. The phylogenetic analysis of 35 sequences showed that some strains of the same species resolved into different monophyletic groups, suggesting species divergence or distinct evolutionary lineages. The species K. gibsonii was found to be the earliest ancestor following sequence-based ancestral analysis, suggesting that it was present in the analysed samples before other bacteria. The Ugba seeds appear to harbour a diverse group of bacteria and will benefit from metagenomic investigations as well as studies of the mechanism of survival and succession to reveal the true nature of the resident flora. This will help safeguard public health and highlight the organism's relevance to food safety surveillance and microbial evolution. Increased knowledge of the resident organisms will also lead to the improvement of fermentation techniques and enhance the quality of the final product.}, } @article {pmid42473567, year = {2026}, author = {Yan, J and Yang, H and Wan, L and Zhao, C}, title = {Oral Histoplasmosis in an Immunocompetent Male Diagnosed by Culture, Histopathology, and MetaCAP.}, journal = {International medical case reports journal}, volume = {19}, number = {}, pages = {596732}, pmid = {42473567}, issn = {1179-142X}, abstract = {BACKGROUND: Histoplasmosis is a systemic fungal infection caused by the dimorphic fungus Histoplasma capsulatum, commonly found in soil contaminated by bird or bat excrement. Oral granulomatous histoplasmosis is a relatively rare presentation that often lacks typical clinical features. Patients may experience persistent oral pain or lesions lasting several weeks, and clinical presentations can mimic malignant tumors or other infectious pathogens, leading to diagnostic challenges.

CASE PRESENTATION: We report a case of oral granulomatous histoplasmosis in a 53-year-old immunocompetent male, initially suspected of having lymphoma or tuberculosis. To our knowledge, this is an exceptional case of oral histoplasmosis diagnosed in an immunocompetent patient through a combination of tissue fungal culture, pathological biopsy, and metagenomic capture sequencing (metaCAP).

CONCLUSION: The case highlights the importance of considering fungal infections in persistent oral lesions of immunocompetent patients. It also demonstrates that metaCAP, alongside conventional culture and histopathology, can facilitate a definitive diagnosis in challenging cases.}, } @article {pmid42473611, year = {2026}, author = {Liu, M and Chen, Y and Xie, P and Xu, W and Huang, S and Liu, B}, title = {A Case of Listeria monocytogenes Meningitis (Complicated) with Hydrocephalus and Occipital Lobe Infarction.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {624063}, pmid = {42473611}, issn = {1178-6973}, abstract = {BACKGROUND: Listeria monocytogenes (LM) meningitis is a rare but severe infection, particularly in immunocompromised patients, often leading to complications such as hydrocephalus, markedly increasing treatment complexity and the risk of poor outcomes.

CASE PRESENTATION: We report a case of LM meningitis in an immunocompromised patient. The illness began with fever and gastrointestinal symptoms, followed by neck stiffness and altered consciousness. LM was identified via blood culture, cerebrospinal fluid (CSF) culture, and metagenomic next-generation sequencing (mNGS). During hospitalization, the patient developed decompensated hydrocephalus and a right occipital lobe infarction, emergent external ventricular drainage (hospital day 4) and subsequent ventriculoperitoneal shunting (hospital day 44) were performed, which were potentially life-saving. After comprehensive treatment and rehabilitation, the patient was discharged on day 85 without significant neurological deficits.

CONCLUSION: Clinical presentation of LM meningitis may be atypical, especially in immunocompromised patients. In such patients, aggressive management of hydrocephalus-including timely CSF diversion-is potentially life-saving. Early pathogen detection through combined blood culture, CSF culture, and mNGS, together with prompt, targeted antimicrobial therapy and dynamic management of neurological complications such as hydrocephalus, is essential for improving clinical outcomes.}, } @article {pmid42474014, year = {2026}, author = {Yu, Y and Zhao, H and He, Y and Zhao, J and Yang, X and Liu, X and Cheng, X}, title = {Therapeutic Effects of the Traditional Chinese Formula Qifuyin on Cognition, Lipid Metabolism, and Gut Microbiota in ApoE4 Mice.}, journal = {Combinatorial chemistry & high throughput screening}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113862073453341260621182306}, pmid = {42474014}, issn = {1875-5402}, abstract = {INTRODUCTION: Apolipoprotein E4 (ApoE4) is the strongest genetic risk factor for sporadic Alzheimer's disease (AD). Qifuyin is a promising herbal formula used clinically for cognitive decline, but its effects on ApoE4-associated cognitive and systemic phenotypes remain unclear. This study aimed to evaluate the effects of Qifuyin on cognitive performance in ApoE4 transgenic mice and to preliminarily explore its associations with lipid metabolism and gut microbiota alterations.

METHODS: Ten-month-old ApoE4 transgenic mice were treated with Qifuyin by gavage for 321 days, once daily for the first 123 days and once every two days thereafter. Cognitive function was assessed using the step-down test, novel object recognition test (NORT), and Morris water maze test (MWM). Aging- and frailty-related phenotypes were evaluated using senescence grading scores. Serum triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), and apolipoprotein B (ApoB) levels were measured to assess lipid metabolism. Gut microbiota composition and functional profiles were analyzed by 16S rRNA and metagenomic sequencing.

RESULTS: Qifuyin treatment significantly reduced error counts and prolonged latency in the stepdown test, increased the 24h preference index in the NORT, shortened escape latency, and increased platform crossings in the MWM in ApoE4 transgenic mice. High-dose Qifuyin reduced aging scores in males and in all doses in females and in the pooled dataset. Qifuyin decreased serum TG and ApoB levels, and increased serum HDL-C levels. 16S rRNA sequencing indicated that Qifuyin increased alpha diversity and shifted beta diversity toward the control profile. At the phylum level, Qifuyin altered the relative abundances of Firmicutes, Bacteroidota, Cyanobacteria, and Synergistota. At the family and genus levels, Qifuyin treatment was associated with increased abundances of Helicobacteraceae, Bacteroidaceae, Helicobacter, and Bacteroides, and a reduced abundance of Ruminococcaceae. Metagenomic annotation analysis showed altered abundances of K02003, K06147, COG1961, CBM37, and GH35-related features.

DISCUSSION: These findings suggest that Qifuyin may benefit ApoE4-associated cognitive and systemic dysfunction through its integrated effects on lipid metabolism and gut microbiota alterations. The microbiota-related changes observed in this study may provide a potential link between peripheral metabolic regulation and cognitive improvement, although their mechanistic significance requires further validation.

CONCLUSIONS: Qifuyin improved cognitive performance and lipid metabolism, and was associated with alterations in gut microbiota composition in ApoE4 transgenic mice. These findings suggest that Qifuyin may exert beneficial effects on cognitive and systemic phenotypes in this model, while the biological significance of specific microbial changes warrants further investigation.}, } @article {pmid42474149, year = {2026}, author = {Liu, H and Chen, M and Zhang, D}, title = {Lactobacillus-fermented feed alters growth performance, fecal short-chain fatty acid contents, metagenomics, and metabolomics in growing pigs.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0040426}, doi = {10.1128/msystems.00404-26}, pmid = {42474149}, issn = {2379-5077}, abstract = {UNLABELLED: This study sought to comprehensively evaluate the impact of Lactobacillus-fermented feed produced with Latilactobacillus curvatus SQ13 on the growth and fecal short-chain fatty acid (SCFA) contents, as well as metagenomic and metabolomic parameters, in growing pigs. One hundred crossbred pigs were randomized into two dietary treatment groups. Animals were given either a basal diet (CON) or a diet containing Lactobacillus-fermented feed (LP) over a 32-day period. The LP group exhibited a significantly reduced feed conversion ratio (FCR) and lower fecal valeric acid concentration compared with the CON group (P < 0.05). Microbial community analysis revealed that the relative abundance levels of Candidatus_Eremiobacterota, Cyanobacteriota, Lacrimispora, and Candidatus_Onthomorpha were markedly increased in the LP group (P < 0.05), whereas Actinomycetota, Pseudomonadota, Solobacterium, and Mitsuokella were significantly decreased (P < 0.05). KEGG pathway analyses indicated that arachidonic acid metabolism, phototransduction-fly, and Th17 cell differentiation were the three most significantly altered pathways. Correlation analysis further demonstrated that FCR was positively associated with Solobacterium abundance and downregulated metabolites, while showing negative correlations with Alistipes and upregulated metabolites. Collectively, these findings suggest that Lactobacillus-fermented feed improves growth efficiency and modulates valeric acid levels in growing pigs, likely through coordinated alterations in gut microbial composition and host metabolic processes. These results offer a potential foundation for the application of fermented feed in swine production systems. .

IMPORTANCE: Our study demonstrated that fermented feed produced by Latilactobacillus curvatus ZLA031 could improve growth efficiency, decrease valeric acid levels in growing pigs, likely through coordinated alterations in fecal microbiota composition, and host metabolic processes. Our work provided both experimental evidence and a theoretical framework supporting the application of Lactobacillus-fermented feed in swine production, while highlighting the need for further mechanistic research.}, } @article {pmid42474199, year = {2026}, author = {Xu, Y and Ren, R and Liu, W and Liu, L and Cui, X and Guo, J and Li, S}, title = {Clinical impact of metagenomic next-generation sequencing for pathogen identification and guided therapy in pediatric intensive care unit patients with severe pulmonary infections.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0037426}, doi = {10.1128/spectrum.00374-26}, pmid = {42474199}, issn = {2165-0497}, abstract = {UNLABELLED: To explore the diagnostic efficiency, clinical concordance, and precision treatment value of metagenomic next-generation sequencing (mNGS) for severe pulmonary infections in children in the pediatric intensive care unit (PICU), and to provide evidence for improving microbiological diagnosis and optimizing anti-infective strategies. A retrospective cohort study included 89 children with severe pneumonia in the PICU in 2024. All underwent routine microbiological testing and mNGS of bronchoalveolar lavage fluid (BALF). Detection rates, pathogen composition, co-infection identification, diagnostic concordance, and treatment impact were analyzed. Metagenomic next-generation sequencing demonstrated high diagnostic sensitivity in the PICU setting, achieving a positive detection rate of 90.0% (80/89) and identifying a diverse spectrum of 103 pathogens, including 50.5% viruses, 43.7% bacteria, 38.8% co-infections (vs 11.6%), and 86.3% diagnostic concordance (vs 55.8%, P < 0.01). Among 46 patients included in the therapeutic outcome analysis (22 in the mNGS-guided group), 21 patients in the mNGS-guided group improved. Multivariate logistic regression analysis, adjusting for confounding factors (age, underlying diseases, PaO2/FiO2 ratio, PRISM III score, and preoperative antibiotic use duration), confirmed that mNGS-guided therapy was an independent protective factor for achieving the primary outcome (OR = 5.23, 95% CI: 1.87-14.61, P = 0.002) and secondary outcomes (C-reactive protein reduction ≥50%: OR = 4.89, 95% CI: 1.72-13.93, P = 0.003; oxygenation improvement: OR = 5.67, 95% CI: 1.98-16.21, P = 0.001). Metagenomic next-generation sequencing demonstrated high diagnostic sensitivity in the PICU setting, guiding precision therapy, and improving prognosis.

IMPORTANCE: It supports metagenomic next-generation sequencing (mNGS) as a supplementary tool for pediatric intensive care unit (PICU) refractory infections, guides anti-infective adjustments, and informs tiered diagnostic pathways for resource-limited settings to optimize cost-effectiveness.}, } @article {pmid42474201, year = {2026}, author = {Palmer, B and Couradeau, EM and Johansen, JR and Kurbessoian, T and Carranza, JO and Stajich, JE and Ward, R and Pietrasiak, N}, title = {Unraveling the diversity and functional potential of cyanosphere microbiomes assembled from terrestrial cyanobacteria.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0104326}, doi = {10.1128/aem.01043-26}, pmid = {42474201}, issn = {1098-5336}, abstract = {The cyanosphere is composed of non-cyanobacterial microorganisms living within the exopolysaccharide sheath of cyanobacteria, interacting with the cyanobacterial hosts and their surrounding environment. Understanding the interactions between cyanobacteria and their cyanospheres can help predict the success of terrestrial cyanobacteria in providing ecosystem services in nutrient-poor environments. However, knowledge of the microbial diversity and functions within the cyanosphere remains limited. Here, we used metagenomic sequencing to reconstruct 415 metagenome-assembled genomes (MAGs) from cyanosphere-associated microbes linked to 56 terrestrial cyanobacteria cultures, representing 12 cyanobacterial orders. Our findings showed that the composition of cyanosphere microbial communities was significantly shaped by environmental factors such as habitat of host origin, including precipitation and temperature. Three microbial genera, Brevundimonas, Devosia, and Sphingopyxis, were present in over 30% of the cyanospheres, suggesting a core cyanosphere microbiome. Functional gene analysis showed a distinction between the cyanobacteria and their associated cyanospheres, with dissimilatory nitrate reduction being the dominant pathway in the cyanosphere, an anaerobic process that retains nitrogen in the host-cyanosphere system in contrast to denitrification. While nitrogen fixation was more common in the cyanobacteria, 15 cyanospheres also contained nitrogen fixation genes, including in hosts that were nitrogen fixation capable themselves. The cyanosphere also contained genes for polysaccharide lyases, indicating a possible link to the exopolysaccharides produced by the cyanobacteria. Given the observed variability in microbial community composition and function across different cyanobacterial hosts, future ecological assessments and restoration efforts involving cyanobacteria should not only focus on the cyanobacteria themselves but also consider their associated microbial communities.IMPORTANCEOur study identifies members of an understudied and under-valued microbial community, the cyanosphere. We used a diversity of terrestrial cyanobacteria to understand how the cyanosphere composition and predicted functions were influenced by the host cyanobacterium and environmental factors using metagenomics. This is a novel approach to studying the cyanosphere, providing insights into the diversity of terrestrial microbial communities. Importantly, our results underscore the need to consider microbial consortia when assessing the ecological potential of cyanobacteria in terrestrial restoration.}, } @article {pmid42474235, year = {2026}, author = {Pettersson, KJ and Demina, T and Eronen-Rasimus, E and Roux, S and Viitamäki, S and Pessi, IS and Oksanen, HM and Assmy, P and Kaartokallio, H and Hultman, J}, title = {Viral genetic diversity and functional potential in polar and subarctic sea ice.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag077}, pmid = {42474235}, issn = {1574-6941}, abstract = {Sea ice plays a critical role in regulating the global climate and serves as a unique habitat for diverse microbial communities. Still, our understanding of viruses in these communities remains limited. To further uncover the diversity and functional potential of viruses in polar and subarctic sea ice, we explored the viral component of Arctic, Baltic Sea, and Antarctic sea ice metagenomes. Altogether, 550 viral operational taxonomic units (vOTUs) were recovered, most of which were putatively classified within the class Caudoviricetes, which comprises bacterial and archaeal tailed double-stranded DNA viruses. Hosts were predicted for 187 vOTUs, with Gammaproteobacteria and Bacteroidia being the most prevalent viral host groups. Potential functions were assigned for 56% of predicted viral gene products, including putative auxiliary metabolic genes (AMGs) involved in oxidative metabolism, photosynthesis, and metabolism regulation under stress conditions. Related viral genomes carrying similar AMGs were detected in other Arctic and more geographically distant freshwater, marine, and ice environments. Genus- and/or family-level links between the studied vOTUs were detected across samples. Our results suggest diverse and complex virus-host interactions in sea ice and highlight the essential roles viruses may play in sea ice ecosystem dynamics across polar and subpolar environments.}, } @article {pmid42474352, year = {2026}, author = {Bergada-Pijuan, J and Pichler, I and Zaheri, M and Kufner, V and Huber, M}, title = {Masking recurrent contaminants in reference sequences improves specificity of clinical metagenomic sequencing.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0039726}, doi = {10.1128/jcm.00397-26}, pmid = {42474352}, issn = {1098-660X}, abstract = {Viral metagenomic next-generation sequencing (mNGS) is a powerful approach for pathogen detection in clinical diagnostics; however, accurate virus identification depends critically on the quality of reference databases. Diagnostic specificity is frequently compromised by erroneous viral classifications, which occur when host- or reagent-derived sequences align to non-viral contaminant regions (such as ribosomal RNA, vector contamination like cytomegalovirus enhancers, and sequencing adapters) embedded within the viral reference sequences. To address this, we present VirMask, a novel computational strategy to systematically identify and mask recurrent contaminant regions within the viral reference sequences. In a first step, VirMask aligns simulated human reads against a viral database and masks host-derived regions. Second, it identifies and masks persistent contaminant regions based on their high prevalence across independent metagenomic data sets. Finally, VirMask employs alignment-based similarity searches to detect and mask homologous regions across multiple reference sequences, thereby reducing noise in mNGS outputs and improving diagnostic specificity. Using data from clinical mNGS runs, we demonstrate that VirMask usefully reduces artefactual detections without impacting true pathogen identification. Specifically, reads erroneously assigned to human viruses decreased by up to 30%, and those assigned to non-human viruses and bacteriophages by more than 99%. Furthermore, validation with a standardized international quality control panel confirmed 100% preservation of true-positive detections, while reducing false-positive human virus calls by up to 89% and overall erroneous assignments by 40%-94%. These results underscore the necessity of rigorous viral database curation and offer a reproducible framework for enhancing diagnostic confidence in mNGS-based clinical virology.IMPORTANCEThe importance of this study lies in addressing a critical bottleneck in clinical metagenomic next-generation sequencing (mNGS): the presence of systematic false-positive viral detections caused by contaminant regions within reference databases. While mNGS is a powerful, unbiased tool for pathogen discovery, its diagnostic reliability is often compromised by "kitome-derived" sequences that align to non-viral segments embedded in viral reference genomes. By introducing VirMask, this research provides a reproducible framework to systematically identify and mask these recurrent artifacts without sacrificing the sensitivity required to detect true pathogens. This targeted refinement of viral databases significantly reduces "noise" in diagnostic outputs, ensuring that clinicians can interpret metagenomic data with higher confidence and avoid misidentifying persistent laboratory contaminants as clinically significant infections.}, } @article {pmid42475242, year = {2026}, author = {Shi, W and Cen, L and Huang, J and Lei, X and Wang, Y and Wang, S and Ying, J and Li, Y and Ma, Y and Fang, Y and Liu, A and Lu, C and Dai, M}, title = {LECT2 deficiency contributes to bile acid metabolic reprogramming and cholestatic liver injury.}, journal = {Hepatology communications}, volume = {10}, number = {8}, pages = {}, doi = {10.1097/HC9.0000000000001007}, pmid = {42475242}, issn = {2471-254X}, mesh = {Animals ; *Bile Acids and Salts/metabolism ; Mice, Knockout ; Mice ; *Intercellular Signaling Peptides and Proteins/deficiency/genetics/metabolism ; Liver/metabolism/pathology ; Disease Models, Animal ; Receptor, Farnesoid X-Activated ; Gastrointestinal Microbiome ; Male ; Receptors, Cytoplasmic and Nuclear/metabolism ; Metabolic Reprogramming ; Fibroblast Growth Factors/metabolism ; *Cholestasis, Intrahepatic/metabolism ; *Cholestasis/metabolism ; Signal Transduction ; Mice, Inbred C57BL ; Humans ; }, abstract = {BACKGROUND: Cholestatic liver injury involves impaired bile acid (BA) formation or flow, leading to toxic hepatic BA accumulation, yet the underlying mechanisms remain poorly understood. Leukocyte cell-derived chemotaxin 2 (LECT2) has been implicated in liver metabolic disorders; however, its specific role in cholestasis remains incompletely understood.

METHODS: ANIT was administered to wild-type (WT) and LECT2 knockout (KO) mice to establish an intrahepatic cholestasis model. Metabolomics and metagenomics were performed to discover the role of BA metabolism and the gut-liver axis in cholestatic liver injury. Clinical samples were analyzed to assess the relationship between LECT2 and cholestatic liver injury.

RESULTS: LECT2 deletion was associated with altered BA synthesis, characterized by a shift toward the classical pathway with upregulation of CYP7A1 and CYP8B1. Under cholestatic conditions, LECT2 deficiency was associated with aggravated liver injury, accompanied by alterations in gut microbiota composition, changes in intestinal FXR-FGF15 signaling, and increased hepatic JNK activation. In KO mice, HDCA supplementation restored the alternative synthesis pathway, FMT reshaped gut microbiota, and antibiotic cocktail treatment suppressed intestinal FXR signaling, each of which was associated with improved cholestatic liver injury. In clinical samples, LECT2 levels were negatively correlated with markers of cholestasis, supporting its potential relevance to disease severity.

CONCLUSION: LECT2 deficiency is associated with aggravated cholestatic liver injury, which may involve altered BA synthesis, gut microbiota dysbiosis, and modulation of intestinal FXR-hepatic JNK signaling. These findings offer new insights into the role of LECT2 in regulating metabolism and identify potential therapeutic targets for managing cholestatic liver injury.}, } @article {pmid42475475, year = {2026}, author = {Durán-Viseras, A and Cha, G and Hatt, JK and Lindner, BG and Benvenuto, EM and Zhang, Y and Kunjapur, AM and Konstantinidis, KT}, title = {A Metagenome-Based Methodology to Track Genomically Recoded Strains and Assess Their Effects on Indigenous Microbes.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c15663}, pmid = {42475475}, issn = {1520-5851}, abstract = {Assessing the effects of the release of biologically contained microorganisms into the environment represents a challenging task as it requires both the tracking of escape events as well as the changes that result in the indigenous microbes, which cannot be effectively determined based on conventional culture-based methodologies. Toward closing this gap, we set up closed, laboratory mesocosms with water from a nearby recreational-use freshwater reservoir that were subsequently spiked with the Escherichia coli strain DEP to simulate an accidental spill of a synthetic organism into the environment. Strain DEP is a chloramphenicol-resistant synthetic auxotroph harboring three redesigned genes encoding nonstandard amino acid (nsAA)-dependent gene products for l-4,4'-biphenylalanine (BipA) dependence. Shotgun metagenome sequencing of the mesocosms revealed a sharp decline in the relative abundance of strain DEP over time, with minimal impact on the indigenous freshwater microbial communities as evidenced by the recovery of these communities to the preperturbation state after 2 days of incubation. Further, there were no observations of transfer of the nsAA-dependent genes to the indigenous populations at the limit of detection of our metagenome sequencing effort or based on culturing on BipA-supplemented media. Collectively, our results show that this particular strain DEP may not pose a serious environmental threat if accidentally released into the environment due to low competitiveness against the indigenous freshwater microbes and the lack of escape mutants. Notably, this work establishes a holistic approach to assess biocontainment efficacy that should be applicable to additional genetically modified organisms.}, } @article {pmid42475510, year = {2026}, author = {Li, R and Dong, W and Yang, Z and Wang, M and Xiong, J and Ma, Y and Hu, X and Yang, Y and Wan, J and Wu, R and Ye, R and Liu, B and Nguyen-Viet, H and Peng, Z and Wang, S and Li, J}, title = {MicroWorldOmics: All-in-one Desktop Solution for Microbiome Profiling, Virome Analysis, and Unexplored "Dark Matter" Discovery.}, journal = {Genomics, proteomics & bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/gpbjnl/qzag059}, pmid = {42475510}, issn = {2210-3244}, abstract = {The large amount of high-throughput sequencing data generated in ecology, medicine, and pharmacology has increased the complexity of data analysis and interpretation. However, the microbiome and virome fields still lack a user-friendly and programming-free desktop application for comprehensive analysis of microbiome and virome data, with a particular gap in virome analysis and "dark matter" exploration. To address this gap, we introduce MicroWorldOmics, a plugin-based desktop application designed to offer a streamlined one-stop solution for life sciences and biomedical research. Its plugin-based architecture allows users to analyze data interactively and in parallel, simplifying tasks that typically require advanced bioinformatics skills. MicroWorldOmics is a comprehensive software suite tailored for microbiome and virome research, featuring 92 sub-applications across four main modules: epidemiology analysis, in-depth metagenomic/amplicon and virome profiling, and "dark matter" exploration. MicroWorldOmics leverages over 80 Python modules and 600 R packages for diverse bioinformatics, statistics, deep learning, and visualization tasks, accommodating multiple input and output formats including GFF3, FASTA, CSV, PNG, JPG, JSON, and TXT. To enhance user productivity, the software is compatible with Windows, Linux, and macOS systems, and includes demo data for easy benchmarking. In summary, MicroWorldOmics is intended to facilitate microbiome and virome data analysis for life sciences and biomedicine researchers without a programming background. It is available at https://hzaurzli.github.io/.}, } @article {pmid42475793, year = {2026}, author = {Lyu, Y and Wu, S and Fan, X and Zhang, Y and Zhang, Q and Wang, S and Feng, Z}, title = {Discovery and characterization of a novel GH6 multifunctional enzyme from soil metagenomic library.}, journal = {Carbohydrate research}, volume = {568}, number = {}, pages = {110046}, doi = {10.1016/j.carres.2026.110046}, pmid = {42475793}, issn = {1873-426X}, abstract = {Cellulases are crucial for converting biomass into renewable energy. Despite extensive research, there remains a significant industrial demand for novel cellulases, particularly those with multi-substrates catalytic activity. This study aimed to identify and characterize a novel cellulase from a high-altitude soil metagenome library using functional screening method. A novel 1218-bp GH6 family hydrolase gene, designated zfy1641, was identified from a Mount Everest soil library. Bioinformatics analysis indicated that it encoded a 405-amino-acid protein (43.7 kDa) and was classified into glycoside hydrolase family 6 (GH6). The target glycoside hydrolase gene was cloned and heterologously expressed, then the recombinant protein was purified, and its biochemical properties and kinetic parameters were characterized. The purified recombinant enzyme exhibited broad substrate specificity, demonstrating significant activity against carboxymethyl cellulose (CMC-Na; 69.87 ± 0.13 U/mg), locust bean gum (125.56 ± 0.18 U/mg) and chitin (77.06 ± 0.08 U/mg). ZFY1641 represented a novel member of the GH6 family, that exhibited detectable reducing sugar release from chitin-a function not previously documented for this family. Moreover, ZFY1641 demonstrated optimal activity at 50°C and pH 5.0, and exhibited moderate thermal stability, tolerance to selected metal ions, and halophilicity under the conditions tested. These characteristics suggest potential utility of ZFY1641 in industrial processes, though further validation is required. This work expanded the substrate diversity of GH6 family enzymes and provided a foundation for the development of new enzymatic preparations with a novel multi-functional GH6 family enzyme.}, } @article {pmid42476086, year = {2026}, author = {Jurvansuu, J and Sipponen, E and Salmivirta, E and Lehto, KM and Havulinna, A and Pitkänen, T and Oikarinen, S}, title = {Wastewater viromics reveals host-structured viral signals and non-human pathogens.}, journal = {Water research}, volume = {305}, number = {}, pages = {126485}, doi = {10.1016/j.watres.2026.126485}, pmid = {42476086}, issn = {1879-2448}, abstract = {Wastewater represents a powerful platform for human virus surveillance. However, the entry of animal- and plant-associated viruses into sewage is heterogeneous and incompletely understood, creating uncertainty about how reliably wastewater reflects non-human virus circulation. Here, we address this by analysing monthly wastewater metagenomic data from two distinct periods (2020-2021 and 2024-2025) across five major Finnish wastewater treatment plant catchments using a targeted hybrid-capture approach to characterise the composition, host range, and spatial distribution of the non-human wastewater virome. Nearly half of the detected viral accessions were non-human, indicating substantial diversity, despite human-associated viruses accounting for 83% of normalised viral reads. Rodent-, livestock-, and bird-associated viruses showed spatial structuring consistent with regional host populations. The wastewater viromics also detected four EU-regulated plant pathogens, including tomato brown rugose fruit virus, which was highly prevalent in wastewater two years before its first official detection in Finland. Together, these results show that wastewater contains structured, host-linked viral signals, supporting its use as an ecological proxy for non-human virus circulation.}, } @article {pmid42476135, year = {2026}, author = {Zhao, W and Wang, J and Chen, C and Jiang, A and Wang, Y and Hu, A and Qi, Q and Chen, Y and Sui, W and Dong, L and Zhang, Y and Xiao, X}, title = {Hadal topography incubates hidden microbial hotspots in the deepest ocean.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.06.015}, pmid = {42476135}, issn = {1934-6069}, abstract = {Plate subduction creates unique topographic features in hadal trenches, yet their influence on microbial ecosystems and the global ocean remains unclear. Here, we conducted a topography-targeted investigation across 6-11 km of water depth within the Mariana Trench, integrating metagenomic, metaproteomic, and geochemical analyses. Coupled with high-resolution topographic mapping, our analyses reveal topography as an overlooked determinant of hadal geochemical and microbial heterogeneity. Convex areas exhibit classical sediment-depth-decay patterns with sparse, cooperative microbial communities. Conversely, concave features maintain higher biomass and activity as well as dense microbial interactions. Critically, slope concave sites incubate previously unrecognized microbial hotspots and may serve as interchange hubs, potentially facilitating genetic exchange and upward dispersal of microorganisms from Earth's deepest regions to the broader ocean. Our findings demonstrate that topographic features, rather than water depth, significantly correlate with organic carbon influx and its microbial turnover rates, enabling predictive modeling of hadal carbon cycling with global implications.}, } @article {pmid42476199, year = {2026}, author = {Hoepers, PG and Nunes, PLF and Almeida, HO and Martins, MM and Bastos, LM and de Oliveira Carvalho, RD and Aburjaile, FF and de Jesus E Silva, B and Sommerfeld, S and de Souza Penha, VA and Alves, LBR and de Carvalho Azevedo, VA and Fonseca, BB}, title = {ENHANCING POULTRY HEALTH AND FOOD SAFETY WITH PROBIOTICS: A STUDY ON Bacillus Velezensis AGAINST Salmonella Heidelberg IN BROILERS.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108717}, doi = {10.1016/j.micpath.2026.108717}, pmid = {42476199}, issn = {1096-1208}, abstract = {The growing concern over antibiotic use and foodborne pathogens such as Salmonella Heidelberg (SH) highlights the need for effective alternative strategies in poultry production. This study evaluated the probiotic potential of Bacillus velezensis (BV) to control SH colonization and modulate gut microbiota and metabolism in broilers. In vitro, BV exhibited inhibitory activity against SH. In vivo, a total of 100 one-day-old broiler chicks were randomly assigned to four treatments (n = 25/group): NC (negative control), PC (positive control, challenged with SH), BV-Neg (BV supplementation without SH challenge), and BV-SH (BV supplementation with SH challenge). Birds were orally challenged at 4 days of age with 0.2 mL of SH (6 × 10[9] CFU/mL). Cecal SH counts, microbial diversity, and fecal metabolomic profiles were evaluated at 7, 14, 21, and 28 days. Data were analyzed using ANOVA, chi-square tests, and multivariate approaches, including principal component analysis (PCA) and multivariate analysis of variance (MANOVA), with significance set at P < 0.05. BV supplementation significantly reduced SH colonization in the cecum at 28 days, with a reduction of 3.53 log CFU/g (∼99.9%) compared to the positive control (P < 0.01), indicating a time-dependent probiotic effect. Microbial diversity was influenced by treatment and age, with BV-supplemented and SH-challenged groups showing higher diversity than NC (P < 0.05). Metabolomic analysis identified 60 analytes across multiple metabolic classes, with BV increasing beneficial compounds such as fatty acyl glucosides, lignin, artemisinin, and taurodeoxycholic acid, while reducing metabolites associated with SH infection. Overall, BV demonstrated a cumulative effect in reducing SH colonization and modulating gut microbiota and metabolism, supporting its potential as a probiotic strategy to improve poultry health and food safety.}, } @article {pmid42476393, year = {2026}, author = {Huang, M and Li, S and Mu, G and Li, X and Yang, Q and Shao, B and Zhang, Q and Tong, Y}, title = {Methanotrophs and Co-occurring Microbial Taxa: Genomic Potential for Carbon, Nitrogen, and Sulfur Cycles in Newly Formed High-altitude Proglacial Lakes.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125274}, doi = {10.1016/j.envres.2026.125274}, pmid = {42476393}, issn = {1096-0953}, abstract = {The extreme and fragile environments of high-altitude proglacial lakes shape unique microbial communities and metabolic networks, serving as active interfaces in the biogeochemical cycles of carbon (C), nitrogen (N), and sulfur (S). However, the metabolic processes underlying microbially driven biogeochemical cycling in these lakes remain poorly understood. In this study, by integrating field investigations and isotopic analyses across multiple seasons, we observed geochemical and genomic evidence consistent with significant microbial methane (CH4) oxidation in the surface sediments of cryo-oligotrophic proglacial lakes in the Nyainqentanglha Range on the Tibetan Plateau. Metagenome-assembled genomes (MAGs) analysis revealed that Methylobacter was the dominant methanotroph in surface sediments, possessing complete pathways for aerobic CH4 oxidation, partial denitrification (nitrate → nitrous oxide), and sulfide oxidation (sulfide → elemental S), suggesting its genetic capacity to potentially participate in C, N, and S transformations. The co-occurring Nitrospira (Palsa-1315) was identified as a key player in the N cycle through complete ammonia oxidation (comammox, ammonia → nitrate), while Rhodoferax and Thiobacillus were considered important contributors via heterotrophic and autotrophic denitrification (nitrate → dinitrogen), respectively. Additionally, Thiobacillus may be the key genus involved in the S cycle through S/sulfide oxidation (S[0]/sulfide → sulfate). Overall, this study reveals the key microbial taxa involved in CH4, N, and S cycling and highlights the potential importance of methanotrophy in rapidly expanding proglacial ecosystems amid ongoing climate warming.}, } @article {pmid42476404, year = {2026}, author = {Lou, J and Chen, J and Zheng, Y and Su, Q and Zhu, Z and Zhu, J}, title = {Biochar for Mitigating the Oxytetracycline Stress of Nitrite-DAMO System: Microbial Metabolic Mechanisms and Metagenomics Research.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125278}, doi = {10.1016/j.envres.2026.125278}, pmid = {42476404}, issn = {1096-0953}, abstract = {Denitrifying anaerobic methane oxidation (DAMO) serves as a critical biogeochemical nexus linking the global carbon and nitrogen cycles to mitigate greenhouse gas emissions. However, ubiquitous antibiotics in DAMO habitats and wastewater systems presents a severe ecological threat, exacerbating methane emissions, nitrogen accumulation, and biotoxicity. Investigating mitigation strategies and mechanisms is essential for addressing these real-world environmental challenges. This study focused on the nitrite-dependent anaerobic methane oxidation (Nitrite-DAMO) system to investigate the comprehensive effects of biochar on denitrification performance and microbial metabolic characteristics under long-term oxytetracycline (OTC) stress (1 mg/L and 10 mg/L), along with the potential mechanisms. Results indicated that biochar significantly mitigated OTC toxicity and effectively enhanced both denitrification and methane oxidation performances. Average denitrification rates in biochar-amended groups reached 0.86 and 0.73 mg/(L·d), while the methane oxidation capacities increased to 2.27 and 1.76 times those of the non-biochar groups. Biochar established physicochemical barriers against antibiotic stress by stimulating extracellular polymeric substances (EPS) and enhancing electron transport system activity (ETSA). High-throughput sequencing and metagenomic analysis revealed that biochar drove microbial community succession, enriching functional bacteria (Candidatus Methylomirabilis and Thauera), while significantly upregulating the abundance of functional genes involved in nitrogen and carbon metabolism pathways (nirK, pmoA/B/C). Crucially, biochar suppressed the proliferation of potential hosts and disrupted transposons-mediated horizontal gene transfer (HGT), thereby substantially mitigating the accumulation and dissemination risks of antibiotic resistance genes (ARGs). The synergistic mitigation mechanisms elucidated herein provide theoretical guidance for in-situ regulation strategies to reduce methane emissions in antibiotic-contaminated wetlands, paddy fields, and river sediments.}, } @article {pmid42476406, year = {2026}, author = {Li, N and Yi, J and Zhu, L and Chen, D and Wang, M and Huang, D}, title = {Nanoconfined humic acid-supported nZVI enhances imidacloprid remediation without compromising soil microbiome or exacerbating ARG health risks.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125277}, doi = {10.1016/j.envres.2026.125277}, pmid = {42476406}, issn = {1096-0953}, abstract = {Pesticide contamination of agricultural soils poses persistent risks to ecosystem function and agricultural sustainability, yet the application of reactive nanomaterials for remediation remains constrained by physicochemical instability and uncertain ecological consequences. Here, we synthesized a nanoconfined humic acid-supported nZVI composite (HA-nZVI) and evaluated its performance in imidacloprid (IMI)-contaminated soil through kinetic analysis, interfacial characterization, metagenomic sequencing, and dual-dimensional ARG risk assessment. HA nanoconfinement improved particle dispersion, increased active-site accessibility, and facilitated interfacial electron shuttling. These effects accelerated predominantly abiotic IMI dissipation, raising the degradation rate by 3.8-fold relative to the unamended control and shortening the half-life to 18.56 d. Despite the accelerated removal, dominant phylum-level abundances fluctuated by less than 3%, suppression of plant-beneficial bacteria (PBB) observed with pristine nZVI was alleviated, and no measurable increase in human- or livestock-associated ARG risk was detected among the 525 identified ARG subtypes. Collectively, these findings show that HA nanoconfinement can couple improved pesticide dissipation with microbiome compatibility and resistome safety, supporting the design of iron-based nanomaterials for sustainable agricultural remediation.}, } @article {pmid42476495, year = {2026}, author = {Chen, M and Cao, J and Fu, S and Han, Y and Zheng, W and Chen, J and Yang, X and Wang, J}, title = {Lambda-cyhalothrin exposure disrupts microbiota-associated bile acid metabolism and enterohepatic feedback in mice.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128813}, doi = {10.1016/j.envpol.2026.128813}, pmid = {42476495}, issn = {1873-6424}, abstract = {Lambda-cyhalothrin (LCT) is a widely used pyrethroid insecticide frequently detected in environmental and food-associated matrices, yet its effects on host bile acid metabolism remain unclear. Male C57BL/6 mice were orally exposed to LCT for 28 days and analyzed using integrated bile acid metabolomics, hepatic and ileal gene-expression profiling, 16S rRNA sequencing, and shotgun metagenomics. LCT reduced hepatic total bile acids but increased plasma and fecal bile acids, indicating compartment-specific bile acid redistribution. This response was accompanied by hepatic Cyp7a1/Cyp27a1 downregulation, selective Cyp8b1 upregulation, altered bile acid transporter expression, and enhanced ileal FXR-FGF15-related feedback responses. LCT also remodeled gut microbial composition and altered bile acid transformation-related functional signatures, particularly those related to 7α-HSDH and 3β-HSDH. Consistently, fecal LCA, 3-ketoLCA, and isoLCA accumulated, consistent with altered microbial LCA oxidation-reduction and epimerization potential. These findings identify microbiota-associated bile acid remodeling as a potential non-neurotoxic metabolic endpoint of pyrethroid-induced gut-liver axis disturbance and provide candidate microbial and host targets for future mechanistic validation.}, } @article {pmid42476558, year = {2026}, author = {D'Agostino, GD and Kim, CH and Park, J and Zhang, Y and Amer, B and Franzosa, EA and Bird, SS and Huttenhower, C and Huh, JR and Devlin, AS}, title = {Comparative Metabolomics Reveals the Production of Sulfated Metabolites by Human Gut Bacteria.}, journal = {Journal of the American Chemical Society}, volume = {}, number = {}, pages = {}, doi = {10.1021/jacs.6c02487}, pmid = {42476558}, issn = {1520-5126}, abstract = {The sulfated metabolome─the collection of sulfate-containing metabolites─is an emerging source of structurally unique bioactive compounds that influence metabolism, immune responses, and neurological function. Recent studies have shown that, in addition to host enzymes, gut bacteria also encode sulfotransferase enzymes (SULTs) that generate sulfated metabolites. However, the substrate scope of characterized gut bacterial SULTs remains narrow, and comprehensive discovery is limited by a lack of methods to detect and assign sulfated metabolites in complex samples. Here, we develop a comparative metabolomics workflow that leverages the universal SULT cofactor 3'-phosphoadenosine-5'-phosphosulfate (PAPS) to incorporate heavy ([34]S) or light ([32]S) sulfur into sulfated metabolites, enabling discovery of microbiome-dependent sulfated compounds. By applying this approach in both "bottom-up" bacterial culture and "top-down" in vivo studies, we find that gut bacteria sulfonate hydroxy fatty acids. We identify a gut commensal microbe, Eubacterium ramulus, that performs this transformation, as well as an enzyme in this bacterium that performs this sulfonation, ErSULT. Metagenomic analyses reveal that ErSULT is prevalent across diverse human gut microbiomes. Together, this workflow and its application demonstrate that sulfated metabolite production by gut bacteria is more widespread than previously appreciated and provide a platform for future studies investigating the biosynthesis and biological functions of microbiome-derived sulfated small molecules.}, } @article {pmid42476661, year = {2026}, author = {Zhang, F and Hu, W and Zhao, X and Fu, B and Lin, Y and Xie, C and Yang, R and Fu, Y and Tan, W and Ye, L}, title = {Comorbid depression exacerbates Gelsemium elegans toxicity via disruption of the Clostridium-LCA-PXR-CYP3A11 metabolic axis.}, journal = {Chinese journal of natural medicines}, volume = {24}, number = {8}, pages = {987-998}, doi = {10.1016/S1875-5364(26)61197-1}, pmid = {42476661}, issn = {1875-5364}, mesh = {Animals ; *Gelsemium/toxicity/chemistry ; Mice ; *Clostridium/metabolism ; Gastrointestinal Microbiome/drug effects ; *Pregnane X Receptor/metabolism/genetics ; Male ; *Depression/metabolism/microbiology/complications ; *Cytochrome P-450 CYP3A/metabolism/genetics ; *Plant Extracts/toxicity ; Indole Alkaloids/toxicity ; Alkaloids ; }, abstract = {Gelsemium elegans (G. elegans) is a toxic medicinal plant traditionally used to treat chronic pain, with its toxicity linked to indole alkaloids such as gelsemine and humantenmine (HMT). Chronic pain often co-occurs with depression, a condition known to disrupt host-microbiota interactions, potentially affecting drug metabolism and toxicity. However, the impact of comorbid depression on the toxicity of G. elegans remains unclear. This study investigates how depression exacerbates the neurotoxicity of G. elegans and explores the role of the gut microbiota-host metabolic axis in this process. Depression-model mice were treated with G. elegans aqueous extract, gelsemine and HMT. Multi-omics approaches, including 16S rRNA sequencing and shotgun metagenomics, were used to analyze microbiota changes under depressive conditions. Functional validation was performed using pseudo-germ-free mice, fecal microbiota transplantation, and supplementation with Clostridium species and lithocholic acid (LCA), as well as pregnane X receptor (Pxr) knockout models. The results showed that depression significantly heightened the neurotoxicity of G. elegans, gelsemine and HMT. Mechanistically, depression reduced Clostridium abundance and LCA levels, impairing PXR activation and downregulating hepatic CYP3A11 expression. This disruption of the Clostridium-LCA-PXR-CYP3A11 axis hindered the detoxification of indole alkaloids, leading to increased systemic exposure and exacerbated neurotoxicity. Restoration of this pathway through Clostridium or LCA supplementation alleviated the toxicity. These findings highlight the role of the Clostridium-LCA-PXR-CYP3A11 axis in the altered toxicity of G. elegans in a depressive state, and suggest that Clostridium species and their metabolites may serve as a potential strategy for mitigating toxicity.}, } @article {pmid42476947, year = {2026}, author = {Su, Z and Liu, T and Zhao, J and Evans, P and Yuan, Z and Guo, J and Zheng, M}, title = {Substantial N2O Accumulation under Acidic Oxic Conditions Driven by Constrained N2O Reduction in a Denitrifying Consortium.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c03705}, pmid = {42476947}, issn = {1520-5851}, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas generated as an intermediate during microbial nitrogen cycling, but it rarely dominates total nitrogen fluxes. Here, we report substantial N2O accumulation in an enriched denitrifying culture supplied with nitrite and acetate and maintained under acidic (pH 4.8-5.0) and oxic conditions (>7 mg O2/L), accounting for around 60-70% of the total nitrogen flux. Metagenomic and metatranscriptomic analyses reveal distinct functional roles among key populations. Ottowia shows high genomic abundance and strong transcriptional activity of cNOR (norB) but lacks nosZ, consistent with an efficient NO-reducing but N2O-accumulating phenotype. A Rhodanobacteraceae lineage exhibits high genomic abundance and active expression of both qNOR and cNOR, together with dominant nosZ transcription, suggesting a potential capacity for both N2O production and reduction. However, the persistence of high N2O levels indicates constrained N2O reduction under these conditions. In contrast, Mycobacterium, despite its low abundance, displays disproportionately high qNOR expression, indicative of a specialized role in NO detoxification. These results suggest that N2O accumulation primarily arises from incomplete denitrification, where N2O formation exceeded net N2O reduction under acidic oxic conditions. The inhibitory effects of low pH, oxygen, and nitrite/free nitrous acid likely limit N2O reductase activity, leading to decoupling between nosZ transcription and function. Together, these findings highlight the importance of constrained N2O reduction in driving emissions under acidic conditions and demonstrate how community-level functional partitioning shapes N2O dynamics in engineered systems.}, } @article {pmid42476978, year = {2026}, author = {Xu, Z and Xing, J and Zeng, X and Wu, Y and Wang, Y and He, Y and Lin, X and Huang, H and Zhao, Z and Wu, H and Guo, Z and Chen, T}, title = {Citywide metagenomics reveals microbial community and resistome dynamics in urban wastewater.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-75771-6}, pmid = {42476978}, issn = {2041-1723}, abstract = {Urban wastewater systems connect hospitals, residential communities, transport hubs, and wastewater treatment plants, creating opportunities for the dissemination of microorganisms and antibiotic resistance genes (ARGs). Here, we conduct a three-month, citywide metagenomic survey of wastewater in Xiamen, China, comprising 252 samples from seven hospital sites (n = 16), 27 residential sites (n = 55), 16 wastewater treatment plant sites (n = 159), and individual international flights (n = 22). Genome-resolved analyses reveal source-specific microbial community structures, resistome profiles, lineage-sharing patterns, and associations between ARGs and mobile genetic elements across wastewater sources. Hospital wastewater harbors the most diverse resistome, while international flight wastewater introduces microbial taxa and ARGs absent from local wastewater networks. Wastewater treatment plants accumulate ARGs from multiple upstream sources, exhibiting frequent lineage sharing and signals of potential horizontal gene transfer. Compared with within-environment sharing, cross-environment lineage sharing is associated with lower nucleotide diversity, consistent with possible genetic bottlenecks. Among potential correlates, pH shows strong non-linear associations with microbial diversity and resistome composition. These findings indicate that urban wastewater systems function as interconnected networks for microbial and ARG dissemination and identify potential hotspots for targeted antimicrobial resistance surveillance.}, } @article {pmid42477049, year = {2026}, author = {Tan, B and Zafra, C and Ng, C}, title = {Comparative genomics of the Nap2-2B clade reveals substrate partitioning and niche diversification among uncultured hydrocarbon-degrading Desulfotomaculales.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-63016-x}, pmid = {42477049}, issn = {2045-2322}, abstract = {Uncultured Nap2-2B bacteria (order Desulfotomaculales; formerly family Peptococcaceae) are frequently detected in methanogenic hydrocarbon-degrading environments, yet their metabolic diversity remains poorly understood. Here, we analysed 17 GTDB r232 metagenome-assembled genomes (MAGs) from four genera within this clade. A bac120 phylogeny places Nap2-2B as a monophyletic family-level lineage within Desulfotomaculales. Glycyl radical enzyme phylogeny and operon context reveal strict substrate partitioning: SCADC1-2-3 encodes alkylsuccinate synthase for aliphatic hydrocarbon activation, 46-80 and UBA4053 encode benzylsuccinate synthase for aromatic activation, and JAIMBK01 lacks hydrocarbon activation genes but retains complete dissimilatory sulfate reduction pathway genes. Pangenome-level pathway reconstruction identifies complementary cofactor biosynthetic potential, notably in cobalamin and pantothenate biosynthesis, consistent with possible cofactor complementation. Genome-scale metabolic modeling suggests that the alkane-degrading SCADC1-2-3 lineage can support syntrophic hexane degradation, whereas the aromatic lineage cannot grow on the alkane FBA test because it lacks AssA and PFOR. A parallel aromatic-substrate FBA for 46-80 MAGs did not yield growth under minimal curation, reflecting the greater complexity of the downstream benzoyl-CoA pathway. Together, these data support a syntrophic guild structured by substrate partitioning, putative cofactor complementation, and distinct electron-disposal strategies that may shape methanogenic hydrocarbon attenuation in anoxic tailings environments.}, } @article {pmid42477236, year = {2026}, author = {Mohamed, ME and Cheng, S and Staley, C and Rashidi, A and Jurdi, NE and Holtan, SG and Jacobson, PA}, title = {Identification of Microbiome Associations with Tacrolimus Pharmacokinetics in Adult Hematopoietic Cell Transplantation Using Population Pharmacokinetic and Machine Learning.}, journal = {Pharmaceutical research}, volume = {}, number = {}, pages = {}, pmid = {42477236}, issn = {1573-904X}, support = {1UM1TR004405/TR/NCATS NIH HHS/United States ; P30CA077598/CA/NCI NIH HHS/United States ; }, abstract = {PURPOSE: Tacrolimus (TAC) is known for its high pharmacokinetic variability which cannot be fully explained by pharmacogenomic (PGx) and clinical variables. We identified gut microbiome associated with TAC pharmacokinetic variability in allogeneic hematopoietic cell transplant (HCT) recipients.

METHODS: In this observational study, metagenomic shotgun sequencing was used to analyze stool microbiome collected within ± 10 days from time of first oral TAC trough at steady state. TAC steady state concentrations (222 IV continuous infusion and 436 oral troughs) were modeled to estimate TAC clearance (CL) and oral bioavailability (F) using nonlinear mixed effects modeling. The effect of clinical covariates, PGx variants and concomitant medications on CL and F were evaluated. Machine learning was used to identify bacterial species associated with variability in F and CL. The identified species were incorporated into the final model, and simulations were conducted to estimate their clinical relevance on oral TAC troughs.

RESULTS: TAC population CL was 6.91 L/h and population F was 64.4%. TAC CL was increased in those with CYP3A5*1 genotype and reduced with voriconazole use and if estimated glomerular filtration rate < 60 ml/min/1.73 m[2]. TAC F increased with laxative use and decreased with corticosteroid use. Limosilactobacillus fermentum had the strongest positive effect on oral TAC troughs while Bacteroides uniformis had the strongest negative effect.

CONCLUSION: Gut microbiome contributes to the inter-patient variability in TAC CL and oral F.}, } @article {pmid42470694, year = {2026}, author = {Yi-Hui, Z and George, S}, title = {Hierarchical Multi-Omics Trajectory Prediction for fecal microbiota transplantation: a novel machine learning framework for small-sample longitudinal multi-omics integration.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {4}, pages = {}, doi = {10.1093/bib/bbag389}, pmid = {42470694}, issn = {1477-4054}, mesh = {Humans ; Multiomics ; *Machine Learning ; *Fecal Microbiota Transplantation ; *Clostridium Infections/therapy/microbiology ; Clostridioides difficile ; Longitudinal Studies ; Predictive Learning Models ; Metagenomics ; }, abstract = {Fecal microbiota transplantation (FMT) has emerged as a highly effective treatment for recurrent Clostridioides difficile infection and is being actively investigated for numerous other conditions. While multi-omics studies have revealed dynamic changes in microbial communities and host metabolism following FMT, existing approaches are primarily descriptive and lack the ability to model individual patient trajectories or identify early biomarkers of treatment response. Small-sample, multi-omics, longitudinal prediction presents unique computational challenges: high dimensionality ($p \gg n$), multi-omics integration, temporal dynamics, and interpretability. Here, we present Hierarchical Multi-Omics Trajectory Prediction (HMOTP), a purpose-built machine learning framework that addresses these challenges through hierarchical feature construction, multilevel attention mechanisms, and patient-specific trajectory prediction. We evaluated HMOTP on 15 patients with recurrent Clostridioides difficile infection who underwent FMT, with lipidomics and metagenomics profiling at four timepoints spanning 6 months. Notably, naively concatenating multi-omics features degraded Random Forest performance ($93.33\%$ to $87.18\%$ accuracy), whereas HMOTP's hierarchical integration benefited from the additional omics layer, demonstrating that its advantage stems from structure, not from access to more data. Through hierarchical interpretability, HMOTP identified key biomarkers and revealed cross-omics associations between host lipid metabolism and microbial energy pathways, demonstrating utility for longitudinal modeling and biological discovery in FMT response. HMOTP provides a generalizable, principled framework for personalized medicine applications across small-sample multi-omics problems. Source code and a demo dataset are publicly available.}, } @article {pmid42470960, year = {2026}, author = {Chen, Y and Han, D and Hu, Q and Xiong, Y and Zhou, X and Wang, Y and Li, D and Yan, J and Yang, J and Zhang, F and Cao, H and Wu, P and Liu, Y and Xia, Y and Sun, J}, title = {Gut-liver axis through microbiota-metabolite interplay driving age-dependent susceptibility to arsenite-induced liver injury in mice.}, journal = {Ecotoxicology and environmental safety}, volume = {322}, number = {}, pages = {120522}, doi = {10.1016/j.ecoenv.2026.120522}, pmid = {42470960}, issn = {1090-2414}, abstract = {Arsenic is a highly toxic metalloid that contributes to many chronic diseases. The liver is a primary target organ because it mediates detoxification and metabolism. However, the differences in susceptibility to age-related arsenic-induced liver injury and their underlying mechanisms remain unclear, particularly regarding the involvement of the gut-liver axis. Young, adult, and old mice ingested arsenic via drinking water. We assessed glucose metabolism, liver injury, and intestinal barrier integrity. To investigate the role of the gut microbiota, we performed metagenomic sequencing on fecal samples. Liver metabolic changes and signaling pathways were analyzed using non-targeted metabolomics and transcriptomics technologies, respectively. This study reveals that aged mice exhibit heightened susceptibility to arsenite-induced liver injury and metabolic disorders. Histological examination and reduced occludin expression confirm this is associated with impaired intestinal barrier function. Metagenomic analysis indicated that arsenite exposure was associated with gut microbiota remodeling in aged mice, characterized primarily by genus-level alterations, including reduced Muribaculaceae-related genera and relative enrichment of genera associated with altered mucosal homeostasis and inflammatory signaling. Metagenomic pathway analysis further suggested shifts in microbial metabolic and inflammatory signaling-related pathways, including changes in insulin/glucagon signaling, glycerolipid metabolism, and NOD-like receptor signaling. Metabolomics detection revealed significant accumulation of uridine diphosphate glucose (UDPG) in the livers of arsenite-exposed aged mice. Transcriptomic analysis revealed upregulation of the mitogen-activated protein kinase (MAPK) signaling pathway, while western blotting confirmed its activation in the liver. These findings suggest that aging is associated with increased susceptibility to arsenite-induced liver injury, potentially involving gut microbiota remodeling, intestinal barrier dysfunction, and hepatic UDPG accumulation. UDPG may function as a metabolic stress-associated factor or potential amplifier of MAPK-related inflammatory signaling, thereby potentially contributing to liver injury. Consequently, a novel gut-liver axis mechanism is revealed, elucidating the intrinsic link between aging and susceptibility to environmentally induced toxic diseases.}, } @article {pmid42471145, year = {2026}, author = {Liang, L and Li, Y and Fu, X and Lin, R and Liu, K and Zhao, Z}, title = {Biochar enhances anaerobic oxidation of methane coupled with Cr(VI) reduction: pyrolysis temperature-dependent electron transfer pathways and regulatory mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135442}, doi = {10.1016/j.biortech.2026.135442}, pmid = {42471145}, issn = {1873-2976}, abstract = {Anaerobic oxidation of methane (AOM) coupled with Cr(VI) reduction offers a promising strategy for synergistic remediation of methane and chromium co-contamination, but is constrained by inefficient interspecies electron transfer (IET). Biochar can facilitate IET via its tunable electrochemical properties, yet how pyrolysis temperature governs this process remains unclear. Herein, biochars prepared at 300 °C (BC300) and 800 °C (BC800) were compared to elucidate their regulatory mechanisms on AOM-coupled Cr(VI) reduction. Biochar amendment significantly improved Cr(VI) removal: BC800 achieved complete reduction of 50.0 mg/L Cr(VI) within 34 days, versus 77.4 % for BC300 and 39.6 % for the control. Electrochemical analysis revealed that BC300 facilitated mediated interspecies electron transfer via redox-active functional groups as electron shuttles, whereas graphitized BC800 facilitated direct interspecies electron transfer (DIET) via its high conductivity, markedly reducing electron transfer resistance and enhancing electron transport system activity. Microbial and metagenomic analyses revealed BC800 enriched Methanospirillum and Geobacter, and upregulated genes encoding DIET-related PilA protein and c-type cytochromes. These findings elucidate a complete electron route, where Methanospirillum transfers electrons generated from methane oxidation to Geobacter via BC800 acting as an electron conduit, and then Geobacter delivers electrons to extracellular Cr(VI) through conductive pili to complete the reduction process, verifying DIET as the core enhancement mechanism. This study demonstrates the prominent application superiority of high-temperature conductive biochar, and provides a robust scientific basis for rational design of functional carbon materials for synergistic methane mitigation and heavy metal remediation.}, } @article {pmid42468699, year = {2026}, author = {Qing, C and Zhou, Y and Wang, Y and Li, P and Hedlund, B}, title = {Arsenic detoxification mediated by mutualistic cross-feeding in a thermophilic microbial consortium.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135440}, doi = {10.1016/j.biortech.2026.135440}, pmid = {42468699}, issn = {1873-2976}, abstract = {Cyanobacteria-dominated microbial mats thrive in arsenic (As)-rich hot springs, but how they cope with As stress remains unclear. This study explored the As detoxification strategy of a photosynthetic microbial mat from a high-As hot spring in Tibet. The photosynthetic mat oxidized arsenite [As(Ⅲ)] under light without external organic carbon sources or electron acceptors. However, As(Ⅲ) was not oxidized by a pure culture of the dominant cyanobacterium isolated from the mat, "Thermoleptolyngbya sichuanensis" XZ-Cy5. Instead, exposure of a growing culture to 5 mM As(Ⅲ) led to rapid loss of chlorophyll and photosynthetic activity. In contrast, a pure culture of the mat-derived heterotroph Chelatococcus sp. XZ-Ab1 could oxidize As(Ⅲ) quickly with the addition of organic carbon and oxygen. A co-culture system demonstrated mutualistic interactions where "T. sichuanensis" XZ-Cy5 secreted organic carbon to facilitate heterotrophic growth of Chelatococcus sp. XZ-Ab1, while Chelatococcus sp. XZ-Ab1 promoted growth of "T. sichuanensis" XZ-Cy5 by oxidizing toxic As(Ⅲ) to the less toxic arsenate. Following growth of the co-culture using [13]CO2, NanoSIMS isotope tracing provided direct evidence of photoautotroph-derived carbon from "T. sichuanensis" XZ-Cy5 to Chelatococcus sp. XZ-Ab1. Metagenomic and genomic analyses indicated several mechanisms for metabolic complementarity between the two strains, including As detoxification by the heterotroph and fixed carbon and nitrogen provision by the cyanobacterium, in addition to oxygen production. Our findings reveal a cooperative survival strategy in extreme environments and provide a novel model for engineering synthetic microbial consortia for As bioremediation.}, } @article {pmid42469266, year = {2026}, author = {Yu, Z and Zhang, K and Zeng, XM and Cheng, X and Zhang, Y and Wang, X and Sun, J and Chen, L and Liu, F and Zhang, Q}, title = {Consequences of agricultural deforestation and subsequent afforestation on soil biodiversity and ecosystem multifunctionality.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-75740-z}, pmid = {42469266}, issn = {2041-1723}, support = {32471650,32430068, 31922060, 32130069//National Natural Science Foundation of China (National Science Foundation of China)/ ; Y2022091//Youth Innovation Promotion Association of the Chinese Academy of Sciences (Youth Innovation Promotion Association CAS)/ ; }, abstract = {The Earth is currently in an era where massive deforestation and afforestation coexist. The impact of large-scale agricultural deforestation and the subsequent afforestation on soil biota multidiversity, ecosystem multifunctionality (EMF), and the relationship between soil biota multidiversity and EMF (BEFm) remain unclear. Here, we investigate 405 paired plots along a 4000 km south-north transect, spanning tropical, subtropical, temperate, and boreal zones. We measure 19 ecological functions and sequence soil biota (including bacteria, fungi, archaea, viruses, protists, and invertebrates) and metagenomes. We find that agricultural deforestation reduces soil multitrophic biodiversity by 25% and EMF by 58%, and afforestation has partially restored them, but pristine levels have not been reached. Agricultural deforestation decouples the positive BEFm relationship across four climatic zones, while afforestation restores the positive BEFm relationship in tropics and subtropics but not in temperate and boreal zones. Afforestation in the warmer zone triggers potential multitrophic cascades to enhance EMF, thereby strengthening BEFm relationship. The changes in biogeochemical-cycling genes induced by afforestation exert more significant driving effects on EMF in the warmer zone than the colder zone. Our study provides integrative evidence that climate modulates the recovery of BEFm relationship and offers multitrophic and metagenomic insights into the mechanisms underlying EMF.}, } @article {pmid42469597, year = {2026}, author = {Shen, Z and Eckert, JK and Saffery, R and Allen, KJ and Walsh, A and , and Deming, C and Chen, Q and Laky, K and Li, JM and Chatman, L and , and Kong, HH and Perrett, KP and Segre, JA and Frischmeyer-Guerrerio, PA}, title = {Shotgun Metagenomics Reveals Skin Microbiome Composition and Function in Infant Atopic Disease.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.70449}, pmid = {42469597}, issn = {1398-9995}, support = {AR084058/NH/NIH HHS/United States ; UM1AI109565/NH/NIH HHS/United States ; APP1146913//National Health and Medical Research Council/ ; GNT2008911//National Health and Medical Research Council/ ; 26-PBII-T1-04//WSU Office of Research/ ; }, abstract = {BACKGROUND: Atopic dermatitis (AD), food sensitization (FS), and food allergy (FA) frequently co-occur in infancy, but the factors underlying distinct atopic phenotypes remain unclear. Although FLG null mutations are major genetic risk factors for AD, they explain only part of disease heritability, suggesting a potential role for the skin microbiome. This study examined how early-life skin microbiome composition and its interaction with host genetics contribute to distinct atopic phenotypes in infancy.

METHODS: We analyzed > 1000 skin swabs from 429 infants in the VITALITY cohort using deep shotgun metagenomic sequencing at 2-3 months (pre-diagnosis) and 12 months (post-diagnosis). Differential abundance, strain-level, and microbial genome-wide association analyses were performed to identify taxonomic and functional features associated with AD, FS, FA, their co-occurrence, and FLG mutation status.

RESULTS: Within AD, microbial signatures differed by co-occurring FA or FS. At 12 months, Staphylococcus epidermidis was enriched in infants with AD alone, whereas infants with AD and FA showed decreased Staphylococcus hominis and Lactococcus species, and increased Dermacoccus nishinomiyaensis and Malassezia slooffiae. At 2-3 months, early skin dysbiosis characterized by enrichment of Staphylococcus species was associated with later development of AD with FS or FA, but not AD alone. Among infants with AD, FLG mutation carriers showed additional microbial shifts, including reduced Streptococcus species and increased M. slooffiae. Strain-level analyses revealed mother-infant sharing of AD-associated taxa, and microbial genome-wide association analyses identified species-specific genes linked to AD severity.

CONCLUSIONS: Infant atopic phenotypes are associated with distinct, phenotype-specific skin microbiome features that emerge before and after disease onset, highlighting the microbiome as a potential target for early risk stratification.}, } @article {pmid42469878, year = {2026}, author = {Li, S and Guo, R and Sun, L and Zhu, P and Wang, T and Zheng, J and Chen, H and Li, H}, title = {Co-production of high-purity floridoside and isofloridoside ameliorates MASH via Parabacteroides goldsteinii-UDCA-FXR enterohepatic axis.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {}, pmid = {42469878}, issn = {1749-8546}, support = {No.2024J422//Ningbo Natural Science Foundation/ ; No.2024020919//Ningbo Top Medical and Health Research Program/ ; No.32373099//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Metabolic dysfunction-associated steatohepatitis (MASH), the progressive form of metabolic dysfunction-associated fatty liver disease (MAFLD), is tightly linked to gut microbiota dysbiosis and disrupted bile acid (BA) homeostasis. Floridoside (Flor), a marine glycoside from the edible seaweed Pyropia haitanensis (P. haitanensis), exerts promising biological activities. However, protocols for its high-purity preparation and the mechanisms underlying its anti-MASH effects remain unclear.

PURPOSE: To develop a protocol for the preparation of high-purity Flor and its isomer isofloridoside (Isoflor) from P. haitanensis, and to elucidate how Flor alleviates MASH via regulating gut microbiota and BA metabolism.

METHODS: High-purity Flor and Isoflor were isolated via integrated chromatography, with their chemical structures confirmed by LC-MS and NMR. Anti-MASH efficacy was evaluated in a high-fat diet (HFD)-induced murine MASH model. The underlying mechanisms were explored using multi-omics analyses, including transcriptomics, gut microbiota metagenomics and BA-targeted metabolomics, and further validated by molecular docking, molecular dynamics simulation and western blotting; the compounds' biosafety was evaluated using zebrafish.

RESULTS: High-purity Flor and Isoflor were successfully isolated, each with a purity of ≥ 99.0%. Both compounds exhibited a favorable biosafety profile and comparable lipid-lowering activity in zebrafish. In HFD-induced murine MASH models, Flor robustly ameliorated HFD-driven obesity, hepatic steatosis, and chronic inflammation, and restored systemic BA homeostasis characterized by a markedly increased non-12-OH/12-OH BA ratio. Meanwhile, Flor treatment dramatically enriched the relative abundance of intestinal Parabacteroides goldsteinii (P. goldsteinii), which showed a significant positive correlation with MASH alleviation and beneficial BAs (e.g., ursodeoxycholic acid (UDCA)). Mechanistically, UDCA exerted its therapeutic effects by antagonizing FXR signaling, upregulating the hepatic protein and mRNA expression of CYP7B1 and CYP27A1, and ultimately promoting the activation of the alternative BA synthesis pathway.

CONCLUSION: High-purity Flor and Isoflor were obtained via an integrated co-production process from P. haitanensis. We hypothesize that Flor may ameliorate MASH by enriching P. goldsteinii and modulating the UDCA-FXR axis to activate the alternative bile acid synthesis pathway, positioning Flor as a promising prebiotic candidate for MASH management.}, } @article {pmid42470286, year = {2026}, author = {Nikam, R and Kalani, K and Beverly, M and Kumar, PS}, title = {The Vape, the Mouth, and the Mycobiome: A Comparative Metagenomic Analysis.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345261450182}, doi = {10.1177/00220345261450182}, pmid = {42470286}, issn = {1544-0591}, abstract = {Electronic nicotine delivery systems (ENDS), including e-cigarettes, are increasingly marketed as safer alternatives to combustible tobacco, yet their effects on oral health remain underexplored. Although the role of ENDS in creating dysbiotic oral bacterial communities is documented, effects on the oral mycobiome remain underexplored. This study compared the subgingival fungal communities of 123 periodontally and systemically healthy e-cigarette-only users, smokers, dual users, former smokers, and never-smokers using whole-genome shotgun sequencing for functional profiling. Taxonomic assignment using Kraken 2 and the PlusPF database identified 98 fungal taxa, and functional annotation with the Kyoto Encyclopedia of Genes and Genomes identified 2,960 fungal genes. Cross-domain bacterial-fungal interactions were interrogated using a correlation threshold of |r| ≥ 0.7 and P ≤ 0.001. E-cigarette users demonstrated a significantly higher α-diversity than smokers and never-smokers did (P < 0.001; P < 0.005) and a mycobiome enriched with Candida albicans, Aspergillus oryzae, and Schizosaccharomyces pombe. Functional profiling revealed enrichment of genes encoding or DNA repair, xenobiotic degradation, membrane transport, and stress response. The mycobiome of dual users and former smokers using e-cigarettes did not differ from that of e-cigarette users. Cross-kingdom networks identified 5- to 10-fold higher bacterial-fungal connectivity in e-cigarette users, with fungi capable of enhanced stress tolerance, DNA repair capacity, and metabolic adaptability acting as network anchors. Our data support an association between e-cigarette use and remodeling of the oral mycobiome and microbiome, driven by enhanced polymicrobial interactions and increased functional complexity, suggesting that assumptions regarding the biological neutrality of e-cigarette aerosols warrant further investigation.}, } @article {pmid42470541, year = {2026}, author = {Ergen, AG and Keskin, E and Akgun, A and Erol, HB and Edis, G and Celik, I and Kaskatepe, B and Erganis, S and Sahin, EA and Gülmez, D and Akdağlı, SA and Ergin, Ç and San Keskin, O and Yardımci, H and Sivri, N and Altug, G and Kalkanci, A}, title = {Environmental Detection of Candidozyma (Candida) auris in Surface Waters of the Gediz Delta, a Critical Coastal Wetland in Türkiye: Expanding One Health Surveillance Perspective.}, journal = {Mycopathologia}, volume = {191}, number = {4}, pages = {}, pmid = {42470541}, issn = {1573-0832}, support = {124S746//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; }, mesh = {*Wetlands ; Temperature ; DNA, Fungal/genetics/isolation & purification ; *Candida auris/isolation & purification/genetics/classification ; Real-Time Polymerase Chain Reaction ; *Water Microbiology ; Hydrogen-Ion Concentration ; *Saccharomycetales/isolation & purification/genetics/classification ; *Candida/isolation & purification/classification/genetics ; }, abstract = {BACKGROUND: Candidozyma auris (syn. Candida auris) is an emerging multidrug-resistant yeast of growing clinical and environmental concern. Despite its increasing detection in healthcare settings worldwide, environmental evidence remains scarce. This study presents the first molecular detection of C. auris DNA in surface waters of Türkiye, within the Ramsar-protected Gediz Delta, as part of the national One Health Surveillance Framework.

METHODS: A total of 80 surface-water samples were collected from five wetland ecosystems Tuz Lake, Kulu Lake, Göksu Delta (Akgöl and Paradeniz Lagoons), Kızılırmak Delta, and Gediz Delta. Physicochemical parameters; temperature, pH, and salinity were recorded in situ using a multi parameter sensor. Environmental DNA was extracted from 2 L of 0.22 µm Sterivex-filtered water and analyzed via qPCR using C. auris-specific (CauF/CauR) and Candida-genus (CauRelF/CauRelR) primer sets. Yeast isolation was performed on CHROMagar™ Candida Plus, and identification was achieved by MALDI-TOF MS.

RESULTS: C. auris DNA was detected in one sample (1.25%), specifically from the Gediz Delta (Sample No. 5651, 38.523° N, 26.892° E), with Ct values 33.8-37.2 confirmed by sequencing. Broader Candida genus signals were observed in 24% of samples. Culture-based analyses yielded no viable C. auris, but 15 yeast isolates were identified, mainly Pichia kudriavzevii (Candida krusei), C. albicans, and Nakaseomyces glabratus (Candida glabrata).

CONCLUSION: The culture-negative yet qPCR-positive finding indicates that C. auris DNA likely persists in aquatic environments as non-viable or residual material. This finding provides early molecular evidence of environmental dissemination and underscores the need for viability assays, culture-based isolation, and metagenomic monitoring integrated within One Health surveillance programmes.}, } @article {pmid42462951, year = {2026}, author = {Jin, Y and Liu, J and Liu, Z and Yuan, Y and Cui, H and Dong, Z and Zhang, F and Lv, M and Hu, L and Zhang, L and Zhou, D and Yang, W}, title = {Linking oral microbiota to clinic air during ultrasonic scaling: Quantitative sequencing and CFD modeling reveal pathogenic aerosol emissions, infection risk, and control strategies.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128796}, doi = {10.1016/j.envpol.2026.128796}, pmid = {42462951}, issn = {1873-6424}, abstract = {Microbial aerosols from dental procedures pose a recognized yet unquantified airborne infection risk. During ultrasonic scaling, we performed multi-site sampling (saliva, air, surfaces) and combined metagenomics with quantitative 16S rRNA and ITS amplicon sequencing to profile viral, bacterial, and fungal communities. Using size-resolved aerosol sampling and absolute quantification, we determined the emission strength and size distribution of pathogenic bacterial aerosols (PBA), which were key inputs for computational fluid dynamics (CFD) simulations performed at ventilation velocities of 0.1, 0.2, and 0.4 m/s, corresponding to air exchange per hour (ACH) of 2.4, 4.7, and 9.4 h[-1], respectively. We first linked patient oral microbiota to clinic aerosols, identifying a shared core of 51 viral, 55 bacterial, and 23 fungal families, of which three bacterial families (Streptococcaceae, Pasteurellaceae, Nocardiaceae) were pathogenic. The emission strength of PBA was ∼3.06×10[3] copies/min, with 66.7% concentrated in the 2.1∼4.7 μm fraction, a size associated with higher deposition in the lower respiratory tract. CFD simulations, fed with real pathogen concentrations and aerodynamic size spectra, revealed that increasing ACH from 0.1 to 0.4 m/s reduced PBA suspension (-26.4%) and surface deposition (-12.7%) during scaling, lowering the inhalation infection risk (IIR) at the dentist's position by 80.8% and keeping overall IIR below 25%. After scaling, lower velocity favours particle removal, supporting a dynamic ventilation strategy (high during treatment, low afterwards). This integrated framework provides a direct scientific basis for infection control in dental operatories.}, } @article {pmid42463489, year = {2026}, author = {Gao, Z and Wu, J and Lucaci, AG and Ouyang, J and Wang, L and Ryon, KA and Elhaik, E and Probst, AJ and Rodó, X and Velavan, TP and Chasapi, A and Ouzounis, CA and Oliveira, M and Dias-Neto, E and Osuolale, O and Poulsen, M and Meleshko, D and Bhattacharyya, M and Ugalde, JA and Tull, A and Rubins, KH and Sierra, MA and Tierney, BT and Prithiviraj, B and Sharma, NK and Munteanu, V and Mangul, S and Kurt, KC and Ushio, M and Mazur-Panasiuk, N and Kopera, K and Marszałek, K and Kowalski, M and Toscan, RB and Branicki, W and Pyrć, K and Łabaj, PP and Subramanian, B and Frolova, A and Burkhart, JG and Deng, Y and Udekwu, KI and Schriml, LM and Hazrin-Chong, NH and Suzuki, H and Lee, PKH and Camargo, AP and Kyrpides, NC and Liu, D and Wang, LF and Mason, CE and Shi, T and , }, title = {Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42463489}, issn = {2041-1723}, support = {32370720//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Virome/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; RNA, Viral/genetics ; Cities ; Animals ; }, abstract = {RNA viruses represent an integral component of human-associated environments and human health. However, the ecology of environmental RNA viruses remains largely unexplored. Here, we analyzed 2922 metatranscriptomic samples collected from urban and surrounding environments-including human-dense settings (e.g., transit hubs, hospitals, banks), alongside peri-urban settings - across 102 cities in 31 countries and constructed the Urban & Peri-urban RNA Virus Atlas (UPVAtlas), comprising 54,945 RNA viruses, 77% of which had not been previously observed. Phylogenetic reconstruction based on RNA-dependent RNA polymerases from UPVAtlas greatly expanded the evolutionary diversity of RNA viruses, leading to the identification of two potential candidate phyla, one candidate class, and several unclassified clades. Host association analyses further revealed the ecological complexity of environmental RNA viruses, with the diversity of vertebrate-related and ESKAPE pathogen-related viruses underscoring the importance of continued monitoring of urban environments for tracking RNA viral prevalence and dynamics, with direct relevance to future public health.}, } @article {pmid42463504, year = {2026}, author = {Côrtes, MF and Luna-Muschi, A and Marchi, AP and Noguera, SLV and Hurtado, R and Espinoza, ES and Ferreira, NE and Da-Costa, AC and Berg, MG and Rodgers, MA and Cloherty, GA and Silveira, CGT and Paranhos-Baccalà, G and Kallas, EG and Mendes-Correa, MC and Costa, SF}, title = {Nasopharyngeal metagenomics of symptomatic healthcare workers provides insights into the respiratory microbiome and antimicrobial resistance.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-59198-z}, pmid = {42463504}, issn = {2045-2322}, abstract = {Respiratory infections represent a significant risk for healthcare workers (HCWs), particularly during viral outbreaks. This study applied metagenomic sequencing to characterize microbial communities and antimicrobial resistance (AMR) genes in nasopharyngeal swabs from HCWs presenting respiratory symptoms. Samples from 161 HCWs collected at a tertiary hospital in 2020-2021 were screened using FilmArray; negative samples were analyzed by metagenomic sequencing. After removal of human reads, sequences were taxonomically classified into viral, bacterial, and eukaryotic groups, and AMR genes were identified. On average, samples consisted of 5% viral reads, 89% bacterial, and 6% eukaryotic. Detected viruses included Enterovirus, human bocavirus(HBoV1), Alphaherpesvirus, and Coronavirus OC43, with one OC43 infection identified exclusively by metagenomic. Bacteria commonly associated with respiratory infections, such as Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis, were frequently observed. Fungi included Schizophyllum commune, Cryptococcus wingfieldii, Pneumocystis murina, and Cryptococcus neoformans. AMR analysis revealed that 65% of samples harbored at least one resistance gene, totaling 112 distinct genes; ermC was the most prevalent, detected in 28% of samples. Predominant classes included macrolide-lincosamide-streptogramin, beta-lactam, aminoglycoside, and tetracycline. These findings demonstrate the utility of metagenomic sequencing for comprehensive pathogen detection and AMR profiling, supporting improved infection control and clinical management in healthcare settings.}, } @article {pmid42463700, year = {2026}, author = {Mani, K and Palanisamy, V and Shrestha, B and Vice, Z and Paudyal, S and Chitlapilly Dass, S}, title = {Metagenomics-based surveillance identifies possible sources of mastitis-associated organisms in organic and conventional dairy farm environments.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00989-z}, pmid = {42463700}, issn = {2396-8370}, support = {2020-67017-30776//National Institute of Food and Agriculture/ ; }, abstract = {Mastitis is one of the most economically significant diseases of the dairy industry. Although farm environments are recognized reservoirs for mastitis pathogens, comprehensive metagenomic comparisons between organic and conventional systems remain limited. We compared the prevalence, diversity, and functional potential of mastitis-associated organisms in one organic and one conventional dairy farm in Texas using shotgun metagenomics. Of 180 samples collected from six environmental sites (teats, liners, parlor floor mats, feed areas, bedding sands, and water troughs), 126 were retained after quality-control exclusions. Taxonomic analysis revealed the prevalence of Pseudomonas fluorescens, Lactococcus garvieae, Escherichia coli, Citrobacter freundii, Enterococcus faecium, and Streptococcus parauberis. Alpha- and beta-diversity analyses indicated similar pathobiome structure between farm types, with niche-specific clustering observed for teat and liner samples. Functional annotation revealed comparable COG category distributions, with toxin-related genes representing the most abundant virulence-associated signatures, followed by lipopolysaccharide synthesis genes; adhesion and capsular polysaccharide genes were relatively more abundant on the organic farm. Metagenome-assembled genomes affiliated with key species confirmed genes related to toxin secretion, lipopolysaccharide biosynthesis, adhesion, and biofilm formation. Collectively, these farms harbored similar mastitis-associated reservoirs but differed in certain virulence-associated signatures, highlighting the need for environment-specific hygiene interventions.}, } @article {pmid42464133, year = {2026}, author = {Chen, Y and Wang, X and Si, Y and Zhang, F and Ding, K and Zhang, J and Wang, J and Zhou, L and Luo, X}, title = {Salt/alkali‑tolerant Streptomyces luteus TRM 45540 improves pepper growth and soil quality in acidic and alkaline soils.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-09509-3}, pmid = {42464133}, issn = {1471-2229}, support = {(Grant No. 32560008)//Study on Spatial Heterogeneity of Microbial Community Structure and Function in Tamarix Shrub Sand Dunes of the Tarim Basin/ ; (2025AB005),//Key Technology R&D and Demonstration of Saline-Alkali Tolerant Carbon-Based Slow-Release Functional Fertilizer/ ; (Grant No. 2025DA008)//Green Preparation of High-Efficiency Acaricidal Microbial Technical Concentrates and Development of Controlled-Release Synergistic Technologies"./ ; }, abstract = {This study evaluated the potential of the salt-alkali-tolerant actinobacterium Streptomyces luteus TRM 45540, isolated from Lop Nur saline-alkali soil in Xinjiang, to alleviate pH-related iron deficiency and promote pepper growth. We hypothesized that this strain could mobilize and compete for soil iron via siderophore production, thereby benefiting plants under variable-pH conditions. To test this hypothesis, we compared its effects with conventional iron fertilizers (EDDHA-Fe6, ferrous sulfate) and compound microbial fertilizer on pepper growth, soil physicochemical properties, and rhizosphere microbial communities in acidic (pH 5) and alkaline (pH 7.69) soils. TRM 45540 exhibited good stress tolerance, growing well at 3%-9% NaCl and pH 9-12. In both soil types, it significantly promoted pepper growth: fresh weight was increased by over 44% in acidic soil relative to the control, while root and stem lengths were elevated by 26%-91% in alkaline soil compared with conventional amendment groups. The strain increased the content of indigenous soluble iron in soil, raising soluble iron to 42 mg/kg[- 1] in acidic soil without exogenous iron addition, neutralized acidic soil toward neutral pH, increased total nitrogen to 6.5 g/kg[- 1], and enhanced phosphorus and potassium availability. Redundancy analysis identified pH and total iron as the dominant factors shaping microbial communities in acidic and alkaline soils, respectively. KEGG pathway enrichment revealed significant changes in organic pollutant degradation, nutrient metabolism, and stress response pathways following TRM 45540 inoculation. The strain enriched functional microorganisms related to siderophore secretion and nitrogen fixation, thereby improving soil microbial diversity and richness, while compound microbial fertilizer was associated with relatively lower microbial community activity. These findings demonstrate that S. luteus TRM 45540, with cross-pH adaptability and functional stability, enhances pepper growth and soil quality via synergistic effects of stress tolerance, nutrient activation (especially iron mobilization), and microbial community regulation. This strain provides a promising microbial inoculant for sustainable pepper production in variable-pH soils, especially saline-alkali soils.}, } @article {pmid42464224, year = {2026}, author = {Zhang, G and Wang, Y and Liu, S and Wu, X and Fu, H and Sun, D}, title = {Clinical randomized comparative study of Laifu Chengqi Decoction enema for treating postoperative peritonitis in children with complicated appendicitis.}, journal = {BMC pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12887-026-07329-w}, pmid = {42464224}, issn = {1471-2431}, support = {2025KJ061//Tianjin Municipal Education Commission Scientific Research Project/ ; }, abstract = {BACKGROUND: Laifu Chengqi Decoction (LF-CQD) is a traditional Chinese medicine enema rooted in classic heat-clearing and purgative formulas traditionally used to relieve abdominal distention, resolve stasis, and restore bowel motility. Its components (e.g., Laifuzi and Dahuang) provide plausible pro-motility and anti-inflammatory actions, supporting its culturally grounded use as a postoperative adjunct in pediatric perforated appendicitis. This study aimed to evaluate the clinical efficacy of LF-CQD enemas in the treatment of postoperative peritonitis in children.

METHODS: This prospective randomized controlled trial included 118 children with perforated appendicitis complicated by peritonitis. The LF-CQD group received LF-CQD retention enemas for 5 days, whereas the control group was administered saline enemas. The primary outcome was time to first passage of flatus (a core marker of gastrointestinal recovery). Key secondary outcomes included time to bowel sound resumption, time to oral intake, preoperative and postoperative day (POD) 3 and 7 inflammatory marker levels, complication rates at 6-month follow-up, antibiotic use, and length of hospital stay.

RESULTS: Gastrointestinal function recovery was significantly faster in the LF-CQD group than in the control group [bowel sound resumption (p < 0.001), flatus (p < 0.001), and oral intake (p < 0.001)]. On POD7, the LF-CQD group exhibited significantly lower inflammatory marker levels than the control group (C-reactive protein level: p < 0.001). Exploratory post-hoc analyses showed greater relative reductions (ΔCRP/ΔWBC) in the LFCQD group at all timepoints (all p < 0.05). Complication rates for intra-abdominal abscess (8.5% vs. 25.4%, p = 0.008) and adhesive intestinal obstruction (5.1% vs. 22%, p = 0.003) were reduced, and antibiotic use duration was shorter (p < 0.001).

CONCLUSIONS: LFCQD enema serves as a safe, well-tolerated adjuvant intervention for children with postoperative peritonitis secondary to complicated perforated appendicitis. It accelerates gastrointestinal function recovery and alleviates postoperative inflammation. However, being a single-center trial with a modest sample size, it yielded large treatment effects for intra-abdominal abscess, adhesive intestinal obstruction, and length of hospital stay; thus, these effect sizes warrant cautious interpretation and require validation in large-scale multicenter trials. Exploratory post hoc analyses also indicated reduced systemic inflammatory marker levels in the intervention group. We hypothesize that LFCQD may modulate inflammatory signaling cascades and promote gut microbiota homeostasis to drive these clinical improvements. However, as no direct assessment of these pathways or metagenomic profiling of the intestinal microbiome was performed during this trial, these mechanistic proposed mechanistic pathways remain speculative and unconfirmed. In conclusion, this study demonstrates clinical associations between LFCQD enema and improved postoperative outcomes, but does not establish definitive causal molecular mechanisms.

TRIAL REGISTRATION: International Traditional Medicine Clinical Trial Registry; ITMCTR2025001634. Retrospectively registered on July 24, 2025, which constitutes an methodological limitation of this trial. All primary and secondary outcomes, inclusion and exclusion criteria, and core study procedures were precisely predefined and finalized in 2019 at the study design stage, prior to the initiation of patient enrollment in January 2020. No post-hoc additions, deletions, or modifications to any trial outcomes were made after patient recruitment, data collection, or statistical analysis. The retrospective registration was merely delayed due to institutional administrative procedures for traditional Chinese medicine clinical trials, without any alteration to the originally designed trial endpoints. The updated Supplementary Material 1 provides a detailed item-by-item comparison between the registered protocol and manuscript-reported outcomes, confirming full consistency and integrity of all pre-specified endpoints.}, } @article {pmid42464266, year = {2026}, author = {He, C and Du, Y and Lloyd, KG and Vishnivetskaya, TA and Rivkina, EM and Jiang, H and Liang, R}, title = {Diversity and potential ecological roles of viruses in Pleistocene permafrost.}, journal = {BMC biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12915-026-02685-6}, pmid = {42464266}, issn = {1741-7007}, abstract = {BACKGROUND: Ancient permafrost, formed during past glacial periods, is widespread in Siberia and other Arctic regions. Even though these soils have remained below 0 °C over geological time periods, the widespread presence of bacteria and archaea in permafrost is well documented. However, the diversity of viruses in ancient permafrost of different geological ages and their potential ecological roles are still poorly understood.

RESULTS: We applied metagenomics to characterize viruses from Middle to Late Pleistocene permafrost sediments from Siberia. A total of 2697 viral operational taxonomic units (vOTUs) were recovered through metagenomic assembly and virus identification. Viral diversity in the Middle Pleistocene permafrost was much higher than that in the Late Pleistocene. The virus communities at different depths of the Middle Pleistocene permafrost showed great similarity to each other but were significantly different from those of the Late Pleistocene, with Azeredovirinae, Peduoviridae, and Fiersviridae being the predominant viruses in Pleistocene permafrost. The viruses were predicted to carry auxiliary metabolic genes potentially involved in cold adaptation and elemental (C and N) biogeochemical cycling in ancient permafrost. The virus-host prediction revealed that microorganisms such as bacteria and archaea are the main hosts and only a few eukaryotic hosts were identified.

CONCLUSIONS: Our results show that permafrost viral communities in Siberia exhibit remarkable diversity and may have played a significant ecological role in ancient permafrost over geological time. While the release of viruses from thawing deep permafrost could pose a relatively small risk to human health and environment, it could have significant impacts on the carbon cycle, potentially influencing climate change feedback in permafrost regions.}, } @article {pmid42464281, year = {2026}, author = {Yu, M and Xiao, Y and Liu, Y and Wang, Z and Zhou, H and Tang, Y}, title = {Sequential Talaromyces marneffei and Legionella pneumophila infections leading to the diagnosis of anti-interferon-γ autoantibody-associated immunodeficiency: a case report.}, journal = {BMC pulmonary medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12890-026-04455-0}, pmid = {42464281}, issn = {1471-2466}, support = {2024YFHZ0273//Science and Technology Department of Sichuan Province-International Science and Technology Innovation Cooperation Project/ ; }, abstract = {BACKGROUND: Opportunistic infections caused by uncommon intracellular pathogens can serve as important clues to underlying immune dysfunction.

CASE PRESENTATION: We report a 57-year-old male who presented with chronic cough, dyspnea, fever, and weight loss. Chest imaging revealed diffuse pulmonary infiltrates and mediastinal lymphadenopathy, mimicking tuberculosis or lymphoma. Despite empirical anti-tuberculosis and broad-spectrum antibiotic therapy, his condition deteriorated. Metagenomic next-generation sequencing (mNGS) and culture confirmed Talaromyces marneffei infection. During antifungal therapy, he developed Legionella pneumophila pneumonia-an unusual sequential infection that raised suspicion of an immune defect. Comprehensive immunological evaluation revealed anti-interferon-γ (anti-IFN-γ) autoantibodies, supporting the diagnosis of AIGA-associated immunodeficiency. The patient had also shown repeatedly indeterminate interferon-γ release assay (IGRA) results, retrospectively suggesting impairment of the IFN-γ pathway.

CONCLUSIONS: This case illustrates that recurrent or sequential infections with intracellular pathogens, particularly Talaromyces marneffei and Legionella pneumophila, should prompt evaluation for cell-mediated immunodeficiency such as AIGA syndrome. Early recognition may facilitate tailored antimicrobial therapy, immunological follow-up, and consideration of immunomodulatory treatment in selected patients.}, } @article {pmid42464402, year = {2026}, author = {Stiffler, AK and Varona, NS and Wallace, BA and Silveira, CB}, title = {Chemical prophage induction selectively removes Vibrio from a pelagic Sargassum-derived multispecies biofilm.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00925-4}, pmid = {42464402}, issn = {2524-6372}, support = {2023349872//National Science Foundation Graduate Research Fellowship Program/ ; 2023353157//National Science Foundation Graduate Research Fellowship Program/ ; 80NSSC23K0676/NASA/NASA/United States ; 2424579//National Science Foundation/ ; }, abstract = {BACKGROUND: Pelagic Sargassum has undergone significant range expansion and dramatic blooms in the Atlantic over the past 15 years. This alga's microbiome provides symbiotic functions that are believed to contribute to its ecological success. Recent research shows that Sargassum-associated bacteria are enriched in integrated prophages compared to the surrounding seawater and that these prophages are inducible by chemical and ultraviolet treatment.

RESULTS: Here, we investigated a Sargassum-derived in vitro multispecies biofilm encompassing the dominant heterotrophic microbial members associated with Sargassum to probe the impacts of prophage induction on the composition of Sargassum microbiomes. Induction was quantified by coverage-based virus-to-host ratios in chemically induced treatments with Mitomycin C and non-induced controls, and the community composition and metabolic profiles were analyzed after Mitomycin C treatment. Chemical induction led to a significant increase in abundance and virus-to-host ratio of viral genomes linked to Vibrio metagenome-assembled genomes. This was accompanied by altered biofilm community composition, with a reduction in Vibrio bacterial abundance that opened niche space for other biofilm members in the genera Pseudoalteromonas, Alteromonas, and Cobetia. The induced Vibrio-associated phages encoded genes involved in quorum sensing, biofilm formation, virulence, and host metabolism. Induction led to the depletion of 17 metabolic modules, including functions related to energy metabolism and nitrogen utilization.

CONCLUSION: Due to the high frequency of lysogeny in the Sargassum microbiome and the susceptibility of prophages to chemical and ultraviolet light induction, these results suggest that prophage integration and induction are mechanisms that contribute to structuring the Sargassum microbiome and its functional profiles, potentially aiding in microbiome flexibility in changing environmental contexts.}, } @article {pmid42464404, year = {2026}, author = {Eriksson, CE and Shipley, L and Clark, DA and Levi, T}, title = {Comparing Accuracy and Biases of DNA Metabarcoding, Hybridization Capture, and Metagenomic Sequencing for Quantifying Herbivore Diets.}, journal = {Molecular ecology resources}, volume = {26}, number = {5}, pages = {e70175}, doi = {10.1111/1755-0998.70175}, pmid = {42464404}, issn = {1755-0998}, support = {WNP00848//USDA National Institute of Food and Agriculture, McIntire-Stennis Project/ ; F23AF03162//Federal Aid in Wildlife Restoration/ ; 2317537//National Science Foundation/ ; }, mesh = {Animals ; *Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; *Herbivory ; *Diet/methods ; Deer/physiology ; Sequence Analysis, DNA/methods ; *Nucleic Acid Hybridization/methods ; Plants/genetics ; }, abstract = {DNA metabarcoding using relative read abundance (RRA) is commonly applied to estimate herbivore diet composition, yet its quantitative accuracy remains uncertain. We assessed taxonomic resolution and quantitative performance of RRA from DNA metabarcoding compared to metagenomic sequencing and hybridization capture, using deer scats from feeding trials and recreated diet samples using plant tissues. All methods recovered plant composition in recreated diets (R[2] = 0.59-0.82), indicating accurate scaling with biomass in the absence of digestion, with only minor bias from amplicon length in DNA metabarcoding. In contrast, RRA from scat samples performed poorly (R[2] < 0.01) across all methods largely due to differential plant digestibility. Correcting for digestibility, measured with acid detergent lignin and acid-insoluble ash, was strongly supported in mixed-effects models and improved prediction of dietary composition, although species-level variation remained. For metagenomic sequencing and hybridization capture, we also evaluated Relative Genome Coverage (RGC), a novel relative abundance metric quantifying the proportion of each plant's chloroplast genome covered by mapped reads, normalized for genome length. RGC further improved correlations in recreated diets (R[2] = 0.82-0.84) and, with hybridization capture, largely overcame digestibility-related biases in scat samples (R[2] = 0.57) without correction. When such corrections are infeasible, hybridization capture with uncorrected RGC may achieve higher quantitative accuracy in scat samples. Our results provide practical guidance for improving molecular herbivore diet analysis and highlight the importance of accounting for digestion-related biases.}, } @article {pmid42464944, year = {2026}, author = {Hazan, S and Bao, G and Goudzwaard, A and Ichim, T and Martin, L and Vidal, AC}, title = {Gut Microbiome Alterations in Cancer and Non-cancer Adults: A Cross-Sectional Metagenomic Study.}, journal = {Technology in cancer research & treatment}, volume = {25}, number = {}, pages = {15330338261470516}, doi = {10.1177/15330338261470516}, pmid = {42464944}, issn = {1533-0338}, mesh = {Humans ; Female ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; *Neoplasms/microbiology/pathology ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Adult ; Aged ; *Bacteria/classification/genetics ; Metagenome ; Retrospective Studies ; }, abstract = {IntroductionPrevious studies found associations between cancer and the gut microbiome. Thus, we aimed to investigate the gut microbiome composition in adults with and without cancer to try to identify specific microbes that may be associated with cancer in a cross-sectional, observational, and retrospective study.MethodsStool samples from sixty participants, n=20 controls, n=25 with aggressive cancer, and n=15 with non-aggressive cancer were analyzed using Metagenomic Next Generation Sequencing. Mann-Whitney U test tests were used to examine differences in the relative abundances of bacterial genera.ResultsCompared to controls, aggressive cancer patients had statistically significantly lower levels of gut Bifidobacterium, Faecalibacterium, and Collinsella, (all p≤0.05), while they had higher levels of gut Bacteroides (p=0.015). Non-aggressive cancer patients had lower levels of gut Bifidobacterium compared to controls, an association that was approaching statistical significance (p=0.054).ConclusionAggressive-cancer patients showed significantly altered levels of key gut microbes compared to controls. These are preliminary associations, and thus further larger studies are needed to confirm these findings.}, } @article {pmid42465056, year = {2026}, author = {Li, Q and Chen, M and Lu, Y and Xu, C and Zheng, Y and Zeng, Z and Xu, D and Qin, W and Zhang, Y}, title = {Close spatial and metabolic association between heterotrophic and ammonia-oxidizing marine Nitrososphaerota.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag173}, pmid = {42465056}, issn = {2730-6151}, abstract = {Following the ubiquitous autotrophic ammonia-oxidizing archaea (AOA), heterotrophic representatives of the marine Nitrososphaerota (HMN) form the second most abundant group within this archaeal phylum. However, their eco-evolutionary strategies remain poorly understood. Previous studies have reported a consistent co-occurrence of HMN with marine AOA (MAOA), prompting a detailed investigation into their potential interaction. Through large-scale (meta)genomic and metatranscriptomic analyses, we reveal that HMN possess ultra-streamlined genomes and globally co-occur with marine AOA. The absence of most B vitamin biosynthesis pathways, incomplete citrate cycle and glycolysis, along with the essential requirement for exogenous amino acids, suggest their potential metabolic dependency on AOA. Meanwhile, catalyzed reporter deposition fluorescence in situ hybridization supports a close physical association between HMN and AOA. The nearly synchronous origins of HMN and AOA after oxygen rise, coupled with HMN's dispersive microhabitats (evidenced by dense, shallow subclades) and extensive horizontal gene transfer between these groups, further support their close relationship-although HMN likely acquired heterotrophic capabilities from bacteria. This study reveals a previously unrecognized association between HMN and AOA, implying a tight coupling between autotrophic and heterotrophic processes in deep-sea habitats.}, } @article {pmid42465060, year = {2026}, author = {Koike, K and Smith, GJ and Okuda, N and Konno, R and Watanabe, S and Kusunoki, Y and Kawakami, S and van Alen, TA and van Kessel, MAHJ and Yamamoto-Ikemoto, R and Lücker, S and Matsuura, N}, title = {Copper availability controls niche differentiation between comammox Nitrospira and ammonia-oxidizing bacteria.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag135}, pmid = {42465060}, issn = {2730-6151}, abstract = {The biological oxidation of ammonia, the first step of nitrification, is central to biological water purification processes for nitrogen removal. For drinking water treatment, particularly sourced from groundwater, low concentrations of available copper often limit the efficiency of nitrification. Copper dosing both enhances nitrification and affects the composition of the nitrifying microbial community. The mechanisms underlying the effect of copper on nitrifying community composition, ammonia oxidation, and subsequent nitrogen removal processes remain unknown. The objective of this study was to confirm the effects of copper availability on the relative abundance of complete (comammox) and canonical ammonia-oxidizing bacteria (AOB) in nitrifying communities within the drinking water treatment plant and to determine differences in their copper transport mechanisms. Comparative metagenomic analysis revealed that, unlike most AOB, many comammox Nitrospira encode PcoB/CopB-type high-affinity copper uptake systems, indicating that they are more competitive in low-copper environments. This niche adaptation was confirmed in laboratory-scale bioreactors, which showed that comammox Nitrospira became dominant under copper-limited conditions, while AOB dominated at high copper concentrations. Furthermore, specific detection of comammox amoA mRNA by catalyzed reporter deposition-fluorescent in situ hybridization confirmed that the transcriptional activity of comammox Nitrospira was higher compared to AOB under copper limitation. Thus, these results suggest that copper availability may play an important role in shaping the dominant ammonia-oxidizing bacterial guild, with potential implications for engineered water treatment processes.}, } @article {pmid42465064, year = {2026}, author = {Zhao, S and Bos, RP and Nakajima, R}, title = {Comparative functional profiles of microbial communities on drifting microplastics and volcanic pumice.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag158}, pmid = {42465064}, issn = {2730-6151}, abstract = {Plastics have been shown in incubation experiments to select for distinct microbial communities from biogenic and inanimate controls, with successional shifts over time. However, few field studies have directly compared microbial communities on free-drifting plastic debris and non-plastic particles. Using shotgun metagenomics, we analyzed the microbial communities adhered to marine microplastics and co-drifting volcanic pumice as a time-tracked control to investigate differences in metabolic potential. Overall, the mature microbial communities on neuston-net collected microplastics and pumice exhibited broad functional and taxonomic similarity, providing suggestive evidence of function convergence. Interestingly, plastic hydrolysis genes, and putative hydrocarbon-degrading bacteria were scarce on both substrates, whereas β-glucan degradation genes were abundant, indicating potential utilization of biofilm-associated carbon sources. Nevertheless, pumice biofilms exhibited substrate-associated enrichment of genes linking to biofilm formation, quorum sensing, nitrogen and phosphonate metabolism, suggesting expanded genomic versatility. Considering the increasing input of anthropogenic and natural inanimate particles may act as environmental perturbations, potentially shaping microbial succession and metabolic potential on floating surfaces. Our findings provide insight into the genomic potential of particle-associated assemblages that stay afloat for months to years, and their metabolic responses to both natural and anthropogenic perturbations.}, } @article {pmid42465072, year = {2026}, author = {Li, S and Zeng, H and Wan, X and Chen, Z and Nong, X and Peng, L and Li, Q and Wang, Y}, title = {Characteristics in the uterine cavity microbiota of infertile women with hydrosalpinx or endometrial polyps revealed by shotgun metagenomics.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1825869}, pmid = {42465072}, issn = {2296-858X}, abstract = {Infertility is a global public health issue, and a favorable endometrial environment is essential for successful assisted reproductive treatment. Endometrial polyps (EM) and hydrosalpinx (HD) are common gynecological disorders impairing the intrauterine milieu, but their impacts on uterine cavity microbiota remain unclear. This study enrolled 75 participants [32 fertile controls (C), 32 EM patients, 11 HD patients] to characterize their uterine cavity profiles using shotgun metagenomic sequencing. The C group showed significantly higher microbial alpha diversity than the two patient groups, with no significant difference between EM and HD groups. At the species level, EM group exhibited marked dysbiosis, characterized by elevated pathogenic bacteria, particularly Streptococcus and Streptococcus pneumoniae. HD featured a marked reduction in overall microbial load, decreased absolute abundance of core beneficial bacteria, and a relative increase in Streptococcus and Streptococcus pneumoniae. This study identifies distinct endometrial microbial profiles for EM and HD, providing novel insights into microbiota-mediated mechanisms of infertility. These subtype-specific signatures support the endometrial microbiota as a potential biomarker for infertility, offering clinical targets for antibiotic selection and therapeutic evaluation.}, } @article {pmid42465457, year = {2026}, author = {Maier, J and Deshmukh, N and Kleiner, M}, title = {High throughput chromatographic ultra-purification of virus-like particles for downstream viromics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.07.09.737491}, pmid = {42465457}, issn = {2692-8205}, abstract = {Virus-like particles (VLPs) are an abundant component of microbiomes with critical ecological roles such as population control through viral predation and horizontal gene transfer. Studying the collection of viruses in microbiomes (the virome) through metagenomics has provided important insights into the composition and functions of VLPs in different environments. However, the current gold-standard method for VLP purification, CsCl density gradient ultracentrifugation (CsCl), is low throughput, time consuming and suffers from biases which limits the ability to study viromes in larger sample sets and can interfere with data interpretation. Here we present an anion exchange (AEX) chromatography-based approach for the purification of VLPs from microbiome samples that allows for significant increases in throughput and reproducibility while achieving VLP purity levels similar to or higher than CsCl. We used microbiome samples of known composition to first establish and evaluate the AEX approaches and compare them to CsCl. We implemented the AEX approach both for fast performance liquid chromatography (FPLC) and in multi-well plates. We compared the VLPs purified with CsCl and AEX using shotgun metagenomic sequencing and found that AEX performs similarly to or better than CsCl for purification of VLPs. AEX purified VLP-fractions captured significantly more viral DNA compared to CsCl. We also found that both AEX and CsCl were capable of capturing viruses present at extremely low relative abundances (<0.001%). Additionally, we found that DNase digestion and CsCl may bias against filamentous phage morphologies. Finally, we purified VLPs from conventional murine feces using AEX and CsCl. AEX purified murine fecal VLPs had a much higher viral DNA content (85%) than CsCl (41%). While there were some differences in viral contigs assembled from AEX and CsCl VLP metagenomes, these method unique viral contigs made up only small proportions (<8%) of the relative abundance in the VLP metagenomes. AEX, particularly in the multi-well format, enables the ultrapurification of VLPs from tens to hundreds of samples in a single day thus facilitating virome studies with the large sample numbers needed for translational and clinical research.}, } @article {pmid42465472, year = {2026}, author = {Deka, N and Nawrocki, EM and Brauer, AL and Chakraborty, S and Cooper, VS and Armbruster, CE}, title = {Optimized Urine Metagenomic Methods Reveal Longitudinal Microbial Community Dynamics and Predictors of Transition from Asymptomatic Colonization to CAUTI.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.07.06.736792}, pmid = {42465472}, issn = {2692-8205}, abstract = {BACKGROUND: Urinary tract infections (UTIs) rank among the most common infections globally, with many linked to indwelling urinary catheters. Our prior culture-based longitudinal evaluation of long-term catheterized nursing home residents revealed persistent asymptomatic colonization by pathogens and demonstrated that CAUTI onset was not necessarily due to new pathogen acquisition. In this study, we optimized metagenomics methods to examine the ecological structure underlying persistent colonization and the transition to infection.

RESULTS: We present a comprehensive longitudinal metagenomic analysis of catheterized urine specimens, revealing colonization dynamics of 69 microbial species across 198 samples from 9 individuals. Descriptive ecological metrics were combined with Bayesian mixed-effects models that accounted for repeated within-participant sampling to identify clusters of co-occurring species, determine the impact of perturbations such as antibiotic exposure and catheter changes on community structure, and identify taxa predictive of infection sign and symptom onset. Longitudinal specimens clustered into three main ecological phenotypes: 1) moderate diversity, unstable communities (3 participants); 2) high diversity, stable communities that resisted disruption even after multiple catheter changes (3 participants); and 3) low diversity, pathogen-dominated communities (3 participants). Catheter changes alone did not significantly disrupt community composition, while antibiotic exposures induced major shifts often followed by re-colonization with the same genera within subsequent weeks. Six clusters of species were identified for which relative abundances correlated across perturbations to the microbial community, including a mutually exclusive Enterobacterales cluster and fastidious-anaerobe group cluster. 24 species were found to correlate with onset of signs and symptoms of infection, 11 of which were missed by standard urine culture.

CONCLUSIONS: The catheterized urinary tract represents a novel ecosystem that is resilient to disruption by catheter changes but susceptible to antibiotic perturbation. Antibiotic exposure did deplete all species associated with signs and symptoms but also depleted potentially benign microbes. Our findings have direct implications for catheter management protocols and antibiotic stewardship in long-term catheterized patients. Prospective evaluation using this framework in a larger cohort can help translate these ecological insights into clinical decision-making tools.}, } @article {pmid42465527, year = {2026}, author = {Vega Brizneda, M and Lum, J and Wang, H and Yetmar, ZA}, title = {Pulmonary Nocardiosis Diagnosed by Plasma Metagenomic Next-Generation Sequencing in a Patient With Recurrent Febrile Neutropenia.}, journal = {Case reports in infectious diseases}, volume = {2026}, number = {}, pages = {2832247}, pmid = {42465527}, issn = {2090-6625}, abstract = {BACKGROUND: Nocardiosis disproportionately affects immunocompromised hosts. Early identification of Nocardia infections is critical as delays can lead to worse outcomes. Species such as N. farcinica are associated with increased risk of dissemination and resistance. Diagnosis of opportunistic infections in immunocompromised populations relies on culture, antigen, or serologic methods that often have limited sensitivity or specificity. Plasma microbial cell-free DNA metagenomic next-generation sequencing (mNGS) offers a noninvasive approach for early diagnosis of opportunistic infections.

CASE PRESENTATION: We report a case of pulmonary nocardiosis in an 87-year-old man with myelodysplastic syndrome and prolonged neutropenia diagnosed by plasma mNGS. He had been hospitalized multiple times with recurrent febrile neutropenia and respiratory symptoms. Standard noninvasive microbiologic workup was unrevealing, but lower respiratory specimens could not be readily obtained. Due to elevated risk of complications from invasive testing, plasma mNGS was used as a complementary tool and identified N. farcinica. Anti-Nocardia therapy was initiated, and his fevers resolved.

CONCLUSION: mNGS is an emerging diagnostic tool that may identify Nocardia species from clinical specimens with a faster turnaround time than culture and enables rapid species identification. Although culture is still recommended for susceptibility testing, mNGS may expedite diagnosis in particular situations. This case supports the role of plasma mNGS as a complementary tool in the evaluation of febrile neutropenia and highlights its diagnostic potential.}, } @article {pmid42465693, year = {2026}, author = {Vaher, K and Kenny, A and Lusarreta Parga, P and Jiménez-Sánchez, L and Turner, H and Smikle, R and Corrigan, A and Cruickshank, H and Rudnicka, M and Fletcher-Watson, S and Bogaert, D and Boardman, JP}, title = {From microbes to milestones: Gut bacterial abundances and functional pathways associate with neurodevelopment following preterm birth.}, journal = {Gut microbiology}, volume = {2}, number = {}, pages = {None}, pmid = {42465693}, issn = {3051-1720}, abstract = {The early life gut microbiome has been identified as a potential driver of neurocognitive development. Evidence for this relationship in preterm children, who are at increased risk of both gut microbiome disruptions and neurodevelopmental impairment, is scarce. In a sample of 73 very preterm infants drawn from a prospective birth cohort, we assessed associations between the neonatal gut microbiome and neurodevelopmental outcomes at 9 months and 2 years. The gut microbiome taxonomic and functional profiles were obtained from stool samples collected prior to NICU discharge using shotgun metagenomics. Neurodevelopment was assessed using a battery of outcome measures. We took a consensus-based analytic approach, applying several different methods to investigate microbiome-outcome relationships and focussing on results which were consistently significant across methods. We found the most robust evidence for associations between the abundances of several gut bacterial species and measures related to autistic traits (e.g. Klebsiella spp.), socio-emotional development, including temperament (e.g. Enterobacter cloacae complex, Veillonella parvula), and executive functioning (Clostridium perfringens). The abundances of functional modules involved in gut-brain signalling, particularly those involved in histamine and quinolinic acid metabolism, were associated with outcome measures related to executive functioning and cognitive-behavioural flexibility. This study provides evidence that the neonatal gut microbiome composition may affect longer-term neurodevelopmental profiles following preterm birth, particularly those related to socio-emotional development, autistic traits and executive functioning.}, } @article {pmid42465842, year = {2026}, author = {Sun, Y and Yang, S and Wang, M and Xu, H and Wang, S}, title = {Predictors for identifying autoimmune encephalitis in pediatric patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1827367}, pmid = {42465842}, issn = {2235-2988}, mesh = {Humans ; Female ; Child ; *Encephalitis/diagnosis/cerebrospinal fluid/immunology ; Retrospective Studies ; Child, Preschool ; Male ; Risk Factors ; ROC Curve ; *Hashimoto Disease/diagnosis/cerebrospinal fluid ; Infant ; Nomograms ; Adolescent ; }, abstract = {OBJECTIVES: This study aimed to identify the independent predictors and develop a predictive model for autoimmune encephalitis (AE) in pediatric populations.

METHODS: This retrospective study comprised 88 pediatric patients with encephalitis (37 AE cases and 51 non- AE cases) at Children's Hospital Affiliated to Shandong University between May 2020 and April 2025. Lasso regression analysis, univariate and multivariate logistic analysis was used to identify autoimmune encephalitis associated risk factors. The nomogram visualized the results. Receiver operating characteristic (ROC) curves, calibration plots, Brier scoring and decision curve analysis (DCA) were used to evaluate the diagnostic model.

RESULTS: 16 clinical variables significantly differed between the autoimmune encephalitis and non-autoimmune encephalitis groups. Lasso regression analysis, univariate and multivariate logistic analysis identified four significant independent predictors: age (OR: 1.44; 95% CI: 1.09-1.91; P = 0.010), proteins in the cerebrospinal fluid/100(C.Protein.100) (OR: 0.80; 95% CI: 0.65-1.00; P = 0.049), chloride in the cerebrospinal fluid(C. Chloride) (OR: 1.38; 95% CI: 1.00-1.92; P = 0.050), and spontaneous remission (OR: 21.14; 95% CI: 3.17-141.17; P = 0.002) were risk factors for autoimmune encephalitis. The predictive model demonstrated excellent discrimination (AUC 0.976, 95% CI 0.947-1.000) and calibration (Hosmer-Lemeshow p = 0.886, R²=0.9796, Brier score 0.052).

CONCLUSIONS: This study established and validated a high-performance predictive model incorporating four clinically accessible parameters for the diagnosis of pediatric autoimmune encephalitis.}, } @article {pmid42465845, year = {2026}, author = {Luo, L and Zhan, J and Wang, Z and Du, X and Li, N}, title = {Application of metagenomic next-generation sequencing in HIV-negative hematogenous disseminated tuberculosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1851741}, pmid = {42465845}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Male ; Female ; *Metagenomics/methods ; Adult ; Middle Aged ; C-Reactive Protein/analysis ; *Mycobacterium tuberculosis/genetics/isolation & purification ; Procalcitonin/blood ; Tuberculosis, Extrapulmonary ; Fibrin Fibrinogen Degradation Products/analysis ; }, abstract = {BACKGROUND: Hematogenous disseminated tuberculosis (Hematogenous disseminated tuberculosis, HDTB) is a rare, critical form of tuberculosis with a high case fatality ratio and is uncommon in HIV-negative patients. Early recognition of this disease is difficult, and limitations of traditional testing methods often lead to delayed diagnosis. This study aims to investigate the value of metagenomic Next-Generation Sequencing (metagenomic Next-Generation Sequencing, mNGS), as a promising tool, in the diagnosis of hematogenous disseminated tuberculosis in HIV-negative (Human Immunodeficiency Virus, HIV) patients.

METHODS: A retrospective analysis was conducted of the clinical data of 10 HIV-negative patients with hematogenous disseminated tuberculosis confirmed by mNGS.

RESULTS: All patients had pre-existing diseases that could lead to impaired immune function. Common symptoms included hyperpyrexia, cough, and dyspnea, and 6 patients developed respiratory failure. C-reactive protein (C-reactive protein, CRP) and procalcitonin (procalcitonin, PCT) levels were both elevated, and PCT was markedly elevated in more than half of the patients, using 0.5 ng/mL as the cutoff value. Most patients had markedly elevated D-dimer levels accompanied by thrombotic events, including 3 patients with concomitant pulmonary embolism. Chest imaging showed patchy pulmonary opacities, and 2 patients had atypical bilateral pleural effusion; these nonspecific findings were easily confused with those of other diseases. Blood mNGS detected Mycobacterium tuberculosis within 2 to 3 days. According to the presence or absence of concomitant pulmonary tuberculosis, the patients were divided into the pulmonary tuberculosis subgroup (pulmonary tuberculosis subgroup, PTB) and the non-pulmonary tuberculosis subgroup (non-pulmonary tuberculosis subgroup, non-PTB). The oxygenation index was significantly lower in the pulmonary tuberculosis subgroup than in the non-pulmonary tuberculosis subgroup (P = 0.037). All cases of pulmonary embolism occurred in the pulmonary tuberculosis subgroup, but the difference was not statistically significant.

CONCLUSIONS: HIV-negative patients with hematogenously disseminated tuberculosis have atypical clinical manifestations and are prone to incorrect diagnosis. The application of mNGS helps shorten diagnostic delays and accelerate disease control, providing an effective supplementary diagnostic pathway when conventional testing methods cannot identify the pathogen.}, } @article {pmid42466125, year = {2026}, author = {Li, H and Gao, H and Tian, J and Wang, X and Jiang, R and Chen, T and Chen, H and Yang, Y and Zhu, C}, title = {tsAMP: a strain-level antimicrobial peptide identification framework based on large language models and pathogen genomic variation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1842380}, pmid = {42466125}, issn = {1664-302X}, abstract = {INTRODUCTION: Facing the global threat of multidrug-resistant bacteria, antimicrobial peptides (AMPs) represent a promising alternative to conventional antibiotics.

METHODS: To improve computational AMP identification and accuracy of strain-level MIC prediction, we developed tsAMP, a comprehensive framework integrating the ESM-1v protein language model with multidimensional feature extraction. The model was trained on AMP and metagenome-derived non-AMP sequences.

RESULTS: tsAMP achieved an F1-score of 0.958 for AMP identification, outperforming state-of-the-art tools. For bacterial inhibition prediction, tsAMP consistently maintained F1-scores above 0.8 across 33 pathogenic species. In strain-specific MIC prediction, it attained high performance (MSE = 0.214, R [2] = 0.634) for 10 bacterial species' strains. To assess predictive reliability, the model was benchmarked against published experimentally determined MIC values for AMPs targeting Micrococcus luteus, yielding low prediction error (MSE = 0.1489) and strong ranking consistency (NDCG = 0.791). Computational benchmarking against published relative MIC data for diverse E. coli strains further demonstrated the model's ranking accuracy (NDCG > 0.85) and consistent strain-level differentiation. Applied to the Mgnify_genome database, tsAMP identified 8,277 putative AMP candidates in silico and revealed distinct predicted antimicrobial activity patterns across pathogens.

DISCUSSION: tsAMP provides a computational framework to facilitate the identification of AMP candidates and support prioritization for downstream experimental characterization. The code is available on GitHub at https://github.com/YangLab-BUPT/tsAMP.}, } @article {pmid42466130, year = {2026}, author = {Kumar, V and Ahmad, F and Rai, A and Kushwaha, A and Parmar, K and Singh, R and Tomar, A and Kumar, C}, title = {Multi-omics and synthetic microbial ecology for engineering climate-resilient phytobiomes in cold-arid agroecosystems: current advances and future perspectives.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1876810}, pmid = {42466130}, issn = {1664-302X}, abstract = {Extreme environmental stressors, including freezing temperatures, strong ultraviolet radiation, and nutrient scarcity, pose a serious threat to global food security in high-altitude cold-arid agroecosystems. Ecological stability depends on the phytobiome, which is made up of plant hosts, their microbiomes, and the edaphic environment. Although plant-associated microbiomes are important in providing stress tolerance, existing management strategies predominantly employ descriptive single-strain inoculants, which often fail under open field conditions due to competitive exclusion and environmental drift. The review summarizes recent mechanistic insights into how psychrotolerant microorganisms modify host physiology to alleviate low-temperature stress. We examine the biophysical and biochemical processes involved, with a particular emphasis on the microbial impact on the host plant's internal ICE1-CBF-COR transcriptional cascade and redox homeostasis, the role of biofilm-mediated extracellular polymeric substances (EPS) in root-zone thermal buffering, and the kinetic inhibition of ice crystallization by antifreeze proteins. Furthermore, we evaluate how genome-scale metabolic modeling can be combined with sophisticated integrated multi-omics approaches, particularly metagenomics, metatranscriptomics, and metabolomics, to create structurally stable synthetic microbial communities (SynComs), going beyond traditional isolation methods. Lastly, we discuss how regional microbial biobanks and ecological network modeling can maximize consortia persistence, addressing the translational obstacles that prevent laboratory-scale efficacy from reproducing in the field. This synthesis presents a methodical approach for creating robust phytobiomes in vulnerable mountain agroecosystems by moving the emphasis from descriptive cataloging to predictable, function-driven synthetic ecology.}, } @article {pmid42466390, year = {2026}, author = {Buro, AW and Gomez, MF and Kim, Y and Ward, NP and Umbarger, M and Ma, L and Vala, A and Hogue, S and Silva, WV and Bailey, A and Pierce, CM and Kim, Y and DeNicola, GM and Byrd, DA and Robinson, LA}, title = {Metagenomic and Metabolomic Correlates of Immunotherapy Response in Non-Small Cell Lung Cancer.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-10107631/v1}, pmid = {42466390}, issn = {2693-5015}, abstract = {Background The gut microbiome may influence cancer treatment response, perhaps by immune system interactions, but studies are limited among non-small cell lung cancer (NSCLC) patients. We investigated associations of the pre-treatment gut microbiome and serum metabolome/lipidome with immune checkpoint inhibitor (ICI) response among patients with stage III-IV NSCLC. Methods We conducted an observational cohort study with fecal and blood collection among 66 patients with stage III-IV NSCLC undergoing ICI therapy, using an updated definition of clinical benefit. Fecal whole genome sequencing, plasma untargeted metabolomics, and serum lipidomics were conducted using liquid chromatography mass spectrometry. Multivariable logistic regression estimated associations of alpha/beta diversity, microbial abundance, metabolites, and lipids with clinical benefit. Microbial taxa, metabolites, lipids, and significant lipids correlations were examined. Results Microbiome composition (beta diversity) differed between participants with and without clinical benefit (P = 0.03). Those with higher relative abundance of Bifidobacterium were less likely (OR per 1-SD = 0.51, 95%CI = 0.25-0.92, P = 0.04) to have clinical benefit. Those with higher Ruminococcus prevalence were more likely (OR = 7.00, 95%CI = 1.80-34.47, P = 0.01) to have clinical benefit. Clinical benefit participants had higher serum concentration of 4-Imidazoleacetate (OR = 6.34, 95%CI = 2.36-22.29, P = 0.001), 6-Bromotryptophan (OR = 3.84, 95%CI = 1.80-10.17, P = 0.002), and lyso-phosphatidylcholines (OR = 4.52, 95%CI = 1.59-17.19, P = 0.01) compared to no clinical benefit, though these findings were not statistically significant after multiple corrections. Conclusions This hypothesis-generating study found Ruminococcus was positively, and Bifidobacterium inversely, associated with ICI response among NSCLC patients. The gut microbiome and related metabolites/lipids were found to be associated with ICI clinical benefit among NSCLC patients. Larger, diverse longitudinal studies are needed to clarify the associations of the microbiome and related metabolites with ICI response among NSCLC patients.}, } @article {pmid42466699, year = {2026}, author = {Touati, A and Boufahja, F and Ben Hamadi, N and Touaitia, R and Idres, T}, title = {Artificial Intelligence Applications in Antimicrobial Resistance: Comprehensive Review of Predictive Models, Diagnostic Innovations, and Clinical Integration.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {}, number = {}, pages = {10766294261467803}, doi = {10.1177/10766294261467803}, pmid = {42466699}, issn = {1931-8448}, abstract = {Antimicrobial resistance (AMR) represents a critical global health crisis, driving increased mortality, treatment failure, and economic burden. Artificial intelligence (AI) offers transformative potential to counter this threat by enhancing detection, diagnostics, and therapeutic precision. This narrative review synthesizes recent advances in AI-based approaches for AMR prediction, antimicrobial discovery, and clinical decision support, drawing on representative peer-reviewed studies published between January 1, 2015, and April 24, 2026. Models such as Deeparg-LS, XGBoost, and vision transformers achieved remarkable predictive accuracy using genomic, spectroscopic, and clinical data (AUC > 0.90; sensitivity/specificity >95%). AI-driven clinical decision support systems reduced antibiotic mismatches by up to 67%, while generative algorithms accelerated antimicrobial peptide discovery with 76% validation success. Deep learning frameworks improved metagenomic resistance profiling, and microscopy-based diagnostics shortened antimicrobial susceptibility testing by 50-70%. However, major challenges persist, including dataset heterogeneity, computational intensity, limited model transferability, and ethical concerns related to data privacy, bias, and interpretability. Emerging strategies such as explainable AI and federated learning show promise in addressing these issues. Overall, AI stands as a pivotal enabler in the fight against AMR, with future progress hinging on interdisciplinary collaboration, standardized validation, and responsible integration into clinical practice.}, } @article {pmid42466871, year = {2026}, author = {Jin, C and Chen, Q and Liu, X and Liu, H and Wang, Y}, title = {The functional structure of foxtail millet rhizoplane microbiome and its association with yield.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0070726}, doi = {10.1128/spectrum.00707-26}, pmid = {42466871}, issn = {2165-0497}, abstract = {UNLABELLED: Root-associated microbial communities profoundly influence plant growth and productivity. Although the rhizosphere microbiome has been extensively studied, the functional distinctiveness and host-specific role of the closely adhering rhizoplane microbiota remain unclear. In this study, we performed deep metagenomic sequencing of both the rhizosphere and rhizoplane microbiomes in foxtail millet (Setaria italica). We constructed a comprehensive non-redundant gene catalog, reconstructed 595 metagenome-assembled genomes (MAGs), and analyzed the co-occurrence networks. Our results revealed that the rhizoplane sustains a core microbial network with greater complexity and connectivity than rhizospheres. Metabolically, the rhizoplane microbiome is enriched in the functions underlying host adaptation, including ammonium production and polysaccharide decomposition. Our results showed that the associations between microbial features (taxonomic and functional) and yield were significantly stronger in the rhizoplane than in the rhizosphere. We identified 22 yield-positive MAGs, primarily from Bacillales, harboring genes for plant growth-promoting traits, such as nutrient solubilization and phytohormone synthesis. Collectively, our findings illustrate that the rhizoplane is not only a subset of the rhizosphere but also a critical host-microbe interface and functional hotspot where specialized microbial processes are directly coordinated to enhance plant performance and yield.

IMPORTANCE: Plant roots selectively recruit diverse and beneficial microorganisms from the surrounding soil, assembling a distinctive rhizosphere microbiome. Substantial research, primarily utilizing amplicon sequencing, has elucidated the taxonomic composition of these rhizosphere communities across a wide range of plant species. The functional architecture, assembly processes, and coexistence mechanisms of the rhizoplane microbiome remain poorly understood, and their link to host plant traits is unclear. We elucidate the taxonomic and functional structural disparities between the rhizosphere and rhizoplane microbiomes, thereby clarifying the composition and functional roles of the rhizoplane microbiome, and further examine the association between the rhizoplane microbiome and millet yield. A deeper understanding of root-associated microbial communities may inform the development of effective agricultural probiotics, thereby enhancing sustainable farming practices. Additionally, the candidate biomarkers identified in this work offer potential targets for improving cultivation practices and supporting the long-term agricultural sustainability of foxtail millet.}, } @article {pmid42466883, year = {2026}, author = {Han, H and Qian, Q and Wu, W and Yang, J and Zhou, J and Sun, W}, title = {Diabetes-associated Parvimonas enrichment and altered lung microbiota profiles in lower respiratory tract infection: an analysis of 632 metagenomes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0404825}, doi = {10.1128/spectrum.04048-25}, pmid = {42466883}, issn = {2165-0497}, abstract = {The homeostasis of pulmonary microbiota is crucial in maintaining human health and modulating disease progression. The stability of pulmonary microbial flora may be associated with diabetes, yet the specific alterations remain poorly characterized. This retrospective observational study aims to analyze the profiles in pulmonary microbiota between individuals with and without diabetes, using metagenomic next-generation sequencing (mNGS). A total of 632 patients were sequentially enrolled, including 77 patients with both pneumonia and diabetes, 46 patients without either pneumonia or diabetes, 499 patients with pneumonia but without diabetes, and 10 diabetic patients without pneumonia. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS (DNA). The lung microbiota of diabetic individuals significantly differs from that of non-diabetic individuals in the non-lower respiratory tract infection (non-LRTI) cohort. Parvimonas was more abundant in the diabetic group. Compared to non-diabetic patients with LRTI, those with diabetes and LRTI showed an increased relative abundance of Parvimonas, but decreased relative abundances of Prevotella and Malassezia. Our analysis revealed a negative correlation between Parvimonas and Malassezia, alongside a positive association of Parvimonas with the expression of antimicrobial resistance genes ICR-Mc and RbpA. This suggests a potential association between Parvimonas enrichment and microbial dysbiosis during infection, although the underlying host-microbe interactions require further validation. Interestingly, Parvimonas abundance showed no significant association with HbA1c levels. Our findings suggest that Parvimonas enrichment is associated with diabetes-related alterations in lower respiratory tract microbiota. Whether microbiota-associated alterations represent clinically actionable targets in diabetic patients with pulmonary infections remains to be determined in prospective and interventional studies.IMPORTANCEThis study reveals significant differences in lung microbiota between diabetic and non-diabetic individuals. Parvimonas was enriched in the diabetic lung, and its abundance correlated with the expression of antimicrobial resistance genes, such as ICR-Mc and RbpA. Surprisingly, microbial dysbiosis was independent of HbA1c levels, indicating that mechanisms other than glycemic control contribute to infection progression. This study suggests that Parvimonas enrichment may be a diabetes-associated microbial feature in bronchoalveolar lavage fluid (BALF) microbiota, but its potential diagnostic or clinical relevance requires validation in future studies. Our work provides a scientific foundation for optimizing infection prevention and advancing precision anti-Parvimonas therapies.}, } @article {pmid42466908, year = {2026}, author = {Fairusya, N and Wang, R and Honda, R}, title = {Plasmid-mediated antimicrobial resistance across One Health sectors: transmission dynamics and surveillance needs.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0019226}, doi = {10.1128/msphere.00192-26}, pmid = {42466908}, issn = {2379-5042}, abstract = {Antimicrobial resistance (AMR) is increasingly recognized as a One Health challenge driven by the continuous exchange of resistant bacteria and resistance determinants across human, animal, and environmental sectors. While genomic surveillance has substantially improved detection of antimicrobial resistance genes (ARGs), most monitoring frameworks remain gene- or isolate-centric, limiting insight into the mechanisms that govern resistance transmission and persistence. Recent evidence indicates that plasmids, self-replicating mobile genetic elements (MGEs) capable of horizontal transfer across bacterial species, play an important role in disseminating clinically relevant resistance determinants across sectors. In this mini-review, we synthesize genomic and ecological evidence demonstrating that a limited number of plasmid incompatibility (Inc) groups recur across human, animal, and environmental reservoirs, often independent of bacterial host lineages. We highlight how plasmid transmission dynamics are shaped by host-independent mobility, ecological generalism, co-selection with accessory traits, and persistence in engineered and natural environments. We further examine why current AMR surveillance approaches, including ARG-centric metagenomics and isolate-based monitoring, systematically overlook these plasmid-mediated processes. Furthermore, we propose that plasmid-resolved analysis represents a critical and currently underutilized complementary layer for One Health AMR surveillance. Integrating plasmid classification and genomic reconstruction into wastewater-based epidemiology and cross-sector monitoring frameworks can improve attribution of transmission pathways, enhance early detection of high-risk resistance, and provide a mechanistic foundation for risk-informed intervention strategies.}, } @article {pmid42467010, year = {2026}, author = {Umekage, S}, title = {Shallow shotgun metagenomic sequencing of wild yeast communities enriched in ethanol-containing koji extract medium.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0034626}, doi = {10.1128/mra.00346-26}, pmid = {42467010}, issn = {2576-098X}, abstract = {I report the shallow shotgun metagenomic sequencing data of three ethanol-enriched wild yeast communities cultured in an ethanol-containing koji extract medium.}, } @article {pmid42467174, year = {2026}, author = {Zhao, M and Shi, Q and Zhao, L and Wang, M and Li, J and Wan, Z and Ouyang, T and Yu, Y}, title = {Severe pneumonia and acute respiratory distress syndrome caused by avian influenza A (H10N3) in a young female: a case report.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {42467174}, issn = {1439-0973}, abstract = {BACKGROUND: Human infection with avian influenza A (H10N3) is a rare but severe emerging zoonotic disease. To date, only a limited number of cases have been reported, which restricts a comprehensive understanding of its clinical features and public health risks. We report the fourth documented case of human H10N3 infection, which is the first to be identified in a female patient. Additionally, we compared the clinical and genomic characteristics of all four cases.

CASE PRESENTATION: A 23-year-old female with no prior comorbidities developed severe pneumonia and acute respiratory distress syndrome due to infection with avian influenza A (H10N3) virus. The patient, working in a fresh market with recent training at a slaughterhouse, presented a one-week history of high fever, cough, and dyspnea. Despite initial broad-spectrum antibiotics, her condition rapidly worsened, requiring mechanical ventilation and veno-venous extracorporeal membrane oxygenation (V-V ECMO). Metagenomic next-generation sequencing of bronchoalveolar lavage fluid, confirmed by the Centers for Disease Control and Prevention, identified avian influenza A (H10N3). Following approximately three months of intensive treatment, the patient recovered and was discharged. Phylogenetic analyses showed that her virus strain was closest to the third human H10N3 case (Kunming, China, 2024). In addition, this strain had a human-adapted substitution (P221) but lacked the G228S substitution in the haemagglutinin protein, suggesting that the latter is not essential for human infection.

CONCLUSIONS: This case highlights the potential for severe human infection by the H10N3 virus. It is imperative that surveillance is enhanced in both human and animal populations.}, } @article {pmid42467233, year = {2026}, author = {Liu, W and Tang, Q and Shen, M and Zhang, L and Jia, X}, title = {Conditional superiorities and unaddressed bottlenecks: a critical review of artificial intelligence for waterborne microbial detection.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-026-13917-8}, pmid = {42467233}, issn = {1432-0614}, abstract = {Although conventional microbial detection approaches for water samples are widely applied, they still suffer from prolonged assay durations (24-72 h), low sensitivity, and the absence of real-time monitoring capacity. Artificial intelligence (AI) has demonstrated conditional advantages in specific experimental environments, such as achieving a sensitivity of 99% for detecting Cryptosporidium and Giardia in low turbidity water (based on approximately 12,000 annotated images, using fivefold cross validation, completed under laboratory conditions); however, such advantages tend to diminish or vanish in high-turbidity water matrices or when training datasets are insufficient. This review critically evaluates four categories of AI-driven approaches: image-based analysis, spectroscopic techniques, genome, and metagenomic sequencing, as well as predictive pollution modeling. While AI helps boost detection efficiency, precision, and analytical capacity, a set of long-standing obstacles restrict its real-world deployment. The main issues involve non-standardized datasets, low model interpretability, weak generalization over various water substrates, and a substantial gap between lab-based performance and on-site operational outcomes. In summary, to fully exploit the capabilities of AI in aquatic microbial detection, greater emphasis should be placed on on-site validation, unified data specifications, and practical performance benchmarks, rather than further algorithmic innovation. This review seeks to provide practical references for scholars and practitioners working in the fields of microbiology, AI and water quality monitoring and management. KEY POINTS: • AI shows favorable performance for microbial detection under lab conditions. • Model performance declines greatly in complex water with many practical barriers. • Standardized data and validation will advance real-world application.}, } @article {pmid42467464, year = {2026}, author = {Savin, M and Hayer, JJ and Mutters, NT and Erler, T and Simon, S and Griesdorn, L and Steinhoff-Wagner, J and Hammerl, JA and Heinemann, C and Probst, AJ}, title = {Lineage-aware comparison of extended-spectrum β-lactamase-producing Escherichia coli from unweaned dairy calves and human references reveals host-structured plasmidomes and co-selection.}, journal = {Microbial genomics}, volume = {12}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001783}, pmid = {42467464}, issn = {2057-5858}, mesh = {Animals ; Cattle ; *Plasmids/genetics ; *Escherichia coli/genetics/isolation & purification/classification/drug effects/enzymology ; *beta-Lactamases/genetics/metabolism ; Humans ; *Escherichia coli Infections/microbiology/veterinary ; Phylogeny ; Germany ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antimicrobial resistance in Escherichia coli is shaped not only by resistance genes themselves but also by their chromosomal or plasmid localization and co-occurrence with biocide/metal resistance genes (BMRGs), virulence-associated genes and mobile genetic elements. We applied chromosome- and plasmid-resolved genomics to 109 extended-spectrum β-lactamase-producing E. coli isolates from unweaned dairy calves (n=484) in Germany and compared them with 479 human-associated reference genomes. Calf isolates were polyclonal and dominated by phylogroups A and B1. Resistance was predominantly plasmid-borne: 41% of isolates carried antibiotic resistance genes (ARGs) exclusively on plasmids, whereas only 4.6% carried ARGs exclusively on chromosomes. The chromosomal-versus-plasmid distribution of acquired ARGs differed significantly across phylogroups (P<0.05) and sequence types (all P<0.01). Conjugative plasmids accounted for 94.6% of plasmid-borne ARG occurrences and carried significantly more ARGs than mobilizable plasmids (P=3.66×10[-42]). ARG and BMRG counts were strongly correlated at the plasmid level (ρ=0.574, P=8.0×10[-41]), and class 1 integrons marked enriched multidrug plasmids with increased ARGs (P=6.22×10[-34]) and BMRGs (P=3.00×10[-29]). At the isolate level, calf isolates carried more acquired ARGs in unadjusted comparisons, but this host-associated difference was largely explained by population structure. At the plasmid level, however, host-associated differences persisted after adjustment: human plasmids carried more ARGs (IRR 1.66, P=0.0017) and showed a strong host×mobility interaction (IRR 4.61, P=4.9×10-8), stronger ARG-BMRG coupling and a higher prevalence of integrons. These findings show that antimicrobial resistance ecology in E. coli is shaped not only by which resistance genes are present, but by where they are located, what they are linked to and how readily their genomic carriers can disseminate.}, } @article {pmid42467473, year = {2026}, author = {Donoso, A and Pérez, AB and Lopez-Dosil, M and Vázquez, A and Gámbaro, F and Sánchez-Seco, MP and Martinez-Martinez, L and Cabrerizo, M and Tarragó, D and Fernandez-Garcia, MD}, title = {Human pegivirus, Toscana virus and herpesviruses identified in cerebrospinal fluid from adults with unexplained neurologic disease, Spain, 2022-2023.}, journal = {The Journal of general virology}, volume = {107}, number = {7}, pages = {}, doi = {10.1099/jgv.0.002302}, pmid = {42467473}, issn = {1465-2099}, mesh = {Humans ; Spain/epidemiology ; Male ; Female ; Adult ; Retrospective Studies ; *Sandfly fever Naples virus/isolation & purification/genetics ; *Pegivirus/genetics/isolation & purification ; Middle Aged ; *Nervous System Diseases/virology/cerebrospinal fluid ; Aged ; *Herpesviridae/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; *Flaviviridae Infections/cerebrospinal fluid/virology ; *Cerebrospinal Fluid/virology ; }, abstract = {Viral central nervous system (CNS) infections in adults frequently remain unresolved after routine diagnostic testing. We applied probe-based viral metagenomic next-generation sequencing (vmNGS) to cerebrospinal fluid samples from adults with suspected CNS infection and negative conventional diagnostics in a retrospective multicentre study conducted in Spain between 2022 and 2023. Among 40 idiopathic cases, vmNGS detected viral sequences in 6 patients without evidence of coinfection: human pegivirus (HPgV, n=3), Toscana virus (TOSV, n=1), herpes simplex virus type 1 (HSV-1, n=1) and varicella-zoster virus (VZV, n=1). Two HPgV-positive patients were transplant recipients, with neurological disease occurring more than 2 years after transplantation, compatible with possible long-term viral persistence in immunocompromised hosts. TOSV genotype B was identified in a patient residing in central Spain, supporting consideration of TOSV in selected cases of unexplained aseptic meningitis during the vector season, including outside traditionally recognized Mediterranean coastal regions. Furthermore, the failure of syndromic panel testing to detect HSV-1 and VZV highlights the need for complementary diagnostic strategies when clinical suspicion remains high. Overall, the detection of unexpected viral sequences, together with missed clinically actionable infections, supports the use of complementary molecular testing in selected cases of unexplained CNS syndromes when routine diagnostics are negative. These findings highlight the added diagnostic value of vmNGS and provide sequence-level data for future studies of viral diversity and molecular epidemiology in neurological disease.}, } @article {pmid42467734, year = {2026}, author = {Dai, G and Yao, S and Chen, W and Zhang, J and Du, X and Zhao, Y and Jin, Z and Zhang, G}, title = {Ephrin B2 and Ephrin B3 are receptors for a novel putative henipavirus with zoonotic potential.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {7}, pages = {e0014557}, doi = {10.1371/journal.pntd.0014557}, pmid = {42467734}, issn = {1935-2735}, abstract = {Next-generation sequencing has accelerated the discovery of novel putative viruses in wildlife reservoirs, while identifying those with zoonotic potential remains challenging. In this study, we report the identification and characterization of Ailong virus, a novel putative henipavirus from previous bat metagenomes in China that utilizes human ephrin B2 (EFNB2) and EFNB3 as functional receptors. Using an integrated approach combining phylogenetic analysis, pseudotyped virus entry assays, antibody blockade assays, and structural modeling, we demonstrate that Ailong virus glycoprotein binds human EFNB2 and EFNB3 with high specificity, mediating pseudovirus entry into both human neuronal and respiratory epithelial cells. Structural analysis revealed the Ailong virus glycoprotein-EFNB2 interface closely resembling that of Nipah virus (NiV), with conservation of all critical receptor-binding residues. Moreover, AiV encodes an exceptionally large phosphoprotein, 1,033 amino acids in length, which is larger than any other known phosphoprotein in the subfamily Paramyxoviridae. Given its receptor usage, structural similarities to NiV, and efficient entry in human airway epithelia, Ailong virus is believed to pose a spillover risk.}, } @article {pmid42467857, year = {2026}, author = {Majumdar, A and Upadhyay, MK and Ghosh, A and Biswas, R and Loizou, IK and Buck, M and Tibbett, M and Giri, B and Moulick, D and Kumar Jaiswal, M and Roychowdhury, T}, title = {Revolutionising Agricultural Sustainability: New 'Furrow Tillage' can Mitigate Short-Term Soil-to-Atmosphere CO2 Flux and Promote Soil-Plant-Microbe Health.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e76645}, doi = {10.1002/advs.76645}, pmid = {42467857}, issn = {2198-3844}, support = {PDF/2022/001418/LS//National Postdoctoral Fellowship scheme, Ministry of Education, Government of India/ ; 101152605//Marie Skłodowska-Curie-UKRI Postdoctoral Fellowship scheme, United Kingdom/ ; EP/Z002664/1//Marie Skłodowska-Curie-UKRI Postdoctoral Fellowship scheme, United Kingdom/ ; }, abstract = {Global agricultural carbon loss demands refined tillage practices. This study evaluates a hybrid furrow tillage field (FTF) approach that combines the bed geometry of conservation tillage with controlled, localised disturbance of conventional tillage. Distinct from strip-tillage and permanent-bed planting, FTF is designed for puddled, lowland rice systems, featuring a continuously water-filled furrow and an alternately wet-dry mid-bed. A two-year, twelve-site field trial across the Gangetic deltaic plain of West Bengal, India, assessed FTF through agronomy, geochemistry, crop physiology, and molecular microbiology, and presented all CO2-flux and labile-carbon results as short-term responses. FTF produced CO2 efflux comparable to no-tillage (3.94-4.38 vs. 2.43-2.84 g C m[-] [2] d[-] [1]) while sustaining nutrient bioavailability close to conventional deep tillage (6.29-7.11 g C m[-] [2] d[-] [1]), demonstrating that hybrid bed-and-furrow geometry can decouple short-term CO2 flux from nutrient-mineralisation benefits. Microbial diversity and gene-ontology profiles indicate active microbial interactions with reduced soil-to-atmosphere CO2 transfer. Molecular modelling identifies AmtB and HypC-HypD as candidate CO2-handling routes; mid-bed physical properties independently contribute to flux reduction. Long-term SOC stability requires multi-year, multi-soil-order validation with isotopic partitioning. The study integrates CO2 flux chambers, Kriging interpolation, elemental bioavailability analysis, plant ultrastructural observation, metagenomics, and molecular modelling.}, } @article {pmid42467901, year = {2026}, author = {Zhang, M and Yu, Y and Zhang, X and Qu, F and Chen, N}, title = {Climate-Driven Harmful Algal Blooms Impair the Coastal Nitrogen Filter and Shift Denitrification Pathways toward N2O Accumulation.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c01472}, pmid = {42467901}, issn = {1520-5851}, abstract = {Climate change is expanding harmful algal blooms (HABs) beyond nutrient-driven paradigms, yet their effects on coastal nitrogen cycling remain poorly understood. Here, we investigated a climate-driven dry-season Phaeocystis globosa bloom in Xiamen Bay, a subtropical coastal embayment, using field observations, isotopic incubations, and metagenomics. Contrary to the conventional view that HABs stimulate denitrification, the bloom suppressed sedimentary denitrification by ∼70% and reduced total dissolved excess gaseous nitrogen (ΔN2 + ΔN2rO) by ∼50% relative to the pre-bloom period. Despite this decline in nitrogen removal, N2O yield (ΔN2O/(ΔN2 + ΔN2O)) increased by approximately an order of magnitude from 0.04% to 0.30%, indicating a shift toward incomplete denitrification. This shift was linked to a sulfur-mediated microbial reorganization. In seawater, sulfur-metabolizing denitrifiers, particularly Roseobacter, capable of utilizing algal-derived sulfur compounds (e.g., DMSP), were enriched and became dominant. These taxa harbored clade I nosZ, whose sensitivity to oxygen and pH likely constrained N2O reduction. In sediments, chemolithoautotrophic sulfur-oxidizing denitrifiers, particularly Sulfurovum, became dominant and were associated with reduced N2 production. Together, these compartment-specific responses weakened denitrification and shifted its end-product composition toward a higher N2O share, revealing a sulfur-coupled microbial mechanism by which climate-driven HABs impair the coastal nitrogen filter.}, } @article {pmid42468181, year = {2026}, author = {Zhang, H and Zhu, L and Zhao, X and Wu, Z}, title = {Metagenomic next-generation sequencing identifies Ureaplasma parvum in culture-negative peritoneal dialysis-associated peritonitis complicated by COVID-19: a case report.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {3}, pages = {117554}, doi = {10.1016/j.diagmicrobio.2026.117554}, pmid = {42468181}, issn = {1879-0070}, abstract = {Ureaplasma parvum is a fastidious, cell wall-deficient urogenital commensal that is rarely reported in peritoneal dialysis-associated peritonitis (PDAP) and often missed by routine culture. We describe a 43-year-old woman with stage 5 chronic kidney disease receiving maintenance peritoneal dialysis who presented with abdominal pain, diarrhea, fever, and cloudy effluent. The effluent nucleated cell count was 223/μL, with 85.3% neutrophils, and CT showed abdominopelvic fluid with mild irregular peritoneal thickening. Empirical broad-spectrum therapy failed, while repeated blood and effluent cultures remained negative. Metagenomic next-generation sequencing (mNGS) of peritoneal effluent identified U. parvum, confirmed by species-specific nucleic acid testing. Doxycycline therapy and catheter removal led to defervescence. Although coronavirus disease 2019 (COVID-19), inflammatory pulmonary changes, and colitis complicated the course, she recovered with targeted and supportive treatment. No recurrence occurred during 2 years of follow-up. However, because paired genital and intestinal specimens were not analyzed, the exact route of infection remains unconfirmed, which is a limitation of this study. CLINICAL TRIALS REGISTRATION: ChiCTR2600120155.}, } @article {pmid42468189, year = {2026}, author = {Wan, S and Huang, W and Zhang, Z and Liu, X and Dong, W and Chen, Y and Ke, L and Yang, Q and Chen, S and Hu, Y and Zhang, Y}, title = {Microbial succession and flavor-related metabolic potential during industrial eight-round mechanized stacking fermentation of Maotai-flavor Baijiu.}, journal = {International journal of food microbiology}, volume = {460}, number = {}, pages = {111975}, doi = {10.1016/j.ijfoodmicro.2026.111975}, pmid = {42468189}, issn = {1879-3460}, abstract = {Mechanized production of Maotai-flavor Baijiu (MFB) is increasingly adopted in the Baijiu industry; however, microbial succession and flavor-related metabolic potential throughout the complete eight-round mechanized stacking fermentation (SF) process remain insufficiently understood. In this study, microbial communities, functional genes, physicochemical properties, and volatile compounds during SF were investigated using metagenomic sequencing and headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC/MS). A total of 168 volatile compounds were detected, of which 41 representative compounds were selected for further analysis. Among them, 15 differential volatiles were identified by PLS-DA, with furfural showing the highest abundance. Microbial profiling revealed pronounced community differentiation and continuous succession across fermentation rounds. Acidity, starch, and reducing sugars were significantly associated with microbial community variation, with acidity and starch exhibiting the strongest associations. In the initial round (R1), microbial communities were mainly derived from raw materials and Daqu. Bacterial communities shifted from lactic-acid-bacteria-enriched communities to those characterized by Kroppenstedtia and Bacillus, whereas fungal communities transitioned from yeast-enriched stages to mold-enriched and mold-yeast coexistence stages. Metagenome-inferred functional annotation, co-occurrence network, and correlation analyses suggested potential links between microbial succession and flavor-related metabolic pathways. Yeasts were mainly associated with ethanol- and organic-acid-related metabolism during the early stage, whereas Bacillus and Kroppenstedtia were linked to predicted starch-degradation and organic-acid-related pathways during the middle and late stages. Overall, this study provides a comprehensive characterization of microbial succession and metagenome-inferred flavor-related metabolic potential during mechanized SF and offers reference data for process monitoring and quality management in MFB production.}, } @article {pmid42468214, year = {2026}, author = {Wei, T and Chen, J and Zhang, Q and Song, M and Lin, Z and Qiu, R and Luo, C}, title = {Effects of maize and peanut cultivation on microbial degradation of dibutyl phthalate in agricultural soil.}, journal = {Ecotoxicology and environmental safety}, volume = {322}, number = {}, pages = {120510}, doi = {10.1016/j.ecoenv.2026.120510}, pmid = {42468214}, issn = {1090-2414}, abstract = {Phthalate esters (PAEs) widely contaminate agricultural soils. Although microbes can degrade PAEs, how plants influence this process remains unclear. Using DNA-stable isotope probing and metagenomics, this study investigated the influence of plants on microbial degradation of PAEs by soil bacteria. Our results revealed that maize and peanut, representing non-legumes and legumes, exerted contrasting impacts on PAE microbial degradation. Specifically, peanut cultivation significantly enhanced PAE biodegradation efficiency by 26.53% compared to unplanted soil, whereas maize inhibited the process by 33.97%. Mechanism-driven analyses indicated that peanut facilitated PAE biodegradation by enriching active degraders and key degrading genes (e.g., pcaF, xylF, and benB-xylY) involved in biodegradation pathway II, recruiting Bacteroidetes, and alleviating nitrogen limitation (evidenced by increased abundances of nrfH, rhlA, and gspD). Furthermore, peanut cultivation promoted synergistic microbial interactions by increasing the diversity of taxa positively correlated with PAE degraders. In contrast, maize inhibited biodegradation by disrupting these processes and energy metabolism. This study sheds light on the plant-specific mechanisms driving PAE dissipation in soil.}, } @article {pmid42458280, year = {2026}, author = {Wu, L and Wang, J and Zhu, J and Li, T and Chen, Y and Luo, L and Zhang, Y and Ning, S and Li, B}, title = {Rare primary small intestinal infection: a case report of Mycobacterium kansasii enteropathy in an immunocompetent patient and literature review.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13817-2}, pmid = {42458280}, issn = {1471-2334}, abstract = {BACKGROUND: Non-tuberculous mycobacteria (NTM) are important opportunistic pathogens that most commonly infect the lungs. Primary involvement of the gastrointestinal tract-especially the small intestine-is exceedingly rare, and small-bowel infection caused by Mycobacterium kansasii (M. kansasii) has seldom been reported.

CASE PRESENTATION: We describe an extremely rare case of primary small-intestinal M. kansasii infection in an immunocompetent young man who presented with prolonged chronic diarrhea and fever. After an extensive but unrevealing diagnostic work-up, the etiology was finally established by microbial metagenomic sequencing of tissue obtained by double-balloon endoscopy. Building on the initial regimen of ethambutol hydrochloride, rifampicin, and clarithromycin-and with subsequent antibiotic adjustments tailored to the patient's evolving symptoms-clinical symptoms resolved completely, and follow-up endoscopy showed mucosal improvement.

CONCLUSION: This case underscores that NTM infection should be considered in the differential diagnosis of unexplained chronic gastrointestinal symptoms and highlights the pivotal role of modern molecular techniques in reaching a precise diagnosis. Detailed analysis of the case together with a review of the literature aims to raise clinicians' awareness and improve management of this rare entity.}, } @article {pmid42458473, year = {2026}, author = {Gupta, E and Sharma, S and Tikar, SN and Dash, PK}, title = {Exploration of viral diversity in Aedes mosquitoes employing different shotgun metagenomic data analysis pipelines.}, journal = {Virology journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12985-026-03249-4}, pmid = {42458473}, issn = {1743-422X}, abstract = {Metagenomics or metaviromics is emerging as a powerful technology for pathogen surveillance and pandemic preparedness. Mosquitoes are important vectors for transmission of many emerging viruses responsible for numerous outbreaks. Monitoring mosquitoes becomes essential to investigate its virome which leads to understanding of disease dynamics and allow preventive actions. In this study, shotgun metagenomic methodology using Ion GeneStudio S5 System was optimized for exploration of viral diversity. A total of 1913 Aedes larvae were collected from Central India during post monsoon season of 2024. Aedes larvae reared to adulthood and processed for sequencing using Ion Torrent S5 platform. Computational analyses were performed using three bioinformatic pipelines: Chan Zuckerberg ID (CZ ID), Genome Detective Platform and the Galaxy Platform. A mock database of 11 known viruses was created as well as publicly available NCBI Sequence Read Archive (SRA) datasets were used to validate all three pipelines. In terms of detection accuracy, Genome Detective and CZ ID performed exceptionally well and therefore may be suitable for future mosquito virome surveillance studies. We found presence of viruses viz. Alphamesonivirus cavallynense and Phasivirus phasiense dominating in all samples. Dengue virus was detected in one sample by CZ ID, whereas Wenzhou sobemo-like virus, Hubei mosquito virus 2, Cell fusing agent virus found most commonly among samples. Other viruses found like Aedes anphevirus (AeAV; genus Glybovirus), Aedes totivirus, Verdadero virus and Chaq-like virus. Variation in the result among different pipelines are likely attributable to incorporation of different viral reference databases, classification algorithms, metrics and analysis parameters. To the best of our knowledge, this study represents the first metagenomic study of mosquitoes using Ion GeneStudio S5 platform in India. The findings provide a comparative evaluation of the metagenomic pipelines and elucidates detailed information of each pipeline and its working for future studies.}, } @article {pmid42458483, year = {2026}, author = {Jiang, Q and Nian, F and Xu, L and Wu, S and Zhang, F and Meng, F and Chen, Z and Tang, W and Shen, X and Dong, L}, title = {Helicobacter pylori promotes hepatocarcinogenesis by abrogating the protective effect of intestinal Bacteroides acidifaciens in females.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08590-4}, pmid = {42458483}, issn = {1479-5876}, support = {NSFC82273027//National Natural Science Foundation of China/ ; 24YF2704900//Shanghai Sailing Program/ ; }, abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) exhibits sexual dimorphism, with a lower incidence observed in females. However, the mechanisms underlying the disruption of this protective effect remain inadequately understood. Helicobacter pylori (Hp) is associated with HCC and can cause gut microbiota imbalances that promote HCC progression. This study explored how Hp might influence female susceptibility to HCC via the gut-liver axis, focusing on gut bacteria and their metabolites.

METHODS: A Hp-infected DEN + CCl₄-induced HCC mouse model was established, and a cohort of 186 HCC patients was analyzed. Fecal metagenomics and serum metabolomics were employed to identify Hp-responsive gut microbes and metabolites. The therapeutic potential of Bacteroides acidifaciens (Ba) and its metabolite 4‑hydroxybenzyl alcohol (4‑HBA), alone or combined with Hp eradication, was evaluated in mouse models and in mechanistic cell-based assays.

RESULTS: Hp increased tumor burden and fibrosis especially in female mice. Hp-positive female patients exhibited larger tumors, more advanced disease stages, higher cirrhosis incidence, and poorer overall survival compared to Hp-negative females. Hp also reduced gut microbiota diversity and decreased female-enriched Ba. The Ba-specific metabolite 4-HBA, which is higher in females and reduced by Hp, suppressed TGF‑β/SMAD signaling by binding to TGFBR2, thereby inhibiting hepatic stellate cell activation and HCC cell proliferation. Ba/4-HBA alleviated Hp-induced liver pathology in both sexes, with the combination of Hp eradication and Ba/4-HBA treatment proving more effective than eradication alone in females.

CONCLUSIONS: Hp exacerbates hepatic fibrogenesis and HCC in females by depleting Ba and its metabolite 4-HBA, which inhibits TGF-β/SMAD signaling through binding to TGFBR2. Supplementation with Ba/4-HBA, particularly when combined with Hp eradication, tend to be a promising microbiota-metabolite-targeted strategy for attenuating female HCC progression.}, } @article {pmid42459144, year = {2026}, author = {Sriram, S and Alsafar, H and Lusa, R and Wang, Y}, title = {Single-Thallus Genomics of Ejectosporus trisporus, an Unculturable Stonefly Gut Fungal Symbiont.}, journal = {Environmental microbiology}, volume = {28}, number = {7}, pages = {e70380}, pmid = {42459144}, issn = {1462-2920}, support = {RGPIN-2020-04293//Natural Sciences and Engineering Research Council of Canada/ ; DGECR-2020-00154//Natural Sciences and Engineering Research Council of Canada/ ; //TD Undergraduate Research Fellowship/ ; //Centre for Environmental Research in the Anthropocene Undergrad Research Fund/ ; //Mitacs Globalink Research Internship Award/ ; }, mesh = {Animals ; *Symbiosis ; Phylogeny ; *Genome, Fungal ; *Insecta/microbiology ; Genomics ; Gastrointestinal Tract/microbiology ; Canada ; }, abstract = {Microorganisms play essential roles in global ecosystems, yet much of their diversity, particularly among fungi, remains unexplored due to challenges in culturing and genomic characterisation. Trichomycetes, an early-diverging lineage of obligate gut symbionts of aquatic insects, exemplify this 'microbial dark matter', as most taxa cannot be maintained in axenic culture. Here, we present the first culture-independent genome assembly of Ejectosporus trisporus, an unculturable Harpellales fungus isolated from the hindgut of a winter stonefly (Allocapnia sp.) in Rouge National Urban Park, Canada. Using a single-thallus genomic approach based on multiple displacement amplification and Illumina short-read sequencing, we generated a 29.3 Mb genome assembly with 76.6% BUSCO completeness, comparable to existing culture-based Harpellales genomes. Phylogenomic analyses using 1241 conserved orthologs placed E. trisporus in a well-supported clade with Zancudomyces culisetae and Capniomyces stellatus, confirming its taxonomic position. Scanning electron microscopy further revealed detailed ultrastructural features of thalli, trichospores, and zygospores. This study demonstrates the feasibility of single-thallus genomics for unculturable fungi and provides the first genomic resource for an unculturable trichomycete species. Our study establishes a valuable basis for future large-scale genomic investigations of early-diverging fungi, enabling further exploration of the symbiosis and ecological roles of these cryptic gut-dwelling fungi.}, } @article {pmid42459798, year = {2026}, author = {Cao, D and Huang, L and Zhang, X and Zhang, X and Zhao, Z and Long, X and Zhu, X and Li, Y}, title = {Lentinan alleviates metabolic dysfunction implicating Parabacteroides goldsteinii-enriched gut microbiota and hepatic lipid metabolism reprogramming through gut-liver axis-associated mechanisms.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1841358}, pmid = {42459798}, issn = {2296-861X}, abstract = {Metabolic disorders represent a global health challenge requiring novel therapeutic strategies targeting the gut-liver axis. This study investigates the protective effects and mechanisms of lentinan, a bioactive polysaccharide from Lentinus edodes, against high-fat diet (HFD)-induced metabolic dysfunction. HFD-fed mice were treated with lentinan. Comprehensive phenotypic assessments, metagenome sequencing, hepatic transcriptomics, and correlation analyses were performed to elucidate mechanisms. Lentinan intervention significantly ameliorated dyslipidemia, hepatic steatosis, systemic inflammation, and intestinal barrier dysfunction in HFD-fed mice. Mechanistically, lentinan induced taxonomically selective gut microbiota remodeling, characterized by substantial enrichment of Parabacteroides goldsteinii (positively correlated with hepatic Plppr3 expression) and reduction of Romboutsia ilealis (negatively correlated with Dgkh and Nfat5), while paradoxically decreasing Akkermansia muciniphila despite metabolic improvements. Hepatic transcriptomics revealed significant downregulation of glycerolipid metabolism and oxidative phosphorylation pathways, directly correlating with reduced lipid accumulation and improved serum biochemistry. Unlike conventional prebiotics, lentinan functions as a precision modulator of specific microbial metabolic functions, particularly L-arginine and uridine 5'-monophosphate (UMP) biosynthesis pathways, which interface with host inflammatory and lipid metabolism. These findings establish lentinan as a promising therapeutic candidate for metabolic syndrome management through coordinated gut microbiota-liver axis modulation, providing a conceptual framework for developing precision microbiome-targeted interventions.}, } @article {pmid42459877, year = {2026}, author = {Romero-Arguelles, R and Ruiz-Ayma, G and Rodriguez-Castro, VA and Gonzalez-Rojas, JI and Gomez-Govea, MA}, title = {Next-generation soil monitoring: linking metagenomics, biosensors, and ecological modeling for sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1861333}, pmid = {42459877}, issn = {1664-302X}, abstract = {Soils represent one of the most complex and dynamic biological systems on Earth, where microbial communities play a central role in regulating ecosystem functions, including nutrient cycling, carbon sequestration, and plant productivity. However, increasing pressures from land-use intensification and climate change threaten soil health and biodiversity, highlighting the need for innovative monitoring and management approaches. In this review, we synthesize current advances in soil microbial ecology, sustainable soil management, environmental sensing technologies, and metagenomics to propose an integrative framework for soil monitoring and prediction. This review integrates environmental sensing, microbiome characterization, ecological modeling, and AI-based analytics into a unified framework for next-generation predictive soil monitoring systems. We discuss how high-resolution environmental sensors enable real-time characterization of soil physicochemical dynamics, while metagenomic approaches provide unprecedented insights into the taxonomic and functional diversity of soil microbiomes. Furthermore, we explore the role of microbial network analysis and ecological modeling in uncovering interaction patterns and predicting ecosystem responses to environmental change. The integration of these tools through machine learning and data-driven approaches is transforming soil science from a descriptive to a predictive discipline. We also address key challenges, including data standardization, scalability, and the interpretation of complex biological datasets. Finally, we highlight emerging directions such as microbiome-informed precision agriculture, microbiome engineering, and the development of soil digital twins. Together, these advances pave the way toward sustainable soil management strategies that enhance ecosystem resilience and agricultural productivity in the face of global change.}, } @article {pmid42460235, year = {2026}, author = {Barthman, B and Klassen, M and Ressing, A and Danielson, K}, title = {Disseminated Culture-Negative Periprosthetic Knee Infection With Multifocal Septic Arthritis Associated With Mycoplasma pneumoniae: A Case Report.}, journal = {Case reports in orthopedics}, volume = {2026}, number = {}, pages = {9426714}, pmid = {42460235}, issn = {2090-6749}, abstract = {We report a case of a 72-year-old woman with Waldenström macroglobulinemia who developed a culture-negative periprosthetic joint infection (PJI) of the right knee following total knee arthroplasty. Despite multiple debridements and broad-spectrum antibiotics, she developed systemic signs of infection and hematogenous spread to multiple native joints, including the contralateral knee, ankle, wrist, and lumbar facet joints. All intraoperative cultures remained negative. A respiratory PCR was performed, which detected Mycoplasma pneumoniae, and metagenomic next-generation sequencing (mNGS) of plasma supported the diagnosis of the pathogen. Based on these findings, therapy was narrowed to doxycycline, resulting in clinical improvement and deferral of further surgery. This case highlights the importance of considering atypical pathogens in culture-negative PJI and demonstrates the utility of mNGS in guiding targeted antimicrobial therapy.}, } @article {pmid42460558, year = {2026}, author = {Fan, L and Sun, F}, title = {Composition and function of biofilm microbial communities reveal high efficiency potential in carbohydrate metabolism in the mariculture.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {94}, number = {1}, pages = {60-69}, pmid = {42460558}, issn = {0273-1223}, support = {ZDYF2021XDNY131//Key Research and Development Project of Hainan Province/ ; }, mesh = {*Biofilms ; *Carbohydrate Metabolism ; Bacteria/metabolism/genetics ; Citric Acid Cycle ; }, abstract = {Biofilms on composite carriers may contribute to organic matter transformation in mariculture effluents, but the taxa and carbon-metabolic functions underlying this process remain unclear. This study employed metagenomic sequencing and functional annotation to comprehensively analyze the microbial composition and metabolic potential involved in glycoside hydrolase (GH), glycolysis, and the tricarboxylic acid (TCA) cycle in biofilms, revealing the functional characteristics of microbial communities in carbon metabolism. The results showed high microbial diversity in various carbon metabolism pathways, with Bacteroidota, Proteobacteria, and Planctomycetota being the dominant phyla, and Flavobacteriales and Planctomycetales being the predominant orders across all metabolic pathways. Functional analysis indicated that key enzymes involved in polysaccharide hydrolysis, glycolysis, and the TCA cycle exhibited high abundance. Core functional genes included polysaccharide hydrolases (GH33, GH109), glycolytic enzymes (glyceraldehyde-3-phosphate dehydrogenase, phosphofructokinase), and TCA cycle enzymes (succinate dehydrogenase, pyruvate dehydrogenase). These profiles suggest that carrier-associated biofilm communities harbor coordinated genetic potential for carbohydrate depolymerization and downstream central carbon metabolism in mariculture effluents. This study offers theoretical and practical guidance for developing efficient and sustainable biofilm-based wastewater treatment systems.}, } @article {pmid42461001, year = {2026}, author = {Zhang, Q and Niu, Z and Li, J and Wei, M and Wang, R and Zhao, J}, title = {Emergent Macrophytes Specifically Regulate Ammonia-Oxidizing Microbial Communities and Functions: Comammox Dominance and N2O Emission Effects.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag178}, pmid = {42461001}, issn = {1365-2672}, abstract = {AIMS: Emergent macrophytes regulate nitrogen-cycling microbial processes in lake riparian zones, though the mechanisms underlying these species-specific effects remain to be fully elucidated. This study investigated the structure, functional activity, and environmental drivers of three ammonia-oxidizing microbial communities in sediments with different emergent macrophytes (Phragmites australis, Typha orientalis, and Thalia dealbata) in Meixi Lake, Changsha.

METHODS AND RESULTS: Metagenomic sequencing, quantitative PCR (qPCR), potential nitrification rate, and N2O yield were integrated to reveal the influence of riparian vegetation on the structural dynamics and ecological effects of ammonia-oxidizing microorganisms. The results indicated that the emergent macrophytes altered the sediment physicochemical properties, thereby exerting certain selective effects on specific ammonia-oxidizing microbial communities. The microbial community structure was similar in the P. australis and T. orientalis sediments, whereas significantly different in the T. dealbata sediment. Comammox Nitrospira dominated across all sediments, with a maximum absolute abundance of 2.10 × 109 copies g-1. Notably, the T. orientalis sediment exhibited the highest comammox-driven potential nitrification rate (1.196 mg N kg⁻¹ d⁻¹), while the T. dealbata sediment showed the highest N2O production rate (3.042 ng N g-1 h-1). Environmental factor analysis revealed that organic matter and plant biomass facilitated N2O emissions driven by comammox and ammonia-oxidizing archaea (AOA), respectively. Furthermore, AOA abundance was positively regulated by pH whereas negatively regulated by ammonium nitrogen (NH₄⁺-N).

CONCLUSIONS: This study demonstrates that different emergent macrophytes influence the nitrogen transformation processes by modulating the abundance and activity of key microbial communities, providing a scientific basis for optimizing plant configuration in ecological restoration to mitigate greenhouse gas emissions.}, } @article {pmid42461036, year = {2026}, author = {Munford, KE and Grégoire, DS and Hug, LA}, title = {Tracking interlinked microbial and geochemical succession over decades in landfilled municipal solid waste.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0031126}, doi = {10.1128/aem.00311-26}, pmid = {42461036}, issn = {1098-5336}, abstract = {Landfills are heterogeneous built environments embedded in natural freshwater systems. They pose increasing risks of groundwater contamination from metal-bearing leachates over time. The interlinked succession of waste decomposition processes, microbial community membership, and metal cycling across a landfill's lifespan has not been explored, reducing our ability to predict the long-term environmental impacts of landfills. Working with 1,647 metagenome-assembled genomes from a single landfill, from samples spanning over 39 years of waste decomposition, we identified changes in landfill biogeochemistry and connected these changes to shifts in microbial community composition and predicted functions over time. Comparing Older (aged 31-39 years) and Newer (aged 3-20 years) waste cells identified significant shifts in the availability of labile carbon, redox-associated processes, and concentrations of mobile metals-all higher in Newer cells. Newer cells were dominated by chemoorganoheterotrophs, while Older cells contained higher proportions of chemolithoautotrophs and organisms with higher metabolic versatility. Metal resistance and metal cycling genes were significantly more abundant in Older cells. Using geochemical data from the time of filling to the present and microbial membership data across six landfill cells of different ages, we developed a conceptual model of landfill characteristics across time. This model connects redox conditions and metal fate, highlighting leachate recirculation as a key process impacting many geochemical parameters and defining site chemistry. Our work highlights the substantial changes occurring over the stabilization phase and provides a conceptual model for understanding this critical, final stage in a landfill's life cycle.IMPORTANCEAging landfills pose significant risks to environmental stability and are currently poorly modeled beyond ~20 years. Our examination of a single landfill across 39 years of waste degradation was a unique opportunity to examine the impact of time within a connected system. Our work connects geochemical data, microbial membership, and predicted function, as well as physical processes (e.g., leachate recirculation). Our conceptual model interlinks these facets across the lifespan of a landfill, providing an empirical data-based model of landfill aging. Previous models were extrapolated from younger waste and did not include the microbial dimension-a critical facet of the landfill ecosystem. Our model clarifies processes taking place in older wastes (30+ years), including oxygen infiltration, that have important implications for methane emission and metal mobility and fate over the longer term.}, } @article {pmid42461050, year = {2026}, author = {Wozniak, KJ and Pan, L and Zhu, D and Corver, J and Kuijper, EJ and Smits, WK and Britton, RA}, title = {Acquisition of a gene cluster in Clostridioides difficile PCR ribotype 023 strains enables xylitol utilization.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0026326}, doi = {10.1128/msphere.00263-26}, pmid = {42461050}, issn = {2379-5042}, abstract = {Hundreds of ribotypes of the gastrointestinal pathogen Clostridioides difficile have emerged over the last three decades, yet the factors driving their emergence are poorly understood. Recently, there has been an increase in infections caused by PCR ribotype 023 (RT023) strains in Europe. We profiled the growth of seven RT023 strains in 190 unique carbon sources and found they were able to grow in xylitol, a sugar alcohol used as a food additive in humans and animals. Other ribotypes of C. difficile tested (n = 19) displayed little to no growth in 0.5% xylitol and were growth-inhibited in higher concentrations of xylitol. Genome sequencing identified that RT023 strains acquired a putative xylitol dehydrogenase (xdh) gene in a mobile genetic element (MGE) that is absent from other C. difficile ribotypes. We created a deletion of xdh in the RT023 strain PRB1128 and observed poor growth in xylitol, indicating that the xdh is necessary for xylitol utilization. Complementation of the xdh mutant with a plasmid-based inducible copy of the xdh gene restored growth in xylitol. We performed competition assays in minibioreactor arrays (MBRAs) and observed that PRB1128 outcompeted the non-xylitol-utilizing strain CD2015 (RT027) in the presence of xylitol. These data support that the xdh gene within RT023 strains provides a fitness benefit for growth in xylitol. Interestingly, the chromosomal locus where the MGE inserted appears to be a hotspot for genetic insertions across clades of C. difficile. Together, this work improves our understanding of the molecular basis for niche adaptation of C. difficile.IMPORTANCEGenetic factors aiding in the emergence of the opportunistic pathogen Clostridioides difficile are poorly understood. Infections with clade 3 (PCR ribotype 023) strains causing severe disease have increased since 2008. Here, we show RT023 strains have the unique ability to utilize xylitol, a sugar alcohol used as a food additive in humans and animals, due to the presence of a xylitol dehydrogenase (xdh) gene within a mobile genetic element (MGE). This xylitol utilization ability confers a fitness benefit in competition against other C. difficile ribotypes, as well as in a fecal community in vitro. Research investigating the underlying genetic factors driving the physiology of C. difficile will improve our understanding of colonization and hypervirulence.}, } @article {pmid42461222, year = {2026}, author = {Schwartz, M and Ladeira, R and Neiers, F and Nicolaï, A and Hocquet, D and Loupiac, C}, title = {Next-Generation Food Enzymology: From Metagenomic Discovery to AI-Driven Biocatalyst Design.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.6c04349}, pmid = {42461222}, issn = {1520-5118}, abstract = {Food enzymology is entering a new era driven by the convergence of metagenomics, artificial intelligence, and synthetic biology. While traditional food processes rely on a limited repertoire of established biocatalysts, metagenomic and multiomics approaches now provide access to vast reservoirs of unexplored enzymatic diversity. Simultaneously, advances in protein structure prediction, functional modeling, and de novo protein design are transforming enzyme discovery from a largely empirical process to a predictive discipline. In this Perspective, we discuss how these technologies will enable the development of tailored biocatalysts for sustainable, precise, and next-generation food processing applications.}, } @article {pmid42461231, year = {2026}, author = {Liu, S and Li, Y and Zeng, X and Sun, Y and Li, L and Jia, Y}, title = {Reversible Control of Microbial As(III) Oxidation by Nitrous Oxide Availability in Flooded Paddy Soils.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c04988}, pmid = {42461231}, issn = {1520-5851}, abstract = {The persistence of arsenite (As(III)) oxidation in flooded paddy soils is difficult to explain once canonical oxidants are rapidly depleted under anoxia. Here we tested whether nitrous oxide (N2O), a prevalent nitrogen-cycle intermediate, reversibly regulates microbial As(III) oxidation and arsenic (As) partitioning in flooded soils. Using two paddy soils with low and high As contents, we conducted (i) three-generation serial-transfer enrichments with exogenous As(III) addition and (ii) continuous-cessation-readdition N2O exposure microcosms targeting native As pools. Across transfer generations, N2O consistently promoted As(III) oxidation under strictly anoxic conditions, while sterilized controls showed no As(III) loss, indicating biological mediation. In native-soil microcosms, porewater As(III) declined during N2O input, rebounded upon N2O withdrawal, and decreased again after N2O readdition, demonstrating reversible control. N2O exposure also shifted As toward amorphous Fe (hydr)oxide-associated operational fractions, consistent with reduced porewater mobility. Metagenomic analyses further showed enrichment of functional genes for As oxidation (aioA, aioB) and N2O reduction (nosZ), with the strongest responses in the high-As soil at day 70 (1 mM vs 0 mM N2O: aioA 13.9-fold, aioB 1.68-fold, nosZ 3.26-fold). These results indicate that N2O availability can act as a reversible control point associated with microbially mediated As(III) oxidation and As redistribution under anoxia, with implications for As mobility and exposure risk in flooded paddy systems.}, } @article {pmid42462345, year = {2026}, author = {Wang, Y and Ye, L and Cao, C and Che, G and Zhang, C and Wei, Q and Hong, Y and Jiang, K}, title = {Metagenomics indicates new taxa in Candidatus Saccharimonadia and proposal of Parviradicicola hetaonensis gen. nov. sp. nov. and Parviputeicola dengkouensis gen. nov. sp. nov. following the rules of the SeqCode.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {5}, pages = {126751}, doi = {10.1016/j.syapm.2026.126751}, pmid = {42462345}, issn = {1618-0984}, abstract = {Candidatus Saccharimonadia is a core lineage within the phylum Patescibacteriota (formerly the bacterial candidate phyla radiation, CPR), yet the class has long lacked a standardized, complete taxonomic framework. This nomenclatural gap severely hinders consistent academic exchange and global research into its diversity, evolutionary history, and ecological roles. Here, we recovered 29 medium- to high-quality Ca. Saccharimonadia metagenome-assembled genomes (MAGs) from groundwater, rhizosphere soil, and saline-alkali soil in the Hetao Irrigation District, Inner Mongolia, China, and performed integrated phylogenomic, genome size evolution, and metabolic analyses alongside reference genomes from the GTDB r220 database. Based on robust polyphasic taxonomic evidence (multi-dimensional phylogenetic analyses, widely accepted genome-wide ANI/AAI thresholds) and SeqCode rules, we formally propose two novel taxa: Parviradicicola hetaonensis gen. nov., sp. nov. (type material: txb011_bin.8.strict[TS]) and Parviputeicola dengkouensis gen. nov., sp. nov. (type material: sgl022_bin.19.orig[TS]), plus two novel families and one novel order. We further identified potential drivers and important associations related to Ca. Saccharimonadia genome size evolution and adaptive metabolic traits. This work refines the Ca. Saccharimonadia taxonomic framework, providing critical genomic references for follow-up research.}, } @article {pmid42462650, year = {2026}, author = {Liu, J and Wang, H and Wang, Y}, title = {Iron limitation induced siderophores production drives interspecies competition in anammox consortia.}, journal = {Water research}, volume = {305}, number = {}, pages = {126446}, doi = {10.1016/j.watres.2026.126446}, pmid = {42462650}, issn = {1879-2448}, abstract = {Anaerobic ammonium oxidation (anammox) relies heavily on iron to sustain the metabolism of its functional bacteria. However, actual wastewater systems are typically characterized by bioavailable iron scarcity, threatening the long-term stability of the nitrogen removal process. To understand how anammox bacteria utilize insoluble ferric iron and how iron availability dictates microbial interactions, we investigated the ecological dynamics of anammox consortia under iron-limited conditions (< 1 mg/L) using combined microbial network and metagenomic analyses. Results revealed that anammox bacteria could utilize endogenous siderophores to acquire trace iron, a strategy that initially sustained high anammox activity and achieved a nitrogen removal efficiency exceeding 70%. Quantitative PCR and functional genes analyses identified the AcsABCDEF and MbnBH systems as the potential siderophores synthesis pathways of anammox bacteria, predominantly attributed to catechol and carboxylate types. Notably, while this siderophore-mediated iron acquisition initially promoted the proliferation of both anammox and denitrifying bacteria, it subsequently triggered intense interspecies competition and cell apoptosis for the scarce iron pool. This competitive exclusion eventually disrupted the stability of the system, causing the nitrogen removal efficiency to plummet below 40% after 60 days. These findings uncover the iron uptake strategies of anammox bacteria and highlight iron availability as a critical regulatory lever for managing microbial interactions, offering a new ecological perspective for maintaining stable anammox processes in wastewater treatment.}, } @article {pmid42462831, year = {2026}, author = {Qiang, H and Jing, Y and Xu, X and Heo, S and Liu, Z and Yue, X and Zhou, A and Fernández-Morales, FJ and Oleskowicz-Popiel, P}, title = {N-(3-oxohexanoyl)-homoserine lactone-assisted enrichment reshapes functional microbial consortia for chain elongation in electrofermentation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135425}, doi = {10.1016/j.biortech.2026.135425}, pmid = {42462831}, issn = {1873-2976}, abstract = {The functional microbial consortia supporting chain elongation determine medium-chain carboxylate recovery from organic wastes, but how signal-molecule-assisted enrichment shapes chain-elongating bacteria (CEB), electroactive bacteria (EAB), and competing guilds in electrofermentation remains unclear. Here, three N-acyl-homoserine lactones: N-butyryl-homoserine lactone (C4-HSL), N-octanoyl-homoserine lactone (C8-HSL), and N-(3-oxohexanoyl)-homoserine lactone (3OC6-HSL), were supplied during microbial enrichment, and the subsequent electrofermentation was conducted fed with sludge fermentation broth. Compared with the Control (without signaling molecules), 3OC6-HSL had the strongest response, increasing caproate production by 94.0%, compared with 16.9% and 27.3% for C4-HSL and C8-HSL, respectively. It also increased the apparent caproate electron transfer efficiency by 20.7 percentage points, increased the abundance of CEB (44.9% vs. 33.2%) and EAB (14.3% vs. 6.6%), and reduced the abundance of homoacetogens (12.1% vs. 33.7%). Co-occurrence network analysis revealed more modular and compact inferred associations, with 25.0% more modules and a 34.7-49.3% shorter average path length. Metagenomic analysis revealed enhanced reverse β-oxidation, QS, chemotaxis, and flagellar assembly potentials, and the expression levels of acetyl-CoA acyltransferase (ACAT/fadA) and acyl-CoA dehydrogenase (ACADS/ACADM) increased by 162.1% and 96.6%, respectively. Clostridium kluyveri dominated the ACAT contribution (85.9%). Overall, enrichment-phase 3OC6-HSL supplementation was associated with a caproate-oriented microbial consortium and improved caproate recovery without continuous signal dosing.}, } @article {pmid42448275, year = {2026}, author = {Wang, Q and Cui, J and Zhang, X and Zhao, H and Xu, X}, title = {Process-specific inhibition of sediment denitrification by metal oxide nanoparticles.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128777}, doi = {10.1016/j.envpol.2026.128777}, pmid = {42448275}, issn = {1873-6424}, abstract = {The continuous accumulation of nanoparticles (NPs) in river sediments poses a potential threat to benthic nitrogen cycling. However, systematic comparisons of their effects on denitrification pathways driven by different electron donors are lacking. This study investigated the impacts of nZVI, nCuO, and nZnO on heterotrophic denitrification (H-DN), iron-based autotrophic denitrification (Fe-AD), and sulfur-based autotrophic denitrification (S-AD) in sediment. An integrated analysis was conducted including denitrification performance, key enzyme activities, extracellular polymeric substance (EPS) responses, microbial community structure, and functional gene abundance. Results revealed process- and particle-specific nanoparticle toxicity. H-DN was sensitive only to nZnO (11.6% reduction in nitrate removal rate). Fe-AD was sensitive to three NPs, with nZnO showing the strongest inhibition (38.7% reduction). In contrast, S-AD exhibited high tolerance. Nitrite reductase (NIR) activity reached 5.1 times that of the control, coupled with lower oxyR abundance, suggesting that sulfide-mediated passivation alleviated oxidative stress. NIR was identified as the common enzymatic target. Microorganisms defended against NP stress by increasing the protein fraction of EPS. nZnO triggered abnormal soluble microbial products (SMP) profiles across all systems, with protein/polysaccharide ratios surging to 45.0-45.3. Metagenomics revealed higher abundances of heavy-metal efflux and oxidative-stress genes in H-DN and Fe-AD under NP stress, imposing an energy trade-off between defense and metabolism; these genes were less abundant in S-AD. Gene abundance-enzyme activity decoupling further cautions that ecological risk assessments based solely on community abundance may underestimate nanoparticle toxicity.}, } @article {pmid42448379, year = {2026}, author = {Feng, Y and Lin, G and Jiang, Z and Shi, W and Deng, L and Dong, J}, title = {A Phenotype-Embedded Mapper Framework Links Microbiome-Metabolome Interaction Modules to Colorectal Cancer.}, journal = {Journal of proteome research}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jproteome.6c00192}, pmid = {42448379}, issn = {1535-3907}, abstract = {Integrative analysis of the gut microbiome and metabolome can help characterize colorectal cancer (CRC)-associated molecular changes that are difficult to resolve from either omics layer alone. However, microbiome-metabolome data are high-dimensional, heterogeneous, and often contain nonlinear or locally confined associations that may be obscured by global linear models. Here, we propose a phenotype-guided topological framework that extends the Mapper algorithm for local interpretation of paired microbiome and metabolome profiles. Disease-associated variation from each omics block was summarized by partial least-squares regression and used to construct a two-dimensional filter space for Mapper graph construction. We further developed an Extended Spatial Analysis of Functional Enrichment strategy (eSAFE) to evaluate the spatial enrichment of phenotypes, individual features, and feature-pair associations on the resulting graph. Applied to paired fecal metagenomic and metabolomic profiles from a CRC cohort, the framework organized samples into phenotype-aligned neighborhoods and identified localized microbial, metabolic, and cross-omics association patterns linked to CRC. Coenrichment analysis further prioritized disease-associated features and interaction modules that were partly distinct from those obtained by univariate differential analysis or supervised sparse multiblock integration. One disease-localized microbiome-metabolome module showed moderate CRC discrimination in internal cross-validation and was enriched for metabolites involved in butanoate and amino acid-related pathways. These results suggest that phenotype-guided topological analysis can provide a complementary, interpretable view of localized multiomics organization in CRC-associated gut ecosystems.}, } @article {pmid42448967, year = {2026}, author = {Sittipo, P and Park, JY and Tiffany, E and Oh, A and Moon, S and Lee, CH and Oh, JS and Kim, TY and Kweon, MN and Choi, J and Song, KH and Lee, DW and Nam, MH and Hong, SJ and Lee, EY and Jeon, SR and Song, HY and Kim, BS and Lee, YK}, title = {Gut microbiome modulation by Veillonella ratti induces resistance to EAE pathogenesis via microbe-derived metabolites.}, journal = {Experimental & molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {42448967}, issn = {2092-6413}, support = {2021M3A9I4027993//National Research Foundation of Korea (NRF)/ ; RS-2023-00219563//National Research Foundation of Korea (NRF)/ ; 2021M3A9I4023974//National Research Foundation of Korea (NRF)/ ; }, abstract = {The progression of multiple sclerosis (MS) is potentially influenced by the microbiome. Elucidating host-microbiome interactions in MS may aid in developing microbiome-based applications; however, these interactions remain unclear. Here, we aimed to elucidate how Veillonella ratti MHL0042, isolated from human infant feces, modulates neuroinflammation and disease severity in experimental autoimmune encephalomyelitis, a murine MS model. Whole metagenomic sequencing revealed that V. ratti MHL0042 reshaped disrupted gut microbiota via microbial interactions throughout the intestinal tract. V. ratti MHL0042 administration significantly reduced central nervous system inflammation, notably decreasing CD4[+]IFN-γ[+] T cell populations and activated spinal cord microglia. Mechanistically, V. ratti MHL0042 depleted pldA-containing bacteria, involved in phosphatidylethanolamine metabolism, thus elevating dioleoyl phosphatidylethanolamine (DOPE) levels. Increased DOPE was not only detected in the intestinal tract but also extended systemically and reflected in the central nervous system. Exogenous DOPE administration recapitulated the attenuation of experimental autoimmune encephalomyelitis pathogenesis by suppressing microglial activation. These findings highlight the therapeutic applicability of the microbiome and underscore its potential in human disease treatment.}, } @article {pmid42449467, year = {2026}, author = {Gan, L and Yang, Z and Zhang, Y and Wang, S and Meng, F and Liu, Y and Dorji, T}, title = {Beyond diversity: the functional mechanisms of microbial adapations under climate change in alpine deserts.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00928-1}, pmid = {42449467}, issn = {2524-6372}, support = {QYXTZX-AL2022-05//Regional Science and Technology Collaborative Innovation Special Project of Ngari in Tibetan Autonomous Region of China/ ; 2019QZKK0600//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; U20A2005//the Joint Key Research Fund under cooperative agreement between the National Natural Science Foundation of China (NSFC) and Tibet Autonomous Region (TAR)/ ; 42122005//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The functional responses of soil microbiomes to concurrent warming and altered precipitation in alpine deserts remain poorly understood, hindering predictions of these fragile ecosystem to climate change. Specifically, the mechanisms by which microbial communities maintain ecosystem function potential despite climate-induced biodiversity changes are unclear.

RESULTS: A three-year field manipulation experiment in an alpine desert grassland on the Qinghai-Xizang Plateau showed that warming and watering acted as distinct ecological drivers. Warming restructured prokaryotic and fungal communities, favored stress-associated taxa, and increasing interkingdom network complexity, indicating tighter microbial associations under climate stress. Although warming reduced microbial richness and diversity, it did not diminish the overall potential for soil nutrient cycling. Instead, functional stability was associated with sustained microbial abundance, network reorganization, and selective changes in nutrient-cycling genes, particularly those involved in nitrogen and phosphorus transformation hosted by specific bacterial phyla. In contrast, watering did not significantly increase mean soil moisture, but altered soil nutrient availability, affecting key microbial groups and their functions, showing an indirect regulation pathway.

CONCLUSIONS: Functional stability in alpine deserts under climate change was maintained not by taxonomic diversity alone, but through abundance-based compensation, community reorganization, and pathway-specific functional shifts. This study provides a mechanistic framework linking climate drivers to microbial community structure and nutrient-cycling potential, offering predictive insights into the responses of cold-arid ecosystems to future climate change.}, } @article {pmid42449846, year = {2026}, author = {Sun, Y and Wang, F and Mao, L and Lu, W and Wu, H and Mao, H and Zhang, Y}, title = {Optimization of Metagenomic Library Construction for Influenza A Virus and SARS-CoV-2: Systematic Comparison of rRNA Depletion Strategies and Fragmentation Orders.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {13}, pages = {}, doi = {10.3390/diagnostics16132065}, pmid = {42449846}, issn = {2075-4418}, support = {2024YFC2309905//National Key R&D Program of China/ ; }, abstract = {Background/Objectives: RNA virus metagenomic sequencing is a core technology for emerging infectious disease prevention and control, as well as for rapid pathogen identification. However, two major bottlenecks hinder its clinical application: the low fraction of informative sequencing reads caused by host rRNA contamination, and insufficient viral genome coverage. This study aimed to optimize the experimental parameters of RNA virus metagenomic sequencing, address the above bottlenecks, and establish a standardized workflow. Methods: Forty-five clinically positive samples (20 influenza virus-positive; 25 SARS-CoV-2-positive) were investigated in three parallel comparative experiments: rRNA depletion versus no depletion; probe-mediated RNase H digestion versus rRNA blocking; and two fragmentation timing strategies (fragmentation before versus after reverse transcription). Sequencing was performed on the GeneMind platform, and key performance metrics were systematically analyzed. Results: Following rRNA depletion, the host sequence proportion in the influenza virus and SARS-CoV-2 samples decreased from 39.5 to 90.5% to 3.6 to 32.2%, while the 10× genomic coverage increased from 0 to 99.4% to 98.1 to 100.0%. The proportion of host sequences captured by probe capture depletion (0.3-16.2%) was significantly (p < 0.05) lower than that captured by rRNA blocking module (14.3-92.3%). No significant differences were observed in the 10× genomic coverage (96.5-100.0%) or the fraction of effective viral reads between the two fragmentation strategies (p > 0.05). rRNA depletion is key to improving library quality, with post-capture probe digestion being optimal. Conclusions: The suggested optimization process will enhance sequencing efficiency and support the standardization of clinical RNA virus identification.}, } @article {pmid42449918, year = {2026}, author = {Smirne, C and Romano, G and Ravanini, P and Crobu, MG and Palumbo, A and Ferrari, G and Mercandino, A and Grossini, E and Pirisi, M and Piralla, A}, title = {Phylogenetic and Genomic Characterization of Whole Genome Sequences of a Herpes Simplex Virus Type 1 Isolate Identified Genomic Variant Characteristics in a Human Subject with Fulminant Hepatitis.}, journal = {International journal of molecular sciences}, volume = {27}, number = {13}, pages = {}, doi = {10.3390/ijms27135640}, pmid = {42449918}, issn = {1422-0067}, support = {PE00000007//European Union/ ; }, mesh = {Humans ; Phylogeny ; *Genome, Viral ; *Herpesvirus 1, Human/genetics/isolation & purification/classification ; Whole Genome Sequencing ; Polymorphism, Single Nucleotide ; *Liver Failure, Acute/virology ; Genomics/methods ; *Herpes Simplex/virology/complications ; }, abstract = {Herpes simplex virus 1 (HSV-1) is a rare cause of acute hepatitis, especially in patients with chronic immunosuppression. We performed whole-genome HSV-1 sequencing with a metagenomics approach on peripheral blood samples from an Italian case of fatal acute liver failure with high circulating HSV-1 (1,129,900,000 copies/mL), followed by phylogenetic analysis. After multiple sequence alignment, a final dataset of 182 whole-genome sequences was selected. The sequenced HSV-1 strain belonged to a phylogenetic clade isolated in Florida in 2002 (OQ724868.1). A characterization of single nucleotide polymorphisms and indels was performed to determine their effects on the viral genome: only one variant, classified as an indel, was detected with a high impact effect (c.905_906insGTTTT) in the UL49A gene, which is known to encode a membrane protein regulating virion morphogenesis, replication and assembly. In addition, this study also detected variants in other genes involved in crucial steps of the HSV-1 life cycle, like alpha-regulation (US7), capsid transport (UL36) and viral polymerase function (UL30). In conclusion, the results of this variant analysis confirmed that in HSV-1 hepatitis, some viral regions may be hotspots for adaptive mutations with a substantial impact on viral replication or immune evasion.}, } @article {pmid42449941, year = {2026}, author = {Wojtyś, M and Górska, EB and Osińska, E and Stępień, W and Gozdowski, D and Gworek, B and Cunha, A and Garcia, INS and Kondras, M and Hewelke, E and Fidler-Jarkowska, J and Chmielewski, J and Orzechowski, S}, title = {Integrating Microbiological Indicators and Shotgun Metagenomics for the Assessment of the Rhizosphere Microbiome of Medicinal Plants.}, journal = {International journal of molecular sciences}, volume = {27}, number = {13}, pages = {}, doi = {10.3390/ijms27135665}, pmid = {42449941}, issn = {1422-0067}, support = {UID/50006 + LA/P/0094/2020//Foundation for Science and Technology/ ; 8762E-385/SPUB /2018/31.07.2018//Ministry of Science and Higher Education/ ; }, mesh = {*Rhizosphere ; *Metagenomics/methods ; *Microbiota/genetics ; *Plants, Medicinal/microbiology ; *Soil Microbiology ; Bacteria/genetics/classification ; Metagenome ; }, abstract = {Medicinal plants are rich sources of bioactive secondary metabolites, yet their long-term effects on the rhizosphere (RS) microbial communities remain poorly understood, particularly with respect to microbial selection and functional potential. This study evaluated the number of selected groups of microorganisms culturable in vitro in the RS and bulk soil (BS) within 10-year monocultures of 11 medicinal plant species, and as a targeted case study, we performed shotgun metagenomic profiling for Allium ursinum. The abundance of microorganisms differed markedly among plant species, indicating species-specific RS selection. Azotobacter spp. showed the strongest variation: they were not detected in the RS of Allium ursinum, Thymus vulgaris, and Carum carvi, whereas higher counts were observed under Artemisia dracunculus (135.1 × 10[2] CFU g[-1] DM), Melissa officinalis (67.1 × 10[2] CFU g[-1] DM) and Calendula officinalis (38.8× 10[2] CFU g[-1] DM). Azotobacter spp. may serve as a sensitive candidate indicator of RS imbalance. Metagenomic analysis of the A. ursinum-associated soil revealed fine-scale taxonomic restructuring, while major functional categories remained broadly similar between the RS and BS. The novelty of this study lies in the development of the Integrated Microbiological Health Soil Index (IMHSI) and the proposal of a Nitrogen Enrichment Index (NEI) as exploratory composite metrics that integrate selected functional microbial groups.}, } @article {pmid42450074, year = {2026}, author = {Sheng, L and Wang, Y and Lu, P and Han, G and Hao, Z and Hou, S}, title = {The Composition and Differentiation of the Seed-Associated Microbiome in Rapeseed Seeds as Studied Through 218 Rapeseed Transcriptomes.}, journal = {International journal of molecular sciences}, volume = {27}, number = {13}, pages = {}, doi = {10.3390/ijms27135801}, pmid = {42450074}, issn = {1422-0067}, support = {CARS-12//China Agriculture Research System/ ; }, mesh = {*Seeds/microbiology/genetics ; *Transcriptome ; *Microbiota/genetics ; *Brassica rapa/microbiology/genetics ; Gene Expression Profiling ; Stress, Physiological ; *Brassica napus/microbiology/genetics ; }, abstract = {Rapeseed is one of the most important oil crops in the world. Its yield and quality are severely restricted by biotic stress and abiotic stress. Rapeseed seeds play a crucial role in the propagation process, and the microorganisms in the seeds can be vertically passed on to the next generation, which greatly affects the quality, yield and growth of rapeseed. However, from a group perspective, there is currently a lack of systematic research on the composition of seed-associated microbiome within rapeseed seeds. This study utilized the transcriptome data of 218 rapeseed seeds that have been published, focusing on analyzing and comparing the dynamic changes and functional differences in the composition of seed-associated microbiome in rapeseed seeds under normal growth and development, biologic stress and abiotic stress conditions. Since we used public transcriptome data without surface sterilisation control, we refered to the detected microorganisms as seed-associated microbiome. The advantage of this study lies in its application of this method to a large-scale sample of rapeseed populations, which systematically revealed the response characteristics of seed-associated microbiome under different stress conditions. Interestingly, some widely distributed genera were not detected, while rare taxa were found under specific conditions, warranting further verification. Since these microorganisms originated from the seeds, their compatibility with plants and colonization ability may far exceed those of soil-derived agents. In the future, high-throughput screening of strains with excellent antagonistic or repellent effects against major diseases and pests of rapeseed can be conducted from these unique seed-associated microbiome. These strains that were confirmed by culture-based, amplicon or metagenomic approaches can then be used to develop seed coating agents or soil inoculants.}, } @article {pmid42450138, year = {2026}, author = {Getsina, M and Tsyba, N and Chernevskaya, E}, title = {Modern Approaches to Diagnosis and Evaluation of Survival Prognosis in Patients with Pancreatic Cancer.}, journal = {International journal of molecular sciences}, volume = {27}, number = {13}, pages = {}, doi = {10.3390/ijms27135867}, pmid = {42450138}, issn = {1422-0067}, mesh = {*Pancreatic Neoplasms/diagnosis/mortality/genetics/metabolism ; Humans ; Prognosis ; *Biomarkers, Tumor/metabolism ; Microbiota ; Metabolomics/methods ; Circulating Tumor DNA/blood ; Early Detection of Cancer ; }, abstract = {Pancreatic cancer is among the most aggressive malignancies, and late diagnosis remains a key challenge. For a systematic review of pancreatic cancer diagnosis and prognosis, Scopus and Web of Science databases were used for the period from 2016 to 2026. The search query included the following keywords and their combinations: pancreatic cancer, diagnosis, early detection, prognosis, biomarkers, metabolomic profiling, CA19-9, microbiome, metagenomic changes, circulating tumor DNA, genomic analysis. Inclusion criteria included only articles published in English. Exclusion criteria included case reports and studies that did not examine pancreatic cancer. Our analysis demonstrates that integrating multi-omics data, particularly combining traditional CA19-9 with circulating tumor DNA (ctDNA) and metabolomic profiles (lipids, amino acids, carbohydrates), significantly improves diagnostic accuracy. Microbiome composition and genomic alterations further refine risk stratification and prognostic assessment. The synergistic use of these biomarkers may facilitate the development of screening, early diagnosis, risk stratification, and treatment optimization. However, the introduction of new diagnostic approaches into clinical practice requires additional verification, standardization and prospective clinical studies.}, } @article {pmid42450507, year = {2026}, author = {Xu, M and Ma, B and Zhu, K and Tu, W and Li, C and Hao, P and Zhang, M}, title = {Research Progress in Multi-Omics Analysis of Dairy Products: Nutritional Quality, Safety Evaluation, and Health Functions.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {13}, pages = {}, doi = {10.3390/foods15132389}, pmid = {42450507}, issn = {2304-8158}, support = {2023YFF1104704//National Key Research and Development Program of China/ ; 2025SNJF021//Zhejiang Provincial Department of Agriculture and Rural Affairs Project/ ; }, abstract = {This review evaluates multi-omics applications in dairy research across nutrition, safety, and health. Through multi-omics integration, we reveal nutrient differences driven by species, rearing practices, and processing techniques, identify protein patterns and allergen profiles, and construct adulteration detection fingerprints and species-specific peptide markers, thereby improving the timeliness and accuracy of safety assessment. The coupling of metagenomics and metabolomics effectively predicts spoilage-related microbial risks, enabling better risk control. Furthermore, multi-omics approaches systematically elucidate the functional mechanisms of bioactive peptides (e.g., ACE-inhibitory peptides), clarify the prebiotic effects of functional oligosaccharides, and build interaction networks between dairy components and gut microbiota. The introduction of machine learning enables origin and shelf-life prediction, as well as the discovery of novel biomarkers, promoting personalized nutrition and precision fermentation strategies. However, the field is currently constrained by severe reproducibility issues arising from the absence of standardized operating procedures, excessive optimism regarding machine learning models that rarely generalize across laboratories or product matrices, and a persistent disconnect between laboratory-scale biomarker discovery and industrial implementation. Without rigorous cross-platform validation and openly shared multi-omics reference datasets, most published markers remain unfit for regulatory or industrial application. Future efforts should establish standardized workflows and expand the evidence base to drive the dairy industry toward safer, healthier, and more traceable directions.}, } @article {pmid42450525, year = {2026}, author = {Oo-Puthinan, S and Limpeanchob, N and Pichitsiri, W and Wangteeraprasert, A and Trisat, K and Chumee, S and Sutheerawattananonda, M}, title = {Safety, Tolerability, and Gut Microbiota Impact of Sericin-Derived Oligopeptides (SDOs) from Yellow Silk Cocoons in Healthy Adults: A Randomized, Double-Blind, Placebo-Controlled Trial.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {13}, pages = {}, doi = {10.3390/foods15132405}, pmid = {42450525}, issn = {2304-8158}, support = {CRP6105022920//Agricultural Research Development Agency/ ; CRP6105022920//Ministry of Agriculture and Cooperatives/ ; }, abstract = {Sericin-derived oligopeptides (SDOs) from the Bombyx mori yellow silk cocoons show strong bioactive properties. However, clinical safety data on SDOs produced by specific enzymatic hydrolysis with a particular serine-rich (20.5%) and aspartic acid-rich (16.9%) composition is required to obtain regulatory approval as a novel food ingredient. This Phase 0 randomized, double-blind, placebo-controlled trial evaluated the short-term safety, tolerability, and gut microbiota effects of SDOs supplementation in healthy adults. Forty-two healthy volunteers were randomized (1:1:1) to receive daily doses of placebo, 0.9 g SDOs or 1.8 g SDOs for eight weeks. Primary safety endpoints included vital signs, hematology, and comprehensive clinical chemistry (renal and hepatic functions). Secondary outcomes included lipid profiles, oxidative stress markers (hs-CRP, TAC, SOD, MDA) and gut microbiota composition analyzed by 16S rRNA metagenome sequencing. Forty-one participants (97.6%) completed the study with high compliance (>98%). No serious adverse events were reported. All primary clinical parameters remained within clinically normal ranges, and no significant differences between groups were observed throughout the study (p > 0.05). No adverse effects on fasting blood glucose, lipid profiles or systemic oxidative stress were observed after SDOs supplementation. Importantly, 16S rRNA sequencing analysis showed that SDOs maintained gut microbial homeostasis throughout the 8-week intervention period, with Bacteroidetes and Firmicutes as the predominant phyla in the core community structure. Oral intake of enzymatically generated SDOs up to 1.8 g/day in healthy adults was well-tolerated with only occasional mild and transient gastrointestinal symptoms that did not appear to be dose-dependent. These first preliminary findings suggest a favorable safety profile for this unique peptide preparation, supporting its potential evaluation as a novel food ingredient and providing a reasonable basis for future, larger-scale trials to evaluate its efficacy in metabolic health.}, } @article {pmid42450613, year = {2026}, author = {Jiang, Z and Chen, J and Ren, Y and Lin, T and Li, S and Shen, F and Qin, B and Li, L and Li, C and Ying, N and Zheng, H}, title = {Gut Microbiomes of Rainbow Trout and Atlantic Salmon: Nutritional Modulation, Mucosal Immunity, and Resistome Risk.}, journal = {Biology}, volume = {15}, number = {13}, pages = {}, doi = {10.3390/biology15131066}, pmid = {42450613}, issn = {2079-7737}, support = {2024TD08//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; 2025QT04//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; 2025ZX03//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; SF2407//Lianyungang Key Research and Development Program/ ; }, abstract = {The gut microbiome of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) is increasingly recognized as a functional interface linking dietary inputs, epithelial barrier integrity, mucosal immunity, environmental stress, disease susceptibility, and antimicrobial-resistance risk in intensive aquaculture. Based on available salmonid studies and relevant evidence from broader fish and aquaculture systems, this review synthesizes current knowledge on salmonid gut microbial composition, nutritional modulation, microbiome-mucosal immune interactions, aquaculture stressors, antibiotic exposure, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metagenomics, multi-omics, and emerging microbiome-informed decision-support tools. Current evidence does not support a universally stable single-core microbiota in these species. Instead, community structure is shaped by developmental stage, freshwater-seawater transition, intestinal segment, digesta versus mucosa sampling, diet, temperature, stress, health status, and methodological workflow. Feed substitution and functional additives can remodel the gut microbiota, but these shifts should be interpreted alongside histology, barrier function, metabolic profiles, immune indicators, and disease-resistance phenotypes. Antibiotic exposure may reduce acute bacterial disease pressure while disturbing community structure and potentially enriching ARGs or ARG-MGE associations. Risk assessment should therefore move beyond ARG abundance toward host-ARG-MGE linkage using shotgun metagenomics, metagenome-assembled genomes, long-read sequencing, Hi-C, and externally validated multi-omics models. Machine learning and artificial intelligence approaches may support feature screening, risk stratification, and decision support, but their application in salmonid gut-health management remains at an early stage and requires external validation across sites, production stages, diets, and seasons.}, } @article {pmid42450643, year = {2026}, author = {Han, Y and Yuan, Z and Liu, B and Liu, T and Zhang, Q and Zhang, Z and Zhang, F and Yuan, H}, title = {Effects of Dietary Nucleotides on Growth Performance, Antioxidant Capacity, Intestinal Morphology and Gut Microbiota of Swamp Eel (Monopterus albus).}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {13}, pages = {}, doi = {10.3390/ani16131936}, pmid = {42450643}, issn = {2076-2615}, support = {2022CFB314//Natural Science Foundation of Hubei Province of China/ ; }, abstract = {This study evaluated how graded dietary nucleotide supplementation (0, 0.25, 0.5, 0.75, 1.0, and 2.0 g/kg) affects growth performance, antioxidant capacity, intestinal morphology, and gut microbiota in swamp eel (Monopterus albus) (initial body weight 10.07 ± 0.92 g). Three hundred sixty fish were randomly assigned to six diets, each in triplicate, for eight weeks. Compared with the control, nucleotide addition significantly increased final body weight, weight gain rate, and specific growth rate, and decreased feed conversion ratio (p < 0.05), with optimal results at 0.75 g/kg (HS3). Survival was 100% in all groups. Supplemented fish showed lower serum and intestinal malondialdehyde levels and higher superoxide dismutase and catalase activities (p < 0.05). Serum total protein, albumin, and triglycerides increased, whereas alanine aminotransferase, aspartate aminotransferase, and γ-glutamyl transpeptidase decreased (p < 0.05), pointing to improved hepatic and lipid metabolism. Intestinal trypsin, lipase, and amylase activities also rose markedly (p < 0.05), peaking in HS3. Histological examination revealed greater mucosal thickness and villus height (p < 0.05); in HS3, these values reached approximately 0.95 mm and 0.87 mm, respectively. Metagenomic analysis showed that 0.75-1.0 g/kg nucleotides increased alpha diversity and restructured the microbial community, enriching Bacteroidetes- and Prevotella-related taxa while reducing Proteobacteria, including Acinetobacter baumannii and Escherichia coli. LEfSe identified dose-specific discriminant taxa, and refined KEGG Level 3 pathway analysis predicted enhanced butyrate and propanoate biosynthesis, starch utilization, and purine/pyrimidine interconversion at moderate doses. Genus-level abundances of Prevotella and Bacteroides correlated inversely with serum oxidative and hepatic stress markers. Quadratic regression estimated the optimal dietary nucleotide level at 764 mg/kg (0.76 g/kg), consistent with the best-performing 0.75 g/kg group. Collectively, 0.75-0.76 g/kg dietary nucleotides optimize growth and intestinal health in M. albus through coordinated improvements in antioxidant status, digestive function, mucosal architecture, and beneficial gut microbiota remodeling.}, } @article {pmid42450707, year = {2026}, author = {Dai, Y and Qiao, Y and Xie, N and Zhu, J and Lin, Q and Xu, B and Dai, Y}, title = {Contrasting Roles of Mobile Genetic Elements and Metal Resistance Genes in Shaping the Gut Resistome of Wild Fish from the Qiantang River.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {13}, pages = {}, doi = {10.3390/ani16132000}, pmid = {42450707}, issn = {2076-2615}, support = {LHZY24C190001//Zhejiang Provincial Natural Science Foundation/ ; }, abstract = {The dissemination of antibiotic resistance genes (ARGs) in riverine ecosystems poses a pressing public health threat, while the mechanisms governing the assembly of the gut resistome in wild fish remain poorly elucidated. This study aimed to elucidate the distributional patterns of ARGs across multiple environmental compartments and to identify factors associated with their variation, particularly the contributions of mobile genetic elements (MGEs) and metal resistance genes (MRGs) to gut resistome variation. Metagenomic sequencing was conducted on 60 samples, comprising water, sediment, and gut contents from three wild fish species (Megalobrama terminalis, Aristichthys nobilis, and Coilia nasus) with distinct feeding habits, collected from four reaches of the Qiantang River basin. A total of 305 ARG subtypes belonging to 23 classes were identified. ARG composition differed significantly across environmental media and host species (permutational multivariate analysis of variance, PERMANOVA; p < 0.01), with host species identity as the primary structuring factor. Variance partitioning analysis (VPA) revealed that MGEs independently explained the largest fraction of ARG variation in A. nobilis (33.8%, p = 0.006), whereas MRGs dominated in C. nasus (33.3%, p = 0.005); in M. terminalis, MGEs and MRGs together accounted for 47.9% of the variation. Metagenomic assembly recovered 2622 ARG-carrying contigs, of which 28.3% (743) were predicted as plasmid sequences; physical co-localization among ARGs, MGEs, and MRGs was detected on both chromosomes and plasmids. Metagenomic binning validated the physical co-localization of ARG-MGE-MRG modules in genera such as Morganella and Burkholderia at the genome level, while plasmid-borne high-risk ARGs were identified in Aeromonas. Risk ranking further revealed significant enrichment of Rank II potentially high-risk ARGs (e.g., mcr-7.1, blaZ) in fish guts, carried by potential pathogens. These findings suggest that horizontal gene transfer involving MGEs and co-selection related to MRGs are closely associated with the fish gut resistome composition in a manner dependent on host ecology, providing a scientific basis for shifting riverine resistance management from concentration-based control toward the interruption of dissemination pathways.}, } @article {pmid42450796, year = {2026}, author = {Wei, Q and Chen, Y and Yang, H and Du, J and Li, H and Song, Z}, title = {Host-Associated and Environmental Microbiota of Hatchery-Reared Sichuan Taimen (Hucho bleekeri): Community Structure and Functional Profiling.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {13}, pages = {}, doi = {10.3390/ani16132089}, pmid = {42450796}, issn = {2076-2615}, support = {BL2023/D-88//the Sichuan Zumuzu River Hydropower Development Company, Ltd./ ; NJTCSC25-2//the Open Project of Sichuan Provincial Key Laboratory of Fish Resources Conservation and Utilization in the Upper Reaches of the Yangtze River/ ; YSCX2035-011//the Project of Original Innovation 2035/ ; SCCXTD-2026-15//the Sichuan Fresh Water Fish Innovation Team/ ; }, abstract = {The diversity and complexity of symbiotic microbiota in fish may significantly influence the host's physiological, metabolic and immunological functions. In order to understand the microbial assembly in Sichuan taimen (Hucho bleekeri), an endangered fish species in the upper reaches of the Yangtze River, the microbiota of the skin, oral cavity and feces of artificially reared individuals and the microbiota of the rearing water were characterized through metagenomic sequencing. The results demonstrated that Pseudomonadota were shared across the skin, oral cavity, feces and rearing water, suggesting that they may constitute a shared microbial group connecting the aquatic environment and host mucosal surfaces. Based on functional prediction analyses, these taxa were potentially associated with organic matter degradation, nutrient cycling, and microbial and immune homeostasis. Likewise, Actinomycetota and Bacillota were consistently detected across multiple mucosal tissues and were predicted to be associated with nutrient transformation, antimicrobial defense, and the maintenance of mucosal microbial stability. Fusobacteriota were detected solely in feces, suggesting a strong tissue-specific colonization capacity. The alpha diversity of the microbiota did not differ significantly among tissues, and the beta diversity revealed strong clustering of host-associated samples and clear separation from water samples. Functional annotation further revealed that the water microbiota exhibited broader yet more dispersed functional potential, whereas host-associated microbiota showed stronger functional specialization closely aligned with host physiological demands. Collectively, the findings are better presented as baseline information for future comparative and hypothesis-driven studies in Sichuan taimen.}, } @article {pmid42451140, year = {2026}, author = {Ibor-Miguel, M and Pérez-Sánchez, D and Marques-Martínez, L and Aura-Tormos, JI and Guinot-Barona, C and Miralles, EG}, title = {Influence of Early Feeding Practices on Oral Microbiota Composition During Infancy and Potential Implications for Early Childhood Caries: A Systematic Review.}, journal = {Nutrients}, volume = {18}, number = {13}, pages = {}, doi = {10.3390/nu18132138}, pmid = {42451140}, issn = {2072-6643}, mesh = {Humans ; Infant ; *Dental Caries/microbiology/epidemiology ; *Microbiota ; *Mouth/microbiology ; Breast Feeding ; Child, Preschool ; Infant, Newborn ; Female ; *Feeding Behavior ; Child ; Infant Nutritional Physiological Phenomena ; Milk, Human ; Infant Formula ; }, abstract = {BACKGROUND: Early feeding practices are among the most influential determinants of the infant oral microbiota during the first years of life. Breastfeeding provides bioactive components-immunoglobulins, human milk oligosaccharides (HMOs), and commensal bacteria-that may shape microbial colonisation patterns with long-term implications for oral health. However, the nature, magnitude, and clinical relevance of these effects remain poorly characterised, particularly with regard to early childhood caries (ECC) risk.

OBJECTIVES: The primary objective was to evaluate the association between early feeding practices and oral microbiota composition during infancy. A secondary exploratory objective was to assess whether feeding-associated microbiota differences had been linked to subsequent dental caries outcomes.

METHODS: A systematic review was conducted in accordance with PRISMA 2020 guidelines. PubMed, Scopus, Web of Science, and Embase were searched from January 2010 to June 2026. Eligible studies compared at least two feeding groups and measured oral microbiota directly using culture-independent methods (16S rRNA gene sequencing, metagenomics, or quantitative PCR targeting multiple taxa). Study selection, data extraction, and risk of bias assessment using the ROBINS-E tool were performed independently. Qualitative synthesis was conducted given clinical and methodological heterogeneity.

RESULTS: Of 8582 records identified, 12 studies met the inclusion criteria (sample size range: 12-448 participants; age range at microbiota assessment: 2 days-14 years, although eligibility was based on feeding exposure during infancy; six countries). Most included studies reported differences in oral microbiota composition associated with feeding type. During the first months of life, breastfed infants generally showed lower oral microbial diversity and higher abundance of Lactobacillus, the Streptococcus mitis group and Bifidobacterium compared with formula-fed infants, who exhibited greater alpha diversity, higher transmission of maternal oral bacteria, and higher abundance of Prevotella and Actinomyces. Effects were most pronounced in the first three months of life and attenuated by 12 months in most cohorts. Only one study reported subsequent dental caries outcomes after early-life microbiota assessment, finding that Streptococcus cristatus abundance at three months was associated with dental caries at nine years of age, and that longer breastfeeding duration (≥12 months) was associated with a distinct microbiota profile and lower caries rates in this single available longitudinal study. Risk of bias was low in two studies, moderate in six, and high in four. Publication bias could not be formally evaluated.

CONCLUSIONS: Early feeding practices are associated with measurable differences in oral microbiota composition during infancy, particularly during the first months of life. However, evidence linking these microbiota differences to subsequent dental caries outcomes remains extremely limited, with only one included study assessing later caries development. Therefore, the clinical significance of feeding-associated microbiota profiles remains uncertain and should be investigated through well-designed prospective longitudinal studies.}, } @article {pmid42451600, year = {2026}, author = {Garcia, J and Silva, J and Alves, MJ and Gouvinhas, I}, title = {Microbiome-Driven Bioactives for Chronic Wound Repair: Microbial Metabolites, Host-Microbe Mechanisms and Paths to Clinical Translation.}, journal = {Molecules (Basel, Switzerland)}, volume = {31}, number = {13}, pages = {}, doi = {10.3390/molecules31132229}, pmid = {42451600}, issn = {1420-3049}, mesh = {Humans ; *Wound Healing/drug effects ; *Microbiota ; Chronic Disease ; *Host Microbial Interactions ; Animals ; Probiotics/therapeutic use ; Skin Microbiome ; Biofilms ; Translational Research, Biomedical ; }, abstract = {Chronic wounds represent a substantial and growing clinical burden, yet durable healing remains difficult to achieve in a large proportion of patients. The skin microbiome plays a central role in this challenge: in healthy tissue, resident microorganisms support barrier integrity and calibrate immune responses, whereas in chronic wounds, community disruption-often combined with persistent biofilm formation-drives non-resolving inflammation, impairs re-epithelialisation, and increases antimicrobial tolerance. As antibiotic resistance escalates, these features strengthen the rationale for microbiome-directed strategies that target wound ecology while reducing reliance on conventional antimicrobials. Current evidence is still dominated by mechanistic and preclinical studies, with only early clinical signals for selected approaches; therefore, next-generation probiotics, including Lactiplantibacillus/Lactobacillus spp., as well as defined prebiotic and postbiotic formulations, should be interpreted as promising adjuncts rather than clinically established therapies. Causal mechanisms, optimal formulations, reproducibility, and patient-level determinants of response remain insufficiently defined, representing a critical knowledge gap that limits translation. Here, we synthesise current evidence linking microbial ecology to key wound-healing pathways and propose a precision framework that integrates metagenomics, transcriptomics, metabolomics, and spatial profiling to map host-microbe interactions, identify predictive biomarkers, and guide stratified therapy. We further highlight combinatorial approaches pairing ecological engineering with biofilm-disruptive materials and immune-modulatory molecules. Realising the potential of these interventions will require mechanism-resolved clinical trials, standardised outcome frameworks, and patient stratification tools-advances that could improve chronic wound management while reducing selective pressure for antimicrobial resistance.}, } @article {pmid42451744, year = {2026}, author = {Yan, S and Li, J and Chen, K and Ren, C and Zhang, S and Chen, Q and Gao, Y and Liu, B}, title = {Metagenomic and Metabolomic Insights into Volatile Flavor Changes and Microbial Community Shifts in Physalis pubescens L. Fermentation by Lactiplantibacillus plantarum.}, journal = {Molecules (Basel, Switzerland)}, volume = {31}, number = {13}, pages = {}, doi = {10.3390/molecules31132377}, pmid = {42451744}, issn = {1420-3049}, support = {CZKYF2025-1-B013//Provincial Research Institutes Scientific Research Operating Funds Project of Heilongjiang Province/ ; }, mesh = {*Fermentation ; *Metagenomics/methods ; *Metabolomics/methods ; *Volatile Organic Compounds/metabolism/analysis ; *Physalis/microbiology/metabolism/chemistry ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; Metabolome ; Fruit/microbiology/chemistry ; *Flavoring Agents/metabolism ; Metagenome ; }, abstract = {Physalis pubescens L. is a seasonal fruit with high nutritional value but a short shelf life that limits its processing and utilization. This study integrated metagenomics and metabolomics to investigate the comparative effects of Lactiplantibacillus plantarum fermentation on volatile flavor metabolites and microbial community composition of P. pubescens by comparing initial (0 h) and post-fermentation (24 h) states. After 24 h of fermentation, 1316 volatile compounds were putatively identified by GC-MS, with 592 metabolites significantly changed and 501 upregulated and 91 downregulated. Key flavor compounds that impart citrus, floral, fruity, and rose notes including D-limonene, geraniol, D-carvone, and phenylethyl alcohol were markedly increased. Metagenomic analysis revealed that L. plantarum rapidly dominated the microbial community (relative abundance surged from <0.05% to ~72%) while effectively suppressing potential spoilage bacteria such as Escherichia coli. Functional gene annotation demonstrated significant enrichment of amino acid, carbohydrate, and fatty acid metabolism pathways, with key enzyme genes (L-lactate dehydrogenase, pyruvate oxidase, acetyl-CoA carboxylase) predominantly assigned to L. plantarum, suggesting their potential contribution to the generation of organic acids, ethanol, and esters. Spearman correlation analysis indicated that Lactobacillaceae genera were significantly positively correlated with terpenoids, phenols, alcohols, and aldehydes. This study provides the first metagenomics-metabolomics insight into the microbial and molecular mechanisms associated with flavor formation in LAB-fermented P. pubescens, offering a theoretical foundation for developing stable and controllable fermented fruit products.}, } @article {pmid42452294, year = {2026}, author = {Huang, J and Zhang, X and Tian, Y and Luo, G and Xie, D and Li, J and Duan, B and Peng, S}, title = {Moss Cover Redirects Soil Organic Carbon from Active Turnover to Mineral-Associated Stabilization in Subalpine Forests.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {13}, pages = {}, doi = {10.3390/plants15132098}, pmid = {42452294}, issn = {2223-7747}, support = {N5132112023000495//Huanglong Nature Reserve/ ; }, abstract = {Understory mosses modify near-surface soil conditions, but how elevation regulates their influence on active and mineral-associated soil organic carbon (SOC) remains unclear. We compared independently selected moss-covered and non-moss-covered soils across a 3200-3500 m elevational gradient and integrated soil physicochemical measurements, microbial biomass (MB), dissolved organic matter (DOM), microbial necromass carbon (MNC), particulate organic carbon (POC), mineral-associated organic carbon (MAOC), metagenomic profiling, and piecewise structural equation modeling. Moss-covered soils consistently contained higher SOC and MAOC, but lower DOM, MB, and generally lower POC, than non-moss-covered soils. MNC showed an elevation-dependent reversal, with higher values under moss cover at 3200 m but lower values under moss cover at 3300-3500 m. Elevation was not a significant uniform driver of MB, DOM, MNC, POC, or MAOC; instead, its influence was mainly reflected in interactions with surface cover and in elevation-related changes in moss-layer structure, diversity, and hydrothermal conditions. Core carbon-fixation and degradation functions remained broadly stable, whereas specific functional modules shifted within moss-covered soils: acetate and acetyl-CoA metabolism genes (ackA and abfD) were relatively abundant at 3300-3400 m, while the polysaccharide-reprocessing gene SGA1 and oxidative-transformation gene katG increased toward higher elevations, and pmoC/amoC rebounded at 3500 m. Structural equation models linked the microbial functional gene system more strongly to POC, whereas MNC was positively associated with MAOC, and the direct POC-to-MAOC pathway was not significant. These findings indicate that moss cover is associated with contrasting SOC allocation patterns and stronger microbial necromass-MAOC coupling, while elevation modulates these relationships indirectly through changes in moss communities, soil microenvironment, and microbial functional potential.}, } @article {pmid42453369, year = {2026}, author = {Cui, Y and Li, Q and Liu, Z and Yu, Y}, title = {Induced Sputum Microbial Diversity and Function Changes in Patients with Acute Exacerbations of Chronic Obstructive Pulmonary Disease by Metagenomic Sequencing: A Cross-Sectional Study.}, journal = {International journal of chronic obstructive pulmonary disease}, volume = {21}, number = {}, pages = {600218}, pmid = {42453369}, issn = {1178-2005}, mesh = {Humans ; *Sputum/microbiology ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology/diagnosis ; Male ; Female ; Aged ; Cross-Sectional Studies ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Disease Progression ; *Microbiota ; Middle Aged ; *Lung/microbiology/physiopathology ; High-Throughput Nucleotide Sequencing ; China ; Phenotype ; Ribotyping ; }, abstract = {PURPOSE: The underlying pathogenesis of acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is closely related to airway microbiota dysregulation. Currently, there is a lack of systematic elaboration based on deep metagenomic sequencing regarding the species-level and functional characteristics of the microbiota during AECOPD, as well as its correlation with clinical phenotypes of the host. This study aims to systematically analyze the taxonomic composition and functional profile changes of the microbiota in induced sputum samples from COPD patients during the stable and acute exacerbation periods using metagenomic next-generation sequencing and to explore their correlations with clinical indicators through metagenomic methods.

PATIENTS AND METHODS: A total of 66 patients with COPD were recruited from the Department of Respiratory and Critical Care Medicine at Jiading District Central Hospital in Shanghai, China. Of these, 49 induced sputum samples were obtained from 47 patients (17 in the stable group; 30 in the acute exacerbation group) after the quality control with DNA extraction and deep metagenomic sequencing. The species annotation and functional analysis were conducted using bioinformatics procedures, and microbial α-diversity analysis, LEfSe analysis was performed to identify differentially expressed markers. Spearman correlation analysis was used to evaluate the correlation between microbial/functional characteristics and a series of clinical indicators.

RESULTS: The α-diversity of the sputum microbiota in AECOPD patients was significantly lower at the species level compared to the stable stage (p < 0.01), and the community structure also underwent significant changes. Functional annotation and comparative analysis further identified 9 KEGG pathways (ko00970, ko04112, ko03420, ko03440, ko03060/ko03070, ko03410, ko04930, and ko00680) and 1 eggNOG functional category (M: Cell wall/membrane/envelope biogenesis) that differed significantly between the two groups. Among them, pathways such as methane metabolism were downregulated in the exacerbation period.

CONCLUSION: This study revealed significant dysregulation of the airway microbiome in AECOPD patients at species-level diversity, community structure, and functional metabolism, providing a molecular basis for the discovery of functional biomarkers and therapeutic targets in the microbiome.}, } @article {pmid42453735, year = {2026}, author = {Shulga, S and Tigunova, O and Andriiash, H and Yemets, A and Blume, Y}, title = {Harnessing plant microbiomes to enhance crop resilience and restore war-affected soils in Ukraine.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1868751}, pmid = {42453735}, issn = {1664-462X}, abstract = {This review presents the current understanding of the rhizosphere microbiome and its potential application for the regeneration of damaged soils. The aim was to examine the issues of soil degradation associated with military actions and the latest developments in microbiome engineering for their application in the bioremediation of damaged lands. The review analyses recent developments and achievements in the study of the microbiome, its role in soil fertility, and plant protection against stress. Various directions and approaches to microbial profiling and addressing relevant pollution issues using developed bioengineered models and constructs have been examined. It has been shown that the most common explosive organic compounds - TNT, hexogen, and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine - and heavy metals - lead, cadmium, zinc, and antimony - account for the greatest soil contamination. The restoration of soils damaged as a result of military actions is feasible through the engineering of a specific soil microbiome (including genera Bacillus, Pseudomonas, and Arthrobackter, as well as arbuscular mycorrhiza). Military-related stress on soil is exerted by a mixture of organic pollutants and heavy metals, and the use of microbial consortia is a promising approach for mitigating their impact. The main economic advantage of such associations is that a consortium not only degrades toxic contaminants but also contains strains capable of nitrogen fixation and phosphorus mobilisation. The economic feasibility of applying synthetic microbial consortia and microbial engineering in war-affected regions is based on balancing the initial costs of research and development against substantial savings in capital investments compared with conventional land remediation methods.}, } @article {pmid42454139, year = {2026}, author = {Wang, Q and Tang, C}, title = {Diagnosis and treatment of severe tuberculosis complicated by ARDS and MODS in a young immunosuppressed host: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1846671}, pmid = {42454139}, issn = {2296-858X}, abstract = {BACKGROUND: Severe tuberculosis (TB) presents with complex clinical manifestations and high mortality. Immunosuppressed hosts are at high risk for TB infection and prone to progress to severe disease.

CASE PRESENTATION: A young female patient was admitted to our Respiratory Intensive Care Unit with fever, cough, and progressive dyspnea. She had a history of nephrotic syndrome and was on long-term corticosteroids and immunosuppressive agents, but without TB screening at baseline. Following admission, she rapidly developed acute respiratory distress syndrome (ARDS), diffuse alveolar hemorrhage, and multiple organ dysfunction syndrome (MODS). While providing broad-spectrum anti-infective therapy, invasive mechanical ventilation, continuous renal replacement therapy, and supportive care to maintain vital signs, we achieved an early definitive diagnosis of disseminated tuberculosis through rapid sputum acid-fast bacilli staining, Mycobacterium tuberculosis nucleic acid testing, and metagenomic next-generation sequencing (mNGS). A multidisciplinary team collaborated to formulate an individualized anti-tuberculosis treatment plan, leading to a favorable clinical outcome.

CONCLUSION: This case highlights the necessity of TB screening in immunosuppressed hosts, early recognition of severe TB, the importance of precise etiological diagnosis, and emphasizing the application of comprehensive treatment strategies in such patients.}, } @article {pmid42454225, year = {2026}, author = {Kafaie, S and Naseri, S and Mahoney, DBJ and Gagie, T and Beiko, RG and Maguire, F}, title = {Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.}, journal = {NAR genomics and bioinformatics}, volume = {8}, number = {3}, pages = {lqag066}, pmid = {42454225}, issn = {2631-9268}, mesh = {*Metagenomics/methods ; *Drug Resistance, Bacterial/genetics ; *Software ; Humans ; }, abstract = {Antimicrobial resistance (AMR) is a major global challenge to human and animal health. The genomic element (e.g. chromosome, plasmid, and genomic islands) and neighbouring genes associated with an AMR gene play a major role in its function, regulation, evolution, and propensity to undergo lateral gene transfer. Therefore, characterizing these genomic contexts is vital for effective AMR surveillance, risk assessment, and stewardship. Metagenomic sequencing is widely used to identify AMR genes in microbial communities but fragmentary short-read data do not directly provide this critical contextual information. Assembly of these reads provides some contextual information but fails to recover many mobile genetic elements. Here, we introduce Sarand, a method retaining some of the sensitivity of read-based methods while providing the genomic context of assembly by extracting AMR genes and their associated context directly from metagenomic assembly graphs. Sarand uses BLAST-based homology searches with coverage statistics to identify and visualize AMR gene contexts while filtering false chimeric contexts. Using both real and simulated metagenomic data, we show that Sarand outperforms metagenomic assembly and other recently developed graph-based tools in terms of precision and sensitivity for this problem. Sarand enables effective extraction of metagenomic AMR gene contexts to better characterize AMR evolutionary dynamics within complex microbial communities.}, } @article {pmid42454401, year = {2026}, author = {Pettinga, D and Fonseca-García, C and Krause, G and Ploemacher, H and Wheeler, T and Clendinen, CS and Handakumbura, P and Egbert, R and Coleman-Derr, D}, title = {Rational reduction of a sorghum SynCom that preserves growth promotion reveals flavonoid-mediated plant-microbe interactions.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71425}, pmid = {42454401}, issn = {1469-8137}, support = {2019-67019-29306//National Institute of Food and Agriculture/ ; DE-AC05-76RL01830//Pacific Northwest National Laboratory/ ; CRIS 2030-12210-003-000D//Agricultural Research Service/ ; DE-AC05-76RL0183//Biological and Environmental Research/ ; }, abstract = {Plant growth is influenced by the composition of its associated microbiome. The inherent complexity and functional redundancy of natural plant microbiomes present a formidable barrier to understanding the myriad biological interactions therein. Efforts have been made to develop synthetic microbial communities (SynComs) that can provide a rigorous and generalizable framework for the rational design of next-generation microbial products for sustainable agriculture. We test multiple strategies for stable, plant growth promoting SynCom design and evaluate the phenotypic and molecular impacts of a successful plant-SynCom interaction. We designed four distinct, reduced-complexity variants of SynCom Sorghum Root Consortium 1 and assessed their capacities for colonization, stability, and plant growth promotion (PGP). To understand the impact on plant performance of our highest performing SynCom variant, we characterized the host's longitudinal transcriptional response to SynCom inoculation and corroborated the results with metabolomics analysis. The top-performing SynCom stably colonized Sorghum bicolor roots and rhizospheres, elicited PGP, and induced dynamic spatiotemporal gene transcription in S. bicolor roots and shoots defined by modulation of growth-defense trade-off machinery and enhanced flavonoid production. The resultant reduced-complexity SynCom is a highly stable, soil-independent, plant growth promoting, and demonstrates the utility of colonization-based selection criteria, integrated with longitudinal transcriptomic and metabolomic characterization.}, } @article {pmid42454923, year = {2026}, author = {Shen, J and Hu, Y and Zou, X and Zhao, X and Li, S and Jiang, Y and Zhu, F}, title = {Impact of corticosteroids on lung antibiotic resistance genes in patients with lower respiratory tract infections.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0208025}, doi = {10.1128/spectrum.02080-25}, pmid = {42454923}, issn = {2165-0497}, abstract = {UNLABELLED: Lower respiratory tract infections (LRTIs) are a major global health concern, complicated by rising antibiotic resistance driven by antibiotic resistance genes (ARGs). Despite its role in the treatment of respiratory diseases, the impact of corticosteroids on ARGs in LRTI patients remains underexplored. Bronchial alveolar lavage (BAL) samples were collected from LRTI patients from two intensive care units (ICUs). Patients were classified into the corticosteroid group (CS group) and the non-corticosteroid group (NCS group) based on corticosteroid use. Next-generation sequencing assessed ARGs and associated microbes, with multivariable logistic regression analyzing the relationship between corticosteroid therapy and ARG accumulation. Ninety-one patients were recruited; the CS group (n = 57) exhibited a distinct ARG profile, marked by higher alpha-diversity and increased prevalence of ARGs than the NCS group (n = 34). The duration of corticosteroid therapy was positively associated with ARG accumulation, with individuals receiving treatment for more than 30 days exhibiting the highest ARG burden. The duration of corticosteroid therapy and the underlying hematological diseases were two independent risk factors for ARG accumulation. Our data provide new evidence that, in patients with LRTIs, extended corticosteroid use is associated with the accumulation of ARGs and modifications in the microbial composition of the lower respiratory tract.

IMPORTANCE: This research provides new evidence that prolonged use of corticosteroid drastically increases antibiotic resistance genes (ARGs) in the lungs of LRTI patients. It reveals a duration-dependent accumulation of ARGs, notably for common broad-spectrum antibiotics. These findings highlight the need to consider ARG burden when evaluating corticosteroid prescribing practices in patients with lower respiratory tract infections.}, } @article {pmid42454926, year = {2026}, author = {Davies, J and Ireland-Hughes, J and Stronati, S and Smith, RP and Oastler, C and Nunez-Garcia, J and Anjum, MF and AbuOun, M}, title = {Exploratory analysis of livestock waste treatment impacts on microbial diversity and antimicrobial resistance gene abundance.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0147626}, doi = {10.1128/spectrum.01476-26}, pmid = {42454926}, issn = {2165-0497}, abstract = {UNLABELLED: The potential spread of antimicrobial resistance (AMR) through agricultural waste is underexplored and may contribute to the dissemination of AMR genes into the environment. This pilot study used metagenomic sequencing to investigate how anaerobic digestion (AD) and on-farm slurry lagoon treatment affect microbial community composition and relative AMR gene abundance in livestock waste. Samples were collected before and after treatment from three AD sites and two on-farm slurry lagoon sites. Taxonomic profiles and diversity metrics were generated from short-read Illumina sequencing, and AMR gene presence and relative abundance were assessed using APHA SeqFinder, an in-house analysis pipeline. AD treatment led to decreased microbial richness and evenness, and reduced the relative abundance of several high-prevalence taxa, including members of the Enterobacteriaceae. On-farm slurry lagoon treatment had a comparatively minor effect on microbial composition. AD was also associated with significant reductions in the relative abundance of genes conferring resistance to macrolides, aminoglycosides, fusidic acid, and beta-lactams. These findings suggest that AD and on-farm slurry lagoon treatment exert distinct effects on microbial communities and AMR gene profiles. The results provide preliminary evidence that AD may contribute to reducing AMR gene burden in agricultural waste, although further investigation across broader temporal scales and treatment methods is needed.

IMPORTANCE: Antimicrobial resistance is a major global health challenge, and agricultural waste is a key environmental reservoir of resistance genes. This study examined how two livestock waste treatments (anaerobic digestion and on-farm slurry lagoon storage) affect microbial communities and relative antimicrobial resistance gene (ARG) abundance. The findings show that anaerobic digestion reduces both microbial diversity and the relative abundance of several resistance genes, while on-farm slurry lagoon treatment has a limited impact. These results highlight the potential for treatment strategies to reduce the environmental spread of resistance.}, } @article {pmid42454932, year = {2026}, author = {Li, J and Xue, S and Hou, L and Zhang, Z and Yuan, K and Chen, X and Kong, C and Wang, L and Gu, B and Liu, X}, title = {Construction and validation of a phenotypic prediction model for bacterial gentamicin resistance using deep learning with gene sequences.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0190625}, doi = {10.1128/spectrum.01906-25}, pmid = {42454932}, issn = {2165-0497}, abstract = {The emergence of bacterial resistance to antibiotics poses a significant threat to human health; thus, there is an urgent need for new strategies in understanding the mechanisms of resistance and further fast prediction of it. Deep learning models offer promising solutions through analyzing genetic sequences in the prediction of bacterial resistance patterns. This study develops and validates a transformer-based deep learning model, DNABERT-2-117M, to predict gentamicin resistance in Klebsiella pneumoniae directly from whole-genome sequences. Our central methodological advance investigates the impact of the DNA tokenization strategy on predictive performance. We prospectively compared a dynamic tokenization approach against conventional fixed-length tokenization. Evaluated through rigorous fivefold cross-validation and on a hold-out test set, the model employing dynamic tokenization achieved superior performance, with a mean F1-score of 0.95 and an area under the curve of 0.97. Our findings establish that optimizing sub-sequence tokenization is crucial for model accuracy, and this dynamic tokenization approach significantly enhances model accuracy for antibiotic resistance prediction from genomic data. This genome-based predictive model represents a scalable and rapid alternative to traditional antibiotic susceptibility testing, offering the potential to accelerate clinical decision-making and improve patient outcomes in managing K. pneumoniae infections.IMPORTANCEThis study addresses a critical gap in diagnostic technologies for hypervirulent, antibiotic-resistant Klebsiella pneumoniae. We introduce a transformer-based deep learning framework that utilizes dynamic tokenization strategies to predict drug resistance directly from genomic sequences. The core significance of our work is the development of a robust genomic prediction model that serves as a foundational component for future diagnostic paradigms. The significance of this work lies in its potential to fundamentally alter clinical timelines. By decoupling resistance prediction from the requirement for phenotypic growth, our approach is a critical step toward next-generation workflows (e.g., clinical metagenomics) that could deliver a complete diagnostic and susceptibility report directly from a patient sample within hours. This represents a scalable, rapid diagnostic platform that promises to accelerate the administration of targeted treatment for high-risk K. pneumoniae infections, with a clear trajectory toward same-day, specimen-to-result diagnostics in the near future.}, } @article {pmid42454939, year = {2026}, author = {Sen, P and Oliver, LL and Makarova, KS and Wolf, YI and Pavloudi, C and Shlafstein, M and Saw, JH}, title = {Hawaiian geothermal fumaroles contain diverse and novel viruses.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0156726}, doi = {10.1128/spectrum.01567-26}, pmid = {42454939}, issn = {2165-0497}, abstract = {UNLABELLED: Viral community structure is known to influence the evolution of microbes in diverse and complex environments. While the diversity of microbes and their viruses have been metagenomically explored in terrestrial hot springs and hydrothermal vent systems, other volcanic features remain remarkably understudied. Fumaroles (steam vents) are geothermal features that heat groundwater with magma, releasing heated water vapor and volcanic gases, such as CO2 and H2S. Fumaroles are physicochemically dynamic compared to terrestrial hot springs-temperatures and gas emissions fluctuate rapidly with volcanic activity. The viral community structures and diversity have never been systematically characterized or explored. We hypothesize that viruses facilitate microbial community adaptation to the harsh and dynamic fumarole environment. Using a sensitive profile-based approach for identification, we identify 383 viral operational taxonomic units (vOTUs) from 46 metagenomes of biofilms hosted near basaltic fumaroles. We estimate two previously undescribed order-level clades of Caudoviricetes (tailed phages), and find evidence of phylogenetic diversification within the fumarole systems. Read-mapping analysis of three sampled geothermal regions shows unexpected diversity and community structure within the geologic system: 99.7% of fumarole vOTUs are shared between distant fumaroles, and 40°C-60°C biofilms have high viral richness and evenness that do not correspond to biofilm microbial composition or diversity. Lastly, we provide the first description of a terrestrial environment dominated by Microviridae, which has only been described in viral communities of deep-ocean hydrothermal vents. Our study offers a unique geological system for the exploration of viral ecology in extreme environments.

IMPORTANCE: Geothermal environments serve as natural laboratories for studying adaptations to extreme conditions that challenge the limits of microbial life and offer insight into early life on Earth. Exploring microbial diversity in these systems reveals how ecological factors shape complex communities in extreme environments. Evidence increasingly shows that viruses influence microbial diversity in terrestrial hot springs and oceanic hydrothermal vents, yet the biogeography of viruses across these systems remains largely unexplored. We present the first metagenomic characterization of viral diversity and ecology in Hawaiian terrestrial volcanic fumaroles. Our results indicate extensive viral dispersal, in contrast to the typically more constrained dispersal observed in hot springs and hydrothermal vent systems. Furthermore, we observe a dominance of ssDNA viruses in fumarole viral communities, a pattern not previously reported in terrestrial systems. Our comprehensive analyses indicate that Hawaiian fumaroles are a valuable system for studying community patterns and the ecological determinants of viral biogeography.}, } @article {pmid42454945, year = {2026}, author = {Oworae, KO and Rabacal, W and Hu, A and Wychrij, DA and Rayens, E and Chapman, TI and Bahl, J and Norris, KA}, title = {Evaluating the impact of immunization with the "pan-fungal" vaccine, NXT-2, on the gut mycobiome and microbiome in non-human primates (NHPs).}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0104726}, doi = {10.1128/spectrum.01047-26}, pmid = {42454945}, issn = {2165-0497}, abstract = {Fungal infections remain a significant public health concern with high mortality, morbidity, and increasing associated health costs. This burden is projected to rise due to expansion of at-risk populations, limited therapeutics, increasing drug resistance, and the emergence of new fungal pathogens. Even with these challenges, there are currently no approved vaccines. We previously developed a "pan-fungal" vaccine candidate, NXT-2, that confers protection against multiple invasive fungal infections such as pulmonary aspergillosis, pneumocystosis, and invasive candidiasis, as well as non-invasive vulvovaginal candidiasis. NXT-2 is a 90 amino acid consensus peptide designed from a conserved region of the fungal antigen (KEX1). We assessed the effect of NXT-2 immunization on gut microbial diversity, composition, and functional capacity in non-human primates. To do this, we monitored changes in the gut mycobiome and microbiome pre- and post-vaccination using ITS2 and metagenomic sequencing, respectively, in Japanese and rhesus macaque cohorts. NXT-2 elicited a robust antibody response without disrupting the gut microbial communities in both macaque species. The mycobiome exhibited stability with no significant changes in alpha and beta diversity, taxonomic composition, or functional guild distributions. The relative abundance of gut resident Candida and Aspergillus species remained stable and was not significantly altered following vaccination. The microbiome showed stability with preserved alpha and beta diversities, taxonomic composition, and functional capacity. Results from this study show the first cross-kingdom analysis demonstrating that antifungal vaccination can achieve protective immunity without perturbing gut microbial communities. This establishes a framework for microbiome-informed vaccine assessment beyond conventional immunogenicity and adverse effect monitoring.IMPORTANCEFungal infections cause millions of deaths annually, yet no vaccines are approved despite growing drug resistance and limited treatment options. NXT-2 is a pan-fungal vaccine that protects against multiple fungal infections such as pneumocystosis, candidiasis, and aspergillosis. Here, we demonstrate in NHPs that NXT-2 elicits robust protective antibody responses without altering gut bacterial or fungal communities. This is the first study to assess antifungal vaccination across both microbial kingdoms and establish that protective antifungal immunity can be achieved while preserving resident microbiota. This work provides a framework for incorporating microbiome assessment into vaccine development beyond conventional immunogenicity and adverse event monitoring.}, } @article {pmid42455045, year = {2026}, author = {Deng, L and Ju, Z and Chen, J and Lin, Y and Zhou, W and Lee, SS and Yung, CCM and Liu, H}, title = {Sulfur-cycling diazotrophs dominate nitrogen fixation in seagrass sediments.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0099326}, doi = {10.1128/aem.00993-26}, pmid = {42455045}, issn = {1098-5336}, abstract = {Diazotrophs, the microbes capable of fixing dinitrogen, are essential for providing bioavailable nitrogen that supports marine primary production. Traditionally, nitrogen fixation in seagrass sediments has been linked primarily to heterotrophic sulfate reduction, leaving the roles of other metabolic processes, like sulfur oxidation, largely unexplored. Here, we employed metagenomic and metatranscriptomic approaches to explore the distribution, metabolic capabilities, and activity of diazotrophs in sediments dominated by the seagrass Halophila ovalis in a subtropical bay in Hong Kong. Our results revealed significantly higher nitrogen fixation rates in seagrass-vegetated sediments compared to adjacent bare sediments, with peak rates occurring in subsurface layers, suggesting that seagrass sediments may serve as hotspots for nitrogen fixation. We recovered 305 metagenome-assembled genomes, including those of diazotrophic sulfur-cycling bacteria. Notably, sulfur-oxidizing Gammaproteobacteria and sulfate-reducing Desulfobacterota emerged as the dominant and active members of the diazotroph community in seagrass sediments, expressing specific genes related to both nitrogen and sulfur metabolic pathways. Furthermore, our findings suggest that sulfate-reducing Desulfobacterota likely drive the high nitrogen fixation rates observed in deeper sediment layers, while sulfur-oxidizing Gammaproteobacteria may play a crucial role in surface layers. This study underscores the important roles of both sulfate-reducing and sulfur-oxidizing bacteria in nitrogen fixation within seagrass sediments, revealing a complex interplay between nitrogen fixation and sulfur metabolism.IMPORTANCESeagrass meadows are vital blue carbon ecosystems found in coastal and estuarine regions, playing a crucial role in carbon sequestration and supporting marine diversity. Traditionally, biological nitrogen fixation, an essential process for supplying bioavailable nitrogen to living organisms, has been primarily associated with heterotrophic sulfate reduction in these ecosystems. Our research offers novel insights into the nitrogen-fixing microorganisms present in the sediments dominated by the seagrass Halophila ovalis. We found that both sulfur-oxidizing and sulfate-reducing bacteria contribute to nitrogen fixation processes in seagrass sediments. This study highlights the intricate connections between nitrogen and sulfur metabolic pathways, providing a more comprehensive understanding of nutrient cycling in coastal ecosystems.}, } @article {pmid42455624, year = {2026}, author = {Signorelli, T and Walker, M and Robertson, J and Quizon, K and Zhang, Y and Reimer, AR and Eagle, SHC}, title = {Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.}, journal = {Microbial genomics}, volume = {12}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001738}, pmid = {42455624}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Benchmarking ; *DNA, Bacterial/isolation & purification/genetics ; Humans ; Microbiota/genetics ; Feces/microbiology ; Nanopores ; *DNA/isolation & purification ; }, abstract = {Oxford Nanopore Technologies (ONT) sequencing offers several advantages for metagenomics, including long reads, rapid turnaround, low upfront cost, scalability and portability. However, for ONT metagenomics, DNA yield, quality and integrity are important considerations when selecting an extraction method. Many metagenomic extraction methods use harsh lysis conditions to extract a wide range of species and provide an accurate community composition, but these conditions can compromise DNA fragment length. Therefore, extraction methods for ONT metagenomics must balance DNA shearing and recovery with representative community lysis. We systematically evaluated DNA extraction methods for ONT metagenomic sequencing using a use case-oriented framework. Among nearly 50 extraction methods screened, 7 were selected for detailed comparison based on suitability for metagenomics, variation in methodology, availability, cost and processing time: Norgen BioTek Corp's Stool DNA Isolation (NG), Zymo Research's ZymoBIOMICS Quick-DNA HMW MagBead (ZMG), Qiagen's DNeasy Blood and Tissue (QBT), Macherey-Nagel's NucleoMag DNA Microbiome (MN), Zymo Research's ZymoBIOMICS DNA Mini Prep (ZMI), Qiagen's DNeasy PowerSoil/QIAamp PowerFecal Pro (PS) and Qiagen's QIAamp Fast DNA Stool Mini (QIA). Methods were tested using Zymo Research's ZymoBIOMICS Microbial Community Standard (MCS), a matrix-free mock community with known composition. DNA extracts were sequenced on an ONT PromethION using the Rapid Barcoding Kit, except QIA due to insufficient DNA yield. Metrics for the method, DNA extracts, sequencing and genomes were evaluated, revealing trade-offs between methods. The two magnetic bead methods, MN and ZMG, produced the highest mean read length N50 values (13.9 and 16.5 kb, respectively) but showed apparent community compositions skewed towards Gram-negative bacteria. In contrast, ZMI and PS maintained a community composition close to expected, with reduced mean read length N50 values (4.5 vs. 7.5 kb). Performance across various metrics is presented in the context of the following use cases: maximizing genome coverage and assembly completeness, preserving composition accuracy, targeting specific species and limiting required resources (equipment, time or budget). The metrics and use case considerations presented offer practical guidance for informed selection of DNA extraction methods for ONT metagenomics. For accurate community composition, ZMI or PS are recommended, while PS and ZMG perform best at maximizing genome coverage and assembly completeness. NG and QBT may be the most economical options, though performance trade-offs were observed. Finally, PS may be the preferred method for time-sensitive diagnostic or field applications.}, } @article {pmid42456224, year = {2026}, author = {Zhang, Y and Wang, D and Su, N and Lu, H and Xu, H and Wan, W and Li, Z and Li, W}, title = {Chronic prosthetic joint infection caused by Coxiella burnetii diagnosed by metagenomic next-generation sequencing: A case report and literature review.}, journal = {Journal of infection and public health}, volume = {19}, number = {9}, pages = {103301}, doi = {10.1016/j.jiph.2026.103301}, pmid = {42456224}, issn = {1876-035X}, abstract = {Prosthetic joint infection (PJI) caused by Coxiella burnetii (C. burnetii) remains a rare but clinically significant diagnostic challenge due to its culture-negative characteristics and nonspecific clinical manifestations. Metagenomic next-generation sequencing (mNGS) has emerged as a valuable tool for identifying fastidious pathogens in culture-negative PJI cases. A patient with a history of joint arthroplasty presented with persistent joint pain and swelling. Despite multiple surgical interventions and prolonged empirical antibiotic therapy, routine bacterial cultures remained negative and the infection recurred. mNGS performed on periprosthetic tissue detected C. burnetii in two independent specimens, while all conventional cultures remained negative. Targeted antimicrobial therapy with doxycycline combined with levofloxacin was initiated, resulting in gradual symptom resolution and sustained clinical improvement during follow-up. This case highlights C. burnetii as an underrecognized cause of culture-negative PJI and demonstrates the clinical value of mNGS for early pathogen identification when conventional diagnostics fail. Repeated detection in independent specimens strengthened diagnostic confidence and enabled timely targeted therapy. Our findings support the early incorporation of mNGS into the diagnostic algorithm for suspected culture-negative PJI. In the present case, targeted doxycycline-levofloxacin therapy following mNGS-based pathogen identification was associated with sustained clinical improvement.}, } @article {pmid42456442, year = {2026}, author = {Wills, OC and Chua, XY and McEvoy, C and Fitzmaurice, M and El-Assaad, F and El-Omar, E and Probst, Y}, title = {A case-control study of the oral microbiome among Australian female adults with relapsing-remitting multiple sclerosis: A pilot study.}, journal = {Multiple sclerosis and related disorders}, volume = {113}, number = {}, pages = {107383}, doi = {10.1016/j.msard.2026.107383}, pmid = {42456442}, issn = {2211-0356}, abstract = {BACKGROUND: There is growing evidence investigating the role of the gut microbiome in the onset and progression of multiple sclerosis (MS). However, the role of the oral microbiome in MS is poorly understood, despite its importance in immune regulation and systemic health.

METHODS: A cross-sectional, case-control, pilot study comparing the oral microbiome among adults with relapsing-remitting MS to matched controls based on age, sex and body mass index (BMI), was conducted. Participants provided fasting oral swabs where DNA was extracted and shotgun metagenomic sequencing performed. Comparative analyses between cases and controls explored alpha-and beta-diversities including differential abundance testing.

RESULTS: Across 24 oral microbiome samples, 355 species from 12 phylum were detected. Alpha diversity was lower in MS at the species level, however, did not reach statistical significance for either richness or Shannon diversity. Beta diversity demonstrated a significant difference using Bray-Curtis dissimilarity with group status accounting for ∼6.7% of the total variation in microbial community structure. Differential abundance testing highlighted Veillonella parvula as the most enriched species among cases (coef=2.56, stderr=0.74, FDR=0.17), while Porphyromonas pasteri (coef=-3.57, stderr=1.02, FDR=0.17) and s__GGB4936_SGB6889 (coef=-4.29, stderr=1.30, FDR=0.17) were predominant among controls.

CONCLUSION: The oral microbiome of Australian females with RRMS differs in a subtle but detectable manner from those without MS, characterised by a non-significant trend towards reduced microbial diversity and distinct compositional clustering based on Bray-Curtis dissimilarity. Findings support the emerging concept of an oral-immune axis in MS, underscoring the need for longitudinal and functional studies to explore causality.}, } @article {pmid42456685, year = {2026}, author = {Steriade, C and Segata, N and Saxena, D}, title = {The role of the gut microbiome in mediating neuroinflammation in immune-based neurological disorders.}, journal = {The Lancet. Neurology}, volume = {25}, number = {8}, pages = {764-780}, doi = {10.1016/S1474-4422(26)00193-6}, pmid = {42456685}, issn = {1474-4465}, abstract = {The gut microbiome can influence brain health by modulating neuroinflammation through various mechanisms, including immune regulation, the production of metabolites that affect neural function, gut and blood-brain barrier integrity, upstream effects via the vagus nerve, upstream migration of gut-resident lymphocytes to the brain, bile acid signalling, and endocrine activity. Changes in gut microbiota have been observed in demyelinating conditions, autoimmune encephalitis, and epilepsy. Gut microbiota composition changes can affect neuroinflammation, disease progression, and treatment outcomes. Advances in microbiome research have improved the potential for clinical translation of findings; but limitations persist, driven by the largely correlational nature of clinical studies and the complexity of microbiome sequencing and interpretation. At present, only the ketogenic diet is routinely recommended by clinicians, whereas other microbiome-based interventions remain investigational. Multiple strategies for manipulating the gut microbiome, including dietary changes, prebiotics, probiotics, postbiotics, and faecal microbiota transplantation, might be used as disease-modifying therapies in the future.}, } @article {pmid42456986, year = {2026}, author = {Yang, C and Xu, Y and Nie, Y and Li, Y and Zeng, XC}, title = {Beyond arsenite: Arsenite-oxidizing prokaryotes drive sulfur compound oxidation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135419}, doi = {10.1016/j.biortech.2026.135419}, pmid = {42456986}, issn = {1873-2976}, abstract = {Arsenite oxidation prokaryotes (AsOPs) contribute significantly to the biogeochemical processes governing arsenic cycling. Since AsOPs can oxidize As[III] to As[V], markedly reducing arsenic toxicity and decreasing its migration potential, they have been widely utilized in the restoration of As[III]-affected sites and in the design of bioreactors for treating As[III]-polluted groundwater. However, it is still unclear whether AsOPs possess additional catalytic activities that may interfere with their bioremediation capacity, highlighting a critical knowledge gap that warrants further investigation. Because arsenic often coexists with sulfur, it was hypothesized that AsOPs may also oxidize reduced sulfur compounds. To verify this hypothesis, an AsOP-enriched culture was successfully established. Metagenomic analysis revealed that ∼ 96.1% of the AsOP metagenome-assembled genomes (MAGs) contained at least one pathway for the oxidation of reduced sulfur compounds, including sulfide, thiosulfate, or sulfite. Functional assays using both the AsOP community and three cultivable AsOP strains demonstrated that AsOPs actively catalyzed anaerobic sulfide oxidation coupled with nitrate reduction to ammonium, leading to complete sulfide oxidation to sulfate and a marked decrease in pH from ∼ 7 to ∼ 3. In addition, AsOP also directly degraded arsenopyrite, releasing As[V] and sulfate and causing acidification (pH 2.5). The findings from this study, for the first time, reveal that AsOP possesses not only As[III] oxidation capability but also anaerobic reduced sulfur compound oxidation activity that may lead to environmental acidification, highlighting the need for extreme caution when applying AsOPs in arsenic bioremediation.}, } @article {pmid42456987, year = {2026}, author = {Zhu, Y and Guo, J and Sun, H and Zhu, M and Shan, W and Lv, X and Qu, Z and Zhang, S and Liu, Y}, title = {Perfluorobutane sulfonate reshapes microbial metabolism and enhances antibiotic resistance and pathogen dissemination in anammox systems.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135422}, doi = {10.1016/j.biortech.2026.135422}, pmid = {42456987}, issn = {1873-2976}, abstract = {As the use of short-chain per- and polyfluoroalkyl substances, particularly perfluorobutane sulfonate (PFBS), continues to increase, their accumulation in wastewater treatment plants (WWTPs) and the associated ecological risks have attracted growing attention. Nevertheless, the impacts of PFBS on the anaerobic ammonium oxidation (anammox) process, as well as its role in the dissemination of antibiotic resistance genes (ARGs) and the proliferation of pathogens, remain poorly understood. In this study, metagenomic analysis combined with multidimensional data integration was employed to systematically investigate the effects of PFBS exposure on anammox performance, microbial metabolism, and ARG dynamics. The results revealed that PFBS exposure significantly deteriorated nitrogen removal, leading to a 10.16% reduction in total nitrogen removal efficiency. Carbon metabolism was inhibited, whereas microbial communities adapted by enhancing antioxidant capacity and electron transport activity. The relative abundance of key anammox functional genes (hzs and hdh) decreased by 54.65% and 57.32%, respectively. Molecular docking analysis demonstrated a strong binding affinity between PFBS and hydrazine dehydrogenase (-8 kcal/mol), suggesting potential interactions. Moreover, PFBS exhibited notable interactions with denitrification-related enzymes, suggesting potential perturbations to denitrification pathways. Additionally, PFBS facilitated the enrichment of ARG and mobile genetic elements (MGE), thereby increasing the potential for MGE-mediated ARG dissemination. PFBS enriched potential pathogenic microorganisms and strengthened their associations with ARGs. Collectively, these findings demonstrate that PFBS exposure compromises anammox performance while simultaneously elevating antimicrobial resistance dissemination and pathogen-associated risks, highlighting its ecological implications in WWTPs.}, } @article {pmid42457325, year = {2026}, author = {Zhang, YY and Gan, MY and Zhu, YQ and Wu, BB and Zhou, WH}, title = {[Application of metagenomic next-generation sequencing in the pathogen spectrum analysis of suspected infections in neonatal blood and cerebrospinal fluid].}, journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics}, volume = {28}, number = {7}, pages = {824-831}, doi = {10.7499/j.issn.1008-8830.2511025}, pmid = {42457325}, issn = {1008-8830}, abstract = {OBJECTIVES: To evaluate the performance of metagenomic next-generation sequencing (mNGS) in detecting pathogens in suspected neonatal sepsis and central nervous system infections.

METHODS: This retrospective study included 648 neonates with suspected sepsis or central nervous system infections, with 734 cerebrospinal fluid and 733 blood samples collected. The pathogen spectra detected by mNGS and traditional culture were compared. Using clinical diagnosis as the gold standard, the diagnostic efficacy of the two methods was analyzed.

RESULTS: The positive rates of pathogen detection by mNGS in cerebrospinal fluid and blood samples were 15.3% and 40.0%, respectively, significantly higher than those of traditional culture (1.4% and 10.7%, respectively). mNGS identified 25 and 40 distinct pathogenic species from cerebrospinal fluid and blood, respectively, exceeding the 4 and 24 species detected by culture. Ureaplasma, Mycoplasma, and other fastidious pathogens difficult to culture were detected exclusively by mNGS. Using clinical diagnosis as the reference, mNGS showed sensitivities of 50.4% (cerebrospinal fluid) and 46.7% (blood), compared to 5.8% and 18.0% for culture.

CONCLUSIONS: mNGS significantly improves pathogen detection rates in neonatal infections compared with traditional culture, provides more comprehensive pathogen information, and holds important clinical value for the precise diagnosis and treatment of neonatal infections.}, } @article {pmid42457685, year = {2026}, author = {Wei, L and Cui, Z and Mu, Z and Li, Y and Deng, F}, title = {Comparative fecal microbiome and metabolome reveal enhanced lignocellulose-degrading potential in Cervus elaphus yarkandensis.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-01002-3}, pmid = {42457685}, issn = {2396-8370}, support = {ygzbhly2025102//School-level project fund of Chongqing Medical and Pharmaceutical College/ ; QN[2025]100//Guizhou Provincial Basic Research Program (Natural Science) Youth Guidance Project/ ; }, abstract = {Reed is rich in lignocellulose and is therefore challenging for many ruminants to use efficiently. The endangered Tarim red deer subspecies Cervus elaphus yarkandensis (TH) inhabits the Tarim Basin, where reed represents an important forage resource, whereas captive observations suggest that the closely related Cervus elaphus songaricus (TS) may exhibit poorer tolerance to reed-rich diets. Here, we compared fecal microbial composition, metagenomic functional potential, metagenome-assembled genome (MAG)-level carbohydrate-active enzyme (CAZyme) profiles, fecal enzymatic activities, in vitro reed-straw degradation capacity, and fecal and serum metabolomic profiles between TH and TS under the same reed-containing feeding conditions. Compared with TS, TH showed higher fecal microbial diversity and increased abundances of fiber-associated taxa, including Ruminococcaceae, Lachnospiraceae, and Alistipes. Shotgun metagenomics and MAG-level CAZyme analysis indicated that TH-associated microbial communities carried a broader repertoire of functions related to lignocellulose degradation and plant-polysaccharide deconstruction. Consistent with these functional profiles, TH fecal samples exhibited higher cellulase and hemicellulase activities, and TH fecal inocula showed greater reed-straw degradation capacity than TS fecal inocula in vitro. Untargeted metabolomics revealed group-specific fecal and serum metabolites related to carbohydrate fermentation, short-chain fatty-acid-related metabolism, and lipid metabolism, which were associated with TH-enriched fiber-degrading taxa and microbial functional pathways. In an exploratory mouse colonization experiment, TH-derived fecal microbiota was associated with changes in fiber-associated microbial taxa, metabolic pathways, fecal metabolites, body weight, and intestinal morphology in antibiotic-treated mice fed a reed-containing diet. Together, these results indicate that TH harbors fecal microbial and metabolic features associated with enhanced lignocellulose and reed-straw degradation capacity. These findings suggest candidate microbiome-associated pathways relevant to reed-rich forage utilization and may help identify microbial and enzymatic resources for lignocellulose bioconversion.}, } @article {pmid42457990, year = {2026}, author = {Danielsson, H and Portlock, T and Hellström, A and Nilsson, A and Sävman, K and Wackernagel, D and Hansen-Pupp, I and Ley, D and Shoaie, S and Uhlén, M and Brusselaers, N and Elfvin, A}, title = {Supplementation with long-chain polyunsaturated fatty acids to extremely preterm infants associates with development of the intestinal microbiota.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {42457990}, issn = {1530-0447}, abstract = {BACKGROUND: Supplementation with arachidonic acid (AA) and docosahexaenoic acid (DHA) to extremely preterm infants reduces the risk of severe retinopathy of prematurity (ROP). The main aim of this study was to explore the involvement of AA:DHA supplementation in the developing gut microbiome, and its possible contribution to the ROP-protective effect. Secondly, additional covariates for microbiome maturation were evaluated.

METHODS: Longitudinal gut microbiome profiles and bacterial gene pathways were characterised using shot-gun metagenomics in 75 extremely preterm infants who participated in a randomized clinical trial on AA:DHA supplementation. Serum protein levels quantified using proximity extension assays were merged with the microbiome data.

RESULTS: AA:DHA supplementation was linked to an increase in relative abundance of Citrobacter koseri and associated with changes in proteins and metabolic pathways. Occurrence of severe ROP was associated with microbiome alpha diversity (Shannon and Evenness) and beta diversity (Bray-Curtis). Additionally, study centre and gestational age at birth impacted the microbiome composition.

CONCLUSION: We conclude that AA:DHA supplementation impacts the microbiome. However, the current study could not determine the causality between the supplementation, microbiome and ROP-decrease. Nonetheless, these findings highlight the complex interplay between external interventions, including nutritional supplements, and the gut microbiome development in extremely preterm infants.

IMPACT: Longitudinal gut microbiome profiles, bacterial gene pathways and serum protein expressions were determined using shotgun metagenomics and proximity extension assays in 75 extremely preterm infants included in a multicentre randomized clinical trial investigating enteral fatty acid supplementation. Dynamic shifts in microbiome and pathway composition were seen from birth to 34 weeks gestational age. Arachidonic acid (AA) and docosahexaenoic acid (DHA) supplementation was linked to an increase in relative abundance of Citrobacter koseri and associated with changes in proteins and metabolic pathways. However, the causality between the supplementation, microbiome, and ROP-decrease could not be determined.}, } @article {pmid42443209, year = {2026}, author = {Xie, YG and Cao, XR and Qi, YL and Chen, L and Mao, YH and Li, Y and Wang, CJ and Li, ZW and Qu, YN and Li, WJ and Hua, ZS}, title = {Genome-resolved discovery of Candidatus Vitaminotrophota reveals carbon fixation and multi-vitamin biosynthetic potential in hot springs.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01093-6}, pmid = {42443209}, issn = {2055-5008}, support = {32400002//National Natural Science Foundation of China/ ; 32471574//National Natural Science Foundation of China/ ; }, abstract = {Geothermal environments harbor abundant microbial diversity, yet rare lineages remain poorly resolved, limiting understanding of ecosystem function and evolutionary innovation under energy limitation. Here, we describe Candidatus Vitaminotrophota, a previously unrecognized bacterial phylum represented by 35 metagenome-assembled genomes (MAGs) from Tengchong hot spring sediments, China. Phylogenomic analyses support a coherent internal taxonomy comprising one order, two families and four candidate genera. Metabolic reconstruction indicates a predominantly anaerobic, mixotrophic lifestyle, with widespread carbon fixation potential via the Wood-Ljungdahl pathway and a noncanonical CODH/ACS architecture featuring divergent acsA paralogs. Nitrogenase structural genes (nifHDK) occur in two genera, suggesting diazotrophic potential in part of the lineage. All MAGs encode complete or near-complete cobalamin and pantothenate biosynthesis pathways, and most retain conserved thiamine pathway components, alongside transport systems consistent with corrinoid and metal acquisition. Ca. Vitaminotrophota dominated community-level cobalamin biosynthetic potential in several samples, reaching 99.11% and accounting for >50% in nearly half of the samples. Conserved flagellar and chemotaxis gene sets suggest capacity to navigate steep physicochemical gradients. These findings expand the phylogenetic and functional landscape of geothermal bacteria and identify Ca. Vitaminotrophota as a candidate contributor to carbon fixation and vitamin-mediated metabolic interactions in nutrient-limited hot springs.}, } @article {pmid42443210, year = {2026}, author = {Wang, YF and Xu, JY and Liu, Y and Ni, B and Zhang, TL and Cui, HL and Qi, FY and Qiao, M and Li, HZ and Gillings, MR and Zhu, YG and Zhu, D}, title = {Divergent mechanisms of active antibiotic resistance gene enrichment in soil driven by pesticide diversity.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-75445-3}, pmid = {42443210}, issn = {2041-1723}, support = {22193062//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Antimicrobial resistance is an escalating global threat, with soils serving as reservoirs and conduits for the dissemination of antibiotic resistance genes (ARGs). Pesticide use in agriculture contributes to ARG proliferation, and ~60% of agricultural soils contain multiple pesticide residues. However, how pesticide diversity influences ARG dynamics in active microbial populations (active ARGs) remains unclear. Here, we evaluate the effects of pesticide diversity on active soil ARGs through a long-term field experiment integrating bioorthogonal non-canonical amino acid tagging (BONCAT), fluorescence-activated cell sorting (FACS), and metagenomics. We show that both low and high pesticide diversity significantly increase active ARG abundance relative to untreated control, whereas total ARG levels remain largely unchanged. The underlying mechanisms differ with pesticide diversity. At low diversity, active ARG co-selection via efflux pumps in Acinetobacter baumannii is a prominent mechanism. At high diversity, elevated reactive oxygen species and SOS responses promote horizontal gene transfer of active ARGs, as validated by culture experiments. These findings demonstrate that increasing pesticide diversity accelerates the emergence and dissemination of active ARGs, highlighting the need for integrated pesticide management strategies that consider both application intensity and diversity to mitigate resistance risks under the One Health framework.}, } @article {pmid42443349, year = {2026}, author = {Yang, Q and Fu, L and Chen, H and Huang, W and Guo, Y and Liu, L and Fu, Q and Liu, T and Chen, F}, title = {An investigation of the abnormalities in the microbiome‑gut‑brain axis in betel quid chewers.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-60616-5}, pmid = {42443349}, issn = {2045-2322}, support = {Qhyb2023-183//the Hainan Provincial Graduate Innovation Research Project/ ; ZDYF2024SHFZ058, ZDYF2023SHFZ096//the Key Science and Technology Project of Hainan Province/ ; 82271977, 82160327//the National Nature Science Foundation of China/ ; YSPTZX202514//the Innovation Platform for Academicians of Hainan Province and Hainan Academician Innovation Platform Scientific Research Project/ ; }, abstract = {Betel quid (BQ) chewing, a prevalent practice affecting over 600 million people globally, is associated with systemic toxicity and neurological alterations. While dysbiosis of the gut microbiota is implicated in neuropsychiatric disorders via the gut-brain axis (GBA), its role in BQ chewers remains unexplored. This exploratory study aimed to investigate whether chronic BQ chewing is associated with gut dysbiosis and alterations in spontaneous brain activity. Fecal samples (n = 30 BQ chewers, n = 19 healthy controls) were subjected to whole metagenome shotgun sequencing (WMGS) to assess microbial composition and function. Amplitude of low-frequency fluctuations (ALFF) values, a resting-state functional magnetic resonance imaging metric reflecting regional spontaneous neural activity, were assessed in a subset of 29 BQ chewers and 21 healthy controls. Group differences in microbiota and ALFF were analyzed using the Wilcoxon rank-sum test and two-sample t-test (adjusted for age, sex, education, smoking and alchohol). Partial Spearman's correlation analysis was performed to link microbial taxa with ALFF alterations. Motivated by the presence of complex polysaccharides and polyphenols in BQ, carbohydrate-active enzyme (CAZyme) profiles were also assessed. Chronic BQ chewers exhibited significant gut microbiome alterations, characterized by reduced microbial diversity, enrichment of pro-inflammatory genera, and depletion of beneficial taxa. Analysis of carbohydrate-active enzymes further revealed altered metabolic potential in BQ chewers. Furthermore, reduced ALFF was observed in the limbic lobe of BQ chewers. At a nominal significance level, Streptococcus abundance correlated positively with limbic ALFF (partial ρ = 0.35, 95% CI [0.07, 0.58], raw p = 0.04), whereas Dorea formicigenerans exhibited a negative correlation (partial ρ = -0.36, 95% CI [- 0.55, - 0.08], raw p = 0.04). Chronic BQ chewing is associated with gut microbial dysbiosis and functional metabolic shifts. Exploratory analyses suggest that these microbial features may correlate with spontaneous neural activity in the limbic lobe, providing preliminary evidence for a potential involvement of the GBA in BQ‑associated neurological sequelae. These findings highlight the need for further investigation into microbiota‑targeted strategies in BQ chewers.}, } @article {pmid42443738, year = {2026}, author = {Carasso, S and Gefen, T and Bakria, R and Bar-Yoseph, H and Geva-Zatorsky, N}, title = {Microbiome changes associated with FMT-mediated clearance of antibiotic-resistant Klebsiella pneumoniae in a murine carriage model.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05354-4}, pmid = {42443738}, issn = {1471-2180}, support = {grant 1571/17 and 3165/20//Israeli Science Foundation/ ; grant FL-000969/FL-001245/FL-001381//CIFAR Azrieli Global Scholars/ ; grant CDA00025/2019-C//Human Frontier Science Program Career Development Award/ ; ERC, ExtractABact, 101078712//the European Union/ ; }, abstract = {Carbapenem-resistant Enterobacterales (CRE), including Klebsiella pneumoniae (KP), pose a significant public health threat due to their resistance to last-line antibiotics. Eliminating CRE colonization in asymptomatic carriers is crucial to prevent the spread of resistance, as carriage often serves as a reservoir that enables the transmission of resistant strains to vulnerable populations. Fecal microbiota transplantation (FMT) has emerged as a potential strategy to restore gut microbiome balance and eliminate CRE colonization. However, the mechanisms driving successful decolonization warrant further research. This study investigates the impact of FMT on gut microbiome composition, CRE-KP clearance and host response, in a mouse model of CRE-KP carriage. Mice colonized with CRE-KP, were treated with FMT or left untreated. Shotgun metagenomics of fecal samples were used to monitor changes in microbiome composition and function. FMT resulted in substantial changes in the gut microbiome, with successful clearance correlating with an expansion of commensal bacteria including Bifidobacterium and Lactobacillus species. Notably, a reduction in K. pneumoniae was also observed in some untreated control mice as the microbiome recovered naturally, also associated with Bifidobacterium expansion. Phage profiling revealed distinct viral populations that were associated with successful decolonization. Flow cytometry was employed to quantify bacterial populations bound by immunoglobulins, providing insight into host immune modulation. These findings suggest potential mechanisms for CRE carriage eradication using microbiome targeted therapies. The results emphasize the importance of microbiome resilience in combating antibiotic-resistant infections and suggest that phage-microbiome interactions could play a role in restoring microbial balance.}, } @article {pmid42443941, year = {2026}, author = {Markkanen, M and Putkuri, H and Kičiatovas, D and Mustonen, V and Virta, M and Karkman, A}, title = {Long-read metagenomics and methylation-based binning support the discovery of antibiotic resistance gene-host associations in complex communities.}, journal = {Genome biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13059-026-04200-0}, pmid = {42443941}, issn = {1474-760X}, support = {364234//Research Council of Finland funding for the Multidisciplinary Center of Excellence in Antimicrobial Resistance Research/ ; 364231//Research Council of Finland funding for the Multidisciplinary Center of Excellence in Antimicrobial Resistance Research/ ; }, abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) circulating among clinically relevant bacteria pose serious challenges to public health. Given the ancient and environmental bacterial origins of ARGs, a better understanding of the carriers of ARGs beyond the clinically most relevant species is urgently needed for longer-term resistance monitoring and intervention measures. While the risks of emerging ARGs from environmental sources have been recognized, the identification bottlenecks stem from the limitations of shotgun metagenomic sequencing and bioinformatic methods.

RESULTS: We use long-read metagenomic sequencing and bacteria-specific methylation profiles to re-establish the links between established (well-described) or latent (absent in databases) ARGs and their bacterial and genetic contexts in wastewater. We analyze base modification data produced by PacBio SMRT sequencing using an in-house pipeline utilizing position weight matrices and UMAP visualizations, which we validate by a synthetic community with known bacterial composition. Our analysis reveals several previously unreported ARGs and ARG-host linkages in wastewater. For instance, we find that Arcobacter, a key wastewater associated taxon and emerging pathogen, carries a latent beta-lactamase gene with high predicted mobility potential. Of the other understudied beta-lactamases, we describe blaMCA within pdif-modules across highly varying contexts suggesting its recent acquisition events. Additionally, we uncover the wastewater resident taxa mediated carriage of clinically important ARGs.

CONCLUSIONS: By linking ARGs to their wider genetic contexts and hosts, our findings shed light on the previously unrecognized carriers of resistance genes in wastewater. The presented approach provides a valuable methodology for early identification of newly arising ARGs and their hosts.}, } @article {pmid42444523, year = {2026}, author = {Santucci, NR and Dike, CR and Hellmann, J and Ollberding, NJ and Duan, Q and Minar, P and Denson, LA and Haslam, DB and Castillo, D and Abu-El-Haija, M}, title = {Gut microbiome in pediatric acute pancreatitis and Crohn's disease versus irritable bowel syndrome and healthy controls.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpn3.70504}, pmid = {42444523}, issn = {1536-4801}, support = {K23DK135797//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; 23DK118190//National Institutes of Health - National Institute of Diabetes and Digestive and Kidney Disease/ ; R03 DK131156/DK/NIDDK NIH HHS/United States ; P30 DK078392/GF/NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati/ ; NCT04131504//Leona M. and Harry B. Helmsley Charitable Trust for the ENvISION study/ ; }, abstract = {OBJECTIVES: Pediatric acute pancreatitis (AP), Crohn's disease (CD), and irritable bowel syndrome (IBS) are associated with gut dysbiosis, but differences and similarities between conditions are unknown. We hypothesized that gut microbial ecology would differ across these disorders.

METHODS: Stool was collected from 120 subjects (AP [n = 30], CD [n = 29], IBS Rome IV [n = 27], and healthy controls [HC, n = 34]). Shotgun metagenomic sequencing was performed on extracted DNA and taxonomic and functional profiles obtained using sylph and HUMAnN3 with default parameters.

RESULTS: Age interquartile range for all participants was 8.1-17.7 years. Shannon diversity was decreased in AP compared to IBS or HC (p < 0.0001) and similar to CD (p = 0.97). CD differed from IBS (p = 0.001) and HC (p < 0.0001) while IBS and HC were similar (p = 0.61). Ordination of the first two principal coordinate analyses axes showed sample clustering by condition (R[2] = 0.12, p < 0.001), and differences between all conditions in pairwise comparisons (p < 0.001). Escherichia coli, Ruminococcus gnavus, Staphylococcus aureus, and Thomasciavelia ramosa remained enriched when all conditions (AP, CD, and IBS) were compared as a single group to HC. Using a random forest machine learning algorithm for species relative abundance, the ability to classify a sample to each condition versus all others was highest for CD (area under the receiver operative characteristic curve, AUC = 0.97), followed by AP (AUC = 0.92), HC (AUC = 0.88), and IBS (AUC = 0.83).

CONCLUSION: Organic disorders (AP and CD) are associated with significant gut dysbiosis than IBS which appears more like HC. Interventions targeting shifts in commensals in AP and CD may be helpful in improving outcomes in both disorders.}, } @article {pmid42445134, year = {2026}, author = {Yang, Q and Chen, Y and Chen, L and Wei, S}, title = {Tropheryma whipplei pneumonia: a retrospective case series of nine patients with treatment response.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1883057}, pmid = {42445134}, issn = {2296-858X}, abstract = {BACKGROUND: The detection of Tropheryma whipplei in respiratory specimens has increased with metagenomic next-generation sequencing (mNGS), yet distinguishing colonization from active infection remains challenging. In clinical settings lacking quantitative PCR or pathological confirmation, practical approaches to guide treatment decisions are urgently needed.

METHODS: We retrospectively analyzed nine patients (January 2019-January 2024) with T. whipplei detected by bronchoalveolar lavage fluid (BALF) mNGS. All patients initially received cefoperazone-sulbactam (3.0 g q8h) as empirical therapy for 3-5 days without improvement. Targeted therapy (ceftriaxone or meropenem combined with doxycycline or trimethoprim-sulfamethoxazole) was subsequently initiated. We describe clinical characteristics and treatment outcomes.

RESULTS: Among nine patients (3 male, 6 female; mean age 59 years, range 32-79), six (67%) were immunosuppressed. Primary manifestations included fever (67%), cough with sputum (89%), and dyspnea (78%). Common laboratory findings were anemia (67%), lymphocytopenia (67%), hypoalbuminemia (100%), and elevated inflammatory markers (78%). Chest CT predominantly showed patchy ground-glass opacities. Eight cases (89%) had co-infections. All patients showed no improvement after initial cefoperazone-sulbactam therapy. After targeted therapy was initiated, eight patients (89%) achieved defervescence within 3-5 days, with resolution of pulmonary infiltrates on follow-up CT within 10-14 days. Among these eight responders, one patient (Case 4) underwent repeat BALF mNGS which demonstrated a >99.99% reduction in T. whipplei (from 6,100,499 to 383 reads), reported in the suspected colonizer list rather than the pathogen panel. One non-responder (Case 8) showed a >99% reduction in T. whipplei read count on repeat BALF mNGS after targeted therapy, but ultimately died of polymicrobial sepsis from multidrug-resistant co-pathogens. No relapse occurred during 1-year follow-up.

CONCLUSION: This retrospective case series suggests that rapid improvement after adding targeted anti-T. whipplei therapy is compatible with possible T. whipplei-associated infection in selected mNGS-positive patients, rather than colonization alone. Sequential mNGS showed marked burden reduction in two cases. These observations require prospective validation.}, } @article {pmid42445282, year = {2026}, author = {Xue, K and Lei, S and Cheng, X and Xu, W and Lin, Z and Zhou, Y and Mao, X and Ge, X and Zhu, H and Zhu, F}, title = {A two-hit ecological framework linking social context to caries-associated microbiome shifts in children.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2677291}, pmid = {42445282}, issn = {2000-2297}, abstract = {BACKGROUND: Dental caries arises from an ecological imbalance within a complex community. How chronic social context relates to ecological heterogeneity and dysbiosis-associated microbial shifts in school-age children remains unclear.

OBJECTIVE: To investigate the associations of left-behind status and caries burden with the salivary microbiome and to explore a two-hit ecological framework linking social context to caries-associated microbial shifts.

DESIGN: In this cross-sectional study, 127 rural children were classified using a 2 × 2 framework based on left-behind status and caries burden. Saliva samples underwent shotgun metagenomic sequencing. Ecological analyses and covariate-adjusted multivariable models were performed.

RESULTS: Alpha diversity did not differ across groups. Global community centroids were similar, whereas within-group dispersion was higher in left-behind children, suggesting greater ecological heterogeneity. After covariate adjustment, no genus-level associations remained significant, whereas several KEGG level 3 pathways related to translation and carbohydrate utilization were positively associated with dmft. Stratified analyses showed concordant caries-related enrichment of Streptococcus, Veillonella, and carbohydrate-utilization pathways across social strata. Ecological subtyping identified Neisseria- and Veillonella-anchored community types.

CONCLUSION: The findings are consistent with a two-hit ecological framework in which social context is associated with greater ecological heterogeneity and cariogenic pressure is associated with reproducible functional shifts. Given the cross-sectional design, this framework should be considered hypothesis-generating.}, } @article {pmid42445283, year = {2026}, author = {Al-Maweri, SA and Ba-Hattab, R and Alomairi, A and Syed, A and Azouni, K and Batta, N and Almeer, F and Assad, R and Al-Mansoori, A and Eltai, NO and Al-Hashimi, N and Al-Hebshi, NN and Almashraqi, AA}, title = {Metagenomic analysis of tongue samples from healthy subjects identifies distinct microbiome orotypes.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2687934}, pmid = {42445283}, issn = {2000-2297}, abstract = {BACKGROUND: The tongue dorsum harbors a complex microbiome that remains incompletely characterized.

OBJECTIVE: This study aimed to characterize the tongue microbiome-including its phageome-in a healthy Qatari population.

DESIGN: Shotgun metagenomic sequencing was performed on tongue-coating samples from 92 systemically healthy adults to comprehensively profile the bacteriome, phageome and functional potential of the tongue microbiome.

RESULTS: Taxonomic profiling revealed a predominantly bacterial community (>99%) dominated by Veillonella, Streptococcus, Neisseria, Rothia, Prevotella, Haemophilus and Pauljensenia. Among low-abundance domains, the fungus Saccharomyces and the protist Entamoeba were most prevalent. Dirichlet-multinomial mixture clustering identified three distinct bacterial 'orotypes' (C1-C3) showing significant compositional separation (PERMANOVA, p = 0.001) and alpha diversity differences at both genus and species levels. A major compositional gradient involved enrichment of Neisseria and Haemophilus in C2, their absence in C3 and intermediate representation in C1. Functional profiling revealed a conserved core of housekeeping pathways across orotypes, wherease adaptive functionsdiffered across orotypes, particularly in the Neisseria/Haemophilus-enriched C2 orotype. The phageome was dominated by Uroviricota (class Caudoviricetes).

CONCLUSION: The findings identify distinct tongue microbiome orotypes with conserved core functions, divergent taxonomic and metabolic profiles, and provide new insights into the tongue phageome, establishing a foundation for investigating their roles in health.}, } @article {pmid42445473, year = {2026}, author = {Zhuang, J and Yu, Z and Jin, C and Qiu, H and Wu, Y and Feng, Q and Zheng, S and Wang, J}, title = {Detection Blind Spots in Microbial Culture, tNGS, and mNGS: Anaerobic Bacterial Infections in the Lung-A Retrospective Analysis of Two Cases.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {611567}, pmid = {42445473}, issn = {1178-6973}, abstract = {Aspiration pneumonia is often associated with specific obligate anaerobic bacteria, particularly oral commensals, as causative agents; however, these infections are frequently misdiagnosed in clinical settings. This retrospective analysis of two patients presenting with fever and cough demonstrates that, in the setting of inconclusive routine microbiological testing and tNGS results, along with ineffective empirical antimicrobial therapy, comprehensive mNGS analysis of BALF microbiota-combined with the presence of high-risk oral factors (such as dental caries and severe periodontitis)-facilitated the diagnosis of anaerobic pneumonia. In both cases, tNGS was unable to detect anaerobic pathogens due to the limited scope of anaerobic bacterial targets in commercial panels. In contrast, comprehensive mNGS, when correctly interpreted in conjunction with clinical context, can detect anaerobic sequences. The key difference lies in that mNGS offers a broader detection capability, but it requires careful correlation with clinical circumstances to distinguish between true pathogens and colonizing bacteria. Specifically, Case 1 revealed the presence of Bacteroides timidum and Fusobacterium nucleatum. Case 2 identified Prevotella oralis, Streptococcus australis, and Actinomyces caries. The administration of targeted anti-anaerobic therapy (metronidazole, ornidazole) subsequently resulted in significant improvement in clinical symptoms and radiographic findings. These cases underscore the diagnostic value of integrating metagenomic next-generation sequencing (mNGS) with clinical risk factor assessment when conventional diagnostics produce negative results.}, } @article {pmid42445487, year = {2026}, author = {Liu, M and Liu, T and Jin, S and Liu, P and Wang, X and Liu, X}, title = {Remodeling of gut bacteriome and virome in acute retinal necrosis: expansion of Enterobacteriaceae-related taxa.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1848524}, pmid = {42445487}, issn = {1664-302X}, abstract = {BACKGROUND: This study was designed to examine the alterations in the gut bacteriome and virome of patients with acute retinal necrosis (ARN), and to explore potential cross-kingdom microbial associations.

METHODS: The gut virome and bacteriome of 10 patients with new-onset ARN and 10 age- and sex-matched healthy individuals (N) were profiled using viral metagenomics and 16S rRNA sequencing, respectively.

RESULTS: The gut bacteriome in ARN patients was significantly altered, with Enterobacteriaceae_A increased at the family level. Genus-level analysis further described higher relative abundances of opportunistic pathogens, such as Escherichia and Klebsiella, alongside lower relative abundances of commensal anaerobes, including Fusicatenibacter and Anaerobutyricum. Exploratory clinical association analysis suggested a positive association between Klebsiella and intraocular pressure, while Fusicatenibacter tended to be further reduced in patients with vasculitis involving the major retinal arteries. Predicted bacterial functional profiling indicated an enrichment in enterobactin biosynthesis and related metabolic pathways. In contrast, differences in the gut eukaryotic virome were limited, and no significant enrichment of fecal Herpesviridae was detected. Virome perturbations predominantly occurred at the bacteriophage level, featuring shifts in predicted bacterial host assignment from commensal bacteria toward opportunistic pathogen-associated taxa and an increased inferred proportion of temperate phages. Exploratory cross-kingdom analysis suggested associations involving Escherichia and three related phage features.

CONCLUSION: Gut dysbiosis in ARN was associated with Enterobacteriaceae-related bacterial remodeling and phage alterations. These findings highlight an ARN-associated bacteriome-phage alteration pattern that warrants validation in larger independent cohorts.}, } @article {pmid42445491, year = {2026}, author = {Luo, L and Cheng, K and Chen, B and Li, Y and Ruan, L and Li, Z and Zhu, S and Zhao, L and Zhang, C and Liu, Y and Li, T}, title = {Depletion of Blautia wexlerae and Parabacteroides distasonis in adiposity-related prehypertension.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1873803}, pmid = {42445491}, issn = {1664-302X}, abstract = {BACKGROUND: Prehypertension is more likely to develop into hypertension in individuals with adiposity. We aimed to explore how adiposity influences prehypertension through gut microbiota.

METHODS: Kaplan-Meier and Cox proportional hazard regression models were employed to evaluate the association between prehypertension and adiposity in 649 individuals. Among them, 197 consented to provide fecal samples and were divided, along with 184 additional participants, into healthy controls (HC), individuals with adiposity and normal tension (Ad-NT), and those with prehypertension (Ad-pHT) based on body mass index (BMI) and blood pressure. Shotgun metagenomic sequencing was performed on fecal samples, followed by taxonomic and functional annotations using MetaPhlAn and HUMAnN. Linear discriminant analysis effect size (LEfSe) was used to analyze differences in microbial species and metabolic pathways across groups. Partial Spearman rank correlation analysis was used to assess microbial interactions, and the relationships among metabolic pathways, species, BMI, and blood pressure.

RESULTS: Elevated BMI independently predicted the risk of prehypertension (adjusted HR = 1.072, 95% CI: 1.002-1.147). We observed the depletion of Blautia wexlerae and Parabacteroides distasonis in populations with Ad-pHT. A multiclass logistic regression model distinguished individuals with Ad-pHT from HC and those with adiposity and normal tension (Ad-NT) (AUC = 0.704). Microbiota-microbiota interactions gradually become complex from HC to Ad-NT to Ad-pHT groups. Blautia wexlerae and Parabacteroides distasonis were associated with pathways involved in carbohydrate degradation (PWY-8004), fermentation (ANAEROFRUCAT-PWY), biosynthesis of secondary metabolites (PWY-6270), amino acid (ARGININE-SYN4-PWY), quinol and quinone (PWY-7992), and nucleoside and nucleotide (PWY-6700).

CONCLUSION: Shifts in Blautia wexlerae and Parabacteroides distasonis, as well as their relationships with pathways (energy metabolism and amino acid biosynthesis), were observed in adiposity-related prehypertension. Blautia wexlerae and Parabacteroides distasonis might represent promising candidates for next-generation probiotics targeting weight management and blood pressure reduction, which require validation in clinical studies.}, } @article {pmid42445502, year = {2026}, author = {Hou, H and Zhang, X and Chen, S and Kong, Y and Yang, S and Gao, Z and Cui, Z and Lv, Z and Yang, Z and Yuan, Y and Feng, B}, title = {Saline-alkali gradients reshape soil microbial network complexity and niche breadth.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1886660}, pmid = {42445502}, issn = {1664-302X}, abstract = {INTRODUCTION: Saline-alkali soils impose combined osmotic, ionic and alkaline constraints on soil microorganisms, yet how bacterial and fungal ecological strategies vary along saline-alkali gradients remains insufficiently resolved.

METHODS: We analyzed 30 composite soil samples from 10 sites across China using bacterial 16S rRNA and fungal ITS amplicon sequencing, soil physicochemical profiling, co-occurrence network analysis, niche breadth classification and PICRUSt2-based functional prediction.

RESULTS: Higher saline-alkali intensity was associated with reduced nutrient availability, lower microbial network complexity and greater network vulnerability. Bacterial specialists showed stronger diversity and compositional responses than generalists, whereas fungal communities displayed comparatively stable patterns across the sampled gradient. Predicted bacterial functional profiles suggested an increased representation of stress-survival-related pathways under high saline-alkali conditions.

DISCUSSION: These findings identify microbial taxa, network properties and predicted functional features associated with saline-alkali soil degradation and provide candidate targets for future culture-based, metagenomic and experimental validation.}, } @article {pmid42445733, year = {2026}, author = {Yang, L and Liu, Y and Li, J and Lv, J and Zhang, Q and Cong, M and Shi, H and Zhang, H}, title = {Bifidobacterium animalis subsp. lactis V9 improves quality of life in advanced gastrointestinal cancer through gut microbiota-metabolite modulation.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag127}, pmid = {42445733}, issn = {2730-6151}, abstract = {Chemotherapy for advanced gastric and esophageal cancer is often limited by severe gastrointestinal and systemic toxicities that profoundly impair patients' quality of life. We conducted a randomized, double-blind, placebo-controlled trial in 104 patients to evaluate whether Bifidobacterium animalis subsp. lactis V9 (V9; 2 × 10[10] CFU/day) mitigates these effects. Participants received V9 or placebo daily for 18 weeks alongside standard chemotherapy. Supplementation with V9 significantly improved EORTC QLQ-C30 scores for overall health status, fatigue, nausea, vomiting, appetite loss, cognitive functioning, role functioning, and insomnia (all P < .01). Integrated metagenomic and metabolomic analyses of stool samples revealed that V9 did not alter overall microbial α- or β-diversity but induced targeted shifts: it enriched beneficial taxa, such as B. pseudocatenulatum, Agathobacter rectalis, and Lachnospira hominis, while depleting pathobionts such as Fusobacterium varium and Enterocloster clostridioformis. These microbial changes correlated with favorable metabolic reprogramming, including increased fecal levels of pyridoxamine, 5'-methylthioadenosine, and palmitoylcarnitine, as well as decreased levels of taurine-conjugated bile acids and several amino acids (P < .05). Critically, these metabolite alterations were significantly associated with clinical improvements. Our findings demonstrate that V9 enhances quality of life during chemotherapy not through global microbiota restructuring, but via precise modulation of functionally relevant bacteria and their metabolic outputs. This supports V9 as a mechanistically grounded, targeted adjuvant therapy to improve resilience and well-being in patients with advanced upper gastrointestinal cancers.}, } @article {pmid42445734, year = {2026}, author = {Storck, V and Ponton, DE and Lawruk-Desjardins, C and Ferriz, LM and Leclerc, M and Kraemer, S and Planas, D and Amyot, M and Walsh, D}, title = {Cross-habitat interactions drive methylmercury contamination in a disturbed river ecosystem: novel metagenomic and biogeochemical insights.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag176}, pmid = {42445734}, issn = {2730-6151}, abstract = {Understanding contaminant dynamics in ecosystems requires considering interactions between habitats-an aspect often overlooked in research. Mercury (Hg) studies typically focus on methylmercury (MeHg) production in sediments, often neglecting the role of biofilms such as periphyton. This study analyzes sediments and periphyton in a disturbed river using biogeochemical and metagenomic approaches. We found that microbial communities differed between habitats, but Hg-methylating microbes were taxonomically similar, with higher abundance in sediments. Organic matter (OM), a key Hg vector, likely affects Hg dynamics differently across habitats: MeHg concentrations increased with increasing terrigenous OM in sediments, whereas in periphyton, MeHg increased with greater contributions of aquatic-derived OM. Surprisingly, periphyton showed higher MeHg concentrations than sediments, despite lower hgcA abundance, the gene associated with MeHg production. Our multi-indicator analysis provides a conceptual model suggesting that MeHg is primarily produced in active sediments (indicated by elevated carbon dioxide and methane), diffuses into the water column (supported by carbon dioxide-MeHg correlations), and accumulates in protein-rich periphyton in shallow, low-flow waters where prolonged exposure can enhance MeHg retention. While some MeHg production occurs in periphyton, especially at a wetland site with thick growth, periphyton at a hydroelectric-impacted site showed the highest MeHg levels despite absent hgcA and methylation activity, pointing towards MeHg retention from the water. As a major food source for primary consumers, periphyton likely redistributes accumulated MeHg through the food web. This study highlights the importance of considering MeHg transfer between habitats and the need to examine entire aquatic ecosystems to fully understand MeHg dynamics.}, } @article {pmid42445853, year = {2026}, author = {Chen, X and Pan, J and Wang, Y and Wei, Y and Zhang, X and Jiang, H and Zhang, L and Wu, G and Chen, B and Xie, J and Tong, P}, title = {Detection and molecular characterization of bovine enterovirus E2 from dairy calves with respiratory disease in Urumqi, Xinjiang, China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1800707}, pmid = {42445853}, issn = {2235-2988}, mesh = {Animals ; Cattle ; China/epidemiology ; Phylogeny ; *Cattle Diseases/virology/epidemiology ; *Enterovirus, Bovine/genetics/isolation & purification/classification ; *Respiratory Tract Infections/veterinary/virology/epidemiology ; Disease Outbreaks/veterinary ; *Enterovirus Infections/veterinary/virology/epidemiology ; Genome, Viral ; Metagenomics ; }, abstract = {INTRODUCTION: Bovine enterovirus (BEV) is a contagious viral agent that can cause respiratory infections and disease outbreaks among calves. This study reports an outbreak that occurred in a population of dairy calves in northern Xinjiang in November 2024.

METHODS: Nasal swab samples were collected from 58 clinically symptomatic calves and analyzed for some bovine respiratory viruses using RT-PCR and viral metagenomic sequencing.

RESULTS: Viral metagenomic analysis annotated only one bovine pathogen, BEV, in respiratory disease samples. RT-PCR further confirmed that BEV was detected in all nasal swab samples from symptomatic dairy calves, while it was not detected in samples from healthy dairy cattle, suggesting that BEV may be the etiological agent of this respiratory disease. One BEV strain, designated XJ-FHT, was successfully isolated and found to be responsible for respiratory illness in calves. Comparative analysis of the whole genome, the encoded polyprotein, and the nucleotide and amino acid sequences of VP1 and P1, along with phylogenetic analysis of VP1 amino acid sequences, classified this isolate as belonging to the E2 subtype.

DISCUSSION: This study provides the first identification of a BEV-associated respiratory disease among calves in Xinjiang, China, in 2024. Molecular characterization and phylogenetic analysis identified the isolated strain as belonging to the E2 subtype. These findings highlight the potential role of BEV in bovine respiratory infections and emphasize the need for continued surveillance and preventive measures.}, } @article {pmid42446199, year = {2026}, author = {Landa, MM and Mendoza, A and Rossoff, J and Rosenthal, A and Chaudhury, S and Muller, WJ}, title = {Plasma metagenomic sequencing testing for diagnosis of invasive fungal infection in children and young adults.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0069926}, doi = {10.1128/spectrum.00699-26}, pmid = {42446199}, issn = {2165-0497}, abstract = {UNLABELLED: Invasive fungal infection (IFI) is challenging to diagnose, often involving invasive sampling. Plasma cell-free metagenomic next-generation sequencing (mNGS) has shown promise in diagnosing infections, but data are limited on specific clinical scenarios in which this test is most helpful. We conducted a retrospective single-center study of children and young adults with high-risk conditions evaluated for IFI between December 2016 and November 2024. Clinical concern for IFI was indicated by (i) evaluation with both serum β-D-glucan and galactomannan testing, (ii) either or both of CT scans of sinuses and chest, and (iii) antifungal treatment either started or broadened. Episodes in which mNGS testing was sent within 30 days of initiation or broadening of antifungal coverage were evaluated to determine the diagnostic performance of mNGS testing, using EORTC-MSG criteria for proven or probable IFI as the comparator. We identified 227 episodes in 180 high-risk patients consistent with clinical concern for IFI. Of these, 45 episodes met EORTC-MSG criteria for proven/probable IFI. Plasma mNGS testing was sent in 36 episodes and identified the causative organism in 28. Positive and negative percent agreement for diagnosis of proven/probable IFI in this population was 77.8% and 90.4%, respectively. Among proven/probable cases with mNGS testing, Candida and Aspergillus were the most commonly identified fungi. Plasma mNGS testing in pediatric and young adult patients at risk for IFI compares favorably with diagnostic criteria used for IFI diagnosis and may be added to the diagnostic evaluation of patients at high-risk of IFI.

IMPORTANCE: Performance of plasma mNGS testing for diagnosis of invasive fungal infection in high-risk pediatric and young adult patients was comparable to the combination of fungal culture and targeted PCR from invasively acquired samples, suggesting that it might allow earlier diagnosis for some patients.}, } @article {pmid42446240, year = {2026}, author = {Tamm, SC and Doster, E and Wolfe, CA and Pinnell, LJ and Crosby, WB and Newcomer, BW and Funk, JL and Richeson, JT and Gow, SP and Valeris-Chacin, R and Woolums, AR and Morley, PS}, title = {Mannheimia haemolytica strain-level diversity in cattle populations.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0404925}, doi = {10.1128/spectrum.04049-25}, pmid = {42446240}, issn = {2165-0497}, abstract = {High-resolution genomic characterization is essential for understanding diversity, pathogenicity, and transmission dynamics of bacterial pathogens. Mannheimia haemolytica (Mh) is the most consequential bacterial agent associated with bovine respiratory disease (BRD) in cattle, as a leading cause of morbidity, mortality, and antimicrobial use. Historically, BRD pathogens, including Mh, have been studied using culture or PCR approaches that provided limited ability to characterize fine-scale genomic variation across communities. Here, we evaluated target-enriched (TE) shotgun sequencing, a culture-independent method capable of strain-level resolution within metagenomic data, for detecting and characterizing Mh in comparison with qPCR and 16S rRNA gene sequencing. Nasal swabs (10 individual and 2 composited DNA samples per pen) and environmental samples (three ropes hung on pen rails and three water bowl swabs per pen) were collected from four pens in each of five distinct cattle populations. DNA was extracted for TE sequencing to identify Mh at both species and genomic sequence variant (GSV) levels, and to characterize antimicrobial resistance genes across the bacterial communities. qPCR was performed to quantify Mh genome copies, and 16S rRNA gene sequencing was used to assess the broader respiratory microbiome. TE sequencing identified Mh in 100% of TE-tested samples and classified multiple GSVs in all but 3 of 121 samples. GSV profiles clustered within housing groups and varied across cattle populations, indicating structured strain-level diversity. In contrast, Mannheimia spp. were detected in only 47.7% of samples by 16S rRNA sequencing. These findings demonstrate that TE sequencing enables sensitive, strain-level characterization of Mh in cattle and environmental samples and reveals substantial within-population genomic diversity not captured by conventional approaches.IMPORTANCETarget-enriched shotgun sequencing enabled sensitive, strain-level detection of Mannheimia haemolytica (Mh), revealing multiple co-circulating genomic sequence variants (GSVs) within and among cattle groups. This demonstrates greater genetic variability of Mh populations in beef cattle than has been previously recognized. The clustering of GSVs within housing groups, together with the overlap between respiratory and environmental samples, is consistent with the hypothesis that contagious transmission contributes to Mh ecology. These results highlight the potential utility of composite nasal swab and environmental samples for future studies evaluating relationships between Mh genomic variation and disease risk.}, } @article {pmid42446350, year = {2026}, author = {Gregory, JB and Harrison, JW and Uehling, JK and Farrer, RA and Ballou, ER}, title = {Phylogenetically diverse Mucorales-Mycetohabitans endosymbiotic interactions identified from whole-genome sequencing using a targeted metagenomic assembly pipeline.}, journal = {Microbial genomics}, volume = {12}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001746}, pmid = {42446350}, issn = {2057-5858}, mesh = {*Symbiosis/genetics ; Phylogeny ; *Mucorales/genetics/classification/physiology ; Whole Genome Sequencing/methods ; Metagenomics/methods ; Metagenome ; Genome, Fungal ; }, abstract = {Endosymbiotic bacteria of the genus Mycetohabitans are obligate intracellular associates of Mucorales fungi, yet the understanding of their diversity, distribution and evolutionary dynamics is in its infancy. By screening 1,696 public sequencing datasets from Mucorales fungi, we detected Mycetohabitans in 46 fungal accessions spanning 5 host taxa across the fungal genera Rhizopus and Apophysomyces. These included 13 previously unreported associations. Genome reconstruction yielded 38 Mycetohabitans metagenome-assembled genomes (MAGs), of which 34 were of high quality. Incorporating these MAGs into genome-based species delimitation expanded known Mycetohabitans diversity from four to nine species-level clusters, including novel host-associated lineages. Re-examination of fungal host identities revealed frequent misidentification of isolates in fungal collection catalogues and/or misannotation in GenBank, with nearly a quarter of positive datasets requiring correction through internal transcribed spacer and genome-scale verification. Host-symbiont associations were non-random under this revised framework, with significant structure detected by contingency analysis and ParaFit. MAG-focused pangenome analysis revealed an open pangenome and mosaic lineage-associated functional traits, including variation in metabolism, secretion, cell-envelope systems, metal resistance, antimicrobial-resistance-associated functions and mobile elements. The most distinctive lineage comprised two Apophysomyces-associated MAGs, provisionally named M. apophysomyceticola, which showed pronounced genome reduction compared with other sampled Mycetohabitans spp. and loss of multiple central metabolic, nutrient assimilation, cofactor biosynthesis, catabolic, stress-response and defence pathways, consistent with reduced metabolic flexibility and increased host dependence. Together, these results show that Mycetohabitans symbioses are more geographically widespread, taxonomically diverse and functionally differentiated than previously recognized. More broadly, this work demonstrates the value of public sequencing repositories for uncovering hidden fungal-bacterial symbioses, while emphasizing that repository-derived patterns must be interpreted considering host misidentification, uneven sampling and incomplete metadata. Overall, our work establishes a global framework for Mycetohabitans diversity and function, with implications for fungal ecology, evolution and clinical mycology.}, } @article {pmid42446470, year = {2026}, author = {Almulhim, F and Narayanasamy, S and Wang, C and Mandal, P and Bensaddek, D and Amad, M and Hong, PY}, title = {Prolonged Stagnation Reduces Treated Wastewater Biostability by Altering Microbial Community: Insights From Metaproteomics.}, journal = {Environmental microbiology}, volume = {28}, number = {7}, pages = {e70372}, doi = {10.1111/1462-2920.70372}, pmid = {42446470}, issn = {1462-2920}, support = {BAS/1/1033-01-01//King Abdullah University of Science and Technology/ ; }, mesh = {*Wastewater/microbiology/chemistry ; Proteomics ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Biofilms ; Metagenomics ; Nitrogen/metabolism ; Denitrification ; }, abstract = {Reclaimed wastewater is increasingly reused for irrigation and other non-potable applications; however, inadequately treated effluent has raised concerns regarding environmental and public health impacts. Water quality in reclaimed distribution systems is shaped by multiple factors, particularly hydraulic stagnation in pipes and storage reservoirs. Stagnation can alter microbial community stability and facilitate persistence of pathogenic taxa. To investigate how prolonged stagnation affects microbial community structure and function, we integrated metagenomics and metaproteomics analyses of biofilms under flow and stagnant conditions over 3, 5 and 7 months. Prolonged stagnation caused pronounced compositional shifts, including strong reductions in nitrogen-removing taxa such as Nitrospira and Nitrosomonas. Correspondingly, key nitrification and denitrification proteins were depleted ≥ twofold under stagnation, indicating impaired nitrogen conversion processes. Stagnation also enriched motility- and transport-related functions and promoted Acidovorax persistence, a genus including phytopathogenic species. In contrast, flow conditions sustained nitrogen-cycling activity, contaminant-degrading enzymes, and quorum-quenching proteins, supporting greater biostability. Overall, our findings show that prolonged stagnation disrupts microbial community balance, suppresses essential nitrogen-cycling and detoxification pathways, and reduces the functional robustness of treated wastewater. Maintaining hydraulic flow within reclaimed water systems is therefore critical for preserving microbial functionality and ensuring safe and reliable reuse in irrigation and other non-potable applications.}, } @article {pmid42446573, year = {2026}, author = {Zhang, C and Zhang, YT and Cao, J and Li, X and Yuan, S and Dai, X and Xu, Y}, title = {Hydrovoltaic Energy Harvesting from Sewage Sludge Induces Its Efficient Anaerobic Digestion.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c01444}, pmid = {42446573}, issn = {1520-5851}, abstract = {The hydrovoltaic effect originates from leveraging water-material interactions to generate electricity. Sewage sludge inherently possesses an abundant porous structure and water-solid interfaces favorable for hydrovoltaic power generation. Herein, we explored the influence of promoting the hydrovoltaic effect of sludge on its subsequent methanogenesis during anaerobic digestion (AD). It was observed that a maximum open-circuit voltage of 0.62 V was achieved from sludge, and in its subsequent AD, the methane production and proportion of methane in biogas increased by 82% and 24.6%, respectively, indicating that the hydrovoltaic effect of sludge enables the direct recovery of electricity and significantly enhances its subsequent methanogenesis. The stable isotope-labeled AD experiments demonstrate that the hydrovoltaic effect enhanced water participation in CO2-reduction methanogenesis. Statistical analyses of variations in physicochemical properties of sludge, key enzymes closely related to electron/proton transfer, and microbial community in AD reveal that the hydrovoltaic effect induced significant enhancement of water-mediated proton-coupled electron transfer-associated methanogenesis, providing a thermodynamic advantage for methanogenic reactions. It was further verified by metagenomic and metatranscriptomic analyses, which showed that the expression levels of key genes associated with the classical and RuBisCO-mediated CO2 reduction methanogenic pathways were almost all significantly upregulated. This study provides a reference for directly recovering electricity from sludge by utilizing inherent properties while inducing efficient AD.}, } @article {pmid42446674, year = {2026}, author = {Jahnavi, S and Devendu, KV and Saha, S and Dey, P and Osborne, WJ}, title = {Marine bacteria and fungi: the hidden treasure of oceans in the biodegradation of microplastics and hydrocarbons integrated with omics technologies.}, journal = {Archives of toxicology}, volume = {}, number = {}, pages = {}, pmid = {42446674}, issn = {1432-0738}, abstract = {Marine microorganisms play a crucial role in maintaining oceanic ecosystem stability by mediating essential biogeochemical cycles, nutrient cycling and natural attenuation of environmental pollutants through diverse metabolic processes. Owing to their remarkable metabolic diversity, marine bacteria, fungi, and archaea possess the ability to utilize complex organic compounds as carbon and energy sources enabling them to transform and degrade a wide range of contaminants in aquatic environments, making them key agents in marine bioremediation. Among these, the most persistent pollutants threatening the marine ecosystem are the Microplastics (MPs) and hydrocarbons, both of which originate largely from anthropogenic activities including plastic waste accumulation, industrial discharge, petroleum extraction and accidental spills. MPs, are plastic particles of size less than or equal to 5 mm, produced due to the fragmentation of larger plastic debris while hydrocarbons consist of complex mixtures of aliphatic and aromatic compounds including polycyclic aromatic hydrocarbons (PAHs) and BTEX compounds. In marine systems, MPs frequently act as carriers for hydrocarbons and other contaminants, facilitating the formation of specialized microbial biofilms known as the plastisphere. Microbial degradation of these pollutants involves sequential processes including surface colonization, enzymatic depolymerization, biofragmentation, assimilation and mineralization. Several studies have reported the potential of marine bacteria and fungi in the degradation of MPs and HCs through the synthesis of key enzymes such as PETase and MHETase for MPs and laccases, peroxidases for HCs. Recent advances in omics technologies including metagenomics, metabolomics, proteomics, and transcriptomics have significantly improved our understanding of microbial community dynamics, degradation pathways, and functional genes involved in pollutant degradation. Therefore, integration of recent technologies alongside conventional methods could enhance the remediation process. In this review, we have collated the collective role of marine microorganisms in the biodegradation of MPs and hydrocarbons, highlighting their key degradation mechanisms, microbial interactions and the contributions of omics based approaches in advancing marine bioremediation research.}, } @article {pmid42446958, year = {2026}, author = {Nguyen-Dinh, T and Hutchinson, TF and Ricci, F and Prayitno, H and Jimenez, L and Eate, V and Leung, PM and Lappan, R and Yoon, S and Wong, WW and Cook, PLM and Greening, C}, title = {Flavobacteria consume nitrous oxide produced by partial denitrifiers in coastal sediments.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag186}, pmid = {42446958}, issn = {1751-7370}, abstract = {Nearly one-fifth of global emissions of the potent greenhouse gas nitrous oxide (N2O) originate from the ocean, particularly from nutrient-polluted coastal regions. Permeable (sandy) sediments, which cover half of the continental shelf worldwide, are potential sources of N2O due to increasing nutrient inputs from urbanization and agriculture. Yet, the microbial processes determining N2O emissions in these dynamic and unique ecosystems remain understudied. Here, we combined environmental measurements, bacterial cultivation, and genomic analyses to understand the microbes and processes controlling N2O cycling in permeable sediments from Port Phillip Bay (Australia). We established a genomic resource comprising 249 metagenome-assembled genomes and 95 new isolate genomes. Genome-based metabolic reconstructions and culture-based gas measurements revealed diverse bacteria in these sediments produce N2O through incomplete denitrification pathways. However, these bacteria co-occurred with highly abundant clade II N2O-reducing bacteria from the Flavobacteriaceae family. Kinetic profiling showed that both clade II nosZ flavobacterial isolates and whole sand communities exhibited a low apparent affinity for N2O under the tested experimental conditions, expanding the currently limited kinetic data available for N2O reducing microorganisms from coastal permeable sediments, including flavobacterial clade II N2O reducers. Collectively, these findings indicate that abundant N2O reducing communities can substantially consume N2O within permeable sediments, thus limiting N2O accumulation despite active N2O production. Together with previous hydrodynamic models predicting low N2O release from permeable sediments, our results highlight the important role of specialized microbial communities in regulating N2O cycling under increasing nutrient pollution.}, } @article {pmid42447082, year = {2026}, author = {Rodríguez, JA and Santos-Bay, L and Narechania, A and Carøe, C and Sirén, K and Mak, SST and Broman Nielsen, I and Ramsøe, M and Pontén, TS and Lillevang, S and Andersen, LT and Gilbert, MTP}, title = {The effect of different milk pretreatment methods on microbiome community development during Herrgårds cheese production and ripening.}, journal = {PloS one}, volume = {21}, number = {7}, pages = {e0350187}, doi = {10.1371/journal.pone.0350187}, pmid = {42447082}, issn = {1932-6203}, mesh = {*Cheese/microbiology ; Animals ; *Milk/microbiology ; *Microbiota/genetics ; Metagenome ; Food Microbiology ; Pasteurization ; Lactococcus lactis/genetics/isolation & purification ; Clostridium tyrobutyricum/genetics/isolation & purification ; }, abstract = {One of the biggest challenges for dairy producers is the substantial variability in final product properties caused by changes in the production environment. In cheese production, this variation is influenced by several factors, particularly the milk base and its pretreatment, which shape the microbiome throughout the process and ultimately affect the cheese's organoleptic characteristics. To examine the impact of three different pretreatments for pasteurised milk- microfiltration, protein fortification, and pasteurisation only (control)- on microbiome dynamics, we generated metagenome sequencing data from 14 cheese production steps across these three production trials at a Danish dairy factory. We constructed three metagenomic co-assemblies, identifying nine high-quality metagenome-assembled genomes. Our analysis revealed that a specific strain of Lactococcus lactis dominates the process, while other minor bacterial species persist at very low abundances (<1%), contributing non-negligibly to product properties. Notably, we detected DNA from Clostridium tyrobutyricum, a known bacterium whose heat-resistant spores may cause dairy spoilage, in pasteurised only and protein-fortified milk trials but was nearly absent in microfiltered milk. To enhance our analyses, we implemented KHILL, a novel k-mer based method, which facilitates metagenomic co-assembly and enables early detection of unwanted microorganisms. Our findings provide industrial dairy producers with a comprehensive view of microbial dynamics during cheese production, offering insights to improve process consistency and product quality.}, } @article {pmid42447281, year = {2026}, author = {Su, Y and Fan, L and Chen, Z and Tang, X and Wang, J and Klümper, U and Shi, G and Han, P}, title = {Nitrification Couples Microbial CO2 Fixation to Warming and Drought Responses in Alpine Grassland Soils.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c17815}, pmid = {42447281}, issn = {1520-5851}, abstract = {Microbial CO2 fixation in alpine grassland soils is highly sensitive to warming and drought. Nitrogen inputs from grazing may stimulate autotrophic nitrifiers, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). These nitrifiers assimilate carbon through CO2 fixation, but how their activity is associated with microbial CO2 fixation under warming and drought remains unclear. Here, we investigated microbial CO2 fixation and nitrification under altered temperature and moisture using urea-amended soil microcosms with [13]CO2 labeling, DNA-stable isotope probing (DNA-SIP), metagenomics, and quantitative PCR. Warming increased CO2 fixation rates to 1.48-2.58 times those at 15 °C under moist conditions, whereas drought reduced it by 59-91%. Nitrification rates were positively correlated with CO2 fixation, whereas the CO2 fixation offset only 1.3-12.1% of associated N2O emissions (measured as CO2 equivalents). DNA-SIP and metagenomics indicated that nitrifiers contributed to microbial CO2 fixation, with AOA showing more pronounced [13]C-labeling under combined warming and drought. Co-occurrence network indicated that AOA occupied more highly connected positions than AOB and NOB. This study provides microbial evidence that warming and drought reshape the linkage between nitrification and microbial CO2 fixation in urea-amended alpine grassland soil microcosms, with implications for carbon-nitrogen cycling and greenhouse-gas feedbacks.}, } @article {pmid42447304, year = {2026}, author = {Cao, J and Ye, Z and Pan, J}, title = {Metagenomics for antimicrobial resistance: from resistome surveillance to mechanistic inference.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0009026}, doi = {10.1128/jb.00090-26}, pmid = {42447304}, issn = {1098-5530}, abstract = {Antimicrobial resistance (AMR) is a global health crisis shaped by complex ecological and evolutionary processes that often occur in polymicrobial communities. Metagenomics enables culture-independent profiling of microbial DNA directly from clinical or environmental samples, providing an unparalleled view of community composition, resistome content, and the mobile genetic elements that drive horizontal gene transfer (HGT). Yet, a recurring challenge is that metagenomic detection of antibiotic-resistance genes does not automatically translate into a mechanistic understanding of resistance phenotypes, nor does it replace culture-based functional validation. Here, we synthesize how modern metagenomics supports AMR research across three linked questions: (i) what resistance determinants are present and how do they change across time and space, (ii) which hosts and mobile genetic elements carry these determinants, and how gene flow can be inferred, and (iii) what evidence is required to move from "resistance potential" to robust mechanistic claims. We emphasize practical design principles (sampling, controls, and contamination management), analytical choices (database and parameter effects), and recent advances, including long-read sequencing for resolving antibiotic-resistance genes context, and rapid clinical metagenomic sequencing for time-sensitive decision support. We propose an evidence ladder for mechanistic inference that integrates metagenomics with targeted assays and culture-dependent experiments. Beyond synthesizing recent advances, this review provides operational tools for critical appraisal and study design: an evidence ladder for mechanistic inference, a decision-gated workflow that ties metagenomic outputs to allowable claim language, a minimum reporting checklist aligned to evidence strength, and a "pitfall → consequence → fix" guide to reduce over-interpretation. To support a more comprehensive, forward-looking view, we also summarize emerging directions that are rapidly reshaping AMR metagenomics-multi-omics integration, single-cell, and epigenetic linkage strategies, CRISPR-enabled enrichment/depletion, and AI-assisted discovery/mining-and clarify where these advances strengthen (or do not strengthen) mechanistic claims within the same evidence ladder.}, } @article {pmid42447582, year = {2026}, author = {Lin, H and Li, X and Wang, X and Yuan, Q and Yang, F and Hu, W and Li, X and Lei, L and Luo, Y}, title = {The antibiotic resistome in oysters across the Chinese coastline: Enrichment, microbial drivers, and implications for health risk.}, journal = {Journal of hazardous materials}, volume = {515}, number = {}, pages = {142811}, doi = {10.1016/j.jhazmat.2026.142811}, pmid = {42447582}, issn = {1873-3336}, abstract = {Oysters extensively farmed in China represent a critical but under-investigated pathway for human exposure to antibiotic resistance genes (ARGs). This study employed metagenomic analysis of 75 samples from representative Chinese oyster farms to explore ARGs distribution in oysters and their surrounding environments, alongside assessing their health risk. Results exhibited significant spatial heterogeneity and marked ARG enrichment in oyster compared to surrounding seawater along the Chinese coastline, with an enrichment factor 2.60 ± 2.43 folds higher. This enrichment is primarily driven by selective retention of specific microbes, particularly the opportunistic pathogen Vibrio, which emerged as a dominant ARG host. Furthermore, the co-occurrence of mobile genetic elements and diverse ARGs, particularly IS91 and tnpA, suggests a high potential for horizontal gene transfer within oyster bacteriome, potentially exacerbating the dissemination of antibiotic resistance. From a public health perspective, the mean estimated daily intake (EDI) of ARGs via oyster consumption was calculated at 1.7E-1 ± 1.7E-1 copies/16S/g/individual. Given that oyster can be consumed raw and harbor pathogenic Vibrio, this ARG exposure may underscores potential health risk for consumers. Integrating the EDI with a resistome scoring system, the Risk Index (RI) demonstrated site-specific health threats that necessitate differentiated management priorities. Collectively, these results provide critical evidence of how marine aquaculture serves as a reservoir for ARGs and highlight the urgent need for integrated surveillance under the One Health approach to mitigate the transmission of antibiotic resistance from marine environments to the human food chain.}, } @article {pmid42447623, year = {2026}, author = {Su, K and Tian, S and Xia, Y and Zhao, X and Huang, J and Hu, S and Ye, J}, title = {Species composition and functional characteristics of the human multi-organ microbiome: A metagenomic study.}, journal = {Journal of forensic and legal medicine}, volume = {122}, number = {}, pages = {103213}, doi = {10.1016/j.jflm.2026.103213}, pmid = {42447623}, issn = {1878-7487}, abstract = {Postmortem microbial communities may provide useful information for forensic microbiology, but species-level and functional profiles across multiple cadaveric anatomical sites remain poorly characterized. Here, shotgun metagenomic sequencing was performed on 144 samples from six anatomical sites, including the oral cavity, nasal cavity, trachea, lung, colon, and anus, collected from 24 human cadavers. A total of 15,301,799,968 raw reads were obtained, and 6565 species were identified, and KEGG pathways were annotated at the L1, L2, and L3 levels. Species-level microbial composition differed significantly among anatomical sites. PERMANOVA with permutations blocked by individual identity showed that anatomical site was the dominant factor explaining microbial community variation (R[2] = 0.3778, p = 0.001, q = 0.001), whereas postmortem interval did not show a significant independent effect within the 1-38-day interval. KEGG functional profiles also differed significantly among anatomical sites at the L2 and L3 levels, and 182 of 214 L3 pathways showed significant site-associated differences after false-discovery-rate correction. Pathway-level mixed-effect models further indicated that anatomical site remained significantly associated with most L3 pathways after accounting for postmortem interval, age, sex, cause of death, and repeated sampling from the same individual. Species-pathway correlation analysis identified significant taxon-function associations, but these were interpreted as correlative rather than direct evidence of species-specific functional contribution. Low-biomass sensitivity analyses indicated that respiratory-site results, especially lung and tracheal findings, should be interpreted cautiously because of high host DNA proportions and low non-host read counts. Inter-site shared occurrence and intra-site co-occurrence analyses further described distributional associations across anatomical sites. This study establishes a multi-site postmortem metagenomic reference framework for characterizing anatomical-site-specific microbial and functional patterns, offering insights into forensic microbiology and postmortem microbial ecology.}, } @article {pmid42447671, year = {2026}, author = {Han, Z and Zhang, H and Li, H and Luan, X and Guruge, SK and Hu, C and Yang, M and Zhang, Y}, title = {Novel bacterial hosts and mobile genetic structure of tet(X) variants in tetracycline-contaminated aquatic environment uncovered by culture and long-read metagenomics.}, journal = {Water research}, volume = {305}, number = {}, pages = {126471}, doi = {10.1016/j.watres.2026.126471}, pmid = {42447671}, issn = {1879-2448}, abstract = {Clinically important tigecycline (3rd-generation tetracycline) resistance tet(X) variants were inferred to have evolutionarily originated from environmental bacteria, and have been recognized among environment, human and animals. However, genetic basis for environmental proliferation and dissemination of tet(X) variants remains ambiguous. This study profiled tet(X) variants at gene, contig, isolate, and community levels in environmental community subjected to long-term stepwise increasing oxytetracycline (1st-generation tetracycline) or tigecycline pressure using long-term microcosm experiments, quantitative PCR, bacterial isolation, whole-genome sequencing, and Nanopore-based long-read metagenomics. We confirmed that both oxytetracycline and tigecycline enriched the abundance of tetracycline resistance genes especially oxytetracycline-enriched tet(X3). Unexpectedly diverse bacterial hosts and genetic structure of tet(X)-positive mobile elements in the environment microbiome were identified using bacterial isolation and long-read Nanopore metagenomics. Pseudomonas defluvii was first reported to carry tet(X3) in the chromosome, forming IS26-tet(X3)-res-ISCR2 circular intermediate to transfer between different DNA molecules. Database mining revealed similar mobile segments have prevailed among animal-derived Acinetobacter species. Unlike the widely reported ISCR2-mediated transfer of tet(X6), we identified a novel mobile multidrug transposon TnAs3 where tet(X6) and class 1 integron co-transferred as its passenger region. Mobile tet(X2)-ere(D)-aadS-erm(F)-blaOXA-347 segment was annotated in Runella, and co-occurrences of tet(X2) and ere(D), aadS, blaOXA-347 were also found in Flavobacterium, Arsenicibacter, Chryseobacterium and Pedobacter. Overall, tetracycline-contaminated aquatic microbiome harboured diverse mobile tet(X)-positive segments which have not yet been acquired by clinical pathogens, and thus served as the genetic pool of tet(X) variants together with indigenous bacterial hosts, especially the newly reported Pseudomonas defluvii. Reducing pollution of older-generation tetracyclines would be a proactive way to mitigate environmental evolution and possible clinical effects of tet(X) variants.}, } @article {pmid42448116, year = {2026}, author = {Wu, J and He, C and Wu, K and Feng, W and Zhou, Q and Yang, Y and Tyagi, RD}, title = {Black soldier fly bioconversion improves agronomic value but sustains resistome risks in silver-bearing sewage sludge compost.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135402}, doi = {10.1016/j.biortech.2026.135402}, pmid = {42448116}, issn = {1873-2976}, abstract = {Agricultural reuse of sewage sludge can improve crop production but may also introduce metals and antibiotic resistance genes (ARGs) into soil-plant systems. We evaluated sludge-derived composts, with and without black soldier fly (BSF) bioconversion, in a red amaranth pot experiment under exposure to silver nanoparticles (Ag-NPs) and silver sulfide nanoparticles (Ag2S-NPs). During composting, BSF was associated with greater dissolved organic matter humification, reduced extractable Ag and co-existing metal concentrations, while Ag exposure selectively reshaped compost microbiota and the BSF gut resistome. However, BSF bioconversion remained the main driver of microbial community reassembly, whereas Ag exposure mainly promoted host turnover and mobile genetic element enrichment rather than broad ARG amplification. After soil application, compost significantly enhanced red amaranth growth. Total biomass increased from 1.3 g pot[-1] in the unfertilized control to 3.8 g pot[-1] with BSF-derived compost and 5.1-5.2 g pot[-1] with BSF-derived Ag2S-NP composts, accompanied by higher shoot N and P concentrations. However, shoot Ag and selected co-existing metals also increased, indicating an agronomic benefit-risk trade-off. Metagenomic analyses showed that compost application reshaped the rhizosphere resistome mainly through host filtering, with ARG dissemination potential linked to the co-localization of ARGs, metal resistance genes, and mobile genetic elements in a limited number of enriched hosts. Plant growth was driven mainly by fertilization and nutrient status, whereas ARG abundance was associated primarily with metals, metal resistance genes, and gene mobility. These findings support BSF-assisted sludge recycling as a promising but risk-aware strategy for agricultural reuse.}, } @article {pmid42448240, year = {2026}, author = {Thompson, KN and Ma, S and Bhosle, A and Nickols, WA and Shen, J and Ghazi, AR and Dang, NH and Zhang, Y and Nzabarushimana, E and Kim, H and Xavier, RJ and Chan, AT and Franzosa, EA and Huttenhower, C and Nguyen, LH}, title = {Harmonized metagenomic signatures of the gut microbiome reveal robust species, functions, and strain links to inflammatory bowel disease.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2026.06.023}, pmid = {42448240}, issn = {1528-0012}, abstract = {BACKGROUND & AIMS: Coupled with well-characterized host genetic and environmental risk factors, alterations of gut microbial communities contribute to risk and severity of inflammatory bowel disease (IBD) and its subtypes, Crohn's disease (CD) and ulcerative colitis (UC). In a rapidly advancing field in which diverse multinational cohorts and molecular methods have been created, highly-resolved microbial traits such as protein function and strain genetics can now be investigated through meta-analysis.

METHODS: We integrated 2,371 stool metagenomes from 542 individuals with IBD and their referent counterparts from the United States, Canada, and Europe, utilizing all seven IBD cohorts in the Human Microbiome Bioactives Resource, which we interrogated using taxonomic, functional, and strain profiling.

RESULTS: We systematically identified the mass expansion of pro-inflammatory, oral-predominant taxa in the IBD gut, such as Veillonella and Streptococcus spp. We also accurately discriminate CD from UC, a clinically challenging problem, using highly-resolved microbial strain genetics (AUC=0.69). Further, we observed disease-specific shifts in carbohydrate metabolism, a likely consequence of small bowel dysfunction in CD, but not UC, as well as perturbations in mucin utilization, increased microbial virulence and invasion cassettes, and loss of carnitine degradation pathways in IBD. Finally, we observed novel and significant differences in the gene carriage among both IBD- and non-IBD-associated taxa, suggesting that strain-specific functional variation may contribute to pathogenesis and disease-related bacterial fitness.

CONCLUSION: Microbial clades responsible for IBD-linked dysbiosis are not uniform, and their functionality in IBD and CD/UC subsets are driven by species and strain lineage-specific variants.}, } @article {pmid42437837, year = {2026}, author = {Devi, U and Ramadass, B and Pullattayil, AK and Vishnu Bhat, B}, title = {Gut Microbiome in Neonatal Necrotizing Enterocolitis - A Comprehensive Review of Evidence.}, journal = {Indian journal of pediatrics}, volume = {}, number = {}, pages = {}, pmid = {42437837}, issn = {0973-7693}, abstract = {Necrotizing enterocolitis (NEC) is one of the most catastrophic gastrointestinal emergency occurring predominantly in preterm neonates. It contributes to substantial neonatal morbidity and mortality. Disturbances in the intestinal microbiome are crucial to disease pathogenesis. In preterm infants, an immature intestinal barrier, dysregulated immune responses, and environmental exposures altogether predispose to alteration in microbial colonization and intestinal inflammation. This review was done to present the current evidence on gut microbiome alterations associated with NEC in preterm infants. A systematic search of the MEDLINE and EMBASE databases was performed using search strategy related to prematurity, intestinal microbiota, and necrotizing enterocolitis. A total of 42 studies assessing microbial composition, microbial progression, or microbial functional patterns in relation to NEC were included. Across the included studies, NEC was commonly preceded by reduced microbial diversity, delayed maturation of anerobic communities, and expansion of Proteobacteria, particularly Enterobacteriaceae family such as Klebsiella and Escherichia. Longitudinal studies further showed that these microbial changes may become evident days to weeks before clinical disease, suggesting a potential window for early risk identification. Functional analyses also showed alterations in microbial metabolic pathways, including short-chain fatty acids, tricarboxylic acid intermediates, volatile compounds, and viral signatures that may lead to epithelial injury and inflammatory signaling. Clinical and environmental factors including antibiotic exposure, mode of delivery, feeding practices, and NICU microbial ecosystem are important determinants of neonatal gut microbiome development. Thus, the current evidence supports a reproducible pattern of intestinal dysbiosis preceding NEC. Better understanding of microbiome dynamics may aid early risk stratification and support microbiome-targeted preventive strategies in vulnerable preterm populations.}, } @article {pmid42437892, year = {2026}, author = {Chen, Y and Lu, S and Zhao, A and Li, M and Gan, X and Wang, Y and Yang, Y and Huang, M and Wang, Q and Niu, T and Zhou, Y}, title = {Blood mNGS: an effective non-invasive diagnostic tool for Pneumocystis jirovecii pneumonia.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05408-7}, pmid = {42437892}, issn = {1471-2180}, support = {2024J0304//the Scientific Research Fund of Yunnan Provincial Department of Education/ ; 202401AY070001-295//the Kunming Medical Joint Special Project of Yunnan Provincial Science and Technology Plan Project/ ; 82370192//National Natural Science Foundation of China/ ; GYYX24003//1.3.5 Project of High Altitude Medicine/ ; 2024NSFSC1746//West China Hospital, Sichuan University, the Natural Science Foundation of Sichuan Province/ ; 2022YFC2406804//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) is a life-threatening opportunistic infection. Colonization is prevalent but cannot be reliably distinguished from active infection by conventional methods. Metagenomic next-generation sequencing (mNGS) is a promising diagnostic tool, but the value of blood mNGS for diagnosis, microbial community comparison, and outcome-related associations in PJP remains unclear.

METHODS: We analyzed 73 suspected PJP patients with paired BALF and blood mNGS. Using strict diagnostic criteria, patients were classified as: PJP (n = 50) and P. jirovecii colonization (PJC, n = 23). Bioinformatic analyses compared compartment-specific microbiota. BALF-blood concordance and associations between P. jirovecii load and outcomes were evaluated.

RESULTS: BALF showed higher α-diversity than blood (both Shannon and Simpson, P < 0.001), whereas β-diversity showed no compartmental segregation. BALF identified 216 species versus 43 in blood; however, the top-10 species were concordantly ranked (90% concordance). Blood mNGS distinguished PJP from PJC with an AUC of 0.80 (specificity 95.7%, sensitivity 62.0% at RPM > 4.8), outperforming BALF mNGS (AUC 0.76), blood PCR (AUC 0.64) and BALF PCR (AUC 0.73). Gram-negative bacteria accounted for a large proportion of blood taxa (75% of top 20 taxa), while BALF showed additional fungal taxa including Aspergillus fumigatus. LEfSe identified matrix-specific taxa: oral commensals in PJC-BALF. Blood P. jirovecii load correlated positively with LDH (r = 0.34, P = 0.0035), CRP (r = 0.34, P = 0.0031), and BDG (r = 0.26, P = 0.025), and was higher in non-survivors (P < 0.05).

CONCLUSION: Blood mNGS may serve as a non-invasive, highly specific complementary tool for PJP diagnosis and broader microbiological assessment.}, } @article {pmid42437920, year = {2026}, author = {Diaz-Canestro, C and Cheung, K and Roche, E and Sarabia, JM and Tse, MA and Xu, A}, title = {Multi-omics signatures of circulating factors associated with cardiorespiratory fitness adaptations in individuals with prediabetes.}, journal = {Cardiovascular diabetology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12933-026-03286-x}, pmid = {42437920}, issn = {1475-2840}, abstract = {BACKGROUND: Patients with insulin resistance exhibit reduced cardiorespiratory fitness (CRF), assessed by peak oxygen consumption (VO2peak), compared with healthy age-matched individuals. Although high-intensity interval training (HIIT) can substantially improve VO2peak, there is considerable interindividual variability in this response. Therefore, further research is needed to elucidate the molecular mechanisms underlying the heterogeneous response of VO2peak to HIIT in individuals with prediabetes.

METHODS: Proteomic analyses of serum samples, along with fecal metagenomic and targeted metabolomic profiling, were conducted in medication-naïve, overweight and obese Chinese men with prediabetes (n = 35; aged 24-62 years). All participants underwent a 12-week HIIT intervention, and biological samples were collected both before and after the intervention to evaluate exercise-induced alterations in circulating proteins, gut microbial composition, and metabolite profiles.

RESULTS: After 12 weeks of HIIT, mean VO₂peak increased by 0.47 L/min with individual responses ranging from 0 to 1.7 L/min. Baseline levels of short-chain fatty acid (SCFA)-producing genera, including Prevotella (β = 105.65, P = < 0.001, FDR = 0.034), Coprococcus (β = 50.22, P = 0.01, FDR = 0.39), and Hungatella (β = 40.72, P = 0.025, FDR = 0.50), were positively associated with ΔVO₂ peak. In contrast, baseline levels of the erythropoiesis-stimulating hormone erythropoietin (EPO) (β = -279.03, P = 0.024, FDR = 0.99) were negatively associated with ΔVO₂ peak. Exercise-induced changes in growth hormone 1 (β = 63.97, P = 0.04, FDR = 0.99) were positively associated with ΔVO₂ peak, whereas exercise-induced changes in BTB and CNC Homology 1 (β = -250.82, P = 0.01, FDR = 0.99), a repressor of heme oxygenase-1, were negatively associated with ΔVO₂ peak. In multiple linear regression analysis including clinical variables, percentage lean mass (β = 64.17, P = 0.0005) was the strongest variable associated with ΔVO₂peak. The clinical model explained 27% of the variance which increased to 37% (P = 0.002) upon inclusion of exercise-associated circulating factors such as EPO.

CONCLUSIONS: Our findings reveal that baseline proteomic and metagenomic signatures are associated with VO₂peak adaptations. These multi-omics signatures may support the clinical implementation of personalized exercise interventions to improve CRF in individuals with prediabetes.}, } @article {pmid42437978, year = {2026}, author = {Xia, J and Meng, L and Fang, Y and Ban, H and Okazaki, Y and Yoshida, T and Endo, H and Nagasaki, K and Ogata, H}, title = {Rapid Diversification of a Natural Heterosigma akashiwo Virus Population during a Host Bloom.}, journal = {Microbes and environments}, volume = {41}, number = {3}, pages = {}, doi = {10.1264/jsme2.ME26018}, pmid = {42437978}, issn = {1347-4405}, mesh = {Japan ; *Genetic Variation ; *Giant Viruses/genetics/classification/isolation & purification ; *Eutrophication ; Phylogeny ; Genome, Viral ; Metagenomics ; Seawater/virology ; Biodiversity ; }, abstract = {Despite the ecological importance of viruses, our understanding of their evolutionary dynamics in natural environments remains limited. This gap is particularly pronounced for giant dsDNA viruses of the phyla Nucleocytoviricota and Mirusviricota. Knowledge on their population genetic dynamics is mostly derived from a small number of laboratory-based experiments, while patterns in nature are rarely observed. To overcome this limitation, we traced the genetic structure and transcription status of Heterosigma akashiwo virus (HaV) using high-frequency, time-resolved sampling during a host bloom in a coastal area of Japan by integrating cell counting, metabarcoding, and metagenomic and metatranscriptomic sequencing. The results obtained revealed that HaV dominated the giant virus community in most samples, with relative abundance up to 56%. Despite its high abundance, the HaV population exhibited a low level of microdiversity, but had a higher pN/pS ratio than other giant viruses in the study site. Microdiversity increased during the early sampling period, peaked mid-sampling, and decreased during the later period, consistent with rapid diversification during viral expansion, which may be driven by both in situ mutations and the succession of pre-existing minor variants. Several accessory genes, including a glycosyltransferase and an endonuclease, were highly expressed, providing functional evidence consistent with host interaction-driven selective pressure during the bloom. Collectively, these results indicate that HaV population dynamics during algal blooms are shaped by host-driven selection acting on standing genetic variations.}, } @article {pmid42438180, year = {2026}, author = {Castells-Ballester, J and Taron, A and Smith, M and Gawron, R and Beaulieu, J and Papa, O and Buss, J and Ong, J and Chen, M}, title = {Development of a Microdroplet-Based Functional Genomic Screening Pipeline by Combination of DNA Nanoflowers and PURExpress Cell-Free Expression.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.6c00061}, pmid = {42438180}, issn = {2161-5063}, abstract = {We present a microfluidic workflow that couples reconstituted in vitro transcription-translation (IVTT) with ultrahigh-throughput droplet screening to directly link genotype and phenotype within complex, heterogeneous DNA pools. The approach employs DNA nanoflowers as clonal, high-copy templates, enabling robust protein expression from single DNA molecules encapsulated in picoliter droplets. When integrated with fluorescence-assisted microdroplet sorting (FADS) and a DNA recovery pipeline that reconstituted selected libraries for subsequent iterative rounds, the platform achieves approximately 400-600-fold enrichment per selection cycle and supports functional discovery and directed evolution entirely independent of host cell expression. As a proof of principle, we demonstrate recovery of the recombinase RecA from an E. coli genomic library screened for single-stranded DNA binders, highlighting the platform's capability to identify DNA-interacting and DNA-modifying enzymes. By eliminating host-derived background activity and toxicity constraints that often complicate lysate- or cell-based metagenomic screens, this method potentially expands access to enzyme classes that have historically been difficult to assay.}, } @article {pmid42438386, year = {2026}, author = {Yuan, D and Cui, X and Zhang, S and Wang, Y and Sun, Y and Xiao, M and Zhang, M and Zheng, L}, title = {Nitrifiers Drive Different N2O Production Patterns in Tropical River Sediments.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c01501}, pmid = {42438386}, issn = {1520-5851}, abstract = {Since the 20th century, global riverine nitrous oxide (N2O) emissions have increased 4-fold; however, the N2O emissions of tropical rivers are still unclear. Here, we employed a series of techniques (closed chamber, biological inhibitor, [15]N-[18]O double tracer, metagenomic sequencing, and reverse transcription qPCR) to analyze in situ N2O flux, potential N2O production rate, and N2O production mechanism of China's tropical rivers. In the 82 sediment samples from the top 10 Hainan rivers, high levels of in situ N2O flux and potential N2O production rate were detected in all samples, indicating that Hainan rivers are significant hotspots of N2O emissions. The higher values were observed in estuary samples (avg: 4.48 ± 0.25 mg m[-2] d[-1], 39.17 ± 3.28 ng N g[-1] d[-1]) compared to nonestuary samples (avg: 1.98 ± 0.16 mg m[-2] d[-1], 21.29 ± 4.68 ng N g[-1] d[-1]). Nitrifier denitrification (ND) dominates the N2O production, and its contribution to estuary samples (avg. 49.31-78.90%) is higher than that for nonestuary samples (avg. 32.27-66.19%). We found that complete ammonia-oxidizing bacteria (comammox) Nitrospira nitrificans and ammonia-oxidizing bacteria (AOB) Nitrosomonas marina cooperate to produce N2O via the ND pathway in estuary samples, and AOB Nitrosomonas europaea produces N2O via the ND pathway in nonestuary samples. Salinity, NH4[+], pH, and total organic matter (TOM) affect N2O production via three key species. Our findings advance the mechanistic understanding of tropical rivers in the tropical N-cycle and global climate change. Ammonium fertilizer management and estuary ecological restoration should be prioritized in tropical river basins.}, } @article {pmid42438737, year = {2026}, author = {Faleiros, CA and Gonçalves, OS and Nunes, AT and Pires, CS and Poleti, MD and Fukumasu, H}, title = {Host breed and geography shape the antiviral defense landscape of the bovine rumen microbiome.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag162}, pmid = {42438737}, issn = {2730-6151}, abstract = {The rumen microbiome represents a complex, phage-rich ecosystem where microbial survival depends on both metabolic cooperation and antiviral defense. However, global and breed-associated variations in rumen prokaryotic immune systems remain poorly understood. Here, we performed the most comprehensive profile to date of antiviral defense systems (DS) in the rumen, analyzing 6530 microbial genomes and metagenome-assembled genomes (MAGs) from diverse cattle breeds and geographic regions. In this global dataset, we identified >90 000 DS, the most abundant of which were restriction-modification, PDC-S01, deoxyribonucleic acid modification systems (DMS_other), AbiE and SoFic, with variations influenced by both host the lineage and geographic region. A more in-depth analysis was performed using two complementary antiviral annotation frameworks for Nellore cattle (Bos indicus) from Brazil. Data exhibited a remarkably enriched antiviral defense repertoire, with over 15 632 DS encoded across 547 high-quality MAGs. These systems were densely clustered in dominant rumen lineages, such as Prevotella, and positively correlated with prophage abundance, consistent with virus-host coevolution. Notably, we also detected viral contigs encoding both antiviral defense and anti-defense genes, underscoring the arms race between the phages and their microbial hosts. Metatranscriptomic data from North America and Oceania revealed high expression levels of toxin-antitoxin modules, clustered regularly interspaced short palindromic repeats components, and restriction enzymes, suggesting a basal level of antiviral activity. These findings reveal the rumen as an antiviral innovation hotspot, highlighting microbiome resilience with implications for ecology, adaptation, and phage-based interventions.}, } @article {pmid42439467, year = {2026}, author = {Luo, Y and Kang, FL and Li, QM and Yang, WC}, title = {Metagenomic Association Uncovers Host Genotype-Structured Rhizobacterial Networks and Novel Taxa That Enhance Soybean Salt Tolerance.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e76373}, doi = {10.1002/advs.76373}, pmid = {42439467}, issn = {2198-3844}, support = {YSBR-011//CAS project for Young Scientists in Basic Research/ ; 2023YFD1200600//National Key Research and Development Program of China/ ; XDA24010205//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDA26030105//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2016QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; }, abstract = {Salinity is an escalating agricultural challenge, yet plant microbiomes offer a promising avenue for improving salt tolerance. Nevertheless, most naturally occurring microbes remain unevaluated for plant growth-promoting function, and systematic approaches to uncover salt-tolerance-enhancing plant growth-promoting rhizobacteria (PGPR) are limited. Here, using soybean as a model, we implement a quantitative framework to characterize rhizosphere microbial networks and nominate novel taxa functionally associated with plant salt tolerance. We introduced a salt tolerance index (STI) to quantify plant salt tolerance and normalize performance across heterogeneous natural soil salinity. Metagenomic sequencing and co-occurrence analysis revealed distinct rhizosphere microbiota structures between tolerant and susceptible soybeans. In tolerant soybeans, Pseudomonas dominated as the hub of a highly interconnected network, whereas susceptible accessions showed a fragmented network dominated by Acinetobacter. Correlation analyses identified bacterial taxa positively associated with STI, including documented salt-tolerant PGPR and novel candidates. Greenhouse experiments showed that one candidate, Thalassospira xiamenensis, enhances soybean salt tolerance and reshapes host ion-transport and oxidative-stress gene expression under salinity, validating our screening strategy. Our culture-independent metagenomic association approach reveals host genotype-structured rhizosphere microbial networks underlying salt tolerance and provides an efficient, labor-saving means for high-throughput identification of salt-tolerant PGPR.}, } @article {pmid42439510, year = {2026}, author = {Hertramph, TL and Dorda, M and Pallenberg, ST and Sauer-Heilborn, A and Ringshausen, FC and Steglich, M and Hansen, G and Tümmler, B and Wiehlmann, L and Rosenboom, I and Dittrich, A-M}, title = {Effects of elexacaftor/tezacaftor/ivacaftor on the nasal microbial metagenome in cystic fibrosis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0060126}, doi = {10.1128/spectrum.00601-26}, pmid = {42439510}, issn = {2165-0497}, abstract = {Mutation-specific cystic fibrosis (CF) transmembrane conductance regulator (CFTR) modulator therapy with elexacaftor/tezacaftor/ivacaftor (ETI) has dramatically improved clinical outcomes for people with CF (pwCF), yet its impact on the nasal microbial metagenome remains insufficiently understood. This prospective, post-approval study investigated the impact of 15-week ETI therapy on sinonasal microbiota of pwCF aged 12 years and older. Whole-genome shotgun sequencing was performed on total DNA from 24 paired nasal lavage samples, with synthetic spike-in controls enabling absolute abundance normalization. Taxonomic profiling was conducted using the Wochenende pipeline. ETI did not induce major shifts in alpha or beta diversity. Instead, the overall microbial community became further dominated by the skin commensals Staphylococcus epidermidis and Cutibacterium acnes, accompanied by a more than twofold increase in total bacterial load. Classical CF pathogens showed divergent trajectories: Pseudomonas aeruginosa tended to decrease, whereas Staphylococcus aureus exhibited a tendency toward increased abundance. Co-occurrence network analysis revealed a transition from a dense, multicomponent baseline network to a single, fully connected, but less densely integrated network following treatment initiation.IMPORTANCEThe nasal cavity represents the primary entry point of microorganisms into the respiratory tract and a potential reservoir for lower airway infection, the major cause of CF disease progression. Using shotgun metagenomics with spike-in controls, this study provides the first genome-wide characterization of how ETI alters microbial load and pathogen dynamics in CF nasal airways. Treatment with ETI strengthened the dominance of skin commensals in the nares while reducing P. aeruginosa. Given the observed increase in S. aureus, further work is needed to determine whether this represents expansion of a typical nasal colonizer or a clinically relevant rise of a key CF pathogen that could act as a reservoir for future lower airway infection.}, } @article {pmid42439573, year = {2026}, author = {van Haren, MHI and Have, Lt and Koopman, PD and Buil, JB and Maat, I and Rahamat-Langendoen, JC and Martens, L and Moorlag, SJCFM and van den Bosch, B and Koenraad, E and Wertheim, HFL and Melchers, WJG and Pas, SD}, title = {Clinical impact of 16S rRNA RC-PCR NGS on infectious disease management.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0002326}, doi = {10.1128/spectrum.00023-26}, pmid = {42439573}, issn = {2165-0497}, abstract = {16S rRNA metagenomics provides a culture-independent method for diagnosing infections with fastidious or uncultivable organisms, guiding targeted therapy, and detecting polymicrobial communities. This study utilizes reverse complement (RC)-PCR next-generation sequencing (NGS) to accurately identify bacterial pathogens from clinical specimens and assess its impact on clinical decision-making, setting it apart from conventional 16S sequencing approaches. A retrospective analysis of an ISO 15189 accredited 16S RC-PCR NGS diagnostic workflow targeting the V1-6 and V9 regions of the 16S rRNA gene was conducted over a 2-year period, including 390 clinical specimens from 316 patients. 16S RC-PCR NGS results were discussed in a multidisciplinary consultation and subsequently reported to the clinic. In total, 1,283 RC-PCR results were analyzed, of which 517 were from clinical specimens, 284 were negative controls, 66 were positive controls, and 416 were from wet lab and bioinformatic pipeline validation. 16S RC-PCR NGS assay detected bacterial taxa in 179/390 (45.9%) of clinical specimens, while 201/390 (51.5%) were negative, and 10/390 (2.6%) yielded uninterpretable results. The specimen types pus, pleural fluid, and heart valves exhibited the highest positivity rate (68% to 70%). Overall, 16S RC-PCR NGS influenced diagnostic decision making in 145/282 (51.4%) clinical cases and guided therapeutic management in 77/282 (27.3%) cases. Results providing definite evidence for either the presence or absence of bacterial infection were considered clinically valuable. Integration of 16S RC-PCR NGS pathogen detection with multidisciplinary consultation markedly improved clinical management, directly impacting diagnosis and treatment of complex clinical cases in a tertiary care setting. The effect was most pronounced in brain abscess patients, where RC-PCR results guided treatment decisions in 9/13 (69.2%) of cases.IMPORTANCETimely and accurate diagnosis is essential for managing serious infections, yet clinicians often face situations where routine laboratory tests do not provide clear answers. This study demonstrates that next-generation sequencing (NGS) of the bacterial 16S rRNA gene can decisively resolve these uncertainties. By revealing whether bacteria are present in clinical specimens, this approach influenced clinical reasoning and supported treatment decisions across a variety of challenging cases. 16S reverse-complement PCR was especially powerful for brain abscesses and infections where the causative microorganism was unclear, providing clarity that directly improved patient care. These findings show that integrating advanced sequencing with expert clinical interpretation can enhance the management of complex infections and support more confident, evidence-based therapy.}, } @article {pmid42440035, year = {2026}, author = {Mathiyazhagan, S and Balu, B and Gunaseelan, RJ and Piliyan, R and Perumal, S and Natesan, M}, title = {Discovery of novel bio-resources from the hidden biodiversity of marine mangrove ecosystems.}, journal = {Environmental geochemistry and health}, volume = {48}, number = {10}, pages = {}, pmid = {42440035}, issn = {1573-2983}, mesh = {*Wetlands ; *Biodiversity ; Animals ; Biological Products ; Fungi/metabolism ; Bacteria/metabolism ; Biotechnology ; Invertebrates/metabolism ; }, abstract = {Marine mangrove wetlands are ecologically complex ecosystems that serve as rich reservoirs of biologically active compounds with significant biotechnological potential. This review synthesizes current knowledge on mangrove-associated microorganisms and biota, including bacteria, fungi, algae, and invertebrates, with emphasis on their bioassay activities and derived bioactive metabolites. Various analytical approaches, including chromatographic techniques, LC-MS/NMR analysis, and in silico tools, have been employed to identify and characterize compounds such as enzymes, polysaccharides, biosurfactants, and antimicrobial peptides. These biomolecules exhibit diverse functional applications in medicine, environmental management, and industrial processes, including nitrogen fixation, bioremediation, and hydrocarbon degradation. The review highlights that mangrove-derived bioactive compounds are influenced by both ecological interactions and environmental conditions. Furthermore, recent advances indicate a shift toward genome-guided discovery using multi-omics and metagenomic approaches, enabling the identification of novel biosynthetic pathways, particularly from unculturable microorganisms. This integrated approach enhances the efficiency of bioactive compound discovery and supports scalable production through synthetic biology. Overall, mangrove ecosystems represent promising platforms for sustainable biotechnological innovation, underscoring the need for their conservation and the development of integrated validation strategies.}, } @article {pmid42440756, year = {2026}, author = {Kraiselburd, I and Susenburger-Lange, R and Balzer, M and Magin, S and Block, K and Consten, L and Dörr, A and Dörr, AK and Gosch, J and Nishad, S and Sachse, S and Thomas, A and Triebs, A and Welling, J and Wilhelm, A and Widera, M and Schmithausen, R and Meyer, F}, title = {Wastewater-based epidemiology for public health - benefits and trade-offs of different molecular methods for the generation of actionable data in a small-town context.}, journal = {Frontiers in public health}, volume = {14}, number = {}, pages = {1828355}, doi = {10.3389/fpubh.2026.1828355}, pmid = {42440756}, issn = {2296-2565}, mesh = {*Wastewater/microbiology ; Humans ; Germany/epidemiology ; *Wastewater-Based Epidemiological Monitoring ; *Public Health ; Metagenomics ; }, abstract = {BACKGROUND: Wastewater-based epidemiology (WBE) is a promising complement to traditional surveillance systems, yet its practical utility and performance in real-world public health settings remain insufficiently characterized. This study aims to evaluate the feasibility and added value of WBE for monitoring infectious disease dynamics at the regional level, with a particular focus on jointly identifying, together with public health authorities, actionable and scalable methodological strategies based on cost, applicability, and the relevance and timeliness of the information generated.

METHODS: Composite influent wastewater samples were collected over 6 weeks from a treatment plant serving a defined district in western Germany. Samples were analyzed using quantitative PCR and both targeted and shotgun metagenomic sequencing. WBE findings were compared with routine case-based surveillance data from the corresponding catchment area.

RESULTS: All pathogens reported through routine public health surveillance during the study period were also detected in wastewater. In addition, WBE identified signals from clinically relevant pathogens not captured by case-based surveillance. Sequencing approaches provided further resolution on pathogen diversity and resistance profiles. The combined use of targeted and untargeted methods revealed differences in sensitivity and resolution, with complementary strengths across approaches, and enabled the definition of a practical, tiered approach to support actionable surveillance at the regional level.

CONCLUSION: This study describes the operational integration of WBE into a regional public health workflow, providing timely, population-level data that complements routine surveillance and can reveal pathogen circulation not captured by reported cases. Building on the established advantages of WBE, our results highlight its practical value when jointly implemented with public health authorities, enabling context-specific, actionable insights that enhance situational awareness, guide targeted local responses and support earlier detection of emerging threats.}, } @article {pmid42441076, year = {2026}, author = {Mohammadzadeh, P and Pilvaieh, A and Dousti, A and Bahrami, MRS and Ziaee, F}, title = {Multimodal characterisation of spontaneous Merkel cell carcinoma in the endangered Caucasian squirrel (Sciurus anomalus pallescens): integrating spatial transcriptomics, imaging mass cytometry and metagenomic sequencing.}, journal = {Journal of veterinary research}, volume = {70}, number = {2}, pages = {321-334}, doi = {10.2478/jvetres-2026-0034}, pmid = {42441076}, issn = {2450-7393}, abstract = {INTRODUCTION: Merkel cell carcinoma is an aggressive neuroendocrine skin malignancy rarely reported in non-domestic species.

MATERIAL AND METHODS: A cutaneous nodule from an endangered Caucasian squirrel (Sciurus anomalus pallescens) was examined using histopathology, immunohistochemistry, imaging mass cytometry, spatial transcriptomics (10× Visium) and metagenomic sequencing.

RESULTS: Histology revealed a high-grade neuroendocrine carcinoma with frequent mitoses (52 per 2.37 mm[2]) and necrosis. Tumour cells were positive for cytokeratin 20 (paranuclear dot pattern), synaptophysin and chromogranin A, with a high Ki-67 index (68%). Spatial analyses delineated a distinct tumour core and combined invasive front and stromal compartments, revealing upregulation of neuroendocrine (atonal basic helix-loop-helix transcription factor 1 and neurogenic differentiation factor 1) and proliferative (marker of proliferation Ki-67) programmes, and activation of phosphoinositide 3-kinase-AKT serine/threonine kinase 1-mechanistic target of rapamycin and mitogen-activated protein kinase pathways. No evidence of Merkel cell polyomavirus was found. The tumour microenvironment was immune-excluded, with programmed-death ligand 1 expression on ~22% of tumour cells and CD8[+] T cells restricted to the stroma.

CONCLUSION: This study provides a comprehensive methodological framework for high-resolution tumour profiling in conservation pathology and highlights the emergence of neoplasia in threatened wildlife.}, } @article {pmid42441094, year = {2026}, author = {Dal, GE and Çelik, B and Sabuncu, A and Yılmaz, M and Kekeç, AI and Dümen, E and İkiz, S and Diker, KS}, title = {Metagenomic analysis of the vaginal microbiota in cows with ovarian cysts.}, journal = {Journal of veterinary research}, volume = {70}, number = {2}, pages = {215-225}, doi = {10.2478/jvetres-2026-0028}, pmid = {42441094}, issn = {2450-7393}, abstract = {INTRODUCTION: This study compared the vaginal microbiota composition of dairy cows with follicular and luteal ovarian cysts using metagenomic analysis.

MATERIAL AND METHODS: Ovarian cysts, which impair reproductive performance through endocrine disruption, were diagnosed by ultrasonography and serum hormone evaluation in Holstein cows 30-60 d postpartum. Forty-five cows were initially included and divided into follicular cyst, luteal cyst and control groups. Vaginal lavage samples were analysed using third-generation sequencing, and taxonomic classification was performed through 16S rRNA gene analysis.

RESULTS: A total of 258 operational taxonomic units (OTUs) were identified, with the highest diversity observed in the control group (mean of 56.8 OTUs) and the lowest in the luteal cyst group (mean of 49.0 OTUs). Proteobacteria was the dominant phylum across all groups (93.4%), followed by Tenericutes (5.9%). Firmicutes, Bacteroidetes and Fusobacteria accounted for less than 1%. At the family level, Burkholderiaceae (62.7%) and Pasteurellaceae (24.0%) were predominant, while of the genera, Ralstonia was the most abundant (62.2%). The luteal group had the highest relative abundance of Burkholderiaceae, whereas Pasteurellaceae was most abundant in the control group.

CONCLUSION: These results indicate that cystic cows exhibit reduced microbial diversity and altered bacterial composition in comparison with healthy animals. The predominance of Proteobacteria and Ralstonia suggests a potential link between endocrine imbalance and changes in the vaginal microenvironment. Hormonal analyses supported the classification of cyst types, with follicular cyst cows showing low progesterone (0.31 ± 0.05 ng/mL) and high oestradiol-17β concentrations (55.57 ± 7.91 pg/mL), whereas luteal cyst cows exhibited higher progesterone (2.89 ± 0.74 ng/mL) and lower oestradiol-17β concentrations (6.19 ± 0.56 pg/mL) (P < 0.001). These results may support future studies evaluating vaginal microbial profiles as complementary indicators of ovarian status in dairy cows.}, } @article {pmid42442076, year = {2026}, author = {Ma, L and Zhang, J and He, X and Wang, Z and Zhao, M}, title = {Hemophagocytic lymphohistiocytosis secondary to disseminated histoplasmosis diagnosed by bone marrow smear microscopy and metagenomic next-generation sequencing: A case report and review of literature.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {3}, pages = {117542}, doi = {10.1016/j.diagmicrobio.2026.117542}, pmid = {42442076}, issn = {1879-0070}, abstract = {Hemophagocytic lymphohistiocytosis (HLH) secondary to Histoplasma capsulatum infection is rare in immunocompetent individuals but is associated with an extremely high mortality rate. Here, we report a case of disseminated histoplasmosis (DHP) in an immunocompetent patient. The pathogen was confirmed by bone marrow smear microscopy and metagenomic next-generation sequencing (mNGS). The patient experienced rapid clinical deterioration and was subsequently diagnosed with HLH secondary to DHP. Following targeted antimicrobial therapy with amphotericin B and immunomodulatory treatment involving etoposide and ruxolitinib, the patient's clinical condition improved. Early clinical manifestations of DHP are often atypical, while conventional diagnostic methods frequently yield negative results in the early stage. This case indicates that bone marrow examination combined with mNGS facilitates early definitive diagnosis. Furthermore, this report rarely describes the sequential morphological changes of Histoplasma capsulatum in bone marrow tissue.}, } @article {pmid42442081, year = {2026}, author = {Shayo, MJ and Kuchaka, D and Beti, M and Kimu, P and Wadugu, B and Jensen, EEB and Kumburu, H and Kazyoba, P and Ali, M and , and Clausen, PTLC and Muro, F and Mmbaga, BT and Kiwelu, I and Alifrangis, M and Aarestrup, FM and Sonda, T}, title = {Identification of enteric viral pathogens in Tanzanian children under the age of five with diarrhea using nanopore-based metagenomic sequencing.}, journal = {Virology}, volume = {623}, number = {}, pages = {111024}, doi = {10.1016/j.virol.2026.111024}, pmid = {42442081}, issn = {1096-0341}, abstract = {Diarrhea continues to be a significant contributor to illness and death among children, especially in low-income settings. In Tanzania, diarrheal disease remains a public health concern with many minors under five seeking healthcare despite the wide coverage of rotavirus vaccine. The diagnosis of pediatric diarrhea in Tanzania primarily focuses on specific viral diseases, which may overlook the broad-spectrum of viral pathogens. In this study, Oxford Nanopore-based metagenomic sequencing was applied to characterize viral pathogens in 200 stool samples from children under the age of five presented with diarrhea. Samples were collected from April 2023 to April 2024 at health facilities in six regions across mainland Tanzania and Zanzibar. At least one known diarrhea linked virus was detected in 31% of the participants. Although no statistical difference could be observed across different age categories, a slightly higher detection was observed in children aged 6-23 months. Human adenovirus was the most frequently detected 16% (32/200) in this study. Rotavirus was the second most frequently detected virus 9.5% (19/200) despite participant vaccination status. Other enteric viruses detected was astrovirus, norovirus, human bocavirus and Aichi virus were detected in 2.5% (5/200), 2% (4/200), 0.5% (1/200) and 0.5% (1/200) of the study participants respectively. Rotavirus showed negative correlation with temperature and relative humidity while human adenovirus was positively correlated to relative humidity. Metagenomics also revealed the presence of non-enteric viral pathogens, including measles and HAdV-C and HAdV-B, within this cohort. This study identified a range of viral pathogens associated with pediatric diarrhea in this cohort, including agents not typically targeted by routine diagnostic assays by using untargeted metagenomic technique direct to the clinical samples. These findings contribute baseline data that could inform future, larger-scale surveillance efforts in Tanzania.}, } @article {pmid42442149, year = {2026}, author = {Hong, M and Ji, L and Gao, J and Zhang, H and Ge, S and Yuan, C}, title = {Granulomatous inflammation in lung and lymph node specimens: A molecularly enhanced pathology-based algorithm for etiologic differential diagnosis.}, journal = {Annals of diagnostic pathology}, volume = {85}, number = {}, pages = {152684}, doi = {10.1016/j.anndiagpath.2026.152684}, pmid = {42442149}, issn = {1532-8198}, abstract = {Granulomatous inflammation is frequently encountered in lung and lymph node specimens and represents a diagnostic challenge because diverse infectious, immune-mediated, exposure-related, and neoplastic conditions may produce overlapping histologic patterns. Necrotizing, non-necrotizing, suppurative, foreign body-type, vasculitic, and malignancy-associated granulomas provide important diagnostic clues but are rarely disease-specific. Conventional pathology-based evaluation, including hematoxylin and eosin assessment, special stains, immunohistochemistry, culture, and serologic or antigen testing, remains the foundation of etiologic diagnosis. However, these methods may be limited by low organism burden, prior antimicrobial therapy, small tissue samples, formalin fixation, and broad etiologic heterogeneity. Molecular methods, including targeted polymerase chain reaction, 16S ribosomal RNA sequencing, internal transcribed spacer sequencing, targeted next-generation sequencing, and metagenomic next-generation sequencing, provide complementary tools for pathogen detection and species-level identification. This review summarizes the major histopathologic patterns and etiologic categories of granulomatous inflammation in lung and lymph node specimens and proposes a molecularly enhanced pathology-based algorithm for diagnostic workup. The goal is not to replace morphology with molecular testing, but to use histopathology to guide molecular assay selection and to interpret molecular findings within the appropriate tissue, microbiologic, radiologic, and clinical context.}, } @article {pmid42442277, year = {2026}, author = {Zhang, X and Han, S and Zhao, A and Wei, B and Chang, X and Song, S and Zhao, Y and Zhao, Z and Zhang, X and Chen, J}, title = {Dietary cypermethrin exposure reshapes the rumen microbiota and enriches antibiotic resistance genes: Metagenomic evidence of co-selection.}, journal = {Ecotoxicology and environmental safety}, volume = {322}, number = {}, pages = {120488}, doi = {10.1016/j.ecoenv.2026.120488}, pmid = {42442277}, issn = {1090-2414}, abstract = {Pesticide residues in crop-derived feedstocks represent a pervasive environmental stressor in agro-ecosystems, yet their role in driving the non-antibiotic co-selection of antimicrobial resistance (AMR) within the ruminant gut reservoir remains poorly understood. This study investigated the physiological trade-offs and indirect mechanisms of resistome expansion in a ruminant model exposed to environmentally relevant levels of cypermethrin. Integrated metagenomic and phenotypic assays revealed that cypermethrin exposure did not impair growth performance, but significantly increased daily feed intake and shifted fermentation profiles toward acetate. This metabolic compensation was supported by a reshaped core microbiome, characterized by increased abundance of fibrolytic consortia (e.g., Fibrobacter, Ruminococcus), enrichment of carbohydrate-active enzymes (GH3, GH5, GH13, and GH43), and upregulation of glycolysis and acetate-producing pathways. However, this metabolic adaptation came at a severe physiological cost, evidenced by systemic oxidative injury and hepatic dysfunction in the host. Crucially, cypermethrin acted as a potent non-antibiotic selective agent that expanded the ruminal resistome and mobilome, specifically, enriching efflux pumps (e.g., oqxA, MexB) confirmed target alteration genes (e.g., vanE). Consequently, dietary cypermethrin exposure forces microbial metabolic compensation at the expense of host hepatic health, while turning the ruminant gut into an overlooked repository for AMR. These findings highlight the critical ecological risks of pesticide-induced resistance co-selection, threatenting the One Health framework. Future research should incorporate multi-dose gradients, evaluate long-term exposure effects using sequential temporal sampling, and utilize non-invasive baseline monitoring across diverse ruminant species to fully elucidate these ecological risks.}, } @article {pmid42442278, year = {2026}, author = {Li, X and Chen, Y and Wang, J and Shu, Y and Lv, G}, title = {Phytotoxic effects and rhizosphere microecological responses of peanut to oxytetracycline and microplastic co-exposure.}, journal = {Ecotoxicology and environmental safety}, volume = {322}, number = {}, pages = {120498}, doi = {10.1016/j.ecoenv.2026.120498}, pmid = {42442278}, issn = {1090-2414}, abstract = {Microplastics (MPs) and antibiotics represent escalating emerging contaminants in global agricultural soils, posing substantial threats to crop health and ecosystem functionality worldwide. However, a comprehensive understanding of their joint toxicity and the underlying rhizosphere mechanisms under co-contamination remains elusive, leaving a critical knowledge gap. This study conducted a pot experiment using the globally cultivated peanut (Arachis hypogaea) exposed to polystyrene (PS) or polylactic acid (PLA) MPs (0.25 and 2% w/w) and oxytetracycline (OTC, 10 mg·kg[-1]), integrating metagenomic sequencing and untargeted metabolomics to elucidate root-zone microecological responses. High-concentration co-exposures significantly suppressed peanut shoot biomass, and OTC was identified as the primary contributor to reduced leaf catalase activity (CAT) (p < 0.01). Metagenomic profiling revealed that co-exposure significantly reshaped the rhizosphere microbiota (R[2] = 0.939, p = 0.001), enriching Pseudomonadota while inhibiting Actinobacteriota. Untargeted metabolomics detected 3789 metabolites, revealing that co-exposure significantly regulated the accumulation of defensive flavonoids (taxifolin and daidzin) and stress-responsive steroids (ponasterone A). Particularly, the combined exposure of PLA MPs and OTC induced the most severe metabolic disruption in the rhizosphere, generating 374 differential metabolites compared to the PLA-alone treatment. Procrustes analysis confirmed a tight coupling between microbial communities and metabolomes (M[2] = 0.619, p = 0.004). Network analysis further identified key regulatory nodes (Nocardioides and taxifolin) that bridge the associations between the rhizosphere microenvironment and plant growth traits. This study demonstrates that microbial shifts and metabolic adjustments are essential in mediating plant responses to multi-pollutant stress, providing crucial theoretical and mechanistic insights for global agricultural environmental risk assessment under co-contamination scenarios.}, } @article {pmid42442320, year = {2026}, author = {Sabater, C and Calvete-Torre, I and Vázquez, X and Cobo-Díaz, JF and Álvarez-Ordoñez, A and Ruas-Madiedo, P and Ruiz, L and Margolles, A}, title = {Metagenomics to assess authenticity and traceability of Asturian Gamonéu PDO cheese: A multi-omic study.}, journal = {International journal of food microbiology}, volume = {460}, number = {}, pages = {111939}, doi = {10.1016/j.ijfoodmicro.2026.111939}, pmid = {42442320}, issn = {1879-3460}, abstract = {Cheese is one of the most widely consumed fermented foods in Europe. The Principality of Asturias (northern Spain) has a broad tradition in cheese making including four cheeses under Protected Designation of Origin (PDO) status (Cabrales, Gamonéu, Casín and Afuega'l Pitu). The added value of PDO food products increases the risk of fraudulently copied cheeses reaching the market. The aim of this work was to develop a novel microbiome-based method contributing to the assessment of the authenticity of Gamonéu PDO cheese. For this purpose, cheese metagenomes and volatile organic compounds (VOCs) profiles were integrated using machine learning (ML) algorithms. Computational models accurately discriminated between samples from 9 Gamonéu PDO cheese producers, as well as between cheeses ripened in different natural caves. Furthermore, they allowed distinguishing PDO and non-PDO Gamonéu-like cheeses produced in the same area. Potential microbial markers of the geographical origin of Gamonéu PDO cheese included Debaryomyces hansenii, Lacticaseibacillus paracasei and Penicillium roqueforti (more abundant in non-PDO cheeses), and Brachybacterium faecium (more abundant in PDO cheeses). Computational models presented in this work may contribute to improving existing traceability methods in the field of fermented foods and may be applied to a wide range of cheese varieties.}, } @article {pmid42442424, year = {2026}, author = {Luo, Z and Zhang, K and Wang, L and Zhang, J and Huang, Y and Lu, X and Zhao, F and Cao, S and Li, J}, title = {Astragalus polysaccharides reshape gut resistome of postpartum dairy cows.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135399}, doi = {10.1016/j.biortech.2026.135399}, pmid = {42442424}, issn = {1873-2976}, abstract = {Antibiotic resistance genes (ARGs) in livestock feces represent an important environmental reservoir of antimicrobial resistance. Natural product intervention is a potential strategy for regulating the gut microbiome of livestock; however, its effects on the gut resistome of postpartum dairy cows remain poorly understood. In this study, we investigated the effects of Astragalus polysaccharides (APS) supplementation on the fecal microbiome, ARGs, mobile genetic elements (MGEs), virulence factors (VFs), and ARG-carrying metagenome-assembled genomes (MAGs) in dairy cows during postpartum period. Alpha and beta diversity analyses showed that APS supplementation did not significantly alter the global resistome, mobilome, or virulome structure. The content of several ARGs and VFs, including AAC(6')-Iw, qacEdelta1, ast, PM_RS00425, and sdrF, significantly decreased in the APS group, and several plasmid-associated MGEs genes showed group-specific changes. Co-occurrence network analysis revealed complex associations between ARGs, VFs, and core bacterial taxa, with Paludibacter and Parabacteroides identified as potential microbial reservoirs of resistance- and virulence-associated genes. Furthermore, 101 metagenome-assembled genomes (MAGs) were recovered, 42 of which carried multiple ARGs. Bin.1, assigned to Scatovivens, had the highest ARG count. APS supplementation reduced the overall ARG load, particularly the ARG contribution in bin.1. However, APS utilization potential was not significantly correlated with ARG density or ARG load across MAGs. Thus, this study provides new insights into APS supplementation and nutritional strategies that can mitigate the fecal ARG burden in dairy production.}, } @article {pmid42442443, year = {2026}, author = {Umair, M and Jamal, Z and Ali, Q and Hakim, R and Rana, MS and Javed, Y and Bugti, AR and Ayub, A and Sabeen, F and Waheed, Y and Salman, M}, title = {Emergence of Reassortant Crimean-Congo Hemorrhagic fever virus lineages, Pakistan, 2023-2024.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105988}, doi = {10.1016/j.meegid.2026.105988}, pmid = {42442443}, issn = {1567-7257}, abstract = {Crimean-Congo hemorrhagic fever virus (CCHFV) remains endemic in Pakistan, yet whole-genome data are limited. During 2023-2024 national surveillance, 151 suspected cases were screened by qRT-PCR; 23 were confirmed at the NIH, Islamabad. Shotgun metagenomic sequencing of 17 cases (15 Pakistan, 2 Afghanistan) generated high-quality genomes, with 65% classified as Asia-1 genotype, while 35% showed segment reassortment involving Asia-2-derived S and/or M segments. Reassortment involved primarily S and M segments, while L segments remained conserved. Phylogenetic analysis revealed Asia-1 sequences closely related to strains from India, Afghanistan, Iran, and the Middle East, whereas Asia-2 sequences clustered with Indian and Central Asian strains, suggesting cross-border and regional viral exchange. S-segment phylogeography indicated northern Punjab (Rawalpindi, Islamabad, Chakwal, Attock) as a region potential involved in viral connectivity. Region-specific mutations (S: G185S, D186N; M: P90L, T122I, M35L, L443S, I1597V) may reflect localized viral evolution. These findings underscore ongoing viral diversification, reassortment, and regional connectivity, highlighting the need for integrated genomic surveillance to guide public health interventions.}, } @article {pmid42442450, year = {2026}, author = {Zhang, Z and Xia, Y and Liu, Y and Tao, L and Ju, F}, title = {Future Climate Scenarios Reduce Antibiotic Resistome-associated Risk but Enrich Specific Soil-borne Pathogens.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125248}, doi = {10.1016/j.envres.2026.125248}, pmid = {42442450}, issn = {1096-0953}, abstract = {Understanding how climate change reshapes the soil resistome, i.e., the collection of antibiotic resistance genes (ARGs), is critical for environmental and public health. Using a representative six-year (2014-2019) metagenomic dataset from a long-term climate manipulation experiment, this study investigated the impacts of future climate scenarios on cropland and grassland soil resistomes. Both simulated climate warming (+0.6°C) and extreme summers (+2.2°C during 2018-2019) significantly altered soil resistome structures, reducing ARG richness by 4.4%-12.5% while increasing the abundance of specific ARG types predominantly carried by gram-positive bacteria by 31.5%-72.8%. Simulated climate and extreme summer also reduced the abundance of high-risk ARGs by 10.0% and 27.2%, respectively, and concomitantly lowered the estimated resistome-associated risk by 18.3% and 36.4%, primarily through selectively filtering their bacterial hosts (e.g., Pseudomonadota). At the same time, future climate scenarios confer a competitive advantage for specific soil-dwelling antibiotic-resistant phytopathogens (e.g., Rhodococcus fascians) and human pathogens (e.g., Mycobacterium spp.), potentially increasing their prevalence and public health relevance in soil ecosystems. These findings highlight the contrasting responses of soil resistomes and pathogen communities under future climate scenarios and underscore the importance of long-term monitoring of soil ARGs and pathogens under the context of on-going global change within a One-Health framework.}, } @article {pmid42442462, year = {2026}, author = {Fukada, A and Suda, K and Watayo, H and Motooka, D and Shinoda, T and Tohya, M and Ishiyama, A and Nishimura, Y and Fujiwara, K and Ochi, T and Goto, H and Nikai, K and Ishii, J and Yamamoto, Y and Okazaki, T and Nakamura, S and Kirikae, T and Yamataka, A and Watanabe, S and Miyano, G}, title = {Characteristics and environmental susceptibility of first-pass meconium microbiota in neonates with congenital intestinal atresia.}, journal = {Journal of pediatric surgery}, volume = {}, number = {}, pages = {163290}, doi = {10.1016/j.jpedsurg.2026.163290}, pmid = {42442462}, issn = {1531-5037}, abstract = {PURPOSE: Whether congenital gastrointestinal atresia (atresia) specifically affects the meconium microbiota because of an altered intrauterine intestinal environment remains unclear. Therefore, we aimed to characterize the meconium microbiota of neonates with congenital anomalies, specifically atresia.

METHODS: Meconium samples were collected from healthy term neonates (control), neonates with congenital malformations other than atresia (other anomalies), and those with atresia who were admitted to the growing care unit or obstetrics ward. Alpha-diversity (Shannon index and observed features) and beta-diversity (principal coordinate analysis) were assessed through 16S rRNA gene sequencing. The microbial composition was examined at the phylum and genus levels, and stratified by delivery mode and mother's antibiotic exposure.

RESULTS: The study included 20 controls, 37 neonates with other anomalies, and 11 with atresia, including esophageal, duodenal, small intestinal, and colonic atresia. Alpha-diversity was the lowest in atresia, particularly with cesarean delivery or maternal antibiotic exposure (p<0.05). Beta-diversity analysis demonstrated that the distribution of microbial profiles significantly differed between the control and atresia groups (p<0.05). At the phylum level, atresia had a high proportion of Bacteroidetes, whereas Firmicutes and Proteobacteria were reduced. Several genera that were abundant in the control were markedly reduced in atresia (p<0.001 vs. control; p<0.01, among 3 groups), with higher Pseudomonas but lower Staphylococcus (p<0.05, vs. control and other anomalies) and Escherichia (p<0.05 vs. other anomalies).

CONCLUSION: Congenital gastrointestinal atresia demonstrated unique meconium microbiota profiles compared with those of healthy neonates and other congenital anomalies. This suggests differences in the intraintestinal environment during the fetal period.

LEVEL OF EVIDENCE: Ⅱ.}, } @article {pmid42442593, year = {2026}, author = {Qi, T and Liu, Q and Li, M and Li, H and Liang, G and Tu, W}, title = {Integrating lung microbiome, amino acid metabolism, and host immune response in elderly patients for severe lower respiratory Infections diagnosis: a multi-omics study.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {}, number = {}, pages = {121232}, doi = {10.1016/j.cca.2026.121232}, pmid = {42442593}, issn = {1873-3492}, abstract = {BACKGROUND: Lower respiratory infections (LRIs) cause significant morbidity and mortality in elderly individuals, but the mechanisms driving severe deterioration remain unclear.

METHODS: This prospective study enrolled 105 patients aged ≥60 with suspected LRIs between October 2024 and April 2025. Bronchoalveolar lavage fluid (BALF) was analyzed using 16S rRNA sequencing, metagenomics, untargeted metabolomics, and cytokine profiling. Multi-omics data were integrated into a tripartite network, and severity-associated signatures were identified via PLS-DA, logistic regression, and ROC analysis.

RESULTS: The cohort included 40 severe (sLRIs) and 65 mild (mLRIs) cases. sLRIs exhibited reduced microbial diversity, shifting from commensal genera to opportunistic pathogens (Klebsiella, Corynebacterium, Elizabethkingia), with Klebsiella pneumoniae as a major bacterial hub. Metabolomics revealed 180 differential metabolites. Phenylalanine and beta-Alanine metabolism emerged as key severity-associated pathways. sLRIs showed accumulation of pro-inflammatory metabolites L-phenylalanine and phenylpyruvic acid. L-3-phenyllactic acid (PLA) served as the central metabolic hub. Cytokine profiling revealed local hyperinflammation (elevated IL-1β, IL-6, IL-8, TNF-α, IFN-γ), with IL-6 as central hubs. Multivariate analysis identified PLA and IL-8 as independently associated with severe status. Combined metabolic-immune signatures achieved high diagnostic accuracy (AUC: 0.858-0.882).

CONCLUSIONS: sLRIs in elderly patients are characterized by microbial dysbiosis, opportunistic pathogen enrichment, and remodeled Phenylalanine and beta-Alanine metabolism that correlates with hyperinflammation. BALF PLA and IL-8 represent promising metabolic-immune biomarkers for severity stratification.}, } @article {pmid42443172, year = {2026}, author = {Mühlberg, L and Ruta, J and Mikirtumov, V and Burton-Smith, R and Murata, K and Kudryashev, M and Okamoto, K and Bogdanow, B and Liu, F}, title = {Integrative structural interactomics reveals protein organization and structure in a giant virus.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42443172}, issn = {2041-1723}, support = {LI 3260/6-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KU 3222/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ERC-STG-2020 No. 949184//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Leibniz-Wettbewerb P70/2018//Leibniz-Gemeinschaft (Leibniz Association)/ ; 24ama121005j0003//Japan Agency for Medical Research and Development (AMED)/ ; 2018-03387 and 2023-01857//Vetenskapsrådet (Swedish Research Council)/ ; CTS23:2703//Carl Tryggers Stiftelse för Vetenskaplig Forskning (Carl Trygger Foundation)/ ; }, abstract = {Giant viruses are large DNA viruses that infect unicellular and multicellular eukaryotes and form exceptionally large extracellular particles. (Meta)genomics and (meta)transcriptomics have provided insight into their diverse coding repertoire, but many of the proteins remain to be characterized as they lack homology with known proteins. Here, we integrate cross-linking mass spectrometry, quantitative proteomics, computational tools and cryo-EM data to characterize the protein architecture of intact melbournevirus particles. Based on this, we allocate 88 viral proteins to different virion sub-compartments and propose topologies of 25 inner membrane proteins. We assign eight components of the capsid in cryo-EM data, including proteins that tether the capsid shell to the membrane, reflecting key points in virion maturation. The data provide a valuable resource and demonstrate the power of an integrative approach to gain system-level structural insights into a poorly characterized biological system.}, } @article {pmid42130477, year = {2026}, author = {Molano, LG and Hirsch, P and Keller, A and Dolejska, M and Palkovicova, J}, title = {HERA: a web server for host element reference-based aligner.}, journal = {Nucleic acids research}, volume = {54}, number = {W1}, pages = {W154-W159}, pmid = {42130477}, issn = {1362-4962}, support = {469073465//Deutsche Forschungsgemeinschaft/ ; //European Commission/ ; 205/2025/FVHE//University of Veterinary Sciences in Brno/ ; 24-12527S//Czech Science Foundation/ ; }, mesh = {*Software ; Internet ; *Plasmids/genetics/chemistry ; Genome, Bacterial ; Sequence Alignment ; Genomics/methods ; }, abstract = {Plasmids play a central role in bacterial adaptation and in the dissemination of antimicrobial resistance, driving a growing need for accessible tools that support their comparative analysis without requiring local computational infrastructure. Although several circular genome visualization platforms exist, most are designed for general bacterial genome analysis rather than focused on plasmid comparison. Host element reference-based aligner (HERA) is a web server for intuitive visualization and comparison of plasmids and other circular molecules through BLAST alignment against reference sequences. Built on interactive circular genome visualization, HERA simplifies comparative genomics by providing an accessible interface for exploring sequence similarity, identifying conserved regions, and analyzing genetic elements without the complexity of traditional local tools. HERA includes a plasmid-oriented annotation pipeline covering replicon and mobility typing, antimicrobial resistance detection, mobile element identification, and homology search against the PLSDB plasmid database. HERA also provides an automatic selection of the reference which is the most appropriate from the uploaded sequences. The web server is available without login or any restriction at https://web.ccb.uni-saarland.de/hera/.}, } @article {pmid42436166, year = {2026}, author = {Chen, Y and Ma, J and Guo, Z and Chen, J and Wang, X and Xiao, J and Hu, D and Yan, J and Deng, W and Nu, Z and He, H and He, W and Luo, J and Zhang, YP and Li, Y}, title = {A rugged life: how host-microbiome adaptations associated with the semi-feral lifestyle of gayal (Bos frontalis).}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01095-4}, pmid = {42436166}, issn = {2055-5008}, support = {CY22624109//Yunnan Provincial Universities Service Key Industry Technology Project - Doctoral Student Industry-Oriented Scientific Research Innovation Training Project/ ; KC-242410789//Graduate Research and Innovation Project of Yunnan University/ ; 2021YFD1200904//National Key Research and Development Program of China/ ; 32470654//National Natural Science Foundation of China/ ; 202407AA110003//Special funds for central guidance of local scientific and technological development/ ; 202601BC070001//Major Program of Yunnan Fundamental Research Projects/ ; XDYC-QNRC-2023-0371//"Xingdian Talent Support Program" Grant of Yunnan Province/ ; }, abstract = {The semi-domesticated gayal (Bos frontalis) is an endangered browsing ruminant inhabiting the rugged Eastern Himalayan foothills, and maintains an energy-intensive lifestyle on nutrient-poor, fiber-rich feed. However, the dietary, microbial, and host physiological features underlying this adaptation remain poorly understood. Here, we analyzed fecal metagenomes from ten bovine populations (n = 334) to characterize dietary composition. Then we profiled the four-chambered (FC) stomach microbiome in adult gayal (Bos frontalis), yak (Bos grunniens), and taurine cattle (Bos taurus). Host transcriptomes were profiled across the FC stomach in adult individuals from gayal, yak and cattle. Dietary analysis revealed a woody plant-dominated, bamboo-rich dietary pattern in gayal. Gastric metagenomes in gayal showed high population-level microbial diversity, pronounced individual-associated community structure, and functional potentials related to aromatic compound transformation, nitrogen metabolism, and metabolic flexibility. Transcriptomes revealed compartment-specific specialization in the gayal stomach, including rumen immune signatures and reticulum contractile/electrophysiological features. Exploratory compartment-level integration further suggested possible consistency between host transcriptomic features and microbial functional potential. Together, these multi-omics findings suggest a host-microbiome system potentially associated with the utilization of chemically complex, low-quality forage, providing a framework for understanding digestive features of browsing ruminants and for conserving host-associated gastrointestinal microbiomes.}, } @article {pmid42436177, year = {2026}, author = {Eriksson, D and Righetti, D and Benedetti, F and Gruber, N and Paoli, L and Salazar, G and Sunagawa, S and Vogt, M}, title = {Nitrogen fixation rates increase with diazotroph richness in the global ocean.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-61132-2}, pmid = {42436177}, issn = {2045-2322}, abstract = {Marine nitrogen fixation is a key process to support and maintain the ocean's primary production, yet our knowledge of the distribution and diversity of the diazotrophic microbes that are capable of fixing nitrogen is very limited. Here, integrating microscopic and metagenomic data, we determine the biogeography and richness of the main diazotrophic taxa across the global ocean. Analyzing 22,000 records and 15 species, we deduce a latitudinal gradient in diazotroph richness, with higher richness to the tropics driven by temperature and nutrient levels. Cyanobacteria dominate in nutrient-poor gyres, while non-cyanobacterial diazotrophs thrive in nutrient-rich zones. Across the global ocean, diazotroph richness is found to correlate positively with nitrogen fixation rates, suggesting a positive biodiversity-ecosystem function relationship. While this relationship is robust to spatial autocorrelation and confounding environmental drivers, spatial dependence in the global datasets and potential unmeasured covariates may influence local-scale inferences. The findings suggest that positive biodiversity-ecosystem functioning relationships with implications for global biogeochemical cycling exist in marine plankton.}, } @article {pmid42436183, year = {2026}, author = {Liu, Z and Wu, H and Howe, S and Zuo, B and Tian, Y and Wang, X and Assress, HA and Shang-Lun Lan, R and Mu, C and Xiao, Y and Huang, Y and Looper, M and Tsai, T and Zhao, J}, title = {Lactiplantibacillus plantarum promotes intestinal goblet cell differentiation via indole-3-lactic acid-AHR signaling in pigs.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01085-6}, pmid = {42436183}, issn = {2055-5008}, support = {Grant No. 32573234//the National Natural Science Foundation of China/ ; Grant No. 32573234//the National Natural Science Foundation of China/ ; Grant No. 32573234//the National Natural Science Foundation of China/ ; Grant No. 32573234//the National Natural Science Foundation of China/ ; Grant No. 2023B10564001//Double First-Class Discipline Promotion Project/ ; Grant No. 2023B10564001//Double First-Class Discipline Promotion Project/ ; Grant No. 2023B10564001//Double First-Class Discipline Promotion Project/ ; Grant No. 2023B10564001//Double First-Class Discipline Promotion Project/ ; USDA-ARS 6026-10700-001-000D//USDA/ ; USDA-ARS 6026-10700-001-000D//Food and Nutrition Service/ ; 2023YFE0124400//National Key Research and Development Program of China/ ; 2025-WPY-00-001//the Guangdong Provincial Special Fund Project for Seed Industry Revitalization/ ; }, abstract = {The swine intestinal microbiota dynamically remodels during development and supports gut homeostasis. However, whether stage-specific microbial shifts, are associated with epithelial development remains poorly understood. Here, longitudinal metagenomic profiling of the swine gut microbiome identified Lactiplantibacillus plantarum as a transiently enriched nursery-stage bacterium positively associated with goblet cell numbers. Dietary supplementation with L. plantarum validated this association, showing increased goblet cell numbers and MUC2 expression in the ileum of nursery piglets. Co-culture with porcine ileum organoids further demonstrated that L. plantarum cell-free supernatant promoted ileal organoid growth and goblet cell differentiation. Integrated untargeted metabolomic analyses of ileal samples and bacterial culture supernatants identified indole-3-lactic acid (ILA) as a potential key microbial metabolite from L. plantarum. Mechanistically, ILA promoted intestinal stem cell proliferation and MUC2 expression, accompanied by increased expression of aryl hydrocarbon receptor (AHR) and its downstream target CYP1A1 in ileal organoids. Consistently, activation of AHR using FICZ increased MUC2 expression, whereas inhibition with CH-223191 suppressed MUC2 expression in ileal organoids. Collectively, these findings uncover a L. plantarum-ILA-AHR signaling axis that promotes intestinal goblet cell differentiation, providing mechanistic insight into microbial metabolite-mediated regulation of epithelial homeostasis during post-weaning period in pigs.}, } @article {pmid42436393, year = {2026}, author = {Zhao, Y and Wang, H and Duan, J}, title = {A rare presentation of clinically diagnosed lyme disease with probable neuroborreliosis, septic shock, and bone marrow suppression: a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13899-y}, pmid = {42436393}, issn = {1471-2334}, support = {2025-HX-27//Evaluation of the effects of acupuncture intervention on central nervous system regulation in septic patients/ ; }, abstract = {BACKGROUND: Lyme disease is rarely considered in critically ill patients from regions not routinely recognised as endemic. Severe presentations including septic shock, central nervous system involvement, and bone marrow suppression may therefore be difficult to recognise, particularly when laboratory confirmation is incomplete.

CASE PRESENTATION: A 60-year-old man from an inland province of northern China was admitted to the intensive care unit with four months of relapsing fever, acute delirium, respiratory distress, and septic shock. During admission, he developed recurrent high-grade fever with migratory erythematous rashes. Collateral history revealed a tick bite approximately 15 months earlier, followed by an expanding erythematous lesion compatible with erythema migrans. Cerebrospinal fluid showed markedly elevated opening pressure (>30 cmH2O), lymphocytic pleocytosis, elevated protein, and a normal CSF-to-serum glucose ratio, consistent with aseptic meningitis. Bone marrow aspiration showed pure red cell aplasia and megakaryocyte maturation arrest. Blood, urine, and cerebrospinal fluid cultures were negative, and metagenomic next-generation sequencing did not identify alternative pathogens. Lyme serology showed isolated IgM positivity with IgG negativity. Confirmatory two-tier testing and CSF Borrelia antibody testing were unavailable in our centre. This patient was therefore classified as clinically diagnosed Lyme disease with probable neuroborreliosis. Treatment with ceftriaxone and doxycycline was followed by defervescence and haematological recovery. At follow-up several weeks after discharge, the patient was afebrile, fully alert, and oriented.

CONCLUSIONS: This case highlights an unusual severe presentation of clinically diagnosed Lyme disease with probable neuroborreliosis, intracranial hypertension, septic shock, and bone marrow suppression. Geographic origin should not preclude diagnostic consideration. In critically ill patients with unexplained fever, cytopenias, and dynamic cutaneous lesions, careful tick exposure history and bedside dermatological assessment may prove decisive where laboratory testing is inconclusive.}, } @article {pmid42437026, year = {2026}, author = {Mohidin, AF and Neshat, SA and Santillan, E and Wuertz, S}, title = {Disturbance intensity shapes universal and context-dependent functional traits in anaerobic microbiomes.}, journal = {Environmental science and ecotechnology}, volume = {32}, number = {}, pages = {100729}, pmid = {42437026}, issn = {2666-4984}, abstract = {Trait-based frameworks, notably Grime's competitor-stress-tolerant-ruderal theory, offer a powerful lens for predicting how environmental fluctuations govern community structure. Yet, classical ecological models assume environments combining extreme stress and intense disturbance are non-viable for sustained colonisation, leaving a critical bottleneck in our ability to predict how microbial systems withstand compounded operational pressures. This gap severely hinders the predictive management of engineered microbiomes critical for global waste-to-energy conversion. Here we extend the application of classic ecological frameworks by demonstrating that anaerobic digester microbiomes deploy distinct, predictable life-history strategies across a 182-day compounded gradient of biomass turnover and organic loading. High-intensity single-event disturbances drive severe volatile fatty acid accumulation (propionate reaching 2,955 mg L[-1]), selectively shifting the microbiome toward stress-tolerant and stress-tolerant-ruderal strategies. Traits associated with ribosome function, molecular chaperones, and enzymatic reactive oxygen species detoxification were particularly enriched under highly disturbed conditions. Conversely, intermediate regimes were associated with ruderal strategies that prioritise rapid growth over resource-uptake efficiency, dropping total chemical oxygen demand removal to 41%. Cross-system comparisons encompassing anaerobic digestion, activated sludge, and soil ecosystems, revealed both universal and context-dependent ecological traits. Survival-associated traits linked to cell maintenance and repair, protective mechanisms, and cell motility were universally associated with stress-tolerant or ruderal strategies across ecosystems, whereas nutrient transport and metabolic traits exhibited greater context dependency. These insights establish a gene-resolved framework that reconciles microbial trait selection with ecological theory, providing a roadmap to engineer microbiome resilience against process failures.}, } @article {pmid42437039, year = {2026}, author = {Goraya, MU and Fatima, G and Hayat, K and Raza, A and Yong, D}, title = {The evolution of diagnostic microbiology: integrating culture-based methods and genomic advances.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21411}, pmid = {42437039}, issn = {2167-8359}, mesh = {Humans ; *Genomics/methods ; *Microbiological Techniques/methods/trends ; Bacteria/genetics/isolation & purification ; *Molecular Diagnostic Techniques/methods ; Machine Learning ; }, abstract = {Over the past several decades, diagnostic microbiology has progressed from traditional culture methods to include modern, culture-independent molecular and metagenomic approaches for diagnosing infectious diseases and guiding antimicrobial therapy. Since the beginning of the twenty-first century, clinical diagnostic microbiology has made considerable strides in optimizing pathogen identification. This progress has been driven by the introduction of optimized sampling methods, advanced diagnostic kits, and new technologies like mass spectrometry for bacterial identification, real-time genomics, and adaptable culture systems. However, the costs of advanced molecular methods are very high, and they require massive instrumentation to reach a clinical diagnosis. Conventional cultures remain cost-effective and can be performed with minimal resource requirements compared to advanced laboratory equipment. However, the most significant challenge with conventional methods is the reporting time of results (several days). Since the newer molecular and genomic methods do not meet all the diagnostic demands, strategies have shifted toward employing techniques with higher precision, sensitivity, and better time efficiency. The integration of artificial intelligence and machine learning is set to redefine diagnostic paradigms, facilitating not only rapid and precise pathogen identification but also addressing foundational limitations in data analysis and interpretation. This review evaluates the synergy between conventional and emerging diagnostic technologies, emphasizing their clinical utility, limitations, and future trajectories for diverse audiences in microbiology and healthcare.}, } @article {pmid42437291, year = {2026}, author = {Griffin, NG and Hughes, AE and Erdody, DS and Berlemont, E and Sweeney, S and Fareghbal, T and Hagedorn, KB and Berlemont, R}, title = {Annotation of glycoside hydrolases in unassembled metagenomes using CAZyOGH.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag137}, pmid = {42437291}, issn = {2635-0041}, abstract = {MOTIVATION: Functional characterization of microbiomes often relies on the sequencing of metagenomic DNA extracted from environmental samples, with current approaches using metagenome-assembled genomes (MAGs). Although glycoside hydrolases (GHs) are central to carbon cycling, accurate annotation of GHs in metagenomic datasets remains challenging due to the multidomain architecture of carbohydrate-active enzymes and the prevalence of unassembled short reads due to limitations in the MAG-generation process.

RESULTS: Here, we present CAZyOGH (CAZymes Open-source GH annotation), a curated reference database for the domain-specific identification of 135 protein domains spanning 99 GH families with well-defined catalytic domain signatures. CAZyOGH focuses on individual GH domains, enabling robust annotation of both assembled and unassembled metagenomic data. We validated CAZyOGH by reanalyzing genomes listed in CAZy db, where predicted GH profiles closely matched reported values. Next, we used CAZyOGH to analyze 12 human gut metagenomes and 12 newly sequenced soil microbiomes to reveal environment-specific GH repertoires. By accurately detecting catalytic domains independent of the genomic context, CAZyOGH improves sensitivity and specificity in short-read metagenomic annotation. This framework provides a scalable and reproducible approach to investigate carbohydrate-active enzymes across ecosystems, advancing our capacity to characterize microbial functional potential in global carbon cycling.

CAZyOGH data is available on figshare (https://figshare.com/projects/CAZyO_GH/267770).}, } @article {pmid42437307, year = {2026}, author = {Guo, Y and Liang, Y and Liu, L and Zhou, Y and Yang, X and Ming, X and Hu, P and Wu, J and Li, D and Hou, D and Xia, S and Wang, X and Zuo, Y}, title = {Decoding preeclampsia: A fusion of multi-view machine learning and multi-omics to identify putative inflammation-related mechanisms.}, journal = {Molecular therapy. Nucleic acids}, volume = {37}, number = {3}, pages = {102992}, pmid = {42437307}, issn = {2162-2531}, abstract = {Preeclampsia (PE) is a leading cause of maternal and fetal morbidity and mortality worldwide, with placental inflammation recognized as a central pathogenic feature, yet the upstream triggers and inflammatory mechanisms remain incompletely understood. Here, we combined placental single-cell transcriptomics with gut metagenomic and metabolomic profiling to characterize inflammatory signatures in PE. Stratified analyses across clinical subgroups-defined by fetal number, onset timing, and fetal sex-revealed that placental single-cell transcriptomics coupled with multi-view machine learning consistently prioritized bacteria-associated inflammatory features across all subgroups. Superimposed on this shared foundation, we identified subgroup-specific trajectories: twin PE exhibited IL-1-dominant inflammation with compensatory antioxidant metabolic shifts, while singleton PE showed IFN-II-associated immune activation. Early-onset PE displayed sexual dimorphism-male fetuses featured bacterial defense pathways, lipid metabolic programs, and trophoblast-confined glycolysis, while female fetuses exhibited angiogenesis, chemotaxis, nitric oxide signaling pathways, and glycolytic reprogramming in immune cells, whereas late-onset PE exhibited comparatively attenuated inflammatory activity. Gut metagenomic profiling revealed enrichment of lipopolysaccharide (LPS)-producing taxa and depletion of beneficial commensals in PE, accompanied by metabolomic alterations that aligned with inflammatory pathways also highlighted in placental analyses. Collectively, these findings reveal a conserved bacteria-associated inflammatory program in PE that is modulated by clinical context and linked to gut microbial dysbiosis.}, } @article {pmid42437513, year = {2026}, author = {Dhande, SS and Mankoskar, NA and Panakkal, HP and Gupta, IR and Bhagat, RP}, title = {Critical Review on Microbial Inulinase Production: Emerging Strategies, AI-Driven Optimization, and Applications.}, journal = {Biotechnology and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1002/bit.70306}, pmid = {42437513}, issn = {1097-0290}, support = {Plan & Stat/RDC/2024-25/1018-21//Dr. Babasaheb Ambedkar Marathwada University/ ; }, abstract = {Microbial inulinases are increasingly recognized as valuable biocatalysts for the sustainable production of high-value products, including fructooligosaccharides, fructose, bioethanol, and organic acids in industries, such as food, pharmaceuticals, and bioenergy. In the last few decades, microbial inulinase research has advanced significantly, from strain selection and fermentation optimization to advanced enzyme engineering and immobilization, improving yields, stability, and reusability. There are still some final bottlenecks, such as low yields, poor thermostability, and high purification costs. This review examines strategies to innovate and overcome these bottlenecks, including novel immobilization strategies that utilize nanomaterials, system-scale bioprocess optimization using artificial intelligence (AI), and bioprospecting extremophiles using metagenomics. The present review discusses how statistical and computational modeling (RSM, ANN, and AI) significantly increases yield and process efficiency, with comments on their relevance to contemporary biorefinery applications. The advanced immobilization approaches significantly enhance operational stability and reusability, allowing for continuous processing. This review situates the development of inulinase as not just an enzymological effort but a multidisciplinary effort involving process engineering and sustainability science. Overall, emphasize is given toward the thought that advancements leaning toward the future will require a synthesis of AI-designed enzyme systems; economical immobilization supports; and incorporation of circular bioeconomy principles through the valorization of agro-wastes. These barriers to knowledge transfer must be resolved if we are to unlock the full bioeconomic potential of microbial inulinase systems.}, } @article {pmid42437546, year = {2026}, author = {Fregolente, LG and Roth, FN and Warncke, JD and Macpherson, AJ and Yilmaz, B and Bassetti, CLA}, title = {The gut-sleep connection: a scoping review into microbiome alterations in sleep-wake and circadian disorders.}, journal = {Sleep medicine}, volume = {147}, number = {}, pages = {109136}, doi = {10.1016/j.sleep.2026.109136}, pmid = {42437546}, issn = {1878-5506}, abstract = {Sleep is fundamental to brain, body, mental, and social health. In parallel, the gut microbiome is increasingly recognized as a key regulator of immune, metabolic, endocrine, and neurophysiological processes. This scoping review explored current evidence on gut microbiome alterations in relation to sleep duration and sleep loss, sleep-wake disorders, and circadian rhythm-related phenotypes. Searches of MEDLINE, Embase, and Cochrane were conducted up to February 2024. Of 2059 records identified, 54 studies met the eligibility criteria. Thirty-eight studies were observational, nine interventional, and seven genome-wide association or Mendelian-randomization studies. The most frequently investigated phenotypes were insomnia (15 studies, 28%), obstructive sleep apnea (12 studies, 22%), circadian rhythm or circadian-misalignment phenotypes (10 studies, 19%), and sleep duration or sleep loss/deprivation (9 studies, 17%). Most studies used 16S rRNA gene sequencing to assess gut microbiota composition and diversity, while shotgun metagenomic sequencing and functional analyses were less common. Across disorders, studies reported alterations in microbial diversity, taxonomic composition, short-chain fatty acid-producing taxa, bile acid-related pathways, inflammatory markers, and cardiometabolic or neurophysiological correlates. However, findings were limited by heterogeneous sleep phenotyping, small sample sizes, cross-sectional designs, variable microbiome methods, and inconsistent control of diet, medication use, body mass index, comorbidities, and stool sampling protocols. Current evidence supports an association between sleep-wake and circadian disturbances and gut microbiome alterations, but causality and disorder-specific microbial signatures remain unresolved. Standardized longitudinal and multi-omics studies are needed to clarify mechanisms and therapeutic potential.}, } @article {pmid42437625, year = {2026}, author = {Souto, LCDS and Ubaid, FK and Hernández, LHA and da Silva, SP and Barbosa, BB and Farias, LDSS and Coelho, TFSB and Cruz, ACR and Mascarenhas, JDP}, title = {New Iflavirus identified in Chiroxiphia pareola birds from an ecotone area in northeast Brazil.}, journal = {Virus research}, volume = {}, number = {}, pages = {199776}, doi = {10.1016/j.virusres.2026.199776}, pmid = {42437625}, issn = {1872-7492}, abstract = {Avian species play a key role in the ecology of viruses, acting as reservoirs, sentinels, and biological carriers across diverse environments. Here, we describe the detection and genomic characterization of a novel iflavirus identified in fecal samples from the Chiroxiphiapareola("blue-backed manakin") collected in areas of the Middle North region of Brazil, Maranhão state. Viral RNA was extracted from pool fecal samples and subjected to next-generation sequencing. De novo assembly and comparative analyses enabled the recovery of a complete picorna-like viral genome of 9,043 nucleotides, comprising a single open reading frame encoding a polyprotein of 2,896 amino acids. Phylogenetic analyses based on the RNA-dependent RNA polymerase (RdRp) domain and the translated polyprotein consistently clustered the virus within the family Iflaviridae, forming a specific clade with reference sequences previously reported in arthropods. Functional domain analysis revealed conserved motifs characteristic of positive-sense single-stranded RNA viruses, including helicase superfamily 3 and RdRp domains. Although iflaviruses are classically associated with arthropod hosts, their detection in avian fecal samples is likely related to dietary intake, suggesting the presence of a transient virome rather than active infection. The sampling area is characterized by increasing environmental degradation, which may favor interactions between wildlife and anthropogenic environments, highlighting the importance of viral surveillance. This study reports, for the first time, the genome of an iflavirus detected in C. pareola, expanding current knowledge on iflavirus diversity and reinforcing the relevance of wildlife-based surveillance in ecologically altered regions under anthropogenic pressure.}, } @article {pmid42430137, year = {2026}, author = {Allen, L and Sheneman, A and Morrow, MA}, title = {Post-wildfire soil bacterial MAGs and metagenome analysis.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0044426}, doi = {10.1128/mra.00444-26}, pmid = {42430137}, issn = {2576-098X}, abstract = {We compare the differences between bacteria in soil affected by a wildfire to an unaffected area from Minnewaska State Park, NY, located in the biodiverse northern Shawangunk Ridge. We detail our metagenomic sequencing data, relative abundance of bacterial phyla, and the taxonomic classification of three MAGs.}, } @article {pmid42430408, year = {2026}, author = {Khan, N and Nasir, MM and Aziz, U and Manzoor, H and Raziq, MF and Hussain, Z and Jabeen, I and Kayani, MUR}, title = {Integrative metagenomics and structural bioinformatics identify explainable gut microbial variants associated with Crohn's disease.}, journal = {PloS one}, volume = {21}, number = {7}, pages = {e0340748}, doi = {10.1371/journal.pone.0340748}, pmid = {42430408}, issn = {1932-6203}, mesh = {*Crohn Disease/microbiology/genetics ; Humans ; *Metagenomics/methods ; *Computational Biology/methods ; Polymorphism, Single Nucleotide ; Molecular Dynamics Simulation ; Bacteroides/genetics ; *Gastrointestinal Microbiome/genetics ; Bacterial Proteins/genetics/chemistry/metabolism ; Colitis, Ulcerative/microbiology/genetics ; }, abstract = {Metagenomics has revealed disease-associated shifts in microbial taxa and functions in inflammatory bowel disease (IBD) patients. However, the role of genomic variation in gut commensals remains poorly understood. Here, we integrated metagenomic profiling, variant calling, and structural bioinformatics to identify disease-associated variants in the gut microbes. Crohn's disease (CD) and ulcerative colitis (UC) showed significant negative associations with Bacteroides uniformis, Bacteroides vulgatus, and Eubacterium rectale. These bacteria exhibited 190,712 single-nucleotide polymorphisms, including 479 CD-specific and 235 UC-specific variants. Variant prioritization identified a CD-specific Val170Leu substitution in the conserved starch-binding domain of the Starch Utilization System D (SusD) protein in B. uniformis. Structural modeling and cyclodextrin docking indicated reduced binding affinity in the mutant, while 200-ns molecular dynamics simulations showed stable ligand retention only in the wild type. These findings suggest that impaired starch metabolism driven by SusD variation may contribute to B. uniformis depletion in CD and demonstrate the value of integrating metagenomics with structural analyses to identify functionally relevant microbial variants.}, } @article {pmid42430554, year = {2026}, author = {Penzotti, P and Gutkind, G and Powers, RA and Power, P}, title = {Environmental species from theTelluria group as the putative origin of bifunctionalβ-lactamases.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0342825}, doi = {10.1128/spectrum.03428-25}, pmid = {42430554}, issn = {2165-0497}, abstract = {β-Lactamases comprise two structurally and evolutionarily well-defined groups: serine- (SBL) and metallo-β-lactamases (MBL). To date, clinically relevant β-lactamases are typically monofunctional DD-peptidases, containing a single active site cavity per molecule. Recently, several genes encoding putative β-lactamases from the four molecular classes (named as LRA) were identified through functional metagenomics in Alaskan soil samples. blaLRA-13 encoded a 609-amino acid protein encompassing a class D and a class C-like β-lactamase fused as a single polypeptide, translated from a single open reading frame (ORF). Furthermore, we identified 20 LRA-13 homologs, one of them found in a Duganella hordei isolate, sharing 91.3% amino acid identity. Predicted structures generated with AlphaFold 3 showed similar conserved architectures encompassing an N-terminal and C-terminal domains compatible with class D and class C β-lactamases, respectively, connected by a short peptide as a linker and containing their characteristic structural features. A maximum likelihood (ML) evolutionary tree showed a close relationship between LRA-13 and the putative β-lactamase from Duganella hordei, a species belonging to the Telluria group, indicating that bifunctional enzymes likely evolved from a common remote ancestor and that their diversification may provide an evolutionary advantage in certain environmental niches. The genetic content of blaLRA-13 and related genes appears to have a conserved synteny. The description of β-lactamases with two catalytic sites constitutes a novel finding and provides a basis for exploring new evolutionary mechanisms.IMPORTANCEβ-Lactamases are enzymes able to destroy β-lactam antibiotics and are divided into two main groups according to their structural and mechanistic features: serine- (SBL) and metallo-β-lactamases (MBL). To date, β-lactamases that represent a threat and are produced by bacterial pathogens contain a unique catalytic "pocket,"i.e., only a single β-lactam molecule is bound and cleaved at a time. LRA-13 and other related proteins seem to contain two different catalytic sites of different kinds (one of them is related to class C β-lactamases and the other to class D enzymes). In this study, we analyzed if these enzymes can represent a different evolutionary path for the β-lactamases.}, } @article {pmid42430840, year = {2026}, author = {Li, QD and Wang, YY and Nwankwo, C and Hu, Y and Dong, XY and Hou, J and Chen, XD and Cui, HL}, title = {Halorubrum marinum sp. nov., Halorubrum rarum sp. nov., Halorubrum wangae sp. nov., Halorubrum shenae sp. nov., and Halorubrum zhoui sp. nov., halophilic archaea from coastal tidal flats, a saline lake, and a marine solar saltern.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {5}, pages = {126750}, doi = {10.1016/j.syapm.2026.126750}, pmid = {42430840}, issn = {1618-0984}, abstract = {Five novel halophilic archaeal strains, designated DTA46[T], DTA98[T], HHNYT27[T], N11[T], and SY-15[T], were isolated from diverse saline environments across various regions of China. Amplicon and metagenome analyses revealed that three amplicon reads were affiliated with strains DTA46[T], HHNYT27[T], and N11[T] while two MAGs related to strains N11[T] and SY-15[T]. The sequence similarities among these five strains and current species of the genus Halorubrum were 93.1%-99.1% and 86.0%-95.9% judged by 16S rRNA and rpoB' genes, respectively. Phylogenomic and comparative genomic analyses revealed their close affiliation with Halorubrum. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values between these strains and existing Halorubrum species ranged from 74.9%-93.6%, 22.3%-58.3%, and 68.3%-93.7%, respectively. All are below the recommended thresholds for species delineation, which supports their classification as novel taxa. The growth characteristics of strains DTA46[T], DTA98[T], HHNYT27[T], N11[T], and SY-15[T] were determined as follows: temperature range 20-60 °C (optima: 35, 37-42, 37, 35, and 42 °C), NaCl concentration 1.4-5.5 M (optima: 2.6, 3.1, 3.1, 3.1, and 5.1 M), and pH range 5.5-9.5 (optima: 8.0, 8.0, 7.0, 7.5, and 7.0). Based on the polyphasic characterization integrating phenotypic, chemotaxonomic, phylogenetic, and phylogenomic evidence, strains DTA46[T], DTA98[T], HHNYT27[T], N11[T], and SY-15[T] are proposed to represent five novel species of the genus Halorubrum, for which the names Halorubrum marinum sp. nov., Halorubrum rarum sp. nov., Halorubrum wangae sp. nov., Halorubrum shenae sp. nov., and Halorubrum zhoui sp. nov. are designated, respectively.}, } @article {pmid42430921, year = {2026}, author = {Li, Z and Xie, R and Zhang, W and Cheng, J and Jia, P and Liu, C and Guo, X and Zhuang, L and Chen, T}, title = {Lead fraction transformation drives microbial functional recovery and coupled nutrient cycling-metal resistance networks in Pb-Zn tailings.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142947}, doi = {10.1016/j.jhazmat.2026.142947}, pmid = {42430921}, issn = {1873-3336}, abstract = {Ecological remediation of lead-zinc (Pb-Zn) mine tailings, characterized by nutrient deficiency and high concentrations of toxic metals, represents a significant environmental challenge. While revegetation is a promising strategy, the underlying microbial functional responses, particularly the coupling between nutrient cycling and heavy metal detoxification, remain insufficiently understood. This study investigated the geochemical evolution and microbial functional succession of a Pb-Zn tailings pond, encompassing fresh tailings, weathering, and revegetation areas. Geochemical analysis, metagenomic sequencing, and the cultivation of the dominant bacterial strain were employed. Results demonstrated that revegetation significantly enhanced microbial α-diversity and shifted community assembly toward stochasticity. Metagenomic analysis revealed a substantial increase in the abundance and diversity of functional genes related to carbon, nitrogen, phosphorus, and sulfur (C/N/P/S) cycling, concurrent with the enrichment of metal resistance genes. The transformation of Pb fraction, specifically a decrease in bioavailable (exchangeable) fractions and an increase in stable (organic-bound, residual) fractions, was identified as the key driver of microbial functional recovery. Co-occurrence network analysis demonstrated a strong synergy between the Pb resistance gene zntA/yhhO and core nutrient-cycling genes. Furthermore, the dominant isolated strain, Pseudomonas aeruginosa QPBII-1, exhibited high Pb(Ⅱ) removal efficiency (98.5%). Multi-faceted characterization indicated its removal mechanism involves extracellular immobilization and intracellular reduction of Pb(Ⅱ) to less toxic Pb(0)/PbO, supported by genomic evidence (e.g., pbrA, narB). This study demonstrates that revegetation fosters an integrated microbial network that couples biogeochemical cycling with metal resistance, providing a mechanistic basis for developing sustainable bioremediation strategies for metalliferous tailings.}, } @article {pmid42431026, year = {2026}, author = {Guhanraj, R and Matharasi, AP}, title = {Integrated anaerobic culture and molecular approaches for periodontal pathogens: Advancements in microbial detection and characterization.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {3}, pages = {117540}, doi = {10.1016/j.diagmicrobio.2026.117540}, pmid = {42431026}, issn = {1879-0070}, abstract = {Periodontal diseases are polymicrobial infections driven by complex interactions between anaerobic pathogens and host immune responses within the periodontal pocket. Accurate detection and characterization of these pathogens are critical for early diagnosis, disease risk assessment, and effective therapeutic intervention. This review aims to critically evaluate conventional anaerobic culture and advanced molecular diagnostic techniques for the detection and characterization of periodontal pathogens, highlighting their respective advantages, limitations, and clinical relevance. A comprehensive analysis of existing literature was conducted focusing on traditional culture-based approaches and emerging molecular technologies, including polymerase chain reaction (PCR), quantitative PCR (qPCR), 16S rRNA gene sequencing, next-generation sequencing (NGS), and multi-omics strategies such as metagenomics, metatranscriptomics, proteomics, and metabolomics. Anaerobic culture remains the gold standard for microbial isolation, enabling phenotypic characterization, antimicrobial susceptibility testing, and functional studies. However, it is labor-intensive, time-consuming, and limited in detecting fastidious, slow-growing, or viable-but-non-culturable microorganisms. In contrast, molecular techniques offer rapid, sensitive, and comprehensive detection of key periodontal pathogens, including Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola. Advanced omics approaches further provide insights into microbial functionality, virulence, and host-microbe interactions. Nevertheless, molecular methods are limited in assessing microbial viability and antimicrobial susceptibility. The integration of culture-based and molecular diagnostic approaches enhances diagnostic accuracy and supports early, targeted therapeutic interventions. This combined strategy facilitates personalized treatment planning, improves clinical outcomes, and helps reduce inappropriate antimicrobial use in periodontal therapy. Both anaerobic culture and molecular diagnostics possess distinct yet complementary strengths. An integrated diagnostic approach combining phenotypic and high-resolution molecular techniques is essential for improving diagnostic accuracy, enabling personalized treatment strategies, advancing precision periodontal care, and contributing to Good Health and Well-Being through improved oral health outcomes and responsible antimicrobial stewardship.}, } @article {pmid42431120, year = {2026}, author = {Osborne, CJ and Deakins, AG and Ergunay, K and Bourke, BP and Linton, YM and Jiang, L and Grieco, JP and Achee, NL and McDermott, EG}, title = {Metagenomic sequencing provides insight into pathogenic and related benign microbes in ticks collected from pastured cattle.}, journal = {Veterinary microbiology}, volume = {320}, number = {}, pages = {111135}, doi = {10.1016/j.vetmic.2026.111135}, pmid = {42431120}, issn = {1873-2542}, abstract = {Biting arthropods (e.g., ticks and mosquitoes) feed on pastured cattle and may serve as sentinels for certain pathogens present in the environment, including those with the capacity to spillover from wildlife into managed herds and humans. Metagenomic next generation sequencing (mNGS)-enabled by applications such as Oxford Nanopore Technologies (ONT)-allows samples to be screened for a diverse array of known and unknown pathogens compared to traditional targeted methods reliant on polymerase chain reaction (PCR). This study examined the utility of mNGS to identify potential pathogens relevant to animal and human health in samples collected from pastured cattle in Arkansas. Twenty Angus calves (Bos taurus) were sampled by collecting whole blood, swabbing the nose, mouth, and peri-anal region, and collecting ticks during a three-minute search. Each sample type was processed according to published procedures, and samples were sequenced using ONT MinION flow cells. mNGS analysis identified potentially pathogenic Theileria, Ehrlichia, and Borrelia species in tick samples. Downstream PCR identified Theileria cervi in 28.89% (13/45) of tick pools and 5.00% (1/20) of blood samples, a Babesia sp. in 6.67% (3/45) tick pools, three Ehrlichia species (E. chaffeensis, E. ewingii, and Panola Mountain Ehrlichia) in 6.61% (8/121) of ticks, and Borrelia lonestari in 2.48% (3/121) of ticks. In conclusion, the mNGS approach illuminated a wide spectrum of suspected microorganisms down to the genus-level, which were further characterized and confirmed as pathogenic species with conventional molecular detection approaches, thereby demonstrating a rigorous approach for a broad-spectrum screen and confirmation framework for pathogen identification.}, } @article {pmid42431299, year = {2026}, author = {Zhang, X and Cai, M and Lin, J and Feng, Z and Wang, W and Jiao, Y and Lu, L}, title = {Multi-year glyphosate exposure impairs soil fertility, microbial communities, nutrient cycling genes, and tea quality in tea plantations.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128689}, doi = {10.1016/j.envpol.2026.128689}, pmid = {42431299}, issn = {1873-6424}, abstract = {Although glyphosate is highly effective for weed control, its potential risks to tea agroecosystems remain a significant concern. Previous studies have shown inhibitory effects on soil microbial communities in tea plantations, yet the multi-year impacts of glyphosate on microbially mediated nutrient cycling remain poorly understood. To address this gap, we conducted a three-year controlled field experiment, applying glyphosate at 0 kg a.i. ha[-1] (CK), 2.3 kg a.i. ha[-1] (G1), and 6.9 kg a.i. ha[-1] (G2), and used metagenomic sequencing to evaluate its effects on soil fertility, microbial communities, nutrient cycling genes, and tea quality. The results showed that glyphosate application significantly increased soil pH but reduced the contents of total organic carbon, total nitrogen, total potassium, available nutrients, and enzyme activities, leading to marked declines in soil fertility. Relative to CK, G2 reduced microbial alpha diversity, with Chao1, Shannon, and Pielou indices decreasing by 33.22%, 14.97%, and 11.50%, respectively. Tea quality was also affected, with free amino acids and caffeine decreasing by 22.67% and 11.30%, respectively, whereas tea polyphenols and the phenol/ammonia ratio increased by 12.16% and 45.08%, respectively. G2 also restructured bacterial communities, including depletion of Actinobacteria and Planctomycetota and more than 70-fold enrichment of Candidatus Rokubacteria. Metagenomic analysis revealed broad suppression of carbon, nitrogen, and phosphorus cycling genes under G2. Overall, these results suggest that repeated glyphosate exposure over three years may alter soil ecological processes and compromise tea quality, highlighting the need for more sustainable weed management strategies and reduced reliance on glyphosate in tea plantations.}, } @article {pmid42431300, year = {2026}, author = {Zou, Y and Wang, D and Chen, W and Jin, Z and Xie, Y and Li, Y and Wang, L}, title = {Shifts of antibiotic resistance genes across an estuarine meandering bend and dissemination risks to offshore oceans.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128757}, doi = {10.1016/j.envpol.2026.128757}, pmid = {42431300}, issn = {1873-6424}, abstract = {Meandering is a fundamental geomorphic feature of rivers that plays a critical role in regulating pollutant attenuation. To elucidate its impact on antibiotic resistance genes (ARGs) distribution in estuarine intertidal sediments, samples were collected from both the landward side (freshwater-dominated) and the seaward side (tide-dominated) of a meander bend during ebb and flood tides. The total relative abundance of ARGs was approximately 2.7 times higher on the landward side, peaking during the ebb tide. Microbial composition analysis showed that genera Acinetobacter and Pseudomonas were dominant at the landward sites, while halophilic genera such as Marinobacter and Exiguobacterium were abundant at the seaward sites. Further analysis of metagenome-assembled genomes (MAGs) demonstrated that the dominant landward genus Acinetobacter acted as a key host of ARGs, with two of four MAGs encoding more than ten ARGs. Notably, the total relative abundance of mobile genetic elements was high but consistent between sides and tidal cycles (p > 0.05). Given this high dissemination risk, we further forecasted the ARGs transfer scenarios to oceanic settings based on a set of offshore MAGs (n = 3626). Three ARGs, i.e., acrA, vanSL, and AAC(2')-Ia, were inferred to have transfer potential, supported by neighboring MGEs detected in marine microorganisms. Analysis of the genomes of predicted recipients in the SRA database confirmed the predicted mobilizations. Together, this study highlights that the meandering planform may serve as a significant barrier, attenuating the discharge of ARGs from terrestrial sources into the marine environment.}, } @article {pmid42431420, year = {2026}, author = {Yang, M and Li, Y and Chen, Y and Zhang, Y and Wang, Y and Liu, Q and Lu, S and Wang, X}, title = {Low-dose sodium acetate-mediated energy compensation stabilizes oxygen-limited urea hydrolysis coupled with partial nitritation/anammox for high-strength urea wastewater treatment.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135374}, doi = {10.1016/j.biortech.2026.135374}, pmid = {42431420}, issn = {1873-2976}, abstract = {The high free ammonia (FA) environment generated during high-strength urea wastewater hydrolysis can impair biological nitrogen removal, while insufficient energy supply under inorganic influent conditions may limit long-term high-load urea hydrolysis. In this study, a continuous-flow two-stage system coupling an up-flow anaerobic filter reactor (UAFR) with a partial nitritation/anammox (PN/A) reactor was developed, and the role of low-dose sodium acetate in stabilizing UAFR urea hydrolysis was investigated. The UAFR showed hydrolysis deterioration under inorganic feeding, whereas hydrolysis performance rapidly recovered after anhydrous sodium acetate equivalent to 100 mg/L chemical oxygen demand was added on day 53. When the influent urea concentration increased to 2000 mg/L, the UAFR maintained a urea removal efficiency above 99.5%, with a urea removal rate of 8.0 kg urea/(m[3]·d). Acetate withdrawal caused a marked increase in effluent urea, indicating that high-load hydrolysis stability was closely associated with continuous acetate supply. Microbial community and metagenomic analyses showed enrichment of fermentative bacteria such as Tissierella and community-level increases in ackA-pta and urease-related genes, suggesting enhanced acetate-associated energy metabolism and urea hydrolysis potential under high-FA stress. After PN/A treatment, the overall total nitrogen removal efficiency reached 73.4%. This study demonstrates that low-dose acetate can stabilize UAFR urea hydrolysis and enable its coupling with autotrophic PN/A for high-strength urea wastewater treatment.}, } @article {pmid42431426, year = {2026}, author = {Tian, Y and Sun, J and Shu, Q and Sun, H and Yang, X and Liu, Y and Zhang, Y and Ding, J and Lan, L and Gong, P and Wang, G}, title = {Spiramycin fermentation residue-derived biochar regulates soil nutrient cycling, microbial communities, and antibiotic resistance gene dynamics.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135372}, doi = {10.1016/j.biortech.2026.135372}, pmid = {42431426}, issn = {1873-2976}, abstract = {Spiramycin fermentation residues (SFR) are hazardous wastes enriched with residual antibiotics, yet they can serve as potential feedstocks for resource recovery after appropriate treatment. In this study, SFR-derived biochar (SFR-BC) was produced by pyrolysis and applied to agricultural soil to evaluate its effects on soil properties, microbial communities, potential pathogenic bacteria, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A 60-day soil incubation experiment was conducted with one control and three SFR-BC application rates of 0.5%, 1.0%, and 2.0%. SFR-BC improved soil physicochemical properties, nutrient status, enzyme activities, and microbial alpha diversity. Metagenomic analysis showed that SFR-BC altered the abundance of functional genes associated with carbon and nitrogen cycling, indicating shifts in microbial functional potential. SFR-BC also changed bacterial co-occurrence patterns, with the high-dose treatment showing a more complex and highly connected network structure during incubation. In addition, high-dose SFR-BC reduced several potential pathogenic bacteria, including major plant pathogenic taxa. SFR-BC decreased soil ARG abundance by 9.38%-33.67% and MGE abundance by 6.49%-27.89% relative to the control, showing a dose-dependent reduction in antibiotic resistance-related genetic elements. Network and PLS-PM analyses further indicated that ARG variation was statistically associated with soil physicochemical properties, microbial diversity, potential bacterial hosts, and MGEs. Overall, these results suggest that SFR-BC can improve short-term soil nutrient status and reduce ARGs, MGEs, and several potential pathogenic taxa under controlled incubation conditions, providing useful evidence for the potential valorization of antibiotic fermentation residues through pyrolysis.}, } @article {pmid42431948, year = {2026}, author = {Neshat, SA and Santillan, E and Wuertz, S}, title = {Uncovering microbial life-history strategies under disturbance: a trait-based computational analysis of anaerobic systems.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01067-8}, pmid = {42431948}, issn = {2055-5008}, abstract = {Trait-based approaches are helpful in simplifying ecosystem complexity to explore disturbance-diversity-function relationships. These frameworks classify organisms based on their functional characteristics-traits that influence growth, survival and reproduction-providing a mechanistic basis to understand how communities respond to changes in their environment. The application of these approaches has been successful in ecology, but to date has only been tested in a few microbial ecosystems, namely, soil microbial communities and aerobic bioreactors treating wastewater. Here, we employed Grime's competitor-stress-tolerant-ruderal framework in replicated mesophilic anaerobic bioreactors exposed to a disturbance (biomass removal) with varied frequencies at a constant number of disturbance events for 90 days. Bioreactors were inoculated with sludge from full-scale anaerobic digesters and fed with a mixture of primary and waste activated sludge. A genome-resolved metagenomics approach was utilised to assess the microbial communities in terms of composition and functional potential. We found that communities across the disturbance range were clustered into three groups, suggesting the adoption of a three-way life-history strategy. This study demonstrates, for the first time, the applicability of trait-based life-history strategies in anaerobic microbial systems under disturbance using genome-resolved techniques, providing a new perspective for understanding and managing microbial ecosystems under disturbance conditions.}, } @article {pmid42431976, year = {2026}, author = {Chattaraj, S and Chatterjee, I and Nandi, R and Mohapatra, PKD and Mitra, P and Mandal, A and Mitra, D and Ganguly, A}, title = {Effect of probiotic Bacillus cereus PKA18 on the overall growth, gut microbiome, and immunity in Clarias magur (Hamilton, 1822).}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-57479-1}, pmid = {42431976}, issn = {2045-2322}, abstract = {The current study evaluated the probiotic potential of Bacillus cereus PKA18, isolated from indigenous Clarias batrachus, as a dietary supplement for the cultivation of Clarias magur fingerlings (In India, the species Clarias batrachus was reclassified as the neotype Clarias magur). Prior to application in fish, Bacillus cereus PKA18 was subjected to safety evaluation, which confirmed negative enterotoxin production, non-hemolytic (γ-hemolysis) behavior on sheep, fish, and human blood agar, and the absence of pathogenic effects or adverse impacts on fish growth following intraperitoneal administration. A total of 240 fingerlings (average weight: 4.96 ± 0.06 g) were randomly assigned to four dietary groups (Control, C1, C2, and C3), each in triplicate, and reared for 60 days in continuous-flow chambers (92 × 61 × 92 cm[3]; 516 L; 5 cm bottom mud). The control group received basal feed without any probiotic additives, while treatment groups were administered feed supplemented with increasing concentrations of B. cereus PKA18: C1 (2 × 10[4] CFU), C2 (2 × 10[5] CFU), and C3 (2 × 10[6] CFU) per 100 g of feed. Fish in the C2 group exhibited significantly (p < 0.05) superior performance in terms of specific growth rate (3.14 ± 0.05), protein efficiency ratio (2.15 ± 0.12), and live weight gain (27.77 ± 1.24 g), along with the lowest feed conversion ratio (1.29 ± 0.11). Serum biochemical analyses showed notable enhancement in total proteins and reduction in hepatic enzymes (ALT, ALP, AST) in C2-fed fish. Antioxidant enzyme activities were significantly higher in the C2 group. These included superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-PX). Malondialdehyde (MDA) levels were lowest in this group. Digestive enzyme activities (protease, amylase, cellulase, xylanase, and lipase) were also significantly higher in the C2 group compared to control. Species-level 16 S rRNA gene analysis demonstrated that probiotic-fed Clarias magur exhibited a marked shift in intestinal microbiota, characterized by dominance of beneficial Cetobacterium spp., enrichment of Bacillus spp., and a significant reduction of opportunistic and pathogenic bacteria compared to the control group. Functional profiling further revealed that probiotic supplementation promoted a more metabolically efficient microbial community, with targeted enrichment of core metabolic and genetic information processing pathways despite lower overall functional abundance. Following a pathogenic challenge with Vibrio vulnificus (MTCC 1145), fish in the control and C2 groups were assessed for immune response. Fish fed C2 have demonstrated enhanced activity of respiratory burst, myeloperoxidase, α2-macroglobulin and antiprotease. Additionally, a significant upregulation of immune-related genes (IL-6 and C3a) was observed in the liver, muscle, and intestinal tissues of fish fed with C2. Post-challenge survivability was found to be highest in the C2 group, indicating improved resistance to vibriosis. Overall, the study identifies 2 × 10[5] CFU/100 g feed of B. cereus PKA18 (C2 feed) as the optimal probiotic dose for promoting growth performance, digestive activity, immune functions and disease resistance in Clarias magur. These findings support its potential application in the conservation-oriented aquaculture of this endangered species.}, } @article {pmid42432469, year = {2026}, author = {Liu, L and Fu, M and Peng, J and Duan, T and Ma, X and Liu, H and Sha, R and Yang, Y and Yan, H and Jia, R and Li, X and An, X and Liu, Y and Lu, Q}, title = {Bio-valorization of Caragana korshinskii forage via a synthetic microbial community.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05353-5}, pmid = {42432469}, issn = {1471-2180}, abstract = {Caragana korshinskii represents a critical ecological and feed resource in arid regions, yet its utilization is severely impeded by the recalcitrant lignocellulose barrier. This study established a cross-kingdom synthetic microbial community (SynCom) to synergistically overcome this bottleneck, integrating Lactobacillus plantarum for rapid acidification with the fibrolytic enzyme secretion of Bacillus subtilis and the oxidative delignification potential of Aspergillus niger. We integrated microbiome profiling and functional prediction to decode the fermentation dynamics and metabolic mechanisms. Results demonstrated that the SynCom (LBA) treatment engineered a robust fermentation system, achieving a significantly higher in vitro dry matter digestibility (49.68%) and neutral detergent fiber digestibility (25.65%) compared to the control (P < 0.05). This enhancement was driven by a directed shift in the microbiome, where Lactobacillus abundance surged to > 95%, effectively suppressing spoilage genera like Staphylococcus and Weissella via competitive exclusion. Metagenomic prediction revealed that the SynCom upregulated key metabolic modules, specifically pyruvate metabolism and amino acid biosynthesis pathways, facilitating rapid acidification and protein preservation. These findings delineate a coordinated degradation-fermentation-preservation process driven by a rationally assembled synthetic consortium, offering a promising and sustainable bio-valorization strategy for converting high-fiber woody biomass into high-quality livestock feed.}, } @article {pmid42432510, year = {2026}, author = {Feng, J and Zhang, B and Lu, W and Liu, H and Liu, Y and Zou, Y and Ma, H}, title = {Streptococcus anginosus group brain abscesses and subdural empyemas: exploratory compartment-specific phenotypes and discharge outcomes in a single-center retrospective cohort study.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13998-w}, pmid = {42432510}, issn = {1471-2334}, abstract = {BACKGROUND: Intracranial suppuration caused by the Streptococcus anginosus group (SAG) includes brain abscess and subdural empyema, but compartment-specific phenotypes and short-term outcomes remain incompletely described. We characterized clinical, radiological, and microbiological features and explored factors associated with poor discharge outcome.

METHODS: We conducted a single-center retrospective cohort study of patients with imaging-confirmed intracranial suppuration and SAG identified by culture and/or metagenomic next-generation sequencing from October 2020 to October 2025. Cases were classified as intracerebral (n = 39), subdural (n = 6), or mixed (n = 7). The primary outcome was Glasgow Outcome Scale (GOS) at discharge; GOS 1-3 defined poor discharge outcome. Analyses were descriptive, with exploratory univariable logistic regression.

RESULTS: A total of 52 patients were included. Patients with subdural empyema were younger and had numerically lower admission functional status than those with intracerebral infection, whereas subdural and mixed-compartment infections showed higher inflammatory-marker levels. Ventricular involvement was uncommon (5/52, 9.6%) and was observed more frequently among patients with poor discharge outcomes in unadjusted comparisons (5/12 vs. 0/40). Complete ring enhancement was confined to intracerebral cases, and S. intermedius was the predominant species. At discharge, 12 patients (23.1%) had poor outcomes, including six in-hospital deaths (11.5%). Lower admission KPS and fever were exploratory univariable associations with poor discharge outcome.

CONCLUSIONS: This study describes compartment-specific clinical, imaging, and microbiological features of Streptococcus anginosus group brain abscesses and subdural empyemas. Ventricular involvement may be a marker of severe disease, but all findings should be interpreted as exploratory and require validation in larger multicenter studies.}, } @article {pmid42432696, year = {2026}, author = {Clarke, MD and Falcione, S and Boghozian, R and Todoran, R and Zhang, Y and Real, MGC and StPierre, A and Joy, T and Jickling, GC}, title = {Metagenomic analysis of blood virome in ischemic stroke reveals an increase in herpesvirus transcripts and host immune activation.}, journal = {Genome medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13073-026-01707-w}, pmid = {42432696}, issn = {1756-994X}, abstract = {BACKGROUND: Viral infections may influence stroke pathophysiology. Several infections have been linked to increased risk of stroke, however our understanding of these viral interactions with immune and host tissue is limited. We performed a transcriptomic analysis of the blood virome following ischemic stroke to study these interactions.

METHODS: Viruses were measured by RNA sequencing of blood from 37 patients with ischemic stroke and 32 matched controls. RNA reads are aligned against a human reference genome, as well as a comprehensive database of human virus genomes. Host gene expression following stroke is examined in relation to the presence of viral transcripts.

RESULTS: Viral RNAs were detected in the blood samples of both ischemic stroke and control groups. Viral reads with a prevalence > 3% and raw counts > 2 were from a total of 6 viral families. This included several human herpesviruses (HHVs), adenoviruses, and papillomaviruses, as well as human pegivirus, respiratory syncytial virus, and human endogenous retrovirus K (HERV-K). Combined, counts from HHVs were higher in stroke compared to control by a fold change of 2.13. Coinfection with multiple HHVs was more common in stroke, with a 1.23 fold increase in the number of detected herpesviruses. Reads from two viral genes were increased in stroke, UL95 from cytomegalovirus (CMV), and EBNA2 from Epstein-Barr virus (EBV). Genes associated with stroke, including APOE, C3, PDGF, and CXCL2 were differentially expressed in stroke samples which contained high counts of one or both of UL95 and EBNA2.

CONCLUSION: Viral RNAs from multiple families can be detected within the human blood virome. HHV transcripts were the most abundant of viral RNAs detected. Among stroke patients, HHV transcripts were more prevalent, with higher counts, and indicated a higher rate of coinfection with multiple HHV species. Expression of the EBV gene EBNA2 and the CMV gene UL95 may relate to changes in immune gene expression following stroke. Further evaluation is needed to determine the effects that the human virome have on stroke risk, immune response to stroke, and long-term outcome.}, } @article {pmid42432805, year = {2026}, author = {He, B and Liu, B and Wang, X and Xia, M and Ding, C and Nazar, M and Cheng, Y and Xiao, D}, title = {Rumen-derived Prevotella and Megasphaera elsdenii mitigate methane production through functional modulation of rumen microbial metabolism.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42432805}, issn = {1674-9782}, support = {2023YFD1300903//National Key Research and Development Program of China/ ; CARS-37//Earmarked Fund for China Agriculture Research System/ ; }, abstract = {BACKGROUND: Enteric methane (CH4) production represents a major energy loss in ruminant systems and contributes substantially to agricultural greenhouse gas emissions. Increasing ruminal propionate production has been proposed as a strategy to redirect metabolic hydrogen away from methanogenesis, although the underlying microbial mechanisms remain incompletely understood.

RESULTS: Four rumen-derived Prevotella strains and one Megasphaera elsdenii strain were isolated, genomically characterized, and evaluated using an in vitro rumen fermentation model. Distinct strain-specific responses were observed. Compared with the control, Prevotella strains RH14 and RH35 significantly reduced CH4 accumulation at 48 h (P < 0.05), coinciding with lower total gas and carbon dioxide (CO2) production, whereas RH3, RH27, and RH19 showed CH4 production comparable to the control. Volatile fatty acid (VFA) profiles showed comparatively smaller differences among treatments, although RH14 maintained relatively greater total VFA and propionate concentrations at later incubation stages. Metagenomic analysis indicated that methane mitigation was associated with reduced relative abundance of methanogenesis-related pathways, particularly hydrogenotrophic methanogenesis (P < 0.05), whereas archaeal community composition remained largely unchanged. However, metagenomic data reflect gene abundance rather than activity and do not directly indicate functional regulation.

CONCLUSIONS: These findings demonstrate strain-specific effects of rumen-derived bacteria on rumen fermentation and methane production. In particular, Prevotella strains RH14 and RH35 showed potential to mitigate methane formation through functional modulation of microbial metabolism, partially displacing rather than completely eliminating methanogens. These results provide a functional basis for the future development of rumen microbial interventions aimed at improving rumen fermentation efficiency and mitigating enteric methane emissions.}, } @article {pmid42433691, year = {2026}, author = {Hasan, M and Schirtzinger, EE and Stancic, S and Affonso, P and Lu, A and Souza-Neto, JA and Klenda, KL and Ferreyra, FM and Noll, LW and Hanzlicek, GA and Retallick, J and Miller, LC}, title = {A targeted PCR approach for the detection of IOLA in canine infectious respiratory disease samples during an atypical CIRD outbreak in winter 2023.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1849862}, pmid = {42433691}, issn = {2297-1769}, abstract = {BACKGROUND: During winter 2023, an atypical canine infectious respiratory disease (aCIRD) outbreak was associated with high case-fatality rates and poor antibiotic response. Preliminary metagenomics investigations claimed partial sequences resembling Infectious Organism Lurking in Human Airways (IOLA), a poorly characterized bacterium first described in humans, in canine respiratory samples. However, its detectability remained uncertain and required systematic molecular investigation.

METHODS: We screened 777 veterinarian-submitted canine respiratory samples from the United States using 16S targeted sequencing for samples positive for Rickettsiales, the lowest taxonomic classification for IOLA. Samples containing sequencing reads classified as for Rickettsiales were tested by PCR assay targeting two IOLA genes (16S rRNA and PrfA). Assays were optimized at 58 °C with 500 nM primers, and products visualized by agarose gel and capillary electrophoresis. Analytical sensitivity was 10[4] copies/μl and 10[4] copies/μl for 16S and PrfA assay, respectively. Candidate amplicons were verified by Sanger sequencing and BLAST analysis.

RESULTS: Of the 777 samples screened, 55 contained sequencing reads classified as Rickettsiales. Forty-five of the 55 samples were negative by 16S rRNA PCR, while 10 samples produced amplicons near the expected size. The PrfA PCR assay was negative across all samples. Sequencing representative samples from those that produced 16S amplicons confirmed nonspecific amplification. Therefore, all 55 samples were negative for IOLA.

CONCLUSION: Dual-target PCR identified no evidence of IOLA in respiratory samples from the 2023 aCIRD outbreak. Non-specific amplification in the 16S PCR assay highlights the need for multi-target validation in novel pathogen detection and supports prioritization of established CIRD pathogens over unverified organisms.}, } @article {pmid42434089, year = {2026}, author = {Őrsi, Á and Laczkó, L and Bőkényné Tóth, R and Freytag, C and Tóth, P and Simay, G and Szabó, N and Kardos, G and Lovas-Kiss, Á}, title = {Microbiota shows major difference in case of two shorebird species with different feeding strategy.}, journal = {Veterinary and animal science}, volume = {34}, number = {}, pages = {100754}, pmid = {42434089}, issn = {2451-943X}, abstract = {Despite the well-known effects of the gut microbiota on mammals, other vertebrates have only recently begun receiving attention in research. Our study focused on describing the cloacal microbiome of Common Snipe (Gallinago gallinago) and Wood Sandpiper (Tringa glareola), using 16S rRNA metabarcoding, to understand how different foraging methods can affect their microbiome. Assessing the host microbial diversity, we found that Shannon- (W = 253, p = 0.099), Simpson- (W = 268, p = 0.168) and inverse Simpson- diversities (W = 268, p = 0.168) did not differ significantly, however, there was a tendency towards the Wood Sandpiper having the higher values. SIMPER analysis revealed that the differences were caused by several bacterial taxa, the biggest contributor being Catellicoccus marimammalinum (mean contribution = 2.76%, p = 0.003) which had greater abundances in Common Snipe (mean relative abundance = 22.76%) than in the Wood Sandpiper (8.27%). We found great differences in Fusobacteria abundances between the hosts, as this phylum had an average abundance of 29.4% in Wood Sandpiper and 8.8% in Common Snipe samples. This difference in their microbiome may be explained by the higher chitin consumption of Wood Sandpiper which is associated with higher Fusobacteria abundance. We found multiple important animal (Mycoplasma iowae, Brachyspira hyodysenteriae) and human pathogens (Campylobacter jejuni, Aeromonas veronii, Vibrio cholerae), some of which are also associated with the growing problem of antimicrobial resistance (Escherichia coli, Enterococcus faecalis). The high prevalence of these pathogens in wild waterbirds should be considered important when assessing human and environmental health hazards.}, } @article {pmid42434393, year = {2026}, author = {Wang, B and Yu, Y and Huang, S and He, Y and Chen, Y and Dong, S and Tang, D and Cheng, Z and Cao, L}, title = {Metabolomic and Metagenomic Correlation Reveals the Network Regulatory Mechanism of Cecal Microbiota Structural Changes Induced by Eimeria tenella.}, journal = {International journal of veterinary science and medicine}, volume = {14}, number = {}, pages = {8}, pmid = {42434393}, issn = {2314-4599}, abstract = {BACKGROUND: Eimeria tenella poses a significant threat to the poultry industry, and understanding the correlation between metabolic changes in cecal tissues and microbial community alterations is crucial for studying parasite-host interactions.

AIMS AND OBJECTIVES: To investigate the associations among dominant bacterial populations, key functional genes, and altered metabolites in cecal tissues and contents during E. tenella infection.

MATERIALS AND METHODS: Metagenomic analysis was first performed on cecal contents to identify the dominant bacterial communities, followed by metabolomic analysis of cecal tissues and contents. Correlation analysis was then conducted to evaluate the relationships among microbial communities, functional genes, and differential metabolites.

RESULTS: Correlation analysis showed that increased potentially pathogenic genera were generally positively associated with upregulated metabolites and negatively associated with downregulated metabolites, whereas reduced commensal genera showed the opposite trend. Shared KEGG pathways co-enriched by differential metabolites and microbial functional genes were identified, mainly involving amino acid metabolism, transport systems, membrane-associated metabolism, and nucleotide metabolism. The metabolites linked to dominant bacterial communities were primarily enriched in pathways such as amino sugar metabolism, sialic acid metabolism, and glycerophospholipid metabolism. These findings reflected complex metabolic reprogramming and interactions between the host and pathogen, especially in cecal tissue repair, immune regulation, and metabolic competition with the pathogen.

CONCLUSION: This study provided valuable insights into parasite-host interactions and laid a foundation for understanding the role of bacterial community-associated metabolites in cecal coccidiosis.}, } @article {pmid42434420, year = {2026}, author = {Al-Maleki, AR and Flores-Treviño, S and Cheah, CW and Abdelhafiz, YA}, title = {Editorial: Microbiota, antibiotic resistance, and host-microbe interactions: a comprehensive exploration of infectious disease dynamics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1899262}, pmid = {42434420}, issn = {2235-2988}, } @article {pmid42434557, year = {2026}, author = {Hossen, N and Mascellino, MT}, title = {Molecular insights into antimicrobial resistance in human bacterial pathogens: mechanisms, resistance genes, and translational diagnostic applications.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1842688}, pmid = {42434557}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) represents one of the most critical global public health challenges. This review provides a comprehensive overview of the molecular foundation of AMR in human bacterial pathogens, including the biology of resistance genes and the importance of the mobile genetic elements-plasmids, transposons, and integrons-in facilitating the rapid horizontal transfer of resistance determinates across the populations. We critically evaluate current and emerging molecular diagnostic platforms - including targeted polymerase chain reaction (PCR), whole-genome sequencing (WGS), clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies, and metagenomics - emphasizing their comparative performance, limitations, and suitability for point-of-care deployment. The review addresses the translational integration of molecular diagnostics into antimicrobial stewardship programmes and real-time AMR surveillance, with particular attention to the persistent gap between laboratory-generated genomic data and actionable clinical decision-making. Emerging evidence suggests that artificial intelligence (AI) and machine learning hold considerable promise for improving resistance phenotype prediction from genomic data and informing personalized antibiotic therapy, although widespread clinical implementation remains in its early stages. The transition from phenotypic to genotypic strategies represents a significant paradigm shift in AMR, with the potential to substantially improve surveillance, diagnostic accuracy, and therapeutic outcomes, provided that outstanding barriers in infrastructure, standardization, and equity are addressed.}, } @article {pmid42434559, year = {2026}, author = {Saraiva, M and Gerilovych, A and Ay, H}, title = {Editorial: Harnessing aquatic microbial symbioses for sustainable aquaculture: unveiling biodiversity and ecosystem dynamics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1897215}, doi = {10.3389/fmicb.2026.1897215}, pmid = {42434559}, issn = {1664-302X}, } @article {pmid42434564, year = {2026}, author = {Diaz, B and House, T and Padala, M and Schoeniger, JS and Mageeney, CM}, title = {HtPIP: High-throughput phage isolation platform increases diversity and reduces isolation time using multiple bacteria.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1845440}, pmid = {42434564}, issn = {1664-302X}, abstract = {Bacteriophages are ubiquitous in nature, but relatively few have been isolated and characterized compared to the number of bacterial strains. Phage biotechnology applications benefit from a diverse library of isolated phages to kill or transfer genetic material to a bacterium of interest. However, scaling up phage discovery for diverse bacterial hosts can be time-consuming and costly. We developed an approach to capture novel phages for multiple bacterial strains in parallel from an environmental sample using commercially available 0.2-μM filter plates. Using this High-throughput Phage Isolation Platform (HtPIP), 12 novel phages were isolated spanning 9 diverse bacterial host genera. Eleven of the isolated phages define new phage species, with nine also defining new genera. The HtPIP was used to discover both DNA and RNA phages, including a Tectiviridae infecting Pseudomonas putida mt-2 and a Leviviricetes infecting a Microbacterium isolate, which represents the first cultured RNA phage infecting a host outside of Proteobacteria. Using a metagenomic approach, we demonstrate that the HtPIP captures a higher proportion of novel phages compared to traditional low-throughput methods.}, } @article {pmid42434567, year = {2026}, author = {Huang, J and Bol, R and Liu, D and Kiladze, E and Lou, X and Wang, H and Zhang, J and Ge, Z and Wang, T}, title = {Multi-omics reveal soil microbial dysbiosis and metabolite toxicity as drivers of blueberry continuous cropping obstacles.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1880203}, pmid = {42434567}, issn = {1664-302X}, abstract = {Blueberry (Vaccinium spp.) are one of the most economically important fruit trees globally. However, due to continuous cropping have limited the industry's ability to produce consistently over the long term, and the mechanism underlying the development of this continuous cropping problem is not yet fully understood. In this study, we applied metagenomic and metabolomic to systematically detect changes in microbial community structure, function and metabolic profiles in rhizosphere and non-rhizosphere soils after different years of continuous blueberry cultivation (0, 2, 4, and 6 years) in Dalian (China). The results showed that continuous cultivation significantly reduced overall microbial diversity and the bacterial and fungal Shannon index, with the decrease being more significant in the rhizosphere soils (P < 0.05). The β diversity analysis showed that the microbial community structure was distinctly separated between cultivation periods, with the most prominent differences in the rhizosphere soils (PERMANOVA, P < 0.01). The increased cultivation duration led to a decrease in the relative abundance of beneficial functional taxa in the microbial community, while the depletion-tolerant and stress-adapted taxa were gradually enriched. Functional annotation analysis showed that KEGG pathways related to stress response, amino acid degradation, and energy metabolism significantly increased, while functions related to nutrient transformation and plant-microbe interactions were weakened (FDR < 0.05). The metabolomic results further showed that 6 years of continuous cultivation significantly reshaped the rhizosphere metabolite composition. This was evidenced by the accumulation of various secondary metabolites in the rhizosphere soil, including metabolites related to potential self-toxicity (e.g., ferulic acid, 3-hydroxyphenylacetic acid, and 2-hydroxycinnamic acid), mainly involved in the pathways of amino acid metabolism, lipid metabolism, and secondary metabolite synthesis. In conclusion, continuous cultivation of blueberry induced pronounced shifts in rhizosphere microbial community structure, function, and metabolite composition, suggesting that these changes may contribute to the development of continuous cropping obstacles (CCO).}, } @article {pmid42434987, year = {2026}, author = {Cusi, MG and Savellini, GG and Cassol, C and Nencioni, C and Bernini, L and Tacconi, D and Alessandri, G and Rizzo, L and Anichini, G and Smura, T and Vapalahti, O}, title = {Molecular evidence of neuroinvasive Sindbis virus infection in humans: detection in cerebrospinal fluid by next generation sequencing.}, journal = {Emerging microbes & infections}, volume = {}, number = {}, pages = {2703397}, doi = {10.1080/22221751.2026.2703397}, pmid = {42434987}, issn = {2222-1751}, abstract = {Sindbis virus (SINV) is a mosquito borne alphavirus causing seasonal outbreaks in northern Europe, Africa and Russia. Neurological involvement in humans is poorly documented, and detection in cerebrospinal fluid (CSF) has not previously been reported. This study provides the first unequivocal evidence of human CNS involvement by detecting SINV RNA directly in the cerebrospinal fluid of four autochthonous patients presenting with acute neurological symptoms in south eastern Tuscany, Italy, July-August 2025. Utilizing metagenomic Next Generation Sequencing (mNGS), we reconstructed complete viral genomes, strongly supporting a causal relationship between SINV and neurological manifestations. Phylogenetic analysis revealed a complex epidemiological landscape in Italy characterized by the co-circulation of Clade D lineages. Our findings fundamentally expand the clinical spectrum of SINV, demonstrating that it is not merely an arthritogenic pathogen, but a neuroinvasive threat to humans. This highlights the critical need to include SINV in the differential diagnosis of viral CNS infections in endemic areas and underscores the urgency for enhanced European laboratory surveillance.}, } @article {pmid42435095, year = {2026}, author = {Aziz, U and Akhoon, RH and Gani, KM}, title = {Wastewater-associated antibiotic resistance in Western Himalayas: prevalence and diversity in a north Indian city of Srinagar, Jammu and Kashmir.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {8}, pages = {}, pmid = {42435095}, issn = {1573-2959}, mesh = {*Wastewater/microbiology ; India ; Himalayas ; Anti-Bacterial Agents/pharmacology ; *Environmental Monitoring ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Cities ; Bacteria/genetics/classification/drug effects ; Escherichia coli ; }, abstract = {Antibiotic-resistant bacteria (ARB) in wastewater have emerged as a major environmental and public health concern, particularly in areas with high urbanization and limited wastewater treatment efficiency. Despite this, limited data exist on the distribution and diversity of ARB in the Western Himalayan region of India. This study addresses this gap by assessing the prevalence, antibiotic resistance patterns, and antibiotic-resistant genes (ARG) diversity of wastewater-associated bacteria in Srinagar, Jammu and Kashmir. A total of 18 influent and effluent wastewater samples were collected from nine wastewater treatment plants (WWTPs) in Srinagar, Jammu and Kashmir, and were examined to investigate antibiotic-resistant bacteria (ARBs). Enterococcus faecium and Escherichia coli were isolated using selective media, identified through Gram staining and 16S rDNA PCR, and assessed for antibiotic susceptibility. Both bacterial species exhibited higher resistance in influent samples compared to effluent samples. Enterococcus faecium showed notable resistance to ampicillin, minocycline, and linezolid, whereas Escherichia coli showed greater resistance to minocycline and nitrofurantoin. Metagenomic analysis revealed that bacteria accounted for 99.98% of the taxonomic composition, with shotgun sequencing identifying diverse antibiotic resistance genes (ARGs), including tet(B), tet36, adeF, adeG, emrK, and acrB, associated with resistance to tetracyclines, fluoroquinolones, and β-lactams. This highlights the urgent need for strengthened antibiotic management practices and enhanced wastewater treatment technologies to limit the spread of resistance elements into aquatic environments.}, } @article {pmid42435326, year = {2026}, author = {Garcia, A and Trivedi, D and Anthony, DC and Swann, JR and Burnet, PWJ}, title = {Glycodeoxycholic and deoxycholic bile acids impair recognition and spatial memory in adult mice, and reduce central CREB-BDNF signaling and cytokine expression with neuroanatomical specificity.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2701471}, doi = {10.1080/19490976.2026.2701471}, pmid = {42435326}, issn = {1949-0984}, mesh = {Animals ; Male ; *Cyclic AMP Response Element-Binding Protein/metabolism/genetics ; Mice ; Female ; Signal Transduction/drug effects ; *Spatial Memory/drug effects ; *Brain-Derived Neurotrophic Factor/metabolism/genetics ; *Deoxycholic Acid/metabolism/administration & dosage ; *Cytokines/metabolism/genetics ; Receptors, N-Methyl-D-Aspartate/genetics/metabolism ; Mice, Inbred C57BL ; Hippocampus/metabolism/drug effects ; Brain/metabolism/drug effects ; Bile Acids and Salts ; }, abstract = {Emerging evidence suggests that bile acids, traditionally recognized for their role in digestion, also influence brain function and memory. This study examined the effects of two microbiota-derived secondary bile acids, deoxycholic acid (DCA) and glycodeoxycholic acid (GDCA), on memory in mice and the associated molecular mechanisms. Male and female mice received daily oral administration of DCA, GDCA, or vehicle, and spatial working and reference memory (Y-maze) and recognition memory (novel object recognition task) were assessed. After testing, gene expression and signaling activity were measured in the frontal cortex and hippocampus. Administration of GDCA after 10 d disrupted recognition memory, whereas DCA intake for 12 d impaired spatial reference memory. Neither bile acid administered for 5 d affected spatial working memory. GDCA reduced NMDA receptor subunit (GluN1, GluN2A) mRNAs and encoded protein and brain-derived neurotrophic factor (BDNF) mRNA expression and attenuated CREB signaling in the frontal cortex, which is consistent with the observed recognition memory deficit. GDCA did not alter the abundance of transcripts encoding bile acid receptors (FXR or TGR5) or their corresponding protein levels. In contrast, DCA modified the FXR and TGR5 mRNAs and proteins in a region-specific manner and decreased CREB signaling in the hippocampus, likely contributing to spatial memory deficits. In the frontal cortex, DCA increased GluA1 phosphorylation and reduced IL-1β and IL-6 expression, which may have helped preserve recognition memory. Exploratory metagenomic analysis of fecal samples showed no significant microbial differences, though subtle, non-significant functional gene changes suggested early adaptations. These findings reveal that DCA and GDCA exert distinct, receptor- and region-specific effects on cognition, identifying bile acids as modulators of microbiome-gut-brain communication.}, } @article {pmid42435590, year = {2026}, author = {Yan, Y and Yang, B and Bao, P and Chen, B and Jia, Y and Lu, H}, title = {Polyethylene microplastics impose reversible redox suppression in sulfur-driven wastewater treatment systems under antibiotic co-stress.}, journal = {Water research}, volume = {305}, number = {}, pages = {126399}, doi = {10.1016/j.watres.2026.126399}, pmid = {42435590}, issn = {1879-2448}, abstract = {Microplastics and antibiotics frequently co-occur in wastewater treatment systems, yet their combined effect on sulfur-driven bioprocesses and the subsequent post-stress recovery remains poorly resolved. In this study, the long-term response of a sulfate-reducing bacteria (SRB) sludge system treating sulfamethoxazole (SMX)-laden wastewater to polyethylene microplastics (PE MPs; 100 - 800 particles/L) was investigated by combining parallel continuous-flow reactors, batch physiological assays, and metagenomic analysis. PE MPs exerted a concentration-dependent but function-differentiated inhibition, in which SMX removal was more sensitive than chemical oxygen demand (COD) removal and sulfate reduction. At 800 particles/L, SMX removal declined from 37.1 ± 4.1% to 30.5 ± 5.2%, accompanied by elevated intracellular reactive oxygen species (ROS; 138.2 ± 4.0%), increased lactate dehydrogenase (LDH) leakage (122.0 ± 7.1% of the control), weakened antioxidant capacity, and a higher dead-cell fraction (29.7 ± 2.0%). Metagenomic analysis further revealed suppression of central carbon metabolism, dissimilatory sulfate reduction, lipid metabolism, and antioxidant defense, indicating that PE MPs disrupted redox homeostasis and thereby constrained energy supply, sulfur-related electron transfer, membrane maintenance, and stress-response capacity. Notably, after PE MPs withdrawal, SMX removal recovered to 37.8 ± 4.0%, and ROS declined to 107.8 ± 2.8% despite continued SMX loading, together with partial restoration of sulfur-related functional potential. These findings support a reversible, redox-mediated metabolic suppression model rather than irreversible functional collapse, providing an engineering basis for the stable application and functional resilience evaluation of sulfur-driven biotechnologies under fluctuating microplastic exposure, while highlighting the need for future enzyme-level verification of ROS-dependent causal mechanisms.}, } @article {pmid42435593, year = {2026}, author = {Zhang, Y and Li, YT and Zhang, Q and Wang, XT and Wang, W and Wang, A and Ma, J and Lee, DJ and Ren, N and Chen, C}, title = {Thiocyanate-driven denitrification with mixotrophic flexibility for real coking wastewater treatment: Novel insights into nitrogen cycling.}, journal = {Water research}, volume = {305}, number = {}, pages = {126438}, doi = {10.1016/j.watres.2026.126438}, pmid = {42435593}, issn = {1879-2448}, abstract = {Industrial coking wastewater, characterized by high thiocyanate (SCN[-]), nitrate, and complex toxic organics, challenges conventional biological nitrogen removal and impedes resource recovery. To shift the treatment objective from mere detoxification to predictable nitrogen partitioning, a SCN[-]-driven biological nitrogen removal (SCN[-]-BNR) bioreactor was operated for 200 days, comprising a 160-day synthetic stoichiometric optimization phase and a 40-day validation phase with undiluted real coking wastewater. We identified the influent SCN[-]-S/NO3[-]-N mass ratio (S/N) as the primary operational lever governing nitrogen fate. Increasing this ratio to ∼4.0 drove >99% nitrate removal, with DNRA contributing 49.1% of the total nitrate reduction. Crucially, [15]N stable isotope tracing and metagenomics elucidated a synergistic cross-feeding mechanism: Chlorobium sp. likely initiates SCN[-] cleavage, followed by cyanate hydrolysis (cynS) and dissimilatory nitrate reduction to ammonium (DNRA, nrfA) driven by distinct populations (SpSt-501 sp. And JADFDR01 sp.). DNRA was highly activated under electron-donor-surplus conditions, directly contributing up to 22.8% of the generated effluent ammonium. This metabolic division of labor proved exceptionally resilient; the mixotrophic consortium maintained stable >95% SCN[-] and >90% NO3[-] removal during real wastewater validation, demonstrating strong tolerance to phenol, quinoline, and salinity. This study provides a verifiable operational-mechanistic framework for engineering next-generation SCN[-]-driven bioreactors, integrating robust complex wastewater detoxification with circular nitrogen management.}, } @article {pmid42435595, year = {2026}, author = {Ma, B and Zhang, C and Li, F and Adamovich, B and Huang, T and Zhang, H}, title = {Iron-manganese co-mediated electron shuttling rewires mixotrophic aerobic denitrification metabolism: Unraveling metabolic complementarity and functional regulation.}, journal = {Water research}, volume = {305}, number = {}, pages = {126447}, doi = {10.1016/j.watres.2026.126447}, pmid = {42435595}, issn = {1879-2448}, abstract = {Electron donor scarcity is the primary bottleneck limiting the biological reduction of elevated nitrate (NO3[-]-N) in eutrophic reservoir water. However, simultaneous microbial aerobic denitrification mediated by iron-manganese redox offers a viable strategy for mitigating nitrogen pollution in such organic electron donor-limited natural aquatic systems. Here, we constructed four bioreactors to investigate the functional regulation and metabolic complementarity underlying the bioremediation of NO3[-]-N via iron-manganese coupling in eutrophic reservoir water. The iron-manganese co-doped reactor system exhibited NO3[-]-N reduction rate of 0.82523-1.01249 mg/L/d, which was higher than that of the other reactors. Furthermore, iron-manganese synergy significantly enhanced phosphorus and organic matter removal in aquatic systems, combining biochemical degradation and physical sedimentation. We also detected the simultaneous occurrence of NO3[-]-N reduction (napA/B, narB/G/H/I, nirS/K, norB/C, and nosZ), aerobic respiration (Cyo, Cyd, Cco, and Cox), and quorum sensing (cciR, expR, lasR, mqsR, solR, sdiA, rpaR, and raiR) via functional gene analysis using a metagenomic database in iron-manganese synergy reactors. Furthermore, functional genes involved in iron redox cycling (korA/B/C/D and fhuF) and manganese oxidation (moxA, mcoA, cotA, and mnxG) were encoded by Nitrospirota, Thermoproteota, Desulfobacterota, and Halobacteriota, potentially facilitating a sustained supply of iron-based electron donors during the operation of iron-only and iron-manganese coupling reactors. Meanwhile, the microbial community exhibited complementary metabolic profiles and higher electron transport chain activity in the iron-manganese synergy reactors. Knowledge of the effects of functional regulation and metabolic complementarity in iron-manganese coupling systems can broaden our grasp of the scientific basis for applying water quality improvement strategies in reservoirs.}, } @article {pmid42435639, year = {2026}, author = {Neofytos, D and Muñoz, P and Averbuch, D and Mikulska, M and Vanbiervliet, Y and Baccelli, F and Vidal, CG and Aguilar-Guisado, M and Blijlevens, N and Akova, M and Calandra, T and Cordonnier, C}, title = {Non-culture based diagnostic tests for detection of bacterial infections in hematology patients with febrile neutropenia: A review by the European Conference on Infections in Leukemia (ECIL-10).}, journal = {Current research in translational medicine}, volume = {74}, number = {3}, pages = {103600}, doi = {10.1016/j.retram.2026.103600}, pmid = {42435639}, issn = {2452-3186}, abstract = {BACKGROUND: Limited data are available on the performance of non-culture-based diagnostics in hematology patients with febrile neutropenia (FN).

METHODS: The European Conference on Infections in Leukaemia (ECIL) 10 group performed a review (2011-2024) on the performance of available in Europe non-culture-based diagnostic methods on blood samples in hematology patients with FN, focusing on bacterial infections. The following tests were included: direct matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), multiplex/specific polymerase chain reaction (PCR), T2-magnetic resonance (T2MR), and metagenomic next generation sequencing (mNGS). A list of 6 predefined pertinent questions was assessed for the performance of each test.

RESULTS: For MALDI-TOF-MS, 4/16 (25%) articles were retained, including 475 hematology patients (98 with FN), with sensitivity ranging from 63 to 92.6%. For multiplex-PCR, 8/293 (2.7%) articles were retained, including 509 hematology patients (209 with FN), with a sensitivity of 80.5% and 100% (2 studies) and one study reporting a specificity of 88.5%. For T2MR, 1/18 (5.6%) article was retained including 648 hematology patients (309 with FN) and sensitivity and specificity of 84.2 and 85.9%, respectively. For mNGS, 6/35 (17%) articles were retained: 459 hematology patients (335 with FN), sensitivity (40-100%) and specificity (40-84%) reported in 3 studies. No articles were found on specific PCR in hematology patients. Improved microbiological documentation was reported in 5, 1, and 5 studies on multiplex-PCR, T2MR, and mNGS, respectively. Faster time to diagnosis was reported in 1, 5, and 1 studies on MALDI-TOF-MS, multiplex-PCR, and T2MR, respectively. Treatment choice was affected by the results of MALDI-TOF-MS, multiplex-PCR, mNGS in 1, 6, and 2 studies, respectively. No significant impact on overall survival or length of stay was reported for any of the tests reviewed.

CONCLUSIONS: Limited evidence exists on the performance of non-culture-based diagnostics in hematology patients. Blood cultures should be routinely used, even if new tests are available, which should be used in conjunction with the routine microbiological techniques, until more quality data are available.}, } @article {pmid42435910, year = {2026}, author = {Almeida, L and Alexandrino, DAM and Lilienthal, T and Karpe, NV and Ribeiro, N and Oliveira, RS and Carvalho, MF and Freitas, M}, title = {Compost microbiomes as reservoirs of cellulolytic microorganisms for cellulosic textile degradation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135373}, doi = {10.1016/j.biortech.2026.135373}, pmid = {42435910}, issn = {1873-2976}, abstract = {Cellulosic textiles, constituting over 30% of global fibre production, are biodegradable but remain challenging to recycle at scale owing to their high crystallinity, chemical finishes, and heterogeneous waste streams. Although microorganisms drive cellulose turnover in natural ecosystems, their potential for transforming anthropogenic cellulosic waste remains largely unexplored. In this study, composting was evaluated both as a sustainable approach to textile biodegradation and a reservoir of cellulolytic microorganisms with biotechnological potential. Biodegradation assays of cotton and lyocell were integrated with shotgun metagenomics and targeted cultivation to identify microbial taxa and enzymes involved in cellulose degradation. Composting trials showed that degradation was strongly influenced by both composting system and fibre composition. Community composting achieved near-complete textile disintegration, while shredded textiles exhibited the highest degradation rates, reaching up to 97%. Shotgun metagenomic revealed a bacterial-dominated community enriched in Actinomycetota and Bacillota and characterised by an abundance of glycoside hydrolases. Culture-based screening recovered 62 microbial isolates, of which Neurospora and Aspergillus exhibited the highest cellulolytic activity (>60%). In vitro assays further showed that cotton was more readily degraded than lyocell, with several isolates achieving >70% mass loss. Metagenomic approach revealed a predominantly bacterial composting community at the sampled stage, whereas cultivation preferentially recovered fungi that, despite their low relative abundance in situ, exhibited strong cellulolytic potential. These findings highlight the potential of composting as a sustainable end-of-life strategy for cellulosic textiles and identify compost microbiomes as valuable reservoirs of cellulolytic microorganisms for the development of sustainable bioprocesses for textile waste treatment.}, } @article {pmid42436017, year = {2026}, author = {Wang, Q and Zhong, W and Huang, H and Yang, X and Liu, X and Ren, Y and He, F and Li, J}, title = {Harnessing microbial modulators to mitigate antibiotic-induced gut dysbiosis: from phytochemicals to faecal microbiota transplantation.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-28}, doi = {10.1163/18762891-bja00123}, pmid = {42436017}, issn = {1876-2891}, abstract = {Antibiotics remain indispensable for the management of infectious diseases; however, their use inevitably perturbs the gut microbiota. Advances in metagenomics and multiomics approaches have demonstrated that antibiotic exposure profoundly disrupts microbial diversity and community structure, leading to the depletion of key commensals, the expansion of opportunistic pathogens, metabolic dysfunction, and the emergence of antimicrobial resistance. These alterations are increasingly associated with a broad spectrum of dysbiosis-related diseases (DRDs), encompassing metabolic, neuropsychiatric, and immune-mediated disorders. To mitigate or reverse antibiotic-induced microbial imbalances, various microbiota-targeted interventions have emerged as promising alternatives or complementary approaches. These include dietary phytochemicals (such as polyphenols, alkaloids, and organosulfur compounds), probiotics, prebiotics, synbiotics, postbiotics, bacteriophage therapy, and faecal microbiota transplantation (FMT). Evidence from in vitro and animal studies has provided mechanistic insights into how these interventions modulate microbial composition and function; however, clinical evidence varies across intervention type. This review summarizes the composition and functional roles of the gut microbiota, outlines the consequences of antibiotic exposure, and provides an overview of the underlying mechanisms, recent evidence, and potential applications of microbiota-targeted interventions in preserving intestinal homeostasis. This review aims to provide a theoretical basis and reference framework for the development of safer and more effective alternatives or adjuncts to antibiotic therapy.}, } @article {pmid42426176, year = {2026}, author = {Latorre, F and Jaillon, O and Sieracki, ME and Cruaud, C and Massana, R and Logares, R}, title = {Global population structure in MAST-4 unicellular marine predators.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10607-z}, pmid = {42426176}, issn = {2399-3642}, support = {CTM2015-69936-P//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; PID2022-137508NB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; RYC-2013-12554//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; CEX2019-000928-S//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; 240904//Norges Forskningsråd (Research Council of Norway)/ ; }, abstract = {Marine heterotrophic flagellates (HFs) are key unicellular predators in marine food webs. Understanding their diversity and distributions is crucial for comprehending ocean ecosystems. MAST-4, an uncultured clade of Marine Stramenopiles, comprises a key group of bacterivorous heterotrophic flagellates (HFs) in the ocean microbiome. While we know that temperature is a major driver of MAST-4's biogeography, the population structure of MAST-4 species remains poorly known, limiting our ability to understand their ecology and adaptations. Here, we investigate the global population diversity and structure of MAST-4 species A, B, C, and E using metagenomics and single-cell genomics data from the Tara Oceans expedition. We find substantial population divergence in MAST-4A and C, with lower divergence in species B and E. Temperature and salinity are the primary factors structuring these populations. Analyses of positively selected genes reveal genomic regions likely involved in population adaptation to different environments. Our findings enhance the understanding of the population diversity and structure of these critical unicellular predators, providing insights into their ecological roles and adaptations in the global ocean. They also contribute to our general understanding of microbial populations, a largely unexplored dimension of biodiversity that plays a crucial role in grasping the impacts of global change.}, } @article {pmid42426205, year = {2026}, author = {Wang, RH and Pan, G and Wang, S and Wang, J and Li, SC}, title = {High-quality phage assembly from metagenomes with PALACE.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {42426205}, issn = {1546-1696}, abstract = {Millions of phage genomes have been mined from metagenomic data recently but the genome completeness remains poor because of the limitations of existing phage detection methods, which rely on metagenomic contigs that fragment phage genomes. Here, we present PALACE, a conjugate-graph-based framework for assembling high-quality phage genomes from metagenomes. PALACE incorporates homology-based and deep-learning-based methods to detect phage signals and constructs a conjugate graph from the metagenomic sample. On simulated data, PALACE generates accurate and complete phage genomes, achieving an F1 score of 0.92-1.00 across simulation settings, outperforming the second-best method by 0.21-0.48. Applying PALACE to 914 gut metagenomic samples from healthy controls and participants with colorectal cancer (CRC) yielded 5,306 high-quality phage genomes, outperforming the second-best benchmark method by 55.98% in median genome completeness. We observed a high degree of functional organization for genes within phage genomes. Phages from participants with CRC exhibited a notable enrichment of metabolic factors, suggesting their adaptation to nutrient availability in the CRC gut environment.}, } @article {pmid42426353, year = {2026}, author = {Marszałek, K and Kowalski, MB and Jagiełło, A and Woźniak, A and Herda, K and Płoski, R and Ossowski, A and Oliveira, M and Zbieć-Piekarska, R and Łabaj, PP and Branicki, W}, title = {Evaluation of targeted Massively Parallel Sequencing methods for forensic metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-026-13944-5}, pmid = {42426353}, issn = {1432-0614}, abstract = {Massively Parallel Sequencing (MPS) is effective for monitoring the microbial composition of environmental samples. Soil microbial signatures are critical for pinpointing the geographic location of forensic evidence, but standard 16S rRNA methods lack species-level resolution. Targeted sequencing panels, consisting of informative DNA fragments, can overcome this shortcoming and are highly desirable for forensic investigations. To address this, we evaluated three target enrichment methods for metagenomic analysis. First, we used Whole Metagenome Sequencing (WMS) data from 134 soil samples across 46 locations in Poland to extract a set of 200 markers. Using these markers, we created prototype targeted sequencing panels to compare two amplicon capture-based methods (Thermo Fisher AmpliSeq™ and Integrated DNA Technologies xGen™) and one hybridization capture-based method (Roche KAPA HyperPlus). The comparison of the technologies was guided by the results of classification of sample origin by machine learning classifier trained on feature profiles from WMS. The methods were assessed on technical parameters including data quality, reproducibility, sensitivity, and practical implementation for forensic laboratories. The performance and precision varied depending on technology and DNA concentration. The Roche KAPA HyperPlus hybridization capture-based method consistently demonstrated superior performance. Across various DNA input quantities, it showed the highest correlation with WMS data and achieved an exceptional F1 score of 0.94 at 5 ng, significantly outperforming the amplicon-based methods. This indicates that hybridization capture is a more robust and accurate approach for forensic soil microbiome profiling, particularly for low-template evidence, providing a highly reliable tool for predicting geographic origin. KEY POINTS: • Targeted Massively Parallel Sequencing methods for forensic soil microbial analysis • Targeted sequencing allowed the determination of the place of origin of soil samples • Roche KAPA HyperPlus: the most accurate classification of the soil samples origin.}, } @article {pmid42426489, year = {2026}, author = {Dimri, A and Sharma, P and Vishvakarma, R and Sharma, S}, title = {Effect of Probiotics on the Gut-Mammary Pathway: Implications on Infant Microbiota Transfer and Development.}, journal = {Current nutrition reports}, volume = {15}, number = {1}, pages = {}, pmid = {42426489}, issn = {2161-3311}, mesh = {Humans ; *Probiotics/administration & dosage/pharmacology ; Female ; *Gastrointestinal Microbiome ; Infant, Newborn ; Milk, Human/microbiology ; Lactobacillus ; Bifidobacterium ; Pregnancy ; Infant ; *Gastrointestinal Tract/microbiology ; Lactation ; *Mammary Glands, Human/microbiology ; }, abstract = {PURPOSE OF REVIEW: Transfer of microbiota from the maternal gut, during lactation, takes place via breastmilk, which establishes an intricate beneficial microbial ecosystem in the gut of the newborn. A healthy gut microbiota influences and enhances the neonatal health, and aids in multidimensional development-metabolically, immunologically, neurologically, and hormonally. Several microorganisms like Lactobacillus and Bifidobacterium get transferred to the infant gut and play a key role in its colonization and programming. Administration of such microbes, or probiotics, to the mother can assist in improving the benefits imparted by breastmilk to the infant, and can also provide health benefits to the mother. In recent years, there has been a focus on related metagenomic studies and the immunological effects of individual genera have also been studied in detail. In this review, we observe the gut-mammary pathway and the different roles played by probiotics in prenatal and postnatal scenarios. We also analyze the level of evidence of potential of some promising probiotic strains in the transfer, establishment, and development of infant gut microbiota based on recently conducted studies.

RECENT FINDINGS: The analysis of recent metagenomic studies proved that strains like Bifidobacterium infantis, Lactobacillus rhamnosus, and Limosilactobacillus reuteri exibit a high level of evidence in benefitting the microbiota transfer as well as establishment, diversification, and development of the infant gut ecosystem. Hence, these strains in particular, can be given as supplements to mothers during pregnancy and lactation, in order to improve their inherent immunity and the overall health of the mother-infant dyad. With the advent of metagenomics, the roles, functions and effects of microbes in the gut-mammary pathway have been re-examined. This review, critically evaluates the recent studies related to gut-mammary pathway and the different roles played by probiotics in prenatal and postnatal scenarios with particular emphasis on the strength and quality of their evidence.}, } @article {pmid42426596, year = {2026}, author = {Bunga, S and Tan, A and Roos, M and Kuersten, S}, title = {RiboZAP: a species-agnostic pipeline for rRNA depletion probe design in metatranscriptomics.}, journal = {BMC bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12859-026-06533-w}, pmid = {42426596}, issn = {1471-2105}, abstract = {BACKGROUND: Metatranscriptomic (MetaT) sequencing provides insights into gene expression and functional activity within microbial communities, but its utility is limited by the high abundance of ribosomal RNA (rRNA), which often accounts for ≥ 90% of total RNA. Efficient rRNA depletion is therefore essential to maximize mRNA coverage and sequencing efficiency. Commercial rRNA depletion kits can effectively reduce rRNA content; they are typically optimized for specific host microbiomes and often underperform in others. For example, probes designed for the human gut microbiome frequently show reduced efficiency when applied to non-human samples such as mouse cecal donor samples-a common model in microbiome research. Regardless of the depletion strategy used, designing rRNA removal probes solely based on a microbiome's taxonomic composition often requires an extensive number of probes, making the approach expensive and difficult to manufacture. To address these challenges, we developed RiboZAP, a species-agnostic computational pipeline that designs custom RNase H depletion probes directly from MetaT sequencing data without prior knowledge of sample composition.

RESULTS: RiboZAP-designed probe sets achieved 43-62% predicted rRNA depletion across both design and independent mouse cecal MetaT samples. Probes performed effectively on non-design samples, with depletion performance consistent with those observed in the design samples. Read composition and taxonomic diversity of residual rRNA, calculated using Shannon diversity indices, showed no evidence of probe-induced bias following depletion. In silico predictions were consistent with previously reported experimental depletion results [1-3], where RiboZAP designed probes improved mRNA recovery up to ~ 75% (P < 0.01). Comprehensive downstream validation demonstrated no bias in differential gene expression (R[2] = 0.96), metabolic pathway profiling (ρ = ~0.92-0.95), or taxonomic composition.

CONCLUSION: In this study, we demonstrate a data-driven, in silico approach for designing additional rRNA depletion probes that perform consistently across samples of the same sample type. Probe sets designed from a subset of samples can be applied to independent samples of the same type. This approach enables estimation of rRNA depletion prior to synthesis, reducing experimental costs, and improving the efficiency of MetaT profiling from complex microbial communities.}, } @article {pmid42426749, year = {2026}, author = {Zhan, S and Zheng, Y and Wu, T and Hou, X and Li, J and Ma, S and Gai, W and Shen, N and Zheng, J}, title = {Nucleosome-targeted host DNA depletion enables automated plasma metagenomic sequencing for sensitive detection of bloodstream pathogens.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08597-x}, pmid = {42426749}, issn = {1479-5876}, support = {F252052//Beijing Natural Science Foundation/ ; BYSYJC2023005//Peking University Third Hospital Fund for Interdisciplinary Research/ ; 2025-VHR-O-SY-21//State Key Laboratory of Vascular Homeostasis and Remodeling Open Research Fund/ ; 2025YFC2609702 and 2025YFC2609700//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Bloodstream infections (BSIs) are leading causes of sepsis-related mortality. Although metagenomic next-generation sequencing (mNGS) enables culture-independent pathogen detection, its clinical utility in plasma is limited by the overwhelming abundance of host cell-free DNA (cfDNA) and labor-intensive manual workflows.

METHODS: A plasma host DNA depletion mNGS (HD-mNGS) assay was developed which integrated nucleosome-targeted host DNA depletion with automated DNA extraction and library preparation. Analytical performance was evaluated through limit of detection, linearity, precision, and contamination control. Clinical performance was assessed in a cohort of 107 patients with suspected BSI and benchmarked against blood culture (BC), conventional microbiological testing (CMT), and standard mNGS without host depletion, using a composite clinical reference standard.

RESULTS: Nucleosome depletion markedly reduced host DNA background by an average of 66-fold, consequently enriching microbial reads by approximately 46.73-fold. The automated HD-mNGS assay exhibited robust analytical sensitivity, with limits of detection (LoD) ranging from 9.1 to 38 genome equivalents (GE) /mL for bacteria and fungi, and from 283 to 321 GE/mL for viruses and excellent linearity across tested concentrations (R[2] = 0.915-0.989). Furthermore, the automated workflow maintained strong quantitative correlation with manual protocols while significantly reducing common skin and environmental contaminants by 71.7% and 83.7%, respectively. In a cohort of 107 patients, HD-mNGS demonstrates improved diagnostic performance for BSI, achieving a significantly higher pathogen detection rate (64.49%) and clinical positive percent agreement (PPA: 95.24%) than standard mNGS, BC, and CMT (P < 0.001). Crucially, HD-mNGS demonstrates enhanced performance in detecting rare, fastidious, and intracellular pathogens (such as Mycobacterium tuberculosis and Rickettsia) that yield extremely low concentrations of circulating DNA, overcoming the limitations of traditional methods while maintaining high overall diagnostic total percent agreement (TPA: 88.79%).

CONCLUSIONS: Nucleosome-targeted host DNA depletion integrated with a fully automated mNGS platform significantly enhances microbial detection in plasma and provides a scalable approach for standardized BSI diagnostics.}, } @article {pmid42426884, year = {2026}, author = {Lei, Y and Xu, Y and Yan, Y and Zhang, J and Zhang, T and Huang, J and Huang, Y and Zhong, J and Wang, X and Zhang, K and Chen, Y}, title = {Multi-omics and functional validation reveal that Methanobrevibacter-derived L-3-aminoisobutyrate alleviates subclinical mastitis in dairy goats via the HSPA1B-p65 signaling pathway.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02464-z}, pmid = {42426884}, issn = {2049-2618}, abstract = {BACKGROUND: Subclinical mastitis (SCM) is prevalent in dairy livestock and compromises milk quality and lactation performance. Although often attributed to bacterial infection, many cases lack identifiable pathogens, suggesting alternative mechanisms. While evidence supports a gut-mammary gland axis, the microbial drivers and microbiota-derived metabolites linking gut dysbiosis to SCM remain unclear. Here, we aimed to identify SCM-associated gut microbial markers, prioritize candidate therapeutic metabolites and define the underlying mechanism.

RESULTS: Based on differences in somatic cell count (SCC) and inflammatory phenotypes across a cohort of 167 mid-lactation Saanen dairy goats, we selected 6 healthy and 6 SCM goats for downstream analyses. By integrating metagenomics, metabolomics, cross-species fecal microbiota transplantation (FMT) and functional validation in vitro and in vivo, we found that SCM was accompanied by reduced milk yield and heightened inflammatory signatures. Compared with the Healthy group, SCM goats exhibited marked remodelling of the gut microbiota, with enrichment of opportunistic taxa (Eubacterium and Blautia) and a pronounced depletion of archaeal Methanobrevibacter spp. Notably, FMT from SCM donors recapitulated mammary inflammatory phenotypes in mice, supporting a causal contribution of gut dysbiosis to mammary inflammation. Joint metagenomic functional profiling and metabolomics further identified the branched-chain amino-acid-derived metabolite L-3-aminoisobutyrate (BAIBA) as significantly enriched in the gut of healthy goats. Moreover, Methanobrevibacter spp. harboured key enzyme genes (vorA, vorB and vorD) implicated in BAIBA biosynthesis. In an LPS-challenged MAC-T model, BAIBA attenuated mammary epithelial inflammation by activating endoplasmic reticulum protein quality control programmes and restoring HSPA1B expression, thereby suppressing NF-κB activation and reducing pro-inflammatory cytokine production. Finally, in naturally infected goats, intramammary administration of BAIBA lowered SCC, highlighting translational potential.

CONCLUSIONS: This study identifies BAIBA as a microbiota-derived metabolite that protects against SCM by restraining mammary inflammation via the HSPA1B-NF-κB axis, establishing a mechanistic gut-mammary link and highlighting a potential non-antibiotic intervention strategy. Video Abstract.}, } @article {pmid42426896, year = {2026}, author = {Tóth, GE and Nagy, A and Costales, JA and Camacho, MA and Burneo, SF and Petersen, M and Bialonski, A and Baum, H and Horváth, B and Heitmann, A and Lühken, R and Schmidt, M and Schmidt-Chanasit, J and Tauber, Z and Cadar, D}, title = {A highly sensitive amplicon sequencing workflow for genomic surveillance of Usutu virus.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, doi = {10.1186/s12985-026-03251-w}, pmid = {42426896}, issn = {1743-422X}, mesh = {Humans ; *Flavivirus/genetics/isolation & purification/classification ; Germany ; *High-Throughput Nucleotide Sequencing/methods ; *Genome, Viral ; *Flavivirus Infections/virology ; Workflow ; Blood Donors ; RNA, Viral/genetics ; Phylogeny ; Genomics/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Genomic surveillance of Usutu virus (USUV) in blood donors is hampered by extremely low viral loads, which usually prevent reliable genome sequencing. We developed and validated a tiled amplicon-based sequencing protocol optimized for low-titer samples. Serial dilutions of four phylogenetically distinct USUV lineages showed ≥ 95% genome recovery above 100 RNA copies/µL and 65-98% recovery between 3 and 100 copies/µL. We applied the method to 27 USUV-positive blood donors from Germany (median 1.70 copies/µL), achieving lineage assignment in 74% and ≥ 70% genome coverage in 63% of samples. This approach enables routine genomic surveillance of USUV in blood donors.}, } @article {pmid42427046, year = {2026}, author = {Guo, YF and Zhan, QY and Huang, LN}, title = {[Clinical characteristics, diagnosis and treatment strategies, and prognostic factors in 47 patients with pulmonary mucormycosis].}, journal = {Zhonghua nei ke za zhi}, volume = {65}, number = {7}, pages = {734-742}, doi = {10.3760/cma.j.cn112138-20260201-00069}, pmid = {42427046}, issn = {0578-1426}, support = {2025ZD01902400//National Science and Technology Major Project/ ; }, mesh = {Humans ; *Mucormycosis/diagnosis ; Male ; Prognosis ; *Lung Diseases, Fungal/diagnosis ; Middle Aged ; Retrospective Studies ; Female ; Antifungal Agents ; Risk Factors ; Adult ; Voriconazole ; }, abstract = {Objective: To summarize the clinical characteristics, diagnostic and therapeutic strategies, and prognostic factors in patients with pulmonary mucormycosis. Methods: The patients with pulmonary mucormycosis admitted to the Department of Respiratory and Critical Care Medicine and the Lung Transplantation Department of China-Japan Friendship Hospital from January 2016 to March 2023 were retrospectively evaluated. High-risk factors, clinical manifestations, imaging findings, microbiological tests, therapeutic interventions, and clinical outcomes were analyzed, and variables were compared between survivors and non-survivors. Intergroup statistical analyses were performed using the chi-squared test, or Fisher's exact test, etc. Results: Of the 47 patients (21 confirmed, 26 clinically diagnosed), 32 (68.1%) were male, and the mean age of the cohort was (48±17) years. High-risk factors were present in 87.2% (41/47) of patients, primarily diabetes mellitus (53.2%, 25/47) and immunosuppression (42.6%, 20/47); 53.2% (25/47) had a history of voriconazole exposure. Hemoptysis occurred in 57.4% (27/47) of patients, of whom 17.0% (8/47) experienced massive hemoptysis; 48.9%(23/47) required interventional or surgical management. Chest CT scans revealed large consolidative opacities (70.2%, 33/47) and thick-walled cavities (48.9%, 23/47), and contrast-enhanced CT identified vascular involvement. The positive rate for lower respiratory tract fungal culture was only 17.1% (6/35), and that of smear microscopy was 18.2% (6/33), whereas the positive rate of metagenomic next-generation sequencing (mNGS) reached 76.0% (19/25), with mNGS of bronchoalveolar lavage fluid reaching 85.0% (17/20). Overall, 34.0% (16/47) of patients were diagnosed exclusively via mNGS. Conventional amphotericin B formulations were administered to 68.1% (32/47) of patients (including 10 who received liposomal amphotericin B); these formulations were associated with an adverse drug reaction rate of 86.7% (26/30), which contributed to only 40.7% (11/27) of these treated patients receiving a full therapeutic dose. Azoles were administered to 91.5% (43/47) of patients (15 received azoles alone), and among those treated with posaconazole, 88.0% (22/25) achieved target plasma concentrations; 48.9% (23/47) received combination therapy consisting of an amphotericin B formulation plus an azole. The survival rate among patients who underwent surgical intervention combined with antifungal therapy was 11/12, which was higher than that of patients who received antifungal therapy alone (28/35). Compared with survivors, non-survivors demonstrated significantly higher incidences of dyspnea (8/8 vs. 14/39, P=0.001), uncontrolled fever (6/8 vs. 12/39, P=0.027), pleural effusion (8/8 vs. 17/39, P=0.003), atelectasis (5/8 vs. 6/39, P=0.016), and severe complications (7/8 vs. 13/39, P=0.015). Furthermore, a significantly lower proportion of non-survivors received adequate antifungal dosing (1/8 vs. 21/39, P=0.037). Conclusions: Pulmonary mucormycosis predominantly occurs in high-risk populations such as those with diabetes mellitus or immunosuppression. Hemoptysis is a prominent clinical manifestation, while imaging findings commonly include large areas of consolidation, thick-walled cavities, and signs of vascular invasion. Early execution of contrast-enhanced chest CT, along with bronchoscopy with bronchoalveolar lavage fluid mNGS, improves the diagnostic yield. Adequate antifungal therapy combined with aggressive surgical intervention may contribute to improved prognosis. Severe complications, dyspnea, uncontrolled fever, pleural effusion, atelectasis, and inadequate antifungal treatment are associated with a poor prognosis, underscoring the need for early recognition and management.}, } @article {pmid42427959, year = {2026}, author = {Wang, L and Ding, K and Yu, S and Guo, Z and Wang, Y and Zeng, L and Yuan, W}, title = {Atypical congenital toxoplasmosis presenting with neonatal jaundice and central nervous system involvement: a case report and therapeutic challenges to limited access to first-line anti-toxoplasma medications.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1874973}, pmid = {42427959}, issn = {2296-2360}, abstract = {BACKGROUND: Congenital toxoplasmosis (CT) is a vertically transmitted infection with a variable clinical spectrum, ranging from asymptomatic infection at birth to severe neurological and ocular sequelae. While the classic triad of hydrocephalus, intracranial calcifications, and chorioretinitis is well characterized, isolated neonatal hyperbilirubinemia as the initial presenting feature is uncommon and may delay diagnosis. We report a case of CT in a Chinese neonate who presented with jaundice and was subsequently found to have subclinical active chorioretinitis, cerebral edema, and bilateral central auditory pathway dysfunction. The case also illustrates therapeutic challenges related to the availability of first-line anti-parasitic agents.

CASE PRESENTATION: A 9-day-old term male infant was admitted for persistent jaundice. He was born at 39 [+] [4] weeks' gestation, with a prenatal history notable only for maternal cat exposure and treated hypothyroidism. Initial serological testing at the referring hospital revealed positive Toxoplasma gondii IgM and IgG. After transfer, two consecutive blood metagenomic next-generation sequencing (mNGS) tests detected T. gondii DNA (reads: 6 and 7). The combination of negative first-trimester maternal serology, postpartum maternal IgM/IgG positivity, neonatal IgM positivity, and repeated detection of T. gondii DNA in neonatal blood strongly supported congenital toxoplasmosis. Cerebrospinal fluid (CSF) analysis showed pleocytosis and elevated protein, while CSF mNGS was negative, possibly reflecting low pathogen burden or compartmentalized infection. Further evaluation demonstrated bilateral active chorioretinitis on fundoscopic examination, abnormal brainstem auditory evoked potentials consistent with bilateral central auditory pathway dysfunction, and brain MRI showing cerebral edema with punctate hemorrhages. Due to initial unavailability of pyrimethamine, azithromycin followed by trimethoprim-sulfamethoxazole was administered; however, no clear improvement in CSF inflammatory indices was observed during this period. After initiation of standard therapy with pyrimethamine, sulfadiazine, and folinic acid, the patient demonstrated rapid clinical improvement and radiological resolution of brain lesions on follow-up MRI, with marked improvement of chorioretinal scars.

CONCLUSIONS: Clinicians should consider congenital toxoplasmosis in neonates with unexplained jaundice, even in the absence of classic clinical manifestations. Comprehensive multi-organ evaluation, including neuroimaging, ophthalmologic examination, and auditory testing, is essential for early disease characterization. Standard pyrimethamine-sulfadiazine-folinic acid therapy may be associated with better clinical and radiological outcomes and should be used when available. Long-term multidisciplinary follow-up is necessary to monitor potential sequelae.}, } @article {pmid42428097, year = {2026}, author = {Hanze Villavicencio, KL and Tanes, C and Malekshahi, C and Cutillo, D and Knoll, MD and Prosperi, C and Kalaycioglu, M and Harris, M and Utz, PJ and Mattei, LM and Beiting, DP}, title = {Microbial and immune determinants of disease severity and death in pediatric pneumonia.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.07.02.26356561}, pmid = {42428097}, abstract = {Pneumonia is a leading cause of death globally and disproportionately affects children in lower- and middle-income countries. To explore microbial and immune correlates of disease and death, we performed metagenomic sequencing of upper respiratory tract (URT) microbiome in 309 children in Mali with pneumonia and 150 age- and season- and site-matched controls. We show that the URT microbiome matures throughout early life and is influenced by breastfeeding. URT microbiome maturation was disrupted during pneumonia resulting in loss of commensal species and expansion of pathobionts, which was linked to disease severity and death. Analysis of serum antibody levels revealed that low levels of passively acquired antibody from mothers, deficient antibody responses to RSV, and persistent autoantibody to cytokines were associated with pneumonia mortality in an age-dependent manner. These findings underscore the complex nature of pneumonia and identify microbial and immune factors for risk stratification and therapeutic interventions in pediatric pneumonia.}, } @article {pmid42428114, year = {2026}, author = {Wang, Q and Wang, BY and Wilus, D and Xie, H}, title = {Effects of Non-Surgical Periodontal Therapy on Dental Plaque Microbiome.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {42428114}, abstract = {Periodontitis, a chronic inflammatory disease affecting approximately 40% of U.S. adults aged 30 years and older, is characterized by dysbiosis of the dental plaque microbiome. However, although scaling and root planing (SRP) is the cornerstone of periodontal treatment, its effects on the taxonomic composition and functional potential of the dental plaque microbiome remain incompletely understood. In this study, we used whole-metagenome shotgun sequencing to characterize taxonomic composition and functional potential in dental plaque microbiomes collected from 39 patients with Stage II or III generalized periodontitis before and 3-4 months after SRP. Consistent with clinical improvement, periodontal therapy significantly reduced bleeding on probing and plaque index. Whole-metagenome shotgun sequencing identified 3.18 million non-redundant genes and 12,353 microbial species across 78 samples, revealing increased gene and species richness after treatment, along with a significant restructuring of microbial community. Established periodontal pathogens, including Porphyromonas gingivalis and Tannerella forsythia , as well as the emerging pathogen Escherichia coli , decreased following treatment, whereas health-associated early colonizers, including multiple Actinomyces species and Streptococcus cristatus , increased. Functional annotation using the Carbohydrate-Active Enzymes (CAZy) database identified treatment-associated differences in several carbohydrate-active enzymes, including multiple glycosyltransferases, indicating remodeling of the predicted functional potential of the dental plaque microbiome. These findings demonstrate that successful SRP promotes coordinated taxonomic and predicted functional remodeling of the dental plaque microbiome and highlight the value of shotgun metagenomic sequencing for characterizing both taxonomic and functional recovery following periodontal therapy.}, } @article {pmid42428252, year = {2026}, author = {Qi, W and Kong, M and Meng, X and Sun, Z and Mei, Z and Pu, Y and Zhou, X and Wang, Q and Qiu, JG and Jiang, BH and Shen, J and Yuan, C and Ji, JS and Wang, X and Kan, H and Zheng, Y}, title = {The Role of Gut Microbiota in the Association between Air Pollution and Cognitive Function in Older Adults.}, journal = {Environmental health perspectives}, volume = {134}, number = {3}, pages = {335-350}, pmid = {42428252}, issn = {1552-9924}, mesh = {Humans ; *Air Pollution/adverse effects/statistics & numerical data ; *Gastrointestinal Microbiome/drug effects ; Aged ; Particulate Matter/adverse effects ; Ozone ; Male ; Female ; *Cognition/drug effects ; *Cognitive Dysfunction/epidemiology ; *Air Pollutants ; *Environmental Exposure/statistics & numerical data ; }, abstract = {BACKGROUND: Growing evidence links air pollution to cognitive dysfunction in older adults. The gut microbiome and circulating metabolites present an important yet unexplored pathway given their crucial role in the gut-brain axis. OBJECTIVES: We aimed to explore the potential roles of gut bacteria, fungi, microbial functional potentials, and circulating metabolites in the association of residential PM2.5 and O3 exposure with cognitive dysfunction. METHODS: We analyzed gut microbiome data from 1,027 older adults using metagenome and internal transcribed spacer sequencing to profile bacterial and fungal taxa, functional pathways, and enzyme abundances. Targeted metabolomics quantified 195 circulating metabolites, such as amino acids and organic acids. Annual average ambient PM2.5 and O3 exposures were estimated by using satellite-based models. Cognitive outcomes, including mild cognitive impairment and cognitive decline, were assessed using the Mini-Mental State Examination and Hasegawa Dementia Scale. Statistical analyses included Microbiome Multivariable Association with Linear Models (with a false discovery rate threshold of 0.25) for microbial associations and multivariate regression for metabolites and cognitive outcomes. RESULTS: Higher PM2.5 and O3 exposures were associated with disturbances in microbial composition, altered taxonomic profiles (e.g., decreased abundances of Blautia obeum and Gordonibacter pamelaeae), and disrupted functional pathways, particularly those regulating 2-oxoglutarate. These findings were partially replicated in an independent population. Higher air pollution levels were associated with increased circulating levels of 2-oxoglutarate and l-glutamine (key metabolites in neurodegenerative progression), which were further linked to higher odds of concurrent mild cognitive impairment (OR: 1.39-1.56) and an increased 2-year risk of cognitive decline (OR: 1.26-1.37). These associations were partially mediated by air pollution-related changes in microbial anaerobic energy metabolism pathways, especially involving 2-oxoglutarate metabolism and the enzyme aspartate transaminase. CONCLUSIONS: Our findings highlight the role of the gut microbiome and microbial metabolites in mediating the detrimental impact of air pollution on cognitive health in older adults, providing new insights into the underlying etiology for future hypothesis generation.}, } @article {pmid42429397, year = {2026}, author = {Romo Bechara, N and Bardeskar, N and Hopkins, HA and Bobay, L-M and Raymann, K}, title = {Genomic and phenotypic diversification of Pseudomonas aeruginosa during sustained exposure to a ciliate predator.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0121326}, doi = {10.1128/spectrum.01213-26}, pmid = {42429397}, issn = {2165-0497}, abstract = {UNLABELLED: Predator-mediated selection is an important ecological force shaping bacterial evolution, but its effects on genomic adaptation and virulence in opportunistic pathogens are not fully understood. Here, we used experimental evolution to study how exposure to the ciliate predator Tetrahymena thermophila affects Pseudomonas aeruginosa. Replicate populations were evolved for 60 days with or without the predator, followed by whole-genome shotgun metagenomic sequencing and phenotypic analyses. Both treatments showed strong selection and evidence of parallel evolution at gene and nucleotide levels, indicating constrained adaptation. However, predator exposure altered evolutionary dynamics. Predator-evolved populations showed a wider distribution of mutation frequencies, with many mutations persisting at intermediate frequencies, consistent with increased clonal interference and ongoing competition among lineages. In contrast, populations evolved without predators showed more high-frequency mutations, consistent with selective sweeps, although some low-frequency variants remained. Despite substantial genomic change, phenotypic outcomes were variable. Virulence in an invertebrate host model did not consistently increase. Instead, evolved isolates showed context-dependent changes, including modest decreases or occasional increases. Competition assays also showed no consistent fitness advantage for predator-evolved isolates, suggesting trade-offs between predator resistance and growth in other environments. Overall, predator-mediated selection reshaped evolutionary dynamics by maintaining diversity and altering the balance of lineages rather than producing uniform increases in virulence. These results highlight how ecological complexity influences adaptive evolution and the context-dependent nature of pathogen traits.

IMPORTANCE: Opportunistic pathogens such as Pseudomonas aeruginosa often evolve in environmental settings before infecting hosts, raising questions about how ecological interactions influence virulence. Predator-mediated selection has been suggested to increase virulence via coincidental evolution, but evidence is inconsistent. Here, we show that exposure to a eukaryotic predator does not consistently elevate virulence but does reshape evolutionary dynamics by altering how mutations spread in populations. Predator-exposed populations retained more intermediate-frequency mutations, consistent with increased clonal interference and ongoing competition among lineages, whereas non-predator populations were dominated by selective sweeps. These differences were also reflected in functional targets of adaptation, with predator exposure favoring mutations in genes involved in environmental sensing and interaction. Together, these findings suggest that ecological complexity shapes the dynamics of adaptation rather than driving a single evolutionary outcome, highlighting that virulence is an emergent property influenced by underlying evolutionary processes.}, } @article {pmid42429454, year = {2026}, author = {Di Leo, D and Nilsson, E and Westmeijer, G and Pinhassi, J and Lundin, D}, title = {nf-core/magmap: Map metatranscriptomes to large collections of genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag501}, pmid = {42429454}, issn = {1367-4811}, abstract = {SUMMARY: The lack of publicly available reference genomes has forced annotation of metatranscriptomes to either use direct alignment of sequence reads to reference databases or de novo assembly. As more and more natural environments are covered by metagenomic surveys, this is rapidly changing. This opens up the possibility of genome-resolved studies of prokaryotic metatranscriptomes by mapping to genomes from public repositories or metagenome-assembled genomes derived from the same environment. Here, we present the nf-core/magmap pipeline that provides a reproducible, easy-to-access, and well-documented workflow for selecting reference genomes, mapping to them, and quantifying features. Genomes can be drawn from public sources or originate from private collections. The pipeline is primarily aimed at prokaryotic communities but can, together with collections of reference mature gene sequences, also be applied to eukaryotes.

The nf-core/magmap pipeline is implemented in Nextflow and part of the nf-core collaboration. The pipeline is available at the nf-core website (https://nf-co.re/magmap) and GitHub (https://github.com/nf-core/magmap).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid42429456, year = {2026}, author = {Flamholz, ZN and Mulay, SA and Leshyk, V and Caporaso, JG and Eisen, JA and Kelly, L and Lloyd, KG and Osburn, MR and Podar, M and Roux, S and Regberg, SAB and Ruff, SE and Tierney, B and Tighe, S and Trembath-Reichert, E and Venkateswaran, K and Woyke, T and Locken, KM and Sapers, HM and Whiteson, K}, title = {Exploring life's hidden majority: microbial dark matter symposium highlights.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0058725}, doi = {10.1128/msphere.00587-25}, pmid = {42429456}, issn = {2379-5042}, abstract = {The Microbial Dark Matter Symposium held on August 28-29, 2025, in Laguna Beach, Orange County, CA, convened a multidisciplinary group of scientists to address the vast unknowns in microbial life-from uncultured taxa and uncharacterized proteins to elusive viruses and spacefaring microbes. Set against a scenic coastal backdrop, the symposium highlighted advances in single-cell genomics, proximity ligation sequencing, and artificial intelligence-ready bioinformatics, while also probing the limits of microbial persistence, metabolism, and ecological distribution. Sessions explored microbial dark matter from multiple dimensions: cultivability, where new strategies are enabling recovery of elusive microbes; functional ambiguity, where metagenomic dark zones are illuminated by computational annotation; and genomic representation, where single-cell methods bridge gaps left by shotgun community sequencing. Researchers shared breakthroughs in identifying atmospheric microbiomes, "dark oxygen" production in groundwater ecosystems, and microbial survival on the International Space Station. The symposium emphasized integration of methods, disciplines, and ecosystems, advancing a collective push to illuminate the microbial dark matter on Earth and beyond. By highlighting emerging tools, pressing questions, and cross-domain insights, the symposium underscored the need for collaborative, open, and adaptive approaches to study the microbial unknown. The meeting marks a pivotal moment in microbiology, where cultivating knowledge of the uncultivated promises transformative understanding of life, everywhere.}, } @article {pmid42429485, year = {2026}, author = {Tian, B and Liu, Y and Su, KJ and Jiang, LD and Lin, X and Qiu, C and Luo, Z and Tian, Q and Shen, J and Shen, H and Zhang, LS and Xiao, HM and Deng, HW}, title = {Multi-omics Analysis Identify Novel Microbiome-Metabolome Signatures Associated with Obesity.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag172}, pmid = {42429485}, issn = {1365-2672}, abstract = {AIMS: Explore the potential microbiome and serum metabolome factors and their interactions associated with obesity.

METHODS AND RESULTS: We performed a systematic multi-omics analysis using paired metagenomic and metabolomic profiles-including untargeted serum metabolomics, lipidomics, and short-chain fatty acids (SCFAs) with body mass index (BMI) from a cohort of 495 US men. Single omics analysis identified 52 gut bacteria species and 31 serum metabolites for potential associations with BMI. Among the identified bacteria, Collinsella stercoris (C.stercoris) (Coef.=-0.147, P=0.015) was negatively associated, whereas Bacteroides fragilis (B.fragilis) (Coef.=0.294, P=1.22E-04) and Veillonella dispar (V.dispar) (Coef.=0.135, P=0.001) were positively associated, these results were further validated by an independent Chinese cohort. Several of the identified metabolites including gamma-glutamylglycine (Coef.=-0.713, P=4.53E-06), asparagine (Coef.=-0.629, P=3.53E-05), glycine (Coef.=-0.952, P=5.28E-09) and serotonin (Coef.=0.566, P=1.78E-04) were associated with these significant bacteria (P<0.05).

CONCLUSION: This multi-omics study identifies key gut bacteria and serum metabolites that interact to associate with host obesity, providing systemic insight into microbiome-host metabolic interactions.}, } @article {pmid42429570, year = {2026}, author = {Sánchez-Nieto, E and Martínez-Abarca, F and Millán, V and Molina-Sánchez, MD and García-Rodríguez, FM and Toro, N}, title = {A UG5 reverse transcriptase-nitrilase antiviral module confers phage immunity in the plant symbiont Sinorhizobium meliloti.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0038126}, doi = {10.1128/spectrum.00381-26}, pmid = {42429570}, issn = {2165-0497}, abstract = {Bacteriophages exert strong selective pressure on soil- and rhizosphere-associated bacteria, including plant-associated symbionts. Reverse transcriptase-associated defense systems of the UG family are widespread across bacterial lineages, yet their ecological roles remain largely undefined. Within this family, UG5 systems are distinguished by reverse transcriptases fused to or associated with a nitrilase domain. Here, we combine phylogenetic, metagenomic, and functional analyses to investigate the evolutionary context and antiviral activity of UG5-associated systems. Phylogenetic analysis of 728 nitrilase domains places UG5-associated nitrilases within a well-supported UG-related radiation encompassing the UG1, UG5, and UG6 families, with UG1 nested within a broader UG5 lineage. Metagenomic analysis further revealed UG5-associated reverse transcriptases in soil- and rhizosphere-derived metagenomes. Based on this observation, we characterized a UG5-large reverse transcriptase (RT)-associated system, here designated DRT11, encoded on the pSymA megaplasmid of Sinorhizobium meliloti RMO17, a nitrogen-fixing symbiont of Medicago sativa. Despite lacking the transmembrane protein typical of canonical UG5-large architectures, DRT11 confers protection against naturally occurring M. sativa rhizosphere phages with podovirus-like morphology. Phage infection assays reveal protection at low multiplicities of infection, consistent with an abortive-infection-like mechanism. Moreover, mutational analyses demonstrate that antiviral activity requires only the RT and its fused C-terminal nitrilase domain, establishing DRT11 as a minimal UG5-associated antiviral system.IMPORTANCEIn this study, we report the functional characterization of a UG5-large reverse transcriptase-associated defense system (DRT11) encoded on the pSymA megaplasmid of the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Using a combination of phylogenetic, metagenomic, genomic, and experimental approaches, we demonstrate that DRT11 functions as a bona fide antiviral defense module, providing protection against naturally occurring rhizosphere phages through a minimal reverse transcriptase-nitrilase architecture. This work establishes direct functional evidence for antiviral activity within the UG5 family and clarifies the evolutionary placement of UG5-associated systems within the broader UG radiation.}, } @article {pmid42429609, year = {2026}, author = {Robertson, CM and Mercado-Evans, V and Larson, AB and Branthoover, H and Ottinger, S and Mejia, ME and Hameed, ZA and Gonzalez, LA and Serchejian, C and Ogilvie, L and Zulk, JJ and Patras, KA}, title = {Type 2 diabetes mellitus exacerbates vaginal group B Streptococcus colonization via impaired mucosal cytokine response.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0002726}, doi = {10.1128/msphere.00027-26}, pmid = {42429609}, issn = {2379-5042}, abstract = {Type 2 diabetes mellitus (T2D) is a metabolic disorder that confers increased risk of microbial infections, including those caused by the opportunistic pathogen group B Streptococcus (GBS). Asymptomatic GBS vaginal carriage is a notable reservoir for infection, but the impact of T2D on the vaginal mucosa and GBS colonization is not fully understood. We employed a diet-induced mouse model of T2D to investigate the impact of diabetes on glucose availability, vaginal microbiome composition, and vaginal cytokines at baseline and in response to GBS. We observed enhanced susceptibility of diabetic mice to GBS vaginal colonization and reproductive tract dissemination. Despite experiencing hyperglycemia, diabetic mice did not exhibit elevated glucose in the reproductive tract. Regarding the vaginal microbiota, diabetic mice had minimal compositional differences, with decreased Mammaliicoccus being the only significant taxonomic variance. Vaginal cytokine profiling revealed consistently depressed cytokines in diabetic mice, beginning with KC at baseline and expanding to eight pro-inflammatory cytokines post-GBS infection. Diabetic mice exhibited decreased proportions of uterine neutrophils and, following GBS exposure, also displayed an expanded vaginal γδ T cell compartment compared with controls. Pairing cytokine observations with GBS colonization revealed a correlation between delayed vaginal IL-1α induction and persistent vaginal GBS, suggesting that vaginal cytokine deficiency may contribute to diabetic GBS phenotypes. Intravaginal supplementation with rIL-1α resolved GBS burden differences between diabetic mice and controls, confirming that deficient vaginal cytokines contribute to diabetic GBS vaginal persistence. These findings advance our understanding of diabetic vaginal mucosal susceptibility to pathogens and support the potential for immunological intervention.IMPORTANCEPeople with T2D are more susceptible to microbial infections, but there is limited understanding of the mechanisms that drive this vulnerability. One possibility is that T2D enhances the colonization of opportunistic pathogens, like GBS, in mucosal reservoirs as a precursor to infection. In this study, we used a diabetic mouse model to test whether diabetes alters the vaginal mucosa to promote GBS colonization. We found that increased vaginal GBS colonization in diabetic mice was not linked to tissue glucose availability or changes in the vaginal microbiome but instead was associated with impaired vaginal immune responses. These findings provide a foundation for translational approaches to reduce GBS persistence and dissemination in at-risk individuals.}, } @article {pmid42429615, year = {2026}, author = {Jiang, K and Xiong, F and Peng, Y and Meng, L and Wang, X and Xu, Y and Tang, T and Gao, H}, title = {Intermittent Fasting Restores Cardiac Lipid Homeostasis in Diabetic Cardiomyopathy in Association With Akkermansia Muciniphila and 1-methyl-L-histidine.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e76528}, doi = {10.1002/advs.76528}, pmid = {42429615}, issn = {2198-3844}, support = {22274115//National Natural Science Foundation of China/ ; 21974096//National Natural Science Foundation of China/ ; LZ26C010002//Zhejiang Provincial Natural Science Foundation of China/ ; LQN26C010004//Zhejiang Provincial Natural Science Foundation of China/ ; }, abstract = {Diabetic cardiomyopathy (DCM) is a major cardiovascular complication of diabetes with limited effective interventions. Using a streptozotocin-induced insulin-deficient, type 1 diabetes-like DCM mouse model, we show that intermittent fasting (IF) improves cardiac function and attenuates myocardial remodeling. Antibiotic-mediated microbiota depletion largely abolished these benefits, whereas fecal microbiota transplantation from IF-treated donors recapitulated cardioprotection, supporting a causal role of the gut microbiota. Metagenomic profiling identified Akkermansia muciniphila (A. muciniphila) as a prominent IF-responsive taxon, and A. muciniphila supplementation alleviated cardiac injury without obvious improvement in glycaemia. Integrated serum and heart metabolomics identified 1-methyl-L-histidine as a microbiota-associated metabolite reduced in diabetes but restored by IF and A. muciniphila. In vitro and ex vivo assays further supported an L-anserine-linked microbial route for 1-methyl-L-histidine generation. Importantly, oral 1-methyl-L-histidine supplementation recapitulated key cardioprotective effects, remodeled cardiac lipid homeostasis, and reduced lipid peroxidation and oxidative injury. Together, these findings support a gut microbiota-metabolite-lipid axis associated with IF-related cardioprotection in DCM and highlight microbial metabolites as tractable targets to complement dietary intervention.}, } @article {pmid42429677, year = {2026}, author = {Sarkar, M and Maddheshiya, A and Tailor, P and Nath, S and Makkar, N and , and Misra, S and Desiraju, BK and Wadhwa, N and Bhatnagar, S and Kshetrapal, P and Mukherjee, S}, title = {Longitudinal shifts in oral microbiome composition and metabolic pathways associated with preterm birth.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0018426}, doi = {10.1128/msystems.00184-26}, pmid = {42429677}, issn = {2379-5077}, abstract = {Oral dysbiosis in pregnant women with oral diseases has been associated with adverse pregnancy outcomes. However, the inter-individual variability in oral microbiome composition of pregnant women without any oral disease, and its role in preterm birth, has not been studied yet. Here, we have collected saliva from 20 term birth (TB) and 20 preterm birth (PTB) delivering women without any self-reported oral disease at three trimesters (n = 120). Microbial DNA was subjected to 16S rRNA gene sequencing for taxonomic classification, and microbial pathways were investigated by PICRUSt2. In a subset of samples, shotgun metagenomic sequencing was done to identify microbial species, their gene families, and their pathways. TB and PTB women were distributed into three distinct oral community types (OCTs). Haemophilus parainfluenzae and Rothia mucilaginosa were associated with TB and PTB, respectively. The chorismate biosynthesis pathway, essential for folic acid biosynthesis, was significantly enriched in TB, whereas the enterobactin biosynthesis pathway that produces iron chelators (siderophores) was significantly enriched in PTB. The heterolactic fermentation pathway that reduces oral pH was enriched in PTB. Our data suggest that oral microbiome changes might have an impact on birth outcomes in women even without any history of self-reported oral disease during the pregnancy period.IMPORTANCEThe importance of this study lies in demonstrating that compositional and functional shifts in the oral microbiome are associated with pregnancy outcomes. Using a longitudinal design across three trimesters in an Indian cohort, we show that pregnant women segregate into distinct oral community types with consistent associations to term birth (TB) and preterm birth (PTB). Importantly, the TB-associated microbiome was enriched in taxa and pathways linked to vitamin and amino acid biosynthesis, including chorismate and threonine metabolism, which are critical for fetal growth. In contrast, PTB was associated with pathways related to iron scavenging and acidification of the oral environment, suggesting a metabolically stressed and dysbiotic state. These findings highlight the oral microbiome as a previously underappreciated, modifiable factor in pregnancy outcomes and underscore its potential relevance for early risk stratification and preventive strategies against PTB.}, } @article {pmid42429741, year = {2026}, author = {Koraimann, G and Hölzl, N and Koller, M and Zarfel, G and Treiber, F}, title = {A complete Candidatus walczuchella monophlebidarum genome assembled from citrus leaf metagenomic sequences.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0062026}, doi = {10.1128/mra.00620-26}, pmid = {42429741}, issn = {2576-098X}, abstract = {We present the complete de novo assembly of a Candidatus Walczuchella monophlebidarum genome (286,606 bp), a flavobacterial endosymbiont of the giant-scale insect Icerya purchasi. The genome was assembled from metagenomic short read Illumina sequences obtained from DNA of citrus leaves collected in Carinthia, Austria in November 2024.}, } @article {pmid42429749, year = {2026}, author = {Cluett, H and Chandler, JC and Bisha, B}, title = {A coding-complete genome sequence of bovine-like coronavirus identified in white-tailed deer (Odocoileus virginianus) in the United States.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0050026}, doi = {10.1128/mra.00500-26}, pmid = {42429749}, issn = {2576-098X}, abstract = {Bovine coronavirus within the Embecovirus subgenus causes respiratory and enteric diseases in domestic cattle. We report a coding-complete genome of bovine-like coronavirus from a white-tailed deer (Odocoileus virginianus) in New Jersey, USA. This genome is 30,988 bp with a guanine-cytosine content of 37%.}, } @article {pmid42429762, year = {2026}, author = {Putman, T and Abdel-Hamid, AM and Galbraith, E and Schimmel, P and Kim, H and Yasuma, T and Alhawsawi, MAB and Boateng, KA and Holmes, J and Duersteler, M and D'Alessandro-Gabazza, CN and Fujimoto, H and Kobayashi, T and Walden, KKO and Rendon, G and Fields, CJ and Zuckermann, FA and Mackie, RI and Son, S and Leistikow, KR and Gabazza, EC and King, MR and Cann, I}, title = {A Bacillus-based direct-fed microbial mixture remodels the gut microbiome to augment the respiratory health of Salmonella-infected pigs.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0097226}, doi = {10.1128/aem.00972-26}, pmid = {42429762}, issn = {1098-5336}, abstract = {Commercial pork production is practiced worldwide and represents a major source of protein for global populations. Pigs, however, are plagued by various diseases that affect their productivity. A common practice is to administer antibiotics in the feed to reduce infections and promote growth. However, antibiotic utilization in pig production has been identified as a source of spread of antibiotic resistance genes, prompting the need for antibiotic alternatives in swine production. Salmonella enterica serotype Choleraesuis and porcine reproductive and respiratory syndrome virus (PRRSV) are two disease agents with a significant impact on the pork industry. In this study, we designed experiments to test the hypothesis that a Bacillus-based direct-fed microbial (DFM) cocktail will alleviate the impact of Salmonella infection alone or in combination with PRRSV. Both single and dual infections resulted in shifts in the cecal microbiota from that of the Control group, with administration of the DFM dampening this effect, especially in the Salmonella-infected group. In the absence of the DFM, the infected pigs exhibited gross changes in the lungs, including tissue hepatization. Significantly, the DFM application suppressed the lesions in the lungs of Salmonella-only infected pigs. Using metagenome-assembled genomes, we found that DFM administration to Salmonella-only infected pigs led to cecal microbiota enriched in the potential to produce immune-stimulating short-chain fatty acids and naturally occurring antimicrobials, including peptides. The putative antimicrobial peptides derived from this study, upon biochemical characterization, could lead to their application as novel antimicrobials in animal agriculture and health.IMPORTANCEAntibiotics, as feed additives, have been integral to commercial pork production. Their use, however, has fostered the spread of antibiotic resistance genes in the environment. In this study, we explored the use of a mixture of naturally occurring bacteria, comprising species of the genus Bacillus, as an alternative to antibiotics in the pig diet. The bacterial mixture reversed disease lesions in the lungs of pigs infected with Salmonella enterica serotype Choleraesuis, a bacterium that causes severe disease in commercial pigs. Our findings suggest that applying the bacterial mixture to the Salmonella-infected pigs shifts the microbes in the gut to a community that is endowed with antimicrobials that mitigate the effects of Salmonella infection. We present data showing the novelty of putative antimicrobials discovered in the present study and postulate that their characterization will yield new antimicrobials that can be used in different sectors of animal production and health. PRRSV was included in the study to model a common bacterial-viral co-infection in swine, as it exacerbates disease severity. This design allowed assessment of whether Bacillus-based DFM could improve outcomes along the gut-lung axis under realistic co-infection conditions.}, } @article {pmid42429885, year = {2026}, author = {Delik, A and Ülger, Y and Albayrak, F and Orhan, U and Unal, U and Gov, E and Dinçer, S}, title = {Machine learning integration of tissue-specific metagenomic signatures for colorectal cancer diagnosis.}, journal = {Journal of applied genetics}, volume = {}, number = {}, pages = {}, pmid = {42429885}, issn = {2190-3883}, abstract = {Colorectal cancer (CRC) represents a significant global health burden. Leveraging machine learning (ML) with metagenomic and tissue-specific data presents new opportunities for improving diagnostic accuracy and understanding the microbiome's role in CRC. This study was conducted to enhance diagnostic efficiency and identify crucial bacterial biomarkers in CRC using various ML models applied to metagenomic data. A total of 33 samples were analyzed, comprising 20 healthy controls and 13 CRC patients. Each sample included demographic data (age, gender) and bacterial information (Bacteroides, Enterococcus, Faecalibacterium, Proteobacteria, Gammaproteobacteria, Firmicutes, Enterobacteriaceae, Clostridia). Six models: Logistic Regression, Naive Bayes, Decision Tree, Support Vector Machine (SVM) with both linear and polynomial kernels and Multilayer Perceptron (MLP) were employed. Performance was evaluated using leave-one-out cross-validation (LOOCV). To address the class imbalance, F1-score was utilized as the primary metric for feature selection. A consensus-based feature elimination strategy, where bacterial features were iteratively removed only if their exclusion improved or maintained the F1-score across the majority of the models was implemented. For the MLP, a grid search was integrated into each iteration to optimize hidden layer architectures and solvers, thereby ensuring that robust performance was achieved for each feature subset. The analysis was conducted using a 10-feature initial set consisting of 2 demographic and 8 microbial features. Model performances were optimized through a consensus-based feature elimination strategy, and it was determined that diagnostic success increased with the exclusion of the Faecalibacterium, Age, and Enterobacteriaceae features during the process. The highest performance was achieved with the SVM model with Linear kernel when Bacteroides was excluded from the 9-feature subset (Table 4), reaching an accuracy of 87.88% and an F1-score of 83.33%. Within the final biomarker set, Enterococcus and Firmicutes were identified as the most critical predictive features due to the sharpest declines in F1-score observed in their absence. This study demonstrates that the systematic elimination of initial clinical and metagenomic features maximizes CRC diagnostic accuracy and model stability. The process, initiated with a 10-feature baseline set was subsequently refined to establish a high-precision diagnostic mechanism with an F1-score of 83.33%. The identified final microbial signatures, consisting of 5-6 taxa, provide a clinically applicable, non-invasive diagnostic foundation with low input requirements.}, } @article {pmid42429927, year = {2026}, author = {Lirio, CPT and Albino, EED and Nisnisan, KKS and Castro, AE}, title = {Gut bacterial community profile of the endemic catfish Arius manillensis from Pasig River, Philippines.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0037026}, doi = {10.1128/mra.00370-26}, pmid = {42429927}, issn = {2576-098X}, abstract = {The Pasig River is a highly urbanized waterway, yet the microbial ecology of its native fauna remains poorly understood. This study provides the first report of the gut bacterial community of the catfish Arius manillensis, revealing bacterial taxa and underscoring the need to study host-associated microbiomes in urban aquatic ecosystems.}, } @article {pmid42430134, year = {2026}, author = {Laureano, G and Lal, V and Mitchell, L and Santillan Olea, E and Tovar, J and Scoles, A and Arun, A}, title = {Meta-genome assembled genome of Agrobacterium oryzihabitans associated with the cultivated yellow-green alga Vaucheria bursata.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0047325}, doi = {10.1128/mra.00473-25}, pmid = {42430134}, issn = {2576-098X}, abstract = {We report a draft metagenome-assembled genome (MAG) of an Agrobacterium species from Vaucheria bursata. The MAG is 89% complete (CheckM2 v1.1.0) with 3,281 predicted genes, providing a basis to explore bacteria-algae interactions and their role in the Vaucheria microbiome.}, } @article {pmid42430136, year = {2026}, author = {Aoki, M and Wakui, N and Hayashi, K and Syutsubo, K}, title = {High-quality metagenome-assembled genome sequences of Bacteroidota and Pseudomonadota bacteria, assembled from a manganese(II)-oxidizing biofilm reactor.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0058826}, doi = {10.1128/mra.00588-26}, pmid = {42430136}, issn = {2576-098X}, abstract = {We report five high-quality, potentially novel metagenome-assembled genomes (MAGs) recovered from a manganese(II)-oxidizing biofilm reactor. Affiliated with Bacteroidota and Pseudomonadota, these MAGs provide a genomic basis for understanding the ecology and metabolic potential of Mn(II)-oxidizing systems and represent a valuable resource for future functional studies of biofilm-mediated metal cycling.}, } @article {pmid42419832, year = {2026}, author = {Chaurasia, A and Ponangi, K}, title = {The microbiome of the head and neck region.}, journal = {Advances in immunology}, volume = {169}, number = {}, pages = {25-51}, doi = {10.1016/bs.ai.2026.03.002}, pmid = {42419832}, issn = {1557-8445}, mesh = {Humans ; *Microbiota/immunology ; *Dysbiosis/immunology/microbiology ; *Head and Neck Neoplasms/microbiology/immunology ; Animals ; *Head/microbiology ; *Squamous Cell Carcinoma of Head and Neck/microbiology/immunology ; }, abstract = {The head and neck region is a host to a diverse and complex microbiome, comprising of very specific microbial communities across different anatomical niches such as the oral cavity, nasal sinuses, pharynx, larynx, salivary glands, and middle ear. The existence of these communities is determined by various factors such as physicochemical conditions, local environment and host genetics playing a critical role in maintaining mucosal integrity, immune modulation, colonization resistance, and thereby achieving metabolic homeostasis. As the human ages, the microbiome constantly evolves, influenced by diet, hormonal changes, and lifestyle even causing disruptions such as dysbiosis linked to diseases like head and neck squamous cell carcinoma (HNSCC). This chapter attempts to explore the anatomical and ecological diversity, site-specific microbial compositions, functional roles, developmental trajectories, and the challenges in understanding these microbial communities. Even though there were significant advances in sequencing technologies helping in identifying the microbial protective and pathogenic potential, hurdles like sampling difficulties and low biomass contamination tend to complicate the research process. Therefore it is of utmost importance to understand the baseline microbiome thereby helping in laying a foundation for studying its role in HNSCC, creating a pathway for microbial diagnostics and curative therapies.}, } @article {pmid42419833, year = {2026}, author = {Jams, J and Jayasinghe, RD}, title = {Introduction.}, journal = {Advances in immunology}, volume = {169}, number = {}, pages = {3-23}, doi = {10.1016/bs.ai.2026.03.005}, pmid = {42419833}, issn = {1557-8445}, mesh = {Humans ; *Microbiota ; *Dysbiosis/microbiology/immunology ; *Mouth/microbiology ; Biofilms ; Animals ; *Head and Neck Neoplasms/microbiology/etiology/immunology ; Host Microbial Interactions ; Host-Pathogen Interactions ; }, abstract = {Microorganisms colonize nearly all anatomical sites of the human body, with the oral cavity hosting one of the most diverse, accessible, and densely populated microbial ecosystems. The oral microbiome comprises a complex consortium of bacteria, fungi, viruses, archaea, and protozoa that inhabit distinct ecological niches. Each niche provides unique physicochemical conditions that shape microbial composition, structure, and function. In addition to oral and dental sites, oral biofilms frequently develop on dental materials, appliances, and prostheses, where surface characteristics such as roughness, hydrophobicity, and chemical composition further influence microbial adhesion and biofilm maturation, leading to marked differences at species and strain levels. Advances in culture-independent molecular technologies, particularly 16S rRNA gene sequencing, shotgun metagenomics, and other multi-omics approaches, have greatly enhanced understanding of oral microbial diversity, functional capacity, and host-microbe interactions beyond the limitations of conventional culture-based methods. In health, the oral microbiome exists in a state of dynamic equilibrium, or eubiosis, which contributes to local and systemic homeostasis. This balance is modulated by host factors such as saliva composition, immune responses, and oral hygiene practices, as well as environmental influences including diet, tobacco use, and alcohol consumption. Disruption of this equilibrium, termed dysbiosis, has been increasingly implicated in the pathogenesis of head and neck cancers. Emerging evidence suggests that microbial dysbiosis may promote carcinogenesis through chronic inflammation, immune modulation, production of carcinogenic metabolites, and direct interactions with epithelial cells. Understanding the microbiology of head and neck cancer therefore provides critical insights into disease initiation, progression, and potential diagnostic and therapeutic strategies.}, } @article {pmid42420265, year = {2026}, author = {Vilar Geraldi, M and Dwibedi, C and Jaiswal, R and Gregori, G and Zhou, X and Lv, B and Zheng, Y and Wang, X and Wu, H and Axelsson, KF and Bäckhed, F and Tremaroli, V and Lorentzon, M}, title = {Gut microbiota associates with frailty in older women.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42420265}, issn = {2041-1723}, support = {2023-01976, 2023-01976, 2022-06725, 2018-05973, 2024-03723,//Vetenskapsrådet (Swedish Research Council)/ ; Lorentzon, 2023-2024//Konung Gustaf V:s och Drottning Victorias Frimurarestiftelse (King Gustaf V and Queen Victoria's Foundation of Freemasons)/ ; 2024-0104//Familjen Erling-Perssons Stiftelse (Erling-Persson Family Foundation)/ ; Lorentzon, 2016//IngaBritt och Arne Lundbergs Forskningsstiftelse (Ingabritt and Arne Lundberg Research Foundation)/ ; KAW 2020.0239//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; }, mesh = {Humans ; Female ; Aged ; *Frailty/microbiology/mortality ; Aged, 80 and over ; *Gastrointestinal Microbiome/genetics/physiology ; Sweden/epidemiology ; Frail Elderly ; Bacteria/classification/genetics/isolation & purification ; Cohort Studies ; }, abstract = {Frailty is a multifactorial geriatric condition linked to increased mortality and adverse health outcomes and is associated with gut microbiome features that differ from those observed in healthy ageing. We analyze gut metagenomic profiles in relation to estimated frailty severity and frailty-related clinical outcomes assessed with an internally developed and validated Frailty Mortality Index (FMI) in the SUPERB cohort, comprising 2,081 Swedish women aged 75-80 years. The FMI is a composite measure that integrates functional, physiological and psychological dimensions associated with frailty and mortality risk, and shows stronger associations with mortality compared to the Charlson Comorbidity Index in the SUPERB cohort. The FMI is inversely associated with microbial diversity, gene richness, and predicted functional capacity, which are linked to physical function, mortality and fall-related injuries. A total of 404 bacterial species are significantly associated with FMI, and most show concordant associations in a Chinese cohort of 1,448 older adults. Here we show microbial signatures linked to frailty and mortality across different continents.}, } @article {pmid42420666, year = {2026}, author = {Ounjai, S and Liu, H and Zhou, Z and Correia, MP and Creedy, TJ and Andújar, C and Arribas, P and Vogler, AP}, title = {Phylogenetic Authentication of Amplicon Sequence Variants in Single-Specimen Metabarcoding of Tropical Insects.}, journal = {Molecular ecology resources}, volume = {26}, number = {5}, pages = {e70178}, pmid = {42420666}, issn = {1755-0998}, support = {//Institute for the Promotion of Teaching Science and Technology/ ; //Biodiversity Initiative of the Natural History Museum/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods/standards ; *Phylogeny ; *Coleoptera/classification/genetics ; Tropical Climate ; *Metagenomics/methods/standards ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA ; Genetic Variation ; DNA, Mitochondrial/genetics ; }, abstract = {High-throughput sequencing (HTS) allows large-scale DNA barcoding of individually tagged specimens ('megabarcoding'), but deep amplicon sequencing produces a mixture of authentic mitochondrial sequences together with nuclear pseudogenes (NUMTs), environmental and cross-sample contaminants, and sequencing artefacts. Standard approaches relying on read clustering or dominant-read selection often fail to classify these types, leading to incorrect taxonomic identifications and species counts. We developed an authentication framework by integrating abundance filtering, phylogenetic placement and taxonomic congruence. The workflow was applied to 18,533 morphospecies of tropical beetles (Coleoptera) from multiple biogeographic regions, which were imaged for family-level identification, prior to individual Illumina barcoding. Sequencing yielded > 36 million reads and 64,544 unique ASVs, which were evaluated against a reference phylogeny of > 13,000 mitogenomes. Authentication succeeded for 86.5% of quality-passing specimens (15,901 ASVs). Non-authentic sequences were technical artefacts (58.0%), environmental contamination including prey DNA (14.2%), intra-individual variants (NUMTs, heteroplasmy; 11.3%) and cross-sample contamination (7.5%). Authentication success and the proportions of failure categories varied markedly across trap types, sampling campaigns, taxonomic groups and sequencing runs. We identified 930 confirmed NUMTs based on consistent co-occurrence patterns and phylogenetic proximity to authenticated haplotypes. Single-specimen HTS data contain substantial biological and technical complexity not resolved by standard filtering methods. Our pipeline-agnostic, phylogenetically informed authentication framework achieves robust recovery of validated barcodes while retaining informative secondary variants, improving the accuracy of molecular ASV data to a standard sufficient for inclusion in barcode reference databases and the phylogenetically informed DNA barcoding of tropical insects.}, } @article {pmid42420833, year = {2026}, author = {Luo, D and Lu, F and Yang, L and Gan, Z and Zhang, X and Zhao, Z and Dong, R}, title = {Harnessing probiotics to combat nonylphenol toxicity: a multiomics approach of gut microbiome remodelling in Silurus meridionalis.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-13161-4}, pmid = {42420833}, issn = {1471-2164}, support = {GZSTYYCYJSTX-202605//Guizhou Modern Agricultural Industry Technology System of China/ ; 2024 (No. 079//the Guizhou Provincial Key Technology R&D Program/ ; 32460918//the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: As a ubiquitous environmental endocrine disruptor, nonylphenol (NP) threatens aquatic organisms, driving the need for sustainable mitigation strategies. While probiotics represent promising eco-friendly supplements, their molecular mechanisms against NP toxicity remain unclear. In this study, S. meridionalis received 7-week of probiotic (Bacillus subtilis and Lactobacillus acidophilus) pretreatment followed by 15 days of NP exposure. Integrated metagenomics, transcriptomics, and metabolomics analyses, with Reverse transcription quantitative real-time PCR (RT‒qPCR) and Enzyme-linked immunosorbent assay (ELISA) validation, were performed to elucidate microbial, genetic and metabolic responses. Growth performance, including the specific growth rate (SGR) and weight gain rate (WGR), was concurrently assessed.

RESULTS: NP exposure significantly suppressed WGR and SGR, and induced gut microbiota dysbiosis alongside and lipid metabolism disorders in S. meridionalis. Probiotic pretreatment effectively reversed these toxic effects and restored the inhibited WGR and SGR. Multiomics integration revealed that the protective effects of probiotics were mediated by a coherent "microbe-host" co-metabolism network across 3 progressive layers: (1) Microbial Remodelling: in which beneficial taxa (e.g., Bacteroides eggerthii and Cetobacterium sp.) were enriched, and the functional capacity for short-chain fatty acid (SCFA) synthesis and ethanolamine metabolism was enhanced; (2) Host Gene Regulation: in which key lipid metabolism genes (ek1, cept1, ept1, mogat2, and abcg2a) were upregulated, and lipase activity was restored; and (3) Metabolic Pathway Activation and Physiological Repair: in which the activity of the NP-suppressed Kennedy pathway was reactivated, thereby promoting phosphatidylethanolamine (PE) and phosphatidylcholine (PC) synthesis and ultimately restoring gut barrier function. These results were further were corroborated by RT‒qPCR and ELISA.

CONCLUSION: This study systematically elucidated that probiotics alleviated NP toxicity by remodelling a "microbiota-host Kennedy pathway gene-metabolite (PE and PC)-growth performance" regulatory network. The key mechanism is the beneficial microbiota activating the host Kennedy pathway and restoring gut phospholipid homeostasis and barrier function. These findings provide a theoretical basis for developing targeted, lipid metabolism focused probiotic feed additives for use in sustainable aquaculture.}, } @article {pmid42421628, year = {2026}, author = {Chen, X and Jamieson, L and Weyrich, LS and Nath, S}, title = {Global Landscape of Publicly Available Human Oral Microbiome Data.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345261456612}, doi = {10.1177/00220345261456612}, pmid = {42421628}, issn = {1544-0591}, abstract = {Despite rapid growth in oral microbiome research, it remains unclear how well publicly available data reflect the diversity of the global human population. This study systematically evaluated the geographic and sampling-type representativeness of publicly available human oral microbiome data. A global meta-research analysis of publicly available human oral microbiome records in the NCBI BioSample database released up to December 31, 2025, was conducted. Records were retrieved, harmonized, and analyzed across 4 dimensions: geographic origin, oral sampling type, temporal trends, and population-adjusted representation using a derived representation index (RI). A total of 222,454 BioSamples from 1,600 studies were identified, spanning 92 countries and 4 major oral sampling-type groups: oral fluids, oral mucosa and surfaces, dental plaque and calculus, and special or lesion-associated sites. Geographic distribution was highly concentrated; nearly half of all geographically annotated samples originated from the United States and China, while 61% of countries worldwide contributed no samples. Low- and middle-income regions, including Central and Southern Asia (RI = -12.76) and Sub-Saharan Africa (RI = -11.21), were underrepresented relative to their population sizes. Sampling-type distribution was similarly uneven, with saliva samples comprising more than half of all samples. In contrast, disease-relevant sites, including carious lesions, periapical lesions, and the dental pulp, each represented less than 0.2% of the dataset. Together, these findings underscore that publicly available human oral microbiome data remain unevenly distributed across geographic origin and sampling types, reflecting structural and practical factors that have persisted over time. Deliberate efforts to improve global representation, sampling diversity, and metadata standardization are needed to build a more scientifically robust oral microbiome evidence base.}, } @article {pmid42421935, year = {2026}, author = {Memida, T and Jaar, JC and Chen, T and Cao, G and Kuriki, N and Abdolahinia, ED and Okamoto, M and Shindo, S and Yamashita, S and He, X and Suzuki, M and Vardar, S and Kawai, T and Han, X}, title = {Hyperglycemia and systemic inflammation differentially shape immune dysregulation, tissue destruction, and microbiota in experimental periodontitis and peri-implantitis in diabetic mice.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1847456}, pmid = {42421935}, issn = {1664-3224}, mesh = {Animals ; *Peri-Implantitis/immunology/microbiology/pathology/etiology ; *Periodontitis/immunology/microbiology/pathology/etiology ; Mice ; *Hyperglycemia/immunology/microbiology ; *Microbiota/immunology ; *Diabetes Mellitus, Experimental/immunology/complications/microbiology ; *Inflammation/immunology ; Disease Models, Animal ; Cytokines/metabolism ; Male ; }, abstract = {AIM: To investigate the impact of hyperglycemia and systemic inflammation on experimental periodontitis/peri-implantitis in diabetic mice, focusing on osteoimmunological dysregulation and oral microbial alteration.

MATERIALS AND METHODS: After implant placement, diabetic db/db mice were treated with Liraglutide, Indomethacin, or both, followed by ligature-induced experimental periodontitis/peri-implantitis. Samples were analyzed for bone loss, inflammatory cytokines, osteoclast activity, RAGE expression, IL-17-associated inflammatory responses, and Treg infiltration. The periodontal/peri-implant microbiota were examined by metagenomics and tested in vitro for inflammatory cytokine induction.

RESULTS: Liraglutide, but not indomethacin, effectively reduced bone loss, immune cell infiltration, RAGE, IL-17A expression, and restored Foxp3[+] Treg presence. Post-treatment cytokine responses were slightly different between peri-implantitis sites compared to those in periodontitis sites. Oral microbiota composition from diabetic mice differed significantly from that of normoglycemic mice. Liraglutide treatment produced the greatest deviation from the ligation-only profile and shifted the microbiome toward normoglycemic control. The peri-implant microbiome was more resistant to interventions than the periodontal communities. Hyperglycemia control alleviated microbiome-induced pro-inflammatory responses in vitro.

CONCLUSIONS: Diabetic hyperglycemia is a more predominant driver than systemic inflammation in exacerbating periodontitis/peri-implantitis tissue destruction, immune dysregulation, and eliciting a pro-inflammatory oral microbial environment. The local inflammatory response and microbial alteration around the tooth and implant were similar but not identical.}, } @article {pmid42421950, year = {2026}, author = {Lu, W and Wang, Y and Zhang, J and Li, Y and Huang, L and Yang, W and Zhou, S and Zhou, M and Chen, Y and Wu, R and Wang, Y and Zhang, H and Wan, J and Xia, F and Zhang, Z and Shen, L}, title = {Fecal microbiome and metabolome dynamics during immunotherapy-based total neoadjuvant therapy in rectal cancer: associations with treatment response and toxicity.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1871586}, pmid = {42421950}, issn = {1664-3224}, mesh = {Animals ; Female ; Humans ; Male ; Mice ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Immunotherapy/adverse effects/methods ; *Metabolome ; Metabolomics ; Multiomics ; *Neoadjuvant Therapy/adverse effects/methods ; *Rectal Neoplasms/therapy/metabolism/microbiology/immunology ; Treatment Outcome ; Clinical Trials, Phase II as Topic ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; }, abstract = {BACKGROUND: Immunotherapy-based total neoadjuvant therapy (iTNT) is a promising strategy for microsatellite-stable locally advanced rectal cancer (LARC), yet therapeutic response and treatment-related toxicity remain heterogeneous. Integrated fecal microbiome and metabolome profiling may provide non-invasive biomarkers and functional clues for optimizing iTNT.

METHODS: We conducted a longitudinal fecal multi-omics study using samples from patients with microsatellite-stable LARC enrolled in the TORCH trial (NCT04518280). A total of 102 fecal samples were collected before treatment, during treatment, and after completion of iTNT. Metagenomic sequencing and untargeted metabolomics were integrated to characterize longitudinal microbial and metabolic changes. We also examined baseline features associated with therapeutic response, and multi-omics signatures linked to hematologic and gastrointestinal toxicities. A murine tumor model treated with radiotherapy plus immunotherapy, with or without GABA supplementation, was used for functional testing of the response-associated metabolite.

RESULTS: iTNT induced longitudinal gut microbiome remodeling. This remodeling was characterized by altered community structure, increased alpha diversity, enhanced microbial network connectivity, enrichment of Firmicutes-associated taxa, and depletion of Bacteroidetes and Proteobacteria. Fecal metabolomic profiles also shifted during treatment, with prominent changes in amino acid-related pathways and significant concordance between microbial and metabolic profiles. Responders were enriched in several Firmicutes-associated genera, including Ruminococcus, Anaerostipes, and Coprobacillus. In contrast, non-responders showed enrichment of Klebsiella and response-associated metabolites including gamma-aminobutyric acid (GABA). Microbial functional and metabolomic pathway analyses showed convergent enrichment of arginine and proline metabolism, which includes an alternative GABA-related metabolic route. Functionally, GABA supplementation weakened the antitumor efficacy of radiotherapy plus immunotherapy and was accompanied by systemic T cell dysfunction. In addition, specific microbial taxa and fecal metabolic features were associated with hematologic toxicity and diarrhea severity, with baseline metabolites showing exploratory potential for toxicity stratification.

CONCLUSION: This study provides a longitudinal fecal microbiome-metabolome resource for iTNT in LARC and identifies candidate microbial and metabolic features associated with treatment response and toxicity. GABA was functionally supported as a response-associated immunomodulatory metabolite, while candidate microbial functional signals warrant further mechanistic validation.}, } @article {pmid42422444, year = {2026}, author = {Lu, T and Sun, S and Teng, T and Zhang, J and Cao, Q and Ren, H}, title = {Bartonella henselae mediastinal lymphadenitis mimicking malignancy with critical airway compression in a child: a case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1871232}, pmid = {42422444}, issn = {2296-2360}, abstract = {Cat-scratch disease, caused by Bartonella henselae, is usually a self-limited infection presenting with regional lymphadenopathy in children. Thoracic involvement is uncommon, and mediastinal lymphadenitis with clinically significant airway compression may closely mimic malignancy. We report a previously healthy 6-year-old boy who presented with persistent fever, mild cough, weight loss, and cervical lymphadenopathy. Chest computed tomography revealed necrotic mediastinal lymphadenopathy forming a mass-like lesion with compression of the right middle lobe bronchus and associated atelectasis. Bronchoscopy showed severe bronchomalacia with approximately 90% luminal narrowing, despite only mild respiratory symptoms. Initial antimicrobial therapy failed to improve the clinical or radiologic abnormalities. Because of constitutional symptoms and a necrotic mediastinal mass, lymphoma was strongly suspected; however, bone marrow examination was unrevealing. During biopsy of the mediastinal lesion, purulent material was encountered. Histopathology demonstrated necrotizing granulomatous inflammation, and metagenomic next-generation sequencing identified Bartonella henselae, establishing the diagnosis of cat-scratch disease. Treatment with doxycycline and rifampin led to prompt resolution of fever and marked radiologic improvement, with substantial relief of airway compression. This case highlights that Bartonella henselae infection can present as a necrotic mediastinal mass with severe but reversible airway compression in children. Cat-scratch disease should be considered in the differential diagnosis of pediatric mediastinal masses, particularly when inflammatory features, cat exposure, and discordant respiratory symptoms are present. Integration of imaging, bronchoscopy, pathology, and molecular testing may prevent misdiagnosis as malignancy and underestimation of airway risk.}, } @article {pmid42422454, year = {2026}, author = {Wang, X and Zhang, Y and Ye, M and Kong, C and Diao, M}, title = {Clinical and stool microbiome correlates of simple post-ERCP hyperamylasemia in children undergoing therapeutic ERCP for pancreatobiliary obstructive disorders: an exploratory pilot study.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1851821}, pmid = {42422454}, issn = {2296-2360}, abstract = {BACKGROUND: Simple post-ERCP hyperamylasemia is a common biochemical finding after therapeutic endoscopic retrograde cholangiopancreatography (ERCP), but pediatric data integrating procedural characteristics with stool microbiome features remain limited.

METHODS: We performed an exploratory single-center observational pilot study of 24 successful therapeutic ERCP procedures in children younger than 18 years with pancreatobiliary obstructive disorders between January 2024 and December 2025. The primary endpoint was simple post-ERCP hyperamylasemia, defined as serum amylase >3 times the upper limit of normal within 24 h after ERCP without new or worsening abdominal pain. Baseline clinical variables, predefined stool microbiome features derived from pre-ERCP metagenomic data (Shannon diversity, Enterococcus abundance, and Bifidobacterium abundance), and intraprocedural variables were compared between groups. Exploratory signal prioritization was used only to identify candidate associations for future validation.

RESULTS: Hyperamylasemia occurred in 8/24 procedures (33.3%). Compared with non- hyperamylasemia group, the affected children had higher baseline gamma-glutamyl transferase and C-reactive protein, longer procedure time, more difficult cannulation, more inadvertent pancreatic duct cannulation, more pancreatic contrast injection, and more rescue precut access. Stool microbiome features in the hyperamylasemia group included lower Shannon diversity, higher Enterococcus abundance, and lower Bifidobacterium abundance. Procedure time and Shannon diversity emerged as the most interpretable combined signals, but all model estimates should be viewed cautiously because of the small event count.

CONCLUSION: In this pilot dataset, simple post-ERCP hyperamylasemia clustered with technically demanding procedures and a low-diversity, Enterococcus-enriched stool microbiome profile. These findings are hypothesis-generating and require prospective multicenter validation before they can inform pediatric ERCP surveillance or risk-stratification research.}, } @article {pmid42422751, year = {2026}, author = {Wang, H and Han, Y and Chen, C and Chen, K and Zhang, Y and Wang, Z and Qi, L}, title = {Moisture-mediated resource availability shapes rhizosphere and bulk soil microbial structure and function post-rainfall.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1752099}, pmid = {42422751}, issn = {1664-302X}, abstract = {INTRODUCTION: Rainfall pulses drive rapid ecological changes in alpine grasslands, but their compartment-specific effects on short-term soil microbial dynamics remain unclear.

METHODS: We investigated the structural and functional responses of rhizosphere versus bulk soil microbiomes associated with Poa alpigena in the Qinghai Lake Basin. Paired soil samples were collected before rainfall and 2 h after a heavy rainfall event and analyzed by shotgun metagenomic DNA sequencing.

RESULTS: Rainfall triggered compartment-specific shifts in microbial community assembly. In the rhizosphere, rainfall significantly reduced alpha diversity (Chao1 and Richness indices) but enhanced community evenness (Simpson and Shannon indices), whereas bulk soil diversity remained relatively stable. DNA-based functional profiling revealed a short-term shift in the rhizosphere from a pre-rain "carbon-oriented" metabolic potential to increased relative abundance of genes involved in central carbon pathways, amino acid degradation, and chemotaxis post-rainfall. Notably, sequences affiliated with Paraburkholderia were significantly enriched in the nitrogen-limited rhizosphere immediately after rainfall, suggesting a potential link to nitrogen cycling. In contrast, bulk soil communities shifted toward gene categories for labile carbon utilization and bacterial secretion systems. Co-occurrence network analysis indicated that rainfall simplified microbial interactions and weakened the coupling between microbial communities and soil physicochemical properties.

DISCUSSION: These findings demonstrate that rainfall pulses trigger rapid, niche-dependent changes in soil microbiomes at the DNA level, driven by moisture-mediated shifts in resource availability, and highlight distinct ecological strategies in rhizosphere and bulk soil compartments.}, } @article {pmid42422832, year = {2026}, author = {Wang, H and Zhu, Y and Cheng, AX and Zhang, C}, title = {Acute retinal necrosis presenting exudative retinal detachment: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1746774}, pmid = {42422832}, issn = {2296-858X}, abstract = {BACKGROUND: Acute retinal necrosis (ARN) is a severe, rapidly progressive viral retinitis that is commonly complicated by rhegmatogenous retinal detachment in its late stage. However, the presentation of ARN with exudative retinal detachment (ERD) in the early phase is exceptionally rare, particularly when caused by varicella zoster virus (VZV) in an adult patient. This report highlights this atypical presentation, which initially occurred without definite evidence of retinal necrosis, posing a diagnostic challenge.

CASE PRESENTATION: A 43-year-old woman presented with acute blurred vision, eye redness, and ocular pain in the left eye of 3 days' duration. Initial clinical examination revealed ciliary congestion, vitritis, optic disc swelling, and a non-rhegmatogenous retinal detachment. Optical coherence tomography demonstrated optic disc and macular edema with intraretinal cystic spaces and a serous retinal detachment temporal to the fovea. Given the atypical presentation, the patient was initially treated with corticosteroids. Two days later, characteristic peripheral retinal necrotic lesions appeared, prompting immediate aqueous humor sampling. Metagenomic testing confirmed VZV infection. The patient was then treated aggressively with systemic intravenous acyclovir, intravitreal ganciclovir injections, and systemic corticosteroids. This regimen led to rapid resolution of the retinal detachment and complete resolution of the retinal lesions, with stable visual acuity maintained at 1 month of follow-up.

CONCLUSION: Exudative retinal detachment is a rare manifestation of early-stage ARN. In uveitis patients presenting with ERD who show a poor response to initial anti-inflammatory therapy, viral infection (particularly VZV) should be considered in the differential diagnosis. Aggressive combined systemic and intravitreal antiviral therapy, alongside corticosteroids, is critical for achieving favorable anatomical and visual outcomes in these challenging cases.}, } @article {pmid42422873, year = {2026}, author = {Pithia, N and Kesavan, K and Lee, A and Yang, S and Kaur, I}, title = {Clinical impact of plasma cell-free DNA metagenomic next-generation sequencing testing in neonatal and infant populations.}, journal = {Antimicrobial stewardship & healthcare epidemiology : ASHE}, volume = {6}, number = {1}, pages = {e201}, pmid = {42422873}, issn = {2732-494X}, abstract = {OBJECTIVE: Plasma cell-free DNA metagenomic next-generation sequencing (cf-mNGS) tests offer the ability to detect microbial DNA from a single blood sample; however, its clinical utility in infants remains incompletely characterized. This study aims to evaluate the real-world clinical impact of plasma cf-mNGS testing in the neonatal and infant population.

DESIGN: Retrospective cohort study.

SETTING: A large academic medical center in Los Angeles, California.

PATIENTS: 95 hospitalized neonates and infants (≤12 months of age).

METHODS: Clinical impact was adjudicated using predefined criteria.

RESULTS: We reviewed 95 unique plasma cf-mNGS testing episodes performed between February 2018 and August 2024. The mean age at testing was 4.2 months (SD, 3.8). All patients were hospitalized in the intensive care unit at the time of testing. Tests were most frequently performed for evaluation of "culture-negative sepsis" (30.5%), unexplained hospital-onset fevers (25.3%), and multiorgan failure (21.1%). Plasma cf-mNGS testing did not influence clinical management in the majority of cases (86.3%; 95% CI, 78.0%-91.8%). Positive clinical impact occurred in 5/95 cases (5.3%; 95% CI, 2.3%-11.7%), where plasma mNGS results assisting in antimicrobial de-escalation/discontinuation or earlier/new diagnoses. Negative clinical impact occurred in 4/95 cases (4.2%; 95% CI, 1.6%-10.3%), with plasma cf-mNGS results prompting unnecessary investigations or treatment.

CONCLUSIONS: Our findings do not support the routine use of plasma cf-mNGS testing for indications including "culture-negative sepsis" in neonatal and infant populations.}, } @article {pmid42423254, year = {2026}, author = {Irshad, F and Nazir, A}, title = {Metagenomic exploration of indigenous bacteria with their bioaugmentation for enhanced phytobial remediation of tannery effluent with Lemna minor.}, journal = {International journal of phytoremediation}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/15226514.2026.2698048}, pmid = {42423254}, issn = {1549-7879}, abstract = {Despite the toxic and persistent nature of tannery effluent (TE), limited research studies have evaluated Lemna minor-based phytobial remediation in real TE. The current study aimed at TE remediation using L. minor with the assistance of indigenous heavy metals (HMs) tolerant bacterial strains. Five coded TE indigenous bacterial strains (S1WC4, S2WC3, S2WC2, S3WC1 and S1WC2), isolated from TE samples were applied in combination with L. minor for treatment of TE dilutions (2%, 5%, 10% and 15%), while pond water (PW) treatments were used as a control. The bacterial community was also profiled through 16S rRNA metagenomic amplicon sequencing. Results showed that treatments aided by consortia demonstrated higher efficiencies for metal removal, i.e., Pb removal ∼80-95%, Cr removal ∼80-90%, Cu removal ∼55-83%, Cd removal ∼70-85%. The consortia treatments also enhanced bioaccumulation factors (e.g.,BAF up to 18.4 for Pb and 8.2 for Cr in 5% TE), with higher biomass and SPAD values compared to control treatments. The TE bacterial community was dominated by stress tolerant bacterial taxa, and the ecological importance of these taxa was evaluated with PICRUSt2-analysis, predicting pathways associated with community survival under HMs stress conditions. Biologically driven removal was confirmed in logistic modeling that showed time-dependent HMs removal. Results of the study, therefore, conclude that bioaugmentation had a significant effect on the performance of the remediation system when compared with control treatments (plant-only treatments).}, } @article {pmid42423734, year = {2026}, author = {Tomar, SS and Khairnar, K}, title = {Upper Respiratory Tract Resistome Exhibits SARS-CoV-2-associated Antimicrobial Resistance Patterns.}, journal = {Current microbiology}, volume = {83}, number = {9}, pages = {}, pmid = {42423734}, issn = {1432-0991}, mesh = {Humans ; *SARS-CoV-2/drug effects/genetics/isolation & purification ; *COVID-19/virology/microbiology ; India ; *Bacteria/drug effects/genetics/classification/isolation & purification ; Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics/drug effects ; }, abstract = {SARS-CoV-2 infection can influence the antimicrobial resistance (AMR) profiles of the upper respiratory tract (URT), although the extent and nature of these alterations remain insufficiently understood. In this study, we analysed 95 URT swab samples, including 48 SARS-CoV-2-positive cases and 47 RT-PCR-negative controls, collected from five districts of central India. Metagenomic DNA sequencing was performed on the Illumina NextSeq 550 platform, and the data were analysed using the Chan Zuckerberg Initiative (CZ ID) pipeline. Alpha diversity indices (Chao1, Shannon, and Simpson) did not differ significantly (p = 0.264, 0.985, and 0.902, respectively). Beta-diversity analysis revealed distinct clustering of SARS-CoV-2 and control resistomes. Differential resistome analysis identified 22 significantly altered AMR genes, of which 21 were enriched in the SARS-CoV-2 group. Pathogen-of-origin analysis linked several AMR genes to opportunistic pathogens, including Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus. Bayesian regression analysis identified SARS-CoV-2 infection as a significant factor associated with increased AMR abundance (β = 1.549, HDI [1.409, 1.691]), whereas age and location were not significantly associated. Results demonstrate an association between SARS-CoV-2 infection and alterations in the URT resistome, warranting further investigation into the mechanisms linking viral infection and antimicrobial resistance.}, } @article {pmid42423979, year = {2026}, author = {Hu, C and Zeng, X and Wu, X and Yan, D and Yuan, J and Qu, L and Dou, M and Yang, Y}, title = {Mechanistic insights into iron cycling-driven nitrogen removal from biogas slurry via coupled iron-based denitrification and Feammox.}, journal = {Environmental geochemistry and health}, volume = {48}, number = {10}, pages = {}, pmid = {42423979}, issn = {1573-2983}, support = {52300222//National Natural Science Foundation of China/ ; 221100320200//Key Science and Technology Project of Henan Province/ ; 242300421224//Natural Science Foundation of Henan Province/ ; 25A610006//Applied Research Plan of Key Scientific Research Projects in Colleges and Universities of Henan Province/ ; }, mesh = {*Denitrification ; *Nitrogen/metabolism/isolation & purification ; *Biofuels ; *Iron/metabolism/chemistry ; Bioreactors/microbiology ; Oxidation-Reduction ; Bacteria/metabolism/genetics ; Ferrous Compounds/metabolism ; }, abstract = {In this study, ferrous-based denitrification was combined with Feammox (Fe(III) reduction coupled with anaerobic ammonium oxidation) to trigger NH4[+] removal through intermittently adding NOx[-] (NO2[-] and NO3[-]) into biogas slurry. The results showed that NOx[-] oxidized Fe(II), then the generated Fe(III) was reduced to Fe(II) again, resulting in a continuous iron cycling and nitrogen removal. On day 35, the total nitrogen removal efficiencies in the NO2[-] (67.52%) and NO3[-]-added (52.32%) groups were significantly higher than that of the control (without NOx[-]) (P < 0.05). Nitrifying and Anammox microorganisms were not detected in the NOx[-]-added reactors, while Feammox functional microorganisms (iron-reducing bacteria) were enriched (1.08%-1.51%), and the electron transfer capacities were also increased by 7.69%-16.08%. Metagenomic analysis showed that the NO3[-] group had more nitrate reductase genes but fewer downstream denitrification genes than the control group, indicating that NO2[-] accumulated as a key intermediate. NO3[-] could not directly oxidize Fe(II), and no nitrate-dependent Fe(II)-oxidizing microorganisms were detected. Moreover, the Fe(II) oxidation products in the NO3[-]-added reactors were identical to those generated by abiotic NO2[-] oxidation, suggesting that NO2[-] produced via partial denitrification was likely responsible for Fe(II) oxidation. Based on this, a possible metabolic pathway coupling nitrogen and iron transformations was proposed, in which partial NO3[-] reduction to NO2[-] may contribute to Fe(II) oxidation and subsequent Fe(III)-mediated NH4[+] removal via Feammox. This study provided a method for dealing with biogas slurry, and also offers a new approach for simultaneously removing NOx[-] and NH4[+].}, } @article {pmid42424147, year = {2026}, author = {Ebel, ER and Kulkarni, AS and Mongad, DS and Olm, MR and Devi, SI and Mir, BA and Ozarkar, S and Sonnenburg, ED and Shouche, YS and Sonnenburg, JL and Dhotre, DP}, title = {Gut microbiomes of tribal communities in India vary with dairy and grain consumption.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2694242}, doi = {10.1080/19490976.2026.2694242}, pmid = {42424147}, issn = {1949-0984}, mesh = {Humans ; India ; Feces/microbiology ; *Diet ; *Edible Grain/metabolism ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; *Dairy Products ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Female ; Gastrointestinal Tract/microbiology ; }, abstract = {Highly diverse gut microbiomes of non-industrialized populations share similarities with ancestral states of symbiosis and are linked to low rates of chronic inflammatory diseases. Yet there is still limited understanding of the diverse array of non-industrialized gut microbiomes throughout the world, including among the tribal populations of India. In this study, we surveyed dietary and fecal microbiome variation among 76 adults from eight tribal communities in four biogeographic regions of India, including Warli on the western coast, Gond and Madia in the northeast Deccan Plateau, Kabui (or Rongmei Naga) in the northeast hills of the Himalayas, and Balti, Boto, Brokpa, and Purigpa in the northwest Trans-Himalayas. Metagenomic and 16S sequencing of fecal samples identified Segatella, Agathobacter, and Faecalibacterium as core members of the gut microbiome of all populations, with Segatella copri (formerly Prevotella copri) dominant at mean 25%-47% relative abundance. Four Trans-Himalayan populations with diets uniquely defined by dairy and diverse cereals had elevated gut alpha diversity and distinct beta diversity, driven by prevalent and abundant Bifidobacterium as well as taxa shared with the ruminant microbiome. Strains of B. adolescentis present in the dairy-consuming populations were genetically distinct from industrialized strains around the world and encoded CAZymes consistent with selection by dairy and grain consumption. The gut microbiomes of a minority of subjects shared taxonomic and functional features with a previously described sample of Californians, suggesting that the pressures posed by globalization could be impacting the microbiomes of tribal populations. These results highlight the nutritional and microbiological contribution of dairy livestock in shaping gut communities and emphasize the large effect that lifestyle can have on the diversity and function of non-industrialized gut microbiomes.}, } @article {pmid42424326, year = {2026}, author = {Brown, CR and Yacoub, MN and Bogan, JE and Buehler, MD and Hoffman, ML and Krumbeck, JA and Loughman, ZJ}, title = {Cloacal microbiome variation in wild and captive Eastern Indigo Snakes (Drymarchon couperi) with and without Cryptosporidium serpentis infection.}, journal = {PloS one}, volume = {21}, number = {7}, pages = {e0350824}, doi = {10.1371/journal.pone.0350824}, pmid = {42424326}, issn = {1932-6203}, mesh = {Animals ; *Cloaca/microbiology/parasitology ; *Cryptosporidium/isolation & purification ; *Snakes/microbiology/parasitology ; *Microbiota ; *Cryptosporidiosis/microbiology/parasitology ; Animals, Wild/microbiology ; }, abstract = {The Eastern Indigo Snake (EIS; Drymarchon couperi), a federally threatened species native to the southeastern United States, serves as a valuable model for examining the effects of captivity and infection on gastrointestinal microbial composition in reptiles. As an alternative to direct gut sampling, we examined the cloacal microbiomes of EISs to evaluate changes in microbial community structure across our study groups. This study assessed the cloacal microbiome of wild and captive EISs using shotgun metagenomic sequencing. Samples were divided into three groups for comparative microbiome analysis: captive snakes positive for Cryptosporidium serpentis (C. serpentis), captive snakes negative for C. serpentis, and wild snakes. Alpha (Shannon index, paired Wilcoxon test) and beta diversity (Bray-Curtis dissimilarity, PERMANOVA, CAP) metrics were used to assess microbial diversity and community composition across groups. Furthermore, a linear discriminant analysis effect size (LEfSe) was used to identify microbial taxa significantly enriched in C. serpentis-positive versus C. serpentis-negative captive snakes. Bacterial, fungal, bacteriophage, nematode, and protozoan taxa were significantly enriched in C. serpentis-positive snakes compared with C. serpentis-negative captive snakes, based on a linear discriminant analysis (LDA) score ≥ 2.5 and p ≤ 0.05. Total taxa species Shannon diversity was consistent between C. serpentis-positive and negative captive snakes (p = 0.55) while wild snake samples were significantly more diverse (p = 0.026). Wild snakes also exhibited a significantly increased Shannon diversity of fungi (p = 0.044), protozoa (p = 0.012), and nematodes (p = 0.008) compared to their captive counterparts. This study offers the first in-depth characterization of the cloacal microbiome in reptiles, specifically in EISs, using shotgun metagenomic sequencing. The findings establish a foundation for exploring microbiota-host interactions with implications for reptile health, disease ecology, and conservation management.}, } @article {pmid42424815, year = {2026}, author = {Tang, Q and Zhang, Y and Garza, DR and Ruan, C and Liu, B and Rocha, U and Shen, P and Wei, Y and Deng, Y and Zhang, J and Richnow, HH}, title = {Virus-mediated fate of antimicrobial resistance genes in livestock manure anaerobic digestion.}, journal = {Water research}, volume = {305}, number = {}, pages = {126401}, doi = {10.1016/j.watres.2026.126401}, pmid = {42424815}, issn = {1879-2448}, abstract = {Antimicrobial resistance (AMR) poses a critical global health challenge, with livestock manure acting as a significant environmental reservoir for antimicrobial resistance genes (ARGs). Anaerobic digestion (AD) is a pivotal process for mitigating ARG dissemination at the livestock-environment-human interface. This study aims to elucidate the global dynamics of ARGs in AD systems, focusing on virus-host interactions and arms race, to identify actionable strategies for AMR control. We analyzed 205 metagenomic (4.5 Tb) and 36 meta-transcriptomic (640 Gb) datasets, including 15 newly generated datasets, revealing that pig manure AD harbors the highest ARG abundance (0.668 ARGs/16S rRNA), while AD systems generally exhibit limited transcriptional activation of ARGs. We constructed a viral dataset for livestock manure AD (GVD_LMAD), comprising 59,316 DNA and 727 RNA viral operational taxonomic units (vOTUs). Virus-host interactions established by CRISPR-Cas spacer, tRNA and homology matches revealed 889 lytic infections of antimicrobial-resistant bacteria (ARB) compared to only 18 ARG transduction events. Further analysis showed that the relative abundance of vOTUs assigned to the reduction role (4.11% ± 3.19%) was substantially higher than that of reproduction (0.72% ± 0.64%) and transduction (0.19% ± 0.30%), demonstrating that, among viral processes, lysis outweighs transduction in contributing to ARG abundance reduction in AD. Furthermore, an antiviral defense system (ADS) catalogue (GADSC_LMAD), derived from 2760 high-quality metagenome-assembled genomes (MAGs) containing 39,307 ADS, with ADS prevalence in ARB (7.8 ± 6.0 per MAG), indicating an intensified virus-host arms race in AD that may shield ARB from phage lysis. The resulting CRISPR-Cas immune network with expressed spacers targets foreign ARG-carrying sequences (primarily plasmids and ICEs), suggesting a mechanism that restricts horizontal gene transfer (HGT) via conjugation and transformation, despite shielding ARB from phage lysis. Collectively, these findings highlight that viral communities significantly contribute to ARG reduction through phage lysis relative to transduction, while the ADS-mediated arms race, despite protecting ARB, constructs a biological firewall that potentially limits HGT of ARGs. This study provides novel insights into virus-host dynamics as a key mechanism for controlling ARG dissemination in AD systems.}, } @article {pmid42425006, year = {2026}, author = {Hao, Q and Jiang, L and Yu, H and Chen, C and Deng, Z and Zhou, H and Deng, Y and Lai, H and Cao, J and Zhang, C}, title = {Hydrostatic pressure drives metabolic strategies for anaerobic hydrocarbon degradation in cold seep sediments: from autonomy to syntrophic cooperation revealed by metagenomics.}, journal = {Marine environmental research}, volume = {221}, number = {}, pages = {108254}, doi = {10.1016/j.marenvres.2026.108254}, pmid = {42425006}, issn = {1879-0291}, abstract = {Petroleum pollution poses a significant threat to marine ecosystems, extending its impact to deep-sea environments. Cold seeps represent unique deep-sea ecosystems and are natural hotspots for studying anaerobic hydrocarbon degradation, yet the specific influence of hydrostatic pressure on the microbial process remains poorly understood. In this study, we established incubation systems with sediments from the Haima cold seep, enriched with n-hexadecane and naphthalene under varying hydrostatic pressures (0.1, 5, and 11 MPa). After seven months, naphthalene degradation consistently exceeded that of n-hexadecane across all pressures, yet was suppressed under high-pressure conditions. Notably, pressure selectively shaped the community structure: Marinobacter and Desulfoscipio were enriched at 0.1 MPa, while Halomonas and Sulfitobacter maintained stable dominance under high pressure. Metagenomic analysis revealed 0.1-bin.35, a bacterium affiliated with Desulfotomaculia, as a key hydrocarbon degrader encoding self-sufficient pathways for hydrocarbon degradation and dissimilatory sulfite reduction. However, under high pressure, dominant Sulfitobacter (5-bin.13, 11-bin.4) likely relied on syntrophy with sulfate-reducing bacteria to complement its incomplete catabolic pathways for hydrocarbons. This study reveals key hydrocarbon degraders in cold seep environments, advancing our understanding of deep-sea hydrocarbon-degrading microbiomes. Moreover, it unveils a possible pressure-induced adaptation strategy from autonomous degradation to syntrophic cooperation, providing insights into their ecological significance and potential applications in deep-sea oil pollutant bioremediation.}, } @article {pmid42425460, year = {2026}, author = {Feng, B and Chen, J and Wang, C and Fu, J and Wang, R and Zhang, J and Zhang, B and Cheng, C}, title = {Fate of antibiotic resistance genes during rural domestic wastewater treatment: Anaerobic unit as enrichment hotspot versus aerobic unit as attenuation zone.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135356}, doi = {10.1016/j.biortech.2026.135356}, pmid = {42425460}, issn = {1873-2976}, abstract = {Rural domestic wastewater treatment systems are important but understudied reservoirs for antibiotic resistance genes (ARGs), whose full-process migration mechanisms remain unclear. Herein, the contribution of each treatment unit of ARGs was investigated using metagenomic methods across two seasons in typical rural domestic wastewater treatment systems. Although a removal efficiency (69 % in winter and 22 % in summer) was observed for ARGs, higher antibiotic residues and temperature dramatically induced ARG occurrence in wastewater and horizontal gene transfer (HGT) risk during wastewater treatment. The ARG abundances in the anaerobic unit increased by 1.6-2.1 fold compared to the regulating pool, primarily driven by elevated mobile genetic element (MGE) activity. In sharp contrast, ARG reduction was achieved through ARG host removal and suppressed HGT potential in the aerobic unit. Notably, mobile ARGs were dominated by tetracycline resistance genes in winter and co-dominated by tetracycline and sulfonamide genes in summer, with most flanked by transposases. Key pathogenic hosts, including Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa carrying ARG-MGE complexes, were primarily concentrated in the regulating pool and the influent, forming high-risk upstream sources of dissemination. Partial least-squares path model highlighted MGEs as the primary drivers, and variance partitioning analysis indicated that MGEs account for 31 % of the explained variation in ARGs during wastewater treatment. In summary, the anaerobic unit was an ARG enrichment hotspot, while the aerobic unit as ARG attenuation zone during wastewater treatment. These findings provide crucial evidence to optimize rural wastewater treatment processes and to target the control of antibiotic resistance.}, } @article {pmid42425523, year = {2026}, author = {Post, SE and Ceisler, HS and Lal, RG and Singh, A and Deen, MA and Bonomo, LE and Cunic, LM and Brito, IL}, title = {Discovery of Novel Glycosidase-Derived Cell-Penetrating Peptides Encoded by Human Gut Commensals.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.6c00031}, pmid = {42425523}, issn = {2161-5063}, abstract = {Intracellular delivery of therapeutics remains a major challenge for modern medicine. To enhance intracellular uptake, therapeutics can be delivered with carrier proteins possessing an inherent cell-penetrating activity. There is an increasing need for new cell-penetrating carriers with diverse biophysical properties and mechanisms of action to transport a wide range of therapeutic cargo. As many cell-penetrating proteins and peptides derive from natural proteins, we sought to mine a previously unexplored community, the human gut microbiome, for cell-penetrating sequences. Here, we performed a high-throughput functional metagenomic screen to identify cell-penetrating protein fragments from the human gut microbiome. We identified protein fragments encoded within glycosidase enzymes from members of the Bacteroidetes phylum that mediate internalization into human cell lines when displayed on the surface of nonpathogenic, noninvasive Escherichia coli. We investigate one fragment, dubbed Gh_112, that adheres to human fibronectin, activates multiple endocytic pathways, and specifically promotes uptake of E. coli into multiple cancerous epithelial cell lines rather than healthy epithelial tissue in vitro. Overall, this work demonstrates that the human gut microbiome is a source of cell-penetrating sequences and expands the known repertoire of cell-penetrating carrier systems.}, } @article {pmid42425637, year = {2026}, author = {Elsheshtawy, A and Clokie, BGJ and Saugh, S and Adler, KD and Michniewski, SM and MacKenzie, S and Clokie, MRJ and Sicheritz-Pontén, T and Albalat, A}, title = {Microbial succession and spoilage dynamics revealed by multi-omics in Norway lobster (Nephrops norvegicus) during ice storage.}, journal = {Food microbiology}, volume = {140}, number = {}, pages = {105151}, doi = {10.1016/j.fm.2026.105151}, pmid = {42425637}, issn = {1095-9998}, abstract = {The Norway lobster (Nephrops norvegicus) is a high-value seafood product with limited shelf-life under chilled storage. This study investigated microbial succession and spoilage dynamics during ice storage (0 °C, 16 days) using an integrated multi-omics approach combining sensory assessment (Quality Index Method), physicochemical indicators (muscle pH and K-value), culture-dependent microbiology, absolute bacterial load quantification (16S rRNA qPCR), 16S rRNA gene amplicon sequencing and shotgun metagenomics. Quality deterioration was characterised by progressive increases in sensory scores, nucleotide degradation and muscle pH, with rejection occurring at day 7. This transition coincided with a marked increase in bacterial load following an initial lag phase (days 0-5), indicating a critical shift in spoilage progression. Amplicon sequencing revealed a transition from a diverse early community (days 0-3) to a Proteobacteria-dominated assemblage from day 5 onwards, driven by increases in Moritella, Pseudoalteromonas and Aliivibrio. Metagenomic analysis further resolved these dynamics at species-level resolution and identified a limited number of dominant taxa associated with mid-to late-stage spoilage. The convergence of sensory rejection, physicochemical changes and microbial restructuring identifies a mid-storage tipping point in spoilage development. By integrating multi-omics with established quality indicators, this study links microbial succession to measurable spoilage outcomes. The dominant taxa are consistent with known spoilage-associated activities, including proteolysis and off-odour production, while highlighting Moritella as a potential contributor in crustacean spoilage. These findings provide a temporal framework for spoilage progression in N. norvegicus and inform targeted strategies for shelf-life management.}, } @article {pmid42426126, year = {2026}, author = {Barcaccia, G and Rambaldi Migliore, N and Gabelli, G and Agostini, V and Palumbo, F and Moroni, E and Nicolini, V and Gao, L and Mattutino, G and Porter, A and Palmowski, P and Procopio, N and Perego, UA and Iorizzo, M and Sharbel, TF and Baima Bollone, P and Torroni, A and Squartini, A and Achilli, A}, title = {DNA signatures preserved in the official 1978 sample collection of the Shroud of Turin.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42426126}, issn = {2045-2322}, support = {rif: 2023-1373//Fondazione Cariplo/ ; DAFNAE1-DOR-00719//University of Padova/ ; MR/Y019989/1//UKRI FLF/ ; 2022Y8BSAL//Ministero dell'Università e della Ricerca/ ; }, abstract = {This research provides novel insights into the diversity of DNA extracted from samples collected from the Turin Shroud in 1978, revealing its biological complexity through rigorous DNA and metagenomic analyses. Our findings highlight its preservation conditions and environmental interactions, offering valuable perspectives into the identified genetic variants, which originated from multiple biological sources. We identified several human mitochondrial DNA (mtDNA) lineages, including K1a1b1a, which matches the 1978 official collector's mitogenome, H2a2 (i.e., the lineage of the mtDNA reference sequence rCRS), H1b, which is common in Western Eurasia, and the rare H33, which is also present in the Near East. Additionally, the reconstructed microbiome of the Shroud reveals a rich tapestry of multiple microbes commonly found on the human epidermis, as well as archaeal communities adapted to high salinity and fungi including molds. These findings are consistent with the preservation conditions experienced by the Shroud over the centuries. The presence of abundant Mediterranean endemic red coral, various cultivated plants (e.g., carrot, wheat, corn, bananas, and peanuts) and domesticated animals (e.g., cattle, pigs, chickens, dogs, and cats) provide a fascinating glimpse into the diverse biological sources of the contaminants that have accumulated on the Turin Shroud over time. Finally, radiocarbon dating of two distinct threads collected from the reliquary is consistent with their use in repair interventions of the Shroud carried out in 1534 and 1694 CE.}, } @article {pmid42276012, year = {2026}, author = {Budzinski, L and Beenken, AE and Sempert, T and Kang, GU and Abbas, A and Lietz, L and Maier, R and Mashreghi, MF and Chang, HD and Alexander, T}, title = {IgG4-related disease has a specific intestinal microbiota signature.}, journal = {EBioMedicine}, volume = {129}, number = {}, pages = {106326}, pmid = {42276012}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; RNA, Ribosomal, 16S/genetics ; Male ; *Immunoglobulin G4-Related Disease/microbiology/diagnosis/etiology ; Middle Aged ; Flow Cytometry ; Aged ; Immunoglobulin G ; Adult ; Cross-Sectional Studies ; Feces/microbiology ; Metagenomics/methods ; }, abstract = {BACKGROUND: While the intestinal microbiome has been implicated in Immunoglobulin-4 related disease (IgG4-RD), it remains poorly characterised. Therefore, we performed a comprehensive microbiome characterisation to identify disease-specific alterations.

METHODS: In this cross-sectional study, cryopreserved stool samples from 28 patients with IgG4-RD were characterised by 16S rRNA gene sequencing and by multiparameter microbiota flow-cytometry to determine their taxonomic composition and phenotype at the single cell level. These data were evaluated in comparison with 24 healthy controls (HC) and assessed for their potential to classify IgG4-RD using random forest classification, with an independent validation cohort (12 IgG4-RD, 12 HC).

FINDINGS: Patients with IgG4-RD exhibited reduced taxonomic diversity and disease-specific alterations in the microbiome compared to HC, characterised by significantly elevated levels of several species within the Bacillota phylum. These taxonomic alterations classified patients and HC with an AUROC of 0.87 (95% CI: 0.77-0.97) but showed reduced performance in the validation cohort (AUROC 0.58, 95% CI: 0.29-0.87). Flow cytometry revealed distinct phenotypic microbiota alterations, robustly distinguishing patients with IgG4-RD from HC in both the training (AUROC 0.9, 95% CI: 0.81-0.99) and validation cohort (AUROC 0.78, 95% CI: 0.59-0.97). The IgG4-RD microbiota were predominantly DNA-low and showed no enhanced endogenous IgG4 coating, neither natively nor after in vitro incubation with autologous serum.

INTERPRETATION: Our study revealed specific alterations in the intestinal microbiota on taxonomic and phenotypic level in IgG4-RD, which potentially reflect different mechanisms of adaptations of the gut microbiota to immune disturbances specific to IgG4-RD. We provide proof-of-concept that this "microbiota fingerprint" may be suitable to identify IgG4-RD in a machine-learning approach and may provide important insights into the complexity of intestinal microbiota alterations in IgG4-RD.

FUNDING: This work was supported by grants from Rolf M. Schwiete Foundation, DFG (German Research Foundation), Innovative Medicines Initiative 2 Joint Undertaking (3 TR), and EFRE-Project.}, } @article {pmid42413090, year = {2026}, author = {Hidalgo, M}, title = {From microscopy to metagenomics: Evolution and challenges in clinical microbiology.}, journal = {Biomedica : revista del Instituto Nacional de Salud}, volume = {46}, number = {Sp. 1}, pages = {5-7}, doi = {10.7705/biomedica.8421}, pmid = {42413090}, issn = {2590-7379}, } @article {pmid42414278, year = {2026}, author = {Zhao, C and Li, Z and Liu, M and Bao, L and Yuan, C and Zhao, Y and Wu, K and Qiu, M and He, Y and Zhang, N and Hu, X and Zhang, Y and Han, F and Fu, Y}, title = {Dissection of mammary cell landscape in ruminal dysbiosis-induced mastitis by single-cell RNA sequencing.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01076-7}, pmid = {42414278}, issn = {2055-5008}, support = {32402956//National Natural Science Foundation of China/ ; 32422086//National Natural Science Foundation of China/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; }, abstract = {Growing evidence has underscored the contribution of gastrointestinal dysbiosis to the onset of mastitis, however, the local cellular changes responsible for the pathological processes of ruminal dysbiosis-induced mastitis (RDIM) are still unclear. Here, we profiled mammary single-cell transcriptomes in goats with RDIM, complemented by ruminal metagenomic and untargeted metabolomic analyses of rumen fluid and serum. Our results indicated that compromised lactation and barrier integrity in LumSec were linked to RDIM. Increased inflammatory macrophages and DCs, γδT and CD4[+] TH cell populations, along with reduced Tex/Treg and B cells were implicated in RDIM. Fibroblasts exhibited increased gene expression related to the extracellular matrix, while lymphatic endothelial cells and Vas-venous structures displayed elevated inflammatory gene expression. Tight junction integrity and apelin signaling pathways were compromised in Vas-capillary during RDIM. Notably, metagenomic analysis indicated that RDIM correlated with reduced ruminal microbial diversity and shifts in microbial community composition. Key metabolic pathways including microbial tryptophan metabolism, secondary bile acid biosynthesis, and vitamin metabolism were significantly diminished during RDIM. Furthermore, tryptophan-induced AHR signaling and secondary bile acid receptor GPBAR1, primarily expressed in vascular endothelial cells and macrophages, respectively, which were reduced during RDIM. Collectively, our study provides a comprehensive atlas of mammary cell landscapes in RDIM, which may enhance the understanding of mastitis pathogenesis.}, } @article {pmid42415156, year = {2026}, author = {Houvessou, GM and Antonieta Alfane, NW and Mahoche, M}, title = {Dynamic, transition and variation of cervicovaginal microbiome and HPV infection and cervical dysplasia and cancer: a systematic review.}, journal = {Infectious agents and cancer}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13027-026-00777-0}, pmid = {42415156}, issn = {1750-9378}, abstract = {BACKGROUND: Cervical cancer is the fourth most common malignancy in women worldwide, with approximately 660,000 new cases and 350,000 deaths annually. The burden falls disproportionately on low- and middle-income countries. Although persistent infection with high-risk HPV (hrHPV) is the necessary cause, most infected women clear the virus spontaneously, implicating additional cofactors, including the cervicovaginal microbiome in determining oncogenic outcomes.

METHODS: PubMed was searched through September 10, 2024, to identify longitudinal studies assessing cervicovaginal microbiota in relation to HPV infection or cervical lesion outcomes at two or more time points. Methodological quality was evaluated using the Newcastle-Ottawa Scale (NOS). Given the substantial heterogeneity, a structured thematic synthesis was performed across three predefined domains: (a) baseline microbiome composition and clinical outcomes; (b) community state type (CST) dynamics and temporal stability; and (c) microbiome changes following treatment.

RESULTS: Twelve studies enrolling 1,663 women across 11 countries met inclusion criteria. NOS scores ranged from 4 to 9. Lactobacillus-dominated CSTs at baseline were consistently associated with HPV clearance and CIN regression, while Lactobacillus-depleted states showed higher transition rates and unfavourable outcomes. Prior L.iners (CST III) dominance was repeatedly linked to favourable outcomes, although evidence on this species remains conflicting. Cervicovaginal dysbiosis frequently preceded HPV persistence or lesion progression.

CONCLUSION: Sustained Lactobacillus-dominated CST stability, rather than dominance by any single species, is the most consistent microbiome factor associated with favourable HPV and cervical lesion outcomes. Standardized longitudinal designs incorporating metagenomic sequencing, frequent sampling intervals, and rigorous confounder adjustment are needed to advance mechanistic understanding.

Not applicable.}, } @article {pmid42415193, year = {2026}, author = {Lechleiter, N and Wedemeyer, J and Junker, J and Sehl-Ewert, J and Homeier-Bachmann, T}, title = {Gastrointestinal parasites of red and roe deer investigated via metagenomics and histology.}, journal = {Parasites & vectors}, volume = {19}, number = {1}, pages = {}, pmid = {42415193}, issn = {1756-3305}, support = {Grant No. 28KIDA001//Federal Ministry of Agriculture, Food and Regional Identity (BMLEH) - Germany/ ; }, mesh = {Animals ; *Deer/parasitology ; *Metagenomics/methods ; Feces/parasitology ; *Gastrointestinal Tract/parasitology/pathology ; *Parasites/genetics/isolation & purification/classification ; Seasons ; Animals, Wild/parasitology ; *Intestinal Diseases, Parasitic/veterinary/parasitology ; }, abstract = {BACKGROUND: Some of the most common pathogens in wildlife are parasites. Since wild cervids are phylogenetically close to a lot of our livestock species, disease dynamics can arise, for example, through shared parasites. Insight into regional patterns, shaped by ecosystems and cross-species relationships, is only slowly emerging and the species-specific knowledge about lifecycle and ecology of parasites is often based on cross-sectional studies and therefore limited. Possibilities for broad and easy investigation of parasites could be the key to widen our understanding of these systems and processes.

METHODS: Here, shotgun metagenomics were investigated as a method for parasite detection in fecal samples of wild ungulates. The results were further validated by histopathological examination of gastrointestinal tissues.

RESULTS: The results from the two methods are in line with similar studies, and while not being identical, complement each other.

CONCLUSIONS: This investigation revealed parasite composition and seasonal dynamics in two species of wild cervid red deer (Cervus elaphus) and roe deer (Capreolus capreolus).}, } @article {pmid42415408, year = {2026}, author = {Li, J and Liu, P and Zhang, Q and Zhao, R and Zhang, J and Zheng, X and Li, B and Zhang, XX}, title = {Temperate Phages Mediate Dual Adaptive Mechanisms That Enhance Microbial Resilience in Antibiotic-Contaminated Wastewater Treatment Systems.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c07049}, pmid = {42415408}, issn = {1520-5851}, abstract = {Temperate phages play crucial ecological roles in engineered microbial communities, yet their adaptive strategies under antibiotic stress remain unclear. Here, metagenomic analysis was used to investigate how temperate phages facilitate host adaptation in activated sludge acclimated to chloramphenicol (CAP). Antibiotic stress markedly reshaped bacterial and temperate phage communities, with dominant degraders (e.g., Sphingomonas and Caballeronia) reaching relative abundances of 6.5-42.0%. Temperate phages exhibited specific adaptive responses by significantly enriching antibiotic resistance genes, including multidrug (arlR and mtrA) and peptide (bcrA) resistance genes, resulting in a 1.56-4.15-fold increase in the phage-derived resistome relative to the control. They also mediated general adaptive responses by encoding auxiliary genes involved in oxidative stress mitigation, DNA repair, biofilm formation, and antiviral defense. Host-phage linkage prediction identified 1045 phage-bacteria interactions, including 11 ARG-harboring viral operational taxonomic units associated with dominant CAP-degrading hosts. Collectively, our findings reveal that temperate phages facilitate microbial resilience in antibiotic-stressed environments by delivering mutualistic genetic traits, encompassing both specific (antibiotic resistance genes) and general (antiviral defense, metabolic, and stress mitigation) adaptive responses, highlighting their ecological significance and potential for enhancing the stability and performance of wastewater treatment systems under pharmaceutical stress.}, } @article {pmid42415516, year = {2026}, author = {Zhou, G and Liu, J and Liu, F and Xiao, Y and Graham, EB and Kuzyakov, Y and Ye, M and Xin, X and Chen, L and Zhang, C and Ma, D and Wu, Z and Zhou, Z and Zhou, J and Liang, Y and Zhang, J}, title = {Resource-Dependent Metabolic and Biogeochemical Consequences of Viruses in Agricultural Soils.}, journal = {Global change biology}, volume = {32}, number = {7}, pages = {e70994}, doi = {10.1111/gcb.70994}, pmid = {42415516}, issn = {1365-2486}, support = {42277336//National Natural Science Foundation of China/ ; 42425703//National Natural Science Foundation of China/ ; SKLSSA2501//Major Program of State Key Laboratory of Soil and Sustainable Agriculture/ ; BK20221561//Natural Science Foundation of Jiangsu Province/ ; CARS-03//China Agriculture Research System/ ; CARS-52//China Agriculture Research System/ ; CX(24)1003//Jiangsu Agricultural Science and Technology Innovation Fund/ ; NMKJXM202401-01//Key Special Projects of the "Science and Technology Revitalizing Inner Mongolia" Action Fund/ ; DE-AC05-76RL01830//Department of Energy, Office of Science, Biological and Environmental Research program and by Pacific Northwest National Laboratory/ ; }, mesh = {*Soil Microbiology ; Agriculture ; *Soil/chemistry ; Carbon/metabolism ; *Viruses/genetics/metabolism ; Metagenome ; Fertilizers ; }, abstract = {Soil viruses are crucial for microbial life, biogeochemical cycles of carbon and nutrients, and for microbial necromass formation. We hypothesized that the effects of viruses on these processes depend on organic matter and nutrient availability in soils. Here, we combined a 34-year long-term fertilization trial, 150 sequenced soil metagenomes, and microcosm experiments to explore how viruses modulate carbon and nutrient dynamics depending on resource availability. We uncovered 2789 viral populations (vOTUs) grouping into 301 viral clusters, 91% of which were previously unknown. Organically fertilized soils harbored most lytic viruses carrying diverse element cycling-related auxiliary viral genes (AVGs) acquired through co-evolution and horizontal gene transfer. Synthesis and heterologous expression assays further indicated that four AVGs (i.e., cbhA, pel, wbpD, GT2) had higher transcript levels in Escherichia coli under nutrient rich than nutrient poor conditions. Addition of virus particles to soils raised microbial carbon use efficiency (CUE; biomass production relative to carbon uptake) and accelerated microbial turnover leading to boosted microbial necromass formation by 14%. Conversely, in soils without organic fertilizers, viruses facilitate bacterial adaptation to stress (e.g., defense system and interference competition) and accelerate microbial decomposition of organic matter. 35 days after virus addition, CO2 and N2O emissions increased by 41% and 52%, respectively. Finally, we propose the Viral Entombing-Priming (VEP) framework to describe the contrasting roles of viruses in carbon and nutrient dynamics depending on soil fertility. This work reveals the viral "Matthew effect" (the rich get richer and the poor get poorer) in resource-rich and resource-poor soils and could unlock nature-based pathways to raise carbon and nutrient retention for sustainable agriculture.}, } @article {pmid42415518, year = {2026}, author = {Dolivet-Maréchal, M and Palacin-Lizarbe, C and Siljanen, HMP and Paul, D and Delort, A and Gervaix, J and Creuzé des Châtelliers, C and Schmidt, S and Cognat, M and Sebag, D and Taugourdeau, O and Schübert, C and Labourdette, N and Bertrand, I and Rossi, LMW and Le Roux, X and Richaume, A and Florio, A}, title = {Vegetation Increases CH4 Emissions and Methanotroph Diversity in Marine Sediments.}, journal = {Global change biology}, volume = {32}, number = {7}, pages = {e70989}, doi = {10.1111/gcb.70989}, pmid = {42415518}, issn = {1365-2486}, support = {101037097//EU Horizon2020/ ; ANR-17-EURE-0018//Graduate School H2O'Lyon/ ; }, mesh = {*Methane/metabolism/analysis ; *Geologic Sediments/microbiology/chemistry ; France ; *Zosteraceae/microbiology/metabolism ; }, abstract = {Seagrass meadows are key blue carbon (C) ecosystems, storing large amounts of organic C over centuries. Their climate benefits may be reduced by methane (CH4) emissions, whose microbial and environmental descriptors in Zostera noltii meadows, dominant seagrass in North-Western Europe, remain poorly understood. We studied CH4 fluxes, CH4-producing and consuming microbial communities and sediment physicochemical parameters in Z. noltii meadows and adjacent bare sediments across seven sites in Arcachon Bay, France. In situ CH4 fluxes were measured at low tide during daytime conditions, providing standardized estimates of peak emissions. Microbial communities were characterized using targeted metagenomics of three functional genes (mcrA, mmoX, pmoA) and quantitative PCR. CH4 fluxes were higher in vegetated than bare sediments (24.4 ± 2.6 vs. 9.4 ± 0.7 μmol m[-2] day[-1]). Mixed linear models and random forest analyses identified C accumulation rate and CO2 flux as the strongest positive descriptors of CH4 fluxes. Vegetated sediments hosted more diverse methanotrophs, while methanogens showed no habitat differences. Four genera (mcrA-Methanolobus, mmoX-Methylocella, pmoA-Methylococcus, Methyloglobulus) emerged as abundant, seagrass-associated, correlated with CH4 fluxes, and highlighted by models. Functional diversity, especially pmoA richness, was a stronger microbial descriptor of CH4 fluxes than gene abundance or a specific genus. Findings indicate Z. noltii meadows enhance C burial and CH4 emission, with methanotroph diversity potentially mitigating CH4 emissions. Our results provide the first integrated assessment of CH4 fluxes and their descriptors in Z. noltii meadows, based on limited temporal coverage capturing the daytime peak emission conditions, highlighting the intertwined nature of C burial and CH4 emissions and the need to account for both in blue C climate assessments.}, } @article {pmid42415914, year = {2026}, author = {Zhang, M and Jiang, J and Yang, B and Zhao, W and Zhang, J and Ma, T and Wang, H}, title = {Integrated multi-omics analysis reveals distinct microbiota-metabolite signatures and a novel HCN2-2-hydroxybutyric acid interaction in inflammatory bowel disease.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1843166}, pmid = {42415914}, issn = {2296-861X}, abstract = {INTRODUCTION: Gut microbiota-derived short-chain fatty acids (SCFAs) exert critical regulatory functions in inflammatory bowel disease (IBD). However, integrated profiling of fecal SCFA signatures alongside gut microbiota composition in ulcerative colitis (UC) and Crohn's disease (CD) remains insufficiently characterized. Furthermore, the molecular mechanisms through which microbiota metabolites engage host protein targets warrant systematic investigation.

METHODS: This study enrolled 30 patients with UC, 20 with CD, and 30 healthy controls, with paired fecal collection. Gut microbiota composition was analyzed by deep metagenomic sequencing, and SCFA concentrations were quantified by gas chromatography-mass spectrometry. Multi-omics integration, correlation network analysis, and Bayesian kernel machine regression were employed to resolve microbiota-metabolite associations. An integrated computational pipeline incorporating molecular dynamics simulations was constructed to evaluate the thermodynamic stability and binding modalities of metabolite-protein interactions.

RESULTS: Both UC and CD patients exhibited significantly reduced gut microbial α-diversity and characteristic community structure alterations. Fecal metabolomic profiling revealed synchronous elevation of 2-Hydroxybutyric acid (2-HB) and isocaproate in both patient groups, whereas butyrate reduction was restricted to UC. Multi-omics correlation analysis identified significant associations between 2-HB and unclassified Veillonella species as well as specific functional modules. Molecular dynamics simulations with an aggregate sampling time of 100 ns revealed a structural basis for the formation of a stable complex between 2-HB and the hyperpolarization-activated cyclic nucleotide-gated channel 2 (HCN2). This interaction was primarily mediated by electrostatic interactions involving Arg659, Arg618, and Arg617 residues alongside hydrophobic contacts, suggestive of potential allosteric modulation.

CONCLUSIONS: This study identifies 2-HB and isocaproate as shared fecal metabolic markers across IBD and provides a structural rationale for the interaction between 2-HB and HCN2. The druggability profile of HCN2 supports its prioritization for mechanistic investigation, with the caveat that functional validation is prerequisite to any inference of therapeutic relevance.}, } @article {pmid42416069, year = {2026}, author = {Wang, J and Lin, K and Zhong, Y and Wu, Z and Lu, T and Lu, W and Wang, W and Ma, C}, title = {Disseminated Mycobacterium kansasii infection with osseous involvement in anti-interferon-γ autoantibody-associated adult-onset immunodeficiency: a case report and literature review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1841472}, pmid = {42416069}, issn = {1664-3224}, mesh = {Humans ; Male ; Middle Aged ; *Mycobacterium Infections, Nontuberculous/immunology/diagnosis/drug therapy ; *Mycobacterium kansasii/immunology ; *Interferon-gamma/immunology ; *Autoantibodies/immunology ; *Immunologic Deficiency Syndromes/immunology/complications/diagnosis ; }, abstract = {BACKGROUND: Anti-interferon-γ autoantibody-associated adult-onset immunodeficiency is a rare acquired immunodeficiency that predisposes patients to recurrent or disseminated opportunistic infections, particularly nontuberculous mycobacterial (NTM) infections. Disseminated Mycobacterium kansasii infection in this setting is uncommon and may radiologically mimic malignancy, leading to diagnostic delay.

CASE PRESENTATION: A 53-year-old Chinese man with untreated chronic hepatitis B virus (HBV) infection presented with cough, chest pain, and back pain. Chest computed tomography and ^18F-FDG PET/CT revealed a left hilar mass, mediastinal and hilar lymphadenopathy, and extensive FDG-avid skeletal lesions, initially suggesting lung cancer with bone metastases. However, repeated pathological examinations, including bronchoscopic brushing, endobronchial ultrasound-guided transbronchial needle aspiration, and cervical lymph node aspiration, failed to confirm malignancy. Targeted next-generation sequencing of bronchoalveolar lavage fluid and metagenomic next-generation sequencing of vertebral tissue both identified Mycobacterium kansasii, supporting disseminated infection with pulmonary and skeletal involvement. Subsequent immunologic testing demonstrated elevated anti-IFN-γ autoantibodies, supporting a clinical diagnosis of AIGA-associated disseminated M. kansasii infection. Antimycobacterial therapy was initiated, but further treatment was complicated by postoperative cholestatic jaundice and high-level HBV viremia, which precluded immediate escalation to immune-directed therapy.

CONCLUSIONS: AIGA-associated disseminated Mycobacterium kansasii infection can closely mimic lung cancer with bone metastases. In patients with tumor-like pulmonary and skeletal lesions but repeatedly nondiagnostic pathology, early integration of pathogen detection and anti-IFN-γ autoantibody testing may help shorten diagnostic delay.}, } @article {pmid42416141, year = {2026}, author = {Chen, D and Li, X and Wang, Z and Huang, L and Qin, L}, title = {Complementary mNGS and traditional testing for bloodstream infections.}, journal = {Open medicine (Warsaw, Poland)}, volume = {21}, number = {1}, pages = {20261494}, pmid = {42416141}, issn = {2391-5463}, abstract = {Bloodstream infections (BSIs) require rapid and accurate etiological diagnosis to guide timely antimicrobial therapy. Conventional diagnostic approaches, particularly blood culture, remain indispensable for antimicrobial susceptibility testing; however, they are limited by prolonged turnaround time and reduced sensitivity, especially following prior antibiotic exposure. Metagenomic next-generation sequencing (mNGS) has emerged as a culture-independent and hypothesis-free diagnostic tool capable of detecting a broad spectrum of pathogens directly from clinical samples. This approach is particularly advantageous for identifying rare, fastidious, and polymicrobial infections, as well as infections in immunocompromised patients. However, its clinical application remains constrained by challenges in distinguishing infection from colonization, interpreting antimicrobial resistance signals, and variability in bioinformatics pipelines. Thus, in the era of integrated diagnosis, mNGS does not replace but powerfully complements traditional methods. Furthermore, we propose a dynamic evidence-weighted integrated diagnostic framework to guide real time clinical decision and improve the clinical applicability of mNGS in bloodstream infections.}, } @article {pmid42416274, year = {2026}, author = {Dang, Y}, title = {How mNGS transforms care for non-verbal elderly stroke patients with pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1814320}, pmid = {42416274}, issn = {2235-2988}, mesh = {Humans ; Aged ; Retrospective Studies ; *Stroke/complications ; Female ; Male ; Sputum/microbiology/virology ; Aged, 80 and over ; *Pneumonia/diagnosis/microbiology/etiology/drug therapy ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Bacteria/isolation & purification/genetics/classification ; Anti-Bacterial Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {BACKGROUND: Stroke-associated pneumonia (SAP) is a severe complication in non-verbal elderly stroke patients, with diagnosis hindered by the low sensitivity and slow turnaround of conventional microbial culture.

METHODS: A single-center retrospective cohort study was conducted on 64 non-verbal elderly SAP patients (≥65 years) admitted to Guangxi Jiangbin Hospital from 2018 to 2022, divided into an mNGS group (n=30, sputum/BALF tested by metagenomic next-generation sequencing) and a control group (n=34, conventional culture). Propensity score matching (1:1) was used to balance baseline characteristics, and clinical outcomes and pathogen detection efficiency were compared between groups. Multivariable Cox regression adjusted for hypoalbuminemia, electrolyte disturbance and stroke severity.

RESULTS: mNGS detected more bacterial pathogens (37 vs.27 in sputum, 37 vs.21 in BALF) and identified 3 viral and 2 atypical pathogens undetectable by culture, with a negative rate of 13.3% (vs.20.0% for sputum culture, 43.3% for BALF culture). 73.3% of mNGS group patients received antimicrobial therapy adjustment. After adjustment, the mNGS group had notably higher 28-day (96.7% vs.76.5%; adjusted HR = 0.32, P = 0.032) and 90-day survival (76.7% vs.44.1%; adjusted HR = 0.41, P = 0.024), lower invasive mechanical ventilation rate (40.0% vs.64.7%, P = 0.048), shorter median antibiotic duration (14 vs.21 days, P = 0.016) and lower median hospitalization costs (¥32,450 vs.¥89,310, P < 0.001).

CONCLUSION: mNGS enables more comprehensive pathogen detection in non-verbal elderly SAP patients, guides targeted antimicrobial therapy, and is associated with improved survival and reduced healthcare resource consumption. However, large-sample multicenter prospective studies are needed to validate these findings due to the study's limitations.}, } @article {pmid42416386, year = {2026}, author = {Wicaksono, WA and Köberl, M and White, RA and Jansson, JK and Jansson, C and Cernava, T and Berg, G}, title = {Plant-specific microbial diversity facilitates functional redundancy at the soil-root interface.}, journal = {Plant and soil}, volume = {523}, number = {2}, pages = {811-825}, pmid = {42416386}, issn = {0032-079X}, abstract = {AIMS: Plant-specific microbial diversity reflecting host-microbe coevolution was frequently shown at the structural level but less on the functional scale. We studied the microbiome of three compartments at the soil root interface (root endosphere, rhizosphere, bulk soil) of medicinal plants cultivated under organic management in Egypt. The study aimed to examine the impact of the rhizosphere on microbial community composition and diversity in desert agricultural soil, as well as to identify specific functions associated with the rhizosphere.

METHODS: The microbiome community structure, diversity, and microbial functioning were evaluated through the utilization of 16S rRNA gene amplicon and shotgun metagenome sequencing.

RESULTS: We found the typical rhizosphere effect and plant-species-specific enrichment of bacterial diversity. The annual plants Calendula officinalis and Matricaria chamomilla (Asteraceae) were more similar than the perennial Solanum distichum (Solanaceae). Altogether, plant species explained 50.5% of the variation in bacterial community structures in the rhizosphere. Our results indicate a stronger effect of the plant species in terms of modulating bacterial community structures in the rhizosphere than in root endosphere samples. The plant-driven rhizosphere effect could be linked to redundant plant beneficial functions in the microbiome, while enrichment of specific genes related to amino acid ion transport and metabolism, carbohydrate transport and metabolism, defense mechanisms, and secondary metabolites biosynthesis were more specific.

CONCLUSIONS: The study explores the microbiome continuum at the soil-root interface of medicinal plant species, revealing significant bacterial community structure shifts and plant specificity. The study provides insights into the essential microbiome components contributing to rhizosphere functionality.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-024-07097-5.}, } @article {pmid42416834, year = {2026}, author = {Zhao, Z and Lu, M and Ying, Y}, title = {Full-term pregnancy after severe gestational psittacosis: a case report and literature review.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1836961}, pmid = {42416834}, issn = {1663-9812}, abstract = {Gestational psittacosis is a rare but high-risk infection caused by Chlamydia psittaci, often leading to severe maternal complications and adverse fetal outcomes. We report a unique case of a 30-year-old woman at 22 + 5 weeks of gestation who presented with acute high fever and respiratory failure following bird exposure. The diagnosis of C. psittaci infection was rapidly confirmed via blood metagenomic next-generation sequencing (mNGS). Following multidisciplinary consultation involving obstetricians, infectious disease specialists, intensivists, respiratory physicians, clinical pharmacists, and neonatologists, an individualized management plan was established to balance maternal infection control, respiratory support, fetal monitoring, and medication safety during pregnancy. The patient was treated with intravenous azithromycin combined with corticosteroids, and her clinical condition stabilized within 2 weeks. Notably, the pregnancy continued to term, resulting in the delivery of a healthy male infant. To our knowledge, this represents the first reported case worldwide of a successful full-term delivery following gestational psittacosis. This case underscores the critical importance of early mNGS-based diagnosis, multidisciplinary collaboration, and appropriate antimicrobial therapy in optimizing maternal and neonatal outcomes, providing a valuable clinical reference for managing this life-threatening zoonosis during pregnancy.}, } @article {pmid42417135, year = {2026}, author = {Walker, WB and Neven, LG}, title = {eDNA analysis of yard waste samples reveals taxonomical diversity, sequence database limitations, and consistencies across sequencing platforms.}, journal = {Journal of insect science (Online)}, volume = {26}, number = {4}, pages = {}, doi = {10.1093/jisesa/ieag062}, pmid = {42417135}, issn = {1536-2442}, support = {//Washington State Department of Agriculture Specialty Crops Block/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *DNA, Environmental/analysis ; High-Throughput Nucleotide Sequencing/methods ; Biodiversity ; Sequence Analysis, DNA ; Insecta/genetics/classification ; Extrachromosomal DNA ; }, abstract = {Timely identification of biological species is often needed for various purposes, including economic reasons, and advances in DNA sequencing technologies have greatly augmented the ability to identify species through the application of DNA barcoding. One such method examines environmental DNA (eDNA) to sample the presence of organisms in an environment without necessarily having direct access to the whole organisms. In recent years, multiple high-throughput sequencing platforms have emerged, and there are differences in the efficiency, effectiveness, and economics across these platforms. In this report, we examine the application of two platforms, from PacBio and Oxford Nanopore Technologies, to sequence COI amplicons from nine barcoded yard waste samples that we previously studied for a different purpose. Here, we observed consistencies across the platforms in the identification of operational taxonomical units (OTUs) from broad swaths of life, most prominently including Bacteria, Amoebozoa, Fungi, Arthropoda, Nematoda, Spiralia, and Viridiplantae. Other taxonomical groupings were also tentatively identified. However, limitations in coverage of the diversity of COI sequences in the public databases rendered species-level identification impossible for many of the OTUs. Insect species were the best represented across all barcoded samples, and both sequencing platforms regarding percentage identity to the best BLAST hits in the databases. Following this, we took an in-depth look at the knowledge of the presence of highly matched species in the locality from where the eDNA samples were derived. Strengths and limitations of this approach in the analysis of eDNA are discussed.}, } @article {pmid42417706, year = {2026}, author = {Oliveira, MEAS and Lucino, D and Garcia, GJY and Bertozzi, BG and Bassinello, PZ and Colombari Filho, JM and Piler de Carvalho, CW and Góes-Neto, A and Rocha, LO and Kabuki, DY and Freitas Silva, O and Takeiti, CY}, title = {Germination and Polishing Reshape Microbial Communities in Japonica and Indica Rice.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.6c02819}, pmid = {42417706}, issn = {1520-5118}, abstract = {Germination is a process used to improve the nutritional quality of rice. However, its impact on rice microbiomes remains poorly understood. This study evaluated the microbiota of two rice ecotypes, low-amylose (Mochi) and high-amylose (BRS Formoso), after germination and polishing using 16S rRNA and ITS amplicon sequencing. Bacterial alpha diversity was highest in commercial brown rice (Shannon index 3.21) and lowest in commercial polished rice (1.50). Beta diversity indicated that germination exerted a similar effect on bacterial community composition in both ecotypes. Principal Coordinate Analysis suggested that polishing did not markedly influence microbiome composition relative to germination. The microbial profiles of Mochi and BRS Formoso were dominated by Pantoea, Pseudomonas, Rhizopus, and Moesziomyces. Overall, germination strongly influenced bacterial and fungal communities, emerging as the main factor shaping microbial structure and dynamics. These findings provide new insights into how processing affects the rice microbiome, with implications for food quality and safety.}, } @article {pmid42417716, year = {2026}, author = {Wang, Y and Luo, X and Ji, Y and Zhu, T and Zhao, Y and Tong, Y and Ni, BJ and Liu, Y}, title = {1,3-Dichloro-5,5-dimethylhydantoin (DCDMH)-Driven Sludge Pretreatment for Organic Carbon Valorization: Mechanistic Insights into Controlled Oxidative Disruption and Hormesis-Mediated Metabolic Reshaping.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c16484}, pmid = {42417716}, issn = {1520-5851}, abstract = {Organic carbon valorization via anaerobic sludge fermentation is intrinsically constrained by biopolymer recalcitrance and methanogenic diversion. We introduced 1,3-Dichloro-5,5-dimethylhydantoin (DCDMH) pretreatment leveraging controlled oxidative disruption and microbial metabolic regulation to boost short-chain fatty acid (SCFA) production. At optimal dosage (0.025 g/g TSS), SCFA yield increased by 192.1%, driven by enhanced substrate liberation and biochemical conversion. Molecular docking and 2D-COS FTIR analyses collectively indicate that the N-Cl moiety of DCDMH preferentially oxidized hydrophobic proteins within extracellular polymeric substances, while the derived HClO could penetrate cells to damage intracellular components. This dual action disrupted structural integrity, accelerating macromolecular substrate release and conversion, and enriching stress-tolerant hydrolytic/acidogenic bacteria. Sustained HClO release established oxidative stress wherein reactive oxygen species (ROS) functioned as metabolic signals beyond mere damage indicators. Moderate intracellular ROS stress stimulated substrate acidogenesis while suppressing methanogenic carbon sinks, and enhanced the gene abundances associated with antioxidant defenses and acidogenic pathways. Crucially, this work reveals for the first time the hormetic effect of DCDMH-derived HClO on acidogenic metabolism, providing a new insight into the application of chlorine-containing disinfectants in related fields.}, } @article {pmid42417728, year = {2026}, author = {Välikangas, T and Fritze, H and Pitkänen, JM and Peltoniemi, K and Järvi-Laturi, E and Christensen, TR and Väisänen, M and Lämsä, J and Paavola, R and Hultman, J}, title = {Environmental variation structures northern peatland soil microbiome composition and function in a reindeer herding area exclosure experiment.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag072}, pmid = {42417728}, issn = {1574-6941}, abstract = {Northern peatlands store large carbon stocks but are sensitive to disturbance. Hydrology, vegetation, herbivory and snow conditions may affect soil microorganisms involved in methane (CH4) cycling and nitrous oxide (N2O) production/reduction. We investigated how reindeer exclusion and snow depth (increased and reduced relative to ambient) manipulations (ongoing for three seasons) influenced archaeal and bacterial communities in a boreal rich fen. Metagenomic (MG) and metatranscriptomic (MT) sequencing were combined with pore-water chemistry and CH4 flux measurements to link the microbiome to ecosystem processes. Microbial communities differed between outside and inside the exclosure. However, these patterns primarily reflected underlying hydrological variation. Slightly wetter inside plots showed higher expression of denitrification genes (norB, nosZ) and lower (nirS+nirK)/nosZ ratios, indicating greater potential for complete denitrification to N2 instead of N2O. Methane dynamics were mainly associated with vegetation: plots associated with Carex rostrata exhibited lower pmoA/mcrA ratios and elevated CH4 fluxes. Snow manipulations had subtle effects: reduced snow depth decreased the expression of taxa dependent on microbial interactions, while effect to the investigated metabolic marker genes was small. Overall hydrology, leading to variations in redox conditions and nutrient availability, together with vegetation appeared as the primary drivers on microbial greenhouse gas processes in this peatland.}, } @article {pmid42417745, year = {2026}, author = {Antunes, TPB and Antunes, E}, title = {Next-generation molecular tools in veterinary parasitology: advances, challenges, and perspectives in the diagnosis of emerging parasites.}, journal = {Revista brasileira de parasitologia veterinaria = Brazilian journal of veterinary parasitology : Orgao Oficial do Colegio Brasileiro de Parasitologia Veterinaria}, volume = {35}, number = {2}, pages = {e016525}, doi = {10.1590/S1984-29612026023}, pmid = {42417745}, issn = {1984-2961}, mesh = {Animals ; *Parasitic Diseases, Animal/diagnosis/parasitology ; *Parasitology/methods/trends ; *Communicable Diseases, Emerging/diagnosis/veterinary/parasitology ; High-Throughput Nucleotide Sequencing ; }, abstract = {Advances in molecular technologies have revolutionized veterinary parasitology, providing highly sensitive and specific tools for the detection, characterization, and surveillance of parasites in domestic and wildlife species. Approaches such as next-generation sequencing, metabarcoding, and metagenomics have significantly enhanced the ability to identify previously unknown or uncultivable species, detect complex coinfections, and deepen our understanding of parasite genetic diversity, evolution, and population dynamics. Beyond their impact on laboratory diagnostics, these tools have proven essential for the early detection of zoonoses, environmental monitoring, and the development of integrated surveillance systems under the One Health framework. This review synthesizes the major technological advances and their practical applications in both global and Latin American contexts, particularly Brazilian, highlighting how the incorporation of these tools has the potential to transform strategies for surveillance, prevention, and response to emerging and re-emerging parasitic diseases. Challenges related to standardization, cost, infrastructure, and technology transfer are also discussed, along with future perspectives for large-scale implementation aimed at strengthening diagnostic capacity and epidemiological surveillance in the face of increasing parasitic threats in a rapidly changing world.}, } @article {pmid42417967, year = {2026}, author = {Lin, Z and Ma, Y and Wu, H and Lu, Z and Zhuang, X and Zhao, M and Peng, S and Lin, F and Zheng, K and Li, Z}, title = {Effects of lemongrass (Cymbopogon citratus) on slaughter performance, meat quality, and intestinal health in Muscovy ducks.}, journal = {British poultry science}, volume = {}, number = {}, pages = {1-17}, doi = {10.1080/00071668.2026.2670474}, pmid = {42417967}, issn = {1466-1799}, abstract = {1. This study tested the effects of dietary lemongrass (LG) supplementation on production performance, meat quality and intestinal health of Muscovy ducks. A 42 d feeding trial used four treatment diets (0%, 2%, 4% or 6% LG) fed as part of a commercial diet after 20 d rearing from day old on a basal diet.2. The results revealed that 6% LG supplementation significantly improved slaughter performance, notably increasing full eviscerated weight (p < 0.05).3. Meat nutritional quality was enhanced by higher amino acids (cysteine and methionine in breast muscle; tyrosine in leg muscle) and beneficial polyunsaturated fatty acids (PUFA) including C22:6n3 (DHA) and C20:5n3 (EPA; p < 0.05).4. Intestinal health was improved, with LG which enhanced duodenal morphology manifested as increased villus length and villus-to-crypt ratio. There was up-regulated gene expression for intestinal barrier proteins (ZO-1, Claudin-1), immune factors (sIgA, IFN-γ) and antioxidant enzymes (SOD, GSH-Px; p < 0.05).5. Metagenomic and metabolomic analyses revealed a restructured caecal microbiota, characterised by increased commensal Ligilactobacillus spp. inhibited pathogenic Burkholderia spp. and increased production of beneficial metabolites, including butyric acid (p < 0.05), which acts as an energy source for enterocytes.6. This trial demonstrated that LG can enhance both growth performance outcomes and meat quality in Muscovy ducks through gut health modulation, supporting its application in sustainable poultry farming.}, } @article {pmid42417977, year = {2026}, author = {Yu, SJ and Stanley, D and Van, TTH and Steel, JC and Bajagai, YS}, title = {Metagenomics comparison identifies shared pathogenic microbiome in humans, pigs and chickens.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-026-13948-1}, pmid = {42417977}, issn = {1432-0614}, support = {PRO-017656//AgriFutures Australia/ ; PRO-017656//AgriFutures Australia/ ; }, abstract = {Integrating human, animal, and environmental health is crucial for combating infectious diseases, as an estimated 60 to 75% of emerging infectious diseases originate from zoonotic sources globally. In this study, we analysed 1274 shotgun metagenomic faecal samples of humans, pigs, and chickens collected across multiple countries to estimate levels of microbial sharing at the species-level genome bins (SGBs) resolution. We confirm that host species, rather than geography, significantly structures the gut microbial community, as shown by alpha and beta diversity analyses. Despite this high host specificity, we identified substantial cross-host sharing of SGBs, including taxa recognised as pathogens such as Escherichia coli, Clostridium perfringens, Clostridium innocuum, Clostridium disporicum, Enterococcus species, and Streptococcus alactolyticus. Core taxa were predominantly host-specific, while non-core taxa were more frequently shared across humans, pigs, and chickens. LEfSe analysis identified distinctive microbial signatures for each host, further supporting differences in community composition. These findings demonstrate that unrelated and geographically distant humans and livestock can harbour highly similar microbial populations with pathogenic potential. This work provides molecular evidence supporting the need for integrated One Health surveillance to better detect, manage, and prevent zoonotic and reverse zoonotic transmission events across interconnected human, animal, and environmental systems. KEY POINTS: • There is substantial cross-host sharing of species-level genome bins, including potential pathogens • Core taxa are predominantly host-specific • Non-core taxa are more likely to be shared across humans, pigs, and chickens.}, } @article {pmid42418234, year = {2026}, author = {Araujo Serrao de Andrade, A and Silverj, A and Josephs, T and Gregory, AC}, title = {Evolving strategies for virus discovery.}, journal = {Microbial genomics}, volume = {12}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001785}, pmid = {42418234}, issn = {2057-5858}, mesh = {*Viruses/genetics/isolation & purification/classification ; Genome, Viral ; *Metagenomics/methods ; *Virome/genetics ; Artificial Intelligence ; Computational Biology/methods ; }, abstract = {Viruses interact with all domains of life and play fundamental roles in shaping biological systems from individual hosts to global ecosystems. Yet their identification remains difficult due to a lack of a universal marker gene and the extensive diversity of viral genomes. Despite this, the speed of viral discovery is quickly increasing, driven by the growing number of virome studies, improved sequencing technologies and the decreased cost of sequencing. In this review, we examine the evolution of virus identification approaches from classical and molecular methods to contemporary genome-resolved and computational frameworks. By aggregating genome-resolved virome studies from 2010 to early 2026 that meet defined criteria (n=502), we synthesize the current landscape of virus identification methods, including similarity-based, sequence-based artificial intelligence (AI) and hybrid approaches. We also highlight the key limitations of the current methods, particularly biases in reference databases that contribute to persistent viral 'dark matter'. Finally, we identify emerging opportunities for the field in structure-based and AI-driven approaches that extend detection beyond sequence similarity and outline how these integrative frameworks are poised to improve virus discovery across ecosystems.}, } @article {pmid42418242, year = {2026}, author = {Robinson, JM and Guentas, L and Breed, MF}, title = {A microbial mirage: when microbiome metrics may obscure ecological meaning.}, journal = {Microbial genomics}, volume = {12}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001777}, pmid = {42418242}, issn = {2057-5858}, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Ecology ; }, abstract = {Metrics such as alpha diversity, inferred functional potential and network complexity have become standard metrics in microbiome research. While they offer convenient ways to summarize complex data, these metrics may sometimes obscure more than they reveal. Alpha diversity, for example, measures richness and evenness. However, two samples may exhibit identical diversity scores, yet one could be dominated by beneficial taxa and the other by pathogens. Similarly, the presence of genes associated with particular functions does not guarantee that those functions are expressed or ecologically relevant under given conditions. Functional inference is also limited by database bias and often lacks empirical validation. Likewise, correlation-based network analyses can produce spurious associations driven by shared environmental covariates, sequencing depth or batch effects. These issues are routinely encountered in genomic workflows - from 16S/ITS amplicon surveys to shotgun metagenomics, genome-resolved metagenomics and gene-centric network analyses - where apparently 'clean' summary metrics can mask very different ecological realities. Here, we use simple, domain-relevant examples to illustrate how over-reliance on these metrics can lead to misinterpretation. Rather than rejecting these approaches, we outline when they are most informative, when they require caution and what complementary analyses can strengthen ecological inference. We propose a practical framework based on four questions: what exactly is being summarized, at what biological level, under which ecological conditions and with what form of validation? While acknowledging their value, we argue for greater critical scrutiny in their application and interpretation, and advocate for approaches that prioritize functional validation, temporal resolution and systems thinking to support more meaningful ecological insight.}, } @article {pmid42418263, year = {2026}, author = {Bai, W and Huang, G and Rao, X and Li, H and Zhou, T and Yang, Y and Wei, W}, title = {Efficacy, Safety, and Mechanism of the Qi-Lian-Xiao-Pi Prescription (WW-1) for Chronic Atrophic Gastritis After Helicobacter Pylori Eradication: Protocol for a Multicenter, Randomized, Double-Blind, Placebo-Controlled Trial.}, journal = {JMIR research protocols}, volume = {15}, number = {}, pages = {e90965}, doi = {10.2196/90965}, pmid = {42418263}, issn = {1929-0748}, mesh = {Humans ; *Gastritis, Atrophic/drug therapy ; *Helicobacter Infections/drug therapy ; Double-Blind Method ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; *Helicobacter pylori/drug effects ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; Female ; Male ; Treatment Outcome ; }, abstract = {BACKGROUND: Chronic atrophic gastritis (CAG) is widely recognized as one of the precancerous lesions of gastric cancer. Helicobacter pylori is one of the important risk factors for CAG and gastric cancer. However, a large proportion of patients with CAG cannot avoid developing gastric cancer even after eradicating H pylori. It is necessary to find a safe and effective treatment to suppress this "inflammation-cancer" progression. The Qi-Lian-Xiao-Pi prescription (WW-1), a traditional Chinese medicine (TCM), has been reported to be effective in the treatment of CAG. However, the evidence is subject to methodological limitations.

OBJECTIVE: This study aimed to evaluate the efficacy, safety, and mechanism of the WW-1 in patients with CAG following successful H pylori eradication.

METHODS: This study is a rigorous parallel-arm, randomized, placebo-controlled, multicenter, double-blinded trial. A total of 110 eligible participants with a confirmed diagnosis of CAG after H pylori eradication are being enrolled and randomly assigned in a 1:1 ratio to either the intervention group (WW-1) or the control group (WW-1 placebo). Key eligibility criteria include confirmed CAG by histopathology, documented successful H pylori eradication, and compliance with predefined inclusion and exclusion criteria. The treatment duration is 24 weeks. Blinded histopathological assessments using the Operative Link on Gastritis Assessment and Operative Link on Gastric Intestinal Metaplasia Assessment staging systems will serve as primary outcomes. Secondary outcomes include improvement rates of gastric mucosal gland atrophy and intestinal metaplasia, as well as TCM syndrome scores. Safety will be assessed through monitoring vital signs, adverse events, blood, urine, and stool tests, liver and kidney function, and electrocardiography. Additionally, gastric mucosal DNA methylation and metagenomic sequencing of digestive tract microbiota (including saliva, tongue coating, gastric, and intestinal samples) will be analyzed to explore potential mechanisms of WW-1.

RESULTS: The funding began in November 2023. The study was officially initiated on April 20, 2025, with the enrollment of the first participant. The final study results, including efficacy outcomes, safety profiles, and mechanistic insights, are expected to be released in October 2026 after comprehensive data analysis and verification.

CONCLUSIONS: This study is designed to determine whether WW-1 can improve CAG by modulating gastric mucosal DNA methylation and the digestive tract microbiota. It represents a prospective clinical trial in TCM that aims to evaluate therapeutic effects on CAG through the regulation of microbiota homeostasis and epigenetic mechanisms. The findings of this study are expected to provide evidence regarding the efficacy and safety of WW-1 and contribute to the development of therapeutic strategies and future drug research for CAG.

DERR1-10.2196/90965.}, } @article {pmid42418319, year = {2026}, author = {Li, Z and Chi, B and Ruan, C and Song, L and Dong, L and Li, A and Zheng, T and Wang, L and Huang, Y and Huang, J and Du, H and Zheng, X and Du, W and Dong, Z and Liu, Y and Huang, L and Dai, X}, title = {A deep-sea rare bacterium exhibits extraordinary metabolic versatility.}, journal = {Cell reports}, volume = {45}, number = {7}, pages = {117671}, doi = {10.1016/j.celrep.2026.117671}, pmid = {42418319}, issn = {2211-1247}, abstract = {The rare biosphere harbors immense microbial diversity, yet most low-abundance taxa remain uncultured and functionally enigmatic. Here, we isolated strain D14[T] from deep-sea water, and propose to classify it as a novel species, Metabolovarius oceani sp. nov., within the novel family Metabolovariaceae fam. nov. M. oceani represents the first cultivated member of the candidate family NORP267, a globally distributed but elusive alphaproteobacterial lineage known only from metagenome-assembled genomes. It possesses broad metabolic capabilities, including CO2 fixation, polyhydroxyalkanoate biosynthesis, complete denitrification and thiosulfate oxidation, and is capable of aerobic growth under both heterotrophic and autotrophic conditions and of anaerobic autotrophic denitrification via thiosulfate oxidation. Despite its versatile metabolic repertoire and global distribution, Metabolovariaceae remains consistently low in abundance across diverse habitats. The isolation of M. oceani permits direct experimental insights into the evolutionary adaptations, physiological resilience, and potential ecosystem roles of rare but metabolically versatile microorganisms within the microbial dark matter.}, } @article {pmid42418574, year = {2026}, author = {Caceres, C and Krasovec, M and Crispi, O and Gourbiere, S and Piganeau, G}, title = {Effect of cellular nutrient economy on the evolution of genome size in phytoplankton.}, journal = {Science advances}, volume = {12}, number = {28}, pages = {eaee2207}, doi = {10.1126/sciadv.aee2207}, pmid = {42418574}, issn = {2375-2548}, mesh = {*Phytoplankton/genetics/metabolism ; *Genome Size ; Selection, Genetic ; *Evolution, Molecular ; *Nutrients/metabolism ; Genetic Drift ; INDEL Mutation ; Models, Genetic ; }, abstract = {The origin of genome size variation remains a central question in evolutionary biology. While energetic costs have been proposed to influence genome size through selection on insertions and deletions (indels), nutrient availability may be a more relevant constraint in primary producers such as phytoplankton. We derived an expression for the selection coefficient of indels based on the phosphorus and nitrogen costs of nucleotides and the cellular nutrient requirements. Selection coefficient estimates indicate that natural selection dominates over genetic drift and favors the fixation of mutations that reduce genome size in phytoplankton with low nutrient requirements. Model predictions are supported by comparative genomics and metagenomic analyses. Together, this model provides a rigorous quantitative framework for understanding genome size evolution, particularly in small cells and oligotrophic environments, highlighting how nutrient limitation drives genome streamlining.}, } @article {pmid42418675, year = {2026}, author = {Zhang, M and Cao, Y and Yao, F and Lin, W and Lan, X and Sun, X and Wang, Y and Tan, Z and Ren, Y and Huang, Y and Sun, W}, title = {Antimonate Reduction Coupled to Anaerobic Ammonium Oxidation in Paddy Soil: Process Evidence and a Putative Syntrophic Microbial Model.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c00276}, pmid = {42418675}, issn = {1520-5851}, abstract = {The coupling of metal(loid) (e.g., Fe(III) and As(V)) reduction with anaerobic ammonium oxidation (anammox) is emerging as a critical process impacting the fate of N and metal(loid)s. Despite the chemical analogs of As and Sb, Sb(V) reduction exhibits different thermodynamics from As(V) reduction, which may constrain its coupling with anammox (termed "Sbammox") and impose stricter limitations on the metabolic pathway. To determine the occurrence and mechanism of Sbammox, Sb-contaminated paddy soil was used to establish the microcosms. Using [15]N isotope tracing, we confirmed the existence of Sbammox with the synchronous [15]N-N2 and Sb(III) productions and their concurrent suppressions by the inhibitor acetylene (C2H2). In contrast to the single-species-driving Asammox and Feammox, a tripartite syntrophic consortium was proposed to mediate Sbammox by DNA-stable isotope probing (SIP) combined with amplicon sequencing and metagenomic analysis. In this consortium, Ramlibacter and Candidatus Brocadia are proposed as the candidate Sb(V) reducer and ammonium oxidizer, respectively, with Geobacter hypothesized to mediate interspecies electron transfer. This distinct microbial strategy suggests that the specific thermodynamic constraints of Sb(V) necessitate a cooperative strategy rather than a solitary metabolic pathway. These findings are essential for understanding the divergent biogeochemical behaviors of As and Sb and underscore a critical dual risk in exacerbating nitrogen loss and Sb toxicity in agro-ecosystems.}, } @article {pmid42418904, year = {2026}, author = {Yu, J and Wan, Y and Peng, Y and Liang, S and Chan, FKL and Ng, SC and Tun, HM}, title = {Multi-cohort evidence for impaired microbial support of the methionine cycle in children with autism spectrum disorder.}, journal = {Psychiatry research}, volume = {364}, number = {}, pages = {117317}, doi = {10.1016/j.psychres.2026.117317}, pmid = {42418904}, issn = {1872-7123}, abstract = {The contribution of gut microbiota to outcomes of autism spectrum disorders (ASD) has been increasingly appreciated in recent years. With the accumulating evidence on ASD-driven alterations of the gut microbiota, heterogeneities arise across different reports. To account for variabilities in gut microbiota, clinical representations of ASD and data processing approaches, as well as limitations in sample sizes among the existing gut microbiota studies for ASD, the present multi-cohort analysis applied a standard bioinformatic and statistical pipeline on the publicly available gut metagenomic sequencing data for 674 samples, including 326 TD and 348 ASD individuals, collected from eight studies across three main geographical regions. Throughout the analysis, we identified taxonomic profiles of the gut microbiota exhibited more pronounced dysbiosis associated with ASD and between-study variations compared to functional profiles. Differentially abundant taxonomic and pathway markers were identified and validated for their consistent response to ASD across different studies. Co-occurring deficits in microbial pathways for salvaging adenosylcobalamin and S-adenosyl-L-methionine and biosynthesis of methionine in children with ASD point to a reduced microbial support for the host methionine cycle. Species from Faecalibacterium, Bacteroides, Blautia and Bifidobacterium were identified as microbial contributors to ASD-deficient microbial pathways, particularly those related to the methionine cycle. Therefore, the generalisable ASD-deficient contributors to the methionine cycle, such as Blautia wexlerae, Bacteroides stercoris and Streptococcus thermophilus, could be further investigated for their role in therapeutic applications for ASD.}, } @article {pmid42418982, year = {2026}, author = {Zhai, Y and Wang, X and Deng, X and Li, X and Hu, B and van der Meer, W and van Loosdrecht, MCM and Liu, G and Pabst, M}, title = {Metagenomic insights into microbial drivers of organic micropollutant removal in wastewater-impacted riverbank filtration.}, journal = {Water research}, volume = {305}, number = {}, pages = {126421}, doi = {10.1016/j.watres.2026.126421}, pmid = {42418982}, issn = {1879-2448}, abstract = {Organic micropollutants (OMPs) in wastewater treatment plant (WWTP) effluent pose persistent risks to aquatic ecosystems and drinking water sources. Riverbank filtration (RBF) is a nature-based treatment process, yet the compartment-specific roles of riverbed sediment and downstream soil in OMP attenuation remain poorly resolved under wastewater-impacted conditions. Here, we combined targeted chemical analysis, OMP property compilation, shotgun metagenomics, EnviPath-based biotransformation annotation, and exploratory network analysis to investigate OMP attenuation in a laboratory-scale RBF system treating real WWTP effluent for 10 months. Nineteen OMPs were monitored along a sequential sediment-soil filtration pathway. Sediment preferentially attenuated hydrophilic or charged compounds, including lidocaine, amantadine, and sotalol, whereas soil contributed more strongly to the attenuation of naproxen, atenolol, and losartan. Metagenomic profiling revealed distinct microbial communities and functional gene repertoires between sediment and soil after long-term operation. Sediment harbored higher relative abundances of genes associated with oxidative xenobiotic transformation, including cytochrome P450-related enzymes, demethylases, dehydrogenases, oxidases, and aromatic compound degradation pathways. An exploratory Spearman network further identified associations among microbial genera, EnviPath-annotated candidate biotransformation genes, and OMP removal rates, including 17 KO-OMP links supported by both correlation and pathway annotation. These findings indicate that sediment and soil develop complementary microbial functional potentials that may support compound-specific OMP attenuation. This study provides a mechanistic basis for optimizing sediment-soil configurations in wastewater-impacted RBF systems and for improving nature-based barriers against diverse OMP mixtures.}, } @article {pmid42418983, year = {2026}, author = {Huang, Y and Liu, P and Wu, J and Li, J and Tuo, J and Zhang, Q and Zhang, XX}, title = {Diverse and ultraviolet-inducible phage-associated antibiotic resistance genes in wastewater treatment plants.}, journal = {Water research}, volume = {305}, number = {}, pages = {126419}, doi = {10.1016/j.watres.2026.126419}, pmid = {42418983}, issn = {1879-2448}, abstract = {Phage-mediated transduction is an underappreciated route of antibiotic resistance gene (ARG) dissemination in wastewater treatment plants (WWTPs), yet the diversity and fate of phage-associated ARGs remain poorly resolved. Here, a 5-year monthly metagenomic survey of 538 influent, activated sludge, and effluent samples from two municipal WWTPs in Nanjing, China, was combined with laboratory-scale UV dose-response experiments to profile the phage-encoded resistome and its fate along the treatment train. A total of 168 phage-associated ARG subtypes spanning 23 drug classes were recovered, approximately 1.7-fold more than catalogued for comparable environments in IMG/VR, with multidrug- and diaminopyrimidine-resistance genes dominating the catalogue and efflux pumps constituting the major resistance mechanism; 64.9 % of subtypes were WWTP-exclusive, highlighting pronounced habitat specificity. Caudoviricetes overwhelmingly carried the ARGs and were primarily putatively linked to Gammaproteobacteria, Betaproteobacteria, and Actinobacteria. Biological treatment markedly restructured the phage-associated resistome (PERMANOVA R[2] = 0.19-0.34, p = 0.001), whereas conventional UV disinfection produced no significant bulk abundance reduction (p > 0.05). Dose-response experiments across 0-80 mJ/cm[2] revealed a biphasic pattern: low-to-moderate doses (10-20 mJ/cm[2]) induced prophages and transiently elevated phage-fraction ARG concentrations by 0.3-0.8 log10 copies/L (≈2- to 6-fold), whereas higher doses (≥40 mJ/cm[2]) drove progressive inactivation. These findings expose a previously underappreciated paradoxical release of phage-associated ARGs within the operational UV window of Chinese municipal reactors and argue for coupling UV with complementary barriers to curb transduction-mediated resistance dissemination.}, } @article {pmid42419029, year = {2026}, author = {Elmaghrabi, MM and Alghamdi, S and Alzeer, S and Magrashi, AM and Bakheet, RH and Alabden, DZ and Alshuhri, S and Abouelhoda, MM and Alrashaid, BA and Tayeb, HT}, title = {Metagenomic investigation of VIM-type metallo-β-lactamase-producing multidrug-resistant Pseudomonas aeruginosa associated with a hospital outbreak across multiple hospital units in Saudi Arabia.}, journal = {Journal of infection and public health}, volume = {19}, number = {8}, pages = {103299}, doi = {10.1016/j.jiph.2026.103299}, pmid = {42419029}, issn = {1876-035X}, abstract = {BACKGROUND: Healthcare-associated infections (HAIs) caused by multidrug-resistant (MDR) Pseudomonas aeruginosa (P. aeruginosa) represent a public health challenge, particularly when associated with VIM-type metallo-β-lactamases (MBLs), which limit therapeutic options. Conventional microbiological methods may underestimate resistance determinants and transmission dynamics. Long-read metagenomic sequencing is a promising approach for Pathogen detection, resistome characterization, and genomic surveillance.

OBJECTIVES: The study's objectives were to characterize the resistome, including detection of the blaVIM gene, assess genomic relatedness and potential transmission dynamics, and evaluate the diagnostic value of metagenomics compared with conventional microbiological approaches.

METHODS: This retrospective infection control investigation included seven hospitalized patients from multiple hospital units. Clinical specimens included blood, respiratory specimens, surgical tissue, and device-associated material. Conventional microbiological investigations included bacterial culture, identification, and antimicrobial susceptibility testing (AST) using the VITEK 2 automated system. Carbapenemase genes were detected using Xpert Carba-R. Long-read metagenomic sequencing was conducted using Oxford Nanopore Technologies (ONT) on the GridION platform. Bioinformatic analysis was performed using the CosmosID platform for taxonomic profiling, antimicrobial resistance gene detection, and genomic relatedness assessment.

RESULTS: Conventional microbiological methods identified carbapenem-resistant Pseudomonas aeruginosa (CRPA) in five cases, whereas ONT sequencing detected the blaVIM gene in all seven samples, demonstrating superior diagnostic sensitivity. A highly conserved resistome profile was identified across all investigated cases, including multiple β-lactamase and aminoglycoside, fluoroquinolone, and polymyxin-associated resistance determinants. Genomic relatedness analysis demonstrated close clustering patterns with minimal genomic variability, suggesting possible circulation of closely related MDR strains.

CONCLUSION: These findings highlight the added value of ONT sequencing in identifying concealed resistance determinants and improving transmission tracking compared with conventional diagnostic approaches. Future investigations involving larger sample sizes and environmental surveillance are needed to further clarify transmission dynamics and potential reservoirs of VIM-producing P. aeruginosa.}, } @article {pmid42419186, year = {2026}, author = {Liu, H}, title = {Computational strategies for uncovering bacterial biocatalysts in the biodegradation of persistent organic pollutants.}, journal = {Computational biology and chemistry}, volume = {124}, number = {Pt 2}, pages = {109222}, doi = {10.1016/j.compbiolchem.2026.109222}, pmid = {42419186}, issn = {1476-928X}, abstract = {The rapid accumulation of persistent organic pollutants (POPs) in soil, sediment, and aquatic environments presents a critical global challenge that demands sustainable and efficient remediation strategies. In this context, computational enzymology has emerged as a powerful framework for accelerating the discovery, validation, and optimization of pollutant-degrading enzymes. However, prior POP-biodegradation reviews have typically treated enzymes, docking, molecular dynamics (MD), metagenomics, and artificial intelligence (AI) as separate topics (e.g., docking-focused reviews (1), metagenomics-focused reviews (2), and structural-mechanism-focused reviews (3) rather than as parts of a single bacterial-enzyme discovery pipeline. This review fills that gap by focusing specifically on bacterial biocatalysts and by integrating structure prediction, docking, MD, metagenomic mining, and machine learning-guided design into one workflow. Its main contribution is a unified framework that links sequence discovery to structural screening, dynamic validation, and experimental prioritization. This work provides a comprehensive synthesis of molecular docking, molecular dynamics (MD) simulations, and integrative artificial intelligence (AI)-driven approaches applied to biodegradation research. We highlight how molecular docking functions as a high-throughput, structure-based filter for prioritizing enzyme-pollutant interactions, while MD simulations supply the essential temporal and mechanistic resolution required to evaluate enzyme flexibility, substrate access pathways, and catalytic competence under realistic environmental conditions. Case studies across diverse pollutant classes including polycyclic aromatic hydrocarbons, organochlorine pesticides, polychlorinated biphenyls, and plastic additives demonstrate that workflows combining docking with microsecond-scale MD and MM-PBSA/GBSA free-energy calculations show markedly higher experimental reproducibility than static docking alone. Beyond individual methods, this article emphasizes the growing importance of integrative computational strategies that unite metagenomics, AI-based structure prediction, enhanced-sampling MD, and machine learning-guided directed evolution within a closed-loop Design-Build-Test-Learn (DBTL) paradigm. Such pipelines enable systematic navigation of vast biological sequence space while simultaneously balancing enzyme stability, conformational flexibility, and catalytic efficiency. Finally, we discuss prevailing challenges encompassing computational cost, structural uncertainty in apo-state predictions, force-field limitations for halogenated substrates, and the translational gap between in silico predictions and environmental field deployment, and outline future directions toward scalable, low-energy, and environmentally robust bioremediation technologies. Collectively, these advances position computational modeling as a cornerstone of next-generation, eco-friendly enzyme discovery.}, } @article {pmid42419222, year = {2026}, author = {Liang, Y and Gao, H and Chen, F and Sun, J and Sun, G and Wang, Z and Li, Y and Liu, H and Geng, M and Li, J and Zhang, Y}, title = {Bilateral intranigral α-synuclein seeding in A53T transgenic mice drives early Parkinsonism and concurrent gut dysbiosis.}, journal = {Biochemical and biophysical research communications}, volume = {830}, number = {}, pages = {154244}, doi = {10.1016/j.bbrc.2026.154244}, pmid = {42419222}, issn = {1090-2104}, abstract = {Heterozygous A53T α-synuclein transgenic mice (M83 line) typically exhibit late-onset Parkinson's disease (PD) symptoms. This study established an accelerated PD model via bilateral intranigral injection of α-synuclein preformed fibrils (PFF) to characterize central and peripheral pathologies. Three-month-old heterozygous A53T mice received bilateral substantia nigra injections of α-synuclein PFF or PBS. Motor function was assessed monthly. Following the onset of motor deficits, the substantia nigra was harvested for immunohistochemistry and colons were harvested for H&E, transcriptomic analysis and western blotting, while gut microbiota composition was assessed using metagenomic sequencing. Three months post-injection, PFF-treated mice exhibited significant motor deficits, dopaminergic neuron loss, and nigral α-synuclein aggregation, with no sex differences. Peripherally, mice displayed increased α-synuclein in colon, impaired gut motility, reduced Occludin expression indicating barrier damage, and colonic inflammation. Metagenomics identified gut dysbiosis characterized by a skewed Bacillota/Bacteroidota ratio, Lactobacillus depletion, and enrichment of inflammation-associated taxa. Bilateral intranigral α-synuclein PFF injection in A53T mice successfully induces an early-onset, progressive PD phenotype encompassing motor impairments, nigrostriatal neurodegeneration. Crucially, the model recapitulates key peripheral manifestations, including gastrointestinal dysfunction and microbial dysbiosis. These findings provide compelling evidence for a descending brain-to-gut pathological axis where central α-synuclein pathology drives distal gut alterations. This optimized model offers a valuable platform for investigating multi-system PD progression and bidirectional brain-gut communication mechanisms.}, } @article {pmid42419237, year = {2026}, author = {Li, T and Xu, J and He, S and Zhao, Q and Liu, J and Shi, Y}, title = {Salinity of oxidation pond effluent regulates the fate of antibiotic resistance genes in the soil-leachate continuum by selecting a salt-adaptive resistome.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142854}, doi = {10.1016/j.jhazmat.2026.142854}, pmid = {42419237}, issn = {1873-3336}, abstract = {Oxidation pond effluent (OPE) reuse can introduce antibiotic resistance genes (ARGs) into agricultural soils. Yet, how OPE salinity regulates ARG fate across the soil-leachate continuum remains poorly understood. Soil column experiments were conducted using three OPE salinity levels with electrical conductivities of 4.35, 8.24, and 13.17 dS/m, combined with high-throughput quantitative PCR and metagenomics. Results showed that although increasing OPE salinity reduced the mean ARG abundance across the soil-leachate continuum, its effects were clearly depth dependent, with slight ARG enrichment of 10.78%-17.26% in surface soil (0-30 cm), a unimodal response in the 30-60 cm layer, and marked reduction of 24.17%-42.60% in deeper soil (60-90 cm) and leachate. More importantly, increasing OPE salinity reduced total ARG abundance by about 14.13% in OPE, but ARG abundance still increased in surface soil after irrigation. Metagenomic analyses showed increasing OPE salinity selectively enriched ARGs related to antibiotic efflux and antibiotic inactivation, indicating that salt-adaptive ARG enrichment better explained topsoil ARG accumulation than total ARG input load alone under OPE irrigation. In addition, surface ARG enrichment was linked to the selection of bacterial groups capable of maintaining ARGs under saline conditions, and the co-localization of salt-tolerance genes, ARGs, and MGEs. In deeper soil and leachate, ARG attenuation was driven mainly by reduced bacterial abundance under continued salinity accumulation. These findings provide a new perspective on ARG risk under saline wastewater irrigation by showing that salinity-driven reshaping of the introduced resistome and salinity accumulation regulate ARG fate and downward transport potential.}, } @article {pmid42419245, year = {2026}, author = {Han, Z and Zhang, Y and Luan, X and Feng, H and Wang, Y and Deng, Y and Hu, C and Yang, M}, title = {Clinically prevalent transposons contribute to erm gene dissemination in the field soil under pseudo-persistent erythromycin contamination.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142927}, doi = {10.1016/j.jhazmat.2026.142927}, pmid = {42419245}, issn = {1873-3336}, abstract = {Clinically relevant antibiotic resistance genes (ARGs) or their ancestral genes are widespread in natural soil microbiome at ultralow abundance. Whether and how long-term antibiotic pressure in soil accelerate dissemination of these ARGs remain unclear. Here, annual cycle of erythromycin exposure at levels around 5-20 μg∙kg[-1] was conducted in previously undisturbed field soil for consecutive five years, to simulate the pseudo-persistent characteristic of antibiotic contamination in soil environment. The primary clinically relevant macrolide resistance genes, rRNA methyltransferase genes (erm genes), were initially rare but gradually enriched, exhibiting a 37.8-fold increase after five years, which was greatly higher than macrolide efflux pump genes and inactivation genes (less than 2.3-fold). Among diverse mobile genetic elements, transposase gene tnpA exhibited potential association with the horizontal transfer of erm genes during long-term erythromycin exposure. From genetic and statistical evidence, enriched erm genes were presumed to locate on Bacilli with mobile transposable elements Tn554 and Tn551, which were clinically prevalent gene clusters in pathogens-Enterococcus and Staphylococcus. Thus, there may be a historical contribution of long-term erythromycin contamination to erm-carrying clinical transposable elements in soil microbiome. Our findings also demonstrated soil erythromycin exposure at levels much lower than laboratory-determined minimal selective concentrations (MSCs) still exhibits long-term effects on erm genes. Taking pseudo-persistent characteristic of antibiotic contamination, we further proposed long-term in-situ assessment with endpoint of clinically relevant ARGs to obtain a real-world MSC in the future studies.}, } @article {pmid42419262, year = {2026}, author = {Gelsinger, DR and Wang, HH}, title = {Toward precision microbiome therapeutics: From black box to blueprint.}, journal = {Cell host & microbe}, volume = {34}, number = {7}, pages = {1157-1161}, doi = {10.1016/j.chom.2026.06.014}, pmid = {42419262}, issn = {1934-6069}, mesh = {Humans ; Metagenomics ; *Gastrointestinal Microbiome/physiology/genetics ; Bacteria/genetics ; Animals ; Gene Editing ; *Precision Medicine/methods ; Microbiota ; }, abstract = {The gut microbiome influences human health, yet microbiome-mediated therapies have lagged as metagenomics identifies gut-colonizing microbes without clarifying functional networks. Prior microbiome "reset" approaches improved clinical outcomes despite limited mechanistic understanding. We argue a critical field inflection point: in situ genome editing of native bacteria enables mechanism-driven, programmable, species-specific therapeutics.}, } @article {pmid42419272, year = {2026}, author = {Crysler, A and de la Fuente-Nunez, C}, title = {Mining the code of life for new antibiotics.}, journal = {Cell host & microbe}, volume = {34}, number = {7}, pages = {1273-1284}, doi = {10.1016/j.chom.2026.06.007}, pmid = {42419272}, issn = {1934-6069}, mesh = {*Anti-Bacterial Agents/pharmacology/chemistry ; *Drug Discovery/methods ; Antimicrobial Peptides/pharmacology ; Humans ; Drug Resistance, Bacterial ; Bacteria/drug effects/genetics ; Generative Artificial Intelligence ; Machine Learning ; }, abstract = {Antimicrobial resistance (AMR) is outpacing antibiotic development, creating an urgent need for discovery strategies that are faster, broader, and more systematic. Here, we review the transition from classical "dirt mining" and phenotypic screening toward digital discovery approaches that treat chemical structures and biological sequences as searchable, engineerable substrates for antibiotic innovation. Modern extensions of conventional screening, including in situ cultivation, co-culture, and microfluidics, have broadened access to previously uncultured microbes. Computer-aided approaches spanning virtual screening, molecular networking, and deep learning have enabled identification of unconventional antibacterial scaffolds from ultra-large chemical libraries. Mining genomes, proteomes, and metagenomes has uncovered antimicrobial peptides, encrypted peptides, and biosynthetic gene clusters encoding novel small-molecule antibiotics. Generative AI now enables design of peptides and small molecules under multiobjective constraints, including potency, toxicity, stability, and resistance risk. Together, these advances point toward discovery platforms that improve novelty, hit rates, and long-term durability in the face of AMR.}, } @article {pmid42419418, year = {2026}, author = {Lin, YR and Tseng, HY and Lai, ZL and Hsueh, PR}, title = {Metagenomic next-generation sequencing facilitates the diagnosis of disseminated Mycobacterium tuberculosis infection in a patient with complex sepsis.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {107918}, doi = {10.1016/j.ijantimicag.2026.107918}, pmid = {42419418}, issn = {1872-7913}, } @article {pmid42419508, year = {2026}, author = {Hering-Peter, C and Schulz, R}, title = {Physiological responses of floc-forming microalgae-bacteria consortia to environmental perturbations.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135341}, doi = {10.1016/j.biortech.2026.135341}, pmid = {42419508}, issn = {1873-2976}, abstract = {Fast-sedimenting microalgae-bacteria consortia (MBC) offer a cost-efficient pathway for biomass harvesting while remediating polluted water bodies in chemostatic photobioreactors. Understanding how abiotic parameters affect floc morphology, sinking properties and metagenomic species composition remains critical for optimization of these specific bioreactors. This study investigated whether fast-sedimenting MBC maintain structural resilience under moderate stress but lose stability beyond critical physiological tipping points. By investigating the physiological boundaries of five environmental factors, we identified clear operational thresholds. Moderate perturbations including light intensities up to 1500 µmol m[-2] s[-1], salinities from 0 to 35 PSU and low antibiotic concentrations showed no statistically significant impact on settling efficiency. In contrast, extreme pH at 12 and temperatures at 45 °C reduced recovery rates by more than 50 % compared to controls maintaining above 87 % efficiency. The surface charge decreased from -27.94 mV to -4.83 mV under acidic conditions at pH 3, indicating electrostatic destabilization of the floc matrix. Dominance of the cyanobacterium Thermoleptolyngbya spp. persisted above 70 % abundance across all treatments. These findings define a safe operating envelope between pH 6-9 and temperatures from 15 to 35 °C necessary to maintain gravity-driven sedimentation. This work provides quantitative boundaries where biological buffering fails, enabling predictive reactor design that avoids biomass washout in continuous cultivation systems.}, } @article {pmid42419510, year = {2026}, author = {He, J and Liu, Y and Zhao, Y and Wei, T and Gong, Z and Wu, Y and Kang, X and Zhang, W and Ma, J and Chu, Z and Wang, R}, title = {Metagenomic insights into the mechanisms of heteroatom-doped, iron-loaded biochar in enhancing anaerobic digestion of waste activated sludge.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135349}, doi = {10.1016/j.biortech.2026.135349}, pmid = {42419510}, issn = {1873-2976}, abstract = {Anaerobic digestion is a crucial technology for resource recovery from waste activated sludge. Enhancing its methane production efficiency using conductive materials is a key research objective. This study aimed to elucidate the mechanisms by which conductive materials promote this process. Three types of biochar(FeS@BC300, FeP@BC600, and FeP@BC900) were prepared by doping bamboo powder with N, P, S and iron salts under pyrolysis conditions at 300-900 °C, and their physical and chemical properties were characterized, including surface functional groups, specific surface area, capacitance, electrical resistance, electron-accepting capacity (EAC), and electron-donating capacity (EDC). These analyses assessed the influence of synthesis parameters. These materials were subsequently introduced into the anaerobic digestion of thermally hydrolyzed sludge to evaluate their impacts on methanogenic performance, microbial community structure, and metabolic pathways. The results show that the FeP@BC600 material, which exhibited the highest EDC, substantially increased microbial cytochrome c production (by 29.2 % compared to the control). This enhancement improved interspecies electron transfer, stimulated ATP synthesis (increased by 41.5 %), and reinforced both hydrogenotrophic and acetoclastic methanogenic pathways, ultimately elevating methane production by 55 %. Integrated analysis of metagenomic data, material properties, and performance metrics revealed that the key mechanism by which FeP@BC600 promotes methanogenesis is through the enrichment of cytochrome c-encoding genes, thereby facilitating direct interspecies electron transfer (DIET) and augmenting ATP synthesis. This study provides a foundation for the subsequent application of conductive materials to enhance anaerobic digestion and offers guidance for the optimized design of such materials.}, } @article {pmid42419591, year = {2026}, author = {Kim, S and Seo, H and Jo, S and Rahim, MA and Hossain, MS and Shuvo, MSH and Jeong, SY and Lee, MY and Kim, KH and Lee, N and Won, JH and Song, HY and Yoon, SY}, title = {Oral Sodium Butyrate Supplementation, Gut Microbiome Modulation, and Reduced Acute Graft-versus-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation.}, journal = {Transplantation and cellular therapy}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtct.2026.07.006}, pmid = {42419591}, issn = {2666-6367}, abstract = {BACKGROUND: Acute graft-versus-host disease (aGVHD) remains a major cause of morbidity and mortality after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Disruption of the gut microbiome during transplantation has been implicated in the pathogenesis of aGVHD, yet clinically applicable strategies to modulate the microbiome in immunocompromised patients remain limited.

OBJECTIVES: To evaluate the association between oral sodium butyrate supplementation and the incidence and severity of aGVHD, and to investigate its impact on gut microbiome recovery following allo-HSCT.

STUDY DESIGN: In this prospective, single-center study, 39 consecutive patients undergoing allo-HSCT received oral sodium butyrate (1,200 mg/day) from neutrophil engraftment to day +100. Outcomes were compared with 18 historical controls treated at the same institution without butyrate supplementation. The primary endpoint was the cumulative incidence of grade II-IV aGVHD by day +100. Secondary endpoints included lower gastrointestinal aGVHD and microbiome characteristics assessed using shotgun metagenomic sequencing. Competing risk analyses were performed to account for death as a competing event.

RESULTS: Butyrate supplementation was associated with a lower incidence of grade II-IV aGVHD (30% vs 53%, p=0.028) and grade III-IV aGVHD (5% vs 34%, p=0.002). Lower gastrointestinal aGVHD occurred in 5% of the butyrate group compared with 40% of historical controls (p<0.001). In multivariable competing risk analysis, butyrate supplementation remained independently associated with reduced grade II-IV aGVHD (adjusted HR 0.31, 95% CI 0.11-0.89; p=0.029) and lower gastrointestinal aGVHD (adjusted HR 0.07, 95% CI 0.02-0.30; p<0.001). Microbiome analysis demonstrated improved recovery of gut microbial diversity at day +100 in the butyrate group, with enrichment of commensal taxa and restoration of fecal butyrate levels.

CONCLUSIONS: Oral sodium butyrate supplementation was associated with reduced incidence and severity of aGVHD, particularly involving the gastrointestinal tract, along with improved microbiome recovery. These findings suggest a potential role for postbiotic-based microbiome modulation in GVHD prevention and warrant validation in randomized controlled trials.}, } @article {pmid42410232, year = {2026}, author = {Li, Y and Li, J and Wang, H and Fan, J and Tang, K and Yan, G and Dong, W and Lan, T}, title = {Ischial tuberculosis: MRI and mNGS enable early diagnosis in the largest reported case series of twenty two patients.}, journal = {International orthopaedics}, volume = {}, number = {}, pages = {}, pmid = {42410232}, issn = {1432-5195}, support = {PYZ24154//The Scientific Research Cultivation Fund of Capital Medical University/ ; SKLSIM-2024108//The 2024 Youth Project of the Open Research Fund of the State Key Laboratory of Neurology and Oncology Drug Development/ ; }, abstract = {PURPOSE: To analyze the clinical features, diagnosis, treatment, and prognosis of ischial tuberculosis (IT), and to evaluate the diagnostic value of MRI and mNGS in the largest reported case series to date.

METHODS: Data from 22 patients with confirmed IT treated between January 2013 and January 2023 were retrospectively reviewed. Diagnosis was based on histopathology, microbiology, and molecular tests.

RESULTS: The mean age was 31.6 years (11 to 67). Common symptoms included gluteal pain (100.0%), sitting-induced pain (81.8%), and local swelling (59.1%). Computed tomography (CT) revealed lesions in 86.4% of patients, while magnetic resonance imaging (MRI) showed abnormalities in all 18 patients examined. The ischial tuberosity was the most common site of involvement (63.6%). The T-cell spot test for tuberculosis infection (T-SPOT.TB), Xpert Mycobacterium tuberculosis/rifampicin resistance assay (Xpert MTB/RIF), and metagenomic next-generation sequencing (mNGS) showed positivity rates of 83.3%, 83.3%, and 100%, respectively. Histopathological granulomas were observed in 77.3%. Overall, 68.2% underwent surgical debridement. All patients achieved clinical cure with no recurrence at a mean follow-up of 34.7 months.

CONCLUSION: IT has an insidious onset. MRI (100% sensitivity) is valuable for early diagnosis, and molecular tests, particularly mNGS (100% detection rate), enhance pathogen detection. Surgical debridement combined with standard chemotherapy achieved clinical cure in all patients, but comparative studies are needed to confirm its superiority over conservative treatment.}, } @article {pmid42410336, year = {2026}, author = {Xie, Y and Cidan, Y and Sun, F and Renqing, C and Cisang, Z and Wang, D and Cideng, D and Basang, W and Zhu, Y}, title = {Bacillus-based probiotic supplementation reshapes rumen bacterial and fungal communities and enhances carbohydrate-degrading functional capacity in weaned yaks.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05372-2}, pmid = {42410336}, issn = {1471-2180}, support = {XZ202401YD0012//Central Government-Guided Local Science and Technology Development Project, Mining and Application of Functional Microorganisms and Enzyme Resources for Efficient Cellulose Degradation in Yaks/ ; CARS-37//Modern Agricultural Industry Technology System for Beef and Yak/ ; QYXTZX-LS2020-01//Breeding and Efficient Propagation of Yaks in Gesangtang of Linzhou County/ ; }, abstract = {This study evaluated the effects of dietary supplementation with Bacillus-based probiotics on growth performance, nutrient digestibility, rumen fermentation, and microbial functional capacity in weaned yaks. Twenty animals were randomly assigned to a basal diet (control group, CON) or the same diet supplemented with Bacillus subtilis and Bacillus licheniformis (probiotic group, PRO) for 90 days. Probiotic supplementation increased average daily gain (P < 0.05) and tended to increase dry matter intake (P = 0.059). In addition, neutral detergent fibre and acid detergent fibre digestibility were improved (P < 0.05), suggesting improved degradation of structural carbohydrates. Rumen fermentation was altered, with increased concentrations of butyrate and isovalerate and reduced ammonia nitrogen, suggesting improved fermentation efficiency and nitrogen metabolism. Microbial analysis showed that probiotics reshaped both bacterial and fungal community structures without affecting α-diversity, indicating selective modulation of key microbial taxa. Notably, the relative abundance of carbohydrate-degrading genera, including Xylanibacter, was increased. Metagenomic analysis further demonstrated changes in microbial functional capacity, as evidenced by increased abundance of carbohydrate-active enzymes and genes associated with cellulose, hemicellulose, chitin, lignin, and starch degradation. These results indicate that Bacillus-based probiotics were associated with improved growth performance and enhanced rumen microbial functional potential related to carbohydrate degradation.}, } @article {pmid42410398, year = {2026}, author = {Xiang, X and Zhu, Y and Wang, T and Cheng, K and Ming, Y}, title = {Association between salivary microbiota-related amino acid metabolic dysregulation and tacrolimus-induced gingival overgrowth following kidney transplantation.}, journal = {BMC oral health}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12903-026-09004-z}, pmid = {42410398}, issn = {1472-6831}, support = {81771722//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Kidney transplant (KT) recipients require lifelong immunosuppressive therapy to prevent allograft rejection. Drug-induced gingival overgrowth (DIGO) is a notable adverse effect of tacrolimus, for which effective preventive or therapeutic strategies are lacking. Dysbiosis of the oral microbiota has been implicated as a major risk factor for DIGO. However, its mechanistic role remains poorly understood.

RESULTS: Twenty KT recipients with newly diagnosed DIGO while receiving tacrolimus were enrolled, along with 20 matched controls with stable graft function. Salivary samples were collected and subjected to metagenomic and untargeted metabolomic profiling. Taxonomic analysis revealed greater microbial heterogeneity in DIGO patients compared to more interconnected communities observed in controls. Periodontitis-associated taxon, including Porphyromonas gingivalis, were enriched in the DIGO group. Multiple differentially expressed microbial genes and metabolites were identified, predominantly enriched in disordered amino acid metabolic pathways. Key metabolites-such as L-proline, carnosine, choline, 5-aminolevulinic acid, and spermidine-showed strong associations with DIGO-related taxon.

CONCLUSION: A strong association was observed between salivary microbial composition, metabolic profiles, and DIGO. The identified microbiota and metabolite alterations suggest a potential link between amino acid metabolic dysregulation and gingival fibroblast-related pathways in DIGO. These findings provide new insights into the biological features of DIGO and offer a foundation for future mechanistic and therapeutic studies.}, } @article {pmid42410808, year = {2026}, author = {Wang, Y and Yang, X and Wang, Q and Shen, T and Wang, W and Qiu, J}, title = {Microbial flora and antimicrobial resistance in dental unit waterlines of Chongqing: An observational cross-sectional laboratory study.}, journal = {Medicine}, volume = {105}, number = {27}, pages = {e49461}, doi = {10.1097/MD.0000000000049461}, pmid = {42410808}, issn = {1536-5964}, mesh = {China ; *Water Microbiology ; Cross-Sectional Studies ; *Dental Equipment/microbiology ; Humans ; *Drug Resistance, Bacterial/genetics ; *Bacteria/isolation & purification/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; }, abstract = {To identify pathogenic bacteria in dental water systems and assess microbial diversity and resistance genes, we collected water samples from 35 dental facilities in Chongqing, China. Using the VITEK 2 COMPACT system, we identified 26 strains and 13 species of opportunistic pathogens in 23 samples exceeding the standard limits. In addition, metagenomic sequencing was performed to investigate microbial diversity and resistance genes. Among the 170 collected samples, 78.2% qualified, with no significant variation across samples. However, there was a statistically significant difference in qualifying rates between hospitals of different levels (χ2 = 7.696, P = .021). Most bacteria (80.8%) were Gram-negative and non-Enterobacteriaceae, with only 1 type belonging to the Enterobacteriaceae family. Notably abundant resistance genes included bacA, adeC, mexT, mdfA, adeJ, mdtK, emrB, and mdtB, predominantly associated with multidrug resistance (relative abundance: 71.42%). The contamination of dental unit waterlines is a concern that cannot be overlooked.}, } @article {pmid42411404, year = {2026}, author = {Bouras, G and Grigson, SR and Durr, L and Papudeshi, B and Mallawaarachchi, V and Vreugde, S and Edwards, RA}, title = {Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny.}, journal = {Current protocols}, volume = {6}, number = {7}, pages = {e70405}, doi = {10.1002/cpz1.70405}, pmid = {42411404}, issn = {2691-1299}, support = {//Australian Research Council/ ; }, mesh = {*Genome, Viral ; *Metagenomics/methods ; *Computational Biology/methods ; *Viruses/genetics ; *Metagenome ; Molecular Sequence Annotation/methods ; *Software ; Bacteriophages/genetics ; Viral Proteins/genetics ; }, abstract = {Viral metagenomics is an increasingly powerful tool for understanding the function and structure of viruses across the diverse environments of our planet. However, decoding the functional potential of prokaryotic viral metagenomes is extremely challenging. Pharokka, Phold, and Phynteny are complementary open-source prokaryotic viral genome annotation tools that utilize a variety of bioinformatics approaches to maximally annotate viral metagenomes. This article describes a protocol for installing and running these tools on a viral metagenomic dataset, followed by visualization of annotations using our client-side Phold Plot web assembly application. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Prokaryotic viral metagenome annotation with Pharokka Basic Protocol 2: Enhanced prokaryotic viral metagenome protein annotation using protein structures with Phold Basic Protocol 3: Further prokaryotic viral metagenome protein annotation using genome synteny and protein language models with Phynteny Basic Protocol 4: Visualization of prokaryotic viral metagenome annotations with Phold Plot web assembly application.}, } @article {pmid42412829, year = {2026}, author = {Wang, S and Du, Y}, title = {VirBinn improves viral genome binning from metagenomic Hi-C through graph diffusion.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {Supplement_1}, pages = {}, doi = {10.1093/bioinformatics/btag271}, pmid = {42412829}, issn = {1367-4811}, support = {//University of Texas Systems STARs Program/ ; }, mesh = {*Genome, Viral ; *Metagenomics/methods ; Animals ; Humans ; *Software ; Metagenome ; Algorithms ; }, abstract = {MOTIVATION: Metagenomic Hi-C provides in situ proximity signals that can improve genome binning and enable virus-host-association analysis. However, viral genome recovery remains difficult because virus-virus Hi-C contact matrices are extremely sparse. Viral genomes are small, often low-abundance, and frequently assemble into short contigs, leaving many true within-genome links unobserved and causing viral bins to fragment.

RESULTS: We present VirBinn, a graph-diffusion framework for viral binning from metagenomic Hi-C. VirBinn enhances virus-virus connectivity through two complementary mechanisms: random-walk-with-restart enhancement on the sparse virus-virus contact graph and host-guided diffusion that propagates viral seeds through the host network to infer indirect virus-virus associations. The enhanced views are integrated and clustered using Leiden community detection to produce viral metagenome-assembled genomes (vMAGs). On dataset-specific simulation benchmarks with ground truth, VirBinn consistently recovers more high-quality vMAGs than Hi-C-based and shotgun-based baselines and substantially increases the number of near-complete genomes. On four real metagenomic Hi-C datasets spanning human gut, pig gut, sheep gut (long-read assembly), and wastewater, VirBinn yields more high-completeness vMAGs under CheckV and produces bins with strong within-cluster contact support. Finally, host linkage analysis using reconstructed host MAGs reveals habitat-specific host-association patterns and plausible host taxonomic profiles.

VirBinn is available at https://github.com/dyxstat/VirBinn. The scripts to reproduce the results and figures in this article are available at https://github.com/dyxstat/Reproduce_VirBinn.}, } @article {pmid42412840, year = {2026}, author = {Zhang, A and Boucher, C and Noyes, N and Yu, YW}, title = {RAmpSim: a thermodynamic simulator for hybridization capture in metagenomic sequencing.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {Supplement_1}, pages = {}, doi = {10.1093/bioinformatics/btag303}, pmid = {42412840}, issn = {1367-4811}, support = {R35GM160134/NH/NIH HHS/United States ; R01AI173928/NH/NIH HHS/United States ; R01AI141810/NH/NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Thermodynamics ; *Nucleic Acid Hybridization/methods ; *Sequence Analysis, DNA/methods ; *Software ; Computer Simulation ; }, abstract = {MOTIVATION: Simulators that generate synthetic datasets help address the lack of ground truth for developing and benchmarking computational tools. Many read simulators assume uniform sampling across reference genomes; however, for newer capture-based sequencing technologies (e.g. TELSeq), this assumption is intentionally broken to oversample regions of interest. Along with systematic biases arising from probe multiplicity, sequence composition, and species abundances inherent to capture-based sequencing, this mismatch between modeling assumptions and the characteristics of real data necessitates the design of a new capture-based sequencing-specific simulator.

RESULTS: We present RAmpSim, a fast simulator that models bait-target hybridization and fragment capture using a thermodynamic nearest-neighbor energy model and Boltzmann-weighted sampling of binding sites. Fragments are generated through multinomial sampling parameterized by bait concentration, binding energy, and genomic abundance before being passed to existing models of platform-specific errors. Implemented in Rust, RAmpSim reproduces empirical within-genome coverage and cross-species enrichment patterns observed in capture-based metagenomic datasets. RAmpSim generally outperforms a uniform baseline with respect to position-based earth mover's distance when compared against the empirical coverage distribution. Classification analysis also shows high recall in recovering empirical high-coverage regions while outperforming a uniform baseline.

AVAILABILITY: Code, example scripts, and data sources are available at https://github.com/az002/RAmpSim.git.}, } @article {pmid42413135, year = {2026}, author = {Hernández-Velázquez, R and Bokulich, NA}, title = {Unlocking the biotechnological potential of traditional fermented food microbiomes.}, journal = {Current opinion in biotechnology}, volume = {100}, number = {}, pages = {103550}, doi = {10.1016/j.copbio.2026.103550}, pmid = {42413135}, issn = {1879-0429}, abstract = {Fermented foods are a globally important source of dietary microbes, cultural heritage, and functional diversity, yet current microbiome research captures only a narrow fraction of this richness. Public sequencing datasets are heavily skewed toward a limited set of regions and fermentation types, leaving vast areas of geographic, substrate, and process diversity underrepresented. This imbalance constrains the discovery of novel microbial species, enzymes, and biosynthetic capacities, and risks accelerating homogenization through standardized starter cultures. We argue that coordinated, ethically grounded global efforts integrating metagenomics, multi-omics, standardized metadata, and biobanking are urgently needed to document, preserve, and responsibly leverage fermented food microbial diversity for sustainable food systems and innovation.}, } @article {pmid42413264, year = {2026}, author = {Hu, N and Feng, Q and Li, C and Liu, Y and Zhu, B and Guo, T and Tong, L and Shi, J and Sanford, RA and Li, S and He, Y and Hu, Y and Jiang, Z and Jiang, Y and Zhao, L and Wang, M and Xu, M and Li, Y and Dong, Y and Shi, L}, title = {Fe(II)-driven abiotic-biotic relay alleviates denitrification bottleneck via chemical nitrite reduction and intracellular carbon.}, journal = {Water research}, volume = {304}, number = {}, pages = {126366}, doi = {10.1016/j.watres.2026.126366}, pmid = {42413264}, issn = {1879-2448}, abstract = {The coexistence of iron and nitrate (NO3[-]) in natural and engineered environments invites complex abiotic and biotic interactions, yet how such abiotic-biotic synergies operate under fluctuating carbon availability and how light modulates them remain poorly resolved. Using a nitrate-reducing, nitrite-accumulating enrichment culture derived from lake sediment, we uncovered a synergistic abiotic-biotic relay that overcame the kinetic bottleneck of denitrification. During initial heterotrophic denitrification of 2 mM NO3[-], 85.10-89.72% of the substrate was accumulated as NO2[-]. In contrast, ferrous iron (Fe(II)) amendment triggered subsequent iron-dependent nitrate reduction (IDNR) and significantly reduced NO2[-] accumulation. Abiotic controls confirmed that Fe(II) chemically reduced the accumulated NO2[-] to the downstream products. In parallel, metagenomic and metatranscriptomic analyses of the bioactive samples demonstrated that these gaseous intermediates (e.g., NO, N2O) were enzymatically reduced to N2 based on upregulated denitrification-associated genes. More importantly, when exogenous acetate was depleted, the community sustained IDNR not through strict autotrophy but via heterotrophic metabolism using intracellular poly-3-hydroxybutyrate (PHB) and microbial necromass as the carbon/energy sources. This metabolic plasticity drove a functional succession from organotrophic denitrifiers (e.g., Pseudomonas) toward PHB- and necromass-utilizing microbial consortia mainly composed of Pseudomonas, Alicycliphilus and some phototrophic populations. Supporting evidence showed that illumination further accelerated the relay via light-driven reactive oxygen species, and secondary iron minerals (e.g., bernalite, lepidocrocite, and goethite) formed as fingerprints of the Fe(II) oxidation. Collectively, this work deciphers a dual-mechanism model, abiotic nitrite reduction followed with endogenous carbon-fueled denitrification, that governed efficient nitrate reduction under carbon-limited conditions. Leveraging such abiotic-biotic relays offers promising strategies for sustainable nitrogen removal in both natural and engineered systems.}, } @article {pmid42413404, year = {2026}, author = {Cao, Z and Gong, H and Qin, H and Wei, T and He, X and Yang, K and Li, X and Wang, Y and Jia, Y and Lan, X and He, W and Jing, X and Long, R and Li, B and Mi, J}, title = {Gut dysbiosis and Escherichia coli-associated enrichment of antibiotic resistance genes in diarrheal yak calves.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142862}, doi = {10.1016/j.jhazmat.2026.142862}, pmid = {42413404}, issn = {1873-3336}, abstract = {Yak grazing systems are fundamental to pastoralist livelihoods on the Qinghai-Tibet Plateau (QTP), and their safe and sustainable development is essential for regional socioeconomic stability. Diarrhea is a multifactorial disease that severely impairs calf growth and may lead to mortality. In this study, we integrated second- and third-generation metagenomic sequencing with untargeted metabolomics to elucidate the underlying mechanisms and associated biosafety risks in yak calves with diarrhea. The results revealed significant gut microbiota dysbiosis in affected calves, characterized by reduced α-diversity and disrupted metabolism of arachidonic acid (AA) and its derivatives. Analysis of 1799 high-quality metagenome-assembled genomes (MAGs; ≥50% completeness and ≤5% contamination) showed a markedly increased relative abundance of Escherichia coli (16.4%) in diarrheal feces, far exceeding that observed in healthy controls. Eight assembled E. coli strains served as major reservoirs of antibiotic resistance genes (ARGs), contributing to high fecal abundances of resistance genes associated with MLS antibiotics (22.1%), bacitracin (21.7%), and β-lactams (19.9%), along with abundant mobile genetic elements (MGEs), including tnpA (21.1%) and IS91 (13.0%). Viral profiling identified E. coli as a key host for bacteriophages belonging to the families Chimeraviridae, Straboviridae, and Suoliviridae. These phages carried ARGs and MGEs that matched those detected in E. coli, potentially facilitating the dissemination of resistance through horizontal gene transfer. StrainPhlAn analysis further demonstrated that multidrug-resistant E. coli strains are widespread even among healthy calves, indicating the presence of a hidden resistome with potential for inter-individual transmission. These findings provide important theoretical guidance for managing yak calf diarrhea and offer valuable references for improving livestock production safety and mitigating antimicrobial resistance on the QTP.}, } @article {pmid42413405, year = {2026}, author = {Zhang, K and Fang, Y and Zhang, L and Zhao, W and Zhang, X and Ye, L}, title = {Dissolved oxygen regulation enhances organic micropollutant removal in wastewater treatment bioreactors.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142887}, doi = {10.1016/j.jhazmat.2026.142887}, pmid = {42413405}, issn = {1873-3336}, abstract = {Organic micropollutants (OMPs) are ubiquitously detected in wastewater and pose potential risks to aquatic ecosystems and human health, making their effective removal a critical objective of wastewater treatment processes. Dissolved oxygen (DO) is a central operational parameter that governs microbial metabolism in biological wastewater treatment processes; however, its long-term role in controlling OMP removal remains insufficiently understood. Here, three bioreactors were operated for 166 days under staged DO conditions ranging from 0.8 to 4.5 mg/L to systematically evaluate the effects of DO on the removal of eight representative OMPs and associated microbial responses. Operating at a low DO level maintained stable removal of conventional pollutants while significantly enhancing the biodegradation of several OMPs, including dimetridazole, ofloxacin, trimethoprim, and sulfamethazine. Despite only minor changes in overall community composition, intermediate and rare taxa exhibited pronounced sensitivity to DO variation, suggesting their potential involvement in OMP biodegradation under low-oxygen conditions. Enzyme activity measurements combined with metagenomic and transcriptomic analyses further revealed that low DO promoted higher activity, abundance, and expression of redox-related co-metabolic enzymes, particularly peroxidases and cytochrome P450 enzymes. These results demonstrate that DO regulates OMP removal primarily by reshaping microbial functional potential and redox metabolism. Overall, this study provides both mechanistic understanding and practical guidance for applying DO regulation to achieve enhanced micropollutant removal in wastewater treatment systems.}, } @article {pmid42413431, year = {2026}, author = {Mitra, S and Ahmed, MF and Yusuf, MA}, title = {Hidden pathways of antimicrobial resistance: A review of environmental metagenomics and exposure risks in low-resource settings.}, journal = {Journal of environmental management}, volume = {414}, number = {}, pages = {130366}, doi = {10.1016/j.jenvman.2026.130366}, pmid = {42413431}, issn = {1095-8630}, abstract = {Antimicrobial resistance (AMR) is increasingly recognised as a One Health challenge in which environmental reservoirs play an important role in the persistence and dissemination of resistance genes. Despite growing recognition that environmental antimicrobial resistance is a critical component of the One Health challenge, the pathways through which antimicrobial resistance genes (ARGs) move between environmental systems and human populations remain incompletely characterised, particularly in low- and middle-income countries where environmental exposures are greatest and surveillance capacity is limited. This review synthesises current knowledge on environmental resistomes across soil, water, sediment and groundwater systems, with a focus on metagenomic and quantitative analytical approaches that have transformed environmental AMR surveillance. Unlike traditional culture-based methods, metagenomics enables comprehensive, culture-independent profiling of microbial communities and their associated resistomes, allowing detection of both known and previously uncharacterised resistance genes, as well as insights into their genetic context and mobility. This has significantly advanced our ability to characterise environmental reservoirs and infer potential transmission pathways at ecosystem scale. Using Bangladesh as an illustrative example of environmental exposure dynamics in rapidly urbanising low- and middle-income settings, we examine how contaminated urban waterways, wastewater discharge, agricultural practices, and seasonal hydrological processes-including monsoon-driven flooding-create interconnected transmission pathways linking environmental, animal, and human microbiomes. We also consider how co-selection pressures from heavy metals and other environmental contaminants contribute to the persistence and amplification of antimicrobial resistance beyond antibiotic-driven selection alone. These dynamics are further intensified by dense surface water networks, strong hydrological connectivity, and limited wastewater treatment infrastructure, which together create high-intensity human-environment interfaces and facilitate large-scale redistribution of antimicrobial resistance genes across environmental compartments. Taken together, these features make Bangladesh an analytically distinctive and tractable model system for understanding environmental AMR dynamics, with relevance to comparable deltaic and monsoon-influenced regions in South and Southeast Asia. Key methodological challenges-including the gap between ARG detection and clinical risk interpretation, biases in resistance gene databases, sampling limitations, and the lack of harmonised environmental surveillance frameworks-are examined alongside emerging tools such as long-read sequencing, functional metagenomics and artificial intelligence-assisted bioinformatic analysis. Finally, we propose an integrated One Health framework linking environmental metagenomics, global surveillance systems and policy interventions to support harmonised, data-driven monitoring and mitigation of environmental AMR across interconnected ecosystems.}, } @article {pmid42413842, year = {2026}, author = {Hu, Y and Shi, S and Liu, Y and Chen, H and Cui, K and Wei, L}, title = {Structure and Function of the Coleoptericin Gene in the Ladybird Beetle Serangium japonicum during Seasonal Development.}, journal = {Developmental and comparative immunology}, volume = {}, number = {}, pages = {105675}, doi = {10.1016/j.dci.2026.105675}, pmid = {42413842}, issn = {1879-0089}, abstract = {[OBJECTIVE]: This study was conducted to explain the relationship between structure and function of coleoptericin in Serangium japonicum, and importance of the differential expression patterns of it between in winter and summer, and to provide a theoretical foundation for the rational application of S. japonicum as a natural enemy in pest control. [METHOD]: The full length cDNA was obtained using rapid amplification of cDNA ends (RACE) technology. Bioinformatics software was employed to predict the structure and physicochemical properties of the coleoptericin protein based on its cDNA sequence. The prokaryotic expression protein were tested activity of anti against three experimental strains of microorganisms through using the pore diffusion method. Additionally, metagenome was sequenced and analyzed to find the proteins' effect on microorganism in S.japonicum. [RESULT]: The full-length cDNA sequence of coleoptericin was found to be 606 base pairs (bp) in length. Its open reading frame (ORF) spanned from nucleotide 48 to 495, totaling 447 bp, and encoded a polypeptide of 149 amino acids. Homology analysis revealed that the deduced amino acid sequence shared the highest similarity (55.1%) with the antimicrobial peptide from Tribolium castaneum. The protein had molecular weight of 17.03 kD and theoretical i-soelectric point of 9.19. Hydrophilicity analysis indicated a grand average of hydropathicity (GRAVY) score of -0.85, suggesting a hydrophilic nature. Furthermore, the protein was predicted to contain one transmembrane domain and a signal peptide. Agar well diffusion assays demonstrated that the prokaryotically expressed coleoptericin exhibited antimicrobial activity against Escherichia coli. Results from Metagenome showed that the abundance of Penicillium was significantly lower in winter compared to summer. [CONCLUSION]: The coleoptericin protein from S.japonicum had a sequence of over 100 amino acid residues and an α-helical secondary structure. For S. japonicum, our results supported that coleoptericin protein could protect the beetle from pathogenic bacteria in winter. Some results from relative reports suggested that coleoptericin protein also could be an antifreeze energy source except for immune function.}, } @article {pmid42413995, year = {2026}, author = {Halford, C and Toriro, R and Rowlands, E and Le Viet, T and Schaap, S and O'Shea, MK and Fletcher, T and Beeching, NJ and Woolley, S and Lukaszewski, R and Gilmour, M and Weller, SA}, title = {Detection of Cryptosporidium hominis by clinical metagenomics in stool samples from an outbreak of diarrhoea among British military personnel in Kenya.}, journal = {BMJ military health}, volume = {}, number = {}, pages = {}, doi = {10.1136/military-2026-003248}, pmid = {42413995}, issn = {2633-3775}, abstract = {INTRODUCTION: Traveller's diarrhoea is a common complaint among deployed military personnel. Maintaining sample integrity prior to diagnostic testing is a key challenge in resource-limited environments. We report the comparison of three long-term ambient temperature stool sample stabilisation matrices for the detection of Cryptosporidium hominis from samples collected during an outbreak among British military personnel stationed in Kenya.

METHODS: A retrospective cohort of stool samples, each stabilised for more than 12 months at ambient temperatures using Flinders Technical Associate (FTA) cards, OMNIgene GUT tubes and DNA Shield faecal collection tubes, were analysed by Nanopore-based clinical metagenomic (CMgs) DNA sequencing and quantitative real-time PCR (qPCR) in the UK. The results were compared with BioFire FilmArray Gastrointestinal Panel testing carried out at the point of sampling in Kenya.

RESULTS: Cryptosporidium DNA was detected in 13/24 (54.2%) OMNIgene GUT samples by CMg following long-term storage, compared with 9/24 (37.5%) of DNA Shield samples. Samples stored on FTA cards did not identify Cryptosporidium DNA by CMg in any sample. OMNIgene GUT samples also had the highest rate of detection of C. hominis DNA by qPCR, with 23/24 samples testing positive, compared with 21/24 and 17/20 of DNA Shield and FTA samples, respectively.

CONCLUSIONS: Samples stored in OMNIgene GUT tubes retained detectable levels of Cryptosporidium DNA in a higher proportion of samples following long-term storage. This study demonstrates the importance of selecting the optimal sample collection and stabilisation matrix for CMg and qPCR based diagnostic testing in austere environments.}, } @article {pmid42414020, year = {2026}, author = {Clister, D and Chandra, QM and Tan, MW and Gunawan, MC and Bibi, A and Ahmed, A and Bastian, M and Meesakul, P and Cao, S and Kim, B and Nurkolis, F and Syahputra, RA}, title = {Microbiome-Based Precision Interventions in Type 2 Diabetes Mellitus: Mechanisms, Modulators, and Translational Opportunities.}, journal = {The Journal of nutrition}, volume = {156}, number = {7}, pages = {101596}, doi = {10.1016/j.tjnut.2026.101596}, pmid = {42414020}, issn = {1541-6100}, abstract = {Type 2 diabetes mellitus (T2DM) is a complex metabolic disease driven by insulin resistance, chronic low-grade inflammation, and impaired glucose regulation. Although pharmacological options have advanced, sustained glycemic control remains elusive due to heterogeneity in disease progression and therapeutic response. Precision medicine offers a framework to individualize interventions, with the gut microbiota emerging as a central determinant of host metabolic and immune regulation. Dysbiosis has been implicated in T2DM through altered microbial metabolites-including short-chain fatty acids, bile acids, branched-chain amino acids, and indole derivatives-that shape insulin sensitivity, inflammatory pathways, and glucose homeostasis. This review critically examined microbiome-targeted strategies such as probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and personalized nutrition, alongside advances in metagenomics and machine learning for biomarker discovery. By integrating mechanistic and translational insights, we highlight opportunities and challenges in implementing microbiome-based precision interventions, underscoring their potential to transform T2DM management.}, } @article {pmid42402588, year = {2026}, author = {Jin, Y and Cui, J and Liu, R and Ma, H and Xu, X and Wu, S and Gan, F and Lu, ZJ and Xu, ZZ}, title = {Conserved 3' stem-loop structures enable comprehensive analysis of bacterial transcription termination in metagenomes.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02454-1}, pmid = {42402588}, issn = {2049-2618}, abstract = {BACKGROUND: Bacterial transcription termination is a critical yet underexplored layer of gene regulation in microbial ecosystems. Existing computational tools, however, primarily focus on predicting transcript 3' ends generated by Rho-independent terminators (RITs) in a few model species, leaving gaps in understanding those generated by Rho-dependent terminators (RDTs) and their diversity across Bacteria.

RESULTS: We developed BATTER (Bacteria Transcript Three Prime End Recognizer), a deep learning-based framework for predicting bacterial transcript 3' termini. BATTER leverages the observation that conserved stem-loop structures are frequently associated with 3' ends of primary transcripts terminated by both RIT and RDT mechanisms across diverse bacterial clades. Compared with existing approaches, BATTER demonstrated superior performance and scalability, enabling a comprehensive analysis of 42,905 representative bacterial genomes. This large-scale application revealed that stem-loop structures exhibit clade-specific properties with greater variations between species than between gene families. Notably, BATTER uncovered that certain Cyanobacteria lineages, despite lacking rho homologs, harbor Rho utilization (RUT)-like sequences near 3' ends, and preliminary experimental validation in E. coli supports their partial functionality in transcription termination. Additionally, BATTER systematically identified pervasive premature termination events in antimicrobial resistance (AMR) genes.

CONCLUSIONS: BATTER enables large-scale comparative genomic analyses of transcription termination, providing a powerful framework to investigate termination-associated transcriptional regulation in microbial communities. The BATTER tool is available at https://github.com/xu-research-lab/BATTER. Video Abstract.}, } @article {pmid42402612, year = {2026}, author = {Cao, L and Zhang, G and Zhang, G and Zhang, F and Li, W and Song, Q and He, J and Zhao, J and Zhang, Z}, title = {Cichorium intybus L. polysaccharide improves growth performance and colonic barrier function in weaned piglets via the microbiota-HDCA-TGR5-Akt-NF-κB signaling axis: validation by FMT and in vitro models.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42402612}, issn = {1674-9782}, support = {32302766//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Weaning stress predisposes piglets to intestinal barrier disruption and gut dysbiosis, which contribute to post-weaning diarrhea and poor feed efficiency. Chicory (Cichorium intybus L.) polysaccharide (CLP) is a fructan-rich prebiotic candidate; however, how CLP reshapes the microbiota-metabolite network to protect the colon remains unclear.

METHODS: In Exp. 1, 96 weaned piglets [Duroc × (Landrace × Yorkshire), 28 days old, 8.03 ± 0.2 kg] were fed a basal diet (CON group) or a 0.5% CLP supplemented diet (CLP group). In Exp. 2, fecal microbiota from piglets were transplanted into dextran sulfate sodium (DSS)-induced mice to confirm the causal role of the CLP-remodeled microbiota. Metagenomic and untargeted metabolomic analyses were employed to identify key microbial species and functional metabolites. In Exp. 3, Caco-2 cells were treated with varying concentrations of hyodeoxycholic acid (HDCA) for 24 h to functionally validate the regulatory effects on TGR5 and FXR expression levels.

RESULTS: The results showed that dietary CLP significantly decreased the feed to gain ratio, diarrhea rate and histology index (P < 0.05), but increased goblet cell numbers (P < 0.05). Metagenomic sequencing revealed that CLP significantly increased microbial α-diversity and remodeled the community structure, specifically enriching beneficial microbes, such as Blautia sp., Eubacterium sp., and Ruminococcus sp. To test microbiota causality, fecal microbiota from CON or CLP piglets was transplanted into antibiotic treated mice followed by DSS challenge. The CLP modified microbiota alleviates DSS induced colitis, upregulated Occludin and ZO-1 expression, and reduced colonic IL-1β and TNF-α levels. Mechanistically, the CLP remodeled microbiota promoted the accumulation of HDCA, which functioned as a signaling ligand to activate the colonic TGR5 receptor. This activation subsequently suppressed the phosphorylation of Akt (P < 0.05), leading to the inhibition of the NF-κB signaling pathway through the reduced phosphorylation of IκBα and the p65 subunit (P < 0.05), thereby effectively abrogating the inflammatory response.

CONCLUSION: Dietary CLP supplementation mitigates weaning induced intestinal injury and inflammation by remodeling the colonic microbiota, specifically enriching HDCA-producing species. The subsequent activation of the HDCA-TGR5-Akt signaling axis inhibits the NF-κB pathway, thereby improving host immune responses and intestinal barrier function.}, } @article {pmid42402715, year = {2026}, author = {Bellucci, M and Mostofa, MG and Benucci, GMN and Kabir, AH and Khan, I and Lombardi, M and Locato, V and Bonito, G and Loreto, F and Sharkey, TD}, title = {Isoprene-Emitting Transgenic Tobacco Shapes Root Microbiome and Enhances Growth of Co-Cultivated Non-Emitting Plants.}, journal = {Plant, cell & environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70698}, pmid = {42402715}, issn = {1365-3040}, support = {IOS-2022495//National Science Foundation (NSF)/ ; DE-FG02-91ER20021//Basic Energy Sciences/ ; FIS00000382//Italian Ministry of University and Research (MUR) Future in Science (FIS) 2021 program/ ; 2022ZYCCJJ//MUR - PRIN 2022/ ; P20229ZW4A//MUR - PRIN 2022/ ; DEVTF2210892//The Company of Biologists/ ; DE-SC0018409//Great Lakes Bioenergy Research Center/ ; }, abstract = {Isoprene is the most abundant biogenic volatile organic compound emitted by terrestrial vegetation. Here we report the impact of isoprene on root-associated microbiomes. Using isoprene-emitting (IE) transgenic tobacco and isogenic non-emitting (NE) controls, we performed co-cultivation experiments in natural soil and analysed plant phenotypes and growth alongside bacterial and fungal communities across root, rhizosphere, and soil niches. NE plants co-cultivated with IE neighbours displayed increased shoot and root biomass, suggesting interactive belowground functions of isoprene. Amplicon sequencing revealed more growth-promoting microbiota in root and rhizosphere of IE plants than NE plants. Both bacterial and fungal growth-promoting microbiota were enriched in IE and NE plants grown in the same pot. However, isoprene-fumigated plant-free soils did not replicate these shifts, indicating that plant-microbe interactions are required for the modulation of the soil microbiome. Our results suggest that isoprene acts as a belowground cue influencing microbiome assembly and indirectly enhancing growth in neighbouring plants. This work uncovers a potential ecological role for isoprene, highlighting how plant-derived isoprene can mediate plant-plant-microbiome interactions and contribute to community-level processes in the rhizosphere.}, } @article {pmid42402854, year = {2026}, author = {Cai, Y and Yan, H and Qin, J and Qiang, Y and Lin, GQ and Wang, H and He, QL and Zhao, Q}, title = {Heterologous Expression of an Abandoned Termite Mound Fungus Gene Cluster Reveals a Protective Aldehyde-Alcohol Cycle and a Candidate Termiticidal Metabolite.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.6c00101}, pmid = {42402854}, issn = {2161-5063}, abstract = {The medicinal fungus Wulingshen, comprising multiple Xylaria species, inhabits deserted termite mounds as sclerotia. To explore the molecular basis of its niche adaptation, we employed a synthetic biology-driven approach. Metagenomic and transcriptomic mining of wild specimens identified a conserved biosynthetic gene cluster. Its heterologous reconstruction in the fungal host Aspergillus oryzae enabled the characterization of a family of α-pyrone metabolites and, crucially, the elucidation of a spatially separated aldehyde-alcohol cycle. In this self-protection system, an extracellular oxidase (WlsA) converts an alcohol precursor to a reactive aldehyde, while an intracellular reductase (WlsE) catalyzes the reverse reaction. The aldehyde product exhibits potent toxicity against termites in vitro, suggesting a potential role in ecological interactions. This work establishes a functional genomics platform that decodes cryptic ecological metabolism by integrating multiomics with heterologous pathway expression, providing a generalizable strategy for discovering and mechanistically understanding niche-specific natural products.}, } @article {pmid42402985, year = {2026}, author = {Asato, Y and Kubo, T and Hashimoto, M and Wakatsuki, T and Sakamoto, H and Tanigawa, T and Kitamura, S and Kadokawa, H}, title = {Bifidobacterium longum BB536 supplementation is associated with increased circulating choline plasmalogen concentrations in non-pregnant, non-lactating dairy cows.}, journal = {Reproduction, fertility, and development}, volume = {38}, number = {10}, pages = {}, doi = {10.1071/RD26107}, pmid = {42402985}, issn = {1448-5990}, mesh = {Animals ; Female ; Cattle ; *Plasmalogens/blood ; Pregnancy ; *Probiotics/administration & dosage ; Dietary Supplements ; Lactation ; *Bifidobacterium ; Animal Feed ; }, abstract = {CONTEXT: Plasmalogens are ether phospholipids implicated in neuroendocrine regulation, including reproductive function. Recent studies have suggested that circulating plasmalogen concentrations are associated with reproductive performance in dairy cows; however, practical strategies to increase these concentrations remain limited.

AIMS: We hypothesised that supplementation with Bifidobacterium longum increases circulating choline plasmalogen concentrations and that this response depends on physiological state.

METHODS: Commercial probiotic products were screened using liquid chromatography-mass spectrometry and metagenomics to identify candidates containing plasmalogen-producing bacteria. A product containing the characterised strain B. longum BB536 and products containing other B. longum strains were selected for in vivo evaluation. Selected products were administered to Holstein cattle, and circulating choline plasmalogen concentrations were measured using an enzyme-based fluorometric assay.

KEY RESULTS: In long-term non-pregnant, non-lactating dairy cows, supplementation with B. longum BB536 significantly increased circulating choline plasmalogen concentrations, with a detectable rise approximately 1 week after the start of treatment and peak concentrations during Days 8-14 (P < 0.05). In contrast, no consistent increase was observed in pregnant, lactating dairy cows. Cross-sectional analysis across pregnancy stages showed significant variation in circulating choline plasmalogen concentrations, with lower concentrations during mid- to late gestation. No adverse effects were observed in ruminal pH, blood lactate concentrations, or bodyweight.

CONCLUSION: These findings suggest that supplementation with B. longum BB536 increases circulating choline plasmalogen concentrations in a state-dependent manner.

IMPLICATIONS: This study has provided new insight into the regulation of plasmalogens in cattle and suggests a potential nutritional approach for modulating reproductive function.}, } @article {pmid42403142, year = {2026}, author = {Zheng, Y and Ruan, P and Chen, H}, title = {Severe <em>Pneumocystis Jirovecii </em>Pneumonia in a Non-HIV Infant: The Diagnostic Value of Metagenomic Next-<br /> Generation Sequencing.}, journal = {Journal of the College of Physicians and Surgeons--Pakistan : JCPSP}, volume = {36}, number = {7}, pages = {961-962}, doi = {10.29271/jcpsp.2026.07.961}, pmid = {42403142}, issn = {1681-7168}, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/drug therapy/microbiology ; *Pneumocystis carinii/genetics/isolation & purification ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Infant ; }, abstract = {Null.}, } @article {pmid42403487, year = {2026}, author = {Calvanese, CM and Valentino, V and Sequino, G and De Vivo, A and Buzzanca, D and Prencipe, S and Demarinis, C and Perri, G and Pontonio, E and Ferrocino, I and Ercolini, D and De Filippis, F}, title = {Lactobacilli, best allies of mental health: a probiogenomic approach to identify potential psychobiotic strains.}, journal = {Current research in food science}, volume = {13}, number = {}, pages = {101490}, pmid = {42403487}, issn = {2665-9271}, abstract = {Targeted dietary strategies and supplements represent a promising approach for the treatment of cognitive problems. Multi-omic approaches may facilitate and accelerate the discovery of new psychobiotic strains and their applications. In this work, we applied metagenomics and comparative genomics to guide the isolation and screening of novel psychobiotic strains from fermented foods. Metagenomes of 1185 fermented food were screened, revealing the occurrence of genes coding for the biosynthesis of neuroactive molecules, supporting the isolation of 73 novel Lactic Acid Bacteria (LAB) strains. Comparative genomic analysis highlighted species-specific patterns, identifying Levilactobacillus brevis, Lactiplantibacillus plantarum, Limosilactobacillus fermentum as potential psychobiotics. In vitro functional screening for the production of neuroactive metabolites confirmed four strains, Lactiplantibacillus plantarum TUCC00000144, Limosilactobacillus fermentum TUCC00000777, Levilactobacillus brevis TO10, Lentilactobacillus diolivorans B92, as the most promising candidates for the development of dietary supplements or innovative fermented food products aimed at supporting mental health.}, } @article {pmid42403498, year = {2026}, author = {Leprohon, H and Tannir, B and Jolicoeur, G and Domingo, MC and Dufresne, PJ and Morency-Potvin, P and Benoit, P and Grandjean Lapierre, S}, title = {Impact of direct from clinical sample sequencing assays for infectious diseases diagnostics: A single-centre retrospective cohort study.}, journal = {Journal of the Association of Medical Microbiology and Infectious Disease Canada = Journal officiel de l'Association pour la microbiologie medicale et l'infectiologie Canada}, volume = {11}, number = {2}, pages = {141-154}, pmid = {42403498}, issn = {2371-0888}, abstract = {BACKGROUND: The analytical performance of bacterial targeted sequencing (BTS), fungal targeted/panfungal sequencing (FTS), and metagenomic next-generation sequencing (mNGS) assays has been previously evaluated and their clinical use is increasing. Limited evidence is available on their true clinical impact on infectious disease diagnosis and treatment.

METHODS: We conducted a 3-year retrospective cohort study including all patients for whom broad-range sequencing assays were performed directly from clinical samples for the detection of bacterial and fungal pathogens. The operational characteristics, diagnostic and therapeutic impacts of the assays were assessed by reviewing patient clinical files and laboratory information system charts.

RESULTS: A total of 279 samples from 185 patients were included. The positivity rates for BTS, FTS, and mNGS were respectively 20.5% (47/229), 20% (9/45), and 20% (1/5). Of these 279 samples, 40 (14.3%) had an impact on patient management. The test results helped to establish a diagnosis in 26 (9.3%) cases and led to treatment modifications in 14 (5%). FTS achieved higher impact rates (26.7%) than both BTS (12.2%) and mNGS (0%). Short turnaround times increase impact rates, and the most impactful tests were those performed on bone and intervertebral disc samples, or in patients with negative culture results due to prior antibiotic administration.

CONCLUSIONS: In this study, the overall diagnostic impact of BTS and FTS was high. Both the diagnostic and treatment impact of those assays can be increased if prescribed in well-selected clinical syndromes and performed on well-selected clinical samples.}, } @article {pmid42404619, year = {2026}, author = {Ramani, RR and Baskaran, S and Arun, KV and Alamelu, S and Arumugamnainar, D}, title = {Salivary metagenomic profiling of Neisseria , Dialister , and Filifactor species in periodontal health and disease using next-generation sequencing.}, journal = {Journal of oral biology and craniofacial research}, volume = {16}, number = {4}, pages = {101482}, pmid = {42404619}, issn = {2212-4268}, abstract = {BACKGROUND: Periodontal diseases represent a complex dysbiosis-driven inflammatory condition, where the transition from health to gingivitis and periodontitis is accompanied by distinct microbial shifts. Emerging evidence highlights the significance of less-studied genera such as Neisseria, Dialister, and Filifactor in shaping periodontal outcomes. This study aimed to investigate the salivary distribution of Neisseria, Dialister, and Filifactor species across periodontal health, gingivitis, periodontitis, and gingival recession using next-generation sequencing (NGS).

METHODS: Whole saliva samples were collected from 40 participants (10 per group) classified according to the American Academy of Periodontology criteria. Microbial DNA was extracted and subjected to 16S rRNA sequencing (V3-V4 region, Illumina MiSeq). Species-level classification was performed using the Human Oral Microbiome Database. Frequency distributions were compared across groups using Fisher's exact test, with significance set at p < 0.05.

RESULTS: Distinct patterns were observed. Several commensal Neisseria species, including N. subflava (p = 0.001), N. elongata(p = 0.015), and N. polysaccharea (p = 0.001), showed significantly reduced prevalence in periodontitis compared with health and gingivitis. In contrast, Dialister pneumosintes exhibited a sharp increase in all diseased groups (p = 0.002). Filifactor alocis was markedly enriched in gingivitis, recession, and periodontitis (p = 0.011), suggesting its strong association with disease states.

CONCLUSION: The findings demonstrate a characteristic microbial shift in saliva: health-associated Neisseria species decline with disease progression, while anaerobic taxa such as D. pneumosintes and F. alocis expand. These results align with the polymicrobial synergy and dysbiosis model and underscore the potential of these species as salivary biomarkers for early detection and monitoring of periodontal disease.}, } @article {pmid42404879, year = {2026}, author = {Dai, P and Feng, J and Cao, J and Fan, D}, title = {Integrative multi-omics profiling reveals coordinated immunometabolic reprogramming and host-microbiome interactions in acute pancreatitis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1828633}, pmid = {42404879}, issn = {1664-3224}, mesh = {Humans ; Multiomics ; *Pancreatitis/metabolism/microbiology/immunology ; Metabolomics ; Gene Expression Profiling ; *Host Microbial Interactions/immunology ; Biomarkers ; Metabolic Reprogramming ; *Gastrointestinal Microbiome/immunology ; Acute Disease ; Female ; Transcriptome ; Male ; Metabolome ; }, abstract = {BACKGROUND: Acute pancreatitis (AP) is a life-threatening inflammatory disorder characterized by diverse etiologies and complex pathophysiological mechanisms involving immune dysregulation, systemic metabolic reprogramming, and gut microbiota disturbances. Although single-omics studies have provided partial insights into AP pathogenesis, comprehensive integrative multi-omics analyses investigating the intricate interactions among immunity, metabolism, and the microbiome in AP remain limited.

METHODS: We conducted an integrative multi-omics analysis of peripheral blood transcriptomics, untargeted plasma metabolomics, and fecal whole-metagenome sequencing in 15 patients with AP and 15 age- and sex-matched healthy controls. Differentially expressed genes (DEGs), metabolites (DEMs), and gut microbial species (DGMs) were identified. Subsequently, functional enrichment analysis, correlation network analysis, and exploratory machine learning approaches were employed to investigate molecular interactions and identify candidate biomarkers.

RESULTS: Transcriptomic profiling identified 4, 776 DEGs, including 409 immune-related genes significantly enriched in the NF-κB, IL-17, and cytokine-cytokine receptor interaction pathways, indicating pronounced inflammatory activation. Metabolomic analysis detected 296 DEMs, with prominent alterations in amino acid and lipid metabolism, mong which 9 metabolites showed potential discriminatory value (AUC > 0.75), with representative metabolites including xanthine, homocarnosine, and tetradecanedioic acid. Metagenomic sequencing revealed significant microbial compositional and functional remodeling, characterized by enrichment of pro-inflammatory taxa such as Escherichia coli and Streptococcus anginosus, alongside depletion of SCFA-producing commensals including Faecalibacterium prausnitzii and Blautia wexlerae. Functional profiling demonstrated disrupted amino acid metabolism, gut-brain signaling, and SCFA synthesis. Multi-omics integration revealed 215 significant correlations between host genes, metabolites, and microbes, highlighting key interaction hubs. An exploratory random forest model identified Lachnospira pectinoschiza, Megamonas funiformis, and SRGN as candidate biomarkers, showing promising classification performance within the current cohort (AUC = 0.951).

CONCLUSIONS: This study provides a systems-level characterization of the immune, metabolic, and microbial alterations in AP. The identified molecular signatures and cross-omics interaction networks offer mechanistic insights into AP pathogenesis and highlight candidate biomarkers that warrant further validation in larger, independent cohorts.}, } @article {pmid42405192, year = {2026}, author = {Scott, CJR and Caccia, S}, title = {metaLoc: protein localisation prediction workflow.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag169}, pmid = {42405192}, issn = {2635-0041}, abstract = {SUMMARY: metaLoc combines existing tools for signal peptide, localisation, and transmembrane helices prediction from protein sequences into a workflow for rapid evaluation of protein datasets. By accepting both protein and nucleotide sequences, the workflow is especially suitable for in silico screening of the growing volumes of sequencing data. With a single command, metaLoc provides a simple, accessible, and user-friendly tool for the bioinformatic investigation of proteomic or metagenomic datasets.

metaLoc is freely available on the GitHub platform (https://github.com/scottc-bio/metaLoc). The metaLoc workflow is implemented in Nextflow with a modular design utilizing isolated Conda environments for reproducibility. An archived version of this release is permanently available at Zenodo (https://doi.org/10.5281/zenodo.18936772).}, } @article {pmid42405317, year = {2026}, author = {Wang, Y and Cai, Y and Peng, Z and Hou, F and Jia, Z}, title = {Molecular insights into atmospheric methane-oxidizing USCγ from desert grassland soil based on metagenome-assembled genome analysis.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag151}, pmid = {42405317}, issn = {2730-6151}, abstract = {Upland Soil Cluster Gamma (USCγ) is a key high-affinity aerobic methanotroph driving atmospheric methane oxidation in grassland soils; however, it has never been obtained in pure culture, and its metabolic processes remain largely unknown. Here, we reconstructed a USCγ metagenome-assembled genome (MAG) containing the complete pmoA gene from desert grassland soil in northwestern China, designated USC_AKS. At the site, USCγ accounted for 9.83% of the microbial community in the 10-20 cm layer. BLASTn of its 16S rRNA gene against the NCBI database (excluding uncultured/environmental sequences) showed 93.03% similarity to the non-methanotroph Thioalkalivibrio sulfidiphilus HL-EbGr7 (order Chromatiales). The closest match among named species was an uncultured bacterium (JN672117) at 97.86% similarity. Its pmoA shares 96.18% similarity with the original USCγ-defining sequence. Phylogenomic analysis placed USC_AKS and seven other USCγ MAGs into a monophyletic group of three subclades, distantly related to culturable Type I methanotrophs. Their genomic average nucleotide identity values are all below 95%, confirming eight distinct species. Like other USCγ MAGs, USC_AKS encodes a complete pmoCAB operon, an XoxF-type methanol dehydrogenase, and enzymes for formaldehyde oxidation to CO2. However, it lacks key ribulose monophosphate (RuMP) cycle genes encoding 3-hexulose-6-phosphate synthase (hps) and 6-phospho-3-hexulose isomerase (phi). The serine cycle also appears incomplete, as these MAGs lack hpr, the gene encoding hydroxypyruvate reductase. Moreover, none encode Rubisco, ruling out the Calvin-Benson-Bassham CO2-fixation pathway. Consequently, the metabolic characteristics of USCγ-particularly its carbon assimilation pathway-remain enigmatic, and obtaining pure cultures or enriched consortia is likely the only route to resolving this mystery.}, } @article {pmid42405318, year = {2026}, author = {Modolon, F and Capo, E and Wardle, DA}, title = {Long-term ecosystem development and retrogression drive microbial specialization for complex organic matter degradation.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag157}, pmid = {42405318}, issn = {2730-6151}, abstract = {Long-term ecosystem development includes a build-up phase followed by a decline (retrogressive) phase characterized by reduced plant productivity and belowground process rates due to reduced nutrient availability. In boreal forests, retrogression is accompanied by soil organic matter (SOM) accumulation, especially in the prolonged absence of fire. However, the role of bacterial communities in SOM dynamics during ecosystem retrogression has been little explored. Using a 5000-year post-fire boreal forest chronosequence, we investigated how long-term succession and retrogression shapes soil bacterial community structure and functional specialization. While the Actinomycetota phylum dominated communities across all chronosequence stages, a significant family-level shift within this phylum occurred in the later (retrogressive) phase, characterized by a transition from Mycobacteriaceae to Streptosporangiaceae. The recovery of metagenome-assembled genomes (MAGs) revealed distinct life-history trade-offs between these families. Streptosporangiaceae MAGs were significantly enriched in genes for degrading phenolics, cellulose, and lignin, and exhibited potential for chitin, lipid and peptide degradation. This positions them as potential decomposers of the primary constituents of stored soil carbon, including plant-derived complex carbohydrates and fungal necromass, during retrogression when fungal activity declines. In contrast, Mycobacteriaceae MAGs are likely to prioritize inorganic phosphate (P i) uptake-by pstS gene enrichment, reflecting adaptation to P availability changes during ecosystem development. Collectively, our results demonstrate that long-term ecosystem retrogression drives shifts in the bacterial communities and functions within the Actinomycetota. These shifts may indicate possible divergent strategies, i.e. recalcitrant carbon turnover versus nutrient scavenging, which could explain shifts in the microbial community as the ecosystem transitions toward retrogressive, nutrient-limited states.}, } @article {pmid42405543, year = {2026}, author = {Anggraini, D and Yovi, I and Elliyanti, A and Safari, D and Syah, NA and Jati, AP and Sarassari, R and Simatupang, ETM}, title = {Metagenomic Analysis of Thoracic Empyema Etiology Through Next-Generation Sequencing Enhances Conventional Culture Techniques.}, journal = {Infection & chemotherapy}, volume = {58}, number = {2}, pages = {214-223}, doi = {10.3947/ic.2025.0159}, pmid = {42405543}, issn = {2093-2340}, abstract = {BACKGROUND: This study aimed to analyze the microbiome of thoracic empyema using metagenomic methods and compare the results with conventional culture methods to increase diagnostic accuracy and enhance antibiotic therapy.

MATERIALS AND METHODS: This study involved 30 patients with thoracic empyema from hospitals in Riau Province, Indonesia. Pleural fluid samples were collected for culture analysis and identification using the Vitek 2 compact system and metagenomic analysis. Patient clinical data were also collected.

RESULTS: Culture methods showed a 40.0% positive rate, with Gram-negative bacteria (Klebsiella pneumoniae and Pseudomonas aeruginosa) predominating. Metagenomics showed a 56.7% positive rate, identifying a more diverse microbiome, including fungi (29.4% abundance), other Gram-negative bacteria (26.5%), and anaerobic bacteria (22.5%). Comparison of the two methods showed 36.7% complete agreement and 23.3% partial agreement, with 40% disagreement, with a Kappa coefficient of 0.416 and P-value of 0.016 (P<0.050).

CONCLUSION: Metagenomic NGS offers significant advantages in detecting the microbiome of thoracic empyema, particularly fungi and anaerobic bacteria, which are often missed by conventional culture methods. This has the potential to improve diagnostic accuracy and optimize antibiotic therapy. Further research with larger sample sizes is needed.}, } @article {pmid42405768, year = {2026}, author = {Berryhill, BA and Gil-Gil, T and Burke, KB and Fontaine, J and Brink, CE and Harvill, MG and Goldberg, DA and Navas, JN and Grabowicz, M and Konstantinidis, KT and Levin, BR and Woodworth, MH}, title = {Enteric populations of Escherichia coli are likely to be resistant to phages due to O antigen expression.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0038626}, doi = {10.1128/msphere.00386-26}, pmid = {42405768}, issn = {2379-5042}, abstract = {Metagenomic data provide evidence that bacteriophage (phage) abound in the enteric microbiomes of humans. However, the contribution of these viruses in shaping the bacterial composition of the gut microbiome and how these phages are maintained remain unclear. We performed experiments with 756 combinations of 54 Escherichia coli and nine phage isolates from four fecal microbiota transplantation (FMT) doses and five laboratory phages as samples of non-dysbiotic human enteric microbiota. We also developed a mathematical model of the population and evolutionary dynamics of bacteria and phage. Our experiments predict that as a consequence of the production of the O antigen, most of the E. coli in the human enteric microbiome will be resistant to infections with the array of co-occurring phages. Our modeling suggests that phages are maintained in these enteric communities due to the high rates of transition between the O antigen-resistant and -sensitive states. Based on our observations and predictions from this theory, we postulate that the phage found in the human gut are likely to play a little role in shaping the strain composition of E. coli of healthy individuals. Although we only investigated E. coli, the mechanism of resistance described here is shared among most of the gram-negative bacteria. Evidence is provided that, as a consequence of O antigen-mediated resistance, the genetically diverse array of bacteriophage in the gut microbiome of humans plays little or no role in determining the densities and distribution of the genetically diverse strain E. coli in this habitat. Our mathematical model predicts and our experiments support the hypothesis that the phage present in the gut microbiome are maintained by replication on the minority of sensitive bacteria generated by the leakiness of O antigen-mediated resistance.IMPORTANCEBacteriophages (phages) are abundant in the human gut, yet whether these viruses shape the bacterial communities living there remains unresolved. Using Escherichia coli and phages isolated from the stool of healthy fecal microbiota transplantation (FMT) donors, together with a mathematical model, we show that the vast majority of gut E. coli are resistant to co-occurring phages because they express the O antigen, a surface structure that masks the receptors phages use to attach. Despite this widespread resistance, phages persist by replicating on a small, continually regenerated subpopulation of sensitive cells, a phenomenon we term leaky resistance. These findings suggest that phages play a little role in determining which E. coli strains dominate the healthy human gut. Because the O antigen is broadly expressed across gram-negative bacteria, this mechanism likely extends well beyond E. coli and helps explain why isolating therapeutic phages against many pathogens is difficult.}, } @article {pmid42406122, year = {2026}, author = {Joseph, S and Abraham, LS and Premachandran, K and Samrot, AV and Thirugnanasambandam, R and Ragavendhar, K and Alodaini, HA and Moubayed, NM and Hatamleh, AA and Mani, RR and Chang, SW and Ravindran, B}, title = {Unravelling Extremophilic Microbiome Diversity and Functional Dynamics in Hypersaline Environment.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02817-z}, pmid = {42406122}, issn = {1432-184X}, support = {REIG-FPS-2025/038//UCSI University/ ; }, abstract = {Solar salt pans are extreme hypersaline environments that represent functionally specialised microbial communities mediating essential biogeochemical transformation. Vedaranyam, a coastal region of the Bay of Bengal containing artificially constructed solar salterns for salt production. There is limited information available on the metagenome diversity and functional profiling of this saltpan, which prompted us to investigate it. Here, we report the first whole metagenome sequencing to explore the dynamics of the functional structure of microbial communities in saltpan during the preharvest and postharvest phases of salt production. Methanobacteriota and Pseudomonadota dominated both phases at the phylum level, while Halobacteria comprised the most abundant class (53.2% preharvest; 48% postharvest). A notable bloom of Dactylococcopsis salina was observed during postharvest (4.28% to 12.67%) and flock doubling of Cyanobacterota relative abundance (5.5% to 10.6%), reflecting photosynthetic primary production following salt removal. Conversely, during postharvest phase sulfur oxidising Guyparkeria halophila reduced 23 fold, while the DMSP accumulating osmolyte producer Salinibaculum marinum dominated preharvest (6.98%). However, functional classification of the metagenome revealed active participation of the microbial community across five major biogeochemical cycles. Encompassing carbon fixation by cyanobacteria and diverse haloarchaea, nitrogen cycling through diazotrophy and denitrification, a cryptic preharvest sulfur cycle coupling sulfate reduction and sulphide oxidation, phase shifted DMSP catabolism, and light driven bacteriorhodopsin through archaeal energy conservation. Metagenomic assembly yielded ten metagenomic assembled genomes (MAGs), revealing the taxonomic diversity and metabolic potential of the dominant halophilic community across biogeochemical cycles. These results provide critical insights into the ecological succession from an anaerobic, chemolithotrophy-rich preharvest microbial community to an aerobic, photosynthetically driven postharvest assemblage, advancing our understanding of microbial biogeochemistry in managed hypersaline ecosystems.}, } @article {pmid42407310, year = {2026}, author = {Jiang, ZQ and Xing, RK and Peng, D and Ren, YH and Wei, TY and Guo, WB and Shen, ZM and Wang, CN and Zhang, FL and Yuan, T}, title = {Compartment-specific host association and mobility shape ARG risk in aquaculture systems.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142895}, doi = {10.1016/j.jhazmat.2026.142895}, pmid = {42407310}, issn = {1873-3336}, abstract = {Antimicrobial resistance in aquaculture threatens environmental and public health, but the risk of ARGs cannot be inferred from abundance alone; host context and mobility potential are essential. Here, we investigated how ecological compartments shape ARG host background, mobility, and risk in aquaculture systems. We analyzed 437 metagenomes from water and sediment in freshwater and marine aquaculture across China using resistome profiling, host assignment, genetic localization, ARG-MGE co-occurrence, a four-tier risk framework, and machine learning. We detected 1413 nonredundant ARG subtypes (28 classes). Water had higher ARG diversity, stronger associations with opportunistic pathogens, and stronger mobility-related signals than sediment. High-risk ARGs were concentrated in water: Rank I ARGs were exclusive to water, and water-specific Rank II ARGs accounted for 7.2% (freshwater) and 6.9% (marine) of total ARG diversity, versus 4.2% (freshwater sediment) and 2.9% (marine sediment). The LightGBM model identified salinity, temperature, and pH as key mobility predictors. Together, these results show that ARG risk in aquaculture is jointly shaped by the ecological compartment, host association, and mobility potential, with water acting as the principal high-risk interface. This risk-oriented analytical framework provides a transferable basis for prioritizing surveillance and intervention in aquaculture environments.}, } @article {pmid42407426, year = {2026}, author = {Dong, F and Hou, A and Hu, X and Wei, L and Sun, F and Xiao, X and Su, X}, title = {Process-dependent niches of rpf-harboring microorganisms regulate nitrogen and carbon functional networks in full-scale activated sludge.}, journal = {Environmental research}, volume = {306}, number = {Pt 2}, pages = {125198}, doi = {10.1016/j.envres.2026.125198}, pmid = {42407426}, issn = {1096-0953}, abstract = {Resuscitating viable but non-culturable (VBNC) microorganisms offers a strategy to unlock hidden metabolic capabilities, enhancing pollutant degradation and system stability in wastewater bioreactors. However, the ecological mechanisms underlying VBNC resuscitation in activated sludge, particularly the role of resuscitation-promoting factor (Rpf) gene-harboring microbial consortia, remain elusive. Here, metagenomic profiling of full-scale anaerobic/anoxic/oxic (A[2]/O) and oxidation ditch processes demonstrates the widespread distribution of rpf-harboring microorganisms in wastewater treatment plants (WWTPs). A[2]/O systems enriched for taxa associated with denitrification and ammonification, while oxidation ditches showed higher abundance of microorganisms involved in nitrification and dissimilatory nitrate reduction to ammonium (DNRA). The two processes configuration harbored distinct sets of rpf-carrying taxa, with Chloroflexota dominating in A[2]/O systems and Nitrospira and Kouleothrix in oxidation ditches. Network analysis further reveals that rpf-harboring taxa may act as ecological connectors between dormant and metabolically active populations, thereby enhancing community cohesion and resilience under fluctuating operational conditions. These findings uncover process-dependent resuscitation ecology shaping activated sludge communities and nutrient transformation pathways, providing a mechanistic foundation for engineering Rpf-mediated microbial interactions to improve biological wastewater treatment.}, } @article {pmid42409195, year = {2026}, author = {Yan, M and Yang, C and Huang, J and Qi, P and Tang, L and Lu, H}, title = {Reactor performance and microbial responses of sulfate-reducing bacteria sludge under stepwise polyvinyl chloride microplastic exposure.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135334}, doi = {10.1016/j.biortech.2026.135334}, pmid = {42409195}, issn = {1873-2976}, abstract = {Plastic pollution, particularly microplastic contamination, poses potential risks to biological wastewater treatment processes. However, the response of sulfate-reducing bacteria (SRB) sludge systems to polyvinyl chloride (PVC) microplastics remains poorly understood. In this study, a laboratory-scale sulfate-reducing up-flow sludge bed (SRUSB) reactor was operated under stepwise PVC microplastic exposure at 0, 20, 100, and 500 particles/L. COD removal and sulfate reduction showed limited changes at 20 and 100 particles/L, whereas 500 particles/L caused transient inhibition followed by gradual recovery within the same reactor. PVC exposure increased intracellular reactive oxygen species (ROS) levels and lactate dehydrogenase (LDH) release, while live/dead staining indicated no marked increase in cell mortality across the operational stages. Stepwise PVC exposure was also accompanied by enrichment of protein-rich loosely bound extracellular polymeric substances (LB-EPS) and accumulation of PVC-derived additives, including BPA and ATBC. Microbial community analysis showed that the relative abundance of SRB-related genera increased from 8.7% to 24.9%, mainly involving increased abundances of Desulfobacter, Desulfococcus, and Desulforhabdus. Metagenomic annotation further revealed genes associated with EPS precursor supply, polysaccharide assembly/export, protein secretion, antioxidant response, aromatic metabolism, ester-bond hydrolysis, and dissimilatory sulfate reduction. Overall, this study provides a longitudinal characterization of reactor performance and associated physiological, chemical, microbial, and community-level genetic responses of SRB sludge under stepwise PVC microplastic exposure, offering useful insights for evaluating sulfate-reducing saline wastewater treatment systems facing microplastic contamination.}, } @article {pmid42409199, year = {2026}, author = {Agostini, F and Baruzzo, V and Fernandez, FR and Satta, A and Raga, R and Penzo, D and Modesti, M and Valerin, MC and Campanaro, S and Treu, L and Zampieri, G}, title = {Discovering hidden candidate plastic-degrading enzymes: Combined multi-omics and machine learning strategy.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135332}, doi = {10.1016/j.biortech.2026.135332}, pmid = {42409199}, issn = {1873-2976}, abstract = {Plastic pollution poses a major threat to the stability of natural ecosystems as well as human health. Microbial enzymes have long been considered a potential resource for targeted biodegradation but, except for a few successful cases, the discovery of efficient enzymes has proved challenging. Aiming to accelerate the process, we propose an approach combining metagenomics, metatranscriptomics and semi-supervised learning that selects promising plastic-degrading candidate enzymes from the proteome of relevant microorganisms. Tested on a dataset of over 10,000 microbial proteins, ranking models consistently prioritize known plastic-degrading enzymes, achieving an area under the cumulative distribution function curve above 0.96, with leave-one-family-out cross-validation indicating that performance is largely retained across protein families. As a case study, this work focuses on mixed microbial cultures exposed for extended periods to polyethylene, polyethylene terephthalate, and polyurethane substrates. The prevalent species after selective enrichment were functionally characterized, finding Rhodococcus aetherivorans as the most relevant species in two of the five cultures under investigation. Among the top-ranked proteins, several have high structural similarity with known enzymes despite not being identified by sequence similarity search. Moreover, according to metatranscriptomics results, several of these enzymes were found to be expressed at the same level or above that of annotated enzymes, suggesting that they may have functional relevance. Overall, this work highlights the potential of integrating multi-omics with data-driven methods for enzyme discovery and for accelerating the development of biotechnological solutions to plastic pollution.}, } @article {pmid42409336, year = {2026}, author = {Wu, J and Lin, M and Fan, Y}, title = {An Unusual Cause of Chronic Hematochezia.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2026.06.025}, pmid = {42409336}, issn = {1528-0012}, } @article {pmid42409355, year = {2026}, author = {Nguyen, HT and Bez, C and Tran, MQ and Tran, LT and Pham, VT and Bertani, I and Venturi, V and Dinh, HT}, title = {Rhizospheric Fungal Communities and Their Role in Biocontrol of Fusarium in Robusta Coffee (Coffea canephora) in Vietnam.}, journal = {The plant pathology journal}, volume = {}, number = {}, pages = {}, doi = {10.5423/PPJ.OA.12.2025.0186}, pmid = {42409355}, issn = {1598-2254}, abstract = {Rhizospheric microbial communities are critical to the health and productivity of coffee plantations. This study investigated the microbiome of robusta coffee (Coffea canephora) across three major cultivation areas in Vietnam (Dak-Nong, Dak-Lak, and Gia-Lai) to assess its role in Fusarium suppression. Using ITS ampliconbased metagenomics and culture-dependent approaches, we analyzed fungal community structure in relation to location, plant age, and health status. Metagenomic analysis revealed no significant differences in bacterial communities between healthy and diseased rhizospheres, whereas fungal communities showed clear distinctions, particularly in young plants (<2 years). These differences diminished in mature plants (≥2 years) but continued to vary with age (2-10 years). Healthy rhizospheres were enriched with beneficial fungi, while diseased soils contained more phytopathogenic genera. Fusarium was prevalent in all regions, with higher abundance in diseased soils, whereas Trichoderma, a known biocontrol agent, was more abundant in healthy soils but declined with plant age. Of 343 fungal isolates, 46 strains exhibited strong antagonistic activity against Fusarium, representing 10 genera, including Aspergillus, Penicillium, Gongronella, and Talaromyces. Although Trichoderma isolates were less frequent, they showed promising biocontrol potential. These findings underscore the role of rhizospheric fungi in managing Fusarium wilt and identify candidate biocontrol agents for sustainable robusta coffee cultivation.}, } @article {pmid42409501, year = {2026}, author = {Huang, C and Zhao, Y and Gu, M and Li, Z and Li, X and Huang, Y and Zhang, C and Zhang, D}, title = {Metagenomic-metabolomic integration elucidates stage-specific dynamics of microbial communities and metabolites driving pork spoilage in commercial supply chains.}, journal = {Food research international (Ottawa, Ont.)}, volume = {240}, number = {}, pages = {119678}, doi = {10.1016/j.foodres.2026.119678}, pmid = {42409501}, issn = {1873-7145}, abstract = {Microbial-metabolic axis drives meat quality deterioration and shelf-life changes along commercial supply chains. This study tracked pork quality and freshness from postmortem processing to retail sale by integrating untargeted metabolomic and metagenomic analyses. Over the first 1700 min postmortem, pork showed a decline in pH and increases in L*, a* and b* values, cooking loss, shear force, total volatile basic nitrogen and total viable counts. At the point of sale, the meat remained in rigor mortis and retained acceptable freshness. Metabolic profiles remained dynamic after warehousing and were further modified by ambient exposure during transport and retail sale. Results revealed that differential metabolites were predominantly enriched in purine metabolism, nucleotide metabolism, lysosome pathway, as well as alanine, aspartate and glutamate metabolism. Likewise, several genera potentially associated with spoilage or contamination-associated bacteria were influenced by commercial condition along the supply chain, with increased abundance of Acinetobacter, Bacillus, Listeria, Psychrobacter, Salmonella andEnterobacter during transport and retail sale, while Listeria, Salmonella andEnterobacter may originate from environmental or processing-associated sources. These findings identify stage-specific metabolic and microbial signatures shaped by commercial handling, such as temperature, relative humidity and provide insights for improving pork quality and safety management during the early postmortem period.}, } @article {pmid42409516, year = {2026}, author = {Moon, SH and Yang, X and Kim, J and Leighton, E and Jun, SR and DiCaprio, E and Gale, C and Chen, S and Li, X and Huang, E}, title = {Comprehensive analyses of carbapenem-resistant and ESBL-producing bacteria in fresh vegetables and their resistome in the United States.}, journal = {Food research international (Ottawa, Ont.)}, volume = {240}, number = {}, pages = {119552}, doi = {10.1016/j.foodres.2026.119552}, pmid = {42409516}, issn = {1873-7145}, abstract = {Carbapenem-resistant and extended-spectrum beta-lactamase (ESBL)-producing bacteria, once largely confined to healthcare settings, are increasingly detected in community environments. Food and the environment may act as important reservoirs for clinically relevant antibiotic-resistant bacteria. A large-scale surveillance study was conducted from 2022 to 2023 to assess antibiotic resistance in retail fresh vegetables across three U.S. regions: the Midsouth, Midwest, and West Coast. A total of 1218 samples representing five vegetable categories (carrots, lettuce, spinach, sprouts/microgreens, and salads) were analyzed for carbapenem-resistant bacteria and ESBL-producing Enterobacterales. Culture-based methods included selective isolation on CHROMagar, antibiotic susceptibility testing, phenotypic evaluation of ESBL and carbapenem resistance, and carbapenemase detection and typing. Whole-genome sequencing of phenotypically resistant isolates was used to identify beta-lactamase genes. Overall, 62 carbapenem-resistant isolates (5.09%) and 70 ESBL-producing Enterobacterales isolates (5.74%) were recovered. Carbapenemase-producing Enterobacterales included 30 Enterobacter strains and one Kluyvera strain, with carbapenem-resistant Enterobacter most frequently isolated from sprouts and microgreens. ESBL-producing strains included 39 Serratia, 20 Enterobacter, 6 Klebsiella, 3 Raoultella, and 2 Rahnella isolates. Comparative genomic analyses showed close similarity between vegetable isolates and human clinical strains. Notably, the carbapenemase gene blaIMI-6 identified in Enterobacter asburiae from microgreens was transferable to Escherichia coli by conjugation. Shotgun metagenomics of 40 samples further confirmed diverse resistance genes. These findings highlight vegetables as potential reservoirs of clinically important antibiotic resistance and emphasize the need for ongoing surveillance in both vegetable products and their production environments.}, } @article {pmid42409884, year = {2026}, author = {Studer Silva Gutierrez, FAO and Morandi, SC and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC}, title = {Influence of smoking on the human ocular surface microbiome and tear proteome.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-60743-z}, pmid = {42409884}, issn = {2045-2322}, abstract = {The ocular surface hosts microbes of low abundance and their genomes, collectively called the ocular surface microbiome (OSM). The OSM is involved in maintaining health and protecting the eye from infection. Although disruption of this microbial balance has been linked to various eye diseases, the effect of smoking, a known risk factor for ocular conditions, on the OSM remains unclear. We analysed ocular samples from smokers (n = 17) and non-smokers (n = 24) using metagenomic sequencing and proteomics approaches to assess both microbial composition and functions, as well as the host protein profiles. Microbial DNA was examined for bacterial, fungal, and viral taxa, with contaminants removed using microDecon. Statistical analyses showed no significant differences in microbial diversity or tear proteins between groups, apart from one bacterial gene. No bacterial, fungal, or viral species were uniquely associated with smoking status. While no clear smoking-related effects were observed in microbial communities or tear proteome composition, the overall stability of tear proteins may reflect intrinsic resilience dynamics that maintain low microbial abundance on the ocular surface.}, } @article {pmid42401772, year = {2026}, author = {Afonso, AC and Lema, JM and Trueba-Santiso, A}, title = {Metaproteomics for Water Biotechnology: Considerations and Study Cases.}, journal = {Advances in experimental medicine and biology}, volume = {1510}, number = {}, pages = {21-44}, pmid = {42401772}, issn = {0065-2598}, mesh = {*Proteomics/methods ; *Biotechnology/methods ; Multiomics ; *Water Purification/methods ; Water Microbiology ; Wastewater/microbiology ; Biofilms ; }, abstract = {This chapter summarizes the current knowledge on the practical, methodological, and interpretative aspects of applying metaproteomics in water biotechnology. We outline the full metaproteomic workflow-from sampling and protein extraction to LC-MS/MS acquisition, database construction, quantitative analysis, and bioinformatic interpretation-and emphasize critical considerations specific to complex matrices such as EPS-rich biofilms, granular sludge, and low-biomass drinking water. Case studies illustrate how metaproteomics can clarify mechanisms of micropollutant degradation, nitrogen-transforming pathways, biofilm functional architecture, and microbial resilience under operational stress. Recent advances in data-independent acquisition, metagenome-informed databases, and integrative multi-omics are shown to substantially improve depth, reproducibility, and functional resolution. Finally, we discuss emerging applications in wastewater-based epidemiology, where metaproteomics complement nucleic-acid-based surveillance by enabling the detection of large biomolecule biomarkers of population health and industrial activity. Although metaproteomics is already being applied across a wide range of water cycle contexts and is producing promising, robust results, several challenges, including limitations in analytical chemistry, database completeness, and bioinformatics workflows, continue to hinder its broader implementation. Continued technical research and innovation are therefore essential to fully unlock its potential in water biotechnology.}, } @article {pmid42401776, year = {2026}, author = {Zapata-Peñasco, I and Herrera-Díaz, J}, title = {Proteomic Sample Preparation for the Petroleum Industry: A Biocorrosion Case Study.}, journal = {Advances in experimental medicine and biology}, volume = {1510}, number = {}, pages = {121-145}, pmid = {42401776}, issn = {0065-2598}, mesh = {*Proteomics/methods ; *Petroleum/microbiology ; Corrosion ; *Oil and Gas Industry ; Biodegradation, Environmental ; Biofilms/growth & development ; *Bacterial Proteins/metabolism ; Sewage/microbiology ; *Bacteria/metabolism/genetics ; }, abstract = {Petroleum-associated environments are among the most chemically complex and biologically extreme systems encountered in the field of industrial biotechnology. Here, microbial activity plays a pivotal role in hydrocarbon biodegradation, reservoir souring, and microbiologically influenced corrosion (MIC). In these systems, proteins constitute the functional interface between microbial metabolism and physicochemical processes affecting infrastructure integrity and environmental impact. This chapter presents an integrated proteomics-based workflow for the characterization of microbial communities inhabiting oil pipeline sludges, with particular emphasis on sample preparation strategies tailored to hydrocarbon-rich, metal-laden, and saline matrices. Optimized phenol-based extraction, electrochemical in vitro corrosion assays, two-dimensional gel electrophoresis, and high-resolution mass spectrometry are combined with metagenomic information to enable robust identification and functional interpretation of proteins involved in redox metabolism, biofilm formation, extracellular electron transfer, sulfur and nitrogen cycling, and stress adaptation. The approach is illustrated through a biocorrosion case study of marine pipeline sludge, revealing key enzymatic systems, including oxidoreductases, hydrolases, cytochromes, ABC transporters, and biofilm-associated structural proteins that mediate metal dissolution and microbial energy conservation. By integrating proteomics with electrochemical measurements and systems-level analysis, this chapter highlights how tailored sample preparation and functional protein profiling can overcome the limitations of culture-dependent methods, providing mechanistic insight into complex petroleum microbiomes. These advances establish proteomics as a critical tool for monitoring, predicting, and ultimately mitigating biocorrosion, as well as for guiding the development of biotechnology-based strategies in the oil and gas industry.}, } @article {pmid42401984, year = {2026}, author = {Pangga, GM and Richmond, A and Hughes, C and Psifidi, A and Xia, D and Blake, D and Ijaz, UZ and Gundogdu, O}, title = {Integrated metabolomics and metagenomics reveal divergent caecal metabolic signatures following commercial gut health interventions in broilers.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00596-z}, pmid = {42401984}, issn = {2524-4671}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, abstract = {BACKGROUND: The intensification of food production systems highlights the need for poultry gut health strategies aligned with One Health goals. Central to this is a balanced gut microbiota, which supports nutrient absorption, immunity, and disease resilience.

RESULTS: We applied integrative multi-omics, combining untargeted LC-MS metabolomics and shotgun metagenomics, to explore the caecal responses of commercial Ross-308 broilers to two widely used gut health interventions: ionophore supplementation (T1) and anticoccidial vaccination (T2). Across 7,554 detected metabolites, we identified candidate metabolic signatures: T1 was marked by trends in prenol lipids, including multiple soyasaponins, and enrichment of cellular stress-related pathways (e.g. glutathione pathway). T2 instead was associated with shifts in aromatic amino acid metabolism, elevating tryptophan-derived indoles such as 5-methoxyindole. While global metabolic profiles did not differ significantly (PERMANOVA p > 0.05), supervised integration (DIABLO algorithm) identified 405 potential metabolite-MAG correlations. Bacteroides fragilis emerged as a dominant associate, correlating positively with a diverse range of metabolites (n = 271). Functional gene analysis suggested a link between Mediterraneibacter spp. and soyasaponin deglycosylation, while Ruminococcaceae UBA3818 showed genomic potential for tryptophan utilisation and indole-linked metabolic steps.

CONCLUSION: Our exploratory findings suggest that prophylactic interventions impact the gut microbiome, resulting in divergent subsets of metabolic features. This highlights the potential of microbiome-informed strategies to improve enteric disease management and advance gut health centred approaches in both veterinary and human contexts.}, } @article {pmid42402030, year = {2026}, author = {Qi, K and Zhang, S and Su, X and Chen, J and Huang, S and Chen, Y and Li, W and Ni, G and Duo, J and Yang, S and Shen, Q and Wang, X and Liu, Y and Wu, P and Yang, H and Ji, L and Wang, X and Zhang, W}, title = {Comparative analysis of gut viromes in four penguin species reveals diverse novel viruses and host-associated differences.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0084825}, doi = {10.1128/msphere.00848-25}, pmid = {42402030}, issn = {2379-5042}, abstract = {Penguins, as distinctive marine birds, play important roles in polar and sub-Antarctic ecosystems, yet the diversity and species-specific distribution of their gut viromes remain insufficiently understood. Here, we used viral metagenomics to characterize the cloacal viromes of four penguin species-Spheniscus humboldti (S. humboldti), Pygoscelis papua (P. papua), Pygoscelis adeliae (P. adeliae), and Aptenodytes forsteri (A. forsteri)-collected at Chimelong Ocean Kingdom. A total of 219 viral sequences representing potentially novel lineages were identified, with more than 94% sharing <80% amino acid similarity with previously known viruses. These sequences were assigned to several viral families, including Parvoviridae, Caliciviridae, Anelloviridae, Circoviridae, and Microviridae, among others. Marked interspecies differences in virome composition were observed: Parvoviridae dominated in S. humboldti, Microviridae were enriched in P. papua, Caliciviridae accounted for a substantial proportion in A. forsteri, and P. adeliae displayed the greatest overall virome diversity. Multiple-virus co-detections, particularly involving Parvoviridae, were frequent in S. humboldti. Phylogenetic analyses showed that many penguin-associated viruses clustered with viruses infecting other avian and fish hosts, suggesting possible dietary or environmental origins of some detected viral sequences. These findings expand current knowledge of penguin gut virome diversity and host-associated differences and provide a valuable foundation for evaluating the ecological roles, health implications, and transmission risks of penguin-associated viruses.IMPORTANCEThis study uncovers significant diversity in the gut viromes of four penguin species, revealing over 219 viral sequences representing potentially novel lineages, many of which showed host-associated distribution patterns. Using viral metagenomics, we identified notable interspecies differences, with Parvoviridae predominating in Spheniscus humboldti and Microviridae being enriched in Pygoscelis papua. These findings highlight the complexity of viral community structures in penguins, including frequent viral co-detections, which could impact host health and ecological adaptation. Additionally, novel bacteriophage communities were identified, emphasizing their potential role in shaping the gut microbiome and influencing viral dynamics. This work provides new insights into viral diversity in wildlife and lays the groundwork for future studies on viral transmission risks and ecological conservation.}, } @article {pmid42402034, year = {2026}, author = {Wu, Y and Wang, Y and Qin, R and Liu, L and Wang, L and Liu, Y and Wang, W and Diao, Q}, title = {Dietary supplementation with fermented compound Chinese herbal medicine reshapes the gastrointestinal microbiota and enhances growth in suckling lambs.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0388925}, doi = {10.1128/spectrum.03889-25}, pmid = {42402034}, issn = {2165-0497}, abstract = {UNLABELLED: This study investigated the effects of a fermented compound Chinese herbal medicine (FCHM) on growth performance, antioxidant capacity, immune function, and gastrointestinal microbiota in suckling lambs. FCHM consisted of 10 herbs fermented with Candida utilis and Bacillus subtilis. Sixty twin Hu lambs (15 days) were randomly fed a basal diet (CON) or the diet supplemented with 0.6% FCHM (Treat) for 45 days. The results indicated that the Treat group exhibited a significant increase in average daily gain (ADG) (P < 0.05). Serum analyses revealed elevated levels of growth hormone (GH), insulin-like growth factor-1 (IGF-1), total antioxidant capacity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and glucose (GLU), whereas malondialdehyde (MDA) and pro-inflammatory cytokines (IL-6 and TNF-α) were reduced (P < 0.05). In the duodenal mucosa, SOD and GSH-Px activities and T-AOC levels were significantly elevated, while MDA content was notably decreased (P < 0.05). Ruminal fermentation profiles showed increased concentrations of propionate and total volatile fatty acids (TVFA) in the Treat group (P < 0.05). Microbiome analysis revealed that FCHM supplementation selectively modulated the ruminal microbial community, enriching beneficial genera such as Prevotellaceae_UCG-003 and Butyrivibrio, while reducing the abundance of potentially harmful genera like Streptococcus, despite no significant changes in the overall community diversity. Metagenomic sequencing further demonstrated the enrichment of KEGG enzymes and carbohydrate-active enzyme genes involved in carbohydrate metabolism and propionate biosynthesis. Correlation network analyses revealed significant associations among specific microbial taxa, serum antioxidant, immune biomarkers, and growth performance. In conclusion, dietary FCHM supplementation improves growth performance in suckling lambs by optimizing ruminal fermentation patterns, selectively regulating gastrointestinal microbiota, and enhancing systemic antioxidant capacity. These findings support the potential of FCHM as a functional feed additive in lamb production systems.

IMPORTANCE: Enhancing growth performance and ensuring gastrointestinal health during the suckling period are critical for lamb productivity and welfare. In the context of the antibiotic-free mandate in animal feed, we evaluated the effects of a fermented compound Chinese herbal medicine (FCHM) on growth, antioxidant status, immune parameters, and gastrointestinal microbiota in lambs. Our findings demonstrate that FCHM improves average daily gain, enhances systemic and mucosal antioxidant capacity, and modulates ruminal and hindgut microbiota by enriching beneficial taxa and suppressing potentially harmful bacteria. These effects are linked to upregulated microbial functions in carbohydrate metabolism and propionate biosynthesis. This study provides a microbial-based mechanism for FCHM as a natural feed additive to promote lamb growth and gastrointestinal resilience, offering a sustainable strategy to support early-life development in ruminant production systems.}, } @article {pmid42402279, year = {2026}, author = {Jiang, C and Wang, Z and Xie, B and Huang, H and Zhan, M and Kim, Y and El-Kady, AA and Su, Y}, title = {Fructose-Induced bioenergetic surplus Unlocks fatty acid biosynthesis pathway dominance over reverse β-Oxidation: Mechanistic insights into High-Caproate production from food waste.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135298}, doi = {10.1016/j.biortech.2026.135298}, pmid = {42402279}, issn = {1873-2976}, abstract = {Chain elongation (CE) is an effective strategy for converting organic wastes into value-added medium-chain fatty acids (MCFAs), wherein electron donors (EDs) dictate process efficiency. However, beyond substrate toxicity and limited reducing power, conventional EDs such as ethanol and lactate impose a chronic bioenergetic constraint: their minimal net ATP yield thermodynamically restricts CE strictly to the energy-neutral reverse β-oxidation (RBO) pathway. To overcome this bioenergetic bottleneck, this study investigated fructose as a high-energy-yielding multidimensional ED to drive n-caproate production from food waste in a mixed-culture system. Herein, the results demonstrated a dose-dependent enhancement of n-caproate, peaking at 12.38 g/L with a remarkable selectivity of 63.0 % (50 g/L fructose dosage). Mechanistically, fructose fermentation established an in-situ synergistic multi-ED microenvironment (fructose, ethanol, and lactate) that buffered toxicity and sustained robust reducing power. More critically, intensive glycolytic flux induced a hyper-energetic intracellular state characterized by abundant ATP and elevated NADH/NAD[+] ratio. Meanwhile, the activities of key enzymes (e.g., phosphofructokinase and butyrate kinase) were significantly stimulated, redirecting carbon flow toward butyrate and n-caproate. This favorable energetic and metabolic environment further selectively enriched Limosilactobacillus spp., which glycolyzed fructose into essential carbon intermediates for CE. Finally, metagenomic profiling revealed that the fructose-induced ATP surplus profoundly enriched genes associated with the ATP-dependent fatty acid biosynthesis (FAB), while suppressing RBO-related genes. This uncovers a paradigm shift from the RBO-dominated route to a FAB-driven mechanism. These findings unravel how a targeted carbohydrate structurally rewires the thermodynamic hierarchy of CE pathways, providing novel mechanistic blueprints for upgrading complex organic wastes into high-value biochemicals.}, } @article {pmid42402284, year = {2026}, author = {Dar, RA and Tsui, TH and Du, Z and Zhang, L and Smoliński, A and Xiang, G and Liu, R}, title = {Integrated metagenomic and metaproteomic insights into current-carrying-coil magnetic field enhanced synergistic methanogenic system and antibiotic resistance gene reduction in cow manure anaerobic digestion.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135326}, doi = {10.1016/j.biortech.2026.135326}, pmid = {42402284}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) is a sustainable strategy for valorizing cow manure (CM). However, the high ammonia (NH3) concentration and low biodegradability of CM limit hydrolysis and methane production. This study investigated the application of a current-carrying-coil-based magnetic field (CCC-MF) to AD of CM. The CCC-MF digesters showed higher soluble chemical oxygen demand and attained 16.59 % higher ammonium nitrogen reduction, contributing to a 37.50 % higher average methane yield than the control. Further, CCC-MF digesters showed higher enzyme activities (alkaline protease + 30 %, acetate kinase + 22 % and hydrazine dehydrogenase + 26 %) and increased microbial metabolic indices (dehydrogenase activity + 17 % and electron transport system activity + 10 %) than the control. Metagenomics analysis revealed that abundances of the bacterial genera Mesotoga, Aminobacterium, Xiashengella, unclassified Candidatus Cloacimonadota, Advenella, Pseudomonas, and Comamonas increased, whereas the acetoclastic methanogen Methanothrix decreased by 2.58 %, accompanied by 2.07- and 1.64-fold increases in hydrogenotrophic methanogens Methanospirillum and Methanobacterium, respectively, in CCC-MF digesters. The abundance of nitrogen dissimilation and assimilation genes NirK, NorB, NarB, NapA, nmo, and GLT1 were enhanced by 1.14, 1.04, 2.30, 1.32, 1.17, and 1.29-fold in CCC-MF digesters compared to the control. Moreover, metaproteomics revealed higher up-regulated differentially expressed proteins in NH3 reduction-related amino acid metabolism pathways in CCC-MF digester compared to control. Additionally, reduced abundances of bacitracin, polymyxin, sulfonamide, and multidrug antibiotic resistance (MAR) gene types were observed in the CCC-MF digesters. The findings suggest that applying CCC-MF may be associated with higher methane production and ammonium reduction, potentially linked to a more favorable synergistic methanogenic system and nitrogen transformation pathways.}, } @article {pmid42402338, year = {2026}, author = {Chakrawarti, A and Cromarty, RT and Basting, CM and Anderson, J and Schroeder, TA and Escandón, K and Shields-Cutler, R and Langat, R and Swanson, E and Soon-Shiong, P and Safrit, JT and Sender, LS and Reddy, S and Miller, JS and Rhein, J and Schacker, TW and Klatt, NR}, title = {Pre-treatment Gut Microbiome Diversity and Function Linked to Cytotoxic and Natural Killer Cell Immune Responses after N-803 Treatment in People with HIV.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciag369}, pmid = {42402338}, issn = {1537-6591}, abstract = {BACKGROUND: N-803, an IL-15 superagonist, is currently being studied in clinical trials as a treatment to reverse HIV latency. However, its effects on the gut microbiome are not well understood.

METHODS: In this exploratory longitudinal metagenomic study, we analyzed fecal microbiomes from 10 ART-suppressed people with HIV at four different timepoints before, during, and after N-803 treatment.

RESULTS: Overall taxonomic and functional diversity did not change significantly, yet beneficial microbial taxa and pathways were nominally enriched after N-803. Specifically, the relative abundance of Faecalibacterium prausnitzii showed a nominal increase after N-803, whereas histidine degradation pathways, often associated with pro-inflammatory mucosal state, decreased. A higher baseline microbial diversity correlated with stronger CD8+ and natural killer (NK) cells activation and reduced frequency of rectal HIV RNA+ cells. MaAsLin2 analyses further identified potentially important associations between short-chain fatty acid (SCFA)-producing taxa and pathways with increased immune activation markers.

CONCLUSIONS: These findings in a limited Phase 1B clinical study suggest that gut microbiome diversity prior to immunotherapy may influence host response. These results provide a basis for further investigation into microbiome-based strategies to improve efforts to cure HIV.}, } @article {pmid42399687, year = {2026}, author = {Wang, X and Wang, H and Wang, X and Liao, H and Yang, J and Jin, H and Hoffnagle, E and Jeon, MK and Cui, Y and Li, X and Liu, X and Chen, X and Liao, L and Dong, Y and Jiang, L and Xiu, Z and Yang, Y}, title = {Fermentative iron reduction by a psychrotolerant Clostridium-dominant consortium enriched from Antarctic penguin-impacted soils.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10434-2}, pmid = {42399687}, issn = {2399-3642}, abstract = {Microbial iron cycling regulates nutrient availability and redox balance in global ecosystems, yet its pathways remain underexplored in ice-free Antarctic terrestrial ecosystems. This study reports the enrichment of a psychrotolerant microbial consortium from penguin-impacted soils on Beaufort Island, Antarctica, capable of reducing Fe(III) to Fe(II) at 4 °C via an anaerobic (likely fermentative) iron-reducing pathway. The consortium was dominated by Clostridium sensu stricto 13 and completely reduced 230 mg L[-1] Fe(III) citrate within three months and drove the biogenic formation of magnetite (Fe3O4). Metagenomic binning yielded four high-quality Clostridium genomes harboring multiple hydrogenases and cold-shock proteins (csp), revealing genomic strategies for energy conservation and psychrotolerance. Hydrogen production was strongly suppressed in the presence of Fe(III) citrate, indicating an intimate coupling of fermentation-derived electron flow to Fe(III) reduction. Our findings reveal a previously unrecognized low-temperature iron reduction mechanism and highlight the ecological significance of anaerobic (likely fermentative) iron reducers in ornithogenic soils-microhabitats enriched in organic matter and metals by penguin guano. This work expands the known diversity of Fe(III)-reducing microorganisms, demonstrates their role in magnetite biomineralization under extreme conditions, and provides insights into microbial modulation of iron speciation in Antarctic ornithogenic soils.}, } @article {pmid42399871, year = {2026}, author = {Du, W and Pan, F and Lan, P and Xie, L and Zheng, C and Wu, H}, title = {Metagenomic next-generation sequencing-guided management of descending mediastinitis and empyema caused by Segatella baroniae: a case report.}, journal = {BMC pulmonary medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12890-026-04465-y}, pmid = {42399871}, issn = {1471-2466}, abstract = {BACKGROUND: Deep neck infections can rapidly progress to descending mediastinitis and empyema, both of which are associated with high morbidity and mortality. Early diagnosis and timely intervention are essential but can be challenging, particularly in infections caused by rare anaerobic pathogens.

CASE PRESENTATION: We report a case of a 63-year-old man presenting with fever and neck pain. Computed tomography revealed extensive cervical emphysema and pneumomediastinum with a large right-sided empyema. The patient developed respiratory failure requiring endotracheal intubation. Endoscopic examination identified a retropharyngeal fistula, and thoracoscopic exploration confirmed communication between the mediastinum and pleural cavity. Combined cervical, mediastinal, and thoracic drainage was performed. Metagenomic next-generation sequencing identified Segatella baroniae as the predominant pathogen, guiding targeted antimicrobial therapy. The patient showed gradual clinical and radiological improvement and was discharged in good condition.

CONCLUSION: This case highlights the importance of early recognition and aggressive surgical management in deep neck infections complicated by descending mediastinitis. Metagenomic next-generation sequencing may facilitate rapid pathogen identification and guide targeted therapy in complex anaerobic infections.}, } @article {pmid42399943, year = {2026}, author = {Fu, Y and Song, X and Wang, H and Sun, J and Chen, J and Liu, T and Qi, K and Shi, Y and Li, F and Huang, X and Yang, H and Zhang, W}, title = {Viral metagenomic analysis of the blood virome in patients with multiple autoimmune diseases.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {42399943}, issn = {1743-422X}, support = {No.SH2022092 and SH2024091//Social Development Projects in Zhenjiang/ ; F202322//Jiangsu Province Maternal and Child Health Research Project/ ; JC-2023-004//Clinical Research Project of the Jiangsu University Affiliated People's Hospital/ ; No. 82341106 and 82550118//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Virome ; *Autoimmune Diseases/virology/blood ; *Metagenomics ; Female ; *Viruses/classification/genetics/isolation & purification ; Male ; Adult ; Middle Aged ; Lupus Erythematosus, Systemic/virology ; }, abstract = {Autoimmune diseases are chronic and heterogeneous disorders resulting from the breakdown of immune tolerance and subsequent tissue damage. Beyond genetic predisposition, viral infections are increasingly recognized as pivotal environmental contributors to disease onset. In this study, we performed comprehensive viral metagenomic profiling of blood samples from 205 patients with systemic lupus erythematosus (SLE), Sjögren's syndrome (SS), ankylosing spondylitis (AS), and undifferentiated connective tissue disease (UCTD). A total of approximately 103.98 million sequencing reads were analyzed, revealing 44 viral families, including 30 DNA and 14 RNA families. RNA viruses dominated the virome composition, accounting for 71% of total reads, with Picobirnaviridae being consistently prevalent and abundant across all disease groups. Alpha and beta diversity analyses revealed significant heterogeneity in viral community structures among different disease groups, with a marked diversity skew observed in the SS group. Disease-specific viral composition patterns were prominent, and the number of core viral species shared across the four groups was limited. Of particular note, Anelloviridae was significantly enriched in the AS and UCTD groups, suggesting its potential as a biomarker for immunosuppressive states. Furthermore, bacteriophages such as Microviridae exhibited differential abundance across groups, reflecting the potential role of virus-microbe-host immune interactions in disease pathogenesis. In conclusion, this study provides a comprehensive profile of the blood virome in four autoimmune diseases, highlighting the potential role of viral communities in immune regulation and offering new perspectives for the development of related biomarkers.}, } @article {pmid42400043, year = {2026}, author = {Wang, Y and Xue, X and Usyk, M and Sharma, A and Anastos, K and Post, WS and Hodis, HN and Wang, Z and Witt, MD and Rinaldo, CR and Brown, TT and Palella, FJ and Gange, S and Kuniholm, MH and Sha, BE and Caron, P and Gerszten, RE and Clish, CB and Guillemette, C and Burk, RD and Kaplan, RC and Qi, Q and Hanna, DB and Peters, BA}, title = {Multi-omics profiles of sex hormone-binding globulin are associated with subclinical atherosclerosis in men with HIV.}, journal = {Genome medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13073-026-01709-8}, pmid = {42400043}, issn = {1756-994X}, support = {R01HL095129/HL/NHLBI NIH HHS/United States ; K01HL169019/HL/NHLBI NIH HHS/United States ; R01HL148094/HL/NHLBI NIH HHS/United States ; R01HL140976/HL/NHLBI NIH HHS/United States ; K01HL137557/HL/NHLBI NIH HHS/United States ; K01HL160146/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: Sex hormones and HIV infection both influence cardiovascular health. However, the association between sex hormones and subclinical atherosclerosis is not fully understood, especially in the context of HIV.

METHODS: Among 321 men (65% with HIV) from the MACS/WIHS Combined Cohort Study, we measured 14 serum sex hormones and sex hormone-binding globulin (SHBG), assessed carotid artery plaque (IMT > 1.5 mm) using high-resolution B-mode ultrasound, and performed metagenomic sequencing on stool samples. In 312 men, we measured 986 plasma metabolites via liquid chromatography-tandem mass spectrometry and 2883 plasma proteins using the Olink Explore 3072 platform. In stratified analyses of men with (MWH) and without HIV (MWOH) and adjusting for covariates and multiple testing, we (1) examined associations of sex hormones with plaque; (2) characterized multi-omics profiles related to sex hormones; and (3) generated sex hormone-related omics scores via linear combination of related species, metabolites, and proteins, respectively, to explore whether these sex hormone-related multi-omics profiles were associated with plaque.

RESULTS: Median age of participants was 62 years (interquartile range: 58-68), and 31.5% had carotid artery plaque. Sex hormones were differentially associated with plaque in MWH and MWOH. In MWH, an inverse association was observed between SHBG and plaque (OR = 0.60 per 1-SD increase, 95% CI: 0.41, 0.90). Furthermore, higher SHBG levels were associated with overall gut microbial composition, lower abundance of species from genera Prevotella, Fibrobacter and Coprococcus, higher levels of certain metabolites (primarily lipid and carnitine metabolites) and proteins enriched in the cell-cell adhesion pathway. Some SHBG-related species (e.g., Mediterranea massiliensis), metabolites (e.g., phosphatidylcholine-based lipids) and proteins (e.g., enriched in immune response pathway) were also associated with plaque in MWH. All three SHBG-related omics scores were inter-correlated and inversely associated with plaque in MWH. In MWOH, estrone-sulfate was positively associated with plaque (OR = 3.80, 95% CI: 1.41, 10.22) but not with any species, metabolites or proteins.

CONCLUSIONS: Higher SHBG, and related microbial species, circulating metabolites, and proteins, were inversely associated with carotid artery plaque. These findings suggested that SHBG may play a protective role in subclinical atherosclerosis in MWH.}, } @article {pmid42400260, year = {2026}, author = {Kim, D and Li, M and Nguyen, TH and Choi, YJ and Jang, S and Kim, M and Kim, YK and Shin, MK and de Guzman, ACV and Park, S}, title = {Vitamin B6 produced by gut microbiome regulates host behavioral phenotypes through dopaminergic metabolism.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2695485}, doi = {10.1080/19490976.2026.2695485}, pmid = {42400260}, issn = {1949-0984}, mesh = {Animals ; Caenorhabditis elegans/microbiology/metabolism ; Humans ; *Dopamine/metabolism ; *Gastrointestinal Microbiome ; *Vitamin B 6/metabolism/biosynthesis ; *Parkinson Disease/microbiology/metabolism/genetics ; Mice ; Pyridoxal Phosphate/metabolism ; Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics/metabolism ; Phenotype ; Escherichia coli/genetics/metabolism ; alpha-Synuclein/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Male ; Mice, Inbred C57BL ; Feces/microbiology ; Disease Models, Animal ; }, abstract = {The gut microbiome modulates host neuropathology, but the mechanisms linking specific microbial genes and metabolites to host phenotypes remain poorly defined. Here, we identify microbiome-derived vitamin B6 (VB6) and its biosynthesis gene as key regulators of host dopaminergic homeostasis. Metagenomic analysis of fecal samples from Parkinson's disease (PD) patients revealed enrichment of biosynthetic pathways for pyridoxal-5'-phosphate (PLP), the active form of VB6, and tyrosine decarboxylase genes. Using E. coli-C. elegans symbiotic models, we demonstrate that the bacterial pdxJ gene, encoding a key enzyme in de novo VB6 synthesis, is essential in regulating host dopaminergic homeostasis. Colonization with pdxJ-deficient bacteria led to reduced host VB6 and dopamine levels, reduced dopaminergic enzyme activity, and altered motor behavior, which were all rescued by VB6 supplementation. In PD-relevant C. elegans models, bacterial PLP biosynthesis modulated α-synuclein aggregation and behavioral deficits associated with human LRRK2 mutations. In mice, colonization with pdxJ-deficient bacteria reduced serum VB6 levels, decreased tyrosine hydroxylase staining in the substantia nigra, and impaired motor coordination, which were rescued by VB6 supplementation. Overall, our results define a bacterial pdxJ-PLP-dopamine axis that links gut microbial metabolism to host dopaminergic phenotypes and suggest bacterial VB6 biosynthesis as a potential modifier of PD risk and a context-dependent therapeutic target.}, } @article {pmid42400618, year = {2026}, author = {Yu, J and Jiang, C and Sakai, Y and Mino, S and Sawabe, T}, title = {The Sea Cucumber Holobiont and Probiotics: Recent Progress on Apostichopus japonicus.}, journal = {Current microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {42400618}, issn = {1432-0991}, support = {JP19K22262//MEXT Kaken/ ; }, mesh = {Animals ; *Symbiosis ; *Probiotics ; *Stichopus/microbiology/physiology/genetics ; *Sea Cucumbers/microbiology/physiology ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {After the first definition of the term "Holobiont" by Margulis in the introduction of symbiosis as "Association throughout a significant portion of the life history" in 1991 [1], the understanding of holobiont has become an important goal in modern biology today [2]. Recent advances in microbial collection, genome/metagenome/transcriptome sequencings, and bioassays for host-microbes interactions push us towards a fuller understanding of holobiont in various aspects of life on Earth. Historically, holobiont and related hologenome concepts have been tested and expanded through research on marine organisms such as coral, fish, sea cucumber, sponge, and squid. In particular, the sea cucumber Apostichopus japonicus is a physiologically and ecologically unique marine invertebrate in which the holobiont can be studied with its significant capability of organ regeneration, presence of microbes in coelomic fluid, their mysterious nutrition connected to slow growth, and improvements in seed production for the bio-conservation of endangered and essential fisheries resources. The animals are also important in evolutionary terms on a branch of the Deuterostomia clade sharing ancestry with humans, so we can also compare to and learn from knowledge on the human-microbes interactions. In this review, recent progress in the sea cucumber A. japonicus holobiont studies, and the discovery of probiotics candidates among its pioneer microbiomes are described. By understanding this recent progress, we expect to stimulate new and further perspectives on basic biology, bio-conservation, and sustainable aquaculture of sea cucumber.}, } @article {pmid42400712, year = {2026}, author = {Song, Y and Mao, C and Liu, P and Yang, G and Kang, L and Li, Z and Zhou, W and Liu, X and Yao, S and Yang, Y}, title = {Microbial community structure and function and their linkages with methane production in sediments of thermokarst lakes on the Tibetan Plateau.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {42400712}, issn = {1869-1889}, abstract = {Thermokarst lakes represent a critical source of atmospheric methane (CH4), owing to large amounts of microbially generated CH4 in sediments. However, the structure and function of lake sediment microbiota, as well as their roles in mediating CH4 production, remain poorly understood across broad geographic scales. Here, we combined high-throughput sequencing, a 224-d anaerobic incubation, and stable isotopic analyses to investigate sediment microbiota and CH4 production across 30 thermokarst lakes along a 1,100 km permafrost transect on the Tibetan Plateau. Our results revealed that lake characteristics (i.e., lake depth and salinity-alkalinity) shaped sediment microbial composition and function. Deeper lakes exhibited enriched methanogenic taxa and pathways. In contrast, shallower lakes with higher salinity-alkalinity were dominated by microbial consortia that suppress net CH4 production via methanotrophs consuming CH4 and sulfate reducers competing with acetoclastic and hydrogenotrophic methanogens. Accordingly, cumulative CH4 production decreased by one order of magnitude from deeper lakes (2.5 log10CH4-C µg/g) to shallow and alkaline lakes (1.3 log10CH4-C µg/g) or salinity-alkalinity lakes (1.1 log10CH4-C µg/g). This variation was modulated by both key microbial consortia and sediment organic carbon and nitrogen supply. Overall, these results disentangled how lake characteristics restructured microbial dynamics to alter sediment CH4 production, and identified critical microbial consortia that could predict spatial variations in sediment CH4 production across thermokarst lakes.}, } @article {pmid42401057, year = {2026}, author = {Zheng, Y and Wang, C and Niu, X and Han, C and Zhang, Z and Yang, H and Zhang, S and Ye, X and Li, L and Lv, J and Ma, Z and Liu, H and Ma, Y and Su, X}, title = {Coupled geochemical profiling and metagenomics reveal controls on phosphine preservation and emission in a eutrophic Estuary.}, journal = {Water research}, volume = {304}, number = {}, pages = {126393}, doi = {10.1016/j.watres.2026.126393}, pmid = {42401057}, issn = {1879-2448}, abstract = {Matrix-bound phosphine (MBP) represents a critical yet poorly constrained component of aquatic phosphorus cycling, and the controls governing its preservation and emission in eutrophic estuarine systems remain incompletely resolved. The spatial controls on MBP preservation and atmospheric phosphine emission across the Pearl River Estuary (PRE) were investigated by integrating sediment phosphorus fractionation, sub-millimeter diffusive gradients in thin films (DGT) profiling, and metagenomic sequencing. Sedimentary MBP was detected at all sites and varied markedly along the estuarine gradient, ranging from 2.38 to 36.85 ng kg[-1] ww, with significant positive correlations with Org-P and TP (p < 0.05). The PRE acted as a net atmospheric source of PH3 during summer, with air-water interface (AWI) fluxes ranging from -5.35 ± 0.63 to 28.90 ± 4.67 ng m[-2] h[-1] and highest emissions concentrated at inner-estuarine nearshore sites. DGT-derived labile P-Fe-S coupling patterns and systematic shifts in microbial metabolic functional potential (e.g., dsrA, mcrA, and ptxD genes) were broadly consistent with the spatial distribution of MBP, suggesting that microscale redox conditions and microbial community function may collectively contribute to reduced-P preservation. The accumulation of Org-P and OM in nearshore depositional zones, driven by terrestrial inputs and local hydrological conditions, may progressively shift sedimentary phosphorus cycling toward pathways that favor reduced-P preservation and sustained atmospheric PH3 emissions. Collectively, these findings offer new insights into the spatial controls on MBP preservation and atmospheric PH3 emission in eutrophic estuarine systems, which are essential to understanding the complex biogeochemical processes that regulate nutrient cycling in these fragile ecosystems.}, } @article {pmid42401342, year = {2026}, author = {Zeng, Y and Zhang, L and Zou, Y and Liu, L and Chen, B}, title = {Enhancing catalytic efficiency of a deep-sea alkaline lipase through integrated engineering of lid-associated dynamics.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135300}, doi = {10.1016/j.biortech.2026.135300}, pmid = {42401342}, issn = {1873-2976}, abstract = {A deep-sea alkaline lipase, MyLip2, fromMoritella yayanosiiwas identified from a metagenomic library of 1,048,576 genes. The wild-type enzyme preferred medium- to long-chain p-nitrophenyl esters, with optimal activity at pH 10.5 and 40 °C, but its specific activity was only 2.93 U/mg toward p-nitrophenyl palmitate. To improve performance, we used a structure- and sequence-guided strategy targeting noncatalytic residues around the catalytic center and lid region. Combinatorial engineering produced triple A271F/V250L/L231P and quadruple A271F/V250L/L231P/T300K (4 M), with comparable specific activities of 743.4 and 745.4 U/mg; 4 M was chosen for its high activity and improved thermal tolerance. This variant showed ∼ 196-fold higher catalytic efficiency (kcat/Km) toward p-nitrophenyl palmitate, with increasedVmax and kcat. Molecular docking, kinetics, and simulations indicated that the substitutions support a more open and catalytically accessible lid conformation, facilitating substrate access and turnover. Comparison with reported lipases indicated that MyLip2 and 4 M combine alkaline preference, medium- to long-chain activity, and improved performance. This work provides a high-performance deep-sea alkaline lipase and suggests that catalytic efficiency can be improved by tuning noncatalytic residues that influence the catalytic-center microenvironment and lid dynamics, without mutating the catalytic triad or redesigning the lid.}, } @article {pmid42401346, year = {2026}, author = {Ping, Q and Chen, X and Jin, Y and Chen, Y and Zheng, M and Wang, L and Li, Y}, title = {Deciphering the structural and stoichiometric regulation of anaerobic digestion: A cross-scale perspective from molecular thermodynamics to methanogenic pathways.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135314}, doi = {10.1016/j.biortech.2026.135314}, pmid = {42401346}, issn = {1873-2976}, abstract = {Proteins and polysaccharides are the predominant organic fractions of waste activated sludge (WAS). However, the regulation mechanisms of their distinct molecular structures and compositional ratios on the efficiency of anaerobic digestion (AD) remain unclear. This study comprehensively investigates their impacts on AD performance, focusing on molecular thermodynamics and functional gene regulation involved in electron transfer, energy conversion, and methanogenic pathways. The results demonstrate that molecular structure is a key factor determining substrate bioavailability. The protein with a mainly β-structure (xylanase) and randomly coiled polysaccharide (pullulan) exhibited superior hydrolysis, acidification, and methanogenic efficiency due to increased enzyme binding affinity. Conversely, α-helical protein and triple-helix polysaccharide displayed restricted enzymatic accessibility. Further studies revealed the combination of xylanase and pullulan at the optimal C/N ratio (35) effectively balanced nutrition, thereby achieving the highest cumulative methane yield. Metagenomic and metatranscriptomic analyses revealed that the optimal structures and C/N stoichiometry not only enriched GH13 enzymes, but also shifted the metabolic pathway from acetoclastic to hydrogenotrophic methanogenesis. Moreover, it enhanced interspecies electron transfer and energy conversion efficiency by promoting NADH dehydrogenases, formate dehydrogenase and heterodisulfide reductase, thereby establishing a highly efficient and stable metabolic network in AD system. These findings provide novel insights into the microbial and biochemical regulation driven by substrate structure and stoichiometry from cross-scale perspective, thereby offering a theoretical basis and regulatory strategy for the efficient resource recovery of waste activated sludge.}, } @article {pmid42401622, year = {2026}, author = {Real, MVF and Vitousek, MN and Sheehan, MJ and Moeller, AH}, title = {The mouse gut microbiota responds to predator odor and predicts host behavior.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01028-1}, pmid = {42401622}, issn = {2055-5008}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; }, abstract = {Chronic stressors can alter the mammalian gut microbiota in ways that mediate host stress responses, but the impacts of acute stressors on these interactions are less well understood. Here, we show that brief exposure of wild-derived mice to predator odor altered gut-microbiota composition, which in turn predicted host behavior. We investigated the individual and combined effects of 15-minute exposures to synthetic fox fecal odor and 30 days of chronic social isolation, an established chronic stressor. Using ethological assays, visceral adipose tissue transcriptomics, and genome-resolved metagenomics, we found that predator-odor exposure significantly affected mouse behavior, gene expression, and gut microbiota. Predator odor-responsive bacteria were associated with the expression of genes involved in anti-microbial defense, and host behavioral responses were predicted by random forest models trained on gut-microbiota profiles. These findings indicate interactions between the gut microbiota and wild-mouse responses to the threat of predation, an ecologically relevant acute stressor.}, } @article {pmid42401690, year = {2026}, author = {Ribero, MN and Schiaffino, MR and Filloy, J}, title = {Grassland afforestation more than forestry intensification shapes soil multifunctionality via microbial compositional change under abiotic constraints.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-60845-8}, pmid = {42401690}, issn = {2045-2322}, support = {UBACyT 2018//Universidad de Buenos Aires/ ; }, abstract = {Soil ecosystem multifunctionality (EMF) is driven by the interplay of abiotic and biological factors, yet how these interactions respond to anthropogenic pressures remains poorly understood. Here, we evaluated how grassland afforestation and its intensification shape soil edaphic conditions, microbial diversity, and EMF along a 200 km grassland-eucalypt plantation transect in Argentina. EMF was estimated, accounting for six ecosystem functions related to nutrient provisioning, organic matter cycling, and pathogen control. Microbial diversity was studied through the taxonomic, functional, and phylogenetic dimensions of prokaryotes, mycorrhizae, and fungal saprotrophs. Abiotic and biotic drivers of individual ecosystem functions and EMF were assessed using correlations, linear mixed models, structural equation models, and Multiple Regressions on distance Matrices. Individual ecosystem functions responded differentially to environmental drivers: functions linked to soil physicochemical processes were primarily associated with edaphic conditions, whereas biologically mediated functions were more closely linked to climate and grassland afforestation. Soil multifunctionality, however, was driven by edaphic and climatic conditions, particularly soil sand percentage and precipitation, with no direct association with microbial alpha diversity or afforestation. In contrast, similarity in fungal composition explained similarity in EMF, suggesting a coupling between microbial composition and soil conditions associated with grassland afforestation. Grassland conversion to commercial forest, rather than forestry intensification, altered individual soil functions and microbial functional composition without further reducing EMF. Overall, our findings indicate that afforestation influences soil EMF through changes in microbial composition, but that these effects are constrained by abiotic drivers.}, } @article {pmid41738567, year = {2026}, author = {Ma, M and Liu, B and Zhou, J and Zhang, J and Zhang, Y and Li, W and Liu, X and Xu, D}, title = {Viral Community Profiling of RNA Viruses in Lesion Tissues From Hyriopsis cumingii With Epidemic Disease via Metatranscriptomics and VirID-Based RdRP Mining.}, journal = {Journal of fish diseases}, volume = {49}, number = {8}, pages = {e70143}, doi = {10.1111/jfd.70143}, pmid = {41738567}, issn = {1365-2761}, support = {2024SKLBC-KF02//National Key Laboratory of Aquatic Animal Disease Control and Healthy Aquaculture, 2024 Open Research Projects/ ; }, mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification/physiology ; Phylogeny ; *Unionidae/virology ; RNA-Dependent RNA Polymerase/genetics ; Metagenomics ; Transcriptome ; Epidemics/veterinary ; *Virome ; Hepatopancreas/virology ; }, abstract = {To identify enriched pathogens and characterise the viral community associated with epidemic disease outbreaks in the freshwater mussel Hyriopsis cumingii, we performed metatranscriptomic sequencing combined with VirID-driven RNA-dependent RNA polymerase (RdRP) mining and phylogenetic analysis using hepatopancreas and intestinal samples from six severely infected individuals. Clinical observations were consistent with hallmark features of epidemic outbreaks. The sequencing yielded 86.2 Gb of raw data, of which 97.1% passed quality control, resulting in 77.7 Gb of high-quality clean data. Taxonomic annotation identified 182 viral species, predominantly unclassified viruses (45% Transcripts Per Million, TPM), followed by members of the phyla Lenarviricota (28%) and Uroviricota (17%). Phylogenetic analysis of RdRP sequences revealed 13 viral supergroups, with the Picorna-Calici supergroup showing the highest abundance (26.2% of annotated viruses) and reaching a prevalence of 39.3% in sample HcAV3. Notably, 89.6% of the identified viral RdRPs exhibited less than 70% amino acid identity to known viral sequences, highlighting the presence of extensive "viral dark matter" in this host species. This study establishes the first viral profile associated with epidemic disease in H. cumingii, providing a baseline for further etiological research on this high-mortality aquaculture disease.}, } @article {pmid42392820, year = {2026}, author = {Li, H and Deng, XF and Chen, H and Wang, P and Xu, HY}, title = {[Metabolomics and metagenomics reveal mechanism of Xinglou Chengqi Decoction in preventing cerebral ischemia-reperfusion injury].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {51}, number = {9}, pages = {2652-2664}, doi = {10.19540/j.cnki.cjcmm.20260107.707}, pmid = {42392820}, issn = {1001-5302}, mesh = {Animals ; *Drugs, Chinese Herbal/administration & dosage ; *Reperfusion Injury/metabolism/prevention & control/drug therapy/genetics ; Rats ; Male ; Metabolomics ; Metagenomics ; Rats, Sprague-Dawley ; *Brain Ischemia/metabolism/drug therapy/genetics ; Humans ; Oxidative Stress/drug effects ; Blood-Brain Barrier/drug effects/metabolism ; Brain/metabolism/drug effects ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; }, abstract = {This study uses a rat model of middle cerebral artery occlusion and reperfusion(MCAO/R) to investigate the mechanism by which Xinglou Chengqi Decoction treats cerebral ischemia-reperfusion injury, employing metabolomics and metagenomics approaches. A rat model of MCAO/R was established to evaluate the neurological function and modified neurological severity scores. Then, the brain tissue pathology, inflammatory mediators, oxidative stress, blood-brain barrier integrity, cerebral edema, and intestinal barrier function were examined to assess the pharmacological effects of Xinglou Chengqi Decoction. Metabolomics analysis of the brain tissue and metagenomics analysis of the intestinal contents were conducted to investigate the metabolism and gut microbiota regulatory mechanisms of Xinglou Chengqi Decoction. The results suggested that Xingluo Chengqi Decoction improved the neural function, reduced the severity of cerebral infarction, attenuated oxidative stress and inflammatory factor levels, boosted blood-brain barrier factor levels, minimized cerebral edema, and strengthened intestinal mucosal barrier protection, thus treating cerebral ischemia-reperfusion injury in rats. Metabolomic analysis of the brain tissue revealed that Xinglou Chengqi Decoction primarily treated ischemic stroke through 14 potential metabolic pathways, including phenylalanine, tyrosine, and tryptophan biosynthesis, valine, leucine, and isoleucine biosynthesis, and phenylalanine metabolism. Metagenomic analysis revealed that administration of Xinglou Chengqi Decoction increased the relative abundance of Firmicutes, Clostridia and Bacilli, Clostridiales and Lactobacillales, and Lachnospiraceae and Oscillospiraceae. In addition, it influenced the biosynthesis of aminoacyl-tRNA, valine, leucine, and isoleucine, along with peptidoglycan synthesis, thereby enhancing the regulatory function of the gut microbiota. Simultaneously, Xinglou Chengqi Decoction exerts therapeutic effects through the gut-brain crosstalk mediated by substances such as amino acids and fatty acids, which act within the biosynthetic and metabolic pathways.}, } @article {pmid42393176, year = {2026}, author = {Gordon, LM and Sevigny, JL and Buck, CB and Murray, MJ and Sidor, IF and Newton, AL and Palisoul, SM and Kelly, M and Nigatu, AS and Simpson, SD and Popov, VL and Waltzek, TB and Tsongalis, GJ and Frasca, S and Thomas, WK}, title = {A novel adomavirus from proliferative skin lesions of a broadnose sevengill shark (Notorynchus cepedianus).}, journal = {Npj viruses}, volume = {}, number = {}, pages = {}, doi = {10.1038/s44298-026-00210-8}, pmid = {42393176}, issn = {2948-1767}, support = {P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM103506/GM/NIGMS NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; P20GM113131/NH/NIH HHS/United States ; 5P30CA023108-37/CA/NCI NIH HHS/United States ; 5P30CA023108-37/CA/NCI NIH HHS/United States ; }, abstract = {In May of 2022, an aquarium-maintained broadnose sevengill shark (Notorynchus cepedianus) developed proliferative skin lesions that prompted pathologic and molecular investigation. Histopathologic examination revealed epidermal hyperplasia consisting of proliferation of spinous epithelial cells with mild dysplasia. Metagenomic sequencing identified a novel adomavirus with an 18,834 base pair circular double-stranded DNA genome. The virus, provisionally named broadnose sevengill shark adomavirus (7AdoV), contains two bidirectionally expressed protein-coding gene sets. Genomic annotation and structural predictions of proteins were used to contextualize 7AdoV phylogenetically and functionally. Transcriptomic analysis showed that expression of the structural late gene set was higher than the replicative early gene set at the time of diagnostic sampling. In situ hybridization using RNAscope technology localized transcripts of the adomavirus Wasp gene to epithelial cells of the hyperplastic epidermis. Infection by this novel adomavirus was associated with superficial and proliferative lesions that were self-limiting and resolved in this shark.}, } @article {pmid42393215, year = {2026}, author = {Nthuku, S and Mordecai, J and Babajide, AA and Makoko, D and Sawadogo, Y and Awe, OI}, title = {The Kenyan Human Gut Virome Catalogue reveals extensive viral diversity and age-dependent community structure.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-60183-9}, pmid = {42393215}, issn = {2045-2322}, abstract = {The human gut virome is a critical yet understudied component of the microbiome that shapes microbial community structure and host-microbe interactions. However, most existing human gut virome reference databases have been constructed predominantly from populations in high-income countries, resulting in the substantial underrepresentation of African populations. To help address this disparity, we developed the Kenyan Human Gut Virome Catalogue (KHGVC), the first comprehensive human gut virome resource for Kenya and the first country-specific human gut virome catalogue from Africa. Using a standardized viromics pipeline applied to 626 fecal metagenomes spanning infants and adults across three Kenyan counties, we reconstructed 116,968 viral operational taxonomic units (vOTUs). Cross-catalogue comparisons revealed extensive novelty where 65.6% of KHGVC's vOTUs larger than 10 kb lacked matches in five major human gut virome databases, and 95% remained unique relative to the Unified Human Gut Virome (UHGV). Temperate bacteriophages accounted for ~ 70% of vOTUs, supporting a major role for lysogeny in gut ecosystem stability. Functional annotation assigned putative roles to ~ 27% of predicted viral proteins, primarily structural and replication-associated functions. Application of KHGVC revealed pronounced age-dependent virome structuring in which infant viromes were less diverse and enriched in Bifidobacterium-infecting phages, including Bifidobacterium longum, whereas adult viromes exhibited greater diversity and expansion of Prevotella-associated phages. Together, the KHGVC substantially expands known human gut viral diversity and provides a foundational reference for Kenyan and African virome research. The KHGVC can be accessed freely through a publicly available interactive web interface (https://igmr.org/software/kenyavirocat).}, } @article {pmid42394019, year = {2026}, author = {Dicko, A and Barro, SG and Sombie, S and Séré, R and Bonkoungou, I}, title = {Applications of Metagenomics and Artificial Intelligence in Characterizing Antimicrobial Resistance in Livestock: A Systematic Review.}, journal = {Studies in health technology and informatics}, volume = {338}, number = {}, pages = {328-332}, doi = {10.3233/SHTI260857}, pmid = {42394019}, issn = {1879-8365}, mesh = {Animals ; *Metagenomics/methods ; *Livestock/microbiology/genetics ; *Artificial Intelligence ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Humans ; One Health ; Machine Learning ; }, abstract = {Antimicrobial resistance (AMR) is an urgent global health threat, intensified by the widespread use of antimicrobials in livestock production. This study synthesizes the current landscape of combining metagenomic sequencing with artificial intelligence (machine learning and deep learning) to characterize, surveil, and predict AMR within the One Health framework. A comprehensive multi-database literature search was conducted, and, following PRISMA guidelines, 10 peer-reviewed studies meeting the inclusion criteria were selected for full synthesis. Metagenomic shotgun sequencing significantly surpasses conventional culture-based methods by directly capturing antimicrobial resistance genes (ARGs) from complex biological communities. AI algorithms substantially outperform traditional bioinformatic tools, achieving high predictive accuracy (AUC-ROC > 0.90) and revealing consistent ARG transfer pathways that link livestock, human, and environmental compartments. Integrating metagenomics with AI delivers a paradigm shift for proactive AMR surveillance. However, standardization, interpretability, and technological adaptation to resource-limited settings-especially in sub-Saharan Africa-remain urgent priorities to inform effective public health policy.}, } @article {pmid42394335, year = {2026}, author = {Sun, X and Ding, M and Li, Y and Mu, D and Wu, J and Yu, X and Zhu, M and Sun, G and Xiang, X}, title = {[Effects and Mechanisms of a multi-strain probiotic on the gut microbiota of healthy mice].}, journal = {Wei sheng yan jiu = Journal of hygiene research}, volume = {55}, number = {3}, pages = {491-498}, doi = {10.19813/j.cnki.weishengyanjiu.2026.03.019}, pmid = {42394335}, issn = {1000-8020}, mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; Male ; Mice ; Mice, Inbred C57BL ; Lactobacillus acidophilus/physiology ; Tryptophan/metabolism ; Indoles/metabolism ; Bifidobacterium animalis/physiology ; Lacticaseibacillus rhamnosus/physiology ; Feces/microbiology ; *Microbiota ; }, abstract = {OBJECTIVE: Systematic evaluation of the regulatory effects of compound probiotics containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 and their ratios on gut microbiota composition and the tryptophan-indole metabolic pathway.

METHODS: 30 male C57BL/6 mice were randomly divided into three groups of ten mice each: Control group, Mix-A group(Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101 and Lactobacillus rhamnosus JL1, in a 1∶1∶1 ratio) and Mix-B group(same bacterial strains, in a 10∶1∶1 ratio). The composite probiotic group received daily oral administration of 0.2 mL probiotic suspension at a total concentration of 1.5 × 10~(10) CFU/mL. The control group received daily oral administration of an equal volume of PBS solution. The experimental intervention lasted for 3 weeks. At the end of the experiment, colon tissues were collected from mice to measure superoxide dismutase(SOD)and catalase(CAT)levels. Fecal samples were collected from mice at mid-and end-experiment time points for metagenomic sequencing and targeted metabolomics analysis.

RESULTS: There were no significant differences in body weight or organ indices among the three groups of mice. CAT levels were significantly higher in the Mix-B group compared to the control group(P<0.05). Metabolomic analysis revealed significantly elevated levels of indole-3-acetic acid(IAA), indole-3-lactic acid(ILA), and indole-3-carbaldehyde(IAld) in fecal samples from the Mix-B group(P <0.05). By day 22, β-diversity analysis revealed distinct microbial community structures across all 3 groups. The Mix-B group exhibited decreased Richness indices and increased dominance of specific bacterial taxa. LEfSe analysis indicated enrichment in Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Bifidobacterium animalis in Mix-A; while Mix-B group showed enrichment in Akkermansia muciniphila, Bacteroides acidifaciens, Clostridium cocleatum, and Anaerotruncus colihominis. Correlation analysis revealed significant positive correlations between Bacteroides thetaiotaomicron, Bacteroides acidifaciens, and Akkermansia muciniphila with indole metabolites including IAA, ILA, and IAld.

CONCLUSION: The compound probiotic combination containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 can safely modulate gut microbiota composition and enhance tryptophan-indole metabolism, which may provide a potential strategy for maintaining gut health.}, } @article {pmid42394341, year = {2026}, author = {Stenger, PL and Majorel, C and Valette, L and Ihage, W and Jardin-Camps, M and Jourand, P and Anton-Leberre, V}, title = {Spatial structuring dominates over seasonality in tropical coastal microbiomes: Insights from New Caledonia's Indo-Pacific lagoon.}, journal = {Journal of environmental quality}, volume = {55}, number = {4}, pages = {e70215}, doi = {10.1002/jeq2.70215}, pmid = {42394341}, issn = {1537-2537}, support = {//CRESICA (Consortium for Research, Higher Education, and Innovation in New Caledonia)/ ; //MITI-CNRS (Mission pour les initiatives transverses et interdisciplinaires)/ ; }, mesh = {New Caledonia ; Seasons ; *Seawater/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Bacteria/classification ; Tropical Climate ; *Environmental Monitoring ; Archaea ; Ecosystem ; }, abstract = {Tropical coastal ecosystems harbor diverse microbes essential for biogeochemical cycling and serve as sentinels of environmental change. However, microbial community profiles remain largely undocumented across the Southwest Pacific. We investigated bacterial communities in coastal and lagoonal waters surrounding Nouméa, New Caledonia, an area under increasing urban pressure. Our objective was to determine whether spatial heterogeneity or seasonal variation primarily structures these communities and how anthropogenic activities shape microbial diversity. Forty-two seawater samples were collected from seven sites spanning anthropized bays, mangrove estuaries, and offshore lagoon waters during hot and cold seasons. We found that spatial gradients explained significantly more variation in community structure (R[2] = 0.25) than seasonal changes (R[2] = 0.04), revealing distinct microbial signatures along the land-to-sea continuum. Coastal and mangrove sites harbored more copiotrophic taxa and elevated levels of predicted pathogen-associated functional pathways, though these predictions are based on 16S rRNA data, and require validation with metagenomic or functional assays. Seasonal shifts mainly involved Cyanobacteria (Synechococcus↑, Prochlorococcus↓ in warm season) and archaeal Marine Group II, reflecting temperature-mediated niche partitioning. This study establishes the first spatial and seasonal microbial inventory for New Caledonian coastal ecosystems, suggesting associations between anthropogenic influence and microbial community health. Spatial dominance highlights the potential value of local management, while temperature sensitivity of key taxa underscores the importance of integrating microbial monitoring into coastal conservation and One Health frameworks.}, } @article {pmid42394361, year = {2026}, author = {Queiroz, VF and Tatara, JM and Jivaji, AM and Given, CJ and Dutra, LAL and Abbas, W and Ricky, Z and Stokke, R and Stensvåg, K and Abrahao, JS and Almeida, GMF}, title = {Isolation of a Cohort of Giant Viruses From Above the Arctic Circle in Northern Norway.}, journal = {Environmental microbiology}, volume = {28}, number = {7}, pages = {e70366}, doi = {10.1111/1462-2920.70366}, pmid = {42394361}, issn = {1462-2920}, support = {311192/A65276//Tromsø Forskningsstiftelse/ ; 101150485//Horizon 2020 Framework Programme/ ; 101162830/ERC_/European Research Council/International ; 315427//Norges Forskningsråd/ ; TMS2020TMT13//Trond Mohn stiftelse/ ; }, mesh = {*Giant Viruses/isolation & purification/classification/genetics ; Arctic Regions ; Norway ; Phylogeny ; *Acanthamoeba/virology ; Mimiviridae/isolation & purification/classification/genetics ; *Seawater/virology ; Fresh Water/virology ; }, abstract = {Viruses are the most abundant biological entities on Earth. Metagenomic data indicates a higher viral abundance of viruses of unicellular eukaryotes in the polar regions, information still not matched by broad isolation efforts using samples collected in these regions. Here we describe a prospection effort using diverse samples collected above the Arctic circle, including freshwater and marine samples from urban areas, deep-sea hydrothermal vents and sea ice samples from the Nansen Basin. We isolated 10 giant viruses capable of infecting Acanthamoeba spp., five representing the Marseilleviridae family and five representing the Mimiviridae family. These viruses are the northernmost isolates found so far in the Nordic countries and consist of a unique cohort of Arctic viruses that differs geographically and temporarily from a cohort already described from the Siberian permafrost. Despite an apparent viral diversity in the samples, the uniqueness of the samples themselves and the use of additional non-amebozoan strains as hosts, our viruses are still representatives of known viral families. In conclusion, here we show the isolation of giant viruses in Northern Norway and highlight the potential host bias towards Acanthamoeba in giant virus prospection, indicating the need to break this bias to diversify the isolation of environmental viruses.}, } @article {pmid42394639, year = {2026}, author = {Zhu, H and Yang, P and Tu, Y and Fu, X and Yang, X and An, N}, title = {A Case Report of Meningitis with Possible Coinfection by Listeria monocytogenes and Mycobacterium tuberculosis (Detected by Metagenomic Next-Generation Sequencing) and Literature Review.}, journal = {Case reports in critical care}, volume = {2026}, number = {}, pages = {9615951}, pmid = {42394639}, issn = {2090-6420}, abstract = {RATIONALE: The study is aimed at exploring the complex clinical scenario of a patient with systemic lupus erythematosus who developed a rare coinfection with Listeria monocytogenes and Mycobacterium tuberculosis. The rationale is to highlight the diagnostic and therapeutic challenges in managing such a case, particularly in the context of immunosuppression and the need for effective antimicrobial therapy. This case underscores the importance of advanced diagnostic techniques like metagenomic next-generation sequencing in identifying coinfections and the critical balance required in treating both infections while managing the underlying autoimmune condition.

PATIENT CONCERNS: This case report presents a 58-year-old female patient who initially manifested thrombocytopenia and was diagnosed with SLE in an external hospital. After treatment, her condition did not improve. On the contrary, she developed a fever and a headache, and her disturbance of consciousness gradually worsened. The patient was admitted to our hospital with a suspected diagnosis of lupus encephalopathy and central nervous system infection.

DIAGNOSES: MRI plain scan showed linear enhancement shadows in the right temporal pole and bilateral cerebellar hemisphere regions on the fluid-attenuated inversion recovery three-dimensional volumetric fluid-attenuated inversion recovery contrast-enhanced scan. Subsequently, NGS of the cerebrospinal fluid detected L. monocytogenes and M. tuberculosis, suggesting a possible mixed infectious meningitis caused by these two pathogens.

INTERVENTIONS: The patient underwent a comprehensive treatment regimen including antiListeria and antituberculosis therapies. Unfortunately, this was followed by the development of liver failure and various other complications. In response, we administered interventions such as blood purification and liver support measures. Furthermore, we organized a multidisciplinary consultation to address the complex medical needs of the patient.

OUTCOMES: Despite aggressive medical interventions, the patient's condition deteriorated. She developed multiorgan failure, which significantly impacted her prognosis. The patient's family elected to withdraw life-sustaining treatment, and the patient passed away within 24 h after discharge.

LESSONS: This case underscores the importance of early and accurate diagnosis, particularly for immunocompromised patients with complex clinical presentations. Identifying mixed infections is crucial, and it also poses a significant challenge in selecting appropriate antimicrobial agents and conducting relevant tests.}, } @article {pmid42394779, year = {2026}, author = {Wishahi, M and Badawy, M}, title = {Letter to the Editor: Urinary infection in European guidelines 2025 vs microbiology culture results in the management of urinary infection.}, journal = {World journal of experimental medicine}, volume = {16}, number = {2}, pages = {115894}, pmid = {42394779}, issn = {2220-315X}, abstract = {We read with great interest the study by Yadav et al published in the World Journal of Experimental Medicine, which postulated a nomogram including patient's critical factors, other than urine sample. European Association of Urology (EAU) published the guidelines on urological infection 2025. The EAU guidelines 2025 of urinary infections (UIs) has classified in two distanced categories: Localized UTs and systemic UTs according to specific patient's symptoms and clinical signs, this new practical classification replaced previous concept of non-complicated urinary tract infection (UTI) against complicated UTI. The new EAU classification categorizes UIs as either localized or systemic, according to the presence of specific clinical signs and symptoms, this new practical classification replaced previous concept of non-complicated UTI against complicated UTI, irrespective of the results of bacteriological findings. In the new classification of UIs, the classification is based on clinical set-up on which the practitioner or urologist will manage the patient. Management of UIs is crucial to consider the urinary and gut microbiota. It was established recently that antibiotic use affects microbiota homeostasis in the gut and urinary tract that will initiate dysbiosis.}, } @article {pmid42394824, year = {2026}, author = {Wu, Y and Cai, H and Wu, Q and Wu, J and Hu, J and Huang, E and Li, Z and Liang, S and Hu, X and Dai, J and Liao, R}, title = {The CRISPR-Cas toolkit for mosquito-borne virus surveillance: detection, tracing, and discovery.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1873187}, pmid = {42394824}, issn = {2235-2988}, mesh = {Animals ; *CRISPR-Cas Systems ; Humans ; *Mosquito-Borne Diseases/virology ; *Epidemiological Monitoring ; *Culicidae/virology ; *Mosquito Vectors/virology ; *Viruses/genetics/isolation & purification/classification ; *Virus Diseases/virology/transmission/diagnosis ; }, abstract = {Mosquito-borne virus surveillance increasingly requires rapid, distributed detection of co-circulating pathogens, serotypes, and lineages across clinical and vector-sampling sites. CRISPR-Cas platforms offer a programmable toolkit for this purpose, but their readiness differs substantially across surveillance functions. Here, we review CRISPR-Cas methods for mosquito-borne virus surveillance across detection, tracing, and discovery-supporting targeted screening. Detection is the most advanced application: selected Cas12- and Cas13-based assays for dengue, Zika, chikungunya, West Nile, Japanese encephalitis, and related mosquito-associated viruses report sub-hour workflows, portable readouts, and targeted serotype- or lineage-marker discrimination. However, performance remains assay-, target-, and sample-matrix-dependent, and validation in pooled mosquito samples and field settings is still limited. Tracing currently relies mainly on validated portable amplicon-sequencing workflows, whereas CRISPR-aided sample-preparation methods such as DASH, FLASH, RAPID-DASH, and Cas9-targeted enrichment remain transferable opportunities for host depletion or target enrichment rather than established mosquito-borne virus genomic-surveillance workflows. For discovery-oriented surveillance, multiplex CRISPR-Cas systems such as CARMEN can support targeted screening of known or near-neighbor viruses represented by predesigned crRNAs, while metagenomic next-generation sequencing remains necessary for divergent or previously unknown viruses. Across these functions, CRISPR-Cas programmability may accelerate parts of assay redesign, but practical retargeting still requires compatible amplification primers, effector-specific target constraints, cross-reactivity assessment, and analytical revalidation. Routine surveillance use will require integrated demonstrations with clinical and pooled-vector samples, comparison against established molecular and sequencing methods, cost validation, and regulatory evidence.}, } @article {pmid42394849, year = {2026}, author = {Ding, J and Liu, F and Zhao, Y and He, Z and Shi, Y and Shu, L}, title = {Protists show high resilience and thrive under multiple chemical stressors.}, journal = {mLife}, volume = {5}, number = {3}, pages = {388-392}, pmid = {42394849}, issn = {2770-100X}, abstract = {Protists are an underexplored but functionally important component of aerobic-activated granular sludge under pollution stress. Using metagenomics, we profiled protistan responses to ciprofloxacin, triclosan, and Cu[2+] (alone or in combination). Protists remained a stable 6.35%-7.88% of the bacterial community, and the consumers were the most abundant groups. Ciprofloxacin showed little effect on protist abundance, while Cu[2+] increased protist abundance, especially consumers. Stress conditions also strengthened predominantly positive protist-bacteria associations, suggesting cross-domain interactions that may enhance community resilience. These results demonstrate that protists are key determinants in stabilizing microbial communities under multiple stressors.}, } @article {pmid42395046, year = {2026}, author = {Kumar, A and Ghosh, D}, title = {Letter to the Editor: Dengue virus as an underrecognized cause of encephalitis in tropical Asia - Bridging diagnostic and surveillance gaps.}, journal = {World journal of virology}, volume = {15}, number = {2}, pages = {118082}, pmid = {42395046}, issn = {2220-3249}, abstract = {Arboviral encephalitis remains a major public health concern in tropical Asia, where the etiology of a substantial proportion of central nervous system infections remains undetermined despite endemic circulation of dengue virus (DENV) and Japanese encephalitis virus. Laboratory confirmation is frequently absent in clinically suspected encephalitis. Perera et al recently published a study in World Journal of Virology, highlight this diagnostic gap by identifying DENV infection in 6.06% of encephalitis cases, including molecular evidence of DENV-3 neuroinvasion. These findings add to the growing evidence that DENV can cause encephalitis and meningoencephalitis across age groups. However, encephalitis in endemic settings is etiologically heterogeneous, and dengue represents only one of several infectious and immune-mediated contributors. Neurological dengue is likely under-recognized due to overlapping clinical presentations and limited diagnostic capacity. The identification of DENV-3 is noteworthy given its recurrent association with neurological disease. Limited concordance between reverse transcription polymerase chain reaction and immunoglobulin M assays reflects challenges related to viral kinetics, timing of specimen collection, and flaviviral serological cross-reactivity. Strengthening surveillance through integrated molecular and serological diagnostic strategies, including multiplex polymerase chain reaction and metagenomic next-generation sequencing, is essential to reduce undiagnosed encephalitis and improve clinical management and public health preparedness in tropical Asia.}, } @article {pmid42395425, year = {2026}, author = {Shih, JB and Zhao, C and Pollard, KS and Lind, AL}, title = {Quantitative detection of gut microbial eukaryotes with EukDetect2 reveals global distribution of commensal protists and association with distinct microbial community structure.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.24.734308}, pmid = {42395425}, issn = {2692-8205}, abstract = {Microbial eukaryotes are prevalent members of host-associated and free-living microbial communities, but are routinely excluded from studies of these communities. Existing methods for eukaryote detection from whole metagenome sequencing are limited by contamination of eukaryotic reference genomes and incomplete taxonomic coverage. Our previously published tool EukDetect addressed these challenges using a curated database of universal BUSCO marker genes, but lacked validated quantitative abundance metrics and was built from a limited number of genomes. Here we present EukDetect2, incorporating a database containing 6,948 microbial eukaryotic genomes representing 6,594 unique species, 2,339 of which are newly added since EukDetect version 1, alongside quantitative metrics for estimating absolute and relative abundance of microbial eukaryotes. Using simulated data, we demonstrate accurate abundance estimation, no false positives from bacterial or host-derived reads, and equivalent or greater sensitivity and specificity than alternative taxonomic profiling tools across a range of microbial abundances and community compositions. Applying EukDetect2 across globally distributed human gut microbiome cohorts, we find that Blastocystis spp. and Dientamoeba fragilis are the most prevalent gut eukaryotes across cohorts, while host-associated fungi are consistently less prevalent than commensal protists. Blastocystis abundance is positively associated with a gut microbial community enriched for fiber-fermenting microbes and depleted for pro-inflammatory and industrialization-associated taxa. EukDetect2 provides sensitive, accurate, and quantitative metrics for investigating microbial eukaryotes from metagenomic samples.}, } @article {pmid42395547, year = {2026}, author = {Kokroko, N and Jayanti, R and Sapoval, N and Nute, MG and Nakhleh, L and Treangen, TJ}, title = {Kente: A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.22.733643}, pmid = {42395547}, issn = {2692-8205}, abstract = {MOTIVATION: Horizontal gene transfer (HGT) shapes bacterial evolution and microbial ecosystems, yet detecting HGT within microbiomes remains a challenge due to fragmented metagenomic assemblies, reference bias, reliance on gene boundaries, and limited ability to model structural mosaicism and patterns across genomes.

METHODS: We present Kente, a novel pangenome graph-based framework designed for HGT detection that aligns metagenomic assembly contigs to a curated database of >600 genus-level bacterial pangenome graphs constructed using minigraph. Kente infers local taxonomic composition along contigs using alignment evidence and classifies candidate transfers using structured clade-transition topologies (e.g., A-B-A sandwich, open tips, and mosaic patterns). A complementary intra-genus module detects inter-species transfers within a single genus graph using segment-level clade annotations.

RESULTS: Across simulated intra- and inter-genus transfer scenarios, Kente achieves higher precision and comparable recall relative to existing gene-centric microbiome HGT detection approaches while reducing false positives from fragmented assemblies. Application to real human gut metagenomes (HMP2, n = 26) demonstrates Kente's ability to detect candidate cross-lineage transfer regions in complex microbial communities. Runtime profiling shows near-linear scaling with input size, enabling efficient analysis of large metagenomic assemblies.

https://github.com/treangenlab/Kente.}, } @article {pmid42395643, year = {2026}, author = {Yang, S and Yu, Q and Zeng, Y and Lu, Y and Xia, C and Cheng, F and Liu, Y and Liu, M and Chen, Y}, title = {Direct viral invasion and tumor-like pulmonary nodules: A fatal case of mpox in a patient with advanced HIV disease.}, journal = {Biosafety and health}, volume = {8}, number = {3}, pages = {228-233}, pmid = {42395643}, issn = {2590-0536}, abstract = {While mpox is typically a self-limiting zoonosis, individuals with advanced human immunodeficiency virus type 1 (HIV-1) infection are at increased risk for severe visceral complications and high mortality. We report a fatal case of fulminant mpox pneumonia in a 38-year-old male with advanced HIV-1 Infection and severe immunosuppression (CD4[+] T-cell count <100 cells/µL). The patient initially presented with characteristic cutaneous lesions but rapidly progressed to dyspnea and respiratory failure. Serial chest imaging revealed diffuse, solid perivascular nodules and patchy consolidations were highly suggestive of pulmonary malignancy. While initial microbiological cultures and clinical presentation (Day 4) suggested bacterial and fungal superinfections, metagenomic next-generation sequencing (mNGS) of lung tissue biopsy identified an overwhelming burden of mpox virus (MPXV; 260,840 sequence reads), cytomegalovirus (CMV) and Epstein-Barr virus (EBV), confirming direct viral invasion of the pulmonary parenchyma. Despite comprehensive treatment with antibiotics, antifungals, CMV-targeted therapy, and mechanical ventilation (specific anti-orthopoxvirus agents were unavailable), the patient succumbed to progressive respiratory failure on Day 31. This case highlights that mpox can manifest as severe necrotizing pneumonia with tumor-like radiological features in patients with acquired immunodeficiency syndrome (AIDS). It underscores the necessity of early pulmonary imaging and molecular testing in high-risk populations to differentiate mpox pneumonia from malignancy or opportunistic infections.}, } @article {pmid42395675, year = {2026}, author = {Almuhanna, AA and Vatte, C and Guo, Q and Elsalamouni, TS and Al-Muhanna, FA and Aboalrihy, AM and Alhabib, HA and Almomen, MF and Alali, RA and Habara, AH and Alrubaish, MA and Alfalah, KM and Cyrus, C and Abdul-Rahman, IS and Keating, BJ and Al-Ali, AK and Wang, C}, title = {Gut microbiota in a Saudi population with chronic kidney disease.}, journal = {World journal of nephrology}, volume = {15}, number = {2}, pages = {118343}, pmid = {42395675}, issn = {2220-6124}, abstract = {BACKGROUND: The gut microbiota (GM) plays an important role in chronic kidney disease (CKD) progression, and dialysis modalities can differentially impact the GM composition and function. There is also limited information on the GM in Arab populations.

AIM: To investigate the distinct microbial profiles and functional alterations associated with hemodialysis (HD) and peritoneal dialysis (PD) in a Saudi Arabian cohort.

METHODS: We performed whole-genome metagenomic sequencing on fecal samples from 189 participants (controls and CKD, HD, and PD patients).

RESULTS: We detected distinct microbial profiles across all patient groups compared with that of the controls. Microbial risk scores derived from differentially abundant taxa accurately distinguished CKD, PD, and HD patients from controls, with area under the curves exceeding 0.9. Compared with HD patients, PD patients exhibited reduced species richness, an increased abundance of opportunistic pathogens (particularly Proteobacteria), and increased virulence. Functional analysis revealed suppressed energy metabolism and activated proinflammatory pathways in PD patients. Cooccurrence network analysis demonstrated decreased microbial community resilience in PD patients, with increased Proteobacteria interactions. Conversely, the HD group showed partial recovery of microbial balance and beneficial metabolic functions, including increased short-chain fatty acid metabolism and reduced lipopolysaccharide biosynthesis.

CONCLUSION: The findings of this study highlight the potential of the microbial profile as a robust biomarker for CKD classification and underscore the differential impacts of different dialysis modalities.}, } @article {pmid42395905, year = {2026}, author = {Li, H and Li, N and Wang, C and Yang, J and Dong, Z and Cai, Z and Li, J and Chen, Y and Zheng, J and Zhu, J}, title = {Dysbiosis and unsustainable delayed gut microbiota development as non-invasive biomarkers for predicting autism spectrum disorder in Chinese children.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1753665}, pmid = {42395905}, issn = {1664-302X}, abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social impairment, restricted interest, repetitive behavior, and stereotypical behavioral patterns. Diagnosing ASD presents considerable challenges; a previous large-sample study in children linked ASD and intestinal flora imbalances.

METHODS: To explore the composition and functional changes of the gut microbiota in children with ASD, shotgun metagenomic sequencing was used to evaluate the gut microbiota of 78 Chinese children (34 with ASD and 44 with typical development [TD] children).

RESULTS: We observed differences in the gut microbiota composition and richness between children with ASD and TD in this cohort. The α-diversity of the gut microbiota in the ASD group fluctuated more with age than that in the TD group, based on cross-sectional data. Age-related dynamic changes in the gut bacteria of TD children were not clearly observed in children with ASD. Gut microbiota of children with ASD showed a higher number of antibiotic resistance genes compared to TD. Additionally, the functional gene pathways related to carbohydrate-active enzymes and amino acid metabolism and synthesis appeared reduced in the ASD group.

DISCUSSION: This exploratory study describes key compositional and functional characteristics of the gut microbiota in Chinese children with ASD. Our preliminary findings identify differential bacterial taxa that may be considered as potential candidates for further investigation as fecal markers, and suggest differences in age-related gut microbiota patterns between ASD and TD children. However, due to the modest sample size, cross-sectional design, and lack of external validation, these results should be regarded as a preliminary exploration and require confirmation in larger, independent cohorts.}, } @article {pmid42396176, year = {2026}, author = {Deb, D and Liguori, F and Shuster, BM and Huang, R and Shoreibah, S and Wang, S and Rojas Ocampo, NE and Murray, KP and Danino, T}, title = {Toward development of soil-derived Bacillus isolates as lung cancer cytotoxic agents.}, journal = {Biodesign research}, volume = {8}, number = {2}, pages = {100074}, pmid = {42396176}, issn = {2693-1257}, abstract = {The wide-ranging impact of the human microbiome on health and disease has sparked growing interest in employing bacteria as live therapeutics. Natural properties of bacteria have been enhanced using synthetic biology to treat diverse diseases, from infections to inflammation and cancer. However, a major obstacle in this area is identifying specific bacterial hosts and molecular payloads that are both safe and effective for specific diseases or cancers. In this study, we explored environmental microbial diversity as a promising source of new therapeutic agents that could be engineered for bacterial drug delivery systems. We collected and characterized soil bacteria from 25 urban public parks, then evaluated their secreted metabolites for anti-cancer activity using both monolayer and three-dimensional spheroid models of lung cancer. Metagenomic analysis, toxicity profiling, and co-culture assays revealed that several Bacillus species isolated from Manhattan park soils produced compounds with strong, dose-dependent cytotoxic effects on lung cancer cells. Furthermore, we demonstrated that Bacillus subtilis-a well-characterized, gram-positive model organism-was capable of colonizing lung tumor spheroids, suggesting its potential as a safe and effective chassis for bacterial cancer therapy. Complementing these experiments, we developed a mechanistic ordinary differential equation (ODE) model of the bacteria-spheroid co-culture that is consistent with our bacterial and spheroid growth data. Overall, our findings highlight a discovery platform for the screening of environmental microbes as chassis or payload sources for microbial cancer therapies.}, } @article {pmid42396177, year = {2026}, author = {Ross, DAN and Lauzon, J and Makarenkov, V and Kembel, SW}, title = {Metagenome-assembled genomes from the temperate forest phyllosphere in Eastern Canada.}, journal = {Access microbiology}, volume = {8}, number = {7}, pages = {}, pmid = {42396177}, issn = {2516-8290}, abstract = {The phyllosphere is host to diverse microbial communities surviving in dynamic environmental conditions and which form important relationships with their hosts. Here, we constructed metagenome-assembled genomes (MAGs) from 25 temperate forest phyllosphere samples collected in Eastern Canada. We found 423 dereplicated MAGs with completeness ≥50% and contamination ≤10%, using a combination of co-assembly strategies. The MAGs were predominantly classified into the bacterial phyla Pseudomonadota (n=197), Actinomycetota (n=88) and Acidobacteriota (n=50) and included two archaeal MAGs in the phylum Thermoproteota. These genomes can help to improve reference database entries of phyllosphere-affiliated microbes, increasing our understanding of phyllosphere microbial phylogenomic and community dynamics and the ecological roles of phyllosphere microbiomes.}, } @article {pmid42396572, year = {2026}, author = {Campos, PE and Collins, PC and Ruane, A and Carlsson, JE and Carlsson, J}, title = {Instance of a Heteroplasmic Mitogenome in Alvinocaridid Shrimp Mirocaris fortunata (Martin & Christiansen 1995) Found at the Moytirra Deep-Sea High-Temperature Hydrothermal Vent Field.}, journal = {Ecology and evolution}, volume = {16}, number = {7}, pages = {e73956}, pmid = {42396572}, issn = {2045-7758}, abstract = {In this study, we report the complete mitochondrial genome of the deep-sea hydrothermal vent shrimp Mirocaris fortunata (Alvinocarididae) from shotgun sequencing data on an individual tail tissue. The 15,923-bp-long sequence displays 98.72% pairwise identity with its closest relative, Mirocaris indica. A significant proportion of the mitochondrial genome (0.63%) corresponds to heteroplasmic sites that were found on 14 of the 37 genes, including cox1, though all such sites induce synonymous mutations. This level of heteroplasmy may serve as the first step for recombination of the mitogenome by paternal leakage and/or a less effective purifying selection in somatic tissues. We also take advantage of the shotgun deep sequencing strategy to assess the metagenomic composition of the sample and are able to detect other deep-sea hydrothermal vent species present at the vent system.}, } @article {pmid42397430, year = {2026}, author = {Liu, Y and Jiang, W and Wang, J and Cheng, S and Cheng, C and Zhang, C and Zhang, J and Liu, C and Zhao, J and Wang, H}, title = {A special multifiber dietary mixture ameliorates Crohn's-like colitis in an IL-10[-]/[-] mouse model by promoting treg differentiation through the ETS1/RUNX1/Foxp3 axis.}, journal = {European journal of nutrition}, volume = {65}, number = {5}, pages = {}, pmid = {42397430}, issn = {1436-6215}, mesh = {Animals ; Proto-Oncogene Protein c-ets-1/metabolism/genetics ; *T-Lymphocytes, Regulatory/metabolism ; Mice ; *Crohn Disease/diet therapy/metabolism ; *Colitis/diet therapy ; Forkhead Transcription Factors/metabolism/genetics ; *Interleukin-10/genetics/metabolism/deficiency ; Disease Models, Animal ; Cell Differentiation/drug effects ; Core Binding Factor Alpha 2 Subunit/metabolism/genetics ; Mice, Knockout ; Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Male ; }, abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory disorder characterized by immune dysregulation. Regulatory T cells (Tregs) play a pivotal role in maintaining mucosal tolerance, and their dysfunction directly contributes to CD pathogenesis.

METHODS: We used interleukin-10[-]/[-] mice to evaluate the therapeutic effects of a special multifiber mixture (MF) on colitis. T cell phenotypes, transcriptional profiles, gut microbiota composition, and N[6]-methyl adenosine (m6A) ribonucleic acid (RNA) methylation were analyzed using flow cytometry, RNA sequencing, metagenomics, and methylated RNA immunoprecipitation-quantitative polymerase chain reaction.

RESULTS: MF significantly reduced intestinal inflammation, restored epithelial barrier function, and promoted Treg differentiation while suppressing Th1/Th17 polarization. Integrated transcriptomic and proteomic analyses identified ETS1 as a negative regulator of Treg differentiation, modulated by gut microbiota-derived S-adenosylmethionine (SAM) through methyltransferase-like protein 3-mediated m6A methylation. MF feeding reduced SAM levels and m6A enrichment on ETS1 messenger RNA, leading to decreased ETS1 expression. Silencing of ETS1 enhanced Foxp3 expression and expanded the Treg population. RUNX1 was identified as a functional interactor of ETS1, with reciprocal expression patterns validated in both mouse models and colonic tissues from patients with CD.

CONCLUSION: MF alleviates colitis by reshaping the gut microbiota and suppressing SAM-dependent m6A methylation, resulting in ETS1 downregulation and the restoration of Treg homeostasis through the ETS1/RUNX1/Foxp3 axis. These findings reveal a mechanistic link between microbiota, epigenetics, and immunity, highlighting MF feeding as a promising nutritional intervention for CD treatment.}, } @article {pmid42397535, year = {2026}, author = {Sharma, R and Gupta, V and Pal, V and Sen, J and Meghvansi, MK and Goel, AK}, title = {Influence of inoculum-to-substrate ratio on process stability and microbial community structure in anaerobic digestion of human faecal matter.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {42397535}, issn = {1614-7499}, abstract = {Anaerobic digestion is a pivotal technology for modern sanitation. This study investigates the impact of inoculum-substrate ratio (ISR) on anaerobic digestion of human faecal matter (HFM). To determine the anaerobic digestion efficiency of HFM, the experiments were conducted using an automatic biomethane potential test system with ISRs ranging from 0.33 to 3. Higher ISRs (1, 2, and 3) resulted in improved volatile solids reduction, increased hydrolysis rates, and higher cumulative methane production compared to lower ISRs. Kinetic modelling revealed that an ISR of 3 exhibited the highest hydrolysis rate constant and shortest lag phase. Analysis of volatile fatty acids showed that higher ISRs mitigated acid accumulation and maintained pH stability. Microbial community analysis demonstrated shifts in bacterial and archaeal populations across different ISRs, with higher ratios fostering greater diversity and abundance of hydrolytic and methanogenic microorganisms. The findings offer essential insights for enhancing the anaerobic digestion of HFM, promoting sustainable waste management and renewable energy production.}, } @article {pmid42397700, year = {2026}, author = {Mills, EG and Evans, KM and Dorazio, AJ and Squires, KM and Sundermann, AJ and Stellfox, ME and Culyba, MJ and Shields, RK and Van Tyne, D}, title = {Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant Enterococcus faecium.}, journal = {Microbial genomics}, volume = {12}, number = {7}, pages = {}, doi = {10.1099/mgen.0.001778}, pmid = {42397700}, issn = {2057-5858}, mesh = {Humans ; *Enterococcus faecium/genetics/isolation & purification/classification ; *Vancomycin-Resistant Enterococci/genetics/isolation & purification/classification ; *Metagenomics/methods ; *Gram-Positive Bacterial Infections/microbiology/transmission ; Gastrointestinal Tract/microbiology ; Genetic Variation ; Metagenome ; }, abstract = {Colonization of the gastrointestinal (GI) tract by vancomycin-resistant Enterococcus faecium (VREfm) often precedes bloodstream infection and serves as a reservoir for onward patient transmission in healthcare settings. Routine clonal isolate-based sequencing often underestimates within-patient diversity and can miss transmission involving low-abundance and co-colonizing strains. Here, we applied culture-enriched metagenomic sequencing to matched GI tract and blood VREfm populations collected ≤14 days apart from 35 patients with positive VREfm blood cultures obtained between 2020 and 2025 at a single hospital. GI tract populations exhibited greater within-patient diversity than bloodstream populations, including multi-strain colonization in five patients. Among single-strain populations, variant analysis suggested distinct environment-specific pressures between the GI tract and bloodstream environments. To assess transmission using culture-enriched metagenomic sequencing, we compared all 70 VREfm populations against 470 contemporary clinical VREfm isolate genomes collected from the same hospital and identified 19 putative transmission clusters including 6 clusters involving multi-strain populations. Together, these results demonstrate how culture-enriched metagenomic sequencing improves resolution for assessing within-patient VREfm diversity and enhances the detection of transmission events that could be missed by clonal isolate-based surveillance.}, } @article {pmid42397950, year = {2026}, author = {Karthik, Y and Nanjareddy, K and Arthikala, MK}, title = {Deciphering soybean-microbiome interactions: from rhizosphere dynamics to sustainable yield enhancement.}, journal = {Plant signaling & behavior}, volume = {21}, number = {1}, pages = {2693436}, doi = {10.1080/15592324.2026.2693436}, pmid = {42397950}, issn = {1559-2324}, mesh = {*Glycine max/microbiology/growth & development/metabolism ; *Rhizosphere ; *Microbiota/physiology ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {The soybean plant (Glycine max L.) is an important crop for valuable food source because of its high levels of protein and oil, thus contributing greatly to a sustainable system for producing food through biological nitrogen fixation. Recent research supports the theory that the soybean-associated microbiome located in the rhizosphere is a crucial regulatory mechanism governing plant growth, nutrient acquisition, and stress tolerance. Additionally, advances in metagenomics, metatranscriptomics, metabolomics, and root exudate profiling via LC‒MS have shown that soybean roots alter the microbial communities found in their rhizosphere by utilizing dynamic chemical signaling and targeted microbial recruitment, thereby enhancing the ecological interpretation of the processes that drive microbiome assembly. Microbial consortia (AMF & PGPR) assess cycling through nutrients, phytohormones, suppressing diseases, as well as having a legacy effects on the productivity of agroecosystems. Factors such as plant genotype, physical and chemical soil properties, and environmental conditions greatly affect the assembly and functioning of the soybean microbiome, thus this is difficult to transfer this information to field applications. Unlike previous reviews focused primarily on biological nitrogen fixation, this review integrates recent advances in multi-omics technologies, species-level microbiome characterization, root exudate chemistry, microbiome-assisted breeding, and translational microbiome engineering approaches to provide a systems-level perspective of soybean-microbiome interactions. while also identifying significant knowledge gaps and future areas of research within this aspect of agriculture.}, } @article {pmid42397959, year = {2026}, author = {Umezawa, K and Tsuji, JM and Tani, Y and Nohara, S and Amann, RI and Fukui, M}, title = {Isolation of Allocrenothrix methanica reveals distinct ecophysiologies of filamentous methanotrophs and adaptations to O2 limitation.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag178}, pmid = {42397959}, issn = {1751-7370}, abstract = {Ferdinand Cohn observed abundant filamentous bacteria in drinking water wells in 1870 that he named Crenothrix polyspora. Subsequent research has revealed the methanotrophic metabolism of Crenothrix bacteria and their disproportionately high activity in stratified lakes compared to unicellular methanotrophs, yet laboratory cultivation has proven elusive, leaving the ecophysiology of Crenothrix bacteria largely unknown. Here we report the isolation of two methanotrophic strains of the "lacustrine Crenothrix" clade from an iron-rich wetland and reveal their unique cell biology and ecology. We demonstrate that the strains are microaerobic and grow as filaments of cells, which are connected by unidirectionally oriented structures. The strains have broad genomic repertoires for addressing O2 limitation that are uniquely associated with lacustrine Crenothrix compared to related clades based on genome data. Aligning with laboratory observations, we identify lacustrine Crenothrix bacteria along potential redox gradients in the wetland at iron-rich snow sites, and we also detect such bacteria in diverse global ecosystems based on public metagenome searches. Together, our data strongly point to an ecophysiology of lacustrine Crenothrix bacteria that is tightly linked to O2 limitation, and we propose that the strains uniquely store or share metabolic intermediates between cells in filaments to thrive under such conditions. Our cultivation-based findings for these strains, which we name Allocrenothrix methanica, provide new insights into the diversity, evolution, and ecology of filamentous methanotrophs, connecting over 150 years of microbiology research and opening vast new opportunities to investigate bacteria contributing to the global methane cycle under O2 limitation.}, } @article {pmid42398003, year = {2026}, author = {Robinson, CRP and Dolezal, AG and Liachko, I and Newton, ILG}, title = {Host Range Breadth Correlates with Genic Diversity in Honeybee Phages.}, journal = {Genome biology and evolution}, volume = {18}, number = {7}, pages = {}, doi = {10.1093/gbe/evag152}, pmid = {42398003}, issn = {1759-6653}, support = {//Costco/Project Apis m/ ; 2005306//NSF IOS Collaborative Research/ ; 2022049//NSF DBI Biology Integration Institutes/ ; //Bill and Melinda Gates Foundation to Phase Genomics/ ; }, mesh = {Animals ; Bees/virology/microbiology ; *Bacteriophages/genetics ; *Host Specificity/genetics ; Genetic Variation ; Evolution, Molecular ; Genome, Viral ; Phylogeny ; Selection, Genetic ; Metagenome ; }, abstract = {Bacteriophages can evolve rapidly. Mutation and recombination via horizontal gene transfer allow them to counter adaptive responses by microbial hosts. However, little is known about the genomic processes underlying phage evolution within an ecological context-especially within natural microbial communities. This is due in part to the difficulty in resolving aspects of phage ecology, such as host range. To better understand the interplay of phage ecology and evolution within natural microbial communities, we combined measures of phage host range in vivo with measures of genome evolution in order to infer the evolutionary pressures acting on phage genomes within individual honeybee worker microbiomes. We show that near-identical phage genomes, cooccurring across multiple honeybee colonies, exhibit large variation with respect to gene modules, despite retaining a highly similar core genome. Estimates of genic diversity suggest deviations from neutral evolutionary models and identify loci under putative diversifying selection. We then use HiC-resolved metagenomics and show that the honeybee gut contains a dense phage community that exhibits a wide degree of host range variation. This variation differed across individual metagenomes in both the number and phylogenetic distance of potential hosts. We show that common measures of genetic variation positively correlate with host range in bee-associated phages and that functional targets of diversifying selection are partitioned differently between broad or narrow host range phages. Our work underscores the high host range variation associated with phages within host-associated microbial communities and provides evidence that this variation impacts rates of phage evolution.}, } @article {pmid42398208, year = {2026}, author = {Yi, Y and Li, D and Li, Y and Wang, H and Yang, D and Yang, S and Xing, S and Wei, S and Yang, J and Guo, H and Luo, Z}, title = {Abrus cantoniensis α-glucan-like polysaccharide alleviates influenza via gut microbial acetate to activate free fatty acid receptor 2/ mitochondrial antiviral signaling protein/interferon-beta pathway.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {159}, number = {}, pages = {158533}, doi = {10.1016/j.phymed.2026.158533}, pmid = {42398208}, issn = {1618-095X}, abstract = {BACKGROUND: The gut microbiota is critical for host defense against influenza. Polysaccharides are known for their microbiota-modulating and immunomodulatory activities; however, the anti-influenza efficacy of homogeneous Abrus cantoniensis polysaccharides (ACP) remains unexplored.

PURPOSE: The present study seeks to clarify the protective role of ACP in influenza and explore its underlying molecular mechanisms.

METHODS: Initially, crude polysaccharides were extracted via ethanol precipitation and subsequently purified by gel chromatography. Systematic structural characterization of ACP was then performed using carbohydrate chemistry techniques, including scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), ultraviolet (UV) spectroscopy, and nuclear magnetic resonance (NMR). The therapeutic efficacy of ACP was assessed by monitoring various indicators such as body weight, survival rate, viral load, and pulmonary pathological changes in mouse models. Furthermore, to elucidate the biological mechanism underlying ACP's anti-influenza activity via regulation of pulmonary interferon-beta (IFN-β) immune networks by intestinal acetate-producing microbiota, multi-omics analyses integrating metagenomics, metabolomics, gene knockout, immunofluorescence, and Western blot were conducted. Finally, the potential anti-influenza effects of ACP via the gut-lung axis were evaluated based on in vivo and in vitro detection of protein expression of IFN-β, free fatty acid receptor 2 (FFAR2), and mitochondrial antiviral signaling protein (MAVS), as well as antiviral interferon-stimulated genes (ISGs).

RESULTS: In this study, we purified a novel polysaccharide, ACP-A1, with a backbone of→4)-α-D-Glcp-(1→,→4)-β-D-Galp-(1→, and →4,6)-α-D-Glcp-(1→ linkages and α-D-Glcp-(1→ branches at O-6. In H1N1-infected mice, oral ACP-A1 alleviated weight loss, increased survival, and reduced lung inflammation and viral load. Metagenomic and targeted metabolomic analyses showed that ACP-A1 enriched Limosilactobacillus reuteri and elevated acetate levels. Fecal microbiota transplantation, FFAR2 inhibition, and MAVS knockout experiments demonstrated that ACP-A1 enhances the FFAR2/MAVS/IFN-β antiviral pathway via microbial-derived acetate.

CONCLUSION: Collectively, our findings elucidate that ACP mitigates influenza virus-induced lung dysfunction by promoting the proliferation of acetate-producing gut microbiota, particularly Limosilactobacillus reuteri, and activating the FFAR2/MAVS/IFN-β antiviral axis in pulmonary immune cells. These findings establish ACP-A1 as a natural polysaccharide regulating IFN-β homeostasis, highlighting its potential for influenza prevention.}, } @article {pmid42398246, year = {2026}, author = {Zhang, Y and Tang, Z and Shangguan, H and Zhu, R and Xie, A and Huang, Q and Su, J and O'Connor, P and Jiang, Y and Sun, X}, title = {Invasive giant African snails as potential reservoirs of antimicrobial resistance and bacterial pathogens in urban park.}, journal = {Journal of environmental management}, volume = {413}, number = {}, pages = {130396}, doi = {10.1016/j.jenvman.2026.130396}, pmid = {42398246}, issn = {1095-8630}, abstract = {Urban parks serve millions of visitors annually, yet antimicrobial resistance (AMR) surveillance programs rarely consider invasive species as environmental reservoirs. Here, we investigated antibiotic resistance genes (ARGs) and potential zoonotic pathogens in invasive giant African snails (Lissachatina fulica) across 23 urban parks in Xiamen, China, with comparative analysis of dog feces and earthworm casts collected from the same parks. Metagenomic profiling revealed that snails harbored extensive ARG diversity (1222 subtypes) comparable to dogs (1,393) and substantially exceeding earthworms (492), with 936 ARG subtypes shared between invasive snails and dogs. Invasive snails also carried substantial relative abundances of potential zoonotic pathogens (mean 15.7% relative abundance), including clinically relevant taxa such as Escherichia, Pseudomonas, and Enterococcus. Phenotypic testing of representative isolates confirmed the presence of antibiotic-resistant bacteria in snail and dog fecal samples. The convergence of broad ARG diversity, substantial potential zoonotic pathogen burdens, and coprophagous behavior suggests that invasive snails may represent previously unmonitored environmental hosts associated with AMR in urban parks. Field observations of snails consuming dog feces, together with the greater resistome similarity between snails and dogs than between snails and earthworms, are consistent with exposure to animal feces as a potential source of ARGs. This study underscores the need to integrate invasive species into One Health AMR surveillance and urban environmental management strategies.}, } @article {pmid42398311, year = {2026}, author = {Guleria, A and Bagal, D and Mishra, S and Mehrotra, S and Srivastava, V}, title = {Phytomicrobiome-based approaches for sustainable crop performance and environmental resilience.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128605}, doi = {10.1016/j.micres.2026.128605}, pmid = {42398311}, issn = {1618-0623}, abstract = {The plant microbiome refers to the dynamic microbial communities including bacteria, fungi, protists, viruses, and nematodes that colonize diverse plant tissues and coevolve intimately with their host. The primary objective of microbiome engineering is to improve plant performance by enhancing tolerance to biotic and abiotic stresses, increasing plant fitness, and boosting crop productivity. By discovering the modern approaches and plant-microbe interactions, many experts can design artificial microbial consortia and other biotechnological tools suited to specific crops and environmental conditions. Therefore, in current work special attention is given to the goals, applications, and advanced tools-such as genome editing, synthetic biology, metagenomics, and AI-driven modelling used to optimize plant-microbe interactions for sustainable agriculture and ecosystem restoration. Further, recent advances in ecological, biochemical, and molecular approaches have also introduced a new paradigm for addressing microbiome-based challenges in agricultural management. In this context, microbiome engineering has emerged as a promising biotechnological strategy aimed at the targeted addition, removal, or modification of microbial community traits to achieve greater specificity and efficacy.}, } @article {pmid42398436, year = {2026}, author = {Funk, T and Zaheer, R and Wobeser, B and Conrad, C and McLeod, L and Gow, S and Otto, SJG and Waldner, CL and McAllister, T}, title = {Evaluating detection of Histophilus somni immunoglobulin-binding protein A DR2 Fic: A species-specific gene target for recombinase polymerase amplification relative to long-read sequencing of respiratory samples from feedlot calves.}, journal = {Research in veterinary science}, volume = {210}, number = {}, pages = {106315}, doi = {10.1016/j.rvsc.2026.106315}, pmid = {42398436}, issn = {1532-2661}, abstract = {Histophilosis is an important cause of morbidity and mortality as well as antimicrobial use in feedlot cattle across North America. Detection of Histophilus somni by culture is challenging, and there is no standardized tool for distinguishing isolates that carry virulence factors most likely to contribute to disease. The DR2 repeat of H. somni-associated virulence factor 'immunoglobulin-binding protein A' (ibpA DR2) harbors a Fic domain that mediates host cell cytotoxicity and is essential for histophilosis. For rapid detection of ibpA DR2 in extracted DNA, we developed a real-time recombinase polymerase amplification (RPA) assay with a runtime of 24 min at 39 °C. DNA from H. somni-RPA-positive respiratory swabs (n = 73) was screened for ibpA DR2 using the novel RPA assay and long-read metagenomic sequencing, as well as nanopore whole-genome sequencing (WGS) of H. somni isolated from the same samples. IbpA DR2 was identified in 71% and 70% of tested samples using RPA and WGS, respectively, and in ≤41% of samples using metagenomic sequencing. The likelihood of detection by RPA did not differ (OR 1.1, 95% CI (0.42, 2.9), P > 0.99) from WGS; however, agreement between these assays was only fair (κ = 0.31). Conversely, RPA (OR 3.4, 95% CI (1.6, 8.2)) and WGS (OR 8.0, 95% CI (2.4, 42)) were more likely (P < 0.001) to detect ibpA DR2 than metagenomic sequencing, likely reflecting limited coverage of H. somni by metagenomics. This study demonstrated that RPA and long-read WGS detected ibpA DR2 with similar frequencies in extracted DNA and H. somni isolates, respectively. Further testing of non-target isolates confirmed the analytical specificity of ibpA DR2 to H. somni. Further investigation of the diagnostic validity for RPA-based ibpA DR2 detection is required in a larger cohort of field samples, as a rapid screening tool for H. somni most likely to contribute to disease.}, } @article {pmid42398457, year = {2026}, author = {Fonseca, A and Kenney, S and Bierly, S and Boney, J and Ganda, E}, title = {Assessing the impact of dietary interventions on the resistomes of broiler chickens.}, journal = {Poultry science}, volume = {105}, number = {10}, pages = {107343}, doi = {10.1016/j.psj.2026.107343}, pmid = {42398457}, issn = {1525-3171}, abstract = {Antimicrobial resistance (AMR) is a major One Health concern, and while natural feed additives such as probiotics and phytotherapeutics are increasingly used as alternatives to antimicrobial growth promoters (AGPs) in poultry production, their potential effects on the selection of antibiotic resistance genes remain poorly understood. Therefore, our objective was to characterize the effects of a probiotic and an essential oils blend on the broiler resistome. Cobb 500 1-day-old chicks (N=320) were randomly allocated in 32 cages, with eight replicates of ten broilers per cage per treatment and were raised until day 21. Treatments consisted of four diets: a basal diet (negative control), a basal diet with Bacitracin Methylene Disalicylate (BMD) at 50 g/ton, a basal diet with an essential oil blend at 100 g/ton, and a basal diet with a probiotic (Bacillus subtilis) at 226.8 g/ton. Excreta samples were collected at three-time points (1, 10, and 21 days) to characterize broilers' resistome. The DNA extracted from these samples was sequenced using shotgun metagenomics on the NovaSeq platform and statistical analyses were done using Kruskal-Wallis and PERMANOVA to assess gene diversity. Across all samples, 823 unique ARGs were identified. These genes spanned a broad spectrum of classes, including multi-compound, metals, drugs, and biocides resistance. No significant differences in alpha diversity of these genes (P = 0.51) were observed between treatment groups; however, AMR gene diversity varied by age (P < 0.001). A statistically significant difference was observed in beta diversity across ages (P = 0.001), but not between treatments (P = 0.95). While age impacted AMR gene diversity, under our experimental conditions, antibiotics or other in-feed additives did not significantly alter broiler resistomes. This study advances poultry AMR surveillance by demonstrating that resistome diversity and composition in broiler chickens are predominantly shaped by age-dependent microbial succession, while neither in-feed antibiotics nor non-antibiotic feed additives induced persistent or treatment-specific alterations in ARG profiles under the conditions tested.}, } @article {pmid42398478, year = {2026}, author = {Gao, Q and Hou, J and Ding, W and Qi, C and Xu, D and Zhou, C and You, G}, title = {Carbon-to-nitrogen stoichiometry shapes divergent intracellular and extracellular antibiotic resistance gene fates through a dissolved organic matter-extracellular polymeric substance-mobile genetic element cascade in cyanobacteria-bacteria co-cultures.}, journal = {Water research}, volume = {304}, number = {}, pages = {126390}, doi = {10.1016/j.watres.2026.126390}, pmid = {42398478}, issn = {1879-2448}, abstract = {The carbon-to-nitrogen (C:N) ratio constrains microbial metabolism, yet whether nutrient stoichiometry controls the differential fates of intracellular (iARGs) versus extracellular antibiotic resistance genes (eARGs) remains unknown. This study aimed to test whether C:N ratios approaching the bacterial threshold elemental ratio (TER) would maximize iARG enrichment through a dissolved organic matter (DOM)-extracellular polymeric substance (EPS)-mobile genetic element (MGE) cascade, while eARG dynamics would be governed by physicochemical processes. Cyanobacteria-bacteria co-cultures at four C:N ratios (5:1, 10:1, 20:1, 40:1) were analyzed using shotgun metagenomics, FTICR-MS, 3D-EEM, untargeted metabolomics, and EPS fractionation. C:N = 10:1 produced the highest iARG abundance (65.1 ± 17.4 TPM, mean ± SD) and a 17-fold iARG/eARG ratio, while eARG showed no significant treatment effect (Kruskal-Wallis p = 0.082, treating triplicate subsamples as observations). FTICR-MS revealed the lowest intensity-weighted O/C (0.334), most negative NOSC (-0.67), and highest molecular diversity (8029 formulas) at C:N = 10:1, indicating a uniquely reduced, aliphatic-enriched DOM pool. (Note: FTICR-MS samples were pooled from triplicate subsamples per treatment, yielding one composite per C:N level; these results are therefore descriptive and unreplicated.) EPS polysaccharide/protein ratios peaked at 2.8, correlating with iARG across treatments (ρ=0.91, p < 0.001) but inversely with eARG (ρ=-0.59, p = 0.044). Guanosine (ppGpp precursor) peaked at C:N = 10:1 (ρ=0.75 with iARG) while UDP-glucose was depleted, confirming active EPS biosynthesis. Piecewise structural equation modeling identified a pathway from C:N through DOM, EPS, and MGE to iARG (R[2]=0.78, Fisher's C p = 0.31), whereas eARG depended on eDNA physicochemical trapping (R[2]=0.41). These findings provide evidence that nutrient stoichiometry acts as a selective control on ARG partitioning, suggesting that C:N monitoring could be incorporated into eutrophic water ARG risk assessment.}, } @article {pmid42398553, year = {2026}, author = {Xu, J and Zhang, X and Sun, W and Zhang, X and Wu, P and Wang, A}, title = {Hydroxylamine steers nitrogen metabolism toward dissimilatory nitrate reduction to ammonium by suppressing competitive denitrification.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135307}, doi = {10.1016/j.biortech.2026.135307}, pmid = {42398553}, issn = {1873-2976}, abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) is important for nitrogen conservation and resource recovery in wastewater treatment, but its efficiency is often limited by competition for electrons and substrates from denitrifiers. Although hydroxylamine (NH2OH) has been shown to modulate various nitrogen transformation processes, its long-term effects on DNRA systems and the underlying microbial ecological responses remain unclear. In this study, the nitrogen transformation performance, electron transfer characteristics, and microbial community succession in DNRA systems were comprehensively investigated under prolonged exposure to 0-5 mg/L NH2OH. The results demonstrated that, with increasing NH2OH concentrations, the system consistently achieved near-complete nitrate removal without nitrite accumulation, and the effluent NH4[+]-N reached up to 51.5 mg/L, indicating a substantial enhancement of DNRA ammonium production. Functional activity analyses and apparent electron-equivalent balance suggested an increased contribution of DNRA to nitrate-reduction-associated electron consumption. Metagenomic analyses further showed that NH2OH could decrease the relative abundances of denitrification-related genes, including nirS, norB, and nosZ, while increasing those of narG and the nrf gene cluster. Building upon the existing DNRA functionality, NH2OH selectively enriched a tolerant DNRA population, exemplified by Ignavibacteriota, and facilitated cross-feeding interactions and electron transfer network remodeling involving fermentative bacteria. Collectively, these findings suggest that NH2OH can weaken denitrification competition and increase the apparent contribution of DNRA to nitrate-reduction-associated electron consumption, thereby enhancing ammonium production. Moreover, these findings may provide a theoretical basis for the future development of DNRA-Anammox coupled processes for high-level nitrogen removal.}, } @article {pmid42398606, year = {2026}, author = {Liu, J and Liu, Y and Zheng, Y and Wang, H and Wang, J and Zhang, Y and Wang, K}, title = {Intestinal metabolic characteristics of Smilax china L. pectic polysaccharide and prediction of its gut microbiota-mediated mechanism.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {153348}, doi = {10.1016/j.ijbiomac.2026.153348}, pmid = {42398606}, issn = {1879-0003}, abstract = {This study aimed to investigate the intestinal metabolic characteristics and mechanisms of the pectic polysaccharide isolated from the medicinal plant Smilax china L. (SCLP). Firstly, in vitro simulated digestion confirmed that SCLP remained stable in simulated digestive fluids. Subsequently, in vivo real-time tracking of intestinal metabolism based on fluorescent labeling revealed that SCLP maintained its prototype in the small intestine and began to be degraded into fragments (Mw < 4000 Da) upon reaching the cecum and colon, where it was retained for prolonged periods. Pseudo-sterile mouse experiments indicated the mediating role of gut microbiota in SCLP metabolism. Furthermore, metagenomic sequencing suggested that SCLP increased the proportion of polysaccharide utilization loci (PULs) from Phocaeicola vulgatus and Bacteroides uniformis, elevated the gene numbers of carbohydrate-active enzymes (CAZymes) including GHs, GTs and CBMs, and activated pathways of carbohydrate metabolism. Finally, in vitro bacterial culture study verified the degradation and utilization of SCLP by Phocaeicola vulgatus and Bacteroides uniformis. In summary, this work elucidates the intestinal metabolic profile of SCLP, providing valuable insights for its further development and utilization.}, } @article {pmid42398615, year = {2026}, author = {Majeed, A and Javaid, MH and Mahreen, N and Hussain, M and Kang, Y and Hussain, K and Su, J}, title = {Nucleic acid and multi-omics approaches for understanding plant-microbiome interactions in grassland ecosystems.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {153356}, doi = {10.1016/j.ijbiomac.2026.153356}, pmid = {42398615}, issn = {1879-0003}, abstract = {Grasslands are among the largest terrestrial biomes and play essential roles in livestock production, carbon sequestration and global food security. The productivity and resilience of these ecosystems are driven by complex molecular interactions between plants and their associated microbiomes. Although recent advances in nucleic acid research and multi-omics approaches have provided new insights into these interactions, the molecular mechanisms underpinning plant-microbiome interactions in these ecosystems remain insufficiently explored. This review synthesizes the latest progress in nucleic-acid and multi-omics approaches to better understand plant-microbiome interactions. It integrates nucleic acid-based technologies with multi-omics frameworks to explain plant-microbiome interactions across molecular, ecological, and management scales. By linking microbial community structure, functional genes, gene expression, metabolite profiles, ecosystem multifunctionality and sustainable grassland management, this review provides a broader framework for translating molecular insights into practical strategies for grassland resilience, productivity, and food security. Advances in amplicon sequencing, shotgun and long-read metagenomics, environmental DNA (eDNA) monitoring, plant and microbiome genome-wide association studies (GWAS) and transcriptomics have provided valuable insights into plant-microbiome interaction. This review highlights how these techniques enable functional and mechanistic understanding by linking microbial diversity with gene expression, nutrient cycling and plant performance. Additionally, long-read sequencing technologies provide genome-resolved analysis, improving the detection of structural and epigenetic variations, which are essential for understanding these interactions. These approaches reveal the role of beneficial microbes in enhancing grassland fertility, ultimately improving grassland productivity. Integrating these findings with metabolomics and phenomics offers a novel approach for predictive modeling in sustainable grassland management. The review concludes by emphasizing the need for standardized protocols, longitudinal field studies and experimental validation through synthetic communities and genome editing to harness plant-microbiome interactions for enhanced productivity and food security.}, } @article {pmid42399247, year = {2026}, author = {Liao, H and Cui, HX and Chen, LX and Duan, CS and Li, J and Zhao, S and Zhu, YG and Su, JQ}, title = {Viral modulation of sulfur-oxidizing bacteria drives organic carbon sink formation during primary succession in deglaciating ecosystems.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-75234-y}, pmid = {42399247}, issn = {2041-1723}, abstract = {Glacier forelands undergo a transition from oligotrophic to eutrophic conditions during primary succession. Reduced sulfur compounds may serve as an energy source for early microbial colonizers, yet the sulfur oxidation potential and key taxa remain largely unknown. Here, we perform a multi‑omics survey across a 130‑year chronosequence on the Tibetan Plateau. Glacial retreat profoundly reshapes both viral communities (61,394 viral operational taxonomic units, vOTUs) and microbial communities (404 metagenome‑assembled genomes, MAGs). Notably, Oxidative Dissimilatory sulfite reductase (Dsr) operon‑encoding Sulfur‑Oxidizing Bacteria (ODSOB) were specifically enriched within the first 1-5 years after retreat. Their associated viruses predominantly follow a "piggyback‑the‑winner" strategy, influencing host cold shock protein evolution and potentially modulating sulfur oxidation via iron‑sulfur (Fe‑S) cluster assembly. Metatranscriptomics reveals elevated expression of the oxidative Dsr operon and Form‑I ribulose‑1,5‑bisphosphate carboxylase/oxygenase (RubisCO) in early stages, coinciding with higher sulfate, sulfite, sulfide, and dissolved inorganic carbon (DIC)‑to‑dissolved carbon ratios compared to later stages. These findings indicate that ODSOB support DIC fixation and sulfide detoxification during early ecosystem development. Collectively, this study uncovers the eco‑evolutionary dynamics between viruses and microbes in developing ecosystems and provides genomic and functional evidence for ODSOB as key drivers of soil formation and primary succession in glacial forelands.}, } @article {pmid42399252, year = {2026}, author = {Dai, D and Wang, P and Zhang, H and Qi, G and Wang, J}, title = {Temporal landscapes of the gut microbiota-host axis reveal mechanisms of age-related eggshell quality decline in laying hens.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01079-4}, pmid = {42399252}, issn = {2055-5008}, support = {32402797//National Natural Science Foundation of China/ ; 32322078//National Natural Science Foundation of China/ ; CARS-40//China Agriculture Research System/ ; ASTIP//Agricultural Science and Technology Innovation Program/ ; }, abstract = {Age-related shifts in the gut microbiota of laying hens significantly affect eggshell quality. However, the temporal interactions of the gut microbiota during the eggshell mineralization cycle remain unclear. Existing research often overlooks the rhythmic synchronization required for mineralization, as well as the specific cellular landscape of the aging intestine that impairs effective host-microbe crosstalk. We integrated 16S rRNA sequencing, metagenomics, untargeted metabolomics, and single-cell RNA sequencing to compare young and aged hens during the initial (7 h post-oviposition) and rapid growth (17 h post-oviposition) phases of eggshell mineralization. Aged hens exhibited significantly lower eggshell strength, thickness, and Ca/P concentrations (P < 0.05), which were associated with mitochondrial cristae disruption and necrocytosis in ileal tissues. 16S and metagenomic analyses revealed that young hens maintain stochastic microbial assembly, whereas aged hens shift toward deterministic processes driven by environmental stress. Rhythmic shifts in Lactobacillus and Ligilactobacillus were observed in young hens, supporting energy metabolism and mineral absorption pathways. In contrast, the aged hen microbiome remained focused on basal survival and oxidative stress responses. scRNA-seq identified nine cell populations, highlighting T cell exhaustion and HIF-1-driven metabolic reprogramming in epithelial cells of aged hens. Mediation analysis identified Ligilactobacillus salivarius as a keystone species that enhances eggshell breaking strength and thickness by increasing rhamnose and tyrosol levels and modulating host CALB1 and BLB2 expression. These findings indicate that aging disrupts proactive host-microbe synergy required for eggshell formation and identify L. salivarius-derived metabolites as promising candidates for restoring mineralization function in aged hens.}, } @article {pmid42399304, year = {2026}, author = {Sun, Y and Cheng, X and Zhou, J and Li, R and Wei, Y and Li, H and Qin, Y and Bao, J and Ren, X and Qu, S and Liu, W}, title = {Bio-stimulants improve tomato growth by regulating the rhizosphere microbiome involved in phosphorus and nitrogen cycling.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-59808-w}, pmid = {42399304}, issn = {2045-2322}, support = {2024CXPT056//the Key R&D Plan of Shandong Province (Competitive Innovation Platform) Project: Green, Ecological and Efficient Modern Agricultural Biological Product Development/ ; }, abstract = {Bio-stimulants are promising environment friendly alternatives to support sustainable agricultural development, capable of boosting crop growth and yield while cutting down excessive dependence on chemical synthetic fertilizers. Nevertheless, the explicit regulatory mechanisms by which bio-stimulants exert the role of growth-promoting functions still remain largely unclear and require further systematic clarification. In this study, we explored the influences of bio-stimulants (rich in humic acid) on tomato growth performance and rhizosphere microbial community assembly via greenhouse trials, and comparatively analyzed the functional differences between foliar spraying and root irrigation application modes. The results demonstrated that bio-stimulants treatment markedly improved tomato aboveground biomass, plant nitrogen and phosphorus accumulation by 17.1%, 27.4% and 22.7%, respectively. Meanwhile, bio-stimulants application effectively raised soil available nitrogen and soil organic matter levels, and further facilitated phosphorus assimilation in tomato plants. Metagenomic sequencing confirmed that bio-stimulants substantially reshaped the overall structure and composition of tomato rhizosphere microbiome. Specifically, they dramatically enriched the relative abundance of core microbial taxa responsible for soil nitrogen fixation and phosphorus solubilization. Collectively, these results clearly elaborate the underlying action mechanism: bio-stimulants optimize rhizosphere micro-ecological environment, enrich functional nutrient-solubilizing microorganisms, improve soil nutrient availability, and ultimately promote nutrient absorption and vegetative growth of tomato plants. This study confirms that bio-stimulants can serve as efficient and reliable regulators to advance green and sustainable crop production.}, } @article {pmid42342250, year = {2026}, author = {Baghbanzadeh, M and Mann, BT and Crandall, KA and Rahnavard, A}, title = {seqLens: Optimizing Language Models for Genomic Predictions.}, journal = {Molecular biology and evolution}, volume = {43}, number = {7}, pages = {}, pmid = {42342250}, issn = {1537-1719}, support = {2109688//National Science Foundation/ ; }, mesh = {*Genomics/methods ; *Models, Genetic ; Large Language Models ; Evolution, Molecular ; Genome ; }, abstract = {Understanding evolutionary variation in genomic sequences through the lens of language modeling has the potential to revolutionize biological research. Yet to maximize the utility of language modeling in genomics, we must overcome computational challenges in tokenization and model architecture adapted to diverse genomic features across evolutionary timescales. In this study, we investigated key elements in genomic language modeling (gLM), including tokenization, pretraining datasets, fine-tuning approaches, pooling methods, and domain adaptation, and applied the language models to diverse genomic data. We gathered two evolutionarily distinct pretraining datasets: one consisting of 19,551 reference genomes, including over 18,000 prokaryotic genomes (115 B nucleotides) and the remainder eukaryotic genomes, and another more balanced dataset with 1,354 genomes, including 1,166 prokaryotic and 188 eukaryotic reference genomes (180 B nucleotides). We trained five byte-pair encoding tokenizers and pretrained 52 gLMs, systematically comparing different architectures, hyperparameters, and classification heads. We introduce seqLens, a family of models based on disentangled attention with relative positional encoding, which outperforms relatively similar-sized models in 13 of 19 benchmarking phenotypic predictions. We further explore continual pretraining, domain adaptation, and parameter-efficient fine-tuning methods to assess trade-offs between computational efficiency and accuracy. Our findings demonstrate that relevant pretraining data significantly boost performance, alternative pooling techniques can enhance classification, tokenizers with larger vocabulary sizes negatively impact generalization, and gLMs are capable of understanding evolutionary relationships. These insights provide a foundation for optimizing genomic language models for identifying diverse evolutionary genomic features and improving genome annotations.}, } @article {pmid42386120, year = {2026}, author = {Nancy, N and Sharma, M and Singh, K and Singh, B and Sharma, PK}, title = {Mutation T71R enhanced the structural stability and functional activity of wild type superoxide dismutase cloned from soil metagenome.}, journal = {Gene}, volume = {}, number = {}, pages = {150294}, doi = {10.1016/j.gene.2026.150294}, pmid = {42386120}, issn = {1879-0038}, abstract = {In this study, we report engineering of three mutations m1, m2, and m3 respectively in the wild type SOD, cloned form soil metagenome. Expressed proteins from wild type and mutants were purified to homogeneity using Ni-NTA affinity chromatography. Biochemical characterization of mutants demonstrated enhanced functional activity at varying pH and temperature compared to wild type and other mutant proteins. Additionally, it also showed increased specific activity of 185 ± 0.75 U/mg compared to 150 ± 0.042 U/mg and 168 ± 0.25 U/mg respectively for mutant m1, m2 and m3. Altogether, it was observed that the relative enzyme activity of mutant m1, m2 and m3 enhanced ∼ 30 %, 10 % and 17 % respectively compared to wild type. Biophysical investigation carried out employing circular dichroism and intrinsic tryptophan fluorescence also demonstrated conformational stability in the secondary and tertiary structure of mutant m1 compared to the wild type at varying pH and temperature. Interestingly, in silico molecular simulation dynamics studies carried out at 300 ns demonstrated structural stability, reduced flexibility and attainment of stable conformation in this mutant form. Molecular simulation analysis revealed that mutation T71R in m1 tends to introduce β-sheet like secondary structure at protein surface, which might enhance residue-residue interactions within this protein, leading to allover enhancement in the stability and activity of this mutant.}, } @article {pmid42386249, year = {2026}, author = {Arenas-Montes, J and Garcia-Fernandez, H and Alcala-Diaz, JF and Boughanem, H and Allais, A and Gutierrez-Mariscal, FM and Arenas-de Larriva, AP and Ojeda-Rodriguez, A and Malagon, MM and Priego-Capote, F and Delgado-Lista, J and Perez-Martinez, P and Camargo, A and Lopez-Miranda, J}, title = {High postprandial endotoxemia is associated with recurrence of cardiovascular events in patients with coronary heart disease: from the CORDIOPREV randomized clinical trial.}, journal = {The American journal of clinical nutrition}, volume = {124}, number = {1}, pages = {101323}, doi = {10.1016/j.ajcnut.2026.101323}, pmid = {42386249}, issn = {1938-3207}, mesh = {Humans ; *Endotoxemia/complications/blood ; Male ; Female ; *Postprandial Period ; *Coronary Disease/complications/blood ; Middle Aged ; Lipopolysaccharides/blood ; Diet, Fat-Restricted ; Recurrence ; Diet, Mediterranean ; Aged ; Gastrointestinal Microbiome ; *Cardiovascular Diseases/etiology ; }, abstract = {BACKGROUND: The translocation into the systemic circulation of proinflammatory bacterial components such as lipopolysaccharide (LPS) has been linked to cardiovascular disease (CVD).

OBJECTIVES: We aimed to evaluate the association between baseline postprandial endotoxemia and the risk of suffering major adverse cardiovascular events (MACE) in patients with coronary heart disease (CHD), as well as the influence of consuming a low-fat (LF) diet or the Mediterranean (MED) diet on the associated risk.

METHODS: Our research was conducted within the framework of the CORDIOPREV Study, a clinical trial which involved 1002 patients with CHD randomly assigned to consume an LF diet or the MED diet for 7 y. A mixed meal was administered at the beginning of the study and after 3 y of follow-up. LPS plasma concentrations were measured by Limulus Amebocyte Lysate (LAL) colorimetric assay and gut microbiota was analyzed using 16S metagenomics.

RESULTS: Baseline postprandial increase in LPS plasma concentrations were associated with recurrence of MACE after a follow-up of 7 y, using Cox regression analysis [hazard ratio (HR):1.42 (1.01, 2.00)]. Patients with moderate LPS postprandial increase and consuming LF diet had higher risk of suffering MACE compared with the MED diet [HR: 1.45 (1.01, 2.09)]. Both diets reduced LPS plasma concentrations and formed a gut microbiota profile associated with a postprandial LPS decrease.

CONCLUSIONS: Our results suggest that the magnitude of postprandial endotoxemia is associated with suffering new MACE in patients with CHD, with the MED diet exercising a higher preventive role than an LF diet. Our results especially are relevant to clinical practice, supporting the measurement of postprandial endotoxemia as a tool for personalized medicine in secondary prevention. This study was registered at clinicaltrials.gov as NCT00924937.}, } @article {pmid42387129, year = {2026}, author = {Kumar, A and Kumar, A and Tyagi, A and Singh, R and Charaya, MU}, title = {A review of bloodstream infections-pathogens, pathogenesis, diagnostic strategies, treatment methods-challenges and future aspects.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42387129}, issn = {1435-4373}, abstract = {PURPOSE: Bloodstream infections (BSIs) remain a major cause of morbidity and mortality worldwide and continue to represent a substantial challenge to modern healthcare systems. These infections arise when pathogenic microorganisms gain access to the bloodstream, triggering systemic inflammatory responses that may progress to sepsis, septic shock, multi-organ dysfunction, and death. This review provides a comprehensive overview of the historical development, epidemiology, pathogenesis, diagnosis, treatment, and future perspectives of BSIs. The major bacterial, fungal, viral, and parasitic pathogens associated with BSIs are discussed, with particular emphasis on their virulence attributes, mechanisms of immune evasion, antimicrobial resistance, and clinical significance.

METHODS: A comprehensive literature review was conducted using peer-reviewed publications, clinical guidelines, surveillance reports, and systematic reviews published between 2010 and mid-2026. Evidence related to bacterial, fungal, viral, and parasitic bloodstream pathogens, host-pathogen interactions, diagnostic modalities, antimicrobial resistance mechanisms, and emerging therapeutic and diagnostic innovations was critically evaluated and integrated.

RESULTS: BSIs continue to impose a substantial healthcare burden, driven by increasing antimicrobial resistance, delayed diagnosis, and diverse pathogen-specific virulence mechanisms. Bacterial pathogens remain the predominant cause of BSIs, whereas Candida species represent the leading fungal agents. Advances in molecular diagnostics, metagenomic sequencing, biomarker-guided testing, and artificial intelligence-assisted analyses have substantially improved rapid pathogen detection and therapeutic decision-making. Precision medicine, genomic surveillance, and novel antimicrobial agents show considerable promise for enhancing clinical management and addressing multidrug-resistant infections.

CONCLUSION: Bloodstream infections remain a major global health challenge due to their complex pathogenesis, increasing antimicrobial resistance, and high associated mortality. Improving patient outcomes requires early and accurate pathogen identification, prompt initiation of targeted antimicrobial therapy, effective antimicrobial stewardship, and continuous epidemiological surveillance. The integration of next-generation diagnostics, artificial intelligence-assisted pathogen detection, genomic surveillance, and precision medicine has the potential to transform BSI diagnosis and management by enabling rapid, individualized therapeutic interventions.}, } @article {pmid42387141, year = {2026}, author = {Zou, P and Wang, X and Zhao, H and Yang, K and Ye, J and Sun, Y and Meng, X and Yi, Z and Xiong, X and Li, W}, title = {Mycobacterium Abscessus Infection after Breast Augmentation: Case Reports and Literature Review.}, journal = {Aesthetic plastic surgery}, volume = {}, number = {}, pages = {}, pmid = {42387141}, issn = {1432-5241}, abstract = {BACKGROUND: Mycobacterium abscessus (M. abscessus) infection following breast augmentation is a rare complication, yet evidence and standardized treatments remain limited. Challenges include diagnostic difficulties and prolonged treatment periods.

METHODS: We report two cases of M. abscessus infection following breast augmentation and conducted a structured narrative review of PubMed literature to explore prevention, diagnosis, and treatment strategies associated with this condition.

RESULTS: The two patients underwent different breast augmentation procedures: one received autologous fat transfer, and the other had a prosthetic implant inserted. Following confirmation of M. abscessus infection via metagenomic next-generation sequencing (mNGS), both patients underwent through surgical debridement and drainage with daily amikacin irrigation. Combination antibiotic therapy was administered, including intravenous amikacin and linezolid, plus oral azithromycin. Both patients demonstrated good tolerance to the prescribed antibiotics, achieving effective infection control without recurrence over a 12-month follow-up period. The rigorous debridement and targeted antibiotic therapy significantly enhanced treatment efficacy.

CONCLUSION: This study reports two rare cases of M. abscessus infection occurring after breast aesthetic surgery. Such infections are difficult to diagnose and are often associated with prolonged treatment courses. We successfully identified the causative pathogen through mNGS and implemented a comprehensive treatment strategy that included multiple surgical debridements, local irrigation, and combination antimicrobial therapy with azithromycin, amikacin, and linezolid, which was associated with favorable clinical outcomes. Rather than establishing a definitive management model, this study provides practical, case-based insights into the diagnosis and management of postoperative M. abscessus infections.

LEVEL OF EVIDENCE V: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .}, } @article {pmid42387381, year = {2026}, author = {Andersson, O and Fagerström, A and Dannenberg, K and Kekki, J and Rode, J and Rangel, I and Lindqvist, CM and Stenmark, B}, title = {Comparison of library preparation protocols and bioinformatic pipelines in high-throughput 16S rRNA gene sequencing.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42387381}, issn = {1471-2180}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Computational Biology/methods ; *Gene Library ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; DNA, Bacterial/genetics ; Microbiota/genetics ; }, abstract = {BACKGROUND: 16S rRNA gene sequencing is widely used for bacterial community profiling in both clinical and research contexts. The expanding availability of library preparation protocols and bioinformatic pipelines increases analytical flexibility but may also introduce method-dependent biases that affect inferred microbial composition and relative abundance estimates. The relative impact of library preparation protocol, amplicon region, and bioinformatic pipeline on species-level taxonomic inference and compositional agreement remains insufficiently characterised. We therefore compared the Illumina 16S Metagenomic Sequencing Library Preparation protocol (V3-V4) and the Zymo Quick-16S Plus NGS Library Prep Kit (V1-V2 and V3-V4) in combination with two bioinformatic pipelines, nf-core/ampliseq and TRANA. Performance was assessed using defined microbial community standards and human faecal and colonic biopsy samples.

RESULTS: Pipeline choice was the dominant driver of variation in inferred community composition, exceeding the effects of amplicon regions and library preparation protocols. Genus-level profiles were broadly concordant across methods. Species-level resolution and agreement with expected community composition differed systematically between pipelines, with TRANA demonstrating lower Bray-Curtis dissimilarities to expected compositions than nf-core/ampliseq. Amplicon region had a secondary, pipeline-dependent effect, while protocol differences were minor. In clinical samples, inter-individual biological variation exceeded technical variation.

CONCLUSIONS: Bioinformatic processing substantially influenced species-level inference in short-read 16S sequencing, highlighting the importance of pipeline selection for microbiome study design and cross-study comparability.}, } @article {pmid42387416, year = {2026}, author = {Ishio, D and Eguchi, H and Hotta, F and Miyamoto, T}, title = {Blepharoconjunctivitis mimicking conjunctival tumor associated with Streptococcus intermedius sinusitis: case report and literature review.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13910-6}, pmid = {42387416}, issn = {1471-2334}, abstract = {Streptococcus intermedius, a commensal bacterium in the human oral cavity, can occasionally cause severe infections in deep tissues. The patient was referred because of a conjunctival tumor. She had severe nasal cavity and periocular tissue inflammation that persisted for over a year. Microbiological examination of the nasal and ocular specimens identified S. intermedius as the pathogenic strain. The inflammation and the conjunctival mass subsided after systemic and topical administration of a susceptible antibiotic. Smear microscopy of the eye and nasal discharge was useful for the differential diagnosis. 16S metagenomic analysis using MinION as an adjunctive diagnostic tool has contributed to the species identification of the pathogenic strain.}, } @article {pmid42387479, year = {2026}, author = {Vastolo, A and Tolone, M and Gannuscio, R and Staropoli, A and Giosa, D and Bonomo, A and Vinale, F and Cutrignelli, MI and Todaro, M}, title = {Impact of Opuntia spp. by-product silage on sheep metabolic profile, rumen fermentation and microbial communities.}, journal = {BMC veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12917-026-05646-x}, pmid = {42387479}, issn = {1746-6148}, support = {cod. U-Gov PRJ-1776; CUP: J83C22000830005//National Recovery and Resilience Plan (PNNR) of Italy: project Biometric-Call PNNR a cascata-Università della TUSCIA/ ; }, abstract = {BACKGROUND: Prickly pear (Opuntia ficus-indica) by-products represent a promising alternative feed resource for improving the sustainability of sheep production systems in Mediterranean areas. This study evaluated the effects of prickly pear by-product (PPB) silages on rumen fermentation, metabolic profile, and rumen microbiome in lactating ewes. Twelve Valle del Belice ewes were assigned to three dietary treatments (control, CTR; prickly pear peel silage, PPP; and pastazzo silage, PPS) in a Latin square design. Blood biochemical parameters, rumen volatile fatty acids (VFA), and metagenomic profiles were analysed.

RESULTS: PPB inclusion did not induce significant changes in blood biochemical parameters, which remained within physiological ranges. Rumen fermentation parameters were significantly affected, with the PPP diet increasing total VFA concentration and promoting a more glucogenic profile through higher propionate production. The rumen microbiome was dominated by Prevotella, which showed higher relative abundance in the CTR diet. PPB supplementation was associated with shifts in microbial functional profiles, including pathways related to polyphenol degradation, vitamin K2 biosynthesis, and central carbon metabolism, partially consistent with observed changes in rumen fermentation. No significant effects were observed on methanogenesis-related pathways.

CONCLUSIONS: Prickly pear by-product silages, particularly prickly pear peel, modulate rumen fermentation and microbial functional profiles in lactating ewes without adversely affecting systemic metabolic status.}, } @article {pmid42387526, year = {2026}, author = {Bing, Y and Yuan, W and Liang, L and Li, J and Chen, Y and Feng, L and Li, X and Li, H and Zhong, J and Wang, L and Tong, Z and Liu, X}, title = {Alterations in the fecal virome and bacteriome-virome interplay in IPAH.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03797-x}, pmid = {42387526}, issn = {1465-993X}, support = {Nos. 82570072, 82170302//Innovative Research Group Project of the National Natural Science Foundation of China/ ; Nos. Ysbz2025004, Ysbz2025005, Ysbz2025006, Ysbz2025007//the Financial Budgeting Project of Beijing Institute of Respiratory Medicine/ ; }, abstract = {BACKGROUND: Idiopathic pulmonary arterial hypertension (IPAH) is a life-threatening cardiovascular disorder characterized by complex multisystem disturbances. Although alterations in the gut microbiota have been reported in IPAH, how the gut virome interacts with bacterial communities and host metabolism remains unclear.

METHODS: We enrolled 28 patients with IPAH and 30 age-matched healthy controls (HCs). Fecal viromes and bacteriomes were profiled by metagenomic sequencing, and serum metabolomic data were integrated to construct virus-bacterium-metabolite interaction networks. Random forest models were used to evaluate the diagnostic potential of virome features.

RESULTS: IPAH patients exhibited markedly reduced gut virome diversity (Shannon, Simpson, and Pielou indices, p < 0.05) and distinct community structures from HCs (p < 0.01). A total of 499 differential viral operational taxonomic units (vOTUs) were identified, accompanied by extensive reorganization of interaction networks. At the phylum level, Hofneiviricota was enriched and Phixviricota depleted, both correlating with clinical indicators. Virus-bacterium associations were markedly increased in IPAH (44,894 vs. 17,920, r > 0.5). Notably, vOTU2967, vOTU1924, and vOTU4522 were elevated and inversely related to Bacteroides, whose depletion was associated with increased lactic acid levels. Mediation analysis confirmed significant indirect virus-bacterium-metabolite effects (p < 0.05). Random forest models based on vOTUs or viral families effectively distinguished IPAH patients from controls, highlighting the exploratory potential of gut virome features for mechanistic insights.

CONCLUSIONS: IPAH is characterized by reduced virome diversity, altered viral taxa, and reorganized virus-bacterium-metabolite networks. These findings suggest that gut viruses may influence disease progression by modulating bacterial metabolism, providing a potential avenue for biomarker discovery and therapeutic intervention.}, } @article {pmid42387604, year = {2026}, author = {Hu, Y and Chen, JS and Zhou, MY and Huang, H and Zhou, YF and Zhou, HY and Lv, ZY}, title = {Dynamic alterations and potential roles of gut microbiota and metabolites in Angiostrongylus cantonensis-infected mice and rats.}, journal = {Infectious diseases of poverty}, volume = {15}, number = {1}, pages = {}, pmid = {42387604}, issn = {2049-9957}, support = {NPRC-2019-194-30//National Parasitic Resources Center of China/ ; 22qntd4804//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; 2021YFC2300800//National Key Research and Development Program of China/ ; 82072303//National Natural Science Foundation of China/ ; YSPTZX202133//Specific Research Fund of the Innovation Platform for Academicians of Hainan Province/ ; ZDYF2020120//Key Research and Development Program of Hainan Province/ ; ZDKJ202003//Major Science and Technology Program of Hainan Province/ ; 2020TTM007//Open Foundation of Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University/ ; }, mesh = {Animals ; Female ; *Angiostrongylus cantonensis/physiology ; Rats, Sprague-Dawley ; *Strongylida Infections/parasitology/microbiology/metabolism ; Rats ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred BALB C ; RNA, Ribosomal, 16S/genetics/analysis ; Biomarkers ; Feces ; }, abstract = {BACKGROUND: Angiostrongyliasis, a food-borne parasitic disease caused by Angiostrongylus cantonensis, is characterized by eosinophilic meningitis or meningoencephalitis, leading to serious central nervous system damage. Current diagnostic methods lack specificity or sensitivity, and the pathogenesis is complex and incompletely understood. This study aimed to comprehensively characterize the dynamic alterations in the gut microbiota and host metabolism in both suitable (rats) and non-suitable (mice) hosts following A. cantonensis infection and to identify potential metabolic biomarkers for early diagnosis.

METHODS: Female BALB/c mice and Sprague Dawley rats (n = 10/group) were infected with 30 or 100 third-stage larvae, respectively. Serum, urine, feces, and brain samples were collected longitudinally. Gut microbiota was analyzed via 16S rRNA gene sequencing and metagenomics. Host metabolism was profiled using untargeted and targeted metabolomics via ultraperformance liquid chromatography-quadrupoles/time of flight-mass spectrometry. Statistical analyses included Wilcoxon rank sum test, linear discriminant effect size analysis, Spearman correlation analysis, orthogonal partial least squares-discriminatory analysis, and receiver operating characteristic curve analysis.

RESULTS: Infection induced significant, host-specific gut microbiota dysbiosis. In infected hosts, Firmicutes decreased (P < 0.05) while Bacteroidetes increased (P < 0.05). A main difference in gut flora structure between infected hosts was observed in Prevotellaceae, which increased significantly in mice (P < 0.05) but decreased in rats (P < 0.05). Metagenomics revealed enhanced carbohydrate metabolism and fatty acid biosynthesis in gut microbes of infected mice, whereas up-regulated amino acid and vitamin metabolism were also observed in infected rats. Infection caused pronounced disruptions in host lipid and bile acid (BA) metabolism, changes in various BA types were closely related to alterations in specific bacterial genera (P < 0.05). Several metabolites, including phosphatidylcholine (16:0/18:1), 2-phenyl acetic acid, 2-octenoylglycine, lysophosphatidylcholine (18:2), O-glucuronide, and 2-carboxylic acid, were identified as potential early diagnostic biomarkers in the mouse model.

CONCLUSIONS: A. cantonensis infection causes profound host-specific dysregulation of the gut microbiome and metabolome, with severe disturbances in Firmicutes, Bacteroidetes, lipid and BA metabolism being central features. These alterations highlight the critical role of the host-gut microbiota-metabolite axis in pathogenesis and offer novel insights for developing diagnostic and therapeutic strategies.}, } @article {pmid42388191, year = {2026}, author = {Zhang, J and Fu, C and Tan, S and Lyu, B and Shu, G and Shi, L and Wu, Y and Guo, P}, title = {How Host Phylogeny, Diet, and Habitat Affect Gut Microbial Diversity in Wild Snakes.}, journal = {Ecology and evolution}, volume = {16}, number = {7}, pages = {e73902}, pmid = {42388191}, issn = {2045-7758}, abstract = {Gut microbiota plays critical roles in host digestion, immune regulation, neurochemical signaling, and metabolic homeostasis. Based on wild snakes (73 individuals from 23 species) from China, we explored the composition, characteristics, and functions of gut microbes across different groups using fecal metagenomic samples; further we explored the relative contributions of host phylogeny, diet, and habitat to the microbial structure. Among 23 wild snake species, the dominant gut microbial phyla were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, with Bacteroides, Salmonella, Citrobacter, and Aeromonas comprising the major genera. Mantel test revealed a significant correlation (r = 0.3173, p = 0.0055) between microbial composition at the genus level and host genetic divergence (p-distance), indicating potential phylogenetic influence on gut microbial profiles. While α-diversity and principal coordinate analysis showed no marked differences across different subgroups. Linear discriminant analysis effect size demonstrated notable differences in the gut microbes of the terrestrial snakes with different diets and vertebrate-feeding snakes with different habitats. Functional annotation of microbial genes indicated enrichment in metabolic processes, as well as environmental and genetic information processing. Carbohydrate-active enzymes were predominantly from GT2, GT4, GT51, and GH23 families. Linear discriminant analysis effect size showed different diets and habitats had distinct differential taxa. Additionally, antibiotic resistance gene profiles varied across groups, with acrB, AcrF, MexB, acrD, and mdtF being most prevalent. Future studies should increase the samples and comprehensively consider different ecological factors to explore the impacts on the composition and functions of snake gut microbes on different evolutionary, which will provide a deeper understanding of the interrelationships between snake gut microbes and their hosts.}, } @article {pmid42388299, year = {2026}, author = {Maccario, L and Otani, S and Szarvas, J and Mortensen, LH and Elberling, B and Møller, KE and Madsen, CEK and Aarestrup, FM and Priemé, A}, title = {Microbial composition of archaeological middens: tracing human footprints through centuries in Greenland's ancient settlements.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809037}, pmid = {42388299}, issn = {1664-302X}, abstract = {The history of Greenland is marked by different waves of Paleo-Inuit immigration from North America from 2,500 BC to the 12th century and from the 10th to 15th century, Norse settlers immigrated from Northwest Europe and flourished in Southwest Greenland with the introduction of domestic livestock. The different Inuit and Norse cultures created middens by dumping and accumulating domestic waste; a latent source of microbes, including potential pathogens, that might have been preserved due to the general wet and cold conditions in the region. The aim of this study was to evaluate whether ancient Arctic settlements might be possible hot-spots for pathogenic agents that may spread to the surrounding environment because of current climate changes. Using metagenomics, we compared the microbial communities and resistomes of 78 samples from middens from different ages and locations in West and South Greenland (two Paleo-Inuit, four Norse and one early Colonial-time middens) to 143 soil samples from nearby surroundings. We found that the middens harbor a distinctive microbial signature enriched in human-associated bacteria. Those include opportunistic pathogens such as Clostridium perfringens and Paeniclostridium sordellii. In some early colonial midden layers, C. perfringens and Paraclostridium tenue together accounted for up to ~40%-50% of MetaPhlAn-derived relative abundance in individual samples. Antimicrobial resistance genes representing 17 resistance classes were detected across all sites, dominated by β-lactam and tetracycline resistance. Transect analyses across an actively eroding midden showed that midden-derived bacteria were confined to local erosion layers and were rapidly replaced by native marine communities, indicating limited environmental dispersal.}, } @article {pmid42388302, year = {2026}, author = {Cao, H and Wang, Q and Ren, W and Wang, A and Tian, W and Zhang, D and Chen, J}, title = {Characterization of the gastric mucosal microbiota in tumoral and peritumoral mucosa in patients with advanced gastric cancer from Northwest China.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1763714}, pmid = {42388302}, issn = {1664-302X}, abstract = {INTRODUCTION: The gastric microbiota affects tumor development and treatment response, yet the characteristics and interactions of mucosal bacteria and fungi in advanced gastric cancer (AGC) remain unclear.

METHODS: Here we analyzed 177 mucosal samples (88 peritumoral and 89 tumoral) from 91 AGC patients in Northwest China using shotgun metagenomic sequencing.

RESULTS: MetaPhlAn4 and Kaiju were used to annotate the gastric mucosal microbial composition. MetaPhlAn4 has identified 12 phyla (no phylum-level differences), 98 genera and 278 species. PERMANOVA revealed age and tumor location significantly influenced microbial composition in tumoral mucosa. Wilcoxon signed-rank test revealed that 10 species including Serratia surfactantfaciens, Pseudomonas protegens, Treponema pectinovorum, Streptococcus anginosus, Bacteroides heparinolyticus, Selenomonas sputigena, and Mogibacterium diversum were significantly enriched in tumoral tissue, whereas five species including Actinomyces graevenitzii, Gemella sanguinis, Porphyromonas pasteri, Helicobacter pylori, and Leptotrichia sp. oral taxon-215 were more abundant in peritumoral mucosa. HUMAnN4 showed tumor-enriched bacteria were involved in metabolic pathways including polysaccharide degradation, biosynthesis of fatty acids, nucleotides, and arginine/histidine/purine/pyrimidine, which were primarily linked to S. surfactantfaciens. Peritumor-enriched bacteria were associated with L-tryptophan biosynthesis, L-arginine degradation, and TCA cycle. Kaiju annotation further revealed 2,429 bacteria, 12 archaea, 74 viruses, 82 fungi, and 63 other eukaryota species, among which the majority of significantly different species were enriched in the tumoral mocusa. Mycobiome analysis revealed eight fungal phyla, 82 genera and 82 species. PERMANOVA revealed that age had a significant effect on fungal composition in peritumoral mucosa, and five species including Saccharomyces cerevisiae, Aspergillus ochraceoroseus, Aspergillus fumigatiaffinis, Mitosporidium daphniae, and Puccinia striiformis were significantly positively correlated with age. Alpha diversity using Shannon index was significantly reduced in peritumoral mucosa at both genus and species levels. Wilcoxon signed-rank test revealed that all the significantly different fungi, including eight phyla, 46 genera, and 42 species were significantly enriched in tumoral mucosa. Correlation analysis indicated tumor-enriched bacteria were positively correlated with tumoral fungi but negatively with peritumoral fungi, suggesting possible synergistic bacteria-fungi interactions.

DISCUSSION: This study comprehensively characterizes the gastric mucosal bacteriome and mycobiome in AGC, illuminates potential microbiota-mediated carcinogenic mechanisms, identifies candidate biomarkers, and fills a regional research gap.}, } @article {pmid42388305, year = {2026}, author = {Zhang, H and Ma, L and Jia, L and Li, Y and Wang, Y and Wang, W and Wu, W and Wang, H and Li, H and Zhang, Y and Chen, G and Hou, K and Dong, J}, title = {Multi-omics analysis reveals the potential for fermented Cordyceps militaris mushroom substrate in laying hens.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1807060}, pmid = {42388305}, issn = {1664-302X}, abstract = {This study examines how varying levels of fermented Cordyceps militaris mushroom substrate (CMMS) in laying hen diets affect production performance, digestive health, immunity, cecal microbiota, metabolites, and quorum-sensing functions. Fermentation reduced CMMS dry matter, NDF, and phosphorus content (p < 0.05). Replacing 30% of the diet with fermented CMMS significantly improved laying rate, egg weight, feed intake, and feed efficiency (p < 0.05), while enhancing yolk color, Haugh units, and lipase activity. A 20% substitution increased nutrient digestibility and immunoglobulin levels (p < 0.05). Metagenomic analysis revealed increased abundance of Phocaeicola, Alistipes, and Parabacteroides (p < 0.05) with enhanced energy metabolism and specific gene families. Metabolomic analysis identified 1,529 differentially expressed metabolites, with carboxylic acids being most prevalent (21.20%), and enhanced taurine/hypotaurine metabolism and GPI-anchor biosynthesis. Parabacteroides showed negative correlations with certain metabolites, while Alistipes correlated positively with PemK/MazF family genes (p < 0.001). CMMS fermented feed proportions influence cecal microbiota, their metabolites, and quorum sensing in laying hens, affecting production, digestibility, immunity, metabolism, and health, demonstrating CMMS potential as alternative poultry nutrition.}, } @article {pmid42388398, year = {2026}, author = {Yu, L and Chong, Z and Yanchun, L and Yingying, H}, title = {The Diagnosis of Human Neurological Infection Caused by Rabies Virus Using Metagenomic Next-Generation Sequencing: Two Case Reports.}, journal = {Case reports in infectious diseases}, volume = {2026}, number = {}, pages = {1910139}, pmid = {42388398}, issn = {2090-6625}, abstract = {The rabies virus (RABV) causes acute progressive and fatal encephalomyelitis. Two case studies of RABV neurological infection identified using metagenomic next-generation sequencing (mNGS) are presented in this paper. A total of 39 RABV sequences were detected using mNGS in the cerebrospinal fluid (CSF) in Case 1. The detected sequences were located in the 0%-35% range of the enriched and amplified region and had a 27 × sequencing depth. A total of 75 RABV sequences were detected using mNGS in the CSF in Case 2. These cases illustrate that mNGS use during the early diagnosis of infectious diseases is critical. They also indicate that RABV can remain latent in the human body for many years. Disease prevention education for people who have experienced bites or scratches by rabid animals is therefore crucial.}, } @article {pmid42388653, year = {2026}, author = {Zhang, X and Sun, E and Zhao, Z and Li, S and Shen, X and Liu, J and He, Q and Wang, Y and Zhao, F and Zhao, H and Zhang, H}, title = {Intervention With Lacticaseibacillus paracaseiPC-01 Fermented Milk Beverage Ameliorates Functional Dyspepsia and Modulates Gut Microbiome: A Pilot Study.}, journal = {Food science & nutrition}, volume = {14}, number = {7}, pages = {e71928}, pmid = {42388653}, issn = {2048-7177}, abstract = {Functional dyspepsia (FD) is a common chronic gastrointestinal disorder characterized by persistent or recurrent epigastric symptoms in the absence of detectable structural abnormalities. In this pilot study, we explored whether a Lacticaseibacillus paracasei PC-01 (PC-01) fermented milk beverage alleviates FD symptoms. Fifty-five patients with FD were randomized into an experimental group (EP, n = 37) receiving the PC-01 fermented milk beverage (5.0 × 10[8] CFU/mL, 200 mL/day) or a control group (CP, n = 18) receiving the active comparator, an acidified milk beverage (non-fermented, without PC-01) (200 mL/day). The interventions lasted 28 days, with symptom scores on the 7-point Global Overall Symptom Scale (GOSS) and Gastrointestinal Symptom Rating Scale (GSRS), and fecal samples were collected at baseline (day 0), 14, and 28. Consumption of the PC-01 fermented milk beverage in this pilot study was associated with improvements in FD symptoms, and a higher effective response rate was observed in the EP group than in the CP group (p = 0.04). Metagenomic analysis revealed that, compared with the CP group, the EP group exhibited significant enrichment of potentially beneficial bacteria (e.g., Blautia) and a reduction in potentially pathogenic bacteria (e.g., Clostridium paraputrificum), accompanied by significant downregulation of the fatty acid β-oxidation I (FAO-PWY) pathway. We acknowledge that the limitation of this pilot study is that the acidified milk beverage used as the control might also exert certain effects on gastrointestinal symptoms and gut microbiota, which could not be fully avoided due to the lack of a fully inert placebo. Collectively, the findings of this preliminary study indicate that the PC-01 fermented milk beverage may alleviate FD-related symptoms and modulate the gut microbiome and metabolic pathways, highlighting its potential in ameliorating FD-associated symptoms. Further large-sample, multi-center, and long-term clinical studies are warranted to verify these preliminary results and establish the long-term efficacy and safety of FD management.}, } @article {pmid42388798, year = {2026}, author = {Sen, P and Oliver, LL and Makarova, KS and Wolf, YI and Pavloudi, C and Shlafstein, M and Saw, JH}, title = {Hawaiian Geothermal Fumaroles Contain Diverse and Novel Viruses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.06.716669}, pmid = {42388798}, issn = {2692-8205}, abstract = {Microbial communities of geothermal habitats are central to understanding the evolution of life on Earth. Metagenomics has provided insight into the role of viruses in shaping microbial diversity of complex environments. However, identification of novel viruses is constrained by lack of marker genes and low nucleotide similarities between related viral taxa. While microbial and viral diversity have been explored in terrestrial hot springs and hydrothermal vent systems, other volcanic features remain underexplored. Fumaroles (steam vents) are geothermal features that heat groundwater with magma, releasing steam and volcanic gases such as CO2 and H2S. Comparatively physicochemically dynamic to hot springs, fumarole temperatures and gas emissions rapidly fluctuate with volcanic activity. Here, we describe viruses identified metagenomically from microbial mats hosted near basaltic fumaroles on the Big Island of Hawaìi. To our knowledge, this is the first systematic survey of fumarole viruses. Our utilization of a sensitive profile-based approach for identification reveals high viral diversity in fumaroles, resulting in estimation of two undescribed order-level clades of Caudoviricetes (tailed phages). Viral metabolic genes provide evidence of viral-mediated adaptation of microbes to fumarole conditions. We describe patterns of viral diversity that diverge from the Bank model of viral ecology, hinting at viral dispersal between biofilms and high viral richness and evenness. Lastly, we provide a description of the first terrestrial geothermal environment dominated by Microviridae, previously only described in viral communities of deep ocean hydrothermal vents. This study offers important findings for exploration of viral ecology in extreme environments.}, } @article {pmid42388836, year = {2026}, author = {Liu, B and Ding, Q and Tang, S and Dong, H and Li, RJ and Gan, M and Wei, J and Zhang, N and Wu, C and Zhang, TH and Yu, HZ and Zheng, Z}, title = {Avian paramyxovirus type 1-associated severe pneumonia in humans: Molecular characterization and zoonotic transmission risk.}, journal = {One health (Amsterdam, Netherlands)}, volume = {23}, number = {}, pages = {101501}, pmid = {42388836}, issn = {2352-7714}, abstract = {BACKGROUND: Avian paramyxovirus serotype 1 (APMV-1, Newcastle disease virus) is a major poultry pathogen. Human infections are rare and typically self-limiting, but its potential to cause severe respiratory disease and the mechanisms underlying cross-species transmission remain understudied.

METHODS: We analyzed a 65-year-old male with severe pneumonia who had contact with sick backyard feeder chickens. Immunocompetence was evaluated via routine blood tests and serum immunoglobulin levels. mNGS identified 40 APMV-1 sequence reads (50.6% microbial abundance) covering 10.78% of the genome. APMV-1 nucleic acid, antigen, and high IgG titers were detected in human specimens. High viral loads were confirmed in chicken and environmental samples. Phylogenetic analysis classified the strain as Class I genotype 1.1.2 1b, genetically identical to poultry-derived viruses, suggesting a potential avian-to-human transmission.

RESULTS: mNGS identified 40 APMV-1 sequence reads (50.6% microbial abundance) covering 10.78% of the genome. APMV-1 nucleic acid, antigen, and high IgG titers were detected in human specimens. High viral loads were confirmed in chicken and environmental samples. Phylogenetic analysis classified the strain as Class I genotype 1.1.2 1b, genetically identical to poultry-derived viruses, providing molecular clues for zoonotic infection.

CONCLUSIONS: APMV-1 Class I genotype 1.1.2 1b can cross the species barrier and cause life-threatening pneumonia in immunocompetent humans. Our findings highlight its underrecognized zoonotic potential, emphasizing the need for enhanced surveillance in avian and human populations and research into determinants of cross-species pathogenicity.}, } @article {pmid42389124, year = {2026}, author = {Zhou, Y and Bian, P and Yang, C and Qu, J and Wang, H and Gao, W}, title = {Differences in carbon sequestration capacity, rhizosphere microorganisms and metabolic functions among different herbaceous plants.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1849153}, pmid = {42389124}, issn = {1664-462X}, abstract = {Mitigating the rapid increase in global CO2 concentrations necessitates a deeper understanding of plant-microbe symbiotic carbon sequestration. While previous research has predominantly focused on woody plants, the carbon sequestration potential and mechanisms of herbaceous plants and their rhizosphere microbiomes remain largely underexplored. To address this gap, this study employed metagenomic technology to systematically investigate the carbon sequestration capacities and metabolic mechanisms of seven plant species and their rhizosphere soil microorganisms. Plant physiological measurements were integrated with microbial functional profiles predicted via PICRUSt2. The results show that the rhizosphere soil microbial communities generally possess functional genes for carbon decomposition and carbon fixation, providing evidence for the coupling of intracellular decomposition and synthesis metabolism in microorganisms. Notably, Spearman correlation analysis established a direct statistical link between plant physiological performance and specific microbial metabolic pathways. These findings demonstrate a functional coupling between plant physiology and rhizosphere microbial carbon metabolism. By linking plant phenotypes to microbial gene pathways, this study reveals that herbaceous plants and their rhizosphere microbiomes form an integrated carbon sequestration system. Therefore, leveraging such plant-soil interactions offers a promising strategy to enhance ecosystem carbon sinks and mitigate rising atmospheric CO2.}, } @article {pmid42389176, year = {2026}, author = {Ubani, O and Ngole-Jeme, VM}, title = {Long-read whole-genome sequencing dataset of microbial communities from industrially and municipally impacted freshwater wetlands in South Africa.}, journal = {Data in brief}, volume = {67}, number = {}, pages = {112987}, pmid = {42389176}, issn = {2352-3409}, abstract = {This article describes a long-read whole-genome shotgun sequencing dataset generated from microbial communities inhabiting industrially and municipally impacted freshwater wetlands in South Africa. Surface water samples were collected from five strategically selected sites exposed to distinct anthropogenic pressures, including industrial effluent discharge, sewage overflow, greywater inputs, informal settlement runoff, and landfill leachate to generate a unique microbial genomic data. Environmental DNA was extracted and sequenced using the PacBio Sequel IIe platform, producing high-fidelity long reads suitable for improved assembly contiguity and functional reconstruction. Post-quality control processing yielded 4.9 × 10[4] to 1.6 × 10[5] HiFi reads per sample, corresponding to 0.34-1.02 Gb of high-accuracy sequence data per site. Long-read assemblies generated between 16,080 and 54,670 predicted protein-coding genes per sample. Taxonomic classification using Kaiju assigned 94.1-99.8% of assembled sequences to reference taxa. Domain-level profiles were exclusively bacterial dominated, with few rare or undetected (0.000-0.001%) archaeal, eukaryotic, or viral representation. Phylum-level composition was strongly dominated by Pseudomonadota (83-95%), followed by Bacillota (3-10%) and Bacteroidota (1-14%), with Actinomycetota consistently below 1%. Functional annotation using the DRAM pipeline identified 9390-31,251 KEGG orthologs, 969-3039 MEROPS peptidases, 13,454-45,103 Pfam domains, and 202-776 carbohydrate-active enzyme (CAZy) genes across assemblies. Distilled metabolic modules indicated the presence of near‑complete electron transport chain complexes (I-V), denitrification-associated pathways, sulfur oxidation and dissimilatory reduction genes, and diverse carbohydrate degradation functions; methanogenesis‑associated modules were not detected among the annotated metabolic pathways recovered in this dataset. The dataset provides genomic coverage of urban wetland microbiomes shaped by mixed industrial and municipal stressors and represents one of the few long-read metagenomic resources available for southern African freshwater wetlands. The availability of assembled contigs, gene annotations, metabolic reconstructions, enables reuse for comparative environmental genomics, biogeochemical modelling, bioremediation gene discovery, resistome screening, and microbial ecology investigations. This high-fidelity long-read sequencing resource expands opportunities for structural and functional analyses of anthropogenically influenced wetland ecosystems and supports future research in environmental biotechnology, bioinformatics-driven ecosystem monitoring, and microbial adaptation to urban pollution gradients.}, } @article {pmid42389349, year = {2026}, author = {Iranzo, J and Wolf, Y and Koonin, E}, title = {Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono?.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9816737/v1}, pmid = {42389349}, issn = {2693-5015}, abstract = {Background Mobile genetic elements (MGEs), including viruses, plasmids, and transposons, are major drivers of evolution in bacteria and archaea. Host-parasite conflicts drive the emergence of a broad variety of defense and counter-defense systems. Recent advances in metagenomics and functional annotation have shown that many defense systems are located on MGEs. The fact that MGEs are, essentially, genomic parasites raises an intriguing question: why do these parasites carry defense systems at high prevalence, often even higher than the host chromosome? Results We developed a simple mathematical model to investigate the factors that promote evolution of defense systems in MGEs and the ecological implications of MGE-encoded defense. Our analysis points to the strength of inter-MGE interference as a key determinant of the evolution of defense systems in MGEs. We identify two qualitatively distinct regimes, depending on the basic reproductive number in mixed coinfections. Weakly interfering MGEs tend to carry low-cost defense systems that enhance the survival of their hosts upon exposure to more damaging MGEs. Although these systems can be occasionally transferred to the host, they typically remain in MGEs. In contrast, strongly interfering MGEs, such as plasmids from the same incompatibility group, can carry high-cost defense systems that are detrimental to the host and the population as a whole, but help their carriers spread by actively replacing their competitors. Conclusions Analysis of our model shows that the key determinant of the evolution and spread of defense systems in MGEs is the strength of cross-MGE interference. Weakly interfering MGEs would serve as 'MGE banks', typically carrying low-cost defense systems that can benefit the host by protecting it from more damaging MGEs. In contrast, strongly interfering MGEs would carry costly defense systems that mediate inter-MGE conflicts but are deleterious to the host. These MGEs could serve as proving ground for emerging defense systems, which might eventually become cost-effective once optimized by selection.}, } @article {pmid42389510, year = {2026}, author = {Al Shareef, ZM and Al-Shahrabi, RM and Sharif-Askari, FS and Yener, B and Bhamidimarri, PM and Bouzid, A and Talaat, IM and Bendardaf, R and Hamoudi, RA and Mote, S and Mall, R and Castiglione, F}, title = {Microbial dysbiosis and inferred functional profiling reveals the potential role of Methylobacterium in prostate cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1760700}, pmid = {42389510}, issn = {2235-2988}, mesh = {Humans ; Male ; *Methylobacterium/genetics/classification/isolation & purification/physiology ; *Prostatic Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Retrospective Studies ; Microbiota/genetics ; Prostate/microbiology/pathology ; }, abstract = {BACKGROUND AND OBJECTIVE: Prostate cancer (PCa) is a leading malignancy in men, with a multifactorial aetiology involving genetic, hormonal, and microbial factors. Although emerging evidence implicates tumour-associated microbial communities in cancer biology, microbial signatures in PCa, particularly in Arab populations, remain underexplored. This study aimed to characterize the prostate tissue microbiota in an Arab cohort and explore associations with clinical features.

METHODS: In this retrospective study, 40 formalin-fixed paraffin-embedded (FFPE) prostate tissue samples (23 PCa and 17 benign prostatic hyperplasia [BPH]) were analysed using 16S rRNA gene sequencing. Microbial diversity, taxonomic composition, and predicted functional potential inferred from 16S data were assessed using DADA2 (v1.30.0), phyllode (v1.46.0), and PICRUSt2 (v2.5.2), with taxonomic classification based on the SILVA database (release 138). Beta diversity differences were tested using PERMANOVA (999 permutations), and differential abundance analyses were corrected using false discovery rate (FDR).

KEY FINDINGS AND LIMITATIONS: PCa tissues demonstrated higher alpha diversity than BPH samples, with greater heterogeneity in beta diversity. Among the identified genera, Methylobacterium was enriched in PCa samples and remained directionally consistent after multivariable adjustment. Exploratory analyses suggested higher abundance in advanced and deceased cases; however, survival findings were limited by sample size. Functional inference indicated enrichment of predicted pathways for carbohydrate and nitrogen metabolism.

CONCLUSIONS: This exploratory study identified Methylobacterium as a candidate microbial signature associated with PCa in an Arab cohort. Given the modest sample size and the inferential nature of functional predictions, these findings require validation in larger prospective studies using direct metagenomic and metabolomic approaches.}, } @article {pmid42389512, year = {2026}, author = {Díaz-Velis, L and Salvador-Sagüez, F and Roach, F and Mancilla, E and Campos, MA and Ruiz-Gil, T and López-Moral, M and Lázaro-Martínez, JL}, title = {Correction: Metagenomic and ribosomal transcript profiles of diabetic foot osteomyelitis in Hispanic patients: underestimated bacteria in biofilm persistence.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1902309}, doi = {10.3389/fcimb.2026.1902309}, pmid = {42389512}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1729196.].}, } @article {pmid42389745, year = {2026}, author = {Ota, Y and Nukui, Y and Gu, Y and Saito, R}, title = {Genomic insights into activated antimicrobial resistance of in situ hospital-wastewater biofilm.}, journal = {Biofilm}, volume = {12}, number = {}, pages = {100377}, pmid = {42389745}, issn = {2590-2075}, abstract = {Antimicrobial resistance (AMR), particularly among carbapenemase-producing organisms, poses a major global health threat. Although hospital wastewater is considered an AMR hotspot, its functional contribution to resistance dynamics remains poorly defined. We developed in situ biofilms in hospital wastewater and applied integrated metagenomic, metatranscriptomic, and culture-based analyses to characterize community structure and gene expression. Biofilms exhibited greater biomass and higher contamination with extended-spectrum β-lactamase-producing Escherichia coli than planktonic wastewater. Biofilms were enriched in surface-adapted Flavobacteriaceae species and a broader array of carbapenemase genes, whereas wastewater showed higher abundance of gut-associated Bacteroidaceae species and virulence factors. Mobile genetic elements linked multiple AMR genes and showed increased expression in biofilms, including bla IMP family carbapenemases. Culture confirmed bla IMP-1 in four biofilm isolates and one wastewater isolate. These findings indicate that hospital-wastewater biofilms can serve as important reservoirs that promote the persistence and potential dissemination of clinically relevant carbapenem resistance.}, } @article {pmid42390233, year = {2026}, author = {Peng, Y and Liu, Q and Lin, X and Xing, F and Li, S and Liu, X and Han, Y and Chen, Y and Dong, X}, title = {Salinity-driven microbial adaptation of hydrocarbon-degrading communities in coastal sediments.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0036926}, doi = {10.1128/msphere.00369-26}, pmid = {42390233}, issn = {2379-5042}, abstract = {Salinity is a major abiotic driver of microbial diversity and metabolic function in coastal ecosystems. While its broad ecological impacts are well established, its role in shaping hydrocarbon-degrading communities and their adaptive mechanisms remains poorly understood. Here, we integrated gene- and genome-resolved metagenomics to investigate how salinity regulates the diversity, ecological interactions, and evolutionary dynamics of aerobic hydrocarbon-degrading microbes in Zhenhai Bay sediments (0.17-28.54 practical salinity units [PSU]). Across the natural salinity gradient, 10 types of hydrocarbon-degrading genes and 30 bacterial genomes spanning four phyla were identified, revealing extensive metabolic potential for the aerobic degradation of both aliphatic and aromatic hydrocarbons. The functional diversity and relative abundance of these genes increased significantly with salinity, accompanied by strong correlations with organic carbon parameters and nitrogen availability. Co-occurrence network analyses showed that hydrocarbon degraders, particularly Gammaproteobacteria, acted as key taxa maintaining community stability under saline conditions. Comparative genomics revealed that these bacteria possess multiple halotolerance strategies, including compatible solute biosynthesis and ion transport, supported by diverse energy-generating pathways. Frequent horizontal gene transfer and duplication of alkane monooxygenases (alkB and cyp153) expanded substrate ranges and enhanced functional diversity in hydrocarbon oxidation, highlighting salinity-driven evolutionary innovation. Together, these findings demonstrate that salinity governs the structure, metabolism, and evolution of hydrocarbon-degrading microbes, promoting microbial adaptation and functional diversification in coastal sediments.IMPORTANCESalinity is a defining feature of coastal ecosystems and a major regulator of microbial processes that support carbon cycling and pollutant degradation. This study highlights that salinity plays a central role in structuring hydrocarbon-degrading microbial communities and shaping their functional capacities and evolutionary trajectories in coastal sediments. By integrating osmoadaptation, metabolic potential, and community organization, our work shows that hydrocarbon degraders function as key links between environmental conditions and ecological processes. Salinity-driven shifts in microbial networks and metabolic strategies illustrate how environmental gradients can foster resilience and stability in highly dynamic coastal systems. Beyond advancing understanding of microbial responses, this study has potential implications for the rational design of bioremediation strategies targeting hydrocarbon pollutants in saline and estuarine environments.}, } @article {pmid42390270, year = {2026}, author = {Varona, NS and Schellenberg, L and Barnes, W and Scholten, Y and Haas, AF and Silveira, C}, title = {Bacteriophage replication strategies are associated with organic matter energy content on coral reefs.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0039526}, doi = {10.1128/msystems.00395-26}, pmid = {42390270}, issn = {2379-5077}, abstract = {Bacteriophages, viruses that infect bacteria, play a crucial role in carbon cycling within marine environments. In coral reefs, dissolved organic matter (DOM) released by benthic primary producers such as algae fuels heterotrophic microbial growth, which can be detrimental to corals. This microbialization process has been associated with the abundance and replication strategies of bacteriophages, but the direct relationship between reef DOM composition and bacteriophage communities remains unclear. Here, we combine metabolomics, metagenomes, and viromes to demonstrate that phage communities have significant relationships with DOM composition on the reefs of Curaçao, Southern Caribbean. While total viral abundances did not significantly correlate with overall dissolved organic carbon (DOC) concentration on these reefs, co-occurrence networks identified thousands of statistically significant associations between free or cell-associated viruses and organic compounds. Cell-associated phages had significantly more positive associations with compounds that had a reduced nominal oxidative state of carbon (NOSC). Furthermore, temperate phages were more frequently correlated with metabolites exhibiting higher Gibbs energy than putatively lytic phages. Six of the ten viruses with the highest number of positive associations with metabolites were temperate (i.e., encoded an integrase or were identified as a prophage), despite this network consisting of approximately 90% lytic viruses. These temperate viruses were predicted to infect members of the genus Sphingobium. Together, these findings reveal a connection between phage replication strategies and DOM energy availability, with potential implications for coral reef biogeochemistry.IMPORTANCECoral reefs are highly dynamic ecosystems where microbial communities and organic matter cycles are intricately linked. This study provides new insights into how bacteriophages interact with dissolved organic matter (DOM) composition, revealing that cell-associated bacteriophages, particularly temperate phages, are associated with more energy-rich organic compounds. These findings suggest that DOM could affect the lysis-lysogeny decision of temperate phages or that lysogeny may play an underappreciated role in shaping the reef carbon cycle. Energy-rich organic compounds have generally been associated with increased algal abundances and coral decline. By demonstrating significant connections between viral infection strategies and the energy content of DOM, our results highlight the potential for phages to influence coral reef biogeochemistry and health.}, } @article {pmid42390352, year = {2026}, author = {Zhong, W and Zhu, Z and Zeng, Z and Wu, J and Xie, X and Li, X and Lv, Q and Li, D and Liu, M and Ward, G and Knol, J and Wopereis, H and Guyard, C and Jingjing, X and Lianyi, H and Wang, B and Li, Y and Roeselers, G and Gong, S}, title = {Early-life gut microbiome-metabolome development trajectories in Chinese infants: a decentralized real-world evidence study.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo02082h}, pmid = {42390352}, issn = {2042-650X}, abstract = {The neonatal period is a critical stage of development during which the gut microbiome profoundly influences both short- and long-term health and nutrition. Its maturation from infancy to childhood is shaped by interacting environmental factors, including feeding mode, birth mode, and geographic location. A clinical study of 445 infants and toddlers (aged 0-24 months) from six socioeconomically diverse regions in China investigated age-related trajectories of gut microbiome and metabolomic development, with a particular focus on feeding mode. The study included a breastfed reference group and a formula-fed group that received an open-label formula containing a prebiotic mixture of short-chain galacto-oligosaccharides and long-chain fructo-oligosaccharides (scGOS/lcFOS, 9 : 1). Longitudinal fecal samples were analyzed using shotgun metagenomic and metabolomic approaches. Feeding mode was strongly associated with variations in gut microbiome structure and function, along with birth mode and geographic location. Bifidobacterium and Bacteroides were the dominant taxa in both groups and exhibited dynamic abundance trajectories over time. Increased Bifidobacterium abundance was correlated with gene functions involved in starch and fatty acid metabolism as well as the fructose-6-phosphoketolase pathway (Bifid shunt). Comparative metabolomic analyses of amino acids and bile acids revealed highly similar metabolic profiles between the two groups. These findings highlight the association between feeding mode with the developing gut microbiome and describe age-dependent trajectories in Chinese children.}, } @article {pmid42390679, year = {2026}, author = {Shao, Z and Zheng, F and Sun, J and Wei, H and Sun, Y and Wang, F}, title = {Response of soil microbiomes to nano-zero-valent iron and biochar in Cr(VI)-contaminated soil remediation.}, journal = {Ecotoxicology (London, England)}, volume = {35}, number = {6}, pages = {}, pmid = {42390679}, issn = {1573-3017}, support = {2021CXGC011206//Major Scientific and Technological Innovation Project of Shandong Province/ ; }, mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; *Iron/chemistry ; *Microbiota/drug effects ; *Chromium ; *Charcoal/chemistry ; *Environmental Restoration and Remediation/methods ; Bacteria/drug effects ; *Metal Nanoparticles ; }, abstract = {Both biochar and nano-zero-valent iron (nZVI) are increasingly used to remediate soils polluted with heavy metals, such as the toxic Cr(VI). However, how soil microbiomes respond to biochar and nZVI applied in Cr(VI)-contaminated soil has not yet been clarified. The current study compared the effects of bare nZVI (B-nZVI) and starch-stabilized nZVI (S-nZVI) at 100 and 1000 mg/kg on soil enzyme activity and microbial communities in Cr(VI)-contaminated soil growing mung bean amended with or without 1% biochar. High-throughput metagenomic sequencing was conducted to determine the evenness (Simpson index), diversity (Shannon index), and richness (Chao-1 index) of soil bacteria, fungi, archaea, and viruses. Soil catalase activity was inhibited by S-nZVI but stimulated by biochar. Soil phosphatase activity was stimulated by both types of nZVI, but not influenced by biochar. The combination of 1000 mg/kg nZVI and biochar decreased bacterial and fungal evenness and diversity, but did not significantly alter their richness. Archaeal communities remained relatively stable across most treatments. The evenness and diversity of viral communities increased significantly at 1000 mg/kg S-nZVI, whereas the richness decreased conversely. PCoA showed that soil microbial community structure was significantly changed by 1000 mg/kg S-nZVI, which diminished Actinobacteria but enriched Cellvibrio. Furthermore, 1000 mg/kg S-nZVI increased the abundances of some genes involved in antioxidant enzymes and the metabolism of Fe and Cr, and decreased the abundance of C-cycling genes significantly. Overall, S-nZVI caused significant perturbations in soil microbial activity and community structure, but these adverse effects were alleviated by the incorporation of biochar.}, } @article {pmid42390736, year = {2026}, author = {Qi, M and Ye, H and Lei, D and Shao, J and Zhou, W}, title = {Metagenomic next-generation sequencing assists in identifying neurosyphilis: a case series.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {42390736}, issn = {1439-0973}, support = {Y20240739//Wenzhou Science & Technology Bureau/ ; }, abstract = {BACKGROUND: Neurosyphilis is a severe manifestation of syphilis caused by Treponema pallidum and remains challenging to diagnose because of heterogeneous clinical presentations and the limited performance of cerebrospinal fluid (CSF) assays. Here, we report four neurosyphilis cases in which CSF metagenomic next-generation sequencing (mNGS) detected T. pallidum and explore its potential value as an adjunctive diagnostic tool.

METHODS: We retrospectively reviewed four HIV-negative adults treated at the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University in whom CSF mNGS detected T. pallidum and the overall clinical assessment supported neurosyphilis. Demographic data, presentations, neuroimaging, CSF parameters, serology, antimicrobial therapy, and outcomes were extracted from the medical records.

RESULTS: All patients had positive syphilis serology and inflammatory CSF profiles with lymphocytic pleocytosis (40-130 cells/µL) and elevated CSF protein (0.70-1.26 g/L). Brain magnetic resonance imaging (MRI) revealed non-specific chronic structural changes in all patients (including white matter hyperintensities, cerebral atrophy, and ventricular enlargement), with no acute ischemic, hemorrhagic, or neoplastic lesions. Bacterial cultures remained negative after 48 h. CSF mNGS detected T. pallidum in all cases (unique reads 8-135; standardized mapped reads number (SMRN) 1-53; genome coverage 0.0260-0.4945%), including three patients whose predominant presentations were neuropsychiatric. Following anti-treponemal therapy with ceftriaxone or penicillin, all patients showed clinical improvement.

CONCLUSIONS: In this case series, CSF mNGS provided direct detection of T. pallidum and supported the diagnosis of neurosyphilis in patients with diverse, often neuropsychiatric presentations when conventional microbiology was non-diagnostic. CSF mNGS may serve as a useful adjunct in selected patients, but results should be interpreted alongside clinical features and CSF inflammation rather than in isolation.}, } @article {pmid42391470, year = {2026}, author = {Plominsky, AM and Peoples, LM and Norenberg, M and Ramirez-Flandes, S and Podell, S and Mullane, KK and Casagrande, D and Roman, C and Pockalny, R and Smith, DC and Belser, C and Poulain, J and Allen, EE and Glud, RN and Ulloa, O and Barber, N and D'Hondt, S and Bartlett, DH}, title = {Minimising decompression and warming during deep seawater collection increases abundance and activity of autochthonous bacteria and archaea.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag064}, pmid = {42391470}, issn = {1751-7370}, abstract = {The deep ocean hosts autochthonous pressure-adapted microorganisms that are unique to this environment, as well as allochthonous pressure-sensitive members transported from shallow depths by vertical advection and particle-sinking. However, conventional sampling instruments decompress and warm deep-sea samples during retrieval, potentially altering microbial properties when studied ex situ. Here, we assess this potential sampling bias by comparing seawater microbial communities collected with or without measures aimed at minimising pressure and temperature effects. When compared to samples collected under pressurised conditions, conventional sampling (using Niskin bottles) was found to affect prokaryotic cells retrieved by reducing their total numbers, diminishing protein synthesis activity (>10%), and also causing overall shifts in the community composition. The most significant compositional change was a > 20% decrease in metagenomic archaeal representation (TACK-group/Thaumarchaeota/Nitrososphaerota). Deep-sea bacterial groups had mixed responses to preserving pressure during retrieval, with some groups exhibiting higher representation when samples were maintained pressurised (e.g., members of the family Pelagibacteraceae, unclassified Thiotricales, Thioglobaceae, and Chitinophagaceae), whereas others increased their representation when decompressed (e.g., Burkholderiaceae, Comamonadaceae, and Oxalobacteraceae). This study reveals the existence of bias introduced by the complete decompression of samples retrieved with traditional instrumentation, as well as a decrease in overall bacterial activity when samples are completely decompressed during retrieval. Additionally, incubations lasting for >24 h were shown to transform the original prokaryotic community composition. Precautions addressing these effects are necessary to enhance the reliability of ex situ measurements and improve our understanding of deep-sea microbial ecology and biogeochemistry.}, } @article {pmid42391838, year = {2026}, author = {Yu, YH and Marín Arancibia, M}, title = {Mesorhizobium bavaricum sp. nov. and Mesorhizobium monacense sp. nov., two novel Lotus-associated species harbouring symbiotic plasmids.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {5}, pages = {126739}, doi = {10.1016/j.syapm.2026.126739}, pmid = {42391838}, issn = {1618-0984}, abstract = {Legumes establish a mutualistic interaction with nitrogen-fixing rhizobia. Lotus japonicus is a model for studying this symbiosis; however, only a limited number of rhizobial species nodulating this host have been taxonomically described. Here, we characterise four Mesorhizobium strains (DC-1.1[T], Qj1B1, DC-1.5[T], and Qj2B2) isolated from root nodules of Lotus japonicus and Lotus burttii. Multi-locus phylogeny and phylogenomic analyses resolved these isolates into two well-supported monophyletic clades. Genome-based comparisons supported their classification as distinct taxa, with strains DC-1.1[T] and Qj1B1 showing 95.2% average nucleotide identity (ANI) and 62.9-63.5% digital DNA-DNA hybridisation (dDDH) values relative to Mesorhizobium newzealandense ICMP 19545[T], whereas DC-1.5[T] and Qj2B2 exhibited 92.5-92.8% ANI and 49.9-50.5% dDDH compared with Mesorhizobium waimense ICMP 19557[T]. Together with chemotaxonomic and physiological traits, these data support the proposal of two novel species, Mesorhizobium bavaricum sp. nov. (DC-1.1[T] and Qj1B1) and Mesorhizobium monacense sp. nov. (DC-1.5[T] and Qj2B2). Metagenomic analyses predicted high environmental prevalence for these novel taxa, particularly within soil habitats. Isolates DC-1.1[T], Qj1B1, and DC-1.5[T] effectively nodulated Lotus burttii and significantly promoted plant growth, whereas Qj2B2 neither nodulated nor enhanced growth. Comparative genomic analysis revealed that the nodulating isolates harbour symbiotic genes (nod, fix, and nif) on symbiotic plasmids, a rare feature in Mesorhizobium strains, whereas Qj2B2 lacks essential nod and nif genes. Consistent with these genomic features, symbiotaxonomic analysis assigned the nodulating isolates to symbiovar loti. These results highlight the potential of these isolates as models for comparative analyses of symbiotic plasmid evolution and horizontal gene transfer.}, } @article {pmid42391940, year = {2026}, author = {Wang, J and Guo, C and Pu, X}, title = {Metabolic filtering as a putative mechanism linking soil metabolome and microbial community assembly along a lake expansion gradient.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128601}, doi = {10.1016/j.micres.2026.128601}, pmid = {42391940}, issn = {1618-0623}, abstract = {Climate-driven lake expansion across the Qinghai-Tibet Plateau induces profound edaphic shifts, but how these abiotic changes shape soil microbial assembly remains unclear. Soil metagenomics and metabolomics were integrated along a 0-10 km spatial gradient at Gahai. Redundancy analysis (RDA) identified moisture (NDWI) and salinity (SI) as primary ecosystem drivers. Structural equation modeling (SEM) provided exploratory evidence consistent with a mediation pathway (P = 0.64, CFI = 1, RMSEA = 0), in which environmental factors potentially influenced microbial community structure indirectly, via reshaping the soil metabolome rather than through a direct path. Moisture availability exerted a strong negative effect on soil metabolic profiles (λ = -0.93), leading to a pronounced negative correlation between the metabolome and microbial community (λ= -0.97). Multi-omics integration attributed this pattern to stress-induced accumulation of defensive metabolites, including Feruloylputrescine and 3-Methylthiopropyl-desulfoglucosinolate. These compounds showed significant negative correlations with dominant genera (e.g., Candidatus Kryptobacter). This "metabolic filtering" is hypothesized to selectively limit the presence of non-adapted taxa based solely on correlational SEM and network analyses, supporting our tentative hypothesis that increasing environmental stress may promote a transition from competitive interactions toward patterns consistent with stronger deterministic filtering. Our exploratory findings suggest that the soil metabolome acts as a functional interface mediating microbial adaptation and strategic resource allocation to lake expansion in this high-altitude saline-alkali system. However, due to regional heterogeneity, these patterns provide a theoretical baseline for plateau lake ecosystems and should be applied with caution to broader geographic areas.}, } @article {pmid42391942, year = {2026}, author = {Castellano-Hinojosa, A and de Freitas, J and de Carvalho, DU and Monus, BD and González-López, J and Strauss, SL and Albrecht, U}, title = {Compartmental and functional responses of the citrus microbiome and resistome to the systemic delivery of oxytetracycline by trunk injection.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128613}, doi = {10.1016/j.micres.2026.128613}, pmid = {42391942}, issn = {1618-0623}, abstract = {Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (CLas), severely limits citrus production worldwide. We investigated how oxytetracycline (OTC) trunk injection affects the citrus holobiont, examining its ability to suppress CLas and improve tree performance while assessing compartment-specific responses of the microbiome and resistome. A field experiment was conducted in CLas-infected sweet orange trees, integrating qPCR pathogen quantification, fruit yield and juice quality measurements, functional pathway analysis, and genome-resolved profiling across leaves, bark, fibrous roots, and the rhizosphere at three time points after injection. OTC reduced CLas abundance in leaves and improved fruit yield and juice quality without altering microbial diversity. No clear OTC-associated shifts in microbial functional pathways were observed in aboveground compartments, and resistome profiles were strongly compartment-dependent but showed no detectable response to OTC treatment. However, pronounced functional shifts were detected in belowground compartments, with consistent reductions in carbon-, nitrogen-, and phosphorus-related pathways and declines in several taxa and metagenome-assembled genomes associated with nutrient turnover. In contrast, stress-tolerance and xenobiotic-responsive microorganisms were enriched. In addition, these belowground responses were associated with low-abundance, rare taxa rather than by changes in alpha diversity or the dominant community, revealing a hidden functional reconfiguration that was concentrated in the root and rhizosphere compartments most relevant to nutrient cycling and long-term soil health. These findings demonstrate that systemically delivered OTC induces targeted, compartment-specific reorganization of microbiome functions rather than broad disruption. By linking physiological improvement with functional and genome-resolved microbial responses, this study highlights the broader ecological consequences of antibiotic interventions in perennial crops.}, } @article {pmid42392368, year = {2026}, author = {Cheng, M and Qin, X and Han, Y and Tan, F and She, M and Zhu, X and Yuan, L and Teng, M and Ou, X and Luo, S and Xiang, P and Chen, L and Yang, F}, title = {Genomic and biosynthetic landscape of high-temperature Daqu microbiome.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135297}, doi = {10.1016/j.biortech.2026.135297}, pmid = {42392368}, issn = {1873-2976}, abstract = {As the core starter for Chinese Baijiu, high-temperature Daqu is produced through open solid-state fermentation with recurrent inoculation by mature Daqu, forming a rich yet largely untapped reservoir of genomes and bioactive compounds. This study constructs the High-temperature Daqu Fermentation Microbiome catalog using 463 metagenomes spanning the full fermentation cycle. The catalog comprises 4,264 metagenome-assembled genomes that are dereplicated into 252 representative genome-based species, 82% of which are absent from current global food microbiome databases. It further contains 14.3 million non-redundant genes, of which 17.3% are novel, and 17,031 biosynthetic gene clusters, of which 62.63% are novel, thereby substantially expanding the known genomic and biosynthetic space of food microbiomes. Genome-resolved analyses revealed a U-shaped ecological trajectory, shifting from early Bacillus velezensis-enriched assemblages to transient dominance of lactic acid bacteria during peak thermogenesis, before returning in late fermentation to thermotolerant, spore-forming Bacillota and Actinomycetota. In parallel, biosynthetic potential was further organized into four recurrent, stage-enriched profiles, from RiPP-rich thermogenic states to mature-state assemblages enriched in PKS-, NRPS-, and terpene-related capacities, with Bacillus, Kroppenstedtia, and Saccharopolyspora constituting the principal biosynthetic reservoir. Together, this work uncovers a largely unexplored genomic and biosynthetic reservoir in high-temperature Daqu fermentation, providing a target resource for mining thermotolerant industrial enzymes, flavor-related genes, and bioactive metabolites with biotechnological potential.}, } @article {pmid42392373, year = {2026}, author = {Long, Y and Zhu, C and Wu, X and Hou, J and Zeng, J and Wu, SL}, title = {Magnetite-driven food waste conversion toward high-value medium-chain fatty acids production through promoted biological processes and electrochemical environment.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135299}, doi = {10.1016/j.biortech.2026.135299}, pmid = {42392373}, issn = {1873-2976}, abstract = {Achieving high-value valorization of food waste (FW) into medium-chain fatty acids (MCFAs) is vital for alleviating environmental pressure and advancing carbon neutrality. However, the inherent electron transfer and metabolic bottlenecks in FW bioconversion process restrains the conversion efficiency of MCFAs. Herein, the performance and comprehensive mechanisms of Fe3O4-enhanced MCFA production were comprehensively studied through integrated batch fermentation tests, bio-electrochemical characterizations, and metagenomic analysis. Results revealed that the optimal dosage of 8 g/L Fe3O4 enhanced caproate production to 3409.32 mg COD/L (a 3.7-fold increase over the control group). Notably, this dosage drove the further elongation of carbon chains, yielding high-energy-density heptanoate (C7) and caprylate (C8), thereby elevating MCFA selectivity from 5.5 % to 38.6 %. Further analysis indicated that Fe3O4 promoted all biological processes (solubilization, hydrolysis, acidogenesis, and chain elongation). Mechanically, Fe3O4 optimized the electrochemical microenvironment, enhancing conductivity and electron transport system (ETS) activity by 32.5 % and 69.1 %, respectively. The correlation-based network analysis confirmed a strong correlation (r > 0.4) between product distribution, iron cycling (Fe[2+] concentration), and conductivity. Metagenomic analysis elucidated that by enriching core functional genera like Clostridium and Sphaerochaeta and associated functional microbial genes, Fe3O4 synergistically promoted the efficient bioconversion of FW into MCFAs. This study offers new mechanistic insights into enhancing MCFA production via magnetite-regulated electron transfer, providing a robust strategy for efficient resource recovery from complex organic wastes.}, } @article {pmid42392375, year = {2026}, author = {Hou, K and Yang, B and Zhao, R and Zhang, J and Duan, Y}, title = {Dose-dependent effects of biochar on low-temperature anammox: reactor performance, community variation, and functional potential.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135296}, doi = {10.1016/j.biortech.2026.135296}, pmid = {42392375}, issn = {1873-2976}, abstract = {Low temperature is a major constraint on the practical application of anaerobic ammonium oxidation (anammox). Although biochar has been reported to improve low-temperature anammox, the effect of dosage remains insufficiently understood. In this study, mature anammox sludge was amended with 0, 3, 7, and 9 g/L bamboo-derived biochar and operated under a stepwise temperature decrease from 35 to 15°C, followed by low-temperature operation for 70 d. Reactor performance, extracellular polymeric substances (EPS), microbial community composition, and metagenomic functional potential were analyzed to clarify the dose effect of biochar. Among the tested dosages, 7 g/L biochar achieved the highest nitrogen removal efficiency (48.6%) at 15°C, which was 12.8 percentage points higher than the control value of 35.8%. Biochar-amended reactors also showed higher EPS contents than the control, and the 7 g/L group better maintained the PN/PS ratio under low-temperature stress. Community analysis indicated a higher relative abundance of Candidatus Brocadia in the biochar-amended groups, especially at 7 g/L. Metagenomic analysis further showed higher abundance of genes associated with nitrogen metabolism, carbon metabolism, and EPS-related precursor synthesis in the 7 g/L group. These results suggest that an appropriate biochar dosage can improve low-temperature anammox performance and is associated with EPS stabilization, enrichment of key functional taxa, and enhanced functional potential. This study provides guidance for biochar dosage optimization in low-temperature anammox systems.}, } @article {pmid42392574, year = {2026}, author = {Vita, AA and Brown, J and Norby-Adams, L and Ghanem, N and Weir, TL and Goldenberg, JZ}, title = {Microbial-derived polyphenol metabolites and the gut microbiota: A scoping review of clinical studies.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101700}, doi = {10.1016/j.tjnut.2026.101700}, pmid = {42392574}, issn = {1541-6100}, abstract = {BACKGROUND: Dietary (poly)phenols are widely recognized for their health-promoting properties, yet their bioactivity is largely contingent upon gut microbial metabolism. Individual differences in microbiome composition lead to variable production of microbial-derived (poly)phenol metabolites (MPMs) and thus contribute to divergent health outcomes.

OBJECTIVE: This scoping review aimed to systematically map the scope of clinical evidence reporting relationships between MPMs and gut microbiota composition and function, highlighting research gaps to guide future investigations.

METHODS: Using pre-defined search criteria, two reviewers identified human clinical studies reporting relationships between metabolite levels and microbiome outcomes.

RESULTS: Fifty-six studies were included. Evidence was frequently focused on phenolic acids (n=20), phytoestrogens (n=18), and urolithins (n=17), with relationships between microbiota and other MPMs only being reported in 1-2 studies. The majority of studies across MPM categories used 16S rRNA gene sequencing for identification of gut microbiota (n=42), among other methods, with only six studies using metagenomic shotgun sequencing, thus limiting taxonomic resolution and functional inference. Findings revealed recurrent associations between specific microbes and MPMs; while some reflected known producer taxa (e.g., Gordonibacter and urolithins), others may represent broader community-level interactions (e.g., Alistipes and equol). However, these results varied across (poly)phenol class, intervention type, and host-specific context.

CONCLUSION: This scoping review identified recurrent microbiota-MPM associations alongside major evidence gaps, including limited functional microbiome characterization and sparse investigation of several MPM classes/subclasses (e.g., resveratrol-, flavanone-, and flavan-3-ol-related MPMs). Future research using standardized, high-resolution multi-omics approaches is needed to improve identification of reproducible microbial signatures and mechanisms underlying (poly)phenol metabolism, and to link these features with functional health outcomes.}, } @article {pmid42379395, year = {2026}, author = {Mannila, E and Gómez-Gallego, C and Muluh, G and Nuotio, P and Koistinen, V and Erawijantari, P and Salminen, S and Lahti, L and Kolehmainen, M and Linderborg, KM}, title = {Oat-rich low-gluten diet modulates plasma short-chain fatty acids without significant changes in fecal microbiome or inflammatory markers - a randomized clinical trial in people with cardiometabolic risk.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101690}, doi = {10.1016/j.tjnut.2026.101690}, pmid = {42379395}, issn = {1541-6100}, abstract = {BACKGROUND: Increasingly popular low-gluten diets (LGDs) are generally low in fiber; however, it is possible to improve the LGD by using oat-based products.

OBJECTIVE: To investigate the changes in fecal microbiome, fasting plasma short-chain fatty acids (SCFAs), and inflammatory markers during a 6-week oat- or rice-rich LGD in individuals with increased cardiometabolic risk.

METHODS: The participants (n=69) were allocated into two parallel groups following a 6-week LGD with either oats or rice. Fasting plasma, stool, and dietary information were collected both at the baseline and at the end of the trial. Fecal microbial communities were analyzed by shotgun metagenomics (Novaseq X Plus) and characterized using MetaPhlAn4. Their functional potential was assessed with HUMAnN3 using the MetaCyc database. Plasma SCFAs were quantified by UHPLC-MS, and inflammatory markers were detected and quantified using a 45-cytokine panel (Olink Target). Diet-group differences over time were assessed with linear mixed-effects model.

RESULTS: Dietary information revealed high-oat and low-rice consumption at the baseline for both groups. Overall, the oat-rich LGD increased circulating SCFAs. Particularly, butyrate increased more during the oat-rich LGD than during the rice-rich LGD (ptimeXgroup=0.033). Regarding changes in the fecal microbiome, the rice group had a higher Shannon diversity index after the intervention than the oat group (ptimeXgroup=0.025), and more changes in the microbiome. This is possibly due to more substantial dietary changes from a low rice consumption compared to the habitual diet in the baseline. No significant differences between or changes within the groups in inflammatory markers were observed.

CONCLUSIONS: Changing to an oat-rich LGD increases fasting plasma SCFA concentrations without significant effects on the fecal microbiome and inflammatory markers in individuals with increased cardiometabolic risk. When there is a regular baseline consumption of oats, adopting a low-fiber rice-rich LGD may shift the microbiome towards potentially unfavorable direction.

NCT05526092, https://clinicaltrials.gov/study/NCT05526092.}, } @article {pmid42379815, year = {2026}, author = {Patel, I and Mammel, M and Gangiredla, J and Mukherjee, A}, title = {Targeted amplicon sequencing for enhanced detection of spiked Shiga toxin-producing Escherichia coli in ready-to-eat romaine lettuce: a proof-of-concept study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0102226}, doi = {10.1128/spectrum.01022-26}, pmid = {42379815}, issn = {2165-0497}, abstract = {The early and accurate detection of low-level pathogenic and indicator organisms in fresh produce is critical for preventing widespread foodborne outbreaks. Contamination of leafy greens with foodborne pathogens, such as Shiga toxin-producing Escherichia coli (STEC), is a significant public health issue, making rapid and sensitive detection methods critical for mitigating outbreaks. Although next-generation sequencing (NGS) is a powerful tool for pathogen identification, challenges remain in detecting low contamination levels in food products. Here, we demonstrate the use of a custom targeted amplicon sequencing (TAS) primer panel targeting species with food safety concerns, including known human foodborne pathogens, opportunistic pathogens, and indicator organisms related to food spoilage. Using a quasi-metagenomics approach, this proof-of-concept study demonstrates that, compared to whole-metagenomic sequencing (WMS), TAS is a rapid and sensitive NGS-based method for detecting low levels of pathogens. Ready-to-eat romaine lettuce was spiked with STEC and incubated in enrichment medium. DNA was isolated at 0.5, 5, and 6 h, and libraries were prepared for both WMS and TAS. The results indicated that TAS was more sensitive than WMS not only at detecting the pathogen at the species level but also at identifying key virulence markers stx1 and stx2. Overall, our targeted sequencing approach provides a rapid and sensitive molecular method to detect and identify foodborne pathogenic bacteria, demonstrating its potential for application in food safety.IMPORTANCEDetecting low-level pathogenic and indicator organisms is critical to prevent foodborne outbreaks. Conventional methods lack speed and sensitivity. While next-generation sequencing methods, such as whole-metagenomic sequencing (WMS), offer a broad microbial landscape view, detecting pathogens at low concentrations within complex food matrices remains challenging. To address this, a targeted amplicon sequencing (TAS) panel was designed to identify species of food safety concern and key indicator organisms. This study demonstrates that TAS is more sensitive than WMS. The application of this TAS assay provides an important bridge between qPCR and WMS by detecting and characterizing pathogens that might be present in low numbers and otherwise missed in an enrichment. TAS allows multiplexing and overcomes the critical limitation of sensitivity in complex samples, providing a robust tool for food safety surveillance. Our findings demonstrate the potential use of targeted next-generation sequencing (NGS)-based methods to mitigate the risk of foodborne illnesses.}, } @article {pmid42379825, year = {2026}, author = {Wang, S and Chen, M and Jiao, D}, title = {ZILA-SRM: a probabilistic framework with zero-inflated latent models for robust strain reconstruction from metagenomes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0410125}, doi = {10.1128/spectrum.04101-25}, pmid = {42379825}, issn = {2165-0497}, abstract = {UNLABELLED: Resolving bacterial strain diversity from shotgun metagenomic data is fundamental to understanding intra-host evolution, transmission dynamics, and phenotypic heterogeneity. However, current probabilistic approaches face a severe "identifiability limit" when disentangling highly similar genomes. Under high-noise conditions, sequencing errors, coverage overdispersion, and collinearity confound standard expectation-maximization algorithms, resulting in overfitting and spurious "ghost" strains. Here, we introduce zero-inflated latent allocation for strain reconstruction from metagenomes with adaptive sparsity regularization (ZILA-SRM) to overcome this barrier through three innovations. First, we integrate a zero-inflated Poisson mixture model to decouple "structural zeros" (true strain absence) from "sampling zeros" (stochastic dropout), addressing overdispersion in standard Poisson-based tools. Second, we impose a convex adaptive sparsity regularization penalty that leverages biological sparsity priors to shrink noise artifacts dynamically. Third, we implement a graph-theoretic refinement step using maximal clique enumeration to resolve haplotype collinearity. Benchmarking against StrainFinder and MixtureS on 702 synthetic data sets shows that ZILA-SRM achieves a 20% improvement in precision in high-complexity scenarios while maintaining over 80% recall for minor variants at 0.5% abundance. Re-analysis of deep-sequencing data from 195 Mycobacterium tuberculosis clinical samples reveals cryptic low-abundance drug-resistant variants in 12% of patients, including a minor clone carrying the rpoB S450L mutation. Furthermore, application to skin microbiome data sets further reveals a strong negative correlation between dominant Staphylococcus aureus and Staphylococcus epidermidis strains, providing genomic evidence for competitive exclusion. These findings establish ZILA-SRM as a robust tool for resolving strain-level diversity in complex metagenomes.

IMPORTANCE: Understanding microbial communities at the strain level is critical because closely related strains can differ dramatically in traits such as drug resistance, virulence, and ecological interactions. However, resolving individual strains from metagenomic sequencing data remains difficult, especially when strains are highly similar or present at low abundance. As a result, biologically meaningful diversity is often obscured or misinterpreted as noise. In this study, we introduce a new framework that improves the reliability of strain reconstruction from complex metagenomic data. By reducing false-positive strain detection while preserving sensitivity to rare variants, our approach enables more accurate characterization of microbial populations. This improved resolution reveals previously hidden subpopulations in clinical and microbiome datasets, providing clearer insights into microbial evolution, competition, and the emergence of clinically relevant traits such as antibiotic resistance.}, } @article {pmid42380482, year = {2026}, author = {Kang, X and He, P and Zhang, H and Lü, F}, title = {Virus-mediated prokaryotic community adaptation dynamics under thermal stress in municipal organic solid waste microbiomes.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10568-3}, pmid = {42380482}, issn = {2399-3642}, abstract = {Temperature influences microbial metabolic activity, which is crucial for biotechnological processes and bioproducts stabilization. However, temperature-driven responses of complex viruses and prokaryotic communities, and the modulatory role of viruses in prokaryotic community within environmental biotechnology systems, remain poorly understood. We developed a continuous thermal stress system with temperature gradients and high-resolution temporal sampling of metagenomics and metatranscriptomics, using municipal organic solid waste as a biological model. An optimized meta-omics pipeline integrating genomic potential and activity was applied to investigate the adaptive dynamics of complex prokaryotic and viral communities. Continuous thermal stress triggered stress responses in paired virus-hosts within the system. Thermal stress exerted distinct effects on temperate and virulent viruses. Viruses formed quasi-symbiotic alliances with their hosts to withstand thermal stress by integrating protein folding genes, stress response, and metabolic function genes, shaping host adaptability under thermal pressure. Equipped with multiple defense and counter-defense systems, viruses accelerated the accumulation of beneficial mutations under thermal stress, enabling them to escape host immunity and intensify competition with prokaryotic communities. This study demonstrates how viruses accelerated both the restructuring and adaptive responses of prokaryotic communities under thermal stress, advancing our understanding of phage-based therapeutic strategies in temperature-variable engineering applications.}, } @article {pmid42381037, year = {2026}, author = {Garcia-Castillo, L and Ferrero, G and Blaževitš, O and Francescato, G and Eliass, AT and Cortez, NE and Beltrà, M and Tarallo, S and Pardini, B and Costelli, P and Naccarati, A and Longo, VD and Penna, F}, title = {Fasting-mimicking diet counteracts gut microbial dysbiosis in experimental lynch syndrome.}, journal = {Cancer & metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40170-026-00446-1}, pmid = {42381037}, issn = {2049-3002}, abstract = {The development of colorectal cancer (CRC) is largely influenced by hereditary factors, with up to one-third of cases linked to genetic predisposition. In parallel, environmental factors such as diet and intestinal microbiota play a significant role. Lynch syndrome (LS), the most common form of hereditary CRC, is due to mutations in DNA mismatch repair genes. Diet interventions such as calorie restriction (CR) can modify the course of the disease, altering nutrient supply and promoting beneficial microbial populations. Fasting-mimicking diets (FMD) are plant-based CR regimens that showed promise in modulating the gut microbiota and suppressing CRC progression in pre-clinical ectopic cancer models. In this study, Villin-Cre/Msh2-floxed (VCM) mice, modelling LS, were subjected to periodic FMD cycles for 10 months. FMD regimen influenced animal weight in a sexually dimorphic manner, stably reducing animal body weight only in males. Moreover, shotgun metagenomic sequencing revealed that FMD mitigated the dysbiotic longitudinal changes associated with cancer onset, preserving beneficial species, such as Lactobacillus johnsonii, and reducing adverse species, such as Escherichia coli. Metabolic pathway analysis also showed significant differences, with FMD preventing the upregulation of pathways involved in amino acid and nucleotide synthesis, potentially promoting tumour growth. Overall, the findings suggest that periodic FMD may result useful in a multimodal approach for LS management, counteracting gut microbiota alterations.}, } @article {pmid42381048, year = {2026}, author = {Porcel Sanchis, D and Pola, M and Engelberts, JP and Guerra-Font, O and Messer, L and Alberola-Mora, I and Escobar Sáez, L and Pérez Gómez, N and Portolés Campo, Á and Valero-Tebar, J and Naya Garmendia, LM and Preciado Barahona, JC and Gil García, R and Arnau, V and McIlroy, SJ and Džunková, M}, title = {Museomics reveals uncultured symbionts with biosynthetic potential in nudibranchs.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02456-z}, pmid = {42381048}, issn = {2049-2618}, abstract = {BACKGROUND: Museum specimens are widely used for PCR-based pathogen detection, yet their potential for metagenomic discovery of beneficial microbes remains underexplored, largely due to difficulties in distinguishing true symbionts from contaminants. Here, we use metagenomics of museum specimens to uncover symbioses in endangered or difficult-to-collect animals, such as nudibranchs. To date, Doriopsilla is the only nudibranch demonstrated to harbor an uncultured symbiont involved in chemical defense, leaving it unclear whether comparable associations occur in other nudibranchs. We hypothesized that bona fide symbionts should belong to abundant, uncultured lineages consistently present across individuals of the same host taxon collected across space and time.

RESULTS: Using ethanol-preserved specimens archived for up to 30 years, we doubled the number of available nudibranch microbiome datasets and found that dominant uncultured symbionts are rare, with most nudibranchs likely relying on alternative chemical defense mechanisms. An exception were Polycera and Felimare that contained two previously unknown symbionts, Candidatus Polyceribacter and Candidatus Felimaribacter, from distinct uncultured orders that are globally rare in marine metagenomes. These symbionts encode diverse biosynthetic gene clusters exhibiting strain- and species-level microdiversity consistent with metabolites previously reported from their hosts. Their restricted host distribution, phylogenetic distinctiveness, and phylogenetic similarity to symbionts of sponges or corals that are not nudibranch prey, support long-term evolutionary specialization and functional convergence. Fine-scale diversification further suggests host-driven microbial adaptation following symbiosis establishment.

CONCLUSIONS: Overall, this study establishes museomics as a robust framework for symbiosis research and advances understanding of the evolutionary and chemical ecology of host-microbe interactions in rare marine invertebrates. Video Abstract.}, } @article {pmid42381185, year = {2026}, author = {Mouanes-Abelin, J and Pomares, C and Montoya, JG and Pondrom, M and Maria, L and Zimmer, AJ and Gomez, CA}, title = {Toxoplasmosis Beyond Transplantation: Diagnostic and Prevention Challenges in a Patient Receiving Targeted Immunomodulators.}, journal = {Transplant infectious disease : an official journal of the Transplantation Society}, volume = {}, number = {}, pages = {e70263}, doi = {10.1111/tid.70263}, pmid = {42381185}, issn = {1399-3062}, abstract = {Toxoplasmosis has long been recognized as a serious complication in immunocompromised host, particularly those with advanced HIV/AIDS, hematopoietic stem-cell transplantation (HSCT), solid-organ transplant (SOT), and hematological malignancies. The rapid expansion of targeted immunomodulators, including chimeric antigen receptor T-cell (CAR-T) therapies, monoclonal antibodies, and small-molecule inhibitors, is creating new at-risk populations beyond traditional transplant settings. We present a 9-year-old boy with high-risk B-cell acute lymphoblastic leukemia (B-ALL), who developed prolonged fever and macrophage activation syndrome (MAS). After an extensive unrevealing workup, disseminated acute toxoplasmosis was identified incidentally on bone marrow aspirate via morphologic identification of tachyzoites and confirmed by Toxoplasma gondii PCR. This case exemplifies the emerging threat of toxoplasmosis in non-transplant immunomodulated hosts and supports three core mitigation strategies. First, baseline Toxoplasma IgG and IgM serology should be obtained in all patients initiating targeted immunotherapy, recognizing that B-cell depletion or hypogammaglobulinemia may render IgG unreliable, and that IgM may be falsely negative, delayed, or persistently positive in immunocompromised individuals. Second, targeted PCR from clinically relevant compartments or metagenomic next-generation sequencing when conventional diagnostics is unrevealing should be applied early. Third, prevention requires a bundled approach: baseline screening, patient education for seronegative individuals, and trimethoprim-sulfamethoxazole prophylaxis with or without serial qPCR monitoring for seropositive patients. Toxoplasmosis is no longer a transplant-exclusive concern. As targeted immunomodulators reshape practice across rheumatology, oncology, neurology, and autoimmune disease, infectious diseases specialists must lead efforts to raise cross-specialty awareness, establish guidelines, and build registries to define the true burden of toxoplasmosis in these growing populations.}, } @article {pmid42381379, year = {2026}, author = {Vaaben, TH and Lützhøft, DO and Hedin, KA and Ahonen, L and Vazquez-Uribe, R and Sommer, MOA}, title = {Multi-omics analysis of saccharomyces boulardii supplementation reveals coordinated microbiome, metabolic, and immune signaling changes accompanying tumor suppression.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2690687}, doi = {10.1080/19490976.2026.2690687}, pmid = {42381379}, issn = {1949-0984}, mesh = {Animals ; *Probiotics/administration & dosage ; Multiomics ; *Saccharomyces boulardii/physiology ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Signal Transduction ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/immunology/microbiology/metabolism/therapy ; Mice ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {The gut microbiome shapes cancer progression and treatment responses, yet scalable microbiome-targeted interventions remain limited. We screened commercial probiotics for activation of the host aryl hydrocarbon receptor (AhR) and identified the yeast Saccharomyces boulardii as a consistent AhR activator. In an immunocompetent syngeneic colorectal cancer model, daily oral gavage of S. boulardii slowed growth of established subcutaneous tumors without detectable tumor colonization. Integrated profiling of the gut microbiome, circulating metabolites, cytokines, and tumor transcriptomes revealed a coordinated systemic response. S. boulardii increased microbial diversity and functionally rebalanced the gut microbiota, enriching taxa with lower genome-encoded biosynthetic autonomy. These changes were accompanied by elevated plasma levels of several indole metabolites, including the AhR agonists 5-hydroxyindole-3-acetic acid (5-HIAA) and indole-3-propionic acid (IPA). Targeted LC-MS/MS showed that S. boulardii can produce 5-HIAA under culture conditions, whereas IPA was not detected, suggesting that increased plasma levels of these metabolites may arise through a combination of probiotic activity and broader microbiome-associated processes. Circulating IL-17A and CTLA-4 were reduced, and tumors exhibited downregulation of programs linked to invasion, inflammation, and KRAS signaling. Multi-omics integration showed strong covariation across microbial, metabolic, immune signaling, and tumor compartments, highlighting coordinated cross-compartment responses during S. boulardii-associated tumor suppression.}, } @article {pmid42381607, year = {2026}, author = {Lv, JL and Zhu, MQ and Gao, T and Pan, Y and Yu, HQ and Min, D and Xiong, YJ and Liu, DF}, title = {Profiling Active Low-Abundance Microbes in As/Sb-Contaminated Soils via d-Amino Acid-Based In Situ Labeling.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c07045}, pmid = {42381607}, issn = {1520-5851}, abstract = {Soil microbial communities play a pivotal ecological role in contaminated environments. However, conventional metagenomic approaches struggle to distinguish between "potential function holders" and "in situ metabolically active executors". Here, we employed a method combining fluorescent d-amino acid labeling, fluorescence-activated cell sorting, and metagenomics (FDAA-FACS-Metagenomics) to capture and profile active microbes in complex soils. The secondary addition of As(V) and Sb(V) enhanced the community's reductive activity toward these metalloids, reshaping the active assemblages. Clostridium was markedly enriched, and several low-abundance members were activated as true executors of the reduction process. MAGs recovered via FDAA-FACS revealed an active core community with functional partitioning: some taxa participated directly in As(V)/Sb(V) reduction, while others contributed to community stability through tolerance and metabolic support. Notably, a Desulfitobacteriaceae genome (MAG29) harbored both arrAB and anrAB gene clusters, a complete Wood-Ljungdahl carbon fixation pathway, and nitrogen fixation genes. These genomic features suggest the potential for a multifunctional metabolic lifestyle involving metalloid reduction, carbon fixation, and nitrogen transformation. Such metabolic versatility may enable MAG29 to contribute to coupled carbon-nitrogen cycling and metalloid transformation under contaminated environmental conditions. These findings emphasize the important ecological roles of rare, metabolically active microbes in metalloid transformation and soil ecosystem functioning.}, } @article {pmid42381665, year = {2026}, author = {Flach, CF and Berglund, F and Osena, G and Huijbers, PMC and Larsson, DGJ}, title = {Sewage surveillance for assessing clinical antibiotic resistance prevalence: Combining metagenomic and phenotypic data.}, journal = {One health (Amsterdam, Netherlands)}, volume = {23}, number = {}, pages = {101485}, pmid = {42381665}, issn = {2352-7714}, abstract = {Surveillance of antibiotic resistance in clinical isolates is a cornerstone for the management of bacterial infections but is limited in large parts of the world, often due to lack of resources. Sewage surveillance has been proposed as a promising, resource-efficient complement to the traditional surveillance approach based on samples from many individual patients. Both phenotypic data on resistance in sewage isolates and abundance of antibiotic resistance genes in sewage have been shown to correlate with resistance prevalence in clinical isolates. Here, we aimed to directly compare and combine an isolate-based and a gene-based sewage surveillance approach to evaluate what best can reflect clinical resistance rates. The two approaches, based on susceptibility testing of collected E. coli isolates and metagenomic sequencing, respectively, were applied to municipal sewage samples collected in ten European countries. The data generated was related to available data on resistance to aminopenicillins, fluoroquinolones, third generation cephalosporins and aminoglycosides prevalence in clinical E. coli isolates using beta regression models. None of the tested individual predictors were superior across all four investigated classes of antibiotics. For modelling of aminopenicillin resistance, a clearly higher R[2] value was obtained when isolate-based and gene-based data was combined as predictors, also after adjusting for the number of included variables. We conclude that there could be a value of including both isolate- and gene-based sewage data for predictions of resistance rates in clinical isolates, while emphasizing the value of linking predictors to specific species and classes of antibiotics.}, } @article {pmid42381921, year = {2026}, author = {Salah, R and AbdElaal, KR and Ghonaim, L and Awe, OI and Moustafa, A}, title = {DeepTaxa: a hybrid CNN-BERT framework for 16S rRNA taxonomic classification.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag166}, pmid = {42381921}, issn = {2635-0041}, abstract = {MOTIVATION: Accurate species-level classification of prokaryotic 16S rRNA sequences remains difficult: existing tools rely on exact alignment, k-mer heuristics, or phylogenetic placement and are limited by incomplete reference databases. Deep learning approaches in microbial genomics have focused largely on whole-genome metagenomics, leaving 16S taxonomy under-supported.

RESULTS: We present DeepTaxa, a hybrid CNN-BERT framework that pairs a multiscale CNN with a transformer trained from scratch on the DNABERT-2 BPE vocabulary, producing parallel rank-specific predictions across the seven Linnean ranks. On the Greengenes2 2024.09 test set, DeepTaxa achieves species-level accuracy of 92.96% and F1 of 0.9212 (3-seed mean; cross-seed standard deviation ≤ 0.0008 F1 at every rank), with F1 above 0.99 from domain through class and a species-level expected calibration error of 0.0242. DeepTaxa exceeds DADA2 (90.05%) and QIIME 2 (85.01%) at the species rank on the same held-out test set, with larger gains over the k-mer-based classifiers SINTAX and Kraken 2. Performance degrades smoothly with decreasing training-set similarity (species F1 from 0.95 to 0.45), and a dedicated V3-V4 amplicon checkpoint reaches 87.55% species accuracy from an approximately 420 bp window.

Source code, trained checkpoints for full-length 16S and V3-V4 amplicons, curated datasets, and reproducible workflows are publicly available at github.com/systems-genomics-lab/deeptaxa and huggingface.co/systems-genomics-lab/deeptaxa.}, } @article {pmid42382111, year = {2026}, author = {Sachula, W and Huimin, L and Yaxing, Z and Ding, Y and Shangxiong, Z and Shengli, L and Haizhou, S and Chunhua, Z}, title = {An integrative multi-omics investigation into the influence of forage type on the volatile flavor profile of Ujumqin sheep mutton.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1856240}, pmid = {42382111}, issn = {2297-1769}, abstract = {China ranks among the leading producers and consumers of mutton globally and the development of nutritional strategies to improve meat quality and sensory attributes. This study investigated the effect of three high-quality forages, i.e., alfalfa hay (ALFA), Leymus chinensis hay (LEYM) and oat hay (OATS) compared to corn stalks-based control diet (CORN) on rumen microbiota, metabolomics profiles, and muscle volatile flavor compounds in lambs through a multi-omics integration approach. Forty male lambs were randomly allocated into four dietary groups (n = 10/group) and fed a concentrated forage supplement for 91 days. From each group, six lambs (n = 6/group; totla 24) were slaughtered. Rumen fluid and longissimus dorsi muscle samples were collected for metagenomics, untargeted metabolomics, and volatile flavor analysis. Differential microbial taxa were identified using LEfSe analysis, followed by integrated Pearson correlation and MetoOrigin analysis to link microbiota, metabolites, and metabolic pathways. Associations with muscle volatile flavor compounds were also assessed. LEfSe analysis identified 4, 3, and 7 differentially abundant rumen microbial taxa in the ALFA, LEYM and OATS groups, respectively, compared to CORN. Integrated analysis showed these taxa correlated with 4, 9 and 11 rumen metabolites via 3, 11 and 7 microbial or host-microbial co-metabolic routes, respectively. These metabolic changes were strongly associated to alterations in muscle volatile flavor compounds. Particularly, the ALFA diet increased volatile compounds associated with fresh, grassy, floral, and citrus-like odors reduced mutton-related Pyrazine (2,5-dimethyl-). The LEYM diet reduced Pentaborane(9) and Pyrazine, which are associated with undesirable mutton like odors. The OATS diet increased 2-Nonanone and Phenylethyl Alcohol (fruity and floral smells), while suppressing n-Decanoic acid and n-Octanoic acid (associated with characteristic mutton aroma). These results showed that high-quality forages improve the mutton flavor by regulating the rumen micro-ecological network and associated metabolic pathways along the forage-microbiota-metabolites-muscle flavor axis. These findings provide a theoretical foundation for precise nutritional interventions aimed at enhancing meat quality in lambs.}, } @article {pmid42382141, year = {2026}, author = {Chigwada, AD and Tekere, M}, title = {Archaea-driven bioremediation of polyolefins and polyesters in extreme environments.}, journal = {Biodesign research}, volume = {8}, number = {3}, pages = {100092}, pmid = {42382141}, issn = {2693-1257}, abstract = {Global plastic production surpassed 436 million metric tonnes in 2023, with polyolefins, polyethylene and polypropylene, and polyesters, polyethylene terephthalate and polybutylene adipate terephthalate dominating the persistent fraction. In extreme environments, these recalcitrant polymers accumulate rapidly: hadal-trench sediments contain microplastic abundances of 71.1 items per kilogram dry weight, while bottom waters reach 2.06-13.51 particles per litre. Abiotic degradation is severely limited by hydrostatic pressure, hypersalinity, low temperature, and anaerobiosis. Although bacterial and fungal pathways have received primary attention, archaea adapted to polyextreme conditions represent an underexplored resource. Landmark discoveries include PET46, a lid-containing feruloyl esterase from uncultured Candidatus Bathyarchaeota in Guaymas Basin deep-sea sediments that hydrolyses semi-crystalline polyethylene terephthalate powder at rates comparable to established bacterial PETases while outperforming them on oligomers. Subsequent metagenomic prospecting identified GuaPA, a distinct Bathyarchaeia-derived PETase capable of film depolymerisation. Deep-sea plastispheres, hypersaline basins, and extraterrestrial analog sites further reveal archaeal colonisation and metabolic versatility. This review synthesises metagenomic, enzymatic, and community-level evidence, critically evaluates archaeal advantages relative to bacteria and fungi, addresses persistent gaps, including limited polyolefin mineralisation and cultivation bias, and outlines priorities for enzyme engineering and consortia design. The work advances sustainable bioremediation strategies aligned with climate-action goals and circular-economy frameworks in extreme and space environments.}, } @article {pmid42382346, year = {2026}, author = {He, B and Xiao, Z and Zou, L and Wei, J and Xiang, Z and Sang, F and Guo, X}, title = {Unveiling the unique gut microbial signatures in colorectal adenomas: establishment and validation of a cross-kingdom microbiome predictive model.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1854806}, pmid = {42382346}, issn = {1664-302X}, abstract = {BACKGROUND: Colorectal adenoma (CA), the main precancerous lesion of colorectal cancer (CRC), originates in approximately 85-90% of CRC cases. With increasing demands for early diagnosis and treatment, gut microbiome research has become a forefront area. While numerous studies have shown that gut bacteria are closely related to the development of colorectal adenomas and cancer, research on viruses, archaea, and fungi is limited.

METHODS: From January 2019 to January 2024, this study collected 296 fecal samples from multiple centers and performed metagenomic analysis using shotgun sequencing. Principal coordinate analysis (PCoA) was conducted based on Bray-Curtis distance at the species level, α-diversity was calculated, and LEfSe analysis identified differential microorganisms. A random forest model was developed to distinguish adenoma patients from healthy individuals, with performance evaluated through internal validation using Bootstrap sampling and external validation with an independent cohort.

FINDINGS: Significant differences in the relative abundance of certain bacteria (e.g., Phocaeicola_vulgatus and Prevotella_copri), fungi (Candida_albicans), archaea (Methanobrevibacter_oralis), and viruses (Streptococcus satellite phage Javan301) were observed in adenoma patients. Spearman correlation analysis revealed complex network relationships among these microorganisms. The prediction model achieved a mean AUC of 0.80 ± 0.05 and an external validation AUC of 0.75, demonstrating stability and generalizability.

CONCLUSION: This study shows significant cross-kingdom microbial signatures in colorectal adenoma patients, providing potential for developing new preventive and therapeutic methods. The predictive model, based on these differential microorganisms, exhibits robust and promising classification performance, offering potential for early adenoma detection.}, } @article {pmid42382358, year = {2026}, author = {Mengjia, C and Bujiang, W and Honghui, C and Qiying, H and Haojun, S}, title = {Biliary tract microbes and common bile duct stones: current status and prospects.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1818256}, pmid = {42382358}, issn = {1664-302X}, abstract = {Common bile duct stones is a common digestive system disease, and about 5%-30% of patients with cholelithiasis are complicated with common bile duct stones. It poses significant challenges to clinical diagnosis and treatment. Although its occurrence is related to traditional factors such as abnormal bile composition and biliary dynamics disorders, the exact pathogenesis has not been fully clarified. In recent years, with the rapid development of high-throughput sequencing and metagenomics and other microbiome technologies, researchers have begun to pay attention to the role of biliary microbiota in the formation of common bile duct stones. More and more evidence indicates that the biliary tract microbes may has been associated with the occurrence and development of stones. This review firstly examines the literature implicating between biliary microorganisms and different types of common bile duct stones. We discuss the various mechanisms of action of biliary tract microorganisms in the occurrence of common bile duct stones. We also evaluated the specific value of microbial markers for diagnostic typing and prediction of recurrence.}, } @article {pmid42382773, year = {2026}, author = {Zhang, D and Song, Y and Bai, Y and Yan, J and Shen, R}, title = {Autoimmune GFAP astrocytopathy with eosinophils on cerebrospinal fluid cytology and isolated spinal cord lesions on MRI: a case report.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1865920}, pmid = {42382773}, issn = {1664-3224}, mesh = {Humans ; Female ; Adult ; *Glial Fibrillary Acidic Protein/immunology ; Magnetic Resonance Imaging ; *Astrocytes/immunology/pathology ; *Spinal Cord/pathology/diagnostic imaging/immunology ; *Eosinophils/immunology/pathology ; Biomarkers ; Autoantibodies/immunology ; }, abstract = {BACKGROUND: Autoimmune glial fibrillary acidic protein (GFAP) astrocytopathy is an autoimmune inflammatory disorder of the central nervous system associated with GFAP-IgG. It most commonly presents as meningoencephalitis, myelitis, or meningoencephalomyelitis. Although MRI abnormalities in the brain and spinal cord are common, isolated spinal cord lesions without corresponding brain MRI abnormalities are uncommon and may pose a diagnostic challenge. Eosinophils identified on cerebrospinal fluid cytology have rarely been reported in this disorder.

CASE PRESENTATION: A 31-year-old woman presented with fever, headache, urinary retention, and meningeal irritation signs. Despite these findings, brain magnetic resonance imaging (MRI) was unremarkable, whereas spinal MRI revealed discontinuous patchy long-segment intramedullary lesions in the thoracic cord. Cerebrospinal fluid (CSF) analysis showed elevated opening pressure, pleocytosis, increased protein, and 10% eosinophils on cytological examination. Infectious studies, including CSF culture and metagenomic next-generation sequencing, were negative. Serum and CSF antibodies against aquaporin-4, myelin oligodendrocyte glycoprotein, and myelin basic protein were negative, whereas CSF GFAP-IgG was positive at a titer of 1:32, while serum GFAP-IgG was negative. Following high-dose intravenous methylprednisolone and an oral prednisone taper, the patient showed marked clinical, CSF, and radiological improvement, with complete resolution of thoracic cord lesions on follow-up MRI.

CONCLUSION: Isolated spinal cord lesions on MRI may represent an important clue to autoimmune GFAP astrocytopathy and should prompt consideration of this diagnosis even in the absence of brain MRI abnormalities. The presence of eosinophils on cerebrospinal fluid cytology may further suggest a distinct inflammatory profile and offer insight into the pathophysiology of the disease.}, } @article {pmid42382960, year = {2026}, author = {Zhang, WJ and Yang, Z and She, JQ and Wu, HL and Xia, ZY and Zhang, D and Suo, LG and Pan, Z and Zhang, Y and Wang, HZ and Hong, J and Zhang, C}, title = {Metagenomic analysis of ocular microbiome in aqueous humor from myopia, cataract, primary open angle glaucoma and Posner-Schlossman syndrome.}, journal = {International journal of ophthalmology}, volume = {19}, number = {7}, pages = {1235-1248}, pmid = {42382960}, issn = {2222-3959}, abstract = {AIM: To characterize the composition and functional features of the aqueous humor microbiome in common ocular diseases, including myopia, cataract, primary open angle glaucoma (POAG), and Posner-Schlossman syndrome (PSS).

METHODS: We performed metagenomic sequencing on 176 aqueous humor samples from patients with cataract (n=37), POAG (n=66), PSS (n=35), and myopia patients (n=38, as controls). Taxonomic profiling, functional annotation, and diversity analyses were conducted to characterize microbial communities, with adjustments for age and gender where appropriate. Associations between microbial features and clinical parameters were evaluated using correlation analyses.

RESULTS: We identified 6635 bacterial, 141 archaeal, 96 eukaryotic, and 108 viral operational taxonomic units (OTUs) in the aqueous humor. The microbiome was dominated by Actinomycetota and Pseudomonadota at the phylum level. Compared to myopia controls, POAG and PSS patients showed significantly reduced alpha diversity after age adjustment (P<0.05), whereas cataract patients showed no significant difference. Additionally, we identified disease-specific microbial signatures including enrichment of Cytomegalovirus (CMV) in PSS. Functional analysis revealed enrichment of distinct metabolic pathways. Finally, correlations were observed between microbiota/pathway abundance and clinical phenotype, though none remained significant after multiple testing correction.

CONCLUSION: This study provides a preliminary characterization of the aqueous humor microbiome in patients with POAG, PSS, cataract, and myopia controls. The identified microbial signatures and functional pathways offer new insights into potential microbiome-mediated mechanisms in ocular pathophysiology and may inform future diagnostic and therapeutic strategies.}, } @article {pmid42383698, year = {2026}, author = {Briggs, FB and Litwiler, J and Montini, F and Fereidan Esfahani, M and Sagen, J and McCauley, JL and Nelson, F and Gregory, S and Brambilla, R and Trapl, ES and Cooke Bailey, JN and Schwerdtfeger, LA and Cox, L and Weiner, H and Tobin, WO}, title = {Tobacco smoking disrupts bile acid and tryptophan metabolism in multiple sclerosis.}, journal = {Multiple sclerosis (Houndmills, Basingstoke, England)}, volume = {}, number = {}, pages = {13524585261454207}, doi = {10.1177/13524585261454207}, pmid = {42383698}, issn = {1477-0970}, abstract = {BACKGROUND: Smokers with multiple sclerosis (MS) experience worse disease, yet underlying mechanisms remain unknown. Smoking disrupts bile acid and tryptophan metabolism in non-MS populations; both pathways involve host-microbiome co-metabolism and have been linked to MS.

OBJECTIVE: Determine whether smoking perturbs these metabolic pathways in MS and whether such alterations statistically mediate smoking's effect on MS severity.

METHODS: We analyzed serum bile acid, tryptophan, and tobacco-related metabolites across four independent MS cohorts (N = 266) using discovery-replication analyses. Mixed-effects regression assessed replicating associations with current smoking and nicotine exposure. Mediation analyses tested if replicating metabolites were potential mediators between smoking and MS severity. Hypothesis-generating metagenomic analyses explored smoking-associated gut-microbial shifts and metabolite correlations.

RESULTS: Current smokers and nicotine-exposed MS subjects had reductions in bile acids and tryptophan metabolites, notably indolepropionate, a neuroprotective, anti-inflammatory gut-microbial metabolite. Lower indolepropionate statistically mediated ~20% of smoking's adverse effect on MS severity. Metagenomic analyses identified potential smoking-enriched MS-linked taxa, and that indolepropionate broadly co-occurs with microbial networks (e.g. Lachnoclostridium appeared inversely associated with indolepropionate in smokers with MS).

CONCLUSION: Tobacco exposure disrupts host-microbiome tryptophan and bile acid metabolism in persons with multiple sclerosis, with indolepropionate depletion partially mediating disease severity, highlighting a potential mechanistic pathway warranting further investigation in MS smokers.}, } @article {pmid42384485, year = {2026}, author = {Crouch, AL and Rambeau, M and Li-Pook-Than, J and Snyder, MP and Henderson, JA and Yracheta, JM and Anderson, MZ}, title = {The gut microbiome of a Northern Plains tribe is in transition between global Indigenous and industrialized populations.}, journal = {Cell reports}, volume = {45}, number = {7}, pages = {116334}, doi = {10.1016/j.celrep.2025.116334}, pmid = {42384485}, issn = {2211-1247}, abstract = {The human gut is shaped by environmental factors, producing distinct microbial communities. Indigenous individuals practicing traditional lifestyles often harbor more diverse microbiota, with taxa often absent in industrialized people. However, little engagement has occurred with American Indian communities in North America who experienced forced relocation and dietary programs during colonization. Here, shotgun metagenomics profiled the gut microbiome of people from a Northern Plains tribe (NPT) reservation in comparison to 12 global populations engaged in traditional, agrarian, or industrialized lifestyles. Analysis of the 532 samples revealed that the NPT microbiota exhibited greater bacterial and archaeal diversity than industrialized populations but reduced diversity compared to global traditional and agrarian populations. Relative to the general United States population, NPT microbiomes encoded more virulence factor and microbial defense genes and fewer CAZyme-encoding genes. These findings suggest that the NPT gut microbiome is in transition between lifestyles associated with global Indigenous and industrialized populations.}, } @article {pmid42384916, year = {2026}, author = {Kok, CR and Mulakken, NJ and Thissen, JB and Martí, JM and Lee, R and Trainer, JB and Goncalves, AR and Ranganathan, H and Avila-Herrera, A and Jaing, CJ and Be, NA}, title = {Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag422}, pmid = {42384916}, issn = {1367-4811}, abstract = {SUMMARY: Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13,897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on January 04, 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health.

AVAILABILITY: Data is available at https://gdo-meta2db.llnl.gov/ and https://zenodo.org/records/17315984.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid42384962, year = {2026}, author = {Narayanan, AK and Philosof, A and Murali, R and Connon, SA and Wegener, G and Orphan, VJ}, title = {Viral communities from long-term anaerobic alkane-oxidizing enrichments encode predicted cell surface adhesion functions.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag172}, pmid = {42384962}, issn = {1751-7370}, abstract = {The anaerobic oxidation of methane and higher C2+ alkanes is a dominant metabolism within hydrocarbon-rich deep-sea sediments and is largely mediated by alkane-oxidizing archaea in metabolic partnership with syntrophic sulfate-reducing bacteria. Although these processes fuel a diverse ecosystem, the viral component of alkane-rich sediments has historically been overlooked. We analyzed the viral assemblages in long-term sediment-free enrichments of alkane-degrading organisms and found that abiotic factors such as incubation temperature had a greater correlation with community composition than with the phylogenetic patterns among individual viral species. No auxiliary metabolic genes (AMGs) directly involved in hydrocarbon oxidation or sulfate reduction were found, but the presence of candidate AMGs involved in heme synthesis pathways common in methane oxidizers hints at a possible viral impact on alkane degradation. We also examined potential host-virus pairs using CRISPR- and tRNA-based methods. Lastly, we identified the presence of nosD-like proteins in viruses from sediment-derived systems that are not present in water column datasets; their distribution, genomic context, and lack of canonical nosD characteristics suggest an alternate adhesion-related role in sediment communities. The number of new viruses obtained from these multi-year enrichment cultures and their potential roles in mediating host physiology illustrate the importance of studying the viral component in laboratory and environmental systems.}, } @article {pmid42385223, year = {2026}, author = {Haque, ME and Rahman, MS and Sultana, M and Begum, A}, title = {Seasonal Restructuring of Microbial Communities and Resistomes in the Shitalakshya River, Bangladesh Revealed by Shotgun Metagenomics.}, journal = {MicrobiologyOpen}, volume = {15}, number = {4}, pages = {e70359}, doi = {10.1002/mbo3.70359}, pmid = {42385223}, issn = {2045-8827}, mesh = {*Rivers/microbiology/chemistry ; *Metagenomics ; Seasons ; Bangladesh ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Water Quality ; Shotgun Sequencing ; }, abstract = {Urban rivers supplying drinking water face mounting pollution and AMR threats. We combined shotgun metagenomics with physicochemical analysis to investigate microbial community and resistome dynamics in Bangladesh's Shitalakshya River, a drinking water source under increasing pollution pressure, during early and peak dry seasons. Peak dry season water quality deteriorated markedly, characterized by hypoxia and elevated nutrient and organic carbon levels, which drove pronounced restructuring of the river microbiome. A distinct shift occurred from Myroides dominance toward a more diverse assemblage enriched in pollution-tolerant and opportunistic genera, notably Comamonas, Brevundimonas, Tissierella, and Aeromonas. Metagenomic profiling revealed a diverse resistome encompassing antibiotic, metal, and biocide resistance genes. Although overall antibiotic resistance gene abundance declined slightly, metal resistance genes increased more than twofold, with strong enrichment of mercury resistance determinants such as merA. Concurrent increases in multidrug efflux pump genes suggested potential co-selection driven by metal and chemical stressors. These findings indicate that dry-season pollutant concentration reshapes both microbial communities and resistance profiles through non-antibiotic selective pressures. Despite limited sampling, this study provides a baseline metagenomic snapshot of antimicrobial resistance dynamics in a climate-stressed urban river system, offering vital insights for pollution abatement and the safeguarding of drinking water safety.}, } @article {pmid42385456, year = {2026}, author = {Hodžić, A and Cizek, V and Kunert, M and Berry, D and Collingro, A}, title = {Qualitative profiling of the gut-specific chlamydial population in Ixodes ricinus ticks.}, journal = {Ticks and tick-borne diseases}, volume = {17}, number = {4}, pages = {102679}, doi = {10.1016/j.ttbdis.2026.102679}, pmid = {42385456}, issn = {1877-9603}, abstract = {Members of the phylum Chlamydiota are obligate intracellular bacteria increasingly recognized across a wide range of arthropod hosts, including ticks. In this study, we investigated the diversity and distribution of chlamydiae in Ixodes ricinus ticks and their potential association with Lyme borreliosis spirochetes. A total of 250 questing nymphal and female I. ricinus ticks were collected from three recreational sites in Vienna, Austria. Individual tick guts were screened for chlamydiae using pan-Chlamydiota PCR assays targeting the 16S rRNA gene, followed by sequencing for taxonomic identification. The presence and abundance of Borrelia burgdorferi sensu lato were quantified by specific qPCR to evaluate potential co-occurrence patterns. Chlamydiota DNA was detected in ticks from all investigated areas, with prevalence varying according to geography and developmental stage. Phylogenetic analyzes revealed high chlamydial diversity within the gut microbiome, predominantly comprising members of the metagenomic family MCF-D, followed by Parachlamydiaceae, Endochlamydiaceae, and Parasimkaniaceae. A positive, albeit not statistically significant, association between Chlamydiota and Borrelia was also observed. These findings indicate that the I. ricinus gut microbiome harbours a diverse assemblage of chlamydiae, suggesting potential ecological and functional relevance. Overall, our study highlights the importance of tissue-specific, single-tick analyzes for elucidating microbiome complexity and advances current understanding of Chlamydiota diversity in the tick vector. Further experimental and multi-omics studies are warranted to elucidate the biological roles of these bacteria in tick physiology and pathogen infection dynamics.}, } @article {pmid42385542, year = {2026}, author = {Zhong, X and Sun, Z and Wu, H and Li, E and Fang, G}, title = {Response of soil nitrogen-cycling functional genes and their associations to nitrogen enrichment in a typical subtropical estuary (Min River), Southeast China.}, journal = {Marine pollution bulletin}, volume = {232}, number = {}, pages = {120078}, doi = {10.1016/j.marpolbul.2026.120078}, pmid = {42385542}, issn = {1879-3363}, abstract = {Soil N-cycling functional genes are easily modified by environmental changes, but insufficient information is available regarding the response of their elaborate associations to nitrogen (N) enrichment in estuarine marsh ecosystem. In this study, a field experiment with four N enrichment levels (NN, 0.0 g N m[-2] yr[-1]; NL, 37.5 g N m[-2] yr[-1]; NM, 50.0 g N m[-2] yr[-1]; and NH, 100.0 g N m[-2] yr[-1]) was conducted in a typical Cyperus malaccensis marsh in the Min River estuary of southeastern China. After 28 and 40 months of sustained N additions (represented by T28 and T40 periods, respectively), the potential impacts of N enrichment on soil N-cycling functional genes and their associations were investigated by metagenomic sequencing. Results showed that although the composition of functional microbial communities showed causality with N enrichment levels, its variation was primarily driven by N-enriched duration as evidenced by the higher interpretability (64.7%). With prolonged the experiment, the diversity of soil N-cycling microbial communities dropped markedly while their richness showed no statistically significant alteration. Within each sampling period, the relative abundances of functional genes involved in organic N metabolism (ONM, glnB, GDH2 and GLT1), assimilatory nitrate reduction (ANRA, narB, nirA, NR and NIT-6), denitrification (nirS, norC and napB), N fixation (nifK/D, vnfH/K/G and anfG), dissimilatory nitrate reduction (DNRA, nrfA and nirB/D), N transport (nrtC/B) and nitrification (pmoB/C-amoB/C) significantly increased with increasing N additions. Compared with the T28 period, the relative abundances of genes involved in ONM (GDH2 and K00261_gdhA), denitrification (narI and nirS), N fixation (nifD/H and vnf/H/K) and N transport (NRT2 and nrtA/C) elevated significantly at T40 period, while those participated in DNRA (nrfH), nitrification (hao) and anammox (hzsB/C) declined markedly. Under N-enriched conditions, the network complexity of functional genes displayed decreases in the LN and MN treatments, followed by a significant increase in the HN treatment. With prolonged the experiment, the positive correlations among functional genes were weakened and the succession of functional microbial communities was driven in a more functionally specialized direction by a few dominant species. This paper found that sustained N enrichment drove the phased reconstruction of gene networks with a continuous weakening of positive associations among functional genes. The findings can guide the policymaking of targeted N load control and estuarine marsh conservation.}, } @article {pmid42385547, year = {2026}, author = {Paietta, EN and Lefkowitz, EJ and Van Der Pol, WJ and Hendrickson, RC and Johnston, RA and Randrianarisoa, SF and Kraberger, S and Razanamahenina, TT and Ramboninarimalala, A and Raherinirina, TG and Raveloson, L and Finley, NL and Scotch, M and Baitchman, E and Yoder, AD and Varsani, A}, title = {Divergent poxvirus identified in a non-native black rat from Madagascar.}, journal = {Virology}, volume = {623}, number = {}, pages = {111021}, doi = {10.1016/j.virol.2026.111021}, pmid = {42385547}, issn = {1096-0341}, abstract = {Non-native rodents serve as bridges between anthropogenic and natural landscapes. They have expanded across the planet alongside humans while bringing competition, predation, and pathogens, such as poxviruses, to naïve ecosystems. Although rodents serve as reservoirs for multiple zoonotic poxviruses, limited research has focused on rodents for identification of unknown poxviruses. Here, we characterized a divergent metagenome-assembled poxvirus, madamurpox virus, from the oral swab of a black rat in southeastern Madagascar. While madamurpox virus shares a phylogenetic relationship with human-infecting molluscum contagiosum virus and bat-associated Rousettus poxvirus, madamurpox virus presents extensive genetic variation and represents a putative new species and genus in the Chordopoxvirinae subfamily. Further, although madamurpox virus has a similar genome organization to molluscum contagiosum virus and Rousettus poxvirus, madamurpox virus lacks key immune modulators seen in molluscum contagiosum virus. Our findings highlight that substantial unexplored poxvirus diversity likely exists in rodents, with globally distributed, non-native rodent populations of increased interest.}, } @article {pmid42385579, year = {2026}, author = {Han, YH and Zou, MZ and Wei, XM and Chen, X and Tong, LC and Zhang, Y and Zhang, H and Chen, Z}, title = {Mining rare earth elements with ammonium sulfate as a leaching agent provokes a significant perturbation in soil microbial function.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142856}, doi = {10.1016/j.jhazmat.2026.142856}, pmid = {42385579}, issn = {1873-3336}, abstract = {The mining of rare earth elements (REEs), which are critical for modern technologies, frequently leads to severe soil degradation, particularly through ammonium sulfate-based in-situ leaching. This study provided a comprehensive metagenomic assessment of how REEs mining reshapes soil ecosystems. We analyzed paired samples from a mined site and an adjacent unmined control in a typical ion-adsorption REEs deposit region in China. Mining activity was associated with profound alterations in soil geochemical profiles. While soil pH decreased from 4.72 to 4.42, total carbon (TC) declined by over two-thirds (from 1.05 to 0.31 g kg[-1]), and total nitrogen (TN) exhibited a significant 22% increase (from 215.60 to 263.26 mg kg[-1]). Regarding REEs, mining caused an approximately 53% reduction in their total content (from 475.83 to 218.82 mg kg[-1]) and a restructured composition (cerium from 28% to 75%, lanthanum from 23% to 5.4%, and neodymium from 18% to 4.8%). Metagenomic analysis revealed that microbial diversity was significantly lower in the post-mining area compared to the unmined control. Bacterial communities shifted from a balanced composition to an oligotroph-dominated state, with p_Acidobacteriota increasing to 41% and the copiotrophic p_Actinomycetota declining from 23% to 10%. Fungal communities transitioned from a p_Basidiomycota-rich (31%) symbiotic state to an p_Ascomycota-dominated (77%), saprotrophic condition. Mantel tests and path analysis identified the mining-induced deterioration of soil physicochemical and nutrient properties (especially pH, TC, and Mg) as a key factor associated with microbial restructuring, rather than REEs depletion itself. Functionally, Kyoto Encyclopedia of Genes and Genomes annotation revealed a widespread suppression of metabolic pathways critical for ecosystem functioning, including C fixation, N metabolism, energy production, and environmental adaptation. The identification of key microbial taxa (e.g., declining p_Actinomycetota and p_Chloroflexota) as biomarkers for soil health, and their strong linkage to decreased C and N cycling functions, offers potential genomic targets for monitoring and guiding the recovery of soil ecosystem services in post-mining landscapes.}, } @article {pmid42385824, year = {2026}, author = {Zhang, W and Ran, G and Li, P and Ke, J and Ji, S and Gao, Y and Bian, R and Wang, Z}, title = {Multi-scale analysis of patterns, risks, and mechanisms of edaphic antibiotic resistance genes on the Qinghai-Tibet Plateau: Integrating regional and national perspectives.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128686}, doi = {10.1016/j.envpol.2026.128686}, pmid = {42385824}, issn = {1873-6424}, abstract = {The Qinghai-Tibet Plateau (QTP), acclaimed as the "Third Pole"," is an ecologically vulnerable region pivotal to global biogeochemical cycles. However, our knowledge of edaphic antibiotic resistance genes (ARGs) across its heterogeneous land-use regimes remains limited. Here, we systematically characterized the patterns, potential risks, and driving mechanisms of ARGs by analyzing soil samples encompassing anthropogenically disturbed soils (ADS) and pristine alpine meadows on the QTP, coupled with comparative analysis of national cropland metagenomic datasets. Metagenomic analysis identified 897 ARG subtypes, with ADS harboring significantly higher ARG abundance, diversity, and horizontal transfer potential compared to pristine alpine meadows. Source tracking analysis confirmed yak feces as the predominant source of soil ARGs, contributing 31.35%-38.33% across different land-use types. At the national scale, QTP croplands exhibited a distinct resistome profile containing 158 unique ARG subtypes, and the abundance of ARG-carrying pathogens was 1.4-fold higher than the national average, with human pathogens being the most prevalent. Non-dominant ARGs were pinpointed as pivotal biomarkers for differentiating land-use types and geographic regions. Rare microorganisms were critical drivers shaping ARG distribution, whereas mobile genetic elements and virulence factors augmented ARG transmissibility and pathogenicity. This study presents the first comprehensive characterization of the soil resistome on the QTP, highlighting that anthropogenic activities have triggered non-negligible ARG contamination in this ecologically vulnerable ecosystem. These findings underscore the urgency of implementing "One Health" strategies to mitigate the spread of antibiotic resistance in high-altitude regions, with far-reaching implications for global public health and ecological security.}, } @article {pmid42385828, year = {2026}, author = {Yin, Z and Zhang, Y and Song, S and Li, C and Shi, J and Yin, Y and Cai, Y}, title = {Co-contamination of antimony and arsenic reshapes resistome, virulome, and virome in poultry feces near the world's largest antimony mine.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128684}, doi = {10.1016/j.envpol.2026.128684}, pmid = {42385828}, issn = {1873-6424}, abstract = {The poultry microbiome and virome are integral to the One Health framework, with significant implications for ecosystem and human health, but their responses to arsenic (As) and antimony (Sb) exposure remain overlooked. Here, we conducted a comprehensive metagenomic characterization of the metal resistome, antibiotic resistome, virulome, and virome in poultry feces collected from the world's largest antimony mining area. We found that As and Sb co-contamination was significantly associated with elevated resistance and virulence. The abundance of metal resistance genes (MRGs) was 1.8-fold higher in the high-Sb group than in the low-Sb group (15,022.27 ± 3,538.47 vs 8,370.24 ± 4,502.07 TPM, P = 0.008), with arsR, arsB, and arsC dominating the MRG profiles. Similarly, antibiotic resistance genes (ARGs) abundance was 1.6-fold higher in the high-Sb group than in the low-Sb group (7,251.00 ± 1,844.34 vs 4,478.95 ± 2,302.69 TPM, P = 0.026), with multidrug resistance genes being the predominant class (8.09% - 58.48%). Metagenome-assembled genomes (MAGs) analysis and contig analysis suggest co-selection of MRGs, ARGs, and virulence factor genes (VFGs). We identified 100,819 viral contigs clustered into 91,004 viral operational taxonomic units (vOTUs), revealing a highly diverse viral community. Members of Enterobacteriaceae (e.g., Klebsiella) and Enterococcaceae (i.e., Enterococcus) were identified as key drivers mediating resistance and virulence dynamics, acting as resistome supercarriers, opportunistic pathogens, and viral hosts. These findings suggest that As-Sb co-contamination is an overlooked but potentially important driver of poultry antimicrobial resistance and pathogenicity, and highlight potential ecological and public health risks in mining-impacted poultry-associated environments.}, } @article {pmid42385829, year = {2026}, author = {Wei, C and Yun, CW and Li, XQ and Lai, LH and Gao, JP and Tang, MP and Zhou, CN and Zhang, YL and Xu, HJ}, title = {Regulatory mechanisms of N2O emissions from latosolic red soil by different ecotypes of earthworms: insights from microbial diversity and metagenomic analysis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128682}, doi = {10.1016/j.envpol.2026.128682}, pmid = {42385829}, issn = {1873-6424}, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas pollutant, but the mechanisms by which different earthworm ecotypes regulate N2O emissions in latosolic red soils remain poorly understood. To address this issue, a microcosm incubation experiment was conducted using three earthworm ecological categories, epigeic Eisenia foetida, endogeic Pontoscolex corethrurus, and anecic Pheretima guillelmi, to investigate their effects on N2O emissions, soil nitrogen-cycling processes, microbial communities, and nitrogen-cycling functional genes in latosolic red soil. The results showed that the three earthworm ecological categories differentially affected N2O emissions by altering soil physicochemical properties, regulating related enzyme activities, and promoting inorganic nitrogen transformation, with endogeic and anecic earthworms exerting stronger stimulatory effects. Earthworm activity reshaped microbial community interactions and altered the relative abundances of key functional genes involved in nitrification, denitrification, assimilatory nitrate reduction, and dissimilatory nitrate reduction to ammonium (DNRA). Integrated analysis indicated that earthworms may jointly influence soil nitrogen transformation and N2O emissions by modifying the soil environment, promoting soil nitrogen transformation processes, and regulating microbial community structure and the relative abundance of nitrogen-cycling functional genes. Due to differences in activity patterns and disturbance intensity, the effects of different earthworm ecological categories varied substantially, with cumulative N2O emissions generally following the order: anecic > endogeic > epigeic.}, } @article {pmid42385873, year = {2026}, author = {Chen, P and Si, H and Wang, J and Xie, J and Gu, C and Ma, W and Liu, X and Sun, Q}, title = {Metagenomic insights into microbial responses to soil amendments and oat cultivar identity in saline-alkali soils.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125147}, doi = {10.1016/j.envres.2026.125147}, pmid = {42385873}, issn = {1096-0953}, abstract = {Host cultivar identity can influence rhizosphere microbiomes, yet its relative importance compared with soil amendment regime in saline-alkali farmland remains insufficiently resolved. Here, we compared how two oat (Avena sativa) cultivars shape soil microbial communities and functions under contrasting amendment regimes. In a field experiment, two oat cultivars, Tianyan 60 (TY60) and Musite (MST), were grown under five treatments: control, bacterial agent, organic manure, silica fume, and their combination. Soil physicochemical properties, enzyme activities, and metagenomic sequencing were used to characterize microbial taxonomic and functional profiles. Amendment regimes strongly altered soil nutrient and enzyme variables, whereas cultivar identity explained more variation than amendment regime in microbial community structure and beta diversity under the tested field conditions. Taxonomically, TY60 showed stronger amendment-associated reassembly, including enrichment of Bacteroidota, Pseudomonadota, and Ascomycota under selected treatments, whereas MST retained a comparatively more stable higher-rank backbone. Network analysis further indicated cultivar-associated differences in microbial community organization. Functionally, organic manure and the combination treatments (MIX3) produced the broadest shifts in C, N, P, and S cycling gene modules, particularly in TY60-associated soils. Null-model analyses showed that stochastic assembly dominated overall, but the dominant stochastic component differed among kingdoms, with bacteria mainly governed by drift, archaea by homogeneous dispersal, and fungi by a more balanced contribution of the drift and homogeneous dispersal. These results indicate that cultivar identity played a stronger role than amendment regime in shaping amendment-associated microbiome and functional shifts in this two-cultivar comparison, highlighting the potential value of combining cultivar choice with organic-microbial inputs to improve rhizosphere multifunctionality in saline-alkali agroecosystems.}, } @article {pmid42385907, year = {2026}, author = {Qiao, Z and Chen, Z and Gong, H and Guo, X and Chen, L and Zhang, X and Zhang, Y}, title = {Exogenous S[0] enhances the degradation of lignocellulose residues in anaerobic digestion: by driving the coenzyme A-dependent NAD(P)H sulforeductase pathway and persulfidation modification of cellulase.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135285}, doi = {10.1016/j.biortech.2026.135285}, pmid = {42385907}, issn = {1873-2976}, abstract = {Lignocellulose residues in food wastes are encapsulated by polysaccharide matrices, forming a "biomass barrier" that hinders their degradation during anaerobic digestion. This study demonstrates that elemental sulfur (S[0]) can serve as a low-cost in-situ enhancer, effectively breaking down this biomass barrier and significantly improving the degradation efficiency and CH4 yield of lignocellulose residues. Anaerobic fermentation experiment showed that the addition of S[0] increased cellulose and hemicellulose removal efficiencies to 94.89% and 96.78%, respectively, while VFAs concentration increased by 54.72%. Methanogenesis experiment further revealed that the optimal S[0] dosage (20 mg/L) achieved a CH4 yield of 378 mL CH4/g VS, which was 1.72 times that of the control. Microbial community analysis indicated a significant enrichment of cellulolytic bacteria, sulfur-reducing bacteria, and syntrophic acidogenic microorganisms. Metagenomic analysis further revealed that S[0] induced the sulfur reduction pathway mediated by Coenzyme A-dependent NAD(P)H Sulfide Oxidoreductase (NSR), with NSR abundance significantly increasing by 74.28%. This pathway can regenerate NAD[+] and maintain redox balance, thereby promoting the degradation of lignocellulose substrates. In addition, the sulfide generated by S[0] reduction stimulated S-persulfidation modification of cellulase active site, converting -SH to the more polar -SSH, enhancing the affinity between cellulases and lignocellulose substrates. This study demonstrates that S[0] can serve as a low-cost in-situ enhancer, effectively breaking down the biomass barrier in food wastes lignocellulosic residues and significantly improving degradation efficiency and CH4 yield.}, } @article {pmid42374043, year = {2026}, author = {Wu, J and Zhang, B and Ma, Y and Kuang, C and Hong, Y}, title = {Recovery of 178 metagenome-assembled genomes from sediments in subterranean estuary.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07716-z}, pmid = {42374043}, issn = {2052-4463}, support = {42476141//National Natural Science Foundation of China/ ; 42276130//National Natural Science Foundation of China/ ; 2025001//Open Fund of Hainan Xisha Marine Environment National Observation and Research Station/ ; 2024312281//Graduate Innovative Research Grant Program of Guangzhou Education Bureau/ ; 2023B1515120029//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2025A03J3103//Science and Technology Projects in Guangzhou/ ; }, abstract = {Subterranean estuaries (STEs), the mixing zones between terrestrial groundwater and seawater, function as critical biogeochemical reactors that buffer anthropogenic pollutants from entering the open ocean. To date, microbial diversity and community structure within STEs remain poorly characterized. Here, we reconstructed 178 metagenome-assembled genomes (MAGs) exclusively from bacteria (no archaeal MAGs identified). All MAGs met medium-quality standards (>70% completeness, <10% contamination), including 59 near-complete (>90%), 47 with completeness over 80%, and 23 over 75% complete genomes. These MAGs spanned 17 bacterial phyla, with Pseudomonadota dominating (30.9%). Crucially, 157 MAGs (88%) are unclassified at the species level based on GTDB assessment, potentially representing novel taxa, including 1 candidate family, 28 candidate genera, and 128 candidate species. This study provides a genomic resource for studying the functional roles of these unclassified taxa in STEs.}, } @article {pmid42374196, year = {2026}, author = {Ye, J and Mao, P and Li, B and Hao, Y and Chen, Y and Li, K}, title = {Metagenomic profiling of gut microbiome in post-cholecystectomy patients with diarrhea: a nested case-control study.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05346-4}, pmid = {42374196}, issn = {1471-2180}, abstract = {BACKGROUND: Cholecystectomy can cause diarrhea, with an incidence as high as 57.2%, seriously impacting patient prognosis. To investigate the gut dysbiosis following cholecystectomy and identify microbial biomarkers and functional genomics associated with post-cholecystectomy diarrhea (PCD), we conducted a nested case-control study within a prospective cohort.

METHODS: We enrolled a cohort of 160 patients. At follow-up completion, 30 patients who developed PCD were matched with 30 non-PCD (NPCD) controls. 16 S rRNA sequencing was used to analyze gut microbiota structure and diversity (mainly at genus level). Representative fecal samples underwent metagenomic sequencing for species level and genetic differential analysis.

RESULTS: The potentially pathogenic bacterial species Coprococcus comes and Blautia sp. were significantly enriched in the gut microbiota of PCD patients, with their abundance positively correlated with the degree of intestinal inflammation. In contrast, the potentially beneficial bacterial species Bacteroides intestinalis and Prevotella copri, known to contribute to lipid metabolism and play a role in modulating gut immunity and suppressing inflammatory responses, were found to be significantly depleted in PCD patients. Further metagenomic functional analysis revealed significant enrichment of pathways related to cell motility, membrane transport, and sulfur metabolism in PCD patients.

CONCLUSIONS: This work identified potential beneficial and pathogenic bacterial species associated with the onset of PCD, as well as significantly enriched functional pathways within the intestinal microbiota. These findings provide a scientific basis for elucidating the relationship between PCD and gut microbiota, and provide candidate microbial signatures and functional pathways that may inform future microbiota-targeted strategies, pending external and mechanistic validation.}, } @article {pmid42374517, year = {2026}, author = {Harvey, E and Van Brussel, K and Holmes, EC}, title = {Empowering One Health with metagenomics.}, journal = {One health outlook}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42522-026-00225-4}, pmid = {42374517}, issn = {2524-4655}, support = {GNT2017197//National Health and Medical Research Council/ ; }, abstract = {In an increasingly connected world a global One Health approach to the management of human, animal and ecosystem health will be critical to effective infectious disease responses. The emergence and rapid global spread of several emerging and re-emerging pathogens in the past decade has highlighted the need for rapid, sensitive and accurate diagnostics. Metagenomics, while commonly used for research purposes for almost two decades, entered the global spotlight during the COVID-19 pandemic. In this review we discuss the impacts that metagenomic studies have had on our understanding of origins, aetiology and ecology of infectious diseases within a One Health context. We also discuss the role of metagenomics in the future of diagnostics and disease surveillance, and outline the challenges and limitations of current metagenomic methods.}, } @article {pmid42374552, year = {2026}, author = {Wan, LY and Zou, J and Li, XM and Zhao, R and Yang, G and Zhang, MY and Xiao, QY and Wei, YD and Gao, JM and Yang, BP and Zhang, C and Jiao, YM and Wang, FS and Song, JW}, title = {Metagenomic next-generation sequencing of cerebrospinal fluid reveals pathogen spectrum and mortality predictors among patients with advanced HIV-1 disease at a tertiary hospital in China.}, journal = {Virology journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12985-026-03234-x}, pmid = {42374552}, issn = {1743-422X}, support = {No. 20250484882//Beijing Nova Program, China/ ; No. 2025ZD01904603//National Science and Technology Major Project/ ; }, abstract = {BACKGROUND: Central nervous system (CNS) infections remain the major causes of morbidity and mortality among people living with HIV-1 (PLWH), particularly in resource-limited settings. However, the clinical characteristics and prognostic indicators of PLWH with suspected CNS infections are not well defined. In this study, we aim to characterize the spectrum of CNS pathogens, clinical characteristics, in-hospital mortality, and factors associated with death among people with advanced HIV-1 disease (AHD) in Guangxi, China.

METHODS: Metagenomic next-generation sequencing (mNGS) was performed to analyze types of infection in cerebrospinal fluid (CSF) from 61 treatment-naive PLWH with suspected CNS infections. Clinical data, routine laboratory tests, and biochemical tests were collected and analyzed.

RESULTS: Among the 61 CSF samples, primarily with AHD, a total of 206 pathogens were identified. Viral pathogens predominated, with Epstein-Barr virus being the most frequently identified, followed by cytomegalovirus. Compared with patients with single-pathogen infection, those with multiple infections (viral, bacterial, and fungal) exhibited significantly lower CD4 T cell counts, higher C-reactive protein levels, and markedly reduced lipid metabolism parameters. However, infection types were not significantly associated with in-hospital death. Multivariate logistic regression analysis identified plasma low density lipoprotein (LDL) and CSF lactate dehydrogenase (LDH) as independent predictors of in-hospital death.

CONCLUSION: In PLWH with AHD and suspected CNS infections, multiple pathogens frequently coexist in the CSF. Plasma LDL and CSF LDH levels were independent predictors of death, indicating their potential value as early risk stratification in AHD.}, } @article {pmid42374590, year = {2026}, author = {Fürnwein, L and Tichy, J and Waldherr, M and Lehner, E and Ortbauer, M and Vassallo, Y and Sipek, B and Sterflinger, K and Piñar, G and Graf, AB}, title = {Uncovering transcriptional processes in microbial communities adapted to differing saline conditions in salt-weathered historic buildings.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02383-z}, pmid = {42374590}, issn = {2049-2618}, support = {Heritage_2020-005_RESTOROMIC//Österreichischen Akademie der Wissenschaften/ ; }, abstract = {BACKGROUND: Microbial colonization of architectural surfaces in historic buildings can cause not only aesthetic damage but also biodeterioration. One example is the colonizing microbiome on salt-weathered architectural surfaces. Halotolerant and halophilic communities on such surfaces produce colored pigments that visually alter cultural heritage sites and could potentially degrade organic binders used for mural paintings. Although the microorganisms involved in these deterioration processes have already been described, detailed information about the molecular processes that allow these communities to succeed, survive, and thrive under such extreme conditions is still lacking.

RESULTS: A combined metagenome and metatranscriptome approach were employed to investigate three sampling sites located in two Austrian historic buildings displaying different environmental and saline compositions. The chapel of St. Virgil (Vienna) is a subsurface, climate-controlled environment. In contrast, the Charterhouse Mauerbach (Lower Austria) is exposed to natural fluctuations in temperature and humidity. DNA and total RNA were extracted from each sampling site simultaneously and sequenced. Two methods for gene assembly were compared and functionally evaluated. Results showed a minor bias in both methods, with improved results when they were combined. Comparison between DNA and RNA showed interesting variations in the taxonomic composition between the DNA- and RNA-based dataset, distinguishing the dormant from the active microbiome. The annotated halotolerance mechanisms in the metatranscriptomes indicated genome and proteome adaptations, showing high GC content, proteome acidification, with elevated aspartate and glutamate levels, and low isoelectric point profiles. Furthermore, the communities used both "salt-in" and "salt-out" osmoregulatory mechanisms. Pigment production was confirmed in all sampling points, revealing diverse pathways for carotenoid biosynthesis. Various protective mechanisms against oxidative stress were detected, such as those against reactive oxygen species (ROS), but also detoxification, protein folding, protein and DNA repair, and RNA chaperones. Key metabolic pathways revealed diverse pathways related to carbon, nitrogen, and sulfur cycling, linked to varying oxygen concentrations within biofilms. The results also highlighted the need for an in-depth analysis of the capabilities of the involved microorganisms.

CONCLUSIONS: The study shows highly specialized and cooperative adaptations, using both "salt-in" and "salt-out" strategies, diverse phototrophic and redox metabolisms that tightly couple C-N-S cycling.}, } @article {pmid42375904, year = {2026}, author = {Panagiotidi, K and Markidis, A and Karamatzanis, I and Almomani, M and Omirou, R and Kosmidou, P}, title = {The Nasopharyngeal Microbiome: A Narrative Review of the Hidden Regulator of Ear, Nose, and Throat (ENT) Inflammations.}, journal = {Cureus}, volume = {18}, number = {5}, pages = {e109921}, pmid = {42375904}, issn = {2168-8184}, abstract = {The nasopharyngeal microbiome is a central regulator of respiratory health. The upper airway microbial community acts as the primary gatekeeper against respiratory pathogens and maintains homeostasis in the upper respiratory tract (URT). This community is established at birth and influenced by the delivery method and antibiotic exposure. Disruptions to this balance are recognised as a major driver of chronic inflammatory ear, nose, and throat (ENT) diseases. This review analyses the literature on the relationship between the nasopharyngeal microbiome and inflammatory ENT diseases. We searched recent literature (2015-2025) via PubMed and Scopus, focusing on 16S rRNA and metagenomic studies of the upper respiratory tract. We examined papers that linked microbial shifts to clinical outcomes in otitis media, rhinosinusitis, and allergic rhinitis, as well as studies applying machine learning to diagnostic modelling. Clinical health is associated with stable colonisation by Dolosigranulum and Corynebacterium. These commensals protect the host by maintaining the mucosal barrier and competing against pathogens. Chronic disease, in contrast, is marked by a bloom of Streptococcus, Haemophilus, or Moraxella. In chronic rhinosinusitis, loss of bacterial diversity and S. aureus biofilm formation often lead to treatment failure. Machine learning tools like Random Forest and XGBoost classifiers have been applied to nasopharyngeal microbiome data. In published cohorts, these models have achieved sensitivity and specificity values of 80-90% for identifying dysbiotic profiles associated with disease, outperforming standard culture in speed and taxonomic resolution. These findings support a shift from broad antibiotic use toward microbiome-informed treatment. Standardising sampling and sequencing methods remains the next necessary step.}, } @article {pmid42376027, year = {2026}, author = {Dong, X and Xiao, R and Gao, C and Huang, S and Meng, X and Yan, X and Bai, Z and Wu, S}, title = {Ruxolitinib combined with azithromycin for scrub typhus-associated hemophagocytic lymphohistiocytosis in a child: a case report and narrative literature review.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1852110}, pmid = {42376027}, issn = {2296-2360}, abstract = {BACKGROUND: Scrub typhus-associated hemophagocytic lymphohistiocytosis (HLH) is a rare but life-threatening complication in children, with reported mortality of 11.9%-30%. Conventional immunomodulation with corticosteroids and intravenous immunoglobulin often provides insufficient control of the hyperinflammatory state, while etoposide-based chemotherapy carries significant toxicity. JAK1/2 inhibition targeting the interferon-gamma pathway represents a promising therapeutic strategy, but its application in scrub typhus-associated HLH has not been previously reported.

CASE PRESENTATION: A 5-year-11-month-old girl with no prior medical history presented with persistent fever, tachypnea, hepatosplenomegaly, and a 0.5 cm eschar in the left axilla after travel to Yunnan Province, China. Laboratory findings revealed pancytopenia (platelets 40× 10[9]/L), hyperferritinemia (>2,000 ng/mL), hypofibrinogenemia (1 g/L), and elevated interferon-gamma (135.48 pg/mL). Bone marrow aspiration demonstrated hemophagocytosis. Metagenomic next-generation sequencing confirmed Orientia tsutsugamushi infection. The patient met six of eight HLH-2004 diagnostic criteria. She was treated with oral ruxolitinib (5 mg twice daily) initiated on the day of admission, followed by intravenous azithromycin (10 mg/kg once daily) after confirmatory testing. Fever resolved within 72 h. Ruxolitinib was temporally associated with rapid clinical improvement, although causal attribution cannot be established due to concurrent therapies. By day 8, platelet count normalized to 240× 10[9]/L, ferritin declined to 1,246 ng/mL, and fibrinogen recovered to 2.4 g/L. The patient was discharged on day 13 with ruxolitinib tapered to 2.5 mg daily. At 3-month follow-up, she remained well with normal laboratory parameters.

LITERATURE REVIEW: Narrative literature review of 66 previously reported pediatric cases from Chinese and English databases (inception to May 2026) plus the present case revealed an overall mortality of 11.94% (8/67). Among these patients, 43 (64.2%) received corticosteroids, 34 (50.7%) received intravenous immunoglobulin, and only 3 (4.5%) received etoposide. The published cases suggest that absence or delay of anti-rickettsial therapy is associated with poor outcomes, though the evidence is limited by case-report bias and confounding.

CONCLUSION: This is the first report of successful JAK1/2 inhibitor therapy in scrub typhus-associated HLH. This case raises a hypothesis worth investigating further-that ruxolitinib combined with azithromycin may achieve rapid disease control with good tolerability. Prospective studies are needed to evaluate the role of targeted JAK inhibition in infection-triggered HLH.}, } @article {pmid42376290, year = {2026}, author = {Onumanyi, V and Ogola, HJO and Ijoma, GN and Semenya, K}, title = {PacBio HiFi sequencing datasets of culture-enriched airborne microbial cave communities from dolomitic Sudwala Caves, South Africa.}, journal = {Data in brief}, volume = {67}, number = {}, pages = {112970}, pmid = {42376290}, issn = {2352-3409}, abstract = {We present a dataset integrating physico-chemical air quality measurements with long-read PacBio HiFi shotgun metagenomic sequences from culture-enriched airborne samples collected in Sudwala Caves, one of the oldest known cave systems in South Africa. This resource provides baseline characterization of airborne microbial communities and associated environmental parameters within a subterranean karst ecosystem. A total of 106 air samples were collected across six different cave compartments and three external reference sites spanning two seasonal periods, the winter-spring transition (September-October 2024) and the summer-autumn window (February-March 2025). Environmental metadata include temperature, relative humidity, particulate matter (PM1.0, PM2.5, PM10), and formaldehyde (HCHO) concentrations, enabling direct linkage between microbial composition and air quality dynamics. Post-quality control of eighteen (18) culture-enriched metagenome datasets yielded 7.7 × 10[4] to 7.8 × 10[5] HiFi reads per sample corresponding to 0.63-6.71 Gb of high-accuracy sequence data per sample. Kaiju classification assigned 65.1-83.4% of assembled sequences to reference taxa. Domain-level profiles were dominated by Bacteria (98.7-99.9% of classified sequences), with minor representation of Eukaryota (0.06-0.15%) and extremely low abundances of Archaea (0.002-0.009%) and Viruses (0.000-0.001%). At the phylum level, airborne bacterial communities were consistently dominated by Bacillota (mean relative abundance: 46.92%), Pseudomonadota (34.28%), and Actinomycetota (15.71%) across all sampling sites and seasons, with Pseudomonadota and Actinomycetota exhibiting proportionally higher representation within cave interior environments relative to outdoor reference sites. At the genus level, Staphylococcus, Bacillus, Microbacterium, Arthrobacter, and Pseudomonas were among the most consistently detected and abundant airborne genera within cave compartments, whilst outdoor aerobiome communities were characterised by greater relative abundances of Planococcus, Sphingomonas, Stenotrophomonas, and Arthrobacter. Functional annotation using the DRAM pipeline identified 1205,651 predicted genes, with 579,682 KEGG orthologs (KO), 62,261 MEROPs peptidases, 904,193 Pfam domains, and 21,859 CAZy genes annotated. This dataset supports investigations of culturable airborne microbial composition, functional capacity, bioaerosol dynamics, and environmental health indicators in dolomitic subterranean karst systems, providing a reference framework for comparative studies of low-biomass atmospheric environments.}, } @article {pmid42376319, year = {2026}, author = {Gu, Z and Tan, Q and Mao, D and Zhang, Y and Wang, Y and He, D and Chen, S}, title = {Metagenomic analysis of human feces reveals gut microbiome role in colorectal cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1828012}, pmid = {42376319}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Multiomics ; High-Throughput Nucleotide Sequencing ; Adult ; Metagenome ; }, abstract = {BACKGROUND: This study aimed to identify the microbiota and specific genes that are closely associated with colorectal cancer (CRC) through metagenomic sequencing and integrative multi-omics analysis.

METHODS: Fecal samples were collected from 11 healthy volunteers and 20 patients with CRC. Genomic DNA was extracted for metagenomic analysis and high-throughput sequencing. Compositional differences and correlations of the gut microbiome were compared based on species and functional diversity.

RESULTS: The overall species composition included 1,980 species, with 1,707 species identified in the CRC group and 1,525 in the healthy control group. Alpha diversity was significantly lower in the CRC group than in the healthy control group (p = 0.014). Beta diversity analysis revealed significant differences between the two groups (stress = 0.1308, p = 0.021). Based on LEfSe analysis, Shigella, Porphyromonas, Proteus, Bacteroides, Alistipes, Fusobacterium, and Escherichia were more abundant in patients with CRC, whereas Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella were significantly more abundant in the healthy control group (p < 0.05).

CONCLUSION: A multidimensional microbial diagnostic model, incorporating Shigella, Porphyromonas, Proteus, Bacteroides, Fusobacterium, Escherichia, Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella, suggests the potential to enhance early CRC screening performance. Furthermore, LptA, tnaA, envC, and argB may represent promising candidates for novel therapeutic targets, warranting further investigation.}, } @article {pmid42376322, year = {2026}, author = {Qin, Q and Ning, YC and Zhu, SN and Ma, JH and Chen, W and Tian, W and Wang, CM and Wu, YF and Li, SL}, title = {Performance of metagenomic next-generation sequencing for bloodstream infections in perioperative critically ill patients- a post-hoc analysis of a prospective, multi-center cohort study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1814969}, pmid = {42376322}, issn = {2235-2988}, mesh = {Humans ; Prospective Studies ; Female ; *Metagenomics/methods ; Critical Illness ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Intensive Care Units ; *Bacteremia/diagnosis/microbiology ; Aged ; Middle Aged ; Sensitivity and Specificity ; Bacteria/genetics/classification/isolation & purification ; Blood Culture ; *Sepsis/diagnosis/microbiology ; }, abstract = {BACKGROUND: Bloodstream infections (BSI) in intensive care unit (ICU) patients are associated with high morbidity and mortality, necessitating rapid and accurate pathogen identification to guide early antimicrobial therapy. However, traditional blood culture (BC) is limited by the long turnaround time and low sensitivity. Metagenomic next-generation sequencing (mNGS) has been applied in infectious disease diagnostics, but its clinical utility for perioperative ICU patients with BSI requires further evaluation.

METHODS: This post-hoc analysis included 219 perioperative ICU patients (from a prospective, multi-center cohort, July 2020-June 2023) who underwent concurrent mNGS and BC testing. The study compared pathogen detection differences between the two methods, and evaluated the diagnostic value of mNGS for clinical BSI based on mNGS-assisted clinical diagnostic criteria. Additionally, the impact of mNGS findings on clinical antimicrobial management was assessed.

RESULTS: mNGS demonstrated a higher overall pathogen detection rate than BC in the 219 enrolled patients (25.1% vs. 9.6%, p < 0.001), with significant advantages in detecting Gram-negative bacteria (13.2% vs. 5.9%, p = 0.009), anaerobes (3.6% vs. 0.5%, p = 0.018), and fungi (6.4% vs. 0.9%, p = 0.002). Mixed-pathogen infections were identified in 20% of mNGS-positive clinical BSI cases, whereas BC-positive cases exclusively had single-pathogen infections. Ultimately, 64 patients (29.2%) were diagnosed with clinical BSIs. The sensitivity and specificity of the mNGS were 85.9% (95% CI: 74.5%-93.0%), and 80.6% (95% CI: 73.4%-86.4%), respectively, and the area under the receiver operating characteristic curve was 0.833 (95% CI: 0.772-0.894). The positive predictive value and negative predictive value were 64.7% (95% CI: 53.5%-74.6%) and 93.3% (95% CI: 87.3%-96.7%), respectively. Additionally, mNGS led to a positive impact in 56 patients (25.6%), manifested by the identification of new pathogens and guidance for targeted therapy, a negative impact in 11 patients (5.0%), and no clinical impact in 152 patients (69.4%).

CONCLUSIONS: For perioperative ICU patients, mNGS demonstrated superior pathogen detection rates, broader microbial spectrum coverage, and enhanced polymicrobial infection detection capability versus BC. mNGS exhibited high diagnostic value for clinical BSI, with the potential to facilitate targeted antimicrobial therapy adjustments.}, } @article {pmid42376574, year = {2026}, author = {Biełło, K and Rodríguez-Caballero, G and Becerra-Mora, D and Dorado-Blanco, N and Sáez-Melero, LP and Moreno-Vivián, C and Luque-Almagro, VM and Olaya-Abril, A and Roldán, MD}, title = {Exploring the Tenebrio molitor gut microbiota response to LDPE and PET: putative genetic indicators and methodological insights.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1746922}, pmid = {42376574}, issn = {1664-302X}, abstract = {Insect gut microbiomes are recognized as potential reservoirs of enzymatic activities relevant to plastic metabolism. Here, we investigated the taxonomic and functional dynamics of the Tenebrio molitor gut microbiota under dietary exposure to low-density polyethylene (LDPE) and polyethylene terephthalate (PET) using 16S rRNA sequencing and shotgun metagenomics. Significant compositional shifts were detected at the ASV level, with plastic-fed cohorts showing enrichment of taxa implicated in xenobiotic metabolism. Predicted functional changes suggested altered abundance of pathways related to aromatic compound processing and redox homeostasis. Metagenomic assembly and functional annotation, performed through a reproducible open-source workflow, revealed several putative proteins with distant homology to enzymes such as phthalate dioxygenases, urethanases, and polyhydroxyalkanoate depolymerases. A metagenome-assembled genome (MAG) assigned to Enterococcus accounted for most recovered protein-coding sequences. Although gene-level comparisons did not show statistically significant differences, Gene Set Enrichment Analysis (GSEA) highlighted ABC transporter signatures and stress-response ATPases under plastic-exposed conditions. Overall, this exploratory study reveals microbial shifts and putative genetic indicators of metabolic potential within the T. molitor gut, providing a reproducible analytical framework for future investigations into the microbial role in plastic bioconversion.}, } @article {pmid42376617, year = {2026}, author = {Lee, YS and Kuo, TF and Yang, G and Liang, YC and Yang, WC}, title = {Bidens pilosa extract and bentonite, a phytogenic formulation, as a feed additive to improve diarrhea and gut microbiota in calves: Effects on feed use and regulation of gut microbiota.}, journal = {Veterinary and animal science}, volume = {34}, number = {}, pages = {100732}, pmid = {42376617}, issn = {2451-943X}, abstract = {Phytogenics are emerging as an alternative approach to maintain animal health and productivity without using antibiotics in the livestock industry. This study investigated the function and mechanism of a phytogenic formulation composed of Bidens pilosa extract and bentonite (BPB) on diarrhea, gut microbiota and growth performance in calves. Twenty-six 15-day-old Holstein Friesian calves were fed control or 0.5% BPB diets for 4 weeks. Their diarrhea, gut microbiota, fecal IgA, and bacterial growth were analyzed using culture-based methods, 16S rRNA sequencing, and statistical analyses. BPB (0.5%) significantly reduced diarrhea, fecal scores, and fecal IgA levels, but increased body weight in calves. Furthermore, metagenomic analysis and selective agar assays indicated that 0.5% BPB decreased three bacterial genera, Campylobacter, Clostridium_sensu_stricto_1, and Escherichia/Shigella, but increased seven other bacterial genera, including Lactobacillus, Ruminococcus, and Bacteroides, in the feces of calves. Mechanistic studies suggested that BPB augmented the proliferation of bacteria associated with beneficial effects, subsequently inhibiting the growth of bacteria associated with harmful effects in the intestines of calves. In conclusion, BPB mitigated diarrhea and gut inflammation and increased body weight gain in calves by modulating the gut microbiota. This modulation involved the upregulation of bacteria with beneficial potential that antagonize the growth of bacteria with pathogenic potential.}, } @article {pmid42376710, year = {2026}, author = {Arguelles, EDLR and Mugikura, K and Sato, S}, title = {Impact of the invasive diatom species Cymbella janischii on riverine microbial biofilm communities and a potential role of bacterially produced zeatin.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70195}, pmid = {42376710}, issn = {1529-8817}, support = {21A402//Japan Society for the Promotion of Science/ ; 23K05398//Japan Society for the Promotion of Science/ ; 26K01814//Japan Society for the Promotion of Science/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; }, abstract = {The diatom Cymbella janischii is an invasive species in Japan, causing nuisance blooms by forming thick mats in rivers. To date, there are no documented studies on the microbiome associations in C. janischii mats or the processes that drive bloom formation. This study used metabarcoding of diatoms, bacteria, and fungi to identify key species and assess the effects of C. janischii blooms on the benthic microbial communities. C. janischii blooms reduced diatom and bacterial species diversity, while fungal diversity remained stable. In addition, the diatom Nitzschia paleacea and the bacterium Flavobacterium sp. were observed to co-occur and vary in abundance, indicating a possible ecological link that may affect mat structure or function. Metagenomic predictions of bacterial functions showed that compared to benthic stones without visible C. janischii mats, mat-associated bacteria had enriched pathways related to the metabolism of carbohydrates, nucleotides, and amino acids, along with zeatin biosynthesis. Zeatin is a cytokinin phytohormone that stimulates plant growth and development. In vitro exposure of C. janischii to varying zeatin concentrations confirmed its growth-promoting effects, inducing cell proliferation and stalk formation. This study shows that zeatin stimulates the growth of C. janischii. The findings of this study provide new insights into microbiome diversity, identifying key taxa associated with C. janischii mats to help better understand bloom formation.}, } @article {pmid42377028, year = {2026}, author = {Lenz, C and Seel, W and Dombrowski, T and Hacker, S and Simon, M-C and Zentgraf, K and Dawczynski, C and Krüger, K}, title = {Signatures in the gut microbiome of German elite athletes: insights from a matched-subgroup analysis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0048926}, doi = {10.1128/msystems.00489-26}, pmid = {42377028}, issn = {2379-5077}, abstract = {Elite athletes undergo intense physical training and experience substantial physiological stress, which could affect the composition and function of their gut microbiome. This study compared the gut microbiomes of 148 German junior and senior elite athletes with those of 108 healthy adults to identify taxonomic and functional features associated with elite athletic status. Group comparisons were conducted between healthy adults, senior athletes, and junior athletes, and a matched-subgroup analysis was performed in adults only, controlling for age, sex, body mass index, and dietary pattern. Significant differences in taxonomic composition were observed between athletes and healthy adults. Healthy adults exhibited greater microbial evenness and diversity than junior athletes, whereas senior athletes displayed higher microbial richness. Principal coordinate analysis revealed distinct clustering by athletic status. Linear discriminant analysis effect size identified taxa such as Escherichia-Shigella as being enriched in athletes. Predictive metagenomic profiling (PICRUSt2) indicated differences in microbial functional potential between adult athletes and matched controls, including pathways related to amino acid metabolism, glycolysis, fatty acid β-oxidation, and quinone biosynthesis. Together, these findings demonstrate distinct taxonomic and predicted functional microbiome signatures associated with elite athletic status.IMPORTANCEElite athletic training and lifestyle are associated with the gut microbiome. Our research has revealed distinct microbial structures in elite athletes, characterized by reduced evenness in junior athletes and increased richness in senior athletes, compared to healthy adults. Matched-subgroup analyses confirmed these group-specific differences. The gut microbiomes of athletes were enriched in pathways related to amino acid biosynthesis, glycolysis, fatty acid β-oxidation, and quinone synthesis. These microbiome features may be relevant for metabolic efficiency and resilience to oxidative stress. Combining taxonomic and functional prediction data from a uniquely characterized cohort of junior and senior elite athletes provides novel insight into microbiome signatures associated with sustained physical and psychological stress, with potential implications for performance, recovery, and health.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT03582020.}, } @article {pmid42377463, year = {2026}, author = {Brenner, T and Skarabis, A and Schaller, SJ and von Groote, T and Putensen, C and Günther, U and Sauer, M and Decker, SO and Dusse, F and Weiss, M and Suchodolski, K and Simon, TP and Rosenberger, P and Moerer, O and Unterberg, M and Schewe, JC and Bracht, H and Hutzl, S and Feißt, M and Marschall, U and Brandenburg, P and Stevens, P and Schmidt, J and Pletz, MW and Berger, MM and , }, title = {Effects of a clinical metagenomics intervention on clinical outcomes, healthcare costs, and health-related quality of life in patients with sepsis or septic shock: results of the randomized-controlled DigiSep trial.}, journal = {Intensive care medicine}, volume = {}, number = {}, pages = {}, pmid = {42377463}, issn = {1432-1238}, support = {01NVF20013//German Innovation Fund/ ; }, abstract = {PURPOSE: Early pathogen detection is crucial in sepsis. We hypothesized that detection of microbial circulating cell-free DNA by metagenomic next-generation sequencing (mNGS) improves clinical outcomes and health-related quality of life without increasing healthcare costs.

METHODS: This randomized, controlled, interventional, open-label, multicenter trial was conducted in 24 intensive care units across Germany. The intervention group (n = 200) received mNGS diagnostics in addition to standard-of-care microbiology, compared with standard-of-care microbiology alone (control group; n = 189). The primary endpoint was the Desirability of Outcome Ranking/Response Adjusted for Duration of Antibiotic Risk (DOOR/RADAR) score.

RESULTS: The DOOR/RADAR score was not significantly improved at 28 days after sepsis onset (intervention group: 3.21 ± 1.54; control group: 3.49 ± 1.51; 95% CI - 0.58 to 0.03). However, other secondary endpoints were improved, including a reduced duration of mechanical ventilation (intervention group: 6.6 ± 9.4 days; control group: 9.3 ± 10.6 days; 95% CI - 5.03 to - 0.34) and faster shock resolution (intervention group: 6.9 ± 7.4 days; control group: 8.8 ± 8.5 days; 95% CI - 3.75 to - 0.04). Health-related quality of life at 90 days (EQ-5D-5L) was improved in the intervention group (0.312 ± 0.386) compared with the control group (0.208 ± 0.373; p = 0.047). In the subgroup with available claims data (33.2% of participating patients), healthcare costs over 180 days did not differ.

CONCLUSION: The DOOR/RADAR score as primary endpoint was not significantly improved by mNGS. Exploratory secondary analyses revealed improvements in secondary endpoints. (Funding: German Innovation Fund; ClinicalTrials.gov number, NCT04571801, registration: 25.8.2020).}, } @article {pmid42377624, year = {2026}, author = {Mwazembe, KJ and Chauhan, A and Pathak, A and Chukwujindu, C}, title = {Isolation and characterization of microalgal growth-enhancing bacteria from a wastewater treatment facility.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42377624}, issn = {1573-0972}, mesh = {*Wastewater/microbiology ; *Microalgae/growth & development/microbiology ; Phylogeny ; *Bacteria/isolation & purification/classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Biomass ; Microbial Consortia ; Coculture Techniques ; Biofuels ; DNA, Bacterial/genetics ; Metagenomics ; Water Purification ; }, abstract = {Microalgae-bacteria interactions represent a promising approach for improving microalgal growth and biomass productivity, with potential applications in biofuel production, wastewater remediation, and the synthesis of value-added bioproducts. In this study, enriched microalgae consortia from the Tallahassee Wastewater Treatment Facility were first characterized using shotgun metagenomic sequencing to assess their taxonomic composition and functional potential. The consortia were dominated by Chlorella species and associated with diverse bacterial communities. Subsequently, bacterial strains were isolated and characterized to evaluate their potential as natural growth enhancers for microalgae. Eight bacterial isolates, Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., Agrobacterium tumefaciens, Citrobacter freundii, Cellulosimicrobium sp., Stenotrophomonas pavanii, and Mycobacterium sp. SMC-4 were identified through 16 S rRNA sequencing and phylogenetic analysis. The influence of these isolates on microalgae was assessed using a membrane-separated coculture system that enabled metabolite exchange without direct cell-to-cell contact. Microalgal growth, monitored through optical density (OD) at 680 nm over 18 days, showed significant enhancement across all bacterial treatments compared to the reference (microalgae without bacteria). The most pronounced effects were observed with Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., and Agrobacterium tumefaciens, which exhibited the highest growth responses. These findings suggest that wastewater-derived bacteria can substantially enhance microalgal growth performance, likely through metabolite-mediated interactions. This study expands the repository of algal-supportive bacterial taxa and highlights the potential of targeted microalgae-bacteria consortia for scalable and sustainable bioprocessing.}, } @article {pmid42377631, year = {2026}, author = {Thakur, A and Gupta, P and Sethi, S and Apreja, M and Ahmed, S and Sharma, L}, title = {Exploring the antibacterial potential of a designed peptide against Gardnerella vaginalis.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42377631}, issn = {1573-4978}, mesh = {*Gardnerella vaginalis/drug effects ; Humans ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Antimicrobial Peptides/pharmacology ; Female ; Vaginosis, Bacterial/drug therapy/microbiology ; Hemolysis/drug effects ; Cell Survival/drug effects ; *Antimicrobial Cationic Peptides/pharmacology ; Peptides, Cyclic/pharmacology ; }, abstract = {BACKGROUND: Bacterial vaginosis (BV) is a common vaginal dysbiosis caused by Gardnerella vaginalis, a facultative anaerobic bacillus. The failure of conventional antibiotics and recurrence of bacterial vaginosis call for alternative novel therapeutic strategies. Antimicrobial peptides (AMPs) provide a targeted, resistance-sparing alternative with their broad-spectrum activity and distinct mode of action.

METHODS: Two AMPs, i.e., TCCP-1 (cyclic) and ZMLP-2 (linear), were designed in silico from proteome sequences of Thymbra capitata and Zataria multiflora already available in NCBI. The designed peptides were chemically synthesized, evaluated for their antibacterial activity, cytotoxicity, hemolytic effects and mechanism of action against G.vaginalis.

RESULTS: TCCP-1, a cyclic peptide with an MIC of 1.95 µg/mL against G. vaginalis showed minimal cytotoxicity even at 100 µg/mL, which is much higher than its MIC value (1.95 µg/mL). TCCP-1 maintained high cell viability at lower concentrations, while a concentration-dependent reduction in viability was observed at higher concentrations. In contrast, ZMLP-2, a linear AMP, showed weak antimicrobial activity with an MIC of 100 µg/mL, exhibited a moderate reduction in cell viability (~ 70-75%) when tested at 100 µg/mL or a concentration below its MIC. Both peptides showed the disruption of bacterial membranes and, therefore, support the re-establishment of healthy vaginal flora. More significantly, TCCP-1 demonstrated efficient antimicrobial activity against G.vaginalis along with decreased cytotoxicity, making it an excellent candidate for future in vivo studies and possible clinical uses.

CONCLUSIONS: Thus, plant-derived AMPs could prove to be useful, targeted, and sustainable alternatives to BV prevention while treating both resistance and recurrence.}, } @article {pmid42377725, year = {2025}, author = {Yun, S and Seo, Y and Yoon, Y}, title = {Prevalence of Microorganisms and Suggestion for Potential Contribution of Microorganisms to Volatile Basic Nitrogen Production in Beef at Current Purchase Stages.}, journal = {Food science of animal resources}, volume = {45}, number = {6}, pages = {1710-1723}, doi = {10.5851/kosfa.2025.e14}, pmid = {42377725}, issn = {2636-0780}, abstract = {This study investigated the prevalence of microorganisms related to meat quality and analyzed volatile basic nitrogen (VBN) levels in beef samples to suggest potential bacteria that might contribute to VBN production at current purchase stages using metagenomic analysis. Seventy beef samples were analyzed for coliform, Escherichia coli, enterohemorrhagic E. coli, Listeria monocytogenes, Salmonella, Staphylococcus aureus, total aerobic bacteria (TAB), Enterobacteriaceae, lactic acid bacteria (LAB), Pseudomonas spp., yeast and molds (YM), and psychrotrophic bacteria (PB). VBN levels ranged from 0.69 to 22.51 mg%. Microbiota from three samples with the highest and three with the lowest VBN levels were analyzed. S. aureus was detected in only one sample at 1.2 Log CFU/g. The cell counts for TAB, coliform, Enterobacteriaceae, LAB, Pseudomonas spp., YM, and PB were 5.1, 1.7, 2.6, 4.2, 1.9, 2.9, and 5.4 Log CFU/g, respectively. Microbiota analysis revealed that samples with high VBN levels had high relative abundances of Lactobacillus and Leuconostoc. This study showed that these relatively abundant LAB were potential bacteria that might contribute to producing more VBN in beef at current purchase stages. However, the potential bacteria were suggested only by metagenomic analysis with a limited sample size without considering the endogenous meat enzymes. Therefore, further research is necessary to identify and isolate these bacteria with a larger sample size while excluding VBN produced by endogenous enzymes. Additionally, environmental factors not included due to the limited objective of this study could also be considered in further research with the different objectives from this study.}, } @article {pmid42377908, year = {2026}, author = {Deng, Y and Borton, MA and Nesbø, CL and Forster, MD and Konhauser, KO and Gingras, MK and Goss, GG and Wrighton, KC and Lanoil, BD and Zhong, C and Alessi, DS}, title = {Geochemistry shapes microbial diversity and selected functional traits in flowback and produced waters from hydraulically fractured formations.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag070}, pmid = {42377908}, issn = {1574-6941}, abstract = {Microbial communities inhabiting hydraulically fractured subsurface waters are increasingly recognized as important components of unconventional oil and gas systems because they can influence water quality, infrastructure integrity, and biogeochemical processes during flowback and production. However, a quantitative cross-basin understanding of their taxonomic diversity, ecological organization, and potential functional variation remains limited. In this study, we analyzed 16S rRNA gene amplicons, metagenomes, and geochemical data from flowback and produced water (FPW) from the Sichuan Basin, China, and conducted a quantitative comparison to data previously reported from the same basin and hydraulic fracturing (HF) regions in North America. Our findings revealed strong co-occurrence patterns among fermentative, sulfidogenic, and methanogenic microorganisms, which emerged as core members of microbial communities across all fractured subsurface environments. Notably, microbial diversity and selected metabolic traits differed across basins in the low-salinity systems of China, whereas high-salinity basins in North America exhibited reduced diversity and more constrained metabolic capabilities. These differences are consistent with salinity acting as an important ecological filter across the analyzed basins. Our results indicate that basin-specific geochemical context, particularly salinity, is closely associated with cross-basin differences in microbial diversity, community composition, and selected metabolic traits in fractured subsurface waters. These findings support the value of integrating geological, geochemical, and microbiological information when interpreting microbial risks and water-management strategies in hydraulic fracturing systems.}, } @article {pmid42378511, year = {2026}, author = {Zhang, R and Wang, B and Lu, J and Wu, J and Liu, X and Zhang, R and Marsili, E and Gong, C}, title = {The Food Additives p-Coumaric Acid Production from Corn Stalk Catalyzed by a Cold-Adapted Carboxylesterase.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.6c05955}, pmid = {42378511}, issn = {1520-5118}, abstract = {p-Coumaric acid is a widely utilized food additive with beneficial biological activities. A novel enzymatic catalysis strategy for the production of p-coumaric acid from lignocellulosic biomass is proposed herein. The gene encoding a carboxylesterase was identified in metagenome-assembled genome and further characterized in the isolated Glutamicibacter soli Em07. The target protein, with a molecular weight of 53 kDa, was successfully obtained through heterologous expression. The carboxylesterase exhibited cold adaptation, with optimal activity at 35 °C and pH 7.0 using 1-naphthyl acetate as substrate, and maintained over 75% of the maximum activity after incubation at 25 °C for 2 h. At 25 °C, 35.9 ± 0.4 μg of p-coumaric acid was obtained from 20 mg of corn stalk via carboxylesterase-mediated catalysis. This work achieves a high p-CA yield from lignocellulosic biomass via low-temperature enzymatic catalysis without pretreatment. The results offer valuable progress toward manufacturing high-value food additives, including p-CA.}, } @article {pmid42378616, year = {2026}, author = {Tyler, RS and Charles, DW and Mills, AG and Alkabab, Y}, title = {Disseminated Mycobacterium immunogenum -associated Hemophagocytic Lymphohistiocytosis after Stem Cell Transplantation.}, journal = {International journal of mycobacteriology}, volume = {15}, number = {2}, pages = {179-182}, pmid = {42378616}, issn = {2212-554X}, abstract = {Secondary hemophagocytic lymphohistiocytosis (HLH) is a life-threatening hyperinflammatory syndrome most commonly triggered by infection, malignancy, or transplant-related immune dysregulation. Rapidly growing mycobacteria are uncommon causes of disseminated infection and have only rarely been reported as infectious triggers of HLH. A 56-year-old immunocompromised woman with a history of allogeneic hematopoietic stem cell transplant presented with recurrent fever, progressive transaminitis, and laboratory features consistent with secondary HLH. Liver biopsy showed granulomatous hepatitis with iron overload. Initial treatment with dexamethasone and anakinra resulted in transient clinical improvement. Less than 2 weeks later, she was readmitted with worsening hepatic dysfunction and found to have acid-fast bacilli in blood and bone marrow cultures, later identified as Mycobacterium immunogenum. Despite targeted antimicrobial therapy, the patient developed progressive hepatic and renal failure and died. To our knowledge, this case represents the first reported case of disseminated M. immunogenum infection precipitating secondary HLH, expanding the recognized clinical spectrum of this rapidly growing nontuberculous mycobacterium and highlights the diagnostic challenges of atypical mycobacterial infection in immunocompromised hosts.}, } @article {pmid42378712, year = {2026}, author = {Mamie, C and Cabalzar-Wondberg, D and Turina, M and Wawrzyniak, M and Misselwitz, B and Zamboni, N and Gottier, C and Lang, S and Rogler, G and Avivar-Valderas, A and de la Rosa, O and Candela, N and Tang, J and Morsy, Y and Scharl, M}, title = {Multiomics analysis dissects the molecular foundation of perianal fistulas associated with Crohn's disease and of cryptoglandular origin.}, journal = {Journal of Crohn's & colitis}, volume = {20}, number = {6}, pages = {}, doi = {10.1093/ecco-jcc/jjag080}, pmid = {42378712}, issn = {1876-4479}, support = {//Takeda Pharmaceutical Company Ltd/ ; }, abstract = {BACKGROUND AND OBJECTIVE: Perianal fistulas, either of cryptoglandular origin (CgF) or associated with Crohn's disease (CDF), have limited treatment options and pose a tremendous burden for affected patients. We recently showed that the epithelial-mesenchymal transition (EMT) contributes to CDF pathogenesis, but detailed mechanisms need further evaluation. Here, we performed multiomics analysis to gain further molecular insights into fistula pathogenesis.

DESIGN: Rectal biopsies, swabs, fistula curettage, and serum samples were derived from patients with either CDF (n = 23) or CgF (n = 17) and analyzed by bulk RNA sequencing, metagenomics, untargeted metabolomics, or multiplex-ELISA, where appropriate.

RESULTS: Transcriptomics revealed striking differences in gene expression between rectal mucosa and fistula tract samples. However, the transcriptomes of CDF and CgF were comparable, and genes involved in EMT, inflammation and tumor necrosis factor signaling were prominent in both fistula types. A set of 18 genes was found to be differentially expressed in CDF and CgF and might allow discrimination. The overall microbiome composition within fistula tracts did not differ between CDF and CgF patients, but there was a significant difference in rectal microbiome compositions. On a species level, we detected an enrichment of disease-specific, pathogenic species in the fistula tracts. Of note, Bacteroides ssp., Fusobacterium animalis, and Staphylococcus aureus prevailed within CDF.

CONCLUSION: Our data demonstrate only minor differences in the transcriptome and the microbiome between CDF and CgF, but clear differences when compared to rectal mucosa biopsies. Thus, our data suggest that the molecular makeup underlying the pathophysiology of fistulas might be comparable between CDF and CgF.}, } @article {pmid42378762, year = {2026}, author = {Liu, J and Tan, Y and Fan, X and Xie, S and Xu, X and Zhu, L}, title = {Exogenous vitamin B12 alleviated inhibition of salinity on anaerobic dichloromethane degradation by reducing cofactor-related constraints and reshaping community functional potential.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142823}, doi = {10.1016/j.jhazmat.2026.142823}, pmid = {42378762}, issn = {1873-3336}, abstract = {Dichloromethane (DCM) frequently co-occurs with high salinity in industrial wastewater, imposing dual stress on anaerobic treatment. However, how anaerobic DCM degraders respond to salt stress and whether exogenous vitamin B12 (VB12, a key cofactor in DCM transformation) can facilitate DCM degradation remain poorly understood. Here, we established long-term enrichments (>800 days) of DCM-degrading consortia under non-saline and salt-stressed conditions (10 g/L NaCl) to investigate how VB12 affected degradation performance, community assembly, and functional potential. Salt stress significantly inhibited DCM degradation, reducing the maximum degradation rate by 71.5%, whereas VB12 substantially alleviated this inhibition and increased the degradation rate to 55.9% of the non-saline control. Metagenomic and co-occurrence network analyses indicated that salinity drove community reassembly and niche differentiation, linking DCM degraders, methanogens/homoacetogens, and fermenters within an inferred producer-cooperator-cross-feeder framework that maintained community stability under salt stress. Functional analyses showed that VB12 was associated with shifts in community functional potential toward hydrogenotrophic/acetoclastic methanogenesis and osmoadaptive metabolism, supporting stress adaptation under saline conditions. Further analysis of the mec (methylene chloride catabolism) cassette suggested that VB12 likely reduced cofactor-related constraints and reinforced downstream product-consuming functions, thereby contributing to the enhanced degradation performance. Notably, a previously uncharacterized Dehalobacteriaceae MAG, D_MAG.168, emerged as a dominant candidate DCM degrader under salt stress. Overall, these findings provide insight into the functional responses of DCM-degrading consortia to VB12 supplementation under salt stress and support the further development of VB12-assisted bioaugmentation strategies for DCM-contaminated saline industrial wastewater.}, } @article {pmid42378793, year = {2026}, author = {Torres, MC and Breyer, GM and da Silva, MERJ and Jank, L and Barreto, F and Dorn, M and Cardoso, MRI and Siqueira, FM}, title = {Swine waste stabilization ponds as hotspots for antimicrobial resistance gene accumulation: a longitudinal metagenomic study.}, journal = {International journal of hygiene and environmental health}, volume = {276}, number = {}, pages = {114857}, doi = {10.1016/j.ijheh.2026.114857}, pmid = {42378793}, issn = {1618-131X}, abstract = {Using next-generation sequencing, this study provides a comprehensive longitudinal assessment of bacterial communities, antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs), and metabolic pathways in a full-scale swine waste treatment system in Brazil. Samples were collected from the first (WSP1) and final (WSP4) waste stabilization ponds of a farrow-to-finish farm during four sampling events between October 2022 and January 2023. Antibiotic molecules were additionally identified and quantified using solid-phase extraction coupled with liquid chromatography-tandem mass spectrometry. Bacterial community composition remained remarkably stable over time. Similarly, the resistome and mobilome showed pronounced temporal stability, although a consistently higher relative abundance of ARGs and MGEs was observed in the final treatment process (WSP4). Genes encoding resistance markers of human-health relevance were detected in WSP4, including Paer_PhoP_CST, associated with polymyxin (colistin) resistance; PRC-1, linked to resistance to third-generation cephalosporins; and quinolone resistance determinants such as adeF, Paer_parE_FLO, and Mtub_gyrB_FLO. Genes encoding efflux pump complexes associated with multidrug resistance were also identified, including Paer_CpxR, PmpM, YajC, MuxB, and MexW. Supporting these findings, fluoroquinolones (ciprofloxacin and norfloxacin), lincomycin, and tetracycline molecules were detected in the waste ponds, indicating sustained selective pressure within the system. The accumulation of clinically relevant resistance determinants in the final of the waste treatment process, whose effluent is reused for agricultural irrigation, highlights waste stabilization ponds as potential hotspots for the persistence and environmental dissemination of antimicrobial resistance. These findings underscore the urgent need for improved monitoring and management of livestock waste treatment systems to mitigate antimicrobial resistance dissemination across agroecosystems.}, } @article {pmid42378969, year = {2026}, author = {Xing, BS and Wu, YF and Zhang, Y and Wang, XC and Li, YY and Chen, R}, title = {Carbon cloth-mediated direct interspecies electron transfer effect on the intensification mechanism of high-load codigestion dynamic membrane bioreactors.}, journal = {Water research}, volume = {304}, number = {}, pages = {126376}, doi = {10.1016/j.watres.2026.126376}, pmid = {42378969}, issn = {1879-2448}, abstract = {Acidification under high organic loading conditions and control of dynamic membrane (DM) thickness remain major challenges in the development of anaerobic dynamic membrane bioreactors (AnDMBR). In anaerobic digestion (AD), conductive materials can promote electron exchange between electron donors and acceptors, thereby accelerating electron transfer and enhancing direct interspecies electron transfer (DIET). These processes can improve methane yield and process stability at higher organic loading rates (OLRs). In this study, a carbon cloth anaerobic dynamic membrane bioreactor (CC-AnDMBR) was constructed and compared with a common nylon mesh anaerobic dynamic membrane bioreactor (NM-AnDMBR) to investigate the impact of DIET reinforcement on system performance and stability. The maximum load tolerance of the system and changes in microorganisms during this process were further evaluated to elucidate the mechanisms underlying enhanced system resilience. At a hydraulic retention time of 6.25 days (OLR of 20.13 g COD/L/day), the methane production rate of the carbon cloth reactor (313.74 ± 41.06 mL/g COD) was significantly greater than that of the nylon mesh reactor (256.02 ± 63.29 mL/g COD). Metagenomic analysis revealed that carbon cloth membranes are more conducive to the enrichment of Geobacter, which can exchange electrons with the dominant archaeal genus Methanosarcina, thereby accelerating the DIET rate within the CC-AnDMBR. The enhanced performance of the carbon cloth reactor was attributed to the higher electrical conductivity, more negative oxidation-reduction potential value, and higher electron transport system activity of the sludge. These characteristics together created a more conducive environment for conductive microorganisms and improved the system's electron transfer rate.}, } @article {pmid42378973, year = {2026}, author = {Min, H and Wang, Y and Wang, Q and Zhang, J and Lin, L and Li, X and Li, B}, title = {Cefpirome biodegradation by enriched bacterial consortia and isolated strain Bosea sp. MYQ: Novel insights on biodegradation pathway and bacterial interaction patterns.}, journal = {Water research}, volume = {304}, number = {}, pages = {126351}, doi = {10.1016/j.watres.2026.126351}, pmid = {42378973}, issn = {1879-2448}, abstract = {Deciphering the metabolic fate of cefpirome is essential for designing more efficient biodegradation strategies. In this study, we integrated second- and third-generation metagenomic sequencing with high-performance liquid chromatography-quadrupole time-of-flight mass spectrometer (HPLC-QTOF-MS) to unravel cefpirome biodegradation by a long-term enriched bacterial consortium and its key isolate Bosea sp. MYQ. Five biodegradation products were detected and mapped onto three cooperative pathways. Among them, four products involved in Pathways 2 and 3 were first identified in cefpirome biodegradation. Genome-scale metabolic modeling and genome-resolved metagenomics jointly revealed a pollutant-degrading network coordinated by two keystone donors, MAG2 (Variovorax) and MAG3 (Bosea sp. MYQ). They were primarily responsible for β-lactam ring-opening and the formation of downstream products, while exporting diverse metabolic intermediates to sustain pathway continuity through cross-feeding. Notably, MAG3 (Bosea sp. MYQ) encodes per-1 and bla, which likely contribute critically to cefpirome degradation by underpinning key β-lactam transformation steps. Complementary functions were provided by auxiliary and rare members, particularly MAG4 (Hyphomicrobium), MAG7 (Pandoraea), MAG10 (Methyloversatilis), and MAG21 (Phenylobacterium). These findings expand the repertoire of cefpirome-degrading microorganisms, reveal previously unrecognized biodegradation pathways, and clarify the microbial interaction network underpinning fourth-generation cephalosporin removal.}, } @article {pmid42379260, year = {2026}, author = {Alamri, MM and Proctor, G and Garcia-Guevara, F and Guennec, AL and Mainas, G and Shoaie, S and Nibali, L}, title = {Multiomics Analyses in Young Grade C Molar Incisor Pattern Periodontitis.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {106871}, doi = {10.1016/j.jdent.2026.106871}, pmid = {42379260}, issn = {1879-176X}, abstract = {OBJECTIVE: To explore the microbial profiles in plaque and saliva and metabolic profiles in saliva and serum collected from young patients (≤25 years old) with grade C molar incisor pattern periodontitis (C/MIP), to compare them to age-matched controls and integrate both omics to elucidate C/MIP pathogenesis.

MATERIAL AND METHOD: Thirty-one young patients with C/MIP and 31 periodontally healthy age-matched controls were recruited. Bacterial profiles were investigated in unstimulated saliva and subgingival plaque using shotgun sequencing metagenomics while metabolic profiles were assessed in saliva using nuclear magnetic resonance and serum using mass spectrometry. Data from both omics analyses were integrated and visualised as interaction networks using Cytoscape software.

RESULTS: C/MIP showed significantly lower levels of several salivary (e.g., dimethylamine, proline, glycine) and serum metabolites, and higher levels of others including methyl indole-3-acetate and sulfosalicylic acid, compared to controls (P<0.001). Fifteen bacteria, of which twelve were associated with C/MIP, were differentially prevalent between groups. The plaque microbiome in C/MIP was enriched with pathogenic species such as D. oralis, C. rectus, T. denticola, and P. endodontalis, while health-associated bacteria like R. mucilaginosa and L. hongkongensis were more prevalent in controls. D. oralis and GGB10485-SGB49305 emerged as potential microbial biomarkers. Notably, metabolites such as DL-glutamine and taurine were significantly associated with periodontal pathogens.

CONCLUSION: C/MIP is marked by a distinct dysbiotic microbiome and altered metabolic profile. While key pathogens and metabolites likely contribute to disease progression, the underlying mechanisms remain only partially understood due to the complexity and incomplete characterisation of many associated factors.

CLINICAL SIGNIFICANCE: This study highlighted the multifactorial nature of C/MIP, driven by microbial dysbiosis, immune disturbances, and metabolic alterations. A comprehensive multi-omics approach offered a foundation for understanding microbial-metabolite dynamics in young patients, and highlighted candidate biomarkers for future diagnostics and therapeutics.}, } @article {pmid42379362, year = {2026}, author = {Piantoni, P and Sardi, MI and Aumiller, T and Khafipour, E and Roman-Garcia, Y and Chakrabarti, A and Dieho, K and Aubert, T and Schroeder, GF}, title = {Effects of increasing doses of a phytogenic product based on condensed tannins and spices on production performance and rumen microbiome of lactating dairy cows fed a low-protein diet.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-28174}, pmid = {42379362}, issn = {1525-3198}, abstract = {The objective of this experiment was to determine the effect of increasing doses of a phytogenic product based on condensed tannins and spices (CTS) on production performance of lactating dairy cows fed a low protein diet. Eight rumen-cannulated Holstein Friesian dairy cows (140 ± 86 DIM; 39.0 ± 5 kg/d milk yield; mean ± SD), were used in a replicated 4 × 4 Latin Square design experiment with 4-wk periods. Treatments were: 0, 10, 20 and 30 g/d CTS (CTR, 10CTS, 20CTS, and 30CTS, respectively). The grass silage and corn silage-based diet was 55.2% forage, 38.7% NDF, 21.0% total starch, and 14.6% CP. Orthogonal contrasts were used to evaluate the linear and quadratic effect of increasing doses of CTS. Results follow the order: CTR, 10CTS, 20CTS, and 30CTS. Increasing doses of CTS quadratically increased DMI (25.4, 25.9, 26.1, and 25.1 kg/d) and milk yield (37.1, 38.5, 37.7, and 36.3 kg/d), tended to increase fat-and-protein-corrected milk (36.9, 37.6, 37.4, and 36.1 kg/d), and did not affect feed or N efficiency (1.45 ± 0.2 and 32.0 ± 2.3%, respectively). Treatments did not affect milk fat yield (1.48 ± 0.2 kg/d) but increasing doses of CTS increased milk protein yield quadratically (1.22, 1.27, 1.26, and 1.20 kg/d). Intermediate doses of CTS tended to increase de novo fatty acid yield (352, 369, 373, and 356 g/d) and decrease trans-10 C18:1 (4.31, 4.05, 4.05, and 4.24 g/d) compared with CTR and 30CTS. Treatments did not affect milk urea concentration (17.8 ± 1.7 mg/dL) or milk crude protein (3.39 ± 0.2%) or fat (4.06 ± 0.2%) content. Rumen pH and time below rumen pH of 5.8 were not affected by level of CTS supplementation. A treatment by time interaction for rumen ammonia concentration indicated that 20CTS and 30CTS increased ammonia concentration 3 h post-feeding compared with CTR and 10CTS (7.72, 7.94, 13.7, and 14.1 mg/dL). The 10CTS treatment decreased rumen propionate concentration only at 3 h post-feeding compared with the other treatments. Apparent DM and NDF total-tract digestibility were not affected by treatments. Shotgun metagenomics were used to evaluate the impact of CTS supplementation on the solid- and liquid-associated rumen microbiome. Treatment effects were only observed in the solid-associated microbiome. Supplementation of CTS linearly decreased α diversity at both the taxa and functional levels, indicating promotion of a leaner microbial community with higher doses of CTS. Differential abundance analysis identified 26 species with large fold changes, including some species with a high presence of cellulases and significant correlations with phenotypic parameters such as DMI, N efficiency, and milk production. In conclusion, a mixture of CTS affected microbiome and rumen metabolism, increasing fat-and-protein-corrected milk yield when fed at 10 and 20 g/d only. This experiment demonstrates the importance of in vivo dose response experiments with phytogenic products to determine optimum dosage for improved rumen metabolism and performance.}, } @article {pmid42282649, year = {2026}, author = {Boyd, AI and Quintanilla, KA and Escapa, IF and Lewis, MA and Kafer, LA and Zeng, XL and Blutt, SE and Ibberson, CB and Lemon, KP}, title = {D-alanine aminotransferase (Dat) promotes Staphylococcus aureus colonization fitness on human nasal respiratory epithelium.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42282649}, issn = {2692-8205}, abstract = {Nasal colonization by Staphylococcus aureus is an established risk factor for invasive infection, yet bacterial determinants promoting fitness on human nasal mucosa remain incompletely defined. To identify genes required for early colonization of human nasal respiratory epithelium, we colonized human nasal epithelial organoids differentiated at air-liquid interface (HNO-ALI) with a high-density transposon (Tn) library of the methicillin-resistant USA300 strain LAC. TnSeq analysis identified 165 genes that met our threshold for candidate colonization fitness factors. Among these, genes involved in D-alanine biosynthesis and use were enriched, including two encoding the enzymes that separately synthesize D-alanine in S. aureus: alanine racemase 1 (alr1) and D-alanine aminotransferase (dat). Disruption of dat reduced colonization fitness in competition with the parental strain by ≥ 1,000 fold across 4 different strains from clonal complexes 8, 5, and 30. In competition with the parental strain during HNO-ALI colonization, a dat::Tn mutant was 34-fold less fit than an alr1::Tn mutant. Genetic complementation with single-copy dat expressed from its native operon promoter restored parental colonization levels. Supplementation with exogenous D-alanine or L-alanine also rescued the dat::Tn colonization defect, whereas D-glutamate did not, consistent with Dat primarily producing D-alanine on nasal mucosa. Complementation with dat under control of a putative 5' intra-operon promoter substantially restored colonization but failed to support growth in chemically defined medium lacking L-alanine, suggesting a new layer of environment-specific regulation of dat transcription. Together, these findings demonstrate that Dat is a major source of D-alanine during colonization of human nasal mucosa and is required for S. aureus fitness in this environment.}, } @article {pmid42366391, year = {2026}, author = {Lai, T and Liu, Y and Duan, Z and Su, S and Ding, H and Dai, Y and Gao, M and Ji, M and Liao, L}, title = {Deep metagenomics uncovers functional adaptations and pathogenic risks in the gut microbiome of Antarctic fur seals (Arctocephalus gazella).}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00919-2}, pmid = {42366391}, issn = {2524-6372}, support = {2022YFC2807501//National Key Research and Development Program of China/ ; 42476264//National Natural Science Foundation of China/ ; }, abstract = {The Antarctic fur seal (Arctocephalus gazella) plays a key role in the Antarctic marine ecosystem by regulating krill, fish, and cephalopod populations through selective foraging, promoting Southern Ocean productivity via excretion, and influencing coastal island ecosystems during breeding season. Despite the importance of the gut microbiota in reflecting diet, health, and environmental adaptation, the gut microbiome of the Antarctic fur seal remains poorly characterized. To address this gap and evaluate its potential as a bioindicator of Antarctic marine environmental health, we employed shotgun metagenomics and 16S rRNA amplicon sequencing on fresh fecal samples collected from four Antarctic fur seals (designated S59, S62, S63, and S64) at King George Island, Western Antarctica. Despite inter-individual variation, both approaches identified Bacillota as the dominant phylum but showed genus-level discrepancies, with Fusobacterium prevailing in metagenomes and Clostridium in 16S amplicons. Viral communities constituted up to 5.3% of the microbiome, including an immunodeficiency-associated Lentivirus. Chitin-degrading capacity was ubiquitous, consistent with the host's krill-based diet. Metagenome-assembled genomes (MAGs) resolved distinct taxonomic contributions to discrete steps of chitin hydrolysis, suggesting that complete depolymerization requires metabolic cross-feeding among functionally complementary taxa. Notably, Helicobacter MAGs were abundant in individual S62, suggesting potential pathogenicity. Additionally, 16 antibiotic resistance gene types were detected, with bacitracin, polymyxin, and multidrug resistance dominating the resistome. These findings not only elucidate the community composition, functional potential, and ecological adaptation of the Antarctic fur seal gut microbiota but also establish a comprehensive baseline for assessing environmental change and human impacts on the Antarctic marine ecosystem, thereby offering valuable scientific data and methodological insights for the conservation of polar marine mammals.}, } @article {pmid42366413, year = {2026}, author = {Li, X and Li, Z and Sun, X and Guo, Y and Pang, Z and Niu, G}, title = {Honghe Bunya-like virus: a novel virus identified in mosquitoes from Yunnan, China.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-13112-z}, pmid = {42366413}, issn = {1471-2164}, support = {SDYJSJGC2025059//Shandong Provincial Department of Education/ ; }, abstract = {BACKGROUND: Arboviruses represent a persistent and escalating threat to global public health, with mosquitoes serving as the principal vectors in their natural transmission cycles and geographic dissemination. Yunnan Province, southwestern China, is a recognized hotspot for arboviral diversity, yet the full spectrum of mosquito-borne viruses circulating in this region remains incompletely characterized.

RESULTS: A total of 3,300 female mosquitoes of four species across four genera were collected from rural areas of Honghe County, Yunnan Province in 2024, and subjected to viral metatranscriptomic sequencing. A previously undescribed bunya-like virus, designated Honghe Bunya-like virus, was identified in two locally dominant hematophagous mosquito species, with minimum infection rates of 0.2% and 0.3%, respectively. The viral genome comprises three single-stranded negative-sense RNA segments (L, M, and S) encoding the RdRp, glycoprotein, and nucleoprotein, respectively, consistent with the canonical architecture of the genus Orthobunyavirus. Phylogenetic analyses placed the virus within Orthobunyavirus across all three segments, though inter-segment topological incongruence was observed; amino acid identities to known orthobunyaviruses (49.7%-71.6%) fell below conspecific thresholds, suggesting a novel species.

CONCLUSIONS: This study expands the known genetic diversity of mosquito-associated virus in southwestern China and, given the phylogenetic affinity to pathogenic orthobunyaviruses and the hematophagous nature of the vector species, raises the possibility of vertebrate infection potential warranting further investigation.}, } @article {pmid42366525, year = {2026}, author = {Kan, J and Morales-Amador, A and Hernandez, Y and Burian, J and Ternei, MA and Brady, SF}, title = {Resistance-CONKAT-seq Guided Discovery of a ClpP Active Natural Product from a Soil Metagenome.}, journal = {ACS chemical biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acschembio.6c00347}, pmid = {42366525}, issn = {1554-8937}, abstract = {The discovery of natural products with specific molecular targets from metagenomes remains challenging. To address this limitation, we developed resistance-CONKAT-seq (resistance co-occurrence network analysis of targeted sequences) which links metagenomic BGCs (biosynthetic gene clusters) to potential modes of action through the identification of colocalized molecular target-based resistance genes. Applying this approach to a soil metagenomic library, we identified the uncharacterized metagenomic azetidopyrroline (MTA) BGC associated with a potential clpP self-resistance gene. Genetic engineering and heterologous expression of the MTA BGC led to the discovery of metaze A and B, which are structurally related azetidopyrroline- and bicyclocarbamate-based natural products, respectively. Metaze B inhibited Mycobacterium tuberculosis caseinolytic protease proteolytic subunit (ClpP) with an IC50 of 1.35 μM. This study expands the chemical diversity of natural product ClpP inhibitors and further demonstrates the applicability of resistance-CONKAT-seq for target-guided discovery of natural products with specific modes of action from complex metagenomes.}, } @article {pmid42366537, year = {2026}, author = {Meusel, I and Manheim, D and Delaney, O and Greene, D and Tobolsky, R and Palya, H and Shapiro, N and Sharma, S}, title = {A Metagenomic Biosurveillance Network for Emerging Infectious Diseases: A Simulation-Based Model.}, journal = {Health security}, volume = {}, number = {}, pages = {23265094261453732}, doi = {10.1177/23265094261453732}, pmid = {42366537}, issn = {2326-5108}, abstract = {In this article, we propose a metagenomic next-generation sequencing (mNGS) system for symptomatic clinical respiratory disease samples in Israel to enable detection early enough to contain novel pathogen outbreaks, limit international spread and expedite countermeasure development. We built an open-source, interactive SEIR (susceptible, exposed, infectious, recovered)-based model extending the work of Sharma et al (2023) for 7 representative known respiratory pathogens with pandemic potential, aiming to estimate costs and detection time for the identification of a novel respiratory pathogen in Israel through a network of mNGS monitoring in hospitals. We find that a novel pathogen with SARS-CoV-2-like characteristics could be detected within 68 days (interquartile range [IQR]: 53 to 80) after the first 2 emergency department presentations and 213 (IQR: 94 to 429) total infections across Israel. This surveillance system would cost US$24 million annually over 10 years when implemented in Israel's 6 largest hospitals, covering 37% of the population. Our open-source interactive model allows policymakers and experts to explore different system configurations and their associated tradeoffs between cost, detection speed, and population coverage.}, } @article {pmid42366621, year = {2026}, author = {Tawfiq, R and Kulmanov, M and Hoehndorf, R}, title = {Evaluating completeness, coherence, and consistency of genome-scale function annotations.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {3}, pages = {}, doi = {10.1093/bib/bbag336}, pmid = {42366621}, issn = {1477-4054}, support = {URF/1/5041-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; REI/1/5235-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; REI/1/4938-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; REI/1/5659-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; 5932//King Abdullah University of Science and Technology (KAUST)-KAUST Center of Excellence for Smart Health (KCSH)/ ; 5940//King Abdullah University of Science and Technology (KAUST)-Center of Excellence for Generative AI/ ; //KAUST Supercomputing Laboratory/ ; }, mesh = {*Molecular Sequence Annotation/methods ; Systems Biology/methods ; *Genome ; *Proteins/genetics/metabolism ; Genomics/methods ; Computational Biology/methods ; }, abstract = {Protein function annotation traditionally follows a reductionist approach, assigning functions to individual proteins acting in isolation. This treats each annotation as an independent fact, disconnected from the broader biological system. However, proteins operate within integrated networks where their functions depend on genomic context and interacting partners. This needs to be reflected in function annotation and evaluation frameworks. We assess whether annotated protein functions could plausibly coexist within a living organism. To achieve this goal, we formalize three criteria grounded in systems biology principles: completeness (presence of essential functions), coherence (satisfaction of functional dependencies), and consistency (absence of mutually exclusive functions). We applied this framework to manually curated function annotations from six model organisms and computational function predictions from seven methods. While model organism annotations largely satisfied our constraints, computational function prediction methods systematically failed to produce biologically plausible genome-scale annotations. Our review reveals a measurable gap between the per-protein objectives of current annotation methods and the system-level criteria that an annotation set must satisfy to describe a viable organism. Our evaluation framework grounded in systems biology principles provides quantitative metrics for evaluating biological plausibility and establishes a foundation for developing system-aware annotation approaches. Augmenting protein-level annotation with system-level criteria offers a tractable path to improving annotation of the rapidly growing collection of sequenced genomes and metagenomes.}, } @article {pmid42366665, year = {2026}, author = {Kuzbekov, SR}, title = {[Microbiota and microbiome of the lacrimal drainage system].}, journal = {Vestnik oftalmologii}, volume = {142}, number = {3}, pages = {91-100}, doi = {10.17116/oftalma202614203191}, pmid = {42366665}, issn = {0042-465X}, mesh = {Humans ; *Microbiota ; *Lacrimal Apparatus/microbiology/physiopathology/pathology ; *Dacryocystitis/microbiology/diagnosis/physiopathology ; *Lacrimal Duct Obstruction/diagnosis ; Anti-Bacterial Agents/pharmacology ; }, abstract = {This review analyzes current concepts of the role of the microbiota and microbiome in the physiology and pathology of the human lacrimal drainage system (LDS). The terms are clearly differentiated: microbiota is the collection of living microorganisms, whereas microbiome also includes their genetic material and habitat. The article describes anatomical features of the LDS and involutional changes in adults (atrophy of the lacrimal puncta, canalicular fibrosis, and nasolacrimal duct stenosis), which predispose to tear stagnation and inflammation. The review includes a comparative analysis of the microbiological spectrum in healthy individuals and patients with dacryocystitis and canaliculitis. The composition of the flora was found to differ substantially depending on age (predominance of S. pneumoniae in children versus Staphylococcus spp. in adults) and geographical region. Metagenomic sequencing data (16S rRNA) demonstrate significantly greater microbial diversity compared with conventional culture methods, revealing a broad spectrum of aerobes, anaerobes, and fungi. The work pays particular attention to regional resistance patterns, including the high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in several Asian countries. Based on the literature data this study proposes and algorithm for empirical antibacterial therapy, taking into account the likely pathogens, as well as the indications for surgical correction, and emphasizes the prospects for creating a national map of the LDS microbiome in the Russian Federation to optimize treatment strategies for dacryocystitis and dacryostenosis.}, } @article {pmid42366735, year = {2026}, author = {Guo, X and Lai, CY and Zhao, HP}, title = {Targeted Acclimation Unlocks Adaptive Evolution of a Methanotrophic Consortium Enabling 3A5MI Elimination and Enhanced Sulfamethoxazole Biodegradation.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c02194}, pmid = {42366735}, issn = {1520-5851}, abstract = {Targeted pollutant exposure is widely used to acclimate microbial communities for enhanced biodegradation of recalcitrant contaminants, yet the evolutionary mechanisms underlying functional reinforcement remain poorly understood. Here, we acclimated a methanotrophic consortium achieving efficient removal of 3-amino-5-methyl-isoxazole (3A5MI) (>90%, >5 mg/L/d) and elucidated the adaptive evolutionary processes behind it. Analyses of mobile genetic elements (MGEs) and horizontal gene transfer (HGT) revealed that dominant Methylococcaceae members served as genetic exchange hubs in the acclimation bioreactor. Integrated metagenomic and metatranscriptomic analyses showed that prolonged 3A5MI exposure activated their MGEs and promoted extensive HGT of genes related to energy generation, oxidative stress defense, and biosynthesis. This adaptive evolution enabled community-level metabolic rewiring, including optimized carbon metabolism to relieve energy limitation, niche differentiation, and specialized transcription of C-N bond catalytic functions. Furthermore, batch experiments and transformation product analyses confirmed that 3A5MI-induced functional traits (e.g., heterocycle hydroxylation and C-N bond catalysis) facilitated complete sulfamethoxazole (SMX) biodegradation. Overall, this study demonstrates the evolutionary plasticity of methanotrophic consortia under targeted acclimation and highlights MGE-driven genetic exchange and metabolic adaptation as key mechanisms that both underpin functional enhancement and support the development of methanotroph-based strategies for the biodegradation of recalcitrant isoxazole-based pollutants.}, } @article {pmid42367190, year = {2026}, author = {Teng, Y and Saghaï, A}, title = {Fermentative nitrite ammonifiers are abundant in soils and ecologically distinct from NrfA-dependent ammonifiers.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag144}, pmid = {42367190}, issn = {2730-6151}, abstract = {Microorganisms can use different enzymes to perform nitrite ammonification, the reduction of nitrite to ammonium, an important process to retain nitrogen in soils. Yet, the organisms mediating this process and their distribution in terrestrial ecosystems remain poorly resolved. Here, we determined the phylogenetic diversity of bacteria performing fermentative nitrite ammonification via the NAD(P)H-dependent nitrite reductase NirB, assessed their distribution across terrestrial ecosystems, and identified their environmental preferences. We found that these organisms are broadly distributed, spanning 29 phyla including Bacillota, Pseudomonadota and Actinomycetota. Screening 1587 globally distributed soil metagenomes using a phylogeny-based approach revealed that fermentative nitrite ammonifiers are ubiquitous across biomes and particularly abundant in Mediterranean forests and desert soils. In these ecosystems, they outnumbered NrfA-dependent ammonifiers, the best characterized ammonifier group to date, suggesting distinct ecological niches for the two groups. Consistent with this, random forest modelling revealed a negative relationship between fermentative nitrite ammonifiers and the carbon-to-nitrate ratio, which contrasts with a preference for high carbon-to-nitrate conditions in NrfA-dependent ammonifiers. However, moisture and salinity emerged as the strongest predictors of the abundance of fermentative nitrite ammonifiers, indicating a high tolerance to osmotic stress in this group. Overall, our results demonstrate that fermentative nitrite ammonifiers are both phylogenetically diverse and environmentally widespread, calling for future efforts to determine the conditions under which they contribute to nitrogen retention in soils.}, } @article {pmid42367193, year = {2026}, author = {Guo, S and McNamara, NP and Bending, GD and Mushinski, RM}, title = {Phosphorus availability mediates pathway-specific nitrogen cycling in stratified peatland microbiomes.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag143}, pmid = {42367193}, issn = {2730-6151}, abstract = {Peatland microbiomes regulate nitrogen (N) cycling processes that control nutrient retention and greenhouse gas emissions in carbon-rich ecosystems. Although depth-driven redox gradients structure microbial communities, how physicochemical stratification shapes the functional versus taxonomic organization of N-cycling microorganisms remains unclear. We used shotgun metagenomics to characterize N-cycling gene distributions, taxonomic affiliations, and metagenome-assembled genomes (MAGs) across depth and vegetation gradients in a temperate blanket bog. Depth emerged as the primary structuring factor, creating functional-taxonomic decoupling. Surface peat (0-20 cm) harbored functionally diverse but taxonomically constrained communities assembled deterministically around nitrification and labile N acquisition, while subsurface peat (20-40 cm) supported taxonomically richer but functionally-simpler communities assembled stochastically and enriched in denitrification and dissimilatory nitrate reduction. Linear mixed-effects models revealed pathway-specific controls on N cycling. Denitrification increased with depth (β = 11.53, P < .05), whereas organic N transformation declined (β = -5.81, P < .05); depth effects on nitrification and N fixation became non-significant after accounting for environmental variables. Phosphorus (P) emerged as the strongest environmental predictor, regulating nitrification (β = 95.40, P < .01), N fixation (β = 128.33, P < .01), organic N transformation (β = 80.53, P < .01), and denitrification (β = -109.63, P < .05), highlighting the importance of P availability in structuring microbial N cycling. This challenges traditional N-limitation paradigms in ombrotrophic systems. MAGs revealed Pseudomonadota as the dominant N-cycling lineage, while incomplete denitrification capacity indicated genetic potential for N2O accumulation in subsurface layers. These findings demonstrate that P availability, rather than N content alone, regulates microbial N transformation capacity in peatlands, with implications for predicting nutrient dynamics under altered hydrological and nutrient deposition regimes.}, } @article {pmid42367641, year = {2026}, author = {Xu, C and Liu, T and Zhang, X and Feng, S}, title = {Application value and challenges associated with plasma cell-free DNA metagenomic sequencing technology in the diagnosis of infections in patients with hematological disorders.}, journal = {Blood science (Baltimore, Md.)}, volume = {8}, number = {3}, pages = {e00304}, pmid = {42367641}, issn = {2543-6368}, abstract = {In patients with hematological disorders, the high risk of complex infections caused by immune dysfunction and intensive therapies poses a major challenge to the use of conventional microbiological tests (CMTs). Plasma cell-free DNA (cfDNA) metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary noninvasive tool that enables unbiased, broad-spectrum, and rapid pathogen identification directly from blood samples. This review summarizes the core applications of plasma cfDNA mNGS in patients with hematological disorders, including the diagnosis of febrile neutropenia, bloodstream infections, focal infections, and infections caused by uncommon/fastidious pathogens. It highlights the advantages of this technology in overcoming antibiotic interference, enabling early detection, and providing diagnostic value in cases without clear infection foci or when invasive sampling is not feasible. This review further discusses how China has facilitated the widespread adoption of this technology through a localized application model, cost reduction, and the development of clinically relevant interpretation models. Nevertheless, challenges remain, such as lower sensitivity than site-specific specimens in focal infections, and the difficulty in predicting antimicrobial resistance (AMR) on the basis of cfDNA mNGS. Future developmental directions should focus on technical optimization (eg, combined plasma cell-fraction testing), quality assurance and quality control management, multidimensional data integration (eg, host immune response analysis), artificial intelligence (AI)-assisted interpretation, and cost reduction through technology popularization and insurance coverage. These efforts will advance cfDNA mNGS from a pathogen detection tool toward an intelligent clinical decision-support platform, ultimately improving the diagnostic accuracy and clinical outcomes of hematological patients with infections.}, } @article {pmid42367778, year = {2026}, author = {Fan, R and Zang, Q and Xu, Y and Gao, L and Zhou, J and Zang, Y}, title = {Metagenomic characterization of gut microbiota in rheumatoid arthritis-associated interstitial lung disease: taxonomic shifts and clinical correlations.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1868704}, pmid = {42367778}, issn = {1664-3224}, mesh = {Humans ; *Arthritis, Rheumatoid/complications/microbiology ; *Lung Diseases, Interstitial/microbiology/etiology ; Female ; *Metagenomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Feces/microbiology ; Aged ; *Bacteria/classification/genetics ; Dysbiosis/microbiology ; *Metagenome ; }, abstract = {BACKGROUND: Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a severe extra-articular manifestation with limited diagnostic biomarkers. While gut microbiota dysbiosis contributes to rheumatoid arthritis (RA) pathogenesis, its specific role in RA-ILD remains poorly characterized.

METHODS: We performed shotgun metagenomic sequencing on fecal samples from 41 participants: 10 RA-ILD patients, 20 RA patients without ILD (RA-non-ILD), and 11 healthy controls (HCs). We assessed alpha and beta diversity, differential abundance (Wilcoxon rank-sum tests with FDR correction), Spearman correlations with clinical parameters, microbial co-occurrence networks, and random forest classification.

RESULTS: Alpha and beta diversity did not differ significantly among groups. After FDR correction, no genus differed significantly between RA-ILD and RA-non-ILD. Exploratory analysis (uncorrected P < 0.05) revealed enrichment of Escherichia/Shigella in RA-ILD (11.72% vs. 2.66%, P = 0.003) and depletion of Roseburia (1.05% vs. 3.77%, P = 0.005) and Ruminococcus (5.98% vs. 7.85%, P = 0.032), while Faecalibacterium showed a trend toward depletion without reaching nominal significance (4.45% vs. 4.66%, P = 0.409). Correlation analysis revealed a dichotomous pattern: pro-inflammatory genera correlated positively with disease activity, while butyrate-producing genera correlated negatively. Co-occurrence network analysis showed RA patients had a more complex network than HC and RA-ILD. Random forest classification identified Bifidobacterium, unclassified_ Oscillospiraceae, and unclassified_Lachnospiraceae as top discriminators between HC and RA, and unclassified_ Bacteroidaceae, Parabacteroides, and Blautia for RA-ILD vs RA.

CONCLUSIONS: RA-ILD is associated with specific gut microbial alterations-notably Escherichia/Shigella enrichment and depletion of Roseburia and Ruminococcus-despite preserved overall diversity. These changes correlate with systemic inflammation and suggest a role for the gut microbiota in RA-ILD pathogenesis via the gut-lung axis. The identified taxa warrant validation as candidate biomarkers in larger cohorts.}, } @article {pmid42367784, year = {2026}, author = {Zheng, X and Li, D and Yao, X and Luo, X and Gao, C and Yan, X}, title = {The gut microbiota-immune-brain axis in post-traumatic stress disorder: mechanistic integration and translational prospects.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1859206}, pmid = {42367784}, issn = {1664-3224}, mesh = {Humans ; *Stress Disorders, Post-Traumatic/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/immunology ; Animals ; *Brain/immunology/metabolism ; Translational Research, Biomedical ; Intestinal Barrier Function ; Neuroimmunomodulation ; }, abstract = {Post-traumatic stress disorder (PTSD) is a complex mental disorder triggered by severe traumatic events. Its pathophysiology involves not only abnormalities in fear memory circuits and neuroendocrine imbalances but also immune dysregulation and alterations in gut homeostasis. In recent years, the gut microbiota, as a crucial regulatory factor connecting the periphery and the central nervous system, has garnered widespread attention for its potential role in the development and progression of PTSD, offering a new integrative perspective for understanding this disorder. This article focuses on the "gut microbiota-immune-brain axis" framework, reviewing evidence related to changes in the composition and function of the gut microbiota in PTSD. It summarizes how these changes may influence neuroplasticity abnormalities and PTSD-related behavioral phenotypes through mechanisms involving microbial metabolite production, modulation of intestinal barrier integrity, immuno-inflammatory responses, regulation of neuroendocrine homeostasis, and blood-brain barrier dysfunction. However, these mechanistic pathways remain incompletely validated in human studies. Existing research suggests that this axis holds significant value in explaining the multisystem pathological features of PTSD. Nevertheless, challenges persist, including ambiguous causal relationships in microbiota-host interactions, limited direct clinical evidence, and insufficient translational research. Current evidence primarily stems from observational studies, preclinical models, and preliminary intervention studies. The explanatory power varies across these evidence levels: population studies primarily establish correlations, animal models facilitate mechanistic validation, metagenomic and metabolic analyses yield functional insights, while clinical intervention data remain exploratory. This article aims to elucidate the key molecular and systemic mechanisms underlying this axis in PTSD and to evaluate the potential translational value and practical limitations of microbial intervention and immune modulation strategies.}, } @article {pmid42367847, year = {2026}, author = {Sparagon, WJ and Lary, S and Ioh, MT and Lin, A and Dhungana, I and Fullmer, CR and Handel, CR and Paudel, R and Burden, J and Deubel, JN and Tayo, MAG and Rodriguez, FE and Swift, SOI and Nakayama, KK and Maaz, TM and Nguyen, NH}, title = {Soil Resistomes in a Tropical Watershed are Indirectly Structured by Bacterial Community Interactions with Soil Properties.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.18.733189}, pmid = {42367847}, issn = {2692-8205}, abstract = {Soils are recognized as reservoirs of antibiotic resistance genes (ARGs) with the potential to transfer to clinical pathogens, creating antimicrobial resistance (AMR) that poses a threat to human health. While large-scale AMR surveys have profiled how diverse biomes shape soil resistomes, less is known about the influence of specific soil properties. Here, we combined metagenomics and 16S rRNA amplicon sequencing with isolate-based approaches to investigate drivers of soil AMR across a tropical watershed from beach to mountaintop in Waimea Valley, O'ahu, Hawai□i. We leveraged functional- and taxonomic-classification of resistances to unravel how soil properties interact with bacterial taxa to structure resistomes. Metagenomic- and isolate-resistomes showed remarkable consistency, including a general gradient of increasing AMR from ridge to beach. Resistome functional composition was significantly correlated with total bacterial community structure. The relationship between resistances and soil properties was primarily dictated by taxonomic composition of each resistance. Rifampin- and Vancomycin-ARGs associated with Actinomycetes negatively correlated with soil physical properties, while resistant genes and isolates from Gammaproteobacteria positively correlated with enzymatic activity metrics. These findings indicate that soil properties structure the resistome indirectly through taxonomic filtering of microbial hosts and challenge the notion that AMR is decoupled from phylogenetic relatedness.}, } @article {pmid42367895, year = {2026}, author = {Cuau, M and Avalon, NE and Ryu, B and Glukhov, E and Almaliti, J and Rego, A and Teixeira, TR and Shingyoji, M and De Souza, ML and Trinidad-Javier, A and Kumpornsin, K and Chen, J and McNamara, CW and Caffrey, CR and Winzeler, EA and Vasconcelos, VM and Leão, PN and Gerwick, WH}, title = {AI-Accelerated Structure Elucidation of Boavistamides A-C, Cyclic Depsipeptides from a Marine Filamentous Cyanobacterium Collected in Cabo Verde.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.13.732064}, pmid = {42367895}, issn = {2692-8205}, abstract = {Boavistamide A (1), a new alkyne-containing cyclic depsipeptide featuring the rare 3-amino-2-methyl-7-octynoic acid (AMOYA) moiety, was discovered along with two structurally related analogs, boavistamides B and C (2 and 3), from a filamentous marine cyanobacterium collected on Boa Vista Island, Cabo Verde. Their isolation was guided by antiplasmodial activity, GNPS MS/MS molecular networking, LC-MS profiling, and dereplication using the MarinLit database. The planar structures of boavistamides A-C (1 - 3) were elucidated through comprehensive HRMS and 1D/2D NMR analyses, with annotation support from AI-based tools SMART-NMR 2.1 and DeepSAT. The absolute configurations were established using Marfey's analysis and L-Phe-OMe coupling, complemented by NMR-based conformational studies. Boavistamides A and B exhibited moderate antiplasmodial activity with no mammalian cell cytotoxicity. Microscopic observations and metagenomic binning identified the producer strain as belonging to the genus Okeania (Microcoleaceae). These results expand the chemical diversity of AMOYA-containing cyanobacterial metabolites and highlight the utility of integrated metabolomics and AI-assisted workflows for natural product discovery from environmental samples.}, } @article {pmid42368165, year = {2026}, author = {Tinker, KA and Ross, DE and Beebe, MN and Bagwell, CE and Smallwood, CR and Davis, RW and Gulliver, DM}, title = {Biogeochemical Assessment of Short-Term Hydrogen Storage in Methane Reservoirs with Field Sample Characterization and Reactor Experiments.}, journal = {ACS omega}, volume = {11}, number = {24}, pages = {34976-34986}, pmid = {42368165}, issn = {2470-1343}, abstract = {Hydrogen is a valuable commodity due to its high energy density and properties as a flexible energy carrier. It is possible to store hydrogen by blending it with methane and utilizing existing natural gas infrastructure. However, adapting current methane storage strategies to withstand the expected biogeochemical processes caused by H2 injection has not been fully explored. In this study, a series of experiments were designed to identify potential geochemical and microbial challenges of storing hydrogen/methane gas blends in existing methane reservoirs. First, fluid samples were collected from two methane reservoirs located in the western United States. The geochemical composition, microbial taxonomy, and metabolic potential of each fluid sample were characterized by utilizing ion chromatography (IC), inductively coupled plasma optical emission spectroscopy (ICP-OES), a Total Organic Carbon (TOC) analyzer, 16S rRNA gene amplicon sequencing, and metagenomic sequencing. Next, fluid samples from one field site (Site 2) were used to complete a series of short-term reactor experiments at reservoir conditions (80 °C and ∼1000 psi) for natural gas (100% CH4) and hydrogen blend (80% CH4/20% H2) storage environments. Both biotic and abiotic (sterilized) measurements were conducted to accurately understand and decouple abiotic and microbially driven processes, with the goal of linking these processes to storage impacts. Overall, the two reservoirs had a high, but variable, total dissolved solids (TDS) concentration, with various organic acids including acetate and propionate. The field sample was characterized by a diverse microbial community with the metabolic capacity for sulfur reduction, iron reduction, and acetogenesis. Across these reactors, there was minimal change in the fluid geochemistry and a minimal (0-5%) decrease of hydrogen gas during the initial storage event (days 1-3). This work contributes to the understanding of the complexities of hydrogen storage and demonstrates the need for additional research.}, } @article {pmid42368245, year = {2026}, author = {Bahr, NC and Kasibante, J and Nsangi, L and Kagimu, E and Ssebambulidde, K and Rutakingirwa, MK and Tugume, L and Ramachandran, PS and Cresswell, F and Meya, DB and Boulware, DR and Wilson, MR and Ellis, J}, title = {Central Nervous System Toxoplasmosis is an Under-Recognized Opportunistic infection in Uganda.}, journal = {Journal of tropical medicine}, volume = {2026}, number = {}, pages = {2158978}, pmid = {42368245}, issn = {1687-9686}, abstract = {In Uganda, Toxoplasma meningoencephalitis remains underdiagnosed due to the low sensitivities and specificities of available diagnostics. In our recent publication, we identified 15 cases of possible Toxoplasma gondii meningoencephalitis by cerebrospinal fluid metagenomic next-generation sequencing in patients with suspected meningitis. We herein discuss, in detail, these cases to highlight the ongoing limitations of utilizing clinical symptoms to diagnose Toxoplasma gondii meningoencephalitis, the importance of access to rapid diagnostics, and the frequency of toxoplasmosis as a possible co-infection with other opportunistic diseases among people with advanced HIV.}, } @article {pmid42368276, year = {2026}, author = {Zhu, H and Lin, Y and Liao, H and Li, X and Xie, Q and Zheng, Y}, title = {Infantile pulmonary abscess due to Mycobacterium abscessus subsp. massiliense identified by integrated mNGS and targeted NGS: a rare case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1828339}, pmid = {42368276}, issn = {2296-2360}, abstract = {BACKGROUND: To describe a rare case of pulmonary infection caused by Mycobacterium abscessus in an infant and to evaluate the complementary diagnostic value of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in identifying non-tuberculous mycobacterial (NTM) infections when conventional testing is inconclusive.

CASE PRESENTATION: A 3-month-old male infant presented with a persistent cough and a right upper-lobe mass, initially suspected to be a congenital malformation or neoplasm. Following inconclusive routine examinations, mNGS was performed on bronchoalveolar lavage fluid (BALF). mNGS detected a single read of M. abscessus in BALF, providing an initial diagnostic clue. Subsequently, a tNGS assay was conducted on both BALF and resected lung tissue to achieve precise species identification. tNGS identified 13,272 reads of M. abscessus subsp. massiliense in BALF and 31,474 reads in lung tissue, confirming the pathogen and enabling precise molecular diagnosis. Histopathological examination revealed granulomatous inflammation with multinucleated giant cells, consistent with NTM infection. Guided by these results, the patient initially received azithromycin and was transferred to a specialized chest hospital, where a multidrug anti-NTM regimen was formulated, including azithromycin, imipenem-cilastatin, cefoxitin, and linezolid. After continued treatment at a local municipal hospital, respiratory symptoms resolved, inflammatory markers improved, follow-up CT showed progressive absorption of the right upper-lobe lesion with a small residual cavity, and the patient was discharged in stable condition without recurrent infections during available follow-up.

CONCLUSION: This case highlights the diagnostic utility of integrating mNGS and tNGS for the accurate identification of rare NTM infections in infants, particularly when routine microbiological tests and imaging findings are inconclusive.}, } @article {pmid42368287, year = {2026}, author = {Li, M and Sun, Z and Jia, T and Ma, M}, title = {Insights into the mechanism of intestinal flora imbalance and immune disorder in co-morbidity of pneumonia and diarrhea in children.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1836762}, pmid = {42368287}, issn = {2296-2360}, abstract = {Pneumonia and diarrhea are the two leading causes of death in children under five years of age, and these two conditions often present as a comorbidity, where the same child experiences respiratory and digestive system infection symptoms simultaneously or sequentially. Clinical data indicate that the incidence of secondary diarrhea in children hospitalized with pneumonia is high, significantly prolonging hospital stays and affecting prognosis. In recent years, the proposal of the gut-lung axis theory has provided a novel perspective for understanding this comorbidity phenomenon. The gut-lung axis refers to the bidirectional regulatory pathway between the gut microbiota and the pulmonary immune system, with the lungs and intestines sharing embryonic origin and a common mucosal immune system. This review systematically reviews the characteristics of gut microbiota dysbiosis and the mechanisms of immune disorders in the context of pediatric pneumonia-diarrhea comorbidity. Clinical studies have shown that children with comorbidity exhibit significant gut microbiota dysbiosis, characterized by a reduction in beneficial bacteria such as Bifidobacterium, an increase in opportunistic pathogens such as Escherichia coli, and decreased microbial diversity. Gut microbiota dysbiosis leads to immune disorders through multiple mechanisms, including reduced short-chain fatty acids, skewed immune cell differentiation, and dysregulated inflammatory factor networks, resulting in Th1/Th2 imbalance, decreased regulatory T cell function, and exacerbated systemic inflammatory responses. Supplementation with microecological preparations such as Saccharomyces boulardii has been shown to significantly shorten hospital stays, diarrhea duration, and fever resolution time, while improving peripheral blood immunoglobulin levels and T-cell subsets, providing evidence-based support for clinical intervention. This review also systematically reviews clinical laboratory indicators associated with comorbidity, including inflammatory markers, immune status indicators, intestinal barrier function markers, and microbiota detection methods, which have important application value in early identification, disease assessment, and treatment monitoring of comorbidity. Future research should further employ metagenomic approaches combined with longitudinal follow-up designs to elucidate the roles of specific bacterial species/strains in gut-lung axis regulation, providing new strategies for precision prevention and treatment of pediatric pneumonia-diarrhea comorbidity.}, } @article {pmid42368316, year = {2026}, author = {Zheng, H and Zhuang, J and Lin, Q and Wang, T and Guo, G and Huang, L and Lin, W}, title = {Study on the role and clinical relevance of gut microbiota in diabetic foot ulcers.}, journal = {3 Biotech}, volume = {16}, number = {7}, pages = {287}, pmid = {42368316}, issn = {2190-572X}, abstract = {UNLABELLED: Diabetic foot ulcers (DFU) are severe and costly complications of diabetes, predisposing to infection, amputation, and mortality, highlighting the urgent need to clarify their mechanisms for optimized clinical management. This study integrated clinical biochemistry data and multi-omics analyses (including metagenomic sequencing) from 11 patients to reveal the critical role of gut microbiota in the pathogenesis of DFU. Results showed significant host metabolic disorders in DFU patients, characterized by hypoalbuminemia (mean ± SD:32.35 ± 6.02 g/L), persistent hyperglycemia (mean ± SD:8.25 ± 3.21 mmol/L), and imbalances in trace elements such as magnesium (mean ± SD:0.84 ± 0.08 mmol/L). Concurrently, the gut microbiota composition was markedly altered, with enrichment of the phylum Bacillota_A (formerly Firmicutes; 48.7% in patients vs. 32.1% in controls) and elevated genetic potential of virulence genes (e.g., type VI secretion systems, capsular polysaccharide gene cps4J/L). Metagenomic tracing revealed that antibiotic resistance genes (ARGs) such as tet(A) and blaOXA-1 were co-localized with mobile genetic elements (MGEs) including IncF plasmids and tnpA transposases. 99.2% of key ARGs shared sequence homology with gut-derived metagenome-assembled genomes (MAGs) and co-localized with MGEs, indicating potential cross-niche transfer capacity. Furthermore, renal (mean ± SD:11.81 ± 5.75 mmol/L) and hepatic (ALT: 35.67 ± 18.22 U/L) dysfunction correlated with aggravated gut dysbiosis and ARG enrichment. In conclusion, this study confirms that host metabolic deficiencies contribute to DFU refractoriness by altering gut microbiota ecology and enhancing horizontal gene transfer of virulence and resistance determinants, providing a novel framework for precision therapies targeting the host-microbe metabolic interface.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04745-8.}, } @article {pmid42368546, year = {2026}, author = {Xue, G and Hu, Y and Xue, H and Wang, X and Bai, H and Du, J and Wang, Y and Huo, H and Li, M and Jiang, W}, title = {Erratum: Biochar enhances cucumber production by modulating rhizosphere microbiota and soil metabolites under continuous cropping systems.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1899816}, doi = {10.3389/fpls.2026.1899816}, pmid = {42368546}, issn = {1664-462X}, abstract = {[This corrects the article DOI: 10.3389/fpls.2026.1726191.].}, } @article {pmid42368826, year = {2026}, author = {Martínez-Noriega, M and Jean-Louis, P and Philippon, M and Sanchez-Flores, A and Gonzalez-Rizzo, S}, title = {Revealing the bacterial diversity and variation of white filamentous microbial mats in marine mangroves of Guadeloupe Island in relation to human activities.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag034}, pmid = {42368826}, issn = {2633-6685}, abstract = {White filamentous microbial mats are complex benthic communities, typically structured by sulfur-oxidizing bacteria from the Beggiatoaceae family, yet their diversity and ecological responses in mangrove ecosystems remain poorly characterized. Here, we provide a high-resolution analysis of bacterial communities associated with white microbial mats in marine mangrove sediments of Guadeloupe using 16S rRNA metabarcoding. Bacterial community composition was compared across sites with different levels of anthropogenic impact (protected, natural, and urban). While overall diversity remained stable, richness differed significantly between conditions, and beta diversity analyses revealed clear compositional structuring along the disturbance gradient. A conserved core microbiome was identified across all sites, whereas rare taxa were detected exclusively in urban sites, including Ferrimicrobium, Thermonospora, Alcanivorax, and Serratia, which has been previously associated with human-induced environmental changes. In contrast, Prosthecochloris and Chlorobaculum were highly abundant in protected sites, whereas Sulfurovum and Sulfurimonas dominated urban environments. The relative abundance of Beggiatoaceae also varied across sites, suggesting sensitivity to anthropogenic disturbance. Despite these compositional shifts, measured physicochemical parameters did not significantly correlate with the community structure, suggesting that microbial mat organization is influenced by fine-scale or unmeasured environmental gradients. Together, these findings indicate that white microbial mats respond to anthropogenic disturbance primarily through taxonomic restructuring rather than loss of diversity, highlighting their potential as sensitive indicators of environmental change in mangrove ecosystems.}, } @article {pmid42368984, year = {2026}, author = {Basbouss-Serhal, I and Fayad, F}, title = {Familial Mediterranean Fever and the Gut Microbiota: A Dual Perspective Review of Current Evidence.}, journal = {Mediterranean journal of rheumatology}, volume = {37}, number = {2}, pages = {302-308}, pmid = {42368984}, issn = {2529-198X}, abstract = {Familial Mediterranean Fever is a well-known autoinflammatory disease resulting from mutations in the MEFV gene. A recent development has linked FMF pathogenesis and mode of expression to the gut micro-biota. There may be a change in the gut microbiota profile of FMF patients, characterised by low diversity and a depletion of beneficial bacteria. Dysbiosis tends to be linked to increased gut permeability, systemic inflammation, and low response to colchicine treatment. Probiotics and prebiotics, in this case, may help restore the previous idyllic state of the microbial balance, along with a reduction in inflammatory markers, thereby demonstrating therapeutic merit. Notably, however, it did argue in some instances that changes in the microbiota were secondary to the genetic and inflammatory nature of FMF itself. It is still important to carry out longitudinal studies of naïve patients that will integrate metagenomics with immune profiling to ascertain whether microbial changes arise from causes, contributions, or coincidence in the pathogenesis of FMF.}, } @article {pmid42369126, year = {2026}, author = {Pang, H and Pi, C and Shen, P and Tang, Z and Bao, E and Luo, X and Zhang, Q}, title = {Case Report: pharmaceutical care in a case of complicated urinary tract infection combined with disseminated Nocardia brasiliensis infection.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1839868}, pmid = {42369126}, issn = {2296-858X}, abstract = {Given the increasing prevalence of multidrug-resistant opportunistic pathogens and the high mortality rate associated with delayed diagnosis of disseminated infections, there is an urgent need for rapid diagnostic tools and closely monitored, individualized anti-infective strategies. This study aimed to explore the critical role of comprehensive pharmaceutical care in managing disseminated Nocardia infections complicated by complicated urinary tract infection (cUTI). Through detailed documentation of a 67-year-old male patient, this study focuses on optimizing antimicrobial regimens based on pathogenetic findings and adjusting treatments for severe adverse reactions. The patient was diagnosed with disseminated Nocardia brasiliensis infection complicated by Enterococcus faecalis urinary tract infection using metagenomic next-generation sequencing (mNGS). The treatment process underwent two critical adjustments. First, during the efficacy optimization phase, the initial empirical meropenem therapy was modified to a reinforced regimen centered on trimethoprim-sulfamethoxazole (TMP-SMX), combined with linezolid and short-term amikacin, effectively controlling the spread of infection. Subsequently, during the safety optimization phase, the patient developed severe thrombocytopenia during sequential oral therapy. Prompt identification and switching to amoxicillin/clavulanate potassium resolved the adverse reactions, enabling successful continuation of subsequent treatment. Follow-up revealed a favorable patient recovery. This case demonstrates that for such complex mixed infections, rapid pathogen diagnosis represented by mNGS serves as the starting point for precision treatment, whereas the intensive combination regimen centered on TMP-SMX forms the foundation for controlling disseminated Nocardia infection. More importantly, the core insight from this case is that successful treatment relies not only on appropriate initial medication, but more critically, on proactive, dynamic pharmaceutical monitoring throughout long-term therapy. This enables early intervention for severe adverse drug reactions and timely, flexible adjustments to treatment regimens, which are essential components for ensuring ultimate therapeutic success in patients with such complex infections.}, } @article {pmid42369553, year = {2026}, author = {Xu, S and Jia, M and Guo, X and Liang, W and Pan, Y and Lin, Y and Li, X and Qiu, H and Hu, D and Yan, D}, title = {Metagenomics and metabolomics analyses of the mechanism of non-expression of natural mating behavior in captive male Malayan pangolins (Manis javanica).}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1828282}, pmid = {42369553}, issn = {1664-302X}, abstract = {Ex situ conservation and captive breeding are important measures for conserving endangered species. However, the reproduction of some wild animals, especially males, is inhibited in captivity, but the underlying mechanism has not yet been elucidated. This study aimed to investigate the microbiota and their functions, metabolites, and their metabolic pathways impacting reproduction employing metagenomics and metabolomics analyses and using male Malayan pangolins with normal (with natural mating behavior) and abnormal (no natural mating behavior) reproduction as the research objects. The results showed that the relative abundance of Proteobacteria, Escherichia coli, and Shigella spp. was significantly higher in the abnormal reproduction (AR) group. However, the relative abundance of Firmicutes and Staphylococcus aureus was significantly higher in the normal reproduction (NR) group. Kyoto Encyclopedia of Genes and Genomes functional pathway enrichment analysis found that citrate cycle (TCA cycle, KO00020) and pyruvate metabolism (KO00620) were significantly enriched in pangolins with AR, whereas gonadotropin-releasing hormone secretion (KO04929) was significantly enriched in pangolins with NR. Metabolites such as tryptophan, arginine, and androgen were significantly enriched in pangolins with AR, whereas L-proline, taurine, choline, and spermidine were significantly enriched in pangolins with NR. Microbiota dysbiosis, energy metabolism disorder, deficiencies in key metabolic pathways and metabolites, and hormonal disturbances are all potential factors contributing to the inability of male Malayan pangolin to express natural reproductive behavior. This study provides evidence for AR of captive pangolins and offers important insights for the conservation of captive endangered species.}, } @article {pmid42369554, year = {2026}, author = {Zi, GR and Zhang, DJ and He, DL and Shu, F and Ou, Y and Ke, CX}, title = {Current status and prospects of nanopore sequencing technology in the detection of pathogenic microorganisms.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1843102}, pmid = {42369554}, issn = {1664-302X}, abstract = {Rapid and accurate detection of pathogenic microorganisms is the key to clinical diagnosis and treatment as well as public health prevention and control. As a representative of the third-generation sequencing technologies, nanopore sequencing technology has brought revolutionary potential to the field of pathogen detection by virtue of its unique advantages such as long read length, real-time sequencing and portable instruments. This paper aims to review the current application status of this technology and prospect its future development. Firstly, the basic principles and the development of mainstream platforms of nanopore sequencing are outlined. Subsequently, its specific applications in the detection of various pathogens including bacteria, viruses, fungi and parasites are systematically elaborated, with a focus on analyzing the practice and remarkable advantages of this technology in scenarios such as direct metagenomic detection without culture, rapid identification of drug resistance and virulence factors, and point-of-care rapid diagnosis. Meanwhile, this paper also objectively discusses the main technical challenges faced in the current application, including the raw read accuracy, the complexity of bioinformatics analysis and the balance between cost and benefit. Finally, the future technological optimization, standardization of data analysis workflows and the expansion of broader clinical application scenarios are prospected. Importantly, this review aims to equip clinical laboratory professionals with a balanced, evidence-based framework to evaluate the readiness, utility, and implementation pathway of nanopore sequencing for specific diagnostic use-cases (e.g., urgent meningitis/endophthalmitis, culture-negative infections, resistance gene detection) within the constraints of a clinical lab, such as cost, turnaround time, and staff expertise, in order to provide new technical perspectives and theoretical support for the precise diagnosis and active surveillance of infectious diseases.}, } @article {pmid42369768, year = {2026}, author = {Papalitsas, C and Mouratidis, I and Patsakis, M and Stogiannos, E and Georgakopoulos-Soares, I and Koulouras, G}, title = {A foundational quantum framework for multi-pattern string matching in k-mer detection.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1802517}, pmid = {42369768}, issn = {2673-7647}, abstract = {MOTIVATION: The exponential growth of publicly available genomic data has created unprecedented opportunities for sequence-based discovery. Locating specific k-mers is fundamental to diverse applications, including metagenomic classification, pathogen and cancer detection, and variant calling yet efficient identification of multiple k-mer patterns across large sequencing data and massive databases remains a significant computational challenge.

METHOD: We implement two quantum algorithms for DNA multi-pattern string matching for k-mer detection, leveraging Grover's amplitude amplification under the idealized quantum random access memory (QRAM) framework. The first algorithm uses an enumerate-m oracle that sequentially checks a loaded text substring against all m patterns achieving O (√S) query complexity for S text positions but requiring O (m · L) work per oracle call. The second algorithm employs nested Grover search with an outer loop over text positions and an inner loop over pattern space, reducing oracle complexity to O(L) while performing O (√S · √m) in total. These asymptotic gains highlight the potential advantages that could be unlocked by future large-scale, low-noise QRAM architectures, positioning our results as a promising proof-of-concept foundation.

RESULTS: This work introduces two quantum implementations of multi-pattern string matching tailored for k-mer detection. Leveraging quantum parallelism and Grover-inspired search primitives, our methods accelerate dictionary-based pattern matching, particularly in contexts involving large sequences, such as genomic data, and extensive pattern sets.

CONCLUSION: While implementation challenges such as QRAM overhead remain, this study demonstrates both the promise and current limitations of quantum-enhanced string matching, establishing a foundational step toward quantum readiness in bioinformatics.

To maximize accessibility and practical use, we provide our methodology at: https://github.com/Georgakopoulos-Soares-lab/quantum-multi-motif-finder.}, } @article {pmid42369969, year = {2026}, author = {Wei, M and Xiao, Z and Du, X and Cao, J and Wu, S and Zhang, R and Yang, X and Fan, C and Lian, J and Kang, W and Wang, C and Ye, C}, title = {mNGS-Identified Mycobacterium porcinum Infection in a Newly Diagnosed Person With HIV Presenting With Recurrent Suppurative Cervical Lymphadenitis.}, journal = {Open forum infectious diseases}, volume = {13}, number = {6}, pages = {ofag373}, pmid = {42369969}, issn = {2328-8957}, abstract = {Although reports of human infection caused by Mycobacterium porcinum (M. porcinum) have gradually increased in recent years, cases occurring in people with HIV (PWH) remain rare, and the association between M. porcinum infection and suppurative cervical lymphadenitis in PWH has not been previously reported. In this case, metagenomic next-generation sequencing was used to rapidly identify M. porcinum from a pus specimen obtained from a newly diagnosed person with HIV presenting with suppurative cervical lymphadenitis as the initial manifestation. Recognition of these rare clinical features may improve understanding of non-tuberculous mycobacterial infections in PWH and their diverse clinical presentations.}, } @article {pmid42370219, year = {2026}, author = {Niu, X and Yu, Q and Gu, J and Lu, B and Shen, W and Tian, J}, title = {Disseminated Mycobacterium avium Complex Infection in an HIV Patient with a History of Talaromyces marneffei: Diagnostic Value of Blind Subculture and Suspected Management Challenges of Immune Reconstitution Inflammatory Syndrome.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {606947}, pmid = {42370219}, issn = {1178-6973}, abstract = {This study reported a 33-year-old male acquired immune deficiency syndrome (AIDS) patient with a 10-year human immunodeficiency virus (HIV) infection history, poor antiretroviral therapy (ART) adherence, and two previous Talaromyces marneffei infections. Self-discontinuation of ART led to severe immunosuppression and disseminated Mycobacterium avium complex (MAC) infection involving the bloodstream and bone marrow. After the restart of ART, the patient developed persistent high fever, which was clinically suspected to be MAC-associated immune reconstitution inflammatory syndrome (IRIS). However, due to the lack of serial HIV viral load and CD4[+] T lymphocyte data, a definitive diagnosis could not be established. The patient was admitted with fatigue, anorexia, and black stool as the main symptoms. MAC infection was confirmed by blood culture, bone marrow culture, and bone marrow metagenomic next-generation sequencing (mNGS) at a higher-level hospital. Notably, after transfer to our hospital, the microbiology laboratory performed blind subculture on routinely negative blood culture bottles and extended the incubation period to 15 days, successfully isolating MAC. This highlights the crucial significance of close clinical-laboratory collaboration and optimized pathogen detection for diagnosing non-tuberculous mycobacteria (NTM) infections. After initial infection control and ART restart, the patient developed recurrent fever. Given the temporal association with ART reinitiation and the dose-dependent correlation between fever and glucocorticoid adjustments, possible MAC-associated IRIS was suspected. The patient's clinical symptoms improved with glucocorticoid therapy, though this does not confirm the diagnosis. Complications including cytomegalovirus reactivation, adverse drug reactions, and human rhinovirus co-infection were managed in a standardized manner. This case suggests that the diagnosis of disseminated MAC infection in severely immunocompromised AIDS patients relies on efficient collaboration between clinicians and laboratories. However, in the absence of confirmatory immunological and virological evidence, the diagnosis of IRIS remains uncertain. Clinicians should remain vigilant for suspected IRIS when restarting ART while acknowledge that limited data may preclude a definitive diagnosis. Individualized comprehensive strategies covering anti-infection, immunomodulation, anti-inflammation, and supportive treatment are the key to managing such complex HIV-related opportunistic infections.}, } @article {pmid42370222, year = {2026}, author = {Chen, M and An, W and Fang, S and Zhang, M}, title = {Efficacy and Safety of Omadacycline in Patients with Mycoplasma Pneumoniae Harboring the 23S rRNA A2063G Mutation.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {601060}, pmid = {42370222}, issn = {1178-6973}, abstract = {OBJECTIVE: Mycoplasma pneumoniae is a major pathogen of community-acquired bacterial pneumonia (CABP). Macrolide-resistant Mycoplasma pneumoniae (MRMP) harboring the 23S rRNA A2063G mutation poses a global therapeutic challenge. Omadacycline, a novel aminomethylcycline approved for CABP, exhibits activity against MRMP. However, real-world data on omadacycline for A2063G-mutated MRMP pneumonia remain limited. In this study, we present our clinical experience with intravenous omadacycline in patients with genetically confirmed A2063G-mutated MRMP pneumonia.

METHODS: We retrospectively analyzed the clinical data of eight patients with MRMP pneumonia confirmed by metagenomic next-generation sequencing (mNGS). All patients had failed prior macrolide or fluoroquinolone therapy and received a 7-day course of intravenous omadacycline. Clinical symptoms, inflammatory parameters, chest CT findings, and safety were evaluated.

RESULTS: Eight patients were included. Significant reductions in inflammatory markers were observed after treatment: the neutrophil count decreased from (6.92 ± 2.13)×10[9]/L to (4.67 ± 1.03)×10[9]/L (P = 0.02), C-reactive protein decreased from (68.17 ± 50.35) mg/L to (14.77 ± 19.34) mg/L (P = 0.01), and serum amyloid A decreased from (497.28 ± 319.79) mg/L to (28.35 ± 32.28) mg/L (P < 0.01). Chest CT showed marked resolution of pulmonary lesions in seven patients. No treatment-related adverse events requiring discontinuation were reported.

CONCLUSION: Omadacycline demonstrates promising clinical efficacy and a favorable safety profile for the treatment of pneumonia caused by A2063G-mutated MRMP, promoting both clinical and radiological recovery. Larger prospective controlled studies are warranted to confirm these findings.}, } @article {pmid42370333, year = {2026}, author = {Mahlich, Y and Sohi, H and Veličković, M and Piehowski, PD and McDermott, JE and Gosline, SJC}, title = {spammR: an R package designed for analysis and integration of spatial multi-omic measurements.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag163}, pmid = {42370333}, issn = {2635-0041}, abstract = {MOTIVATION: Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance profiles for multiple different omics types and associated microscopy imaging data, as well as their analysis in a spatial context. However, most analytical tools are designed for spatial transcriptomics platforms and are challenging to use in other contexts such as mass spectrometry-based measurements or metagenomics.

RESULTS: To this end we present spammR (spatial analysis of multi-omics measurements in R), an R package that enables end-to-end analysis with a specific focus on mass-spectrometry derived spatial omics datasets with the goal of integration across multiple data types (e.g. sequencing, metabolites, proteins) within the same tissue.

spammR is implemented in R. The package is currently installable from GitHub (https://pnnl-compbio.github.io/spammR/).}, } @article {pmid42370706, year = {2026}, author = {Schiml, VC and Stalder, K and Várnai, A and Bergaust, LL and Bakken, LR and Arntzen, MØ}, title = {Microbial consortia mediating lignocellulose turnover and denitrification in eutrophic lake sediment enrichments.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0057726}, doi = {10.1128/msystems.00577-26}, pmid = {42370706}, issn = {2379-5077}, abstract = {Lignocellulose is a major component of plant biomass and is recalcitrant, with efficient degradation typically requiring oxygen-dependent oxidative and carbohydrate-active enzymes (CAZymes). Anaerobic turnover is slower but can be supported by microbes capable of nitrate respiration, including denitrifiers and dissimilatory nitrate reduction to ammonium (DNRA) bacteria, which may use nitrate or nitric oxide as alternative oxidants. Anoxic layers beneath the oxic zones of eutrophic lake sediments, where nitrate penetrates from surface waters, provide a natural habitat for such organisms. To investigate these processes, we established nitrate-amended enrichments from organic-rich sediments of 10 eutrophic lakes and applied gas kinetics alongside metagenomics and metaproteomics to characterize the microbial communities. We identified a set of core microbial metagenome-assembled genomes (MAGs) present in all enrichments, dominated by Pseudomonadota, Bacteroidota, Verrucomicrobiota, and Actinomycetota, which played key roles in denitrification and fermentation. Lignocellulose degradation, however, was largely carried out by species outside the core microbiome-that is, different key degraders between lakes, suggesting lake-specific specialization. Among these, we observed potential respiratory DNRA pathways and a broad repertoire of CAZymes targeting various lignocellulose subfractions. Interestingly, many MAGs also encoded nitric oxide dismutases (NODs), enzymes postulated to convert NO to molecular oxygen and dinitrogen gas. Together, these findings advance our understanding of anaerobic biomass degradation and nitrogen cycling in eutrophic freshwater sediments, while highlighting the unexplored functional diversity of NOD-containing bacteria as an intriguing open question for future research.IMPORTANCELignocellulose, the main structural component of plant biomass, represents a vast reservoir of organic carbon in natural environments. Although lignocellulose breakdown is commonly associated with oxygen-rich conditions, it also occurs in oxygen-depleted habitats such as lake sediments, where the responsible microbes and processes are poorly understood. This study reveals how diverse microbial communities can degrade lignocellulose while respiring nitrate, linking carbon turnover to nitrogen cycling in anoxic environments. By identifying shared and lake-specific microbial strategies, as well as a widespread but poorly characterized class of enzymes associated with nitric oxide metabolism, our work advances our understanding of anaerobic biomass degradation. These insights have implications for ecosystem functioning in nutrient-rich waters and for the development of sustainable, oxygen-free biotechnological processes.}, } @article {pmid42370707, year = {2026}, author = {Victorsen, A and Knutson, TP and Bolender, L and Jung, S and Ferrieri, P and Thyagarajan, B and Hilt, EE}, title = {Validation of an integrated metagenomic pipeline combining optimized wet-lab processing and tiered reporting for CSF pathogen detection.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0366625}, doi = {10.1128/spectrum.03666-25}, pmid = {42370707}, issn = {2165-0497}, abstract = {UNLABELLED: Metagenomic next-generation sequencing (mNGS) in the infectious disease diagnostic space has been gaining traction and is popular for aiding in the diagnosis of central nervous system infections. However, many challenges and obstacles remain in making this technology a gold standard for infectious disease diagnostic testing. One major challenge is being able to distinguish between the clinically relevant organisms from background contamination. We performed a validation study for mNGS on cerebrospinal fluid (CSF) that utilized positive clinical samples and contrived samples that incorporated a bioinformatics pipeline that can better distinguish between background contamination and clinically relevant organisms and used a three-tiered reporting algorithm meant to decrease the inherent subjectivity that comes with interpreting and reporting data from clinical metagenomic sequencing. The validation of this assay and category-based reporting pipeline revealed an overall concordance of 91.8%, with a sensitivity of 100% and a specificity of 72.4%. In addition, we improved the detection of clinically relevant RNA viruses to almost 100% in the CSF by modifying the wet lab processing of the sample. This bioinformatics pipeline with a category-based reporting algorithm will provide more confidence in reporting microorganisms detected with this technology, mNGS, and improving patient care.

IMPORTANCE: Metagenomic next-generation sequencing (mNGS) can offer a broad, unbiased approach for the detection of infectious pathogens and has shown promise in diagnosing central nervous system infections. Despite its potential, clinical implementation remains limited by challenges in distinguishing clinically relevant organisms from background contamination. This study validated an mNGS assay for cerebrospinal fluid that incorporates an optimized bioinformatics pipeline with a three-tiered reporting algorithm designed to reduce subjectivity and enhance diagnostic confidence. The assay also has improved detection of clinically relevant RNA viruses through modified wet-lab processing. These findings support the clinical utility of a structured, category-based reporting approach for mNGS, advancing its reliability as a diagnostic tool in infectious disease testing.}, } @article {pmid42370713, year = {2026}, author = {Trubl, G and Roux, S and Kellom, M and Vyshenska, D and Tomatsu, A and Singh, K and Kimbrel, JA and Eloe-Fadrosh, E and Malmstrom, RR and Pett-Ridge, J and Blazewicz, SJ}, title = {Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0113625}, doi = {10.1128/msystems.01136-25}, pmid = {42370713}, issn = {2379-5077}, abstract = {Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied genome-resolved stable isotope probing viromics (SIP-viromics), combining H2[18]O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined virome assemblies. Only 22% of vOTUs exhibited significant [18]O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76-5.15% of total virions per gram of soil, with viral loads ranging from 3.15 × 10[10] to 6.59 × 10[10] virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome length reinforced that persistent virions represented the majority of the extracellular viral pool post-wet-up, regardless of parameter assumptions. Host predictions linked both active and persistent vOTUs primarily to Actinomycetota and Pseudomonadota-bacterial groups known to rapidly resuscitate following rewetting-suggesting that some viruses exhibit rapid turnover, while others persist over longer timescales, forming a stable viral pool capable of reinitiating infections during favorable conditions. These results demonstrate that SIP-viromics can distinguish newly produced from persistent virions and reveal predicted host-associated, lineage-level patterns consistent with lytic infection and virion production. Our findings advance understanding of soil virus-host interactions and highlight the ecological role of persistent virions as a genetic reservoir contributing to microbial turnover and biogeochemical cycling following environmental disturbance.IMPORTANCESoil viruses influence microbial survival, nutrient cycling, and ecosystem recovery after environmental disturbance, yet it remains difficult to determine which viruses are newly produced versus those persisting in the environment. By integrating H2[18]O stable isotope probing with viromics, this study introduces SIP-viromics, a framework that directly distinguishes newly produced from persistent extracellular virions in situ. Unlike conventional viromics, which primarily catalogs viral diversity, SIP-viromics enables quantification of active viral replication and persistence. Following rewetting of a seasonally dry grassland soil, most virions persisted without detectable replication, while only a small subset became active. Active viruses were primarily associated with bacterial groups known to rapidly recover after wet-up, linking viral activity to host physiological responses. These findings show that soil viruses can persist as stable reservoirs of genetic material while retaining the potential to rapidly reactivate under favorable conditions.}, } @article {pmid42370731, year = {2026}, author = {Bresette, N and Ericsson, AC and Woods, C and Lin, A-L}, title = {MeLSI: Metric Learning for Statistical Inference in microbiome community composition analysis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0040726}, doi = {10.1128/msystems.00407-26}, pmid = {42370731}, issn = {2379-5077}, abstract = {Microbiome beta diversity analysis relies on distance-based methods, including permutational multivariate analysis of variance (PERMANOVA) combined with fixed ecological distance metrics (Bray-Curtis, Euclidean, Jaccard, and UniFrac), which treat all microbial taxa uniformly, regardless of their biological relevance to community differences. This "one-size-fits-all" approach may miss subtle but biologically meaningful patterns in complex microbiome data. We present Metric Learning for Statistical Inference (MeLSI), a novel machine learning framework that learns data-adaptive distance metrics optimized for detecting community composition differences in multivariate microbiome analyses. MeLSI employs an ensemble of weak learners using bootstrap sampling, feature subsampling, and gradient-based optimization to learn optimal feature weights, combined with rigorous permutation testing for statistical inference. The learned metrics can be used with PERMANOVA for hypothesis testing and with principal coordinates analysis for ordination visualization. Comprehensive validation on synthetic benchmarks and real data sets shows that MeLSI maintains proper type I error control while delivering competitive or superior statistical power for detecting subtle community shifts and, crucially, supplies interpretable feature-weight profiles that clarify which taxa drive group separation. On the DietSwap data set, MeLSI was the only method to achieve significance at α = 0.05, demonstrating that adaptive weighting can detect diet-induced community shifts that fixed metrics miss. Across all data sets, the learned feature weights identified biologically relevant taxa while providing actionable insight that no fixed distance metric can supply. MeLSI therefore offers a statistically rigorous tool that augments beta diversity analysis with transparent, data-driven interpretability.IMPORTANCEUnderstanding which microbes differ between groups of interest could reveal therapeutic targets and diagnostic biomarkers. However, current analysis methods treat all microbes equally (similar to using the same ruler to measure everything, regardless of what matters most). This means subtle but biologically important differences may go undetected, especially when only a few key species drive disease states while hundreds of "bystander" species add noise. Metric Learning for Statistical Inference (MeLSI) solves this by learning which microbes matter most for each specific comparison. In comparing male and female gut microbiomes, MeLSI identified specific bacterial families driving the differences, providing actionable biological insights that standard methods miss. This capability is particularly crucial for detecting early disease biomarkers, where differences are subtle and masked by biological variability. By telling researchers not just whether groups differ, but which specific microbes drive those differences, MeLSI accelerates the path from microbiome data to testable biological hypotheses and clinical applications.}, } @article {pmid42370747, year = {2026}, author = {Plominsky, AM and Oliver, A and Henriquez-Castillo, C and Podell, S and Minich, JJ and Augyte, S and Lowell-Hawkins, J and Sims, NA and Allen, EE}, title = {Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens.}, journal = {mBio}, volume = {}, number = {}, pages = {e0338225}, doi = {10.1128/mbio.03382-25}, pmid = {42370747}, issn = {2150-7511}, abstract = {The biotransformation of macroalgal biomass represents a major catabolic challenge due to its structurally diverse polysaccharides and inhibitory polyphenols. Unlike terrestrial lignocellulosic substrates, macroalgal polysaccharides contain multiple monomer types, branching patterns, and sulfation states. Additionally, toxic macroalgal polyphenols have been shown to inhibit both microbial growth and their catalytic enzymes. While herbivorous fishes have evolved specialized gut microbiota to process these substrates, the enzymatic pathways remain poorly characterized, with few experimentally validated polysaccharide utilization loci or biochemically defined marine sulfatases, and limited understanding of polyphenol degradation. Here, we developed in vitro microcosms, based on the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens, to temporally resolve the activity of the microbial guilds involved in macroalgal polysaccharide and polyphenol transformation. First, parallel cDNA/DNA amplicon sequencing was employed to distinguish the natural active fraction from transient gut microbiome taxa that became inactive/dead after their ingestion. Four medium combinations were able to propagate between 96% and 99% of the active hindgut microbial families, reproducing the cooperative degradation dynamics observed in vivo. Metagenomic and metatranscriptomic profiling of these four optimized in vitro microcosms served as models to assess the stepwise functional successions occurring in the natural gut microbiome. Early Gammaproteobacteria expressed enzymes linked to polyphenol detoxification and alginate degradation, followed by Bacillota, Bacteroidota, and Verrucomicrobiota guilds targeting more recalcitrant sulfated polysaccharides and polyphenols. Together, these results identified temporal and taxonomic coordination as key features of macroalgal biomass deconstruction, providing an experimentally tractable model for discovering novel carbohydrate-active enzymes and elucidating poorly understood pathways of marine polyphenol degradation.IMPORTANCESeaweed represents a source of sustainable biomass for various applications, but scalable industrial methods struggle to break down seaweed biomass into intermediate products due to the complexity of its constituents. Fish of the genus Kyphosus feed on different seaweed types by leveraging gastrointestinal bacteria to neutralize inhibitory polyphenols and convert their polysaccharides into simple sugars. This study identifies microbial groups that are transcriptionally active in natural fish hindgut microbiomes and how to propagate these active microbial communities in vitro. This enabled assessing how distinct microbial guilds act in succession to transform complex polysaccharides and polyphenols. Notably, this is the first study to assess the biotransformation capacities of macroalgal polyphenols by complex in vitro hindgut microbiomes of a generalist herbivorous fish. These findings advance our ecological understanding of cooperative degradation in marine gut symbioses and establish a tractable platform for discovering new enzymes and pathways with potential applications in algal biomass utilization.}, } @article {pmid42371112, year = {2026}, author = {Tang, A and Cao, Q and Wang, M and Li, W and Xu, H and Wang, Y and Niu, H and Wang, H and Ma, G and Jia, K and Feng, X and He, C and He, J and Alballa, MM and Liao, X and Tian, T and Qin, B and Yang, N and Wei, J and Sun, J and Wang, Y and Cheng, Y and Wu, Q and Yang, J and Wang, Q and Wang, X and Liu, X}, title = {The effectiveness of a plant-based milk with fermented brown rice on constipation symptoms via gut microbiota modulation: a double-blind randomized controlled trial.}, journal = {European journal of nutrition}, volume = {65}, number = {5}, pages = {}, pmid = {42371112}, issn = {1436-6215}, support = {DW080038K0000004//Xi'an Jiaotong University/ ; 82011530197//National Natural Science Foundation of China/ ; 202405212//Feihe Research Grant/ ; }, mesh = {Humans ; *Constipation/microbiology/diet therapy ; *Oryza ; Double-Blind Method ; Female ; *Plant-based Milk ; Adult ; *Gastrointestinal Microbiome/physiology ; Animals ; Middle Aged ; Fermentation ; Fermented Foods ; }, abstract = {PURPOSE: To evaluate the effects of a plant-based milk with fermented brown rice on constipation symptoms in patients with functional constipation and to identify post-intervention gut microbial alterations that may underlie potential mechanisms.

METHODS: This is a randomized controlled trial among 100 participants with functional constipation. Participants were randomly assigned to the intervention group (plant-based milk with fermented brown rice, 2 bottles/day, 500 ml in total), or the control group (an isocaloric plant protein milk, equivalent dose) for 3 weeks. The primary outcome is complete spontaneous bowel movement (CSBM) rate, while secondary outcomes include score of individual symptoms assessment of constipation, bowel movement frequency (BMF), and gut microbial changes (metagenomics).

RESULTS: A total of 99 participants completed the intervention. CSBM and BMF increased, and GSRS scores decreased over time in both groups, with no significant between-group differences. The plant-based milk with fermented brown rice relieved constipation symptoms more than the control group did, with significant between-group differences in straining, bloating and abdominal pain (all P < 0.05). The intervention group showed increases in 8 species, including three beneficial species in the genus Blautia, associated with relief of abdominal pain after the intervention. Meanwhile, machine learning models identified gut microbiota features predicting intervention responders.

CONCLUSION: Our study did not find between-group difference in CSBM, while the plant-based milk with fermented brown rice showed greater effectiveness in relieving constipation symptoms and optimizing gut microbiota. Functional species benefiting intestinal health in response to the intervention were also identified.

CLINICAL TRIAL REGISTRY: This study has been registered in the Chinese Clinical Trial Registry (https://www.chictr.org.cn/, ChiCTR2400088688).}, } @article {pmid42371206, year = {2026}, author = {He, Y and He, G and Zhang, Q and Song, Y and Zhong, Z and Guo, Z and Xiong, J and He, T}, title = {Efficiency of nitrogen and phosphorus cycling in paddy soils is directly driven by functional gene-microbe co-occurrence networks and indirectly controlled by soil physicochemical properties.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42371206}, issn = {1573-0972}, support = {42367039//National Natural Science Foundation of China/ ; 42267038//National Natural Science Foundation of China/ ; 2022YFD1901505//the National Key Research and Development Program of China/ ; }, mesh = {*Phosphorus/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Nitrogen/metabolism ; Oryza/growth & development ; *Nitrogen Cycle ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenome ; China ; Microbiota/genetics ; }, abstract = {Rice productivity in karst regions is often constrained by low nitrogen (N) and phosphorus (P) use efficiency, yet the attributes associated with reduced nutrient cycling function in medium- and low-yield paddy fields remain unclear. We selected five representative paddy soil profiles in Qianxi City, Guizhou Province, comprising one high-yield field, one medium-yield field and three low-yield fields characterised by sandy soil, water deficit or waterlogging. These profiles contained 23 diagnostic horizons, yielding 23 composite soil samples for analyses of soil physicochemical properties, enzyme activities, metagenome-derived functional gene abundance and microbial community composition. Integrative analyses, including redundancy analysis, co-occurrence networks, random forest modelling and structural equation modelling (SEM), were used to evaluate attributes associated with nitrogen and phosphorus cycling functional potential. Across paddy field types, N- and P-cycling functional genes showed distinct abundance patterns. In the waterlogged low-yield field, the abundance value of nifH reached 525.33 reads, 5.3-fold higher than that in the high-yield field. Genes associated with organic P mineralisation and regulation, including phoD, phoU and ppnK, ranged from 608 to 2,480 reads across field types. Microbial taxonomic profiles associated with N- and P-cycling functions also differed among paddy fields. Available phosphorus showed the strongest association with P-cycling functional profiles (Mantel r = 0.72). SEM showed that gene-related variables were positively associated with integrated N and P cycling functional potential (path coefficient = 0.567, P < 0.01), whereas soil microbial variables were negatively associated with this potential (- 0.619, P < 0.01). These results identify attributes associated with nutrient cycling constraints in karst paddy fields and provide a basis for targeted nutrient management.}, } @article {pmid42371248, year = {2026}, author = {Tlaskalová-Hogenová, H and Hrnčíř, T and Štěpánková, R and Trebichavský, I and Hudcovic, T and Šplíchal, I and Šplíchalová, A and Šinkora, M and Funda, D and Sánchez, D and Kverka, M and Jirásková Zákostelská, Z and Kostovčíková, K and Coufal, Š and Procházková, P and Roubalová, R and Vannucci, L and Miler, I}, title = {Gnotobiology: from 19th-century global foundations to 21st-century omics - six decades of Czech contribution to microbiome research.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {42371248}, issn = {1874-9356}, support = {22-12533S, 22-21356S, 23-05645S, 25-16094S, 26-21469S//Czech Science Foundation (GAČR)/ ; LUAUS23014//Ministry of Education, Youth and Sports of the Czech Republic/ ; CZ.02.01.01/00/22_008/0004597//European Union - Next Generation EU (Operational Programme Johannes Amos Comenius)/ ; LX22NPO5102//European Union - Next Generation EU (National Institute for Cancer Research, Programme EXCELES)/ ; RVO: 61388971//Institute of Microbiology of the Czech Academy of Sciences/ ; NU21-04-00443, NU22-09-00493, NU22J-05-00056, NU23-01-00288, NU23-04-00381, NU23-05-00133, NW24-06-00509, NW24-07-00042, NW25-04-00079//Czech Health Research Council (AZV ČR)/ ; }, abstract = {Gnotobiology, from the Greek gnotos (meaning 'known') and bios (meaning 'life'), is a research discipline that uses organisms with a defined microbiological status to study the interaction between hosts and microbes. This review traces six decades of Czech gnotobiology, beginning with the launch of a dedicated gnotobiology programme at Nový Hrádek in 1962 by Jaroslav Šterzl, whose visionary aims anticipated by decades the current recognition of the microbiota as a central determinant of immune and broader physiological function. The site - originally established in 1953 as the Biological Station - was thereby transformed into one of only four gnotobiological laboratories worldwide at that time and the first in Central and Eastern Europe. The facility pioneered the rearing of germ-free piglets, rats, rabbits, and mice, establishing the experimental foundation for the laboratory's work on immune ontogeny, mucosal immunity and tolerance, and microbiota-host interactions in immune development and regulation. This review discusses the key discoveries made using these models. Among them, work at the Institute of Microbiology (Prague and Nový Hrádek) demonstrated that germ-free animals have underdeveloped lymphoid tissue and impaired adaptive immunity. The review also describes the subsequent development of gnotobiotic models of human metabolic, immune-mediated, neoplastic, and neuropsychiatric diseases. The completion of the Human Genome Project in 2001 and the emergence of microbial metagenomics in the early 2000s sparked renewed interest in host-microbe interactions and led to a rediscovery of gnotobiotic approaches as essential tools for establishing causation in microbiome research. We examine how integrating these approaches with high-throughput sequencing, metabolomics, and other omics technologies has shifted the focus from cataloguing the microbiome to mechanistically dissecting host-microbe interactions. Finally, we outline future directions, including humanized gnotobiotic models, microbiota-based therapeutics, and the convergence of gnotobiology with personalized medicine and synthetic biology.}, } @article {pmid42371328, year = {2026}, author = {Pattani, V and Kaneriya, J and Joshi, K and Sanghvi, G}, title = {Microbial Metabolic Strategies for Environmental Detoxification: From Enzymatic Mechanisms to Synthetic Biology and Omics.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {42371328}, issn = {1559-0291}, abstract = {Microorganisms play a pivotal role in environmental detoxification by utilizing their metabolic pathways to degrade, transform, or immobilize toxic pollutants such as hydrocarbons, heavy metals, pesticides, and industrial effluents. This review explores microbial enzymatic systems, including oxidoreductases, hydrolases, and transferases, that facilitate pollutant breakdown. Various bioremediation strategies, such as bioaugmentation, biostimulation, and phytoremediation-assisted microbial degradation, are discussed alongside advances in synthetic biology and metabolic engineering, which enhance microbial efficiency for targeted detoxification. The potential of microbial consortia in tackling complex contamination scenarios is also examined. Additionally, omics-based approaches, including metagenomics, transcriptomics, and proteomics, provide deeper insights into microbial community dynamics and metabolic capabilities. Challenges such as environmental limitations, regulatory concerns, and sustainability issues are critically analyzed. By integrating microbiology with biotechnological innovations, microbial metabolism can be effectively harnessed for large-scale pollution mitigation, offering ecofriendly and cost-effective solutions to address global environmental challenges and promote sustainable industrial practices.}, } @article {pmid42372060, year = {2026}, author = {Jiang, H and Zhang, M and Khan, RAA and Zhao, J and Hou, J and Liu, T}, title = {Trichoderma enriches Burkholderia via cross-feeding of degradation intermediates to enhance atrazine degradation and alleviate soybean phytotoxicity.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag152}, pmid = {42372060}, issn = {1751-7370}, abstract = {The widespread agricultural use of atrazine threatens soil health, and residual phytotoxicity in corn-soybean rotation systems necessitates sustainable remediation strategies. By leveraging the atrazine-degrading fungus Trichoderma lentiforme HN154, we achieved an 80.3% removal of atrazine (500 mg/kg) in non-sterilized soils from a corn planting system within 14 days, 22.1% higher degradation than in sterilized soil, while concurrently alleviating phytotoxic symptoms in soybean plants. Metagenomic analysis revealed that colonization by T. lentiforme HN154 drove restructuring of microbial networks, enriching the keystone family Burkholderiaceae, which was strongly associated with atrazine catabolism and four key catabolic enzymes (EC 3.5.4.43 (atzB), EC 3.5.1.131 (atzE), EC 3.5.1.54 (atzF), EC 3.5.4.42 (atzC)). Among 23 rhizosphere isolates, the Burkholderia strains Bur-4, Bur-5, and Bur-14 showed the highest atrazine degradation rates (26.3% - 29.4%) within 72 h. A Trichoderma-Burkholderia synthetic consortium further enhanced remediation by boosting plant antioxidant defenses (SOD, POD, CAT) and reducing oxidative damage (MDA). Mechanistically, intermediates (hydroxyatrazine and biuret) generated during T. lentiforme HN154-mediated degradation stimulated Burkholderia chemotaxis, swarming and swimming motility, while cross-feeding on these metabolites synergistically accelerated bioaugmentation (the Trichoderma-Burkholderia synthetic consortium achieved rapid atrazine degradation of 86.3% within 168 h). This study reveals tripartite interactions among exogenous microbial degraders, pollutant metabolites, and indigenous microbiota, offering a strategic foundation for microbiome-guided, precision bioaugmentation to restore soil ecological health and crop resilience.}, } @article {pmid42372843, year = {2026}, author = {Capuano, N and Giannattasio, A and Impemba, S and Belgiorno, V and Folliero, V and Buonerba, A and Franci, G}, title = {Microplastics as Emerging Viral Vectors: Nexus, Mechanisms, Ecological Implications and Health Risks.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125138}, doi = {10.1016/j.envres.2026.125138}, pmid = {42372843}, issn = {1096-0953}, abstract = {Microplastics (MPs) have emerged as pervasive environmental pollutants with complex implications for ecological and human health. Beyond their chemical toxicity and persistence, MPs act as dynamic microhabitats supporting microbial colonization and viral adsorption. This review provides a comprehensive overview of the physicochemical characteristics, environmental distribution, and degradation pathways of the most common polymeric MPs, including polystyrene, polyethylene, polypropylene, polyvinyl chloride, polyurethane, polyethylene terephthalate, polydimethylsiloxane, and biobased polyesters. Particular attention is given to the virus-microplastic interface, highlighting how MPs serve as vectors that enhance viral persistence, transport, and infectivity. Experimental and metagenomic evidence demonstrates that both enveloped and non-enveloped viruses can adhere to MPs via electrostatic and hydrophobic interactions, often mediated by biofilm and eco-corona formation. These interactions extend viral stability across environmental compartments and can modulate host immune responses, exacerbating infection outcomes. By integrating physicochemical, microbiological, and toxicological perspectives, this review emphasizes that MPs are not inert residues but active ecological interfaces that can reshape viral ecology and increase public-health risks. Future studies combining molecular, environmental, and epidemiological approaches are essential to quantify the real impact of MP-virus interactions on ecosystem balance and infectious-disease dynamics.}, } @article {pmid42372850, year = {2026}, author = {Gong, X and Zhang, L and Xu, A and Huang, Z and Wang, C and Yang, T and Liang, H and Zhang, M and Zhan, X and Peng, Y and Gao, D}, title = {Root Exudates Recruit Beneficial Microbes to Promote Anammox-Driven Nitrogen Cycling in Wetland.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125149}, doi = {10.1016/j.envres.2026.125149}, pmid = {42372850}, issn = {1096-0953}, abstract = {Anammox bacteria serve as a major biological sink in nitrogen (N) cycling within wetland, yet the hydrophyte root exudates-mediated microbial interplay mechanism that sustain their activity and ecosystem function remain unclear. To address this gap, we established flow-controlled microcosms planted with Iris pseudacorus, combined with [15]N stable isotope tracing and metagenome-assembled genomes (MAGs) analysis. Our findings revealed that root exudates significantly enhanced in-situ anammox rates (rhizosphere: 5.9±2.0 mg N/(m[3]·d), non-rhizosphere: 0.4±0.02 mg N/(m[3]·d), p<0.001), leading to a remarkable enrichment of anammox bacteria in the rhizosphere (6.5×10[7] copies/g dry sludge, p<0.001). We further uncovered a previously overlooked partial denitrification pathway that supplied nitrite, substantially increasing anammox contributions to rhizosphere N removal (16.6±4.1%). Key bioactive components, flavonoids and amino acids, selectively recruited beneficial rhizobacteria affiliated to Pseudomonadota and Bacteroidota. MAGs-based analysis revealed that these microbial taxa encoded pathways for producing essential substrates (nitrite loop) and metabolites (cofactor, biotin) supporting anammox metabolism. The symbiotic interaction facilitated the survival and metabolic activity of anammox bacteria in the oligotrophic rhizosphere habitat. These findings unveil a natural plant-microbiota interaction that effectively enhances the sustainability of N cycling and provide new insights for optimizing nitrogen removal strategies in engineered wetland systems.}, } @article {pmid42372852, year = {2026}, author = {Wang, Y and Yan, C and Jin, J and Li, Z and Zhou, H and Tang, J and Wang, X and Li, H}, title = {Straw incorporation and strawsphere formation shape the fate of antibiotic-resistant human pathogens in agricultural soil.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125142}, doi = {10.1016/j.envres.2026.125142}, pmid = {42372852}, issn = {1096-0953}, abstract = {Antibiotic-resistant human pathogens (ARPs) in soil pose a latent threat to public health. However, how ARPs evolve in agricultural soil after straw incorporation remains unclear. This study combined a metagenomic analysis of 230 soil samples from typical straw-incorporated regions in China and controlled microcosm experiments to assess the effects of straw incorporation on soil ARPs. The influence of straw incorporation on ARPs was management practice-dependent. Semi-quantity short (4 cm) straw incorporation significantly decreased the total abundances of ARPs by 17.4%. A redundancy analysis revealed that elevated levels of alkali hydrolyzable nitrogen, available potassium and total organic carbon as well as virus abundance were key factors associated with the reduction in ARPs in straw-incorporated soil. Moreover, scanning electron micrographs revealed that the straw surface developed a coccoid bacterium-dominated biofilm, forming a distinct ecological niche, the strawsphere. A KEGG pathway annotation suggested that lignocellulose-degrading microbes in the strawsphere serve as a potential source of ARP-antagonistic microorganisms. Structural equation models further identified straw fragment length as a critical parameter for the fates of ARPs both in soil and the strawsphere. The study elucidated the critical roles of straw incorporation and the resulting 'strawsphere' in controlling ARPs in agricultural soil.}, } @article {pmid42372901, year = {2026}, author = {Edwards, M and Sanchez-Ramos, L}, title = {Likelihood ratios enhance clinical interpretation of metagenomic prediction of early-onset neonatal sepsis in preterm premature rupture of membranes (Letter-to-the-Editor).}, journal = {American journal of obstetrics and gynecology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajog.2026.06.023}, pmid = {42372901}, issn = {1097-6868}, } @article {pmid42372926, year = {2026}, author = {Kwon, CY and Choi, YH and Kim, H and Han, K and Jang, D and Hwangbo, H}, title = {Gut microbial signature for frailty discrimination: a metagenomic meta-analysis of 28 independent cohorts.}, journal = {Experimental gerontology}, volume = {}, number = {}, pages = {113223}, doi = {10.1016/j.exger.2026.113223}, pmid = {42372926}, issn = {1873-6815}, abstract = {Frailty, a clinical syndrome of multisystem decline and homeostatic vulnerability, is a critical public health priority. While the gut microbiome regulates immune and metabolic signaling, current evidence remains fragmented. We performed a metagenomic meta-analysis of 955 individuals from 28 independent cohorts across 24 countries to identify universal microbial signatures and develop a generalizable discriminative model. Frailty was determined using a Proxy Frailty Index based on the deficit accumulation model. Following refinement to isolate signatures from disease-specific dysbiosis, we used Firth's penalized regression for biomarker discovery and validated a Random Forest (RF) model via leave-one-study-out cross-validation. Shannon diversity exhibited a significant and sharp decline during the transition from robust to pre-frail states (p = 0.0006), manifesting at the earliest stages of physiological decline. We identified 16 microbial biomarkers characterized by the progressive attrition of core symbionts, such as Coprococcus eutactus, and the opportunistic expansion of pathobionts, including Enterococcus gallinarum. Sensitivity analysis in a healthy sub-cohort (n = 499) confirmed that these shifts occur independently of chronic clinical diagnoses and their associated confounding effects (p = 0.036). The 16-species RF model, predominantly driven by Collinsella massiliensis, achieved a corrected mean area under the receiver operating characteristic curve of 0.7572 across 5 eligible cohorts. Gut microbial restructuring is a sentinel biological hallmark of frailty that occurs independently of aging-related diseases. This study establishes a microbial signature broadly applicable across European and East Asian populations that serves as a high-fidelity, non-invasive metric for precision geriatric assessment.}, } @article {pmid42372963, year = {2026}, author = {Cui, Q and Wang, F and Shan, X and Ding, L and Qiu, X and Zhang, B and Li, X and Liang, X and Guo, X}, title = {Biodegradable polylactic acid microplastics affect nutrient cycling during the entire crop growth cycle: Implications for soil ecosystem multifunctionality.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128664}, doi = {10.1016/j.envpol.2026.128664}, pmid = {42372963}, issn = {1873-6424}, abstract = {While microplastics (MPs) have been extensively studied for their effects on soil nutrient cycling, their influence on ecosystem multifunctionality (EMF) across the entire crop growth cycle remains poorly understood. This study systematically investigated the impacts of a model biodegradable MP, polylactic acid (PLA), on soil microbiomes and EMF across different maize incubation periods. Results of 16S rRNA amplicon sequencing and metagenomic analysis revealed that PLA-MPs decreased bacterial community α-diversity, co-occurrence network complexity, and stability throughout the 120-day incubation period. Particularly, PLA-MPs exerted more pronounced effects at early incubation stages (30 and 60 days), and these effects were intensified with increasing PLA-MP concentrations. PLA-MPs suppressed anaerobic carbon fixation (porA, porB, frda) and pyruvate metabolism (ppdk), while promoting fermentation (L-lactate dehydrogenase), nitrogen fixation (nifD, nifH, nifK, anfG), and microbial phosphorus (P) acquisition (phoD, phn cluster). Over the entire incubation period, PLA-MP-induced shifts in nutrient cycling enhanced soil carbon (C) function by 37.6-569%, while decreasing nitrogen (N) and P functions by 8.40-22.4% and 16.8-56.2%, respectively. Path analysis revealed that PLA-MPs altered soil properties and bacterial community diversity, which in turn regulated functional genes and these individual soil functions, thereby reducing EMF by 2.05-27.0% (R[2] = 0.923), with bacterial community diversity as the primary driver of EMF (standardized path coefficient of 0.978). These findings underscore the impacts of PLA-MPs on EMF in the soil-crop system throughout the entire maize growth cycle, advancing the understanding of the agroecological safety of biodegradable MPs.}, } @article {pmid42373490, year = {2026}, author = {Shen, Y and Zhang, DT and Shi, WX and Ma, CN and Huo, D and Yang, P and Wang, QY and Feng, ZM}, title = {[Epidemiological characteristics of test-negative severe acute respiratory infections during the 2024-2025 surveillance years in Beijing].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {47}, number = {6}, pages = {1114-1119}, doi = {10.3760/cma.j.cn112338-20260104-00004}, pmid = {42373490}, issn = {0254-6450}, support = {2026-2G-30124//Capital's Funds for Health Improvement and Research/ ; BJRID2026-001//Beijing Research Center for Respiratory Infectious Diseases/ ; 20252D01900800//National Science and Technology Major Project of China/ ; }, mesh = {Humans ; Middle Aged ; Adult ; Adolescent ; Child ; Child, Preschool ; *Respiratory Tract Infections/epidemiology/microbiology ; Male ; Female ; Young Adult ; Infant ; Beijing/epidemiology ; Aged ; Infant, Newborn ; High-Throughput Nucleotide Sequencing ; Acute Disease ; }, abstract = {Objective: To analyze the epidemiological characteristics of cases with severe acute respiratory infection (SARI) in Beijing who tested negative for 22 common respiratory pathogens by nucleic acid testing, and to explore the potential pathogen spectrum using metagenomic next-generation sequencing (mNGS). Methods: Data were obtained from the Beijing Acute Respiratory Infectious Disease Surveillance Network. Hospitalized SARI cases from week 40 of 2024 to week 39 of 2025 were included. All cases were tested for 22 common respiratory pathogens using nucleic acid assays. Among those test-negative results, 50 specimens were randomly selected for mNGS analysis. Multivariable logistic regression was performed to identify factors associated with test-negative results. Results: A total of 7 202 SARI cases were included, of whom 4 212 (58.5%) tested negative for all 22 common respiratory pathogens. The proportion of negative results increased with age, with 32.9% (322/978) in children aged 0-5 years, 69.1% (972/1 407) in adults aged 18-59 years, and 65.0% (2 506/3 856) in those aged ≥60 years, the difference was statistically significant (all P<0.001). Multivariable analysis showed that age was independently associated with negative results (18-59 years: aOR=4.62, 95%CI:3.85-5.55; ≥60 years: aOR=4.08, 95%CI:3.49-4.78). Upper respiratory samples were more likely to test negative. Among 48 valid mNGS samples, 32 pathogens were identified. At least one pathogen was detected in 44 cases (93.6%), and multiple infections were common (37 cases, 84.1%). Human herpesvirus 7 (20 cases) was most frequently detected, followed by Stenotrophomonas maltophilia (16 cases), Human herpesvirus (15 cases), and Streptococcus pneumoniae (12 cases). Conclusions: A high proportion of SARI cases in Beijing tested negative for common respiratory pathogens, and age played an important role. mNGS identified predominantly opportunistic pathogens and herpesviruses, and did not detect novel pathogens with clear respiratory significance. These findings indicate that the current SARI surveillance covers the most common respiratory pathogens.}, } @article {pmid42373646, year = {2026}, author = {Howells, AEG and Robinson, K and Silva, MG and Cook, E and Fifer, L and Boyer, G and Hoehler, T and Shock, EL}, title = {Methanotrophy under extreme alkalinity in a serpentinizing system.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72513-6}, pmid = {42373646}, issn = {2041-1723}, support = {NNA15BB02A//NASA | NASA Astrobiology Institute (NAI)/ ; EAR-1515513//National Science Foundation (NSF)/ ; EAR-1949030//National Science Foundation (NSF)/ ; EAR-2149016//National Science Foundation (NSF)/ ; }, abstract = {Serpentinization produces hyperalkaline, H2- and CH4-rich fluids that support microbial life and serve as analogs for ocean worlds such as Enceladus. While methane production in these systems has been well studied, methane consumption-especially under high pH-remains poorly understood. Here, we present isotopic, geochemical, and genomic evidence for hyperalkaliphilic (pH > 11) methanotrophy in the Samail ophiolite of Oman. Using models that account for fluid mixing and gas exsolution, we identify δ[13]CH4 enrichment that cannot be explained by abiotic processes alone. The enrichment of [13]CH4 co-occurs with methanotroph 16S rRNA gene sequences, particularly in fluids formed by mixing CH4-rich, reduced fluids with oxidant-rich waters. Shotgun metagenome sequencing reveals a metagenome-assembled genome affiliated with Methylovulum, encoding a complete methane oxidation pathway, multiple carbon assimilation routes, and Na[+]/H[+] antiporters-adaptations likely enabling growth above pH 11. Our findings highlight the viability of methanotrophy under extreme high pH conditions and provide a framework for interpreting δ[13]CH4 signals in serpentinizing environments on Earth and beyond.}, } @article {pmid42374042, year = {2026}, author = {Chen, X and Chen, C and Zhang, P and OuYang, X and Ma, H and Chen, W and Li, T and Han, J and Wang, Y and Wang, H and Zhou, Q and Cheng, G and Zhou, W and Yu, Z and Zhou, W and Wang, M and Zeng, S}, title = {Bifidobacterium animalis reshapes the bile acid pool and prevents neonatal jaundice: a clinical microbiome study from correlation to causation.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01057-w}, pmid = {42374042}, issn = {2055-5008}, support = {2024YFC2707700//National Key R&D Program of China, Key Special Project for "Reproductive Health and Maternal and Child Health Security"/ ; 82571963//the National Natural Science Foundation of China/ ; 2025A1515012162//Natural Science Foundation of Guangdong Province, China/ ; JCYJ20250604145739052//Shenzhen Science and Technology Innovation Bureau/ ; Y2024001//the Research Initiation Fund of Longgang District Maternity & Child Healthcare Hospital of Shenzhen City/ ; }, abstract = {Neonatal jaundice (NJ) affects 60-80% of neonates, yet the underlying microbial mechanisms remain elucidated, despite known links between gut dysbiosis and bilirubin and bile acid (BA) metabolism. Through two-stage shotgun metagenomic-metabolomic analysis of 150 fecal samples from 120 neonates, we identified key taxa linked to bile acid (BA) metabolism in moderate-to-severe NJ. Furthermore, multi-omics integration revealed significant interkingdom correlations among gut phages, bacteria, and BAs. Dysbiosis featured enriched Streptococcus and Escherichia, depleted Bifidobacterium animalis, and group-specific phage signatures. In the independent clinical validation cohort, jaundice intervention normalized the dysbiotic profile, demonstrating significant suppression of pathogenic taxa concomitant with restoration of B. animalis abundance. In vitro, B. animalis subsp. lactis Y103-OTU5 remodeled BA via deconjugation. In a phenylhydrazine hydrochloride (PHZ)-induced murine model of hemolytic jaundice, oral administration of isolated B. animalis subsp. lactis Y103-OTU5 significantly attenuated hyperbilirubinemia and hepatic inflammation, likely via Cyp7a1/Cyp7b1-dependent modulation of BA synthesis and detoxification pathways. Structural equation modeling revealed a tripartite regulatory network: phages indirectly modulated BA through bacterial remodeling, while B. animalis directly regulated BA pathways, positioning it as a potential therapeutic candidate for hemolysis-associated neonatal jaundice. Collectively, these findings reveal a gut phage-bacteria-BA network in NJ, highlighting B. animalis as a therapeutic candidate with dual modulation of BA metabolism and phage-bacteria interactions.}, } @article {pmid42365131, year = {2026}, author = {Zhu, S and Yang, Z and Zhao, H and Ma, Y and Chen, K and Qi, D}, title = {Rainfall Drives Differentiation of Plant Rhizosphere Microbial Communities in Two Different Types of Alpine Wetlands: A Perspective Based on a Carbon-Water Coupling Framework.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02823-1}, pmid = {42365131}, issn = {1432-184X}, support = {Qing[2025]TG04//Demonstration of Techniques for Wetland Protection, Restoration, and Carbon Sink Capacity Enhancement in the Qinghai Lake Basin - Qinghai Provincial Finance Budget/ ; }, abstract = {The alpine wetlands of the Qinghai-Tibet Plateau are confronting significant ecological challenges due to drastic shifts in precipitation patterns. Elucidating the response mechanisms of rhizosphere microbial communities in wetland plants to precipitation events is critical to understanding ecosystem resilience. In this study, sandy wetlands at Niaodao and riverine wetlands at Haergai in the Qinghai Lake basin were selected as study sites. Using Poa alpigena rhizosphere and non-rhizosphere soils as the research subjects, metagenomic DNA sequencing combined with environmental factor analysis was employed to compare the microbial community responses before and after a single pulse precipitation event. The results showed that Proteobacteria and Actinobacteria were the dominant phyla in both wetland types (combined relative abundance > 70%). Rainfall induced a differentiated restructuring of soil microbial community composition across different habitats. In rhizosphere soils, rainfall significantly reduced microbial alpha diversity. Co-occurrence network analysis revealed that the rhizosphere community shifted from a competition-coexistence pattern before rainfall to a cooperative adaptation pattern after rainfall, with significant increases in modular cohesion and the proportion of positive correlations. Metagenomic analysis indicated that the number of differentially abundant metabolic pathways in soil microorganisms increased markedly after rainfall, rising to 46 and 40 pathways in the rhizosphere and non-rhizosphere, respectively (compared to 3 and 31 before rainfall), indicating a shift from carbon reserve metabolism to energy-producing metabolism. Total carbon and water content were identified as the core environmental factors jointly regulating community assembly. This study reveals the mechanism by which regional background, precipitation disturbance, and the rhizosphere effect synergistically drive the succession of microbial communities in alpine wetlands, providing a new paradigm for understanding ecosystem adaptation to climate change.}, } @article {pmid42365389, year = {2026}, author = {Park, JH and Lee, KL and Lee, YM and Choi, JY and Heo, YR and Oh, SM and Lee, D and Kim, S and Lee, HW and Poon, CTC and Hong, WH and Moon, HB and Mok, S and Lee, CY and Kim, MA and Yuen, AHL and Seok, SH and Kim, BY and Kim, SW}, title = {From traumatic oral fibroma to fatal pneumonia: a multidisciplinary postmortem investigation in a long-term monitored Indo-Pacific bottlenose dolphin (Tursiops aduncus).}, journal = {BMC zoology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40850-026-00277-z}, pmid = {42365389}, issn = {2056-3132}, support = {No. RS-2025-25432543//National Research Foundation of Korea/ ; No. RS-2022-NR072403//National Research Foundation of Korea/ ; }, abstract = {BACKGROUND: An Indo-Pacific bottlenose dolphin (Tursiops aduncus) in the coastal waters of Jeju Island, Republic of Korea, exhibited an oral mass and mandibular deformity over a documented 6-year period, including 3 years of intensive longitudinal monitoring by our research team. A multidisciplinary approach combining imaging, pathology, microbiology, and omics analyses was used to assess the dolphin.

RESULTS: Post-mortem computed tomography confirmed a mandibular fracture at the oral mass site. Histopathological examination of the oral mass revealed prominent fibroblast proliferation and collagen deposition. Fibropapillomas and desmoid tumors were excluded based on viral detection assays and β-catenin accumulation analysis, supporting a diagnosis of trauma-induced fibroma. Transcriptomic analysis of the tumor tissues identified highly expressed genes associated with extracellular matrix remodeling, myofibroblast activation, and epithelial differentiation, supporting a reactive fibrotic rather than malignant phenotype. Gross necropsy revealed multiple suppurative pulmonary lesions, abundant foamy fluid within the respiratory tract, and diatoms within the pulmonary tissue. Metagenomic sequencing revealed a polymicrobial infection, with Parvimonas micra as the predominant organism. Collectively, these findings are most consistent with aspiration pneumonia, with severe secondary pulmonary infection considered a major contributor to death. In addition, analysis of halogenated organic contaminants revealed accumulation levels consistent with those typically observed in aged individuals, and no evidence was identified indicating a direct causal role in the terminal disease process.

CONCLUSIONS: To the best of our knowledge, this is the first study to characterize the pathological features and proposed pathogenic mechanism of traumatic fibroma in a marine mammal, and the first confirmed case of pulmonary abscessation associated with Parvimonas micra infection in this taxonomic group. Overall, these findings provide valuable baseline data for the health monitoring and conservation of marine mammal populations.}, } @article {pmid42365784, year = {2026}, author = {Chen, Q and Zheng, J and Zeng, L and You, Y and Zhuang, X and Meng, F and Wang, L}, title = {A 1-year-old boy with near-complete tracheobronchial obstruction from endobronchial tuberculosis.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {3}, pages = {117533}, doi = {10.1016/j.diagmicrobio.2026.117533}, pmid = {42365784}, issn = {1879-0070}, abstract = {A one-year-old boy was referred to our respiratory department for further evaluation of obstructing endobronchial lesions. The lesions were detected on chest computed tomography (CT) performed at another hospital after the patient presented with cough and worsening wheezing. Physical examination revealed tachypnea and diminished breath sounds bilaterally without rales. The patient was receiving supplemental oxygen. Notably, his medical history was significant for an admission at 21 days of age for persistent cough, right upper lung atelectasis, and sputum analysis that revealed Bordetella pertussis, Acinetobacter baumannii, and rhinovirus. Despite advanced testing, including bronchoalveolar lavage acid-fast staining, tuberculin skin testing, and metagenomic next-generation sequencing, the diagnosis was initially missed and was ultimately established only after multi-institutional pathology review with deeper histologic recuts identifying a rare acid-fast bacillus. This case demonstrates a rare but high-risk presentation of pediatric tuberculosis: near-complete tracheobronchial obstruction due to endobronchial tuberculosis (EBTB) in an infant.}, } @article {pmid42365883, year = {2026}, author = {Wu, W and Wang, W and Liu, H and Ganigué, R and Zhang, J and Liu, B and Liu, G and Wang, A}, title = {Multi-omics analysis reveals propanol is superior electron donor for odd-chain elongation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135265}, doi = {10.1016/j.biortech.2026.135265}, pmid = {42365883}, issn = {1873-2976}, abstract = {Chain elongation from organic wastes has primarily targeted even-chain carboxylates, leaving the production of equally valuable odd-chain compounds underexplored. Propanol, abundant in industrial wastewater, offers a promising electron donor to address this gap, yet the underlying metabolic pathways and microbial consortia driving efficient odd-chain elongation remain unclear. The present study systematically investigated the characteristics of odd-chain elongation. The results demonstrated that the propanol-acetate (PA) group, using propanol as the electron donor and acetate as the electron acceptor, achieved an excellent selectivity of 84% for n-valerate and n-heptanoate, compared with 55% in the conventional ethanol-propionate (EP) group. Multi-omics analysis guided the specialized metabolic route construction, showing that electrons from propanol oxidation are channeled to drive acetyl-CoA synthesis from acetate and activate the reverse β-oxidation pathway. The propionate generated from propanol oxidation serves as the initial three-carbon backbone for odd-chain carboxylates generation. The keystone microorganisms for propanol-based odd-chain elongation are suggested to be Clostridium kluyveri and Oscillibacter valericigenes. Techno-economic analysis confirmed the metabolic selectivity inherent to the PA group confers superior economic resilience, yielding higher profitability than the EP group. This work positions propanol-based chain elongation as an efficient and economically viable strategy for the targeted production of valuable odd-chain carboxylates from propanol-containing wastewater.}, } @article {pmid42366019, year = {2026}, author = {Wang, D and Wang, F and Sun, S and Huang, L and Sun, K and Li, Z and Feng, J}, title = {Microbe-Metabolite Interactions in Cave Soils Synergistically Regulate the Environmental Persistence of Pseudogymnoascus destructans.}, journal = {Environmental microbiology}, volume = {28}, number = {7}, pages = {e70367}, doi = {10.1111/1462-2920.70367}, pmid = {42366019}, issn = {1462-2920}, support = {32430066//National Natural Science Foundation of China/ ; 32300425//National Natural Science Foundation of China/ ; }, mesh = {*Soil Microbiology ; *Caves/microbiology ; *Ascomycota/isolation & purification/genetics/physiology ; Seasons ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Soil/chemistry ; China ; Microbiota ; Nitrogen Cycle ; }, abstract = {Pseudogymnoascus destructans (Pd), the causative agent of bat white-nose syndrome, persists in cave soils and acts as a chronic source of infection, yet the environmental processes governing this reservoir remain unclear. We performed seasonal sampling of bat cave soils in Northeast China and combined metagenomic, untargeted metabolomic and physicochemical analyses to identify drivers of Pd loads. Pd abundance tracked strong seasonal gradients in temperature, soil water content, electrical conductivity and nitrogen availability. The microbial community structure exhibited pronounced seasonal variation, primarily associated with pH, and was governed predominantly by stochastic ecological processes. Nitrogen-cycling genes showed a switch from nitrogen fixation and nitrification in summer to denitrification and nitrate reduction in winter. Antibiotic resistance genes and mobile genetic elements covaried with core bacterial taxa, while antifungal metabolites such as tetracycline, glycitin and chrysin were positively associated with putatively antagonistic genera (e.g., Rhodanobacter, Pseudomonas, Streptomyces, and Bacillus), indicating a microbe-metabolite defence network. Structural equation modelling revealed a temperature-driven cascade linking nutrient cycling, microbial communities, metabolite profiles and Pd loads. Our results show that seasonal dynamics of Pd in cave soils emerge from interactions between climate-regulated soil processes and microbe-metabolite feedbacks, with implications for environmental control of pathogenic fungi.}, } @article {pmid42050399, year = {2026}, author = {Li, CJ and Zhao, Y and Tang, M and Chu, X and Zhan, PC and Jiang, XW and Tian, JY and Hai, X and Lu, YF and Yang, LL and Zhi, XY}, title = {Comparative population genomics reveal the genetic features associated with the plant host adaptation of Clostridium butyricum.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {42050399}, issn = {1471-2164}, support = {32560005//National Natural Science Foundation of China/ ; }, mesh = {*Clostridium butyricum/genetics/physiology/classification/isolation & purification ; *Host Adaptation/genetics ; Phylogeny ; Genetic Variation ; *Metagenomics ; Genomics ; Genetics, Population ; Genome, Bacterial ; }, abstract = {BACKGROUND: Plants are increasingly considered as secondary reservoirs for enterics. However, little is known about their population dynamics and the genetic mechanisms during plant colonization. Clostridium butyricum is a gut symbiont of humans and animals and, rarely, a pathogen. Here, 55 strains of C. butyricum isolated from the roots of Paris polyphylla var. yunnanensis provided a new model for understanding plant-host adaptation of enterics. RESULTS: These strains, along with 67 non-endophytic C. butyricum strains (nECB), were examined for population structure, revealing that they diverged into four well-defined lineages, whereas endophytic C. butyricum strains (ECB) from different sources were scattered across two lineages. The population diversity estimate confirmed the genetic distinctiveness among four lineages and uncovered distinct evolutionary processes that might drive the divergence of ECB-related lineages. Frequent gene flow between ECB and nECB suggested that plant-host colonization does not lead to genetic isolation. Extensive recombinations within and between lineages demonstrated the major role of recombination in shaping population genetic structure and diversification in C. butyricum. Additionally, the endophytic variance analysis identified several genes associated with CRISPR, defense systems, and metabolism that contribute to endophytic colonization by C. butyricum. CONCLUSION: This study provides novel insights into the ongoing adaptation of C. butyricum to plant hosts and illuminates the genetic mechanisms underlying this host transition. By elucidating population structure, gene flow, recombination patterns, and candidate adaptive genes, our findings advance the understanding of host-associated evolution in enteric bacteria.}, } @article {pmid42363297, year = {2026}, author = {Wang, Y and Liu, M and Dogra, SK and Vidal, K and Godin, JP and Darwish, N and Wei, X and Reymond, L and Li, Q and Dong, J and Vyllioti, AT and Bettler, J and Kennedy, E and Wang, K and Zhai, Q and O'Regan, J and Samuel, TM and Cai, W}, title = {Effects of an infant formula containing a whey protein concentrate on feeding tolerance and markers of intestinal immune defense in Chinese infants.}, journal = {BMC nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40795-026-01395-0}, pmid = {42363297}, issn = {2055-0928}, abstract = {BACKGROUND: Human milk (HM) bioactive components can have immune modulatory functions, impact the gut microbiome, and may result in functional benefits when added to infant formula (IF). In this single-arm, prospective, intervention study, we tested the effectiveness of an IF with a whey protein concentrate co-enriched in α-lactalbumin, milk fat globule membrane (MFGM), and Sn-2 palmitate resulting in protein and lipid profiles observed in HM. The outcomes tested were feeding tolerance, Bifidobacteria abundance, and intestinal and immune health of Chinese infants.

METHODS: Predominantly formula-fed (FF) and breastfed (BF) infants were enrolled between 3 and 28 days and assigned to the FF (N = 60) or BF (N = 60) group, per their feeding practice, for 6 weeks. The primary endpoint was Infant Gastrointestinal Symptom Questionnaire (IGSQ) index score assessed using a validated IGSQ-13 questionnaire after 6 weeks of intervention; non-inferiority of FF vs BF was tested. Secondary endpoints included fecal Bifidobacteria abundance assessed using shotgun metagenomics sequencing; fecal short chain fatty acids (SCFAs) analyzed by ultra-performance liquid chromatography-tandem mass spectrometry; fecal markers of immune response, inflammation, intestinal barrier integrity (secretory immunoglobulin A sIgA), cytokines, calprotectin, α1 antitrypsin, lipocalin-2) assessed using enzyme-linked immunosorbent assay; stool consistency assessed using gastrointestinal (GI) diary; anthropometric assessments; quality of life; physician reported adverse events; and use of medications.

RESULTS: Good GI tolerance was observed in both groups at V2 (mean ± SD IGSQ score FF: 19.9 ± 7.4; BF: 16.8 ± 4.2); difference of means 1.35 [95% CI: -1.312, 4.012]). After 6 weeks, Bifidobacterium genus relative abundance was not significantly different between the groups. Total SCFAs were significantly higher (p < 0.05) in the FF versus BF group, driven by increased levels of valeric and propanoic acids (p < 0.05 for both). The IGSQ domain scores, stool consistency, fecal markers of immunity, inflammation, and intestinal barrier integrity (except lipocalin-2 which was significantly higher in BF vs FF), anthropometric Z-scores, common illnesses, antibiotic use, and adverse events were not significantly different between groups at week 6.

CONCLUSIONS: Our results support the effectiveness of this tested infant formula in supporting good GI tolerance, growth, specific intestinal and immune health markers, and Bifidobacteria abundance similar to that of the BF group.

TRIAL REGISTRATION: NCT04880083 (2021-05-06).}, } @article {pmid42363646, year = {2026}, author = {Torres Sánchez, ED and Martínez Nieto, M and González Alvarez, GE and Rodríguez Montaño, R and Alarcón-Sánchez, MA and Heboyan, A and Gutiérrez Maldonado, AF and Varela Hernández, JJ and Lomelí Martínez, SM}, title = {Helicobacter pylori in oral and gastric pathologies: a narrative review of potential bidirectional pathogenic interactions.}, journal = {Annals of medicine}, volume = {58}, number = {1}, pages = {2533434}, doi = {10.1080/07853890.2025.2533434}, pmid = {42363646}, issn = {1365-2060}, mesh = {Humans ; *Helicobacter pylori/pathogenicity/isolation & purification ; *Helicobacter Infections/microbiology/complications/immunology ; *Periodontitis/microbiology ; *Mouth/microbiology ; *Gastritis/microbiology ; }, abstract = {The association between periodontal diseases and gastrointestinal conditions, particularly those associated with Helicobacter pylori and systemic inflammation, has garnered increased scientific attention because of its clinical and public health implications. These diseases, which affect both the oral cavity and the digestive system, have shared pathophysiological mechanisms that link inflammatory processes and bacterial transmission pathways. The possible presence of H. pylori in the oral cavity has sparked interest regarding its potential colonization of periodontal tissues and acting as an extragastric reservoir. This narrative review describes H. pylori's possible survival mechanisms in this oral microenvironment and its clinical significance in the interaction between oral and gastric conditions. We propose that periodontitis might promote gastric H. pylori infection by stimulating systemic inflammation, and oral colonization might serve as a reservoir for gastric reinfection. Future studies may involve advanced technologies such as metagenomics and proteomics. The eradication of H. pylori in the oral cavity may provide a strategy to prevent gastric reinfection. The findings described herein highlight the importance of this bacterium in two different pathologies sharing a close anatomical relationship.}, } @article {pmid42363687, year = {2026}, author = {Redmile, C and Sutherland, D and Devane, M and Taylor, W and Busby, I and Glackin, A and Gilpin, B and Chambers, T}, title = {The Establishment of an Indigenous-Led Drinking Water Monitoring Program Leveraging qPCR and Metagenomics Testing in New Zealand.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {98}, number = {7}, pages = {e70471}, doi = {10.1002/wer.70471}, pmid = {42363687}, issn = {1554-7531}, support = {ESR2411//Ministry of Business, Innovation and Employment/ ; TN/PWC/19/UoOWTC//Ministry of Business, Innovation and Employment/ ; }, mesh = {New Zealand ; *Drinking Water/microbiology/analysis ; *Metagenomics/methods ; *Environmental Monitoring/methods ; Humans ; Water Quality ; Water Microbiology ; Maori People ; }, abstract = {An Indigenous-led monitoring program was established in partnership with the South Island Māori (Indigenous population of New Zealand [NZ]) tribe of NZ to understand and improve local drinking water safety. The aims of the project were to: (1) establish an Indigenous-led drinking water monitoring program; (2) utilize a full suite of monitoring tools to understand source water hazards and treatment efficacy; and (3) test the effectiveness of advanced water sampling techniques in Indigenous communities. Advanced sampling techniques were used for fecal source tracking to identify existing public health hazards and to provide assurance that any remedial interventions were effective. The program trained a total of 27 individuals from 16 different Indigenous communities in water quality sampling and helped to identify and address six microbial water quality issues. This project underscored the benefits of engaging Indigenous Peoples in governance and decision-making processes and in alleviating systemic barriers that prevent Indigenous communities from realizing safe water quality and sufficient water infrastructure.}, } @article {pmid42363849, year = {2026}, author = {Wang, X and Wang, H and Wang, X and Zhang, M and Cui, Y and Liao, H and Yang, J and Zou, Y and Jiang, L and Li, X and Yang, Y}, title = {Metagenome-assembled genome of Oscillospiraceae bacterium strain ZGZL, an anaerobic chloromethane-degrading bacterium enriched from rice paddy soil.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0028726}, doi = {10.1128/mra.00287-26}, pmid = {42363849}, issn = {2576-098X}, abstract = {Oscillospiraceae sp. strain ZGZL is an anaerobic bacterium capable of degrading chloromethane. Here, we report the metagenome-assembled genome sequence of strain ZGZL, which has a genome size of 2.04 Mb and a G+C content of 52.56%.}, } @article {pmid42363855, year = {2026}, author = {Pham, EQ and Gaulke, CA and Eisen, JA and Dandekar, S}, title = {Metagenome-assembled genomes recovered from the gut microbiomes of simian immunodeficiency virus-infected rhesus macaques.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0042826}, doi = {10.1128/mra.00428-26}, pmid = {42363855}, issn = {2576-098X}, abstract = {Rhesus macaques are widely used model organisms for studying human biology, yet relatively few metagenome-assembled genomes (MAGs) are available from their microbiome. Here, we report 159 MAGs recovered from simian immunodeficiency virus-infected macaques, including those treated either with antiretroviral therapy or 10-hydroxystearic acid.}, } @article {pmid42364055, year = {2026}, author = {Xu, Q and Sun, L and Han, X and Zhang, Q and Jiang, W and Zhu, S}, title = {Multi-kingdom gut microbiota analyses define bacterial-fungal interplay in multiple type 2 diabetes cohorts.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {42364055}, issn = {1869-1889}, abstract = {The role of the gut microbiome in type 2 diabetes (T2D) remains incompletely defined, particularly across microbial kingdoms and diverse populations. Here, we conducted a meta-analysis of 3,857 fecal metagenomes from six international cohorts, profiling bacteria, fungi, archaea, and viruses. Using supervised machine-learning models trained on harmonized multi-kingdom profiles with cross-cohort validation, we identified conserved alterations in T2D, characterized by reduced bacterial and viral diversity and increased fungal and archaeal diversity. A cross-kingdom panel of 33 microbial markers derived from these models achieved robust diagnostic performance (AUR-OC=0.82), outperforming single-kingdom models. Notably, Saccharomyces cerevisiae was consistently depleted in T2D and inversely correlated with glycemic indices. In mice, oral S. cerevisiae supplementation improved glucose tolerance and insulin sensitivity while reducing the abundance of Eggerthella lenta and Klebsiella pneumoniae, bacterial taxa previously linked to adverse metabolic and inflammatory phenotypes. Together, our findings highlight the diagnostic value and mechanistic relevance of multi-kingdom microbial signatures in T2D and position S. cerevisiae as a potential fungal probiotic candidate for metabolic intervention.}, } @article {pmid42364169, year = {2026}, author = {Pan, P and Zhou, NY}, title = {Metabolic interactions enable aerobic degradation of the environmental pollutant BDE-47.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag163}, pmid = {42364169}, issn = {1751-7370}, abstract = {As a prevalent congener of polybrominated diphenyl ethers (PBDEs), 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) poses significant environmental and health risks due to its persistence and bioaccumulation. However, the limited understanding of the microbial degradation mechanism of BDE-47 has hindered the development of effective bioremediation strategies. Here, we decipher an aerobic catabolic pathway of BDE-47 mediated by metabolic relay within a synthetic consortium composed of two environmental isolates, Rhizorhabdus wittichii YL-JM2C and Cupriavidus necator JMP134. Bioaugmentation with this consortium achieved complete removal of BDE-47 in real wastewater samples. The molecular basis underlying this cooperative degradation was elucidated through the heterologous expression and functional characterization of key enzymes involved. Namely, the dioxygenase TcsAaAb from strain YL-JM2C catalyzed the initial conversion of BDE-47 into 2,4-dibromophenol (2,4-DBP) and 3,5-dibromocatechol (3,5-DBC). As a dead-end intermediate in strain YL-JM2C, the former (2,4-DBP) was subsequently transformed into the latter (3,5-DBC) by the hydroxylase TfdB from strain JMP134. The resulting 3,5-DBC was catabolized through the downstream ortho-cleavage pathway present in both strains. These key enzymes for BDE-47 degradation coexist across diverse environments, including soil, seawater, and marine sediments. Global marine metagenomic profiling revealed a significant enrichment of these catabolic signatures in the Mariana Trench, implying that microorganisms in the hadal zone possess the genetic potential for PBDE catabolism. This study unveils previously unrecognized aerobic catabolic mechanisms for BDE-47 within natural ecosystems, offering promising bioremediation strategies for PBDE-contaminated environments.}, } @article {pmid42364365, year = {2026}, author = {Manning, VA and Moore, PA and Medina, AR and Trippe, KM}, title = {Genome-resolved metagenomics of an acid-tolerant nitrifying biofilm suggests cooperative nitrogen cycling at low pH.}, journal = {The Science of the total environment}, volume = {1046}, number = {}, pages = {181954}, doi = {10.1016/j.scitotenv.2026.181954}, pmid = {42364365}, issn = {1879-1026}, abstract = {Ammonia emissions from animal feeding operations are a major source of nitrogen loss and environmental pollution. Nitrifying bacteria used within ammonia scrubbers offers a promising strategy to recover nitrogen for fertilizer; however, the acidic environment within air scrubbers generally inhibits nitrification and sustained nitrification at low pH remains poorly understood. Here, we present a genome-resolved analysis of an acid-tolerant nitrifying community (ATNC) enriched from a laboratory bioreactor operating at pH values between 4 and 4.6 that was previously shown to support nitrification. Long-read metagenomic sequencing yielded 12 high-quality metagenome-assembled genomes accounting for 94.7% of community abundance, including four phylogenetically distinct Nitrospira representing both comammox and canonical nitrite-oxidizing lineages, alongside heterotrophic species of Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and a filamentous Ktedonobacterales strain. Genomic reconstruction suggested niche partitioning in nitrogen cycling, with comammox Nitrospira encoding the capacity for complete nitrification and Rhodanobacteraceae harboring genes associated with denitrification. Acid tolerance and biofilm persistence were associated with diverse ion-transport systems, alternative respiratory complexes, extracellular polymeric substance biosynthesis, and expanded repertoires of secreted proteases and carbohydrate-active enzymes that facilitate matrix turnover and carbon scavenging. Within the biofilm, Chloroflexi likely contribute structural scaffolding, while heterotrophs appear to be adapted for extracellular organic matter turnover and to act as metabolic partners. Together, these findings suggest that metabolic cooperation, functional redundancy, and biofilm-mediated resource sharing may support nitrification under acidic conditions. This work provides genome-resolved insight into the microbial processes potentially underpinning nitrification-enhanced ammonia capture and identifies candidate genomic features relevant to optimizing nitrogen recovery while minimizing denitrification-driven losses in engineered systems.}, } @article {pmid42364424, year = {2026}, author = {Chambers, LM and Spakowicz, D and Chalif, J and O'Connor, R and Kistenfeger, Q and Mehra, Y and Mohssen, M and Abdeen, C and Haight, P and Nagel, C and Neff, R and Cohn, D and Copeland, LJ and Backes, F and Cosgrove, C and Hays, J and Dravillas, C and McLaughlin, E and O'Malley, D}, title = {PRO-PLATINUM: A randomized, double-blind, placebo controlled study to investigate the efficacy of a probiotic intervention on the gut and vaginal microbiome of ovarian cancer patients undergoing treatment with platinum chemotherapy.}, journal = {Gynecologic oncology}, volume = {211}, number = {}, pages = {74-78}, doi = {10.1016/j.ygyno.2026.06.016}, pmid = {42364424}, issn = {1095-6859}, abstract = {BACKGROUND: PRO-PLATINUM evaluates whether a 5-strain probiotic formulation can favorably modulate the gut microbiome during platinum-based chemotherapy in ovarian cancer (OC), while assessing feasibility, safety, and translational correlates of response and toxicity.

PATIENTS AND METHODS: PRO-PLATINUM is an IRB-approved, randomized, double-blind, placebo-controlled trial enrolling 124 patients with stage II-IV or platinum-sensitive recurrent high-grade OC receiving platinum-based chemotherapy. The study opened to enrollment in February 2026. Participants are randomized 1:1 to a 5-strain probiotic (WBF-038) or placebo, stratified by newly diagnosed advanced versus recurrent disease. The intervention contains inulin and five microbial strains: Akkermansia muciniphila, Anaerobutyricum hallii, Clostridium beijerinckii, Clostridium butyricum, and Bifidobacterium infantis, and is administered orally twice daily beginning within seven days of cycle 1 and continuing through seven days after the completion of cycle 6. Eligible patients must have ECOG performance status 0-2, adequate organ function, and no major probiotic-related contraindications. Stool, blood, and vaginal samples are collected at baseline, cycle 3, and cycle 6; tumor tissue is collected at surgery when available. The primary endpoint is change in gut microbiome composition by whole-genome metagenomic sequencing. Secondary endpoints include intervention adherence, biospecimen feasibility, recurrence-free survival, and overall survival. Exploratory endpoints include toxicity, postoperative infections, stool consistency, diet, medication and antibiotic exposure, quality of life, symptom burden, serum metabolomic and immune profiling, vaginal and tumor microbiome composition, and associations between microbial features and clinical outcomes.

CONCLUSIONS: PRO-PLATINUM will evaluate treatment feasibility and safety and generate prospective translational data to inform future microbiome-directed strategies to improve treatment tolerance, quality of life, and outcomes in OC patients.}, } @article {pmid42364687, year = {2026}, author = {Sun, J and Han, X and Sun, X and Qin, H and Yang, D and Shangguan, M and Lu, J and Li, H and Li, Y and Bao, M}, title = {Geochemical and Microbial Functional Responses of Surface Soil to Simulated Low-Concentration CO2 Leakage from Geological Storage.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125132}, doi = {10.1016/j.envres.2026.125132}, pmid = {42364687}, issn = {1096-0953}, abstract = {Geological CO2 storage may pose environmental risks if leaked CO2 migrates into near-surface soils. To evaluate early surface-soil responses to low-concentration CO2 exposure, a 42-day aerated soil microcosm experiment was conducted using a control group and two CO2 treatment levels of 2,000 and 10,000 ppm. Soil physicochemical properties, dissolved cations, metal fractions, enzyme activities, bacterial community composition, and metagenomic functional profiles were analyzed. Sustained CO2 exposure increased electrical conductivity and HCO3[-] concentrations, whereas soil pH remained within a narrow weakly alkaline range. Sequential extraction showed limited redistribution of selected metals among operationally defined fractions, but no evidence of extensive metal mobilization was observed. Among microbial indicators, FDA hydrolase activity responded significantly to CO2 exposure, whereas microbial community structure, alpha diversity, and overall KEGG and CAZy functional profiles remained largely stable. Representative carbon- and nitrogen-cycling genes were influenced mainly by incubation time rather than CO2 concentration. Under the tested short-term, low-concentration, aerated microcosm conditions, the soil system exhibited considerable buffering capacity and resistance to CO2 exposure. The observed effects were mainly expressed as minor changes in soil solution chemistry and selected functional indicators rather than pronounced geochemical deterioration or microbial community restructuring. These findings provide experimental evidence and insights into the geochemical buffering capacity and microbial response mechanisms of surface soil systems under potential leakage scenarios of underground CO2 storage. The findings offer scientific references for environmental risk assessment of CO2 geological sequestration and the selection and interpretation of sensitive monitoring indicators.}, } @article {pmid42364737, year = {2026}, author = {Hajjar, C and Saint-Criq, V and Thomas, M and Butel, MJ and Bazarbachi, A and Abifadel, M}, title = {The Lung Microbiome in Hematopoietic Stem Cell Transplantation: Immune Interactions, Clinical Consequences, and Emerging Interventions.}, journal = {Respiratory medicine}, volume = {}, number = {}, pages = {109004}, doi = {10.1016/j.rmed.2026.109004}, pmid = {42364737}, issn = {1532-3064}, abstract = {Hematopoietic stem cell transplantation (HSCT) offers curative potential for hematologic malignancies and immune disorders, yet pulmonary complications remain major contributors to non-relapse morbidity and mortality. Traditionally attributed to immune suppression and graft-versus-host disease (GvHD), these complications are increasingly recognized to involve disruption of pulmonary microbial communities. A growing body of clinical and experimental evidence indicates that HSCT-associated perturbations in the lung microbiome, driven by conditioning, antimicrobials, immune injury, and infection, are associated with distinct post-transplant pulmonary phenotypes and, in some cohorts, with mortality risk. Whether these microbial shifts represent causal contributors to lung injury or contextual biomarkers of immune vulnerability remains unresolved, and this distinction carries direct implications for microbiome-targeted intervention. Dysbiotic shifts in the lung have been associated with both infectious and non-infectious complications, including idiopathic pneumonia syndrome, bronchiolitis obliterans syndrome, and fibrotic lung disease. Gut-lung microbial crosstalk may amplify or reflect systemic immune dysfunction, though the directionality of this relationship remains incompletely characterized. Multi-omics approaches, integrating metagenomics, metatranscriptomics, and metabolomics, are beginning to define the host-microbiome interaction signatures that distinguish injury subtypes and predict outcomes. This review synthesizes mechanistic insights into lung microbiome-immune interactions after HSCT, critically appraises the methodological constraints on the current evidence base, and evaluates microbiome-based interventions, including fecal microbiota transplantation, inhaled postbiotics, and precision antimicrobials, as candidate strategies for respiratory protection in transplant recipients, while acknowledging that prospective interventional evidence in this population remains limited.}, } @article {pmid42364789, year = {2026}, author = {DiSilvestro, AN and Wesolowski, LT and Williams, BD and Warren, LK and Athrey, G and White-Springer, SH}, title = {Short-term provision of moderate dietary starch alters fecal microbiota but does not exacerbate exercise-induced inflammation in yearling Quarter Horses.}, journal = {Journal of equine veterinary science}, volume = {}, number = {}, pages = {106071}, doi = {10.1016/j.jevs.2026.106071}, pmid = {42364789}, issn = {0737-0806}, abstract = {BACKGROUND: Energy-dense feeds commonly provided to equine athletes may be high in starch, which alter gastrointestinal microbiota and could promote systemic inflammation.

AIMS/OBJECTIVES: To test the hypothesis that exercise-induced inflammation would be greater in horses receiving a starch- versus fiber-based concentrate.

METHODS: Quarter Horses (mean±SD 16±1mo; 337±30kg) received either a fiber-based control (CON; 7 fillies, 8 geldings) or an isocaloric, isonitrogenous starch concentrate (STARCH; 8 fillies, 7 geldings) for 24d. Fecal metagenomics were evaluated on d0 and 21. Blood inflammatory mediators were quantified on d0, d21, and surrounding a 2-h submaximal exercise test (SET) on d22.

RESULTS: On d21, CON horses had greater Lactobacillaceae (∼5.7% vs. ∼2.4% in STARCH), while STARCH had greater Lachnospiraceae (∼38% vs. ∼32% in CON) but diet alone did not impact inflammatory markers. On d22, CRP increased at 24h post-SET in all horses (P<0.0001). By 48h, CRP returned to pre-SET in STARCH but remained elevated in CON (P=0.0005), resulting in greater CRP in CON than STARCH at 48h (P=0.02). TNFα increased from pre-SET to 1h in STARCH horses (P=0.02), then returned to pre by 6h. In CON horses, TNFα increased at 24h (P=0.04) and remained elevated at 48h (P=0.0005). Throughout the SET, CON had greater IL-10 than STARCH horses (P=0.005). SAA, IL-4, IL-8, and vascular endothelial growth factor (VEGF)-A were differentially impacted by the SET but were unaffected by diet.

CONCLUSION: Contrary to our hypothesis, fiber-fed horses appeared to elicit a more robust acute inflammatory response to exercise than starch-fed horses despite an altered gastrointestinal microbiome.}, } @article {pmid42364824, year = {2026}, author = {Zhang, H and Xie, G and Jiang, L and Li, M and Ding, J and Mei, C and Xiong, X}, title = {Effects of different function-oriented hydrochars on anaerobic digestion of hydrothermal wastewater: Focusing on microbial community function and organic degradation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135266}, doi = {10.1016/j.biortech.2026.135266}, pmid = {42364824}, issn = {1873-2976}, abstract = {To elucidate the coupling relationships among hydrochar characteristics, microbial responses, and organic matter removal during anaerobic digestion of hydrothermal treatment wastewater (HTTWW-AD), raw hydrochar (HC), alkali-modified hydrochar (AHC), and iron-modified hydrochar (IHC) were prepared. Excessive microbial anabolic metabolism and limited hydrolysis-acidification efficiency were identified as the main causes of the low methane yield in HTTWW-AD. HC, AHC, and IHC increased methane yield by 115.97%, 148.25%, and 135.42%, respectively, and the methane content also increased by 9.86% - 12.50%. Metagenomic analysis revealed that microorganisms in the control (CK) system were under higher stress, whereas hydrochar addition promoted the enrichment of hydrolytic and acidogenic bacteria (HAB) and alleviated microbial stress. AHC further enriched Methanothrix and Methanobacterium, thereby enhancing both acetoclastic and hydrogenotrophic methanogenesis. The enhanced reductive methanogenesis was likely associated with its high electron-donating capacity (EDC). IHC enriched exoelectrogenic HAB, suggesting that Fe/N-related active sites may facilitate extracellular electron transfer. Gas chromatography-mass spectrometry analysis showed that HC favored the removal of ketones, N-containing heterocycles, and alcohols, whereas AHC was more effective for acids, N-containing heterocycles, and alcohols. IHC promoted the removal of diverse organic compounds, particularly ketones, phenols, and esters. These differences were associated with the enrichment of potential degraders (Hydrogenophaga, Sphaerochaeta, Mesotoga, Bacteroides, and Paludibacter), possible adsorption at surface-active sites, and Fe(III)/Fe(II)-cycle-mediated redox activation. Overall, hydrochars effectively promoted hydrolysis-acidification during HTTWW-AD. Hydrochars enriched with electron-donating functional groups favored methanogenic conversion, whereas Fe/N-related active sites were more beneficial for the removal of recalcitrant organic compounds.}, } @article {pmid41073888, year = {2025}, author = {Michel, A and Leoz, M and Nesi, N and Petat, H and Ar Gouilh, M and Charbonnier Le Clezio, C and Marguet, C and Hassel, C and Plantier, JC}, title = {Impact of RNA extraction on respiratory microbiome analysis using third-generation sequencing.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {908}, pmid = {41073888}, issn = {1471-2164}, mesh = {*Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Fungi/genetics/isolation & purification/classification ; Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification ; *Respiratory System/microbiology ; *RNA/isolation & purification ; }, abstract = {BACKGROUND: The respiratory microbiome, which comprises bacteria, fungi, and viruses, plays a crucial role in respiratory health and disease. However, its study is limited by the low microbial biomass in respiratory samples and the dominance of host RNA. Metatranscriptomics offers comprehensive insights into active microbial communities and their interactions with the host but requires optimized RNA extraction protocols for robust and unbiased analysis. This study evaluated two RNA extraction kits—one employing chemical lysis (CL) and another combining chemical and mechanical lysis (CML)—to determine their effectiveness for metatranscriptomic analysis of respiratory samples. RESULTS: The CML protocol significantly increased double-stranded DNA (dsDNA) library yields, leading to higher sequencing read counts for both sample types (p < 0.0001). The read length was unaffected by the lysis protocol for the BAL and NPS samples. Taxonomic profiling revealed that CML enhanced the detection of robust microorganisms, such as gram-positive bacteria and fungi, without compromising viral detection. CONCLUSIONS: The CML protocol demonstrated superior recovery of genetic material, particularly for fungi and gram-positive bacteria, making it better suited for comprehensive metatranscriptomic analyses. These findings underscore the need for tailored RNA extraction strategies on the basis of sample type and research objectives. Optimized metatranscriptomic protocols are pivotal for advancing our understanding of the respiratory microbiome and its role in health and disease.}, } @article {pmid42350828, year = {2026}, author = {Botta, A and Messina, C}, title = {Hantavirus infection: Neurologic manifestations should not be overlooked.}, journal = {Journal of neurovirology}, volume = {32}, number = {4}, pages = {}, pmid = {42350828}, issn = {1538-2443}, mesh = {Humans ; *Orthohantavirus/pathogenicity ; *Hemorrhagic Fever with Renal Syndrome/virology/immunology/diagnostic imaging/complications/pathology ; *Hantavirus Infections/virology/complications ; Blood-Brain Barrier/virology/immunology/diagnostic imaging ; *Hantavirus Pulmonary Syndrome/virology/immunology/diagnostic imaging ; }, abstract = {Hantavirus infection is primarily associated with hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS), with predominant renal and pulmonary involvement. However, neurological manifestations affecting both the central nervous system (CNS) and peripheral nervous system (PNS) are increasingly recognized. We conducted a narrative review of the literature to summarize the current evidence regarding hantavirus-associated neurological involvement. Reported CNS manifestations included encephalitis, encephalopathy, seizures, meningitis, neurocognitive alterations, posterior reversible encephalopathy syndrome, transverse myelitis, and cerebral hemorrhage. PNS involvement appeared less frequent and included Guillain-Barré syndrome, cranial nerve palsies, neuropathic pain, and sensory disturbances. Neuroimaging findings were heterogeneous, while cerebrospinal fluid analysis often demonstrated nonspecific inflammatory changes. Advanced molecular techniques such as metagenomic next-generation sequencing may improve diagnostic sensitivity, particularly in immunocompromised patients. Current evidence suggests that neurological involvement may result from endothelial dysfunction, neuroinflammation, immune-mediated injury, blood-brain barrier disruption, and, in selected cases, direct viral neuroinvasion. Greater clinical awareness is needed to improve recognition of neurological complications during hantavirus infection. Further prospective studies are required to better define the epidemiology, pathogenesis, and optimal diagnostic approaches of hantavirus-associated neurological disease.}, } @article {pmid42351266, year = {2026}, author = {Chen, T and Xiao, J and Li, S and Peng, R and Xu, Y and Zhuang, Y and Zhao, X and Sha, M and Wang, J and Ma, J and Wang, W and Gao, J and Ma, M and Li, S and Cao, Z and Liu, S}, title = {Differential rumen and hindgut microbiome and metabolome in Holstein female calves with divergent feed efficiency.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02446-1}, pmid = {42351266}, issn = {2049-2618}, abstract = {BACKGROUND: Significant environmental problems have challenged animal agriculture, improving feed efficiency in animals has become a vital research direction for sustainable agriculture. Bacteria play a critical role in the feed efficiency of animals. However, our current understanding of bacteria communities in the gastrointestinal tract of high-feed efficiency animals and their metabolic mechanisms remains unclear.

RESULTS: Twenty Holstein female calves were used in this multi-omics study that integrated metagenomic and metabolomic analyses of 20 Holstein female calves to investigate feed efficiency, as measured by residual feed intake (RFI). From an initial cohort of 84 calves, the 10 with the highest RFI (HRFI, low efficiency) and the 10 with the lowest RFI (LRFI, high efficiency) were selected at 84 days of age. Rumen fluid, feces, and serum samples from these calves were collected for subsequent analyses. We found that LRFI calves harbored rumen and fecal microbiomes with significantly different community structures and co-occurrence networks compared to HRFI calves. Multi-omics integration identified robust microbial and metabolite biomarkers discriminating RFI groups. These microbiomes were functionally linked to differential nutrient utilization, LRFI calves were characterized by enhanced starch and protein digestibility coupled with propionate-oriented fermentation, associated with key species like Erysipelotrichaceae_bacterium and Hungatella_sp. Conversely, HRFI calves showed higher fat digestibility and acetate production. Notably, serum glutamate was enriched in LRFI calves despite lower intake, correlating with potential microbial metabolites (ribitol, taurine). Subsequent validation confirmed that glutamate supplementation in mice improved nitrogen metabolism and gut barrier function.

CONCLUSIONS: In summary, this multi-omics study reveals that high feed efficiency in calves is associated with distinct microbial ecosystems characterized by functions such as starch degradation and propionate production, where glutamate metabolism serves as a central node. Video Abstract.}, } @article {pmid42351291, year = {2026}, author = {Liu, J and Coker, MO and Osazuwa-Peters, N and Peter, O and Idemudia, NL and Schlecht, NF and Obuekwe, O and Eki-Udoko, FE and Bromberg, Y}, title = {Whole metagenome sequencing: not deep enough for complete microbial function recovery.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02448-z}, pmid = {42351291}, issn = {2049-2618}, abstract = {BACKGROUND: Whole metagenome shotgun sequencing (WMS) is widely used to profile microbial function. However, technical variability in sequencing and analysis often obscures true biological patterns. Large-scale studies are particularly susceptible to batch effects, such as differences in sequencing depth and platform and annotation strategies, as well as sample-to-flow-cell assignments. However, the relative effects of these factors on functional inference in such studies have yet to be systematically evaluated. We analyzed oral-rinse WMS data from 671 Nigerian youths aged 9-18, sequenced on two Illumina platforms. Microbial molecular functionality encoded in these data was annotated using the mi-faser/Fusion pipeline, to capture the broad functional repertoire, and HUMAnN 3/EC numbers pipeline to characterize curated enzymatic activities. We then quantified how technical factors and batch effects shaped the recovery of microbial functionality.

RESULTS: Three findings of our work were most salient. First, we observed that the choice of annotation strategy traded off between breadth and specificity of functional coverage. Second, we found that low-prevalence functions were disproportionately lost at shallow sequencing depths, indicating that in, e.g., case-control studies with few representatives of the minor class, sequencing depth could critically impact study resolution. Finally, using our newly developed model relating sequencing depth to functional recovery, we demonstrated that increasing sequencing depth does not directly or proportionally improve functional recall. That is, at as little as 10% of this study's sequencing depth, 30% of the estimated complete microbiome functional repertoire was detectable. However, even at the full depth used in this study, we were only able to recover an estimated 60% of that complete functional repertoire. We further showed that despite biomes differences in functional diversity and host contamination levels (e.g., soil, fecal), incomplete functional recovery at commonly used sequencing depths was consistently observed.

CONCLUSIONS: Together, these findings and our depth-to-function mapping framework provide practical guidelines for the design and interpretation of WMS studies. Coordinating sequencing depth planning with annotation strategy, experimental design, and rigorous batch control is thus essential for robust detection of microbial functions and for ensuring reproducible microbiome insights. Video Abstract.}, } @article {pmid42351509, year = {2026}, author = {Wang, M}, title = {Nanopore Sequencing in Mycobacterial Diagnostics: Clinical and Laboratory Roles of mNGS and tNGS.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/diagnostics16121850}, pmid = {42351509}, issn = {2075-4418}, support = {No. 20220919Y060//Hangzhou Science and Technology Commission/ ; }, abstract = {Background/Objectives: Nanopore sequencing is increasingly used in mycobacterial diagnostics, where clinical microbiologists and diagnostic laboratories must decide when broad metagenomic next-generation sequencing (mNGS) or focused targeted next-generation sequencing (tNGS) is most appropriate. This review examined reported clinical and laboratory roles of nanopore mNGS and tNGS in tuberculosis (TB) and nontuberculous mycobacterial (NTM) settings. Methods: Targeted searches of PubMed/MEDLINE, Embase, Web of Science Core Collection, and Scopus were refreshed on 4 April 2026. Thirty-five records spanning original clinical studies, evidence syntheses, and guideline-context documents were included. Results: Nanopore mNGS is most useful for broad organism detection and diagnostic rescue in unresolved pulmonary and extrapulmonary presentations, particularly when first-line testing is negative, discordant, low-yield, or when mixed infection is suspected. Nanopore tNGS appears better aligned with predefined TB confirmation and resistance-focused workflows because targeted regions allow more standardized interpretation. Agreement is strongest for rifampicin- and isoniazid-related resistance targets. In NTM settings, evidence is stronger for detection and species identification than for disease-level diagnosis. Common implementation constraints include pre-analytical variation, contamination control, host-background interference, inconsistent bioinformatics, and limited workforce capacity. Conclusions: A practical tiered approach is supported in which mNGS is positioned mainly for diagnostic rescue and discovery, whereas tNGS is considered for predefined workflows requiring standardized target interrogation and resistance-associated mutation reporting under local validation and quality systems.}, } @article {pmid42351718, year = {2026}, author = {Tîrziu, AT and Romanescu, M and Ciordas, PD and Mercea, N and Munteanu, M and Horhat, FG and Chis, AR and Preda, MA}, title = {Metagenomic Profiling of the Gut Microbiome in Age-Related Macular Degeneration-A Pilot Study.}, journal = {Biomedicines}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/biomedicines14061290}, pmid = {42351718}, issn = {2227-9059}, support = {CNFIS-FDI-2024-F-0451//Consiliul National pentru Finantarea Invatamantului Superior/ ; }, abstract = {Background/Objectives: Age-related macular degeneration (AMD) is a multifactorial retinal disease involving inflammatory, metabolic, and genetic factors. Increasing evidence suggests that the gut microbiome may contribute to systemic pathways involved in retinal homeostasis. This exploratory pilot study investigated gut microbiome alterations in AMD patients and controls using long-read whole-genome sequencing. Methods: Bacterial DNA was extracted from fecal samples and analyzed using Oxford Nanopore sequencing, followed by taxonomic profiling, alpha and beta diversity analyses, and differential abundance testing. Results: AMD patients showed significantly reduced microbial diversity, reflected by lower richness, Shannon and Simpson indices. Species-level beta diversity analyses revealed significant differences in microbial community composition, particularly with Bray-Curtis metrics, alongside increased inter-individual microbial heterogeneity in AMD samples. Differential abundance analyses identified the depletion of several potentially beneficial commensal taxa, including Faecalibacterium prausnitzii and Parabacteriodes distasonis, whereas Staphylococcus aureus was enriched in AMD patients. Comparisons between wet and dry subtypes showed no significant differences in alpha or beta diversity. Conclusions: Overall, the findings support the presence of gut microbial dysbiosis in AMD characterized by reduced diversity, abundance-driven community shifts, and increased microbiome heterogeneity. Given the small cohort size, cross-sectional design and lack of functional analysis, these results should be considered preliminary and hypothesis-generating.}, } @article {pmid42351858, year = {2026}, author = {Chen, X and Yuan, H and Li, X}, title = {Methane Yield, Substrate Conversion, Microbial Community Structure and Metabolic Pathways During Anaerobic Digestion of Natural Cellulosic Biomass.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/bioengineering13060613}, pmid = {42351858}, issn = {2306-5354}, abstract = {Three natural celluloses (softwood pulp, straw grass pulp, and degreased cotton) were used for anaerobic digestion tests to research methane yield, substrate conversion and microbial community structure, and further supplemented and clarified the metabolic pathway mechanisms of anaerobic digestion of cellulosic biomass. The results showed that natural cellulose could be significantly degraded and converted into methane by anaerobic microorganisms. The cumulative specific methane yields of wood pulp fiber (F1), straw pulp fiber (F2), and degreased cotton fiber (F3) were 373.57 ± 10.70 mL/g VS, 349.15 ± 13.20 mL/g VS and 346.16 ± 1.60 mL/g VS, respectively. The corresponding biodegradability values were 93.97%, 85.95% and 84.32%. Although the fermentation cycles in F1, F2, and F3 were identical (T95 was 12 days), the three groups exhibited distinct biogas production patterns. Metagenomic analysis indicated that F1 and F2 were dominated by the acetoclastic methanogenesis pathway, while the proportion of the hydrogenotrophic methanogenesis pathway increased in F3. Meanwhile, the cell motility pathway category was significantly enriched in F3. These results supplement the existing research on the anaerobic digestion of natural cellulose and provide theoretical support for the efficient anaerobic bioconversion of natural cellulosic biomass.}, } @article {pmid42352020, year = {2026}, author = {Zhang, BY and Wang, YQ and Yang, R and Zhang, Y and Jiang, DZ and Ji, LH and Mao, YF and Tang, B and Zhang, XM}, title = {Gut Microbiota-Mediated Histidine Deficiency Drives Testicular Ferroptosis Induced by Bisphenol F Exposure.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/antiox15060714}, pmid = {42352020}, issn = {2076-3921}, support = {No. 32573319 and No. 32172803//National Natural Science Foundation of China/ ; }, abstract = {Bisphenol F (BPF), a widespread environmental contaminant and a major substitute for the restricted bisphenol A (BPA), has raised increasing concerns regarding its potential male reproductive health risks, yet its underlying mechanisms remain poorly understood. This study investigates the mechanisms underlying BPF-induced testicular damage, focusing on the interplay among gut microbiota (GM) dysbiosis, histidine metabolism disruption, and ferroptosis. Using a mouse model exposed to BPF (50, 100, and 200 mg/kg/day) for 28 days, we observed significant testicular pathology, including seminiferous tubule atrophy, vacuolation, and blood-testis barrier (BTB) impairment. Metagenomic and metabolomic analyses revealed GM dysbiosis and suppressed intestinal histidine metabolism, accompanied by decreased abundance of beneficial taxa (e.g., Bacteroides, Ligilactobacillus) and increased potential pathobionts (e.g., Akkermansia, Mucispirillum). BPF exposure was associated with reduced testicular histidine levels and decreased expression of the histidine transporter-related marker LAT1, suggesting impaired histidine availability and a possible alteration in LAT1/CD98-mediated transport; however, direct inhibition of LAT1/CD98 transport activity was not experimentally demonstrated. BPF exposure was accompanied by ferroptosis-related alterations in the testes, including mitochondrial damage, iron accumulation, lipid peroxidation, and downregulation of the xCT-GSH-GPX4 antioxidant axis. In vitro experiments using mouse Sertoli cells (mSCs) confirmed BPF-induced ferroptosis, which was mitigated by the exogenous histidine supplementation. Histidine administration in vivo ameliorated testicular damage, restored BTB integrity, and reversed ferroptotic markers. Our findings support a working model in which a GM-histidine-testis axis may contribute to BPF-induced reproductive toxicity, while further functional studies are required to establish direct causality and transporter-level mechanisms.}, } @article {pmid42352268, year = {2026}, author = {Tita, GV and Fogas, CR and Slavescu, KC and Tantau, VM and Medan, SA and Serban, DE}, title = {Persistent Gut Microbiota Dysbiosis in Pediatric Crohn's Disease: A Next-Generation Sequencing Pilot Study.}, journal = {Biomolecules}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/biom16060801}, pmid = {42352268}, issn = {2218-273X}, mesh = {Humans ; *Crohn Disease/microbiology ; *Dysbiosis/microbiology/genetics ; Pilot Projects ; Female ; Male ; Child ; *Gastrointestinal Microbiome/genetics ; *High-Throughput Nucleotide Sequencing ; Prospective Studies ; Adolescent ; Metagenomics ; Eubacteriales ; }, abstract = {Background: Crohn's disease (CD) is characterized by gut microbiota alterations including reduced microbial diversity, loss of commensal species, and increased abundance of opportunistic taxa. Methods: This prospective study was conducted between 2022 and 2024 at the Emergency Clinical Hospital for Children, Cluj-Napoca. Children with CD and healthy controls were evaluated. The gut microbiota was analyzed using shotgun metagenomics. Bioinformatic processing assessed alpha and beta diversity, core microbiome composition, and differential taxa. Results: Ten patients with CD and eight healthy children were included; five patients were re-evaluated after a median interval of 14 weeks. The Shannon index was significantly lower in CD patients compared with controls (p = 0.037). Beta diversity analysis suggested partial separation between CD at diagnosis and controls (p = 0.041). An inverse correlation was observed between the Shannon index and the clinical score (p = 0.028). Ruminococcus gnavus was among the taxa contributing to group separation. At follow-up, all patients were in clinical remission, while 80% had achieved biological remission and mucosal healing. They showed persistently reduced alpha diversity and distinct microbial communities compared with controls (p = 0.028 and p = 0.005, respectively). Conclusions: Pediatric CD was correlated with dysbiosis that persisted despite remission. Reduced alpha diversity was associated with greater disease severity at diagnosis.}, } @article {pmid42352384, year = {2026}, author = {Brown, JL and Mahadevan, P and Middlebrooks, M}, title = {Bacterial Community Composition and Functional Potential of the Kleptoplastic Sea Slug Elysia papillosa.}, journal = {Biomolecules}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/biom16060918}, pmid = {42352384}, issn = {2218-273X}, support = {OURI//University of Tampa/ ; }, mesh = {Animals ; *Gastropoda/microbiology ; *Microbiota ; *Bacteria/genetics/classification ; Phylogeny ; }, abstract = {Certain sacoglossan sea slugs, often known as "solar-powered sea slugs", are a group of marine gastropods that have the unique ability to photosynthesize by stealing functional chloroplasts from algae. The sacoglossan Elysia papillosa can maintain functional chloroplasts for up to two weeks after feeding. The microbiome of these slugs may play a crucial role in their metabolism, immunity, development, but more importantly their photosynthesis. Shotgun metagenomic sequencing was conducted on four samples of E. papillosa in order to characterize their microbiome. Sequences were classified and relative abundance was quantified with Centrifuger and functional data was examined using SqueezeMeta. Bacteria were analyzed by taxonomic groups and hypothesized function to the sea slug was determined with literature analysis. All samples were dominated by phyla Actinomycetota, Bacillota, Patescibacteriota, and Pseudomonadota. The presence of the phyla Bacteroidota and Bacillota was notable in all samples, which contain species known to produce enzymes that break down polysaccharides. It is possible that these bacteria could assist in degradation of the polysaccharide xylan found in the cell walls of Penicillus, the algal food source of E. papillosa. One species that was found in all samples was Cutibacterium acnes which has been shown to be an important component of the gut microbiota in other marine invertebrates and may provide the host with vitamin B12 and other beneficial nutrients. Many of these bacteria may be opportunistic rather than commensal. As a result, more research is required to describe the interactions between the slug and its microbiome, but this preliminary report provides a valuable starting point for identifying the microbiome make-up to further understanding of these relationships.}, } @article {pmid42353029, year = {2026}, author = {Xu, HJ and Liu, QL and Zhang, YF and Cuan, SN and Jia, Z and Qiao, D}, title = {Metagenomic Insights into Gut Microbiota Alterations Following Dendrobium huoshanense Water Extract Intervention in Streptozotocin-Induced Type 1 Diabetic Rats.}, journal = {International journal of molecular sciences}, volume = {27}, number = {12}, pages = {}, doi = {10.3390/ijms27125308}, pmid = {42353029}, issn = {1422-0067}, support = {no//the platform of the Traditional Chinese Medicine Institute of Anhui Dabie Mountain/ ; }, mesh = {Animals ; *Dendrobium/chemistry ; Rats ; *Plant Extracts/pharmacology/chemistry ; *Diabetes Mellitus, Experimental/drug therapy/microbiology ; *Diabetes Mellitus, Type 1/drug therapy/microbiology/chemically induced ; *Gastrointestinal Microbiome/drug effects ; Male ; Metagenomics/methods ; *Hypoglycemic Agents/pharmacology ; Rats, Sprague-Dawley ; Streptozocin ; Water/chemistry ; Metagenome ; }, abstract = {Dendrobium huoshanense water extract (DHWE) exhibits hypoglycemic effects in streptozotocin-induced type 1 diabetic (STZ-T1D) rats. However, its regulatory impact on the gut microbiota of T1D rats remains largely unclear. In this study, metagenomic sequencing was employed to characterize alterations in the gut microbiota of STZ-T1D rats following DHWE intervention, aiming to explore associations between DHWE-mediated gut microbial changes and T1D-related phenotypes. The results showed that 1300 mg/kg·BW/day DHWE did not significantly affect gut microbial α-diversity (p > 0.05), but drove the β-diversity structure toward that of normal rats. Meanwhile, DHWE significantly reduced the Bacteroidota/Bacillota ratio (p < 0.05), Megamonas (p < 0.01), Megamonas funiformis (p < 0.01), and notably increased the relative abundances of Adlercreutzia (p < 0.01), Adlercreutzia equolifaciens (p < 0.01) in STZ-T1D rats. Furthermore, functional annotation revealed that DHWE enriched multiple metabolic pathways, including streptomycin biosynthesis, ansamycins biosynthesis, galactose metabolism, ether lipid metabolism, and caprolactam degradation. Collectively, these findings demonstrate that DHWE reshapes gut microbiota composition and function in STZ-T1D rats, offering new clues regarding how gut microbial changes may contribute to the modulatory effects of Dendrobium huoshanense in T1D conditions.}, } @article {pmid42353070, year = {2026}, author = {Dang, X and Hanson, BA and Lopez, M and Miller, J and Koralnik, IJ}, title = {Cross-Compartment Virome Profiling in Human Immunodeficiency Virus Infection and Substance Use Disorder Reveals Brain-CSF-Periphery Discordance and Hepatitis B Virus in Central Nervous System.}, journal = {International journal of molecular sciences}, volume = {27}, number = {12}, pages = {}, doi = {10.3390/ijms27125349}, pmid = {42353070}, issn = {1422-0067}, mesh = {Humans ; *Brain/virology ; *HIV Infections/virology/cerebrospinal fluid/complications ; *Substance-Related Disorders/virology/cerebrospinal fluid/complications ; *Virome ; *Hepatitis B virus/genetics/isolation & purification ; Female ; *Central Nervous System/virology ; Male ; *Hepatitis B/virology/cerebrospinal fluid ; Viral Load ; Adult ; }, abstract = {The diversity and abundance of the brain virome is an active field of investigation. However, how the brain virome relates to the presence of viruses outside of the nervous system remains unclear. The rationale for this study is that analyses across multiple biologically linked compartments within the same individuals provide an important opportunity to evaluate virome discordance and viral burden. To characterize viral prevalence and burden across anatomical compartments, we applied the targeted viral enrichment method ViroFind to matched postmortem brain (n = 66), cerebrospinal fluid (CSF; n = 24), and peripheral samples (spleen, peripheral blood mononuclear cells, and lymph nodes; n = 66) from individuals with and without human immunodeficiency virus (HIV) infection and substance use disorder (SUD) in the National NeuroAIDS Tissue Consortium. We detected nucleic acids from 27 viruses representing 12 taxa. Several viruses, including adenovirus, torque teno virus, Epstein-Barr virus, human herpesvirus 6 and 7, cytomegalovirus, parvovirus, and JC polyomavirus, showed significant inter-compartment differences in prevalence or burden. CSF exhibited lower overall viral diversity than brain or peripheral samples, whereas peripheral samples showed the highest viral burden. CNS viral detection was more likely when the same virus was also detected in the periphery. We also detected HBV and HCV in CNS samples despite them not being classically regarded as neurotropic. Broader virome profiling showed greater peripheral viral burden and diversity in HIV-positive than HIV-negative individuals, whereas SUD was not associated with overall viral burden differences. These findings highlight important cross-compartment differences in viral detection, including occurrence of occult HBV infection within the CNS, and support the value of CNS-periphery comparisons in virome studies. These findings can contribute to improved diagnosis and management of viral infections.}, } @article {pmid42353346, year = {2026}, author = {Wang, Y and Han, Y and Wang, C and Wang, Z and Guan, Z and Li, N and Pan, J}, title = {Microbial Contamination, Degradation Characteristics of Dominant Bacteria on the Hull of the Nanhai No. 1 Shipwreck.}, journal = {International journal of molecular sciences}, volume = {27}, number = {12}, pages = {}, doi = {10.3390/ijms27125631}, pmid = {42353346}, issn = {1422-0067}, mesh = {*Wood/microbiology/metabolism ; *Bacteria/isolation & purification/genetics/classification/metabolism ; Biodegradation, Environmental ; Anti-Bacterial Agents/pharmacology ; }, abstract = {To clarify the microbial contamination and wood degradation risk of the Nanhai No. 1 shipwreck hull and verify on-site antibacterial agent effectiveness, microbial samples were collected and analyzed via SEM, metagenomic sequencing, bacterial isolation, enzyme activity detection, and antibacterial experiments. The results showed that Actinomycetota was the dominant phylum, and Brachybacterium, Microbacterium, and Brevibacterium were the dominant genera. Seven bacterial strains were isolated and purified, among which Brevibacterium sp. (NH.SH-B6) had the strongest wood degradation ability, possessing cellulase, LiP, MnP, and Lac activities. When cultured with hull wood as the sole carbon source, LiP was the dominant degrading enzyme of NH.SH-B6, and its maximum enzyme activity was achieved under the optimal conditions of pH = 7, 10% NaCl, 1000 mg/L FeSO4, and no PEG400 added. 50 mg/mL cinnamaldehyde and 0.5% isothiazolinone K100 had good inhibitory effects on the isolated bacteria, and bacterial proliferation was due to incomplete antibacterial agent spraying. This study clarifies the microbial degradation risk of the Nanhai No. 1 shipwreck hull and provides a scientific basis for optimizing the on-site protection strategy of the shipwreck.}, } @article {pmid42353397, year = {2026}, author = {Walther, B and Bouilloux, F and Vayer, P and Douablin, A and Walther, F}, title = {An Ecological Framework for Interpreting the Canine Gut Microbiome.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/ani16121787}, pmid = {42353397}, issn = {2076-2615}, abstract = {The intestinal microbiome is increasingly recognized as an important determinant of canine gastrointestinal health. However, interpreting microbiome sequencing data remains challenging because most analytical approaches rely on taxonomic descriptions, alpha diversity indices, or dysbiosis indices derived generally from a limited number of microbial ecological interpretation targets. While shotgun metagenomic approaches increasingly allow the identification of microbial communities, such analyses remain costly and are not yet widely accessible in routine veterinary settings. The objective of this study was to develop an integrative interpretation framework based on widely accessible biomarkers combining fecal calprotectin and 16S rRNA gene sequencing data. These data enabled the generation of complementary ecological dimensions of gut microbiome organization: biological inflammation assessed through fecal calprotectin, microbiological inflammatory pressure estimated through a Microbiological Inflammatory Score (MIS), and microbiome stability measured by a Microbiome Resilience Score (MRS) derived from alpha diversity, functional balance, and dominance structure. Fecal microbiome profiles obtained by 16S rRNA gene sequencing were analyzed in a real-life cohort of privately owned dogs. Alpha diversity, taxonomic weighting, abundance-dependent dominance rules, beta diversity based on Bray-Curtis dissimilarity, distance to a reference microbiome core, and a 16S-derived dysbiosis score were integrated into a multidimensional interpretation model. Strong ecological associations were observed between resilience, microbial diversity, and dysbiosis-related metrics. Microbiome resilience strongly correlated with Shannon diversity (Spearman ρ = 0.98, p < 0.001), while the reconstructed 16S-derived dysbiosis score showed a more moderate positive correlation with MIS (Spearman ρ = 0.41, p = 0.004), supporting the partially independent ecological dimensions captured by the framework. The results revealed a continuum ranging from stable microbiomes to inflammatory dysbiosis. Most dogs clustered near a reference microbiome core characterized by low microbiological inflammatory pressure and high resilience, whereas a subset of microbiomes showed elevated MIS values, reduced resilience, increased compositional distance from the reference core, and higher dysbiosis index values. These findings support the value of a multidimensional experimental framework integrating inflammation, dysbiosis, and resilience to improve interpretation of canine microbiome profiles under real-life conditions.}, } @article {pmid42353476, year = {2026}, author = {Kiani, A and Jurgens, G and Gonzalez-Ortiz, G and Walk, CL and Rinttilä, T}, title = {Investigation of the Effect of TiO2 as a Dietary Marker on Broiler Intestinal Fermentation: Combination of Ex Vivo Simulation and In Vivo Approach.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/ani16121867}, pmid = {42353476}, issn = {2076-2615}, abstract = {The impact of dietary inert digestibility markers on gut microbiota and intestinal fermentation remains poorly understood. This study investigated the effects of dietary titanium dioxide (TiO2) supplementation at 4 kg/t feed, representing a typical dose used in animal nutrition studies, on fermentation dynamics and microbial composition in broiler chickens using combined ex vivo and in vivo approaches. Ex vivo fermentations were conducted using ileal and caecal microbiota and substrates collected from 32-day-old broiler chickens. Titanium dioxide (TiO2) was supplemented directly to the fermentations, and gas production and short-chain fatty acid (SCFA) profiles were used as the main outcome measures. In parallel, 392 broiler chickens were fed diets with or without TiO2 for 32 days, and ileal and caecal digesta were analysed for fermentation end-products and microbial composition using shotgun metagenomic sequencing. A second ex vivo experiment was performed using microbiota adapted to dietary TiO2. In the first ex vivo model, TiO2 reduced gas production and acetic acid concentration in the ileum (p < 0.05), whereas in the caecum it increased gas production, total eubacterial counts, and branched-chain fatty acids (BCFAs) (p < 0.05). In vivo, TiO2 did not affect growth performance or organ development but significantly increased isobutyric acid and total BCFA concentrations in the caecum (p < 0.05). Metagenomic analysis revealed increased caecal alpha diversity (Shannon index) and enrichment of taxa associated with amino acid metabolism, including Massilicoli timonensis, Blautia merdavium, Rubneribacter badeniensis, and Mediterraneibacter caccavium. The second ex vivo experiment showed similar trends, with increased gas and BCFA production. Collectively, these findings indicate that TiO2 can modulate intestinal fermentation and microbial composition in a segment-specific manner, suggesting that dietary markers may not be biologically inert.}, } @article {pmid42353508, year = {2026}, author = {Shi, K and Zhou, X and Li, K and Dai, J and Shen, Y and Wu, Z and Zhang, X and Yu, Q and Chen, S}, title = {Multi-Omics Analysis Reveals the Gut-Mediated Mechanism Underlying the Seasonal Non-Laying Phenotype in Zhedong White Geese (Anser cygnoides domesticus).}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/ani16121899}, pmid = {42353508}, issn = {2076-2615}, abstract = {As a precious indigenous goose resource in China, the Zhedong white goose occupies an essential position in the domestic goose industry. However, this breed spontaneously enters a prolonged non-laying period of over two months per year, which greatly limits egg production capacity and restricts the economic development of the goose industry. Herein, this study systematically compared serum physiological indices and serum and fecal metabolome, as well as fecal microbial communities, between laying and non-laying Zhedong white geese, aiming to reveal the key regulatory mechanisms underlying reproductive stage transition. Physiological analyses indicated that non-laying geese had higher serum levels of GnRH, PRL, APOA, and T-AOC, whereas the concentrations of LH, E2, TNF-α, IL-1, and calcium were significantly reduced; FSH, PROG, and BA levels showed no significant differences between the two groups. Metabolomic analysis identified 277 upregulated and 403 downregulated DAMs in feces, and 386 DAMs in serum. The shared enriched pathways across serum and fecal samples encompassed arginine biosynthesis, histidine metabolism, and pantothenate and CoA biosynthesis, as well as steroid hormone biosynthesis. A total of 120 DAMs overlapped in two specimens, and the non-laying geese presented pronounced depletion of tryptophan-derived metabolites and steroid hormone-related metabolites. Metagenomic results showed no significant difference in gut microbial alpha diversity between groups, while their microbial community structures were clearly differentiated. A total of 774 upregulated and 854 downregulated microbial species were screened in non-laying geese, and these differential microbes were primarily enriched in pathways associated with reproductive hormone signaling, steroid biosynthesis and energy metabolism. Multi-omics correlation analysis verified close associations between differential microbes and reproductive-related metabolites. Certain probiotic strains, including Pediococcus pentosaceus and Lactococcus raffinolactis, were positively correlated with steroid hormones and tryptophan metabolites, and their abundances declined obviously in the non-laying stage. Collectively, this study elaborates the holistic changes in serum biochemistry, gut metabolome and microbiome in geese at different reproductive stages. The dysregulation of amino acid and steroid hormone metabolism, combined with the loss of beneficial intestinal microbes, jointly induces the non-laying phenotype. This study provides new perspectives for understanding the gut-reproductive axis and supplies promising biomarkers to improve the laying performance of geese.}, } @article {pmid42353537, year = {2026}, author = {Liu, Y and Zhang, G and Gao, H and Fang, M and Jiang, L and Kong, Y and Liu, Q and Wang, P and Zhang, S and Li, Y}, title = {Metavirome Analysis of Viruses Carried by Dairy Cows in Shaanxi, Gansu and Ningxia, China.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {12}, pages = {}, doi = {10.3390/ani16121928}, pmid = {42353537}, issn = {2076-2615}, support = {32130104//National Natural Science Foundation of China/ ; 2023BCF01038, 2024BBF02017//the Ningxia Hui Autonomous Region Key R&D Projects/ ; }, abstract = {Dairy cows are economically significant ruminants in China, and the dairy industry is closely linked to food safety and the agricultural economy. However, various factors such as pathogenic microorganisms often lead to frequent diseases in dairy cows. Furthermore, as potential hosts for diverse viruses, dairy cows can harbor zoonotic pathogens, which pose a threat to public health. The Shaanxi-Gansu-Ningxia region boasts abundant natural resources and extensive pastures. It is a major animal husbandry base in Northwest China, and dairy farming plays a significant role in the local economy. However, research on dairy cow virus diversity in this region remains limited; epidemic prevention and control capabilities are constrained, and the risk of disease outbreaks is elevated. In this study, 790 dairy cow samples were collected from 13 large-scale farms and free-range households in the Shaanxi-Gansu-Ningxia region from 2021 to 2023. Sample types consisted of nasal and anal swabs. Six viral metagenomic libraries were constructed and analyzed using high-throughput sequencing and bioinformatics methods, leading to the identification of 51 viral families. These comprised 16 positive-sense single-stranded RNA virus families, one Retroviridae family, four double-stranded RNA virus families, 21 double-stranded DNA virus families, and nine single-stranded DNA virus families. Among these, RNA viruses were represented by families such as Astroviridae, Coronaviridae, Caliciviridae, Picornaviridae, and Picobirnaviridae; DNA viruses were primarily detected in Circoviridae, Papillomaviridae, Genomoviridae, and Smacoviridae. Alpha diversity analysis revealed no significant differences in viral diversity and abundance among the three regions (p > 0.05); however, significant differences were observed in the read counts and proportions of RNA and DNA viruses across the provinces. Phylogenetic analysis further indicated that viruses carried by dairy cows exhibit considerable genetic diversity and pose potential cross-species transmission risks. This study established a reference database for the dairy cow virome in the Shaanxi-Gansu-Ningxia region, elucidated the phylogenetic relationships of key viruses, and provided a scientific basis for future monitoring and prevention of dairy cow viruses.}, } @article {pmid42353547, year = {2026}, author = {Liu, L and Narrowe, AB and Firrman, J and Mahalak, KK and Chetty, VJ and Lemons, JMS and Baudot, A and Van den Abbeele, P}, title = {Perfluorooctanoic Acid (PFOA) Alters the Structure of the Gut Microbial Community and Colonoid Transcription.}, journal = {Current issues in molecular biology}, volume = {48}, number = {6}, pages = {}, doi = {10.3390/cimb48060542}, pmid = {42353547}, issn = {1467-3045}, support = {8072-41000-108-00-D//United States Department of Agriculture/ ; }, abstract = {Perfluorooctanoic acid (PFOA) is an environmentally persistent chemical that enters the gastrointestinal tract (GIT) via the food chain, posing a harmful, long-term threat to human health. In response to this challenge, research on the PFOA-GIT interaction is thriving. Currently, studies on the effect of PFOA on the epithelial cells of the GIT and those on its influence on the microbial community are often implemented separately, and less attention has been paid to the combinational effects of the chemical, the gut microbiome and metabolome. In the present study, we co-cultured fecal samples from healthy adults aged 25-70 in the ex vivo SIFR[®] simulator, adding PFOA at 10 mg/L to represent the accumulated effects of long-term exposure. The results obtained from bacterial cell counting by flow cytometry and shotgun metagenomic sequencing revealed that PFOA was broadly disruptive to the microbiome and that Pseudomonadota emerged as the dominant phylum by replacing Bacteriodota and Bacillota, including key members of short-chain fatty acid-producing groups. Bacterial culture media with and without PFOA were collected and used in human colonoid cell culture for TEER and transcription measurement. It was shown that the PFOA-impacted microbial culture had stronger effects on the cell's protective functions, in terms of tissue junction tightening, mucin biosynthesis, and immune response, than either untreated bacterial culture or PFOA alone. The results point out the possibility that the combination of PFOA and PFOA-impacted bacterial metabolites more strongly induces a change in epithelial cells' protective function than either one alone.}, } @article {pmid42353629, year = {2026}, author = {Iorizzo, M}, title = {Microbial α-L-Rhamnosidases: Regioselective Biocatalysts for Flavonoid Biotransformation and Nutraceutical Applications.}, journal = {Current issues in molecular biology}, volume = {48}, number = {6}, pages = {}, doi = {10.3390/cimb48060625}, pmid = {42353629}, issn = {1467-3045}, abstract = {Microbial α-L-rhamnosidases are increasingly recognised as selective biocatalysts in food biotechnology, nutraceutical production, and health-related applications. These glycoside hydrolases catalyse the hydrolysis of terminal alpha-L-rhamnose residues from flavonoids, terpenoids, saponins, and other glycosylated natural products, thereby modulating sensory properties, solubility, intestinal absorption, and biological activity. While their traditional uses include debittering citrus juice and enhancing wine aroma, recent evidence demonstrates their wider value in selective flavonoid biotransformation, production of rare mono-glycosylated derivatives, probiotic fermentations, and microbiome-associated metabolism. This review summarises microbial sources, catalytic mechanisms, CAZy classification, substrate specificity, structure-function relationships, analytical methods, industrial process engineering, and emerging applications in functional foods and targeted nutraceutical applications. Particular attention is given to the distinction between alpha-(1→2)- and alpha-(1→6)-linked substrates, the production of isoquercitrin and prunin, recombinant enzyme platforms, immobilised biocatalysts, and potential future opportunities arising from metagenomics, synthetic biology, and AI-assisted protein engineering.}, } @article {pmid42353668, year = {2026}, author = {Kerek, Á and Husz, LH and Szarka, E and Tornyos, GÁ and Jerzsele, Á}, title = {Integrated Phenotypic and Sequencing-Based Resistome Assessment of Antimicrobial Resistance Determinants in a Sample of Commercial Farm-Animal Probiotic Products.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/antibiotics15060544}, pmid = {42353668}, issn = {2079-6382}, support = {RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; }, abstract = {Background/Objectives: Probiotic feed additives are increasingly used in livestock production as antimicrobial-sparing tools, yet viable microbial products should not introduce clinically relevant antimicrobial resistance genes (ARGs) into the intestinal resistome. This study evaluated farm-animal probiotic products using an integrated phenotypic, metagenomic and mobilome-aware safety framework. Methods: Seven commercially available products intended for poultry, pigs, cattle or horses were assessed using product metadata, culture-based recovery, broth microdilution minimum inhibitory concentration (MIC) profiling and Illumina short-read sequencing as a screening-level resistome approach. Reads were quality controlled, assembled, screened using the Comprehensive Antibiotic Research Database (CARD)/Resistance Gene Identifier (RGI) workflow and interrogated for plasmid-, phage- and insertion sequence/mobile genetic element-associated genomic context. Results: MIC profiles were generated for viable bacterial isolates representing Enterococcus faecium, Pediococcus acidilactici, Pediococcus pentosaceus and Bacillus subtilis. One labelled Lactobacillus plantarum component was not recovered as viable culture, and one labelled P. acidilactici component was recorded as P. pentosaceus. Sequencing-based resistome screening identified 30 antimicrobial resistance (AMR)-associated CARD antibiotic-resistant organism (ARO) hits belonging to 13 determinants across six ARG-positive coded products, while one coded product had no retained CARD/RGI hit. Profiles were dominated by recurrent Enterococcus-associated background determinants, including aac(6')-Ii, msrC and eatAv. Plasmid prediction was positive for five hits, whereas no iMGE- or phage-associated ARG context was detected. No vanA/vanB, mcr, optrA, poxtA, cfr, extended-spectrum β-lactamase (ESBL) or carbapenemase gene was detected. Conclusions: The investigated products did not show evidence of high-priority mobile ARG carriage. Nevertheless, AMR-associated determinants and occasional predicted mobile contexts support routine integrated MIC-sequencing-based resistome-mobilome assessment of veterinary probiotic products. Because short-read assemblies do not fully resolve plasmid architecture or transferability, mobile-context predictions should be considered screening-level indicators requiring confirmatory long-read or functional testing for higher-priority findings.}, } @article {pmid42353692, year = {2026}, author = {Elton, L and Lutimba, S and Mateos, AD and Frosini, SM and Jepson, R and Williams, A and Ali, S and Heaphy, J and Pang, V and Commins, L and O'Brien, C and Yetiş, Ö and Caine, E and Ward, I and Muzslay, M and Yui, S and Karia, K and Shore, E and Rofael, S and Mack, D and Atkinson, C and McHugh, TD and Wey, EQ}, title = {Comparison of Environmental Microbiomes, Resistomes and Plasmidomes from a Human Tertiary Hospital and Companion Animal Veterinary Hospital in London, UK.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/antibiotics15060568}, pmid = {42353692}, issn = {2079-6382}, support = {N/A//Royal Free London NHS Foundation Trust/ ; }, abstract = {Background: Human hospitals and veterinary centres are hotspots for resistant microbes and plasmids, and metagenomic sequencing offers an agnostic insight into microbiomes, resistomes, and mobilomes, informing strategies for reducing AMR spread. Methods: Environmental samples, including wastewater and surface swabs, were taken from a tertiary human hospital ward (36 samples) and a companion animal veterinary hospital (48 samples) in London. Whole DNA was extracted and metagenomic sequencing undertaken using Oxford Nanopore Technologies' MinION. Data were analyzed for microbiomes, resistomes and mobilomes and compared. Results: Microbial diversity analyses highlight higher richness across human hospital (HH) environmental samples, but more evenness in veterinary hospital (VH) environmental samples. Diversity showed distinct microbial communities in the HH and VH samples. There were significantly more total antimicrobial resistance gene (ARG) types (p < 0.0001) in the environmental HH samples compared with the environmental VH samples. There was a significantly higher mean number of Enterobacteriales plasmid types (p ≤ 0.0001) in the HH samples. There were significantly more total Gram-Positive plasmid types (p ≤ 0.0001) in the VH samples. Discussion: This research highlights the presence of human and animal pathogens, ARGs and mobile genetic elements in clinical environments, underscoring the importance of multisectoral surveillance. Integrating taxonomic, resistome, and mobilome analyses provides a better understanding of the potential for AMR dissemination at the human-animal-environment interface. This provides insights relevant for the development of targeted surveillance and mitigation strategies within a OH framework.}, } @article {pmid42353998, year = {2026}, author = {Margasoiu, I and Pînzariu, AC and Manole, LM and Spoială, EL and Păduraru, G and Ghiga, G and Popa, IP and Șerban, DN and Șerban, IL and Trandafir, LM}, title = {Gut Microbiome Responses to Nutritional and Lifestyle Interventions in Pediatric Obesity: A Systematic Review Toward Precision Nutrition.}, journal = {Children (Basel, Switzerland)}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/children13060828}, pmid = {42353998}, issn = {2227-9067}, support = {SMIS code 351058//Grigore T. Popa University of Medicine and Pharmacy/ ; }, abstract = {Background: Childhood obesity is increasingly associated with gut microbiome dysbiosis. This systematic review (PROSPERO CRD420251131354) evaluates evidence from studies published between 2020 and 2026 assessing how nutritional and lifestyle interventions influence gut microbiota in children with obesity. Methods: A systematic search of PubMed, EMBASE and EBSCO identified 21 interventional studies involving children aged 5-18 years with obesity, with the last search conducted in April 2026. Interventions comprised prebiotics, probiotics, synbiotics, postbiotics, high-fiber diets, calorie-restricted dietary approaches, and lifestyle modifications such as physical activity. Microbiome outcomes were analyzed using 16S rRNA sequencing, quantitative real-time polymerase chain reaction (qPCR), or metagenomics. Risk of bias was evaluated using the RoB 2 and ROBINS-I (version 2) tools. Due to substantial heterogeneity in study design, participant characteristics, intervention types, and analytical methods, a meta-analysis was not feasible. Results: Across 21 studies, nutritional interventions included measurable but heterogeneous alterations in gut microbiome composition. Inulin supplementation was associated with a significant increase in alpha diversity and with higher relative abundances of Bifidobacterium, Blautia, Megasphaera, Subdoligranulum, and Eubacterium coprostanoligenes. Synbiotic supplementation increased Prevotella and Dialister and reduced the Firmicutes/Bacteroidetes ratio. High-fiber dietary interventions increased Faecalibacterium, Bifidobacterium, and Clostridium, while reducing Bacteroides, and were associated with shifts in metabolic pathways related to carbohydrate, lipid, and nucleotide metabolism. Calorie-restricted diets and combined diet-exercise interventions increased beneficial taxa such as Akkermansia muciniphila, improved microbial diversity, and correlated with favorable metabolic and anthropometric outcomes. Overall, nutritional and lifestyle interventions in pediatric obesity were associated with taxon-specific and context-dependent microbiome changes, rather than uniform restructuring. Conclusions: Nutritional interventions can modulate gut microbiota diversity, composition, and predicted function in pediatric obesity; however, the observed effects vary substantially across studies. The limited number of trials, small sample sizes, and methodological heterogeneity underscore the need for larger, standardized studies to better define clinical and therapeutic implications.}, } @article {pmid42354149, year = {2026}, author = {Bai, F and Cai, C and Zhang, T and Xu, L and Liu, Y and Liu, R and Ma, Z and Jiang, M and Gao, J and Zhang, J and Yu, X and Tang, T and Chen, J and Yao, S}, title = {Comparative Analysis of Microbial Community Structure and Functional Traits of Baijiu Daqu Across Diverse Geographical Regions in China.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/foods15122182}, pmid = {42354149}, issn = {2304-8158}, support = {YQY25-SW-210//China National Research Institute of Food and Fermentation/ ; ZQ2023JC-GC03//Science and Technology Innovation Program of Sinolight Corporation/ ; }, abstract = {Daqu is a key starter used in Baijiu production, and its microbial composition and associated metabolic functions play critical roles in fermentation performance and flavor development. This work aimed to reveal how Daqu-making temperature regulates microbial community divergence and subsequent metabolite formation via multi-omics analysis so as to provide theoretical guidance for Daqu quality control. In this study, physicochemical analysis, metagenomic sequencing, and metabolomic profiling were combined to investigate the microbial community structure, functional differentiation, and metabolite characteristics of nine Daqu samples collected from six major Baijiu-producing regions in China. The temperature during Daqu preparation was found to be a primary factor driving microbial community assembly and functional specialization. Medium-temperature Daqu exhibited higher saccharifying activity (up to 867 U) and greater microbial diversity with the enrichment of amino acid metabolism-related pathways, indicating enhanced protein degradation and amino acid utilization for the formation of flavor precursors. In contrast, high-temperature Daqu showed stronger capacities for carbohydrate degradation and conversion, particularly in starch and sucrose metabolism, which were closely associated with the enrichment of thermotolerant fungi and bacteria. LEfSe analysis identified 47 distinct microbial biomarkers (LDA score > 3.0), which could differentiate between medium- and high-temperature Daqu. Redundancy analysis indicated that environmental factors (moisture and acidity) together with functional properties (fermentation, esterification, liquefaction, and saccharification) act as key drivers of microbial functional patterns. Metabolomic analysis further revealed that medium-temperature Daqu had higher abundances of esters and fatty acids, whereas high-temperature Daqu had higher proportions of alcohols and ketones. Taken together, these results provide a multi-omics perspective on temperature-driven microbial functional differentiation in Daqu and offer a scientific basis for quality-oriented regulation and process optimization in Baijiu production.}, } @article {pmid42354792, year = {2026}, author = {Pan, Z and Bao, J and Liu, X and Ge, G and Zhao, M}, title = {Metagenomic Insights into Regional Differences in the Rhizosphere Microbial Communities of Stellera chamaejasme L. in Inner Mongolia.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061167}, pmid = {42354792}, issn = {2076-2607}, support = {CARS-34//China Agriculture Research System/ ; }, abstract = {Rhizosphere microorganisms are important components of grassland ecosystems, but the rhizosphere microbiome of the poisonous and medicinal plant Stellera chamaejasme L. remains poorly characterized. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition, community structure, differentially enriched taxa, and KEGG-based functional potential of rhizosphere microbial communities associated with S. chamaejasme from three typical steppe regions in Inner Mongolia. Acidobacteria, Proteobacteria, and Actinobacteria were the dominant phyla, while Sphingomonas, Bradyrhizobium, and Streptomyces were among the dominant genera. Genus-level profiles and ordination analysis showed region-associated community patterns, and rarefaction curves indicated that sequencing depth was sufficient to capture most detectable taxa. LEfSe analysis identified region-associated differentially enriched taxa, including Sphingomonas-, Bradyrhizobium/Nitrospira-, and Streptomyces/Solirubrobacter-associated taxa. KEGG annotation suggested broadly similar major functional categories across regions, with some differences in the relative abundance of metabolic pathways. These results provide baseline metagenomic information on S. chamaejasme rhizosphere communities. Because of the limited replication and lack of soil physicochemical measurements, ecological mechanisms should be tested in future studies.}, } @article {pmid42354802, year = {2026}, author = {Hao, D and Yu, X and Sun, X and Cheng, D and Ding, H and Wang, Y and Li, Y and Geng, Z and Xu, G}, title = {Thermophilic Microbial Inoculant Promotes Lignocellulose Degradation During Green Waste Composting.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061177}, pmid = {42354802}, issn = {2076-2607}, support = {PTYX202514//Fundamental Research Funds for the Central Universities/ ; Liao[2025]TG03//China Central Financial Forestry and Grassland Science and Technology Promotion Demonstration Project/ ; }, abstract = {Thermophilic microbial inoculant (CI) has been demonstrated to optimize the green waste composting (GWC) process. The pathways through which it enhances lignocellulose degradation remain unclear. This study evaluated composting performance under four treatments: CI, effective microorganisms (EM), Phanerochaete chrysosporium (WF), and natural composting (CK). To elucidate the biological differences between efficient lignocellulose-degrading systems and CK, metagenomic analyses were conducted on CI and CK based on lignocellulose degradation rates. The results indicated that CI inoculation did not negatively affect the compost heating process and produced a nitrogen-rich, safe, and mature compost product. Compared to other treatments, CI increased the lignocellulose degradation rate by 3.66% to 31.8%. Metagenomic analysis revealed that CI inoculation enriched genes encoding glycoside hydrolases (GHs), glycosyl transferases (GTs), carbohydrate esterases (CEs), and carbohydrate-binding modules (CBMs) across multiple composting phases, positively impacting dominant carbohydrate-active enzyme (CAZyme) families including AA3, CE1, and CE7. CI inoculation also elevated the relative abundance of lignocellulose-degrading microorganisms (0.70~2.73%), simplified microbial network structure, and strengthened microbial cooperation. Within the microbial network, Chryseolinea, Protaetiibacter, and unclassified_f__Burkholderiaceae were identified as core taxa involved in lignocellulose degradation. Redundancy analysis (RDA) identified temperature as the primary factor influencing biological factors, with CI improving composting efficiency by optimizing the microenvironment. Collectively, this work provides a novel strategy for microbial inoculant application in composting and offers new perspectives for identifying core taxa, contributing to advancing composting efficiency.}, } @article {pmid42354818, year = {2026}, author = {Yang, Z and Xv, W and Cai, Y and Gu, H and Feng, Y}, title = {Long-Term Application of Fermented Fertilizer Attenuates the Accumulation of Antibiotic Resistance Genes in Aquaculture Sediment.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061193}, pmid = {42354818}, issn = {2076-2607}, abstract = {Aquaculture sediments are increasingly recognized as important reservoirs of antibiotic resistance genes (ARGs). Although thermophilic fermentation is widely used to reduce ARGs and pathogens in manure, most biosafety assessments stop at the fertilizer product itself, leaving unresolved whether these benefits persist after application to aquaculture sediments. Here, we compared inorganic fertilizer (IF), raw manure (RM), and fermented fertilizer (FF) to test whether fermentation confers sustained biosafety benefits in aquaculture pond sediments. After a 6-month co-culture period, sediment samples were analyzed using shotgun metagenomic sequencing, ARG and mobile genetic element (MGE) profiling, antibiotic residue determination, and network analyses. Long-term fertilization significantly altered sediment physicochemical properties, microbial community composition, and resistome structure. Among the three groups, the RM exhibited the highest total ARG abundance and the greatest number of unique ARG subtypes, with significant enrichment of multidrug resistance genes as well as pathogen-, disease-, and host-associated mobile genetic elements (MGEs). In contrast, the FF group showed the lowest total ARG abundance and fewest unique ARG subtypes, along with suppression of pathogen-associated MGEs, indicating that FF can effectively reduce the risk of ARG dissemination. However, the potential impact of residual antibiotics still warrants attention. Redundancy analysis showed that TC and TN primarily explained bacteriome and resistome variation under RM, whereas pH, EC, AP, and AK were more strongly associated with FF. Co-occurrence analysis further suggested that fertilizer-driven microbial community shifts may regulate ARG persistence and potential cross-ecosystem dissemination. Overall, fermented fertilizer attenuated, but did not eliminate, manure-derived resistance risks in aquaculture sediments. These findings support fermented fertilizer as a safer management option than raw manure and highlight the need for integrated risk assessment combining ARGs, MGEs, microbial hosts, and antibiotic residues.}, } @article {pmid42354826, year = {2026}, author = {O'Donald, SN and Patel, F and Keen, P and Hanson, LA and Cunningham, F and Lawrence, ML and Tekedar, HC}, title = {Hi-C Metagenome Deconvolution of Double-Crested Cormorant (Nannopterum auritum) Fecal Samples Demonstrates Feasibility of Linking Microbial Genomes, AMR Genes, and Mobile Elements in Avian Microbiomes.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061198}, pmid = {42354826}, issn = {2076-2607}, support = {N/A//New York Institute of Technology/ ; }, abstract = {The double-crested cormorant (Nannopterum auritum), a piscivorous bird endemic to North America, frequently forages in aquaculture ponds during migration and wintering, contributing to economic losses in catfish-producing regions of the southern United States. While interactions between cormorants and aquaculture systems are well documented, their associated microbial communities and genetic elements remain less characterized. In this exploratory study, Hi-C-enabled metagenomics was applied to fecal samples from two cormorants to generate a genome-resolved, descriptive analysis of gut microbial composition and to associate bacterial genomes with mobile genetic elements (MGEs), antimicrobial resistance genes (ARGs), and putative virulence-associated genes. Metagenome-assembled genomes (MAGs) included taxa reported in aquatic or animal-associated environments, including Edwardsiella tarda, Plesiomonas shigelloides, Clostridium perfringens, and Campylobacter volucris. ARGs were detected across multiple MAGs, with E. tarda harboring the greatest diversity. Hi-C-enabled linkage of plasmids and phages to putative hosts, providing structural insight into microbial organization. Analyses are descriptive (n = 2) and do not include statistical comparisons or diversity metrics. These findings demonstrate the utility of Hi-C for resolving gene-host associations and provide a framework for future studies of microbial connectivity in One Health contexts.}, } @article {pmid42354835, year = {2026}, author = {Mohammed, MZ and Linhares, DCL and Zeller, MA and Silva, GS and Rademacher, C and Peterson, C and Trevisan, G}, title = {Genetic Characterization of PRRSV Diversity and Detection of Other Pathogens in Live Virus Inoculation Material Used in Breeding Herd Stabilization Programs.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061207}, pmid = {42354835}, issn = {2076-2607}, support = {GR-028677//American Association of Swine Veterinarians Foundation/ ; IPPA 23-120//Iowa Pork Producers Association/ ; }, abstract = {Live virus inoculation (LVI) is widely used for porcine reproductive and respiratory syndrome virus (PRRSV) stabilization, yet preparation practices and pathogen composition remain poorly characterized. This study aimed to evaluate variability in LVI preparation, quantify PRRSV genomic load, and detect additional swine pathogens. A survey was conducted to document LVI preparation methods, and samples were analyzed using reverse-transcription quantitative PCR (RT-qPCR) for PRRSV quantification and next-generation sequencing for PRRSV and the metagenomic characterization of additional pathogens. Among 61 LVI samples, substantial variability was observed in preparation practices and viral composition, with 31 distinct PRRSV variants identified and seven samples containing multiple strains. PRRSV RNA concentrations ranged from 10[1.69] to 2.52 × 10[8] copies/mL. Metagenomic analysis detected a complete or near-complete genome for PRRSV, porcine parvovirus, and porcine circovirus type 2. Genome fragments of porcine sapovirus, porcine rotavirus, porcine astrovirus, and bacterial genetic material from Salmonella spp., Pseudomonas spp., Streptococcus spp., and Escherichia coli were also detected. These findings highlight substantial heterogeneity in LVI materials and encourage the use of next-generation sequencing to verify LVI PRRSV composition and screen for co-existing pathogens, reinforcing the need for standardized preparation protocols and further investigation into optimal viral dosing for effective immunization.}, } @article {pmid42354848, year = {2026}, author = {Gou, F and Zhao, Q and Han, Y and Sun, Y and Ding, W and Chen, J and Jin, S}, title = {Effects of Dietary Concentrate-to-Roughage Ratio on Rumen Microbiota, Functional Profiles, and Fermentation Characteristics in Yak.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061223}, pmid = {42354848}, issn = {2076-2607}, support = {2024-NK-109//Qinghai Provincial Science and Technology Department/ ; }, abstract = {This study investigated the effects of different concentrate-to-roughage ratios on the rumen microbial community, functional potential, and fermentation characteristics in yak. Forty Qinghai Plateau-type yaks (8-9 months, 68.725 ± 18.973 kg) were randomly assigned to four dietary groups with concentrate-to-roughage ratios of 80:20 (C80), 65:35 (C65), 50:50 (C50), and 35:65 (C35). After a 15-day adaptation period, animals were fed for 105 days. Rumen contents were analyzed using metagenomic sequencing combined with fermentation parameter measurements. High-concentrate diets (C80 and C65) were associated with increased relative abundance of starch-degrading and propionate-producing bacteria, such as Prevotella and Succiniclasticum, whereas low-concentrate diets (C50 and C35) were associated with higher abundance of cellulolytic bacteria, including Ruminococcus and Fibrobacter. Functional analysis indicated increased relative abundance of genes involved in glycolysis (ko00010), propanoate metabolism (ko00640), and energy-related pathways in high-concentrate groups, while fiber degradation and methane-related pathways were relatively higher in low-concentrate groups. Rumen fermentation parameters showed a significant decrease in pH with increasing concentrate level (p = 0.001), and NH3-N concentrations differed among treatments (p = 0.036). Dietary concentrate-to-roughage ratio significantly influences rumen microbial composition, functional potential, and fermentation characteristics in yak. A moderate concentrate level (approximately 65:35) may contribute to a more balanced rumen microbial and fermentation profile under the conditions of this study.}, } @article {pmid42354871, year = {2026}, author = {Qiu, Q and Sun, X and Li, H and Zhou, D and Huo, H}, title = {Plastic Degradation Potential and Metagenomic Analysis of an Enriched Gut Microbial Consortium from Tenebrio molitor.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061246}, pmid = {42354871}, issn = {2076-2607}, support = {52230003//National Natural Science Foundation of China/ ; }, abstract = {Plastic pollution has become an increasingly severe global environmental issue, highlighting the urgent need for efficient and sustainable biodegradation strategies. In this study, an enriched gut microbial consortium, NE-01 derived from Tenebrio molitor, exhibited significant degradation activity toward polystyrene (PS), polyethylene (PE), and polyethylene terephthalate (PET). Metagenomic sequencing revealed that Pseudomonas and Proteobacteria were the dominant taxa, maintaining high community diversity and providing a microbial foundation for the degradation of plastics and other complex organic compounds. Functional annotation and metabolic pathway analysis indicated that xenobiotic biodegradation and metabolism occupied a large proportion of the metabolic network, suggesting the consortium's potential for degrading exogenous pollutants. Several key genes associated with the degradation of aromatic and halogenated compounds, such as benzoate, toluene, styrene, and bisphenol A, were identified. Metabolic reconstruction further suggested possible degradation pathways for PS, PE, PET, and the plasticizer di(2-ethylhexyl) phthalate (DEHP). This study preliminarily demonstrated that the T. molitor gut-derived microbial consortium harbors multiple plastic-degrading genes and provides a theoretical basis for developing green, microbe-based strategies for plastic degradation.}, } @article {pmid42354876, year = {2026}, author = {Yue, Y and Jiang, Y and Zhang, Y and Xiao, T and Hao, H and Wang, Q and Tong, Z and Zhang, J and Chen, H}, title = {Duration of Spent Mushroom Substrate Return Affects Microbial Assembly and Nitrogen Metabolism to Promote Functional Stabilization in Rice-Mushroom Crop Rotation Systems.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061251}, pmid = {42354876}, issn = {2076-2607}, support = {T2024310//Shanghai Agricultural Science and Technology Innovation Project/ ; 24YF273800//Shanghai Sailing Program/ ; 202509/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Spent mushroom substrate (SMS) return is a vital strategy for agricultural waste recycling and soil fertility improvement, yet its ecological impacts of duration remain poorly understood. This study employed metagenomic sequencing to explore soil fertility, microbial dynamics, and nitrogen cycling across different SMS return durations (0, 1, and 3 years) within rice-mushroom crop rotation systems. Soil nutrients (organic matter, total nitrogen, total phosphorus) initially decreased and then increased throughout the rice growth cycle. The one-year return (y1) induced early nutrient depletion, whereas the three-year return (y3) significantly enhanced late-stage nutrient accumulation. With increasing duration, bacterial and archaeal assembly shifted from stochastic toward deterministic processes, while fungal diversity and stochasticity decreased continuously. Co-occurrence network analysis demonstrated that SMS return increased network complexity and intercommunity competition. This transition was accompanied by a functional shift in keystone taxa from those responsive to exogenous organic matter in y1 to those mediating nitrogen fixation, anammox, and sulfur metabolism in y3. Nitrogen cycling in y1 increased potential N2O emission risks through nirS upregulation and nosZ downregulation, whereas y3 mitigated inorganic nitrogen loss by upregulating gene abundances of ammonia assimilation, nitrification, and DNRA genes. Notably, the structure of nitrogen-cycling genes fluctuated in y1 but was resilient to y0 levels in y3. These findings demonstrated that while initial SMS return triggered ecological fluctuations and environmental risks, continuous return (y3) achieved functional stability by reshaping microbial niches. This study highlights the importance of SMS return duration in balancing soil fertility enhancement with environmental risk mitigation in sustainable paddy ecosystems.}, } @article {pmid42354906, year = {2026}, author = {Cao, YF and Wang, YR and Zheng, PX and Wang, XC and Xu, L and Sun, C}, title = {Multi-Omics Reveals the Impact of Domestic Wastewater Input on the Dissolved Organic Carbon Pool and Microbial Community in the Qiantang River Estuary.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061282}, pmid = {42354906}, issn = {2076-2607}, support = {32370006//National Natural Science Foundation of China/ ; Y24C010009//Zhejiang Provincial Natural Science Foundation/ ; }, abstract = {Estuarine ecosystems face intense anthropogenic pressures, yet systematic research on how domestic wastewater influences the dissolved organic carbon (DOC) pool via microbial community regulation remains limited. In this study, we conducted a microcosm experiment simulating wastewater input into the Qiantang River and integrated multi-omics (16S rRNA sequencing, metagenomics, metatranscriptomics, and FT-ICR MS) to elucidate the mechanism. Results showed that: (1) Wastewater input increased initial DOC and changed its degradation pattern: slower decay but higher removal. (2) Compared to the control, the wastewater-amended group exhibited a decreased fluorescence intensity contribution of carboxyl-rich alicyclic molecule (CRAM)-like compounds, indicating reduced chemical stability of recalcitrant DOC (RDOC). (3) Wastewater drove directional microbial succession from catabolic-dominant taxa (e.g., Comamonas, Citrobacter) to anabolic-dominant taxa (e.g., Reyranella), shifting metabolism from pollutant degradation to endogenous synthesis, thereby lowering the system's efficiency in forming stable RDOC. (4) Multi-omics revealed a "stimulation-balance" functional response: early activation of xenobiotic degradation and signal transduction (day 2), followed by a shift to anabolic metabolism (day 28). This functional transition, driven by microbial succession, ultimately reduced RDOC stability. Our findings reveal that wastewater reshapes the microbial carbon pump, providing a theoretical basis for assessing estuarine carbon sink responses to pollution control measures.}, } @article {pmid42354916, year = {2026}, author = {Zhang, X and Lu, C and Lu, L and Meng, L and Liu, Y and Ma, B}, title = {Metagenome-Assembled Genomes Support the Proposal of Candidatus Flavobacterium genomatis from the Northeast Black Soil Ecosystem.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061292}, pmid = {42354916}, issn = {2076-2607}, support = {2024YFD1501800//National Key R&D Program of China/ ; 2024ZD1000603//National Key Science and Technology Special Project for Deep Earth Research/ ; 42277283//National Natural Science Foundation of China/ ; 2024C03131//Key R&D Program of Zhejiang Province/ ; 2024Z267//Key R&D Program of Ningbo/ ; GZC20251786//National Program for Funding Postdoctoral Researchers/ ; }, abstract = {Soils are critical microbial habitats that support terrestrial ecosystem functioning and harbor numerous uncultured and functionally uncharacterized microbial groups. The black soil region in northeast China is a key agricultural ecosystem globally, yet the classification and functional understanding of its crucial microbial groups remain underexplored. In this study, we identified three high-completeness metagenome-assembled genomes (MAGs) from the Global Mollisols Genomic Atlas (GMGA). Phylogenetic and comparative genomic analyses identified these genomes as representing a novel evolutionary branch within the genus Flavobacterium, classified under the phylum Bacteroidota. Their novel taxonomic position is further supported by average nucleotide identity (ANI) and average amino acid identity (AAI) thresholds, demonstrating significant divergence from all known reference genomes. Functional annotation indicated that this species possesses strong plant polysaccharide degradation potential and a chemoheterotrophic lifestyle, together with environmental stress tolerance and a specialized nitrogen metabolic network adapted to agricultural inputs, thereby conferring a metabolic advantage in black soil environments characterized by high organic matter input and marked seasonal fluctuations. In addition, global distribution analysis showed that this lineage is widely distributed across diverse ecosystems and is significantly enriched in soil habitats, particularly in environments with fluctuating carbon sources and high organic matter inputs. The new species is most abundant in temperate soils, with the northeast black soil region of China emerging as a key hotspot. Based on these findings, and because no pure culture is currently available, we propose Candidatus Flavobacterium genomatis based on genome-resolved metagenomic evidence and in alignment with the International Code of Nomenclature of Prokaryotes rules for uncultivated prokaryotes. Our results expand the known species diversity of the genus Flavobacterium and suggest potential ecological roles of uncultured black-soil microbes in carbon and nitrogen cycling, including possible involvement in N2O reduction under suitable environmental conditions.}, } @article {pmid42354965, year = {2026}, author = {He, Z and Wang, B and Jin, D and Tian, M and Gong, L}, title = {Effects of Rice Straw Incorporation on Paddy Soil Microbiome and Metabolome Throughout the Crop Growth Period.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061341}, pmid = {42354965}, issn = {2076-2607}, support = {2024BS1002;2026CY3515;2025XKJS8528//Liaoning Academy of Agricultural Sciences/ ; 2025JH2; 101300068//Liaoning Province Applied Basic Research Program/ ; }, abstract = {Rice straw incorporation is a paddy soil management practice that can reduce environmental pollution, mitigate soil degradation, and minimize nutrient loss. In this study, temporal shifts in soil microbial communities and metabolic profiles were investigated across three key rice growth stages-pre-planting (BS), tillering (TI), and harvest (HA)-to elucidate the ecological effects of straw incorporation. The Shannon diversity and Pielou evenness indices were significantly higher under straw incorporation than under the control at the BS and TI stages, but significantly lower at the HA stage. Straw incorporation also increased the relative abundance of key bacterial taxa, including Polaromonas sp. AER18D145, Sphingomonas sediminicola, and Thiobacillus denitrificans. Functional annotation indicated that the microbial community was mainly associated with amino acid biosynthesis and glycolysis. Metabolomic analysis revealed significant changes in steroids and their derivatives, terpenoid lipids, and carboxylic acids and their derivatives. Three metabolites-3-hexa-isoprenyl-4,5-dihydroxybenzoic acid, LysoPE (16:1(9Z)/0:0), and stachyose-differed significantly across all stages, suggesting their potential as metabolic indicators of straw incorporation. KEGG enrichment analysis identified significant alterations in arachidonic acid, purine, galactose, and pyrimidine metabolism. Redundancy analysis further revealed positive associations of LysoPE (16:1(9Z)/0:0) and stachyose with Brevundimonas sp. Root608 and Polaromonas sp. AER18D145.}, } @article {pmid42354967, year = {2026}, author = {Romero-Ricardo, L and López, Y and Lopez-Mejia, Y and García, A and Contreras-Martínez, H and Galeano, K and Gastelbondo, B and Fragoso, P and Paternina, L and Arrieta, G and Mattar, S}, title = {Metagenomic Analysis Reveals Viral Diversity in Phlebotomine Sand Flies from Caribbean Region in Colombia.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061343}, pmid = {42354967}, issn = {2076-2607}, support = {BPIN 2020000100322//Ministry of Science, Technology and Innovation/ ; }, abstract = {Phlebotomine sand flies are dipterans that transmit leishmaniasis, bartonellosis, and arboviruses of public health importance. Colombia is a tropical country with high annual incidences of arboviruses, such as dengue and, more recently, yellow fever, all of which have similar symptoms. This study characterized the viruses circulating in phlebotomine sand flies in two departments in the Colombian Caribbean. Between August 2023 and December 2024, a descriptive study was conducted in the Departments of Córdoba and Cesar in Colombia. Four municipalities were selected per department, and four insect captures were performed using CDC light traps. Specimens were taxonomically identified and organized into groups according to species and study area, and total RNA was extracted for NGS analysis. Short sequences were quality-assessed, assembled using MEGAHIT to obtain contigs, and classified using DIAMOND-MEGAN6 to select viral genomic sequences for phylogenetic analysis. Thirteen viral families were identified, including a virus from the family Rhabdoviridae in Pi. evansi in the department of Cesar and another from the family Dicistroviridae in Lutzomyia gomezi in both departments. Two genome segments of the family Phenuiviridae were found in Lutzomyia gomezi in the department of Córdoba, Colombia. Sand flies harbor a diverse range of viral families, some of which are previously undescribed, and can be studied to determine their taxonomy and assess their potential to infect vertebrate cells or their interactions with medically important pathogens such as Leishmania spp.}, } @article {pmid42354972, year = {2026}, author = {Diakoumopoulou, D and Slavko, A and Papadimitriou, K and Karoussis, IK and Nikolaou, C and Chatzipanagiotou, S and Ioannidis, A}, title = {Subgingival Microbiota Shifts Following Diode Laser-Activated Indocyanine Green Treatment in Periodontitis: A Pilot 16S rDNA Study.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061347}, pmid = {42354972}, issn = {2076-2607}, support = {485/03-07-2023/OPN: 9Ρ5Ι46Ψ8Ν2-83Φ//National and Kapodistrian University of Athens/ ; }, abstract = {Periodontal disease is driven by a dysbiotic subgingival microbiota enriched in anaerobic pathogens, and novel antimicrobial strategies are needed to complement conventional therapy. This pilot study assessed changes in the subgingival microbiota following diode laser-activated indocyanine green-based treatment (EmunDo) using 16S rDNA amplicon sequencing of paired samples collected before and after therapy. Microbiome analysis revealed compositional shifts across all taxonomic levels, with reductions in disease-associated genera including Porphyromonas, Treponema, Fretibacterium, and Prevotella, and relative increases in taxa more commonly associated with periodontal health, such as Streptococcus, Actinomyces, and Haemophilus. Functional prediction further suggested treatment-associated variation in metabolic categories. Overall microbial richness was preserved between groups. These findings suggest that EmunDo treatment was associated with a restructuring of the subgingival microbiota toward a less dysbiotic profile, warranting further investigation in larger controlled studies using higher-resolution approaches such as shotgun metagenomics.}, } @article {pmid42354979, year = {2026}, author = {de Sousa, LC and Caeiro, AJ and de Carvalho, CCCR}, title = {Screening of Marine Bacteria for Lipase Activity and Application as Whole-Cell Biocatalysts.}, journal = {Microorganisms}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/microorganisms14061355}, pmid = {42354979}, issn = {2076-2607}, support = {no. 101000327, project FuturEnzyme//European Union/ ; UID/04565/2025//Fundação para a Ciência e Tecnologia/ ; LA/P/0140/2020//Fundação para a Ciência e Tecnologia/ ; }, abstract = {Several strategies can be employed for the identification of novel microbial lipases. Despite the increasing importance of metagenomics in bioprospecting, significant limitations in the expression of recombinant proteins, and lipases in particular, remain. Culture-based bioprospecting approaches are, therefore, still valuable. In this work, a collection of bacterial isolates, mainly of marine origin, was screened for lipase activity through a culture-based approach. Screening for lipolytic bacteria was performed in solid media containing olive oil emulsions and rhodamine B. Positive isolates were subsequently grown in liquid media, to confirm lipase production. Significant hydrolytic activity towards the triglyceride substrates tributyrin and triolein could be observed with the biomass produced, although no lipase activity could be detected in the culture supernatants. Six isolates presenting high activity were characterized as whole-cell biocatalysts, and all were found to be active at temperatures ranging between 25 and 65 °C, and at pH values between 6 and 10.5. Genomic analyses of two of these Gram-negative lipase-producing isolates revealed the presence of several hypothetical genes encoding for lipolytic enzymes, including outer cell-bound enzymes, predicted through the application of machine-learning tools. These natural isolates, containing cell-associated lipases, may therefore be of special interest for application as whole-cell biocatalysts.}, } @article {pmid42355557, year = {2026}, author = {Ang, MY and Chen, L and Song, L and Lipovich, L and Choo, SW}, title = {Responsible Use of Large Language Models in Microbial Genomics and Bioinformatics: A Life-Science Framework for Reliability, Reproducibility, and Risk-Aware Interpretation.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/life16061032}, pmid = {42355557}, issn = {2075-1729}, support = {5000105//High-Level Talent Recruitment Program for Academic and Research Platform Construction/ ; }, abstract = {Large language models (LLMs) are increasingly adopted in life-science research for scientific writing, coding, literature synthesis, workflow troubleshooting, and preliminary data interpretation. In microbial genomics and bioinformatics, their appeal is clear because researchers routinely integrate genome annotations, antimicrobial resistance profiles, virulence determinants, taxonomic assignments, microbiome outputs, workflow scripts, and primary literature. Yet this domain also highlights major risks, including hallucinated biological claims, inaccurate citations, irreproducible code, unsupported genotype-to-phenotype inference, and inappropriate clinical or public health framing. This narrative review examines responsible LLM use in microbial genomics as a representative life-science setting where interpretation depends on database provenance, validated workflows, expert assessment, and reproducible evidence chains. It considers applications in genome annotation, antimicrobial resistance interpretation, virulence analysis, microbiome and metagenomics workflows, coding support, and scientific writing. The review further presents MicrobeGuardGPT as a conceptual reliability framework for assessing LLM-assisted microbial genomics outputs before scientific, clinical, or public health use. By connecting task domains, evidence verification, expert validation, and reliability classification, the framework supports risk-aware LLM integration in bioinformatics. Responsible implementation will require domain-specific benchmarks, curated database linkage, transparent reporting, reproducible workflows, human oversight, and governance standards tailored to biological interpretation across research, diagnostic, surveillance, outbreak-response, educational, and translational contexts.}, } @article {pmid42355602, year = {2026}, author = {Schroeder, TH and Eliwi Alsaffan, M and Stäudle, H and Dervishi, A}, title = {Influence of Ongoing Antibiotic Therapy on the Detection of Pathogenic Microorganisms Using Metagenomic Next-Generation Sequencing and Blood Culture in ICU Patients.}, journal = {Journal of clinical medicine}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/jcm15124434}, pmid = {42355602}, issn = {2077-0383}, abstract = {Background: Blood cultures often yield negative results in critically ill patients, particularly after antimicrobial therapy has started. Plasma metagenomic next-generation sequencing enables culture-independent pathogen detection, but its diagnostic performance relative to blood cultures, especially under ongoing antibiotic exposure in ICU populations, remains unclear. Methods: In this retrospective single-center study, we analyzed adult ICU patients who underwent plasma metagenomic next-generation sequencing testing with paired contemporaneous blood culture between March 2023 and September 2024. Patients were classified according to antibiotic exposure at the time of sampling, and the diagnostic yield and performance of metagenomic next-generation sequencing and blood culture were compared overall and stratified by duration of antibiotic exposure. Results: A total of 393 paired metagenomic next-generation sequencing-blood culture samples from 302 ICU patients were analyzed. Blood culture positivity was significantly lower in patients receiving antibiotics at the time of sampling (10.4% vs. 30.4%), whereas metagenomic next-generation sequencing positivity for bacteria remained stable (52.6% vs. 50.8%). With increasing antibiotic exposure, blood culture yield declined sharply, while metagenomic next-generation sequencing detection showed minimal variation. Overall, the concordance of metagenomic next-generation sequencing compared with blood culture as a comparator was 75.3%, with a negative predictive value of 88.0%. Across all subgroups, metagenomic next-generation sequencing demonstrated a higher diagnostic yield than blood culture, with the greatest relative advantage in antibiotic-treated patients. Conclusions: In critically ill patients receiving antimicrobial therapy, blood culture diagnostic yield is markedly reduced, whereas plasma metagenomic next-generation sequencing maintains pathogen detection across varying durations of antibiotic exposure. Metagenomic next-generation sequencing represents a valuable complementary diagnostic tool alongside blood cultures in pretreated ICU patients.}, } @article {pmid42355677, year = {2026}, author = {He, C and Zou, H and Jiang, Z and Zhou, Y and Ying, B}, title = {Metagenomic Next-Generation Sequencing for Pulmonary Tuberculosis Diagnosis and Infection Risk Factor Analysis in AECOPD Patients: A Single-Center Retrospective Study.}, journal = {Journal of clinical medicine}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/jcm15124507}, pmid = {42355677}, issn = {2077-0383}, support = {2024ZD0533100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2024ZD0533106//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; ZYGD23036//1. 3. 5 project for disciplines of excellence from West China Hospital of Sichuan University/ ; 2024YFFK0225//Science and Technology Department of Sichuan Province/ ; }, abstract = {Background: Pulmonary tuberculosis (TB) is a significant trigger of acute exacerbations of chronic obstructive pulmonary disease (AECOPD), so its timely and accurate diagnosis is essential. Also, the risk factors for TB occurrence in this population remain unclear. This study aimed to evaluate the performance of metagenomic next-generation sequencing (mNGS) for TB diagnosis in AECOPD patients, as well as to identify the associated risk factors. Methods: A retrospective observational cohort of 659 AECOPD patients with suspected pulmonary infection was enrolled. The microbial cell-free nucleic acids in bronchoalveolar lavage fluid samples were extracted and subjected to mNGS detection. The clinical data for each patient were collected from the hospital information system. The statistical analyses were performed with SPSS version 25.0. Results: A total of 170 cases, included for final analyses, were categorized into TB (n = 41), bacterial infection (n = 73), and non-infective control (n = 56) groups. Among these groups, the TB group had the highest intensive care unit (ICU) admission rate (46.34%) and longest median hospital stay (19.50 days) (p < 0.01). For TB diagnosis, mNGS demonstrated a greater sensitivity (86.00%), a lower specificity (93.30%), and a higher area under the curve (AUC, 0.877) than TB-DNA detection (70.21%, 100%, 0.848, respectively) and Xpert Mycobacterium tuberculosis/rifampicin (MTB/RIF) assay (63.83%, 100.00%, 0.870, respectively). Notably, mNGS identified the bacterial or viral co-infections in 18.00% of TB cases. Furthermore, the stringently mapped read number determined by mNGS showed a positive correlation with ICU admission rate (r = 0.76) and in-hospital mortality (r = 0.77). The lower body mass index (BMI) and reduced natural killer (NK) cell count were identified as the independent risk factors in the TB group (both p < 0.05). Conclusions: For the diagnosis of pulmonary TB in AECOPD patients, mNGS demonstrated comparable performance to TB-DNA detection and Xpert MTB/RIF assay, and also mNGS identified co-infections. In addition, a lower BMI and reduced NK cell count were identified as the independent risk factors for TB occurrence in this cohort.}, } @article {pmid42355923, year = {2026}, author = {Mammadov, RA and Roest, HP and Fuhler, GM and Su, J and Visseren, T and Janssen, HLA and Porte, RJ and Murad, SD and Hansen, BE and van der Laan, LJW and Peppelenbosch, MP}, title = {Association of FUT2 rs601338 Genotype with Colonic Mucosal Microbiome Composition, Post-Transplant Bacteremia, and All-Cause Mortality After Liver Transplantation for Primary Sclerosing Cholangitis: A Retrospective Cohort Study.}, journal = {Journal of clinical medicine}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/jcm15124755}, pmid = {42355923}, issn = {2077-0383}, abstract = {Background/Objectives: Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease frequently requiring liver transplantation (LTx). The gut-liver axis, host genetics, and microbial dysbiosis are thought to contribute to disease progression and post-transplant outcomes. The FUT2 rs601338 polymorphism influences mucosal fucosylation, host-microbial interactions, and susceptibility to infection. This study aimed to investigate the association between FUT2 genotype, colonic mucosal microbiome composition, post-transplant bacteremia, and all-cause mortality in a retrospective single-center PSC cohort. Methods: This retrospective cohort study included PSC patients who underwent LTx at Erasmus MC University Medical Center (Rotterdam, The Netherlands) between 1987 and 2015. Pre-transplant archival formalin-fixed paraffin-embedded (FFPE) colonic biopsy specimens were available for microbiome analysis. Of 169 transplanted patients, FFPE tissue was available for 98 individuals, and FUT2 rs601338 genotyping was successfully performed in 87 patients. Patients were classified as FUT2 non-secretors (AA, n = 28) and secretors (GA/GG, n = 59). Post-transplant bacteremia was assessed based on clinically indicated blood cultures during follow-up. Colonic mucosal microbiome composition was analyzed using 16S rRNA gene sequencing. Results: FUT2 non-secretors showed a distinct colonic mucosal microbiome profile compared with secretors, characterized by differential abundance of selected taxa within Proteobacteria, Firmicutes, and Bacteroidetes. Post-transplant bacteremia occurred in 30 patients and was more frequent among non-secretors (43%) compared with secretors (15%). Both FUT2 non-secretor status and post-transplant bacteremia were associated with reduced all-cause post-transplant survival in Kaplan-Meier analysis and remained associated with mortality in multivariable regression models. Specific microbial taxa were also showed associations with bacteremia, mortality, and established prognostic scores, including the Amsterdam-Oxford Model and Mayo Risk Score. Conclusions: FUT2 genotype is associated with alterations in colonic mucosal microbiome composition, post-transplant bacteremia, and all-cause mortality in PSC patients undergoing liver transplantation. These findings suggest a potential interplay between host genetics, intestinal microbiota, and infectious complications after transplantation. Given the retrospective design, limited sample size, and use of archival FFPE tissue, all findings should be interpreted as exploratory and hypothesis-generating. Prospective multicenter studies using standardized sampling and high-resolution metagenomic approaches are warranted for validation.}, } @article {pmid42357036, year = {2026}, author = {Osipov, DO and Rozhkova, AM and Volkov, PV and Zorov, IN and Sinitsyna, OA and Trofimchuk, ES and Moskvina, MA and Grokhovskaya, TE and Yaroslavov, AA and Sinitsyn, AP}, title = {Changes in Mechanical Properties and Structure of PET Films Treated with Metagenome-Derived LCC[ICCG] PETase Heterologously Expressed in Penicillium verruculosum.}, journal = {Polymers}, volume = {18}, number = {12}, pages = {}, doi = {10.3390/polym18121510}, pmid = {42357036}, issn = {2073-4360}, support = {126030218233-1//The Ministry of Education and Science of the Russian Federation/ ; }, abstract = {This study examines the nature of enzymatic degradation of polyethylene terephthalate (PET) films mediated by a novel recombinant LCC[ICCG] PETase enzyme preparation based on P. verruculosum fungus. The investigation was conducted using amorphous PET samples and PET samples with varying degrees of crystallinity as substrates for PETase-catalyzed hydrolysis under different temperature and pH conditions. Mechanical testing revealed that enzymatic treatment reduced the yield stress by 20-25%, tensile strength by approximately twofold, and elongation at break by 5-10 times, while the deformation mechanism remained unchanged. Enzymatic degradation under acidic conditions was ineffective, whereas increasing the pH to 9-10 markedly accelerated PET degradation and the associated deterioration of mechanical properties. Thermal analysis (TGA, DSC) and microscopy (optical and scanning electron microscopy) demonstrated that degradation was localized at the polymer surface, leading to the formation of cavities, cracks, and submicron-sized pores rather than bulk material disintegration. An inverse correlation was observed between PET crystallinity and susceptibility to enzymatic degradation: samples with crystallinity below 13% could be almost completely degraded, whereas samples with crystallinity above 30% exhibited little or no measurable weight loss over the same period. Low-crystallinity PET underwent rapid degradation accompanied by a transient increase in crystallinity, while highly crystalline PET primarily accumulated surface defects that nevertheless caused a substantial loss of mechanical strength. Consequently, the experimental data obtained in this study provide useful information for understanding PET degradation and for future studies on enzymatic PET recycling. The systematization of feedstock characteristics and the elucidated patterns of enzymatic degradation will enable optimization of pretreatment, enzymatic hydrolysis, and monomer recovery process parameters, thereby facilitating the eventual production of secondary raw materials.}, } @article {pmid42357147, year = {2026}, author = {Chen, X and Hou, C and Yu, H and Xie, J}, title = {Enhanced Yield of GmJAG1-Edited Soybeans Accompanied by Improved Function of the Rhizosphere Microbiome.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/plants15121828}, pmid = {42357147}, issn = {2223-7747}, support = {2023YFF1001600//National Key R&D Program of China/ ; }, abstract = {In the present study, we investigated how soybean yield is enhanced upon editing of the gene GmJAG1 and the consequent influence on the structure and function of the rhizosphere microbiome. Field trials revealed that gene-edited (GE) soybeans had a 55.22% increase in yield without concomitant changes in root length. Metagenomic sequencing of the rhizosphere soil microbiome showed that, compared with the corresponding non-edited line (CK), the alpha diversity of the GE groups remained unaltered, whereas beta diversity differed significantly at the soybean reproductive (R2) stage. Notably, the rhizosphere microbiome of GE soybeans at the R2 stage exhibited enrichment of functional pathways related to transport, amino acid biosynthesis, and central metabolism. These findings suggest that GmJAG1 editing may shape the functional profile of the rhizosphere microbiome, which could potentially contribute to yield gains. This work offers a novel microbiological perspective for understanding the mechanisms by which yield may be improved in GE crops.}, } @article {pmid42357170, year = {2026}, author = {Wang, P and Yin, D and Fu, G and Yi, X and Guo, Z}, title = {Nitrogen Input Alters Root Exudation of Kandelia obovata and Nitrogen Cycling in Constructed Mangrove Wetlands.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/plants15121851}, pmid = {42357170}, issn = {2223-7747}, support = {32271704//National Natural Science Foundation of China/ ; 2022A1515010562//Basic and Applied Basic Research Foundation of Guangdong Province/ ; JCYJ20230808105410020//The Shenzhen Science and Technology Project/ ; }, abstract = {The role of mangrove root exudates in mediating the nitrogen cycle, particularly under high dissolved inorganic nitrogen (DIN) input, in coastal ecosystems remains unclear. This research investigated variation in the root exudates, and nitrogen transformation and output, in constructed mangrove wetlands planted with Kandelia obovata under high, moderate, and low nitrogen-input levels (PCWs-H, PCWs-M, and PCWs-L, respectively). PCWs-H promoted increased root density and biomass accumulation, enhancing soil nitrogen sequestration, whereas PCWs-L induced greater specific root length, specific root surface area, and number of root tips. These changes directly influenced denitrification efficiency. Hydroxymethoxyphenylcarboxylic acid-O-sulfate and Arg-Ser released in root exudates under PCWs-H might act as potential denitrification inhibitors, thereby suppressing denitrifiers and impairing dissolved nitrogen purification. Elevated nitrogen loading predominantly limited denitrification, resulting in relative NO3[-]-N removal rates of PCWs-H < PCWs-M < PCWs-L (p < 0.05). Compared with PCWs-H and PCWs-L, the enhanced soil organic nitrogen storage under PCWs-M was associated with flavonoids in root exudates. Metagenomic analysis showed that denitrification was the dominant nitrogen removal pathway. Nitrogen loading influenced the effects of root exudates on the microbial community. Under PCWs-H, triterpenoids promoted norBC and nirK/S abundance but depressed amoABC abundance. Sterols and flavonoids in exudates under PCWs-L depressed nosZ abundance, instead activating dissimilatory nitrate reduction to ammonium. Compared with PCWs-H and PCWs-L, N2O emissions were minimal under PCWs-M. This study revealed that mangrove root exudates mediate the nitrogen cycle in mangrove wetlands, providing a theoretical basis for local authorities to manage DIN inputs and mitigate N2O emissions.}, } @article {pmid42357267, year = {2026}, author = {Dumitru, CN and Dumitru, AO and Goroftei, L and Niculet, E and Ignat, MD and Baroiu, L and Nechita, A and Balan, G}, title = {Pharmacomicrobiomics of Non-Antibiotic Drugs: Mechanisms and Clinical Consequences of Gut Microbiota Alterations.}, journal = {Pharmaceutics}, volume = {18}, number = {6}, pages = {}, doi = {10.3390/pharmaceutics18060651}, pmid = {42357267}, issn = {1999-4923}, support = {NA//"Dunarea de Jos" University of Galati/ ; }, abstract = {Background: The gut microbiota constitutes a metabolically active "second genome" that profoundly modulates drug pharmacokinetics, pharmacodynamics, and adverse reaction profiles. Beyond antibiotics, widely prescribed non-antibiotic pharmacotherapies exert clinically relevant pharmacomicrobiomic effects with implications for therapeutic optimisation and pharmacovigilance. Methods: This narrative review, conducted following PRISMA 2020 reporting principles (without PROSPERO pre-registration), searched PubMed/MEDLINE, Scopus, Web of Science, and Cochrane Library (January 2015-December 2024) for evidence on proton pump inhibitors (PPIs), metformin, NSAIDs, statins, SGLT2 inhibitors, and oral iron. Evidence tables included clinical human studies with molecular microbiota characterisation (16S rRNA or shotgun metagenomics), ≥20 participants, and a control arm; preclinical data informed mechanistic synthesis. Results: Of 68 eligible studies, 20 met criteria for the evidence tables. PPIs significantly remodelled gut microbiota composition with enrichment of oral-origin taxa ("oralisation of the gut"), associating with Clostridioides difficile infection and SIBO. Metformin enriched Akkermansia muciniphila and butyrate producers, contributing causally to glycaemic efficacy. NSAIDs compromised barrier integrity, with synergistic dysbiosis under PPI co-prescription. Statins correlated with reduced prevalence of the dysbiotic Bact2 enterotype. SGLT2 inhibitor data remained discordant. Oral iron consistently enriched Enterobacteriaceae at the expense of beneficial commensals.}, } @article {pmid42357653, year = {2026}, author = {Sholes, SL and Norton, S and Gonzalez, A and Gaspar, JM}, title = {MGtree: A Fast and Flexible Alignment-Based Metagenomics Pipeline.}, journal = {Viruses}, volume = {18}, number = {6}, pages = {}, doi = {10.3390/v18060643}, pmid = {42357653}, issn = {1999-4915}, support = {n/a//Merck & Co., Inc., Rahway, NJ, USA (United States)/ ; }, mesh = {*Metagenomics/methods ; Phylogeny ; Humans ; Norovirus/genetics/classification ; Genotype ; *Sequence Alignment/methods ; Computational Biology/methods ; Genome, Viral ; *Software ; Papillomaviridae/genetics/classification ; Human Papillomavirus Viruses/genetics/classification ; }, abstract = {Metagenomics analysis is a critical tool in identifying and typing viral samples to aid surveillance, clinical, epidemiological, and other workflows. Despite advances in sequencing technology and analysis pipelines, there are still limitations that lead to reduced taxonomic resolution or false positives from highly recombinant or challenging samples. Here we describe MGtree, a novel metagenomics pipeline that utilizes a combination of full-length read alignments and phylogenetic analysis to classify samples of interest. We demonstrate that MGtree accurately genotypes viral samples from challenging norovirus and HPV datasets. MGtree outperforms the popular metagenomics programs Kraken2 and Centrifuge, and it succeeds with low-input samples where de novo assembly fails. MGtree's correct assignments across highly mutant and coinfected samples highlights its ability to resolve viral genotypes and its potential to improve classification precision in complex samples.}, } @article {pmid42357654, year = {2026}, author = {Paoli, JE and Trovão, NS and Odoom, T and Mohktar, Q and Buabeng, KB and Adu, B and Tasiame, W and Anderson, B and Tawiah-Yingar, DNY and Subramaniam, K and von Fricken, ME and Mensah, GI and Mietzsch, M and McKenna, R and Johnson, SAM and Mavian, CN}, title = {One Health Genomic Surveillance at Human-Animal Interfaces in Rural Ghana Reveals Underreported Viruses of Zoonotic and Economic Concern.}, journal = {Viruses}, volume = {18}, number = {6}, pages = {}, doi = {10.3390/v18060644}, pmid = {42357654}, issn = {1999-4915}, support = {N/A//University of Florida/ ; }, abstract = {Under a One Health framework, viruses of veterinary and zoonotic importance pose significant threats to animal and human health, food security, and livelihoods, particularly in regions with intense human-animal interactions. In West Africa, despite recent advances in surveillance programs, important gaps remain in understanding viral diversity and cross-species transmission at wildlife-livestock interfaces. We conducted metagenomic surveillance to characterize viruses circulating across livestock, domestic animals, and wildlife in rural Ghana in 165 animals sampled across five regions. Viral RNA from serum and tissue samples was sequenced with the Illumina platform, and genomes were de novo assembled with MEGAHIT. Phylogenetic relationships were reconstructed using Bayesian approaches. We report the first genomic sequences of porcine parvovirus 3, canine parvovirus, rotavirus A genotype R16, and bovine hepacivirus subtype B from Ghana in over a decade. Phylogenetic analyses revealed intercontinental linkages between Africa and Europe for parvoviruses, persistence of hepacivirus lineages, and evidence of cross-species transmission for rotavirus. Notably, detection in apparently healthy animals highlights underrecognized circulation, gaps in vaccination effectiveness, trade-related biosecurity vulnerabilities, and the role of wildlife in viral maintenance and transmission. Our findings reveal dynamic viral diversity and connectivity across animal populations and ecological interfaces, emphasizing the fluid and interconnected nature of pathogen circulation within One Health systems. By integrating metagenomics and phylogenetics, this study provides a scalable framework for enhancing surveillance capacity, enabling the early detection of emerging threats and informing targeted strategies to mitigate zoonotic and economically important viral diseases in West Africa.}, } @article {pmid42357666, year = {2026}, author = {Lai, T and Liu, F and Li, G and Hua, L}, title = {ViroBioTree: A Tree-Structured Biological Evidence Retrieval Framework for Viral Protein Function Annotation.}, journal = {Viruses}, volume = {18}, number = {6}, pages = {}, doi = {10.3390/v18060656}, pmid = {42357666}, issn = {1999-4915}, support = {Grant No. 2026GXNSFAA00640099//Natural Science Foundation of Guangxi province/ ; Guike AD25069086//the Science and Technology Project of Guangxi/ ; }, mesh = {*Viral Proteins/genetics/metabolism ; *Molecular Sequence Annotation/methods ; *Computational Biology/methods ; Humans ; Open Reading Frames ; SARS-CoV-2/genetics ; Genome, Viral ; *Software ; }, abstract = {Accurate viral protein function annotation is essential for genomic surveillance, yet conventional retrieval-augmented generation (RAG) pipelines often fragment biological evidence into fixed-length text chunks, disrupting relationships among ORFs, annotations, structural domains, sequence motifs, residue mappings, and model-derived attention evidence. We propose ViroBioTree, a tree-structured biological evidence retrieval framework for downstream viral protein evidence review rather than a new primary annotation classifier. Built as an evidence organization layer on ViralMultiNet-derived ORF-level predictions and annotations, ViroBioTree converts sequence, annotation, structure, and attention evidence into typed biological nodes and traceable edges, then performs deterministic multi-channel recall, evidence-aware reranking, balanced TopK selection, rule-based verification, and node-cited report generation. In a demo benchmark, ViroBioTree achieved its strongest deterministic proxy performance on structure-explanation tasks, with Precision@K = 1.0, Recall@K = 1.0, and diversity = 0.52; these values reflect expected node-type and tag agreement rather than independent biological correctness. A bounded full-scale SARS-CoV-2 index contained 39,800 ORF rows, 80,000 attention records, 199,418 nodes, and 495,886 edges. In a stratified full20k diagnostic evaluation, ViroBioTree showed task-dependent advantages over LlamaIndex vector retrieval for conflict detection, evidence retrieval, and structure explanation, while LlamaIndex remained competitive or stronger for annotation-rich function annotation. A cross-family Influenza A Virus (IAV) diagnostic audit showed that the schema can represent IAV evidence namespaces while explicitly exposing missing formal ORF inputs, missing attention evidence, and unavailable residue/PDB assertions. Supplementary robustness, external sanity-check, diversity-risk, expert-evaluation, domain-tool positioning, and cross-family audit analyses supported traceability, report quality, and conservative evidence handling, but also showed that stable Precision@K under query perturbation does not necessarily imply stable retrieved evidence sets. ViroBioTree operates offline and deterministically, but does not address raw-read assembly, base calling, primary ORF prediction, or wet-lab validation. Its results should be interpreted as proxy and expert-reviewed evidence for traceable viral protein evidence retrieval and report generation rather than as direct validation of biological function annotation.}, } @article {pmid42357739, year = {2026}, author = {Xue, T and Zhang, B and Wang, Z and Ma, Y and Shen, Q and Ding, J and Yang, X}, title = {Rapid Metagenomic Detection of Brucella abortus During a Two-Case Bovine Abortion Investigation in Inner Mongolia, China.}, journal = {Veterinary sciences}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/vetsci13060541}, pmid = {42357739}, issn = {2306-7381}, abstract = {Abortion in cattle entails substantial economic loss, and rapid identification of abortigenic pathogens is critical for timely on-farm response and reduction in human exposure risk. In 2024, two Holstein cows from a small farm in Inner Mongolia aborted in close succession without an obvious cause. Vulvar swabs from both cows, one afterbirth sample, and whole blood from one aborted fetus were collected. Shotgun metagenomic sequencing was performed, followed by host-read removal, taxonomic profiling with Kraken2, de novo assembly of Brucella-aligned reads, and whole-genome comparison. Serological tests, Gram-stained smears, and Brucella genus- and species-specific qPCR assays were used as orthogonal verification. Putative resistance and virulence determinants were screened against CARD and VFDB. Brucella reads were detected in all samples, with the highest relative abundance in the 138-afterbirth (96%). qPCR assays detected Brucella DNA and B. abortus-specific signals in all four samples. A draft Brucella genome was assembled from the 138-afterbirth sample and was phylogenetically placed within B. abortus, showing relatedness to previously circulating Chinese lineages. Cows 138 and 198 were RBT-positive with SAT titres of 1:100 (++). No acquired Brucella resistance genes were identified in CARD. Within 72 h of sample receipt, B. abortus was reported to the farm and local authorities and emergency biosecurity measures were implemented. This field investigation shows that metagenomic sequencing, when combined with conventional serology, microscopy, and targeted qPCR, can support rapid etiological investigation when culture is delayed, hazardous, or biosafety level 3 facilities are unavailable.}, } @article {pmid42357757, year = {2026}, author = {Ma, L and Qu, J and Li, X and Liu, Y}, title = {Ecological Reassembly of the Milk Microbiome and Its Associated Resistome During the Dry Period in Dairy Cows.}, journal = {Veterinary sciences}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/vetsci13060559}, pmid = {42357757}, issn = {2306-7381}, support = {2023YFD1800100//National Key Research and Development Program of China/ ; No. IFR-06//the Agricultural Science and Technology Innovation Program/ ; }, abstract = {The aim of this study was to characterize the coordinated dynamics of the mammary microbiome, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) across the dry period, calving, and early lactation. The mammary microbiome undergoes substantial ecological changes across these stages, yet the coordinated dynamics of microbial composition, ARGs, and MGEs remain poorly understood. Here, shotgun metagenomic sequencing was performed on mammary secretion samples collected before dry-off (BM), immediately after calving (ACM), and one month postpartum (AM). The mammary microbiome exhibited a clear "exposure-bottleneck-reassembly" trajectory. BM was characterized by high microbial diversity and the enrichment of environmentally associated taxa, whereas ACM displayed a pronounced immunological bottleneck with markedly reduced microbial diversity and network complexity. During AM, microbial communities partially recovered but remained distinct from the BM state, indicating persistent ecological restructuring after calving. ARGs and MGEs showed parallel dynamics, with broad resistome and mobilome diversity in BM, a sharp contraction in ACM, and a selective re-expansion in AM. Network analysis further revealed maximal ecological complexity in BM, increased ARGs/MGEs connectivity in ACM, and partial stabilization in AM. These findings demonstrate that host physiological transitions, together with dry cow therapy (DCT), drive the coordinated remodeling of the mammary microbiome, resistome, and mobilome across the dry period.}, } @article {pmid42358061, year = {2026}, author = {Morvil, N and Goh, WGW and Zheng, C and Sutjipto, S and Ng, DHL and Zambon, M}, title = {Navigating the Future of Respiratory Infections: Key Insights From International Congress in Singapore, 17-20 September 2025.}, journal = {Influenza and other respiratory viruses}, volume = {20}, number = {7}, pages = {e70276}, doi = {10.1111/irv.70276}, pmid = {42358061}, issn = {1750-2659}, mesh = {Humans ; Singapore ; *Respiratory Tract Infections/prevention & control/diagnosis/epidemiology/drug therapy/therapy/virology ; Antiviral Agents/therapeutic use ; Animals ; }, abstract = {BACKGROUND: The 8th International Society for Respiratory Viruses (ISRV) Antiviral Group Conference, held jointly with the 3rd International Meeting on Respiratory Pathogens in Singapore (17-20 September 2025), examined evolving approaches to prevention and management of respiratory infections. This report summarizes the major themes and perspectives that emerged across the meeting.

METHODS: We reviewed plenary sessions, thematic symposia and panel discussions and synthesized recurring concepts relevant to clinical practice and preparedness. Discussions were organized into key domains, including therapeutics, host response, vaccination, surveillance, diagnostics and research infrastructure.

RESULTS: Presentations highlighted the development of long-acting and broadly active antivirals, interest in combination therapy and early treatment, and increasing recognition that inflammatory host responses contribute substantially to disease severity. Advances in vaccines targeting conserved viral components and long-acting monoclonal antibodies were discussed, along with the growing role of adaptive platform trials and harmonized clinical endpoints. A recurring theme was the transition from pathogen-centred management to a broader framework incorporating host responses. Speakers also emphasized integrated surveillance using genomic sequencing, metagenomics and rapid point-of-care diagnostics within a One Health framework addressing zoonotic spillover.

CONCLUSIONS: The meeting illustrated how clinical care, translational science and public health preparedness are becoming increasingly interconnected. Sustained investment in surveillance systems, clinical trial platforms and access to therapeutics will be necessary to translate scientific progress into routine care and to strengthen readiness for future epidemics and pandemics.}, } @article {pmid42358249, year = {2026}, author = {He, L and Huang, Y and Li, H and Zhu, B and Zhang, Z and Wu, J and Zhou, S and Zhan, Q and Wu, K and Wu, F}, title = {Novel insights into gut microbiota alterations in major depressive disorder with suicidal ideation: a metagenomic analysis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1843301}, pmid = {42358249}, issn = {1664-302X}, abstract = {INTRODUCTION: Suicidal ideation in major depressive disorder (MDD) is common, yet its biological mechanisms and biomarkers remain unclear. The gut microbiota, a key component of the gut-brain axis, has been implicated, but current evidence is limited.

METHODS: We analyzed fecal samples from 141 participants, including 52 healthy controls (HCs) and 89 first-episode, drug-naïve MDD patients, further classified into suicidal ideation (SI, n = 57) and non-suicidal ideation (NSI, n = 32) groups using the Beck Scale for Suicide Ideation (BSSI). Shotgun metagenomic sequencing with HUMAnN3-based taxonomic and functional profiling was performed. Microbial diversity, differential abundance, and partial correlation analyses with suicidal ideation severity were conducted to identify key microbial taxa associated with suicidal ideation. For functional difference analysis, MaAsLin2 was employed across four levels: KEGG Orthology (KO), KEGG pathways, CAZy, and MetaCyc pathways. Mediation analysis was used to assess potential mediating effects between suicidal ideation and key microbial taxa after adjustment for age, sex, education, and BMI.

RESULTS: No significant differences were observed in overall microbial diversity. Bacteroides cellulosilyticus was enriched in HCs and showed a significant negative association with suicidal ideation severity. Functionally, compared with the NSI group, patients with suicidal ideation exhibited reduced microbial capacities related to peptidoglycan biosynthesis. Mediation analysis further indicated that B. cellulosilyticus may modulate suicidal ideation through pathways involved in carbohydrate transport and metabolism, vitamin K2 biosynthesis, and DNA repair.

CONCLUSION: Bacteroides cellulosilyticus may act as a potentially protective microbial species, negatively regulating suicidal ideation, possibly by enhancing carbohydrate metabolism and short-chain fatty acid production. Notably, this species has received limited attention in the context of psychiatric disorders, highlighting its potential as a novel microbial target. These findings provide new microbiome-based insights into suicidal ideation in MDD.}, } @article {pmid42358254, year = {2026}, author = {Duan, G and Kong, L and Duan, S and Nie, S and Gu, W}, title = {Research progress on emerging and important Tick-Borne pathogens.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1866307}, pmid = {42358254}, issn = {1664-302X}, abstract = {Ticks are important vector arthropods, which can carry and transmit a variety of pathogenic microorganisms, and pose a serious threat to global public health. This study reviews the research progress of the main and emerging tick-borne pathogens, such as Lyme disease related Borrelia, Rickettsia, Babesia, Thrombocytopenia Syndrome Virus (SFTSV), Tick-borne Encephalitis Virus (TBEV), Alongshan virus (ALSV), etc., focuses on their genomic diversity, pathogenicity, transmission and immune escape, co- infection. In addition, the application of new detection technology [Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), metagenomic next-generation sequencing (mNGS), microfluidics] in Tick-Borne pathogens is summarized.It highlights current research limitations, including delayed vaccine development and inadequate surveillance systems. Finally, future research directions are prospected, providing theoretical references for the prevention and control of tick-borne diseases.}, } @article {pmid42358269, year = {2026}, author = {Hou, Z and Shi, M and Gou, S and Liao, D and Hu, C and Zhang, Q and Zhang, X and He, L and Ba, Y and Zhang, Y and Li, Y and Zhou, K and Wang, H and Song, L}, title = {Relative contributions of vegetation and soil properties to microbial community structure and function in alpine and subalpine meadows of the southeastern Tibetan Plateau.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1847498}, pmid = {42358269}, issn = {1664-302X}, abstract = {INTRODUCTION: Ongoing climate warming is expected to promote the upward expansion of subalpine meadows and the gradual replacement of alpine meadows on the southeastern margin of the Tibetan Plateau. However, the mechanisms by which these vegetation transitions reshape belowground microbial taxonomic composition and metabolic functional potential remain poorly understood.

METHODS: We investigated soil microbial community structure and functional potential in alpine meadow (AM) and subalpine meadow (SM) ecosystems in the Napahai Basin by integrating vegetation surveys, soil chemical analyses, enzyme activity assays, and metagenomic sequencing.

RESULTS AND DISCUSSION: Altitudinal differences in hydrothermal conditions were associated with pronounced divergence in plant community composition and soil nutrient status between the two meadow types. Although microbial α-diversity did not differ significantly, β-diversity analyses revealed distinct taxonomic and functional differentiation. Functional annotations based on CAZymes and KEGG indicated that variation in microbial functional potential was closely associated with coordinated changes in carbon, nitrogen, and phosphorus availability, suggesting that microbial metabolic strategies shifted along the environmental gradient. Random forest and partial least squares path modelling further showed that plant community composition exerted a stronger direct influence on microbial functional configuration than soil-mediated indirect effects. These findings highlight the prominent role of vegetation in shaping microbial functional potential and underscore the sensitivity of belowground ecological processes to vegetation transitions along environmental gradients in high-elevation meadow ecosystems.}, } @article {pmid42358428, year = {2026}, author = {Chen, Y and Tian, D and Bai, Y and Xu, J and Liu, S and Wang, Y and Li, X}, title = {Case Report: Listeria monocytogenes meningitis complicated by an acute exacerbation of chronic obstructive pulmonary disease: the key diagnostic role of metagenomic high-throughput sequencing.}, journal = {Frontiers in medical technology}, volume = {8}, number = {}, pages = {1801483}, pmid = {42358428}, issn = {2673-3129}, abstract = {BACKGROUND: Listeria monocytogenes is an opportunistic foodborne pathogen that causes severe invasive infections, such as meningitis, primarily in immunocompromised individuals, the elderly, and pregnant women. Diagnosis is often challenging due to nonspecific early symptoms.

CASE DESCRIPTION: A 67-year-old male with a history of chronic obstructive pulmonary disease (COPD) presented with a 4-day history of persistent high-grade fever and altered mental status. Initial empirical antibiotic therapy (meropenem) proved ineffective.Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) definitively identified L.monocytogenes. The patient was diagnosed with "Listeria monocytogenes meningitis complicated by an acute exacerbation of chronic obstructive pulmonary disease". Patients with pathogenic bacterial infections completed a 21-day course of ampicillin and sulbactam sodium and a 14-day course of gentamicin, resulting in a rapid improvement in clinical symptoms and biochemical parameters.

CONCLUSION: This case underscores the critical role of mNGS in the aetiological diagnosis of central nervous system infections, especially when conventional methods are inconclusive. It highlights the need for a high index of suspicion for listeriosis in elderly patients with comorbidities presenting with unexplained fever and neurological decline.}, } @article {pmid42358480, year = {2026}, author = {Flores, GD and Damon, ZF and Ford, M and Gancz, NN and Savoca, PW and Esfand, SM and Chu, KA and Querdasi, FR and McCann, CF and Westman, JG and Labus, JS and Clewett, D and Parr, AC and Hsiao, EY and Jacobs, J and Silvers, J and Callaghan, BL}, title = {A protocol for the Teen Bugs study: An integrative, multi-omics approach to understanding the role of the gut microbiome and mesocorticolimbic system in adolescent mental health following early adverse caregiving.}, journal = {Brain, behavior, & immunity - health}, volume = {55}, number = {}, pages = {101275}, pmid = {42358480}, issn = {2666-3546}, abstract = {Caregiving-related early adversities (crEAs) are potent risk factors for the development of internalizing psychopathology (e.g., depression, anxiety). Alterations to the dopaminergic mesocorticolimbic system, which supports the construction of reward-related experiences, are commonly observed following crEA exposure and are thought to mediate this risk. Indeed, many internalizing disorders are characterized by disruptions in how reward-related information is represented and used to guide affective and motivational states. Critically, the effects of crEA on mesocorticolimbic functioning may be shaped by input from peripheral systems, such as the gut microbiome, though such bottom-up signaling has been markedly understudied in humans. The Teen Bugs study was thus developed to identify gut microbiome-dependent metabolic pathways linking crEA exposure to mesocorticolimbic functioning and internalizing symptoms in adolescents, a group that experiences a disproportionate incidence of psychopathology relative to other age groups and is underrepresented in the gut microbiome literature. Adolescents aged 12-15 years, with and without histories of crEA exposure, will be followed across three timepoints over five years. At each timepoint, participants will complete a semi-structured clinical interview, a reward-guided decision-making task, and self-report questionnaires assessing mental health, previous caregiving experiences, reward-related behaviors, as well as developmental and lifestyle factors. Participants will also undergo multimodal neuroimaging that leverages MRI-based proxy markers of dopaminergic neurobiology and provide stool and blood samples for metagenomic and metabolomic profiling, respectively. This integrative design has the potential to clarify developmentally salient mechanisms that may serve as novel therapeutic targets for youth most at risk of, or already experiencing, internalizing psychopathology.}, } @article {pmid42358948, year = {2026}, author = {Fu, J and Shan, J and Xu, H and Zhu, Z and Yang, P and Wang, Q and Han, J and Cao, G}, title = {Altered GABA and secondary bile acids in Guillain-Barré syndrome: association with gut dysbiosis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1849216}, pmid = {42358948}, issn = {1664-3224}, mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; *Guillain-Barre Syndrome/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Female ; *Bile Acids and Salts/metabolism/blood ; Male ; *gamma-Aminobutyric Acid/metabolism/blood ; Adult ; Middle Aged ; Metabolomics/methods ; Metabolome ; Metagenomics ; Feces/microbiology ; Aged ; }, abstract = {OBJECTIVE: Guillain-Barré syndrome (GBS) is a rare, immune-mediated inflammatory disease of the complex peripheral nervous system that often follows acute infections, and may also be associated with long-term 'silent infections'. Long-term "silent infections" can alter the gut microbiota, which in turn may contribute to immune-mediated inflammatory diseases. Emerging evidence suggests that gut dysbiosis and altered serum metabolites are associated with GBS, but the causative link between GBS and gut microbiota remains unclear. Therefore, this study aimed to evaluate the association between gut microbiota structure and serum metabolic profile in GBS.

METHODS: Untargeted metabolomics profiling of serum and metagenomics sequencing of stool samples were performed to capture the global metabolic and microbial differences between GBS subjects and healthy controls. Multivariate statistical analyses, including PLS-DA, were applied to identify distinct clustering patterns and differential abundances of metabolites and gut microbiota. Pearson's correlation analysis was used to estimate the correlations between abundance of gut microbiota and serum metabolic profile. Seven different media were used to isolate the potential pathogens from GBS stool samples.

RESULTS: The metabolome data revealed that gamma-aminobutyric acid (GABA) metabolism and secondary cholic acid metabolism were perturbed in GBS. Specifically, GABA was increased significantly (approximately 14.3-fold), while multiple secondary cholic acids (methyl deoxycholate, glycodeoxycholic acid, glycolithocholic acid, taurolithocholic acid, and coprocholic acid) were decreased significantly in GBS subjects. Regarding the gut microbiota identified via metagenomic sequencing of stool samples, Ligilactobacillus salivarius, Enterocloster bolteae, and the opportunistic pathogenic Klebsiella pneumonia were notably more abundant in GBS subjects, while Bacteroides sp., Roseburia hominis and Paraprevotella xylaniphila were decreased significantly. In addition, pathogens such as K. pneumoniae were also isolated from GBS subjects. Further analysis of the metagenomic data revealed enrichment of prokaryotic genes involved in the GABA biosynthesis pathway, while genes associated with secondary cholic acid metabolism pathways were decreased in gut microbiome in GBS subjects. On this basis, correlation analysis revealed that changes in GABA were associated with altered levels of gut microbes including Enterococcus species, Ligilactobacillus salivarius and Enterocloster bolteae, whereas changes in secondary cholic acids were positively correlated with altered levels of Bacteroides species and Roseburia species.

CONCLUSION: GABA metabolism and secondary cholic acid metabolism were significantly disturbed in GBS subjects, potentially resulting from the dysbiosis of the gut microbiota. K. pneumonia and other no gut microbes were significantly enriched and isolated in GBS and may contribute to the inflammatory response in this immune-mediated inflammatory disease. These findings also suggest that GABA may be a promising biomarker for the diagnosis of GBS and that modulation of gut microbiota might impact the clinical course of GBS.}, } @article {pmid42359020, year = {2026}, author = {Wei, BH and Da, HJ}, title = {Purulent Pericarditis Caused by Polymicrobial Periodontal Pathogens (Tannerella forsythia, Fusobacterium nucleatum, and Porphyromonas gingivalis): A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {598156}, pmid = {42359020}, issn = {1178-6973}, abstract = {BACKGROUND: Purulent pericarditis is a rare, life-threatening infection, most commonly caused by bacteria such as Staphylococcus aureus. We report an exceptional case of hematogenously disseminated infection probably originating from the oral cavity, highlighting a novel pathogen profile.

CASE PRESENTATION: We report a 66-year-old male with no history of periodontal disease or oral procedures presented with purulent pericarditis and a concomitant subphrenic abscess. Metagenomic next-generation sequencing (mNGS) of pericardial fluid revealed a polymicrobial infection with three periodontal pathogens: Tannerella forsythia, Fusobacterium nucleatum, and Porphyromonas gingivalis. The patient was treated with pericardiocentesis, targeted antibiotics, and organ support, resulting in clinical stabilization.

CONCLUSION: This case provides clinical evidence that a consortium of periodontal pathogens can disseminate hematogenously to cause severe metastatic infections in sterile sites, even in individuals without overt oral disease. It underscores the need to consider occult oral origins in infections of unknown source and illustrates the value of comprehensive molecular diagnostics in identifying fastidious organisms, although it remains undetermined whether both conditions were secondary to the same source.}, } @article {pmid42359168, year = {2026}, author = {Mundt, B and Kant, R and Grzybek, M}, title = {Viral pathogens in urban rats: A one health systematic review of global surveillance evidence.}, journal = {One health (Amsterdam, Netherlands)}, volume = {23}, number = {}, pages = {101468}, pmid = {42359168}, issn = {2352-7714}, abstract = {BACKGROUND: Commensal rats (Rattus norvegicus and Rattus rattus) thrive in urban environments worldwide, where they live near humans and may act as reservoirs for viral pathogens of public health relevance. Although rats are increasingly recognised as sentinels of urban environmental health, the diversity and distribution of viral infections circulating in urban rat populations remain incompletely characterised within a One Health framework.

OBJECTIVES: This systematic review synthesises global evidence on viral pathogens detected in urban rats, focusing on rat hepatitis E virus/Rocahepevirus ratti and human-associated hepatitis E virus/Paslahepevirus balayani where distinguishable, Seoul virus (SEOV), SARS-CoV-2, and additional viral taxa identified through targeted surveillance or, in rare cases, metagenomic approaches.

METHODS: Following PRISMA 2020 guidelines, five electronic databases were searched for primary studies reporting viral detection in urban Rattus spp. Eligible studies underwent screening, structured data extraction and quality appraisal. Viral prevalence was summarised descriptively by pathogen and geographic region.

RESULTS: A total of 70 studies met the inclusion criteria, spanning Europe, Asia, North America, South America and the Caribbean. HEV and SEOV were the most frequently reported viruses, with prevalence varying widely between regions. HEV prevalence ranged from low levels in parts of Europe and Asia to high levels in North America. SEOV was detected across all regions, with particularly high prevalence in parts of Asia and the Americas. SARS-CoV-2 was not detected in European rats but was reported at low to moderate prevalence in the Americas. Numerous additional viral pathogens were identified.

CONCLUSIONS: Urban rats globally harbour diverse viral communities, including pathogens with zoonotic potential. Surveillance remains uneven and methodologically heterogeneous. Integrating rat biomonitoring into coordinated One Health surveillance systems is critical to strengthen early warning capacity and mitigate zoonotic risk.}, } @article {pmid42359352, year = {2026}, author = {Lyu, C and Zhou, Q and Xiao, X and Bai, X and Pu, Y and Zhu, H and Zhao, M and Meng, J and Lyu, H}, title = {Metagenomics next-generation sequencing of plasma combined with blood cells for improving the prognosis of early infection in patients with hematologic disorders: a real-world cohort study in northern China.}, journal = {Frontiers in molecular biosciences}, volume = {13}, number = {}, pages = {1662559}, pmid = {42359352}, issn = {2296-889X}, abstract = {INTRODUCTION: Infection is a leading cause of death in hematologic disorder patients. While plasma metagenomic next-generation sequencing (mNGS) is widely used, no studies have explored the clinical value of whole blood mNGS, combining plasma and blood cells, in these patients.

METHODS: We retrospectively analyzed the results of whole blood mNGS testing from 231 blood samples of hematological disorders patients with suspected infections. The diagnostic performance of whole blood mNGS and its clinical impacts on treatment were assessed based on the final clinical diagnosis.

RESULTS: mNGS testing in both plasma and whole blood showed significantly higher pathogen detection rates than blood culture (72.29%, 77.06% vs. 21.65%, P < 0.001). The total concordance rate of whole blood mNGS was also significantly higher than that of blood culture, conventional microbial testing, and plasma mNGS when compared to the final clinical diagnosis. Of the 101 pathogens detected by whole blood mNGS, 13 were missed by plasma mNGS. As a result, whole blood mNGS demonstrated a broad pathogen detection capability, especially in patients with non-hematologic malignancies or hematopoietic stem cell transplantation. Regarding treatment, whole blood mNGS had a positive impact on 72.73% of all patients, and 75.15% patients with pulmonary infections. It helped rule out infection in a timely manner, reduce or stop unnecessary antibiotic use, and enabled 77.88% of infected patients to benefit from whole blood mNGS sequencing.

DISCUSSION: Whole blood mNGS assays, combining plasma and blood cells, significantly improved pathogen detection rates and optimized antibiotic therapy in patients with hematological diseases and pulmonary infections or bloodstream infection. This approach facilitates the early management of patients with hematologic disorders who are at risk of infection.}, } @article {pmid42359485, year = {2026}, author = {Addy, HPK and Amedorme, D and Osei-Poku, P and Kwarteng, A}, title = {Predicted Functional Potentials of Bacterial Communities in Fermented Maize Products From Ghana, Nigeria, and Benin via 16S rRNA Amplicon Sequencing and PICRUSt2.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70272}, doi = {10.1002/mbo3.70272}, pmid = {42359485}, issn = {2045-8827}, mesh = {RNA, Ribosomal, 16S/genetics ; *Zea mays/microbiology ; *Fermented Foods/microbiology ; Ghana ; Nigeria ; Benin ; *Microbiota/genetics ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Sequence Analysis, DNA ; Phylogeny ; Lactobacillus/genetics/metabolism ; DNA, Bacterial/genetics ; }, abstract = {Fermented maize products are integral to the diets of many African communities. Despite their cultural significance and health benefits, little is known about the metabolic potential of their microbial populations. This study utilized 16S rRNA amplicon sequencing data from the NCBI to characterize the functional capabilities of microbiomes in six maize-based fermented foods. Quality assessment and taxonomic classification were performed using QIIME2 with the SILVA 138 database, while functional predictions were generated with PICRUSt2 and analyzed in R. Taxonomic profiling revealed that Firmicutes dominated all samples, reaching peak abundance in Mawe (94.9%) and S37_Fermented_Maize (91.4%). Proteobacteria were elevated in S19_Fermented_maize (up to 36.5%) and S38_Dehulled_Maize (16.0%). At the genus level, Lactobacillus was most abundant in S5_Mawe (82.2%) and S6_Mawe (79.6%), while Acetobacter peaked in S19_Fermented_maize (32.7%). Regarding functional predictions, Lactobacillus appeared to drive key KEGG Orthologs and pathways, specifically ABC transporters, transcriptional regulation, and DNA replication mechanisms. In contrast, Weissella and Streptococcus contributed notably to peptide/nickel transport, L-lactate dehydrogenase (EC 1.1.1.27), and nucleotide biosynthesis. Acetobacter was prominent in Ogi, showing a connection with site-specific methylation (EC 2.1.1.72) and phospholipid synthesis (PHOSLIPSYN-PWY). Notably, commercial Mawe samples exhibited higher predicted activities related to transposase activity (K07496), energy metabolism, and peptidoglycan maturation (PWY0-1586). These findings demonstrate that while traditional fermentation processes maintain a consistent set of metabolic functions predominantly driven by Lactobacillus, distinct variations exist depending on product type and production approach. These predicted functions provide a baseline for further experimental validation of the metabolic contributions of microbial communities in fermented maize products.}, } @article {pmid42359789, year = {2026}, author = {Lakey, BD and Wozniak, KJ and Britton, RA and Tabor, JJ}, title = {Mucin-derived sugars act as metabolic brakes controlling growth initiation in Akkermansia muciniphila.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2691334}, doi = {10.1080/19490976.2026.2691334}, pmid = {42359789}, issn = {1949-0984}, mesh = {*Mucins/metabolism/chemistry ; Animals ; Humans ; *Akkermansia/growth & development/metabolism ; Mice ; Gastrointestinal Microbiome ; Polysaccharides/metabolism ; *Dietary Sugars/metabolism ; Colon/microbiology ; Citric Acid Cycle ; *Verrucomicrobia/growth & development/metabolism ; }, abstract = {Akkermansia muciniphila is a key member of the gut microbiota and plays important roles in host metabolism and health. In the colon, A. muciniphila extracts nutrients from oligosaccharide-rich mucin glycans that comprise the mucosa. However, this environment is complex and shaped by dietary inputs, microbiome metabolism, and mucin glycan composition varying across hosts, gastrointestinal regions, and physiological states. How strains of A. muciniphila integrate these nutrient signals into growth initiation and niche colonization remains unclear. Here, we compare physiological responses of a human- and mouse-derived strain of A. muciniphila, finding that dietary sugars differentially affect these isolates, suggesting host-associated tuning of metabolic capacity. In contrast, several mucin-derived sugars impose a conserved, concentration-dependent delay in growth initiation, implicating the lag phase as a critical metabolic checkpoint for growth. Genetic suppressor analysis identified sugar kinases and a component of the tricarboxylic acid cycle as genetically encoded control points linking glycan sugar exposure to the energy balance required for growth. These findings demonstrate that mucin-derived sugars function as both nutrients and metabolic stressors, regulating growth initiation. We propose that A. muciniphila employs metabolic "brakes" to coordinate growth with mucin composition, putatively linking host glycan landscapes to microbial physiology and ecological fitness within the mucus layer.}, } @article {pmid42360122, year = {2026}, author = {Banerjee, P and Al-Bayer, S and Calaor, J and Weber, S and Graham, NR and Andersen, JC and Economo, EP and Kennedy, S and Krehenwinkel, H and Gillespie, RG and Roderick, GK and Rogers, HS and Puliafico, KP}, title = {Comparison of Environmental DNA and Bulk DNA Metabarcoding for Assessing Terrestrial Arthropod Diversity Across Three Habitat Types on Guam.}, journal = {Molecular ecology resources}, volume = {26}, number = {5}, pages = {e70172}, doi = {10.1111/1755-0998.70172}, pmid = {42360122}, issn = {1755-0998}, support = {RC21-1034//Strategic Environmental Research and Development Program/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; *Arthropods/genetics/classification ; *Biodiversity ; *Ecosystem ; Electron Transport Complex IV/genetics ; *Metagenomics/methods ; }, abstract = {DNA-based methods offer a rapid and cost-effective way for detecting species occurrence and monitoring biodiversity; among them, bulk DNA metabarcoding is well-established, and recently developed environmental DNA (eDNA)-based methods offer a non-lethal alternative. With a goal to develop suitable methods for assessing insect biodiversity for understudied island ecosystems where DNA reference libraries are incomplete, we compared established bulk DNA metabarcoding methods with eDNA across three replicated terrestrial ecosystem types (degraded forest, limestone forest, and grassland) on the island of Guam. Using two mitochondrial COI primer pairs, we performed bulk DNA metabarcoding of standard entomological collection methods (Malaise traps, pan traps, and vegetation beating), and compared the assessment of biodiversity with that from different eDNA sources (flowers, leaves, tree trunks, and spider webs). In our samples, eDNA and bulk DNA metabarcoding both detected a large proportion of overall taxa (OTUs, 86.6% and 60.3%, respectively). Although bulk DNA metabarcoding detected significantly more taxa, eDNA proved to be a reasonable non-lethal alternative. As expected, because of limitations in existing reference databases for understudied systems, species-level identification was achieved for only a few OTUs. Overall, the sampling approach was the dominant driver of arthropod diversity, explaining ~17% of the observed variation, while habitat type accounted for ~4%. Thus, each sampling approach captured some unique diversity and contributed to the complementary effect of maximizing detection. For rapid biodiversity surveys of terrestrial arthropods, we recommend integrating metabarcoding approaches, and in sensitive ecosystems where specimen capture is undesirable, eDNA offers a powerful non-lethal alternative to monitor diversity and community change.}, } @article {pmid42360286, year = {2026}, author = {Shi, Q and Chen, C and Bai, T and Zhang, S and Wu, Y and Wu, H and Luo, H and Chen, Y and Zheng, S and Meng, X and Wu, Y and Gao, J and Wang, Z and Chen, H}, title = {Protein-Free Diet Aggravates Food Allergy Response via the Consumption of Glycochenodeoxycholic Acid in a Murine Model.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.6c03218}, pmid = {42360286}, issn = {1520-5118}, abstract = {Amino acid-based formulas (AAFs) are increasingly consumed in infants with food allergy (FA), while the effects of their long-term consumption on FA remain poorly known. This study investigated the effects of the long-term consumption of AAFs on FA by subjecting neonatal mice to an amino acid-based diet (AAD). Long-term consumption of AAD exacerbated allergic symptoms, Th2 responses, and mast cell activation and concurrently suppressed the differentiation of CD103[+] DCs and Tregs in the MLN. Furthermore, integrated metabolomics and metagenomics analysis revealed that AAD induced intestinal microbiota dysbiosis and altered the systemic metabolome, characterized by a marked depletion of Bacteroides and glycochenodeoxycholic acid (GCDCA). Critically, oral supplementation with GCDCA effectively attenuated the FA response in AAD-fed mice. In summary, our findings suggest that long-term consumption of AAD aggravates FA via GCDCA depletion, which highlights the necessity to avoid the excessive use of AAFs and positions GCDCA supplementation as a promising therapeutic strategy for FA.}, } @article {pmid42360299, year = {2026}, author = {Drahun, I and Chukwunta, A and Ayodele, A and Pilling, BG and van Herk, WG and Cassone, BJ}, title = {Bacteriomes, cryptic forms and evolution of a common wireworm pest species, Hypnoidus bicolor.}, journal = {Insect molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imb.70054}, pmid = {42360299}, issn = {1365-2583}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Like other insects, coleopterans harbour dynamic bacteriomes that shape core aspects of their life history. The bacteriomes of several wireworm species (Coleoptera: Elateridae) have been described; however, little research has been undertaken to determine the factors that influence their structure and composition. These soil-dwelling larvae of click beetles are significant agricultural pests in the Canadian Prairies, with the most ubiquitous species, Hypnoidus bicolor, delineated into two genetically distinct clades and both sexual and parthenogenetic populations. In this study, we collected 69 H. bicolor adults and larvae from nine populations spanning three Prairie provinces and subjected them to Sanger and 16S rRNA gene sequencing to determine their clade and characterize their bacteriome, respectively. Combined with long-term surveillance, we provide compelling evidence that the parthenogenetic and sexual populations are associated with different clades. Development, sampling location and host genetics all contributed to the plasticity of H. bicolor bacteriomes. These differences are largely attributed to gut bacterial community composition of larvae, whereas, in adults, they appear driven by overall community structure as well as differences in the presence/absence of taxa and within-clade/population variance. Several notable genera emerged from our study, including Alphaproteobacteria and Rickettsiella endosymbionts that predominated in the parthenogenetic clade. Incorporation of this research into integrative pest management and reclassification of H. bicolor into a cryptic species complex is also discussed. Overall, this study advances our understanding of Elateridae bacteriomes, including factors that contribute to their richness and community composition.}, } @article {pmid42360358, year = {2026}, author = {Meier, DV and Greve, A and de Beer, D and Abed, RMM and Woebken, D}, title = {Sulfide-oxidizing potential and hypersalinity tolerance strategies in salt-crust covered coastal microbial mats.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag166}, pmid = {42360358}, issn = {1751-7370}, abstract = {Hypersaline microbial mats are dense microbial ecosystems capable of performing nearly complete element cycling under harsh conditions including near-saturation salinity. Our previous study of salt-crust covered microbial mats showed that oxygenic photosynthesis was inhibited at salt saturation, while phototrophic sulfide oxidation persisted despite well-known sulfide-oxidizing taxa being undetectable. In this study, we analyzed metagenome-assembled genomes (MAGs) from the same mats to identify sulfide-oxidizing taxa and adaptations enabling oxygenic phototrophs to survive salt saturation. We extended the dataset by including morphologically identical mats exposed to lower salinity regimes to identify metabolic capabilities specifically selected for by saturation-level salinity. The phototrophic sulfide oxidation capability was found in nearly all cyanobacterial MAGs, in some Chloroflexota, and in abundant Rhodovibrio populations previously not known to oxidize sulfide. Furthermore, we found clear indications of Haloarchaea-like potassium-based osmoregulation in Bradymonadaceae (Myxococcota) adding another taxon to the few known potassium-accumulating bacteria. Despite lower oxygen concentrations, salt-crust covered mats showed smaller proportions of fermenters and higher proportions of aerobic microorganisms than lower salinity mats. We compared the genetic signatures of hypersalinity and desiccation tolerance in cyanobacterial MAGs from this study to genomes from desiccation-prone environments such as desert soils and small freshwater streams. Genomes of hyperhalophilic cyanobacteria were characterized by lack of certain potassium transporters and catalase genes and presence of additional osmolyte transporter subunits and sulfide-oxidation genes. We hypothesize that during salt saturation the oxidative stress for mat dwelling cyanobacteria is lowered, while the ability to oxidize sulfide provides them with energy when oxygenic photosynthesis is inhibited.}, } @article {pmid42360629, year = {2026}, author = {Liu, KJ and Gao, Y and Yang, X and Xia, Y and Lu, C and Li, ZR and Chu, X and Huang, H and Xu, P and Shi, M and Yuan, K and Yang, H}, title = {Diagnostic Performance and Cost-Effectiveness of BALF mNGS in Older Adults with Pulmonary Infections.}, journal = {Infectious diseases and therapy}, volume = {}, number = {}, pages = {}, pmid = {42360629}, issn = {2193-8229}, support = {KQTD20200820145822023//Shenzhen Science and technology innovation Commission foundation/ ; JCYJ20240813120110015//Shenzhen Science and technology innovation Commission foundation/ ; JCYJ20230807095204008//Shenzhen Science and technology innovation Commission foundation/ ; No. LCYJ2021008//Key Program for Clinical Research at Peking University Shenzhen Hospital/ ; }, abstract = {INTRODUCTION: Pulmonary infections in elderly patients cause high morbidity and mortality. Conventional culture has low sensitivity and slow turnaround, delaying targeted therapy. Metagenomic next-generation sequencing (mNGS) is an emerging technology, but its diagnostic performance and cost-effectiveness are unclear. This study therefore aims to evaluate its diagnostic performance compared to conventional culture in older adults with pulmonary infections and to assess its cost-effectiveness.

METHODS: From March 2020 to March 2023, 522 patients (aged 55-69 years) diagnosed with pulmonary infections were enrolled at Peking University Shenzhen Hospital. Of these, 168 patients underwent simultaneous mNGS and conventional culture testing using bronchoalveolar lavage fluid (BALF) samples, while the remaining 354 patients received culture testing alone. Pathogen detection results were compared to assess the diagnostic performance of mNGS versus traditional culture methods. Additionally, cost-effectiveness analyses of the two diagnostic strategies-as well as the impact of mNGS testing timing post-admission-were conducted in the overall cohort and across stratified subgroups.

RESULTS: Among the 168 patients who underwent both tests, mNGS identified a greater diversity and abundance of microorganisms than culture (overall detection: 89.88% vs. 26.79%; pathogen detection: 67.86% vs. 18.45%, p < 0.001). mNGS testing yielded a net economic benefit of 1202.70 CNY per patient overall and 3831.15 CNY among pathogen-positive cases. Delaying mNGS testing tended to be associated with increased hospitalization length of stay (LOS) and costs, with the most pronounced difference observed around 6 days after admission (p < 0.001). Early mNGS testing (within 6 days of admission) provided a net benefit of 6346.00 CNY.

CONCLUSIONS: BALF-based mNGS showed higher positivity rates and a broader pathogen detection spectrum compared to conventional culture methods in this study. Early implementation of mNGS shows strong potential to guide the treatment of pulmonary infections and reduce healthcare costs for elderly and aging patients.}, } @article {pmid42361430, year = {2026}, author = {Horowitz, ML and Shrestha, A and Feng, KH and Pelton, CA and Wells, R and Allen, RF and Clauss, TM and Stokka, D and Cavin, JM and Walsh, MT and Holmes, EC and Allison, AB}, title = {Viral etiology of orogenital papillomatosis and squamous cell carcinoma in bottlenose dolphins in the southeastern United States.}, journal = {Virology}, volume = {623}, number = {}, pages = {111015}, doi = {10.1016/j.virol.2026.111015}, pmid = {42361430}, issn = {1096-0341}, abstract = {Orogenital papillomatosis and squamous cell carcinoma is an emerging yet poorly understood complex disease of bottlenose dolphins (Tursiops truncatus and T. erebennus), both in the wild and under managed care. Previous studies have indicated a potential role of papillomaviruses and/or herpesviruses in the development of oncogenesis, although unbiased metagenomic approaches to examine the disease-associated virome in biopsied lesions have not been performed. Herein, we determined the viruses present in oral and genital lesions from both wild and managed care bottlenose dolphins from the southeastern United States through deep sequencing. The sampled dolphins were infected with two closely related but phylogenetically distinct lineages of delphinid gammaherpesvirus. Multiple different papillomaviruses were also detected, including a new species and several novel types of Tursiops papillomaviruses. Delphinid gammaherpesviruses were detected more often and at higher levels than papillomaviruses in both wild and managed care dolphins, although co-infections with both viruses were common. Additionally, we demonstrate that oral and genital swabs are an effective method for detecting viral infection in dolphins with or without lesions, providing a simple, non-invasive surveillance tool and an adjunct to surgical tissue biopsies. To build diagnostic tools for further study on viral diseases of bottlenose dolphins, we immortalized primary cells from oral frenulum biopsies via retroviral transduction of the simian virus 40 large T antigen gene, which was confirmed by immunoassays and chromosomal mapping. Elucidating the etiologic agent(s) and malignant transformation process of this important disease of dolphins may ultimately lead to the development of targeted therapeutics and/or preventative recommendations.}, } @article {pmid42361635, year = {2026}, author = {Tian, L and Lu, JN and Zhang, Y and Zhang, Q and Jiang, G and Yin, Y and Li, L and Fei, YH and Yang, Y and Ruan, Z and Guo, Y and Wang, S and Tang, YT and Chao, Y and Qiu, R}, title = {Overlooked dissemination risk of resistomes in mining soil environments.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142779}, doi = {10.1016/j.jhazmat.2026.142779}, pmid = {42361635}, issn = {1873-3336}, abstract = {Global mining significantly alters soil microbial communities and enriches antibiotic resistance genes (ARGs) via metal co-selection. However, the dissemination of mining-associated resistomes into surrounding ecosystems remains poorly understood. We conducted a national-scale metagenomic investigation of 416 soil samples to characterize the mining resistome and its dissemination potential. Mining soils were notably enriched in bacitracin resistance genes. Host analysis revealed that 60% of ARG-carrying genomes in downstream farmland were shared with mining sites, while source tracking indicated that 57% of quinolone resistance genes in farmlands likely originated from mining areas. Bipartite network analysis further supported this resistome connection from mines to agricultural soils. Using an optimized risk assessment framework, we identified 14 high-risk ARGs, 50% of which were previously unreported. These high-risk ARGs exhibited distinct latitudinal distributions, often associated with uncharacterized hosts. This study provides the first systematic, national-scale evidence of ARG dissemination from mining environments to agricultural ecosystems. By identifying overlooked high-risk ARGs, this research fills critical knowledge gaps in evaluating resistomes from extreme environments and offers essential insights for managing ARG dissemination risks.}, } @article {pmid42361757, year = {2026}, author = {Lyu, Y and Bi, X and Tan, Y and Jiang, J and Zhang, Y and Zhou, M and Chen, G and Guo, G}, title = {SANI® process enables sustainable coking wastewater treatment: performance, microbial mechanisms and detoxification.}, journal = {Water research}, volume = {304}, number = {}, pages = {126354}, doi = {10.1016/j.watres.2026.126354}, pmid = {42361757}, issn = {1879-2448}, abstract = {Coking wastewater (CW), characterized by high organic concentration, high toxicity, and poor biodegradability, poses significant challenges for biological treatment. The sulfate reduction-autotrophic denitrification-nitrification (SANI®) process, known for its robustness in treating municipal wastewater with high salinity and low sludge production, has not yet been explored for CW treatment under high-toxicity conditions. This study established a lab-scale continuous-flow SANI system treating real CW at stepwise increasing concentrations (30 %→60 %→100 % of real CW ratio) to investigate toxic pollutants removal performance and sulfur-mediated degradation mechanisms. The SANI process achieved efficient and stable removal of carbon (COD 83.5 %, TOC 93.3 %), nitrogen (NH4[+]-N 97.5 %, TN 85.1 %), and characteristic toxic pollutants (volatile phenols >99 %, SCN[-] >99 %) during 100 % CW treatment, with effluent biotoxicity substantially reduced. 16S rRNA gene sequencing revealed functionally complementary microbial consortia: sulfur-reducing genera (Gudongella, Desulfitobacterium) dominated the anaerobic reactor; mixotrophic denitrifiers (Thauera, Comamonas) enriched in the anoxic reactor; and nitrifiers (Nitrospira) coupled with sulfur-oxidizers (Thiobacillus) prevailed in the aerobic reactor. Metagenomic analysis elucidated complete nitrogen/sulfur metabolic networks and typical toxic pollutant degradation pathways: SCN[-] degradation proceeded via the CNO pathway, while phenol degradation followed the meta-cleavage pathway after hydroxylation. This study pioneers SANI process for sulfur-rich real CW treatment, demonstrating it enables simultaneous removal of carbon, nitrogen, and toxic pollutants-offering a breakthrough low-carbon alternative for industrial wastewater.}, } @article {pmid42361875, year = {2026}, author = {Liu, C and Che, C and Huang, P and Gao, J and Wang, S and Ji, B}, title = {Dual carbon source driven metabolic coupling shapes microalgal-bacterial granular sludge stability.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125119}, doi = {10.1016/j.envres.2026.125119}, pmid = {42361875}, issn = {1096-0953}, abstract = {Microalgal-bacterial granular sludge (MBGS) is a viable technology for wastewater treatment, yet its operational stability is often limited under single-carbon conditions due to metabolic imbalance. In this study, six dual carbon strategies were evaluated to investigate their roles in regulating system stability and pollutant removal. The results showed that carbon source composition strongly influenced reactor performance, potentially by pH buffering, thereby reshaping microenvironmental conditions and microbial community structure. Among all conditions, the acetate-glucose system achieved the highest stability, with simultaneous removal of COD (91.1%), NH4[+]-N (96.8%), and PO4[3-]-P (96.9%). Metagenomic analysis and system performance indicated that proton consumption during acetate assimilation likely offset acidification from glucose fermentation, maintaining a favorable alkaline niche (pH 10.0-10.2) that enriched functional bacteria (e.g., Thauera, 4.1%) and enabled simultaneous nitrogen and phosphorus removal. In contrast, the glycerol-glucose system induced severe acidification (pH < 4.0), which suppressed bacterial activity and shifted the community toward acid-tolerant fungi (e.g., Fusarium, 38.9%), resulting in functional deterioration. These findings suggest that pH buffering likely serves as a key regulatory parameter linking carbon metabolism to system stability. Rational pairing of carbon sources with complementary proton fluxes may provide a practical strategy to enhance MBGS robustness and offers a generalizable framework for carbon-source design in biological wastewater treatment.}, } @article {pmid42361876, year = {2026}, author = {Chen, S and Zhang, C and Li, P and Li, S and Xing, H and Zhao, Z and Zhang, C and Zhou, D and Huo, H}, title = {Tightened Coupling of Organic Nitrogen and Organic Carbon Synthesis Governs Integrity of Soil Organic Matter in Black Soils.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125123}, doi = {10.1016/j.envres.2026.125123}, pmid = {42361876}, issn = {1096-0953}, abstract = {Soil organic matter (SOM) underpins fertility and carbon sequestration in black soils, yet the regulatory role of soil organic nitrogen (SON) in SOM stabilization remains poorly resolved. Herein, a total of 246 cropland black soils samples spanning three SOM gradients (10 g/kg interval) collected before spring plowing were analyzed using integrated multi-spectroscopic techniques and metagenomics to unravel chemical transformations and microbial mechanisms linking nitrogen and carbon processes. Results demonstrated that SOM accumulation drove a compositional transition from labile polysaccharides-C toward persistent alkyl-C, aromatic-C and aromatic-N containing structures. SON emerged as a dominant regulator of both SOM accumulation and stabilization by promoting aromatization and nitrogen incorporation, thereby enhancing aromaticity and structural persistence. Metagenomic evidences revealed intensified microbial coordination between soil organic carbon (SOC) and SON synthesis under high SOM conditions. On average, 64.8% microbial species encoded concurrent capacities for SOC and SON synthesis under favorable SOM enrichment status. 79.4% higher microbial network interaction and 83.3% stronger coupling intensity between SOC and SON synthesis were observed in favorable SOM enrichment status. Above improvements were attributed to coordinated upregulation of five SOC synthesis pathways and six SON synthesis pathways, with increases ranging from 21% to 57.5% and 24% to 99.8%, respectively. Overall, this study demonstrates that SON is not only a passive component but also an active driver that couples microbial carbon-nitrogen metabolism to govern SOM integrity, providing a novel biological perspective for understanding SOM integrity in black soils.}, } @article {pmid42361879, year = {2026}, author = {Ge, Z and Wang, S and Zhang, N and Li, Y and Huang, D and Zhang, J}, title = {Habitat-dependent viral dynamics and auxiliary metabolism in ecological floating beds: implications for biogeochemical function.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125118}, doi = {10.1016/j.envres.2026.125118}, pmid = {42361879}, issn = {1096-0953}, abstract = {Ecological floating beds (EFBs), plant-substrate floating treatment systems, have been widely implemented in aquatic ecological restoration, where microbes play crucial roles in nutrient cycling and material transformation. However, the ecology of viruses in EFBs remains poorly understood. Here, prokaryotic and metagenome-derived viral communities in a full-scale EFB were analyzed over 12 months utilizing 84 samples from biofilms, plant roots, and surrounding water. Viral communities, dominantly by Caudoviricetes (96.7%), exhibited temporal and habitat-dependent responses that contrasted with their prokaryotic hosts. Deterministic processes, primarily temperature and total organic carbon, shaped viral community composition and auxiliary metabolic gene (AMG) repertoires. Temperate viruses were enriched in biofilms and roots (8.91%-13.45%) compared to water (7.75%), indicating distinct interactions with attached prokaryotes and highlighting these niches as potential metabolic hotspots. Virus-host linkage analyses connected viruses to dominant prokaryotes and revealed abundant AMGs (n = 3,703; 238 types), including genes implicated in carbon, phosphorus and sulfur transformations. Furthermore, prokaryotic C/N/P/S-cycling gene repertoires showed stronger coupling in attached habitats, whereas viruses carrying element-cycling AMGs were relatively more abundant in water. These findings provide a genome-resolved view of habitat-dependent viral community structure and auxiliary metabolic potential in EFBs, identifying attached habitats as important compartments for future validation of virus-host interactions and their possible links to restoration-related biogeochemical processes.}, } @article {pmid42361932, year = {2026}, author = {Ying, Y and Zheng, X and Yang, J and Ye, H and Dong, Z and Ji, Y and Li, S and Tan, X and Zhang, W}, title = {Tong-Xie-Yao-Fang Ameliorates IBS-D: Potential Role of Alistipes finegoldii-associated Gut Tryptophan Indole Metabolism.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {122061}, doi = {10.1016/j.jep.2026.122061}, pmid = {42361932}, issn = {1872-7573}, abstract = {Irritable bowel syndrome with diarrhea (IBS-D) is a prevalent chronic gastrointestinal condition characterized by visceral hypersensitivity, low-grade mucosal inflammation, and impaired epithelial barrier integrity. Current therapies remain limited, highlighting the need for more alternative strategies. Tong-Xie-Yao-Fang (TXYF), a classical Chinese herbal formula, has shown clinical efficacy in IBS-D, however, the mechanisms underlying its therapeutic effects remain unclear.

AIM OF THE STUDY: This study aimed to investigate whether and how TXYF exerts therapeutic effects by modulating colonic tryptophan metabolism, with a particular focus on the gut microbiota.

MATERIALS AND METHODS: IBS-D model was induced by combining chemical irritation and wrap restraint stress in C57BL/6J mice, and multi-omics approaches were employed to identify specific microbiota and metabolites modulated by TXYF. The multi-omics findings were further verified in vivo and in vitro.

RESULTS: TXYF treatment significantly alleviated IBS-D symptoms in our model. Non-targeted metabolomics identified the tryptophan-indole pathway as a key axis modulated by TXYF, with indole-3-acetic acid (IAA) emerging as a prominent differential metabolite in colonic tissue. Western blot analysis showed that TXYF activated the aryl hydrocarbon receptor (AhR) in the colon. Integrative metagenomic and metabolomic analyses revealed a strong association between Alistipes finegoldii and colonic indole and IAA levels. Consistent with these findings, transplantation of A. finegoldii combined with tryptophan supplementation, or administration of IAA alone, recapitulated the therapeutic effects of TXYF against IBS-D. In vitro, both IAA and faecal supernatant from TXYF-treated mice protected against tumour necrosis factor-induced epithelial barrier disruption in an AhR-dependent manner.

CONCLUSION: Collectively, the present study suggests that the therapeutic efficiency of TXYF against IBS-D is closely associated with its ability to modify microbiota-derived colonic IAA production, with gut microbiota member Alistipes finegoldii playing a key role in this effect.}, } @article {pmid42361963, year = {2026}, author = {Loc, DH and Sulesco, T and Tóth, GE and Lühken, R and Schmidt-Chanasit, J and Velavan, TP}, title = {First Mosquito-Based Molecular Evidence of Tembusu Virus in Vietnam.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108927}, doi = {10.1016/j.ijid.2026.108927}, pmid = {42361963}, issn = {1878-3511}, abstract = {BACKGROUND: Mosquito borne flavivirus diversity in Vietnam remains incompletely characterized. Tembusu virus (TMUV), an emerging flavivirus associated with ducks and other avian hosts, has been reported in poultry in Vietnam, but molecular evidence from field-caught mosquitoes has been lacking.

METHODS: We screened 10,658 mosquitoes representing four major arbovirus vector species including Aedes aegypti, Ae. albopictus, Culex quinquefaciatus, Cx. tritarniorhynchus, collected across multiple ecological settings in Vietnam. Mosquitoes were grouped into 586 pools and tested using broad range RT-PCR assays targeting flaviviruses and alphaviruses. Positive flavivirus amplicons were subjected to sequencing, and one TMUV positive pool underwent deeper sequencing and phylogenetic analysis.

RESULTS: The Cx. tritaeniorhynchus pool (25 specimens) collected in rural southern Vietnam yielded a TMUV draft genome. In the complete genome phylogeny, the Vietnamese mosquito derived sequence clustered within a distinct monophyletic clade comprising strains from China, Thailand, Taiwan, and Vietnam.

CONCLUSIONS: These findings provide the first mosquito-based molecular evidence of a TMUV related virus in Vietnam and suggest that mosquito surveillance can reveal previously unrecognized viral diversity and transmission patterns.}, } @article {pmid42362546, year = {2026}, author = {Vemuganti, V and Kang, JW and Zhang, Q and McGregor, ER and Hilser, JR and Aquino-Martinez, R and Harding, S and Harpt, JL and Beck, KR and Bussan, H and Kuehn, JF and Deming, Y and Studer, R and Johnson, SC and Asthana, S and Zetterberg, H and Blennow, K and Engelman, CD and Allayee, H and Anderson, RM and Ulland, TK and Bäckhed, F and Bendlin, BB and Rey, FE}, title = {Gut bacterial metabolite imidazole propionate potentiates Alzheimer's disease pathology.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74744-z}, pmid = {42362546}, issn = {2041-1723}, abstract = {The gut microbiome modulates metabolic and neurovascular processes implicated in Alzheimer's disease and related dementias (ADRD), but the underlying mechanisms remain unclear. Here, we identify the bacterial metabolite imidazole propionate (ImP) as a modifier of ADRD pathology. In a cohort of 1196 cognitively unimpaired adults, higher plasma ImP levels were associated with lower preclinical cognitive scores and biomarkers of ADRD, both cross-sectionally and longitudinally. Fecal metagenomic analysis linked putative ImP producers to ADRD phenotypes. Genome-wide integrative analysis revealed a locus on chromosome 12 associated with both plasma ImP levels and AD risk in humans, supporting a host genetic contribution to ImP regulation and a causal role of this metabolite in AD. In mice, chronic ImP administration exacerbated AD-like pathology. ImP impaired brain endothelial barrier and promoted tau hyperphosphorylation in primary neurons, an effect blocked by glycogen synthase kinase-3β inhibition. Together, this study links ImP to hallmarks of neurodegeneration and suggests that targeting ImP may represent a potential strategy to modify ADRD risk.}, } @article {pmid42362550, year = {2026}, author = {Falshaw, N and Ducarmon, QR and King, A and Grundler, F and Mesnage, R}, title = {Remodelling of the gut virome after long-term fasting.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42362550}, issn = {2055-5008}, abstract = {Long-term fasting is a promising strategy to restore metabolic health. Emerging evidence suggests that the gut microbiome may mediate some of fasting benefits, but the role of its viral component remains poorly understood. Using shotgun metagenomic data from a single-arm, monocentric fasting intervention, this study profiled the gut virome (n = 89 individuals, n = 241 samples) before and after 9.8 days of fasting (~ 250 kcal/day) as well as one and three months afterwards. Fasting induced a transient loss of viral diversity and a shift toward increased representation of virulent phages. External dataset validation identified 49 phages showing reproducible directional changes during fasting. Many were linked to bacterial hosts, showing concordant shifts, including depletion of Faecalibacterium-associated phages and enrichment of Bacteroides-associated phages. Cross-domain network analyses revealed denser viral-bacterial networks at the end of fast, with enriched connections to butyrate producers, suggesting phages may participate in the fasting-induced restructuring of microbial networks involving health-associated taxa. Collectively, these findings indicate that fasting remodels the gut virome cross-domain associations through reproducible, functionally relevant phage-host interactions, with reorganisation persisting for up to three months and occurring in parallel with improvements in cardiometabolic markers.}, } @article {pmid42362787, year = {2026}, author = {Sinha, B and Khandeparker, L}, title = {Seasonal variation in plastic-associated biofilm microbial assemblages: a microcosm approach.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {7}, pages = {}, pmid = {42362787}, issn = {1573-2959}, abstract = {Plastic pollution in natural ecosystems creates novel niches, known as the "Plastisphere", that host heterogeneous microbial communities shaped by substrate type and environmental conditions. This study explored the effects of seasonal variation on the plastisphere evolution on different plastic substrates, oxo-degradable carrier bags (Oxo), oxo-degradable garbage bags (Oxo-G), normal plastics (N), and snack packets (Sn) for 30 days in a microcosm experiment using ambient water from the monsoon-influenced Zuari estuary. The results indicated that the early-stage (day 5) plastisphere was dominated by fast-growing r-strategists, such as Alpha- and Gamma-proteobacteria as well as Campylobacterota-related lineages, whereas mature biofilms (day 30) showed increased abundance of secondary colonisers, including Planctomycetota, Actinomycetota, and Bacteroidota. The oxo-degradable plastics emerged as preferred substrates, likely due to their prooxidant-mediated abiotic degradation and the novel nature of the conditioning film. Salinity, in conjunction with nutrient concentrations, emerged as a major driver of microbial abundance in the plastisphere. Though the putative pathogens, such as Vibrio spp. and total coliforms, were present at very low abundance in the aged plastisphere during the SW-Mon and PostM seasons, their persistence indicates their resilience even under nutrient-limited conditions. Although a closed microcosm system probably introduced bottle effects, influencing temporal changes in nutrient levels and microbial abundance, the study provides baseline insights into substrate- and season-driven patterns of plastisphere development. Overall, these findings underscore the dynamic interplay among various factors, including plastic types and seasonal environmental shifts, in shaping plastisphere maturation. This has potential implications for public health and ecosystem functioning in the natural marine environment. Employing functional metagenomics analysis in future in situ studies of plastisphere communities can provide further insights and is a way forward for predicting associated ecological risks.}, } @article {pmid41499025, year = {2026}, author = {Cunanan, DJ and Carandang, THDC and Pilapil, JD and Cunanan, DJ and Mollasgo, AG and Manalo, GNS and Co, GS and Rosch, J and Carroll, K and Notarte, KI}, title = {Nanopore sequencing for microbiological diagnosis of bacterial pneumonia: A systematic review and meta-analysis.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {45}, number = {4}, pages = {1077-1091}, pmid = {41499025}, issn = {1435-4373}, abstract = {PURPOSE: Accurate and timely diagnosis is essential to ensure effective management of bacterial pneumonia to improve patient outcomes. This study aims to evaluate the use of metagenomic nanopore sequencing in the microbiological diagnosis of pneumonia compared to standard diagnostic procedures. METHODS: A comprehensive literature search across multiple databases was performed. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy 2 (QUADAS-2) tool. Pooled sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic odds ratio (DOR), and area under the curve (AUC) were determined. RESULTS: Thirteen studies were included in the systematic review, with eight eligible for meta-analysis. In the microbiological diagnosis of bacterial pneumonia, the overall sensitivity of nanopore sequencing using both MinION and GridION platforms is 86.08% (95% CI 75.96–92.37) while specificity is 84.97% (95% CI 75.94–91.02). Results show a high PPV (85.13%; 95% CI 77.72–90.38) and high NPV (85.27%; 95% CI 76.79–91.01). Nanopore sequencing also has a high diagnostic value based on the computed AUC (0.922) and DOR (40.68; 95% CI 11.22–147.48). Sensitivity analyses suggest a trend toward higher diagnostic accuracy for bacterial pneumonia with the MinION device and lower accuracy with the GridION platform. We also found that accuracy is higher when the focus of diagnosis is ventilator-associated pneumonia (VAP) and when endotracheal aspirate alone is utilized as the sample type. CONCLUSIONS: Nanopore sequencing offers faster, real-time results compared to traditional culture. It also shows higher specificity than short-read metagenomic next-generation sequencing (mNGS), particularly in ventilator-associated pneumonia. Further research is warranted for subgroup analyses to optimize the use of nanopore sequencing in detecting bacterial pneumonia.}, } @article {pmid41511674, year = {2026}, author = {Yin, Q and Mei, X and Ma, Y and Zheng, M}, title = {Central nervous system infections caused by carbapenem-resistant klebsiella pneumoniae after CAR T-cell therapy in a patient with preexisting colonization: a case report and literature review.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {45}, number = {5}, pages = {1491-1499}, pmid = {41511674}, issn = {1435-4373}, support = {81974005//National Natural Science Foundation of China/ ; Y-SYBLD2022MS-0055//the Beijing Xisike Clinical Oncology Research Foundation/ ; 2025AFD777//the Joint Fund for Innovation and Development of Natural 205 Science Foundation of Hubei Province/ ; }, abstract = {OBJECTIVE: To investigate the risk factors for corresponding infections following chimeric antigen receptor (CAR) T-cell infusion in Carbapenem-resistant Enterobacteriaceae (CRE) carriers and to provide insights for managing such cases. METHODS: A retrospective analysis was performed on the clinical presentation, laboratory findings, treatment, and prognosis of a patient with preexisting colonization who developed CRE intracranial infection after CAR T-cell therapy. A systematic review of the literature was conducted to explore optimal antibiotic strategies for CRE-associated central nervous system infections. RESULTS: Carbapenem-resistant Klebsiella pneumoniae was detected in perianal swabs before preconditioning chemotherapy, and the patient subsequently received high-dose corticosteroids for cytokine release syndrome and immune effector cell-associated neurotoxicity syndrome following CAR T-cell infusion. Despite broad-spectrum coverage, recurrent fevers and convulsions ensued. Metagenomic next-generation sequencing of cerebrospinal fluid on day +14 confirmed Kbsiella pneumoniae infection, later identified as a multidrug-resistant strain. Clinical and microbiological clearance was achieved following combination therapy centered on intravenous ceftazidime-avibactam, supplemented with intrathecal polymyxin B, guided by antibiotic susceptibility testing. The patient ultimately died three months later due to lymphoma progression. CONCLUSION: Defining optimal management strategies for CRE carriers is essential to integrate infection risk mitigation into the personalized framework of CAR T-cell therapy.}, } @article {pmid41654923, year = {2026}, author = {Dong, R and Lu, Y and Zheng, J and Zhuang, Y and Ma, Y and Cao, L and Li, Y and Kane, Y and Zhang, C and Li, YY}, title = {First-year dynamics of the plasma virome and cytokine profile in infants born to mothers with syphilis.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41654923}, issn = {1479-5876}, support = {202403AC100011//Key research and development program of Yunnan Province/ ; RLXZ20230001//The "Xingdian Talents" Support Project of Yunnan Province/ ; YWLCYXZX2023300076//The Project of AIDS Bureau of Yunnan Province, the Yunnan Province Clinical Center for Skin Immune Diseases/ ; 2024XKTDYS01//The First-Class Discipline Team of Kunming Medical University/ ; 82203934//The National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The early-life development of the human plasma virome and its immunological implications remain poorly understood. We aimed to explore the dynamic interplay between viral colonization and immune maturation in infancy. METHODS: We conducted a retrospective longitudinal study of the plasma virome and cytokine profile in a cohort of 77 pregnant women with syphilis and their 89 infants. Plasma samples were collected from mothers at delivery and infants at multiple time points (the first day, and at 3, 6, 9 and 12 months of age). Virome composition was characterized via metagenomic sequencing, and 27 cytokine concentrations were quantified using multiplex immunoassays. The impacts of delivery mode, feeding patterns, and anti-syphilitic treatment on the development of plasma virome were investigated. Mother-infant vertical transmission of anelloviruses was validated by phylogenetic analysis with MEGA (v1.2.9). RESULTS: The infant plasma virome was composed mainly of host-associated viruses (42.5%, primarily Anelloviridae) and phages (45.5%). Phages dominated the neonatal plasma virome at birth, but declined accompanied with a rapid expansion of host-derived viruses (96.1% at 12 months) during the first year of life. Human-host viruses were rarely detected in neonates at birth, with their richness and abundance increaing notably after 3 months of life. Shared human-host viruses with mothers were observed at the neonates at birth and increased in virus number and abundance in the first year of life. Mother-to-infant perinatal vertical transmission of anelloviruses were validated by transmission cluster analysis using all identified anelloviruses ORF1 lineages at delivery. Delivery mode, environment exposure, and feeding pattern had no significant effect on virome diversity. Compared with their mothers, the neonates exhibited higher plasma levels of eotaxin, FGF basic, GM-CSF, MCP-1, MIP-1α, MIP-1β, VEGF, IFN-γ, IL-5, IL-9, IL-10, IL-17 A, and TNF-α at birth. During months 3 to 6, infant IL-6 levels declined, while IL-13 and IP-10 levels gradually increased. From month 3, Anelloviridae abundance positively correlated with IL-6, IL-9, IL-10, IP-10, MCP-1, MIP-1α, MIP-1β, and TNF-α in infants, and with MCP-1 and MIP-1α in maternal plasma. CONCLUSION: Our findings reveal dynamic developmental trajectories of the virome and immune system and suggest that early virome exposures may influence immune development, providing a basis for future maternal-child health interventions.}, } @article {pmid41779333, year = {2026}, author = {Hu, Y and Li, A and Qiu, S and Zhu, T and Guo, J and Zhang, W and Zhao, C and Lyu, Y}, title = {Characteristics of Multispecies Bacterial Cocultures for the Removal of Ammonia, Nitrate, and Nitrite from Water.}, journal = {Applied biochemistry and biotechnology}, volume = {198}, number = {5}, pages = {3811-3830}, pmid = {41779333}, issn = {1559-0291}, support = {2025AFD305//Hubei Provincial Natural Science Foundation - Yichang Innovation and Development Joint Fund/ ; }, abstract = {The removal of ammonia, nitrate, and nitrite from wastewater is essential for controlling nitrogen pollution. However, the efficiency of biological nitrogen removal is often limited by the scarcity of highly active bacterial strains. In this study, a coculture system, designated YEM003, was constructed using eight nitrogen-metabolizing bacterial strains isolated from the same activated sludge. YEM003 exhibited robust nitrogen removal performance, effectively eliminating ammonia, nitrate, and nitrite from wastewater under varying oxygen conditions. Metagenomic analysis revealed enrichment of key genes involved in nitrogen metabolism and elucidated nitrogen removal pathways of YEM003. Due to the unbalanced abundance distribution of the eight strains in YEM003, the contributions of each strain to the nitrogen removal metabolism in different wastewaters differed significantly. Overall, YEM003 exhibits comprehensive and efficient biological nitrogen removal capabilities and shows strong potential for application in wastewater nitrogen removal processes.}, } @article {pmid41803286, year = {2026}, author = {Zhu, C and Zhu, Y and Gao, H and Wang, X and Guo, Y and Sun, H and Qi, M and Zhang, B and Hu, Y}, title = {Long-Term Preservation of Humid Earthen Sites: Shelter Efficacy, Essential Oil Dynamics, and Microbial Adaptation.}, journal = {Current microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {41803286}, issn = {1432-0991}, support = {2023C03G1752302//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; }, abstract = {This study evaluates the long-term conservation of humid earthen archaeological sites using protective shelters and plant essential oil treatments at the Laohuling Dam (Liangzhu, China), a UNESCO World Heritage site. Over seven years (2017–2024), structural deterioration, biological colonization, and microbial community dynamics were monitored through field surveys, amplicon sequencing (16 S rRNA and ITS), and shotgun metagenomics. Protective shelters effectively reduced large-scale structural damage and higher-plant colonization; however, enclosed and climate-controlled conditions promoted persistent microbial biofilms in high-humidity zones. Oregano essential oil treatments rapidly eliminated visible biofilms and suppressed recolonization for approximately 6–8 months, but did not prevent long-term microbial recovery. Post-treatment communities shifted from phototrophic and biofilm-forming taxa toward fast-growing, opportunistic heterotrophs, predominantly affiliated with Pseudomonadota. Metagenomic analyses revealed a stable resistome across consecutive treatment years. The high abundance of multidrug resistance genes (e.g., adeF, β-lactam- and CAMP-associated genes) primarily reflected the dominance of Pseudomonadota-related taxa rather than evidence of resistance evolution driven by essential oil application. No significant increase in resistance gene diversity or abundance was detected. These findings demonstrate that sheltering and essential oil treatments are effective short-term conservation tools but reshape microbial succession rather than eliminating biological risks. Long-term preservation of humid earthen sites therefore requires integrated strategies combining microclimate control, low-bioreceptivity materials, and continuous microbial monitoring.}, } @article {pmid41998050, year = {2026}, author = {Gao, Y and Kim, J and Wu, R and Chowdhury, NB and Lee, JY and Nicora, CD and Moore, RJ and Monroe, ME and Jansson, JK and Burnum-Johnson, KE}, title = {Metaproteomics uncovers the functional capacity of a soil microbiome.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47816-9}, pmid = {41998050}, issn = {2045-2322}, support = {Early Career Research Program//U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research/ ; }, abstract = {The soil microbiome plays a vital role in key ecosystem processes, but its functional capacity remains poorly understood. Microbial activities underpin many applications in environmental biotechnology, such as nutrient cycling, contaminant degradation, and the recovery and transformation of minerals and elements. However, analyzing the complex soil metaproteome is challenging. Here, we propose an approach to explore soil metaproteomes, which will improve our understanding of the metabolic potential within the soil microbiome. As a proof of concept, we generated high-quality metaproteomes from native prairie soil using high-resolution tandem mass spectrometry. Over 15,000 peptides were identified using paired metagenomes. By using lowest common ancestor method, the peptides were conservatively assigned to 21 bacterial, fungal, and archaeal phyla or superphyla, including rare soil bacterial phyla such as Candidatus Tectomicrobia, as well as viruses. Functional analysis at the pathway level was performed using complementary KEGG and MetaCyc databases, revealing essential biogeochemical cycles, such as carbon and sulfur cycling. By combining taxonomic and functional analyses, we disentangled the relative contributions of individual soil microbial phylum-level taxon to community metabolic functions. This study highlights the importance of taxon-resolved functional analysis enabled by soil metaproteomics, surpassing the capabilities of other single-omics methods. It offers new insights into how individual microbes function within complex soil microbiomes, paving the way for more targeted microbial strategies to improve system performance in bioeconomy applications.}, } @article {pmid42029951, year = {2026}, author = {Kallistova, A and Savvichev, A and Toshchakov, S and Tutubalina, N and Rusanov, I and Petrova, K and Kadnikov, V and Beletsky, A and Zakharova, E and Ravin, N and Pimenov, N}, title = {Structure and Metabolic Potential of Microbial Communities in High-altitude Lake Enriched with Dissolved Organic Carbon.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {42029951}, issn = {1432-0991}, support = {22-14-00038-C//Russian Science Foundation/ ; 22-14-00038-C//Russian Science Foundation/ ; 22-14-00038-C//Russian Science Foundation/ ; 22-14-00038-C//Russian Science Foundation/ ; }, abstract = {It is evident that climate change is causing glaciers to melt at an accelerated rate. This has a noticeable impact on the hydrological regime of high-altitude lakes, as well as the activity of microbial communities. However, the impact of climate change on microbial processes, abundance and diversity of microbial communities in high-altitude lakes remains to be elucidated. The objective of the study was to evaluate the structure, activity and metabolic capacity of microbial communities inhabiting the high-altitude Caucasus lake. Analytical and radiotracer methods were used together with 16S rRNA profiling, and metagenome analyses. Elevated concentrations of dissolved organic carbon (DOC) were observed in both the water column of the lake (12.2–19.4 mg/l) and the pore water of the sediments (6.3–15.8 mg/l). The intensity of photosynthesis in water column was very low. The bulk of phototrophs concentrated on the sediment surface where we suggest they produce organic matter due to sufficient light penetration and warming of the overlying water. The elevated DOC concentrations facilitated the activity of diverse heterotrophic microorganisms, resulting in oxygen depletion and activation of anaerobic processes in sediments. In case of an increase in the average annual temperature of the region, it is possible to predict the transformation of the lake into a eutrophic meromictic reservoir with constantly anoxic water layers, where sulfate reduction and methanogenesis would assume a pivotal role.}, } @article {pmid42047869, year = {2026}, author = {Gloanec, N and Huré, M and Bailly, L and Petit, É and Loutelier-Bourhis, C and Goux, D and Coëffier, M and Ribet, D}, title = {Pilosibacter rotomagensis sp. nov., a Butyrate-Producing Bacterium Isolated from Human Faeces.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {42047869}, issn = {1432-0991}, support = {SUMONING ANR-22-CE14-0064-01//Agence Nationale de la Recherche/ ; Labex SynOrg ANR-11-LABX-0029//Agence Nationale de la Recherche/ ; ANR-18-EURE-0020 XL CHEM//Agence Nationale de la Recherche (FR)/ ; }, abstract = {Isolating bacteria from the human gut microbiota and analyzing their phenotypes is essential for complementing the data obtained by metagenomics and for characterizing the functions of these microorganisms in human physiology. In this study, we isolated bacteria from the gut microbiota of healthy individuals and identified an uncharacterized bacterial strain that we designated HC1M1C21T. Phylogenetic analyses based on 16S rRNA and whole genome sequences indicated that this strain belongs to the family Lachnospiraceae. The closest relative of strain HC1M1C21T is Pilosibacter fragilis CSJ-4T (97.0% 16S rRNA gene sequence identity). P. fragilis was initially classified in the family Clostridiaceae. Based on our phylogenetic analyses, we propose to transfer the genus Pilosibacter from the family Clostridiaceae to the family Lachnospiraceae. HC1M1C21T has a DNA G + C content of 48.7%. This strain is anaerobic, Gram-stain-positive, non-motile and non-spore-forming. HC1M1C21T cells appear as single rods or chained rods with tapered ends. Optimal growth was observed at 37°C, at pH between 5.7 and 7.0 and at salinity below 10 g/L. HC1M1C21T is a potent butyrate producer. On the basis of these data, HC1M1C21T represents a novel species from the genus Pilosibacter, for which the name Pilosibacter rotomagensis sp. nov. is proposed. The type strain of P. rotomagensis is HC1M1C21T (= DSM 119410T=LMG 33828T).}, } @article {pmid42062386, year = {2026}, author = {Szklenarik, G and Dora, D and Szincsak, S and Acquah, CK and Biswas, A and Horváth, M and Galffy, G and Lohinai, Z}, title = {The gut mycobiome and inter-kingdom microbial networks are linked to COPD severity in lung cancer patients.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47296-x}, pmid = {42062386}, issn = {2045-2322}, abstract = {Chronic obstructive pulmonary disease (COPD) is increasingly recognized as a systemic disorder affecting host–microbiome interactions beyond the airways. Although bacterial alterations in COPD have been documented, the gut mycobiome and its ecological integration with bacterial communities remain unexplored. In this study, we profiled the gut mycobiome of 61 non-small-cell lung cancer (NSCLC) patients stratified by COPD severity using ITS2 sequencing and analyzed 47 overlapping patients with available metagenomic data to construct cross-kingdom bacterial–fungal networks. Alpha diversity, assessed by Shannon, Simpson, and Chao1 indices, did not differ significantly between patients with and without severe COPD. Partial least squares discriminant analysis (PLS-DA) revealed partial separation of the two groups, with COPD severity explaining 6% of overall compositional variance (R[2]=0.06, p = 0.058). COPD-severe patients exhibited a significantly reduced Ascomycota/Basidiomycota ratio (p = 0.039) and lower relative abundance of Mucoromycota. Analysis of compositions of microbiomes (ANCOM) identified Myrothecium and Lasiodiplodia crassispora enriched in severe COPD, while Helotiales_unclassified and Phallus atrovolvatus were more abundant in non-severe cases. Fungal co-occurrence networks demonstrated reduced connectivity and modularity in severe COPD compared with non-severe COPD. Cross-kingdom analyses integrating bacterial genera revealed strengthened Candida–Enterococcus/Clostridium hubs and weakened Faecalibacterium/Roseburia–yeast associations in severe disease. Keystone analysis showed increased centrality for Candida, Aspergillus, Enterococcus, and Clostridium, and decreased centrality for Akkermansia and Roseburia. A compositional balance classifier achieved high discriminatory power (AUC = 0.88) in distinguishing COPD-severe from non-severe patients. These findings indicate that COPD severity is not characterized by major diversity loss but by guild-specific compositional shifts and extensive network rewiring, favoring oxygen-tolerant, opportunistic taxa over short-chain fatty acid–associated commensals.}, } @article {pmid42343068, year = {2026}, author = {He, G and Liu, T and Xing, J and Rao, L and Chen, S and Xie, C and Wei, G and Quan, X}, title = {In Situ Quorum Quenching Effect Induced by Negative Potential on Electro-Conductive Membranes for Membrane Fouling Control in Membrane Bioreactors.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c04557}, pmid = {42343068}, issn = {1520-5851}, abstract = {Membrane fouling is a major impediment to the widespread application of membrane bioreactors (MBRs) for water treatment. In recent years, the electro-conductive membrane bioreactor (E-MBR) has demonstrated efficacy in mitigating membrane fouling. The application of a negative potential to the electro-conductive membrane promotes electrostatic repulsion, effectively displacing negatively charged extracellular polymeric substances (EPS) away from the membrane surface. However, given the established vital role of quorum sensing (QS) in membrane fouling development, the interference of the negative potential on QS-mediated EPS secretion and biofilm formation has been largely overlooked. Herein, we found that the negative potential applied to the electro-conductive membrane could effectively suppress the QS process, thereby inducing the in situ quorum quenching (QQ) effect. The application of negative potential significantly reduced the levels of the signal molecule C14-HSL as well as EPS. Metagenomic analysis indicated that the relative abundance of the "signal transduction mechanism" pathway was suppressed, and the functional genes encoding C14-HSL receptor proteins belonging to "LuxR family" was downregulated in the cake layer of E-MBR. Density functional theory calculations and molecular dynamics simulation results revealed that the application of negative potential enhanced the electrostatic repulsion between the membrane and C14-HSL and induced the conformational changes of the LuxR protein, which synergistically induced the in situ QQ effect. This study provides a novel perspective on the antifouling mechanism in E-MBR.}, } @article {pmid42343220, year = {2026}, author = {Nichols, H and Molokin, A and Davies, CP and Maloney, JG}, title = {Exploring shotgun metagenomic data to detect microeukaryotic pathogens in wildlife.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05298-9}, pmid = {42343220}, issn = {1471-2180}, support = {8042-32000-112-00-D//USDA, ARS/ ; }, abstract = {BACKGROUND: Microeukaryotic parasites of the intestinal tract are an understudied group of organisms that infect humans and many other animals. Targeted sequencing methods focused on individual loci are usually employed for detection of these parasites, making comprehensive studies of microeukaryotic parasite diversity within hosts or other systems difficult. Exploratory approaches such as shotgun metagenomic sequencing to survey the diversity of microeukaryotic parasites in new and existing datasets are not well developed.

RESULTS: Utilizing existing datasets from 12 goose fecal samples, we explored some of the benefits and challenges of using shotgun metagenome sequencing to detect microeukaryotic parasites. We demonstrated the importance of careful curation of read classification data to avoid erroneously linking pathogens to hosts or environments as unsupported classifications were common in the data and varied widely depending on analysis parameters. However, we were able to establish strong support for the presence of sequences of Eimeria and Enterocytozoon bieneusi. In addition, examination of trichomonad reads indicated that parasite reads mapping to human pathogens unlikely to colonize geese may in fact represent cryptic microeukaryotic species that are not included in existing curated databases opening new potential avenues of study.

CONCLUSIONS: Taken together these findings support the idea that exploring microeukaryotic parasite diversity within shotgun metagenomic datasets can be beneficial to our understanding of the presence and diversity of these organisms in wildlife hosts.}, } @article {pmid42343233, year = {2026}, author = {Suenaert, P and Segers, A and Rymenans, L and Devroye, H and Moll, JM and Cani, PD and de Vos, WM}, title = {Effect of pasteurized Akkermansia muciniphila MucT on insulin sensitivity, body composition, and GLP-1 production in subjects with metabolic syndrome: impact of low baseline gut Akkermansia levels.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2690689}, doi = {10.1080/19490976.2026.2690689}, pmid = {42343233}, issn = {1949-0984}, mesh = {Humans ; *Metabolic Syndrome/metabolism/microbiology/therapy ; Female ; Middle Aged ; *Glucagon-Like Peptide 1/metabolism ; Male ; *Insulin Resistance ; Double-Blind Method ; *Probiotics/administration & dosage ; *Body Composition ; Adult ; Akkermansia ; *Verrucomicrobia ; Gastrointestinal Microbiome ; Pasteurization ; Prediabetic State/metabolism ; Aged ; }, abstract = {Pasteurized Akkermansia muciniphila MucT was found to improve barrier function in preclinical models and a proof-of-concept study in obese and prediabetic adults. Here, we describe the results of a double-blind placebo-controlled multicenter (Ireland and Germany) trial in 142 adults with metabolic syndrome, with or without prediabetes. The primary endpoint of whole-body insulin sensitivity (Matsuda index) did not differ after 4-months of daily administration of capsules containing 30 billion cells of pasteurized A. muciniphila MucT compared to placebo in the intention-to-treat subjects. Subsequent exploratory analyses showed that 3-months intake of pasteurized A. muciniphila MucT already improved HOMA-based hepatic insulin sensitivity in prediabetic (12%; p = 0.05) and 63-y-or-older-age subgroups (p = 0.05) while increasing post-OGTT excursion of the insulinotropic hormone glucagon-like peptide 1 (GLP-1) over placebo (p < 0.01). Further analysis of the gut microbiota by deep metagenomic analysis showed minor effects of the intervention but revealed that the baseline microbial composition differed from that in matched healthy adults. We found that participants with low baseline Akkermansia gene counts experienced significant health improvements and GLP-1 excursion after 3-months of treatment with pasteurized A. muciniphila MucT over the placebo. These benefits included improved insulin sensitivity (as shown by Matsuda and HOMA-S indices) and GLP-1 excursion (post-OGTT) (p < 0.05), reductions in body weight (p = 0.06) and decreased trunk fat (p < 0.05). In conclusion, daily supplementation with pasteurized A. muciniphila MucT has the potential to improve health markers in overweight or obese normo- or dysglycemic adults with the most significant improvements in subjects with low baseline intestinal Akkermansia levels, who are apparently truly in need of this intervention. Clinical trial registration no.: NCT05114018 clinicaltrials.gov.}, } @article {pmid42343345, year = {2026}, author = {Huang, H and Ye, X and Gu, D and Huang, E and Yu, X and Ai, L and Deng, J and Guo, P and Liu, H and Chen, Y and Wang, R and Luo, Y and Chen, P}, title = {Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03786-0}, pmid = {42343345}, issn = {1465-993X}, support = {2024ZD0533100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2022B1111020003//2021 Guangdong Province Key Areas Research and Development Plan "Biosafety Technology" Key Project/ ; 2023P-TS46//Featured Clinical Technique of Guangzhou/ ; 0720240122//Guangdong Provincial Center for Disease Control and Prevention Supports Talent Projects/ ; }, abstract = {BACKGROUND: Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) improves pathogen detection in severe pneumonia-related sepsis, but sampling is invasive and prone to false-positive results. Blood is easier to obtain, and broad-spectrum targeted NGS (tNGS) of microbial cell-free DNA may offer a practical alternative to BALF-based testing. We evaluated the diagnostic and prognostic value of blood-based bstNGS.

METHODS: In this retrospective cohort, 122 adults with suspected severe pneumonia-related sepsis and paired BALF and blood samples underwent BALF-mNGS, blood-bstNGS and blood-mNGS. Pathogens were adjudicated using a composite clinical reference. We assessed blood-BALF concordance, compared diagnostic performance across methods, and examined whether blood-bstNGS could down-weight likely false-positive BALF-only detections and stratify prognosis.

RESULTS: BALF-mNGS identified 414 microorganisms; 51% were adjudicated as causative or possibly causative, corresponding to 85.24% of patients. Among these pathogenic microorganisms, blood-bstNGS detected 45.02%, significantly more than blood-mNGS (22.27%), and nearly all pathogens detected by blood-mNGS were also detected by blood-bstNGS. Against the clinical reference, blood-bstNGS showed higher sensitivity (63.46%) than blood-mNGS (35.58%), conventional microbiological tests (CMTs) (49.04%), and blood culture (9.62%). Organisms detected only in BALF but not in blood were less likely to be classified as causative. Patients with concordant blood-bstNGS and BALF-mNGS profiles had significantly lower 30-day and 90-day mortality.

CONCLUSIONS: In severe pneumonia-related sepsis, blood-bstNGS provides sensitive, non-invasive pathogen detection. It acts as a complementary tool rather than a replacement for BALF-mNGS, offering an important diagnostic alternative when BALF is unavailable and improving specificity and prognostic utility when used in combination.}, } @article {pmid42343457, year = {2026}, author = {Wang, C and Li, S and Liu, Y and Zhao, X and Wang, F and You, Y and Zhao, X}, title = {Temporal dynamics of rhizosphere microbiome assembly and carbon-phosphorus coupling in poplar-medicinal plant intercropping systems.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02453-2}, pmid = {42343457}, issn = {2049-2618}, abstract = {BACKGROUND: Intercropping can reshape the rhizosphere microbiome, but how specific companion plants influence nutrient cycling and host growth remains unclear. We proposed that intercropping poplar with medicinal plants creates distinct rhizosphere niches that select for microbial communities with distinct functional potential, thereby improving tree nutrition.

RESULTS: Intercropping significantly promoted poplar growth, with increases in diameter at breast height (DBH) of 15.33%, 14.3%, and 15.23% in systems with Anemarrhena asphodeloides, Belamcanda chinensis, and Saposhnikovia divaricata, respectively. Intercropping did not change microbial alpha diversity but led to plant-specific shifts in beta diversity with clear seasonal dynamics. Metagenomic analyses revealed corresponding shifts in the functional potential of microbial communities related to carbon (C) and phosphorus (P) cycling, including genes such as frdC, aldB, ppk2, and phnH. Intercropping, particularly with S. divaricata, was associated with an increased genetic potential for microbial C metabolism and​ a heightened potential for P solubilization. These co-occurring shifts in genetic potential were correlated with greater P accumulation in poplar leaves. Network analysis showed distinct temporal microbial co-occurrence patterns across intercropping treatments, with A. asphodeloides supporting the most interconnected community linked to P mobilization. Three bacterial genera (Priestia, Pseudomonas, Acinetobacter) were strongly associated with key soil nutrient pools. Re-inoculation experiments confirmed their functional roles: Priestia sp. increased N and P retention in the rhizosphere; Pseudomonas sp. promoted plant growth, suggesting a role in​ stimulating plant secondary metabolism; and Acinetobacter sp. enhanced organic C mineralization.

CONCLUSIONS: Intercropping with specific medicinal plants structures the rhizosphere microbiome through niche differentiation. This restructuring leads to distinct patterns of microbial functional potential, centered on C and P metabolism, which correlate with improved poplar nutrient acquisition and growth. Our findings, integrating metagenomic inference with experimental validation, provide a framework for selecting companion plants to steer the rhizosphere microbiome toward beneficial functional outcomes in agroforestry systems. Video Abstract.}, } @article {pmid42343580, year = {2026}, author = {Cuau, M and Avalon, NE and Ryu, B and Glukhov, E and Almaliti, J and Rego, A and Teixeira, TR and Shingyoji, M and L De Souza, M and Trinidad-Javier, A and Kumpornsin, K and Chen, J and McNamara, CW and Caffrey, CR and Winzeler, EA and Vasconcelos, VM and Leão, PN and Gerwick, WH}, title = {AI-Accelerated Structure Elucidation of Boavistamides A-C, Cyclic Depsipeptides from a Marine Filamentous Cyanobacterium Collected in Cabo Verde.}, journal = {Journal of natural products}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jnatprod.6c00391}, pmid = {42343580}, issn = {1520-6025}, abstract = {Boavistamide A (1), a new alkyne-containing cyclic depsipeptide featuring the rare 3-amino-2-methyl-7-octynoic acid (AMOYA) moiety, was discovered along with two structurally related analogs, boavistamides B and C (2 and 3), from a filamentous marine cyanobacterium collected on Boa Vista Island, Cabo Verde. Their isolation was guided by antiplasmodial activity, GNPS MS/MS molecular networking, LC-MS profiling, and dereplication using the MarinLit database. The planar structures of boavistamides A-C (1-3) were elucidated through comprehensive HRMS and 1D/2D NMR analyses, with annotation support from AI-based tools SMART-NMR 2.1 and DeepSAT. The absolute configurations were established using Marfey's analysis and l-Phe-OMe coupling, complemented by NMR-based conformational studies. Boavistamides A and B exhibited moderate antiplasmodial activity with no mammalian cell cytotoxicity. Microscopic observations and metagenomic binning identified the producer strain as belonging to the genus Okeania (Microcoleaceae). These results expand the chemical diversity of AMOYA-containing cyanobacterial metabolites and highlight the utility of integrated metabolomics and AI-assisted workflows for natural product discovery from environmental samples.}, } @article {pmid42343765, year = {2026}, author = {Qiu, X and Lei, Z and Wang, J}, title = {[Effects of graphene sol on the root growth of tomato seedlings and the rhizosphere soil microbiota].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {42}, number = {5}, pages = {2103-2113}, doi = {10.13345/j.cjb.250783}, pmid = {42343765}, issn = {1872-2075}, support = {Y2022036//the Youth Innovation Promotion Association CAS/ ; }, mesh = {*Solanum lycopersicum/growth & development/drug effects ; *Plant Roots/growth & development/drug effects ; *Seedlings/growth & development/drug effects ; *Rhizosphere ; *Soil Microbiology ; *Graphite/pharmacology ; *Microbiota/drug effects ; Soil/chemistry ; Nitrogen/metabolism ; }, abstract = {Graphene exhibits broad application potential in agriculture due to its unique physical and chemical properties. In home gardening, low survival rates of seedlings during the early transplanting stage represent a common challenge, yet whether graphene can ameliorate this problem remains underexplored. This study analyzed the root growth rate, soil nutrients, and soil microbiota of tomato seedlings in response to graphene sol treatment. The results revealed that graphene sol at concentrations of 50 mg/L and 100 mg/L promoted root growth, while that at higher concentrations exhibited inhibitory effects. Furthermore, all tested concentrations of graphene sol led to a decrease in soil organic matter content and an increase in available nitrogen content. Metagenomic sequencing revealed that 50 mg/L and 100 mg/L graphene sol treatments enhanced the abundance of soil microorganisms that promote humus and organic matter decomposition, participate in soil nitrogen cycling, and mediate heavy metal metabolism. In conclusion, appropriate concentrations of graphene sol can improve the root growth, increase the soil nitrogen availability, and enrich specific beneficial microorganisms of tomato seedlings during the early transplanting stage. These findings provide a theoretical reference for the rational application of graphene-based materials in home gardening.}, } @article {pmid42343869, year = {2026}, author = {Liang, P and Zhang, X and Cai, S and Hu, Z and Dong, L}, title = {Invasive aspergillosis in autoimmune inflammatory rheumatic diseases: epidemiology, risk factors, diagnosis, management and challenges.}, journal = {Annals of medicine}, volume = {58}, number = {1}, pages = {2685285}, doi = {10.1080/07853890.2026.2685285}, pmid = {42343869}, issn = {1365-2060}, mesh = {Humans ; *Rheumatic Diseases/immunology/complications/drug therapy/epidemiology ; Risk Factors ; *Autoimmune Diseases/immunology/complications/drug therapy/epidemiology ; Aspergillus/immunology/isolation & purification ; Immunosuppressive Agents/adverse effects ; Immunocompromised Host ; *Opportunistic Infections/epidemiology/diagnosis/immunology ; Antifungal Agents/therapeutic use ; *Invasive Pulmonary Aspergillosis/epidemiology/diagnosis ; Aspergillosis/diagnosis/epidemiology ; }, abstract = {BACKGROUND: Invasive aspergillosis (IA) is a life-threatening opportunistic fungal infection caused by Aspergillus species. In recent years, IA appears to have become more frequently reported among patients with autoimmune inflammatory rheumatic diseases (AIIRD), likely reflecting the broader use of immunosuppressive therapies, with incidence in high-risk AIIRD subgroups reported to reach approximately 6.7% in selected cohorts.

OBJECTIVE: This review aims to summarize the current evidence on the epidemiology, susceptibility mechanisms, risk factors, clinical presentation, diagnosis, and management of IA in AIIRD, and to outline the clinical practical challenges in this population.

METHODS: This narrative review was informed by a structured literature search of PubMed, Embase, Web of Science, and Google Scholar for studies on IA in AIIRD published up to August 2025.

RESULTS: IA in AIIRD patients generally appears to arise from multiple interacting factors, including compromised host immunity, immunosuppressive therapy, the underlying rheumatic disease itself, comorbidities, and environmental exposures. Aspergillus infection and the resulting anti-Aspergillus immunity may also induce or exacerbate autoimmune inflammation. Invasive pulmonary aspergillosis is the most commonly reported manifestation, typically presenting with nonspecific respiratory symptoms, and disseminated infection tends to occur in the setting of profound immunosuppression. Early, integrated microbiologic testing (e.g. serum or bronchoalveolar lavage galactomannan, culture, polymerase chain reaction, and next-generation sequencing) together with serial imaging examination may facilitate earlier detection and guides care. Although robust AIIRD-specific evidence remains limited, current practice generally favour a multidisciplinary, individualized approach incorporating timely antifungal therapy and careful modulation of immunosuppression. Reported mortality remains high, ranging from 25% to 85% across AIIRD cohorts, particularly when diagnosis and treatment are delayed.

CONCLUSIONS: IA is a serious and likely under-recognized infection in AIIRD patients. Multiple determinants appear to increase infection risk, and symptoms and imaging manifestations can mimic rheumatic disease activity, potentially contributing to diagnostic delay. Current epidemiological and clinical data on AIIRD-IA remain limited, and further studies are needed to refine risk stratification, establish diagnostic criteria tailored to AIIRD patients, and inform more evidence-based management strategies.}, } @article {pmid42343917, year = {2026}, author = {Krasaesin, A and Wongbanthit, Y and Chaiboonyarak, T and Wang, DH and Alinejad-Rokny, H and Samaranayake, L and Pongpanich, M and Porntaveetus, T}, title = {Shotgun metagenomic profiling reveals ecological and functional alterations of the oral microbiome in craniosynostosis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2687219}, pmid = {42343917}, issn = {2000-2297}, abstract = {OBJECTIVE: To elucidate the microbial drivers underlying of craniosynostosis (CS) , which involves premature suture fusion and secondary dentofacial malformations likely to increase dental disease burden.

METHODS: Shotgun metagenomic sequencing of supragingival plaque from 44 participants (22 CS patients and 22 matched healthy controls, aged 6-17 years) were performed, following by bioinformatics evaluation.

RESULTS: Beta diversity demonstrated significant differences between groups (p < 0.01), whereas alpha diversity trended lower in the CS cohort. Taxonomic profiling revealed a dysbiotic signature in CS with high caries burden, defined by the enrichment of saccharolytic and anaerobic taxa (Scardovia, Actinomyces sp. oral taxon 448, Selenomonas sp. F0473, and Treponema lecithinolyticum)) alongside reduced health-associated genera like Haemophilus and Neisseria. Functional pathway analysis indicated metabolic remodeling, with upregulated fructan biosynthesis and starch degradation III pathways, consistent with caries-active biofilms.

CONCLUSION: These findings demonstrate that orofacial anomalies in CS favor the assembly of an acidogenic, virulent plaque biofilm. The first shotgun metagenomic profile of the oral microbiome in CS establishes a foundation for future investigations. Furthermore, clinical management of CS should extend beyond structural correction to incorporate microbiological monitoring and preventive strategies, reducing the elevated risk of dental disease in this vulnerable population.}, } @article {pmid42343927, year = {2026}, author = {González-Ramírez, IS and Song, MJ and Mehlferber, EC and Mishler, BD}, title = {Off-target metagenomics: Leveraging whole genome sequencing to study the bacteriome of the liverwort Calasterella californica.}, journal = {Applications in plant sciences}, volume = {14}, number = {3}, pages = {e70064}, pmid = {42343927}, issn = {2168-0450}, abstract = {PREMISE: The recovery of non-target organism reads, especially when whole organisms are sampled, constitutes a great opportunity for studying microbial communities. The increase in whole genome sequencing feasibility and the development of new marker-based pipelines enable the use of short reads to study bacterial communities associated with organisms.

METHODS: We utilized population genomic data of the liverwort Calasterella californica obtained through the California Conservation Genomics Project to characterize the composition of its associated bacterial communities and explore its variation across the geographic space.

RESULTS: The bacterial communities associated with C. californica were dominated by the methanotroph Methylobacterium and other Hyphomicrobiales, a group that includes well-known plant symbionts. While diversity metrics of bacteria composition were similar across localities, we found significant differences in the relative abundance of a few taxa across California regions, likely driven by differences in precipitation and temperature seasonality.

DISCUSSION: Our results support previous observations that liverwort bacterial communities are not randomly assembled, suggesting a potential role of the plant in determining community composition, an emerging pattern that deserves more attention. The novel off-target metagenomics approach can be applied to any population-level resequencing where whole organisms are sequenced, opening the door to exciting avenues of microbiome research using repurposed data from landscape genomics.}, } @article {pmid42343969, year = {2026}, author = {Schaerer, LG and Anderson, RS and Chan, J and De Long, SK}, title = {Acetate to caproate: metagenomic insights into functional shifts in a methane-arrested anaerobic bioreactor.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag035}, pmid = {42343969}, issn = {2633-6685}, abstract = {Methane-arrested anaerobic digestion (AAD) is a waste management strategy that produces carboxylic acid precursors to industrial products (fuels, bio-based polymers, and pharmaceuticals) from organic wastes. A major challenge preventing application of AAD is highly variable product profiles resulting from an inability to control the microbial communities underlying waste decomposition and product biosynthesis. Over time, lactic acid bacteria (LAB) often dominate AAD bioreactors and overproduce shorter chain acids causing acidosis. Here an AAD bioreactor where caproic acid production increased from an average of 3.9 g/l to an average of 12.3 g/l when the feedstock was switched from manure and paperboard to food waste. Time series shotgun metagenomics is used to investigate how microbial dynamics drive performance shifts. The dominant LAB shifted from Lactobacillus amylovorus spp. to Lactiplantibacillus pentosus spp. following the feedstock switch, corresponding with increased diversity and relative abundance (26.2%) of Caproicibacter spp. (putative chain elongator). Additionally, L. amylovorus MAGs encoded biosynthesis genes to produce the bacteriocin helveticin often produced by LAB to target closely related species. Lactiplantibacillus pentosus MAG.84 encodes bacteriocin-degrading enzymes and helveticin resistance genes, suggesting putitive mechanisms for bacteriocin resistance. These results suggest that bacteriocins may be an underappreciated mechanism for shaping microbial community dynamics in AAD.}, } @article {pmid42343970, year = {2026}, author = {Das, R and Kumar, R and Tamang, B}, title = {Microbial community structure, functional potential, probiotic signatures, and MAG reconstruction of fermented bamboo shoots from Northeast India.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag032}, pmid = {42343970}, issn = {2633-6685}, abstract = {Fermented bamboo shoot (FBS) products are widely consumed traditional foods across the Northeast region (NER) of India, yet their microbiome structure, functional capacity, biosynthetic potential, and safety attributes remain insufficiently explored. Here, comparative shotgun metagenomics of ten traditional FBS products from six NER states was used to address these gaps integrating previously generated metagenomic data from Tripura with newly generated datasets from Manipur, Meghalaya, Arunachal Pradesh, Nagaland, and Sikkim thereby bringing the total number of samples to 24. Taxonomic profiling revealed a predominance of lactic acid bacteria, primarily members of Lactiplantibacillus, Levilactobacillus, Lactobacillus, Lactococcus, and Pediococcus, with pronounced product- and region-specific community signatures. Functional annotation demonstrated predominance of genes involved in carbohydrate metabolism, stress response, quorum sensing, ABC transporters, vitamin biosynthesis, and energy metabolism, supporting strong probiotic-associated functional potential across FBS types. AntiSMASH analysis enabled the identification of diverse biosynthetic gene clusters (BGCs) responsible for the production of various secondary metabolites, including bacteriocins, non-ribosomal peptides, terpenes, and siderophores, with higher biosynthetic diversity observed in Mesu (Sikkim), Tuaithar (Manipur), Lung-Seij (Meghalaya), and Bastenga (Nagaland). Antimicrobial resistance (AMR) profiling revealed a generally low resistome burden, dominated by intrinsic resistance determinants, with FBS Sikkim and Tripura exhibiting the lowest AMR prevalence among all products. High-quality metagenome-assembled genomes affiliated with Lactiplantibacillus plantarum, Lactobacillus acetotolerans, and Pediococcus pentosaceus exhibited conserved probiotic traits, carbohydrate-active enzymes, biosynthetic pathways, and a limited presence of mobile genetic elements. Overall, the microbiome-based comparative analysis provides a framework for understanding the microbial community structure and functional potential across the NER, demonstrating broad probiotic potential and biosynthetic richness, with mesu samples from Sikkim showed a comparatively consistent distribution of functional pathways, biosynthetic gene clusters, and AMR-related features relative to the other FBS samples analysed.}, } @article {pmid42343982, year = {2026}, author = {van Mourik, DJM and Balvers, M and Jansen, VLBI and de Jonge, PA and Coppens, M and Nieuwdorp, M and Middeldorp, S and Eikenboom, JCJ and Voorberg, J and van Mens, TE}, title = {Cross-Reactivity of Antiphospholipid Antibodies with Gut Commensal Proteins in Antiphospholipid Syndrome.}, journal = {TH open : companion journal to thrombosis and haemostasis}, volume = {10}, number = {}, pages = {a28685248}, pmid = {42343982}, issn = {2512-9465}, abstract = {BACKGROUND: Antiphospholipid syndrome (APS) is an autoimmune disease characterized by the persistent presence of antiphospholipid antibodies (aPL), mainly targeted against β2 glycoprotein 1 (β2GP1). The autoimmune response to β2GP1 is aimed at several B-cell and T-cell epitopes. Molecular mimicry of these epitopes by gut commensal proteins, so-called mimotopes, causing cross-immunization, might contribute to the formation of aPL.

OBJECTIVE: To study the potential role of gut microbiome cross-immunization in APS by examining cross-reactivity of aPL with gut commensal mimotope-containing proteins.

METHODS: Fecal microbial metagenome of APS patients was determined using shotgun sequencing. An in-house developed in silico pipeline was used to identify gut commensal proteins that show sequence homology with known β2GP1 B and T cell epitopes in the metagenomic data. An enzyme-linked immunosorbent assay was used to test the identified microbial proteins for IgG cross-reactivity, with plasma of 21 APS patients and 17 control participants.

RESULTS: The in silico pipeline resulted in the identification of six gut commensals with a B cell and T cell β2GP1 epitope homologue. Of these, YjjG family noncanonical pyrimidine nucleotidase, one of the candidate-β2GP1 B cell mimicking proteins, showed significantly increased IgG reactivity in APS patients compared to control participants, as well as higher binding of a specific anti-β2GP1 monoclonal antibody than a negative control.

CONCLUSION: Our study shows reactivity of IgG antibodies to YjjG family noncanonical pyrimidine nucleotidase from Roseburia amylophila in APS patients. Insights into the origins of antibody formation may yield new therapeutic targets for improvement of APS treatment.}, } @article {pmid42344006, year = {2026}, author = {Tepson, JA and Agyirifo, DS}, title = {Microbial Ecology at the Nexus of Food Safety and Biotechnology With Ecological Mechanisms, Risks, and Emerging Innovations.}, journal = {International journal of food science}, volume = {2026}, number = {}, pages = {6618960}, pmid = {42344006}, issn = {2314-5765}, abstract = {Food systems are complex microbial ecosystems in which microorganisms play dual and often contrasting roles as agents of foodborne contamination and as essential drivers of food production and biotechnological innovation. Microbial ecology provides an integrative framework for understanding how microbial interactions, environmental conditions, and human interventions shape food safety outcomes and technological processes. This narrative integrative review is aimed at synthesizing current literature on microbial ecology at the nexus of food safety and food biotechnology and at identifying key research gaps and future directions. In this study, peer-reviewed journal articles addressing microbial interactions, contamination pathways, and ecological mechanisms relevant to food safety and biotechnology published between 2015 and 2025 were retrieved from major scientific databases and were synthesized using a narrative integrative approach. The review highlights ecological factors including microbial competition, stress adaptation, and biofilm formation across pre- and postharvest environments. At the same time, these same ecological principles are harnessed in food biotechnology to drive controlled fermentations, enhance shelf life through biopreservation, develop functional probiotics and enzymes, and engineer microbial systems via synthetic biology. Advances in high-throughput sequencing technologies, including whole genome sequencing, metagenomics, and multiomics integration, are identified as transformative tools for linking food-associated microbial community structure to functional outcomes. Despite significant progress, challenges remain in translating ecological insights into reliable industrial and regulatory practices due to microbial complexity, data integration limitations, and safety considerations. The review positions microbial ecology as a strategic framework for advancing food safety, biotechnological innovation, and sustainable food systems.}, } @article {pmid42344497, year = {2026}, author = {Yu, W and Yang, P and Ding, M and Guo, L and Liu, Y and Zhou, D and Gu, C}, title = {Acute pancreatitis temporally associated with COVID-19 pneumonia in a patient with post-tuberculosis chronic pulmonary aspergillosis: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1828229}, pmid = {42344497}, issn = {2296-858X}, abstract = {This report describes a 59-year-old woman with a history of malignancy and post-tuberculosis lung disease complicated by chronic cavitary pulmonary aspergillosis. She was admitted with worsening hemoptysis and underwent bronchial artery embolization. However, she subsequently developed massive post-procedural hemoptysis, requiring mechanical ventilation. Sputum metagenomic next-generation sequencing detected SARS-CoV-2 and bacterial pathogens, prompting Paxlovid treatment for COVID-19 pneumonia. While her respiratory symptoms improved, epigastric pain developed. Based on elevated serum amylase/lipase and CT-confirmed peripancreatic inflammation, she was diagnosed with acute pancreatitis. One year later, pulmonary tuberculosis and liver metastasis recurred. This case highlights acute pancreatitis temporally associated with COVID-19 pneumonia in a patient with multiple competing risk factors. Further, this case underscores the diagnostic complexity of structural lung disease with overlapping infections such as COVID-19 and stresses on the need for long-term surveillance.}, } @article {pmid42344668, year = {2026}, author = {Huang, F and Zhang, Z and Zhao, Y and Ye, S and Gan, M and Li, X and Zhang, Y and Chen, L and Zhang, Y and Chen, L and Wang, T and Huang, J and Zhang, X}, title = {Altitude-Associated Divergence of the Gut Microbiome in Endangered Forest Musk Deer: Evidence From Integrated Metagenomics, Metabolomics, and Culturomics.}, journal = {Evolutionary applications}, volume = {19}, number = {6}, pages = {e70285}, pmid = {42344668}, issn = {1752-4571}, abstract = {High-altitude environments expose mammals and their gut symbionts to multifaceted stressors-hypoxia, cold, and intense UV radiation. Whether gut microbial communities undergo compositional restructuring in response to these stressors, and whether such restructuring carries translational value for captive conservation, remain unresolved questions. Here, we integrated deep shotgun metagenomics (≥ 15 Gb per sample), untargeted fecal metabolomics, and culturomics in 75 captive forest musk deer (Moschus berezovskii Flerov, 1929) housed at high altitude (~3900 m) and low altitude (~1450 m) facilities under uniform husbandry. Neutral community modeling showed a greater contribution of deterministic processes at high altitude (only 34.3% of species conformed to neutral expectations vs. 89.3% at low altitude), consistent with stronger environmental filtering. At high altitude, we observed enrichment of a functionally coherent guild of short-chain fatty acid (SCFA)-producing bacteria-centered on Flavonifractor plautii, Intestinimonas butyriciproducens, and Enterococcus faecium-that formed antagonistic co-occurrence networks with opportunistic pathogens including Clostridioides difficile and Campylobacter species, mirroring SCFA enrichment in phylogenetically diverse high-altitude mammals. Fecal metabolomics revealed coordinated shifts in urolithin biosynthesis, branch-specific regulation of the tryptophan-kynurenine pathway, and energy metabolism remodeling, all robustly predicted by microbiome composition via neural network modeling. Culturomics yielded seven safety-validated isolates with confirmed gastrointestinal stress tolerance and broad-spectrum pathogen-antagonistic activity in vitro. These findings provide an actionable framework for altitude-informed facility siting, fecal microbiota transplantation (FMT) donor selection, host-derived probiotic development, and non-invasive health surveillance in captive endangered species, and are broadly transferable to other taxa facing microbiome-associated disease pressure in captivity.}, } @article {pmid42344740, year = {2026}, author = {Zhang, X and Huo, H and Hu, L and Yang, F and Hu, X and Deng, Y and Feng, C and Wang, H and Huo, J}, title = {Dietary Lonicera japonica supplementation modulates cecal gut microbial composition and metabolomic profiles in weaned piglets.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1804735}, pmid = {42344740}, issn = {2297-1769}, abstract = {Weaning is a critical developmental stage in piglets and is often associated with intestinal dysbiosis, metabolic disturbances, and impaired gut barrier function. Phytogenic feed additives have emerged as promising natural alternatives to antibiotics for improving gut health. Lonicera japonica, a traditional medicinal and edible plant rich in bioactive compounds, exhibits well-documented antimicrobial, antioxidant, and immunomodulatory properties; however, its effects on the gut microbiota-metabolite axis in weaned piglets remain poorly understood. In this study, weaned piglets were fed either a basal diet (control group) or a Lonicera japonica-supplemented diet (experimental group). Cecal contents were collected for metagenomic sequencing to characterize gut microbial composition and for untargeted LC-MS-based metabolomic profiling. Functional pathway enrichment and microbe-metabolite correlation network analyses were conducted to elucidate potential mechanisms. Lonicera japonica supplementation significantly improved evenness in terms of microbial species richness and reshaped microbial community structure, characterized by the enrichment of beneficial taxa, including Firmicutes and Eubacterium coprostanoligenes, and a concomitant reduction in opportunistic pathogens such as Proteobacteria and Escherichia coli. KEGG pathway analysis revealed the upregulation of microbial pathways related to translation, replication, and energy metabolism, alongside the downregulation of stress-response-associated pathways. Metabolomic profiling demonstrated distinct metabolic signatures between groups, with elevated levels of unsaturated fatty acids, amino acid derivatives, and organic acids, and reduced bile acid intermediates in the Lonicera japonica-treated piglets. Correlation network analysis further revealed strong positive correlations between SCFA-producing bacteria and beneficial metabolites, underscoring a reinforced microbiota-metabolite axis. Collectively, these findings indicate that Lonicera japonica supplementation promotes a healthier and more stable gut ecosystem in weaned piglets through coordinated modulation of microbial composition, functional potential, and metabolic outputs. This study provides novel insights into microbiota-metabolite interactions underlying phytogenic interventions and supports the use of Lonicera japonica as a natural feed additive to enhance intestinal health and resilience during weaning.}, } @article {pmid42344904, year = {2026}, author = {Guo, R and Chen, Q and Kong, L and Huang, A and Li, Y and Li, C}, title = {Anti-NMDAR and anti-MOG antibody double-positive encephalitis temporally associated with cytomegalovirus detection in cerebrospinal fluid: a case report.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1805851}, pmid = {42344904}, issn = {1664-3224}, mesh = {Humans ; Male ; Middle Aged ; *Cytomegalovirus/immunology/genetics ; *Cytomegalovirus Infections/immunology/diagnosis/drug therapy/cerebrospinal fluid/complications ; *Autoantibodies/cerebrospinal fluid/blood ; *Receptors, N-Methyl-D-Aspartate/immunology ; Antiviral Agents/therapeutic use ; DNA, Viral/cerebrospinal fluid ; Myelin-Oligodendrocyte Glycoprotein ; }, abstract = {The co-occurrence of MOG and NMDAR antibodies has been reported in a limited number of cases and is termed the overlapping syndrome (MNOS). Viral coinfections have been identified in a subset of patients with MNOS. Herein, we report the first case of MNOS with concomitant cytomegalovirus (CMV) infection detected in cerebrospinal fluid, a finding that helps to further explore the relationship between viral infection and MNOS. A previously healthy 49-year-old man developed fever and behavioral abnormalities following prodromal symptoms. Metagenomic next-generation sequencing (NGS) of the CSF identified CMV DNA with high confidence (specific reads: 362; relative abundance: 85.97%). Serology was positive for CMV IgG but negative for IgM; serum CMV-DNA detected by real-time PCR was negative. Positivity for anti-NMDAR antibodies and anti-MOG antibodies in the CSF, whereas only anti-MOG antibodies were detected in the serum. The patient's condition gradually improved after treatment with antiviral agents, corticosteroids, and intravenous immunoglobulin. The main limitations of this report include the lack of detection of CMV-DNA in CSF by real-time PCR, as well as the absence of dynamic assessment of serum/CSF CMV IgG/IgM, anti-NMDAR, and MOG antibody titers. Clinical vigilance for coexisting autoimmune encephalitis should be heightened following viral infections.}, } @article {pmid42345796, year = {2026}, author = {Mancini, P and Brandtner, D and Cordeschi, G and Iaconelli, M and Mastrantonio, V and La Rosa, G and Porretta, D}, title = {Exploratory Metaviromic Analysis of the Sea-Rock Pool Mosquito Aedes mariae and the Water of Its Breeding Habitat.}, journal = {Biology}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/biology15120940}, pmid = {42345796}, issn = {2079-7737}, abstract = {The mosquito-associated virome may modulate host biology and influence vector competence, highlighting the importance of understanding its composition. Here, a metagenomic analysis was conducted to characterize the virome of the sea-rock pool mosquito Aedes mariae across sexes and developmental stages, together with water from its sea-rock pool breeding site in San Felice Circeo (Italy). A total of 51 viral taxa were identified, including viruses associated with bacteria and archaea (39%), plants, algae, fungi, and protists (35%), vertebrates (8%), and invertebrates (18%), including insect-specific viruses such as Mesoniviridae, Baculoviridae, Nudiviridae, Iridoviridae and Totiviridae. Twenty-five percent of the taxa were shared across samples, suggesting acquisition from breeding-site water and persistence across stages during development. Interestingly, the need for host genome filtering highlights the potential sequence similarity between viral and mosquito genomes, which may reflect the presence of endogenous viral elements or historical virus-host interactions. These findings represent the first characterization of the virome of Aedes mariae and highlight the role of aquatic breeding sites in shaping mosquito virome. Finally, we argue the importance of adequate sequencing depth and host genome filtering to capture the diversity of the mosquito virome.}, } @article {pmid42345825, year = {2026}, author = {Zhakypbek, Y and Toktar, M and Kossalbayev, BD and Yang, Q and Shi, Q and Tursbekov, S and Belkozhayev, AM and Abseyt, AS and Kezembayeva, G and Kamarkhan, T}, title = {Soil Bacterial Community Structure and Functional Potential in the Caspian Drylands of Western Kazakhstan.}, journal = {Biology}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/biology15120969}, pmid = {42345825}, issn = {2079-7737}, support = {BR24993218//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {Dryland soils of the Caspian region of western Kazakhstan are exposed to environmental stress, including drought, alkalinity, low soil organic matter content, and anthropogenic pressure. In this preliminary study, bacterial communities were investigated in 18 soil samples collected from six sampling groups across Makat (M1, M2), Isatay (I1, I2), and Beyneu (B1, B2) districts. Soil physicochemical properties were measured, and bacterial diversity was analyzed using 16S rRNA gene sequencing of the V3-V4 region. Community composition analysis indicated spatial heterogeneity among the sampled groups. M1 and I1 showed the highest taxon richness, whereas B2 contained the highest number of unique taxa. Genus-level profiles showed that B1 and M2 were mainly associated with Rubrobacter and related actinobacterial taxa; B2 contained higher proportions of Marinobacter, Tychonema, Qipengyuania, and Halomonas; and I2 was enriched with Antarcticibacterium, Salinimicrobium, Rhodococcus, Gillisia, Marinobacter, Dietzia, and Pontibacter. Correlation analysis showed that several bacterial taxa were associated with soil organic matter content, total nitrogen, total phosphorus, exchangeable cations, and pH, although the overall Mantel relationship between soil properties and community structure was not significant. FAPROTAX-based prediction indicated differences in putative heterotrophic, nitrogen-related, sulfur-related, and hydrocarbon-associated functional categories among sites. Because FAPROTAX predictions are based on taxonomic composition, these results should be interpreted only as putative functional potential and not as evidence of actual microbial metabolic activity. These findings suggest that the sampled Caspian dryland soils contain distinct bacterial assemblages and taxa with potential ecological relevance; however, their role in dryland soil resilience or bioremediation should be verified through future culture-based, metagenomic, and functional validation studies.}, } @article {pmid42346014, year = {2026}, author = {Domingues, R and Pires, JCM}, title = {Bioinformatics Strategy for 16s and 23s rRNA Metabarcoding Data.}, journal = {Biotech (Basel (Switzerland))}, volume = {15}, number = {2}, pages = {}, pmid = {42346014}, issn = {2673-6284}, support = {UID/00511/2025 and UID/PRR/00511/2025//Fundação para a Ciência e Tecnologia/ ; LA/P/0045/2020//Fundação para a Ciência e Tecnologia/ ; }, abstract = {Understanding biological communities is essential for elucidating ecosystem structure and function. Metabarcoding based on ribosomal RNA (rRNA) genes, particularly 16S and 23S, is widely used to characterise bacterial and microalgal communities. However, analysing high-throughput sequencing data generated by platforms such as the Illumina MiSeq remains challenging due to fragmented bioinformatics tools, complex parameterisation, and limited accessibility for non-specialist users. In this study, a comprehensive and user-friendly bioinformatics pipeline is proposed for the analysis of 16S and 23S paired-end metabarcoding data. The workflow integrates all critical processing steps, including read merging, primer and adapter trimming, quality filtering, dereplication, chimaera removal, and clustering into Operational Taxonomic Units (OTUs). Taxonomic assignment is performed using curated reference databases, namely EZBioCloud for bacterial communities and µgreen for microalgae. The pipeline was developed in Python 3.11 and incorporates validated tools such as VSEARCH and Cutadapt, ensuring robustness and computational efficiency. Additionally, modules for alpha and beta diversity analysis are included to support comprehensive ecological interpretation. The main novelty of this work lies in providing a unified, GUI-based framework that enables the standardised processing of dual-marker (16S/23S) metabarcoding data within a single environment. In its current implementation, SOMBA supports the analysis of each marker through separate but harmonised workflows, ensuring consistency in parameterisation, processing steps, and output structure. This approach provides an accessible and standardised solution that bridges the gap between raw sequencing data and reliable biological insights, supporting applications in environmental microbiology and biotechnology.}, } @article {pmid42346116, year = {2026}, author = {Khan, SU and Chauhan, V and Chaudhary, AA and Khan, M}, title = {The Gut-Brain-Immune Axis: Multi-Omics Insights into Neurodegenerative and Metabolic Diseases.}, journal = {Cells}, volume = {15}, number = {12}, pages = {}, pmid = {42346116}, issn = {2073-4409}, support = {DDRSP-2601//Imam Mohammad ibn Saud Islamic University/ ; }, mesh = {Humans ; Multiomics ; *Neurodegenerative Diseases/immunology/metabolism ; Animals ; *Brain/immunology/metabolism ; *Metabolic Diseases/immunology/metabolism ; Gastrointestinal Microbiome ; Metabolomics ; }, abstract = {The axis linking the gut to the brain to the immune system connects all tissues involved-bacteria, immune cells, metabolism and the CNS-through a multidirectional communication network. Several studies have confirmed that when this axis is disrupted, it can be responsible for Alzheimer's disease, Parkinson's disease, obesity, type 2 diabetes, and NAFLD, and the main consequences come from increased systemic inflammation, altered regulation of immune cells, the production of microbial metabolites that alter signals to the immune cells and nervous system, increase in oxidative stress, breakdown of the gut barrier, and more. In recent years, advanced multi-omics technologies, such as metagenomics, transcriptomics, metabolomics, proteomics, and single-cell sequencing, have provided significant advancement in our understanding of all of the interacting nodes involved in the gut-brain-immune axis. These advanced sequencing technologies can characterize the microbial communities, host immune cells, metabolic profiles, and the degree of cell heterogeneity during a specific disease. Combining multi-omics information can reveal a few shared pathways between neurodegenerative and metabolic disorders, such as NF-κB, NLRP3 inflammasome activation, mitochondrial dysfunction, changes in SCFA metabolism, and the alteration of microbial populations in Alzheimer's and Parkinson's disease; metabolic dysbiosis and increased risk for Parkinson's disease; or changes in gut-to-brain-to-immune signaling contributing to diabetes complications and NAFLD. Artificial intelligence (AI) and machine learning are becoming promising tools for detecting biomarkers from these datasets, extracting knowledge, interpreting systems biology, and helping with developing precision medicine. In this review, we summarize current evidence that supports the role of the gut-brain-immune axis in neurodegenerative and metabolic diseases, highlighting results gained with the utilization of multi-omics approaches. We will describe the key microbial, immune, and metabolic pathways involved in pathogenesis and therapeutic approaches including psychobiotics, tailored nutrition, modulation of the microbiome, and metabolite interventions, discussing future perspectives of the translation of the gut-brain-immune axis knowledge into clinical practice.}, } @article {pmid42346385, year = {2026}, author = {Li, J and Xu, X and Wang, H and Gao, R and Li, B and You, X}, title = {Relationship Between Calcium and Gut Microbial Composition and Metabolic Pathways in Children with Autism.}, journal = {Metabolites}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/metabo16060405}, pmid = {42346385}, issn = {2218-1989}, support = {531100006787540685//Chinese Academy of Medical Sciences & Peking Union Medical College/ ; }, abstract = {Background/Objectives: Trace elements may influence autism spectrum disorder (ASD) severity through interactions with the gut microbiota and microbial metabolic functions, but calcium-related evidence remains limited. This cross-sectional study examined associations among hair calcium, gut microbial taxa, metabolic pathways, and behavioral phenotypes in children with ASD. Methods: We analyzed 183 children with ASD who had behavioral assessments, hair calcium measurements, and fecal shotgun metagenomic sequencing data. Participants in the lowest and highest calcium quartiles were first compared to characterize group-level microbiome differences. Full-sample analyses then tested associations among continuous hair calcium, microbial taxa, metabolic pathways, and behavioral measures after covariate adjustment. Benjamini-Hochberg false discovery rate correction was applied for multiple testing. Results: Hair calcium was positively associated with CARS, ATEC-Total, ATEC-1, and ATEC-3 scores, with the strongest associations involving ATEC-1 and ATEC-3. Alpha and beta diversity did not differ significantly between calcium quartile groups, but group-based microbiome analyses identified 63 differential species and 22 differential MetaCyc pathways. Full-sample integrated analyses connected calcium-associated microbial taxa, metabolic pathways, and ASD behavioral measures. Conclusions: Hair calcium was associated with ASD behavioral severity, selected gut microbial species, and microbial metabolic pathways. These findings support an association framework connecting longer-term calcium-related mineral profiles, gut microbial functional potential, and behavioral phenotypes, providing a basis for future longitudinal and multi-omics studies.}, } @article {pmid42346775, year = {2026}, author = {He, Z and Nie, Y and Li, C and Sun, G and Zheng, W and Liu, H and Geng, M and Tian, J and Zhang, Y}, title = {GV-971 Ameliorates Chronic Restraint Stress-Induced Depression-like Phenotypes Accompanied by Reshaping of the Microbiota-Gut-Brain Axis.}, journal = {Marine drugs}, volume = {24}, number = {6}, pages = {}, pmid = {42346775}, issn = {1660-3397}, support = {2024CXPT029, 2025CXPT011//Key R&D Program of Shandong Province, China/ ; ZR2024QH615//Shandong Provincial Natural Science Foundation/ ; SYS202205//Shandong Laboratory Program/ ; }, mesh = {Animals ; *Depression/drug therapy/etiology ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; *Stress, Psychological/drug therapy ; *Brain-Gut Axis/drug effects ; *Oligosaccharides/pharmacology ; Restraint, Physical ; Disease Models, Animal ; *Antidepressive Agents/pharmacology ; Mice, Inbred C57BL ; Brain/drug effects/metabolism ; Phenotype ; Hippocampus/drug effects/metabolism ; Intestinal Barrier Function ; }, abstract = {Depression is increasingly linked to microbiota-gut-brain axis dysfunction, yet current monoaminergic antidepressants show limited efficacy. This study investigated the therapeutic potential and underlying mechanisms of GV-971, a marine-derived oligosaccharide, in a chronic restraint stress (CRS) mouse model. We first established that 8 h of daily restraint for 4-8 weeks induces a stable depression-like phenotype characterized by behavioral despair and significant reduction in peripheral monoamine neurotransmitters (5-HT and norepinephrine). GV-971 treatment robustly attenuated CRS-induced depression- and anxiety-like behaviors, restored hippocampal serotonin levels, reduced elevated plasma corticosterone concentrations, and ameliorated CRS-induced adrenal cortical hyperplasia. Mechanistically, GV-971 significantly suppressed neuroinflammation by inhibiting microglial hyperactivation in the prefrontal cortex and hippocampus. Concurrently, it repaired intestinal barrier dysfunction, evidenced by reduced permeability, restored mucosal integrity, and recovered goblet cell numbers. Crucially, integrated shot-gun metagenomics and plasma metabolomics revealed that GV-971 not only reshaped microbial taxonomy but also functionally recalibrated the gut ecosystem. It enriched beneficial taxa (e.g., Bifidobacterium pseudolongum, Bacteroides uniformis) and specific metabolic pathways, leading to increased short-chain fatty acids (valeric and caproic acids) and a significant reduction in plasma levels of tryptophan-kynurenine pathway metabolites, specifically the neurotoxic compounds kynurenine and quinolinic acid. Fecal microbiota transplantation (FMT) from GV-971-treated donors partially recapitulated the antidepressant and gut-protective effects in CRS recipients, confirming a causal role for the remodeled microbiota. Collectively, GV-971 exerts antidepressant effects by coordinately remodeling the gut microbiota, normalizing tryptophan and SCFA metabolism, restoring gut barrier integrity, and dampening central neuroinflammation, supporting its potential as a novel gut-brain axis-targeted therapy for depression.}, } @article {pmid42347203, year = {2026}, author = {Widyarman, AS and Udawatte, NS and Ma, SSSS and Theodorea, CF and Richi, M and Poedjiastoeti, W and Seneviratne, CJ}, title = {Nutritional Stunting Is Linked to Reduced Oral Microbiome Stability and Reconfigured Microbial Networks in Children: A Pilot Intervention Study.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/pathogens15060591}, pmid = {42347203}, issn = {2076-0817}, mesh = {Humans ; Child ; Pilot Projects ; Female ; Probiotics/administration & dosage ; Male ; *Microbiota ; *Growth Disorders/microbiology/complications ; Mouthwashes/administration & dosage ; *Mouth/microbiology ; Saliva/microbiology/chemistry ; Oral Health ; Bacteria/classification/genetics ; Oils, Volatile/administration & dosage ; }, abstract = {This non-randomized, open-labelled, controlled pilot trial investigated the impact of stunting on oral health and the oral microbiome, and evaluated the effect of 14-day probiotic or essential oil mouthwash interventions in children aged 8-12 years. Thirty-six participants (18 stunted, 18 non-stunted) were randomized into three parallel arms: probiotic lozenges (Limosilactobacillus reuteri DSM 17938 + ATCC PTA 5289), essential oil mouthwash, or water control. D-25OH level was assessed with ELISA, OHI-S, and PBI were examined, and oral microbiome was analyzed using 16S metagenomic sequencing. Stunted children demonstrated significantly higher gingival inflammation (PBI, F = 10.57, p = 0.002), reduced microbial alpha diversity, reductions in commensal Streptococcus spp., and increases in pathobionts, including Parvimonas micra, Fusobacterium nucleatum, and Tannerella forsythia. Beta-diversity analysis revealed distinct microbial communities (p = 0.001), with network analysis identifying these anaerobes as keystone hubs in stunted individuals. Salivary vitamin D and oral hygiene indices (OHI-S) also differed by stunting status. Fourteen-day interventions produced only modest, non-significant improvements in clinical indices and failed to induce significant shifts in microbial diversity or composition. These findings indicate that nutritional stunting is independently associated with oral dysbiosis and gingival inflammation. Short-term antiseptic interventions appear insufficient to reverse established microbial shifts, highlighting the need for sustained, integrated nutritional-oral health strategies.}, } @article {pmid42347234, year = {2026}, author = {Wojnarowski, K and Cholewińska, P and Zhao, D and Hasegawa, Y and Denk, D and Palić, D}, title = {Rapid Culture-Independent Detection of Fish Pathogens Using Oxford Nanopore Technologies: Case-Based Insights Across Multiple Species and Tissues.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/pathogens15060622}, pmid = {42347234}, issn = {2076-0817}, mesh = {Animals ; *Fish Diseases/microbiology/diagnosis ; *Bacteria/genetics/classification/isolation & purification ; *Nanopore Sequencing/methods ; Fishes/microbiology ; Metagenomics/methods ; *Bacterial Infections/veterinary/diagnosis/microbiology ; }, abstract = {Rapid and accurate diagnosis of infectious diseases in aquaculture is essential for preventing major economic and ecological losses. Traditional culture-based methods focus on isolation of individual pathogens, and often are burdened with extended processing times, particularly during investigations of polymicrobial infections. Application of Oxford Nanopore Technologies (ONT) sequencing offers a rapid, culture-independent workflow for the identification of bacterial and fungal pathogens directly from fish tissues. Swab and organ samples from four cases (1: Salmo spp.; 2: Cyprinus carpio; 3: Salvelinus fontinalis; 4: Heniochus acuminatus) were analyzed using ONT long-read sequencing for metagenomic screening and bioinformatic classification. The results revealed case-, species-, and tissue-specific microbial profiles, with external tissues showing higher microbial diversity and internal organs enriched in pathogenic taxa. Dominant pathogens included Streptococcus iniae, Aeromonas hydrophila, Pseudomonas spp., and Saprolegnia parasitica, alongside opportunistic zoonotic bacteria such as Escherichia coli and Acinetobacter baumannii. We demonstrate the potential for diagnostic application of ONT sequencing in investigations and detection of multi-pathogen infections, including assessments of microbial community structure changes during disease outbreaks in aquatic species. The presented workflow enables rapid, cost-effective, and comprehensive pathogen profiling, supporting early disease surveillance and improved management in aquatic veterinary practice.}, } @article {pmid42347240, year = {2026}, author = {Chen, J and Wang, H and Li, Y and Xiao, Y and Yan, Y and Zhang, Y and Lu, X}, title = {Scenario-Driven Rapid Testing for Top Pathogens in Pediatric Respiratory Infections: Clinical and Economic Value from Emergency Triage to Precision Anti-Infective Management in the PICU.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/pathogens15060628}, pmid = {42347240}, issn = {2076-0817}, support = {WJ2025Z010//Health Commission of Hubei Province/ ; WJ2021M262//Health Commission of Hubei Province/ ; WX23A90//Wuhan Health Commission/ ; 32270528//National Natural Science Foundation of China/ ; CX20240883//Hunan Provincial Postgraduate Research and Innovation Project/ ; }, mesh = {Humans ; *Respiratory Tract Infections/diagnosis/drug therapy/microbiology/virology ; *Triage ; Intensive Care Units, Pediatric ; Rapid Diagnostic Tests ; Child ; Anti-Bacterial Agents/therapeutic use ; *Anti-Infective Agents/therapeutic use ; }, abstract = {Pediatric respiratory infections remain among the leading causes of emergency department visits, hospitalization and pediatric intensive care unit (PICU) admission. Although most acute respiratory infections in children are viral, clinical manifestations overlap substantially among viral, bacterial and atypical pathogens, creating diagnostic uncertainty and promoting empirical antimicrobial use. Rapid antigen tests, nucleic acid amplification tests, multiplex respiratory panels and metagenomic sequencing have expanded the ability to detect pathogens within clinically actionable timeframes. However, evidence from pediatric emergency trials indicates that rapid pathogen detection alone does not necessarily reduce antibiotic prescribing or healthcare costs. These findings suggest that the value of rapid diagnostics depends less on analytical breadth than on whether testing is applied to the right child, in the right clinical scenario and within a predefined decision pathway. This narrative review reorganizes the evidence around a scenario-driven top-pathogen framework. Top pathogens are defined as organisms that, in a specific age group, syndrome, season or care setting, have high prevalence, severe disease potential, transmissibility, treatment implications, antimicrobial resistance relevance or infection-control value. We discuss how top-pathogen testing should differ across emergency triage, inpatient ward management, severe pneumonia, PICU care, hospital-acquired pneumonia, ventilator-associated pneumonia and outbreak settings. We further examine the economic mechanisms through which rapid testing may generate value, including reduced unnecessary antibiotics, timely antiviral therapy, optimized isolation, shorter length of stay, reduced repeated testing and prevention of healthcare-associated transmission. Finally, we propose implementation principles centered on diagnostic stewardship, antimicrobial stewardship, local epidemiology and real-world cost-effectiveness evaluation. A scenario-driven top-pathogen strategy may provide a practical bridge between broad syndromic testing and precision infectious disease management in children.}, } @article {pmid42347253, year = {2026}, author = {Yean, S and Prasetyo, DB and Chao, S and Vuth, L and Prot, M and Baidaliuk, A and Bonnet, S and Simon-Loriere, E and Boyer, S}, title = {Combining PCR and Metagenomic Approaches to Reveal Tick-Borne Pathogens in Ticks Collected from Livestock and Companion Animals in Cambodia.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/pathogens15060641}, pmid = {42347253}, issn = {2076-0817}, mesh = {Animals ; Cambodia/epidemiology ; *Tick-Borne Diseases/veterinary/epidemiology/microbiology ; *Metagenomics/methods ; *Polymerase Chain Reaction/methods ; *Livestock/parasitology ; Cross-Sectional Studies ; Cattle ; *Ticks/microbiology/virology/parasitology ; Dogs ; Tick Infestations/veterinary ; Bacteria/genetics/isolation & purification/classification ; }, abstract = {In Cambodia, livestock production plays an important role in the national economy and food security, yet tick-borne diseases remain an underrecognized constraint on animal health and productivity. Domestic animals may also serve as reservoirs of zoonotic pathogens in this predominantly rural setting. To address the lack of baseline molecular data on tick-borne pathogens in Cambodia, we conducted a cross-sectional study of ticks collected from November 2022 to April 2023 across 24 provinces. Ticks were collected from various hosts and environments, including cats, cattle, dogs, goats, pangolins, pythons, wild pigs, and bat cave floors, representing urban, rural, farm, wildlife rescue center, and forest fringe habitats. A total of 1526 ticks belonging to nine species were pooled into 352 samples and screened using conventional PCR (cPCR) targeting Anaplasma, Ehrlichia, Babesia, and Coxiella. Additionally, a subset of Rhipicephalus microplus ticks was analyzed using metatranscriptomic next-generation sequencing (NGS). Rhipicephalus microplus ticks collected from cattle tested positive for Anaplasma marginale (1.1% of pools) and Ehrlichia minasensis (0.9% of pools), whereas Rhipicephalus linnaei ticks collected from dogs were positive for Anaplasma platys (0.3% of pools) and Babesia canis (2.0% of pools). A high prevalence of Coxiella-like endosymbionts (15.6% of pools) was found in R. microplus from both cattle and goats. Metatranscriptomic analysis also identified six tick-associated viruses in R. microplus from cattle; with Guangdong tick manly virus being the most dominant (32.5% of samples); followed by Zhangzhou Totiv tick virus 1 (15.0%), Jingmen tick virus (5.0%), and Mogiana tick virus; Rhipicephalus-associated rhabdo-like virus; and Rhipicephalus-associated flavi-like virus; each at 2.5%. These findings provide the first molecular evidence of numerous bacterial, protozoal, and viral pathogens circulating in R. microplus and R. linnaei in Cambodia. The study highlights the need for integrated One Health surveillance to better understand, prevent, and control tick-borne diseases in the region.}, } @article {pmid42347401, year = {2026}, author = {Zheng, L and He, Y and Yan, Y and Li, Q and Zhang, L and Xing, Z and Lu, X}, title = {Characteristics, Ecological Risks, and the Impacts on Soil Carbon Cycling of PAH Pollution in the Soil of a Retired Coking Plant in Zaozhuang, Northern China.}, journal = {Toxics}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/toxics14060503}, pmid = {42347401}, issn = {2305-6304}, abstract = {During the industrial restructuring in China, numerous outdated coking enterprises were phased out. Despite the cessation of production for several years, the soil in the production area of the retired coking plant remains heavily contaminated with polycyclic aromatic hydrocarbons (PAHs), which continue to adversely affect soil health. However, research on the pollution characteristics of soil PAHs under prolonged PAH exposure and the associated changes in functional genes related to soil carbon cycling is still inadequate. This study aims to identify the pollution characteristics and ecological risks of PAHs in the coking plant and to investigate the effects of long-term PAH contamination from abandoned coking plants on the functional genes involved in soil carbon cycling. It was found that PAHs in the soil were predominantly composed of high-molecular-weight PAHs (HMW-PAHs), which constituted 65.7% to 83.4% of the total PAH content. The total concentration of PAHs in the surface soil ranged from 3.79 to 554 mg·kg[-1], with an average concentration of 147.6 mg·kg[-1]. Source analysis based on isomer ratios indicated that PAHs primarily originated from the combustion of coal and biomass. Utilizing the toxicity equivalent factor (TEF) method, we found that the PAH levels in the CA group exceeded the Serious Risk Concentration, indicating that PAH pollution poses a potential threat to the ecological environment. Metagenomic analysis revealed that the gene abundance of alpha-amylase in the CA group was significantly higher than that in the OLA group (p < 0.05), suggesting that prolonged exposure to PAHs has enhanced the starch hydrolysis capabilities of soil microorganisms. The findings of this study refine methods for assessing the risks associated with soil PAH contamination and provide a theoretical foundation for the risk management and reuse of retired coking plant sites.}, } @article {pmid42347555, year = {2026}, author = {Jacob, SM and Akinbo, SY and Ajakaye, OG and Ekpo, UF and Omoruyi, Z and Agbana, T and Makau-Barasa, L and Aderogba, MO and Diehl, JC and Bell, D and Bayegun, AA and Okungbowa, MA and A-Enegela, J and Akinbo, FO}, title = {Molecular Identification of Schistosoma Species Associated with Atypical Urinary Eggs in Abuja (Nigeria): Evidence of Potential Zoonotic Transmission.}, journal = {Tropical medicine and infectious disease}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/tropicalmed11060170}, pmid = {42347555}, issn = {2414-6366}, abstract = {Schistosomiasis remains a major public health concern in Nigeria. We molecularly characterized Schistosoma eggs obtained from human urine to identify species and assess the presence of hybrid schistosomes in Abuja, Nigeria. Urine samples were collected from 1887 participants aged five years and above. Samples were examined for Schistosoma eggs using light microscopy. A total of 507 (26.9%) were positive for any form of Schistosoma while 91 (4.8%) had atypical Schistosoma eggs. DNA extracted from pooled ova was analyzed using metagenomic sequencing, read mapping, phylogenetic analysis, and BLASTn confirmation. Molecular analyses identified genetic signatures associated with both S. haematobium and S. bovis within pooled human urine samples, indicating the co-circulation of multiple schistosome species in the study area. Phylogenetic analyses based on trans-ITS and mitochondrial COX1 markers supported the presence of distinct nuclear and mitochondrial schistosome lineages. However, because sequencing was performed on pooled egg samples, the findings cannot distinguish between true recombinants and mixed infections involving co-circulating parental species. These findings highlight the potential complexity of schistosome transmission dynamics in endemic communities and underscore the need for enhanced molecular surveillance, especially single-parasite genomic approaches, and integrated One Health investigations to better understand schistosome transmission and its implications for control and elimination efforts in Nigeria.}, } @article {pmid42347906, year = {2026}, author = {Liu, Y and Lin, H and Zhu, M and Chen, X and Yu, Z and Peng, D and Dong, G and Ni, Y and Fu, J}, title = {Gut microbiota dysbiosis and short-chain fatty acid alterations in pediatric new-onset type 1 diabetes with ketoacidosis.}, journal = {Journal of endocrinological investigation}, volume = {}, number = {}, pages = {}, pmid = {42347906}, issn = {1720-8386}, support = {2023C03047//Key Research and Development Program of Zhejiang Province/ ; 2021YFC2701900//Key Technologies Research and Development Program/ ; 82370863//National Natural Science Foundation of China/ ; 82502105//National Natural Science Foundation of China/ ; LKLY25H180005//Natural Science Foundation of Zhejiang Province/ ; LQN25H040005//Natural Science Foundation of Zhejiang Province/ ; }, abstract = {PURPOSE: Diabetic ketoacidosis (DKA) stands as the most common acute hyperglycaemic complication in children with type 1 diabetes (T1D) and remains associated with considerable morbidity and mortality. Although gut dysbiosis has been reported in newly diagnosed T1D, the gut microbiota and microbial metabolites during DKA onset remain poorly characterized.

METHODS: Shotgun metagenomic sequencing was performed on fecal samples from 96 newly diagnosed T1D children, including 32 presenting with DKA upon admission. Short-chain fatty acids (SCFAs) were quantified using gas chromatography/mass spectrometry (GC/MS). Comparative and correlation analyses were conducted to explore differences in gut microbial composition, SCFA levels, and their association with clinical indicators of DKA severity.

RESULTS: Children with DKA exhibited distinct gut microbial compositions, with marked β-diversity separation from non-DKA individuals. The DKA group was characterized by an enrichment of potential pathogens and a significant depletion of SCFA-producing genera, including Anaerobutyricum, Dialister, Ruminococcus, Roseburia, Dorea, and Butyricicoccus. Correspondingly, fecal SCFA levels were significantly reduced in the DKA group. Moreover, SCFAs and their producing bacteria were strongly correlated with clinical indices of DKA severity. Mediation analysis suggested that reductions in SCFAs, particularly propionic acid and butyric acid, were associated with metabolic alterations linking SCFA-producing bacteria to DKA.

CONCLUSION: This study provides a comprehensive characterization of gut microbiota and SCFA alterations in T1D children at DKA onset. The depletion of SCFA-producing bacteria and their metabolites reflects metabolic disturbances associated with DKA, and highlights SCFAs and their producers as candidate metabolic features warranting further validation as biomarkers and therapeutic targets.}, } @article {pmid42347915, year = {2026}, author = {Huang, CH and Lu, IC and Lin, CW and Hsieh, MT and Chiang, IH and Lai, PH and Liu, IT and Chen, JS}, title = {Gut microbiota profiles across intrinsic capacity strata in community-dwelling older adults using full-length 16S rRNA sequencing.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {42347915}, issn = {2509-2723}, support = {NSTC 112‑2314‑B‑650‑001‑MY3//National Science and Technology Council/ ; EDAHP111045//E-Da Hospital/ ; EDAHP113004//E-Da Hospital/ ; EDAHS113021//E-Da Hospital/ ; }, abstract = {Intrinsic capacity (IC), introduced by the World Health Organization, provides a multidimensional framework for evaluating functional aging across locomotion, cognition, sensory, psychological, and vitality domains. However, gut microbial features associated with IC among community-dwelling older adults remain incompletely understood. In this exploratory cross-sectional study, we enrolled 52 community-dwelling older adults and assessed gut microbiota using full-length 16S rRNA sequencing. Participants were stratified into IC quartiles, and additional analyses examined composite IC and domain-specific IC scores as continuous measures. Alpha diversity indices were not significantly associated with composite IC after false discovery rate correction, although vitality showed nominal positive associations with observed features and Chao1 richness (both rho = 0.316, P = 0.024, q = 0.288). PERMANOVA did not show statistically robust differences in beta diversity across IC quartile groups using Bray-Curtis distance (R[2] = 0.061, P = 0.060, q = 0.383), weighted UniFrac distance (R[2] = 0.083, P = 0.140, q = 0.436), or unweighted UniFrac distance (R[2] = 0.063, P = 0.211, q = 0.443). Selected bacterial taxa, including Ruminococcaceae, Lachnospiraceae, Alistipes, and Faecalibacterium, showed nominal associations with composite or domain-specific IC measures, but none remained significant after FDR correction or covariate-adjusted regression. In PICRUSt2-predicted functional analyses, several COG features related to transport systems, multidrug efflux, and site-specific recombination were positively associated with the vitality domain after false discovery rate correction. Because functional profiles were inferred from 16S rRNA sequencing rather than directly measured by shotgun metagenomics, metabolomics, or inflammatory biomarkers, these findings should be interpreted as exploratory and hypothesis-generating. This study identifies candidate microbiota and predicted functional features for future longitudinal and mechanistic studies of multidimensional functional aging.}, } @article {pmid42348069, year = {2026}, author = {Ernst, S and Dirschka, T}, title = {The Bacterial Landscape of Facial Skin: From Homeostasis to Skin Conditions.}, journal = {Dermatology and therapy}, volume = {}, number = {}, pages = {}, pmid = {42348069}, issn = {2193-8210}, abstract = {The human facial skin microbiome is a complex and dynamic ecosystem that plays a central role in maintaining skin health, immune regulation, and preventing dermatological skin conditions. Cutibacterium acnes (C. acnes) and Staphylococcus epidermidis (S. epidermidis) are the most prominent bacterial species, with shifts in their relative abundance correlating with skin site, age, skin site, and health status. Exploring the facial microbiome offers exciting opportunities, though it requires careful methodological consideration. Sampling techniques vary in invasiveness and depth, which can influence the accuracy and reproducibility of microbiome profiles. While traditional cultivation methods provide valuable insights, they often miss nonculturable microbes, limiting the view of microbial diversity. Molecular approaches such as amplicon sequencing and metagenomics enable a more comprehensive understanding of microbial communities, even though they currently cannot distinguish between viable and nonviable microbes. Addressing these challenges will help unlock the full potential of facial microbiome research. A balanced facial skin microbiome is associated with healthy skin, whereas a dysbiosis of C. acnes and S. epidermidis is commonly observed in acne-prone skin and more pronounced clinically manifest acne. A comprehensive understanding of the diversity and distribution of C. acnes phylotypes, as well as distinct lineages of S. epidermidis associated with skin disorders, is crucial for developing targeted, microbiome-based cosmetic and medical treatments. Emerging strategies aim to restore microbial balance by leveraging the skin's native microbiota, including probiotic approaches. These strategies represent a promising yet still emerging approach, as current clinical evidence remains limited and further well-controlled studies are required, although they may offer benefits by enhancing microbial diversity and supporting skin barrier function.}, } @article {pmid42348335, year = {2026}, author = {Biswa, BB and Mori, H and Toyoda, A and Fujiwara, K and Kurokawa, K and Koide, T}, title = {Increased abundance of Limosilactobacillus reuteri in the gut of selectively bred high-tameness mice and its association with behavioural changes.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {33}, number = {3}, pages = {}, doi = {10.1093/dnares/dsag006}, pmid = {42348335}, issn = {1756-1663}, support = {JPMJSP2104//JST/ ; 19KK0177//JSPS/ ; 24K01951//JSPS/ ; //Research Organization of Information and Systems/ ; }, mesh = {Animals ; Male ; Female ; *Limosilactobacillus reuteri/isolation & purification/genetics ; Mice ; Oxytocin/blood ; *Behavior, Animal ; *Gastrointestinal Microbiome ; Feces/microbiology ; Selective Breeding ; Pyruvic Acid/blood ; }, abstract = {Domestication alters animal behaviour, particularly tameness. We previously established 2 tamed mouse groups by selective breeding for active tameness-defined as the motivation to approach a human hand-from genetically heterogeneous wild-derived mouse stock, together with 2 nonselected control groups. Genetic analyses identified loci associated with active tameness, but their low heritability suggested contributions from nongenetic factors. We therefore hypothesized that the gut microbiota, which has been shown to influence brain function, contributes to behavioural changes associated with active tameness. To test this hypothesis, we conducted shotgun metagenomic analyses of faecal samples from 10 males and 10 females (80 individuals total) from the 2 tamed and 2 nonselected groups. Tamed mice exhibited markedly higher levels of active tameness, accompanied by elevated blood concentrations of oxytocin and pyruvate. While overall taxonomic and functional diversity of the gut microbiota was largely unchanged, the abundance of Limosilactobacillus reuteri was significantly increased in the tamed mice. Administration of a pyruvate-secreting L. reuteri strain to nonselected mice elevated blood oxytocin levels and enhanced active tameness, although plasma pyruvate levels were not increased. These findings suggest that L. reuteri is associated with behavioural modulation, potentially via oxytocin-related pathways, and provide mechanistic insight into microbial contributions to animal domestication.}, } @article {pmid42348560, year = {2026}, author = {Mani, K and Palanisamy, V and Shrestha, B and Vice, Z and Paudyal, S and Chitlapilly Dass, S}, title = {Insights into spatial dynamics of the microbiome and resistome across the conventional and organic dairy farms.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0352336}, doi = {10.1371/journal.pone.0352336}, pmid = {42348560}, issn = {1932-6203}, mesh = {Animals ; *Dairying/methods ; *Microbiota/genetics ; Cattle ; Milk/microbiology ; Farms ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Metagenomics ; Organic Agriculture ; }, abstract = {Antimicrobial resistance (AMR) poses a serious global threat to human and animal health. While AMR has been reported in various environments, its distribution across different ecological compartments within dairy farms remains poorly characterized. In this study, we used large-scale shotgun metagenomic sequencing to characterize the microbiome and resistome across multiple sampling sites within one organic and one conventional dairy farm, including teats, liners, water troughs, feed area, milking parlour mats, bedding sand, and milk. Our results indicate that microbial community composition and resistance gene profiles were largely comparable between the two study farms, with sample type (ecological niche) exerting a stronger influence on community structure than farm management type. Pseudomonadota, Bacillota, and Actinomycetota were the dominant phyla, while Aerococcus, Glutamicibacter, and Pseudomonas were the most prevalent genera. Glycopeptide resistance genes were the most abundant ARG class, followed by lincosamide and tetracycline resistance genes. Milk samples exhibited a distinct microbiome and resistome composition compared to environmental samples. Strong correlations between microbiome structure, resistome profiles, virulence factors, and metal resistance genes were observed across farm niches, highlighting the interconnected nature of microbial communities and resistance elements across dairy farm environments. These findings provide foundational data for targeted surveillance and management strategies to mitigate antimicrobial resistance in dairy production systems.}, } @article {pmid42349033, year = {2026}, author = {Cárdenas-Conejo, Y}, title = {GenomoBase: A comprehensive resource for the family Genomoviridae.}, journal = {Virology}, volume = {623}, number = {}, pages = {111018}, doi = {10.1016/j.virol.2026.111018}, pmid = {42349033}, issn = {1096-0341}, abstract = {The family Genomoviridae comprises circular single-stranded DNA viruses reported from fungi, plants, animals and environmental samples. Although metagenomics has accelerated their discovery, genomic sequences, annotations and metadata remain dispersed across repositories. Here we present GenomoBase (https://www.genomobase.org), a curated resource that integrates genomic, ecological and bibliographic data for all 237 ICTV-recognized genomovirus species. GenomoBase incorporates Serratus-filtered SRA screening outputs, enabling prioritization of metagenomes for targeted re-analysis. As a proof of concept, a targeted bait-and-assemble workflow of one prioritized SRA run reconstructed two candidate complete circular genomovirus genomes from metagenomic reads, both below the 78% species demarcation threshold for genomoviruses. Overall, GenomoBase supports comparative analyses and taxonomically informed exploration of public metagenomes.}, } @article {pmid42349155, year = {2026}, author = {Li, YY and Lin, L and Wen, L and Li, XY}, title = {Rapid adaptation and enrichment of salt-tolerant anammox via dosing of chemical enhancers in packed-bed biofilm reactor.}, journal = {Water research}, volume = {304}, number = {}, pages = {126343}, doi = {10.1016/j.watres.2026.126343}, pmid = {42349155}, issn = {1879-2448}, abstract = {The application of anammox-based processes for saline wastewater treatment is constrained by the scarcity of salt-tolerant seed sludge and the lengthy adaptation periods. To overcome this challenge, exogenous chemical enhancers, hydrazine (N2H4, 5 mg/L) and glycine betaine (GB, 30 mg/L), were introduced and evaluated for their roles in facilitating salt-adapted anammox biofilms enrichment from freshwater seed in packed-bed biofilm reactors. Hydrazine addition for 15 days increased the nitrogen removal rate from approximately 50 to 441.1 mg N/(L·d) within 70 days, which was substantially higher than that achieved through natural acclimation (192.2 mg N/(L·d)). When GB was subsequently supplemented for 30 days to the naturally acclimated reactor, its nitrogen removal rate rapidly increased to 1000 mg N/(L·d) within 30 days and further to 3000 mg N/(L·d) within 60 days, catching up the reactor receiving N2H4 from the outset. According to community analysis, performance recovery coincided with immediate shift from Ca. Brocadia to Ca. Kuenenia, with its relative abundance surged ∼15-fold within 20 days, highlighting the remarkable stimulatory effect of enhancers on Ca. Kuenenia's proliferation. Inferred from KEGG pathway studies, N2H4 primarily enhanced oxidative phosphorylation and ATP synthesis, providing energetic support for early recovery of the proton motive force and osmotic balance. In contrast, GB stabilized cellular osmotic conditions and membrane structures, enabling reallocation of metabolic resources toward antioxidant defense, cellular repair, and folate biosynthesis under saline stress. This alleviated the energetic burden associated with ion transport and lipid remodeling, thereby promoting sustained recovery of the anammox community.}, } @article {pmid42349523, year = {2026}, author = {Muqaddas, K and Mahnoor, and Hayat, O and Islam, A and Khan, R and Naz, S}, title = {Cutaneous Leishmaniasis Promotes Skin Microbial Dysbiosis and Exacerbation of Local Inflammatory Responses.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108655}, doi = {10.1016/j.micpath.2026.108655}, pmid = {42349523}, issn = {1096-1208}, abstract = {Cutaneous leishmaniasis (CL) is a neglected tropical disease caused by protozoan parasites belongs to the genus Leishmania transmitted to humans by the bite of the infected female sand fly. Increasing evidence suggested that alterations in the skin microbiome may influence local inflammatory responses and disease progression in CL. This study aimed to investigate the microbial community shifts associated with CL lesions using paired lesional and contralateral healthy skin samples from infected individuals (n = 8). Leishmania tropica was identified in all clinical samples by ITS-1 real-time PCR analysis. Microbiome profiling was performed using 16S rRNA gene amplicon sequencing followed by quality filtering, taxonomic classification using Kraken2/Bracken and statistical analysis. Phylum level analysis demonstrated altered microbial composition in lesional skin, with predominance of Proteobacteria. At the genus and species levels, lesional samples exhibited reduced microbial evenness and enrichment of opportunistic bacterial genera, including Stenotrophomonas, Pseudomonas, Acinetobacter, and Staphylococcus. In comparison, contralateral healthy skin indicated dominance of environmental and commensal bacteria such as Luteibacter, Methylobacterium, and Paracoccus, representing a relatively stable microbial community (FDR p ≥ 0.05). Alpha diversity analysis showed reduced microbial diversity in CL infected samples, whereas beta diversity analysis indicated clear difference between CL infected and contralateral skin microbiomes. The findings indicate that CL is associated with localized microbial dysbiosis characterized by altered community structure. These findings highlight the significance of skin microbiome as a contributing factor in CL pathogenesis and suggest that microbiome targeted approach may complement existing therapeutic strategies.}, } @article {pmid42349567, year = {2026}, author = {Wang, J and Wen, J and Zhang, X and Zhang, X and Wu, P}, title = {Sulfide-mediated anammox performance under antibiotics stress: Linking antibiotic resistance genes, functional microbes and nitrogen-sulfur metabolism.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135244}, doi = {10.1016/j.biortech.2026.135244}, pmid = {42349567}, issn = {1873-2976}, abstract = {Anaerobic ammonium oxidation (anammox), a sustainable and energy-efficient biological nitrogen removal process, is vulnerable to antibiotic stress during stable operation, while the mechanism of functional recovery mediated by sulfides remains unclear. This study systematically analyzed the response characteristics of the anammox process under sustained high-concentration oxytetracycline (OTC) and sulfamethoxazole (SMX) exposure, and further evaluated the potential of sulfide as an exogenous regulatory factor to mitigate antibiotic stress. Results indicate that sustained high concentration OTC and SMX exposure impaired the system's nitrogen removal performance, while the removal efficiencies of ammonium and nitrite successfully recovered to 85% and 83%, respectively, following sulfide addition. Metagenomic analysis suggested that the addition of sulfide was accompanied by an increased abundance of potential genes related to sulfur and nitrogen metabolism. Moreover, sulfide may alleviate antibiotic stress by facilitating metabolic interactions related to electron transfer and increasing the potential for SMX degradation. Furthermore, under OTC and SMX stress, a 20% increase in the abundance of Brocadia sapporoensis harboring ARGs was closely associated with the addition of sulfide. This study elucidates the biological mechanisms by which sulfides mitigate antibiotic stress, providing a theoretical basis for recovery strategies of anammox under an intensified stress model.}, } @article {pmid42349748, year = {2026}, author = {Ortega-Yago, A and Rubio, P and Ulldemolins, P and Baeza-Oliete, J and Bas, P and Bas, T}, title = {What's new in spinal instrumentation-related infections.}, journal = {Revista espanola de cirugia ortopedica y traumatologia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.recot.2026.06.008}, pmid = {42349748}, issn = {1988-8856}, abstract = {Infections associated with spinal instrumentation represent one of the most complex complications in spine surgery and frequently involve biofilm-forming pathogens that compromise the effectiveness of antimicrobial therapies. Diagnosis-particularly in chronic cases-requires the use of advanced microbiological techniques, such as implant sonication, next-generation metagenomic sequencing, and prolonged culture incubation. Therapeutic strategies depend on the chronicity of the infection and the stability of the implant, ranging from surgical debridement with retention of osteosynthesis material to staged delayed re-instrumentation. Empirical antibiotic therapy should be initiated promptly and subsequently adjusted according to microbiological results. Prevention remains a fundamental pillar and includes strict perioperative optimization. Favorable outcomes rely on early detection, a multidisciplinary team approach, and individualized surgical and antimicrobial management based on accurate clinical and radiological assessment.}, } @article {pmid42349820, year = {2026}, author = {Zhou, Y and Zhong, WJ and An, XL and Huang, FY and Guo, XY and Gao, MK and Xu, MR and Huang, X and Li, H and Zhang, B and Springael, D and Su, JQ}, title = {FThe ISChip: A High-Throughput qPCR Array for Absolute Quantification of Insertion Sequences across the One Health Continuum.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128649}, doi = {10.1016/j.envpol.2026.128649}, pmid = {42349820}, issn = {1873-6424}, abstract = {Insertion sequences (IS) are pivotal mobile genetic elements that shape bacterial genome plasticity and act as critical drivers of environmental genetic hazards by accelerating the dissemination of antimicrobial resistance. However, high-throughput, absolute quantification of IS elements across diverse environmental matrices remains a significant technical challenge, as conventional short-read metagenomics often lacks the sensitivity and resolution required for profiling low-abundance and highly repetitive targets. Here, we developed ISChip, a high-capacity qPCR array for the multiplexed absolute quantification of 183 prevalent IS elements, serving as a robust quantitative complement to metagenomics. The platform was rigorously validated using 119 primer sets, demonstrating high specificity, efficiency, and a superior absolute sensitivity (limit of quantification: 23-28 copies per reaction) compared to conventional qPCR. We applied ISChip to 69 anthropogenically impacted samples spanning 13 matrices, including air, wastewater, soil, and human/animal feces, representing a comprehensive One Health continuum. Our results revealed a distinct compartmentalization of IS communities and identified wastewater, sludge, sediments, and human feces as primary IS hotspots. Notably, we discovered a highly conserved "core IS assemblage" in human feces, suggesting a unique niche for IS-driven microbial evolution. By providing a scalable and absolute quantitative framework, this study uncovers the extreme spatial magnitude of these biological hazards, serving as a powerful tool for monitoring genetic pollution across the One Health framework.}, } @article {pmid42350342, year = {2026}, author = {Lyu, R and Zhou, P and Li, Z and He, Q and Fu, X and Wen, W and Zhang, C and Zhang, T}, title = {[HLA-B27 alters gut microbial composition and promotes susceptibility to intestinal inflammation].}, journal = {Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology}, volume = {42}, number = {6}, pages = {499-510}, pmid = {42350342}, issn = {1007-8738}, abstract = {Objective This study aimed to investigate the impact of human leukocyte antigen B27 (HLA-B27)/β2m gene expression on the gut microbiota and metabolites, and to elucidate its role in the pathogenesis of spinal arthritis (SpA)-associated intestinal inflammation. Methods Transgenic mice expressing HLA-B27/β2m without spontaneous inflammation were employed. Integrated multi-omics analyses, including metagenomics and metabolomics, were conducted to profile microbial and metabolic changes at prenatal, early colonization, and stable colonization stages. Inflammatory susceptibility was further assessed using a dextran sulfate sodium (DSS)-induced colitis model. Results Expression of HLA-B27/β2m significantly altered the gut microbiota structure, promoting the expansion of Gram-negative bacteria and inhibiting Gram-positive populations. Metabolomic profiling revealed enhanced arachidonic acid metabolism, elevated levels of pro-inflammatory metabolites such as prostaglandins, and a reduction in anti-inflammatory flavonoids. These findings collectively indicated a pro-inflammatory intestinal microenvironment, which was corroborated by exacerbated colitis upon DSS challenge in animal models. Conclusion The HLA-B27/β2m gene modulates gut microbial composition and metabolic balance, predisposing the intestine to inflammatory responses. These results provide novel mechanistic insights into the "gut-joint axis" in SpA pathogenesis.}, } @article {pmid42350492, year = {2026}, author = {Dini, H and Chenghang, S and Tong, X and Yixin, L and Tianchun, P and Shunfu, H and Yanqiang, Y and Yibo, H}, title = {Integrated analyses of metagenomics, metabolomics and culture-based assays reveal functional roles of gut microbiota in Felidae.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01066-9}, pmid = {42350492}, issn = {2055-5008}, support = {32370552//National Natural Science Foundation of China/ ; 32325010//National Natural Science Foundation of China/ ; 2023YFF1304800//National Key Program of Research and Development of Ministry of Science and Technology/ ; }, abstract = {The functional roles of gut microbiota in carnivores remain poorly understood. Here, we integrated metagenomics, metabolomics, proteomics and culture-based functional assays to characterize metabolic potential of gut microbiota across 14 captive Felidae species. Comparative metagenomics analysis revealed that the Felidae gut microbiome is distinct from that of non-Felidae and reflects carnivorous dietary patterns. Genus-level core microbiota were dominated by Clostridium, Collinsella and Bacteroides, with functional enrichment in carbohydrate and amino acid metabolism. Of 219 reconstructed metagenome-assembled genomes (MAGs), 27 were identified as core MAGs containing proteases- and lipases- encoding genes, with ATP-dependent Clp proteases predominating and enriched KEGG orthologs mainly associated with amino acid metabolism. Fecal metabolomics identified 1316 metabolites shared among Felidae species, with KEGG analysis showing they were involved in amino acid and lipid metabolism and significantly enriched in protein digestion and absorption pathway. The amino acid- and lipid-related metabolites were correlated with the relative abundance of core MAGs. Culture-based assays revealed proteolytic and lipolytic activities across isolates, supported by proteomics evidence of predominant ATP-dependent proteases. In vitro fermentation with representative isolates generated fatty-acid-dominated metabolites consistent with fecal metabolomic profiles. Together, our findings demonstrate that Felidae gut microbiota play a critical role in amino acid metabolism for carnivory.}, } @article {pmid42350494, year = {2026}, author = {Beiko, RG and Tolman, J and Barawi, SS and Fares, M and Murthy, SSN and Knox, T and Mackie, CM and Grundke, I and Jeffery, NW and Stanley, RRE and Sieben, V and LaRoche, J}, title = {Automated eDNA and eRNA profiling for biodiversity monitoring in marine and freshwater ecosystems.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-58421-1}, pmid = {42350494}, issn = {2045-2322}, abstract = {Biodiversity monitoring is essential to measure the impacts of pollution, invasive species, and the longer-term effects of climate change. Automated samplers enable temporally flexible, remote collection of environmental DNA (eDNA), improving access to time-sensitive events. The Dartmouth Ocean Technologies (DOT) Preserving eDNA Sampler has proven effective in multi-month marine deployments, but further validation is needed across a broader range of habitats and water chemistries, and to establish its suitability for collection and assessment of environmental RNA (eRNA). In this study, we collected samples near the surface (1-1.5 m depth) of a brackish pond, a freshwater lake, and two marine harbours. We identified patterns of species turnover consistent with transitions among aquatic environments, including invasive species such as smallmouth bass and chain pickerel in the freshwater lake. Automated deployment in Halifax Harbour following a significant rainfall event detected nearly ten times as many probable fecal-associated bacteria by proportion at this site relative to Lunenburg Harbour. Preserved eRNA allowed the identification of taxa below the eDNA limit of detection. Our pilot study demonstrates the feasibility of using the DOT sampler for longer-term biomonitoring in a diverse range of aquatic habitats, yielding ecological insights that would not be attainable through manual sampling alone.}, } @article {pmid42350644, year = {2026}, author = {Suissa, D and Fidelle, M and Reich, E and Pham, TN and Thomas, S and Björk, JR and Liu, P and Zhao, L and Kitaoka, K and Piard, E and Lebhar, I and Tian, AL and Thelemaque, C and Alves Costa Silva, C and Deutsch, E and Loriot, Y and Segata, N and Piccinno, G and Hospers, GAP and Maleki Vareki, S and Silverman, MS and Lenehan, JG and Bataille, V and Boulate, D and Kuznetsova, T and Weersma, RK and Messaoudene, M and Durand, S and van der Aalst, CM and de Koning, HJ and Schuler-Thurner, B and de Vries, IJM and Rafie, E and Saliby, RM and Machaalani, M and Haferkamp, S and Schilling, B and Porcari, S and Ciccarese, C and Iacovelli, R and Cremolini, C and Choueiri, TK and Elkrief, A and Kroemer, G and Heinzerling, L and Chamoto, K and Ianiro, G and Routy, B and Derosa, L and Paragios, N and Zitvogel, L}, title = {Metabolic determinants of cancer immunotherapy outcomes identified by plasma profiling.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {42350644}, issn = {1546-170X}, abstract = {Immune-checkpoint inhibitors benefit a subset of patients with advanced cancer, and the metabolic determinants of response remain unclear. Here, using targeted metabolomics and metagenomics, we profiled 4,336 plasma samples from 1,714 patients across five tumor types and 16 cohorts spanning Europe and North America, longitudinally sampled during five immune-checkpoint inhibitor-based treatment modalities, including fecal microbiota transplantation. A multimodal machine-learning framework integrating 154 metabolites with clinical variables identified five metabolites, age, body mass index and renal function as predictors of 12-month progression-free survival. The model achieved areas under the curve of 0.88 in training and 0.73 in validation cohorts of 105 and 30 patients, respectively and generalized across seven external cohorts. Histidine was a favorable prognostic feature of survival, whereas long-chain fatty acids and succinate were negatively associated with outcome. Histidine supplementation enhanced antitumor immunity in mice. Histidine-rich diets improved progression-free survival in patients lacking dysbiotic microbiome signatures associated with histidine catabolism.}, } @article {pmid42337002, year = {2026}, author = {Guéguen, LM and Mathieu, A and Pelletier, S and Woo, A and Misra, N and Moreau, M and Perin, O and Droit, A}, title = {META-DIFF: a k-mer-based pipeline that detects differentially abundant sequences in metagenomics whole genome sequencing.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-59138-x}, pmid = {42337002}, issn = {2045-2322}, abstract = {Traditional case-control metagenomic studies are constrained by their dependence on taxonomic and functional databases. Because annotation occurs before differential analysis, they are limited to known elements and keep function and taxonomy separate. Although binning strategies have emerged to reconstruct genomes and mitigate this issue, they still require an assembly step, preventing the use of all available sequencing data. Here, we introduce META-DIFF, a pipeline based on differentially abundant k-mers independently of any prior annotation. From those k-mers, it reconstructs longer sequences and provides biological context, as well as the best set of unitigs to discriminate between conditions. Across both taxonomy-centric and functionally-centric benchmarks, it showed robust performance and displayed great reproducibility. It also behaved more conservatively than did other univariate methodologies, i.e. it maintained a high precision at the expense of recall, particularly in conditions of low fold-change and limited sequencing depth. The efficacy of META-DIFF was further validated through its application to a real-world colorectal cancer dataset, which produced both confirmatory and novel results compared with those of previous publications. The pipeline is able to exploit all reads and identify differentially abundant elements, including unknown DNA, prior to annotation. With the guidelines provided, META-DIFF provides users with great exploratory power to unravel microbiome changes.}, } @article {pmid42337243, year = {2026}, author = {Hoskinson, C and Dai, DLY and Petersen, C and Moraes, TJ and Mandhane, PJ and Simons, E and Kozyrskyj, AL and Azad, MB and Subbarao, P and Turvey, SE}, title = {Saccharomycetes and Malassezia fungi associate with early-life gut maturation and allergic disease risk in childhood.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42337243}, issn = {2041-1723}, support = {[274CHI] and [EC1-144621]//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; [274CHI] and [EC1-144621]//AllerGen (AllerGen National Center of Excellence)/ ; [274CHI] and [EC1-144621]//Genome Canada (Génome Canada)/ ; }, mesh = {Humans ; *Malassezia/genetics/isolation & purification/physiology ; Infant ; Feces/microbiology ; *Dermatitis, Atopic/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; Mycobiome ; Male ; Female ; Child, Preschool ; *Food Hypersensitivity/microbiology/immunology ; Child ; Metagenome ; Metagenomics ; *Hypersensitivity/microbiology ; }, abstract = {While early-life gut bacterial microbiota maturation has been well studied and linked to childhood disease, the development of the gut mycobiome remains poorly understood. Few studies have defined fungal succession in infancy, and even fewer have integrated fungal and bacterial maturation, allowing interkingdom analysis within the same individuals. In this study, we analyzed a subset of the CHILD Study Cohort (n = 1409 participants) and generated both ITS2 amplicon and shotgun metagenomic sequencing data from infant stool samples (n = 2256 samples). We hypothesized that the infant mycobiome follows predictable developmental trajectories that influence childhood health outcomes. We found that fungi are reliable biomarkers for gut maturation, with the notable emergence of Saccharomyces and Malassezia as some of the strongest indicators across both fungi and bacteria. Fungal composition was strongly associated with infant age (R = 0.79, p < 0.001) and with the later development of both atopic dermatitis (adj. p = 0.029) and food allergy (adj. p = 0.013). Further, differences in fungal development coincided with changes in key gut immune-modulating metabolites such as butyrate and glycerol, indicating the functional importance of infant gut mycobiome maturation in early-life immune development. Together, these results highlight the early life mycobiome as a potential therapeutic target to mitigate allergic disease development.}, } @article {pmid42337676, year = {2026}, author = {Gorji, AE and Xue, B and Yan, T and Sadkowski, T and Chen, X and Cristobal-Carballo, O and Morrison, S and Razban, V and Smith, L and Stergiadis, S and Theodoridou, K and Shirali, M}, title = {Apple pomace and hempseed cake can reduce methane intensity (CH4/DMI) and alter the rumen microbiome in dairy cows: a shotgun metagenomic approach.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42337676}, issn = {1674-9782}, support = {Project No. 21/5/01//Department of Agriculture, Environment and Rural Affairs (DAERA)/ ; }, abstract = {BACKGROUND: With growing attention to environmental impacts, the dairy sector is increasingly focused on implementing strategies that lower methane emissions and enhance sustainability while maintaining productivity and economic viability. Utilizing agro-industrial by-products as alternative feed ingredients supports circular economy goals, lowers feed costs, and may benefit rumen fermentation and environmental performance in dairy cows.

METHODS: Forty-five mid-lactation Holstein cows were assigned to three diets, Control, Apple Pomace (AP), or Hempseed Cake (HC) for 24 d. Feed intake, milk yield, rumen fermentation, methane emissions, and nutrient use were measured. Rumen samples underwent shotgun metagenome sequencing and bioinformatics analysis to assess microbial and functional changes.

RESULTS: Values are reported as mean ± SEM. Shotgun metagenomic sequencing revealed that both supplements significantly increased the relative abundance of Bacteroidota (AP: 56.7% ± 2.8%, P = 0.032; HC: 54.5% ± 3.4%, P = 0.048) compared to the Control (48.2% ± 3.1%). Concurrently, Bacillota (formerly Firmicutes) abundance decreased, significantly reducing the Bacillota/Bacteroidota ratio (formerly the Firmicutes/Bacteroidetes ratio) from 0.81 ± 0.06 (Control) to 0.58 ± 0.05 for AP (P = 0.012) and 0.64 ± 0.05 for HC (P = 0.034). Functional analysis showed that AP increased the abundance of Segatella bryantii (2.1-fold, P < 0.01), associated with a 1.52-fold enrichment in propionate metabolism pathways (P = 0.019). Phenotypically, AP significantly reduced the acetate-to-propionate ratio (AP: 2.41 vs. Control: 4.50; P = 0.0075) and methane emissions per unit of dry matter intake (CH4/DMI) (AP: 20.33 vs. Control: 24.27 g/kg; P = 0.016). HC supplementation upregulated fiber-degrading taxa such as Xylanibacter ruminicola (1.6-fold) and enriched xylanase families (GH10: 1.58-fold, P = 0.035), alongside a significant reduction in methane intensity (CH4/DMI). Total methane output, feed intake, and milk yield were not significantly changed by treatments (P > 0.05).

CONCLUSIONS: In this short-term (24-d) controlled feeding study in mid-lactation Holstein cows, AP and HC were associated with distinct microbial and functional shifts alongside lower methane intensity, with AP linked to propanoate-related signals and HC to fiber-degrading functions; however, ruminal H2 concentration and methanogenesis/hydrogen-metabolism markers were not quantified, so the proposed mechanisms should be interpreted as plausible inferences rather than direct physiological evidence.}, } @article {pmid42338488, year = {2026}, author = {Chen, B and Chen, J and Feng, Z and Lv, H and Lin, Q and Jiang, G}, title = {Gut microbiota reconstruction after liver transplantation and its association with early postoperative infections in patients with liver failure.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1845273}, pmid = {42338488}, issn = {2235-2988}, mesh = {Humans ; *Liver Transplantation/adverse effects ; Female ; *Gastrointestinal Microbiome ; Retrospective Studies ; *Postoperative Complications/microbiology ; Dysbiosis/microbiology ; Male ; *Liver Failure/surgery/complications ; Probiotics/administration & dosage/therapeutic use ; Middle Aged ; Metagenomics ; Feces/microbiology ; Adult ; *Bacterial Infections/microbiology/epidemiology ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {BACKGROUND: Postoperative infection remains a major cause of morbidity after liver transplantation (LT) in patients with liver failure. Increasing evidence suggests that gut microbiota dysbiosis may contribute to infection risk, but its dynamic changes after LT are not fully understood.

METHODS: This retrospective study included 60 patients with liver failure who underwent LT and developed postoperative infection-related risk. Patients were divided into a probiotic group and a non-probiotic group. Fecal samples were collected before transplantation and on postoperative days 7, 14, 21, and 28. Metagenomic sequencing was performed to analyze gut microbial composition, diversity, and antibiotic resistance genes.

RESULTS: The probiotic group showed a significantly lower rate of postoperative bacterial infection, especially intra-abdominal infection. After LT, gut microbiota gradually recovered in both groups, but restoration was faster in the probiotic group. The non-probiotic group showed persistent dysbiosis, characterized by enrichment of opportunistic pathogens such as Enterococcus and Klebsiella, whereas beneficial genera including Bifidobacterium and Lactobacillus were more abundant in the probiotic group. Antibiotic resistance genes were also more enriched in the non-probiotic group.

CONCLUSION: Early postoperative gut microbiota reconstruction is closely associated with infectious complications after LT, and modulation of gut microbiota may help improve postoperative outcomes.}, } @article {pmid42338489, year = {2026}, author = {Tang, C and Li, B and Chen, J and Liu, X and She, C}, title = {Causal relationship between gut microbiota and adenomyosis: metagenomics sequencing and Mendelian randomization.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1772864}, pmid = {42338489}, issn = {2235-2988}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; *Adenomyosis/microbiology/etiology ; *Mendelian Randomization Analysis ; *Metagenomics/methods ; Middle Aged ; Adult ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: Emerging evidence implicates the gut microbiota in the pathogenesis of adenomyosis (AM); however, whether this association is causal and through which mechanisms it operates remain largely unknown.

METHODS: To interrogate potential causal relationships, we performed a two-sample Mendelian randomization (MR) analysis leveraging inverse-variance weighting (IVW) as the primary estimator, complemented by MR-Egger, weighted median, and weighted mode approaches, to evaluate the causal effects of gut microbial taxa and microbiota-derived metabolic pathways on AM. We further conducted mediation analyzes to delineate the role of circulating immune-cell phenotypes in this process. In parallel, in an independent clinical cohort, 22 patients with AM and 23 age-matched healthy controls recruited from the health-screening center of our institution were enrolled according to stringent inclusion and exclusion criteria (including antibiotic-use history and long-term local residency) and subjected to shotgun metagenomic sequencing. Significant differences in the types of bacterial communities were observed between the AM group and the control group. Subsequently, the results were cross-compared with those of the MR study using the Linear Discriminant Analysis Effect Size (LEfSe) method, and further verified using the ANCOM-BC method to determine the common microbial characteristics.

RESULTS: MR analysis identified ten microbial taxa and ten metabolic pathways with evidence of potential causal associations with AM. Of these, nine taxa and five pathways were associated with a reduced risk of AM, including Alistipes indistinctus (OR = 0.847, 95% CI = 0.754-0.951, p = 0.005, p~FDR~ > 0.05), Ruminococcus torques (OR = 0.818, 95% CI = 0.712-0.941, p = 0.005, p~FDR~ > 0.05), class Deltaproteobacteria (OR = 0.780, 95% CI = 0.629-0.967, p = 0.024, p~FDR~ > 0.05), family Desulfovibrionaceae (OR = 0.780, 95% CI = 0.629-0.967, p = 0.024, p~FDR~ > 0.05), order Desulfovibrionales (OR = 0.780, 95% CI = 0.629-0.967, p = 0.024, p~FDR~ > 0.05), Parasutterella excrementihominis (OR = 0.875, 95% CI = 0.784-0.977, p = 0.017, p~FDR~ > 0.05), Ruminococcus bromii (OR = 0.836, 95% CI = 0.718-0.972, p = 0.020, p~FDR~ > 0.05), Bacteroides finegoldii (OR = 0.919, 95% CI = 0.855-0.987, p = 0.020, p~FDR~ > 0.05), and the genus Parasutterella (OR = 0.886, 95% CI = 0.797-0.986, p = 0.026, p~FDR~ > 0.05); the five protective pathways comprised dTDP-L-rhamnose biosynthesis (OR = 0.819, 95% CI = 0.674-0.995, p = 0.045, p~FDR~ > 0.05), lactose and galactose degradation (OR = 0.818, 95% CI = 0.689-0.972, p = 0.022, p~FDR~ > 0.05), the reductive TCA cycle (OR = 0.919, 95% CI = 0.851-0.993, p = 0.032, p~FDR~ > 0.05), allantoin degradation to glyoxylate (OR = 0.907, 95% CI = 0.830-0.991, p = 0.030, p~FDR~ > 0.05), and glycolysis I (from glucose-6-phosphate) (OR = 0.850, 95% CI = 0.747-0.967, p = 0.013, p~FDR~ > 0.05).Conversely, one taxon and five pathways were associated with an increased risk of AM: the genus Lactobacillus (OR = 1.083, 95% CI = 1.008-1.164, p = 0.030, p~FDR~ > 0.05), degradation of glucose and glucose-1-phosphate (OR = 1.202, 95% CI = 1.056-1.369, p = 0.005, p~FDR~ > 0.05), peptidoglycan biosynthesis (in Enterococcus faecium) (OR = 1.138, 95% CI = 1.007-1.285, p = 0.039, p~FDR~ > 0.05), pyruvate fermentation to acetone (OR = 1.118, 95% CI = 1.001-1.248, p = 0.048, p~FDR~ > 0.05), glycerol degradation to butanol (OR = 1.118, 95% CI = 1.011-1.237, p = 0.031, p~FDR~ > 0.05), and de novo pyrimidine deoxyribonucleotide biosynthesis (OR = 1.216, 95% CI = 1.063-1.390, p = 0.004, p~FDR~ > 0.05).Mediation analysis revealed that the immune phenotype "CD24 on CD24[+]CD27[+] B cells" mediated the pathway from Ruminococcus bromii to AM, accounting for 32.91% of the total effect (p = 0.020).Shotgun metagenomic profiling of the clinical cohort demonstrated no significant differences in α-diversity or β-diversity between the AM and control groups. At the phylum level, the relative abundance of Desulfobacterota was significantly decreased in the AM group (p< 0.05), and at the genus level, Alistipes was similarly reduced (p< 0.05). LEfSe analysis further indicated enrichment of Escherichia and Clostridium in the AM group, whereas Desulfobacterota and Rikenellaceae were enriched in the Control group. Matching the aforementioned results with the Mendelian randomization (MR) outcomes revealed that Desulfovibrionales and Desulfovibrionaceae constituted the shared microbial taxa. This finding was subsequently re-validated and confirmed using the ANCOM-BC method.

CONCLUSIONS: Integrating genetic causal inference with clinical metagenomic validation, this study provides convergent evidence that specific gut microbial taxa, their associated metabolic pathways, and immune-cell-mediated mechanisms may be causally implicated in the development of AM. These findings offer a framework for future microbiota-targeted preventive and therapeutic strategies against AM.}, } @article {pmid42338795, year = {2026}, author = {Chen, J and Wei, J and Liu, T and Chen, J and Yuan, Y and Zhang, F and Zhang, J}, title = {Gut microbiome dynamics in autism: a prospective nested case-control study demonstrates microbial-clinical associations following rehabilitation interventions.}, journal = {Frontiers in neuroscience}, volume = {20}, number = {}, pages = {1820904}, pmid = {42338795}, issn = {1662-4548}, abstract = {BACKGROUND: Children with autism spectrum disorder (ASD) commonly exhibit gut microbiota dysbiosis and metabolic abnormalities, yet the mechanisms linking these changes to clinical symptoms remain unclear.

OBJECTIVE: This study employed a nested case-control design and multi-omics approaches to evaluate the effects of rehabilitation intervention on clinical symptoms and gut microbiota in children with ASD, identify distinct microbial-metabolic signatures, and explore their mechanistic links with sleep disorders and developmental abilities.

METHODS: Within a prospectively established pediatric cohort (n = 45), we implemented a nested case-control design including 26 ASD children (18 males, 8 females; mean age 61.79 ± 11.15 months) and 19 age- and sex-matched healthy controls. All ASD participants received standardized rehabilitation therapy (2 h/day, 5 days/week for 6 months) comprising occupational therapy and cognitive-linguistic training. Primary outcomes included comprehensive clinical assessments [Griffiths Development Scales-Chinese (GDS-C), Children's Sleep Habits Questionnaire (CSHQ), Autism Behavior Checklist (ABC), Childhood Autism Rating Scale (CARS)] and longitudinal multi-omics analysis (metagenomic sequencing and LC-MS-based metabolomics). Association analyses were performed with FDR correction (q < 0.05).

RESULTS: Following the 6-month rehabilitation intervention, significant clinical improvements were observed in sleep quality (CSHQ total and subscores) and developmental performance (GDS-C). Multi-omics profiling revealed distinct biological signatures in ASD children compared to healthy controls, characterized by elevated Intestinibacter_bartlettii and reduced levels of ornithine and siderophore nonribosomal peptide biosynthesis. Crucially, correlation analysis demonstrated that, after FDR correction, ornithine levels were significantly positively correlated with multiple GDS-C developmental domains, while tyrosine was associated with parasomnias. These findings establish a potential mechanistic link where amino acid metabolism connects gut microbial shifts to clinical phenotypes.

CONCLUSION: This study demonstrates that rehabilitation intervention synchronously ameliorates clinical symptoms and modulates the gut-metabolic profile in ASD. The identified associations between specific metabolites (ornithine and tyrosine) and clinical outcomes suggest a metabolic mechanism underlying the gut-brain axis, highlighting the potential of these metabolites as biomarkers for therapeutic monitoring. Further large-scale studies are needed to validate these findings.}, } @article {pmid42338857, year = {2026}, author = {Baumgartner, EE and Weltin, L and Whitten, JP and Fahey, TE and Baumgartel, PB and Farrell, JJ}, title = {An Unusual Infectious Cause of Abdominal Pain: Non-typhoidal Salmonella Aortitis Complicating an Endovascular Aortic Stent Graft.}, journal = {Cureus}, volume = {18}, number = {5}, pages = {e109509}, pmid = {42338857}, issn = {2168-8184}, abstract = {Non-typhoidal Salmonella (NTS) is a rare but life-threatening cause of infectious aortitis and mycotic aneurysm formation, predominantly affecting immunocompromised patients and those with pre-existing vascular pathology or prosthetic hardware. Diagnosis is frequently delayed due to its non-specific clinical presentation and the poor sensitivity of conventional blood cultures. A 73-year-old immunocompromised woman with a history of penetrating aortic ulcer and prior endovascular aortic stent graft placement presented with progressive abdominal pain and para-aortic soft tissue thickening encasing the infrarenal aorta. Blood cultures were negative; however, CT-guided peri-aortic tissue aspiration and metagenomic next-generation sequencing (mNGS; Karius test) identified Salmonella enterica serovar Enteritidis susceptible to ampicillin, ceftriaxone, levofloxacin, nalidixic acid, and trimethoprim/sulfamethoxazole. The most probable infection source was the patient's prolonged daily consumption of unpasteurized eggs from backyard chickens. She was treated with intravenous (IV) ceftriaxone for 30 days followed by 18 months of oral cephalexin suppression, with significant radiographic improvement at three-month follow-up. Surgical intervention was deferred given her high operative risk from metastatic malignancy and multiple comorbidities. This case is notable for its documentation of culture-negative NTS aortitis complicating an endovascular stent graft, in which mNGS was essential for pathogen identification. It further highlights the importance of eliciting detailed dietary exposure history in high-risk patients, the novel diagnostic challenge posed by concurrent autoimmune disease mimicking non-infectious vasculitis, and the feasibility of antibiotic-only management in carefully selected surgical non-candidates.}, } @article {pmid42338881, year = {2026}, author = {Wang, H and Wang, Y and Yang, L and Feng, J and Tian, S and Chen, L and Huang, W and Liu, J and Wang, X}, title = {Correction: Integrated 16S rRNA sequencing and metagenomics insights into microbial dysbiosis and distinct virulence factors in inflammatory bowel disease.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1852209}, doi = {10.3389/fmicb.2026.1852209}, pmid = {42338881}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2024.1375804.].}, } @article {pmid42338883, year = {2026}, author = {Goktas, NT and Guven, S and Dinleyici, EC}, title = {The combination of Lactobacillus acidophilus DSMZ 26280 and Limosilactobacillus reuteri DSMZ 25441 has an impact on clinical course and gut microbiota of children with acute infectious diarrhea.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1792126}, pmid = {42338883}, issn = {1664-302X}, abstract = {INTRODUCTION: Previous studies and society guidelines have proposed probiotics as a complementary therapy for acute infectious diarrhea, which may shorten the disease course, yet strain-specific effects and microbiome correlates remain incompletely defined. We aim to evaluate the effect of a combination of Lactobacillus acidophilus and Limosilactobacillus reuteri on the duration of diarrhea and gut microbiota composition in children with acute infectious diarrhea.

PATIENT AND METHODS: In a prospective, randomized, controlled, open-label trial at a tertiary pediatric emergency department (March-August 2024), children aged 1-6 years with acute infectious diarrhea lasting less than 24 h were allocated 1:1 to standard therapy (oral rehydration ± intravenous fluids) with or without 5-day probiotic (L. acidophilus DSMZ 26280; 108 CFU) and (L. reuteri DSMZ 25441; 108 CFU). Primary outcomes were duration of diarrhea and the proportion diarrhea-free at 72 h. The secondary outcome measures included the proportion of diarrhea-free children during first 10th day of the study. A subgroup analysis for gut microbiota composition at Day 0, 10th and 30th days of the study have been performed.

RESULTS: Of 145 enrolled children, 79 in the probiotic group (34 girls, 45 boys) and 66 in the control (30 girls and 36 boys); baseline demographics were comparable. The duration of diarrhea was significantly reduced in the probiotic group compared to the control group (46.4 ± 29.6 h vs. 81.6 ± 38.5 h, p < 0.001). The percentage of diarrhea-free children was significantly larger in the probiotic group at 72 h compared to the control (86.0% vs. 33.3%, p < 0.001). Persistence of diarrhea was lower in the probiotic group at 24, 48, and 96 h (all p < 0.001) and at day 6 (2.5% vs. 15.1%; p < 0.05); by days 7-10, persistence was rare in both groups. The probiotic combination is well-tolerated, and no adverse events have been reported. Alpha diversity indices were unchanged within/between groups. Bray-Curtis and Jaccard PCoA showed no between-group separation; unweighted UniFrac revealed differences within the probiotic group (day 1 vs. day 30) and between groups at day 30 (p < 0.05). LEfSe indicated enrichment of taxa associated with recovery in the probiotic arm and control group, and there is difference between group at Day 30.

CONCLUSION: This study evaluates a specific combination of L. acidophilus DSMZ 26280 and L. reuteri DSMZ 25441 in a randomized controlled setting, adding to the growing body of strain-specific probiotic research in pediatric acute infectious diarrhea. Adding probiotics to treatment is well-tolerated and reduces the duration of diarrhea by approximately 35 h when it starts in the early hours of infection. This probiotic combination use is associated with modest phylogenetics shifts in gut microbiota composition, with enrichment of certain taxa that have been previously associated with gut homeostasis in other contexts; however, their functional and clinical significance in this setting remains unclear. Larger blinded trials are warranted to confirm durability and detailed metagenomic analysis including metabolomics.}, } @article {pmid42338911, year = {2026}, author = {Huang, Y and Chen, F and Yu, Z and Sheng, X and Wen, S and Zhang, X and Tang, W and Huang, M}, title = {Integrated analysis of physicochemical properties, microbiome, and flavor profiles for differentiating two aroma grades of sauce-flavor Daqu.}, journal = {Food chemistry: X}, volume = {37}, number = {}, pages = {104092}, pmid = {42338911}, issn = {2590-1575}, abstract = {Aroma characteristics are critical indicators for evaluating sauce-flavor Daqu quality. This study systematically compared physicochemical properties, enzyme activities, microbiomes, and flavor profiles of first-grade (GF) and second-grade (GS) aroma Daqu. GF had higher total acidity, amino nitrogen content, acid protease activity, a lower pH, and was correlated with enrichment of bacteria potentially associated with flavor precursor production such as Kroppenstedtia guangzhouensis and Kroppenstedtia eburnea. GS showed higher liquefying/cellulase activities and pH, and was associated with dominance by hydrolytic fungi such as Paecilomyces variotii and off-odor-related Oceanobacillus. HS-SPME-GC-MS combined with VIP and OAV analyses identified 11 differential volatile compounds. Aldehydes were strongly correlated with positive aroma grading and may serve as potential indicators associated with grade differentiation, while GS accumulated dimethyl trisulfide correlating with off-odors. The findings reveal the relationships between multi-omics characteristics and aroma grade differentiation of Daqu, and provide theoretical support for Daqu quality evaluation and production regulation.}, } @article {pmid42338938, year = {2026}, author = {Zhong, L and Xia, K and Fan, Y}, title = {Sigmoid colonic tuberculosis presenting as a colovesical fistula mimicking colorectal malignancy: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1857599}, pmid = {42338938}, issn = {2296-858X}, abstract = {BACKGROUND: Intestinal tuberculosis (ITB) most commonly involves the ileocecal region. Isolated sigmoid colonic tuberculosis complicated by a colovesical fistula is extremely rare and may closely mimic colorectal malignancy or Crohn's disease (CD).

CASE PRESENTATION: A 73-year-old man presented with subacute diarrhea, fever, and lower urinary tract symptoms. Laboratory tests showed markedly elevated inflammatory markers and anemia. Cross-sectional imaging demonstrated segmental thickening of the sigmoid colon, pericolic lymphadenopathy, multiple serous effusions, and findings consistent with a colovesical fistula, including bladder wall disruption and intravesical gas. Colonoscopy revealed a circumferential stenosing lesion with irregular ulceration, raising strong suspicion for colorectal malignancy or CD.

Initial histopathology showed only mixed inflammatory cell infiltration without granulomas or malignant cells, and empirical antimicrobial therapy failed to control the fever. Given the positive immunological testing for tuberculosis and persistent clinical suspicion, acid-fast bacilli staining and metagenomic next-generation sequencing (mNGS) were performed on colonic biopsy tissue. Acid-fast bacilli were detected, and mNGS identified Mycobacterium tuberculosis complex, confirming ITB. Standard anti-tuberculosis therapy was initiated, leading to rapid clinical improvement, complete endoscopic mucosal healing, and radiological resolution of the colovesical fistula.

CONCLUSION: This case highlights that ITB can present as an isolated tumor-like sigmoid lesion complicated by fistula formation. When routine histology is nondiagnostic, especially in the absence of granulomas, integration of imaging, immunological testing, special staining, and molecular diagnostics may be crucial for early diagnosis, avoidance of misdiagnosis, and timely targeted treatment.}, } @article {pmid42339070, year = {2026}, author = {Happi, AN and Ogunsanya, OA and Sijuwola, AE and Saibu, FM and Akano, K and Ayinla, AO and Daodu, RO and Page, B and Olumade, TJ and Oguzie, JU and Oluniyi, PE and Adedokun, OA and Fadele, J and Nwofoke, C and Elias, OT and Ogundana, KE and Lawal, OZ and Nosamiefan, I and Okolie, J and Adelabu, A and Lombardi, K and Eller, LA and Broach, E and Prins, PA and Heeney, JL and Modjarrad, K and Njatou, TLFA and Parker, ZF and McCauley, M and Vasan, S and Parker, E and Collins, ND and Michael, NL and Happi, CT}, title = {Genomic epidemiology and evolutionary analysis of Lassa virus from small mammals suggest bidirectional viral movement across humans and animals.}, journal = {Virus evolution}, volume = {12}, number = {1}, pages = {veag032}, pmid = {42339070}, issn = {2057-1577}, abstract = {Lassa fever is a viral haemorrhagic fever that poses a persistent public health threat in several West African countries, particularly Nigeria. The scarcity of Lassa virus (LASV) sequences isolated from small mammal reservoirs limits our knowledge and understanding of LASV genomic diversity and transmission dynamics. To address this knowledge gap, we sampled 1189 small mammals, including mice, rats, and shrews, from two LASV-endemic states in southern Nigeria (Ondo and Ebonyi States) and tested them for the presence of LASV RNA using reverse transcription-quantitative polymerase chain reaction. Selected quantitative polymerase chain reaction-positive samples were subjected to whole genome sequencing and small mammal speciation through next-generation sequencing outputs. We recorded an overall polymerase chain reaction positivity rate of 61.6%, with rat species demonstrating the highest LASV prevalence. We also conducted a serosurvey of 269 small rodents using indirect Enzyme-Linked Immunosorbent Assay (ELISA) and obtained an overall anti-LASV seroprevalence of 45%. Using the Nextera XT metagenomic sequencing protocol, we produced 55 LASV partial (n = 28) and full-length genomes (n = 27) from small mammals sampled, all of which clustered within sublineage 2g. LASV sequences generated from this study suggest that LASV variation is mostly driven by location, as isolates from this study tend to cluster more closely with other isolates collected from within the same region, rather than by collection date or host. However, samples collected from Ebonyi State were more closely related to isolates collected in Ondo State than to isolates from Edo, despite a larger physical distance. Overall, the data from this study suggest free movement of the virus across states in Nigeria, among humans and various non-human taxa. The finding of LASV in additional small mammal hosts suggests that the virus reservoir is vast and may include many small mammals not well-characterized.}, } @article {pmid42339199, year = {2026}, author = {Acosta-España, JD and Altamirano-Jara, JB and Herrera-Yela, A and Estrella, F and Palacios, S}, title = {Metagenomic identification of Acanthamoeba Rhysodes in chronic skin lesion: Case report and literature review.}, journal = {JAAD case reports}, volume = {73}, number = {}, pages = {160-164}, pmid = {42339199}, issn = {2352-5126}, } @article {pmid42339286, year = {2026}, author = {Dang, Y and Kong, J}, title = {A double pathogen strike: COVID-19 and talaromycosis Co-infection in a patient with post-tuberculosis lung disease.}, journal = {Respiratory medicine case reports}, volume = {62}, number = {}, pages = {102450}, pmid = {42339286}, issn = {2213-0071}, abstract = {An 80-year-old woman from rural Guangxi with post-tuberculosis lung disease (PTLD) (hereinafter referred to as PTLD)presented with one month of cough and fever. One month prior, she had ingested raw rodent meat-a known exposure for Talaromyces marneffei. Chest HRCT showed bilateral tree-in-bud opacities superimposed on prior left lung destruction. Conventional microbiological tests, including acid-fast bacilli smears, were negative. A nasopharyngeal swab was positive for SARS-CoV-2 (cycle threshold 17). Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified both T. marneffei and SARS-CoV-2. Her CD4[+] count was 344/μL and HIV serology was negative. She received nirmatrelvir-ritonavir and sequential amphotericin B followed by voriconazole, with clinical and radiological improvement. This case illustrates that PTLD may serve as a local anatomical risk factor for talaromycosis even without systemic immunodeficiency.}, } @article {pmid42339375, year = {2026}, author = {Tomasi, N and Banchi, E and Manna, V and Celussi, M}, title = {Surface sediments prokaryotic communities: five years of 16S rRNA amplicon sequencing data from the northernmost part of the Mediterranean Sea.}, journal = {Data in brief}, volume = {67}, number = {}, pages = {112971}, pmid = {42339375}, issn = {2352-3409}, abstract = {Surface sediments harbour diverse prokaryotic communities that play a key role in biogeochemical cycling and provide valuable insights when compared with water column communities, allowing for a more comprehensive understanding of marine ecosystem functioning. Specifically, this dataset presents prokaryotic community data from 16 surface sediment samples collected seasonally from June 2020 to May 2025 at the C1-LTER station (45°42'2.99″ N, 13°42'36.00″ E; DEIMS.iDhttps://deims.org/96969205-cfdf-41d8-979f-ff881ea8dc8b) in the Gulf of Trieste, located in the northeastern Adriatic Sea (Mediterranean Sea). Extracted DNA was sequenced following the 16S Metagenomic Sequencing Library Preparation protocol and run on an Illumina NovaSeq 6000 System. Raw reads were filtered and denoised with DADA2, and taxonomic assignment was performed against the Silva 138.2 99% reference database. The dataset provides useful insights into prokaryotic communities and their seasonal variability over five years. Moreover, a focus on specific taxa is provided, such as Cyanobacteriota and Archaea, highlighting patterns of community variability in the sediment. Finally, it shows seasonal stability and generally consistent taxa distribution over time, as indicated by the high proportion of shared taxa at each taxonomic level. The raw data, deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA1442017, include two sets of sequencing reads obtained from surface sediment samples using the Illumina MiSeq and Illumina NovaSeq 6000 sequencing platforms, for a total of 27 16S rRNA gene sequencing FASTQ files. Overall, these data provide valuable insight into the surface sediment community in the northernmost part of the Mediterranean Sea, contributing to long-term research on sediment prokaryotic communities.}, } @article {pmid42339699, year = {2026}, author = {Patel, D and Heidenblut, M and Mau, RL and Wagner, WP and Schwartz, E and Dijkstra, P and Hungate, BA and Ceja-Navarro, JA}, title = {Protist Predation Rapidly Reshapes Soil Microbial Gene Expression Linked to Nutrient Processing, Resistance, Virulence, and Gene Mobility Traits.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c18948}, pmid = {42339699}, issn = {1520-5851}, abstract = {Protists are ubiquitous soil predators that regulate bacterial communities and biogeochemical cycling, yet how their predation alters expression of nutrient-cycling genes and traits linked to antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) in natural soils remains poorly understood. Here, we used a short-term soil microcosm experiment to distinguish the effects of moisture-stimulated resident protists from enhanced predation by an introduced exogenous predatory protist community. Using quantitative stable isotope probing (qSIP) and metagenomic and metatranscriptomic analyses, we tracked protist activity and microbial responses over 3 days. Enhanced predation rapidly reshaped transcriptionally active microbial communities, increasing expression of nitrogen and phosphorus cycling genes while concurrently elevating diversity and transcription of ARGs, VFs, and MGEs, including multidrug-efflux systems, motility-, biofilm-related traits, and phage-associated elements. Metagenome-assembled genome─resolved analyses showed that some resident soil populations were activated by wet-up and remained transcriptionally active under predation pressure, encoding nutrient-cycling, resistance, virulence, and mobility traits that contributed to the functional background of wetted soils. These results suggest that, even over short time periods, protist predation links soil nutrient processing with environmentally relevant resistance and genetic mobility pathways, acting as a crucial ecological driver of gene expression related to nutrient processing and microbial interaction traits during environmental change.}, } @article {pmid42340399, year = {2026}, author = {Mattar, MM and Eraqi, WA and Zaki, MB and Elkashlan, AM and Abouzid, KAM and Aziz, RK and Yassin, AS and Elbehery, AHA}, title = {Metagenomic Analysis of Rural Groundwater Viromes Reveals Bacteriophage Contributions to Groundwater Microbial Ecology.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02818-y}, pmid = {42340399}, issn = {1432-184X}, abstract = {Groundwater ecosystems host diverse microbial communities, yet the diversity and ecological roles of their associated viral genomes remain poorly characterized. Here, we investigated viral community composition, diversity, host associations, lifestyles, and auxiliary metabolic potential in groundwater from three hand pumps located in Toukh, Qalyubia, Egypt, representing distinct local surroundings and potential contamination pressures. Using complementary viral detection approaches and a quality assessment workflow, we recovered 9,534 non-redundant viral contigs spanning a wide range of viral genome quality. Taxonomic profiling revealed dominance of tailed dsDNA bacteriophages (Uroviricota/Caudoviricetes) across all pumps, with ~ 99% of contigs not assigned below the class level. Whereas the viral composition of pump 3 was distinct and its diversity was consistently higher, pumps 1 and 2 clustered together, a pattern mirrored across taxonomic scales and diversity metrics. The majority of predicted viral hosts belonged to phylum Pseudomonadota, followed by Actinomycetota, Bacillota and Bacteroidota, with levels that varied between pumps. Correlation and network analyses showed strong concordance between the relative abundance of bacteria and the abundance of viruses that potentially infect them. Lifestyle prediction indicated a descending relative abundance of viruses with lysogenic lifestyle from pumps 1 through 3. Auxiliary metabolic genes (AMGs) related mainly to nucleotide, amino acid, and cofactor metabolism were detected in all pumps, with distinct pump-specific repertoires suggesting localized viral metabolic strategies. Together, these results demonstrate that groundwater viromes are ecologically structured and highly novel, with the potential ability to modulate host metabolism, highlighting their potential role in shaping subsurface microbial communities.}, } @article {pmid42341025, year = {2026}, author = {Wohl, DL and Belder, PT and Mitchell, BD}, title = {A comparative analysis of the oral microbiome of Amish and non-Amish individuals to strengthen our understanding of variation within the oral microbiome.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0350558}, doi = {10.1371/journal.pone.0350558}, pmid = {42341025}, issn = {1932-6203}, mesh = {Humans ; *Microbiota/genetics ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; *Amish ; Female ; Male ; Oral Health ; Adult ; Middle Aged ; Dental Plaque/microbiology ; Bacteria/genetics/classification ; }, abstract = {More than 700 phylotypes associated with the oral cavity collectively comprise the oral microbiome. Study of microbiomes has advanced our understanding of human health. Little is known about the oral microbiome of the Old Order Amish population, a distinct ethnoreligious group who choose to stay separate from mainstream society to preserve their traditional, faith-based way of life. This research was to generate a novel characterization of the Amish oral bacterial microbiome and, using a comparative study design, provide metagenomic analyses of potential variations between generated profiles of the Amish and non-Amish. Next-generation sequencing of 16S rRNA genes of supragingival plaque and saliva samples was used. Analysis between oral health habits from surveys (e.g., fluoride use, frequency of dental visits) and markers within the microbiomes were used to assess the extent of variation due to oral health habits or other factors. Samples were analyzed from 14 Amish and 13 non-Amish individuals. Using non-parametric analyses, alpha and beta diversity were measured to assess core microbiomes, abundance, and sample dissimilarity. Compared to non-Amish, Amish experienced significantly lower frequency of dental visits (p < 0.001) and fluoride use (p < 0.001), but no difference in frequency of teeth brushing (p = 0.198) was observed. Alpha-diversity of observed species differed significantly between Amish and non-Amish samples (H = -3.89, p = 0.002). Beta-diversity which accounted for relative taxon abundance and presence, as well as other metadata such as fluoride use, frequency of dental visits, and teeth brushing indicated, for both saliva and plaque, samples clustered by grouping and their covariates. The five primary phyla typically associated with the oral microbiome were the dominant phyla in both Amish and non-Amish individuals, although Proteobacteria were proportionally fewer in Amish samples. We conclude the oral microbiome between the Old Order Amish and rural non-Amish are distinctly different, which may reflect observed differences in lifestyle and oral health habits.}, } @article {pmid42341423, year = {2026}, author = {Zheng, J and Yao, DY and Lu, YY and Luo, SJ and Liang, XX}, title = {Diagnostic utility of metagenomic next-generation sequencing for determining the etiology of thoracolumbar spine infections.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {3}, pages = {117517}, doi = {10.1016/j.diagmicrobio.2026.117517}, pmid = {42341423}, issn = {1879-0070}, abstract = {OBJECTIVE: This study evaluated the diagnostic performance of metagenomic next-generation sequencing (mNGS) in identifying the etiological agents of thoracolumbar spine infections and examined its clinical relevance in facilitating timely diagnosis and therapeutic decision-making.

METHODS: A total of 54 patients with suspected thoracolumbar spinal infection admitted to the Department of Spinal Orthopedics between June 1, 2022, and January 15, 2026, were enrolled. Tissue specimens from all patients underwent microbial culture, histopathological examination, and metagenomic next-generation sequencing (mNGS). Based on established clinical diagnostic criteria, patients were classified into an infection group (n = 49) and a non-infection group (n = 5). The pathogen detection rate, and diagnostic sensitivity of mNGS and conventional culture were compared using the paired χ² test.

RESULTS: Among the 54 patients with suspected thoracolumbar spine infection, the male-to-female ratio was 2:1. The overall positive detection rate of mNGS was 75.9% (41/54), which was significantly higher than that of microbial culture at 57.4% (31/54) (χ² = 4.500, p < 0.05). When clinical diagnosis served as the reference standard, mNGS demonstrated greater sensitivity for diagnosing thoracolumbar spinal infections compared to microbial culture (83.7% vs. 63.3%), and this difference reached statistical significance (χ² = 4.500, p < 0.05).

CONCLUSION: mNGS shows a high pathogen detection rate and superior sensitivity for diagnosing thoracolumbar spinal infection, providing valuable support for clinical diagnosis and guiding therapeutic management in suspected cases.}, } @article {pmid42341424, year = {2026}, author = {Tsuboi, I and Inoue, S and Hirayama, T and Mitsui, Y and Watanabe, M and Hirakawa, H and Sadahira, T}, title = {Gut, vaginal, and urinary microbiome alterations in women with genitourinary syndrome of menopause: A systematic review.}, journal = {Maturitas}, volume = {211}, number = {}, pages = {109031}, doi = {10.1016/j.maturitas.2026.109031}, pmid = {42341424}, issn = {1873-4111}, abstract = {BACKGROUND AND OBJECTIVE: Genitourinary syndrome of menopause (GSM) is a chronic condition caused by estrogen deficiency, encompassing vaginal dryness, dyspareunia, and urinary symptoms. Alterations in the vaginal, urinary, and gut microbiome may contribute to GSM pathophysiology. We synthesize the evidence on microbiome composition and diversity across these compartments in postmenopausal women with GSM.

METHODS: PubMed, Scopus, and Embase were searched from inception to April 2026 for studies assessing the microbiome in postmenopausal women with GSM using 16S rRNA gene sequencing, metagenomics, or culture-based methods.

RESULTS: Twenty-three studies (5027 participants) were included: 15 examined the vaginal microbiome, seven the urinary microbiome, and one the gut microbiome. Postmenopausal women consistently showed reduced Lactobacillus abundance and increased microbial diversity. Estrogen therapy partially restored Lactobacillus dominance but did not uniformly improve symptoms. In the SWAN cohort (n = 1320), sexual pain was the only GSM symptom independently associated with a specific community state type (CST IV-C1; OR 2.26, 95% CI 1.20-4.23). Specific species showed associations with distinct symptom domains: Prevotella with urinary symptoms, Finegoldia magna with recurrent urinary tract infection, and Streptococcus with sexual pain. Parallel Lactobacillus depletion and pathobiont enrichment across all three compartments pointed toward a vaginal-bladder-gut axis, potentially linked through estrobolome disruption and bacterial translocation.

CONCLUSION: The postmenopausal genitourinary microbiome is characterized by Lactobacillus depletion and increased diversity, but microbiome restoration alone does not predict symptom resolution. The shared microbial alterations across compartments suggest a vaginal-bladder-gut axis that may collectively drive GSM, but this requires multi-compartment longitudinal validation. PROSPERO registration: CRD420261335478.}, } @article {pmid42341530, year = {2026}, author = {Lu, B and Wang, P and Hu, J and Qian, J and Shen, J and Tang, S and Zong, Y}, title = {Aqueous PFOS exposure decouples gaseous carbon loss from mineral-associated carbon retention in controlled wetland-interface mesocosms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {406}, number = {}, pages = {128638}, doi = {10.1016/j.envpol.2026.128638}, pmid = {42341530}, issn = {1873-6424}, abstract = {Wetland interfaces regulate greenhouse-gas exchange and carbon retention, yet contaminant exposure may disrupt the relationship between these two processes. Whether aqueous perfluorooctane sulfonate (PFOS), a persistent aquatic contaminant, alters this relationship remains unclear. Here, we used a controlled rhizobox mesocosm with paired planted and unplanted treatments across an aqueous PFOS gradient (0, 10, 100, and 1000 μg L[-1]) to resolve plant-mediated and background soil responses. We combined endpoint, time-weighted 24-h CO2 and CH4 flux partitioning with [13]CO2 tracing of root-derived carbon, rhizosphere priming estimates, soil organic carbon fractionation into particulate organic carbon (POC) and mineral-associated organic carbon (MAOC), and metagenomic profiling. PFOS induced clear exposure-dependent and non-linear responses. Low-to-medium PFOS stimulated root-associated CO2 fluxes and maintained positive rhizosphere priming, whereas high PFOS suppressed rhizosphere CO2 and root respiration, weakened net plant CO2 uptake, and shifted soil organic carbon priming to a net negative response. In contrast, at H-P, MAOC was significantly higher than the control in both bulk and rhizosphere compartments, indicating that mineral-associated carbon retention can persist even when biological carbon processing weakens. Metagenomic profiling further suggested compartment-specific microbial filtering, reduced genetic potential for polymer depolymerization, and reweighted methane-related functions under PFOS exposure. Together, these results show that aqueous PFOS exposure can decouple gaseous carbon loss from mineral-associated carbon retention in controlled wetland-interface mesocosms. These findings indicate that lower gaseous carbon release under PFOS exposure should not be interpreted straightforwardly as stronger carbon-retention function or enhanced carbon sequestration, particularly without longer-term field validation.}, } @article {pmid42341576, year = {2026}, author = {Gupta, G and Fortin, RM and Labrie, S and Filteau, M}, title = {Genomic insights and antifungal potential of Pseudomonas species isolated from maple sap, including the novel species Pseudomonas acericola sp. nov. and Pseudomonas edsoni sp. nov.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126738}, doi = {10.1016/j.syapm.2026.126738}, pmid = {42341576}, issn = {1618-0984}, abstract = {Fungal contamination poses a significant challenge in maple sap collection systems and postproduction processes, which affects the quality and shelf life of maple syrup. As an alternative to chemical treatments, microorganisms offer promising biocontrol potential. This study investigates nine Pseudomonas strains isolated from maple sap for their antifungal activity and genomic features. Whole-genome sequencing followed by comparative genomic analysis identified five distinct Pseudomonas species, including two previously uncharacterized taxa for which we propose the names Pseudomonas acericola sp. nov. and Pseudomonas edsoni sp. nov., in accordance with the nomenclatural guidelines of the SeqCode. Strain distributions from metagenome recruitment suggest they originate from sapwood, and previous metataxonomic data show that the amplicon sequence variant matching P. edsoni predominated maple sap samples. Genome mining using antiSMASH and BAGEL4 identified gene clusters associated with the synthesis of antifungal compounds, such as hydrogen cyanide, siderophores, cyclic lipopeptides, and ribosomally synthesized peptides. Antifungal assays demonstrated inhibitory activity against food spoilage fungi, with P. edsoni strains being active against Kluyveromyces lactis. The absence of activity in the cell-free supernatant and the presence of Type VI secretion systems in the genomes point toward contact-dependent mechanisms. Collectively, these findings reveal previously unrecognized taxonomic diversity and ecological specialization in maple sap-associated Pseudomonas, providing a basis for the rational development of Pseudomonas-based antifungal strategies in maple syrup production and quality control.}, } @article {pmid42341885, year = {2026}, author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and Giosuè, A and Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L}, title = {Ultra-processed food intake and its associations with atherogenic dyslipidemia, glycemic control, and gut microbiome features in adults with type 1 diabetes from Southern Italy.}, journal = {Diabetes research and clinical practice}, volume = {}, number = {}, pages = {113373}, doi = {10.1016/j.diabres.2026.113373}, pmid = {42341885}, issn = {1872-8227}, abstract = {AIMS: To examine the associations between ultra-processed food (UPF) intake, glycemic control, cardiovascular risk factors, and gut microbiome in adults with type 1 diabetes (T1D).

METHODS: In 253 adults with T1D, diet was assessed using the EPIC food-frequency questionnaire, and UPFs classified according to NOVA. Evaluations included lipid profile, HbA1c, and continuous glucose monitoring metrics. In a subgroup (n = 103), gut microbiota composition/function was analyzed using shotgun metagenomic sequencing and beta-diversity assessed by PERMANOVA. Associations were examined using multivariable regression models adjusted for age and Mediterranean diet adherence.

RESULTS: Mean UPF intake was 15.5 % of total food intake. Higher UPF intake was independently associated with higher triglycerides (β per 20 g/1000 kcal = 3.62 mg/dL; 95 %CI 1.16-6.08) and lower HDL-cholesterol (β =  - 0.98 mg/dL; 95 %CI - 1.72 to - 0.24). Sugar/artificially sweetened beverages were positively associated with triglycerides and animal-based UPFs inversely associated with HDL cholesterol. In participants on multiple daily injections or open-loop systems, ready-to-eat mixed dishes were positively associated with HbA1c. Microbiome beta-diversity significantly differed according to UPF intake. Triglycerides positively associated with microbial pathways (ketogluconate, tetrapyrrole, and acetate metabolism).

CONCLUSION: Higher UPF intake was associated with atherogenic dyslipidemia, poorer glycemic control in selected groups, and gut microbiome alterations in adults with T1D. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.}, } @article {pmid42341953, year = {2026}, author = {Cao, S and Han, YC and Wang, XC and Chen, R and Xing, BS}, title = {Unraveling the short- and long-term effects of lignocellulosic pretreatment derivatives on the anaerobic co-digestion of corn straw and food waste: Digester performance, microbial community, and metabolic mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135234}, doi = {10.1016/j.biortech.2026.135234}, pmid = {42341953}, issn = {1873-2976}, abstract = {Lignocellulosic pretreatment hydrolysates often contain inhibitory derivatives, particularly furan inhibitors (furfural and 5-hydroxymethylfurfural) and phenolic compounds, which can suppress anaerobic digestion. In this study, a CS/FW mesophilic AcoD system was investigated through short-term single- and mixed-inhibitor batch tests and long-term operation in two continuous stirred tank reactors (CSTRs), with mixed-inhibitor concentrations increased stepwise at fixed ratios. The results revealed that the maximum concentrations of furfural, phenol, and 5-hydroxymethylfurfural tolerated by the AcoD system were 100, 50, and 50 mg/L, respectively, in short-term batch tests, whereas during long-term operation, twofold greater concentrations in the same ratio were tolerated, leading to a 4.2 % increase in methane yield compared with that of the control. At high concentrations of 1000:500:500 mg/L, the hydrolysis, acidification, and methanogenesis rates were strongly suppressed. Furfural showed the strongest inhibition on polysaccharide and protein degradation, indicating that hydrolysis was the main affected stage during AcoD. Metagenomic analysis revealed that the relative abundance of Methanobacterium increased from 39.03 % to 69.50 %, indicating a selective microbial adaptation. In contrast, the overall abundance of genes involved in both acetoclastic and hydrogenotrophic methanogenesis decreased, suggesting a reduction in community-level methanogenic functional potential, which was consistent with the observed 97.4 % decline in methane yield. Meanwhile, the relative abundances of oxidative stress defense genes, katE (EC:1.11.1.6) and GPX (EC:1.11.1.9), in the test group increased by 10.2 % and 19.9 %, respectively, indicating enhanced antioxidant capacity of the microbial community. These findings provide insights into the management of inhibitor-rich pretreatment hydrolysates during AcoD of CS and FW.}, } @article {pmid42342666, year = {2026}, author = {Jia, X and Jiang, L and Gong, Y and Chu, X and Yu, W and Du, J and Zhang, J and Shang, X and Wang, P and Wang, J and Li, Y and Wang, Z and Zhou, R and Li, Z and Zhu, Y and Wu, B and Li, J and Yang, Q}, title = {Fusobacterium periodonticum promotes colorectal tumorigenesis via decanoic acid-driven neutrophil chemotaxis.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74591-y}, pmid = {42342666}, issn = {2041-1723}, abstract = {Gut microbiota dysbiosis and immune dysregulation are closely associated with the development of colorectal cancer. Identifying the mechanistic links among specific microbial species, metabolites, and immune responses is crucial for uncovering novel insights into its pathogenesis. Here we show, through metagenomic and metabolomic analyses of clinical cohorts, that Fusobacterium periodonticum is significantly enriched in colorectal cancer patients and strongly correlated with elevated decanoic acid levels. Single-cell transcriptomic results further reveal tissue-specific neutrophil enrichment in colorectal cancer tissues, characterized by high CXCL8 expression and activation of neutrophil-related immune pathways. Cellular experiments demonstrate that decanoic acid induces late apoptosis/necrosis of neutrophils, enhances their chemotaxis through a pertussis toxin-sensitive G-protein-dependent mechanism, and upregulates genes involved in leukocyte migration and tumorigenesis. Mouse models further confirm that F. periodonticum colonization increases intestinal dysplasia and decanoic acid levels, and that decanoic acid intervention promotes tumor progression by facilitating neutrophil infiltration and modulating the local immune microenvironment. Our study reveals an important role of F. periodonticum in colorectal tumorigenesis via decanoic acid-medicated neutrophil chemotaxis, providing mechanistic insights into the pathogenesis of colorectal cancer.}, } @article {pmid42342687, year = {2026}, author = {Rubbab, B and Adenwalla, A and Spottiswoode, N and Haston, JC and Firmani, S and Singh, S and Rajaram, V and Ramos, J and Ali, IKM and Whittemore, B and Hanners, NW}, title = {Neurosurgical Biopsy and Resection for Diagnosis and Treatment of Balamuthia mandrillaris Amebic Encephalitis, United States.}, journal = {Emerging infectious diseases}, volume = {32}, number = {7}, pages = {}, doi = {10.3201/eid3207.260725}, pmid = {42342687}, issn = {1080-6059}, abstract = {We report a systematic case review of antemortem neurosurgical resections and biopsies and outcomes including new lesions after procedure and survival in Balamuthia mandrillaris granulomatous amebic encephalitis. The investigation was prompted by a 5-year-old patient in the southwestern United States who was treated with nitroxoline, the 2021 Centers for Disease Control and Prevention regimen, and underwent 2 resections; initial resection site recurrence and a new lesion after resection prompted the question whether complete resection versus biopsy is associated with better outcomes. We conducted a literature review and found no substantial difference between neurosurgical resection versus biopsy-only groups. Limitations include case review, number of cases, and incomplete data available. Additional analyses comparing neurosurgical outcomes with outcomes of those diagnosed via blood or cerebrospinal fluid and metagenomic next-generation sequencing might provide more definitive answers. This case and systematic review provide evidence that treatment with nitroxoline and neurosurgical resection could contribute to survival in Balamuthia encephalitis case-patients.}, } @article {pmid42342731, year = {2026}, author = {Schäfer, C and Bonatelli, ML and Burgos, IMT and Kleinsteuber, S and Machado, D and Øyås, O and Harms, H and Sträuber, H}, title = {Functional roles of degraders and non-degraders in anaerobic trophic networks converting lignocellulose into monocarboxylates.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {42342731}, issn = {2055-5008}, support = {100572058//Sächsische Aufbaubank/ ; 100572058//Sächsische Aufbaubank/ ; 100572058//Sächsische Aufbaubank/ ; 323134//Norges Forskningsråd/ ; 323134//Norges Forskningsråd/ ; }, mesh = {*Lignin/metabolism ; Metagenomics ; Xylans/metabolism ; *Carboxylic Acids/metabolism ; Anaerobiosis ; Fermentation ; Ethanol/metabolism ; Metabolic Networks and Pathways ; *Bacteria/metabolism/classification/genetics ; Cellulose/metabolism ; Microbial Consortia ; Lactic Acid/metabolism ; Acetic Acid/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Lignocellulose is a promising renewable resource for anaerobic biochemical production, but its microbial conversion remains challenging. To elucidate metabolic networks in lignocellulose-degrading consortia, inocula of various origins were enriched on cellulose or xylan. Community composition and metabolic functions were revealed by amplicon sequencing, metagenomics, genome-scale metabolic modelling, and metabolic simulations. In cellulose-enriched communities, Fibrobacter and Lacrimispora consistently dominated as primary cellulose degraders, whereas Bacteroides likely functioned as secondary degraders. Acetic acid (up to 1.3 g l[-1]) and CO2 were the main fermentation products. Xylan enrichments produced C2-C6 fatty acids (up to 3.9 g l[-1]), lactic acid (up to 1.2 g l[-1]), ethanol (up to 1.2 g l[-1]), CO2, and H2. Clostridium dominated one xylan community and produced mainly butyric acid, while Bifidobacterium dominated another and produced mainly lactic acid. Caproic acid production was experimentally observed in one xylan enrichment. Metagenomic annotations and metabolic simulations suggest that Lacrimispora amygdalina degraded xylan and Robinsoniella peoriensis consumed xylobiose as a secondary consumer, both likely producing ethanol and lactic acid that supported caproic and butyric acid production by Caproicibacter fermentans. Integrated analysis identified functional guilds and clarified the roles of degraders and non-degraders, providing a blueprint for engineering synthetic consortia for sustainable biochemical production.}, } @article {pmid42342987, year = {2026}, author = {Saw, JH and Shlafstein, MD and Pavloudi, C and Monsalve, N and Prescott, RD and Chain, PSG and Decho, AW and Donachie, SP}, title = {Amplicon and metagenomic data from fumarole-associated geothermal features of Hawai'i.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07734-x}, pmid = {42342987}, issn = {2052-4463}, support = {2442122//National Science Foundation/ ; 1711856//National Science Foundation/ ; LANLF59T//Office of the Chief Information Officer, U.S. Department of Energy/ ; 80NSSC18K1064/NASA/NASA/United States ; }, abstract = {The Hawaiian Islands are among the most geologically and volcanically active places on Earth. While the Hawaiian Archipelago is known for its animal and plant diversity, much less is known about microbial diversity in the area's diverse habitats. In this study, we focused on steam vent associated biofilms found on the most volcanically active island of Hawai'i, also known as the Big Island. From 46 samples from various biofilms and associated features around fumaroles emitting water steam, we generated amplicon and metagenomic sequences. This represents a total of 276 Gbp of raw sequencing data. From the shotgun metagenomic data, we constructed 363 non-redundant medium- to high-quality metagenome-assembled genomes (MAGs) that are at least 70% complete and with less than 5% contamination. Of these, ten MAGs belong in the domain Archaea, and 353 belong in the domain Bacteria. This dataset could provide valuable insights into microbial diversity and ecology around volcanic features in Hawai'i and elsewhere.}, } @article {pmid42332682, year = {2026}, author = {Zhu, Q and Duan, Q and Wang, F and Shao, ZJ and Hu, W and Bi, YK and Wang, X and Li, JL and Zhu, D and Lv, ZH and Yang, ZF and Yin, YR}, title = {Characterization of an alkali- and glucose-tolerant β-glucosidase from Karamay saline-alkali soil and its structural basis for glucose tolerance.}, journal = {BMC biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12896-026-01191-5}, pmid = {42332682}, issn = {1472-6750}, support = {32560004 and 32570003//National Natural Science Foundation of China/ ; 202501AU070181 and 202501AT070411//Yunnan Applied Basic Research Projects/ ; XZ202501ZY0019//the Science and Technology Projects of the Xizang Autonomous Region/ ; 230212528080//the Xingdian Talent Support Program of Yunnan Province/ ; 2025DNS01//the Dali Prefecture Science and Technology Bureau/ ; }, abstract = {BACKGROUND: Industrial applications of β-glucosidases are often constrained by high salinity, alkaline conditions, and glucose inhibition.

RESULTS: A glycoside hydrolase family 1 β-glucosidase, B0-BG40, was mined from the metagenome of saline-alkali soil in Karamay, Xinjiang, China. When heterologously expressed in Escherichia coli, B0-BG40 exhibited optimal activity at 45 °C and pH 8.6, retaining > 60% of its maximal activity over 20-55 °C and pH 5.6-9.6. The enzyme was highly stable at 25 °C, 40 °C and 45 °C and under alkaline conditions, maintaining > 85% residual activity after prolonged incubation and showing activity enhancement following incubation at pH 8.0-10.0. B0-BG40 also tolerated up to 2.0 M NaCl and 4.0 M glucose, and displayed weak glucose inhibition (Ki = 1033.5 mM). Combined with the results of protein homology modeling and molecular docking, a reasonable mechanistic hypothesis was proposed: the excellent glucose tolerance of the enzyme may be related to its narrow and deeply recessed catalytic channel, and this special channel structure could hinder glucose molecules from entering the active site.

CONCLUSIONS: B0-BG40 is a salt-, alkali-, and glucose-tolerant β-glucosidase with strong potential for applications in food and feed processing and cellulosic ethanol production.}, } @article {pmid42332773, year = {2026}, author = {Liang, X and Zhu, L and Li, J and Li, Y and Ivey, KL and Lee, KH and Eliassen, AH and Chan, AT and Huttenhower, C and Zhang, C and Hu, FB and Qi, Q and Hu, Y and Rimm, EB and Sun, Q}, title = {Circulating imidazole propionate and coronary heart disease risk: interplay between histidine intake, fiber, and gut microbiome.}, journal = {BMC medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12916-026-05012-6}, pmid = {42332773}, issn = {1741-7015}, support = {UM1 CA186107/NH/NIH HHS/United States ; HL060712/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; HL035464/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; DK119268/DK/NIDDK NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; U01CA152904/CA/NCI NIH HHS/United States ; DK120870//National Heart, Lung, and Blood Institute (NHLBI)/ ; }, abstract = {BACKGROUND: Imidazole propionate (ImP), a microbial metabolite of histidine, may impair glucose metabolism, but its relevance to coronary heart disease (CHD) risk and potential diet-microbiota regulations remain unclear. We aimed to examine prospective associations of plasma ImP levels and histidine intake with CHD risk, to identify ImP-predicting gut microbes, and to investigate diet-microbiome interactions influencing ImP levels.

METHODS: Associations of ImP and histidine with CHD risk were evaluated using Cox models in 7,432 participants from Nurses' Health Study (NHS), NHSII, and Health Professionals Follow-up Study. Microbiome-diet interactions influencing ImP levels were assessed using fecal metagenome and 7-day diet record data in 296 men from the Men's Lifestyle Validation Study, with replication in the Mind-Body Study.

RESULTS: Higher plasma ImP was associated with increased CHD risk (HR comparing extreme quintiles = 1.82; 95%CI = 1.17-2.81; p-trend = 0.002), while histidine intake showed a non-significant inverse association. Although histidine intake was not associated with ImP levels, the intake of fiber, especially pectin, emerged as a key negative predictor. We identified 17 distinct ImP-predicting species, including Clostridium and Blautia species. A parametric ImP-microbial score was constructed based on these species to represent the microbial capacity of producing ImP. Further functional characterization uncovered that the microbial urocanate reductase gene urdA was also associated with cardiovascular risk markers. No significant interaction was observed between histidine intake and the microbial score on ImP levels, but ImP levels increased with higher histidine intake and higher microbial score only under low pectin intake (p for 3-way interaction = 0.01). Similar interactions were seen for total fiber (p = 0.09), soluble fiber (p = 0.09), and insoluble fiber (p = 0.11), without statistical significance.

CONCLUSIONS: ImP, but not its dietary precursor histidine, was associated with a higher CHD risk. The gut microbial metabolism of ImP appeared context-dependent, with ImP production from histidine associated with a higher ImP-producing microbial capacity and lower fiber intake. These findings highlight the potential role of dietary fiber and gut microbiome in modulating diet-health associations related to ImP metabolism.}, } @article {pmid42333020, year = {2026}, author = {Habiba, MU and Rahman, MM and Augustin, MA and Varela, C and Morris, H and Bozkurt, H}, title = {Traditional Fermented Dairy Products as Reservoirs of Bifidobacterium With Probiotic Potential: From Microbial Diversity to Functional Characterization.}, journal = {Comprehensive reviews in food science and food safety}, volume = {25}, number = {4}, pages = {e70540}, doi = {10.1111/1541-4337.70540}, pmid = {42333020}, issn = {1541-4337}, support = {//Adelaide University/ ; //University of Adelaide Research Scholarship/ ; }, mesh = {*Probiotics ; *Bifidobacterium/physiology/isolation & purification ; *Cultured Milk Products/microbiology ; Fermentation ; Animals ; Food Microbiology ; Humans ; *Dairy Products/microbiology ; }, abstract = {Traditional fermented dairy products (TFDPs) are complex microbial ecosystems that may serve as reservoirs of many microorganisms, including those with probiotic potential such as Bifidobacterium species and lactobacilli. Although bifidobacteria are widely used as probiotic microorganisms in defined formulations, their occurrence, persistence, and functional relevance within TFDPs remain incompletely understood. This review critically synthesizes current evidence on the diversity, ecological roles, and traits associated with probiotic potential of Bifidobacterium spp. detected in TFDPs, including raw-milk fermentations, artisanal dairy products, and selected controlled dairy systems. Species such as Bifidobacterium animalis, Bifidobacterium longum, Bifidobacterium bifidum, and Bifidobacterium breve have been reported across yogurt, kefir, airag (traditional Mongolian fermented dairy beverage from mare milk), and raw milk cheeses, often at low abundance or as transient microbial community members. Many isolates from fermented dairy products exhibit traits commonly associated with probiotic functionality, including acid/bile tolerance, adhesion capacity, exopolysaccharide production, and antimicrobial activity. However, most reports remain limited to presence/absence or in vitro assays, with limited in vivo or clinical validation. Advances in molecular and omics-based approaches have improved detection, characterization, and safety evaluation; however, translation into validated applications remains constrained by challenges in isolation, viability, and strain-level confirmation. Importantly, detection of bifidobacteria in TFDPs does not confer probiotic status, which requires strain-level identification, demonstrated safety, adequate viable counts at consumption, and clinical evidence of health benefit. Collectively, TFDPs, as culturally embedded microbial reservoirs, may support the discovery of novel bifidobacterial strains for future development of functional foods or probiotic products following rigorous validation.}, } @article {pmid42333270, year = {2026}, author = {Ibitoye, OA and Anyanwu, CN and Agbaje, AB and Fasogbon, IV and Dangana, RS and Akinola, SA and Tibyangye, J and Adam, AA and Aja, PM}, title = {Advances in the detection of antimicrobial resistance in aquatic environments: a methodological perspective.}, journal = {Biology methods & protocols}, volume = {11}, number = {1}, pages = {bpag029}, pmid = {42333270}, issn = {2396-8923}, abstract = {Antimicrobial resistance (AMR) is a global health and environmental challenge, driven by complex interactions among microbial communities, resistance genes, and selective pressures in various ecological niches. Traditional surveillance procedures often fall short in capturing the full diversity and dynamics of resistance reservoirs in the environment. This review examines the integration of artificial intelligence (AI) and machine learning (ML) with next-generation sequencing (NGS) technologies for comprehensive resistome profiling. We discuss advances in multi-omics approaches, particularly metagenomics, microbiome-based analytics, and metatranscriptomics. We also highlight computational workflows that enable high-resolution mapping of resistance genes, their mobile genetic elements, and host associations. The role of AI/ML in resistome prediction, classification, and source tracking, as well as the incorporation of environmental metadata for contextual interpretation is discussed based on the selected literature. Moreover, we assess current challenges and propose future directions for developing standardized, scalable, and interpretable bioinformatic pipelines in AMR surveillance. This review primarily elucidates the potential of integrated AI-omics platforms to revolutionize aquatic environmental AMR monitoring and inform risk assessment and mitigation strategies.}, } @article {pmid42334513, year = {2026}, author = {Zhang, X and Du, L and Jin, X and Sun, J and An, G and Li, L and Yang, P and Li, F}, title = {Nocardia brasiliensis endophthalmitis initially misdiagnosed as uveitis: a case report.}, journal = {Journal of ophthalmic inflammation and infection}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12348-026-00602-0}, pmid = {42334513}, issn = {1869-5760}, support = {YXKC2020026//Henan Provincial Health Commission/ ; 82301271//National Natural Science Foundation of China/ ; 82230032//National Natural Science Foundation of China/ ; 82101108//National Natural Science Foundation of China/ ; 2025Hx39//First Affiliated Hospital of Zhengzhou University/ ; SBGJ202101011//Health Commission of Henan Province/ ; }, abstract = {BACKGROUND: Endophthalmitis caused by Nocardia brasiliensis is extremely rare and typically affects immunocompromised individuals, frequently leading to severe vision loss due to diagnostic delays. We report a case of N. brasiliensis endophthalmitis in an older man without prior history of systemic immunosuppression but with newly identified diabetes mellitus, characterized by an indolent initial course followed by fulminant progression.

CASE PRESENTATION: A 67-year-old man without known systemic immunosuppression presented with a two-month history of recurrent right-eye pain and redness, followed by rapid vision loss and a hypopyon. Aqueous humor analysis and metagenomic sequencing identified N. brasiliensis. Despite intravitreal amikacin, systemic antimicrobial therapy, and subsequent pars plana vitrectomy with silicone oil tamponade, intraocular inflammation advanced, resulting in worsening corneal opacification, irreversible structural damage, and a final best-corrected visual acuity of light perception.

CONCLUSIONS: N. brasiliensis endophthalmitis may progress rapidly and result in severe, irreversible ocular damage, even in patients without overt systemic immunodeficiency. Early microbiologic identification and prompt, targeted antimicrobial therapy combined with timely surgical intervention are critical, although visual outcomes may remain poor in advanced cases.}, } @article {pmid42334609, year = {2026}, author = {Zheng, Y and Chen, C and Guan, D and Huang, Y and Xiong, L and Liu, R}, title = {Viral community dynamics and functional succession in advanced drinking water treatment processes.}, journal = {Archives of microbiology}, volume = {208}, number = {9}, pages = {}, pmid = {42334609}, issn = {1432-072X}, mesh = {*Drinking Water/virology/microbiology ; *Water Purification/methods ; Bacteria/genetics/classification/isolation & purification ; *Viruses/genetics/classification/isolation & purification ; China ; Metagenomics ; Water Microbiology ; }, abstract = {Viruses play a significant role in microbial ecology, yet their impact on drinking water systems remains poorly understood. We collected water from different treatment process streams of an ozone-bioactivated carbon (O3-BAC) advanced drinking water treatment plant in eastern China. DNA viral metagenomic sequencing was then performed to analyze viral abundance, community structure, diversity, host prediction, virulence factors, potential viral pathogens, and functional genes, including carbohydrate-active enzymes (CAZymes), auxiliary metabolic genes (AMGs), and antibiotic resistance genes (ARGs). The results revealed that treatment reduced viral abundance and diversity, although certain taxa not detected in raw water or sedimentation water (e.g., Preplasmiviricota) were detected in sand-filtered water and finished water. Caudoviricetes were the most abundant viruses in the water treatment process. The virus host types were predominantly bacteria, mainly Lactobacillus, Mycoplasma, Staphylococcus, Bacillus, and Streptococcus. Functional analysis revealed viral involvement in carbohydrate degradation via CAZymes and modulation of host metabolism through AMGs and ARGs to support viral replication. Potential human pathogens were identified within Poxviridae and Herpesviridae. This study provides novel insights into DNA viral ecological dynamics in engineered water systems and supports enhanced pathogen control strategies.}, } @article {pmid42334937, year = {2026}, author = {Ma, C and Liu, S and Won, S and Koslicki, D}, title = {MetagenomicKG: a knowledge graph for metagenomic applications.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag421}, pmid = {42334937}, issn = {1367-4811}, abstract = {MOTIVATION: The sheer volume and variety of genomic content within microbial communities makes metagenomics a field rich in biomedical knowledge. To traverse these complex communities and their vast unknowns, metagenomic studies often depend on distinct reference databases, such as the Genome Taxonomy Database (GTDB), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), for various analytical purposes. These databases are crucial for the genetic and functional annotation of microbial communities. Nevertheless, the inconsistent nomenclature or identifiers of these databases present challenges for effective integration, representation, and utilization. Knowledge graphs (KGs) offer an appropriate solution by organizing biological entities from different databases to standardized identifiers, allowing their interrelations to be captured into a cohesive network regardless of the naming conventions used in each source. The graph structure not only facilitates the unveiling of hidden patterns but also enriches our biological understanding with deeper insights. Despite KGs having shown potential in various biomedical fields, their application in metagenomics remains underexplored.

RESULTS: We present MetagenomicKG, a novel knowledge graph specifically tailored for metagenomic analysis. MetagenomicKG integrates taxonomic, functional, and pathogenesis-related information on the human microbiome sourced from various databases, and further connects these with existing biomedical KGs to expand the biological network. Through various case studies involving the human microbiome, we demonstrate its utility in enabling hypothesis generation regarding the relationships between microbes and diseases, generating sample-specific graph embeddings, and providing robust pathogen prediction.

CODE AVAILABILITY: The source code and technical details for constructing the MetagenomicKG and reproducing all analyses are available on GitHub at https://github.com/KoslickiLab/MetagenomicKG. The data used in this manuscript, including the pre-built files and use case input data, are archived on Zenodo with DOI: 10.5281/zenodo.17546861.

SUPPLEMENTARY INFORMATION: available at Bioinformatics online.}, } @article {pmid42334999, year = {2026}, author = {Masukawa, H and Kobayashi, R and Watanabe, J and Tanizaki, A and Morono, Y and Ito, M and Terada, T and Takaki, Y and Tsuda, M and Matsui, Y and Arai, T and Takai, K and Kameya, M and Arai, H and Yamamoto, M}, title = {Electrosynthetic bacterial growth under conditions simulating electric discharge in deep-sea hydrothermal fields.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag108}, pmid = {42334999}, issn = {1751-7370}, abstract = {Microbial electrosynthesis is a metabolic process in which extracellular electrons are utilized as the primary energy source for carbon fixation. While microbial electrosynthesis has been proposed as a novel concept for ecological primary production, our understanding of how such microorganisms are distributed in natural environments remains limited. In this study, we constructed a laboratory-scale electrochemical cultivation system that simulates electric discharge conditions in deep-sea hydrothermal fields. Microscopic counts revealed increased cell numbers in the electrochemical culture, and 16S rRNA gene analysis revealed a significant enrichment of a novel Thiomicrorhabdus species. Quantitative PCR confirmed proliferation and enrichment of a metagenome-assembled genome (MAG), named the SREC-4. Electrochemical cultivation with 13C-labeled CO2 as a substrate indicated significant 13C incorporation specifically in Thiomicrorhabdus cells including MAG SREC-4. The genome of MAG SREC-4 revealed the possession of the putative extracellular electron uptake pathway in addition to the autotrophic sulfur-oxidizing aerobic respiration pathways typically found in Thiomicrorhabdus members. The putative extracellular electron uptake pathway was found in a phylogenetic clade in Thiomicrorhabdus mainly formed by strains derived from hydrothermal fields. These results provide the direct experimental evidence from enrichment cultures derived from hydrothermal fields that an organism inhabiting deep-sea hydrothermal fields can grow electrosynthetically, and suggest that this ability is shared by other Thiomicrorhabdus species, specifically those found in similar environments. This finding suggests electrosynthetic growth may be widely distributed in Thiomicrorhabdus populations dwelling in deep-sea hydrothermal fields, the largest natural electrogenic environment on Earth.}, } @article {pmid42335476, year = {2026}, author = {Valentino, V and De Filippis, F and Ercolini, D}, title = {Fermented foods: lessons learned from metagenomics.}, journal = {Current opinion in biotechnology}, volume = {100}, number = {}, pages = {103545}, doi = {10.1016/j.copbio.2026.103545}, pmid = {42335476}, issn = {1879-0429}, abstract = {Thanks to the standard microbiology protocols of isolation and culturing, hundreds of strains have been isolated from fermented foods throughout the last decades, and phenotypic traits linked with pro-technological properties and health claims have been investigated. However, culture-independent metagenomic analyses have revealed an unexpected microbial diversity in foods fermented spontaneously or by undefined starter cultures. Here, we report the most groundbreaking advancements in the understanding of fermented foods ecology by presenting case studies where metagenomics has been applied, contributing to identifying novel species in silico or to deciphering the microbiome structure associated with spontaneous fermentations. We also highlight the potential of metagenomics in supporting the identification of potential probiotics and discuss the future ahead, particularly focusing on the integration of multi-omics approaches.}, } @article {pmid42335503, year = {2026}, author = {Liu, LM and Fang, HB and Wang, YF and Zhang, YL and Yu, QQ and Zhang, WY and Liu, J and Miao, H and Zhao, YY}, title = {Niaoduqing particles ameliorated tubulointerstitial fibrosis by suppressing IκB/NF-κB signalling pathway via inhibiting host- and gut microbiota-mediated tryptophan co-metabolism.}, journal = {Microbiological research}, volume = {311}, number = {}, pages = {128592}, doi = {10.1016/j.micres.2026.128592}, pmid = {42335503}, issn = {1618-0623}, abstract = {Tubulointerstitial fibrosis (TIF) is an inevitable outcome of progressive chronic kidney disease (CKD). Niaoduqing particles (NDQ) were developed for the treatment of CKD. However, the molecular mechanisms underlying the effect of NDQ on TIF remain unclear. Fecal gut microbiota (GM) and serum metabolites were analyzed using metagenomics and metabolomics in unilateral ureteral obstruction (UUO)-induced TIF rats. NDQ treatment attenuated UUO-induced TIF in rats in a dose- and time-dependent manner. The increased abundance of eight pathogenic bacteria, including Bacillus wiedmannii, Enterococcus mundtii and Fusobacterium varium, showed strong positive correlations with TID scores, whereas the reduced abundance of two probiotic bacteria, Ruminococcus flavefaciens and Clostridium celatum, showed strong negative correlations with tubulointerstitial damage (TID) scores. NDQ treatment reversed these aberrant microbial alterations, indicating its capacity to remodel GM dysbiosis. TID scores were strongly correlated with host- and GM-mediated tryptophan co-metabolites, including indoxyl sulfate, tryptamine and indole-3-acetic acid, in both TIF- and NDQ-treated TIF rats, and NDQ intervention normalized these metabolic disturbances. Notably, Fusobacterium varium and Enterococcus faecium exhibited strong linear correlations with indoxyl sulfate, indole-3-acetic acid, and indole-3-aldehyde in the TIF rat model. Furthermore, NDQ suppressed IκB/NF-κB signaling pathway in both TIF rats and TGF-β1-induced NRK-52E cells. These inhibitory effects were partially reversed by NF-κB p65 knockdown. This study is the first to demonstrate that NDQ alleviates TIF by reshaping microbial dysbiosis and modulating host- and GM-mediated tryptophan metabolism. These findings support that NDQ mitigates TIF by suppressing IκB/NF-κB signaling pathway through regulation of host-microbiota-derived tryptophan metabolism.}, } @article {pmid42335537, year = {2026}, author = {Gong, H and Xian, ZN and Hu, J and Luo, J and Wang, Y and Liu, X and Zhu, N}, title = {Low-intensity electrical stimulation enhances phthalate ester biodegradation by activated sludge through real-time multi-scale regulation.}, journal = {Water research}, volume = {304}, number = {}, pages = {126306}, doi = {10.1016/j.watres.2026.126306}, pmid = {42335537}, issn = {1879-2448}, abstract = {Phthalate esters (PAEs) are ubiquitous contaminants that are poorly removed by conventional biological treatment processes. This study investigated the enhancement of PAE biodegradation in activated sludge under low-intensity electrical stimulation. A single-chamber electrostimulated aerobic microbial system (EAMS) was established and operated at 0.6-2.1 V to explore the physiological, genetic, and community-level responses of microorganisms. Moderate stimulation (0.9-1.5 V, electric field strength 180-300 V·m[-1], current 10.6-136.0 μA, current density 0.5-6.8 mA·m[-2]) increased the biodegradability of the three PAEs by 11%-20%. Electrical stimulation significantly enhanced the physiological activity and community synergy of the microbial community dominated by non-electroactive bacteria. Metagenomic and metatranscriptomic analyses revealed that the genomic abundance of PAE-degrading genes was unchanged, but their expression was strongly upregulated (20-40-fold). Electrical stimulation enhanced PAE biodegradation by activating the metabolic and transcriptional machinery of the resident microbial community, rather than by selecting for specific degraders. This activation led to elevated expression of key degradation genes and consequently improved biodegradation efficiency. These findings suggest that electrical stimulation acts as a functional activator of indigenous microbial communities, providing a rapid and broadly applicable strategy for improving biodegradation efficiency without requiring extensive community restructuring.}, } @article {pmid42335557, year = {2026}, author = {Sun, X and Jia, C and Song, X and Zhao, X and Han, M and Yin, H and Zhang, P}, title = {Incorporating benthic microbial thresholds into ecological carrying capacity to sustain ecosystem services of coastal oyster farming.}, journal = {Journal of environmental management}, volume = {413}, number = {}, pages = {130316}, doi = {10.1016/j.jenvman.2026.130316}, pmid = {42335557}, issn = {1095-8630}, abstract = {Oyster aquaculture provides crucial ecosystem services by mitigating coastal eutrophication. However, intensive farming frequently leads to benthic organic overloading, which threatens this bioremediation capacity. Current Ecological Carrying Capacity (ECC) assessments focus on the interaction between yield and pelagic metrics, leaving a critical management loophole regarding benthic sediment health. To address this gap, we conducted a large-scale benthic environmental and metagenomic investigation across five intensive oyster (Crassostrea gigas) farming areas in the Shandong Peninsula, China. Our results revealed that biodeposit-driven organic loading promoted total sulfur (TS) accumulation, triggering a non-linear functional regime shift in the benthic nitrogen cycle. Breakpoint analysis identified a critical threshold at a sedimentary TS concentration of 0.89 g kg[-1], beyond which the denitrification was redirected toward dissimilatory nitrate reduction to ammonium (DNRA), concurrently elevating the risk of greenhouse gas (N2O) emissions. Crucially, a profound spatial decoupling was observed between macroscopic farming yield and benthic micro-ecological status. Shallow-water areas with low yields suffered severe benthic degradation, whereas deep-water areas sustaining highly intensive yields maintained robust eutrophication mitigation functions. This paradox underscores the decisive role of the ecosystem's assimilative capacity over absolute farming load. These findings challenge the traditional yield-focused Ecological Carrying Capacity (ECC) assessments. We therefore advocate for incorporating thresholds of microbial-driven biogeochemical potentials into the ECC management framework to ensure the holistic sustainability of coastal aquaculture.}, } @article {pmid42335767, year = {2026}, author = {Li, T and Guo, T and Cui, M and Cao, Y and Zhi, Z and Wang, P and Li, Q and Zhang, J}, title = {Rearing systems shape the successional dynamics of the gut microbiota, resistome, and mobilome in Lueyang Black-boned chickens.}, journal = {Poultry science}, volume = {105}, number = {10}, pages = {107322}, doi = {10.1016/j.psj.2026.107322}, pmid = {42335767}, issn = {1525-3171}, abstract = {Understanding the ecological factors shaping antimicrobial resistance (AMR) dissemination in agricultural environments is critical for global "One Health". Here, we performed metagenomic sequencing to investigate the impact of intensive cage-reared (CR) and free-range (FR) systems on the gut microbiota, resistome, and mobilome dynamics of Lueyang Black-boned chickens across different production stages. Our analyses revealed that distinct rearing systems drove resistome alterations by reshaping microbial community assembly and horizontal gene transfer (HGT) pathways. Specifically, the CR system imposed strong deterministic stress, thereby enriching opportunistic taxa (such as Desulfovibrio) and promoting a highly connected but topologically fragile microbial network. Conversely, the FR system exhibited a higher total abundance of commensal resistance genes, a process mainly driven by diverse transposon-mediated integrations including tnpA and ISBf10. In contrast, the CR system was associated with high-risk, clinically relevant resistance determinants. These included extended-spectrum beta-lactamases and multidrug resistance cassettes. Targeted network tracking unmasked highly divergent potential host-vector-ARG associations. Resistance expansion under confined CR conditions showed strong vector-dependency, being fundamentally linked to the broad-host-range plasmid IncQ1 alongside clinically relevant mobilization elements, including Class 1 integrons. Longitudinally, the FR resistome achieved ecological stabilization. In contrast, the CR microbiota exhibited continued genetic flux, continuously acquiring transient resistance elements during the observed production period. These findings demonstrate that welfare-friendly rearing management serves as a critical ecological intervention to limit the proliferation of mobile, high-risk resistance traits. Ultimately, future agricultural surveillance must transition beyond quantifying total resistance gene abundance to prioritize functional risk assessments and mobilization potential.}, } @article {pmid42335821, year = {2026}, author = {Rehman, A and Wang, X and Yousaf, M and Wang, J and Li, Z}, title = {Biotransformation of Microcystin-LR in marine sediments: Mechanism and global potential.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142754}, doi = {10.1016/j.jhazmat.2026.142754}, pmid = {42335821}, issn = {1873-3336}, abstract = {Microcystin-LR (MC-LR), a potent hepatotoxin produced during cyanobacterial harmful algal blooms, can be transported from freshwater systems to coastal marine environments through riverine discharge and estuarine mixing, yet its environmental fate in coastal sediments remains poorly understood. Here, we investigated the biotransformation mechanism of MC-LR in coastal sediments using LC-MS/MS, metagenomics, metabolic modeling, molecular docking, and genome binning. The results showed that MC-LR was transformed primarily via co-metabolism, following pseudo-first-order kinetics. Notably, we identified a novel biotransformation pathway in the marine environment that differs from the conventionally recognized mlr-dependent pathway observed in terrestrial systems. Biotransformation in marine sediments involves peptide ring opening, formation of linear MC-LR, stepwise peptide shortening, and conversion of the Adda-containing fragment into smaller aromatic compounds. Metabolic modeling and ecological network analysis further revealed that the microbial community facilitates this co-metabolic biotransformation through a cross-feeding mechanism, in which different taxonomic groups share complementary functions for co-substrate transformation, peptide bond cleavage, and aromatic compound degradation. Metagenomic profiling and genome binning demonstrated that MC-LR transformation is coupled with glutathione metabolism, and key genes involved in MC-LR transformation (e.g., CAAX, pepA, pepN, paaA, paaG, paaZ) were mainly associated with members of the Pseudomonadota, Myxococcota, and Acidobacteriota. Global screening of publicly available MAGs revealed that CAAX genes linked to MC-LR transformation are widely distributed across aquatic environments, with 16,209 CAAX-containing MAGs identified from 498 sampling locations worldwide, including 6892 marine MAGs from 317 oceanic sites. Overall, this study clarifies the biotransformation mechanism of MC-LR in marine sediments and highlights the widespread genetic potential for its biotransformation across global aquatic environments.}, } @article {pmid42335822, year = {2026}, author = {He, T and Liu, J and Li, Y and Ohgami, N and Wei, X and Peng, T and Zhang, X and Zhang, R and Du, J and Deng, Y and Jiang, H and Zhang, P and Zhang, Y}, title = {Long-term groundwater arsenic exposure is associated with altered arsenic methylation capacity and gut microbiota composition in a rural Chinese population.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142658}, doi = {10.1016/j.jhazmat.2026.142658}, pmid = {42335822}, issn = {1873-3336}, abstract = {This study investigated the relationship between long-term groundwater arsenic exposure, arsenic methylation capacity, and gut microbiota in adults from rural northern China. Arsenic detoxification relies in part on methylation processes, and growing evidence suggests that the gut microbiome may participate in arsenic biotransformation, yet population-based data integrating exposure, metabolism, and microbial profiles remain scarce. We recruited 258 participants from two neighboring villages supplied by centralized wells with contrasting arsenic levels (control, n = 138; exposure, n = 120). Total urinary arsenic was measured in all participants, and arsenic species were quantified in a subgroup (n = 60) to derive primary and secondary methylation indices (PMI and SMI). Fecal metagenomes were sequenced to characterize taxonomic composition and functional potential based on KEGG and GO annotations. Individuals in the exposure village showed higher levels of urinary inorganic arsenic and methylated metabolites. While PMI was comparable between groups, SMI was significantly reduced among exposed individuals, indicating impaired secondary methylation. Arsenic exposure was also associated with pronounced alterations in gut microbial diversity and community structure. Several anaerobic taxa, largely linked to fermentative metabolism, were positively associated with SMI after multivariable adjustment. Functional analyses further revealed differences in pathways related to transport, environmental sensing, and metabolism. These findings suggest that chronic arsenic exposure is associated with reduced methylation efficiency and shifts in gut microbial composition and function, and that the gut microbiome may contribute to interindividual variability in arsenic metabolism and toxicity.}, } @article {pmid42335936, year = {2026}, author = {Ter Horst, PAG and Marshall, IPG and Egas, RA and Klomp, R and Schutgens, MAW and van Alen, T and Jetten, MSM and Slomp, CP and Welte, CU}, title = {Electrogenic CH4 oxidation on a bioanode: putative extracellular electron transport system in Methylobacter sp.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag067}, pmid = {42335936}, issn = {1574-6941}, abstract = {Aerobic methanotrophs are frequently detected in oxygen-limited, stratified coastal environments. Known adaptations, including high-affinity terminal oxidases and oxygen-binding bacteriohemerythrins, help explain methane oxidation at extremely low oxygen concentrations, yet their activity and ecological role under fully anoxic conditions remain uncertain. Here, we show that an anoxic, poised-anode bioelectrochemical system inoculated with a methane-oxidizing sediment enrichment produced methane-dependent current, with rapid current loss upon methane removal and recovery after re-addition. Metagenomic analysis revealed the selective enrichment of a Methylobacter population encoding a porin-cytochrome complex and numerous multiheme c-type cytochromes, suggesting extracellular electron transfer potential. A complementary phylogenomic survey across Methylococcales identified homologs of this gene cluster in multiple lineages, but with a scattered phylogenetic distribution indicative of modular acquisition. Comparative synteny further revealed conserved gene order across genomes, supporting horizontal transfer of the locus as a functional unit. Together, these results demonstrate that aerobic methanotrophs may employ extracellular electron transfer strategies to dissipate methane-derived electrons when oxygen-dependent respiration is constrained.}, } @article {pmid42336533, year = {2026}, author = {Yu, L and Jiang, L and Liu, C and Wang, S and Zhu, G}, title = {High co-occurrence but low heterogeneity of virulence factors and resistance genes in farmland soil.}, journal = {Journal of environmental sciences (China)}, volume = {166}, number = {}, pages = {273-282}, doi = {10.1016/j.jes.2025.11.031}, pmid = {42336533}, issn = {1001-0742}, abstract = {Virulence factors (VFs), antibiotic resistance genes, and metal resistance genes in farmland soil pose significant threats to food security, soil health, and human well-being. Numerous studies have reported on the characteristics and hazards of resistance genes in the soil, but the co-occurrence of VFs and resistance genes has received little attention as a potential threat to the ecological environment. Here, we investigated the mechanism of interaction between VFs and resistance genes in farmland soil samples worldwide, especially in China, the most antibiotic-contaminated country. Metagenomics and metagenome binning analysis provided direct evidence that VFs and resistance genes could co-occur universally in the same microbial cell in farmland soil, dramatically enhancing the pathogenic ability of soil microorganisms and severely raising the threat to ecological security. We found that the spatial distribution of resistance genes and VFs in farmland topsoil exhibited low heterogeneity. These findings contribute to our understanding of VFs and resistance genes in farmland soil, which is beneficial for ensuring the healthy development of agriculture and food security.}, } @article {pmid42336534, year = {2026}, author = {Zhai, F and Li, B and Zhao, X and Zhao, P and Yang, S and Li, X and Wang, T and Liu, G and Yan, P}, title = {Bioelectrochemical mitigation of soil antibiotic resistance: Disruption of bacteriophage transmission and resistant hosts.}, journal = {Journal of environmental sciences (China)}, volume = {166}, number = {}, pages = {283-294}, doi = {10.1016/j.jes.2025.11.008}, pmid = {42336534}, issn = {1001-0742}, abstract = {The proliferation of antibiotic resistance genes (ARGs) in environment poses a threat to global public health. Although microbial fuel cell (MFC) has been demonstrated to mitigate ARG amplification, the mechanism remains unclear. This study employed metagenomic sequencing combined with the DeepARG-LS model for profiling ARGs and further analyzed the effects of MFCs on them in tetracycline-contaminated soil. Consequently, tetracycline addition (AT treatment) elevated total ARG abundance by 31 %, whereas MFC application (MT treatment) reduced it by 12 %. The deep learning model revealed a 38 % reduction in the richness of ARG subtypes in the MT compared to the AT. Proteobacteria dominated as ARG hosts, accounting for 78 % of ARGs in the AT, but declined by 18 % in the MT. Notably, the archaeal Nitrososphaeraceae was identified as a host for tetA(48). Species-level analysis identified 12 ARG-carrying bacterial taxa, the abundance of most of which was suppressed (abundance) by MFCs. The richness of ARGs host bacteria was 38 % lower in the MT treatment than that in the AT treatment. Meanwhile, the abundance of the indole biosynthesis gene (tryptophanase, EC 4.1.99.1) exhibited a consistent trend with the richness of ARGs hosts. Mechanistically, the suppression of ARG-host bacteria may be attributed to enhanced indole biosynthesis (as indicated by increased tryptophanase abundance), coupled with reduced abundances of mobile genetic elements (84 %) and virulence factors (11 %), and a decline in phage-mediated ARG transmission (19 %). Overall, these findings provide insights into bioelectrochemical controlling ARG dissemination in soils.}, } @article {pmid42336879, year = {2026}, author = {Feng, C and Lu, H and Bian, J and Wang, H and Jia, H and Li, X and Yang, M and Song, H and Tan, W and Wang, L}, title = {Phage-mediated expansion of the virulence gene types and enhanced ecological integration of pathogens in wild mice from human-impacted environments.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01054-z}, pmid = {42336879}, issn = {2055-5008}, support = {2025ZD01900200//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project/ ; }, abstract = {Wild mice are crucial in the transmission of infectious diseases; however, quantitative indicators for evaluating risk of virulence factors transmission are still lacking. We combined metagenomics and network analysis to evaluate ecological connectivity and functional gene profiles of microbial communities in wild mice from human-impacted environments (HE) and woodland environments (WE). We found that the pathogen centrality was significantly higher in HE than in WE (p < 0.001). Random Forest Model suggested habitats, phage abundances, and antibiotic resistance genes (ARGs) counts were crucial factors influencing virulence factor genes (VFGs) counts (p < 0.05). Structural Equation Model revealed that habitats affected VFGs (p < 0.01) via phages mediation (p < 0.05), while ARGs directly affected VFGs (p < 0.001). Although VFG counts were significantly higher in HE (p < 0.001), their expression levels did not differ between two habitats (p = 0.2952), indicating that VFG diversity was not necessarily accompanied by higher virulence expression. This study highlights the mediating role of phages and the direct contribution of ARGs in shaping the virulence-associated genetic repertoire, underscoring the importance of a One Health perspective that considers human impacts on microbial communities in infectious disease surveillance.}, } @article {pmid42336888, year = {2026}, author = {Liu, Y and Xiong, G and Gao, L and Li, Y and Zhou, X and Yao, H and Wei, G and Yang, M and Yin, Y and Peng, J and Dong, L and Zhang, G}, title = {Foliar metal micronutrients reshape rhizosphere soil multifunctionality by filtering microbial life-history strategies.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01071-y}, pmid = {42336888}, issn = {2055-5008}, support = {2022YFC3501802, 2022YFC3501803, and 2022YFC3501804//National Key Research and Development Program/ ; 2023-I2M-2-006//CAMS Innovation Fund for Medical Sciences(CIFMS) Grant/ ; CI2023E002, CI2024E003//Chinese Academy of Chinese Medical Sciences/ ; CI2026A03809//Chinese Academy of Chinese Medical Sciences/ ; 82304663//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ16-XRZ-072, ZZ17-YQ-025, ZXKT22052, and ZXKT22060//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; Z181100006218020//Beijing Nova Program/ ; }, abstract = {Foliar application of metal micronutrients is increasingly adopted in intensive cultivation systems, yet its potential ecological risks to rhizosphere functions remain poorly understood. Here, using the medicinal plant Panax notoginseng as a model, we conducted a gradient foliar amendment experiment with iron (Fe), zinc (Zn), and copper (Cu) to evaluate how aboveground metal inputs regulate rhizosphere soil multifunctionality (MF) through microbial life-history strategies. By integrating 16S rRNA amplicon sequencing, metagenomics, root transcriptomics, and a newly developed quantitative Yield-Acquisition-Stress tolerance (qYAS) framework, we disentangled the microbial mechanisms underlying divergent functional responses to metal amendments. Foliar Fe significantly enhanced multifunctionality, including nutrient provision and element cycling, while Cu and Zn reduced nutrient provision and element cycling, but enhanced plant pathogen abundances. These changes were closely associated with shifts in bacterial life-history strategies: Fe promoted Y-strategists characterized by efficient carbon use, streamlined genomes, and high network connectivity, whereas Cu and Zn enriched AS-strategists with larger genomes and negative associations with multifunctionality. Partial least squares path modeling (PLS-PM) further identified microbial strategies as key mediators linking foliar metal inputs, plant performance, soil properties, and multifunctionality. This study provides a trait-based microbial framework for evaluating foliar metal fertilization and guiding safer nutrient management.}, } @article {pmid42336979, year = {2026}, author = {Solymosi, N and Pap, B and Nagy, SÁ and Tóth, AG and Kevély, FJ and Maróti, G and Csabai, I and Kóthay, K and Magyar, D}, title = {Metagenomic peek into a corn mummy.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-59149-8}, pmid = {42336979}, issn = {2045-2322}, abstract = {Numerous studies have shown that metagenomics has opened a dimension in reading the contents of archaeological remains as time capsules. Corn mummies are ritual objects from ancient Egypt, created by forming human-shaped figures from cereal grains grown in a mixture of water and earth. The aim of our study was to determine whether ancient DNA could be preserved in the mummy, and if so, which organisms it might have originated from. To find answers, we performed metagenomic analyses on samples taken from a corn mummy dating to the second half of the third century BC. Alongside a number of clearly modern contaminants, we identified organisms that cannot be excluded as being of historical origin. Besides considerable amounts of bacterial sequences belonging to the genus Bacillus, Mesobacillus, Metabacillus, Neobacillus, Niallia, Peribacillus and Paenibacillus, we also found traces of plants, animals, and humans. Sequences assigned to the genus Triticum showed the highest similarity to ancient T. turgidum ssp. dicoccum specimens from Egypt and the southern Levant. The fragments identified as of Lepidopteran origin showed the greatest similarity to Sphingidae genomes. Analysis of the human-derived sequences revealed L3 (mtDNA), E, and J (Y chromosome) haplotypes, which are common lineages in Africa today.}, } @article {pmid42135082, year = {2026}, author = {Saranya, RG and Ramesh Babu, K and Viswanathan, P}, title = {Corrigendum to "Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR" [Life Sci. 393 (2026) 124336].}, journal = {Life sciences}, volume = {398}, number = {}, pages = {124457}, doi = {10.1016/j.lfs.2026.124457}, pmid = {42135082}, issn = {1879-0631}, } @article {pmid42135536, year = {2026}, author = {Adedire, DE and Onilude, AA and Odeniyi, OA and Nash, O and Semenya, K and Unuofin, JO}, title = {Snapshot reflection of the seasonal resilience and diversity of fungal phylotypes in the tropical Ikogosi spring.}, journal = {Environmental science and pollution research international}, volume = {33}, number = {17}, pages = {8264-8275}, pmid = {42135536}, issn = {1614-7499}, mesh = {Seasons ; *Fungi ; Biodiversity ; Geologic Sediments ; Microbiota ; Phylogeny ; }, abstract = {Freshwater ecosystems like rivers, streams, and springs harbour diverse microbial communities, including fungal and bacterial phylotypes. These communities are an important part of the aquatic ecosystem, playing key roles in biogeochemical cycles. However, research on the seasonal differences concerning the fungal diversity of Ikogosi Warm Spring's sediments and water has been lacking. In this pilot study, we aimed to bridge this gap by employing high-throughput DNA sequencing to examine the fungal microbiome of this spring during the wet and dry seasons. Metagenomic DNA was extracted from water and sediment samples from different locations of the spring, and the fungal ITS1 region was sequenced using Illumina HiSeq technology. Sequences were processed with the DADA2 pipeline in R, enabling comprehensive taxonomic and diversity analyses. In addition, the spring's sediment and water physicochemical characteristics were assessed, and the impact of environmental variables on fungal communities was examined using redundancy analysis. Taxonomic analysis revealed that the spring was dominated by Ascomycota and Basidiomycota, irrespective of seasonal differences. In water samples, Ascomycota represented 62.0% (wet season) and 89.0% (dry season), while Basidiomycota accounted for 37.7% and 10.7%, respectively. Sediments exhibited a similar dominance, with Ascomycota comprising 65.1% in both seasons and Basidiomycota contributing 34.8% (wet season) and 33.5% (dry season). Alpha diversity indices indicated that fungal diversity was higher during the dry season than in the wet season, with no significant difference at p < 0.05. Redundancy analysis showed that some physicochemical factors, such as potassium and sulphate ions in water samples, were associated with seasonal patterns. These factors also influenced fungal communities in the spring, such as Cladosporium, Trichosporon, and Meyerozyma.}, } @article {pmid42135633, year = {2026}, author = {Basu, U and Ahanger, SA and Song, T and Gai, X and Hu, X}, title = {Ecological and genomic dynamics of the soil microbiome under sustained pressure from Phytophthora nicotianae, the causal agent of tobacco black shank disease.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05137-x}, pmid = {42135633}, issn = {1471-2180}, support = {202405AD350100, 2023530000241003/YNDG202302XJ02//Yunnan Applied Fundamental Research Projects and the Yunnan Provincial Tobacco Monopoly Bureau/ ; }, abstract = {BACKGROUND: Soil-borne pathogens threaten global agriculture, yet soil microbiome adaptation to persistent pathogen pressure is poorly understood. This study characterized the ecological and genomic long-term shifts in a tobacco field soil microbiome under sustained Phytophthora nicotianae pressure. We conducted a six-year longitudinal metagenomic study in a field with a documented history of tobacco black shank disease. Comparative analysis of the rhizosphere microbiome from Year_1 and Year_6 was performed using shotgun sequencing, non-redundant gene catalog construction, and functional annotation against specialized databases.

RESULTS: Our analysis revealed a profound genetic remodelling, with 45.6% (116,529) of 255,258 genes showing significant differences in abundance (p < 0.05, |log2FC| ≥ 1). This restructuring was systematic, characterized by significant enrichment of the soil antibiotic resistome, where 45.88% of antibiotic resistance genes were differentially abundant and showed a distinct trend toward increased abundance. The functional potential for carbohydrate metabolism was reorganized, with 53.2% of CAZymes (Carbohydrate-Active enZYmes) genes showing differential abundance and a predominant depletion. Analysis of COG (Clusters of Orthologous Groups) revealed a strategic functional trade-off, with significant enrichment of defense-related categories like secondary metabolite biosynthesis (+ 52.9%) alongside a reduction in growth-related processes. Such functional changes were ultimately driven by an taxonomically homogenized community, as indicated by a major reduction in species level alpha diversity (Shannon index: 5.52 to 5.31) that coexisted with a 14.8% significant increase in species level abundance, which showed a selective enrichment of a subset of dominant taxa.

CONCLUSION: Sustained pathogen pressure triggers a coordinated, multi-level adaptive succession, reshaping the genetic, functional, and taxonomic structure of the soil microbiome into a more defended and specialized state.}, } @article {pmid42136553, year = {2026}, author = {Yang, L and Chen, X and Jia, A and Liu, Q and Chu, J}, title = {Atypical Streptococcus sinensis infective endocarditis complicated by bacterial meningitis: A case report and literature review.}, journal = {The Journal of international medical research}, volume = {54}, number = {5}, pages = {3000605261447124}, pmid = {42136553}, issn = {1473-2300}, mesh = {Humans ; Male ; *Meningitis, Bacterial/microbiology/drug therapy/complications/diagnosis ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; *Streptococcus/isolation & purification/genetics ; *Endocarditis, Bacterial/microbiology/drug therapy/complications/diagnosis ; *Streptococcal Infections/microbiology/drug therapy/complications/diagnosis ; RNA, Ribosomal, 16S/genetics ; Vancomycin/therapeutic use ; *Endocarditis/microbiology/complications/drug therapy ; Mitral Valve/microbiology ; Ceftriaxone/therapeutic use ; Echocardiography ; }, abstract = {Infective endocarditis caused by Streptococcus sinensis complicated by bacterial meningitis is exceedingly rare. We report a case of a middle-aged man who initially presented with ischemic symptoms in both lower limbs. Echocardiography revealed mitral valvular vegetations, and blood cultures confirmed S. sinensis. During antibiotic therapy, the patient developed somnolence, dysarthria, and left-sided weakness. Metagenomic next-generation sequencing of cerebrospinal fluid detected S. sinensis, thereby confirming infective endocarditis complicated by bacterial meningitis. Given the high surgical risk, combination antimicrobial therapy with vancomycin and ceftriaxone was administered. The patient's consciousness recovered, and inflammatory and cerebrospinal fluid parameters gradually normalized. This case demonstrates that S. sinensis-associated infective endocarditis can occur in patients with immunocompetent status and often involves the mitral valve, with potential intracranial complications. Early identification by blood culture, metagenomic next-generation sequencing, and 16S rRNA sequencing enables precise pathogen diagnosis. Standardized antibiotic therapy and individualized surgical assessment are crucial to optimize outcomes. For patients with neurological complications, multidisciplinary management is essential to improve survival and long-term prognosis.}, } @article {pmid42136736, year = {2026}, author = {Takahashi, Y and Sada, RM and Matsuo, H and Yamamoto, S and Matsuzaki, S and Okada, A and Sunada, A and Takao, M and Yamamoto, G and Chuang, CK and Liu, CH and Kutsuna, S}, title = {Diagnostic challenges in postoperative pelvic infections associated with Metamycoplasma hominis: a two-case analysis using metagenomic sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1823299}, pmid = {42136736}, issn = {2235-2988}, mesh = {Humans ; Female ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; *Mycoplasma hominis/genetics/isolation & purification ; Middle Aged ; *Pelvic Infection/diagnosis/microbiology ; *Postoperative Complications/diagnosis/microbiology ; DNA, Bacterial/genetics ; Adult ; *Mycoplasma Infections/diagnosis/microbiology ; }, abstract = {Postoperative gynecological infections may present diagnostic challenges, particularly in the presence of fastidious genital mollicutes and inherently mixed microbial DNA, both of which limit the diagnostic performance of microbiological methods, including Gram staining, conventional culture, 16S rRNA gene PCR followed by Sanger sequencing. This study aimed to illustrate the limitations of conventional microbiological methods in the diagnosis of gynecologic pelvic infections and highlight key considerations for the clinical use of metagenomic next-generation sequencing (mNGS), based on two contrasting cases of postoperative pelvic infections associated with Metamycoplasma hominis (M. hominis). In both cases, neither conventional culture nor 16S rRNA gene PCR/Sanger sequencing identified the causative organism, and shotgun mNGS was subsequently performed. Although the mNGS findings differed markedly between the two cases, M. hominis was considered the most plausible pathogen. These two cases show that the clinical relevance of organisms detected by mNGS should not be judged by read counts alone, particularly in non-sterile specimens or after antibiotic exposure. Even low-abundance reads may represent clinically meaningful pathogens when interpreted within the clinical context. They also highlighted the value of mNGS as a complementary diagnostic tool for gynecological pelvic infections when conventional diagnostic methods are intrinsically limited.}, } @article {pmid42136790, year = {2026}, author = {Ariyasiri, A and Altaf, A and Mirza, H and Rehman, M}, title = {Genomics for precision surgical source control in anti-microbial resistant infections: A global review with focus on resource-limited settings.}, journal = {Pakistan journal of medical sciences}, volume = {42}, number = {411AASC}, pages = {S151-S156}, pmid = {42136790}, issn = {1682-024X}, abstract = {BACKGROUND & OBJECTIVE: Antimicrobial resistance (AMR) critically threatens surgical safety, impairing perioperative prophylaxis and complicating infection management. Timely surgical source control is essential but relies on accurate microbiological diagnosis. Conventional culture-based methods are slow and insensitive, often leading to empirical broad-spectrum therapy. This review evaluates the role of advanced genomic diagnostics in enhancing surgical source control for AMR infections, with a focus on challenges and opportunities in low- and middle-income countries (LMICs) like Pakistan.

METHODOLOGY: A narrative review was conducted via a structured search of PubMed, Google Scholar, and ScienceDirect (January 2015-October 2025). Studies involving genomic tools in the management of AMR-related surgical infections were included. Evidence was synthesized thematically, covering genomic platforms, clinical applications, implementation barriers, and LMIC specific perspectives.

RESULTS: Genomic tools, particularly metagenomic next-generation sequencing (mNGS) and rapid multiplex PCR, demonstrate superior sensitivity (80.6-95.45%) and faster turnaround times (e.g., roughly 27 hours for mNGS) compared to culture. They improve pathogen detection in complex infections (e.g., prosthetic joints, necrotizing soft tissue), guide targeted antibiotic therapy, and can reduce broad-spectrum use. However, major implementation barriers exist, including high costs, need for specialized infrastructure and expertise, bioinformatic challenges, and ethical data concerns, which are especially pronounced in LMICs.

CONCLUSION: Genomic diagnostics offer a powerful approach to accelerate and refine surgical source control in the era of AMR. Strategic investments in local capacity, affordable platforms, and integration with antimicrobial stewardship are needed to realize their potential for improving surgical outcomes, particularly in resource-limited settings.}, } @article {pmid42136862, year = {2026}, author = {Feng, Z and Quan, H and Li, M and He, D and Han, Y and Zou, C and Zhang, W and Chang, J and Lu, M}, title = {Distinct microbial and functional alterations across skin sites and disease severity in pediatric atopic dermatitis: a prospective study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1805596}, pmid = {42136862}, issn = {2296-858X}, abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin condition frequently associated with microbial dysbiosis.

OBJECTIVE: This study examined the diversity, composition, and functional profiles of the skin microbiome in children with varying degrees of AD in different skin regions.

METHODS: Skin samples were collected from 12 AD patients and 12 healthy controls. Genomic DNA underwent shotgun metagenomic sequencing to analyze alpha and beta diversity, taxonomic composition, and functional profiles, including the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), virulence factors and pathogen-host interactions (PHI).

RESULTS: Significant differences were observed in Shannon's diversity index and Chao1 diversity index between severity groups (p = 0.007 and 0.004). Cluster analysis revealed partial clustering by severity, with significant differences between mild and moderate groups (p = 0.042) and between moderate and severe groups (p = 0.036). Staphylococcus and Streptococcus dominated the abundance profile in AD samples. Functional analysis revealed alterations in epidermal microbial activity during AD onset and across different severity levels.

CONCLUSION: Pediatric AD involves site- and severity-specific microbial shifts. This functional dysregulation and enrichment of virulence factors may push barrier dysfunction and inflammation, suggesting that the microbiome is a critical target for future therapies.}, } @article {pmid42136870, year = {2026}, author = {Zhou, Y and Chen, L and Wang, L and Zhao, Z and Tu, J and Chen, H and Wang, S}, title = {Cavitary nodule caused by Emergomyces orientalis in a diabetic patient: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1829356}, pmid = {42136870}, issn = {2296-858X}, abstract = {Emergomyces orientalis is a rare thermally dimorphic fungus belonging to the family Ajellomycetaceae. It exists in the environment as a mold producing conidia, which are inhaled and transform into yeast-like cells at body temperature to cause disseminated infections. While primarily associated with immunocompromised individuals, especially those with HIV. Diagnosis remains challenging due to its morphological similarity to Blastomyces dermatitidis and the frequent failure of routine cultures. Thus, molecular methods such as metagenomic next-generation sequencing (mNGS) have become crucial for early identification. This case report describes a 51-year-old man with type 2 diabetes mellitus presented (T2DM) with a 10-day history of back pain, pharyngeal discomfort, and scant sputum. Chest CT showed multiple bilateral pulmonary nodules, one of which had cavitated. mNGS of a percutaneous lung biopsy confirmed Emergomyces orientalis. Histopathology also supported the diagnosis. The patient was discharged on oral itraconazole after partial symptomatic improvement, with outpatient follow-up arranged. Two months of antifungal therapy resulted in mild reduction of cavitary lesions on follow-up CT.}, } @article {pmid42137133, year = {2025}, author = {Kazemifard, N and Norouzi-Beirami, MH and Baradaran Ghavami, S and Ghanbari-Maman, L and Zali, MR and Shahrokh, S and Kavousi, K}, title = {Microbiome-microRNA interactions in inflammatory bowel disease: insights from metagenomic and transcriptomic data analysis.}, journal = {Gastroenterology and hepatology from bed to bench}, volume = {18}, number = {SI}, pages = {85-96}, pmid = {42137133}, issn = {2008-2258}, abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD) is a chronic inflammation of the gastrointestinal tract, the precise origins of which remain not fully elucidated. This study investigates the complex relationship between gut metagenomics and host transcriptomics in IBD patients, focusing on Ulcerative Colitis (UC) and Crohn's Disease (CD).

METHOD: One proposed theory suggests that microRNAs produced by the host may significantly influence IBD development by impacting the gut microbiota. Conversely, the gut microbiome may regulate the expression of host microRNAs, leading to dysfunction in the intestinal epithelium. An enrichment analysis was conducted to pinpoint associated pathways. To unravel this intricate interplay, the study utilized data from the IBDMDB database, selecting samples from adult individuals.

RESULT: The dataset comprised 50 paired metagenomic and host transcriptomic samples, including 8 controls, 18 UCs, and 24 CDs. Computational analyses and network constructions were applied to identify relationships between bacterial species, microRNAs, and other transcripts.

CONCLUSION: This research offers valuable insights into the dynamic relationship between the gut microbiome and human transcriptomics in IBD, providing a deeper understanding of potential disease mechanisms. Furthermore, it sheds light on the complex tripartite network connecting bacterial species, microRNAs, and transcripts, contributing to a comprehension of IBD pathogenesis and the identification of novel therapeutic targets.}, } @article {pmid42137225, year = {2026}, author = {Meknas, A and Bessonov, K and Eagle, SHC and Peterson, CL and Robertson, J and Ricker, N and Signorelli, T and Nash, J and Reimer, A}, title = {Sequenoscope: a modular tool for nanopore adaptive sequencing analytics and beyond.}, journal = {Access microbiology}, volume = {8}, number = {5}, pages = {}, pmid = {42137225}, issn = {2516-8290}, abstract = {This article presents Sequenoscope: a bioinformatics pipeline for analysing Oxford Nanopore Technologies (ONT) adaptive sampling sequencing data. Sequenoscope features three main modules: filter_ONT for filtering raw reads and creating a FASTQ file with a subset of reads for further analyses, analyze for generating sequencing and read mapping statistics against the provided reference taxon sequences and plot for interactive data summarization, comparison, and visualization between two datasets/test conditions. Here, we demonstrate the ability of the pipeline to analyse ONT adaptive sampling sequence data and provide examples of the outputs users can expect using data we generated. Adaptive sampling was performed on two ZymoBIOMICS Microbial Community DNA Standards, log-distributed (Cat# D6311) and even-distributed (Cat# D6306) formulations, with targeted depletions of Listeria monocytogenes. By comparing the test and control experimental data in FASTQ files from the sequencing runs, Sequenoscope showed that depletion of L. monocytogenes was successful by providing users with parameters to compare such as taxon coverage, read length and types of pore-level decisions made during sequencing. Although Sequenoscope was designed for ONT adaptive sampling data analysis, it supports short-read data from other sequencing platforms such as Illumina, allowing for the direct comparison of any two experimental conditions or cross-platform benchmarking.}, } @article {pmid42137573, year = {2026}, author = {Sun, J and Gao, W and Tan, H}, title = {The role of targeted next-generation sequencing and ultrasound in diagnosing fetal cytomegalovirus infection: a case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1734139}, pmid = {42137573}, issn = {2296-2360}, abstract = {BACKGROUND: Cytomegalovirus (CMV) infection is a leading cause of congenital infection and neonatal morbidity. Conventional diagnostic methods, such as polymerase chain reaction (PCR) and amniocentesis, remain important in the diagnosis of congenital CMV infection, although each method has its own limitations in clinical practice.

CASE PRESENTATION: A 31-year-old woman, gravida 3 para 1, presented for routine prenatal evaluation. At 18 weeks of gestation, ultrasound revealed echogenic bowel and fetal ascites. Amniocentesis at 19 weeks showed normal chromosomal results, but targeted next-generation sequencing (tNGS) detected CMV DNA with a high viral load, confirming intrauterine infection.

RESULTS: Despite counseling regarding poor fetal prognosis, the patient chose to continue the pregnancy under close ultrasound surveillance. Progressive hydrops fetalis was observed at 23 weeks, and the pregnancy was terminated at 24 weeks.

CONCLUSION: This case suggests that combining tNGS with ultrasound may provide complementary diagnostic information in selected cases of suspected fetal infection. In this patient, tNGS supported the identification of CMV in amniotic fluid when conventional genetic testing was unremarkable. However, as this is a single-case report, the broader diagnostic performance and clinical utility of tNGS require further validation in larger studies.}, } @article {pmid42137610, year = {2026}, author = {Oguzie, JU and Cummings, DB and Groves, JT and Hagan, AG and Rodriguez, J and Hernandez-Vidal, G and Moreno-Degollado, G and Shittu, I and Marushchak, LV and Nguyen-Tien, T and Trujillo-Vargas, CM and Silva, DB and Li, F and Richeson, JT and Schneider, NE and Gray, GC}, title = {Detection and Genomic Characterization of Novel Respiratory Viruses in US and Mexican Cattle Farms.}, journal = {Transboundary and emerging diseases}, volume = {2026}, number = {}, pages = {3247802}, pmid = {42137610}, issn = {1865-1682}, mesh = {Animals ; Cattle ; United States/epidemiology ; *Cattle Diseases/virology/epidemiology ; Mexico/epidemiology ; *Respiratory Tract Infections/veterinary/virology/epidemiology ; Farms ; Humans ; Genome, Viral ; *Viruses/isolation & purification/genetics/classification ; *Virus Diseases/veterinary/epidemiology/virology ; }, abstract = {Respiratory virus infections in cattle cause an estimated more than $1 billion in production losses and can threaten human health. During February 2024 to May 2025, we employed a One Health approach to surveil for respiratory viruses among cattle, farm workers, and environmental samples from 11 US and Mexican beef or dairy cattle farms. We studied nasal and ocular swabs from cattle, nasal swabs from cattle workers, bioaerosol samples, and other environmental farm samples using molecular and virological techniques. Among 26 distinct viruses identified in cattle, we detected bovine nidovirus 1, influenza D virus (D/OK-like and D/660-like), bovine coronavirus, bovine rhinitis A and B viruses, bovine respirovirus 3 and bovine respiratory syncytial virus (BRSV); 11 of the 26 detected viruses were non-bovine-associated. Two bovine rhinitis A virus was markedly divergent (provisionally designated BRAV-4). Environmental metagenomics additionally identified influenza D virus, bovine coronavirus, and bovine rhinitis B virus. One human nasal swab tested positive for SARS-CoV-2 (cladeLF.7.3). Our findings reveal the presence of emerging, co-circulating, and environmentally linked pathogens at the human-animal-environment interface, underscoring the constant need for One Health surveillance to safeguard livestock and mitigate zoonotic risk.}, } @article {pmid42137790, year = {2026}, author = {Qi, J and Zhang, K and Zhan, C and Lu, X and Chen, X and Li, X and Zhang, C and Wang, H and Tu, C and Tong, W and Dai, L and Zeng, D}, title = {Microbial and metabolic crosstalk in the rhizosphere shapes the divergent drought resilience of contrasting rice genotypes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1788826}, pmid = {42137790}, issn = {1664-302X}, abstract = {Drought is a major constraint on rice production, yet the coordinated responses of rhizosphere microbial communities and metabolites across rice genotypes with contrasting drought tolerance remain insufficiently understood. In this study, we combined metagenomic and metabolomic analyses to investigate drought-induced changes in the rhizosphere of three rice genotypes with distinct ecological backgrounds: the drought-sensitive cultivar Bhutan, the upland rice genotype TGR78, and Oryza rufipogon K111. Field experiments were conducted under well-watered and drought conditions, and rhizosphere soil samples were collected for multi-omics profiling. Drought stress reduced plant height and panicle number in all three genotypes, but the magnitude of these effects differed among genotypes. Bhutan showed the greatest reduction in plant height (42.1%) and the largest number of differential metabolites (146), indicating a stronger drought response at both phenotypic and metabolic levels. In contrast, TGR78 and K111 displayed relatively greater phenotypic stability under drought stress. Metagenomic analysis revealed pronounced genotype-dependent shifts in rhizosphere bacterial community composition, whereas metabolomic profiling showed distinct changes in metabolite accumulation patterns among genotypes. Correlation analysis further demonstrated that drought substantially reshaped rhizosphere microbe-metabolite associations, shifting the interaction network from broadly positive and highly connected under well-watered conditions to more selective associations under drought stress. Collectively, these results indicate that rice drought adaptation is associated with genotype-dependent reorganization of the rhizosphere microbiome and metabolic profile. This study provides new insight into rhizosphere-mediated drought responses in rice and offers a basis for developing microbiome-informed strategies for drought-resilient crop improvement.}, } @article {pmid42137793, year = {2026}, author = {Adeleke, RA and Machailoe, TME and Malemagovha, M and Olanrewaju, OS and Alayande, KA and Obi, LU and Makinde, OM}, title = {Diversity and functional potential of bacterial and fungal endophytes in traditional food wrapping leaves reveal implications for artisanal food safety and quality.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1641069}, pmid = {42137793}, issn = {1664-302X}, abstract = {Plant leaves are widely utilised globally for the packaging and serving of traditionally prepared foods. The microbial communities associated with these wrapping leaves, particularly endophytes, are recognised to potentially influence food quality, safety, and preservation. Specifically, certain endophytes can enhance sensory attributes and nutritional value through fermentative processes, while the presence of harmful microorganisms may lead to spoilage and pose a risk of foodborne illness. This study utilised 16S rRNA, ITS metabarcoding and metagenomic functional analysis (PICRUSt2) to comprehensively investigate the composition and infer the putative functional potential of putative endophytic bacterial and fungal communities present in 53 samples of four different food wrapping leaves. The leaves examined included Thaumatococcus daniellii (n = 10), Alstonia macrophylla (n = 18), Theobroma species (n = 14), and Megaphrynium macrostachyum (n = 11). Distinct microbial community profiles were observed across the different leaf types. Highest bacterial species richness and community variability were detected in A. macrophylla samples, reflected by Principal Coordinates Analysis (PCoA) values (PCoA1 = 43.97%; PCoA2 = 10.68%). Conversely, M. macrostachyum exhibited the greatest fungal species richness and variability (PCoA1 = 20.08%; PCoA2 = 8.72%). Taxonomic analysis identified Proteobacteria as the dominant bacterial phylum and Stenotrophomonas as the dominant bacterial genus. Other notable bacterial taxa included the phyla Bacteroidota and Firmicutes, and genera such as Pseudomonas, Faecalibacterium, and Bacteroides. For fungal communities, Ascomycota was the dominant phylum. Additional fungal taxa included the phylum Basidiomycota and genera Cryptococcus, Candida, and Meyerozyma. A core microbiome analysis revealed that 42 bacterial (notably Stenotrophomonas and Chryseobacterium) and 7 fungal taxa (notably Pleosporaceae and Ascomycota) were shared across all examined wrapping leaves. The identified microbial communities (e.g., Lactobacillus and Geotrichum) encompass taxa with potential beneficial roles, such as enhancing food fermentation and potentially contributing to human gut health upon consumption of the packaged food. However, the detection of potentially pathogenic and toxigenic bacterial taxa highlights a possible public health risk associated with the use of these leaves. Further investigation into the specific functionalities of these associated bacteria and fungi is essential to maximise their beneficial applications while simultaneously mitigating potential health risks posed by harmful strains.}, } @article {pmid42137803, year = {2026}, author = {Liu, Y and Chen, C and Gao, J}, title = {Topological characteristics and longitudinal dynamics of co-abundance networks involving beneficial commensal bacteria in the pig gut microbiome and its association with average daily gain.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1818141}, pmid = {42137803}, issn = {1664-302X}, abstract = {Microorganisms are intricately interrelated with each other in the gut microecosystem, which influences the colonization and functional roles of probiotics. However, how these interactions dynamically change during host development and whether their topological features influence host phenotypes, such as average daily gain (ADG), remain poorly understood. In this study, we performed metagenome analysis for 2,311 fecal samples collected from a specifically designed eight genetically divergent breed intercrossed mosaic F6 and F7 population, at three developmental ages of 25 days (D25), 120 days (D120), and 240 days (D240) of each individual, covering pre-weaning to market. By constructing their microbiota co-abundance networks, we systematically characterized dynamic changes in beneficial commensal bacteria involved co-abundance networks in the pig gut microbiome across three ages. We elucidated conserved and variable co-abundance features involving these bacteria across developmental stages. We observed that the cross-age stable co-abundance correlations of beneficial commensal bacteria were maintained by a large set of weak correlations. A subset of age-shared co-abundance correlations remained variable across different ages in correlation strength and direction. Topological analysis revealed that beneficial commensal bacteria involved co-abundance networks were highly age-specific. Among the three age stages sampled in this study, the D120 stage represented a critical window for the structural and functional reorganization of gut microbiota. Using metagenomic sequencing data at the D120, we identified two guilds that were significantly associated with ADG from D120 to D240. Guild 1 included short chain fatty acid-producing taxa and was positively associated with ADG, whereas Guild 2 tended to self-utilization of energy and was negatively associated with ADG. We also inferred the ecological interaction mechanisms of ADG-associated microbial communities using genome-scale metabolic models. These findings provided a theoretical basis for stage-specific intervention in the pig gut microbiome using probiotics to improve production traits.}, } @article {pmid42137806, year = {2026}, author = {Doughan, GE and Walthart, BK and Schau, CE and Skoland, KJ and Mou, KTY and Brown, JT and Bonnema, JL and Plummer, PJ and Zhang, D and Li, G and Karriker, LA}, title = {Presence of antimicrobial resistance genes in biofilms from swine drinking water pipes before and after treatment with peracetic acid.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1770950}, pmid = {42137806}, issn = {1664-302X}, abstract = {Biofilms can be problematic to swine drinking water systems as they can harbor pathogens, decrease water quality, and may contribute to antimicrobial treatment failure. Water-administered antimicrobials are used for disease treatment in swine populations, yet, little is known about water line ecology and the impact it can have on antimicrobial resistance and stewardship. Water line cleaning and disinfection may aid in removal of water line biofilms, improve swine health, and antimicrobial stewardship. Water line samples were collected pre-treatment (0), 24 h post-treatment with 0.78% CID 2000 Pro (peracetic acid) (1), and 3, 5, 7, 14, 21, 42, 56, and 77-days post-treatment from six wean-to-finish swine farms in Iowa, USA. Biofilm was aseptically extracted from the interior of the water line pipe (n = 119) and submitted for metagenomic analysis to detect antimicrobial resistance genes (ARGs). This study demonstrates high prevalence of ARGs in swine water line biofilms that could confer resistance to both medically important antimicrobials to humans and animals such as aminoglycosides, beta-lactams, fluoroquinolones, colistin, and fosfomycin. From 115 samples, a frequency of 3,904 ARGs were reported, with 184 unique ARGs defined. Four samples contained no ARGs. One hundred and fifty-one integron genes representing three classes were found in 115 of 119 samples, indicating mechanisms of potential spread of multiple drug resistance. ARGs and integron genes combined were significantly lower on average by 10 unique ARGs/ integron genes 24-h post-treatment (1) when compared to pre-treatment (0) counts (p-value = 0.01). The number of unique ARG and integron genes quickly rebounded and were not statistically significant compared to pre-treatment counts on post-treatment dates 3, 5, and 7 (adjusted p-value ≥ 0.05), and by post-treatment date 14, unique ARG and integron genes were significantly higher than pre-treatment (adjusted p-value = 0.012). This study demonstrates that swine water line biofilms can harbor antimicrobial resistance genes which could have potential clinical impacts on pig health and treatment response.}, } @article {pmid42137815, year = {2026}, author = {Geng, S and Shi, X and Zhang, Q and Yang, J and Yang, C and Yang, L}, title = {Organic fertilizer enhances microbial functional genes related to nitrogen and phosphorus cycling in rubber tree (Hevea brasiliensis) rhizosphere.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1833968}, pmid = {42137815}, issn = {1664-302X}, abstract = {INTRODUCTION: Nitrogen (N) and phosphorus (P) are the essential nutrient for rubber growth. However, the effect of organic fertilizer application on soil microbial communities and functional genes related to N and P cycling in rubber plantation are unclear.

METHODS: A field trial was established in a rubber plantation with two treatments: organic fertilizer (OF) and an unfertilized control (CK). In this study, we used metagenomics analysis to examine the structural and functional alterations in the microbial community within the rhizospheric soil of rubber when organic fertilizers were applied.

RESULTS: Results showed that compared with the CK treatments, the OF treatment significantly increased soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), alkali-hydrolyzable nitrogen (AN), and available phosphorus (AP) contents. Taxonomic analysis revealed that OF treatment significantly enriched the phyla Pseudomonadota and Myxococcota, and the genera Pseudolabrys and Gaiella. At the functional level, organic fertilization significantly up-regulated key genes associated with N cycling, including organic N metabolism (gltB), N transport (nrtA, nrtB, nrtC), denitrification (norB, nosZ), nitrification (nxrB), and dissimilatory nitrate reduction (napA, napC). Regarding the P cycle, organic fertilization leads to the downregulation of the high-affinity phosphate transporter gene pstS and the concurrent upregulation of genes governing organic P mineralization (phnA, phoN), regulation (phoB), polyphosphate synthesis (ppk1), and polyphosphate degradation (spoT, relA). The variation partitioning analysis (VPA) results indicated that pH, SOM, and nitrogen nutrients (comprising TN and AN) explained 71.52% of the variation in the abundance of nitrogen-cycling functional genes, while pH, SOM, and phosphorus nutrients (comprising TP and AP) explained 64.95% of the variation in the abundance of phosphorus-cycling functional genes.

CONCLUSION: In summary, the application of organic fertilizer reshapes soil microbial communities and enhances the functional potential for nitrogen (N) and phosphorus (P) cycling. Our study provides a mechanistic basis for developing sustainable nutrient management strategies to optimize N and P bioavailability in tropical rubber agroecosystems.}, } @article {pmid42137872, year = {2026}, author = {Parrino, J and Sunshine, J and Tripp, K and Shaffer, M and Sughra, U and Procházková, N and Jara, M and Moll, JM and Noble, R and Muir, L and McIntyre, E and Guduk, E and Zachariah, D and Vernochet, C and Frahm, N and Schmidt, AC}, title = {Impact of Bifidobacterium infantis supplementation on growth, health outcomes, and gut microbiome features in underweight infants from Pakistan.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1783141}, pmid = {42137872}, issn = {2296-861X}, abstract = {BACKGROUND: Alterations in the gut microbiome are implicated in infant malnutrition. Bifidobacterium longum subspecies infantis (B. infantis), a commensal common in breastfed infants, has been shown to have reduced abundance in malnourished infants. This trial (NCT05952076) evaluated if B. infantis strain Bi-26 supplementation could improve growth and health outcomes in underweight infants in Pakistan.

METHODS: In this double-blind, randomized, placebo-controlled trial, 40 infants aged 30-120 days (d) with a weight-for-age Z score (WAZ) below -2 received daily oral Bi-26 or placebo for 28d, with follow-up to d90 for safety. The primary endpoint was change in WAZ from baseline to d56. The intended sample size was 396 infants but study was terminated early due to operational delays. Total B. infantis levels microbiome, metabolome, and cytokine profiles were assessed.

RESULTS: Bi-26 supplementation increased fecal B. infantis levels at d28 (p = 0.001) and d56 (p = 0.03) but did not result in significant change in WAZ (p = 0.69) or weight gain (p = 0.56) compared to placebo. Fewer adverse events (AEs) occurred in the Bi-26 group compared to placebo (40% vs. 80% of infants; 17 vs. 49 events). Probiotic engraftment was impacted by presence of baseline endogenous B. infantis, suggesting that Bi-26 complemented rather than outcompeted endogenous strains. Bi-26 altered microbiome composition with transient alterations in function and metabolite abundance that reverted to baseline by d56, without cytokine differences between groups. B. infantis levels and Bifidobacterium-community types were associated with fewer AEs but not changes in WAZ or weight.

DISCUSSION: Bi-26 supplementation had an acceptable safety profile but did not improve growth. The findings of this trial support further evaluation of B. infantis strains in larger studies of underweight infants across diverse LMIC settings. Future trials should determine whether sustained metabolic and functional remodeling can translate into measurable improvements in growth and health outcomes.

CLINICAL TRIAL REGISTRATION: https://www.clinicaltrials.gov/study/NCT05952076, NCT05952076.}, } @article {pmid42137970, year = {2026}, author = {Feser, M and Arend, D and Beier, S and Bolger, M and Lübke, NC and Meister, M and Steilen, L and Usadel, B and Scholz, U}, title = {Evolving bioinformatics services - the journey of KPI metrics with Scorpion.}, journal = {Journal of integrative bioinformatics}, volume = {}, number = {}, pages = {}, pmid = {42137970}, issn = {1613-4516}, abstract = {Key Performance Indicators (KPIs) are essential for evaluating project success and establishing control mechanisms to monitor development, performance, and user acceptance of services in joint projects. However, the absence of standardized frameworks and effective monitoring tools, combined with service providers' reluctance due to fears of comparability, has limited their adoption in scientific contexts. To address this gap, we developed Scorpion, a flexible tool for KPI monitoring in project management. Scorpion enables service providers to retain control over their metrics while supporting centralized reporting. It offers both web-based and programmatic access, with features for KPI submission, visualization, and user and service management. Initially created for bioinformatics and biodiversity projects, Scorpion is applicable across diverse domains. It is particularly valuable for initiatives like the German National Research Data Infrastructure (NFDI), where funding agencies require KPI reporting for evaluation. We present the Scorpion framework, highlighting its design principles, features, and potential to improve project management practices. Use cases illustrate how Scorpion enhances KPI monitoring efficiency and accuracy, contributing to better impact evaluation, quality assurance, and informed decision-making in project and service management.}, } @article {pmid42138445, year = {2026}, author = {Ndhlovu, K and Salawu-Rotimi, A and Bopape, FL and Mtsweni, PN and Babalola, OO and Hassen, AI}, title = {Elucidating the Functional and Taxonomic Diversity of Soil Microbial Communities From Three Commercial Soybean Farms in South Africa.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70360}, pmid = {42138445}, issn = {1758-2229}, support = {135456//National Research Foundation (NRF), South Africa/ ; }, mesh = {South Africa ; *Glycine max/growth & development/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Bradyrhizobium/genetics/isolation & purification/classification ; Metagenomics ; Nitrogen Fixation ; Phylogeny ; *Biodiversity ; Farms ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Prior to the introduction of the exotic inoculant strain of Bradyrhizobium, South African soils lacked the rhizobia that nodulate soybean. Five decades of soybean inoculation practice resulted in the establishment of the Bradyrhizobium population in many soybean growing fields. However, there is no record of the magnitude of this establishment and its impact on the taxonomic and functional abundance of other microbes. Here we use a shotgun metagenomics approach to elucidate the taxonomic and functional profiles of the soil microbes from selected commercial soybean farms in South Africa. Metagenomics of the total sequences revealed that Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria and Bacteroitedes are the prevalent phyla which differed in their relative abundance. Bradyrhizobium was the predominant genus at all three locations. Predicted functions detected genes essential for nitrogen metabolism, including nitrogen fixation, which have been unveiled in this study at a higher rate in all locations investigated. This study uncovers the microbial communities associated with soybean soils in South Africa. The study also generated vital information on the establishment of Bradyrhizobium spp. in the soils of soybean farms, providing a clue on whether inoculation of soya beans is always necessary. The findings, however, warrant further field investigations before any recommendations are rendered.}, } @article {pmid42138618, year = {2026}, author = {Ran, L and Mao, Y and He, B and Pan, H and Ma, H}, title = {Wildfire-Altered Soil Water-Extractable Organic Matter Drives Divergent Greenhouse Gas Emissions in Anaerobic Subsurface Soils.}, journal = {Environmental science & technology}, volume = {60}, number = {21}, pages = {15078-15088}, doi = {10.1021/acs.est.6c04642}, pmid = {42138618}, issn = {1520-5851}, mesh = {*Greenhouse Gases ; *Soil/chemistry ; *Wildfires ; Water ; Methane ; Carbon Cycle ; Soil Microbiology ; }, abstract = {Intensifying global climate change has increased wildfire frequency. Wildfire-altered soil water-extractable organic matter (burned-WEOM) is hydrologically transported to unburned areas, profoundly affecting cross-ecosystem carbon-nitrogen cycling and greenhouse gas (GHG) emissions. Taking soils from unburned subtropical forests as the research object, this study combined anaerobic incubation with high-resolution mass spectrometry and metagenomic sequencing to elucidate the regulatory mechanisms of burned-WEOM on soil GHG emissions under anaerobic conditions. The results showed that burned-WEOM increased CO2 emissions by 17.0%, induced a 164.6% surge in N2O emissions, and simultaneously inhibited CH4 emissions by 52.9%. With unique properties of high unsaturation and strong electron exchange capacity, burned-WEOM not only reshapes soil organic matter composition but also drives differential GHG emissions by enhancing complete carbon fixation pathways and recalcitrant carbon decomposition, increasing the abundance of anaerobic methane oxidation (AMO) genes and methanotrophs, enriching denitrifying microorganisms (especially fungi), and boosting N2O-generating gene activity without altering the reduction pathway. Moreover, WEOM molecular characteristics drive differences in GHG emissions: CH4 is mainly fueled by reduced, unsaturated lipid-like compounds, N2O is associated with nitrogen-rich, complex aromatic compounds, and CO2 has a broader range of source substrates. This study provides insights that may improve mechanistic understanding of postfire GHG dynamics and inform process representations in climate models.}, } @article {pmid42138754, year = {2026}, author = {Guimarães, LO and Couto, RDS and Reginato, SL and Mucci, LF and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, E}, title = {Wyeomyia confusa Lispivirus (WcLispV-SP): a novel neotropical mosquito virus in the Lispiviridae family.}, journal = {Archives of virology}, volume = {171}, number = {6}, pages = {}, pmid = {42138754}, issn = {1432-8798}, mesh = {Animals ; Phylogeny ; Genome, Viral ; *Culicidae/virology ; Open Reading Frames ; Brazil ; Viral Proteins/genetics ; RNA, Viral/genetics ; *Mononegavirales/genetics/classification/isolation & purification ; RNA-Dependent RNA Polymerase/genetics ; }, abstract = {Metatranscriptomic analysis of Wyeomyia confusa mosquitoes collected in the Atlantic Forest (Pindamonhangaba, São Paulo, Brazil) led to the identification of a previously uncharacterized virus, designated Wyeomyia confusa Lispivirus (WcLispV-SP), classified within the family Lispiviridae, genus Canmovirus. The viral genome consists of a negative-sense single-stranded RNA (ssRNA-) of 12,698 nucleotides, encoding six open reading frames (ORFs): nucleoprotein (N), two hypothetical proteins (HP/1 and HP/2), glycoprotein (G), ORFan protein, and RNA-dependent RNA polymerase (RdRp-L). Phylogenetic analysis supports the classification of WcLispV-SP as a distinct species within the genus Canmovirus. Structural analysis of the RdRp revealed conserved domains and catalytic motifs characteristic of members of the order Mononegavirales, supporting its functional integrity. These findings expand the known diversity of the Lispiviridae family and highlight the utility of metagenomic approaches for the discovery and characterization of RNA viruses associated with Neotropical sylvatic mosquitoes.}, } @article {pmid42138983, year = {2026}, author = {Touceda-Suárez, M and Ponsero, AJ and Barberán, A}, title = {Urban greenspaces harbour distinct plasmid communities enriched in heavy metal resistance and competitive traits in arid soils.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {5}, pages = {}, pmid = {42138983}, issn = {1465-2080}, mesh = {*Plasmids/genetics ; *Soil Microbiology ; *Metals, Heavy/pharmacology ; Soil/chemistry ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Gene Transfer, Horizontal ; Metagenome ; Microbiota/genetics ; Cities ; Humans ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Plasmids drive horizontal gene transfer, a fundamental mechanism for soil bacterial evolution and antibiotic resistance emergence. In arid regions, the transformation of natural soils into urban greenspaces introduces dramatic environmental changes that influence the adaptive strategies of soil micro-organisms. Additionally, urban greenspaces can act as interfaces of antibiotic resistance spread between environmental and human microbiomes. Here, we inferred plasmids from soil metagenomes of urban greenspaces in Tucson, AZ, USA, and nearby natural arid habitats. We found urban greenspaces to select for plasmids that carried genes that confer competitive advantages, including motility, prokaryotic defence and resistance to heavy metals. Notably, urban greenspace plasmids exhibited reduced diversity (genetic and functional variants), which could in turn constrain their adaptability to rapid environmental changes. These findings underscore the importance of plasmids as agents mediating soil microbial adaptation to human activities.}, } @article {pmid42139081, year = {2026}, author = {Shen, H and Song, J and Li, J and Hu, Y and Peng, N and Zhao, S}, title = {Dietary niches drive microbial community assembly, network reorganization, and symbiont evolution in freshwater fish gut microbiomes.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42139081}, issn = {1751-7370}, support = {NWZZJ2025-2027-05//Major Project of Hubei Agricultural Microbial Industry Development-Innovative Bio-feed Development and Demonstration of Straw-Based Feed Utilization/ ; }, mesh = {Animals ; *Symbiosis ; Fresh Water ; *Fishes/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; China ; *Diet ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Host diet is a fundamental ecological factor shaping the assembly and evolution of host-associated microbiomes, yet how dietary niches influence the structure of microbial associations and functional adaptation in freshwater fish remains poorly understood. This study selected five dominant farmed freshwater fish species in China with distinct feeding habits (herbivory, omnivory, filter-feeding, and carnivory) and systematically investigated the adaptive mechanisms of their gut microbiomes by integrating metagenomics, targeted cultivation, comparative genomics, and in vitro assays. We show that dietary niches exert a strong deterministic effect on microbial community assembly, leading to pronounced differences in ecological network topology, including connectivity, modularity, and keystone taxa. Cetobacterium was detected in all five fish species but exhibited a higher relative abundance in omnivorous (16.0%) compared to carnivorous fish (5.4%), suggesting that it may be a core genus within the gut microbiota of freshwater fish. Comparative genomics further revealed that Cetobacterium symbionts exhibit streamlined genome architectures and conserved core metabolic functions, indicative of adaptive evolution toward stable host-associated lifestyles. Guided by metagenomic insights, we isolated multiple Cetobacterium strains displaying host-adapted functional traits, linking community-level ecological patterns to cultivable symbiont resources. In summary, our findings demonstrate that freshwater fish guts function as ecological niches that deterministically structure microbial community assembly and drive symbiont evolution, providing a conceptual framework for understanding host-microbiome co-adaptation in aquatic ecosystems.}, } @article {pmid42139090, year = {2026}, author = {Parienti, JJ and Yang, SS and Grinspoon, S}, title = {Selected Industry Highlights From IDWeek 2025.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {82}, number = {Supplement_4}, pages = {S85-S86}, doi = {10.1093/cid/ciag206}, pmid = {42139090}, issn = {1537-6591}, mesh = {Humans ; *HIV Infections/complications/drug therapy ; High-Throughput Nucleotide Sequencing ; }, abstract = {This supplement presents scientific reports from industry-sponsored IDWeek 2025 symposia, highlighting selected advances in infectious diseases and HIV care through clinical case scenarios. One article explores therapeutic approaches to metabolic complications in people with HIV, emphasizing treatment strategies and the clinical reasoning that supports individualized management of excess adiposity. The second examines the clinical integration of metagenomic next-generation sequencing for diagnosing central nervous system infections, outlining both its opportunities and limitations within current diagnostic pathways.}, } @article {pmid42139092, year = {2026}, author = {Waldrop, G and Reddy, SP}, title = {Metagenomic Next-generation Sequencing in Central Nervous System Infections: Clinical Strategies, Evidence, and Best Practices.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {82}, number = {Supplement_4}, pages = {S92-S99}, doi = {10.1093/cid/ciag120}, pmid = {42139092}, issn = {1537-6591}, support = {//Delve Bio/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology ; Immunocompromised Host ; Female ; Middle Aged ; }, abstract = {BACKGROUND: Central nervous system (CNS) infections are diagnostically challenging due to their nonspecific clinical presentations and wide array of potential pathogens. The rising population of immunocompromised patients further complicates this landscape, increasing the prevalence of atypical and opportunistic infections that are often missed by conventional testing.

OBJECTIVE: This article provides guidance on the use and clinical interpretation of cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) in suspected CNS infections.

DISCUSSION: We highlight the paradigm shift from targeted molecular testing to agnostic mNGS, emphasizing key factors that impact diagnostic utility, including specimen handling, neuroanatomical factors, host inflammatory response, and pathogen kinetics. Using illustrative cases, we demonstrate how these biological and technical variables influence test sensitivity and result adjudication. We further discuss the impact of mNGS on clinical decision-making and current limitations regarding cost and turnaround time.

CONCLUSIONS: Cerebrospinal fluid mNGS is a transformative diagnostic tool, particularly for unusual presentations and in immunocompromised hosts. However, it does not replace clinical judgment and requires careful multidisciplinary interpretation. When integrated thoughtfully with clinical and laboratory data, mNGS can meaningfully reduce the diagnostic gap in CNS infections.}, } @article {pmid42139793, year = {2026}, author = {Jibril, AH and Alencar, ALF and Olsen, JE and Hounmanou, YMG}, title = {Effect of age, severity of diarrhoea, number of pathogens present and blooming of E. coli on metagenomic characteristics of stools from Danish dairy calves with diarrhoea.}, journal = {Veterinary microbiology}, volume = {319}, number = {}, pages = {111070}, doi = {10.1016/j.vetmic.2026.111070}, pmid = {42139793}, issn = {1873-2542}, mesh = {Animals ; *Diarrhea/veterinary/microbiology/epidemiology ; *Feces/microbiology ; Cattle ; *Cattle Diseases/microbiology/parasitology/epidemiology ; *Escherichia coli/genetics/isolation & purification ; Denmark/epidemiology ; Metagenome ; Age Factors ; Metagenomics ; *Escherichia coli Infections/veterinary/microbiology ; Severity of Illness Index ; }, abstract = {BACKGROUND: Calf diarrhoea causes substantial welfare and economic losses, and it is one of the major drivers of antimicrobial use. This study aimed to characterize the faecal microbiome of diarrhoeic calves, with a specific focus on Escherichia coli, and to assess whether microbial profiles vary with age, diarrhoea severity, and high E. coli abundance in the absence of other detectable enteric pathogens.

METHODS: Stool samples from Danish diary calves (n = 32) below 4 weeks of age were collected from 11 herds and were analysed using direct long-read sequencing (mgt) as well as analyses of a subset of samples by swiping microbiota from faecal samples grown on McConkey agar plates (plate-swipe). Metagenomes were analysed to characterise community structure (Shannon α-diversity; Bray-Curtis PCoA with PERMANOVA) and to assess differential abundance at the species level while adjusting for sample type (mgt/plate swipe), herd, age, number of other pathogens detected by qPCR (rotavirus, coronavirus, Cryptosporidium parvum, Salmonella Dublin, Clostridium perfringens A, B, C, Eimeria and Escherichia coli F5) and recorded as presence/absence and summarised into infection classes (None/Mono/Co-2/Co-3 +). Binning was performed to build metagenome assembled genomes (MAGs) of E. coli.

RESULTS: Microbiome structure was dominated by methodological and contextual factors: sample type (direct metagenomic vs plate swipe) and herd explained far more variation than clinical severity and age. Metagenomic species profiles from plate swabs were comparatively homogeneous and E. coli-rich, whereas direct metagenomes captured higher diversity. Differential abundance identified species enriched with increasing diarrhoea severity and with infection classes, while pathogen-specific contrasts (e.g., C. perfringens A-positive vs negative) revealed discrete sets of bacterial co-occurrences. Classical pathotype markers (virulence-genes) were uncommon among E. coli MAGs.

CONCLUSIONS: Long-read metagenomics revealed insignificant influence of severity of diarrhoea, age below 4 weeks and number of pathogens detected in stool samples on diversity and microbial communities in diarrheic dairy calves. In contrast, large variation was observed between herds. On average, E. coli constituted about half of the microbiota. MAGs generated by binning indicated non-specific blooming of strains without particular virulence genes.}, } @article {pmid42139982, year = {2026}, author = {Yuan, M and Dong, S and Luo, J and Li, Y and Li, YA and Wen, W and Zhao, R}, title = {Habitat-driven taxonomic and functional differentiation of microbial communities across water and sediments in a large eutrophic shallow lake deciphered by metagenomics.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128553}, doi = {10.1016/j.micres.2026.128553}, pmid = {42139982}, issn = {1618-0623}, mesh = {*Lakes/microbiology ; *Metagenomics/methods ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; Ecosystem ; Metagenome ; Phylogeny ; *Water Microbiology ; Carbon/metabolism ; Nitrogen/metabolism ; Eutrophication ; China ; Biodiversity ; }, abstract = {Shallow lakes in arid and semi-arid regions are vulnerable to hydrological fluctuations and nutrient loading. However, the composition and functional traits of microbial communities and their roles in mediating internal nutrient cycling across the water column and sediments remain poorly understood. Here, we applied an integrated metagenomic framework to investigate microbial community structure and metabolic potential in Wuliangsuhai Lake, a typical eutrophic shallow lake in the Yellow River Basin. Read-based taxonomic profiling revealed pronounced habitat-driven community differentiation, with significantly higher microbial diversity and evenness in sediments than in water. Both habitats were dominated by Pseudomonadota, while water was enriched in Cyanobacteriota, Actinomycetota, and Bacteroidota, and sediments in Actinomycetota, Thermodesulfobacteriota, and Bacillota. Contig-based functional profiling based on a non-redundant catalog of 9.45 million genes showed clear habitat-specific divergence. Sediments were significantly enriched in pathways associated with complex carbon degradation, reductive nitrogen transformations, and sulfur redox metabolism. Genome-resolved analysis recovered 974 non-redundant metagenome-assembled genomes spanning 54 phyla, including one putative novel lineage. Metabolic reconstruction indicated community-wide dominance of heterotrophic carbon oxidation and fermentation, while methanogenic potential was largely confined to sediments. Nitrogen cycling was biased toward reductive processes, and sulfur cycling showed strong representation of both sulfite oxidation and sulfate/sulfite reduction. Metabolic weight scores further revealed a clear functional division of labor among major microbial lineages, with Pseudomonadota contributing broadly across multiple biogeochemical processes. These results indicate pronounced sediment-water functional differentiation in eutrophic shallow lakes, with sediments primarily supporting metabolic processes related to internal nutrient turnover.}, } @article {pmid42140024, year = {2026}, author = {Mu, Y and Zhang, H and Pan, Y and Tian, Z and Huang, Y and Yang, L and Zhang, C and Zhao, C and Li, D and Liu, X and Jiang, L}, title = {Deciphering the mechanisms underlying regional heterogeneity of high-temperature Daqu through integrated electronic sensory, volatilome, and microbiome analysis.}, journal = {International journal of food microbiology}, volume = {457}, number = {}, pages = {111847}, doi = {10.1016/j.ijfoodmicro.2026.111847}, pmid = {42140024}, issn = {1879-3460}, mesh = {*Microbiota ; Bacteria/classification/genetics/isolation & purification/metabolism ; Fungi/classification/isolation & purification/genetics/metabolism ; Hot Temperature ; China ; *Volatile Organic Compounds/analysis ; Taste ; Humans ; *Alcoholic Beverages/microbiology/analysis ; Food Microbiology ; *Wine/microbiology/analysis ; }, abstract = {High-temperature Daqu (HTD) is crucial for shaping the style of Moutai-flavor Baijiu, but its quality characteristics exhibit geographical and spatial heterogeneity, resulting in diminished typicity of products from non-core production regions. Therefore, this study employed multiphase detection techniques to analyze HTD samples from the typical region (Guizhou) and emerging region (Shandong), along with their surface and inner layers. Guizhou HTD possessed superior biochemical activity (especially on the surface) and higher response values for W1W, W2W, umami, and salty sensors. It also showed higher concentrations of key flavor compounds, such as pyrazines, acids, and alcohols. Targeted amplicon sequencing showed Kroppenstedtia, Thermoascus, and Thermomyces dominated all samples, but Guizhou HTD had greater microbial diversity and richness. Metagenomics indicated a higher proportion of bacteria in Guizhou HTD, represented by Kroppenstedtia eburnea and Oceanobacillus indicireducens, whereas fungi were more prevalent in Shandong HTD, with Paecilomyces varioti, Aspergillus chevalieri, and Rasamsonia emersonii as the dominant species. Functional annotation demonstrated that carbohydrate metabolism and amino acid metabolism were core biological functions of HTD, with gene abundances showing Guizhou > Shandong and inner > surface. Furthermore, species-enzyme contribution and metagenome-assembled genomes analyses confirmed that HTD exhibited functional redundancy at the ecological scale, yet the species responsible for these functions displayed regional specificity, explaining the phenotypic heterogeneity between Guizhou HTD and Shandong HTD. These findings highlight the pivotal role of the production region in HTD quality and offer insights for improving Moutai-flavor Baijiu flavor in non-core regions.}, } @article {pmid42140051, year = {2026}, author = {Missaoui, Y and Venditti, M and Zhang, L and Vaccaric, F and Abelouah, MR and Abouda, S and Gaaieda, S and Puglisi, E and Lucini, L and Minnucci, S and Banni, M}, title = {Microplastic-induced gut dysbiosis and metabolic alterations in juvenile European seabass (Dicentrarchus labrax): A multi-omics approach.}, journal = {Marine pollution bulletin}, volume = {230}, number = {}, pages = {119879}, doi = {10.1016/j.marpolbul.2026.119879}, pmid = {42140051}, issn = {1879-3363}, abstract = {Environmental microplastics (MPs) are increasingly recognized as emerging contaminants with the potential to disrupt intestinal homeostasis in marine organisms. However, most experimental evidence is based on pristine particles rather than environmentally weathered forms. This study investigated the intestinal effects of environmentally derived microplastics (EMPs) in juvenile European seabass (Dicentrarchus labrax) using an integrated multi-omics approach. Fish were exposed for five days to two concentrations of EMPs (0.5 and 1 mg/kg of feed), followed by analyses combining histological, transcriptomic, metabolomic, and metagenomic endpoints. EMP exposure led to significant particle accumulation in gut tissues, predominantly consisting of small polyethylene fragments. Gene expression and immunofluorescence analyses revealed activation of p53 and Caspase-3 mediated apoptosis together with NF-κB and IL-6 driven inflammatory signalling, indicating concurrent oxidative and immune stress. Untargeted metabolomics identified marked alterations in lipid metabolism, redox regulation, and amino acid turnover, consistent with mitochondrial dysfunction and impaired energy homeostasis. Parallel metagenomic profiling revealed subtle but coherent shifts in gut bacterial communities, with enrichment of pollutant-tolerant taxa such as Acidovorax and Halioglobus and reduction of beneficial commensals such as Ligilactobacillus. Multi-omics data integration demonstrated a coordinated restructuring of microbial and metabolic networks underlying host physiological stress. Collectively, these findings highlight the intestine as a primary target of microplastic toxicity and provide mechanistic insight into early biological responses to environmentally realistic microplastic exposure in marine fish.}, } @article {pmid42140215, year = {2026}, author = {Hughes, N and Sathiananthamoorthy, S and Sergaki, C}, title = {Antimicrobial resistance surveillance through wastewater: methodological considerations for metagenomic approaches and public health perspectives.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101400}, doi = {10.1016/j.lanmic.2026.101400}, pmid = {42140215}, issn = {2666-5247}, abstract = {Antimicrobial resistance (AMR) is a recognised global threat with substantial predicted impact on lives, agriculture, and the economy. Metagenomic sequencing is being increasingly used for AMR surveillance and detection, given its capacity for community-level AMR profiling with high-level resolution. This technology has seen an explosion of surveillance efforts and data generation; however, the variation between workflows has direct implications on the sequencing results and their interpretation. In this Personal View, we summarise aspects of the sequencing workflow that need to be considered during metagenomic study design, for meaningful and reliable population-based surveillance. We reflect on the vital role of standardisation for capturing the ground truth of AMR and data comparability and reproducibility, and in addition, review the limitations of the various phenotypic and genotypic methods of AMR detection. We further highlight complex mechanisms of resistance to antimicrobials that could hinder our ability to confidently assess the true AMR burden in the environment and those that are often overlooked during surveillance.}, } @article {pmid42140378, year = {2026}, author = {Tan, MW and Clister, D and Chandra, QM and Wangsa, CE and Simone, CN and Umaya, C and Choi, J and Park, S and Rani, A and Akter, S and Kim, B and Kim, SH and de Azambuja Ribeiro, RIM and Syahputra, RA}, title = {Circulating microbial metabolites and the gut-prostate axis in prostate cancer: Implications for laboratory biomarkers and therapeutic response.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {590}, number = {}, pages = {121086}, doi = {10.1016/j.cca.2026.121086}, pmid = {42140378}, issn = {1873-3492}, abstract = {Prostate cancer progression and treatment response are influenced not only by tumor genomics and androgen receptor signaling but also by systemic host-microbiome interactions along the gut-prostate axis. Increasing evidence indicates that gut microbial metabolism produces bioactive compounds that circulate in human body fluids and can influence immune regulation, hormone metabolism, and therapeutic outcomes. This review synthesizes current evidence on microbiome-derived metabolites that may serve as measurable biomarkers relevant to prostate cancer biology and clinical laboratory diagnostics. Microbial metabolism of dietary substrates generates circulating molecules-including short-chain fatty acids, secondary bile acids, indole derivatives, polyamines, and endotoxin-associated signals-that can modulate inflammation, epithelial barrier integrity, and systemic immune responses involved in tumor progression. In addition, intestinal microbes participate in steroid transformation and enterohepatic cycling of hormones, potentially influencing circulating androgen and estrogen levels that contribute to androgen-driven prostate cancer development and adaptation under androgen deprivation therapy. Importantly, many of these microbial metabolites are detectable in serum or plasma using validated analytical platforms such as liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry, supporting their potential integration into laboratory biomarker panels. Emerging multi-omics approaches combining metagenomics, metabolomics, host transcriptomics, and immune profiling are beginning to clarify mechanistic links between microbial activity and therapy response, including variability in outcomes with androgen-targeted agents, chemotherapy, radiotherapy, and immune checkpoint inhibitors. From a clinical chemistry perspective, characterization of circulating microbiome-derived metabolites may enhance the diagnostic and prognostic performance of established biomarkers such as prostate-specific antigen while providing new opportunities for non-invasive monitoring of disease progression and treatment response. Establishing reproducible microbial metabolic signatures across diverse patient populations will be essential to translate microbiome-informed biomarkers into next-generation diagnostic and prognostic tools in prostate cancer management.}, } @article {pmid42140478, year = {2026}, author = {Sheidae Mehne, Z and Honarjou, E and Khamoushi Kahdouee, M}, title = {Chronic infections of the spine: A systematic review of microbial etiologies, diagnostic approaches, and treatment outcomes.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {169}, number = {}, pages = {108769}, doi = {10.1016/j.ijid.2026.108769}, pmid = {42140478}, issn = {1878-3511}, mesh = {Humans ; Treatment Outcome ; Chronic Disease ; *Spinal Diseases/microbiology/diagnosis/therapy ; Mycobacterium tuberculosis/isolation & purification ; Spine/microbiology ; Tuberculosis, Spinal/diagnosis/microbiology/therapy ; }, abstract = {OBJECTIVES: Chronic spinal infections are uncommon but potentially devastating conditions, frequently associated with delayed diagnosis, heterogeneous microbiology, and complex management. Existing evidence remains fragmented, and a comprehensive synthesis of microbial etiologies, diagnostic approaches, and treatment outcomes is needed.

METHODS: A systematic review was conducted in accordance with PRISMA guidelines. PubMed, Scopus, Web of Science, and Embase were searched for studies published between October 2015 and September 2025 involving adult patients with chronic spinal infections. Data were extracted on causative pathogens, diagnostic modalities, medical and surgical interventions, and clinical outcomes. Risk of bias was assessed using standardized methodological criteria.

RESULTS: Fifty-five studies comprising 3036 patients were included. Mycobacterium tuberculosis was the most frequently identified pathogen, followed by Brucella species and pyogenic bacteria. Metagenomic next-generation sequencing (mNGS) demonstrated the highest diagnostic yield, with reported sensitivities ranging from 82% to 92%, and showed particular utility in detecting mixed or atypical infections. Biomarker-based and RNA-derived assays demonstrated promising performance in differentiating tuberculous spondylitis from other spinal conditions. Surgical interventions, including minimally invasive and combined approaches, were associated with high fusion and neurological recovery rates.

CONCLUSION: Chronic spinal infections show marked microbiological heterogeneity. Integrating molecular diagnostics with tailored surgical and antimicrobial strategies may improve diagnostic accuracy and clinical outcomes.}, } @article {pmid42140665, year = {2026}, author = {Vollmers, J and Correa Cassal, M and Kaster, AK}, title = {Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.280099.124}, pmid = {42140665}, issn = {1549-5469}, abstract = {Because the majority of microbial organisms still evade cultivation attempts, genomic insights into many taxa are limited to cultivation-independent approaches. However, current methods of metagenomics and single-cell genome sequencing have individual drawbacks, which can limit the quality and completeness of the reconstructed genomes. Current attempts to combine both approaches still use whole-genome amplification techniques, which are prone to bias. Here, we propose a novel approach for the purpose of genome reconstructions that utilizes the potential of cell sorting for targeted enrichment and depletion of different cell types to create distinct cell fractions with sufficient DNA amounts, circumventing amplification. By distributing sequencing efforts over these fractions as well as the original sample, coassemblies become highly optimized for coabundance variation-based binning approaches. "Midi-metagenomics" enables accurate metagenome-assembled genome (MAG) reconstruction from individual sorted samples with higher quality than coassembly and binning of multiple distinct samples and therefore improves analyses of uncultivated microorganisms.}, } @article {pmid42140743, year = {2026}, author = {Lee, JB and Baek, S and Kim, DK and Kwon, BE and Ahn, JS and Nagasaka, M and Davar, D and Park, H and Kim, H and Im, J and Yang, J and Yang, E and Shin, GH and Choi, S and Kwon, JE and Kim, JM and Kang, SY and Kim, Y and Park, SY and Kim, JH and Oh, HS and Chalita, M and Min, A and Cho, BC}, title = {Phase I trial of CJRB-101 plus pembrolizumab in patients with metastatic non-small cell lung cancer, head and neck squamous cell carcinoma and melanoma.}, journal = {Journal for immunotherapy of cancer}, volume = {14}, number = {5}, pages = {}, pmid = {42140743}, issn = {2051-1426}, mesh = {Humans ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Female ; Male ; Middle Aged ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology ; Aged ; *Squamous Cell Carcinoma of Head and Neck/drug therapy/pathology ; *Melanoma/drug therapy/pathology ; *Lung Neoplasms/drug therapy/pathology ; Mice ; *Head and Neck Neoplasms/drug therapy/pathology ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; Animals ; Adult ; }, abstract = {BACKGROUND: Dysbiosis of gut microbiome leads to resistance to immunotherapy in various advanced solid tumors. CJRB-101 is a live biotherapeutic product consisting of a novel strain belonging to the species Leuconostoc mesenteroides. To modulate the tumor microenvironment, CJRB-101 was combined with pembrolizumab.

METHODS: Preclinical efficacy and mechanistic studies were performed using humanized non-small cell lung cancer (NSCLC) patient-derived xenograft (PDX) models. This is a multicenter, first-in-human, two-part, phase I, open-label study of CJRB-101 (1×10[11] or 4×10[11] colony forming unit (CFU)/day) plus pembrolizumab (200 mg every three weeks (Q3W)) in advanced NSCLC, melanoma, and head and neck squamous cell carcinoma in both immune checkpoint inhibitor (ICI)-naive and ICI-refractory settings. The primary endpoint was to assess the dose-limiting toxicities (DLTs), adverse events, and preliminary activity of the combination treatment. Exploratory endpoints included stool metagenomics analysis and pharmacodynamics parameters.

RESULTS: In four PDX models, CJRB-101 with pembrolizumab demonstrated enhanced antitumor efficacy, showing a tumor growth inhibition (TGI) of 77.3% in the CJRB-101 monotherapy group and 61.9% in the combination group, which was significantly improved compared with pembrolizumab alone. A distinct M2-to-M1 repolarization was observed and validated in vitro. Notably, increased activation of cytotoxic T cells was observed, suggesting an immune-mediated antitumor mechanism of CJRB-101. A total of 42 patients were enrolled in the low-dose cohort (one capsule once a day; n=6) and high-dose cohort (two capsules two times a day, n=36). Metastatic NSCLC accounted for 86% (n=36) and 67% (n=28) of the patients were refractory to ICIs. None of the patients experienced DLT. In ICI-naïve NSCLC (n=12) with programmed death-ligand 1 (PD-L1) >50%, the overall response rate (ORR) and disease control rate (DCR) were 58% and 75%, respectively. The ORR was 5% and DCR was 41% in the ICI-refractory NSCLC (n=22) with an ORR of 5% and DCR of 41%. After a median follow-up of 15.6 months and 8.9 months for ICI-naïve and ICI-refractory NSCLC, the median progression-free survival was 9 months (95% CI 5.6 to not reached) and 1.8 months (95% CI 1.6 to 4.3), respectively. CJRB-101 plus pembrolizumab was well-tolerated, and none of the patients experienced grade >3 treatment-related adverse events.

CONCLUSIONS: Early clinical data show encouraging antitumor response of CJRB-101 plus pembrolizumab in ICI-naïve metastatic NSCLC with PD-L1 >50%.

TRIAL REGISTRATION NUMBER: NCT05877430.}, } @article {pmid42140896, year = {2026}, author = {Blázquez-Sánchez, P and Gunkel, J and Useini, A and Zlobin, A and Zakary, JD and Schöler, A and Graefe, N and Engelberger, F and Cantanhede, F and Frank, R and Zhao, Z and Zarei, A and Butenschön, E and Matysik, J and Zimmermann, W and Sträter, N and Sonnendecker, C and Künze, G}, title = {Computational engineering of the polyester hydrolase PHL7 for efficient poly(ethylene terephthalate) degradation in biocatalytic recycling processes.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42140896}, issn = {2041-1723}, support = {887913//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ScaDS.AI//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, mesh = {*Polyethylene Terephthalates/metabolism/chemistry ; Biocatalysis ; *Protein Engineering/methods ; *Hydrolases/metabolism/genetics/chemistry ; Recycling ; Enzyme Stability ; Biodegradation, Environmental ; Molecular Dynamics Simulation ; Metagenome ; *Bacterial Proteins/metabolism/genetics/chemistry ; }, abstract = {Polyethylene terephthalate (PET) plastic waste causes serious environmental pollution due to insufficient recycling rates. Enzymatic PET depolymerization offers a sustainable recycling strategy, but limited stability and activity of current PET-degrading enzymes restrict practical implementation. Here, we engineer Polyester Hydrolase Leipzig 7 (PHL7), a PET hydrolase from a compost metagenome, to enhance its stability and catalytic performance under recycling-relevant conditions. Using Rosetta PROSS-based computational design combined with rational mutagenesis, we introduce up to 24 mutations, generating variants with melting temperatures of 88-95 °C and over 110-fold higher activity in 0.1 M phosphate buffer compared to the parent enzyme. Benchmarking shows that the best variants (R4M6, R4M9, and R4M10) match or exceed the performance of established engineered PET hydrolases, including ICCG and LCC-A2, and approach that of TurboPETase across multiple conditions. Under high substrate loadings, the PHL7-R4 variants degrade 75-78% of 10% (w/w) PET within 24 h at 65 °C, outperforming ICCG, while an optimized variant R4M10-H185Y achieves up to 84% degradation of 20% (w/w) PET. X-ray structure determination and molecular dynamics simulations reveal key stabilizing and activity enhancing mechanisms. These engineered PHL7 variants represent robust biocatalysts for scalable enzymatic PET recycling.}, } @article {pmid42140961, year = {2026}, author = {Li, CW and Liao, HX and Callaway, RM and Su, ZY and Zou, JK and Liu, A and Wu, YR and Fang, YQ and Peng, SL and Chen, BM}, title = {Divergence among species with "good competitor" and "good cultivator" strategies promotes asymmetric facilitation among co-invaders.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42140961}, issn = {2041-1723}, support = {32471739//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023A1515010669//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; }, mesh = {*Introduced Species ; *Asteraceae/microbiology ; Species Specificity ; Microbiota ; Ecosystem ; Bacteria/genetics ; }, abstract = {Facilitative interactions among co-invaders may lead to invasional meltdown, accelerating non-native species accumulation and exacerbating ecological impacts over time. However, it remains unclear why certain non-native combinations promote facilitation while others do not, and may even constrain invasions. To address this question, we examine six invasive species in the Asteraceae family along two strategic dimensions: competitiveness and capacity to cultivate invader-promoting microbial communities. We then create experimental combinations to mix "good competitors" and "good cultivators" to varying degrees to form a "strategic divergence" gradient. We hypothesize greater strategic divergences generate more intense facilitations, whereas similar strategies generate inhibitions. Strategic divergence correlates with facilitation, but interactions are asymmetric: strong competitive suppressors of natives benefit from co-invasions with weaker competitors that cultivate favorable microbial environments but the performance of the latter are generally suppressed by the strong competitors. Metagenomic sequencing further indicates that good cultivators may promote facilitation by repelling pathogens (Ascomycota) and deterring microbes that might be exclusively beneficial for natives (Proteobacteria, Firmicutes, and Planctomycetota). Our results provide empirical evidence for the importance of strategic divergence among invasive species and offer a mechanistic basis for predicting which combinations of co-invading species might generate facilitation and which might result in inhibition.}, } @article {pmid42141123, year = {2026}, author = {Han, S and Wu, Z and Wu, Y and Wang, Z and Qian, P and Chu, J and Li, J and Zhuang, J and Yang, X}, title = {Decoding the human gut bacterial plasmids in colorectal cancer.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10278-w}, pmid = {42141123}, issn = {2399-3642}, abstract = {Gut plasmids show heightened sensitivity to gut microenvironmental changes compared to their bacterial hosts. To explore their significance in colorectal cancer (CRC), we analyzed metagenomic data from 863 participants (312 CRC, 387 high-risk, 164 low-risk). Plasmid and bacterial profiles were characterized, along with trace elements and metabolites. Differential analysis, functional gene assessment (ARG, MGE, MRG, VFGB), random forest modeling, and structural equation modeling (SEM) were applied. In terms of overall abundance, plasmids in both the high-risk and CRC groups exhibited a decreasing trend. Gut plasmids significantly influenced the functional genes (ARG, MGE, MRG, VFGB) of their bacterial hosts. Six key bacterial hosts (Enterobacterales, Bucrkholderiales, Hyphomicrobiales, Lactobacillales, Bacteroidales, Campylobacterales) and 12 plasmid markers were identified. The plasmid-based model effectively predicted CRC risk. SEM revealed that trace elements (e.g., Ni), metabolites (e.g., 5-Hydroxytryptophol), and host bacteria (e.g., Campylobacterales, Enterobacterales) predominantly exerted negative effects on most plasmids, whereas Ni exhibited a positive influence on plasmids NZ_CP013564.1, NZ_CP024312.1, and NZ_CP48284.1. We characterized the composition of gut plasmids and their bacterial hosts, explored the impacts of gut plasmids on bacterial functionality, and mapped multi-omics interaction networks linking plasmids, hosts, and metabolic features.}, } @article {pmid42141277, year = {2026}, author = {Jiao, S and Pan, H and García-Palacios, P and Tu, H and Zhang, Y and Liu, Y and Gao, H and Chen, B and Peng, Z and Chen, S and Qi, J and Liang, C and Li, X and Wang, Y and Jin, C and Gao, M and Liu, J and Wang, Y and Zhao, J and Jiang, L and Romero, F and Banerjee, S and Yang, Y and Lu, Y and Delgado-Baquerizo, M and van der Heijden, MGA and Wei, G}, title = {Agricultural soil microbiomes are structurally and functionally more resistant to warming than adjacent natural ecosystems.}, journal = {Nature food}, volume = {7}, number = {5}, pages = {428-440}, pmid = {42141277}, issn = {2662-1355}, mesh = {*Soil Microbiology ; *Microbiota ; *Ecosystem ; Agriculture ; Soil/chemistry ; Climate Change ; Global Warming ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Agricultural soil microbiomes experience frequent disturbance from intensive management and may therefore be better equipped to withstand climate warming than microbiomes in undisturbed natural soils. Here we test this by combining a continental-scale warming microcosm experiment across 100 paired agricultural-natural sites with a global meta-analysis and three microbiome manipulation experiments (microbial suspensions, cross-inoculation and synthetic communities). Agricultural soils showed a higher resistance of soil multifunctionality to warming than natural soils, consistent across the meta-analysis. Resistance of microbial community composition was the strongest predictor of functional resistance and was confirmed in artificial soils inoculated with agricultural versus natural microbial suspensions. Introducing soil microbiomes from agricultural ecosystems into previously undisturbed natural soils enhanced functional resistance to warming. Metagenomic analysis revealed that microbial life-history strategies play a crucial role in regulating the resistance of soil microbial community to warming, with communities dominated by stress-tolerant strategies conferring significantly stronger resistance. Our work highlights the potential of microbiome engineering to strengthen ecosystem functioning under climate change.}, } @article {pmid42141292, year = {2026}, author = {Ghori, R and Ramadoss, D and Ramsland, PA and Blanch, EW and Ammanabrolu, BS}, title = {Comparative metagenomic analysis of microbial communities: unravelling microbial communities from the great Rann of Kachchh and coastal saltpans, Gujarat, India.}, journal = {Extremophiles : life under extreme conditions}, volume = {30}, number = {1}, pages = {}, pmid = {42141292}, issn = {1433-4909}, mesh = {*Microbiota ; India ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Salinity ; *Metagenome ; }, abstract = {Hypersaline environments exhibit extreme physiochemical conditions yet support diverse microbial communities. These communities are not only ecologically important but also possess substantial potential for biotechnological exploitation. In this study, we employed a comparative metagenomic approach to assess microbial diversity using two distinct methodologies: (1) direct DNA extraction from raw sediment, and (2) DNA extraction following halophilic enrichment in selective media. Sediment samples were collected from multiple sites and pooled together within the Rann of Kachchh and close-by saltpans and were analysed using 16S rRNA sequencing coupled with bioinformatics pipelines. The results revealed pronounced differences in microbial community composition between the two approaches. Raw sediment samples exhibited significantly higher alpha diversity, with dominant taxa including Halobacterota, Cyanobacteria, and Desulfobacterota, with a substantial proportion of unclassified genera. In contrast, enriched samples were dominated by fast-growing, culturable genera such as Halobacterium, Alkalibacillus, and Candidatus haloredivivus. Principal Coordinate Analysis (PCoA) of beta diversity demonstrated distinct clustering between raw and enriched communities, even within samples from the same sites, underscoring the selective bias introduced by enrichment procedures. These findings emphasise that the methodological choice strongly influences the observed microbial diversity. The aim of this study was to compare microbial community composition in raw hypersaline sediments and enrichment cultures using metagenomic sequencing, to evaluate how enrichment selectively favours specific halophilic taxa. This comparative approach allows identification of the microbial groups that rapidly proliferate under controlled hypersaline conditions, thereby complementing direct environmental sequencing. By integrating both direct and enrichment-based metagenomic approaches, a more comprehensive understanding of microbial community structure in hypersaline environments can be achieved.}, } @article {pmid42141512, year = {2026}, author = {Li, Y and Sun, J and Dai, Z and Jin, LN and Chen, Z and Lin, D and Zhu, L}, title = {Antibiotic Metabolites Are an Overlooked Driver of Resistance Dissemination in Plant Systems.}, journal = {Environmental science & technology}, volume = {60}, number = {23}, pages = {16540-16551}, doi = {10.1021/acs.est.6c04146}, pmid = {42141512}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents ; Drug Resistance, Microbial ; Lactuca ; Tetracycline ; }, abstract = {Antibiotic pollution in agroecosystems is widely recognized, yet the risks posed by their metabolites remain insufficiently addressed. Using lettuce as a model, we investigated how tetracycline (TC) and its metabolites, anhydrotetracycline (ATC) and epitetracycline (ETC), contribute to the dissemination of antibiotic resistance genes (ARGs). TC primarily accumulated in roots and declined during translocation, whereas ATC exhibited greater persistence and became the predominant residue through in planta transformation. At environmentally relevant concentrations (≤0.1 mg·L[-1]), ATC more effectively expanded the mobilizable resistome than the parent compound by inducing reactive oxygen species, activating the SOS response, increasing membrane permeability, and promoting RP4 plasmid conjugative transfer. These processes facilitated the acquisition of multidrug resistance and the colonization of plant tissues by human pathogens, including Stenotrophomonas maltophilia and Pseudomonas aeruginosa, thereby increasing ARG burdens in both rhizosphere and phyllosphere compartments. Metagenomic analysis further confirmed the coselection of nontetracycline ARGs, such as aph3'-I and catB, and the enrichment of efflux systems (acr/emr) in pathogenic bacteria. Our findings challenge the parent-compound-centered paradigm of antibiotic risk assessment by identifying ATC as a key high-risk driver of ARG dissemination in food plants and highlighting the need to incorporate transformation products into future management strategies.}, } @article {pmid42141881, year = {2026}, author = {Nagy, A and Erdélyi, K and Molnár, Z and Lőrincz, RB and Nagy, O and Koroknai, A and Csonka, N and Kerényi, K and Forgách, P and Horváth, E and Soltész, Z and Nagy, G and Takács, M and Barcsay, E and Szomor, K and Tóth, GE and Cadar, D}, title = {Hungary as a source of West Nile virus diversity and spread in Europe: insights from the 2024 transmission season.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {31}, number = {16}, pages = {}, pmid = {42141881}, issn = {1560-7917}, mesh = {Humans ; Hungary/epidemiology ; *West Nile virus/genetics/isolation & purification/classification ; *West Nile Fever/epidemiology/transmission/virology ; Animals ; Phylogeny ; Phylogeography ; *Culex/virology ; Seasons ; Birds/virology ; Europe/epidemiology ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; Bayes Theorem ; Incidence ; Male ; Mosquito Vectors/virology ; Middle Aged ; }, abstract = {BACKGROUNDWest Nile virus (WNV) has become established across Europe, with Hungary serving as a key transmission hub since 2004. Following reduced activity during 2020-22, the 2024 season marked a resurgence with the largest geographical distribution ever recorded in Europe.AIMTo analyse the 2024 WNV transmission season in Hungary using a One Health approach and characterise circulating strains within the European phylogeographic context using comprehensive genomic surveillance.METHODSComplete and near-complete genome sequencing was performed on 55 specimens from 38 humans, 15 birds and two Culex pipiens mosquito pools using amplicon-based next-generation sequencing. Phylogeographic analysis incorporated 637 European WNV genome sequences (2004-24) with time-scaled Bayesian phylogenetic reconstruction and continuous spatial diffusion modelling.RESULTSHungary reported 113 human WNV cases in 2024 (n = 111 autochthonous, 2 imported), a 3.7-fold increase from 2023 (incidence: 1.16 vs 0.31 per 100,000 population). Neuroinvasive disease predominated (92%, n = 104) with a 7.9% case fatality rate. All 55 sequenced strains belonged to WNV lineage 2. Phylogeographic analysis revealed Hungary's central role in European WNV dissemination since 2004, with multiple introductions and local diversification across distinct clades. Continuous spatial modelling identified Hungary as a persistent transmission hub with bidirectional viral flow to neighbouring countries, contributing to northward expansion.CONCLUSIONHungary remains a critical WNV transmission hub in Central Europe with established endemicity of multiple lineage 2 clades. The analysis highlights Hungary's role as both a recipient and major source of European WNV diversity, emphasising the need for coordinated surveillance and climate-adapted preparedness strategies.}, } @article {pmid42142571, year = {2026}, author = {Malešević, M and Matijašević, D and Kljajević, N and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K}, title = {Seasonal shifts in the Belgrade airborne resistome and virulome: A metagenomic perspective.}, journal = {Environmental research}, volume = {303}, number = {Pt 2}, pages = {124700}, doi = {10.1016/j.envres.2026.124700}, pmid = {42142571}, issn = {1096-0953}, mesh = {*Seasons ; *Air Microbiology ; Serbia ; *Microbiota ; *Metagenome ; Metagenomics ; *Bacteria/genetics ; Environmental Monitoring ; }, abstract = {The atmosphere is a dynamic reservoir for microorganisms and antimicrobial resistance genes (ARGs), yet the seasonal interplay of microbial communities, resistance and virulence determinants with environmental conditions remains poorly characterized, particularly in polluted urban areas. This study presents year-round (summer 2024-spring 2025) shotgun metagenomic monitoring of airborne microbiomes across the Belgrade metropolitan area, a European air pollution hotspot. While community composition shifted seasonally, with an enrichment of Bacillota in autumn and stress-tolerant genera in winter, opportunistic pathogens including Pseudomonas and Acinetobacter were detected year-round. The airborne resistome and mobilome exhibited pronounced seasonal restructuring, with winter showing the highest diversity of resistance genes and plasmid-associated sequences. Mobility-associated genes, including unique toxins and plasmid maintenance systems, were also most prominent in winter. Pathogen-host interaction profiling revealed a functional shift from respiratory and colonization-associated Gram-positive taxa such as Streptococcus pneumoniae and Staphylococcus aureus in autumn to enteric pathogens like Escherichia coli and Salmonella enterica in winter. Network analysis showed that winter formed the densest co-occurrence network, suggesting enhanced potential for co-selection of resistance and virulence traits. Specific plasmid-associated ARGs displayed seasonal patterns, with blaCTX-M linked to multiple plasmids in summer, while blaTEM and aph genes were more prominent in winter. Our findings illustrate that seasonal variations in the airborne genetic landscape are linked to environmental factors and fluctuating reservoirs of clinically relevant resistance and virulence determinants. This highlights the need for integrated longitudinal aerobiome surveillance to understand its implications for public health within the One Health framework.}, } @article {pmid42142769, year = {2026}, author = {Zhang, Z and Hu, Y and Zu, G and Dang, Q and Sun, X and Wu, Y}, title = {Molecular mechanisms of dissolved organic matter transformation and microbial interactions in composting.}, journal = {Bioresource technology}, volume = {456}, number = {}, pages = {134880}, doi = {10.1016/j.biortech.2026.134880}, pmid = {42142769}, issn = {1873-2976}, mesh = {Animals ; *Bacteria/metabolism ; Carbon ; Chickens ; *Composting/methods ; *Dissolved Organic Matter/metabolism/chemistry ; *Food Loss and Waste ; Manure ; Mass Spectrometry ; *Soil Microbiology ; Thermodynamics ; }, abstract = {Industrial composting of food waste digestate (FW) and chicken manure (CM) involves distinct dissolved organic matter (DOM) transformation pathways and different microbial interaction mechanisms. This study used Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and shotgun metagenomics (for microbial community profiling) to compare interactions between DOM and microbial communities in the two composting processes. Results show that FW is dominated by labile organic matter (OM). This dominance increases the degree of DOM oxidation and the relative abundance of CHO. This labile carbon environment selected for a simplified microbial community dominated by key genera, yet facilitated active potential molecular transformations (PMTs) of DOM. These PMTs were characterized by an increase in thermodynamically limited processes (TLPs), indicating a carbon source-oriented pathway. In contrast, PMTs of DOM in CM favor thermodynamically favorable processes (TFPs), exhibiting higher aromaticity and CHOS abundance. The microbial community remains highly diverse, strongly connected, and functionally complementary, forming a synergistic network that supports coupled nitrogen-sulfur transformations. Environmental factors differentially regulate the two systems. This study indicates that the initial chemical properties of the composting feedstock fundamentally shape the PMTs of DOM pathways and the microbial communities they drive, providing an important theoretical basis for optimizing organic solid waste resource recovery processes.}, } @article {pmid42142806, year = {2026}, author = {Samuelsen, Ø and López-Causapé, C and Aarestrup, FM and Bortolaia, V and Brouwer, MSM and Cantón, R and Egli, A and Grad, YH and Hamprecht, A and Haussler, S and Holt, KE and Hopkins, KL and Howden, BP and Jeannot, K and Kahlmeter, G and Köser, CU and Mathers, AJ and Naas, T and Pournaras, S and Ruppé, E and Schön, T and Stoesser, N and Turnidge, J and Werner, G and Wright, GD and Giske, CG and Oliver, A}, title = {The role of whole genome sequencing in antimicrobial susceptibility prediction of bacteria: 2025 update from the European Committee on Antimicrobial Susceptibility Testing Subcommittee.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2026.05.012}, pmid = {42142806}, issn = {1469-0691}, abstract = {SCOPE: The 2017 European Committee on Antimicrobial Susceptibility Testing (EUCAST) subcommittee report on the role of whole genome sequencing (WGS) in antimicrobial susceptibility testing (AST) concluded that WGS antimicrobial susceptibility prediction (WGS-ASP) was not a sufficiently robust alternative to AST to guide clinical decision making at that stage and that more evidence was required [1]. Since then, the use of WGS, bioinformatic tools, machine learning (ML)/artificial intelligence (AI), databases, and prediction approaches has greatly expanded, along with an increased knowledge of resistance mechanisms and their contribution to antimicrobial susceptibility. In response, a new EUCAST ad hoc subcommittee was established in 2024 to review the literature, with the aim of assessing the current potential and limitations of WGS-ASP.

METHODS: As in the previous report, the subcommittee reviewed the literature on a 'by organism' basis but expanded the list to also include enterococci, Haemophilus influenzae, and Bacteroides fragilis in addition to those already included in the first version: Enterobacterales, Pseudomonas aeruginosa, Acinetobacter baumannii, Neisseria gonorrhoeae, Staphylococcus aureus, Streptococcus pneumoniae, Clostridioides difficile, and Mycobacterium tuberculosis. Additional sections were included to cover advances in metagenomics, other omics technologies and ML/AI. The full report was compiled and reviewed by all subcommittee members before public consultation in November 2025.

Significant progress has been achieved in WGS-ASP, with growing evidence supporting its ability to distinguish wild-type from non-wild-type isolates and, consequently, susceptible from resistant strains, particularly for M. tuberculosis and when clinical breakpoints align with the epidemiological cut-off (ECOFF). Despite these advances, important challenges remain before WGS-ASP can be adopted as a clinical decision-making tool. Addressing these gaps will require integrated phenotypic and genotypic surveillance to strengthen the evidence base for complex resistance mechanisms and newer antimicrobial agents, alongside comparative assessments that consider both ECOFF and clinical breakpoints. The analyses will require reference method phenotypic AST and high-quality genomic data. It is critical to ensure that datasets reflect the target populations and encompass the full spectrum of antimicrobial susceptibility, while developing unified interpretation frameworks and harmonized bioinformatics tools to standardize outputs. Robust external quality assessment schemes will be essential for clinical validation, and emerging technologies such as AI and ML offer promising avenues to enhance predictive accuracy. Finally, improvements in cost and turnaround time, coupled with evaluations of setting-specific cost-effectiveness, will be key to enabling practical implementation of WGS-ASP.}, } @article {pmid42143007, year = {2026}, author = {Zhang, XD and Shen, XN and Liu, CX and Liu, ZH and Ao, X and Che, TY and Ran, TJ and Li, HL and Zhang, Y and Zhou, CH and Zou, DW}, title = {Analysis of gut microbiome dynamics in patients with type 1 autoimmune pancreatitis before and after glucocorticoid treatment.}, journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pan.2026.05.002}, pmid = {42143007}, issn = {1424-3911}, abstract = {BACKGROUND: Type 1 autoimmune pancreatitis (AIP) is a rare inflammatory pancreatic disease. Emerging evidence suggests that gut microbiota dysbiosis may contribute to the pathogenesis of type 1 AIP. However, no study has systematically characterized gut microbiota alterations before and after glucocorticoid treatment in patients with type 1 AIP.

METHODS: Fecal samples were collected from 45 healthy controls (HC), 61 patients with type 1 AIP before glucocorticoid treatment, and 27 patients after glucocorticoid treatment for metagenomic sequencing. To investigate the potential role of Streptococcus anginosus in the development of type 1 AIP, heat-killed Streptococcus anginosus was administered by oral gavage in an AIP mouse model.

RESULTS: Significant differences in both α-diversity and β-diversity were observed among HC and the pre- and post-treatment groups. Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus, Streptococcus anginosus, and Streptococcus salivarius, along with decreased abundances of Blautia and Dorea formicigenerans. Moreover, the abundances of Streptococcus and Streptococcus anginosus were reduced in the post-treatment group. In the AIP mouse model, oral gavage with heat-killed Streptococcus anginosus significantly increased the pancreatic pathological injury score.

CONCLUSIONS: Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus and Streptococcus anginosus, which were reduced in the post-treatment group. In addition, heat-killed Streptococcus anginosus exacerbated pancreatic injury in the AIP mouse model.}, } @article {pmid42143215, year = {2026}, author = {Martínez, S and Cerdeiras, MP and Douterelo, I and Ijaz, UZ}, title = {Biofilm and sediment phases as key components of microbial community dynamics within secondary drinking water distribution systems.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05149-7}, pmid = {42143215}, issn = {1471-2180}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, abstract = {BACKGROUND: Secondary drinking water distribution systems (SDWDS), particularly rooftop storage tanks, are critical components of water supply infrastructure in many regions, yet the ecological processes governing microbial community development within these systems remain poorly characterized. Here we present a year-long, phase-resolved metagenomic study of an operational full-scale SDWDS in Uruguay to assess how environmental conditions and surface materials are associated with microbiome dynamics across bulk water, biofilm and sediment phases. We integrated amplicon sequencing, whole-genome sequencing (WGS) metagenomics, culture-based microbiology and physicochemical analyses over a one-year period.

RESULTS: Microbial communities associated with biofilm and sediment phases consistently exhibited higher richness and diversity than bulk water, with marked seasonal variation. Biofilms formed on concrete and polyethylene surfaces followed distinct successional trajectories, indicating material-associated patterns in community development. Seasonal increases in temperature were associated with greater similarity in community composition across phases, while functional richness remained comparatively stable over time. Functional pathways related to energy production, stress response, and antibiotic resistance showed phase- and time-dependent enrichment, particularly in mature biofilms. Across the system, Proteobacteria, Actinobacteriota, and Bacteroidota were persistent taxa. Temperature and pH were the primary variables associated with temporal shifts in water-phase microbial communities, with chlorine residuals contributing to additional variation.

CONCLUSIONS: Together, these findings provide in situ ecological insight into microbial succession and phase-specific community dynamics in drinking water storage systems, highlighting the importance of long-term observations in real-world engineered environments.}, } @article {pmid42143222, year = {2026}, author = {Yao, Y and Li, Z and Luo, L and Lu, X and Wang, H}, title = {Central nervous system infection associated with Human herpesvirus 7 presenting with predominant persecutory delusions as initial psychiatric manifestations after allogeneic stem cell transplantation: a rare case report with diagnostic and therapeutic implications.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13040-z}, pmid = {42143222}, issn = {1471-2334}, support = {82300248//National Natural Science Foundation of China/ ; 82100143//National Key Research and Development Program of China grant 2022YFC2304600/ ; }, abstract = {BACKGROUND: Human Herpesvirus 7 (HHV-7)-associated central nervous system (CNS) infection is an extremely rare complication following allogeneic hematopoietic stem cell transplantation (allo-HSCT), with no prior reports of initial presentation dominated by psychiatric symptoms.

CASE PRESENTATION: We report a unique case of a 14-year-old female with high-risk acute lymphoblastic leukemia (ALL) who developed acute persecutory delusions and auditory hallucinations as the sole initial manifestations 54 days post-allo-HSCT. Brain magnetic resonance imaging (MRI) revealed multifocal lesions in the right frontal lobe and bilateral parieto-occipital regions. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) confirmed the presence of HHV-7, establishing the diagnosis of HHV-7-associated CNS infection. The patient achieved complete clinical and radiological remission following a comprehensive treatment regimen combining antiviral therapy, glucocorticoids, intravenous immunoglobulin (IVIG), and antipsychotic medication.

CONCLUSIONS: This is the first documented case of HHV-7-associated CNS infection post-allo-HSCT presenting with persecutory delusions as the initial symptom, expanding the clinical spectrum of HHV-7-related CNS complications in immunocompromised hosts. Our findings emphasize the importance of considering atypical viral encephalitis in the differential diagnosis of acute psychiatric symptoms post-allo-HSCT and highlight the value of early neuroimaging and CSF mNGS for timely diagnosis and targeted intervention.}, } @article {pmid42143235, year = {2026}, author = {Zhong, M and Zhang, H and Yan, H and Li, Y and Zhu, D and Hu, S and Tan, L and Peng, L and Xie, X and Lan, G}, title = {Clinical characteristics, diagnosis and prognosis of Talaromyces marneffei pneumonia in kidney transplant recipients: a retrospective study.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13557-3}, pmid = {42143235}, issn = {1471-2334}, support = {2025JJ70074//Natural Science Foundation of Hunan Province/ ; 2024JJ2088//Natural Science Foundation of Hunan Province/ ; 2023JJ30755//Natural Science Foundation of Hunan Province/ ; 82370760//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Talaromyces marneffei (TM) is an opportunistic dimorphic fungus that increasingly affects immunocompromised individuals, including kidney transplant recipients. However, data on the clinical features, diagnosis, treatment, and prognosis of Talaromyces marneffei pneumonia (TMP) in this population remain limited.

METHODS: This retrospective study included 8 HIV-negative kidney transplant recipients diagnosed with TMP at the Second Xiangya Hospital of Central South University between January 2015 and January 2025. Clinical data, including demographic characteristics, clinical manifestations, imaging findings, microbiological results, treatment regimens and outcomes, were collected and analyzed.

RESULTS: The cohort consisted of 7 males and 1 female with a mean age of 45.12 ± 9.03 years. The median time from transplantation to TMP onset was 356.5 days (IQR, 302.75-771.75). All patients presented with fever, and chest CT showed diverse pulmonary lesions, including nodules and patchy opacities. Metagenomic next-generation sequencing (mNGS) was the primary diagnostic tool, identifying TM in 7 cases (87.5%), with a mean diagnostic time of 5 ± 2.56 days, while conventional culture was positive in only 3 cases. All patients received antifungal therapy, mainly amphotericin B for induction followed by oral azoles for maintenance. Immunosuppressive regimens were adjusted during treatment. All patients achieved clinical cure without severe adverse events, and graft function remained stable.

CONCLUSIONS: TMP is a rare but serious infection in kidney transplant recipients receiving long-term immunosuppression. Early diagnosis using mNGS combined with conventional culture can improve detection efficiency. Timely antifungal therapy with amphotericin B followed by azole maintenance, along with careful adjustment of immunosuppressants, is associated with favorable prognosis.}, } @article {pmid42143297, year = {2026}, author = {Feng, J and Wang, Y and Han, J and Li, J and Xu, W and Hu, X}, title = {Gestational psittacosis: a systematic review of clinical manifestations and outcomes.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13575-1}, pmid = {42143297}, issn = {1471-2334}, support = {2025359//Scientific Research Project of Chengdu Municipal Health Commission/ ; 2025GZX002//Primary Health Care Research Project of Ganzi County People's Hospital/ ; 2024-YF09-00021-SN//Key Research and Development Support Program of Chengdu Science and Technology Bureau/ ; SCKFKY20250217//2025 Scientific Research Project of Sichuan Rehabilitation Medical Association/ ; }, abstract = {BACKGROUND: Gestational psittacosis is a rare but severe zoonotic infection caused by Chlamydia psittaci. This systematic review aims to evaluate the clinical characteristics, diagnostic challenges, therapeutic interventions, and maternal-fetal outcomes of this condition.

METHODS: A systematic search was conducted in PubMed, Embase, Web of Science, CNKI, and Wanfang Data from inception to October 31, 2025. Two investigators independently performed study selection and data extraction encompassing maternal demographics, clinical manifestations, laboratory findings, diagnostic modalities, antimicrobial regimens, and maternal-fetal outcomes.

RESULTS: A total of 32 cases from 30 publications were included. The median maternal age was 29 years (IQR: 26-32), and the median gestational age at diagnosis was 26.5 weeks (IQR: 21-30). All patients presented with fever (32/32, 100%), and common symptoms included headache (17/32, 53%), cough (15/32, 47%), and dyspnea (15/32, 47%). Severe disease was frequent: 66% (21/32) required intensive care unit (ICU) admission, 34% (11/32) required endotracheal intubation, and maternal mortality was 13% (4/32). Thrombocytopenia (26/32, 81%), hepatic dysfunction (27/32, 84%), renal impairment (18/32, 56%), and disseminated intravascular coagulation (DIC) (15/32, 47%) were the most prominent laboratory abnormalities. Diagnostic approaches evolved from serology to molecular methods. Recent studies have demonstrated the potential value of metagenomic next-generation sequencing (mNGS) in diagnosis, but further research is needed to confirm its clinical utility. The overall fetal and neonatal mortality was 68% (21/31 with available data), primarily due to stillbirth, spontaneous abortion, or therapeutic induction. These estimates reflect outcomes among reported cases and may overestimate true population-level risk.

CONCLUSION: Gestational psittacosis is a rare but life-threatening infection associated with substantial maternal morbidity and a high risk of fetal loss, although these outcomes may be influenced by publication bias. mNGS has facilitated earlier diagnosis in recent case reports; however, comparative performance data for gestational psittacosis remain limited.

TRIAL REGISTRATION: PROSPERO, CRD420251275911 (Registered 30 December 2025).

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid42143373, year = {2026}, author = {Huntington, CA and Bonavita, CM and Wells, HL and Tiemann, JD and Navarrete-Macias, I and Johnson, RF and Hensley, LE and Anthony, SJ}, title = {Optimization of environmental air sampling for viral metagenomics in a cave-roosting bat assemblage.}, journal = {One health outlook}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42522-026-00218-3}, pmid = {42143373}, issn = {2524-4655}, support = {#2412522//NSF/ ; }, abstract = {BACKGROUND: Environmental air sampling holds significant potential as a tool for viral surveillance. Its use in agricultural and indoor settings has demonstrated its feasibility and effectiveness but despite this, it has rarely been used in wildlife settings.

METHODS: To enable future applications, we optimized key parameters in air sampling methodology using a cave-roosting bat assemblage as a model system. We systematically investigated the impact of sampling conditions (flow rate, sampling duration, and sampling location/deployment time) and post-sampling treatments (DNA/RNA Shield ratios and secondary filtration) on three viral metrics - total mammalian virus abundance, mammalian RNA virus abundance, and Shannon diversity index - generated from next-generation sequencing data.

RESULTS: We first showed that air sampling can recover broad viral diversity, including alphacoronaviruses and betacoronaviruses. The sampling conditions for maximizing viral metrics were larger air sample volumes (≥24,000 liters) and sampling inside the cave while the bats were roosting, as opposed to at the cave entrance during emergence. Post-sampling treatments had limited impact on viral metrics, but their application may vary depending on the objectives of the study.

CONCLUSION: This work provides a proof-of-concept for applying air sampling for wildlife viral surveillance in a cave-roosting bat assemblage and identifies key sampling parameters.}, } @article {pmid42143423, year = {2026}, author = {Faghihinezhad, M and Eshghdoostkhatami, Z and Cupples, AM}, title = {Characterization of multiple trichloroethene, cis-dichloroethene and 1,1-dichloroethene degrading propanotrophic communities.}, journal = {Journal of environmental management}, volume = {408}, number = {}, pages = {129957}, doi = {10.1016/j.jenvman.2026.129957}, pmid = {42143423}, issn = {1095-8630}, mesh = {*Trichloroethylene/metabolism ; Biodegradation, Environmental ; *Dichloroethylenes/metabolism ; Rhodococcus/metabolism ; Propane/metabolism ; }, abstract = {Aerobic cometabolism offers a viable strategy for the remediation of chlorinated solvent plumes at oxic sites where anaerobic approaches are limited. Here, propane-enriched mixed cultures (derived from agricultural soils and an impacted site sediment) which previously degraded 1,4-dioxane, were evaluated for their capacity to also degrade trichloroethene (TCE), cis-1,2-dichloroethene (cDCE), and 1,1-dichloroethene (1,1-DCE) over successive transfers. Sustained biodegradation of TCE and cDCE was observed across multiple enrichments and cultures enriched on one compound generally degraded the other. In contrast, 1,1-DCE biodegradation was restricted to a subset of cultures and removal times increased over transfers. Further, 1,1-DCE removal was absent at elevated concentrations, both trends consistent with inhibitory or toxic effects. Whole genome sequencing analyses revealed pronounced substrate-dependent selection of microbial communities, with cDCE-degrading cultures being dominated by Mycobacterium and Mycolicibacterium, whereas TCE-degrading cultures were dominated by Rhodococcus. Rhodococcus metagenome-assembled genomes (MAGs) in the TCE degrading cultures classified as R. opacus or R. wratislaviensis. 1,1-DCE degrading cultures were dominated by Pseudonocardia, although the associated MAGs contained a truncated propane monooxygenase alpha subunit, suggesting other enzymes were responsible for 1,1-DCE transformation. Functional gene analysis identified both group 5 (prmABCD) and putative group 6 propane monooxygenases (although their expression was not examined). Together, these results demonstrate that substrate-specific pressures govern propanotrophic community structure and function, and highlight distinct roles of key actinobacterial genera in chlorinated ethene cometabolism. These findings support the development of propane-based bioaugmentation strategies for the treatment of mixed chlorinated solvent contamination under aerobic conditions.}, } @article {pmid42143455, year = {2026}, author = {Jia, W and Li, J and Wang, K and Cheng, L and Jin, N and Yang, Q and Zhang, D and Xia, X and Xu, N and Wang, M and Meng, J and Zhu, Y and Ding, A}, title = {Convergent shifts in microbial communities: Petroleum hydrocarbon contamination suppresses matrix heterogeneity.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142349}, doi = {10.1016/j.jhazmat.2026.142349}, pmid = {42143455}, issn = {1873-3336}, mesh = {*Groundwater/microbiology/chemistry ; *Hydrocarbons/analysis ; *Water Pollutants, Chemical/analysis ; *Petroleum/analysis ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology/chemistry ; *Microbiota/drug effects ; Bacteria/genetics/metabolism ; Petroleum Pollution ; }, abstract = {Accurate characterization of microbial communities in aquifers is essential for understanding groundwater ecosystem responses to petroleum hydrocarbon contamination. However, existing studies have focused primarily on groundwater, largely overlooking the coupled interactions between groundwater and aquifer sediments, which may bias aquifer-scale evaluations of microbial functional potential. In this study, contaminated groundwater and corresponding aquifer sediment samples were collected from a petroleum hydrocarbon impacted site, together with uncontaminated groundwater and sediment samples outside the contaminant plume as controls. Petroleum hydrocarbon concentrations and principal component analysis (PCA) revealed comparable contamination levels in groundwater and aquifer sediments. Integrating 16S rRNA gene sequencing analysis and metagenomic sequencing analysis, we found that microbial communities in contaminated groundwater exhibited broader niche breadth, higher niche overlap, and increased representation of low-molecular-weight carbon (LMW-C) metabolism, particularly pathways associated with ribose and amino sugar utilization. In contrast, aquifer sediment communities showed higher abundances of multidrug efflux pump genes and functional pathways involved in naphthalene and benzene degradation (PAH-C and MAH-C). Further correlation and community assembly analyses indicated that petroleum hydrocarbon contamination was the primary driver shaping microbial communities in both matrices, overriding intrinsic physicochemical differences. Meanwhile, sediment-specific properties, such as stronger sorption capacity for organic matter and differences in microbial lifestyles contributed to the observed divergence between groundwater and sediment communities. Overall, this study demonstrates that contamination induced selection dominates microbial community assembly in aquifers, and provides a mechanistic basis for improving the evaluation of natural attenuation potential and informing remediation strategies in contaminated aquifer systems.}, } @article {pmid42143457, year = {2026}, author = {Zhang, Z and Lv, M and Wang, R and Wang, B and Du, R and Lou, Y and Wang, C and Jiang, X and Hou, H and Li, Z and Chen, F}, title = {Micro-nano biochar interfaces promote adsorption-reduction coupling to accelerate bioelectrodechlorination in groundwater.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142393}, doi = {10.1016/j.jhazmat.2026.142393}, pmid = {42143457}, issn = {1873-3336}, mesh = {*Charcoal/chemistry ; *Groundwater/chemistry ; *Trichloroethylene/chemistry ; *Water Pollutants, Chemical/chemistry ; Adsorption ; Electrodes ; Water Purification/methods ; Halogenation ; Biofilms ; Oxidation-Reduction ; }, abstract = {Chlorinated aliphatic hydrocarbons (CAHs), such as trichloroethylene (TCE), are frequently detected high-toxicity contaminants in groundwater. Bioelectrodechlorination provides a sustainable alternative for CAHs remediation, but its practical application is hindered by limited interfacial reactivity due to low CAHs bioavailability and inefficient electron supply. Herein, we propose the construction of biochar-based functional electrodes featuring micro-nano interfacial architectures with hierarchical porosity, excellent biocompatibility, and enhanced interfacial extracellular electron transfer (EET) relative to carbon felt, which strengthened the coupling among local contaminant enrichment, cathode-associated biofilm development, and interfacial electron transfer, thereby accelerating TCE reductive dechlorination. The biochar-modified electrode increased the TCE dechlorination rate by 3.67-fold and reduced the interfacial charge-transfer resistance by 1.79-fold. Cathodic polarization at -0.5 V (vs. SCE) achieved the optimal balance between performance and energy efficiency, delivering 98.7% removal within 48 h at a low energy consumption of 4.1 Wh kg[-1] TCE, whereas less negative or more negative potentials decreased dechlorination efficiency by 4.3-11.0%. Under optimized conditions, TCE was efficiently removed and predominantly converted to cis-1,2-DCE. Biochar functionalization promoted biofilm development and selectively enriched electroactive and dechlorinating populations. Metagenomic analysis revealed marked upregulation of reductive dehalogenase genes (tceA, rdhA) and EET-related genes (cytc-c, e-pilin, and riboflavin). Environmental-economic benchmarking further demonstrated that biochar-based bioelectrodechlorination outperforms organic carbon-driven bioreduction and conventional electroreduction in removal efficiency, electron utilization, process controllability, and material sustainability.}, } @article {pmid42143575, year = {2026}, author = {Zhang, P and Zhao, M and Cheng, Z and Ding, Y and Xia, S and Guo, J}, title = {Bile acid metabolism dysregulation following Helicobacter pylori eradication promotes plasmid-mediated antimicrobial resistance in the gut microbiome.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42143575}, issn = {1751-7370}, mesh = {Animals ; *Bile Acids and Salts/metabolism ; *Plasmids/genetics ; *Helicobacter Infections/drug therapy/microbiology ; *Helicobacter pylori/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice ; *Gastrointestinal Microbiome/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; Humans ; Metagenomics ; Escherichia coli/genetics/drug effects ; Feces/microbiology/chemistry ; Metabolomics ; Male ; Female ; Mice, Inbred C57BL ; }, abstract = {Antimicrobial resistance (AMR) transmission within the gut microbiome poses a major health risk during antibiotic exposure, primarily via horizontal gene transfer (HGT). However, how antibiotic-induced metabolic remodeling of the intestinal environment modulates plasmid-mediated AMR dissemination remains unclear. Herein, integrating metagenomics, metabolomics, in vitro conjugation assays, and in vivo mouse models, we show that Helicobacter pylori eradication therapy reshapes gut metabolism in ways that enhance transfer of antibiotic resistance genes (ARGs). Metagenomic analysis revealed the expansion of Escherichia populations and the enrichment of plasmid-borne ARGs after H. pylori eradication. Fecal filtrates from treated individuals significantly increased conjugation frequencies of the broad-host-range plasmid RP4 in E. coli. Metabolomic profiling identified a pronounced accumulation of primary bile acids, including glycocholic acid, taurocholic acid, glycochenodeoxycholic acid, and taurochenodeoxycholic acids, which could increase bacterial membrane permeability, induce the SOS response, and upregulate conjugation and pilus assembly genes, thereby accelerating ARG transfer. Molecular docking further suggested these bile acids may likely participates in interacting with global plasmid repressors KorA/KorB, derepressing conjugation operons. In mice, H. pylori eradication therapy elevated fecal primary bile acid levels and significantly promoted in vivo plasmid transfer, with the critical role of bile acids further confirmed through interventions using the bile acid sequestrant cholestyramine or glycocholic acid. Together, these findings demonstrate that dysregulation of bile acid metabolism due to H. pylori eradication creates a permissive gut niche for plasmid-mediated ARG dissemination, providing mechanistic insight into how clinical antibiotic regimens can unintentionally promote microbiome-associated AMR risk.}, } @article {pmid42143599, year = {2026}, author = {Dong, A and Paju, S and Leskelä, J and Manzoor, M and Putaala, J and Ylikotila, P and Könönen, E and Pussinen, P and Zaric, S}, title = {Microbial burden of periodontal diseases and its clinical application: The stage, grade, and furcation matter.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jper.70140}, pmid = {42143599}, issn = {1943-3670}, support = {SGL023/1035/AMS_/Academy of Medical Sciences/United Kingdom ; //Medical Research Council Impact Acceleration Account/ ; 202108410182//Engineering and Physical Sciences Research Council/ ; //Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences/ ; //Revealing the Etiology/ ; //Sigrid Jusélius Foundation/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; //Finnish Medical Foundation/ ; //Finnish Dental Society Apollonia/ ; //King's-China Scholarship Council/ ; }, abstract = {BACKGROUND: Periodontal diseases are associated with dysbiotic oral microbial communities, but clinically applicable measures that reflect microbial burden across disease severity and progression remain limited. This study aimed to assess the oral microbial burden of periodontal diseases by evaluating salivary and subgingival lipopolysaccharide (LPS) activity and lipoteichoic acid (LTA) levels, to explore their relationships with microbial dysbiosis and clinical periodontal parameters in individuals with periodontal health (n = 52), gingivitis (n = 194), and periodontitis of varying stages, grades, and furcation involvement (n = 78), and to assess their diagnostic potential.

METHODS: Saliva and subgingival plaque samples from 324 SECRETO cohort participants were analyzed for microbial virulence factors using a recombinant Factor C assay for LPS and enzyme-linked immunosorbent assay (ELISA) for LTA. Microbial dysbiosis was assessed using a sequencing-derived, simplified dysbiosis index, calculated from subgingival 16S rRNA gene sequencing and salivary shotgun metagenomic profiles, based on the relative abundances of health-associated and periodontitis-associated taxa.

RESULTS: Subgingival LPS activity was significantly higher in periodontitis patients compared to healthy individuals and increased progressively across disease stages and grades. Salivary LPS activity differed only by periodontal diagnosis and correlated with full-mouth bleeding score (FMBS). LTA levels showed no statistical variations across periodontal conditions. Subgingival LPS activity and LPS/LTA ratio were strongly associated with simplified dysbiosis index. Salivary dysbiosis index was significantly higher in patients with furcation involvement. Receiver operating characteristic (ROC) analyses identified subgingival LPS, salivary LPS, and simplified dysbiosis index as diagnostic biomarkers with good clinical utility (area under the curve [AUC] 0.59-0.87).

CONCLUSIONS: This study highlights the importance of periodontitis diagnoses, stages and grades of periodontitis and furcation involvement as determining factors for increased salivary and subgingival bioburden. In addition, LPS activity could be used as a reliable periodontal biomarker, while the LPS/LTA ratio is an indirect indicator of microbial dysbiosis.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01934725.

PLAIN LANGUAGE SUMMARY: Periodontitis is a common inflammatory disease that affects the tissues supporting the teeth and can lead to tooth loss and broader health consequences if not properly managed. This study explored whether measures of oral microbial burden, particularly bacterial components such as lipopolysaccharide (LPS) and lipoteichoic acid (LTA), could help explain differences in periodontal disease severity and progression. Saliva and subgingival plaque samples were analyzed from individuals with periodontal health, gingivitis, and different stages and grades of periodontitis. We found that microbial burden, especially subgingival LPS activity, increased consistently with more severe and rapidly progressing forms of periodontitis and was closely associated with clinical signs of inflammation. In contrast, LTA levels showed limited variation across disease categories. Importantly, LPS-related measures demonstrated good ability to distinguish periodontal health from disease. These findings suggest that assessing microbial burden, particularly LPS activity, may provide clinically useful information beyond traditional periodontal assessments and could support improved disease classification, risk assessment, and the development of more personalized periodontal care strategies.}, } @article {pmid42143831, year = {2026}, author = {Deng, Y and Yuan, X and Xu, Y and Jiang, H and Xue, J and Jiang, Y and Wang, Y}, title = {Acetoclastic methanogenesis associated with arsenic methylation in a reducing aquifer: Pathway-specific patterns and mechanistic insights.}, journal = {Water research}, volume = {301}, number = {}, pages = {126114}, doi = {10.1016/j.watres.2026.126114}, pmid = {42143831}, issn = {1879-2448}, mesh = {*Groundwater/chemistry ; *Arsenic/metabolism/chemistry ; Methylation ; *Methane/metabolism ; Water Pollutants, Chemical ; }, abstract = {The distribution of methylated arsenic (MeAs) in reducing groundwater systems remains incompletely understood, in part due to uncertainties regarding how specific methanogenic pathways may influence arsenic biomethylation, a critical issue in arsenic biogeochemistry and risk assessment. To explore this question, we integrated hydrogeochemical characterization, carbon isotopic tracing, metagenomic analysis, and pathway-specific enrichment experiments, focusing on MeAs-rich alluvial-lacustrine aquifers in the central Yangtze River Basin. A strong positive correlation between arsM and mcrA abundances (r = 0.84, p < 0.001) points to a co-occurrence of genetic potential for arsenic methylation and methanogenesis in the studied aquifer. Metagenome-assembled genome (MAG) analysis showed a pathway-specific distribution of arsM gene, a higher proportion of acetoclastic methanogen MAGs harbored complete arsM genes (14.29 %), compared to methylotrophic (9.09 %) and hydrogenotrophic (0.00 %) methanogens. In pathway-specific enrichment assays under controlled laboratory conditions, acetoclastic cultures exhibited the highest capacity for stepwise arsenic methylation (MMA and DMA production), with methylation efficiency reaching approximately 10.2 %, whereas methylotrophic cultures produced only transient MMA and hydrogenotrophic cultures showed minimal methylation. These observations provide insights into pathway-dependent differences in methanogen-associated arsenic methylation, highlighting a possible biogeochemical link between methanogenesis and arsenic cycling in the studied aquifer. These findings contribute to understanding potential controls on MeAs occurrence in reducing groundwater and provide a basis for further investigations in comparable hydrogeological settings.}, } @article {pmid42144568, year = {2026}, author = {Rui, Z and Wang, X and Yu, C}, title = {Trichoderma koningiopsis-assembled synthetic PGPR community manage Fusarium damping-off and promote growth of Pinus massoniana seedlings.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70924}, pmid = {42144568}, issn = {1526-4998}, support = {QKEZDZX[2024]010//the Guizhou Provincial Major Scientific and Technological Program/ ; theNationalNaturalScienceFoundationofChina//32160375/ ; }, abstract = {BACKGROUND: Fusarium oxysporum causes damping-off disease in Pinus massoniana seedlings. While Trichoderma koningiopsis can enhance seedling resistance by regulating rhizosphere plant growth-promoting rhizobacteria (PGPR), the specific bacterial compositions and their role in disease resistance remained undefined. To elucidate this mechanism, we used amplicon and metagenomic sequencing to identify T. koningiopsis-assembled PGPR. Synthetic PGPR communities were constructed from isolated strains to validate their effects on disease suppression and growth promotion.

RESULTS: Microbial community analysis indicated that T. koningiopsis reshaped the bacterial community: Actinospica, Dyella, and Streptomyces decreased in presence, and Bacillus and Arthrobacter increased. A total of 153 PGPR strains were isolated from the T. koningiopsis-inoculated treatment. Of these, eight strains demonstrated significant inhibitory effects against F. oxysporum, ranging from 33.81% to 59.52%. Four synthetic communities (SynComs) (C1, C2, HT, and 2K) were further constructed, exhibiting superior inhibitory effects against F. oxysporum compared to individual strains. Compared to the control, the C2 and HT SynComs increased seedling height by 10.18% and 9.44%, and reduced disease incidence by 50% and 36.67%, respectively. These treatments also enhanced protective enzyme activity and alleviated membrane damage. At the molecular level, the C2 and HT SynComs boost plant resistance by modulating the plant hormone and mitogen-activated protein kinase (MAPK) signaling pathways, thereby activating the expression of crucial resistance genes such as PR1, FLS2, and CAT1.

CONCLUSION: Trichoderma koningiopsis alters the composition of rhizosphere PGPR community. The synthetic PGPR community assembled under the influence of T. koningiopsis effectively enhances damping-off resistance and promotes the growth of Masson pine seedlings. © 2026 Society of Chemical Industry.}, } @article {pmid42145141, year = {2026}, author = {Sreekumaran, S and V K, P and M N, A and Premnath, M and P S, S and P R, P and Mathew, J and E K, R}, title = {Comparative Human-Poultry Fecal Resistome Profiling from Broiler Farms Reveals Diverse Antimicrobial Resistance Genes.}, journal = {Foodborne pathogens and disease}, volume = {}, number = {}, pages = {15353141261449964}, doi = {10.1177/15353141261449964}, pmid = {42145141}, issn = {1556-7125}, abstract = {Indiscriminate use of over-the-counter antibiotics has led to the rapid emergence of resistant genes in bacteria, with the ultimate crisis to global health. One of the prominent sectors with the antimicrobial resistance (AMR) concern is the farm animals that exist in close contact with humans where the environmental conditions are favorable for the rapid dissemination of pathogenic organisms and resistance genes. Hence, to understand the threat with environmental AMR, a detailed molecular insight is very important. In this study, fecal samples from both poultry and associated humans were studied by metagenomics analysis. From the results, a primary understanding on the microbial diversity difference could be generated from the selected samples. Here, the poultry samples were identified to have more microbial diversity. At the same time, several pathogens were found to be shared commonly between the hosts. Upon detailed examination, several AMR genes were also observed to be common between the poultry and human samples. The results of the study are highly relevant in light of the "One Health" concept where an integrated approach is targeted.}, } @article {pmid42145647, year = {2026}, author = {Xing, J and Xu, Z and Zhang, Y and Zhang, H and Zheng, L and Zhang, M and Guo, W and Liu, J and Pan, Y and Zhang, J and Jie, Z and Baele, G and Li, C and D'Souza, A and Zhao, J and Li, J and Chen, T and Wu, H}, title = {Longitudinal cross-species transmission of microbiomes and resistomes across farmers, animals and environment.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.06.26352545}, pmid = {42145647}, abstract = {Understanding the acquisition and dissemination of microbiomes and antimicrobial resistance genes (ARGs) that circulate across human-animal-environment interfaces remains a central One Health challenge, largely because of complex ecological interactions and multiple confounding factors. Although occupational exposure is known to influence the microbiomes and resistomes of farmers, how environmental compartments involve in this system is unclear. Here, we conducted a one-year longitudinal study combining strain-resolved metagenomics (500 metagenomes) with isolate-based whole-genome sequencing (28 isolates) in an ecologically managed, antibiotic-free farming ecosystem spanning animals, farmers, environmental compartments and non-exposed individuals. Assembling 6,075 species-level genomes, we show that animal-associated occupancy reshapes the microbiome and resistome of occupationally exposed farmers and their surrounding environments. Animals and their associated habitats formed the dominant interface for both strain sharing and ARG dissemination across connected ecological compartments, whereas village residents and surrounding river samples - used as ecological controls - showed limited integration into this sharing network. Tracking a frequently shared lineage further revealed within-lineage genetic turnover together with selection-consistent changes following cross-species spread, suggestive of ecological selection across hosts and habitats. Finally, we identify Klebsiella pneumoniae as the most widespread ESKAPE pathogen in this ecosystem, with repeated occurrence across animal, human and environmental compartments, consistent with a neglected but clinically critical broad profile of ecological generalist. Together, these findings identify animals as central interfaces for microbiome and resistome sharing and show how agricultural ecosystems can sustain circulation of opportunistic pathogens and resistance determinants across human-animal-environment interfaces even in the absence of routine antibiotic use.}, } @article {pmid42146067, year = {2026}, author = {Cooper, G and Ayotte, SH and Du, ML and Wood, JD and Opp, B and Bothner, B and Peyton, BM}, title = {Arsenic detoxification within thermo-alkaline biofilms.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1783099}, pmid = {42146067}, issn = {1664-302X}, abstract = {INTRODUCTION: The fundamental principles driving community composition and dynamics of microbial mats in thermoalkaline springs are largely uncharacterized. High in not only temperature but also arsenic (As), the microbial populations of Yellowstone National Parks (YNP), USA thermal springs require unique detoxification mechanisms to survive and carry out basic biological functions.

METHODS: While many studies have focused on which microorganisms are present, few studies have integrated the use of metagenome sequencing, imaging techniques, and mass spectrometry to gain insight into how structure and function of the mat dwelling organisms might be impacted by the high arsenical species in the ecosystem.

RESULTS: Here, we demonstrate via metagenome sequencing that community composition, including microbial genera Roseiflexus, Thermus, and Synechococcus, and as detoxification abilities change with mat depth and distance from the springs. Arsenical speciation confirmed the generation of bioarsenicals by mat-dwelling microorganisms. Microscopy revealed stratification of microorganisms in the mat, potentially reflecting their arsenic redox capabilities.

DISCUSSION: These data demonstrate how microbial mats are modular, stratified systems that shape and are shaped by environmental and geochemical gradients. Together, these findings characterize novel complexity and associations between geochemical cycles of metals and metabolic adaptations necessary for microorganisms to inhabit thermal springs. In conclusion, these findings demonstrate physiochemical heterogeneity of microbial mats in YNP.}, } @article {pmid42146533, year = {2026}, author = {Steininger, HM and Iglesias-Aguirre, CE and Panzer, AR and Durack, J and McKean, M and Cabana, MD and Diamond, S and Lynch, SV}, title = {Carbohydrate Metabolism Differs in Infants by Asthma-risk Status and is Associated with the Functional Potential of Bacteroides cellulosilyticus.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42146533}, issn = {2692-8205}, abstract = {Childhood atopic disease is linked to delayed gut microbiome development and metabolic dysfunction, however microbial drivers remain unclear. To explore microbial correlates of asthma risk during a time of active gut microbiome development, we analyzed stool from 6-month-old infants at high asthma risk (HR) or healthy controls (HC), using Genome-resolved metagenomics (HR=7; HC=12) and untargeted metabolomics (HR=11; HC=15). We recovered 82 bacterial species-level metagenomic-assembled genomes (MAGs). Global Taxonomic composition did not differ by asthma risk. Anticipating that key differences might associate with specific genomes, a machine-learning approach pinpointed Bacteroides cellulosilyticus, Hungatella effluvii, and Enterocloster aldenensis as linked with asthma risk status. All three species were more abundant in HC infants and the B. cellulosilyticus genome was enriched for carbohydrate metabolism genes relative to other MAGs. Metabolomic profiling revealed variance associated with asthma risk (PERMANOVA, R[2]=0.069, p=0.016). HR fecal metabolomes were enriched in simple sugars, whereas HC contained more nitrogenous compounds. Integrative genome-metabolic modeling of compounds that significantly differentiate asthma-risk groups revealed risk-dependent interactions with community-encoded metabolic potential (CEP), for arabinose and agmatine, whose fecal concentrations are linked with B. cellulosilyticus and H. effluvii functional traits respectively. These findings suggest that microbial-influenced metabolic differences associate with asthma risk at 6 months, with B. cellulosilyticus and H. effluvii emerging as candidate bacteria influencing this observed metabolic remodeling.}, } @article {pmid42146661, year = {2026}, author = {Miller, CJ and Pope, CE and Lavitt, MH and Caverly, LJ and LiPuma, JJ and Penewit, K and Lewis, JD and Salipante, SJ and Hoffman, LR}, title = {The Unified Human Virome Database: A toolkit for expanded human virome analysis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42146661}, issn = {2692-8205}, abstract = {Current approaches for computationally analyzing viruses within human microbiomes often rely on databases largely composed of fragmented viral genomes from gastrointestinal samples, limiting identification of viruses exclusively found outside the gastrointestinal tract and analyses requiring high-quality genomes. To address these issues, we created the Unified Human Virome Database (UHVDB), comprising 575,497 high-quality, annotated viral genomes from human gastrointestinal, airway, skin, and urogenital sample metagenomes. We developed an associated toolkit that uses UHVDB to characterize viruses and their potential activity from metagenomes, then applied this toolkit to 1,983 airway sample metagenomes from people with cystic fibrosis. Over half of detected viruses lacked evidence of potential activity and were detected transiently. UHVDB is nearly three times larger than prior viral databases and its ability to identify likely active viruses enables rigorous analysis of viruses from diverse human sample types, expanding the capacity to define virus contributions to health and disease.}, } @article {pmid42146906, year = {2026}, author = {Orletskaia, VA and Olekhnovich, EI}, title = {Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types.}, journal = {Computational and structural biotechnology journal}, volume = {35}, number = {1}, pages = {0065}, pmid = {42146906}, issn = {2001-0370}, abstract = {Despite the recognized role of the gut microbiome in modulating immune checkpoint inhibitor efficacy, the ecological principles governing this relationship remain elusive. Moving beyond cataloging specific bacteria, we investigated whether general ecosystem properties determine clinical outcome. Through genome-resolved metagenomic analysis, we constructed a comprehensive catalog from 951 stool metagenomes and subsequently analyzed a curated subset of 624 samples from 11 multicancer cohorts, with melanoma (72.7%, n = 456) and other cancer types collectively accounting for 27.3% (n = 171), including gastrointestinal, non-small-cell lung, breast, ovarian, and other types. Our catalog comprises 3,816 operational genomic units and reveals the key ecological determinants of immune checkpoint inhibitor response. Clinical benefit was associated with gut ecosystems dominated by prevalent, autochthonous taxa. Indeed, the population frequency of a taxon was a positive predictor of its favorable outcome association. Functionally, responder-associated microbes were enriched in genomic capacity for complex carbohydrate metabolism, including specialized mucin degradation and amino acid biosynthesis. In contrast, nonresponse was characterized by enrichment of low-prevalence, exogenous oral and food-derived bacteria and enriched for replication-associated pathways. Our results support an ecological interpretation of the "Anna Karenina principle" in microbiomes: response is linked to a stable, functionally coherent microbial community, whereas nonresponse represents a destabilized state with high individual variability. This reframes the search for biomarkers from individual taxa to the assessment of ecosystem stability and functional coherence, providing a foundation for microbiome-targeted strategies to improve cancer immunotherapy outcomes.}, } @article {pmid42147179, year = {2026}, author = {Belger, C and Wirbel, J and Maghini, D and Carstens, N and van Coller, A and Beasley, JC and Melzheimer, J and Berkman, AY and Strauss, WM and Hetem, RS and Hazelhurst, S}, title = {The Gut Microbiome Profile of Lions in Etosha National Park, Namibia.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {42147179}, issn = {2693-5015}, abstract = {BACKGROUND: The gut microbiome plays a crucial role in carnivore ecology, diet, and health, yet remains poorly characterised in African lions (Panthera leo melanochaita). Previous studies of lion microbiomes have primarily focused on small numbers of captive individuals maintained on controlled diets of Asian origin, reporting Fusobacteriota and Firmicutes as dominant phyla. Some recent literature has begun to describe microbiome composition in free-living African lions; however, genome-resolved analyses and detailed functional characterisation of the wild African lion gut microbiome remain lacking.

RESULTS: We present the first comprehensive gut microbiome analysis of free-living African lions, including novel MAGs generated from examining 23 fresh faecal samples from 20 individuals in Etosha National Park, Namibia. The African lion gut was dominated by Bacteroides (22.1%) and Phocaeicola (13.3%) - two related genera - contrasting sharply with the captive lions where Fusobacterium (Bhopal, India) and Firmicutes (Rotterdam, Netherlands) predominate. This divergence likely reflects dietary differences, captivity effects and possibly allopatric separation. While recent work has begun to characterise taxonomic composition in wild African lions, our study extends these findings through the reconstruction of 318 bacterial and 102 viral metagenome-assembled genomes (MAGs) from combined short- and long-read sequencing data. Most MAGs shared <95% average nucleotide identity with existing reference genomes, indicating largely novel species. Supplementing the GTDB database with these MAGs reduced unclassified reads from 24.5% to 9.2%, demonstrating the substantial gaps in existing carnivore gut microbiome databases. Functional analysis revealed metabolic pathway enrichment, particularly for purine metabolism-critical for processing the lions' high-purine diet-with nearly complete pathways for degrading adenine and guanine to urea.

CONCLUSIONS: This study provides the first in depth description of the microbial taxa in the African lion gut microbiome. Genera in the Bacteroidaceae family dominated. There are large differences with the metagenomics of the n = 3,4 hybrid and Asiatic lions on controlled diets reported in prior studies. The discovery of over 300 novel MAGs significantly expands microbial reference databases and underscores the unique and understudied nature of apex carnivore microbiomes. These findings show critical microbial contributions to carnivore nutrition and establish a foundation for microbiome-based approaches to wildlife health monitoring and conservation management of threatened lion population.}, } @article {pmid42148043, year = {2026}, author = {Huang, CY and Nuwagira, E and Tisza, M and Kim, M and Tayebwa, M and Vieira, J and Lam, N and Wallach, E and Wiens, M and Tsai, AC and Valeri, L and Vallarino, J and Allen, JG and Lai, PS}, title = {Effect of Household Air Pollution on the Gut Microbiome and Virome of Adult Women Living in Uganda.}, journal = {Environmental health perspectives}, volume = {134}, number = {1}, pages = {75-90}, pmid = {42148043}, issn = {1552-9924}, mesh = {Humans ; Uganda ; Female ; *Gastrointestinal Microbiome ; *Air Pollution, Indoor/statistics & numerical data/adverse effects ; Adult ; *Virome ; Middle Aged ; }, abstract = {BACKGROUND: Emerging observational studies suggest that air pollution can influence the gut microbiome. However, this association is often highly confounded by factors, such as diet and poverty. The gut virome may influence respiratory health independent of the gut microbiome. We recently demonstrated in a randomized waitlist-controlled trial (ClinicalTrials.gov NCT03351504) that a clean lighting intervention reduced the level of personal exposure to air pollution among adult women in rural Uganda. OBJECTIVES: To determine the effect of a solar lighting intervention on changes to the gut microbiome and virome and secondarily to determine the association between these changes on lung health. METHODS: Between 2018 and 2019, we collected stool samples and assessed respiratory symptoms and spirometry from 80 adult women living in rural Uganda at baseline and 12 and 18 months postrandomization. The intervention group received a solar lighting system after randomization, while the waitlist-controlled group received one at 12 months. Deep metagenomics sequencing of stool was performed and profiled for nonviral and viral taxonomic composition. The primary analysis focused on pre- vs postintervention changes due to power considerations, adjusting for potential confounding by age, diet, antibiotic use, and season. A sensitivity analysis was conducted using intention-to-treat principles. When comparing pre- vs postintervention periods, we used sparse partial least-squares models to identify nonviral and viral signatures of reduced air pollution exposure. Mixed effects models were used to evaluate changes in health outcomes as well as associations between microbial signatures of reduced air pollution exposure and health. RESULTS: The average age was 39.2 years. The solar lighting intervention led to larger changes in viral compared to nonviral microbial community structure and differential abundance of bacteria, eukaryotes, and viruses. Provision of solar lighting systems was associated with a reduction in the presence of respiratory symptoms from 57.1% to 36.1% (p = 0.002), while there was no impact on lung function. Microbiome and virome signatures had AUCs of 0.74 and 0.76, respectively, in predicting pre- vs postintervention stool samples. Microbiome signatures were associated with a lower risk of respiratory symptoms (OR = 0.68 (0.49 - 0.94), p = 0.020). CONCLUSION: Among adult women living in rural Uganda, both nonviral and viral components of the gut microbial community changed after a clean lighting intervention. Microbiome signatures reflective of lower air pollution exposures were associated with improved respiratory symptoms. These observations suggest that air pollution may influence lung health through the gut-lung axis, warranting further exploration in future intervention studies.}, } @article {pmid42148573, year = {2026}, author = {Raad, R and Mann, A and Pal, A and Parra, A and Strawn, L and Hamilton, A and Critzer, F and den Bakker, HC}, title = {Metagenomic profiling of bacterial (16S) and fungal (ITS) communities on d'Anjou pears during long-term controlled-atmosphere storage.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0411725}, doi = {10.1128/spectrum.04117-25}, pmid = {42148573}, issn = {2165-0497}, abstract = {D'Anjou pears are routinely stored for up to nine months under controlled-atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears' natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends, and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability, or whether bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas (19.2% relative abundance [RA]) and Acinetobacter (3.31% RA). Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium (23.3% RA), Penicillium (9.28% RA), Botrytis (0.33% RA), and Mucor (0.14% RA) present at different storage stages.IMPORTANCEThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and possibly improve food safety throughout the supply chain.}, } @article {pmid42148581, year = {2026}, author = {Wang, K and Zhang, D and Shen, K and Qiu, Y and Deng, B and Zhou, J and Qiu, S}, title = {Multi-omics characterization of new and aged Daqu reveals region-specific microbial succession and metabolic signatures in Maotai-flavor liquor fermentation.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0377525}, doi = {10.1128/spectrum.03775-25}, pmid = {42148581}, issn = {2165-0497}, abstract = {Daqu is an essential fermentation starter that drives the formation of the characteristic flavor of Maotai-flavor liquor, yet the ecological and metabolic mechanisms underlying its regional differentiation and maturation remain poorly resolved. Here, we performed genome-resolved metagenomic and untargeted metabolomic analyses on 48 new and aged Daqu samples collected from four major Maotai-flavor liquor-producing regions in Guizhou Province, China. We reconstructed 163 high-quality metagenome-assembled genomes (MAGs) spanning 16 bacterial and 3 archaeal phyla and identified 2,642 metabolites across ionization modes. Distinct regional microbial signatures were observed, with Jinsha Daqu showing the greatest genomic diversity and unique MAGs, whereas Maotai Daqu exhibited the highest community similarity with other regions. Aged Daqu significantly increased microbial richness and functional capacity, enriching thermophilic and spore-forming taxa (e.g., Bacillus, Lentibacillus, Kroppenstedtia) and enhancing carbohydrate-active enzymes (GH13, GH43, and GH3), amino acid degradation, lipid metabolism, and secondary metabolic pathways. Metabolomic profiling revealed elevated amino acid derivatives, fatty acids, esters, and phenolic compounds in aged Daqu, indicating intensified biochemical activity. Multi-omics integration linked dominant microorganisms-including Bacillus thuringiensis, Actinomycetaceae bacterium, and Methylocaldum szegediense to pyrazine biosynthesis, amino acid catabolism, and lipid oxidation, forming coordinated microbial-metabolite modules that underlie region-specific flavor precursor formation. These findings establish a mechanistic model in which microbial terroir, aging-driven succession, and metabolic specialization jointly shape the maturation and flavor potential of Maotai-flavor liquor.IMPORTANCEThis study provides the first genome-resolved, multi-omics framework for understanding how geographic origin and storage aging co-regulate the ecological assembly, functional specialization, and metabolic transformation of Maotai-flavor liquor. By linking specific MAGs, functional pathways, and key flavor precursors, our results offer mechanistic insights into microbial terroir and provide a scientific foundation for microbiome-guided optimization of Maotai-flavor liquor quality.}, } @article {pmid42148582, year = {2026}, author = {Yu, L and Li, H and Yu, H and Zhou, Y and Wang, X and Luo, L}, title = {Inoculation of Bacillus velezensis SD24 enhancing the accumulation of tea catechin secondary metabolites.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0346925}, doi = {10.1128/spectrum.03469-25}, pmid = {42148582}, issn = {2165-0497}, abstract = {Tea (Camellia sinensis) is a globally significant economic crop, and its desirable quality and health benefits are largely credited to catechin derivatives. Plant growth-promoting rhizobacteria (PGPR), such as Bacillus velezensis, are well-known for enhancing the environmental fitness and disease resistance of plants. However, the regulation of their impact on tea catechin biosynthesis remains unclear. While previous studies have focused on PGPR-facilitated growth promotion in crops like tomatoes and rice, the physiological mechanisms by which microbes regulate secondary metabolism in tea-especially under co-inoculation conditions-remain largely underexplored. This study examined the effects of B. velezensis SD24, isolated from tea rhizosphere soil, on catechin derivative accumulation of tea leaves by altering gene expression and the rhizosphere microbiome. Strain SD24 exhibited broad-spectrum antimicrobial activity against various pathogens due to behaving antimicrobial gene clusters. Tea plants inoculated with SD24 showed significantly increased levels of catechin derivatives in their leaves. This was likely achieved by upregulation of leucoanthocyanidin reductase and anthocyanidin reductase within the phenylpropanoid pathway. Additionally, chlorophyll content was increased. Transcriptomic analysis revealed a notable enrichment in biosynthesis of secondary natural products among the tea genes activated by SD24 inoculation. Metagenomic analysis further demonstrated that SD24 inoculation led to a restructuring of the tea rhizosphere microbiome. Notably, co-inoculation with Piriformospora indica, a beneficial endophytic fungus, suppressed SD24-induced gene expression and catechin accumulation, underscoring its antagonism toward SD24. These findings suggest that B. velezensis SD24 enhances tea quality, probably by transcriptionally activating the synthesis of catechin derivatives, a process associated with the restructuring of the rhizosphere microbiome.IMPORTANCEThe mechanisms through which plant growth-promoting rhizobacteria (PGPR) influence secondary metabolism in perennial crops remain poorly understood. This study demonstrates that Bacillus velezensis SD24, a tea rhizosphere isolate, significantly enhances the accumulation of health-beneficial catechin derivatives in tea leaves. This quality improvement is associated with transcriptionally upregulating key biosynthetic genes (LAR and ANR) and concurrently restructuring the rhizosphere microbiome. Furthermore, we reveal a critical antagonistic interaction, where the beneficial fungus Piriformospora indica suppresses these SD24-induced effects. Our findings provide crucial insights into how specific PGPR strains may directly enhance tea quality by affecting host plant metabolism and the root microbiome, highlighting the complex and tailored microbial interactions that could be harnessed for sustainable agriculture.}, } @article {pmid42148731, year = {2026}, author = {Qiu, H and Zhang, Z and Qian, H}, title = {Evolutionary plasticity of cyanobacteria under persistent anoxia: mechanistic insights from marine blue holes and global ecological implications.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {6}, pages = {e0025126}, pmid = {42148731}, issn = {1098-5336}, mesh = {*Oxygen/metabolism ; *Cyanobacteria/genetics/physiology ; *Synechococcus/genetics/physiology/metabolism ; *Seawater/microbiology ; Anaerobiosis ; *Biological Evolution ; Adaptation, Physiological ; }, abstract = {Cyanobacteria are generally viewed as obligate oxic photoautotrophs. However, this paradigm was challenged by Z. Li, H. Zhang, T. Wei, L. He, and Y. Wang in Applied and Environmental Microbiology(92:e02576-25, 2026, https://doi.org/10.1128/aem.02576-25); this group identified transcriptionally active Synechococcus in the dark, permanently anoxic Yongle Blue Hole using integrated metagenomic and transcriptomic analyses. This finding suggests adaptive streamlining under long-term oxygen limitation, expands the recognized ecological range of phototrophic microorganisms, and highlights the potential relevance of microbial adaptation to future ocean deoxygenation.}, } @article {pmid42148775, year = {2026}, author = {Shi, W and Liu, L and Wu, L and Wang, X and Peng, Y and Liu, X and Li, C and Xu, J and Wu, Z and Dong, X and Zheng, Q}, title = {Salinity-driven adaptations and evolution of DNA viruses in estuarine-coastal ecosystems.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0035426}, doi = {10.1128/msystems.00354-26}, pmid = {42148775}, issn = {2379-5077}, abstract = {UNLABELLED: Salinity gradients drive microbial diversity and evolution in estuarine-coastal ecosystems, yet viral adaptation remains less well understood. We used metagenomics to study viral adaptation and functions in three representative estuarine-coastal regions in China. Our results reveal salinity-associated adaptations in DNA viruses, with viruses enriched in medium- to high-salinity environments exhibiting higher frequencies of acidic isoelectric points and charged amino acids compared to those enriched in low-salinity environments. Viral genomes encode diverse genes related to ion transporters and organic osmolyte metabolism, suggesting potential roles in osmotic stress responses. Viral microdiversity also varied systematically along the salinity gradient, indicating reduced genetic variation and stronger purifying selection under more saline conditions. Furthermore, we identified diverse AMGs linked to nutrient cycles, with salinity-driven enrichment revealing viral roles in host metabolism. Overall, our findings highlight salinity as a key driver of viral evolution and functional potential in estuarine-coastal ecosystems, providing new insights into how viruses adapt to environmental gradients.

IMPORTANCE: Salinity is a defining environmental gradient in estuarine-coastal systems, yet its role in shaping viral molecular evolution remains poorly understood. By integrating metagenomes, viromes, and metatranscriptomes across three estuaries, this study demonstrates that salinity exerts a strong and consistent imprint on DNA viruses. Increasing salinity selects for viral genomes encoding ion-transport and osmolyte-related proteins and drives systematic shifts in viral proteome composition toward osmoadaptive physicochemical properties. At the population level, higher salinity is associated with reduced viral microdiversity and stronger purifying selection, indicating constrained evolutionary space under osmotic stress. Viral auxiliary metabolic gene repertoires are structured along salinity gradients, with functional differentiation in carbon, nutrient, and nucleotide metabolism. Together, these findings identify salinity as a key evolutionary filter linking viral physiological adaptation, evolutionary dynamics, and functional potential in estuarine and coastal ecosystems.}, } @article {pmid42148776, year = {2026}, author = {Guo, J and Xiang, Z-w and Hu, F-f and Zhang, S-x and Han, W-j and Ding, X and Wang, X and Ye, M-l and Chen, J-h and Rao, T and Wu, L-l and Lian, G-h and Zhang, W and Huang, Y and Chen, Y}, title = {Turicibacter sanguinis is a candidate gut microbial pathobiont that promotes metabolic dysfunction-associated steatohepatitis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0029226}, doi = {10.1128/msystems.00292-26}, pmid = {42148776}, issn = {2379-5077}, abstract = {UNLABELLED: Emerging evidence points to the gut microbiota's involvement in metabolic dysfunction-associated steatohepatitis (MASH), yet the specific causative microbes remain largely unidentified. This study aimed to identify and functionally characterize candidate microbial pathobionts to MASH progression. Differentially abundant microbes were identified by 16S rRNA sequencing in a choline-deficient, L-amino acid-defined, high-fat diet MASH model, validated in other animal MASH models and in public clinical metagenomic data sets, then screened for consistently altered gut taxa. A candidate underwent functional validation via directed oral administration in mice. Mechanisms were explored through bile acid profiling by UHPLC-MS/MS and FXR signaling analysis by qPCR and immunohistochemistry. Additionally, fecal samples from MASH patients before and after treatment were analyzed to correlate microbial abundance with treatment response. Turicibacter sanguinis was consistently enriched in all MASH models and public data sets, with abundance correlating positively with liver injury markers. Its increased abundance exacerbated steatosis, inflammation, and fibrosis in healthy and diseased mice. Mechanistically, Turicibacter sanguinis altered bile acid composition, thereby increasing conjugated and decreasing unconjugated species, and inhibited hepatic FXR signaling, accompanied by suppressed SHP and elevated CYP7A1 and SREBP1c expression, which is consistent with enhanced bile acid synthesis and lipid accumulation. Futhermore, after pharmacotherapy, reduced Turicibater sanguinis levels correlated positively with alanine aminotransferase (ALT) and aspartate aminotransferase (AST) improvements. In conclusion, Turicibacter sanguinis is a clinically relevant microbial pathogen that exacerbated MASH by inducing bile acid dysregulation and suppressing FXR signaling, highlighting its potential as a candidate biomarker for disease monitoring and motivating future evaluation of targeted microbiome interventions.

IMPORTANCE: Metabolic dysfunction-associated steatohepatitis (MASH) is a growing global health problem with limited treatment options. Although the gut microbiome has been implicated in MASH, the specific bacterial strains that directly drive disease progression remain largely unknown. This study identified Turicibacter sanguinis as a candidate gut microbial pathobiont that promotes MASH, demonstrating its significant enrichment in both animal models and patient samples. By disrupting hepatic metabolic signaling, this bacterium promotes bile acid synthesis and exacerbates liver fat accumulation, inflammation, and fibrosis. Following effective treatment, its abundance decreased significantly in patients. These findings indicate that Turicibacter sanguinis holds promise as a potential target for developing novel microbiome-based diagnostic and therapeutic approaches for MASH.}, } @article {pmid42149293, year = {2026}, author = {Fulke, AB and Ratanpal, S}, title = {Integrated pragmatic approach of bioinformatics and cheminformatics for tracking the fecal pollution in an urban marine environment.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {6}, pages = {}, pmid = {42149293}, issn = {1573-2959}, mesh = {*Environmental Monitoring/methods ; *Feces/microbiology/chemistry ; *Computational Biology ; *Water Pollution/statistics & numerical data/analysis ; *Cheminformatics ; Cities ; *Water Pollutants, Chemical/analysis ; Humans ; }, abstract = {Fecal contamination in urban marine environments poses an alarming global threat to public health, ecosystems, and economies. Traditional fecal indicator bacteria (FIB) methods, while accessible, suffer from delayed results and inability to differentiate pollution sources. To overcome this, microbial source tracking (MST) employs molecular techniques like qPCR to rapidly identify specific origins (human, animal) using genetic markers. Complementary chemical source tracking utilizes distinct chemical signatures (e.g., sterols and pharmaceuticals) for detection, offering low limits and temporal stability. The burgeoning fields of bioinformatics and cheminformatics are crucial for processing the complex, high-volume data generated by these advanced methods. Bioinformatics tools analyze metagenomic data for microbial community profiling and source attribution, while cheminformatics automates the acquisition of chemical-specific data for environmental exposure modeling, enhancing efficiency and transparency. An integrated pragmatic approach leverages these capabilities with Geographic Information Systems (GIS) and remote sensing. GIS serves as a unifying platform, integrating diverse spatial, temporal, sensor, and analytical data to enable comprehensive spatial analysis, real-time monitoring, and predictive modeling of fecal plumes. Hence, this review is aimed toward this holistic framework, which is essential for effective, targeted management strategies to safeguard water quality.}, } @article {pmid42149451, year = {2026}, author = {Edelkamp, J and Lousada, MB}, title = {In Situ Laser-Capture Microdissection for Detection of Components of the Hair Follicle and Scalp Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3031}, number = {}, pages = {233-242}, pmid = {42149451}, issn = {1940-6029}, mesh = {*Hair Follicle/microbiology ; *Laser Capture Microdissection/methods ; *Microbiota/genetics ; Humans ; *Scalp/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; }, abstract = {Laser-capture microdissection (LCM) enables the study of the hair follicle (HF) microbiome in relation to hair health and disease with high spatial resolution. It allows the precise excision of specific HF regions, each containing a unique and conserved microbiome, from full-length HFs encompassing all relevant HF compartments. With LCM, cross-contamination with microbiota from neighboring regions is minimized. Coupled with 16S rRNA gene or metagenomic shotgun sequencing, LCM offers great potential to assess region-specific microbiome changes, particularly in HF-associated disorders.}, } @article {pmid42149452, year = {2026}, author = {Edelkamp, J and Lousada, MB}, title = {Viable vs. Nonviable Microbiota Evaluation of the Hair Follicle and Scalp Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3031}, number = {}, pages = {243-259}, pmid = {42149452}, issn = {1940-6029}, mesh = {Humans ; *Hair Follicle/microbiology ; *Microbiota/genetics ; *Scalp/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; In Situ Hybridization, Fluorescence/methods ; Propidium/analogs & derivatives/chemistry ; Azides/chemistry ; Microbial Viability ; Real-Time Polymerase Chain Reaction/methods ; }, abstract = {Various hair follicle (HF)-associated disorders, such as acne vulgaris, hidradenitis suppurativa, and alopecia areata, are linked to dysbiosis, an imbalance between resident and pathogenic microbes. Characterization of the HF and skin microbiome employs techniques such as 16S rRNA gene sequencing and metagenomic shotgun sequencing, with the latter providing comprehensive taxonomic and functional insights. However, relic DNA from dead microbes and free environmental DNA can persist in samples, meaning that metagenomic data does not exclusively reflect living microbiota. For functional studies on HF dysbiosis or to assess potential therapeutic interventions, we describe here how propidium monoazide (PMA) treatment can be performed before (metagenomics) sequencing to distinguish viable microbial communities. Furthermore, we exemplify qPCR and (fluorescent) in situ hybridization (ISH) of two alternative viability screening methods for the HF and scalp microbiome.}, } @article {pmid42149940, year = {2026}, author = {Sandi, JD and Brock-Fisher, TM and Kallon, TMPS and Paye, MF and Fofanah, IU and Nosamiefan, D and Kamara, MS and Teh, AJ and Turay, A and Wilkason, C and Baudi, I and Tomkins-Tinch, C and I'Anson, C and Stachler, E and Pekar, JE and Ozonoff, A and Park, D and Happi, C and Sabeti, PC and Grant, DS}, title = {Characterization of the first complete genome sequence of yellow fever virus (YFV) in Sierra Leone: Implications for public health.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {5}, pages = {e0014354}, pmid = {42149940}, issn = {1935-2735}, support = {U19 AI110818/AI/NIAID NIH HHS/United States ; }, mesh = {Sierra Leone ; *Yellow fever virus/genetics/isolation & purification/classification ; *Genome, Viral ; Humans ; Phylogeny ; *Yellow Fever/virology/epidemiology ; Male ; Public Health ; Sequence Analysis, DNA ; Whole Genome Sequencing ; Genotype ; }, abstract = {Yellow fever virus (YFV), a mosquito-borne orthoflavivirus that causes severe hemorrhagic disease, is endemic in parts of South America and Africa, yet genomic data from Sierra Leone is lacking despite ongoing case-based surveillance. Using hybrid-capture metagenomic sequencing, we generated a complete 10,611 nt YFV genome (98% coverage) from an adult male patient who reported to the Kailahun Government Hospital with fever and muscle pain. Phylogenetic analysis assigned the genome to the West African II genotype via the YFV Nextstrain build. The Sierra Leone genome showed 57 substitutions, three of which were non-synonymous (NS2B: N79S, NS3: V515I, and NS5 (RdRp domain): A643V), relative to its most recent common ancestor with other genomes from Senegal and the Netherlands. Bayesian phylogenetics estimated the time to the most recent common ancestor with these genomes as January 14, 2001 (95% HPD: December 17, 1987 - April 28, 2009), potentially indicative of long-standing transmission within West Africa that has not been genomically characterized, rather than specific localization to Sierra Leone. Together, these findings underscore the need for expanded genomic surveillance to monitor YFV spread and evolution.}, } @article {pmid42150467, year = {2026}, author = {Wang, X and Zhang, Y and Yu, J and Yang, S and Zhang, T and Song, J and Sun, Z}, title = {Metagenomic insights into nitrate- and sulfate-enhanced anoxic biodegradation of PAHs in subsurface soil.}, journal = {Ecotoxicology and environmental safety}, volume = {318}, number = {}, pages = {120281}, doi = {10.1016/j.ecoenv.2026.120281}, pmid = {42150467}, issn = {1090-2414}, mesh = {*Nitrates/metabolism ; Biodegradation, Environmental ; *Polycyclic Aromatic Hydrocarbons/metabolism/analysis ; *Soil Microbiology ; *Soil Pollutants/metabolism/analysis ; *Sulfates/metabolism ; Metagenomics ; *Bacteria/metabolism/genetics ; Soil/chemistry ; }, abstract = {Anoxic biodegradation is pivotal for remediating PAH-contaminated subsurface soils, yet its mechanisms remain poorly understood. In this study, nitrate and sulfate were used as electron acceptors to stimulate the anoxic biodegradation of PAHs in soil by indigenous bacteria. A 180-day anoxic incubation experiment was conducted, coupled with high-throughput sequencing for bacterial community composition, quantitative PCR for microbial abundance, metagenomic sequencing for functional gene profiling, and gas chromatography-mass spectrometry for PAH quantification, to characterize microbial community properties, key functional genes, and their contributions to PAH degradation. After 180 days of incubation, the addition of electron acceptors significantly increased the abundances of total and potential PAH-degrading bacteria (which increased by 0.11-0.24 and 0.09-0.46 orders of magnitude per gram of soil, respectively) and promoted the removal of 3- and 4-ring PAHs (59-64% and 26-33%, respectively). Notably, the degradation efficiency followed the order of NO3[-] > mixed electron acceptors > SO4[2-], revealing a clear preference for nitrate. Nitrate amendment selectively enriched key PAH-degrading taxa like Bacillus. Metagenomic analysis revealed the underlying microbial mechanisms: the functional pathway ko00624 (PAH degradation) was enriched, and the abundances of 15 key genes (e.g., pcaH, ligB, and pht5) involved in upstream and downstream metabolic steps were positively correlated with degradation efficiency. Comparative analysis showed that differences across treatments stemmed primarily from ‌elevated expression of shared core genes (e.g., pht4, phdG, nidB), with nitrate (SN) treatment showing the greatest enrichment. These findings elucidate electron acceptor-driven anoxic PAH transformation, highlighting nitrate's dual role as a nutrient and favorable electron acceptor, and provide a basis for targeted subsurface bioremediation.}, } @article {pmid42150504, year = {2026}, author = {Pan, Z and Wang, W and Torabi, E and Zhang, M and Su, Z and Xu, X and Yin, Y and Xu, W and Duan, Y and Chen, J and Maróti, G and Huang, Q}, title = {Multi-metal contamination is associated with microbial network simplification and functional adaptation in paddy soils: Insights from genome-resolved metagenomics.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142406}, doi = {10.1016/j.jhazmat.2026.142406}, pmid = {42150504}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity/analysis ; Metagenomics ; *Metals, Heavy/toxicity/analysis ; Oryza ; China ; Adaptation, Physiological ; Metagenome ; *Microbiota/drug effects ; Bacteria/genetics ; }, abstract = {The spatial heterogeneity of multi-metal contamination and its ecological consequences for soil microbial communities remain poorly characterized on a national scale, particularly within paddy ecosystems. This study investigated microbial ecological and genomic responses to heavy metal stress across 48 paddy soils from major rice-growing regions in China, categorized into low (LMS), moderate (MMS), and high (HMS) contamination levels. Our results indicate that multi-metal contamination triggered a significant restructuring of microbial communities, which was accompanied by increased alpha diversity and the enrichment of metal-tolerant taxa (e.g., Planctomycetes and Cyanobacteria). Conversely, microbial co-occurrence networks exhibited systematic simplification as contamination levels increased, characterized by reduced connectivity and a significant loss of keystone taxa. This suggests a transition from functionally redundant communities to modularized, survival-oriented network configurations. Metagenomic analysis revealed positive correlations between metal contamination and the abundance of nitrogen, phosphorus, and sulfur-cycling genes, while carbon-cycling genes remained relatively stable. Furthermore, genome-resolved metagenomics demonstrated widespread co-localization of metal resistance genes (MRGs) and nutrient cycling genes within metagenome-assembled genomes, particularly among key taxa (e.g., Burkholderiaceae, MBNT15). Collectively, these findings elucidate the mechanistic basis of microbial adaptation to multi-metal stress in paddy soils, providing critical insights for optimizing soil health management, developing targeted bioremediation strategies, and enhancing environmental risk assessment frameworks for contaminated agricultural ecosystems.}, } @article {pmid42150526, year = {2026}, author = {Thompson, LR}, title = {Microbial ecology: Rise of the planet of the microbes.}, journal = {Current biology : CB}, volume = {36}, number = {10}, pages = {R432-R434}, doi = {10.1016/j.cub.2026.03.072}, pmid = {42150526}, issn = {1879-0445}, mesh = {*Microbiota/genetics ; Metagenomics ; Ecosystem ; *Bacteria/genetics ; *Metagenome ; }, abstract = {A long-standing tenet of microbiology is that Earth's microbiomes are structured by environment, not geography. In a new study, Kim et al. report the largest metagenomic analysis yet performed, revealing that microbial generalists transcend these boundaries, ferrying genes - including antibiotic resistance determinants - across ecologically distant habitats.}, } @article {pmid42150690, year = {2026}, author = {Kruger, F and den Haan, R}, title = {Adaptive laboratory evolution and rational engineering enabled xylose utilisation and xylan conversion in natural isolates of Saccharomyces cerevisiae.}, journal = {Journal of biotechnology}, volume = {417}, number = {}, pages = {17-30}, doi = {10.1016/j.jbiotec.2026.05.007}, pmid = {42150690}, issn = {1873-4863}, abstract = {Second-generation biofuels produced from renewable lignocellulosic biomass (LCB) are attractive alternatives to environmentally damaging, non-renewable fossil fuels. A key challenge in converting LCB to bioethanol is the incomplete utilisation of all available sugars. To address this, the hemicellulose fraction, consisting mainly of xylan, should be converted to the desired product alongside cellulose. This study aimed to develop natural isolate strains of Saccharomyces cerevisiae capable of xylose utilisation and xylan degradation. Strains YI13, YI59 and FIN1 were selected for potential industrial applications due to their high fermentation performance levels under environmental stress and enhanced ethanol production compared to laboratory strains. Xylose utilisation was achieved in these strains by introducing heterologous xylose isomerase (XI) and xylulokinase (XKS) gene cassettes and a xylose transporter (XTR), followed by adaptive laboratory evolution (ALE) in minimal xylose media. The evolved strains were further engineered for cell-associated xylosidase and secreted xylanase activities, yielding variants with strong enzyme activities, optimized xylose metabolism, and high ethanol production from both xylose and xylan. The final engineered version of YI13 showed the best xylose and xylan conversion, with maximum ethanol titres of ∼7.1 g/L from 20 g/L xylose and ∼4.7 g/L from 40 g/L xylan, among the highest ethanol titres from polymeric xylan by direct microbial conversion reported to date. The development of these S. cerevisiae strains provides a useful platform for future development of robust xylan-converting S. cerevisiae strains for large-scale ethanol production, although validation on real-world lignocellulosic feedstocks is still required.}, } @article {pmid42151282, year = {2026}, author = {Visci, G and Notario, E and Defazio, G and Caratozzolo, MF and Cox, SN and Fosso, B and Marzano, M and Pesole, G}, title = {Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-49725-3}, pmid = {42151282}, issn = {2045-2322}, support = {PNC0000002 - CUP: B53C22006420001//Ministero dell'Università e della Ricerca/ ; PNC-EJ-2022-23683266 PNC-HLS-DA//Ministero dell'Università e della Ricerca/ ; H93C22000560003//Regione Puglia/ ; }, abstract = {Two culture-independent methods, amplicon-based sequencing and shotgun metagenomics, have significantly advanced the study of microbial communities. To date, short-read sequencing technologies have enabled high accuracy and deep coverage, while long-read sequencing approaches are increasingly being applied to improve genome assembly, despite challenges related to sequencing errors and nucleic acid input requirements. In this benchmark study, we compared the shotgun metagenomics approach across three sequencing technologies, Illumina (short reads), PacBio and Nanopore (long reads), using a 20-species commercial mock microbial community with even species representation. Specifically, we evaluated the effectiveness of the data generated by each platform in reconstructing genomes and identifying specific known taxa, as well as in understanding their functional potential, considering annotated genes, the length of predicted proteins and the number and types of inferred functions. Illumina sequencing provided high-throughput and high-quality data, but its limited read length precluded complete genome assembly. This affected the functional analysis, leading to an underestimation of coding and non-coding genes. Nanopore sequencing yielded the longest reads, resulting in more contiguous assemblies, although it was affected by higher error rates and the choice of assembly method. PacBio offered the best balance between read length and base accuracy, but with a lower number of reads. This affected genome coverage for certain taxa, influencing the quality of their assemblies, the completeness of MAGs (Metagenome Assembled Genomes), and the accuracy of functional annotation. Nevertheless, PacBio successfully retrieved MAGs for all mock community species, and the genome annotation was consistent with the reference. Evaluating the strengths and limitations of different NGS technologies and assembly strategies, this benchmark provides a practical framework for selecting the most suitable approach for optimizing data quality in microbiome genome characterization, according to study-specific goals.}, } @article {pmid42151303, year = {2026}, author = {de Tacca, LMA and Lima, RN and de Oliveira, MA and Pascoal, PV and Bambil, D and Rosinha, GMS and Signor, D and Freire, M and Rech, E}, title = {The soil microbiome of the Caatinga drylands in Brazil.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-50433-1}, pmid = {42151303}, issn = {2045-2322}, support = {20-122//Conrad Prebys Foundation/ ; }, abstract = {Drylands cover a significant portion of the Earth's surface and play a key role in maintaining global ecological balance. The Caatinga, with its unique biodiversity adapted to the extreme conditions of this semi-arid region, offers a valuable opportunity to expand our knowledge about these ecosystems. Here, this work reveals the high microbial diversity in the soil and rhizosphere of the Caatinga, with the roots presenting more specialized communities. Bacteria such as Bacilli, Alphaproteobacteria and Firmicutes excelled in critical functions such as nutrient cycling. The Interplant differences suggested the influence of root exudates. Altogether, the metagenomic study of interactions between microorganisms in the rhizosphere of selected plants revealed microbial biodiversity and contributed to our understanding of nutrient cycling, plant growth and resistance to water stress. In addition, they demonstrate biotechnological potential to address global challenges such as desertification and food security.}, } @article {pmid42151510, year = {2026}, author = {de Souza Pereira, LF and Tavares, TCS and Martins, DT and Dias Dantas, CW and de Souza, FOR and Prazeres, MCC and Faturi, C and Rogez, HLG and Ramos, RTJ and Cardenas Alegria, OV and Ribeiro Carneiro Nunes, A}, title = {Characterization of defensome genes and mobile genetic Elements in different types of pasture soil agroecosystems from the Brazilian Amazon.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42151510}, issn = {1618-1905}, abstract = {The Amazon rainforest represents nearly 40% of the world's tropical forests and has undergone extensive conversion to pasture, profoundly altering soil microbial communities. Given that bacteriophage-driven selective pressure shapes bacterial defense systems (the defensome) as well as mobile genetic elements (MGEs), we examined the diversity and distribution of these genetic components in native forest soils and in pasture soils under two management regimes (with and without fertilization) in the Brazilian Amazon. Metagenomic sequencing revealed pronounced differences in bacterial community structure between forest and pasture sites (R = 0.942), whereas phages communities exhibited no significant variation. Pasture soils-particularly those under fertilization-showed higher abundances of functional genes and mobile genetic elements, including conjugative plasmid-associated genes and insertion sequences. Defensome analyses indicated an increased prevalence of retrons and Pycsar systems in managed soils, while a greater diversity of defense genes was observed in non-fertilized pastures. A strong positive correlation was observed between defensome diversity and MGE diversity, suggesting coordinated dynamics between viral selective pressure and horizontal gene transfer. These findings indicate that forest-to-pasture conversion reshapes microbial functional potential and amplifies genetic mechanisms linked to phage defense and gene mobility, with potential consequences for ecosystem functioning and the dissemination of antimicrobial resistance.}, } @article {pmid42151682, year = {2026}, author = {Blackburn, D and Rahman, B and Saroyia, AP and Parish, AJ and Driscoll, M and Szewczyk, NJ and Vanapalli, SA and Samuel, BS}, title = {Defining Microbiome Impact on Host Physiology During Spaceflight Using Caenorhabditis elegans.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3000}, number = {}, pages = {251-275}, pmid = {42151682}, issn = {1940-6029}, mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology ; *Space Flight ; *Microbiota ; Weightlessness ; *Host Microbial Interactions ; }, abstract = {Microbiome-integrated Caenorhabditis elegans cultivation methods enable investigation of host-microbiome interactions in the context of space-relevant stresses using three key innovations: introduction of live bacterial communities replacing chemically defined media, implementation of auxin-inducible degradation systems to prevent progeny production, and development of complementary hardware platforms. Polyethylene bags provide gas-permeable cultivation environments for large populations with complex microbiomes supporting downstream molecular analyses, while NemaCapsules with micropillar arrays and passive culturing chambers allow real-time phenotypic assessment through on-orbit imaging, transforming our ability to correlate molecular signatures with physiological outcomes in microgravity.}, } @article {pmid42152463, year = {2026}, author = {Forshee, MD and Nachman, EJ and Shenoy, ER and Danhof, HA and Ermann Lundberg, L and Roos, S and Britton, RA}, title = {Limosilactobacillus reuteri promotes melatonin release from human intestinal organoids via 5'ectonucleotidase activity.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2670854}, pmid = {42152463}, issn = {1949-0984}, mesh = {*Melatonin/metabolism ; *Limosilactobacillus reuteri/metabolism/growth & development/enzymology ; Humans ; *Organoids/metabolism/microbiology ; *Intestines/microbiology ; Probiotics ; Adenosine/metabolism ; }, abstract = {Strains of Limosilactobacillus reuteri have been used to prevent or treat various conditions; however, the mechanisms by which they exert beneficial effects are not completely understood. Infant colic is one example in which L. reuteri DSM 17938 reduces clinical symptoms. While the etiology of colic is unknown, abnormal melatonin levels in infants have been suggested as a possible contributor. L. reuteri DSM 17938 has been shown to produce adenosine from AMP via production of the extracellular enzyme 5'ectonucleotidase (5'NT). Adenosine is a potent signaling molecule that impacts several important aspects of host physiology, including the release of melatonin from the pineal gland in the brain. A second major source of melatonin production is enteroendocrine cells in the intestine. We hypothesized that the adenosine generated via the 5'NT activity of L. reuteri DSM 17938, would stimulate melatonin release from human intestinal organoids. Here, we characterized the growth conditions that impact L. reuteri DSM 17938 5'NT activity, including carbon source utilization and required metal cofactors. We found zinc to be an essential cofactor for 5'NT activity by L. reuteri and observed carbon utilization altered 5'NT activity levels. Stachyose and raffinose increased levels of 5'NT activity while sucrose decreased 5'NT activity. We demonstrated that L. reuteri DSM 17938 stimulates melatonin release from pediatric human intestinal organoids in a 5'NT-dependent manner. Surprisingly, adenosine was necessary, but not sufficient, for the induction of epithelial melatonin release, thereby suggesting that an additional secreted factor was also required. Furthermore, L. reuteri BG-R46[®], an evolved strain of DSM 17938 that is known to express higher 5'NT activity, was shown to induce higher levels of melatonin secretion. Taken together, this work identifies zinc and carbon sources as key factors altering L. reuteri 5'NT activity levels and demonstrates that the L. reuteri strains stimulate intestinal melatonin release via 5'NT.}, } @article {pmid42152762, year = {2026}, author = {Yang, W and Guo, J}, title = {Unveiling the Hidden Resistome: A Comprehensive Risk Assessment of Latent Antibiotic Resistance Genes in China's Wastewater.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70330}, doi = {10.1111/1462-2920.70330}, pmid = {42152762}, issn = {1462-2920}, support = {2021YFD1600400//National Key Research and Development Program of China/ ; }, mesh = {*Wastewater/microbiology ; China ; Risk Assessment ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Metagenome ; Genes, Bacterial ; Escherichia coli/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; }, abstract = {Wastewater systems are important reservoirs of antibiotic resistance genes (ARGs), but the ecological and health risks of numerous latent ARGs (LARGs) remain unclear. In this study, we analysed 636 wastewater metagenomic samples from China and constructed a database containing 1587 LARGs. Across all environments, LARGs encoding serine-β-lactamases were the most abundant and prevalent. A comprehensive risk assessment, integrating host pathogenicity, gene mobility and environmental prevalence, was performed on 561 LARGs identified in metagenome-assembled genomes. Most LARGs exhibited low levels across all three dimensions, suggesting limited transmission risk. Nevertheless, 37 high-risk LARGs were identified, indicating non-negligible threats. Functional validation showed that the top three extremely high-risk LARGs significantly enhanced host resistance to ampicillin and ciprofloxacin when expressed in Escherichia coli, while AlphaFold3 revealed typical resistance protein folding, further supporting their functional activity. Horizontal gene transfer analysis indicated that these high-risk genes have disseminated from wastewater to natural water bodies such as rivers via plasmid-mediated mechanisms. Collectively, wastewater acts not only as an 'accumulation pool' for LARGs but also as a potential source releasing 'super-risky' resistance gene into the environment. Therefore, urgent efforts are needed to monitor and control these high-risk LARGs and their mobile genetic elements to block their environmental spread.}, } @article {pmid42152807, year = {2026}, author = {Jing, M and Chen, X and Jiang, M and Fang, H and Zhu, X and Jin, X and Jiao, Y and Hou, N and Gong, W and Liu, A}, title = {Microbial and Metabolic Correlates of Endometrial Dysfunction in Polycystic Ovary Syndrome: A Translational Study.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1471-0528.70266}, pmid = {42152807}, issn = {1471-0528}, support = {//Hangzhou Joint Fund of the Zhejiang Provincial Natural Science Foundation of China/ ; //Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; }, abstract = {OBJECTIVE: Women with polycystic ovary syndrome (PCOS) exhibit a substantially increased risk of miscarriage, yet the underlying mechanisms remain inadequately understood. This study aimed to investigate whether specific gut microbial dysbiosis and metabolic disturbance are associated with and may potentially contribute to endometrial dysfunction and adverse pregnancy outcomes in women with PCOS.

DESIGN: Prospective cohort study integrated with mechanistic experiments.

SETTING: Women's Hospital, School of Medicine, Zhejiang University, China (2022-2024).

POPULATION: A total of 110 women with PCOS and 110 age- and body mass index-matched controls were enrolled.

METHODS: We performed 16S rRNA and metagenomic sequencing of gut microbiota, with untargeted and targeted serum metabolomics. Functional validation was conducted using primary human endometrial stromal cells and a PCOS rat model intervened with Parabacteroides merdae (P. merdae) supplementation or faecal microbiota transplantation.

MAIN OUTCOME MEASURES: Gut microbiota composition, serum metabolites, endometrial senescence markers, and pregnancy outcomes.

RESULTS: Women with PCOS exhibited significantly higher miscarriage rates than controls, accompanied by a marked depletion of P. merdae abundance and elevated serum levels of branched-chain amino acids, particularly isoleucine. Exogenous isoleucine induced cellular senescence in human endometrial stromal cells in a dose-dependent manner. Restoration of P. merdae levels in the PCOS rat model resulted in decreased serum isoleucine levels, amelioration of the senescent endometrial phenotype, and reduction in the fetal resorption rate.

CONCLUSIONS: These findings suggest that P. merdae depletion and the concurrent accumulation of isoleucine may be associated with endometrial senescence and elevated risk of miscarriage, suggesting the possible involvement of a gut microbiota-metabolite pathway in PCOS-related reproductive dysfunction. These results also provide a mechanistic basis for future translational investigations.}, } @article {pmid42152996, year = {2026}, author = {Chauhan, G and Bisht, N and Gautam, P and Arya, M and Kumari, A and Verma, D and Sharma, M}, title = {Cloning and Heterologous Expression of a Novel Thermo-Alkalistable GH-10 Xylanase (rXyn-GM) Retrieved from Tapovan Hot-Spring Soil Metagenome and its Characterization for Kinetic Parameters.}, journal = {Indian journal of microbiology}, volume = {66}, number = {2}, pages = {417-430}, pmid = {42152996}, issn = {0046-8991}, abstract = {UNLABELLED: A cellulase-free xylanase gene of 927 bp size (Xyn-GM) was isolated from the metagenomic library of the Tapovan Hot Spring in Uttarakhand, India. This gene encodes a 308-amino acid xylanase enzyme classified under the glycoside hydrolase family 10 (GH-10). The Xyn-GM gene was introduced into the pET28a (+) vector and expressed in host cells of Escherichia coli BL21 (DE3). The recombinant xylanase (rXyn-GM), with a molecular weight ~ 32.5 kDa, was isolated through a one-step purification process using Ni[2][+]-NTA affinity chromatography. The purified enzyme exhibited broad thermostability (50-100 °C) and pH stability (4.0-11.0), with optimal activity at 70 °C and pH 9.0. Its activity increased by 67% in the presence of 1 mM Mn[2][+]. rXyn-GM retained ~ 65% activity after 2 h at 50 °C and 60 °C and ~ 75% activity at pH 9.0 after 3 h. It showed a preference for beechwood xylan, with kinetic parameters Km 20.9 mg/mL and Vmax 156.25 µmol/mg/min. Furthermore, rXyn-GM catalysed the production of xylo-oligosaccharides from beechwood xylan, suggesting its potential utility as prebiotics in the food and pharmaceutical industries.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01480-1.}, } @article {pmid42153006, year = {2026}, author = {Yadav, S and Shipra, }, title = {Impact of Climate Change on Zoonotic Diseases and Antimicrobial Resistance.}, journal = {Indian journal of microbiology}, volume = {66}, number = {2}, pages = {280-291}, pmid = {42153006}, issn = {0046-8991}, abstract = {UNLABELLED: Climate change along with infectious disease and antimicrobial resistance are imposing threat to public health globally. Climate change mediates frequent rise in antimicrobial resistance leading to the emergence of zoonotic vectors. Both climate change and AMR contribute significantly to global morbidity and mortality and impose burden on the healthcare sector. Overexploitation of antimicrobials in various sectors causes broader dissemination of AMR. Therefore, the application of a holistic "One Health Approach" is required to combat both climate change and antimicrobial resistance. Increasing public awareness about the negative consequences of climate change and antimicrobial resistance is essential. Also, the discovery of new antimicrobials has become the need of the present world. The application of metagenomics has the potential to shed light on microbial community dynamics (taxonomic abundance and predominant biochemical pathways) in response to climate change. The application of modern tools like functional metagenomics has the potential to yield new antimicrobial compounds for combating AMR.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01430-3.}, } @article {pmid42153318, year = {2026}, author = {Chasapi, MN and Kontis, N and Lehmann, R and Tasneem, R and Patel, NS and Khan, SA and Martínez de Morentin, X and Chasapi, IN and Aplakidou, E and Galaras, A and Aldakheel, L and Su, M and Baltoumas, FA and Venkateswaran, K and Lagani, V and Gómez-Cabrero, D and Tegnér, J and Pavlopoulos, GA and Soares Rosado, A}, title = {Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {3}, pages = {}, pmid = {42153318}, issn = {1477-4054}, support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; //KAUST Visiting Student Research Program (VSRP)/ ; 28787-VIROMINE//Hellenic Foundation for Research and Innovation (H.F.R.I.)/ ; 23592-EMISSION//Research Projects to Support Faculty Members and Researchers/ ; }, mesh = {*Computational Biology/methods ; Culture Techniques ; Environmental Microbiology ; *Extremophiles/genetics/isolation & purification/metabolism ; Machine Learning ; }, abstract = {Life thrives in Earth's most inhospitable environments, from boiling hydrothermal vents to hypersaline lakes and frozen polar deserts, thanks to the remarkable adaptations of extremophilic microorganisms. The study of these organisms has rapidly evolved from early cultivation-based discoveries to a data-rich discipline powered by advanced omics technologies. This review comprehensively outlines the current landscape and future directions in extremophile research, emphasizing the pivotal role of bioinformatics, machine learning (ML), and data-driven approaches. We begin by charting the evolution of methodologies, from innovative in situ cultivation techniques and robust biomolecule extraction protocols to modern multi-omics workflows (metagenomics, transcriptomics, proteomics, and metabolomics) that decode the genetic and functional basis of extremophiles. We then catalogue essential bioinformatics resources and specialized databases critical for annotating extremophile genomes and uncovering their unique adaptive strategies, including protein stabilization and syntrophic metabolic relationships. Finally, we explore the transformative potential of artificial intelligence (AI) and ML in overcoming fundamental challenges in the field. These include predicting the functions of uncharacterized "hypothetical" proteins, identifying novel extremozymes, modeling complex genotype-phenotype relationships, and guiding the targeted engineering of industrially relevant strains. By synthesizing insights across these domains, this review highlights how integrating computational biology and AI is poised to unlock the full biotechnological potential of extremophiles and redefine the boundaries of life itself.}, } @article {pmid42153323, year = {2026}, author = {Wang, J and Liu, Y and Liu, F and Hou, T and Chen, S and Liu, S and Liu, Y}, title = {DCVBin: a novel binning method for single-sample metagenomes based on DNA language model and variational autoencoder.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {3}, pages = {}, pmid = {42153323}, issn = {1477-4054}, support = {62303193//National Natural Science Foundation of China/ ; 20230101064JC//Science and Technology Development Plan Project of Jilin Province, China/ ; //Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Metagenomics/methods ; *Metagenome ; Humans ; Algorithms ; *Software ; Computational Biology/methods ; Autoencoder ; }, abstract = {DNA contigs binning is necessary to reconstruct metagenome-assembled genomes. Current metagenomic DNA contigs binning methods often leverage coverage profiles across multiple related metagenomes and have demonstrated strong performance on co-assembled contigs. However, in single-sample scenarios where coverage information is rare, their performance drops significantly, limiting the in-depth development of metagenomics at the individual sample level. To address this issue, we propose DCVBin, a novel single-sample metagenomic contigs binning method that incorporates semantic features extracted from a DNA language model. Specifically, our approach continues pretraining on a DNA language model to capture more domain-specific semantic representations, which are then integrated with 4-mer frequencies using a variational autoencoder. Clustering is subsequently performed using the k-means algorithm, in which the number of clusters is determined by single copy genes. Experimental results on six publicly available datasets demonstrate that DCVBin achieves high-accuracy single-sample metagenomic binning and outperforms other state-of-the-art methods. Furthermore, DCVBin is included into a disease diagnostic framework that is evaluated on a cohort of gut metagenomes from people with colorectal cancer and healthy people. The framework is shown to be accurate in predicting colorectal cancer using gut metagenomes and has identified a list of potential microbial biomarkers.}, } @article {pmid42153643, year = {2026}, author = {Jeilu, O and Simachew, A and Hartmann, EM and Alexandersson, E and Johansson, E}, title = {CAZyme fold architecture is conserved between disparate environments despite extreme sequence divergence.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0048526}, doi = {10.1128/msystems.00485-26}, pmid = {42153643}, issn = {2379-5077}, abstract = {Microbial carbohydrate-active enzymes (CAZymes) underpin carbon cycling across Earth's ecosystems; however, how contrasting environments shape CAZyme diversity and structural conservation remains poorly understood. Here, we applied shotgun metagenomics to compare the carbohydrate-degradation potential of two functionally prolific but physicochemically opposed ecosystems: the alkaline-saline soda lakes of the East African Rift Valley and the anaerobic ruminant gut. From 34 metagenomes (12 soda lake and 22 rumen), we recovered 371 quality-filtered metagenome-assembled genomes, of which 84% of soda lake and 52% of rumen MAGs represented novel species. Rumen communities, dominated by Bacteroidota, Fibrobacterota, and Bacillota, exhibited significantly higher taxonomic diversity and were enriched in carbohydrate catabolism and fermentation pathways. Soda lake communities, dominated by Pseudomonadota, displayed greater evolutionary divergence (lower RED scores) and were enriched in pH homeostasis, oxidative and osmotic stress, sulfur cycling, and carbon fixation pathways. To assess whether structural conservation persists despite extreme sequence divergence, we predicted three-dimensional structures for 12 representative enzymes from six glycoside hydrolase families (GH1, GH3, GH5_11, GH9, GH10, and GH28) using AlphaFold 3. All 12 structures adopted canonical GH family folds with high confidence (pTM 0.75-0.97). These results demonstrate that environmental selection drives distinct taxonomic and functional strategies for carbon processing while preserving three-dimensional CAZyme architecture, positioning soda lake and rumen metagenomes as complementary reservoirs for bioprospecting industrially relevant enzymes.IMPORTANCECarbohydrate-active enzymes, or CAZymes, are the molecular machines that microorganisms use to break down plant material and other complex sugars, and they underpin both the global carbon cycle and many industrial processes, from biofuel production to food, feed, and textile manufacturing. In this study, we compared the CAZyme repertoires of two microbial worlds that could hardly be more different: the alkaline, salty soda lakes of the East African Rift Valley, and the anaerobic stomachs of cattle, sheep, and goats. We show that although these communities are taxonomically distinct and their enzyme sequences have diverged dramatically, the three-dimensional shapes of their key carbohydrate-degrading enzymes remain remarkably well preserved. Soda lakes, in particular, hold a large pool of previously uncharacterised enzymes, identifying them as a promising, largely untapped source of robust biocatalysts for sustainable biotechnology and industrial applications.}, } @article {pmid42153646, year = {2026}, author = {Revel-Muroz, AZ and Sonets, IV and Chistyakov, AS and Vasiluev, PA and Surovoy, YA and Ivanova, VA and Kozlovskaya, LI and Khokhlova, OE and Fursov, MV and Fursova, NK and Ulianov, SV and Tyakht, AV}, title = {Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0013926}, doi = {10.1128/msphere.00139-26}, pmid = {42153646}, issn = {2379-5042}, abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, particularly in intensive care units, where vulnerable patients are frequently exposed to multidrug-resistant microorganisms. The human gut microbiome serves as a key reservoir for AMR genes, which can disseminate to other body sites, including the lungs, especially during severe illness. We applied Hi-C metagenomics to stool samples from 11 critically ill COVID-19 patients and analyzed microbial isolates from their lungs to investigate intra-host transmission of AMR genes. Plasmid-resolved microbial interaction networks revealed AMR gene sharing across 13 bacterial genera, primarily from Firmicutes and Proteobacteria, with evidence of plasmid-mediated transfer across phylum boundaries and between gut and lung compartments. Notably, we identified genetically identical Klebsiella pneumoniae strains colonizing both the gut and lungs of a single patient, as well as shared plasmids carrying qnrS-1 and blaCTX-M-231 resistance genes between gut Escherichia coli and lung K. pneumoniae. In addition to bacterial pathogens, Candida yeast species isolated from both niches harbored resistance genes to multiple antifungal classes, including azoles. These findings underscore the dynamic, cross-compartmental nature of AMR dissemination within the human body and highlight the importance of integrative surveillance strategies to control resistance in clinical settings.IMPORTANCEWhile COVID-19 itself caused severe illness, many deaths were ultimately due to secondary microbial infections-often worsened by antibiotic resistance. Plasmids, which shuttle resistance genes between bacterial species, are key players in their spread, yet their roles in transmission, especially across body sites such as the gut and lungs, are to be elucidated. The use of Hi-C metagenomics allowed us to map bacterium-plasmid links in the guts of severe COVID-19 patients and reconstruct high-quality genomes of opportunistic fungi. Comparing these with lung-derived isolate genomes, we gained insight into possible intra-host dissemination routes of resistance genes. Preparing for future pandemics will require not only rapid pathogen detection but also tools to monitor microbiome health and resistance dynamics, and understanding how treatments and microbial imbalances shape infection risks.}, } @article {pmid42153961, year = {2026}, author = {Zhu, B and Chen, S and Diao, Y and Wang, W and Huang, Y and Liang, L and Lu, X and Han, R and Guo, M and Li, Z and Wang, S and Li, H and Liu, C and Zhou, J and Xiong, D and Li, X and Ning, Y and Shi, X and Wu, F and Wu, K}, title = {Dissecting the Ecological Structure of Health and Disease in the Global Gut Microbiome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17087}, doi = {10.1002/advs.202517087}, pmid = {42153961}, issn = {2198-3844}, support = {2023YFC2414500//National Key Research and Development Program of China/ ; 2023YFC2414504//National Key Research and Development Program of China/ ; 2025YFC3410000//National Key Research and Development Program of China/ ; 2025YFC3410005//National Key Research and Development Program of China/ ; 82271953//National Natural Science Foundation of China/ ; 82301688//National Natural Science Foundation of China/ ; 2023B0303020001//Key Research and Development Program of Guangdong/ ; 2023B0303010003//Key Research and Development Program of Guangdong/ ; 2024A1515013058//Natural Science Foundation of Guangdong Province/ ; 2025A1515010507//Natural Science Foundation of Guangdong Province/ ; 2023A1515011383//Natural Science Foundation of Guangdong Province/ ; 2019B121203008-KJ-2024-040/KJ-2024-041//Guangdong Key Laboratory of Battery Safety at Guangzhou Institute of Energy Testing/ ; 2025A03J3357//Science and Technology Program of Guangzhou/ ; ZDYN-2024-A-121//Clinical Collaboration Project on Integrated Traditional Chinese and Western Medicine for Major and Difficult Diseases/ ; 2024SRP200//Research Capacity Improvement Project of Guangzhou Medical University/ ; GCAAL2022001//Guangzhou Key Clinical Specialty (Clinical Medical Research Institute), the Announcement and Leading Science and Technical Foundation of Guangzhou Civil Affairs/ ; 2023B04J0106//Guangzhou Planned Project of Science and Technology/ ; 2025B04J0011//Guangzhou Planned Project of Science and Technology/ ; }, abstract = {The gut microbiota plays a crucial role in human health, but its coordinated ecological dynamics remain largely unclear. We present Wiredancer, a novel scalable framework based on similarity-constrained non-negative matrix factorization (NMF), which extracts continuous and overlapping microbial ecological factors (MEFs). By integrating 20,178 metagenomes spanning 36 countries and over 50 disease states, Wiredancer identified three robust and interpretable MEFs delineating the health-disease continuum. MEF1, the dysbiotic factor dominated by Bacteroides uniformis, was elevated in disease populations; MEF2, the protective factor characterized by Prevotella copri, was reduced compared with the healthy group; and MEF3, the intermediate factor represented by Bifidobacterium adolescentis, reflected a mixed ecological configuration between MEF1 and MEF2. MEFs exhibited high reproducibility across individuals and longitudinal cohorts, but showed significantly increased variability in disease, consistent with the Anna Karenina principle and highlighting disrupted ecological stability. These findings were validated in the largest Chinese metagenomic cohort of major psychiatric disorders, where MEFs were associated with clinical symptoms, peripheral biomarkers, and disease subtypes, and remained essentially stable under short-term treatment. Together, Wiredancer provides a generalizable strategy to define microbiome states and decode ecological transitions, offering new opportunities for precision diagnostics and stratified medicine in complex disorders.}, } @article {pmid42154322, year = {2026}, author = {Greaves, JC and Rodriguez, RA}, title = {Revealing the hidden burden: wastewater-based epidemiology for underreported and emerging infectious diseases in communities.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {6}, pages = {}, pmid = {42154322}, issn = {1573-2959}, mesh = {Humans ; *Wastewater/virology/microbiology ; *Communicable Diseases, Emerging/epidemiology ; *Wastewater-Based Epidemiological Monitoring ; }, abstract = {Wastewater-based epidemiology (WBE) has become a transformative tool for infectious disease surveillance, providing population-level insights that complement and extend traditional case-based reporting. This review examines the expanding role of WBE in identifying and characterizing underreported, novel, and emerging human pathogens. Evidence reveals that wastewater analysis consistently detects enteric, respiratory, and neglected pathogens that are often missed by clinical systems, thereby revealing the hidden burden of infection within communities. Sequencing-based studies have identified numerous novel and divergent human viruses, highlighting the extensive diversity of the human virome. The frequent co-detection of multiple viral taxa also suggests that interactions and co-infections may influence viral evolution, disease manifestation, and transmission. Despite methodological challenges in quantification and biological validation, WBE has proven capable of detecting both known and novel pathogens before they are clinically recognized. Future developments in long-read sequencing, bioinformatics, and global data integration will enhance the precision and scope of wastewater genomics, positioning it as a central element of early-warning and One Health surveillance frameworks. By illuminating the unseen spectrum of infectious agents, WBE bridges environmental and clinical domains, offering a scalable and equitable strategy for global pathogen discovery and public health preparedness.}, } @article {pmid42154337, year = {2026}, author = {Sain, M and Rani, S and Singh, SP and Pothal, P and Yadav, S and Suttee, A and Kumar, A and Kumar, S and Ranawat, P and Singh, G and Barnwal, RP}, title = {The Influence of Gut Microbiome on Alpha-Synuclein Aggregation: Implications for Parkinson's Disease Pathogenesis.}, journal = {Molecular neurobiology}, volume = {63}, number = {1}, pages = {}, pmid = {42154337}, issn = {1559-1182}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/metabolism/pathology/microbiology ; *alpha-Synuclein/metabolism ; Animals ; Dysbiosis ; *Protein Aggregates ; }, abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder traditionally characterized by dopaminergic neuronal loss in the substantia nigra and the accumulation of misfolded α-synuclein (α-syn) aggregates. While genetic susceptibility and environmental exposures are well-recognized contributors to PD, growing evidence indicates that disease initiation and progression may also involve peripheral mechanisms originating in the gastrointestinal (GI) tract. Early non-motor symptoms such as constipation, along with the presence of α-syn pathology in the enteric nervous system, have led to increasing interest in the gut-brain axis as a critical modulator of PD pathogenesis. Recent literatures reveal that gut microbiota dysbiosis can influence neurodegeneration through immune activation, intestinal barrier dysfunction, and altered production of microbial metabolites, including short-chain fatty acids, bile acids, lipopolysaccharides, and tryptophan-derived compounds. However, the precise molecular mechanisms by which these microbial factors modulate α-syn aggregation, propagation, and clearance remain incompletely understood. In this article, we review current clinical and experimental literature linking gut microbiota alterations to α-syn pathology, with particular emphasis on inflammatory signaling, microbial metabolites, and impaired proteostatic pathways that promote α-syn misfolding. We further integrate emerging concepts of "body-first" and "brain-first" PD subtypes and discuss proposed routes of α-syn transmission from the enteric to the central nervous system, including vagal, hematogenous, and immune-mediated pathways. By highlighting underexplored mechanistic connections between gut dysbiosis and α-syn biology, this review underscores the potential of microbiome-targeted strategies for early diagnosis and disease modification. A deeper understanding of gut-brain communication may ultimately enable personalized therapeutic approaches and reshape current paradigms of PD pathogenesis.}, } @article {pmid42154370, year = {2026}, author = {Benekos, K and Katsanos, A and Laspas, P and Panos, GD and Vagiakis, I and Fousekis, FS and Luca, R and Zhou, B and Kostoulas, C and Georgiou, I and Katsanos, KH and Skondra, D and Konstas, AG}, title = {An Update and Overview of the Ocular and Extraocular Microbiome and Its Impact on Ophthalmic Care.}, journal = {Advances in therapy}, volume = {}, number = {}, pages = {}, pmid = {42154370}, issn = {1865-8652}, abstract = {The microbiome has been described as the last human "organ" and is currently the topic of great research interest worldwide. The application of culture-independent methods, like 16S ribosomal next-generation sequencing, has offered researchers the opportunity to identify bacterial populations that were impossible to detect previously using conventional culture methods. Further standardization of these new approaches to characterizing the microbiome is desirable. The present review discusses the mounting evidence suggesting that alterations in the microbiome and microbial metabolites, such as short-chain fatty acids in the gut, mouth, and ocular surface, may play a key role in the pathogenesis of ocular pathologies such as ocular surface disease, glaucoma, uveitis, age-related macular degeneration, and diabetic retinopathy. Clarifying the probable role of the microbiome in ocular diseases would not only offer valuable insights into pathogenesis but could also enable the development of novel therapeutic approaches. As yet, microbial-based therapeutic applications in ophthalmology are limited. Nevertheless, recently emerging strategies utilizing probiotics and prebiotics, or even fecal transplantation to regulate microbiome composition, offer promising research avenues for developing future innovative therapies for ocular diseases. Further studies employing standardized methodological protocols are needed to ensure the reproducibility of results and to eventually unlock the precise links between the microbiome and the eye.}, } @article {pmid42154390, year = {2026}, author = {Khan, I and Irfan, M and Bacha, AS and Khan, I and Ali, Y and Li, Z}, title = {Host-Microbiota Metabolic Interactions in Atherosclerosis: Oral, gut, and Blood Perspectives.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42154390}, issn = {1867-1314}, abstract = {Atherosclerosis is a chronic inflammatory disease influenced by host-microbiota interactions beyond traditional risk factors. Microbial communities in the oral cavity, gut, and blood contribute to vascular dysfunction through metabolic and immune mechanisms, yet an integrated perspective across these compartments remains lacking. This narrative review synthesizes current evidence on the distinct and interconnected roles of oral, gut, and blood microbiotas in atherosclerosis pathogenesis. We critically evaluate key microbial metabolites, trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), and secondary bile acids, and their mechanisms of host metabolic and immune modulation. We also examine cross-compartment interactions, emerging multi-omics approaches, and the translational potential of microbiota-targeted interventions. Oral pathogens promote systemic inflammation and endothelial activation. Gut-derived metabolites such as TMAO exacerbate foam cell formation and impair reverse cholesterol transport, whereas SCFAs exert protective effects via immune modulation and gut barrier maintenance. Emerging evidence suggests that blood microbial components contribute to vascular inflammation, though methodological challenges remain. Multi-omics integration (metagenomics, metabolomics, host genomics) reveals interconnected metabolic networks linking microbial activity to atherosclerosis. Microbiota-targeted strategies, including dietary modulation, TMA lyase inhibitors, and probiotics, show promise for risk stratification and therapeutic intervention. The human microbiota regulates atherosclerosis through immunometabolic metabolites, offering promising biomarkers and therapeutic targets. However, clinical translation requires addressing interindividual variability, establishing causality, and standardizing methodologies. This review provides an integrated framework for leveraging microbiota-host interactions in precision cardiovascular medicine.}, } @article {pmid42154500, year = {2026}, author = {Pouder, E and Alain, K and Mieszkin, S}, title = {Phylogenomic and metabolic insights into iron reduction metabolism in the genus Deferribacter belonging to the order Deferribacterales.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42154500}, issn = {2057-5858}, mesh = {*Phylogeny ; *Iron/metabolism ; Oxidation-Reduction ; Hydrothermal Vents/microbiology ; Genome, Bacterial ; Metabolic Networks and Pathways/genetics ; }, abstract = {Iron is one of the most important elements of the Earth, yet its bioavailability is limited in oceanic environments. In this context, deep-sea hydrothermal ecosystems represent one of the major sources of iron. While some microorganisms involved in its biogeochemical cycle, particularly in Fe(III)-reduction, have been isolated from these ecosystems, the molecular mechanisms underpinning metabolic pathways remain hypothetical and incomplete. Therefore, this study aims to investigate the global metabolism of bacteria within the Deferribacter genus, isolated from hydrothermal systems and a petroleum reservoir, with a specific focus on the Fe(III)-reduction metabolism to identify genes potentially involved in this pathway. This study revealed a conserved carbon metabolism across the four species, while their energetic metabolism exhibited notable differences. These species appear to be able to use different elements as electron sources, showing their ability to adapt to different ecological (micro)niches, particularly in deep-sea hydrothermal vents. The marker genes known for Fe(III)-reduction were identified, with a contrast between the strains isolated from hydrothermal systems and the one isolated from a petroleum reservoir. To further explore this pattern, the study was extended, including 14 genomes of representative strains and 36 metagenome-assembled genomes affiliated to the Deferribacterales order. Phylogenomic analysis revealed a distribution pattern within this order that correlates with environmental origin. Canonical marker genes of Fe(III)-reduction were also identified, with their distribution primarily aligned with specific ecological niches.}, } @article {pmid42154842, year = {2026}, author = {Wang, D and Wang, N and Liu, J and Zhao, C and Xing, X}, title = {The diagnostic value of fine-needle aspiration cytology in the early diagnosis of pulmonary cryptococcosis.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {68}, number = {}, pages = {e33}, pmid = {42154842}, issn = {1678-9946}, mesh = {Humans ; *Cryptococcosis/pathology/diagnosis ; Biopsy, Fine-Needle/methods ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Lung Diseases, Fungal/pathology/diagnosis ; Early Diagnosis ; Adult ; Aged ; Lung/pathology/microbiology ; }, abstract = {Pulmonary cryptococcosis, an invasive fungal infection caused by Cryptococcus spp., is often misdiagnosed as tuberculosis or lung cancer due to overlapping clinical and radiological features, leading to treatment delays. In this descriptive study, we aim to characterize the diagnostic findings and clinical utility of fine-needle aspiration cytology (FNAC) in a series of patients with pulmonary cryptococcosis, within the context of other available diagnostic modalities. We retrospectively analyzed 10 patients with pulmonary cryptococcosis who underwent imaging-guided percutaneous lung aspiration. Wright-Giemsa-stained cytology smears were examined under oil immersion, enabling clear visualization of the characteristic morphological features of Cryptococcus. In this case series, FNAC provided a rapid cytological diagnosis within two hours in all 10 cases, consistent with the results obtained by metagenomic next-generation sequencing (mNGS) and serological testing. In contrast, conventional smear microscopy showed lower detection rates, and histopathology required longer processing times. The use of FNAC facilitated early diagnosis, enabling timely initiation of antifungal therapy and helping to avoid unnecessary surgical interventions. Our findings suggest that cytomorphological evaluation by FNAC is a rapid and valuable diagnostic tool in the early clinical management of pulmonary cryptococcosis, effectively complementing existing diagnostic methods.}, } @article {pmid42154957, year = {2026}, author = {Lorca, R and Bretagne, MC and Boizeau, L and Cappy, P and Allenbach, Y and Rodriguez, C and Salem, JE}, title = {Immune checkpoint inhibitor myocarditis: a metagenomic investigation of infectious pathogens.}, journal = {European heart journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/eurheartj/ehag371}, pmid = {42154957}, issn = {1522-9645}, } @article {pmid42155010, year = {2026}, author = {Kim, JS and Loe, A and Ma, SF and Ranjan, P and Lipinski, JH and Mikhail, SG and Gurczynski, SJ and Zhou, X and Huffnagle, GB and Downward, JE and Metcalf, JD and Falkowski, N and Stringer, KA and Dickson, RP and Huang, Y and Moore, BB and Martinez, FJ and Murray, S and Noth, I and O'Dwyer, DN}, title = {Gut microbiota associate with disease severity and survival in idiopathic pulmonary fibrosis.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajrccm/aamag249}, pmid = {42155010}, issn = {1535-4970}, abstract = {RATIONALE: Gut microbiota modify immunity. Dysregulated immunity plays a key role in the pathogenesis of IPF. However, the role of gut microbiota in IPF pathogenesis is unknown.

OBJECTIVES: Determine associations between gut microbiota, disease severity and lung transplant-free survival in IPF.

METHODS: Gut microbiota from patients enrolled in the CleanUP-IPF trial were characterized using fecal swab samples (n = 411). CleanUP-IPF investigated the clinical efficacy of long-term anti-microbials in IPF. 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing were performed to comprehensively profile gut microbial communities. Associations between baseline microbiota with disease severity, transplant-free survival, and treatment heterogeneity were analyzed using principal component analysis, multivariate generalized linear models, additive models and Cox regression models.

MEASUREMENTS AND MAIN RESULTS: Gut microbiota composition varied significantly with sex, age, and proton pump inhibitor use. Gut microbial diversity and community composition were significantly associated with impaired gas exchange (percent predicted (pp) DLCO). Several genera including the Lachnospiraceae unclassified genus were associated with improved transplant-free survival (HR 0.34 95% CI 0.14-0.87, P = .02) in patients not assigned to anti-microbial treatment. Patients with a higher abundance of the Lachnospiraceae unclassified genus exposed to long term co-trimoxazole had worse survival (HR 6.09 95% CI 1.36-27.27, P = .02). Survival in pirfenidone treated patients was significantly associated with a higher abundance of the gut Lachnospiraceae unclassified genus.

CONCLUSIONS: In exploratory post-hoc analysis, gut microbiota correlated with disease severity, associated with treatment heterogeneity and transplant-free survival in patients with IPF.}, } @article {pmid42155550, year = {2026}, author = {Pandit, S and Hazra, S and Dinda, SK and Bhattacharjee, B and Basu, A and Pradhan, B and Kumar, K and Manna, D}, title = {Advances in the detection of deadly free-living amoebae (FLA).}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {2}, pages = {117465}, doi = {10.1016/j.diagmicrobio.2026.117465}, pmid = {42155550}, issn = {1879-0070}, mesh = {Humans ; *Amebiasis/diagnosis/parasitology ; *Molecular Diagnostic Techniques/methods ; *Amoeba/isolation & purification/genetics/classification ; Balamuthia mandrillaris/isolation & purification ; Naegleria fowleri/isolation & purification ; Specimen Handling ; }, abstract = {Free-living amoebae (FLA), including Naegleria fowleri, Acanthamoeba castellanii, Balamuthia mandrillaris, and Sappinia pedata, are ubiquitous protozoa capable of causing severe infections such as primary amoebic meningoencephalitis (PAM), granulomatous amoebic encephalitis (GAE), and Acanthamoeba keratitis (AK). Early diagnosis remains challenging due to disease rarity, nonspecific clinical presentation, and limited access to specialized laboratory methods. Rapid and accurate detection is critical for patient management and public health response, particularly amid changing environmental exposures. This review summarizes current diagnostic approaches in clinical and environmental contexts, including specimen handling, microscopy, culture, immunohistochemistry, antigen detection, and molecular methods such as conventional PCR, real-time PCR, multiplex qPCR, LAMP, and metagenomic next-generation sequencing. Environmental surveillance, biomarker discovery, quality assurance, and standardized protocols are also discussed. By evaluating strengths and limitations of available tools, this review highlights diagnostic gaps and future priorities to enhance sensitivity, turnaround time, and global accessibility.}, } @article {pmid42155712, year = {2026}, author = {Geng, R and Huang, B and Duan, Z and Zhao, F and Lü, X and Jiang, Z and Yi, Y}, title = {Antimicrobial Efficacy and Food Application Potential of Bacteriocins LL3 and LL4 from Traditional Dairy-Derived Lactococcus lactis.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2026-28309}, pmid = {42155712}, issn = {1525-3198}, abstract = {To combat foodborne pathogens like Salmonella, this study employed an activity-based screening followed by metagenomic mining of the active isolates to discover and characterize bacteriocins from Inner Mongolian dairy products. From the 15 active isolates, Lactococcus lactis D63 and D64 were identified as harboring a putative biosynthetic gene cluster (BGC) encoding 2 bacteriocins, LL3 and LL4. Both peptides form amphipathic α-helical structures that disrupt bacterial membranes, leading to intracellular leakage and cell death. They exhibited effective antimicrobial activity, particularly against Salmonella Typhimurium. Crucially, when applied in a simulated milk model under standard refrigeration (4°C), synthesized LL4 demonstrated robust preservative efficacy by effectively controlling S. Typhimurium, showing comparable performance to the commercial preservative Nisin. Genetic analysis revealed that this BGC exhibits low basal transcription under standard laboratory growth conditions and shares high homology with plasmid elements, suggesting it is a mobile genetic element acquired via horizontal gene transfer. This study presents LL3 and LL4 as promising natural preservatives and validates metagenomic mining as an efficient strategy for uncovering antimicrobial genes.}, } @article {pmid42155775, year = {2026}, author = {Yao, X and Zhu, Y and Gao, P and Liu, T and Zhang, X and Liu, W and Li, J and Li, D and Zhang, Y and Zhang, Z}, title = {Limitations of endogenous denitrification in low carbon-to-nitrogen wastewater treatment: Insights into carbon allocation imbalance and metabolic adaptation.}, journal = {Bioresource technology}, volume = {456}, number = {}, pages = {134915}, doi = {10.1016/j.biortech.2026.134915}, pmid = {42155775}, issn = {1873-2976}, mesh = {*Carbon/metabolism ; *Denitrification ; *Nitrogen/metabolism ; *Wastewater/chemistry/microbiology ; *Water Purification/methods ; Bioreactors/microbiology ; *Adaptation, Physiological ; Polyhydroxyalkanoates/metabolism ; Bacteria/metabolism ; Glycogen/metabolism ; Sewage/microbiology ; }, abstract = {Endogenous denitrification (EnD) has been identified as a promising strategy for enhancing nitrogen removal from wastewater with a low carbon-to-nitrogen (C/N) ratio. However, the mechanisms limiting its effectiveness under carbon-starved conditions remain insufficiently understood. This 160-day study compared denitrification performance, carbon allocation, and metabolic responses in two sets of anaerobic/aerobic/anoxic-sequential batch reactors (A/O/A-SBR) under low (3-5) and high (10-15) C/N ratios. Under low C/N, total nitrogen (TN) removal decreased to 69.90 ± 13.31%, with effluent NO3[-]-N accounting for 87.43 ± 14.40% of TN. Concurrently, microbial activity was inhibited. Compared with high C/N ratio, microorganisms under low C/N preferentially allocated limited carbon to extracellular protein (PN) rather than to intracellular polyhydroxyalkanoates or glycogen. PN constitutes 47.39 ± 2.38% of the total internal carbon sources in unit sludge and functions primarily to maintain cellular structural stability. This carbon allocation pattern imposes limitations on the supply of carbon sources available for the EnD process. In addition, despite the enrichment of EnD functional bacteria (15.22 ± 2.03%), functional genes were primarily directed toward survival-related pathways (xenobiotics biodegradation and metabolism and amino acid synthesis). Constraints on energy metabolism further limited carbon utilization and denitrification. Concurrently, while the dispersion of denitrification-related genes under low C/N maintained system stability across multiple bacterial genera, it concomitantly reduced denitrification efficiency. This metabolic shift further limited EnD. This study provides novel insights into constraints on EnD from the perspectives of carbon source allocation and microbial metabolic adaptation, thereby establishing a theoretical foundation for the treatment of low C/N wastewater.}, } @article {pmid42155781, year = {2026}, author = {Wang, J and Liu, S and Wang, Z and Guo, Y and Liu, J and Shi, L}, title = {Coupling heterotrophic and hydrogenotrophic partial denitrification via gel-based bio-carriers: microbial mechanisms and metabolic modeling.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {134914}, doi = {10.1016/j.biortech.2026.134914}, pmid = {42155781}, issn = {1873-2976}, mesh = {*Denitrification/physiology ; *Hydrogen/metabolism ; *Heterotrophic Processes ; *Models, Biological ; Bioreactors/microbiology ; *Bacteria/metabolism/genetics ; Gels ; Nitrates/metabolism ; Nitrites/metabolism ; }, abstract = {Partial denitrification (PD) has emerged as a pivotal technology for addressing the limited nitrite (NO2[-]) supply that hinders the widespread application of anammox, as it efficiently provides NO2[-]. However, its reliance on organic carbon sources restricts its broad implementation. In this study, a system of heterotrophic coupled with hydrogen-autotrophic PD was established using polyvinyl alcohol gel bio-carriers. Operated under a low COD/NO3[-]-N ratio of 2.00 for 90 days, the system achieved remarkable performances, with a NO2[-] transformation ratio (NTR) of 85.50 ± 3.10% and a nitrate (NO3[-]) removal rate (NRR) of 84.70 ± 5.00%. Metagenomic analysis revealed the effective enrichment ofHydrogenophaga(23.90%) as a key hydrogen-autotrophic denitrifier, which formed a functionally complementary consortium with heterotrophic denitrifiers (e.g.,Dokdonella). The abundance ratio of NO2[-] reduction genes in autotrophic to heterotrophic bacteria was 1.3:1. Furthermore, a putative metabolic model was constructed, which posits a potential cross-feeding interaction characterized by "hydrogen production by heterotrophs and consumption by autotrophs." The hydrogenase (EC:1.12.99.6) was proposed as a potential key gene facilitating this synergy between heterotrophic and autotrophic bacteria. The increased abundance ratio of nitrate reductase to nitrite reductase genes to 2.07 was identified as the key factor promoting the high accumulation of NO2[-]. Material characterization confirmed that the gel carriers possessed a hierarchical porous structure, with a mesopore-dominated pore size distribution conducive to hydrogen diffusion and the aggregation of functional microbial communities, thereby providing a stable micro-environment. This study offers a novel technological pathway for stable NO2[-] supply in the treatment of low-carbon wastewater.}, } @article {pmid42155841, year = {2026}, author = {Zhang, M and Sun, H and Ren, Y and Chen, K and Yan, G and Li, B and Huang, Y and Tan, Z and Sun, W}, title = {Thiosulfate drives vanadium natural attenuation in oligotrophic mine tailings: Insights from DNA-SIP and metagenomics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {403}, number = {}, pages = {128368}, doi = {10.1016/j.envpol.2026.128368}, pmid = {42155841}, issn = {1873-6424}, mesh = {*Thiosulfates/metabolism/chemistry ; *Mining ; *Vanadium/metabolism/analysis ; Metagenomics ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; Bacteria/metabolism/genetics ; Oxidation-Reduction ; }, abstract = {Vanadium (V) accumulation in mine tailing ponds represents a persistent contamination source, posing severe risks to the surrounding ecosystems. Microbial V(V) reduction represents a key pathway of V detoxification, immobilization and attenuation. While thiosulfate (S2O3[2-]), a prevalent byproduct in tailing ponds, is thermodynamically capable of driving V(V) reduction, the occurrence of the S2O3[2-]-driven V(V) reduction and its underpinning microbial mechanisms remain elusive. Here, we investigated the potential of S2O3[2-] to fuel V(V) natural attenuation in the tailing sediment. Microcosm experiments demonstrated that S2O3[2-] amendment significantly accelerated V(V) reduction rates by 1.8-fold compared to thiosulfate-free controls, confirming a stoichiometric coupling between V(V) reduction and S2O3[2-] oxidation. Pseudomonas, Symbiobacterium and Actinotalea were proposed as the active autotrophic taxa responsible for this coupling process using DNA-stable isotope probing (SIP) combined with metagenomics. Metabolic reconstruction revealed a resilient microbial network based on functional redundancy. These key taxa harbored denitrification-related reductases (NarGHI, NapAB, and NirS/K) and respiratory electron-transfer components (cytochrome c oxidases), together with distinct thiosulfate oxidation genes including thiosulfate dehydrogenase (TsdA/DoxD) and sulfurtransferases (TST/GlpE), indicating potential pathways for the S2O3[2-]-driven V(V) reduction process. These findings expand our understanding of the coupled S-V biogeochemical cycle and highlight the intrinsic natural attenuation capacity of tailing environments. This work provides a mechanistic basis for assessing the environmental fate and mobility of vanadium in oligotrophic habitats.}, } @article {pmid42156214, year = {2026}, author = {Wang, H and Chen, N and Feng, C and Mei, D and Gao, H and Liu, T}, title = {Carbon availability dictates the stability of nitrate-vanadium co-remediation in stratified biofilters.}, journal = {Water research}, volume = {302}, number = {}, pages = {126137}, doi = {10.1016/j.watres.2026.126137}, pmid = {42156214}, issn = {1879-2448}, mesh = {*Nitrates/metabolism ; *Carbon/metabolism ; Biodegradation, Environmental ; *Vanadium/metabolism/chemistry ; *Filtration/methods ; Denitrification ; *Water Pollutants, Chemical/metabolism ; Groundwater/chemistry ; }, abstract = {Thermodynamic hierarchies constrain the bioremediation of groundwater co-contaminated with nitrate (NO3[-]) and pentavalent vanadium (V(V)), denitrification preferentially consumes electron donors that would otherwise support metal reduction. Here, we show that spatial stratification of lignocellulosic residues (wheat straw → corn straw → corncob) can transiently alleviate competition between these competing processes, although system performance remains ultimately governed by carbon availability and kinetics. Over 330 days of operation, the stratified biofilter exhibited a biphasic response: (i) a carbon-sufficient phase (0 - 88 d) that enabled synergistic co-removal, increasing NO3[-] and V(V) loading capacities by up to 6.3-fold and 4.0-fold, respectively, relative to single-substrate controls; and (ii) a carbon-limited phase (88 - 330 d) in which denitrification persisted (>50% removal) while V(V) reduction collapsed (≈0%). Spatially resolved metagenomics (n = 15) revealed the mechanism as a thermodynamic "metabolic triage": under carbon limitation, microbial communities maintained denitrification pathways but selectively down-regulated V-reduction modules (sulfite reductase and multiheme cytochromes) by 59% - 69%. While distinct functional niches emerged-characterized by rapid efflux (top), deep reduction (middle), and sequestration (bottom), spatial organization alone could not override thermodynamic limits. Our findings establish that sustained metal co-remediation requires dynamic carbon management strategies to actuate latent genetic potential, providing a design framework for overcoming competitive inhibition in engineered aquifers.}, } @article {pmid42156216, year = {2026}, author = {Deng, X and Wang, Y and Zhu, H and Guo, Y and Wang, Q and Han, J and Yu, K and Zhou, B}, title = {Metagenomic profiling of resistome and mobilome dynamics in diverse freshwater aquaculture modes.}, journal = {Water research}, volume = {302}, number = {}, pages = {126133}, doi = {10.1016/j.watres.2026.126133}, pmid = {42156216}, issn = {1879-2448}, mesh = {*Aquaculture ; *Fresh Water ; Animals ; Metagenomics ; *Drug Resistance, Microbial/genetics ; *Metagenome ; }, abstract = {The widespread presence of antibiotic resistance genes (ARGs) in aquaculture environments poses a growing threat to public health. However, comprehensive understanding of ARG distribution and transmission potential across different freshwater aquaculture modes remains limited. This study employed integrated short- and long-read metagenomic sequencing to characterize the resistome, mobilome, and associated microbial communities across three predominant freshwater aquaculture modes (grass carp, crayfish, and crab ponds), using water, sediment, and intestinal samples analyzed at both contig and metagenome-assembled genome (MAG) levels. The results revealed that aquaculture modes and environmental media jointly shaped microbial and ARG compositions. At the contig level, the crayfish system harbored the highest relative abundance of both ARGs and mobile genetic elements (MGEs), with gut samples consistently emerging as the dominant reservoir across all modes. A significant positive correlation between ARG and MGE alpha diversity indicated that the gut microbiome, particularly in crayfish, provides a selective environment that co-enriches resistance genes and their mobile carriers. High-risk core ARGs (Rank I) were at least 19 times more abundant in the crayfish gut than in any other compartment, underscoring the intestinal microbiome as a hotspot for clinically relevant resistance accumulation. At the MAG level, over half of the recovered MAGs met near-complete or high-quality thresholds, and approximately 38% of ARG-carrying MAGs were classified as multidrug-resistant (MDR). MDR MAG abundance was significantly higher in gut than in sediment and water samples, with the crayfish gut as the most enriched compartment. Critically, several crayfish-associated MDR MAGs affiliated with Klebsiella aerogenes carried virulence factor genes (VFGs) and exhibited ARG-MGE-VFG co-localization within prophage sequences, suggesting phage-mediated co-dissemination of resistance and virulence traits. These findings highlight the intestinal microbiome of aquaculture species as a critical hotspot for resistance dissemination and provide a scientific basis for evaluating freshwater aquaculture-associated ARG risks under the One Health framework.}, } @article {pmid42156414, year = {2026}, author = {Maziers, N and Le Chatelier, E and Plaza Oñate, F and Fromentin, S and Thirion, F and Pons, N and Borruel, N and Casellas, F and Torrejon, A and Robles-Alonso, V and Manichanh, C and Varela, E and Derrien, M and Veiga, P and Oozeer, R and Sunagawa, S and Lombard, V and Terrapon, N and Henrissat, B and , and Guarner, F and Ehrlich, SD}, title = {Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44895-6}, pmid = {42156414}, issn = {2045-2322}, support = {ANR-11-DPBS-0001, MetaGenoPolis (MGP)//Agence Nationale de la Recherche/ ; FP7-HEALTH-F4-2007-201052, MetaHIT//Seventh Framework Programme/ ; }, abstract = {Inflammatory bowel diseases affect ever-increasing numbers of individuals worldwide. Alterations of the intestinal microbiome were reported for Crohn's disease and at relapse in Ulcerative Colitis (UC); they were not clearly detected in UC at remission. Here we report the characterization of the microbiome by quantitative metagenomics in a cohort of 121 individuals, composed of 65 UC adult patients in remission and 56 healthy controls. A cross-sectional comparison revealed substantial microbiome differences, patients in remission having lower microbiome richness and paucity of the Ruminococcus species driven enterotype. The observed microbiome alterations allowed robust classification of patients by intestinal species abundance, yielding an area under the curve (AUC) of 0.87 in a Receiver-Operator Characteristic (ROC) analysis. Loss of richness was linked to an aggressive UC phenotype and to the importance of past relapses; it was associated with a worse IBD quality of life score (IBDQ-36). Unexpectedly, onset of inflammatory bouts, as assessed by white blood cell count and fecal calprotectin levels, was associated with higher richness; in a longitudinal study of patients at high risk of disease flare, we observed a link between increasing gut microbiome richness over time and calprotectin level, in turn related to clinical inflammatory response and relapse.}, } @article {pmid42156610, year = {2026}, author = {Liu, Y and Shao, Q and Zhang, C and Zhang, F and Liu, J and Li, Y and Huang, Z}, title = {The dual role of gastric microbiota dysbiosis in gastric cancer progression and therapy.}, journal = {International journal of clinical oncology}, volume = {}, number = {}, pages = {}, pmid = {42156610}, issn = {1437-7772}, support = {82460559//National Natural Science Foundation of China/ ; 25JRRA1264//Gansu Provincial Joint Scientific Research Fund Major Project/ ; GSWSKY2024-06//Gansu Province Health Industry Science and Technology Innovation Major Projects/ ; CY2022-YB-A04//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; CY2024-MS-B18//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; No.CY2023-MS-B17//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; }, abstract = {Gastric cancer (GC) ranks among the most prevalent malignant neoplasms globally and is one of the leading causes of cancer-related mortality. The gastric microbiota, as a crucial component of the human microecosystem, plays a pivotal role in maintaining human health through its ecological balance. In recent years, with the advancement of technologies such as metagenomics, the dysbiosis of gastric microbiota has increasingly become a focal point of research, particularly in understanding its role in the initiation, progression, and treatment of GC. This review elucidates the current understanding of the roles played by gastric microbiota and their metabolic products in the progression of GC. Additionally, it summarizes and prognosticates the translational value and clinical significance of gastric microbiota in the diagnosis, prognosis, and treatment of GC. The gastric microbiota assumes a dual role in the progression and treatment of GC. Further in-depth studies on the interactions and mechanisms between gastric microbiota and the host represent an emerging and valuable area in the field of GC research.}, } @article {pmid42156647, year = {2026}, author = {Ravikrishnan, A}, title = {Unlocking the Metagenome: Pipeline for Microbiome Data Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {1-23}, pmid = {42156647}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Software ; Workflow ; Sequence Analysis, DNA/methods ; Humans ; Data Analysis ; }, abstract = {Metagenomic technologies have revolutionized our understanding of microbes in different spheres of life, revealing the massive diversity and complex functionalities of microbial communities across various environments. Shotgun metagenomics, which involves sequencing the DNA of all the organisms in a sample, is emerging as a powerful tool in assessing the microbial content. Unlike the traditional culturing approach, the shotgun metagenomic technology provides a comprehensive view of the entire microbial community, including potential functions that the organisms could be performing. In this chapter, we describe a typical bioinformatics workflow to generate the taxonomic profiles from metagenomic sequencing data and demonstrate a few basic statistical analyses that can be performed from this data to generate insights. In addition, we discuss the experimental and analytical considerations that must be taken into account while generating and making inferences from metagenomic data. Lastly, we provide insights on automating the workflow for consistent and reproducible large-scale analyses.}, } @article {pmid42156648, year = {2026}, author = {Yugandhar Reddy, BS and Sripradha, S and Kumar, A}, title = {Targeted Metagenomics Using Next-Generation Sequencing Methods.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {25-32}, pmid = {42156648}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Microbiota/genetics ; Metagenome ; Humans ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomics allows the discovery of the full diversity of all microbes present in a given niche. The technique is very powerful and has allowed very significant advances delineating the role of the microbiome in several disciplines including health, agriculture, ecology, industry, etc. Here, we describe the method required for processing of samples for metagenomic analysis using Next-Gen sequencing.}, } @article {pmid42156649, year = {2026}, author = {Rangamaran, VR and Sushmitha, TJ and Tamilmani, KK and Murugesan, H and Gopal, D}, title = {Exploring the Ocean's Microbial World: Techniques and Protocols for Microbiome Research.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {33-46}, pmid = {42156649}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Oceans and Seas ; *Seawater/microbiology ; Computational Biology/methods ; }, abstract = {Marine microbiomes play a crucial role in oceanic ecosystems, influencing biogeochemical cycles, climate regulation, and marine biodiversity. Accurate characterization of these microbial communities requires standardized protocols for sample collection, processing, sequencing and data analysis. This chapter provides a comprehensive guide to essential methodologies for marine microbiome research including field sampling strategies, DNA and RNA extraction techniques, high-throughput sequencing approaches (such as 16S rRNA amplicon sequencing and metagenomics) and bioinformatics pipelines for data interpretation. Additionally, we discuss quality control measures, best practices for reproducibility, and challenges associated with marine microbiome profiling. By adopting standardized methodologies, researchers can generate reliable, comparable datasets that enhance our understanding of marine microbial ecology and its broader environmental implications.}, } @article {pmid42156650, year = {2026}, author = {Miliotis, G and Tumeo, A}, title = {Shotgun Metagenomic Analysis of Microbial Community Dynamics in Wastewater Treatment Through Constructed Wetlands.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {47-73}, pmid = {42156650}, issn = {1940-6029}, mesh = {*Wetlands ; *Metagenomics/methods ; *Wastewater/microbiology ; *Water Purification/methods ; *Microbiota/genetics ; Metagenome ; Computational Biology/methods ; Water Microbiology ; }, abstract = {Constructed wetlands (CWs) offer a sustainable, nature-based solution to wastewater treatment, supporting diverse and dynamic microbial communities that drive nutrient cycling, pollutant degradation, and pathogen removal. This chapter presents an end-to-end methodology for performing shotgun metagenomic analyses on microbial populations from CW influent and effluent. We detail approaches for site selection, sample collection, filtration, DNA extraction, and the incorporation of positive and negative controls to ensure reproducibility and data quality. Two modular bioinformatic workflows encompassing quality control, assembly, taxonomic/functional annotation, and metagenome-assembled genome recovery are described alongside options for detecting antimicrobial resistance genes, pathogens, toxins, and plasmids. In addition, an example workflow for the calculation of alpha and beta diversity is provided. Guidelines for data standardization, replication, and compliance with community-driven reporting standards (MIMS, MIMAG) are also included. Incorporating this protocol will facilitate standardized, reproducible insights into CW microbial dynamics, thereby informing ecological understanding and guiding practical interventions that enhance wastewater treatment efficacy and improve public health outcomes.}, } @article {pmid42156652, year = {2026}, author = {Kosmopoulos, JC and Anantharaman, K}, title = {Computational Microbial and Viral Ecology Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {83-141}, pmid = {42156652}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; Metagenome ; *Microbiota/genetics ; *Viruses/genetics/classification ; Virome ; Bacteriophages/genetics ; Bacteria/genetics ; Archaea/genetics ; }, abstract = {The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics have revealed that interactions between diverse groups of community members such as archaea, bacteria, and viruses (bacteriophages) are common and have significant impacts on entire microbiomes. Thus, to have a well-developed understanding of microbes as they naturally exist in the environment, biological entities of all kinds must be studied together. While numerous protocols for metagenome analysis exist, comprehensive published protocols for the simultaneous analysis of viruses and prokaryotes together are scarce. Further, as bioinformatic methods for microbiology rapidly advance, existing metagenomic tools and pipelines require frequent re-evaluation. This ensures the adherence to best practices for microbiome and metagenomic data analysis. Here, we offer an expansive approach for the joint analysis of bulk sequence data from a mixed microbial community (metagenomes) and viral-sized fraction communities (viromes). This chapter serves as a beginner's-level guide for researchers with limited bioinformatics expertise who wish to engage in multiscale metagenome and virome analyses. We cover steps from initial study design to sequence read processing, metagenome assembly, quality control, virus identification, microbial and viral genome binning, taxonomic characterization, species-level clustering, and host-virus predictions. We also provide the bioinformatic scripts used in our workflow for reuse in one's own computational methods. Lastly, we discuss additional approaches a researcher can take after processing data with this workflow.}, } @article {pmid42156658, year = {2026}, author = {Roma Pi, J and Heinken, A}, title = {Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {233-260}, pmid = {42156658}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; Humans ; *Gastrointestinal Microbiome/genetics ; Precision Medicine/methods ; Software ; *Microbiota/genetics ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; Systems Biology/methods ; }, abstract = {High-throughput metagenomic sequencing techniques such as 16S rRNA and shotgun sequencing have enabled an unprecedented understanding of the structure and function of microbiome communities such as the human gut microbiome. Tailored dietary or therapeutic interventions targeting the microbiome could advance personalized medicine; however, predicting such interventions requires predictive systems biology methods. Constraint-Based Reconstruction and Analysis (COBRA) is a mechanistic systems biology approach that relies on detailed genome-scale reconstructions of a target organism's metabolism. A resource of genome-scale reconstructions of human microbes, AGORA, and its expansion in size and scope, AGORA2, have been developed through a semi-automated refinement pipeline, DEMETER. A user-friendly analysis pipeline, mgPipe, allows building and interrogating personalized models of microbiome communities from AGORA and AGORA2. Through sample-specific simulations, mgPipe can stratify patients and controls by the distinct metabolic capabilities of their microbiomes, starting from the processed metagenomic sequencing data. Building on this functionality, the protocol provides a comprehensive workflow for the contextualization of metagenomics data through personalized, mechanistic modeling. Comprehensive tutorials for the DEMETER and mgPipe workflows are presented, which will enable both systems biologists and microbiome scientists to contextualize metagenomic data and perform mechanistic simulations of diet-microbiome-host interactions.}, } @article {pmid42156769, year = {2026}, author = {Chen, R and Luo, S and Feng, Y and Maestre, FT and Sáez-Sandino, T and Gross, N and Le Bagousse-Pinguet, Y and Ochoa, V and Gozalo, B and Guirado, E and García-Gómez, M and Valencia, E and Asensio, S and Martínez-Valderrama, J and Mendoza, BJ and Abades, S and Alfaro, F and Barrett, M and Berdugo, M and Pastor, JLB and Blaum, N and Boldgiv, B and Bowker, M and Castro, H and Chu, H and Cutler, NA and Dai, Z and Deák, B and Durán, J and Espinosa, CI and Fajardo, A and Fan, K and Foronda, A and Fraser, LH and Geissler, K and Grebenc, T and Moltanvan, EG and Hart, SC and Kindermann, L and Köbel, M and Laanisto, L and le Roux, PC and Liancourt, P and Linstädter, A and Louw, MA and Macek, P and Maggs-Kölling, G and Makhalanyane, TP and Manzaneda, AJ and Marais, E and Montesinos, D and Mora, JP and Moreno, G and Munson, SM and Muñoz-Rojas, M and Nair, GR and Neuhauser, S and Nunes, A and Plaza, C and Pueyo, Y and Rey, PJ and Rey, A and Ríos, AL and Rodríguez, A and Lozano, BR and Roman, R and Ruppert, JC and Salah, A and Singh, J and Throop, HL and Travers, S and Nahberger, TU and Uuganbayar, M and Valkó, O and Wang, L and Williams, MA and Xiong, C and Xu, J and Zaady, E and Ma, B and Singh, BK and Delgado-Baquerizo, M}, title = {Functional restructuring of the global soil microbiome under multiple stressors.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73231-9}, pmid = {42156769}, issn = {2041-1723}, support = {42577352//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Microbes, as the planet's most abundant and diverse organisms, drive soil functions globally and are vulnerable to environmental stressors triggered by global change. Yet, knowledge regarding the impacts of multiple environmental stressors on their functional profiles as well as the consequences for soil functionality largely remains unknown. Here, we analyze two global-scale datasets including information on soil metagenomics and multiple environmental stressors. We find that across terrestrial ecosystems worldwide, up to 60% of all functional genes significantly shift when soil microbes experience the high-level of concurrent stressors. In this regard, the relative abundances of genes involved in microbial growth are negatively linked to the increasing number of stressors. Conversely, those genes linked to stress resistance and energy production exhibit positive responses. Taken together, our findings highlight a significant restructuring of global soil functional microbiomes in response to multiple environmental stressors. Consequently, such restructuring drives community-level shifts in matter and energy reallocations, thereby impacting the maintenance of soil functionality under the projected global change.}, } @article {pmid42156772, year = {2026}, author = {Bamberger, T and Muller, E and Algavi, YM and Greenier, A and Adjangba, C and Slikas, E and Brassington, L and Mariner, B and McCoy, B and Harrison, BR and Partida-Aguilar, M and Marye, A and Harris, A and Rout, E and , and Avery, A and Promislow, DEL and Snyder-Mackler, N and Borenstein, E}, title = {Mapping the canine gut microbiome: insights from the Dog Aging Project.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73193-y}, pmid = {42156772}, issn = {2041-1723}, support = {U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; }, abstract = {Companion dogs (Canis lupus familiaris) offer a unique model for studying the gut microbiome and its relation to aging due to their cohabitation with humans, sharing similar environments, diets, and healthcare practices. Here, we present the Dog Aging Project (DAP) Precision cohort, a large population-wide study of the canine gut microbiome. This cohort encompasses over 900 dogs of diverse breeds, environments, and demographics living across the United States. Coupling fecal shotgun metagenomic sequencing with phenotypic and environmental surveys and clinical lab tests, we explore the intricate relationships between microbiome composition, aging, and key factors such as health and living conditions. Our analyses identify multiple factors associated with microbiome composition, including dietary preferences such as commercial versus home cooked nutrition, and behaviors such as coprophagy (feces eating). In addition, we find age-associated gradual shifts in microbiome composition, supporting the development of a metagenomics-based population-level model for canine age prediction based on microbial signatures. We further examined which age-associated microbial patterns observed in humans are recapitulated in dogs by comparing our cohort with the Lifelines-DEEP cohort. Overall, these findings offer insights into the role the gut microbiome plays in our four-legged companions, with potential implications for veterinary medicine and translational aging research.}, } @article {pmid42157110, year = {2026}, author = {Al Achkar, N and Privitera, GF and Arena, D and Nicotra, R and Ciccarello, L and Rizzo, GF and Pulvirenti, A and Spatafora, M and Restuccia, C and Branca, F}, title = {Exogenous microbial consortia modulate rhizosphere microbiome and yield of grafted tomato grown in the mediterranean greenhouse.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-08962-4}, pmid = {42157110}, issn = {1471-2229}, support = {CN00000022//AGRITECH National Research Center (European Union Next-Generation EU, PIANO NAZIONALE DI RIPRESA E RESILIENZA, PNRR - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4-D.D. 1032 17/06/2022)/ ; }, abstract = {BACKGROUND: The adoption of sustainable agricultural practices for intensive horticultural production could determine less damage to the ecosystem is a fundamental need increasing worldwide. In this trial the effect of two commercial microbial consortia, applied on two hybrid rootstocks of tomato grafted by two scions, were evaluated both on yield components and on the compositions of the rhizosphere microbiome. The rhizosphere was collected from each grafting combination, in both treated and non-treated plots. Microbiome DNA extracted was then sequenced by amplifying two specific regions ITS1-1F for fungus and 16SV34 for bacteria.

RESULTS: At the morphological level, the effect of microbial consortia application on the total production and yield showed to be highly dependent on the grafting combination, yield increased by 9.1, 10.3 and 12.6% in treated plots of Auto S2, R1/S1 and R1/S2 respectively but registered a reduction of 22.4% in NG.S2 and 9.3% in R2/S2 plots. The metagenomic sequencing revealed that fungal community composition was significantly influenced by both grafting combinations and microbial treatments (especially on the relative abundance of major phyla; Ascomycota and Basidiomycota), whereas bacterial communities exhibited stronger shifts in response to microbial consortia application than to grafting combinations. Correlation analysis between the rhizosphere microbial taxa, yield, and root weight highlighted significant associations supporting the potential of combined use of these practices. Notably, although the inoculated microorganisms were detected at low abundance or were not detectable in treated soils, pronounced shifts in the overall microbiome structure were observed, suggesting indirect yet significant ecological effects of the consortia.

CONCLUSION: This study demonstrates that microbial consortia and grafting synergistically enhance tomato productivity and modulate rhizosphere microbial communities in the monoculture degraded soil under intensive Mediterranean greenhouse conditions. These findings advance current understanding of plant genotype × microbial consortium interactions by demonstrating that microbial inoculant relevant effects are highly modulated by plant genotype and can indirectly restructure rhizosphere microbial assemblages, contributing to the development of more sustainable and resilient horticultural systems.}, } @article {pmid42157119, year = {2026}, author = {Li, QX and Luo, LZ}, title = {Cutaneous MAC infection in an immunocompetent patient: a case report confirmed by mNGS.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13549-3}, pmid = {42157119}, issn = {1471-2334}, abstract = {BACKGROUND: Cutaneous infections caused by non-tuberculous mycobacteria (NTM) are rare. Atypical clinical manifestations and the need for precise microbiological identification often result in misdiagnosis and underdiagnosis.

CASE PRESENTATION: A 65-year-old immunocompetent female initially presented with papular urticaria. Her symptoms improved transiently after anti-inflammatory treatment, but the lesions rapidly progressed to generalized erythematous nodules and ulcers accompanied by fever and lymphadenopathy. Routine microbiological culture and histopathological examination yielded negative results, while metagenomic next-generation sequencing (mNGS) identified Mycobacterium avium complex (MAC) as the causative pathogen.Triple antimicrobial therapy (clarithromycin, doxycycline, and levofloxacin) a favorable clinical response. This case indicates that cutaneous non-tuberculous mycobacterial (NTM) infection has atypical clinical manifestations and is frequently misdiagnosed as common cutaneous eruptions. mNGS can serve as a key diagnostic tool for suspected cutaneous NTM infection, effectively reducing misdiagnosis and missed diagnosis and providing a reliable basis for clinical diagnosis and treatment.

CONCLUSION: Cutaneous MAC infection, though rare, may occur in immunocompetent individuals. Clinicians should suspect NTM infection in treatment-refractory skin lesions. mNGS is valuable for etiological diagnosis when conventional tests are negative.}, } @article {pmid42157131, year = {2026}, author = {Ji, T and Cheng, R and Lu, M}, title = {mNGS and IL-5: potential early diagnostic clues for clonorchiasis before eosinophil rise - a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13612-z}, pmid = {42157131}, issn = {1471-2334}, support = {2022YFC2303203-01//National Key R&D Program of China/ ; Z-2017-24-2202//Specialized Research Fund for Pathogenic Metagenomics of the Bacterial Infection and Drug Resistance Prevention of the Chinese Medical Association/ ; }, abstract = {Clonorchiasis, caused by Clonorchis sinensis, often evades early diagnosis in non-endemic regions due to its nonspecific presentation and the delayed appearance of eosinophilia. We report an informative case of a 56-year-old male with acute fever, abdominal pain, and hepatitis, where conventional diagnostics and initial antimicrobial therapy failed. In this case, metagenomic next-generation sequencing (mNGS) of blood identified C. sinensis-specific reads, and cytokine profiling revealed a marked elevation in interleukin-5 (IL-5) before the onset of peripheral eosinophilia. Targeted treatment with praziquantel led to rapid clinical resolution. This case suggests the potential of integrating mNGS and IL-5 monitoring as early diagnostic tools for clonorchiasis, which can allow for intervention prior to classical biomarker emergence.}, } @article {pmid42157143, year = {2026}, author = {Sheng, G and Zhao, C and Jiang, L and Zhang, X and Gao, F}, title = {Talaromyces marneffei infection of central nervous system in an immunocompetent child in a nonendemic area: a case report and literature review.}, journal = {BMC pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12887-026-06996-z}, pmid = {42157143}, issn = {1471-2431}, abstract = {BACKGROUND TALAROMYCES MARNEFFEI: (T. marneffei, formerly Penicillium marneffei) is a rare fatal fungus endemic in Southeast Asia and southern China. T. marneffei infections mainly occur in HIV-infected adults, and commonly involves the skin, lung, and reticuloendothelial system. T. marneffei infections of isolated central nervous system (CNS) in immunocompetent pediatric patients in nonendemic areas have rarely been reported. CASE PRESENTATION: We report a rare case of T. marneffei-induced disseminated encephalomyelitis in an immunocompetent girl from a nonendemic area of Eastern China. The main clinical manifestations were abdominal pain with distension and abnormal gait. Contrast-enhanced magnetic resonance imaging (MRI) revealed both brain and spinal cord lesions. The infection status of T. marneffei was quickly determined via the metagenomic next-generation sequencing (mNGS) of spinal cord biopsy tissue. T. marneffei induced disseminated encephalomyelitis was diagnosed. Following successful antifungal treatment with amphotericin B liposomes and voriconazole, the child recovered gradually. To date, only 3 cases of T. marneffei infection of the central nervous system in non-HIV-infected pediatric patients have been reported in the literature. Among them, one child had inborn errors of immunity, and the other two children were from endemic areas. Moreover, the clinical manifestations of those 3 reported cases were disseminated with common infection sites in the lungs. our patient represents a unique case of an immunocompetent child from a nonendemic area with isolated CNS infection. CONCLUSIONS: We report this rare case and aim to promote pediatric clinicians' recognition of T. marneffei isolated CNS infection in immunocompetent pediatric patients from nonendemic regions. Furthermore, the early use of mNGS is recommended when non-HIV-infected pediatric patients present with unexplained clinical manifestations and poor response to conventional treatments. Timely diagnosis and appropriate antifungal therapy can improve patient prognosis.}, } @article {pmid42157342, year = {2026}, author = {Jing, Y and Liu, S and Leng, L and He, J and Wang, T and Guan, Y and Su, Z and Zhang, W and Li, Y and Luan, P and Cheng, B and Wang, N and Li, H}, title = {Microbiota transplantation and multi-omics profiling integration unveil the mechanism of Alistipes communis-driven abdominal fat deposition in chickens.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42157342}, issn = {1674-9782}, support = {No. 2022YFF1000201//National Key Research and Development Program of China/ ; No. NK20221001//National Major Agricultural Science and Technology Project/ ; No. 32272863//National Natural Science Foundation of China/ ; No. CARS-41//The earmarked fund for CARS-41/ ; }, abstract = {BACKGROUND: Emerging evidence highlights strong correlations between the cecal microbiome and abdominal fat deposition (AFD) in chickens. However, the specific microbial species driving this process remain unclear. This study aims to identify the key microbe and elucidate its underlying mechanism in regulating chicken AFD.

RESULTS: First, cecal microbiota transplantation confirmed a causal relationship between the cecal microbiota and AFD. Subsequently, metagenomic and metatranscriptomic integrations identified Alistipes communis as a key microbe implicated in AFD. Finally, in vivo gavage integrated with multi-omics revealed that A. communis enhances AFD by disrupting host tryptophan and histidine metabolism. This was evidenced by the elevated concentrations of amino acid metabolism-related metabolites, including L-phosphoarginine and spermine in the cecum.

CONCLUSIONS: This study provides direct evidence that the cecal microbiome serves as a key driver in chicken AFD and identifies A. communis as a critical AFD regulator, offering valuable insights into the gut microbiome's role in host obesity.}, } @article {pmid42157352, year = {2026}, author = {Pérez-Pérez, L and Galisteo, C and Castillo-Peinado, LLS and Tomé-Rodríguez, S and Priego-Capote, F and Carvajal, A and Arguello, H}, title = {Metabolomic signatures of colonic infection by Brachyspira hyodysenteriae.}, journal = {Veterinary research}, volume = {57}, number = {1}, pages = {}, pmid = {42157352}, issn = {1297-9716}, support = {PRE2020-093762//Spanish Ministerio de Ciencia, Innovación y Universidades/ ; LE088P23//Junta de Castilla y León/ ; }, mesh = {Animals ; Swine ; *Brachyspira hyodysenteriae/physiology ; *Swine Diseases/microbiology/metabolism ; *Gram-Negative Bacterial Infections/veterinary/microbiology/metabolism ; *Metabolome ; Colon/metabolism/microbiology ; Gastrointestinal Microbiome ; *Dysentery/veterinary/microbiology/metabolism ; Feces/microbiology ; Metabolomics ; }, abstract = {Despite swine dysentery's relevance in the pork industry, there are still gaps in our understanding of its pathogenesis and the impact of the infection in the gut. This study aimed to characterize the in vivo colonic metabolome of pigs experimentally infected with Brachyspira hyodysenteriae at the onset of fecal shedding (Early_inf group, n = 6) and during acute clinical disease characterized by mucohemorrhagic diarrhea (Acute_inf group, n = 8) compared with non-infected controls (n = 16). The metabolic profile of the colonic contents changed progressively with disease severity, showing an intermediate pattern in the Early_inf group between the control and the Acute_inf groups (p < 0.05). In acute disease, the metabolome was defined by increased concentrations of amino acids, carnitine derivatives, arachidic acid, 1,2-butanediol, and lactic acid, along with decreased levels of anti-inflammatory compounds. In the Early_inf group, increases were observed in amino acids, organic acids, amines, myo-inositol, quinoline, and 1,2-butanediol, whereas linolenic acid and oxalic acid decreased. Integrated analysis of the colonic metabolome and metagenome revealed a strong correlation between metabolic and microbial profiles, particularly in the Acute_inf group, where differential metabolites were associated with B. hyodysenteriae, Campylobacter hyointestinalis, and Velocimicrobium ethanolgignens. Metabolites showed high predictive potential for the disease stage, with lactic acid and arachidic acid being key markers of acute infection and dihydroxyacetone and leucine distinguishing early infection. Overall, this study reveals significant alterations in the colonic metabolome and its association with the microbiota during swine dysentery, providing new insights into the pathophysiology of the disease and contributing to the development of improved prevention and treatment strategies.}, } @article {pmid42157462, year = {2026}, author = {Singh, HW and Gutleben, J and Bogdanov, A and Chase, AB and Demko, A and Podell, S and Haley, B and Jensen, PR}, title = {Multi-Omic Assessment of Microbial Communities and Their Polyketide Biosynthetic Potential Across Abyssal Sediments.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70320}, doi = {10.1111/1462-2920.70320}, pmid = {42157462}, issn = {1462-2920}, support = {R01GM085770/NH/NIH HHS/United States ; }, mesh = {*Geologic Sediments/microbiology ; *Polyketides/metabolism ; Phylogeny ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Polyketide Synthases/genetics/metabolism ; Metagenome ; Seawater/microbiology ; Biodiversity ; Multiomics ; }, abstract = {Microbially-derived polyketides include some of today's most valuable medicines, yet their discovery has focused on a narrow subset of Earth's microbial biodiversity. Although understudied biomes such as marine sediments have been targeted, these efforts have focused on samples collected from shallow waters. In contrast, abyssal marine sediments (4000-6000 m), which comprise > 80% of the ocean floor, remain poorly explored. This leaves foundational gaps in our understanding of deep-sea microbial diversity and its relationship to biosynthetic potential. Here, we used culture-independent approaches to characterise microbial taxonomic and biosynthetic diversity in abyssal sediments collected from three geochemically distinct plains along an 880 km transect. Sediment communities varied in both taxonomic (16S rRNA gene) and biosynthetic (ketosynthase domain) composition across sites and relative to nearshore sediments, suggesting they harbour unique opportunities for natural product discovery. Ketosynthase phylogenies revealed abyssal clades that diverged from experimentally characterised polyketide synthase pathways, further supporting biosynthetic novelty. Metagenome-assembled genomes linked unique ketosynthase domains to the poorly studied phylum Gemmatimonadota. Sediment metabolomes provided evidence of chemical novelty, with < 10% of the features detected matching previously reported spectra. These baseline findings indicate that abyssal sediments represent reservoirs of unexplored polyketide biosynthetic diversity.}, } @article {pmid42158361, year = {2026}, author = {Louise Jespersen, M and Kjærgaard Munk, K and Fjermedal, S and Pilgaard, B and Meyer, AS and Aarestrup, FM and Otani, S}, title = {A Hadza-enriched Prevotella/Segatella xyloglucanase shows sequence conservation and functional specialization.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2673265}, pmid = {42158361}, issn = {2993-3935}, abstract = {Bacteria can adapt to their environment through changes in their genetic material. A large proportion of gut bacteria are shaped by host-specific diet, including complex carbohydrates. The bacterial abundance, genetic content within the same bacterial species, and sequence-level variation in genes encoding similar carbohydrate-processing enzymes may therefore vary across hosts with different diets. We previously found that the abundance of diet-degrading genes varies between hominid host populations from Tanzania. We therefore hypothesized that, in addition to these abundance differences, selective pressure could act on individual gene sequences. Here, we investigated Tanzanian hominid gut microbiome differences at the taxonomic, genetic, structural, and functional levels. We analyzed 15,146 metagenome-assembled genomes (MAGs) spanning 1563 species and identified one species with striking host-associated separation. In particular, sequence variation in a xyloglucanase-encoding gene correlated strongly with the host population. This gene was highly conserved in the Hadza population, suggesting a role in the processing of diet-associated polysaccharides. Sequence differences and structural modeling revealed amino acid substitutions near the catalytic site, and biochemical assays using xyloglucan showed that representative variants differed in activity under identical assay conditions. Collectively, our findings suggest that host lifestyle and diet contribute to population-associated sequence variation in genes encoding enzymes involved in degrading polysaccharides.}, } @article {pmid42158572, year = {2026}, author = {Wong, E and England, J and Jagadeesan, V}, title = {Scedosporium apiospermum Infective Endocarditis With Brain Abscesses in a Lung Transplant Recipient: Review of the Literature and Evaluating the Use of Next-Generation Sequencing.}, journal = {Case reports in infectious diseases}, volume = {2026}, number = {}, pages = {8041837}, pmid = {42158572}, issn = {2090-6625}, abstract = {Scedosporium apiospermum is an emerging cause of invasive mold infection in immunocompromised hosts, often with central nervous system involvement and limited susceptibility to amphotericin B. We describe a 36-year-old lung transplant recipient who presented with fever, meningismus, and multiple enhancing brain lesions nine months post-transplant. Cerebrospinal fluid studies, including metagenomic next-generation sequencing (mNGS), were negative. Cardiac imaging revealed a pedunculated right ventricular septal mass, and plasma cell-free DNA (cfDNA) testing (Karius) identified S. apiospermum. Subsequent brain biopsy and thrombectomy confirmed the diagnosis by histopathology and culture. Following surgical removal of the cardiac mass and treatment with voriconazole, the patient improved with near resolution of brain lesions. This case highlights disseminated S. apiospermum endocarditis diagnosed by plasma cfDNA despite negative CSF mNGS, underscoring that site-specific mNGS may be falsely negative in compartmentalized infections. Plasma cfDNA testing can complement conventional and tissue-based diagnostics for early detection of disseminated mold infections in transplant recipients.}, } @article {pmid42158968, year = {2026}, author = {Shi, Z and Huang, F and Luo, C and Yang, L and Chen, Y and Qiao, C and Wang, R and Wang, Y and Yan, Y and Wang, L and Fan, L and Shen, W}, title = {Gut Microbiota Alterations in Myelodysplastic Neoplasms Are Associated With Immune Dysfunction and the Therapeutic Mechanism of Hypomethylating Agents.}, journal = {Cancer medicine}, volume = {15}, number = {5}, pages = {e71946}, pmid = {42158968}, issn = {2045-7634}, support = {82200151//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Myelodysplastic Syndromes/drug therapy/immunology/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Dysbiosis/immunology ; Case-Control Studies ; DNA Methylation/drug effects ; Feces/microbiology ; Aged, 80 and over ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Adult ; }, abstract = {BACKGROUND: Myelodysplastic neoplasms (MDS) represent a group of heterogeneous clonal disorders characterized by immune dysregulation in their pathogenesis. Gut microbiota dysbiosis plays a critical role in immune modulation.

METHODS: We collected the fecal samples of 23 newly diagnosed MDS, 10 hypomethylating agents (HMA) treated MDS and 13 age and sex matched healthy controls (HC), and analyzed the gut microbiota compositions and functional pathways using metagenomic next-generation sequencing (mNGS).

RESULTS: Distinct microbial compositions were observed between newly diagnosed MDS and HC. Notably, the Veillonellaceae family was significantly enriched in MDS patients. Specific bacteroid species demonstrated significant correlations with lymphocyte subtypes, functional activation status, and serum inflammatory cytokines. Functional profiling revealed altered metabolic pathways in newly diagnosed patients, particularly in amino acid metabolism and ATP synthesis. Notably, glutamine/glutamate and tryptophan metabolism pathways were hyperactive in untreated MDS but downregulated following HMA treatment.

CONCLUSIONS: The gut microbiota altered in MDS patients and was associated with immune dysregulation and inflammation, which may contribute to MDS pathogenesis and mediate therapeutic effects of HMA treatment, highlighting the gut microbiota-metabolism axis as a potential therapeutic target for MDS management.}, } @article {pmid42159114, year = {2026}, author = {Li, Y and Liu, J and Hu, W and Li, C and Zhang, L and Qiu, S and Zhu, S}, title = {The Value of Second-Generation Metagenomic Sequencing in the Diagnosis of Respiratory Infections.}, journal = {Clinical laboratory}, volume = {72}, number = {5}, pages = {}, doi = {10.7754/Clin.Lab.2025.250525}, pmid = {42159114}, issn = {1433-6510}, mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; Male ; Female ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Retrospective Studies ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Adult ; *Bacteria/genetics/isolation & purification ; Young Adult ; Aged, 80 and over ; }, abstract = {BACKGROUND: This study aimed to compare the results of metagenomic next-generation sequencing (mNGS) and conventional culture detection of pathogenic bacteria in bronchoalveolar lavage fluid (BALF) of patients with respiratory tract infections and analyze the influencing factors and clinical significance of mNGS positive detection.

METHODS: We retrospectively analyzed BALF samples from 90 respiratory infection patients at the First People's Hospital of Yongkang City from June 1, 2024, through January 28, 2025, using mNGS and conventional culture testing to compare the positivity rate, pathogen distribution, and consistency of the two methods. The relationship between mNGS detection positivity and clinical indicators of patients and patient prognosis was analyzed.

RESULTS: The positive rate of mNGS detection was 77.78%, while the positive rate of conventional culture detection was 44.44%, and the difference was statistically significant (p < 0.05). mNGS can detect a wider variety of pathogens, mainly gram-negative bacilli, fungi, and atypical pathogens. mNGS has moderate consistency with conventional culture detection results in bacteria, fungi, and atypical pathogens, but low consistency in viruses and para-sites. The positive detection of mNGS is related to factors such as patient age, underlying diseases, peripheral blood white blood cells, and C-reactive protein, which are risk factors affecting the positive detection of mNGS.

CONCLUSIONS: The pathogenic diagnosis of mNGS in BALF of patients with lower respiratory tract infections is su-perior to conventional culture detection; it can detect more and a wider range of pathogens, helping to promote rational drug use and improve patient prognosis in clinical practice.}, } @article {pmid42159601, year = {2026}, author = {Yang, Y and Lian, S and Li, X and Tang, Y and Su, Y and Zhang, Z and Li, M and Guo, Y and He, Z and Shen, Y}, title = {Unveiling metagenomic and metabolomic signatures in mild and severe pneumonia caused by Mycoplasma pneumoniae in children.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42159601}, issn = {2057-5858}, mesh = {Humans ; *Mycoplasma pneumoniae/genetics/pathogenicity/metabolism ; *Pneumonia, Mycoplasma/microbiology/metabolism/diagnosis ; Female ; Male ; Child, Preschool ; Child ; *Metagenomics/methods ; *Metabolomics/methods ; Prospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Infant ; Severity of Illness Index ; Microbiota ; Machine Learning ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Background. Mycoplasma pneumoniae (MP) is a common causative pathogen of community-acquired pneumonia in children, with clinical presentations ranging in severity. Early stratification and timely intervention are essential for improving patient outcomes. However, a major clinical challenge lies in the limited ability to accurately distinguish between mild and severe cases based solely on early clinical indicators.Methods. This prospective real-world study investigated the differences in microbiome and metabolomics between mild and severe MP pneumonia (MPP) in children. Bronchoalveolar lavage fluid samples were collected from 153 children and subjected to metagenomic sequencing and non-targeted metabolomic analysis. Meanwhile, to enhance early diagnostic accuracy, this study developed a machine learning classification model and validated it using a third-party validation set.Results. The results revealed significant alterations in the abundance of specific bacterial communities in the severe group, most notably the coexistence of MP and Alphainfluenzavirus influenzae, which may contribute to disease exacerbation through synergistic pathogenic mechanisms. Furthermore, the macrolide resistant rate of MP in the severe group exceeded 80%, emphasizing the importance of appropriate antibiotic selection. Metabolomic analysis showed a significant enrichment of metabolites related to cellular energy metabolism and immune regulation in severe cases. The model demonstrated exceptional predictive performance, achieving an area under the curve ranging from 0.909 to 0.991, which significantly outperformed conventional clinical stratification methods.Conclusions. These findings elucidate the distinct pathophysiological mechanisms underlying both mild and severe MP infections and provide a promising framework for improving early diagnosis and personalized treatment strategies in paediatric MPP.}, } @article {pmid42159642, year = {2026}, author = {Ortigoza, PYA and Luiz, FN and Ghellere, GJ and Meyer, RF and Rosa, LH and Passarini, MRZ}, title = {Biogas production using the microbial community present in the soil from Deception Island, maritime Antarctica.}, journal = {Environmental science and pollution research international}, volume = {33}, number = {17}, pages = {8426-8435}, pmid = {42159642}, issn = {1614-7499}, support = {118/2024//Institutional Program to Support Research Groups/ ; 440218/2023-3//CNPq PROANTAR/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Methane/biosynthesis ; *Biofuels ; Archaea/genetics/metabolism/classification ; Islands ; }, abstract = {The current energy crisis is increasing the production of sustainable energy, such as biogas, a fuel generated by the anaerobic digestion of organic waste. The use of oat, an agricultural waste, makes the anaerobic digestion more sustainable. Antarctic microbial communities can utilize a wide range of substrates and adapt to different temperatures. Thus, this study evaluated methane production through an innovative approach, using microbial enrichment, and assessed archaeal diversity through metagenomic techniques in Antarctic soils, Deception Island, Maritime Antarctica. Metagenomic analyses showed low archaeal diversity and abundance. The Euryarchaeota (95.2%) and Methanobrevibacter were the most abundant and frequent phylum and genus, respectively. The average biogas production values were 595 LN kg VS[-][1] and 561 LN kg VS[-][1] in tests with individual oat (IO) and oat with enriched mixed culture (O + MC), respectively. However, O + MC showed a higher methane production, 4% (319 LN kg VS[-][1]) more than the results from the IO test with inoculum. Soils from Deception Island may represent a promising source of methanogenic communities capable of producing methane using agricultural waste as an alternative for energy production. Future studies are needed to understand the methane production using soil samples from cold environments.}, } @article {pmid42159838, year = {2026}, author = {Dos Santos Miranda, T and Cosentino, MAC and Moreira, FRR and Schiffler, FB and Coimbra, A and Mouta, R and Medeiros, G and Girardi, DL and Wanderkoke, V and Lima, M and de Oliveira, TH and Francisco, TM and Soffiati, FL and Ferreira, SS and Ruiz-Miranda, CR and Soares, MA and D'arc, M and Dos Santos, AFA}, title = {Fecal virome of paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) in Rio de Janeiro, Brazil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {42159838}, issn = {1678-4405}, mesh = {Animals ; *Feces/virology ; *Porcupines/virology ; Brazil ; *Virome ; Genome, Viral ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Viruses/classification/genetics/isolation & purification ; }, abstract = {The Paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) is a rodent species (Rodentia, Erethizontidae) widely distributed in the Brazilian Atlantic forest. However, little is known about their viral diversity. In this study, we aimed to evaluate, using high-throughput sequencing (HTS), the virome of the feces of seven healthy adult free-living porcupines from Silva Jardim, Rio de Janeiro, Brazil. Total viral nucleic acid was extracted and used for the library preparation for HTS using the Illumina MiSeq platform. The bioinformatics pipeline included quality control, with taxonomic assignments by Kraken2 and Diamond. Unclassified RNA viruses were investigated for viral genome characterization. A total of 41 viral families were classified, of which only seven were validated by both taxonomic analysis tools, including bacteriophages, vertebrate viruses, and unclassified RNA viruses. The most abundant bacterial reads identified belonged to the phylum Proteobacteria. In addition, in-depth analyses of RNA viruses revealed the presence of the Tombusviridae family, a group of plant-infecting viruses possibly associated with the host's diet. This study provides new insights into the fecal virome of Paraguayan hairy dwarf porcupines, contributing to the knowledge of microbial diversity in Erethizontidae and supporting non-invasive virome studies in wildlife.}, } @article {pmid42159959, year = {2026}, author = {Zhang, Z and Jiang, F and Li, Z and Lin, L and Qi, B and Han, D and Ran, C and Mao, S and Wang, J and Zhou, Z and Wang, M and Li, J and Wang, G and Kang, S and Zhang, T}, title = {Animal gut microbes and microbiomes in the 21st century and beyond.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {42159959}, issn = {1869-1889}, abstract = {Animal gut microbiomes-comprising bacteria, archaea, fungi, viruses, and protozoa-are fundamental to host evolution, physiology, and ecosystem resilience. This review synthesizes 21st-century advances in their diversity, spatiotemporal dynamics, and functional roles across the animal kingdom. Although high-throughput metagenomics has transformed the field, major biases remain: most studies still focus on domesticated vertebrates and fecal samples, leaving substantial "microbial dark matter" in wild hosts, invertebrates, and non-bacterial domains unexplored. We highlight how gut microbiomes mediate adaptation to environmental extremes, including hypoxia, temperature stress, and toxins, and how industrialization disrupts these communities, contributing to biodiversity loss and disease risk. We further integrate eco-evolutionary theory, multi-omics, and spatial modeling to clarify cross-kingdom interactions and functional networks. Finally, we discuss translational applications-including probiotics, fecal microbiota transplantation (FMT), phage therapy, and synthetic consortia-and emphasize the need for global collaborative initiatives, artificial intelligence (AI)-driven discovery, and standardized databases to unlock the full potential of animal gut microbiomes for biodiversity conservation, climate resilience, and planetary health in the coming decades.}, } @article {pmid42160933, year = {2026}, author = {Geng, C and Deng, T and Ren, K and Chen, X and Xue, S and Chen, L and Huang, C and Xu, M}, title = {Divergent structure but convergent metabolic organization of tetrabromobisphenol A degrading microbial consortia from aerobic and anaerobic conditions.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142454}, doi = {10.1016/j.jhazmat.2026.142454}, pmid = {42160933}, issn = {1873-3336}, mesh = {*Polybrominated Biphenyls/metabolism ; *Microbial Consortia ; Biodegradation, Environmental ; Anaerobiosis ; Aerobiosis ; Bacteria/metabolism/genetics ; }, abstract = {Microbial consortia drive the degradation of persistent pollutants through complex metabolic interactions. However, how these interactions are reconfigured under contrasting redox conditions to maintain functional efficiency remains a fundamental question in microbial ecology. Here, we used a top-down enrichment approach to investigate the collaborative degradation of tetrabromobisphenol A (TBBPA) under both aerobic and anaerobic conditions, integrating sequential transfer cultivation, metagenomics, network analysis, pure culture experiments, and predictive modeling. Sequential transfers significantly (p < 0.05) enhanced TBBPA degradation efficiencies under both regimes, driving distinct structural successions in the microbial communities. Specialist taxa such as Sphingopyxis (aerobic) and Novosphingobium (anaerobic) were phase-specifically enriched, whereas generalists like Pseudomonas and Comamonas emerged as highly interconnected keystone taxa under both conditions. Pure culture experiments and genomic reconstruction indicated functional partitioning among different taxa, where specialists might mediate debromination and β-scission by haloalkane dehalogenase and cytochrome P450, respectively. Furthermore, generalists harbored genetic modules for downstream ring-cleavage pathways, collectively forming a metabolic network that partitions degradation steps across the community. Partial least squares (PLS) regression and random forest analysis supported this functional partitioning and indicated that the overall TBBPA degradation is an emergent community property driven by community‑level interactions. This study suggests a principle of structure-divergent but convergent metabolic organization in collaborative TBBPA-degrading consortia, providing a mechanistic basis for designing synthetic communities to optimize bioremediation of brominated pollutants across diverse environmental settings.}, } @article {pmid42161086, year = {2026}, author = {Ziliani, A and Bovio-Winkler, P and Pabst, M and Cabezas, A and Etchebehere, C and Garcia, HA and López-Vázquez, CM and Brdjanovic, D and van Loosdrecht, MCM and Rubio-Rincón, FJ}, title = {Glycine-mediated microbial interactions in biological phosphorus removal systems.}, journal = {Water research}, volume = {302}, number = {}, pages = {126057}, doi = {10.1016/j.watres.2026.126057}, pmid = {42161086}, issn = {1879-2448}, mesh = {*Phosphorus/metabolism/isolation & purification ; *Glycine/metabolism ; Bioreactors/microbiology ; Bacteria/metabolism/genetics ; Waste Disposal, Fluid/methods ; Carbon/metabolism ; *Microbial Interactions ; Wastewater ; }, abstract = {Amino acids are less studied substrates in enhanced biological phosphorus removal (EBPR) systems. Glycine, a prevalent amino acid in wastewater, was used in this study to evaluate its role in EBPR processes. We operated a sequencing batch reactor (SBR) for over three months with glycine as the sole carbon source to investigate phosphorus removal performance and microbial dynamics using chemical and molecular analyses. The reactor supported EBPR activity, with glycine enabling anaerobic phosphorus release followed by aerobic uptake. The dissolved organic carbon to phosphorus (DOC:P) removal ratio of 100:9.9 closely matched values reported for systems dominated by polyphosphate-accumulating organisms (PAOs), and net phosphorus removal (20 mg PO4-P L[-1]) fell within the range reported for laboratory-scale EBPR systems fed with mixed carbon sources. Community analyses showed enrichment of Saccharimonadales alongside putative PAOs, including Ca. Phosphoribacter and Ca. Propionivibrio. Genome-resolved analyses indicate distinct but complementary metabolic potentials, including glycine transformation and lactate-related pathways, suggesting distributed carbon processing within the community. Together, these findings expand the understanding of amino acid utilization in EBPR systems and identify potential metabolic linkages that influence phosphorus removal under glycine-fed conditions.}, } @article {pmid42161088, year = {2026}, author = {Liu, Q and Zhang, Y and Gong, H and Zhou, S and Yang, J and Zhu, D and Huang, Z and Zhu, Y and Niu, H and Dai, X}, title = {Microbial-driven molecular transformation of dissolved organic matter in water-jet loom wastewater reclamation: An integrated FT-ICR MS and metagenomic investigation.}, journal = {Water research}, volume = {302}, number = {}, pages = {126124}, doi = {10.1016/j.watres.2026.126124}, pmid = {42161088}, issn = {1879-2448}, mesh = {*Wastewater/chemistry ; Bioreactors ; Metagenomics ; *Dissolved Organic Matter ; Waste Disposal, Fluid ; Mass Spectrometry ; }, abstract = {Water-jet loom wastewater, a major textile effluent in China, contains recalcitrant dissolved organic matter (DOM) derived from synthetic sizing agents and lubricants, whose incomplete removal constrains high-quality water reuse. Although Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomics provide high-resolution molecular and genetic insights, optimizing treatment efficacy remains hindered by a fragmented understanding of the intricate links between molecular transformations and their microbial drivers. This study established a reactomic-genomic paradigm coupling potential mass difference (PMD)-based molecular network analysis with metagenomic enzyme annotation in a full-scale membrane bioreactor (MBR) system (10000 m[3]·d[-1]). Over 8,000 molecular formulae were resolved across the treatment train. The results revealed that the dissolved air flotation unit prior to MBR selectively removed hydrophobic lipids and aliphatic/peptide-like compounds, leading to the relative enrichment of lignins/CRAM-like recalcitrant matter. The bioreactor served as the major zone of molecular turnover, with oxidation and depolymerization identified as the dominant transformation classes. These transformations were consistent with the enrichment of a Sphingomonadaceae-associated functional guild and abundant oxygenase-related genes, highlighting the role of microbial oxidation in aromatic transformation. Furthermore, a source-oriented framework revealed MBR effluent DOM as a spatially assembled mixture of three components. The recalcitrant influent-derived fraction dominated total effluent intensity (74.3%), while the bioreactor-emergent fraction constituted a consistent biogenic baseline (12.0%). In contrast, the membrane-associated emergent fraction contributed to molecular diversity (45.4% of unique formulae) but weakly to total intensity (9.7%). These findings indicate that the key challenge for high-quality reuse lies in controlling persistent and compositionally complex DOM. This framework provides a molecular basis for targeted process optimization and supports the transition of textile wastewater treatment from discharge compliance toward chemistry-informed reuse.}, } @article {pmid42161089, year = {2026}, author = {Schoenmakers, S and Nieuwenhuijse, DF and Reiss, I and van der Meeren, L and Mulders, CE and Molenkamp, R and Fraaij, PLA and van Boheemen, S}, title = {No detection of relevant virus-specific DNA or RNA sequences in the placenta.}, journal = {Placenta}, volume = {181}, number = {}, pages = {168-174}, doi = {10.1016/j.placenta.2026.05.010}, pmid = {42161089}, issn = {1532-3102}, mesh = {Female ; Humans ; Pregnancy ; *Placenta/virology ; *DNA, Viral/analysis ; *RNA, Viral/analysis ; Pre-Eclampsia/virology ; Adult ; *Virome ; Cesarean Section ; }, abstract = {INTRODUCTION: The existence of a placental bacterial microbiome remains a subject of active debate, with recent studies challenging earlier claims of a resident microbial community. While the role of bacterial and viral pathogens in placental infection and adverse pregnancy outcomes is well established, the potential existence of a resident placental (non-pathogenic) virome remains largely unexplored. Given the placenta's vital role in fetal development, our study aimed to investigate whether viral genetic material is present in placental tissue, rather than to identify viral pathogens, in both uncomplicated and complicated pregnancies using viral metagenomic capture sequencing.

METHODS: Placental biopsies were obtained from three pregnancy groups: (1) delivered by elective caesarean section (n = 6), (2) delivered by emergency caesarean section (n = 6), and (3) complicated by preeclampsia (n = 5). Samples were processed using VirCapSeq VERT, a targeted enrichment strategy for vertebrate viruses, followed by Illumina NovaSeq 6000 sequencing.

RESULTS: High quality sequencing yielded an average of 46.6 million reads per sample, with >99.6% of reads aligned to the human genome, and <0.4% of non human sequences. Across all samples, only 12 viral contigs were identified, corresponding to bacteriophages, human endogenous retroviruses, and human gammaherpesvirus 4 (not confirmed by PCR), mostly with low read counts.

CONCLUSIONS: Our study found no evidence supporting the presence of a resident placental virome. Together with existing data on the absence of a bacterial microbiome, these findings support the concept that the placenta does not harbor a detectable microbial or viral community under controlled sampling conditions.}, } @article {pmid42161263, year = {2026}, author = {Ni, M and Junker, K and Liu, Y and Fan, Y and Li, Y and Qiao, W and Zhang, XS and Ksiezarek, M and Mead, EA and Tourancheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Davey, LE and Fang, G}, title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.}, journal = {Cell host & microbe}, volume = {34}, number = {6}, pages = {1033-1049.e8}, pmid = {42161263}, issn = {1934-6069}, support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Epigenesis, Genetic ; *Gastrointestinal Microbiome/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Adaptation, Physiological/genetics ; DNA Methylation ; Fecal Microbiota Transplantation ; Infant ; *Bacteria/genetics/drug effects ; Metagenomics ; Probiotics ; Feces/microbiology ; Akkermansia ; }, abstract = {The human microbiome continuously adapts to variations in diet and host physiology. Epigenetic phase variation (ePV) mediated by bacterial DNA methylation can generate phenotypic heterogeneity within clonal populations. ePVs have been characterized in human pathogens, but their roles in commensals remain unclear. Here, we cataloged ePVs in infant and adult gut microbiomes, revealing genome-wide and site-specific ePV in response to antibiotics and fecal microbiota transplantation. Long-read metagenomics revealed genome-wide ePV mediated by structural variations of DNA methyltransferases. Analysis of public short-read metagenomic datasets further revealed a high prevalence of genome-wide ePVs in the human microbiome. Site-specific ePVs were identified and associated with antibiotics or probiotic engraftment. Focusing on an Akkermansia muciniphila isolate, we find a specific ePV regulating mucC, a gene of unknown function but whose heterologous expression enhances bacterial tolerance to antibiotics via a bet-hedging strategy. Thus, epigenetic modifications are used by gut bacteria to adapt to fluctuating environments.}, } @article {pmid42161874, year = {2026}, author = {, and , }, title = {[Expert consensus on laboratory diagnosis of inflammatory bowel disease (2026)].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {60}, number = {}, pages = {1-17}, doi = {10.3760/cma.j.cn112150-20260413-00324}, pmid = {42161874}, issn = {0253-9624}, support = {82472361//Natural Science Foundation of China/ ; }, abstract = {In recent years, the incidence of inflammatory bowel disease (IBD) in China has shown a significant upward trend. The invasive nature of colonoscopy limits its widespread application in population screening and long-term follow-up, while conventional laboratory parameters still suffer from insufficient sensitivity and specificity. A single test is inadequate for comprehensively assessing the complex pathophysiological processes of IBD. To enhance diagnostic efficacy, it is necessary to establish a multi-index combined evaluation system, integrating comprehensive assessments across dimensions such as inflammatory activity, nutritional metabolism, coagulation function, and infection risk. This consensus integrates relevant hematological and fecal laboratory markers, establishes a stratified application pathway covering initial screening, differential diagnosis, activity monitoring, and efficacy evaluation, and standardizes the clinical application scenarios of indicators such as fecal calprotectin (FC), the anti-Saccharomyces cerevisiae antibody (ASCA)/perinuclear anti-neutrophil cytoplasmic antibody (pANCA) panel, CRP (C-reactive protein)/ESR (erythrocyte sedimentation rate), and NLR (neutrophil-to-lymphocyte ratio). Furthermore, this consensus systematically reviews the clinical potential of cutting-edge technologies, including 16S amplicon sequencing, metagenomic sequencing, and microRNA detection, highlighting their significant prospects in analyzing microbial community structure, identifying occult pathogens, and assessing host regulation. This consensus aims to optimize non-invasive testing strategies for IBD, reduce misdiagnosis and improper treatment, and provide a standardized framework for tiered diagnosis and treatment as well as precision prevention and management.}, } @article {pmid42162115, year = {2026}, author = {Ranasinghe, PD and Barazanji, N and Bednarska, O and Bergman Jungeström, M and Lundberg, P and Keita, ÅV and Walter, S and Simon, R}, title = {High-resolution metagenomic characterization of gut microbiota composition and functional pathways in irritable bowel syndrome.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42162115}, issn = {2045-2322}, mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; *Metagenomics/methods ; Adult ; Middle Aged ; Feces/microbiology ; *Metagenome ; Case-Control Studies ; }, abstract = {Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder characterized by abdominal pain, altered bowel habits, and frequent comorbidity with anxiety and depression. The gut microbiota has been implicated in gut-brain axis (GBA) dysfunction, but consistent microbial signatures remain unclear. We performed whole metagenome shotgun sequencing of stool samples from 63 female patients with moderate to severe IBS and 34 female healthy controls and assessed microbial composition and functional pathways. Microbial richness and diversity were slightly reduced in IBS, though with high variability and no robust separation from controls. Differential abundance analyses revealed enrichment of Streptococcus sp. and the sulfate-reducing bacterium Desulfovibrio piger in IBS, alongside reductions in Bifidobacterium and Methanobrevibacter. Functional profiling identified 39 differentially abundant pathways: amino acid biosynthesis (e.g., L-isoleucine, L-threonine) was more prominent in IBS, while carbohydrate degradation pathways (e.g., galactose, stachyose) were enriched in healthy controls. These findings indicate modest but significant IBS-associated shifts in gut microbial composition and function that may contribute to IBS symptoms. However, high intra-group variability underscores the complexity of IBS and highlights the need for larger, multi-omics studies to define robust microbial markers. These results contribute to a growing body of evidence emphasizing the complexity of gut microbiota-host interactions and the need for high-resolution, systems-level approaches in microbiome-associated disorders.}, } @article {pmid42162191, year = {2026}, author = {Han, D and Liu, C and Yang, B and Yu, F and Liu, H and Lou, B and Shen, Y and Tang, H and Zhou, H and Zheng, S and Chen, Y}, title = {Author Correction: Metagenomic fingerprints in bronchoalveolar lavage differentiate pulmonary diseases.}, journal = {NPJ digital medicine}, volume = {9}, number = {1}, pages = {}, doi = {10.1038/s41746-026-02769-1}, pmid = {42162191}, issn = {2398-6352}, } @article {pmid42162287, year = {2026}, author = {Svanella-Dumas, L and Marais, A and Faure, C and Bergey, B and Comte, R and Candresse, T}, title = {Repeated identification of plant-associated polerovirus 3 (PaPV3) and of a novel polerovirus in the virome of French grain cereals.}, journal = {Archives of virology}, volume = {171}, number = {6}, pages = {}, pmid = {42162287}, issn = {1432-8798}, support = {ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ViroCAP//Ministère de l'Agriculture, de l'Agroalimentaire et de la Forêt/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; }, mesh = {*Edible Grain/virology ; Genome, Viral ; Phylogeny ; *Hordeum/virology ; *Luteoviridae/genetics/classification/isolation & purification ; *Plant Diseases/virology ; France ; *Virome/genetics ; Metagenomics ; }, abstract = {Two novel poleroviruses were repeatedly identified by metagenomics in French barley over the 2018-2023 period. One showed ~ 98.5% nucleotide (nt) identity with plant-associated polerovirus 3 (PaPV3) identified by metagenomics in Slovenia, while the second represents a novel species for which the name barley virus H (BVH) is proposed. Both viruses show a typical polerovirus genome organization but do not have ORF6 or ORF7. In French cereals samples, the most prevalent polerovirus was barley virus G (6.4%) followed by BVH (2.3%), cereal yellow dwarf virus RPV (CYDV-RPV, 1.8%) and PaPV3 (0.9%) suggesting the novel poleroviruses to be as prevalent as CYDV.}, } @article {pmid42162448, year = {2026}, author = {Bharadava, K and Makarani, N and Kaushal, RS}, title = {Co-selection of antimicrobial and heavy metal resistance in aquatic microbial communities at the water interface.}, journal = {Environmental geochemistry and health}, volume = {48}, number = {8}, pages = {}, pmid = {42162448}, issn = {1573-2983}, mesh = {*Metals, Heavy/pharmacology/toxicity ; *Water Microbiology ; *Drug Resistance, Bacterial ; *Water Pollutants, Chemical ; Wastewater/microbiology ; *Drug Resistance, Microbial ; Humans ; *Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; }, abstract = {Antimicrobial resistance (AMR) and heavy metal resistance (HMR) in aquatic ecosystems are increasing global health concerns driven by anthropogenic pollution of water systems. Municipal wastewater, hospital effluents, industrial discharge, agricultural runoff, and aquaculture activities contribute to the persistence and dissemination of resistant microorganisms and resistance genes in aquatic environments. Clinically important waterborne pathogens, including Escherichia coli, Salmonella Typhi, Shigella spp., and Vibrio cholerae, readily acquire resistance under continuous environmental stress conditions. Heavy metals further enhance AMR persistence through co-selection and cross-resistance mediated by mobile genetic elements carrying both antimicrobial and heavy metal resistance genes. This review summarizes the major environmental drivers, molecular mechanisms, and dissemination pathways associated with AMR-HMR interactions in aquatic systems. Recent advances in wastewater-based epidemiology, metagenomic surveillance, and resistance monitoring are highlighted as emerging tools for environmental and public health assessment. Current mitigation approaches, including advanced oxidation processes, membrane bioreactors, nanomaterial-based filtration, and microbial bioremediation, are also evaluated. A multidisciplinary One Health framework is essential for limiting environmental resistance dissemination and protecting human, animal, and ecosystem health.}, } @article {pmid42162574, year = {2025}, author = {Panneerselvam, R and Karuppannan, M and S C, GP and Durairaj, E}, title = {Impact of Sevoflurane on the Murine Gut Microbiota: Longitudinal Characterization of Diversity Alterations and Dysbiosis Metrics Using Metagenomics.}, journal = {Asian journal of anesthesiology}, volume = {63}, number = {1}, pages = {20-29}, doi = {10.6859/aja.202503_63(1).0003}, pmid = {42162574}, issn = {2468-824X}, mesh = {Animals ; *Sevoflurane/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Female ; *Anesthetics, Inhalation/pharmacology ; *Dysbiosis/chemically induced/microbiology ; *Metagenomics/methods ; Feces/microbiology ; Longitudinal Studies ; Sex Factors ; }, abstract = {BACKGROUND: General anesthetics can alter the gut microbiota, but the longitudinal and sex-specific effects of sevoflurane remain unclear. This study examined whether a single exposure to sevoflurane anesthesia induces significant compositional changes in the murine gut microbiome over two weeks, with a secondary focus on sex-specific patterns of alteration.

METHODS: A controlled animal exposure study was conducted at a tertiary-care academic laboratory animal facility in southern India, approved by an institutional animal ethics committee. Twenty albino mice (6-8 weeks old, ~12 g; both females and males) were randomized to sevoflurane or control groups, subdivided by sex. All animals were housed under standard conditions and completed the study protocol. Experimental animals underwent a single 4-hour exposure to sevoflurane in a controlled chamber; controls experienced identical procedures without sevoflurane. Primary endpoints were gut microbiota alpha and beta diversity (Bray-Curtis distance, Shannon, Simpson indices, richness), phylum- and genus-level differential abundance, and derived Firmicutes: Bacteroidetes and Proteobacteria metrics from serial fecal samples across five time points up to Day 14.

RESULTS: Sevoflurane exposure led to significant beta diversity separation between groups at both phylum (P = 0.004) and genus levels (P = 0.034), with additional sex effects (P = 0.035 for genus level); alpha diversity indices were significantly reduced in males (P = 0.0079), but not in females. Phylum-level differential abundance was significant in females but not in males. Group and sex effects were present throughout, and derived dysbiosis metrics varied temporally and by sex Conclusion: A single prolonged exposure to sevoflurane induces significant, durable, and sexually dimorphic shifts in the murine gut microbiome. These findings highlight the importance of considering sex as a biological variable in studies of anesthetic effects on gut health.}, } @article {pmid42162897, year = {2026}, author = {Wang, C and Liu, X and Wan, S and Xie, F and Dai, J and Chen, W and Qu, L and Zhang, L and Li, N and Du, X and Zhu, H and Hua, J}, title = {BLOS1 overexpression enhances goat immune response to Brucella LPS through augmented autophagy with associated gut microbiota remodeling.}, journal = {Veterinary journal (London, England : 1997)}, volume = {318}, number = {}, pages = {106706}, doi = {10.1016/j.tvjl.2026.106706}, pmid = {42162897}, issn = {1532-2971}, abstract = {Biogenesis of lysosome-related organelles complex 1 subunit 1 (BLOC1S1, also known as BLOS1) is a key gene involved in phagosome-lysosome maturation, transport, and autophagosome fusion, and it plays a crucial role in host resistance to Brucella infection. This study aimed to examine the effects of BLOS1 overexpression (oeBLOS1) on the stress response of goat macrophages and on intestinal microbiota composition. Peripheral blood mononuclear cells (PBMCs) were isolated from oeBLOS1 and wild-type (WT) goats and differentiated into macrophages. These macrophages were then stimulated with Brucella LPS to assess cytokine secretion and autophagy levels. Metagenomic sequencing was also performed to analyze the structural and functional profiles of the rectal fecal microbiota in these goats. After Brucella LPS stimulation, oeBLOS1 goat macrophages rapidly activated the NF-κB and TLR4 signaling pathways, promoting the synthesis and secretion of cytokines such as TNF-α (P < 0.05). Brucella LPS challenge also significantly increased the transcription of autophagy-related genes such as LAMP2 and BECN1, enhancing autophagic activity and bacterial clearance (P < 0.05). Furthermore, oeBLOS1 altered the intestinal microbiota, significantly enriching pathways linked to membrane transport and cell motility, and reducing the abundance of virulence factors and opportunistic pathogens, which may contribute to intestinal immune homeostasis. In summary, oeBLOS1 may help counteract Brucella LPS-induced infection by promoting the immune response, enhancing autophagy. In addition, it is associated with remodeling gut microbial function, suggesting a potential role in disease resistance.}, } @article {pmid42163161, year = {2026}, author = {Guan, X and Shen, XL and Hao, YN and Dong, ZQ and Chen, JM}, title = {Complex correlations between mitochondrial DNA variants and gut microbiome in major depressive disorder: a genome-wide association analysis.}, journal = {BMC psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12888-026-08132-8}, pmid = {42163161}, issn = {1471-244X}, abstract = {BACKGROUND: Gut microbiota disturbances and impaired mitochondrial function are both linked with the development of major depressive disorder (MDD). However, little is known about how they interact in MDD.

METHODS: We used shotgun metagenomic sequencing to explore fecal microbiome based on 63 MDD patients and 30 healthy controls (HCs). Then we performed GWAS for the discriminative taxonomic features of gut microbiota to identify genetic associations between gut microbiome and mitochondrial DNA (mtDNA) in MDD.

RESULTS: Characteristic gut microbiome-based features, including significant differences in gut microbiota composition and 101 differentially enriched gut microbial species, were found in MDD group vs. HC group. 68 mitochondrial single-nucleotide polymorphisms (mtSNPs) shared between the two groups were identified through GWAS at a Bonferroni-corrected significance level of p < 0.05. The genetic variants and their associated gut microbes were mapped to mitochondrial genome, most of which were located in coding regions, including MT-ND, MT-ND4L, MT-ND5, MT-ND6; MT-CO, MT-CO3; MT-RNR, MT-RNR, and MT-TE. Manhattan plots showed 9 mtSNPs in MDD group and 10 mtSNPs in HC group were associated with 20 gut microbial species at a significance of -log10(p) >20. Furthermore, Sankey diagram was used to visualize the relationships of gut microbiota and mtDNA. 36 mtSNPs (-log10(p) >5) were shown to be associated with 54 gut microbes in crosslinked patterns.

CONCLUSIONS: The current findings provide substantial evidence that complex interactions between gut microbiota and mtDNA contribute to MDD, which enables a better understanding of MDD pathogenesis and suggests new leads for future investigations.

CLINICAL TRIAL NUMBER: ChiCTR2000029703. Registration Date: Feb. 9[th], 2020. Registration Details are available at the website of Chinese Clinical Trial Registry (https://www.chictr.org.cn).}, } @article {pmid42163620, year = {2026}, author = {Lu, D and Lu, J and Yang, P and Lou, L and Li, W and Zhou, Y}, title = {Microbiome and Lipidomics Reveal the Mechanism of Eight Zhes Decoction on MAFLD.}, journal = {Combinatorial chemistry & high throughput screening}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113862073460107260407065758}, pmid = {42163620}, issn = {1875-5402}, abstract = {INTRODUCTION: The therapeutic potential of Eight Zhes Decoction (EZD) against metabolic dysfunction-associated fatty liver disease (MAFLD) is well-recognized; however, the underlying biological pathways are not well understood. To address this gap, an integrated investigation using both lipidomics and metagenomics was conducted to reveal the mechanistic rationale behind the effects of EZD.

METHODS: A MAFLD mouse model was established using a Methionine-Choline-Deficient (MCD) diet combined with CCl₁. The mice were treated with EZD for four weeks. Hepatic injury was assessed via H&E, Oil Red O, and Masson staining. Untargeted hepatic lipidomics and shotgun metagenomics were employed to profile lipid species and the gut microbiota composition, respectively.

RESULTS: Histopathological analysis confirmed that EZD significantly alleviated hepatic steatosis, ballooning degeneration, and fibrosis. Lipidomics identified 277 differential lipids; EZD treatment notably downregulated 24 TGs and modulated pathways related to arachidonic acid metabolism and bile secretion. Metagenomics revealed that EZD reshaped the gut microbiota, significantly increasing the abundance of Alistipes sp. while reducing the abundance of Faecalibaculum rodentium.

DISCUSSION: Correlation analysis demonstrated that the restored Alistipes sp. was negatively correlated with multiple hepatic TGs, whereas Faecalibaculum rodentium was positively correlated with lipid accumulation.

CONCLUSION: EZD mitigates MAFLD in mice by synergistically regulating hepatic lipid metabolism and gut microbiota. Specifically, the therapeutic effect involves restoring Alistipes sp. and modulating the gut-liver axis, providing experimental evidence for the clinical application of EZD.}, } @article {pmid42164149, year = {2026}, author = {Scutari, R and Fox, V and Mastropaolo, M and Fini, V and Mussa, M and Bigliano, P and Colagrossi, L and Vrenna, G and Perinzano, A and Scabini, S and Perno, CF and Calcagno, A}, title = {Case Report: Beyond conventional diagnostics: mNGS support in a complex immunocompromised patient diagnosis.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1791094}, pmid = {42164149}, issn = {2296-858X}, abstract = {Next-generation metagenomic sequencing (mNGS) enables the direct and unbiased detection of pathogens from clinical samples, overcoming the limitations of standard methods. It is particularly valuable in immunocompromised patients and in cases of complex infections. We report the case of a man in his 40s, born in North Africa, who was admitted with progressive skin and soft-tissue lesions after a minor foot trauma. The initially localized infection rapidly worsened, leading to bilateral pneumonia, acute respiratory failure, disseminated intravascular coagulation, and death. Histopathological examination revealed granulomatous inflammation with alcohol-resistant bacilli and an undiagnosed cutaneous T-cell lymphoma associated with hemophagocytic syndrome. Conventional microbiological tests identified multiple pathogens, including influenza A virus, herpes simplex virus 1 (HSV-1), Candida albicans, Enterococcus faecalis, Proteus mirabilis, and Pseudomonas aeruginosa; however, their heterogeneous distribution and isolation from non-sterile sites hindered etiological interpretation. Cultures and molecular assays for Mycobacterium species were negative despite findings of histological examination suggestive of granulomatous inflammation with alcohol-resistant bacilli. To clarify the diagnosis, mNGS was performed on blood, serum, and lymph node samples using host DNA depletion and Illumina sequencing. Bioinformatic analysis revealed a diverse microbial landscape, with the detection of Fusarium pseudograminearum, Mycobacterium canettii, and Ralstonia sp., alongside low-level viral sequences [Epstein-Barr virus (EBV) and HSV-1]. These results reflected the patient's severe immune deficiency, characterized by a marked depletion of CD8[+] T cells and NK cells. Although the results became available too late to influence treatment, mNGS provided crucial diagnostic insights, demonstrating its ability to uncover hidden or rare pathogens. Early application of mNGS could significantly improve diagnostic precision and therapeutic decisions in critically ill immunocompromised patients.}, } @article {pmid42164154, year = {2026}, author = {Wang, S and Wang, X and Sun, K and Jin, Z and Ma, J}, title = {Pulmonary sarcoidosis complicated with pulmonary cryptococcosis: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1822801}, pmid = {42164154}, issn = {2296-858X}, abstract = {Pulmonary sarcoidosis is an idiopathic granulomatous disorder primarily affecting the lungs and mediastinal lymph nodes. Pulmonary cryptococcosis, an opportunistic mycosis caused by Cryptococcus species, may occur concurrently with sarcoidosis, presenting substantial diagnostic challenges, particularly in treatment-naïve patients. A 63-years-old previously healthy female presented with insidious-onset dyspnea and low-grade fever. Chest computed tomography (CT) showed mediastinal and hilar lymphadenopathy, accompanied by small nodules in the right lower lobe. She was diagnosed with pulmonary sarcoidosis at a local hospital and started on prednisone, with symptomatic improvement. However, follow-up imaging showed enlargement and cavitation of the right lower lobe nodules. Admission laboratory tests, including inflammatory markers and fungal serology, were all unremarkable. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) identified sequences of Cryptococcus neoformans. Histopathological examination of mediastinal lymph node specimens confirmed the presence of non-necrotizing granulomas, which is consistent with a diagnosis of sarcoidosis. Meanwhile, the right lower lobe lung biopsy revealed positive staining for Cryptococcus. The patient was treated with fluconazole, resulting in radiological resolution. This case highlights the importance of considering pulmonary cryptococcosis as a potential complication in treatment-naïve sarcoidosis patients who present with abnormal chest shadows. Underlying immune dysregulation in sarcoidosis may obscure both clinical and radiological findings, thereby complicating the diagnostic process.}, } @article {pmid42164315, year = {2026}, author = {O'Connor, BRW and Allen, D and Quinn, M and Kozey, M and Léveillé, RJ and Whyte, LG}, title = {Bipolar investigation of near-surface glacial ice reveals an active microbial ecosystem driven by photosynthesis and chemolithoautotrophy.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag105}, pmid = {42164315}, issn = {2730-6151}, abstract = {Despite extreme conditions including freezing temperatures, low water activity, and few nutrients, active microorganisms are thought to inhabit glacial ice, yet little is known about their identities and methods of survival. We used flow cytometry, cultivation, metagenomics, and metatranscriptomics to characterize viable and active microbial communities from near-surface englacial ice from White Glacier in the Canadian High Arctic and Johnsons Glacier on Livingston Island, Antarctica. The ice, though low in microbial biomass (10[4] cells/ml), harbors communities capable of growth at subzero temperatures (-5°C), high salinity (12% NaCl), and low pH (pH 3). The communities of both poles were different, with metagenome-assembled genomes (MAGs) from White Glacier belonging to Cyanobacteriota and novel phyla and MAGs from Johnsons Glacier belonging to Pseudomonadota and Actinomycetota. Despite this, both glacial communities shared key metabolic functions, including aerobic respiration, aerobic carbon monoxide oxidation, sulfide oxidation, and denitrification. Metatranscriptomics from White Glacier revealed dominant Cyanobacteriota, performing oxygenic photosynthesis and carbon fixation and accompanied by active lithoautotrophs performing metabolisms such as carbon fixation via the 3-hydroxyproprionate cycle, anoxygenic photosynthesis, sulfide oxidation, and nitrate reduction/denitrification. These metabolisms appear to support an active heterotrophic community performing aerobic respiration and aerobic carbon monoxide oxidation. This study highlights the distinct but functionally similar microbial communities in Arctic and Antarctic glaciers, hinting that there may be a core set of metabolisms required for surviving in englacial ice and suggesting that similar communities could persist in glacial ice on Mars or the icy outer moons, Europa and Enceladus.}, } @article {pmid42164317, year = {2026}, author = {Domínguez-Huerta, G and Cabello, AM and Santos-Bruña, JJ and Mercado, JM and Ferrera, I}, title = {Ecology of prokaryotic DNA viruses in a highly impacted coastal lagoon revealed through comparative and temporal metagenomics.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag110}, pmid = {42164317}, issn = {2730-6151}, abstract = {Coastal lagoons are highly productive ecosystems, yet their prokaryotic viruses remain poorly studied. The Mar Menor, a hypersaline coastal lagoon in south-eastern Spain, is under strong anthropogenic pressure from continuous agricultural runoff, leading to severe eutrophication. To assess the impact of these unique conditions on viral assemblages, we analyzed a 3-year metagenomic time series of picoplankton communities. We reconstructed the lagoon's prokaryotic DNA viral communities and compared them with their counterparts in open Mediterranean Sea waters to reveal how environmental variability shapes their structure. Viral communities in the Mar Menor showed higher viral operational taxonomic unit relative abundances and diversities and were distinct from those offshore. Temporally, community structure was correlated with water transparency and silicate concentration. The putative hosts of the lagoon viruses were copiotrophic rather than oligotrophic compared to the open sea, and their composition shifted in response to episodic environmental disturbances. Temperate virus levels did not consistently support either the piggyback-the-winner or refugium models, spatially or temporally, indicating that viral replication strategies are governed by factors more complex than trophic status or environmental variability alone. Auxiliary viral genes (AVGs) encoding 2-oxoglutarate/Fe(II)-dependent oxygenase and DNA methyltransferase emerged as potentially relevant functions in the lagoon, as they were more frequent than in the Mediterranean Sea. Similar to targeted hosts, AVG-specific temporal relative abundance patterns were strongly shaped by local disturbances. This study provides the first metagenomic insight into viruses of the Mar Menor, revealing viral ecology in a dynamic, eutrophic lagoon, with implications for predictive models of nutrient cycling.}, } @article {pmid42164318, year = {2026}, author = {Aizpurua, O and Brenner, E and Martin-Bideguren, G and Garin-Barrio, I and Cabido, C and Alberdi, A}, title = {Beyond the core microbiome: endemic bacteria drive functional and microdiversity differences across salamander populations.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag106}, pmid = {42164318}, issn = {2730-6151}, abstract = {Population-specific variation in animal microbiomes is well documented, yet the functional consequences and underlying mechanisms remain poorly understood. To address this, we conducted genome-resolved metagenomic analyses on gut and skin microbiomes from four populations of Pyrenean brook salamanders (Calotriton asper) inhabiting two distinct environments: Pyrenean subalpine brooks and Atlantic montane streams. From paired faecal and skin swab samples, we reconstructed 539 and 43 metagenome-assembled genomes, respectively, and examined taxonomic composition, metabolic capacity, and microdiversity across environments. Although alpha diversity remained similar across environments, both gut and skin microbiomes exhibited significant differences in community composition and functional potential between environments. Partitioning the gut microbiome into core, endemic, and marginal fractions revealed a dominant core community-shared across environments and accounting for over 85% of reads-that did not drive functional divergence. Instead, functional differences were primarily shaped by low-abundance, population-specific endemic bacteria. Atlantic salamanders hosted endemic taxa with significantly greater metabolic potential and higher strain-level microdiversity than those at the Pyrenees. These patterns were not associated with broad-scale dietary differences and may reflect environmental influences such as temperature and nutrient availability. Our findings highlight the relevance of rare, endemic bacteria in driving microbiome function and underscore the power of genome-resolved metagenomics to uncover functional and evolutionary dynamics in wild host-microbe systems.}, } @article {pmid42164663, year = {2026}, author = {Glapa-Nowak, A and Nowak, JK and Kurek, S and Walkowiak, J}, title = {What a pickle-a metagenomic perspective on the cucumber fermentation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809866}, pmid = {42164663}, issn = {1664-302X}, abstract = {Food fermentation involves an interplay between multiple strains and species. This delicate composition during fermentation has been investigated so far using both classical and molecular methods; however, the results remain difficult to interpret. In this perspective article, we discuss the spontaneous fermentation of cucumber from organic and commercial cultivation (from 1st day to 90th day) based on our preliminary data from a nanopore sequencing study. The present study is the first to report the occurrence of coagulase-negative cocci in cucumber fermentation [Staphylococcus saprophyticus (0.01%) and Staphylococcus schleiferi (0.03%)]. Furthermore, we conclude that own-cultivation cucumbers may exhibit a lower incidence and diversity of phages, which have practical implications for designing future studies as well as for direct consumers. Our data also show that, even in the absence of phages (own-cultivation cucumbers <1%), lactic acid bacteria dominance occurs, which contrasts with previous conclusions and contributes to the discussion on the role of phages in maintaining the balance between Enterobacteriaceae and lactic acid bacteria in plant fermentation. The powerful metagenomic approach provides a broader understanding of the day-to-day and sample-to-sample diversity within microbiome communities. The maturity of the fermentation product may play a significant role in exerting specific biological actions. This should be accounted for before planning an intervention study.}, } @article {pmid42164669, year = {2026}, author = {Yuan, B and Li, C and Wang, Q and Yao, Q and Guo, X and Wang, Z}, title = {Maize stover mulching combined with an optimized fertilization strategy reshapes rhizosphere microbial communities and functions in greenhouse potato.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1670904}, pmid = {42164669}, issn = {1664-302X}, abstract = {Protected cultivation systems offer opportunities for improving potato productivity but are often constrained by inefficient maize stover utilization and suboptimal fertilization practices. In this study, a 4 × 4 factorial experiment was conducted using the potato cultivar 'Jishu No. 1' to decode the rhizosphere microbial mechanisms underpinning plant growth and yield enhancement under greenhouse conditions. We hypothesized that integrated management (the synergy between stover mulching and fertilization) would modify the soil microenvironment, thereby reshaping microbial community assembly patterns and functional gene distributions. The results showed that while split fertilization combined with moderate stover mulching (F2S2, 8,500 kg·hm[-2] stover mulching) was most effective in enhancing plant physiological status, full topdressing combined with the same mulching level (F3S2) achieved the highest agronomic productivity, increasing total yield to 42.33 t·hm[-2]. Metagenomic analysis revealed that the F3S2 strategy significantly reshaped the rhizosphere microbiome, characterized by higher α-diversity and the enrichment of pathways related to carbon metabolism and carbohydrate processing. Notably, F3S2 promoted the recruitment of copiotrophic taxa, particularly Actinobacteriota, whose relative abundance was significantly and positively correlated with soil organic phosphorus (r = 0.623, p < 0.05). In contrast, oligotrophic groups like Acidobacteriota were relatively less abundant in nutrient-rich treatments. These findings demonstrate that moderate stover mulching combined with dynamic fertilization provides a high-resource niche that favors functional microbial groups, thereby driving rhizosphere nutrient cycling to support potato performance. This study underscores the importance of optimized stover and fertilizer management strategies in protected cultivation.}, } @article {pmid42165181, year = {2026}, author = {Zhang, B and Zhang, J and Duan, F and Xuan, Z and Sun, T and Lu, L}, title = {Enzymatic Galactosylation of Erythritol Enhances Antibacterial Activity against Cariogenic Streptococcus mutans.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {21}, pages = {16527-16538}, doi = {10.1021/acs.jafc.5c14195}, pmid = {42165181}, issn = {1520-5118}, mesh = {*Streptococcus mutans/drug effects/genetics/physiology/growth & development ; *Erythritol/chemistry/pharmacology/metabolism ; *beta-Galactosidase/genetics/metabolism/chemistry ; *Anti-Bacterial Agents/pharmacology/chemistry/metabolism ; *Bacterial Proteins/genetics/metabolism/chemistry ; *Dental Caries/microbiology ; Biofilms/drug effects ; *Galactose/metabolism ; Escherichia coli/genetics/metabolism ; }, abstract = {Erythritol is a widely used sweetener with beneficial properties and bioactivities, including the inhibition of Streptococcus mutans, a bacterium that induces dental caries. Galactosylation of compounds is an attractive method for improving antimicrobial activity. In this study, a novel metagenomic β-galactosidase gene, bga7, was successfully expressed in Escherichia coli. The recombinant enzyme was used to galactosylate erythritol, generating a high yield (93.6%) of galactoside product at a concentration of 2 U/mL upon incubation with 20 mM o-nitrophenyl-β-d-galactopyranoside and 0.5 M erythritol at 40 °C and pH 9.0 for 4 h. The product was confirmed to be β-galactosyl-erythritol by MS and NMR analysis. This galactoside demonstrated significantly enhanced inhibition of both the planktonic growth of S. mutans and biofilm formation compared to erythritol alone. Further investigation into the mechanism revealed that the galactoside suppressed the transcriptional levels of four important genes (gtfB, ftf, srtA, and spaP) associated with bacterial adhesion and biofilm formation.}, } @article {pmid42165232, year = {2026}, author = {Nap, B and Thinnes, CC and Thiele, I}, title = {Whole-body metabolic modelling and its prospects in precision nutrition.}, journal = {The Proceedings of the Nutrition Society}, volume = {}, number = {}, pages = {1-19}, doi = {10.1017/S0029665126103061}, pmid = {42165232}, issn = {1475-2719}, abstract = {Nutrition has long been investigated with respect to its influence on human health. With the availability of various omics data, such as metagenomics and metabolomics, novel insights have been obtained into the influence of nutrition, particularly concerning the gut microbiome. The gut microbiome plays an important role in the breakdown of food-derived compounds and in producing essential bioactive metabolites required for human health. However, this wealth of information made the interactions between nutrition and human health increasingly intricate, and unravelling these links is complex. This review covers the concepts of genome-scale metabolic modelling as a tool to understand the links between nutrition, the gut microbiome and human metabolism and its applications. Genome-scale metabolic modelling treats metabolism as a mathematical problem which was used to develop models of human metabolism that incorporate physiology and organ-specific metabolism, known as whole-body metabolic models (WBMs). WBMs can incorporate physiological data, such as sex, weight, and body fat percentage, as well as nutrition in the form of its metabolite constituents. Finally, the gut microbiome can also be incorporated through a mathematical representation of the species present, based on stool metagenomics. WBMs have already been applied to understand gut microbiome-host co-metabolism in various non-communicable diseases. However, challenges remain, as metabolites measured in food items in public databases typically cover only common metabolites, and engagement with end-users such as nutritionists and policymakers is limited. Nevertheless, WBMs represent a promising step towards digital metabolic twins and thus personalised nutrition and medicine.}, } @article {pmid42165805, year = {2026}, author = {Brown, TL and Ng, DYK and Savva, GM and Elek, CKA and Docherty, JAD and Cook, R and Ansorge, R and Telatin, A and Kutter, E and Adriaenssens, EM}, title = {The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42165805}, issn = {2057-5858}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/physiology ; *Colon/microbiology/virology ; Escherichia coli/virology/genetics ; Bacteria/genetics/virology/classification ; Phage Therapy ; Feces/microbiology ; }, abstract = {The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacterial gastrointestinal disease, and commercial preparations such as the Intesti bacteriophage cocktail can be taken orally to target bacterial pathogens. However, interactions between these phages and the native gut microbiota are understudied. To investigate the impact of phage treatment, we used simulated gut models seeded with healthy donor microbiota from three individuals, sequenced the DNA and analysed the bacterial and viral portions from samples obtained over time. Each donor had a unique bacterial composition that diverged with time. When comparing phage-treated to control samples, we observed that Escherichia coli abundance accounted for the largest portion of bacterial community variance and was more associated with the controls. The lower abundance in phage-treated samples may have resulted from the lytic action of phages from the cocktail. Additionally, our analyses of the viral portion revealed a phage bloom exclusive to phage-treated samples. A highly abundant phage in this bloom was matched with the Intesti bacteriophage cocktail, showed similarity to Enterobacteria phage phi92 and provided evidence of productive infection within the model. While we did observe fluctuations in relative abundance of additional viral sequences in the presence of the phage cocktail, these changes were often transient. Furthermore, we detected only slight differences from typical members of the virome and low numbers of active prophages. Our experiments suggest that the phage cocktail had minimal interruption to the native gut microbiota within the model.}, } @article {pmid42165964, year = {2026}, author = {Chen, S and Hua, Y and Chen, D and Jiang, X}, title = {Laboratory diagnosis of brucellosis: evolving synergy between serological testing and next-generation sequencing.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42165964}, issn = {1435-4373}, abstract = {BACKGROUND: Brucellosis is an animal‑to‑human infection that is hard to identify in practice; its signs are vague and the laboratory tools used in routine care have clear limits. Bacterial culture is regarded as the reference test; the procedure is slow and has modest sensitivity, and in many hospitals clinicians rely mainly on serologic assays when they make a diagnosis. Over the past decade clinical microbiology laboratories have increasingly used next‑generation sequencing (NGS) as a tool for pathogen identification, especially metagenomic NGS (mNGS). In patients with suspected bru-cellosis clinicians and laboratory staff often see a mismatch between test results, with serological assays suggesting infection but NGS reports failing to detect Brucella, a gap between serology and sequencing that remains a frequent and unresolved problem in routine diagnosis.

OBJECTIVE: This review brings together available data on how serological tests and sequencing-based methods in both metagenomic and targeted formats contribute to the laboratory diagnosis of human brucellosis and where they fall short.

CONCLUSION: It describes biological and technical sources of false-positive serology and false-negative sequencing and sets out a practical integrated way to judge and confirm mismatched findings so that laboratories and clinicians can use conventional and molecular tools together and reach sound decisions when brucellosis is suspected.}, } @article {pmid42166146, year = {2026}, author = {Besteman, MS and Alaux, E and Doloman, A and Tahon, G and Ettema, TJG and Sousa, DZ}, title = {Uncovering syntrophic potential from genome-resolved metagenomics of suspended and granular anaerobic digestion sludges.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {6}, pages = {}, pmid = {42166146}, issn = {1574-6941}, support = {0.24.002.002//Ministry of Education, Culture and Science, Netherlands/ ; VI.C.192.016/NWO_/Dutch Research Council/Netherlands ; 817834/ERC_/European Research Council/International ; }, mesh = {*Metagenomics ; Anaerobiosis ; *Sewage/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Oxidation-Reduction ; Phylogeny ; Fatty Acids/metabolism ; *Metagenome ; Sequence Analysis, DNA ; Archaea/genetics/classification/metabolism ; }, abstract = {Syntrophic microbial interactions are fundamental to the degradation of organic matter (e.g. fatty acids), playing a central role in natural anoxic ecosystems and engineered systems such as anaerobic digestion (AD). Despite their ecological and biotechnological importance, only a limited number of (obligate) syntrophic fatty-acid oxidizers have been successfully isolated. In this study, microbial communities from suspended and granular sludge samples were characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomics. Network analysis of the 16S rRNA gene amplicon data revealed strong positive associations between methanogens and known syntrophic fatty-acid oxidizers, particularly in granular sludge samples. 743 High-Completion Metagenome Assembled Genomes (HC-MAGs) were recovered. This comprehensive HC-MAGs dataset provides a valuable resource for identifying novel microorganisms with genomic potential for syntrophic oxidation of butyrate, propionate, and acetate. This analysis identified multiple interesting novel targets, including the families DTU052 and CALXsZ01 (class Syntrophomonadia) as potential butyrate oxidizers; the families UBA6807, PHBD01, FEN-1087, and FEN-1099 (class Syntrophia) as potential propionate oxidizers; and genus DTU068 (family Thermacetogeniaceae) together with the family-level lineage 4572-78 (phylum Chloroflexota) as potential acetate oxidizers. These findings highlight granular sludges as a reservoir for previously uncharacterized syntrophic microorganisms. The recovered HC-MAG dataset also provides a framework to further elucidating fatty-acid oxidizing bacterial lineages within complex anaerobic communities.}, } @article {pmid42166340, year = {2026}, author = {Sato, M and Kanaly, RA and Mori, JF}, title = {Genomic and transcriptomic insights into Achromobacter-Sphingobium co-colonization within polycyclic aromatic hydrocarbon-exposed bacterial communities.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {5}, pages = {}, pmid = {42166340}, issn = {1465-2080}, mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; *Sphingomonadaceae/genetics/metabolism/growth & development ; Biodegradation, Environmental ; Genome, Bacterial ; *Transcriptome ; *Achromobacter/genetics/metabolism/growth & development ; Soil Microbiology ; *Achromobacter denitrificans/genetics/metabolism ; Phylogeny ; Genomics ; Soil Pollutants/metabolism ; Gene Expression Profiling ; Microbial Consortia ; }, abstract = {Efficient and complete biodegradation of polycyclic aromatic hydrocarbons (PAHs), which are persistent and genotoxic petroleum hydrocarbon pollutants, is often considered to require the cooperative activities of multiple bacterial groups, and bacterial (meta)genomic investigations of PAH-exposed ecosystems have contributed to elucidating such interactions. In this study, two bacterial isolates representing dominant genera within a PAH-grown soil bacterial consortium, Achromobacter xylosoxidans strain KK8 and Sphingobium barthaii strain KK22, were utilized as model organisms to investigate the relationship between these bacterial genera during PAH biodegradation. Strain KK8 has previously been characterized as incapable of biodegrading PAHs; thus, Achromobacter in the consortium appears to grow under metabolic dependence on PAH biodegradation products (i.e. salicylic acid) provided by the pioneer PAH-degrading Sphingobium. This metabolic relationship was evidenced through complete genome sequencing and functional gene analysis of strain KK8 conducted in the present study. To further elucidate potential interactions between Achromobacter and Sphingobium, cell-free filtrate-exchange experiments were performed using these isolates, revealing that strain KK8 exhibited a significantly shortened growth lag phase in the presence of the filtrate of strain KK22. Subsequent transcriptomic profiling of strain KK8 indicated that exposure to the Sphingobium filtrate up-regulated functional genes likely associated with Achromobacter colonization, including genes involved in biofilm formation (pga genes) or cell division (fts genes). Enhanced biofilm formation of strain KK8 in response to strain KK22 filtrate was additionally evidenced by biofilm assays. Taken together, these results suggest that the high abundance of Achromobacter within the consortium may be stimulated by Sphingobium when they are present together, potentially via extracellular signalling molecule(s). As the co-occurrence of Achromobacter and Sphingobium has been repeatedly documented in PAH-degrading bacterial communities, elucidating the mechanisms underlying their specific interspecies co-colonization during PAH biodegradation shall be valuable for the future biotechnological applications utilizing these bacteria.}, } @article {pmid42166940, year = {2026}, author = {Ali, S and Chaudhary, AA and Sheikh, WM and Ali, MAM and Chopra, C and Dar, MA and Wani, AK and Bashir, SM}, title = {Genome-resolved metagenomics of the tumour microbiome: From strain diversity to functional cancer ecology.}, journal = {Pathology, research and practice}, volume = {285}, number = {}, pages = {156543}, doi = {10.1016/j.prp.2026.156543}, pmid = {42166940}, issn = {1618-0631}, mesh = {Humans ; *Neoplasms/microbiology/genetics ; *Microbiota/genetics ; *Metagenomics/methods ; *Tumor Microenvironment/genetics ; Multiomics ; Animals ; }, abstract = {Advances in genome-resolved metagenomics, spatial transcriptomics, and single-cell sequencing have revealed that tumour-associated microbes are not random contaminants but structured, functionally heterogeneous components of the tumour microenvironment. Strain-level genomic reconstruction uncovers substantial intra-species diversity, encompassing accessory genes, mobile elements, and metabolic modules that collectively influence genotoxicity, immune modulation, drug metabolism, redox regulation, and biofilm formation. These microbial traits often assemble into convergent functional guilds that drive DNA damage, immune polarization, therapeutic resistance, and metastatic potential across tumour types. Integrative multi-omics analyses demonstrate that only a subset of detected microbial taxa is transcriptionally and metabolically active within tumours, underscoring the importance of combining metatranscriptomics, proteomics, metabolomics, and spatial profiling to delineate biologically meaningful host-microbe interactions. Spatial and single-cell mapping further reveal that intratumoural microbes occupy defined intracellular and extracellular microniches often aligned with hypoxic regions, myeloid-rich aggregates, T-cell exclusion zones, and metabolically reprogrammed epithelial states, reinforcing their role as active participants in tumour physiology rather than passive passengers. Mechanistic evidence now indicates that tumour-resident microbial ecosystems modulate responses to chemotherapy, immune checkpoint blockade, and radiotherapy, while contributing to premetastatic niche conditioning. Low-abundance but high-impact keystone microbial genomes can exert a disproportionate influence on tumour progression and therapeutic outcomes, providing new opportunities for biomarker discovery and microbiome-targeted interventions. This review integrates genome-resolved, spatial, and functional perspectives to propose an onco-metagenome framework that links tumour microbial ecology to cancer evolution, immune regulation, and translational intervention.}, } @article {pmid42166998, year = {2026}, author = {Wu, Q and Zheng, Y and Xia, Y and Ge, C and Deng, H and Zhao, Y and Luo, J and Feng, D}, title = {Decoding the seagrass plastisphere: Metagenomic insights into biogeochemical cycling of biogenic elements and ecological consequences.}, journal = {Environment international}, volume = {212}, number = {}, pages = {110311}, doi = {10.1016/j.envint.2026.110311}, pmid = {42166998}, issn = {1873-6750}, mesh = {Carbon/metabolism ; Ecosystem ; *Metagenome ; Metagenomics ; Nitrogen/metabolism ; Phosphorus/metabolism ; Sulfur/metabolism ; Aquatic Organisms ; *Water Pollutants/metabolism ; *Hydrocharitaceae/genetics/metabolism ; Plastics/metabolism ; *Water Microbiology ; }, abstract = {Seagrass meadow, a crucial blue carbon ecosystem, is increasingly threatened by plastic pollution. Plastic debris in this sensitive ecosystem creates a new microbial habitat known as "plastisphere". However, the functional role of plastisphere, particularly in driving the cycling of key biogenic elements, remains poorly understood. This knowledge gap raises concerns over potential disruptions to elemental fluxes and subsequent ecological consequences. Here, metagenomic analysis was employed to investigate the metabolic profile of in-situ plastisphere in seagrass meadow, with particular focus on carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) biotransformation. The obtained results revealed that plastisphere microbes were taxonomically distinct from those in natural environments of the seagrass meadow, and these inhabitants were capable of driving diverse metabolic pathways. However, >75% functional gene similarity indicated a significant functional overlap between the plastisphere and natural environments. This niche enriched genes related to heterotrophic organic C degradation (27.71% ± 3.28%) and oxidation (17.86% ± 2.04%) pathways, organic N metabolism (62.18% ± 8.57%) mainly through GS-GOGAT pathways and denitrification (8.70% ± 4.06%), polyphosphate degradation (22.89% ± 2.20%) and organic P mineralization (17.50% ± 1.70%), as well as assimilatory/dissimilatory sulfate reduction (30.60% ± 3.49%) and thiosulfate disproportionation (13.57% ± 2.89%) metabolic pathways. Metabolic linkage within seagrass plastisphere was facilitated by highly connected taxa including Silicimonas and Erythrobacter, which linked electron-donating processes (including organic C degradation and S oxidation) to electron-accepting pathways (e.g., sulfate/nitrate reduction, C fixation). These interactions established the plastisphere as a potential biogeochemical hotspot, potentially amplifying the risks of CO2/N2O emission, H2S accumulation, nutrient competition with seagrass and potential eutrophication from imbalanced P mobilization, ultimately threatening the health and stability of seagrass ecosystem.}, } @article {pmid42167281, year = {2026}, author = {Bambakidis, T and Liu, S and Wettengel, AM and Holmes, RM and Dinga, BJ and Koning, AA and McIntyre, PB and Borton, MA and Mann, PJ and Crump, BC}, title = {Congo River Bacterioplankton Genomic Diversity Reflects Water Travel Time, Wetland Habitats, and Greenhouse Gases.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70327}, doi = {10.1111/1462-2920.70327}, pmid = {42167281}, issn = {1462-2920}, support = {DEB-1840243//National Science Foundation/ ; OCE-0851101//National Science Foundation/ ; OCE-0851015//National Science Foundation/ ; DGE-0718123//National Science Foundation/ ; DEB-1501836//National Science Foundation/ ; 52379057//China Natural Science Foundation/ ; //David and Lucile Packard Foundation/ ; //U.S. Geological Survey/ ; 10.46936/10.25585/60001289//Joint Genome Institute/ ; }, mesh = {*Wetlands ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Greenhouse Gases/analysis/metabolism ; Congo ; RNA, Ribosomal, 16S/genetics ; *Plankton/genetics/classification ; Ecosystem ; Methane/metabolism ; Phylogeny ; Carbon Cycle ; Biodiversity ; Metagenome ; }, abstract = {Tropical rivers are major contributors to global carbon cycling, yet the microbial communities driving these transformations remain largely uncharacterized. We investigated bacterioplankton communities along the northwest Congo watershed using 16S rRNA and metagenomic sequencing, paired with hydrological, biogeochemical, and greenhouse gas data. In large rivers, community composition correlated with temperature and water travel time, while smaller streams were shaped by nutrient chemistry and landscape. Most sites were dominated by Burkholderiales, but composition varied, especially in DOC-rich Cuvette Centrale wetland streams that hosted distinct communities associated with high methane and CO2, and low oxygen. Indicator species analysis identified specific taxa and metagenome-assembled genomes (MAGs) strongly associated with long travel times, wetlands, and methane, including methanotrophs (Methylcoccaceae, Methylophilaceae, Methylomonas) and MAGs encoding diverse carbon-processing metabolisms. For global context, Congo and northern Thailand river bacterioplankton were more similar to each other than to temperate Connecticut River communities, possibly reflecting shared tropical features such as high precipitation, temperature, and travel time. As in temperate systems, bacterioplankton in large tropical rivers are shaped by temperature and hydrology, while smaller tropical streams reflect localized environmental drivers. The striking similarity of tropical river bacterioplankton from Africa and Asia suggests the primacy of environmental controls on river bacterioplankton.}, } @article {pmid42167521, year = {2026}, author = {Wolacewicz, M and Decewicz, P and Valdes, ME and Iaconi, OS and Todiras, M and Ferdohleb, A and Rodriguez-Mozaz, S and Borrego, CM and Dziewit, L}, title = {The occurrence and removal of antibiotic residues and antibiotic resistance genes in the largest European constructed wetland at Orhei (Moldova).}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {402}, number = {}, pages = {128381}, doi = {10.1016/j.envpol.2026.128381}, pmid = {42167521}, issn = {1873-6424}, mesh = {*Wetlands ; *Anti-Bacterial Agents/analysis ; *Waste Disposal, Fluid/methods ; Wastewater/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical/analysis ; *Genes, Bacterial ; Bacteria/genetics ; }, abstract = {Constructed wetlands (CWs) are increasingly promoted as low-cost, nature-based solutions for wastewater treatment, particularly in low- and middle-income countries (LMICs), yet their performance in removing pharmaceutical compounds, antibiotic resistance genes (ARGs), and bacterial pathogens remains insufficiently characterized under real-field-scale conditions. Here, we investigated the fate of pharmaceutical compounds (including antibiotic residues), wastewater bacterial communities, and the associated ARGs in the largest European passive treatment system, the vertical-flow CW of Orhei (Moldova), serving nearly 26,000 inhabitants. Metagenomic profiling revealed 783 bacterial families, with a reduction from 33 families in raw sewage to 25 in the final effluent and clear enrichment of autochthonous wetland taxa. A total of 150 ARG types conferring resistance to 16 antibiotic classes were detected. The cumulative ARG load decreased by approximately 78% from influent to effluent. ARGs conferring resistance to fosfomycin, nitroimidazoles, rifamycins, streptothricin, oxazolidinones, and pleuromutilins were not detected in the final effluent, suggesting effective removal to below the detection limit of the applied metagenomic method, while sulfonamide resistance genes (sul1, sul2) persisted across all stages. Out of 29 antibiotic residues analyzed, 13 (including two sulfamethoxazole metabolites) were detected, together with 14 non-antibiotic pharmaceuticals (out of 30 residues analyzed). The removal of individual antibiotics ranged between 85 and 100%, and for other pharmaceuticals between 34 and 100%, although some compounds (e.g., carbamazepine, 10,11-epoxycarbamazepine, alprazolam) showed negative removals. Environmental risk assessment (risk quotients, RQ) indicated no significant risk to freshwater biota (RQ < 0.1) for all detected compounds in the treated effluent. Results demonstrated that a large-scale CW in the LMIC context can substantially reduce antibiotic residues and ARGs, supporting its role as an effective, nature-based component of One Health-oriented wastewater management.}, } @article {pmid42167540, year = {2026}, author = {Wang, W and Liu, H and Jiang, K and Posum, W and Lu, Z and Chen, X}, title = {A rare case of Porphyromonas endodontalis lung abscess mimicking lung cancer on imaging: the diagnostic value of postoperative metagenomic next-generation sequencing.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {169}, number = {}, pages = {108821}, doi = {10.1016/j.ijid.2026.108821}, pmid = {42167540}, issn = {1878-3511}, mesh = {Humans ; Male ; *Lung Abscess/microbiology/diagnosis/diagnostic imaging/surgery ; *Lung Neoplasms/diagnosis/diagnostic imaging ; Aged ; Diagnosis, Differential ; High-Throughput Nucleotide Sequencing ; *Bacteroidaceae Infections/diagnosis/microbiology/diagnostic imaging ; *Porphyromonas endodontalis/genetics/isolation & purification ; Metagenomics ; Tomography, X-Ray Computed ; }, abstract = {This case highlights the diagnostic challenge of a Porphyromonas endodontalis lung abscess mimicking lung cancer. A 67-year-old male presented with a right lower lobe mass suggestive of malignancy. Following wedge resection, pathology confirmed an abscess. Metagenomic next-generation sequencing (mNGS) of the tissue revealed a microbial profile dominated by oral anaerobes of Porphyromonas endodontalis. Postoperative mNGS identified the oral origin of infection and prompted periodontal treatment, leading to full recovery. This report reveals the decisive value of postoperative mNGS in correcting a diagnosis of infection mimicking lung cancer. It emphasizes that oral anaerobic infections can present as "tumor-like" pulmonary lesions. This case suggests that oral infection sources should be considered in the differential diagnosis of challenging pulmonary lesions and highlights the potential value of a multidisciplinary approach that includes dental evaluation.}, } @article {pmid42167986, year = {2026}, author = {Thomas, J and Ananthanarayanan, V and Padmanabhan, S}, title = {Metagenomic analysis of oral microbiome around zinc oxide nanoparticle-coated mini-implants: A split-mouth trial.}, journal = {Journal of the World federation of orthodontists}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ejwf.2026.03.003}, pmid = {42167986}, issn = {2212-4438}, abstract = {BACKGROUND: This study aimed to evaluate the changes in the oral microbiome surrounding zinc oxide nanoparticle (NP)-coated orthodontic mini-implants using whole-genome metagenomic sequencing and to compare the microbial colonization and clinical stability with uncoated orthodontic mini-implants.

METHODS: A randomized split-mouth trial was conducted on 12 orthodontic patients requiring bilateral skeletal anchorage in the maxillary arch. Each patient received one zinc oxide NP-coated mini-implant and one uncoated implant. The implants were coated using radiofrequency magnetron sputtering. Peri mini-implant crevicular fluid samples were collected at 1 week (T1), 4 weeks (T2), and 3 months (T3) postinsertion, and the pooled sample at each time point was subjected to whole-genome shotgun metagenomic sequencing. Taxonomic and functional profiles were analyzed using Kraken and MEGAN6, with diversity indices calculated via the VEGAN R package. Stability was assessed using a 4-point semiquantitative mobility scoring.

RESULTS: Alpha diversity indices (Shannon and Chao1) showed no comparable differences between coated and uncoated mini-implants at any time point. Descriptive analysis of pooled metagenomic samples showed lower relative abundance or absence of peri‑implant pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Parvimonas micra, around coated implants. Functional gene analysis revealed reduced expression of bacterial motility, chemotaxis, and ribosomal pathways in the coated group. All mini-implants remained clinically successful during follow-up. Mobility scores were significantly lower at 1 month (P = 0.04), but not at 3 months (P = 0.102).

CONCLUSIONS: Within the constraints of pooled metagenomic analysis, zinc oxide NP-coated mini-implants were associated with a lower relative abundance of selected peri‑implant pathogens and differences in functional pathway profiles compared with uncoated implants. Overall microbial diversity did not differ significantly between groups. Both implant types remained clinically stable, although coated implants showed reduced early mobility at 1 month. These findings should be interpreted as exploratory, and further validation through patient-level metagenomic studies is warranted.}, } @article {pmid42168196, year = {2026}, author = {Bowie, KR and Luhung, I and Burke, TR and Roberts, SC and Martinello, RA and Gerstein, M and Peccia, J and Healy, HG}, title = {Disinfection of hospital sink drains enriches pseudomonadota and efflux pump-mediated antibiotic resistance in reestablished biofilms.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73533-y}, pmid = {42168196}, issn = {2041-1723}, support = {1S10OD030363-01A1//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, abstract = {Antimicrobial resistant pathogens and associated infections represent major public health threats affecting healthcare facilities, with sink drain biofilms serving as reservoirs for many of these bacteria. Despite attempts at sink drain biofilm disinfection and removal, drain biofilms inevitably regrow, and disinfection may shape the returning microbial communities and their resistance profiles. We applied culture-based and metagenomic approaches to study these drain disinfection effects on microbial community abundance, taxonomy, and antimicrobial resistance in operational hospital sinks. Drain biofilms regrew to baseline densities in approximately four days. Regrown biofilms contained more viable carbapenem-resistant bacteria and were dominated by Pseudomonadota, including Cupriavidus and Pseudomonas. Long-read sequencing revealed an increase in multidrug efflux pump genes after disinfection, which confer broad resistance to antibiotics and disinfectants. This work provides mechanistic insights into how disinfection influences sink drain biofilm ecology and the enrichment of antimicrobial resistance, with implications for infection prevention strategies in healthcare environments.}, } @article {pmid42168704, year = {2026}, author = {Zhang, X and Mallick, H and Rahnavard, A}, title = {Meta-analytic microbiome target discovery for immune checkpoint inhibitor response in advanced melanoma.}, journal = {Communications medicine}, volume = {6}, number = {1}, pages = {}, pmid = {42168704}, issn = {2730-664X}, support = {2109688//National Science Foundation (NSF)/ ; 2109688//National Science Foundation (NSF)/ ; }, abstract = {BACKGROUND: Immune checkpoint inhibitors have transformed melanoma therapy, yet only a subset of patients achieve durable responses. Gut microbes have been linked to response, but reported biomarkers vary across studies. We aim to identify reproducible microbial features and test their generalizability across cohorts and treatment settings.

METHODS: We reprocessed stool metagenomic sequencing data from 15 melanoma cohorts (763 samples from 484 individuals), including 12 cohorts treated with immune checkpoint inhibitors alone and 3 trials combining immune checkpoint inhibitors with fecal microbiota transplantation. Using a unified analysis pipeline, we profiled microbial species, metabolic pathways, and biosynthetic gene clusters, and analyzed their associations with treatment response using Tweedie regression, random-effects meta-analysis, and multimodal integration with leave-one-dataset-out validation.

RESULTS: Here, we show that responders in immune checkpoint inhibitor-only cohorts are enriched for several short-chain fatty acid-producing commensals, whereas non-responders show higher abundance of taxa associated with disrupted gut communities. In fecal microbiota transplantation plus immune checkpoint inhibitor trials, response associates with distinct communities and shifts in amino-acid, nucleotide and cofactor metabolism. Across cohorts, multiview prediction models repeatedly select gene clusters linked to antimicrobial peptides and surface polysaccharides, but cross-study discrimination remains modest.

CONCLUSIONS: Microbiome signatures of response are treatment-context dependent and are not captured by a single universal species. These harmonized findings prioritize microbial taxa and functions for mechanistic studies and future microbiome-informed interventions.}, } @article {pmid42168837, year = {2026}, author = {Tong, L and Liu, Y and Han, F and Jiang, Y and Ying, S and Zhang, B and Cheng, Y and Liu, Z and Shi, Y and Xu, M and Tang, C and Sui, S and Chen, T}, title = {Exploring microbial ecology in public swimming pools: a metagenomic investigation of community structure and environmental correlates.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05157-7}, pmid = {42168837}, issn = {1471-2180}, support = {GWVI-4//The Key Projects in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025)/ ; }, abstract = {Epidemiological studies have identified correlations between swimming and outbreaks of various infectious diseases. However, a comprehensive understanding of the pathogens present in public swimming pool water has yet to be systematically established. Swimming pool water samples were collected from 20 indoor public swimming pools in Shanghai, China during the summer of 2023. After quality inspection of the extracted nucleic acid, the qualified samples were subjected to metagenomic sequencing to profile the microbial communities of swimming pool water. A total of 24,035 microbial species were identified with the abundance of bacteria (99.46%), followed by archaea (0.29%), viruses (0.20%), and fungi (0.05%), including 441 pathogenic species, 23 of which were classified as biosafety level 3 (BSL-3) microorganisms. Environmental sources constituted the dominant origin (86.00%) of the pool water microbiome. Additionally, suburban pools demonstrated greater microbial diversity than urban pools (P < 0.05). The abundance of viruses exhibited a positive correlation with the concentration of urea in pool water (r = 0.31, P < 0.05). This study demonstrated that swimming pool water serves as a potent reservoir and mixing vessel for various highly pathogenic microorganisms. Effective water quality management strategies are essential to mitigating the potential public health threats of public swimming pools.}, } @article {pmid42168845, year = {2026}, author = {Zhao, Q and Zuo, S and Liu, S and Wang, J and Tang, J and Zou, X and Leng, Y and Li, X and Zhou, M and Tian, J and Wang, P}, title = {Integrative multi-omics analysis reveals host-microbiome metabolic alterations and candidate biomarkers in Parkinson's disease.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05168-4}, pmid = {42168845}, issn = {1471-2180}, support = {2023AFD045//Hubei Provincial Natural Science Foundation / Joint Fund Project Cultivation Project/ ; 2023BCB140//Hubei Provincial plan of science and technology key research project/ ; 2023XKQT1//The Advantages Dicipline Group (Medicine) Project in Higher Education of Hubei Province (2021-2025)/ ; }, abstract = {Alterations in the gut microbiome have been increasingly implicated in Parkinson's disease (PD), but the associated metabolic changes remain incompletely understood. Here, we applied an integrative multi-omics approach combining shotgun metagenomic sequencing and untargeted LC-MS-based plasma metabolomics to investigate host-microbiome alterations in PD. Fecal and plasma samples were collected from 30 PD patients and 30 healthy spouse controls. Significant differences in microbial diversity and taxonomic composition were observed between the two groups. Taxonomic profiling revealed marked gut microbial dysbiosis in PD, including altered abundances of Phocea massiliensis, Bacteroides sp900766005, and Alistipes_A indistinctus. Metabolomic analysis identified 86 significantly altered plasma metabolites, including glycerophospholipids, indoleacetic acid, and kynurenic acid. Integrative pathway analysis suggested links between microbial functional alterations and host metabolic changes. Machine-learning analyses identified three biomarker panels that distinguished PD patients from controls in validation datasets, with the highest area under the curve (AUC) reaching 0.92. In silico molecular docking further suggested potential interactions between several metabolite biomarkers and alpha-2-macroglobulin (A2M) or the human B[act] spliceosome. Overall, these findings provide an integrative view of host-microbiome metabolic alterations associated with PD and highlight candidate biomarkers and exploratory host-metabolite associations for further investigation.}, } @article {pmid42169289, year = {2026}, author = {Li, Y and Liu, X and Li, C and Xu, X and Tang, C and Zhou, G and Liu, Y and Blank, I}, title = {Elucidating microbial succession and aroma-active metabolite formation in hybrid dry-fermented sausage analogues with texturized pea protein: Integrating flavoromics, metabolomics, and metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {237}, number = {}, pages = {119324}, doi = {10.1016/j.foodres.2026.119324}, pmid = {42169289}, issn = {1873-7145}, mesh = {*Metabolomics/methods ; *Meat Products/microbiology/analysis ; *Odorants/analysis ; Fermentation ; *Metagenomics/methods ; Volatile Organic Compounds/analysis ; *Pea Proteins/metabolism ; Animals ; Gas Chromatography-Mass Spectrometry ; Taste ; Food Microbiology ; Humans ; Microbiota ; Swine ; Tandem Mass Spectrometry ; }, abstract = {Hybrid dry-fermented sausage analogues with texturized pea proteins (TPPs) are emerging, yet flavor formation mechanisms remain unclear. We combined quantitative descriptive analysis with complementary HS-SPME-GC-MS/HS-GC-IMS volatilomics, UHPLC-MS/MS untargeted metabolomics, and marker-gene microbiome sequencing across sausages with different fermentation and ripening stages to map key aroma and their potential microbial and metabolic drivers. Sensory data showed rising fruity, cocoa-chocolate and nutty notes. In total, 47 volatiles were identified by GC-MS and 40 by GC-IMS. Screening of odorants based on relative odor activity value (rOAV) consistently highlighted seven odorants, with a shift from hexanal-dominated raw profiles to linalool-dominated processed profiles, indicating suppression of aldehyde-derived off-notes and enrichment of terpene/ester notes. Metabolomics detected 2467 metabolites, dominated by lipids and organic acids, and short-peptide enrichment suggested intensified proteolysis supplying aroma precursors. Bacterial succession exceeded fungal variation, with Latilactobacillus and Staphylococcus as core taxa. The integrated dataset provides practical markers and microbial/process cues to enhance flavor quality of sustainable hybrid fermented meats.}, } @article {pmid42169351, year = {2026}, author = {Yang, S and Fu, X and Yang, Z and Zhang, T and Lu, C and Yi, L and Zhao, Q and Gu, Y and Wang, S}, title = {Metagenomic sequencing reveals the similarities and differences in microbial community structure and diversity between fermented whey and Rubing cheese, a fresh goat milk cheese.}, journal = {Food research international (Ottawa, Ont.)}, volume = {237}, number = {}, pages = {119400}, doi = {10.1016/j.foodres.2026.119400}, pmid = {42169351}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Animals ; Goats ; *Metagenomics/methods ; Fermentation ; *Whey/microbiology ; *Food Microbiology ; Biogenic Amines/analysis ; China ; Milk/microbiology ; *Microbiota ; Bacteria/genetics/classification ; }, abstract = {Rubing cheese is a traditional handmade goat milk cheese in Yunnan, China, and the fermented whey used in its production affects its quality and safety. This study employed metagenomic sequencing to systematically characterize the microbial communities in fermented whey and Rubing cheese and to quantitatively analyze their biogenic amine (BA) contents. Metagenomic analysis revealed that Rubing cheese had higher microbial diversity than fermented whey. Approximately 403 microbial species were identified in Rubing cheese, and 209 were identified in fermented whey. Notably, fermented whey was rich in lactic acid bacteria (LAB), such as Lactobacillus delbrueckii (L. delbrueckii), Lentilactobacillus hilgardii (Le. hilgardii), and Lacticaseibacillus paracasei (La. paracasei). In contrast, Rubing cheese contained a high abundance of Escherichia coli (E. coli). The total BA content was low in both fermented whey (20.25 mg·kg[-1]) and Rubing cheese (4.69 mg·kg[-1]). These findings provide a scientific basis for establishing standardized production processes for developing functional starter cultures in the industrialization of Rubing cheese production.}, } @article {pmid42169753, year = {2026}, author = {Song, D and Zhong, X and Zhang, G and Chen, J and Xue, Y and Yang, L}, title = {Linking geographic flavor signatures to microbial origin in high-temperature Daqu: An integrated metaproteomics and metabolomics approach.}, journal = {Food chemistry: X}, volume = {36}, number = {}, pages = {103952}, pmid = {42169753}, issn = {2590-1575}, abstract = {Elucidating the molecular architecture of microbial terroir is vital for precision fermentation, yet functional decoupling between taxonomic abundance and in situ expression remains a fundamental challenge. To resolve this "abundance-activity paradox," we integrated metaproteomics, metabolomics, and metagenomics across the Chishui River gradient. We identified distinct chemosensory fingerprints: upstream thermotolerant consortia (Bacillus and Oceanibacillus) specialize in 2,3,5,6-tetramethylpyrazine biosynthesis mediated by bacterial acetolactate decarboxylase, while downstream microbiota (Weissella and Debaryomyces) prioritize alcohol and ester formation. Crucially, metaproteomic profiling unmasked the "rare biosphere" as a primary driver of core metabolic fluxes. While Bacillus was genomically dominant, keystone functional taxa-specifically low-abundance fungi like Hyphopichia and Paecilomyces-were the actual executors of rate-limiting starch hydrolysis. Furthermore, functional resilience was uniquely maintained through robust fungal co-occurrence networks despite geographic constraints. This study challenges abundance-centric paradigms, providing an activity-based framework for the rational design of synthetic microbial consortia to standardize flavor while preserving regional identity.}, } @article {pmid42169756, year = {2026}, author = {Chen, Y and Yu, K and Sun, Y and Yan, Y and Yin, G and Wang, J and Li, X and Tang, S and Pronyk, P and Xia, Y}, title = {Plastic leachates drive conjugative transfer of antibiotic resistance genes.}, journal = {Environmental science and ecotechnology}, volume = {31}, number = {}, pages = {100705}, pmid = {42169756}, issn = {2666-4984}, abstract = {Plastic pollution pervades aquatic ecosystems worldwide, releasing leachates that interact intimately with microbial communities. Antibiotic resistance genes (ARGs) disseminate rapidly through horizontal gene transfer via plasmid conjugation, posing a severe and accelerating threat to public health and environmental stability. While microplastic particles are known to promote ARG exchange within biofilms, the influence of soluble chemical leachates derived from degrading plastics has remained unclear. Here we show that photodegraded leachate from polyvinyl chloride (PVC)-a widely used material in water infrastructure-substantially enhances conjugative transfer of ARGs in both laboratory model systems and natural aquatic microbiomes. Exposure increased transconjugant abundance up to 26.4-fold and conjugation efficiency up to 44.6-fold, with non-monotonic responses modulated by leachate concentration and microbial community diversity. Characterization of the leachate revealed high proportions of biolabile dissolved organic matter alongside additives; mechanistic assays demonstrated that these effects arise through elevated intracellular reactive oxygen species (21% increase), activation of the SOS response and DNA-repair pathways, increased extracellular protein production facilitating cell-cell contact, and compensatory adjustments in the electron transport chain that maintain ATP homeostasis. These results demonstrate that plastic leachates act as potent but previously overlooked facilitators of ARG dissemination beyond the physical effects of microplastics. Our findings reveal a critical synergy between plastic pollution and the global antimicrobial-resistance crisis, underscoring the urgent need for targeted regulations on plastic additives and degradation products in aquatic systems.}, } @article {pmid42170025, year = {2026}, author = {Higashi, K and Ishikawa, H and Kurokawa, K and Mori, H}, title = {PZLAST-MAG: full length protein sequence similarity search server of large-scale MAG proteins.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag129}, pmid = {42170025}, issn = {2635-0041}, abstract = {MOTIVATION: Metagenome-assembled genomes (MAGs) provide access to novel protein sequences from uncultured microbes, offering invaluable resources for studying protein diversity, structure prediction, and evolutionary analysis. However, despite the explosive growth of MAG-derived protein data, tools enabling fast and accurate similarity searches against large-scale MAG protein datasets remain limited.

RESULTS: We present PZLAST-MAG, a web server for ultra-fast sequence similarity searches against 0.4 billion MAG-derived protein sequences (0.1 trillion amino acids) from over 210 000 MAGs indexed in Microbiome Datahub. Implemented on PEZY-SC3 MIMD many-core processors, PZLAST-MAG achieves high accuracy and speed, with performance comparable to widely used tools such as DIAMOND and MMseqs2 based on our benchmark analyses. In addition to tabular alignments, PZLAST-MAG provides interactive visualizations of phylogenetic and environmental distributions and co-occurrence patterns of homologous proteins across MAGs. This combination enables rapid homolog mining of functionally important genes across diverse microbial lineages while simultaneously revealing their taxonomic and ecological contexts. Two use case analyses indicate its utility for homolog mining of metabolic enzyme genes and plasmid-derived genes.

PZLAST-MAG is provided as a web-based service and is freely available at https://pzlast.nig.ac.jp/pzlast/mag without requiring registration.}, } @article {pmid42170880, year = {2026}, author = {Ershova-Menze, E and Westgaard, JI and Hjellnes, H and Falkenhaug, T}, title = {Optimising Zooplankton DNA Metabarcoding: Methodological Considerations for Large-Scale Monitoring.}, journal = {Molecular ecology resources}, volume = {26}, number = {4}, pages = {e70149}, doi = {10.1111/1755-0998.70149}, pmid = {42170880}, issn = {1755-0998}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Zooplankton/genetics/classification ; Animals ; Biodiversity ; DNA/genetics/isolation & purification ; *Metagenomics/methods ; Electron Transport Complex IV/genetics ; }, abstract = {DNA metabarcoding is becoming an increasingly common approach in ecological monitoring of marine and freshwater planktonic communities, yet methodological choices along the metabarcoding workflow and data post-processing approaches remain highly inconsistent across studies, limiting the ability to track biodiversity trends, detect range shifts, or integrate datasets across monitoring programs. This study addresses this methodological bottleneck by combining controlled experimental comparisons with a comprehensive literature synthesis to identify how protocol decisions-from sample preservation and DNA extraction to sequencing platforms and taxonomic assignments-affect the results of COI metabarcoding and its interpretation. Overall biodiversity and community patterns were recovered by all combinations of tested methods, supporting the notion that patterns identified through DNA metabarcoding are robust and comparable across studies. We identify TES (Tris-EDTA-SDS) buffer, optionally paired with at-sea homogenisation, as a practical alternative to ethanol preservation for large-scale monitoring surveys. We show that integrating several classification methods and reference databases for taxonomic assignment improves diversity estimates and confidence in the assignments, and advocate for increased use of tools like BOLDigger that facilitate manual curation of ambiguous/erroneous references. Finally, we demonstrate that introducing stricter filtering thresholds reduces the effect of false positives, pseudogenes and lab-specific contamination, and make comparisons of data generated by different laboratories and methodological configurations more robust, although potentially at the expense of excluding rare taxa. While we intentionally refrain from recommending a universal best practices protocol, this study aims to provide a practical roadmap to help enhance the reliability and reproducibility of marine zooplankton monitoring via DNA metabarcoding.}, } @article {pmid42171141, year = {2026}, author = {Tagliamonte, S and Neill, HR and Murphy, BÓ and Pourshahidi, KL and De Filippis, F and Ercolini, D and Gill, CIR and Natalia, K and Curran, B and Nicole, M and Mary, S and Dobani, S and Fontana, M and Vitaglione, P}, title = {Dietary N-acylethanolamines are bioaccessible in the small intestine and modulate postprandial hormonal responses: a randomized crossover trial in subjects with ileostomy.}, journal = {Food & function}, volume = {17}, number = {11}, pages = {5106-5117}, doi = {10.1039/d5fo03328d}, pmid = {42171141}, issn = {2042-650X}, mesh = {Humans ; Female ; Postprandial Period ; Male ; Cross-Over Studies ; *Ileostomy ; Double-Blind Method ; Middle Aged ; *Ethanolamines/metabolism/administration & dosage ; *Intestine, Small/metabolism ; Adult ; Aged ; Endocannabinoids ; Blood Glucose/metabolism ; *Gastrointestinal Hormones/metabolism ; }, abstract = {N-Acylethanolamines (NAEs) are bioactive lipid mediators involved in the regulation of appetite, inflammation, and gut-brain signaling. This study investigated the metabolic fate of dietary NAEs following the consumption of two test meals with differing NAE contents in subjects with ileostomy and evaluated their effects on gastrointestinal hormones, glycaemia, and appetite regulation. An acute, double-blind, randomized, crossover postprandial study was conducted in ileostomy patients who consumed either a high-NAE meal (HNM) or a low-NAE meal (LNM) on two separate occasions. Ileal fluid and plasma samples were collected over an 8-hour postprandial period for analysis of NAEs and endocannabinoids (ECs). Baseline ileal microbiota composition was assessed. At the end of the 8-hour period, participants completed a buffet meal test to evaluate ad libitum energy intake. Dietary NAEs were significantly recovered in ileal fluids after HNM intake, with concentrations approximately 3-fold higher than those after LNM, suggesting partial digestion and release from the food matrix. No significant differences in postprandial plasma NAE concentrations were observed between meals. HNM consumption led to higher postprandial levels of plasma insulin, C-peptide, and glucose-dependent insulinotropic polypeptide, despite no differences in glycemic response or subsequent ad libitum energy intake. Metagenomic analysis identified clusters of ileal microbial taxa associated with circulating lipid profiles, suggesting a role of the small intestinal microbiota in the metabolism of NAEs and ECs. Dietary NAEs reach the small intestine at active concentrations and may influence local signaling via GPR119, with microbiota composition influencing their release from food.}, } @article {pmid42171373, year = {2026}, author = {Schroer, HW and Beghini, F and Raygoza Garay, JA and Christakis, NA and Bosch, DE}, title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0030526}, doi = {10.1128/msystems.00305-26}, pmid = {42171373}, issn = {2379-5077}, abstract = {Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.}, } @article {pmid42171625, year = {2026}, author = {Paietta, EN and Johnston, RA and Kraberger, S and Randrianarisoa, SF and Razanamahenina, TT and Ramboninarimalala, A and Velontsara, JB and Raherinirina, TG and Raveloson, L and Finley, NL and Baitchman, E and McAdoo, BG and Yoder, AD and Varsani, A}, title = {Mammal-infecting DNA viruses identified in lemurs and rodents in Madagascar mirror the evolutionary history of their hosts.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42171625}, issn = {2057-5858}, mesh = {Animals ; Madagascar ; *Lemur/virology ; *DNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; *Rodentia/virology ; Rats/virology ; Metagenomics ; Genome, Viral ; }, abstract = {Given that some DNA viruses have been found to exhibit virus-host co-evolution and establish lifelong infection, mammals with unique evolutionary histories in island ecosystems likely host exceptionally diverse viruses. Madagascar is inhabited by endemic non-human primate and rodent lineages interacting with expansive populations of introduced non-native rodents across the island. Using a viral metagenomic workflow on 189 oral swabs of lemurs and rodents in southeastern Madagascar, we characterized genomic sequences of DNA viruses in the families Adenoviridae, Circoviridae, Orthoherpesviridae, Papillomaviridae, Parvoviridae and Polyomaviridae and assessed their phylogenetic relationships to known viruses. Endemic lemurs and tufted-tailed rats displayed particularly novel DNA viral diversity mirroring the geographic isolation and subsequently rich evolutionary history of their hosts. Notably, we provide the first coding-complete sequences in lemurs of herpesviruses, polyomaviruses, adeno-associated viruses and circoviruses. In contrast, the DNA viral communities of black rats in Madagascar were similar to those found in globally distributed black and brown rat populations, given their broad geographic spread and relatively recent introduction to the island. Given the scarcity of viral research in natural populations of lemurs and rodents in Madagascar despite the island's exceptional biodiversity and escalating anthropogenic pressures, this study provides a genomic and phylogenetic foundation for DNA viruses infecting Malagasy lemurs and rodents.}, } @article {pmid42171661, year = {2026}, author = {Goodall, T and Busi, SB and Jones, B and Thorpe, A and Griffiths, RI and Redhead, J and Hulmes, L and Hulmes, S and Ridding, L and Peyton, J and Pereira, G and Gweon, HS and Read, DS and Pywell, R}, title = {Taxonomic filtering accompanies functional expansion during long-term soil restoration.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42171661}, issn = {1751-7370}, support = {BBX011089/1//UK Research and Innovation/ ; NE/S005137/1//UK Research and Innovation/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Bacteria/classification/genetics ; Grassland ; Metagenomics ; United Kingdom ; Ecosystem ; Biodiversity ; }, abstract = {The restoration of species-rich calcareous grasslands is a critical conservation objective, yet the recovery of the invisible below-ground microbiome remains poorly quantified compared to above-ground vegetation. Using a unique 143-year land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly across arable, regenerating (23 and 67 years), and ancient grasslands. By integrating vegetation surveys with soil physiochemistry, microbial profiling, and shotgun metagenomics, we identified a decoupling between floral and edaphic recovery. While the diversity of vegetation recovered relatively rapidly, approaching ancient grassland levels within 23-67 years, soil properties exhibited persistent legacy effects and slow convergence. Bacterial richness decreased with restoration age; this taxonomic contraction was conversely matched by an expansion in inferred metagenomic functional potential. This was reflected in increased functional gene richness and shifts in the relative abundance of specific SEED-annotated functions towards metabolic pathways associated with complex carbon cycling and stress tolerance. These shifts were congruent with the emergence of specific, unnamed genera belonging to Pseudomonadota and Actinomycetota, and the Bacillota species Pristimantibacillus. The soil ecosystem remained distinct from the 143-year stage even after 67 years of recovery, characterized by persistent legacy phosphorus and a slow accumulation of soil organic matter. These findings suggest that passive regeneration alone may be insufficient for full soil functional recovery, and that strategies targeting microbial assembly and long-term carbon dynamics warrant further evaluation.}, } @article {pmid42171933, year = {2026}, author = {Xu, Y and Sun, X and Xu, S and Deng, S and Zhang, Y}, title = {Clinical profile of microsporidial keratoconjunctivitis in healthy individuals of China -new species and neglected risk factors.}, journal = {Journal of ophthalmic inflammation and infection}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12348-026-00596-9}, pmid = {42171933}, issn = {1869-5760}, abstract = {OBJECTIVE: To characterize microsporidial keratoconjunctivitis (MKC) in immunocompetent individuals in Mainland China, including novel etiologies and risk factors.

METHODS: A prospective analysis of 20 MKC patients in 2025, including clinical features, pathogens (via corneal scrapings and metagenomic sequencing), risk factors and etc. RESULTS: All patients were misdiagnosed for a median of 1 month. Patients (mean age 28.5 years, 13 F) showed Encephalitozoon hellem (65.0%), E. bieneusi (15.0%, first reported in MKC), and Vittaforma corneae (15.0%). Key risks included bird contact (70.0%, mostly psittacines), contact lens use (40.0%), and water exposure (15.0%). The most common symptom was redness (85.0%); limbal fluorescein positivity occurred in 65.0%. Topical 0.02% PHMB cured 90.0% of 20 cases; one recurrence followed treatment stop. Some E. hellem cases linked to parrots showed potential zoonotic transmission.

CONCLUSION: MKC in China involves E. bieneusi and parrot-associated E. hellem. Limbal staining aids diagnosis; PHMB is effective. Zoonotic risks related to Psittacine birds and contact lens use require clinical attention.}, } @article {pmid42172047, year = {2026}, author = {Delgado, LF and Ortís Sunyer, J and Laczny, CC and Hickl, O and May, P and Wilmes, P}, title = {PathoFact 2.0: an integrative pipeline for the prediction of antimicrobial resistance genes, virulence factors, toxins and toxin-associated proteins, and biosynthetic gene clusters in metagenomes.}, journal = {GigaScience}, volume = {15}, number = {}, pages = {}, pmid = {42172047}, issn = {2047-217X}, support = {C23/BM/18091896//Luxembourg National Research Fund/ ; ERC-CoG 863664/ERC_/European Research Council/International ; }, mesh = {*Virulence Factors/genetics ; *Multigene Family ; *Metagenome ; *Software ; Machine Learning ; *Drug Resistance, Bacterial/genetics ; *Computational Biology/methods ; Bacterial Toxins/genetics ; }, abstract = {BACKGROUND: Antimicrobial resistance genes (ARGs) and virulence factors (VFs) are central contributors to the global health crisis surrounding drug-resistant infections.

FINDINGS: We introduce PathoFact 2.0, an enhanced pipeline for improved ARG, VF, toxin, and biosynthetic gene clusters (BGCs) prediction. Key improvements include an updated machine learning (ML) model for VF identification, expanded hidden Markov model profiles for VFs and toxin-associated proteins, a new ML model for toxin and toxin-associated proteins identification, and the integration of antiSMASH 7.0 for predicting BGCs.

CONCLUSIONS: Our upgrades make PathoFact 2.0 a more powerful and user-friendly platform for predicting microbiome-based pathogenicity and resistance, providing a crucial tool for better understanding and addressing the challenges posed by antimicrobial resistance and infectious diseases.PathoFact 2.0 is available at https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2. It is compatible with Linux operating systems.}, } @article {pmid42172141, year = {2026}, author = {Long, K and Gravel-Pucillo, K and Waldron, L and Davis, S and Oh, S}, title = {Large-scale manual curation and harmonization of metadata from metagenomic and cancer genomic repositories: challenges and solutions.}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, pmid = {42172141}, issn = {1758-0463}, support = {/CA/NCI NIH HHS/United States ; U24CA289073/NH/NIH HHS/United States ; 3U24CA180996-10S1/NH/NIH HHS/United States ; }, mesh = {*Metadata/standards ; Humans ; *Data Curation/methods ; *Neoplasms/genetics ; *Databases, Genetic ; *Metagenomics ; *Genomics ; }, abstract = {Public omics repositories contain vast amounts of valuable data, but their metadata suffers from extreme heterogeneity, unstandardized terminologies, and quality issues that severely limit data reusability and cross-study integration. While prospective metadata standards exist, the majority of published omics data remain in non-standardized formats requiring retrospective harmonization. We performed comprehensive manual curation and harmonization of metadata, such as participant characteristics and study conditions, from 212 027 omics samples across 468 studies in two repositories: curatedMetagenomicData (93 studies, 22 588 samples) and cBioPortal (375 studies, 189 438 samples). Through systematic ontology mapping, we consolidated redundant, dispersed information into far fewer harmonized columns, reduced unique values, and increased the completeness of major attributes. This curation process revealed common metadata quality issues, including typos, inconsistent terminologies, misplaced values, conflicting annotations, and inappropriately merged information across attributes. We document the challenges, decisions, and solutions during this large-scale metadata harmonization. The harmonized metadata, accessible through the OmicsMLRepoR Bioconductor package, enables repository-wide queries and cross-study analyses previously challenging with heterogeneous metadata. Our experience provides practical guidance for similar curation efforts and demonstrates the value of investing in retrospective metadata improvement for existing public omics resources.}, } @article {pmid42172324, year = {2026}, author = {Freschlin, CR and Yang, KK and Romero, PA}, title = {Scalable and cost-efficient custom gene library assembly from oligopools.}, journal = {Science advances}, volume = {12}, number = {21}, pages = {eady2279}, pmid = {42172324}, issn = {2375-2548}, support = {R01 GM150929/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gene Library ; Software ; *Oligonucleotides/genetics ; Computational Biology/methods ; }, abstract = {Advances in metagenomics, deep learning, and generative protein design have enabled broad in silico exploration of sequence space, but experimental characterization is still constrained by the cost and scalability of DNA synthesis. Here, we present OMEGA (Oligo-based Multiplexed Efficient Gene Assembly), a low-cost, accessible method for assembling hundreds to thousands of full-length genes in parallel using standard laboratory techniques. OMEGA computationally fragments target genes into short, high-fidelity Golden Gate-compatible oligonucleotides that can be ordered as a pooled library and assembled across multiplexed subpools. We systematically optimized the number of fragments per gene and orthogonal ligation sites per reaction and determine that OMEGA can assemble up to 2.6-kilobase constructs using as many as 70 Golden Gate sites. To validate the approach, we assembled and functionally screened a library of 810 natural and synthetic green fluorescent protein variants, recovering 94 to 97% of target sequences with high uniformity. OMEGA enables precision library construction at scale, with per-gene costs as low as $1.50, and offers a broadly applicable solution for bridging computational protein design with high-throughput experimental validation. We have developed OMEGA as an open-source software package and an easy-to-use Colab notebook to facilitate community adaptation.}, } @article {pmid42172586, year = {2026}, author = {Singh, R and Gupta, P and Singh, R and Basant, N}, title = {Environmental Antibiotic Contamination and AMR: Integrating Pathways, Impacts, and AI-Driven Mitigation.}, journal = {Environmental toxicology and chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/etojnl/vgag115}, pmid = {42172586}, issn = {1552-8618}, abstract = {The widespread contamination of the environment with antibiotic residues is a significant factor contributing to the global crisis of antimicrobial resistance. Antibiotics from various sources, such as effluents from municipal and hospital wastewater treatment plants, agricultural runoffs, discharges from pharmaceutical manufacturing and improper disposal of expired or unused medicines, create selective pressures in the spread of antibiotic resistance genes. These environmental reservoirs act as hotspots for horizontal gene transfer, facilitating the emergence of multidrug-resistant pathogens. Conventional detection methods including culture-based assays, chromatographic quantification, and molecular diagnostics, provide essential insights but are limited by low throughput, reduced sensitivity to new Antibiotic Resistance Genes, and challenges in real-time monitoring across complex environments. Recent advances, such as whole-genome sequencing, metagenomics, and biosensor-based detection, help to address these gaps by enabling more comprehensive surveillance of the resistome. Artificial intelligence further enhances these approaches by improving data interpretation and pattern recognition, thus complementing traditional and molecular methods rather than replacing them. This review examines the pathways of environmental antibiotic contamination, ecological and health impacts of Antimicrobial Resistance (AMR), and limitations of conventional detection methods. It aims to clarify how these pathways contribute to the AMR crisis, assess the effectiveness of existing surveillance techniques, and identify gaps in current research.}, } @article {pmid42172842, year = {2026}, author = {Chen, X and Tan, QG and Pan, K and Xiao, A and Cheng, H and Wang, X}, title = {Vegetation of exotic fast-growing species Sonneratia apetala increases the potential of methylmercury production: Insights from carbon bioavailability, microbial metabolism and mercury methylators.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142469}, doi = {10.1016/j.jhazmat.2026.142469}, pmid = {42172842}, issn = {1873-3336}, mesh = {*Methylmercury Compounds/metabolism ; *Carbon/metabolism ; Geologic Sediments/microbiology/chemistry ; Methylation ; Bacteria/metabolism/genetics ; China ; }, abstract = {Mangrove sediments are hotspots for neurotoxic methylmercury (MeHg) production, with litter-derived organic carbon strongly affecting mercury (Hg) methylation. However, the specific role of carbon bioavailability in regulating net MeHg production remains unclear. This study investigated sediments vegetated by exotic fast-growing Sonneratia apetala (SA) and native Kandelia obovata (KO) in southern China. Contrary to the expectation that larger carbon pools enhance methylation, MeHg levels were 2.1-2.6 times higher in SA sediments despite KO containing 1.2-4.2 times more total organic carbon. This disparity was driven by carbon bioavailability: SA sediments exhibited a significantly higher proportion of available carbon (34-50%) compared to KO (28-36%), which stimulated microbial activity and enriched Hg-methylating microbes (1.4-3.3 times higher in hgcAB gene abundance). Metagenomics showed that SA not only promoted key Hg-methylating taxa (e.g., Desulfobacterales, Syntrophobacteria) but also upregulated their metabolic pathways for labile carbon use and methyl transfer to Hg. Our results demonstrate that carbon bioavailability, governed by species-specific litter chemistry, is the key driver of net MeHg production. The findings provide an in-depth understanding of Hg biogeochemistry by linking soil carbon quality to microbial metabolic networks, and offer novel insights for evaluating the ecological risks associated with exotic species in mangrove restoration.}, } @article {pmid42172844, year = {2026}, author = {Xu, Y and Xie, T and Zhong, W and Yang, G and Zhang, W}, title = {Probable disseminated Mycobacterium avium complex infection in an apparently immunocompetent patient: A case report and literature review.}, journal = {Journal of infection and public health}, volume = {19}, number = {7}, pages = {103245}, doi = {10.1016/j.jiph.2026.103245}, pmid = {42172844}, issn = {1876-035X}, mesh = {Humans ; *Mycobacterium avium-intracellulare Infection/diagnosis/drug therapy/microbiology/pathology ; *Mycobacterium avium Complex/isolation & purification/genetics ; High-Throughput Nucleotide Sequencing ; Osteomyelitis/microbiology/diagnosis ; Anti-Bacterial Agents/therapeutic use ; Immunocompetence ; Skin Ulcer/microbiology ; Male ; }, abstract = {Disseminated Mycobacterium avium complex (MAC) infection is rare in immunocompetent hosts. This often leads to diagnostic delays. We report a challenging case of an apparently immunocompetent patient with pulmonary lesions, osteomyelitis, and skin ulcers. While routine cultures were pending, metagenomic next-generation sequencing (mNGS) rapidly identified MAC, enabling timely treatment. Subsequent culture and species identification confirmed the pathogen as Mycobacterium colombiense. Systematic reviews since 2000 have shown that skeletal and pulmonary involvement are common in this population. Diagnosis has gradually incorporated molecular biological techniques, and with timely treatment, patient outcomes are generally favorable. Our findings highlight the limitations of traditional microbiology and demonstrate that mNGS is a vital adjunctive tool for slow-growing pathogens. We conclude that disseminated MAC should be considered in refractory multifocal infections, even without recognized immunodeficiencies. Early molecular diagnosis, individualized multidrug therapy, and rigorous follow-up are essential for clinical remission.}, } @article {pmid42172850, year = {2026}, author = {Li, Y and Shi, B and Li, D and Li, YA and Yuan, M and Luo, J and Dong, S and Wen, W and Zhao, R}, title = {Microbial community shift and functional reorganization from influent to effluent in wastewater treatment plants on the Qinghai-Tibet Plateau.}, journal = {Journal of environmental management}, volume = {409}, number = {}, pages = {130036}, doi = {10.1016/j.jenvman.2026.130036}, pmid = {42172850}, issn = {1095-8630}, mesh = {Tibet ; *Wastewater/microbiology ; RNA, Ribosomal, 16S ; *Waste Disposal, Fluid ; *Microbiota ; Bacteria ; Altitude ; Metagenomics ; }, abstract = {Wastewater treatment plants (WWTPs) on the Qinghai-Tibet Plateau play a critical role in safeguarding fragile high-altitude aquatic ecosystems. However, microbial community structure and functional characteristics in the influent and effluent in high-altitude WWTPs remain poorly understood. Here, we integrated 16S rRNA gene amplicon sequencing with metagenomic gene-centric profiling and genome-resolved reconstruction to investigate influent and final effluent microbiomes from 18 municipal WWTPs across five cities in Qinghai Province. The results showed that alpha diversity was comparable between influent and effluent, whereas microbial community composition differed significantly. Co-occurrence networks revealed a simplified and more modular interaction pattern in effluent, accompanied by fewer keystone taxa compared with influent. Metagenomic analyses showed that major metabolic pathways were retained across treatment stages, but their relative abundances declined toward effluent. Genome-resolved analyses further indicated this treatment-associated functional reorganization primarily reflected shifts in the taxa and genomic coverage supporting these pathways, rather than replacement of pathway categories. Pseudomonadota accounted for the largest proportion of metabolic contributions across carbon, nitrogen, and sulfur transformation pathways, while multiple pathways persisted in effluent but were encoded by fewer genomes with lower coverage. Denitrification-associated steps, particularly nitric oxide and nitrous oxide reduction, constituted major genome-level contributions to nitrogen removal potential. Notably, Patescibacteria were significantly enriched in effluent and exhibited highly simplified genomes dominated by energy-conserving traits. These results reveal treatment-associated microbial and functional reorganization in plateau WWTPs and provide a genome-resolved framework for interpreting microbial metabolic potential in high-altitude wastewater systems.}, } @article {pmid42172982, year = {2026}, author = {Yan, S and Zhang, Y and Fan, Q and Jia, W and Dai, Y and Li, X and Lu, S and Sheng, Y and Sun, S and Lin, R and Tang, Y and Zhao, C}, title = {Evodiamine targets ZO-1 to ameliorate cholestatic liver disease: Intestinal homeostasis as the core mediator of gut-liver axis repair and bile acid metabolism remodeling.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {157}, number = {}, pages = {158288}, doi = {10.1016/j.phymed.2026.158288}, pmid = {42172982}, issn = {1618-095X}, mesh = {Animals ; Homeostasis/drug effects ; Male ; *Zonula Occludens-1 Protein/metabolism ; *Bile Acids and Salts/metabolism ; Liver/drug effects/metabolism ; Rats ; Rats, Sprague-Dawley ; *Quinazolines/pharmacology ; *Cholestasis/drug therapy/metabolism ; Gastrointestinal Microbiome/drug effects ; Intestines/drug effects ; Fecal Microbiota Transplantation ; Disease Models, Animal ; *Liver Diseases/drug therapy/metabolism ; }, abstract = {BACKGROUND: Cholestatic liver disease (CLD) is a complex and multifactorial chronic disorder that requires a systematic and integrative management. Evodiamine (EVO), a natural alkaloid derived from Evodiae Fructus, has demonstrated significant therapeutic potential in ameliorating digestive diseases. However, the beneficial effects of EVO on CLD and the underlying mechanisms remain poorly understood.

OBJECTIVE: This study aims to elucidate the mechanisms through which EVO modulates the progression of CLD, with a particular focus on the regulation of gut-liver axis homeostasis.

METHODS: The therapeutic efficacy of EVO in bile duct ligation (BDL)- and α-naphthyl isothiocyanate (ANIT)-induced CLD rat models was systematically evaluated. An integrative approach combining network pharmacology with multi-omics analyses (transcriptomic, metagenomic sequencing, targeted bile acid metabolomics) was employed to identify significantly altered molecular networks. Fecal microbiota transplantation (FMT) was conducted to validate the functional role of gut microbiota in the hepato-intestinal protective effects. Direct molecular targets as well as the functional validation were confirmed through molecular docking, pull-down assays, surface plasmon resonance and cellular thermal shift assay.

RESULTS: EVO achieved significant synchronous hepato-intestine protection in both CLD rats: it markedly ameliorated hepatic injury and hepatic fibrosis, downregulated pro-inflammatory cytokine levels, while preserving intestinal barrier integrity and alleviating intestinal inflammation. Mechanistically, EVO exerted these protective effects by directly targeting the tight junction protein ZO-1 and enhancing its expression and stability. Furthermore, EVO restored intestinal microbial homeostasis, corrected dysregulated BA metabolism-specifically normalizing deoxycholic acid (DCA) levels. FMT experiments demonstrated that the synchronous hepato-intestinal beneficial effects of EVO were partially mediated by gut microbiota.

CONCLUSION: EVO exerts a protective effect against CLD by directly targeting ZO-1 to strengthen intestinal barrier function, thereby restoring gut microbial balance and rebalancing BAs metabolism (especially DCA levels) in the gut-liver axis. This study uncovers a novel ZO-1-dependent mechanism of EVO in CLD, highlighting EVO as a promising candidate for the treatment of CLD and providing new insights into gut-liver axis-targeted therapies.}, } @article {pmid42173380, year = {2026}, author = {Du, S and Ding, S and Zhao, Y and Wang, Y and Ju, F and Wu, D}, title = {Maintaining oxygen above a critical threshold prevents acetate-driven phytotoxicity in industrial-scale aerobic composting: metagenomic, MAG, and enzyme-activity evidence.}, journal = {Bioresource technology}, volume = {456}, number = {}, pages = {134949}, doi = {10.1016/j.biortech.2026.134949}, pmid = {42173380}, issn = {1873-2976}, mesh = {*Oxygen/metabolism/pharmacology ; *Acetates/toxicity ; *Composting/methods ; Aerobiosis ; Germination/drug effects ; *Metagenomics/methods ; }, abstract = {Aerobic composting is a key route for organic-waste valorization, yet product utilization is often constrained by phytotoxicity and low germination index (GI), particularly under oxygen-limited operation. Here, we developed an actionable oxygen-control window (O2 ≥ 10% v/v) to mitigate acetate-associated GI inhibition by integrating process monitoring with inhibitor profiling of GI extracts, metagenomics/metagenome-assembled genomes (MAGs), and pyruvate dehydrogenase (PDH) activity measurements. Three composting modes were implemented to create contrasting oxygen regimes: mechanical composting (MC; well-aerated), forced aeration composting (FC; intermittently oxygen-limited), and static composting (SC; ventilation-supported static aerobic). Chemical profiling and mixed-effects/regression analyses identified acetate as the dominant GI-inhibiting compound relative to other candidates (e.g., ammonium, formate, chloride). A bench-scale oxygen-gradient validation experiment (0-21% O2) confirmed an oxygen dose-response of acetate accumulation: acetate reached 1163.5 and 865.4 mg/L at 0% and 5% O2, but remained near baseline at ≥ 10% O2 (85.8 and 80.2 mg/L at 10% and 21% O2, respectively; 24 h), defining an oxygen window for suppressing acetate build-up. To probe mechanism, KEGG-based pathway mapping showed that acetate-linked functions were dominated by pyruvate metabolism, and high-acetate states were associated with reduced PDH-related functional gene abundance (PDHA/B) and lower PDH activity. MAG co-occurrence and correlation analyses further linked acetate-associated states to specific MAG-level contributors (including Thermobifida fusca). Together, these results support a PDH-linked metabolic constraint under oxygen limitation that promotes acetate persistence and GI inhibition, and provide operational guidance to maintain in-pile O2 ≥ 10% (v/v) to reduce acetate-driven phytotoxicity in industrial composting of readily acidogenic wastes.}, } @article {pmid42173516, year = {2026}, author = {Ogasawara, K and Uno, K and Tamahara, T and Asano, N and Sudo, K and Kusano, K and Tanabe, M and Kaise, Y and Shindo, T and Shimoyama, Y and Kanno, T and Koike, T and Shimizu, R and Masamune, A}, title = {Antibiotics treatment promotes squamocolumnar junction tumor progression via tumor immune evasion in K19-Wnt1/C2mE mice fed high-fat diet and acidic bile salts.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {331}, number = {1}, pages = {G38-G59}, doi = {10.1152/ajpgi.00056.2026}, pmid = {42173516}, issn = {1522-1547}, support = {19K08434//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 23K07368//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 24K13105//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Anti-Bacterial Agents/pharmacology/toxicity ; *Tumor Escape/drug effects ; Male ; Mice ; *Bile Acids and Salts ; Dysbiosis/chemically induced ; STAT1 Transcription Factor/metabolism ; Wnt1 Protein/genetics/metabolism ; STAT3 Transcription Factor/metabolism ; Disease Progression ; B7-H1 Antigen/metabolism ; Humans ; Gastrointestinal Microbiome/drug effects ; Cell Proliferation/drug effects ; Mice, Inbred C57BL ; Interferon-gamma/metabolism ; }, abstract = {Clinical studies suggested that antibiotics (ABx) administration might increase esophagogastric junction adenocarcinoma risk, but the underlying mechanisms remain unclear. We previously demonstrated that the administration of a high-fat diet (HFD) and acid bile salts (ABS) to K19-Wnt1/C2mE mice might promote the metabolic-driven tumor growth at the squamocolumnar junction (SCJ) cooperatively with gut dysbiosis. To clarify whether ABx-induced dysbiosis promotes tumorigenesis, we evaluated the effects of HFD + ABS ± ABx treatment on tumor immune evasion in mice. In HFD + ABS + ABx-treated mice, SCJ tumor growth with increased tumor cell proliferation and infiltration of inflammatory cells positive for CD8, programmed cell death protein 1, and programmed cell death-ligand 1 (PD-L1) was observed, along with apoptosis suppression. Protein expressions of interferon-gamma (IFNγ) and phosphorylated signal transducer and activator of transcription (p-STAT) 3 were upregulated in the tumors of the HFD + ABS + ABx group, whose p-STAT1 expression was equivalent to that of the control group. The mice exhibited insulin resistance and metabolic endotoxemia, and metagenomic analysis of their ileal excrement revealed dysbiosis with a decrease in butyrate-producing bacteria and bacterial butanoate metabolism activity. Moreover, IFNγ stimulation of human-derived NUGC-4 cells increased the protein expression of PD-L1, p-STAT1, and p-STAT3, all of which decreased in response to STAT inhibitors. Transfection with small interfering RNA targeting STAT1 or STAT3 did not attenuate PD-L1 induction, which was inhibited by the combined knockdown. Therefore, oral HFD + ABS + ABx administration to K19-Wnt1/C2mE mice may promote SCJ tumors through tumor immune evasion via IFNγ-STAT1/STAT3-PD-L1 signaling, along with metabolic endotoxemia.NEW & NOTEWORTHY Coadministration of antibiotics with a high-fat diet and acid bile salts exacerbated dysbiosis, insulin resistance, and systemic inflammation, thereby promoting tumor progression via tumor immune evasion at the squamocolumnar junction (SCJ) in K19-Wnt1/C2mE mice. In the tumor, interferon-gamma-induced programmed death-ligand 1 through the activation of signal transducer and activator of transcription 1 (STAT1) and STAT3. Understanding the link between dysbiosis and tumor immunity might aid in the development of new immunotherapies for SCJ tumors.}, } @article {pmid42173938, year = {2026}, author = {van Beek, N and Bargheet, A and Jian, C and Noordzij, HT and Ponsero, A and Pettersen, VK and Korpela, KE}, title = {Metagenomic survey of pathogen prevalence in the infant gut.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47440-7}, pmid = {42173938}, issn = {2045-2322}, support = {101039583//ERC Starting Grant/ ; }, abstract = {The human microbiota impacts our health and well-being from infancy throughout our lives. Besides mutualistic and commensal strains, it also contains opportunistic pathogens. Infants may be especially vulnerable to opportunistic pathogen colonisation due to their immature immune systems and low microbial diversity.The study aims to examine associations between opportunistic pathogen prevalence and factors such as breastfeeding, antibiotic use, birth-mode, and the presence of other bacterial taxa. This study analysed 3981 publicly available shotgun metagenomes collected from 1275 infants and 415 mothers across ten countries to identify species that may be considered opportunistic pathogens in the infant gut. The prevalence of C. difficile was decreased in breastfed infants and in those carrying Faecalibacterium and Dorea spp. S. aureus carriage was negatively associated with antibiotic use and positively with skin contact and breastfeeding. K. pneumoniae was acquired later in life and was more prevalent in premature infants, and less commonplace in vaginal deliveries without antibiotics. Our findings indicate that opportunistic pathogen prevalence in the infant gut is influenced by medical and caregiving practices and may be modifiable through targeted interventions. Reducing the spread of these opportunistic pathogens could contribute to global efforts against early life infections.}, } @article {pmid42174003, year = {2026}, author = {Kumari, R and Ghosh, C and Kumar, R and Shakya, R and Kumar, S and Saini, AK}, title = {Assessment of water quality and microbial contamination in institutional water resources: a necessity to understand health risks.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53672-4}, pmid = {42174003}, issn = {2045-2322}, support = {project grant MH-32/2024//R&D cell, Miranda House, University of Delhi, India/ ; }, abstract = {Lack of regular monitoring of water sources may lead to undetected contamination, posing serious health risks and necessitating regular water quality assessments. Sampling for physicochemical, microbial analyses, and online surveys across three higher education institutions was done to evaluate water quality. Spatiotemporal variations among physicochemical parameters showed that the pH, EC, and TDS decreased during the wet season, reflecting the dilution effect of rain. However, DO increased from 0.67 to 4.83 ppm, indicating better aeration. PCA showed seasonal variability, whereas the correlation matrix highlighted both positive and negative interrelationships between temperature-pH (- 0.25), DO-ORP (0.11), and TDS-EC (1.00). Potentially toxic metals were either negligible or not detected. Metagenomics revealed the presence of 29 bacterial phyla, 61 classes, 124 orders, 241 families, and 457 genera. Canonical correspondence analysis showed the influence of Mo, EC, salinity, and TDS on Bacteroidota, Chloroflexota, Cyanobacteriota, and Planctomycetota, whereas Verrucomicrobiota, Acidobacteriota, Chlamydiota, Candidatus Melainabacteria, Bdellovibrionota, and Deinococcota were affected by Ni, pH, and COD. Pathogen mapping revealed the presence of Vibrio, Pseudomonas, Enterobacter spp., etc., responsible for diseases such as cholera, diarrhea, and typhoid. Also, occupants' perception about the water quality emphasizes the need for better management of drinking water in HEIs.}, } @article {pmid42174021, year = {2026}, author = {Min, U and Kim, J and Kim, J and Jin, H and Oh, H and Ahn, S and Shin, H and Lee, W}, title = {Spicy food intake and dietary factors shape the gut microbiome and metabolism of mucin and short-chain fatty acids in healthy adults.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53556-7}, pmid = {42174021}, issn = {2045-2322}, abstract = {Whether spicy food intake independently modulates mucin metabolism and short-chain fatty acid (SCFA) production or depends on co-ingested factors such as alcohol remains poorly understood. Herein, shotgun metagenomics characterized gut microbial composition, functional pathways, and their relationship with spicy food intake, alcohol consumption, and intestinal fatty acid-binding protein (I-FABP) and liver fatty acid-binding protein (L-FABP) levels in 229 healthy Korean adults. Alcohol intake was positively correlated with urinary I-FABP levels indicating mild epithelial stress, whereas spicy food intake was not associated with either FABP biomarker. Consumption of highly spicy foods resulted in increased abundance of SCFA-producing and mucin-metabolizing taxa, along with mucin degradation and SCFA production. Individuals with high alcohol intake showed stronger enrichment of mucin-degrading taxa with reduced SCFA flux and increased abundance of Proteobacteria and Fusobacteria. The cross-classified dietary groups exhibited distinct mucin and SCFA activity patterns. The Drink-High-Spicy-High (DHSH) group displayed elevated mucin turnover and SCFA production with dysbiosis. These findings suggest that spicy food may modulate mucus layer metabolism in a context-dependent manner, whereas alcohol more consistently perturbs mucin-SCFA networks and epithelial integrity.}, } @article {pmid42174437, year = {2026}, author = {van Bemmelen, J and Nika, I and Baaijens, JA}, title = {Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12874-w}, pmid = {42174437}, issn = {1471-2164}, abstract = {BACKGROUND: Over the past decades, genome databases have expanded exponentially, often incorporating highly similar genomes at the same taxonomic level. This redundancy can hinder taxonomic classification, leading to difficulties distinguishing between closely related sequences and increasing computational demands. While some novel taxonomic classification tools address this redundancy by selecting a subset of genomes as references, insights regarding the impact of different reference genome selection methods across taxonomic classification tools are lacking.

RESULTS: We systematically evaluate genome selection and dereplication methods on bacterial and viral datasets using simulated metagenomic samples and a bacterial mock community. For bacterial species-level profiling, incorporating all available genomes generally yields the highest accuracy, while having a limited impact on computational resource usage. In contrast, for highly similar bacterial strain-level and SARS-CoV-2 lineage-level datasets we find that selection significantly improves abundance estimation accuracy. Incorporating location-based metadata further enhances viral profiling performance by prioritizing locally relevant genomes. Across viral experiments, smaller reference sets significantly reduce memory and runtime requirements during both indexing and profiling, although this comes at an additional pre-processing cost.

CONCLUSIONS: Reference genome selection influences both accuracy and computational efficiency in taxonomic profiling, but its benefits seem context- and resolution-dependent. Our results demonstrate that reference set design does not have a one-size-fits-all solution, and that selection strategies should be adapted based on the biological and computational setting.}, } @article {pmid42174665, year = {2026}, author = {Nolan, S and Trego, A and Waters, N and Thorn, C and Fenton, O and Richards, KG and O'Flaherty, V and Ijaz, UZ and Abram, F}, title = {Using feeding regime as a microbial selective pressure to optimise biogas production and digestate sanitisation from slurry-based anaerobic digestion.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00902-x}, pmid = {42174665}, issn = {2524-6372}, support = {14 F847//Irish Department of Agriculture, Food and Marine/ ; }, abstract = {BACKGROUND: The urgent need to adopt sustainable agricultural practices has positioned anaerobic digestion (AD) as a pivotal technology. Indeed, slurry-based AD can mitigate agricultural pollution by capturing greenhouse gas from stored slurry and converting it into biomethane, a valuable source of renewable energy, while generating digestate that can be used as fertiliser. For such a strategy to be effectively and widely deployed however, AD must be optimised. To this end, efforts have typically focused solely on biogas yields, yet improvements in pathogen load reduction may potentially negate the need for a costly pasteurisation step. Hence, optimisation of AD for sanitisation as well as improved biogas output is desirable. To address this, we set up triplicate 10-L CSTR bioreactors, which were fed with a combination of slurry and fats, oils and grease for 216 days. An organic loading rate (OLR) of 2 g VS L[-1] d[-1] was used throughout the trial, with a retention time of 21 days. For the first 98 days, bioreactors were fed each weekday (Monday to Friday), with 3 × feedstock on Fridays to maintain the OLR over the weekend. On Day 99 and for the remainder of the trial, the feeding regime was changed to every three days, still maintaining the 2 g VS L[-1] d[-1] OLR. The change in feeding regime was prompted by a noticeable increase in E. coli removal on Mondays, indicating that feeding regime could potentially function as a controllable ecological selection pressure.

RESULTS: After an initial period of adaptation to the new operating conditions (from day 99-150), the change in feeding regime resulted in improved E. coli removal, achieving consistently the required reduction in numbers to satisfy EU sanitisation standards (< 1000 CFU g[-1]). Additionally, methane production increased significantly in all bioreactors with an average of 58% higher methane yield per gram VS fed when compared to the previous 5-day feeding regime. Interestingly, process optimisation led to a more tailored microbial community as revealed by metagenomics. Specifically, we observed selection for improved carbon oxidation, syntrophic acetate oxidation and methanogenesis, as well as overall reduced microbial richness and decreased functional diversity. This could potentially lead to a reduced ecosystem stability however the emergence of Methanosarcina prevalence, known for its robustness, together with the detection of the two main methanogenic pathways-acetoclastic and hydrogenotrophic-after process optimisation might confer some resistance against future perturbations. The impact of microbial shifts on ecosystem stability needs to be further assessed experimentally.

CONCLUSIONS: Taken together, we demonstrate that feeding regime can function as a microbial selection pressure in anaerobic digestion. The switch from a 5-day to a 3-day feeding regime led to shifts in microbial pathways, underpinning the simultaneous improvement in methane production and E. coli removal. While further research is required to assess the impact of the observed microbial community dynamics on system stability, our findings suggest that full scale on-farm AD operators could explore the effects of feeding intervals on their process performance.}, } @article {pmid42175291, year = {2026}, author = {Dicko, A and Barro, SG and Somda, NS and Sombie, S and Bandaogo, O and Sanou, G and Esona, MD and Bonkoungou, JIO}, title = {Application of Metagenomics and Artificial Intelligence for Pathogen Characterization in Domestic Animals and Epizootic Prediction: A Systematic Review and Meta-Analysis.}, journal = {Studies in health technology and informatics}, volume = {336}, number = {}, pages = {2095-2096}, doi = {10.3233/SHTI260622}, pmid = {42175291}, issn = {1879-8365}, mesh = {Animals ; *Metagenomics/methods ; *Artificial Intelligence ; *Animals, Domestic/microbiology ; *Disease Outbreaks/veterinary/prevention & control ; *Animal Diseases/diagnosis/microbiology ; }, abstract = {Sub-Saharan Africa suffers devastating animal health losses exceeding $20 billion each year. By combining metagenomics with artificial intelligence (AI), a promising path emerges for faster diagnostics and proactive disease prediction. Our PRISMA-guided review of 1,225 studies reveals that metagenomics achieves 94.2% diagnostic sensitivity (compared to 67.3% with conventional methods), while AI dramatically shortens turnaround from 48-72h to just 4-8h, offering a valuable 14-18 day early warning window for epizootics.}, } @article {pmid42175403, year = {2026}, author = {Tang, R and Wang, R and Han, Y}, title = {Mycobacterium avium complex pulmonary disease in rheumatoid arthritis-associated interstitial lung disease under non-biologic immunomodulatory therapy: A case report.}, journal = {Medicine}, volume = {105}, number = {21}, pages = {e48801}, pmid = {42175403}, issn = {1536-5964}, mesh = {Humans ; Male ; *Lung Diseases, Interstitial/complications/drug therapy/etiology ; Aged ; *Arthritis, Rheumatoid/complications/drug therapy ; *Mycobacterium avium-intracellulare Infection/drug therapy/diagnosis/complications/etiology ; Mycobacterium avium Complex/isolation & purification ; }, abstract = {RATIONALE: Rheumatoid arthritis (RA) is a well-recognized risk factor for nontuberculous mycobacterial infections, especially among patients receiving glucocorticoids or biological disease-modifying antirheumatic drugs. However, cases of Mycobacterium avium complex (MAC) pulmonary disease in RA patients without such immunosuppressive therapies are rarely reported, which challenges the conventional risk stratification.

PATIENT CONCERNS: A 78-year-old male with a 3-year history of RA and interstitial lung disease (ILD) presented with progressive dyspnea and chest tightness. He had no fever, joint swelling, or typical infection flares. Before admission, he was treated with Tripterygium Glycosides and Iguratimod (non-biologic, non-glucocorticoid agents).

DIAGNOSIS: The patient had chest tightness and weight loss. Chest high-resolution computed tomography showed asymmetric progression of ILD, along with tree-in-bud signs, centrilobular nodules, and suspicious fibrocavities. Bronchoscopy revealed necrotizing granulomatous inflammation, and quantitative metagenomic sequencing of bronchoalveolar lavage fluid confirmed MAC (no drug-resistant genes detected).

INTERVENTIONS: The patient was put on a 4-drug anti-MAC regimen (rifampicin, azithromycin, ethambutol, amikacin). However, he was lost to follow-up after being transferred to a tuberculosis specialist hospital. He eventually died of unknown causes, and there were prior reports of his nonadherence to treatment.

OUTCOMES: For RA patients with ILD who show asymmetric imaging progression or discordant inflammatory markers, it is crucial to actively screen for atypical pathogens like MAC, even in the absence of glucocorticoid or biologic exposure. This case highlights the necessity of expanding nontuberculous mycobacterial infection risk assessment beyond traditional immunosuppressive therapies in RA-ILD patients.

LESSONS: For patients with autoimmune disease-associated interstitial pneumonia, particularly those with progressive interstitial lung disease (ILD) despite stable autoimmune serology, proactive screening for atypical pathogens such as nontuberculous mycobacteria is critical. When imaging shows asymmetric lesions, tree-in-bud opacities, centrilobular nodules, or fibrocavitary changes, clinicians should prioritize comprehensive etiological evaluation - including bronchoscopy and histopathology - to avoid misdiagnosing these opportunistic infections.}, } @article {pmid42175735, year = {2026}, author = {Li, J and Liu, Q and He, C and Zhu, Y and Yin, C and Pang, X}, title = {Microbial Life-History Strategies and Functional Gene Regulation Drive Soil Nitrogen and Phosphorus Bioavailability During Succession in an Arid Valley Ecosystem.}, journal = {Molecular ecology}, volume = {35}, number = {10}, pages = {e70408}, doi = {10.1111/mec.70408}, pmid = {42175735}, issn = {1365-294X}, support = {32572029//National Natural Science Foundation of China/ ; 2025ZYD0007//Sichuan Province Science and Technology Support Program/ ; XZ202501JX0012//Science and Technology Projects of Xizang Autonomous Region, China/ ; DJ-ZDXM-2024-28//Power Construction Corporation of China/ ; }, mesh = {*Nitrogen/metabolism ; *Soil Microbiology ; *Phosphorus/metabolism ; *Ecosystem ; *Soil/chemistry ; Microbiota/genetics ; Tibet ; Metagenomics ; Bacteria/genetics ; }, abstract = {Arid valley ecosystems are highly vulnerable to environmental change and face accelerating degradation due to climate warming and anthropogenic disturbance. Although soil microorganisms are known to drive nutrient cycling during succession, their adaptive strategies under persistent nutrient limitation remain poorly understood. This study integrated metagenomics, enzymatic stoichiometry and co-occurrence network analysis to investigate microbial community composition, life-history strategies, and nitrogen (N) and phosphorus (P) cycling functional genes along a successional gradient in an arid valley on the southeastern Tibetan Plateau. We found that microbial communities experienced consistent N limitation throughout succession, which shaped their functional potential and biogeochemical roles. Notably, during the transition from bare soil to biological soil crusts (BSCs), shifts in microbial life-history strategies towards resource acquisition (A-strategy) were accompanied by increased network complexity. Key functional genes, particularly those involved in nitrification (nxrB, amoC), dissimilatory nitrate reduction (nirB, nifH, nirD), inorganic P solubilization (gcd, ppk) and organic P mineralization (phnJ, phoA, phnM, phnI), were significantly upregulated during the BSCs stage. These genetic traits facilitated the transformation of organic and mineral nutrients into bioavailable forms, thereby supporting ecosystem development. This is manifested as a higher bioavailability of DON (+110%) and Bio-P (+97%) in the BSCs stage compared to bare land. Our results demonstrate that microbial communities adapt to resource constraints through trait-based strategies and functional gene regulation, highlighting the BSCs stage acts as a critical biogeochemical trigger in early succession. These insights advance our understanding of microbial-mediated nutrient cycling in arid ecosystems and inform restoration strategies under global change.}, } @article {pmid42175741, year = {2026}, author = {Yuan, S and Wang, X and Chang, Z and Zhang, B and Wang, M and Yu, J and Chen, Z}, title = {Climate Change Elevates the Risk of Antibiotic Resistance in Global Surface Ocean.}, journal = {Global change biology}, volume = {32}, number = {5}, pages = {e70929}, doi = {10.1111/gcb.70929}, pmid = {42175741}, issn = {1365-2486}, support = {42277386//National Natural Science Foundation of China/ ; 24JCYBJC01900//Tianjin Natural Science Foundation/ ; }, mesh = {*Climate Change ; *Drug Resistance, Microbial/genetics ; Oceans and Seas ; *Microbiota ; Virulence Factors/genetics ; *Seawater/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Understanding how climate change affects antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in marine microbiomes is critical to safeguarding global health, yet a systematic, global-scale analysis of their responses and associated health risks remains lacking. Here, we analyzed 890 surface-ocean metagenomic samples, the largest dataset collected using a standardized sampling pipeline to date. Our analysis revealed distinct biogeographical patterns in the composition of ARGs and VFGs across spatial and temporal gradients. Using machine learning, we mapped global distributions of ARGs and VFGs across the surface ocean by leveraging their strong associations with climate-releated environmental factors, revealing clear differences between polar and low-latitude areas. We then quantified the community-level antibiotic resistance risk and identified global risk zones, finding that high-risk regions are the least extensive and occur primarily at low latitudes. Furthermore, we estimated how this risk would change under future climate scenarios, suggesting that anthropogenic climate change is projected to increase the antibiotic resistance risk index of the surface ocean by altering environmental factors, most notably carbonate concentrations. Under the SSP5-8.5 scenario, which respresents a high greenhouse gas emissions pathway, the risk index is projected to rise across 33.0% (95% CI: 32.2%-33.5%) of the surface ocean by 2100, mainly in low-latitude regions, driven by an increase in genes involved in antibiotic efflux, inactivation, and motility. In contrast, effective greenhouse-gas mitigation would limit this increase to 3.7% (95% CI: 3.4%-4.1%). This study advances our understanding of how climate shapes marine antibiotic resistome and underscores the urgency of climate mitigation.}, } @article {pmid42176010, year = {2026}, author = {Davolos, D and Chimenti, C and Fassio, G and Russini, V and Lepri, A and Nocella, E}, title = {Understanding Hepatopancreas-Associated Microbiota in the Supralittoral Tylos ponticus (Crustacea, Isopoda, Oniscidea): Insights from Next-Generation Sequencing Approaches.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {42176010}, issn = {1432-184X}, mesh = {Animals ; *Isopoda/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; *Hepatopancreas/microbiology ; Metagenome ; Metagenomics ; Lignin/metabolism ; Phylogeny ; Italy ; }, abstract = {Tylos isopods, which are found exclusively in supralittoral beaches, play an important ecological role in the harsh sea-land interface contributing significantly to lignocellulose degradation. Herein, we investigated the hepatopancreatic microbiota in the oniscidean isopod Tylos ponticus Grebnitzky, 1874 from an Italian supralittoral zone characterized by the accumulation of beached leaves from the seagrass Posidonia oceanica. To characterize this Tylos-microbe system, we combined three Next Generation Sequencing techniques: 16S rRNA gene metabarcoding, whole-genome sequencing of cultured hepatopancreatic bacteria and shotgun metagenomic sequencing of uncultured bacterial communities. Comparative analyses revealed that some bacterial taxa were associated with the hepatopancreas of T. ponticus but were also detected in the supralittoral sandy beach where the detritivores Tylos live. However, distinct components of the microbial community may be adapted within the hepatopancreas. Moreover, the assembled and annotated genomes of hepatopancreatic bacteria allowed us to identify genes encoding lignocellulose-degrading CAZymes for a better understanding of the role of symbionts in aiding lignocellulose degradation. Finally, our shotgun sequencing data confirmed the presence of an uncultured Candidatus Hepatoplasma (Mollicutes) in the hepatopancreas of T. ponticus, with the provisional taxonomic assignment as Candidatus Hepatoplasma cf. vulgare Tp. We compared this data with recently reported metagenome-assembled genomes of uncultured Hepatoplasmataceae members from isopods, including Candidatus Tyloplasma litorale identified from the semiterrestrial isopod Tylos granuliferus, Candidatus Hepatoplasma vulgare from the terrestrial isopod Armadillidium vulgare, and Candidatus Hepatoplasma scabrum from the terrestrial isopod Porcellio scaber. In such a scenario, a deeper understanding of halophilic bacteria in the supralittoral zone also has broad relevance to applied research, particularly to the biotechnological sector related to marine biomass conversion and plastic degradation.}, } @article {pmid42176043, year = {2026}, author = {Khan, I and Naeem, I and Ali, S and Gulbin, M and Iqbal, A and Shafiq, M}, title = {Metagenomic surveillance identifies a high-risk antibiotic resistance profile in community wastewater: a pilot study from Pakistan.}, journal = {Naunyn-Schmiedeberg's archives of pharmacology}, volume = {}, number = {}, pages = {}, pmid = {42176043}, issn = {1432-1912}, abstract = {Environmental antimicrobial resistance surveillance in low- and middle-income countries (LMICs) faces critical data gaps, particularly in Pakistan, where approximately 90% of municipal wastewater is discharged untreated. In the absence of systematic monitoring in regions like Khyber Pakhtunkhwa, we conducted a pilot shotgun metagenomic sequencing study on two strategically selected community wastewater sites in Mardan. To translate complex metagenomic data into actionable public health intelligence, we developed the Antibiotic Resistance Risk Index (ARRI), a novel framework integrating antibiotic resistance gene (ARG) proportional abundance, pathogen taxonomic expansion, and WHO priority weighting. Our analysis revealed that the urban site (MCW2) exhibited a "critical" resistance profile, characterized by a 54% increase in ARG allelic richness (628 unique variants) despite a 19.9% decline in total relative ARG abundance. Taxonomic compositional changes consistent with an aerobic shift, including a 34-fold decline in Thermodesulfobacteria and a 46% increase in Pseudomonadota, were observed alongside an increased proportion of WHO priority pathogens, including Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli. This site served as a reservoir for last-resort resistance determinants, including blaNDM, blaIMP, blaCTX-M, and mcr, which emerged exclusively in the urban drainage environment. The resistome contained 159 ARG families and 26 MGE types. Network analysis showed that 90.8% of ARG-MGE pairs exhibited coordinated increase in relative abundance, with all carbapenemase-linked pairs showing parallel trends. Consequently, ARRI scores escalated from 8.7 (moderate risk) to 34.2 (critical risk) at the urban site. These findings reveal the environmental circulation of hospital-associated resistance through decentralized sanitation infrastructure, representing a convergence of hospital-associated and community resistance profiles in LMIC settings. This study demonstrates that risk-weighted surveillance enables high-resolution, actionable AMR monitoring, providing a baseline methodology for environmental AMR surveillance in resource-limited settings.}, } @article {pmid42176229, year = {2026}, author = {Cagle, GA and Baiser, B and Bernardin, JR and Bittleston, LS and Young, EB and Gray, SM and Freedman, ZB}, title = {Carbon regime structures functional trait trajectories during primary succession in microorganisms.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag134}, pmid = {42176229}, issn = {1751-7370}, abstract = {Primary succession is a foundational process in ecology, but how microbial communities shift functionally during succession, and whether these dynamics follow predictable patterns, remains unresolved. We conducted a systematic review of functional primary succession in microorganisms and applied a consistent metagenomic pipeline to evaluate functional richness, rRNA operon copy number (RRN), and average genome size (AGS) over time. We also explored the yield-acquisition-stress (Y-A-S) life-history framework using functional gene annotations. Across autotrophic systems, RRN tended to decrease and AGS tended to increase during succession, whereas heterotrophic systems exhibited more variable trajectories. These consistent shifts in autotrophic systems suggest a transition from early colonization by copiotrophic taxa with small genomes and high RRN toward later-stage communities with larger genomes, lower RRN, and greater functional versatility. In contrast, heterotrophic systems showed heterogeneous trait trajectories, likely reflecting variation in the timing and predictability of organic inputs. Topic modeling further revealed that early successional stages were enriched in stress-tolerance genes, followed by shifts toward other strategies over time. While certain trait patterns such as RRN and AGS appeared broadly conserved, changes in life-history strategies during succession were context dependent and shaped by resource dynamics and system type. These findings suggest that microbial successional trajectories are structured by differences in resource availability, particularly whether systems are driven by autotrophic inputs or constrained by externally supplied carbon sources.}, } @article {pmid42176246, year = {2026}, author = {Chen, Y and Wang, S and Chen, A and Lin, Z and Wang, H and Li, W and Liu, J and Yao, J and Tian, D and Lei, Y and Liu, M}, title = {Multi-omics Analysis Reveals the Protection of a Quadruple Probiotic Mixture in Experimental Autoimmune Hepatitis.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42176246}, issn = {1867-1314}, support = {2025M782000//China Postdoctoral Science Foundation/ ; 2023AB006//Shangrao Science and Technology Bureau/ ; 202303021221195//Fundamental Research Program of Shanxi Province/ ; 82270558//National Natural Science Foundation of China/ ; }, abstract = {Autoimmune hepatitis (AIH) is a chronic progressive inflammatory liver disease with a rising global incidence. The treatment of AIH remains challenging because first-line drugs show limited efficacy and systemic side effects. Gut microbiota plays a crucial role in the pathogenesis of AIH, leading to growing interest in developing probiotic-based therapies. In this study, we used multi-omics analysis to investigate the therapeutic effects of a quadruple probiotic mixture (Probiotic-quad) consisting of Bifidobacterium infantis, Lactobacillus acidophilus, Enterococcus faecalis, and Bacillus cereus in a well-established chronic AIH murine model. Our results showed that Probiotic-quad treatment significantly alleviated AIH progression, as evidenced by lower serum liver enzyme levels, ameliorated hepatic inflammatory infiltration and histopathological damage. Metagenomic sequencing results showed that gut dysbiosis in AIH mice was partially reversed after Probiotic-quad administration. Additionally, the integrity of the intestinal epithelial barrier was restored, accompanied by a reduction in serum lipopolysaccharide levels. Untargeted metabolomic and transcriptomic analysis revealed that Probiotic-quad treatment was linked to alterations in hepatic metabolism, including the citrate cycle and tryptophan metabolism, and was associated with reduced activation of the NF-κB and NOD-like receptor signaling pathways. These findings suggest that Probiotic-quad treatment ameliorates AIH severity and is potentially associated with changes in hepatic immune responses, metabolism, gut microbiota, and intestinal barrier function, highlighting its potential as an adjuvant therapy for AIH.}, } @article {pmid42176375, year = {2026}, author = {Zhang, Y and Wang, R and Su, X and Lang, T and Li, D}, title = {Freeze-thaw specifically regulates microbiome patterns and phosphorus acquisition strategies in the lake-groundwater interaction zone.}, journal = {Water research}, volume = {302}, number = {}, pages = {126129}, doi = {10.1016/j.watres.2026.126129}, pmid = {42176375}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Phosphorus/metabolism ; *Freezing ; *Microbiota ; Geologic Sediments ; }, abstract = {Freeze-thaw regulates phosphorus cycling in lake-groundwater interaction zones (LIZ) of seasonally frozen regions, where microorganisms and their functional traits play indispensable roles. However, the spatiotemporal dynamics of phosphorus pools and their driving mechanisms in the LIZ remain poorly understood, especially with insufficient quantitative evidence. Using absolute quantitative metagenomics, this study investigated the LIZ of Lake Chagan, a typical eutrophic lake in the seasonally frozen region. Results showed that Losses of Fe-P (44.69%) and Res-P (35.47%) dominated sediment phosphorus dynamics. Freeze-thaw induced opposing trends in diversity and similarity of PCGs-microbial communities between sediment and the lake-groundwater. The assembly of PCGs-microbial communities shifted from stochastic to deterministic processes in lake-groundwater, while stochastic processes persisted in sediments. DIP and DOP in lake-groundwater were driven by genes involved in P-uptake and transport (r = 0.65 and 0.40, respectively, P<0.05), while phosphorus release from sediments was co-regulated by inorganic P-solubilization and organic P-mineralization genes (r = 0.89 and -0.36, respectively, P<0.05). Microbial taxa harboring complete phosphorus cycling pathways (42.2%) and organic P-mineralization genes (48.1%) were relatively rare, with Pseudomonadota as the dominant phylum (65.2% and 57.0%, respectively). This study reveals medium-specific adaptive strategies of microorganisms and PCGs-mediated phosphorus cycling mechanisms, providing scientific support for predicting eutrophication risks and managing lake ecosystems in seasonally frozen regions.}, } @article {pmid42176511, year = {2026}, author = {Li, K and Jin, F and Tan, S and Zeng, X and Yuan, D and Shu, F and Chen, J and Ouyang, JM and Zhang, L and Li, C and Zhu, J}, title = {Cinchonain Ia inhibits uric acid reabsorption by binding to the TRP-459 residue of the GLUT9 protein.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {157}, number = {}, pages = {158292}, doi = {10.1016/j.phymed.2026.158292}, pmid = {42176511}, issn = {1618-095X}, mesh = {Animals ; *Hyperuricemia/drug therapy/metabolism ; *Uric Acid/metabolism/blood ; Male ; *Plant Extracts/pharmacology/chemistry ; *Polygonum/chemistry ; *Glucose Transport Proteins, Facilitative/metabolism/chemistry ; Rats ; Kidney/drug effects/metabolism ; Rats, Sprague-Dawley ; Mice ; Liver/drug effects/metabolism ; Humans ; }, abstract = {BACKGROUND: Hyperuricemia, a chronic metabolic disorder resulting from purine metabolism abnormalities, imposes a substantial burden on patients, their families, and society. Consequently, discovering more efficient prevention strategies and treatment drugs is of crucial importance. Polygonum capitatum (Buch.-Ham. ex D. Don) H. Gross is a plant belonging to the Polygonaceae family and Polygonum genus. Polygonum capitatum can reduce uric acid levels and alleviate gouty arthritis; However, whether its aqueous extract contains other uric acid-lowering active components besides quercetin and gallic acid still requires further research.

PURPOSE: This study aims to investigate the protective effects and potential mechanisms of Polygonum capitatum aqueous extract on liver and kidney function, while also identifying new potential pharmacologically active components for hyperuricemia within the extract.

METHODS: This study established a hyperuricemia rat and mice model and a uric acid-induced renal injury cell model. Liquid chromatography-tandem mass spectrometry was employed to analyze the active components of Polygonum capitatum aqueous extract. The target was analyzed by proteomics. Metagenomics and spatial metabolome were used to analyze gut microbes and metabolites associated with liver and kidney injury. Finally, SPR, DARTS, and CETSA were used to assess the binding potential of active components to targets. Additionally, mutant plasmids were constructed to analyze the binding sites between pharmacologically active components and their targets.

RESULTS: The aqueous extract of Polygonum capitatum significantly reduced serum uric acid levels and alleviated renal injury in the hyperuricemia rat model, with no apparent damage on liver tissue morphology or hepatic function indicators. Metagenomic and spatial metabolomics analyses demonstrated that the extract increased the relative abundance of beneficial gut microbiota and decreased that of harmful bacteria. It also modulated the levels and distribution of renal metabolites such as l-arginine and N-acetylglucosamine, reduced lipid oxidation in the kidney. Proteomics analysis suggests that renal GLUT9 may be one of the action targets of this extract. LC-MS/MS analysis indicated that the chemical composition of the extract underwent significant changes after entering rat blood and undergoing renal metabolism. Specifically, serves as a new active component in Polygonum capitatum aqueous extract, Cinchonain Ia was found to bind to the TRP-459 residue of GLUT9, inhibiting its expression and thereby reducing uric acid reabsorption in vivo and in vitro, and alleviated oxidative stress, inflammation, and tissue damage. However, overexpression of GLUT9 markedly reversed the inhibitory effects of Cinchonain Ia on inflammation and injury.

CONCLUSIONS: The aqueous extract of Polygonum capitatum prevents liver damage and alleviates kidney injury by regulating gut microbiota and renal metabolites. Furthermore, Cinchonain Ia, as one of its active components, can bind to the TRP-459 residue of the GLUT9 protein and inhibit its expression, thereby suppressing uric acid reabsorption and lowering serum uric acid levels.}, } @article {pmid42176589, year = {2026}, author = {Kuerban, Z and Shao, Y and Jiang, R and Shi, Y and Ma, Y and Li, H and Mei, X and Xu, Y and Dong, C and Shen, Q}, title = {Trichoderma modulates Pseudomonas metabolism: Co-inoculation enhances phosphorus acquisition of Pyrus betulifolia in calcareous soil.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128552}, doi = {10.1016/j.micres.2026.128552}, pmid = {42176589}, issn = {1618-0623}, mesh = {*Phosphorus/metabolism ; Soil Microbiology ; *Trichoderma/physiology/metabolism ; Rhizosphere ; *Pseudomonas/metabolism/genetics ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Pyrus/microbiology/growth & development/metabolism ; Biomass ; Microbiota ; Metagenome ; Plant Roots/microbiology ; }, abstract = {Phosphorus (P) is poorly available in calcareous soils, limiting pear growth. We evaluated whether Trichoderma brevicompactum TB2 improves P availability and the rhizosphere microbiome. This study used Trichoderma brevicompactum TB2 to investigate the regulatory mechanisms influencing rhizosphere phosphorus transformation and microbiome structure in pear seedlings. Four treatments were analyzed: sterilized soil control (SSC), sterilized soil with TB2 (SST), natural soil control (NSC), and natural soil with TB2 (NST). SST and NST treatments significantly increased plant height, biomass, and soil available phosphorus (AP) while reducing soil pH compared to SSC and NSC. Notably, only the NST treatment significantly enhanced plant phosphorus content and accumulation. Compared to NSC, NST led to significant restructuring of the rhizosphere microbial community (via 16S rRNA) and functional differentiation in phosphorus cycling (as shown by metagenomics), including increased abundances of key phosphorus-metabolism genes (phnN, phnL, phnP, gcd) and improved organic phosphoester hydrolysis and transport pathways. Metagenome-assembled genomes (MAGs) identified five high-quality gcd-containing MAGs, including those from Bacteroidota (bin43, bin16) and Pseudomonas (bin53, bin72, bin13), with a bin13-match strain isolated from the NST rhizosphere. Pot trials confirmed that inoculation with TB2 or PSE significantly improved plant biomass and phosphorus nutrition indices compared to CK. Co-inoculation with TB2 and PSE elicited synergistic effects that exceeded those of the individual inoculants. In natural calcareous soil, TB2 enhances pear growth by recruiting P-solubilizing Pseudomonas and activating rhizosphere P cycling. This offers a practical route to improve P-fertilizer efficiency in orchards.}, } @article {pmid42176630, year = {2026}, author = {Wu, Y and Ma, W and Sun, Y and Tang, J and Xu, X and Zhu, J and Miao, J and Li, M and Zeng, J and Gou, K and Song, Y and Zou, J}, title = {From active defense to cross-kingdom alarm: Rhizosphere microenvironment remodeling in soybean under polylactic acid nanoplastics and cadmium Co-stress.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142470}, doi = {10.1016/j.jhazmat.2026.142470}, pmid = {42176630}, issn = {1873-3336}, mesh = {*Rhizosphere ; *Glycine max/drug effects/metabolism/genetics ; *Cadmium/toxicity ; *Polyesters/toxicity ; *Soil Pollutants/toxicity ; Plant Roots/drug effects/metabolism ; Stress, Physiological ; Flavonoids/biosynthesis ; Soil Microbiology ; }, abstract = {As foundational components of the food web, plants face significant environmental threats caused by the coexistence of micro/nanoplastics (MNPs) and heavy metals. This study investigates the combined effects of cadmium and biodegradable polylactic acid nanoplastics on soybean. Under co-exposure conditions, toxicity progressively diminishes from the roots to the leaves of soybeans. By integrating root transcriptomics, root exudate metabolomics, rhizosphere soil metagenomics, and soil physicochemical analyses within a Bayesian structural equation modeling framework, we identified the Flavonoid biosynthesis pathway as a central mediating hub in the rhizosphere microenvironment under combined stress. Soybean roots modulated this pathway as a response strategy, which concurrently served as a signal for rhizosphere microbes to downregulate energy-intensive processes such as Methane metabolism, facilitating microbial adaptation. The down-regulation of the Flavonoid biosynthesis pathway in root exudates further altered rhizosphere soil properties, creating a feedback loop that amplified the expression of stress-related genes in soybean roots.}, } @article {pmid42176697, year = {2026}, author = {Yao, J and Zhu, T and Tian, W and Xu, J and Nie, M and Wan, J}, title = {Artificial reefs alter viral communities and functional traits in coastal waters.}, journal = {Marine environmental research}, volume = {220}, number = {}, pages = {108131}, doi = {10.1016/j.marenvres.2026.108131}, pmid = {42176697}, issn = {1879-0291}, abstract = {Artificial reefs (ARs) are widely deployed as engineered coastal structures to enhance habitat complexity and support marine resource management, yet their impacts on marine viral ecology remain poorly understood. Viruses regulate microbial communities and biogeochemical processes, and their functional traits are sensitive to environmental change. Here, we investigated how artificial reefs influence viral community composition, functional gene profiles, and virus-environment interactions across paired reef and non-reef sites in coastal shelf systems. Using an integrated viromic and metagenomic approach, we compared viral assemblages in both seawater and sediments under artificial reef influence. ARs significantly modified seawater physicochemical conditions, including pH, sulfate concentration, dissolved oxygen, and salinity, whereas sediment properties remained largely unchanged. These environmental differences coincided with distinct virus-environment association patterns across habitats. Notably, artificial reefs were associated with viral functional profiles characterized by a reduced genomic representation of lysis-related genes and an increased representation of genes involved in DNA replication and nucleotide metabolism. Network analyses further showed differences in the balance of positive and negative virus-host correlations between AR and non-AR sites. Together, these results indicate that engineered coastal structures are linked to habitat-specific patterns in viral functional traits and virus-host associations. Our findings highlight viruses as sensitive indicators of anthropogenic habitat modification and underscore the importance of incorporating viral dynamics into assessments of microbial and biogeochemical responses in engineered coastal ecosystems.}, } @article {pmid42176766, year = {2026}, author = {Avolio, E and Olivito, I and Minervini, D and Soda, T and De Bartolo, A and Rocca, C and Alò, R and Facciolo, RM}, title = {Neuronutrition in ASD: Involvement of gut microbiota, oxidative stress and inflammatory markers.}, journal = {Neuroscience and biobehavioral reviews}, volume = {187}, number = {}, pages = {106775}, doi = {10.1016/j.neubiorev.2026.106775}, pmid = {42176766}, issn = {1873-7528}, mesh = {Humans ; *Autism Spectrum Disorder/immunology/metabolism/microbiology/physiopathology ; *Oxidative Stress/physiology ; Animals ; *Gastrointestinal Microbiome/physiology ; *Inflammation/immunology/metabolism ; *Neuroinflammatory Diseases/immunology/metabolism ; Probiotics ; }, abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder displaying altered human behaviors, such as social interaction impairments, stereotypical/repetitive activities and emotional dysregulation. Children with ASD are often affected by gastrointestinal problems and gut microbiota dysbiosis. Inflammation and immune dysfunction are key contributors to ASD, as shown by high proinflammatory cytokines and oxidative stress. Indeed, notable implication of the nuclear factor kappa B in the severity of ASD derives from its ability to amplify neuroinflammation. This narrative review focused attention on neuronutrition and gut microbiota manipulation for mitigation of ASD symptoms, including neuroinflammation and oxidative stress. Studies in both rodents and humans with ASD have revealed that both pure and mixed Lactobacillus and Bifidobacterium were effective in ameliorating behavioral symptoms and GABA/glutamate imbalance. Often, the combined use of probiotics and prebiotics can have greater health benefits in ASD. Additionally, dietary interventions and microbiota transfer therapies along with low-to-moderate-intensity exercise have been proposed to improve gastrointestinal and behavioral symptoms. However, despite some encouraging results, biases in the neuronutrition/microbiota literature still exist. Indeed, many studies rely on small sample sizes, cross-sectional designs, and heterogeneous populations that differ in diet, medications, and comorbidities. In this context, the development of a precision diet tailored to individual gut microbiome profiles will allow for a broader understanding of the microbial ecosystem and relative therapeutical applications. Hence, by integrating metagenomics, metabolomics, epigenomics, with evaluation of environmental and nutritional factors, it will be possible to significantly improve the quality of life for people with ASD and their families.}, } @article {pmid42176818, year = {2026}, author = {Dorofeev, A and Pelevina, A and Gruzdev, E and Beletsky, A and Berestovskaya, Y and Litti, Y and Mardanov, A and Pimenov, N}, title = {Development of an Azonexus- and Competibacter-enriched phosphate-accumulating community in the anaerobic/anoxic sequencing batch reactor: Cooperative denitrification.}, journal = {Bioresource technology}, volume = {456}, number = {}, pages = {134959}, doi = {10.1016/j.biortech.2026.134959}, pmid = {42176818}, issn = {1873-2976}, mesh = {*Denitrification ; *Bioreactors/microbiology ; Anaerobiosis ; *Phosphates/metabolism ; Sewage/microbiology ; *Rhodocyclaceae/metabolism ; *Batch Cell Culture Techniques ; }, abstract = {Denitrifying polyphosphate-accumulating organisms (DPAOs) enable simultaneous N and P removal, however, reliable strategies for enriching stable DPAO communities and their metabolic interactions remain insufficiently understood. In this study, DPAO-enriched cultures were developed in a sequencing batch reactor operated under anaerobic/anoxic conditions with acetate as C source. For three independent experiments, activated sludge, collected at different times, was used as the inoculum. Within 0.5-2 months, all experiments exhibited definitive DPAO phenotype dynamics. After 100-200 days of operation, the microbial community was consistently co-dominated by two genera: Azonexus (19-35 %), representing DPAOs, and Competibacter (23-31 %), representing denitrifying glycogen-accumulating organisms (DGAOs). Metagenomic reconstruction revealed that neither Azonexus nor Competibacter harbored the full complement of denitrification genes. The Azonexus metagenome-assembled genome encoded napAB (nitrate reductase), nirS (nitrite reductase), and nosZ (nitrous oxide reductase), while the Competibacter MAG possessed only norBC (nitric oxide reductase) genes. This genomic complementarity provides evidence that complete denitrification in this system could be achieved through cooperation between DPAOs and DGAOs. Consequently, the observed lower phosphorus removal efficiency, compared to anaerobic/aerobic systems, is attributed to the reduced biomass yield of DPAOs and the high essential abundance of DGAOs. These results clarify the ecological role of Azonexus as a DPAO dependent on partnership with DGAOs. Furthermore, the selective conditions favoring Azonexus development in enhanced nutrient removal systems, are evaluated. This work reveals a possible mechanism of syntrophic cooperation between DPAO and DGAO, which has direct implications for the development of resource-saving biological processes for nutrient removal.}, } @article {pmid42176923, year = {2026}, author = {Pi, D and Zhou, F and Huang, S and Yan, H and Pan, J and Yang, Q and Pan, M and Zhang, Y}, title = {Atractylodes lancea (Thunb.) DC polysaccharide alleviates MASH by regulating the 1‑carbon cycle through intestinal flora remodelling.}, journal = {International journal of biological macromolecules}, volume = {368}, number = {}, pages = {152668}, doi = {10.1016/j.ijbiomac.2026.152668}, pmid = {42176923}, issn = {1879-0003}, mesh = {Animals ; *Atractylodes/chemistry ; *Polysaccharides/pharmacology/chemistry ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; Liver/drug effects/metabolism/pathology ; *Carbon/metabolism ; *Fatty Liver/drug therapy/metabolism ; Disease Models, Animal ; }, abstract = {Metabolic-associated steatohepatitis (MASH) is a severe stage of Metabolic-associated fatty liver disease (MAFLD). Currently, effective pharmacological therapies for MASH are extremely limited. An Atractylodes lancea (Thunb.) DC polysaccharide (ALP) was isolated from Atractylodes lancea (Thunb.) DC, and its preventive effect on MASH and the potential mechanism were investigated. Mice were fed a high-fat and methionine/choline-deficient diet (HFMCD) to induce MASH. MASH model mice were then treated with ALP at low (50 mg/kg/d) or high (100 mg/kg/d) dosages. Faecal metagenomics, nontargeted metabolomics sequencing, biochemical and pathological analyses, ELISAs, western blotting and other detection techniques were conducted to elucidate the mechanism by which ALP alleviates MASH. The research results indicate that both the low-dose (50 mg/kg/d) and high-dose (100 mg/kg/d) of ALP can effectively alleviate MASH, but the high-dose has a more significant effect. ALP effectively reduced liver lipid accumulation and inflammation in MASH model mice by regulating the 1‑carbon cycle through intestinal flora remodelling. ALP may be a promising natural candidate for the treatment of MASH.}, } @article {pmid42177038, year = {2026}, author = {Strobel, KM and Leibel, SL and Bhute, S and Aja, E and Jacobs, JP and Calkins, K}, title = {Gut microbial differences and function in infants with gastroschisis: a pilot prospective cohort study.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-14}, doi = {10.1163/18762891-bja00121}, pmid = {42177038}, issn = {1876-2891}, abstract = {Newborns with gastroschisis hospitalised in the neonatal intensive care unit (NICU) are at risk for a disrupted gut microbiome. Infants with gastroschisis are particularly vulnerable to a dysbiotic microbiome; they require prolonged parenteral nutrition (PN) due to intestinal dysmotility, which often leads to growth faltering (GF). This pilot study's goals were to (1) compare the gut microbiome in infants with gastroschisis to infants admitted to the NICU without congenital anomalies, (2) identify differences in the gut microbiome between infants with gastroschisis requiring prolonged PN and those who do not, and (3) compare the microbiome in infants with gastroschisis with GF to those without GF. This was a multi-site prospective cohort study including 17 infants born with gastroschisis and 16 infants with a gestational age greater than 34 weeks admitted to the NICU without congenital anomalies (controls). Prolonged PN was defined as more than 28 days. GF was defined as a decline in weight or length z-score from birth to discharge of ≤-0.8. Stool samples were collected weekly during hospitalisation and analysed by shotgun metagenomics to assess bacterial composition, diversity, and function. Gestational age and birth weight were similar in the gastroschisis group and the control group. Infants with gastroschisis showed increased Staphylococcus aureus and decreased Bifidobacterium longum. Those requiring prolonged PN had a reduced abundance of genes in the glucosidase pathway compared to those who did not. Infants with GF showed a lower abundance of genes involved in the NAD-diphosphatase pathway compared to those without GF. Infants with gastroschisis display a distinct microbial composition and function compared to NICU infants without this condition. Among infants with gastroschisis, differences in bacterial functional capacity were observed in those who required prolonged PN and developed GF.}, } @article {pmid42177062, year = {2026}, author = {Adamek, M and Yılmaz, TM and Erdogmus, S and Moore, S and Ziemert, N}, title = {The ARTS toolset: Resistance-based genome mining for systematic prioritization of bioactive gene clusters.}, journal = {Methods in enzymology}, volume = {730}, number = {}, pages = {35-60}, doi = {10.1016/bs.mie.2025.08.023}, pmid = {42177062}, issn = {1557-7988}, mesh = {*Multigene Family ; *Software ; Genome, Bacterial ; Genome, Fungal ; Fungi/genetics/metabolism ; *Bacteria/genetics/metabolism ; *Computational Biology/methods ; Biological Products/metabolism ; Data Mining/methods ; Genomics/methods ; Metagenome ; }, abstract = {Natural products, especially those produced by bacteria and fungi, have been a rich source of antibiotics and other medically important compounds. Advances in genome sequencing have revealed that many microorganisms harbor far more biosynthetic potential than previously known, but identifying which gene clusters are most likely to produce bioactive compounds remains a major challenge. One promising strategy is to look for genes that protect the producing organism from its own toxic products-so-called resistance genes-which often appear near the biosynthetic genes. In this chapter, we introduce the ARTS toolset, a collection of computational tools designed to identify such resistance-linked biosynthetic gene clusters in microbial genomes. ARTS 2.0 allows users to analyze bacterial genomes and metagenomes, ARTS-DB provides access to precomputed results from tens of thousands of genomes, and FunARTS adapts the approach for fungal genomes. We describe how each tool works and provide examples to guide their use, with additional online tutorial videos provided by the authors.}, } @article {pmid42177063, year = {2026}, author = {Sélem-Mojica, N and Magaña-Lemus, MÁ and Rosiles-Loeza, PY and Barona-Gómez, F}, title = {Bringing CORASON to Windows: Exploring fungal natural products through biosynthetic gene clusters.}, journal = {Methods in enzymology}, volume = {730}, number = {}, pages = {61-73}, doi = {10.1016/bs.mie.2026.03.001}, pmid = {42177063}, issn = {1557-7988}, mesh = {*Multigene Family ; *Biological Products/metabolism ; *Fusarium/genetics/metabolism ; Phylogeny ; *Software ; Genome, Fungal ; *Biosynthetic Pathways/genetics ; *Computational Biology/methods ; }, abstract = {Biosynthetic gene clusters (BGC) are genomic regions that encode the production of specialized metabolites, including antibiotics, pigments, and toxins. While BGC are traditionally classified into broad categories such as NRPS, PKS, and terpene clusters, these classes often overlook finer relationships among gene clusters that produce structurally or functionally related compounds. Tools like BiG-SCAPE and BiG-SLiCE have been developed to address this issue by organizing BGC into gene cluster families (GCFs). CORASON complements these tools by enabling phylogenetic reconstruction of BGC, identifying conserved core genes, and visualizing GFCs as a continuum of variation in gene presence/absence and sequence identity. Although CORASON is incorporated in BiG-SCAPE visualization, it is also a standalone tool initially designed for bacterial genomes annotated via RAST and implemented through Docker in Linux environments. Here, we demonstrate CORASON's broader applicability using fungal GenBank files and its installation via Conda on Windows. As a case study, we examine metagenome-assembled genomes (MAGs) from Fusarium domesticum, a lesser-known member of the Fusarium genus, which is often present in food-associated microbiomes. Unlike its pathogenic relatives (F. oxysporum, F. graminearum), F. domesticum remains understudied, making it an interesting target for genomic mining. This work expands the accessibility of CORASON for fungal genome analysis and highlights its potential in uncovering novel biosynthetic potential in overlooked microbial taxa.}, } @article {pmid42177457, year = {2026}, author = {Zhang, H and Abbas, Z and Li, H and Zhu, Y and Hu, X and Si, D}, title = {Synergistic fungal-enzymatic fermentation of corn straw enhances nutritional value, microbial stability, and bio-feed quality.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05190-6}, pmid = {42177457}, issn = {1471-2180}, support = {2024TSYCTD0016//Xinjiang Uygur Autonomous Region "Tianshan Talents" Cultivation Program/ ; }, abstract = {Valorizing mature, dry corn straw into nutritional animal feed is constrained by its recalcitrant lignocellulosic matrix, while conventional silage methods face stability and logistical limitations. Existing enzymatic and bacterial approaches often lack synergistic efficacy and fail to mitigate pathogen risk in dry biomass systems. We engineered a two-stage fungal-enzymatic fermentation strategy employing a consortium of Aspergillus niger LFB-AN14, Coriolopsis trogii LFB-F1, Bacillus subtilis LFB-BS7, and Pediococcus acidilactici A62, integrated with cellulase, xylanase, and laccase under optimized conditions (1% inoculation, 5:5:1:1 ratio, 37 °C, 21 days). Our results demonstrated that the bacterial-enzyme co-treatment (Group A3) significantly reduced fiber content, with neutral detergent fiber (NDF) and acid detergent fiber (ADF) decreasing by 22.6% and 29.1%, respectively, compared to the control (p < 0.001). Lignin degradation was enhanced, accompanied by a 4.5-fold increase in water-soluble carbohydrates (WSC). The metabolic profile revealed elevated lactic acid production (36.54 g/kg FM) and the suppression of undesirable byproducts such as propionic and butyric acids. Microbial community analysis revealed a dominant shift toward Pediococcus (> 50% abundance) and inhibition of pathogenic Enterobacter spp. Structural analyses (SEM, FTIR) confirmed extensive lignocellulose deconstruction, particularly through carbonyl and hydroxyl functional groups. Metagenomic analysis revealed upregulated Auxiliary Activity (AA) enzymes and cellulosome modules, elucidating the mechanistic basis for enhanced degradation. KEGG enrichment highlighted enhanced aromatic compound metabolism and yeast proliferation, reflecting superior metabolic efficiency. This integrated fungal-enzymatic approach establishes a safe, scalable, and metabolically efficient strategy for transforming agricultural residues into high-quality bio-feed, resolving key challenges in fiber digestibility, pathogen control, and storage stability for sustainable livestock production.}, } @article {pmid42178356, year = {2026}, author = {Chen, S and Xu, S and Muhammad, ZUA and Wang, X and Guo, K and Tao, J and Li, M and Wang, H and Zhang, C and Hou, S}, title = {Two-hourly resolved microbial and viral dynamics in the subtropical Daya Bay.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07491-x}, pmid = {42178356}, issn = {2052-4463}, support = {JCYJ20220530115401003//Shenzhen Science and Technology Innovation Commission/ ; JCYJ20220530115401003//Shenzhen Science and Technology Innovation Commission/ ; 4241003//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Planktonic microbial and viral communities are fundamental drivers of biogeochemical cycling and energy flow in marine ecosystems. These communities display substantial variability in their composition at daily to sub-daily scales, which cannot be captured by conventional low-frequency monthly or weekly sampling. To reveal these high-resolution dynamics, we performed a time-series sampling of planktonic microbial and viral communities in the subtropical Daya Bay at 2-hour intervals over 3 days. Seawater samples were subjected to metagenomic and metatranscriptomic sequencing for the cellular size fraction (>0.2 μm) and metagenomic sequencing for the viral size fraction (0.02-0.2 μm). This approach enabled us to capture fine-scale temporal variations in the genomic composition and transcriptional activities of microbial and viral communities. The resulting comprehensive dataset, including 700 metagenome-assembled genomes (MAGs) and 118,242 viral operational taxonomic units (vOTUs), provides a valuable resource for investigating the metabolic potentials and dynamic interactions within natural planktonic microbial-viral assemblages in subtropical bay ecosystems, offering insights into their ecological roles that are inaccessible through low-temporal-resolution sampling.}, } @article {pmid42178395, year = {2026}, author = {Sharaf, H and Bobay, LM}, title = {MetaStrainer: accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {6}, pages = {}, pmid = {42178395}, issn = {1367-4811}, support = {R01GM132137//National Institutes of Health (NIGMS)/ ; }, mesh = {*Metagenomics/methods ; Genotype ; *Software ; *Bacteria/genetics/classification ; Algorithms ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; }, abstract = {MOTIVATION: Metagenomics provides broad insights from microbial communities, but more biological relevant phenotypes are attributed to subtle changes at the strain-level rather than species. Despite development of several tools using different algorithms, resolving individual strains from short-read pair-end sequencing data remains challenging.

RESULTS: Here we present MetaStrainer, a tool capable of reconstructing strain genotypes from metagenomic data. Compared with existing approaches, MetaStrainer substantially increases genotype accuracy, correctly identifies the number of strains, and accurately estimates their relative abundances. Accuracy of reconstructed genotypes is robust to choice of mapping reference.

AVAILABILITY: MetaStrainer is implemented in Python 3. Source code and instructions are available on GitHub at www.github.com/lbobay/MetaStrainer and on Zenodo: 10.5281/zenodo.17872331.}, } @article {pmid42178569, year = {2026}, author = {Garritano, AN and J Hill, L and Ribeiro, B and Damasceno, T and Medeiros, L and Duarte, G and L S Vilela, C and Majzoub, ME and Allen, MA and Nappi, J and S Peixoto, R and Thomas, T}, title = {Ammonia oxidation and recalcitrant carbon degradation fuel mixotrophic growth in the symbiont community of a deep-sea sponge.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42178569}, issn = {2049-2618}, support = {BAS/1/1095-01-01//KAUST/ ; ANP 21005-4//ANP, Brazil/ ; }, mesh = {Animals ; *Porifera/microbiology ; *Ammonia/metabolism ; *Symbiosis ; Oxidation-Reduction ; *Archaea/metabolism/genetics/classification/isolation & purification ; *Microbiota ; *Carbon/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics/methods ; Autotrophic Processes ; Carbon Cycle ; Seawater/microbiology ; }, abstract = {BACKGROUND: Sponges are important members of shallow-water, benthic ecosystems, where they often rely on their microbial symbionts to acquire organic or inorganic carbon. Sponges are also found in the deep sea, however, how they metabolically interact there with their symbionts remains underexplored. Here, we combined metagenomic, metatranscriptomic and stable-isotope labelling approaches to investigate the metabolic activities of the microbial community of the deep-sea sponge Calyx sp.

RESULTS: Approximately 84% of the total estimated microbial abundance was composed of nine heterotrophic phyla, whilst the remaining 16% consisted of two autotrophic ammonia-oxidising archaea. Metatranscriptomic analysis revealed the high expression of genes involved in the degradation of recalcitrant polysaccharides of algal origin, suggesting that an undegraded fraction of marine snow plays a role in the nutrition of this deep-sea holobiont. Additionally, we detected active ammonia oxidation and carbon fixation pathways in the autotrophic community members and, through ex situ incubations with labelled carbonate show a potential to fix 13.67 mg CO2 per g dry weight in a year.

CONCLUSIONS: This study highlights the mixotrophic lifestyle of a deep-sea sponge microbiome, expanding our knowledge of the sponge-microbe symbiosis in the oligotrophic environment of the deep ocean. Video Abstract.}, } @article {pmid42178714, year = {2026}, author = {Zeamer, AL and Lai, Y and Loew, E and Sanborn, V and Tracy, M and Jo, C and Ferdinand, D and Ward, DV and Bhattarai, SK and Drake, J and McCormick, BA and Bucci, V and Haran, JP}, title = {Microbiome functional gene pathways are indicative of cognitive performance in older adults at risk for Alzheimer's disease.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2676162}, pmid = {42178714}, issn = {1949-0984}, mesh = {Humans ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Aged ; Female ; Male ; *Cognition ; Middle Aged ; *Cognitive Dysfunction/microbiology ; Aged, 80 and over ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Cohort Studies ; Metagenomics ; Metabolic Networks and Pathways/genetics ; }, abstract = {Disturbances in the gut microbiome are increasingly correlated with neurodegenerative disorders, including Alzheimer's disease. Multiple lines of emerging evidence are consistent with the microbiome's involvement in disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby influencing disease pathology through the "microbiota-gut-brain axis." Currently, the copathologies contributing to cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in the gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (aged 60 y or older) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiome samples. Subjects were classified as healthy controls, exhibiting mild cognitive impairment, or having dementia based on clinical assessments. Using metagenomic sequencing and gene pathway analyses, we found that certain microbial-encoded metabolic pathways correlated with worse cognitive performance. Specifically, genes involved in the urea cycle, polyamine synthesis, or the metabolism of methionine and cysteine predicted worse cognitive performance. Our study suggests that the gut microbiome composition may be linked to cognitive impairment along the AD continuum and points to microbial metabolic pathways that may potentiate disease.}, } @article {pmid42178721, year = {2026}, author = {Schulze, K and Goldschmidt, I and Melk, A and Boehne, M and Woltemate, S and Ballmaier, M and Kleiner, S and Lehmann, E and Kramer, M and Vital, M}, title = {Altered SIgA-targeting of gut microbiota is associated with long-term dysbiosis in pediatric solid organ transplant recipients.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2675078}, pmid = {42178721}, issn = {1949-0984}, mesh = {Humans ; *Dysbiosis/microbiology/immunology/etiology ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; *Immunoglobulin A, Secretory/immunology/genetics ; *Transplant Recipients ; Tacrolimus/adverse effects ; Bacteria/classification/genetics/isolation & purification ; Adolescent ; Immunosuppressive Agents/adverse effects/therapeutic use ; *Organ Transplantation/adverse effects ; Feces/microbiology ; Child, Preschool ; Liver Transplantation/adverse effects ; }, abstract = {The composition of the gut microbiota (GM) is altered in solid organ transplantation (SOT) recipients, where the degree of dysbiosis is associated with long-term survival and is believed to be influenced by immunosuppression therapy. At the interface stands secretory (S)IgA, however, little is known about its role in governing dysbiosis in the context of SOT. We performed quantitative metagenomic analyses of the GM accompanied by SIgA sequencing in 48 pediatric SOT recipients (age = 10.6 ± 4.7 y) receiving either heart (n = 11), kidney (n = 10) or liver transplantation (n = 27), and compared the results to age-matched healthy controls (HC, n = 16). We confirmed compositional and functional dysbiosis in SOT recipients, with the degree of dysbiosis being associated with tacrolimus (TAC) levels. Overall, SOT recipients exhibited higher SIgA levels than HC, along with an increased percentage of bacteria targeted and altered target spectra. Furthermore, altered SIgA responses were associated with the degree of dysbiosis. A mechanistic model connecting immunosuppression, GM composition and SIgA-targeting is proposed, suggesting that GM dysbiosis in SOT recipients is mediated by the immune system through the SIgA response; direct drug-mediated effects on fecal communities were not observed in in vitro experiments. Our study provides new insights into factors that contribute to persisting dysbiosis in SOT recipients.}, } @article {pmid42180198, year = {2026}, author = {Nnorom, MA and Du, B and Wang, Z and Tian, Z and Hough, R and Avery, L and Saroj, D and Guo, B}, title = {Dynamics of the Microbiome and Antibiotic Resistome in Hyper-Mesophilic Anaerobic Digestion of Cattle Manure Assisted with Granular Activated Carbon.}, journal = {ACS environmental Au}, volume = {6}, number = {3}, pages = {435-448}, pmid = {42180198}, issn = {2694-2518}, abstract = {The use of conductive materials, such as granular activated carbon (GAC), for optimization of the anaerobic digestion (AD) process has garnered attention in recent years; however, its impact on the dynamics of the microbiome and resistome in continuous AD systems remains unclear, especially under temperature variation. This study combined culture-based bacterial enumeration and shotgun metagenomics to investigate the impact of two GAC application strategies, suspended and packed, on the fate of pathogens (viable Escherichia coli) and ARGs during the AD of cattle manure at 40 and 45 °C. The results show that GAC mitigated the process imbalance and shock induced by temperature transition. The microbial community in the AD sludge was highly impacted by temperature but not GAC, while GAC biofilms showed notably higher archaeal abundance. All AD reactors reduced viable E. coli, with the highest reduction occurring in the packed GAC reactors (95.70-96.24%), followed by the suspended GAC (94.53-95.69%), and then the non-GAC (92.77-94.24%). Culturable tetracycline-resistant bacteria were reduced below the quantification limit in all reactors. Reduction of ampicillin-resistant bacteria showed stochastic trends at 40 °C but improved at 45 °C, indicating limited impact by GAC. ARGs and mobile genetic elements (MGEs) were reduced in all reactors at comparable levels, regardless of GAC addition. Temperature transition exerted a mixed effect, with higher reduction of some resistance classes (MLS, tetracycline, and multidrug) and lower reduction of others (bacitracin, aminoglycoside, beta-lactam, and streptothricin). Mantel test and Procrustes analysis revealed a significant correlation between the resistome and the bacterial community, inferring that shifts in the ARG host population were a major determinant of the fate of ARGs. Overall, GAC was beneficial to reactor stability but had a minimal influence on the reduction of E. coli, ARGs, and MGEs. It is highly recommended to monitor antimicrobial resistance using both culture-based and culture-independent methods.}, } @article {pmid42180259, year = {2026}, author = {He, J and Ning, Y and Liang, H and Qin, J and Wei, Y and Liang, S and He, Z and Yin, S}, title = {Special pathogen infections presenting with neck mass as the initial manifestation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1767591}, pmid = {42180259}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Middle Aged ; Adult ; Aged ; *Neck/pathology/microbiology ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology/pathology/drug therapy ; *Mycoses/diagnosis/microbiology/pathology/drug therapy ; *Talaromyces/isolation & purification ; Nontuberculous Mycobacteria/isolation & purification ; China ; Lymphadenopathy/microbiology ; }, abstract = {BACKGROUND: The etiology of neck masses is complex. Infections caused by Talaromyces marneffei (TM) and nontuberculous mycobacteria (NTM) are uncommon but often present with insidious clinical manifestations, leading to frequent misdiagnosis.

METHODS: We collected and analyzed data from 13 patients with TM/NTM infections presenting with neck masses at The First Affiliated Hospital of Guangxi Medical University and The Second Affiliated Hospital of Guangxi Medical University. Clinical manifestations, laboratory findings, infection sites, pathogen types, treatments, and outcomes were described and analyzed.

RESULTS: Of the 13 patients, six were male and seven female, with a median age of 57 years (range, 27-73 years). All patients were residents of Guangxi and tested positive for anti-interferon-γ autoantibodies (AIGAs), with titers of 1:2500 in 12 patients and 1:500 in one. The median time from symptom onset to diagnosis was 5 months (range, 1-19 months). Common clinical features included lymphadenopathy (13/13), fever (11/13), respiratory symptoms (10/13), and rash or skin ulceration (8/13). Frequent laboratory abnormalities included leukocytosis (11/13), neutrophilia (11/13), elevated erythrocyte sedimentation rate (12/13), and elevated C-reactive protein (13/13). Coinfection with two or more pathogens was observed in 12 patients. The lungs and lymph nodes were involved in all 13 patients, followed by bone (11/13), skin or soft tissue (8/13), bloodstream or bone marrow (3/13), and nasopharynx (3/13). Neck mass specimens yielded NTM in nine cases and TM in four. NTM was most frequently identified by metagenomic next-generation sequencing (mNGS), whereas TM was detected by culture. The median follow-up duration was 28 months (range, 1-86 months). During follow-up, 6 patients (46.2%) experienced disease exacerbations. Among the 13 patients, 12 achieved clinical improvement after pathogen-directed antimicrobial therapy, while one patient died.

CONCLUSION: Neck masses have diverse etiologies. TM and NTM infections presenting initially as neck masses are rare and easily misdiagnosed as tuberculosis, malignancy, or lymphoma. Culture and mNGS are crucial diagnostic tools for TM and NTM, respectively. Clinicians should maintain a high index of suspicion for these infections, particularly in immunocompromised patients in endemic regions.}, } @article {pmid42180316, year = {2026}, author = {Chen, X and Zhang, M and Yang, L and Chen, Y and Chi, Y and Zhao, Y and Ma, Z and Li, Y and Wang, X}, title = {CRISPR spacer profiling and prophage mining reveal diverse bacteriophages associated with Streptococcus Mutans.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2674332}, pmid = {42180316}, issn = {2000-2297}, abstract = {BACKGROUND: Streptococcus mutans is a key cariogenic bacterium. Current antimicrobials lack species specificity, while phage-based approaches remain experimental and require more S. mutans phage isolates.

OBJECTIVE: To profile the diversity of S. mutans-associated phages and strain-level heterogeneity in phage exposure using genome-informed CRISPR spacer and prophage analyses.

MATERIALS AND METHODS: We compiled 944 publicly available S. mutans genomes and dereplicated them into 735 non-redundant strains. CRISPR-Cas systems, spacers, spacer targets, and putative prophages were identified, quality-assessed, and functionally annotated. Phylogenetic relationships of (pro)phages were evaluated using terminase large subunit proteins, and comparative genomics compared spacer-positive and spacer-negative strains.

RESULTS: CRISPR systems were detected in 548/735 strains, yielding 14,263 spacers, 1,864 phage-targeting spacers mapped to 110 viral genomes, including 41 cultured isolates, 51 metagenome-assembled phages, and 18 uncultured viral genomes. The most frequently targeted cultured phage was phiKSM96, whereas metagenome-assembled Caudoviricetes ctNo011 showed broader targeting. Prophage mining identified 186 regions in 130 strains, including 37 of ≥ medium quality and elements related to ctNo011 and phiKSM96. TerL phylogeny showed that most high-quality endogenous prophages clustered with phiKSM96 and ctNo011.

CONCLUSION: These findings reveal a vast, uncultivated phage repertoire targeting S. mutans, providing a critical genomic roadmap to guide the future isolation of novel phages for caries prevention.}, } @article {pmid42180431, year = {2026}, author = {Mallawaarachchi, V and Bouras, G and Wick, RR and Grigson, SR and Papudeshi, B and Edwards, RA}, title = {agtools: a software framework to manipulate assembly graphs.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag126}, pmid = {42180431}, issn = {2635-0041}, abstract = {MOTIVATION: Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler in constructing longer genomic fragments. Apart from their core use in assemblers, assembly graphs have become increasingly important in a range of downstream applications such as metagenomic binning, plasmid detection, viral genome resolution, and haplotype phasing. However, there is a need for a comprehensive tool that allows programmatic access to manipulate assembly graphs (e.g. parse, convert, filter, and analyze) across different assembly graph formats.

RESULTS: Here we present agtools, an open-source Python framework to manipulate assembly graphs produced by commonly used assemblers. agtools provides a command-line interface for tasks such as assembly graph format conversion, segment filtering, and component extraction. It also exposes a Python package interface to load, query, and analyze assembly graphs from popular genome and metagenome assemblers. This enables streamlined assembly-graph-based analyses that can be integrated into other bioinformatics software and workflows.

The source code of agtools is hosted on GitHub at https://github.com/Vini2/agtools and the documentation is available at https://agtools.readthedocs.io/. agtools can also be installed from Bioconda (https://anaconda.org/bioconda/agtools) and PyPI (https://pypi.org/project/agtools/).}, } @article {pmid42180728, year = {2026}, author = {Wang, T and Wang, M and Zhao, L and Tang, G and Hou, L}, title = {Case Report: Pulmonary brucellosis presenting as multiple cavitary lung lesions on imaging.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1814731}, pmid = {42180728}, issn = {2296-858X}, abstract = {Pulmonary brucellosis is a rare focal manifestation of human brucellosis with non-specific clinical features. Predominant imaging findings include pneumonia, pleural effusion, pulmonary nodules, abscesses, and interstitial changes. Multiple cavitary lesions are exceptionally rare. Herein, we report a case of bilateral multiple pulmonary cavities in a 76-year-old man with a 2-year history of intermittent cough, sputum production, and progressive dyspnea that acutely worsened 10 days prior to admission with intermittent fever, anorexia, and fatigue. Chest computed tomography (CT) revealed bilateral upper lobe irregular mass-like opacities and multiple nodules with heterogeneous density, punctate calcifications, and cavitation; multiple microcavitations in the right middle and lower lobes and the left lower lobe; and enlarged, calcified hilar and mediastinal lymph nodes. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid identified Brucella species, which was confirmed by positive serology. After 3 days of doxycycline (0.1 g bid po) and rifampicin (0.6 g qd po), followed by 140 days of doxycycline (0.1 g bid po), rifapentine (0.6 g biw po), and levofloxacin (0.5 g qd po), along with silibinin meglumine tablets 0.1 g tid po for hepatoprotective therapy, the patient became afebrile with significant symptomatic improvement. Repeat chest CT demonstrated reduction in the right upper lobe consolidation/cavity and left upper lobe consolidation, resolution of the right lower lobe cavity, and complete resolution of the microcavitations. This case underscores that pulmonary brucellosis should be considered in the differential diagnosis of cavitary lung lesions in patients with livestock exposure and that prolonged combination antibiotic therapy can achieve favorable clinical and radiological outcomes.}, } @article {pmid42181109, year = {2026}, author = {Wunderer, M and Mullaymeri, A and Wagner, AO and Prem, EM}, title = {Comparative phenotypic and genomic analysis of the methanogen Methanomethylovorans thermophila L2FAW and its phylogenomic placement within the Genome Taxonomy Database.}, journal = {Access microbiology}, volume = {8}, number = {5}, pages = {}, pmid = {42181109}, issn = {2516-8290}, abstract = {The genome of the methylotrophic methanogen Methanomethylovorans thermophila L2FAW is not included in the Genome Taxonomy Database (GTDB) so far, even though the strain was first described in 2005. To evaluate its genomic characteristics and placement in the GTDB, we sequenced the genome of M. thermophila L2FAW via Illumina shotgun and Oxford Nanopore sequencing and subsequently did hybrid assembly. The assembled genome consists of 2.25 Mbp (contigs ≥500 bp) with a G+C content of 40 mol%. The quality of the genome is good, which is already apparent from the low L50 (=1) and L90 (=2) metrics. Our assembled genome was highly similar to the metagenome-assembled genome Methanomethylovorans sp014361205 (GCA_014361205.1_ASM1436120v1_genomic) with an average nucleotide identity of 99.9%. Even though KEGG Mapper Reconstruction results revealed that M. thermophila L2FAW harbours all the enzymes necessary for acetoclastic and hydrogenotrophic methanogenesis and gapseq predicted formate as a potential substrate for M. thermophila L2FAW, no metabolic activity could be observed on acetate, H2-CO2 (80:20 vol/vol, 2,000 mbar) and on a mixture of H2-CO2 and formate in lab tests; thus, the obligate methylotrophic lifestyle of the phenotype was confirmed.}, } @article {pmid42181159, year = {2026}, author = {Bressuire, C and Thirion, F and Chiaravano, L and Ngom, SI and Marion, R and Gilles, M and Quinquis, B and Mathieu, E and Berland, M and Blottière, HM and Le Bourgot, C and Béra-Maillet, C}, title = {Short-chain fructo-oligosaccharides modulate gut microbiota composition and metabolism: dose-response assessment in an ex vivo gut model.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2674335}, pmid = {42181159}, issn = {2993-3935}, abstract = {Short-chain fructo-oligosaccharides (scFOS) are prebiotic fiber rapidly fermented in the colon and known to stimulate beneficial bacteria, such as Bifidobacterium spp. and Lactobacillaceae. While their overall effects on the gut microbiota are established, the dose-response relationship remained only partially characterized. This study aimed to determine the minimum effective dose of scFOS required to modulate gut microbiota composition and functions. An ex vivo chemostat model was used to simulate colonic fermentation with different doses of scFOS (1 to 10 g/d). Microbiota composition and metabolic activity were assessed by qPCR, short-chain fatty acid (SCFA) quantification, and shotgun metagenomics. An increase in scFOS dose led to higher SCFA levels, particularly acetate and butyrate, along with a modification in microbial composition, with a minimum significant effective dose of 2.5 g/d. Significant increase in Bifidobacterium adolescentis, Anaerostipes hadrus, and Clostridium innocuum was observed at the same dose. Functional analysis revealed an enrichment of GH32 genes in the pangenomes of species positively impacted by scFOS. These findings demonstrate that low doses of scFOS can effectively modulate the gut microbiota and enhance SCFA production, supporting their use in dietary interventions aimed at improving intestinal health.}, } @article {pmid42182002, year = {2026}, author = {Chen, S and Hu, X and Pan, W and Chen, T and Xie, X and Zhang, Y}, title = {Integrated metagenomic and culture-dependent profiling reveals electric shavers as selective reservoirs for multidrug-resistant opportunistic pathogens.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1839764}, pmid = {42182002}, issn = {1664-302X}, abstract = {INTRODUCTION: Personal care items are commonly viewed as passive vehicles for microbial transfer; however, the physicochemical stresses they impose may actively shape microbial persistence, community composition, and the distribution of resistance-associated determinants. Electric shavers may therefore constitute an underrecognized anthropogenic niche for the enrichment of clinically relevant antimicrobial resistance traits.

METHODS: We sampled electric shavers from 10 individuals at early (day 2) and mature (day 21) usage stages, generating 8 high-quality metagenomes and recovering 97 viable isolates spanning 16 bacterial species. Deep metagenomic sequencing, combined with whole-genome sequencing of 45 representative isolates, was used to resolve the ecological, functional, and evolutionary features of shaver-associated microbiomes.

RESULTS: Shaver-associated community assembly was dominated by stringent environmental filtering, which promoted the repeated enrichment of stress-adapted lineages across hosts, notably Acinetobacter ursingii MLST3244 and Klebsiella pneumoniae MLST995 and MLST23. We further identified recurrent mobile genetic element-associated resistance islands and plasmid backbones in different host cohorts, suggesting repeated selection under shared anthropogenic pressures rather than direct evidence of de novo convergent evolution. Importantly, viable Klebsiella pneumoniae isolates co-carried extended-spectrum β-lactamase genes such as bla SHV and major virulence determinants, while metagenomic profiling detected reads assigned to mcr- and tet(X)-like gene variants at the community level, targeted PCR further confirmed the presence of these resistance determinants.

DISCUSSION: Because routine shaving can generate barrier-disrupting micro-abrasions, electric shavers may function as selective reservoirs for multidrug-resistant bacteria. Our findings reveal a previously overlooked exposure interface through which everyday personal care practices may promote the enrichment and persistence of clinically important resistance and virulence determinants.}, } @article {pmid42182003, year = {2026}, author = {Li, F and Liu, X and Hou, W and Dong, H and Hu, J and Chen, H and Zhong, Y and Wu, Y and Xu, X and Ding, Y}, title = {Archaeal communities as indicators of hydrothermal influence in the Tianxiu vent field, Northwest Indian Ocean.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1837947}, pmid = {42182003}, issn = {1664-302X}, abstract = {Deep-sea hydrothermal sediments represent critical zones for archaea-driven biogeochemical cycling, yet the ecological differentiation of archaeal communities across hydrothermal gradients remains poorly understood. Here, we used 16S rRNA gene amplicon sequencing of sediment cores from two contrasting sites in the Tianxiu hydrothermal field of the Northwest Indian Ocean, and performed metagenomic analysis on the near-vent BC12 sediments, to investigate archaeal community composition, co-occurrence patterns, and metabolic potential in response to the hydrothermal activity. Comparative analysis revealed marked divergence between near-vent site BC12 and far-vent site JL218P. The site BC12, under stronger hydrothermal influence, was enriched in Hydrothermarchaeia, along with Nanoarchaeia and Thermoplasmata, and exhibited a more complex, highly connected co-occurrence network. Correlation analyses further showed that Hydrothermarchaeia abundance was significantly associated with hydrothermal-related geochemical gradients, supporting this lineage as a potential indicator of hydrothermal influence. Metagenomic analysis of BC12 further revealed Hydrothermarchaeia genomes encoding the Wood-Ljungdahl carbon fixation pathway, while genome-centric functional inference suggested enhanced potential for methanogenesis and hydrogen oxidation. In contrast, JL218P was dominated by Nitrososphaeria, showed limited vertical variation, and formed a simpler network structure, with predicted functional profiles more closely associated with nitrification and aerobic ammonia oxidation. Together, these findings identify hydrothermal-related geochemical heterogeneity as a major driver of archaeal community composition, ecological organization, and metabolic differentiation in deep-sea sediments, and advance our understanding of the ecological drivers structuring deep-sea hydrothermal ecosystems.}, } @article {pmid42182018, year = {2026}, author = {Abilda, Z and Isgandarov, I and Kanat, R and Daurov, D and Sapakhova, Z and Zhambakin, K and Daurova, A and Begaliyeva, D and Choi, K and Shamekova, M}, title = {Genome-resolved metagenomics reveals co-selection of antibiotic and metal resistance in chronically polluted industrial soils.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1829529}, pmid = {42182018}, issn = {1664-302X}, abstract = {INTRODUCTION: Chronic heavy metal contamination can restructure soil microbiomes and may co-select for antibiotic resistance, yet genome-resolved evidence from industrial soils remains limited.

METHODS: In this study, we applied Oxford Nanopore long-read metagenomic sequencing to soil samples collected across industrially influenced sites in East Kazakhstan to characterize strain-level community composition, profile antibiotic resistance genes and metal resistance genes, and relate these patterns to soil physicochemical properties.

RESULTS: Across all samples, we identified 3,053 strains, with Actinobacteria and Proteobacteria together accounting for 94.1% of the total community. Heavy metal concentrations varied markedly among sites. The resistome comprised antibiotic resistance genes from several drug classes and 238 distinct metal resistant genes, with aminoglycoside, glycopeptide, and multidrug resistance dominating the antibiotic resistance gene profile, while czcA, ruvB, arsM, and arsT were among the most abundant Metal resistant genes. Multivariate analyses showed that heavy metals, particularly Zn, significantly shaped microbial community structure as well as antibiotic resistance gene and metal resistance gene composition, and redundancy analysis identified Zn and soil pH as the principal environmental drivers. Network analyses further revealed that Bradyrhizobium icense and Conexibacter woesei acted as key super-hosts linking ARGs and MRGs, supporting heavy metal-driven co-selection within the soil microbiome.

DISCUSSION: Together, these findings show that long-read genome-resolved metagenomics can uncover how chronic industrial pollution maintains metal-adapted microbial communities while promoting the persistence and potential dissemination of antibiotic resistance in soil ecosystems.}, } @article {pmid42182023, year = {2026}, author = {Duan, J and Chen, Y and Zhang, X and Li, C and Gao, T and Li, K}, title = {Metagenomic analysis suggests that tomato root-knot nematode infestation disrupts rhizosphere microbial networks, consistent with reduced disease suppression.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1798902}, pmid = {42182023}, issn = {1664-302X}, abstract = {INTRODUCTION: The rhizosphere microbiome serves as a critical line of defense for plant health and soil-borne disease suppression. However, the underlying mechanisms by which root-knot nematodes (RKN), a devastating soil-borne pathogen, undermine putative disease-suppressive function through destabilizing microbial interaction networks remain poorly understood.

METHODS: This study employed metagenomic sequencing coupled with microbial co-occurrence network analysis to systematically compare the community structure, interaction network topology, and functional gene profiles of the rhizosphere microbiome between healthy and RKN-infected tomato plants.

RESULTS: Our findings revealed that RKN infection significantly altered the community structure of bacteria, fungi, and viruses. This disturbance was associated with a systematic simplification and loss of modularity within microbial interaction networks. Specifically, intra-domain bacterial networks exhibited reduced scale and connectivity, whereas fungal networks showed strengthened internal cohesion. Cross-kingdom interactions (e.g., bacteria-fungi) were severely weakened, resulting in a topological imbalance characterized by "tight within domains, loose between domains." Functional profiling further indicated a distinct metabolic reprogramming in the infected rhizosphere, with a shift in resource allocation from growth and biosynthesis toward core energy acquisition and stress response.

DISCUSSION: Collectively, our results suggest that the putative decline in disease-suppressive function following RKN infection may be mechanistically rooted in the destabilization of microbial cooperative networks and the consequent loss of functional redundancy. This study provides a novel network-level ecological framework for understanding plant-microbe-pathogen interactions and lays a theoretical foundation for microbiome-based ecological management strategies against soil-borne diseases.}, } @article {pmid42182035, year = {2026}, author = {Qian, W and Han, A and Al Hatmi, AMS and Wang, Y and Rafiq, M and Cui, G and Zhou, S and Li, S and Kang, Y}, title = {Concordance between environmental resistomes and pathogenic phenotypes: a case study of multidrug-resistant Klebsiella pneumoniae in a drinking water source in Guizhou, China.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1810806}, pmid = {42182035}, issn = {1664-302X}, abstract = {INTRODUCTION: The persistence of antibiotic resistance in aquatic environments poses a public health concern, particularly when drinking water sources act as reservoirs for multidrug-resistant opportunistic pathogens. However, the linkage between environmental resistomes and the resistance phenotypes of cultivable bacteria remains under-characterized. This case study investigated this relationship in a karst drinking water source in Guizhou, China.

METHODS: Surface water samples from seven sites were analyzed for antibiotic residues using LC-MS/MS. Metagenomic sequencing was conducted on selected contamination hotspots to characterize microbial communities and antibiotic resistance genes (ARGs). Cultivable bacteria were isolated, identified via 16S rRNA sequencing, and tested for antimicrobial susceptibility. To validate resistance mechanisms, a multidrug-resistant Klebsiella pneumoniae isolate was analyzed for tetA expression using RT-qPCR.

RESULTS: Antibiotic residues were detected across all sites, with sulfonamides and tetracyclines being the most prevalent. Consistent with this chemical pressure, metagenomic analysis identified corresponding ARGs, including sul1 and tet(Q), which functionally clustered with mobile genetic elements. From the contaminated matrix (sample W2), a multidrug-resistant Klebsiella pneumoniae strain (B8) was recovered. Mechanistic validation revealed a 2.78-fold upregulation of the tetA efflux pump gene in this strain.

DISCUSSION: These findings demonstrate a concordance among chemical selection pressures, environmental resistomes, and active resistance phenotypes. The results indicate that drinking water sources can harbor and maintain clinically relevant resistant bacteria, supporting the implementation of integrated surveillance strategies to evaluate biological risks.}, } @article {pmid42182110, year = {2026}, author = {Zhang, Z and Holton, M and Ferrer, DM and Tripp, AD and Richter, A and Dixit, PD and Urtecho, G}, title = {Metagenome-scale Modeling to Assess Microbiome Metabolic Complementarity for Precision Microbiota Transplantation Therapies.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42182110}, issn = {2692-8205}, abstract = {Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable, in part because existing computational models do not fully capture the metabolic compatibility between donor and recipient communities. Here, we present a metagenome-scale metabolic modeling framework that quantifies metabolic niche complementarity between donor and recipient microbiomes to predict transplantation outcomes. Using MICOM-derived community metabolic models, we show that donor taxa whose metabolic flux profiles are more dissimilar from the recipient community engraft at significantly higher rates in both murine and human FMT cohorts. In a human IBS trial, metabolic models accurately predicted post-FMT community composition via leave-one-out cross-validation and recapitulated disease-associated alterations in short-chain fatty acid, sulfur, and gas metabolism. We then performed 2,548 in silico FMT simulations between IBS-D/M patients and donors from the OpenBiome biobank to demonstrate a platform for personalized donor screening. This screen identified super-donors characterized by high taxonomic diversity, broad metabolic niche coverage, and community interaction networks dominated by cross-feeding rather than competition, as quantified by a flux-derived ecological network balance index that strongly predicted engraftment potential. This framework provides a mechanistic, scalable tool for rational donor-recipient matching that could guide personalized microbiome-based therapies.}, } @article {pmid42182295, year = {2026}, author = {Kumar, A and Keerthipati, P and Lotana, H and White, T and Jones, E and Prescrille, J and Webb, T and Zhu, Y and Somakhin, A and Johnson, D and Tsymbalyuk, O and Simard, M and Qin, X and Ge, Y and Zhang, H and Dilipkumar, S and Gonzalez-Juarbe, N and Drake, WP}, title = {The Vagus Nerve conducts viable translocation of gut flora to the lungs that impacts interstitial lung disease severity in mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.15.725489}, pmid = {42182295}, issn = {2692-8205}, abstract = {Communication between gut microbiota and extraintestinal organs is increasingly recognized, yet elucidation of relevant translocation mechanism(s) remains enigmatic. Vagus neuroanatomy and reports of vagal protein transfer to extraintestinal organs suggest that this "superhighway" could translocate bacteria. Here we explore whether the vagus superhighway can translocate bacteria to extraintestinal organs. Gavage of green fluorescent protein-expressing Escherichia coli (GFP- E. coli) into germ-free (GF) or specific-pathogen free (SPF) C57BL/6 mice yielded high bacillary loads in the stomach and lungs, followed by the heart, stool and peripheral muscles, despite negative blood cultures. Notably, confocal microscopy and culture revealed GFP- E. coli within the vagus nerve within five minutes of gavage suggesting rapid translocation. Metagenomic analysis of stool, lung, heart, vagus nerve, and muscle from non-gavaged SPF mice demonstrated significant microbial overlap, supporting that bacterial translocation occurs despite the presence of endogenous microflora. Remarkably, subdiaphragmatic vagotomy performed prior to GFP- E. coli gavage resulted in marked reductions of bacterial transduction in the lungs and other extraintestinal organs, except muscle. Furthermore, vagotomy significantly reduced lung fibrosis in SPF mice following intranasal bleomycin administration. In lung cancer patients undergoing lobectomy, vagotomy inhibited postsurgical reductions in forced vital capacity. These findings identify the vagus nerve as a literal gut-lung axis, facilitating viable bacterial translocation and influencing lung severity.}, } @article {pmid42182444, year = {2026}, author = {Wright, JT and Yendluri, S and Thomas, NC and Butterfield, CN and Dangerfield, TL and Taylor, DW}, title = {Structural and kinetic insights into a metagenomics-derived Cas12a with high specificity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.13.724879}, pmid = {42182444}, issn = {2692-8205}, abstract = {CRISPR-Cas12a nucleases provide an attractive alternative to Cas9 due to their compact RNA scaffold, T-rich PAM requirement, and improved target specificity. However, the mechanistic features that govern activity and discrimination across Cas12a orthologs remain incompletely understood. Here, we characterize Cas12a-MG29-1, a highly active and specific nuclease identified through metagenomic mining, using cryogenic electron microscopy, mutational analysis, and kinetic modeling. The Cas12a-MG29-1 structure reveals repositioned flexible loops near the distal end of the R-loop, including reduced engagement of one loop region and additional contacts formed by a second distal loop. Structure-guided mutagenesis and loop-swap experiments indicate that distal R-loop architecture modulates target discrimination in a context-dependent manner. Single-turnover cleavage and stopped-flow measurements show that Cas12a-MG29-1 and AsCas12a form reversible R-loops with similar kinetics but differ in strand cleavage following R-loop formation. Global kinetic modeling demonstrates that Cas12a-MG29-1 exhibits accelerated non-target strand cleavage, shifting kinetic partitioning toward product formation. This faster irreversible commitment provides a mechanistic explanation for enhanced activity and specificity without altering initial target interrogation. Together, these findings identify distal R-loop interactions and catalytic commitment as key determinants of Cas12a function and provide a framework for interpreting and engineering next-generation Cas12a orthologs.}, } @article {pmid42182637, year = {2026}, author = {Cai, X and Pang, S and Tang, C and Li, S}, title = {Relationship between airway stents and airway microorganisms: a literature review.}, journal = {Journal of thoracic disease}, volume = {18}, number = {4}, pages = {418}, pmid = {42182637}, issn = {2072-1439}, abstract = {BACKGROUND AND OBJECTIVE: Airway stent placement is widely used for the management of airway stenosis; however, it can be associated with complications such as granulation, stent migration, and infection, all of which affect patient outcomes. Among these complications, infection is a major concern, yet the relationship between airway stents and microbial colonization remains insufficiently studied. This review aims to summarize the current evidence on the effects of airway stents on the airway microbiome and to discuss their potential clinical implications.

METHODS: A literature search was conducted in PubMed for relevant studies published from database inception to December 31, 2025. Search terms included "airway stent", "tracheal stent", "bronchial stent", "airway microbiome", "biofilm", and "respiratory infection". Relevant studies were screened according to predefined criteria, and the available evidence was narratively synthesized.

KEY CONTENT AND FINDINGS: Available evidence suggests that airway stents can alter the airway microenvironment and facilitate microbial colonization, most commonly involving Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus), and Klebsiella pneumoniae (K. pneumoniae). Both metallic and silicone stents lead to similar microbial profiles, dominated by P. aeruginosa and S. aureus. Although microbial colonization frequently occurs after stent implantation, colonization does not necessarily reflect clinically significant infection, and microbiological findings should be interpreted in the clinical context. Most clinical studies report an increased risk of respiratory infection following airway stent placement. In certain specific clinical situations, such as patients with tracheoesophageal fistula, infection rates may decrease after stenting due to restoration of airway integrity. Conventional culture-based methods remain adequate for detecting common respiratory pathogens, while emerging techniques such as metagenomic next-generation sequencing (mNGS) enable broader characterization of airway microbial communities.

CONCLUSIONS: Airway stents appear to alter the airway's microbial environment by promoting the growth of potentially pathogenic microorganisms. Different stent materials, including silicone stents and self-expanding metallic stents (SEMS), seem to affect the biofilm formation on the stents' surface, which may influence microbial colonization. More studies with larger sample sizes, standardized methodologies, and advanced techniques like metagenomic sequencing are needed to further clarify the microbial changes and improve clinical management.}, } @article {pmid42182855, year = {2026}, author = {Jia, Y and Zhu, Y and Cai, H}, title = {Polymicrobial Multidrug-Resistant Infection and Fatal Bowel Ischemic Perforation After Urgent Heart Transplantation in a VA-ECMO-Bridged Recipient: A Case Report.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {604688}, pmid = {42182855}, issn = {1178-6973}, abstract = {Post-transplant infection caused by multidrug-resistant organisms (MDROs) is a major challenge in heart transplantation, especially in recipients requiring veno-arterial extracorporeal membrane oxygenation (VA-ECMO) before surgery. We describe a 52-year-old man with non-ST-elevation myocardial infarction and refractory cardiogenic shock who required VA-ECMO, intra-aortic balloon pump support, continuous renal replacement therapy, and mechanical ventilation before urgent heart transplantation. Before transplantation, he had active pneumonia. Donor respiratory culture grew Acinetobacter baumannii, Pseudomonas aeruginosa, and Staphylococcus aureus, whereas donor blood culture and blood metagenomic next-generation sequencing (mNGS) were negative. After transplantation, serial mNGS and conventional cultures revealed rapidly progressive polymicrobial infection involving Stenotrophomonas maltophilia, Burkholderia multivorans, carbapenem-resistant Acinetobacter baumannii, carbapenem-resistant Klebsiella pneumoniae, and vancomycin-resistant Enterococcus faecium. Antimicrobial therapy was repeatedly adjusted, and VA-ECMO was successfully discontinued on postoperative day 13. However, on postoperative day 16, the patient developed bowel ischemia with gastrointestinal perforation, followed by feculent peritonitis, persistent septic shock, progressive multiorgan dysfunction syndrome, and death on postoperative day 24. This case shows that perioperative infection control in VA-ECMO-bridged urgent heart transplant recipients requires more than broad-spectrum antimicrobial escalation. It requires careful assessment of preoperative infection controllability, interpretation of mNGS in conjunction with culture-based susceptibility testing, and early investigation of occult abdominal ischemia when clinical deterioration is unexplained.}, } @article {pmid42183063, year = {2026}, author = {Zhang, J and Chen, C and Hu, Y and Jia, S and Li, B and Hu, W and Jia, Y and Li, D and Liu, Y}, title = {Interaction between microorganisms and flavour products during cigar fermentation promoted by citrus Reticulata-"Chenpi" derived Enterobacter G5Z-2: based on multi-omics studies and microbial profiles.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {14}, number = {}, pages = {1785975}, pmid = {42183063}, issn = {2296-4185}, abstract = {INTRODUCTION: Cigar fermentation is crucial for developing its characteristic aroma, exogenous microorganisms can be used to enhance fermentation. It is reported that the citrus reticulata 'Chachi' (Chenpi, a traditional fermented ingredient) extract can improve the flavor of cigarette. However, there is no report on the influence of Chenpi-derived microorganisms on the fermentation process and flavor quality of cigar tobacco leaves (CTLs) till now.

METHODS: A fermentation strain (Enterobacter hoffmannii, G5Z-2) was isolated from Chenpi, and it was applied as a bioaugmentation agent in CTLs fermentation. A multi-omics approach, including metagenomics and metabolomics, was employed to investigate its impact.

RESULTS: Inoculation with G5Z-2 significantly altered the microbial community structure, suppressing native Pseudomonas and reducing overall alpha diversity while enriching beneficial genera like Aspergillus and Staphylococcus. Metabolomic analysis revealed substantial restructuring of metabolic pathways, particularly the enrichment of amino acid metabolism (such as arginine biosynthesis and phenylalanine metabolism) and nicotinate/nicotinamide metabolism. This led to accelerated degradation of proteins and amino acids, providing precursors for Maillard reaction, and a marked increase (57.5%) in total volatile flavour compounds, including key aroma constituents from carotenoid and cembranoid degradation.

CONCLUSION: The Chenpi-derived E. hoffmannii G5Z-2 optimises the fermentation process by modulating the microbial consortium and driving metabolic shifts towards favourable flavour development, demonstrating significant potential for improving the quality of Chinese-style cigars.}, } @article {pmid42184066, year = {2026}, author = {Al Awawdeh, S and Shafie, NH and Ishak, AH and Mohd Esa, N and Loh, SP and Nurdin, A}, title = {Green tea polyphenol-iron oxide chitosan nanoparticles modulate gut microbiota and regulate metabolic pathways.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42184066}, issn = {1573-0972}, support = {GP-IPS/2023/9772000//Universiti Putra Malaysia/ ; FRGS/1/2018/SKK10/UPM/02/5//Ministry of Higher Education, Malaysia/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Polyphenols/pharmacology/chemistry/administration & dosage ; Rats, Sprague-Dawley ; Male ; Rats ; *Chitosan/chemistry ; *Tea/chemistry ; *Metabolic Networks and Pathways/drug effects ; Liver/metabolism/drug effects ; *Nanoparticles/chemistry ; *Ferric Compounds/chemistry ; Proteome ; Proteomics ; Bacteria/classification/genetics/drug effects ; }, abstract = {Green tea polyphenols (GTPP) exhibit antioxidants, anti-inflammatory, and anticancer properties; however, their poor bioavailability limits clinical translation. Nanoparticle-based formulations may enhance absorption and therapeutic potential. This study investigates the therapeutic effects of GTPP encapsulated in iron oxide chitosan nanoparticles (GTPP-IOCHNP) on gut microbiota and hepatic proteome, with particular attention to pathways relevant to inflammation, drug metabolism, and tumorigenesis. Male Sprague Dawley rats were administered a single oral dose of GTPP or GTPP-IOCHNP (200 mg/kg). Cecal microbiota composition was analyzed by metagenomic sequencing, while liver proteome alterations were assessed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Metagenomic analysis revealed that GTPP-IOCHNP promoted Actinobacteriota and Collinsella, both linked to reduced inflammation and improved gut health, while inhibiting Bacteroides and Ruminococcus genera associated with intestinal barrier dysfunction, inflammation, and nephropathy. Blautia was significantly enriched (p < 0.05), supporting short chain fatty acid production, modulation of lipid and carbohydrate metabolism, and transformation of polyphenols into bioactive antioxidant metabolites. Proteomics profiling identified 20 differentially expressed hepatic proteins (p < 0.05). GTPP-IOCHNP significantly downregulated cytochrome P4502D26 (CYP2D6), indicating modulation of CYP2D6 mediated drug metabolism, and suppressed glutamate dehydrogenase 1, implicating inhibition of glutamine-driven energy metabolism linked to cancer and hyperinsulinism. Conversely, significant upregulation of elongation factor 1-alpha-1 (eEF1A1), albumin, and adenosine kinase (ADK) highlighted improved GTPP absorption, systemic transport, and regulation of hepatic energy metabolism. The integrative metagenomic and proteomic analyses reveal that GTPP-IOCHNP improves polyphenol bioavailability by modulating gut microbial ecology and hepatic metabolic pathways, offering a mechanistically driven platform for therapeutic advancement.}, } @article {pmid42184159, year = {2026}, author = {Pavlovska, M and Prekrasna-Kviatkovska, Y and Zotov, A and Dzhulai, A and Dykyi, E and Huettel, B and Fuchs, BM and Amann, RI and Teeling, H and Sidhu, C}, title = {Phytoplankton dynamics shape bacterioplankton community structure and metabolism during the austral summer-autumn transition in the Western Antarctic Peninsula.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {6}, pages = {}, pmid = {42184159}, issn = {1574-6941}, support = {//Scientific Committee on Antarctic Research/ ; 542264307//German Research Foundation/ ; 569718716//German Research Foundation/ ; }, mesh = {Antarctic Regions ; *Phytoplankton/metabolism/genetics/classification ; Seasons ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Diatoms ; Seawater/microbiology ; Polysaccharides/metabolism ; *Microbiota ; }, abstract = {Seasonal changes in Antarctic coastal waters trigger pronounced shifts in microbial community composition and function, yet sparse spatial and temporal coverage currently limits our understanding of phytoplankton-bacterioplankton coupling. This study combines metagenomic and metatranscriptomic analyses of marine bacterioplankton with environmental data to address the functional dynamics of planktonic communities off the Western Antarctic Peninsula during the austral summer-autumn transition. Diatoms dominated the phytoplankton community, with generally low biomass and abundance, yet a species-specific succession was observed. The bacterioplankton community structure shifted from dominance of copiotrophic taxa (e.g. Polaribacter) towards oligotrophic lineages (e.g. SAR11) adapted to low-nutrient conditions, accompanied by a decrease in microbial carbohydrate-degradation activity. The capacity to degrade algal-derived polysaccharides varied between community members, with ß-glucan, α-glucan, chitin, and host glycan utilization present in all, and fucose, β-galactan and trehalose degradation restricted to specific taxa. DMSP metabolism also showed taxonomic specificity and was shaped by both physical (ice melt and fluctuations in solar irradiation) and biological factors (phytoplankton succession). Together, these findings reveal a complex, taxon-specific coupling between bacterioplankton and phytoplankton communities in the Western Antarctic Peninsula, linking community structure to likely functional gene expression and highlight how Antarctic bacterioplankton drives carbon and sulfur turnover in a polar marine ecosystem.}, } @article {pmid42184529, year = {2026}, author = {Wang, R and Chen, H}, title = {Metagenomic insights into vertical migration of soil antibiotic and metal(loid) resistance genes under long-term organic fertilizer application and irrigation.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142479}, doi = {10.1016/j.jhazmat.2026.142479}, pmid = {42184529}, issn = {1873-3336}, mesh = {Manure ; Animals ; *Fertilizers ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Cattle ; *Agricultural Irrigation ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Soil/chemistry ; Chickens ; Metals, Heavy/analysis ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; }, abstract = {Agricultural irrigation is associated with antibiotic resistance gene (ARG) transmission and resistome succession through the integration of exogenous and indigenous soil communities. However, the long-term field-scale impacts of organic irrigation on vertical resistome migration and its ecological consequences remain underexplored. This study employed metagenomic analyses and field surveys to bridge these knowledge gaps. The results showed that ARGs and metal(loid) resistance genes (MRGs) were most abundant and diverse at 0-20 cm depth, with distinct characteristics in deeper layers depending on manure type. Cattle manure-irrigated soils exhibited a greater potential for vertical ARG diffusion than chicken manure-irrigated soils, despite lower surface-level enrichment. ARG distribution was more strongly associated with groundwater and soil background factors than with organic fertilizer inputs. Mobile genetic elements (MGEs) and heavy metal concentrations were key factors associated with resistome succession. Compared to the control, contigs associated with both ARGs and MRGs increased 5.8-fold and 3.1-fold in chicken and cattle manure-irrigated soils, respectively, suggesting a potentially important role for prophages. While control contigs were distributed in deeper layers, irrigated soils showed pronounced surface enrichment. Irrigation was linked to increased network density and complexity, with chicken manure-irrigated soils exhibiting higher levels of antibiotic-resistant bacteria (ARB). Notably, opportunistic pathogens carrying ARGs, including Ralstonia pickettii and Stenotrophomonas maltophilia, were enriched in irrigated profiles. Microbiome, MGEs, and abiotic factors were collectively associated with resistome succession, with deterministic processes contributing substantially to community assembly. This study provides new insights into the vertical distribution and inferred succession of the resistome in organically irrigated soils.}, } @article {pmid42184535, year = {2026}, author = {Ma, B and Li, F and Zhang, C and Deng, Y and Sekar, R and Chen, Z and Wang, M and Zamyadi, A and He, S and Huang, T and Guo, J and Zhang, H}, title = {Multivalent manganese-mediated synergistic aerobic denitrification boost nitrogen removal in oligotrophic aquatic systems: Insight into microbial functional and metabolic complementarity.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142496}, doi = {10.1016/j.jhazmat.2026.142496}, pmid = {42184535}, issn = {1873-3336}, mesh = {*Manganese/chemistry/metabolism ; *Denitrification ; *Nitrogen/metabolism ; Bioreactors ; *Bacteria/metabolism/genetics ; *Water Pollutants, Chemical/metabolism ; Aerobiosis ; Water Purification/methods ; }, abstract = {Efficient nitrogen removal from oligotrophic lakes and reservoirs necessitates the development of innovative, eco-friendly strategies to mitigate the limitation of organic electron donors. We engineered four multivalent manganese (Mn) composite-functionalized bioreactors for oligotrophic water remediation, which demonstrated a sustained total nitrogen removal efficiency exceeding 97.66% over five operational cycles. Manganese powder-doped activated carbon achieved the highest nitrate removal rate, ranging from 0.29956 to 0.39831 mg/L/d. Immobilization with sodium alginate has mitigated manganese oxidative corrosion, thereby resulting in more sustained long-term reactive performance. Furthermore, denitrifying bacteria synergistically promote the enrichment of phosphorus-accumulating microorganisms and manganese-oxidizing bacteria (Burkholderiaceae, Methylophilaceae, and Azospirillaceae), which play pivotal roles in denitrification and manganese cycling, within Mn addition (MNA) reactors. Correlation analyses revealed stronger co-occurrence patterns between denitrification genes and manganese-oxidizing genes in the MNA reactors compared to the control. The abundance of ATP-binding cassette transporter genes, particularly encoding lipopolysaccharide transport (wzt) and lipoprotein release (lolD), increased by 1.37-1.90-fold and 1.31-1.80-fold, respectively, in the MNA reactors relative to the control reactor. Furthermore, the metabolic complementarity network suggested that MNA not only promoted community metabolic competition and complementarity effects but also enhanced higher energy production and respiratory activity. These findings establish a manganese-driven microbial enhancement strategy for sustainable nitrogen removal from polluted surface waters, offering new opportunities for eco-engineered water treatment.}, } @article {pmid42184563, year = {2026}, author = {Hull, R}, title = {RNA viruses are an integral part in evolution of all organisms.}, journal = {Virology}, volume = {621}, number = {}, pages = {110950}, doi = {10.1016/j.virol.2026.110950}, pmid = {42184563}, issn = {1096-0341}, mesh = {*RNA Viruses/genetics/physiology/classification ; Symbiosis ; *Evolution, Molecular ; *Biological Evolution ; Animals ; Genome, Viral ; Host-Pathogen Interactions ; Virus Replication ; Humans ; Retroviridae/genetics/physiology ; }, abstract = {RNA viruses are intracellular symbiotic obligate parasites, needing host factors and energy for their replication with forms of symbiosis ranging from antagonism (pathogenic, not contributing to host metabolism) to mutualism (contributing benefits to the host as well as making demands on host metabolism). As a group, they have several unusual features: a) metagenomic studies suggest that they are probably are the most common group of viruses infecting all organism species and are the most abundant biological entity on earth; b) they have existed ever since the Last Universal Common Ancestor from which all living organisms have evolved; c) a high proportion of their species have + strand RNA genomes, or are retroviruses, that replicate without proof-reading creating many variants (quasispecies); d) they replicate in organelles within the endoplasmic reticulum and other membranes which connect to other organelles and to membrane and metabolic network systems. This paper brings together these facts presenting the hypothesis that RNA viruses and retroviruses form host/mutualistic virus symbionts as an evolutionary unit with the viral responses to evolutionary stresses being rapid and linking closely with the slower host genomic responses. The hypothesis is presented with a background of evolution of organisms and viruses, drivers of evolution, and the evolutionary natural selection pathway from the sources of stresses to impact and molecular reactions to stresses entering the basic organism body, the cell.}, } @article {pmid42184767, year = {2026}, author = {Chen, D and Ibrar, M and Yan, F and Sun, G and Xue, R and Jia, A and Zhou, J and Gao, Y and Ma, C and Wang, M and Zhang, J and Ma, Z and Liu, L}, title = {The rising power of females: Dioecious shrub enhances soil organic carbon sequestration via fungal necromass in chronosequence of desertified alpine grassland restoration.}, journal = {Journal of environmental management}, volume = {409}, number = {}, pages = {130022}, doi = {10.1016/j.jenvman.2026.130022}, pmid = {42184767}, issn = {1095-8630}, mesh = {*Grassland ; *Soil/chemistry ; *Soil Microbiology ; *Carbon Sequestration ; Carbon ; *Fungi ; Rhizosphere ; Tibet ; }, abstract = {Desertification-induced soil organic carbon (SOC) loss poses a major environmental threat to the alpine grasslands of the Qinghai-Tibet Plateau, jeopardizing ecological security and sustainability. While pioneer shrub introduction has yielded positive ecological outcomes, the mechanisms of SOC recovery remain poorly understood. We investigated the effects of a widely used dioecious shrub on rhizosphere SOC dynamics across a 20-year restoration chronosequence, employing a comprehensive framework that combined root exudation measurements, soil physicochemical analysis, metagenomics, and biomarker profiling to decipher the mechanism. Our results reveal that microbial-derived carbon dominated rhizosphere SOC accrual, contributing 20.1-22.0% to the total SOC pool, over 50 times more than plant-derived carbon (0.1-0.4%). The microbial pool was predominantly fungal necromass (>93%), correlated with declining root exudation and suppressed carbon-degrading gene abundance during restoration. In the 20th year after recovery, a striking divergence in the effects of male and female shrubs on rhizosphere SOC became apparent, with female shrubs sustaining 15% more microbial necromass and 47% more lignin phenols than males. Our findings highlight that SOC restoration in the rhizosphere of pioneer shrubs is predominantly driven by a fungal-mediated microbial carbon pump. Moreover, the preferential use of female shrubs offers a dual benefit: enhancing long-term rhizosphere SOC sequestration and controlling shrubs encroachment. This sex-informed strategy therefore provides a scalable framework for degraded alpine grasslands and serves as a transferable model for other drylands undergoing warming-wetting transitions, where alleviated water limitation increasingly enables vegetation-microbe-mediated carbon stabilization.}, } @article {pmid42184943, year = {2026}, author = {Cai, Q and He, J and Qiu, W and Wang, Y and Fang, K and Zou, X and Aili, A and Zhong, Y and Zhang, J}, title = {In situ assembly of the humic acid-protein conductive network facilitates chain elongation for medium-chain fatty acids anaerobic production from waste activated sludge.}, journal = {Bioresource technology}, volume = {456}, number = {}, pages = {134964}, doi = {10.1016/j.biortech.2026.134964}, pmid = {42184943}, issn = {1873-2976}, mesh = {*Sewage/microbiology/chemistry ; *Humic Substances ; *Fatty Acids/biosynthesis ; Anaerobiosis ; *Proteins/metabolism ; }, abstract = {Biosynthesis of medium-chain fatty acids (MCFAs) from waste activated sludge (WAS) is primarily limited by intracellular reductive stress (NADH accumulation) and energy shortages. This work demonstrates that humic acid (HA), functioning as a redox mediator, effectively enhances the carbon chain elongation (CE) process. Optimal HA supplementation (1000 mg/L) increased the peak MCFAs yield by 98.3%, driving a fundamental shift in the dominant product spectrum from short-chain fatty acids (SCFAs) to MCFAs. Combined metagenomic and electrochemical analyses reveal that this enhancement originates from HA-mediated spatial and metabolic integration across multiple scales. Macroscopically, HA complexes with proteins to construct a conductive biopolymer network. Functioning as a highly efficient extracellular electron sink, this network significantly accelerates transmembrane electron discharge to consume excess intracellular electrons. This rapid electron extrusion alleviates reductive stress and relieves product feedback inhibition on dehydrogenases, concurrently inducing an elevated cellular energy charge (ATP surge). Subsequently, feedback regulation driven by this high-energy state suppresses the competitive acetogenic branch (Pta-ackA pathway), effectively preventing carbon loss. Dominated by the highly enriched CE taxon Candidatus_Microthrix, the microbial consortium exhibits a robust metabolic potential to channel carbon into synergistic RBO and FAB pathways. This metabolic shift, fueled by abundant precursors and energy, effectively circumvents acidic toxicity by rapidly consuming SCFAs. These findings elucidate the critical role of HA in reshaping microbial redox homeostasis, providing a robust mechanistic foundation for high-value carbon recovery engineering from complex solid wastes.}, } @article {pmid42185267, year = {2026}, author = {Zhou, YL and Feng, JC and Lu, R and Chen, Z and Mara, P and Tao, X and Liu, J and Huang, Y and Hu, J and Yao, J and Edgcomb, VP and Teske, A and Wang, X and Zhang, S}, title = {Diversification in ANME-1 archaea is associated with the presence of highly variable genomic hotspots.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73573-4}, pmid = {42185267}, issn = {2041-1723}, support = {42494884//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42325603//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Anaerobic methanotrophic (ANME) archaea have been primarily documented by metagenomic analysis of environmental samples. The mechanisms that drive their diversification and speciation are poorly understood. Here we analyse the phylogenomic diversity at the species and strain levels of clade ANME-1 from deep-sea cold seeps, as a model system with a well-studied phylogenetic framework. We reconstruct high-quality circular metagenomic-assembled genomes (cMAGs) and identify highly variable genomic hotspots that distinguish them. Genomic differentiation and diversification in ANME-1 is associated with genes involved in prokaryotic defense systems, transport mechanisms and methane metabolism. In addition, heterologous expression of ANME-1 hicAB operons supports their proposed role as toxin/antitoxin systems, possibly involved in mediating responses to environmental stresses.}, } @article {pmid42185302, year = {2026}, author = {Nishisaka, CS and Quevedo, HD and Pellegrinetti, TA and de Almeida Godoy, F and Rossmann, M and Mendes, LW and Mendes, R}, title = {Bacterial inoculation drives microbiome-mediated resistance to a soil-borne pathogen in wheat.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01021-8}, pmid = {42185302}, issn = {2055-5008}, support = {2020/06077-9//São Paulo Research Foundation (Fapesp)/ ; 2025/11610-1//São Paulo Research Foundation (Fapesp)/ ; 402654/2023-4//National Council for Scientific and Technological Development (CNPq)/ ; }, abstract = {Soil microbiomes are fundamental to plant health, mediating nutrient cycling, stress tolerance, and pathogen defense. However, soil-borne pathogens such as Bipolaris sorokiniana severely constrain wheat productivity. Despite growing interest, the mechanisms by which beneficial bacterial inoculation reshapes rhizosphere microbial communities to enhance disease resistance remain poorly understood. Here, we isolated three bacterial strains, Streptomyces virginiae CMAA1738, Paenibacillus ottowii CMAA1739, and Pseudomonas inefficax CMAA1741, with antagonistic activity against B. sorokiniana, and evaluated their effects on wheat under controlled conditions. Through plant bioassays, bacterial inoculation reduced disease severity by ~60% and promoted root growth. Metataxonomic and metagenomic analyses revealed shifts in the structure and functional potential of the rhizosphere microbiome. Structural equation modeling indicated that inoculation was the primary driver of microbiome restructuring and disease suppression. Notably, inoculation restored the diversity of plant growth-promoting genes and biosynthetic gene clusters reduced by pathogen infection, enriching functions associated with stress tolerance, nutrient metabolism, and secondary metabolite production. In addition, Random Forest analysis revealed that variation in disease severity under pathogen pressure was associated with differences in bacterial community composition. Together, these findings demonstrate that bacterial inoculation can restructure the rhizosphere microbiome and restore key functional traits linked to plant resilience.}, } @article {pmid42185318, year = {2026}, author = {Nguyen, UT and Salamzade, R and Sandstrom, S and Swaney, MH and Townsend, EC and Wu, SY and Cheong, JZA and Sardina, JA and Ludwikoski, I and Rybolt, M and Wan, H and Carlson, CM and Ferro, J and McArthur, O and Suh, WS and Zarnowski, R and Andes, DR and Currie, CR and Kalan, LR}, title = {Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73524-z}, pmid = {42185318}, issn = {2041-1723}, support = {U19AI142720//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R35GM137828//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, abstract = {The skin microbiome forms a protective barrier to pathogens, including through the production of antimicrobial metabolites. Here, we present EPIC[HHS], a large and taxonomically diverse skin microbiome culture collection of 968 strains from eight body sites. EPIC[HHS] captures >95% of cumulative species-level abundance across 268 skin metagenomes. It includes isolates present at <0.1% relative abundance and the cultured representatives for eight species not previously isolated, markedly expanding current skin microbiome resources. A contact-independent screen assaying ~14,000 pairwise interactions against 22 pathogens revealed widespread antagonism with striking enrichment for antifungal activity. Finally, functional genomic analysis, including 287 EPIC[HHS] isolate genomes, demonstrated a diverse landscape of skin-associated biosynthetic gene clusters that are mostly uncharacterized. Together EPIC[HHS], its functional and genomic characterization, establishes the skin microbiome as a reservoir for specialized metabolism and provides a platform for microbiome-based antimicrobial discovery.}, } @article {pmid42185326, year = {2026}, author = {Hoggard, M and Gios, E and Tee, HS and Geoghegan, JL and Handley, KM}, title = {DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73439-9}, pmid = {42185326}, issn = {2041-1723}, abstract = {Viruses are ubiquitous albeit individually constrained by host-range. Less well understood are environmental limitations on virus proliferation. To investigate estuarine viral diversity, niche constraints, and traits of environmental adaptation, we analyse metagenomic and metatranscriptomic data from an estuarine salinity gradient, including water and sediment. We then expand our analysis to globally-distributed viral genomes. Viral distributions vary by estuary habitat, reflecting prokaryote community patterns, and highlighting that virus-host interactions are strongly influenced by environment. Viral lineages, up until approximately the rank of genus, are largely partitioned by ecological niche based on factors such as salinity and the aquatic-terrestrial divide. Across habitat boundaries, viruses feature osmoadaptive traits similar to their prokaryote hosts. These include slightly elevated ratios of acidic to basic amino acids and decreased protein isoelectric points at higher salinities, particularly in virus major tail and capsid proteins, which are not solely explained by reliance on host machinery. Further studies are needed to determine the primary driver of these modifications in viruses (e.g. environment or host) and whether these traits restrict virus distributions beyond host-range limitation. Overall, our findings indicate that successful proliferations of viruses into distinct biomes (e.g. freshwater, saline, terrestrial) are rare, with viruses constrained to specific ecological niches.}, } @article {pmid42185942, year = {2026}, author = {Wang, Y and Peng, Y and Wang, B and Di, M and Xi, M and Yao, Z and Shi, C and Feng, Q and Yin, D and Li, J and Xu, X and Zhang, R and Peng, X}, title = {A preliminary metagenomic and metabolomic investigation into the effects of Aspergillus niger cultures on microbial homeostasis and antibiotic resistance gene profiles in the rumen of fattening sheep.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42185942}, issn = {1674-9782}, abstract = {BACKGROUND: Under high-concentrate feeding conditions, ruminants often experience rumen microecological imbalance and dysfunction, which can impair growth performance and increase the risk of antibiotic resistance gene (ARG) dissemination.

RESULTS: To evaluate the ameliorative effects of Aspergillus niger (A. niger) cultures, fattening sheep were randomly allocated into the following five groups: a control group (CON), a control diet supplemented with 250, 500, or 1,000 mg/kg A. niger cultures (designated as LA, MA, and HA, respectively); and an antibiotic group supplemented with 5,000 mg/kg chlortetracycline premix (AN). Microbial community analysis indicated that several bacterial taxa, including Succinivibrio sp900317105, Prevotella sp002353485, Quinella sp017515635, Quinella sp015206805, and Prevotella sp900320255, were significantly enriched in the A. niger culture-supplemented groups (P < 0.05). ARG profiling showed that the abundance of tetracycline resistance genes was significantly lower in all A. niger groups compared with the CON and AN groups (P < 0.05), while β-lactam resistance genes were significantly reduced in the HA group (P < 0.05). Furthermore, the abundances of Rank I and Rank II ARGs were significantly higher in the AN group than in the other groups, whereas the abundances of Rank II and Rank IV ARGs were significantly lower in the A. niger culture groups than in the CON and AN groups. Metabolomic analysis further demonstrated that supplementation with A. niger cultures significantly decreased the concentration of N-decanoyl-L-homoserine lactone (P < 0.05) while increasing the levels of N-3-oxotetradec-7Z-enoyl-L-homoserine lactone, indole-3-methyl acetate, and indole-3-propionic acid (P < 0.05).

CONCLUSIONS: These findings suggest that A. niger cultures can reduce the abundance of ARGs and mitigate the risk of ARG dissemination by modulating the rumen microbial community and associated metabolites.}, } @article {pmid42185948, year = {2026}, author = {Michalik, A and Majewska, E and Andriienko, V and Nowak, KH and Stroiński, A and Łukasik, P}, title = {Stable nutritional endosymbiosis across cryptic diversity of a leafhopper species complex.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12986-3}, pmid = {42185948}, issn = {1471-2164}, support = {2021/41/B/NZ8/04526//Narodowe Centrum Nauki/ ; 2018/31/B/NZ8/01158//Narodowe Centrum Nauki/ ; }, abstract = {BACKGROUND: Ancient nutritional symbioses underpin the ecological success of many sap-feeding insects. In 'true hoppers' - the hemipteran suborder Auchenorrhyncha, obligate bacterial partners provide essential amino acids lacking in plant phloem diets. However, the stability and persistence of such associations across the diversity of hoppers are poorly understood, and investigations are often complicated by insufficiently resolved host identity.

RESULTS: Here, we combined multitarget amplicon sequencing, metagenomics, and microscopy to assess the compositional and functional diversity of the microbiota across Polish, Swedish, and Austrian populations of leafhoppers morphologically identified as Verdanus abdominalis. Host COI data revealed pronounced cryptic genetic diversity, indicating several deeply divergent lineages within the characterized collection, but limited microbiota variation among populations. 16S rRNA amplicon data confirmed the consistent presence of the ancient bacterial endosymbionts Candidatus Sulcia muelleri and Candidatus Nasuia deltocephalinicola, and metagenomics showed that their reduced but complementary genomes jointly encode the complete set of essential amino acid biosynthesis pathways required by the host. Other microbes were uncommon in these symbioses. Microscopy corroborated these findings, revealing conserved bacteriome organization and spatial separation of Sulcia and Nasuia within distinct bacteriocytes.

CONCLUSIONS: Our results demonstrate that the Sulcia-Nasuia dual symbiosis remains evolutionarily stable across cryptic Verdanus diversity, underscoring the robustness of ancient nutritional partnerships despite ongoing host diversification.}, } @article {pmid42186028, year = {2026}, author = {Larroya, A and Romera-Giner, S and Tolosa-Enguís, V and Rodríguez-Ruano, SM and Andrés-García, S and Soro-Conde, I and Codoñer, P and Sanz, Y}, title = {Gut microbiota and western dietary patterns associated with behavioral problems in children and adolescents: a cross-sectional study.}, journal = {Nutrition journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12937-026-01335-5}, pmid = {42186028}, issn = {1475-2891}, abstract = {BACKGROUND: Childhood and adolescence are crucial periods for brain development, during which multiple environmental factors, including gut microbiota and dietary habits, play important roles. However, the combined impact of those factors on neurodevelopment and mental disease risk remains largely unexplored. Here, we aimed to investigate the relationships between gut microbiota and diet and their role in classifying behavioral problems that may precede mental disorders in children and adolescents.

METHODS: We performed a cross-sectional study, including data from 335 subjects, including 202 children (5-10 years) and 133 adolescents (11-17 years). Gut microbiota was analysed in stools by shotgun metagenomics. Dietary habits, lifestyle factors and emotional and behavioral difficulties were screened using validated questionnaires. Penalized Logistic Regression models were trained to classify individuals into Healthy and Behavioral Problem groups based on microbial diversity, differential abundance of bacterial species, dietary patterns, and food and nutrient intakes. Mediation analyses were applied to assess whether gut microbiota mediates the effect of diet on behavioral problems.

RESULTS: A Western diet characterized by poor adherence to dietary recommendations was consistently associated with behavioral problems in all age groups. Individuals with behavioral problems exhibited distinct gut microbiota profiles characterized by lower levels of short-chain fatty acid-producing bacteria (particularly butyrate-producing species) and higher levels of potential pathogens (e.g., Campylobacter coli and Lautropia mirabilis), linked to poor dietary choices. Furthermore, we evidenced the mediation role of the gut microbiota in the association between dietary patterns and food groups and behavioral problems. In adolescents, L. mirabilis was identified as a mediator of the relationship between a Western diet and behavioral problems, while Anaerostipes rhamnosivorans mediated the relationship between fish consumption and behavioral problems. Gut microbiota data enhanced the classification accuracy of logistic regression models for identifying individuals with behavioral problems over models based solely on dietary data.

CONCLUSION: Integrating dietary habits and gut microbiota data enables more accurate stratification of children and adolescents at risk for behavioral problems. Our findings may help to refine dietary interventions targeting the gut microbiota to improve mental health outcomes in these vulnerable populations.}, } @article {pmid42186092, year = {2026}, author = {Wang, L and Li, F and Ma, Z and Ungerfeld, EM and Zhang, T and Zhang, Z and Liu, X and Zhang, Q and Zhang, X}, title = {Yeast culture promotes butyrate produced fibrolytic bacteria as intracellular hydrogen sink in the rumen.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02436-3}, pmid = {42186092}, issn = {2049-2618}, support = {32308686//The National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Yeast culture (YC) supplementation is widely adopted to mitigate rumen pH depression and alleviate the inhibition of fiber degradation under starch-rich diets. Yet, the underlying microbial mechanisms, particularly how yeast culture orchestrates fibrolytic communities and affects metabolic hydrogen flow in the rumen, remain a critical knowledge gap. Accordingly, elucidating the microbial basis by which yeast culture modulates fiber degradation and hydrogen utilization under starch-rich diets is of both theoretical and practical importance.

METHODS: We conducted a study with growing lambs receiving starch-rich diets that differed only in yeast culture supplementation (CON 0%, YC 1%). We evaluated their growth performance, apparent total-tract digestibilities, rumen fermentation end-products, and the rumen metagenome.

RESULTS: The YC treatment increased the lambs' final body mass (P = 0.02), average daily gain (P = 0.03), digestibilities of neutral detergent fiber (P < 0.001) and acid detergent fiber (P < 0.001), and rumen pH (P < 0.05), and tended to increase organic matter digestibility (P = 0.09). In addition, total VFA concentrations, particularly butyrate, were higher at 6 h post-morning feeding (P = 0.01). Fibrolytic and hydrogenotrophic taxa (e.g., Ruminococcus_E and Quinella) and CAZyme families, including GH43, GH31, GH9, and GH35, were enriched by the YC treatment, as were bacteria involved in fiber degradation and butyrate production. Furthermore, none of the top five YC treatment-enriched bacterial genomes contained any hydrogenase genes, which indicates that this butyrogenic fibrolytic consortium is significantly different from the hydrogen-producing fiber-degrading microorganisms we are familiar with.

CONCLUSION: Yeast culture supplementation promoted the proliferation of a distinct butyrogenic consortium that degrades fiber while apparently disposing intracellularly metabolic hydrogen generated during fermentation, rather than releasing it as H2. These findings provide a microbial basis for understanding how yeast culture improves fermentation efficiency under starch-rich diets and suggest that selecting yeast culture products capable of promoting butyrogenic fibrolytic bacteria may be beneficial for ruminant performance and rumen stability. Video Abstract.}, } @article {pmid42186552, year = {2026}, author = {Méndez-Sánchez, D and Pomahač, O and Valt, M and Bourland, WA and Čepička, I}, title = {An extensive morphological and molecular characterization of the neglected class Odontostomatea (Ciliophora).}, journal = {Marine life science & technology}, volume = {8}, number = {2}, pages = {289-323}, pmid = {42186552}, issn = {2662-1746}, abstract = {UNLABELLED: Odontostomatid ciliates, known for over a century, were historically classified within various taxonomic groups of Ciliophora Doflein, 1901 until their reclassification into the class Odontostomatea. Despite the recognition of 25 valid species, most descriptions predate the advent of silver impregnation and sequencing methods. Consequently, many species were described based solely on observations of live specimens, leading to incomplete or ambiguous records. To date, redescriptions of only three species include 18S rRNA gene sequences data, and their evolutionary relationships remain unresolved. In this study, we investigated 32 populations representing 15 species-including three newly described-across the genera Discomorphella, Epalxella, Limnomylestoma gen. nov., Mircalla gen. nov., Mylestoma, Pelodinium, Saprodinium, and Tostonella gen. nov. Comprehensive analyses were conducted using in vivo microscopy, silver impregnation, and scanning electron microscopy. We also designed specific primers to amplify the partial 18S rRNA gene of various odontostomateans and retrieved additional 18S rRNA sequences from environmental metatranscriptomic and metagenomic datasets. This study represents the most extensive investigation of Odontostomatea to date, confirming the monophyly of the class by revealing the position of Epalxella, reconstructing its internal phylogeny, identifying two main odontostomatean lineages, and revealing its remarkable diversity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-026-00352-x.}, } @article {pmid42186601, year = {2026}, author = {Zhang, Z and Jia, Z and Zhang, X and Zou, W and Chen, J}, title = {Late-onset cytomegalovirus pneumonia after autologous stem cell transplantation for angioimmunoblastic T-cell lymphoma: a case report.}, journal = {Therapeutic advances in infectious disease}, volume = {13}, number = {}, pages = {20499361261450721}, pmid = {42186601}, issn = {2049-9361}, abstract = {This case report illustrates a diagnostic and therapeutic challenge in a highly immunocompromised host: severe pneumonia occurring late after autologous hematopoietic stem cell transplantation (auto-HSCT). A 57-year-old male with angioimmunoblastic T-cell lymphoma (AITL) presented with hypoxemic respiratory failure 1 year post-auto-HSCT, a timeline extending beyond the typical high-risk period for opportunistic infections. A profoundly low CD4+ T-cell count (172/µL) was identified as the key predisposing factor. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) enabled rapid, unbiased pathogen detection, confirming cytomegalovirus (CMV) pneumonia (viral load: 3.0 × 10[4] copies/mL) with Klebsiella pneumoniae coinfection. An integrated management strategy was instituted, comprising early empiric coverage for Pneumocystis jirovecii pneumonia, targeted therapy with ganciclovir and levofloxacin, and adjunctive immunomodulation using intravenous immunoglobulin and corticosteroids. This comprehensive approach resulted in full recovery, highlighting that the severity of immune suppression-rather than time since transplantation alone-determines infection risk. This case challenges the conventional time-based risk paradigm and supports immune-guided surveillance. It underscores the transformative role of mNGS in diagnosing complex infections in immunocompromised patients and advocates for a management paradigm that concurrently addresses pathogen eradication and host immune dysfunction.}, } @article {pmid42186944, year = {2026}, author = {Patin, NV and Pitz, K and Kimbrough, K and Archer, F}, title = {Beyond Biodiversity: Incorporating Uncertainty Into Metabarcoding Data for Improved Inference of Ecological Relationships.}, journal = {Molecular ecology resources}, volume = {26}, number = {4}, pages = {e70160}, doi = {10.1111/1755-0998.70160}, pmid = {42186944}, issn = {1755-0998}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; Bayes Theorem ; }, abstract = {Metabarcoding sequence data from environmental DNA (eDNA) is rapidly expanding as a powerful method for biodiversity surveys. In order to interpret these data, tools are needed that account for the uncertainty associated with eDNA sampling, sequencing and analysis. The data resulting from eDNA marker gene analysis differ from many traditional methods of biodiversity surveys because they are highly complex, sparse and compositional. Methodological biases produce uncertainty at every step of the sampling and sequencing process. Thus, it is critical that users have a way of interpreting eDNA results that accounts for their compositional nature and models the uncertainty resulting from factors like patchy sampling, PCR amplification biases and variable sequencing depth. Here, we introduce MAMBO: Metabarcoding Analysis using Modeled Bayesian Occurrences. MAMBO simulates in silico replication and models the uncertainty surrounding the sequencing and analysis process. Further, it uses these modelled sequence count data to correlate two sets of marker genes with a Bayesian regression, facilitating the linkage of different groups targeted by these assays. Compared with correlational network analyses, MAMBO overcomes many of the limitations to robust statistical analyses of eDNA marker gene data and provides an opportunity for new insight into ecological patterns over space and time.}, } @article {pmid42187250, year = {2026}, author = {Liu, X and Kwok, L-Y and Zhang, W}, title = {Integrated gut microbiota and metabolome signatures revealed by deep metagenomic sequencing in post-stroke cognitive impairment with type 2 diabetes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0024426}, doi = {10.1128/spectrum.00244-26}, pmid = {42187250}, issn = {2165-0497}, abstract = {UNLABELLED: Post-stroke cognitive impairment (PSCI) is significantly exacerbated in individuals with type 2 diabetes mellitus (T2DM), yet the underlying gut microbial and metabolic mechanisms remain unclear. In this study, baseline fecal samples from 28 diabetic PSCI (PSCI-DM) patients and 29 matched non-PSCI non-diabetic controls were subjected to deep metagenomic sequencing and untargeted metabolomics. Although alpha diversity was preserved, subtle but meaningful shifts were observed in bacterial and fungal composition. The PSCI-DM group exhibited depletion of beneficial butyrate-producing taxa, including Lachnospira spp. and Butyribacter intestini, and enrichment of Butyricimonas virosa. Five fungal species, including Torulaspora globosa and Pichia kudriavzevii, were significantly reduced. Metabolomic profiling identified 45 differentially abundant metabolites, with decreases in neuroprotective compounds, such as 9-oxononanoic acid, C16-ceramide, and nootkatone, and increases in metformin and bile acid derivatives. Abundances of microbial functional pathways linked to energy metabolism were elevated, while those involved in cofactor and neurotransmitter precursor synthesis were reduced. Significant correlations were found between specific microbes and metabolites, suggesting coordinated dysregulation across kingdoms. However, only a limited subset of microbial features remained independently associated with cognitive performance. Specifically, metabolites Nb-palmitoyltryptamine and pipecolic acid, and fungal species Pichia kudriavzevii showed significant correlations with Montreal cognitive assessment (MoCA) scores for cognitive impairment. These findings reveal a tripartite gut ecosystem signature in PSCI-DM and provide a mechanistic foundation for microbiota-targeted therapeutic strategies.

IMPORTANCE: In the context of type 2 diabetes, post-stroke cognitive impairment represents a clinically prevalent yet mechanistically underexplored condition with limited therapeutic options. This study combined metagenomic sequencing with non-targeted metabolomics to reveal the coordinated dysregulation of bacteria, fungi, and host-related metabolites in the gut of type 2 diabetes mellitus with post-stroke cognitive impairment (PSCI-DM) patients. The research indicates that cognitive impairment is not solely related to the overall decline in microbial diversity, but also involves the targeted reduction of neuroprotective butyrate-producing bacteria, the absence of specific gut fungi, and the corresponding reduction in neural activity and lipid metabolites. These findings collectively establish the gut microbiota-metabolite characteristics of PSCI-DM patients, providing a theoretical basis for targeted probiotic intervention measures to prevent or alleviate cognitive decline in diabetic patients after stroke.}, } @article {pmid42187318, year = {2026}, author = {Tang, Y and Lin, Z and Liu, Z and Guo, J and Yang, C and Feng, L and Wang, Y and Zhang, P and Chen, Y}, title = {Impact of Corneal Microbial Latency Detected by Metagenomic next-generation sequencing on Postoperative Recovery Following Keratorefractive lenticule extraction.}, journal = {Journal of cataract and refractive surgery}, volume = {}, number = {}, pages = {}, doi = {10.1097/j.jcrs.0000000000001979}, pmid = {42187318}, issn = {1873-4502}, abstract = {PURPOSE: To investigate the microbial species latent in corneas of healthy individuals and determine whether small incision lenticule extraction (SMILE) serves as a risk factor for pathogen reactivation.

SETTING: The Ophthalmology Department of Peking University Third Hospital, Beijing, China.

DESIGN: Prospective Cohort Study.

METHODS: Metagenomic next-generation sequencing (mNGS) was employed to analyze the microbial composition of corneal lenticules from SMILE. Based on the results, patients were categorized into Viral Group (VG) and Non-Viral Pathogen Group (NVPG). Two Matched Groups (MG1 and MG2) were established by selecting pathogen-negative individuals at a 1:4 ratio relative to two positive groups. Using SPSS to analyze baseline characteristics, preoperative ocular parameters and postoperative ocular parameters among groups.

RESULTS: Among the detected pathogens, latent Herpesviruses were identified in 9 cases (4.31%), Papillomavirus were 4 cases (1.91%), and non-viral pathogens were 20 cases (9.57%). Both VG and NVPG groups showed no significant differences in baseline characteristics or preoperative ocular parameters compared with MG groups. In postoperative ocular parameters, no significant differences were found between VG and MG1, though intergroup variations in intraocular pressure and corneal thickness were observed (p>0.05). However, NVPG demonstrated significantly poorer results than MG2 in 1 month-spherical equivalent (p=0.033) and corneal epithelial staining (p=0.044).

CONCLUSION: These findings indicate pathogen latency does not affect ocular status and SMILE surgery is unlikely to reactivate latent viruses or exerts minimal influence. Viral latency has almost no impact on postoperative recovery, while latent non-viral pathogens may interfere with postoperative recovery.}, } @article {pmid42187703, year = {2026}, author = {Sun, Q and Li, J and Xu, G and Zhou, C and Lei, K and Jiang, W}, title = {Source-Specific Nitrogen Inputs Are Associated with Pathway Partitioning Between Denitrification and DNRA in River Water.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, pmid = {42187703}, issn = {2079-7737}, support = {Lishui City Key R&D Program Projects.(2023zdyf03)//Lishui Ecological and Environmental Monitoring Center of Zhejiang Province/ ; }, abstract = {Understanding how external nitrogen sources regulate nitrogen fate in river water is critical for improving nitrogen removal and reducing greenhouse-gas risk. Here, short-term microcosm incubations were conducted using source water as the background matrix and seven representative source inputs. By integrating hydrochemical analyses, bacterial community profiling, metagenomics, RT-qPCR, and process-rate measurements, we evaluated source-dependent shifts in nitrogen-cycling pathways. Manure-related inputs generated the highest organic and nitrogen loading, suppressed nitrification, enhanced nrfA (cytochrome c nitrite reductase) abundance and transcription, and promoted DNRA, indicating a shift toward nitrogen retention via ammonium regeneration. In contrast, sewage-related inputs maintained relatively high NO3[-] availability, elevated nirS (cytochrome cd1 nitrite reductase) and nosZ (nitrous oxide reductase) expression, and enhanced denitrification, but also increased N2O production. Metagenomic, transcriptional, and rate-based evidence consistently identified 12 h as a critical window for source-dependent pathway redistribution, highlighting the importance of short-term monitoring for detecting rapid nitrogen-cycle responses following pollution inputs. These findings support source-oriented nitrogen management that considers both nitrogen loading and hydrochemical controls on nitrate fate.}, } @article {pmid42187710, year = {2026}, author = {Singh, S and Tiwari, H and Singh, M and Gautam, V and Gautam, A and Gautam, HK}, title = {Expanding the Microbial Genomic Landscape and Biotechnological Applications of CRISPR-Cas Systems.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, pmid = {42187710}, issn = {2079-7737}, support = {(File No.: ANRF/IRG/2025/000135/LS)//Anusandhan National Research Foundation (ANRF)/ ; CST/D-1187//Council of Science and Technology, Uttar Pradesh, India (CST-UP)/ ; }, abstract = {The CRISPR-Cas systems, identified initially as adaptive immune mechanisms in bacteria and archaea against viral threats, have rapidly evolved into transformative tools in genetic engineering and biotechnology. These RNA-guided systems are broadly classified into Class 1, comprising multi-subunit complexes, and Class 2, characterized by compact single-effector protein, such as Cas9, Cas12, and Cas13. Their remarkable structural and functional diversity enables microorganisms to adapt to diverse ecological niches, offering a vast repertoire of genome-editing strategies. Beyond their natural role in maintaining genome integrity and defense, CRISPR-Cas systems have been extensively repurposed for precise genome modification, transcriptional regulation, epigenetic editing, and nucleic acid detection. Recent advances in computational mining of microbial genomes and metagenomes have uncovered a broad range of novel CRISPR effectors with unique properties, distinct protospacer adjacent motif (PAM) requirements, RNA-targeting capabilities, miniature architectures, and promiscuous cleavage activities that significantly expand the molecular biology toolkit. The development of CRISPR-based technologies such as base editing, prime editing, gene knock-in/out, and live-cell DNA/RNA imaging exemplifies the versatility of these systems. Despite the challenges associated with delivering complex Class 1 systems, both classes are now being actively harnessed across diverse microbial platforms. Concurrently, the CRISPR-Cas research, particularly for guide RNA (gRNA) design and activity prediction, has revolutionized target specificity and editing efficiency. This review presents a comprehensive overview of CRISPR-Cas system diversity, their genomic landscape in microorganisms, and their cutting-edge biotechnological applications. It also emphasizes the transformative potential of CRISPR in synthetic biology, therapeutics, diagnostics, environmental remediation, and agriculture, while also addressing the ethical and biosafety considerations surrounding its deployment. As CRISPR-Cas systems continue to evolve, they stand at the forefront of innovations that bridge natural microbial immunity with engineered precision tools for next-generation biotechnology.}, } @article {pmid42187714, year = {2026}, author = {Peng, D and Huang, T and Kang, W}, title = {Evolutionary Strategies for Heavy Metal Resistance: Genomic Plasticity in Pseudomonas Versus Stability in Aeromonas and Bacillus.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, pmid = {42187714}, issn = {2079-7737}, support = {2025QT02//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; 2024FY100200//Science & Technology Fundamental Resources Investigation Program/ ; }, abstract = {Heavy metal resistance represents a critical microbial trait shaped by lineage-specific evolutionary pressures, yet its genomic foundations and diversification across major bacterial taxa remain poorly resolved. This study presented a comparative pangenomic analysis of Aeromonas (n = 32), Bacillus (n = 123), and Pseudomonas (n = 350)-three phylogenetically and ecologically distinct genera frequently enriched in metal-contaminated environments and exhibiting notable differences in resistance architectures. All three genera exhibited open pangenomes, with fitted expansion indices of 0.003 (Aeromonas), 0.03 (Bacillus), and 0.04 (Pseudomonas), each showing strong model fit (R[2] > 0.98). Pseudomonas harbored a significantly greater number of resistance genes, with copper and zinc resistance genes exceeding 25 per strain in some cases. Most heavy metal resistance genes across the three genera were subject to purifying selection (dN/dS < 1), and no significant expansion or contraction of these gene families was observed (p > 0.05). The presence of these genera and their lineage-specific resistance determinants may serve as bioindicators of heavy metal exposure, offering valuable references for assessing contamination levels through environmental metagenomics.}, } @article {pmid42187862, year = {2026}, author = {Mills, N and Mills, N and Suwannarach, N and Noirungsee, N and Kumla, J and Inwongwan, S and Yongsawas, R and Saksunwiriya, C and Domethong, V and Shoocongdej, R and Disayathanoowat, T}, title = {Fungal Communities Associated with Wooden Coffins in a Prehistoric Burial Cave.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, pmid = {42187862}, issn = {2309-608X}, support = {2021//U.S. Ambassador's Fund for Cultural Preservation/ ; }, abstract = {Phi Man Long Long Rak Cave, located in Mae Hong Son Province, northern Thailand, is a prehistoric burial site containing ancient wooden coffins that have undergone biodeterioration, likely due to fungal activity. Both culture-dependent and culture-independent approaches were employed to characterize fungal communities and assess their roles in wood degradation. Culture-dependent analysis identified five Aspergillus isolates from the wooden coffins, most of which produced cellulolytic and hemicellulolytic enzymes; some isolates also produced organic acids, indicating significant degradative potential. Culture-independent analysis revealed a community dominated by Aspergillus, together with additional taxa such as Penicillium and Ceriporia that were not detected by cultivation, highlighting greater community diversity and demonstrating the complementarity of the two methods. Functional prediction indicated a predominance of saprotrophic fungi. The presence of shared dominant taxa between soil and coffin-associated substrates suggests ecological connectivity at the soil-coffin interface, although the direction of dispersal cannot be determined from the present data. All tested fungicides inhibited fungal growth, with the highest efficacy observed in the formulation containing the highest proportion of active components. Taken together, these findings provide insights into fungal biodeterioration processes and inform conservation strategies.}, } @article {pmid42188011, year = {2026}, author = {Li, X and Deng, W and Zhang, Z and Tong, H and Cao, Y}, title = {Revealing the Formation Mechanism of Key Metabolites During Japonica Rice Storage Driven by Microbial Functional Genes.}, journal = {Metabolites}, volume = {16}, number = {5}, pages = {}, pmid = {42188011}, issn = {2218-1989}, support = {2023010714-JH3/107//Liaoning Provincial Science and Technology Plan Project General Project/ ; 254358.//China Postdoctoral Science Foundation Project/ ; }, abstract = {BACKGROUND: To elucidate the evolution of metabolites and fungal communities during storage of fragrant japonica rice (Liaoxiangjing 1396), and to investigate the biosynthetic mechanisms of key compounds and their association with quality deterioration, this study examined rice samples stored under simulated conditions for 16 months.

METHOD: Samples were collected at 4-month intervals (designated R20, R14, R13, R12, and R11). Metabolites were identified using GC-MS non-targeted metabolomics, while fungal community structure was analyzed through metagenomics. Core mechanisms were further elucidated via PLS-DA, KEGG pathway enrichment, and multiomics association analysis.

RESULT: Results demonstrated that the fatty acid content of rice increased initially and then stabilized (from 12.24 mg/g in R20 to 17.63 mg/g in R12). A total of 263 metabolites were identified, with oxygenated organic compounds (38 species) and lipids/lepidid molecules (24 species) as the predominant categories. Twelve key differential metabolites were screened from the R20 and R12 groups, involving five major metabolic pathways, including amino acid metabolism and lipid metabolism. In the fungal community, Pseudomonas (60.2%) and Pantoea (38.19%) were dominant taxa, with a specific Pantoea species (Pantoea sp.) identified as a core potential biomarker. Multiomics association analysis revealed that Klebsiella dominated the ndhB energy metabolism pathway, while multiple bacteria cooperatively regulated the mcp chemotaxis pathway, interacting with monosaccharide and amino acid accumulation.

CONCLUSIONS: This study reveals that the storage quality deterioration of fragrant japonica rice is driven by the "metabolite-microbe-pathway" chain regulation, and the dynamic changes in key metabolites and fungal communities can serve as quality early warning targets.}, } @article {pmid42188051, year = {2026}, author = {Deng, H and Zhang, R}, title = {TCM-Derived Natural Compounds Targeting the Gut Microbiota in Metabolic Dysfunction-Associated Steatotic Liver Disease: Gut-Liver Axis Mechanisms, Safety Considerations, and Translational Challenges.}, journal = {Metabolites}, volume = {16}, number = {5}, pages = {}, pmid = {42188051}, issn = {2218-1989}, abstract = {The occurrence and development of metabolic dysfunction-associated steatotic liver disease (MASLD) are closely related to intestinal flora imbalance, intestinal barrier damage, and gut-liver axis dysfunction. Due to their multi-target regulatory effects and advantages in intestinal microecological intervention, Chinese herbal monomers have shown promising application prospects in the prevention and treatment of MASLD. However, basic research on their toxicity still lags behind, and issues related to safety and clinical translation urgently need attention. This article systematically reviews the research progress on how flavonoids, triterpenoids, alkaloids, and polysaccharides improve hepatic steatosis, inflammatory responses, and metabolic disorders from a toxicological perspective by reshaping the intestinal microbiota, repairing the intestinal mucosal barrier, regulating short-chain fatty acid and bile acid metabolism, and synergistically acting on signaling pathways such as TLR4/NF-kB, FXR, TGR5, SIRT1, and the NLRP3 inflammasome. Furthermore, by combining methods such as 16S rRNA sequencing, metagenomics, metabolomics, and multi-omics integration, the article analyzes their application value and limitations in toxicological mechanism research, and discusses the translational bottlenecks faced by Chinese herbal monomers in pharmacokinetics, bioavailability, quality standardization, targeted delivery, and toxicological safety. Existing evidence indicates that Chinese herbal monomers have a three-in-one intervention advantage of microecological remodeling-metabolic regulation-inflammation inhibition, but their long-term medication safety, toxic target organs, dose-effect/toxicity relationships, and potential drug interactions still need further clarification. This article aims to provide a systematic reference for the safety evaluation and clinical translational research of Chinese herbal monomers in the prevention and treatment of MASLD.}, } @article {pmid42188128, year = {2026}, author = {Sontigun, N and Thanawan, N and Fungwithaya, P}, title = {Epidemiology and Antimicrobial-Resistant Genes of Family Staphylococcaceae in Musca domestica: Case Studies from Chicken Farm, Pig Farms, and Residential Areas in Southern Thailand.}, journal = {Insects}, volume = {17}, number = {5}, pages = {}, pmid = {42188128}, issn = {2075-4450}, support = {KREF186729//King Mongkut's Institute of Technology Ladkrabang Research Fund/ ; }, abstract = {The major Staphylococcaceae family is recognized as opportunistic pathogens colonizing human and animal skin, mucous membranes, and environments. Musca domestica, the house fly, plays a role in the transmission of AMR bacteria. This study focused on examining the epidemiology and antimicrobial-resistant genes of the family Staphylococcaceae in M. domestica through metagenomic analysis, using samples collected from three animal farms and two residential areas in southern Thailand. Fifty M. domestica were collected from five places surrounding Walailak University, including one chicken farm (CF1), two pig farms (PF2 and PF3), and two residential areas (H1 and H2). All samples were dispatched for analysis using shotgun metagenomic sequencing and analyzed using FastQC, MultiQC, FASTQ, MEGAHIT, QUAST, ABRicate, AMRFinderPlus, ResFinder, ARG-ANNOT, MEGARES, PlasmidFinder, VFDB, Kraken2, Krona and Python. Our findings describe the taxonomic composition of Staphylococcaceae taxa in M. domestica from different environments; the representation of the family Staphylococcaceae in CF1, PF2, PF3, H1, and H2 was recorded at 2%, 0.7%, 0.2%, 0.2%, and 2% of this phylum, respectively. The average populations discovered were Staphylococcus (37.4%), Mammaliicoccus (17.4%), and Macrococcus (10.3%), respectively. Trimethoprim-resistant genes (dfrG and dfrE) were found only in CF1, PF2, and H1. Interestingly, fosfomycin-resistant genes were found only in M. domestica within residential areas. Our findings pertain to the Staphylococcaceae population in M. domestica within residential areas, which exhibited varying multidrug-resistance genes, particularly those resistant to fosfomycin.}, } @article {pmid42188162, year = {2026}, author = {Tao, M and Zhang, J and Fan, Y}, title = {Metagenomic Analysis of Gut Microbiome Across Developmental Stage of Asian Corn Borer (Ostrinia furnacalis).}, journal = {Insects}, volume = {17}, number = {5}, pages = {}, pmid = {42188162}, issn = {2075-4450}, support = {Grant No. 32402469//National Natural Science Foundation of China/ ; }, abstract = {Ostrinia furnacalis is one of the most important agricultural pests in Asia. Previous studies utilizing 16S rRNA sequencing have established a foundational understanding of the taxonomic composition of its gut microbiota; however, the dynamic functional transitions across the host's entire life cycle remain poorly understood. In this study, we used metagenomic sequencing to systematically characterize the gut microbiome across six groups representing different life stages and sexes of O. furnacalis: first-instar, third-instar, and fifth-instar larvae, pupae, and adults (both males and females). Microbial richness and evenness vary significantly across six groups representing different life stages and sexes. Species richness is highest in the first-instar larvae (L1D2), while evenness is relatively high in both first- and third-instar larvae (L1D2 and L3D2). Additionally, no sex-based differences were observed in either indicator during the adult stage. Enterococcus mundtii is the primary species driving community succession and rapidly achieves dominance after the third-instar stage. Co-occurrence network analysis revealed that the first-instar larval network exhibits the highest complexity, with positive correlations accounting for 96.6% of all edges. Conversely, the fifth-instar larvae exhibits the greatest proportion of negative correlation edges at 29.13%, while the pupal stage network is the most dispersive, indicating microbial reorganization during metamorphosis. Functional annotation reveals that carbohydrate and amino acid metabolism pathways are significantly enriched during the larval stage. In contrast, the pupal stage is characterized by enrichment in environmental information processing and a notable increase in polysaccharide lyases (PLs). This shift indicates that the microbiota transitioned from degrading plant polysaccharides to foraging host-derived glycans. The number of resistance genes in the first-instar larvae is significantly higher than that in all other groups representing different life stages and sexes. Collectively, this study systematically reveals the dynamic succession patterns of the gut microbiome throughout the life cycle of O. furnacalis and provides a theoretical foundation for the development of microbiome-based pest management strategies.}, } @article {pmid42188886, year = {2026}, author = {Yi, C and Nicolas, CS and Sun, Z and Wang, Q and Dong, T and Wu, Y}, title = {Effects of a Novel Prebiotic and Postbiotic Dietary Supplement on Gut Microbiota, Intestinal Barrier Markers, and Inflammation in Healthy Dogs.}, journal = {Veterinary sciences}, volume = {13}, number = {5}, pages = {}, pmid = {42188886}, issn = {2306-7381}, support = {202404810411350//Virbac China/ ; }, abstract = {Although prebiotics and postbiotics support gastrointestinal health, evidence for their combined effects in dogs remains limited. This study evaluated a novel prebiotic and postbiotic supplement in healthy dogs undergoing a dietary transition. Thirty-six healthy adult dogs were randomly assigned to control group (CON, high-protein basal diet with placebo chew) or treatment group (TRT, the same basal diet with chew containing prebiotics [baobab fruit pulp and acacia gum] and postbiotics [inactivated Lactobacillus acidophilus and selected yeast fractions]) for a 28-day formal trial following a 7-day adaptation period. The primary outcomes evaluated included clinical fecal scores, specific biomarkers of intestinal barrier function and inflammation, fecal short-chain fatty acids, and microbiota structure. Following the 7-day adaptation, formal trial baseline, fecal scores were already within the healthy range and remained optimal without differing between groups throughout the study. Compared with CON, the TRT group showed lower fecal calprotectin and serum diamine oxidase levels, and higher fecal butyrate (p < 0.05). Metagenomic analysis revealed increased abundances of Bacteroidota, Oscillospiraceae, Prevotellaceae, and Prevotella in TRT (p < 0.05). Overall, in healthy dogs, this supplementation was associated with favorable microbiota modulation and modulated biomarkers of intestinal barrier and inflammation within normal ranges, without altering clinical fecal endpoints.}, } @article {pmid42188905, year = {2026}, author = {Yao, Y and Yang, Z and Xie, T and Zhang, Y and Huang, F and Meng, C and Wu, Y}, title = {Multi-Omics Analyses of the Gut Microbiota and Metabolism in Cats with Different Body Conditions and the Effects of Fecal Microbiota Transplantation.}, journal = {Veterinary sciences}, volume = {13}, number = {5}, pages = {}, pmid = {42188905}, issn = {2306-7381}, abstract = {Obesity is increasingly recognized in domestic cats and is associated with metabolic disturbances such as insulin resistance and dyslipidemia. The gut microbiota is considered an important regulator of host metabolism, yet its role in feline obesity remains unclear. In this study, a multi-omics approach was used to investigate gut microbiota composition and metabolic profiles in cats with different body conditions and to evaluate the effects of fecal microbiota transplantation (FMT) on the feline gut microbiota and overall metabolism. In Experiment 1, twenty-four cats were classified as obese, normal, or lean, and their gut microbiota and serum metabolites were analyzed. In Experiment 2, fecal microbiota from obese or lean donors were transplanted into recipient cats. Although overall microbial diversity and community structure did not differ significantly among groups, Coriobacteriaceae and Collinsella were enriched in obese cats, whereas Enterobacteriaceae-related taxa were more abundant in normal-weight cats. Serum metabolomics revealed alterations mainly related to amino acid and antioxidant metabolism, including O-acetylcarnitine, glutathione, and tryptophan metabolism. FMT shifted the recipient gut microbial communities toward their respective donor profiles (obese or lean) but did not significantly affect body weight or routine serum biochemical parameters during the experimental period. These findings suggest that gut microbiota remodeling may influence metabolic processes prior to detectable phenotypic changes in cats.}, } @article {pmid42189102, year = {2026}, author = {Zheng, H and Xie, X and Zhang, L and Cai, Y and Zhang, Q and Yang, F and Liu, X and Basitere, M and Wei, C and Qiu, G}, title = {Intralineage Diversity and Global Biogeography of Ca. Phosphoribacter.}, journal = {Environmental science & technology}, volume = {60}, number = {22}, pages = {15964-15976}, doi = {10.1021/acs.est.5c18078}, pmid = {42189102}, issn = {1520-5851}, mesh = {*Metagenome ; *Phosphorus/metabolism ; Phylogeny ; *Actinobacteria/genetics/metabolism ; Sewage/microbiology ; }, abstract = {In wastewater treatment plants (WWTPs), the newly defined polyphosphate-accumulating organism (PAO) "Candidatus Phosphoribacter" demonstrated important contributions to phosphorus removal. However, their phylogenetic and metabolic diversity, as well as ecological distributions, remain largely uncharacterized. By sequencing 81 activated sludge samples from 34 provinces in China and integrating 747 WWTP metagenomes from six continents, we recovered 166 metagenome-assembled genomes (MAGs) of this genus, expanding the number of Ca. Phosphoribacter MAGs by 17 times and identifying 12 novel species. Biogeographical analysis demonstrated their distinct intercontinental distribution. The coexistence of cosmopolitan species and regionally dominant ones was observed globally as a result of metabolic differentiation. Ancestral gene family reconstruction indicated that this genus underwent a streamlining process dominated by gene loss. Vertically inherited ppk2 and horizontally acquired phoU jointly underpinned the genetic basis of a PhoU-dysregulation-driven polyphosphate phenotype. Comparative genomics revealed broad metabolic potential, including versatile carbon utilization, α-glucan metabolism, and three complementary denitrifying phenotypes. Metatranscriptomic analyses further supported glucose uptake and potential α-glucan cycling as a carbon storage polymer. Overall, this study establishes the most comprehensive genomic framework of Ca. Phosphoribacter, elucidates their functional metabolisms, ecological roles, and global distributions, providing new insights into Ca. Phosphoribacter-mediated enhanced biological phosphorus removal (EBPR) for improved engineering implementation and system sustainability.}, } @article {pmid42189287, year = {2026}, author = {Candeliere, F and Busi, E and Cerri, S and Sola, L and Lombardi, M and Greco, S and Pedroni, S and Amaretti, A and Raimondi, S and Chiavelli, C and Vitale, MG and Bertolini, F and Depenni, R and Franchini, G and Dominici, M and Rossi, M}, title = {Enterotype-specific microbial biomarkers of immune checkpoint inhibitor response revealed by large-scale integrated metagenomic analysis.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00262-026-04432-w}, pmid = {42189287}, issn = {1432-0851}, support = {PE00000019//NextGenerationEU/ ; }, abstract = {The gut microbiota appears to play a critical role in modulating antitumor immune responses and influencing the efficacy of cancer immunotherapy drugs such as immune checkpoint inhibitors. However, the identification of consistent microbial biomarkers of response remains a significant challenge. This lack of consensus is largely driven by multi-source heterogeneity, including geographic variations in lifestyle, and high inter-individual variability. We hypothesize that these inconsistencies arise because microbiome composition is not uniform but organized into distinct enterotypes. To address this, we performed an integrated metagenomic analysis of 569 fecal samples from oncological patients affected by different tumor types treated with immunotherapy. The samples were clustered into two main enterotypes, E1 and E2, each of them containing two subclusters. A total of 166 species (e.g., Collinsella spp., Blautia spp., Bacteroides spp.) were identified as enterotype-specific biomarkers. A preliminary independent concordance assessment of these biomarkers was conducted in 19 oncologic patients with exceptional response to immunotherapy, providing an initial confirmation of selected enterotype-associated signals. Furthermore, we evaluated the predictive potential of gut microbiota profiles for immunotherapy outcomes through machine learning techniques. The models showed encouraging, albeit moderate, performance in the heterogeneous full dataset, supporting the potential of microbiome-based stratification as an exploratory framework for patient classification, while indicating that further validation is needed before clinical application.}, } @article {pmid42189388, year = {2026}, author = {Chen, P and Ma, M and Li, Y and Chen, X and Xu, Z and Guo, J and Hu, X and Lv, L and Guo, J and Liu, G}, title = {Food processing-derived carbon dots disrupt male fertility via the gut-testis axis.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {42189388}, issn = {1869-1889}, abstract = {Carbon dots (CDs) are unintentionally formed during thermal processing of food and are emerging environmental pollutants that may pose health risks. We investigated the reproductive toxicity of food-derived CDs via the gut-testicular axis by exposing male mice to environmentally relevant doses (25 and 100 mg kg[-1] d[-1]) for 15 weeks. Multi-omics analysis (including metagenomics, transcriptomics, and metabolomics) revealed that CDs significantly altered the gut microbiota composition, reducing beneficial bacteria (Akkermansia muciniphila, P<0.01) while increasing pathogenic bacteria (Desulfovibrionaceae, P<0.001). Functional analysis revealed upregulation of the lipopolysaccharide (LPS) biosynthesis pathway (P<0.001) and reduced levels of barrier-protective tryptophan metabolites. Time-series studies established a mechanistic sequence: microbiota disruption (days 1-3), intestinal barrier dysfunction (days 3-5), blood-testis barrier damage (days 5-7), testicular inflammation, and reproductive dysfunction. Dose-dependent testicular toxicity included reduced testosterone synthesis (P<0.001), impaired spermatogonial stem cell maintenance due to downregulation of PLZF, and impaired fertility. Testicular transcriptomics analysis revealed activation of the IL-17 signaling pathway and inhibition of steroidogenesis. This study provides comprehensive evidence that CD induces male reproductive toxicity through microbiota-dependent mechanisms, emphasizing the environmental health implications of dietary nanoparticle exposure.}, } @article {pmid42189604, year = {2026}, author = {Lopes, F and Martinez-Martinez, D and Späth, MR and Hoyer-Allo, KJR and Strubl, S and Cukoski, S and Knieps, L and Brodesser, S and Göbel, H and Schwarz, G and van den Berg, BM and Rabelink, TJ and Schermer, B and Benzing, T and Müller, RU and Beyer, A and Cabreiro, F and Koehler, FC}, title = {The Interplay between Gut Microbiota and Diet-Induced Kidney Protection.}, journal = {Kidney360}, volume = {}, number = {}, pages = {}, doi = {10.34067/KID.0000001219}, pmid = {42189604}, issn = {2641-7650}, abstract = {BACKGROUND: On the one hand, dietary interventions are known for their pivotal role in regulating diversity, composition as well as function of the gut microbiome. On the other hand, specific diets show an immense potential in preventing kidney injury from various damaging stimuli in rodents and recent findings, in turn, highlight a central role of gut microbiota in kidney health and disease.

METHODS: Three protective dietary regimens - a fasting mimicking diet, a diet depleted in sulfur containing amino acids and caloric restriction - were examined in parallel in a rodent model of ischemia-reperfusion injury. To delineate the diet-induced effect on gut microbiota in response to ischemic kidney damage we used comparative shotgun metagenomics for taxonomic as well as functional profiling. We further examined the renal metabolic response using comparative transcriptomics to unravel the interplay between gut microbiota and kidney protection.

RESULTS: Beneficial dietary preconditioning strategies changed the composition of gut microbiota in an IRI-dependent manner. Using ternary plots to investigate the role of dietary interventions over time before and after ischemic insult, we detected a central role of Lachnospiraceae that commonly expanded in response to renal IRI in dietary-preconditioned mice. Further functional profiling of gut microbiota in our model revealed an increase in plasma levels of bacterial derived short chained fatty acids in diet-induced kidney protection. Comparative bulk transcriptomics in our model, in turn, pointed towards the metabolic use of these bacterial derived short-chained fatty acids in kidneys of protected mice.

CONCLUSIONS: As proximal tubules lack sufficient glycolytic capacity, products of microbial metabolism may serve as an additional energy source to fulfill their high demands when withstanding ischemic damage. Our data shed light on a close interplay between gut microbiota and diet-induced kidney protection calling for further research at the crossroads of microbiology, metabolism and molecular nephrology.}, } @article {pmid42190464, year = {2026}, author = {Yergalyiev, T and Roth, C and Rodehutscord, M and Seifert, J and Camarinha-Silva, A}, title = {Age, strain, and gut section shape the microbiome of commercial laying hens.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107152}, pmid = {42190464}, issn = {1525-3171}, abstract = {Gut microbiota, among other factors, may influence the overall performance of laying hens. To investigate how host genetics and age shape microbial communities, we profiled the gut microbiome of two commercial laying hen strains, Lohmann Brown-Classic and Lohmann LSL-Classic, across five anatomical sections (crop, gizzard, duodenum, ileum, caeca) at five ages spanning pullet development through late lay (10, 16, 24, 30, 60 weeks of age). We extracted RNA from the luminal content and performed 16S rRNA gene amplicon sequencing based on complementary DNA. Both strain and age had highly significant effects on community composition. The greatest shifts occurred between early development (10 weeks) and the onset of lay (16-24 weeks). To link taxa to function, we applied shotgun metagenomics to samples taken at 16 and 24 weeks, revealing strain-specific changes in functional profiles associated with the transition into egg production. We identified three groups of bacterial species that increased in abundance during the transition: lactic-acid producers (such as Lactococcus raffinolactis, Ligilactobacillus aviarius, Lactobacillus pontis, etc.), potential probiotic bacteria (Megasphaera stantonii, Megamonas funiformis, Phocaeicola coprophilus, etc.), and opportunistic or egg-associated pathogens (Comamonas testosteroni, Aeromonas caviae, Acinetobacter johnsonii, etc.). Corresponding shifts were also observed in the functional profiles of inositol phosphate metabolism. Moreover, MAG-based analyses reported two bacterial species - Gallibacterium anatis and Megamonas hypermegale, to contain high numbers of myoinositol-related genes. Together, our results demonstrate that genetic background and production phase both drive dynamic, section-specific changes in the gut microbiome of laying hens.}, } @article {pmid42190784, year = {2026}, author = {Qadeer, A and Nazir, MJ and Muhammad, S and Azim, R and Wang, Q and Hussain, MM}, title = {Decoding heavy metal tolerance in rice: Nucleic acid-based technologies shaping global food security.}, journal = {International journal of biological macromolecules}, volume = {370}, number = {}, pages = {152693}, doi = {10.1016/j.ijbiomac.2026.152693}, pmid = {42190784}, issn = {1879-0003}, abstract = {Global rice production is critically threatened by heavy metal contamination, particularly cadmium (Cd) and arsenic (As), which compromises yield, diminishes grain nutritional quality, and exposes billions of consumers to nephrotoxic and carcinogenic risks. Conventional remediation strategies (soil amendments, water management, phytoremediation) are prohibitively expensive, temporally protracted, and fundamentally reactive, while conventional breeding is constrained by linkage drag, polygenic trait architecture, and absence of natural alleles that restrict toxic metal uptake from essential mineral nutrition. This review critically examines how nucleic acid-based technologies have fundamentally reconfigured the discovery-to-deployment pipeline for heavy metal tolerance in rice. We trace the progression from early QTL mapping and positional cloning of transporters through population-scale GWAS and pan-genomics, which have resolved the full allelic series at these loci, to contemporary CRISPR-mediated genome editing, that generated transgene-free, field-validated low-accumulating lines. Transcriptomic, epigenomic, and metagenomic tools have further illuminated the dynamic stress response, non-coding regulatory networks, and rhizosphere microbiome contributions to metal exclusion. Translational case studies including Japan's marker-assisted deployment of OsHMA3 for Cd mitigation and South Asia's development of OsLsi2-edited low-As lines demonstrate that these technologies are not merely academic instruments but operational solutions. However, specificity-versus-essentiality dilemma, multi-metal antagonism (Cd/As redox conflict), and profound regulatory divergence (SDN-1 exemption in the Americas, Japan, and India versus GMO classification in the EU) remain formidable barriers. We conclude that nucleic acid technologies constitute the cornerstone of a second Green Revolution focused on grain quality and safety, contingent upon sustained investment in synthetic biology, digital integration, and internationally harmonized governance frameworks.}, } @article {pmid42190825, year = {2026}, author = {Li, Y and Qu, C and Sun, H and Li, C and Rehman, F and Guo, J}, title = {Distinct associations between polycyclic aromatic hydrocarbons with different molecular weights and antibiotic resistance gene distribution in river sediments of the Loess Plateau, China.}, journal = {Environmental research}, volume = {304}, number = {}, pages = {124845}, doi = {10.1016/j.envres.2026.124845}, pmid = {42190825}, issn = {1096-0953}, mesh = {China ; *Polycyclic Aromatic Hydrocarbons/analysis/chemistry ; *Geologic Sediments/chemistry/microbiology ; *Rivers/chemistry/microbiology ; *Water Pollutants, Chemical/analysis ; *Drug Resistance, Microbial/genetics ; Molecular Weight ; *Genes, Bacterial ; Bacteria/genetics/drug effects ; Environmental Monitoring ; Microbiota ; }, abstract = {Although polycyclic aromatic hydrocarbons (PAHs) are widely recognized to influence the distribution of antibiotic resistance genes (ARGs), the roles of PAHs with different molecular weights in shaping ARG patterns remain underexplored. It is hypothesized that different molecular weight PAHs can influence ARGs dissemination through shifts in microbial diversity. Here, the spatial distribution and concentrations of PAHs in Beiluo River sediments were evaluated, followed by an assessment of their relationships with ARG distribution and microbial community structure across 18 sampling sites. Metagenomic sequencing was used to characterize the distribution patterns of ARGs, mobile genetic elements (MGEs), and microbial communities. The partial least squares path model (PLS-PM) suggested that PAH molecular weight was differentially associated with microbial community structure and ARG distribution. Low- and medium-molecular-weight PAHs (PHE and ANT) were positively associated with the dominating phylum Pseudomonadota, which may act as potential ARG hosts and promote the transmission of dominant ARGs, especially bacitracin- and multidrug resistance genes. In contrast, the α-diversity indices of Acidobacteriota, which exhibited relatively low abundance, were negatively correlated with high-molecular-weight PAHs (BbF). The co-occurrence network analysis further suggested that this phylum may serve as a potential host for MLS- and tetracycline resistance genes. Overall, these results contribute to the understanding of interactions among persistent organic pollutants, microbiota, and ARGs in human-disturbed rivers and support the ecological risk evaluation and management of PAH-contaminated aquatic systems.}, } @article {pmid42190956, year = {2026}, author = {Xia, R and Cui, B and Li, G and Zhou, H and Luo, W and Xu, Z}, title = {Integrated metagenomics unravels the microbial mechanisms driving greenhouse gas and odor emissions during composting.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {134984}, doi = {10.1016/j.biortech.2026.134984}, pmid = {42190956}, issn = {1873-2976}, mesh = {*Metagenomics/methods ; *Greenhouse Gases/analysis/metabolism ; *Composting ; Methane ; *Odorants/analysis ; *Bacteria/metabolism/genetics ; Nitrous Oxide/analysis ; Hydrogen Sulfide ; Temperature ; }, abstract = {While composting is widely used for the resource recovery of organic waste, it is complicated by greenhouse gas and odor emissions. An integrated analysis of emission characteristics and elemental metabolism mechanisms is essential for targeted control strategies. Using integrated metagenomics and modular network analysis, this study identified the biotic and abiotic factors driving gaseous emissions. Results showed that methane (CH4) and nitrous oxide (N2O) emissions mainly occurred during the mesophilic and cooling stages, whereas ammonia (NH3) and hydrogen sulfide (H2S) peaked at the thermophilic stage. Initially, acidogens (e.g. Klebsiella) and methanogens (e.g. Methanobacterium) promoted CH4 production via aceticlastic (e.g. ackA gene) and hydrogenotrophic (e.g. frhB gene) pathways. Meanwhile, nitrate-reducing bacteria and denitrifiers converted nitrate nitrogen to N2O via assimilatory/dissimilatory reduction and denitrification pathways, respectively. As temperature increased into the thermophilic stage, CH4 and N2O production decreased due to the thermal inhibition of acidogens and nitrate-reducing bacteria. However, intense mineralization of organic nitrogen/sulfur compounds released ammonium and sulfate ions, leading to NH3 volatilization and microbial H2S production by sulfate-reducing bacteria (e.g. Desulfitibacter) via synergistic assimilatory/dissimilatory sulfate reduction pathways. Reduced thermal inhibition at the cooling stage restored activity of acidogens and methanogens, which drove CH4 emission via all four pathways. Denitrifiers (e.g. Pusillimonas) with nirS and norC genes and nitrifiers (e.g. Devosia) with hao genes were also enriched, increasing N2O production. Nevertheless, N2O was ultimately reduced to N2 by denitrifiers carrying nosZ at the mature stage. These findings provide fundamental insights for developing targeted strategies to mitigate gaseous emissions during composting.}, } @article {pmid42191017, year = {2026}, author = {Cavone, C and De Paola, D and Naclerio, G and Bucci, A and Barra Caracciolo, A and Rutigliano, A and Cotugno, P and Rolando, L and Savino, I and Grenni, P and Celico, F and Uricchio, VF and Ancona, V}, title = {Lavandula angustifolia and microbial bioaugmentation synergistically reshape rhizosphere microbiome and enhance heavy metals removal in historically contaminated soils.}, journal = {New biotechnology}, volume = {94}, number = {}, pages = {121-135}, doi = {10.1016/j.nbt.2026.05.013}, pmid = {42191017}, issn = {1876-4347}, abstract = {Heavy metal contamination poses a serious threat to soil ecosystems and requires sustainable remediation approaches capable of restoring both chemical quality and microbial functionality. This study evaluates the effectiveness of plant-assisted bioremediation (Lavandula angustifolia) and bioaugmentation with a selected bacterial consortium of four strains (Gordonia amicalis, Rhodococcus erythropolis, Acinetobacter puyangensis, and A. tibetensis) in soils that have been historically contaminated with multiple pollutants - such as heavy metals (HMs) and polychlorinated biphenyls (PCBs). Microcosms were created with four treatments, i.e. Historically Contaminated Soil (HCS), Plant-assisted bioremediation (PLANT), microbial bioaugmentation (BIOAUG) and the combination of plant-assisted bioremediation and bioaugmentation (PLANT+BIOAUG) and monitored over a 90-days period through chemical analyses, 16S rDNA sequencing, diversity metrics, differential abundance tests and functional prediction. The PLANT+BIOAUG combination demonstrated the highest removal efficiency of Pb (44.75%) and Sn (66.87%), suggesting a robust synergistic interaction between plant and microbial inoculum. Microbial α-diversity remained stable across treatments, while β-diversity analyses (Bray-Curtis, PERMANOVA p = 0.001) revealed significant community restructuring. Taxonomic analyses highlighted shifts in key genera and an enrichment of bacterial families associated with metal transformation, redox processes, and stress tolerance. The functional prediction identified 7959 KEGG functions, with the combined treatment showing the highest functional redundancy in metal efflux systems, siderophore production, electron transport pathways, and EPS/biofilm formation. Overall, integrating L. angustifolia with a metal-resistant microbial consortium could improve both contaminant removal and microbial functional potential, supporting a robust and sustainable strategy for the remediation of multi-contaminated soils. These results provide valuable insights into synergistic plant-microbe processes and offer practical guidelines for in situ bioremediation within the framework of the circular economy and nature-based models.}, } @article {pmid42192344, year = {2026}, author = {Liu, L and Su, P and Gong, F and Wang, A and Wang, X and Yang, L and Mo, W and Jiang, T}, title = {Diagnosis and management of mixed Chlamydia abortus and psittaci pneumonia guided by metagenomic next-generation sequencing: a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13691-y}, pmid = {42192344}, issn = {1471-2334}, support = {2023SK4077//the China Hunan Provincial Clinical Medical Technology Demonstration Base for Cardiac Arrest Diseases/ ; }, abstract = {BACKGROUND: Chlamydia abortus primarily causes abortion and stillbirth in animals and is associated with pregnancy-related complications in humans. However, it is an extremely rare cause of pneumonia in humans. While Chlamydia psittaci is a well-established respiratory pathogen, pneumonia resulting from a co-infection with both species has not been previously reported.

CASE PRESENTATION: A 57-year-old male presented with fever, cough, and shortness of breath. Imaging revealed extensive pulmonary inflammation and consolidation, which rapidly progressed to respiratory failure. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) confirmed a mixed infection with Chlamydia abortus and Chlamydia psittaci. Following the early initiation of targeted doxycycline therapy, the patient's clinical symptoms and pulmonary imaging showed significant improvement, leading to a full recovery and hospital discharge.

CONCLUSIONS: To our knowledge, this study reports the first case of atypical pneumonia caused by a mixed Chlamydia abortus and Chlamydia psittaci infection in a male patient, thereby expanding the clinical spectrum of these zoonotic pathogens. The case exhibited a "clinical-imaging dissociation," characterized by severe radiographic changes alongside relatively mild clinical symptoms. When conventional diagnostic methods failed to identify the pathogens, mNGS provided a rapid and precise diagnosis. Guided by this result, early targeted therapy with doxycycline achieved a marked therapeutic effect, preventing progression to severe disease and an adverse outcome.

TRIAL REGISTRATION: Not applicable.}, } @article {pmid42192666, year = {2026}, author = {Liu, L and Wang, M and Wang, X and Liu, Y and Li, Z}, title = {Root Exudates Are Linked to Antibiotic Resistance Gene Variation by Modulating Rhizosphere Microbial Community Assembly Under Swine Wastewater Irrigation.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42192666}, issn = {2079-6382}, support = {242300420230//Natural Science Foundation of Henan Province/ ; }, abstract = {Background: Irrigation with swine wastewater may increase the dissemination risk of antibiotic resistance genes (ARGs) in the rhizosphere and alter root exudate composition. However, the relationship between root exudates and ARG dynamics under swine wastewater irrigation remains poorly understood. This study therefore aimed to clarify how root exudates are connected with ARG dynamics under swine wastewater irrigation. Methods: To address this, untargeted metabolomics and metagenomic sequencing were combined to characterize rhizosphere ARG composition, microbial community structure, and root exudate profiles in different soybean cultivars under swine wastewater irrigation. Results: The results showed that irrigation water source and soybean cultivar were associated with variation in soil ARG composition and changes in plant root metabolic profiles. Under wastewater irrigation, the relative abundances of secondary metabolites in root exudates were generally elevated, particularly those of organic nitrogen compounds and organic oxygenated compounds. Cultivar-related variation remained evident in rhizosphere microbial communities and ARG profiles, and differences in exudate composition among cultivars became smaller. Irrigation water source and soybean cultivar were associated with changes in ARG dynamics. This association was mainly linked to variation in rhizosphere microbial community structure rather than direct effects of root exudates on ARGs. Xanthine and 3-isobutylpentanedioic acid, identified as key root exudates, increased under wastewater irrigation and were related to variation in the potential ARG host genus SCGC-AG-212-J23 and the related ARGs. In contrast, 5-methylheptan-3-one decreased under wastewater irrigation and was correlated with variation in SCGC-AG-212-J23, Gp6-AA40, and the related ARGs. Conclusions: Swine wastewater irrigation and soybean cultivar altered root metabolism, which were linked to variation in rhizosphere microbial communities. These changes may have collectively contributed to shifts in rhizosphere ARGs. This could provide a basis for understanding the ecological relationships among root exudates, microorganisms, and ARGs under swine wastewater irrigation.}, } @article {pmid42192676, year = {2026}, author = {Hassen, KA and Fafetine, J and Augusto, L and Mandomando, I and Garrine, M and Marcos, R and Sileshi, GW}, title = {Mobile Genetic Elements Associated with Antimicrobial Resistance Across One Health Interfaces in Africa: A Systematic Review and Meta-Analysis.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42192676}, issn = {2079-6382}, support = {500003545//Centre of Excellence in Agri-Food Systems and Nutrition (CE-AFSN), Eduardo Mondlane Univer-sity/ ; }, abstract = {Background: High infectious disease burden and uncontrolled antibiotic usage across human, animal, and environmental contaminants make antimicrobial resistance (AMR) a growing public health problem in Africa. Mobile genetic elements (MGEs) such plasmids, transposons, integrons, conjugative elements, and phages help spread AMR via horizontal gene transfer (HGT) across human, animal, food, and environmental sources. Despite growing evidence for antibiotic resistance genes (ARGs), Africa lacks a one-health-focused synthesis of mobile genetic element-mediated AMR. Objective: This systematic review and meta-analysis aimed to consolidate information on MGEs and ARGs in AMR dissemination throughout Africa's one health interface. Methods: The literature was searched using PubMed, Scopus, and ScienceDirect. Observational. molecular epidemiology, whole genome sequencing (WGS), and metagenomic investigations of MGE-associated AMR in Africa were eligible. The study selection, data extraction, and quality assessment were performed by two independent reviewer and quality was graded using ROBVIS 2 utilizing Rayyan software. Narrative synthesis, random-effect meta-analysis, subgroup analysis, and meta-regression were utilized. Results: A total of 109 studies were included, with 91 studies contributing to the meta-analysis. MGEs reported were plasmids (71.7%) and integrons (54.8%). ARGs carried by MGEs were blaCTMX-M-15 (78.6%), Sul2 (69.6%), blaTEM (59.1%), and tetA (49.9%). Horizontal gene transfer was seen in 259 instances; however, transmission was unclear. In 442 observations, transmission pathways across human, animal, and environmental interfaces showed AMR prevalence of 75.1% in human, 98.0% in human-animal, and 61.3% in one health interface. Whole-genome sequencing was the most frequently used method for detecting MGEsThe pooled pathogen and AMR prevalence rates were 73.3% (95% CI: 60.5-83.7%) and 94% (95% CI: 85-98%), with significant heterogeneity (I[2] = 97.8% and 97.4%, respectively). The prevalence of Escherichia coli was 93% and Salmonella enterica 85% in subgroup analysis. Fluoroquinolones, aminoglycosides, and beta-lactams were prevalent in humans (89.7%) and human-animal interactions (98.0%) according to AMR Class. Conclusions: Horizontal gene transfer has propagated MGE-mediated antimicrobial resistance across human, animal, and environmental interfaces in Africa. To combat AMR in Africa, coordinated, genomics-informed One Health surveillance and antibiotic stewardship are needed. Due to variability and publication bias, these data should be considered cautiously. Pooled data may only show descriptive patterns, and not necessarily precise continent-wide prevalence estimates.}, } @article {pmid42192677, year = {2026}, author = {Carneiro, PAM and Santos, LRD and Jardim, R and Silva, CBDGE and Araújo, FR and Dávila, AMR}, title = {Resistome and Mobilome Profiling of Raw Cow and Buffalo Milk from the Brazilian Amazon via Shotgun Metagenomics.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42192677}, issn = {2079-6382}, support = {408696/2024-9//Beef Cattle National Science and Technology Institute/CNPq/ ; }, abstract = {Background/Objectives: Antimicrobial resistance (AMR) is a global health threat, with raw milk serving as a potential reservoir for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). This study characterized the resistome and mobilome of raw milk from cows (Bos taurus) and water buffalo (Bubalus bubalis) in the Brazilian Amazon, a region where unpasteurized dairy consumption is culturally ingrained. Methods: Using shotgun metagenomic sequencing, we analyzed 32 pooled milk samples from extensive and semi-intensive farms in the Manaus Metropolitan Region. Results: Sequencing yielded over 3.1 million contigs. While cow milk showed a higher prevalence of positive samples (80%), buffalo milk exhibited a significantly higher abundance and diversity of ARG-associated contigs (301 contigs vs. 85 in cows). Clinically relevant genes were identified, including AbaQ, ArnT, and KpnF, alongside complex multi-AMR cassettes co-occurring with plasmids and widespread viral sequences (dominated by Caudoviricetes). Integrons were ubiquitous in cattle and highly prevalent in buffalo samples. Conclusions: These findings indicate that raw milk in the Amazon harbors a rich reservoir of resistance determinants and MGEs, likely driven by farm-level antibiotic usage. This underscores a critical food safety risk and highlights the need for One Health-based surveillance in the region.}, } @article {pmid42192724, year = {2026}, author = {Skotareva, AE and Sokolova, EA and Voronina, EN}, title = {West Siberian Soil Resistome: Mobile Antibiotic Resistance in Agricultural Microbiomes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42192724}, issn = {2079-6382}, support = {125012300671-8//Russian state-funded project/ ; }, abstract = {Background/Objectives: Soil microbiomes in agroecosystems are natural reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), creating conditions for horizontal gene transfer (HGT) to clinically relevant bacteria. Southern West Siberia-a globally significant grain-producing region-lacks metagenomic characterization of its soil resistome. This study aimed to establish the first baseline profile of resistome and mobilome composition for West Siberian agricultural soils. Methods: Twelve composite soil samples were collected from agroecosystems under seven crop types across diverse soil types in southern West Siberia (September 2022). Shotgun metagenomics was performed on an Illumina NovaSeq 6000 platform. Taxonomic profiling used Kraken2/Bracken; ARG annotation used Prokka/DeepARG (identity ≥ 70%, probability score ≥ 0.8); while MGE characterization used Platon, HMMER v3.3.2, and Prokka-based integrase annotation. Resistome load was normalized to the single-copy housekeeping gene rpoB; ARG-MGE associations were defined as co-localization within 10 kb on the same contig. Results: Microbial communities were dominated by Pseudomonadota and Bacillota, with a stable core of Streptomycetaceae, Nitrobacteraceae, and Sphingomonadaceae. Normalized resistome load (N/rpoB 2.30-5.37) indicated moderate anthropogenic pressure. Dominant ARGs included efflux pumps (emrA, drrA, tetA, bcr, fsr), target modification (lnrL), and lipid A modification (arnA) genes. Class 1 integron integrase (intI1/rpoB 0.64-1.59) was detected in all 12 samples, exceeding unity in 9 of 12. ARG-MGE co-localizations were found in 11 of 12 samples. In sample Mg_155, genes emrA-emrB and bcr (NODE_16) and arnA and lnrL (NODE_6) were each independently associated with distinct prophage IntA integrase copies within Pseudomonas contigs, documenting multiple parallel horizontal transfer events encompassing resistance to five antibiotic classes. Conclusions: This work establishes the first metagenomic baseline of resistome and mobilome for West Siberian agroecosystems. The obtained data indicate moderate anthropogenic pressure on soil microbiomes, consistent with temperate agricultural systems with limited organic fertilizer input. The detected ARG-MGE co-localizations and evidence of prophage-mediated transfer of resistance determinants beyond their natural hosts suggest that mobilization potential in the region warrants consideration in future AMR monitoring programs.}, } @article {pmid42193165, year = {2026}, author = {Liang, Y and Wang, H and Wang, Z and Zhang, Y and Tu, W and Zhou, J and Diao, Y and Pei, H and Huang, J and Zhou, X and Tan, Y}, title = {High-Fiber Diet Supplemented with N-Carbamylglutamate Modulates Uterine Microbiota, Metabolites, and Transcriptome to Improve Reproductive Efficiency in Sows.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42193165}, issn = {2076-3921}, support = {No.2023ZD04046//Biological Breeding-National Science and Technology Major Project/ ; 2025M780240//China Postdoctoral Science Foundation/ ; NO.2025(05)//Livestock and Poultry Breeding and Healthy Farming Technology/ ; }, abstract = {Uterine microbiome homeostasis and antioxidant capacity are critical for sow fertility. While high-fiber diets and N-carbamylglutamate (NCG) individually enhance sow fertility, their synergistic effects on the antioxidant status, microbiota, metabolites, and transcriptome remain unclear. Here, sows were assigned to the low-fiber (3.73%) or high-fiber (7.46% crude fiber) group, each without or with 0.05% NCG, throughout the 114-day gestation. Sex hormones and antioxidants in serum were detected. Multi-omics approaches were employed to investigate the impact of a high-fiber diet supplemented with NCG (H + N) on uterine microbiota, metabolites, and gene expression profiles. The study revealed that H + N significantly increased total antioxidant capacity (T-AOC) level in serum. Metagenomic analysis revealed an increased abundance of Clostridium disporicum in the uterine microbiota. Plasma metabolomics identified hydroxylysine as a key metabolite mediating this effect, and this metabolite was positively correlated with elevated abundance of Clostridium disporicum. Subsequent transcriptomic profiling revealed activation of the PI3K-Akt signaling pathway, closely linked to improved T-AOC level. Overall, these findings demonstrated that H + N could modulate the uterine microbiota (specifically Clostridium disporicum), increase hydroxylysine production, and activate the PI3K-Akt signaling pathway. These effects further enhanced hormonal activity and antioxidant capacity, ultimately improving sow reproductive efficiency.}, } @article {pmid42193259, year = {2026}, author = {Zhang, MY and Ke, ZZ and Deng, PL and Qin, YY and Mo, SL and Qiu, LT and Xu, JJ and Tong, CX and Song, JL}, title = {Rhamnocitrin Ameliorates the Intestinal Fibrosis in DSS-Induced Colitis Mice by Modulating Host-Metabolites and Remodeling the Gut Microbiome.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42193259}, issn = {2076-3921}, support = {82273630//National Natural Science Foundation of China/ ; 81960590//National Natural Science Foundation of China/ ; 81760589//National Natural Science Foundation of China/ ; 81560530//National Natural Science Foundation of China/ ; }, abstract = {Ulcerative colitis (UC) is characterized by barrier disruption, microbiota dysbiosis, fibrosis, and impaired autophagy. We investigated the effects of Rhamnocitrin (Rha) in dextran sulfate sodium (DSS)-induced chronic UC mice using histological analysis, molecular assays, and multiomics profiling. Rha alleviated weight loss and colon shortening; improved mucus secretion and tight junction protein expression; suppressed NLRP3 inflammasome activation; activated autophagy via AMPK activation and consequent Akt/mTOR inhibition; and attenuated colonic fibrosis. Multiomics analysis integrating 16S rRNA sequencing, metagenomics, and metabolomics revealed that Rha remodels the gut microbiota and is associated with elevated levels of beneficial metabolites, including butyrate in the colon, glutamate and γ-aminobutyric acid in the liver, and α-linolenic acid in the serum. Correlation analysis revealed close associations between microbiota and metabolite alterations, and improved barrier integrity, reduced inflammation, and attenuated fibrosis. These findings suggest that Rha ameliorates chronic UC by modulating autophagy, microbiota composition, and host metabolism across the gut-liver axis.}, } @article {pmid42193752, year = {2026}, author = {Guo, T and Wan, B and Ye, Y and Zhang, Y and Mao, M and Li, R and Fang, Y and Lu, Y and Shao, R and Wu, Y and Wang, Y and Wu, J and Yang, H}, title = {A Prevotella-Rich Gut Microbiota and Microbial CAZymes Are Associated with Half-Diving Length in Ducks.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {10}, pages = {}, pmid = {42193752}, issn = {2076-2615}, support = {2024YFF1000900//National Key Research and Development Program of China/ ; 32302739//National Natural Science Foundation of China/ ; 32360830//National Natural Science Foundation of China/ ; 20243BCE51147//Ganpo Juncai Support Program/ ; QN2023015//Ganpo Juncai Support Program/ ; 20232ACB215003//Natural Science Foundation of Jiangxi Province/ ; }, abstract = {The gut microbiota is closely associated with host growth by nutritional metabolism and immune homeostasis. Half-diving length, a key indicator of duck development and production efficiency, correlates with economic traits like body weight and slaughter yield, yet its link to gut microbiota remains unclear. This study combined metagenomic and metabolomic analyses to explore the association between gut microbiota and duck half-diving length. We found distinct microbial communities between ducks with high (H) and low (L) half-diving lengths: the H group had more carbohydrate-active enzymes (CAZymes) genes (p < 0.05), especially glycoside hydrolases (GHs), and was enriched in MAG3173 (Prevotella sp000431975), which features complete carbohydrate and amino acid metabolic pathways and key CAZymes. Metabolomics revealed slightly higher short-chain fatty acids (SCFAs) levels in the H group, but glycerophospholipids, particularly phosphatidylinositol (PI), were significantly upregulated (p < 0.05). The Prevotella-rich microbial structure in the H group is potentially linked to enhanced polysaccharide degradation capacity and altered SCFAs abundance. This metabolic shift may be associated with host energy supply and lipid metabolic profiles, thereby influencing duck growth. Collectively, this study found significant correlations between duck half-diving length and gut microbial composition, functional capacity, and intestinal metabolic signatures. The study proposes the hypothesis of a potential Prevotella-CAZymes-glycerophospholipid metabolism axis, which might offer a theoretical reference and candidate microbial targets for understanding the microbe-phenotype association in waterfowl.}, } @article {pmid42193766, year = {2026}, author = {Qiu, G and Bai, H and Shi, J and Xue, Y and Wang, T and Qin, S and Zhou, X and He, K}, title = {Metagenomic and Metabolomic Analysis of Intestinal Excrement Differences Between Natural Hatching and Artificial Peeling out of the Shell in Nipponia nippon.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {10}, pages = {}, pmid = {42193766}, issn = {2076-2615}, support = {ZJXRDQ-2025-JC28//the Project for Enhancing the Reproductive Capacity of the Red-crowned Crane/ ; }, abstract = {The Nipponia nippon is a critically endangered species, and its breeding efforts are of vital importance for its conservation. Although artificial shell removal is sometimes employed in current breeding programs to increase survival rates, it may also have unknown impacts on chicks' development. To investigate the influence of artificial shell removal on the gut microbiota composition in Nipponia nippon, metagenomic sequencing and untargeted LC-MS/MS analyses were performed. Samples from the early, mid, and late stages of natural hatching (ZE, ZM, ZL) and artificial shell removal (RE, RM, RL) were compared. Results indicated that the natural hatching groups formed a unique, highly diverse, and stable community by the late stage (ZL). Conversely, artificial peeling caused the microbial community succession to stagnate at an intermediate state. The RL group experienced a sharp decline in alpha diversity and a significant enrichment of opportunistic pathogens, such as Edwardsiella, Clostridium, and Fusobacterium. Functionally, the microbial community in the RL group remained in a stage of expanding basic functions rather than reaching an advanced equilibrium state. Metabolomic analysis confirmed this developmental arrest, revealing abnormal accumulations of organic acids, such as citric acid, and indole derivatives in the RL group. This indicates metabolic dysregulation, stress, and altered microbial-host chemical signaling. Furthermore, the significant biomarker Edwardsiella was strongly correlated with multiple differential metabolites in the RL group. Ultimately, these results indicate that artificial peeling intervention disrupts environmental adaptation and induces metabolic alterations in the intestinal development of the Nipponia nippon chicks.}, } @article {pmid42193830, year = {2026}, author = {Zhou, K and Shi, H and Kong, X and Ma, W and Kang, J and Che, H and Hua, Y}, title = {Wuwei Jianpi San Improves Growth Performance and Immune Status in Yaks Through Modulation of Rumen Microbiota and Host Metabolism.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {10}, pages = {}, pmid = {42193830}, issn = {2076-2615}, support = {CARS-37, CARS-07G-13//China Agriculture Research System of MOF and MARA/ ; No. Gaufx-03J01//Fuxi Foundation of Gansu Agricultural University/ ; 24YFNA016//Gansu Provincial Key Research and Development Program - Agriculture Field/ ; KJZC-2025-14//Modern Cold and Drought Characteristic Agricultural Science and Technology Sup-port Project of Gansu Province/ ; }, abstract = {To investigate the effects of Wuwei Jianpi San (WJPS), a Chinese herbal compound feed additive, on rumen microecology, host metabolism, and immune function in healthy yaks (Bos grunniens), and to determine the optimal supplementation level, 32 yaks with similar initial body weight were randomly assigned to four groups: a control group and three groups receiving 0.5%, 1.0%, or 2.0% WJPS for 90 days. Growth performance, hematological indices, serum antioxidant and immune parameters, tryptophan metabolites, ruminal short-chain fatty acids (SCFAs), and rumen microbiota were analyzed. WJPS supplementation improved growth performance, as shown by a reduced feed-to-gain ratio in all treated groups and tended to increase average daily gain in the 2.0% group. It also enhanced hematological, antioxidant, and immune status, evidenced by increased white blood cell (WBC) and lymphocyte (Lym) counts and elevated interleukin-2 (IL-2), immunoglobulin G (IgG), and superoxide dismutase (SOD) levels. Moreover, 2.0% WJPS increased total SCFAs, acetate, and n-butyrate, while WJPS reduced kynurenine pathway metabolites, including kynurenine, 3-hydroxykynurenine, and quinolinic acid. Metagenomic analysis showed that WJPS tended to shape rumen microbial composition by increasing Bacillota and decreasing Bacteroidota, and these microbial changes were associated with host immune indices and tryptophan metabolism. Overall, 2.0% WJPS showed the best comprehensive effect.}, } @article {pmid42195821, year = {2026}, author = {Wang, X and Liu, X and Han, G and Erdene, K and Bai, C and Cao, Q and Zheng, Y and Hai, L and Ao, C}, title = {Allium mongolicum Regel-Mediated Rumen Microbiota Intervention Modulates Hepatic Metabolome to Reduce 4-Alkyl Branched-Chain Fatty Acids in Lamb Longissimus Thoracis Muscle.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, pmid = {42195821}, issn = {2304-8158}, support = {32260839//National Natural Science Foundation of China/ ; }, abstract = {Deposition of three key 4-alkyl branched-chain fatty acids (KBCFA), including 4-methyloctanoic acid (MOA), 4-ethyloctanoic acid (EOA), and 4-methylnonanoic acid (MNA), causes the gamey flavor in sheep meat. This study integrated metagenomics and metabolomics to evaluate how Allium mongolicum Regel (AMR) supplementation (15 g/d) and rumen fluid transplantation (RFT) modulate rumen microbiota and hepatic metabolism to reduce KBCFA in lamb longissimus thoracis muscle. The experiment consisted of two phases. In Phase I, twelve 3-month-old male Dorper × Small Tailed Han sheep (25 ± 1 kg) were selected as the rumen donor group. These sheep were supplemented with 15 g/d/head of AMR powder in their basal diet until the end of the experiment. In Phase II, thirty 3-month-old male Dorper × Small Tailed Han sheep (23 ± 2 kg) were randomly assigned to one of three groups (n = 10 per group): the control group (STG), which was fed the basal diet and received a physiological saline transplant; the AMR group, which was fed the basal diet supplemented with 15 g/d/head of AMR powder and received a physiological saline transplant; and the rumen fluid transplant group (RTG), which was fed the basal diet and received a rumen fluid transplant from the donor group. Compared to the STG, results showed that the MOA, EOA, and MNA in the AMG decreased by 64.51%, 54.72%, and 49.34%, respectively. Similarly, the MOA, EOA, and MNA in the RTG were reduced by 63.13%, 56.17%, and 49.60%, respectively (p < 0.001). For the rumen metagenome, AMR enriched the genus Prevotella, while RFT increased Butyrivibrio. Hepatic metabolomics revealed a distinct shift where AMR elevated amino acid derivatives and RFT enhanced carnitine-related metabolites. These alterations indicate a potential metabolic shift associated with amino acid metabolism and mitochondrial β-oxidation, rather than lipid elongation. We postulate that this coordinated regulation across the rumen-liver-muscle axis may alter the availability of lipogenic precursors for KBCFA synthesis, ultimately contributing to improved meat flavor.}, } @article {pmid42195847, year = {2026}, author = {Song, D and Yang, L and Zhang, C}, title = {Omics-Guided Construction of Microbial Consortia for Reproducible Traditional Fermented Foods and Beverages.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, pmid = {42195847}, issn = {2304-8158}, support = {32460269//National Natural Science Foundation of China/ ; MTXYTD202501//The Science and Technology Innovation Team of Moutai Institute/ ; Qiankehe Platform Talent-ZDSYS [2023] 007//Guizhou Key Laboratory of Microbial Resources Exploration in Fermentation industry/ ; XYNJ20240104//Moutai Institute & Guangdong Li'er'an Chemical Industry Group Co., Ltd./ ; }, abstract = {Traditional fermented foods and beverages (TFFB) rely on complex microbial communities that generate distinctive flavors, nutritional attributes, and cultural value, but spontaneous or empirically controlled fermentations often limit reproducibility. Defined microbial consortia (DMCs) provide a promising route for improving fermentation controllability and product consistency, although overly simplified starters may fail to reproduce the ecological robustness and sensory complexity of traditional systems. This review focuses on how multi-omics and culturomics can support rational DMC design in TFFB. We summarize how metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics reveal community structure, functional potential, active expression, metabolic output, and cultivable strain resources. Particular attention is given to translating multi-omics evidence into strain prioritization through the identification of keystone microorganisms that drive core fermentation functions and helper microorganisms that support ecological or metabolic stability. We further propose an Assembly-Assessment-Redesign (A-A-R) framework for iterative DMC optimization, linking strain selection, functional validation, performance evaluation, and consortium redesign. Finally, we discuss key challenges, including cross-omics integration, experimental verification of microbial functions, standardized validation criteria, and the transfer of laboratory-designed consortia to industrial fermentation systems.}, } @article {pmid42195939, year = {2026}, author = {Chen, P and Du, G and Chen, J and Fang, F}, title = {Construction of Synthetic Microbial Community with Core Microorganisms for Soy Sauce Fermentation.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, pmid = {42195939}, issn = {2304-8158}, support = {32172182//National Natural Science Foundation of China/ ; }, abstract = {Core microbes and succession of the microbial community greatly influence soy sauce fermentation process. This study identified seven functionally important core microbes, including Weissella paramesenteroides, Lactiplantibacillus plantarum, Tetragenococcus halophilus, Pediococcus pentosaceus, Zygosaccharomyces rouxii, Candida orthopsilosis, and Aspergillus oryzae for soy sauce fermentation, based on dominant taxa, co-occurrence relationships, and volatile-associated taxa analysis. Four distinct fermentation phases were identified for soy sauce fermentation based on metagenomics and metabolomics data correlation analyses. Acceptable fermentation performance and comparable soy sauce flavor compounds were achieved using a temporal synthetic microbial community for fermentation. The synthetic microbial community was assembled with inoculation of dominant lactic acid bacteria (LAB) in the immediate early phase, other LAB in early and middle phases, and yeasts in the late phase. Glutamate and 4-ethylguaiacol were identified as soy sauce fermentation indicators for early to middle and late fermentation phases, respectively. These results may provide a possible solution for achieving precise control over the brewing process and improving the flavor and quality of soy sauce.}, } @article {pmid42196007, year = {2026}, author = {Duo, Q and Zhao, Y and Osman, H and Shao, W and Zhao, Y}, title = {Correlation Between Microbial Communities and Volatile Organic Compounds in Camel Milk at Different Lactation Stages in Xinjiang, China.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, pmid = {42196007}, issn = {2304-8158}, support = {2023B02034-1//Xinjiang Academy of Agricultural Sciences/ ; XJARS-11-09//Xinjiang Academy of Agricultural Sciences/ ; xjnkywdzc-2026002-10//Xinjiang Academy of Agricultural Sciences/ ; }, abstract = {The aroma of camel milk is a key sensory indicator for evaluating its quality and flavor. Camel milk collected at different lactation stages exhibits unique flavor characteristics. However, no systematic study has yet explored the aroma characteristics and variation patterns of camel milk across these stages. This study employs HS-SPME-GC-MS, multivariate statistical analysis, and metagenomics to systematically reveal differences in aroma formation in camel milk across lactation periods and their interactions with microbial communities. A total of 577 metabolites is detected. Through OPLS-DA screening, 24 key differential flavor compounds are identified. ROAV analysis indicates that 2,4-undecadienal and (E)-2-undecenal are the main contributors to the fatty, creamy, fresh green, and citrus aromas of camel milk. Some compounds are more abundant in colostrum, while others are richer in mature milk. For microbiota, colostrum is dominated by Proteobacteria, Psychrobacter, and Janthinobacterium, whereas mature milk is dominated by Acinetobacter and Moraxella. Mature milk shows significantly higher alpha diversity and species richness. Spearman correlation analysis shows that core bacterial groups such as Enterococcus and Lactococcus are significantly positively correlated with characteristic flavor compounds, including aldehydes and lactones. This finding suggests that HS-SPME-GC-MS, combined with multivariate analysis, effectively distinguishes patterns associated with microbes and flavor metabolites in camel milk at different lactation stages, which provides a theoretical basis for quality control and further processing of camel milk.}, } @article {pmid42196140, year = {2026}, author = {Dobretsov, S and Rittschof, D and Peng, L and Yang, JL}, title = {Functional Microbiomes at the Interface: Mediators in Marine Biofouling and Larval Settlement.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196140}, issn = {1422-0067}, support = {CL/SQU-SHOU/AGR/24/01//Sultan Qaboos University/ ; }, mesh = {Animals ; *Biofouling ; *Microbiota ; Larva/microbiology ; Biofilms/growth & development ; Quorum Sensing ; Ecosystem ; *Aquatic Organisms/microbiology ; }, abstract = {Natural and artificial marine surfaces are rapidly colonized by microscopic communities, including propagules of some macrofoulers, in a process called biofouling. These microbiomes play an important role in modulating the evolving microbial community, as well as the attachment and settlement of other invertebrate larvae. Microbiomes act as biochemical and biophysical interfaces in marine communities. This review explores the gene-level processes that underlie microbial functions relevant to biofouling and larval settlement, such as quorum sensing, extracellular polymeric substance (EPS), and innate immune system components, as well as biosynthetic and degradative processes that generate signaling molecules. We critically evaluate current knowledge on how microbial metabolites promote or inhibit larval recruitment in corals, barnacles, polychaetes, and bivalves, and how omics-based approaches are uncovering the functional potential of biofilm communities. We evaluate how these interactions influence ecosystem services, such as habitat structuring, reef resilience, and coastal infrastructure maintenance.}, } @article {pmid42196196, year = {2026}, author = {Wang, Y and Liu, X and Gao, R and An, Y and Ren, C and An, L}, title = {Characteristics of Gut Microbiota in Patients with Chronic Obstructive Pulmonary Disease Based on Metagenomics and Metabolomics.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196196}, issn = {1422-0067}, support = {CYFH202318//Beijing Chao-Yang Hospital/ ; 20250484825//Beijing Municipal Science and Technology Commission/ ; CFH2026-2-1043//Beijing Municipal Health Commission/ ; 2025ZD0548900//National Health Commission of the People's Republic of China/ ; }, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism ; *Metagenomics/methods ; *Metabolomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Aged ; Middle Aged ; Feces/microbiology ; Multiomics ; Metabolome ; Biomarkers ; RNA, Ribosomal, 16S/genetics ; China ; Case-Control Studies ; }, abstract = {The gut-lung axis is important in Chronic Obstructive Pulmonary Disease (COPD) pathogenesis; however, most studies rely on low-resolution 16S rRNA sequencing, and integrated multi-omics investigations in Chinese COPD populations are scarce. A total of 104 participants including 74 stable COPD patients and 30 healthy controls from northern China were recruited, and shotgun metagenomic sequencing and untargeted metabolomics were performed. Results showed that alpha diversity of the gut microbiota did not differ significantly between COPD patients and healthy controls, whereas beta diversity showed clear separation. Marked differences in microbial composition from phylum to species levels (e.g., Oscillospiraceae) and altered microbial functions (signal transduction, antibiotic resistance, etc.) were observed in COPD patients. Metabolomic profiling identified 497 differential fecal metabolites and 1260 differential serum metabolites in COPD patients. Importantly, serum riboflavin levels were significantly reduced and positively correlated with pulmonary function indices as well as the key differential gut microbial functional gene K11752. Serum metabolite eremopetasinorol exhibited high diagnostic accuracy for COPD (AUC = 0.947, 95% CI: 0.8-0.98), surpassing fecal metabolites and microbial features. This study provides integrated metagenomic and metabolomic characterization of gut microbiota alterations in Chinese COPD patients, offering novel insights for biomarker discovery and targeted intervention strategies.}, } @article {pmid42196214, year = {2026}, author = {Kiouri, DP and Batsis, GC and Messaritakis, I and Souglakos, J and Chasapis, CT}, title = {Mapping of Phenotype Specific Host-Microbiome Protein-Protein Interaction Networks in Colorectal Cancer Using Deep Learning.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196214}, issn = {1422-0067}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/genetics ; *Protein Interaction Maps ; *Deep Learning ; Phenotype ; *Gastrointestinal Microbiome ; *Protein Interaction Mapping/methods ; *Host Microbial Interactions ; }, abstract = {Colorectal cancer (CRC) pathogenesis is driven by complex protein-protein interactions (PPIs) between the host and the gut microbiome, yet these molecular dialogs remain largely unmapped. This study utilizes a Deep Learning framework, enhanced by protein structure embeddings, to predict approximately 8.9 billion interspecies PPIs from clinical metagenomic data. The model achieved high accuracy with an AUROC of 0.9960, identifying a high-confidence interactome representing roughly 16% of evaluated protein pairs. Phenotype-specific analysis revealed that while microbial hubs shift-transitioning from metabolic enzymes in healthy states to transport and regulatory proteins in CRC-the primary human targets remain remarkably consistent across both cohorts. These core human interactors are predominantly metalloproteins and regulators of ubiquitination, apoptosis, and zinc transport, suggesting these pathways are primary focal points for microbial manipulation regardless of disease state. Furthermore, co-occurring bacterial genera exhibit over 99% overlap in host target profiles, indicating significant functional redundancy in microbial engagement with the host. These findings suggest that CRC probably arises from network-level perturbations of stable host signaling hubs, offering a blueprint for identifying novel therapeutic targets and biomarkers.}, } @article {pmid42196222, year = {2026}, author = {Zhang, X and Cai, L and Bai, Y and Peng, F}, title = {Comparative Metagenomic Studies Reveal Different Evolutionary Directions of Synthetic Indoor Microbial Communities Under Different Nutritional Conditions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196222}, issn = {1422-0067}, support = {2022YFC2807501//Ministry of Science and Technology of the People's Republic of China/ ; NYWSWZX2025-2027-11//Major Special Project on Agricultural Microbial Industry Development in Hubei Province/ ; NIMR-2025-8//the R&D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People's Republic of China/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; Nutrients ; }, abstract = {The relationship between microorganisms and human health is inseparable. In today's increasingly urbanized world, the relationship between indoor microbial communities and human health is particularly close. Studies have shown that the composition of indoor microbial communities is influenced by various factors, including temperature, humidity, and nutrient conditions. However, research on how to alter indoor microbial community structures by adjusting nutrient components to improve human health is still limited. In this work, we constructed artificial microbial communities composed of common indoor microorganisms, and analyzed the species composition, metabolic capabilities, antibiotic resistance, and virulence of the microbial communities before and after cultivation using metagenomic sequencing technologies and metatranscriptomic sequencing technologies. We then assessed their community characteristics and evolutionary direction under different nutrient conditions. Overall, when the nutrient conditions were altered and reduced, the evolutionary direction of indoor microbial communities changed significantly. Specifically, this evolutionary direction was manifested in a taxonomic succession of community composition, with marked shifts in the relative abundances of constituent species, as well as in a significant alteration of the community-level metabolic functions. In-depth research in this field can help improve the composition of indoor microbial communities, thereby benefiting human health and public health construction in urbanized environments.}, } @article {pmid42196433, year = {2026}, author = {Zeng, Y and Lau, EYT and Ye, S and Lu, J and Zhang, R and Hu, R and Liang, JQ}, title = {Fecal Cloacibacillus porcorum Improves Non-Invasive Diagnosis of Colorectal Adenoma in the Hong Kong Population.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, pmid = {42196433}, issn = {1422-0067}, support = {MRP/058/20//ITF-MRP, Hong Kong/ ; N/A//Hong Kong Ph.D. Fellowship Scheme (HKPFS)/ ; }, mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; *Adenoma/diagnosis/microbiology ; *Feces/microbiology ; Female ; Hong Kong/epidemiology ; Male ; Middle Aged ; Aged ; Biomarkers, Tumor/genetics ; Metagenomics ; ROC Curve ; }, abstract = {We previously developed a four-marker panel for the diagnosis of colorectal cancer (CRC) and adenoma. This study aimed to identify novel bacterial markers to improve adenoma detection using metagenomics and qPCR. Candidate markers were identified from metagenomic data (n = 492) using ANCOM-BC2 and Spearman's rank correlation analysis and were subsequently validated in an independent cohort (n = 426). Diagnostic performance was assessed both individually and in combination with our previously identified markers and FIT. Metagenomic analysis identified 21 candidate markers that increased along the normal-adenoma-carcinoma axis. Two top candidates, Cloacibacillus porcorum (Cp) and Intestinimonas butyriciproducens, were validated via qPCR and showed significant correlations with metagenomic abundances (both p < 0.0001). ROC analysis demonstrated that Cp levels significantly distinguished CRC and adenoma from controls, whereas I. butyriciproducens distinguished only CRC. The prevalence of Cp was significantly higher in adenoma and CRC than in controls (all p < 0.05). Multivariate analysis confirmed that Cp was independently associated with CRC and adenoma diagnoses. Adding Cp to the four-marker panel improved diagnostic sensitivity from 44.8% to 58.7% for adenoma and from 85.7% to 88.6% for CRC (specificity = 85%). When further combined with FIT, Cp improved sensitivity from 47.6% to 64.3% for adenoma and from 95.2% to 96.2% for CRC (specificity = 84.6%). C. porcorum is a novel bacterial marker that may aid in the non-invasive diagnosis of colorectal adenoma.}, } @article {pmid42196657, year = {2026}, author = {Zafar, I and Shafiq, S and Khan, MS}, title = {Wastewater Treatment Challenges and Circular Reuse for One Health Sustainability: A Review.}, journal = {International journal of environmental research and public health}, volume = {23}, number = {5}, pages = {}, pmid = {42196657}, issn = {1660-4601}, mesh = {*Wastewater/analysis ; *One Health ; *Waste Disposal, Fluid/methods ; *Water Purification/methods ; Humans ; *Recycling ; Environmental Monitoring ; }, abstract = {Wastewater is a complex and dynamic issue, particularly at the human-animal-environment interface, bearing biological and chemical hazards that may serve as a resource for transmission pathways for pathogens, antimicrobial resistance (AMR) determinants, heavy metals, pharmaceutical residues, per- and polyfluoroalkyl substances (PFAS), and microplastics. Rising global health issues necessitate effective wastewater treatment and advanced research to support risk-informed circular management within a one health framework, incorporating wastewater-based epidemiology (WBE), multi-omics approaches, nanobiotechnology, and green technologies. Inadequate wastewater treatment and uncontrolled discharge result in the generation of more than 380 billion cubic meters of wastewater annually worldwide, contributing to ecological degradation, the spread of AMR, and long-term toxicological risks. Despite significant advances in wastewater treatment, several challenges remain, including complex contaminant mixtures, limited detection and monitoring technologies, variable treatment efficiency, and weak regulatory and governance frameworks. This review highlights key wastewater treatment issues and presents recent advances in WBE and multi-omics approaches, such as metagenomics, resistome profiling, virome analysis, and chemical fingerprinting for contaminant monitoring and public health risk assessment. This review also examines circular reuse strategies focused on water reclamation, nutrient recovery, bioenergy production, and resource recovery, with particular emphasis on nature-based systems, hybrid biological-physicochemical treatment platforms, and green nanobiotechnology as promising approaches to improve treatment performance while minimizing environmental impacts. In conclusion, this review highlights the importance of integrated and sustainable wastewater management approaches within the One Health framework to address emerging challenges and promote environmental resilience, public health protection, and circular resource recovery.}, } @article {pmid42197004, year = {2026}, author = {Wang, M and Lyu, Y and Zhang, J and Wang, Y and Yang, Y and Mao, YH}, title = {FMT from Exercise and Konjac Glucomannan Preconditioned Donors Rescues Antibiotic-Induced Dysbiosis with Enhanced Ecological Restoration in Mice.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, pmid = {42197004}, issn = {2072-6643}, support = {2023ZDZX2035; 2024ZDZX2061//Guangdong Scientific Research Platform and Projects for the Higher-educational Institution (Key Area Project)/ ; SL2024A04J01093//the Guangzhou Fundamental and Applied Research/ ; No.82030098//National Natural Science Foundation of China/ ; S202410585045 and 202410585015//the College Students Innovation and Entrepreneurship Training Program/ ; 2023A1515010004//the Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {Animals ; *Dysbiosis/therapy/chemically induced/microbiology ; *Fecal Microbiota Transplantation/methods ; *Mannans/pharmacology ; *Anti-Bacterial Agents/adverse effects ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; *Physical Conditioning, Animal ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Although antibiotics have a wide range of applications in medical clinical practice and possess significant clinical value, their inevitable contribution to gut microbiome dysbiosis warrants attention. Our previous research has confirmed that the combined intervention of exercise and konjac glucomannan (KGM) has a better regulatory effect on gut dysbiosis in mice compared with individual interventions.

METHODS: This study aims to further investigate whether this effect can be transmitted through fecal microbiota transplantation (FMT), and to compare the recovery effects of autologous FMT (a-FMT), fecal microbiota transplantation after exercise combined with KGM intervention (EK-FMT), and combinative intervention with exercise and KGM (EXE-KGM) on gut microbiome dysbiosis. Sample sizes ranged from five to six animals.

RESULTS: The results showed that the a-FMT group recovered α diversity the fastest, including Chao, Shannon, and Simpson indices(p < 0.05), within 2 weeks after transplantation when compared with the CTL group. At the end of the experiment, the Bray-Curtis distance of the a-FMT group was closest to the CTL group, while the EXE-KGM group had delayed recovery, there was no significant difference between the EK-FMT group and the EXE-KGM group. Metagenomic analysis and metabolomics analysis indicated that the arginine synthesis and metabolism pathways (KEGG: map00471, map00473, arginine biosynthesis) played a core role in the restoration of the microbiota.

CONCLUSIONS: The results of this experiment indicate that EK-FMT group can partially transfer the regulatory effects of combined exercise and KGM intervention, a-FMT accelerates the recovery speed of the gut microbiome and arginine metabolism may play an important role in it. This finding provides a theoretical basis and practical direction for special populations to receive special donor fecal treatment.}, } @article {pmid42197026, year = {2026}, author = {Alsinani, Y and Rostamkhani, F and Shirvani, H}, title = {Exercise and the Gut Microbiome: From Mechanisms to Clinical Applications.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, pmid = {42197026}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Exercise/physiology ; Fatty Acids, Volatile/metabolism ; }, abstract = {Background/Objectives: The gut microbiome is a critical regulator of host metabolism, immunity, and the gut-brain axis. Exercise is a promising non-pharmacological modulator of microbial ecology, yet human evidence remains heterogeneous and the translational gap persists. This narrative review synthesizes mechanisms, human and animal evidence, and future directions for the exercise-gut microbiome axis. Methods: PubMed, Scopus, Web of Science, and SID were searched for articles published between January 2000 and February 2025. Keywords included exercise, physical activity, gut microbiome, gut microbiota, short-chain fatty acids, and gut-muscle axis. From 218 initial records, 89 original studies (47 human, 42 animal) met inclusion criteria and were critically appraised. Results: Exercise modulates the gut microbiome via splanchnic hypoperfusion, hyperthermia, altered transit time, and immune-mediated barrier regulation. Moderate-intensity continuous training consistently increases alpha diversity and enriches butyrate-producing taxa (Faecalibacterium prausnitzii, Roseburia hominis) and mucin-degrading Akkermansia muciniphila. High-intensity interval training transiently increases intestinal permeability in untrained individuals but, following adaptation, stimulates butyrate production via lactate cross-feeding metabolism-a recent breakthrough. Effects are transient and reversible upon detraining. Animal models establish causality through fecal microbiota transplantation; human randomized controlled trials demonstrate modest, intensity-dependent, and highly individualistic responses. Emerging evidence supports the gut-muscle axis in sarcopenia and personalized exercise prescription guided by microbiome profiling. Conclusion: Exercise shows promise as a low-cost modulator of the gut microbiome for enriching health-associated taxa and improving metabolic outcomes. Definitive evidence linking exercise-induced microbial shifts to enhanced athletic performance in humans remains lacking. Future research requires diet-controlled randomized controlled trials with ≥12-week interventions, shotgun metagenomics, and mechanistic validation of the gut-muscle axis in humans.}, } @article {pmid42197087, year = {2026}, author = {Yang, H and Li, J and Ren, S and Chai, X and Lu, J and Yan, H and Lu, Y}, title = {Gut Microbiota Changes Following Aerobic Exercise in Malnourished Octogenarians: An Assessor-Blinded Intervention Study Stratified by Nutritional Status.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, pmid = {42197087}, issn = {2072-6643}, support = {2020YFC2002902//Beijing Sport University/ ; }, mesh = {Aged, 80 and over ; Female ; Humans ; Male ; *Exercise/physiology ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; *Malnutrition/microbiology/therapy ; Nursing Home Residents ; Nursing Homes ; Nutrition Assessment ; *Nutritional Status ; }, abstract = {BACKGROUND/OBJECTIVES: Global population aging is associated with a rising prevalence of malnutrition among adults aged ≥80 years. Gut dysbiosis is linked to immune decline and impaired nutrient absorption, and aerobic exercise may enhance microbial diversity. This study investigated gut microbiota changes after a 12-week aerobic exercise intervention in octogenarians stratified by nutritional status.

METHODS: A total of 129 nursing home residents (≥80 years) were classified via the Mini Nutritional Assessment Short-Form (MNA-SF) into a healthy group (HG, MNA-SF ≥ 11) and a malnourished group (MG, MNA-SF < 11). Both groups underwent a 12-week brisk walking intervention (three sessions/week, 1 h/session, 40-60% heart rate reserve). Fecal samples were collected at baseline and post-intervention and were analyzed via shotgun metagenomic sequencing.

RESULTS: A total of 36 participants completed the intervention (HG = 17, MG = 19). Within-group baseline-to-post-intervention analysis showed no significant changes in alpha or beta diversity in the MG. However, post-intervention between-group comparison revealed higher microbial richness and diversity in the MG vs. the HG, with enrichment of taxa including Faecalibacterium prausnitzii and Streptococcus salivarius. Functional analysis revealed significant enhancements in metabolic pathways related to amino acid biosynthesis, protein synthesis, and quorum sensing in the MG. In contrast, the HG showed limited shifts in microbial diversity but an increase in species involved in carbohydrate metabolism.

CONCLUSIONS: After 12 weeks, the malnourished group showed higher post-intervention microbial richness and diversity than the healthy group, with differences in taxonomic and predicted functional profiles. Without a non-intervention control group, the microbiota differences observed during the 12-week aerobic exercise period can only be considered observational associations, not causal. Additionally, the high dropout rate (72.1%) limits the generalizability of the findings.

CLINICAL TRIAL REGISTRATION: The Chinese Clinical Trial Registry on 19 October 2022 (ChiCTR2200064801).}, } @article {pmid42197123, year = {2026}, author = {Rojas-Flores, SJ and Liza, R and Nazario-Naveda, R and Díaz, F and Delfin-Narciso, D and Cardenas, MG and Cabanillas-Chirinos, L}, title = {Mapping the Convergence of Frontier Technologies for Major Environmental Challenges: A Chemical and Molecular Perspective on the Use of AI for Climate Action and Antimicrobial Resistance.}, journal = {Molecules (Basel, Switzerland)}, volume = {31}, number = {10}, pages = {}, pmid = {42197123}, issn = {1420-3049}, mesh = {*Artificial Intelligence ; *Climate Change ; Metagenomics ; Humans ; *Drug Resistance, Microbial ; }, abstract = {The planet faces the critical interconnected challenges of climate change and antimicrobial resistance (AMR); these two crises mutually reinforce each other, threatening global health and ecosystem stability. This study conducts a systematic documentary analysis to map the convergence and identify the structural gaps between two key technological domains: artificial intelligence (AI) for climate action and molecular methods for AMR. The methodology was based on a corpus of 179 scientific documents indexed in Scopus (2010-2025), analyzed with data science tools to identify trends, collaborations, and impact. Quantitative results revealed clear leadership by the United States, accounting for 37.4% of publications, followed by China (26.8%); this leadership reflects the concentration of high-throughput molecular surveillance infrastructure and data science clusters essential for monitoring the environmental resistome. In terms of scientific impact, Spain showed the highest average, with 32.8 citations per article. The most influential work, a review on food security and sustainability, accumulated 275 citations. Network analysis identified authors such as Zhu, Yongguan, with 240 citations in total, as central nodes in international collaborations. Thematically, metagenomics and machine learning emerged as mature and interconnected research cores. This analysis confirms a solid yet still fragmented relationship between the two fields. The analysis reveals that, while metagenomic tools dominate the current literature, a gap persists in correlating genotypic resistance potential with functional phenotypic expression under changing climatic stressors. The results confirm a solid yet still fragmented foundation, highlighting the need for hybrid platforms that transition from descriptive bibliometrics to functional integration for designing systemic solutions. Future work should prioritize the development of hybrid platforms, such as intelligent biosensors, and collaborative governance frameworks that accelerate effective responses to these dual crises.}, } @article {pmid42197331, year = {2026}, author = {Manoharan, RK and Shin, HD and Lee, Y and Baek, S and Moon, E and Park, YB and Cho, J and La, IJ and Lee, DH and Han, KI and Srinivasan, S}, title = {Shotgun Metagenomic Analysis of Gut Microbiota and Antibiotic Resistance Genes in a High-Fat Diet Mouse Model Treated with Heat-Killed Lactiplantibacillus plantarum beLP1.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197331}, issn = {2076-2607}, abstract = {The gut microbiota is a central regulator of metabolic function, and its disruption by a high-fat diet (HFD) is strongly linked to obesity and metabolic impairment. This study evaluated the potential of heat-killed Lactiplantibacillus plantarum beLP1 (beLP1[®]) in alleviating HFD-induced metabolic and microbial imbalances in mice. Male C57BL/6N mice were fed an HFD for 10 weeks, with or without daily oral supplementation of beLP1 (≥3 × 10[10] cells). Compared with untreated HFD mice, beLP1 supplementation reduced serum triglycerides by 35% and lowered liver enzymes AST and ALT by 17% and 36%, respectively. Blood glucose levels remained similar to the HFD group throughout the study period. Shotgun metagenomic analysis revealed that beLP1 restored gut microbial diversity, increased beneficial taxa such as Akkermansia and Faecalibaculum high. and reduced pro-inflammatory species including Streptococcus sp., Mucispirillum schaedleri and Clostridium cocleatum. These microbial changes were associated with partial normalization of the Firmicutes/Bacteroidota ratio and improvements in antibiotic resistance gene (ARG) profiles. Specifically, in silico analysis of the short-chain fatty acid (SCFA) synthesis pathways indicated that the potential for acetate and propionate production was maximized in the beLP1 group, resulting in the highest relative abundance among all groups. This functional enhancement directly correlated with the enrichment of key SCFA-producing taxa, particularly Akkermansia muciniphila, confirming that increased bacterial abundance suggests an enhanced functional potential for SCFA production. Furthermore, beLP1[®] induced a selective modulation of gut ARGs, significantly reducing specific subtypes such as tetracycline and multidrug efflux genes, despite a slight increase in vancomycin resistance markers. Overall, our findings suggest that beLP1[®] attenuated the rate of body weight gain during the initial weeks of HFD exposure and significantly improved markers of hepatic stress and lipid metabolism.}, } @article {pmid42197333, year = {2026}, author = {Zhao, Z and Wang, X and Wen, F and Zhao, F and Zhang, M and Menghe, B}, title = {Integrated Metagenomic and Metabolomic Profiling Identifies Predictive Biomarkers for Overweight Status in a Mongolian Population.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197333}, issn = {2076-2607}, support = {2018YFE0123500//Special Funds for International Science and Technology Cooperation of China/ ; }, abstract = {Mongolians have high overweight prevalence linked to their nomadic lifestyle and diet, but gut microbiota studies in this population are scarce. This study used fecal metagenomic and serum metabolomic analyses of 96 Mongolian participants (normal-weight n = 55, overweight n = 41) to characterize gut microbiome alterations and identify weight-related biomarkers. The analyses revealed that Parabacteroides distasonis, Barnesiella intestinihominis, and Alistipes onderdonkii were significantly reduced in overweight individuals (p < 0.05). Concurrently, the metabolites such as beta-cryptoxanthin, p-cresol, and ribothymidine were significantly down-regulated in the overweight group (p < 0.05). Random forest models from the three datasets showed a strong diagnostic ability for microbial families (AUC > 0.70). A subsequent integrated multi-kingdom classifier that combined microbiota and metabolite data achieved the highest performance (AUC = 0.818). Key features with high predictive contributions were identified, including Lactobacillus crispatus, Alistipes onderdonkii, and Parabacteroides distasonis, and metabolites, such as beta-cryptoxanthin, p-cresol, and picolinic acid. These results show the random forest model has high predictive value for distinguishing normal weight and overweight individuals. In summary, this study identified specific gut microbiota and serum metabolomic profiles linked to overweight in Mongolians. Multi-omics integration established a diagnostic biomarker model, laying a theoretical basis for microbiome-targeted weight management interventions.}, } @article {pmid42197335, year = {2026}, author = {Naranjo-Moran, J and Ratti, MF and Vera-Morales, M}, title = {Microorganisms from Antarctica: A Review of Their Potential in the Bioremediation of Hydrocarbon-Contaminated Soils.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197335}, issn = {2076-2607}, abstract = {Antarctica's extreme cryospheric conditions impose severe thermodynamic constraints on the natural attenuation of hydrocarbon pollutants. Despite the Antarctic Treaty System's protections, the footprint of human logistics has left persistent reservoirs of petroleum hydrocarbons that threaten endemic biodiversity. This review critically synthesizes the state-of-the-art in Antarctic bioremediation, moving beyond traditional culture-dependent studies to integrate recent multi-omics breakthroughs (2020-2025). We analyze the molecular mechanisms limiting bioavailability in frozen soils and highlight the adaptive strategies of psychrophilic consortia, including the modification of membrane fluidity and the expression of cold-active enzymes (e.g., RHDs, AlkB). Notably, we discuss emerging findings on novel long-chain alkane degradation genes (almA, ladA) identified in 2025, which challenge previous assumptions about recalcitrance. Furthermore, the review evaluates the engineering bottlenecks of in situ versus ex situ strategies, emphasizing the synergistic potential of bacterial-fungal co-cultures and the ecological necessity of "climate-smart" remediation to mitigate methane emissions from thawing permafrost. By bridging the gap between fundamental microbial genetics and applied field engineering, we propose a roadmap for the next generation of biotechnological solutions in the warming polar environment.}, } @article {pmid42197351, year = {2026}, author = {Huang, W and Liang, J and Chan, P and Liu, Z and Guo, L}, title = {Probiotics Exert Colonization Resistance Against F. nucleatum subsp. polymorphum: Disruption by Antibiotics and Underlying Molecular Mechanisms.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197351}, issn = {2076-2607}, support = {81670982//National Natural Science Foundation of China/ ; }, abstract = {Fusobacterium nucleatum (F. nucleatum), a key oral pathogen, promotes colorectal cancer (CRC) progression via gut translocation. Although gut probiotics provide colonization resistance against pathogens, antibiotic-induced dysbiosis may facilitate F. nucleatum integration and increase the risk of CRC. The mechanisms underlying probiotic-F. nucleatum antagonism and antibiotic modulation remain unclear. A 33-strain probiotic consortium and F. nucleatum subsp. Polymorphum (F. polymorphum) ATCC 10953 were co-cultured. The inhibitory effects of probiotics on F. nucleatum and the impacts of antibiotics (ABXs) on the microbial community structure in the co-culture system and on the probiotic-mediated inhibition of F. nucleatum were evaluated using spent medium assays, plate confrontation tests, growth curves, qRT-PCR, metagenomic sequencing, and transcriptomics. Hydrogen peroxide/pH/lysine assays and coaggregation models were performed to probe the associated mechanisms. Probiotics strongly inhibited the growth of F. nucleatum in a dose-dependent manner, primarily via organic acids, while F. nucleatum enriched amino acid/vitamin biosynthesis pathways without major growth suppression. Antibiotics weakened probiotic antagonism, shifted species abundance (↓ L. plantarum, ↑ L. paracasei), induced adaptive stress responses in F. nucleatum (↑ nucleotide metabolism, propanediol degradation, pdxS), and reduced lysine biosynthesis. Lysine supplementation restored probiotic abundance and disrupted F. nucleatum coaggregation. Multi-strain probiotics exert potent colonization resistance effects against F. nucleatum, mainly through organic acids and metabolic interference. Antibiotic-induced dysbiosis impairs this protective effect and may promote the persistence of F. nucleatum, which has been implicated in CRC risk. Targeted probiotic strategies may offer novel preventive approaches.}, } @article {pmid42197355, year = {2026}, author = {Feletti, R and Mori, A and Zaffagnini, A and Castilletti, C and Pomari, E}, title = {The Human Virome in Infectious Diseases: Insights from Chronic and Acute Infections Across Body Sites-A Narrative Review.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197355}, issn = {2076-2607}, support = {PE00000007, INF-ACT//EU funding within the MUR PNRR/ ; 5MIL-VISA L1P17//Italian Ministry of Health/ ; }, abstract = {The human virome, comprising eukaryotic viruses, bacteriophages, and viral genetic material, is a dynamic component of the microbiome with growing relevance in infectious diseases. This narrative review is structured to: (i) summarize the general composition of the human virome and methodological challenges, including the fraction of unclassified viral "dark matter"; (ii) describe virome alterations in chronic infections; and (iii) explore site-specific virome dynamics across respiratory, intestinal, and genito-urinary tracts in both chronic and acute infections. In chronic viral infections such as HIV, HBV, HCV, and HPV, a recurrent feature is the expansion of Anelloviridae-particularly torque teno virus-reflecting impaired immune surveillance rather than direct pathogenicity, suggesting their potential as surrogate biomarkers of immune competence. Evidence on virome changes in chronic bacterial and parasitic infections remains limited, highlighting a critical knowledge gap. Acute infections are associated with compartment-specific shifts in eukaryotic viruses and bacteriophage communities, often paralleling changes in bacterial populations and inflammatory responses, with implications for disease severity. Despite advances in metagenomic approaches, a substantial proportion of viral sequences remains unclassified, limiting functional interpretation. Nevertheless, virome profiling provides an ecosystem-level perspective, offering insights beyond single-pathogen detection and supporting emerging applications in diagnostics, immune monitoring, prognosis, and infectious disease surveillance.}, } @article {pmid42197366, year = {2026}, author = {Huang, Z and Chen, S and Fan, A and Chen, Y and Cai, Q and Zeng, T and Zheng, W and Yang, Y}, title = {Iron-Containing Flocs Derived from Environmental Emergency Response Influenced Nitrogen Cycling Driven by Microorganisms in River Sediments.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197366}, issn = {2076-2607}, support = {PM-zx703-202204-155//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; PM-zx097-202506-204//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; }, abstract = {In situ coagulation is regarded as the most effective measure in response to the frequent metal spills in China. Excessive coagulant is often used in pursuit of extremely high removal rates of contaminants. Yet the secondary ecological impact of the iron-containing coagulation flocs left on the river sediments after emergency response is still unclear. In the current study, we investigated the impact of flocs derived from three different iron-based coagulants, polymeric ferric sulfate (PFS), polymeric ferric chloride (PFC), and ferric chloride (FeCl3), on microbial communities in sediment based on microcosm experiments. Metagenomics, quantitative PCR, and determination of ammonia oxidation potential were adopted to elucidate community shifts. The results indicate that the community structure and function of microorganisms in sediments have been affected, especially processes and species related to nitrogen cycling, and the effect was coagulant-specific. Flocs retrieved from FeCl3 caused a more pronounced decline in diversity, shifts in community composition, and decreased potential ammonia oxidation. Ammonia-oxidizing archaea (AOA) was more sensitive to iron-containing flocs than ammonia-oxidizing bacteria (AOB), while PFS-flocs tended to reduce multiple genes involved in nitrate reduction. This indicates that the pre-polymerization of inorganic coagulants may be the primary factor leading to different microbial ecological effects. Sulfate, on the other hand, may affect specific biogeochemical processes due to its competition for electron donors. Our results confirmed that even without heavy metals as contaminants, coagulant flocs alone could present an effect on nitrogen cycling in sediments. The results will provide a scientific basis for environmental emergency decision-making: in emergency response to metal pollution incidents, the use of coagulants should be limited to only the necessary level.}, } @article {pmid42197381, year = {2026}, author = {Li, X and Liang, X and Hao, P and Wu, J and Liu, D}, title = {Compound Yeast Culture Reshapes Gut Microbiota and Functional Pathways to Enhance Antioxidant Capacity and Immune Homeostasis in Suckling Calves.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197381}, issn = {2076-2607}, support = {2022YFDZ0051//Inner Mongolia Autonomous Region Science and Technology Project/ ; BR22-11-17//Basic Scientific Research Business Project of Universities directly under the Inner Mongolia Autonomous Region/ ; 2023-JSGG-5//National Center of Technology Innovation for Dairy/ ; YLXKZX-NND-012//First-class Disciplines of Inner Mongolia Scientific Research Special Program/ ; }, abstract = {Diarrhea in suckling calves is associated with impaired growth, oxidative stress, immune dysfunction, and intestinal microbial dysbiosis. This study evaluated the effects of compound yeast culture (CYC) supplementation on growth performance, fecal characteristics, antioxidant capacity, immune function, and gut microbiota in diarrheic Holstein calves. Thirty-six approximately 7-day-old calves were enrolled, including 12 healthy calves (CON) and 24 diarrheic calves randomly assigned to a diarrhea group (DIA) or a CYC-supplemented group (DIA-YC; 50 g/d for 30 days). The experimental period lasted 60 days. Compared with the DIA group, calves in the DIA-YC group showed significantly higher average daily feed intake and average daily gain (ADG) during days 31-60 and across the entire period (p < 0.05), with a trend towards increased body weight. Fecal scores were significantly elevated in diarrheic calves during the early and mid-stages but were markedly reduced by CYC supplementation from days 7 to 30; no significant difference was observed between DIA-YC and CON during days 16-30 (p > 0.05). Diarrheic calves exhibited oxidative stress, characterized by decreased total antioxidant capacity (T-AOC) and increased malondialdehyde (MDA). CYC supplementation significantly increased T-AOC, superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) activities, while reducing MDA levels (p < 0.05). Immune analysis showed higher serum IgG and IL-10 levels and lower TNF-α levels in the DIA-YC group, along with improved intestinal barrier indicators, including diamine oxidase (DAO) activity and endotoxin levels. Metagenomic analysis revealed that diarrhea reduced microbial richness and diversity and altered community structure, whereas CYC partially restored microbial diversity and increased beneficial genera such as Prevotella, Coprococcus, Ruminococcus, and Parabacteroides. Functional analysis indicated that CYC enhanced pathways related to immune regulation, energy metabolism, and antioxidant function. CYC supplementation alleviates oxidative stress and immune dysfunction by modulating gut microbiota, thereby improving growth performance and reducing diarrheal severity in calves.}, } @article {pmid42197408, year = {2026}, author = {Qie, T and Lin, D and Fan, Q and Sun, G and Wang, H and Liu, Z and Liu, X}, title = {Responses of Soil Nitrogen-Cycling Microbial Communities and Functional Potential to Grazing Intensities in Alpine Meadows.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197408}, issn = {2076-2607}, support = {KLGE202209//State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems/ ; 32260354//National Natural Science Foundation of China/ ; KLGE-2024-01//State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems/ ; 2023-QN-46//Lanzhou Science and Technology Bureau/ ; 2500011004//Gansu Agricultural University/ ; }, abstract = {Although grazing is a key driver of nitrogen cycling in alpine meadow soils, a systematic understanding of how different grazing intensities shape the structure and functional potential of soil nitrogen-cycling microbial communities remains lacking. In this study, soil samples were collected under five grazing intensities (no grazing, light grazing, moderate grazing, heavy grazing, and extreme grazing) and metagenomic sequencing was employed to analyze variations in nitrogen-cycling microbial communities and functional genes. The results showed that bacteria were the dominant group in nitrogen-cycling communities (relative abundance: 93.99-98.98%), with significant community differentiation across grazing intensities. Light grazing maintained relatively high microbial diversity, whereas moderate and heavy grazing led to more pronounced differences in community composition. Functional gene analysis identified 41 nitrogen-cycling-related genes, primarily involved in denitrification, nitrate reduction, and ammonia assimilation. Light grazing enhanced nitrate reduction and glutamate synthesis; moderate grazing exhibited the strongest ammonia assimilation potential; heavy grazing significantly increased denitrification activity, indicating an elevated risk of nitrogen loss; and under extreme grazing, both the number and abundance of nitrogen-cycling functional genes declined markedly, with functional composition becoming simplified. Collectively, light grazing is more conducive to maintaining the balance between soil microbial diversity and nitrogen-cycling function in alpine meadows, whereas overgrazing disrupts the equilibrium between microbial communities and nitrogen metabolism. This study provides a microbiological basis for the restoration of degraded alpine meadows and sustainable grazing management.}, } @article {pmid42197422, year = {2026}, author = {Shaik, SM and Schiro, G and Laubitz, D and Madan, JC and Kelley, CP and Daines, M and Rice, SA and Ghishan, FK and Kiela, PR}, title = {Functional Shifts in Gut Microbiota and Associated Metabolites Suggest Gut-Brain Axis Dysregulation in Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections (PANDAS).}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197422}, issn = {2076-2607}, support = {NA//Alex Manful Fund/ ; RFGA2022-010-23//Arizona Department of Health Services/ ; }, abstract = {Background: Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal infections (PANDAS) are characterized by neuropsychiatric symptoms linked to immune dysregulation. Emerging evidence highlights the role of host-microbiome interactions in modulating neuro-immune functions via gut-brain axis signaling; however, its contribution to PANDAS pathophysiology remains poorly understood. Methods: We conducted microbiome analysis from samples collected across multiple sites of PANDAS patients including nasal, throat and stool. We performed an integrated multi-omics analysis of stool samples from pediatric PANDAS cases and healthy controls, including discordant twin pairs. Microbial composition and function were assessed using 16S rRNA gene sequencing, shotgun metagenomics, while untargeted metabolomic profiling was performed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS). Results: PANDAS cases exhibited reduced alpha diversity and significantly altered beta diversity compared to controls, indicating shifts in gut microbial composition. Shotgun metagenomic analysis revealed differential enrichment of functional pathways, including diminished quorum sensing, altered gamma-aminobutyric acid (GABA) biosynthesis, and microbial degradation processes. Multiple gut-brain modules (GBMs) and gut metabolic modules (GMMs) associated with neurotransmission, transport activities and metabolism were significantly perturbed in PANDAS. Metabolomic profiling showed reduced functional diversity and distinct clustering of metabolic profiles, with differential abundance of amino acids, bile acids, and neuroactive compounds. Integrative analysis further identified disrupted microbe-metabolite networks allied to gut-brain signaling. Conclusions: Our findings reveal significant functional shifts in gut microbiota composition, functional capacity and metabolite profile in PANDAS, suggesting dysregulation of the gut-brain axis signaling. This study provides a foundation for development of microbiome-based biomarkers and therapeutic strategies for pediatric neuropsychiatric disorders.}, } @article {pmid42197470, year = {2026}, author = {Zheng, Y and Wu, R and Feng, H and Wu, X and Yang, Y}, title = {Temperature Elevation Alters the Gut Antibiotic Resistome and Carbohydrate-Active Enzymes in the Desert Lizard Eremias roborowskii.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197470}, issn = {2076-2607}, support = {32560265//National Natural Science Foundation of China/ ; 32260118//National Natural Science Foundation of China/ ; 2023TSYCQNTJ0034//the second group of Tianshan Talent Training Program: Youth Support Talent Project/ ; XJAUGRI2025030//Xinjiang Agricultural University Graduate Research Innovation Program/ ; }, abstract = {In the context of global warming, the resulting persistent thermal stress has become a critical environmental factor influencing the structural and functional homeostasis of gut microbiota in reptiles. In this study, Eremias roborowskii, a desert lizard endemic to the extreme heat conditions of the Turpan Basin, was selected as an ideal model for evaluating the ecological impacts of global warming. Meanwhile, a 60-day controlled laboratory experiment was conducted, exposing the lizards to normal (30 °C ± 1 °C), elevated (37 °C ± 1 °C), and high (42 °C ± 1 °C) temperatures to reflect future climate scenarios. Using shotgun metagenomic sequencing, the gut microbiota was characterized to investigate the dynamics of the antibiotic resistance genes (ARGs) and carbohydrate-active enzymes (CAZymes) under heat stress. The results reveal that elevated temperature selectively promotes heat-tolerant gut microbiota, such as Tetragenococcus and Faecalicatena, by altering host energy metabolism and modulating heat stress adaptation to maintain intestinal homeostasis. Moreover, the observed increase in resistome diversity and richness under elevated temperature may be attributed to temperature-induced shifts in gut microbial composition, particularly the enrichment of heat-tolerant ARG-carrying bacterial taxa. Metabolic changes in CAZymes were caused by gut microbiota remodeling, which optimized carbon utilization and preferentially allocated cell wall synthesis and repair. Furthermore, the pentose phosphate pathway and amino acid biosynthesis pathways were upregulated, providing NADPH for antioxidant defense and precursors for protein synthesis, respectively, thereby contributing to the maintenance of microbial cellular homeostasis. Our study provides a theoretical basis for understanding functional gene adaptation strategies in wildlife microbiomes due to climate change.}, } @article {pmid42197480, year = {2026}, author = {Duran Yunga, ER and Rodriguez Coyago, ML}, title = {Structure and Function of the Dental Plaque Microbiome in Eubiosis: A Systematic Review of Ethnic-Racial Influences.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197480}, issn = {2076-2607}, abstract = {While a conserved core microbiome is shared across healthy individuals, significant interindividual taxonomic variation exists; however, the specific influence of genetic ancestry on supragingival plaque structure in eubiosis remains unclear. This systematic review analyzed evidence regarding taxonomic variations in supragingival plaque associated with ethnicity in systemically healthy populations. A search was conducted in PubMed, Scopus, ScienceDirect, and Scielo following PRISMA 2020 guidelines, covering literature up to October 2025. Cross-sectional studies using genomic sequencing or metagenomics were included, with quality assessed via the GRADE system. Six studies met eligibility criteria. Results identified a universal core microbiome structurally dominated by Corynebacterium spp. and Streptococcus spp. However, distinct ethnic-specific taxonomic signatures emerged, such as the enrichment of Fusobacterium spp. in African Americans and Corynebacterium spp. in Caucasians, alongside the exclusive presence of Sneathia spp. in Burmese individuals. Although a basal microbial architecture necessary for homeostasis exists, ethnicity acts as a biological filter defining distinctive bacterial profiles and differential susceptibilities. These findings suggest that while the core microbiome is conserved, the composition of peripheral species in the dental plaque hedgehog structure varies according to ancestry. This supports a transition from standardized dental care to personalized medicine oriented towards the patient's biological heritage.}, } @article {pmid42197517, year = {2026}, author = {Albastaki, A and Smith, J}, title = {Choosing Between Short-Read 16S, Full-Length ONT 16S, and Long-Read Shotgun Metagenomics for Soil Microbiome Studies: A Critical Review of the Benchmarking Evidence.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197517}, issn = {2076-2607}, abstract = {Studying soil microbiomes is challenging because soil contains thousands of microbial species at vastly different abundances. The choice of sequencing method has a strong effect on which of these species are detected and how the community is described. Three approaches now dominate soil microbiome research: short-read 16S rRNA amplicon sequencing on Illumina platforms, full-length 16S sequencing on Oxford Nanopore Technologies (ONT) platforms (particularly the R10.4.1 flow cell), and long-read shotgun metagenomics. Each has distinct biases that shape the recovered community, yet researchers routinely select a method based on cost, understanding, or local expertise rather than on a clear knowledge of what each approach methodically over- or under-represents. Here, we review head-to-head benchmarking studies that have applied two or more of these methods to the same soil or directly comparable samples. We show that while long-read and short-read 16S approaches generally converge on dominant taxa and on between-sample differences, they disagree substantially on alpha diversity estimates, rare taxon detection, and the relative abundances of entire phyla. The R10.4.1 flow cell chemistry has narrowed but not eliminated the accuracy gap with Illumina, and shotgun metagenomics reveals systematic biases in both short and long-read assembly that depend on population diversity within the sample. We synthesise this evidence into an evidence-based decision framework tied to specific research questions and recognise the gaps in soil-specific benchmarking that limit current methods. Rather than asking which platform is "best," we argue that method choice should be framed as an important part of study design, with the biases of the chosen method acknowledged and, where possible, controlled for.}, } @article {pmid42197550, year = {2026}, author = {Zhang, S and Li, G and Zhu, E and Zhao, Y and Yang, X and Huang, S and Zheng, Z}, title = {Rhizosphere Microbial Community and Metagenomic Annotation Responses in a Vallisneria natans-Sediment Microcosm Exposed to Trifluenfuronate and Fluopyram.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, pmid = {42197550}, issn = {2076-2607}, support = {2023YFD1700403//the National Key Research and Development Program of China/ ; 2024R054//Zhejiang Shuren University/ ; }, abstract = {Rhizosphere microorganisms play central roles in nutrient cycling and contaminant transformation in sediment-associated freshwater systems, yet their responses to newer pesticides remain insufficiently characterized. In this study, a 28-day Vallisneria natans-rhizosphere sediment microcosm was used to compare the effects of trifluenfuronate and fluopyram at nominal concentrations of 0.01, 0.1, and 1 mg L[-1]. Bacterial community composition was assessed using 16S rRNA gene sequencing, and shotgun metagenomic data were used to evaluate relative functional annotation patterns. Plant physiological traits and rhizosphere sediment enzyme activities were measured as ecological context for interpreting microorganism-associated responses. Fluopyram, particularly at 1 mg L[-1], produced clearer ordination-level shifts in rhizosphere bacterial community composition than trifluenfuronate, although pairwise treatment separation was not statistically resolved after multiple-testing correction. Annotation-based metagenomic profiles also differed between the two pesticides: stronger exposure was associated with reduced relative signals for several xenobiotic-, transport-, and regulation-related annotations, while high-dose fluopyram showed a methane-metabolism-related annotation signal and high-dose trifluenfuronate showed relative enrichment of secondary-metabolism-related annotations. These microbial and annotation-profile responses coincided with stronger inhibition of V. natans growth and greater suppression of rhizosphere sediment enzyme activities under fluopyram exposure. Overall, fluopyram induced more consistent microorganism-associated response patterns than trifluenfuronate in the tested rooted macrophyte-sediment microcosm. The results highlight the sensitivity of rhizosphere microbial communities and metagenomic annotation profiles to pesticide exposure in sediment-associated freshwater systems.}, } @article {pmid42197616, year = {2026}, author = {Wang, W and Yang, W and Song, W and Huang, S and Lai, J and Zhou, Z and Wang, P and Wang, B}, title = {Rhizosphere Microbial Effects on Soil Quality of Pinus massoniana and Schima superba Mixed Plantations.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, pmid = {42197616}, issn = {2223-7747}, support = {2023YFD2200902//National R&D Program of China/ ; CAFYBB2024ZA021//Fujian Sanming Demonstration and Model Construction Project of China/ ; }, abstract = {This study aimed to reveal the rhizosphere microbial community structure, carbon-nitrogen-phosphorus (C-N-P) nutrient cycling processes, and functional gene characteristics of Pinus massoniana and Schima superba in mixed forests. Furthermore, we sought to elucidate the microbial mechanisms by which mixed-species afforestation enhances soil quality improvement, providing a theoretical basis in soil microbiology for the cultivation of these mixed forests. The research subjects included pure P. massoniana plantations (CLPs), pure S. superba plantations (CLSs), and individual P. massoniana (HJP) and S. superba (HJS) trees within mixed plantations (HJLs). We collected rhizosphere and bulk soil samples to analyze their physicochemical properties and enzyme activities. Metagenomic sequencing was employed to profile the rhizosphere microbial communities and functional genes involved in C-N-P cycling. Furthermore, by integrating a functional gene co-occurrence network analysis with structural equation modeling (SEM), we systematically elucidated the coupling relationships among the stand types, soil properties, microbial communities, and nutrient cycling. Mixed planting significantly improved soil quality; compared to the CLP and CLS forests, the nitrate nitrogen (NO3[-]-N) content in the mixed forest soils increased by 121.01% and 120.10% (p < 0.05), and the activity of urease (URE) also significantly increased by 123.99% and 49.56%, respectively. Mixing significantly altered the microbial community structure. In the bacterial community of the mixed forests, the abundance of nitrogen-fixing and potentially phosphorus-solubilizing bacteria from the genera Paraburkholderia and Burkholderia increased. In the fungal community, the arbuscular mycorrhizal fungus Rhizophagus, which possesses a nutrient absorption advantage, exhibited absolute dominance, with its relative abundance ranging from 14.84% to 88.81%. The abundances of genes associated with denitrification and phosphorus starvation regulation were significantly upregulated in the mixed forests; notably, the abundance of phosphorus starvation regulation genes in the HJSs was 18.84% higher than that in the CLSs. A co-occurrence network analysis demonstrated that the proportion of positive correlation edges in the HJP nitrogen cycling network reached as high as 75.0%, and the average degree of the HJS phosphorus cycling network (2.691) surpassed that of the CLSs. The structural equation modeling further revealed that the association strength between the fungi and phosphorus cycling genes in the mixed forests increased to R[2] = 0.915 (p < 0.01) from R[2] = 0.213 in the pure forests. This mixed planting practice transforms nutrient cycling from a resource-competitive mode to a microbially synergized mode, thereby forming an efficient endogenous nutrient cycling system. This synergistic rhizosphere microbial effect is a key internal mechanism for overcoming nutrient bottlenecks and should serve as a diagnostic indicator of soil recovery in the ecological restoration of degraded pine forests.}, } @article {pmid42198637, year = {2026}, author = {Malleret, B and Kwak, ML and Chavatte, JM}, title = {Accelerating Progress on Ticks and Tick-Borne Diseases in Southeast Asia: Regional Challenges, Evidence Gaps, and Priorities (2023-2025).}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {42198637}, issn = {2076-0817}, support = {NUHSRO/2025/017/T1/Seed-Sep24/Adhoc/01//Ministry of Education/ ; }, mesh = {Animals ; Humans ; Asia, Southeastern/epidemiology ; Evidence Gaps ; *Tick-Borne Diseases/epidemiology/prevention & control ; *Ticks/microbiology ; Congresses as Topic ; }, abstract = {Southeast Asia (SEA) faces persistent gaps in regional understanding and control of ticks and tick-borne diseases (TBDs) despite recent advances (2023-2025). The second international symposium on ticks and TBDs in SEA (Singapore, August 2025), following the inaugural 2023 meeting in Cambodia, served as a catalyst for regional exchange that informed this perspective. SEA's ecological and host diversity supports complex tick-host-pathogen networks, yet evidence remains fragmented due to uneven sampling that has largely focused on livestock and peri-urban environments. Key constraints include limited taxonomic resolution driven by outdated or incomplete identification keys, under-sampling of soft ticks (Argasidae), and the absence of harmonized, open-access regional reference resources (including DNA barcodes and MALDI-TOF MS spectral databases). While MALDI-TOF MS, proteomics, AI-assisted identification, and next-generation sequencing/metagenomics are increasingly applied, their broader regional uptake is limited by the absence of harmonized, open-access reference resources (including DNA barcodes and MALDI-TOF MS spectral databases). Broad ecological surveys and integrated animal and human surveillance remain limited, and vector competence studies are constrained by the scarcity of SEA-derived tick colonies and cell lines. Regional data and recent findings (2024-2026) confirm circulation of multiple TBPs (including Anaplasma, Babesia, Borrelia, Coxiella, Ehrlichia, Rickettsia, and Theileria) and highlight emerging viral findings, including southward reports of Bandavirus dabieense. Human infestations and non-communicable tick bite outcomes (e.g., tick paralysis and alpha-gal syndrome) are recognized but remain under-reported due to low clinical awareness and limited diagnostics. Importantly, the diagnostic chain is further disrupted by missed/insufficient specimen collection at the point of care, and by constrained capacity to identify (especially immature) ticks to species level-limitations compounded by the absence of harmonized, open-access regional reference resources. The symposium identified six priorities: (1) full completion and regional validation of tick identification keys for adults (in progress) and immatures (to be initiated), plus an open-access DNA barcode library anchored by curated, voucher-based collections from all SEA countries; (2) harmonization of molecular and proteomic diagnostic platforms, including expansion of regional MALDI-TOF MS and NGS protocols and reference databases; (3) development of tick colonies and cell lines from locally prevalent species to support vector competence, vaccine, and acaricide testing; (4) expansion of One Health surveillance with enhanced ecological sampling at wildlife-livestock-human interfaces; (5) establishment of open-access, region-wide data platforms for integrated tick, TBP, and ecological metadata sharing; and (6) sustained investment in human resources, training, and policy advocacy to raise research and public health visibility of ticks and TBDs.}, } @article {pmid42198700, year = {2026}, author = {Mansour, O and Fadeev, AV and Perederiy, AA and Ksenafontov, AD and Boyarintseva, AY and Danilenko, DM and Lioznov, DA and Komissarov, AB}, title = {Whole-Genome Phylogenetic Characterization of Human Parainfluenza Virus Type 4 Circulating in St. Petersburg, Russia.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, pmid = {42198700}, issn = {1999-4915}, support = {TVKQ-2024-0003, registration number 124020500002-4//Ministry of Health of the Russian Federation (Project #TVKQ-2024-0003 "Complex approach to genetic characterization and early identifications of pathogens with epidemic and pandemic potential using metagenomic sequencing")/ ; }, mesh = {Humans ; *Phylogeny ; Russia/epidemiology ; *Genome, Viral ; Genetic Variation ; Whole Genome Sequencing ; *Parainfluenza Virus 4, Human/genetics/classification/isolation & purification ; *Rubulavirus Infections/virology/epidemiology ; }, abstract = {Human parainfluenza virus type 4 (hPIV4) remains poorly characterized compared with other hPIV serotypes and information on its genomic diversity is particularly limited for Russia and Eastern Europe. In this study, we report the first complete genome sequences of hPIV4 isolates from Russia and place them in the context of global hPIV4 genetic diversity. Eight hPIV4 viruses were isolated in cell culture from respiratory samples collected from hospitalized children in Saint Petersburg between 2017/2018 and 2023/2024. Complete viral genomes were recovered using a metagenomic whole-genome amplification approach based on SMART-9N technology. Phylogenetic analysis of 178 complete hPIV4 genomes showed clear separation into hPIV4a (n = 132) and hPIV4b (n = 46) subtypes. Based on genetic distance approach, hPIV4a formed two major clusters, with the dominant cluster B subdivided into four subclusters (B1-B4); and subcluster B4 further resolved into four genetic lineages. All Russian isolates belonged to the subcluster B4 and were distributed among multiple co-circulating lineages. In contrast, hPIV4b genomes segregated into three distinct clusters, reflecting structured genetic diversity within the subtype. Collectively, this study provides, to the best of our knowledge, the first p-distance-based framework for hPIV4 whole-genome classification and contributes new complete genome sequences for an underrepresented region.}, } @article {pmid42198703, year = {2026}, author = {Wang, Z and Liu, Z and Zeng, J and Li, J and Cheng, J and Qi, X and Li, J and Bai, S}, title = {Annual Dynamics and Functional Traits of Viral Communities in Tropical Intertidal Sands of Sanya Bay.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, pmid = {42198703}, issn = {1999-4915}, support = {423RC548//Hainan Provincial Natural Science Foundation of China/ ; KJRC2023C14//Department of Science and Technology of Hainan Province/ ; 41506139//National Natural Science Foundation of China/ ; }, mesh = {Seashore ; *Geologic Sediments/virology ; Seasons ; Metagenomics ; *Bays/virology ; *Viruses/classification/genetics/isolation & purification ; Tropical Climate ; Phylogeny ; *Virome ; }, abstract = {Viruses are key regulators of marine microbial communities, yet their temporal dynamics in tropical intertidal sediments remain poorly characterized. We conducted a year-long metagenomic survey of sandy intertidal sediments in Sanya Bay (60 monthly samples from five sites) to examine viral taxonomy, community structure, lytic proteins, and auxiliary metabolic genes (AMGs). Within the classifiable fraction, the assemblages were consistently dominated by Assiduviridae. However, NMDS analysis revealed a significant overall seasonal shift, with October-December samples separating from the rest of the year. Co-occurrence network analysis identified five co-occurrence modules with distinct temporal patterns, alongside a concurrent decline in module abundance and lytic proteins in October. Functional annotation showed that cysteine and methionine metabolism, primarily driven by DNA methyltransferases, was identified as a highly represented AMG category among the annotated functions, while other pathways displayed seasonal variability. Collectively, these findings suggest that although characterized by a classifiable fraction dominated by Assiduviridae, the highly complex tropical intertidal viral communities undergo substantial seasonal reorganization in structure and functional potential.}, } @article {pmid42198741, year = {2026}, author = {Jia, L and De, R and Li, Z and Han, Z and Liu, L and Dong, H and Feng, S and Liu, R and Zhao, L}, title = {A Prolonged Norovirus Infection and the Molecular Evolution of Human Norovirus Within-Host in a Child with Burkitt Lymphoma.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, pmid = {42198741}, issn = {1999-4915}, support = {Discipline Leader -02-20//Beijing Municipal Health Commission/ ; }, mesh = {Humans ; *Burkitt Lymphoma/virology/complications ; *Evolution, Molecular ; *Norovirus/genetics/classification/isolation & purification ; Phylogeny ; *Caliciviridae Infections/virology/complications ; Genome, Viral ; Child ; Feces/virology ; High-Throughput Nucleotide Sequencing ; Mutation ; }, abstract = {It has been reported that chronic infection of human norovirus (HuNoV) may potentially serve as a reservoir for viral variants with the possibility to evade population immunity or alter the binding sites of HBGA receptors. In this study, a child diagnosed with Burkitt lymphoma and positive for HuNoV determined by real-time PCR (qPCR) firstly in 15 August 2016, was followed up until 20 March 2018, and 26 fecal specimens and one vomitus were collected to trace the evolutionary characteristics of HuNoV by phylogenetic analysis, meta-genomics next-generation sequencing (mNGS), and temporal evolutionary analysis of VP1 among 23 specimens positive for HuNoV. There were 15 specimens with partial RdRp gene sequences forming an independent cluster with sequences of GII.P31, 14 with the region C sequences and 11 with P domain sequences of VP1 gene clustered together with HuNoV GII.4 Sydney_2012. All these sequences showed that mutations accumulated nearly in a time order, and more mutations were shown in the key epitopes A-E or near the binding sites for HBGA in subdomain P2 with higher evolutionary rates. Analysis of NGS data identified intra-host viral quasi-species, and two genome sequences of the same length from mNGS were assembled from N705, with mutations located in the region of subdomain P2 (1171 nt-1202 nt) which led to five amino acid mutations. In conclusion, the accumulated mutations of HuNoV, especially in subdomain P2, were explored in a child with Burkitt lymphoma, and the sequencing of HuNoV from immunocompromised individuals was proven critical for monitoring intra-host quasi-species evolution and potential variant emergence, providing basic data for clinical infection control.}, } @article {pmid42198763, year = {2026}, author = {Kim, MJ and Kim, YJ and Ha, HJ and Park, JS and Rini, IA and Lee, S and Lee, TK}, title = {Biological Trajectory of Virophage Research and the Emergence of Marine Virophages: A Scoping Review.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, pmid = {42198763}, issn = {1999-4915}, support = {RS-2021-KS211475//Korea Institute of Marine Science and Technology Promotion/ ; }, mesh = {*Virophages/genetics/physiology ; Genome, Viral ; Giant Viruses/genetics ; *Aquatic Organisms/virology ; Seawater/virology ; Metagenome ; Virus Replication ; }, abstract = {Virophages are satellite viruses that depend on the replication machinery of giant double-stranded DNA viruses and influence the structure and dynamics of viral communities through multilayered interactions among giant viruses, their hosts, and virophages. Since the discovery of the Sputnik virophage in 2008, virophages have been increasingly recognized for their roles in regulating giant virus replication, contributing to host defense mechanisms, and shaping the evolution of mobile genetic elements. However, quantitative syntheses examining how virophage research has developed over time, particularly in marine environments, remain limited. Here, we conducted a bibliometric analysis of virophage research published between 2008 and 2025 using the Web of Science Core Collection. By comparing an overall virophage research corpus with a marine virophage sub-corpus, we assessed publication and citation trends, collaboration structures, and keyword-based intellectual and thematic evolution. Our results show that virophage research has gradually transitioned from an early phase dominated by landmark discoveries and experimental model systems to a data-intensive stage driven by genome- and metagenome-based analyses and computational approaches. Although marine virophage studies represent a relatively small proportion of the total literature, they exhibit sustained citation impact and form a distinct research axis within the field. In particular, marine-focused studies emphasize metagenomic discovery, genome sequence alignment, and the analysis of mobile genetic elements such as polinton-like viruses, highlighting the role of marine environments in accelerating the intellectual transition of virophage research. Collectively, these findings demonstrate that virophage research has moved beyond a "discovery and definition" phase toward data-driven integrative interpretation, with marine virophage research emerging as a key domain for understanding the structure and evolutionary dynamics of marine viral ecosystems.}, } @article {pmid42199008, year = {2026}, author = {Lépine, G and Davila, AM and Cueff, G and Pickering, G and Ichou, F and Perreau, C and Lefranc-Millot, C and Gilles, M and Thirion, F and Mariotti, F and Rémond, D and Fouillet, H and Polakof, S}, title = {Increasing plant protein sources in the diet modulates gut microbiota and tryptophan metabolism in men at cardiometabolic risk.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2677951}, pmid = {42199008}, issn = {1949-0984}, mesh = {Humans ; Male ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cross-Over Studies ; Middle Aged ; *Plant Proteins/metabolism/administration & dosage ; Adult ; Diet ; Cardiometabolic Risk Factors ; Metabolome ; Indoles/metabolism ; Bacteria/classification/isolation & purification/genetics/metabolism ; }, abstract = {This study investigated the effect of partially substituting dietary animal with plant protein (PP) sources on the fecal microbiota composition and metabolome in men with increased cardiometabolic risk. In a randomized, controlled, crossover feeding trial (NCT04236518), 19 men with high plasma triglycerides and waist circumference completed two 4-week isoenergetic diets: a flexitarian diet high in PP sources (FLEX, 64% PP) and a more animal-based control diet (CON, 36% PP). Fecal microbiota (shotgun metagenomics: taxa and metabolic pathways) and metabolome (targeted LC-MS) profiles were assessed before and after each diet and integrated with the host plasma metabolome. Delta values (Δd28-d1) were computed (n = 15 participants with all samples available), inter-individual variation was extracted to account for cross-over design, and OPLS-DA analyses comparing FLEX and CON Δd28-d1 were performed. Variables were selected based on their contribution to the diet discrimination effect (VIP > 1.5) and significant differences between groups (p-value < 0.05 from the paired Wilcoxon signed-rank test). The gut microbiota diversity remained unchanged, but FLEX reduced taxa associated with animal-based diets (e.g., Alistipes putredinis). Compared to CON, FLEX increased fecal xanthurenic acid and decreased the genetic potential for indole production. Combined with previously reported plasma changes (increased indole propionic acid and decreased indoxyl sulfate after FLEX), these findings suggest a shift away from indole production toward kynurenine and indole propionic acid-related tryptophan pathways, possibly driven by higher fiber intake, particularly from legumes. A one-month flexitarian diet thus modulated in men specific microbial taxa and metabolism, particularly tryptophan catabolism. These coordinated changes in microbial composition, functional potential, and metabolites indicate that diets higher in PP sources influence gut microbiota activities relevant to cardiometabolic health.}, } @article {pmid42199353, year = {2026}, author = {Bergot, M and Lefevre, CT and Grouzdev, DS and Menguy, N and Ortet, P and Denis, Y and Viollier, E and Jézéquel, D and Monteil, CL}, title = {Magnetotactic Bdellovibrionota from a ferruginous spring.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag116}, pmid = {42199353}, issn = {2730-6151}, abstract = {Magnetotactic bacteria form a highly diverse group of microorganisms, yet early exploration of their diversity was largely centered on the Pseudomonadota. More recently, metagenomic studies have revealed that magnetotaxis, a form of chemotaxis guided by Earth's magnetic field, is widespread in other deep-branching phyla for which little to no ecological or biological information is available beyond that inferred from their genomes. For most of them, the morphology, ultrastructure and magnetosome chain characteristics responsible for the magnetic guidance remain unknown. While screening extreme environments for novel magnetotactic species, we observed magnetotactic Bdellovibrionota in the anoxic and ferruginous sediments of the Fontaine Goyon spring (France). We characterized their cell morphology and ultrastructure using magnetic enrichment, a single-cell sorting approach, and high-resolution electron microscopy. Cells display the morphology typical of the few predatory bacteria described in this phylum, and biomineralize, on average, five irregularly faceted, bullet-shaped magnetite magnetosomes along the concave side of the cell. Metagenomic analysis of approximately 100 cells revealed a potentially predatory and heterotrophic lifestyle adapted to low-O2 conditions. It also suggests a flexible respiratory metabolism under varying redox conditions, using iron as an alternative terminal electron acceptor. Exploring the diversity of Bdellovibrionota in public databases, we found 21 metagenome-assembled-genomes containing magnetosome genes. None of them harbor the canonical mamK actin-like gene implicated in aligning magnetosomes in described magnetotactic models. Affiliated to an undescribed class, we propose a classification scheme for the magnetotactic Bdellovibrionota species representing the class Bdellonasia class nov., for which no species had been formally described.}, } @article {pmid42199424, year = {2026}, author = {Zhao, L and Wang, Q and Chen, J and Wang, J}, title = {Multi-omics analyses reveal significant differences in the gut microbiota and metabolites in children with Kawasaki disease in Northwest China.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1767902}, pmid = {42199424}, issn = {1664-3224}, mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/metabolism ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Child, Preschool ; Metagenomics/methods ; China/epidemiology ; *Metabolome ; Metabolomics/methods ; Infant ; Feces/microbiology ; Bacteria/classification/genetics ; Child ; }, abstract = {BACKGROUND: Kawasaki disease (KD) is a systemic vasculitis characterized by mucocutaneous lymph node syndrome and aberrant immune activation. Previous studies have indicated substantial disruptions in the gut microbiota during the acute phase of KD. However, the detailed characteristics of the gut microbiota and metabolome in children with KD, as well as their clinical relevance, remain poorly understood.

METHODS: 31 children with KD (KDs) and age/sex-matched healthy controls (HCs) were enrolled to collect their fecal and blood samples. Shotgun metagenomic sequencing and untargeted metabolomic analyses were conducted on these samples.

RESULTS: Significant reductions in alpha diversity and microbial richness were observed in the gut microbiota of KDs at both species and genus levels. Pathogenic species including Enterococcus avium, Streptococcus peroris and Clostridioides difficile were significantly abundant in the KDs group, while beneficial species containing Faecalibacterium prausnitzii, Anaerostipes hadrus, Akkermansia muciniphila, Eubacterium hallii, Agathobaculum butyriciproducens, Ruminococcus bicirculans, and Roseburia intestinalis were markedly decreased. A total of 49 metabolic pathways were differentially enriched between the two groups, with 22 pathways including nucleotide, carbohydrate, energy, and amino acid metabolism being abundant in KDs, while the other 27 pathways were enriched in HCs. For metabolites, both fecal and blood metabolomes exhibited significant alterations. Notably, fecal metabolites including indole, L-tryptophan, L-lactic acid, 5-HETE, indol-3-acetamid, tetraethylammonium and dopaquinone were elevated in KDs, whereas butyrate, methylxanthine, phosphocholine, methylhistidine, ADP-ribose, vitamin A acid, and chenodeoxycholic acid were reduced. In plasma, cholesterol, phosphocholine, porphobilinogen, pantothenate, cortisol, bile acids and related compounds were enriched in KDs, while amino acids, indole and tryptamine derivatives, nucleotides, nucleic acids, and sugar metabolites were more abundant in HCs.

CONCLUSIONS: This study represents the first systematic multi-omics investigation of KD in a pediatric population from Northwest China. It establishes a foundational resource characterizing the gut microbiome and metabolome in KD, offering novel biological insights, suggesting potential therapeutic targets, and supporting further mechanistic and clinical research.}, } @article {pmid42199698, year = {2026}, author = {Li, Q and Wang, X and Zhang, S and Wang, H and Li, X and Zhao, F}, title = {mNGS-Supported Interpretation of Staphylococcus pettenkoferi Bloodstream Infection After Intracerebral Hemorrhage: A Case Report.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {611927}, pmid = {42199698}, issn = {1178-6973}, abstract = {PURPOSE: Staphylococcus pettenkoferi is an uncommon coagulase-negative staphylococcus whose recovery from blood may be difficult to interpret because of the frequent contamination associated with this bacterial group. We report a case in which peripheral-blood metagenomic next-generation sequencing (mNGS) and repeated blood cultures supported clinically significant bloodstream infection after intracerebral hemorrhage.

PATIENTS AND METHODS: We described the clinical course, imaging findings, microbiological results, and antimicrobial management of an 85-year-old man admitted to the intensive care unit after intracerebral hemorrhage with intraventricular extension. Peripheral-blood mNGS and two sets of peripheral blood cultures were obtained during early fever evaluation.

RESULTS: Peripheral-blood mNGS, performed on samples obtained immediately after ICU admission and before neurosurgical intervention or intracranial device placement, detected S. pettenkoferi within 24 h. At 72 h, both peripheral blood culture sets yielded the same organism. Concordant results from mNGS and repeated peripheral blood cultures, together with the clinical context, supported clinically significant bloodstream infection rather than simple contamination. The respiratory tract was considered a presumed source in the setting of clinically suspected aspiration-related pulmonary infection, although it was not microbiologically confirmed.

CONCLUSION: This case highlights the need for cautious interpretation of uncommon coagulase-negative staphylococci recovered from blood. Peripheral-blood mNGS may provide early etiologic support, but conventional blood culture remains essential for confirmation and antimicrobial susceptibility testing.}, } @article {pmid42200417, year = {2026}, author = {Lin, L and Gao, G and Sun, S and Wu, X and Fan, S and Wang, H and Zhou, F and Zhang, X}, title = {Host-independent metagenomics reveal gut bacteria contribution to Delia antiqua growth by vitamin B6 provision.}, journal = {Insect molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imb.70046}, pmid = {42200417}, issn = {1365-2583}, support = {2024KJI002//Young Innovation Team Project of Higher Education in Shandong Province/ ; 2024ZDZX10//QLU Major Innovation Projects of Education-Industry Integration Pilot/ ; SDAIT-31-04//Shandong Province Key Agricultural Project for Application Technology Innovation/ ; 32272530//National Natural Science Foundation of China/ ; }, abstract = {Insect guts host a diverse and abundant array of microorganisms. These microbes improve host fitness by extensively involving in a range of crucial physiological processes, which have mainly been revealed by high-throughput sequencing, particularly metagenomics. However, it is almost impossible to make an accurate and complete distinction between the genetic functions of microbial symbionts and insect hosts without host genome data. By comparing metagenomic data from gut germ-free and nonaxenic larvae, we accurately identified the data belonging to the gut microbiome of the onion maggot Delia antiqua (Diptera: Anthomyiidae). Besides, a correlation between bacteria of the genus Wohlfahrtiimonas (Gammaproteobacteria: Pseudomonadaceae) and vitamin B6 metabolism was detected through collinearity analysis. Furthermore, in vitro tests confirmed that the gut bacterium Wohlfahrtiimonas larvae contributed to the growth of D. antiqua larvae via the independent synthesis of vitamin B6. This study provides a comprehensive view of the gut bacterial diversity in D. antiqua and reveals a functional profile that is strictly specific to the gut microbiota of this species. It has preliminarily revealed the functional differentiation between insect hosts and their symbiotic microorganisms. This study also offers a technical reference for the study of microbial symbiotic functions in other insect-microbe symbioses without host genomic data.}, } @article {pmid42200512, year = {2026}, author = {Vergara, E and Khaleque, HN and Neira, G and Watkin, ELJ and Valdés, JH and Holmes, DS}, title = {Sulphur metabolism as a key factor in the evolution of environmental adaptation of Acidihalobacter.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001732}, pmid = {42200512}, issn = {2057-5858}, mesh = {Phylogeny ; *Sulfur/metabolism ; *Adaptation, Physiological/genetics ; *Rhodobacteraceae/genetics/metabolism/classification ; Genome, Bacterial ; Evolution, Molecular ; Hydrothermal Vents/microbiology ; Australia ; Oxidation-Reduction ; Italy ; Metagenome ; Pacific Ocean ; Bacterial Proteins/genetics/metabolism ; }, abstract = {This study compares predicted sulphur metabolism genes across four Acidihalobacter type strains and two metagenome-assembled genomes (MAGs), revealing genomic differences that appear to correspond to ecological specialization. Phylogenomic analysis separates the species into two clades: clade I includes Acidihalobacter ferrooxydans from a geothermal region in Italy and the two MAGs derived from deep-sea hydrothermal vents in the Pacific Ocean, while clade II comprises Acidihalobacter aeolianus and Acidihalobacter prosperus from a geothermal region in Italy and Acidihalobacter yilgarnensis from a saline and acidic drainage in Australia. Variations in sulphide/quinone oxidoreductases (SQRs) across the species, in particular in Ah. ferrooxydans and Ah. yilgarnensis, likely relate to the availability and speciation of sulphur substrates, which are strictly governed by local redox potential (Eh) and metal redox cycling in their respective habitats. Notably, only Ah. ferrooxydans (clade I) lacks the canonical sulphur/thiosulphate oxidation (Sox) system for thiosulphate oxidation found in clade II and instead encodes components of an alternative S4I pathway. We hypothesize that this difference reflects an adaptation to dynamic microniches going from highly reduced (sulphide-rich) to oxidized metastable sulphur intermediates. In contrast, the retention of the Sox system in clade II suggests a distinct strategy permitting greater metabolic versatility under fluctuating Eh-pH conditions.Differences in clade I terminal oxidases (cbb3-type cytochrome, bc1 complex) and regulatory elements appear to support further adaptation to environments with elevated H2S, setting this clade apart from clade II members. These adaptations, mainly evidenced by gene redundancy, gene loss and horizontal gene transfer, seem to reflect a unique ecological microniche and evolutionary trajectory for Ah. ferrooxydans distinct from other members of the genus, particularly from a sulphur-based energy metabolism perspective.}, } @article {pmid42200521, year = {2026}, author = {Wright, RJ and Fisher, BR and Comeau, AM and Langille, MGI}, title = {From classification to confirmation: verifying taxonomic classifications by mapping metagenomic reads to reference genomes.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001739}, pmid = {42200521}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Bacteria/classification/genetics ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Microbiota/genetics ; }, abstract = {Obtaining high precision while maintaining high recall is an ongoing problem for metagenomic taxonomic classification in microbial ecology research. Parameter adjustments can achieve this in simulated samples, but in real samples - especially from environments like marine and soil - the proportion of classified reads drops sharply with precision increases. We, therefore, suggest verification of metagenomic taxonomic classifications obtained from a tool like Kraken by mapping their assigned reads to reference genomes to assess genomic coverage. In simulations, filtering the identified species to only those with ≥0.5% reference genome coverage removed 99.7% of false-positive taxa. Applying this method to samples from real datasets requires a more nuanced approach that considers sequencing depth, whether the samples are high- or low-microbial biomass, and database completeness with respect to the sampled environment. Nevertheless, we show that clinically relevant Kraken-identified taxa, such as Helicobacter pylori identified in human stool samples, lack any reads mapping to their reference genome and are likely false positives driven by contaminating phage sequences within reference genomes. Similarly, in human blood and lung tumour datasets, only 18 and 11 species, respectively, have ≥1% reference genome coverage and likely represent sample collection or sequencing contaminants. Marine and soil samples pose additional challenges due to lower representation in reference databases, leading to low nucleotide identity between sequenced reads and reference genomes and similarity only at higher taxonomic ranks. We recommend genome coverage checking to researchers in all fields of microbial ecology and provide an open-source pipeline on GitHub (GeCoCheck): https://github.com/R-Wright-1/GeCoCheck.}, } @article {pmid42200658, year = {2026}, author = {Blanchard, JL}, title = {Learning R with generative AI in a metagenomic data science course.}, journal = {Journal of microbiology & biology education}, volume = {}, number = {}, pages = {e0034325}, doi = {10.1128/jmbe.00343-25}, pmid = {42200658}, issn = {1935-7877}, abstract = {Generative artificial intelligence (AI) tools are increasingly used by students in introductory coding courses; however, evidence-based guidance for integrating these tools into biology education remains limited. We examined student experiences with generative AI in a beginner R programming course focused on metagenomic data analysis. An anonymous survey (n = 43) captured quantitative ratings and qualitative reflections on how AI influenced learning, productivity, and problem-solving practices. Most respondents entered the course with little to no prior coding experience (79%) and reported frequent AI use throughout the semester, indicating that AI quickly became embedded in students' workflows. Students rated AI as highly helpful for suggesting R code, explaining syntax and logic, and brainstorming analyses, with over 70% endorsing each use case. However, AI errors were common: over 90% of students encountered incorrect output at least sometimes, including domain-specific misinterpretations and overcomplicated or syntactically incorrect code. Notably, students identified a need for clearer instructional support in core AI-mediated practices. The most frequent recommendation for course redesign was to introduce foundational R concepts prior to AI use, highlighting a threshold-competency principle for effective AI integration. Together, these findings suggest that generative AI can support novice coders but does not substitute for foundational instruction. Effective AI integration requires deliberate pedagogical scaffolding and reflection rather than code generation alone. These principles are likely to remain critical as AI tools become more capable and more widely adopted in undergraduate biology education.}, } @article {pmid42200756, year = {2026}, author = {Harrison, LB and Sohani, ZN and Lasry, D and Cheng, MP and Lee, TC and Babiker, A and Kadri, SS and Lawandi, A}, title = {Rapid Microbiological Diagnostics for Sepsis: Narrative Review of Current and Prospective Approaches.}, journal = {Critical care explorations}, volume = {8}, number = {6}, pages = {e1415}, pmid = {42200756}, issn = {2639-8028}, mesh = {Humans ; *Sepsis/diagnosis/microbiology ; Blood Culture/methods ; Molecular Diagnostic Techniques/methods ; *Microbiological Techniques/methods ; Rapid Diagnostic Tests ; }, abstract = {OBJECTIVES: In this review, we aim to provide critical care clinicians with a concise introduction to the current and prospective tools that exist for rapid diagnostics in sepsis employed in the microbiology laboratory. Our objective is to provide a primer for clinicians to engage with their colleagues in the microbiology laboratory for the selection and implementation of new and emerging tools.

DATA SOURCES: The primary literature, restricted to peer-reviewed sources, was queried using relevant search terms (e.g., sepsis, rapid diagnostics, microbiology, etc) using PubMed and Google Scholar (until February 2025), as well as review of citations of relevant articles.

STUDY SELECTION: After initial searches, literature was screened by each author responsible for the sections of this review: blood culture-based methods (L.B.H.), nonblood culture-based molecular diagnostics (D.L.), and antigen-based methods (Z.N.S.). Titles and abstracts of individual articles were reviewed by the respective section authors and articles describing microbiological diagnostic techniques that decrease the turnaround time for the identification of microorganisms and/or antimicrobial susceptibility testing with relevance to the diagnosis of sepsis were retained.

DATA EXTRACTION: Data from individual studies was extracted by each respective section author using Zotero reference management software and synthesized narratively.

DATA SYNTHESIS: Rapid diagnostics for sepsis can be broadly divided into three categories: those applied to incubated positive blood culture specimens, and culture-independent approaches applied directly to clinical specimens, which can be further divided into those based on the direct detection of the nucleic acids of microorganisms, and those based on the detection of antigens. Blood culture-based approaches rely on biological amplification of microorganisms present but aim to measure this amplified signal directly to speed identification of microorganisms or antimicrobial resistance relative to traditional plate-culture-based workflows. Nucleic acid and antigen detection methods can be performed directly on clinical specimens, and so promise more rapid diagnostics in sepsis, but with method-specific tradeoffs in sensitivity, specificity, and interpretation.

CONCLUSIONS: Evolutionary refinements of blood culture-based diagnostic approaches have decreased time to actionable information significantly while emerging and established culture-independent approaches can reduce time to actionable information to a few hours. In aggregate these interventions may have important clinical benefits, yet significant heterogeneity exists in the applicability and availability of technologies.}, } @article {pmid42201023, year = {2026}, author = {Rehman, A and Awais, M and Baloch, HNUA and Leghari, MO and Ahmad, A and Javed, H}, title = {Sputum Liquid Biopsy for Lung Cancer Screening, Diagnosis, Subtyping, Surveillance, Response Prediction, and Prognostication: A Scoping Review.}, journal = {Medical sciences (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {42201023}, issn = {2076-3271}, mesh = {Humans ; *Lung Neoplasms/diagnosis/pathology/metabolism ; *Sputum/metabolism ; Liquid Biopsy/methods ; Biomarkers, Tumor ; Prognosis ; *Early Detection of Cancer/methods ; }, abstract = {Background/Objectives: Liquid biopsy (LB) is transforming cancer care by enabling minimally invasive tumor profiling. While current research and clinical pathways mostly focus on blood LB, sputum represents a non-invasive, readily available respiratory specimen that may offer unique advantages for lung cancer (LC) care. Despite its potential, the maturity, breadth, and clinical applicability of sputum-based LB remain elusive. Methods: We conducted a scoping review to systematically map the existing literature on sputum LB in LC. Electronic databases were searched for studies evaluating sputum-derived biomarkers-cytologic, genomic, epigenetic, transcriptomic, proteomic, metabolomic, metagenomic, and extracellular vesicle-derived products-across the LC care continuum. Study designs, technologies, clinical contexts, and reported outcomes were extracted and synthesized qualitatively. Results: The literature demonstrated substantial heterogeneity in sputum collection, processing, and analytical platforms. Early work focused on cytometry and genetic alterations, while recent studies increasingly explore DNA methylomics, microRNAs, extracellular vesicle-derived products, and multi-omics approaches. The evidence suggests potential utility of sputum biomarkers for early detection and risk stratification, particularly in high-risk populations, with emerging data supporting roles in molecular subtyping, response monitoring, prognostication, and surveillance. However, few studies report prospective validation, direct comparison with blood-based LB, or impact on actual patient outcomes. Conclusions: Sputum LB is a promising yet underdeveloped modality in LC care. This scoping review highlights technological innovations alongside significant methodological heterogeneity and translational gaps. Future research should focus on standardization, prospective validation, impact on patient outcomes, and integration with blood- and other body fluid-based LB, as well as imaging biomarkers. This will enable incorporation of sputum-based LB into actual clinical pathways of LC care.}, } @article {pmid42201143, year = {2026}, author = {Zhang, W and Eleftherianos, I and Mohamed, A and Smagghe, G and Chakkalakkal, G and Al-Akeel, R and Toprak, U and Tettamanti, G and Keyhani, N and Renault, D}, title = {Evolution, multifunctionality, and agricultural potential of insect microbiomes and the holobiont concept.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag137}, pmid = {42201143}, issn = {1751-7370}, abstract = {Insect-associated microbiomes, as co-evolved members of the holobiont, play pivotal roles in host physiology, ecological resilience, and evolutionary innovation. This review synthesizes recent advances in understanding microbial symbionts' contributions to metabolic adaptation, insecticide detoxification, and immune modulation. Framed within hologenome theory-which posits host-microbe assemblages as units of natural selection-we explore co-evolutionary dynamics driving mutualistic specialization and adaptive plasticity. Cutting-edge tools like genome editing and metagenomics reveal how gut microbiota mediate cross-kingdom interactions, insecticide resistance, and reproductive fitness. Intriguingly, microbial symbionts can enhance host resistance through detoxification while sensitizing hosts to specific toxins, highlighting context-dependent trade-offs. Targeted manipulation of microbial consortia-via detoxification disruption or symbiont engineering-offers new avenues for sustainable pest control, though ecological risks demand rigorous biosafety protocols. A paradigm shift toward holobiont-centered models promises unified strategies for sustainable agriculture and biodiversity conservation in the Anthropocene.}, } @article {pmid42201824, year = {2026}, author = {Lin, X and Asif, M and Li, W and Zhang, B and Li, Y and Yu, Y and Jiang, X}, title = {Long-Term Straw Return Reverses Antibiotic Resistance Accumulation in Maize Rhizosphere through Integrated Soil-Microbial Mechanisms.}, journal = {Environmental science & technology}, volume = {60}, number = {22}, pages = {15544-15556}, doi = {10.1021/acs.est.5c11371}, pmid = {42201824}, issn = {1520-5851}, mesh = {*Zea mays ; *Rhizosphere ; *Soil Microbiology ; Fertilizers ; Soil/chemistry ; *Drug Resistance, Microbial ; Agriculture ; Pseudomonas ; }, abstract = {The impact of long-term agricultural cultivation on antibiotic resistance has emerged as a critical environmental concern. However, previous studies have primarily examined organic fertilizers, and the effects of sustained chemical fertilizer use combined with straw incorporation over extended periods remain poorly understood. Here, we employed a 25-year field trial combined with metagenomic analysis to investigate the differential effects of chemical fertilization and straw incorporation on soil antibiotic resistance gene (ARG) dynamics in the maize rhizosphere. Results showed that long-term cultivation progressively increased ARG and virulence factor gene (VFG) abundance. Metagenomic analyses suggested that shifts in Pseudomonas populations and microbial metabolic pathways were associated with elevated levels of ARGs in the rhizosphere. Field inoculation with a synthetic Pseudomonas community further increased the ARG abundance, accompanied by reduced genomic GC content and enrichment of specific metabolic pathways. In contrast, straw amendment treatments reduced Pseudomonas abundance and soil acidification while increasing the soil total carbon and lignin degradation functional capacity. Our findings indicate that long-term straw incorporation represents a promising strategy for controlling antibiotic resistance dissemination in agricultural systems, offering valuable insights into sustainable crop management practices.}, } @article {pmid42201863, year = {2026}, author = {Kaptan, D and Flemming Elvers, AC and Kjær Knudsen, A and Schroeder, H and Hollund, HI}, title = {Histological and metagenomic analysis of microbial communities in archaeological human bones.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0340244}, pmid = {42201863}, issn = {1932-6203}, mesh = {Humans ; *Bone and Bones/microbiology/pathology ; *Metagenomics/methods ; *Archaeology ; *Microbiota/genetics ; Bacteria/genetics/classification ; Fungi/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Norway ; Phylogeny ; }, abstract = {Buried archaeological bones tend to be heavily degraded by microorganisms. This type of biodegradation was already identified in the 19th century and remains a subject of continuous investigation. However, the underlying processes are still not fully understood, and the organisms responsible for the decay have not been clearly identified. Technological advances in genetic sequencing now allow detailed study of the bone microbiome. And yet, identifying the species causing the observed bioerosion has proven challenging. Relatively few studies have combined the investigation of bone degradation by microscopy, so-called histotaphonomy, with metagenomic analyses. This study aims to bridge this gap. We utilize a large set of human bone samples from medieval cemeteries in south-western Norway. Detailed microscopic analyses have been carried out, showing diverse levels of preservation. The extent of bioerosion is correlated with the results from metagenomic analyses as well as environmental factors. Microbiome diversity is greater and more evenly distributed in well-preserved bones with limited bioerosion, particularly those recovered from burials beneath church floors, contrasting with outdoor cemeteries. Fungal taxa were detected in only a single sample in the metagenomic data despite histological evidence of fungal structures, and their role in bone bioerosion remains unclear. Our findings show that preservation state is strongly associated with microbiome composition. The most prevalent genus found was Streptomyces, supporting previous research suggesting that bacteria within this group could be involved in bone bioerosion.}, } @article {pmid42201897, year = {2026}, author = {, }, title = {Editorial Note: Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0350242}, pmid = {42201897}, issn = {1932-6203}, } @article {pmid42202516, year = {2026}, author = {Sun, X and Lin, Z and Ni, SQ}, title = {Multidrug-resistant bacteria contribute to core bacterial community and ARGs persistence during full-scale pharmaceutical wastewater treatment.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142513}, doi = {10.1016/j.jhazmat.2026.142513}, pmid = {42202516}, issn = {1873-3336}, mesh = {*Wastewater/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Bacteria/genetics/drug effects ; *Genes, Bacterial ; Waste Disposal, Fluid ; Drug Industry ; Water Pollutants, Chemical ; }, abstract = {Pharmaceutical wastewater treatment plants (WWTPs) are confronted with a wide range of contaminants, resulting in the accumulation of antibiotic resistance genes (ARGs) and the evolution of multidrug-resistant (MDR) bacteria. However, the ecological roles of these MDR residents during full-scale wastewater treatment remain unclear. In this study, the core bacterial communities as well as potential MDR bacteria for industrial WWTPs were firstly categorized out. Taxa belonging to MDR bacteria were frequently detected to persist with low relative abundance across different treatment units, even in the effluent. Then, the occurrence and health risk of ARGs were evaluated. Certain abundant and prevalent ARGs, such as fabG, macB, and adeF, were found to exhibit high prevalence. Some pivotal mobile genetic elements, acting as key network hubs, can link MDR bacteria with a broad range of ARGs. Finally, the result showed that several metagenome-assembled genomes recovered from the effluents were not only classified as MDR bacteria harboring ARGs with high risk, but also served as important members of the core bacterial community. These findings provide critical insights into the ecological roles of MDR bacteria during the full-scale pharmaceutical wastewater treatment, and emphasize the urgent need for real-time monitoring of wastewater-borne MDR bacteria for ecological health.}, } @article {pmid42202519, year = {2026}, author = {Li, X and Wang, Y and Dang, X and Zhang, Y and Zhao, C and Hou, S and Li, B and Ma, F and Hao, L and Zhu, T}, title = {Molecular mechanism by which high temperature and RecBCD synergistically lower strand-separation barriers and promote destabilization of representative efflux-pump ARG fragments (macB/tetA) during hyperthermophilic composting.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142445}, doi = {10.1016/j.jhazmat.2026.142445}, pmid = {42202519}, issn = {1873-3336}, mesh = {*Hot Temperature ; *Composting ; *Bacterial Proteins/genetics ; Molecular Dynamics Simulation ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents ; Metagenomics ; Antiporters ; }, abstract = {Hyperthermophilic composting (HC) effectively mitigates antibiotic residues and antibiotic resistance genes (ARGs), yet the molecular basis of ARG-derived DNA destabilization under extreme heat remains unclear. Here, we established an HC system reaching 87.3 ℃ (∼360 K) and combined metagenomics, AlphaFold prediction, molecular dynamics (MD), and free-energy calculations to investigate representative efflux-pump ARG fragments (macB/tetA). HC removed oxytetracycline, enrofloxacin, and sulfamethoxazole by 98.44%, 92.34%, and 99.63%, respectively, while overall ARG abundance declined markedly. Metagenomics identified 796 ARGs, dominated by efflux mechanisms, and qPCR confirmed multi-order decreases in macB and tetA. Nucleic acid processing/degradation genes, including recD/RecBCD-related homologs, were enriched during the high-temperature phase and negatively associated with ARG abundance. Based on these data, we constructed a candidate RecBCD model from metagenomic recB/recC/recD homologs. MD showed that this model maintained overall structural integrity at 360 K. AlphaFold predicted end-loaded candidate RecBCD-DNA complexes (ipTM/pTM ≈ 0.89-0.90) with local duplex opening. Subsequent MD revealed that RecBCD-bound DNA became more flexible, displayed weakened/reorganized hydrogen-bond networks, and sampled more multistate free-energy basins. Umbrella sampling further showed that strand-separation PMFs at 360 K were ∼25-30 kJ·mol[-1] lower than at 330 K, with tetA exhibiting a lower barrier and greater thermal sensitivity than macB. Together, these results support a working model in which high temperature lowers DNA stability and strand-separation barriers, thereby facilitating candidate RecBCD-mediated loading and local processing of representative efflux-pump ARG-derived DNA fragments during HC.}, } @article {pmid42202778, year = {2026}, author = {Nogal, A and Wang, K and Thompson, KN and Kim, H and Bhosle, A and Piccinno, G and Maharjan, S and Upreti, C and Nguyen, LH and Segata, N and Rimm, EB and Garrett, WS and Chan, AT and Huttenhower, C and Song, M}, title = {Long-lasting gut microbiome and fecal metabolome alterations after colorectal adenoma removal and their relationship to colorectal cancer.}, journal = {Cell host & microbe}, volume = {34}, number = {6}, pages = {1135-1150.e6}, doi = {10.1016/j.chom.2026.05.001}, pmid = {42202778}, issn = {1934-6069}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/surgery/metabolism ; Female ; *Feces/microbiology/chemistry ; *Adenoma/microbiology/surgery ; *Metabolome ; *Gastrointestinal Microbiome ; Case-Control Studies ; Middle Aged ; Aged ; Metagenomics ; Metagenome ; }, abstract = {Although the gut microbiome is implicated in colorectal cancer (CRC), microbiome and metabolome alterations along the adenoma-carcinoma sequence remain unclear. Here, we profile stool metagenomes obtained from 354 women 12.1 ± 4.8 years following adenoma resection and from their 1:1-matched controls, as well as stool metabolomes from 184 pairs. Metagenomic profiles are compared with those from 14 independent CRC case-control studies. Microbial composition differs between adenoma cases and controls and agrees with CRC-associated alterations (Pearson's rho = 0.26, p < 0.0001). Thirty-one microbes, including Faecalibacterium prausnitzii and Flavonifractor plautii, are altered in both conditions and correlate with lifestyle factors. Thirty metabolites and 7 sub-pathways, particularly sphingolipids, are associated with adenomas. Adenomas also exhibit disease-specific microbe-metabolite associations, including those between Bilophila wadsworthia and alanine-containing dipeptides. These findings reveal gut microbial and metabolomic alterations detectable years after adenoma resection, supporting the presence of an altered microbiome along the adenoma-CRC continuum.}, } @article {pmid42202790, year = {2026}, author = {Toubon, G and Boulund, F and Escobedo, CM and Brunius, C and Engstrand, L and Larsson, SC and Nordin, E and Schuppe-Koistinen, I and Wolk, A and Wittenbecher, C and Landberg, R}, title = {Gut microbiome composition and functional potential associate with incident type 2 diabetes in 4,685 adults from a Swedish prospective cohort.}, journal = {Cell reports. Medicine}, volume = {7}, number = {6}, pages = {102835}, doi = {10.1016/j.xcrm.2026.102835}, pmid = {42202790}, issn = {2666-3791}, mesh = {*Diabetes Mellitus, Type 2/microbiology/epidemiology ; Humans ; Female ; Sweden/epidemiology ; *Gastrointestinal Microbiome/genetics ; Aged ; Prospective Studies ; Male ; Incidence ; Eubacteriales ; }, abstract = {Cross-sectional studies link gut microbiome alterations to type 2 diabetes (T2D), but prospective evidence remains limited. We aim to identify taxonomic and functional features associated with future T2D risk. We analyze shotgun metagenomic data from 4,685 participants (mean age, 73.9 years; 49.0% women) in the Swedish SIMPLER cohort, followed for a median 5.3 years, during which 383 developed T2D. Six species are associated with increased T2D risk: Desulfovibrio piger, Alistipes communis, Alistipes finegoldii, Akkermansia muciniphila, Ruminococcus gnavus, and GGB3614_SGB4886 (Lachnospiraceae), while three are protective: Erysipelotrichaceae bacterium, Coprococcus catus, and Clostridia unclassified SGB6317. We observe context-specific associations, including a dietary fiber-modified effect for A. muciniphila indicative of diet-dependent patterns. Three gut metabolic modules are associated with incident T2D: asparagine degradation (higher risk), mannose degradation, and the non-oxidative pentose phosphate pathway (lower risk). These prospective findings offer insights into T2D etiology and may support microbiome-informed strategies for risk prediction and prevention.}, } @article {pmid42203111, year = {2026}, author = {Wang, L and Bai, L and Li, H and Zhang, P and He, F}, title = {A case of imported infection in China: Initially treatment-unresponsive schistosomiasis coinfection with bladder tuberculosis.}, journal = {Indian journal of medical microbiology}, volume = {62}, number = {}, pages = {101157}, doi = {10.1016/j.ijmmb.2026.101157}, pmid = {42203111}, issn = {1998-3646}, abstract = {Schistosoma haematobium, endemic to sub-Saharan Africa, causes urogenital disease, differing from Schistosoma japonicum, which affects the hepatointestinal system and is the only endemic schistosome in China. A Chinese male with persistent hematuria after prolonged occupational exposure in Angola was initially attributed to S. japonicum. Following failed treatment, metagenomic sequencing confirmed S. haematobium infection, and subsequent urethral resection detected Mycobacterium tuberculosis DNA, establishing concurrent bladder tuberculosis. This case highlights the need for molecular diagnostics in patients with hematuria after sub-Saharan exposure and the immunomodulatory risks posed by helminth infections.}, } @article {pmid42203372, year = {2026}, author = {McCann, P and Megaw, J and Gobert, GN}, title = {Parasite-associated microbiomes: An unseen microenvironment.}, journal = {Advances in parasitology}, volume = {131}, number = {}, pages = {31-70}, doi = {10.1016/bs.apar.2026.03.001}, pmid = {42203372}, issn = {2163-6079}, mesh = {Animals ; Humans ; *Microbiota ; *Host-Parasite Interactions ; *Parasites/microbiology/physiology ; Symbiosis ; }, abstract = {Parasites harbor diverse microbial ecosystems that include not only bacteria but also archaea, fungi, viruses and microbial eukaryotes. These parasite-associated microbiomes, long overlooked, are now recognized as important determinants of parasite development, fitness, virulence and interactions with hosts across medical, veterinary, agricultural and ecological systems. However, current understanding of parasite-associated microbiomes remains fragmented, with most studies focusing on a narrow set of human parasites, relying heavily on bacterial surveys and rarely capturing the full multi-kingdom diversity of microbial partners. Important challenges include expanding research to encompass neglected parasite groups and their non-bacterial associates, establishing causal links between microbiome members and parasite phenotypes, and overcoming the technical barriers posed by low-biomass, host-contaminated and/or experimentally intractable systems. Progress will also depend on developing robust reference genomes and analytical tools that can resolve multi-kingdom communities and integrate parasite and symbiont biology. This chapter synthesizes current knowledge across helminths, protozoa, ectoparasites and plant-infecting parasites. We consider how microbiome manipulation may contribute to parasite control while recognizing the evolutionary and ecological complexities involved in altering host-parasite-microbiome interactions. Embracing an explicitly multi-kingdom, holobiont-focused perspective promises to illuminate fundamental aspects of parasitism. Such knowledge may contribute to new avenues for mitigating the impact of parasitic diseases on human and animal health, food security and ecosystems.}, } @article {pmid42203690, year = {2026}, author = {Fullam, A and Prasoodanan, PKV and Kuhn, M and Bork, P and Schmidt, TSB}, title = {microntology: a lightweight, data-driven controlled vocabulary to describe earth's microbial habitats.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {6}, pages = {}, pmid = {42203690}, issn = {1367-4811}, support = {12/RC/2273-P2//Research Ireland/ ; }, mesh = {*Ecosystem ; *Vocabulary, Controlled ; *Metagenomics/methods ; *Earth, Planet ; *Software ; }, abstract = {MOTIVATION: Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and consolidated vocabularies.

RESULTS: We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k metagenomic samples from public repositories.

AVAILABILITY: microntology controlled vocabulary terms and term hierarchies (doi: 10.5281/zenodo.19730167), and curated annotations for 305 626 metagenomic samples (doi: 10.5281/zenodo.18164252) are available via Zenodo and spire.embl.de/downloads. Underlying code is available via github.com/grp-schmidt/microntology and Zenodo (doi: 10.5281/zenodo.20323497). User feedback, suggestions and bug reports are welcome at github.com/grp-schmidt/microntology/issues.}, } @article {pmid42203770, year = {2026}, author = {So, Y and Pichler, MJ and Kappel, SS and Jin, C and Eriksen, C and Chatzigiannidou, I and Andersen, MHB and Tsiamis, V and Lukassen, MV and Skytthe, LE and Teneberg, S and Kristiansen, K and Brix, S and Aunsholt, L and Abou Hachem, M}, title = {Dual human milk oligosaccharide-fibre utilisation is a selection cue for the weaning gut microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73297-5}, pmid = {42203770}, issn = {2041-1723}, support = {1026-00386B//Natur og Univers, Det Frie Forskningsråd (Natural Sciences, Danish Council for Independent Research)/ ; }, abstract = {Gut microbiome (GM) maturation in early life follows organised taxonomic successions, yet how the weaning diet impacts these trajectories remains underexplored. Here, we collected faecal samples at pre-, early and late weaning from seven mother-infant dyads forming the Milkome cohort, designed to evaluate the contribution of human milk oligosaccharides (HMOs) to GM maturation during weaning (NCT07026526). Surprisingly, all preweaning infant faecal consortia grew on multiple dietary fibres, consistent with the prevalence of fibre-degradation genes in their metagenomes. Utilisation of both HMOs and dietary fibres was discovered as a metabolic hallmark of the weaning GM, as supported by metagenomics and the growth of faecal consortia on HMOs, following their enrichment on fibres. The growth of a defined consortium on weaning-mimic substrates, further showed that distinct Clostridia simultaneously deploy HMO and fibre utilisation pathways, which confers competitive growth against HMO- or fibre-utilising bifidobacteria. Metagenomics, culturomics and HMO-utilisation profiles of 137 maternal isolates were concordant with retention of the HMO-utilisation capacity by the adult GM. Our findings highlight dual HMO-fibre utilisation as an unrecognised selection cue of core adult GM species during weaning, which outlines a plausible mechanism of GM maturation in early life and extends the importance of HMOs to the weaning transition.}, } @article {pmid42203854, year = {2026}, author = {Bostanci, N and Antony, AT and Silbereisen, A and Esmaili, T and Krog, MC and Sterpu, I and Bashir, Z and Engstrand, L and Wiberg-Itzel, E and Nielsen, HS and Hugerth, LW and Schuppe-Koistinen, I}, title = {Shotgun metagenomic mapping of saliva reveals insights into diversity and function of the oral microbiome in pregnancy.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42203854}, issn = {2045-2322}, mesh = {Humans ; Female ; Pregnancy ; *Saliva/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Adult ; *Mouth/microbiology ; Shotgun Sequencing ; Cross-Sectional Studies ; Metagenome ; Bacteria/genetics/classification ; }, abstract = {The oral microbiome is a complex and dynamic microecosystem that fluctuates continually throughout the lifespan of a woman. Nevertheless, the function of the oral microbiome in reproductive health is not yet fully understood. Monitoring oral health and providing necessary dental care before and during pregnancy could help maintain a balanced oral microecology and support healthier microbial transfer to newborns. Here, we aimed to compare the salivary microbiome of pregnant and non-pregnant women using shotgun metagenomics to describe their taxonomic and functional composition and assess whether the resulting data is better explained by the reproductive stage. We conducted a comparative cross-sectional study involving pregnant women (n = 71; gestational age 37-42 weeks) and non-pregnant women (n = 143 with regular menstrual cycles; 3 saliva samples per participant across different menstrual phases). Shallow shotgun metagenomic sequencing was used to characterize both taxonomic and functional profiles of the oral microbiome. Socransky's color complex analysis was performed to assess group differences in key microbial complexes. Quantitative PCR was used to validate the abundance of selected oral bacteria. Participant data, including demographic, behavioral, clinical, and oral health variables (such as dentist visits), were collected and incorporated as covariates to adjust for potential confounding effects. Additionally, a sensitivity analysis was performed by excluding participants with identified behavioral or clinical risk factors. Ten phyla including Actinomycetota, Bacteroidota, Chloroflexota Bacillota, Fusobacteriota, Pseudomonadota, Spirochaetota, Synergistota Candidatus Saccharimonadota and Mycoplasmatota, 102 genera, and 410 species were identified. Pregnant women had lower saliva microbiome diversity, driven by reduced richness but unchanged evenness. The microbial composition varied between the groups, even after adjusting for confounding factors. Differential abundance analysis, adjusted for potential confounders, identified 25 species that significantly differed between groups (q < 0.05), with 13 taxa more than three-fold higher in pregnant women. Notably, red complex species were more abundant in pregnant women (p < 0.05). Functional pathway analysis identified 40 modules that differed by pregnancy status. These results further suggest a connection between pregnancy and changes to the oral microbiome in women. As many of these changes are in a pro-inflammatory direction, further research is warranted to assess its potential impact on pregnant women and their newborns.}, } @article {pmid42204574, year = {2026}, author = {Dinesh, D and Morgan, XC and Jensen, J and Bjornevik, K and Schwarzschild, MA and Ascherio, A and Huttenhower, C and Palacios, N}, title = {Shotgun Metagenomic Profiling of the Gut Virome in Prodromal and Confirmed Parkinson's Disease.}, journal = {Annals of neurology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ana.78243}, pmid = {42204574}, issn = {1531-8249}, support = {RF1AG075922/GF/NIH HHS/United States ; R01AG085320/GF/NIH HHS/United States ; R01NS097723/GF/NIH HHS/United States ; UM1 CA186107/GF/NIH HHS/United States ; }, abstract = {We conducted a nested case-control study within the Nurses' Health Study and the Health Professionals Follow-up Study to examine the role of the gut virome (GV) in Parkinson's disease (PD). We applied a novel metagenomic virome profiling approach, Bioinformatic Application for Quantification and Labeling of Viral taxonomy (BAQLaVa), to prospectively collected metagenomic data from 62 participants with PD, 123 healthy controls, and 90 participants with prodromal PD (pPD). Multivariate linear modeling identified 3 viral genome bins (VGBs) that were elevated in PD: MVG081219 (β = 0.86, q = 0.013), MVG041501 (β = 0.95, q = 0.048), MVG081211 (β = 0.66, q = 0.048) and one VGB, MVG098915 (β = -1.42, q = 0.047) that was depleted in participants with PD compared to controls. These four VGBs were similarly associated with pPD. This work suggests that the GV has potential as a future biomarker for PD. ANN NEUROL 2026.}, } @article {pmid42204631, year = {2026}, author = {Fu, YT and Deng, YP and Duan, DY and Peng, YY and Liu, YL and Zhang, Y and Xu, ZK and Elsheikha, HM and Liu, GH}, title = {Insights into the microbiota profile of Pediculus humanus capitis using metagenomic next-generation sequencing and molecular detection of unexpected pathogen DNA in Hunan Province, China.}, journal = {Parasites & vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-026-07471-5}, pmid = {42204631}, issn = {1756-3305}, support = {2024JJ6548//the Hunan Natural Science Foundation Youth Fund Project/ ; 32473057//the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The head louse, Pediculus humanus capitis, remains a significant public health concern affecting millions of people worldwide and has been implicated as a potential vector for multiple human pathogens. Characterization of the microbiota of head lice could improve our understanding of their public health significance and potential role in pathogen transmission. Here, we characterize the microbiota of head lice and investigate microbiota differences among different clades of head lice.

METHODS: Head lice were collected from Hunan Province, China, and classified into clade A and clade B (CACB) using polymerase chain reaction (PCR)-based genotyping. The microbiota of pooled CACB of head lice samples (n = 46) was investigated by metagenomic shotgun sequencing and comparatively analysed at the phylum, genus, and species levels. In addition, the prevalence of potential pathogen DNA in head lice samples (n = 204) was assessed using real-time PCR with stringent negative controls.

RESULTS: We obtained non-redundant CACB microbial gene catalog comprising 79,232 genes, of which 4.70% (3,722 genes) were taxonomically assigned. The relative abundance of bacteria (2.52%) was higher than that of eukaryotes (2.04%), viruses (0.11%), and archaea (0.02%). Comparative analysis identified 655 and 750 unique genes in CACB, respectively. The dominant phyla in the CACB of head lice were Proteobacteria. At the genus level, DNA sequences corresponding to Anaplasma (25.98%; 53/204), Mycobacterium (24.02%; 49/204), Chlamydia (23.53%; 48/204), Ehrlichia (10.29%; 21/204), and Vibrio (0.49%; 1/204) were detected, suggesting the presence of bacterial DNA from these taxa.

CONCLUSIONS: Our results provide a preliminary characterization of the annotated fraction of the CACB microbiome in head lice. The high proportion of unannotated genes (>95%) underscores the limited representation of louse-associated microbial genomes in public databases and suggests  substantial, yet unexplored, microbial diversity. The detection of pathogen DNA does not confirm organism viability or vector competence,however it may suggest prior exposure, mechanical carriage, or residual DNA from blood meals. These exploratory findings contribute new insights into the microbiota associated with human lice.}, } @article {pmid42204733, year = {2026}, author = {Fang, Q and Liu, J and Xuan, C and Li, C and Jiang, X and Zhang, S and Li, Q and Liu, X and Liu, Q and Zhang, L and Wang, Y and Cui, J and Qu, Y and Zhang, J and Li, P and Chen, X}, title = {Targeting the gut‒kidney axis for lupus nephritis treatment: multimechanism regulatory strategies and evidence from Traditional Chinese medicine.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {}, pmid = {42204733}, issn = {1749-8546}, support = {2022YFC3602000//the National Key Research and Development Program of China/ ; 82274327//the National Natural Science Foundation of China/ ; 32141005//the National Natural Science Foundation of China/ ; }, abstract = {Lupus nephritis (LN) treatment remains challenging because of the limited efficacy and substantial side effects of conventional immunosuppressive therapies. Traditional Chinese medicine (TCM), with its holistic and multitarget approach, offers unique therapeutic potential. The emerging gut-kidney axis theory provides a new framework for understanding LN pathogenesis by linking gut dysbiosis and intestinal barrier injury to renal inflammation. This review systematically examines the role of gut-kidney axis dysregulation in LN progression and establishes connections between the TCM spleen-kidney correlation theory and this modern concept. Accumulating evidence suggests that TCM compounds and active ingredients alleviate renal injury and improve LN through multiple mechanisms. TCM compounds modulate the gut microbiota composition, enhance intestinal barrier integrity, reduce endotoxin translocation, and suppress systemic inflammation. These findings position the gut-kidney axis as a critical target for TCM intervention. Through multicomponent synergy, TCM restores gut homeostasis and inhibits aberrant immune responses. Future studies should integrate multiomics approaches, including metagenomics and metabolomics, and prospective clinical trials should dynamically track the gut microbiota and metabolite profiles in LN patients. Such investigations will clarify the precise mechanisms by which TCM modulates the gut-kidney axis and facilitate the development of personalized TCM-based therapeutic strategies.}, } @article {pmid42204882, year = {2026}, author = {Jiang, Y and Zhao, J and Chen, Z and Jiang, N and Lu, C and Zhang, Y and Chen, H}, title = {Long-Term Effects of Straw-Biochar Application and Fertilization Gradients on Black Soil Carbon Sequestration via Prokaryote-Fungus-Protist Interactions and Metagenomic-Metabolite Linkages.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70339}, doi = {10.1111/1462-2920.70339}, pmid = {42204882}, issn = {1462-2920}, support = {2022YFD1500302//National Key Research and Development Program of China/ ; 42277282//National Natural Science Foundation of China/ ; 2022A1515010861//Basic and Applied Basic Research Foundation of Guangdong Province/ ; JCYJ20250604174440054//Shenzhen Natural Science Foundation in Basic Research Fund/ ; JCYJ20220530150201003//Shenzhen Natural Science Foundation in Basic Research Fund/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/metabolism/genetics/physiology ; Metagenomics ; *Charcoal ; *Carbon Sequestration ; Bacteria/metabolism/genetics/classification ; *Fertilizers/analysis ; China ; Microbiota ; Carbon/metabolism ; Metagenome ; }, abstract = {Here, we conducted a seven-year field experiment in black soils of Northeast China to evaluate the effects of carbon (C) management, that is, control, straw return (SD), straw-biochar (BC), and a combined amendment (SDBC), with three fertilization levels (N0: unfertilized control, N60: 60% of conventional rates, N100: conventional rates) on soil microbiomes, metagenomics, and metabolomics. Results showed that BC significantly elevated soil total C (+15%), total N (+10%), and NH 4 + $$ {\mathrm{NH} } _4^{+} $$ (+63%) relative to controls. Microbial community analyses revealed that SD increased prokaryotic richness but reduced protist diversity, whereas BC and SDBC suppressed fungal diversity. Integrated metagenomic and metabolomic profiling uncovered microbial functional adaptations to rich-C conditions under BC and SDBC, characterized by downregulated C metabolism-related genes and concurrent accumulation of lipid-associated metabolites. Crucially, BC decreased the abundance of bacterial virulence factors, contrasting with SD elevating pathogenic potentials. Among three fertilization levels, the reduced rates of N60 optimized microbial network complexity and minimized pathogen invasion risks more effectively than conventional rates of N100 without compromising soil fertility. Collectively, by deciphering prokaryote-fungus-protist interactions and metagenomic-metabolite linkages, our research highlights that straw-derived biochar application and optimized fertilization offers a sustainable strategy to foster beneficial microbial associations, suppresses pathogenic potential, and enhances carbon storage.}, } @article {pmid42205184, year = {2026}, author = {Wang, X and Wang, H and Liu, J and Zhang, H and Zhou, XJ}, title = {Gut Virome Characteristics and Network Alterations in IgA Nephropathy.}, journal = {Kidney international reports}, volume = {11}, number = {7}, pages = {106550}, pmid = {42205184}, issn = {2468-0249}, abstract = {INTRODUCTION: Emerging evidence implicates gut microbiota dysbiosis in the pathogenesis of IgA nephropathy (IgAN), yet the contribution of the gut virome remains unexplored. This study aimed to characterize virome signatures and virus-microbiota interactions in IgAN.

METHODS: We performed a rigorously matched case-control study including 32 patients with biopsy-proven IgAN and 32 healthy controls. Fecal viral-like particles and bacterial communities were profiled using metagenomic sequencing and full-length 16S ribosomal RNA (rRNA) sequencing. Statistical analysis included diversity, differential abundance, network analysis, and correlation with clinical indices.

RESULTS: IgAN subjects displayed significant reductions in gut virome richness (severe IgAN vs. healthy controls, P = 0.03), with a lower relative abundance of Caudoviricetes in severe IgAN (P = 0.045) and enrichment of Tectiliviricetes in mild disease (P = 0.03). We identified 113 differentially abundant bacteriophage contigs (82 up, 31 down; false discovery rate < 0.05); key predicted hosts shifted toward Bacteroides, Clostridium, and Roseburia in IgAN, whereas Faecalibacterium and Alistipes prevailed in controls. Viral and bacterial alpha diversity correlated in healthy controls but not in IgAN (r = 0.38, P = 0.03 vs. r = 0.04, P = 0.81). IgAN virome encoded more glyco-modifying enzymes (P < 0.05), with strong correlations to estimated glomerular filtration rate (eGFR) (r = 0.65, P = 0.001). Viral and bacterial alpha diversity were significantly correlated with proteinuria and gross hematuria (r = 0.18-0.25, - < 0.05).

CONCLUSION: This study describes potential alterations in gut virome diversity, bacteriophage composition, bacteriome-virome relationships, and predicted functional profiles in IgAN, suggesting potential relevance of the gut virome to intestinal ecological alterations.}, } @article {pmid42205574, year = {2026}, author = {Liao, G and Xiao, J and Zhang, B and Wang, S and Wan, X and Zhang, C and Lyu, C and Yan, B and Zhao, Y and Kang, C and Zhang, Y and Yuan, F and Zhao, Z and Chen, Y and Guo, L and Zhang, Y}, title = {Enhancement of genetic potential for soil carbon and nitrogen cycling by organic fertilizer substitution improves the ecological environment for licorice cultivation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1758116}, pmid = {42205574}, issn = {1664-302X}, abstract = {BACKGROUND: Excessive chemical fertilizer application has become a core bottleneck restricting the green and sustainable cultivation of Glycyrrhiza uralensis (licorice). Partial organic fertilizer substitution can improve soil microecology and licorice growth traits, yet its regulatory effects on microbial functional genes mediating soil carbon (C) and nitrogen (N) cycling remain unclear.

RESULTS: Using metagenomic sequencing, we investigated the effects of six fertilization regimes [100% organic fertilizer (OF100), 100% chemical fertilizer (OF0), and organic-inorganic combinations (OF25, OF50, OF75)] on the genetic potential of soil C and N cycling, as well as soil properties and licorice growth traits in bulk and rhizosphere soils of licorice. Organic substitution significantly altered the abundance of C and N cycling-related functional genes: OF100 significantly increased the abundance of genes associated with methane oxidation (pmoA/amoA), carbon degradation (pel, cbh) and nitrification (pmoB/amoB), while OF0 significantly upregulated the methanogenesis-related gene mttA and downregulated nitrogen degradation genes; optimized fertilization (OF50) significantly reduced the abundance of genes linked to excessive carbon degradation (malZ) and nitrogen loss genetic potential (nirK), and markedly increased the abundance of genes for carbon fixation (pccA) and nitrogen mineralization (GDH). PERMANOVA revealed that soil compartment (bulk vs. rhizosphere) explained 62.87% of the total variation in functional gene profiles, which was 5.67 times higher than the contribution of fertilization regime (11.10%).

CONCLUSION: Rational organic-inorganic fertilization effectively regulates soil microbial functional genes related to C and N cycling, optimizes soil nutrient cycling potential, reduces nutrient loss risk, and enhances nutrient supply efficiency for licorice growth. These findings provide a scientific basis for fertilizer management optimization and sustainable cultivation of licorice.}, } @article {pmid42205899, year = {2026}, author = {Patil, BL and Shanmugaraj, C and Madhusudan, M}, title = {Metagenomic profiling of endophytic microbiomes associated with fruit pulp and seed kernels of different mango varieties reveals conservation of bacterial communities in seed kernels.}, journal = {3 Biotech}, volume = {16}, number = {6}, pages = {222}, pmid = {42205899}, issn = {2190-572X}, abstract = {UNLABELLED: Bacterial and fungal communities associated with mango pulp and seed kernels from eight Indian mango varieties were profiled using 16 S rRNA and ITS amplicon sequencing. Bacterial diversity was consistently higher in seed kernels (647 ± 238 OTUs) than in pulp tissues (196 ± 112 OTUs). Seed kernel-associated bacterial communities were dominated by Firmicutes (35.8-44.0%) and Bacteroidota (16.8-35.8%) and showed high compositional consistency across varieties, with core genera including Prevotella, Ruminiclostridium, and Lachnoclostridium. In contrast, pulp-associated bacterial communities were enriched in Proteobacteria (6.5-88.5%) and Actinobacteria (4.4-34.6%) and exhibited pronounced inter-varietal variability, particularly in the relative abundance of Bacteroidota (0.8-53.8%). Fungal communities displayed lower richness (14-72 OTUs) and higher variability, with Candida kruisii (15-67%) and Hanseniaspora uvarum (up to 86%) as dominant taxa. Non-metric multidimensional scaling and hierarchical clustering revealed clear tissue-driven segregation of bacterial communities, whereas fungal assemblages showed weaker tissue-associated structuring. Seed kernels harbored approximately 3.3-fold more unique bacterial OTUs than pulp tissues, with the Amrapali seedkernel exhibiting the highest richness (789 OTUs). Across varieties, 82% of kernel-associated bacterial OTUs were shared, compared with 31% in pulp, indicating a conserved kernel microbiome and a more variable, cultivar-specific pulp microbiome. These results highlight strong tissue-level compartmentalization of mango-associated bacterial communities across cultivars.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04848-2.}, } @article {pmid42205903, year = {2026}, author = {Hameed, A and Ghate, SD and Shastry, RP}, title = {Fecal functional metagenomics reveals increased gut Bacillota/Pseudomonadota (Firmicutes/Proteobacteria) ratio and altered bacterial CAZyme profile in human colorectal cancer.}, journal = {3 Biotech}, volume = {16}, number = {6}, pages = {230}, pmid = {42205903}, issn = {2190-572X}, abstract = {UNLABELLED: Gut microbial dysbiosis has been implicated in the onset and/or progression of colorectal cancer (CC). We recently identified the emergence of low-abundance bacterial taxa affiliated with the phylum Bacillota in the gut microbiome of CC patients, as revealed by 16S rRNA gene amplicon sequencing. Here, we subjected the fecal samples from CC (n = 4) and healthy control (HC, n = 4) participants to functional metagenomics using the Illumina Novaseq 6000 platform. Metagenome-assembled genomes (MAGs) showed compositional differences among bacterial phylotypes in CC and HC. Species observed, richness (Chao1), and diversity (Shannon's) were high in CC, whereas species abundance peaked in HC. The Bacillota to Pseudomonadota ratio was high (> 3-fold) in CC (2.45) as compared to HC (0.70). MAGs revealed a decline in the distribution frequency of COGs involved in carbohydrate transport and metabolism (G), inorganic ion transport and metabolism (P), and unknown function (S) in CC. However, CC and HC samples exhibited marginal variations in terms of G/P (1.29 and 1.18, respectively) and G/S (0.35 and 0.40, respectively) ratios. Analysis further revealed a significant increment in glycosyltransferases GT1, GT2 and GT4, particularly in CC. In contrast, the glycoside hydrolases GH5 and GH9 declined in CC. GT/GH ratios were found to increase > 2-fold in CC (3.94) compared with HC (1.37). The present pilot-scale dataset-specific work reflects perseverance of Bacillota, significant decline in Pseudomonadota, a stable G/P and G/S ratios and enrichment of glycosyltransfererases in CC. Further transcriptomic-based studies in larger cohorts are warranted to gain insights into the implications of dysbiosis and its pathophysiological relevance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04882-0.}, } @article {pmid42206066, year = {2026}, author = {Zhang, Q and Li, S and Wang, X and Sun, Y and Liu, J and Gao, J and Deng, C and Zhao, W and Ma, Y and Quan, J and Yin, Q and Jian, D and Zhang, R and Qi, R}, title = {Multi-metal contamination shapes abundance, co-occurrence, and mobility potential of resistance and virulence genes in mining-impacted soils.}, journal = {Infectious medicine}, volume = {5}, number = {2}, pages = {100260}, pmid = {42206066}, issn = {2772-431X}, abstract = {BACKGROUND: Antimicrobial resistance is a growing global public health concern, posing a serious threat to human health. This study aimed to characterize the composition and distribution of microbial communities, metal resistance genes (MRGs), antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) under multi-metal stress and assess the impacts of metal and soil properties on the diversity, abundance, carrying rate (proportion of gene carriers), co-occurrence rate (proportion of microorganisms co-carrying multiple gene types), and mobility potential (MP, likelihood of horizontal gene transfer) of these genes.

METHODS: Soil samples were collected from eight sampling sites within a metal mining area (metal-contaminated soil group, MS) and four sites located more than 3 km away from the mining area (control group). Metal concentrations and physicochemical properties of the soils were measured using standard methods. Metagenomic sequencing was performed to characterize the composition and distribution of the microbiome, resistome, and virulome. Statistical modeling was applied to examine the effects of heavy metal content and soil properties on the relative abundance, co-occurrence, and mobilome potential of the three gene types.

RESULTS: Fe, V, Cr, and Cu primarily promoted the diversity, carrying rate, and co-occurrence rate of microbial communities, MRGs, ARGs, and VFGs. In contrast, Ni and Zn exhibited overall inhibitory effects. For every unit increase in Fe and V, the MP of MRGs and VFGs was associated with an increase of 3.0 × 10⁻⁵ and 1.2 × 10⁻⁵, respectively. A per 1 mg/kg increase in Cr and Cu was correlated with a decrease of 4.3 × 10⁻⁵ and 1.1 × 10⁻⁴ in the MP of ARGs and of MRGs, respectively. Positive correlations were found between the MP of plasmid‑mediated ARGs and Cr, and between transposon‑mediated ARGs and Cr/V. The MP of transposon‑mediated MRGs correlated positively with Fe, while Cu correlated negatively with plasmid‑mediated ARGs but positively with insertion sequence‑mediated ARGs. Ni concentration was positively associated with the MP of IS‑mediated VFGs.

CONCLUSIONS: Metals alter the composition and distribution of microbial communities, MRGs, ARGs, and VFGs. A key mechanism underlying this regulation is the modulation of their mobile potential, which either facilitates or restricts horizontal gene transfer.}, } @article {pmid42206150, year = {2026}, author = {Sun, K and Wang, F and Niu, T and Wang, H and Liu, Y and Guo, L and Wang, X and Hou, X}, title = {Metagenomic and metabolomic insights into the rhizosphere of Paeonia suffruticosa 'Luoyang Hong' across a continuous cropping chronosequence.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1754999}, pmid = {42206150}, issn = {1664-462X}, abstract = {The cultivation of Paeonia suffruticosa 'Luoyang Hong', a valuable ornamental crop, faces significant challenges due to replanting issues. However, the dynamics of its rhizosphere micro-ecosystem under continuous cropping remain poorly understood. This study systematically investigates the successional patterns of the rhizosphere micro-ecosystem over a 12- to 42-year chronosequence to identify the underlying drivers of these issues. Using an integrated multi-omics approach combining metagenomics and non-targeted metabolomics, we deciphered the rhizosphere mechanisms associated with replanting issues in Paeonia suffruticosa 'Luoyang Hong'. Based on differential changes in metabolites within the soil and root systems, key substances such as succinic acid, trans-ferulic acid, vanillic acid, and Leu-Val-Arg-Lys were identified. The microbial succession demonstrated a distinct temporal progression. Initially, at the 12-year stage, the rhizosphere was enriched with beneficial bacterial genera. However, around the 20-year stage, the abundance of these beneficial genera significantly declined. Subsequently, at the 34-year stage, the community shifted to a dominance of genera associated with organic matter degradation. Finally, at the 42-year stage, a partial recovery of certain beneficial genera and their functions was observed. Despite this recovery, the overall system continued to exhibit signs of continuous degradation. Integrated multi-omics analysis further revealed significant positive correlations, such as that between N,N-dimethyldodecylamine N-oxide and several differential microbial genera, underscoring the complex interactions between metabolites and microbes. Our findings provide a systematic perspective on the micro-ecological dynamics in the rhizosphere of Paeonia suffruticosa 'Luoyang Hong', offering deeper insights into replanting issues and supporting future mitigation strategies.}, } @article {pmid42206286, year = {2026}, author = {Oladejo, OA and Ibiwoye, DO and Faniyi, AA and Ayoola, MO and Oguntunji, AO and Ayansina, AD and Dahunsi, SO}, title = {Dynamics of enzyme and metabolic profile of broilers fed black soldier fly (Hermetiailucens) larvae-based diets.}, journal = {Biochemistry and biophysics reports}, volume = {46}, number = {}, pages = {102618}, pmid = {42206286}, issn = {2405-5808}, abstract = {This study investigated the impact of replacing fishmeal with black soldier fly larvae meal (BSFLM) on growth performance, microbial enzyme activity, and metabolic functions in broiler chickens. A total of fifty Arbor Acre Plus chicks were distributed across five dietary groups, including a control (100% fishmeal) and four diets containing increasing levels of BSFLM (25%, 50%, 75%, and 100%) in a completely randomized design. Broilers were reared over eight weeks, and cecal samples were subjected to 16S rRNA metagenomic sequencing to profile gut microbial enzyme activities and metabolic functions. Results revealed a progressive increase in microbial enzyme abundance and functional metabolic pathways with higher BSFLM inclusion, particularly in the 50% (T3) and 100% (T5) groups. Key enzymes, including ABC-2-type ATP-binding proteins, RNA polymerase sigma factors, and carbohydrate-active enzymes, were significantly upregulated, supporting enhanced carbohydrate fermentation, amino acid biosynthesis, and central carbon metabolism. Metabolic pathway analysis indicated a dietary shift from carbohydrate-driven fermentation in the control group to a more protein- and lipid-centered metabolism in BSFL-fed birds, with T3 showing a balanced metabolic profile and T5 exhibiting hyper-metabolic activity. These findings demonstrate that BSFLM can replace fishmeal without compromising gut health and may even enhance microbial functionality, with a 50% replacement emerging as an optimal inclusion level to sustain balanced microbial metabolism.}, } @article {pmid42206340, year = {2026}, author = {Huerta, AI and Joglekar, P and Totsline, N and D'Amico-Willman, KM and Ritchie, DF}, title = {Plant-associated phages across scales: ecological and evolutionary principles for a neglected virosphere.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1951}, pages = {}, doi = {10.1098/rstb.2025.0124}, pmid = {42206340}, issn = {1471-2970}, support = {//National Institute of Food and Agriculture/ ; //Foundation for Food and Agriculture Research/ ; }, mesh = {*Bacteriophages/physiology/genetics ; *Plants/virology/microbiology ; *Microbiota ; *Biological Evolution ; }, abstract = {Bacteriophages are abundant and influential members of plant-associated microbiomes, yet their ecological and evolutionary roles are less explored than those of marine, soil or clinical virospheres. This gap limits our capacity to predict phage-bacterium interactions, understand microbial community dynamics and design robust phage-based strategies for managing diseases in plants. Here, we synthesize emerging evidence across spatial, temporal and biological scales to outline key principles that govern phage ecology in plant systems. Drawing on insights from well-characterized environments, including oceans, soils and the human gut, we highlight how spatial structure, host population genetics, environmental heterogeneity and fluctuating selection jointly shape infection outcomes and coevolution in plant microbiomes. Recent genomic and metaviromic findings further reveal that plant-associated phages can exhibit both long-term genomic stability and localized adaptive divergence, underscoring the importance of scale-aware ecological frameworks. We also identify major technical and conceptual bottlenecks that impede discovery, including plant and bacterial host-DNA contamination and the limited number of phage genomes isolated from plant ecosystems. By linking these ecological principles to applied challenges, such as the inconsistent field performance of phage-based biocontrol, this perspective offers a roadmap for advancing phage biology in plant systems and for resolving this neglected virosphere. This article is part of the theme issue 'Wild plant pathosystems'.}, } @article {pmid42206370, year = {2026}, author = {Chen, L and Lin, L and Wang, Z and Yu, L and Ren, B and Zhou, S and Wang, P and Li, Y and Lu, E and Dong, Z}, title = {Fusobacterium nucleatum-Derived Isoleucine Exacerbates Aneurysm by Inducing Ferroptosis in Vascular Smooth Muscle Cells.}, journal = {Arteriosclerosis, thrombosis, and vascular biology}, volume = {}, number = {}, pages = {}, doi = {10.1161/ATVBAHA.126.324050}, pmid = {42206370}, issn = {1524-4636}, abstract = {BACKGROUND: Bacterial communities and their metabolites are increasingly recognized as key contributors to cardiovascular disease, yet their role and mechanistic involvement in abdominal aortic aneurysm (AAA) pathogenesis remain insufficiently defined.

METHODS: Dental plaques from patients with AAA and matched healthy controls were subjected to metagenomic sequencing, and corresponding plasma samples underwent untargeted metabolomic profiling. In vivo, mice were topically exposed in the oral cavity to Fusobacterium nucleatum (Fn) followed by AngII (angiotensin II) infusion to evaluate its impact on AAA progression. A homologous recombination-based ilvE deletion strategy was used to confirm the role of Fn in isoleucine biosynthesis. Molecular assays were performed to assess ferroptosis-related signatures and histone acetylation in smooth muscle cells, while chromatin immunoprecipitation-quantitative polymerase chain reaction verified the specific acetylation target. In addition, dietary restriction of isoleucine was introduced in the AAA murine model to explore therapeutic relevance.

RESULTS: Patients with AAA showed a marked enrichment of Fn in dental plaque, and topical application of Fn aggravated AngII-induced AAA in mice. Elevated plasma isoleucine concentrations were observed in both human AAA and experimental models. Genetic deletion of ilvE in Fn diminished bacterial isoleucine release and mitigated AAA development in mice. Mechanistic analyses revealed that Fn-derived isoleucine promoted ferroptosis in smooth muscle cells through H3K9ac (histone H3 lysine 9 acetylation)-dependent transcriptional activation of ACSL4 (acyl-CoA [coenzyme A] synthetase long-chain family member 4), a core regulator of ferroptosis. Dietary isoleucine restriction in the AngII-induced model reduced H3K9ac, suppressed ferroptosis, and alleviated aneurysmal progression.

CONCLUSIONS: Fn-derived isoleucine drives ferroptosis in smooth muscle cells via H3K9ac-mediated activation of ACSL4, delineating a microbiota-metabolite-epigenetic axis in AAA pathogenesis and nominating dental plaque Fn abundance and circulating isoleucine as exploratory biomarker candidates requiring larger, independent validation.}, } @article {pmid42206586, year = {2026}, author = {Yeo, S and Park, H}, title = {Dereplication-assisted culturomics enables strain-level ecological analysis of the human gut microbiome.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2681840}, pmid = {42206586}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Enterococcus faecium/isolation & purification/classification/genetics ; Metagenomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Bifidobacterium/isolation & purification/classification/genetics ; }, abstract = {Recent advances in culturomics have enabled large-scale recovery of microbial isolates from the human gut, generating extensive culture collections that bridge metagenomic predictions and experimental validation. However, these isolate resources remain largely underutilized, as conventional culturomics prioritizes the discovery of novel species while massive collections of commensal isolates persist as unexplored biological datasets. Dereplication, particularly based on MALDI-TOF MS spectral features, has been largely regarded as a logistical tool for managing redundancy rather than an analytical asset. Here, we reposition dereplication as an analytical framework for interpreting large-scale culturomics datasets and resolving strain-level ecological patterns. We applied the SPeDE pipeline to a comprehensive collection of 2,231 isolates, including Bifidobacterium spp. and Enterococcus faecium, recovered from healthy donor feces. Spectrum-derived operational isolation units (OIUs) revealed host-associated strain-level repertoires and lineage-like clustering within species. Notably, distinct spectral clusters observed in E. faecium corresponded to clade-level patterns identified through shotgun metagenomic analysis. These findings demonstrate that dereplication-assisted culturomics can extend beyond redundancy control to enable high-resolution ecological interpretation of cultured microbiome datasets. By reframing dereplication as a bridge between large-scale isolate generation and strain-level microbiome ecology, this study outlines a conceptual and practical direction for the next phase of human microbiome research in the post-culturomics era.}, } @article {pmid42206864, year = {2026}, author = {Zhao, R and Biddle, JF}, title = {Community structure and methylation of microbes in an artificially forced sediment core.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0353325}, doi = {10.1128/spectrum.03533-25}, pmid = {42206864}, issn = {2165-0497}, abstract = {Epigenetic modifications, such as DNA methylation, may be used in prokaryotes for the adaptation of microbes to external environmental changes. In this study, we examined the microbial community structure, recovered the genomes of the dominant microbes, and tracked methylation in several dominant microbes in a 23-cm artificial sediment core formed in a settling tank that mimics the sediment formation process. Our results indicated that the prokaryotic communities only showed minor variations with depth and were dominated by bacteria (especially taxa of Deltaproteobacteria, Gammaproteobacteria, and Bacteroidota), while archaea (dominated by Bathyarchaeia) accounted for <5% of the total communities throughout the core. We detected methylation by analyzing metagenome sequencing data of methyl-specific enzyme-digested and undigested DNA. We recovered 72 high- or medium-quality metagenome-assembled genomes for the dominant taxa, for 7 of which we detected distinct downcore methylation patterns. This work highlights the diverse processes of epigenetic modification in response to the sediment burial process, which may have a long-term impact on the overall community fitness in the evolving energy-limited conditions in marine sediments.IMPORTANCEThis work reports changes in the epigenetic profiles of microbes buried in a sediment column formed under a controlled, artificially created environment. This approach removes confounding variables of bioturbation and changes in sediment flux. We also use an approach that is accessible for low amounts of DNA to determine methylation status.}, } @article {pmid42207030, year = {2026}, author = {Ren, P and Kan, Z and Wei, B and Qin, W and Lu, S}, title = {Yellow tea extract ameliorates dexamethasone-induced hepatic steatosis by modulating the gut-liver axis and reshaping microbial metabolites: a multi-omics insight.}, journal = {Food & function}, volume = {17}, number = {12}, pages = {5410-5424}, doi = {10.1039/d6fo01620k}, pmid = {42207030}, issn = {2042-650X}, mesh = {Animals ; Mice ; Liver/metabolism/drug effects ; *Plant Extracts/pharmacology ; Male ; *Gastrointestinal Microbiome/drug effects ; *Dexamethasone/adverse effects ; *Fatty Liver/chemically induced/drug therapy/metabolism ; *Tea/chemistry ; Mice, Inbred C57BL ; Multiomics ; Camellia sinensis/chemistry ; }, abstract = {Long-term glucocorticoid therapy, exemplified by dexamethasone (DEX), frequently induces hepatic steatosis, posing a significant clinical challenge. Yellow tea (YT), a lightly fermented tea, is rich in polyphenols and polysaccharides, yet its protective effects against DEX-induced liver injury remain underexplored. This study investigated the hepatoprotective mechanisms of a yellow tea water extract (YT) using a DEX-induced mouse model, integrated with transcriptomic, metagenomic, and metabolomic analyses. YT intervention (500 mg[-1] kg[-1] day[-1] for 6 weeks) significantly attenuated DEX-induced hepatocellular injury, as evidenced by reduced serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, decreased hepatic triglyceride (TG) and total cholesterol (TC) accumulation, and suppressed systemic inflammation (lipopolysaccharide (LPS) and tumor necrosis factor-alpha (TNF-α)). Hepatic transcriptomics and subsequent reverse transcription quantitative PCR (RT-qPCR) validation revealed that YT upregulated the antioxidant genes nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1) while downregulating the lipogenic gene sterol regulatory element-binding protein 1c (SREBP-1c) and upregulating the fatty acid oxidation gene peroxisome proliferator-activated receptor alpha (PPAR-α). Gut microbiota analysis showed that YT reshaped the microbial community, notably enriching beneficial taxa such as Bifidobacterium pseudolongum and members of the Muribaculaceae family. Serum metabolomics indicated that this microbiota remodeling was associated with the restoration of perturbed metabolic pathways, notably tryptophan metabolism. Correlation analysis further linked specific microbial shifts with improved metabolic and inflammatory markers. Collectively, these integrated transcriptomic, metagenomic, and metabolomic findings demonstrate that YT alleviates DEX-induced hepatic steatosis through dual mechanisms involving direct hepatic antioxidant and lipid metabolic regulation and systemic modulation via the gut-liver axis, positioning it as a promising dietary strategy against glucocorticoid-associated metabolic complications.}, } @article {pmid42207032, year = {2026}, author = {Giani, N and John, J and Campbell, B}, title = {Shotgun metagenomics and metatranscriptomics of soil microbial communities under monoculture and polyculture cover crops.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0030926}, doi = {10.1128/mra.00309-26}, pmid = {42207032}, issn = {2576-098X}, abstract = {Here, we present 30 metagenomes, 21 metatranscriptomes, and 334 metagenome-assembled genomes collected from soils under different cover crop species. This data set will be useful for studying microbial interactions, especially functional redundancy, with relevance to agricultural management and sustainability.}, } @article {pmid42207051, year = {2026}, author = {Sutanto, TPW and Pratama, A and Ishii, E and Iida, T and Matsuda, S}, title = {TsrA modulates type III secretion system 2 expression as a co-regulator of H-NS in Vibrio parahaemolyticus.}, journal = {Journal of bacteriology}, volume = {208}, number = {6}, pages = {e0055625}, pmid = {42207051}, issn = {1098-5530}, support = {20K07428, 23K06529//Japan Society for the Promotion of Science/ ; 23K14521, 25K18800//Japan Society for the Promotion of Science/ ; 23K05637//Japan Society for the Promotion of Science/ ; 2024N068//Shionogi Infectious Disease Research Promotion Foundation/ ; //BIKEN Foundation/ ; }, mesh = {*Vibrio parahaemolyticus/genetics/pathogenicity/metabolism ; *Bacterial Proteins/genetics/metabolism ; *Gene Expression Regulation, Bacterial ; *DNA-Binding Proteins/genetics/metabolism ; *Type III Secretion Systems/genetics/metabolism ; Virulence/genetics ; Transcription Factors/genetics/metabolism ; Virulence Factors/genetics ; }, abstract = {Vibrio parahaemolyticus, a gram-negative marine bacterium, is a major cause of seafood-borne gastroenteritis worldwide. This pathogen relies on type III secretion system 2 (T3SS2), which is encoded on a pathogenicity island, for its enteropathogenicity. Expression of T3SS2 is activated by a regulatory pathway centered on the transcriptional activator VtrB, which is antagonized by the xenogeneic silencer, histone-like nucleoid-structuring protein (H-NS). However, the complete transcriptional network is not yet fully understood. In this study, we identified TsrA as a negative regulator of T3SS2 gene expression. TsrA is a small protein conserved among Vibrio species that lacks a putative DNA-binding motif but has been implicated in the regulation of virulence genes in Vibrio cholerae. In V. parahaemolyticus, deletion of tsrA increased VtrB production and T3SS2 secretion, thereby enhancing T3SS2-dependent pathogenicity. Transcription of vtrB occurs via a two-step activation process, in which TsrA affects the primary activation step, thereby modulating VtrB production. We further provide experimental evidence that TsrA physically interacts with H-NS via its C-terminal region, which correlates with its regulatory activity on vtrB expression. A systematic mutational analysis of the C-terminal 26 residues revealed several residues critical for TsrA regulatory activity. Moreover, the regulatory effect of TsrA on T3SS2 gene expression was dependent on H-NS, demonstrating that TsrA functions in concert with H-NS. Thus, our findings provide new insights into the regulatory mechanisms of virulence gene expression in V. parahaemolyticus by defining the role of TsrA in this network, while also placing TsrA among H-NS co-regulators.IMPORTANCENucleoid-associated proteins (NAPs) play key roles in virulence gene regulation in bacteria. The best-studied NAP is H-NS, which often functions with co-regulators to fine-tune gene expression. TsrA, a small protein lacking a DNA-binding motif conserved among Vibrio species, has been suggested to be functionally related to H-NS in Vibrio cholerae, although its mechanism remains unknown. Here, we demonstrate that TsrA negatively regulates the expression of type III secretion system 2 (T3SS2), a major virulence determinant of Vibrio parahaemolyticus, an important seafood-borne pathogen. TsrA modulates the transcription of vtrB, which encodes the essential activator for T3SS2 expression, through direct physical interaction with H-NS. Our findings reveal a molecular link between TsrA and H-NS, providing mechanistic insights into NAP- and TsrA-mediated regulation of virulence in Vibrio.}, } @article {pmid42207344, year = {2026}, author = {Cagirgan, OY and Korkmaz, S and Diker, KS}, title = {Intestinal microbiome in necrotic enteritis infection of broiler and comparison of treatment alternatives.}, journal = {Tropical animal health and production}, volume = {58}, number = {5}, pages = {}, pmid = {42207344}, issn = {1573-7438}, support = {VTF-190002//Bilimsel Araştırma Projeleri Birimi, Aydın Adnan Menderes Üniversitesi/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Clostridium Infections/veterinary/microbiology/drug therapy ; *Poultry Diseases/microbiology/drug therapy ; *Enteritis/veterinary/microbiology/drug therapy ; Clostridium perfringens/physiology ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Bacillus/physiology ; *Probiotics/administration & dosage ; Amoxicillin/therapeutic use/administration & dosage ; Necrosis/veterinary/microbiology ; Male ; }, abstract = {Clostridium perfringens is the primary causative agent of necrotic enteritis (NE), a gastrointestinal disease that leads to substantial economic losses in poultry. This study aims to characterize the intestinal microbiome of chickens and assess the effects of Bacillus velezensis on gut microbiota and recovery from necrotic enteritis, comparing its efficacy to antibiotic treatment. The experiment involved five groups, each consisting of 16 chickens. The first group, the start-of-challenge (DB) group, included day-old chicks. The second group, the post-challenge control (DS) group, was reared until the end of the trial. The third group was infected with C. perfringens (NE group). The fourth group received both C. perfringens and B. velezensis (BV group), while the fifth group was treated with C. perfringens and amoxicillin (AB group). All chickens were euthanized via cervical dislocation following the experimental infection. Fecal samples collected from the cecum underwent 16 S rRNA gene-based metagenomic analysis, and the resulting data were statistically evaluated. Macroscopic examination after euthanasia revealed pathological changes in the intestines of chickens in the NE group, which had received only C. perfringens. Their intestines appeared swollen, with slight mild mucosal hemorrhage. In contrast, no macroscopic lesions were observed in the DB, DS, BV, or AB groups. Microbiome analysis showed a decline in microbial diversity within the NE group. The BV group exhibited a microbial composition most similar to that of healthy animals, followed by the AB group. The study concludes that B. velezensis could serve as an alternative to prophylactic antibiotics in mitigating the adverse effects of necrotic enteritis on the gut microbiome.}, } @article {pmid42207373, year = {2026}, author = {Shao, C and Li, J and Huang, C and Tang, M and Zeng, J and Zhou, W and Zhang, D and Zeng, G and Wang, J and Hua, T and Zhong, C and Hu, J and Xu, X}, title = {Clinical utility of metagenomic next-generation sequencing in precision diagnosis of infectious diseases: a retrospective study based on bronchoalveolar lavage fluid, blood, and cerebrospinal fluid.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42207373}, issn = {1435-4373}, support = {20170522160421261//Bao'an District Science and Technology Program/ ; 2023B110008//Guangdong Provincial Clinical Research Center for Laboratory Medicine/ ; }, abstract = {RESEARCH BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a culture-independent pathogen identification method, which can directly sequence all nucleic acids present in clinical samples, and has shown transformative potential in the diagnostic field of complex, critical and emerging infectious diseases, but its clinical application value has not been fully evaluated. This study aims to compare the diagnostic efficacy of mNGS and traditional microbiological testing (TMT), and evaluate its impact on clinical decision-making.

RESEARCH METHODS: This retrospective study analyzed the data of the laboratory information system (LIS) of patients who received both mNGS and TMT testing.

RESEARCH RESULTS: In samples of bronchoalveolar lavage fluid (BALF), blood and cerebrospinal fluid (CSF), the positive rates of mNGS were 86.70%, 77.17% and 53.57% respectively, which were significantly higher than the corresponding positive rates of TMT (41.38%, 14.13%, 17.86%). Clinical correlation analysis showed that 77.84%, 66.20% and 73.33% of the positive mNGS results of the three types of samples were of clinical significance respectively. 15.34%~29.58% of the cases adjusted their treatment regimens according to the positive mNGS results, and 33.33%~61.54% of the cases adjusted their treatment regimens according to the negative mNGS results. Most patients who had their treatment adjusted showed improvement or relief of symptoms. Overall, various pathogenic microorganisms were detected in more than 60% of the samples.

RESEARCH CONCLUSION: This study confirms the significant advantages of mNGS in the precise diagnosis of infectious diseases, as well as its value in guiding individualized treatment strategies.}, } @article {pmid42208188, year = {2026}, author = {Gilevska, T and Rotaru, AE and Anestis, K and Fonseca, A and Kümmel, S and Krauss, M and Inostroza, PA and Bonaglia, S}, title = {Wastewater-impacted Skagerrak Sea microbiomes anaerobically demethylate micropollutants.}, journal = {Water research}, volume = {302}, number = {}, pages = {126138}, doi = {10.1016/j.watres.2026.126138}, pmid = {42208188}, issn = {1879-2448}, mesh = {*Water Pollutants, Chemical/metabolism ; *Microbiota ; Geologic Sediments/microbiology ; *Wastewater/microbiology/chemistry ; Anaerobiosis ; Caffeine/metabolism ; Carbon Isotopes ; Bacteria/metabolism/genetics ; Naproxen/metabolism ; Demethylation ; Methane/metabolism ; Archaea/metabolism/genetics ; *Seawater/microbiology ; Oceans and Seas ; }, abstract = {Methylated micropollutants such as naproxen and caffeine persist in wastewater effluents and accumulate in coastal sediments, including Hakefjorden, Skagerrak Sea, yet their anaerobic fate and role in methane emissions remain unresolved. In particular, it is unclear whether pollutant-derived methyl groups are routed mainly to CO2 or can be transformed into CH4 in sulfate-rich coastal sediments. Our primary objective was to resolve this routing by tracing the fate and microbiome responses to [13]C-labeled naproxen and caffeine in sediment microcosms. We show that naproxen underwent rapid O-demethylation to desmethylnaproxen, with 90% ± 15.5% removed within 25 days, producing primarily [13]CO2 and some [13]CH4. Naproxen enriched methylotrophic and hydrogenotrophic Methanomicrobia, alongside Lokiarchaeia, Bathyarchaeia, and bacterial taxa like Eubacterium (Alkalibaculum A sporogenes) and Syntrophomonadaceae. Metagenomics revealed O-demethylation genes in enriched bacterial MAGs affiliated with uncultured Thermoanaerobaculia, indicating a bacterial demethylation potential. In contrast, caffeine was largely recalcitrant to degradation (∼85% ± 5% remaining), yet its [13]C-labeled N-methyl groups fueled trace [13]CH4 production. These results show that methylated micropollutants can activate both bacterial and archaeal demethylation pathways in coastal sediment microbiomes.}, } @article {pmid42208292, year = {2026}, author = {Majumdar, A and Bagchi, D and Kotta-Loizou, I and Buck, M}, title = {The One Health resistome: Integrating environmental, microbial, and human antimicrobial resistance surveillance and risk analysis in the digital age.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142431}, doi = {10.1016/j.jhazmat.2026.142431}, pmid = {42208292}, issn = {1873-3336}, mesh = {Humans ; Risk Assessment ; *Drug Resistance, Microbial/genetics ; *One Health ; *Environmental Monitoring/methods ; *Drug Resistance, Bacterial/genetics ; Machine Learning ; }, abstract = {Antimicrobial resistance (AMR) and antibiotic resistance (ABR) represent one of the most pressing global health threats, driven by the complex interplay between human, animal, and environmental factors. The One Health resistome framework recognises that resistance genes circulate continuously across clinical, agricultural, and environmental compartments through horizontal gene transfer, co-selection mechanisms, and anthropogenic contamination. This comprehensive review synthesises current evidence on integrated AMR surveillance, examining how digital technologies are transforming our capacity to monitor, predict, and respond to resistance emergence. Key advances include whole-genome sequencing enabling high-resolution pathogen tracking, metagenomics revealing environmental resistome diversity, machine learning algorithms predicting resistance phenotypes with > 85% accuracy, and point-of-care diagnostics extending sophisticated testing to resource-limited settings. Geographic information systems facilitate spatial hotspot identification, while wastewater-based surveillance provides early warning capabilities, detecting resistance genes before clinical manifestation. Despite technological progress, substantial challenges persist: fragmented data streams across sectors, lack of standardised environmental monitoring methods, limited laboratory capacity in low- and middle-income countries, and chronic underfunding. Emerging technologies, portable nanopore sequencing, CRISPR-based diagnostics, artificial intelligence, and blockchain-enabled data governance promise to address these gaps. Realising comprehensive One Health resistome surveillance requires sustained investment in interoperable digital infrastructure, international standardisation, capacity building, and political commitment to cross-sectoral coordination, prioritising equitable global implementation.}, } @article {pmid42208296, year = {2026}, author = {Wang, Q and Ma, Y and Niu, J and Liu, Y and Chao, C and Zhao, Y}, title = {Enhanced anti-toxicity memory of Cr(VI)-4-CP stressed denitrification by bio-promoter: Microbial cooperation and multi-path electron transfer drive toxics transformation-migration.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142497}, doi = {10.1016/j.jhazmat.2026.142497}, pmid = {42208296}, issn = {1873-3336}, mesh = {*Chromium/toxicity/chemistry/metabolism ; *Chlorophenols/toxicity/metabolism/chemistry ; *Water Pollutants, Chemical/toxicity/metabolism/chemistry ; *Denitrification/drug effects ; Electron Transport ; Molybdenum/chemistry ; Extracellular Polymeric Substance Matrix/metabolism ; Adenosine Triphosphate/metabolism ; Bacteria/metabolism ; Bioreactors ; }, abstract = {Coexisting heavy metals and organic pollutants in industrial wastewaters posed synergistic inhibition to denitrification by activating dissimilatory nitrate reduction and disrupting electron supply-consumption balance. Taking Cr(VI) and 4-chlorophenol (4-CP) as representative pollutants, this study proposed a combined bio-promoter composed of growth factors and phosphomolybdic acid (PMo12) to accelerate recovery and establish anti-toxicity memory under compound stress. The promoter restored over 90% nitrogen removal within 9 T and maintained 63.6% nitrogen removal under Cr(VI)-4-CP re-stress. Compared to first-stress, the recovered system reduced 37.44 mg/L more Cr(VI) and kept 4-CP below 5 mg/L, thus rapidly relieving Cr(VI)-4-CP toxicity and increasing the supply of direct electron donor nicotinamide adenine dinucleotide (NADH, 65.5%) and energy source adenosine triphosphate (ATP, 27.8%). Meanwhile, the enhanced extracellular polymeric substance (EPS) ensured 11.15 mg/g mixed liquid suspended solids (MLSS) more chromium immobilization with 97.9% distributed intercellularly, preventing Cr(VI) from invading cells and minimizing intracellular oxidative damage. The biofilm-fixed Mo (4.28 mg/g MLSS) shortened electron transfer distance to NO3[-]-N, which, combined with a 17.3% increase in cytochrome (cyt.c), formed a new mode of multi-path electron transfer. Microbacterium with glucose-4-CP co-metabolism and denitrification functions contributed 13.0% of the recovered community, transforming glucose and 4-CP competitive metabolism into collaborative metabolism, further enhancing the anti-toxicity memory, and ensuring efficient denitrification performance.}, } @article {pmid42208547, year = {2026}, author = {Goldberg, H and Dyhrman, ST and DeMers, MA and Braakman, R and Hennon, GMM}, title = {Forces Shaping Diversity of Hydrogen Peroxide Detoxification Potential in Ocean Microbial Ecosystems.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70315}, doi = {10.1111/1462-2920.70315}, pmid = {42208547}, issn = {1462-2920}, support = {OCE-1937715//National Science Foundation/ ; OCE-2019589//National Science Foundation/ ; }, mesh = {*Hydrogen Peroxide/metabolism ; *Seawater/microbiology ; *Catalase/genetics/metabolism ; Ecosystem ; Oceans and Seas ; *Bacteria/genetics/metabolism/classification ; Bacterial Proteins/genetics/metabolism ; Metagenome ; *Microbiota ; Genome, Bacterial ; }, abstract = {Microbial communities have evolved interactions to support growth and essential ecosystem functions. For example, marine cyanobacteria like Prochlorococcus lack the catalase genes (katE, katG and manganese catalase) required for detoxifying freely-diffusible hydrogen peroxide, relying on co-occurring catalase-carrying 'helper' microbes for this function. However, the eco-evolutionary forces shaping catalase distribution are not well understood. We examined genomes, metagenome-assembled genomes (MAGs), and metagenomes to assess catalase gene distributions across diverse marine prokaryotes-including within the known 'helper' genus Alteromonas-and across surface ocean ecosystems. Within Alteromonas, most genomes contain two katE copies, while katG copy number varies across species. Across ecosystems, the Altermonadaceae family is the predominant katE carrier. Some taxa (e.g., SAR202) lack all catalases, highlighting their dependence on 'helpers'. Overall, streamlined genomes, including from SAR11, generally have one katG copy and lack katE, while larger genomes with higher GC content characteristic of copiotrophs have more copies of both catalases. Finally, in free-living communities, katG gene frequency increases with decreased particulate organic carbon (POC) concentrations, whereas in particle-associated communities, katE gene frequency increases with elevated POC. Together, these observations suggest that hydrogen peroxide detoxification capabilities are widespread and shaped by the contributions of particle-associated microbes to total community metabolism.}, } @article {pmid42208809, year = {2026}, author = {Korva, M and Bogovič, P and Knap, N and Kogoj, R and Slunečko, J and Zakotnik, S and Suljič, A and Resman Rus, K and Pozvek, P and Strle, F and Avšič-Županc, T and Petrovec, M}, title = {Emerging human pathogen: Identifying Spiroplasma ixodetis as a frequent cause of unlocalised febrile illness.}, journal = {The Journal of infection}, volume = {93}, number = {1}, pages = {106776}, doi = {10.1016/j.jinf.2026.106776}, pmid = {42208809}, issn = {1532-2742}, mesh = {Humans ; Female ; *Spiroplasma/isolation & purification/genetics/classification ; Male ; Adult ; Aged ; Middle Aged ; *Communicable Diseases, Emerging/microbiology/epidemiology/diagnosis ; Prevalence ; *Gram-Negative Bacterial Infections/epidemiology/microbiology/diagnosis ; RNA, Ribosomal, 23S/genetics ; Young Adult ; Sequence Analysis, DNA ; Real-Time Polymerase Chain Reaction ; Cohort Studies ; DNA, Bacterial/genetics/chemistry ; RNA, Ribosomal, 16S/genetics ; Aged, 80 and over ; *Fever/microbiology ; Adolescent ; }, abstract = {OBJECTIVES: Febrile illness without clear localisation presents a significant diagnostic challenge due to non-specific symptoms and diverse aetiologies. Spiroplasma ixodetis, an emerging tick-associated pathogen previously linked mainly to congenital cataracts, has not been well characterised in adults. We investigated the prevalence and clinical features of S. ixodetis infection in adults with acute febrile illness without localisation.

METHODS: Shotgun metagenomic sequencing identified S. ixodetis in the initial 209 patient cohort and the sequences were used to developed a novel real-time PCR assay targeting the 23S rRNA gene. Initial cohort screening was followed by testing 128 patients from an additionally selected targeted cohort. Positive results were confirmed by sequencing of 16S and 23S rRNA genes.

RESULTS: S. ixodetis DNA was confirmed in 7.2% patients from the initial and in 35.2% patients from the additional cohort (60 in total). All were identified in the period from April to October and 57% reported a recent tick-bite. Clinical presentation was homogenous, characterised by fever, headache, bicytopenia and liver enzyme abnormalities. Outcomes were favourable, with 15% requiring hospitalisation.

CONCLUSION: This study identifies S. ixodetis as a previously unrecognised cause of adult febrile illness without localisation, bridging the gap between previously published data between tick studies and isolated human case reports.}, } @article {pmid42208810, year = {2026}, author = {Vasil, E and Papanicolas, LE and Miller, SJ and Shoubridge, AP and Taylor, SL and Rogers, GB}, title = {Exposure to antibiotics with anaerobe coverage in later life is associated with higher enteric pathobiont carriage.}, journal = {The Journal of infection}, volume = {93}, number = {1}, pages = {106774}, doi = {10.1016/j.jinf.2026.106774}, pmid = {42208810}, issn = {1532-2742}, mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Female ; Male ; *Carrier State/microbiology/epidemiology ; Aged, 80 and over ; *Bacteria, Anaerobic/drug effects ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Aged ; Nursing Home Residents ; Prevalence ; }, abstract = {OBJECTIVES: Infections involving enteric bacteria commonly cause hospitalisation and death in long-term residential aged care (LTC) populations. The risk of such infections has been linked with antibiotic-associated depletion of gut anaerobic commensals and the resulting increase in asymptomatic carriage of gut pathobionts. We sought to determine how antibiotic characteristics, particularly activity against anaerobes, influence pathobiont prevalence in LTC residents.

METHODS: Stool samples from 164 LTC residents (median age: 87.9 years, interquartile range: 81.3-93.0 years) underwent metagenomic analysis. Associations between prior antibiotic exposures (categorised according to anaerobe coverage and type) and gut microbiome characteristics were explored using multivariable models.

RESULTS: Of the 164 participants, 138 (84.1%) carried at least one enteric pathobiont. Compared to those with no prior antibiotic exposure, treatment with anaerobe covering (EAC) antibiotics was associated with higher rates of pathobiont carriage (β=1.36, P=0.010) and higher overall pathobiont relative abundance (β=3.53, P=0.013). In contrast, exposure to antibiotics with limited anaerobe coverage (LAC) showed no such associations. Investigation of commonly prescribed EAC and LAC antibiotics (amoxicillin-clavulanate and cefalexin, respectively) were consistent with these findings, with higher detection (β=1.60, P=0.007) and relative abundance (β=3.32, P=0.039) of pathobiont species in amoxicillin-clavulanate recipients. Pathobionts with greater representation included both species with inherent resistance (i.e. Enterococcus faecium) and sensitivity (i.e. Klebsiella pneumoniae) to amoxicillin-clavulanate.

CONCLUSIONS: Antibiotics that deplete commensal anaerobes are associated with pathobiont prevalence in the gut, even where pathobiont species are sensitive to the administered antibiotic. Off-target disruption of commensal anaerobes should be considered when selecting antibiotic treatments, particularly for LTC individuals.}, } @article {pmid42208932, year = {2026}, author = {Lv, H and Jin, S and Li, L and Ma, S and Wang, Y and Zhang, Y and Guo, K}, title = {Diagnostic accuracy of metagenomic next-generation sequencing for invasive pulmonary aspergillosis: A systematic review and meta-analysis.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {170}, number = {}, pages = {108827}, doi = {10.1016/j.ijid.2026.108827}, pmid = {42208932}, issn = {1878-3511}, abstract = {OBJECTIVES: To systematically evaluate the diagnostic accuracy of metagenomic next‑generation sequencing (mNGS) for invasive pulmonary aspergillosis (IPA), and to compare its sensitivity and specificity with conventional methods.

METHODS: Meta‑analysis was performed to pool sensitivity, specificity, and diagnostic odds ratio (DOR). The comparison test between mNGS and conventional diagnostic methods was conducted through pairwise comparisons, and effect size was expressed using the risk difference (RD) and 95% confidence interval.

RESULTS: Twelve studies were included, the pooled sensitivity of mNGS was 0.75 (95% CI: 0.65-0.84), specificity 0.93 (95% CI: 0.84-0.97), DOR 35.69 (95% CI: 13.70-92.97). The comparative analysis showed mNGS had higher sensitivity compared with galactomannan (RD = 0.22, 95% CI: 0.16-0.29), culture (RD = 0.40, 95% CI: 0.26-0.55), and (1→3)-β-d-glucan (BDG) (RD = 0.23, 95% CI: 0.09-0.37). For BDG assay, mNGS also demonstrated superior specificity (RD = 0.12, 95% CI: 0.04-0.20).

CONCLUSION: mNGS demonstrates promising diagnostic accuracy for IPA, with favorable sensitivity and specificity, and shows higher sensitivity than several conventional methods. BALF is the preferred specimen, and combined testing with multiple sample types improves diagnostic yield.}, } @article {pmid42208954, year = {2026}, author = {Baker, B and Baz Lomba, JA and Bitilinyu-Bangoh, J and Berglöf, A and Bombaywala, S and Calvert-Joshua, T and Kaboré, B and Kingpriest, P and Lang, T and Levy, JI and Lompo, P and Lyimo, E and Martens, L and Mavoko, HM and Mesuere, B and Moremi, N and Mulder, N and Ndure, SL and Rameto, MA and Rinke de Wit, TF and Sebukoto, H and Smith, E and Tahita, MC and Tevuzula, VM and Tippett Barr, BA and Tiwari, A and Tran, T and Ubomba-Jaswa, E and Van Den Bossche, T and Wolday, D and Krolicka, A and Baraka, V and Pitkänen, T and Lood, R}, title = {Project ODIN: advancing environmental genomic surveillance for public health across sub-Saharan Africa.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101426}, doi = {10.1016/j.lanmic.2026.101426}, pmid = {42208954}, issn = {2666-5247}, abstract = {Persistent SARS-CoV-2 transmission, ongoing mpox outbreaks, and the continued spread of endemic diseases such as typhoid fever and cholera underscore the urgent need for global, multiomics surveillance. In this Personal View, we present Project ODIN, a consortium of European and African partners launched in 2023 that aims to meet this challenge by deploying innovative systems for near real-time pathogen detection and actionable public health insights. The project is a collaboration between high-income and low-income countries in northern Europe and sub-Saharan Africa. Focusing on low-income and middle-income countries, ODIN integrates metagenomics with mobile laboratory systems for comprehensive pathogen monitoring across diverse environments. ODIN emphasises standardised sampling, bioinformatics pipelines, and data-sharing protocols to ensure reliable, interoperable results while addressing infrastructure and resource limitations. By bridging gaps in genomic surveillance, these initiatives seek to strengthen outbreak preparedness, improve pathogen detection, monitor antimicrobial resistance, and provide a holistic approach to One Health challenges. Together, these innovations could advance global surveillance capacity-particularly in under-resourced regions-paving the way for effective disease control and evidence-based policy making.}, } @article {pmid42209028, year = {2026}, author = {Hoeter, K and Marriott, L and Neuberger, EWI and Dagwadordsch, U and Kumar, RS and Simon, P and Bodenstein, M and Kersaudy-Kerhoas, M}, title = {Plasma metagenomic cfDNA sequencing identifies pathogens in culture-negative sepsis following urinary pouch rupture.}, journal = {BMJ case reports}, volume = {19}, number = {5}, pages = {}, pmid = {42209028}, issn = {1757-790X}, mesh = {Humans ; Female ; *Sepsis/microbiology/diagnosis/drug therapy/blood ; Anti-Bacterial Agents/therapeutic use ; *Cell-Free Nucleic Acids/blood ; *Pseudomonas Infections/diagnosis/drug therapy/blood ; Metagenomics/methods ; *Klebsiella Infections/diagnosis/drug therapy/blood ; Rupture, Spontaneous ; Klebsiella/isolation & purification/genetics ; }, abstract = {A patient with a complex urological history presented with abdominal pain and respiratory distress after catheter dysfunction. She underwent emergency surgery for a ruptured urinary pouch. Sepsis was later diagnosed based on clinical deterioration, including tachycardia, fever, an elevated respiratory rate and raised inflammatory markers, but blood cultures remained negative. A metagenomic microbial cell-free DNA (cfDNA) assay (iSEP-SEQ), performed early from plasma as part of a research protocol, identified Klebsiella and Pseudomonas at the genus level. Results were obtained retrospectively and were not available in real time; therefore, they did not alter immediate management. These findings were confirmed by cultures from drainage fluid and urine. Broad-spectrum antibiotic treatment led to clinical improvement. This case highlights the limitations of conventional microbiological methods in culture-negative sepsis and illustrates the role of cfDNA-based metagenomic testing as an adjunctive and complementary diagnostic tool for early, accurate pathogen detection. Early use of such tools may support timely and targeted management in complex infectious disease presentations.}, } @article {pmid42209192, year = {2026}, author = {Leggio, M and Schramm, S and Dietz, L and Ocón, B and Wirtz, S and Puertolas Balint, F and Yilmaz, B and Petzold, J and Liu, LJ and Dedden, M and Ekici, A and , and Meng, X and Bingham, D and Ullrich, KA and Heltmann-Meyer, S and Günther, C and Hildner, K and Atreya, R and Atreya, I and Müller, TM and Gerlach, RG and Schroeder, BO and Macpherson, A and Butcher, EC and Neurath, MF and Zundler, S and , }, title = {The endogenous peptide GPR15L shapes the intestinal microbiota to counteract colitis.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337619}, pmid = {42209192}, issn = {1468-3288}, abstract = {BACKGROUND: The peptide GPR15L is produced by colonic epithelial cells and has been implicated in T cell recruitment to the large intestine. However, its role in chronic colitis has been unclear so far.

OBJECTIVE: To explore the role of GPR15L in the pathogenesis of experimental colitis and IBD.

DESIGN: We studied how genetic deletion or overexpression of Gpr15l as well as rectal application of recombinant GPR15L alters the course of acute dextran sodium sulfate colitis and T cell transfer colitis. The impact of GPR15L on microbiota was explored with co-housing, littermate and faecal microbiota transfer studies, by 16S rRNA sequencing as well as anti-microbial assays and shotgun metagenomics. The expression of GPR15L was evaluated across three independent cohorts of patients with IBD and correlated to microbial diversity and flare-free survival.

RESULTS: GPR15L clearly mitigated experimental colitis, but this was independent of T cell recruitment and GPR15. Instead, we observed that the effects of GPR15L were mediated by altered microbiomes in the large intestine and, consistently, showed that GPR15L acts as an antimicrobial peptide under anaerobic conditions and shapes microbial communities towards a homeostatic phenotype. Rectal supplementation of GPR15L counteracted experimental colitis. In patients with IBD, GPR15L expression was decreased in active inflammation, correlated with microbial diversity and was associated with flare-free survival.

CONCLUSIONS: GPR15L is a host-defence peptide that plays a beneficial role in the pathogenesis of intestinal inflammation. It seems promising to further evaluate its potential as a future therapeutic approach in IBD.}, } @article {pmid42209465, year = {2026}, author = {Ghiotto, G and Zampieri, G and Orellana, E and Chatzis, A and Kougias, PG and Camargo, A and Roux, S and Campanaro, S and Kyrpides, NC and Treu, L}, title = {Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73084-2}, pmid = {42209465}, issn = {2041-1723}, abstract = {Microbial bioconversions are shaped by environmental perturbations and the adaptation of resident microbiomes. Prokaryotes coexist with bacteriophages, yet their coevolutionary trajectories remain underexplored. Here, we investigate the effects of a cultivation vessel leak on an anaerobic consortium performing carbon dioxide reduction. Using time-series shotgun metagenomic sequencing, we reconstruct microbial and viral genomes to track community shifts. We further apply single-nucleotide variant profiling and CRISPR array analysis to monitor viral microdiversity and host defense mechanisms. After bioaugmentation restores bioconversion efficiency, the consortium undergoes pronounced restructuring, with new dominant taxa emerging from the rare biosphere. We identify patterns consistent with phage predation selectively removing certain species, while others exhibit resilience to infection. This shift aligns with a widespread viral outbreak and a transient increased frequency of single nucleotide variants in bacterial CRISPR-Cas defense genes. Expansion of CRISPR spacers further supports that CRISPR-mediated processes influence microbial resilience. Concurrently, phages infecting resilient hosts exhibited adaptive evolution, marked by high genetic heterogeneity. Selective pressure varies across their genomes, targeting infectivity genes and protospacer-adjacent motifs. These findings highlight a dynamic evolutionary arms race driven by the selection of beneficial genetic variants, providing a mechanistic framework for multi-omics investigations, and informing biotechnological applications, including phage-based microbiome manipulation.}, } @article {pmid42209510, year = {2026}, author = {Dommann, J and Sprecher, VP and Beisel, C and Ballmer, D and Hürlimann, E and Coulibaly, JT and Keiser, J and Schneeberger, PHH}, title = {Combined high-quality metagenomics reveals off-target effects of albendazole, ivermectin-albendazole and moxidectin-albendazole on the human gut bacteria.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01018-3}, pmid = {42209510}, issn = {2055-5008}, support = {101019223/ERC_/European Research Council/International ; 101019223/ERC_/European Research Council/International ; }, abstract = {Human whipworm infections caused by Trichuris trichiura and Trichuris incognita remain a major public health problem, affecting over 400 million people globally and responding poorly to standard benzimidazole chemotherapy. Ivermectin-albendazole and moxidectin-albendazole have emerged as promising combination therapies, but recent in vitro evidence suggests that ivermectin and moxidectin may also affect gut bacteria. We therefore characterized their off-target effects on the gut microbiome in a randomized controlled trial including 204 Trichuris spp.-infected individuals in Côte d'Ivoire treated with albendazole (400 mg), ivermectin-albendazole (200 µg/kg/400 mg), or moxidectin-albendazole (8 mg/400 mg). By combining Illumina short reads and Nanopore long reads, we recovered over 800 high-quality metagenome-assembled genomes. Albendazole and moxidectin-albendazole induced taxonomic shifts with only mild functional consequences. In contrast, individuals receiving higher absolute ivermectin doses based on their bodyweight (≥ 15 mg) showed pronounced changes in taxonomic composition and microbial function, whereas the resistome remained largely stable. These findings confirm that ivermectin can exert antibacterial off-target effects in the human gut beyond those previously observed in vitro. Given its central role in parasite control, its broader microbiome effects warrant careful evaluation in future treatment strategies.}, } @article {pmid42209552, year = {2026}, author = {Olszyński, RM and Mann, DG and Zakrzewski, PK and Peszek, Ł and Ács, É and Shemesh, S and Trobajo, R}, title = {Nitzschia excavata sp. nov. (Bacillariaceae), a new diatom species from a post-mining reservoir revealed by morphology, molecular phylogeny, and metabarcoding-based biogeography.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42209552}, issn = {2045-2322}, support = {RRF 2.3.1 21 2022 00008//Széchenyi Plan Plus programme/ ; RRF 2.3.1 21 2022 00008//Széchenyi Plan Plus programme/ ; }, mesh = {*Diatoms/genetics/classification/ultrastructure ; *Phylogeny ; *DNA Barcoding, Taxonomic ; Phylogeography ; Mining ; DNA, Ribosomal/genetics ; Poland ; }, abstract = {The Bogdałów post-mining reservoir (Poland) represents a slightly alkaline, moderately mineralised ecosystem formed by flooding a former lignite pit. Its anthropogenic origin and stable physicochemical conditions have enabled the development of species-rich diatom assemblages, particularly numerous Nitzschia (Bacillariaceae) species. To explore this diversity, an integrative approach combining microscopy and DNA-based analyses was employed. Morphological examinations were performed using light and scanning electron microscopy, as well as confocal laser scanning microscopy. Molecular phylogenetic analyses were based on the sequencing of the nuclear SSU rDNA and the chloroplast rbcL and psbC gene markers. This comprehensive study led to the discovery and formal description of Nitzschia excavata sp. nov., distinguishable by unique morphological features and a phylogenetically distinct lineage. Furthermore, environmental DNA metabarcoding and metagenomic database searches revealed sequences identical or closely related to the N. excavata sp. nov. lineage in freshwater habitats across Europe and China, indicating that this taxon has an unexpectedly broad distribution. These findings underscore the value of integrating classical morphological analysis with multi-marker molecular data in diatom taxonomy and demonstrate that anthropogenic habitats may support taxa with broader distributions than previously recognized. The study highlights the important role of metabarcoding and metagenomics in revealing cryptic diversity and clarifying the biogeographic patterns of newly described species.}, } @article {pmid42209868, year = {2026}, author = {Ajeh, IJ and Ikukpla'si, OSI}, title = {The non-bacterial oncobiome: the role of the mycobiome and virome in tumor plasticity.}, journal = {Journal of the Egyptian National Cancer Institute}, volume = {38}, number = {1}, pages = {}, pmid = {42209868}, issn = {2589-0409}, mesh = {Humans ; Tumor Microenvironment ; *Neoplasms/pathology/microbiology/virology ; *Mycobiome ; *Virome ; Epithelial-Mesenchymal Transition ; Cell Plasticity ; }, abstract = {Tumor plasticity, the capacity of malignant cells to undergo reversible phenotypic switching, is a fundamental driver of lineage diversion and therapeutic resistance. While the bacterial microbiome is a recognized modulator of the tumor microenvironment (TME), the non-bacterial oncobiome, comprising the mycobiome (fungi) and virome (viruses), represents a critical but under-explored frontier in cellular adaptability. This review synthesizes current evidence regarding the mechanistic contributions of fungal and viral constituents to tumor plasticity and characterizes the molecular cross-talk that facilitates host cell reprogramming. We conducted a structured narrative synthesis of literature indexed in PubMed, Scopus, and Web of Science (2020-2026), focusing on high-throughput studies such as ITS sequencing, metagenomics NGS (mNGS), and single-cell network analyses. We specifically evaluated evidence concerning the activation of host pattern recognition receptors and the subsequent transcriptional rewiring of lineage-defining markers. Emerging data indicate that fungal dysbiosis, particularly involving Candida and Malassezia species, triggers the Dectin-1/STAT3 signaling axis, a known inducer of epithelial-mesenchymal transition (EMT). Concurrently, the virome, ranging from integrated oncoviruses to reactivated endogenous retroviruses (ERVs), is shown to hijack the Wnt/ β-catenin pathway, enforcing a progenitor-like stemness state. This inter-kingdom synergy promotes an immune-excluded niche, effectively shielding plastic sub-populations from cytotoxic stress and targeted therapies. The non-bacterial oncobiome provides genomic momentum and inflammatory cues necessary to lower the threshold for phenotypic switching. This review highlights that stabilizing the TME ecosystem through ecologically targeted therapy may be a prerequisite for overcoming drug resistance and improving clinical outcomes in refractory cancers.}, } @article {pmid42210135, year = {2026}, author = {Feng, W and Xiao, H and Hu, B and Chen, T and Hu, H and Guo, L and Guo, X and Zhu, L and Liu, G}, title = {Clinical characteristics, diagnosis, and management of central nervous system aspergillosis in children: a single-center experience.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13675-y}, pmid = {42210135}, issn = {1471-2334}, support = {2024-1-2092//Capital's Funds for Health Improvement and Research/ ; 2-1-2-6-15//2022 Beijing Major Epidemic Prevention and Control Specially Construction Project/ ; PX2024042//Beijing Municipal Administration of Hospitals Incubating Program/ ; }, abstract = {BACKGROUND: Central nervous system (CNS) aspergillosis is a severe and frequently misdiagnosed infection in pediatric patients. Systematic pediatric data on its clinical, radiological, diagnostic, and therapeutic features remain limited.

METHODS: We retrospectively identified children aged 0-18 years with proven or probable CNS aspergillosis admitted to Beijing Children's Hospital between January 2010 and December 2024. Demographic, clinical, laboratory, and imaging data were collected. Treatment regimens and clinical outcomes were systematically evaluated.

RESULTS: Sixteen patients were included (12 males), with a median age of 5 years. Hematological malignancies were the most common predisposing factor. Notably, 25% (4/16) of patients lacked identifiable predisposing conditions. Clinical presentations were nonspecific, with fever, seizures, and impaired consciousness being the most common features, and an initial misdiagnosis occurred in 56.3% (9/16) of cases. In contrast to the low yield of cerebrospinal fluid (CSF) cultures, CSF metagenomic next-generation sequencing (mNGS) detected Aspergillus nucleic acids in all tested patients (7/7). Magnetic resonance imaging (MRI) most commonly revealed irregular cerebral abscesses (14/16), frequently accompanied by meningeal enhancement (14/16) and obstructive hydrocephalus (10/16). Among evaluable patients receiving initial voriconazole monotherapy, a partial response was observed in 22.2% (2/9). Conversely, higher response rates were observed with regimens containing liposomal amphotericin B (L-AmB), including initial combination therapy (75.0%) and salvage treatment (80.0%). The all-cause mortality rate was 37.5% (6/16), and moderate-to-severe disability was present in 30.0% (3/10) of survivors.

CONCLUSIONS: Pediatric CNS aspergillosis can occur across a broad risk spectrum, often with nonspecific symptoms, leading to frequent misdiagnosis. Our findings support the early incorporation of CSF mNGS and comprehensive neuroimaging (including whole-neuraxis MRI when clinically indicated) to facilitate timely diagnosis and assess dissemination. The observed high rate of progression with initial voriconazole monotherapy and the relatively favorable responses associated with regimens containing L-AmB highlight the need for prospective pediatric studies to refine initial treatment strategies in severe disease.

CLINICAL TRIAL REGISTRATION: Not applicable.}, } @article {pmid42210369, year = {2026}, author = {Pangestu, HS and Yang, I and Natasha, A and Rajoriya, S and Hennisa, H and Park, J and Park, K and Kim, J and Kim, SG and Klein, TA and Kim, HC and Oh, Y and Song, JW and Kim, WK}, title = {Molecular prevalence, genomic characterization, and zoonotic potential of novel paramyxovirus and hepacivirus in Alexandromys fortis, Republic of Korea.}, journal = {Veterinary research}, volume = {57}, number = {1}, pages = {}, pmid = {42210369}, issn = {1297-9716}, support = {ProMIS ID C0039-09-ME//Global Emerging Infections Surveillance Branch (GEIS)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion/ ; RS-2023-KH140418//Government-wide R&D to Advance Infectious Disease Prevention and Control, Republic of Korea/ ; 2024-ER2502-00//Korea National Institute of Health Research Project/ ; RS-202300249142//Basic Science Research Program through the NRF by the Ministry of Education/ ; NF22SA0082041//Novo Nordisk Foundation PAD award to CBL/ ; U01 AI151810/AI/NIAID NIH HHS/United States ; 2023R1A2C2006105//Basic Research Program through the NRF grant funded by the Korean government (MSIT)/ ; RS-2024-00400152//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through High-Risk Animal Infectious Disease Control Technology Development Program, funded by Ministry of Agriculture, Food and Rural Affairs/ ; }, mesh = {Animals ; Republic of Korea/epidemiology ; *Genome, Viral ; Phylogeny ; *Arvicolinae/virology ; *Paramyxoviridae Infections/veterinary/epidemiology/virology ; *Rodent Diseases/virology/epidemiology ; *Zoonoses/virology/epidemiology ; Prevalence ; *Paramyxoviridae/genetics/isolation & purification ; *Hepatitis C/virology/epidemiology/veterinary ; }, abstract = {Rodents are substantial reservoirs of zoonotic viruses with regular human exposure restricted to a limited number of species. Numerous rodent species have been shown to harbor emerging viruses, including paramyxoviruses and hepaciviruses. Reed voles (Alexandromys fortis), a rodent species that inhabits grasslands and riparian environments throughout East Asia, remain poorly characterized in terms of their viral diversity. In this study, 258 A. fortis specimens collected from rural areas in Gyeonggi Province, Republic of Korea (ROK) were screened for paramyxoviruses and subjected to metagenomic next-generation sequencing. Genome characterization, phylogenetic and cophylogenetic assessments, and prediction of signal peptidase cleavage sites were performed to analyze the molecular features of the identified viruses. Zoonotic potential was evaluated using a genome-based machine-learning model. A nearly complete genome of a novel paramyxovirus, designated as Pyeongtaek Alexandromys paramyxovirus (PyAPV), was identified in six A. fortis specimens, with all sequences clustering within the genus Jeilongvirus. A nearly complete genome of a rodent-associated hepacivirus was also obtained from four specimens and classified as a distinct lineage within the species Hepacivirus J. These findings demonstrate the role of A. fortis as a natural reservoir of emerging viruses and expand current knowledge of rodent-associated viral diversity in the ROK.}, } @article {pmid42210378, year = {2026}, author = {Han, J and Liu, J and Wang, T and Dong, B and Zhang, F and Li, S and Zou, Q and Li, D}, title = {Temporal variations in the gut microbiota of François' langur (Trachypithecus francoisi): implications for adaptation to seasonal dietary change and conservation.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00580-7}, pmid = {42210378}, issn = {2524-4671}, abstract = {Despite growing research on gut microbiota in wild primates, seasonal functional dynamics of the gut microbiota in this endangered folivorous species remain poorly understood. This study investigates the seasonal variations in the gut microbiota of François' langur (Trachypithecus francoisi) and their implications for dietary adaptation and conservation. Using shotgun metagenomic sequencing, fecal samples were collected across four seasons within the Mayanghe National Nature Reserve in China (n = 24). The study identified significant seasonal shifts in microbial diversity and composition. While alpha diversity metrics reflecting community evenness (Shannon and Simpson equivalents) remained stable (Padj > 0.05), species richness (Hill number, q = 0) was significantly lower in Fall compared to Spring and Winter (Padj = 0.013). Results revealed that dominant phyla included Bacillota and Bacteroidota, with a significant enrichment of Faecalibacterium during Fall. Functional analysis showed a predominance of carbohydrate metabolism, which remained stable at broad metabolic levels; however, fine-scale functional units (KOs and CAZy families) exhibited distinct seasonal signatures. A moderate correlation between taxonomic and functional profiles (Mantel r = 0.43, P = 0.001) suggests a partial decoupling. These findings highlight the ecological plasticity of the gut microbiota and underscore how taxonomic flexibility enables functional homeostasis, aiding the physiological resilience of endangered primates in fluctuating environments.}, } @article {pmid42210496, year = {2026}, author = {Gourabi, MJR and Kargar, M and Kamali, A and Sharahi, JY}, title = {Fungal-Bacterial Interactions in Polymicrobial Infections: Hidden Threats.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70320}, pmid = {42210496}, issn = {2045-8827}, mesh = {Humans ; *Coinfection/microbiology/drug therapy ; Biofilms/growth & development ; *Microbial Interactions ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Candida albicans/physiology ; *Bacteria/drug effects ; *Fungi/physiology/drug effects ; *Mycoses/microbiology ; *Bacterial Infections/microbiology ; }, abstract = {Polymicrobial infections involving fungi and bacteria represent a major and increasingly recognized clinical challenge, in which interkingdom interactions significantly amplify disease severity, antimicrobial resistance, and treatment failure. Rather than passive co-existence, fungal-bacterial communities form highly coordinated systems driven by physical adhesion, quorum sensing, metabolic interdependence, and biofilm-mediated structural reinforcement. These cooperative interactions, exemplified by pairs such as Candida albicans-Staphylococcus aureus and Pseudomonas aeruginosa-Aspergillus fumigatus, promote the development of treatment-recalcitrant biofilms with enhanced immune evasion and multidrug tolerance. The global rise of multidrug-resistant (MDR) and extensively drug-resistant (XDR) pathogens has further intensified this burden, with polymicrobial biofilms now representing a post-antibiotic clinical scenario in which therapeutic failure is driven not by individual resistant organisms but by emergent, cooperative resistance architectures. Conventional diagnostic approaches remain insufficient, as culture-based methods frequently fail to capture the complexity of mixed microbial communities. Emerging technologies such as MALDI-TOF mass spectrometry, metagenomic sequencing, and fluorescence in situ hybridization offer improved resolution but are not yet fully integrated into routine clinical practice. Therapeutically, increasing evidence indicates that monotherapy is inherently inadequate in polymicrobial infections due to the emergent nature of microbial cooperation. Effective management therefore requires combination strategies that simultaneously target multiple pathogens and their shared biofilm infrastructure. These include antibiotic-antifungal combinations, phage therapy, enzymatic and nanoparticle-mediated biofilm disruption, metabolic interference, and host-directed immunomodulation. Importantly, recent advances also highlight the role of biophysical properties such as biofilm viscoelasticity and matrix stiffness as critical and previously underappreciated therapeutic targets. This review uniquely integrates biochemical, biophysical, and therapeutic dimensions of polymicrobial infections into a unified systems-level framework in which microbial cooperation is the central driver of pathogenesis, resistance, and treatment failure. Fungal-bacterial interactions are thereby positioned along a dynamic continuum from commensalism to pathogenesis, shaped by host susceptibility and environmental perturbations. Future progress will depend on interdisciplinary strategies combining multi-omics technologies, precision diagnostics, and microbiome-informed therapeutic design to effectively disrupt these complex microbial networks.}, } @article {pmid42210528, year = {2026}, author = {Zhou, X and Zhang, M and Zhou, J and Han, J}, title = {Multi-target effects of Limosilactobacillus reuteri RE225 on hyperuricemia through xanthine oxidase inhibition, nucleoside degradation, gut microbiota modulation, and renal TLR4-NF-κB suppression.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70749}, pmid = {42210528}, issn = {1097-0010}, support = {2024S138//Ningbo Public Welfare Research Program/ ; //K.C. Wong Magna Fund of Ningbo University/ ; }, abstract = {BACKGROUND: Hyperuricemia, a major risk factor for gout and kidney disease, requires safe and effective dietary strategies beyond conventional pharmacotherapy. This study investigated the multi-target effects of the food-grade probiotic Limosilactobacillus reuteri RE225 on hyperuricemia. It was evaluated in vitro for xanthine oxidase (XOD) inhibition and nucleoside degradation, and in vivo in hyperuricemic mice gavaged daily with low or high doses of RE225 (1 × 10[6] or 1 × 10[9] CFU). Serum uric acid (UA), XOD activity, inflammatory cytokines, intestinal permeability markers - fluorescein isothiocyanate-dextran (FITC-dextran), lipopolysaccharide (LPS), and d-lactate - and renal TLR4/NF-κB signaling were quantified. Fecal metagenomics and Kyoto Encyclopedia of Genes and Genomes ortholog (KO) profiling were used to assess microbiota structure and function.

RESULTS: Limosilactobacillus reuteri RE225 dose-dependently inhibited XOD and degraded more than 50% of nucleosides in vitro. In vivo, RE225 reduced serum urate, restored intestinal barrier function, suppressed inflammation, and downregulated renal TLR4/NF-κB signaling. Metagenomic analysis showed that L. reuteri RE225 reversed UA-induced loss of microbial richness and evenness, enriched Faecalibaculum and Erysipelotrichaceae, and shifted functional profiles from proliferation- and inflammation-related modules (K02315, K02970, and K03496) toward carbohydrate utilization and genetic stability pathways (K01784 and K07491).

CONCLUSION: Limosilactobacillus reuteri RE225 shows promise as a dietary intervention for the management of hyperuricemia. © 2026 Society of Chemical Industry.}, } @article {pmid42210827, year = {2026}, author = {Syatrawati, and Kuswinanti, T and Nasruddin, A and Rosmana, A and Hikmahwati, }, title = {Metagenomic Insights into Rhizosphere Fungal Communities Across Different Rice Cultivation Systems.}, journal = {Pakistan journal of biological sciences : PJBS}, volume = {29}, number = {3}, pages = {147-159}, doi = {10.3923/pjbs.2026.147.159}, pmid = {42210827}, issn = {1812-5735}, mesh = {*Oryza/microbiology/growth & development ; *Rhizosphere ; *Metagenomics/methods ; *Fungi/genetics/classification ; Soil Microbiology ; Agriculture/methods ; }, abstract = {Background and Objective: Rhizosphere fungi play a crucial role in nutrient cycling and plant protection, yet most are difficult to cultivate using conventional methods. Consequently, their ecological functions remain largely unknown. Therefore, metagenomic approaches allow for comprehensive and accurate mapping of fungal taxonomic profiles without the need for cultivation and this study investigated the variation of rhizosphere fungi across different rice cultivation systems to elucidate their diverse potentials. Materials and Methods: A metagenomic approach was employed to identify fungi originating from the rhizosphere of rice cultivated in various field conditions, including irrigated, rainfed and organic rice fields. The diversity of fungi from rhizosphere samples was assessed to comprehend the relationships and metrics within the rice cropping systems utilized by farmers. Results: The findings indicated that the rhizosphere fungal index from organic rice fields exhibited the highest Shannon and Simpson index values compared to those from irrigated and rainfed rice fields. Conclusion: Metagenomic analysis revealed that the most dominant fungal diversity at the family level was Trichocomaceae, at the genus level was Talaromyces and at the species level was Talaromyces wortmannii.}, } @article {pmid42211404, year = {2026}, author = {Su, L and Zhang, Y and Xie, Y and Wu, J and Yang, Y and Li, Y and Huang, Y and Liu, X and Wei, X and Chen, Q}, title = {Integrated metabolomics and gut microbiota analyses reveal the protective effects of matrine in ulcerative colitis.}, journal = {Frontiers in chemistry}, volume = {14}, number = {}, pages = {1826894}, pmid = {42211404}, issn = {2296-2646}, abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic inflammatory bowel disease driven by gut microbial dysbiosis and metabolic dysfunction. Matrine, a natural alkaloid with anti-inflammatory properties, shows therapeutic potential; however, its mechanisms involving the coordinated modulation of bacteria, fungi, and host intestinal luminal metabolism remain unclear.

METHODS: We evaluated the therapeutic efficacy of matrine using a dextran sulfate sodium (DSS)-induced murine model of ulcerative colitis. Disease severity was assessed via the disease activity index, colon length, and histopathology. Integrated multi-omics approaches, including metagenomics, ITS fungal sequencing, and untargeted metabolomics of intestinal luminal contents, were employed to systematically characterize the regulatory effects of matrine on gut bacteria, fungi, and metabolic profiles.

RESULTS: Here, we demonstrated that oral matrine significantly alleviated disease severity in a DSS-induced UC mouse model, as evidenced by improved disease activity index, colon length, histopathology, and restoration of tight junction proteins. Integrated multiomics revealed that matrine restored bacterial homeostasis-suppressing Escherichia while enriching SCFAs-producing taxa (Muribaculum, Paramuribaculum, Clostridium). Metagenomic predictions revealed that matrine treatment reversed the model-induced suppression of carbohydrate metabolism and bile acid biosynthesis while upregulating depleted CAZy enzyme families, thereby correcting dysregulated metabolic functions in colitis. Furthermore, matrine rebalanced the mycobiota by normalizing the Ascomycota/Basidiomycota ratio. Intestinal luminal contents untargeted metabolomics identified 43 matrine-responsive metabolites, implicating correction of bile acid metabolism, attenuation of leukotriene-mediated inflammation, and reversal of acylcarnitine-driven epithelial energy disruption. Critically, pro-inflammatory metabolites correlated positively with Escherichia and negatively with beneficial symbionts.

CONCLUSION: Our findings established that matrine exerted protective effects in UC through a unified "microbiota-metabolism" axis, highlighting its promise as a multi-target therapeutic agent for UC.}, } @article {pmid42211783, year = {2026}, author = {Ding, F and Li, Y and He, T and Wang, Y and Li, Y and Huang, Y and Yin, G and Yang, J and Liu, Y and Li, Y and Li, T and Hou, L and Liu, M}, title = {Deciphering the drivers of antibiotic resistance gene transmission in the megacity: Co-occurring contaminants and bacterial community.}, journal = {Eco-Environment & Health}, volume = {5}, number = {2}, pages = {100242}, pmid = {42211783}, issn = {2772-9850}, abstract = {Urban waters are widely contaminated with co-occurring microplastics and antibiotics. Human-land interactions (e.g., wastewater discharge, stormwater runoff, and land use) drive contaminant distribution and antimicrobial resistance. Nevertheless, there is a lack of systematic research evaluating the role of co-occurring contaminants in shaping the spread of antibiotic resistance genes (ARGs). In this study, a metagenomic approach was used to characterize the diversity and distribution of ARGs based on contaminant co-occurring patterns. The random forests and partial least squares path model (PLS-PM) were used to identify and prioritize the factors impacting ARGs, leading to a thorough environmental health ecological risk evaluation. Industrial waters, especially pharmaceutical factories, were significant reservoirs and hotspots for the development of ARGs. Urban estuaries further gathered and amplified the effects of co-occurring contaminants, thereby enhancing the prevalence of ARGs. The potential spread of ARGs was dominated by contaminant co-occurring patterns in urban waters, whereas microbial communities dominated in sediments. Urban zoning comprehensively affected environmental health risks, indicating that environmental management strategies, such as controlling pollution sources and implementing remediation, should prioritize water bodies in agricultural areas and sediments in commercial/residential areas.}, } @article {pmid42211787, year = {2026}, author = {Zhang, R and Chen, YK and Zhu, QY and Feng, RY and Liu, H and Ma, MM and Wang, XJ}, title = {Metagenomic profiling of ocular surface microbiome alterations in patients with progressive supranuclear palsy-Richardson's syndrome.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100605}, pmid = {42211787}, issn = {2666-5174}, abstract = {This study employed shotgun metagenomic sequencing to characterize the ocular surface microbiome in 20 progressive supranuclear palsy-Richardson's syndrome (PSP-RS) patients, 17 Parkinson's disease (PD) patients, and 30 healthy controls (HC). Comparative analysis revealed that PSP-RS patients exhibited significantly altered microbial β-diversity compared to HC, while PD patients showed no such significant changes. Both patient groups demonstrated decreased abundance of g_Vibrio, with PSP-RS patients additionally showing marked increases in g_Acinetobacter and g_Anaerococcus. Importantly, correlation analyses identified that increased g_Acinetobacter abundance was positively associated with ocular motor impairment severity, while elevated g_Anaerococcus levels correlated with both freezing of gait severity and longer disease duration in PSP-RS patients. This is the first shotgun metagenomic investigation of the ocular surface microbiome in PSP-RS and these findings provide evidence that specific alterations in the ocular surface microbiome may contribute to PSP-RS pathogenesis and disease progression.}, } @article {pmid42211840, year = {2026}, author = {Pesantes, N and Barberá, A and Pérez-Rocher, B and Artacho, A and Vargas, SL and Moya, A and Ruiz-Ruiz, S}, title = {Correction: Influence of mental health medication on microbiota in the elderly population in the Valencian region.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1861757}, doi = {10.3389/fmicb.2026.1861757}, pmid = {42211840}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1094071.].}, } @article {pmid42211849, year = {2026}, author = {Du, R and Xu, C and Zhao, D and Zeng, H and Cheng, Y and Tang, K and Cai, P and Zhang, Y}, title = {Contrasting microbial iron metabolism in sediments from oxic and hypoxic estuaries.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1824768}, pmid = {42211849}, issn = {1664-302X}, abstract = {Estuarine sediments are pivotal zones for iron (Fe) cycling, mediated by microbial communities and coupled to carbon, nitrogen, sulfur and phosphorus transformations. However, the microbial iron metabolic processes in estuarine sediments remain poorly characterized, particularly under hypoxia. This study compared metagenomes from the Oujiang River Estuary, an oxic estuary, and the Yangtze River Estuary, a seasonally hypoxic estuary, complemented by sediment core incubations to assess geochemical responses to deoxygenation. The taxonomic affiliations of iron metabolism-related genes in the oxic estuary were homogeneous with depth, dominated by Proteobacteria and Thermodesulfobacteriota. In contrast, the hypoxic estuary exhibited strong stratification, with the surface enriched in Proteobacteria and deeper horizons dominated by Chloroflexota and Candidatus Bathyarchaeota. The surface sediments of the hypoxic estuary at 0-8 centimeters below the seafloor showed a hotspot with co-enrichment of dissimilatory iron reduction (e.g., mtrABC) and iron oxidation genes (e.g., mtoA) relative to both deeper layers in the same estuary and the oxic estuary, consistent with elevated genetic potential for Fe redox turnover. This hotspot also harbored high-affinity Fe acquisition systems (siderophores, inorganic Fe transporters, and heme uptake), suggesting the potential for microbial competition for iron. Co-occurrence networks connecting Fe metabolism with carbon, nitrogen, sulfur and phosphorus cycling were more complex in the hypoxic estuary than in the oxic estuary, revealing strong associations between Fe acquisition/redox cycling and organic matter turnover. A 16-day incubation of sediment cores from the oxic estuary showed that short-term deoxygenation enhanced dissolved Fe, phosphate, and ammonium release. Overall, our results suggest that bottom-water hypoxia is associated with major shifts in microbial iron metabolism potential, with implications for iron-organic matter interactions and nutrient regeneration under coastal deoxygenation.}, } @article {pmid42211850, year = {2026}, author = {Li, L and Liu, R and Yang, H and Zhao, Y}, title = {Metagenomic sequencing reveals structural and functional differentiation of rhizosphere bacterial communities driven by nitrogen and potassium deficiency associated with root rot of Schisandra chinensis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1827096}, pmid = {42211850}, issn = {1664-302X}, abstract = {BACKGROUND: Frequent incidence of root rot in Schisandra chinensis impairs its yield and quality, yet the rhizosphere microecological mechanism driving this incidence remains unclear.

METHODS: To clarify this mechanism, healthy and root rot-infected S. chinensis plants were analyzed in this study. The plant growth, rhizosphere soil physicochemical properties, and the structural and functional differences in rhizosphere bacterial communities under both conditions were analyzed.

RESULTS: Our results showed that root rot significantly inhibited S. chinensis growth and pathogen colonization-induced rhizosphere acidification, with reduced hydrolyzable nitrogen (HN) and available potassium (AK). Analysis of the intergroup differences in bacterial species revealed that the healthy rhizosphere was enriched with Acidobacteriota, Luteitalea, Pseudomonadota, Pseudolabrys, and Methylomirabilota, whereas infected rhizosphere was dominated by Gaiella (Actinomycetota), Gemmatimonas (Gemmatimonadota), Bradyrhizobium, and Sphingomicrobium (Pseudomonadota). Functional annotation based on COG, KEGG, and CAZy databases revealed that the bacteria of the healthy rhizosphere were enriched in defensive-cooperative functions (synergistic metabolism, secondary metabolite synthesis, complex carbon metabolism), while those of the infected rhizosphere exhibited simplified survival functions (individual metabolism, ABC transport, simple carbohydrate metabolism). Redundancy analysis identified HN and AK as key nutrients driving community differentiation in the rhizosphere.

CONCLUSION: This study revealed that root rot in S. chinensis is closely associated with an imbalance in the rhizosphere environment-bacterial community-function system, with healthy plants exhibiting specific core bacterial biomarkers and more complex synergistic metabolic networks, while HN and AK are key nutrients influencing rhizosphere bacterial communities. This study clarifies the rhizosphere microecological mechanism associated with S. chinensis root rot, providing a theoretical basis for its control.}, } @article {pmid42212564, year = {2026}, author = {Kim, Y and Kim, JK and Her, M and Kong, HS and Moon, JS and Yun, CS}, title = {Shotgun Metagenomic Diagnosis of Unidentified Pathogens in Hepatic Necrosis Samples from Samgye Chickens.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {}, number = {}, pages = {1-235}, doi = {10.1080/03079457.2026.2674233}, pmid = {42212564}, issn = {1465-3338}, abstract = {Chicken infectious anemia virus (CIAV), infectious bursal disease virus (IBDV), and Eimeria spp. are major immunosuppressive pathogens in chickens that predispose host to secondary infections, including Clostridium septicum-associated hepatic necrosis. In this case, shotgun metagenomic sequencing was applied to identify C. septicum that could not be isolated by traditional bacterial culture in Samgye chickens. Six 35-day-old Samgye chicken carcasses were submitted for disease diagnosis, histopathological examination, and bacterial and viral isolation/identification were performed. Pooled liver samples were subjected to shotgun metagenomic sequencing to identify microbial composition, virulence factors, and antimicrobial resistance genes. Samgye chickens exhibited dorsal dermatitis, hepatic necrosis, and splenomegaly. Histopathology revealed hepatic necrosis with bacterial colonies and lymphoid depletion. PCR detected CIAV, antigenic variant IBDV, chicken astrovirus, and Eimeria, whereas bacterial culture yielded no growth. Shotgun metagenomic analysis identified C. septicum as predominant bacterium, and CIAV as dominant viral pathogen. The α-toxin and the antimicrobial resistance tetA(P) genes were detected from liver samples. This is the first report of concurrent CIAV, avIBDV, Eimeria spp., and C. septicum infection from Samgye chickens in South Korea, suggesting that immunosuppressive infections may predispose chickens to C. septicum-associated hepatic necrosis and highlight the diagnostic utility of shotgun metagenomic sequencing.}, } @article {pmid42212611, year = {2026}, author = {Sauer, P}, title = {[Current trends in sepsis diagnosis - from classic culture to advanced molecular identification].}, journal = {Klinicka mikrobiologie a infekcni lekarstvi}, volume = {32}, number = {1}, pages = {24-29}, pmid = {42212611}, issn = {1211-264X}, mesh = {Humans ; *Sepsis/diagnosis/microbiology ; Blood Culture ; *Molecular Diagnostic Techniques/trends ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {Sepsis is a critical condition characterized by life-threatening organ dysfunction caused by a dysregulated host response to infection, where each hour of delay in initiating adequate therapy increases mortality by 7-10%. This paper summarizes current trends in microbiological diagnostics, moving from the gold standard of blood culture toward advanced molecular identification. The traditional culture-based process is limited by a time lag of 12-48 hours. Modern approaches include accelerating identification from positive blood cultures using MALDI-TOF MS and RAST methods, which reduce the time to targeted treatment. Significant innovation is represented by culture-independent technologies such as T2MR, SepsiTest-UMD, Cube Dx, and InfectID-BSI, enabling pathogen detection directly from whole blood within a few hours. The future of sepsis diagnosis is further enhanced by digital PCR for absolute quantification of bacterial load, metagenomic sequencing (mNGS) for identifying unexpected pathogens, and transcriptomics for assessing the host immune response. Integrating these technologies with artificial intelligence (AI) predictive models paves the way for precision medicine and personalized care for septic patients. Keywords: sepsis, blood culture, molecular diagnostics, PCR, mNGS, MALDI-TOF MS, artificial intelligence.}, } @article {pmid42212684, year = {2026}, author = {Liu, J and Zhao, P and Jiang, D and Li, S and Jin, C and Xu, D and Wang, X and Chen, Y and Tang, B and Qu, X}, title = {Decoding the microbiome: artificial intelligence-targeted gut microenvironment breakthroughs in personalized cancer therapy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2672791}, pmid = {42212684}, issn = {1949-0984}, mesh = {Animals ; Humans ; *Artificial Intelligence ; *Colorectal Neoplasms/microbiology/therapy/diagnosis ; *Gastrointestinal Microbiome ; Multiomics/methods/trends ; *Precision Medicine/methods ; *Tumor Microenvironment ; }, abstract = {The gut microbiome functions as a key regulator of tumorigenesis and progression, thereby modulating tumor development and treatment outcomes (including chemoresistance, immunotherapy efficacy, and adverse effects) through its influence on the immune microenvironment and metabolite-mediated signaling pathways. Recent advances in multiomics technologies (metagenomics, metabolomics, and transcriptomics) have generated large-scale, comprehensive, and heterogeneous datasets whose complexity exceeds the capabilities of manual analysis, thus necessitating the implementation of artificial intelligence-based approaches. This review systematically examines the crucial role of the gut microbiome in tumorigenesis, with particular emphasis on colorectal cancer (CRC), specifically addressing its utility as a diagnostic and prognostic biomarker. Furthermore, building upon existing applications of artificial intelligence (AI) in microbiome research and cancer diagnosis and treatment, this review presents an AI-driven precision intervention framework and delineates personalized treatment strategies.}, } @article {pmid42212786, year = {2026}, author = {Zielińska, K and Pantiukh, K and Łabaj, PP and Kosciolek, T and Org, E}, title = {A large-scale comparative metagenomic analysis of short-read sequencing platforms indicates high taxonomic concordance and functional analysis challenge.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0171425}, doi = {10.1128/msystems.01714-25}, pmid = {42212786}, issn = {2379-5077}, abstract = {UNLABELLED: Driven by the increasing scale of microbiome studies and the rise of large, continuously expanding population cohorts, the volume of sequencing data is growing rapidly. As such, ensuring the comparability of data generated across different sequencing platforms has become a pressing concern in efforts to uncover robust links between the microbiome and human health. In this study, we conducted a comprehensive comparison of taxonomic and functional profiles from 1,351 matched human gut microbiome sample pairs, sequenced using both the MGISEQ-2000 (MGI) and NovaSeq 6000 (Illumina NovaSeq) platforms. Taxonomic profiles showed high concordance within and between platforms: 96.44% ± 5.96% of species were shared between MGI-MGI pairs, and 92.07% ± 5.20% were shared between MGI and NovaSeq pairs. The proportion of platform-specific species was low, at 3.42% for MGI-MGI comparisons and 5.89% for MGI-NovaSeq comparisons. No significant differences in Shannon diversity were observed for either within-platform or between-platform comparisons. However, functional profiles revealed notable discrepancies between platforms, which were attributed to differences in pre-sequencing protocols.

IMPORTANCE: Our findings demonstrate robust taxonomic comparability between MGI and NovaSeq platforms, while revealing systematic functional differences that should be carefully considered in cross-platform metagenomic studies.}, } @article {pmid42212790, year = {2026}, author = {Zielińska, K and Pantiukh, K and Org, E and Łabaj, PP and Kosciolek, T}, title = {Moving from a taxonomic to a functional perspective in global microbiome analysis requires optimizing multiplexing ratios.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0014426}, doi = {10.1128/msystems.00144-26}, pmid = {42212790}, issn = {2379-5077}, abstract = {Next-generation sequencing has revolutionized microbiome research, yet the transition from taxonomic to functional profiling remains a major technical challenge. While marker gene sequencing provides a widely accessible ecological view, it often lacks the resolution for actionable insights. This perspective argues that shifting to whole metagenomic sequencing is essential for mapping functional potential, such as antimicrobial resistance, and metabolic pathways. However, we identify a critical bottleneck: excessive multiplexing. High multiplexing ratios reduce the number of unique molecules per sample, leading to high duplication rates and the stochastic dropout of low-abundance genes. We demonstrate that functional profiles are far more sensitive to these library complexity issues than taxonomic ones. We recommend prioritizing total sequencing depth and reducing multiplexing to ensure sufficient unique coverage. Additionally, adopting long-read or hybrid architectures is vital for providing the genomic context necessary for strain-level resolution. These optimizations are prerequisites for robust global microbiome synthesis and translational science.}, } @article {pmid42212800, year = {2026}, author = {Yabe, S and Zheng, Y and Takahashi, S and Yang, C and Nose, Y and Yamazaki, S and Okuma, N and Rachmania, MK and Ningsih, F and Sjamsuridzal, W and Sato, M and Toyooka, K and Ichihashi, Y}, title = {Chromid-like secondary replicons as predicted key sites of biosynthetic gene clusters in Ktedonobacteria.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0019726}, doi = {10.1128/msystems.00197-26}, pmid = {42212800}, issn = {2379-5077}, abstract = {UNLABELLED: Soils harbor immense biosynthetic gene cluster (BGC) diversity that mediates microbial interactions, yet this potential remains unevenly mapped and poorly characterized across diverse bacterial lineages. Ktedonobacteria (phylum Chloroflexota) are an actinomycete-like lineage widely distributed in terrestrial soils, including oligotrophic volcanic deposits; however, their secondary metabolism and genome architecture remain poorly characterized. Here, we integrate targeted cultivation from volcanic soils at Mount Zao (Japan) with genome-resolved metagenomics and comparative analysis of public genomes to examine biosynthetic potential across 183 ktedonobacterial genomes. We identified 1,546 BGCs and grouped them into 1,162 non-redundant gene-cluster families (GCFs) using antiSMASH and BiG-SLiCE. Nearly one quarter of genomes encoded ≥10 distinct GCFs, and several family-level clades exhibited high GCF richness that approached that of Streptomyces within our data set, highlighting a putatively biosynthetically rich yet underexplored soil bacterial lineage. Most ktedonobacterial BGCs were highly divergent from current reference collections and exhibited unusually low intra-genomic redundancy, suggesting broad putative chemical diversity. Long-read assemblies from 10 cultured strains revealed recurrent 1.6-3.5 Mb ECE-like contigs with chromid-like features, but distinct maintenance features. These replicons were consistently enriched in BGCs and mobility-associated genes, with mobility loci concentrated near BGC boundaries. Collectively, our results expand the phylogenetic landscape of soil biosynthetic diversity and highlight ECE-like contigs as major genomic reservoirs for secondary metabolism in Ktedonobacteria.

IMPORTANCE: Soil bacteria produce many of the small molecules that become medicines and help microbes interact with each other. Yet most of this chemical diversity remains unexplored because many soil lineages are difficult to cultivate and remain genomically underrepresented. Much of what we know comes from well-studied groups such as actinomycetes, leaving many soil lineages largely unexplored. We analyzed 183 genomes from Ktedonobacteria, an actinomycete-like group within the phylum Chloroflexota that is widespread in terrestrial soils, including nutrient-poor volcanic deposits. We uncovered a large and diverse set of gene clusters predicted to produce secondary metabolites, many of which lack close counterparts in current reference collections. We also show that these clusters are concentrated on large ECE-like contigs with chromid-like features, pointing to a dedicated genomic reservoir that can accumulate and reshuffle biosynthetic traits. Our results expand the known sources of soil biosynthetic diversity and provide a foundation for future cultivation and functional characterization of Ktedonobacteria metabolites.}, } @article {pmid42213267, year = {2026}, author = {Gulnihol, S and Abdukhamid, N and Rustam, T and Firdavs, U and Gholami, AA}, title = {Methodological concerns in the association between gut microbiota and sarcopenia: from cross‑sectional associations to statistical fragility.}, journal = {Aging clinical and experimental research}, volume = {38}, number = {1}, pages = {}, pmid = {42213267}, issn = {1720-8319}, mesh = {Humans ; *Sarcopenia/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Aged ; Iran ; }, abstract = {This commentary critically appraises the cross‑sectional study by Nasrollahizadeh et al. on gut microbiota and sarcopenia in Iranian older adults. Key limitations include; after FDR correction for twelve bacterial genera, no significant differences remained between groups; Akkermansia lost significance in sensitivity analyses; Lactobacillus showed a confidence interval including 1.00; four primer pairs lacked validation with no MIQE‑compliant efficiency data; the cross‑sectional design precludes causal inference; and no sample size justification was reported. The study offers valuable hypothesis‑generating data, but evidence remains preliminary. Future longitudinal studies with metagenomic approaches are essential.}, } @article {pmid42213269, year = {2026}, author = {Song, X and Cai, D and Yu, X and Zhang, X and Zhu, W}, title = {Effects of different cultivation methods on microbial community structure of lettuce based on metagenomic analysis.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {42213269}, issn = {1678-4405}, support = {Z2021067//Tianjin Municipal Transportation Commission Science and Technology Development Plan Project/ ; Tasks of the Key Laboratory for Microbiological Food Safety Risk Monitoring in Jiangsu Province (2023-2025)//Tasks of the Key Laboratory for Microbiological Food Safety Risk Monitoring in Jiangsu Province (2023-2025)/ ; }, mesh = {*Lactuca/microbiology/growth & development ; Soil Microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Hydroponics/methods ; *Microbiota ; Metagenome ; Biodiversity ; }, abstract = {BACKGROUND: Lettuce cultivation primarily involves two methods: traditional soil-based cultivation and modern hydroponic systems. However, research on the microbial community structure of lettuce under these distinct cultivation approache is still limited.

METHOD: This study employed whole-genome shotgun metagenomic sequencing (metagenomic sequencing) to analyze the impact of soil-based and hydroponic cultivation systems on the microbial community structure and functional profiles of lettuce.

RESULTS: The microbial diversity index of soil samples was significantly higher than that of hydroponic samples, indicating a more diverse and complex microbial community in the soil environment. Key functional phylum, including Acidobacteriota and Actinomycetota, were more abundant in soil samples, supporting nutrient cycling and plant-microbe interactions through pathways involved in carbon metabolism, organic matter decomposition, and antibiotic biosynthesis. In contrast, hydroponic samples were dominated by Cyanobacteriota and Verrucomicrobiota, with enrichment of pathways associated with stress response, including quorum sensing, ABC transporters, and oxidative phosphorylation. Although α-diversity did not differ significantly between cultivation systems, their microbial community composition and functional profiles were markedly distinct: soil-grown lettuce exhibited enrichment in sugar catabolism and synergistic prokaryotic metabolic functions, whereas hydroponic lettuce showed a predominance of energy metabolism and enrichment of viral-related pathways. Furthermore, differential distribution of antibiotic resistance genes underscores the role of environmental selective pressures in shaping microbial functional adaptations.

CONCLUSION: This study demonstrates that different cultivation methods significantly influence the microbial community structure and function in lettuce. These findings provide a theoretical foundation for optimizing cultivation systems and offer scientific guidance for precisely modulating microbial functions to promote lettuce growth and health.}, } @article {pmid42213733, year = {2026}, author = {Wheelahan, JW and Vaz, PK and Legione, AR and Hartley, CA and Rourke, NL and Lynch, M and McMeekin, B and Dobson, EC and Devlin, JM}, title = {Virological investigation and comparative genomic analysis of elephant endotheliotropic herpesvirus 1B infection in an Australian captive herd of Asian elephants (Elephas maximus).}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0345964}, pmid = {42213733}, issn = {1932-6203}, mesh = {Animals ; Australia ; *Elephants/virology ; *Genome, Viral ; Genomics ; *Herpesviridae/genetics ; *Herpesviridae Infections/veterinary/virology ; Phylogeny ; Viral Load ; Fatal Outcome ; }, abstract = {Elephant endotheliotropic herpesviruses (EEHV) pose a significant threat to the conservation of Asian elephants (Elephas maximus) worldwide, with a high mortality rate in young elephants. However, several components of EEHV virology remain underexplored, particularly for EEHV1B. This study describes a fatal case of EEHV1B infection in a nine-year-old Asian elephant from an ex situ conservation herd, examining herd viral dynamics, tissue viral loads and comparative genomics. This elephant succumbed to haemorrhagic disease within three days of developing clinical signs, despite therapeutic intervention. Quantitative PCR (qPCR) was performed on serial trunk washes and whole-blood surveillance samples collected before and after the clinical event, as well as on post-mortem tissues preserved in different storage media (DNA/RNA Shield, RNALater, and viral transport medium). Metagenomic next-generation sequencing of infected tissues was performed to characterise the complete viral genome, analyse variation from other published EEHV genomes and assess for evidence of viral recombination between EEHV subspecies. The affected elephant demonstrated a marked viraemia at onset of clinical disease, with viral load peaking at 5.47 x 106 viral genome equivalents per mL of blood, one day after the onset of clinical signs. Samples stored in viral transport medium yielded the greatest viral and host DNA recovery by qPCR, although tissues stored at -80 °C without media were still suitable for molecular detection. Whole genome sequencing demonstrated 96.0% pairwise nucleotide identity between the assembled genome (EEHV1B_AUP_01_2023, GenBank accession: PX651398) and the previously reported EEHV1B sequence (KC462164), and a maximum of 90.9% identity to published EEHV1A genomes, with evidence of recombination between the viral subspecies at several genomic regions. Viral recombination between EEHV subspecies may have significant implications for the pathogenesis of EEHV disease, the reliability of molecular diagnostics and the efficacy of vaccinations and anti-viral therapy.}, } @article {pmid42213849, year = {2026}, author = {Meijer, J and Skiadas, P and Rainey, PB and Hogeweg, P and Dutilh, BE}, title = {Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.}, journal = {Science advances}, volume = {12}, number = {22}, pages = {eaeb8246}, pmid = {42213849}, issn = {2375-2548}, mesh = {*Bacteriophages/genetics/physiology ; *Soil Microbiology ; *Evolution, Molecular ; Ecosystem ; *Composting ; Metagenomics ; Phylogeny ; Genome, Viral ; }, abstract = {Bacteriophages play critical roles in microbial ecosystems, yet their dynamics in complex natural communities remain poorly understood compared to simplified laboratory systems. Here, we tracked viral dynamics in 20 compost-derived microbial communities over 1 year. Communities formed two alternative stable types, each dominated by distinct cellulose degraders and comprising hundreds of genera. In one community type, we observed massive, parallel outbreaks of Theomophage, a previously uncharacterized member of the Schitoviridae, reaching up to 74% of metagenomic reads-the largest bacteriophage outbreak documented to date. Despite extensive replication, Theomophage displayed notable genetic stability during outbreaks and over time. In contrast, the experimental migration of viral communities triggered rapid evolution driven by recombination and the accumulation of newly arising mutations, particularly after colonization of communities of the alternative type in which the phage was initially absent. These results reveal the spatial and temporal scales at which bacteriophage microdiversity evolves in complex ecosystems and show that viral mixing, likely common in nature, can rapidly accelerate phage evolution.}, } @article {pmid42214271, year = {2026}, author = {Lin, Y and Roy, S and Hagedoorn, PL}, title = {Microbial melanin-like material: A factor beyond influencing the brown color of activated sludge.}, journal = {Water research}, volume = {303}, number = {}, pages = {126195}, doi = {10.1016/j.watres.2026.126195}, pmid = {42214271}, issn = {1879-2448}, abstract = {Melanin is a group of phenolic-quinone pigments. Natural melanin is nearly ubiquitous; found in all types of living organisms, ranging from mammals to bacteria. However, its presence and biosynthesis genomic potential in activated sludge have not been investigated. To explore this potential, melanin-like material was extracted from activated sludge collected from a municipal wastewater treatment plant. The extracted melanin-like material was characterized through biochemical analyses in comparison to synthetic melanin and humic acids that are commercially available. Metagenomic analysis of microbial community members in activated sludge and detection of tyrosine-derived melanin synthesis genes was performed. Additionally, the potential application of the extracted melanin-like material as a natural pigment was evaluated by testing its ability to color wool yarn. It was found that melanin-like material extracted from activated sludge accounted for around 11% of sludge dry mass. The isolated material displayed intrinsic autofluorescence, strong UV absorption, high oxidative stability, and free radical-rich EPR signal. FTIR analysis indicated a mixed polymer dominated by pyomelanin-like structures with eumelanin features, distinguishing it from synthetic melanin and humic acid. Metagenomic screening of the sludge community revealed widespread genomic potential for pyomelanin monomeric precursors biosynthesis across key functional genera (e.g. genera Zoogloea, Nitrotoga, Nitrosomonas, Ca. Accumulibacter, Azonexus, Ca. Competibacter, Propionivibrio, and Rhodoferax). These results suggest that microbial melanin-like material is an overlooked contributor to sludge coloration. Furthermore, the extracted pigment exhibited high affinity and wash fastness on wool fibers, demonstrating its potential for valorization as a sustainable biobased colorant.}, } @article {pmid42214309, year = {2026}, author = {Guo, N and Chen, J and Lei, Z and Qu, L and Xie, W and Yin, K and Yang, Y}, title = {Evidence for the connectivity of antibiotic resistance genes between seamount and coastal environments.}, journal = {Ecotoxicology and environmental safety}, volume = {319}, number = {}, pages = {120325}, doi = {10.1016/j.ecoenv.2026.120325}, pmid = {42214309}, issn = {1090-2414}, mesh = {*Geologic Sediments/microbiology ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; *Seawater/microbiology ; *Bacteria/genetics ; China ; Anti-Bacterial Agents/pharmacology ; Environmental Monitoring ; }, abstract = {Antibiotic resistance genes (ARGs) have drawn global attention and are ubiquitously detected in marine environments. Seamounts, prominent seafloor features with high biodiversity, may be hotspots for ARG proliferation and transfer. However, little is known about the existence, microbial associations, or connectivity with terrestrial sources of ARGs in seamounts. In this study, high-throughput sequencing approaches were employed to investigate the distribution, hosts, mobility, and coastal connectivity of ARGs in sediments from the Zhongnan Seamount, South China Sea. The most abundant ARG types were elfamycin, aminoglycoside, and tetracycline. ARG abundance was significantly higher in abyssopelagic zone sediments, suggesting the seamount acts as a sink and deep-sea regions are a major ARG reservoir. Results indicated high horizontal gene transfer potential, with key genes EF-Tu, rpsJ, parC, and parE as predominant mediators. Metagenome-assembled genomes identified 36 bacterial genera as ARG hosts, dominated by Methylomirabilota and Pseudomonadota. The source tracking and genetic connectivity analysis revealed a clear input of coastal ARGs to the seamount, emphasizing the need to investigate global ARG dissemination and its potential ecological effects. Overall, these findings identify the seamount environment as a deep-sea ARG hotspot, providing valuable insights into the prevalence, hosts, and sources of ARGs in the marine ecosystem.}, } @article {pmid42214347, year = {2026}, author = {Peredo, EL and Kulp, R and Rodriguez, F and Weintraub, MN and Anand, M and Bixler, S and Koller, J and Lee, C and Mathai, D and Tuytschaevers, S and Kumar, G}, title = {Metagenome-assembled genomes from biological soil crusts in sandy sediments of Kitty Todd Nature Preserve, OH, USA.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0038026}, doi = {10.1128/mra.00380-26}, pmid = {42214347}, issn = {2576-098X}, abstract = {Biological soil crusts (BSCs) are complex structures composed of prokaryotes, green microalgae, fungi, and small mosses that bind soil particles together. To further understand the microbial composition and interactions among members of these consortia, we investigated the microbial diversity of BSCs found in a xeric patch in northwestern Ohio.}, } @article {pmid42214368, year = {2026}, author = {Karmarkar, B and Dhotre, D}, title = {Harnessing gut microbiome enzymes: Segatella copri and Stenotrophomonas maltophilia prolyl peptidases degrade gliadin peptides and improve epithelial barrier function in a celiac disease model.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0321425}, doi = {10.1128/spectrum.03214-25}, pmid = {42214368}, issn = {2165-0497}, abstract = {UNLABELLED: Celiac disease (CeD) is an autoimmune enteropathy triggered by gluten-derived peptides that resist gastrointestinal digestion, notably the proline-rich 33-mer and 11-mer gliadin epitopes. Here, we describe a rational, metagenome-based strategy to identify gut microbiome-derived prolyl peptidases capable of degrading these immunogenic peptides. Integrating metagenomic mining with structure-based in silico screening, we identified two novel enzymes PSP692 from Segatella copri and PSP464 from Stenotrophomonas maltophilia. Recombinant expression, purification, and characterization confirmed their activity under physiologically relevant conditions: PSP692 efficiently degrades the 33-mer at pH 6, while PSP464 targets the 11-mer at pH 4. Functional assays using CaCo-2 cell line, both in bi- and tri-dimensional assays, demonstrated that degradation of gliadin peptides by PSP692 and PSP464 significantly restored the expression of tight junction proteins (ZO-1 and occludin), reduced IL-6 secretion, and improved barrier integrity. These findings establish a foundational strategy for the discovery of microbiome-derived glutenases and provide both a compelling case and a methodology for data-driven discovery of functional enzymes that degrade immunogenic gliadin peptides, with translational potential as adjunct therapies in CeD and gluten-related disorders.

IMPORTANCE: Celiac disease affects 1.4% of the global population, and, as of date, a gluten-free diet (GFD) is the only therapy available. Adherence to GFD is difficult, and inadvertent exposure to gluten still occurs. To address this, various approaches are utilized to develop adjuvant therapies. These include recombinant enzymes that, to date, have been discovered by serendipity. We have outlined and validated a method to identify enzymes with potential from metagenomic data, which will also be validated experimentally.}, } @article {pmid42214386, year = {2026}, author = {Sun, H and Dulencin, A and Kirn, TJ and Vo, J and Liachko, I and Rao, D and Manzano-Santana, J and Patel, E and Looi, C and Horton, DB and Barrett, E and Weidner, M and Bachmann, G and Panettieri, RA and Connor, BA and Rogova, M and Nagy-Szakal, D and Couto-Rodriguez, M and Kotwal, S and Wu, Q and Simon, J and Blaser, MJ and Dominguez Bello, MG}, title = {Autologous fecal microbiota transplantation restores the infant gut microbiome and metabolome after antibiotics: a case report.}, journal = {mBio}, volume = {}, number = {}, pages = {e0071126}, doi = {10.1128/mbio.00711-26}, pmid = {42214386}, issn = {2150-7511}, abstract = {UNLABELLED: Antibiotic exposure during infancy disrupts gut microbiome assembly during a critical developmental window. Strategies to restore these ecosystems remain limited. In the REPAIR trial (NCT06609980), eight infants were followed longitudinally; two received amoxicillin for otitis media, and one subsequently underwent autologous fecal microbiota transplantation (aFMT) using stool collected prior to antibiotic exposure. Shotgun metagenomics, Hi-C-assisted resistome profiling, and untargeted metabolomics were performed on samples collected before and after antibiotics. Amoxicillin treatment was associated with displacement of community structure, enrichment of antibiotic resistance genes (ARGs), and altered fecal metabolites, including short-chain fatty acids, bile acids, acylcarnitines, bilirubin derivatives, tricarboxylic acid (TCA) cycle metabolites, and amino acids. In the non-restored infant, microbiota composition and ARG profiles remained persistently altered during follow-up, accompanied by sustained metabolic divergence. In contrast, the aFMT-treated infant demonstrated convergence toward pre-antibiotic community structure, directional restructuring of ARG carriers -including reduction of β-lactam and tetracycline resistance genes- and metabolite profiles trending toward the pre-antibiotic baseline across analytical platforms. Although limited to a case-based comparison, these findings provide integrated ecological and functional evidence that aFMT may promote recovery following antibiotic perturbation during early-life microbiome development and support the rationale for larger controlled clinical trials.

IMPORTANCE: Antibiotic exposure in early life disrupts the developing gut microbiome during a critical window of host-microbe interaction. However, the extent to which these disturbances resolve naturally, or can be actively reversed, remains unclear. In this study, we use longitudinal sampling in infants to examine microbiome recovery following antibiotics, with and without autologous fecal microbiota transplantation (aFMT). We show that antibiotic exposure leads to coordinated disruptions in microbial composition, antibiotic resistance genes, and metabolic profiles. While partial recovery spontaneously occurs over time, faster and more extensive restoration toward the pre-antibiotic state is observed following aFMT. These findings provide insight into the ecological dynamics of microbiome reassembly in early life and highlight the potential of using controlled perturbations to understand microbiome resilience.

CLINICAL TRIALS: This study is registered with ClinicalTrials.gov as NCT06609980.}, } @article {pmid42214591, year = {2026}, author = {Zhu, Y and Li, D and Ma, B and Zhang, T and Zeng, H and Zhang, J and Li, S and Ding, F}, title = {Effluent-released sludge in granular anammox systems: nitrogen transformation potential and potential biosafety concerns.}, journal = {Environmental research}, volume = {305}, number = {Pt 1}, pages = {124887}, doi = {10.1016/j.envres.2026.124887}, pmid = {42214591}, issn = {1096-0953}, abstract = {Granular anaerobic ammonium oxidation (anammox) sludge enables effective biomass retention and supports the stable operation of anammox reactors. During long-term operation, however, effluent-released sludge (ERS) is continuously washed out with the effluent, exhibiting physicochemical and microbial characteristics that differ markedly from those of retained sludge (RS). The functional role and biosafety implications of ERS remain poorly understood. In this study, RS and ERS from the same granular anammox reactor were systematically compared in terms of nitrogen removal performance, microbial community composition, functional gene profiles, and biosafety-related features. RS maintained high anammox activity, whereas ERS showed reduced anammox performance but was characterized by a pronounced enrichment of comammox Nitrospira, supporting more diverse nitrogen transformation pathways. Metagenomic and 16S rRNA analyses further indicated the co-occurrence of comammox Nitrospira and heterotrophic denitrifiers in ERS, suggesting a potential metabolic linkage involving nitrate production and partial reduction to nitrite that may complement anammox activity. Functional pathway analysis revealed diminished autotrophic carbon fixation in ERS, alongside enhanced heterotrophic metabolism and cobalamin biosynthesis. In parallel, ERS exhibited elevated abundances of antibiotic resistance genes and pathogenic taxa. Collectively, these results demonstrate that ERS represents a functionally distinct biomass fraction with unique microbial and metabolic characteristics, as well as potential biosafety implications, warranting further consideration in the evaluation and management of granular anammox systems.}, } @article {pmid42214592, year = {2026}, author = {Zhu, Y and Liu, H and Yi, Y and Li, Z and Ye, J}, title = {Agricultural allochthonous dissolved organic matter is associated with microbial functional differentiation in methane- and nitrogen-related gene profiles in rural rivers.}, journal = {Environmental research}, volume = {305}, number = {Pt 1}, pages = {124865}, doi = {10.1016/j.envres.2026.124865}, pmid = {42214592}, issn = {1096-0953}, abstract = {Agricultural non-point source (ANPS) pollution introduces chemically complex dissolved organic matter (DOM) into rural rivers, yet how different agricultural practices structure DOM-microbial differentiation at the molecular scale remains unclear. Here, we compared rivers polluted by three dominant ANPS subtypes-aquaculture (AQ), livestock and poultry farming (LP), and crop farming (CF)-across winter and summer in Shanghai, China, by integrating Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) with 16S rRNA gene sequencing and metagenomics. Distinct DOM-microbial differentiation patterns were identified among ANPS subtypes. AQ was characterized by higher proportions of heteroatom-rich compounds (30.6%) and higher-molecular-weight compounds, LP by more aromatic and lignin-/tannin-associated molecular features (AI_mod = 0.261), and CF by CHOS-enriched (26.8%) but overall lower DOM chemodiversity. These molecular fingerprints co-occurred with differences in microbial diversity, community assembly (βNTI), and co-occurrence network topology, indicating relatively stable DOM-microbial templates shaped by long-term agricultural inputs. Seasonal variability further modified DOM composition and microbial differentiation, but responses differed among ANPS subtypes. Event-driven systems (AQ and LP) exhibited pronounced winter-summer shifts, whereas the background-dominated system (CF) showed weaker temporal variability but more persistent DOM-microbial coupling patterns. Low-to medium-molecular-weight (m/z 100-550) DOM fractions showed the strongest co-variation with nitrogen- and methane-related functional gene potentials, suggesting molecular-weight-dependent associations between DOM composition and microbial functional gene profiles. Overall, these findings suggest that ANPS pollution comprises source- and season-specific DOM-microbial templates that can be distinguished using molecular and functional indicators, providing a basis for source-oriented monitoring and targeted management of agriculturally impacted rural river systems.}, } @article {pmid42214594, year = {2026}, author = {Zhang, Y and Zhang, L and Zhang, S and Yang, C and Wang, Z and Si, G and Peng, Y}, title = {Synergistic antibiotic-laden wastewater treatment doubles denitrification rate in a pilot mineral-based autotrophic biofilter by breaking microbial spatial-metabolic constraints.}, journal = {Environmental research}, volume = {304}, number = {}, pages = {124860}, doi = {10.1016/j.envres.2026.124860}, pmid = {42214594}, issn = {1096-0953}, mesh = {*Denitrification ; *Wastewater/chemistry/microbiology ; *Anti-Bacterial Agents ; Autotrophic Processes ; Sulfides ; *Waste Disposal, Fluid/methods ; Bacteria/metabolism ; *Water Pollutants, Chemical/metabolism ; Pilot Projects ; Iron ; Filtration ; *Bioreactors/microbiology ; }, abstract = {The practical application of pyrite-based autotrophic denitrification biofilters (PADB) is limited by their low nitrogen removal rate (NRR). This study demonstrates that in a pilot-scale PADB (750 L) treating NO3[-]-N wastewater, heterotrophic bacterial consortia (HBs) severely impair the denitrification activity of autotrophic denitrifying bacteria (ADB) through network encapsulation and metabolic shunting. However, after switching to treating composite wastewater containing antibiotics, the system achieved an antibiotic removal rate of 95.12%. And it's NRR from 32.37 to 63.15 mg N/(L·d), representing a 0.95-fold enhancement. Integrated co-occurrence network and metagenomic analyses revealed a three-stage cascade reaction underlying this improvement: (i) The antibiotic stress halted carbon-feeding from ADB and hydrolytic-acidifying bacteria to HBs (fermentation gene abundance decreased by 1.89-58.45%), depriving HBs of energetic and substrate support and resulting in their selective elimination (0.63-fold decrease in relative abundance). This relieved ADB's metabolic burden and shortened their physical distance to pyrite; (ii) Elevated electron and energy demand in ADB activated dormant genes for electron shuttle synthesis (menC/E: 0 to 342/402 TPM) and upregulated sulfur metabolism genes (∼3.9-fold), enhancing pyrite dissolution and electron harvesting; (iii) This augmented electron flow stimulated ADB's carbon fixation pathway (Calvin-Benson-Bassham cycle genes upregulated 14.89-fold) and amplified energy metabolism (1.33-1.55-fold enhancement in glycolysis and Tricarboxylic Acid cycle), supplying ample material and energy for ADB proliferation and denitrification. Consequently, ADB enrichment accelerated 509-fold, while the abundance of key denitrification genes (napA/B, nosZ) increased by 2.1-11.04-fold. These molecular and population-level changes doubled the system's NRR compared to its original level.}, } @article {pmid42214595, year = {2026}, author = {Pan, W and Zhang, L and Liang, L and Du, L and Guo, X}, title = {Nanoplastics reshape nitrogen cycling in submerged macrophyte systems: A metagenomic perspective.}, journal = {Environmental research}, volume = {304}, number = {}, pages = {124885}, doi = {10.1016/j.envres.2026.124885}, pmid = {42214595}, issn = {1096-0953}, mesh = {*Nitrogen Cycle/drug effects ; Metagenomics ; Rhizosphere ; *Water Pollutants, Chemical/toxicity ; Nitrogen/metabolism ; *Magnoliopsida/metabolism/drug effects ; Bacteria/metabolism/genetics ; Microbiota/drug effects ; }, abstract = {Nanoplastics (NPs) pose a potential risk to aquatic ecosystems. Submerged macrophytes are critical for nitrogen removal, but how nitrogen cycling responds to NP-induced stress remains unclear. This study used Myriophyllum aquaticum to evaluate nitrogen cycling in submerged macrophyte-sediment systems exposed to 100 nm polystyrene (PS) NPs at 10, 100, and 1000 μg/L, integrating stable isotope tracing and metagenomic profiling to explore microbial community and nitrogen-cycling gene responses across rhizosphere and non-rhizosphere compartments. Low PS-NP exposure (10 μg/L) slightly increased the NH4[+]-N removal efficiency to 81.5%, whereas medium and high PS-NP exposures (100 and 1000 μg/L) reduced the NH4[+]-N removal efficiency, with values around 70.9%. Low doses stimulated nitrification (NO3[-]-N accumulation) and high doses inhibited N2O emissions; δ[15]N tracing showed disrupted NH4[+]-N to N2 reduction. Plant-only microcosms had the highest N2O release (1.37 mg, 1.5% of total N). Metagenomics revealed concentration-dependent, spatially distinct microbial community shifts: low PS-NPs increased rhizosphere α-diversity, while high concentrations depleted Proteobacteria, enriched Acidobacteria/Bacteroidetes, and reduced key nitrogen-cycling genera (e.g., Dechloromonas, Accumulibacter). In the rhizosphere, denitrification genes (nirK/S,nosZ) were upregulated by 2.5- and 3-fold, respectively, while DNRA (nrfA) and nitrogen fixation (nifH) genes were downregulated by 1.7- and 2.3-fold. Network and canonical correspondence analyses indicated stronger environmental filtering in bulk sediments (explaining 52.0% of variance) and spatially structured nitrogen metabolic pathway reorganization. These findings show concentration-dependent PS-NP exposure differentially shapes microbial community composition and nitrogen-cycling functions in rhizosphere and bulk sediments.}, } @article {pmid42214685, year = {2026}, author = {Jiang, TA and Prioult, G and Quann, E}, title = {Microbial Biotransformation of Polyphenols and Bioactive Substrates: Implications for Metabolite-Guided Synbiotics.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101621}, doi = {10.1016/j.tjnut.2026.101621}, pmid = {42214685}, issn = {1541-6100}, abstract = {Dietary bioactive compounds-including polyphenols, alkaloids, lignans, and amino acid-derived substrates-exert well-established effects on human health, but are constrained by poor bioavailability. Only 5%‒10% of ingested polyphenols are absorbed in the proximal gastrointestinal tract; the remainder undergoes biotransformation by colonic microbiota into a diverse repertoire of bioactive metabolites. Accumulating evidence indicates that these microbially derived metabolites, rather than their parent compounds, are the primary mediators of systemic benefits, owing to superior bioavailability, metabolic stability, anti-inflammatory and antioxidant activity, and greater specificity in modulating host metabolic and signaling pathways. Production of these metabolites varies markedly among individuals due to differences in gut microbiota composition, giving rise to distinct metabolic phenotypes-termed metabotypes-that strongly influence clinical and nutritional responsiveness. This review synthesizes recent advances in the microbial biotransformation of dietary polyphenols, amino acids, glucosinolates, and related substrates, and examines how these pathways influence metabolic, cardiometabolic, neurocognitive, and immune outcomes. We further evaluate emerging evidence supporting synergistic synbiotics-targeted combinations of probiotics with specific polyphenol or bioactive precursors-as a strategy to standardize and enhance the generation of beneficial microbial metabolites. These synbiotic strategies demonstrate the capacity to convert non-producers into producers, reduce interindividual variability in metabolite output, and improve clinically relevant outcomes in metabolic dysfunction, inflammation-driven disorders, and aging. Together, these findings position metabolite-guided synbiotics as a promising paradigm for precision nutrition. Integration of metagenomics, metabolomics, and computational modeling will enable individualized prediction of metabolite-production capacity and accelerate translation of microbiota-targeted interventions.}, } @article {pmid42214867, year = {2026}, author = {Lu, J and Zhang, S and Guo, Y and Wu, H and Hu, Z and Kong, Q and Zhang, J}, title = {Magnetite-facilitated AHL-mediated quorum sensing enhances nitrate removal and mitigates nitrous oxide emissions in constructed wetlands under polycyclic aromatic hydrocarbons stress.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142523}, doi = {10.1016/j.jhazmat.2026.142523}, pmid = {42214867}, issn = {1873-3336}, mesh = {*Quorum Sensing/drug effects ; *Nitrates/metabolism ; *Wetlands ; *Polycyclic Aromatic Hydrocarbons/toxicity ; *Nitrous Oxide/metabolism/analysis ; *Acyl-Butyrolactones/metabolism ; *Water Pollutants, Chemical ; *Ferrosoferric Oxide/chemistry ; }, abstract = {The performance of constructed wetlands (CWs) in removing nitrate (NO3[-]-N) and mitigating nitrous oxide (N2O) emissions can be impaired by trace organic pollutants like polycyclic aromatic hydrocarbons (PAHs). Magnetite has been widely applied as a substrate to regulate nitrogen transformation in CWs; however, its potential role in mediating quorum sensing (QS) to alleviate PAH-induced inhibition remains unclear. In this study, conventional CWs (CW-A) and magnetite-amended CWs (CW-B) were established to evaluate NO3[-]-N removal and N2O emissions and the associated mechanisms under PAH-stress conditions. Results indicated that CW-B maintained a high NO3[-]-N removal efficiency (90.14%), whereas CW-A exhibited a marked decline from 65.06% to 47.32%. Magnetite amendment reduced N2O emissions by 68.97% compared with CW-A. Furthermore, the enhanced performance of CW‑B was closely linked to the strengthening of QS. CW-B sustained elevated levels of acyl-homoserine lactone (AHL) signaling molecules (e.g., C8-HSL) under PAH stress, while these signals were suppressed in CW-A. Metagenomic analysis revealed enrichment of key functional genera (e.g., Tessaracoccus and Pseudomonas) and genes associated with QS and nitrogen transformation (e.g., luxI, nirS, and nosZ) in CW-B, supporting enhanced NO3[-]-N removal and reduced N2O emissions. The reinforced QS further promoted interspecies electron transfer and enhanced microbial network robustness and resilience. Additionally, PAHs stimulated the DNRA process and enhanced the abundance of DNRA-related genes (i.e., nrfA and nrfH) in both CWs, leading to increased effluent total nitrogen. Overall, this study elucidates a magnetite-mediated QS mechanism that enhances nitrogen transformation and microbial metabolic stability in CWs under PAH stress.}, } @article {pmid42215097, year = {2026}, author = {Wang, Z and Ding, Y and Cheng, S and Xun, Z and Li, Z and Zhu, M and Zhao, X and Hu, W and Meng, X and Zhang, S and Qiu, L}, title = {Integrating multi-omics to link core and region-specific microbiota to flavor metabolism in medium-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {238}, number = {}, pages = {119428}, doi = {10.1016/j.foodres.2026.119428}, pmid = {42215097}, issn = {1873-7145}, mesh = {*Alcoholic Beverages/microbiology/analysis ; Bacteria/metabolism/classification ; China ; Fermentation ; *Flavoring Agents/metabolism ; *Food Microbiology ; Fungi/metabolism/classification/genetics ; Gas Chromatography-Mass Spectrometry ; Metabolomics/methods ; Metagenomics ; *Microbiota/physiology ; *Multiomics ; *Taste ; Temperature ; Volatile Organic Compounds/analysis/metabolism ; }, abstract = {Medium-temperature Daqu (MTD) is a critical fermentation starter for strong-aroma Baijiu, where its complex microbiota governs flavor development. We combined metagenomics with GC-MS metabolomics to analyze 15 MTD samples from six major producing regions in China, moving from descriptive profiling to mechanistic insight. Although microbial communities exhibited substantial regional variation, a conserved core microbiota emerged, consisting of eight fungal genera, including Aspergillus and Rhizopus, and five bacterial genera such as Bacillus. Beta diversity analysis indicated that producer-specific practices were more influential than geography in structuring these communities. Functional metagenomic profiling showed enriched pathways for carbohydrate, amino acid, and ester metabolism. Volatile metabolite analysis identified 94 compounds, primarily esters, with 12 common to all samples. We constructed multi-omics correlation networks to predict functional linkages, which notably connected genera like Talaromyces and Aspergillus to key flavor esters. Based on these predictions, we isolated Wickerhamomyces anomalus and Bacillus velezensis from Daqu. In vitro validation demonstrated their functional roles: W. anomalus produced ethyl acetate, while co-culturing B. velezensis with Saccharomyces cerevisiae significantly enhanced the yield of ethyl decanoate and ethyl laurate. This work delineates both the core and region-specific metabolic features of MTD and translates multi-omics correlations into confirmed microbial activities. It thereby establishes a targeted framework for identifying flavor-active microorganisms, offering a scientific foundation for quality control and directed bioaugmentation in Daqu production.}, } @article {pmid42215200, year = {2026}, author = {Jones, RC and Visger, CJ and Lopez, CA}, title = {The microbiota of wild fermented cider from U.S. west coast apples.}, journal = {Food microbiology}, volume = {139}, number = {}, pages = {105120}, doi = {10.1016/j.fm.2026.105120}, pmid = {42215200}, issn = {1095-9998}, mesh = {*Malus/microbiology ; Fermentation ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Alcoholic Beverages/microbiology/analysis ; *Yeasts/isolation & purification/classification/genetics/metabolism ; United States ; Food Microbiology ; Fruit/microbiology ; }, abstract = {Traditional methods to produce apple cider rely on wild fermentations, where the indigenous microbes present on the fruit and environment transform the pressed apple juice, or must, to cider. The identification of the diverse bacteria and yeast responsible for wild fermentations is an important step in designing practices that promote desired microbes while preventing expansion of spoilage microbes. Here, we sought to survey the microbial communities found in wild fermented ciders from the western United States using shotgun metagenomics sequencing in packaged cider. There, we found a substantial diversity of bacteria and yeast genomic sequences; however, despite variation in apple origin and cidery, there was consistent identification of Oenococcus oeni, Lentilactobacillus hilgardii, and Brettanomyces bruxellensis. Additionally, Tatumella ptyseos, a member of the plant-associated Erwiniaceae, was identified in all cider batches, with T. ptyseos representing one of the most abundant observed taxa in some batches. Analysis of the identified T. ptyseos strains suggests the presence of adaptations to a cider environment that include carbohydrate fermentation, methionine salvage, and nutrient iron and zinc scavenging. These results provide preliminary support that the microbial communities established in fermenting cider contain core constituents that may stratify based on key metabolic characteristics or adaptations to a low nutrient, high competition environment.}, } @article {pmid42215210, year = {2026}, author = {Chen, L and Wang, G and Hu, Z and Teng, M and Cao, Q and Qin, X and Du, H and Yang, F and Tu, H and Wang, L}, title = {From diversity to stability: Acidification, antagonism, and resistance driven by Acetilactobacillus jinshanensis during jiang-flavor baijiu fermentation.}, journal = {Food microbiology}, volume = {139}, number = {}, pages = {105130}, doi = {10.1016/j.fm.2026.105130}, pmid = {42215210}, issn = {1095-9998}, mesh = {Fermentation ; Hydrogen-Ion Concentration ; Metagenomics ; *Wine/microbiology/analysis ; Microbiota ; Microbial Consortia ; Metabolomics ; }, abstract = {As a quintessential pillar of Chinese traditional industry, Baijiu relies on solid-state fermentation, a complex ecological succession process driven by highly diverse microbial consortia. While such systemic complexity often introduces stochasticity and uncertainty, baijiu solid-state fermentation is typically dominated by specific keystone species that exhibit remarkable resilience, maintaining high abundance while exerting top-down control over community structure and function. However, the mechanisms enabling these species to emerge from intensely competitive environments remain poorly understood. In this study, we employed Acetilactobacillus jinshanensis, a predominant species in the Moutai-flavor Baijiu microbiome, as a model to address these ecological questions. By integrating shotgun metagenomics, metatranscriptomics, and a pH-dependent generalized Lotka-Volterra model, we demonstrate that A. jinshanensis not only orchestrates environmental acidification but also reshapes the community landscape through active competitive inhibition. Leveraging comparative genomics and AlphaFold3-based structural predictions, we identified a unique GH25-LysM antibacterial module in A. jinshanensis predicted to target peptidoglycan with high specificity, potentially contributing to the suppression of acid-tolerant competitors. Furthermore, targeted metabolomics revealed a novel acid-resistance mechanism centered on an intra- and extracellular choline cycle, which significantly bolsters the organism's fitness under extreme acidic stress via metabolic modulation. Overall, we pinpoint a coupled mechanism set that explains the diversity-to-stability transition driven by A. jinshanensis in fermentation microbial community, offering process-relevant rules for improving reproducibility.}, } @article {pmid42215376, year = {2026}, author = {Kiguchi, Y and Suzuki, Y}, title = {Giants within: a new class of microbial mobile elements.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2026.05.004}, pmid = {42215376}, issn = {0168-9525}, abstract = {Prokaryotes harbor a diverse spectrum of extrachromosomal elements (ECEs), which are intracellular replicons maintained independently of the primary chromosome. Historically, the ECE research field has focused on relatively small ECEs, such as plasmids. However, the advent of long-read sequencing has revealed that prokaryotes also harbor various types of giant ECEs, spanning hundreds of kilobases to over 1 Mb, that were not hitherto recognized. In this review, we describe how long-read sequencing has enabled the discovery of giant ECEs and compare the genetic architectures and functional repertoires of several recently characterized examples. The functions of most genes in these ECEs remain uncharacterized, and current computational tools frequently misclassify or overlook them. We further discuss how the discovery of these giant ECEs challenges existing classification frameworks that attempt to distinguish megaplasmids, chromids, and chromosomes. Together, these findings highlight giant ECEs as a largely unexplored layer of microbial genetics, whose characterization will have broad implications for our understanding of microbial adaptation and horizontal gene transfer.}, } @article {pmid42215825, year = {2026}, author = {Lv, J and Wang, JH and Wang, YY and Huang, J and Chen, FR and Fang, S and Wang, XJ and Li, ZT and Shi, YP and Guo, L}, title = {Gut microbial alterations and functional shifts in patients with hypertriglyceridemia: insights from a northwestern Chinese metagenomic study.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42215825}, issn = {1618-1905}, support = {2025JC-YBMS-916//Shaanxi Natural Science Foundation of China/ ; No. 81702067 and 82560411//National Natural Science Foundation of China/ ; }, abstract = {Although hypertriglyceridemia (HTG) is a significant contributor to lipid-associated pathologies such as atherosclerotic cardiovascular disease, its regulation by host‒microbiome interactions remain insufficiently characterized. While the gut microbiota (GM) is known to influence cholesterol metabolism, its specific role in systemic triglyceride (TG) homeostasis, particularly in non-Western populations, is poorly defined. This study aimed to identify preliminary robust GM signatures associated with HTG and to assess their translational potential using integrated multiomics and explainable machine learning approaches. In a cross-sectional investigation of 50 well-phenotyped adults from Northwest China, we combined 16S rRNA sequencing, shotgun metagenomics, and ensemble machine learning (LightGBM/XGBoost) to elucidate the associations between the GM and TGs. Microbial features were rigorously linked to serum lipid profiles through dual-algorithm validation and SHAP interpretability analysis, while functional potential was assessed via KEGG pathway mapping. Subjects with HTG exhibited a distinct gut microbial configuration, marked by consistent enrichment of Faecalibacterium and Bacteroides coprocola (positively correlated with serum TG levels) and depletion of Bifidobacterium pseudocatenulatum and Lactobacillus salivarius (inversely correlated). Machine learning converged on five exploratory consensus biomarker taxa, three of which were independently confirmed by LEfSe analysis (Faecalibacterium). Functional profiling further revealed the upregulation of microbial starch and sucrose metabolism pathways in the HTG cohort. Our findings establish a preliminary gut microbial signature for HTG patients and suggest context‑dependent associations of butyrate-producing taxa such as Faecalibacterium. By integrating multiomics with explainable artificial intelligence, this work addresses key challenges in reproducibility and mechanistic inference in microbiome research. These results pave the way for novel microbiota-targeted therapeutic strategies, including precision probiotics and dietary interventions, to modulate lipid metabolism, pending further validation in expanded cohorts and functional studies.}, } @article {pmid42215894, year = {2026}, author = {Russell, T and Formiconi, E and Murphy, A and Hortion, J and McElroy, M and Casey, M and Cuartero, LG and Mee, JF and Jahns, H and Kelly, C and Byrne, J and Feeney, ER and Mallon, PW and Gautier, VW}, title = {One health viral metagenomics for pathogen surveillance: robust mNGS workflows for viral detection and genome recovery from swab and tissue specimens.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05105-5}, pmid = {42215894}, issn = {1471-2180}, support = {101132970, EU4H-2022-DGA-MS-IBA3//European Commission/ ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is an untargeted approach that enables detection of pathogens directly from samples without prior knowledge of their genetic sequences. In the context of pandemic preparedness and One Health surveillance, there is a pressing need for robust viral mNGS workflows that perform reliably across diverse hosts sample types and pre-analytical conditions.

RESULTS: The study evaluated two shotgun mNGS workflows, one for swabs and one for complex tissue matrices, using a reference repository of clinical and post-mortem samples. The panel comprised swabs and tissue samples positive for 18 DNA and RNA viruses (including 12 species) from nine host species and nine anatomical sites, encompassing a range of transport media, storage temperatures and processing timelines. Quality control metrics were embedded throughout nucleic acid extraction, library preparation and sequencing to monitor performance and support interpretation. Overall, 88.9% of 18 DNA and RNA viruses previously detected by PCR were identified, including from samples with low nucleic acid concentrations (< 1 ng/µl) and variable integrity and purity. The workflows identified viral co-infections that had not been detected by prior targeted testing, as well as Phocid herpesvirus 7 (PHV7) for which no complete reference genome was initially available.

CONCLUSIONS: These results demonstrate the feasibility and robustness of the swab and tissue mNGS workflows for virus identification across a range of complex clinical specimens supporting their use in investigations of suspected viral diseases of unknown aetiology and is currently being evaluated for early detection of emerging viral threats at the animal-human interface.}, } @article {pmid42216070, year = {2026}, author = {Liu, LM and Zhang, YL and Zhou, JT and Yu, QQ and Zhang, WY and Wang, WF and Pang, SD and Miao, H and Zhao, YY}, title = {Ureic clearance granule ameliorates chronic kidney disease by reshaping microbial dysbiosis via modulating bile acid metabolism.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {}, pmid = {42216070}, issn = {1749-8546}, support = {82274192//National Natural Science Foundation of China/ ; 82474062//National Natural Science Foundation of China/ ; LHZSZ25H270001//Natural Science Foundation of Zhejiang Province/ ; 2023-ZDLSF-26//Shaanxi Key Science and Technology Plan Project/ ; }, abstract = {BACKGROUND: Chronic kidney disease (CKD) is a highly prevalent global public health problem that inevitably leads to renal failure. Although renin-angiotensin system blockers, as first-line therapy, can reduce proteinuria, they cannot prevent the progression to end-stage renal disease. Therefore, the development of new treatment strategies is urgently required. The uremic clearance granule (UCG) was widely used in patients with CKD. However, the underlying molecular mechanisms of UCG for CKD treatment remain unclear.

METHODS: Fecal gut microbiota and serum metabolites were analyzed using metagenomics and metabolomics, respectively. The expression of extracellular matrix components, Takeda G protein-coupled receptor 5 (TGR5), glucagon-like peptide-1 receptor (GLP-1R), and nuclear factor kappa B (NF-κB) p65 was examined by in adenine-induced CKD rats.

RESULTS: UCG improved renal function and alleviated kidney fibrosis in adenine-induced CKD rats. Mechanistically, significantly altered gut bacteria, including Helicobacter hepaticus, Gemella hemolysans, Bacteroides ovatus, Lactococcus cremoris, Bacteroides fragilis, Alistipes finegoldii, and Eubacterium limosum, showed strong linear correlations with serum creatinine levels in CKD rats. UCG treatment improved aberrant changes in these gut bacteria, indicating that UCG can reshape gut microbiota dysbiosis. Microbial-derived metabolites act as a bridge between gut microbiota and host. Further analysis showed that serum bile acids, including ursodeoxycholic acid (UDCA), taurodeoxycholic acid, and hyodeoxycholic acid (HDCA), were strongly correlated with serum creatinine levels in CKD rats, and these aberrant metabolites were reversed by UCG treatment. Notably, both UDCA and HDCA showed strong linear correlations with Bacteroides ovatus, Lactococcus cremoris, Bacteroides fragilis, and Eubacterium limosum, suggesting that UCG regulates microbial-derived metabolites. Moreover, UCG treatment upregulated protein expression of TGR5, GLP-1R, and downregulated NF-κB p65 protein expression in the kidney tissues of CKD rats, indicating that renoprotective effects of UCG are associated with modulation of microbial dysbiosis, regulation of bile acid metabolism and improvement of TGR5, GLP-1R, and NF-κB signaling.

CONCLUSIONS: This study is the first to demonstrate that UCG ameliorates CKD and renal fibrosis by reshaping microbial dysbiosis and microbial-derived bile acid metabolism. Altered gut microbiota and metabolites may serve as biomarkers to evaluate efficacy of UCG. UCG may exert its renoprotective effects by enhancing TGR5, GLP-1R, and NF-κB p65 expression through regulating microbial dysbiosis-mediated bile acid metabolism.}, } @article {pmid42216221, year = {2026}, author = {Zhang, K and Duan, C and Chen, J and He, Q and Jin, Y and Liu, J and Lin, R and Han, C}, title = {Bone marrow mesenchymal stem cells synergize with fusobacterium nucleatum to drive colorectal tumorigenesis via gut microbiome dysbiosis.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00839-z}, pmid = {42216221}, issn = {1757-4749}, support = {2024M761069//Postdoctoral Research Foundation of China/ ; 82470679//National Natural Science Foundation of China/ ; 2023YFC2307001//National Natural Science Foundation of China/ ; 82170570//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The oncogenic role of F. nucleatum (Fn) in colorectal cancer (CRC) is increasingly recognized, yet its interaction with host stromal components, such as bone marrow mesenchymal stem cells (BMSCs), remains poorly understood. Building on our previous discovery that BMSC-derived Wnt3a promotes Fn-driven tumorigenesis, this study aims to investigate the synergistic interplay between BMSCs and F. nucleatum in CRC pathogenesis via the gut microbiome.

METHODS: Based on the established Apc[Min/+] mouse model of CRC, animals were randomly assigned to four experimental groups: control, Fn-only, BMSCs-only, and Fn+BMSCs co-treatment group. Gut microbiota composition was continuously analyzed over 8 weeks by metagenomic sequencing. Metagenomic functions were predicted using PICRUSt2.

RESULTS: The Fn+BMSCs co-treatment group exhibited the highest enrichment of F. nucleatum and the greatest reduction in microbial diversity. Fn+BMSCs co-treatment induced a distinct pro-tumorigenic shift, marked by a decline in symbiont Lactobacillus and an increase in pathobiont Escherichia-Shigella. Metagenomic analysis revealed a unique enhancement of butanoate metabolism in the Fn+BMSC co-treatment group. Furthermore, a profoundly elevated LPS level was discovered in the Fn+BMSCs co-treatment group, indicating hyperactivation of the pro-inflammatory and proliferative TLR4/NF-κB pathway.

CONCLUSIONS: Our findings demonstrate that BMSCs synergize with F. nucleatum to create a tumorigenicmicroenvironment by driving microbial dysbiosis, reprogramming metabolic pathways, and amplifying pro-inflammatory signaling. Our findings reveal that BMSCs fuel CRC progression via multiple mechanisms: by altering the gut microbiome ecology and, as previously discovered, by providing oncogenic Wnt3a signals. Targeting the synergistic BMSC-Fn axis may thus offer a novel therapeutic strategy for CRC.}, } @article {pmid42216275, year = {2026}, author = {Wong, ELY and Otte, J and Schmitt, I}, title = {Chloroplast and Mitochondrial Genomes of the Lichen-Symbiotic Green Alga Trebouxia Illuminate Evolutionary Relationships and Climate Associations and Yield New Phylogenetic Markers.}, journal = {Genome biology and evolution}, volume = {18}, number = {6}, pages = {}, pmid = {42216275}, issn = {1759-6653}, support = {//Centre for Translational Biodiversity Genomics/ ; LOEWE/1/10/519/03/03.001(0014)/52//Hessian Ministry of Science and Research, Arts and Culture/ ; }, mesh = {*Phylogeny ; *Genome, Mitochondrial ; *Lichens/genetics ; Symbiosis ; *Genome, Chloroplast ; *Chlorophyta/genetics/classification ; *Evolution, Molecular ; Climate ; }, abstract = {The green-algal genus Trebouxia (Trebouxiophyceae, Chlorophyta) is the most common photosynthetic symbiont of lichens, displaying high phylogenetic diversity, and worldwide distribution across all climate zones. These single-celled terrestrial algae are valuable systems to study diversification, environmental adaptation and species interactions, yet genomic resources remain limited. We present over 30 new chloroplast and mitochondrial genomes of Trebouxia species, extracted from PacBio metagenomes of diverse Umbilicaria lichens from multiple climate zones. The genomes represent previously identified operational taxonomic units (OTUs) Trebouxia jamesii (A03), T. sp. (A04), T. incrustata (A06), T. vagua (A10), T. sp. (S02), T. sp. (S03), T. sp. (S04), T. suecica (S05), T. sp. (S08), T. angustilobata (S09), T. simplex (S10), T. sp. (S20) and T. barrenoae (S28); a newly designated OTU T. sp. (A57), and several Single-Occurrence Sequences (SOS) from clades A, I, and S. Up to four Trebouxia OTUs were found within a single thallus. Organelle genomes vary considerably in size and structure. The consensus phylogenies from chloroplast (77 genes) and mitochondrial (32 genes) genes are largely congruent with the nuclear ITS tree, differing mainly in the derived clade S sections. All genes are under purifying selection, with mitochondrial genes exhibiting higher nucleotide diversity and hence phylogenetic resolution than chloroplast genes. Certain gene and protein features correlate with temperature variability, and some (such as GC content, arginine, and valine content) mirror findings in mycobiont nuclear genomes from the same samples and highlight shared signatures of environmental adaptation. We designed primers for new, variable phylogenetic markers, including chloroplast genes ftsH and rpoC1, and mitochondrial genes ATP1, ATP6, and ND6. Overall, this study advances our understanding of organelle genome evolution in Trebouxia and provides valuable resources for future ecological and evolutionary research.}, } @article {pmid42216291, year = {2026}, author = {Zwartjes, MSZ and de Jonge, PA and van de Laar, AW and Bruin, SC and Meijnikman, AS and Groen, AK and Gerdes, VEA and Nieuwdorp, M}, title = {Adipose Tissue Inflammation, Oxidative Stress, and Altered Adipogenesis Are Associated With Dyslipidemia in Obesity: A Multiomics Profiling Study.}, journal = {Journal of the American Heart Association}, volume = {15}, number = {11}, pages = {e047397}, doi = {10.1161/JAHA.125.047397}, pmid = {42216291}, issn = {2047-9980}, mesh = {Humans ; *Oxidative Stress ; *Dyslipidemias/metabolism/genetics/etiology ; Male ; Female ; *Adipogenesis/genetics ; Multiomics ; Cross-Sectional Studies ; Middle Aged ; *Adipose Tissue/metabolism ; Adult ; Adipokines/blood ; *Obesity, Morbid/surgery/complications/metabolism ; Metabolomics ; *Inflammation/metabolism ; Bariatric Surgery ; Longitudinal Studies ; Gene Expression Profiling ; Obesity ; }, abstract = {BACKGROUND: Obesity is an important risk factor for cardiometabolic disease, including dyslipidemia and atherosclerotic cardiovascular disease. Although the role of the liver in dyslipidemia is established, the contribution of adipose tissue is less clear. This study aims to clarify the role of adipose tissue in lipid metabolism and dyslipidemia.

METHODS: We conducted a cross-sectional analysis of 125 patients from the BARIA (The Immune System and Microbial Tone in Relation to NAFLD/NASH Before and After Bariatric Surgery in the Morbidly Obese in Amsterdam) longitudinal cohort study undergoing bariatric surgery. Comprehensive phenotyping included fasting untargeted plasma metabolomics, lipid, lipoprotein, adipokine profiling, RNA sequencing, and fecal shotgun metagenomics. Tissue transcriptomic and plasma metabolites were compared between individuals with and without dyslipidemia.

RESULTS: Dyslipidemia was present in 43 of 125 individuals (34.4%), with higher triglycerides (1.62 versus 1.24 mmol/L), apoB (apolipoprotein B; 93.15 versus 81.81 mg/dL), and lower high-density lipoprotein (1.02 versus 1.35 mmol/L) and apoAI (136.40 versus 161.35 mg/dL). Plasma adipokines showed limited differences: leptin concentrations were lower in dyslipidemia in unadjusted analysis but reduced after adjustment for age, sex, and body weight (adjusted P=0.057). RNA sequencing identified altered gene expression of liver, jejunum, visceral and subcutaneous adipose tissue, most pronounced in subcutaneous adipose tissue. Dyslipidemia was associated with adipose tissue pathways related to inflammation, oxidative stress, and adipogenesis. Plasma metabolomics revealed associations with endocannabinoid-like, secondary bile acid, plasmalogen, butyrate, and sphingolipid metabolites. Gut metagenome analysis found modest differences.

CONCLUSIONS: Dyslipidemia in obesity is associated with transcriptomic alterations in adipose tissue, including subcutaneous adipose tissue, involving inflammation, oxidative stress, and adipogenesis. These findings support a role of adipose tissue in lipid regulation beyond hepatic pathways.}, } @article {pmid42217053, year = {2026}, author = {Ortiz-Gasca, A and Aguirre-Noyola, JL and Ruiz-Rivas, M and de Los Santos-Villalobos, S and Trejo-Aguilar, D and Gómez-Godínez, LJ}, title = {Molecular markers for the study of arbuscular mycorrhizal fungi.}, journal = {Archives of microbiology}, volume = {208}, number = {8}, pages = {}, pmid = {42217053}, issn = {1432-072X}, mesh = {*Mycorrhizae/genetics/classification/isolation & purification ; Genetic Markers ; DNA, Fungal/genetics ; Metagenomics/methods ; DNA, Ribosomal/genetics ; Soil Microbiology ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are central components of terrestrial ecosystems and agroecosystems. However, their accurate identification remains methodologically challenging due to their complex biology and the limitations of traditional morphological approaches. Over the past three decades, molecular tools have profoundly reshaped AMF research, shifting from spore-based identification and Sanger sequencing of ribosomal markers toward high-throughput amplicon sequencing and, more recently, metagenomic frameworks that enable community-level and functional analyses. This review critically examines the conceptual and technical evolution of AMF identification strategies, comparing morphological characterization, ribosomal DNA markers (SSU, ITS, LSU), multilocus approaches, metabarcoding, and whole-genome metagenomics. We analyze their taxonomic coverage, resolution, and methodological biases, including primer specificity, intragenomic rDNA variation, database limitations, and bioinformatic pipeline effects. Attention is given to how marker selection influences ecological interpretation, cross-study comparability, and functional inference. Finally, we propose practical guidelines for aligning marker choice with study objectives and outline validation strategies-such as mock communities, curated reference databases, and multi-marker integration-to improve reproducibility and taxonomic robustness. By integrating historical perspective, methodological evaluation, and applied recommendations, this review provides a decision-oriented framework to support more accurate and comparable assessments of Glomeromycota diversity.}, } @article {pmid42217383, year = {2026}, author = {Kong, T and Du, Z and Zhou, J and Zheng, Z and Zhang, J and Zhang, S and Jiang, F and Sun, X and Huang, W and Zhang, R and Li, F and Lin, W and Lan, X and Cao, Y and Yan, G and Sun, W}, title = {Assimilatory sulfate reduction potential in the plastisphere microbiome is linked to plastic mineralization in sulfur-rich mining-impacted river sediments.}, journal = {Water research}, volume = {303}, number = {}, pages = {126182}, doi = {10.1016/j.watres.2026.126182}, pmid = {42217383}, issn = {1879-2448}, abstract = {Microbial communities colonizing plastic surfaces are shaped by environmental factors, yet the role of sulfur in plastisphere assembly and plastic fate remains poorly understood. Here, we collected plastic debris from sulfur-rich, mining-impacted river sediments to characterize plastisphere microbiomes and evaluate their potential roles in plastic transformation. Paenibacillus spp. were identified as core plastisphere members, and their distribution was strongly associated with total sulfur concentrations. Metagenomic binning suggested that Paenibacillus harbored genomic potential associated with plastic transformation/mineralization and sulfate assimilation. An isolate of Paenibacillus provided further laboratory-based evidence that sulfate amendment may support plastic mineralization, although the precise in situ mechanism remains to be clarified. Because both the metagenome-assembled genome and the isolate genome encoded an almost complete assimilatory sulfate reduction pathway but lacked a complete dissimilatory sulfate reduction pathway, the observed sulfate depletion is more conservatively interpreted as sulfate uptake coupled with assimilatory sulfate reduction and subsequent sulfur assimilation into biomass rather than canonical sulfate respiration. Together, these findings suggest that sulfate availability and assimilatory sulfur metabolism may represent underappreciated controls on plastic turnover in sulfur-rich environments by supporting plastic-associated carbon transformation. This study links plastic-carbon fate to local sulfur cycling and provides new insight into microplastic persistence in sulfur-rich aquatic ecosystems.}, } @article {pmid42217591, year = {2026}, author = {Zhang, J and Liu, J and Tian, Y and Jia, W and Zhang, G and Lyu, A and Lyu, H}, title = {Metabolic interactions of host-gut microbiota: Shaping the future of precision diagnosis and therapeutic discovery in gastrointestinal cancers.}, journal = {Pharmacological research}, volume = {229}, number = {}, pages = {108273}, doi = {10.1016/j.phrs.2026.108273}, pmid = {42217591}, issn = {1096-1186}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Gastrointestinal Neoplasms/diagnosis/metabolism/microbiology/therapy/drug therapy ; Animals ; Metabolomics ; Precision Medicine ; }, abstract = {This collection of reviews and research articles highlights the diagnostic and therapeutic potential of gut microbial metabolites across various gastrointestinal cancers, including but not limited to hepatobiliary and pancreatic cancers, gastric cancer, and cholangiocarcinoma. Numerous gut microbial metabolites have been observed to mechanistically regulate cancer cell proliferation and development, supporting their utility as molecular biomarkers for clinical diagnosis and as targets for precision interventions. However, most functional metabolites derived from both host cancer tissues and the gut microbiota remain structurally unidentified; their functional features are largely unexplored due to limitations in conventional measurement technologies. To address these challenges, we propose a transformative functional metabolomics approach-S[2]M[2]ART (Single-Cell Spatial Metabolomics Metagenomics-Artificial Intelligence Recombinational Toolkit)-which will leverage AI-powered multimodal omics and single-cell, spatially-resolved analyses to decode the molecular functions and mechanisms of these metabolites in gastrointestinal cancer development. Collectively, this innovative technique will substantially enhance the applicability and translational potential of microbial metabolites in gastrointestinal cancers and beyond.}, } @article {pmid42217781, year = {2026}, author = {Kim, S and Kang, MG and Oh, S and Jang, KB and Kim, Y}, title = {Genome-based characterization of flavor development via metabolic interactions between Lentilactobacillus kefiri and Kluyveromyces marxianus during milk kefir fermentation.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2026-28435}, pmid = {42217781}, issn = {1525-3198}, abstract = {Kefir, a fermented milk product comprising complex consortia of bacteria and yeasts, develops its characteristic flavor through coordinated microbial interactions. In this study, we investigated flavor compound biosynthesis and development by kefir-derived lactic acid bacteria and yeast during kefir fermentation, integrating genome-based predictions with metabolite validation. Metagenomic analysis identified Lactobacillus and Kluyveromyces as predominant genera in both kefir grains and fermented milk kefir. Lentilactobacillus kefiri SLAM023B and Kluyveromyces marxianus SLAM005Y were isolated and subjected to hybrid genome sequencing on Illumina and Nanopore platforms. Functional annotation via KEGG pathway mapping revealed featured pathways including amino acid and fatty acid metabolism, as well as interconversion of alcohol, aldehyde, and acid, contributing to the formation and generation of flavor compounds. Notably, K. marxianus SLAM005Y produced fruity fusel alcohols, whereas L. kefiri SLAM023B contributed fatty acid-derived precursors. The coculture of the 2 strains significantly enhanced ester synthesis, particularly ethyl acetate and isoamyl acetate, imparting fruity and creamy sensory notes to the fermentation profile. In addition, increases in ethyl octanoate and C6/C8 fatty acids introduced fruity and cheese-like characteristics, while levels of grassy aldehydes were reduced. Correlation analysis supported the complementary metabolic roles and potential cross-feeding mechanisms between the strains, which help explain the development of kefir flavor. Taken together, this study provides a genomic and functional framework to examine cooperative metabolism in kefir and identifies molecular targets for improving the sensory properties of fermented dairy products.}, } @article {pmid42217859, year = {2026}, author = {Qin, W and Zhang, H and Wang, H and Zhou, J and Wang, F}, title = {Pharmaceutical-driven disinfection by-products formation and antibiotic resistance gene enrichment under intensified chlorination during pandemic.}, journal = {Journal of environmental sciences (China)}, volume = {165}, number = {}, pages = {1-10}, doi = {10.1016/j.jes.2025.06.056}, pmid = {42217859}, issn = {1001-0742}, mesh = {Halogenation ; *Disinfection/methods ; *Drug Resistance, Microbial/genetics ; Pandemics ; *Disinfectants ; *Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/analysis ; *Chlorine ; Anti-Bacterial Agents ; Wastewater/chemistry ; }, abstract = {Intensified chlorine disinfection during pandemic is widely implemented in hospital and municipal wastewaters to inactivate pathogens. However, high concentrations of residual chlorine in treated wastewaters might bring secondary environmental risks. This study investigated the impacts of intensified chlorine disinfection on disinfection by-product (DBP) formation from six commonly used pandemic-related drugs and antibiotic resistance gene (ARG) enrichment in sewage. Results showed that high chlorine dosage of 2000 µmol/L led to DBP yields and estimated toxicity that were 1-2 orders of magnitude higher than those under normal chlorine dosage of 40-100 µmol/L. Intensified chlorine disinfection and drug overuse during the pandemic evidently increased the contribution of drugs as precursors to DBPs formation (29.2 %-78.8 %) in sewage. Two antibiotics emerged as major dichloroacetonitrile precursors, two bromine expectorants dominated haloacetic acids and Br-DBP formation, while two ICMs were critical precursors of iodinated acetamides. These DBPs were the main contributors to the estimated toxicity of the chlorinated drugs. Bromine expectorants produced DBPs with yields and estimated toxicity 1-2 orders of magnitude greater than other drugs. Metagenomic sequencing results showed that low chlorine up-regulated ARGs and related mobile genetic elements, driving ARGs enrichment and horizontal transfer. High chlorine in short term inhibited the total ARGs, but enriched the multidrug resistance gene subtypes related to the efflux/mutation pathway and transfer, thereby selected highly chlorine-resistant bacteria with strong antibiotic resistance. These findings reveal the environmental risks of intensified chlorine disinfection and suggest that optimizing chlorine dosage is crucial to mitigate these environmental risks and protect public health.}, } @article {pmid42217876, year = {2026}, author = {Xiao, Y and Ouyang, Q and Wen, X and Tong, H}, title = {Coupling mechanisms between microbial arsenic metabolism and carbon cycling in arsenic-contaminated groundwater.}, journal = {Journal of environmental sciences (China)}, volume = {165}, number = {}, pages = {269-276}, doi = {10.1016/j.jes.2025.10.032}, pmid = {42217876}, issn = {1001-0742}, mesh = {*Arsenic/metabolism/analysis ; *Groundwater/chemistry/microbiology ; *Water Pollutants, Chemical/metabolism/analysis ; *Carbon Cycle ; China ; Bacteria/metabolism ; *Water Microbiology ; Carbon/metabolism ; }, abstract = {Microorganisms in groundwater play a critical role in global carbon (C) cycling. However, how arsenic (As) contamination influences microbially mediated As cycling and its coupling with C metabolism remains poorly understood. Herein, we investigated the associative coupling of microbial function genes between As and C cycling in groundwater from a typical As-contaminated industrial site in southern China. Metagenomic analyses revealed that As concentrations governed microbial community assembly, leading to distinct community structures and dominant taxa. Key microbial groups, including Pseudomonadota and Euryarchaeota, exhibited dual metabolic capabilities for both As and C transformation. Compared to the Safe group (As < 10 μg/L), the Toxic group (As > 10 μg/L) displayed greater dissimilarities in the distribution of As- and C-related functional genes. A strong correlation between As- and C-cycling genes suggests a potential trade-off mechanism between microbial As resistance and organic C utilization. Furthermore, microbial function gene-based co-occurrence networks demonstrated more complex and stable network structures in the Toxic group. The enhanced coupling between As-C functional genes likely increased microbial community resilience against environmental stressors. While observed As-C coupling mechanisms may extrapolate to chemically analogous groundwater systems, their quantitative contribution to global C budgets requires validation across diverse biogeographic contexts. This study offers novel insights into the complex coupling network between As and C metabolic pathways in groundwater microbial communities and underscores their broader implications for global biogeochemical C cycling.}, } @article {pmid42217938, year = {2026}, author = {Dwivedi, S and Agnihotri, R and Kumar, V and Mishra, S and Tiwari, RK and Adhikari, D and Sharma, P and Kumar, S and Verma, T and Gupta, A and Sinam, G and Pandey, V}, title = {Scientific evidence validating spiritual beliefs for controlling pathogenic microbes in the Ganga river.}, journal = {Journal of environmental sciences (China)}, volume = {165}, number = {}, pages = {93-106}, doi = {10.1016/j.jes.2026.01.083}, pmid = {42217938}, issn = {1001-0742}, mesh = {*Rivers/microbiology ; Archaea ; Bacteria ; *Water Microbiology ; Microbiota ; Bacteriophages ; Biodiversity ; }, abstract = {During the Kumbh, the Ganga at the Sangam in Prayagraj, where it meets the Yamuna, showed greater microbial diversity than either river before their confluence. Mass bathing altered the density and diversity of archaea, bacteria, phages and viruses, while fungi, protozoans, cyanobacteria, green algae and diatoms remained largely unaffected. Notably, this study was the first to report archaeal phages, cyanophages and mycophages in the river system. Archaea species richness was higher in the Yamuna (127 spp. during Pre Kumbh), whereas bacterial diversity was greater in the Ganga (2764 spp.). The Ganga exhibited a higher relative abundance of skin, oral and gut archaea and bacteria, except for gut bacteria, which were more prevalent in the Yamuna. Skin and gut archaea showed strong positive correlations with the number of devotees (r = 0.818 and r = 0.870, respectively), while oral archaea were less affected. Pathogenic microbes with high fatality rates were more common in the Yamuna. Variations in archaeal, bacterial, phage and viral communities were influenced by physico-chemical parameters, ion levels, nutrient content and devotee's load. The Ganga exhibited higher phage diversity and a greater phage-to-bacteria ratio than the Yamuna. Hence, phages regulate the pathogenic bacteria through predator-prey dynamics, consequently reducing infection risks. Despite mass bathing by over 100 million devotees, which sharply increased nutrient and pollution levels, no endemic or epidemic outbreaks were reported.}, } @article {pmid42218119, year = {2026}, author = {Fessler, JL and Olm, MR and Engleman, EG and Sonnenburg, JL}, title = {Integration of donor microbiota following FMT correlates with anti-PD-1 response in melanoma.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73465-7}, pmid = {42218119}, issn = {2041-1723}, support = {R21CA290426//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; }, abstract = {Fecal microbiota transplantation (FMT) has shown promise in improving anti-PD-1 therapy in melanoma, but the underlying microbial features remain poorly defined. We performed a strain-resolved metagenomic meta-analysis across three independent FMT plus anti-PD-1 melanoma trials (n = 41). Across cohorts, therapeutic benefit was linked to successful integration of donor microbiota, rather than increased diversity or engraftment of specific species. Responders acquired more donor-derived strains, exhibited greater post-FMT similarity to their donor, and maintained a more stable microbiome. Following FMT, non-responders' microbiomes showed greater taxonomic instability, larger fluctuations in estimated microbial load, and increased abundance of pathogen-associated secretion system genes, whereas responders showed enrichment for microbial functions involved in community-level metabolism and communication. Finally, shifts in tumor-infiltrating immune profiles tracked with clinical outcomes and microbiome changes. Together these findings highlight that distinct patterns of microbiome restructuring, including stable community transitions and altered functional capacity, are associated with anti-PD-1 response following FMT.}, } @article {pmid42218218, year = {2026}, author = {Zhu, G and Yang, G}, title = {Multikingdom microbiome-based machine learning enables multiple sclerosis diagnosis.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01030-7}, pmid = {42218218}, issn = {2055-5008}, support = {32571054 and 82371350//National Natural Science Foundation of China/ ; C7014-24GF//Research Grant Council of the Government of Hong Kong SAR/ ; Institute Digital Medicine internal grant (9229501-13-YG)//City University of Hong Kong/ ; }, abstract = {Emerging evidence suggests a role for the gut bacteria in the pathogenesis of multiple sclerosis (MS); however, the role of other microorganisms and their diagnostic potential for MS remain poorly explored. Here, we analyzed large-scale metagenomic data derived from fecal samples (discovery cohort n = 1152; total n = 1306 across 3 geographically diverse cohorts). Subsequently, we utilized multikingdom gut microbiome data to develop machine learning models to distinguish MS patients from healthy controls. Our analysis identified distinct microbiome alterations, revealing 90 bacterial, 3 fungal, 2 viral species, 119 KEGG orthology genes, and 17 metabolic pathways significantly associated with MS. Machine learning models integrating multikingdom taxonomic and functional features achieved the area under the receiver operating characteristic curves (AUCs) of 0.977 for males and 0.978 for females. On external validation datasets, the ensemble models yielded AUCs of 0.813 in males and 0.745 in females, while the 30-marker models reached AUCs of 0.849 and 0.763, respectively. Notably, the accuracy of the model was associated with Faecalibacterium spp. and L-methionine biosynthesis pathways, which were less abundant in MS patients. Collectively, our findings highlight the potential application of multikingdom and functional gut microbiome markers as non-invasive biomarkers for MS.}, } @article {pmid42218514, year = {2026}, author = {Fabre, V and Robinson, ML and Martino, F and Monge, R and Forastiero, A and Corso, A and Pasteran, F and Karyakarte, R and Randive, B and Singh, S and Naik, M and Prasad, HB and Schwab, KJ and Simner, PJ and Berman, Y and Foy, WI and Salinas, AB and Gupta, A and Lu, J and Vasquez, AM and Noble-Wang, J and Moser, KA and Perry-Dow, KA and Patrick, M and Rock, C}, title = {Environmental reservoirs of carbapenem-resistant organisms in the intensive care unit: a multicenter longitudinal study in two middle-income country hospitals.}, journal = {Antimicrobial resistance and infection control}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13756-026-01768-x}, pmid = {42218514}, issn = {2047-2994}, support = {75D30121D12750/CC/CDC HHS/United States ; }, abstract = {BACKGROUND: There is limited data regarding environmental reservoirs of carbapenem-resistant organisms (CRO) during non-outbreak settings in resource-limited hospitals, or the role of these reservoirs in healthcare transmission.

METHODS: Prospective longitudinal study in which sinks and high-touch surfaces (HTS) were sampled prior to room cleaning in intensive care units (ICUs) in two hospitals (hospital A, Argentina, and hospital B, India), July 2023-February 2024. Selective media was used to recover CROs. Whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) pairwise analysis were performed on environmental and clinical isolates to evaluate bacterial transmission dynamics. Metagenomic sequencing was performed to evaluate bacterial diversity of environmental samples.

RESULTS: Of 541 environmental samples collected, 47.9% in hospital A and 97.5% in hospital B grew at least one CRO. Most CROs tested for the presence of a carbapenemase were positive (63.9-91.0% for hospital A and B isolates, respectively). Carbapenemase producer (CP)-Acinetobacter baumannii and CP-Pseudomonas spp. predominated in HTS and sinks samples, respectively, in hospital A; while CP-Klebsiella pneumoniae predominated in hospital B samples. WGS of 113 CRO isolates and SNP analysis demonstrated certain lineages established enduring reservoirs in the ICUs environment (e.g., blaVIM-36 P. aeruginosa ST395 isolates with 2-9 SNP difference were detected in sinks over 7 months). Several clusters involving environmental and clinical isolates that shared an epidemiological link and displayed ≤ 10 SNP difference were identified (e.g., blaOXA-23 A. baumannii ST195 isolated from three unique patients who stayed in the same private room on sampling months 4, 5, 6 and 7, and from HTS of that room on sampling month 5 displayed 0-3 SNP difference). Metagenomic analysis identified additional AMR genes of clinical importance.

CONCLUSIONS: CROs were abundant and persisted in the ICU environment in countries with high prevalence of MDROs. Our data suggests movement of clones between the environment and patients.}, } @article {pmid42218533, year = {2026}, author = {Kim, W and Kim, JE and Hong, YS and Hwang, DW and Kim, J and Lee, JS and Shin, JH and Kim, TW and Nagarkar, D and Byrd, A and Sung, CO and Kim, SY}, title = {Dynamics of tumor ecosystems and microbiome in response to neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis.}, journal = {Genome medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13073-026-01680-4}, pmid = {42218533}, issn = {1756-994X}, support = {ASA-1 project//This work was supported by the imCORE Network on behalf of F. Hoffmann-La Roche (ASA-1 project)./ ; }, abstract = {BACKGROUND: This study aims to explore the effects of neoadjuvant atezolizumab, bevacizumab, leucovorin, 5-fluorouracil, and oxaliplatin (ABFOLFOX) in patients with unresectable colorectal liver metastases (CRLM), focusing on the molecular dynamics of tumor ecosystems (TE) of CRLM and their impact on treatment outcomes.

METHODS: The study comprises two cohorts with CRLM tissue samples analyzed with RNA sequencing and immunohistochemical staining: cross-sectional cohort A (n = 60, CRLM treated with or without neoadjuvant chemotherapy) and prospectively registered cohort B (n = 20 with serial sampling and treated with ABFOLFOX). Shotgun metagenomic sequencing was performed for stool samples from cohort B.

RESULTS: Durable disease control (PFS ≥ 24 months) was observed in 35% (7/20) of patients receiving ABFOLFOX. Analysis revealed a progressive increase in the immunogenic microenvironment within CRLM tissues upon the addition of therapeutic agents, specifically bevacizumab, and the most significant TE changes in CRLM were observed in those treated with ABFOLFOX in cohort B. The monocyte lineage was significantly associated with benefit from ABFOLFOX. Good responders exhibited improved immune response and notable activation of the SP140 transcription factor regulon. Moreover, microbiome analysis revealed that high abundance of Prevotella was positively correlated with good response and enhanced immune environment within the tumor. Causal mediation analysis suggested that the gut microbiome partially links the ABFOLFOX treatment response to the tumor microenvironment.

CONCLUSIONS: ABFOLFOX enhances the TE immune profile of CRLM, which is further augmented by the gut-liver axis characterized by Prevotella abundance, and can induce durable disease control in a subgroup of patients.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT03698461. May 08, 2019 (prospectively registered).}, } @article {pmid42218921, year = {2026}, author = {Guo, F and Fu, W and Topalović, O and Zhang, Q and Li, K and Li, H and Qing, X}, title = {Genomic insights into nematode microbiomes reveal novel endosymbionts Rickettsiella.}, journal = {Molecular phylogenetics and evolution}, volume = {223}, number = {}, pages = {108650}, doi = {10.1016/j.ympev.2026.108650}, pmid = {42218921}, issn = {1095-9513}, abstract = {BACKGROUND: Bacterial endosymbionts are key drivers of invertebrate ecology and evolution. While the diversity and functional role of the nematode microbiome remain poorly explored.

METHODOLOGY: We reconstructed and characterized 108 metagenome-assembled genomes from 10 published and 15 newly sequenced nematode genomes.

PRINCIPAL FINDINGS: We report the first evidence of Rickettsiella in nematodes and discovered novel endosymbionts Cardinium and Wolbachia in plant-parasitic nematodes. The nematode microbiome is enriched with genes for carbohydrate metabolism and the biosynthesis of essential amino acids and vitamins, indicating a potential primary role in host nutrition. Notably, mobile genetic elements like prophages and insertion sequences (IS) are widespread and carry passenger genes involved in vitamin biosynthesis, suggesting horizontal gene transfer facilitates metabolic adaptation. Genomic reduction in the nematode Rickettsiella lineage, reveals extensive gene loss, particularly in amino acid biosynthesis. Crucially, we find no evidence of purifying selection on its residual nutritional pathways, and thus cannot clearly support a mutualistic role for this association.

CONCLUSION: Our findings expand the known host range of major endosymbiont groups and reveal a spectrum of symbiotic relationships in nematodes, from putative mutualism driven by nutritional supplementation to associations with neutral or parasitic traits, shaped by pervasive horizontal gene transfer and reductive genome evolution.}, } @article {pmid42219044, year = {2026}, author = {Shil, S and Datta, SP and Banerjee, D and Paul, S and Khatua, A and Chowdhury, J and Koner, GS and Das, AK and Mukherjee, A and Karmakar, UK and Haldar, S and Debnath, A}, title = {Hypervariable region-specific detection of an avian gut pathobiont in multi-primer 16S rRNA metagenomics: the V9 region identifies Gallibacterium anatis undetected by conventional V3-V4 approaches.}, journal = {Journal of microbiological methods}, volume = {246}, number = {}, pages = {107565}, doi = {10.1016/j.mimet.2026.107565}, pmid = {42219044}, issn = {1872-8359}, mesh = {Animals ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Pasteurellaceae/genetics/isolation & purification/classification ; Chickens/microbiology ; DNA Primers/genetics ; Cecum/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; *Poultry Diseases/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; *Pasteurellaceae Infections/veterinary/microbiology/diagnosis ; }, abstract = {Hypervariable region (V-region) selection critically determines which taxa are resolved in 16S rRNA amplicon surveys, yet most commercial poultry gut microbiome studies rely on the V3-V4 primer pair optimised for Illumina short-read platforms. The Ion GeneStudio S5 Prime with multi-primer 16S chemistry simultaneously amplifies six variable regions (V2, V3, V4, V67, V8, V9) from a single library, providing an unprecedented opportunity to benchmark region-specific taxonomic resolution in the same sample set without inter-library bias. 29 commercial broiler caecal samples (HEALTHY n = 10; DISEASED n = 19) were analysed per-V-region on the Ion GeneStudio S5 Prime using the Ion 16S Metagenomics Kit, yielding 46,542 classified reads distributed across six V-regions. From a total sequencing depth of 342,716-1,358,797 reads per sample. Independent ASV-level validation was performed using QIIME2 v2024.10 DADA2 (738 ASVs, SILVA 138), confirming all primary findings. V3 contributed the highest read volume (14,818 reads, 31.8%) and resolved the most genera (52 unique). V9 contributed the fewest reads (2831, 6.1%) but the highest number of region-exclusive genera (11), including the avian pathobiont Gallibacterium anatis. Critically, 121 of 220 total G. anatis reads (55%) were recovered exclusively via V9 primers; zero G. anatis reads were detected by V3 across all 29 samples.". In a parallel differential abundance analysis, G. anatis was the most significantly enriched taxon in diseased caecal microbiota (DESeq2 padj = 1.45 × 10[-6]), a finding that would have been entirely missed by a conventional V3-V4 workflow. In silico analysis of one of the samples from this set, found G. anatis (GenBank PX986441.1) confirmed absence of the 341F primer binding site. Mean sequence identity was uniformly high across all regions (98.74-99.05%), confirming that V9 underperformance is a coverage rather than quality issue. These findings demonstrate significant primer bias in single-region 16S workflows applied to poultry gut microbiome research, with direct implications for diagnostic assay design and pathobiont surveillance programmes.}, } @article {pmid42219122, year = {2026}, author = {Wang, X and Huang, Y and Xu, J and Lin, B and Chen, X and Li, ZH}, title = {Exogenous floc-granule replacement regulates particle-size distribution and signaling-associated ecological responses in aerobic granular sludge.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {135039}, doi = {10.1016/j.biortech.2026.135039}, pmid = {42219122}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Particle Size ; Bioreactors/microbiology ; Extracellular Polymeric Substance Matrix/metabolism ; Aerobiosis ; Flocculation ; *Signal Transduction ; Bacteria/metabolism/genetics ; Acyl-Butyrolactones/metabolism ; Biological Oxygen Demand Analysis ; }, abstract = {Aerobic granular sludge (AGS) operation remains constrained by excessive granule enlargement, particle-size redistribution, and structural instability. In this study, exogenous floc-granule replacement was evaluated as a chemical-free, in situ particle-size management strategy for AGS. A conventional granulation reactor (R1) and an exogenous floc-granule replacement reactor (R2) were operated in parallel to compare granulation dynamics, reactor performance, extracellular polymeric substances (EPS), extracellular acyl-homoserine lactones (AHLs), respiration, bacterial partitioning, metagenomic functional gene profiles, and microbial co-occurrence patterns. During the first replacement window, R2 maintained smaller and more uniform granules than R1, with mean particle size of 220 μm on Day 83 compared with 378 μm in R1. R2 also maintained comparable chemical oxygen demand and NH4[+]-N removal performance and showed lower nitrite accumulation during rapid granulation. Particle-size regulation was accompanied by lower extracellular AHL accumulation, altered EPS composition, and distinct respiratory allocation, reflecting higher autotrophic-to-heterotrophic respiration ratio in R2 than in R1 on Day 82 (0.10 vs. 0.07). Comparative characterization indicated that exogenous flocs represented a distinct biomass fraction with smaller particle size, lower protein-to-polysaccharide ratio, and lower extracellular AHL accumulation than endogenous flocs and mature granules. Metagenomic and co-occurrence network analyses showed higher abundance of quorum quenching (QQ)-related genes and greater representation of QQ- or combined quorum sensing /QQ-associated taxa in R2. Overall, exogenous floc-granule replacement represents a tunable structure-based strategy for regulating AGS particle-size distribution, but its effectiveness should be further evaluated according to application scenario.}, } @article {pmid42219517, year = {2026}, author = {Velando, F and Molina, L and Hurtado, I and van Dillewijn, P and Segura, A}, title = {Aeonium decorum as a microbial recruitment platform for atmospheric polycyclic aromatic hydrocarbons mitigation in urban gardens.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00914-7}, pmid = {42219517}, issn = {2524-6372}, abstract = {BACKGROUND: In the context of the Sustainable Architecture, green roofs, green walls, green belts or urban farms are becoming popular infrastructures in cities and have been proposed as promising elements to ameliorate air pollution. Atmospheric contaminants are deposited not only on the foliar surface of plants, but also in soils. Plants may interact with pollutants, but their associated microbiomes (epiphytic, endophytic and rhizospheric) may harbor contaminant-degrading bacteria which could play an important role in pollutant mitigation. Therefore, we explored the effects of atmospheric contaminants, using naphthalene as a model compound, on some of the living elements of urban gardens (plants and microbiomes).

RESULTS: Exposure to gaseous naphthalene had weak effects on Aeonium decorum and Trifolium repens plants (measured as efficiency of photosystem II), and on soil bacterial diversity. Although the presence of naphthalene is not the major driver of soil bacterial community structure, metagenomic and qPCR analysis revealed an increase in polycyclic aromatic hydrocarbon (PAH)-ring hydroxylating dioxygenases in Aeonium planted soils, suggesting a positive effect of this plant species for the selection of potential contaminant-degrading microbes. We have also observed an increment in Pseudomonas (known for their capacity to degrade contaminants) and Solimonas in response to naphthalene. Validation of tools designed to evaluate the exposure of plants to atmospheric contaminants was performed creating urban gardens planted with A. decorum plants and exposed to environmental conditions.

CONCLUSIONS: Our results suggest that Pseudomonas and Solimonas could be used as markers for biodegradation. A. decorum is proposed as a good candidate for amelioration of atmospheric contaminants and gardens constructed with these plants carried PAH degrading bacteria on leaf surfaces indicating that they have the capacity to respond to the presence of contaminants.}, } @article {pmid42219665, year = {2026}, author = {Recio, MI and de la Torre, J and Rocha-Martin, J and de la Mata, I and Ramos, JL}, title = {A Biotechnological Approach to Enzyme-Based Fertilisers: Immobilisation of Acid Phosphatases.}, journal = {Microbial biotechnology}, volume = {19}, number = {6}, pages = {e70385}, pmid = {42219665}, issn = {1751-7915}, support = {PID2021-123469OB-IOO//Agencia Estatal de Investigación/ ; MICIU/AEI/10.13039/501100011033//Agencia Estatal de Investigación/ ; PREDOC_01447//Consejería de Conocimiento, Investigación y Universidad, Junta de Andalucía/ ; }, mesh = {*Acid Phosphatase/metabolism/chemistry ; *Enzymes, Immobilized/metabolism/chemistry ; Hydrogen-Ion Concentration ; Enzyme Stability ; Clay ; *Fertilizers/analysis ; Aluminum Silicates/chemistry ; *Biotechnology/methods ; Temperature ; Soil/chemistry ; }, abstract = {We explore enzyme-based technologies as sustainable alternatives to conventional chemical fertilisers, addressing the challenges associated with using enzymes in free or immobilised form for agricultural applications. We use the metagenome-derived Class A acid phosphatase M2-32, selected for its high activity, broad pH tolerance and thermophilic properties, and evaluated its immobilisation on clay minerals to enhance stability and applicability in soils. Several clays were tested as immobilisation supports. Bentonite caused complete enzyme inactivation, while kaolin formed aggregates and was unsuitable. In contrast, palygorskite, sepiolite and agrozeolite adsorbed more than 99% of the added enzyme. However, only a fraction of the immobilised enzyme retained catalytic activity, with optimal performance observed at moderate protein loading (40-80 μg protein). Among the tested supports, palygorskite consistently provided the highest specific activity (22,000 ± 2200 U/mg), followed by sepiolite (11,000 ± 730 U/mg), whereas agrozeolite (2250 ± 40 U/mg) showed comparatively low activity. ATR-FTIR spectroscopy confirmed successful enzyme immobilisation without significant alteration of the clay structures. Immobilised M2-32 preserved a broad pH range (between 4 and 8.5) and thermophilic behaviour similar to the free enzyme, remaining active up to 50°C. Immobilisation increased substrate affinity while reducing Vmax relative to the free enzyme. To assess environmental compatibility, the effects of free and palygorskite-immobilised M2-32 on soil microbial communities were evaluated using corn rhizosphere microcosms with different organic matter contents. Metabarcoding high-throughput sequencing revealed that microbial diversity and community structure were primarily shaped by soil type, plant presence and incubation time. Enzyme application, whether free or immobilised, did not significantly alter microbial diversity or composition. Overall, these results support palygorskite-immobilised M2-32 as a promising, environmentally compatible candidate for enzyme-based fertiliser development.}, } @article {pmid42219690, year = {2026}, author = {Zhu, P and Yuan, X and Wang, X and Shi, Y}, title = {Application of Nano Silica Is Associated With Enhanced Wheat Resistance to Fusarium Crown Rot via Regulation of Metabolic Pathways and Soil Microbial Community.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70343}, doi = {10.1111/1462-2920.70343}, pmid = {42219690}, issn = {1462-2920}, support = {SDAIT0107//Shandong Modern Agricultural Technology & Industry System/ ; SDNYXTTG-2023-30//Agricultural Major Technology Collaborative Promotion Plan Project in Shandong Province/ ; }, mesh = {*Triticum/microbiology ; *Fusarium/physiology ; *Soil Microbiology ; *Silicon Dioxide/pharmacology ; Metabolic Networks and Pathways/drug effects ; *Microbiota/drug effects ; *Plant Diseases/microbiology/prevention & control ; *Disease Resistance/drug effects ; Lignin/metabolism ; *Nanoparticles ; }, abstract = {Nano silica (NS) has promising agricultural applications, yet its effects and mechanisms in enhancing wheat resistance to Fusarium crown rot (FCR) caused by Fusarium pseudograminearum (FP) remain underexplored. Here, we conducted a pot experiment with 200 mg/L NS, integrating soil metagenomics, plant physiology, and metabolomics to investigate this process. Soil metagenomic analysis revealed that NS was associated with reshaped microbial community structure and distinct functional pathway variations (GO/KEGG annotations). In wheat, NS treatment was linked to activated fructose/mannose metabolism and phenylpropanoid biosynthesis, increasing SOD and POD activities by 14.5% and 169.9% and reducing MDA content by 37.0%. It was also associated with upregulated lignin-related enzymes (PAL, C4H, and 4CL) and their encoding genes, thus promoting lignin accumulation, enhancing stem strength, and restoring cellulose content. Our findings suggest a potential dual mechanism: NS-associated soil microbiome changes coincide with improved plant antioxidant capacity and defence gene expression, reinforcing stem integrity to alleviate FCR, providing new insights for eco-friendly FCR management.}, } @article {pmid42219901, year = {2026}, author = {Yang, J and Shi, T and Du, Z and Wang, Y and Shen, J and Wu, C and Fu, B}, title = {Sub-inhibitory polyether ionophores enhance resistance plasmid transfer and transiently perturb the broiler gut resistome.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {81}, number = {6}, pages = {}, doi = {10.1093/jac/dkag190}, pmid = {42219901}, issn = {1460-2091}, support = {32141002//National Natural Science Foundation of China/ ; 81991535//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Ionophores/pharmacology/administration & dosage ; *Plasmids/genetics ; Chickens/microbiology ; Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/drug effects ; *Drug Resistance, Bacterial/genetics/drug effects ; Polyether Compounds ; Cecum/microbiology ; *Gene Transfer, Horizontal/drug effects ; *Bacteria/drug effects/genetics ; Polyether Polyketides ; Conjugation, Genetic/drug effects ; Pyrans ; }, abstract = {BACKGROUND: Chronic sub-inhibitory antimicrobial exposures may shape antibiotic resistance (AMR) dissemination at the animal, food and environment interface. Polyether ionophore coccidiostats remain widely used in poultry production, yet their influence on AMR dissemination at sub-inhibitory exposure is unclear.

OBJECTIVES: To determine whether sub-minimum inhibitory concentration (MIC) polyether ionophores enhance resistance plasmid transfer in vitro and to characterize their effects on gut microbiota and resistome dynamics in vivo during and after administration.

METHODS: We investigated the effects of representative polyether ionophores at sub-MICs on resistance spreading phenotypes in vitro and gut resistome dynamics in VREfm-challenged broilers. In vitro plasmid conjugation and related phenotypes were quantified, and in vivo caecal microbiota and resistome were profiled by 16S rRNA gene sequencing and shotgun metagenomics.

RESULTS: Sub-MIC polyether ionophores increased plasmid conjugation, copy number and biofilm formation in Enterococcus spp., whereas no comparable effects were observed in Escherichia coli. In vivo, salinomycin temporarily disrupted caecal microbiota development and, at Day 20, suppression of indigenous taxa (e.g. Faecalibacterium) was accompanied by a transient surge in VREfm colonization and vanA abundance; resistome expansion was non-persistent. After salinomycin cessation, recovery of beneficial genera like Akkermansia was associated with reduction of the total resistance gene burden towards pre-treatment baseline by Day 42.

CONCLUSIONS: Polyether ionophores can promote resistance dissemination phenotypes in vitro, but gut ecological resilience may limit long-term impacts after cessation of exposure under recommended dosing conditions. The transient resistome surge during the treatment suggests increased shedding and potential environmental dissemination via manure, warranting surveillance and risk assessment.}, } @article {pmid42221085, year = {2026}, author = {Liu, F and Yang, K and Wu, M and Li, P and Luo, L}, title = {Case Report: Basal ganglia brain abscess caused by Nocardia farcinica.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1798434}, pmid = {42221085}, issn = {2296-858X}, abstract = {We report a rare case of Nocardia farcinica brain abscess in the basal ganglia, detailing its diagnosis, management, and rehabilitation. Diagnosing brain abscess based solely on clinical and imaging findings remains extremely challenging. Fortunately, metagenomic next-generation sequencing (mNGS) proved valuable in this case by rapidly identifying the pathogen, thereby facilitating targeted antibiotic therapy. This case highlights the importance of differentiating brain abscess from ischemic stroke and intracranial tumors. After completing a full course of anti-infective therapy and comprehensive rehabilitation, the patient achieved significant recovery in activities of daily living (ADL).}, } @article {pmid42221483, year = {2026}, author = {Yang, H and Liu, S and Chen, X and Yin, C and Xiao, L and Xu, W and Lv, S and Xie, L and Yin, C}, title = {Gut microbiota-associated immunomodulation contributes to the protective effects of fluvastatin against endometriosis in a mouse model, accompanied by increased Akkermansia muciniphila abundance.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1762444}, pmid = {42221483}, issn = {1664-302X}, abstract = {BACKGROUND: Endometriosis (EMs) is a chronic inflammatory disease characterized by tumor-like growth behavior and limited therapeutic options. Increasing evidence suggests that gut microbiota may contribute to EMs progression by promoting chronic inflammation and immune dysregulation. Fluvastatin, a lipid-lowering agent, exhibits anti-inflammatory, anti-tumor, and immunomodulatory effects and has also been reported to influence microbial homeostasis. However, the relationship among fluvastatin treatment, gut microbiota, and EMs progression remains unclear. This study aimed to investigate this relationship.

MATERIALS AND METHODS: A mouse model of EMs was established by autologous uterine tissue transplantation, followed by oral fluvastatin administration for 3 weeks. Lesion growth, inflammatory responses, and immune characteristics were evaluated by histology, quantitative PCR, flow cytometry, immunofluorescence, and immunohistochemistry. Gut microbiota involvement was assessed using antibiotic-mediated microbiota depletion and fecal microbiota transplantation (FMT). Microbial composition was analyzed by metagenomic sequencing. The role of Akkermansia muciniphila was evaluated by direct oral supplementation.

RESULTS: Fluvastatin significantly reduced the volume and mass of ectopic lesions and decreased the mRNA expression of pro-inflammatory cytokines. It was also associated with changes in macrophage polarization-related markers and reduced abnormal activation of splenic immune cells. Antibiotic-induced gut microbiota depletion attenuated the protective effects associated with fluvastatin treatment, whereas FMT from fluvastatin-treated mice partially transferred similar protective changes. Metagenomic analysis revealed that fluvastatin reshaped gut microbiota composition and increased the abundance of Akkermansia muciniphila. Moreover, oral supplementation with Akkermansia muciniphila attenuated EMs progression and was associated with anti-inflammatory and immune-related changes similar to those observed after fluvastatin treatment.

CONCLUSION: These findings suggest that the protective effects associated with fluvastatin treatment are accompanied by changes in gut microbiota composition, including increased abundance of Akkermansia muciniphila. Gut microbiota may contribute to the beneficial effects of fluvastatin in EMs. These results support the potential value of microbiota-informed therapeutic strategies for EMs.}, } @article {pmid42221497, year = {2026}, author = {Taussig, R and Peralta, R and Bustamante, JP}, title = {A pilot proof-of-concept study of microbial and botanical diversity in honey samples from Necochea, Argentina.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1833002}, pmid = {42221497}, issn = {1664-302X}, abstract = {INTRODUCTION: Honey is a complex biological matrix containing plant-derived, microbial, and viral components that reflect both environmental and hive-associated processes. Traditional methods for determining botanical origin, such as melissopalynology, have limitations in resolution and scope. In this context, untargeted shotgun metagenomics emerges as a promising integrative approach for comprehensive honey characterization.

METHODS: This pilot study explored the feasibility of applying an untargeted shotgun metagenomic approach to honey samples from Necochea, Buenos Aires province, Argentina. Two honey samples and a pollen control sample from Rosa chinensis were subjected to DNA extraction, shotgun library preparation, and sequencing on an Illumina NextSeq 500 platform.

RESULTS: The control sample showed exclusive assignment to Rosa chinensis, supporting the validity of the analytical workflow. In both honey samples, plant-derived sequences were predominantly assigned to Helianthus annuus (common sunflower) and Eucalyptus grandis (rose gum), consistent with the regional flora. Key bacterial taxa included Paenibacillus larvae in one sample, Acinetobacter johnsonii in the other, and Apilactobacillus kunkeei, Bradyrhizobium sp., Sphingobium yanoikuyae, and Stutzerimonas stutzeri in both. Apis mellifera filamentous virus was detected in both samples.

DISCUSSION: Given the limited sample size, these findings should be interpreted as exploratory and hypothesis-generating. Nevertheless, this proof-of-concept supports the potential of untargeted metagenomics as an integrated tool for the simultaneous characterization of botanical origin, microbial communities, and viral content in honey, offering advantages over targeted amplicon-based approaches. Future studies with larger and systematically designed cohorts will be necessary to validate and extend these observations.}, } @article {pmid42221499, year = {2026}, author = {Chang, N and Li, N and Li, W and Xue, J and Zheng, Y and Zhao, C and Zhang, S and Zhang, Y and Yin, G and Bao, M and Shen, W}, title = {Control efficacy and groundwater risk of antibiotic resistance genes in semi-arid landfill leachate treatment: seasonal insights and engineering implications.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1807935}, pmid = {42221499}, issn = {1664-302X}, abstract = {Landfill leachate is a critical reservoir of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), posing prominent risks to groundwater, especially in semi-arid regions. This study focused on the performance of landfill leachate treatment system in Hohhot (Inner Mongolia, semi-arid region), investigating the seasonal variation across three seasons (spring, summer, and autumn), migration characteristics, and control effect of ARGs/MGEs through process optimization-oriented monitoring. Metagenomic sequencing was employed to analyze four key matrices (raw leachate, ultrafiltration effluent, treated leachate, and adjacent groundwater) across three seasons. The treatment system achieved efficient removal of conventional pollutants but failed to eliminate ARGs, MGEs, and antibiotic-resistant bacteria. Instead, it enriched high-risk hosts (e.g., Pseudomonas_E) and transposases (e.g., tnpA), exacerbating horizontal gene transfer potential. ARGs abundance showed pronounced peaks in summer and autumn among the sampled seasons. Notably, the resistome profile of treated leachate was highly similar to that of groundwater, indicating incomplete ARG containment and hydrological connectivity between the treatment system and groundwater. A dual-track health-environmental risk framework was applied to the detected ARG subtypes, revealing that overall risk burden was concentrated in a small set of high-priority determinants. The top contributors were dominated by mobility- and co-selection-linked markers (intI1, tnpA, IS6100, IS26, and qacE△1) together with clinically relevant resistance genes (sul1, aacA, and aadA), underscoring the coupling between resistance functions and genetic mobility in the leachate-groundwater continuum. Collectively, these findings indicate that semi-arid landfill systems can act as both sinks and sources of high-risk resistance determinants, and they highlight the need to integrate ARGs/MGEs-targeted treatment upgrades, seasonally adaptive operational strategies, and risk-based dual-track monitoring into leachate management. This study therefore provides actionable engineering insights for optimizing leachate treatment performance and mitigating cross-media contamination in water-scarce environments.}, } @article {pmid42221583, year = {2026}, author = {David Hanna, LB and Steinig, E and Bond, K and Lim, CK and Ramachandran, PS}, title = {Enrichment techniques for clinical metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1723747}, pmid = {42221583}, issn = {2235-2988}, mesh = {*Metagenomics/methods ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Polymerase Chain Reaction/methods ; CRISPR-Cas Systems ; }, abstract = {Metagenomic next-generation sequencing (mNGS) offers a powerful, hypothesis-free approach for pathogen detection in clinical samples, allowing the identification of both known and novel microorganisms. However, the predominance of host nucleic acid in most samples poses a significant challenge, often overshadowing low-abundance pathogen sequences and increasing the cost of mNGS due to the high sequencing depth required. Enrichment techniques which selectively amplify pathogen-specific sequences can help to overcome this challenge, improving the sensitivity, specificity, and overall efficiency of mNGS - albeit while compromising the hypothesis-free nature and breadth of shotgun mNGS. As such, they can augment the use of mNGS in clinical scenarios where a more targeted approach is needed. This review provides a comprehensive analysis of the main enrichment techniques currently employed in the field, including PCR-based enrichment, CRISPR-Cas9 enrichment, molecular inversion probes (MIP), nanopore adaptive sequencing (AS), and hybridisation capture-based methods. We evaluate each method on a range of metrics including methodology, cost, sensitivity, specificity, and ease of integration into clinical workflows, as well as describing their application to date for purposes including pathogen detection, antimicrobial resistance profiling, and whole-genome sequencing across diverse clinical sample types. Current limitations and future directions for refinement and implementation of these techniques are also discussed. By summarising the current landscape and latest advancements in mNGS enrichment strategies, this review aims to guide the optimisation of mNGS workflows in clinical diagnostics and highlight key areas for future research.}, } @article {pmid42221911, year = {2026}, author = {Gazulla, CR and Ferrera, I and Balagué, V and Marín-Vindas, C and González-Vega, A and Escánez-Pérez, J and Fraile-Nuez, E and Arrieta, JM and Gasol, JM and Sánchez, O}, title = {Diversity and community structure of aerobic anoxygenic phototrophic bacteria are shaped by the deep chlorophyll maximum.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag076}, pmid = {42221911}, issn = {2730-6151}, abstract = {The surface ocean exhibits strong vertical gradients in light irradiance, nutrients, and temperature, shaping the phytoplankton distribution, which often defines a deep chlorophyll maximum (DCM). Aerobic anoxygenic phototrophic (AAP) bacteria inhabit the euphotic zone, with their abundances generally following the chlorophyll a variability. While AAP bacterial communities are known to differ across regions with contrasting environmental conditions, their vertical distribution remains poorly understood. We hypothesized that the diversity and community structure of AAP bacteria vary across the vertical gradient, in relation to changes in environmental variables and following the DCM profile. To test this hypothesis, we studied the composition of AAP communities at different depths along the DCM structure in the South and Central Atlantic Ocean, by means of amplicon sequencing of the pufM gene. The results show significant differences in richness, community structure, and taxonomic composition of samples from different layers of the DCM, highlighting the dependence of AAP bacteria on its structure. Remarkably, the use of primers with broad phylogenetic coverage enabled the recovery of several AAP phylogroups previously detected only through metagenomics. We show that they represent a significant fraction of marine AAP communities, provide clues about their ecological preferences, and confirm their association with the family Candidatus Luxescamonaceae.}, } @article {pmid42222018, year = {2026}, author = {Ye, J and Ye, L and Sun, W and Xie, S and Lai, Z}, title = {A case of infective endocarditis caused by Streptococcus gordonii complicated with bacterial meningitis and cerebral infarction -- Application of metagenomic next-generation sequencing (mNGS).}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02608}, pmid = {42222018}, issn = {2214-2509}, abstract = {This study reports a case of infective endocarditis (IE) caused by Streptococcus gordonii. The patient presented with cerebral infarction as the initial manifestation, complicated by bacterial meningitis and mitral regurgitation. The diagnosis of Streptococcus gordonii-induced infective endocarditis was facilitated by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF). Streptococcus gordonii was detected by CSF mNGS within 40 h after admission, which was 30 h earlier than the positive result of blood culture. During anti-infective therapy, the patient experienced recurrent thromboembolic events and underwent emergency mechanical thrombectomy due to occlusion of the left vertebral artery. Despite aggressive treatment, the patient eventually died of heart failure. This case indicates that Streptococcus gordonii is a rare pathogen of infective endocarditis, and its clinical presentation complicated by cerebral infarction and bacterial meningitis is distinctive; particularly, complex cases requiring mechanical thrombectomy are extremely rare in clinical practice. As an important complement to conventional bacterial culture, mNGS can shorten diagnostic delay, especially in patients with negative blood or CSF cultures. For patients with concurrent cerebral infarction and meningitis, the possibility of infective endocarditis should be highly suspected, and indications for valve replacement surgery should be evaluated as early as possible in high-risk cases.}, } @article {pmid42222019, year = {2026}, author = {Wang, F and Xie, C and Zhao, M and Pan, Y and Xie, Y and Wang, X and Zhu, W and Xie, Y}, title = {VV-ECMO-supported management of severe ARDS secondary to melioidosis sepsis: A case report and concise review.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02612}, pmid = {42222019}, issn = {2214-2509}, abstract = {Melioidosis, caused by Burkholderia pseudomallei (B. pseudomallei), is a life-threatening tropical infection that is frequently underdiagnosed because of its heterogeneous and nonspecific clinical presentation. We report a critically ill patient from an endemic area who developed fulminant pneumonia that progressed to septic shock and severe acute respiratory distress syndrome. Despite empirical broad-spectrum antimicrobial therapy, respiratory failure worsened, prompting early etiologic investigation with metagenomic next-generation sequencing, which identified B. pseudomallei and was subsequently confirmed by culture. The patient required early venovenous extracorporeal membrane oxygenation (ECMO) for refractory hypoxemia. Management included a targeted antimicrobial therapy in accordance with current guidelines and CT-guided drainage of a pulmonary abscess as definitive source control. The patient achieved full recovery without recurrence at follow-up. Early identification of the causative pathogen and timely source control were central to the management of melioidosis-associated severe ARDS. Advanced supportive measures, including ECMO, may be considered in selected patients with refractory hypoxemia as part of management involving multiple specialties.}, } @article {pmid42222035, year = {2026}, author = {Liu, YH and Fang, SR and Chen, W and Wu, YF and Liu, DK and Li, T}, title = {Comparative Study of Confirmed versus Suspected Cases of Vibrio vulnificus Infection in Chaoshan District, Guangdong, China.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {613123}, pmid = {42222035}, issn = {1178-6973}, abstract = {OBJECTIVE: To compare the epidemiological, clinical, and laboratory data of patients with confirmed and suspected Vibrio vulnificus infection in Chaoshan District, Guangdong.

METHODS: This retrospective study analyzed 25 confirmed cases and 23 suspected cases of V. vulnificus infection at the First Affiliated Hospital of Shantou University Medical College from January 2014 to December 2025. A confirmed case was defined by the presence of a positive result from culture and/or mNGS and a suspected case by the experience of a clear marine trauma followed by rapidly progressive soft tissue manifestations, but without etiological confirmation of V. vulnificus infection after exclusion of other infectious etiologies. The epidemiological history, early clinical manifestations, routine blood parameters, and in-hospital outcomes of the two groups were compared.

RESULTS: The confirmed group had a greater severity of soft tissue infection (84.0% vs 26.0%, P<0.01) and more involved sites (88.0% vs 47.8%, P<0.01). The laboratory data indicated the confirmed group had more abnormalities in markers of tissue injury (creatinine kinase, lactate dehydrogenase), coagulation function (platelets, prothrombin time, international normalized ratio), liver function (aspartate transaminase, total bilirubin), renal function (serum creatinine), and lipid and nutritional markers (all P<0.05). The confirmed group also had significantly higher rates of in-hospital mortality (32.0% vs 0%), multi-organ dysfunction syndrome (36.0% vs 0%), and surgical intervention (60.0% vs 30.4%), and a greater economic burden (all P<0.001).

CONCLUSION: There are significant differences in the early clinical manifestations, routine blood parameters, and in-hospital outcomes for patients with confirmed and suspected V. vulnificus infection.}, } @article {pmid42222136, year = {2026}, author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC}, title = {Protist community sites and structure under two barn management systems at a commercial dairy.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1803341}, pmid = {42222136}, issn = {2813-4338}, abstract = {INTRODUCTION: Investigations into the location and load of protists in the environment arounddairies are scarce but are essential to maintaining the health of livestock.Moreover, the design of dairy barns has fluctuated over the decades to maximizecattle health and milk production without regard to influences on environmentalmicrobiomes. Beyond cost, the major emphasis of barn design is the managementof appropriate temperature and comfort for cattle. However, there havebeen no corresponding investigations into whether these design changes affect protist communities within barns.

METHODS: In this study, community shotgun metagenomic analysis was used to define the spatial composition and relative abundance of protist communities from 118 samples of manure, lagoons, troughs, and house and stable flies at a commercial dairy implementing two free-stall management systems: flow-through and cross-vent. Sequence reads were mapped to the CosmosID database. Viability was not assessed; therefore, results reflect DNA detection only not viability or disease occurrence.

RESULTS: The protist composition differed significantly between dairy components. Ecological findings showed that troughs and lagoons harbored high protist diversity, including the possible pathogen Neobalantidium coli and potential carriers Paramecium biaurelia and Acanthamoeba. Manure had the lowest protist diversity. Stable flies carried more protist taxa than house flies. Both fly species uniquely carried the non-pathogenic alveolate parasite Hammondia hammondi. The water mold plant pathogen Pseudoperonospora cubensis was identified in all sample types. Of the total relative abundance of protists, 2.10% were amoebas, 7.63% alveolate parasites, 62.71% water molds, 23.31% ciliates, 1.74% foraminifera, and 2.50% diatoms.

DISCUSSION: These results describe preliminary spatial overlaps and possible avenues of dissemination, providing a basis for assessing appropriate management systems and identifying protist reservoir sites within dairy operations.}, } @article {pmid42222213, year = {2026}, author = {Zhou, Y and Lai, Y and Zhou, F and Wang, X and He, X and Jin, J and Zhang, R}, title = {Morphological analysis of bronchoalveolar lavage fluid in diagnosing pulmonary aspergilloma in a patient with rheumatoid arthritis: A case report.}, journal = {Experimental and therapeutic medicine}, volume = {32}, number = {1}, pages = {191}, pmid = {42222213}, issn = {1792-1015}, abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disorder that primarily affects the joints and may be associated with systemic complications. Patients with RA have an increased susceptibility to opportunistic infections, attributable to inherent immune dysregulation as well as immunosuppressive therapies, including tocilizumab, particularly among those with comorbidities or high disease activity. Notably, the use of tumor necrosis factor inhibitors, such as adalimumab and etanercept, has been associated with a higher incidence of invasive pulmonary aspergillosis and chronic pulmonary aspergillosis. The present study reports a rare case of pulmonary aspergilloma in a 75-year-old female RA patient with prior tuberculosis and long-term tocilizumab use. The patient was diagnosed via bronchoalveolar lavage fluid morphology, fungal culture, Aspergillus galactomannan assay, metagenomic next-generation sequencing and pathology, and the patient achieved symptom resolution and improved imaging after 6 months of treatment with voriconazole. These findings underscore the need for vigilant monitoring and individualized management strategies in this patient population.}, } @article {pmid42222492, year = {2026}, author = {Tran, TTT and Nguyen, OTK and Hoang, PH and Nguyen, NP and To, HTM and Nguyen, HQ}, title = {Metagenomic and metabolomic analyses of fecal samples from civet-digested coffee in Vietnam.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21262}, pmid = {42222492}, issn = {2167-8359}, mesh = {*Feces/microbiology/chemistry ; Vietnam ; *Coffee/metabolism/microbiology ; *Metabolomics ; *Metagenomics ; *Gastrointestinal Microbiome/genetics ; Fermentation ; Humans ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/metabolism ; Animals ; }, abstract = {BACKGROUND: Civet-digested coffee originates from the feces of civets that consume coffee cherries, where microbial fermentation in the gastrointestinal tract imparts distinctive flavor attributes, thereby enhancing its global reputation and market value. Gut microbiota is considered important drivers of coffee-bean fermentation, potentially shaping the unique and region-specific flavor characteristics of civet-digested coffee. To address this context, the present study integrated metagenomic and metabolomic analyses to compare the gut microbiota and secondary metabolites involved in coffee-bean fermentation inside Vietnamese civets.

METHODS: Fecal samples were collected under two dietary conditions: a standardized one containing 20% protein, 6% fiber, and 0.4-1.5% lysine, and the same diet supplemented with coffee cherries. Metagenomic 16S rRNA sequencing and untargeted ultra-performance liquid chromatography quadrupole time-of-flight (UPLC-QTOF) revealed clear differences between the two groups.

RESULTS: Integrated metagenomic and metabolomic analyses revealed clear distinctions between the two groups. Civets on the coffee-cherry diet exhibited higher microbial diversity at the family and genus levels. Specifically, among 31 classified bacterial genera showing a trend toward significant differences in abundance, Enterococcus and Escherichia/Shigella decreased, whereas Gluconobacter, and Pseudomonas increased following the diet shift. Metabolomic profiling identified 46 metabolites across both ionization modes, and strong correlations were observed between microbial genera and metabolite profiles. Specifically, 6-hydroxyangolensic acid methyl ester, 4-aminobenzoic acid and caffeine were more abundant in civets on a coffee-cherry diet, meanwhile the other nine metabolites were more prevalent in the normal diet. Overall, the findings demonstrate that civet gut microbiota and metabolic output were highly responsive to dietary inputs, and that coffee cherries promoted a unique fermentation environment. This represents the first integrative metagenomic and metabolomic study of civets consuming coffee in Vietnam, providing valuable insights into microbial contributions to coffee fermentation.}, } @article {pmid42222536, year = {2026}, author = {Yang, H and Zhao, L}, title = {Clinical characteristics and prognostic analysis of patients with herpesvirus meningitis/encephalitis based on cerebrospinal fluid mNGS positivity.}, journal = {Frontiers in neurology}, volume = {17}, number = {}, pages = {1808867}, pmid = {42222536}, issn = {1664-2295}, abstract = {BACKGROUND: Herpes viruses are a major cause of meningitis/encephalitis in adults. However, their individual clinical phenotypes and outcomes remain incompletely delineated. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) offers a powerful tool for precise pathogen identification, facilitating the comparison of distinct herpes virus infections.

METHODS: This retrospective cohort study analyzed 66 patients with CSF-mNGS confirmed herpes virus meningitis/encephalitis at a single center between October 2019 and August 2025. The cohort was stratified into five etiological groups: herpes simplex virus type 1 (HSV-1, n = 10), herpes simplex virus type 2 (HSV-2, n = 5), varicella-zoster virus (VZV, n = 27), Epstein-Barr virus (EBV, n = 15), and human herpesvirus 7 (HHV-7, n = 9). Demographic, clinical, laboratory, and neuroimaging data were collected. Outcomes were assessed using the Glasgow Outcome Scale (GOS) at 3 months post-discharge.

RESULTS: Distinct clinical phenotypes were observed. HSV-1 encephalitis typically presented with psychiatric symptoms, seizures, and temporal lobe involvement on MRI. HSV-2 infection manifested primarily as a febrile headache syndrome with minimal brain parenchymal involvement. VZV infection was associated with the most intense CSF inflammatory response (highest WBC and protein), a higher incidence of hypoglycorrhachia (25.9%) and hypochloridia (40.7%), and unique complications like cranial neuritis and vasculopathy. EBV infections occurred in older patients and showed features overlapping with HSV-1. HHV-7 infected a significantly younger population and was strikingly associated with elevated intracranial pressure (ICP ≥ 330 mmH2O in 33.3%). Multivariate analysis identified a longer interval from symptom onset to hospitalization (OR: 1.118, p = 0.025) and an abnormal EEG (OR: 0.066, p < 0.001) as independent predictors of an unfavorable outcome (GOS < 5). Antiviral or steroid therapy was not significantly associated with prognosis in this cohort.

CONCLUSION: CSF-mNGS reveals distinct and clinically significant phenotypic differences among various herpesvirus meningitis/encephalitis. VZV is characterized by a vigorous CSF inflammatory response and vascular complications, while HHV-7 predominantly affects younger adults and is significantly associated with intracranial hypertension. These findings underscore the value of mNGS in enabling pathogen-directed diagnosis and management, moving beyond syndromic approaches.}, } @article {pmid42222738, year = {2026}, author = {Park, JH and Chung, J and Lee, HJ and Na, HS}, title = {Comparison of 16S rRNA gene amplicon and whole-genome shotgun metagenomic sequencing for subgingival oral microbiome profiling.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2679807}, pmid = {42222738}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease driven by a dysbiotic subgingival microbiome. While 16S rRNA gene amplicon sequencing is widely used, whole-genome shotgun (WGS) metagenomics is increasingly applied for higher taxonomic and functional resolution.

OBJECTIVE: The aim of this study was to directly compare 16S rRNA gene amplicon (V1-V2) sequencing and WGS metagenomic sequencing using matched subgingival plaque samples from patients with periodontitis.

METHODS: Subgingival plaque samples from 28 patients with periodontitis were analyzed using both 16S rRNA gene amplicon (V1-V2) sequencing and WGS metagenomics. Taxonomic composition, microbial diversity, differential abundance and functional analysis were compared across platforms.

RESULTS: WGS generated markedly higher read counts than 16S rRNA gene amplicon but showed wide variability in non-human reads, whereas 16S rRNA gene amplicon yielded a consistent proportion of non-chimeric reads. High taxonomic overlap was observed at the phylum level but declined at higher taxonomic ranks. WGS preferentially detected taxa such as Actinomyces, Corynebacterium and Olsenella, while the 16S rRNA gene amplicon more frequently captured Saccharibacteria (TM7) and low-abundance taxa. Core genera, including Rothia, Neisseria and Cardiobacterium showed comparable abundance patterns across platforms. When patients were grouped depending on probing pocket depth (PPD), LEfSe analysis resulted in platform-specific enrichment patterns. Functional analyses revealed shared central pathways, such as pyruvate metabolism, while 16S-based PICRUSt2 emphasized reductive and degradative pathways and WGS-based HUMAnN highlighted oxidative and biosynthetic pathways. Notably, WGS-based functional profiles were strongly influenced by microbial read depth.

CONCLUSIONS: This comparative analysis demonstrates that 16S rRNA gene amplicon (V1-V2) sequencing and WGS both robustly capture core subgingival microbial signatures. While WGS provides higher species-level and functional resolution, the resolution was strongly constrained by microbial read depth in host-rich subgingival samples. These findings provide practical guidance for selecting appropriate sequencing strategies and optimizing sample preparation when designing WGS-based periodontal microbiome studies.}, } @article {pmid42222901, year = {2026}, author = {Dong, Y and Hu, D and Yang, R and Xin, T and Guan, Y and Zhu, X and Ding, Y and Cui, S and Wang, R and Wang, X and Niu, Y and Kong, X}, title = {Early-Life Obesity Leaves a Metabolic Memory That Accelerates Aging-Related Decline Through the Gut Microbiota-GABA Axis.}, journal = {Molecular nutrition & food research}, volume = {70}, number = {11}, pages = {e70513}, doi = {10.1002/mnfr.70513}, pmid = {42222901}, issn = {1613-4133}, support = {2024YFF1106004//National Key Research and Development Program/ ; PL2025H095//Natural Science Foundation of Heilongjiang Province/ ; }, mesh = {Animals ; *gamma-Aminobutyric Acid/metabolism/pharmacology ; *Aging/metabolism/physiology ; *Obesity/metabolism/microbiology/etiology ; *Gastrointestinal Microbiome/physiology ; Diet, High-Fat/adverse effects ; Male ; Oxidative Stress ; Rats ; Lipid Metabolism ; }, abstract = {Childhood obesity is a critical public health concern. Whether diet-induced transient obesity during development negatively impacts later-life health remains unclear, and mechanisms are poorly understood. This study investigates whether these effects persist into aging and employs integrated omics to explore underlying mechanisms. Using a high-fat diet (HFD) to induce transient developmental obesity in post-weaning rats and larval Drosophila, we examined the long-term effects on aging metabolic health in both species. Transient developmental obesity in rats was linked to accelerated aging, weight loss, worsened metabolism, colonic inflammation, and oxidative stress. Metabolomics revealed persistent gamma aminobutyric acid (GABA) dysregulation associated with intestinal ammonia levels, and gut metagenomics showed a reduction in Lactobacillales, correlating with adverse health outcomes. In Drosophila, exogenous GABA extended HF-diet lifespan. It reduced trehalose, triglycerides (TG), and oxidative stress; concurrently, it restored intestinal Lactobacillus and activated the phosphotransferase system (PTS), thereby improving metabolic homeostasis and redox status. Transient developmental obesity is associated with reduced gut Lactobacillus abundance, which may contribute to decreased GABA levels and subsequent disruption of glucose (GLU) metabolism, potentially involving the PTS pathway. These interconnected alterations may ultimately lead to systemic dysregulation of GLU and lipid metabolism and redox homeostasis in later life, compromising overall health and longevity.}, } @article {pmid42223080, year = {2026}, author = {An, SY and Kim, I and Hong, SH and Kim, EH and Suh, JY}, title = {AcrIIA8 is a putative phage structural protein of the HTJ2 family that does not inhibit Streptococcus pyogenes Cas9.}, journal = {Protein science : a publication of the Protein Society}, volume = {35}, number = {7}, pages = {e70651}, pmid = {42223080}, issn = {1469-896X}, support = {RS-2025-23525174//National Research Foundation of Korea/ ; RS-2024-00440614//National Research Foundation of Korea/ ; BDB-2025-04-04230007//Korea Institute of Marine Science & Technology Promotion/ ; }, mesh = {*Streptococcus pyogenes/enzymology/genetics/virology ; *CRISPR-Associated Protein 9/antagonists & inhibitors/chemistry/metabolism ; *Viral Structural Proteins/chemistry/metabolism/genetics ; *Bacteriophages/chemistry ; }, abstract = {Anti-CRISPR (Acr) proteins are phage-encoded anti-defense factors that suppress CRISPR-Cas immunity in bacteria. AcrIIA8 was previously identified as an inhibitor of Streptococcus pyogenes Cas9 (SpyCas9) through functional assays of metagenomic libraries. Here, we report that AcrIIA8 does not inhibit SpyCas9 in biochemical assays under a range of buffer conditions and temperatures. The solution structure and dynamics of AcrIIA8 reveal a six-stranded β-barrel fold with flexible β1-β2 and β2-β3 loops, characteristic of phage virion-assembly proteins. In addition, genomic context analysis places AcrIIA8 and its homologs within conserved prophage morphogenetic regions at the position expected for type II head-tail joining (HTJ2) proteins. We further detected no interaction between AcrIIA8 and SpyCas9 in NMR titration experiments, suggesting that they do not specifically associate. Taken together, these findings argue against assigning AcrIIA8 as a SpyCas9 inhibitor and instead support its annotation as a putative phage structural protein of the HTJ2 family.}, } @article {pmid42223254, year = {2026}, author = {Petricciuolo, M and Carnevali, A and Torboli, A and Postinghel, M and Guasticchi, A and Foladori, P and Cadonna, M and Federici, E}, title = {Wastewater-Based Assessment of Antimicrobial Resistance and Bacterial Communities in Urban and Rural Areas in the Province of Trento (Italy).}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70319}, pmid = {42223254}, issn = {2045-8827}, support = {//CINECA/ ; //Ministero dell'Università e della Ricerca/ ; }, mesh = {Italy ; *Bacteria/drug effects/genetics/isolation & purification/classification ; *Anti-Bacterial Agents/pharmacology ; *Wastewater/microbiology ; *Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rural Population ; Sewage/microbiology ; }, abstract = {Wastewater-based epidemiology (WBE) can supplement clinical surveillance for assessing the spread of antimicrobial resistance (AMR) across the population. We have analyzed sewage samples from seven wastewater treatment plants in the Province of Trento (Italy) using both culture-based and metagenomic DNA methods to investigate the prevalence of antimicrobial-resistant bacteria (ARBs) and resistance genes in urban and rural areas. ESBL-Escherichia coli prevalence was higher in urban areas than in rural ones. As determined by qPCR and dPCR, intI1 and genes associated with widespread resistances, namely, to tetracyclines (tetA), sulfonamides (sul1), and fluoroquinolones (qnrS), were abundant regardless of the area of origin. Among the genes coding for clinically relevant resistances, only that related to macrolides resistance (ermB) was abundant, while the others, namely, those to third-generation cephalosporins (blaCTX-M), carbapenems (blaKPC), vancomycin (vanA), and methicillin (mecA), were detected at much lower concentrations. Further, the abundances of ermB, blaKPC, and vanA were significantly higher in urban areas. 16S rRNA amplicon sequencing showed the occurrence of complex bacterial communities and the abundance of Acinetobacter, Pseudomonas, and Streptococcus, genera that may include ARBs reported in the WHO Bacterial Priority Pathogens List, with the latter showing higher prevalence in urban areas. Taken together, our data highlights the importance of implementing WBE studies across geographical areas with different characteristics in terms of vocation, number of municipalities, and population size, such as urban and rural ones. By providing a comprehensive understanding of AMR at the population level, this approach can inform and support more effective public health interventions.}, } @article {pmid42223272, year = {2026}, author = {Borton, MA and Oliverio, AM and Narrowe, AB and Villa, JA and Rinke, C and Hoyt, DW and Liu, P and McGivern, BB and Bechtold, EK and Ellenbogen, JB and Daly, RA and Smith, GJ and Angle, JC and Flynn, RM and Freiburger, AP and Louie, KB and Stemple, B and Northen, TR and Henry, C and Miller, CS and Morin, TH and Bohrer, G and Wrighton, KC}, title = {Mapping the soil microbiome functions shaping wetland methane emissions.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0068025}, doi = {10.1128/msystems.00680-25}, pmid = {42223272}, issn = {2379-5077}, abstract = {Accounting for only 8% of Earth's land cover, freshwater wetlands remain the foremost contributors to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more than land cover or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane-cycling microorganisms, contrasting with theoretically expected responses to hydrological perturbations. Co-expression analyses, coupled with depth-resolved methane measurements, revealed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil-derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production.IMPORTANCESoil microbial ecology is increasingly recognized as essential to climate mitigation, but realizing its full potential requires shifting from static genome inventories to dynamic assessments of microbial activity. This study shows that methane-cycling microbes exhibit stable, depth-stratified expression patterns, even in response to major redox and flooding shifts, undermining assumptions that water-table manipulations common in wetland management can alone reduce methanogenesis. Instead, methane cycling is shaped by spatially organized, transcriptionally active networks involving not only methanogens but also methanotrophs, fermenters, and iron reducers. These findings expose the limitations of genome-only models and highlight the need for soil diagnostics that capture in situ activity. Together, we provide a foundation for developing activity-based microbiome tools, embedding microbial functions into Earth system models, and designing interventions that move beyond "single-lever" strategies and instead work with the structure and dynamics of microbial communities as complex, layered systems.}, } @article {pmid42223530, year = {2026}, author = {Pokharel, SK and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, DC}, title = {Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag140}, pmid = {42223530}, issn = {1751-7370}, abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Time-lapse microscopy revealed that Archangium exhibited reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate) but maintained robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.}, } @article {pmid42224759, year = {2026}, author = {Xu, M and Qi, S and Yu, X and Han, S and Xiao, R and Guo, J and Wang, C and Zhu, N and Lu, H}, title = {Resistome risks of biological wastewater treatment communities: A global dataset of activated sludge, anaerobic digestion, and anammox.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142561}, doi = {10.1016/j.jhazmat.2026.142561}, pmid = {42224759}, issn = {1873-3336}, abstract = {Activated sludge (AS), anaerobic digestion (AD), and anammox (AMX) systems are widely used for wastewater treatment. Their microbial communities harbor resistomes, including but not limited to antibiotic resistance genes (ARGs) and metal resistance genes (MRGs), which may pose potential risks to human and ecological health if they are mobilized or transferred to pathogenic hosts. However, cross-process comparisons of resistome risks are limited at a global scale. This study analyzed 225 metagenomic datasets (210 public: 70 each for AS, AD, AMX; plus 15 in-house AMX) to assess resistome risks and identified key influential factors. Overall, within the constraints of current data availability, North America, Europe and Asia systems exhibited comparable risk levels. AD systems exhibited more than 2-fold higher human health resistome risks (potentials for human pathogens of acute resistance concern to acquire ARGs) than AS and AMX systems. Mesophilic and co-digestion AD systems posed 30-90% higher risks than thermophilic and mono-digestion systems with higher abundance of pathogens, ARGs, and MRGs. AMX systems, otherwise, showed higher ecological resistome risks (overall mobility of ARGs/MRGs and potentials for pathogen acquisition) than AS and AD. The conservative AMX communities contained core taxa that harbor 19.8% more ARGs/MRGs per genome and exhibit 31.4% higher horizontal gene transfer potential than non-core taxa. Key operating factors influencing resistome risks included temperature for AD, and organic loading, influent antibiotics and heavy metals for AMX. These findings provide insights into future wastewater treatment towards improved efficacy and reduced resistome risks.}, } @article {pmid42224761, year = {2026}, author = {Ma, S and Zhao, B and Jing, G and Han, M and Wang, M and Shan, X and Wang, Z and Lu, S and Liu, X and Wu, F}, title = {Vertical stratification and distribution patterns of the ARG resistome in Fuxian Lake: Insights from a global baseline.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142528}, doi = {10.1016/j.jhazmat.2026.142528}, pmid = {42224761}, issn = {1873-3336}, abstract = {Deep lakes are critical reservoirs for antibiotic resistance genes (ARGs), yet global ARG dynamics and vertical mechanisms remain poorly constrained. By combining metagenomics with a global comparative analysis across 17 plateau lakes and 83 Fuxian Lake samples, this study investigates ARG distribution from macro- to micro-scales. The macro-scale analysis identified Longitude, Latitude, and Temperature (all p-values < 0.05) as dominant constraints on ARG abundance. A distinct, synergistic mechanism drives vertical stratification: ARG enrichment occurs in the deep layer (50-150 m) at the lake center, but enrichment shifts to the shallow layer (0-40 m) in the tourism area. This complex pattern is governed by a biotic-abiotic synergy. Specifically, ARG dynamics in the deep layer are jointly regulated by biotic factors and physicochemical constraints such as pH and ORP. Differences observed at the local scale, including the increase in ARG abundance and rare-to-core conversion, contrast with broader patterns observed across plateau lakes. This study provides the first global distribution spectrum of ARGs in plateau lakes and reveals crucial interactive patterns. The persistent presence of high-risk ARGs and critical priority pathogens necessitates heightened vigilance. We propose controlling anthropogenic inputs and mitigating the risk of deep sediment pollutant release as crucial strategies for these vital freshwater resources.}, } @article {pmid42224764, year = {2026}, author = {Sun, Y and Yu, Z and Wu, C and Wang, J and Feng, X}, title = {First insights into agricultural practice-driven mobilization and methylation of arsenic and mercury in soil with implications for groundwater risk mitigation.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142530}, doi = {10.1016/j.jhazmat.2026.142530}, pmid = {42224764}, issn = {1873-3336}, abstract = {The migration of heavy metals from soils to groundwater via karst conduits (e.g., dolines) in karst terrains threatens the safety of anthropogenic water supplies. Despite widespread recognition of contamination risks, the underlying mechanisms governing the transformation and mobilization of heavy metals, particularly those mediated by agricultural activities, remain inadequately characterized. Here, we systematically studied the impact of rice straw return (RS) on the biogeochemical transformation processes of both arsenic (As) and mercury (Hg) from a co-polluted soil in karst regions using a combination of geochemical, microbial, and spectroscopic approaches. The results indicated that RS enhanced the desorption of As from Fe(III)oxyhydroxides and methylation of As(III). Metagenomic sequencing analyses revealed that RS increased the abundance of Fe-reducing bacteria (FeRB) and As-methylating microorganisms, which collectively drive As mobilization and transformation. Furthermore, RS promoted the release of Hg from Fe(III)oxyhydroxides and stimulated methylmercury (MeHg) formation, primarily due to the increased abundance of Hg-methylating microbes and hgcAB genes, as well as enhanced Hg availability through the transformation of HgS into organic matter bound Hg and nano-HgS. These findings are essential for predicting As and Hg leaching risks from soils to groundwater under the influence of agricultural practices in karst regions worldwide.}, } @article {pmid42224874, year = {2026}, author = {Kenzi, M and Benbernou, M and Khelifa, H and Tbahriti, HF}, title = {Machine learning-based prediction of antibiotic resistance gene distribution in agricultural soils under different climate change scenarios.}, journal = {The Science of the total environment}, volume = {1042}, number = {}, pages = {181905}, doi = {10.1016/j.scitotenv.2026.181905}, pmid = {42224874}, issn = {1879-1026}, mesh = {*Climate Change ; *Soil Microbiology ; *Machine Learning ; Agriculture ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Predictive Learning Models ; Boosting Machine Learning Algorithms ; Random Forest ; *Environmental Monitoring/methods ; }, abstract = {Antibiotic resistance genes (ARGs) in agricultural soils represent a major public health concern, as climate change is believed to augment their dissemination and abundance. Understanding the impact of future climate change scenarios on ARG abundance is essential to implement predictive and proactive One Health strategies. In this study, a total of 2301 soil samples from 67 countries across six continents were compiled from three global metagenome databases, namely NCBI SRA, MG-RAST, and JGI IMG/M. Six machine learning models, namely LightGBM, XGBoost, Random Forest, Support Vector Machines, Deep Neural Networks, and Logistic Regression, were used to predict ARG distribution patterns in agricultural soils, and their performance was evaluated using stratified 10-fold cross-validation with metrics such as AUC-ROC, precision, recall, F1 score, and Matthews Correlation Coefficient. WorldClim 2.1 and CMIP6 models were used to project ARG distribution under three Representative Concentration Pathway scenarios, namely RCP 2.6, RCP 4.5, and RCP 8.5, for the years 2050 and 2070. The LightGBM model achieved the best predictive performance, with an AUC-ROC of 0.957 (95% CI: 0.951-0.963), substantially higher than that of the other models, while the Deep Neural Networks model achieved an AUC-ROC of 0.891. The LightGBM model demonstrated high stability across cross-validation folds, with minimal fold-to-fold variance, defined as the standard deviation of AUC-ROC scores across the 10 folds (SD = 0.008). SHAP feature importance analysis identified soil temperature, pH, and organic carbon content as the top three factors influencing ARG relative abundance, with SHAP values of 0.342, 0.287, and 0.251, respectively. Annual precipitation and soil moisture level were also identified as significant contributors to ARG distribution. SHAP dependency plots revealed critical thresholds for ARG relative abundance, with a sharp increase observed independently when soil temperature exceeds 18 °C and when soil pH drops below 6.5. Furthermore, a non-linear accelerating increase in ARG abundance risk was observed as climate change intensity worsened across scenarios. Projections for future climate change scenarios indicate a potential 34.7% increase in high-risk ARG zones by the year 2070, with the largest changes expected in South Asia, Sub-Saharan Africa, and Mediterranean regions. Paired t-tests revealed significant differences in performance among all models (p < 0.001). These findings demonstrate that gradient-boosting methods such as LightGBM outperform deep learning approaches for ARG prediction from soil microbiome data, offering higher accuracy and interpretability. As climate change is projected to increase ARG risks in a non-linear manner, the development of climate-adaptive agricultural practices and global surveillance systems is urgent. This framework provides actionable risk-mapping tools to support precision farming and region-specific policy interventions within the One Health approach.}, } @article {pmid42225156, year = {2026}, author = {Feng, S and Bao, Y and Zhu, X and Wu, J and Chen, W and Huang, D and Zhou, T and Meng, L and Lee, CH and Li, D and Huang, M}, title = {Biodegradable versus persistent nanoplastics reshape nitrogen metabolism and biofilm architecture in denitrifying biofilters.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {135048}, doi = {10.1016/j.biortech.2026.135048}, pmid = {42225156}, issn = {1873-2976}, mesh = {*Microplastics/metabolism/toxicity ; Wastewater/chemistry/microbiology ; *Water Purification/methods ; Biodegradable Plastics/analysis/metabolism ; Biodegradation, Environmental ; Bioreactors/microbiology ; Nitrogen Cycle ; *Nitrogen/analysis/metabolism ; Filtration/instrumentation/methods ; Extracellular Polymeric Substance Matrix/metabolism ; Polyesters/analysis/metabolism ; *Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/analysis ; Denitrification/physiology ; }, abstract = {The presence of nanoplastics (NPs) in biological wastewater treatment systems is an emerging concern. Nevertheless, their differential influence on critical biofilm-mediated processes has yet to be fully elucidated. In this study, denitrifying biofilters were exposed to biodegradable polylactic acid nanoplastics (PLA-NPs) and non-biodegradable polystyrene nanoplastics (PS-NPs) to simulate both typical and cumulative high-exposure scenarios. Results showed that long-term NP stress significantly reduced the denitrification performance, with a maximum inhibition of 35% in total nitrogen (TN) removal. Mechanistically, PLA and PS induced distinct biofilm remodeling strategies. PLA exposure enhanced nitrate assimilation pathways, promoting nitrogen sequestration into microbial biomass. In contrast, PS-NPs elicited concentration-dependent stress responses. Low PS exposure was associated with reduced extracellular polymeric substances (EPS) and enhanced carbohydrate degradation potential, whereas high PS concentrations were linked to altered EPS composition, decreased microbial diversity, and directional succession toward stress-tolerant genera. Metagenomic analysis revealed shifts in central carbon metabolic strategies, including enhanced gluconeogenesis and EPS precursor synthesis under NP exposure. Differences in substrate bioavailability between PLA and PS treatments further contributed to distinct carbon utilization patterns within the biofilms. Overall, this study demonstrates that NP biodegradability governs biofilm functional stability, nitrogen transformation, and denitrification performance, providing mechanistic insight into NP-biofilm interactions in engineered systems.}, } @article {pmid42225158, year = {2026}, author = {Wang, M and Wang, H and Liang, X and Li, J and Wang, C and Cui, L and Yang, S and Lin, J and Yang, Q and Yang, Z}, title = {Enhanced phenanthrene degradation in microalgae-bacteria systems: Mechanistic roles of exogenous and indigenous degraders.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {135034}, doi = {10.1016/j.biortech.2026.135034}, pmid = {42225158}, issn = {1873-2976}, mesh = {*Phenanthrenes/metabolism ; Biodegradation, Environmental ; *Microalgae/metabolism/growth & development ; *Bacteria/metabolism ; Biomass ; *Chlorella vulgaris/metabolism/growth & development ; Extracellular Polymeric Substance Matrix/metabolism ; Biofilms ; }, abstract = {This study investigates the synergistic mechanisms of phenanthrene (PHE) biodegradation using Chlorella vulgaris consortia with exogenous (EB) and indigenous (IB) bacteria. Results showed that both cooperative systems significantly enhanced algal growth and PHE removal, with biomass increasing by 17.2% (C.v-EB) and 75.0% (C.v-IB), and biodegradation rates reaching 75.3%-78.4%. Mechanistically, C.v-EB relied on enzymatic antioxidant responses (SOD and CAT) and a protein-rich extracellular polymeric substance (EPS) shield to mitigate oxidative stress. In contrast, C.v-IB exhibited superior resilience through non-enzymatic redox regulation (glutathione/thioredoxin systems) and the formation of a dense, biofilm-like EPS matrix supported by active transport genes (wzm/wzt). Metagenomic analysis revealed that C.v-IB possessed higher metabolic redundancy and energy production efficiency, organized into a coordinated "Degradation-Defense-Communication" genomic architecture via quorum sensing. Furthermore, both consortia expanded the metabolic landscape of PHE, effectively eliminating intermediate toxicity through divergent pathways. These findings provide a systematic framework for developing robust algal-bacterial biotechnologies for the remediation of polycyclic aromatic hydrocarbons in wastewater.}, } @article {pmid42225249, year = {2026}, author = {Nie, X and Qin, J and Liu, M and Wang, H and Hou, K and Duan, Y}, title = {Process-level design of engineered microalgal-bacterial systems for carbon-efficient nitrogen removal from low C/N wastewater: carbon/electron redistribution revealed by metabolic network analysis.}, journal = {Environmental research}, volume = {305}, number = {Pt 1}, pages = {124883}, doi = {10.1016/j.envres.2026.124883}, pmid = {42225249}, issn = {1096-0953}, abstract = {Carbon scarcity in low carbon-to-nitrogen (C/N) wastewater limits electron donor availability and constrains biological nitrogen removal. Although microalgal-bacterial symbiosis (MBS) is a promising low-input alternative, the mechanisms that sustain nitrogen removal under carbon-limited conditions remain unclear. Here, process-level characterization and metagenomic analysis were combined to investigate community assembly and carbon/electron redistribution in engineered MBS systems. Under the tested conditions, a balanced algae-to-bacteria ratio (1:1) created the most stable niche and achieved >97% NH4[+]-N removal with minimal nitrate accumulation, indicating effective coupling of nitrification, denitrification, and assimilation. Extracellular polymeric substances (EPS) dynamics showed a shift from accumulation to reutilization during prolonged carbon limitation: polysaccharides decreased in the later stage as external chemical oxygen demand (COD) was depleted, suggesting mobilization of EPS as an internal carbon source. Consistently, tricarboxylic acid (TCA) cycle genes (e.g., IDH, OGDH, mdh) were enriched whereas glycolysis-related genes (e.g., GAPDH, PGK) declined, indicating a shift in metabolic potential toward greater generation of reducing equivalents. Overall, the results suggest that EPS functions as a dynamic carbon reservoir and that algae-bacteria interactions promote carbon/electron redistribution under carbon-limited conditions. This study provides a process-level basis for designing carbon-efficient wastewater treatment systems.}, } @article {pmid42226305, year = {2026}, author = {Grundler, F and Ducarmon, QR and Holley, A and Knufinke, M and Strathmeyer, S and Heelemann, S and Geyer, R and Martínez-Téllez, B and MacArthur, MR and Zeller, G and Wilhelmi de Toledo, F and Mesnage, R}, title = {Health benefits of a five-day at-home modified fasting program: a randomised controlled trial.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {42226305}, issn = {1756-994X}, support = {ALTF 1030-2022//EMBO postdoctoral fellowship/ ; RYC2022-036473-I//MCIN/AEI/10.13039/501100011033/ ; }, mesh = {Humans ; Female ; *Fasting ; Adult ; Male ; Blood Pressure ; Weight Loss ; Metabolomics ; Middle Aged ; Biomarkers ; }, abstract = {BACKGROUND: Fasting is one of the most cost-effective methods to improve cardiometabolic health. We tested a 5-day hypocaloric (~ 600 kcal/day) and ketogenic, modified fasting program (MFP) in a two-arm randomised controlled trial, where sixty-four healthy subjects were randomised to MFP or control group.

METHODS: We randomly assigned 64 participants to a group receiving the MFP or to a group of participants who were told to continue with their usual eating behaviour and lifestyle (control group). The changes in blood pressure and body weight were considered as primary endpoints. Secondary outcomes included ketosis, glucose and lipid metabolism, inflammatory markers, antioxidant capacity and well-being. Biological pathways and metabolic processes were explored with nuclear magnetic resonance blood metabolomics and gut metagenomics analyses. Outcomes were assessed at baseline, end of the MFP, after food reintroduction, and one month later.

RESULTS: MFP participants (n = 32) experienced weight loss compared to controls (- 0.52 ± 0.03 kg vs. - 0.03 ± 0.02 kg, p < 0.001). Changes in blood pressure caused by the MFP were non-significant at the end of the fasting period. However, blood pressure was significantly reduced following food reintroduction (systolic: -0.56 ± 0.12 mmHg vs. - 0.16 ± 0.12 mmHg, p < 0.05 and diastolic: -0.36 ± 0.08 mmHg vs. - 0.01 ± 0.08 mmHg, p < 0.01). Serum biochemistry showed the MFP reduced glucose levels and coagulation factors. The MFP also significantly increased physical well-being. Blood metabolomics revealed a significant decrease in chronic inflammation markers. Shotgun metagenomics of the gut microbiome showed significant changes in relative abundance of 11 bacterial species and in the genomic repertoire of 52 carbohydrate-active enzymes (CAZymes), reflecting an increase in families metabolising host-derived glycan substrates. None of these differences in gut microbiome and blood metabolome were shown to be statistically different from the control group one month after the intervention. Comparing MFP effects with a previous cohort's 5-day prolonged fasting showed similar metabolic changes.

CONCLUSIONS: This MFP is safe and transiently improves cardiometabolic health and physical well-being in healthy individuals.

CLINICAL TRIAL REGISTRATION: This trial was prospectively registered at ClinicalTrials.gov (NCT05821660) on 6 April 2023 prior to the start of patient recruitment.}, } @article {pmid42226423, year = {2026}, author = {Xu, Q and Zhang, X and Tian, H and Yang, X and Zhang, J and Li, H and Ma, Z and Zhang, D and Huang, K and Zhang, Y and Zhao, Y and Li, X and Zhao, L and Cheng, J and Xu, D and Li, F and Weng, X and Wu, W and Wang, W}, title = {Integrating rumen microbiome and host metabolome to investigate feed conversion ratio across different fattening stages in Hu sheep.}, journal = {Animal bioscience}, volume = {}, number = {}, pages = {}, doi = {10.5713/ab.260317}, pmid = {42226423}, issn = {2765-0189}, abstract = {OBJECTIVE: Feed conversion ratio (FCR) is a crucial economic trait in animal breeding and management and is also of great significance for environmental sustainability. This study aimed to investigate the potential regulatory mechanisms of FCR in sheep by integrating rumen microbiota and host metabolome through multi-omics analysis.

METHODS: FCR data were collected from 127 male Hu sheep. Extreme individuals were selected for rumen metagenomic and serum metabolomic analyses to identify key factors driving FCR across early and late fattening stages.

RESULTS: Bacteroides, Prevotella, and other genera were identified as dominant taxa in the rumen across both stages, suggesting their involvement in FCR regulation. Notably, Nocardia tengcongensis differed significantly between the highest FCR values (HF) and lowest FCR values (LF) groups at different stages, indicating its potential as a predictive biomarker of feed efficiency. Functional analysis revealed that the pentose phosphate pathway (M00004) and lysine biosynthesis via the succinyl-DAP pathway (M00016) were enriched in the LF group, whereas the methanogenesis pathway (M00357) was significantly enriched in the HF group, indicating increased methane production. Thirteen metabolites consistently differed between HF and LF across fattening stages and may serve as predictive biomarkers. In addition, the abundance of Prevotella and Bacteroides increased over time and showed significant correlations with key metabolites.

CONCLUSION: These findings suggest strong interactions between rumen microbiota and host metabolites that may collectively influence FCR, providing new insights into microbial and metabolic regulation of feed efficiency and a theoretical basis for optimizing feeding strategies in sheep.}, } @article {pmid42227278, year = {2026}, author = {Li, W and Wang, Z and Fu, H and Ma, YR and Gu, Y and Zhuang, JL and Zhao, YX and Liu, YD and Yang, Q and Shapleigh, JP and Jin, RC and Guo, J and Kartal, B and Rittmann, BE}, title = {A Novel Freshwater Anammox Species of Candidatus Loosdrechtia Thriving Under Dual Salinity and Sulfate Stresses.}, journal = {Environmental science & technology}, volume = {60}, number = {23}, pages = {16629-16640}, doi = {10.1021/acs.est.6c03295}, pmid = {42227278}, issn = {1520-5851}, mesh = {Fresh Water ; Oxidation-Reduction ; Salinity ; Sulfates ; *Planctomycetes/classification/isolation & purification ; }, abstract = {Anaerobic ammonium oxidation (anammox) bacteria are key players in the global nitrogen cycle and are widely applied in energy-efficient nitrogen removal processes. However, their activity is often inhibited in saline and sulfate-rich environments. Here, we report the discovery and characterization of Candidatus Loostrechtia thiotolerans (HSAMX1), a novel nonmarine anammox species that became dominant under combined high salinity (3% by weight) and high sulfate concentrations (∼86 mM). Through integrated metagenomic and metatranscriptomic analyses, we reveal the physiological and molecular strategies enabling HSAMX1 to thrive under dual-stress conditions. In response to osmotic stress, HSAMX1 activated ion export systems and subsequently synthesized organic osmoprotectant solutes to maintain cellular homeostasis. It also encoded and strongly expressed the sulfide:quinone oxidoreductase (SQR) gene, which accounted for over 90% of the total community SQR transcription. Intriguingly, HSAMX1 did not emerge under either salinity or sulfate stress alone, suggesting a previously unrecognized niche shaped by the interactions of these two stressors. These findings expand our understanding of nonmarine anammox diversity and identify a promising candidate for nitrogen removal in sulfate-laden, saline wastewater.}, } @article {pmid42227352, year = {2026}, author = {Pérez-Carrasco, V and Uroz-Torres, D and Soriano-Lerma, A and Soriano, M and García-Salcedo, JA and Arias-Moliz, MT}, title = {Association Between the Root Canal Microbiome and Apical Lesion Size: An Observational Shotgun Metagenomic Study.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.70190}, pmid = {42227352}, issn = {1365-2591}, support = {//European Society of Endodontology/ ; }, abstract = {AIM: The aim was to characterize the taxonomic and functional composition of the microbiome involved in primary endodontic infections and to evaluate their association with the periapical lesion size using shotgun metagenomic sequencing.

METHODOLOGY: Samples from primary root canal infections diagnosed with apical periodontitis were analysed with shotgun sequencing. Samples were classified according to the lesion size as small (< 3 mm) or large (> 7 mm). The bacterial DNA copies in each group were quantified by qPCR. Taxonomic and functional annotations were made using Bracken/Kraken2 and HUMAnN3 software. Species richness, Shannon, Simpson and Pielou indices were used to measure alpha diversity. The similarity of the bacterial communities between study groups was evaluated by Principal Coordinate Analysis based on Bray-Curtis distances. The ALDEx2 package was used to infer the differences between species, and the edgeR package for KEGG pathways. For all statistical analyses, p < 0.05 was considered as significant.

RESULTS: A total of 49 samples were analysed, 27 with small lesions and 22 with large lesions. Species richness and Shannon indices showed differences between both groups, whereas no differences were seen according to Simpson and Pielou indices. A different community composition (PERMANOVA, p = 0.0019) was observed between the two groups. Three species were significantly enriched in the large lesion samples, Filifactor alocis, Lachnospiraceae bacterium oral taxon 500 and Olsenella uli, while three others were enriched in small lesion samples, Acinetobacter baumannii, Acinetobacter pittii and Cutibacterium acnes. Functionally, benzoate, flavonoid and steroid degradation, the sphingolipid signalling pathway and proteasome function were enriched in samples with large lesions. Monoterpenoid biosynthesis, phospholipase D signalling, the sulphur relay system and staurosporine biosynthesis were enriched in small lesions.

CONCLUSIONS: Teeth with large periapical lesions harbour greater bacterial loads and exhibit a more diverse microbial community than those with small lesions. Differences in species-level taxonomic composition were observed between both groups. Functionally, large lesions are enriched in pathways associated with immune evasion and pro-inflammatory activity, whereas small lesions are characterized by pathways related to apoptosis, metabolic adaptation and anti-inflammatory processes. These findings suggest that lesion severity is also shaped by the functional potential of the microbiome to modulate host inflammation.}, } @article {pmid42227741, year = {2026}, author = {Duan, J and Marques, AD and Hogenauer, M and Hwang, Y and Zhang, Y and Timperman, A and Higgins, S and Wilson, NG and Fitts, EA and Lim, HK and Bittinger, K and Moustafa, AM and Collman, RG and Bushman, FD}, title = {Optimizing methods for virome analysis based on studies of a synthetic viral community.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0018826}, doi = {10.1128/msystems.00188-26}, pmid = {42227741}, issn = {2379-5077}, abstract = {Studies of whole viral populations-the "virome"-are yielding exciting new insights into biological systems, but methods are still being optimized. Here, we describe generation and use of a synthetic viral community and its use to evaluate technical challenges arising in virome analysis. We spiked the mock community into different human sample types, then passed the samples through different virus enrichment protocols and analyzed by Illumina sequencing. Compared with direct metagenomic sequencing, VLP enrichment protocols greatly increased viral read yields from stool and saliva. Four methods for DNA amplification were compared, with three showing over-amplification of small circular ssDNA viruses, most notably GenomiPhi. Studies of viral particle stability in the presence of nuclease showed that most viral genomes were stable when protected in viral particles, but phage MS2 RNA was unexpectedly labile under some of the conditions tested. Comparison of Illumina 1,000-cycle sequencing versus 300-cycle sequencing showed that longer reads supported generation of longer viral genome assemblies. We tested bacteriophage T4 DNA modified with glucosyl-hydroxymethylcytosine (ghmC) and hydroxymethylcytosine (hmC) and found that both were readily detected, though the recovery of ghmC-modified DNA was reduced compared with T4 genomes with unmodified cytosine. These studies together with published data help provide guidance for virome researchers optimizing analytical protocols.IMPORTANCEA challenge in characterizing the human virome in health and disease is identifying optimal methods for enriching the viral content of samples. Due to the tremendous abundance and diversity of viruses, capturing as broad of a range of viruses as possible for analysis is difficult and potentially complicated by unrecognized biases. This report presents the use of a synthetic viral community for methods optimization in virome studies and illustrates the feasibility and challenges of current virus enrichment strategies for high-throughput virome analysis of different human sample types.}, } @article {pmid42227750, year = {2026}, author = {Becker, DJ and Dyer, KE and Olbrys, BL and Hightower, MG and Allira, M and Demory, B and Lock, LR and Taylor, KN and Bhata, NN and Hernandez, SM and Lawson, PA and Youssef, NH and Miller, SL and Elshahed, MS and Verrett, TB and Clark, KL}, title = {Molecular detection of relapsing fever Borrelia puertoricensis in migratory Mexican free-tailed bats.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0008526}, doi = {10.1128/msphere.00085-26}, pmid = {42227750}, issn = {2379-5042}, abstract = {UNLABELLED: Bats have been increasingly recognized to host relapsing fever borreliae as well as borreliae that form novel clades adjacent to the Lyme borreliosis group. However, the genetic diversity and zoonotic potential of bat-borne borreliae remain poorly understood, in part because most work to date has focused on bats in the tropics. Fewer bat-borne Borrelia surveys have been conducted in temperate zones, where many bats undertake seasonal migrations that may facilitate pathogen dispersal. We surveyed blood from nearly 400 Mexican free-tailed bats (Tadarida brasiliensis) during their seasonal occupancy in Oklahoma, USA, during 2022 and 2023, for Borrelia spp. Targeted PCR of the 16S rRNA and flaB genes revealed high nucleotide identity to Borrelia puertoricensis, and shotgun metagenomics further demonstrated high amino acid identity to strains isolated from argasid ticks and human blood. This represents the first detection of Borrelia puertoricensis in bats and only the second detection within wild vertebrate hosts. Infection prevalence was low but comparable to that of other borreliae in bats. Our findings suggest that Mexican free-tailed bats may contribute to the dispersal of this emerging tick-borne bacterial pathogen in North America.

IMPORTANCE: Bacteria in the genus Borrelia are primarily spread by ticks and cause either Lyme borreliosis or relapsing fever. Substantial work has demonstrated the degree to which rodents and songbirds can contribute to the enzootic cycles and dispersal of these human diseases, but comparatively less attention has been paid to the role of wild bats, particularly in temperate regions. We here report human-relevant findings from a two-year, seasonal survey of migratory Mexican free-tailed bats (Tadarida brasiliensis) in Oklahoma, USA. We tested nearly 400 bats and identified Borrelia puertoricensis, a relapsing fever species that could infect humans. Importantly, this represents the first detection of Borrelia puertoricensis in bats and only the second detection in wild vertebrate hosts, expanding the known host range of this emerging tick-borne pathogen. Given the known migratory routes of Mexican free-tailed bats, our results have implications for the role that bats may play in tick-borne pathogen dispersal in North America.}, } @article {pmid42227946, year = {2026}, author = {Wang, H and Wang, X and Xiu, Z and Wei, H and Cai, H and Chen, J and Zhang, T and Yang, Y}, title = {Substrate-driven microbial specialization and cooperative dechlorination of chlorinated pollutants in estuarine ecosystems.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0023526}, doi = {10.1128/aem.00235-26}, pmid = {42227946}, issn = {1098-5336}, abstract = {Organohalide-respiring bacteria (OHRB) are globally distributed, yet their ecological roles in marine environments remain poorly understood, with few isolates characterized from these systems. Here, we describe a stable anaerobic consortium from estuarine sediments that performs sustained dechlorination of 1,1,2-trichloroethane (1,1,2-TCA) to vinyl chloride (VC) at a rate of 126.3 ± 0.9 µM d[-1]. This activity was associated with the stable co-enrichment of two key populations, Dehalogenimonas and Desulfitobacterium, which increased to dominate the community at 49.7% and 32.5%, respectively. Metagenome-assembled genomes confirmed both populations represent novel species with distinct genomic adaptations. Dehalogenimonas sp. strain H harbors 24 putative reductive dehalogenase genes and complete ectoine biosynthesis pathways (ectABC) essential for osmotolerance, while Desulfitobacterium sp. strain Y represents the first cultivated marine-associated member of this genus. Proteomic analysis confirmed active expression of multiple reductive dehalogenases from strain H, strongly supporting its role as the primary dechlorinator. Concurrently, physiological and genomic data suggest that strain Y is strongly co-selected under 1,1,2-TCA-amended conditions and likely occupies a crucial supportive niche. Alongside its extensive metabolic versatility that likely buffers the consortium against environmental fluctuations, its complete de novo corrinoid biosynthesis pathway implies a complementary role as a vitamin B12 provider for the extreme corrinoid-auxotrophic strain H. This study provides evidence for a stable co-enrichment consistent with nutritional niche differentiation within native microbial communities and suggests a potential cooperative interaction between novel Dehalogenimonas and Desulfitobacterium species, advancing our understanding of halogen cycling in coastal ecosystems.IMPORTANCEEstuaries serve as critical interfaces between terrestrial and marine ecosystems, yet the microbial processes governing chlorinated pollutant fate in these vulnerable zones remain largely unexplored. Our discovery of a novel partnership between Dehalogenimonas and Desulfitobacterium species challenges the conventional understanding that Desulfitobacterium is restricted to terrestrial habitats. Integrative multi-omic and physiological analyses reveal that Dehalogenimonas strain H serves as the highly specialized primary dechlorinator, while Desulfitobacterium strain Y is stably co-enriched and exhibits genomic potential to sustain the consortium by providing essential corrinoid cofactors. The identification of genomic determinants underlying salt tolerance in Dehalogenimonas, including ectoine and mannosylglycerate biosynthesis pathways, provides mechanistic insights into OHRB adaptation to fluctuating salinity. These findings have direct implications for developing bioremediation strategies for contaminated coastal sites and highlight the importance of characterizing microbial diversity in transitional ecosystems.}, } @article {pmid42228562, year = {2026}, author = {Werner, L and Nissenbaum-Toren, T and Fibelman, M and Leibovitzh, H and Cohen, NA and Brenner, M and Lobel, L and Maharshak, N}, title = {Antibiotic disruption of the gut microbiome triggers IBD-like proteolytic activity.}, journal = {Cell reports}, volume = {45}, number = {6}, pages = {117478}, doi = {10.1016/j.celrep.2026.117478}, pmid = {42228562}, issn = {2211-1247}, abstract = {Antibiotics (Abx) are essential in medicine but can disrupt gut microbiota, potentially contributing to inflammatory bowel diseases (IBDs). This study employed fecal metagenomics and metaproteomics to evaluate the effects of Abx in patients with pouchitis, ulcerative colitis (UC), and non-IBD controls. Each group displayed distinct microbiome profiles, with metaproteomes more affected by Abx than metagenomes. Proteomic analysis revealed increased pancreatic protease activity and fecal proteolytic activity in all groups, except in patients without IBD before Abx, consistent with impaired epithelial barrier integrity. Abx also decreased bacterial protease inhibitors, which may control proteolysis and help maintain gut balance. These findings emphasize the importance of understanding Abx-induced proteolytic shifts in IBD and highlight metaproteomics as a valuable tool for studying host-microbiome interactions. Future research should explore the molecular mechanisms that regulate bacterial protease inhibitor levels and their effects on intestinal health.}, } @article {pmid42229136, year = {2026}, author = {Delgado, N and Fernández, KG and Zambrano-Alegría, C and Espinosa, ZYD and Ramos-Cabrera, E}, title = {Physiological and microbial alterations induced by pesticides in agricultural systems: A bioassay- and 16S rRNA-based approach.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142560}, doi = {10.1016/j.jhazmat.2026.142560}, pmid = {42229136}, issn = {1873-3336}, abstract = {The extensive use of pesticides in agricultural production systems has increased interest in understanding their potential impacts on soil environmental dynamics. This study evaluates the effects of pesticide application on Lactuca sativa L. and soil microbiota. An initial field survey identified the main active ingredients commercial pesticides, followed by bioassays assessing germination and early development of Lactuca sativa, as well as soil microbial structure through physiological assessments and metagenomic analyses based on 16S rRNA gene sequencing, during a three-week soil experiment. Thirty active ingredients were identified in 92 agricultural products. Chlorpyrifos was identified as one of the most commercialized insecticides, where insecticides represented 69% of marketed phytosanitary products, mainly organophosphates (18%) and pyrethroids (21%), despite its hazardous classification and ban in several countries. Germination assays showed a hormetic response at low dose (2200 mg/L), reaching 70% germination compared with 51% in the control, while the germination index decreased to 75% at the recommended dose (4400 mg/L). Statistical analyses revealed inhibition of hypocotyl elongation (p = 0.001) and cotyledon development (p = 0.029). Soil microbiome analysis showed that high chlorpyrifos concentrations reduced microbial richness and diversity, while beta diversity analyses explained 99% of the variance among treatments. Proteobacteria, Burkholderiales, and Sphingomonadales increased under pesticide exposure, indicating microbial adaptation and biodegradation potential. Functional prediction using PICRUSt2 revealed enrichment of genes K03381, K00446, K01048, and K01560 associated with potential organophosphate degradation pathways. These findings demonstrate that chlorpyrifos induces ecological and seedling alterations even at agronomically recommended concentrations. highlighting the need to strengthen sustainable pesticide management and environmental monitoring strategies.}, } @article {pmid42229568, year = {2026}, author = {Dang, R and Xiao, L and Zhou, L and Liu, J and Liang, Z and Wang, Y and Song, W and Wang, X and Chu, X and Zhang, X and Song, Y and Song, W and Han, G}, title = {Asymmetric microbial community reassembly under 7-year experimental precipitation decouples soil carbon storage in a coastal wetland.}, journal = {Environmental research}, volume = {305}, number = {Pt 1}, pages = {124851}, doi = {10.1016/j.envres.2026.124851}, pmid = {42229568}, issn = {1096-0953}, abstract = {Climate-driven extremes in precipitation are fundamentally altering the hydrological regimes of wetland ecosystems. However, the mechanistic understanding of how soil microbial communities and their metabolic functions respond to precipitation change, and how these responses regulate soil organic carbon (SOC) dynamic, remains limited. Here, we leveraged a 7-year precipitation manipulation experiment (±40%) in a coastal wetland and applied genome-resolved metagenomics to systematically examine microbial community structure, ecological networks, and key biogeochemical functions (carbon fixation and degradation). We found that although microbial community structure showed no pronounced response to increased precipitation, decreased precipitation reorganized the community, as evidenced by higher β-diversity and more complex co-occurrence networks with strengthened positive interactions. Compared with dominant species, rare species played a more important role in maintaining the stability of microbial networks. Functional potential for carbon degradation and fixation remained relatively stable under decreased precipitation. In contrast, increased precipitation concurrently suppressed degradation of polysaccharides and aromatic compounds, and some carbon fixation pathways, such as Acetyl-CoA (rAcCoA) pathway. Collectively, decreased and increased precipitation induced asymmetric responses in microbial communities, with decreased precipitation primarily reshaping community composition but having little effect on functional potential, whereas increased precipitation predominantly altered functional profiles without substantially changing community structure. We further found microbial community reassembly decoupled SOC content. Together, this study highlights that prolonged precipitation extremes shape coastal wetland microbiomes through divergent ecological trajectories; however, these microbial shifts may not necessarily translate directly into changes in soil carbon storage.}, } @article {pmid42229596, year = {2026}, author = {Lou, D and Duan, J and Zhou, B and Zhou, H and Wang, Y and Yang, J and Cui, J and Ma, X and Tan, J and Duan, H}, title = {Characterization and activity enhancement of a novel thermostable 3-quinuclidinone reductase through modulating the microenvironment of catalytic residues.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {135058}, doi = {10.1016/j.biortech.2026.135058}, pmid = {42229596}, issn = {1873-2976}, mesh = {Molecular Dynamics Simulation ; Enzyme Stability ; *Oxidoreductases/metabolism/chemistry/genetics ; Catalytic Domain ; *Quinuclidines/metabolism ; *Temperature ; Biocatalysis ; Mutation ; Thermodynamics ; Kinetics ; }, abstract = {The biocatalytic synthesis of chiral alcohols offers a sustainable alternative to traditional chemical catalysis, yet the lack of robust, high-efficiency enzymes remains an industrial bottleneck. Here, a novel thermostable 3-quinuclidinone reductase (SdQR) was discovered via metagenomic mining of hot spring environments and biochemically characterized. Among the candidates, the H161Q variant, situated proximal to the conserved catalytic triad, emerged as a high-potential lead. Experimental validation revealed that the H161Q mutation yielded a 16-fold increase in catalytic efficiency (kcat/Km) over the wild-type enzyme while preserving its exceptional thermostability. Molecular dynamics (MD) simulations and MM-PBSA calculations elucidated the mechanistic basis for this enhancement: the mutation establishes a "structurally rigid yet physicochemically fluid" microenvironment. This subtle shift optimizes the hydrophobic landscape within the active pocket and modulates cofactor binding thermodynamics, lowering the desolvation energy barrier without compromising the robust structural scaffold. This study provides a highly potent biocatalyst for the asymmetric synthesis of (R)-3-quinuclidinol, and highlights a sophisticated engineering paradigm for the precise physicochemical fine-tuning of catalytic microenvironments in industrial enzymes.}, } @article {pmid42229597, year = {2026}, author = {Besharati Fard, M and Kwon, S and De Vrieze, J and Wu, D}, title = {Long-term inhibition under continuous perfluorooctanoic acid exposure during anaerobic digestion of waste microalgal-bacterial aerobic granular sludge: Metagenomic-metatranscriptomic insights.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {135056}, doi = {10.1016/j.biortech.2026.135056}, pmid = {42229597}, issn = {1873-2976}, mesh = {*Caprylates/pharmacology ; *Fluorocarbons/pharmacology ; *Sewage/microbiology ; Anaerobiosis/drug effects ; *Microalgae/metabolism/drug effects ; *Bacteria/metabolism/drug effects/genetics ; Aerobiosis/drug effects ; *Metagenomics ; Methane/biosynthesis/metabolism ; Bioreactors/microbiology ; Fatty Acids, Volatile/metabolism ; Biofuels ; Biological Oxygen Demand Analysis ; }, abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) is a promising wastewater treatment technology, but the effect of residual perfluorooctanoic acid (PFOA) on the anaerobic digestion of waste MB-AGS (WMB-AGS) remains poorly understood. This study evaluated PFOA effects (100, 500, and 1000 µg/L) on anaerobic digestion of WMB-AGS by comparing short-term single-exposure batch assays with long-term semi-continuous digestion. Under control conditions, methane production reached 76 ± 2 mL CH4/g volatile solids. Relative to the control, methane yield changed marginally in the presence of PFOA, indicating no measurable inhibition in a single-exposure biochemical methane potential (BMP) assay. In contrast, during continuous exposure in the semi-continuous digester, biogas output decreased after introducing 1000 µg/L PFOA (31 ± 1 to 19 ± 1 mL/day) and coincided with increased residual soluble chemical oxygen demand. During 3-day hydrolysis-acidogenesis tests, total volatile fatty acids increased from 82 ± 9 mg/L (control) to 122 ± 12 mg/L (1000 µg/L), suggesting greater accumulation of fermentation intermediates in the early digestion phase. The PFOA distribution showed substantial partitioning into extracellular polymeric substance fractions and sludge solids, with 28.3% remaining in supernatant, 23.2% in loosely bound extracellular polymeric substances, 16.0% in tightly bound extracellular polymeric substances, and 32.6% in sludge solids with no transformation products. Multi-omics analysis supported that dominant microbial communities remained broadly stable, whereas reduced transcription of glycolysis and pyruvate-to-acetyl-coenzyme A conversion genes was consistent with soluble organic accumulation and reduced biogas production. Overall, single-exposure BMP assays underestimated the long-term operational impact of continuous PFOA exposure during anaerobic digestion of WMB-AGS.}, } @article {pmid42229598, year = {2026}, author = {Dong, C and Pan, J and Li, Y and Liu, M and Li, Y and Zhao, Z and Zhang, Y}, title = {Direct interspecies electron transfer-based simplified microbial consortia for high-efficiency conversion of lignocellulose to methane: Construction, metabolic pathway and performance optimization.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135043}, doi = {10.1016/j.biortech.2026.135043}, pmid = {42229598}, issn = {1873-2976}, abstract = {Establishing direct interspecies electron transfer (DIET)-based methanogenic pathway is likely to address the technical bottlenecks involved in long periods and low rates of methanogenesis during anaerobic digestion of lignocellulose. However, the efficiency of DIET is limited by low abundance of electroactive bacteria and electron competition with conventional methanogenic pathway. Here, we combined cow manures with paddy soils/marine sediments as initial inocula, and constructed two simplified microbial consortia (DIETsimp) for conversion of lignocellulose to methane via a 'top-down' selection. Both DIETsimp dramatically shortened periods of methanogenesis (ca. 15-16 vs 25-40 d, this study vs present level) and increased methane production rates (ca. 32 vs 10-25 mL/gVS·d). Lowering pH dramatically increased conductivity of both DIETsimp, similar to that was found in electrically conductive pili of Geobacter sulfurreducens. Meanwhile, the intensities of characteristic peaks in electrochemical Fourier transform infrared spectra associated with c-type cytochrome in both DIETsimp dramatically increased. Metagenomic analysis showed that, Methanosarcina mazei, capable of accepting electrons via DIET, and electroactive species, Sphaerochaeta globosa and Clostridium aceticum, were the dominant archaea and bacteria in both DIETsimp, respectively. The potential DIET-based methanogenic pathway during anaerobic digestion of lignocellulose that S. globosa and C. aceticum metabolized intermediates (e.g. xylose, glucose, pyruvate and acetate) and transferred electrons to M. mazei for the reduction of CO2 to methane was proposed. At last, we optimized culture conditions (including inoculum ratio, C/N and period) to maximize the performances of both DIETsimp via combining the single-factor experiments with response surface methodology.}, } @article {pmid42229914, year = {2026}, author = {Li, H and Yang, L and Chen, B and Zhang, L and Zhu, J and Zhang, H and Lin, L}, title = {Pneumococcal Rib Osteomyelitis With Concurrent Lung and Chest Wall Abscess in an Infant.}, journal = {Pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1542/peds.2025-073077}, pmid = {42229914}, issn = {1098-4275}, abstract = {We present a rare case of a 7-month-old infant with a complex invasive Streptococcus pneumoniae infection involving rib osteomyelitis, a pulmonary abscess, and a chest wall abscess. The patient presented with persistent fever and no respiratory symptoms. On day 9, chest radiography was performed because of persistent fever and marked leukocytosis, consistent with the American College of Radiology Appropriateness Criteria that recommend imaging in febrile infants with high fever (≥39°C) or elevated white blood cell counts (≥20 000/mm3). On day 14, the emergence of a chest wall mass prompted escalation to ultrasonography, which provided noninvasive assessment of soft tissue involvement. Subsequent contrast-enhanced computed tomography scans were undertaken to delineate the extent of contiguous spread, evaluate rib destruction, and exclude alternative diagnoses. Microbiological cultures of sputum and aspirated pus, along with metagenomic sequencing, confirmed the presence of macrolide-resistant S. pneumoniae. Because of benzylpenicillin and cephalosporin allergy, intravenous linezolid was selected, resulting in rapid clinical improvement. A 6-week course (intravenous infusion followed by oral) led to complete resolution on imaging, with no recurrence over 5 years. This case underscores the importance of appropriate imaging modalities in febrile infants without respiratory symptoms and the need to consider extrapulmonary spread in chest wall masses. It highlights the diagnostic value of metagenomic sequencing and susceptibility testing in guiding individualized antimicrobial therapy, particularly in macrolide-resistant settings.}, } @article {pmid42230119, year = {2026}, author = {Alexander, JL and Mullish, BH and Thomas, L and Weersma, RK and Sokol, H and Roberts, LA and Edwards, LA and Emmanuel, A and Gerasimidis, K and Hall, LJ and Iqbal, TH and Kinross, JM and McIlroy, J and Monaghan, TM and Sergaki, C and Shawcross, DL and Stewart, CJ and Lamb, CA and Williams, HRT and Hansen, R and Hold, G}, title = {Recent advances in our understanding of the gut microbiome: an analysis from the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2026-338252}, pmid = {42230119}, issn = {1468-3288}, abstract = {At around 10 years ago, at the time of the first publication by the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology, recognition of the gut microbiome's importance in health and disease was transitioning from fringe interest towards major global pursuit. A decade on, we appraise the considerable progress made in the field, while acknowledging ongoing challenges. Earlier human work characterising the 16S rRNA gene amplicon signature of particular conditions in small cohorts has been superseded by larger, multicentre studies with extensive metadata. Studies increasingly employ shotgun metagenomics and other 'omic' techniques-coupled with refined bioinformatic tools and disease models-to better characterise perturbation in gut microbiome functionality. The arrival of 'gold standard' pipelines for microbiome analysis and increased mechanistic validation of signals are key developments towards more clinically-translatable outcomes. Novel clinical areas where the gut microbiome has relevance have emerged, including early life and the efficacy of certain treatments (including immune checkpoint inhibitors and vaccination). Enthusiasm for 'microbiome diagnostics and treatments' has grown, but barriers to widespread adoption remain. Faecal microbiota transplant (FMT) is established for treating recurrent Clostridioides difficile infection, with donor-derived 'next generation' FMT products licensed for this condition in certain countries. Beyond FMT, other microbial therapeutic techniques-including nutritional, bacteriophage and probiotic therapies-show promise, but have not fulfilled their high expectations yet. Gut microbiome research is now well-established and shows significant translational potential; the future focus will be translational work to drive its utility in clinical diagnostics, prognostics and therapeutics.}, } @article {pmid42230654, year = {2026}, author = {Li, J and Liang, X and Liu, P and Zhu, W and Jin, W and Mao, S and Xie, F}, title = {Rumen-derived Pichia membranifaciens modulates the rumen microbiome and metabolome and mitigates methane emissions in dairy cows.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01029-0}, pmid = {42230654}, issn = {2055-5008}, abstract = {Methane emissions from ruminants represent a significant environmental challenge and dietary energy loss. While yeasts are potential rumen modulators, specific methane-mitigating species remain poorly characterized. Here, we screened 73 rumen-derived strains in vitro, identifying Pichia membranifaciens M12 as the most effective candidate, reducing methane output by 17.1%. Subsequently, a randomized block trial with 36 dairy cows compared a control group with P. membranifaciens M12 supplementation at 2.5 and 5 × 10[11] CFU/cow/day. Methane yield per unit of dry matter intake significantly decreased in the high-dose group (18.7%, P = 0.003), without compromising lactation performance and animal health. Multi-omics analyses revealed that M12 suppressed hydrogenotrophic methanogens (e.g., Methanobrevibacter) and hydrogen-producing bacteria (e.g., Ruminococcus and Fibrobacter), while enriching specific eukaryotic taxa like Orpinomyces and Entodinium. Metabolomic profiling indicated a significant dose-dependent accumulation of metabolites. Metagenomic function analysis demonstrated the decreased abundance of key methanogenesis genes (e.g., mcrABCDG) and increased abundance of hydrogenase (hyaABC), lactate-forming (ghrB), and propionate-forming (mcmA1 and lcdB), suggesting a redirection of reducing equivalents from methanogenesis toward propionate synthesis, alongside enhanced butyrate production. These findings demonstrate that P. membranifaciens M12 mitigates methane emissions via coordinated ecological and metabolic modulation, highlighting its potential as a sustainable strategy for low-carbon ruminant production.}, } @article {pmid42230804, year = {2026}, author = {Linh, LTK and My, TN and Thi Tran, N and Song, LH and Nurjadi, D and Boutin, S and Velavan, TP}, title = {Metagenomic profiling reveals shared resistome signatures between humans and pigs in Vietnamese smallholder farms.}, journal = {npj antimicrobials and resistance}, volume = {4}, number = {1}, pages = {}, pmid = {42230804}, issn = {2731-8745}, support = {PACE-UP; DAAD Project ID: 57592343//Deutscher Akademischer Austauschdienst/ ; }, abstract = {Antimicrobial resistance (AMR) is a global health concern, yet the extent of resistant genes and microbial exchange between humans and livestock in low- and middle-income countries remains underexplored. Vietnam, an AMR hotspot, was studied using shotgun metagenomic sequencing of paired faecal samples from pigs and caretakers across 50 small-scale farms. Results revealed 10,270 antimicrobial resistance genes (ARGs) representing 550 unique types, including clinically relevant mcr, blaOXA-58, and optrA genes. Pigs showed higher total AMR abundance, while workers harboured richer resistomes. Approximately 52% (288/550) of ARGs were shared between hosts, dominated by aminoglycoside, β-lactam, and tetracycline resistance genes, often co-located with mobile genetic elements, indicating horizontal transfer potential. Closely related Escherichia coli strains were identified in both hosts, consistent with strain sharing or exposure to common sources beyond individual farms. These findings highlight the human-pig interface as an important setting for shared AMR signatures and support the need for integrated One Health surveillance and antimicrobial stewardship.}, } @article {pmid42231385, year = {2026}, author = {Hu, J and Fan, D and Xiao, C and Kang, C and Shi, J and Li, Y and Liu, J and Shen, L and Lin, N}, title = {Curcumin supplementation during high-altitude exposure modulates body composition and its relationship with gut microbiota: a randomized controlled trial.}, journal = {Nutrition journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12937-026-01343-5}, pmid = {42231385}, issn = {1475-2891}, support = {2022NSFSC1422//Natural Science Foundation of Sichuan Province/ ; KJS2525//Open Research Project of the Provincial Key Laboratory of Prevention and Translational Medicine for Major Chronic Diseases at Soochow University/ ; }, abstract = {BACKGROUND: Body composition is crucial for athletic performance and linked to the gut microbiota. Curcumin shows potential to promote muscle regeneration and modulate fat metabolism, but evidence from high-altitude populations remains scarce. This study aimed to evaluate the effects of curcumin on body composition at high altitudes, and explore potential role of gut microbiota.

METHODS: A total of 102 male Han participants was randomized to curcumin (812 mg/d) or placebo groups for 1-week pre-acclimatization and 6-week high-altitude acclimatization. Body composition was assessed via bioelectrical impedance analysis and gut microbiota was analyzed through metagenomic sequencing.

RESULTS: After high-altitude acclimatization, curcumin significantly reduced the percent body fat (PBF, P = 0.030). Soft lean mass (SLM), skeletal muscle mass (SMM) and fat free mass (FFM) were increased in both groups, but the curcumin group exhibited greater increases although without significant difference. Curcumin supplementation significantly attenuated the upper-limbs FFM and arm muscle circumference reduction (P < 0.05). The relative abundance of Eubacterium sp. CAG:180 was significantly negative with SLM and SMM (P < 0.05). Curcumin significantly increased the abundance of Bifidobacterium pseudocatenulatum, Eubacterium sp. CAG:274 and Eubacterium eligens (P < 0.01). Higher abundance of Eubacterium sp. CAG:274, Roseburia inulinivorans, and Bifidobacterium pseudocatenulatum were observed in high-skeletal muscle index participants. Lachnospira pectinoschiza, Clostridium leptum, and Eubacterium sp. CAG:274 were more abundant in low-PBF participants.

CONCLUSIONS: Curcumin supplementation might increase muscle mass gain and reduce PBF during high-altitude acclimatization that may correlate with changes in gut microbiota composition, and their causal association remains to be further verified.

TRIAL REGISTRATION: Chinese Clinical Trail Registry, ChiCTR220005965. Registered on May 5, 2022.}, } @article {pmid42231497, year = {2026}, author = {Vayena, G and Giangeri, G and Gaspari, M and Ghofrani-Isfahani, P and Tsapekos, P and Kougias, PG and Angelidaki, I}, title = {Ecological and metabolic restructuring of anaerobic microbiomes under sulfate stress via magnetite-enhanced cooperative networks.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02443-4}, pmid = {42231497}, issn = {2049-2618}, abstract = {BACKGROUND: Anaerobic digestion systems with elevated sulfate often suffer reduced methane yields, challenged by the competition between sulfate-reducing bacteria and methanogens, and inhibited by hydrogen sulfide introduction. The present work explores the role of magnetite in improving anaerobic digestion performance under elevated sulfate conditions by chemically influencing the anaerobic system and reshaping microbial interaction patterns.

RESULTS: Magnetite addition mitigated hydrogen sulfide toxicity via precipitation and increased methane production by 19%. Genome-centric metagenomics revealed a notable proliferation of the methanogenic population in the magnetite-amended reactors, consistent with the elevated methane output in the presence of both magnetite and sulfate, without suppressing sulfate-reducing, homoacetogenic, or syntrophic acetate-oxidizing activity. Magnetite was associated with enhanced methanogenesis and a strengthened cooperative syntrophic network among the four microbial guilds, in line with more efficient carbon and electron flow despite sulfate stress. Community genome-scale metabolic modeling supported these trends, validating the feasibility of the proposed interaction network and indicating that interspecies metabolite transfer between partners is stoichiometrically feasible, supporting the observed community behavior.

CONCLUSIONS: This study demonstrates the role of magnetite not only as a hydrogen sulfide scavenger but also as a community modulator, promoting resilient direct electron transfer-based networks, ultimately unlocking higher-efficiency biogas production in sulfate-impacted digesters. Our findings support the concept that interactions between sulfate-reducers and hydrogenotrophic methanogens are not purely competitive, and that conductive materials such as magnetite can enhance their metabolic coupling even under sulfate stress. Video Abstract.}, } @article {pmid42231509, year = {2026}, author = {Sarhan, MS and Samadelli, M and Zink, A and Maixner, F}, title = {The Iceman's microbiome: unveiling millennia of microbial diversity and continuity.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42231509}, issn = {2049-2618}, support = {FESR1078-MummyLabs//European Regional Development Fund/ ; }, mesh = {*Mummies/microbiology ; *Microbiota/genetics ; Humans ; Metagenomics/methods ; DNA, Ancient/analysis ; *Ice Cover/microbiology ; Sequence Analysis, DNA ; *Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; Phylogeny ; Biodiversity ; }, abstract = {BACKGROUND: The Iceman mummy, a 5300-year-old natural alpine glacier mummy, provides a unique opportunity to study ancient microbial ecosystems. However, disentangling the mummy's endogenous microbiome from modern environmental contaminants introduced during three decades of conservation remains a significant challenge.

RESULTS: By integrating culture-dependent and culture-independent approaches, including amplicon sequencing, shotgun metagenomics and de novo metagenomic assembly, as well as isolate-level genomics, we performed a comprehensive characterization of the Iceman's microbial landscape. We identified three distinct microbial drivers: endogenous post-mortem succession, ancient glacier-derived relicts, and modern anthropogenic introduction. Metagenomic analysis of internal tissues revealed anaerobic bacteria, including ancient gut taxa, including such as Romboutsia hominis, Clostridium moniliforme, Eubacterium sp., Ruminococcus bromii, Kineothrix sp., Treponema succinifaciens, Enterousia sp., and Huintestinicola butyrica. These taxa, characterized by ancient DNA (aDNA) damage profiles (C to T deamination frequency), show high similarity to ancestral, non-Westernized human gut communities, providing a rare baseline for Copper Age intestinal ecosystems. Conversely, we identified a shift in the external mycobiome, marked by the recent proliferation of psychrophilic yeasts, including Glaciozyma watsonii, Mrakia robertii, Phenoliferia glacialis, and Goffeauzyma sp. While internal bacterial communities remained stable, these external yeast populations showed increased relative abundance and reduced DNA damage signatures between 2010 and 2019, indicating active, modern colonization. Furthermore, strain-level analysis of Pseudomonas sp. 5C2 confirmed that specific environmental strains have successfully colonized the mummy, persisting across multiple tissue sites with minimal genetic divergence.

CONCLUSIONS: Our study demonstrates that the Iceman is not a static relic but a dynamic biological interface. The coexistence of ancient, endogenous gut microbes and modern, psychrophilic colonizers highlights the potential for ongoing microbial activity even at sub-zero temperatures. These findings underscore that maintaining strict environmental parameters is essential to prevent these specialized microbial communities from transitioning from latent persistence to active microorganisms. Video Abstract.}, } @article {pmid42231528, year = {2026}, author = {Wang, W and Fortuna, R and Mayengbam, S and Seerattan, RA and Mu, C and Rios, JL and Abughazaleh, N and Vaghef Mehrabani, E and Noye Tuplin, EW and Hart, DA and Sharkey, KA and Herzog, W and Reimer, RA}, title = {Multiomics insights into the effects of prebiotics on physical function and metabolism in adults with obesity and knee osteoarthritis.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2679516}, pmid = {42231528}, issn = {1949-0984}, mesh = {Animals ; *Prebiotics/administration & dosage ; *Obesity/metabolism/microbiology/physiopathology/complications ; *Osteoarthritis, Knee/metabolism/microbiology/physiopathology ; Rats ; Multiomics ; Humans ; *Gastrointestinal Microbiome ; Male ; Disease Models, Animal ; }, abstract = {Knee osteoarthritis (OA) is a prevalent, painful, degenerative disease lacking effective disease-modifying drugs. The rise in obesity has increased the prevalence of metabolic OA, underscoring the need for effective management to delay or prevent knee replacement. Prebiotics confer improvement in physical function and metabolic health in adults with comorbid knee OA and obesity by unknown mechanisms. Here, we integrated metagenomic and metabolomic analyzes to investigate prebiotic fiber-linked mechanisms along the gut-knee axis. By reshaping the composition and function of the gut microbiota, prebiotics increased diet-derived carbohydrate availability, mitigated excessive host-glycan degradation and mucosal barrier disruption, reduced systemic inflammation and metabolic dysregulation, ultimately enhancing metabolic health and improving physical performance. In a diet-induced obese rat model, prebiotics reduced tibial cartilage degeneration and synovial membrane thickening, conferring protection against OA onset and progression through a common inflammatory pathway. Our findings provide mechanistic evidence supporting the therapeutic potential of prebiotic supplementation as a conservative management in humans and as a preventive approach for obesity-related knee OA in a preclinical rat model, mediated through the gut-joint axis.}, } @article {pmid42232316, year = {2026}, author = {Webster, NS and Bell, SC and Luter, HM and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the sponge, Rhopaloeides odorabile Thompson, Murphy, Bergquist & Evans, 1987 (Dictyoceratida: Spongiidae) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {211}, pmid = {42232316}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Rhopaloeides odorabile (Porifera; Demospongiae; Dictyoceratida; Spongiidae). The genome sequence has a total length of 291.63 megabases. Most of the assembly (98.17%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.42 kilobases. From the metagenome data, we recovered 162 bins, of which 96 were high-quality MAGs. R. odorabile displays a characteristic high microbial abundance sponge profile, with MAGs representing diverse phyla (i.e., Acidobacteriota, Pseudomonadota, and Chloroflexota) and candidate phyla (i.e., Ca. Latescibacteria, Ca. Poribacteria, and Ca. Tectomicrobia).}, } @article {pmid42232360, year = {2026}, author = {Li, Y and Yi, G and Han, Z and Fu, J and Xu, L}, title = {Comparison of mNGS microbial detection profiles between percutaneous lung aspiration biopsy and bronchoalveolar lavage fluid in infective pneumonia.}, journal = {Open medicine (Warsaw, Poland)}, volume = {21}, number = {1}, pages = {20261445}, pmid = {42232360}, issn = {2391-5463}, abstract = {OBJECTIVES: To compare the mNGS-based microbial detection profiles of percutaneous lung aspiration biopsy (PLAB) and bronchoalveolar lavage fluid (BALF) in patients with infective pneumonia under real-world clinical sampling strategies.

METHODS: The study included 166 patients with infective pneumonia, of whom 54 underwent PLAB to obtain unfixed fresh lung tissue from the lesion site, while 112 underwent fiberoptic bronchoscopy to obtain BALF.

RESULTS: In the BALF group, 3 pathogens of high concern and 5 suspected pathogens, totaling 8 types of pathogens, were detected. In contrast, in the PLAB group, 1 pathogen of high concern and 1 suspected pathogen, totaling 2 types of pathogens were detected. Cumulatively, 348 pathogens were identified in the BALF group. In the PLAB group, 96 pathogens were identified cumulatively, p<0.001. In the BALF group, the most frequently detected pathogen was Streptococcus pneumoniae, with 19 strains of Mycobacterium tuberculosis among the special pathogens. In the PLAB group, the most frequently detected pathogen was Epstein-Barr virus (EBV) (14.58 %).

CONCLUSIONS: BALF and PLAB showed different mNGS microbial detection patterns under different clinical sampling strategies. Because of the retrospective non-paired design, these findings should be interpreted as descriptive comparative data rather than proof of the superior diagnostic performance of either sampling method.}, } @article {pmid42232489, year = {2026}, author = {Huang, Y and Yang, M and Liu, J and Zhang, M and Penttinen, P and Zhang, L and Ge, L and Zhang, X and Zhao, N}, title = {Phage succession and putative mechanisms of microbial community regulation in Sichuan radish paocai (traditional Chinese fermented vegetable).}, journal = {Food chemistry: X}, volume = {36}, number = {}, pages = {103997}, pmid = {42232489}, issn = {2590-1575}, abstract = {Spontaneous fermentation of Sichuan paocai is shaped by complex microbial and environmental factors, yet phage communities remain understudied. This study presents integrated viromic and metagenomic analysis of radish paocai combined with metabolite profiling to elucidate phage diversity, dynamics, ecological roles, and sources. Time-series metagenomics revealed Lactiplantibacillus increasing from 11% to 71%, while viromics showed phages comprising 78% of viral contigs, with Uroviricota reaching 88% by day 5. Host prediction indicated that 89% of phages targeted Lactiplantibacillus, mainly L. plantarum. Correlation analysis suggested that core phages were associated with fermentation-related metabolites, including volatile compounds (e.g., decanal), implicating that phages might influence metabolism by modulating host activity. Functional annotation showed phage encoded amino acid and carbohydrate metabolism genes, suggesting auxiliary metabolic roles. Source analysis suggested that most phages in radish paocai may be derived from bacterial prophages. This work advances understanding of phage diversity and ecological function in fermented vegetable ecosystems.}, } @article {pmid42232626, year = {2026}, author = {Han, X and Zhang, L and Zhang, R and Liu, W}, title = {Case Report: Multiple organ dysfunction syndrome in a preterm infant secondary to respiratory syncytial virus and bacterial co-infection.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1825002}, pmid = {42232626}, issn = {2296-2360}, abstract = {This article reports a case of a 1-month 11-day-old preterm infant, born at 36 + 6 weeks gestation, who presented to an outside hospital emergency department with a persistent cough that had not improved over four days. During this period, the infant progressively developed respiratory distress and lethargy. The infant subsequently developed cardiopulmonary arrest, underwent cardiopulmonary resuscitation, and was transferred to our hospital under endotracheal intubation with positive pressure ventilation. Respiratory pathogen polymerase chain reaction testing of a throat swab was positive for respiratory syncytial virus (RSV), while sputum and bronchoalveolar lavage fluid culture and blood metagenomic next-generation sequencing (mNGS) detected Haemophilus influenzae and S. pneumoniae. After 22 days of hospitalization and treatment including invasive mechanical ventilation, antibiotic adjustment, intravenous immunoglobulin (IVIG), and dexamethasone, the infant was discharged without further complications. Metagenomic next-generation sequencing provides rapid diagnostic evidence for mixed infections, while integrated interventions, including IVIG, short-course corticosteroids, and nutritional support, effectively modulate immune responses.}, } @article {pmid42232631, year = {2026}, author = {Gao, L and Wen, Y and Jing, X}, title = {Case Report: Cervical lymphadenitis resulting from Pseudomonas aeruginosa diagnosed by metagenomic next-generation sequencing.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1795457}, pmid = {42232631}, issn = {2296-2360}, abstract = {Pediatric cervical lymphadenitis is usually caused by Staphylococcus aureus and Streptococcus pyogenes. Cases resulting from Gram-negative bacteria are rare. Herein, we report the case of an 11-year-old boy who developed cervical lymphadenitis. He was diagnosed with a Pseudomonas aeruginosa infection through metagenomics next-generation sequencing of blood and biopsy. After treatment with meropenem, the patient's condition improved and he was discharged. Lymphadenitis may be caused by Gram-negative opportunistic pathogens. Metagenomic next-generation sequencing can help identify the underlying cause.}, } @article {pmid42232653, year = {2026}, author = {Fan, F and Wang, B and Jia, R and Lyu, J and Han, F}, title = {Amelioration of tic disorder by Jujuboside A via gut microbiota remodeling and intestinal 5-HT signaling.}, journal = {Frontiers in neuroscience}, volume = {20}, number = {}, pages = {1760647}, pmid = {42232653}, issn = {1662-4548}, abstract = {BACKGROUND: Tic disorder (TD) is a common chronic neuropsychiatric condition manifesting during childhood and adolescence. Jujuboside A (JuA) may alleviate TD symptoms; however, the mechanisms underlying its therapeutic effects remain unclear.

METHODS: We established a rat model of TD and used histological techniques to evaluate the effects of JuA on pathological changes. We also measured 5-hydroxytryptamine (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) levels and assessed tryptophan hydroxylase 1 (TPH1) mRNA expression. Finally, we analyzed the gut microbiota composition in fecal samples using 16S rRNA metagenomic sequencing.

RESULTS: JuA administration alleviated pathological changes in rats with TD, increased 5-HT and 5-HIAA levels, and upregulated TPH1 mRNA expression. Compared with no treatment, JuA treatment increased the proportion of Bacteroidia, Muribaculaceae, Bacteroidales, and Bacteroidota, while reducing that of Bacilli, Lactobacillaceae, Lactobacillus, Lactobacillales, and Firmicutes.

CONCLUSION: These findings indicate that JuA mitigates TD progression, potentially by remodeling the gut microbiota and regulating 5-HT levels.}, } @article {pmid42232910, year = {2026}, author = {Oskolkov, N}, title = {Refining filtering criteria of Kraken family of tools for accurate taxonomic profiling of ancient metagenomic data.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1603339}, pmid = {42232910}, issn = {1664-302X}, abstract = {Taxonomic profiling is a key component of ancient metagenomic analysis, however it is also susceptible to false-positive identifications. In particular, taxonomic classification tools from the Kraken family, such as Kraken2 and KrakenUniq, are highly sensitive to the choice of filtering options. To address this issue, various filtering approaches have been proposed. In this study, I conduct a comprehensive benchmarking of different filtering strategies for Kraken family of tools using simulated microbial and environmental ancient metagenomic data. I evaluate these approaches based on the balance between sensitivity and specificity of ground truth reconstruction (F1-score), and propose an optimal thresholding strategy tailored to specific sequencing depths in ancient metagenomic datasets.}, } @article {pmid42232914, year = {2026}, author = {Chamberlain, EJ and Boulton, W and Connors, E and Calianos, T and Bowman, JS and Creamean, JM and Mock, T and Kim, HH}, title = {From microbial diversity to functional potential using dimensionality reduction.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786397}, pmid = {42232914}, issn = {1664-302X}, abstract = {The high dimensionality of microbial diversity data from 'omics observations can be reduced using Machine Learning, with many recent studies showcasing ML utility for exploratory ecological feature finding and process prediction. Here, we compare the Self Organizing Map (SOM) dimensionality reduction method to the well-documented sample-based Principal Coordinate Analysis (PCoA) and taxa-based Weighted Gene Correlation Network Analysis (WGCNA) using near daily 16S rRNA gene amplicon sequencing data from the 2019 to 2020 MOSAiC International Arctic Drift Expedition. We then map k-means clustering outputs from each method to available metagenomes, extracting functionally distinct seasonal microbial ecotypes in the surface Arctic Ocean. Our results indicate the SOM method better represented expected seasonal transitions and identified a greater number of metabolically distinct functional groups than the more traditional PCoA ordination. Ultimately, we identified four community ecotypes with distinct taxonomic and functional cut-offs driven by seasonality, water mass, and substrate turnover, highlighting the importance of succession in functional diversity for the central Arctic Ocean. These results reinforce ML dimensionality reduction as a meaningful translator in the mining of historical amplicon datasets to address modern mechanistic questions and potentially provide 'omics informed ecotype diversity to leverage in mechanistic biogeochemical models.}, } @article {pmid42233252, year = {2026}, author = {Hashmi, L and Rehman, SU and Jabeen, F and Kayani, MUR}, title = {GUTAID: a curated database linking gut microbial antigens to autoimmune mechanisms.}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, pmid = {42233252}, issn = {1758-0463}, support = {//Metagenomics Discovery Lab at the SINES/ ; //NUST/ ; }, mesh = {Biocuration ; Humans ; *Autoimmune Diseases/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity/immunology ; *Antigens, Bacterial/immunology ; Animals ; *Databases, Protein ; }, abstract = {Gut dysbiosis is widely recognized as a contributor to autoimmune diseases, as it can lead to the expression of microbial antigens that disrupt immune regulation through specific molecular mechanisms. However, existing resources do not systematically link gut microbial antigen sequences to the specific autoimmune mechanisms through which they act. Here, we present GUTAID (Gut Microbes in Autoimmune Disorders), a literature-curated database of gut microbial antigens annotated with experimentally supported autoimmune mechanisms. Peer-reviewed studies published from October 1970 to September 2024 were manually screened, yielding 73 potential antigens that operate through nine molecular mechanisms, including protein citrullination, epitope spreading, molecular mimicry, and immune modulation, amongst others. The corresponding protein sequences were retrieved from UniProtKB, and redundancy was removed with MMseqs2. For the database implementation, data were delivered through a lightweight LAMP (Linux-Apache-MySQL/MariaDB-PHP) stack with server-side HTML/Bootstrap rendering, MySQL indexing, and HTTPS-secured downloads. Users can browse, keyword-search, or bulk-download sequence archives via a five-tab interface (Home, Downloads, Search, Team, and About). GUTAID thus enables mechanism-oriented exploration of gut microbial antigens and supports downstream biomarker and therapeutic discovery in autoimmune research. Database URL: https://gutaid.mgdiscoverylab.com/.}, } @article {pmid42233644, year = {2026}, author = {Dubin, CA and Zhao, C and Pollard, KS and Oskotsky, T and Golob, JL and Sirota, M}, title = {Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0149825}, doi = {10.1128/msystems.01498-25}, pmid = {42233644}, issn = {2379-5077}, abstract = {The vaginal microbiome plays a central role in reproductive health. Vaginal microbiome dysbiosis is associated with many adverse reproductive health outcomes, but most studies have focused on associations at the species level. The potential contribution of intraspecies microbial variation, especially gene content differences across bacterial strains, remains underexplored in reproductive health contexts. The Metagenomic Intra-Species Diversity Analysis (MIDAS) framework enables such analyses, but depends on comprehensive reference databases. We constructed a MIDAS-compatible pangenome database from over 18,000 genomes in the Vaginal Microbiome Genome Collection (VMGC). Compared to the Genome Taxonomy Database (GTDB)-derived reference, the VMGC-derived database expanded the pangenomes of prevalent vaginal species, better capturing vaginal-specific intraspecies diversity. Applying this database to vaginal samples from a cervical dysplasia cohort, we identified 13 Lactobacillus crispatus accessory genes significantly associated with cervical dysplasia, including a HicAB toxin-antitoxin system, three transcriptional regulators, and three phage-derived genes. These findings highlight the utility of body site-specific reference resources and shotgun metagenomic sequencing for uncovering intraspecies microbial variation relevant to reproductive health.IMPORTANCEThe vaginal microbiome plays a critical role in reproductive health, and different bacteria from the same species can carry different genes that influence how the strains interact with the host and other microbes. These strain-level differences are often overlooked when microbiomes are analyzed only at the species level. Existing genomic reference databases are heavily biased toward gut and environmental bacteria, leaving the genetic diversity of vaginal microbes understudied. We built a specialized reference database from over 18,000 vaginal bacterial genomes that better reflects this diversity. We then applied this resource to quantify gene-level variation in vaginal samples from a cervical dysplasia cohort. Focusing on Lactobacillus crispatus, a prevalent and often beneficial vaginal species, we identified 13 genes that were more common in women with cervical dysplasia than in controls. This work demonstrates that body site-specific genomic resources are essential for uncovering strain-level bacterial differences relevant to reproductive health.}, } @article {pmid42233648, year = {2026}, author = {Hu, J and Zhang, H and Miao, H and Chang, W and Zheng, J and Hu, F and Zhang, D and Guo, W and Hu, P and Han, R and Wang, J and Li, L and Wang, X}, title = {Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0399325}, doi = {10.1128/spectrum.03993-25}, pmid = {42233648}, issn = {2165-0497}, abstract = {UNLABELLED: This study aimed to compare the analytical characteristics and diagnostic performance of short-read next-generation sequencing (NGS) and long-read third-generation sequencing (TGS) for metagenomic pathogen detection, using defined mock communities and clinical bronchoalveolar lavage fluid (BALF) samples. Mock evaluations included microbe-host gradient mixtures (D1/D2) and six complex microbial panels (M1-M6). Sequencing was performed on Illumina, MGI, and Oxford Nanopore Technologies (ONT) platforms. Clinical validation was conducted on 62 BALF samples. Diagnostic performance was assessed against culture, clinical microbiological tests (CMT), and a composite reference standard (CRS). Turnaround times for Illumina and MGI were approximately 18-20 h and 14-19 h, respectively, whereas the ONT workflow was completed within 4-6 h. The microbe-to-host DNA ratio significantly influenced sequencing performance. Depletion of host DNA notably enhanced ONT detection, reducing the false-negative rate for low-abundance microorganisms from 43.3% to 6.7%. For all mock samples, both the Illumina and MGI platforms demonstrated 100% sensitivity and showed highly concordant detection profiles. In clinical specimens, when evaluated against the composite reference standard, the positive percent agreement (PPA) values of NGS and TGS were 93.3% and 90.7%, respectively, with corresponding negative percent agreements (NPAs) of 77.6% and 83.3%. Both platforms identified numerous pathogens that were missed by culture, especially in polymicrobial infections. Among 22 CRS-defined polymicrobial samples, culture identified all pathogens in only 2 cases, whereas NGS and TGS achieved full pathogen recovery in 18 and 17 cases, respectively. Within the evaluated workflows, short-read sequencing showed slightly higher sensitivity and overall stability, whereas host-depleted ONT offered a substantial turnaround-time advantage and may serve as a useful complementary approach in complex or time-sensitive clinical scenarios.

IMPORTANCE: Rapid and accurate identification of the microbes causing pneumonia is essential for choosing effective treatment, yet current diagnostic tests are slow and often miss important pathogens. We systematically compared two major DNA sequencing strategies-established short-read platforms and newer long-read nanopore sequencing-using both carefully designed mock communities and real bronchoalveolar lavage samples from patients. We show when removal of human DNA is essential, how mixed infections are best captured, and what trade-offs exist between speed and sensitivity. Our results provide practical guidance on how hospitals can implement sequencing-based diagnostics, when rapid nanopore testing can complement conventional short-read workflows, and how to interpret sequencing read counts in day-to-day clinical decision-making.}, } @article {pmid42233650, year = {2026}, author = {Kane, M and Moukaha Doukanda, SF and Sankhé, S and Sow, B and Ndione, MHD and Mhamadi, M and Dieng, M and Diop, SMBS and Seye, S and Mbanne, M and Faye, O and Barry, MA and Sembene, PM and Loucoubar, C and Fall, G and Diallo, A and Diagne, CT and Dia, N and Diagne, MM}, title = {Evaluating myxovirus resistance protein A-based rapid testing combined with pathogen sequencing for arboviral and incidental viral infection surveillance in Senegal.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0339225}, doi = {10.1128/spectrum.03392-25}, pmid = {42233650}, issn = {2165-0497}, abstract = {Accurate differentiation between viral and bacterial infections remains challenging in resource-limited, arbovirus-endemic settings, leading to antibiotic misuse and diagnostic uncertainty. Myxovirus resistance protein A (MxA), an interferon-induced host biomarker, may offer a pathogen-agnostic approach to improve rapid diagnosis and clinical triage. We evaluated the performance of an MxA rapid diagnostic test (RDT) using archived samples from febrile patients collected during dengue virus (DENV) and chikungunya virus (CHIKV) outbreaks in Senegal. We tested 171 blood samples from patients with acute febrile illness using an MxA RDT and RT-qPCR for DENV and CHIKV. Samples with discordant results (MxA-positive and RT-qPCR-negative) underwent metagenomic and hybrid-capture Illumina-based sequencing to detect missed infections. Sequencing data were analyzed using maximum-likelihood phylogenetics to assess viral lineage placement. The MxA RDT demonstrated moderate-to-high sensitivity (70.0%-85.1%, depending on virus) and moderate specificity (70.2%) for detecting primary arboviral infections. Among discordant samples, sequencing revealed previously missed pathogens, including DENV serotype 3 (genotype III), Parvovirus B19 (B19V), and Torque teno virus (TTV). Detection of B19V and TTV highlights the broader clinical utility of host-response biomarkers to uncover unexpected viral pathogens in high-diversity settings. MxA's longer persistence than viral RNA enables detection of recent infections missed by PCR. Combined with sequencing, this broadens the diagnostic window, improves clinical triage, and supports identification of underdiagnosed viruses. Future research should integrate MxA testing into routine clinical care and surveillance protocols to enhance outbreak responses in resource-limited regions.IMPORTANCETimely and equitable viral diagnosis is vital in outbreak-prone regions where advanced laboratories are scarce. This study shows how a simple, rapid test for the host biomarker myxovirus resistance protein A can provide real-time detection of viral infections such as dengue and chikungunya, even in remote or frontline health centers. When paired with pathogen sequencing, the test also uncovers infections that standard PCR may miss. This integrated approach demonstrates how field-deployable diagnostics can operate both during and between epidemics, strengthening outbreak preparedness, improving patient triage, and advancing laboratory equity worldwide.}, } @article {pmid42233654, year = {2026}, author = {Wang, W and Li, Y and Liang, Y and Wang, J and Zhang, Z and Zhang, Y and Xiao, C and Hao, H}, title = {Age-driven shifts of the camel gut microbiome and resistome in extensively reared dromedary camels.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0318325}, doi = {10.1128/spectrum.03183-25}, pmid = {42233654}, issn = {2165-0497}, abstract = {UNLABELLED: Camels are uniquely adapted to arid environments and are commonly raised in extensive grazing systems. The composition of their gut microbiome and antimicrobial resistance genes (ARGs) is expected to change with host development, but age-related patterns have not been well described. In this study, we analyzed fecal samples from juvenile (approximately 6 months old) and adult (6 years) dromedary camels kept under the same grazing management, with no recorded therapeutic antibiotic treatments during the study period. Shotgun metagenomic sequencing was used to profile bacterial communities, ARGs, and mobile genetic elements (MGEs). Juvenile camels showed lower alpha diversity and greater inter-individual variation than adults, and their gut communities were dominated by facultative anaerobes such as Escherichia and Streptococcus. Adult camels carried more stable, fiber-adapted communities enriched in Bacteroidaceae and Prevotellaceae. In parallel with these microbiome changes, the resistome also differed by age. Juveniles carried a wider range of ARGs, with higher contributions from multidrug efflux pumps and vancomycin resistance genes. Adults had a smaller and more concentrated set of ARGs, mainly β-lactamase and tetracycline resistance genes, together with lower ARG richness and diversity. MGEs also showed distinct age-related patterns: transposase genes were more common in juveniles, whereas insertion sequence-associated genes were more abundant in adults, suggesting age-specific routes of potential ARG mobility. Overall, these data indicate that maturation of the camel gut microbiome is accompanied by a reduction and focusing of the resistome and by a shift in the dominant types of MGEs. This study provides an age-stratified reference for ARG reservoirs and MGE-associated ARG mobility in camels studied under conditions with no recorded therapeutic antibiotic treatments and may be useful for future work on antimicrobial resistance in extensively managed livestock.

IMPORTANCE: Antimicrobial resistance is often studied in animals heavily exposed to antibiotics, leaving a gap in our understanding of its natural development. Camels, rarely treated with antibiotics, offer a unique model. By comparing juvenile and adult gut microbiomes, we found that early-life communities are diverse, unstable, and rich in mobile resistance genes, while adult communities are more stable and carry fewer mobile elements. These findings establish a natural baseline for how resistance genes emerge and settle without drug pressure, providing critical insights for One Health strategies aimed at limiting the spread of resistance in livestock and wildlife.}, } @article {pmid42233680, year = {2026}, author = {Grettenberger, CL and Macalady, JL and Hamilton, TL}, title = {Metabolic diversity of Ferrovaceae and potential contributions to iron oxidation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0070026}, doi = {10.1128/aem.00700-26}, pmid = {42233680}, issn = {1098-5336}, abstract = {Active and abandoned metal and coal mines generate acidic, metal-laden water that pollutes downstream areas, commonly referred to as acid mine drainage (AMD). AMD is host to microbial communities, including acidophilic iron oxidizers. Microbially mediated iron oxidation is a desirable (bio)remediation strategy for AMD. Ferrovaceae are Fe-oxidizing bacteria observed in AMD globally and thus could be an asset for bioremediation strategies. To better understand the potential for Ferrovaceae to contribute to AMD bioremediation, we analyzed 240 genomes and metagenome-assembled genomes from Ferrovaceae, including sequences from AMD sites with high iron oxidation rates. Based on our analyses, the phylogenetic and physiological diversity of this group is greater than previously known. We found that while all taxa are likely capable of iron oxidation using a cyc-2 like protein, some may also be capable of iron oxidation using an Mto-like protein. We also identified Ferrovaceae that are likely capable of anoxygenic phototrophy. Our findings indicate that multiple Ferrovaceae populations co-occur and suggest that differences in physiology may promote niche differentiation along resource axes. Physiologically diverse iron oxidizer communities could support a more resilient microbial community, resulting in higher iron oxidation rates and potentially more efficient bioremediation, and thus our results also indicate that future studies that link taxonomy with iron oxidation activity are warranted.IMPORTANCEAcid mine drainage (AMD) pollutes watersheds worldwide. Microbial communities can be leveraged to improve AMD bioremediation because they drive biogeochemical processes in these ecosystems. In AMD streams, iron-oxidizing microbial populations remove iron from the AMD effluent by precipitating iron oxides, which absorb other metals. These communities vary across sites and differ in how rapidly they oxidize iron. The factors that contribute to iron oxidation rates are not well understood, making it difficult to design effective bioremediation strategies. Ferrovaceae populations are widespread in AMD globally, including in sites with exceptionally high rates of iron oxidation. To examine the potential for Ferrovaceae to be key components of bioremediation strategies, we examined the genomic content and functional potential of Ferrovaceae in publicly available metagenomic data sets. Our analysis uncovered several new species of Ferrovaceae as well as an expanded metabolic potential for this group. Comparative genomics suggests that functional diversity leads to co-occurrence of multiple Ferrovaceae species at the same sites. The presence of multiple iron-oxidizing taxa with distinct physiology could be beneficial for bioremediation strategies.}, } @article {pmid42233768, year = {2026}, author = {Éles, ZB and Rahmani, L and Gyöngyösi, E and Szarka, K and Rebenku, I and Veress, G and Major, T and Kónya, J and Szalmás, A}, title = {Sublineage-Specific A45S Polymorphism Alters the Biological Function of the Human Papillomavirus 11 E7 Protein.}, journal = {Journal of medical virology}, volume = {98}, number = {6}, pages = {e70997}, doi = {10.1002/jmv.70997}, pmid = {42233768}, issn = {1096-9071}, support = {FK125038//National Research, Development and Innovation Office/ ; //Hungarian Academy of Sciences/ ; //Faculty of Medicine, University of Debrecen/ ; //Richter Gedeon Talentum Foundation/ ; }, mesh = {Humans ; *Papillomavirus E7 Proteins/genetics/metabolism ; *Human papillomavirus 11/genetics/pathogenicity ; Amino Acid Substitution ; Keratinocytes/virology ; *Polymorphism, Genetic ; *Host-Pathogen Interactions ; Protein Binding ; Oncogene Proteins, Viral ; }, abstract = {The E7 oncoprotein of human papillomavirus (HPV) plays a crucial role in viral pathogenesis and replication. Although it is generally highly conserved across HPV genotypes, naturally occurring E7 variants can display functional differences that may affect viral persistence, oncogenic potential, and host cellular responses. The prevalent HPV11 A2 sublineage is characterized by a distinctive amino acid substitution at position 45 (A45S) within the E7 protein. In comparative analyses of transfected primary keratinocytes and HPV-negative cancer cells, we here demonstrate that the A45S substitution enhances the interaction of HPV11 E7 with key cellular targets, including pRb family proteins and PTPN14. A further consequence is an increased ability to target both PTPN14 and pRb family proteins for degradation. Functionally, these differences are exemplified by the S45 variant's enhanced ability to activate E2F-driven gene expression, particularly resulting in elevated mRNA levels of key factors involved in homologous recombination-mediated repair of DNA double-strand breaks, a pathway critical for preserving genomic integrity. Together, these findings indicate that the A45S substitution imparts high-risk-like molecular properties to the low-risk HPV11 E7 oncoprotein. To our knowledge, this is the first report to identify a functionally significant alteration in HPV11 E7 activity resulting from a naturally occurring sequence variation. Understanding the underlying mechanisms could provide new strategies for targeting the therapeutically challenging HPV-associated conditions, such as recurrent respiratory papillomatosis.}, } @article {pmid42234268, year = {2026}, author = {Hoseini, R and Hoseini, Z and Heydarpour, B and Faraji, M}, title = {A systematic review of molecular signaling in the muscle-brain-gut axis: exercise-induced myokines and microbial metabolites as key mediators.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42234268}, issn = {1573-4978}, mesh = {Humans ; Myokines/metabolism ; *Exercise/physiology ; *Muscle, Skeletal/metabolism/physiology ; Signal Transduction ; *Gastrointestinal Microbiome/physiology ; *Brain/metabolism/physiology ; *Brain-Gut Axis/physiology ; Animals ; }, abstract = {Exercise physiology is evolving from an organ-based framework toward a systems-level understanding, where molecular interactions between muscle, brain, and the gut microbiome critically influence performance and health. This review systematically examines the genetic, molecular, and cellular bases of this triad, with a focus on translational insights for disease prevention and human optimization. A systematic search of PubMed, Embase, and Web of Science was conducted up to October 2023 to identify studies exploring molecular pathways linking skeletal muscle, cognitive/affective function, and gut microbiota in exercise contexts. Inclusion criteria were original research articles investigating at least two components of the muscle-brain-gut axis. Exclusion criteria included non-English articles, conference abstracts, and studies without molecular data. The PRISMA 2020 guidelines were followed. The search strategy is detailed in Supplementary Material. Evidence was categorized into Grades 1 through 4 based on methodological rigor, omics integration, reproducibility, and translational relevance to human physiology and disease models. Analysis included 154 studies encompassing 987 molecular associations. Among these, 59 associations (Grades 1-2) provided robust evidence for genetically and functionally validated pathways, including myokine-mediated (e.g., irisin, BDNF) and microbially derived metabolites (e.g., SCFAs, tryptophan derivatives) that modulate neuroplasticity, mitochondrial function, inflammation, and HPA axis activity. Psychobiological factors influenced microbial composition, illustrating bidirectional gut-brain-muscle signaling. Most associations (n = 952) were limited by methodological variability or insufficient mechanistic depth. The integration of multi-omics platforms (metagenomics, metabolomics, proteomics) emerges as a key tool for personalized exercise interventions and biomarker discovery. This review synthesizes molecular evidence for the muscle-gut-brain axis as an integrative determinant of exercise responsiveness and disease resilience. We highlight genetic and metabolic pathways with diagnostic and therapeutic potential, aligning with the development of molecular tools for precision medicine. Future interdisciplinary research should leverage artificial intelligence and longitudinal omics to translate these mechanisms into targeted strategies for performance enhancement and disease prevention.}, } @article {pmid42234577, year = {2026}, author = {Faure, R and Faure, U and Truong, T and Derzelle, A and Lavenier, D and Flot, JF and Quince, C}, title = {SNooPy: a statistical framework for long-read metagenomic variant calling.}, journal = {Nucleic acids research}, volume = {54}, number = {10}, pages = {}, pmid = {42234577}, issn = {1362-4962}, support = {101088572//ERC/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBX011089/1//Earlham Institute Strategic Programme/ ; BBS/E/ER/230002C//Earlham Institute Strategic Programme/ ; BB/CSP1720/1//Core Strategic Programme/ ; BBS/E/T/000PR9818//Core Strategic Programme/ ; BBS/E/T/000PR9817//Core Strategic Programme/ ; BB/CCG2220/1//Core Strategic Programme/ ; }, mesh = {*Metagenomics/methods ; *Polymorphism, Single Nucleotide ; Humans ; *Software ; Algorithms ; Haplotypes ; Deep Learning ; Genome, Human ; }, abstract = {Current long-read single-nucleotide variant callers were designed primarily for genomic data-particularly human genomes. While some have been used on metagenomic data, their underlying assumptions and training procedures fail to account for the inherent complexity of metagenomic samples. To date, no long-read variant caller has been purpose-built for metagenomic applications. To address this gap, we present SNooPy, a single nucleotide polymorphism (SNP)-calling tool that implements a new statistical framework tailored to long-read metagenomic data. Unlike previous genomic methods, our approach makes no assumptions about the number of haplotypes present, their evolutionary relationships, or their sequence divergence. We demonstrate that SNooPy outperforms both traditional statistical and deep learning-based SNP callers. Our results suggest that future integration of this framework with deep learning approaches could further enhance variant-calling performance. SNooPy is freely available on github.com/rolandfaure/snoopy.}, } @article {pmid42234710, year = {2026}, author = {Liu, F and Lai, T and Xu, W and Li, G}, title = {ViralMultiNet: A structure-aware multimodal framework for viral protein function prediction in wastewater surveillance.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0349393}, pmid = {42234710}, issn = {1932-6203}, mesh = {*Wastewater/virology ; *Viral Proteins/genetics/chemistry/metabolism ; *SARS-CoV-2/genetics/isolation & purification ; Humans ; COVID-19/virology ; Metagenomics/methods ; }, abstract = {Accurate functional annotation of viral proteins is essential for genomic surveillance, yet rapid viral evolution causes "functional drift" that challenges conventional sequence-only models. These models often lack interpretability and struggle with fragmented sequences from complex environmental samples such as wastewater. We developed ViralMultiNet, a structure-aware multimodal framework that integrates multi-scale k-mer encodings (4-7-mers) with functional semantic embeddings derived from UniProt annotations. Using a curated Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) dataset of 66,011 samples from wastewater metagenomics (NCBI SRA: SRX28474964), we implemented gated multimodal fusion and triple knowledge distillation to transfer structural insights from a teacher to a student model. Model performance was evaluated via 5-fold cross-validation and external validation on emerging variants. Training efficiency was optimized using Low-Rank Adaptation and Flash Attention. ViralMultiNet achieved robust classification performance with a macro F1 score of 0.921 ± 0.004, accuracy of 0.928 ± 0.003, and AUC of 0.983 in cross-validation. The distilled student model matched teacher performance within a negligible margin (<0.003 F1 difference) while reducing training time by 40.4% (from 94.3 to 56.2 minutes per epoch). Interpretability analysis revealed that model attention peaks consistently aligned with experimentally validated functional domains of the SARS-CoV-2 Spike protein, including the receptor-binding domain (residues 319-541), S1/S2 cleavage site (681-685), and fusion peptide (816-835). ViralMultiNet offers a scalable, interpretable solution for viral protein function prediction. Its ability to generalize across variants and map attention to critical biological regions supports deployment in wastewater-based early warning systems, enhancing global pandemic preparedness.}, } @article {pmid42235107, year = {2026}, author = {Candia-Herrera, D and Guerra, M and Carrasco-Fernández, J and Campos-Quiroz, C and Garcia-Gomez, M and Igual, JM and Carro, L and Castro, JF}, title = {Whole genome-based reclassification of the genus Metabacillus: Proposal for five novel genera, Chryseobacillus gen. nov., Cohnibacillus gen. nov., Salimetabacillus gen. nov., Pantoeobacillus gen. nov., and Lutimetabacillus gen. nov. and the description of one novel bacterial species, Chryseobacillus diguaensis sp. nov. isolated from soil in the Digua reservoir.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126734}, doi = {10.1016/j.syapm.2026.126734}, pmid = {42235107}, issn = {1618-0984}, abstract = {Comprehensive phylogenomic and comparative genomic analyses were conducted to clarify the taxonomic boundaries of the genus Metabacillus. Phylogenetic trees reconstructed from a set of single-copy orthologous proteins (SCOPs) revealed that the genus, as currently defined, is polyphyletic. The type species of the genus Metabacillus and its closest relatives formed a consistent clade, herein designated as Metabacillus sensu stricto. The remaining species were grouped into three well-supported clades: Kandeliae, Indicus, and Mangrovi, and two single-taxon lineages: M. arenae and M. lacus. The phylogenomic delineation found in these divergent taxa was corroborated by either inconsistent distribution patterns or the absence of previously defined conserved signature indels (CSIs) specific to Metabacillus. Genomic metrics, including Average Nucleotide Identity (ANI), Average Amino acid Identity (AAI), and digital DNA-DNA hybridization (dDDH) further supported the taxonomic delineation proposed here. The observed genomic divergence was mirrored by phenotypic differences, including variations in GC content ranges. Based on this polyphasic evidence, we propose the reclassification of the genus Metabacillus taxa into five novel genera: Chryseobacillus gen. nov. (encompassing the Kandeliae clade), Cohnibacillus gen. nov. (M. lacus), Salimetabacillus gen. nov. (M. arenae), Pantoeobacillus gen. nov. (Indicus clade), and Lutimetabacillus gen. nov. (Mangrovi clade). The core lineage is retained as Metabacillus sensu stricto, for which an emended description of the genus Metabacillus is also provided. A novel bacterial strain, designated as MAU-250[T], was isolated from a soil sample collected on the shore of an artificial reservoir in the Andean foothills of the Maule Region in central Chile. Public metagenome screening supported a low-abundance taxon with broad ecological adaptability, preferentially associated with soil habitats. A polyphasic analysis based on phenotypic traits and genomic distances (78.0% ANIb and 19.8% dDDH against its closest relative) also supported its designation as a novel species, for which the name Chryseobacillus diguaensis sp. nov. is proposed. The type strain is MAU-250[T] (=RGM 3146[T] = IMI 507634[T]).}, } @article {pmid42235155, year = {2026}, author = {Zhang, YF and Li, MY and Zhang, Y and Ding, H and Yun, L and Li, ZY}, title = {Genome-resolved analysis reveals successional dynamics and functional transitions in chicken gut archaea across the broiler growth cycle.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107186}, pmid = {42235155}, issn = {1525-3171}, abstract = {Archaea are indispensable members of the gut microbiota, playing important roles in host metabolism and gut homeostasis. Despite their ecological significance, the archaeal community within the chicken gut remains poorly understood, particularly regarding its taxonomic diversity, functional potential, and successional dynamics throughout the broiler growth cycle. In this study, we employed a metagenome-assembled genome (MAG) approach to systematically characterize the composition, phylogeny, and functional shifts of the chicken gut archaea. We constructed a genome catalog comprising 172 non-redundant archaeal MAGs, encompassing 11,796 protein clusters. Community analysis revealed that alpha diversity indices differed significantly across growth stages, suggesting that the archaeal community becomes increasingly robust and functionally complex as the host matures. Functional annotation further demonstrated broad metabolic versatility, with distinct metabolic profiles emerging across multiple functional modules at different ages. This study reveals the dynamics of chicken gut archaeal communities and their potential functional characteristics across different production stages, providing a basis for future research into their ecological roles and possible associations with host gut ecosystem stability.}, } @article {pmid42235160, year = {2026}, author = {Lu, T and Chen, Y and He, Q and Zheng, B and Deng, D and Xiong, X}, title = {Gut bacterial species, serum metabolites, and serum cytokines associated with broodiness in chickens.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107187}, pmid = {42235160}, issn = {1525-3171}, abstract = {Increasing evidence suggests that the gut microbiota, serving as a "virtual endocrine organ", potentially modulates reproductive behavior in poultry via the gut-brain and gut-ovary axes. Broodiness in hens inhibits egg-laying activity and causes major economic losses in native chicken breeds, but its micro-physiological basis remains unclear. This study used shotgun metagenomic sequencing to delineate the cecal bacterial species associated with brooding status in Chinese Kangle chickens. We identified 34 cecal bacterial species exhibiting significantly varying abundances between the broodiness and control groups, including six species (e.g., Bacteroides sp. An51A and Phocaeicola barnesiae) that were significantly enriched in the broodiness group. Additionally, 28 species significantly enriched in the control group were screened. Among them, Subdoligranulum variabile and Oribacterium asaccharolyticum served as key biomarkers for distinguishing brooding status in Kangle chickens and were associated with functional shifts in the cecal microbiome. Non-targeted metabolomic analysis identified 17 differential metabolites, among which seven (e.g., (13E) -11a-hydroxy-9,15-dioxoprost-13-enoic acid and d-arabitol) were defined as metabolic markers of the broody state and were significantly associated with Subdoligranulum variabile and Oribacterium asaccharolyticum. In addition, our results suggest that serum cytokines, such as IFN-γ and IL-22, are potentially associated with the broody state and the alterations in both serum metabolites and the gut microbiota (e.g., Subdoligranulum variabile and Oribacterium asaccharolyticum). These findings provide a new insight into the mechanisms underlying reproductive behavior in poultry and offer a theoretical basis for alleviating broodiness through microecological interventions, thereby improving the reproductive efficiency of indigenous chicken breeds.}, } @article {pmid42235395, year = {2026}, author = {Li, Y and Zhu, T and Tao, C and Li, S and Cheng, H and Chen, W}, title = {Threshold-dependent control of ARG removal in global wastewater treatment plants: Molecular mechanisms of low-abundance functional genes deciphered via metagenomics and explainable AI.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142574}, doi = {10.1016/j.jhazmat.2026.142574}, pmid = {42235395}, issn = {1873-3336}, abstract = {Wastewater treatment plants (WWTPs) serve as critical barriers against the dissemination of antibiotic resistance genes (ARGs) from urban water environments to nature, yet the molecular mechanisms governing their biological removal remain poorly understood. By combining experimental metagenomic data from 19 Chinese WWTPs with additional data from 31 global WWTPs (50 WWTPs in total), an explainable machine learning (ML) framework was developed. The RFE-SHAP (Recursive Feature Elimination-SHapley Additive exPlanations) based on feature importance was applied to identify key biological features driving ARG removal. The study revealed that low-abundance microbial functional genes particularly those involved in DNA repair, energy metabolism, and quorum sensing exhibit threshold-dependent control over ARG attenuation. ML models (BFGs-GBDT) incorporating the RFE-SHAP-selected functional genes achieved exceptional predictive accuracy (R[2]test = 0.967), outperforming taxonomy-based models (average R[2]test = 0.805). Strikingly, these functionally critical genes, despite their low abundances (0.04 - 0.15%), exerted disproportionate influence on ARG removal efficiency, challenging the prevailing high-abundance-centric paradigm in WWTPs design. The findings not only elucidated the molecular mechanisms of ARG mitigation but also provided a predictive framework for precision engineering of microbial communities to enhance ARG elimination. This study advances wastewater treatment strategies from empirical ARG removal to mechanism-driven environmental risk control.}, } @article {pmid42235463, year = {2026}, author = {Lin, Q and Mei, X and Zheng, H and Meng, J and He, F and Yang, B and Ru, X and Su, M and Wang, D and Tan, N and Fang, J and Fu, S and Ouyang, N and Yang, Z and Jiang, S and Zhang, Y}, title = {Optimisation and validation of capture mNGS for predicting antimicrobial resistance.}, journal = {EBioMedicine}, volume = {129}, number = {}, pages = {106319}, pmid = {42235463}, issn = {2352-3964}, abstract = {BACKGROUND: Antibiotic resistance critically compromises bacterial infection treatment. While antimicrobial susceptibility testing (AST) remains the standard for resistance assessment, its culture dependence is time-consuming. Clinical metagenomic next-generation sequencing (mNGS) offers rapid pathogen detection and antibiotic resistance gene (ARG) profiling. However, low ARG detection sensitivity and unclear genotype-phenotype correlations limit its clinical utility.

METHODS: We developed capture mNGS approach with probe-based ARG enrichment and a host-attribution algorithm for precise ARG-bacteria linkage. Its ARG detection sensitivity was comparatively analysed against standard mNGS. Using phenotypic AST as reference, we then evaluated the clinical predictive value of capture mNGS-detected ARGs in a retrospective cohort from Sun Yat-sen Memorial Hospital (SYSMH) and an external cohort from Liuzhou Worker's Hospital (LWH). In addition, a prospective cohort from SYSMH was used to explore the clinical utility of ARG detection by mNGS.

FINDINGS: Compared to standard mNGS, capture mNGS significantly enhanced ARG detection sensitivity, achieving a 44-fold increase in sequencing depth. In our retrospective cohort, key resistance genes detected by capture mNGS accurately predicted phenotypic resistance: blaCTX-M achieved a sensitivity of 1.00 (95% CI: 0.86, 1.00) and specificity of 1.00 (95% CI: 0.59, 1.00) for ceftriaxone resistance prediction, with an area under the receiver operating characteristic curve (AUC) of 0.93 (95% CI: 0.87, 0.99). BlaKPC demonstrated a sensitivity of 0.94 (95% CI: 0.73, 1.00) and specificity of 1.00 (95% CI: 0.95, 1.00) for carbapenem resistance (AUC = 0.97, 95% CI: 0.92, 1.00). Similarly, blaOXA-23 exhibited a sensitivity of 0.95 (95% CI: 0.82, 0.99) and specificity of 1.00 (95% CI: 0.69, 1.00) for carbapenem resistance (AUC = 0.97, 95% CI: 0.94, 1.00), which was externally validated in the LWH cohort. In addition, mecA showed a sensitivity of 0.94 (95% CI: 0.71, 1.00) and specificity of 0.94 (95% CI: 0.81, 0.99) for oxacillin resistance (AUC = 0.94, 95% CI: 0.87, 1.00). Whereas blaTEM/blaSHV showed higher false-positive rates for cephalosporin resistance and ErmB/ErmC showed lower sensitivity (0.6, 95% CI: 0.32, 0.84) for macrolide-lincosamide-streptogramin (MLS) resistance. Capture mNGS reported results (median turnaround time (TAT): 24.71 h (IQR 22.74-41.00)) were shorter than AST (median TAT: 73.16 h (IQR 54.19-93.42)). In a prospective cohort, the time to guide antibiotic therapy based on reported positive ARGs was significantly shorter than that based on reported resistant phenotypes from AST.

INTERPRETATION: These results highlight that ARGs can be leveraged to rapidly and accurately predict bacterial resistance phenotypes with high sensitivity and specificity, thereby guiding antibiotic management in clinical practice.

FUNDING: The National Natural Science Foundation of China, the Guangdong Science and Technology Department, Science and Technology Projects in Guangzhou.}, } @article {pmid42235671, year = {2026}, author = {Peng, D and Liu, X and Wang, L and Pan, Y and Kang, B and Liu, X and Xu, R and Cheng, Y}, title = {A multi-omics signature of microplastic exposure and its clinical, metabolic, and microbial correlates in colorectal cancer.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {405}, number = {}, pages = {128426}, doi = {10.1016/j.envpol.2026.128426}, pmid = {42235671}, issn = {1873-6424}, abstract = {Microplastics (MPs) are emerging environmental contaminants with potential human health implications, yet their distribution and biological effects in colorectal cancer (CRC) remain unclear. Here, we investigate the presence of MPs in blood, tumor, and peri-tumor tissues from CRC patients using a multi-omics approach. We find that MPs, particularly polyvinyl chloride (PVC) and polyethylene (PE), are more abundant in tumor and peri-tumor tissues than in blood. Tissue-specific MPs were associated with clinical traits, serum metabolites, and gut microbes. Functional analysis suggested MP-related alterations in microbial pathways involving carbohydrate metabolism, fatty acid degradation, and bile acid biosynthesis. Our findings provide the first integrative evidence suggesting potential links between MPs exposure to metabolic and microbial dysregulation in CRC patients.}, } @article {pmid42235696, year = {2026}, author = {Tang, P and Shuai, H and Yang, Z and Cen, Q and Mao, Y and Wang, J and Zhou, Y}, title = {Contributions and mechanisms of bioclogging-induced oxygen-limited microsites to nitrogen removal in porous media.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135059}, doi = {10.1016/j.biortech.2026.135059}, pmid = {42235696}, issn = {1873-2976}, abstract = {Nitrate (NO3[-]-N) in wastewater treatment plant (WWTP) effluents has become a contributing factor to the increasing eutrophication risk in receiving waters, whereas the relatively high dissolved oxygen (DO, approximately 7-8 mg L[-1]) in effluents constrains NO3[-]-N removal. Constructed wetland systems based on porous media are major technologies for advanced treatment of WWTP effluents. Although bioclogging in such systems is usually regarded as a negative phenomenon, it may create favorable anoxic microenvironments for denitrification through transport confinement. In this study, vertical saturated flow-through porous-media columns were established to systematically elucidate how bioclogging reshapes oxygen transport and drives microbial functional reorganization under bulk-oxic conditions. The results showed that hydraulic conductivity (k) decreased from 27.5 and 18.1 cm s[-1] in Groups A and B, respectively, to < 0.03 cm s[-1], while NO3[-]-N removal increased from 61 to 64% during start-up to 88-91% at day 24. The two-dimensional plate experiment directly captured the full evolution of pore-scale oxygen-limited microenvironments from discrete patches to connected structures. DO heatmaps further showed that bioclogging-induced transport confinement generated nested confined oxygen-limited microsites within an otherwise bulk-oxic flow field. Denitrification-related genes were enriched in the clogging-affected upper and intermediate layers, indicating that efficient denitrification was more likely associated with bioclogging-induced confined oxygen-limited microsites than simply with medium depth. Metagenomic analysis further revealed a metabolic division of labor within the microbial community, with Ectobacillus mainly associated with upstream nitrate reduction, Nitrospira and Chitinophagaceae playing complementary roles in downstream steps, and Ignavibacterium exhibiting genomic signatures consistent with enhanced organic-carbon metabolism and potential reducing-equivalent generation. Overall, bioclogging coupled bulk-oxic and locally oxygen-limited functions through transport confinement and community-level metabolic partitioning, providing new mechanistic insights into stable nitrogen removal under high-DO effluent conditions.}, } @article {pmid42235698, year = {2026}, author = {Zhou, X and Yu, Z and Liao, H and Wang, Y and Zhuang, L and Zhou, S}, title = {Bacteria and viruses associated with antibiotic resistome in hyperthermophilic co-composting of cow manure and mushroom residue.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135075}, doi = {10.1016/j.biortech.2026.135075}, pmid = {42235698}, issn = {1873-2976}, abstract = {Antibiotic resistance in livestock-derived wastes represents a critical environmental and public health concern. Here, we applied genome-resolved metagenomic analysis to characterize antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and associated viral communities during co-composting of cow manure and mushroom residue. By day 20, hyperthermophilic composting (HTC) achieved markedly higher ARG removal (93%) than conventional thermophilic composting (TC, 84%). This enhanced performance was associated with the enrichment of thermophilic taxa (e.g., Bacillaceae and Sporolactobacillaceae) and the suppression of mesophilic ARG reservoirs (e.g., Enterobacteriaceae and Pseudomonadaceae). Genome-resolved analysis further revealed that a majority of multidrug-resistant ARB were eliminated during HTC, particularly Klebsiella pneumoniae and Escherichia coli harboring diverse ARGs and virulence factor genes. These high-risk pathogens were predicted to be targeted by a subset of lytic phages, including those affiliated with Autographiviridae and Schitoviridae, suggesting a potential role of lytic phages in suppressing resistance- and virulence-associated ARB. Collectively, these findings provide genome-resolved insights into the coordinated roles of thermophile-driven suppression and phage-mediated predation of ARB in ARG removal, highlighting HTC as a promising strategy for safer manure recycling and resistance risk mitigation.}, } @article {pmid42235960, year = {2026}, author = {Chongdar, N and Goyal, A and Damare, SR}, title = {Genomic Survey of Carbon Monoxide Dehydrogenases Reveals Their Widespread Distribution in Marine Habitats.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70375}, pmid = {42235960}, issn = {1758-2229}, support = {DST/INSPIRE/04/2021/002518//Department of Science and Technology, Govenrnment of India/ ; }, mesh = {Phylogeny ; *Seawater/microbiology ; *Aldehyde Oxidoreductases/genetics/metabolism ; Ecosystem ; Carbon Monoxide/metabolism ; *Multienzyme Complexes/genetics/metabolism ; *Bacteria/genetics/enzymology/classification ; *Aquatic Organisms/genetics/enzymology ; Oxygen/metabolism ; Oceans and Seas ; }, abstract = {Most carbon monoxide (CO) produced in the ocean is consumed by microorganisms encoding carbon monoxide dehydrogenases (CODHs), thereby significantly reducing the flux of CO from the ocean to the atmosphere. CODHs are of two types based on the metal content of their active sites: the oxygen-sensitive, nickel-containing Ni-CODH and the oxygen-tolerant, molybdenum-copper-containing Mo-CODH. Although CODHs have been reported from specific marine environments, their combined distribution across ocean ecosystems remains unclear. Here, we analyzed the NCBI non-redundant protein database and identified 1969 Ni-CODH and 864 Mo-CODH genes from marine prokaryotes spanning diverse oceanic ecosystems. Using metagenomic analyses across three marine biomes, we showed that oxygen availability selectively constrains Ni-CODH gene abundance, but not Mo-CODHs. Thus, Ni-CODHs are restricted to oxygen-limited niches, while Mo-CODHs occur across both oxygenated and oxygen-limited marine environments. Phylogenetic analyses indicated that all previously described CODH clades are represented in the marine ecosphere, highlighting their evolutionary diversity. Genome context analyses suggest that approximately 50% of the marine Ni-CODH potentially participate in carbon fixation via the Wood-Ljungdahl pathway, whereas most marine Mo-CODH likely contribute to the supplementary energy conservation. Together, these results provide an integrated view of CODH distribution and potential function in marine ecosystems.}, } @article {pmid42236101, year = {2026}, author = {Borghi, E and Tassi, L and d'Orsi, G and Uzzau, S and Pivari, F and Ricci, E and Longoni, G and Mingarelli, A and Previtali, R and Berardi, R and De Diego, L and Vigano', I and Olivotto, S and Compierchio, E and Veggiotti, P and Canevini, MP and Vignoli, A}, title = {Microbiota-gut-brain axis and treatment resistance in epilepsy: a multicentre prospective study protocol (CARE).}, journal = {BMJ open}, volume = {16}, number = {6}, pages = {e111607}, pmid = {42236101}, issn = {2044-6055}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Anticonvulsants/therapeutic use ; *Brain/physiopathology ; Diet, Ketogenic ; *Drug Resistant Epilepsy/therapy/microbiology ; *Epilepsy/therapy ; *Gastrointestinal Microbiome/physiology ; Italy ; Longitudinal Studies ; Prospective Studies ; Quality of Life ; Vagus Nerve Stimulation ; }, abstract = {INTRODUCTION: Approximately one-third of people with epilepsy (PWE) experience resistance to treatment, including pharmacological therapies, epilepsy surgery, vagus nerve stimulation (VNS) and dietary interventions such as the ketogenic diet (KD). Emerging evidence suggests that the gut microbiota may influence seizure susceptibility and treatment response through the microbiota-gut-brain axis, potentially contributing to treatment resistance. The MiCrobiota-gut-brain Axis in Resistant Epilepsy project investigates how gut microbial features and associated host epigenetic signatures affect clinical outcomes in PWE undergoing diverse treatment strategies.

METHODS AND ANALYSIS: This is a multicentre, prospective, longitudinal study involving four clinical centres in Italy and one self-financing partner. Participants aged 3-50 years will be enrolled and stratified into four intervention cohorts: newly diagnosed drug-naïve epilepsy scheduled to start anti-seizure medications, focal drug-resistant epilepsy (DRE) undergoing epilepsy surgery, DRE receiving VNS, and DRE initiating KD. Clinical assessments (including body mass index calculation, self-reported monthly seizure count, dietary evaluation, quality of life scale and gastrointestinal symptoms scale), electroencephalography, MRI and biological sample collection (stool and blood) will be obtained at baseline and longitudinally at two or three timepoints over a 12-month observation period. Gut microbiota changes over time will be assessed via metagenomics (using 16S ribosomal RNA sequencing) and metaproteomics; the associated host DNA methylation profiles will be obtained from blood using Illumina EPIC arrays. Primary endpoints include identification of microbial or host methylation changes predictive of therapeutic response (ie, reduction from baseline in monthly seizure count) to the intervention. Data will be analysed using multivariate models and mixed-effect regression. Further, omics data and corresponding metadata will be integrated using multi-omics approaches to identify molecular signatures biomarkers predictive of treatment response and prognosis in PWE.

ETHICS AND DISSEMINATION: The study received ethical approval from the Research Ethic Board (Comitato Etico Territoriale Lombardia 3, ID 4896 - parere numero 4896_17.07.2024_N_bis). All participants or their legal guardians will provide written informed consent. Results will be disseminated through peer-reviewed publications, conference presentations or lay summaries targeting patient organisations.

TRIAL REGISTRATION NUMBER: ClinicalTrials.gov Identifier NCT07010445, registered on 2 May 2025.}, } @article {pmid42236489, year = {2026}, author = {Kehl, AJ and Taylor-Kearney, L and Jaffe, AL and Pereira, JH and Lee, J and Hammel, M and Waldburger, LM and Yeow, C and Valentin-Alvarado, L and Adams, PD and Banfield, JF and Siegel, JB and Prywes, N and Shih, PM}, title = {Diversity-driven biochemical survey reveals widespread dimerization throughout the rubisco superfamily.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73982-5}, pmid = {42236489}, issn = {2041-1723}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, abstract = {Rubisco is the entry point of nearly all organic carbon into the biosphere and is present in all domains of life. Despite its global importance, biochemical studies of this enzyme superfamily have been limited to a relatively narrow set of subclades. Recent advances in metagenomics have dramatically reshaped our understanding of both microbial and rubisco diversity; however, biochemical characterization of these sequences has not kept pace with the exponential growth in sequence data. To better survey the functional and structural diversity of rubisco, we systematically sample and synthesize a library of diverse rubisco sequences with an emphasis on clades that are sparsely represented in the biochemical literature. Our updated phylogenetic analysis reveals that many deep‑branching rubiscos assemble as dimers, supporting a dimeric origin for the superfamily - in contrast to the ecologically dominant hexadecameric form I. Additionally, we discover and structurally characterize an unusually large catalytic subunit among characterized rubiscos, originating from a early-branching subclade with secondary structural elements not present in canonical rubisco architectures.}, } @article {pmid42236734, year = {2026}, author = {Wei, Y and Xiao, J and He, J and Zhang, K and Xu, C and Zhang, N and Cheng, L}, title = {An integrated global resource of wetland microbiomes linking environmental metadata, community profiles, and genome-resolved metabolic traits.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07581-w}, pmid = {42236734}, issn = {2052-4463}, support = {32501490//National Natural Science Foundation of China/ ; 32501489//National Natural Science Foundation of China/ ; 32571850//National Natural Science Foundation of China/ ; 32430070, 32025024 and 92251305//National Natural Science Foundation of China/ ; LQ24C030001//Zhejiang Provincial NSFC/ ; LQ21C030009//Zhejiang Provincial NSFC/ ; LZ24C030001//Zhejiang Provincial NSFC/ ; JYB2025XDXM909//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; }, abstract = {Wetlands are biogeochemical hotspots pivotal to global carbon and nutrient cycling, yet genome-resolved studies across diverse wetland types remain limited. To address this, we constructed a global wetland metagenomic dataset, integrating environmental metadata, community profiles, and genome-resolved metabolic traits. This dataset comprises 1,962 samples-including 129 newly sequenced field-collected samples-from lakes, rivers, paddies, marshes, and coastal wetlands, spanning water, soil, and sediment habitats. We generated comprehensive taxonomic profiles for all 1,962 samples, and used 251 samples to reconstruct 5,704 sample-specific metagenome-assembled genomes (MAGs). These MAGs were subsequently dereplicated to establish a normalized, non-redundant catalog of 4,164 representative genomes. We further mapped gene repertoires to 549 KEGG modules to decode the metabolic potential of all 5,704 MAGs. This dataset depicts an overview of microbial genomic diversity across global wetlands and provides a comprehensive resource for understanding the metabolic capabilities, ecology, and evolution of wetland microbiomes.}, } @article {pmid42237168, year = {2026}, author = {Hou, X and Fu, Y and Jia, Z and Hou, L and Yin, Y and Xu, K}, title = {Multi-omics elucidates the regulatory mechanisms of tryptophan in gut health of weaned piglets.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42237168}, issn = {2524-4671}, support = {CARS-35//China Agriculture Research System of MOF and MARA/ ; 2023JJ20043//Natural Science Foundation of Hunan Province Project/ ; 32372913//National Natural Science Foundation of China/ ; 2023RC3204//Science and Technology Innovation Program of Hunan Province/ ; }, abstract = {Tryptophan (Trp), an essential amino acid (AA) implicated in diverse physiological and pathological processes, remains incompletely characterized in its mechanisms regulating intestinal health in weaned piglets. In this study, 27 weaned Bama miniature pigs with highly homogeneous genetic characteristics (6.200 ± 0.242 kg) were randomly divided into three groups and fed a basal diet, a diet supplemented with 0.5-fold Trp, or a diet supplemented with 1.5-fold Trp for 21 days. We used multi-omics approaches to investigate the mechanisms by which Trp regulates intestinal health through dietary interventions with different concentrations. Both Trp-supplemented groups exhibited significantly reduced diarrhea incidence (P = 0.012) and improved intestinal morphology compared to the control group (P < 0.05). While Trp-targeted metabolomics showed no statistically significant alterations, metagenomic analysis revealed Trp-driven microbial remodeling, characterized by increased α-diversity, elevated abundances of Deferribacteres, Turicibacter, Clostridials_Bacteria, and Turicibacter_Sanguinis, alongside decreased Tenericutes and Chryseobacterium. Transcriptome analysis further identified immune-related pathways as central targets of Trp action. Subsequent cytokine quantification confirmed Trp's immunomodulatory effects: pro-inflammatory cytokines (IL-1β, IL-6, IL-17) decreased, while anti-inflammatory IL-10 increased. Collectively, our findings demonstrate that Trp alleviates weaning-associated intestinal dysfunction by reshaping microbial ecosystems and regulating immune homeostasis.}, } @article {pmid42237383, year = {2026}, author = {Zhang, J and Shi, X and Peng, S and Zhang, C and Qiao, S and Yu, H}, title = {Icariin shapes post-withdrawal fecal resistome dynamics in layer hens.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42237383}, issn = {1674-9782}, support = {B2024064//Hubei Provincial Department of Education Scientific Research Project/ ; 2025RZ026//Research and Innovation Initiatives of Wuhan Polytechnic University/ ; 202409//Open Fund of Hubei Province Key Laboratory of Animal Nutrition and Feed Science/ ; 32402807//Young Scientists Fund of the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: While the livestock industry actively seeks alternatives to antibiotics, residual low-dose exposures continue to drive the spread of antibiotic resistance genes (ARGs). Icariin, a plant-derived compound, is recognized for improving poultry growth and immunity. However, it remains unclear how this compound influences the environmental persistence of ARGs, mobile genetic elements (MGEs), and horizontal gene transfer (HGT) during the vulnerable recovery phase after antibiotic withdrawal.

RESULTS: We designed a two-phase feeding trial with laying hens, using longitudinal metagenomic sequencing to track post-withdrawal resistance dynamics. Following initial exposure to a low-dose antibiotic mixture that established a baseline of elevated resistance, hens received either a basal diet, an icariin-supplemented diet, or a copper sulfate-supplemented diet. The data indicate that icariin supplementation consistently reduced the burdens of both ARGs and MGEs. It also suppressed the potential for HGT and restricted the diversity of microbial hosts harboring these resistance elements. Conversely, copper sulfate-a traditional metal-based additive-exacerbated resistance risks by expanding both the abundance and the host range of ARGs and MGEs. Across all treatments, the population of Escherichia and the prevalent ARG subtype bacA correlated strongly with total resistance loads, tracking the overall resistome burden.

CONCLUSIONS: Compared to conventional copper sulfate treatments, icariin facilitates a safer ecological recovery in the poultry gut by actively lowering ARG and MGE reservoirs after antibiotic withdrawal. These genomic insights, combined with its known physiological benefits, support icariin as a sustainable feed additive. Furthermore, the Escherichia-bacA correlation provides a reliable, streamlined indicator for monitoring resistance risks in farm environments. However, as these findings rely on short-term fecal metagenomic tracking, further validation through multi-environment studies is warranted.}, } @article {pmid42237400, year = {2026}, author = {Liu, J and Huang, W and Wu, X and Ma, Y}, title = {Coronavirus disease 2019-associated encephalitis and concomitant subdural hematoma: a case report.}, journal = {Journal of medical case reports}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13256-026-06148-y}, pmid = {42237400}, issn = {1752-1947}, support = {82171350//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Coronavirus disease 2019 (COVID-19), induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents a global pandemic with evolving viral variants. In addition to respiratory symptoms, a growing trend of reports indicates that the central nervous system could also be affected in COVID-19 patients.

CASE PRESENTATION: Herein, we reported a case of a 61-year-old Chinese male with fever, psychiatric symptoms, and concomitant subdural hemorrhage. Although naso-oropharyngeal swab tests for SARS-CoV-2 ribonucleic acid detections were negative, the metagenomic next-generation sequencing from cerebrospinal fluid (CSF) samples showed the exclusive positive finding of SARS-CoV-2. The patient was diagnosed with probable COVID-19-associated encephalitis, and was recovered after receiving anti-infection medications, high-dose methylprednisolone pulses (1 g/day for 5 days), and subsequent intravenous immunoglobulin (0.4 g/kg body weight for 5 days) therapies.

CONCLUSION: Our case underscores the importance that for patients with fever and unexplained neuropsychiatric symptoms, it is recommended to conduct CSF testing to screen for possible pathogen infections, and to perform cranial imaging promptly to detect concomitant lesions.}, } @article {pmid42237409, year = {2026}, author = {Guo, D and Chen, Y and Wu, Y and Cheng, J and Lin, Y and Lai, W and Ma, W and Yang, H and Han, L and Ma, L and Jia, H and Liu, X}, title = {Multi-omics characterization of the skin microbiota reveals the anti-aging roles of Stenotrophomonas maltophilia.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02433-6}, pmid = {42237409}, issn = {2049-2618}, support = {WDZC20220819134430002//Shenzhen Science and Technology Program/ ; QD2021005N//Scientific Research Start-up Funds/ ; }, abstract = {BACKGROUND: Shifts in the skin microbiome have shown a close link to chronological age. However, the contribution of the skin microbiome in skin-aging phenotypes remains unclear.

RESULTS: To explore this, we performed phenotypic, metabolomic, metagenomic, and functional analyses on a cohort with divergent skin-aging phenotypes. Genome-scale metabolic models (GEMs) integrated with metabolomic analysis revealed that Stenotrophomonas maltophilia, enriched in the younger group (categorized by AI-predicted age and skin elasticity), utilizes the glutathione cycle to maintain redox homeostasis. Cellular experiments showed its metabolites enhanced GSH synthesis and alleviated oxidative-stress-induced phenotypic skin-aging by upregulating key genes in fibroblasts, including GCLM, PGD, SOD2, and NQO1. In addition, GEMs highlighted its potential in maintaining youthful skin phenotypes through the regulation of host metabolic pathways involving betaine, lysolecithin, and porphyrin. In parallel, Acinetobacter guillouiae was found to influence host melanin metabolism by degrading dopamine (DA) and 3-methoxytyramine (3-MT), offering potential therapeutic strategies for mitigating pigmentation.

CONCLUSIONS: Our findings highlight the dynamic interplay between skin microbiota and the host in phenotypic skin-aging, offering new insights for designing interventions to maintain youthful skin. Video Abstract.}, } @article {pmid42237424, year = {2026}, author = {Yang, L and Chen, J}, title = {mPower: a real data-based power analysis tool for microbiome study design.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02427-4}, pmid = {42237424}, issn = {2049-2618}, support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; }, abstract = {Power analysis is a critical step in designing a microbiome study. Existing power calculation tools for microbiome studies mainly rely on parametric models of the sequencing counts, which underestimate the complexity of microbiome data and could produce overly optimistic power estimates. In this work, we present a new simulation-based power analysis tool, mPower, for microbiome study design. The tool uses a real data-based semi-parametric simulation framework to generate realistic microbiome data, upon which the power assessment is performed. Coupled with a select differential analysis tool, our power tool supports different study designs, including cross-sectional, case-control, and matched-pair studies, with or without confounders. It allows power analysis for both community-level and taxon-level testing. By using microbiome reference datasets from different environments, the users could perform power calculation based on the environment of interest. The mPower is primarily designed for 16S amplicon sequencing data, and it also incorporates a parametric simulation framework that enables power analysis for shotgun metagenomic data. We showcase the application of mPower with several real-world examples. The web interface of mPower is available at https://microbiomestat.shinyapps.io/mPower/. Video Abstract.}, } @article {pmid42237575, year = {2026}, author = {Tilves, C and Xiao, S and Tanaka, T and Differding, MK and Spira, AP and Ferrucci, L and Mueller, NT}, title = {Longitudinal associations of the gut microbiome with arterial stiffness in US adults: findings from the Baltimore Longitudinal Study of Aging.}, journal = {American journal of epidemiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/aje/kwag119}, pmid = {42237575}, issn = {1476-6256}, abstract = {The gut microbiome affects arterial stiffness in experimental murine models; however, evidence in human longitudinal studies is lacking. In this study, we investigated longitudinal between-person (average) and within-person (change) associations of microbiome features with arterial stiffness. We assessed the fecal microbiome using whole genome metagenomic sequencing, and arterial stiffness using carotid-femoral pulse wave velocity (cfPWV). Our analytic sample consisted of 349 adults from the Baltimore Longitudinal Study of Aging, who contributed 915 visits between 2013-2019. Using linear mixed models, we found higher microbiome evenness and butyrate-producing bacteria were associated with lower cfPWV on average (between-person), but changes in diversity were not associated with changes in cfPWV (within-person). Several potentially pathogenic bacteria were positively associated with cfPWV, both between- and within-person. Butyrate-production pathways were inversely associated with cfPWV between-person and borderline within-person. Trimethylamine-production genes were positively associated with cfPWV between-person and borderline within-person. In addition, changes in other functional pathways including peptidoglycan biosynthesis and L-arginine biosynthesis were associated with changes in cfPWV. In conclusion, cfPWV was associated with both between-person and within-person differences in gut microbiome features, with strength and consistency depending on the feature. These results can inform which microbiome features to target in interventions to improve arterial stiffness.}, } @article {pmid42237904, year = {2026}, author = {Lei, H and Du, S and Li, C and Yung, L and Wang, P and Leung, LY and Graham, CA and Yen, HL and Li, Y and Lucaci, AG and Mason, CE and Lee, PKH}, title = {Sustained Chlorination of Hospital Surfaces Restructures the Microbiome and Virome and Diversifies Resistance Genes.}, journal = {Environmental science & technology}, volume = {60}, number = {23}, pages = {16514-16525}, doi = {10.1021/acs.est.6c01505}, pmid = {42237904}, issn = {1520-5851}, mesh = {*Microbiota ; Halogenation ; Hospitals ; Disinfection ; *Virome ; Drug Resistance, Microbial/genetics ; }, abstract = {Routine disinfection can reduce microbial burden on hospital surfaces in the short term, but its long-term impacts on surface microbiomes and antimicrobial resistance dynamics remain unclear. We conducted a year-long metagenomic study of 197 in situ hospital surface samples subjected to sustained chlorination to investigate changes in microbiomes, resistomes, and phage-host interactions. Microbial α-diversity increased during the early months, with a decline in dominant Enterobacteriaceae and enrichment of taxa including Propionibacteriaceae and Micrococcaceae, indicating niche replacement. Over time, both diversity and previously suppressed taxa approached baseline levels, suggesting adaptation to sustained disinfection, with evidence of functional shifts. Viral communities exhibited similar temporal dynamics, with composition and relative abundance distinctly shifting. Concurrently, the resistome underwent substantial, largely irreversible restructuring, with decreased total relative abundance and increased diversity of antibiotic resistance genes (ARGs). Chlorination also reduced ARG mobility and pathogenic potential, indicated by weakened co-occurrence with mobile genetic elements and virulence factor genes and lower predicted resistome risks. Phage and host relative abundances remained strongly correlated, although a shift toward lytic viral lifestyles occurred, potentially limiting phage-mediated ARG dissemination. These findings highlight disinfection as both a microbial control measure and ecological pressure, underscoring the need for ecologically informed strategies to manage clinical antimicrobial resistance.}, } @article {pmid42237982, year = {2026}, author = {Utreja, S and Andreani, GA and Mahmood, S and Patel, MS and Buck, MJ and Rideout, TC}, title = {Dietary pulse prebiotic fibre intake in a rat obese pregnancy model alters maternal caecal microbiome and protects against steatosis in newly weaned offspring.}, journal = {Journal of nutritional science}, volume = {15}, number = {}, pages = {e37}, pmid = {42237982}, issn = {2048-6790}, mesh = {Animals ; Female ; Pregnancy ; *Dietary Fiber/administration & dosage/pharmacology ; *Cecum/microbiology ; Rats, Sprague-Dawley ; *Prebiotics/administration & dosage ; Male ; *Fatty Liver/prevention & control ; *Maternal Nutritional Physiological Phenomena ; Fatty Acids, Volatile/metabolism ; Rats ; *Gastrointestinal Microbiome/drug effects ; Lactation ; Weaning ; *Obesity ; Liver/metabolism ; }, abstract = {We assessed if supplementation of an obese-inducing diet with yellow pea fibre throughout pre-pregnancy (PP), gestation, and lactation could influence maternal gut microbiome composition and improve metabolic health and liver steatosis in newly weaned rat male and female offspring. Forty female Sprague-Dawley rats were fed a low (CON) or high (HC) calorie diet for a 6-week PP period. At the end of PP, HC animals were randomly assigned to either remain on the HC diet or the HC diet with yellow pea fibre (HC + FBR) for an additional 4-weeks prior to mating and throughout gestation and lactation. At the end of lactation, caecal microbiome profile was evaluated in mothers with shotgun metagenomic sequencing, and newly weaned male and female pups were assessed for serum biochemistry and hepatic fat outcomes. Maternal obesity reduced the beta-diversity of the maternal microbiome and lowered total caecal short-chain fatty acid (SCFA) concentration. HC + FBR consumption increased caecal SCFA concentration and differentially altered the maternal caecal microbiome profile of several species that have been linked with hepatic steatosis including Bifidobacterium pseudolongum, Porphyromonas gingivalis, and several Provetella species. Newly weaned offspring from HC mothers exhibited hepatic steatosis; however, male and female pups from HC + FBR mothers demonstrated normalised liver lipid concentrations (cholesterol and triglyceride) and an increase in caecal acetate and propionate concentrations. Findings suggest that maternal obesity enhances the risk of liver steatosis in offspring and that maternal dietary fibre supplementation may have a protective influence that is partly mediated through changes in the caecal microbiome profile and activity.}, } @article {pmid42238272, year = {2026}, author = {Gallina, G and Pizzi, C}, title = {Reference-free k-mer based dissimilarity measures for metagenomes comparison.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1788907}, pmid = {42238272}, issn = {2673-7647}, abstract = {MOTIVATION: Metagenomics plays a crucial role in unraveling the relationship between microbial communities and the environment in which they live, allowing the development of food and environmental control techniques. Similarly, the study of microbial environments within the human body plays a crucial role towards precision medicine. In these contexts, the problem of metagenomic samples comparison is among the most challenging from the computational point of view due to the size of the datasets and to the incompleteness of microbial databases. Thus, the ability to define and efficiently compute reference-free dissimilarity measures is key to the development of effective and practical tools for metagenomes comparison.

RESULTS: In this work, we present a systematic experimental validation of reference-free k -mer-based dissimilarity measures. To this purpose, we investigate the correlation between two popular ecological dissimilarity measures, Bray-Curtis and Jaccard, computed using reference-free and reference-based k -mer approaches, for 12 ≤ k ≤ 31 . Our experiments cover both simulated and real metagenomics settings (samples from the human body and the oceans), and consider both linear and ranking correlation between the computed values. Our results support the hypothesis that the two definitions are indeed correlated for a wide range of values of k , and promote the development of efficient reference-free computational tools based on k -mer statistics for metagenomes comparison.}, } @article {pmid42238651, year = {2026}, author = {Zhang, Q and Zhang, X and Cao, M and Ma, J and Yan, R and Wang, H and Jia, S}, title = {Study on the Role and Mechanism of γδ T Cells in Atherosclerosis Under a High-Fat Diet.}, journal = {Reviews in cardiovascular medicine}, volume = {27}, number = {5}, pages = {48002}, pmid = {42238651}, issn = {2153-8174}, abstract = {BACKGROUND: This study aimed to investigate the effects of γδ T cell inhibition under a high-fat diet (HFD) on metabolic function, immune inflammation, gut microbiota, and atherosclerosis (AS) progression in ApoE [-/-] mice.

METHODS: ApoE [-/-] mice were assigned to three groups: a control group (normal diet), a model group (HFD), and an intervention group (HFD + γδ T cell receptor (TCR) monoclonal antibody). After 12 weeks, flow cytometry was used to assess γδ T cell levels, and cytokines (interferon-gamma (IFN-γ), IL-17A) were measured. Inflammatory markers in blood and adipose tissue were quantified, gut microbiota composition was analyzed via fecal metagenomics, and atherosclerosis was evaluated using Oil Red O, Masson's trichrome, and hematoxylin and eosin (HE) staining methods.

RESULTS: The HFD activated γδ T cells and increased pro-inflammatory cytokines in ApoE [-/-] mice. Treatment with the γδ TCR monoclonal antibody suppressed γδ T cells, reduced IFN-γ and IL-17A expression, improved lipid profiles, and decreased tumor necrosis factor-alpha (TNF-α), IL-1β, and IL-6 levels. Gut microbiota analysis showed an increase in beneficial bacteria, and histological staining (Oil Red O, HE, and Masson's trichrome) confirmed a reduction in atherosclerotic lesion burden.

CONCLUSION: The γδ T cells contribute to AS development under the HFD. Inhibition of γδ T cells reduces inflammation, improves gut microbiota composition, and attenuates atherosclerosis progression.}, } @article {pmid42238901, year = {2026}, author = {Zhao, T and Chen, Y and Sun, H}, title = {A case of severe Legionella pneumonia treated with omadacycline and nemonoxacin.}, journal = {Respiratory medicine case reports}, volume = {62}, number = {}, pages = {102437}, pmid = {42238901}, issn = {2213-0071}, abstract = {Severe Legionella pneumophila pneumonia carries high mortality, and treatment is challenged by emerging resistance to conventional fluoroquinolones/macrolides and diagnostic delays. Novel agents such as omadacycline and nemonoxacin show theoretical promise, yet robust clinical evidence in legionellosis is lacking. We report a 59-year-old man with severe community-acquired pneumonia(sCAP) who initially received empiric ceftazidime-avibactam plus nemonoxacin. Respiratory failure did not improve, and the inflammatory markers did not decline. Subsequent bronchoalveolar lavage fluid metagenomic next-generation sequencing(BALF-mNGS) and urinary Legionella antigen confirmed Legionella pneumonia. We then switched to dual therapy with omadacycline and nemonoxacin. The combination led to rapid improvements in inflammatory markers, hypoxemia, and creatine kinase levels. This case provides a clinical rationale for using omadacycline plus nemonoxacin as salvage therapy in severe Legionella pneumonia when conventional regimens fail.}, } @article {pmid42239023, year = {2026}, author = {Tang, F and Liu, H and Xi, L and Li, C and Wang, X and Wang, B}, title = {Solid-phase enrichment uncovers a hidden Salmonella transmission chain in a recurrent pediatric household cluster: a case report.}, journal = {Frontiers in public health}, volume = {14}, number = {}, pages = {1820049}, pmid = {42239023}, issn = {2296-2565}, mesh = {Humans ; Male ; Child, Preschool ; *Salmonella Infections/transmission/diagnosis/microbiology ; Feces/microbiology ; Recurrence ; *Salmonella/isolation & purification ; Family Characteristics ; Metagenomics ; Shotgun Sequencing ; }, abstract = {OBJECTIVES: To describe a household cluster of recurrent pediatric non-typhoidal Salmonella (NTS) infection and compare the yield of conventional culture, solid-phase enrichment, and shotgun metagenomic sequencing across symptomatic children and household contacts.

METHODS: Longitudinal fecal specimens from a 4-year-old boy (Mo) with three discrete NTS episodes in 2 months, his monozygotic twin (TB), and three adult co-residents were processed by conventional culture; specimens from Episode 2 onwards and all contact specimens additionally received solid-phase enrichment, and a subset shotgun metagenomics. Isolates were characterized by VITEK 2, XbaI-PFGE, and whole-genome sequencing.

RESULTS: None of Mo's episodes met sepsis criteria (peak WBC 12.52 × 10?/L, CRP 5.46 mg/L, PCT 1.14 ng/mL); TB had one self-limited episode, both parents had brief symptomatic periods, and the grandmother was asymptomatic. Conventional culture was positive only at Mo's first episode, whereas solid-phase enrichment recovered Salmonella from three culture-negative pediatric acute-phase specimens (Mo 4.12, TB 4.16, Mo 5.1). Adult contacts were negative by both culture-based methods, but metagenomic sequencing detected Salmonella reads in all three. Mo_0412 and TB_0416 were S. enterica serovar Enteritidis ST11, with identical cgMLST, 99.9966% ANI, and 97% PFGE similarity, indicating a clonal household source. Mo received antibiotics across four classes during his recurrences, vs. two sequential agents in TB.

CONCLUSION: Conventional culture, solid-phase enrichment, and metagenomic sequencing functioned as complementary modalities, each recovering Salmonella the others missed, supporting a tiered diagnostic strategy for household NTS investigation. Cumulative antibiotic exposure may have contributed to Mo's differential susceptibility, a hypothesis warranting prospective study.}, } @article {pmid42239051, year = {2026}, author = {Lalgudi, C and Kotaka, M and Yaffe, E and Lopez, JA and Yu, FB and Ng, K and Sonnenburg, JL and Good, BH and Huang, KC and Shi, H}, title = {Path-dependent recovery of the gut microbiome after antibiotics emerges from coupled ecological and evolutionary dynamics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.22.727306}, pmid = {42239051}, issn = {2692-8205}, abstract = {Recovery of the gut microbiome after antibiotic exposure is often incomplete and variable, and the processes underlying this variation remain unclear. We performed longitudinal shotgun metagenomic sequencing of 2876 daily fecal samples from replicated humanized and conventional mouse cohorts exposed to controlled antibiotic perturbations. Metagenomic profiling recapitulated ecological trajectories previously observed by 16S sequencing, while revealing extensive strain-level dynamics, including reproducible sweeps of standing variants and de novo mutations in antibiotic target sites and regulatory loci. We also identified genetic changes whose effects depended on community composition, competitive release, and perturbation history. Cross-housing experiments revealed bidirectional strain transfer, with antibiotic-induced niche clearance enabling replacement of resident strains. In parallel, phage dynamics were heterogeneous and clustered by cage. Together, these findings show that post-antibiotic microbiome recovery is a path-dependent process shaped by selection, transmission, and phage activity, producing divergent outcomes even among closely matched communities exposed to the same perturbations.}, } @article {pmid42239166, year = {2026}, author = {Ghadermazi, P and Emerson, JB and Olm, MR}, title = {ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42239166}, issn = {2692-8205}, abstract = {Strain-resolved metagenomics characterizes microbial communities at nucleotide-level resolution, enabling researchers to differentiate identical from closely related organisms and characterize population structure and gene content variation. Here we introduce ZipStrain, a program that performs highly accurate strain-resolved metagenomics over 500× faster than available methods while offering superior RAM management. Applied to a dataset of 2,754 samples spanning human populations, we identify a strain-sharing gradient across social relationships, reveal striking variation in clonal structure across bacteria and bacteriophage, and pinpoint genes whose nucleotide identity deviates from genome-wide expectations. ZipStrain is distributed as an open-source Python package and accompanying Nextflow pipeline at https://github.com/OlmLab/ZipStrain.}, } @article {pmid42239183, year = {2026}, author = {Cirolia, G and Gustafson, JT and Aswani, A and Wolf, A}, title = {Performance of IBD machine learning classifiers varies across microbiome training data independent of geographic diversity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.21.727052}, pmid = {42239183}, issn = {2692-8205}, abstract = {Microbiome-based machine learning classifiers show increasing promise for disease identification across gastrointestinal, metabolic, and immune-mediated conditions. Inflammatory bowel disease (IBD), a chronic immune-mediated disorder associated with disruption of the gut microbiome, has been a particularly successful application area. However, while many predictive models achieve high performance within individual datasets, their ability to generalize across independent populations and geographic contexts remains unclear. Here, we tested whether model class and training dataset composition influence model generalizability across geographically diverse evaluation studies. We compiled seven publicly available shotgun metagenomic studies spanning five geographic regions, comprising 697 individuals with IBD or healthy controls. We trained 246,986 model configurations across seven model classes and five distinct training dataset combinations and evaluated top-performing models on independent studies from the USA, Ireland, Germany, Israel and China. Extreme gradient boosting and random forest models showed the highest and most consistent performance across training datasets, a ranking that was maintained on independent evaluation studies. However, models trained on geographically diverse datasets did not outperform those trained on USA-only datasets. Instead, model performance was strongly dependent on the evaluation study itself, with consistent differences in achievable accuracy across studies. Despite most models achieving similar AUC scores, there was limited overlap in the key microbial species identified. Furthermore, even for the small set of disease predictive microbes shared between models, the direction of enrichment between IBD or healthy subjects often varied in opposing directions across study populations. These findings suggest that study-specific factors constrain generalization and may help explain the lack of consistent microbiome-based biomarkers for IBD.}, } @article {pmid42239221, year = {2026}, author = {Keown, RA and Sikkema, AP and Barbone, VA and Ferrell, BD and Donnelly, OB and Iredell, SC and Zatopek, KM and Brumm, PJ and Mead, DA and Lohman, GJS and Wommack, KE and Polson, SW}, title = {Single amino acid substitution in DNA Polymerase I dramatically alters infection dynamics of bacteriophage T7.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42239221}, issn = {2692-8205}, abstract = {Viruses constitute a significant proportion of Earth's genetic diversity, yet most remain uncharacterized beyond their sequences in viral metagenomes. Linking viral genotypes to phenotypes-especially enzyme function to phage infection dynamics-is challenging due to the lack of cultured virus-host systems. DNA polymerase I (PolA), essential for genome replication in ~25% of dsDNA phages, provides an opportunity to explore these connections. In phage T7, residue 526 is critical for nucleotide incorporation, with previous in vitro evidence indicating impacts on enzyme efficiency and fidelity. Previous analyses identified three substitutions at this position (Tyr/Y, Phe/F, Leu/L) linked with deeply rooted viral PolA clades. Mutation impacts at residue 526 were tested in vitro and in vivo. The Y526F protein exhibited a 50% reduction in specific activity, and when introduced via High Complexity Golden Gate Assembly into T7 demonstrated a 53% decrease in burst size and significantly longer latent period compared to wild type. The Y526L protein exhibited a 97% decrease in activity, and the Y526L phage was incapable of completing its lifecycle. These findings confirm historical biochemical data, provide in vivo context for these mutations in the T7-E. coli system, and offer experimental support for genotype-to-phenotype associations in viral PolA, informing viral metagenomics studies.}, } @article {pmid42239239, year = {2026}, author = {Cho, Y and Tsuboyama, K and Litberg, TJ and Jung, MD and Obisesan, A and Wang, Q and Phoumyvong, CM and Thibeault, J and Ovchinnikov, S and Rocklin, GJ}, title = {Accurate protein stability prediction for small domains using mega-scale experiments.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42239239}, issn = {2692-8205}, abstract = {Predicting absolute protein folding stability is a long-standing challenge in biophysics, with broad applications in protein design and in understanding genetic variation and evolution. Physics-based simulations have shown limited success at predicting stability and are often computationally intractable, and machine learning methods have been constrained by the lack of sufficiently large experimental datasets. We recently introduced cDNA display proteolysis, a cell-free approach that can measure folding stability for nearly one million protein domains in parallel. Here, we applied this method to measure stability for 1.8 million diverse protein domains 60-80 amino acids in length primarily taken from the MGnify metagenomic database and spanning over 200,000 sequence families. Using this new "MGnify Stability dataset", we developed the predictive models SaProtΔG and ESM3ΔG, which accurately predict absolute folding stability for small domains with root mean squared error of 0.8 kcal/mol over a 6 kcal/mol range (Spearman rank correlation of 0.88). These predictors show high accuracy at predicting effects of substitutions, insertions, and deletions, successfully identify global trends toward higher stability in thermophilic organisms, and improve discrimination of stable and unstable computationally designed proteins. Our results illustrate how megascale biophysical measurements can complement existing evolutionary and structural data to enable accurate absolute stability prediction for small domains.}, } @article {pmid42239480, year = {2026}, author = {Qian, J and Ghadermazi, P and Maret, S and Kemp, JF and Frank, D and Melanson, EL and Hendricks, AE and Krebs, N and Tang, M and Olm, MR}, title = {IgA Targeting in the Infant Gut Is Modulated by Diet and Increasingly Directed Towards Persistent Species.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.19.726352}, pmid = {42239480}, issn = {2692-8205}, abstract = {BACKGROUND: IgA is the dominant antibody in the human gut and a key regulator of host-microbe interactions. Infants begin to produce IgA at around 6 months old and receive large quantities of IgA via human milk, but technical limitations have prevented species-level characterization of IgA binding in early life. This has left basic knowledge gaps about which species are targeted by IgA in infancy, and how modifiable lifestyle factors like breastfeeding and complementary feeding impact IgA targeting.

RESULTS: Here we adapt Metagenomic Immunoglobulin Sequencing (MIg-Seq) for low-biomass infant fecal samples and apply this optimized protocol to 32 longitudinal samples from 16 infants enrolled in the MINT trial, a four-arm randomized controlled trial comparing meat-based, dairy-based, plant-based, and reference complementary feeding patterns, with fecal sampling at 6 and 12 months (pre and post intervention). Infant IgA targeting mirrors adults at the phylum level, with both age groups showing significantly higher IgA targeting of Pseudomonadota and lower targeting of Bacteroidota relative to other phyla. During the substantial microbiome compositional shifts noted between 6 and 12 months, IgA targeting is significantly more stable than the microbiome itself. Among persistent colonizers, IgA targeting strengthens significantly from 6 to 12 months, with the most pronounced effect observed for Bifidobacterium , a finding robust across all dietary arms and feeding modes. The feeding arm to which infants were enrolled was not significantly associated with IgA binding, but several nutrient-specific associations were discovered. Animal-derived nutrients, particularly cholesterol, are strongly positively correlated with IgA targeting of Bifidobacterium longum , while plant-derived carotenoids are positively associated with IgA targeting of Flavonifractor plautii and Ruminococcus gnavus .

CONCLUSIONS: This study introduces an experimental and computational framework for species-level IgA profiling in the infant gut. The progressive strengthening of IgA targeting of Bifidobacterium and other beneficial persistent colonizers suggests a role for IgA in reinforcing beneficial microbes during infancy. The nutrient-specific dietary effects on IgA targeting reveal the immunological consequences of the complementary feeding period, and highlight a contrast between animal-versus plant-based diets. Together, these findings point to early nutritional interventions and IgA-based therapeutics as promising tools for promoting healthy immune-microbiome development.}, } @article {pmid42239539, year = {2026}, author = {Jiang, X and Chen, B and Wang, Q and Liu, Y and Li, N and Zhang, L}, title = {Structural variation analysis suggests strain-level maternal-infant microbial transmission in early life.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1765801}, pmid = {42239539}, issn = {2235-2988}, mesh = {Humans ; Female ; Metagenomics ; Infant ; *Infectious Disease Transmission, Vertical ; *Microbiota/genetics ; *Genomic Structural Variation ; *Bacteria/genetics/classification ; Infant, Newborn ; Metagenome ; Mothers ; Longitudinal Studies ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; }, abstract = {INTRODUCTION: Structural variations (SVs)-large, functionally consequential genomic alterations-serve as high-resolution markers for strain-level differentiation in the human microbiome, yet their relevance to vertical transmission of the maternal microbiota and early-life colonization remains unclear.

METHODS: Using metagenomic data from a 98-pair longitudinal mother-infant cohort and a 25-pair multi-niche cohort, we profiled microbial taxa, functions, and SVs, characterized variable SVs (vSVs), deletion SVs (dSVs), and transmitted SVs (tSVs), and evaluated the potential influence of delivery mode, feeding regimen, and maternal ecological niches.

RESULTS: We identified 5,578 SVs across 51 reference strains, with infants showing increasing SV diversity during the first year of life, and observed significantly greater SV similarity within mother-infant pairs than unrelated pairs. Abundance-based analysis identified 90 microbial species shared between mothers and infants. However, when incorporating SV-based tracking, only 14 strains showed patterns consistent with sustained maternal contribution across time points. Furthermore, exploratory subgroup analyses suggested that both delivery mode and feeding regimen may influence the vertical transmission patterns of maternal microbial strains and transmitted SVs. Functionally, tSVs were enriched in pathways linked to carbohydrate, amino acid, and lipid metabolism, as well as transport and environmental adaptation modules such as T4SS. Multi-niche analysis further suggested that the maternal gut showed the strongest inferred signal of SV-supported strain sharing with both the infant gut and oral microbiota.

DISCUSSION: Together, these findings suggest that microbial SVs can serve as complementary markers for investigating maternal contribution and vertical transmission-related strain-level patterns in early-life microbiome development, providing new insights into microbial inheritance and early-life health trajectories.}, } @article {pmid42239987, year = {2026}, author = {Zhao, C and Zhang, L and Wang, Y and Yang, G and Ren, C and Cao, X and Yu, Q and Jin, B and Men, Y and Liu, H and Zhang, J}, title = {Microbial Dehalogenation of 3,5,6-Trichlorooctafluorohexanoic Acid under Different Reducing Conditions.}, journal = {Environmental science & technology}, volume = {60}, number = {23}, pages = {16805-16817}, doi = {10.1021/acs.est.5c17496}, pmid = {42239987}, issn = {1520-5851}, mesh = {Halogenation ; Fluorocarbons ; Biodegradation, Environmental ; *Caproates/metabolism ; }, abstract = {Chlorinated polyfluoroalkyl substances (Cl-PFAS) have emerged as promising alternatives to legacy PFAS due to their enhanced microbial reactivity and improved environmental degradability. However, their transformation mechanisms under environmentally relevant reducing conditions remain poorly characterized. This study investigated the microbial dehalogenation of 3,5,6-trichlorooctafluorohexanoic acid (CTFE3), a representative Cl-PFAS, under nitrate-, sulfate-, iron-reducing, and methanogenic conditions. Microbial defluorination was observed across all reducing environments, with higher total defluorination efficiencies (∼60%) under nitrate- and sulfate-reducing conditions compared to iron-reducing and methanogenic conditions (∼30%) under the tested experimental conditions. Proposed biotransformation pathway analysis suggested that CTFE3 underwent more diverse and sequential hydrolytic dechlorination under nitrate- and sulfate-reducing conditions, which was associated with more extensive defluorination. Genes associated with hydrolytic dechlorination were consistently enriched under these conditions, but not in iron-reducing or methanogenic environments. Metagenomic binning further identified key taxa (e.g., Methyloversatilis discipulorum, Herbaspirillum seropedicae, Paracoccaceae, and Rhodobacteraceae-related bacteria) harboring both hydrolytic dechlorination and nitrate/sulfate-reduction genes, suggesting their involvement in CTFE3 hydrolytic dechlorination and subsequent defluorination. This study demonstrates that reducing conditions play an important role in shaping CTFE3 transformation patterns and highlight hydrolytic dechlorination as a viable pathway associated with extensive microbial defluorination, thereby offering insights for sustainable Cl-PFAS remediation.}, } @article {pmid42240391, year = {2026}, author = {de Sousa, LP and Calderon Fajardo, AA and Brandão, MM and Maia de Oliveira, V and Romero, GQ}, title = {Metagenome-assembled genomes of four novel bacterial species from Atlantic rainforest stream sediments in Brazil.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0033626}, doi = {10.1128/mra.00336-26}, pmid = {42240391}, issn = {2576-098X}, abstract = {Here, we report draft genome sequences of four novel bacterial species from Atlantic rainforest stream sediments in southeastern Brazil. The genomes represent distinct lineages within Nitrospirota and Pseudomonadota (average nucleotide identity <95% to known species) and encode diverse metabolic capabilities, including nitrification, denitrification, and aromatic compound degradation.}, } @article {pmid42240519, year = {2026}, author = {Gharbi, M and Abbassi, MS}, title = {Bacteria as anticancer agents: bioactive metabolites, engineered platforms, and translational mechanisms.}, journal = {Letters in applied microbiology}, volume = {79}, number = {6}, pages = {}, doi = {10.1093/lambio/ovag050}, pmid = {42240519}, issn = {1472-765X}, mesh = {*Antineoplastic Agents/pharmacology/metabolism/chemistry ; Humans ; *Bacteria/metabolism/genetics/chemistry ; *Biological Products/pharmacology/metabolism ; *Neoplasms/drug therapy ; Drug Discovery ; Animals ; }, abstract = {Bacteria represent a vast and underexplored reservoir of bioactive compounds with significant anticancer potential. Numerous bacterial taxa, particularly actinomycetes, Bacillus, Pseudomonas, and marine-derived species, produce structurally diverse metabolites exhibiting cytotoxic, cytostatic, pro-apoptotic, immunomodulatory, and anti-angiogenic activities against cancer cells. Clinically established agents such as actinomycin D and bleomycin highlight the therapeutic relevance of bacterial natural products, while recent discoveries continue to expand the repertoire of bioactive polyketides, peptides, alkaloids, and proteins. These compounds act through multiple mechanisms, including DNA intercalation, induction of apoptosis, cell cycle arrest, metabolic disruption, and modulation of the tumor microenvironment. Advances in metagenomics, genome mining, and synthetic biology have enabled the identification and activation of previously silent biosynthetic gene clusters, significantly enhancing drug discovery potential. In addition to metabolite-based anticancer agents, advances in synthetic biology have enabled the development of engineered bacterial platforms capable of selectively colonizing tumors, delivering therapeutic molecules, and activating prodrug therapies within the tumor microenvironment. Despite ongoing challenges related to toxicity, limited yield, selectivity, and clinical translation, bacterial-derived compounds remain a promising frontier in oncology. This review summarizes bacterial sources, bioactive metabolites, molecular mechanisms, preclinical and clinical applications, and future prospects for developing effective and safe anticancer strategies.}, } @article {pmid42240631, year = {2026}, author = {Hernández-Velázquez, R and Hernández-Avilés, JS}, title = {Metagenomic insight into the diversity and biogeochemical functions of microbial communities in the maar tropical Lake Atexcac.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {6}, pages = {}, pmid = {42240631}, issn = {1465-2080}, mesh = {*Lakes/microbiology/chemistry ; Metagenomics ; Mexico ; *Metagenome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Sulfur/metabolism ; Tropical Climate ; Carbon/metabolism ; Phylogeny ; Biodiversity ; Nitrogen/metabolism ; }, abstract = {Warm monomictic maar lakes in tropical regions represent dynamic systems where thermal stratification generates strong vertical gradients in oxygen availability and redox conditions, shaping microbial community structure and function. Lake Atexcac (Puebla, Mexico) undergoes seasonal stratification and episodic whiting events that provide a framework to examine microbial responses to changing hydrodynamic conditions. In this study, we applied deep shotgun metagenomic sequencing to characterize the taxonomic composition and functional potential of microbial communities across the epilimnion, metalimnion and hypolimnion during two contrasting stratification phases: early stratification associated with a whiting event and a later, well-established stratification period.Metagenomic profiles revealed a clear vertical organization of microbial communities, with samples clustering primarily according to thermal strata and the metalimnion displaying the highest genetic differentiation. Genome-resolved analyses enabled the recovery of a large number of metagenome-assembled genomes, with marked differences in their vertical distribution between hydrodynamic phases. The recovered genomes encompassed diverse metabolic pathways related to carbon, nitrogen and sulphur transformations, reflecting the heterogeneous redox conditions along the water column. Notably, sulphur-related metabolisms were widespread across strata, and Chlorobiota-affiliated genomes and metagenomic reads were consistently detected in suboxic layers. These organisms were found to harbour diverse thiosulphate disproportionation pathways and are thought to play an important role in the sulphur cycle that has not previously been reported in this type of lacustrine system.Overall, this study provides a genome-resolved perspective on microbial diversity and metabolic potential in a stratified tropical maar lake and establishes a baseline for future comparative and process-oriented studies integrating water column and sediment microbial communities.}, } @article {pmid42241759, year = {2026}, author = {Tabish, RW and Lin, Y and Rochell, SJ and Pacheco, WJ and Bailey, MA and Dozier, WA and Robinson, K and Hauck, R}, title = {Cecal metagenome and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations[1].}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107151}, pmid = {42241759}, issn = {1525-3171}, abstract = {This study evaluated the effects of dietary fiber supplementation on broiler gut health during a subclinical enteric challenge. Birds were assigned to either an unchallenged control or a challenged control, followed by six dietary treatments applied to challenged birds. These treatments included 3% oat hulls (OH), 3% soy hulls (SH), and four combinations of 1.5% OH or SH with 1.5% wheat middlings (WM) or sugar beet pulp (SBP). A randomized complete block design was used with 2,160 day-old YP × Ross 708 male broiler chicks allocated to eight treatments, each with nine replicate floor pens and 30 birds per pen. Birds were inoculated with Eimeria followed by Clostridium perfringens, and cecal samples were collected at 21 days of age for shotgun metagenomic and transcriptomic analyses. The enteric challenge significantly reduced microbial diversity, depleted butyrate-producing bacteria, and enriched pathways associated with bacterial growth and virulence while triggering inflammatory signaling and suppressing proliferative pathways in the host. Supplementation with dietary fiber modulated these responses through distinct yet complementary mechanisms. The group receiving OH with WM enriched butyrate-producing bacteria, including Faecalibacterium prausnitzii, reduced C. perfringens abundance, and downregulated inflammatory pathways. Birds fed OH with SBP showed increased populations of lactic acid producing bacteria and Bifidobacterium animalis while suppressing TNFα, NF-κB and IFNγ signaling. Diets containing SH combinations enhanced metabolic pathways related to pyruvate fermentation and stachyose degradation, primarily driven by Lactobacillus species. Despite having distinct microbial compositions, all fiber treatments restored epithelial proliferation pathways in the host transcriptome, indicating convergent potentially beneficial effects on intestinal health. Integration of bacteriome and transcriptome data revealed coordinated relationships between specific bacterial species, including Stutzerimonas stutzeri, Bacteroides caecae, and Eubacteriaceae bacterium ES3, and host genes involved in immune function and energy metabolism. These findings provide a mechanistic framework for developing targeted nutritional strategies using specific fiber combinations to enhance gut resilience in antibiotic-free broiler production systems.}, } @article {pmid42241815, year = {2026}, author = {Zhang, S and Liu, X and Cheng, R and Huang, C and Zhang, Z and Long, S and Yang, Q}, title = {Elucidating the Feammox nitrogen transformation pathway: Key intermediates and putative multi-species metabolic cooperation in a long-term Feammox-dominant system.}, journal = {Water research}, volume = {303}, number = {}, pages = {126223}, doi = {10.1016/j.watres.2026.126223}, pmid = {42241815}, issn = {1879-2448}, abstract = {The emerging Fe(Ⅲ) reduction coupled to anaerobic ammonia oxidation (Feammox) process offers a promising approach toward carbon neutrality in wastewater treatment. However, its nitrogen transformation pathway and metabolic mechanism remain unclear. This study established a Feammox-dominant sequencing batch reactor (Fe-SBR) and operated it for 515 days, achieving an ammonia removal efficiency of 97.9 ± 4.5% during the stable phase. Feammox was confirmed as the dominant process for NH4[+]-N conversion, accounting for 83.2% of ammonia transformation. NH2OH, NO, and N2O were identified as key intermediates in the Feammox nitrogen transformation pathway. By integrating metagenomic analysis of functional gene dynamics with metagenome-assembled genomes (MAGs), a potential coupled iron-nitrogen (Fe-N) metabolic pathway was proposed. This pathway suggested that the Feammox process might be accomplished through multi-species metabolic cooperation, with MtrC-mediated extracellular electron transfer potentially serving as the key link coupling nitrogen transformation to the iron redox cycle. These findings provide novel insights into the Feammox metabolic pathway and lay a theoretical foundation for the future precise control and optimization of this process.}, } @article {pmid42241861, year = {2026}, author = {Li, Y and Li, P and Li, H and Zhuang, L and Wang, L}, title = {Case study: Metagenomic analysis of microbial restructuring and nitrogen metabolism under probiotic and Chinese herb applications during post-antibiotic-ban shrimp farming.}, journal = {Journal of environmental management}, volume = {410}, number = {}, pages = {130128}, doi = {10.1016/j.jenvman.2026.130128}, pmid = {42241861}, issn = {1095-8630}, mesh = {Animals ; *Aquaculture ; *Nitrogen/metabolism ; Anti-Bacterial Agents ; *Probiotics ; Metagenomics ; China ; Microbiota ; Penaeidae ; }, abstract = {China's 2020 aquaculture antibiotic ban has driven widespread use of probiotics and Chinese herbs in shrimp farming, yet their ecological effects on microbial communities remain unclear. This case study investigated three commercial Litopenaeus vannamei ponds in eastern China that exhibited contrasting nitrite accumulation and production outcomes under a post-antibiotic ban regime using probiotics and Chinese herbs. All ponds received daily Bacillus licheniformis probiotics and weekly supplements of Effective Microorganisms and a multi-herb blend, including Coptis, Elsholtzia, Sophora, Ligusticum, and Artemisia argyi. Our analysis revealed that Firmicutes-dominated communities replaced typical Proteobacteria-dominated microbiomes. Pond A, characterized by stable production, maintained low nitrite levels (a peak of 0.5 mg/L) and was dominated by Planococcus. In contrast, Ponds B and C, which exhibited elevated nitrite accumulation (peaks of 1.3 mg/L for Pond B and 1.5 mg/L for Pond C) and reduced production, were dominated by Paenisporosarcina. Metagenomic reconstruction indicated that this difference may result from aberrant nitrogen-transforming pathways. Paenisporosarcina correlated positively with nitrite accumulation, whereas Planococcus exhibited negative correlations. Virulence factor gene analysis revealed low abundance of pathogenic Vibrio spp.-associated genes. Importantly, even high-nitrite ponds exhibited minimal antibiotic resistance genes, including the absence of common aquaculture-associated ones such as those conferring resistance to sulfonamides (sul1, sul2), quinolones (qnr), and tetracyclines (tet), confirming the effectiveness of the antibiotic ban. Our case findings indicate that Paenisporosarcina dominance is linked to nitrite accumulation, highlighting a potential target for microbiome management in antibiotic-free shrimp farming.}, } @article {pmid42241983, year = {2026}, author = {Bettera, L and Buzzanca, D and Levante, A and Cirlini, M and Saadoun, JH and Martinengo, N and Chiarini, E and Faccia, M and Zeppa, G and Calasso, M and Alessandria, V and Gatti, M}, title = {Cheeseomics of Grana Padano PDO cheese: Microbial diversity and flavour profiles compared to non-PDO cheeses.}, journal = {International journal of food microbiology}, volume = {459}, number = {}, pages = {111881}, doi = {10.1016/j.ijfoodmicro.2026.111881}, pmid = {42241983}, issn = {1879-3460}, abstract = {Protected Designation of Origin (PDO) schemes define technological constraints that may shape cheese microbiota and, consequently, volatilome and sensory quality. Here, a "cheesomics" approach to compare Grana Padano PDO (n = 13) with hard cooked cheeses of the same type and ripening time (9 months) produced outside the PDO framework (non-PDO; n = 15). Shotgun metagenomics was used to characterize bacterial and fungal communities and functional profile, while the volatilome was profiled by HS-SPME/GC-MS and sensory attributes were evaluated by trained ONAF panelist. A subset of samples (4 PDO and 4 non-PDO) was further analysed by flash profiling. Lactic acid bacteria dominated all samples, but distinct community and functional signature differentiated PDO and non-PDO cheeses. Grana Padano PDO showed higher sensory scores for odor/aroma and taste (p-value < 0.05), together with a more consistent microbiological profile. Non-PDO cheeses were more heterogeneous and displayed higher abundance of lipid-derived volatiles, including short- to medium-chain free fatty acids and methyl ketones, whereas PDO samples were associated with compounds such as pentanal and 2,5-dimethylpyrazine. Multivariate integration of taxa, VOCs and sensory data revealed partial separation between groups, supporting group-specific co-variation patterns. Functional profiling showed higher contributions (p-value < 0.05) of fermentation-related functions and cellular/extracellular polysaccharides in PDO cheeses, suggesting that sensory performance is not driven by VOC abundance alone. Fungal DNA was detected at very low level and showed limited relevance from a dairy microbiology perspective. Overall, the PDO production framework was associated with a measurable microbiological and metabolic imprint and with enhanced sensory performance relative to comparable non-PDO cheeses.}, } @article {pmid42242027, year = {2026}, author = {Li, J and Ji, J and Ma, X and Xu, Z and Zhou, L and Guan, Y and Ling, X and Jia, X and Xi, B and Zhao, M}, title = {Bifidobacterium longum alleviation of metabolic dysfunction-associated steatotic liver disease: A multi-omics landscape of microbiota and metabolome reconfiguration.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128569}, doi = {10.1016/j.micres.2026.128569}, pmid = {42242027}, issn = {1618-0623}, mesh = {Animals ; Male ; Mice ; *Bifidobacterium longum/physiology ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; *Fatty Liver/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; Intestinal Barrier Function ; Liver/metabolism/pathology ; *Metabolic Diseases ; *Metabolome ; Metagenomics ; Mice, Inbred C57BL ; Multiomics ; *Probiotics/administration & dosage ; }, abstract = {The gut microbiome-host metabolism axis plays a critical role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). Although the probiotic Bifidobacterium longum (B. longum) shows promise in ameliorating metabolic disorders, its functional impact on the microbiome-metabolome interplay in MASLD remains elusive. Herein, we established a MASLD mouse model using a high-fat, high-fructose (HFHF) diet and conducted integrated multi-omics analyses, including liver transcriptomics, gut metagenomics, and serum metabolomics, following B. longum intervention. B. longum supplementation effectively attenuated systemic metabolic dysfunction, hepatic steatosis, and intestinal barrier impairment in MASLD. This amelioration was driven by a two-pronged functional reorganization: the restoration of intestinal integrity and a profound remodeling of the hepatic transcriptome, featuring the downregulation of crucial mediators within the CD14-TLR4-NF-κB signaling cascade, including Cd14 and Runx1. Such functional reorganization coincided with a reconfigured gut microbiota, characterized by an increased abundance of beneficial taxa (e.g., Parabacteroides distasonis, Muribaculum intestinale) and suppression of opportunistic pathobionts (e.g., Ruminococcus gnavus, Clostridioides difficile). Furthermore, these microbial shifts were intrinsically linked to a reconfigured serum metabolome, highlighted by the enrichment of protective tryptophan-derived metabolites (e.g., indole-3-propionic acid) and the reduction of detrimental ones (e.g., 17α-methyltestosterone, 7-HDoHE). Collectively, our results suggest that B. longum mitigates MASLD through modulation of the gut microbiota and host serum metabolome, supporting its potential as a probiotic candidate for the management of metabolic health.}, } @article {pmid42242076, year = {2026}, author = {Bai, H and He, LY and Qiao, LK and Gao, FZ and Liu, YS and Ying, GG}, title = {Human-associated microbial inputs and bacterial-fungal ecological coupling shape antibiotic resistance risk in environmental dust.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142602}, doi = {10.1016/j.jhazmat.2026.142602}, pmid = {42242076}, issn = {1873-3336}, abstract = {Environmental dust represents a critical exposure matrix, yet the relationships between multi-kingdom dust microbiomes and antimicrobial resistance (AMR)-associated health risks remain insufficiently characterized. We applied shotgun metagenomics to dust samples from pharmaceutical factories, a dairy farm, railway stations, and schools to comprehensively characterize bacterial, fungal, and viral communities, alongside resistome structure. Microbial community composition exhibited significant differences across all three domains among the sampled environments. Specifically, dust from railway stations displayed the strongest human-associated microbial signal and harbored the highest diversity of antibiotic resistance genes (ARGs), and MetaCompare-derived AMR risk. Functional analyses revealed shared bacterial-fungal metabolic organization, with cross-domain taxonomic and functional associations pointing to structured ecological coupling. Variation partitioning analysis showed that shared explanatory components accounted for most of the variation in MetaCompare-based human-health AMR risk, particularly the overlap among bacterial composition, humanization, and fungal functional structure. Notably, Candida and Aureobasidium emerged as divergent fungal indicators, tracking microbiome humanization and resistome risk in opposite directions. By contrast, viral auxiliary metabolic genes accounted for only 3.92% of the abundance-weighted virome, consistent with a host-linked auxiliary layer rather than a dominant independent pathway. Collectively, these findings demonstrate that AMR-related signatures in environmental dust are shaped by the interplay of human-associated microbial inputs and ecologically coupled bacterial-fungal interactions.}, } @article {pmid42242079, year = {2026}, author = {Yang, F and Zhang, M and Tan, Y and Yuan, Z and Liu, W and Wu, Y and Li, F}, title = {Alkaline woody peat shifts CO2 emissions to CH4 by modulating microbial cross-feeding in Cd-contaminated paddy soil.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142498}, doi = {10.1016/j.jhazmat.2026.142498}, pmid = {42242079}, issn = {1873-3336}, abstract = {Alkaline organic amendments are widely used to remediate cadmium (Cd)-contaminated paddy soils by alleviating acidification and reducing Cd bioavailability, yet their impacts on greenhouse gas emissions remain unclear. Here, we examined how alkaline woody peat (WP) regulates carbon fluxes and microbial interactions in Cd-contaminated paddy soil. Anaerobic incubation and greenhouse pot experiments, together with in situ methane monitoring and metagenomic analyses, were used to compare alkaline-modified WP with acidic WP, CaO alone, and unamended controls. Alkaline WP (AWP-2) increased soil pH from 5.5 to 7.35 and decreased exchangeable Cd from 32% to 13%, confirming its remediation effectiveness. However, this was accompanied by marked changes in greenhouse gas emissions: methane production increased by up to 3.9-fold, while carbon dioxide emissions declined. Metagenomic analyses showed that alkaline WP strongly enriched methanogenic archaea, particularly Methanosarcina, whose relative abundance reached 26.6% compared with 4.2% in the control, while suppressing microbial populations associated with CO2-generating pathways. Functional gene profiles revealed increased abundance of mcrA and reduced representation of genes involved in complete acetate oxidation (maeA, pdc, sucA, porA, aceE, and icd). Genome-resolved analysis further showed that some microbes positively associated with methanogens lacked key genes involved in acetate oxidation to CO2 (e.g., aceE), suggesting a reduced capacity for CO2 generation from acetate and a greater tendency to retain carbon as acetate, thereby potentially favoring acetoclastic methanogenesis. Overall, these results highlighting a potential trade-off between Cd remediation and greenhouse gas mitigation and the need to incorporate microbially driven carbon fluxes into environmental risk assessments of alkaline amendments in contaminated paddy soils.}, } @article {pmid42242448, year = {2026}, author = {Ammar, M and Fang, Y and Saqib, M and Xiao, J and Sial, AU and Wu, Q and Mansoor, MK and Wu, X and Moaaz, M and Butt, MU and Hafeez, R and Iqbal, K and Zohaib, A and Shen, S and Deng, F}, title = {Metagenomic and serological evidence of emerging tick-borne viruses in livestock, humans, and rats in Pakistan.}, journal = {Virologica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.virs.2026.06.001}, pmid = {42242448}, issn = {1995-820X}, abstract = {Tick-borne viruses (TBVs) pose significant emerging threats to public and veterinary health worldwide. In Pakistan, the potential threats posed by TBVs extend far beyond Crimean-Congo hemorrhagic fever virus (CCHFV), which causes outbreaks and severe hemorrhaging with a high fatality rate among humans each year. However, the full extent of the tick-borne virome remains largely unexplored. This study presents the metagenomic profiling of viruses in livestock-associated ticks from Pakistan. Eighty-seven ticks belonging to the genera Ixodes, Rhipicephalus, Haemaphysalis, and Hyalomma species from livestock in Punjab. These ticks were subsequently grouped into 11 pools for RNA sequencing. Our analysis revealed extensive viral diversity, identifying sequences related to 31 viruses spanning at least 11 families. New strains of Jingmen tick virus (JMTV), brown dog tick phlebovirus 2 (BDTPV-2), and Liman tick virus (LMTV) were characterized, confirming their presence in the region. Serological surveys performed among 319 livestock, 253 humans, and 214 rats detected antibodies against these viruses, indicating host exposure. Notably, the presence of JMTV-neutralizing antibodies was confirmed in two livestock animals, one human, and one rat, providing evidence of productive infection. Our findings significantly expand the known diversity and distribution of TBVs in Pakistan, establish the preliminary baseline of the tick virome in the country, and provide serological evidence of cross-species exposure to emerging TBVs. This study highlights the underestimated risk of tick-borne viral zoonoses in Pakistan and underscores the urgent need for enhanced surveillance and risk assessment.}, } @article {pmid42242497, year = {2026}, author = {Han, J and Lisco, A and Che, Y and Anderson, MV and Laidlaw, E and Kim, CS and Hou, P and Conlan, S and Proctor, DM and Lee-Lin, S and Amirkhani, A and Holmes, CJ and Suh, GS and Brownell, I and , and Segre, JA and Sereti, I and Kong, HH}, title = {Expansion of pathogens and restoration of human skin microbiome in CD4 T-cell lymphopenia.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2026.05.019}, pmid = {42242497}, issn = {1523-1747}, abstract = {The microbiome and host immune system maintain a dynamic homeostatic equilibrium at the skin interface. Prior studies have shown that the skin microbiome is profoundly altered in immunodeficient conditions. Patients with idiopathic CD4 lymphopenia (ICL), a rare clinical syndrome with obscure cause, and people living with HIV (PLWH) are two etiologically distinct groups of individuals with CD4 T-cell lymphopenia. We conducted shotgun metagenomic sequencing, metagenome assembly, and read-based mapping to characterize the multi-kingdom taxonomic diversity of skin microbiomes in patients with ICL and PLWH who were followed longitudinally before and after antiretroviral therapy (ART) initiation. Compared with healthy individuals, the skin microbiomes of patients with ICL and ART-naïve PLWH showed greater inter-individual variation and higher relative abundances of eukaryotic viruses. Both patient groups carried pathogenic microbes, including high-oncogenic-risk human papillomaviruses (HPVs) and dermatophytes such as Trichophyton rubrum, which were rarely seen in healthy individuals. In PLWH, high-oncogenic-risk HPV types persisted after 2 months of ART but were mostly cleared after 14 months. The loss of peripheral blood CD4 T-cells was associated with shifts in the skin microbiome and a relative expansion of pathogenic microbes. Investigating microbiome dynamics during immunodeficiency and subsequent immune reconstitution provides additional insights into host-microbial interactions.}, } @article {pmid42243106, year = {2026}, author = {Lee, M and Kim, D and Song, JH and Park, SJ and Chang, JY}, title = {Efficacy of Lactococcus lactis WiKim0124 in Fat-, Sucrose-, and Fat/Sucrose-Induced Obesity Models.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00915-3}, pmid = {42243106}, issn = {2396-8370}, support = {KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; }, abstract = {Lactococcus lactis WiKim0124 (WiKim0124), a probiotic strain isolated from kimchi, has previously shown anti-obesity effects in high-fat diet (HFD) models. This study investigated whether WiKim0124 and its formulated version, SW01, exert consistent anti-obesity efficacy across distinct diet-induced obesity models through modulation of host lipid metabolism and gut microbial function. In 3T3-L1 adipocytes and FFA-treated HepG2 cells, both treatments inhibited lipid accumulation and modulated lipid metabolism-related markers, indicating enhanced fatty acid oxidation and reduced lipogenesis. In C57BL/6 J mice fed HFD, high-sucrose (HSuc), or HFD + HSuc diets, daily oral administration of WiKim0124 or SW01 significantly reduced body weight gain, adipose tissue mass, and hepatic lipid accumulation. WiKim0124 and SW01 significantly enhanced fatty acid oxidation pathways, as evidenced by increased expression of the markers PPARα, CPT-1α, and UCP2. Gut microbiota analysis showed increased Bacteroidetes and enrichment of Akkermansia muciniphila in treated groups. Shotgun metagenomic functional profiling revealed enhanced short-chain fatty acid-related pathways and enzymes, with distinct patterns depending on treatment and dietary stressors. Microbial functional responses were most pronounced in the HFD + HSuc model, supporting a diet-dependent mode of probiotic action. Together, these findings demonstrate consistent anti-obesity efficacy of WiKim0124 and support the translational potential of its formulated application through integrated modulation of host metabolism and gut microbial function.}, } @article {pmid42243452, year = {2026}, author = {Das, R and Medhi, MC and Tamang, B}, title = {Microbial diversity and its links to retinol pathways and aroma compounds in ethnic fermented rice beverages of Assam.}, journal = {AMB Express}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13568-026-02062-0}, pmid = {42243452}, issn = {2191-0855}, abstract = {Traditional fermented rice beverages are produced through complex microbial fermentation processes that influence their physicochemical characteristics and metabolite composition. In this study, metagenomic sequencing and GC-MS/MS-based metabolomics were integrated to characterize four indigenous rice beverages: Black Rohi Modh (BR), Rohi Modh (RH), Jou Bidwi (JOU), and Sai Mod (SM). All beverages were mildly acidic, with pH values ranging from 4.1 to 4.5 and titratable acidity between 0.58 and 0.72% lactic acid. Ethanol content varied among samples, with BR showing the highest concentration (8.13% v/v), followed by JOU and RH (approximately 5.5% v/v), while SM exhibited the lowest level (4.28% v/v). Antioxidant activity differed across beverages, with RH and BR demonstrating higher DPPH radical scavenging activity and SM showing the highest ferric reducing antioxidant power (96.93 µmol/mL). Metagenomic analysis generated 57.69 Mb of assembled sequences, identifying 48 microbial phyla and 1,785 species, with Eukarya accounting for 66.12% of the total community. Ascomycota predominated in BR and JOU, whereas Bacillota was more abundant in RH. The genus Saccharomyces was consistently dominant across samples. Functional annotation indicated enrichment in metabolic pathways related to carbohydrate and amino acid metabolism, as well as genes associated with ethanol biosynthesis and retinol metabolism pathways, reflecting microbial metabolic potential rather than direct vitamin production. Metabolomic profiling identified 113-167 metabolites per beverage, with 93 compounds shared among all samples. Correlation analysis revealed significant associations between Saccharomyces cerevisiae and short-chain fatty acids (ρ = 0.62-0.71, FDR < 0.05), indicating a strong positive relationship between microbial abundance and metabolite production.}, } @article {pmid42243513, year = {2026}, author = {Yi, J and Zhao, Y and Li, Z and Chen, A and Tang, Z and Zheng, L and Ge, H and Yu, Q and Liu, W and Xiang, J and Tang, J}, title = {M.globosa promotes lung cancer progression and M2 macrophage polarization through oxidative phosphorylation.}, journal = {NPJ precision oncology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41698-026-01528-5}, pmid = {42243513}, issn = {2397-768X}, support = {2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2403084//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; }, abstract = {The lungs are colonized by a variety of microbes which play a significant role in lung cancer progression. In this study, we conducted an in-depth analysis of metagenomic sequencing data obtained from alveolar lavage fluid (ALF) samples of patients with non-small-cell lung cancer (NSCLC) at different clinical stages. The nested qPCR was used to validate the abundance of key fungi and establish a correlation between fungi abundance and patient prognosis. We found that elevated levels of M.globosa correlated with patients at stage1B-3 and worse prognosis. M.globosa enhanced the proliferation of lung cancer cells and promoted tumor growth in vivo by promoting M2-like macrophage polarization, which was primarily driven by oxidative phosphorylation (OXPHOS) activation. The inhibition of OXPHOS in tumor-bearing mice using metformin significantly retarded the tumor growth induced by M. globosa. Together, our clinical observations and experimental findings suggest that intracellular M. globosa infection may contribute to lung cancer progression through immunometabolic remodeling of macrophages.}, } @article {pmid42243631, year = {2026}, author = {Bauer, C and Reger, N and Rustem, HAL and Tisza, M and Triosi, CL and Javornik Cregeen, S and Ghobrial, L and Gitter, A and Wu, F and Surathu, A and Deegan, J and Mena, KD and Petrosino, J and Boerwinkle, E and Hanson, BM and Maresso, AW}, title = {SeqBoard: a genomics-based data dashboard for comprehensive wastewater virome monitoring.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {}, number = {}, pages = {}, doi = {10.1093/jamia/ocag088}, pmid = {42243631}, issn = {1527-974X}, support = {//S.B. 1780, 87th Legislature, 2021 Reg. Sess./ ; U19 AI44297/NH/NIH HHS/United States ; //Anonymous Foundation/ ; //UTHealth Houston Seed/ ; //Baylor College of Medicine/ ; //Alkek Foundation Seed/ ; }, abstract = {OBJECTIVES: To develop the first public-facing dashboard that translates genomic sequencing data from wastewater into accessible and actionable community information concerning human pathogenic viruses, representing a shift to sequencing-based public health wastewater monitoring.

MATERIALS AND METHODS: We developed SeqBoard, a user-friendly dashboard that displays sequencing information from the total wastewater virome. The dashboard integrates diverse expertise and components, including data processing and analysis, visualization and management, security, and stakeholder engagement and feedback. We implemented a 3-tiered system for user interactions, customized to the general public, public health officials, and genomics experts.

RESULTS: SeqBoard provides an intuitive interface for presenting genomic information as species-specific trend lines, level indicators, and all-site aggregates. It translates complex sequencing data into public health insights, including reporting on dozens of viruses of concern with modules for detections, variant information, and genomic context.

DISCUSSION: The prevention of the next pandemic will require comprehensive pan-monitoring of deadly viruses and their evolution. Genomics-based dashboards will be essential for early detection of viral activity before significant clinical manifestation, thereby allowing public health systems to provide warnings, ready actions, and develop vaccines.

CONCLUSION: SeqBoard shows that sequencing data can be translated into useful public health information, serving as a model for future sequencing-based pathogen dashboards. The dashboard is publicly available at https://tephi-ww.uth.edu/public-dashboard and represents the first publicly available dashboard providing pan viral genomic detection data for wastewater monitoring.}, } @article {pmid42243719, year = {2026}, author = {Almutrafy, AM and Aloufi, AS and Al-Andal, A and Refai, MY and Tashkandi, M and Alnahari, AA and Bagabas, SS and AlDowsari, FMF and Abuauf, HW and Alshehrei, FM and Alshareef, SA and Abulfaraj, AA and Hassan, RN and Jalal, RS}, title = {Comprehensive in silico analysis of eggNOG-annotated orthologous genes infers functional dynamics and energy metabolism in the microbiome of Abutilon fruticosum.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-09123-3}, pmid = {42243719}, issn = {1471-2229}, support = {PNURSP2026R357//Princess Nourah bint Abdulrahman University Researchers Supporting Project/ ; }, abstract = {BACKGROUND: Abutilon fruticosum is an ecologically and pharmacologically important wild Malvaceae species whose rhizospheric microbiome remains poorly resolved at the level of orthologous-group (OG) genes. Shotgun metagenomic sequencing and eggNOG/COG-based annotation were used to compare rhizosphere and bulk-soil microbiomes, quantify OG repertoires, and infer in silico functional modules.

RESULTS: Principal coordinate and Bray-Curtis analyses of COG categories revealed clear functional segregation between rhizosphere and bulk communities, with the rhizosphere enriched in high-abundance OGs linked to energy metabolism, nutrient transport, stress response, and secondary metabolism. Computational ranking identified a cohort of highly recurrent OGs, predominantly associated with Actinobacteria and Proteobacteria but also with Streptophyta, that dominate the predicted functional landscape and are markedly more abundant in silico in rhizospheric soil. Using eggNOG/COG assignments, ten interacting putative functional modules were delineated in silico, encompassing NADH-quinone oxidoreductase-centered bioenergetics, ABC-type nitrogen and sulfur acquisition, fatty-acid and propionate catabolism, sulfur scavenging and detoxification, cell-envelope and biofilm formation, multidrug efflux, DNA maintenance, environmental sensing and transcriptional regulation, specialized competition/protection, and mobile genetic elements. Conceptual, hypothesis-generating frameworks integrating selected modules posit that rhizosphere dominance could arise from the coordinated coupling of ATP/proton motive force (PMF) generation with high-affinity nutrient uptake, sulfur and carbonyl detoxification, iron-sequestering and antioxidant secondary metabolism, and stress-responsive multidrug efflux, based on our analyses.

CONCLUSIONS: These predictions suggest that specific OG cohorts act as keystone energetic, metabolic, and defense hubs in the A. fruticosum rhizosphere and provide testable hypotheses for future experimental work linking module-level functions to root colonization, stress tolerance, and plant performance. (249 words).}, } @article {pmid42243998, year = {2026}, author = {Li, S and Sun, Y and Tong, X and Zhang, Z and Ma, X and Li, D and Min, L}, title = {Near-complete inhibition of rumen methanogenesis via microbial and enzymatic modulation using a low dose of Asparagopsis taxiformis combined with 3-nitrooxypropanol.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42243998}, issn = {1674-9782}, support = {SKXRC2025487//Youth S&T Talent Support Programme of Guangdong Provincial Association for Science and Technology/ ; 2024CXTD13//Guangdong Modern Agro-industry Technology Research System/ ; 202408440440//China Scholarship Council/ ; NYQS202613//Special Funding for the Construction of the High-Level Academy of Agricultural Sciences/ ; 2026A1515010802//Guangdong Basic and Applied Basic Research Foundation/ ; }, abstract = {BACKGROUND: Enteric methane (CH4) from ruminants represents a major contributor to agricultural greenhouse gas emissions. The red seaweed Asparagopsis taxiformis (A. taxiformis) is a highly effective CH4 emission inhibitor, but its large-scale application is restricted by limited biomass availability. This study evaluated whether reducing the inclusion level of A. taxiformis (0.32% dry matter, DM) combined with 3-nitrooxypropanol (3-NOP; 0.05% DM) could maintain a high inhibitory efficacy, and elucidated the underlying microbial mechanisms through in vitro fermentation and metagenomics analysis.

RESULTS: The combined treatment decreased CH4 production by 98.21% (P < 0.01) without impairing DM degradation, and markedly shifted rumen fermentation towards propionate, lowering the acetate-to-propionate ratio (1.59 vs. 2.65; P < 0.01). Metagenomic profiling revealed substantial reductions in the abundance of Methanobrevibacter and Ruminococcus, along with increased levels of propionate-associated bacteria such as Prevotella, Treponema, Eubacterium, and Selenomonas (P < 0.01). Functionally, the combined treatment downregulated key enzymes in hydrogenotrophic and methylotrophic methanogenesis, including methyl-coenzyme M reductase (EC:2.8.4.1) and tetrahydromethanopterin S-methyltransferase (EC:2.1.1.86), thereby blocking terminal methanogenic steps.

CONCLUSIONS: Collectively, these results demonstrate that co-supplementation with A. taxiformis and 3-NOP achieves near-complete methanogenesis inhibition at drastically reduced seaweed dosage through coordinated changes in fermentation patterns, microbial community structure, and methanogenic enzymatic pathways. This approach provides a practical strategy to overcome biomass limitations of A. taxiformis and warrants validation in long-term in vivo trials.}, } @article {pmid42244002, year = {2026}, author = {Ansari, MH and Staubach, F and Alacatli, N and Obbard, DJ}, title = {A diverse gut virome in natural populations of Drosophila melanogaster.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42244002}, issn = {2524-4671}, abstract = {BACKGROUND: Drosophila melanogaster is not only one of the most important models of antiviral immunity in invertebrates, but is also a powerful model for research of the gut microbiome. Although recent studies have continued to improve our knowledge of the fly gut microbiota, the viral component of the microbiome has remained unexplored.

RESULTS: Here we explore the viral component of the Drosophila melanogaster gut microbiome using deep metagenomic DNA sequencing. We recovered 3040 non-redundant viral contigs, most of which were bacteriophage-associated sequences, resulting in 167 viral Metagenome-Assembled Genomes. Many of these sequences showed limited similarity to reference viruses and included bacteriophages related to tailed double-strand DNA phage lineages, with putative links to major gut-associated bacteria of D. melanogaster, including Lactobacillus, Acetobacter, and Gluconobacter. Our functional annotation and discovery of auxiliary metabolic genes suggested that these bacteriophages encode putative functional potential related to microbial metabolism and genetic information processing. We also identified evidence of known fly pathogens Drosophila Kallithea nudivirus, Vesanto bidna-like virus, and Drosophila Linvill Road densovirus, some of which were common in our studied populations.

CONCLUSIONS: Our findings reveal a complex and diverse phage community in the D. melanogaster gut microbiome, paving the way to study host-phage related research in the natural microbial communities.}, } @article {pmid42244030, year = {2026}, author = {Wang, Y and Zhang, Y and Feng, L and Han, Q and Yu, Q and Li, H}, title = {Host Ecology Shapes Gut Pathogen Evolution: An Eco-Evolutionary Trade-Off in Plateau Wildlife.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70344}, doi = {10.1111/1462-2920.70344}, pmid = {42244030}, issn = {1462-2920}, support = {32471575//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Lagomorpha/microbiology ; *Host-Pathogen Interactions ; *Biological Evolution ; Virulence Factors/genetics ; *Gastrointestinal Tract/microbiology ; *Bacteria/genetics/isolation & purification/classification ; Animals, Wild/microbiology ; Ecosystem ; }, abstract = {The intestinal tracts of plateau wildlife function as crucial reservoirs for diverse pathogens. However, the mechanisms through which host ecology influences pathogen community assembly and their interactions remain unclear. By comparing the subterranean-living plateau zokor (Eospalax baileyi) with the aboveground plateau pika (Ochotona curzoniae) across a two-and-a-half-year study, this work provides evidence that the distribution and transmission dynamics of pathogens, virulence factor genes (VFGs), and pathogen-host interaction (PHI) genes are determined by animals' distinct niches. The results demonstrate a clear eco-evolutionary trade-off: the plateau zokor, inhabiting stable yet pathogen-enriched burrow systems, exhibited higher abundances of pathogens, VFGs, and PHI genes in its gut, and formed complex co-occurrence networks. In contrast, the plateau pika, under diverse environmental exposure, possessed higher pathogen and gene diversity but lower overall abundance, alongside simpler interaction networks indicative of opportunistic colonization. Metagenomic binning indicated a close association among VFGs, PHI genes, and mobile genetic elements (MGEs), pointing to their possible joint transfer. Additionally, animal weight and precipitation were identified as key drivers of pathogen dynamics. These findings indicate that the gut sits at the crossroads of animal and environmental health, highlighting how host-mediated pathogen evolution across distinct niches shapes the broader One Health dynamics of the plateau ecosystem.}, } @article {pmid42244179, year = {2026}, author = {Wang, Y and Zhu, Z and Zhang, Y and Luo, Q and Niu, T and Liu, Y and Chen, J and Yang, R and Zhu, S and Chen, H}, title = {Dynamic microbiome turnover and glycerol-3-phosphate-linked metabolic adjustments underlie resilience to desiccation in intertidal algae.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71330}, pmid = {42244179}, issn = {1469-8137}, support = {2021Z103//Major Scientific and Technological Project of Ningbo/ ; CARS -50//China Agriculture Research System of MOF and MARA/ ; 32373099//National Natural Science Foundation of China/ ; //Ningbo Yongjiang Talent Program/ ; 2021C02069 -9//Key Scientific and Technological Grant of Zhejiang for Breeding New Agricultural (Aquaculture) Varieties/ ; }, abstract = {Tolerance to extreme dehydration has emerged across the tree of life, yet current understanding relies heavily on terrestrial host traits. Marine lineages facing rapid, tide-driven hydration oscillations remain largely unexplored. We used Pyropia haitanensis as a model to determine if intertidal resilience arises from a coordinated holobiont strategy. We integrated time-resolved microbiome profiling and metagenomics. Mechanisms were validated through multi-omics of desiccation-stressed bacterial isolates, inoculation, and antibiotic-depletion experiments, and host physiological assessment. Rapid drying reshaped the microbiome through selective loss of osmosensitive taxa and occupation by stress-tolerant lineages, whereas rehydration promoted selective recolonization and network recovery. Metagenomic analysis revealed enrichment of functional potential for microbial antioxidant, osmoprotective, and extracellular polysaccharide pathways, alongside enrichment of glycerol-3-phosphate (G3P) ABC transporter modules. Host G3P secretion increased, creating a selective nutrient niche that recruited symbionts possessing specialized G3P transporters. Inoculation and microbiota-depletion experiments established a causal role for the microbiome in host resilience. Keystone isolates Sulfitobacter sp. and Alteromonas sp. utilized host-derived G3P to fuel complementary protective mechanisms, with their combination outperforming either taxon alone. These findings highlight an integrated host-microbiome partnership shaped by tidal filtering, a cross-domain strategy that buffers hydration stress and supports intertidal resilience and mariculture practices.}, } @article {pmid42244577, year = {2026}, author = {Ettinger, CL and Eisen, JA}, title = {Phoronids and their tubes harbor distinct microbiomes compared to surrounding sediment.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.05.28.596327}, pmid = {42244577}, issn = {2692-8205}, abstract = {Phoronids are a phylum of animals with only ∼12 described species, all of which are marine filter feeders that build external tubes for shelter and produce chemical deterrents against predators. Many tube-building invertebrates host distinct microbial communities and even have obligate symbionts for survival in sulfur-rich marine sediments. However, the microbiome of phoronids has only recently begun to be described. To address this, we surveyed the composition of the microbiome of the phoronid, Phoronopsis harmeri , using 16S rRNA gene amplicon and metagenomic sequencing. We found that the phoronid microbiome was dominated by members of the orders Campylobacterales, Desulfobulbales, and Desulfobacterales. We also found that the microbiomes of tubes and phoronids were less diverse than that of surrounding sediment, and that the microbiomes of phoronids, tubes and surrounding sediment were all distinctly structured. Based on analysis of metagenomic data, and even though we were only able to recover low quality MAGs of abundant taxa, we found preliminary evidence that taxa associated with phoronids and their tubes likely participate in sulfur cycling pathways. Future work should perform more robust metagenomic sequencing and chemical analysis to assess if there is a link between known phoronid chemical defenses and microorganisms. Overall, this study provides foundational insight into the microbial communities associated with phoronids and these initial findings suggest that these communities may play an important role in sulfur cycling in marine sediments.}, } @article {pmid42244712, year = {2026}, author = {Iranzo, J and Wolf, YI and Koonin, EV}, title = {Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono?.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.25.727639}, pmid = {42244712}, issn = {2692-8205}, abstract = {BACKGROUND: Mobile genetic elements (MGEs), including viruses, plasmids, and transposons, are major drivers of evolution in bacteria and archaea. Host-parasite conflicts drive the emergence of a broad variety of defense and counter-defense systems. Recent advances in metagenomics and functional annotation have shown that many defense systems are located on MGEs. The fact that MGEs are, essentially, genomic parasites raises an intriguing question: why do these parasites carry defense systems at high prevalence, often even higher than the host chromosome?

RESULTS: We developed a simple mathematical model to investigate the factors that promote evolution of defense systems in MGEs and the ecological implications of MGE-encoded defense. Our analysis points to the strength of inter-MGE interference as a key determinant of the evolution of defense systems in MGEs. We identify two qualitatively distinct regimes, depending on the basic reproductive number in mixed coinfections. Weakly interfering MGEs tend to carry low-cost defense systems that enhance the survival of their hosts upon exposure to more damaging MGEs. Although these systems can be occasionally transferred to the host, they typically remain in MGEs. In contrast, strongly interfering MGEs, such as plasmids from the same incompatibility group, can carry high-cost defense systems that are detrimental to the host and the population as a whole, but help their carriers spread by actively replacing their competitors.

CONCLUSIONS: Analysis of our model shows that the key determinant of the evolution and spread of defense systems in MGEs is the strength of cross-MGE interference. Weakly interfering MGEs would serve as 'MGE banks', typically carrying low-cost defense systems that can benefit the host by protecting it from more damaging MGEs. In contrast, strongly interfering MGEs would carry costly defense systems that mediate inter-MGE conflicts but are deleterious to the host. These MGEs could serve as proving grounds for emerging defense systems, which might eventually become cost-effective once optimized by selection.}, } @article {pmid42244725, year = {2026}, author = {Steinberger, AJ and Nickodem, CA and Leite de Campos, J and Kates, AE and Goldberg, TL and Safdar, N and Sethi, AK and Shutske, JM and Ruegg, PL and Suen, G and Hite, JL}, title = {Antimicrobial use contributes to resistance gene enrichment across cattle groups on commercial dairy farms.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.22.726633}, pmid = {42244725}, issn = {2692-8205}, abstract = {Antimicrobial use (AMU) in agricultural systems is frequently linked to antimicrobial resistance (AMR). Yet, the scale at which AMU reshapes host-associated resistomes remains unclear. This gap arises, in part, from the scarcity of farm-level AMU data from commercial production systems. Here, we combine detailed AMU records from commercial dairy farms with metagenomic analyses of bovine fecal resistomes from calves, lactating cows, sick cows, and cull cows. At a broad level, resistome profiles were similar regardless of farm AMU. Resistance associated with historically common antibiotics, such as tetracyclines, was frequent on low- and high-AMU farms, indicating that some resistance classes are ubiquitous in dairy systems regardless of current AMU. In contrast, resistance to other drug classes varied systematically with AMU. Higher AMU was associated with increased resistance to aminoglycosides, β-lactams, and macrolides, drug classes that are critical for treating mastitis and bovine respiratory disease. Resistance gene richness and diversity were highest in calves, underscoring the importance of accounting for host traits alongside AMU when evaluating resistance patterns. Together, these findings underscore the need for detailed, farm-level AMU data to understand how management practices shape AMR and to inform strategies for sustaining the effectiveness of existing antimicrobials in agricultural and public-health contexts.}, } @article {pmid42244773, year = {2026}, author = {Espinoza, JL and Dupont, CL and Phillips, A}, title = {Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for (pan)genome-resolved metagenomics and metatranscriptomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.07.14.664802}, pmid = {42244773}, issn = {2692-8205}, abstract = {Functional profiling of metagenomes and metatranscriptomes is essential for understanding microbial community capabilities, yet current methods require computationally expensive translated-search alignments that scale poorly to the large genome-resolved reference databases now common in the field. We introduce Leviathan, an open-source software package for integrated taxonomic and functional profiling that operates at both genome and pangenome resolution. Leviathan combines Sylph for ultra fast alignment-free taxonomic profiling with Salmon for pseudo-alignment-based read quantification in DNA-space against genome-resolved gene catalogs, bypassing the translated-search step that dominates runtime in existing approaches. For each (pan)genome, Leviathan functional profiling produces dual metrics: pathway abundance from aggregated gene-level quantification and pathway coverage from graph-based assessment of enzymatic step completeness. On CAMI-I and CAMI-II datasets, Leviathan achieved up to 74-fold faster runtimes and 14-fold lower memory usage compared to HUMAnN, while improving genome-level assignment accuracy by up to 12% and pangenome-level accuracy by up to 5%. We demonstrate Leviathan's applicability through two case studies: a marine plastisphere metagenomics dataset where differential coverage analysis revealed metabolic shifts between early and mature biofilm communities and a dental caries metatranscriptomics dataset where pangenome-resolved co-expression network analysis identified organism-specific transcriptional patterns diagnostic of health and disease states. Leviathan is available at https://github.com/jolespin/leviathan.}, } @article {pmid42245494, year = {2026}, author = {Hu, Z and Chen, C}, title = {Revealing gut microbiota profiles and their influencing factors in commercial boars of three breeds by a large-scale metagenome study.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1825304}, pmid = {42245494}, issn = {1664-302X}, abstract = {Boars play a critical role in pig production. Numerous studies have reported important effects of the gut microbiota on pig production traits. However, whether the gut microbiota is associated with reproduction traits in boars remains largely unknown. Understanding the gut microbial composition and its influencing factors in large-scale boar populations is an essential first step to investigate this association. In this study, shotgun metagenomic sequencing was performed on fecal samples of 1,651 commercial boars from three breeds raised in three pig farms to uncover their gut microbial structures. We observed significant differences in boar gut microbial compositions across three breeds, even when raised in the same farm. Permutational multivariate analysis of variance (PERMANOVA) within-farm breeds and with-age stages found that the effect size of each factor on boar gut microbial composition varied across farms and age stages. Breeds accounted for 2% ~ 9% of the variance of boar gut microbial compositions in different farms. We then identified gut microbial taxa enriched in each boar breed using MaAsLin2. Lactic acid and butyrate-producing taxa, such as Lactobacillus amylovorus and Faecalibacterium prausnitzii, were enriched in Duroc boars; Akkermansia muciniphila and Lactobacillus reuteri showed the enrichment in Landrace boars, accompanied by increased relative abundance of Enterobacteriaceae members. Meanwhile, the species from Bacteroides, Prevotella, and Treponema had higher abundances in the gut of Large White pigs than in the other two pig breeds. We also identified bacterial species enriched in each of the three age stages. These breed and age-associated microbial enrichment patterns might reflect the combined effects of long-term genetic selection of pig breeds, age, and differences in feeding diets. The results of this study provide important insights for further investigating the effects of gut microbiota on boar reproductive traits and for developing strategies to modulate the gut microbiota to improve boar health and production performance.}, } @article {pmid42245495, year = {2026}, author = {Kuźniar, A and Das, AP and Goraj, W}, title = {Editorial: Unveiling microbiome interactions and functions in soil hotspots.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1820854}, doi = {10.3389/fmicb.2026.1820854}, pmid = {42245495}, issn = {1664-302X}, } @article {pmid42245502, year = {2026}, author = {Abdulsamad, MA and Bardaa, S and Elleuch, M and Mathlouthi, NEH and Ben Ali, M}, title = {Metagenomic characterization of infected diabetic foot ulcers in North Africa: microbial diversity, virulome, and resistome profiling.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1825173}, pmid = {42245502}, issn = {1664-302X}, abstract = {This study provides the first shotgun metagenomic characterization of infected diabetic foot ulcers (DFUs) from North Africa. We analyzed two independent datasets with distinct roles: 25 non-infected US DFUs (PRJNA506988) served as an ecological reference cohort to characterize depth-stratified microbial community patterns and pre-infection ARG ecology; 15 infected Libyan DFUs constituted the primary characterization cohort. Metagenomic sequencing, taxonomic classification, resistome and virulome profiling, and metagenome-assembled genome (MAG) reconstruction were performed. In the US reference cohort, depth-dependent community shifts were documented: Fusobacteriota predominated in deeper ulcers, while Staphylococcaceae and Pseudomonadaceae were enriched in superficial wounds. Eighty ARGs were detected across depth groups, including mecA and the mexAB-oprM efflux system, in clinically non-infected wounds. In the Libyan cohort, four major opportunistic pathogens were identified: Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter baumannii, and Corynebacterium striatum. From sample M13, a high-quality P. aeruginosa MAG (99.68% completeness, 0.89% contamination) was reconstructed, classified as ST664 and carrying 220 virulence factors, 60 antibiotic resistance genes (all confirmed by RGI v6.0.2), and 213 mobile genetic elements. These findings represent the first genomic evidence of ST664 in a North African DFU and underscore the need for metagenomics-guided antimicrobial stewardship in chronic wound management.}, } @article {pmid42245511, year = {2026}, author = {Otto, SJG and McLeod, L and McCarthy, EL and Funk, T and Lacoste, SR and Chai, Z and Links, MG and Barlow, LD and Gow, SP and Ramsay, D and Zaheer, R and McAllister, TA and Stothard, P and Hill, JE and Waldner, CL}, title = {Laboratory tests for bovine respiratory bacteria and antimicrobial resistance in commercial feedlot cattle: comparing culture, long-read metagenomics, and recombinase polymerase amplification.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1806062}, pmid = {42245511}, issn = {1664-302X}, abstract = {INTRODUCTION: The risk to humans and animals from antimicrobial resistance (AMR) has increased the emphasis on antimicrobial stewardship in food animal agriculture. Current stewardship recommendations include increasing diagnostic laboratory testing to inform antimicrobial use for bovine respiratory disease (BRD) management in beef feedlot production, yet the performance of newer molecular and sequencing-based diagnostic tests in commercial settings remains poorly characterized.

METHODS: Using nasopharyngeal swabs collected from commercial feedlot calves as part of Canadian surveillance, this study evaluated diagnostic laboratory testing approaches for detecting key bacterial BRD pathogens (Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasmopsis bovis) and associated AMR genes. Bayesian latent class models (BLCMs) were applied to compare traditional culture and antimicrobial susceptibility testing (AST) or qPCR with long-read metagenomic sequencing and recombinase polymerase amplification (RPA). Differences in detection of target bacteria and phenotypic or genotypic AMR were assessed across the early feeding period and between age cohorts.

RESULTS: This represents the first large-scale field evaluation of a recently developed, long-read metagenomic sequencing protocol implemented by a commercial laboratory for detecting BRD bacteria and AMR in respiratory samples (n = 760) collected by private veterinarians from western Canadian beef feedlots. Detection patterns for BRD bacteria and AMR using culture/AST and metagenomics were often similar between fall-placed calves and yearlings, but with differences from RPA. Detection of BRD bacteria had low sensitivity (< 65% for most organisms/tests), but higher specificity (>90% for all organisms/tests). Detection of macrolide and tetracycline resistance had low but variable sensitivity, with higher estimates for AST compared to metagenomics and RPA, and higher but variable specificity (>90% for most resistance outcomes/tests). Despite not using any targeted enrichment, metagenomic sequencing detected M. bovis although with a sensitivity lower than qPCR or RPA. Estimates of predictive value were most informative across the largest range of prevalence for AST, followed by metagenomics and then RPA.

DISCUSSION: This work demonstrates the potential for large scale implementation of long-read metagenomic sequencing to support antimicrobial stewardship and AMR surveillance for feedlot cattle. The estimates of clinical diagnostic performance and predictive values provide evidence-based guidance for three different laboratory tests for BRD management.}, } @article {pmid42245748, year = {2026}, author = {Li, JZ and Guan, SY and Zhang, JF and Zheng, JN}, title = {Acute Q Fever in an Elderly Traveler with Multiple Comorbidities Diagnosed by Blood mNGS and Resolved with Omadacycline.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {610202}, pmid = {42245748}, issn = {1178-6973}, abstract = {This article reports a case of acute Q fever in a 61-year-old man. The patient mainly presented with high fever and cough. Extensive multi-system investigations failed to identify an etiology. On the fourth day of admission, the diagnosis of acute Q fever was confirmed by rapid detection of Coxiella burnetii nucleic acid sequence by blood metagenomic Next-Generation Sequencing (mNGS). With the treatment of intravenous omadacycline, the fever was controlled within 24 hours and the clinical symptoms significantly improved. Subsequent sequential therapy with oral doxycycline was administered, and the patient was discharged successfully. This case highlights the value of mNGS in the rapid diagnosis of rare or zoonotic pathogens in patients with fever of unknown origin, especially in patients with potential exposure to endemic areas. Furthermore, the novel tetracycline antibiotic omadacycline, demonstrating favorable efficacy and safety despite the patient's liver dysfunction, offers a valuable treatment option for rapid control of acute Q fever symptoms, especially in severe cases or those intolerant to doxycycline.}, } @article {pmid42245929, year = {2026}, author = {Yan, W and Wang, X and Shi, K and Wang, L}, title = {Atypical Legionella pneumophila encephalopathy lacking respiratory symptoms and radiographic lesions: A Case Report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1828042}, pmid = {42245929}, issn = {2296-858X}, abstract = {This report details an unusual case of Legionella pneumophila encephalopathy in a 29-year-old male who presented with acute altered consciousness and extreme agitation, notably lacking any respiratory symptoms or typical meningeal signs. Extensive imaging, including chest CT and cranial MRI, revealed no pulmonary infiltrates or structural brain lesions. Cerebrospinal fluid (CSF) analysis demonstrated an aseptic profile with elevated protein, and CSF metagenomic sequencing returned negative. The diagnostic dilemma was ultimately resolved using whole-blood targeted next-generation sequencing (tNGS), which detected Legionella sequences. The patient achieved a rapid and complete neurological recovery following a combined regimen of levofloxacin and high-dose glucocorticoids. This case underscores that Legionella infection can manifest as an isolated, toxin- and immune-mediated encephalopathy without preceding clinical pneumonia. It highlights the critical rescue value of early molecular screening (such as tNGS) in unexplained encephalopathy and supports the judicious use of early steroid intervention to halt the aseptic neurotoxic cascade.}, } @article {pmid42246002, year = {2026}, author = {Ren, JM and Zhang, XY and Liu, XP and Pei, LH and Jiang, WP and Zhang, XM and Ding, H and Huang, JS}, title = {Specimen-specific differences in clinical metagenomic sequencing reporting patterns in hospitalized patients: a single-center retrospective observational study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1823283}, pmid = {42246002}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Hospitalization ; Male ; Female ; Cerebrospinal Fluid/microbiology ; }, abstract = {Clinical metagenomic next-generation sequencing (mNGS) is increasingly used in hospitalized patients, but finalized reporting patterns vary across specimen types in routine practice. We conducted a single-center retrospective observational study using routine clinical mNGS data from January 1, 2024, to December 31, 2025. A specimen-specific first-order design retained only the first eligible mNGS order per patient within each specimen category during the study window. Orders were grouped as bronchoalveolar lavage fluid (BALF), blood, cerebrospinal fluid (CSF), and tissue for primary comparisons; heterogeneous "Other" specimens were described separately. The primary endpoint was report-interpreted any-positive at the order level. We summarized specimen-specific report-interpreted positivity, pathogen-group detection, the most frequently reported organisms ranked by order-level report presence, and mixed detections among positive orders. ICU-associated analyses were included as contextual descriptive stratification only. The cohort included DNA-only orders and a subset of PMseq-RNA-tested orders; RNA virus analyses were restricted to PMseq-RNA-tested orders, and DNA-only orders were treated as not tested for RNA virus fields. Among 1, 981 included specimen-specific first orders, BALF accounted for 973, blood 473, CSF 240, and tissue 122. Report-interpreted any-positive differed by specimen type, with BALF highest (876/973, 90.0%; 95% CI, 88.0-91.8%), followed by tissue (95/122, 77.9%; 95% CI, 69.7-84.3%), blood (343/473, 72.5%; 95% CI, 68.3-76.3%), and CSF (63/240, 26.2%; 95% CI, 21.1-32.2%). Among positive orders, at least 2 distinct standardized pathogens were reported in 672/876 BALF orders (76.7%), 182/343 blood orders (53.1%), 39/95 tissue orders (41.1%), and 8/63 CSF orders (12.7%). Across the four primary specimen groups, the most frequently reported organisms included Epstein-Barr virus (n = 485), Candida albicans (n = 285), and cytomegalovirus (n = 262), together with Klebsiella pneumoniae and Acinetobacter baumannii; these rankings reflect report-level frequency rather than adjudicated pathogenic roles, particularly for latency- or reactivation-prone viruses. Of included orders, 277 (14.0%) underwent PMseq-RNA testing. These findings characterize specimen-specific differences in clinical mNGS reporting patterns and provide a specimen-context-aware reference for interpreting routine inpatient reports.}, } @article {pmid42246191, year = {2026}, author = {Das, D and Dixit, R and Pandey, M}, title = {The Biliary Multi-Omics Landscape: Integrating Microbiome and Metabolomics in Gallbladder Carcinogenesis.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.70462}, pmid = {42246191}, issn = {1440-1746}, abstract = {BACKGROUND: Gallbladder cancer (GBC) is a highly aggressive malignancy with a dismal prognosis, frequently diagnosed at advanced stages. While cholelithiasis is a primary risk factor, the role of the biliary microbiome and its metabolic products in driving carcinogenesis is increasingly recognized. This review synthesizes multi-omics data to elucidate the interplay between microbial dysbiosis and metabolomic shifts in GBC.

METHODS: A systematic literature search was conducted on PubMed (up to January 2026) focusing on biliary bacteria, the gut-bile axis, and multi-omics markers. A narrative synthesis integrated findings from metagenomic, metaproteomic, and metabolomic studies involving human cohorts and experimental models.

RESULTS: GBC is characterized by profound biliary dysbiosis, specifically the enrichment of Enterobacteriaceae, Streptococcus, and Helicobacter species. This taxonomic shift triggers a pro-carcinogenic metabolomic flux, where microbial 7α-dehydroxylation converts primary bile acids into secondary bile acids, such as deoxycholic acid (DCA), which induce DNA damage and promote tumor growth. Metaproteomic signatures identify bacterial proteins (e.g., QDR3, ompA) that facilitate biofilm formation and oxidative stress evasion. Furthermore, emerging paradigms like cross-species horizontal gene transfer (HGT) suggest that microbial genetic material can directly modulate host oncogenic pathways.

CONCLUSION: The GBC multi-omics landscape reveals a complex gut-bile axis where microbial and chemical factors converge. These integrated signatures offer potential as noninvasive biomarkers for early diagnosis and precision therapy.}, } @article {pmid42247317, year = {2026}, author = {Zeng, Y and Wang, S and Zhang, Q and Miao, H and Xu, J and Li, W}, title = {Successful management of Legionella pneumonia in an immunocompromised infant presenting with generalized pustular rash: A case report.}, journal = {Science progress}, volume = {109}, number = {2}, pages = {368504261458101}, pmid = {42247317}, issn = {2047-7163}, mesh = {Humans ; Male ; *Immunocompromised Host ; Infant ; *Exanthema/drug therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; *Legionnaires' Disease/drug therapy/immunology/microbiology ; *Legionella/drug effects ; }, abstract = {Legionella infection is rare in children, and extrapulmonary manifestations are even less commonly reported. Cutaneous involvement, particularly in the form of generalized pustular eruptions, may present significant diagnostic and therapeutic challenges, especially in immunocompromised patients. We report a male infant under 6 months with X-linked severe combined immunodeficiency (XL-SCID) who presented with a disseminated pustular rash as the predominant clinical feature. Initial blood and pus cultures were negative, and empirical antimicrobial therapy showed limited clinical response. Metagenomic next-generation sequencing (mNGS) was subsequently performed and identified Legionella as the causative pathogen. Based on this finding, the antimicrobial regimen was adjusted to include a macrolide antibiotic combined with trimethoprim-sulfamethoxazole (TMP-SMX), resulting in significant clinical improvement and eventual recovery. This case highlights the atypical presentation of Legionella infection with predominant cutaneous manifestations in children, particularly in the context of primary immunodeficiency, and underscores the diagnostic value of mNGS in cases with inconclusive conventional testing. Early application of advanced molecular diagnostics and timely optimization of targeted antimicrobial therapy are crucial for improving outcomes in rare and complex pediatric infections.}, } @article {pmid42247440, year = {2026}, author = {Levade, I and Delisle, B and Fournier, É and Therrien, C}, title = {RNA metagenomic profiling of mosquito viromes associated with Vector-Borne diseases in Quebec, Canada.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0350663}, pmid = {42247440}, issn = {1932-6203}, mesh = {Animals ; Quebec ; *Metagenomics/methods ; Phylogeny ; *Culicidae/virology ; *Virome/genetics ; Genome, Viral ; Mosquito-Borne Diseases ; *Mosquito Vectors/virology ; *RNA, Viral/genetics ; Arboviruses/genetics/classification ; }, abstract = {Mosquitoes harbor diverse viral communities, including both medically important arboviruses and insect-specific viruses, yet the viromes of mosquito populations in northern temperate regions remains poorly characterized. In this study, we used metagenomic sequencing to analyse pools of archived mosquito samples from Québec, Canada representing multiple species previously identified as arbovirus carriers. Our analyses identified 60 viral species, including three arboviruses, several insect-specific viruses, and multiple dual-host non-pathogenic viruses, revealing the rich viral diversity present in these mosquito populations. Phylogenetic analysis of complete viral genomes demonstrated genetic relationships with viruses reported from diverse geographic regions. We describe, a newly proposed bipartite Culex tombus-like virus and report the complete resolution of thirty-five viral genomic sequences. These results highlight the utility of metagenomic approaches for comprehensive characterization of the mosquito virome and underscore their potential to enhance surveillance of emerging arboviruses, including West Nile virus, in Québec and similar northern ecosystems.}, } @article {pmid42247515, year = {2026}, author = {Piñero, M and Librado, P}, title = {Genomic evidence for limited entomophagy in ancient Europeans.}, journal = {Science advances}, volume = {12}, number = {23}, pages = {eaec6939}, pmid = {42247515}, issn = {2375-2548}, mesh = {Animals ; Humans ; *Chitinases/genetics ; *DNA, Ancient/analysis ; Europe ; *European People/genetics/history ; *Insecta/classification/genetics ; Metagenomics ; *Diet/history ; History, Ancient ; }, abstract = {To meet the rising food demands of our growing population, the Food and Agriculture Organization proposed edible insects as sustainable sources of animal protein. Although hundreds of million people already consume insects around the tropics, western societies remain averse to entomophagy. To trace whether ancient Europeans consumed insects, we here apply two complementary genomic approaches. Metagenomic screening on 745 ancient anatomically modern human dental calculus returned limited insect DNA traces, with read abundances well below those observed in Neanderthals, western chimpanzees, and gorillas. In addition, genes encoding stomach-expressed chitinases show two of the most significant signatures of latitudinal differentiation genome-wide. Clines are consistent with evolutionary benefits of entomophagy in tropical regions and with expression quantitative trait locus data supporting low chitin digestibility in present-day Europeans. Ancient genomes confirm that both clines already existed at the onset of agriculture and persisted despite massive migrations. Together, our findings support occasional and possibly incidental insect consumption in Europe over the past ~9000 years.}, } @article {pmid42247592, year = {2026}, author = {Boulay, A and Németh, V and Criel, B and Stock, M and De Baets, B and Galiez, C and Rousseau, E and Briers, Y and Vázquez, R}, title = {PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery.}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, pmid = {42247592}, issn = {1758-0463}, support = {#325947//FRQNT/ ; //NSERC/ ; 1S91526N//FWO/ ; 1S38519N//FWO/ ; #307935//FRQS/ ; 01P10022//BOF/ ; }, mesh = {*Bacteriophages/genetics/enzymology ; *Metagenomics/methods ; *Viral Proteins/genetics ; *Databases, Protein ; *Software ; *Metagenome ; }, abstract = {As biology becomes increasingly data-driven, so does the field of phage lysins, enzymes that degrade bacterial cell walls and offer promising alternatives to traditional antibiotics. Five years ago, we introduced PhaLP, a centralized resource for Phage Lytic Protein sequences and associated metadata to support global research efforts. Here, we present PhaLP 2.0, an enhanced database designed to address key challenges in computational lysin research by integrating newly identified lysins from thousands of metagenomes. To expand the known diversity of lysins beyond that of cultured phages, we developed SUBLYME, a protein-embedding-based machine-learning Software designed to Uncover and classify Bacteriophage Lysins from Metagenomic datasets. Using embeddings derived from the well-curated sequences of the original PhaLP database, we trained support vector machines to distinguish lysins from non-lysins in viromes and classify them as endolysins or virion-associated lysins. The models achieved an average F1 score of 98% on held-out clusters. SUBLYME enabled the discovery of 743 000 new lysin sequences from EnVhogDB, a virome-derived protein database, increasing the number of known lysin clusters 40-fold, from 1000 to 40 000. SUBLYME and PhaLP 2.0 are accessible online at https://github.com/Rousseau-Team/sublyme and https://phalp.ugent.be, respectively. Together, these advances establish PhaLP 2.0 as a comprehensive and scalable portal for lysin discovery, classification, and sequence analysis, paving the way for future antibacterial applications and evolutionary insights.}, } @article {pmid42247807, year = {2026}, author = {Sadia, H and Amin, A and Khalid, N and Ahmed, I}, title = {Antimicrobial resistance and virulence in polymicrobial chronic wound infections: A metagenomic perspective.}, journal = {Journal of infection and public health}, volume = {19}, number = {8}, pages = {103280}, doi = {10.1016/j.jiph.2026.103280}, pmid = {42247807}, issn = {1876-035X}, abstract = {BACKGROUND: Chronic wound infections represent a significant clinical and public health challenge due to their polymicrobial nature and the increasing burden of antimicrobial resistance (AMR). Conventional culture-based diagnostics often fail to capture the full microbial diversity and resistance potential associated with these infections.

METHODS: Chronic wound samples persisting for more than 15 days were collected from patients at a tertiary-care hospital in Pakistan. Samples are categorized into five groups: lower leg (ll-H1), upper leg (ul-H2), foot (ft-H3), chest (ct-H4) and catheter (ca-H5). Shotgun metagenomic sequencing was employed alongside routine culture-based methods to characterize microbial communities, antimicrobial resistance genes, and virulence determinants. Taxonomic and functional profiling were performed to assess microbial diversity and resistance patterns across wound subgroups.

RESULTS: Metagenomic analysis revealed a predominance of Proteobacteria, Bacteroidetes, and Actinobacteria. Clinically relevant pathogens, including Achromobacter xylosoxidans, Staphylococcus aureus, and Pseudomonas aeruginosa, were frequently detected, along with less commonly reported taxa such as Achromobacter insolitus and Stenotrophomonas maltophilia. Multiple antimicrobial resistance gene clusters and biofilm-associated virulence factors were identified, indicating substantial multidrug resistance potential. Site-specific analysis showed that Pseudomonas aeruginosa dominated ul-H2 (∼32%), while Enterobacter hormaechei was most abundant in ft-H3 (∼40%). Culture-based methods primarily recovered common aerobic pathogens, whereas metagenomics detected additional opportunistic and unculturable taxa, highlighting the limitations of routine diagnostics. Resistome analysis identified ARGs conferring resistance to β-lactams, aminoglycosides, fluoroquinolones, tetracyclines, and macrolides.

CONCLUSIONS: Chronic wound infections in Pakistan harbor diverse polymicrobial communities with substantial antimicrobial resistance and virulence potential. Shotgun metagenomics provides a more comprehensive characterization than culture-based methods by detecting additional pathogens and resistance determinants across wound sites. These findings support the integration of metagenomic diagnostics to improve clinical decision-making, strengthen antimicrobial stewardship, and guide infection control strategies in resource-limited healthcare settings.}, } @article {pmid42248018, year = {2026}, author = {Park, S and Shin, JH and Lee, HH and Lee, JG}, title = {Cover crop incorporation maintains the methane oxidation potential and lowers methane emissions in plastic-film-mulched upland arable soils.}, journal = {Journal of environmental management}, volume = {410}, number = {}, pages = {130115}, doi = {10.1016/j.jenvman.2026.130115}, pmid = {42248018}, issn = {1095-8630}, mesh = {*Methane/metabolism ; *Soil/chemistry ; Oxidation-Reduction ; Soil Microbiology ; Zea mays ; Plastics ; *Agriculture/methods ; Crops, Agricultural ; Oxygenases ; }, abstract = {Plastic film mulching can transform upland arable soils from sinks for methane (CH4) into sources by limiting gaseous exchange and creating hypoxic microsites. We explored whether incorporating cover crops can help reduce CH4 emissions by maintaining methanotroph functional potential in the presence of mulching. We conducted a field experiment in an upland maize field to compare NPK fertilization and cover crop incorporation, both with and without mulching. We combined CH4 flux measurements with methane oxidation potential (MOP) assays and shotgun metagenomics to analyze CH4-cycling communities and functional gene profiles. Cover crop incorporation under mulching (M-CC) reduced cumulative CH4 emissions by 55% compared with NPK fertilization under mulching (M-NPK) and maintained 17% higher MOP. By contrast, particulate methane monooxygenase (pMMO) genes did not show a uniform enrichment under M-CC. However, M-CC demonstrated higher abundances of genes associated with hydrogenase activity, single-carbon (C1) metabolism, electron transport, and antioxidant biosynthesis. Specifically, there was a 21% to 67% increase in hydrogenase genes, a 14% to 55% rise in C1 metabolism genes, a 28% to 54% increase in electron transport genes, and a remarkable 280% elevation in the antioxidant biosynthesis gene egtD. Using plastic film mulching with incorporated cover crops maintained MOP and promoted greater microbial biomass and metabolic flexibility. These effects were linked to lower CH4 emissions and reduced yield-scale CH4 emissions, all without compromising maize yield.}, } @article {pmid42248101, year = {2026}, author = {Xu, Z and Zhang, L and Zhu, D and Zhi, S and Ashbolt, NJ and Li, G and Luo, W and Nghiem, LD}, title = {Optimising composting to reduce plasmid and integrative conjugative element conjugation to minimise antibiotic resistomes in livestock manure for safe organic fertilisation.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142573}, doi = {10.1016/j.jhazmat.2026.142573}, pmid = {42248101}, issn = {1873-3336}, abstract = {Antimicrobial resistance is a critical threat to organic fertilizer production from livestock manure by composting. This study provides new insights to the dynamics of antimicrobial resistance genes (ARGs) during composting to propose strategies for their elimination. Results from genome-resolved metagenomics, meta-analysis, and quantitative assessment showed temperature and moisture content as key factors governing ARG dynamics during composting. Although integrative conjugative elements (ICE) could be transferable by some thermophilic bacteria, composting temperature to above 60 °C reduces mobile ARGs driven by plasmid conjugation for elimination. Further controlling moisture content to low than 60% inhibits the secretion of extracellular polymeric substances to restrain ARG rebound by ICE conjugation, particularly at the maturation stage of composting. These results are significantly useful for China, where swine manure accounted for most of livestock manure-derived ARGs (91.5%). Applying findings from this study to optimise the composting of livestock manure could reduce ARG proliferation by up to 59.3% in China.}, } @article {pmid42248258, year = {2026}, author = {Guo, Y and Jia, X and Chen, Y and Xu, S and Ming, T and Kong, F and Xu, J}, title = {Inhibiting methanogenesis with medium-chain fatty acids: strategy for rapid start-up and stable operation of food waste chain elongation systems.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135078}, doi = {10.1016/j.biortech.2026.135078}, pmid = {42248258}, issn = {1873-2976}, abstract = {Converting food waste (FW) into medium-chain fatty acids (MCFAs) via chain elongation (CE) is an economical and eco-friendly approach, but methanogenic competition remains a key challenge limiting CE efficiency. Traditional inhibition methods (e.g., pH regulation, hydraulic/solids retention time control, chemical additives) require strict operation or external inputs, causing non-specific microbial inhibition, high costs and environmental risks. Innovatively, MCFAs can inherently suppress methanogens with obvious advantages. However, their inhibition mechanisms and dependence on concentration and carbon chain length remain unclear. This study investigated the effects of butyric acid (C4), caproic acid (C6), and caprylic acid (C8) at different concentrations on methane production, medium- and short-chain fatty acids accumulation, and microbial dynamics in FW anaerobic fermentation. The results indicated that the inhibitory effect was primarily driven by undissociated fatty acids, with the potency increasing with longer carbon chain lengths. Notably, C8 at a low undissociated concentration (0.05 mM) completely inhibited methanogenesis. Higher concentrations of C4, C6, and C8 effectively sustained hydrolysis and acidogenesis while promoting CE and leading to the accumulation of caproic acid and caprylic acid. Metagenomic analysis showed that a decline in methanogenesis-related functional genes was accompanied by an increase in reverse β-oxidation related functional genes. These findings provide a feasible strategy for rapid start-up and stable operation of FW-based CE systems, and present a sustainable route for FW valorization toward high-value biochemicals.}, } @article {pmid42248259, year = {2026}, author = {Gai, T and Zhang, J and Zhang, S and Zhang, L and Li, X and Wu, Y and Yang, Y and Liu, X and Shi, G and Yang, M}, title = {Performance and mechanisms of a biochar-enhanced partial nitritation/anammox process for the treatment of silane tower wastewater.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135083}, doi = {10.1016/j.biortech.2026.135083}, pmid = {42248259}, issn = {1873-2976}, abstract = {The increasing discharge of silane tower wastewater, characterized by high ammonia (NH4[+]-N) and the presence of silane derivatives, poses significant challenges to biological nitrogen removal processes. In this study, a partial nitritation/anammox (PN/A) sludge system was enhanced through the addition of sludge-derived biochar (SBC). The results demonstrated that SBC effectively improved the nitrogen removal performance of PN/A sludge during the treatment of silane tower wastewater. Under low-proportion silane tower wastewater conditions, SBC rapidly promoted R2 sludge granulation within 19 d during phase I. During phase IV, when 100% silane tower wastewater was used as the influent, the NH4[+]-N and total nitrogen removal efficiencies of R2 were stably maintained at 80%-83%. These improvements were mainly attributed to the ability of SBC to promote sludge granulation, enrich functional microorganisms, and enhance extracellular electron transfer (EET) performance. SBC addition enabled the sludge to maintain higher levels of tightly bound extracellular polymeric substances rich in hydrophobic amino acids (HAAs). This study found that SBC-promoted EET was more strongly associated with anammox bacteria than with ammonia-oxidizing bacteria, resulting in a more pronounced enhancement of specific anammox activity than specific ammonia oxidation rate. Metagenomic and metatranscriptomic analyses further revealed that SBC enhanced the biosynthetic pathways and transcriptional expression of genes associated with HAA synthesis in PN/A sludge. Overall, this study provides a novel enhancement strategy for the application of PN/A processes in the treatment of complex industrial wastewater with high NH4[+]-N concentrations.}, } @article {pmid42248305, year = {2026}, author = {Janes, VA and Stalenhoef, JE and van der Putten, BCL and Koster, LAM and Jakobs, ME and van Dissel, JT and de Jong, MD and Schultsz, C and Mende, DR}, title = {Metagenomic sequencing as a diagnostic tool for urine culture negative febrile urinary tract infection.}, journal = {The Journal of infection}, volume = {93}, number = {2}, pages = {106783}, doi = {10.1016/j.jinf.2026.106783}, pmid = {42248305}, issn = {1532-2742}, abstract = {OBJECTIVES: The diagnosis of febrile urinary tract infection (fUTI) by urine culture is hampered by antibiotic pre-treatment. We investigated urine metagenomics to diagnose fUTI in patients with positive blood but negative urine cultures.

METHODS: We performed shotgun metagenomic sequencing on 41 culture-positive and 19 culture-negative urine samples from fUTI patients, comparing urine metagenomics to blood and urine culture including antimicrobial susceptibility testing (AST). mOTUs3.1 performed metagenomic pathogen detection and ResFinder2.0 antimicrobial drug resistance (AMR) gene detection (standard settings). Whole genome sequencing (WGS) was performed on blood culture isolates from culture-negative urine samples. BWA-MEM and sylph aligned metagenomic pathogen reads to their respective WGS assemblies.

RESULTS: Metagenomics detected the blood culture isolate in 39/41 culture-positive and 17/19 culture-negative urine samples. 11/19 urine culture-negative patients were pre-treated with antibiotics, versus 8/41 urine culture-positives. The blood culture isolate was the most abundant pathogen in 33/41 culture-positive and 15/19 culture-negative urine samples. A median of 93.2% of pathogen-specific metagenomic reads mapped to their WGS assemblies with a median ANI of 98.7% (n=11). Genotypic AMR detection and phenotypic AST matched in 38-96% of cases.

CONCLUSIONS: Urine metagenomics successfully detected the causative pathogen in urine culture-negative fUTI patients. Genotypic AMR prediction requires further investigation.}, } @article {pmid42248407, year = {2026}, author = {Tan, Y and Sun, J and Chen, X and Wang, Y and Zhang, C and Gong, L and Cui, X}, title = {Chronic Papillary Conjunctivitis as a Novel Ocular Manifestation of Rickettsia felis Infection: A Case Report.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108861}, doi = {10.1016/j.ijid.2026.108861}, pmid = {42248407}, issn = {1878-3511}, abstract = {PURPOSE: To report the first case of chronic papillary conjunctivitis caused by Rickettsia felis infection.

CASE: A 27-year-old man presented with a four-year history of unilateral papillary conjunctivitis refractory to multiple antibiotic courses. Examination revealed tarsal conjunctival injection, papillary hypertrophy, mucopurulent discharge, and eyelid laxity with entropion. The patient had a history of cat ownership for 5-6 years, suggesting possible exposure to the cat flea, and remained systemically asymptomatic without fever, rash, or lymphadenopathy. Metagenomic next-generation sequencing (mNGS), serology, and histopathology confirmed Rickettsia felis infection. Given the chronic intracellular nature of the infection, the patient received an extended 2-month course of oral doxycycline (100 mg twice daily) combined with topical therapy, with marked improvement observed by week 8 and subsequent entropion repair surgery.

CONCLUSION: This represents the first reported case of chronic, isolated rickettsial conjunctivitis without systemic involvement or Parinaud's oculoglandular syndrome features. This case highlights the importance of considering rickettsial infection in chronic, treatment-refractory conjunctivitis and demonstrates the value of metagenomic sequencing for diagnosis.}, } @article {pmid42248728, year = {2026}, author = {van Dorst, J and Taylor, N and Pushpakumara, BLDU and Tan, ZT and Buchanan, DD and Haber, PS and Nash, E and Visser, S and Volovets, A and Sivam, S and Ooi, CY}, title = {Genotoxic pks + E. coli is strongly associated with ileocolonic neoplasia in adults with Cystic Fibrosis.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2026.05.016}, pmid = {42248728}, issn = {1873-5010}, abstract = {BACKGROUND: Polyketide synthase island-positive (pks+) Escherichia coli is a genotoxic gut bacterium linked to colorectal cancer (CRC) tumorigenesis via the genotoxin colibactin. In adults with Cystic Fibrosis (CF), there is an increased incidence and earlier development of CRC but the biological mechanisms underlying this increased risk remain incompletely understood. We aimed to determine the prevalence of pks+ E. coli in adults with CF.

METHODS: Stool samples and DNA were analyzed from the SCREENCF study cohort. Metagenomic libraries were sequenced on the NovaSeq X Plus platform, using Illumina protocols. Detection of the pks island was assessed with polymerase chain reaction (PCR) targeting the clbB gene.

RESULTS: Of the 49 CF participants; pks+ E. coli was detected in 1/35 (3%) of the no pathology (NORMAL) group, 5/12 (42%) in the adenomatous polyps (AP) group, and 2/2 (100%) in the ileocolonic cancer (ICC) group. Individuals with any ileocolonic neoplasia were 34 times more likely to harbor pks+ E. coli than those with NORMAL colonoscopy findings (OR = 34.0, 95% CI 5.00-691, p = 0.002). The presence of pks+ E. coli correlated with higher overall E. coli burden (p = 0.0009), but not with fecal inflammation, other genotoxic bacterial species or overall bacterial composition.

CONCLUSION: pks+ E. coli is infrequently detected among adults with CF, but its presence is associated with ileocolonic neoplasia, indicating a potential role in pathogenesis. If validated in larger cohorts, pks+ E. coli could provide a clinically meaningful biomarker for early detection, risk stratification and a potential target for precision intervention.}, } @article {pmid42248819, year = {2026}, author = {Peng, D and Zhou, J and Xiong, M and Chen, Y and Zhang, Y and Hu, Y and Yang, Y and Xu, J and Zheng, Y and Xu, D}, title = {Gut Microbiota Dysbiosis Drives Lethal Bacterial Enteritis in Sturgeons: Insights From Ex Vivo Cultivation and Metagenomic Investigations.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e70218}, doi = {10.1111/jfd.70218}, pmid = {42248819}, issn = {1365-2761}, support = {D-8006-25-0392//Shanghai Aquatic Wildlife Conservation and Research Center/ ; K2025-02-08-00-12-F00043//Shanghai Municipal Commission of Agriculture and Rural Affairs/ ; }, abstract = {The Chinese sturgeon (Acipenser sinensis) and Yangtze sturgeon (A. dabryanus) are critically endangered flagship species. To investigate the intestinal microbial changes associated with bacterial enteritis in captive populations, we integrated bacterial isolation with metagenomic sequencing to characterize both healthy and maladjusted gut microbiomes. Healthy sturgeons exhibited a stable microbiota dominated by the beneficial Cetobacterium. In contrast, enteritis was consistently associated with severe dysbiosis, characterized by the depletion of these commensals and the massive expansion of opportunistic pathogens, notably Aeromonas and Citrobacter. Culture-based analyses identified A. veronii, C. freundii and Plesiomonas shigelloides as the dominant cultivable bacteria from diseased individuals; these isolates harboured diverse virulence traits and were multidrug-resistant. Crucially, both sturgeon species showed highly similar microbial responses and pathogenic profiles during enteritis. These findings indicate that sturgeon enteritis is closely correlated with a dysbiosis-driven syndrome. Establishing the healthy baseline provides a critical theoretical foundation for screening autochthonous probiotics and developing targeted pathogen control strategies. Furthermore, the striking cross-species commonality validates the Yangtze sturgeon as a viable surrogate model for advancing disease management and conservation in the difficult-to-breed Chinese sturgeon.}, } @article {pmid42248870, year = {2026}, author = {Vasquez, YM and Romero, MF and Bowers, RM and Rohwer, RR and McMahon, KD and Woyke, T and Schulz, F}, title = {Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73437-x}, pmid = {42248870}, issn = {2041-1723}, support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; }, abstract = {Giant viruses play crucial ecological roles in aquatic ecosystems, yet their evolutionary dynamics in response to environmental changes, particularly in freshwater environments, are not well understood. We analyzed a 20-year time series (2000-2019) of 471 co-assembled metagenomes from Lake Mendota (USA) to reconstruct 1512 giant virus metagenome-assembled genomes, providing insights into viral genome evolution. Viruses in the order Imitervirales dominate the virome, remaining consistent across seasons and years. Our findings reveal gene duplication (23% of genes) and horizontal gene transfer (29% of genes) as key drivers of genomic innovation. A co-occurrence network analysis indicates increased virus-host interactions following the introduction of an invasive predatory zooplankton in 2009, highlighting potential hosts in Bigyra, Perkinsea, and Euglenozoa. While single nucleotide polymorphism analysis shows predominantly purifying selection in viral genes, there is a significant increase in positively selected genes post-invasion, particularly those related to infection. Comparative evolutionary analyses reveal that giant viruses exhibit genome-wide substitution rates similar to co-occurring bacteria but significantly slower than smaller dsDNA phages, suggesting both stability and adaptability. Our study demonstrates that freshwater giant viruses employ various evolutionary strategies to respond to environmental change. These results underscore their significant yet often underappreciated role in freshwater ecosystem dynamics.}, } @article {pmid42249277, year = {2026}, author = {Guanglin, W and Xiuwen, K and Rong, H}, title = {Awake VV-ECMO for severe pneumonia caused by Elizabethkingia anophelis: a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13735-3}, pmid = {42249277}, issn = {1471-2334}, abstract = {BACKGROUND: Elizabethkingia anophelis is phenotypically similar to E. meningoseptica and is often misidentified by conventional methods, delaying appropriate therapy. Awake venovenous extracorporeal membrane oxygenation (VV-ECMO) avoids complications of deep sedation and mechanical ventilation, but its role in severe pulmonary infection with rare pathogens remains underexplored.

CASE PRESENTATION: We report a 62-year-old male with chronic hepatitis B who developed type I respiratory failure and septic shock unresponsive to conventional support. VV-ECMO was initiated on January 23, and awake ECMO management was implemented to preserve spontaneous breathing and cough reflex. Serial metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid revealed influenza A H1N1, Aspergillus fumigatus, and multidrug-resistant bacteria (Detailed mNGS results are provided in Supplementary Table 2). On day 32, sputum culture suggested E. meningoseptica, but subsequent mNGS identified E. anophelis (322,376 reads). The anti-infective regimen was adjusted to minocycline-based combination therapy. Under awake ECMO support, the patient's infection markers gradually improved, and he was successfully weaned from ECMO on day 38 and from mechanical ventilation thereafter. He was discharged after recovery.

CONCLUSION: This case demonstrates that awake ECMO can serve as an effective respiratory support platform in complex severe pneumonia. When conventional testing reports E. meningoseptica, clinicians should suspect possible E. anophelis infection, and timely mNGS is recommended for accurate species identification. Minocycline-based combination therapy appears promising for E. anophelis infections.

CLINICAL TRIAL: Not applicable.

CLINICAL PEARL: In critically ill patients with suspected Elizabethkingia infection, do not rely solely on phenotypic identification; use mNGS to distinguish Elizabethkingia anophelis from Elizabethkingia meningoseptica, and consider early minocycline-based therapy.}, } @article {pmid42249286, year = {2026}, author = {Qiu, X and Li, W and Zhang, M and Lei, S and Chen, H and Wang, X and Miao, Y and Yu, Z and Wu, Y and Hou, Z}, title = {The impact of hydrogen sulfide on gut microbiota of diabetic mice with lower limb arterial ischemia.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05167-5}, pmid = {42249286}, issn = {1471-2180}, support = {H2020206490//Natural Science Foundation of Hebei Province/ ; 20230095//Medical Science Research Subject Plan of Hebei/ ; PD2023002//Clinical Medicine Postdoctoral Research Support Program of Hebei Medical University/ ; B2024003014//Hebei Province Yanzhao Golden Talent Program/ ; H2024206134//Key Project of Natural Science Foundation of Hebei Province (Class A)/ ; }, abstract = {BACKGROUND: The prevalence of hindlimb ischemia (HLI) associated with diabetes mellitus (DM) is high. However, its prevention and treatment face significant challenges. This study explored the effects of hydrogen sulfide (H2S) intervention in mice with DM and HLI, while concurrently investigating its regulatory effects on gut microbial homeostasis.

METHODS: The diabetic model in C57BL/6J mice was established through intraperitoneal injection of streptozotocin. The HLI model was created by ligating and severing the femoral artery, with subsequent initiation of a 21-day exogenous H2S intervention. Fecal samples from the mice were collected at four time points: before model establishment, 3 days after successful induction of the diabetes model, 3 days after establishment of the HLI model, and after 21 days of H2S intervention for metagenomic analysis. Body weight, blood glucose levels, and hindlimb blood flow in the mice were monitored. Additionally, functional assessment and histopathological examination of the ischemic skeletal muscle were performed to evaluate contractile and morphological properties.

RESULTS: H2S administration significantly enhanced hindlimb blood perfusion and restored plasma H2S concentrations in diabetic mice with HLI, concurrently improving both function and morphological integrity of the ischemic skeletal muscle. Bacterial abundance at the phylum level showed changes over the course of the experiment, particularly in Bacteroidetes and Firmicutes. In the DM + HLI group, the Firmicutes-to-Bacteroidetes ratio was significantly elevated; however, H2S treatment downregulated this alteration. H2S intervention modulated the abundance of various bacterial species, increasing Lactobacillus murinus and Faecalibacterium prausnitzii, while simultaneously downregulating inflammation-related bacteria such as Ruminococcus sp. JE7A12. Microbial network analysis revealed that the DM + HLI and H2S groups had lower network complexity than the control group. Furthermore, functional metagenomic profiling identified 28 differentially expressed genes, which were annotated to 8 primary and 30 secondary KEGG pathways, with 6 genes specifically enriched in carbohydrate metabolism pathways.

CONCLUSION: Exogenous H2S administration improved hindlimb blood perfusion, restored contractile function, and preserved morphological integrity of ischemic skeletal muscle in diabetic mice with HLI. Concurrently, H2S treatment altered the abundance of gut microbiota, improving microbial balance. Targeting the gut microbiota via H₂S suggests a potential translational avenue that warrants causal investigation for the treatment of diabetic limb ischemia. Further studies are warranted to establish causal relationships and elucidate the underlying mechanisms linking H2S, gut microbiota, and vascular recovery.}, } @article {pmid42249504, year = {2026}, author = {Liu, Y and Xie, Y and Yang, J and Deng, Y and Liu, D and Chang, J and Tang, J and Zhao, H and Chen, X and Tian, G and Liu, G and Cai, J and Jia, G}, title = {Integrated gut metagenomic and muscle proteomic analysis reveals the role of dietary fermented extruded brewers' spent grain in enhancing pork quality through the gut-muscle axis.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42249504}, issn = {1674-9782}, support = {No. 2021ZDZX0009//Sichuan Science and Technology Program/ ; }, abstract = {BACKGROUND: The fact that feeding pigs with probiotic-fermented agricultural by-products improves pork quality has been repeatedly demonstrated and widely applied, but the underlying mechanisms remain unclear. This study explored the effects of fermented extruded brewers' spent grain (FEBSG) on meat quality in growing-finishing pigs, as well as its regulatory mechanisms.

METHODS: Sixty Duroc × Landrace × Yorkshire pigs (52.25 ± 2.10 kg) were randomly assigned to five dietary treatments, in which FEBSG replaced 0, 5%, 10%, 15%, and 20% of soybean meal (SBM). The experiment spanned 10 weeks.

RESULTS: Compared with the control, 20% FEBSG significantly increased final body weight, average daily feed intake, and average daily gain, while decreasing feed to gain ratio (P < 0.05). Both 15% and 20% FEBSG improved carcass characteristics and meat quality, including higher carcass weight, loin eye area, and intramuscular fat content, along with lower drip loss and shear force (P < 0.05). These treatments also enhanced flavor-related amino acids and unsaturated fatty acids (P < 0.05), and improved umami and sweet taste profiles. Moreover, 20% FEBSG increased muscle fiber density and reduced fiber diameter, upregulated MyHC I, MyHC IIa, PGC-1α, AMPKα1, TFAM, and SDH activity, and downregulated MyHC IIb and LDH activity (P < 0.05). Proteomic analysis identified 69 differentially expressed proteins, with enrichment in AMPK and PPAR signaling pathways. Metagenomic analysis revealed increased abundance of short-chain fatty acid-producing bacteria, including Clostridium, Lactobacillus, Prevotella, and Bartonella. Correlation analysis demonstrated associations between gut microbiota diversity and meat quality traits, as well as between dominant microbial genera and differentially expressed proteins, volatile fatty acids, muscle fiber characteristics, and the AMPK/PGC-1α/TFAM signaling pathway.

CONCLUSIONS: Partial replacement of SBM with FEBSG positively influenced growth performance and pork quality in pigs, with the underlying mechanisms may involve the activation of the AMPK/PGC-1α/TFAM signaling pathway via the gut-muscle axis, thereby enhancing mitochondrial biogenesis, muscle development, and metabolism.}, } @article {pmid42249511, year = {2026}, author = {Stahl, S and Widmaier, H and Sakk, V and Nalapareddy, K and Kissmann, AK and Rosenau, F and Mulaw, MA and Haslam, DB and Geiger, H}, title = {Aging of the adaptive immune system affects the gut microbiome and systemic levels of vitamin B6.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42249511}, issn = {2049-2618}, support = {GRK 2254 HEIST//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Aging/immunology ; Mice ; *Gastrointestinal Microbiome/immunology ; *Adaptive Immunity ; *Vitamin B 6/blood/metabolism ; Mice, Inbred C57BL ; Intestinal Mucosa/immunology/microbiology ; Immunity, Mucosal ; Ileum/immunology/microbiology ; }, abstract = {BACKGROUND: Age-associated dysregulation of the gut microbiota is a hallmark of aging and has been linked to multiple age-related diseases, yet upstream host factors driving these changes remain incompletely defined. Extensive bidirectional crosstalk between gut microbiota and mucosal immunity has been described. Aging is accompanied by a progressive decline in immune function, collectively termed aging-associated immune remodeling (AAIR). AAIR encompasses widespread compositional and functional changes that impair an effective response to pathogens, vaccines, and tissue damage. We examined whether AAIR is an upstream host factor influencing the composition of the microbiome upon aging.

RESULTS: Hallmarks of AAIR were also present in the ileal lamina propria, including reduced naïve CD4[+] and CD8[+] T cell populations and expansion of memory and regulatory T cell subsets. To test whether mucosal AAIR reflects intrinsic aging of the hematopoietic system, we used an HSC transplantation model where young RAG1[-/-] recipients develop an adaptive immune system derived exclusively from either young or aged donor HSC in an otherwise young host environment. Recipients of aged HSCs recapitulated key features of mucosal AAIR, particularly loss of naïve T cells, demonstrating that AAIR in the ileal LP is driven at least in part by aged HSCs. Shotgun metagenomic sequencing of fecal samples revealed that ileal AAIR is associated with alterations in gut microbiota. In detail, there was a reduced abundance of taxa associated with the vitamin B6 (VB6) biosynthesis and salvage pathways. Accordingly, VB6 levels in serum were reduced in mice with aged immune systems.

CONCLUSION: Our findings link AAIR to reduced microbial VB6 pathway abundance and lower systemic VB6 availability, suggesting that immune aging shapes the functional output of the microbiome in ways that diminish its VB6 biosynthetic capacity. This postulates an immune-microbiome-VB6 association that warrants further investigations for therapeutic strategies to increase VB6 levels upon aging. Video Abstract.}, } @article {pmid42249581, year = {2026}, author = {Xi, Y and Liping, Z and Yating, X and Yang, X and Jian, C and Caiyun, C and Shuwen, L and Zian, Z and Xiaojian, Y and Shuwen, H and Wei, W}, title = {Genomic Map of Escherichia coli and Single Nucleotide Polymorphism Markers in Colorectal Cancer.}, journal = {Microbial biotechnology}, volume = {19}, number = {6}, pages = {e70397}, pmid = {42249581}, issn = {1751-7915}, support = {2023GZ86//Public Welfare Technology Application Research Program of Huzhou/ ; 2025KY328//Medical and Health Research Project of Zhejiang Province/ ; }, mesh = {*Escherichia coli/genetics ; *Polymorphism, Single Nucleotide ; *Colorectal Neoplasms/microbiology ; Humans ; Genome, Bacterial ; Genetic Markers ; Gastrointestinal Microbiome ; Case-Control Studies ; Chromosome Mapping ; Multilocus Sequence Typing ; }, abstract = {Gut microbial single nucleotide polymorphisms (SNPs) offer stable, specific genetic markers for disease diagnosis. Escherichia coli (E. coli), a dominant gut bacterium, is associated with colorectal cancer (CRC), but limited enteric reference genomes hinder SNP annotation in intestinal strains. Metagenomic sequencing profiled gut microbiota in 200 CRC patients and 200 healthy controls. The E. coli strain WDP was fully sequenced via PacBio single-molecule technology for genome assembly and functional annotation. Wilcoxon tests identified differentially abundant microbes, while Lasso regression models integrated microbial features (bacteria, viruses, virus-host pairs) and E. coli SNPs to predict CRC risk. E. coli abundance did not differ between groups, but genomic analysis revealed 7460 CRC-associated SNPs. The SNP-based model achieved superior accuracy (92.86% training, 93.33% testing, 84.00% validation) and AUC (0.986, 0.983, 0.913), outperforming models based on microbial abundances (e.g., Staphylococcus capitis, Zindervirus) or virus-host interactions. PacBio-generated E. coli genomic maps enable precise SNP annotation, establishing E. coli SNPs as highly accurate biomarkers for CRC risk prediction. This approach leverages microbial genetic stability to advance non-invasive early detection, offering a novel target for precision microbiome-based diagnostics.}, } @article {pmid42249721, year = {2026}, author = {Liu, H and Xu, J and Guo, Y and Lei, Z and Wang, N and Wei, W and Qu, L and Li, M and Feng, Y and Xie, W}, title = {Stepwise Gradient in Fundamental Individualised Niche Differentiation Across Soil Microbiomes.}, journal = {Molecular ecology}, volume = {35}, number = {11}, pages = {e70422}, doi = {10.1111/mec.70422}, pmid = {42249721}, issn = {1365-294X}, support = {SML2023SP218//Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 92051117//National Natural Science Foundation of China/ ; 41776137//National Natural Science Foundation of China/ ; }, mesh = {*Soil Microbiology ; Temperature ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; *Microbiota/genetics ; Seasons ; *Ecosystem ; Metagenomics ; }, abstract = {Individual microbes often respond differently to the same environment, yet the magnitude of such niche variation inherent to individuals remains unresolved and is anticipated to differ substantially from community-level average responses. We conducted metagenomic binning on monthly time-series soil samples from three sites across seasonal cycles. By considering 440,571 genes as dimensions of the fundamental individualised niche (FIN), we traced FIN trajectories of archaea and bacteria during warming, cooling, and turning periods. We found that neither mean temperature nor temperature difference had a significant effect on FIN breadth or overlap. Instead, we discovered a temporally constant, stepwise gradient of niche differentiation across taxonomic categories. At the interdomain level (Archaea vs. Bacteria), niche overlap is approximately 25%, rising to ~40% at the interphylum level and ~60% at the interorder level. This discontinuous gradient likely marks the limit boundaries of niche variation, is closely linked to functional synergy within FINs, and provides a preliminary comparable ecological carrying capacity for each niche step, particularly regarding the interdomain balance.}, } @article {pmid42250066, year = {2026}, author = {Fu, Y and Jiang, H and Peng, D and Bai, Z and Wang, S and Liu, H and Zhang, W and Shang, W}, title = {Fecal Microbiome and Serum Metabolome Profiles of the Ovarian Failure Mouse Model.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {42250066}, issn = {1559-0291}, support = {KFKT-2024-KY-019//the Key Project Program of the 2024 Scientific Research Fund, Chinese Association of Rehabilitation Medicine/ ; }, abstract = {Ovarian dysfunction is closely associated with reproductive aging and systemic metabolic disturbances; however, the underlying microbial and metabolic mechanisms remain unclear. In this study, we analyzed fecal microbiome and serum metabolome profiles in young (7-week-old) and aged (12-month-old) female C57BL/6J mice using shotgun metagenomic sequencing and untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry. Microbial and metabolic data were processed using QIIME2, HUMAnN, and MetaboAnalyst 5.0. Differential taxa and metabolites were identified using DESeq2 and linear discriminant analysis effect size (LEfSe), and their associations were evaluated using Spearman's correlation analysis. Our results showed that aged mice exhibited significant alterations in gut microbiota composition, including a decreased abundance of Firmicutes and an increased abundance of Bacteroidetes, along with enrichment of the genera Alistipes and Akkermansia. Serum metabolomic profiling identified 246 differential metabolites, primarily involved in amino acid and energy metabolism pathways. Integrated analysis revealed that tryptophan metabolism represents a key pathway linking microbial dysbiosis with systemic metabolic alterations. Notably, enriched microbial taxa, including Akkermansia muciniphila and species within the genus Alistipes, were strongly correlated with tryptophan-related metabolites. These findings indicate that ovarian failure is associated with coordinated alterations in the gut microbiome and serum metabolome, converging on tryptophan metabolism. This study provides new insights into host-microbiome-metabolite interactions in ovarian failure and highlights potential microbial and metabolic targets for therapeutic intervention.}, } @article {pmid42250131, year = {2026}, author = {Gao, X and Qin, R and Li, S and Yang, Y and He, J}, title = {Congenital tuberculosis transmitted via the placenta: identification by metagenomic next-generation sequencing.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42250131}, issn = {1435-4373}, support = {grant number: kryc-yq-2127//Kuanren Talents Program of the second affiliated hospital of Chongqing Medical University/ ; }, abstract = {BACKGROUND: Congenital tuberculosis (CTB) is a rare disease with high mortality in neonates. Early diagnosis is crucial but often delayed due to atypical clinical and imaging manifestations.

CASE PRESENTATION: We report a 36-day-old female infant presenting with recurrent fever. Laboratory data showed leukocytosis and neutrophilia with mildly elevated C-reactive protein. Chest computed tomography revealed extensive ground-glass opacities, multiple subpleural nodules, and necrotic hilar and mediastinal lymphadenopathy. The asymptomatic mother was subsequently found to have diffuse miliary nodules on chest CT. Conventional tuberculosis tests (acid-fast smear, culture, GeneXpert, T-SPOT.TB) were negative in both the infant and mother. Metagenomic next-generation sequencing (mNGS) of the placental tissue detected 10 specific Mycobacterium tuberculosis sequences, and Ziehl-Neelsen staining confirmed acid-fast bacilli. Both mother and infant responded well to anti-tuberculosis therapy.

CONCLUSIONS: CTB should be considered in neonates with persistent pulmonary infection unresponsive to broad-spectrum antibiotics. Examination of placental tissue using mNGS is a valuable diagnostic tool for confirming transplacental tuberculosis transmission.}, } @article {pmid42250135, year = {2026}, author = {Das, K and Jaiswal, P and Priya, H and Sangwan, S and Paul, S and Prasanna, R and Grover, M}, title = {Microbial innovations for climate-resilient agriculture: mechanisms, applications, and emerging technologies.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42250135}, issn = {1573-0972}, mesh = {*Agriculture/methods ; Soil Microbiology ; Climate Change ; Crops, Agricultural/microbiology/growth & development ; Microbiota ; Stress, Physiological ; Ecosystem ; Biotechnology ; Mycorrhizae ; }, abstract = {Agriculture is increasingly challenged by climate change-driven stresses, including rising temperatures, erratic rainfall, soil degradation, with increased frequency of pests and disease outbreaks. This disrupts crop productivity and threatens global food security, underscoring the urgent need for sustainable, adaptive strategies, which are environment-friendly. Microorganisms, integral to soil health, nutrient cycling, and plant stress physiology, offer promising nature-based solutions for climate resilient agriculture. Yet their potential remains underutilized due to technical, ecological, and socio-economic barriers that hinder widespread adoption. This review addresses these research gaps and practical challenges, while outlining future perspectives for scaling up microbe-based technologies through integration with omics and AI tools. The major points addressed in this review are (1) Major advances in microbial applications that directly support crop resilience and ecosystem sustainability. It examines recent progress made towards enhancing the effectiveness of biofertilizers (including mycorrhizal fungi), biopesticides and developing novel products, detailing how these innovations enhance nutrient acquisition, regulate phytohormonal balance, improve water-use efficiency, mitigate abiotic stresses such as drought, salinity, heat and pH, and minimize losses incurred due to pathogen and pests; (2) Mechanistic insights into microbial mediation of nutrient cycling, soil aggregation, and stress alleviation in terms of plant-microbe or soil-plant microbiome networking; (3) The role of emerging biotechnological tools, including metagenomics, microbiome engineering, and synthetic biology, that enable the design of more effective and context-specific microbial interventions that can be integrated with artificial intelligence (AI) and machine learning (ML) tools for precise application (4) Emphasis on both the benefits and constraints of microbial inoculants is documented as well as novel strategies for their effective use as sustainable solutions for climate ready agriculture. Ultimately, microbial innovations are positioned as pivotal in building climate-resilient agroecosystems capable of sustaining productivity and reducing environmental footprints.}, } @article {pmid42250463, year = {2026}, author = {Xia, L and Lu, L and Liu, M and Jiao, J and Liu, L and Meng, L and Liu, Y and Li, W and Lu, C and Ma, B}, title = {Proposal of Edaphobacterium genomatis gen. nov., sp. nov. within the family Casimicrobiaceae from metagenome-assembled genomes in accordance with the SeqCode.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126735}, doi = {10.1016/j.syapm.2026.126735}, pmid = {42250463}, issn = {1618-0984}, abstract = {Casimicrobiaceae strains inhabit various environments, but their ecological roles in natural soils remain mostly unclear. By actively targeting specific high-altitude datasets during our Global Mollisols Genomic Atlas (GMGA) mining efforts, we discovered a previously unknown lineage within this family. This novel group is represented by five metagenome-assembled genomes (MAGs) recovered from oligotrophic soils in the Southern Brazilian Highland Grasslands, a unique environment within the broad Pampas black soil region. Phylogenetic and comparative genomic analyses showed these five MAGs form a distinct monophyletic clade within Casimicrobiaceae. Their novel taxonomic status is supported by Average Nucleotide Identity (ANI) thresholds, showing clear divergence from all known reference genomes. Functional annotations suggest a chemoorganotrophic lifestyle with microaerobic respiration capacity, while trace-gas scavenging genes indicate potential lithoheterotrophy for maintenance energy under nutrient limitation. Additionally, an autonomous ACC deaminase system and specialized nutrient scavenging pathways (organophosphonate and taurine utilization) highlight its adaptive capacity for rhizosphere interactions and survival in oligotrophic environments. Screening 22,976 public metagenomes demonstrated a widespread global distribution, primarily inhabiting diverse soil (86.4%) and plant-associated (7.0%) environments. Based on these analyses, we propose the name Edaphobacterium genomatis gen. nov., sp. nov. for this novel taxon following the SeqCode (Code of Nomenclature of Prokaryotes Described from Sequence Data) rules. Our results uncover hidden species diversity and highlight the specific functional roles of uncultured microbes in nutrient-limited highland niches within fertile black soil regions.}, } @article {pmid42250813, year = {2026}, author = {Kadam, R and Jo, S and Panwar, NL and Kim, T and Park, J}, title = {Metagenomic insights into metabolic limitations and biosafety implications of rendered pig carcass anaerobic digestion.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135081}, doi = {10.1016/j.biortech.2026.135081}, pmid = {42250813}, issn = {1873-2976}, abstract = {Global livestock production has intensified, increasing the biosecurity and environmental risks associated with animal mortality management. This study evaluated the feasibility of anaerobic digestion (AD) as a sustainable valorization route for rendered pig carcasses using long-term performance monitoring and whole-metagenome shotgun sequencing. During operation at an organic loading rate (OLR) of 1.0-2.0 kg-VS/m[3]/d, the reactor achieved peak methane (CH4) yields of 400-430 mL-CH4/g-VS and an organic matter removal efficiency > 70%. The buffering capacity generated through carcass proteolysis contributed to maintaining reactor performance under increasing loading conditions. However, increasing the OLR to 3.0 kg-VS/m[3]/d triggered process instability, decreasing the CH4 yield and increasing the total volatile fatty acids (TVFAs) to > 6,000 mg/L, specifically dominated by propionic and butyric acids. Metagenomic analysis identified a specialized consortium dominated by the syntrophic acetogen Cloacamonas and acetoclastic methanogen Methanosaeta during reactor operation at moderate OLRs. Functional profiling revealed that although the community possessed efficient hydrolytic and syntrophic acetate oxidation pathways, propionic acid accumulation and lower completeness of propionate oxidation pathways suggested potential limitations in syntrophic propionate oxidation at elevated OLRs. Furthermore, biosafety-related assessments suggested that AD may offer potential biocontainment advantages over traditional carcass disposal methods based on reduced prevalence of antimicrobial resistance genes and virulence-associated factors. These findings provide a metabolic framework for optimizing carcass-based AD as a viable substrate for renewable energy recovery.}, } @article {pmid42250815, year = {2026}, author = {Xie, C and Li, D and Li, J and Li, J and Yin, M and Wu, Y and Zhang, C and Luo, R and Zhu, Y and Zhang, Z and Zheng, Z and Peng, Y}, title = {Molecular mechanism of anammox granular sludge disintegration caused by polyethylene terephthalate micro/nanoplastics: a new perspective based on quorum sensing.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135060}, doi = {10.1016/j.biortech.2026.135060}, pmid = {42250815}, issn = {1873-2976}, abstract = {Quorum sensing (QS) regulates the synthesis and secretion of extracellular polymeric substances (EPS), which are essential for maintaining the structural stability of anaerobic ammonium oxidation (Anammox) granular sludge. However, the molecular mechanism linking polyethylene terephthalate micro/nanoplastics (PET-MNPs)-induced QS disruption to EPS inhibition remains unclear. This study investigated the effects of two PET-MNP sizes (80 μm and 300 nm) on Anammox granular sludge under different exposure concentrations. PET-MNPs significantly reduced nitrogen removal performance and caused surface cracking, structural loosening, and granule disintegration. EPS analysis showed that PET-MNPs decreased EPS content, altered protein secondary structure, and increased hydrophilic functional groups, thereby weakening sludge bioadhesion. Metagenomic and metatranscriptomic analyses indicated that PET-MNPs inhibited the abundance and expression of genes involved in the Anammox process, tricarboxylic acid cycle, glycolysis/gluconeogenesis, and Wood-Ljungdahl pathway, resulting in insufficient ATP, NADH, and metabolic precursors required for EPS synthesis. Meanwhile, methionine and fatty acid metabolism were suppressed, limiting precursor supply for acyl-homoserine lactone (AHL) synthesis. Molecular docking showed that PET oligomers could stably bind to LuxR and potentially hinder AHL-LuxR complex formation. Exogenous AHL supplementation promoted EPS re-secretion, confirming the important role of QS imbalance in PET-MNPs-induced EPS reduction. Overall, PET-MNPs destabilized Anammox granular sludge through the combined effects of particle-induced physical damage and oligomer-mediated molecular interference. This study elucidates the molecular mechanism of MNP-induced Anammox granule disintegration and provides a theoretical basis for assessing the ecological risks of emerging pollutants in biological wastewater treatment.}, } @article {pmid42250818, year = {2026}, author = {Liu, Y and Qian, Z and Peng, Y and Zhang, T and Li, Z and Shi, S and Gu, H}, title = {Enhancing ethanol-driven chain elongation via iron speciation: impacts on metabolic flux and dual FAB/RBO pathway activation.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135088}, doi = {10.1016/j.biortech.2026.135088}, pmid = {42250818}, issn = {1873-2976}, abstract = {Anaerobic chain elongation (CE) has emerged as a promising technology for upgrading low-value organic substrates into high-value medium-chain fatty acids (MCFAs); however, achieving targeted metabolic flux and efficient electron transfer remains challenging. To address this, this study explores the role of iron speciation in enhancing chain elongation (CE) driven by ethanol. Two iron-modified activated carbons, Fe3O4@AC and ZVI@AC, were evaluated to assess their impact on microbial metabolic networks. Results revealed that Fe3O4@AC significantly enhanced caproate production (4600.0 mg/L) and electron transfer efficiency (87.0 %), while ZVI@AC triggered a diversion towards alcohol production (940.61 mg/L n-butanol). The superior performance of Fe3O4@AC was attributed to its semiconductive properties, which facilitated interspecies electron transfer (potentially via DIET-like mechanisms) and balanced electron flow, promoting the activation of both fatty acid biosynthesis (FAB) and reverse β-oxidation (RBO) pathways. Metagenomic analysis revealed a shift in microbial community composition, with Massilibacterium enrichment under Fe3O4@AC, highlighting the importance of tailored material design for targeted MCFA production. These findings provide insights into optimizing microbial metabolism for enhanced CE efficiency.}, } @article {pmid42250890, year = {2026}, author = {Ticho, AL and McRae, AN and Cifuentes, L and Fredrick, T and Anazco, D and Espinosa, MA and Garcia Cordova, JM and Romanos, M and Villamarin, J and Johnson, S and Lennon, R and Hurtado Andrade, MD and Chen, J and Camilleri, M and Acosta, AJ}, title = {A Subphenotype of Obesity With Reduced Enteroendocrine Glucagon-Like Peptide 1 Synthesis and Enhanced Tirzepatide Response.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2026.05.019}, pmid = {42250890}, issn = {1528-0012}, abstract = {BACKGROUND & AIMS: Obesity is a heterogeneous disease characterized by different pathophysiological and behavioral traits that influence response to glucagon-like peptide 1 (GLP-1)-based therapies. We previously identified an obesity phenotype characterized by fast gastric emptying (GE) and increased postprandial hunger. We aimed to elucidate pathophysiological mechanisms in this phenotype by evaluating plasma enteroendocrine hormones and mucosal gene expression and to evaluate treatment response to tirzepatide across subphenotypes.

METHODS: A total of 483 adults with obesity underwent solid meal GE (SGE by scintigraphy), postprandial appetite assessment using a visual analogue scale, and plasma enteroendocrine hormone profiling. Gaussian mixed modeling identified phenotypic clusters. Associations with plasma short-chain fatty acids and fecal metagenomics were explored. A separate cohort (n = 31) underwent colonic mucosal biopsies with quantification of GCG (GLP-1) and PYY messenger RNA. Retrospective evaluation of weight loss in participants treated with tirzepatide among each cluster was performed (n = 61).

RESULTS: Three clusters were identified based on SGE and GLP-1. One cluster demonstrated fast SGE, increased postprandial hunger, and discordantly low postprandial GLP-1 (termed dc-GE/GLP-1; n = 130 [26.9%]), as well as lower plasma peptide YY and cholecystokinin. dc-GE/GLP-1 showed higher plasma short-chain fatty acid levels, without significant differences in fecal microbial composition. Compared with concordant clusters (c-GE/GLP-1; n = 353 [73.1%]), dc-GE/GLP-1 had decreased mucosal messenger RNA expression of GCG (GLP-1) and PYY. At 6 months of tirzepatide, dc-GE/GLP-1 was associated with greater weight loss compared with c-GE/GLP-1 (21.5% vs 11.7%).

CONCLUSIONS: We identified a subphenotype of obesity with fast GE and discordantly low GLP-1 plasma levels, reduced mucosal hormone synthesis, and enhanced weight loss to tirzepatide. Further studies are needed to identify mechanisms contributing to GLP-1 deficiency in this subphenotype of obesity.}, } @article {pmid42251226, year = {2026}, author = {Kim, E and Jang, ES and Nam, Y and Hwang, HJ and Lee, YJ and Kim, TG and Hong, C and Lee, SR}, title = {The human microbiome as a source of novel bioactive natural products: structures, bioactivities, and biosynthetic insights.}, journal = {Journal of natural medicines}, volume = {}, number = {}, pages = {}, pmid = {42251226}, issn = {1861-0293}, support = {2025-glocal-02-004-511-002//Ministry of Education and Busan Metropolitan City/ ; RS-2025-23525419//National Research Foundation of Korea/ ; RS-2024-00403999//Korea Basic Science Institute/ ; WISET-2025-392//Ministry of Science and ICT, South Korea/ ; }, abstract = {The human microbiome, comprising trillions of microorganisms in distinct anatomical locations such as the gut, oral cavity, skin, and vagina, has emerged as a source of bioactive natural products with diverse scaffolds. Through co-evolution with the host, the human microbiome produces small molecules tailored to physicochemical environments that contribute to immune regulation, epithelial barrier maintenance, pathogen defense, and neurochemical signaling. Recent advances in metagenomics, single-cell genomics, synthetic biology, and integrated omics approaches have enabled rapid discovery and structural elucidation of biosynthetic gene clusters (BGCs) and metabolites. Cultivation-driven and genome mining strategies combined with omics analyses have improved the efficiency of discovering microbiome-derived drug leads. These metabolites mediate competitive and cooperative interactions within microbial ecosystems and hold high promise for therapeutic applications such as immunomodulators, anti-infectives, and neuroactive agents. This review outlines the structural features, biosynthetic pathways, and bioactivities of key metabolites across major microbial niches, together with strategies for their discovery, highlighting their potential in advancing drug development and human health.}, } @article {pmid42251252, year = {2026}, author = {Lockwood, S and Ranaivoson, HC and Randriambolamanantsoa, TH and Razanajatovo, N and Raharinosy, V and Ahyong, V and Héraud, JM and Dussart, P and Lacoste, V and Brook, CE}, title = {Identifying viral infections through metagenomic Next Generation Sequencing of undiagnosed respiratory fevers in Madagascar (2014-2019).}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13715-7}, pmid = {42251252}, issn = {1471-2334}, support = {P200A210054//U.S. Department of Education/ ; GCE/ID OPP1211841//Bill and Melinda Gates Foundation/ ; }, abstract = {BACKGROUND: Respiratory illness contributes to substantial global morbidity and mortality. In Madagascar, an island nation off the southeastern coast of the African continent, hospital-based public health surveillance for respiratory pathogens screens for common respiratory viruses. However, many cases remain undiagnosed.

METHODS: We conducted metagenomic Next Generation Sequencing (mNGS) to identify the pathogen profile of 102 undiagnosed febrile patients who presented to public hospitals with respiratory symptoms and screened negative on a 14-virus multiplex RT-qPCR. We analyzed the diversity of the respiratory microbiome of each patient from mNGS data and identified viral infections potentially linked to undiagnosed fever. We assembled whole genome consensus sequences of viruses with sufficient read depth and coverage, characterized each phylogenetically, and identified any discrepancies with the primers used in the multiplex RT-qPCR panel. Finally, we compared all whole genome sequences against publicly available global databases in a phylogenetic analysis.

RESULTS: We identified evidence of infection by a wide range of known human viruses in approximately two thirds (64.7%) of study participants from nine different families of viruses and generated 30 complete or nearly complete consensus sequences of known respiratory viruses including orthopneumoviruses, metapneumoviruses, rhinoviruses, coronaviruses, parainfluenza virus, and bocaparvovirus. mNGS-attributed evidence of infection was predominantly due to orthopneumovirus (also called respiratory syncytial virus [RSV]; n = 24; n = 8 previously diagnosed) and rhinovirus (n = 18) detections, despite previous negative RT-qPCR results for the majority of these cases. Finally, phylogenetic analysis identified two distinct phylogenetic clusters of RSV subtype A, suggesting local transmission following distinct international introductions for this virus.

CONCLUSION: mNGS provides a sensitive pan-pathogenic tool for virus detection. We demonstrate the diversity of viruses associated with undiagnosed respiratory fevers in Madagascar, emphasize the importance and relevance of the existing respiratory surveillance in the country, and highlight the interconnectedness of regional respiratory infection dynamics with global networks of respiratory pathogen transmission.}, } @article {pmid42251689, year = {2026}, author = {Tao, M and Zhang, Z and Dai, L and Zeng, Y and Zhang, X}, title = {Metagenomic insights into potential horizontal transfer of resistance/virulence genes in gut microbiota from patients with Crohn disease.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izag090}, pmid = {42251689}, issn = {1536-4844}, support = {2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; 32101368//National Natural Science Foundation of China/ ; 1053320242393//Fundamental Research Funds for the Central Universities of Central South University/ ; }, abstract = {BACKGROUND: Unraveling the potential horizontal transfer of resistance genes/virulence genes (RGs/VGs) in gut microbiota from patients with Crohn disease (CD) is an interesting but poorly characterized issue.

METHODS: Quantitative assessment was performed to estimate the relative abundance and diversity of RGs/VGs/mobile genetic elements (MGEs). Differential analysis was applied to identify the CD-specific enriched genetic subtypes. A species-RGs/VGs/MGEs association network was constructed to explore possible co-occurrence patterns of these genetic elements across potential microbial hosts. Integrated with topological metrics and Zi-Pi computational modeling, co-occurrence network analysis was conducted to characterize potential associations among RGs, VGs, and MGEs.

RESULTS: Comparative metagenomic analyses indicated that the microbiome in group CD exhibited significantly higher relative abundance of RGs compared to that in healthy controls (HC; P = .040), with 131 specific RG/VG subtypes (eg, acrA/T6SS) exhibiting marked enrichment (P < .05). The co-occurrence network revealed intensified interconnectivity between RGs/VGs and MGEs in group CD, in which MGEs accounted for 71% of network nodes (vs 60.80% in HC), and 99.14% of the edges were positively correlated (vs 93.60% in HC). Network topology and Zi-Pi analysis further suggested reduced modularity (0.709 vs 0.979 in HC) and enhanced intergene connectivity (average degree: 12.288 vs 2.156; average weighted degree: 23.359 vs 3.688 in HC). There were no network hubs (0 vs 5 in HC) but abundant modular hubs (60 vs 25 in HC), peripheral nodes (2317 vs 1549 in HC), and connectors (61 vs 36 in HC), which may reflect conditions favorable for enhanced gene transfer potential. Cross-species transfer events were predicted across clinical-environmental-commensal boundaries, exemplified by tet(M) dissemination between Clostridioides difficile and Bacteroides sp., probably implying progressive erosion of ecological barriers.

CONCLUSIONS: Collectively, we inferred that the gut microbiome of CD patients might represent a high-risk reservoir for the horizontal transfer of pathogenic determinants, which may pose a potential threat for public health and biosecurity.}, } @article {pmid42251704, year = {2026}, author = {Farace, PD and Marrero Diaz de Villegas, R and Mon, ML and Soria, MA and Talia, PM}, title = {Structural insights into predicted thermophilic GH5 cellulases for industrial lignocellulose bioconversion.}, journal = {Journal of biomolecular structure & dynamics}, volume = {}, number = {}, pages = {1-22}, doi = {10.1080/07391102.2026.2683872}, pmid = {42251704}, issn = {1538-0254}, abstract = {Lignocellulosic biomass can be converted into biofuels and other valuable bioproducts, but it must first undergo physicochemical and enzymatic degradation. Among the various enzymes involved in lignocellulose degradation, thermophilic glycoside hydrolase family 5 (GH5) cellulases have gained significant attention given their ability to sustain enzymatic activity at temperatures exceeding 60 °C. These high temperatures not only accelerate enzymatic reactions, improving reaction rates and process efficiency, but also enhance substrate solubility and reduce the risk of microbial contamination, making them highly valuable for the paper, food, feed, pharmaceutical, and biofuel industries. In this work, we identified five GH5 cellulases with predicted thermophilic properties from termite gut metagenomes and evaluated their structural features using machine-learning classification, comparative structural modeling, interatomic contact analysis, and temperature-dependent flexibility simulations. The candidates, spanning GH5 subfamilies 2, 25, 37, 39, and 40, displayed high structural confidence (pLDDT > 90) and aliphatic indices comparable to those of thermophilic references. Analysis of amino acid composition analysis revealed enrichment in aromatic and charged residues. Hydrophobic contact densities were consistently higher than in mesophilic controls and aligned with thermophilic benchmarks. Temperature-dependent flexibility simulations showed restrained RMSF profiles, more closely resembling the thermophilic reference enzyme than to the mesophilic control. These findings are consistent with a thermophilic profile, pending experimental confirmation, and provide useful insights for the selection and engineering of GH5 cellulases for high-temperature biotechnological applications.}, } @article {pmid42251735, year = {2026}, author = {Dennu, L and Devic, M and Rigonato, J and Falciatore, A and Lozano, JC and Vergé, V and Mariac, C and Joli, N and Jaillon, O and Sabot, F and Bouget, FY}, title = {Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: insights into genetic diversity and function of outlier chromosomes.}, journal = {The Plant journal : for cell and molecular biology}, volume = {126}, number = {5}, pages = {e70982}, pmid = {42251735}, issn = {1365-313X}, support = {ANR-20-CE20-0024//Agence Nationale de la Recherche/ ; }, mesh = {*Phytoplankton/genetics ; *Genetic Variation/genetics ; Phylogeny ; Metagenome/genetics ; Genomics ; Metagenomics ; *Chromosomes/genetics ; }, abstract = {Population-scale genome sequencing has become essential for exploring genetic diversity and adaptation, particularly in land plants. In contrast, eukaryotic phytoplankton resources remain limited to model reference genomes or community-level metagenomics, leaving a gap in understanding intraspecific variation and evolutionary processes. To address this, we developed a comprehensive biological and genomic resource for the cosmopolitan and ecologically important genus Bathycoccus. Extensive metagenomic data from across the world Ocean are available for this genus, and previous studies have identified four Bathycoccus species and reconstructed 34 metagenome-assembled genomes (MAGs). Here we report 28 high-quality strain genome sequences using a combination of Oxford Nanopore Technologies long reads and Illumina short reads and associated biological resources. These include 24 Bathycoccus prasinos strains spanning a latitudinal gradient from 40° to 78° N, a reference genome for Bathycoccus calidus, and three genomes of the recently identified B3 clade, which we propose as the Bathycoccus catiminus species. Comparative analyses of sequenced genomes with MAGs highlight the complementarity between resources: While MAGs capture environmental diversity and uncover uncultured taxa, the cultured strain genomes provide complete, non-chimeric high-quality assemblies that resolve structural variations and haplotype-level diversity not detected in MAGs. These include the big outlier chromosome, a putative sexual chromosome revealing a second mating type, and extensive variability in the small outlier chromosome, associated with viral resistance and genome plasticity. Together, these biological and genomic resources establish B. prasinos as a powerful model for studying diversity, adaptation, and evolution of eukaryotic phytoplankton in the ocean, complementing existing global metagenomic datasets.}, } @article {pmid42251775, year = {2026}, author = {Sahnan, S and Morandini, V and Ferrer, M and Onrubia, A and Torralvo, C and Kaján, GL and Harrach, B and Varsani, A and Kraberger, S}, title = {Four lineages of adenoviruses identified in raptors sampled in Spain.}, journal = {Virology}, volume = {623}, number = {}, pages = {110990}, doi = {10.1016/j.virol.2026.110990}, pmid = {42251775}, issn = {1096-0341}, abstract = {Adenoviruses infect a wide range of vertebrate species from fish to humans, including an especially large number of avian species. This study utilized viral metagenomic workflow coupled with targeted PCR to identify and characterize adenoviruses from cloacal swabs collected from 50 black kites (Milvus migrans), 11 ospreys (Pandion haliaetus), and 35 common kestrels (Falco tinnunculus) sampled in Spain. A total of eleven adenoviral genomes were determined from black kites (n = 8) and common kestrels (n = 3). Amino acid pairwise comparison of the DNA polymerase protein coupled with phylogenetic analysis shows that these viruses fall into four adenovirus lineages: two in the genus Aviadenovirus (raptor adenovirus 2 and 3) and two in the genus Siadenovirus (raptor adenovirus 1 and 4). The genomes of raptor adenovirus 1 and raptor adenovirus 2 belong to the classified species Siadenovirus raptoris and Aviadenovirus falconis, respectively, whereas raptor adenovirus 3 and 4 represent putative new species. This study expands the known host range of raptor-infecting viruses in the species Siadenovirus raptoris and Aviadenovirus falconis to include black kites and common kestrels, respectively. We also expand on the diversity knowledge of adenoviruses in black kites.}, } @article {pmid42251975, year = {2026}, author = {Chen, C and Wang, M and Sun, L and Cheng, X and Deng, H and Li, RH}, title = {Phosphorus metabolism regulates the trade-off between phosphorus removal and sludge reduction.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135096}, doi = {10.1016/j.biortech.2026.135096}, pmid = {42251975}, issn = {1873-2976}, abstract = {Sludge reduction decreases the phosphorus export flux through waste sludge discharge, thereby increasing the risk of effluent phosphorus instability. However, the regulatory role of phosphorus in sludge reduction remains unclear. Here, side-stream phosphorus recovery was introduced into an anaerobic side-stream reactor (ASSR) based sludge reduction system to redirect phosphorus export from sludge discharge to physicochemical recovery, enabling investigation of how phosphorus flux redistribution regulates sludge reduction. Two parallel systems, a conventional ASSR system (SBR-ASSR) and an ASSR system coupled with phosphorus recovery (SBR-ASSR-PR), were comparatively evaluated using phosphorus mass balance, endogenous respiration analysis, cryptic growth modeling, and metagenomic profiling. Phosphorus recovery increased total phosphorus removal from 77.8% to 97.3% and total nitrogen removal from 72.5% to 82.1%, while reducing the observed sludge yield by 28%. Phosphorus mass balance showed that 34.7% of influent phosphorus was rerouted through the recovery pathway, reducing phosphorus discharge via waste sludge from 74.9% to 57.5%. The resulting lower system phosphorus levels restructured microbial metabolic allocation, suppressing biosynthesis while enhancing decay and substrate reutilization, with the cryptic growth contribution increasing from 35.9% to 46.9%. Metagenomic profiling corroborated this metabolic shift, revealing significant changes in key genes and pathways related to phosphorus cycling, energy maintenance, and denitrification. These findings show that phosphorus metabolism can regulate microbial growth-decay allocation, and that side-stream phosphorus recovery can coordinate nutrient removal, phosphorus recovery, and sludge minimization by restructuring internal phosphorus fluxes and microbial metabolic allocation.}, } @article {pmid42252081, year = {2026}, author = {Wang, F and Xie, J and Fu, T and Pu, K and Wu, Q and Li, Q}, title = {Negative CSF mNGS Results and Early Shunt Placement in Post-Infectious Hydrocephalus: A Retrospective Cohort Study.}, journal = {World neurosurgery}, volume = {}, number = {}, pages = {125104}, doi = {10.1016/j.wneu.2026.125104}, pmid = {42252081}, issn = {1878-8769}, abstract = {OBJECTIVE: To evaluate the impact of pre-shunt cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) guidance on the timing of ventriculoperitoneal (VP) shunt surgery and clinical outcomes in patients with post-infectious hydrocephalus (PIH), and to explore the value of mNGS in different clinical scenarios.

METHODS: In this retrospective cohort study, we included 42 patients with PIH who underwent VP shunt surgery at our institution between January 2019 and December 2025. Patients were divided into two groups according to whether pre-shunt CSF mNGS was performed: the mNGS group (n = 19) and the non-mNGS group (n = 23). Primary outcomes included recovery to shunt time (RTS), first negative to shunt time (NTS), decisional shunt to actual shunt time (DTS), and postoperative antibiotic time (PAT). Secondary outcomes included postoperative hospital stay (POHS), functional outcomes (mRS and GCS), POD 90 mortality, infection recurrence, and reoperation.

RESULTS: Compared with the non-mNGS group, the mNGS group demonstrated significantly shorter NTS (3 [IQR 1-4] days vs. 9 [IQR 4.5-17] days, P = 0.002), DTS (2 [IQR 1-3.5] days vs. 8 [IQR 6-18] days, P < 0.001), and PAT (0 [IQR 0-2] days vs. 4 [IQR 0-10] days, P = 0.010). No significant differences were observed between the two groups in RTS (P = 0.135), functional outcomes, mortality, infection recurrence, or reoperation.

CONCLUSIONS: Pre-shunt CSF mNGS testing significantly shortens NTS, DTS, and PAT in patients with PIH without compromising clinical outcomes. The mNGS-guided shunt strategy is safe and feasible, supporting its potential clinical application.}, } @article {pmid42252233, year = {2026}, author = {Dou, ZX and Liu, C and Zhang, Y and Wang, ZQ and Zhao, L}, title = {[A case of microsporidial keratoconjunctivitis].}, journal = {[Zhonghua yan ke za zhi] Chinese journal of ophthalmology}, volume = {62}, number = {6}, pages = {468-472}, doi = {10.3760/cma.j.cn112142-20251002-00402}, pmid = {42252233}, issn = {0412-4081}, mesh = {Humans ; Male ; *Keratoconjunctivitis/microbiology/diagnosis/drug therapy ; *Microsporidiosis/diagnosis/drug therapy ; Adolescent ; *Eye Infections, Fungal/microbiology/drug therapy/diagnosis ; }, abstract = {A 15-year-old male patient presented with recurrent photophobia, lacrimation, and blurred vision in both eyes for 3 years. He had been repeatedly diagnosed with "bilateral keratitis (unknown etiology)"at other hospitals and failed to respond to multiple topical medications. Initially diagnosed as bilateral Thygeson superficial punctate keratitis, he was treated with 0.5% loteprednol etabonate suspension eye drops and other medications. However, his symptoms worsened after 3 weeks of treatment. Subsequently, corneal epithelial tissue metagenomic testing and scrape cytological examination were performed, confirming the diagnosis of bilateral microsporidial keratoconjunctivitis. The treatment regimen was adjusted to topical application of 1% voriconazole eye drops, 0.3% gatifloxacin ophthalmic gel, and 0.1% tacrolimus eye drops. After 3 weeks of treatment, the patient's visual acuity in both eyes recovered to 1.0, conjunctival hyperemia was alleviated, and corneal epithelial punctate infiltration and fluorescein staining improved. One month after treatment, his symptoms were basically relieved, with the corneal infiltration and palpebral conjunctival papillae resolved. No recurrence was observed during the one-year follow-up.}, } @article {pmid42252320, year = {2026}, author = {Zhou, J and Qiao, Y and Chen, H and Li, L and Su, W}, title = {Spatial scaling of metagenomic diversity reveals ecological disruption in the gut microbiome of gout patients.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-55351-w}, pmid = {42252320}, issn = {2045-2322}, support = {No: 24JRRJ001//Provincial Science and Technology Plan (Basic Research Plan-Natural Science Foundation) Project of Gansu Province in 2024/ ; }, abstract = {Gout, a painful inflammatory arthritis, is characterized by hyperuricemia and monosodium urate crystal deposition, with growing evidence linking its pathogenesis to gut microbiome dysbiosis. However, traditional diversity metrics fail to capture the complex spatial organization of microbial communities. This study addresses this gap by applying the novel metagenomic Diversity-Area Relationship (m-DAR) model to investigate scaling laws in the gout microbiome-quantifying how metagenomic diversity changes with the number of individuals sampled. Our analysis of gut microbiomes from gout patients and healthy controls revealed fundamental ecological disruptions. We found that gout microbiomes exhibited significantly altered scaling patterns: they showed greater inter-individual dissimilarity (higher z-values) at the level of rare genes (q = 0), but weaker scaling of dominant genes (q = 1-3) compared to healthy controls. Crucially, the maximal accrual diversity (MAD) was substantially lower in gout patients, indicating a severely constrained potential for total microbial gene diversity. Furthermore, profiling of metagenomic functional gene clusters (MFGCs) uncovered widespread functional perturbations, including increased diversity scaling for carbohydrate-active enzymes (CAZy) but decreased scaling in essential metabolic pathways (KEGG, KO). These results demonstrate that the gout gut microbiome is defined by a loss of ecological structure, featuring reduced homogeneity in dominant taxa, expanded rare biosphere variation, and an overall collapsed diversity capacity. This work introduces an ecological framework for characterizing dysbiosis in gout that complements traditional diversity metrics and may inform the development of microbiome-based therapeutic strategies. Further research is needed to translate these ecological patterns into clinical applications.}, } @article {pmid42252423, year = {2026}, author = {Becerra-Lucio, PA and Pérez-Rueda, E and Dias, GM and Labrín-Sotomayor, NY and Mendoza-Mendoza, A and Partida-Martínez, LP and Zarza, E and Peña-Ramírez, YJ}, title = {Environmental contributors to bacterially dominated fermenting consortia of artisanal Mezcal.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05199-x}, pmid = {42252423}, issn = {1471-2180}, support = {786763//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; IN220523//PAPIIT-DGAPA UNAM/ ; 5103711808 2021-2024//El Colegio de la Frontera Sur/ ; Omics Unravel Mezcal, a Drink with a Complex Spirit//Química Valaner-MGI Mexico/ ; }, abstract = {The production of spontaneously fermented beverages worldwide relies on native microorganisms acquired incidentally through cross-contamination from environmental reservoirs. We examined the microbiota involved in Mezcal fermentation, exploring their origins, dynamics, and ecology. Using shotgun metagenomics, we analyzed four batches of Mezcal, spanning the entire production process from crop to distillation. Bacterial genera such as Leuconostoc and Lentilactobacillus dominated the fermentation samples, whereas Bacillus was the most abundant in the environmental samples. Fermenting yeasts, such as Saccharomyces, accounted for only ~ 10% of the microbial abundance. No significant differences in microbial community structure were observed between the sampled batches, fermentation times, or depths of the fermentation tanks. Weevil samples clustered with fermentation and plant samples, suggesting they may serve as natural reservoirs for Leuconostoc and Lentilactobacillus. Functional differences were observed in COGs related to secondary metabolism during fermentation and correlated with sensory notes identified by a panel of expert tasters, suggesting that variations in the sensory profiles of the final spirit are directly linked to the metabolic products of genes associated with secondary metabolism. Our work analyzed the spontaneous fermentation microbiota, providing fundamental insights into its natural reservoirs and its contribution to Mezcal terroir.}, } @article {pmid42252476, year = {2026}, author = {Wei, C and Wang, Y and Chen, Z}, title = {Comprehensive analyses of archaeal viral genomes reveal genomic characteristics, divergence, and host interactions.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02445-2}, pmid = {42252476}, issn = {2049-2618}, abstract = {BACKGROUND: The ecological significance of bacteriophages has been extensively investigated, while the role of archaeal viruses across different environments remains poorly understood.

RESULTS: Here, we present the Archaeal Viral Genome Database (AVGD), a comprehensive survey of archaeal viruses across eight distinct habitat types, including 3708 archaeal viral genomes, with genome sizes ranging from 3 to 188 kb, identified from 64,521,709 putative viral genomes using 40 public metagenomic datasets, an integrated public viral genome database (IGN), and pig gut viral databases. Our analysis revealed that the majority (92.93%) of archaeal viruses in the AVGD belong to the class Caudoviricetes. Phylogenetic analysis showed that many archaeal viruses diverged with their respective habitats. Using CRISPR spacer matching, we characterized the host composition of these archaeal viruses and uncovered competitive interaction networks between archaeal viruses and other archaeal viruses targeting the same host or different hosts. Furthermore, we identified 129,067 coding genes from 3708 archaeal viral genomes, most of which were associated with essential archaeal viral cellular functions, including replication, assembly, and packaging. Archaeal viruses also encoded a variety of auxiliary metabolic genes, anti-CRISPR (Acr) proteins for evading host immunity, and DNA methyltransferases for escaping host restriction-modification systems.

CONCLUSIONS: Together, this study provides a valuable resource and offers new insights into the ecological roles and host interactions of archaeal viruses across diverse environments. Video Abstract.}, } @article {pmid42252506, year = {2026}, author = {Galtier, A and Warinner, C and Velsko, IM}, title = {Ancient species diversity and niche adaptation in Tannerella and Porphyromonas revealed through pangenomics.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evag136}, pmid = {42252506}, issn = {1759-6653}, abstract = {De novo assembly of ancient and modern bacterial metagenomes can shed light on evolution and ecology of bacterial species that are challenging to culture. Tannerella and Porphyromonas are bacterial genera linked to periodontal disease, and understanding their evolution may reveal insights into their role in oral disease development. We performed pangenomic and phylogenetic analyses on a global set of isolates and metagenome-assembled genomes of the genera Tannerella (n=238) and Porphyromonas (n=976), including 66 genomes from ancient dental calculus samples (up to 14,800 years old), and modern oral samples from present-day living populations. We identify a novel species of oral Tannerella in modern and ancient humans, which we call Ca. Tannerella abscondita, that is related to and often mistaken for Tannerella forsythia but differs in its virulence repertoire. We reveal distinct niche tropism in Tannerella species and Porphyromonas pasteri, but not Porphyromonas gingivalis. There is limited phylogeographic structuring, and virulence genes are homogeneously distributed across continents and oral niches. Saliva-derived strains of T. forsythia and P. gingivalis from Oceania and T. serpentiformis and P. pasteri from Asia show enrichment of pseudogenes related to ecological niche transitions. A phylogenetic analysis of the P. gingivalis major fimbrial protein gene fimA reveals the genes cluster by genotypes, and that no ancient genes are found in genotypes I and Ib. Using de novo assembly for bacterial pangenomics improves the representation of oral genera found in reference databases and enhances our ability to study the evolutionary history of these taxa.}, } @article {pmid42252693, year = {2026}, author = {Jourdain, L and Leininger, A and Pacheco, AR and Gu, W}, title = {Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag145}, pmid = {42252693}, issn = {1751-7370}, abstract = {Microbial ecosystems often sustain stable metabolic functions despite pronounced taxonomic turnover, yet the mechanisms underlying such reproducible functional states remain poorly understood. Here, we investigated how physicochemical constraints shape functional convergence in anaerobic digestion communities using replicated serial enrichments seeded from four distinct inocula. Across three pH levels and six substrate regimes, replicate communities from different inocula consistently converged toward reproducible metabolite profiles, with pH emerging as the dominant organizing factor. Community composition became progressively environment-driven over time, and after 30 generations, pH explained the largest fraction of compositional variance (PERMANOVA R2 = 0.21, P = 0.001), followed by substrate. Genome-resolved metagenomics revealed that convergence was accompanied by strong pH-dependent structuring of redox-balancing and terminal electron-sink pathways, whereas upstream carbohydrate-entry pathways were conserved. Taxonomic convergence was incomplete and scale-dependent: the ability to correctly assign communities to their inoculum declined from 75% at the genus level to 53% at the phylum level, indicating increasing similarity across inocula at coarser taxonomic resolution despite persistent fine-scale variability. Despite this taxonomic flexibility, communities assembled under identical conditions consistently recruited similar sets of metabolic pathways organized into comparable network architectures. Functional redundancy analyses showed high redundancy and flexible taxonomic implementation for upstream fermentative processes, contrasted with lower redundancy and stronger convergence for terminal methanogenic functions. Together, these results demonstrate that reproducible metabolic function in AD emerges from environmentally constrained assembly of shared metabolic network architectures, rather than deterministic fixation of species composition, highlighting environmental control of metabolic organization as a central principle governing microbiome function.}, } @article {pmid42252802, year = {2026}, author = {Stang, A and Illig, T and Hiller, K and Weilert, H and Schmidt, R and Gronauer, R and Seifert, M}, title = {Lowered Abundance of Gut Bacteriophage Species Is Associated With Human Cancer Cachexia.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {17}, number = {3}, pages = {e70324}, pmid = {42252802}, issn = {2190-6009}, support = {3465//Asklepios Proresearch, Asklepios Hospitals Hamburg, Germany/ ; }, mesh = {Humans ; *Cachexia/etiology ; *Bacteriophages/genetics ; Male ; Female ; *Gastrointestinal Microbiome ; Aged ; *Neoplasms/complications ; Metagenomics/methods ; Metagenome ; Feces/microbiology ; Middle Aged ; }, abstract = {BACKGROUND: Cancer cachexia exemplifies a high medical need condition without effective treatment. Recent studies implicated bacterial gut microbiome alterations to cancer cachexia. Whether the gut bacteriophage profile, an important microbiome component for health and disease, is also related to cancer cachexia remains unknown. We aimed to profile gut microbiome alterations in human cancer cachexia with attention on bacteriophages.

METHODS: We performed shotgun metagenomic sequencing in stool samples from 78 cachectic and 42 noncachectic patients (53% male, mean age 67 ± 8 years) with newly diagnosed, advanced-stage (UICC IV) gastrointestinal cancers. Cachexia was defined according to the main criterion agreed upon international consensus (weight loss [WL] adjusted to body mass index [BMI]). Obtained DNA short-reads were used for k-mers-based, phage-inclusive matching with reference databases, de novo phage assembly and inferring microbiome-encoded functions. We replicated significance-based statistical and prediction-oriented machine-learning analyses in 2022 and 2025 generated metagenome datasets to incorporate the recent change by the International Committee on Taxonomy of Viruses (ICTV) from morphology-based (valid until 2022) to revised genome-based phage taxonomy into microbiome findings of cachexia.

RESULTS: Cachectic and noncachectic patients differed significantly regarding BMI (mean 20.9 vs. 26.4 kg/m2), WL (mean -6.5 vs. -0.2 kg), survival (median 5 vs. 13 months) and clinical cachexia domains (e.g., C-reactive proteine and appetite loss) (all p < 0.001) but not for other clinical covariables (e.g., cancer type) (all p > 0.05). Read-based mapping (2022/2025) identified 1.312/1.513 species (74/39 phage species), and de novo assembly resulted in 4.184/4.209 contigs (corresponding to 65/39 phage species). Concordantly, both analyses (2022 and 2025) showed that prevalent cachexia associated significantly with beta-diversity (Bray-Curtis distance, PERMANOVA, p < 0.05), but not to alpha-diversity (Shannon-Index, ANOVA, p > 0.05), reduced microbiome-encoded detoxification functions (e.g., enriched microbial β-glucuronidase and depleted bacterial efflux pumps) and lowered abundance of bacterial species with false-discovery-rate (FDR)-corrected p < 0.05 (2022: Faecalibacterium prausnitzii, Roseburia intestinalis, Streptococcus species and Lachnospiraceae species; 2025: Faecalibacterium species, Ruminococcus gauvreauii and Intestinibacter bartlettii). Further, lowered abundance of bacteriophages associated with cachexia, predominantly affecting double-stranded (2022: Caudovirales, Siphoviridae, FDR-corrected p < 0.05; 2025: Myoviridae, Siphoridae, p < 0.05) but also single-stranded (2022: Inoviridae, Microviridae, p < 0.05; 2025: Inoviridae; p < 0.05) DNA phage species. In machine-learning models, bacteriophages were top-ranked cachexia predictors (2022: Caudovirales, Siphoviridae; 2025: Myoviridae, Siphoridae). Accuracy was highest when only phage contigs were taken into account (correctly classified instances: 75.0%-85.8%; AUC: 0.703-0.916).

CONCLUSIONS: The previously unknown link between gut bacteriophages and human cancer cachexia expands the scope for basic, translational and clinical microbiome-targeted research in an area of significant unmet medical need.

TRIAL REGISTRATION: Study Box of the German Cancer Society (Registration Number ST-U069, Date: 29 May 2018).}, } @article {pmid42253890, year = {2026}, author = {Liu, Y and Xie, H and Song, Z and Huang, M and Li, M}, title = {Massive ascites and adnexal masses mimicking malignancy: A case report of Chlamydia trachomatis infection diagnosed by metagenomic next-generation sequencing.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02616}, pmid = {42253890}, issn = {2214-2509}, abstract = {OBJECTIVE: Chlamydia trachomatis (C. trachomatis) is the most commonly reported bacterial sexually transmitted infection among sexually active women. Although often asymptomatic or associated with non-specific clinical manifestations, it can cause inflammatory exudates and encapsulated fluid collections that are similar to adnexal masses on imaging. In rare cases, it may also present with massive ascites, a constellation of findings that may mimic ovarian malignancy.

CASE: We report the case of a 32-year-old female with a nearly 3-month history of abdominal pain, adnexal masses and massive ascites. The initial workup did not reveal obvious evidence of infection and cytological examination showed no malignant cells. However, advanced gynecological originated cancer could not be fully excluded. Metagenomic next-generation sequencing (mNGS), which detected C. trachomatis in ascitic fluid, facilitated the diagnosis. The patient showed satisfactory clinical improvement following doxycycline treatment.

CONCLUSION: For young, sexually active women presenting with unexplained ascites and adnexal masses, after excluding malignancy and common infectious diseases such as tuberculosis, C. trachomatis infection should be considered. Modern etiological detection methods, such as mNGS, can be employed to facilitate the diagnosis.}, } @article {pmid42254105, year = {2026}, author = {Habib, E and Urooj, I and Barry, HD and Awais, M and Kumari, M and Hajj, F}, title = {AI-programmable therapeutics via metagenomic foundation models for rare phage-mediated autoimmune modulations: early translational risks and benefits.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {6}, pages = {3905-3906}, pmid = {42254105}, issn = {2049-0801}, } @article {pmid42254157, year = {2026}, author = {Arif, L and Abbasi, MM and Raza, AA and Samadi, A}, title = {From microbiome profiling to precision medicine: diagnostic and therapeutic potential in gastrointestinal disorders: current evidence, challenges, and future directions.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {6}, pages = {3348-3359}, pmid = {42254157}, issn = {2049-0801}, abstract = {Gastrointestinal (GI) disorders, affecting millions globally (approximately 1.5 billion people with IBS alone), impose a significant healthcare burden and remain challenging to diagnose and manage. Current approaches are often invasive or symptom based, highlighting an urgent need for more precise and personalized strategies. The gut microbiome may offer novel diagnostic biomarkers and therapeutic targets, potentially transforming patient care. It supports GI and systemic health via metabolism, immune modulation, and neurochemical signaling. The dysbiosis of the gut microbiota contributes significantly to the pathogenesis of various GI disorders, including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), colorectal cancer (CRC), and small intestinal bacterial overgrowth. This narrative review critically evaluates the diagnostic potential of microbiome profiling and its clinical applications in developing personalized therapeutic strategies. We examine cutting-edge techniques such as 16S rRNA sequencing, metagenomics, and metabolomics, and discuss how dietary modulation, precision probiotics, and fecal microbiota transplantation are being increasingly used to reshape gut microbial composition. However, it is critical to note that while microbiome alterations show consistent associations with GI diseases, current evidence remains largely observational and associative. To date, no microbiome-based test has achieved regulatory approval or clinical validation as a standalone diagnostic tool for IBD, IBS, or CRC, and therapeutic applications remain investigational with modest clinical benefits in select conditions. Additionally, we highlight the translational challenges of integrating microbiome-based diagnostics into mainstream clinical practice and propose future research imperatives. This review provides a balanced perspective on the promise and challenges of integrating microbiome-based approaches into clinical gastroenterology, while proposing actionable research priorities to guide future investigations toward clinically validated, patient-centered diagnostic, and therapeutic solutions.}, } @article {pmid42254407, year = {2026}, author = {Liang, Y and Hu, J and Wang, Z}, title = {A case of severe psittacosis in a hemodialysis patient-the critical role of detailed medical history and next-generation sequencing.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1825118}, pmid = {42254407}, issn = {2296-858X}, abstract = {An 80-year-old male patient on maintenance hemodialysis was admitted with "high fever and cough." Pulmonary imaging suggested pneumonia, but his condition deteriorated rapidly despite empirical broad-spectrum antimicrobial therapy (covering bacteria, atypical pathogens, and fungi), progressing to respiratory failure and delirium. He was transferred to the intensive care unit for continuous renal replacement therapy. Routine microbiological tests (blood culture, sputum culture, respiratory pathogen PCR) were all negative. Detailed history revealed that the patient had kept a parrot for over a month prior to illness onset. Metagenomic next-generation sequencing of blood and sputum specimens detected abundant Chlamydia psittaci sequences. Following confirmation, treatment was adjusted to oral minocycline combined with intravenous azithromycin. The patient's temperature gradually normalized, neuropsychiatric symptoms resolved, and pulmonary imaging showed marked improvement, ultimately leading to successful discharge. This case highlights the importance of considering zoonotic pathogens in immunocompromised patients with refractory pneumonia. Detailed history-taking and metagenomic next-generation sequencing (mNGS) technology are crucial for early diagnosis. Early use of mNGS should be strongly considered in immunocompromised patients with severe pneumonia unresponsive to empiric therapy and negative routine workup, particularly when epidemiological clues such as bird exposure are present.}, } @article {pmid42254409, year = {2026}, author = {Kong, H and Pan, J and Liu, J and Liang, M and Liu, L and Niu, H and Li, Y}, title = {Successful management of severe Pneumocystis jirovecii pneumonia with inhaled nitric oxide and individualized ventilatory strategies in an immunosuppressed patient: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1808578}, pmid = {42254409}, issn = {2296-858X}, abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have improved survival in extensive-stage small-cell lung cancer (SCLC) but may cause checkpoint inhibitor pneumonitis (CIP). Management of CIP often requires prolonged high-dose corticosteroids, leading to profound immunosuppression and increased risk of opportunistic infections. Among these, Pneumocystis jirovecii pneumonia (PJP) is a life-threatening complication in non-HIV patients and carries higher mortality than HIV-associated PJP. Early etiological diagnosis is therefore essential. We report a case of severe PJP diagnosed by metagenomic next-generation sequencing (mNGS) and successfully managed with comprehensive respiratory support.

CASE PRESENTATION: A 69-year-old HIV-negative man with extensive-stage SCLC received four cycles of etoposide-platinum chemotherapy plus adebrelimab. Subsequently, CIP developed and required prolonged high-dose methylprednisolone therapy. He was transferred to our hospital for progressive dyspnea. Evaluation showed severe hypoxemia (PaO₂/FiO₂ 185 mmHg) and markedly elevated serum 1,3-β-D-glucan (3327.99 pg./mL). Bronchoalveolar lavage fluid mNGS identified P. jirovecii as the predominant pathogen, with Klebsiella pneumoniae, Pseudomonas aeruginosa, and Candida albicans indicating mixed pulmonary infection. The patient received trimethoprim-sulfamethoxazole, cefoperazone-sulbactam, and caspofungin. Worsening respiratory failure required endotracheal intubation and mechanical ventilation. Lung recruitment maneuvers, individualized positive end-expiratory pressure titration, and adjunctive inhaled nitric oxide progressively improved oxygenation, allowing successful extubation and eventual discharge.

CONCLUSION: Severe PJP should be considered in non-HIV patients receiving corticosteroids for CIP. mNGS enabled rapid pathogen identification and targeted therapy. Comprehensive respiratory support, including optimized mechanical ventilation and inhaled nitric oxide, may be valuable in managing life-threatening opportunistic infections in immunosuppressed patients.}, } @article {pmid42254474, year = {2026}, author = {Sparaciari, FE and Saylors, K and Chan, M and Perez, S and Firth, C and Horwood, PF and Karlsson, EA}, title = {Operationalizing metagenomic data from environmental surveillance for one health decision-making in live animal markets: Findings from a multisectoral workshop in Cambodia.}, journal = {Dialogues in health}, volume = {8}, number = {}, pages = {100312}, pmid = {42254474}, issn = {2772-6533}, abstract = {BACKGROUND: Live animal markets (LAMs) are recognized as hotspots for zoonotic disease emergence. Environmental surveillance (ES), particularly when paired with metagenomic sequencing, offers an advanced and actionable approach to pathogen detection in high-risk settings. However, the complexity of metagenomic data and the lack of user-friendly communication tools hinder its integration into routine public health decision-making.

METHODS: We conducted an exploratory qualitative participatory workshop study with descriptive analysis. A three-day multisectoral workshop was held in Phnom Penh, Cambodia, in May 2024, bringing together stakeholders from health, agriculture, and environment sectors to explore how metagenomic ES data can be visualized, understood, and applied. Through simulation exercises, surveys, and interviews, the workshop evaluated user preferences for data formats, thresholds for action, and decision-making strategies.

FINDINGS: In total, 52 participants attended the workshop and ten completed semi-structured interviews. Participants discussed their preferred familiar visualizations (bar, pie, and line charts) and intuitive color-coded thresholds (e.g., traffic-light schemes). While digital dashboards were welcomed, analog, printer-friendly formats remained essential due to infrastructure constraints. Key barriers to ES integration included limited bioinformatics capacity, lack of inter-ministerial coordination, and minimal ES prioritization at the provincial level.

INTERPRETATION: Metagenomic ES data can inform public health actions when visualization tools are tailored to end-user needs and embedded in multisectoral governance. This exploratory participatory workshop generated preliminary stakeholder-informed insights and an initial draft roadmap for future implementation planning in Cambodia. Further expert-led and funded work is needed to validate visualization tools, pathogen-specific thresholds, escalation pathways, and operational use under real-world surveillance conditions.}, } @article {pmid42254492, year = {2026}, author = {Chang, Z and Wang, X and Zhao, M and Zhang, X and Li, S and Liu, Y and Zhang, S and Wang, J and Wang, X}, title = {MARM: a framework for malignancy risk prediction from host-derived CNV in bronchoalveolar lavage fluid mNGS data with microbial admixture.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1846545}, pmid = {42254492}, issn = {1664-302X}, abstract = {Early identification and risk assessment of malignancy are essential for improving clinical decision-making and patient outcomes. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) data contain both microbial and host-derived signals, and a key challenge in extending such data to tumor-associated applications is the robust extraction of host features with discriminative value for malignancy from this complex, admixed background. To address this problem, we developed MARM, a malignancy risk prediction method centered on host-derived copy number variation (CNV). Using host-derived reads from BALF mNGS data, MARM performs genome-wide window-based coverage quantification, normalization and bias correction, reference baseline construction, and principal component-based denoising to derive window-level CNV features for malignancy risk modeling. In addition, a pseudo-label-based extension strategy was introduced to incorporate weakly labeled samples through high-confidence screening, and the performance of XGBoost, Random Forest, and generalized linear models (GLM) was systematically evaluated using CNV features, microbial features, and combined features. Models built on host-derived CNV features consistently outperformed those based on microbial features and achieved performance comparable to combined-feature models, while joint modeling did not provide a stable additional benefit. These findings indicate that, under the current data setting and feature construction strategy, CNV represents a more stable and informative discriminative signal than microbial features. Among the evaluated classifiers, XGBoost showed the best compatibility with window-level CNV features and outperformed Random Forest and GLM overall. On the independent validation set, the pseudo-label-enhanced MARM achieved the best overall performance, with a sensitivity of 0.686, specificity of 0.975, accuracy of 0.847, and Youden index of 0.671. By contrast, microbial features did not show stable independent discriminative ability, and combined modeling did not yield clear or sustained performance gains. Together, these results indicate that, in microbially admixed BALF mNGS data, host-derived CNV is more suitable than the evaluated microbial features as the core modeling signal for malignancy risk prediction. MARM provides a new methodological framework for malignancy prediction in complex clinical samples and offers a reference for deeper exploitation of host-derived signals in mNGS data and related auxiliary diagnostic applications.}, } @article {pmid42254517, year = {2026}, author = {Liu, S and Luo, X and Zhou, J and Wang, L and Li, R and Luo, Z and Li, N and Xiao, S and Zhang, P}, title = {A comparative study of the gut microbiome and fecal metabolome in hypertensive patients from middle-temperate and tropical cities of China: Daqing and Haikou.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1801806}, pmid = {42254517}, issn = {1664-302X}, abstract = {BACKGROUND: Geographic variations in climate and lifestyle may be associated with hypertension (HTN) through alterations in the gut microbiota and its metabolites. This study aimed to comparatively analyze the gut microbiome and fecal metabolome of hypertensive patients from two Chinese cities characterized by distinct climatic conditions: Daqing (middle-temperate climate) and Haikou (tropical climate). The objective was to identify gut microbial and metabolic characteristics associated with geographic differences and to provide insights into HTN prevention and management.

METHODS: A cross-sectional study was conducted between May and December 2024, involving hypertensive patients from Daqing and Haikou. Fecal samples were collected from 28 hypertensive patients in Daqing (DQ group) and 32 in Haikou (HK group), and analyzed using shotgun metagenomic sequencing and untargeted metabolomics.

RESULTS: Differences in microbial composition and metabolite profiles were observed between the two groups. Using ALDEx2 analysis at the genus level, 34 genera were identified as differentially abundant between the DQ and HK groups. After adjusting for potential confounding variables, including age, body mass index, smoking, and drinking status, 6 genera remained significantly associated with geographic grouping. A logistic regression model based on these genera achieved an area under the curve (AUC) of 0.8069, with Pseudescherichia showing the highest individual discriminatory performance (AUC = 0.7925). Functional analysis suggested that pathways such as xylene degradation and biofilm formation were relatively reduced in the DQ group. Metabolomic analysis identified 38 differentially abundant metabolites, including 15-hydroxyeicosatetraenoic acid (15-HETE), 7α,25-dihydroxycholesterol, the putative metabolite (3-hydroxypentadecanoyl) lysine, and ginsenoside Rg3. Dysregulated pathways were mainly involved in glycerophospholipid metabolism, ABC transporters, and choline metabolism. Correlation analysis revealed potential associations between differential microbes and metabolites.

CONCLUSION: Distinct gut microbiome and metabolome profiles were observed between hypertensive patients from the two geographic regions. These findings suggest potential associations between environmental factors and host-microbiome-metabolite interactions.}, } @article {pmid42254837, year = {2026}, author = {Schmelz, P and Eckensperger, S and Osvatic, J and Séneca, J and Alzubaidy, H and Petersen, JM}, title = {Host depletion kits improve microbiome analyses in environmental samples: seagrass as a test case.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag082}, pmid = {42254837}, issn = {2730-6151}, abstract = {All plants and animals associate with specific communities of symbiotic microorganisms. Characterizing the diversity and functions of these communities is essential for understanding their roles in host health; however, such efforts are often hindered by the dominance of host-derived material in, e.g. DNA extractions. Although various commercial host DNA depletion kits have been developed to overcome these challenges, they have not yet been systematically tested on environmental samples. We used Zostera marina, globally the most widespread seagrass species, as a test case to assess the effectiveness of three different commercially available host DNA depletion kits: QIAamp DNA Microbiome Kit, HostZero Microbial Enrichment Kit, and NEBNext Microbiome DNA Enrichment Kit, when compared to the widely used DNeasy PowerSoil Pro Kit. All three host depletion kits substantially reduced the relative proportion of host DNA, as assessed by 16S rRNA gene amplicon sequencing, and enriched previously identified seagrass-associated bacteria. Furthermore, in metagenomes, only samples processed with host depletion methods allowed for the assembly of metagenome-assembled genomes with high completeness and low contamination. Metagenomic analysis further enabled the recovery of seagrass root core microbiome members, including previously undetected members of the family Sedimenticolaceae, highlighting the value of these techniques for uncovering novel host-associated microbial diversity in environmental samples such as marine plants.}, } @article {pmid42255303, year = {2026}, author = {Xue, G and Hu, Y and Xue, H and Wang, X and Bai, H and Du, J and Wang, Y and Huo, H and Li, M and Jiang, W}, title = {Biochar enhances cucumber production by modulating rhizosphere microbiota and soil metabolites under continuous cropping systems.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1726191}, pmid = {42255303}, issn = {1664-462X}, abstract = {Biochar, a soil amendment with diverse regulatory functions, has been widely applied to enhance soil conditions. However, its underlying mechanism for alleviating continuous cropping obstacles, from the perspective of rhizosphere microbe-metabolite-plant coupling, remains to be further elucidated. Using cucumber (Cucumis sativus L.) as the model crop, this study explored the rhizosphere-mediated effects of biochar application under continuous cropping conditions via the analytical methods of metagenomics and metabolomics. Six biochar application rates (0, 5, 10, 20, 30, and 40 t ha[-][1]) were tested. All biochar treatments significantly improved cucumber yield by 20%-50%, with the C30 and C40 treatments producing the most pronounced yield enhancement. C10, C20, C30 and C40 treatments had a positive effect on cucumber quality, soil physicochemical properties and enzymatic activities. Vitamin C and soluble protein peaked in C20, whereas some sugar indicators decreased across all biochar treatments. Urease activity was significantly elevated under C20, C30, and C40 treatments. Notably, the C40 treatment led to marked increases in total nitrogen, available phosphorus, and sucrase activity. Biochar amendments also enriched key bacterial phyla involved in carbon and nitrogen cycling, including Actinobacteria, Bacteroidetes, Chloroflexi, and Bacillota. Medium to high application rates (C20, C30, C40) upregulated various secondary metabolic pathways associated with biotic stress resistance, including the biosynthesis pathways of phenylpropanoids, various alkaloids, and the metabolic pathway of phenylalanine. High biochar application rate (C40) characterized lipid metabolism as the core responsive pathway and significantly downregulated galactose metabolism. This study reveals that biochar application represents a promising strategy to mitigate continuous cropping obstacles of cucumber by enhancing nutrient cycling, enzyme activities, soil metabolite composition, and the rhizosphere microbial community in facility systems of the cold and arid northern regions of China.}, } @article {pmid42255362, year = {2026}, author = {Sun, Y and Kei, K and Qiu, JW and Martín-Durán, JM and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the feather duster worm, Sabellastarte sp. h YS-2021 (Sabellida: Sabellidae) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {274}, pmid = {42255362}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Sabellastarte sp. h YS-2021 (feather duster worm; Annelida; Polychaeta; Sabellida; Sabellidae). The genome sequence has a total length of 1 786.39 megabases. Most of the assembly (97.94%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 15.35 kilobases. From the metagenome data, we recovered 5 bins, of which one was a high-quality MAG.}, } @article {pmid42255501, year = {2026}, author = {Huo, S and Liu, W and Lv, C and Liu, B and Xue, J and Hong, Y and Hao, Y and Chen, M and Xu, A and Tan, X and Feng, X and Li, S}, title = {The re-emergence of psittacosis in China: a scoping review of epidemiology, diagnostics, and One Health priorities.}, journal = {Science in One Health}, volume = {5}, number = {}, pages = {100158}, pmid = {42255501}, issn = {2949-7043}, abstract = {Psittacosis caused by Chlamydia psittaci has re-emerged in China as sporadic cases and localized outbreaks. However, current knowledge remains fragmented across the clinical, veterinary, epidemiological, and public health fields. This scoping review mapped studies on psittacosis in China, identified major knowledge gaps, and defined priorities for research, clinical management, and prevention and control. Following the Arksey and O'Malley framework and Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR), China National Knowledge Infrastructure (CNKI), Wanfang, PubMed, Web of Science, and Embase were searched for studies published between 1 January 1985 and 31 December 2025 and synthesized eligible studies with descriptive statistics and thematic analysis. A total of 424 studies were included. Research interest showed recent sharp increases and was concentrated in Eastern and Central China. Case reports and series dominated the literature, whereas analytic epidemiology, standardized surveillance, and high-resolution molecular studies remained limited. Reported cases were most often documented in middle-aged and older adults with avian exposure, including pet birds and poultry, and the reported occurrence showed a winter-spring pattern. Pneumonia was the predominant clinical presentation, and severe cases could progress to acute respiratory distress syndrome and multi-organ dysfunction. Metagenomic next-generation sequencing (mNGS) was the most frequently reported diagnostic method in recent studies, while PCR and serology remained important complementary tools. Overall, the literature is growing rapidly, but remains uneven in geographic coverage, study design, and integration across human, animal, and environmental sectors. These findings support broader One Health surveillance, stronger analytic and molecular epidemiology, and more standardized approaches to diagnosis, source investigation, and prevention in China.}, } @article {pmid42256215, year = {2026}, author = {Li, C and Ye, X and Chen, Y and Shen, M and Zhou, Z and Jiang, H and Hu, L and Pan, H and Shen, D and Lin, Y and Wang, L}, title = {Pathogen spectrum of pulmonary infections in kidney transplant recipients and the diagnostic value of mNGS: a sputum and BALF study based on clinical decision-making.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1742153}, pmid = {42256215}, issn = {2235-2988}, mesh = {Humans ; *Sputum/microbiology/virology ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; *Kidney Transplantation/adverse effects ; Female ; Retrospective Studies ; Male ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; *Transplant Recipients ; *Clinical Decision-Making ; *Respiratory Tract Infections/microbiology/diagnosis ; Adult ; Bacteria/isolation & purification/classification/genetics ; Metagenomics ; Fungi/isolation & purification/classification/genetics ; Viruses/isolation & purification/classification/genetics ; Coinfection/microbiology/diagnosis ; }, abstract = {BACKGROUND: Pulmonary infection is a common and severe post-transplant complication in kidney transplant recipients (KTRs). Their long-term immunosuppression results in an extremely complex pathogen spectrum. Compared with conventional etiological detection methods, metagenomic next-generation sequencing (mNGS) enables rapid and broad-spectrum pathogen identification. However, compared with bronchoalveolar lavage fluid (BALF), research on the diagnostic value of sputum - used as a non-invasive sample - for pulmonary infections in KTRs remains limited.

METHODS: A retrospective study included 77 kidney transplant recipients (KTRs) with pulmonary infections admitted from July 2021 to January 2025. BALF (n=37) or sputum (n=40) was collected for mNGS. Ninety-two non-immunosuppressed patients with pulmonary infections, treated during the same period and with BALF for mNGS, were also included. We compared pathogen profiles between the two groups and evaluated the diagnostic performance for KTRs pulmonary infections between BALF and sputum.

RESULTS: The pathogen spectrum in KTRs was dominated by viruses (43.0%) and opportunistic fungi (20.0%), whereas bacteria (67.97%) predominated in the non-immunosuppressed group. The co-infection rate was significantly higher in KTRs than in the non-immunosuppressed group (67.57% vs. 35.87%, P<0.001). In the KTRs cohort, the sputum group had a much higher prevalence of heart disease than the BALF group (52.5% vs. 2.7%, P<0.001). The positive detection rates of sputum and BALF mNGS showed no statistical difference (97.5% vs. 91.89%, P = 0.268), but sputum mNGShad a higher concordance rate with the clinical composite diagnosis (95.0%) compared to BALF mNGS (81.08%). In both specimen types, mNGS achieved a significantly higher pathogen detection rate than conventional tests (P<0.001 for both), with poor agreement between the two approaches (Kappa < 0.2).

CONCLUSION: The pathogen spectrum of pulmonary infections in KTRs differs significantly from that in non-immunosuppressed patients. It is characterized by a predominance of viruses and opportunistic fungi. mNGS is superior to conventional methods for making an etiological diagnosis. Non-invasive sputum mNGS is a valuable diagnostic alternative in KTRs, particularly for patients unable or unwilling to undergo invasive procedures.}, } @article {pmid42256221, year = {2026}, author = {Giju, JK and John, S and Sivadas, A and Prabhakar, M and K, K and Sunilkumar, D and Nair, BG and Pal, S and Prakash, V}, title = {From dysbiosis to precision medicine: targeting the microbial-metabolic axis in IBD management.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1826972}, pmid = {42256221}, issn = {2235-2988}, mesh = {Animals ; Humans ; *Dysbiosis/complications/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; *Inflammatory Bowel Diseases/immunology/microbiology/therapy ; Intestinal Barrier Function ; Precision Medicine/methods ; *Probiotics/therapeutic use ; Diet Therapy ; Fatty Acids, Volatile/biosynthesis ; Plant Preparations/therapeutic use ; Antimicrobial Peptides/physiology ; Immunomodulation ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition that has a rapidly changing global epidemiology. IBD has been traditionally viewed as a primary immune system dysfunction, but emerging evidence more accurately describes IBD as a perturbance of the intricate balance between host immunity, the intestinal microbiome, and intestinal metabolism. Although genetic and environmental components have long been recognized as contributors, accumulating evidence increasingly highlights the pivotal role of microbial dysbiosis in the pathogenesis of IBD. In patients with IBD, intestinal dysbiosis, which is often characterized by reduced Firmicutes and increased pro-inflammatory bacteria, triggers a cascade of pathogenic events. These pathogenic events include impaired epithelial barrier function, dysregulated immune activation against luminal antigens, and immune reprogramming. Central to these processes are functional changes in microbial metabolism, particularly in pathways involving short-chain fatty acids (SCFAs), bile acids, and redox homeostasis, which critically contribute to the development of chronic mucosal inflammation. The current therapeutic backbone of IBD-including aminosalicylates, biologics, and immunomodulators-largely targets the inflammatory response. However, the challenges such as primary non-response, secondary loss of response, and systemic side effects are often problematic. Consequently, there is an urgent need to develop novel therapeutic and preventive strategies that target the underlying microbial and metabolic causes of the disease rather than modulating immune responses. This review integrates the pathomechanistic implications of the microbiome-metabolic axis in the maintenance of gut homeostasis and its disruption in IBD, with particular emphasis on the global epidemiology of the disease. We further evaluate emerging therapeutic and preventive strategies aimed at restoring the microbiome-metabolic axis, including fecal microbiota transplantation (FMT), probiotic therapy, bacteriophage therapy, and helminth-based therapies. In addition, we explore the potential of advanced approaches such as microbiome engineering and precision genome editing to enable highly personalized therapeutic paradigms. By bridging microbial ecology with clinical pathology, this review highlights the transformative potential of targeting the host-microbiota interface to achieve improved long-term outcomes in IBD.}, } @article {pmid42256253, year = {2026}, author = {Huang, W and Wang, S and Zhang, Y and Gao, M and Zhong, N and Hao, C and Janak, LP and Wang, L and Meng, S and Zhao, W and Zeng, S}, title = {Streptococcus mutans exacerbates gut microbiota dysbiosis in SHANK3 [-/-] autism model mice via the oral-gut axis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2681259}, pmid = {42256253}, issn = {2000-2297}, abstract = {BACKGROUND AND OBJECTIVE: Autism spectrum disorder (ASD) is associated with gut microbiota dysbiosis, yet the impact of oral pathobiont translocation via the oral-gut axis remains unclear. This study investigated how Streptococcus mutans (S. mutans), a primary cariogenic pathogen, influences gut microbial structure and function in an ASD mouse model.

METHODS: SHANK3 knockout (SHANK3[-/-]) and wild-type (WT) mice were divided into four groups: WT control, WT S. mutans-gavaged (WT-S.m), SHANK3[-/-] control, and SHANK3[-/-] S. mutans-gavaged (SHANK3-S.m). Mice were gavaged with S. mutans UA159 twice weekly for five weeks, followed by fecal metagenomic sequencing (n = 6 per group).

RESULTS: S. mutans translocated to the gut in both gavaged groups but did not achieve enhanced colonization in SHANK3[-/-] mice. S. mutans gavage significantly altered the gut microbiota structure in both WT and SHANK3[-/-] mice. In the ASD model, S. mutans gavage led to a significant enrichment of potential pathobionts (e.g. Duncaniella dubosii, Muribaculum gordoncarteri) and a decrease in beneficial bacteria (e.g. Bacteroides caecimuris, Bacteroides faecium). LEfSe analysis identified Parascardovia denticolens and Bacteroides heparinolyticus as specific biomarkers for the SHANK3-S.m group. Microbial networks showed reduced stability in SHANK3-S.m mice, with Enterocloster bolteae as a key node. Functional analysis revealed suppressed butanoate metabolism and enhanced neuroinflammation-related pathways.

CONCLUSION: Although S. mutans colonized only transiently, it provoked exacerbated ecological instability and pro-inflammatory metabolic alterations in ASD model mice, underscoring the role of the oral-gut-brain axis in ASD.}, } @article {pmid42256259, year = {2026}, author = {Dewan, A and Mascellino, MT}, title = {Computational and multi-omics systems biology for precision microbiome therapeutics.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1842701}, pmid = {42256259}, issn = {2813-4338}, abstract = {The human gut microbiome represents a complex and dynamic therapeutic target whose effective interrogation requires system-level analytical approaches beyond single-omics or reductive methods. This mini-review synthesizes recent advances in computational modeling and multi-omics integration relevant to the development of predictive, patient-tailored microbiome therapies. We critically assess the analytical strengths and limitations of genome-scale metabolic models (GEMs); generalized Lotka-Volterra and ODE-based community models; agent-based simulations; and statistical machine-learning frameworks and examine how their integration with metagenomics, metatranscriptomics, metaproteomics, and metabolomics can help bridge microbial functional potential with clinically relevant phenotypes. Representative applications-including MintTea for disease module identification, gNOMO2 for integrative microbiome profiling, and AGORA-based community metabolic modeling-illustrate the translational scope of these frameworks across inflammatory, metabolic, and infectious disease contexts. Hybrid ML-GEM frameworks have not yet been directly applied to FMT outcome prediction; however, the mechanistic principles underlying both approaches - metabolic compatibility modeling and data-driven responder stratification - suggest a compelling direction for future investigation, contingent on prospective validation in adequately powered and independent clinical cohorts. Persistent methodological challenges-such as data heterogeneity, batch effects across sequencing platforms, incomplete multi-omics coverage, and limited interpretability of complex machine-learning models-are being actively addressed through standardized preprocessing pipelines, explainable Artificial intelligence (AI) strategies, and federated analytics. While federated approaches enable privacy-preserving, multi-institutional model training, they introduce additional constraints related to non-identically distributed data, communication overhead, and uneven computational capacity. Overall, the convergence of mechanistic modeling, data-driven learning, and distributed analytical infrastructures may assist in advancing microbiome research from a largely correlational perspective toward mechanistic and ultimately prescriptive frameworks for precision microbiome medicine.}, } @article {pmid42256958, year = {2026}, author = {Elendu, C and Debua, AT and Okolo, EH and Sadiq, HO}, title = {Immune Checkpoint Inhibitor Pneumonitis Complicated by Invasive Pulmonary Aspergillosis in COPD: Diagnostic and Therapeutic Challenges.}, journal = {Clinical case reports}, volume = {14}, number = {6}, pages = {e72755}, pmid = {42256958}, issn = {2050-0904}, abstract = {Checkpoint inhibitor-associated pneumonitis complicated by invasive pulmonary aspergillosis represents a diagnostic challenge in ICI-treated patients, particularly those with COPD receiving corticosteroid therapy. Persistent or worsening respiratory abnormalities despite immunosuppressive treatment should prompt reassessment for superimposed fungal infection, including bronchoscopy, BALF analysis, and microbiologic testing to facilitate diagnosis and targeted therapy.}, } @article {pmid42257244, year = {2026}, author = {Moulignier, A and Heran, F and Lallemand, F and Bourdillon, P}, title = {Human Pegivirus Encephalitis With Brain Detection and Response to Sofosbuvir Ledipasvir.}, journal = {Annals of clinical and translational neurology}, volume = {}, number = {}, pages = {}, doi = {10.1002/acn3.70450}, pmid = {42257244}, issn = {2328-9503}, abstract = {Human pegivirus (HPgV-1) has been associated with severe encephalomyelitis in immunocompromised patients. Its neurological spectrum remains poorly defined. We report a slowly progressive encephalitis in a person living with well-controlled HIV, characterized by white matter abnormalities and inflammatory cerebrospinal fluid (CSF). HPgV RNA was detected in CSF and brain tissue by metagenomic sequencing, with no alternative pathogen identified. Following off-label treatment with sofosbuvir/ledipasvir, the patient showed sustained clinical improvement, normalization of CSF findings, and disappearance of detectable HPgV RNA. This observation expands the clinical context of HPgV-1 detection and supports further investigation of its role in central nervous system disease.}, } @article {pmid42257696, year = {2026}, author = {Nebauer, DJ and Nelson, T and Romanis, C and Neilan, BA and Timms, VJ}, title = {Taxonomy bias in metagenome-assembled genome recovery.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, pmid = {42257696}, issn = {2057-5858}, mesh = {*Metagenome ; *Metagenomics/methods ; Shotgun Sequencing ; *Bacteria/classification/genetics ; Genome, Bacterial ; Phylogeny ; Base Composition ; Sequence Analysis, DNA/methods ; }, abstract = {The recovery of metagenome-assembled genomes (MAGs) from shotgun metagenomic sequencing is rapidly expanding the availability of representative genomes. However, this practice may skew the representation of specific taxa in real-world datasets. This bias is attributed primarily to the known inefficiencies of sequence-by-synthesis platforms in amplifying GC-rich and AT-rich sequence fragments. Here, we recover 216 medium- and high-quality MAGs from an Australian wetland site. Notably, no MAGs were recovered for some dominant cyanobacterial and proteobacterial species known to be present. A new protocol involving read-based classification and alignment to the MAG dataset demonstrated the highly efficient recovery of low-GC organisms in the Actinobacteria and Bacteroidota phyla. Additionally, the recovery of lost taxonomic information was demonstrated through unmatched sample mapping. The findings suggest a bias towards the recovery of smaller, low-GC organisms in MAG recovery, potentially skewing the global representation of microbial diversity. Our pipeline is made publicly available as a tool to help researchers estimate taxonomic losses following MAG recovery efforts.}, } @article {pmid42258415, year = {2026}, author = {Pan, S and Chen, H and Sun, J and Xu, X and Gao, C}, title = {Species Identification And Antibiotic Susceptibility Testing Of The Nocardia Genus: Advances And Clinical Challenges.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {231}, pages = {}, doi = {10.3791/69977}, pmid = {42258415}, issn = {1940-087X}, mesh = {*Nocardia/drug effects/classification/genetics/isolation & purification ; Humans ; *Anti-Bacterial Agents/pharmacology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Microbial Sensitivity Tests/methods ; Nocardia Infections/microbiology/drug therapy/diagnosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The genus Nocardia comprises bacteria widely distributed in nature that can cause infections in both humans and animals. Due to their diverse clinical manifestations and prolonged culture time, infections are frequently misdiagnosed or overlooked. In recent years, advances in biological techniques have markedly improved molecular diagnostic methods, enabling more precise species identification. However, the increasing issue of antimicrobial resistance poses significant challenges for clinical management, particularly among immunocompromised patients, for whom treatment is more complex. Although multiple therapeutic agents are currently available, rising resistance rates highlight the critical importance of antibiotic susceptibility testing. This review discusses molecular identification methods for Nocardia species, including recent advances in 16S rRNA gene sequencing, multilocus sequence analysis (MLSA), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), whole-genome sequencing (WGS), and metagenomic next-generation sequencing (mNGS). The advantages and limitations of each technique are explored, with particular emphasis on their applications in detecting antibiotic resistance. The review also examines the clinical implementation of these molecular technologies, highlighting their contributions to rapid Nocardia identification, improved diagnostic accuracy, and reduced misdiagnosis. Finally, current limitations and future research directions are discussed, with particular attention to challenges related to cost, sensitivity, and standardization.}, } @article {pmid42258525, year = {2026}, author = {Siegers, JY and Auerswald, H and Maquart, PO and Szentiványi, T and Guillebaud, J and Hoem, T and Li, X and Suor, K and Pum, L and Khun, L and Nuon, S and Chea, K and Heang, V and Bienes, KM and Su, YCF and Duong, V and Nouhin, J and Boyer, S and Karlsson, EA}, title = {Discovery of a novel coltivirus in a newly identified Bat Bug Species (Heteroptera: Cimicidae) in Cambodia.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {6}, pages = {e0014372}, pmid = {42258525}, issn = {1935-2735}, mesh = {Animals ; Cambodia ; Phylogeny ; *Chiroptera/parasitology ; *Coltivirus/isolation & purification/genetics/classification ; Sequence Analysis, DNA ; Chlorocebus aethiops ; RNA, Viral/genetics ; Vero Cells ; Genome, Viral ; }, abstract = {Bats and their ectoparasites are significant reservoirs and potential vectors of emerging zoonotic pathogens, yet the viral diversity within bat-associated arthropods remains poorly characterized. This study reports the identification of a novel coltivirus (order Reovirales), provisionally designated Stricticimex coltivirus (SCCV), in a newly described bat bug species, Stricticimex phnomsampovensis, collected from cave-dwelling wrinkle-lipped free-tailed bats (Mops plicatus) in Cambodia. Metagenomic sequencing and phylogenetic analysis revealed that SCCV clusters within the Coltivirus genus, showing closest similarity to Tai Forest Reovirus (TFRV) previously isolated from African bats. SCCV was detected in 18.4% of examined bat bugs and successfully isolated in VeroE6 cells, with replication confirmed in multiple mammalian cell lines. The discovery of SCCV extends the known diversity and geographic range of coltiviruses and highlights bat ectoparasites as overlooked hosts of potentially zoonotic viruses. These findings underscore the importance of integrated One Health surveillance targeting both bats and their ectoparasites to better assess the risk of pathogen spillover in biodiverse regions with high human-animal contact.}, } @article {pmid42258549, year = {2026}, author = {Vanhnollat, C and Chonephetsarath, S and Somlor, S and Vungkyly, V and Soulaphy, T and Vongsanga, S and Etobayeva, IV and Bigot, T and Wong, G and Letizia, AG and Brey, PT and Buchy, P and Vongphayloth, K}, title = {Detection and genetic characterization of Tembusu virus and other flaviviruses from mosquitoes in Lao PDR.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0351023}, pmid = {42258549}, issn = {1932-6203}, mesh = {Animals ; *Flavivirus/genetics/isolation & purification/classification ; Laos ; Phylogeny ; Female ; *Culicidae/virology ; Genome, Viral ; *Mosquito Vectors/virology ; Flavivirus Infections/virology ; Humans ; Mosquito-Borne Diseases ; }, abstract = {BACKGROUND: Lao People's Democratic Republic (Lao PDR), located in Southeast Asia and known for its rich biodiversity, is part of a region recognized as a hotspot for emerging and re-emerging infectious diseases. Among flaviviruses, dengue virus (DENV) and Japanese encephalitis virus (JEV) are recognized public health threats. However, other reemerging mosquito-borne flaviviruses may also infect humans and cause diseases. Despite that, their distribution and public health impact in Lao PDR are not well understood due to limited past surveillance.

METHODOLOGY: Mosquitoes were collected using CDC light traps from 2021 to 2024, as part of vector and pathogen surveillance studies conducted across six provinces. A total of 2,548 female mosquitoes, representing 100 species from 11 genera, were collected and morphologically identified. Of these, 1,622 mosquitoes were pooled into 1,008 "mini pools" according to species and collection site. The pools were screened for flaviviruses by nested RT-PCR. Positive samples were further analysed by metagenomic sequencing, and coding-complete genomes were recovered and subjected to phylogenetic analysis.

PRIMARY RESULTS: We recovered thirteen coding-complete genomes through metagenomic sequencing, which included one Tembusu virus (TMUV) strain (TMUV/Mos_L010) from Culex vishnui mosquitoes and 12 other insect-specific flaviviruses (ISFVs). Phylogenetic analysis placed TMUV/Mos_L010 in cluster 3, closely related to a TMUV strain known to be pathogenic to dolphins in Thailand, with more than >99% bootstrap support for amino acid homogeneity. The detected ISFVs were part of the classical insect-specific flavivirus (cISFV) lineage and were further classified into five subgroups according to their associated mosquito genera: Aedes (1), Anopheles (1), Culex (2), and Uranotaenia (1).

CONCLUSIONS: This study documents the first detection of TMUV in Laotian mosquitoes and extends the known distribution of cluster 3 TMUV strains. The discovery of diverse ISFVs shows the rich and underexplored virome among Laotian mosquito populations. These findings highlight the need for enhanced arbovirus surveillance and ecological research to assess zoonotic risks of spillover infections in Southeast Asia.}, } @article {pmid42258623, year = {2026}, author = {Mosquera, RA and Magana-Ceballos, IG and De Jesus Rojas, W and Huang, X and Koochak, H and Tellez, ME and Castillo-Moguel, JA and Bishehsari, F and Mahdavinia, M and Ramos-Benitez, MJ and Harris, T and Yadav, A and Owens, K and Lemus-Rangel, R and Romero, M and Zuleta, S and Luz, A and Baltazar-Fernandez, A and McBeth, KE and Hashmi, S and Rosario Ortiz, G and Santoyo-Rios, J and Loyo-Rodriguez, JF and Colasurdo, GN}, title = {Multi-Omics Analysis Defines Endotypes and Systemic Inflammation in Primary Ciliary Dyskinesia: A Comparison with Healthy Controls.}, journal = {Annals of the American Thoracic Society}, volume = {}, number = {}, pages = {}, doi = {10.1093/annalsats/aaoag152}, pmid = {42258623}, issn = {2325-6621}, abstract = {INTRODUCTION: Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterized by chronic airway inflammation and progressive lung injury. The inflammatory profile and systemic involvement remain poorly defined. We applied integrated multi omics (transcriptomics, proteomics, and metagenomics) to characterize inflammatory signatures and explore saliva as a noninvasive marker of systemic inflammation. These findings may support improved disease characterization and inform therapy and monitoring.

METHODS: This cross sectional, multicenter study included participants with PCD and healthy controls from Houston, Texas; Puerto Rico; and Mexico. Demographic and clinical data were collected in the absence of acute infection. Oral swabs underwent a bulk inflammatory transcriptomic profiling of 590-genes using NanoString nCounter® and microbiome evaluation via metagenomic sequencing. High sensitivity NULISA™ proteomic profiling of 250-proteins was performed on both saliva and plasma, with results correlated across omic layers. Pathway and gene set analyses were conducted using nSolver Advanced Analysis.

RESULTS: Seventy-six participants were enrolled: 51 with PCD and 25 healthy controls. PCD patients, especially those older than 10 years and those with microtubular defects, showed markedly elevated inflammatory gene and protein expression in saliva and plasma. Five inflammatory endotypes were identified: Neutrophilic protease dominant, Dipeptidyl Peptidase 1(DPP‑1) profile (78%); neutrophilic recruiting, high‑Th17 (71%); eosinophilic dominant, high‑Th2 (51%); Th2/Th17‑high (47%), and Th2/Th17‑low (25%). PCD demonstrated increased neutrophil, and CD45‑related gene expression and activation of ten inflammatory pathways, including NF‑κB, oxidative stress, T‑cell-receptor, TREG, Th17, TNF, Th1, Th2, TGF-B signaling, and TLR (P < .01). Saliva and plasma showed strong molecular concordance. Microbiome analysis revealed significant shifts in diversity and abundance linked to inflammatory pathways.

DISCUSSION: These findings show that PCD is characterized by baseline inflammatory activity with marked endotypic heterogeneity, most frequently involving neutrophilic-immune pathways driven by DPP1-associated protease activity and Th17-mediated neutrophil recruitment, while a distinct subset of patients demonstrates a Th2-predominant inflammatory endotype. Salivary inflammatory profiling, which closely mirrors plasma, may offer a practical, non-invasive approach to capturing this patient-level heterogeneity and monitoring systemic immune activity and treatment response, especially with the new anti-inflammatory medications for bronchiectasis.}, } @article {pmid42259326, year = {2026}, author = {Martins, MF and Govindan, R and Almaghlouth, NK and Kirby, JE and Kentoffio, KJ and Farmakiotis, D and Le-Mahajan, A}, title = {A fatal case of Legionella micdadei prosthetic valve endocarditis diagnosed by plasma microbial cell-free DNA metagenomic sequencing.}, journal = {The Lancet. Infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/S1473-3099(26)00223-9}, pmid = {42259326}, issn = {1474-4457}, abstract = {We report a fatal case of Legionella micdadei prosthetic valve endocarditis in a patient who was immunocompromised, characterised by an indolent outpatient course followed by rapid clinical deterioration into mixed shock secondary to valve dehiscence and sepsis. The diagnosis was made by plasma microbial cell-free DNA metagenomic next-generation sequencing (mcfDNA-mNGS) and confirmed by buffered charcoal yeast extract culture of valve tissue. This case underscores the diagnostic limitations of conventional methods in culture-negative endocarditis, the evolving role of mcfDNA-mNGS in culture-negative endocarditis, and the absence of current culture-negative endocarditis guidelines addressing timely diagnosis for patients who are at risk of rapid deterioration. In this Grand Round, we briefly review the state of diagnostics for culture-negative endocarditis and the particularities of Legionella endocarditis. We also propose a framework for deciding when to consider early metagenomic testing, balancing the potential strengths of this technology with its limitations and cost.}, } @article {pmid42259450, year = {2026}, author = {Yang, W and Wang, X and Li, H and Liu, W and Chen, Z and Ren, B and Guo, T and Guo, J}, title = {Enhanced co-removal of nitrate and tetracycline from wastewater by iron-nitrogen-doped carbon: synergistic role of pyridinic nitrogen and iron.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135105}, doi = {10.1016/j.biortech.2026.135105}, pmid = {42259450}, issn = {1873-2976}, abstract = {Co-pollution of nitrate and tetracycline (TC) poses a critical barrier to efficient biological treatment due to impaired electron transfer, diminished microbial metabolic activity, and disrupted community structure. To address this challenge, this study synthesized an iron-nitrogen-doped carbon material (Fe-NC) featuring electron-withdrawing pyridinic nitrogen and Fe active sites. Under co-contaminated conditions, the nitrate and TC removal efficiencies of the TC/Fe-NC200 system were 100 % and 96 %, which were 21.27 and 2.18 times higher than those of the TC system. Material characterization indicated that Fe-NC might act as an electron transfer station, promoting the removal of nitrate and TC through Fe[3+]/Fe[2+] cycling. Electrochemical analyses showed that Fe-NC promotes the secretion of cytochrome c and flavin mononucleotide, accelerating extracellular electron transfer. Enzyme activity assays indicated that Fe-NC enhances intracellular electron transfer by activating key redox enzymes and upregulating associated gene expressions. Electron transfer system activity and metagenomic analysis further demonstrated that Fe-NC improves microbial respiration and increases the abundance of dominant taxa such as Bacteroidota (11.96 %) and Chryseobacterium (12.00 %), which support both TC degradation and microbial stress tolerance. These mechanistic insights establish a novel, bio-electroactive function for Fe-NC, in which the synergistic effects of Fe redox cycling and pyridinic nitrogen coordination led to improved electron flow, microbial function, and pollutant breakdown. This work not only reveals a previously unexplored pathway for biological co-removal of nitrate and antibiotics but also provides a scalable strategy for enhancing bioremediation efficiency in complex wastewater systems.}, } @article {pmid42259455, year = {2026}, author = {Wang, Y and Huang, Y and Yin, D and Gong, B and Fan, G}, title = {A segmented electron donor dosing strategy for enhancing thiosulfate-driven partial denitrifying efficiency: Insights into sulfur oxidation pathway, electron transfer and metagenomic microbial ecology.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135106}, doi = {10.1016/j.biortech.2026.135106}, pmid = {42259455}, issn = {1873-2976}, abstract = {Thiosulfate-driven partial denitrification (TPD) is a highly efficient denitrification process that exhibits good stability when coupled with Anammox. This study aimed to enhance the performance of the TPD system by employing different electron donor dosing strategies. The data show that the NO3[-]-N removal efficiency (NRE) and NO2[-]-N accumulation efficiency (NAE) in the segmented dosing group reached 98 % and 90 %, respectively. The study indicates that segmented electron donor dosing significantly enhances the activity of the electron transport chain. Specifically, Complex I and Complex III are associated with electron utilization by nitrate reductase (Nar) and nitrite reductase (Nir). The increased activity of Complex I and the inhibited activity of Complex III in the segmented dosing group contribute to improved NRE and NAE. Metagenomic analysis revealed that Thiobacillus predominated and served as the key functional species for Nar, Nir, and sulfur oxidation. Combined with qPCR analysis, segmented dosing significantly increased the expression levels of functional genes and elevated the NarG/(NirK + NirS) ratio, which further facilitated the accumulation of NO2[-]-N. Furthermore, the segmented dosing group possessed a complete sulfur oxidation pathway capable of fully oxidizing S2O3[2-] to SO4[2-], suggesting a reduced metabolic potential for S[0] production within the system. Overall, this study offers a potential strategy for ensuring a stable supply of nitrite in future anaerobic ammonium oxidation processes.}, } @article {pmid42259841, year = {2026}, author = {Deng, F and Fan, Y and Yan, J and Zhang, X and Guo, Y and Li, M and Peng, Y and Zhao, L and Liu, F and Zheng, Y and Deng, B and Deng, J and Chen, S and Jiang, H and Chai, J and Zhao, J and Li, Y}, title = {Genome-resolved and culture-based atlas of the feline gut microbiome enables host-adapted probiotic development.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01038-z}, pmid = {42259841}, issn = {2055-5008}, abstract = {Domestic cats (Felis catus) depend on their gut microbiome for metabolism, immunity, and pathogen defense, yet its genomic characterization remains limited. We combined large-scale metagenomics and culturomics to define the feline gut microbiome and identify indigenous probiotic candidates. Analysis of 412 feline fecal metagenomes produced 2852 strain-resolved metagenome-assembled genomes (MAGs) grouped into 514 species-level genome bins, including 106 putative novel taxa. This catalog revealed 24 core species and two enterotypes: ET-P, deaminated by Prevotella, and ET-CB, enriched for Collinsella, Blautia, Bifidobacterium, Ligilactobacillus, MAG-based screening prioritized 113 candidate probiotic species. Culturomics recovered 2904 isolates representing 110 species-level taxa, including 75 putative novel species and a candidate novel genus. Six feline-derived isolates were selected for downstream testing, and five exhibited favorable probiotic traits in vitro, including acid and bile tolerance, anti-Escherichia coli activity, and favorable cytokine responses. In a pathogenic Escherichia coli-induced dirrhea model in cats, a five-strain indigenous consortium improved fecal scores and reduced IL-2, IL-1β, and IL-6, with TNF-α suppression superior to antibiotics or a commercial probiotic. These results establish FelMGDB as a resource for feline microbiome research and highlights indigenous probiotics as promising interventions for feline gut health.}, } @article {pmid42260308, year = {2026}, author = {Li, L and DU, L}, title = {[Clinical value of cerebrospinal fluid metagenomic next genera-tion sequencing in diagnosing neonatal intracranial infections].}, journal = {Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences}, volume = {}, number = {}, pages = {1-10}, doi = {10.3724/zdxbyxb-2025-0965}, pmid = {42260308}, issn = {1008-9292}, abstract = {OBJECTIVES: To evaluate the diagnostic performance of cerebrospinal fluid (CSF) metagenomic next generation sequencing (mNGS) for neonatal intracranial infections and its impact on clinical decision making.

METHODS: A retrospective observational study was conducted. Neonates admitted to the Children's Hospital, Zhejiang University School of Medicine from 2020 to 2025 with suspected intracranial infection who underwent CSF mNGS were enrolled. The sensitivity of mNGS and its concordance with CSF culture and PCR were calculated. Clinical impact was assessed using predefined criteria, and samples were categorized into positive impact and no impact groups to identify independent factors influencing the clinical utility of mNGS.

RESULTS: Among 61 neonates with suspected intracranial infection, 48 were confirmed. Pathogens were identified in 18 cases, of which 9 were detected exclusively by mNGS, accounting for 50% of etiological diagnoses. The sensitivity of mNGS was 31.3% (95% CI: 18.7%-46.3%), higher than that of culture PCR (18.8%, 95% CI: 8.9%-32.6%), but the difference was not statistically significant (P=0.15). The positive and negative concordance rates between mNGS and culture PCR were 66.7% (95% CI: 29.9%-92.5%) and 76.9% (95% CI: 60.7%-88.9%), respectively. mNGS positively influenced clinical decisions in 37.7% (23/61) of patients: 12 cases with positive results guided etiological diagnosis and treatment adjustment, and 11 cases with negative results led to antibiotic de escalation or discontinuation. Multivariate analysis identified a positive mNGS result as an independent factor associated with positive clinical impact (OR = 22.127, P<0.01).

CONCLUSIONS: CSF mNGS provides valuable support in etiological diagnosis and clinical decision making for neonatal intracranial infections.}, } @article {pmid42260359, year = {2026}, author = {Lu, F and Li, Y and Chen, X and Chen, Y and Li, C and Nong, G and Liu, J and Wei, Q}, title = {Community-acquired pseudomonas aeruginosa pneumonia in immunocompetent children: a study of 7 cases.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13768-8}, pmid = {42260359}, issn = {1471-2334}, support = {AD22035219//Guangxi Clinical Research Center for Pediatric disease/ ; 2025GXNSFAA069702//The National Natural Science Foundation of Guangxi/ ; }, abstract = {BACKGROUND: To characterize the clinical features and outcomes of community-acquired Pseudomonas aeruginosa (PA) pneumonia in immunocompetent children.

METHODS: A retrospective analysis was conducted on seven immunocompetent children with community-acquired PA pneumonia hospitalized between January 2015 and June 2025. Pneumonia was defined by acute respiratory symptoms with new radiographic infiltrates. PA infection was confirmed by culture from sterile sites/lower respiratory tract or metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid.

RESULTS: All patients were male (n = 7). Age distribution was as follows: 1-12 months (n = 3), 13-36 months (n = 1), 37-60 months (n = 1), and ≥ 61 months (n = 2). Median age at onset was 18.0 months (IQR: 8.0-123.0). All patients presented acutely with fever and cough; two developed respiratory failure within 72 h. Additional clinical features included dyspnea (n = 4), lung rales (n = 4), hemoptysis (n = 3), chest pain (n = 2), and wheezing (n = 1). Chest imaging showed lobar consolidation (n = 5) or mass-like consolidation (n = 2). A total of seven cases were identified, with PA confirmed by culture in four patients and by mNGS of bronchoalveolar lavage fluid in three patients. All isolates were susceptible to anti-pseudomonal β-lactam antibiotics except aztreonam. Complications included definite or suspected empyema (n = 5), pyopneumothorax (n = 3), and bacteremia (n = 2). Three patients required pediatric intensive care, two received invasive mechanical ventilation, two underwent closed thoracic drainage, and one required decortication. There were no deaths, but 4 patients sustained significant residual lung injury secondary to necrotizing pneumonia.

CONCLUSION: Although rare, community-acquired PA pneumonia in immunocompetent children is associated with severe disease and pulmonary complications. Initial therapy with anti-pseudomonal β-lactam antibiotics appears effective in improving outcomes. Repeated cultures are recommended in the cases who remain symptomatic.}, } @article {pmid42260652, year = {2026}, author = {Le Moigne, A and Andrei, AŞ and Pernthaler, J}, title = {Linking stochastic assembly to functional potential, redundancy, and trait patterns in bacterial communities.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02442-5}, pmid = {42260652}, issn = {2049-2618}, abstract = {BACKGROUND: Stochastic processes shape the taxonomic composition of microbial assemblages. However, their impact on community functioning remains subject to debate, mainly due to functional redundancy. Little is known on the links between stochasticity and functional redundancy. Here, we assessed how stochastic assembly influences redundancy, functional potential, and trait patterns in twenty parallel lake-water bacterial communities enriched under originally identical conditions. Using gene- and genome-resolved metagenomics, we tested whether incomplete dispersal of genes required for cellobiose uptake and processing-"functional dispersal limitation"-explained variation in cellobiose use.

RESULTS: Several communities were composed of genomes that held the required genes but these communities did not utilize cellobiose, rejecting the notion of "functional dispersal limitation." We quantified redundancy across major functional categories such as signaling, regulation, and transport. Functional redundancy reflected the stochastic assembly from the total set of genomes. It was lower within than between communities, likely reflecting limiting similarity vs. habitat-driven functional convergence. Category-resolved patterns of functional dissimilarity were conserved across various diversity scales and even across randomly sampled sets of 28,000 bacterial genomes from the Genome Taxonomy Database. Among these categories, functions mediating environmental and microbe-to-microbe interactions and genetic information processing had highest and lowest dissimilarity, respectively. Aquatic bacteria showed the greatest differentiation across most categories.

CONCLUSIONS: Stochastic assembly of bacterial communities shaped the functional trait distribution. Functional redundancy inferred from the metagenomes largely reflected the trait patterns of the total set of MAGs. Functional redundancy and dissimilarity varied according to functional category. Comparison with a null model constructed from genomes of the GTDB allowed us to identify functional selection with various strengths according to the functions. While stochasticity diversified community composition, functional patterns remained conserved, reflecting shared ecological and evolutionary constraints tempered by habitat. Hence, using null models as a reference is important to interpret functional redundancy and may provide a more accurate understanding of how stochastic assembly and ecological constraints shape community-level functional organization. Video Abstract.}, } @article {pmid42260783, year = {2026}, author = {Hao, M and Sha, Y and Gao, J and Niu, J and Xu, Y}, title = {Concurrent Spinal Dural Arteriovenous Fistula and Varicella-Zoster Virus Meningoencephalitis Unmasked by Corticosteroid-Associated Deterioration: A Case Report on the Diagnostic Value of Serial mNGS.}, journal = {Current medical imaging}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115734056496224260602072444}, pmid = {42260783}, issn = {1573-4056}, abstract = {BACKGROUND: Concurrent spinal dural arteriovenous fistula (SDAVF) and varicella-zoster virus (VZV) meningoencephalitis are exceptionally rare, and overlapping features can delay diagnosis. This case adds to the literature by illustrating how corticosteroid exposure before exclusion of vascular and infectious mimics may be followed by neurological deterioration, and by emphasizing the diagnostic value of serial metagenomic next-generation sequencing (mNGS).

CASE PRESENTATION: A 48-year-old man developed insidious bilateral lower-limb weakness that progressed to numbness, sphincter dysfunction, and near-paralysis. Initial spinal magnetic resonance imaging showed diffuse thoracolumbar cord lesions; cerebrospinal fluid studies were mildly inflammatory, and myelitis was suspected. He received methylprednisolone pulse therapy followed by oral corticosteroids without improvement. One month later, he presented with fever, severe headache, vomiting, worsening paralysis, and altered mental status. Cerebrospinal fluid demonstrated marked pleocytosis, hypoglycorrhachia, and elevated protein, and mNGS detected abundant VZV sequences. Brain imaging showed hydrocephalus, meningeal enhancement, multifocal ischemic lesions, and intracranial arterial stenoses, consistent with VZV meningoencephalitis and vasculopathy. After external ventricular drainage, intravenous acyclovir, dexamethasone for cerebral edema, and empirical anti-tuberculosis therapy, serial mNGS showed a reduced VZV burden. Repeat spinal imaging revealed tortuous perimedullary vessels and hemosiderin deposition, and angiography confirmed SDAVF from the left T10 intercostal artery. The fistula was coagulated. At 12-month follow-up, he regained slight right-leg movement and partial sensory recovery above L1.

CONCLUSION: Progressive myelopathy with atypical inflammatory features should prompt vascular evaluation and pathogen testing. Serial mNGS can identify coexisting infection, guide therapy, and help avoid hazardous empirical corticosteroid use when the diagnosis remains uncertain.}, } @article {pmid42261054, year = {2026}, author = {Foster, NR and Holman, LE and Armbrecht, L and Courtin, J and Jensen, T and Pedersen, MW and Schreiber, L and Schroeder, H and Seersholm, FV and Zampirolo, G and Bohmann, K and Zimmermann, HH}, title = {A Roadmap for Using Hybridisation Capture-Based Target Enrichment of Ancient Environmental DNA in Palaeoecology.}, journal = {Molecular ecology resources}, volume = {26}, number = {5}, pages = {e70152}, pmid = {42261054}, issn = {1755-0998}, support = {101105307//European Union's Horizon Europe Marie Sklodowska-Curie Actions/ ; 856488//European Union's Horizon 2020 Research and Innovation Program/ ; //Independent Research Fund Denmark/ ; DP250100886//Australian Research Council (ARC)/ ; DP250103420//Australian Research Council (ARC)/ ; }, mesh = {*DNA, Ancient/isolation & purification ; *Nucleic Acid Hybridization/methods ; *DNA, Environmental/isolation & purification/genetics ; *Metagenomics/methods ; *Paleontology/methods ; }, abstract = {Recovering ancient DNA from environmental samples is transforming the way we understand historical ecosystems. While high-throughput sequencing of the total DNA in environmental samples (shotgun metagenomic sequencing) reveals the taxonomic contents of these samples, the genetic signals of some taxa (e.g., eukaryotes) can be weak compared to the background levels of DNA from organisms such as bacteria, requiring deep sequencing approaches that are costly. Thus, to increase cost-effectiveness, pre-sequencing enrichment of target DNA can be advantageous. One technique to enrich this target DNA is hybridisation capture, where short RNA or DNA baits are designed to match, bind and isolate specific stretches of DNA. Hybridisation capture has previously been applied to recover DNA from ancient skeletal remains, but it is only beginning to emerge as an approach to characterise organisms from ancient environmental samples. Thus, there is limited information on establishing hybridisation capture workflows for ancient environmental DNA applications, including the limitations and advantages. This mini review focuses on establishing a roadmap for the applications of hybridisation capture to ancient environmental DNA samples.}, } @article {pmid42262077, year = {2026}, author = {Ran, S and Fu, S and Dai, T and Wei, H and Peng, J and Zhou, Y}, title = {Multi-omics profiling of gut-serum axis dynamics in gestational sows with different reproductive performance.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0113225}, doi = {10.1128/spectrum.01132-25}, pmid = {42262077}, issn = {2165-0497}, abstract = {UNLABELLED: Sustainable swine production hinges on optimizing sow reproductive efficiency, yet mechanisms driving healthy litter size and weak piglet rates remain unclear. This study categorized sows into high (group H) and low (group L) healthy litter size groups based on median performance. Multi-omics analyses (16S rRNA sequencing, metagenomics, and serum metabolomics) revealed distinct fecal microbiota and metabolic profiles between groups. The results showed significant differences in microbiota composition between groups L and H. Group H exhibited a marked increase in Bacteroidetes abundance (particularly Prevotella sp. CAG1092), concurrent with reduced Firmicutes populations. Metabolomic analysis identified 197 differentially abundant metabolites, with 85 metabolites significantly enriched in group H. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that the differentially abundant metabolites were mainly involved in amino acid synthesis and metabolism, and multiple amino acid metabolic pathways were associated with polyamine synthesis. The correlation results showed a significant correlation (P < 0.05) between these metabolites and litter size as well as litter weight. For instance, Prevotellaceae NK3B31 abundance positively correlated with L-alanine, urea, and securinine, while Prevotella sp. CAG1092 exhibited direct associations with reproductive performance. These findings suggest that gut microbiota dysbiosis may disrupt amino acid homeostasis and polyamine regulation, potentially serving as mechanistic links to reproductive efficiency. Reproductive performance dynamically shapes gut microbiota and systemic metabolism in gestating sows, with litter size influencing fecal metabolite diversity and microbial structure. This integrative analysis establishes a framework for improving both sow productivity and economic viability in pig farming.

IMPORTANCE: Optimizing sow reproductive efficiency is vital for sustainable swine production. This study identifies gut microbiota dysbiosis and metabolic imbalances as key drivers of litter size variability. Sows with lower productivity displayed marked reductions in Bacteroidetes (notably Prevotella spp.) and disrupted amino acid/polyamine metabolism, directly linking microbial shifts to poorer litter outcomes. Integrated multi-omics approaches revealed strong correlations between specific taxa (Prevotella sp. CAG1092), metabolites (L-alanine and urea), and reproductive metrics, underscoring the gut-reproductive axis. These findings elucidate mechanistic connections between microbial ecosystems and host physiology, providing a foundation for targeted strategies like microbiota modulation or dietary interventions to enhance metabolic homeostasis and farrowing success. By bridging microbial ecology with livestock productivity, this work advances practical solutions to improve both animal health and agricultural profitability within precision farming frameworks.}, } @article {pmid42262118, year = {2026}, author = {Sommer, AJ and Ferrandis-Vila, M and Mamerow, S and Berens, C and Menge, C and Wei, S and Wang, Q and Aarestrup, FM and Otani, S and Sapountzis, P}, title = {Impact of ceftiofur administration and Escherichia coli inoculation on the calf fecal microbiome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0050126}, doi = {10.1128/msystems.00501-26}, pmid = {42262118}, issn = {2379-5077}, abstract = {The cattle gastrointestinal tract harbors a diverse community of microorganisms, including pathogenic and commensal strains of Escherichia coli. Antimicrobial use in cattle can disrupt the gut microbiome, leading to shifts in bacterial diversity and abundance. Here, we combined shotgun metagenomics and single-cell sequencing to assess how ceftiofur antibiotic treatment impacted microbial diversity and structure. At the start of the experiment, ceftiofur was administered intramuscularly in parallel with the inoculation of a cocktail of extended-beta-lactamase-producing E. coli strains to simulate environmental exposure and acquisition of resistant strains while animals are under antibiotic treatment. Fecal samples were collected from both the antibiotic-treated (ceftiofur and inoculation) and control (inoculation only) calves over the course of 35 days. Read mapping to genome and gene databases showed substantial differences in microbial richness and beta diversity between treatment groups. Treatment group-enriched taxa included Bacteroidaceae and Fibrobacter, which were more abundant in samples that did not receive ceftiofur, and Akkermansia in ceftiofur-treated calves. In ceftiofur-exposed animals, we observed a gradual loss of virulence factors alongside increased abundances of beta-lactam resistance genes, including cfxA5 and cfxA6, likely encoded by CAG-485 (Muribaculaceae). We further profiled individual cells using single-cell sequencing, which revealed a high number of Clostridium carrying macrolide resistance genes lnu(P) and mph(N) in both ceftiofur-treated and control samples. Overall, our complementary approaches reveal distinct remodeling of the calf microbiome following antibiotic and E. coli administration, tied to key functional genes that can be assigned to specific genera or recurrently detected across diverse taxa.IMPORTANCECattle serve as natural reservoirs of zoonotic strains of Escherichia coli, which can cause severe gastrointestinal infections in humans. Antibiotic usage on cattle farms can drive the emergence of antimicrobial-resistant bacterial strains and alter the underlying cattle gastrointestinal microbiome. Consequently, there is a need to understand how antibiotic administration impacts population dynamics of cattle rumen and intestinal microbes. In this study, we combined both shotgun metagenomics and single-cell genomics on feces from ruminating calves to determine microbiome changes following administration of both ceftiofur and E. coli cocktails. We observed considerable variation in the prevalence and abundance of virulence factors, antimicrobial resistance-related genes, and taxa with key roles in animal nutrition and health between the microbiomes of antibiotic-treated and antibiotic-free calves, with potential implications for their subsequent development and overall well-being.}, } @article {pmid42262136, year = {2026}, author = {Iacovacci, J and Cannon, N and McCulloch, JA and Rancati, T and Trinchieri, G}, title = {Differential co-occurrence analysis: a method to extract ecological modules from clinical microbiome data.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0028426}, doi = {10.1128/msystems.00284-26}, pmid = {42262136}, issn = {2379-5077}, abstract = {UNLABELLED: The human microbiota plays a pivotal role in health, with widespread alterations implicated in conditions ranging from inflammatory disorders to cancer. While correlation-based network analyses have illuminated ecological interactions within these communities, the host environment uniquely mediates microbial relationships, demanding new methods to capture dynamic, condition-dependent modules of species interactions. Here, we present a statistical framework termed differential co-occurrence analysis, which identifies blocks of taxa whose collective presence is strengthened or weakened under distinct host states. By leveraging recent advances in metagenomics that enable detailed taxonomic profiling and higher-order interaction discovery, our method transcends traditional pairwise correlation constraints. Conceptually akin to associative rule mining, it diverges through the integration of robust statistical modeling, directly extracting interactions that differ significantly between conditions. This approach offers a refined lens to dissect microbiota ecology and could pave the way for new insights into microbiome-associated disease mechanisms.

IMPORTANCE: The research on the role of the intestinal microbiota in the onset of cancer and as a modulator of anticancer treatments, including chemotherapeutics and immune checkpoint inhibitors, is helping medicine to identify novel strategies for cancer prevention, for the delivery of more effective treatments, and in reducing treatment side effects and complications. Within this context, it is of crucial importance to approach the analysis of clinical microbiome data with an ecology-oriented perspective and to develop bioinformatics tools able to identify functional interactions in bacterial communities of patients from observational cohort studies. Clinical microbiome datasets are typically high dimensional, comprising numerous taxa measured across relatively few samples. This imbalance increases the risk of statistical overfitting and undermines the robustness of analytical findings. However, recent advances in metagenomic bioinformatics pipelines and reference databases have enabled the comprehensive extraction of genetic information from microbiome samples, facilitating the precise characterization of bacterial species presence and absence. In our manuscript, we describe a statistical computational method that we named differential co-occurrence analysis, which focuses on the analysis of the co-presence of microbiota taxa across samples associated with different host conditions. The proposed method can reveal modules of interacting taxa that are strengthened or weakened when the host condition changes (e.g., when passing from a healthy state to a disease state). The method is general and applicable to a broad range of ecological datasets featuring presence/absence data structures. Furthermore, the method accommodates the analysis of higher-order co-occurrence patterns beyond pairwise co-occurrence, thereby enabling the investigation of higher-order interactions, whose detection and identification are a major challenge in ecological network analysis.}, } @article {pmid42262316, year = {2026}, author = {Gao, B and Chen, L and Xu, W and Liu, G and Wei, M and Shen, W and Tu, P and Shan, J}, title = {Uncovering the Hidden Risks: How PLA and PLGA Microplastics Disrupt Gut Microbiota and Metabolic Health.}, journal = {Chemical research in toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.chemrestox.5c00556}, pmid = {42262316}, issn = {1520-5010}, abstract = {Biodegradable plastics are often promoted as an eco-sustainable alternative to conventional polymers. However, their potential to degrade into microplastics still poses significant health risks. Commonly used materials such as polylactic acid (PLA) and poly(lactic-co-glycolic acid) (PLGA) have been widely adopted across various industries. While the toxicity of PLA microplastics has been studied extensively, the biological effects of PLGA microplastics remain largely unknown. Through metagenomic sequencing and untargeted metabolomic profiling, we evaluated the impacts of both PLA and PLGA microplastics on gut bacteria, fungi, virulence factors, microbial metabolic pathways, and metabolites in feces, serum, and liver tissue in this study. Our results demonstrate that both types of biodegradable microplastics disrupt gut microbiota and host metabolic homeostasis. PLA exposure provoked more pronounced changes in gut bacteria, fungi, virulence factors, and fecal and hepatic metabolites. In contrast, microbial metabolic pathways and serum metabolites were more strongly affected by PLGA. Several altered features were common to both microplastics, including enrichment of hepatic metabolic pathways related to valine, leucine, and isoleucine biosynthesis; one-carbon pool by folate; glycine, serine, and threonine metabolism; pantothenate and CoA biosynthesis; taurine and hypotaurine metabolism; and cysteine and methionine metabolism. Other disturbances were material-specific, such as UMP biosynthesis pathways, which were altered exclusively by PLA, while palmitate biosynthesis and unsaturated fatty acid biosynthesis were affected only by PLGA. These findings advance our understanding of the distinct and shared health risks posed by different biodegradable microplastics, providing a clearer basis for assessing their long-term safety.}, } @article {pmid42262390, year = {2026}, author = {Weissman, JL and Walling, A and Ducklow, H and Zakem, EJ}, title = {Genomic Traits Associated with Copiotrophy Decouple from Maximum Growth Rate Predictions Along Temperature Gradients.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag147}, pmid = {42262390}, issn = {1751-7370}, abstract = {Maximum growth rate is often used as a primary axis of functional variation in studies of microorganisms, in part because emerging tools make it straightforward to estimate from genomic and metagenomic data. However, temperature, via its influence on reaction kinetics, may act as a confounder in studies that measure genomic signatures of growth optimization across environments. Observations suggest that growth optimization need not always indicate rapid growth. For example, strong temperature gradients are the norm across much of the world's oceans, where deep-ocean microbes show elevated signals of genomic growth optimization relative to the faster-growing communities at the surface. Looking across environments, we find a negative relationship between genomic growth optimization and optimal growth temperature, leading to the potential decoupling of genomic traits associated with copiotrophy from maximum growth rate, particularly when measured along a temperature gradient. Our results suggest that, as a result of temperature's confounding effects, genomic signatures of growth optimization often better predict the ecological roles and functional genomic content of microorganisms than do growth rates themselves. Finally, we suggest reframing copiotrophy as growth beyond a thermodynamic baseline maximum growth rate, rather than in relation to a static rate cutoff.}, } @article {pmid42263510, year = {2026}, author = {Ergunay, K and Bourke, BP and Kamau, M and Fustec, B and Osborne, CJ and Mutura, J and Lebunge, R and Ochieng, G and Onyango, T and Cruz, A and Campos, M and Pott, MC and Romero, U and Deakins, AG and Paoli, J and Liao, HM and von Fricken, ME and McDermott, EG and Jiang, L and Grieco, JP and Achee, NL and Linton, YM}, title = {Unbiased long read metagenomic screening reveals diverse jingmen tick virus genomes across continents.}, journal = {Virology}, volume = {623}, number = {}, pages = {110999}, doi = {10.1016/j.virol.2026.110999}, pmid = {42263510}, issn = {1096-0341}, abstract = {Jingmen tick virus (JMTV) is an emerging tick-associated virus related to flaviviruses. Substantial information gaps remain on the epidemiology and public health impact of JMTV, despite evidence for symptomatic human infections, detection in potential zoonotic reservoirs and widespread global circulation. Using an unbiased metagenomics approach based on long read sequencing, we screened field-collected ticks (n = 3232) of various life stages from locations of spillover risk across continents, from Eastern Africa (Kenya), Central America (Belize), and North America (Arkansas, United States). Signals of virus detection were observed in 32.9% of the pooled samples comprising adult, nymph and larvae stages. JMTV genome segments were assembled in 16.7% of the pools with initial virus detection. Adult ticks comprising Amblyomma gemma, Hyalomma rufipes, Rhipicephalus. evertsi and Rhipicephalus pulchellus from Kenya yielded complete JMTV genome assemblies. Evidence for tick-associated arbo-jingmenviruses was described for the first time in Belize, identified as complete genome segments encoding for non-structural virus proteins in pooled larvae. Analysis of globally distributed complete JMTV genomes revealed a considerable geographic partitioning of diversity and two significantly supported virus clades and genomic underrepresentation in many regions with documented virus activity. Further investigations and expanded screening are needed to elucidate JMTV and arbo-jingmenvirus global epidemiology.}, } @article {pmid42263617, year = {2026}, author = {Chen, C and Li, J and Wang, F and Cheng, M and Sheng, T and Ahmed, Z and Hu, J and Zhou, Y}, title = {Auxiliary fermentation with Pediococcus acidilactici C1 reshapes flavor formation in sufu: An integrated metagenomic, flavoromic and non-targeted metabolomic deciphering.}, journal = {Food chemistry}, volume = {521}, number = {}, pages = {149979}, doi = {10.1016/j.foodchem.2026.149979}, pmid = {42263617}, issn = {1873-7072}, abstract = {Sufu, a traditional Chinese fermented soybean product, relies on spontaneous microbial succession for flavor, leading to high variability. Starter-assisted fermentation improves flavor; this study explores sufu flavor differences and mechanisms between spontaneous and Pediococcus acidilactici C1-inoculated processes. The findings demonstrated that inoculation with P. acidilactici C1 markedly enhanced the diversity and concentration of flavor compounds in sufu. Notably, 12 key taste-active free amino acids were detected, with glutamate up by 14% and aspartic acid showing an approximate 20-fold increase. A total of 15 key volatile flavor compounds were characterized, among which 8 were newly uncovered, namely ethyl 2-methylbutanoate, ethyl acetate, ethyl butyrate, ethyl caprylate, ethyl 2-ethylhexanoate, ethyl propionate, isoamyl acetate and 3-octanol. Metagenomics revealed enrichment of genes related to carbohydrate transport, amino acid/lipid metabolism, while non-targeted metabolomics confirmed metabolic remodeling. Multi-omics analyses showed P. acidilactici C1 reprogrammed carbon flux and boosted amino acid/lipid-derived volatile biosynthesis, enabling flavor-enhancing starter development.}, } @article {pmid42263645, year = {2026}, author = {Xing, Y and Huang, X and Luo, J and Wei, D and Chen, H and Sun, X}, title = {Active carbon-fixing microbes and their role in carbon fixation in mangrove sediments.}, journal = {Marine pollution bulletin}, volume = {231}, number = {}, pages = {119962}, doi = {10.1016/j.marpolbul.2026.119962}, pmid = {42263645}, issn = {1879-3363}, abstract = {Mangroves are vital blue carbon ecosystems, yet the microbial drivers of carbon fixation in their soils remain poorly understood. Here, this study investigated the patterns of drivers carbon-fixing microbes and their functional genes across three representative mangrove bays in the Beibu Gulf of the South China Sea (Lianzhou Bay, Maowei Sea and Zhenzhu Bay) using an integrated geochemical and metagenomic approach. The findings showed that: (1) the distribution of total organic carbon (TOC) in mangrove soils was significantly influenced by tidal zonation and mangrove plants, with TOC content in the mid-tidal zone consistently exceeding that in adjacent mudflats by 1.5- to 2.3-fold (p < 0.01); (2) potential dominant carbon fixation pathways inferred from soil microbial communities may vary significantly across different areas, including chemolithoautotrophic taxa (e.g., Nitrospira, Thiobacillus), phototrophic cyanobacteria (e.g., Synechococcus, Cyanobium), and mixotrophic assemblages. Correspondingly, the relative abundances of key functional genes (e.g., narH, narG, fabB, oadB) exhibited significant differences among these bays; (3) environmental factors including salinity, nutrients, and heavy metals jointly influenced the accumulation of carbon fixation genes and their microbial hosts, collectively explaining 63.9% of community variation at the species level. This study provides a mechanistic understanding of microbial functional diversity that underpins carbon cycling in mangrove soils, offering quantitative insights for the conservation and management of blue carbon ecosystems under anthropogenic pressures.}, } @article {pmid42263665, year = {2026}, author = {Ueland, K and Elahi, T and Rasmussen, M and Wolfe, AE and Purcell, H and Chakka, SR and Mirimo-Martinez, M and Persinger, H and Johnson, K and Boynton, AM and McMillen, K and Byelykh, M and Biernacki, MA and Yeh, AC and Ali, N and Manjappa, S and Wuliji, N and Fredricks, D and Bleakley, M and Holmberg, LA and Peled, JU and Schenk, J and Raftery, D and Ma, J and Hill, GR and Neuhouser, ML and Lee, SJ and Markey, KA}, title = {Plant-based whole-food diets are feasible during auto-HCT and are associated with dose-dependent microbiome modulation.}, journal = {Blood advances}, volume = {}, number = {}, pages = {}, doi = {10.1182/bloodadvances.2026020270}, pmid = {42263665}, issn = {2473-9537}, abstract = {Plant-based whole foods may represent a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing auto-HCT for multiple myeloma, a population in whom intestinal dysbiosis has been linked with inferior survival. We conducted a single-arm clinical trial at our center, in which participants undergoing auto-HCT (n = 22) received fresh, pre-prepared, plant-based meals for 5 weeks spanning conditioning, neutropenia, and early recovery, with the goal of supporting the consumption of nutrient-dense, high-fiber foods. The primary endpoints were feasibility and tolerability, defined by successful enrollment, and patient-reported intake of study meals. Dietary intake was quantified using prospective food diaries and 24‑hour dietary recall surveys. Secondary endpoints included changes in gut microbiome composition and function assessed by shotgun metagenomic sequencing and stool short-chain fatty acid (SCFA) measurements. The intervention was feasible and generally well tolerated, with all participants consuming delivered meals to some degree, with adherence sufficient to support planned dietary and correlative analyses. Greater intake of study meals was associated with more pronounced shifts in gut microbial communities, including enrichment of SCFA-producing taxa and compositional changes consistent with a fiber-responsive microbiome. Stool SCFA concentrations increased from baseline to the end of the intervention, suggesting a functional impact of the dietary strategy on microbial metabolite production during the peri-transplant period. These findings demonstrate that a plant-based meal delivery intervention is implementable during auto-HCT and suggest dose-dependent modulation of the gut microbiome and its metabolic output. The trial is registered at ClinicalTrials.gov (NCT06559709).}, } @article {pmid42263908, year = {2026}, author = {Figueroa-Ortiz, C and Schoninger, S and Chan, JL and Bermudez, TA and Li, Y and Cander, S and Mcgonagle, B and Bacon, CW and Kalchiem-Dekel, O and Chawla, M and Lin, R and Tamari, R and Shaffer, BC and Perales, MA and Redelman-Sidi, G and Shahid, Z and Loganathan, R and Kamboj, M and Papanicolaou, G and Lee, YJ}, title = {Tuberculosis After Allogeneic Hematopoietic Cell Transplant: A 15-Year Case Series Highlighting Diagnostic Challenges.}, journal = {Transplantation and cellular therapy}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtct.2026.06.007}, pmid = {42263908}, issn = {2666-6367}, abstract = {BACKGROUND: Tuberculosis (TB) is an uncommon but potentially fatal complication after allogeneic hematopoietic cell transplant (HCT). Diagnosis is often delayed due to nonspecific clinical presentations, limited sensitivity of screening tests for latent TB infection, and slow turnaround of conventional TB diagnostic methods.

OBJECTIVE: The study aim is to describe the clinical and diagnostic characteristics of allogeneic HCT recipients with TB in the era of molecular and sequence based diagnostic methods.

STUDY DESIGN: We conducted a retrospective review of microbiologically confirmed TB cases among HCT recipients at a tertiary cancer center from 2010 to 2025. We detail clinical, demographic, and diagnostic characteristics including metagenomic next-generation sequencing (mNGS) testing of bronchoalveolar lavage (BAL) and blood (Eurofins Viracor, Lenexa, KS) for two individuals.

RESULTS: Ten patients were diagnosed with active TB at a median of 122 days post-HCT (range: 36-2,557). The median age was 53 years, and 6 were males. Except for one patient, all patients were foreign-born. Pre-HCT TB screening was performed in 7 patients; however, only 3 had positive (tuberculin skin test, n=1; interferon-gamma release assay [IGRA], n=2), and 1 had indeterminate IGRA results. All patients had abnormal CT chest findings compatible with latent TB. Nine of 10 patients presented with either fever or cough, while one patient was asymptomatic with incidental radiographic abnormalities. TB was diagnosed by MTB PCR in 8 cases, 4 patients had disseminated TB, and 3 died. mNGS results were available in two patients. In both cases MTB was detected in BAL, and in one, MTB was detected in the blood. Among 9 patients with available susceptibility testing data, moxifloxacin resistance was identified in one case.

CONCLUSIONS: In our cohort, post-HCT TB occurred mainly in foreign-born patients. Infection was diagnosed early after transplant and was frequently disseminated, with high mortality. These results underscore the limitations of current screening methods, and the diagnostic challenges of post-HCT TB.}, } @article {pmid42263990, year = {2026}, author = {Meng, Q and Zeng, W and Zhang, J and Liu, H and Li, S and Peng, Y}, title = {Efficient nutrient removal from low C/N municipal wastewater using a phototrophic biofilm system integrating simultaneous nitrification-denitrification and phosphorus removal (SND).}, journal = {Environmental research}, volume = {305}, number = {Pt 2}, pages = {124859}, doi = {10.1016/j.envres.2026.124859}, pmid = {42263990}, issn = {1096-0953}, abstract = {Microalgae-bacteria systems based on phosphorus-accumulating organisms (PAOs) offer low-energy and low-carbon-emission solutions for wastewater treatment, but their performance declines with low carbon-to-nitrogen (C/N) ratios municipal wastewater. In this study, a phototrophic biofilm system capable of coupling simultaneous nitrification-denitrification with phosphorus removal (P-SNDPRB) was developed to enhance low C/N ratios (3.32-4.11) municipal wastewater treatment. Before biofilm integration, total nitrogen (TN) removal was below 75%. After integration, TN removal increased to over 82%, while organic matter and phosphorus removal efficiencies remained at 85% and 90% in the P-SNDPRB system, respectively. Microalgae photosynthesis supplied oxygen to the biofilm, enabling denitrification. Chemometric and metagenomic analyses revealed denitrification and phosphorus accumulating metabolism (PAM) as key pathways for nitrogen and phosphorus removal. Flow cytometry sorting showed that biofilm spatial distribution promoted synergistic interactions among Accumulibacter, Competibacter, Nitrosomonas, Chlorella, and Cyanobacteria, further enhancing nitrogen and phosphorus removal. This study provides a low-energy and sustainable approach for the treatment of municipal wastewater with a low C/N ratio.}, } @article {pmid42264042, year = {2026}, author = {Zheng, Y and Li, X and Jia, Z and Qi, Y and Yin, H}, title = {Microbial-mediated attenuation of carbonaceous organics within urban sewers: Insights from in-pipe sediments microbial communities and metagenomic analyses.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135134}, doi = {10.1016/j.biortech.2026.135134}, pmid = {42264042}, issn = {1873-2976}, abstract = {Sewer sediments consist of diverse microbial communities that actively engage in the degradation of carbonaceous organics, adversely impacting influent quality of wastewater treatment plants. Yet, the underlying biological mechanisms within actual sewers remains underexplored. This study elucidated the microbial-mediated attenuation mechanisms in actual gravity sewers, with integrated approaches including sediments scanning electron microscopy, flow cytometry, extracellular polymeric substances (EPS) characterization, and metagenomic sequencing. Along the 3.56 km trunk sewer, chemical oxygen demand and five-day biological oxygen demand decreased by 55.1 % and 53.9 %, respectively. A spatial shift from anoxic to anaerobic conditions was observed along the sewer, accompanied by increased sediment microbial cell density (2.17 × 10[6]-2.57 × 10[7] cells/g SS) and EPS accumulation (2.22-17.69 mg/g VSS). The downstream enrichment of tryptophan- and tyrosine-like EPS components was consistent with the formation of larger and denser sediment aggregates (21.45-51.55 μm). Metagenomic analysis revealed a spatial shift in carbonaceous organics transformation potential, with upstream sediments enriched in fermentation-related microbial communities and genes associated with simple organic hydrolysis, while downstream reaches showed higher relative abundances of genera and genes associated with complex fatty acid and amino acid transformation through Embden-Meyerhof-Parnas pathway and tricarboxylic acid cycle. Downstream enrichment of pentose phosphate pathway-related genes further supported increased microbial resilience and biosynthetic potential under low-oxygen conditions. These findings underscore the sewer's role as pre-bioreactors, and strengthening sewer maintenance to minimize sediments accumulation is crucial for preventing excessive in-sewer organic matter loss.}, } @article {pmid42264047, year = {2026}, author = {Xu, YY and Tan, X and Dang, CC and Zhao, ZC and Fang, R and Fan, L and Ren, NQ and Xie, GJ and Wu, YN}, title = {Metagenomic insights into Thermus-mediated sulfur oxidation, nitrogen cycling, and thermoadaptation in thermophilic autotrophic denitrification bioreactors.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135137}, doi = {10.1016/j.biortech.2026.135137}, pmid = {42264047}, issn = {1873-2976}, abstract = {Thermus species are widely recognized as a key group of heterotrophic denitrifiers mediating carbon, nitrogen, and sulfur cycling in geothermal habitats, and have attracted extensive research attention for their thermostable enzyme resources. However, their autotrophic denitrification potential remains poorly characterized, and the systems-level mechanisms underlying their thermal adaptation remain incompletely understood. This study presents three high-quality metagenome-assembled genomes (MAGs) of Thermus from autotrophic sulfur-based denitrification bioreactors. These MAGs encode the complete genetic potential for the Calvin-Benson-Bassham cycle, reductive tricarboxylic acid cycle, and 3-hydroxypropionate bicycle for inorganic carbon fixation. Thermus strains employ a distinct sulfide oxidation route: HS[-] is first oxidized to polysulfides or glutathione persulfide by fccAB, then condensed with sulfite to form thiosulfate via rhodanese, and finally completely oxidized to sulfate by complete sox cluster. T. scotoductus (MAG1) carries genes for nitrate reduction (narGHI) and dissimilatory nitrate reduction to ammonium (nrfA and nrfH). As conspecific strains, MAG2 and MAG3 harbor abundant denitrification genes (nar, nirK, norBC), indicating strong substrate-driven metabolic plasticity. A protein-protein interaction network further elucidated the systems-level thermoadaptive survival mechanisms of T. scotoductus, identifying chaperone-mediated protein homeostasis and DNA repair-dependent genomic stability as core adaptive strategies, alongside orphan nodes (e.g., aceE, lpd, nuoC) with potential independent functions. Collectively, these findings advance our understanding of Thermus' metabolic plasticity, offer valuable thermostable resources for high-temperature wastewater treatment and industrial applications, and bridge critical knowledge gaps in the autotrophic metabolism and thermoadaptive regulation of thermophilic bacteria-laying a robust genomic foundation for the development and optimization of high-temperature biotechnological processes.}, } @article {pmid42264152, year = {2026}, author = {Gibbons, JA and Nelson, RM and Dabrowski, CN and Narkhede, A and Szalacha, LA and Kneusel, ML and Maru, JS and Huszar, MR and Hoang, LK and Schiavo, V and Eddins, AC and Georgieff, MK and Neu, J and Donovan, SM and Groer, MW and Ho, TT}, title = {Enteral iron dose effect on iron storage, intestinal barrier, and gut microbiome in preterm infants: a randomized clinical trial.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {101389}, doi = {10.1016/j.ajcnut.2026.101389}, pmid = {42264152}, issn = {1938-3207}, abstract = {BACKGROUND: Preterm infants routinely receive enteral iron supplementation to support growth, replace phlebotomy losses, and prevent iron deficiency. However, concerns regarding potential harms, including those on the gut microbiome, have contributed to recommendations for lower dosing.

OBJECTIVES: This study aimed to compare the effects of 2 enteral iron doses on gut health in very-low-birth-weight preterm infants. We hypothesized that higher iron dose would increase abundances of pathogenic bacteria, intestinal inflammation, and barrier dysfunction.

METHODS: This randomized, double-blind clinical trial assigned preterm infants born <1500 g to receive either the recommended dose, 2 mg/kg/d, or a higher dose of 6 mg/kg/d of total enteral iron. The primary outcome was the fecal microbiome after 2 wk on iron, assessed by metagenomic sequencing. Secondary outcomes included biomarkers of intestinal inflammation and barrier function (fecal calprotectin, urinary claudin-3, and urinary intestinal fatty acid-binding protein). Iron status, adverse events, and auditory brainstem response latencies at 36 wk postmenstrual age were also evaluated.

RESULTS: Among 151 randomly assigned infants who received study iron (77 low dose; 74 high dose), bacterial diversity, individual taxa, virulence potential, bacterial overgrowth, and iron-related functional genes were not significantly different between the treatment groups. In the subgroup analysis of singletons, treatment groups demonstrated significant differences in temporal shifts in overall bacterial community structure. Infants receiving 2 mg/kg/d had higher posttreatment urinary claudin-3 concentrations, indicating possible differences in intestinal permeability, and a higher prevalence of iron deficiency than those receiving 6 mg/kg/d. Other biomarkers, clinical outcomes, adverse events, and auditory latencies did not differ between groups.

CONCLUSIONS: Enteral iron supplementation at 6 mg/kg/d was associated with improved iron status and lower intestinal barrier dysfunction, without evidence of harms on gut microbiome compared with the recommended 2 mg/kg/d dose. These findings do not support concerns regarding gut microbiome disruption as a justification for lower iron dosing in preterm infants. This trial was registered at clinicaltrials.gov as NCT04497012.}, } @article {pmid42264207, year = {2026}, author = {Laovechprasit, W and Avila-Reyes, VA and Stacy, BA and Young, KT and Harris, HS and Tuttle, AD and Sirpenski, G and Kennedy, AE and Innis, CJ and Norton, TM and Zirkelbach, B and Stanton, JB}, title = {Surveillance of gastrointestinal viruses of free-ranging and rehabilitated Sea turtles in the United States.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {142}, number = {}, pages = {105966}, doi = {10.1016/j.meegid.2026.105966}, pmid = {42264207}, issn = {1567-7257}, mesh = {Animals ; *Turtles/virology ; United States/epidemiology ; Phylogeny ; Genome, Viral ; *Viruses/classification/genetics/isolation & purification ; *Gastrointestinal Diseases/veterinary/virology ; *Gastrointestinal Tract/virology ; }, abstract = {Sea turtle populations are imperiled globally, primarily due to anthropogenic threats. However, non-anthropogenic factors, such as infectious diseases, can affect their population stability. Viruses are common causes of gastrointestinal disease in many species, and gastrointestinal signs are regularly observed among sea turtles, but little is known about enteric viruses in sea turtles. Establishing basic knowledge of viral diversity and evolutionary relationships is a necessary step towards understanding potential health impacts. This study investigated the viral genome contents of seventy-seven gastrointestinal specimens from six species of sea turtles with varying health conditions from the Atlantic and Pacific coasts of the United States. Forty-eight, non-plant and non-bacteria infecting viruses were detected (≥5 viral-like reads per sample) through random RNA sequencing. Detected viral sequences were then confirmed and characterized by semi-targeted, strand-switching sequencing, which provided deeper sequencing metrics allowing for phylogenetic characterization (>10× depth) for nineteen viruses across eight viral families, including seven putative novel viral species, one putative novel genus, and eleven likely novel viral sequences from taxa that lack established species demarcation criteria. Sixteen RNA viruses were characterized: four double-stranded RNA viruses (Partitiviridae, Totiviridae, and Picobirnaviridae), eleven positive-sense single-stranded RNA viruses (Caliciviridae, Dicistroviridae, unclassified Hepelivirales, and unclassified Picornavirales), and one negative-sense bisegmented RNA virus (Chuviridae). Three DNA viruses were also identified (Parvoviridae, Circoviridae, and unclassified Cressdnaviricota). Viruses identified in this study were often genetically related to viruses previously known to infect aquatic invertebrates and fish. This study provides baseline knowledge of viral communities in sea turtles and will serve as a foundation for future hypothesis-driven research to understand their relevance to sea turtle health.}, } @article {pmid42264211, year = {2026}, author = {Bhadelia, N and Gikandi, I and Lassmann, B}, title = {Regional Signals Preceding the 2026 Bundibugyo Virus Disease Outbreak.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108862}, doi = {10.1016/j.ijid.2026.108862}, pmid = {42264211}, issn = {1878-3511}, abstract = {BACKGROUND: The May 2026 Bundibugyo virus disease (BVD) outbreak in the Democratic Republic of the Congo was declared a Public Health Emergency of International Concern after substantial undetected community transmission. We describe regional surveillance signals detected by the Biothreats Emergence, Analysis, and Communications Network (BEACON), our open access event based surveillance program, in the weeks preceding outbreak declaration.

METHODS: We reviewed BEACON reports of VHF-compatible illness clusters detected in the transboundary DRC-Uganda-Burundi-South Sudan region during March-April 2026, prior to the May 15 laboratory confirmation of BDBV.

RESULTS: BEACON detected four temporally proximal VHF-compatible illness signals: (1) March 9, North Kivu Province-suspected Ebola case under investigation with unresolved laboratory results; (2) March 10, Kasaï Province-fatal hemorrhagic illness with secondary cases and negative Ebola PCR; (3) March 30, Burundi-35-case undiagnosed cluster near the DRC border with 5 deaths, negative testing for major filoviruses and >200 pathogens, pending metagenomic sequencing; (4) April 22, South Sudan-three suspected VHF cases with negative initial testing. All four signals shared a similar diagnostic phenotype: VHF-compatible presentation, mobilization of investigation teams, negative initial testing, and no publicly reported confirmed etiology. None were formally reported to have been resolved.

CONCLUSIONS: Our detection of four unresolved VHF signals preceding the confirmed BDBV outbreak highlights gaps in formal follow-up mechanisms for negative cases and fragmented regional diagnostic coordination. In light of confirmed BDBV circulation and Africa CDC's identification of 10 countries at high risk for spread, these preceding signals warrant urgent retrospective investigation and laboratory.}, } @article {pmid42264215, year = {2026}, author = {Hou, P and Che, Y and Han, J and Deming, C and Amirkhani, A and Kim, CS and Taylor, ME and Velez, D and Cho, E and Holmes, CJ and Suh, G and Castelo-Soccio, L and , and McDermott, DH and Murphy, PM and Segre, JA and Kong, HH}, title = {Permissive skin microbiomes in WHIM syndrome: HPV and pathogen expansion.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2026.05.024}, pmid = {42264215}, issn = {1523-1747}, abstract = {Warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome is a rare inborn error of immunity (IEI) caused by hyperfunctional pathogenic variants in CXC chemokine receptor 4 (CXCR4), predisposing individuals to recurrent bacterial skin and airway infections and warts. The targeted CXCR4 antagonist plerixafor has shown efficacy in wart regression and potential reduction in bacterial infection frequency. Here, we investigated skin microbiomes of 11 patients with WHIM syndrome using shotgun metagenomics, compared to healthy controls. WHIM skin microbial communities displayed greater inter-individual variability, with highly diverse human papillomavirus profiles and expansion of airway-associated pathogens on the skin. Among patients receiving plerixafor therapy, we observed shifts in the viral composition and a downward trend in viral abundances. Together, these findings demonstrate the distinctive and permissive skin microbiome in WHIM syndrome and highlight the potential microbiome-modulating effects of targeted CXCR4 antagonism.}, } @article {pmid42264245, year = {2026}, author = {Zhao, Y and Zhang, Y and Tang, S and Peng, T and Bagadi, AH and Jia, X and Wei, Z and Han, J and Li, L and Liu, X and Kong, W and Song, S and Wei, C and Wang, J}, title = {Structural elucidation and gut barrier-protective effects of a glucomannan polysaccharide fraction from Lanzhou lily bulbs.}, journal = {International journal of biological macromolecules}, volume = {371}, number = {}, pages = {152899}, doi = {10.1016/j.ijbiomac.2026.152899}, pmid = {42264245}, issn = {1879-0003}, abstract = {Food-derived dietary polysaccharides have attracted increasing attention as functional ingredients for ulcerative colitis (UC) management. In this study, a homogeneous polysaccharide, designated LDP, was isolated from the bulbs of Lilium davidii var. willmottiae (Lanzhou lily). Structural analyses showed that LDP had a weight-average molecular weight (MW) of 5.082 × 10[3] g/mol and was mainly composed of alternating →4)-α-D-Manp-(1 → and →4)-β-D-Glcp-(1 → residues with minor branching. Conformational analysis and molecular dynamics (MD) simulations indicated that LDP adopted an extended semi-flexible coil conformation in aqueous solution. In dextran sulfate sodium (DSS)-induced colitis mice, LDP markedly alleviated disease symptoms, as evidenced by improved survival, reduced body weight loss, a lower disease activity index and attenuated histopathological injury. Mechanistically, LDP enhanced intestinal barrier integrity, significantly increased acetic acid levels and partially restored short-chain fatty acid (SCFA)-associated beneficial taxa, including Lactobacillaceae, Bifidobacterium, Allobaculum and members of Erysipelotrichaceae/Erysipelotrichia. Integrated metagenomic, proteomic, Western blot and immunological analyses further indicated that LDP attenuated intestinal inflammation by suppressing the TAB1/MAP2K4-centered MAPK signaling pathway, as evidenced by reduced TAB1 and MAP2K4 expression and decreased p38 phosphorylation, and by restoring the Th17/Treg balance in mesenteric lymph nodes (MLNs). These findings suggested that LDP alleviated DSS-induced colitis through coordinated regulation of gut microbiota, microbial metabolism, MAPK inflammatory signaling and mucosal immunity.}, } @article {pmid42264341, year = {2026}, author = {Zhu, K and Sun, W and Wang, Z and Zha, Y and Qu, X and Wang, B and Zhang, H}, title = {Environmental ubiquity but limited host taxonomic distribution of co-occurring metal(loid)-resistance genes and persistent organic pollutant-transformation genes in global inland waters.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {405}, number = {}, pages = {128552}, doi = {10.1016/j.envpol.2026.128552}, pmid = {42264341}, issn = {1873-6424}, abstract = {Human activities have transformed inland waters into reservoirs of co-contamination by heavy metals and persistent organic pollutants, driving microbial adaptation through metal-resistance genes (MRGs) and POP-transformation genes (POPTGs). However, the global biogeography and ecological drivers of these co-occurring functional genes and their hosts remain unresolved. Here, leveraging 1593 metagenomes, we investigate the global distribution, microbial hosts, co-occurrence patterns, and drivers of MRGs and POPTGs in inland waters. Key MRG subtypes (e.g., ruvB, pstB, arsB) and POPTGs (e.g., hdt, linJ, bphA) co-occurred in phylogenetically constrained hosts-predominantly Proteobacteria (e.g., Pseudomonas, Acidovorax)-exhibiting dual resistance to Cr/Cu and transformation of aromatic/chlorinated POPs. The positive correlations linked MRG-POPTG to mobile genetic elements, suggesting horizontal gene transfer accelerates multi-pollutant resistance. Our findings highlight known POPTGs and MRGs occur together, which is ubiquitous in the environment but restricted to a limited number of taxa (approximately 3.8% ratio of the total 4129 non-redundant MAGs). Finally, a global map of MRG-POPTG-carrying MAGs (MPCMs) abundance is generated, where climatic and anthropogenic factors explained MPCMs hot spots in South Asia, Southeast Asia, South America.}, } @article {pmid42264402, year = {2026}, author = {Li, C and Tan, Y and Ma, S and Wang, J and Bai, W and Li, Z and Gao, S and Zhao, Q and Qin, J and Ye, Z}, title = {Concentration-dependent roles of hydrazine in immobilized denitrifying biofilm for industrial wastewater treatment.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135122}, doi = {10.1016/j.biortech.2026.135122}, pmid = {42264402}, issn = {1873-2976}, abstract = {Hydrazine-bearing industrial wastewater is challenging to treat biologically because hydrazine can simultaneously act as a reducing substrate and a microbial inhibitor. In this study, an immobilized denitrifying biofilm system was used to evaluate the concentration-dependent effects of hydrazine on denitrification performance, electron contribution, and microbial response under anoxic conditions. Under sufficient co-substrate conditions, 5-10 mg/L hydrazine was effectively removed, with a maximum removal efficiency of approximately 94%, while stable denitrification was maintained. Nitrogen-15 isotope tracing showed that approximately 31% of the electrons released from hydrazine oxidation were transferred to denitrification-coupled nitrate reduction, indicating that hydrazine can partially contribute reducing equivalents in the denitrifying biofilm. However, elevated hydrazine concentrations impaired hydrazine oxidation and denitrification, induced nitrite and ammonium accumulation, and reduced carbon utilization. Mechanistic analyses showed that this deterioration was associated with oxidative stress, membrane damage, and inhibition of key enzymes, particularly nitrite reductase and hydroxylamine oxidoreductase. Metagenomic analysis further revealed a stress-induced shift in the microbial community from central carbon metabolism toward compensatory pathways. Overall, this study provides mechanistic and process-level insights into the feasibility and operational limitations of using immobilized denitrifying biofilms for treating hydrazine-bearing industrial wastewater.}, } @article {pmid42264404, year = {2026}, author = {Li, Z and Wang, L and Wang, B and Wang, S and Liu, T and Peng, Y}, title = {Controlled transition from anammox to partial denitrification-anammox system enhanced nitrogen removal: Microbial community succession and organic matter management.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135121}, doi = {10.1016/j.biortech.2026.135121}, pmid = {42264404}, issn = {1873-2976}, abstract = {Integrated partial denitrification-anammox (PDA) offers a sustainable strategy for mainstream wastewater treatment. However, the dynamic transitions and microbial mechanisms during the shift from anammox to coupled PDA remain inadequately characterized. In this study, a PDA system was systematically established by the gradual replacement of nitrite with nitrate and controlled increases in acetate concentrations. Subsequently, acetate was replaced with sludge fermentation liquor (SFL) as the organic carbon source. The process achieved progressive enhancement in nitrogen removal, which stabilized at 93.9%-96.1%. The contribution of anammox in nitrogen removal accounted for > 74% of influent total nitrogen. Concurrently, the mean particle size increased from 85.6 μm to 387.5 μm, and this granulation process significantly improved the stability of the PDA system. 16S rRNA sequencing revealed a marked enrichment of Candidatus Brocadia (0.3% to 4.6%) and Thauera (5.8% to 17.3%). Furthermore, metagenomic analysis confirmed the high abundance of anammox-related genes (hdh, hzs) and higher abundance of the genes encoding nitrate reductase (narG/H/I, napA/B) compared to nitrite reductase genes (nirS/K). This metabolic bias reinforced the PD ecological niche, ensuring stable PDA functionality when SFL was used as the carbon source. Notably, enhanced activity of polysaccharide and protein hydrolase highlighted the critical roles of hydrolysis and acidogenesis in sustaining non-competitive PD performance, particularly under SFL conditions. This study provides a potentially reproducible strategy for the cultivation of PDA communities from anammox inoculum, elucidating microbial dynamics and functional stability during process transitions. These findings provide valuable insights for efficient wastewater treatment by replacing external chemical carbon sources to improve the recovery and utilization of sludge resources.}, } @article {pmid42264456, year = {2026}, author = {Wildbur, C and Dawson, RA and Roy, S and Ah-Peng, C and Espenberg, M and Hernández, M}, title = {Carbon monoxide oxidizers in soils of different ages from Piton de la Fournaise volcano.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {7}, pages = {}, doi = {10.1093/femsec/fiag062}, pmid = {42264456}, issn = {1574-6941}, support = {DHF\R1\211076//Royal Society Dorothy Hodgkin Research Fellowship/ ; RF\ERE\210050//Royal Society Research Fellows Enhanced/ ; RF\ERE\231066//Royal Society Research Fellows Enhanced/ ; NE/X018180/1//NERC Discipline Hopping for Discovery Science/ ; //European Union/ ; GA 101075426//ERC/ ; }, mesh = {*Soil Microbiology ; *Carbon Monoxide/metabolism ; RNA, Ribosomal, 16S/genetics ; Oxidation-Reduction ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenome ; *Volcanic Eruptions ; Phylogeny ; Aldehyde Oxidoreductases/genetics/metabolism ; Multienzyme Complexes/genetics/metabolism ; Soil/chemistry ; }, abstract = {Volcanic soils provide a unique environment for studying microbial colonization and succession due to their extreme conditions and distinct geochemical profiles. This study focused on carbon monoxide (CO)-oxidizing microbial communities in volcanic soils at Piton De La Fournaise, Réunion Island. Soil samples from three sites (corresponding to eruptions in 1401, 1559, and 2007) were analysed to assess microbial community structure using 16S rRNA gene sequencing and metagenomic analysis to identify functional genes involved in CO oxidation. Phylum-level analysis showed higher relative abundance of Acidobacteriota and Chloroflexota, lower abundances of Actinomycetota and Bacteroidota, and relatively stable levels of Pseudomonadota, while class-level patterns included rising Alphaproteobacteria and Acidobacteriia, with Ktenobacteria emerging in the 1401 site. CO dehydrogenase-related genes were found in 17 metagenome-assembled genomes across all sites. The CO consumption rate by microbes in soils was measured. CO-oxidizing microbes were present across soil ages, with detectable activity in the 2007 site and greatest activity in the 1401 site, suggesting that these microbes actively use CO as an energy source even in soils with primary vegetation, contrary to general understanding. The findings suggest intricate dynamics of microbial succession in volcanic soils and may challenge conventional expectations about community complexity over time.}, } @article {pmid42265111, year = {2026}, author = {Campese, L and Longo, A and Pelletier, E and Delmont, TO and Ambrosino, L and Miralto, M and Mele, BH and Alberti, A and Labadie, K and Oliveira, PH and Perdereau, A and Wincker, P and , and Iudicone, D}, title = {Eukaryotic MAGs from the NEREA observatory: expanding the coastal microbiome dataset.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07571-y}, pmid = {42265111}, issn = {2052-4463}, support = {101082021//MARCO-BOLO/ ; ID: 862923//AtlantECO/ ; 101081642//OBAMA-NEXT/ ; }, abstract = {Marine ecosystems are hotspots of biodiversity and biogeochemical activity, yet much of their complexity remains largely inaccessible without genome-resolved data. Here we present a curated dataset of 52 eukaryotic metagenome-assembled genomes (MAGs) reconstructed from samples collected between April 2019 and January 2020 at three NEREA (Naples Ecological REsearch for Augmented observatories) sites in the Gulf of Naples. NEREA is a coastal observatory integrating physical, chemical and biological measurements with state-of-the-art metagenomics. The eukaryotic MAGs have an average completeness of ~55% and genome size of ~20 Mb. Predicted proteins were functionally annotated against UniProtKB, InterPro, and eggNOG databases, and each MAG was taxonomically classified using a curated RNA polymerase A reference dataset. The recovered MAGs encompass diverse eukaryotic lineages, primarily Ochrophyta, Chlorophyta and Haptophyta. Building on the Tara Oceans eukaryotic MAG legacy, this release represents the first reconstruction of eukaryotic MAGs from a coastal time series, enabling temporal and functional analyses of eukaryotic plankton.}, } @article {pmid42265123, year = {2026}, author = {Murchie, TJ and Cocker, SL and Baleka, S and Vogel, NA and Natola, L and Karpinski, E and Tirlea, D and Barrera, MA and Grant, DM and Morien, E and Long, GS and Rutledge, LY and Zazula, GD and Jensen, BJ and Froese, DG and Poinar, HN}, title = {Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42265123}, issn = {2041-1723}, mesh = {Animals ; *DNA, Ancient/analysis ; *Sciuridae/genetics ; *DNA, Environmental/genetics/analysis ; Fossils ; Permafrost ; Phylogeny ; Mammoths/genetics ; Ecosystem ; Yukon Territory ; DNA, Mitochondrial/genetics ; Bison/genetics ; Genome, Mitochondrial ; Metagenomics ; *Feces/chemistry ; Plants/genetics ; }, abstract = {Permafrost-preserved ground squirrel (Urocitellus) burrows in Yukon, Canada contain coprolites (palaeofaeces) that span from the Holocene to at least the Middle Pleistocene (~700 kya). Using shotgun metagenomics and targeted enrichment, we recover a rich, multi-taxon spectrum of ancient environmental DNA from these pellets, including: plants, insects, microbes, and megafauna consistent with eastern Beringian ecosystems. These coprolites consistently preserve an abundance of eukaryotic DNA, enabling the assembly of >18 mitochondrial genomes (ground squirrel, snowshoe hare, steppe bison, horse, and mammoth), and revealing previously unrecognized diversity within Arctic Urocitellus, including a ~700 kya lineage that predates divergence among several extant clades. Characteristic damage patterns, positive/negative controls, and in silico taxon validations strongly support aDNA authenticity, and comparisons with regional permafrost datasets indicate minimal post-depositional leaching. These results show that permafrost coprolites can yield high-resolution records of Quaternary ecosystems and multi-organism population histories, providing a powerful complement to sedimentary and skeletal ancient DNA.}, } @article {pmid42265319, year = {2026}, author = {Gionchetta, G and Lee, J and Hansen, O and Beck, K and Bürgmann, H}, title = {Invasion dynamics of antimicrobial-resistant E. coli in river biofilms: impacts on the resistome, microbiomes, and horizontal gene transfer.}, journal = {npj antimicrobials and resistance}, volume = {}, number = {}, pages = {}, doi = {10.1038/s44259-026-00232-5}, pmid = {42265319}, issn = {2731-8745}, support = {ID 100010434//La Caixa Foundation/ ; 186531/SNSF_/Swiss National Science Foundation/Switzerland ; }, abstract = {River biofilms are frequently exposed to invasion by antibiotic-resistant bacteria (ARB) due to episodic or chronic wastewater inputs, yet the ecological processes governing the fate of invaders and their resistance plasmids remain poorly understood. We experimentally exposed river-grown biofilms from sites differing in microbial diversity and wastewater impact to a genetically tagged ARB Escherichia coli carrying a transferable IncPα plasmid with the nptII resistance gene. Over two weeks, we tracked invader and plasmid dynamics using qPCR and plasmid-to-genome ratios as a proxy for horizontal gene transfer (HGT), complemented by 16S rRNA gene sequencing and metagenomics. Both quantification approaches yielded consistent results: the invader transiently established in all biofilms, peaking within 48 h and declining to near-background levels after 14 days. Decreasing plasmid-to-genome ratios indicated limited HGT and progressive plasmid loss. Biofilms impacted by wastewater showed slower declines, suggesting greater plasmid persistence in disturbed environments and increased abundance of specific indigenous antimicrobial resistance genes of public health concern. While the overall resistome exhibited short-lived shifts, and indigenous resistomes remained largely stable. These findings demonstrate that invader-biofilm interactions are dynamic and shaped by community context, supporting the One Health framework and highlighting how environmental conditions modulate antimicrobial resistance risks in freshwater ecosystems.}, } @article {pmid42265550, year = {2026}, author = {Lu, R and Dumonceaux, T and Anzar, M and Zovoilis, A and Antonation, K and Barker, D and Corbett, C and Nadon, C and Robertson, J and Eagle, SHC and Lung, O and Rudar, J and Surujballi, O and Wajnberg, G and Laing, C}, title = {MNBC-ME categorizes viral and plasmid sequences within metagenomes and identifies putative species or plasmid host.}, journal = {BMC bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12859-026-06497-x}, pmid = {42265550}, issn = {1471-2105}, support = {CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; }, abstract = {BACKGROUND: Plasmids and viruses are two types of mobile genetic elements (ME), that rely on host cells to reproduce and propagate themselves. Recently, metagenomics has greatly facilitated the discovery and characterization of new plasmids and viruses, which relies on accurate identification of these reads in metagenomes. Some state-of-the-art tools can identify plasmid or viral reads, while others are able to identify the probable host or source species of these reads. Since the Minimizer-based Naïve Bayes Classifier (MNBC) tool accurately classifies chromosomal and viral reads to the species level, we extended it to develop the MNBC-ME tool that can also identify plasmid reads and their putative host species.

RESULTS: A standard reference- and test-sequence framework using simulated variable-length reads was used to benchmark MNBC-ME with eleven other state-of-the-art tools for ME identification: DeepMicroClass, geNomad, PPR-Meta, viralVerify, Plasmer, PlasClass, PlasX, VIBRANT, DeepVirFinder, HOTSPOT, and MOSTPLAS. MNBC-ME was the most consistent tool at classifying chromosomal, viral and plasmid reads of variable lengths, in contrast to the other tools whose precision or recall dropped below 50% in some circumstances. MNBC-ME also exceeded 65% and 70% performance in predicting host genus and family of plasmid reads, respectively.

CONCLUSIONS: MNBC-ME is tool for identification of both short and long viral- and plasmid-originated reads across a wide variety of read types. It also identifies potential low-level host taxa for plasmid reads, and source taxa for chromosomal and viral reads. It is freely available at https://github.com/ComputationalPathogens/MNBC-ME and can be found as the 'mnbc-me' package in bioconda.}, } @article {pmid42265587, year = {2026}, author = {Liang, X and Li, J and Liu, P and Lai, Z and Huang, S and Xie, F and Jin, W and Mao, S}, title = {Rumen ecological distribution of Pichia yeasts and their effects on rumen fermentation and microbial community.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05281-4}, pmid = {42265587}, issn = {1471-2180}, support = {32272896//The National Natural Science Foundation of China/ ; 32361143788//The National Natural Science Foundation of China/ ; QTPY2026017//The Fundamental Research Funds for the Central Universities/ ; }, abstract = {Yeast supplementation has been widely studied to enhance rumen fermentation and feed efficiency, yet developing efficient yeasts adapted to the rumen environment remains a challenge. In this study, two rumen-derived Pichia strains (Pichia membranifaciens M12 and Pichia kudriavzevii Y4) were evaluated using in vitro rumen fermentation experiments, including a control and three supplementation groups (2 × 10[5], 2 × 10[6], and 2 × 10[7] CFU/mL) for each strain. Results indicated that the two strains did not affect pH but significantly reduced concentrations of ammonium nitrogen (NH3-N) and microbial crude protein (MCP). At 24 h, NH3-N decreased by up to 13.3% and MCP by 18.5%, while at 48 h, NH3-N showed a reduction of up to 22.0% and MCP decreased by up to 5.7%. P. membranifaciens significantly increased the concentration of total volatile fatty acids by 15.4% and elevated the proportions of acetate and propionate at 48 h. Microbial community analysis revealed that these shifts in fermentation parameters were associated with an altered bacterial community structure. Specifically, P. membranifaciens enriched cellulolytic bacteria (Ruminococcus), while reducing amylolytic and proteolytic taxa (Prevotella), and promoted the propionate‑producer (Succiniclasticum). These findings suggested that P. membranifaciens has the potential to influence rumen microbiota. Further examination of the in vivo prevalence of Pichia yeasts species via ITS (n = 72; average parity 2.8 ± 1.1) revealed a lower prevalence and relative abundance for P. membranifaciens compared to P. kudriavzevii. Metagenomic analysis (n = 8; average parity 2.7 ± 0.9) detected both species at low abundances. Overall, this study indicated that rumen-derived Pichia yeasts have the capacity to modulate rumen fermentation, with P. membranifaciens warranting further in vivo evaluation.}, } @article {pmid42265917, year = {2026}, author = {Nakamura, K and Okazaki, A and Motooka, D and Matsumoto, N and Hasegawa, Y and Fukuda, S and Yabe, M and Sugiura, A and Yatsuka, Y and Fushimi, T and Onuki, T and Aida, Y and Ohtake, A and Murayama, K and Okazaki, Y}, title = {Nanopore-based haplotype-resolved X-chromosome inactivation analysis for clinical severity assessment in X-linked disorders: an AIFM1 family study with proof-of-concept application to a mosaic PDHA1 carrier.}, journal = {HGG advances}, volume = {}, number = {}, pages = {100632}, doi = {10.1016/j.xhgg.2026.100632}, pmid = {42265917}, issn = {2666-2477}, abstract = {X-chromosome inactivation (XCI) modifies disease severity in females with X-linked variants, but clinically applicable high-resolution assessment remains limited. We report a family with an AIFM1 variant showing marked intrafamilial phenotypic variability and evaluated whether haplotype-resolved nanopore sequencing can inform clinical interpretation. Targeted long-read sequencing was performed in a severely affected hemizygous male, his asymptomatic heterozygous mother, and a severely affected heterozygous sibling. In the hemizygous male, the sample served as a technical control, with all reads mapping to a single haplotype, consistent with a hemizygous X chromosome. Among heterozygous carriers with the identical variant (c.506C>T; p.Pro169Leu), XCI correlated with severity: the affected sibling showed 84% skew favoring activation of the pathogenic allele, whereas the mother showed preferential inactivation (20%). This family-based study shows that using nanopore sequencing for haplotype-resolved X-inactivation (XCI) analysis may provide a practical framework for selected X-linked disorders with variable expressivity.}, } @article {pmid42266244, year = {2026}, author = {Lin, X and Du, Y and Mai, H and Zhang, X}, title = {Voriconazole-Induced Agranulocytosis in a Cirrhotic Patient with Influenza-Associated Pulmonary Aspergillosis: A Case Report.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {607868}, pmid = {42266244}, issn = {1178-6973}, abstract = {The diagnosis and treatment of influenza-associated pulmonary aspergillosis (IAPA) present significant challenges, and voriconazole, as the first-line treatment for IAPA, rarely causes the serious adverse event of agranulocytosis. We first report a case of voriconazole-associated agranulocytosis in a patient with IAPA complicated by cirrhosis and systematically describe the complete process of diagnosis, treatment, and adverse event management. A 68-year-old male with a history of liver cirrhosis presented with cough, dyspnea, and fever. Testing confirmed influenza A, and chest computed tomography (CT) showed diffuse bilateral pulmonary inflammation. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) and culture detected Aspergillus fumigatus, confirming the diagnosis of IAPA. The patient received voriconazole. On Day 20 of hospitalization, agranulocytosis developed and resolved after voriconazole discontinuation and granulocyte colony-stimulating factor (G-CSF) administration, consistent with voriconazole-associated agranulocytosis. After neutrophil recovery, voriconazole was resumed with leukocyte support and close monitoring of complete blood counts (CBC) and drug levels. At one-month follow-up, no recurrence of infection or agranulocytosis was observed. This case emphasizes the value of mNGS in timely diagnosis of IAPA, underscores the importance of closely monitoring CBC in such patients during triazole antifungal therapy, and proves the feasibility of resuming antifungal treatment-including the cautious re-administration of the initially sensitizing agent under strict monitoring-after the correction of agranulocytosis. These findings contribute to a better understanding of the disease and may help to optimize its clinical management.}, } @article {pmid42266457, year = {2026}, author = {Stach, TL and Deep, A and Madge Pimentel, I and Buchner, D and Borton, MA and Soares, AR and Starke, J and Bornemann, TLV and Rehsen, PM and Dreger, KL and Boenigk, J and Vos, M and Leese, F and Beisser, D and Probst, AJ}, title = {Complex compositional and metabolic response of river sediment microbiomes to multiple anthropogenic stressors.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycaf079}, pmid = {42266457}, issn = {2730-6151}, abstract = {Rivers face constant anthropogenic stress, resulting in significant changes in microbial community composition. What remains unclear is whether stream microbiomes exhibit distinct resilience patterns in composition and/or activity upon exposure to different stressors. By subjecting 64 river-connected mesocosms to multiple stressors, we show that sediment microbiomes of small lowland rivers are highly sensitive to low flow velocity. This stress results in altered community compositions incapable of mitigating the applied stressor within a two-week timeframe despite functional stability (inferred via metagenomics). Transcriptomics revealed a systematic heat shock response in the community and a highly active, metabolically versatile, uncharacterized anaerobic keystone species. Increases in temperature (+ 3.5°C) or salinity (+ 0.5 mS/cm) elicited minor responses at community and transcriptomic levels (e.g. upregulation of photosystems). Following a two-week recovery, transcriptomic-inferred stress responses vanished completely, underscoring the river microbiome resilience. Given the complex community responses observed at the activity and compositional levels, we conclude that maintaining natural river flow is vital to preventing energy loss and reduced microbiome activity in river sediments.}, } @article {pmid42266956, year = {2026}, author = {Lu, J and Zhong, J and Qiu, W and Zhang, Q}, title = {Intrathecal combined with intravenous eravacycline for the treatment of multisite carbapenem-resistant Acinetobacter baumannii infections (intracranial, pulmonary, and bloodstream) in a post-trauma adolescent female: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1829527}, pmid = {42266956}, issn = {2296-858X}, abstract = {BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a leading cause of hospital-acquired infection among critically ill patients, with extremely limited therapeutic options, particularly for central nervous system (CNS) infections. Eravacyline, a novel fully synthetic fluorocycline, demonstrates potent in vitro activity against CRAB but exhibits poor penetration across the blood-brain barrier (BBB).

CASE PRESENTATION: A 17-years-old female with severe traumatic brain injury developed concurrent intracranial, pulmonary, and bloodstream CRAB infections. Initial systemic antimicrobial therapy, including intravenous colistin and eravacycline, failed to control the intracranial infection. After switching to a regimen incorporating intrathecal eravacycline (initial dose 2 mg, followed by 5 mg daily) combined with high-dose intravenous cefoperazone-sulbactam and nebulized colistin, the patient showed rapid clinical and microbiological improvement. Serial cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) revealed a dramatic reduction in pathogen load, with eventual eradication of CRAB.

CONCLUSION: This case highlights the potential role of intrathecal eravacycline as a salvage therapy for CRAB meningitis, particularly in cases of multifocal, extensively drug-resistant infection. Further pharmacokinetic and safety studies are warranted to optimize its use in CNS infections.}, } @article {pmid42267106, year = {2026}, author = {Wu, Y and Gao, Q and Yang, H and Wang, Y and Lang, L and Liu, B and Jiang, X and Li, D and Wang, X and Xun, J and Zhang, Q}, title = {Multi-omics analysis identifies gut microbiota-glutamine axis contributing to the pathogenesis of reflux esophagitis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1805181}, pmid = {42267106}, issn = {1664-302X}, abstract = {BACKGROUND: Reflux esophagitis (RE), a common gastroesophageal reflux disease characterized by esophageal mucosal inflammation, is closely associated with gut microbiota dysbiosis and metabolic abnormalities. The glutamine-glutamate metabolic pathway regulates inflammation and mucosal barrier function, but its role in RE and association with gut microbiota remain unclear. This study aimed to characterize gut microbiota and serum metabolites in RE patients via integrated multi-omics (focusing on the gut microbiota-glutamine axis), and verify the activation status of this pathway in RE inflammatory models and the anti-inflammatory effect of its targeted inhibition.

METHODS: RE patients and healthy controls (HCs) were enrolled. Fecal metagenomic sequencing and serum untargeted metabolomics (LC-MS/MS) were performed to identify differential gut microbiota and serum metabolites between the two groups, followed by Pearson correlation analysis to explore their associations. In vitro experiments were conducted on human esophageal epithelial cells (HEECs) divided into four groups: normal, inflammatory, glutamine-supplemented, and inflammatory + glutamine + glutaminase inhibitor (BPTES) groups. qPCR was used to detect the mRNA expression of glutamine-glutamate pathway molecules (GLS, c-Myc, SLC1A5), mucosal barrier markers (ZO-1, Occludin), and pro-inflammatory cytokines (IL-8, IL-6, IL-1β, TNF-α). Intracellular concentrations of glutamine, glutamate, and α-ketoglutarate were measured, and the anti-inflammatory effect of BPTES was verified.

RESULTS: RE patients showed significant differences in gut microbiota diversity and composition compared with HCs, with Bacteroidota, Pseudomonadota, Escherichia coli, and Klebsiella pneumoniae as dominant taxa. Serum metabolomics revealed elevated glutamine and glutamate in RE patients, which were identified as key differential metabolites related to RE pathogenesis. Pearson analysis revealed that alterations in serum metabolite profiles of RE patients were significantly correlated with changes in gut bacterial abundance. Notably, glutamate-glutamate (Glu-Glu) metabolism exhibited negative correlations with multiple bacterial genera (Acrocarpospora, Limnobacter, Pseudobacter, Shewanella, and Tropicimonas). In vitro, inflammatory HEECs exhibited increased intracellular glutamine, glutamate, and α-ketoglutarate, upregulated glutamine-glutamate pathway molecules and pro-inflammatory cytokines, and downregulated mucosal barrier markers. Exogenous glutamine alone failed to alleviate inflammation, while combined with BPTES significantly reversed pathway activation and mitigated inflammation in inflammatory HEECs.

CONCLUSION: RE patients exhibit significant gut microbiota dysbiosis (dominated by Bacteroidota, Pseudomonadota, Escherichia coli, and Klebsiella pneumoniae) and abnormal glutamine metabolism (elevated serum glutamine and glutamate). Pearson analysis reveals that the glutamine-glutamate pathway correlates negatively with multiple bacterial genera (Acrocarpospora, Limnobacter, Pseudobacter, Shewanella, and Tropicimonas). The glutamine-glutamate pathway is activated in inflammatory esophageal epithelial cells, and targeted GLS inhibition by BPTES reverses pathway activation and mitigates inflammation. These findings highlight the gut microbiota-glutamine axis as potential diagnostic biomarkers and therapeutic targets for RE, providing new insights into pathogenesis and a basis for novel clinical interventions.}, } @article {pmid42267107, year = {2026}, author = {Mathyk, BA and Shukla, R and Kumar, V and Mishra, SP and Pandya, S and Patten, N and Gerardi, K and Beatty, HW and Persad, AH and Imudia, AN and Yadav, H and Jain, S}, title = {Parabolic flight induces site specific microbiome changes in women.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1817099}, pmid = {42267107}, issn = {1664-302X}, abstract = {INTRODUCTION: The vaginal microbiome plays a central role in women's health by supporting immune function, maintaining mucosal homeostasis, and preventing infections. Spaceflight and its analogs can induce acute physiological stress, which can alter host microbiome interactions. While other studies have analyzed the microbiome changes at certain body sites, the female-specific microbiome changes have not been explored in depth in space medicine research.

METHODS: Pre- and post-parabolic flight vaginal and oral microbiome were analyzed via metagenomic shotgun sequencing to assess taxonomic composition and metabolic pathways. Host DNA and bad quality sequences were removed using the KneadData tool. Taxonomic and functional profiles were analyzed with MetaPhlAn and HUMAnN. Microbiome data were integrated with stress response parameters including cortisol, proinflammatory cytokines, and urinary short-chain fatty acids.

RESULTS: Both alpha- and beta diversity analysis showed minimal impact of parabolic flight on oral microbiome while vaginal microbiome showed significant differences. Taxonomic profiling showed marked restructuring of the vaginal microbiome, characterized by increased Firmicutes dominance and enrichment of Lactobacillus species, particularly Lactobacillus crispatus and Lactobacillus jensenii, whereas oral microbiome stayed relatively stable. Overall, only 2.54% of oral species showed significant postflight changes compared to 57.9% of vaginal species (p < 0.0001). Random Forest model identified L. crispatus as a key discriminator of postflight vaginal microbiome composition. Metabolic pathway analysis revealed minimal postflight pathway redistribution in saliva samples but greater number of changes in the vaginal microbiome, with significant postflight enrichment of fatty acid biosynthesis and nucleotide metabolism. Vaginal samples demonstrated a threefold greater proportion of altered metabolic pathways compared to oral samples. In addition, urinary acetate, butyrate, and valeric acid levels were significantly reduced postflight. Salivary cortisol increased postflight and positively correlated with L. jensenii.

CONCLUSION: Parabolic flight induces body site-specific microbiome changes in reproductive age women, with greater taxonomic and functional metabolic remodeling in the vaginal microbiome than in the oral microbiome. These findings highlight the sensitivity of the vaginal microbial ecosystem to spaceflight stressors and underscore the need for longitudinal and mechanistic studies to determine the persistence, clinical significance, and potential health implications of these changes during longer duration space missions.}, } @article {pmid42267128, year = {2026}, author = {Daurova, A and Daurov, D and Sapakhova, Z and Kanat, R and Abilda, Z and Toishimanov, M and Isgandarov, I and Mukhametov, A and Volkov, D and Shamekova, M and Zhambakin, K}, title = {Rhizosphere microbiome dynamics and plant adaptation to abiotic stress in major oilseed crops: a review.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1832403}, pmid = {42267128}, issn = {1664-462X}, abstract = {Abiotic stresses, such as drought, salinity, extreme temperatures, nutrient deficiencies, and heavy metal contamination, severely limit oilseed crop productivity under accelerating climate change. This review synthesizes recent advances in understanding the critical role of soil and plant-associated microbiomes in conferring stress tolerance to major oilseed species, including rapeseed (Brassica napus), sunflower (Helianthus annuus), soybean (Glycine max), and sesame (Sesamum indicum). Beneficial microorganisms, particularly plant growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi (AMF), and endophytes, enhance plant tolerance through an integrated network of biochemical, physiological, and molecular mechanisms. Biochemically, they modulate phytohormone levels (e.g., IAA and ABA), produce osmoprotectants, and regulate antioxidant systems (e.g., SOD, CAT, POD) to mitigate oxidative damage. Physiologically, these processes contribute to improved root architecture, water-use efficiency, nutrient acquisition, and ion homeostasis under stress conditions. At the molecular level, microorganisms influence gene expression and signaling pathways associated with stress responses, including activation of stress-responsive genes and metabolic adjustments. These interconnected mechanisms collectively strengthen plant resilience by coordinating metabolic regulation, cellular protection, and adaptive responses within the plant-microbiome system. Agroecological practices (soil type, crop rotation, tillage, fertilization) strongly shape microbial community assembly and functional potential, while multi-omics approaches (metagenomics, metatranscriptomics, metabolomics) reveal stress-driven restructuring and adaptive metabolic shifts in the rhizosphere. Emerging tools such as synthetic microbial consortia (SynComs) and targeted microbiome engineering offer promising, sustainable alternatives to conventional breeding and chemical interventions, enhancing soil health, nutrient cycling, and agroecosystem resilience with reduced environmental footprint. This review presents a comprehensive synthesis with a specific focus on oilseed crops, integrating current knowledge on microbiome dynamics under multiple abiotic stress conditions-an area that remains comparatively underrepresented in the literature. It examines key microbial groups driving adaptation, evaluates omics-based insights into plant-microbiome interactions, identifies critical research gaps, and outlines future directions for microbial inoculants and climate-resilient oilseed production systems.}, } @article {pmid42267141, year = {2026}, author = {Hardies, SC and Park, J and Cho, BC and Hwang, CY}, title = {Alishewanella Phage LSH1 from the Sea Surface Microlayer Provides a Novel Minimalistic View of the Siphoviral Hub Structure.}, journal = {Computational and structural biotechnology journal}, volume = {35}, number = {1}, pages = {0131}, pmid = {42267141}, issn = {2001-0370}, abstract = {LSH1 is a novel lytic siphovirus isolated, together with its host in the genus Alishewanella, from the surface microlayer of a brackish tidal reservoir in South Korea and characterized with respect to growth properties, genome sequence, gene annotation, mass spectrometry, and electron microscopy. Sequence analysis shows that LSH1 shares only distant similarity to other cultured phages, although a closer metagenomic neighborhood can be defined. LSH1 represents the first isolate from a large, previously unsampled family-level sector of the viral tree. Transmission electron microscopy revealed a tail end distinct from the best structurally characterized siphoviral prototypes and similar in appearance to Salmonella phage Jersey, the prototype of a large structurally uncharacterized group named Guernseyvirinae. Therefore, Jersey was included in the comparative analysis with LSH1. A combination of hidden Markov model comparisons and AlphaFold reconstruction was used to clarify the structural relationships of these phages. Both have structural homologs of portions of the canonical bacteriophage lambda tail hub but lack the lambda components associated with receptor recognition linked to ejection triggering in that system. The LSH1 and Jersey tail hubs are of different sequence lineages, but each represents a relatively minimalistic version of the siphoviral tail hub, with distinct candidates for the structural location of their antireceptors. This study explores the capability of AlphaFold to rapidly augment the relatively few structurally characterized phages with models for diverse variants, fleshing out how much variation there is and perhaps leading to a better treatment of how this variation is evolving.}, } @article {pmid42267567, year = {2026}, author = {Liu, BZ and Zhao, XY and Sun, ZW and Wang, J and Zeng, JT and Huang, Y and Cai, KQ and Zhao, JG and Yang, SH and Yuan, JL}, title = {Gut microbiota remodeling in HBB-mutant cynomolgus monkeys reveals blood-gut axis disruption associated with β-thalassemia-related gastrointestinal dysfunction.}, journal = {Zoological research}, volume = {47}, number = {3}, pages = {811-826}, doi = {10.24272/j.issn.2095-8137.2025.141}, pmid = {42267567}, issn = {2095-8137}, mesh = {Animals ; *beta-Thalassemia/genetics/complications/veterinary/microbiology ; *Macaca fascicularis ; *Gastrointestinal Microbiome/physiology ; Mutation ; *Gastrointestinal Diseases/veterinary/microbiology/etiology/genetics ; *beta-Globins/genetics/metabolism ; Male ; }, abstract = {Gastrointestinal symptoms frequently accompany anemia caused by HBB mutations, such as β-thalassemia; however, the mechanisms linking disordered hemoglobin biology to intestinal dysfunction remain incompletely understood. In this study, HBB-mutant cynomolgus monkeys were generated and analyzed together with wild-type (WT) controls through integrated metabolomic and metagenomic profiling. HBB mutation was associated with a marked shift in gut microbial ecology, characterized by reduced microbial diversity and altered abundances of Lactobacillus and Bacteroides. Metabolic profiling revealed broad perturbation of amino acid, lipid, energy, and immune-related metabolic pathways, with 3-oxooctadecanoic acid (HMDB0254633) emerging as a discriminative metabolite between WT and HBB-mutant animals. Multiomics integration indicated that HBB mutation reshaped microbiota-metabolite interactions and may thereby affect host metabolism and immune responses. To examine the functional relevance of this metabolite, 3-oxooctadecanoic acid was administered to C57BL/6 mice with castor oil-induced diarrhea. High-dose treatment alleviated diarrhea severity, improved stool parameters, limited body weight loss, and partially restored gut microbial composition. These findings provide non-human primate evidence that β-thalassemia-associated HBB mutation disrupts intestinal microbiota homeostasis and metabolic output, identifying 3-oxooctadecanoic acid as a candidate biomarker and potential regulator of gastrointestinal dysfunction. This study provides a valuable framework for understanding how host genetic variation contributes to gut microbiome remodeling and gastrointestinal manifestations in β-thalassemia.}, } @article {pmid42267811, year = {2026}, author = {Gołębiowska, J and Woodhouse, JN and Tobias-Hünefeldt, SP and Grossart, H-P}, title = {Salinity-driven niche partitioning of aquatic viruses in one of Europe's largest estuaries.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0080726}, doi = {10.1128/aem.00807-26}, pmid = {42267811}, issn = {1098-5336}, abstract = {UNLABELLED: Viruses are a vital part of the aquatic food web and hold a profound role in carbon and energy cycling at different trophic levels. Despite the rising interest in aquatic viruses, very few studies were conducted in estuaries, where freshwater and marine communities meet along the salinity gradient. We present a paired analysis of metagenomic and metatranscriptomic data focusing on the viral fraction derived from seasonal sampling between May 2021 and November 2022 in one of Europe's largest estuaries, the temperate mesotidal Elbe River downstream of Hamburg. Our results reveal a sharp delineation of viral communities along specific salinity niches and provide evidence for their adaptation. This implicates viruses as a structural component of microbial and phytoplankton ecology across the estuary. We provide a detailed overview of the spatiotemporal distribution of viruses, including taxonomy and hosts, which emphasizes the role of giant viruses (Megaviricetes) in waters of lower salinity and RNA viruses in marine environments. We identify, besides salinity, total dissolved phosphate and temperature as the main drivers of estuarine viral communities. We find a broad spectrum of metabolic pathways, potentially altered by viruses via auxiliary metabolic genes. Potential metabolisms impacted included the underlying carbon processes like photosynthesis or methane metabolism, but may also extend to some xenobiotics and antibiotics metabolisms in this anthropogenically altered estuary. This is the first detailed molecular study of viruses in the Elbe Estuary, shedding light on viral communities and their ecological roles in controlling microbial populations at the base of the estuarine food web.

IMPORTANCE: Estuaries are the interfaces between marine and limnic waters, with their own specific hydrological and biochemical processes due to, e.g., salinity gradients, tides, and terrestrial inflows. In particular, they are sites of intensive carbon cycling. Their often high economic importance causes substantial anthropogenic pressure on the ecosystem. All of these result in extremely complex factors interacting and influencing microbial populations. Our study provides a first comprehensive overview of the viral communities in Europe's largest estuary. We made an attempt to disentangle the numerous environmental parameters, and we highlight salinity as the most important factor, providing evidence of its multidimensional influence on the estuarine virome. Our findings deepen our understanding of viral communities and their interactions with microbes and bring us a step closer to their role in aquatic food webs, particularly in carbon turnover in estuaries.}, } @article {pmid42267859, year = {2026}, author = {Shittu, OE and Enagbonma, BJ and Babalola, OO}, title = {Functional Metagenomics Insights Into the Allium ampeloprasum Rhizosphere Microbiome Under Different Fertilization Regimes.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70307}, pmid = {42267859}, issn = {2045-8827}, support = {//International Centre for Genetic Engineering and Biotechnology (ICGEB) through Grant CRP/ZAF22-03 awarded to OOB/ ; }, mesh = {*Rhizosphere ; *Metagenomics ; Soil Microbiology ; *Allium/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Fertilizers/analysis ; Soil/chemistry ; }, abstract = {Fertilization practices shape the taxonomy, functional composition, and metabolic functions of the microbiome within the rhizosphere. Nonetheless, the impacts of various fertilization approaches on the functional composition of Allium ampeloprasum rhizosphere microbiomes remain underexplored. This study investigated how biofertilizers and chemical fertilizers impact the microbial functional categories of the A. ampeloprasum rhizosphere, hypothesizing that fertilization systems influence the metabolic profile. The genomic DNA was successfully extracted from the collected soil samples and processed via shotgun metagenomics sequencing. The application of biofertilizers enhanced the rhizosphere microbiome, revealing similar microbial orders across all plots, although plot G2 was uniquely enriched with those belonging to phyla Bacteroidota, Proteobacteria, actinobacteria, Myxococcota, and Verrucomicrobiota. Biofertilizers promoted a broader range of microbial functions, primarily at EggNOG level 1. Notably, the α diversity significantly differed (p < 0.05) among the soil samples. The functional diversity was linked to the soil physicochemical attributes, particularly the carbon and moisture contents, as illustrated by the RDA. Biofertilizer increases microbial diversity, underscoring the need to understand the rhizosphere microbiome to advance sustainable agricultural methods.}, } @article {pmid42268526, year = {2026}, author = {Mohit, and Verma, S and Yadav, A and Venkatesh, V}, title = {Multi-omics insights into immunometabolic dysregulation in neonatal sepsis for precision medicine.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42268526}, issn = {1573-4978}, mesh = {Humans ; *Neonatal Sepsis/metabolism/immunology/genetics/therapy ; Multiomics ; Infant, Newborn ; *Precision Medicine/methods ; Metabolomics/methods ; Proteomics/methods ; Genomics/methods ; Biomarkers/metabolism ; }, abstract = {Neonatal sepsis remains a major global health challenge, contributing substantially to morbidity and mortality despite many advances. Conventional diagnostics often fail to capture the disease complexity and immune dysregulation, leading to delayed diagnosis and sub-optimal treatment. Recent advances in multiomics, including genomics, transcriptomics, proteomics, metabolomics and metagenomics are transforming molecular understanding by enabling a precise view of host-pathogen interactions. These approaches also provide critical insights into metainflammation, a state of chronic, low-grade immune and metabolic dysregulation, playing a pivotal role in neonatal immune vulnerability. Integrating multi-omics with meta-inflammatory profiling may support future risk stratification, biomarker discovery, and precision-oriented neonatal sepsis care. However, clinical translation requires further validation, platform standardization, and feasibility assessment in NICU settings. Such insights may establish the foundation of P4 medicine by emphasizing prediction, prevention, personalisation, and participation in neonatal care. Multi-omics integration may support endotype identification, and data-driven clinical communication after adequate validation. Overall, this review highlights how multiomics and metainflammation driven frameworks may improve mechanistic understanding of neonatal sepsis and guide future development of clinically feasible precision-medicine approaches.}, } @article {pmid42268876, year = {2026}, author = {Fatima, Z and Surette, MD and Marttala, S and Leto, D and Jayaratne, P and Smaill, F and Smieja, M and Hasan, MR}, title = {Microbiome analysis of bronchoalveolar lavage (BAL) specimens from immunocompromised patients with pneumonia compared to those from healthy volunteers.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0351562}, pmid = {42268876}, issn = {1932-6203}, mesh = {Humans ; *Immunocompromised Host ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; *Microbiota/genetics ; Female ; Middle Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; *Pneumonia/microbiology/immunology ; Aged ; Healthy Volunteers ; Metagenomics ; Case-Control Studies ; Bacteria/genetics/isolation & purification/classification ; COVID-19 ; SARS-CoV-2 ; }, abstract = {BACKGROUND: Metagenomic sequencing of bronchoalveolar lavage (BAL) specimens is increasingly being applied for the diagnosis of lower respiratory tract infections, offering agnostic pathogen detection and a faster turnaround time. While metagenomic sequencing of BAL specimens can reveal a wide range of organisms, their clinical relevance is often unclear because of the challenge of distinguishing true pathogens from background taxa. This study compared the BAL microbiomes of immunocompromised patients with pneumonia to those of healthy volunteers, with the aim of assisting clinical interpretation of metagenomics-based approaches for diagnosing pneumonia in this patient population.

METHODS: BAL specimens from healthy control volunteers (n = 20) were collected during a COVID-19 vaccine trial, while residual BAL specimens from immunocompromised patients (n = 52) were obtained from the Hamilton Regional Laboratory Medicine Program (HRLMP) after standard culture and PCR testing. 16S rRNA gene amplicon sequencing was performed using Nanopore technology. Reads were classified using Minimap2 in EPI2ME, and microbiome analyses were conducted using the vegan and MaAsLin2 packages in RStudio (v2026.1.1.403).

RESULTS: Immunocompromised patients showed significantly lower bacterial read counts and reduced alpha diversity (p < 0.0001; Wilcoxon Rank-Sum test), along with higher inter-sample heterogeneity. In contrast, BAL samples from healthy controls exhibited a more homogeneous microbial profile dominated by anaerobic Gram-negative genera, including Prevotella, Veillonella, Selenomonas, and Fusobacterium. Beta diversity analyses using Bray-Curtis and Jaccard distance metrics demonstrated significant compositional separation between cohorts (PERMANOVA p = 0.001), with tight clustering of healthy controls and marked dispersion among immunocompromised samples. Differential abundance analysis identified 96 significantly altered species (q < 0.05), with immunocompromised patients showing depletion of anaerobic commensals and enrichment of clinically relevant pathogens, including Stenotrophomonas maltophilia, Enterococcus spp., Mycoplasma spp., and Nocardia spp.

CONCLUSION: Immunocompromised patients demonstrated a markedly disrupted and heterogeneous BAL microbiome, characterized by a loss of anaerobic commensals and an enrichment of potentially pathogenic taxa. This study provides a characterization of the dysbiotic state in immunocompromised pneumonia, offering a baseline reference for future longitudinal studies and clinical trials aimed at improving the interpretation of metagenomic findings in this patient population.}, } @article {pmid42269300, year = {2026}, author = {Lo, HY and Hsiao, YT and Wu, YJ and Whang, LM and Chen, WH and Tung, HH}, title = {Persistence and dynamics of antibiotic resistome in a drinking water supply system with booster chlorination.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142622}, doi = {10.1016/j.jhazmat.2026.142622}, pmid = {42269300}, issn = {1873-3336}, abstract = {Due to the extensive use of antibiotics worldwide, the prevalence of antibiotic resistance genes (ARGs) in aquatic environments has become a major public health concern. This study investigated the ARGs in a drinking water supply system, with particular emphasis on booster chlorination in the distribution network. To elucidate the dynamics of the antibiotic resistome, environmental DNA was extracted from water collected from five different sections, and the resistome profiles were subsequently reconstructed with metagenome assembly. Our findings revealed that 35 core ARGs persisted but decreased in concentration during water treatment and early distribution, with genes resistant to bacitracin, multidrug, and rifamycin being the most prominent. However, a notable surge of ARGs was observed at the terminal distribution segment. This increase was linked to changes in the resistome structure, which were primarily associated with shifts in the microbial community and, within the DWDS specifically, also linked to horizontal transfer mediated by mobile genetic elements (MGEs) under chlorine stress from booster chlorination. Microbial communities within the drinking water distribution system (DWDS) shifted distinctly from those in the water treatment plant. Under re-chlorination pressure, the chlorine-tolerant Mycobacteriales and the biofilm-forming Hyphomicrobiales and Rhodobacterales became the predominant taxa. Additionally, metagenome-assembled genomes (MAGs) reconstruction further identified that Hyphomicrobium and Mycobacterium were the main ARG carriers in the DWDS, with the latter as the main putative host for the core ARGs. Overall, this study demonstrated that booster chlorination in the water distribution system while controlling microbial regrowth, may simultaneously facilitate ARG dissemination. These findings highlight the need to optimise re-chlorination practices to balance microbial growth control while minimising ARG proliferation in DWDS.}, } @article {pmid42269354, year = {2026}, author = {Petersen, J and Ringel, V and Päuker, O and Frühling, A and Rohde, M and Jarek, M and Spröer, C and Bunk, B and Huber-Fischer, K and Pradella, S and Freese, HM and Koblitz, J and Neumann-Schaal, M and Brinkmann, H}, title = {Think pink 2.0 - Description of Roseobacter cerffii sp. nov., isolated from the chromerid alga Vitrella brassicaformis, and reclassification of Sulfitobacter sabulilitoris as Billmartinia sabulilitoris, gen. nov., comb. nov.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126731}, doi = {10.1016/j.syapm.2026.126731}, pmid = {42269354}, issn = {1618-0984}, abstract = {A Gram-stain-negative, aerobic, pink-pigmented bacterial strain A03A-229[T] was isolated from a non-axenic culture of the chromerid alga Vitrella brassicaformis CCMP3155, which originates from the Great Barrier Reef in Australia. Complete genome sequencing revealed the presence of seven circular replicons, representing one chromosome, two chromids and four plasmids. The 142-kb DnaA-like I chromid, which contains the photosynthesis gene cluster (PGC), traces of ubiquinone-11 and the ability to reduce nitrate are diagnostic for A03A-229[T]. Genomic, physiological, and chemotaxonomic data provided clear evidence that strain A03A-229[T] (= DSM 112523[T] = CECT 31310[T]) represents a new species of the genus Roseobacter, for which the name Roseobacter cerffii sp. nov. is proposed. R. cerffii A03A-229[T] represents the tenth described species of the genus Roseobacter, but phylogenetic (meta-)genome analyses indicated the presence of at least 27 different species. Reconstruction of the metabolic pathways of the genus Roseobacter revealed a highly conserved metabolism with lineage specific adaptations for the formation of compatible solutes and a surprising abundance of four GAPDH genes. The ability to perform aerobic anoxygenic photosynthesis, which is mediated by the PGC, is responsible for the eponymous pink color of this genus, while it only occurs scattered in the sister genus Sulfitobacter. Our phylogenomic analyses provided clear evidence for a distinct taxonomic status of strain Sulfitobacter sabulilitoris HSMS-29[T] (= KACC 19870[T] = NBRC 113549[T]). Based on its phylogenetic position, low average amino-acid identities (AAI) and a PufC-type PGC, we propose the reclassification of this strain as Billmartinia sabulilitoris gen. nov., comb. nov.}, } @article {pmid42269462, year = {2026}, author = {Riveros, A and Kwon, H and Impellitteri, CA and Jiang, D}, title = {Nitrate reshapes electron partitioning and Se[0] formation during continuous electro-microbial treatment of mixed selenium oxyanions.}, journal = {Water research}, volume = {303}, number = {}, pages = {126244}, doi = {10.1016/j.watres.2026.126244}, pmid = {42269462}, issn = {1879-2448}, abstract = {Selenium in flue-gas-desulfurization (FGD) wastewater occurs as mixed selenate and selenite oxyanions, and requires both aqueous removal and reduction to elemental selenium to prevent secondary waste generation. Here, we introduce a continuous-flow electro-microbial platform that couples flow-electrode capacitive deionization (FCDI) with bio-electrochemical systems (BES) to achieve voltage-driven removal and bio-mediated reduction within a compact reactor configuration. During 41 days of operation treating mixed selenium oxyanions (10 mg Se L[-1] each) in fortified water samples with FGD-relevant nitrate concentrations (20 mg L[-1]), the system achieved removal efficiencies of 84-95% for selenite and 54-78% for selenate. Nitrate unexpectedly enhanced apparent elemental selenium yield from 70% to 99% under 2 V, but decreased selenium-specific Faradaic efficiency from 20% to 8%, likely due to a combination of electron flux diversion and co-respiration between nitrogen and selenium oxyanions. Metagenomics suggested that genes associated with indirect selenium transformation (cysIJ, trxA/B, gshA/B, and ybbN) were 45-115x more abundant than genes encoding dedicated selenate reductases. Together, these results demonstrate FCDI-BES as a promising platform for treating selenium and potentially other redox-active oxyanions and highlight the importance of studying electron-acceptor competition in similar systems.}, } @article {pmid42269501, year = {2026}, author = {Ghose, M and Parab, AS and Manohar, CS}, title = {Metagenome-based analysis of xenobiotic degradation potential in urban mangrove sediments under chronic anthropogenic impact.}, journal = {Marine pollution bulletin}, volume = {231}, number = {}, pages = {119970}, doi = {10.1016/j.marpolbul.2026.119970}, pmid = {42269501}, issn = {1879-3363}, abstract = {Urban mangrove sediments receive continuous inputs of industrial and domestic pollutants, yet the microbial basis of pollutant transformation in these chronically impacted systems remains insufficiently resolved. This study investigated xenobiotic degradation potential in sediments from two urban mangrove locations along the Mandovi estuary, Goa, India, through reanalysis of previously generated shotgun metagenomic data. The assembled metagenomes showed enrichment of degradation pathways associated with aromatic and aliphatic pollutants commonly linked to urban contamination. A high representation of oxidoreductases and related aromatic transformation functions indicated that xenobiotic processing is closely linked to redox regulation and central carbon metabolism. Pathway completeness did not consistently correspond with relative abundance, suggesting that lower-abundance pathways may still retain structurally coherent degradation capacity. Hydrocarbon-specific annotation revealed the coexistence of aerobic and anaerobic activation strategies, consistent with adaptation to the redox heterogeneity of mangrove sediments. Xenobiotic- and hydrocarbon-associated functions were linked mainly to Pseudomonadota, Actinomycetota, Shewanella, and a substantial fraction of unresolved bacterial lineages, indicating that undercharacterized taxa may contribute importantly to pollutant-processing potential. Supportive metagenome-assembled genome analysis showed that recovered genomes encoded complementary subsets of degradation functions, although these genomes should be treated as illustrative examples rather than representatives of the whole community. Comparison between locations revealed similar core degradation functions but variation in secondary pathways, likely reflecting differences in local pollutant inputs and sediment conditions. These results show that urban mangrove microbiomes retain a functionally structured and redox-adapted metagenomic repertoire for xenobiotic and hydrocarbon degradation, highlighting their relevance to pollutant transformation, environmental monitoring, and native community-based bioremediation.}, } @article {pmid42269618, year = {2026}, author = {Eriksson, D and Schiller, J and Schickele, A and Priest, T and Mankowski, A and Faucher, E and Ustick, LJ and Kuhn, M and Miravet-Verde, S and Ruscheweyh, HJ and Clerc, C and Gruber, N and Sunagawa, S and Bork, P and Vogt, M}, title = {Variations in the latitudinal diversity gradients of the ocean microbiome.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.05.016}, pmid = {42269618}, issn = {1934-6069}, abstract = {Latitudinal diversity gradients (LDGs), which typically decline from the equator to the poles, are a pervasive macroecological pattern. However, their generality and drivers in the ocean microbiome remain widely unresolved. We integrated global-scale metagenomic data with habitat modeling to study marine microbial LDGs across seasons and depths. Surface mixed-layer microbiomes exhibit diversity peaks at (sub)tropical latitudes and a poleward decline, whereas mesopelagic communities (200-1,000 m) show no latitudinal diversity structuring. Taxonomic resolution reveals that the mixed-layer LDG is underpinned by Alphaproteobacteria and Cyanobacteriia, while other taxa exhibit distinct or contrasting LDGs. Diversity structuring also varies by seasons and regions and is governed by temperature and nutrient availability. Together, these findings highlight that, within the ocean microbiome, LDGs are not universal but reflect lineage-specific ecological strategies and responses to environmental gradients. Our study provides fundamental insights into the structuring of ocean microbiome diversity and lays the foundation for predicting responses to environmental change.}, } @article {pmid42269619, year = {2026}, author = {Guo, Y and Wang, Z and Li, D and Wang, L and Lan, H and Guo, F and Zhao, Z and Liu, Z and Meng, L and Shen, X and Wang, M and Zhao, W and Zhang, W and Kong, C and Shi, L and Sun, Y and Seim, I and Jiang, A and Ma, K and Su, Z and Zhang, N and Ji, Q and Chen, J and Chen, K and Qi, C and Li, B and He, B and Liu, Y and Zhou, J and Zheng, Y and Zhang, H and Wang, Y and Han, M and Yang, T and Tong, J and Zhang, Y and Wang, Z and Xu, X and Chen, J and Liu, Y and Chen, H and Zeng, T and Wei, X and Li, C and Yang, H and Wang, B and Liu, X and Shao, C and Zhang, W and Gu, Y and Xiao, X and Xu, X and Wang, J and Mock, T and Fan, G and Li, Y and Liu, S and Dong, Y}, title = {The genetic repertoire of deep-sea microbiome: From sequence to structure and function.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.05.009}, pmid = {42269619}, issn = {1934-6069}, abstract = {The deep sea, as the largest and maybe most hostile environment on Earth, is still underexplored, especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea microbial genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures and use it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity and substantial structural conservation of proteins. Especially, proteins involved in replication, recombination, and repair were identified as being under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as an evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.}, } @article {pmid42269751, year = {2026}, author = {Sun, X and Li, S and Liang, J and Wang, C and Bai, Y and Mao, J and Qu, J}, title = {From correlation to causality: Identifying potential environmental drivers of pathogenic antibiotic-resistant bacteria in river water using causal machine learning.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {405}, number = {}, pages = {128570}, doi = {10.1016/j.envpol.2026.128570}, pmid = {42269751}, issn = {1873-6424}, abstract = {Pathogenic antibiotic-resistant bacteria (PARB) pose a serious public health threat within the One Health framework, yet identifying their potential environmental drivers in complex aquatic systems remains a challenge. This study systematically compared correlation analysis, explainable machine learning, and causal machine learning within a unified framework. Both Spearman correlation and explainable machine learning identified numerous potentially important factors, notably non-antibiotic pharmaceuticals such as carbamazepine and bezafibrate. However, causal inference via double machine learning, which controls for confounders and interaction effects, revealed a distinctly different driver profile. Under predefined assumptions, this approach estimated potential causal effects for dissolved oxygen, the nitrate-to-ammonium ratio, specific antibiotics (roxithromycin, azithromycin), and non-antibiotic compounds (acenaphthene, 2-chloroanthracene). Taxon-specific analysis further showed that Aeromonas aligned closely with the overall PARB causal profile, whereas Pseudomonas responded primarily to oxidation-reduction potential. Functional profiles suggested potential stress-adaptation mechanisms related to signal transduction and metabolic regulation pathways. By shifting from associative prediction to causal inference, this causal machine learning-guided framework provides a robust analytical basis for identifying environmental drivers and informing targeted management of PARB risks in aquatic ecosystems.}, } @article {pmid42270066, year = {2026}, author = {Shi, H and Wang, L and Wu, Y and Cai, B}, title = {Synergistic mechanisms by which arbuscular mycorrhizal fungi regulate hyphosphere bacterial communities and functional genes to suppress potential N2O production under tetracycline stress.}, journal = {Environmental research}, volume = {305}, number = {Pt 2}, pages = {125020}, doi = {10.1016/j.envres.2026.125020}, pmid = {42270066}, issn = {1096-0953}, abstract = {Tetracycline (TC), a widely used veterinary antibiotic, frequently accumulates in agricultural soils and disrupts nitrogen (N) cycling, thereby enhancing nitrous oxide (N2O) emissions. However, biologically based mitigation strategies and their underlying mechanisms remain poorly understood. In this study, a soybean pot experiment was conducted with four treatments: control, arbuscular mycorrhizal fungi (AMF) inoculation, TC addition, and AMF combined with TC. By integrating hyphosphere-specific sampling, potential N2O production rate measurements, 16S rRNA gene sequencing, quantitative PCR, metagenomics, and partial least squares path modeling, we systematically elucidated AMF-mediated regulation of N2O production under TC stress. TC significantly increased potential N2O production rate (+21.2%), primarily by selectively suppressing the terminal denitrification step, as evidenced by reduced nitrous oxide reductase (NOS) activity and decreased abundance of the nosZ gene, resulting in denitrification pathway disruption and N2O accumulation. In contrast, AMF inoculation under TC stress reduced potential N2O production rate by 29.5%, restoring it to control levels. Mechanistically, AMF improved hyphosphere soil properties (e.g., increased SOC and TN and enhanced TC dissipation) and selectively enriched functionally competent and TC-tolerant denitrifiers, particularly nosZ-harboring taxa such as Streptomyces, thereby repairing denitrification pathway completeness. Path modeling further demonstrated that AMF mitigated N2O production both directly by enhancing N-cycling microbial functional capacity and indirectly by optimizing soil physicochemical conditions. Our findings reveal the microbial and molecular mechanisms underlying antibiotic-enhanced N2O emissions and highlight AMF as a low-input, nature-based environmental biotechnology strategy to simultaneously remediate antibiotic-contaminated soils and mitigate agricultural greenhouse gas emissions.}, } @article {pmid42270094, year = {2026}, author = {Deng, L and Gao, X and Guo, C and Hu, X and Qi, J and Wang, J and Huang, X and Zhang, Y and Hu, Z and Wang, H and Hong, B}, title = {Structural and Functional Alterations of Microbiome in Upper and Lower Respiratory Tract in Patients With NSCLC.}, journal = {Cancer control : journal of the Moffitt Cancer Center}, volume = {33}, number = {}, pages = {10732748261460118}, pmid = {42270094}, issn = {1526-2359}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology/pathology ; *Microbiota ; *Lung Neoplasms/microbiology/pathology ; Bronchoalveolar Lavage Fluid/microbiology ; Female ; Case-Control Studies ; Male ; Sputum/microbiology ; Prospective Studies ; Middle Aged ; *Respiratory System/microbiology ; Bacteria/isolation & purification/genetics ; Aged ; Fungi/isolation & purification ; }, abstract = {IntroductionThe airway microbiome plays a pivotal role in lung cancer development, but the microbiome characteristics in upper and lower respiratory tract of non-small cell lung cancer (NSCLC) patients remains unclear.MethodsThis was a prospective case-control study. The study included 60 samples from NSCLC patients and non-cancer controls: 23 sputum (SP) samples (14 NSCLC, 9 controls) and 37 bronchoalveolar lavage fluid (BALF) samples (21 NSCLC, 16 controls). Metagenomic sequencing was performed to characterize microbial composition and diversity, differential taxa, inter-kingdom networks, and functional profiles for bacteria and fungi.ResultsFor bacterial community, BALF samples from NSCLC tend to show higher alpha diversity than that of non-cancer controls (Shannon p = 0.046, Simpson p = 0.089), whereas SP samples from NSCLC show a trend toward lower alpha diversity (Shannon p = 0.053, Simpson p = 0.033). For fungal community, alpha diversity shows no significant difference between NSCLC and non-cancer groups in either SP (Shannon p = 0.250, Simpson p = 0.480) or BALF (Shannon p = 0.800, Simpson p = 0.700) samples. Beta diversity exhibits differences in bacterial community composition between NSCLC and non-cancer controls in both SP (p = 0.018) and BALF samples (p = 0.015), while fungal communities appear relatively stable (p = 0.611 for SP; p = 0.611 for BALF). LEfSe and Random Forest analyses identify bacterium Porphyromonas SGB2015 and fungus Psilocybe cubensis significantly enriched in BALF samples from NSCLC, whereas no species is enriched in SP samples. Cross-kingdom network indicates increased complexity and connectivity in NSCLC-associated microbial communities. Functional analysis shows the enrichment of biosynthetic pathways in SP samples and metabolic pathways in BALF samples from NSCLC.ConclusionThese findings suggest that NSCLC may be associated with compositional, structural, and functional alterations of the airway microbiome, with potentially distinct patterns between upper and lower respiratory tract.}, } @article {pmid42270219, year = {2026}, author = {Zhang, Z and Zhang, K and Hou, Q and Yang, C and Guo, Z and Li, Y and Wang, C and Wang, Y}, title = {Microbial ecology and flavor formation mechanisms of high-temperature Daqu in the Huang-Huai River basin and adjacent regions: A comparative study from eastern Henan, Jiaodong peninsula, and southern Anhui.}, journal = {Food research international (Ottawa, Ont.)}, volume = {239}, number = {}, pages = {119489}, doi = {10.1016/j.foodres.2026.119489}, pmid = {42270219}, issn = {1873-7145}, mesh = {China ; Fermentation ; *Hot Temperature ; *Microbiota ; *Taste ; *Food Microbiology ; Bacteria/metabolism/classification/genetics ; Rivers ; Flavoring Agents ; *Fermented Foods/microbiology ; }, abstract = {High-temperature Daqu (HTD) serves as a critical fermentation starter for sauce-aroma type Baijiu. Although strong-aroma Baijiu dominates production in the Huang-Huai River Basin and surrounding regions, knowledge regarding the microbial ecology and flavor-forming potential of HTD in this area remains limited. In this study, we collected HTD samples from Eastern Henan, Jiaodong Peninsula (Qingdao), and Southern Anhui, and performed physicochemical analyses, enzyme activity assays, electronic sensory evaluation, and metagenomic sequencing. Significant differences in microbial community structure were observed among the three regions. Nevertheless, Kroppenstedtia eburnea, Aspergillus chevalieri, and Aspergillus oryzae were consistently dominant across all sites. Compared with the other two regions, HTD from Qingdao showed markedly higher abundances of Bacillus velezensis, Bacillus licheniformis, and Bacillus amyloliquefaciens. However, the overall relative abundance of Bacillus spp. in the Huang-Huai region was lower than that typically reported in HTD from Hubei and Guizhou provinces. Physicochemical factors, particularly density and acidity, were the primary drivers of microbial community heterogeneity and flavor profile variation across regions. Metagenomic analysis revealed a relatively complete dimethylpyrazine synthesis pathway in Qingdao Daqu, whereas the other two regions appeared to depend more on multi-species cooperation. Limosilactobacillus fermentum, enriched in Qingdao samples, harbored key acetoin synthesis genes and showed strong potential for tetramethylpyrazine (TTMP) precursor accumulation. Additionally, gene-potential profiling identified Pichia kudriavzevii as the main candidate for higher alcohol production. Subsequent validation confirmed that isolated P. kudriavzevii strains produced 2-phenylethanol, a key bitter volatile compound in sauce-flavor Baijiu. These results elucidate the regional microbial mechanisms underlying flavor formation in HTD for sauce-aroma Baijiu production in the Huang-Huai River Basin and adjacent areas, providing a theoretical basis for targeted starter culture improvement.}, } @article {pmid42270261, year = {2026}, author = {Vandana, and Gupta, S and Sharma, R and Pandey, A and Bishnoi, M and Rawal, R and Das, S and Singh, DP}, title = {Polyphenols-rich Indian barberry berries extract alleviates inorganic arsenic exposure-induced cognitive impairments and associated gut microflora alterations.}, journal = {Food research international (Ottawa, Ont.)}, volume = {239}, number = {}, pages = {119548}, doi = {10.1016/j.foodres.2026.119548}, pmid = {42270261}, issn = {1873-7145}, mesh = {Animals ; *Polyphenols/pharmacology ; *Plant Extracts/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Fruit/chemistry ; *Cognitive Dysfunction/chemically induced/prevention & control/drug therapy ; *Arsenic/toxicity ; Male ; *Rubus/chemistry ; Oxidative Stress/drug effects ; Antioxidants/pharmacology ; Disease Models, Animal ; }, abstract = {Arsenic, a globally prevalent environmental toxin that can lead to neuro-behavioural changes. Oxidative stress and activation of inflammatory cascades are prominent mechanisms underlying these effects. The present study investigated the effects of polyphenol-rich extracts from Berberis aristata (Indian barberry) against inorganic arsenic-induced cognitive impairments in a murine model and presented mechanistic insights into its functional food properties. Response Surface Methodology (RSM)-guided hydro-alcoholic extracts were prepared and chemically characterized for their antioxidant activity, total phenolic contents (TPC) and free radical scavenging activities (RSA). UHPLC and LC-MS-based profiling of polyphenols, anthocyanins, and proanthocyanidins was performed. In-vitro toxicity studies in hepatic and colonic cancer cell lines, followed by in-vivo evaluation of these extracts in inorganic arsenic-exposed mice for spatial navigation tasks and passive avoidance-based learning were performed. Further assessments included neurotransmitter levels, histopathological investigations, qRT-PCR-based gene expression analysis, inflammatory cytokines and oxido-nitrosative stress markers in the brain and gastrointestinal tract, Evan's blue dye-based ileum permeability, and short chain fatty acids (SCFAs) estimation, along with Oxford Nanopore-based 16S rRNA metagenomics in cecal contents and PICRUSt2-based functional prediction of metagenomic data. RSM-optimized methods for polyphenol extraction yielded extracts with high TPC and RSA, with flavanols, phenolic acids, and proanthocyanidins identified as major polyphenols, and no in-vitro toxicity was observed. The extracts significantly prevented arsenic exposure-induced cognitive impairment, altered neurotransmitter turnover, neuroinflammation and gastrointestinal tract inflammation, oxidative stress-induced damage, increased ileum permeability, SCFA alteration, and gut microbial dysbiosis. These findings underscore the therapeutic/preventive potential of this polyphenol-rich extract against environmental toxicant-induced neurotoxicity, potentially involving gut microbiota-associated pathways.}, } @article {pmid42270391, year = {2026}, author = {Nakaya, Y and Hashimoto, K and Fukushima, K and Fatimah, M and Matsumoto, Y and Funauchi, A and Tsukaguchi, A and Yamauchi, K and Miyazaki, A and Iwahashi, Y and Tone, M and Naito, M and Shiroyama, T and Hirata, H and Takeda, Y and Nakamura, S and Kumanogoh, A}, title = {Mycobacterium brisbanense Pulmonary Disease Treated with a Macrolide-Based Multidrug Regimen: A Case Report.}, journal = {Internal medicine (Tokyo, Japan)}, volume = {}, number = {}, pages = {}, doi = {10.2169/internalmedicine.7351-26}, pmid = {42270391}, issn = {1349-7235}, abstract = {A 73-year-old woman with a history of tracheostomy for tracheomalacia and bronchiectasis developed a worsening productive cough with progressive nodular/bronchocentric opacities on computed tomography. She was diagnosed with Mycobacterium brisbanense pulmonary disease based on repeated sputum culture results. Antimicrobial susceptibility testing revealed a low minimum inhibitory concentration for clarithromycin, and whole-genome sequencing confirmed the absence of the erm gene. Owing to repeated smear positivity and clinical progression, macrolide-based multidrug therapy was initiated, resulting in both clinical and radiographic improvements. To our knowledge, this is the first reported case of M. brisbanense pulmonary disease in Japan, thus highlighting its potential pathogenicity.}, } @article {pmid42270613, year = {2026}, author = {Deng, C and Cai, H and Luo, K and Liu, S and Chen, Q and Sun, W and Ni, J}, title = {Nitrate-reducing bacteria bridge nitrogen cycling and antibiotic resistance in river ecosystems.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74161-2}, pmid = {42270613}, issn = {2041-1723}, support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {River ecosystems, crucial components of the global nitrogen cycle, are increasingly affected by antibiotic pollution. However, the mechanistic interplay between nitrogen cycling and antibiotic resistance genes (ARGs) dissemination remains poorly understood, limiting effective ecological risk assessments. Here, we identify nitrate-reducing bacteria (NRBs), key drivers of denitrification and greenhouse gas mitigation, as dual-functional hubs that co-regulate nitrogen turnover and ARG dissemination under antibiotic stress. By integrating 173 metagenomes and 10 metatranscriptomes from the Yangtze River, we reconstruct 4200 metagenome-assembled genomes (MAGs) and find that NRBs harbor ~69% of actively transcribed ARGs in river microbiomes, with antibiotic pressure as the dominant ecological driver. Simulated microcosms exposed to antibiotic gradients reveal a hormetic response, where environmentally relevant concentrations enhanced both NRB-driven denitrification efficiency and ARG dissemination. Multi-omics analyses further reveal antibiotic-driven horizontal gene transfer as the predominant selective force co-shaping ARG and nitrate reduction gene dynamics, accelerating both nitrogen cycling and ARG spread. These findings establish NRBs as central hubs bridging antibiotic resistance and nitrogen metabolism, providing a mechanistic framework for predicting co-selection dynamics and mitigating cascading ecological impacts. Our work highlights the need to integrate microbial co-metabolic functions into pollution control strategies and redefine ecological risk assessments in antibiotic-polluted ecosystems.}, } @article {pmid42270686, year = {2026}, author = {Lee, S and Lee, H and Kim, JW and Kim, HJ and Lee, KJ}, title = {Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53382-x}, pmid = {42270686}, issn = {2045-2322}, abstract = {Objective evaluation of sequencing resolution is crucial for comparing technologies and ensuring reproducibility in microbiome analysis. Specifically, a systematic approach is necessary to quantitatively assess the effect of various platforms and experimental conditions on species-level resolution. Therefore, this study quantitatively evaluated multiple strategies, including 16S V3-V4 (16P), full-length 16S rRNA gene (16F), and whole metagenome shotgun sequencing (WMS), using a commercial DNA-based mock community (MC) and a domestically developed whole-cell MC (Korea MC [KMC]). The WMS strategy included 12 combinations of input DNA concentrations and sequencing output levels. A total of 64 WMS libraries were constructed for KMC samples, and 112 sequencing datasets were analysed. Taxonomic resolution was assessed using an adjusted F1-score integrating detection sensitivity and abundance-level reproducibility. Qualitatively examining the detected species against the expected species across platforms, WMS showed a true positive abundance ratio of over 90%, 16F was observed to have an average of 60%, and 16P was observed to have an average of less than 10%. The combination of 10 ng input and 10 gigabases output consistently yielded the highest species-level resolution. However, reduced performance was observed in some MCs under 1 ng or 100 ng DNA input conditions. Detection sensitivity varied by taxon and condition. Specifically, Streptococcus pneumoniae and Cryptococcus neoformans were detected only under high-input or -output conditions, whereas Escherichia coli exhibited optimal accuracy at intermediate inputs. Acinetobacter species demonstrated reduced resolution as input DNA increased. KMC samples showed species- and format-specific variability in DNA extraction efficiency. This study presents a quantitative evaluation of species-level resolution across sequencing conditions using defined mock communities. The results highlight how sequencing configuration and taxon-specific characteristics can influence detection performance and provide insights for interpreting microbiome sequencing results under different experimental conditions.}, } @article {pmid42271018, year = {2026}, author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG}, title = {Disruption of the spinal cord-gut axis alters microbial dynamics and carbohydrate cross-feeding in the gut.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10447-x}, pmid = {42271018}, issn = {2399-3642}, support = {890085//Craig H. Neilsen Foundation (Neilsen Foundation)/ ; ABI#2149505//National Science Foundation (NSF)/ ; DBI#2022070//National Science Foundation (NSF)/ ; }, abstract = {Spinal cord-gut communication regulates gut bacteria, yet the underlying mechanisms remain poorly understood. Previous studies relied primarily on gene markers with limited functional analysis or genome-resolved snapshots from small cohorts. Here, we assessed microbiome dynamics via genome-resolved metagenomics on 333 samples from male and female C57BL/6 mice collected before and up to six months after surgical disruption of the spinal cord-gut axis. This resulted in 6,635 microbial draft genomes as a foundation for a new "Mouse B6 Gut Catalog" that significantly expands species and strain representation for this widely used laboratory mouse strain. Sampling revealed that disrupted spinal cord-gut signaling causes persistent, lesion-severity-, sex-, and time-specific shifts in microbial community composition, with consistent depletion of Lactobacillus johnsonii. Feeding purified L. johnsonii to spinal cord-injured mice prevented metabolic defects and systemic inflammation caused by disruption of the spinal cord-gut axis. Analyses using genome-resolved and community-based metabolic profiling indicated altered carbohydrate sharing and utilization of gut microbes, potentially depleting L. johnsonii, providing a genome-inferred mechanism for future hypothesis testing. This study improves murine microbiome catalogs, illustrates how metagenome-informed microbial interventions can provide a mechanistic understanding to improve host health, and underscores the vital role of a healthy spinal cord in regulating gut ecosystem function.}, } @article {pmid42271211, year = {2026}, author = {Ying, K and Song, X and Chen, J and Wang, Y and Wu, H and Zhang, Q and Yang, X and Peng, W and Wu, H and Zhang, W and Zhang, Q}, title = {Metagenomic characterization and genetic profiling of hepatic viromes in Marmota himalayana from the Three-River-Source region of Qinghai Province.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05231-0}, pmid = {42271211}, issn = {1471-2180}, support = {2024-SF-124//the Key research and development and transformation plan of Qinghai Province/ ; 2023YFD1801300//the National Key Research and Development Program of China/ ; }, abstract = {The Himalayan marmot (Marmota himalayana) is a keystone species in the Tibetan Plateau ecosystem and serves as a potential reservoir host for multiple zoonotic pathogens. To characterize its hepatic virome, this study conducted a systematic analysis of 70 marmot liver samples collected from the Three-River-Source Region in Qinghai Province using viral metagenomics. We identified more than 60 viral species belonging to 13 families. The species accumulation curve indicated that the sequencing effort captured the majority of the viral diversity present. Community analysis revealed that the family Retroviridae was the dominant viral group across all samples, though significant heterogeneity was observed among geographically distinct populations. Specifically, the relative abundance of Anelloviridae was markedly higher in the Chengduo group, whereas Parvoviridae exhibited exceptionally high library-specific enrichment in specific libraries. Furthermore, the study successfully assembled complete or near-complete genomic sequences of multiple strains belonging to the families Polyomaviridae, Anelloviridae, and Parvoviridae. Phylogenetic analysis demonstrated that these newly identified viral strains were most closely related to known marmot-origin viruses, clustering within distinct, host-specific evolutionary clades. This clustering pattern indicating host-associated of the viruses with their marmot hosts. Previous virome studies in marmots have primarily focused on the gut, peripheral blood, and other extrahepatic tissues, with no systematic viral metagenomic profiling of the liver in this species to date. The findings offer crucial scientific insights for the early warning and control of wildlife-origin diseases on the Tibetan Plateau.}, } @article {pmid42271238, year = {2026}, author = {Bi, JG and Wang, YH and Li, PK and Liu, Q and Zheng, X}, title = {Metagenomic insights into regional gut microbiota variation of invasive Spodoptera frugiperda across the Gaoligong Mountains.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05259-2}, pmid = {42271238}, issn = {1471-2180}, support = {202102AA310055//the Supported by the Major Science and Technique Programs of Yunnan Province/ ; YNWRQNBJ2020101//the Young Top Talents of the High-level Talents Training Support Program in Yunnan Province/ ; 202305AM340031//the Lower Nu River, Mountain Agroecosystem, Observation and Research Station of Yunnan Province/ ; 2026J1054//the Yunnan Provincial Department of Education Science Research Fund Project/ ; }, abstract = {BACKGROUND: The invasive pest Spodoptera frugiperda poses a potential threat to the ecological security of western Yunnan, using the Gaoligong Mountains as an important cross-border corridor and overwintering site. However, the potential role of gut microbiota in the local adaptation of S. frugiperda during its invasion remains poorly understood.

METHODS: Adult populations were monitored using sex pheromone traps, and metagenomic sequencing was performed on larval gut microbiota from different regions of the Gaoligong Mountains. The gut microbial composition and functional potential were analyzed, with specific focus on the microbial traits potentially associated with host adaptation and invasion.

RESULTS: S. frugiperda populations persisted year-round in the Gaoligong Mountains, with adult activity peaking from January to May. Microbial diversity was highest in southern samples. Enterococcus, typically dominant in S. frugiperda, displayed low abundance in the central and northern regions. In contrast, Providencia emerged as the dominant genus specifically at the Pianma site (PM, along the China-Myanmar border), where the gut microbiota exhibited higher abundance of site-specific functional genes compared to other regions. These genes encoded proteins including type 1 subunit membrane proteins and outer membrane-targeting proteins. Additionally, the PM samples showed a higher relative abundance of genes K07345, K07347, and K15125. Functional annotation highlighted a strong potential for vancomycin degradation and an enrichment of diverse antimicrobial resistance-associated genes, with adeL being the most abundant.

CONCLUSIONS: These findings suggest that the PM area may represent an important gateway or a priority monitoring site for the transboundary invasion of S. frugiperda, underscoring the urgency of strengthening local management of invasive pests.}, } @article {pmid42271362, year = {2026}, author = {Zhang, Z and Lu, T and Dong, B and Liu, J and Zhang, Y and Li, S and Liu, H and Li, X and Guan, T and Guo, H and Yan, Q and Lei, Z and Yu, X and Wang, L and Kang, J and Li, L and Zhao, D}, title = {Gut fungal signatures in colorectal cancer and their potential for supporting diagnosis: a multi-cohort metagenomic analysis.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {42271362}, issn = {1479-5876}, support = {82370563//National Natural Science Foundation of China/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; *Metagenomics ; *Fungi/genetics ; Cohort Studies ; *Gastrointestinal Microbiome/genetics ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is influenced by host factors and environmental exposures that shape gut microbial ecosystems. Although bacterial and viral alterations in CRC have been widely investigated, the role of gut fungi remains underexplored, partly because of their low biomass and the limited availability of well-curated fungal reference genomes.

METHODS: We conducted a large-scale metagenomic analysis across 9 publicly available cohorts comprising 1,433 fecal samples to characterize CRC-associated fungal alterations and fungal-bacterial co-abundance patterns. The predictive value of microbial signatures was assessed using LASSO and random forest models, with external validation performed in 6 independent cohorts comprising 272 samples.

RESULTS: Multi-cohort analysis revealed CRC-associated alterations in gut fungal community structure and selected diversity measures. Differential abundance analysis identified 15 fungal species with recurrent changes across cohorts. Among them, Saccharomyces cerevisiae c86 and Trichophyton rubrum c61 showed predominant enrichment in healthy controls, whereas Barnettozyma c122 and Pseudopithomyces c302 showed predominant enrichment in CRC. Fungal-only models exhibited limited standalone predictive capacity. However, integrating fungal features with bacterial biomarkers modestly improved CRC prediction performance compared with bacterial-only models. In external validation, the random forest-based fungal-bacterial model increased the mean AUC from 0.722 to 0.762, with improved AUCs in 5 of the 6 validation cohorts.

CONCLUSIONS: This study suggests that CRC is associated with gut fungal dysbiosis and supports the exploratory value of gut fungal signatures as adjunctive features in microbiome-based CRC prediction models. These findings highlight the importance of incorporating fungal communities into CRC microbiome research while emphasizing the need for prospective and mechanistic validation.}, } @article {pmid42271421, year = {2026}, author = {Stanford, J and Supple, H and Collins, CE and Clarke, ED}, title = {Associations between diet, metabolome, gut microbiota and blood pressure in Australian adults.}, journal = {Nutrition journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12937-026-01336-4}, pmid = {42271421}, issn = {1475-2891}, abstract = {PURPOSE: Early metabolomic and microbial markers of blood pressure (BP) dysregulation may be detectable before clinical hypertension develops. This exploratory study aimed to examine associations among dietary intake, BP, metabolomic profiles (plasma and urine), and gut microbiota composition. A secondary aim was to assess whether circulating metabolites mediate relationships between significant dietary factors and BP.

METHOD: This was a cross-sectional analysis of baseline data from a randomised cross-over trial. Usual dietary intake was assessed using the Australian Eating Survey (AES)[®] - Heart version Food Frequency Questionnaire. In-clinic BP measurements were measured and participants provided plasma, urine, and stool samples. Plasma and urine were analysed via untargeted metabolomics. Stool samples were collected for shotgun metagenomic sequencing, though metagenomic data was not included in this analysis. Associations between BP, individual metabolites, microbial taxa, and alpha diversity were assessed using linear regression with false discovery rate (FDR) correction. Causal mediation analysis was performed using nonparametric bootstrapping.

RESULT: Thirty-four Australian adults (mean age: 38.4 ± 18.1 years; 52.9% female) had complete data at baseline. Nut intake (servings/day and % energy) was the only dietary factor significantly associated with systolic BP (SBP), with higher intake linked to a 1.13 mmHg reduction. Twenty-nine plasma lipid metabolites were significantly associated with SBP after FDR correction. Of these, nine lipid-related metabolites, particularly 1,2-dilinoleoyl-GPC (18:2/18:2) and 1-linoleoyl-GPC (18:2), were observed to partially mediate the nut-SBP relationship. No urinary metabolites or microbial taxa were significantly associated with BP.

CONCLUSIONS: In this exploratory cross-sectional study, specific lipid metabolites were associated with SBP and partly accounted for the nut-SBP association. These hypothesis-generating findings suggest potential biomarkers of nut intake and BP regulation, warranting confirmation in larger longitudinal, interventional, and mechanistic studies.

TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (Registration number ACTRN12622001321730, Registration date 12/10/2022).}, } @article {pmid42271469, year = {2026}, author = {Xing, J and Jiang, Z and Jing, X and Li, Y and Guo, F and Liu, P and Liu, Z and Sun, N}, title = {Analysis of gut microbiota and intestinal mucosal neurotransmitter changes and their correlation in adolescent depression mice.}, journal = {Annals of general psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12991-026-00686-x}, pmid = {42271469}, issn = {1744-859X}, abstract = {BACKGROUND: Adolescent depression is a major mental health disorder with increasing prevalence and substantial long-term consequences. Although growing evidence suggests that the gut-brain axis is involved in depression, the relationships among gut microbiota, intestinal mucosal neurotransmitters, and adolescent depression remain insufficiently understood. This knowledge gap limits a better understanding of the pathophysiological mechanisms underlying adolescent depression and the identification of potential microbiota-related targets. Therefore, this study aimed to investigate alterations in gut microbiota and intestinal mucosal neurotransmitters, as well as their correlations, in an adolescent mouse model of depression.

METHODS: We established an adolescent depression mouse model using chronic unpredictable mild stress (CUMS), and collected data with the Smart video tracking system. We collected intestinal contents and mucosal tissues from mice. We analyzed gut microbial composition using metagenomic sequencing and quantified mucosal neurotransmitters with liquid chromatography-tandem mass spectrometry (LC-MS/MS). We analyzed correlations among gut microbiota, intestinal mucosal neurotransmitters, and behavioral indicators.

RESULTS: Mice in the CUMS group exhibited a significantly reduced sucrose preference rate in the sucrose preference test (P < 0.001); a significantly prolonged immobility time in the forced swim test (P < 0.01); and a significantly decreased total movement distance in the open field test (P < 0.01). No significant intergroup difference was observed in the tail suspension test. Regarding the gut microbiome, the CUMS group showed significantly lower Simpson index (P = 0.018) and Pielou's evenness index (P = 0.022). Beta diversity analysis indicated a statistically significant but modest between-group difference in community structure (ANOSIM R = 0.145, P = 0.03); this finding was supported by PERMANOVA (Bray-Curtis; pseudo-F = 1.675, R² = 0.0897, P = 0.033). LEfSe (Linear discriminant analysis Effect Size) analysis suggested 27 candidate taxa with discriminatory signals between groups (nominal P < 0.05; exploratory). Neurotransmitter analysis demonstrated that levels of 5-HIAA (5-hydroxyindoleacetic acid), 5-HT (serotonin), 5-HTP (5-hydroxytryptophan), and Kyn (kynurenine) in the colon were significantly decreased in the CUMS group, whereas levels of PA (phenylethylamine) and NE (norepinephrine) were significantly elevated (P < 0.05). Spearman correlation analysis found that Lactobacillus and Lactobacillus acidophilus correlated positively with sucrose preference and negatively with immobility in the forced swim test. Lactobacillus acidophilus also showed a positive correlation with 5-HT pathway metabolites: 5-HIAA, 5-HT, 5-HTP, and Kyn.

CONCLUSION: Adolescent mice exposed to CUMS showed depression-relevant behavioral alterations, shifts in gut microbiota composition, and changes in 5-HT pathway metabolites. Gut microbiota dysbiosis was significantly associated with alterations in 5-HT pathway metabolites. Because this study is correlational, causal relationships require validation in future interventional studies.}, } @article {pmid42271556, year = {2026}, author = {Kaushik, S and Borck, J and Flatow, E and Frishman, WH and Aronow, WS}, title = {Blood Culture-Negative Infective Endocarditis: A Review.}, journal = {Cardiology in review}, volume = {}, number = {}, pages = {}, pmid = {42271556}, issn = {1538-4683}, abstract = {Blood culture-negative infective endocarditis (BCNIE) represents a diagnostically challenging subset of infective endocarditis in which routine blood cultures remain negative despite fulfillment of Duke-ISCVID diagnostic criteria. BCNIE arises primarily from prior antibiotic exposure, infection with fastidious or nonculturable organisms, or noninfectious conditions that mimic endocarditis. Common fastidious pathogens include Coxiella burnetii, Bartonella species, Brucella species, Tropheryma whipplei, fungi, and nutritionally variant streptococci. Because delayed pathogen identification may postpone targeted therapy, BCNIE is associated with increased diagnostic complexity and substantial morbidity and mortality. Modern evaluation relies on a multimodal strategy integrating serologic testing, prolonged culture incubation, histopathology, advanced molecular diagnostics, and multimodality imaging. Emerging molecular techniques, including 16S/18S polymerase chain reaction and metagenomic next-generation sequencing, have significantly improved microbiologic yield, particularly from excised valve tissue, and are now incorporated into updated Duke-ISCVID criteria. Echocardiography remains central to diagnosis, while cardiac computer tomography and 18 fluoro-2-deoxy-D-glucose positron emission tomography/computer tomography provide complementary value in prosthetic valve disease and detection of periannular complications. Management requires empiric antimicrobial therapy followed by organism-directed treatment once a pathogen is identified, with surgery frequently necessary for heart failure, uncontrolled infection, fungal disease, or structural complications. Multidisciplinary endocarditis teams are increasingly recognized as essential to optimizing outcomes in this complex disease process.}, } @article {pmid42271557, year = {2026}, author = {Wassel, MA and Makabe-Kobayashi, Y and Iqbal, MM and Huang, C and Amano, M and Shimizu, A and Mandario, MAE and Takatani, T and Sakakura, Y and Hamasaki, K}, title = {Tetrodotoxin (TTX) reshapes the functional potential of the gut microbiome in juvenile tiger pufferfish (Takifugu rubripes) across salinity gradients.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42271557}, issn = {2524-4671}, support = {22K05822 and 25K09271//JSPS KAKENHI/ ; No. JURCAOSIRG23-08//Interdisciplinary Collaborative Research Program of the Atmosphere and Ocean Research Institute, The University of Tokyo/ ; }, abstract = {BACKGROUND: The gut microbiota of aquatic organisms responds dynamically to environmental stressors such as salinity fluctuations. However, how microbial communities respond to combined environmental and dietary stressors, and how these interactions influence functional potential, remains incompletely understood. Here, we investigated whether dietary administration of tetrodotoxin (TTX), a neurotoxin naturally accumulated by juvenile tiger pufferfish (Takifugu rubripes), alters gut bacterial community composition and functional potential across salinity gradients.

RESULTS: Juvenile T. rubripes were reared under four salinity conditions (34.0, 17.0, 8.5, and 2.1 ppt) and fed either a control or TTX-containing diet (1.22 MU/g). Integrated 16S rRNA gene amplicon and shotgun metagenomic analyses revealed that salinity was the primary driver of gut microbiota structure, with only 5.1% of amplicon sequence variants (ASVs) shared across salinity levels. In contrast, TTX ingestion induced salinity-dependent shifts in specific bacterial taxa rather than broad community restructuring. Core taxa, including Arcobacteraceae, Mycoplasma, Brevinema, and Vibrio, were consistently detected across treatments but exhibited pronounced changes in relative abundance and functional potential under salinity and toxin stress. Metagenomic profiling indicated that Arcobacteraceae encode genetic modules for amino acid and B vitamin biosynthesis that are absent or incomplete in the host genome, suggesting metabolic complementarity. TTX ingestion reduced the genetic representation of these biosynthetic pathways at specific salinities, particularly those associated with Arcobacteraceae. Conversely, phenylalanine biosynthesis potential enriched in TTX-fed fish, primarily associated with Vibrio spp., indicating a possible microbial functional adaptation to toxin administration. Despite these microbiome and functional shifts, TTX ingestion did not affect host growth.

CONCLUSIONS: Dietary neurotoxin administration reshaped gut microbiome functional profiles in a salinity-dependent manner, highlighting microbiome plasticity and improving our understanding of host-microbiota-environment interactions relevant to aquaculture health management.}, } @article {pmid42271572, year = {2026}, author = {Peugnet, G and Pisapia, C and Ménez, B and Watkinson, M and Lecourt, L and Peugnet, N and Bouchez, J and Bruxelles, L and Gérard, E}, title = {Ghost-rocks' microbiota: metagenomic insights into their influence on the biogeochemistry of karstic cave and groundwater.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {6}, pages = {}, pmid = {42271572}, issn = {1574-6941}, support = {//CNRS/ ; ANR-24-CE01-6539-01//French National Research Agency/ ; }, mesh = {*Groundwater/microbiology/chemistry ; *Caves/microbiology/chemistry ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics ; South Africa ; *Geologic Sediments/microbiology ; Metagenome ; Oxidation-Reduction ; }, abstract = {Microbial communities in the critical zone drive key geochemical processes, but many subsurface habitats remain poorly characterized. Ghost-rock karst systems in particular represent unexplored microbial niches. Here, we provide the first genome-resolved metagenomic comparison of ghost-rock and groundwater microbial communities from the Sterkfontein karst system (South Africa). Ghost-rock and groundwater communities host distinct taxonomic and metabolic assemblages. Groundwater communities are dominated by chemolithotrophs capable of oxidizing sulfur- and nitrogen-bearing compounds, and by heterotrophs degrading refractory, plant-derived organic matter. In contrast, primary producers in ghost-rocks likely rely on atmospheric chemosynthesis via trace gas oxidation, while glycogen metabolism and necromass recycling point to adaptations to oligotrophic and fluctuating hydrological conditions. Groundwater taxa with metal-interacting pathways may initiate bedrock colonization via metal oxidation, whereas ghost-rock communities include potential metal reducers that could drive iron and manganese oxide dissolution and influence trace element mobility. Together, these results underscore ghost-rocks as active microbial and geochemical hot spots within karst systems that may play a non-negligible role on biomineralization/bioweathering processes and on shaping (sub)terrestrial landscapes and global biogeochemical cycles.}, } @article {pmid42272236, year = {2026}, author = {van der Meulen, LWJ and Bergmans, ME and Assil, S and Klarenbeek, N and de Kam, ML and Tibboel, AJ and Brach, T and Herpers, BL and Frieling, J and de Jong, V and Freyee, B and van Doorn, MBA and Rissmann, R and Niemeyer-van der Kolk, T}, title = {S. aureus colonization and clinical symptoms remain stable upon topical XZ.700 treatment: Results of a double-blind randomized clinical trial in patients with mild to moderate atopic dermatitis.}, journal = {British journal of clinical pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1002/bcp.70630}, pmid = {42272236}, issn = {1365-2125}, support = {//Micreos Human Health B.V./ ; }, abstract = {AIM: Recovering dysbiosis may improve atopic dermatitis (AD) symptoms. XZ.700 is a recombinant chimeric endolysin that specifically targets Staphylococcus aureus and could be a new treatment option for patients with AD. The aim of this first-in-human study was to evaluate the safety, tolerability and efficacy of topical XZ.700 and explore the pharmacodynamic effects in patients with mild to moderate AD.

METHOD AND MATERIALS: This study consisted of Part A and Part B. In Part A, subjects were randomized and received XZ.700 10 μg/g, XZ.700 30 μg/g, XZ.700 100 μg/g or vehicle twice daily for 7 days on nonlesional skin and on all lesions (1% ≤ BSA ≤ 10%). In Part B, subjects received XZ.700 100 μg/g or vehicle on all lesions twice daily for 14 days (1% ≤ BSA ≤ 15%). Clinical scores and patient-reported outcomes were recorded. Pharmacodynamic measurements were taken.

RESULTS: In total, 35 patients completed the study. Tolerability of XZ.700 was acceptable. XZ.700 100 μg/g showed no evidence of effect on cultured S. aureus (estimated difference -52.9% CFU/mL; 95% CI -88.4% to 90.8%), oSCORAD (1.03; 95% CI -5.20 to 7.26) or EASI (-0.534; 95% CI -2.48 to 1.41). Furthermore, XZ.700 treatment did not result in a significant reduction in the relative abundance of S. aureus via metagenomics or other pharmacodynamic outcomes.

CONCLUSION: Tolerability and safety of short-term topical administration of XZ.700 100 μg/g for 14 days were acceptable in most participants; however, some local application-site events occurred, and one hypersensitivity reaction led to discontinuation. XZ.700 did not demonstrate target engagement or clinical benefit vs. vehicle under the tested conditions.}, } @article {pmid42272618, year = {2026}, author = {Top, FK and Boussiengui, LG and Sall, NC and Faye, M}, title = {First identification of Molluscum contagiosum poxvirus from human in Senegal.}, journal = {Journal of public health in Africa}, volume = {17}, number = {1}, pages = {1586}, pmid = {42272618}, issn = {2038-9922}, abstract = {Herein, we report on the first identification of a human case of Molluscum contagiosum virus (MOCV) in Senegal. In 2024, a male child living in Diamniadio, Dakar region, with no history of travel, tested positive for MOCV. The aetiology was identified using metagenomic sequencing in the framework of the ongoing preparedness activities for the 2024 mpox public health emergency of international concern (PHEIC). Given the overlapping clinical features of MOCV infection and mpox, further research on MOCV is warranted in the West African region, particularly in the current context of high mpox circulation.}, } @article {pmid42272701, year = {2026}, author = {Luo, L and Guo, Z and Chen, W and Zheng, Y and Chen, C and Li, Q and Wang, N and Ji, Y and Hua, J}, title = {Mycobacterium abscessus infection in a young man with cystic fibrosis: a case report and literature review.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1737211}, pmid = {42272701}, issn = {2296-2360}, abstract = {BACKGROUND: Cystic fibrosis (CF) is a rare autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Although relatively common in Caucasian populations, CF is rare in China, where it frequently presents with non-specific respiratory symptoms, leading to delayed diagnosis and frequent coinfections with multidrug-resistant pathogens.

CASE REPORT: A 21-year-old man presented with a 6-year history of recurrent productive cough and intermittent fever over the past 6 months. Imaging revealed bronchiectasis with evidence of infection. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid identified Staphylococcus aureus and Mycobacterium abscessus. Further investigations revealed pancreatic lipomatosis, congenital absence of seminal vesicles, and fat-soluble vitamin deficiencies. CF diagnosis was confirmed by elevated sweat chloride concentration (88 mmol/L) and biallelic CFTR mutations. Clinical stability was achieved through a quadruple antimycobacterial regimen (linezolid, moxifloxacin, azithromycin, and minocycline) combined with systemic supportive care. CFTR modulator therapy was deferred due to limited access and financial constraints.

CONCLUSION: We report a case of CF in a Chinese patient presenting with nontuberculous mycobacterial infection, a condition rarely documented in East Asian populations. We provide a review of the relevant literature, aiming to emphasize the importance of early recognition of CF, personalized antimicrobial strategies, and improved access to essential medications.}, } @article {pmid42272754, year = {2026}, author = {Wu, H and Shi, L and Wang, C and Liang, Y and Huang, C}, title = {Integrative metagenomic and metabolomic analysis reveals a gut microbiota-metabolite-immune axis in pediatric allergic rhinitis with functional constipation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779298}, pmid = {42272754}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; *Metabolomics ; *Constipation/microbiology/immunology/metabolism/complications ; *Gastrointestinal Microbiome/genetics ; *Rhinitis, Allergic/microbiology/immunology/metabolism/complications ; Child ; Female ; Feces/microbiology ; Male ; Amino Acids/metabolism ; Multiomics ; Bacteria/classification/genetics ; Metabolome ; }, abstract = {OBJECTIVE: This study aimed to delineate the alterations in the gut microbiome and host amino acid metabolism in children with comorbid allergic rhinitis and functional constipation (ARFC), and to explore their links with clinical allergy markers.

METHODS: We performed shotgun metagenomic sequencing and amino acid-targeted metabolomics on fecal samples from 19 children with ARFC and 16 age-matched healthy controls (HC). Microbial community structure, differentially abundant taxa, and metabolic profiles were analyzed. Integrative analyzes, including correlation networks and machine learning modeling, were employed to investigate microbiota-metabolite-host interactions.

RESULTS: Significant beta-diversity distinction was found between ARFC and HC gut microbiota (PCoA R[2]=0.228, P = 0.001). ARFC children exhibited enrichment of mucin-degrading Bacteroidota (e.g., Bacteroides, Phocaeicola) and depletion of beneficial Bacillota (e.g., Bifidobacterium, Blautia). Metabolomics identified 50 differentially abundant metabolites, with widespread downregulation of immunomodulatory amino acids including L-glutamine and γ-aminobutyric acid (GABA). Enriched pathways involved mTOR and FoxO signaling, and neurotransmitter synapses. Integration revealed significant correlations between specific microbial genera (e.g., Bacteroides, Proteus) and metabolites (e.g., kynurenine), and between gut species (e.g., Bacteroides thetaiotaomicron) and serum IgE levels. A machine learning model integrating key microbial and metabolic features, evaluated under a rigorous leave-one-out cross-validation framework, demonstrated robust discriminative performance in this cohort (AUC = 0.946).

CONCLUSION: This multi-omics study unveils a distinct "gut dysbiosis-metabolite dysregulation-immune dysfunction" axis in ARFC children. The synergistic shift towards a mucolytic, pro-inflammatory microbiota alongside deficient immunomodulatory metabolite production, which correlates with clinical allergy markers, provides a novel mechanistic framework for this comorbidity and highlights potential diagnostic biomarkers for future validation.}, } @article {pmid42272841, year = {2026}, author = {Qiu, X and Qiang, L and Wang, Y and Li, B and Lei, Z and Wang, J}, title = {Triptolide clears Staphylococcus aureus infection by targeting XIAP to induce host apoptosis while maintaining gut microbiota homeostasis.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1834558}, pmid = {42272841}, issn = {1663-9812}, abstract = {BACKGROUND: Staphylococcus aureus (SA) remains a global health threat due to its increasing drug resistance and intracellular persistence, which compromise the conventional antibiotic efficacy. Host-directed therapy (HDT) has emerged as a promising alternative by modulating host immunity. With multi-targeting and immunomodulatory properties, traditional Chinese medicine (TCM) monomers represent ideal candidates for HDT. However, their ability to promote host immunity-mediated SA clearance remains largely unexplored.

METHODS: Forty-one TCM monomers potentially regulating host apoptosis, a core mechanism of the host innate immune defense against intracellular pathogens, were screened to identify a compound that promotes the clearance of intracellular SA and methicillin-resistant SA (MRSA). The mechanism was investigated in infected macrophages using transcriptomics, proteomics, molecular dynamics simulations, and biochemical assays. The physiological function of the TCM monomer was examined in infected mice through lung pathology and multi-omics analysis, including transcriptomics, proteomics, metagenomics, and metabolomics.

RESULTS: Triptolide was identified as a potent facilitator of host immunity-mediated intracellular clearance of SA and MRSA, without exerting direct bactericidal effects. Mechanistically, triptolide directly binds to the X-linked inhibitor of apoptosis protein (XIAP), disrupting its interaction with caspases to relieve their inhibition and thereby induce apoptosis. Furthermore, in murine infection models, triptolide treatment reduced bacterial loads, alleviated inflammation, and induced macrophage apoptosis in lungs, concurrently maintaining microbiota homeostasis and improving metabolic function.

CONCLUSION: This study establishes a proof of concept for triptolide as a HDT candidate against SA and MRSA infections, which not only enhances host apoptosis-mediated pathogen clearance but also maintains host microbiota and metabolic homeostasis.}, } @article {pmid42272967, year = {2026}, author = {Frisch, S and Aliyazdi, S and Rehner, J and Schmartz, G and Gevaerd, C and Latta, L and Veldung, B and Becker, SL and Keller, A and Schaefer, UF and Loretz, B and Vogt, T and Lehr, CM}, title = {Staphylococcal proliferation on skin models to investigate novel anti-infective treatments against dysbiosis.}, journal = {Bioengineering & translational medicine}, volume = {11}, number = {3}, pages = {e70124}, pmid = {42272967}, issn = {2380-6761}, abstract = {Inflammatory skin conditions like Acne inversa are characterized by dysbiosis, an imbalance of commensal and pathogenic bacteria, posing challenges for specific treatments. Consequently, we investigated how biofilm formation, low-nutrition skin environments, and air interfaces influence susceptibility to anti-infective treatments in mixed bacterial cultures. To achieve this in a cost-effective and reproducible manner, we developed a simplified substrate made of gelatin, hyaluronic acid, chondroitin sulphate, and alginate (=Gel-Alg). This in vitro model simulates biofilm cultivation on skin surfaces for aerobic bacteria. We selected Staphylococcus aureus and Staphylococcus epidermidis as two clinically relevant strains, which are also abundant in Acne inversa. We tested single and mixed cultures under different conditions: (i) nutrient broth, (ii) Gel-Alg substrate, (iii) EpiDerm™ commercial skin model, and (iv) ex vivo human skin. Proliferation, measured by colony-forming units, was comparable across most conditions, except for human skin. Metabolic activity, assessed via Presto Blue staining, revealed significant differences. Dual-species cultivation and quantification by viability PMA qPCR indicated dominance of S. epidermidis over S. aureus in skin-like environments. Treatments with biofilm-dissolving rhamnolipids, the antibiotic vancomycin, and combinations thereof demonstrated varying efficacy in single and mixed cultures. While the drug combination could almost completely eradicate staphylococcal biofilms in broth, susceptibility varied in skin-like models and moreover strongly depended on temperature (37°C vs. 32°C). In conclusion, this study suggests that reductionistic models, while mimicking key features, could be valuable for early selective antimicrobial drug development for specific applications like Acne inversa therapy.}, } @article {pmid42273068, year = {2026}, author = {Moradi, Z and Alinizi, HR and Mehrvar, M}, title = {Genomic characterization of broad bean wilt virus 1 (Fabavirus alphaviciae) from Iran including phylogenetic relationships.}, journal = {3 Biotech}, volume = {16}, number = {7}, pages = {256}, pmid = {42273068}, issn = {2190-572X}, abstract = {UNLABELLED: The complete genome of a broad bean wilt virus 1 (BBWV1; Fabavirus alphaviciae) isolate (BBWV1-IR) was recovered from an uncultivated Plantago lanceolata plant in Iran by viral metagenomics and validated by RT-PCR. RNA1 (5,779 nucleotides) contains a single ORF encoding replication-associated proteins (Pro-Co, HEL, VPg, Pro, RdRp), while RNA2 (3,414 nucleotides) harbors two overlapping ORFs encoding the large and small coat proteins (LCP and SCP) and two additional proteins (VP47 and VP37). Comparative analyses revealed that BBWV1-IR shared 81-92% and 79.5-83% nucleotide identity in RNA1 and RNA2, respectively, with global isolates. No intragenic recombination was detected; however, reassortment analysis identified three distinct events, including one involving BBWV1-IR, whose RNA1 segment likely originated from Austrian (major) and UK (minor) parental lineages. ORF1 and ORF2a showed substantial variability and high haplotype diversity, with VP37 displaying the greatest nucleotide diversity. Evolutionary analyses indicated that BBWV1 genes were predominantly shaped by negative selection, with essential replication proteins (HEL and Pro) under strong purifying pressure, while VP47 and VP37 experienced more relaxed constraints. A few codons in ORF1 and ORF2a were under episodic positive selection. Phylogenetic analysis clustered 19 non-recombinant isolates into two major clades (A and B), with BBWV1-IR positioned in subclade I of clade A alongside geographically distant isolates, reflecting human-mediated long-distance dispersal. Incongruent clustering of ORF1 and ORF2a in several isolates supports RNA segment reassortment as a key driver of novel variant emergence. Collectively, these findings highlight the roles of mutation, selection, reassortment, and gene flow in shaping BBWV1 evolution, exemplified by the Iranian isolate.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04905-w.}, } @article {pmid42273206, year = {2026}, author = {Montgomery, A and Nupp, S and Gray, CR and Jay, ZJ and Edgcomb, V and Hatzenpichler, R}, title = {Tracking active heterotrophic microbial communities in the Guaymas Basin deep biosphere with BONCAT-FACS.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag111}, pmid = {42273206}, issn = {2730-6151}, abstract = {The marine deep biosphere harbors microbial communities that drive organic matter transformations and biogeochemical cycles. Previous work on these communities has focused either on genomic characterization or metabolic activity measurements. However, to understand microbial ecophysiology in the deep biosphere, taxonomic identity and metabolic function must be connected on both single-cell and ecosystem scales. In this work, we optimized a bioorthogonal noncanonical amino acid tagging fluorescence-activated cell sorting (BONCAT-FACS) workflow for low-biomass deep-biosphere sediments obtained during International Ocean Discovery Program Expedition 385 (IODP 385). BONCAT-FACS with 16S rRNA gene amplicon sequencing as well as metagenomics of sediment communities was applied to characterize translationally active communities in hydrothermally altered subsurface sediments of the Guaymas Basin. Our results revealed a heterotrophic microbial population throughout all sediments examined, with taxa translationally active down to our deepest sampling point, 154 m below the seafloor. Based on 16S rRNA gene identities, the translationally active microbial community was dominated by heterotrophic members of the Gammaproteobacteria, Bacilli, Deinococci, and Alphaproteobacteria. These taxa are likely key contributors to cycling the large quantities of hydrothermally altered organic matter in Guaymas Basin sediments. To further elucidate the metabolic capacity of active taxa, we mapped 16S rRNA gene amplicons to metagenome assembled genomes (MAGs) previously obtained from IODP 385. These MAGs contained genes associated with C1 metabolism, carbohydrate degradation, and fermentation, indicating that active taxa leverage these metabolisms for energy conservation. Our results demonstrate that BONCAT-FACS provides high-throughput and single-cell insights into the metabolic activity of microbes in the low-biomass marine subsurface.}, } @article {pmid42274245, year = {2026}, author = {Christian, WC and Jay, ZJ and Tolic, N and Nicora, CD and Livingstone, R and Trimmer, S and McDermott, TR and Hatzenpichler, R}, title = {Proteomic stress response by a novel methanogen enriched from the Great Salt Lake.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0041226}, doi = {10.1128/spectrum.00412-26}, pmid = {42274245}, issn = {2165-0497}, abstract = {Methanogenic archaea affect the climate through their production of the greenhouse gas, methane. However, it is unclear how a changing climate and other anthropogenic influences impact methanogen physiology and consequent methane flux. The Great Salt Lake (GSL) is an environment that has been heavily impacted by human activity, more than doubling its salt concentration since the last methanogen was cultured from it in 1985. In this study, we enriched a novel methanogen, for which we propose the name Candidatus Methanohalophilus hillemani, from the GSL at a time when its salinity reached a historical high. Interestingly, Ca. M. hillemani does not increase the expression of energy-conservation or osmotolerance proteins when challenged with salinity or oxygen. In contrast, Ca. M. hillemani prioritizes trace metal uptake and immune functions in response to the presence of the sulfate-reducing bacterium Desulfovermiculus. 16S rRNA gene amplicon data from GSL shore soils with extremely high and variable methane flux indicated the presence of Ca. M. hillemani. Our results show that Ca. M. hillemani is active when challenged with environmental stressors and contributes to the methane flux emanating from the GSL.IMPORTANCEMethanogens are microbes that affect the climate through their production of the greenhouse gas, methane. Changes in climate and land-use patterns are drying up saline lakes, damaging their unique economic and ecological value. As lake levels across the globe fall, it is unclear how methanogens and the amount of methane they produce will concurrently shift. In this study, we measured high methane output from the Great Salt Lake (GSL) across seasons and identified a novel methanogen as part of a larger methanogenic community that is responsible for these emissions. We cultured this novel methanogen from GSL sediments and determined that its methane production was largely unaffected by stress conditions. Our findings indicate that methanogens in saline environments, including a novel cultivated species, may be important and continued sources of methane as salinity increases.}, } @article {pmid42274374, year = {2026}, author = {Madi, N and Sayeed, A and Cato, ET and Creasy-Marrazzo, A and Islam, K and Khabir, IU and Islam, T and Khan, ZH and Bhuiyan, TR and Begum, Y and Freeman, E and Vustepalli, A and Brinkley, L and Kamat, M and Bailey, LS and Basso, KB and Qadri, F and Khan, AI and Shapiro, BJ and Nelson, EJ}, title = {Ranked placement of phage predation as a determinant of dehydration severity among cholera patients in Bangladesh.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag286}, pmid = {42274374}, issn = {1537-6613}, abstract = {Virulent bacteriophages (phages) can kill bacterial prey, potentially reducing burden of infection. In cholera, a high phage to Vibrio cholerae ratio is associated with mild dehydration, yet the relative importance of this ratio in disease severity remains unclear. We used machine learning to rank select host, microbial, and environmental factors as determinants of dehydration severity in over 600 cholera patients from across Bangladesh. We found the phage:pathogen ratio ranked among the top classifiers for mild dehydration, behind age and location. We advocate that phage predation be included as a key factor in cholera characterization for scientific, clinical and epidemiological applications.}, } @article {pmid42275101, year = {2026}, author = {Zhu, XY and Hopkins, FE and Airs, R and Widdicombe, CE and Wilkinson, B and Tarran, GA and Woodward, EMS and Carrión, O and Curson, ARJ and Ma, Q and Hanwell, L and Yang, GP and Christie-Oleza, JA and Lea-Smith, DJ and Zhang, XH and Todd, JD}, title = {Predicted shifts in bacterial and algal contributions to DMSP and DMS dynamics during a coastal spring-summer bloom.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag141}, pmid = {42275101}, issn = {1751-7370}, abstract = {Ubiquitous marine microalgae and bacteria produce the abundant organosulfur compound dimethylsulfoniopropionate (DMSP) and/or catabolise it to climate-active gases, such as dimethylsulfide (DMS), with major consequences for global biogeochemistry and climate. However, their relative and dynamic roles in DMSP synthesis and catabolism remain poorly resolved, particularly during natural bloom events. Here, we combined metagenomics and metatranscriptomics, with measurements of intracellular/particulate DMSP (DMSPp), DMS concentrations and DMSPp production rates, as well as microscopy and flow cytometry, to predict the key microbes and enzymes driving DMSP/DMS dynamics during a spring-summer bloom in the Western English Channel. Microalgae and bacteria expressing the DMSP synthesis genes DSYB/DSYE and dsyB were likely major and significant DMSP producers, respectively, except during the largest observed DMSP spike. This spike coincided with elevated Synechococcus and autotrophic flagellate biomass but minimal DMSP synthesis gene expression. Axenic Synechococcus strains contained no detectable DMSP, implying flagellates with novel DMSP synthesis genes were likely responsible. Microbial DMSP import potential far exceeded catabolism, suggesting strong selection for DMSP uptake. Bacteria were the major predicted DMSP degraders, with DMSP demethylation potential dwarfing cleavage. However, the highest DMS concentrations were linked to Haptophyta expressing the DMSP lyase gene Alma, implying the significance of algal DMSP cleavage. Methanethiol-dependent DMS production was also likely important, with bacterial mddH transcripts coinciding with another major DMS spike. Overall, these results imply dynamic and contrasting roles of microalgae and bacteria, and their pathways, in coastal DMSP/DMS and sulfur cycling.}, } @article {pmid42275884, year = {2026}, author = {Zhao, J and Zuo, M and Cao, L and Li, Q and Zhang, R and Wu, H and Yuan, J and Lv, C and Yu, Y and Lu, J}, title = {The neutral and acidic polysaccharides from Ginseng are metabolized by specific gut microbial taxa and confer immunomodulatory effects.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {158}, number = {}, pages = {158400}, doi = {10.1016/j.phymed.2026.158400}, pmid = {42275884}, issn = {1618-095X}, mesh = {*Panax/chemistry ; *Polysaccharides/pharmacology/metabolism/chemistry ; Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Immunologic Factors/pharmacology ; Fatty Acids, Volatile/metabolism ; Male ; Fermentation ; }, abstract = {BACKGROUND: Ginseng (Panax ginseng C. A. Mey.) exerts immunomodulatory effects partly mediated by its polysaccharides and interactions with gut microbiota. However, due to the structural complexity of ginseng polysaccharides, knowledge of their oral fate and direct microbiota interactions remains limited.

PURPOSE: This study aims to elucidate the oral fate of neutral and acidic polysaccharides in ginseng, analyze core gut microbiota genera and their immunomodulatory effects mechanisms.

METHODS: Structural analysis was conducted on neutral and acidic polysaccharides from ginseng. Thereafter, in vitro digestion and fermentation were performed, with metagenomic and metatranscriptomic profiling. The results were validated in conventional and pseudo‑germ-free immunosuppressed mouse models, and the immunomodulatory mechanisms of the core gut microbiota were investigated.

RESULTS: The in vivo and in vitro findings indicated that neutral and acidic polysaccharides exhibit different digestive properties and gut microbiota degradation patterns, differ in short-chain fatty acid production tendencies, bind to GPR-41/43 receptors, upregulate MAPK-p38 phosphorylation, and promote proliferation of intestinal immune cells.

CONCLUSION: This work systematically elucidated the digestive characteristics of ginseng polysaccharides and laid the groundwork for future studies on the specificity and structure-function relationships of plant-derived polysaccharides.}, } @article {pmid42275949, year = {2026}, author = {Zheng, Y and Su, F and Li, H and Wu, H and Cui, P and Song, F}, title = {Wetland succession reshapes microbial degradation of plant- and microbial-derived carbon.}, journal = {Journal of environmental management}, volume = {411}, number = {}, pages = {130154}, doi = {10.1016/j.jenvman.2026.130154}, pmid = {42275949}, issn = {1095-8630}, mesh = {*Wetlands ; *Carbon/metabolism ; *Soil Microbiology ; Bacteria/metabolism ; Biodegradation, Environmental ; Fungi/metabolism ; China ; Plants/metabolism ; Soil/chemistry ; }, abstract = {Plant- and microbial-derived organic carbon require distinct microbial enzymes, but how wetland succession regulates these substrate-specific degradation pathways in estuarine soils remains unclear. We collected 0-10 cm soils from four wetland types in the Liaohe River Estuary, China-tidal flat, restored wetland, Suaeda salsa wetland, and reed wetland-with three independent replicate sites per type. Shotgun metagenomic sequencing, CAZy annotation, taxonomic annotation, co-occurrence networks, and Mantel tests were used to examine CAZyme genes targeting plant-, fungal-, and bacterial-derived carbon. We identified 16,346,752 CAZyme-encoding sequences assigned to 749 families. Carbon-cycling gene composition differed significantly among wetland types (ANOSIM R = 0.37, p = 0.034). Gene diversity was higher in early to mid-successional stages, whereas the abundances of plant-, fungal-, and bacterial-derived carbon degradation genes increased along succession. Lignocellulose-degrading genes were most enriched in reed wetland, including AA3, CBM9, and CE1. Microbial hosts shifted markedly, with Bacteroidota increasing from 8.53% to 38.28% among plant-derived carbon degraders. Plant-derived carbon degrader networks were densest in tidal flat soils, suggesting a transition from stress-associated microbial associations to resource-specialized assemblages. Environmental controls were substrate-specific: plant-derived genes correlated only with nitrate, fungal-derived genes with moisture, nitrogen, salinity, and electrical conductivity, and bacterial-derived genes with none of the measured variables. These findings reveal substrate-specific microbial mechanisms linking wetland succession to carbon turnover and identify Bacteroidota, AA3, and nitrate availability as candidate indicators for restoration assessment and carbon-sequestration management.}, } @article {pmid42276429, year = {2026}, author = {Kang, X and He, P and Zhang, H and Lü, F}, title = {Multi-omic insights into thermal regulation of the resistome through composting-simulating microcosm system.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135119}, doi = {10.1016/j.biortech.2026.135119}, pmid = {42276429}, issn = {1873-2976}, abstract = {Composting is a crucial biosecurity practice that stabilizes organic waste and reduces biological hazards prior to land application, with temperature as a major driver of resistome succession. However, compost temperature is a dependent, composite factor jointly determined by microbial metabolism and management practices. The regulatory pathways of temperature on resistome remain unclear. In this study, temperature gradients from 50°C to 65°C were applied to biowaste in a composting-simulating microcosm system to investigate the genomic and functional regulatory pathways of antimicrobial resistance genes (ARGs) using high-temporal-resolution metagenomic and metatranscriptomic analyses. The succession dynamics of ARGs under temperature-controlled incubation were demonstrated from the ecological niche perspective. Our results revealed that the genomic potential and transcriptional activity of ARGs responded asynchronously to temperatures. ARG sensitivity to temperature was category-specific, with 60°C representing a critical threshold for genomic-level removal of ARGs. The context-anchored members drove the resistome's response trends during temperature-controlled incubation, while abundance-based dynamics did not show significant kinetic shift under elevated temperatures. Temperature shaping the resistome through intra-lineage ARG reduction within context-anchored members rather than community succession. Unassociated fragment members showed transient abundance fluctuations at 55°C. Both context-anchored and unassociated fragment ARG carriers maintained transcriptional homeostasis during temperature-controlled incubation. Viruses had a limited impact on the community resistome. Our study demonstrated temperature-driven regulation of the resistome, providing a basis for optimizing ARG management in composting.}, } @article {pmid42276430, year = {2026}, author = {Cai, Q and He, J and Qiu, W and Wang, Y and Fang, K and Zou, X and Aili, A and Zhong, Y and Pan, X}, title = {Industrial red mud establishes redox-active interfaces to steer metabolic pathways toward chain elongation in sludge anaerobic fermentation.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135151}, doi = {10.1016/j.biortech.2026.135151}, pmid = {42276430}, issn = {1873-2976}, abstract = {Medium-chain fatty acids (MCFAs) production from waste activated sludge (WAS) provides a promising route for sludge valorization, but is often limited by inefficient hydrolysis and restricted interspecies electron transfer. This study evaluated industrial red mud (RM) as a conductive and alkaline regulator to enhance anaerobic chain elongation (CE). With 5 g/L RM addition, MCFAs yield reached 12.6 g COD/L, representing a 164% increase over the control. Spectroscopic analysis showed that the strong alkalinity of RM altered protein secondary structures, facilitating substrate hydrolysis while maintaining stable pH favorable for CE. Increased release of humic-like substances was observed, and electrochemical evidence suggested that the adsorption of these redox mediators onto the RM surface potentially facilitated the formation of redox-active interfaces, which contributed to the enhanced electron transfer capacity. Microbial network analysis demonstrated that RM acted as a topological hub, restructuring the community into a synchronized syntrophic consortium (hydrolysis-acidogenesis-CE) and highly enriching key CE bacteria. Metagenomic analysis revealed an increase in the abundance of genes encoding conductive membrane proteins (cytochromes and Mtr-associated), suggesting a potential enhancement in direct interspecies electron transfer. Meanwhile, RM increased the gene abundance of the CE key pathway (reverse β-oxidation pathway), thereby favoring the genetic potential for MCFAs accumulation. These findings establish a sustainable 'waste-treating-waste' framework, utilizing RM-driven electron reservoirs to facilitate the high-value conversion of WAS in anaerobic systems.}, } @article {pmid42276515, year = {2026}, author = {Hassanien, A and Saadaoui, I and Sayadi, S}, title = {Archaea as a Resource for Sustainable Biotechnology: From Extremophiles to Valuable Products.}, journal = {Biochimie}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biochi.2026.06.006}, pmid = {42276515}, issn = {1638-6183}, abstract = {Archaea, a remarkable domain of microorganisms, possess extraordinary survival capabilities that enable them to thrive in the most extreme environments on Earth, including high temperatures, extreme pH, oxygen-deprived habitats, and high salinity. Modern ecological studies have revealed their broad distribution and ecological roles, but traditional culture techniques do not accurately capture the structure of archaeal communities in such settings. This review provides an integrated and up-to-date synthesis of tools used to assess archaeal biodiversity, with particular emphasis on high-throughput culture-independent strategies, including metagenomics, functional metagenomics, and multi-omics. We also provide a quantitative, up-to-date mapping of archaeal biodiversity and bioproduct research (2010-2024), highlighting methodological trends and underexplored niches that are not emphasized in previous reviews. These advancements in archaeal studies have allowed scientists to investigate numerous archaeal strains for potential biotechnological applications and products, and to explore novel genes that lead to the discovery of new metabolites and bioactive molecules. Building on this framework, we critically analyze the current and emerging biotechnological applications of archaea. focusing on metabolites, enzymes, biopolymers, and biofuels, as well as identifying the major scientific and technical bottlenecks that hinder their translation into industrial scale. Finally, we outline key research priorities for utilizing archaeal resources in development of more sustainable and environmentally friendly biotechnologies.}, } @article {pmid42276765, year = {2026}, author = {Diao, Y and Li, J and Wang, L and Zhang, Q and Xu, C and Peng, A and Lu, C and Lai, B and Chen, R and Chen, J and Pei, X}, title = {Microbiological characteristics of granulomatous lobular mastitis revealed by metagenomic sequencing.}, journal = {Journal of clinical pathology}, volume = {}, number = {}, pages = {}, doi = {10.1136/jcp-2026-210744}, pmid = {42276765}, issn = {1472-4146}, abstract = {AIMS: Granulomatous lobular mastitis (GLM) is a rare, chronic, benign inflammatory disease of the breast with an unclear aetiology. This study aimed to characterise the microbial features of GLM using metagenomic next-generation sequencing (mNGS) and to provide potentially relevant microbial clues for clinical evaluation.

METHODS: Twenty fresh lesion tissue samples were collected from 15 female patients with GLM, including one representative sample per patient and five additional deep tissue samples. Clinical data collection, mNGS, bioinformatics analysis and data interpretation were performed to characterise the microbial profiles of GLM lesions.

RESULTS: In this study, all patients presented with palpable breast masses, breast pain and abscess formation. More than half showed increased white blood cell counts, neutrophil percentages, C reactive protein levels and erythrocyte sedimentation rates together with decreased lymphocyte percentages. Based on genus-level filtering, mNGS identified 16 bacterial genera, 14 fungal genera and 3 viral genera, revealing a complex but bacteria-dominated microbial profile. The most frequently detected bacterial genera were Corynebacterium, Cutibacterium, Acinetobacter, Staphylococcus and Hathewaya, with marked interpatient variation in relative abundance, while fungal profiles were relatively more concentrated. In five patients with both superficial and deep tissue samples, microbial profiles differed across sampling depths, particularly for bacterial composition.

CONCLUSIONS: mNGS revealed a complex, bacteria-dominated microbial profile in GLM lesions and indicated that sampling depth may influence the detected microbial profiles. These findings may provide useful clues for clinical evaluation, but the pathogenic significance of these micro-organisms remains to be elucidated.}, } @article {pmid42277004, year = {2026}, author = {Clark, JR and Chirman, D and Prakash, H and Terwilliger, A and McNeese, M and Ross, M and Tisza, M and Javornik Cregeen, SJ and Hopkins, L and Deegan, J and Troisi, CL and Boerwinkle, E and Mena, K and Wu, F and Kimata, JT and Johnson, M and Gregory, D and Fletcher, FE and Giordano, TP and Maresso, AW}, title = {Statewide multi-year wastewater sequencing reveals dual origins of HIV-1 signal.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74140-7}, pmid = {42277004}, issn = {2041-1723}, support = {U19AI14429//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P30AI161943//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01DA059394//U.S. Department of Health & Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; }, abstract = {Human immunodeficiency virus 1 (HIV-1) is a retrovirus which has infected 90 million people and resulted in over 40 million deaths. Despite advances in diagnostics, treatment, and prophylaxis, HIV-1 continues to spread due to undiagnosed and untreated infections. Traditional monitoring methods are ineffective when access to testing is limited or people do not seek care, particularly given the long period between infection and symptom onset, allowing undetected transmission to continue. Here, we use a hybrid-capture sequencing approach to track HIV-1 signal in municipal wastewater in 15 different cities over nearly 3 years. We obtain near-complete genomic coverage of HIV-1, enabling detailed genomic analysis. Surprisingly, there are a substantial number of research-associated retroviral vector sequences recovered. Using computational competitive mapping, we identify specific genomic regions that differentiate authentic HIV-1 from vector-derived inputs. In an exploratory analysis of sites with available clinical data, wastewater-derived circulating HIV-1 reads show a positive correlation with community-level HIV diagnosed prevalence that was robust to exclusion of individual high-prevalence sites. This study identifies lentiviral vector contamination as a confounding factor in wastewater HIV-1 detection, recovers authentic circulating HIV-1 signal through an original classification framework, and provides initial evidence that the resulting signal tracks community HIV burden.}, } @article {pmid42277027, year = {2026}, author = {Wacker, EM and Rühlemann, MC and Franke, A and Ellinghaus, D}, title = {TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42277027}, issn = {2041-1723}, support = {EL 831/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167/2 - 390884018//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Metagenome/genetics ; *Software ; Humans ; *Metagenomics/methods ; Reproducibility of Results ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA/methods ; Shotgun Sequencing ; Workflow ; }, abstract = {Metagenomic shotgun sequencing data from over 600,000 metagenomes are publicly available in repositories such as NCBI's Sequence Read Archive (SRA). Technically advanced and easy-to-use best-practice metagenome software workflows for raw data pre-processing, assembly of metagenome-assembled genomes, and taxonomic and functional annotation of metagenome-assembled genomes are needed for reproducible analysis and harmonization of large-scale metagenomic datasets. We introduce TOFU-MAaPO (Taxonomic Or FUnctional Metagenomic Assembly and PrOfiling), a portable, automated single-command Nextflow pipeline for large-scale analysis of metagenomic short-read sequencing data. It analyzes metagenome files locally or directly from the SRA using accession or study IDs. In a benchmark against three established metagenome software pipelines, the TOFU-MAaPO workflow yielded 12%, 42% to 77% more high-quality metagenome-assembled genomes, likely reflecting the integration of multiple complementary binning tools with a unified refinement strategy. Using its assembly-free taxonomic abundance profiling module, we also automatically downloaded 16,462 uniquely identifiable and accessible human gut metagenome samples from the SRA and taxonomically annotated them against the Genome Taxonomy Database on a high-performance cluster in less than 55 hours, including download time. TOFU-MAaPO makes large metagenome projects more accessible to individual research groups and is freely available at https://github.com/ikmb/TOFU-MAaPO .}, } @article {pmid42277260, year = {2026}, author = {Jie, Z and Liang, W and Ding, Q and Liu, X and Zhang, Y and Chen, N and Li, S and Tong, X and Gao, H and Lu, R and Huang, X and Guo, R and Chen, J and Zhu, J and Zhang, Z and Liu, N and Xie, Z and Wang, X and Qi, L and Li, Y and Xiao, L and Zhang, S and Jin, X and Xu, X and Yang, H and Wang, J and Zhao, F and Jia, H and Kristiansen, K and Zhang, T and Hao, L and Zhu, L and Chen, C}, title = {Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {42277260}, issn = {1546-1718}, abstract = {The vaginal microbiome is essential for women's health, yet its genomic diversity and interaction with the host remain incompletely characterized. Here we present the Global Vaginal Metagenome-assembled Genomes catalog, an extensive repository of vaginal microbial genomes generated by integrating 10,665 in-house Chinese metagenomes, with 2,967 publicly available metagenomes and 1,433 bacterial isolates. The catalog comprises 65,055 genomes from 890 prokaryotes, 11 eukaryotes and 6,590 viral taxonomic units, many not represented in public reference databases. We investigate virus-bacteria interactions, revealing conserved phages-host associations. We then identify substantial intraspecies genomic and functional variations displaying population-specific patterns. A metagenome-genome-wide association study identifies seven host genetic loci associated with vaginal species at study-wide significance and replicated in at least one independent cohort, notably connecting the gene OPRK1 with the potential pathogen Ureaplasma urealyticum. In summary, our research provides a comprehensive reference for future studies on genotype-phenotype interplay within the human vaginal microbiome.}, } @article {pmid42277454, year = {2026}, author = {Amoia, SS and Giampetruzzi, A and Antònio, LF and Tomàs Pais da Cunha, A and Minafra, A}, title = {A new putative carlavirus identified by metagenomic analysis in a wild weed in Angola.}, journal = {Archives of virology}, volume = {171}, number = {7}, pages = {}, pmid = {42277454}, issn = {1432-8798}, mesh = {Genome, Viral ; Metagenomics ; *Plant Diseases/virology ; Phylogeny ; *Carlavirus/genetics/isolation & purification/classification ; Angola ; *Plant Weeds/virology ; High-Throughput Nucleotide Sequencing ; Open Reading Frames ; RNA, Viral/genetics ; }, abstract = {A metagenomic analysis was performed by high-throughput sequencing (HTS) to identify viruses infecting a wild weed collected in Seles (Angola), which exhibited clear yellowing symptoms. The analysis led to the discovery of a putatively novel carlavirus, tentatively named 'Seles weed carlavirus'. The complete genome sequence, consisting of 8,597 nucleotides, poly-A tail excluded, exhibited the typical organization of members of the genus Carlavirus, including the replicase polyprotein (ORF1); the triple gene block (ORFs 2-4); the coat protein (ORF5) and an RNA-binding protein (ORF6). The replicase polyprotein and coat protein gene regions of the newly described virus shared the highest amino acid sequence identity with the corresponding sequences of cowpea mild mottle virus (51.40%) and Hainan betaflexivirus (63.08%), respectively. The infection was further confirmed by RT-PCR with multiple specific targeted primer pairs, whose related amplicons were cloned and sequenced.}, } @article {pmid42277703, year = {2026}, author = {Cumley, N and Quick, J and Brier, T and Wilkinson, S and Kent, C and Hassan-Smith, Z and Loman, N and Hassan-Smith, G}, title = {Pathogen detection in central nervous system infections: moving metagenomic sequencing closer to clinical practice.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13276-9}, pmid = {42277703}, issn = {1471-2334}, abstract = {BACKGROUND: Central nervous system infections (CNSI) contribute significantly to global disability and mortality, but the causative agent is often undetected. Metagenomic sequencing offers the potential to enhance diagnostic sensitivity, particularly in cases of unusual or partially treated infections. However, caution is required in interpretation of metagenomics data due to technical artefacts from contamination or non-specific read mapping which can reveal a broad spectrum of biologically plausible but diagnostically unlikely organisms.

METHODS: This study compares the performance of metagenomic sequencing with standard clinical microbiology methods using cerebrospinal fluid (CSF) from patients with CNSI and non-infected control samples. To evaluate sensitivity of different laboratory approaches, we sequenced DNA and RNA metagenomic libraries extracted from CSF, using both cell-free and cellular fractions. We then devised a set of simple, easily interpreted yet rigorous filters tailored for clinical metagenomics to generate a framework for result interpretation that can be readily applied by clinical scientists.

RESULTS: We demonstrate that composite filtering strategies are essential to reduce misleading signals and support standardised workflows. Additionally, our results suggest that a cell-free sample preparation approach can improve confidence in identifying clinically relevant pathogens, highlighting the impact of sample preparation on results quality.

CONCLUSION: In this study we describe a reproducible method that can be incorporated into a practical framework for clinical application of metagenomic sequencing in CNSI diagnostics.}, } @article {pmid42277905, year = {2026}, author = {Serrano-Gómez, G and Zaida, S and Pons-Tarín, M and Mayorga, L and Maria, TC and Natalia, B and Francisco, G and Manichanh, C}, title = {Microbial, functional, and virulence biomarkers associated with familial risk of Crohn's disease and ulcerative colitis.}, journal = {Biomarker research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40364-026-00950-y}, pmid = {42277905}, issn = {2050-7771}, support = {PI20/00130//Instituto de Salud Carlos III/ ; PID23-147387OB-100//Ministerio de Ciencia, Innovación y Universidades/ ; SGR 00459//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; }, abstract = {BACKGROUND: First-degree relatives of patients with inflammatory bowel disease (IBD) carry elevated disease risk and offer a unique window into preclinical gut microbiome alterations. We investigated whether familial IBD risk is associated with intermediate, disease-specific, or shared gut microbiome configurations in both Crohn's disease (CD) and ulcerative colitis (UC), the two main form of IBD.

METHODS: Using shotgun metagenomics, we analysed fecal samples from CD (n = 68) and UC (n = 77) patients, their healthy first-degree relatives (CD-HFDRs, n = 37; UC-HFDRs, n = 30), and unrelated healthy controls (HCs, n = 497), integrated species-level taxonomy, MetaCyc functional pathways, and virulence factor gene (VFG) profiling, with differential abundance analyses adjusted for relevant covariates.

RESULTS: HFDRs exhibited preserved alpha diversity but intermediate dysbiosis relative to patients and HCs. CD-HFDRs shared CD-associated taxonomic alterations, including depletion of Faecalibacterium prausnitzii, and enrichment of adherence- and invasion-associated VFGs, with 16 of 18 HFDR-enriched VFGs also elevated in CD patients. CD-HFDR functional pathway profiles nonetheless closely resembled those of HCs, revealing a dissociation between taxonomic and functional dysbiosis. Random forest classifiers distinguished HFDRs from HCs with strong performance: species- and VFG-based models achieved an AUCs of 0.966 in CD, and 0.946 in UC. Top predictive features were depletion of F. prausnitzii and enrichment of the E. coli adhesin gene fdeC. UC-HFDRs showed subtler alterations but comparable classifier performance.

CONCLUSIONS: IBD first-degree relatives harbour a transitional gut microbiome between health and disease, more pronounced in CD, with F. prausnitzii depletion and pathobiont virulence genes emerging as robust microbiome-based risk indicators.}, } @article {pmid42278013, year = {2026}, author = {Mei, Z and Zhou, H and Du, H and Liu, K and Gao, C and Sheng, Z and Gong, Y}, title = {Heat Stress Induces Metabolic and Physiological Imbalance in Laying Hens, Accompanied by Hepatic Transcriptomic, Cecal Microbial, and Metabolomic Alterations.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {11}, pages = {}, pmid = {42278013}, issn = {2076-2615}, support = {2023ZD0405203//the Biological Breeding-National Science and Technology Major Project/ ; 2023ZD0407106//the Biological Breeding-National Science and Technology Major Project/ ; HBZY2023B007//the Hubei Fund for Seed Industry High-Quality Development Project/ ; 2025HBSTX4-04//the Earmarked Fund for Hubei Agriculture Research System/ ; 2018YFE128100//the National Key Research and Development Program of China/ ; 2023BBA029//he Major Program of Hubei Province/ ; }, abstract = {Heat stress is a major constraint to productivity and physiological homeostasis in laying hens. This study investigated integrated responses to acute heat stress using a multi-omics approach, including performance traits, serum biochemical parameters, histology, hepatic transcriptomics, cecal metagenomics, and metabolomics. Acute heat stress impaired productive performance, as reflected by changes in egg production and reduced eggshell strength, and induced systemic physiological disturbances, including increased stress- and injury-related blood indicators and disrupted metabolic and electrolyte balance. Histological analysis confirmed liver and intestinal tissue damage. Hepatic transcriptomics revealed inflammatory activation and suppression of metabolic pathways, particularly those involved in lipid metabolism, energy production, and redox homeostasis. Cecal metagenomic and metabolomic analyses showed altered microbial composition and functional potential, along with disruptions in amino acid, lipid, and energy metabolism. Collectively, these findings suggest that acute heat stress is associated with coordinated inflammatory responses and metabolic reprogramming, together with liver and intestinal injury and gut microbiota-metabolite alterations. The study provides a framework for understanding early heat stress responses and highlights potential targets for nutritional and microbiota-based interventions in poultry production. Importantly, serum biochemical indicators such as D-lactic acid and aspartate aminotransferase may serve as potential early biomarkers for monitoring heat-stress-induced physiological disturbances.}, } @article {pmid42278142, year = {2026}, author = {Yuan, Z and Xie, F and Ding, Y and Li, X and Ghonaim, AH and Jiang, C and Ren, M and Li, S}, title = {Dietary Fiber Levels Modulate Intestinal Mucosal Architecture and the Microbiome-Metabolome Axis to Support Immune Homeostasis in Brooding Wanxi White Geese.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {11}, pages = {}, pmid = {42278142}, issn = {2076-2615}, abstract = {Dietary fiber is a critical determinant of intestinal health, yet its optimal inclusion level for WWG during the critical brooding period remains undefined. This study aimed to evaluate the effects of varying dietary CF levels (approximately 3%, 5%, and 9%) on the intestinal morphology, immune function, and microbiome-metabolome axis of brooding WWG. A total of 120 one-day-old goslings were randomly assigned to the three dietary treatments for a 28-day trial. Histological analysis revealed that the 9% CF diet significantly improved gut morphology, yielding superior villus-to-crypt ratios in the jejunum and ileum. Molecular assays indicated that higher fiber levels (5-9%) upregulated the expression of nutrient transporters (SGLT1 and GLUT2). Concurrently, the 9% CF diet effectively suppressed the potent pro-inflammatory cytokine TNF-α in the jejunum while appropriately upregulating IL-6 and NF-κB, indicating enhanced mucosal immune vigilance and structural maturation. Multi-omics integration (shotgun metagenomics and LC-MS metabolomics) demonstrated that specific fiber levels significantly shifted microbial abundances, specifically enriching Bacteroidetes and Actinobacteria. These microbial shifts were strongly correlated with enriched metabolic pathways, notably lysine biosynthesis and purine metabolism, which synergistically support mucosal homeostasis. Collectively, these findings demonstrate that a 9% dietary CF inclusion is an effective nutritional strategy to optimize intestinal architecture and microbial-metabolic profiles in brooding WWG.}, } @article {pmid42278211, year = {2026}, author = {Shematorova, EK and Shpakovski, GV}, title = {Molecular Evolution of the Archaeal DNA-Dependent RNA Polymerase: Cooperative Changes in Subunit Composition and Specific Domains of Small Subunits.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278211}, issn = {1422-0067}, support = {thematic plan 1ф.4.1//National Research Center "Kurchatov Institute"/ ; }, mesh = {*DNA-Directed RNA Polymerases/genetics/chemistry/metabolism ; *Evolution, Molecular ; *Archaea/genetics/enzymology ; Protein Subunits/genetics/chemistry ; *Archaeal Proteins/genetics/chemistry/metabolism ; Phylogeny ; Amino Acid Sequence ; Protein Domains ; }, abstract = {The subunit composition and tertiary structure of DNA-dependent RNA polymerases in archaea, bacteria, and eukaryotes are currently well understood. The single RNA polymerase of archaea resembles the nuclear RNA polymerase II of eukaryotes in its composition and consists of 10-12 subunits. Perhaps the only exception that seems to confirm this rule is the Rpo8 subunit (homologue of the eukaryotic Rpb8), which only some classes of archaea have. The development of metagenomic sequencing has led to a significant revision of the classification system of prokaryotes, in particular to the identification of a number of new Archaea evolutionary lineages. This makes it possible to analyze the subunit composition and structure of RNA polymerase of all currently isolated archaeal phyla. Our analysis shows that the Rpo8 subunit is present only in the RNA polymerase of Archaea species from the Thermoproteota of the Thermoproteati superphylum and from the whole superphylum Promethearchaeati, formerly known as the Asgard. After analyzing the changes in the small Rpo6 subunit (homologue of eukaryotic Rpb6), functionally interacting with Rpo8, we noticed that the largest number of changes in the primary and domain structures of this small subunit occurred in archaeal phyla that lack Rpo8. Shortened forms of Rpo6 without N- or C-terminal regions were observed only in representatives of archaea with an RNA polymerase that does not contain the Rpo8 subunit. Our analysis shows that the changes in Rpo6 are an adaptation of a multisubunit transcription complex to the disappearance of Rpo8. Most likely, the Rpo8 subunit was present in the RNA polymerase of the Last Common Ancestor of Archaea (LCAA) and, in the course of evolution, disappeared in the superphyla Euryarchaeota and Nanobdellati and two divisions of the Thermoproteati superphylum: Bathyarchaeota and Thaumarchaeota.}, } @article {pmid42278252, year = {2026}, author = {Mechri, S and Najjari, A and Croze, S and Ouzari, HI and Le Roes-Hill, M and Tounsi, S and Lachuer, J and Jaouadi, B}, title = {Unraveling the Taxonomic Diversity and Functional Potential of the Tunisian Salterns, Abbassia and Thyna, via Integrated 16S-18S Amplicons and Shotgun Metagenomics.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278252}, issn = {1422-0067}, support = {101079425//Centre of Biotechnologie of Sfax/ ; }, mesh = {*Metagenomics/methods ; Tunisia ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Archaea/genetics/classification ; Shotgun Sequencing ; Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; }, abstract = {Hypersaline environments are unique ecosystems harboring specialized microbial communities with significant biotechnological potential. This study provides a comprehensive characterization of the taxonomic diversity and functional potential of two Tunisian salterns, Abbassia (Kerkennah) and Thyna (Sfax), using an integrated approach that combines 16S/18S rRNA gene amplicons (Illumina and full-length Nanopore) with shotgun metagenomics. Taxonomic profiling revealed a high species richness (S ≈ 1250 taxa); however, the Abbassia site was characterized by extreme taxonomic polarization, with over 95% of the community dominated by specialized halophilic Bacillota (Salinicoccus and Jeotgalicoccus). In contrast, Thyna exhibited a more even distribution dominated by Pseudomonadota and methanogenic Archaea. Beyond taxonomy, functional annotation via the HUMAnN 3.0 pipeline identified site-specific metabolic specializations. Abbassia was enriched in biosynthetic pathways and robust stress-response mechanisms, including ectoine biosynthesis and ppGpp-mediated stringent response, reflecting adaptation to stable hypersaline conditions. Conversely, Thyna's microbiome prioritized energy extraction and nutrient recycling, with a high abundance of fermentation and glyoxylate cycle pathways. These findings demonstrate that environmental filtering shapes not only the microbial structure but also the metabolic landscape, highlighting the ecological plasticity of microbial life in extreme Tunisian salterns.}, } @article {pmid42278256, year = {2026}, author = {Al-Ansari, MM and Mahmood, SM and Al-Alwan, M}, title = {The Human Breast Microbiome: From Homeostasis to Malignancy, Mechanistic Insights and Therapeutic Perspectives.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278256}, issn = {1422-0067}, support = {RAC# 2240005//King Faisal Specialist Hospital & Research Centre/ ; }, mesh = {Humans ; Female ; *Breast Neoplasms/microbiology/therapy/pathology ; *Microbiota ; *Homeostasis ; *Breast/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Although human mammary glands were traditionally considered sterile, accumulating evidence has established the presence of distinct microbial communities that may have colonized breast tissue primarily via retrograde nipple flow or via hematogenous or lymphatic translocation from other body sites. Comparative studies reveal differences in the microbiota of healthy and diseased breast tissues, with variations in microbial signatures across breast cancer subtypes and in comparison with adjacent normal tissues. This review synthesizes current evidence on the composition of the breast microbiome, the factors shaping its development, and alterations it undergoes in inflammatory and malignant breast diseases. Furthermore, the article discusses mechanistic insights, methodological challenges, and future therapeutic perspectives based on published studies employing culture-independent approaches, such as 16S rRNA gene sequencing and metagenomic analyses. Key host-related factors influencing breast-associated microbial communities, including hormonal regulation, environmental exposure, diet, and therapeutic interventions, are explored. The existing literature is assessed to identify key associations between the breast microbiome and host signaling pathways, as well as the significant challenges that remain unresolved, including low biomass contamination, inter-study variability, limited longitudinal data, and an incomplete understanding of causality. Addressing these limitations is critical for advancing microbiome-based diagnostic and therapeutic strategies for breast disease.}, } @article {pmid42278324, year = {2026}, author = {Ilinskaya, O and Vagin, K and Kurdy, W and Yakovleva, G and Karamova, N and Zelenikhin, P and Kolpakov, A and Zuev, Y}, title = {Biomineral Complex with Probiotic and Detoxifying Properties for Recovery After Radiotherapy.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278324}, issn = {1422-0067}, support = {24-14-00059//Russian Science Foundation/ ; }, mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; Mice ; *Gastrointestinal Microbiome/drug effects/radiation effects ; Chromosome Aberrations/radiation effects/drug effects ; RNA, Ribosomal, 16S/genetics ; *Radiotherapy/adverse effects ; Radiation-Protective Agents/pharmacology ; Male ; Lactobacillus ; *Minerals/pharmacology ; *Dysbiosis/etiology ; }, abstract = {Radiotherapy is a highly effective, safe cancer treatment, and about half of all cancer treatments involve lifesaving radiotherapy. Despite huge advances in technology that have made it safer and more effective, it is still not without side effects. They differ from patient to patient and can include fatigue, nausea, skin reactions, and hair loss, but dysbiosis is the most common complication associated with radiotherapy. Probiotics aimed at restoring the microbiome have found widespread use, but the problem of their rapid inactivation in the gastrointestinal tract has not yet been solved. Our study aims to confirm the effectiveness of a novel biomineral complex, based on a powdered clinoptilolite containing a rock loaded with lactobacilli for restoring the intestinal microbiome of mice exposed to radiation. Based on the 16S rRNA gene analysis, alpha-diversity and dynamics of changes in the fecal metagenome, as well as the functional potential of mice exposed to radiation, were studied, and the prospects of administering the biomineral complex to achieve positive effects were assessed. NMR analysis of the mineral carrier was carried out, and its safety was confirmed. Moreover, per os administration of the complex following irradiation led to a reduction in the level of chromosomal aberrations induced by irradiation. Thus, the biomineral complex has a microbiome-restoring effect and reduces radiation-induced clastogenesis.}, } @article {pmid42278475, year = {2026}, author = {Ermakov, VS and Falah, K and Nigam, SK}, title = {A Kidney-Microbiome Short- and Medium-Chain Fatty Acid Loop Mediated by OAT1: Implications for the Remote Sensing and Signaling Theory.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278475}, issn = {1422-0067}, support = {R01 DK109392/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Organic Anion Transport Protein 1/metabolism/genetics ; Signal Transduction ; Mice ; *Kidney/metabolism/microbiology ; *Fatty Acids, Volatile/metabolism ; Mice, Knockout ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Short-chain fatty acids (SCFAs) and medium-chain fatty acids (MCFAs) include small organic anions derived from the gut microbiome that interact with organic anion transporters of the SLC22 family, many of which are expressed in the kidney proximal tubule. According to the Remote Sensing and Signaling Theory (RSST), crosstalk between organs (e.g., gut-liver-kidney axis, gut-brain axis) and the gut microbiome is mediated by metabolites and signaling molecules transported by multi-specific "drug" transporters. The renal drug transporter OAT1 (SLC22A6) is also a major transporter of gut-microbiome products and uremic toxins (e.g., indoxyl sulfate); it has been shown to act as part of a regulatory feedback loop involving the gut microbiome. SCFAs, especially propionate and butyrate, have been shown to play a central role in the transcriptional regulation of OAT1 through HDAC inhibition. By fecal metagenomics analyses of Oat1 knockout mice, we now find that propionate synthesis is among the most altered pathways in the gut microbiome. In contrast, these pathways were only minimally altered in the Oat3 (Slc22a8) knockout. Metabolomics analyses indicate that serum propionate derivatives (e.g., propionyl glycine) and 3-hydroxybutyrate are dependent on OAT1 in the knockout mice and in humans treated with probenecid, an OAT1 inhibitor. The gut microbiome of the Oat1 knockout mice also exhibited greater fatty acid synthesis, which generates odd-chain-length fatty acids (e.g. heptanoate) when propionate is available. Overall, the data, especially when considered in light of in vitro experiments of others, indicates the in vivo existence of a feedback loop connecting gut-microbiome-derived SCFAs and MCFAs to kidney proximal tubule uptake via OAT1. This bidirectional feedback loop in turn regulates OAT1 expression through HDAC inhibition. The feedback loop is clearly consistent with the Remote Sensing and Signaling Theory-in particular, the centrality of multi-specific "drug" transporters in organ crosstalk and host-microbiome interactions via small molecules with "high information content." The key role of OAT1 function in maintaining tubular secretion in CKD supports the importance of this RSST loop in renal pathophysiology. Modulating this RSST loop could have therapeutic value in chronic kidney disease and other contexts.}, } @article {pmid42278495, year = {2026}, author = {Zielińska, E and Kycia, K and Mikołajczuk-Szczyrba, A and Piłka, N and Juszczuk-Kubiak, E}, title = {GABA-Producing Bacteria as Potential Psychobiotics in Gut-Brain Axis Regulation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278495}, issn = {1422-0067}, support = {NdS-II/SN/0238/2023/01"//Ministry of Science and Higher Education/ ; }, mesh = {Humans ; *gamma-Aminobutyric Acid/metabolism/biosynthesis ; *Brain/metabolism/physiology ; Animals ; *Probiotics ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism ; *Brain-Gut Axis ; }, abstract = {γ-Aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the central nervous system (CNS) and plays a vital role in maintaining neural balance, regulating mood, and reducing stress responses. Recent metagenomic studies of the gut microbiome have shown that various bacterial species, especially those in the genera Lactobacillus, Bifidobacterium, and Bacteroides, isolated from the human gut and environmental sources such as fermented foods, contain glutamate decarboxylase (GAD) systems that enable GABA production. Microbially produced GABA can influence the microbiota-gut-brain (MGB) axis by activating neural, endocrine, and immune signalling pathways that are crucial for maintaining gut and brain homeostasis. Emerging evidence suggests that supplementation with GABA-producing bacteria, known as psychobiotics, may improve neurotransmitter balance, modulate cytokine production, strengthen the integrity of the intestinal barrier, and alleviate anxiety- and depression-related behaviours. This review summarises current knowledge of GABA-producing bacterial strains derived from the human gut and food environments and explores their potential as emerging psychobiotics in modulating gut-brain communication and mental health.}, } @article {pmid42278559, year = {2026}, author = {Li, CC and Sun, DS and Lien, TS and Lin, GL and Cheng, CF and Tsai, KW and Wu, WS and Hu, CT and Lin, MD and Lin, WY and Yang, CH and Liou, JW and Chang, HH}, title = {TiO2 Nanoparticles Trigger Gut-to-Gill Bacterial Translocation and Dysbiosis in Zebrafish.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278559}, issn = {1422-0067}, support = {111-2320-B320-006-MY3, 112-2320-B-320-007, 114-2320-B-320-004//National Science and Technology Council/ ; TCMMP114-01, TCAS111-02, TCAS112-02, TCAS113-04, TCRD112-033, TCRD113-041, TCRD114-029, TCRD115-030//Tzu Chi Foundation/ ; }, mesh = {Animals ; *Titanium/toxicity/chemistry ; *Zebrafish/microbiology ; *Dysbiosis/microbiology/chemically induced ; *Gills/microbiology/drug effects ; *Bacterial Translocation/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Nanoparticles/toxicity ; RNA, Ribosomal, 16S/genetics ; *Metal Nanoparticles/toxicity/chemistry ; }, abstract = {Titanium dioxide nanoparticles (TiO2-NPs) are widely produced and persist in aquatic ecosystems, yet their indirect effects on host-microbe interactions remain poorly defined. By using zebrafish (Danio rerio) as a sentinel species, this study investigated the effects of subchronic 5 mg/L TiO2-NP exposure. Dynamic light scattering was utilized to characterize the bimodal aggregates (peaks at 917 and 46,841 nm; surface charge: +22.08 mV) that define the environmental state of TiO2-NPs. Parallel 16S rRNA metagenomic profiling on Day 6, prior to mortality, revealed profound gut dysbiosis. A marked increase in Chao1 richness (p < 0.01), alongside a catastrophic 333-fold reduction in beneficial Cetobacterium and an 856-fold enrichment of pathogenic Mycobacterium, was observed. Beta-diversity and hierarchical clustering analyses revealed a striking convergence between gut and gill microbial signatures, supporting a gut-to-gill translocation model. These results suggest that TiO2-NPs exposure induces intestinal dysbiosis, facilitating opportunistic bacterial migration via internal (gut-blood-gill) or external (fecal-water-gill) pathways. This study identifies dysbiosis-driven secondary infection as a novel, overlooked mechanism of nanoparticle toxicity, necessitating a shift in ecological risk assessments toward host-microbe interactions.}, } @article {pmid42278576, year = {2026}, author = {Kozhakhmetov, S and Kushugulova, A and Vinogradova, E and Rakhmankulova, A and Terzic, M and Bapayeva, G and Aimagambetova, G and Kamzayeva, N and Kim, Y and Primbetov, B and Imankulova, B and Kongrtay, K and Kadroldinova, N and Galym, M and Makhambetova, S and Nurgaliyeva, K and Abdiyeva, Z and Zhumakanova, Z and Baktybayeva, D and Smagulova, B and Ukybassova, T}, title = {Cervicovaginal Mycobiome Restructuring by HPV and Bacterial Community State Types in a Kazakhstani Shotgun Metagenomic Cohort: Lactobacillus iners as a Candida-Permissive Niche Associated with α-9 HPV in Cytologically Normal Women.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278576}, issn = {1422-0067}, mesh = {Humans ; Female ; *Lactobacillus/genetics/physiology ; *Vagina/microbiology/virology ; *Candida/genetics/physiology ; *Cervix Uteri/microbiology/virology ; *Papillomavirus Infections/virology/microbiology ; *Mycobiome/genetics ; Metagenomics/methods ; Adult ; Microbiota ; Shotgun Sequencing ; Middle Aged ; *Human Papillomavirus Viruses/genetics ; }, abstract = {Cervicovaginal dysbiosis is an established co-factor of high-risk human papillomavirus (HPV) persistence and cervical neoplastic development, yet most studies address the bacterial compartment in isolation, leaving fungal communities and bacterial-fungal cross-kingdom interactions underexplored, particularly in Central Asian populations. We performed shotgun metagenomic sequencing (mNGS) of cervicovaginal samples from 311 Kazakhstani women undergoing routine cervical screening. HPV status was determined using combined PCR and mNGS methods, and cervical screening was completed using liquid-based cytology (NILM, ASC-US, LSIL, ASC-H). Bacterial, viral, and fungal taxa were profiled from a single shotgun dataset with Kraken2 pipeline. Bacterial community state types (CSTs) were determined based on dominant bacterial species, functional gene content was annotated against KEGG using eggNOG, and covariate-adjusted associations were estimated using MaAsLin3. Mycobiome β-diversity differed significantly by HPV status (p = 0.003). In particular, Candida positivity was significantly associated with HPV presence and with high-risk α-9 HPV in cytologically normal (NILM) samples (OR = 3.6, [1.6-9.6], p ≤ 0.001). Covariate-adjusted analysis was consistent with this positive association (q < 0.05). Concurrently, among CSTs, Lactobacillus iners-dominated CST III and dysbiotic Gardnerella vaginalis-dominated CST IV showed a 3-fold higher Candida albicans prevalence (p < 0.01). Further analysis demonstrated that, functionally, both of these CSTs had depleted capacity for lactate metabolism (ko00620, p < 0.0001) and, in particular, for the genetic capacity for pyruvate-dependent H2O2 generation (half that of the L. crispatus-dominated CST I). These findings support L. iners as a metabolically permissive rather than protective Lactobacillus and suggest cross-kingdom functional signatures as candidate biomarkers for HPV acquisition and persistence in Central Asia, a region previously absent from the cervicovaginal microbiome literature.}, } @article {pmid42278616, year = {2026}, author = {Gajic, I and Jovicevic, M and Kekic, D and Kabic, J and Vicic, I and Lukovic, B and Tomic, A and Sovljanski, O and Skoric, M and Sikanic, I and Jankovic, M and Smitran, A and Bozic, L and Golic, B and Basic, J and Karabasil, N and Opavski, N}, title = {Evolving Approaches to Bacterial Identification: A Review of Classical and Modern Techniques.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, pmid = {42278616}, issn = {1422-0067}, support = {7042//Scientific Fund of the Republic of Serbia/ ; }, mesh = {*Bacteria/genetics/classification/isolation & purification ; Humans ; Animals ; *Bacterial Infections/diagnosis/microbiology ; Metagenomics/methods ; *Bacterial Typing Techniques/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Infectious diseases remain a major global health concern, with a growing burden of antimicrobial resistance and consequent higher mortality in the human population. Accurate bacterial identification is fundamental across clinical, veterinary, agricultural, and research settings, supporting effective diagnosis, antimicrobial stewardship, infection control, food safety, and environmental monitoring; however, conventional approaches are limited by time constraints, reduced sensitivity, and challenges in detecting fastidious or uncultivable organisms. This review provides a comprehensive overview of classical and advanced methods, including microscopy, culture, biochemical testing, immunological and serological assays, proteomic and spectroscopy-based techniques, and molecular approaches, such as polymerase chain reaction (PCR), digital PCR, DNA hybridization, 16S rRNA gene sequencing, whole-genome sequencing, and metagenomics. The integration of artificial intelligence has further enhanced analytical performance. Nevertheless, harmonization of bioinformatics frameworks remains essential, as variability in algorithm-defined cut-off values limits standardized implementation of whole-genome sequencing in routine laboratories. Emerging technologies, including CRISPR-based diagnostics and phage- and nanomaterial-based detection systems, offer promising alternatives. Overall, the integration of these approaches is expected to improve the accuracy, speed, and applicability of bacterial identification across diverse settings; however, these advances should be implemented cautiously, with standardization remaining a key priority alongside technological modernization.}, } @article {pmid42279294, year = {2026}, author = {Newell, LF and Twohey, E and Sweetnam, J and Skendzel, S and Stingle, J and Vartanian, KA and Davis, BA and Layman, CE and Carbone, L and Ray, K and Fei, SS and Karstens, L and He, FC and El Jurdi, N and Blaes, AH and Meyers, G and Cook, RJ and Baraki, A and Dengel, DR and Holtan, SG}, title = {Attenuation of Immune Senescence Markers After Intensive Cancer Therapy Through Resistance Training: A Pilot Study.}, journal = {Cancers}, volume = {18}, number = {11}, pages = {}, pmid = {42279294}, issn = {2072-6694}, abstract = {Background: Chemotherapy and radiation accelerate aging of multiple systems, including the immune and musculoskeletal systems. Resistance training may mitigate some of the late physiologic effects of cancer therapy. Methods: We developed a community-based pilot study of resistance training for long-term cancer survivors meeting criteria for pre-frailty or frailty (N = 8; 6 allogeneic hematopoietic cell transplant, 1 autologous hematopoietic transplant, 1 breast cancer survivor) and their caregivers (N = 8 healthy controls) consisting of a baseline assessment, 10 weeks of personalized resistance training at least once weekly as a group and as many additional times on an individual basis as their schedule allowed, and an end-of-study assessment to measure change in strength and body composition. Blood samples were collected at the start of the study and after the 10-week training program to assess changes in peripheral blood mononuclear cell DNA methylation patterns, gene expression measured by RNA sequencing, and stool microbiome analysis using metagenomics. The median number of resistance training sessions was 25 sessions. Results: Cancer survivors and controls both more than doubled their squat and press volume after 10 weeks. At baseline, cancer survivors exhibited a pro-inflammatory transcriptomic and epigenetic profile with elevated interferon signaling and reduced naïve T cell signatures compared to healthy controls, consistent with immune senescence. After 10 weeks of resistance training, these differences normalized, suggesting that exercise exerted anti-inflammatory and immune-restorative effects in cancer survivors at both gene expression and methylation levels. Ten fecal microbial pathways that were lower in relative abundance in patients compared with controls at baseline were no longer significantly different post-exercise. Conclusions: Our data suggest that in addition to beneficial changes in body composition, resistance training may exert an immune restorative effect in cancer survivors.}, } @article {pmid42279452, year = {2026}, author = {Yang, L and Meng, W and Yang, T and Zhu, Y and Wang, Z}, title = {Microbiomics: Novel Biomarkers of Colorectal Cancer Diagnosis and Prognosis.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {11}, pages = {}, pmid = {42279452}, issn = {2075-4418}, abstract = {With colorectal cancer (CRC) accounting for over 1.9 million new cases and 930,000 deaths globally in 2020, there is a critical need for innovative indicators to forecast disease advancement and therapeutic outcomes. The gut microbiome has emerged as a fertile area for discovering such diagnostic and prognostic signals. This narrative review collected current evidence on intestinal microorganisms and their metabolic products as candidate markers for CRC control. Intestinal communities influence malignancy through diverse mechanisms, including metabolic shifts, immune modulation, inflammation, proliferation/apoptosis regulation, genotoxicity, and mucosal barrier disruption. Pathogenic species, such as Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis, facilitate tumorigenesis via FadA-mediated signaling and Th17/IL-17 responses. In contrast, beneficial taxa like Faecalibacterium prausnitzii and Akkermansia muciniphila provide protective effects through short chain fatty acid production. Macrophage phenotype physiological equilibrium is altered and inflammatory status fluctuates under the former. Metabolically, hydrogen sulfide damages mitochondrial DNA and secondary bile acids stimulate cellular proliferation. While 16S rRNA sequencing and shotgun metagenomics are established detection strategies, innovative platforms like organoids and gene arrays remain in the exploratory stage. Clinical data indicates that F. nucleatum aligns with advanced tumor stage, and its combined detection with colibactin-producing E. coli achieves high sensitivity for early-stage screening. Additionally, A. muciniphila levels can anticipate the efficacy of PD-1 blockade immunotherapy. Microbiota-derived tools represent a transformative direction in oncology. Future research must focus on standardizing protocols and validating multi-marker panels to enhance clinical translation.}, } @article {pmid42279756, year = {2026}, author = {Abaalkhail, MA and Mohamed, SHS and Aljurbua, MS and Alkhuraisi, RA and Aladhadh, M}, title = {Microbial Diversity of Spontaneously Fermented Camel Milk.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {42279756}, issn = {2304-8158}, abstract = {Camel milk is widely consumed in the world's arid and semi-arid regions because of its favorable nutritional profile and associated human health benefits. The indigenous microbiota of raw camel milk is diverse and composed of different bacterial and fungal groups. This community drives spontaneous milk fermentation, resulting in a variety of traditional products, including Gariss, Shubat, Chal, Dhanaan, Lfrik, and Suusac (or Suusa), depending on geographic region and cultural practice. This fermented milk has improved sensory, nutritional, and health profiles, as well as an extended shelf life, compared to raw milk. Fermentation alters the microbial community structure, with lactic acid bacteria (LAB) consistently becoming dominant, while yeasts and molds are also detected in some products. These patterns have been identified using both culture-dependent and culture-independent approaches, including 16S rRNA gene sequencing and whole-genome shotgun metagenomics. However, the milk's microbial composition is highly variable and is influenced by the original composition, geographical location, fermentation and hygiene practices. The detection of opportunistic pathogens such as E. coli, Salmonella and Listeria in some traditional products raises important food safety concerns. This review presents current knowledge on fermented camel milk microbiology using a cross-regional approach, identifying key gaps in microbial safety and process standardization to support wider acceptance and potential commercialization.}, } @article {pmid42280335, year = {2026}, author = {Barba-de la Rosa, AP and Treviño, S and Ovando-Vázquez, C and De León-Rodríguez, A and Calva-Cruz, OJ and Barrera-Pacheco, A and Espitia-Rangel, E}, title = {Dietary Supplementation with Amaranth Protein Isolate Modulates the Gut Microbiota in Children with Overweight and Obesity: A Nonrandomized Trial.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280335}, issn = {2072-6643}, support = {A3-S-37825//Consejo nacional de ciencia y tecnologia mexico/ ; }, mesh = {Humans ; Child ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; *Amaranthus/chemistry ; Body Mass Index ; Blood Glucose/metabolism ; *Pediatric Obesity/microbiology/blood ; *Plant Proteins/administration & dosage/isolation & purification/pharmacology ; *Overweight/microbiology ; Cholesterol/blood ; Insulin/blood ; Triglycerides/blood ; Feces/microbiology ; }, abstract = {BACKGROUND: Overweight and obesity are chronic diseases that result from complex interactions including genetics, environment, eating behaviors, and limited access to a healthy diet. Amaranth protein (AmProt) has several health benefits, but no studies have examined its effects on the modulation of children's gut microbiota. The work aimed to analyze serum levels and changes in gut microbiota in children aged 8-10 years with different body mass index (BMI) values after supplementation with AmProt.

METHODS: Participating children were allocated into three groups according to their BMI: normal weight (NW), overweight (OW), and with obesity (OB). Children received AmProt for 90 days. Levels of fasting blood glucose, cholesterol, triglycerides, and insulin were analyzed before and after diet supplementation. HOMA-IR and adinopectin/leptin ratio were evaluated. Feces were collected and metagenome analysis was carried out.

RESULTS: No changes in glucose levels were observed across groups and treatments; however, cholesterol and triglycerides levels tended to decrease. The HOMA-IR value increased in relation to BMI and no changes were observed after treatment. Firmicutes were highly abundant in all groups. The lower abundance of Ruminococcus was observed in the OW and OB groups. In the OW group, Blautia, Butyricicoccus, and Roseburia were also observed in increased abundance. In all groups, AmProt consumption tended to increase the abundance of Coproccus, Prevotella, and Collinsella. Conclusions: Supplementation of the children's diet with AmProt showed an improvement in serum cholesterol and triglyceride levels, which could be related to changes in the microbiota related to lipid metabolism.}, } @article {pmid42280338, year = {2026}, author = {Zhang, S and Liu, K and Shi, L and Yan, C and Wang, A and Liu, A and Guo, H and Xie, A and Kong, XJ}, title = {Development of a Metagenomics-Guided Personalized Synbiotic Protocol for Children with Autism Spectrum Disorder: An Exploratory Case Series.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, pmid = {42280338}, issn = {2072-6643}, support = {92436//Boston Children's Hospital/ ; 233263//Massachusetts General Hospital/ ; }, mesh = {Humans ; *Synbiotics/administration & dosage ; *Metagenomics/methods ; Child, Preschool ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; Child ; Female ; Pilot Projects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Treatment Outcome ; *Precision Medicine/methods ; }, abstract = {BACKGROUND/OBJECTIVES: Gut microbiota dysregulation has been increasingly implicated in the pathophysiology of autism spectrum disorder (ASD), yet clinical responses to standardized probiotic interventions remain inconsistent, likely reflecting substantial inter-individual variability in baseline microbiome composition, host-microbe interactions, immune tone, and metabolic function. Here, we present a pilot implementation of a metagenomics-guided, personalized synbiotic intervention in children with ASD using the Systematic Microbiome Assessment and Reconstruction Therapy (SMART) framework.

METHODS: Seven children (aged 5-12 years) underwent longitudinal fecal shotgun metagenomic profiling, and dietary habits, food sensitivities, and regional dietary background were recorded as contextual factors potentially influencing microbiome composition and response to intervention. Individualized synbiotic formulations were constructed based on microbial taxonomic composition and inferred functional capacity and iteratively refined over time. Gastrointestinal outcomes were assessed through caregiver-reported clinical observations, whereas behavioral changes were evaluated using standardized instruments.

RESULTS: Several participants demonstrated improvements in gastrointestinal symptoms and selected behavioral domains. Notably, in a subset of participants, improvements in gastrointestinal function preceded measurable behavioral changes.

CONCLUSIONS: Although limited by a small sample size and lack of a control group, these findings provide preliminary evidence supporting the feasibility of implementing a metagenomics-guided personalized synbiotic framework in ASD and generate hypotheses for future investigation. This work presents a preliminary conceptual framework for integrating microbial composition and inferred functional profiling into individualized intervention design and highlights the potential value of microbiome-informed stratification in future studies of treatment response. Larger controlled studies with objective outcome measures are warranted to further evaluate feasibility, reproducibility, and potential clinical utility.}, } @article {pmid42280669, year = {2026}, author = {Zhang, L and Dong, J and Zhao, J and Jiang, H and Zhang, W}, title = {Rhizosphere Functional Plasticity and the Keystone Taxon Sphingomonas Facilitate Sweet Cherry Adaptation to Semi-Arid Stress.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {42280669}, issn = {2223-7747}, support = {2023LHMS03007//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; }, abstract = {Translocation of elite cultivars across distinct climatic regions often induces transplantation shock. Although the rhizosphere microbiome can facilitate host acclimation, the underlying functional mechanisms remain unclear. Here, we investigated microbiome-mediated adaptation in "Hongdeng" sweet cherry (Prunus avium L.) moved from a humid coastal region (Dalian, DL) to a semi-arid inland habitat (Hohhot, HS). We integrated plant physiological assays, metagenomic sequencing, and structural equation modeling (SEM) to compare the source population (DL), the introduced population (HS), and a locally acclimated reference cultivar ("Summit", HSY). The introduced trees adjusted physiologically to the semi-arid environment by elevating proline levels and antioxidant enzyme activities. Although environmental stress reduced microbial alpha diversity, the core taxonomic framework persisted. Community assembly analysis indicated that the semi-arid climate intensified environmental filtering. Network analysis identified Sphingomonas as a keystone taxon; notably, it maintained a highly connected topological role despite a stable relative abundance. Furthermore, structural equation modeling showed that the environmental stress index positively correlated with the upregulation of microbial DNA repair pathways (R = 0.81, p < 0.001). Ultimately, the SEM demonstrated that environmental stress primarily shapes microbial functional profiles rather than driving species turnover, thereby contributing to host adaptation. The successful establishment of introduced sweet cherry in semi-arid regions is tied more closely to rhizosphere functional plasticity than to taxonomic restructuring. These findings highlight the role of the keystone taxon Sphingomonas in maintaining rhizosphere homeostasis, offering a theoretical framework for targeted microbiome engineering to mitigate transplant shock and enhance crop resilience.}, } @article {pmid42280715, year = {2026}, author = {Beckett, T and Hesse, U}, title = {Transcriptome Profiling of Leaves and Roots from Rooibos (Aspalathus linearis) Using Oxford Nanopore Sequencing.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, pmid = {42280715}, issn = {2223-7747}, support = {PMDS22062326365//National Research Foundation/ ; N/A//Rooibos Council of South Africa/ ; }, abstract = {Rooibos (Aspalathus linearis) is one of the few endemic South African plants that has achieved economic importance and international acclaim, mostly as a herbal tea. Plant production, limited to a small mountainous region in South Africa, is at risk as commercial rooibos longevity is in decline, mostly due to low stress tolerance. Transcriptome data can serve to identify molecular markers for improved stress response, which would speed up selection and facilitate the establishment of breeding programmes. Previously, rooibos leaf transcriptomes have been sequenced using Illumina, which yields short reads, hampering correct reassembly of full-length transcripts. Here, we established Oxford Nanopore-based, long-read transcriptome analysis for leaf and root samples from rooibos. We report on potential pitfalls in data pre-processing (PolyA tail trimming and rRNA removal), and compare two assemblers (RATTLE and RNA-Bloom2) and two clustering algorithms (VSEARCH and CD-HIT). The best assembly comprising 169,122 transcripts was generated using RNA-Bloom2 with short-read polishing, followed by CD-HIT clustering. Of the 95,054 predicted proteins, only 67% were also present in the Illumina dataset. The remainder comprised substantially shorter, mostly full-length sequences from a wide range of primary and secondary biosynthesis pathways. Functional annotation indicated that this transcriptome represents a high-quality, comprehensive resource for data mining. In the leaf fraction, comparative transcriptomics identified overexpressed rooibos transcripts potentially involved in photosynthesis, photorespiration and carbon fixation. In the roots, overexpressed transcripts encoded enzymes potentially involved in regulation of root growth and secondary metabolite biosynthesis. These transcripts may represent first targets for molecular marker development.}, } @article {pmid42281243, year = {2026}, author = {Stanford, J and Hoedt, EC and Gómez-Martín, M and Clarke, ED and Duncanson, K and Burrows, T and Collins, CE}, title = {Contrasting dietary patterns remodel gut microbial function and generate multi-omic signatures associated with cardiometabolic markers.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2685381}, pmid = {42281243}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Feces/microbiology ; Biomarkers/urine/blood ; Female ; Adult ; Male ; *Diet ; Australia ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Cross-Over Studies ; Middle Aged ; Metabolome ; Metabolomics ; Blood Pressure ; }, abstract = {Diet is a modifiable determinant of gut microbiome composition, yet the impact of contrasting whole-dietary patterns on microbial metabolic capacity and coordinated host metabolic signatures remains incompletely characterized. In a randomized crossover feeding trial, 34 Australian adults were provided with a Healthy Australian Diet (HAD), aligned with national dietary guidelines, and a Typical Australian Diet (TAD), reflecting average population intake for two weeks each, separated by a two-week washout. Fecal microbiome composition and function were assessed using shotgun metagenomics, plasma and urine metabolites by untargeted metabolomics, with cardiometabolic markers including blood pressure, plasma lipids, and glucose quantified. HAD was associated with reduced taxonomic and functional alpha diversity relative to baseline, with no change following TAD. Species-level responses were modest, 105 functional pathways differed between diets, with 99 increasing following HAD, predominantly related to amino acid and nucleotide biosynthesis and vitamin/cofactor metabolism. Multi-omic integration using DIABLO achieved strong discrimination of dietary responses (held-out accuracy 91.7%; permutation p = 0.005). In total, 77 individual omic feature-cardiometabolic outcome associations survived FDR correction (q < 0.05), spanning microbial gene functions, plasma metabolites, and urinary metabolites linked to cholesterol, blood pressure, and triglyceride responses. These exploratory findings suggest that integrated microbiome-metabolome profiling may capture inter-individual variation in dietary cardiometabolic responses, though replication in larger, independent, robustly designed studies is needed before translational personalized nutrition strategies can be assessed.}, } @article {pmid42281420, year = {2026}, author = {Góngora, E and Altshuler, I and Ellis, M and Okshevsky, M and Greer, CW and Whyte, LG}, title = {In Situ Mesocosm Experiment Shows the Capability of the Microbial Community of a Canadian High Arctic Shoreline to Degrade the New Generation of Ship Fuels.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c10583}, pmid = {42281420}, issn = {1520-5851}, abstract = {The warming effects of climate change are leading to a reduction in sea ice, which could open new shipping routes across the Arctic, leading to the possibility of hydrocarbon spills washing onto a shoreline. The behavior and biodegradability of new low-sulfur fuels (LSFs), currently being used by vessels worldwide, has not been assessed on Arctic beaches. We deployed mesocosm experiments on a remote Canadian high Arctic beach for 33 days using two LSFs (marine diesel and ultra-low-sulfur fuel oil, ULSFO) and Bunker C fuel oil (currently being phased out). Bunker C was mostly removed from beach sediments by natural attenuation (14.6% biodegradation, 62.8% nonbiological removal), while the LSFs were more easily biodegraded (37.6-72.8% biodegradation, 2.9-10.0% nonbiological removal). Native beach sediment microorganisms, including putatively novel taxa, adapted to the presence of fuel by expressing multiple aliphatic hydrocarbon biodegradation genes, but only few aromatic hydrocarbon degradation genes. Our results suggest that, while not as biodegradable as marine diesel, ULSFO appears to be a more environmentally friendly alternative to Bunker C due to its higher biodegradability under in situ Arctic environmental conditions. However, limited aromatic hydrocarbon biodegradation under cold and nutrient-poor environmental conditions could negatively affect the efficacy of natural attenuation.}, } @article {pmid42282013, year = {2026}, author = {Dobbler, PT and Ravi, A and Větrovský, T and Pěchoučková, E and Nemec, A and Kyselková, M}, title = {Single-contig bacterial genomes recovered from cattle fecal metagenomes at farms with variable antibiotic use.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9715194/v1}, pmid = {42282013}, issn = {2693-5015}, abstract = {Cattle feces represent a complex microbial reservoir with implications for animal health and the environmental dissemination of microorganisms and antibiotic resistance genes. Metagenomic studies have shown that cattle fecal communities are dominated by Bacillota and Bacteroidota, whereas low-abundance taxa, including potential pathogens, often remain underrepresented due to methodological detection limits. Here, we present 84 single-contig, medium- to high-quality metagenome-assembled genomes (MAGs) recovered from cattle feces after enrichment for bacteria able to grow in acetate-supplemented minimal medium. The MAGs were classified within the phyla Actinomycetota (20 MAGs), Bacillota (5), Bacteroidota (21), Patescibacteriota (5), and Pseudomonadota (33), with 41 MAGs representing putative novel taxa at species to family level. Nineteen MAGs carried antibiotic resistance genes and six MAGs were assigned to opportunistic pathogenic species. This dataset thus provides a genomic resource for studies of bacterial diversity and antimicrobial resistance at the animal-environment interface within a One Health framework.}, } @article {pmid42282041, year = {2026}, author = {Schutz, C and Queiroz, A and Mota, T and Ward, A and Barr, D and Janssen, S and Shey, M and Wilkinson, R and Wilkinson, K and Burton, R and Lelouvier, B and Andrade, B and Meintjes, G}, title = {Microbial product translocation and mortality in adults hospitalised with HIV-associated tuberculosis: a prospective observational cohort study.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9856875/v1}, pmid = {42282041}, issn = {2693-5015}, abstract = {Background: HIV-associated tuberculosis (HIV-TB) results in unacceptably high mortality rates despite appropriate treatment. Patients hospitalized with HIV-TB often have disseminated tuberculosis and sepsis syndrome which may result in gastro-intestinal barrier dysfunction and facilitate microbial product translocation. Microbial product translocation may contribute to HIV-TB deaths by driving systemic inflammation. Objectives: To assess microbial product translocation and gastrointestinal epithelial damage in patients hospitalized with HIV-TB and the association with 12-week mortality and biomarkers of tuberculosis dissemination. To describe the bacterial blood microbiome (abundance and diversity) in patients with HIV-TB, its association with mortality and tuberculosis dissemination and compare to outpatient controls. Methods: Patients hospitalized with a new diagnosis of HIV-TB were enrolled and prospectively followed for 12 weeks. Markers of microbial product translocation and gastrointestinal damage were measured in a subset (n=373) and bacterial 16s rDNA was quantitated and metagenomic sequencing performed in 235 patients. Microbial product translocation and gastrointestinal epithelial damage marker concentrations were compared between hospitalized patients who died and survivors and inpatients compared to HIVpositive outpatient controls. Logistic regression analysis was performed to determine associations with mortality. Bacterial abundance, diversity and immune perturbation was measured and analysed across patient outcome groups and in patients with tuberculosis dissemination. Results: Patients hospitalized with HIV-TB had significantly higher concentrations of bacterial 16s rDNA, soluble CD14 (sCD14), lipopolysaccharide binding protein (LBP), trefoil factor 3 (TFF3) and lower endotoxin core antibody IgM (EndoCAB), compared to outpatient controls. Soluble CD14 and TFF3 were significantly higher and EndoCAB lower in inpatients who died versus survivors. TFF3 was independently associated with mortality. LPS, sCD14, LBP, EndoCAB and TFF3 showed significant trends in patients with positive biomarkers of tuberculosis dissemination. Metagenomic sequencing showed higher diversity in hospitalised HIV-TB patients compared to controls, but diversity was not different between outcome groups. Mycobacterium genus proportions were increased in hospitalised patients who died compared to survivors. Conclusion: We found evidence of increased gastrointestinal epithelial damage and microbial product translocation in patients hospitalized with HIV-TB and in patients with positive biomarkers for tuberculosis dissemination, however, only TTF3 (a marker of gastrointestinal epithelial damage), was independently associated with mortality.}, } @article {pmid42282268, year = {2026}, author = {Frame, LA and Warren, A and Al Qalam, A and Corr, PG and Farah, M and Karam, M and Rangoussis, K and Fahim Devin, M and Celikkol, Z and Gordon, L and Villarreal, D and Catto, E and Udam, Y and Thompson, K and Lubinski, O and Samman, A and Badawi, A and Hack, H and Hunter, M and Hines, I and Servetas, S and Jackson, SA and Hasan, NA and Kogan, M}, title = {Brain health and the gut microbiome (bMicrobiome Study): a proof-of-concept, feasibility study integrating shotgun metagenomics, metrology, and multidimensional phenotyping across the cognitive aging spectrum.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2679810}, pmid = {42282268}, issn = {2993-3935}, abstract = {BACKGROUND: Associations between the gut microbiome and cognitive decline remain inconsistent, reflecting methodological variability, small cohorts, and limited integration of behavioral and lifestyle factors. The microbiota-gut-brain axis may influence cognition through metabolic, immune, and neuroendocrine pathways affecting mood, decision-making, and health behaviors.

METHODS: This prospective, proof-of-concept study integrated multidimensional phenotyping with metagenomic sequencing (shotgun) in adults (50-90 y) around Washington, DC. Participants were classified as healthy controls (HC) or mild cognitive impairment (MCI) by clinical history; early Alzheimer's disease (eAD) participants were unable to complete study requirements. Longitudinal assessment used Boston Cognitive Assessment (BoCA), patient-reported outcomes (PROMIS-29), dietary intake and quality (DietID™), readiness-for-change (adapted URICA), at-home stool sample collection.

RESULTS: Seventeen participants completed sufficient assessments (HC n = 11; MCI n = 6). Substantial overlap in gut microbiome composition was observed between HC and MCI. Poorly characterized or uncommon taxa drove trends; unassigned taxa were common. Assessment revealed high diet quality and variability in dietary patterns and key components (vegetables, whole grains, fat, fish). Participants demonstrated high readiness to engage in nutritional behavior change, with individuals with MCI reporting greater concern about maintaining changes and a stronger desire for external support.

CONCLUSIONS: Integrating multidimensional phenotyping with metagenomics is feasible in cognitive decline. Findings highlight biological and behavioral heterogeneity, limitations of species-level inference, and diet and behavioral readiness as modifiable contextual factors.}, } @article {pmid42282663, year = {2026}, author = {Torres-Morales, J and Dewhirst, F and Kauffman, KM and Mark Welch, J and Borisy, G}, title = {Site-specialization of human oral Porphyromonas species.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.02.729646}, pmid = {42282663}, issn = {2692-8205}, abstract = {Site-specificity within the human oral cavity reflects adaptation mechanisms such as genome divergence and metabolic specialization. Members of the genus Porphyromonas are distributed across oral sites in health and disease, yet the specific distribution of taxa and the functional basis of their site-specificity remain poorly understood. We analyzed 1,242 metagenomes from nine oral sites in healthy individuals and 24 subgingival plaque samples from individuals with periodontitis. Competitive mapping to a dereplicated genus-level pangenome of 84 reference genomes, combined with phylogenomic, gene-level detection, and functional profiling, revealed distinct site-specific distribution patterns, ecotype differentiation, and metabolic specialization across Porphyromonas taxa. Porphyromonas pasteri was the most abundant and widespread taxon in healthy subjects, comprising two ecotypes--one mucosal, one plaque-associated. Porphyromonas gingivalis was rare in healthy subjects but present in periodontal disease, although detected in only half of periodontitis samples. P. gingivalis exhibited the broadest metabolic repertoire, suggestive of a survival strategy adaptive to disparate conditions. In contrast, Porphyromonas catoniae, restricted to healthy dental plaque, lacked biosynthetic pathways for cobalamin, biotin, and serine, implying nutritional dependency on other taxa or the host. Porphyromonas endodontalis, detected in subgingival plaque across both health and disease, also lacked several metabolic pathways. A 44 kb conjugative element identified in P. gingivalis was detected across healthy and periodontitis subgingival plaque microbiomes independently of the P. gingivalis chromosome, indicating horizontal transfer. These findings reveal genomic divergence and complex metabolic specialization among Porphyromonas taxa, refining our understanding of their role in the ecological structure of the human oral microbiome.}, } @article {pmid42282812, year = {2026}, author = {Jiang, AK and Grant, MR and Arp, G and Dufault-Thompson, K and Clarke, AM and Li, Y and Lehman, D and Jarmusch, AK and Hall, B and Jiang, X}, title = {Discovery of BilV reveals a multienzymatic basis for bilirubin reduction across vertebrate gut microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.01.729425}, pmid = {42282812}, issn = {2692-8205}, abstract = {Gut bacteria reduce bilirubin to urobilinogen, allowing it to be excreted through feces and urine, but studies have long noted a heterogeneous mixture of partially reduced bilirubin-derived intermediates, suggesting that multiple enzymes are involved. Here we identify bilirubin vinyl reductase (BilV), a novel Old Yellow Enzyme family reductase encoded in the genomic neighborhood of the known bilirubin reductase (bilR). Using heterologous expression and LC-MS/MS, we show that BilR acts on the methine bridges in the bilirubin reduction pathway; co-expression with BilV enables vinyl-group reduction and complete conversion to urobilinogen. In bacterial genomes, bilV co-occurs primarily with the bilR -insertion subtype and is largely absent alongside bilR -short. Analysis of 1,197 gut metagenomes across 14 vertebrate species reveals that this differential co-occurrence shapes pathway availability across hosts: carnivores and omnivores carry balanced bilR and bilV , whereas avian microbiomes, dominated by bilR -short, are depleted for bilV . These findings establish that bilirubin reduction to urobilinogen involves two enzymes with complementary regioselectivity, and that their distribution across vertebrate gut microbiomes varies in concert with host bile pigment chemistry.}, } @article {pmid42283066, year = {2026}, author = {Zhang, J and Liang, J and Lv, F and Guo, Z}, title = {Maternal vaginal colonization screening for term singleton pregnancy: comparative evaluation of metagenomic next-generation sequencing (mNGS) versus real-time quantitative PCR (qPCR).}, journal = {Practical laboratory medicine}, volume = {50}, number = {}, pages = {e00542}, pmid = {42283066}, issn = {2352-5517}, abstract = {OBJECTIVE: To investigate the distribution characteristics of potential high-risk pathogens for early-onset neonatal infection in maternal vaginal secretions, and to perform a head-to-head comparative evaluation of detection performance for target pathogens between metagenomic next-generation sequencing (mNGS) and real-time quantitative polymerase chain reaction (qPCR), with conventional bacterial culture as the reference standard.

METHODS: A total of 294 valid maternal vaginal secretion samples were prospectively collected and tested in parallel using qPCR, mNGS, and conventional bacterial culture. The Chi-square test was used to compare the differences in pathogen detection rates among the three methods. Receiver operating characteristic (ROC) curve was plotted to calculate the area under the curve (AUC) and 95% confidence interval (CI), to systematically evaluate the detection performance of the two methods for target pathogens.

RESULTS: The spectrum of potential early-onset neonatal pathogens in maternal vaginal secretions, ranked by detection rate, was as follows: Staphylococcus aureus, Streptococcus agalactiae, Ureaplasma urealyticum, Listeria monocytogenes, and Campylobacter fetus. The detection rates of these target pathogens by qPCR, mNGS, and bacterial culture showed high consistency, with no statistically significant difference in detection rates among the three methods (all P > 0.05). ROC curve analysis showed that the AUC values of both qPCR and mNGS for the above major pathogens were all above 0.90, which were significantly different from the null hypothesis of AUC = 0.5 (all P < 0.05), indicating good detection performance; while there was no significant difference in AUC values between qPCR and mNGS (all P > 0.05). In addition, Listeria monocytogenes (3 cases) and Campylobacter fetus (1 case) were only detected by qPCR and mNGS, while not isolated by conventional culture.

CONCLUSION: This head-to-head comparative study confirms that both mNGS and targeted qPCR have high accuracy and consistency for detecting potential early-onset neonatal pathogens in maternal vaginal secretions. We propose a tiered antenatal screening strategy for maternal vaginal pathogenic colonization: qPCR is recommended as the first-line tool for routine antenatal screening due to its high cost-effectiveness and rapid turnaround time, while mNGS is reserved for high-risk pregnant women (e.g., preterm premature rupture of membranes, clinical chorioamnionitis), culture-negative suspected infection cases, or scenarios requiring comprehensive pathogen profiling, to take full advantage of its unbiased, broad-spectrum detection capability. This integrated screening strategy requires further prospective validation with paired neonatal clinical outcome data to confirm its value in the prevention and early intervention of early-onset neonatal infection.}, } @article {pmid42283067, year = {2026}, author = {Wei, F and Wang, X and Lv, H and Xia, H and Gan, G and Chen, X and Liu, X and Chen, H and Zhao, L}, title = {Identification of a potential novel Staphylococcus species via genomic sequencing: A neonatal infection case report.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02631}, pmid = {42283067}, issn = {2214-2509}, abstract = {BACKGROUND: Coagulase-negative Staphylococci (CoNS) are common symbiotic Gram-positive bacteria colonizing human skin and mucous membranes with lower virulence than Staphylococcus aureus. As crucial pathogens of neonatal infections, they often harbor multiple drug resistance genes and can induce neonatal pneumonia, sepsis, suppurative meningitis, and other clinical manifestations.

CASE PRESENTATION: A preterm neonate at 29[+1] weeks' gestation complicated by respiratory distress syndrome and pneumonia received empirical ceftazidime and penicillin for 8 days. The condition initially improved but suddenly deteriorated on postnatal day 17 with septic shock, fever, and anemia. Routine tests suggested Staphylococcus capitis infection, and targeted anti-infective and supportive treatments relieved symptoms. Given the inconsistenty between the infection severity and that of typical Staphylococcus infections, metagenomic next-generation sequencing (mNGS) and whole-genome sequencing (WGS) were further performed, identifying a potential novel Staphylococcus species closely related to Staphylococcus warneri. Nevertheless, the origin of this potential novel species remains unclear, which needs further verification.

CONCLUSION: For neonates with sudden clinical deterioration, intractable infection or ambiguous conventional microbial results, mNGS and WGS facilitate accurate pathogen identification and treatment adjustment. This potential novel strain discovery highlights the importance of enhanced vigilance against bacterial multidrug resistance and the emergence of potential novel pathogens in neonatal care.}, } @article {pmid42283460, year = {2026}, author = {Tothero, GK and Keffer, JL and Emerson, D and Fleming, EJ and Chan, CS}, title = {Distinguishing Leptothrix and Sphaerotilus genera by an integrated genomic-phenotypic analysis supported by new Leptothrix genomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0176825}, doi = {10.1128/msystems.01768-25}, pmid = {42283460}, issn = {2379-5077}, abstract = {The Sphaerotilus-Leptothrix group of bacteria includes one of the first described microorganisms, Leptothrix ochracea, an uncultured type strain, plus isolates of Leptothrix and Sphaerotilus. This group is unified by the ability to form sheaths and oxidize metals, although L. ochracea exhibits obvious ecological, morphological, and functional differences from the rest of Sphaerotilus-Leptothrix. Recently, there have been calls to combine the group into one genus, Sphaerotilus; however, these studies lacked adequate genomic representation of L. ochracea. Here, we present a comprehensive comparative genomic analysis of the Sphaerotilus-Leptothrix group, including expanded representation of L. ochracea, a closely related novel species, Leptothrix toolikensis, and two new isolates (Leptothrix mechoopdaensis). Analysis of 38 genomes resolves three phylogenetic and functional groups: the ochracea-type Leptothrix (Group 1), the mobilis-type Leptothrix (Group 2), and Sphaerotilus (Group 3). Group 1 genomes form a separate genus based on average nucleotide identity and alignment fraction. The genomes clearly diverge from the rest of Sphaerotilus-Leptothrix in phylogeny, size, and metabolic potential. Group 1 genomes are much smaller (2.59-3.04 Mb) than those of Groups 2 (4.55-6.06 Mb) and 3 (3.94-5.07 Mb), while encoding more metal oxidases and fewer carbohydrate-active enzymes. Group 2 clusters with Group 3 phylogenetically and is similar in organic carbon metabolisms but maintains more metal oxidation genes. Group 2 members lack homogeneity in phenotype and genotype, suggesting that additional isolates and genomes are needed for confident classification. However, Group 1 genomes (L. ochracea and L. toolikensis) show clear divergence, precluding their inclusion in Sphaerotilus and supporting the retention of the genus Leptothrix.IMPORTANCEResearchers have long noted differences in metal oxidation, morphology, and ecology among Sphaerotilus-Leptothrix, but longstanding confusion over phylogeny and genus boundaries led to inconsistent taxonomic classification between the two genera. This confusion stems from previous work that used isolates that are unavailable or lost distinguishing traits in culture, and from limited genomic data. Furthermore, the Leptothrix type strain L. ochracea has never been isolated. This study provides molecular evidence that substantiates calls to reassign some Leptothrix members to the genus Sphaerotilus but adds to an emerging body of evidence that Group 1 L. ochracea and now L. toolikensis represent a functionally distinct lineage. While genomic similarity metrics left taxonomic divisions unclear, integrating metabolic potential with phylogeny resolved genus boundaries based on clear functional groupings. This polyphasic approach for delineating genera clarifies longstanding taxonomic confusion and refines our understanding of functional diversity both across and within Sphaerotilus-Leptothrix lineages.}, } @article {pmid42283524, year = {2026}, author = {Hashimoto, K and Fukushima, K and Nakamura, S and Kida, H}, title = {Reply to Rojas-Ponce, "Operational considerations for implementing culture-free mycobacterial sequencing in routine laboratory settings".}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0056426}, doi = {10.1128/jcm.00564-26}, pmid = {42283524}, issn = {1098-660X}, } @article {pmid42283633, year = {2026}, author = {Gómez-Gallego, T and Udaondo, Z and Palacios-Ferrer, R and Díaz-Martínez, L and Ramos, JL}, title = {Development of advanced bioinformatic profiles to improve the detection and functional understanding of fungal acid phosphatases.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0210625}, doi = {10.1128/aem.02106-25}, pmid = {42283633}, issn = {1098-5336}, abstract = {We have retrieved approximately 9,000 protein sequences annotated as fungal acid phosphatase or phytase from the UniProtKB database. Following stringent quality filtering, a curated dataset comprising 3,058 high-confidence sequences was assembled. Phylogenetic analysis resolved these enzymes into eight distinct clades, representing distinct groups of fungal acid phosphatases: purple acid phosphatases, phytases, and groups containing both phytases and acid phosphatases annotations. Based on this classification, we have developed three representative protein profiles referred to as Prf-A-Fungal_phos, Prf-B-Fungal_phos, and Prf-C-Fungal_phos, each designed to capture the phylogenetic and functional diversity of these enzyme families. Heat-map analyses confirmed the breadth and high specificity of these profiles. Application of these profiles to public protein and metagenomic databases enabled the identification of hundreds of previously uncharacterized fungal proteins, with a broad taxonomic distribution and notable prevalence in the Ascomycota and Basidiomycota phyla. Functional validation through heterologous expression of selected candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, supporting the accuracy of the in silico predictions. By integrating large-scale bioinformatics with experimental validation, this study provides robust tools for the discovery of novel fungal phosphatases and for investigation of their ecological roles in nutrient-limited environments.IMPORTANCEFungal acid phosphatases are critical enzymes in global phosphorus cycling, yet no dedicated bioinformatic tools exist to comprehensively identify and classify them across fungal diversity. Here, we present the first PROSITE generalized profiles specific to fungal acid phosphatases, derived from a curated data set of over 3,000 high-confidence sequences spanning eight phylogenetic groups. These profiles exhibit high specificity and sensitivity, enabling the detection of hundreds of previously uncharacterized proteins from public protein databases. Experimental expression of representative candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, validating our in silico predictions. By bridging large-scale bioinformatics with functional validation, this study delivers robust resources to uncover novel fungal phosphatases and to explore their ecological roles in nutrient-limited environments. The developed profiles will advance metagenomic annotation, support soil and environmental microbiology research, and foster biotechnological innovation in sustainable phosphorus management.}, } @article {pmid42283754, year = {2026}, author = {Chen, X and Fang, Z and Li, S and Wu, Q and Liu, W and Xiang, L and Liu, Q and Tan, L and Weng, Q}, title = {Isolation and genomic analysis of a novel Pseudomonas phage from karst cave in China.}, journal = {Archives of virology}, volume = {171}, number = {7}, pages = {}, pmid = {42283754}, issn = {1432-8798}, mesh = {*Genome, Viral ; *Caves/virology/microbiology ; *Pseudomonas Phages/genetics/isolation & purification/classification ; Phylogeny ; China ; *Pseudomonas/virology ; DNA, Viral/genetics ; Sequence Analysis, DNA ; Genomics ; Geologic Sediments/virology ; }, abstract = {Bacteriophages (phages) in extreme environments like karst caves remain largely unexplored. Here, we report vB_Psp_JHDO137a, a novel phage isolated from cave sediment infecting Pseudomonas sp. The 41,530-bp dsDNA genome places it within the genus Ghunavirus (family Autographiviridae). Notably, its genome lacks auxiliary metabolic genes (AMGs), in contrast to AMG-rich profiles reported in cave metagenomic surveys and underscoring the necessity of isolation-based approaches to complement environmental sequencing data.}, } @article {pmid42283827, year = {2026}, author = {Wiśniewski, P and Maździarz, M and Kwietniewska, K and Krawczyk, K}, title = {Shifts in Rhizosphere Bacterial Community Composition and Predicted Functional Potential Associated with Impatiens parviflora Invasion in Temperate Forest.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02807-1}, pmid = {42283827}, issn = {1432-184X}, support = {No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; }, abstract = {Impatiens parviflora is a widespread invasive plant in temperate European forests, yet its influence on rhizosphere microbial communities remains poorly understood. This study provides initial metagenomic insights into taxonomic shifts and predicted functional potential of bacterial communities associated with this invader. Rhizosphere soils were collected from eight I. parviflora-invaded and eight non-invaded control plots in a mixed coniferous forest in northern Poland and analysed using Oxford Nanopore shotgun sequencing, with functional inference performed using the taxonomy-dependent FAPROTAX database. Bacterial richness was significantly higher in invaded soils, whereas Shannon and Simpson diversity indices did not differ between treatments, indicating an expansion of rare taxa without changes in overall diversity structure. The invaded rhizosphere was characterised by a uniform depletion of dominant bacterial orders, with no significantly enriched taxa detected, contrasting with the selective enrichment of microbial groups often reported for other invasive plant species. FAPROTAX-based predictions indicated consistently lower inferred abundances of 37 metabolic processes in invaded plots, including those related to nitrogen cycling and degradation of complex plant polymers. Because these functional predictions are derived from taxonomic composition, they represent inferred ecological potential rather than measured activity. Overall, these results generate testable hypotheses regarding plant-soil feedbacks and highlight the utility of long-read metagenomics for exploring microbial dynamics potentially contributing to the ecological success of I. parviflora in temperate forests.}, } @article {pmid42284845, year = {2026}, author = {Wang, W and Sun, X and Hao, R and Li, F}, title = {Algal community composition drives lake greenhouse gas emissions via dissolved organic matter transformation and microbial processing.}, journal = {Journal of environmental management}, volume = {411}, number = {}, pages = {130177}, doi = {10.1016/j.jenvman.2026.130177}, pmid = {42284845}, issn = {1095-8630}, mesh = {*Lakes ; *Greenhouse Gases ; *Dissolved Organic Matter ; Eutrophication ; Diatoms ; Cyanobacteria ; }, abstract = {Lakes are important sources of greenhouse gases, yet bloom-driven emissions are often assessed from total algal biomass, ignoring algal functional composition. This study examined how cyanobacteria (Microcystis aeruginosa), green algae (Chlorella vulgaris), diatoms (Cyclotella meneghiniana), and dominance-based mixtures regulate DOM transformation and CO2/N2O production under eutrophic conditions. It integrated to pure-culture experiments, water-sediment microcosms, sterilization controls, DOM fluorescence spectroscopy, gas monitoring, and metagenomics to resolve an algae-DOM-microbe-gas cascade. Cyanobacteria produced protein-like DOM and stimulated carbon mineralization, with CO2 exceeding 20 mmol L-1 by day 36; cyanobacteria-dominant mixtures followed a similar high-CO2 trajectory. Green algae generated tyrosine-like DOM and caused the strongest NO2[-] accumulation, reaching 5.21 mg L[-1] by day 21, corresponding to the highest N2O production; this pattern also occurred in green-algae-dominant mixtures. Diatom-only and diatom-dominant treatments favored humic-like DOM, organic carbon retention, and the weakest short-term CO2/N2O accumulation. Sterilization reduced inorganic carbon and greenhouse gas production, supporting microbial control. Background summer metagenomics provided functional context, showing algal-DOM turnover potential through carbon metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, and the TCA cycle, while nirK and other nitrogen genes indicated capacity for substrate-driven incomplete nitrogen reduction. Functional differentiation among Candidatus_Planktophila, Limnohabitans, Rhodoferax, and Cyanobium linked DOM processing with potential gas-production pathways. These results show algal community composition, rather than biomass alone, regulates greenhouse gas production by shaping DOM quality, nutrient intermediates, and microbial C-N pathways. Incorporating algae composition into greenhouse gas assessment, this novel algae-DOM-microbe-gas framework provides mechanistic support for improving eutrophication management and lake-emission mitigation.}, } @article {pmid42284910, year = {2026}, author = {Fu, J and Li, Z and Hu, C and Yao, L and Cao, M and Dong, Y and Wang, P and Liang, Y and Tong, L and Shi, J}, title = {Metagenomic insights into the distribution and potential influencing factors of antibiotic resistance genes in historically polluted lake sediments.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {298}, number = {}, pages = {107898}, doi = {10.1016/j.aquatox.2026.107898}, pmid = {42284910}, issn = {1879-1514}, abstract = {Lake sediments serve as time-integrated archives of the evolution and persistence of environmental antibiotic resistance genes (ARGs), providing insights into how sustained environmental pressures shape resistome structure in human-impacted lake systems. Industrially polluted lakes, as systems subjected to strong anthropogenic disturbance, are characterized by high-intensity contaminant loading in sediments; however, the accumulation patterns and environmental factors associated with ARG persistence in such environments remain poorly understood. This study investigated the horizontal and vertical distributions and potential influencing factors of ARGs along sediment depth gradients (0-40 cm, 40-80 cm, and 80-120 cm) in a lake historically polluted by industrial activities (Ya'er Lake). Results indicated that bacitracin (27.3-43.6%) and multidrug resistance genes (25.4-33.1%) dominated the resistome, with pronounced enrichment in shallow sediments near discharge outlets, reflecting the influence of legacy pollution inputs. ARGs exhibited significant vertical stratification (p < 0.05): highest abundance in shallow layers, peak diversity in middle layers, and shifts with depth of key subtypes. Host-tracking assigned ARGs to 34 major genera across four phyla, with Pseudomonadota, Actinomycetota, Bacillota, and Thermodesulfobacteriota identified as the major ARG hosts. Microbial communities and mobile genetic elements (MGEs) jointly shaped ARG persistence, with shallow sediments showing broader host-MGE coupling and deeper sediments showing stronger signatures of environmental filtering and selective MGE-mediated maintenance. Overall, ARGs shifted from surface enrichment associated with historical wastewater inputs to a more selective persistence pattern with burial depth, indicating contaminated lake sediments as long-term reservoirs and potential dissemination sources of ARGs.}, } @article {pmid42284942, year = {2026}, author = {Yang, X and Peng, AD and Huang, YH and Cheng, JH and Zhong, HT and Zhou, HT and Liu, PQ and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG}, title = {Ecological risk assessment of 1,4-thioxane and its remediation by a synthetic microbiome based on a sulfur transformation system: From multi-omics to water application.}, journal = {Water research}, volume = {303}, number = {}, pages = {126258}, doi = {10.1016/j.watres.2026.126258}, pmid = {42284942}, issn = {1879-2448}, abstract = {Among the chemicals in weapons abandoned by Japan in China during World War II, 1,4-thioxane, a typical degradation product of mustard gas, has environmental persistence and potential ecological risks. However, its toxicity mechanism and efficient remediation strategy remain unclear. This study first employed multi-omics technologies (16S sequencing, metagenomics, and metabolomics) to analyze the toxic effects of 1,4-thioxane (0-100 mg·L[-1], 120 days) on water microecology. Subsequently, an efficient degrader, Pseudomonas sp. M1, was screened, and transcriptome analysis revealed significant upregulation of Fe-S cluster assembly-related genes (sufB, sufU, sufS), which are key components of the SUF sulfur conversion system. These three genes were heterologously expressed in Escherichia coli to construct three engineered strains, each capable of degrading 1,4-thioxane via the SUF system. When mixed in equal proportions to form a synthetic microbiome, they completely degraded 100 mg·L[-1] 1,4-thioxane in culture medium within 16 h and achieved 100% removal in simulated polluted water within 15 days. Integrated multi-omics analysis demonstrated that 1,4-thioxane is highly persistent (residual rate > 98%) but significantly inhibits nitrogen cycling, manifested by NH4[+] accumulation (1.5-3.1-fold increase) and NO3[-] depletion (24.9-87.6% decrease), along with reduced ammonia monooxygenase, nitrite oxidoreductase, and nitrate reductase activities (67.8-91.0%, 53.2-90.1%, and 42.8-80.9% reductions, respectively). Ionome analysis showed K and P accumulation and Mo depletion; 16S sequencing revealed reduced microbial diversity, suppression of nitrogen-cycling genera, and enrichment of Pseudomonas; metagenomics uncovered widespread suppression of nitrogen metabolism pathways, dysregulation of antibiotic resistance genes, and decreased viral abundance; and metabolomics confirmed global inhibition of the alanine-aspartate-glutamate pathway. This is the first study to combine multi-omics toxicity analysis with synthetic microbiome remediation based on the SUF sulfur conversion system. The findings provide a theoretical basis and technical support for ecological risk assessment and bioremediation of sites contaminated by relic Japanese chemical weapons.}, } @article {pmid42285959, year = {2026}, author = {Lyu, C and Wang, Z and Zhao, R and Zhao, H and Liu, S and Lian, H and Wang, X}, title = {Preoperative gut microbial network alterations and BCAA-Related metabolic disturbance in postoperative delirium after cardiac surgery: a prospective matched multi-omic study.}, journal = {Translational psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41398-026-04161-9}, pmid = {42285959}, issn = {2158-3188}, abstract = {Postoperative delirium (POD) is a frequent neuropsychiatric complication after cardiac surgery, yet the biological basis of individual susceptibility remains unclear. In this prospective cohort study, 317 adults undergoing elective on-pump cardiac surgery were enrolled and followed for POD during the first 7 postoperative days. Thirty patients who developed POD were then matched 1:1 with 30 non-POD controls by age, sex, and primary diagnosis for multi-omic analyses. Preoperative fecal samples were collected from the first bowel movement after admission and before prophylactic antibiotic administration, and postoperative fecal samples were collected from the first postoperative bowel movement. Paired fecal samples underwent shotgun metagenomic sequencing, and perioperative serum samples underwent untargeted metabolomic profiling. Preoperatively, α- and β-diversity were comparable between groups, but patients who subsequently developed POD exhibited a less connected and less integrated microbial network structure. Postoperatively, gut microbial composition differed significantly between groups (PERMANOVA R[2] = 0.053, P < 0.001). Metagenomic profiling identified 35 differentially abundant species and 16 differentially enriched KEGG level 3 pathways, with POD-associated features showing inferred functional shifts toward amino-acid catabolism, including branched-chain amino acid (BCAA)-related pathways. Untargeted metabolomics demonstrated marked perioperative remodeling in both groups, but POD was associated with a 27-metabolite panel characterized predominantly by lower postoperative levels or impaired recovery, with pathway enrichment converging on valine, leucine, and isoleucine metabolism. Integrative analyses further linked POD-associated microbial taxa with amino-acid catabolic pathways and lower levels of BCAA-related serum metabolites. These findings suggest that POD is associated with preoperative alterations in microbial network organization and a postoperative microbiome-metabolome disturbance pattern centered on amino-acid metabolism, particularly the BCAA axis.}, } @article {pmid42286003, year = {2026}, author = {Hensen, ADO and Harmanus, C and Verbeek-Menken, PH and Koopman, JPR and Lamers, OAC and Roozen, GVT and Janse, JJ and Balke-Buijs, M and van der Stoep, MYEC and Meij, P and van Amerongen-Westra, IM and Schipper, P and Crul, C and Pattacini, L and Rox, K and Farowski, F and Tsakmaklis, A and Vehreschild, MJGT and Kuijper, EJ and Smits, WK and Roestenberg, M}, title = {Experimental human colonisation with non-toxigenic Clostridioides difficile: a placebo-controlled randomised clinical trial.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74327-y}, pmid = {42286003}, issn = {2041-1723}, support = {101007799//Innovative Medicines Initiative (IMI)/ ; }, abstract = {Clostridioides difficile infections remain a major global healthcare burden, underscoring the need for novel therapies. Human colonisation models provide mechanistic insight into C. difficile colonisation and facilitate identification of novel intervention targets. We conducted a placebo-controlled, randomised clinical trial (NCT05693077) administering non-toxigenic C. difficile (NTCD) capsules to healthy participants to assess safety and colonisation as primary endpoints, and microbiota susceptibility as a secondary endpoint. A total of 69 healthy participants (18-45 years), not previously colonised with C. difficile and without recent antibiotic use, were enrolled following a health assessment. NTCD capsules administered for five consecutive days at low or high dose, was safe with no dose-response relationship in colonisation outcomes. Vancomycin pretreatment induced colonisation success: with 5% colonisation without, 32% after one day, and 84% after five days vancomycin pretreatment. Some participants that cleared vancomycin rapidly acquired non-challenge C. difficile strains prior to NTCD challenge. Microbiota profiling (using shotgun metagenomics) revealed reduced α-diversity and pronounced community restructuring. These findings highlight the impact of antibiotic-mediated microbiota disruption, the widespread environmental presence of C. difficile, and the feasibility of meaningful microbiota assessment in small-scale intervention trials, thereby providing a robust tool to investigate this globally impactful infection.}, } @article {pmid42286360, year = {2026}, author = {Morelli, S and Romano, S and Cosenza, G and Abate, S and Lombardi, L and Pilli, E}, title = {A damage-aware NGS workflow for conservative species identification from ultra-degraded DNA.}, journal = {Analytical and bioanalytical chemistry}, volume = {}, number = {}, pages = {}, pmid = {42286360}, issn = {1618-2650}, abstract = {Species identification from highly degraded DNA remains a major challenge across ecology, conservation genetics, wildlife forensics, and museum science, where samples are often scarce, contaminated, and embedded in complex matrices. Under these conditions, standard reference-based and metagenomic classifiers are prone to false-positive assignments, particularly when ultra-fragmented DNA and conserved genomic regions are not explicitly accounted for. Here, we present a damage-aware next-generation sequencing (NGS) workflow for conservative species identification from minute quantities of highly degraded DNA, designed to minimize misclassification in low-input and damage-rich datasets. The workflow integrates micro-sampling, half-uracil-DNA-glycosylase (half-UDG) library preparation, PCR duplicate removal, multi-genome mapping against a curated reference panel, and a post-mapping read-ubiquity classifier that distinguishes species-specific reads from those shared across conserved loci. Using collagen-rich substrates as a proof-of-concept, we demonstrated accurate species attribution from samples as small as 1 mm[2], including mixtures and mineral-containing matrices. The workflow reliably identifies dominant biological sources, reduces false-positive assignments driven by conserved genomic regions, and remains robust to common physical and chemical treatments such as swelling, heating, and plaster addition. Overall, this study provides a proof-of-concept framework for conservative species identification in challenging degraded DNA contexts. The workflow may be adaptable to a broader range of degraded DNA contexts-including wildlife monitoring, regulatory enforcement, forensic investigations, and the analysis of processed biological materials-although further validation across diverse matrices will be required.}, } @article {pmid42286394, year = {2026}, author = {Shen, Q and Chen, J and Chen, Y and Liu, J and Mao, L and Shi, W and Ndjekadom, A and Wang, J and Wang, X and Liu, Y and Yang, S and Ji, L and Wu, P and Tong, F and Yang, H and Zhang, W}, title = {Metagenomic characterization of the virome of Aedes albopictus in Anhui Province, China, with phylogenetic analysis of CRESS-DNA viruses and Parvoviridae.}, journal = {Virus genes}, volume = {}, number = {}, pages = {}, pmid = {42286394}, issn = {1572-994X}, support = {22KJA320001//Jiangsu Province Higher Education Basic Science (Natural Science) Research Project/ ; No. 2023YFD1801300//National Key Research and Development Program of China/ ; No. 82341106//National Natural Science Foundation of China/ ; }, abstract = {Aedes albopictus is a globally important mosquito species capable of transmitting a variety of viruses. In this study, a total of 440 Ae. albopictus individuals were collected from Fanchang, Anhui Province, and 22 tissue libraries were constructed for metagenomic sequencing. A total of 649,930,614 reads were obtained and assembled into 209,335 contigs, of which 18,339 showed similarity to known viral proteins, spanning 13 viral families including both DNA and RNA viruses. Because several DNA virus-related sequences were recovered from the dataset, we further focussed on CRESS-DNA virus-related sequences and members of the family Parvoviridae. Phylogenetic analysis showed that three CRESS-DNA virus-related sequences clustered within Smacoviridae and Genomoviridae, while two Parvoviridae genomes were assigned to Brevihamaparvovirus and Protoparvovirus. These findings provide a metagenomic overview of the Ae. albopictus-associated virome in Anhui Province and provide baseline information on mosquito-associated DNA virus-related sequences in this region.}, } @article {pmid42286497, year = {2026}, author = {Gao, X and Sanui, A and Rasmika Dewi, DAP and Lucaci, AG and Mason, CE and Suzuki, H}, title = {Shotgun metagenomic dataset of surface microbiomes at a train station in Shinagawa, Tokyo.}, journal = {BMC genomic data}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12863-026-01451-5}, pmid = {42286497}, issn = {2730-6844}, support = {U54AG089334//National Institute for Health and Care Research/ ; JPMJCR20H1//JST CREST/ ; 20K10436//JSPS KAKENHI/ ; JAHMEC.G-02, 2022//Japan Architectural Health, Management and Education Center Research grant/ ; }, abstract = {OBJECTIVES: The urban microbiome is a significantly underexplored ecosystem which contributes to the health and resilience of the human population and less is known about the microbiome of urban transportation systems that commuters interact with daily. Shotgun metagenomic sequencing data from swab samples were collected at a representative medium-scale urban commuter railway station in Tokyo, Japan, with daily passenger volumes on the order of tens of thousands, in October 2021. The dataset was generated as part of the nationwide "Urban Microbiomes in Japan" project and provides a resource for comparative analyses of urban microbial diversity and future public health surveillance studies in urban environments.

DATA DESCRIPTION: Three surface swab samples were collected in October 2021 from concrete floor areas near ticket gates at a major railway station in Shinagawa, Tokyo. Samples were collected using Isohelix swabs with DNA/RNA Shield stabilization solution. Metagenomic DNA was extracted and subjected to shotgun sequencing, generating 2 × 150 bp paired-end reads.}, } @article {pmid42286668, year = {2026}, author = {Lawther, K and Dimonaco, NJ and Donnelly, P and Guinguina, A and Krizsan, SJ and Huws, SA}, title = {Dietary inclusion of Asparagopsis taxiformis significantly reduces methane emissions in dairy cows by mechanistically altering vitamin B12-dependent and other methanogenesis precursor pathways.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02447-0}, pmid = {42286668}, issn = {2049-2618}, abstract = {BACKGROUND: Ruminant products are widely consumed due to their high protein and micronutrient content, but ruminant production contributes significantly to greenhouse gas emissions, with methane (CH4) accounting for 33% of anthropogenic emissions. CH4 is generated via fermentative processes by the rumen microbiome, primarily through hydrogen utilisation by methanogenic archaea. Feeding beef cattle the red seaweed Asparagopsis taxiformis (ASP) has been shown to reduce CH4 emissions by up to 80%. However, the microbial mechanisms underlying this reduction remain poorly understood. In this study, Nordic Red dairy cows (122 ± 13.7 days in milk) were fed grass silage and concentrate (60:40 dry matter basis) either with or without 0.5% ASP (organic matter basis) in a Latin square design, and rumen fluid was collected 19 days into each of the 3 experimental periods.

RESULTS: ASP supplementation reduced CH₄ yield by 54% (g CH₄/kg DM). Metagenomic analysis revealed genes encoding pyruvate and propionate production pathways were more abundant in ASP treated animals, while those associated with acetate and CH₄ were reduced. Additionally, genes encoding vitamin B12 biosynthesis enzymes showed reduced abundances (e.g., adenosylcobinamide-GDP ribazoletransferase, EC 2.7.8.26, -29.92%). Vitamin B12 and its related cofactors are critical for methanogenic methyltransferases and C1 metabolism. Dominant taxa including Prevotella and Methanobrevibacter declined, while less abundant taxa increased their contribution to methane-related pathways, indicating niche displacement and community restructuring. CONCLUSION : ASP supplementation modulates the rumen microbiome through mechanisms extending beyond direct methanogen inhibition. The reduced abundance of genes involved in C1 metabolism and vitamin B12-dependent methanogenic processes suggest methane suppression is linked to broader restructuring of microbial metabolic networks. The redistribution of methane-related functions from dominant taxa to a wider taxonomic community indicates ecological reorganisation and functional resilience of the rumen microbiome. Collectively, these results reveal the multiple modes of action of ASP, establishing its promise as an effective methane mitigation strategy. Video Abstract.}, } @article {pmid42286752, year = {2026}, author = {Abedini, R and Salekdeh, GH and Hashemi, M}, title = {Beyond metagenomics: culturomics uncovers aerobic and facultative anaerobic bacterial diversity in the camel gut.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42286752}, issn = {2524-4671}, abstract = {While metagenomics has transformed our view of microbial ecosystems, culture-based methods remain indispensable for accessing microbial functionality and biotechnological potential. In this study, we applied a culturomics strategy to explore the diversity, abundance, and distribution of culturable aerobic and facultative anaerobic bacteria along the gastrointestinal tract of dromedary camels (Camelus dromedarius) grazing on pristine desert flora. Using six culture media-including modified YCFA formulations-we isolated 97 bacterial species across 42 genera, 31 families, and four phyla: Firmicutes, Proteobacteria, Actinomycetota, and Bacteroidota. Strikingly, 88.6% of this diversity was recovered using YCFA-based media, and four candidate novel species were identified. The rumen harbored the most diverse and Gram-positive-dominated community, whereas the small intestine was enriched with Gram-negative taxa, many with pathogenic potential. These findings highlight the camel's unique physiological adaptation to extreme arid environments, characterized by efficient fiber degradation under nutrient- and water-limited conditions and the presence of stress-tolerant gut microbes capable of resisting acidic and osmotic challenges. Overall, this study establishes a foundational understanding of the camel gut microbiota and underscores the complementary power of culture-dependent methods to metagenomics. Future integration with anaerobic culturing and multi-omics analyses will further unveil the ecological and biotechnological potential of desert-adapted microbial life.}, } @article {pmid42286784, year = {2026}, author = {Yu, Y and Wu, H and Ji, H and Hu, Y and Fang, Y and Lin, Y and Zhang, Y and Zhou, Y}, title = {Metagenomic analysis reveals resistome characteristics and high-risk resistance genes in the pig nasal cavities, feces, and farm dust.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00589-y}, pmid = {42286784}, issn = {2524-4671}, support = {2024-2026QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; 32402702//National Natural Science Foundation of China/ ; LMS25C170002//Natural Science Foundation of Zhejiang Province/ ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) poses a threat to global public health. Swine farms are critical AMR reservoirs. Comprehensive resistome profiling and risk assessment across pig-associated niches remain limited. Metagenomic analysis of antibiotic resistance genes (ARGs) in pig nasal cavities, feces, and farm dust was performed.

RESULTS: Nasal and dust samples exhibited significantly increased ARG diversity and abundance compared with feces. We identified 78 potentially hazardous ARGs and proposed an improved risk classification framework integrating host promiscuity, mobility, and human health risks. These ARGs were classified into four risk levels: 25 Level I (current high risk), 25 Level II (potential future threats), 18 Level III (host-promiscuous but nonmobile), and 10 Level IV (host-specific). High-risk ARGs mainly confer aminoglycoside, macrolide-lincosamide-streptogramin (MLS), and tetracycline resistance. Metagenome-assembled genome (MAG) analysis revealed that bacterial taxa enriched in ARGs were predominant in nasal and dust samples. Moreover, these environments presented higher mobile genetic element (MGE) abundance and similar ARG-MGE co-occurrence patterns. Notably, 74.12% of the mobile ARGs were predicted to be plasmid-borne, and these ARGs tended to be assigned higher health risk levels than chromosomal ARGs.

CONCLUSIONS: These findings provide a practical framework for ARG risk assessment and highlight the nasal cavity and dust as underappreciated but important AMR reservoirs in pig farms.}, } @article {pmid42286862, year = {2026}, author = {Othman, EM and Bencurova, E and Ferretti, P and Bork, P and Rodriguez Del Rio, A and Huerta-Cepas, J and Caruana, I and Abdel-Latif, R and Akash, A and Albacete, A and Lafi, F and Dandekar, T and Naseem, M}, title = {Diet and microbiome shape small-molecule cytokinin pools in mammals.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2679497}, pmid = {42286862}, issn = {1949-0984}, mesh = {Animals ; *Cytokinins/blood/metabolism ; Humans ; Mice ; *Diet ; *Gastrointestinal Microbiome ; *Mammals/metabolism ; Metabolomics ; Metagenomics ; Feces/chemistry ; Swine ; Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; }, abstract = {Cytokinins (CKs) are adenine-derived metabolites traditionally characterized as plant hormones, yet their origin, distribution, and functions in mammalian systems remain largely undefined. Using integrated metabolomics, microbiome, and metagenomics approaches, we provide a systematic characterization of CK occurrence and potential sources in mammals. Serum profiling across five animal species revealed consistent detection of multiple CK derivatives, with concentrations markedly lower than in plant tissue. The CK storage form, zeatin-O-glucoside, predominated in mammalian sera, followed by trans-zeatin and kinetin, indicating a CK composition distinct from that in plants. Species-specific differences, such as reduced trans-zeatin in mice and lower kinetin in humans, further suggest divergent regulatory patterns. In mice, CKs were present in vascular tissues of the kidney, heart, and liver, demonstrating systemic distribution. Dietary manipulation showed that starvation significantly reduced CK abundance in serum, colon, feces, and urine, confirming that diet is a major contributor to the mammalian CK pool. Meta-omics analysis of gut microbiomes identified CK-related genes across multiple microbial taxa, with the highest representation in human microbiomes, followed by those of mouse and pig. Germ-free mouse experiments showed substantially lower CK levels than conventionally raised counterparts, establishing a microbiome-dependent contribution. Collectively, our findings identify CKs as diet and microbiome modulated metabolites in mammals, warranting future investigation to elucidate their physiological significance in mammalian biology.}, } @article {pmid42287197, year = {2026}, author = {De Visscher, J and Tytgat, B and Hodgson, DA and Wilmotte, A and Willems, A and Verleyen, E and Vyverman, W}, title = {Functional genetic potential of benthic microbial mat communities in Arctic, Antarctic, and sub-Antarctic lakes.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {7}, pages = {}, pmid = {42287197}, issn = {1574-6941}, support = {SD/BA/03A//Belgian Science Policy Office/ ; //EU Horizon 2020 InterAct project MiBiPol/ ; SD/CA/01A//Belspo project HOLANT/ ; //Research Foundation Flanders/ ; }, mesh = {*Lakes/microbiology ; Antarctic Regions ; Arctic Regions ; *Microbiota/genetics ; Ecosystem ; Metagenomics ; *Bacteria/genetics/classification ; }, abstract = {Benthic microbial mat communities are key drivers of ecosystem functioning in polar lakes and ponds, forming the base of aquatic food webs and contributing substantially to nutrient cycling. Although Arctic, sub-Antarctic, and Antarctic microbial mats differ in community composition, their functional genetic potential remains poorly understood. We applied shotgun metagenomic sequencing to study 17 microbial mat communities from Arctic and (sub-)Antarctic lakes differing in salinity, catchment vegetation, and climatic conditions. Stress response genes, especially cold stress, and phosphorus cycling and metabolism genes were highly abundant in all lakes. A large proportion of functional genes was shared between regions, with core functions dominated by transport mechanisms and energy production. However, clear differences in particular gene abundances were observed. Several East-Antarctic lakes and inland ponds in the Transantarctic Mountains showed a dominance of oxygenic photosynthesis and Calvin cycle genes for carbon fixation, likely reflecting the dominance of Cyanobacteriota. In Arctic and sub-Antarctic lakes with catchment vegetation and higher arthropod abundances, lignin and chitin degradation genes were more important. Our study shows that, despite distinct biogeographic patterns in community composition, the functional genetic potential of polar lake microbial mats mainly reflects climatic and local environmental conditions, emphasizing specific adaptations to extreme polar environments.}, } @article {pmid42287489, year = {2026}, author = {da Silveira Bastos, IMA and Cardoso, MS and Laux, M and Ribeiro, RR and García, GJY and Bahia, PA and de Sousa, PMV and Alves, BGT and de Rezende, DHC and Rosado, AS and Bezerra, JDP and Landell, MF and Melo, VMM and Tavares, TCL and Góes-Neto, A}, title = {Worldwide diversity and ecology of mangrove fungi: a systematic review of ITS metabarcoding studies and a quantitative, integrative analysis of raw sequence data.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42287489}, issn = {1573-0972}, mesh = {*Fungi/classification/genetics/isolation & purification ; *DNA Barcoding, Taxonomic ; *Biodiversity ; *Wetlands ; *Mycobiome ; Basidiomycota/genetics/classification ; Geologic Sediments/microbiology ; *Rhizophoraceae/microbiology ; Ecosystem ; Ascomycota/genetics/classification/isolation & purification ; Phylogeny ; }, abstract = {Fungi are integral components of the mangrove microbiome, playing critical roles in decomposition, nutrient cycling, and symbiosis. Our study synthesizes the findings from a global systematic review of fungal ITS metabarcoding studies conducted in mangrove ecosystems. This review consolidates data from 23 original research articles (1,154 samples) and provides a comprehensive overview of the diversity, community structure, and ecological functions of fungi in these critical coastal habitats. The analyses revealed a consistent core fungal mycobiome in mangroves worldwide. This community is dominated by Ascomycota, with Basidiomycota as the second most abundant phylum. A consistent set of ten highly abundant genera underpins this core community, and fungal diversity and composition are strongly influenced by the specific substrate. Non-rhizospheric sediment harbors the highest diversity, while live plant organs host a more specialized and less diverse community, slightly dominated by potential plant pathogens. Rhizospheric sediment supports a unique assemblage rich in wood-decomposing fungi. The primary ecological role of fungi in mangroves is decomposition, which is essential for breaking down lignocellulosic litter, cycling nutrients, and storing carbon in sediments. A surprisingly high relative abundance of fungi classified as plant pathogens was identified on mangrove plant tissues, suggesting an underappreciated role of fungal diseases in these ecosystems. Metabarcoding provides a far broader view of fungal diversity than traditional collection and culturing methods. It has uncovered a vast number of uncultured taxa and has been particularly effective in revealing the significant, and likely underestimated, presence of macrofungi in mangrove soils. Our study also highlights that current short-read metabarcoding can severely underestimate certain fungal groups, particularly the endomycorrhizal Glomeromycota, due to technical limitations. Altogether, our synthesis provides a global baseline against which future mangrove mycobiome studies can be benchmarked.}, } @article {pmid42287798, year = {2026}, author = {Winssy, TD and Anandham, R and Maragatham, S and Uma, D and Karthikeyan, S and Balachandar, D}, title = {Long-term nutrient management shapes soil microbial and metabolic signatures in a century-old semi-arid agroecosystem.}, journal = {Journal of environmental management}, volume = {411}, number = {}, pages = {130209}, doi = {10.1016/j.jenvman.2026.130209}, pmid = {42287798}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Soil/chemistry ; Nitrogen ; Carbon ; Agroecology ; Agriculture ; Fertilizers ; Microbiota ; }, abstract = {Semi-arid tropical soils inherently contain low soil organic carbon (SOC) and limited nutrient reserves, resulting in poor productivity. Intensive cropping with synthetic fertilizers, further deteriorate soil quality and impair ecosystem functioning. In contrast, organic amendments alone or combined with synthetic fertilizers sustain soil biodiversity through microbially mediated processes. However, how long-term nutrient management shapes soil microbiomes and their functional diversity in semi-arid tropical systems remains largely unknown. To address this gap, we investigated a 116-year-old long-term nutrient management experiment using a multi-omic framework. Shotgun metagenomics characterized the total microbiome (bacteria, archaea, and eukaryota) and associated carbon- and nitrogen-cycling genes under four contrasting nutrient management practices: unfertilized control, inorganic fertilizer alone (IC), organic amendment alone (OM), and integrated nutrient management combining organic and inorganic inputs (INM). OM and INM significantly improved soil nutrient stocks, SOC, microbial biomass, and enzyme activities compared with IC and Control. These treatments also enhanced microbial diversity and shifted communities toward copiotrophic and functionally beneficial taxa, whereas IC and Control were dominated by stress-tolerant oligotrophs. Pathway analysis showed that carbon fixation dominated the C-cycling gene pool, with alternative autotrophic pathways prevailing over the Calvin cycle, particularly under OM and INM. These treatments also supported higher abundances of methanogenic and decomposition-associated genes, indicating enhanced carbon turnover. Nitrogen-cycling functions exhibited pathway-specific responses: OM enriched N-fixation and assimilatory nitrate reduction genes, whereas INM enhanced denitrification and dissimilatory nitrate reduction pathways. IC showed increased nitrification potential but the weakest biologically regulated N pathways. Volatomics profiling showed that OM and INM produced more diverse and metabolically active volatile organic compounds that were strongly associated with SOC and key biological attributes. Collectively, our study underscores the importance of carbon-rich organic inputs in rebuilding soil carbon stocks, reinforcing biological processes, and enhancing nutrient cycling for long-term sustainability of agriculture in semi-arid tropical regions.}, } @article {pmid42287872, year = {2026}, author = {Wu, J and Wang, B and Li, Y and Zhang, X and Peng, Y and Liu, Q and Zhang, C and Lian, B and Cao, H and Li, K and Wang, H}, title = {Divergent responses of prokaryotic and eukaryotic microbiomes drive assembly, stability, and functional dynamics in the Bohai sea.}, journal = {Marine environmental research}, volume = {220}, number = {}, pages = {108193}, doi = {10.1016/j.marenvres.2026.108193}, pmid = {42287872}, issn = {1879-0291}, abstract = {Coastal oceans, critical for biodiversity and biogeochemistry, are increasingly altered by anthropogenic pressures that interact with natural spatiotemporal variability. However, the relative influence of spatial versus temporal drivers on microbiomes assembly, association, and function remains unclear. To resolve this, we integrated multi-kingdom amplicon and metagenomic sequencing to analyze microbial communities across spatial (Laizhou Bay vs. open Bohai Sea) and temporal (seasonal to interannual) gradients in the Bohai Sea, a semi-enclosed coastal system heavily influenced by recurrent human activities. Our results demonstrate that temporal variation exerts relatively stronger influences than spatial heterogeneity on the structure and dynamics of microbial communities in the Bohai Sea. Microeukaryotes exhibited the greatest responsiveness to spatiotemporal change, followed by archaea, with bacteria showing the highest stability. Archaeal and microeukaryotic communities were primarily governed by stochastic processes, whereas bacterial assembly transitioned from deterministic to stochastic control along spatiotemporal gradients. Microbiome co-occurrence networks were increasingly complex but less stable under spatiotemporal variability, dominated by competitive interactions and demonstrating a clear complexity-stability trade-off. Metagenomic analysis revealed a scale-dependent hierarchy of environmental drivers regulating metabolic pathways, with temperature predominant at the regional scale, DO in summer, and DON within homogeneous sub-regions. Two parallel microbial strategies for coping with anthropogenic pressure were identified, including enhanced catabolic pathways for xenobiotic degradation and a seasonally dynamic, mobile antibiotic resistome. This study provides a multidimensional and systematic perspective by demonstrating that temporal dynamics are the principal regulator of coastal microbiomes structure, stability, and function, with critical implications for predicting the responses of anthropogenically stressed coastal ecosystems under continuous environmental change.}, } @article {pmid42287875, year = {2026}, author = {Yang, X and Wu, P and Li, C and Zheng, Q and Shi, X and Su, H and Wang, T and Xiong, X and Liu, Y and Xiao, Y and Xu, S and Zou, J and Liu, Y}, title = {Bacterial communities and antibiotic resistance genes in seawater adjacent to inhabited and uninhabited xisha coral reef islands: Insights from 16S rRNA and metagenomic sequencing.}, journal = {Marine environmental research}, volume = {220}, number = {}, pages = {108197}, doi = {10.1016/j.marenvres.2026.108197}, pmid = {42287875}, issn = {1879-0291}, abstract = {The Xisha coral reefs are highly biodiverse ecosystems in the South China Sea, China. Bacterial communities drive energy flow and biogeochemical cycling in coral-reef ecosystems, and serve as indicators of reef health. Yet the composition and dynamics of both bacterial assemblages and ARGs within the Xisha coral reefs remain poorly resolved. This study used 16S rRNA amplicon and metagenomic sequencing to compare bacterial community structure across surface and bottom waters, and surface-water ARGs profiles, in Beijiao Reef (BJ; an uninhabited reef) and Qilianyu Islands (QLY; an inhabited island) of the Xisha Islands. The results revealed bacterial community composition, bacterial co-occurrence network structure, and ARGs profiles differed markedly between the two reef areas. Dominant genera-Prochlorococcus_MIT9313, Salinimonas, Synechococcus_CC9902, Vibrio, and Alteromonas-were significantly more abundant in BJ (p < 0.05), whereas QLY showed higher abundances of Planococcus, Psychrobacter, Jeotgalibacillus, Salinicoccus, and Marinococcus (p < 0.05). The QLY bacterial co-occurrence network exhibited greater complexity (higher clustering coefficients and modularity), whereas the BJ network was simpler but displayed significantly higher closeness-centrality values (p < 0.001). Surface waters of the Xisha Islands were dominated by tetracycline, aminoglycoside, and macrolide resistance genes, whereas sulfonamide and multidrug resistance genes were less abundant. In addition, ARGs concentrations in BJ were slightly higher than those in QLY, suggesting that human habitation may not be a key environmental factor influencing ARGs concentrations in the seawater of the Xisha Islands. Correlation analysis showed that high-abundance ARGs in BJ (msbA, RanA, tetB(P), tet(T)) were linked to phototrophic Prochlorococcus_MIT9313 and Synechococcus_CC9902, whereas QLY dominant ARGs (baeS, patB, MexW) correlated with Gram-negative Vibrio and Pseudomonas. These ARGs are involved in bacterial efflux mechanisms, reflecting adaptive responses to environmental stress. This study provides valuable insights for assessing water quality and evaluating the impacts of human habitation pressure on coral reef ecosystems in the Xisha Islands.}, } @article {pmid42287910, year = {2026}, author = {Li, H and Li, Y and Zhang, Z and Li, X and Zhao, K and Fan, Z and Liu, K}, title = {The ablation cycle drives glacier microbiome dynamics and downstream dissemination risk of the resistome.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142686}, doi = {10.1016/j.jhazmat.2026.142686}, pmid = {42287910}, issn = {1873-3336}, abstract = {Glacial ecosystems on the Tibetan Plateau undergo pronounced hydrological shifts across the glacial ablation cycle, driven by the onset and retreat of the Indian summer monsoon. To elucidate how transitions between four distinct hydrological ablation stages (pre-ablation, early ablation, late ablation, and frozen) shape microbial community structures and antibiotic resistance gene (ARG) profiles, we analyzed 112 samples collected across four stages from multiple glacier catchments on the southeastern Tibetan Plateau using metagenomic sequencing. Our results indicated that warmer stages favored thermotolerant Proteobacteria and reduced overall community diversity and evenness. ARG abundances exhibited ablation-dependent fluctuations, with Betaproteobacteria identified as predominant potential hosts. Furthermore, ARGs and virulence factors associated with mobile genetic elements were enriched during early and late ablation stages relative to the frozen stage, suggesting elevated potential for horizontal gene transfer coinciding with peak meltwater discharge. Notably, while upstream meltwaters generally exhibited higher ARG abundances, the upstream-downstream disparity tended to diminish from the pre-ablation to the late ablation stage, likely reflecting enhanced microbial mixing driven by glacier melt. Together, these findings reveal that glacier meltwater microbiomes are primarily shaped by ablation dynamics rather than spatial heterogeneity. More importantly, dynamics across the glacial ablation cycle drive shifts in meltwater hydrology that facilitate the downstream environmental mobility of glacial resistomes, posing growing antimicrobial resistance risks within the One Health framework.}, } @article {pmid42288243, year = {2026}, author = {Huiling, Y and Jinghui, Z and Xinxin, Y and Hang, J and Jianxiang, W and Lina, Z and Ping, XU and Chao, Z and Jianming, MO and Jing, D and Haixia, LI and Jie, LI and Ling, JI and Chang, LU}, title = {Diagnostic Performance and Clinical Impact of Metagenomic Next-Generation Sequencing in 841 Patients with Suspected Lower Respiratory Tract Infections: A Four-Year Retrospective Study from a Tertiary Hospital in Shenzhen, China.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108885}, doi = {10.1016/j.ijid.2026.108885}, pmid = {42288243}, issn = {1878-3511}, abstract = {BACKGROUND: Accurate pathogen identification is critical for managing lower respiratory tract infections (LRTIs), particularly in suspected polymicrobial infection or after empiric treatment failure. Although metagenomic next-generation sequencing (mNGS) has been increasingly used in clinical practice, its long-term diagnostic performance and clinical impact in LRTIs have not been systematically evaluated in a large single-center cohort.

METHODS: We conducted a retrospective cohort study of 841 hospitalized patients with suspected LRTIs who underwent bronchoalveolar lavage fluid (BALF) testing by both mNGS and conventional culture between December 2021 and December 2025. Positive detection rates, polymicrobial identification, pathogen distributions across age and underlying disease categories, method concordance, and clinical impact were evaluated.

RESULTS: mNGS yielded significantly higher overall and polymicrobial detection rates than culture. Pathogen profiles differed between mNGS and culture and varied across age and underlying diseases subgroups. Over half of pathogens were identified exclusively by mNGS, and over half of these mNGS-exclusive detections influenced diagnostic and antimicrobial management. Furthermore, Mycobacterium tuberculosis complex, nontuberculous mycobacteria, Cryptococcus neoformans, and Pneumocystis jirovecii retained clinical significance even at low sequencing read counts.

CONCLUSIONS: In this real-world cohort, mNGS expanded pathogen detection, improved recognition of mixed infections, and provided meaningful clinical value in LRTI.}, } @article {pmid42288291, year = {2026}, author = {Chen, K and Zhang, X and Li, G and Luo, W and Zhou, H and Shen, Y and Nghiem, LD}, title = {Mechanistic insights into nitrogen loss during food waste composting revealed by metagenomic and qPCR analyses under varying substrate C/N ratios.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135157}, doi = {10.1016/j.biortech.2026.135157}, pmid = {42288291}, issn = {1873-2976}, abstract = {Nitrogen loss during composting can be substantial; however, it can be reduced by applying new insights to better control the substrate C/N ratio and optimise overall composting performance. This study provides mechanistic insights into how substrate C/N governs nitrogen loss during kitchen waste composting. By combining nitrogen speciation analysis, qPCR, and metagenomics analyses, this study explored the potential biochemical mechanisms of nitrogen loss. The results showed that a high substrate C/N ratio significantly reduced nitrogen loss by approximately 37 % (C/N of 25) and 47 % (C/N of 30) compared to the baseline C/N of 20. A higher substrate C/N ratio enhanced nitrogen fixation and assimilation processes while suppressing ammonification and denitrification related potential. The relative abundance of key ammonification-related genera (e.g. Thermobifida and Leuconostoc) and denitrification-related genera (e.g. Pseudomonas and Geobacillus) were decreased at a high substrate C/N ratio, resulting in synergistic mitigation of NH3 and N2O emissions. A small reduction in germination index was observed at substrate C/N ratio of 30 compared with 25. Overall, the results suggest the need to optimize substrate C/N ratio for nitrogen conservation while maintaining overall composting performance.}, } @article {pmid42288625, year = {2026}, author = {Shin, DW and Oh, S and Hong, YJ and Park, KU}, title = {Direct microbiota profiling of apheresis-associated products for microbiological insights in cell therapy.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-57771-0}, pmid = {42288625}, issn = {2045-2322}, abstract = {Cellular therapies require rigorous prevention of bacterial contamination during cell collection, manufacturing, and infusion. We characterized 16 S rRNA profiles in blood-derived specimens obtained during leukapheresis. Leukapheresis donors provided five specimen types: buffy coats (BCs), whole-blood plasma (WBP), apheresis plasma stored at room temperature for 24 h (AP24) and 72 h (AP72), and saliva. Species-level identification was performed using next-generation sequencing-based 16 S rRNA analysis and a database-weighted method. In total, 40 samples from eight donors were analyzed. Plasma specimens (WBP, AP24, and AP72) exhibited higher alpha diversity than saliva (Shannon index, p < 0.05). Beta diversity analysis identified three distinct clusters corresponding to BC, plasma specimens, and saliva (permutational multivariate analysis of variance, p = 0.001). Streptococcus oralis subsp. tigurinus was predominant across all specimens types, Bifidobacterium kashiwanohense predominated in blood-derived specimens, and Enhydrobacter aerosaccus was observed exclusively in plasma specimens. Skin swab culture performed before and after venipuncture site disinfection exhibited no bacterial growth post-disinfection, suggesting that skin-derived carryover is unlikely to fully explain the detected microbial DNA signals. This study provides microbial DNA profiles of various blood-derived specimens obtained during leukapheresis. These findings provide preliminary reference information that may assist interpretation of molecular microbial signals in cellular therapy manufacturing.}, } @article {pmid42288650, year = {2026}, author = {Yang, Y and Guo, Y and Xu, T and Wu, Y and Cao, J and Wen, Z and Liu, S}, title = {Enrichment risk and drivers of manure-derived antibiotic resistance genes in black soldier fly larval gut.}, journal = {npj antimicrobials and resistance}, volume = {}, number = {}, pages = {}, doi = {10.1038/s44259-026-00237-0}, pmid = {42288650}, issn = {2731-8745}, support = {ASTIP//the Agricultural Science and Technology Innovation Program/ ; 2022YFD1301800//National Key R&D Program of China/ ; CARS-42-10//China Agriculture Research System of MOF and MARA/ ; 325QN438//Hainan Provincial Natural Science Foundation of Chin/ ; }, abstract = {Black soldier fly larvae (BSFL) are promising for converting animal manure into protein; however, the risk of antibiotic resistance gene (ARG) enrichment in the larval gut during this process remains unclear. Here, we employed metagenomic and metatranscriptomic analyses to investigate this risk during BSFL conversion of duck manure. Our results demonstrated that within the BSFL treatment system, ARG abundance and diversity in manure decreased significantly over time. Concurrently, total abundance and transcriptional activity of ARGs in the larval gut were significantly lower than those in manure. However, comparative sequence analysis suggested the potential for ARG exchange between bacterial communities in manure and larval gut. Klebsiella, Escherichia, Citrobacter, and Pseudomonas were identified as the primary hosts in the gut. The enrichment and dynamics of these manure-derived ARGs were jointly driven by shifts in physicochemical properties (notably organic matter and total nitrogen), mobile genetic elements, and the bacterial community. Validation experiments demonstrated that modulating these key physicochemical drivers can mitigate ARG abundance in the larval gut. Overall, this study highlights the potential enrichment risk of manure-derived ARGs in the BSFL gut, identifies key hosts and drivers, and provides actionable mitigation strategies for safer BSFL application.}, } @article {pmid42289139, year = {2026}, author = {Kevill, JL and Knight, ME and Jain, Y and Marsden, KA and Williams, RC and Herridge, K and Courtene-Jones, W and Robins, P and Malham, SK and Jones, DL}, title = {Fate and transport of viruses, bacteria and antimicrobial resistance associated with wet wipes and microplastics through wastewater treatment to coastal waters.}, journal = {Water research}, volume = {303}, number = {}, pages = {126281}, doi = {10.1016/j.watres.2026.126281}, pmid = {42289139}, issn = {1879-2448}, abstract = {Microplastics (MPs) in wastewater are increasingly recognised as potential vectors for pathogens and antimicrobial resistance (AMR), yet their role across treatment remains poorly understood. This study tracked viral, bacterial, and AMR associations with MPs from hospital wastewater through to coastal receiving waters, including simulated combined sewer overflow (CSO) events, using quantitative real-time PCR, and shotgun metagenomics. MP concentrations found naturally in the wastewater matrix, declined from 467 to 33 particles L[-1] during WWTP passage, achieving 93% removal. Norovirus (GI and GII) and bacteria colonised beads and wet wipes throughout, with wet wipes retaining higher viral and AMR loads than plastic beads, likely due to structural complexity. Sequential sampling across treatment stages showed a reduction in norovirus and bacterial loads by ∼1 log, yet pathogens remained detectable on beads and wet wipes in final effluent. NoV GI predominated, while NoV GII concentrations and the class I integron-integrase (intI1) gene varied by treatment stage and sample type. Metagenomics showed enrichment of potentially pathogenic genera (Aeromonas, Pseudomonas, Flavobacterium) in bead and wet wipe biofilms, and network analysis identified associations between Aeromonas and clinically relevant beta-lactam resistance genes (OXA, CTX). Shifts at the activated sludge stage indicated bead and wet wipe associated communities in effluent reflect treatment microbiota rather than influent sources. Environmental MP concentrations are below those required to deliver an infectious viral dose, suggesting MP-mediated transmission is unlikely under normal conditions. However, during CSO events, beads and wet wipes retained high viral loads and may act as pathogen transport vectors. These findings highlight CSO management as a priority for reducing MP-associated pathogen risks in receiving waters.}, } @article {pmid42289215, year = {2026}, author = {Dai, J and Tan, X and Ma, J}, title = {Artificial intelligence in clinical metagenomic pathogen detection: A critical review of pipeline integrations, challenges, and future directions.}, journal = {Journal of microbiological methods}, volume = {247}, number = {}, pages = {107592}, doi = {10.1016/j.mimet.2026.107592}, pmid = {42289215}, issn = {1872-8359}, abstract = {Metagenomic next-generation sequencing (mNGS) has expanded the scope of clinical diagnostics by enabling culture-independent detection of microorganisms in patient samples. However, mNGS clinical utility remains constrained by substantial computational demands, reference database biases, and the persistent challenge of distinguishing true pathogens from host background, commensal flora and environmental contamination. Traditional alignment and k-mer-based bioinformatics pipelines frequently struggle to balance speed, sensitivity, and the ability to detect highly divergent or novel organisms. This review critically synthesizes the current landscape of Artificial Intelligence (AI) and Machine Learning (ML) applications across the mNGS diagnostic pipeline, examining deep learning architectures-including Convolutional Neural Networks (CNNs), Long Short-Term Memory networks (LSTMs), and Transformers-as integrated into raw read processing, host sequence depletion, primary taxonomic classification, and ancillary detection of antimicrobial resistance (AMR) and virulence factors. While several AI methodologies report high classification accuracy in benchmarking studies, we note that most performance claims derive from simulated datasets or controlled mock communities rather than prospective clinical validation. Significant gaps persist, including limited AI integration in front-end signal optimization, inadequate automated clinical reporting, absence of standardized benchmarking metrics, and unresolved questions regarding data leakage, reproducibility, and generalizability. Successful clinical translation will require addressing the interpretability limitations of current explainable AI approaches, navigating complex and evolving regulatory landscapes for Software as a Medical Device (SaMD), and bridging the gap between computational feasibility and demonstrated patient-outcome benefit. The development of genomic foundation models and multi-modal clinical integration holds promise for advancing mNGS toward real-time, actionable diagnostics, though substantial evidence gaps remain between current proof-of-concept demonstrations and validated clinical deployment.}, } @article {pmid42289247, year = {2026}, author = {Lin, Y and Nie, B and Liu, X and Zhang, Q}, title = {Mechanistic insights into superior biofilm formation with heterotrophic nitrification-aerobic denitrification bacteria under polypropylene microplastic stress.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135159}, doi = {10.1016/j.biortech.2026.135159}, pmid = {42289247}, issn = {1873-2976}, abstract = {Microplastics may disturb microbial activity and biofilm development in biological wastewater treatment systems, yet the response of three-dimensional rotating biological contactor start-up biofilms to polypropylene microplastic stress remains unclear. This study evaluated a biofilm initiation strategy using heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria (H-3D-RBCs) and compared it with activated sludge-inoculated systems (A-3D-RBCs) under polypropylene microplastic (PP-MP) exposure. H-3D-RBCs showed superior resistance to PP-MP disturbance, with total nitrogen removal decreasing by only 14 %, compared with an approximately 60 % decline in A-3D-RBCs. Respiratory activity inhibition remained below 15 % in H-3D-RBCs but exceeded 90 % in A-3D-RBCs. 16S rRNA gene sequencing showed that PP-MP reduced species richness and diversity in A-3D-RBCs and was associated with a > 90 % loss of core denitrifying genera, including Corynebacterium and Pseudoxanthomonas, whereas H-3D-RBCs maintained community stability and enriched Pseudoxanthomonas to 13.8 %. Metagenomic analysis indicated that PP-MP impaired nitrification and denitrification potential in A-3D-RBCs, as reflected by decreased genes encoding AMO and HAO, a 51.78 % decrease in nosZ abundance, and enhanced dissimilatory nitrate reduction to ammonium (DNRA), which likely intensified competition with denitrification and promoted nitrogen conversion to ammonia. In contrast, H-3D-RBCs suppressed DNRA and maintained high nosZ abundance. Untargeted metabolomics further showed that PP-MP was associated with metabolic disorders in A-3D-RBCs, especially disruptions in alanine, aspartate, and glutamate metabolism and arginine biosynthesis, whereas H-3D-RBCs preserved these key nitrogen metabolic processes. Overall, this study identifies key vulnerabilities of nitrogen-removal biofilms under PP-MP disturbance and provides multi-omics evidence to support the development of microplastic-resistant biofilm wastewater treatment systems.}, } @article {pmid42289444, year = {2026}, author = {Masuoka, H and Miyatake, T and Park, J and Negishi, H and Kurokawa, R and Tsuchihashi, H and Makino, S and Suda, W}, title = {Fatigue-associated gut bacteria in Japanese healthy adults characterized by metagenomic analysis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-56821-x}, pmid = {42289444}, issn = {2045-2322}, support = {J24K18210//Japan Society for the Promotion of Science, Japan/ ; J24K01676//Japan Society for the Promotion of Science, Japan/ ; }, abstract = {Emerging evidence suggests that fatigue caused by accumulated stress may serve as a prodromal symptom of psychiatric disorders, and gut microbiome dysbiosis has been reported in many such conditions. However, little is known about microbial and metabolic signatures associated with fatigue in otherwise healthy individuals. This study aimed to investigate associations between fatigue, the gut microbiome, and fecal metabolites in healthy Japanese adults. We identified characteristic microbial and metabolic differences specific to fatigued healthy individuals. Taxonomic analysis revealed a reduction in potentially beneficial bacteria and an enrichment of Escherichia coli in their gut microbiome. Functional profiling demonstrated enrichment of KEGG orthologs related to oxidative stress and depletion of energy-producing pathways. Correspondingly, key energy metabolites such as citrate were decreased. Notably, some fatigue-associated bacterial alterations overlapped with findings from external datasets on psychiatric disorders and myalgic encephalomyelitis/chronic fatigue syndrome, suggesting associative overlap in gut microbial alterations. These findings suggest associations between host fatigue and gut microbiome alterations involving oxidative stress and impaired energy metabolism. The consistent overlap of fatigue-associated microbial changes with those observed in psychiatric disorders highlights the potential relevance of gut microbial signatures in fatigue-related biological states. This study provides a foundation for future studies on gut microbial and metabolic pathways.}, } @article {pmid42289756, year = {2026}, author = {Jia, P and Dong, L and Ma, T and Bi, Y and Tu, Y and Diao, Q}, title = {Variations in methane emissions from dairy cows: associations with rumen microbial synergy and metabolic pathway divergence.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42289756}, issn = {1674-9782}, support = {2024YFD1300200//the National key Research and Development Program/ ; CAAS-ASTIP//the Agricultural Science and Technology Innovation Program/ ; }, abstract = {BACKGROUND: Methane (CH4) is a metabolic by-product of rumen microbial fermentation, contributing significantly to global warming and dietary energy loss. Elucidating the mechanisms underlying natural variation in rumen methanogenesis is essential for the development of effective CH4 mitigation strategies. Here, we applied rumen metagenomics to identify the microbial mechanisms for differences in enteric CH4 emissions among dairy cows.

RESULTS: Enteric CH4 emissions from 111 lactating dairy cows under normal feeding conditions were utilized to characterize the natural variation in rumen methanogenesis. Metagenomic analysis revealed that the comprehensive effects of bacteria involved in starch degradation, lactate metabolism, and volatile fatty acid biosynthesis provide distinct amounts of hydrogen for rumen methanogenesis in high-methane-producing (HMP) and low-methane-producing (LMP) cows. Ciliate protozoa were universally abundant in HMP cows (P < 0.05), whereas methanogens enrichment exhibited heterogeneity, with the dominant methanogen Methanobrevibacter exhibiting negative correlations with the other 11 methanogens (P < 0.05). Six nutrient metabolic pathways modulating methanogenesis were identified, and HMP-associated methanogenesis was further driven by upregulated formate metabolism and acetoclastic pathways (P < 0.05). Random forest model analysis screened 34 microbial genera as biomarkers for CH4 production.

CONCLUSIONS: This study excluded extrinsic confounders exist for rumen microbiome and CH4 emissions in dairy cows. These findings elucidated the causal microbial and metabolic mechanisms underlying rumen methanogenesis, providing actionable targets for microbiome-based strategies to mitigate CH4 emissions from livestock farming.}, } @article {pmid42290500, year = {2026}, author = {Oriquat, G and Abdelgawwad El-Sehrawy, AAM and K Abdulsahib, W and Waleed Mustafa, W and Jyothi, SR and Priyadarshini Nayak, P and Janney, JB and Singh, G and Sinha, A and Yazdi, F}, title = {Probiotic, synbiotic effects on the gut-liver axis: omics-enabled mechanisms and therapeutic windows.}, journal = {Future microbiology}, volume = {21}, number = {8}, pages = {777-794}, doi = {10.1080/17460913.2026.2684877}, pmid = {42290500}, issn = {1746-0921}, mesh = {*Synbiotics/administration & dosage ; Humans ; *Probiotics/therapeutic use/administration & dosage ; *Liver/metabolism/microbiology ; Multiomics ; *Gastrointestinal Microbiome/physiology ; Animals ; *Liver Diseases/therapy/microbiology ; Proteomics ; Metabolomics ; }, abstract = {The gut-liver axis is a two-way communication network where gut microbes and their metabolites affect liver function, while the liver regulates the intestinal environment through bile acids, immune factors, and antimicrobial substances. Disruption of this balance contributes to various liver diseases, including nonalcoholic fatty liver disease, alcohol-associated liver disease, cirrhosis, and liver cancer. Probiotics and synbiotics are potential therapies that aim to restore microbial balance, strengthen the intestinal barrier, and regulate inflammation and metabolism. Recent omics technologies, such as metagenomics, metabolomics, transcriptomics, and proteomics, have helped uncover how these interventions influence important pathways involving short-chain fatty acids, bile acids, and microbial metabolites. Studies suggest that probiotics and synbiotics may improve liver health through effects on metabolism, immune regulation, and fibrosis, although results vary depending on the specific microbial strains and patient characteristics. Emerging approaches include next-generation probiotics, targeted synbiotic combinations, and personalized microbiome-based treatments. Combining multi-omics data with digital health tools may help identify patients who are most likely to benefit. Overall, microbiota-targeted therapies show promise as personalized strategies for managing liver diseases, but further research is needed to overcome challenges in translating findings into consistent clinical applications.}, } @article {pmid42290753, year = {2026}, author = {Yang, C and Li, M and Yang, S and Pan, J and Ding, Y and Yang, J}, title = {Correction: Channel selection of metagenomic next-generation sequencing in infants pathogen detection: a multicenter cross-sectional study.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1835424}, doi = {10.3389/fped.2026.1835424}, pmid = {42290753}, issn = {2296-2360}, abstract = {[This corrects the article DOI: 10.3389/fped.2025.1632123.].}, } @article {pmid42291119, year = {2026}, author = {Park, J and Jang, KB and Kang, MG and Kyung, J and Yoon, J and Ryu, S and Kim, Y}, title = {Comparative pangenome analysis of methanogenic archaea from diverse ecosystems reveals potential targets for methane mitigation in rumen microbiome.}, journal = {Journal of animal science and technology}, volume = {68}, number = {3}, pages = {935-953}, pmid = {42291119}, issn = {2055-0391}, abstract = {Rumen methanogenesis is a major biological contributor to methane emissions in ruminants, yet the extent to which functional markers align with taxonomic relationships and how genome content varies across habitats, remains poorly resolved. In this study, we integrated broad phylogenetic frameworks with pangenome-resolved analysis to characterize methanogenic archaea from diverse ecosystems, including seawater, freshwater, sewage, rumen, human gut, soil, and cockroach sources. By combining these insights with pangenome reconstruction and KEGG-based pathway mapping of methanogenesis, we reveal key evolutionary and functional patterns. Notably, phylogenies based on 16S rRNA and mcrA genes showed limited concordance: only two clades exhibited overlap between trees, with most clustering patterns lacking environmental specificity. This discrepancy reflects the deep conservation of 16S rRNA compared with the evolutionary plasticity of mcr genes, shaped by lateral gene transfer, gene loss, and pathway modularity. The pangenome comprised of 8,695 orthogroups across 71 genomes, with core and soft-core genes enriched in translation, amino acid metabolism, and coenzyme biosynthesis, while the shell contained many poorly annotated orthogroups, highlighting annotation gaps in archaeal genomes. KEGG analysis revealed habitat-specific signatures: rumen methanogens were notably depleted in genes of the acetyl-CoA pathway, whereas human gut methanogens lacked key cofactor biosynthesis modules, including those for coenzymes M, B, F420, and methanofuran. From rumen-derived shotgun metagenomes, we identified 53 methane-producing, 4 canonical methanogenic, 10 potential competitor, and 1 methanotrophic metagenome-assembled genomes based on functional gene content. Competitor candidates included nitrate-reducing and Wood-Ljungdahl pathway-utilizing acetogens, suggesting hydrogen redirection under high-hydrogen or inhibitor conditions. These findings support a functional marker strategy that integrates 16S rRNA with pathway-specific genes and a pangenome framework to enhance ecological interpretations of methanogens and to prioritize potential targets for methane mitigation in ruminants.}, } @article {pmid42291259, year = {2026}, author = {Feng, S and Liu, Q and Chen, Y and Kang, D and Zou, S}, title = {Different grazing intensities affect soil nitrogen cycling by altering microbial nitrogen metabolism in alpine wetlands.}, journal = {iScience}, volume = {29}, number = {6}, pages = {116009}, pmid = {42291259}, issn = {2589-0042}, abstract = {Grazing significantly affects soil nitrogen cycling in eastern Qinghai-Tibet Plateau alpine wetlands. Grazing did not alter soil microbial α-diversity, but shifted community composition via metagenomic analysis. Moderate and heavy grazing reduced soil total and active nitrogen contents by 53.8%-92.0% vs. light grazing, significantly decreased abundances of nitrification genes (amoA and hao) and ammonium assimilation gene (glnA), while increased dissimilatory nitrite reduction to ammonium gene (nirB) by 142.1%. A nitrification bottleneck from impaired nitrification drove active nitrogen decline, and structural equation modeling identified nitrogen cycle gene abundance as the key driver. This study reveals microbial nitrogen cycling mechanisms and provides a scientific basis for sustainable grazing management in alpine wetlands.}, } @article {pmid42291297, year = {2026}, author = {Ma, M and Wang, L and Chen, M and Shi, S and Gui, X and Huang, X}, title = {Metagenomic next-generation sequencing reveals microbial community characteristics during acute exacerbations of interstitial pneumonia and their associations with clinical phenotypes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1809022}, pmid = {42291297}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Lung Diseases, Interstitial/microbiology/diagnosis ; Female ; *Metagenomics/methods ; *Microbiota/genetics ; Retrospective Studies ; Male ; Bacteria/classification/genetics/isolation & purification ; Aged ; Phenotype ; Middle Aged ; Sensitivity and Specificity ; Metagenome ; }, abstract = {OBJECTIVE: Accurate pathogen detection is crucial for clinical management of interstitial lung diseases (ILDs), but conventional culture methods (CMT) have limited sensitivity. This study evaluated the diagnostic performance of metagenomic next-generation sequencing (mNGS) versus CMT in ILD patients and characterized differences in lower respiratory microbiome between stable (Stable) and acute exacerbation (AE) stage, as well as their associations with clinical indicators.

METHODS: We retrospectively analyzed ILD patients admitted between September 2021 and November 2023. Multidisciplinary discussion (MDT)-based comprehensive diagnosis served as the reference standard. We compared the sensitivity, specificity, and accuracy of mNGS and CMT. Microbiome analyses were performed to assess community composition and diversity in the Stable and AE groups, and to explore correlations with clinical features (e.g., frequency of exacerbations, oxygenation index, inflammatory markers).

RESULTS: The sensitivity of mNGS (95.60%) was significantly higher than that of CMT (32.20%). In 61.80% of patients, only mNGS yielded positive results, highlighting its diagnostic advantage. A total of 77 microorganisms were detected; bacteria accounted for 66.67% (e.g., Streptococcus pneumoniae, Haemophilus parainfluenzae). Among fungi, Candida albicans and Pneumocystis jirovecii predominated. Microbial diversity was significantly lower in the AE group than in the Stable group (p < 0.01). Candida albicans (p = 0.032) and Abiotrophia defectiva (p=0.011) were enriched in AE, whereas Haemophilus parainfluenzae (p = 0.038) and Prevotella pallens (p = 0.022) were more abundant in Stable. Correlation analyses showed that Candida albicans was positively associated with exacerbation frequency (p < 0.05), while Streptococcus salivarius correlated positively with the oxygenation index. Abiotrophia defectiva was positively associated with Erythrocyte Sedimentation Rate (ESR) and body temperature, but negatively associated with lymphocyte count.

CONCLUSION: Patients in the AE group exhibited altered microbial community structures, and increased fungal colonization may be associated with disease progression, suggesting new targets for clinical intervention.}, } @article {pmid42291302, year = {2026}, author = {Wang, R and Yang, H and Zhang, C and Zi Neng, X}, title = {The complexity of invasive fungal diseases in the intensive care unit: evaluation of metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1820501}, pmid = {42291302}, issn = {2235-2988}, mesh = {Humans ; *Intensive Care Units ; *Invasive Fungal Infections/diagnosis/microbiology/drug therapy ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Retrospective Studies ; Middle Aged ; Immunocompromised Host ; Male ; Aged ; *Fungi/genetics/classification/isolation & purification ; Adult ; Antifungal Agents/therapeutic use ; }, abstract = {BACKGROUND: In the intensive care unit (ICU), a subset of adult individuals who are non-neutropenic and lack conventional host risk factors frequently develop fungal infections, which constitute a major mortality risk in this population. This patient group has received limited attention to date, and research on diagnostic approaches remains insufficient. This research looks into whether metagenomic next-generation sequencing (mNGS) could be used to diagnose this group of people.

METHODS: We performed a retrospective analysis of 106 individuals with invasive fungal infections between July 2022 and February 2025. These patients were divided into two groups: immunocompetent and immunocompromised. Demographic and clinical characteristics were analyzed and compared between the two groups. The diagnostic value of mNGS was carefully assessed, and its diagnostic performance was contrasted with that of conventional microbiological tests (CMTs). In addition, the impact of mNGS results from different specimen types on clinical management and antifungal treatment decisions was summarized.

RESULTS: Among the 106 adult patients, 66.26% were immunocompetent, but many of them had underlying comorbidities. A total of 81 pathogens were identified, of which 74 were detected by mNGS and 44 by CMTs. The predominant fungal pathogens included Candida species, Pneumocystis jirovecii, and Aspergillus fumigatus. mNGS showed a distinct superiority in identifying uncommon pathogens and mixed infections, with its total positive rate markedly exceeding that of CMTs. mNGS results led to beneficial modifications in clinical management for 75 patients (70.75%). The clinical impact varied by specimen type, including bronchoalveolar lavage fluid (BALF; 61 cases), blood (14 cases), and other sterile body fluids (31 cases), with blood specimens yielding the least clinical benefit.

CONCLUSION: In the ICU, a substantial number of invasive fungal infections occur among patients without classical host risk factors. mNGS offers substantial benefits in identifying fungal pathogens and mixed infections, hence enhancing the diagnostic efficacy of invasive fungal diseases (IFDs). The extent of clinical benefit is affected by the kind of specimen provided for testing.}, } @article {pmid42292195, year = {2026}, author = {Borgio, JF and Sharma, HS and Almandil, NB and AbdulAzeez, S and van der Spek, PJ}, title = {Editorial: Molecular informatics in personalized medicine, volume II.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1861955}, doi = {10.3389/fmed.2026.1861955}, pmid = {42292195}, issn = {2296-858X}, } @article {pmid42292299, year = {2022}, author = {Oliveira, C and Shakiba, E and North, D and McGraw, M and Ballard, E and Barrett-D'Amico, M and Glazko, G and Rahmatallah, Y}, title = {16S rRNA Gene-Based Metagenomic Analysis of Rhizosphere Soil Bacteria in Arkansas Rice Crop Fields.}, journal = {Agronomy (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {42292299}, issn = {2073-4395}, abstract = {The rhizomicrobiome is composed of microbes that live in association with plant roots. From nutrient cycling to carbon sequestration, soil microorganisms have provided a solid base for natural and agricultural ecosystems to function. The relationship between plant roots and soil microorganisms is especially relevant in food staples such as rice (Oryza sativa L.), as the various properties of these microbes can influence crop yield and plant health, thereby affecting a major portion of the food supply for an ever-growing world population. In this study, we used 16S rRNA gene-based metagenomic analysis to investigate the impact of crop rotation and soil cultivation methods (no-till or tillage) on rhizosphere bacterial diversity and composition in eight crop fields in Arkansas. Illumina MiSeq sequencing revealed 56 Phyla, with four major Phyla: Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes. Soil microbial communities in the samples studied were phylogenetically diverse but with a stable community structure. Crop rotation and tillage did not significantly affect bacterial diversity.}, } @article {pmid42292361, year = {2026}, author = {Jiang, H and Lu, E and Liu, Q and Li, Z and Zhu, Y}, title = {Etiological study of pulmonary infections following solid organ transplantation using metagenomic next-generation sequencing and development of a risk prediction model: a retrospective cohort study.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1734832}, pmid = {42292361}, issn = {1664-3224}, mesh = {Humans ; Retrospective Studies ; *Metagenomics/methods ; Female ; *High-Throughput Nucleotide Sequencing ; Male ; Middle Aged ; *Organ Transplantation/adverse effects ; Prognosis ; Risk Assessment ; Adult ; *Respiratory Tract Infections/etiology/diagnosis/microbiology ; Risk Factors ; }, abstract = {OBJECTIVE: To analyze the pathogenic etiology of pulmonary infection after solid organ transplantation and construct a prognostic prediction model based on metagenomic next-generation sequencing (mNGS) technology, systematically identifying key predictors to provide evidence for clinical risk stratification and individualized interventions.

METHODS: Clinical data were retrospectively collected from patients who developed pulmonary infection after liver or kidney transplantation at a single hospital between January 2020 and December 2023. All patients underwent mNGS detection of bronchoalveolar lavage fluid or sputum for pathogen identification. Collected data included demographic characteristics, transplant-related parameters, underlying diseases, laboratory test results, mNGS pathogen detection outcomes, and prognostic indicators. The dataset was randomly divided into a training set (n=262) and a test set (n=66). Within an AutoML framework, model hyperparameters were optimized using the Improved Dharma Optimization Algorithm (IDRA). Feature importance was validated bidimensionally via LASSO regression and SHAP interpretable models, with an interactive MATLAB-based decision support system developed.

RESULTS: The overall positive detection rate of pathogens by mNGS significantly exceeded that of conventional methods (84.76% vs. 61.89%, P<0.001). No statistically significant differences existed in baseline characteristics or laboratory indicators between the training and test sets (all P>0.05), confirming randomized stratified sampling validity. Both cohorts showed highly consistent proportions of poor prognosis events (training set: 27.48% vs. test set: 28.79%, χ[2]=0.045, P = 0.832). The prediction model achieved a ROC-AUC of 0.9694 and PR-AUC of 0.9690 in the training set, and ROC-AUC of 0.9206 (95% CI: 0.854-0.987) with PR-AUC of 0.9273 (95% CI: 0.867-0.988) in the test set, outperforming comparative models. Fourteen key variables were ultimately selected: mNGS bacterial detection, mNGS fungal detection, procalcitonin (PCT), C-reactive protein (CRP), mNGS viral detection, white blood cell count, creatinine, post-transplantation time, neutrophil percentage, diabetes, age, total bilirubin, alanine aminotransferase (ALT), and lymphocyte percentage. The feature overlap rate with AutoML-screened variables was 78.6% (11/14). SHAP analysis revealed descending importance ranking: mNGS bacterial detection, mNGS fungal detection, PCT, etc.

CONCLUSION: Integrating multidimensional clinical data with explainable machine learning techniques, this study confirms the central role of pathogenic etiology characteristics in prognostic prediction for post-transplant pulmonary infection and demonstrates the potential for real-time risk assessment to inform clinical decisions. However, prospective validation across diverse care settings is required to establish its efficacy as an interventional guide. This work offers innovative tools and methodological frameworks to advance precision diagnosis and management, subject to ongoing refinement through multicenter collaboration.}, } @article {pmid42292462, year = {2026}, author = {Xing, Y and Wang, J and Li, X and Yin, X}, title = {Behind the mask of relapsing bimodal encephalitis: herpesvirus 7 and Epstein-Barr virus associated with Hashimoto's encephalopathy: a case report.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1782631}, pmid = {42292462}, issn = {1664-3224}, mesh = {Adult ; Female ; Humans ; Autoantibodies/blood ; Electroencephalography ; *Encephalitis/diagnosis/virology/drug therapy ; *Encephalitis, Viral/virology/diagnosis/drug therapy ; *Epstein-Barr Virus Infections/complications/virology/diagnosis ; *Hashimoto Disease/virology/diagnosis/drug therapy ; *Herpesvirus 4, Human/physiology ; *Herpesvirus 7, Human/physiology ; Magnetic Resonance Imaging ; Recurrence ; }, abstract = {BACKGROUND AND PURPOSE: Relapsing bimodal encephalitis in adults remains poorly characterized. We describe a case of relapsing viral encephalitis followed by secondary autoimmune-mediated encephalitis and explore its potential underlying mechanisms.

CASE DESCRIPTION: A previously healthy adult female initially presented with fever and headache; brain magnetic resonance imaging (MRI) showed punctate white matter hyperintensities, and electroencephalogram revealed background slowing with intermittent δ waves. Initial cerebrospinal fluid (CSF) analyses were suggestive of viral encephalitis. Although no pathogen was identified by CSF metagenomic next-generation sequencing (mNGS), she responded favorably to empirical antiviral therapy. 22 days after discharge, she was readmitted with decreased responsiveness, hypersomnia, and acute psychosis. Concurrent MRI revealed progressive white matter lesions. CSF analysis demonstrated oligoclonal bands restricted to the CSF, while autoimmune encephalitis antibody panels were negative. Serum autoantibodies (anti-SSA/SSB, anti-thyroglobulin, and thyroid peroxidase) were elevated. Considering probable autoimmune encephalitis, intravenous immunoglobulin and methylprednisolone were administered, leading to clinical and serological remission with radiological improvement. After 22 months, the patient relapsed with similar clinical manifestations, beginning with fever and headache, followed by decreased responsiveness, and subsequently developed an acute mental disorder. Repeat CSF mNGS detected human herpesvirus 7 (HHV-7) and Epstein-Barr virus (EBV), accompanied by new white matter lesions and recurrent thyroid autoantibodies. The patient responded favorably to the same treatment. At one-month follow-up, the patient developed hyperthyroidism.

CONCLUSION: HHV-7 and EBV with long latency are likely associated with a cascade of autoimmune encephalitis, presenting as relapsing bimodal encephalitis. Thyroid autoantibodies-rather than conventional neuronal antibodies-appear central to the autoimmune phase, consistent with Hashimoto's encephalopathy.}, } @article {pmid42292537, year = {2026}, author = {Jung, CG and Gautam, S and Song, Y and Poorey, K and Mishra, U}, title = {Spatiotemporal Dynamics of the Relative Abundance of Soil Nutrient-Degrading Enzyme-Encoding Genes Across Continental US Ecoregions.}, journal = {Ecology and evolution}, volume = {16}, number = {6}, pages = {e73869}, pmid = {42292537}, issn = {2045-7758}, abstract = {Understanding the spatiotemporal patterns in the relative abundance of soil extracellular enzyme-encoding genes is critical for predicting microbial responses to environmental change and their potential role in nutrient cycling. Yet, integrating novel metagenomic observations with spatiotemporal environmental gradients to infer regional patterns and future trajectories has remained unclear. To address this gap, we applied a machine learning (ML) approach, integrating soil metagenomic data with environmental variables-soil properties, topography, vegetation, and climate-to predict the relative abundance of enzyme-encoding genes for soil carbon (C), nitrogen (N), and phosphorus (P) across surface soils of the continental United States. We assessed potential responses under future emission scenarios (SSP2-4.5 and SSP5-8.5) by comparing a baseline (1985-2014) to a future period (2071-2100). The ML model explained 57%-63% of baseline variation. Precipitation was identified as the most influential factor for the relative abundance of C- and N-degrading enzyme-encoding genes, while slope length, representing horizontal distance that water can travel downslope, was the primary driver for P-degrading enzyme-encoding genes abundance. Projections revealed spatially heterogeneous shifts across continental US ecoregions: the relative abundance of C- and N-degrading enzyme-encoding genes decreased in wetter ecoregions and increased in drier ecoregions under future climate, while P-degrading enzyme-encoding genes abundance decreased significantly in semiarid and Mediterranean ecoregions. This study demonstrates the utility of metagenomic data for mapping soil genetic potential and predicting its regional response to environmental change, to inform ecosystem management strategies.}, } @article {pmid42292847, year = {2026}, author = {You, Q and Jin, M and Zhou, B and Huang, C and Lin, Z and Hu, J and Xue, J and Chen, X and Xiao, Y and Li, R and Zong, Y and Wu, M and Zhang, T and Liu, H}, title = {Gut microbiome components predict response to neoadjuvant short-course radiotherapy followed by camrelizumab and chemotherapy in locally advanced rectal cancer (UNION): a prospective study.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1829108}, pmid = {42292847}, issn = {1663-9812}, abstract = {BACKGROUND: Although the gut microbiome shapes responses to anti-tumor immunotherapy and chemotherapy, its predictive value for neoadjuvant short-course radiotherapy (SCRT) followed by camrelizumab (CAM) and CAPOX in patients with locally advanced rectal cancer (LARC) has not been defined. This exploratory study aimed to evaluate whether the gut microbiome is associated with response to neoadjuvant SCRT followed by CAM and CAPOX.

METHODS: We obtained a total of 77 fecal samples from 36 patients with LARC, including 17 assigned to the long-course chemoradiotherapy (LCRT) group and 19 to the SCRT group. Samples were collected at three time points: baseline, after radiotherapy, and after chemoimmunotherapy. DNA was extracted, followed by metagenomic sequencing to profile microbiota dynamics during neoadjuvant treatment.

RESULTS: In this pilot analysis, we observed significant differences in the gut microbiota between the SCRT and LCRT treatment cohorts. Specifically, Bifidobacterium and Dorea were significantly enriched following completion of SCRT sequential CAM and CAPOX therapy. Further analysis revealed that the relative abundances of these two genera changed significantly only before and after the SCRT regimen, with no notable changes observed in the LCRT group. Preliminary ROC analysis suggested potential utility of these taxa for predicting treatment response, though validation in larger cohorts is needed.

CONCLUSION: The gut microbiome offers potential biomarkers that may stratify response to SCRT followed by CAM and CAPOX, representing a promising exploratory finding with potential clinical relevance.

CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/, identifier NCT04928807.}, } @article {pmid42293010, year = {2026}, author = {de Oliveira, SAS and Sheat, S and Margaria, P and Lima, AL and Dos Santos, JA and Rocha, HS and da Silveira, HF and Ramos de Jesus, C and Winter, S}, title = {Association of Rhizoctonia theobromae with cassava witches' broom outbreak in Brazil and genetic relatedness to Southeast Asian isolates.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1799146}, pmid = {42293010}, issn = {1664-462X}, abstract = {BACKGROUND: A new cassava disease outbreak was identified in indigenous communities in Oiapoque, Amapá, Brazil, characterized by stunting, proliferation of thin shoots, broom-like leaf formations, and apical dieback. These symptoms are consistent with Cassava Witches' Broom Disease (CWBD), previously reported in other regions of South America and Asia.

METHODS: Metagenomic profiling, molecular diagnostics, phylogenetic analyses, and multilocus genotyping were used to investigate microbial communities associated with symptomatic cassava plants.

RESULTS: Rhizoctonia (Ceratobasidium) theobromae was identified as the predominant fungal species associated with symptomatic plants. Genetic analyses indicated a close relationship between Brazilian isolates and Asian reference strains, suggesting a possible transcontinental introduction and supporting an association between R. theobromae and CWBD. This represents the first confirmed report of R. theobromae in Brazil, expanding its known geographic distribution in the Americas.

CONCLUSION: The detection of this quarantine pathogen represents a potential threat to cassava production, food security, and preservation of indigenous cassava landraces in Brazil. These findings reinforce the need for surveillance, phytosanitary measures, and further studies on emerging fungal pathogens associated with cassava diseases.}, } @article {pmid42293020, year = {2026}, author = {Yutong, Z and Yaling, L and Wei, Y and Fengling, S}, title = {Spatiotemporal dynamics of rhizosphere microbial communities in alfalfa across saline-alkali agro-ecosystems.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1792882}, pmid = {42293020}, issn = {1664-462X}, abstract = {The rhizosphere represents a highly active plant-soil interface, where microorganisms play critical roles in the growth and development of alfalfa and in regulating local ecosystem processes. However, the mechanisms by which alfalfa rhizosphere microorganisms respond to spatiotemporal variation in saline-alkali environments remain poorly understood. Here, we collected alfalfa plants from one- to eight-year-old stands across three pastoral regions differing in soil type and characterized their rhizosphere soils. Using soil physicochemical analyzes, soil enzymology, and metagenomics, we examined how rhizosphere microbial communities respond to temporal and spatial variation in saline-alkali soils. Our findings indicate that alfalfa rhizosphere microecology may maintain rhizosphere health by modulating soil physicochemical properties, reducing peroxidase activity, enhancing reductase activity, and increasing the abundance of beneficial microorganisms. These results underscore the potential value of introducing exogenous beneficial bacteria to shape indigenous rhizosphere microecology.}, } @article {pmid42293161, year = {2026}, author = {Nunez, H and Straub, TJ and Imam, N and Goad, D and Mueller, NT and Mars, RAT and Sew Hoy, C and Paullin, T and Sukhum, KV}, title = {Age-specific early-life gut microbiome associations with eczema and food allergies during early immune development.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1804117}, pmid = {42293161}, issn = {2813-4338}, abstract = {INTRODUCTION: Eczema and food allergy commonly emerge during infancy and are linked to changes in the gut microbiome, yet it remains unclear when microbiome differences associated with allergic disease first appear during development.

METHODS: We analyzed age-stratified shotgun metagenomic data from 97 children aged 4-36 months, including physician-confirmed cases of eczema or food allergy and non-allergic controls, excluding recent antibiotic or probiotic exposure. Microbial taxa, functional pathways, and composite microbiome metrics were evaluated across three developmental stages: early infancy (4-6 months), mid-infancy (6-12 months), and toddlerhood (12-36 months).

RESULTS: Differences between allergic and non-allergic children were minimal before 6 months of age but became more apparent during mid-infancy and persisted into toddlerhood. Allergic conditions were associated with reduced abundance of fiber-fermenting and butyrate-producing taxa, enrichment of facultative and inflammation-associated microbes, lower microbiome maturation scores, and shifts in metabolic and inflammatory functional capacity.

DISCUSSION: These findings suggest that gut microbiome divergence associated with allergic disease becomes more apparent during mid-infancy, highlighting a developmentally relevant period for understanding early immune disruption. The results support further longitudinal and interventional studies aimed at clarifying whether earlier microbiome-targeted strategies may help modify progression along the atopic march.}, } @article {pmid42293411, year = {2025}, author = {Liu, M and Gong, J and Liu, Y and Yu, J and Hu, Z and Liu, Z}, title = {Multi-omics reveals circadian regulation of bone homeostasis by gut microbiota metabolites: mechanisms and chronotherapeutic implications.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1719445}, pmid = {42293411}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Animals ; *Homeostasis ; *Circadian Rhythm ; *Bone and Bones/metabolism/physiology ; Bone Remodeling ; Metabolomics ; Fatty Acids, Volatile/metabolism ; Osteogenesis ; }, abstract = {The gut-bone axis plays a pivotal role in skeletal health, yet the integration of multi-omics approaches to elucidate circadian metabolite-bone interactions remains limited. This review synthesizes evidence from metagenomics, metabolomics, and germ-free models to uncover how microbiota-derived metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan derivatives, and gaseous molecules-orchestrate bone remodeling in osteoporosis, osteoarthritis, and bone malignancies. Many studies demonstrate that SCFAs inhibit osteoclastogenesis via GPR43/HDAC signaling and promote osteoblast metabolic reprogramming, while bile acids enhance osteogenesis through FXR/Wnt/β-catenin activation. Tryptophan metabolites repair intestinal barrier integrity and modulate osteoimmunity via the AhR pathway. Single-cell omics reveal circadian oscillations of metabolite receptors (e.g., GPR43, FXR) in bone stromal cells, linking microbial diurnal rhythms to epigenetic regulation of bone turnover. We propose a novel "metabolite-immune-bone triad" model, highlighting microbiome-driven immunometabolic reprogramming as a central regulator of skeletal homeostasis. These insights advance precision microbial therapeutics and chrono-nutritional strategies, bridging multi-omics discoveries with clinical applications for bone disorders.}, } @article {pmid42293516, year = {2026}, author = {Zou, Y and Liu, L and Chen, H and Luo, Z and Zhu, Z and Li, Z and Lin, B and Zhuang, Z and Li, W and Yang, Q and Yang, X and Zhou, H and Luo, M and Dai, D}, title = {Study protocol for a randomized controlled trial of fecal microbiota transplantation via different routes in children with moderate-to-severe autism spectrum disorder.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1829532}, pmid = {42293516}, issn = {1664-302X}, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) shows promise for autism spectrum disorder (ASD) by modulating the gut-brain axis, but the optimal delivery route remains unknown. Our previous single-arm study suggested efficacy of nasojejunal FMT in children with moderate-to-severe ASD, yet could not exclude placebo effects or compare routes. This randomized controlled trial aims to determine the most effective and tolerable FMT administration route.

METHODS: This single-center, randomized, triple-blind, double-dummy, placebo-controlled, three-arm parallel-group trial will enroll 75 children (aged 3-16 years) with moderate-to-severe ASD [Childhood Autism Rating Scale, Second Edition (CARS-2) ≥36]. Participants are randomized 1:1:1 to: (1) FMT via nasojejunal tube + sham colonoscopy (FMT-NJT); (2) active FMT via colonoscopy with transendoscopic enteral tube placement (first session) + two subsequent infusions via the indwelling tube + sham nasojejunal intubation (FMT-C); (3) placebo via both routes (sham procedures). Three FMT/placebo sessions (5 mL/kg, max 100 mL) are administered over 5 days. Primary outcome is change in CARS-2 score from baseline to Week 24. Secondary outcomes include changes in Social Responsiveness Scale, Autism Behavior Checklist, Gastrointestinal Symptom Rating Scale, Short Sensory Profile, Children's Sleep Habits Questionnaire, gut metagenomic profiles (baseline, Weeks 2,6,12,24,48), and adverse events.

RESULTS: This is a study protocol; no results are available.

CONCLUSIONS: This first head-to-head comparison of FMT routes in pediatric ASD will provide high-level evidence to guide treatment standardization, directly addressing the translational gap identified in our preliminary work.}, } @article {pmid42293521, year = {2026}, author = {Liu, Z and Xiahou, Y and Li, J and Wu, F and Fan, Y and Liu, R and Zhou, M and Ding, Z and Zhang, Y and Chen, C and Huang, L and Ai, H}, title = {Metagenomic analysis of the DNA virome communities in swine lungs.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1798033}, pmid = {42293521}, issn = {1664-302X}, abstract = {Viruses play critical roles in shaping microbial communities and regulating host metabolism. Investigating the lung virome of pigs can inform swine health management and provide a comparative resource for studies of the human lower respiratory virome. However, viral communities in the porcine lower respiratory tract remain poorly characterized. In this study, lung-associated viral communities were investigated using virus-like particle (VLP) enrichment and DNA metagenomic sequencing of 49 lung-derived samples collected from 17 domestic pigs and 20 wild boars. A total of 18,412 viral operational taxonomic units (vOTUs) were identified. Among the 2,559 vOTUs with genome completeness ≥50%, nearly 95% did not cluster with sequences in current viral reference databases at the species-level threshold (ANI ≥ 95% and AF ≥ 85%), suggesting putative viral novelty in the porcine lung while also reflecting incomplete reference database coverage. Meanwhile, 10,819 vOTUs (accounting for 58.8% of the total 18,412 identified vOTUs) were assigned to known viral taxa, spanning 29 viral orders and 65 viral families. The most prevalent viral families were Microviridae, Circoviridae, Smacoviridae, Adintoviridae, and Autographiviridae. Host prediction linked a subset of vOTUs to putative bacterial hosts, mainly from Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota. In addition, we identified 191 vOTUs carrying 40 auxiliary metabolic genes (AMGs) mapped to 31 metabolic pathways. These AMGs were mainly associated with sulfur metabolism, cysteine and methionine metabolism, folate biosynthesis, and one-carbon pool by folate pathways. Comparative analysis under this study design showed that domestic pigs harbored higher viral diversity with a greater number of unique vOTUs (n = 12,611) than wild boars (n = 3,072). Domestic pigs viromes were enriched in Circoviridae and Microviridae, whereas wild boars showed higher relative abundances of Adintoviridae and Genomoviridae. Putative AMGs related to coenzyme synthesis and DNA methylation were more frequently detected in domestic pigs, whereas AMGs associated with nucleotide biosynthesis and cofactor metabolism were enriched in wild boars. These findings characterize the composition and functional potential of lung-associated DNA viral communities in pigs and provide a resource for future respiratory virome studies.}, } @article {pmid42293528, year = {2026}, author = {Seth, N and Bansal, M and Mazumdar, S and Mazumdar-Leighton, S and Lakhanpaul, S and Vats, S and Arafat, Y and Babu, CR}, title = {Functional diversity in bacterial communities of an integrated constructed wetland used for in situ bioremediation of sewage.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1803785}, pmid = {42293528}, issn = {1664-302X}, abstract = {Constructed wetlands (CWs) offer effective, economical, environment-friendly and energy-efficient solution to growing challenges of increasing sewage and wastewater loads in urban areas. Although microbial communities form an integral component of constructed wetlands for sewage treatment, functional processes and their dynamics during sewage bioremediation in constructed wetlands remain largely uncharacterized. Moreover, the association of specific bacterial taxa with remediation of different sewage and water quality parameters remains largely unclear. This study explored the functional diversity likely associated with microbial communities of a constructed wetland system used for in situ remediation of 1 MLD (Million Liters per Day) sewage without external energy input since 2014. Different bacterial functional groups in the sludge from a stabilization pond and from rhizospheric sediments of the integrated constructed wetland were predicted using a 16S rRNA gene metagenomic sequencing dataset. Correlation analysis, multivariate statistics and a co-occurrence network were used to assess the bacterial groups associated with changes in water quality as it flows through different components of the integrated CW and highlight association patterns predicting major exchanges which might be operating in the microbial communities. While stabilization pond microbiome was dominated by bacterial groups such as Firmicutes, Desulfobacterota and Methylomirabilota known to be involved in carbon fermentation, sulphate reduction and methanogenesis, the rhizospheric sediments showed prevalence of bacteria associated with nitrogen reduction including Nitrospirota and Planctomycetota contributing to improved sewage quality parameters. Such results indicated complex microbial interactions involving bacteria from diverse functional groups sustaining bioremediation in the CW. The identification of primary bacterial taxa along with their putative functions can help in designing strategies to improve sustainable, nature-based wastewater treatment by CW systems.}, } @article {pmid42293535, year = {2026}, author = {González-Reguero, D and Robas-Mora, M and García Ordiales, E and Fernández-Pastrana, VM and Penalba-Iglesias, D and Probanza Lobo, A and Jiménez Gómez, PA}, title = {Recovery of organic waste from a wastewater treatment plant, improved with plant growth promoting bacteria: model of Quercus suber L.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1754063}, pmid = {42293535}, issn = {1664-302X}, abstract = {Cork oaks (Quercus suber L.) are key tree species in Mediterranean ecosystems, playing a crucial role in fire mitigation due to their thick, fire‑resistant bark, while also contributing to biodiversity conservation and soil stability. Integrating waste valorization strategies with biofertilizers based on plant growth‑promoting bacteria (PGPB) may enhance reforestation efficiency. This study evaluated different irrigation regimes under controlled phytotron conditions, including water, organic fertilizer derived from a wastewater treatment plant (WWTP), and sterilized WWTP fertilizer, combined with Bacillus pretiosus CECT30673[T] and Pseudomonas agronomica CECT30673[T]. Microbial functional diversity (Shannon index), antibiotic resistance profiles, and rhizosphere community structure were assessed using 16S rRNA‑based metagenomic analyses, including taxonomic composition, beta diversity, and genus‑level relative abundances. Plant performance was evaluated through biomass production, stem length, and nutritional parameters, including protein composition, sugar content, and fatty acid profile. The application of PGPBs together with WWTP‑derived fertilizers resulted in a significant increase in plant biomass and stem length compared to traditional water irrigation. Nutritional quality was also significantly improved, with higher protein, sugar, and fatty acid contents. Additionally, the combined treatments reduced minimum inhibitory concentrations (MICs) within the rhizosphere microbial community while maintaining its functional and structural stability. These results demonstrate that combining PGPBs with WWTP‑derived matrices enhances cork oak growth and nutritional quality without disrupting native soil microbiomes, supporting their potential as sustainable tools for Mediterranean reforestation.}, } @article {pmid42293540, year = {2026}, author = {Velaz Martín, M and Rießland, H and Rabe, KS and Niemeyer, CM}, title = {Primer choice shapes microbial community interpretation across habitats and informs short-term structured enrichment in environmental and applied systems.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1838890}, pmid = {42293540}, issn = {1664-302X}, abstract = {Microbial communities play central roles in ecosystem functioning across natural and engineered environments, yet their accurate characterization remains challenging due to methodological biases in amplicon sequencing. Primer choice can strongly influence taxonomic resolution, diversity estimates, and ecological interpretation. Here, we systematically compared primer performance across multiple ribosomal marker genes (16S, 18S, 28S rRNA, and ITS) and contrasting habitats, including soil, wastewater, and a photobioreactor-derived suspension. Amplicon-based profiles were benchmarked against shotgun metagenomic data. Primer choice significantly affected community composition, diversity metrics, and concordance with metagenomic profiles across all habitats and markers. Although 16S rRNA gene primers targeting the V3 region showed the highest agreement, no primer set fully reconstructed community structure. Applying the best-performing primer to a structured soil enrichment system using MESIF chips revealed rapid divergence from native soil and convergence toward less diverse communities, consistently favoring copiotrophic, surface-associated taxa while characteristic soil taxa declined. Across the 21-day incubation period, MESIF-associated communities diverged strongly from native soil, whereas medium-specific differences were comparatively smaller. This suggests that early enrichment was dominated by colonization of the structured matrix, while longer incubations and functional analyses will be needed to resolve substrate-specific selection. Overall, our findings highlight primer selection as a critical factor in microbial community analysis and show that combining optimized amplicon sequencing with structured cultivation enables reproducible enrichment, improved community monitoring, and targeted recovery of functionally relevant microorganisms. These insights are relevant for environmental monitoring, wastewater treatment, biotechnology, and controlled environment agriculture.}, } @article {pmid42293542, year = {2026}, author = {Liu, L and Liu, J and He, J and Xing, Y and Zhang, D and Zhang, X and Ma, C and Xu, M and Li, R and Peng, M and Mei, S}, title = {Multi-kingdom gut microbiota analysis identifies bacterial-viral association in multiple myeloma.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1798330}, pmid = {42293542}, issn = {1664-302X}, abstract = {INTRODUCTION: Alterations in the gut microbiome are closely associated with the progression of multiple myeloma (MM). Previous research has predominantly focused on the bacterial components of the microbiota; however, the virome, a significant component of the microbiota, also plays a critical role, with bacteriophages influencing bacterial community composition and evolution.

METHODS: This study utilized shotgun metagenomic sequencing of fecal samples to explore the interaction between the gut microbiota and MM development. Fecal samples from 28 MM patients and 20 healthy controls were analyzed to evaluate microbial diversity. Taxonomic profiling of both bacterial and viral communities was performed using the Kraken2 classifier.

RESULTS: Our analysis confirmed microbial dysbiosis in MM patients and revealed concomitant changes in both bacterial and viral communities. At the phylum level, this study identified a significant increase in the relative abundance of Pseudomonadota (from 1.63 to 8.88%, p < 0.001) and a decrease in Bacillota in MM patients compared to controls. Furthermore, several viral taxa were notably enriched in the MM cohort, including the phylum Heunggongvirae (linear discriminant analysis [LDA] = 4.74, p = 0.00003), phylum Uroviricota, and genus Punavirus (specifically Punavirus RCS47). Functional analysis demonstrated shifts in microbial metabolic pathways associated with MM, including a reduced capacity for amino acid and secondary bile acid biosynthesis and an enrichment of pathways associated with biofilm formation and cationic antimicrobial peptide (CAMP) resistance.

DISCUSSION: This multi-kingdom metagenomic analysis reveals distinct bacterial and viral signatures associated with MM, enhancing our understanding of gut microbial dysbiosis in the disease. These findings lay the groundwork for future mechanistic investigations and highlight the importance of validating these results in larger, independent cohorts.}, } @article {pmid42293553, year = {2026}, author = {Ali, M and Srivastava, A and Arora, PK}, title = {Probiotics: multifunctional microorganisms for human health and biotechnological applications.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1847515}, pmid = {42293553}, issn = {1664-302X}, abstract = {Probiotics are live microorganisms that, when ingested in sufficient amounts, can have a beneficial impact on health. As crucial agents in maintaining gut homeostasis, enhancing immunity, and preventing of numerous diseases, they are fundamentally important. Probiotic function is based on pathogen inhibition, the release of antimicrobial substances, immune modulation, and the enhancement of the intestinal barrier integrity. Technological advances in the area, including molecular identification, microencapsulation methods, and metagenomics, have also been discussed. In addition, research methodologies for several subclasses of probiotics including Lactobacillus and Bifidobacterium continually being investigated. The role of probiotics in health of human, along with existing challenges related to probiotic viability and strain specificity, has also been discussed. This review highlights the growing understanding of probiotics and underscores their potential for optimizing human health and therapeutic applications.}, } @article {pmid42293554, year = {2026}, author = {Behera, BK and Ren, W and Kumar, A}, title = {Editorial: Biodegradation of agricultural pesticides.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1874629}, pmid = {42293554}, issn = {1664-302X}, } @article {pmid42293560, year = {2026}, author = {Tenea, GN and Jarrín-V, P and Reyes, P}, title = {Metagenomic insights into postbiotic-mediated modulation of strawberry surface microbiome and metabolic activity.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1841388}, pmid = {42293560}, issn = {1664-302X}, abstract = {INTRODUCTION: The increasing demand for sustainable alternatives to chemical disinfectants in postharvest fruit handling has incentivized exploration into microbiome-based interventions. We evaluated the impact of lactic acid bacteria (LAB)-derived postbiotic formulations (FF1, FF2, FF3) and a commercial disinfectant (CD) on the microbial community structure of the strawberry fruit surface.

METHODS: Taxonomic and functional changes in the microbial communities were evaluated using shotgun metagenomic sequencing, enabling comprehensive profiling of microbial composition and functional potential through gene family abundance, EggNOG functional categories, KEGG pathways, and MetaCyc metabolic reconstruction. The tested formulations consisted of a precipitated peptide-protein extract (PP) from Weissella cibaria UTNGt21O (FF2), used as the antimicrobial agent, and an exopolysaccharide (EPS) from W. confusa UTNCys2-2 (FF3), serving as a biopolymer carrier, applied in combination (FF1: PPGt21O + EPSCys2-2) or individually.

RESULTS: Our integrated analysis revealed that the highly suppressive formulation, FF1, outperformed the CD by fundamentally restructuring the microbial landscape. Taxonomically, FF1 notably reduced the abundance of key opportunistic spoilage or hazardous organisms. Rather than acting as an indiscriminate biocide, FF1 functioned as a targeted ecological disruptor. Functional profiling (eggNOG, KEGG, and MetaCyc) suggested potential shifts in functional capacity, including a reduced relative abundance of genes associated with translation machinery, cellular membrane expansion (stearate biosynthesis), and host lipid degradation (fatty acid β-oxidation). In parallel, the FF1-treated microbiome showed a higher relative abundance of genes linked to stress-response functions, including heat shock proteins and cell wall-related processes such as peptidoglycan maturation. In contrast, less restrictive formulations (FF2 and FF3) permitted the proliferation of opportunists such as Pseudomonas spp. and Xanthomonas fragariae, accompanied by active energy-consuming and tissue-degrading metabolic signatures.

CONCLUSION: These findings suggest possible underlying mechanisms of LAB-derived postbiotics, demonstrating that FF1 forces the surface microbiome into a metabolically restricted, non-degradative survival state, potentially contributing to the preservation of postharvest strawberry quality.}, } @article {pmid42293865, year = {2026}, author = {Zhang, H and Zhang, W and Yao, D and Li, X and Ali, HSM and Xi, J and Liang, Y and Zhao, F and Yu, S and Yu, K}, title = {Scion varieties and nitrogen levels affect carbon and nitrogen assimilation in apple via modulating rhizosphere microbial structure and function.}, journal = {Horticulture research}, volume = {13}, number = {3}, pages = {uhaf334}, pmid = {42293865}, issn = {2662-6810}, abstract = {The efficiency of carbon and nitrogen uptake in apple trees is co-regulated by plant genotype and rhizosphere microbial communities. However, the mechanisms by which different scion varieties modulate microbial structure and function under varying nitrogen levels remain poorly understood. In this study, Malus sieversii was used as the rootstock, onto which three scion cultivars (M. sieversii, Malus domestica cv. Hanfu, and Malus domestica cv. Red Fuji) were grafted under two nitrogen regimes. A combination of [13]C/[15]N isotope labeling, Illumina MiSeq amplicon sequencing, and metagenomic analysis was employed to elucidate how scion-rootstock interactions and nitrogen availability affect carbon and nitrogen acquisition. Under nitrogen-deficient conditions, Red Fuji exhibited stronger root activity and larger root surface area, indicating enhanced nutrient foraging capacity. Conversely, under nitrogen application, Hanfu showed significantly greater [13]C and [15]N uptake, with 5.7-fold and 1.6-fold higher [13]C accumulation in roots and stems, respectively, and markedly higher [15]N utilization efficiency in roots and leaves compared with M. sieversii. In parallel, Hanfu under nitrogen input showed enrichment of beneficial microbial taxa and more complex microbial co-occurrence networks. Metagenomic analysis and random forest analyses revealed that the relative abundance of specific functional genes related to carbon and nitrogen transformation (rbcL, abfA, napB/C, nasA) was significantly higher under specific scion-nitrogen combinations, contributing to enhanced microbial carbon fixation and nitrogen reduction. Collectively, these results demonstrate that scion genotype modulates rhizosphere microbial structure, physiological root traits, and carbon-nitrogen distribution patterns, thereby improving nutrient uptake efficiency under different nitrogen inputs.}, } @article {pmid42293986, year = {2026}, author = {Lou, L and Li, X and Zhang, P and Wu, H and Chen, H and Ma, J and Zhang, K}, title = {Eravacycline-Cefiderocol Combination Therapy for Carbapenem-Resistant Acinetobacter baumannii Infective Endocarditis: A Case Report and Brief Review of the Literature.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {615678}, pmid = {42293986}, issn = {1178-6973}, abstract = {BACKGROUND: Infective endocarditis (IE) caused by carbapenem-resistant Acinetobacter baumannii (CRAB) is rare and associated with limited treatment options because of extensive antimicrobial resistance.

CASE PRESENTATION: We hereby present a case of prosthetic valve endocarditis (PVE) caused by CRAB, presenting with fever, persistent bloodstream infection, cerebellar hemorrhage, and aortic valve vegetation. The application of a novel combination therapy comprising eravacycline and cefiderocol effectively eliminated the bloodstream infection. Concomitantly, the monitoring of adverse reactions and the subsequent adjustment of medication and dosage ensured the favorable safety. Although bloodstream infection and valve vegetation were controlled, progressive perivalvular leakage indicated the need for timely surgical intervention when clinically feasible.

CONCLUSION: This case indicates that eravacycline combined with cefiderocol may represent a novel and effective treatment option for refractory IE caused by carbapenem-resistant Gram-negative pathogens, including PVE caused by CRAB.}, } @article {pmid42294186, year = {2026}, author = {Saenko, EV and Kuznetsova, MV and Nesterova, LY and Valtsifer, IV and Levin, LY and Zaitsev, AV and Karipova, MO and Strelnikov, VN and Valtsifer, VA}, title = {Analysis of Microbial Tolerance and Physicochemical Properties of HFA‑E Hydraulic Fluids Used in Mechanized Mine Roof Supports.}, journal = {ACS omega}, volume = {11}, number = {22}, pages = {31925-31939}, pmid = {42294186}, issn = {2470-1343}, abstract = {This study presents a comparative analysis of microbial tolerance and physicochemical properties of HFA-E (fire-resistant hydraulic fluid, aqueous-based, emulsion type) hydraulic fluids based on commercial "Hydrotol-ITCh HFAE" and "Fimitol P87 AF" concentrates used in mining hydraulic roof support systems. Metagenomic analysis revealed distinct microbial community structures in the two fluids. The Hydrotol-ITCh HFAE-based fluid microbiota consisted predominantly of Bacteria (99.77%), especially Proteobacteria, while the Fimitol P87 AF-based fluid exhibited a more complex and taxonomically diverse community, including a significant proportion of Archaea (47.09%) and Bacteria (52.92%) from groups such as methanogens (Methanobacteriaceae) and sulfate-reducing bacteria (Desulfovibrionaceae), respectively. In vitro tests confirmed the inherent antimicrobial activity of the fluids, which significantly reduced planktonic microbial viability and eradicated the majority of bacteria. The physicochemical properties of the fluids remained stable even under high initial bacterial load, confirming their reliability during microbial contamination. However, under industrial conditions, the Hydrotol-ITCh HFAE-based fluid demonstrated lower contamination and higher emulsion stability (pH reduced to 8.5 after one year of operation versus 6.5 for "Fimitol P87 AF"), which reduced the risk of biocorrosion and the need for additional treatments. This study emphasizes the importance of comprehensive monitoring of microbial diversity and physicochemical parameters for predicting the service life of hydraulic systems, developing effective biocides, and minimizing risks to equipment and personnel. The obtained data can be used to optimize hydraulic fluid compositions and their operational strategies.}, } @article {pmid42294227, year = {2026}, author = {Tan, AJ and Li, TR and Yang, JJ and Li, XL and Li, WQ and Yu, JW}, title = {Liraglutide and Dapagliflozin Synergistically Reshape Gut Microbiota and Metabolic Profiles to Ameliorate Type‑2 Diabetes in Mice.}, journal = {ACS omega}, volume = {11}, number = {22}, pages = {32363-32379}, pmid = {42294227}, issn = {2470-1343}, abstract = {Background: Type-2 diabetes mellitus (T2DM) poses a formidable global health challenge, characterized by persistent hyperglycemia resulting from insulin resistance and progressive β-cell dysfunction. Liraglutide (LIRA), a GLP-1 receptor agonist, and dapagliflozin (DAPA), an SGLT2 inhibitor, are established therapies with complementary mechanisms. However, the potential synergy of their combination, particularly through modulation of the gut microbiota and host metabolism, remains incompletely understood. To elucidate the gut microbiota-metabolite axis underlying the therapeutic effects of combination therapy in T2DM, we explored the interplay between β-cell function, fecal microbiota composition, and microbial metabolites. Methods: A T2DM mouse model was induced by a high-fat diet and streptozotocin. Mice were treated for 4 weeks with LIRA, DAPA, or their combination (COM). We assessed glycemic control, insulin sensitivity, pancreatic islet morphology, serum biochemistry, gut microbiota (shotgun metagenomic sequencing), and plasma metabolome (nontargeted metabolomics). Integrated multiomics analysis was performed to elucidate microbiota-metabolite interactions. Results: Combination treatment demonstrated superior efficacy compared to monotherapies, resulting in significantly greater improvements in body weight, glucose tolerance, insulin sensitivity, lipid profiles, and liver function. Histologically, COM most effectively restored pancreatic islet architecture, increased β-cell mass, and normalized α/β-cell ratio. Metagenomic analysis revealed that COM induced a unique and restorative remodeling of the gut microbiota, distinct from monotherapies. This was characterized by suppression of pathobionts (e.g., Klebsiella and Enterorhabdus) and enrichment of beneficial taxa (e.g., Akkermansia, Lactobacillus, and Faecalibaculum). Metabolomics profiling showed that COM extensively normalized the diabetic plasma metabolome. Key altered pathways included tryptophan metabolism, sphingolipid metabolism, and branched-chain amino acid degradation. Integrated correlation analysis unveiled significant associations between specific microbial genera and host metabolites, suggesting a functional gut microbiota-metabolite axis underpinning the synergistic benefits. Conclusions: The combination of liraglutide and dapagliflozin exerts synergistic antidiabetic effects that extend beyond glycemic control to encompass pancreatic protection and systemic metabolic improvement. This synergy is mechanistically linked to collaborative remodeling of the gut ecosystem and consequent normalization of host metabolic pathways. Our findings provide a novel rationale for this combination therapy and highlight the gut microbiota as a pivotal target for T2DM management.}, } @article {pmid42294679, year = {2026}, author = {Henkel, JV and Røy, H and Jørgensen, BB and Rotaru, A-E and Jovicic, D and Marshall, IPG and Jiang, C and Nielsen, PH and Singleton, CM and Arz, HW and Plewe, S and Kjeldsen, KU}, title = {Desulfatiglans-related bacteria associated with conductive mineral particles in marine subsurface sediments.}, journal = {mBio}, volume = {}, number = {}, pages = {e0083826}, doi = {10.1128/mbio.00838-26}, pmid = {42294679}, issn = {2150-7511}, abstract = {UNLABELLED: Acetate is a key intermediate in anaerobic mineralization of organic matter in marine sediments. Recent observations suggest that acetate is oxidized syntrophically in the methanic zone of marine sediments, and that electrically conductive mineral particles could provide niches for electroactive microbial communities that perform this process. We combined radiotracer measurements, a novel procedure for ferromagnetic mineral particle extraction, and metagenomic analyses to examine this process in Baltic Sea sediments. Our results confirm that acetate is oxidized syntrophically across and below the sulfate-methane transition zones of the sediments, where the transfer of reducing equivalents from acetate oxidation to CO2 fuels methanogenesis. Ferromagnetic particles consistently occurred throughout the geochemical zones and mainly consisted of the electrically conductive minerals magnetite and pyrite-greigite. The microbial communities associated with ferromagnetic particles were dominated by members phylogenetically affiliated with the bacterial genus Desulfatiglans. Known Desulfatiglans species are dissimilatory sulfate reducers; however, metagenome-assembled genomes indicate that Desulfatiglandales populations associated with ferromagnetic particles lack genetic potential to respire sulfate. Instead, they may grow by acetate oxidation coupled with extracellular electron transfer, consistent with a conductive mineral-associated lifestyle. We hypothesize that Desulfatiglans relatives are acetate-oxidizing partners in a syntrophic process facilitated by interspecies electron transfer via conductive particles. We identified cytochrome-rich ANME-1 archaea as the predominant methane-cycling microorganisms associated with ferromagnetic particles; however, their potential role as methanogenic syntrophic partners remains uncertain. Overall, our study reveals that distinct microbial communities are associated with ferromagnetic particles and shows conductive minerals as a niche for electroactive microorganisms in marine sediments.

IMPORTANCE: Acetate is a central intermediate in the anaerobic breakdown of organic matter. In Baltic Sea sediments at and below the sulfate-methane transition zone, we observed acetate oxidation to carbon dioxide at rates similar to methane formation from carbon dioxide reduction, a pattern indicative of syntrophic acetate oxidation. Previous enrichment studies suggest that electrically conductive mineral surfaces can facilitate this process. Motivated by this observation, we extracted ferromagnetic conductive particles from sediments and compared particle-attached microbial communities with bulk sediment. Particle-attached communities were distinct and enriched in the bacterial genus Desulfatiglans. Their genomes lacked genes for sulfate respiration, yet encoded traits consistent with acetate oxidation and extracellular electron transfer. Our findings suggest conductive minerals as distinct microbial niches and highlight Desulfatiglans-related bacteria as a potential key organism in particle-associated acetate oxidation.}, } @article {pmid42294682, year = {2026}, author = {Ai, C and Tang, X and Han, H and He, Y and Zhang, H and Liu, C and Liao, H and Zhou, S}, title = {Active prophages as key drivers of microbial adaptation in global soil ecosystems.}, journal = {mBio}, volume = {}, number = {}, pages = {e0069326}, doi = {10.1128/mbio.00693-26}, pmid = {42294682}, issn = {2150-7511}, abstract = {Soils harbor the most complex microbial diversity on Earth, in which bacteria are ubiquitously infected by temperate phages. While integrated prophages often enhance host fitness, active (inducible) prophages are traditionally perceived as "molecular time bombs" due to their intrinsic lysis threat. This dual nature has raised fundamental questions about the true contribution of temperate phages to microbial adaptation and ecosystem stability. To address this gap, we conducted a global-scale integrative analysis by synthesizing 123,207 high-quality bacterial genomes, 183 soil-specific viromic data sets, and 3,749 metagenomes. We established the Global Soil Active Prophage Database (GSAPD), comprising 21,397 high-confidence active prophages, which we found to represent 34.3% of the total soil viral population within our analytical framework. Our comparative genomic analysis reveals that active prophages possess significantly larger genomes and greater genetic complexity compared with their dormant counterparts. Crucially, by mapping phage-encoded auxiliary metabolic genes (AMGs) across diverse biomes, we found that active prophages are disproportionately enriched in key pathways for carbon, nitrogen, and sulfur cycling, as well as specialized resistance mechanisms against heavy metal toxicity. These findings suggest that active prophages act as dynamic reservoirs of functional diversity. We demonstrate that their lytic potential is not merely a survival risk, but a sophisticated mechanism underpinning host environmental adaptation and niche expansion. Ultimately, this study provides a comprehensive global catalog of soil viral pathways and redefines the role of temperate phages as pivotal drivers of microbial evolution and biogeochemical cycling in terrestrial ecosystems.IMPORTANCESoils contain immense microbial diversity, yet the ecological role of temperate phages-especially their active (inducible) forms-remains poorly understood. This study provides the first global-scale assessment of active prophages in soils, revealing that they are widespread and functionally distinct from dormant forms. By building a comprehensive database and integrating multi-omics data, we show that active prophages are enriched in genes linked to key biogeochemical processes and stress resistance. These findings challenge the traditional view of active prophages as purely harmful agents and instead highlight their role as dynamic contributors to microbial function and adaptation. Our work offers new insights into how viruses shape ecosystem processes and provides a valuable resource for future studies on soil microbial ecology and nutrient cycling.}, } @article {pmid42294703, year = {2026}, author = {Kady, MR and Britton, RA}, title = {Revised complete genome sequences of Limosilactobacillus reuteri DSM 20016[T] and ATCC PTA-6475 and confirmation of an intragenic macrosatellite in adhesin gene cmbA.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0400525}, doi = {10.1128/spectrum.04005-25}, pmid = {42294703}, issn = {2165-0497}, abstract = {UNLABELLED: Cell and mucus binding protein A (CmbA) is a cell-wall-anchored adhesin common to human isolates of Limosilactobacillus reuteri, which governs mucosal adhesion in vitro. Recent attempts to sequence cmbA in different L. reuteri strains revealed significant genomic inconsistencies with the publicly available closed genome sequences, especially with that of the L. reuteri type strain, DSM 20016[T]. We report here a revised closed genome sequence for DSM 20016[T] and a closed genome sequence for the closely related L. reuteri ATCC PTA-6475 (MM4-1A). Hybrid long- and short-read sequencing demonstrated that two genomic regions totaling 40 kbp, previously thought to be absent in DSM 20016[T], were in fact intact. The cmbA gene, present in one of these regions, is the longest predicted gene in both genomes and was confirmed to contain an intragenic tandem repeat region. In DSM 20016[T], the region consists of 11 identical ~290 bp tandem direct repeats totaling 3.2 kbp, while ATCC PTA-6475 has 8 repeats totaling 2.3 kbp. This macrosatellite posed a challenge to PCR-based approaches to confirm the length of the gene. Polyacrylamide gel electrophoresis of cell wall extracts from ATCC PTA-6475 showed a ~160 kDa band, which was absent from a cmbA-knockout strain, consistent with the expected size based on whole-genome sequencing and confirmed by mass spectrometry to be CmbA. Overall, we present refined publicly available genome sequences for two frequently studied L. reuteri strains and validate the length of a large gene with a conspicuously high number of identical tandem repeats.

IMPORTANCE: Studies comparing bacterial genomes and routine cloning work often implicitly assume that the closed genome sequences available from public databases are accurate. However, as technologies improve and we gain new data, inconsistencies can arise which prompt the resequencing of strains, sometimes with surprising results. We show here that a significant sequencing assembly artifact led to a large gap in the publicly available closed genome of the Limosilactobacillus reuteri type strain which has remained uncorrected for nearly two decades, despite a vast body of L. reuteri work over that time. Another region contained a large stretch of repetitive intragenic DNA that still posed a challenge to modern PCR techniques. Therefore, in addition to being useful to L. reuteri biologists, this work serves as an important reminder of the intrinsically experimental nature of sequencing data; it usually pays to resequence early and often.}, } @article {pmid42294704, year = {2026}, author = {He, Y and Wang, X and Li, S and Zhang, C and Xu, M and Zhou, Y and Sanford, RA and Liang, R and Zhu, Y and Yang, D and Dan, L and Mao, X and Zhang, L and Sun, W and Jiang, Y and Hu, Y and Jiang, Z and Li, Y and Song, W and Hu, N and Zhao, L and Dong, Y and Shi, L}, title = {Ecological plasticity of Halanaerobium microorganisms across terrestrial saline to hypersaline subsurface environments.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0138126}, doi = {10.1128/spectrum.01381-26}, pmid = {42294704}, issn = {2165-0497}, abstract = {UNLABELLED: Members of the genus Halanaerobium are widely distributed in hypersaline environments, including oil and gas reservoirs, and saline lake sediment. However, a comprehensive understanding of their physiological traits, metabolic capacities, adaptive strategies, and biogeography remains limited. In this study, a strictly anaerobic and halophilic strain, H. saccharolyticum_B KY39 was isolated from produced water in the Zhongyuan Oilfield, China. Strain KY39 grew at 20-45°C, 2-30% salinity, pH 5.3-9.0, and up to 50 MPa hydrostatic pressure. It could ferment various carbohydrates (e.g., glucose, xylose, sucrose, and maltose) or use mannitol and pyruvate as electron donors under Fe(III)-reducing conditions. Comparative genomic analyses of 31 high-quality Halanaerobium strains revealed an open pangenome. Genes involved in osmotic and pressure stress responses, including those related to osmoprotectant biosynthesis and ion transport, were highly conserved. The thiosulfate sulfurtransferase (TST) gene, responsible for converting thiosulfate to sulfite, was universally present. Notably, compared to the strains from saline lakes, those from oil and gas reservoirs possessed larger genomes and harbored a broader repertoire of genes related to peptidoglycan biosynthesis, nitrogen fixation, sulfur metabolism, biofilm formation, and carbohydrate uptake, suggesting enhanced metabolic flexibility and environmental adaptation. Moreover, a survey of the available metagenomes revealed that Halanaerobium species were globally distributed across diverse environments exhibiting a broader salinity range. In addition to oil and gas reservoirs and saline lakes, they also widely reside in soils, fermented foods, and marine ecosystems. Collectively, these findings advance the systematic understanding of ecological plasticity and metabolic versatility of Halanaerobium, shedding light on their ecological roles and potential industrial impacts.

IMPORTANCE: Members of the genus Halanaerobium are prominent inhabitants of surface and deep subsurface hypersaline environments, yet their ecological roles and adaptive strategies remain poorly understood. Here, through the isolation of a novel strain from the production fluid of an oil field combined with comparative genomic analyses across the genus, we revealed the metabolic versatility, stress tolerance, and global distribution of Halanaerobium. Our findings underscore the ecological plasticity, functional diversity, and niche differentiation within this genus, providing fundamental insights into its potential industrial and environmental applications.}, } @article {pmid42294714, year = {2026}, author = {Sajib, MSI and Oravcova, K and Brunker, K and Everest, P and Fuentes, M and Wilson, C and Murphy, ME and Forde, T}, title = {Rapid and modular workflows for same-day sequencing-based detection of bloodstream infections and antimicrobial resistance determinants using culture-enriched samples.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0324025}, doi = {10.1128/spectrum.03240-25}, pmid = {42294714}, issn = {2165-0497}, abstract = {UNLABELLED: Bloodstream infections (BSI) are a major global health concern, and existing diagnostic methods are too slow to guide targeted antibiotic therapy for critically ill patients. Rapid metagenomic next-generation sequencing (mNGS) can facilitate swift microbiological diagnosis, but identification is challenged by significant host versus bacterial DNA in blood and blood culture media. To accelerate reporting time, we developed M-15, a rapid mNGS-based host DNA depletion workflow optimized for culture-enriched samples, validated with suspected BSI blood culture samples and rapid culture-enriched spiked blood. M-15 was benchmarked with five commercial/published protocols, combined with rapid mNGS, and tested on blood culture samples (n = 33) from suspected BSI cases identified on BACT/ALERT-VIRTUO. To determine whether it is possible to utilize M-15 mNGS prior to blood culture flagging positive, a rapid enrichment method was tested starting with 1-10 colony-forming units of the top 15 bacterial species causing BSI spiked into BACT/ALERT medium enriched with 10 mL sheep blood. All six chemical depletion protocols reduced host DNA by 2.5 × 10[0]- to 4.1 × 10[6]-fold, with the in-house M-15 protocol performing best. With BACT/ALERT specimens, M-15 mNGS identified 28/28 mono-bacterial and 2/4 multi-bacterial species. With rapid culture enrichment and M-15 mNGS, <18% DNA was classified as host, and all bacterial species tested (n = 10) were correctly identified. M-15 mNGS accurately predicted phenotypic AMR/susceptibility for 90.3% (232/257) of drug/bacteria combinations from BACT/ALERT-positive samples. This study demonstrates that M-15 mNGS can facilitate species and AMR gene detection within 5-7 hours of BACT/ALERT positivity and possibly 13-15 hours of sample collection. Further clinical validation is required to assess its performance and the potential to improve patient outcomes in BSI.

IMPORTANCE: Bloodstream infections (BSI) are among the leading global health challenges, and traditional culture-based diagnostic methods are too slow (often taking >48 hours) to guide critical clinical interventions. This study demonstrates the development and utility of M-15 metagenomic next-generation sequencing (mNGS), a modular Oxford Nanopore-based chemical host DNA depletion and metagenomic sequencing workflow applied to enriched blood culture media for the same-day detection of bacterial etiologies and their antimicrobial resistance (AMR) genes. The selective chemical host DNA depletion method (M-15) described in this study can remove approximately 4.1 × 10[6]-fold unwanted host DNA from whole blood, providing high-resolution genomic information from the bacteria at a fraction of the sequencing time/cost (approximately £120-£160/sample). We have tested this workflow on culture-positive clinical and rapid enriched spiked blood samples and demonstrated its ability to identify bacterial species and AMR genes between 5 and 7 hours post blood culture positivity. Based on our in vitro experiments using rapid enrichment, we believe similar results could be achieved within 13-15 hours from blood sample collection. Although further clinical validation is required, especially to fully assess the rapid version of the protocol, M-15 mNGS offers a promising advancement in BSI diagnosis. This workflow is modular and can be expanded in the future to adapt for other infections, which makes it a versatile tool to improve patient outcomes in sepsis.}, } @article {pmid42294728, year = {2026}, author = {Mao, Z and Jiang, M and Zhao, Z and Xu, S and Wang, H and Chen, K and Duan, J and Chen, Z and He, D and Xing, P and Wu, QL}, title = {Biofilm-forming traits enrich the plasmid diversity and functional potential in particle-attached bacteria in coastal ecosystems.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0046026}, doi = {10.1128/spectrum.00460-26}, pmid = {42294728}, issn = {2165-0497}, abstract = {UNLABELLED: Planktonic microorganisms play a central role in aquatic biogeochemical processes and are commonly divided into particle-attached (PA) and free-living (FL) fractions. Although these two lifestyles differ in ecological strategy, the contribution of plasmids to their niche differentiation remains poorly resolved. Here, we conducted a plasmid-centric metagenomic analysis of two anthropogenically impacted coastal ecosystems in South China, the Pearl River Estuary (PRE), and Daya Bay (DYB), to determine the environmental and biological drivers of plasmid diversity, and their functional potenitial. We found that plasmid diversity was jointly shaped by different fractions and environmental stressors. The PA fraction contained significantly higher plasmid abundance and richness than the FL fraction, and was enriched in multifunctional and conjugative plasmids. These plasmids were associated with genes adapting to the PA lifestyle or microenvironments, suggesting linkage between particle attachment and plasmid maintenance. Structural equation modeling indicated that different fractions shaped plasmid diversity primarily through biofilm-forming genes. Along an anthropogenic gradient from DYB to PRE, increasing pollution levels were accompanied by higher plasmid diversity and greater abundances of antibiotic and metal resistance genes. Plasmid diversity was strongly correlated with resistance gene abundance. The enrichment of transferable plasmids in the PA fraction, where cell densities are high and intercellular distances are close, suggested that particle-associated habitats favor genetic exchange and the persistence of resistance traits. Together, these results demonstrate that particle-associated microbial communities represent key reservoirs of plasmid diversity and resistance potential in coastal ecosystems and highlight the combined influence of lifestyles and anthropogenic stress on plasmid-mediated microbial adaptation.

IMPORTANCE: Plasmids play an important role in microbial adaptation by mediating horizontal gene transfer, yet the ecological contexts that favor their persistence and diversification in natural environments remain poorly understood. This study showed that particle-attached microbial communities in coastal waters harbored substantially higher plasmid diversity and resistance potential than free-living communities, and that this enrichment is strongly linked to biofilm-associated traits. By demonstrating how particulate habitats and pollution gradients jointly shape plasmid diversity and resistance gene abundance, our findings identify particle-associated microenvironments as critical reservoirs for plasmid-mediated functions in coastal ecosystems. These results advance understanding of how microbial lifestyle and human activities influence microbial evolution and the environmental dissemination of resistance traits.}, } @article {pmid42294989, year = {2026}, author = {Thomas, PW}, title = {Hidden Fungal DNA Structures May Shape Sequencing Outcomes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {48}, number = {6}, pages = {e70153}, pmid = {42294989}, issn = {1521-1878}, mesh = {*DNA, Fungal/chemistry/genetics ; Genome, Fungal ; *Fungi/genetics ; Nucleic Acid Conformation ; *Sequence Analysis, DNA/methods ; }, abstract = {Fungal DNA is systematically under-detected in shotgun metagenomics, likely due in part to physical barriers like melanized cell walls and complex DNA conformations. Additionally, Oxford Nanopore Technologies sequencing with native fungal DNA often results in rapid pore clogging and unusual translocation dynamics, possibly due to intrinsic, yet undescribed, structural complexities. Exploring these signals could reveal novel fungal genome architectures, enhance sequencing accuracy, and drive advances in fungal biology.}, } @article {pmid42295167, year = {2026}, author = {Jonouchi, D and Shenoy, S and Saintlouis, R and Singh, A and Kashyap, D and Bhargavi, C and Mansoor, R and Mansoor, E and Honnavar, P}, title = {Vaginal microbiome composition in pregnant and non-pregnant women: community structure, population variation, clinical impact, and metagenomics approaches.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0054225}, doi = {10.1128/iai.00542-25}, pmid = {42295167}, issn = {1098-5522}, abstract = {The vaginal microbiome plays a critical role in reproductive health and undergoes characteristic remodeling during pregnancy that influences maternal and neonatal outcomes. Although the non-pregnant vaginal microbiome shows substantial inter-individual variability, pregnancy is associated with reduced microbial diversity and increased dominance by Lactobacillus species, creating a protective environment for fetal development. Disruption of this balance, termed vaginal dysbiosis, has been linked to adverse obstetric and neonatal outcomes. This narrative review synthesizes current evidence on pregnancy-associated vaginal microbiome dynamics, with emphasis on community state types (CSTs), gestational changes, population-specific variation, and clinical implications. We review studies that use 16S rRNA sequencing, next-generation sequencing, and shotgun metagenomics to characterize microbial composition across pregnancy and the postpartum period. Lactobacillus-dominated communities, particularly those dominated by Lactobacillus crispatus, are consistently associated with microbiome stability and favorable pregnancy outcomes, whereas high-diversity anaerobic communities (CST IV) are linked to bacterial vaginosis, preterm birth, miscarriage, gestational diabetes mellitus, and infection-related complications. The vaginal microbiome composition varies significantly across racial, ethnic, and geographic populations. African-descended populations more often show L. iners-dominant or diverse anaerobic profiles, whereas European populations more commonly show L. crispatus dominance. Future longitudinal and mechanistic studies across diverse populations are needed to establish causality and evaluate microbiome-based interventions to improve maternal and neonatal health.}, } @article {pmid42295179, year = {2026}, author = {Guitart-Matas, J and Ramayo-Caldas, Y and González-Rodríguez, O and Giler-Baquerizo, N and Migura-Garcia, L and Ballester, M}, title = {Implementation of a high-throughput microfluidic platform for antimicrobial resistance surveillance in swine production systems.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, pmid = {42295179}, issn = {2057-5858}, mesh = {Animals ; Swine/microbiology ; Metagenomics/methods ; Feces/microbiology ; *Microfluidics/methods ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/drug effects ; Shotgun Sequencing ; }, abstract = {Antimicrobial resistance poses a serious threat to public health worldwide and demands interventions with a One Health perspective. A key challenge is determining the collection of antimicrobial resistance genes of a specific environment, also known as the resistome. Surveillance and monitoring of the resistome are essential for tracking the emergence and dissemination of resistance mechanisms. In this study, we took advantage of shotgun metagenomics and metatranscriptomics sequencing data of piglets treated with different post-weaning diarrhoea treatments to generate an antimicrobial resistance gene catalogue of the pig gut microbiome during pre-weaning and post-weaning stages. The selected catalogue, comprising a total of 102 genes and representing the majority of antibiotic classes, has been implemented in the microfluidic Biomark[™] X9 System and validated using total DNA and RNA extracted from piglets' faecal samples. Additionally, this platform has been verified by demonstrating a strong and statistically significant correlation with resistome quantification data from both metagenomic and metatranscriptomic sequencing. Overall, the microfluidic qPCR platform implemented here demonstrated enhanced detection of low-abundance targets, successfully identifying genes and transcripts that remained below the stochastic detection threshold of shotgun sequencing. This approach enables high-throughput monitoring and surveillance of antimicrobial resistance, providing a critical tool to support the reduction of antimicrobial use in farms.}, } @article {pmid42295208, year = {2026}, author = {Chaudhary, A and Lin, X and Vitaterna, MH and Auch, B and Liachko, I and Green, SJ}, title = {Metagenome-assembled genome sequence of an uncultured Roseburia sp. generated from mouse fecal DNA from the International Space Station.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0104725}, doi = {10.1128/mra.01047-25}, pmid = {42295208}, issn = {2576-098X}, abstract = {The effects of spaceflight stressors, such as microgravity, cosmic radiation, and confinement, on the host physiology and gut microbiome remain unclear. Here, we report the metagenome-assembled genome (MAG) sequence of an uncultured Roseburia sp. strain that showed a significant gravity dose response in the gut microbiome of mice during spaceflight.}, } @article {pmid42295273, year = {2026}, author = {Mawire, P and Gregori, MNJ and Makumbi, JP and Bezuidt, OK and Makhalanyane, TP}, title = {High-quality metagenome-assembled genomes of carbon-degrading, sulfate-reducing, and sulfur-oxidizing Acidobacteriota from Sub-Antarctic Marion Island soils.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0034226}, doi = {10.1128/mra.00342-26}, pmid = {42295273}, issn = {2576-098X}, abstract = {Here, we present high-quality Acidobacteriota metagenome-assembled genomes (n = 20) belonging to understudied lineages (UBA7541 [n = 13] and SbA1 [n = 7]) from sub-Antarctic soils. Nutrient cycling genes were prevalent in these MAGs, which provide a resource for understanding the ecological role of Acidobacteriota in extreme environments.}, } @article {pmid42295521, year = {2026}, author = {Ferdous, J and Islam, SMR and Chakma, K and Hasan, MM and Tanni, AA and Ahmed, R and Sikder, U and Biswas, S and Siddiki, AZ and Crandall, KA and Rahnavard, A and Hussain, MH and Sharifuzzaman, SM and Chowdhury, MSN and Mannan, A}, title = {Antimicrobial resistance and gut microbiome profiles in wild and cultured shrimp (Penaeus monodon) from the coast of the northern Bay of Bengal, Bangladesh.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {7}, pages = {}, pmid = {42295521}, issn = {1573-2959}, mesh = {Animals ; *Penaeidae/microbiology ; Aquaculture ; Bangladesh ; *Gastrointestinal Microbiome ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Bays ; Bacteria/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Environmental Monitoring ; }, abstract = {The coastal waters of Bangladesh support rich aquatic biodiversity, including the commercially important shrimp Penaeus monodon. However, antimicrobial resistance (AMR) poses a growing threat to aquaculture, ecosystem stability, and human health. In this study, we investigated bacterial AMR profiles and characterized the gut microbiomes of wild (Natural) and cultured P. monodon from the northern Bay of Bengal, Bangladesh. Culture-based and biochemical methods were used to identify bacterial pathogens of shrimp shells, and antimicrobial susceptibility was assessed using the disc diffusion method. Shotgun metagenomic sequencing was used to characterize gut microbial diversity and identify antibiotic resistance genes (ARGs). All Klebsiella isolates were resistant to ampicillin (100%) and showed high resistance to azithromycin (83%) and nitrofurantoin (73%). Pseudomonas isolates were 93.10% resistant to ampicillin, whereas Vibrio isolates had notable resistance to azithromycin (71.05%) and colistin (63.16%). Metagenomic analysis revealed comparable alpha diversity between wild and cultured shrimp, with Vibrio being predominant in both groups and V. parahaemolyticus as the most abundant species. Cultured shrimp harbored greater microbial diversity, including additional genera such as Shewanella, Lactococcus, and Enterobacter. A total of 30 ARGs were detected, primarily associated with β-lactams and tetracycline resistance. Cultured shrimp exhibited a broader ARG spectrum, reflecting potential anthropogenic impacts on aquaculture practices. These findings suggest that cultured shrimp environments can serve as reservoirs of resistant bacteria and ARGs. Therefore, improved antimicrobial stewardship and regular monitoring are essential to curb the spread of AMRs in marine ecosystems.}, } @article {pmid42295988, year = {2026}, author = {Soge, OO and Fifer, H and Alexander, S and Buss, SN}, title = {Diagnostics and novel laboratory approaches to combat Neisseria gonorrhoeae antimicrobial resistance.}, journal = {Expert review of molecular diagnostics}, volume = {}, number = {}, pages = {}, doi = {10.1080/14737159.2026.2689689}, pmid = {42295988}, issn = {1744-8352}, abstract = {INTRODUCTION: Neisseria gonorrhoeae (gonococcus, GC) has developed resistance to all antimicrobials recommended for gonorrhea treatment, owing to its genetic plasticity and capacity to acquire antimicrobial resistance (AMR). This review examines the crucial role of diagnostics and novel laboratory approaches in mitigating the spread of GC-AMR and in preserving the long-term effectiveness of current and future antimicrobials for gonorrhea.

AREAS COVERED: Recent advances in diagnostics and novel laboratory approaches for detection of GC-AMR, enhancing GC-AMR surveillance and clinical management of gonorrhea.

EXPERT OPINION: The rapid emergence and global dissemination of multidrug-resistant GC including ceftriaxone-resistant strains poses a grave challenge to current gonorrhea control and prevention strategies. The implementation of rapid diagnostics and novel laboratory approaches can, when used appropriately, support the rapid detection of GC-AMR, ensure timely treatment, reduce transmission, and preserve last-line antibiotics by enabling resistance-guided therapy. These diagnostics and novel laboratory approaches are also crucial for the early detection of emerging resistance to antimicrobials recently approved by the FDA, and other antimicrobials currently under development and anticipated for future clinical use. Integrating culture-based GC-AMR surveillance with rapid molecular assays targeting genetic determinants of AMR offers a comprehensive approach for robust monitoring and timely response to the ever-evolving GC-AMR.}, } @article {pmid42296170, year = {2026}, author = {Diale-Makhongela, MO and Mpai, T and Bopape, FL and Mtsweni, P and Salawu-Rotimi, A and Shargie, NG and Gerrano, AS and Morey, L and Kubheka, B and Hassen, AI}, title = {16S rRNA-based metagenomics insights into the microbial diversity and functional attributes of soils from the rhizosphere of selected C4 crops of farms in Mpumalanga and Limpopo provinces, South Africa.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0347776}, pmid = {42296170}, issn = {1932-6203}, mesh = {*Rhizosphere ; *RNA, Ribosomal, 16S/genetics ; South Africa ; *Soil Microbiology ; *Metagenomics/methods ; *Crops, Agricultural/microbiology ; Pennisetum/microbiology/growth & development ; Sorghum/microbiology/growth & development ; Soil/chemistry ; Bacteria/genetics/classification ; Phylogeny ; Farms ; Biodiversity ; Carbon/metabolism ; }, abstract = {The rhizosphere serves as a hub for a variety of microorganisms that are highly beneficial to crop production and improvement of soil health. However, intensive farming practices including utilization of agrochemicals can cause a decline in microbial diversity that could severely compromise soil health and crop productivity. Here we investigated the taxonomic abundance and functional diversity of the microbial communities of sorghum and pearl millet rhizosphere soil samples from sixteen farms in Mpumalanga and Limpopo Provinces of South Africa. Soil samples were collected at the rhizosphere of sorghum and pearl millet crops and pooled into 34 samples. The soil samples were used for 16S rRNA amplicon sequencing analysis, soil physicochemical properties, and community-level physiological profiles. The results indicated that carbon utilization was highest in the majority of soil samples from Jane Furse, which also demonstrated greater microbial richness. The 16S rRNA amplicon sequencing analysis provides insight into the relative abundance of soil microbial communities, where at phylum level Planctomycetes, Proteobacteria, and Actinobacteria were the most predominant in all farms, but their relative abundances varied. Our results revealed that physicochemical properties could affect microbial abundance and diversity. The distance-based redundancy analysis (dbRDA) explained 46.8% of the variation in the soil bacterial community structure, with Mn, Fe, NO3[-]-N, and Ca identified as the key soil physicochemical variables shaping community composition. Thus, this study may contribute to advancing sustainable agricultural practices by providing baseline data that may inform future bioinoculant development.}, } @article {pmid42296229, year = {2026}, author = {Yu, Q and Liu, F and Xu, R and Jie, J and Tang, M and Li, D and Gu, Y and Song, L}, title = {Bronchoscopic Cytology and Metagenomic Sequencing to Differentiate Cancer Treatment-related and Infectious Lung Injury.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {231}, pages = {}, doi = {10.3791/70725}, pmid = {42296229}, issn = {1940-087X}, mesh = {Humans ; *Bronchoscopy/methods ; Bronchoalveolar Lavage Fluid/cytology/microbiology ; *Metagenomics/methods ; *Lung Injury/diagnosis/microbiology/etiology/pathology/genetics ; *High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Patients with cancer treatment-related lung injury (CTLI) frequently present with non-specific respiratory symptoms and radiological changes that closely mimic infectious pneumonia or tumor progression, presenting a significant challenge for a definitive diagnosis. Traditional diagnostic processes, mainly evaluated through blood biomarkers and standard microbial cultures, usually cannot make a clear diagnosis and take too much time. Here, we present a comprehensive protocol to diagnose CTLI by combining bronchoalveolar lavage fluid (BALF) cytological analysis with metagenomic next-generation sequencing (mNGS). The procedural workflow consists of three primary stages. First, standardized bronchoscopy is performed to obtain high-quality BALF samples. Second, conducting cytological analysis of the obtained BALF samples provides a snapshot of the lung microenvironment. This allows identification of inflammatory features and screening for malignant cells to exclude tumor progression. Finally, mNGS is utilized to identify or exclude active infectious etiologies. This advanced genomic technique achieves rapid, highly sensitive, and unbiased pathogen detection, successfully overcoming the limitations of traditional cultures. Representative results using this method demonstrate that this approach can effectively distinguish immune-related pneumonitis from active pulmonary infections or tumor progression. Compared with traditional diagnostic methods, this protocol has the advantage of quickly and accurately distinguishing CTLI from infectious etiologies and occult malignancies. Ultimately, this standardized workflow clarifies clinical diagnoses, guides critical treatment decisions, and improves patient outcomes.}, } @article {pmid42296622, year = {2026}, author = {Pravara, R and Praveen, R and Seema, B}, title = {Microbial allies in a cotton pest: A descriptive account of associated microbiota dynamics in Dysdercus cingulatus across development.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {60}, number = {}, pages = {101902}, doi = {10.1016/j.cbd.2026.101902}, pmid = {42296622}, issn = {1878-0407}, abstract = {BACKGROUND: Hemipteran insects harbour several symbiotic partners, mainly bacteria, which play pivotal roles for hosts like dietary provision, support overall physiology, xenobiotic degradation and manipulate/regulate behaviour. Most of these symbionts usually reside and operate from the digestive tracts of the animals. Cotton is one of the major cash crops in India and Dysdercus cingulatus (D. cingulatus) though a secondary pest, is causing significant destruction of cotton bolls, poor lint quality and reduce oil content of seeds. Premature opening of cotton bolls often leads to bacterial and fungal infections, thus resulting in extensive economic loss worldwide. D. cingulatus is a hemimetabolous insect that comprises of developmental stages like egg, nymph (5 instar stages), and adult. The present work explored the ontogeny specific diversity in the associated microbiota and predicted their probable functional inputs in D. cingulatus.

RESULTS: The data obtained using 16S rRNA gene sequencing (NovaSeq 6000) revealed presence of members of Proteobacteria (65.83%), Firmicutes (24%), Actinobacteria (10%) phyla throughout the ontogeny of D. cingulatus. Highest alpha diversity of these symbiotic bacteria was recorded in the third instar nymphs in contrast to rest of the developmental stages. Among all the observed genera, Stenotrophomonas, Hungatella and Glutamicibacter were predominant from egg to adult stages. MicFunPred, a tool used for predicting the probable functional inputs of these symbionts, hinted at their probable stage specific contribution in crucial biochemical pathways such as polyketide biosynthesis, ascorbate/aldarate metabolism, pentose phosphate and glyoxylate cycles, steroid hormone and peptidoglycan biosynthesis, and glycolysis/pyruvate metabolism.

CONCLUSIONS: The primary investigations on the ontogenetic composition and diversity of associated microbiota, suggest dynamic shifts in D. cingulatus, concurrent with their probable functions/roles in the host development and metabolism. To the best of our knowledge, this is the first report on symbiotic microbiota variation across the developmental stages of D. cingulatus that provides preliminary descriptive observations that may guide future functional and experimental investigations into microbiota-based pest management.}, } @article {pmid42296787, year = {2026}, author = {Lu, HB and Kong, LY and Chen, L and Chen, GJ}, title = {Janthinobacterium foliorum sp. nov., isolated from the decayed leaves of wild alpine rhododendron.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126736}, doi = {10.1016/j.syapm.2026.126736}, pmid = {42296787}, issn = {1618-0984}, abstract = {Janthinobacterium strains, which belong to the family Oxalobacteraceae, have attracted considerable attention due to their ability to synthesize violacein and degrade polyphenols. Wild alpine rhododendrons dominate the mountainous vegetation in southwestern China, and their leaf litter decomposition contributes to humification in alpine lakes. The Janthinobacterium strains may play a key role in the decomposition of these leaf litters. In 2025, metagenomic approaches combined with isolation and cultivation methods were applied to investigate microbial resources in stacked decayed leaves from these alpine lakes. The predominant phyla are Pseudomonadota and Actinomycetota with the relative abundances of 47.9% and 39.9%, respectively. The relative abundance of genus Janthinobacterium is only 0.1% in the community, but 11 Janthinobacterium strains were isolated. Based on the ANI and phylogenomic analyses, strains Du111 and Du118 should represent a novel species, for which the name Janthinobacterium foliorum sp. nov. is proposed. The ANI and AAI values between Janthinobacterium aestuarii and Janthinobacterium violaceum are 95.5% and 97.1%, respectively, implying that the recent proposed J. violaceum is the synonym of J. aestuarii. Comparative genomic analyses further reveal that not each of Janthinobacterium strains could produce violacein and prodigiosin, but most Janthinobacterium strains have the potential for participating in the decomposition of lignin and cellulose. This study clarifies the novel role of Janthinobacterium strains, showing that the isolated strains do not represent a novel taxonomic species but have adapted to the alpine microenvironment associated with Rhododendron leaf litter.}, } @article {pmid42297107, year = {2026}, author = {Cr, P and Krishna, V and Sethuraman, N and Nambi P, S and Ramasubramanian, V and Balaguru, P and Gopalakrishnan, R}, title = {Diagnostic utility of 16S rRNA meta genomic next-generation sequencing in clinical Infectious Diseases practice: a retrospective study from South India.}, journal = {Indian journal of medical microbiology}, volume = {}, number = {}, pages = {101166}, doi = {10.1016/j.ijmmb.2026.101166}, pmid = {42297107}, issn = {1998-3646}, abstract = {OBJECTIVES: 16S rRNA sequencing is an emerging diagnostic tool for bacterial syndromes caused by fastidious pathogens and in culture negative infections. However, it can pose significant challenges from pre-analytic to post-analytic phase due to sampling issues, lack of an approved platform and test characteristics. We aimed to evaluate the diagnostic performance of 16S rRNA sequencing in sterile site samples compared to conventional microbiological techniques [CMT] and a composite reference standard [CRS] METHODS: We conducted a retrospective study at a tertiary hospital from January 2022 to July 2024. We included clinical data of patients with sterile site samples processed for both CMT and 16S rRNA sequencing. Sequencing used the Credence Genomics pipeline.

RESULTS: 166 samples met the inclusion criteria: 97 tissue, 35 pus, and 34 fluid samples. Pathogen detection rate was 42.8% [71/166] by CMT and 58.4% [97/166] by 16S rRNA. Concordance between methods was 50.6%. Sensitivity and specificity of 16S rRNA against CMT was 60.6% and 43.2%; and 69.4% and 66.7% against CRS respectively. CMT showed 54% sensitivity and 92.9% specificity against CRS. Combined testing improved sensitivity to 84.7% and accuracy was 78.9%.

CONCLUSION: 16S rRNA sequencing provides incremental diagnostic sensitivity over conventional microbiological techniques but at the cost of reduced specificity. Its routine frontline use as a standalone diagnostic tool is not supported by our findings. Instead, it may be best reserved for selected culture-negative cases with high clinical suspicion, where results can be interpreted in conjunction with clinical, radiological, and microbiological data by experienced clinicians.}, } @article {pmid42297247, year = {2026}, author = {Yang, S and Xing, KY and Tao, YF and Wang, JY and Liu, KH and Zhang, M and Xu, XR and Zhu, L and Wei, W}, title = {Metagenomics-guided targeted isolation and mechanistic elucidation of haloalkaliphilic bisphenol A-degrading microorganisms.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135172}, doi = {10.1016/j.biortech.2026.135172}, pmid = {42297247}, issn = {1873-2976}, abstract = {Bisphenol A (BPA), a typical endocrine-disrupting compound, poses significant environmental risks. Efficient bioremediation in high-salinity and alkaline environments, such as saline-alkaline industrial wastewater and landfill leachate, remains challenging due to the lack of microorganisms capable of maintaining activity under extreme conditions. Here, this study developed a strategy integrating metagenomic functional prediction with targeted enrichment and isolation. Soil microcosm experiments combined with metagenomic analyses identified soda saline-alkaline soils with high BPA degradation potential, and predicted microbial degradation predominantly via hydroxylation, with archaeal involvement also suggested. Guided by these predictions, 14 saline-alkaline-tolerant BPA-degrading bacterial strains (13 genera) and 20 haloalkaliphilic archaeal strains (16 genera) were successfully isolated. The proportion of BPA-degrading archaea (95.24%) was higher than bacteria (58.33%), challenging the view that this function is restricted to bacteria and fungi. Genomic analyses revealed bacterium Pseudomonas reidholzensis SAS-B12 and archaeon Natronomonas gomsonensis SR-A11 degrade BPA via hydroxylation, with differing downstream ring-cleavage pathways. SR-A11 also exhibited high laccase activity, suggesting multi-enzyme synergistic degradation. Response surface methodology optimization showed SAS-B12 achieved ∼50% BPA degradation under simulated saline-alkaline wastewater (pH 8.3, salinity 2.3%), and SR-A11 achieved similar efficiency under extreme conditions (pH 9.8, salinity 23.6%). This study expands the phylogenetic diversity of BPA-degrading microorganisms and provides microbial resources, enzymatic insights, and methodological support for targeted bioremediation in saline-alkaline wastewater.}, } @article {pmid42297252, year = {2026}, author = {Li, Q and Zhang, Q and Huang, D and Chen, S and Zhang, B}, title = {Electrically enhanced, Nature-Driven microbial attenuation of chromate and dichloromethane in groundwater.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135175}, doi = {10.1016/j.biortech.2026.135175}, pmid = {42297252}, issn = {1873-2976}, abstract = {Natural attenuation is a nature-based approach that relies on intrinsic biogeochemical and microbial processes to mitigate mixed heavy metals and organic pollutants in aquifer, yet its efficiency is limited by electron donor scarcity and suppressed microbial activity. Here, a low-energy bioelectrochemical strategy that uses a mild electric field (0.6 V) was introduced to sustainably stimulate the attenuation of chromate [Cr(VI)] and dichloromethane (DCM) co-contamination in groundwater. With minimal electrical input, Cr(VI) and DCM removal reached 95.0 ± 2.6% and 95.2 ± 0.5%, substantially outperforming the no-voltage and single-pollutant systems. The electric field alleviated electron-donor limitations and metabolic inhibition, enabling efficient and energy-conserving bioremediation. Mineralogical and spectroscopic analyses (SEM-EDS, XPS, XRD) confirmed the reduction of Cr(VI) to Cr(III) precipitates (e.g., Cr2O3) and the progressive dechlorination and mineralization of DCM. Integrated metagenomic and metatranscriptomic profiling revealed active functional guilds (e.g., Sphingopyxis, Pseudomonas, Hyphomicrobium) expressing key genes for chromate reduction (yieF, chrA), dehalogenation (dhlA, dcmA), and electron-shuttling metabolism (ribE). This work demonstrates an applicable remediation technology that can be powered by renewable electricity and integrated into secure groundwater management systems. It offers a pathway for environmentally safe pollutant mitigation by harnessing nature-based microbial processes, supporting the transition toward enhanced natural attenuation.}, } @article {pmid42297258, year = {2026}, author = {Wei, S and Wang, L and Li, Y and Wang, B and Wang, T and Li, J}, title = {Cometabolic degradation of ofloxacin by aerobic methane oxidation coupled with denitrification: Identification of degraders, helper bacteria, and metabolic networks.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135168}, doi = {10.1016/j.biortech.2026.135168}, pmid = {42297258}, issn = {1873-2976}, abstract = {The aerobic methane oxidation coupled with denitrification (AME-D) system enables simultaneous nitrogen removal and antibiotics cometabolic degradation, yet the underlying microbial ecological mechanisms remain poorly understood. This work took ofloxacin (OFL) as a typical antibiotic pollutant and established long-term stable sequencing-batch AME-D reactors to explore their nitrogen removal efficiency and OFL degradation sustainability under antibiotic stress. A multi-omics approach combining metagenomics, metaproteomics, and metabolomics was adopted to identify the core degraders and functional helper bacteria, and unravel the synergistic metabolic interactions sustaining the system's performance. Results indicate that the AME-D cometabolic system maintains high-efficiency nitrogen removal capacity and achieves effective OFL degradation under OFL stress. The piperazine ring is the primary reactive site of OFL, undergoing ring cleavage to form intermediate products. Multi-omics results demonstrate that microbial community structure is significantly reshaped by OFL pressure. Aerobic methane-oxidizing bacteria (MOB) are identified as core degraders, which mediate OFL cometabolism via methane monooxygenase (pMMO/sMMO) and supply available electron donors. Denitrifiers and stress-tolerant auxiliary bacteria form synergistic networks by optimizing nitrogen metabolism, activating efflux pumps and regulating antioxidant defenses, which maintains system functional stability under high OFL stress. Fluorescence in situ hybridization (FISH) verification confirms that MOB, nitrifiers and denitrifiers form compact spatial interaction structures in sludge, which provide favorable conditions for interspecific substance exchange and electron transfer. This study clarifies the multi-scale functional maintenance mechanism of AME-D cometabolic system, offering theoretical support for the treatment of antibiotic-laden wastewater and ecological risk control of antibiotic resistance.}, } @article {pmid42297276, year = {2026}, author = {Maas, MAM and Rutjes, SA and Bossers, A and Stege, PB and van der Plaats, RQJ and Kuiper, I and van der Ark, KCH and de Roda Husman, AM}, title = {Use of metagenomics for the detection of pathogens in the environment: A scoping review.}, journal = {Environmental research}, volume = {305}, number = {Pt 2}, pages = {125050}, doi = {10.1016/j.envres.2026.125050}, pmid = {42297276}, issn = {1096-0953}, abstract = {Pathogens in the environment may pose a threat to our ecosystem and public health by causing infectious disease outbreaks. Early detection and identification are crucial for effective surveillance, outbreak prevention, and source attribution. However, analyzing environmental samples (e.g., air, soil, water, biowaste) is challenging due to their complex composition. Testing for each pathogen, known and undiscovered ones, is not possible yet. Metagenomic shotgun sequencing offers a promising approach for pathogen-agnostic DNA detection in these matrices. This review provides guidance and recommendations for experimental design, DNA extraction, library preparation, sequencing, and bioinformatics, and underscores the need for standardized protocols and inter-laboratory studies. This scoping review addresses metagenomic methodologies for pathogen detection in environmental matrices by highlighting current practices, challenges and limitations, and provides guidance for researchers and practitioners. Following the PRISMA guidelines, we identified 81 relevant studies from 6034 initial records. Most studies utilized Illumina short-read sequencing, with fewer using long-read platforms like Oxford Nanopore Technologies or Pacific Biosciences. DNA extraction protocols varied, with a trade-off between DNA yield and preserving community structure. Few studies reported inter-laboratory comparisons or standardized workflows. Selection of bioinformatics tools and reference databases significantly influenced taxonomic classification, yet reporting of analytical parameters was often incomplete. This review highlights the need for appropriate controls and increased transparency in reporting applied methods and settings. Methodological diversity and unreported gaps hinder reproducibility and comparability, while a systematic approach in environmental metagenomics holds great promise for pathogen and ecosystem monitoring.}, } @article {pmid42297323, year = {2026}, author = {Li, Y and Hu, Y and Cheng, S and Fang, H and Guo, Y}, title = {Compound-specific effects of phthalate esters on nitrogen cycling and N2O emissions in paddy soils under contrasting moisture regimes.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {405}, number = {}, pages = {128593}, doi = {10.1016/j.envpol.2026.128593}, pmid = {42297323}, issn = {1873-6424}, abstract = {Phthalates (PAEs) are commonly used as plasticizers and agrochemical additives, easily released and accumulated in soils. As emerging organic pollutants, how PAEs affect soil nitrogen (N) cycling remains unclear. Here, a 91-day microcosm experiment was conducted to investigate the response of functional microorganisms and nitrous oxide (N2O) emissions to dimethyl phthalate (DMP) and di(2-ethylhexyl) phthalate (DEHP) enrichment under different moisture regimes. Metagenomic analysis showed that PAE type, rather than concentration, predominantly shaped microbial community structure and N-cycling functional profiles. Under unflooded conditions, DEHP increased cumulative N2O emissions by 42%, accompanied by enhanced nitrification potential, higher abundances of amoA and hao, and enrichment of Nitrosospira. Conversely, DMP and co-exposure treatments reduced cumulative N2O emissions by 49.24-67.86%, together with suppressed autotrophic nitrification and increased denitrification module abundance. Under flooded conditions, DMP and co-exposure increased nosZ abundance and enriched Telmatospirillum, indicating a greater potential for N2O reduction. In addition, PAE exposure increased the complexity of microbial co-occurrence networks and strengthened associations between functional taxa and N-cycling genes. Structural equation modelling showed that PAE-induced shifts in soil pH, dissolved organic carbon, and inorganic N pools jointly regulated nitrification and denitrification pathways, thereby determining N2O emission patterns. These findings highlight the potential for plasticizer contamination to reshape nitrogen transformation and nitrogen loss pathways in paddy soils under contrasting moisture regimes.}, } @article {pmid42297331, year = {2026}, author = {Fan, S and Li, Y and Zhang, L and Xie, S}, title = {Experimental evidence for the role of phages in mitigating antibiotic resistance genes in mangrove sediments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {405}, number = {}, pages = {128589}, doi = {10.1016/j.envpol.2026.128589}, pmid = {42297331}, issn = {1873-6424}, abstract = {The ecological role of bacteriophages (phages) in mitigating or proliferating antibiotic resistance genes (ARGs) in mangroves remains elusive due to the lack of direct experimental validation. Climate change-driven seawater encroachment introduces non-native phages into mangrove ecosystems, yet the potential impacts of this process on ARG spread have not been elucidated. Here, we established flooded microcosms inoculated with phage suspensions derived from native and non-native mangrove sediments, thus simulating phage input disturbance caused by climate change. Our results revealed distinct phage-host interaction patterns: non-native phages exerted short-term disturbances on bacterial communities, but neither phage source altered the bacterial or resistome structure. Nevertheless, phages specifically influenced the composition and dynamics of ARGs, with non-native phages showing stronger regulatory effects. Furthermore, 77 ± 2.1% of viral operational taxonomic units (vOTUs) were lytic, and 154 out of 185 phage-antibiotic-resistant bacteria (ARB) links were lytic, indicating that lytic phages played a dominant role in controlling ARB abundance and promoting ARG mitigation, whereas 0.68 ± 0.46% of host-infecting lysogenic phages carried ARGs, contributing little to ARG proliferation. Moreover, only 3.2 ± 0.56% vOTUs carried ARGs, resulting in negligible phage-mediated transduction for ARG dissemination. This study provides the first direct experimental evidence for the impacts of phages from different sources on the fate of ARGs in mangrove ecosystems, and offers novel insights into the ecological mechanisms underlying the spread of ARGs in the context of global climate change.}, } @article {pmid42297767, year = {2026}, author = {Song, YC and Shi, C and Stratton, KG and Ayala-Ortiz, C and Stohel, I and Freire-Zapata, V and Tfaily, MM and Eloe-Fadrosh, E and Graham, EB}, title = {Continental-scale integration of soil metagenomes and organic matter chemistry reveals ubiquitous microbial capacity for chemically-recalcitrant carbon decomposition.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42297767}, issn = {2041-1723}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism/chemistry ; *Metagenome ; *Bacteria/metabolism/genetics/classification ; Archaea/metabolism/genetics/classification ; *Organic Chemicals/metabolism/chemistry ; }, abstract = {Soil organic matter (SOM) decomposition by microorganisms is a major uncertainty in predicting terrestrial carbon-atmosphere feedbacks, partly because we lack understanding of the microbial diversity involved in depolymerizing different carbon pools across environmental gradients. We address this gap using a continental-scale dataset pairing shotgun metagenomes with high-resolution SOM chemistry, assembling 0.76 Tbp of prokaryotic MAGs (828 genomes) and identifying 66,727 SOM molecules from 47 standardized U.S. soil cores selected using respiration rates from 106 soils. Integrating these datasets reveals widespread microbial potential for depolymerizing chemically-recalcitrant SOM previously considered stable. We uncover complementary metabolic specialization between genera affiliated with two abundant bacterial orders, Rhizobiales and Chthoniobacterales, and an archaeal order, Nitrososphaerales. This metabolic partitioning is consistent across soil depths and activity levels, suggesting coordinated decomposition of complex SOM through distinct but complementary biochemical strategies. The metabolic potential for depolymerization of chemically-recalcitrant compounds is supported by the abundance of these molecules across the soils, as indicated by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS), and by flux balance analysis of metabolic models. Our results show that a substantial portion of ostensibly stable SOM remains vulnerable to microbial decomposition, a mechanism not captured in current Earth System Models.}, } @article {pmid42298252, year = {2026}, author = {Biter, R and Regney, M and Schmidt, AE and Swanson, N and Elrod, M and Lescroël, A and Burnham, C and Jongsomjit, D and Winquist, S and Pennycook, J and Ainley, DG and Dugger, KM and Ballard, G and Kraberger, S and Varsani, A}, title = {Novel avian papillomaviruses identified in a south polar skua sampled on Ross Island, Antarctica.}, journal = {Archives of virology}, volume = {171}, number = {7}, pages = {}, pmid = {42298252}, issn = {1432-8798}, support = {1935870//National Science Foundation/ ; }, mesh = {Animals ; Antarctic Regions ; Phylogeny ; Genome, Viral ; *Papillomaviridae/genetics/isolation & purification/classification ; *Papillomavirus Infections/veterinary/virology ; *Charadriiformes/virology ; *Bird Diseases/virology ; DNA, Viral/genetics ; }, abstract = {Papillomaviruses are small circular DNA viruses that infect epithelial cells of their hosts. Avian papillomaviruses are poorly sampled/documented compared to those infecting humans. We used a viral metagenomic approach to identify viruses from the oral swab taken from a deceased south polar skua (Stercorarius maccormicki) found at Cape Royds, Ross Island, Antarctica in late 2024. We identified three papillomaviruses and determined their complete genomes, Stercorarius maccormicki papillomavirus (SmacPV) 1-3. SmacPV1 is the most divergent of the three SmacPVs, sharing 62% genome-wide pairwise identity to SmacPV2 and SmacPV3 and <63.5% to other avian papillomaviruses. The genomes of SmacPV2 and SmacPV3 represent two new papillomavirus types sharing 82.4% genome-wide pairwise identity with each other and <72% to other papillomaviruses. SmacPV2 and SmacPV3 phylogenetically cluster with sequences of the Rissa tridactyla papillomavirus 1 from black-legged kittiwake (Rissa tridactyla), Larus smithsonianus papillomavirus 1 from American herring gull (Larus smithsonianus) and Fratercula arctica papillomavirus 1 from Atlantic puffin (Fratercula arctica), and they collectively represent a new papillomavirus species. These are the first papillomaviruses to be identified in Stercorarius spp. and add to the handful of known papillomaviruses in identified avian species. We also expand the known host range of papillomaviruses in Antarctic animals, which previously included Adélie penguins (Pygoscelis adeliae), Weddell seals (Leptonychotes weddellii), Antarctic fur seals (Arctocephalus gazella), leopard seals (Hydrurga leptonyx) and emerald notothen (Trematomus bernacchii).}, } @article {pmid42298353, year = {2026}, author = {Strokach, A and Zakharevich, N and Aginova, V and Grigoryevskaya, Z and Petukhova, I and Bagirova, N and Romanov, M and Dyachkova, M and Morozov, M and Veselovsky, V and Kanaeva, V and Kalinin, D and Larin, A and Shitikov, E and Klimina, K}, title = {Gut microbial markers of immunotherapy response in melanoma: a cross-cohort analysis including the first Russian dataset.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2681788}, pmid = {42298353}, issn = {1949-0984}, mesh = {Humans ; *Immunotherapy ; *Melanoma/therapy/microbiology/immunology/drug therapy ; *Gastrointestinal Microbiome ; Female ; Cohort Studies ; *Bacteria/classification/genetics/isolation & purification ; Male ; Russia ; Metagenomics ; Metagenome ; *Immune Checkpoint Inhibitors/therapeutic use ; Middle Aged ; Aged ; Treatment Outcome ; Adult ; }, abstract = {Melanoma is an aggressive malignancy with a significant risk of mortality. In recent years, treatment strategies have undergone a paradigm shift with the advent of immunotherapy, particularly immune checkpoint inhibitors (ICIs). Despite notable clinical success, a substantial proportion of patients fail to respond or eventually develop resistance to ICIs. Emerging evidence highlights the gut microbiota as a critical modulator of host immune responses and is one of the potential determinants of immunotherapy efficacy. We performed a cross-cohort analysis of gut microbiome profiles from melanoma patients treated with ICIs. The study integrated the first Russian cohort (62 patients) with six previously published international datasets, comprising a total of 490 patients across seven cohorts. In all cases, metagenomic sequencing was performed using various Illumina platforms, and raw sequencing data were processed using a unified bioinformatic pipeline. Analysis revealed 527 metagenome-assembled genomes (MAGs) significantly associated with treatment outcome: 239 with response and 288 with non-response. Notably, the species Faecalibacterium sp900539945, Phocaeicola vulgatus, Bifidobacterium adolescentis, Faecalibacterium taiwanense, and Gemmiger qucibialis were consistently associated with response, while Enterobacter ludwigii was linked to non-response. Analysis of the Russian cohort revealed both conserved and population-specific microbial signatures, highlighting the coexistence of globally shared and region-dependent microbiome features. Our results also show that species-level annotations may obscure opposing response associations within the same taxa, highlighting the need for MAGs or strain profiling. Together, this study demonstrates that cross-cohort analysis enables the identification of robust and reproducible bacterial markers of immunotherapy response, providing a foundation for microbiome-based prediction and modulation strategies in melanoma.}, } @article {pmid42298382, year = {2026}, author = {Raj, K and Sharma, P and Riyaz, M and Shouche, YS and Multani, K and Sharma, M and Dhaliwal, M}, title = {Decoding the functional landscape and resistome profile of the gut microbiome in the Pangwala tribal community of India.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05248-5}, pmid = {42298382}, issn = {1471-2180}, support = {S(File No.R.12020/13/2018-HR)//Department of Health Research, Government of India/ ; S(File No.R.12020/13/2018-HR)//Department of Health Research, Government of India/ ; }, abstract = {BACKGROUND: The human gut microbiome consists of a complex and diverse community of commensal microorganisms and has been under extensive research consideration in the past few decades. Although several recent studies have targeted the determination of bacterial composition of the ecosystem, the knowledge about the mycobiome, virome, and functional attributes of the same remains scarce. The aim of the present study was to investigate the functional and resistome profile of the gut microbiome in the Pangwala tribal community of India using a combined Whole Metagenome Shotgun (WMS) sequencing and bioinformatics approach.

RESULTS: The findings revealed a remarkable diversity of microorganisms inhabiting the gut of both groups, with similar level of diversity among the dominant genera like Prevotella, Bifidobacterium and Succinivibrionaceae. The mycobiome was dominated by the subkingdom Dikarya (74%), while Fungi incertae sedis accounted for 23% of the total fungal species in both groups. The virome analysis showed the dominance of the Caudoviricetes class, with bacteriophages being the most dominant. Moreover, functional analysis identified the prominent metabolic pathways and the key gene families involved in the pathways, highlighting Prevotella copri as the major contributor. Additionally, the study identified the resistome and showed that there were more than 100 potential antibiotic-resistant genes (ARGs) and high levels of resistance to vancomycin in both groups.

CONCLUSION: This study presents a comprehensive overview of the gut microbiome in the Pangi population, detailing both in its taxonomic structure and functional traits. The results show that, despite the high degree of diversity in the gut microbiome, there seems to be evident functional redundancy, which underlines a core stable microbiome. The resistome profile offers complete exploratory picture of the resistome and establishes a valuable baseline for future studies. Furthermore, we anticipate that these findings will add valuable insights to understand the Antimicrobial resistance (AMR) stewardship in the light of one health aspect.}, } @article {pmid42298622, year = {2026}, author = {Wang, F and Sang, Y and Guo, J and Fu, Y and Yang, M and Shan, F and Chen, Y and Zhang, S and Li, X and Li, J and Zhang, L}, title = {Dietary glycyrrhizic acid improves growth performance and modulates upper respiratory microbiota in weaned piglets.}, journal = {BMC veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12917-026-05622-5}, pmid = {42298622}, issn = {1746-6148}, support = {231111111600//Henan Province Key Research and Development Plan Project/ ; 251111113300//Henan Province Key Research and Development Plan Project/ ; CARS-35//the National Pig Industry Technology System/ ; }, abstract = {BACKGROUND: Natural products with dual immunomodulatory and antimicrobial functions offer promising strategies to reduce antibiotic use in livestock. Glycyrrhizic acid (GA), the principal bioactive component of licorice, has demonstrated anti-inflammatory and antiviral properties, yet its translational potential in swine health remains underexplored. This study evaluated the efficacy of GA in weaned piglets under commercial nursery conditions as an antibiotic alternative. A total of 225 weaned piglets were assigned to five groups: negative control (CON, basal diet), farm routine (FA, conventional antibiotics), and three GA-supplemented groups (GLL, 0.65 g/kg; GLM, 1.3 g/kg; GLH, 2.6 g/kg).

RESULTS: The result showed that dietary GA supplementation (2.6 g/kg) numerically improved growth performance and reduced cough scores, although not statistically significant. GA significantly decreased the diarrhea index and improved skin scores. GA also significantly increased serum IgG and IgM levels in piglets and showed a trend toward higher IgA levels. Furthermore, GA exhibited a trend toward lowering serum IL‑1β levels while upregulating IFN‑γ and IL‑10 levels. Regarding antioxidant parameters, GA significantly upregulated T‑SOD, GSH‑PX, and CAT activities and downregulated LDH activity. Metagenomic analysis revealed that high‑dose glycyrrhizic acid (GA) significantly increased the abundance of Alloprevotella, while decreasing the abundances of Moraxella pluranimalium and 11 other pathogenic species associated with respiratory diseases and lung injury, including Glaesserella parasuis, Mesomycoplasma hyorhinis, Mesomycoplasma hyopneumoniae, Streptococcus suis, among others, thereby reshaping the upper respiratory tract microbiota of pigs.

CONCLUSIONS: Collectively, these findings support GA as a viable non-antibiotic strategy for improving immune function, antioxidant capacity, and respiratory health in weaned piglets.}, } @article {pmid42298631, year = {2026}, author = {Yan, Q and Li, M and Wang, G and Zhang, A and Li, Y and Guo, R and Zhang, Y and Yang, W and Zhang, Y and Liu, X and Li, X and Zheng, N and Wang, L and Fan, S and Ma, R and Lu, T and Zhou, S and Guan, T and Xing, G and Li, S and Wang, L and Li, Y}, title = {Cross-kingdom microbial associations characterize responsiveness to fecal microbiota transplantation in patients with irritable bowel syndrome.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08269-w}, pmid = {42298631}, issn = {1479-5876}, abstract = {BACKGROUND: Precise outcome prediction for fecal microbiota transplantation (FMT) in irritable bowel syndrome (IBS) remains a clinical challenge. The roles of the gut virome and its interplay with bacteria in FMT efficacy are particularly underexplored. This secondary analysis aimed to conduct an exploratory, hypothesis-generating investigation into these cross-kingdom dynamics.

METHODS: We conducted a secondary, integrative analysis of a published cohort, performing longitudinal, cross-kingdom metagenomic profiling on 83 samples from 22 IBS patients and healthy donors. We integrative approach combined microbial diversity, species-specific biomarker identification, bacterial-viral associated networks, and exploratory random forest modeling to identify microbial features associated with FMT outcomes.

RESULTS: IBS patients showed higher bacterial and viral alpha diversity than donors. Cross-kingdom profiling identified 223 bacterial and 724 viral biomarkers. Donor-enriched biomarkers were predominantly health-associated Bacteroidetes (e.g., B. ovatus, B. faecis), whereas pre-FMT-enriched biomarkers were largely Firmicutes (e.g., B. obeum) with potential pathobiont roles. The Effect and No effect groups displayed different microbial trajectories. Although both groups shifted toward a donor-like composition initially, only responders maintained a stable donor-like ecology throughout the 12-month follow-up, supported by more resilient bacterial-viral association networks. Exploratory random forest modeling highlighted microbial features, such as R. pickettii, with high relative importance for outcome discrimination. However, permutation testing (p = 0.548-0.616) confirmed that model performance on this small cohort did not exceed chance level, underscoring the risk of overfitting and the exploratory nature of these computational findings.

CONCLUSIONS: This integrative re-analysis provides preliminary evidence that cross-kingdom gut microbiome profiles are strongly associated with FMT outcomes in IBS. Successful outcomes appear linked to sustained donor-like remodeling and stable bacterial-viral networks. Our findings are primarily hypothesis-generating and offer a framework of candidate biomarkers for future validation in larger cohorts. This work underscores the necessity of external validation to develop robust, microbiome-based tools for personalized FMT therapy.}, } @article {pmid42298685, year = {2026}, author = {Yanagawa, Y and Yoshida, N and Makiuchi, T and Kawashima, A and Uemura, H and Aoki, T and Mizushima, D and Gatanaga, H and Watanabe, K}, title = {Multi-omics profiling and bile-acid exposure assays implicate a gut microbiome-parasite axis linked to persistent Entamoeba histolytica carriage.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00845-1}, pmid = {42298685}, issn = {1757-4749}, support = {IN-JP-380-5724//Gilead Sciences/ ; JP26K10011//Japan Society for the Promotion of Science/ ; JP23fk0108680h0001//Japan Agency for Medical Research and Development/ ; }, abstract = {Asymptomatic Entamoeba histolytica (Eh) carriage is a major transmission reservoir, yet how the gut ecosystem-particularly microbiota-derived metabolites such as secondary bile acids-supports persistent colonization remains unclear. We investigated whether gut microbiome-metabolite features are associated with Eh carriage and could influence parasite phenotypes METHODS: We integrated shotgun metagenomics from a prospectively screened outpatient cohort (n=36) with functional in vitro assays. An ordinal stepwise model across detection states (Eh-, Eh_qPCR, Eh_Cyst) was used to identify candidate microbial features, followed by bile-acid exposure assays and transcriptomic profiling to evaluate impacts on parasite fitness and metronidazole susceptibility in vitro RESULTS: Microbiome profiling suggested taxon-specific shifts rather than wholesale dysbiosis. Community-level beta diversity showed no significant separation, whereas genus richness was higher in Eh_Cyst (unadjusted p=0.046). Multivariable modeling yielded concordant directional but non-significant trends (all q>0.9), highlighting Firmicutes genera including Coprococcus, Ruminococcus, and Catenibacterium as candidate taxa. We then evaluated deoxycholic acid (DCA), a microbiota-modified secondary bile acid. In vitro, 100 μM DCA extended Eh survival under nutrient-limited conditions and reduced metronidazole susceptibility after pretreatment. Transcriptomic profiling showed that DCA induced a distinct response, including an 8.34-fold induction of the ABC transporter P-glycoprotein-2 and upregulation of lipid remodeling and stress-response genes, supporting a bile acid-driven adaptive program consistent with intestinal persistence CONCLUSIONS: Our findings suggest that secondary bile acids, exemplified by DCA, can reprogram Eh gene expression and attenuate metronidazole susceptibility in vitro. In the context of cyst-associated microbiome signatures, this supports the plausibility of a microbiome-bile acid-parasite axis that may promote persistence in asymptomatic carriers and could influence treatment efficacy.}, } @article {pmid42298736, year = {2026}, author = {Amat, S and Holman, DB and Luecke, SM and Gzyl, KE and Anas, M and Stokka, G}, title = {The bovine ocular microbiome: a multi-approach study of composition and antimicrobial activity.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00587-0}, pmid = {42298736}, issn = {2524-4671}, support = {20-21-2022; 22-14-0231; 24-30-0265//North Dakota State Board of Agricultural Research and Education/ ; }, abstract = {BACKGROUND: Despite widespread use of antimicrobials and vaccines, the incidence of infectious bovine keratoconjunctivitis (IBK), or pinkeye, continues to increase in North American beef cow-calf operations. Recent research suggests that there is potential for the commensal ocular microbiome to help mitigate IBK. Therefore, this study characterized the ocular microbiome of cattle with and without IBK using culture-based methods and shotgun metagenomic sequencing and assessed the ability of commensal bacteria to inhibit Moraxella spp. in vitro. Ocular swabs (n = 143) were collected from IBK-affected (n = 102) and healthy cattle (n = 41) before antimicrobial treatment from North Dakota herds. Bacteria were cultured aerobically and anaerobically on five different media and the isolates were identified. A subset of swabs (37 IBK-affected; 12 healthy) underwent shotgun metagenomic sequencing. The genomes of 31 isolates, including Moraxella bovoculi, Moraxella bovis, and commensal bacteria, were also sequenced. Fifty-two commensal isolates were screened for inhibition of Moraxella spp. using an agar slab method, with five isolates further tested by qPCR for inhibition in the presence of the culturable ocular microbiome.

RESULTS: The 351 bacterial isolates taxonomically identified represented 61 genera from three phyla. The majority of isolates belonged to Bacillus (25.9%), Streptococcus (11.1%), Staphylococcus (10.1%), and Moraxella (9.4%) genera. Shotgun metagenomic analysis revealed significant differences in ocular microbial species composition between IBK-affected and healthy cattle (R² = 0.05; P = 0.015) based on Bray-Curtis dissimilarity. Dominant bacterial species included Cutibacterium acnes, Mannheimia pernigra, Mesomycoplasma bovoculi, Moraxella bovis, and Moraxella bovoculi. Eight bacterial species, including Bifidobacterium globosum and Bacillus licheniformis, were more abundant in healthy cattle, while Arthrobacter luteus was enriched in IBK cases. Thirty-seven high-quality metagenome-assembled genomes were also recovered, with 27% classified as Mesomycoplasma bovoculi. Moraxella spp. genomes exhibited strain-specific antimicrobial resistance and virulence gene diversity. Seventeen commensal isolates inhibited Moraxella, with Weizmannia coagulans, Lentilactobacillus buchneri, and Paenibacillus polymyxa showing strong activity. Selected isolates maintained inhibitory effects in co-culture with the ocular microbiome.

CONCLUSION: The ocular surface of beef cattle is inhabited by a diverse microbiome that includes several bacterial strains that have the potential to be used as therapeutics to inhibit IBK pathogens.}, } @article {pmid42298774, year = {2026}, author = {Chen, X and Ding, S and Tang, H and Yang, Q and Yuan, L and Zhang, A and Li, Y and Wang, Q and Yan, X and Wang, Z and Wang, M and Zheng, Z}, title = {Monochromatic light reprograms transcription, metabolism, and rhizosphere microbial communities in Salvia miltiorrhiza.}, journal = {Plant signaling & behavior}, volume = {21}, number = {1}, pages = {2686334}, pmid = {42298774}, issn = {1559-2324}, mesh = {*Salvia miltiorrhiza/metabolism/radiation effects/microbiology/genetics ; *Rhizosphere ; *Light ; *Microbiota/radiation effects ; Gene Expression Regulation, Plant/radiation effects ; *Transcription, Genetic/radiation effects ; }, abstract = {Salvia miltiorrhiza is a valuable medicinal plant with diverse pharmacological applications and high market demand. Light quality is a critical environmental factor regulating plant growth, secondary metabolism, and interactions with rhizosphere microorganisms. However, the effects of short-term, pure monochromatic light exposure on S. miltiorrhiza remain largely unexplored. In this study, we employed integrated transcriptomic, metabolomic, and rhizosphere metagenomic analyzes to investigate the responses of S. miltiorrhiza under different monochromatic light conditions: ultraviolet (UV), blue (B), red (R), and far-red (FR), with white light (WL) as the control. GO enrichment analysis indicated that all monochromatic light treatments activated defense responses, while specific pathways related to light stimulus, wounding, and reactive oxygen species were uniquely enriched under B, R, and FR light. Metabolomic analysis showed a general decrease in metabolite abundance under monochromatic light compared to WL, with the R treatment inducing the highest number of significantly upregulated metabolites. Integrated KEGG pathway analysis of differential transcripts and metabolites highlighted the enrichment of secondary metabolic pathways, including diterpenoid, monoterpenoid, and phenylpropanoid biosynthesis. Notably, quantitative HPLC analysis confirmed that UV, R, and FR light significantly promoted the accumulation of dihydrotanshinone I and tanshinone IIA, while decreasing salvianolic acid A content. Metagenomic analysis revealed that monochromatic light, especially B light, reduced rhizosphere microbial alpha diversity and altered the abundance of specific bacterial families and species. Functional gene annotation also showed treatment-specific shifts in microbial metabolic potential and virulence factors. In conclusion, short-term monochromatic light culture, particularly R and FR, effectively modulates the transcriptome and metabolome of S. miltiorrhiza, enhancing the accumulation of key bioactive tanshinones, while simultaneously reshaping its rhizosphere microbial community. These findings offer a potential light-based strategy for improving the quality of S. miltiorrhiza.}, } @article {pmid42299582, year = {2026}, author = {Yu, Y and Wang, C and Pan, X and Ding, C and Chen, J}, title = {Metagenomic profiling of biliary microbiota reveals distinct microbial and functional features in cholelithiasis and cholecystic polyps.}, journal = {Medicine}, volume = {105}, number = {24}, pages = {e49251}, pmid = {42299582}, issn = {1536-5964}, support = {2022YFC2804205//National key research and development program of China/ ; }, mesh = {Humans ; *Cholelithiasis/microbiology ; *Metagenomics/methods ; *Polyps/microbiology ; *Microbiota/genetics ; Female ; *Bile/microbiology ; Male ; *Metagenome ; Middle Aged ; Aged ; }, abstract = {Cholelithiasis and cholecystic polyps are common gastrointestinal conditions, and recent studies suggest that biliary microbiota dysbiosis may be closely associated with their pathogenesis. In this small cohort (n = 11), bile samples were aseptically collected during surgery from 6 patients with cholelithiasis and 5 patients with cholecystic polyps. Metagenomic sequencing was performed to investigate differences in the microbial composition and functional profiles between the 2 groups. The results revealed that the microbial α diversity of bile from patients with cholelithiasis was significantly greater than that of the polyp group, with significant differences in the Richness, Chao1, ACE, and Shannon indices (P < .05). β-diversity analysis further revealed distinct differences in microbial community composition across the groups. Linear discriminant analysis effect size analysis revealed Pseudomonadota as the only phylum enriched in the polyp group, whereas the cholelithiasis group was enriched with multiple phyla, such as Campylobacterota, Bacillota, and Fusobacteriota, and 35 genera, such as Bacteroides, Mucilaginibacter, and Pedobacter. Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis indicated that the microbial community in the cholelithiasis group was significantly associated with neurodegenerative disease-related pathways, while the microbial community in the polyp group was enriched in pathways related to ribosomes and fluid shear stress. This study highlights the potential role of biliary microecological imbalances in the development of biliary diseases and provides a theoretical basis for exploring pathogenesis and microbiota-based therapeutic strategies.}, } @article {pmid42299645, year = {2026}, author = {Paulsen, J and Sharrett, ST and Mumey, D and Larsen, EM and Nguyen, NK and Lendemer, J and Calabria, LM and Hoffman, JR and Magori, K and Allen, JL}, title = {Helitrons are enriched in lichenized fungi with long generation lengths and small distribution sizes.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkag153}, pmid = {42299645}, issn = {2160-1836}, abstract = {Transposable elements (TEs) have the potential to drive genome evolution by introducing mutations and causing structural instability and chromosomal rearrangements, particularly under conditions like environmental or genetic stress. In this study, we generated 18 new long-read based metagenomically assembled reference genomes for lichenized fungi, which form obligate mutualistic symbioses with algae or cyanobacteria. We used the new genomes and 10 publicly available genomes to investigate the relationships between species traits (i.e., dominant reproductive mode, distribution size, and generation length) and the abundance and spatial distribution of TEs using a phylogenetic comparative framework. We found that species with smaller distribution sizes and longer generation lengths had a higher genomic DNA transposon load. Specifically, their genomes were enriched with Rolling Circle transposons, which contradicts previous research that has identified high proportions of retrotransposons in rare species. Disproportionate distributions of TEs in rare and range-restricted species may disrupt genomic stability, decrease fitness, and be reflective of species experiencing a greater degree of stress. Conversely, greater TE activity may be an important source of novel genetic diversity in isolated populations with limited gene flow. Further research is needed to understand the potential mechanisms driving TE proliferation in rare species' genomes, and if TE content is predictive of increased extinction risk.}, } @article {pmid42299860, year = {2026}, author = {Barandouzi, ZA and Eng, T and Khanna, N and Shelton, J and Scott, I and Patel, P and Remick, J and Jin, R and Meador, R and Bruner, DW}, title = {Gut Microbiome Associations With Depressive Symptoms in Women With Gynecologic Cancer: A Longitudinal Study.}, journal = {Biological research for nursing}, volume = {}, number = {}, pages = {10998004261461549}, doi = {10.1177/10998004261461549}, pmid = {42299860}, issn = {1552-4175}, abstract = {About one-quarter of women diagnosed with gynecologic cancer experience depressive symptoms. While the precise mechanism remains unclear, little is known about the association between gut microbiota and depressive symptoms in gynecologic cancer. Thus, this study aimed to evaluate the associations between gut microbiota and depressive symptoms in women with gynecologic cancer over cancer treatment. Thirty-seven women with cervical or endometrial cancer were followed at pre-treatment (T0), 6-8 weeks (T1), and 6 months post-radiation (T2). Depressive symptoms were assessed using the Patient Health Questionnaire-9 (PHQ-9). Rectal swabs were collected at each visit and sequenced for the V4 region of the 16S rRNA gene. MaAsLin2 models evaluated cross-sectional associations between gut microbial taxa and depressive symptoms at each time point, whereas GEE models assessed longitudinal associations over the course of cancer treatment. The patients had an average age of 60 years, and 43% were Black. At baseline (T0), 24% of patients exhibited depressive symptoms, which decreased to 21% at T1 and further to 13% at T2. GEE models showed that lower α-diversity (Shannon index, p = 0.05), dissimilar β-diversity (Bray-Curtis distance, p = 0.02), and reduced abundance of the genus Ruminococcus (p = 0.02) were predictive factors associated with depressive symptoms throughout cancer treatment. Higher depressive symptoms were longitudinally associated with lower gut microbial Shannon diversity, dissimilar microbial community composition, and lower abundance of the genus Ruminococcus. Larger longitudinal studies using shotgun metagenomic sequencing are needed to validate these findings and further elucidate the microbial mechanisms underlying depressive symptoms in women with gynecologic cancers.}, } @article {pmid42300105, year = {2026}, author = {Wilson, SMG and Oliver, A and Alkan, Z and Patil, BS and Kable, ME and Lemay, DG}, title = {Association between dietary polyphenol intake and polyphenol-utilizing bacteria in healthy adults.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo00158k}, pmid = {42300105}, issn = {2042-650X}, abstract = {Dietary polyphenols are bioactive compounds with a bidirectional impact on the gut microbiome; they shape the microbial community and are transformed through bacterial metabolism. However, there are limited studies pairing metagenomic and dietary data to investigate the relationship between polyphenol intake and the taxonomic and functional profiles of the human gut microbiome. We examined if dietary polyphenol intake associates with microbial composition and polyphenol utilization capacity. Healthy adults participated in a cross-sectional study balanced for age, sex, and BMI. Polyphenol intake was previously estimated by mapping multiple 24 h dietary recalls to the Food Database (FooDB). We coupled intake with microbial taxonomic and functional profiles from shotgun-sequenced fecal metagenomes (n = 313). Microbial reads were mapped to dbPUP, a database with 60 experimentally characterized, gut-associated polyphenol utilization proteins (PUPs). We assessed the relationship of polyphenol intake on microbial diversity, abundance of microbes with PUP genes, PUP gene counts, and select lipopolysaccharide (LPS) producers, accounting for age, sex, BMI, fiber intake, and diet quality. Specific polyphenols associated with an increased abundance of nine PUP-containing genera. We found 117 associations between polyphenol intake and microbial PUP genes, with 85 associations involving hydrolysis PUPs. Diversity in polyphenol intake was positively associated with diversity in PUP genes but not with microbial diversity. Lastly, we detected a positive relationship between intake of olive-related polyphenol classes and abundance of order Bacteroidales, a producer of immunoinhibitory LPS. Dietary polyphenol intake may influence the gut microbiome's capacity for polyphenol utilization, particularly its hydrolytic activity, without impacting taxonomic diversity or composition.}, } @article {pmid42300247, year = {2026}, author = {Götze, S and Beemelmanns, C}, title = {Advances in the discovery and functional analysis of Anti-infective and immunomodulatory natural products from host-associated microbiomes.}, journal = {Natural product reports}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6np00003g}, pmid = {42300247}, issn = {1460-4752}, abstract = {Covering: 2018 to 2025Over recent years, metagenomic-driven studies have revealed an enormous encoded repertoire for the biosynthesis of secondary metabolite scaffolds within host-associated microbiota, yet only a small fraction of these chemical scaffolds has been characterized. This review focuses on recent discoveries of natural products with anti-infective and immunomodulatory properties derived from diverse host-associated microbiomes, covering the period from 2018 to 2025. The selected examples span a wide range of anti-infective and immunomodulatory activities, underscoring the deep integration of microbial secondary metabolism with host physiology, while also highlighting the need for more targeted and efficient combined approaches to fully exploit the predicted biosynthetic capacity of microbiomes for anti-infective research and beyond.}, } @article {pmid42300737, year = {2026}, author = {Bueno de Mesquita, CP and Stallard-Olivera, E and Fierer, N}, title = {Predicting oxygen levels in microbial habitats using a metagenome-based approach.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0054526}, doi = {10.1128/msystems.00545-26}, pmid = {42300737}, issn = {2379-5077}, abstract = {Oxygen is a primary driver of the distribution and activity of microbial life. Since oxygen levels are often difficult to measure in situ, one potential solution is to use bacteria as bioindicators of oxygen levels. As bacteria range from obligate aerobes to obligate anaerobes, quantification of bacterial community oxygen preferences could be used to infer variation in oxygen levels and bacterial metabolic strategies. After using ensemble machine learning to select the 20 most important genes that predict oxygen tolerances in individual bacteria, we established a relationship between the abundance ratio of aerobic:anaerobic indicator genes and the proportional abundance of aerobic bacteria using simulated metagenomes with varying ratios of known aerobes and anaerobes. We developed a tool, OxyMetaG, that takes metagenomic reads as input, extracts bacterial reads, maps reads to the 20 genes, and predicts oxygen availability in any sample on a scale from 0% to 100% (completely anoxic to completely oxic). We tested OxyMetaG on a suite of metagenomes with measured or inferred oxygen levels across a variety of environmental and host-associated samples. To demonstrate its utility, we applied OxyMetaG to 540 surface soils, showing that surface soils are predominantly oxic, but wetter sites with finer textures have relatively less oxygen. Finally, we applied OxyMetaG to 73 human gut samples, showing that in the first 3 years of life, human guts progress from oxygen levels as high as 61% down to 0%. We expect OxyMetaG to have broad utility for characterizing oxygen levels in both modern and ancient microbial habitats.IMPORTANCEOxygen is one of the most important environmental variables affecting microbial activity and composition, but is often difficult to measure in situ. We developed a tool, OxyMetaG, that leverages differences in bacterial gene content across known aerobic and anaerobic taxa to predict the oxygen level of a given sample directly from shotgun metagenomic reads. OxyMetaG works on samples with low sequencing depth and avoids computationally expensive genome assembly, which often captures only a fraction of the microbial community in a given environment. With OxyMetaG, bacteria can be used as bioindicators of oxygen availability over broader time scales than just a single measurement and provide crucial environmental context in cases where oxygen has not been or cannot be measured. OxyMetaG is publicly available and can be used to answer a wide variety of ecological questions in both environmental and host-associated systems.}, } @article {pmid42300757, year = {2026}, author = {Li, B and Li, S and Pei, Y and Sun, X and Ding, C and Yu, J and Zhou, M and Han, J and Yang, H and Wan, Y}, title = {Tibetan kefir grain-fermented milk attenuates DSS-induced colitis through coordinated regulation of intestinal barrier function, inflammation, and gut microbiota.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo01565d}, pmid = {42300757}, issn = {2042-650X}, abstract = {This study evaluated the prophylactic efficacy of Tibetan kefir grain-fermented milk (Kefir-milk) in a dextran sulfate sodium (DSS)-induced colitis model and examined host- and fermentation-related changes associated with the intervention. Kefir-milk pretreatment attenuated disease activity, reduced colon shortening, and alleviated histopathological injury. These changes were accompanied by improved intestinal barrier-related readouts, including higher expression of ZO-1, Occludin, and MUC2, together with lower colonic MPO, TNF-α, IL-1β, and IL-6 levels. 16S rRNA profiling showed improved α-diversity, partial restoration of overall community structure, enrichment of Muribaculaceae and other genera commonly linked to intestinal homeostasis, and suppression of Escherichia-Shigella. Shotgun metagenomics indicated that the final Kefir-milk matrix was dominated by Lactobacillus-related taxa, while untargeted UPLC-HRMS/MS metabolomics revealed broad fermentation-associated remodeling of the milk metabolome, including altered relative abundances of features annotated as hippuric acid, p-cresyl sulfate, leucic acid, and phenyllactic acid. In LPS-challenged RAW264.7 macrophages, sterile filtered water-soluble extracts from Kefir-milk modulated polarization-associated marker expression and reduced pro-inflammatory cytokine responses at both transcript and protein levels. Collectively, these findings indicate that Kefir-milk attenuated DSS-induced colitis under the present experimental conditions and was associated with concurrent changes in barrier-related markers, gut microbiota, and the milk metabolome.}, } @article {pmid42300775, year = {2026}, author = {Hawkes, CG and Carroll, BO and Moylan, AD and Stiker, MEJ and Wang, T and Serrano, MG and Ridlon, JM and Miller, DP}, title = {Genomic and phenotypic insights into the novel species Selenomonas lamontii type strain ATCC 33150, currently described as Selenomonas sputigena.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0034126}, doi = {10.1128/spectrum.00341-26}, pmid = {42300775}, issn = {2165-0497}, abstract = {Selenomonas sputigena is an anaerobic, gram-negative bacterium found in the human mouth and upper respiratory tract. This organism is emerging as an important contributor to human health and disease. In the oral cavity, S. sputigena contributes to periodontitis and is associated with early childhood caries. Much of our current understanding of the genus Selenomonas and its relation to human health derives from studies of a single species, S. sputigena, and is further limited to the type strain, ATCC 35185. As S. sputigena is emerging as a significant contributor to human health, we sought to characterize the S. sputigena ATCC 33150 strain. Genomic analyses revealed that ATCC 33150, previously described as S. sputigena, is a novel Selenomonas sp., and we propose the name Selenomonas lamontii. Phenotypic comparison to S. sputigena reveals that S. lamontii grows more slowly and to a lower density in vitro. S. lamontii is more motile than S. sputigena and does not form surface-attached biofilms. Re-analysis of existing metagenomic data revealed the consistent presence of ATCC 33150 across all samples, with significantly elevated relative abundance in periodontitis-associated saliva compared to healthy donor controls. Collectively, we have identified ATCC 33150 as a new Selenomonas sp. and conducted one of the first direct comparative studies of traits relevant to colonization and persistence among Selenomonas spp.IMPORTANCERecognizing that strain ATCC 33150, historically described as Selenomonas sputigena, is a previously undescribed species has important implications for microbial systematics, physiology, and pathogenesis. Accurate taxonomic assignment underpins all downstream biological interpretation (e.g., comparative genomics, microbiome composition studies, virulence studies, and metabolic modeling). The identification of a novel species, therefore, refines the phylogenetic framework of the genus Selenomonas, enables more precise genotype-phenotype correlations, and may uncover previously unrecognized adaptations relevant to oral biofilm ecology and host interactions. Beyond taxonomy, this discovery strengthens the foundation and rigor of future mechanistic studies and provides context for discrepancies in previous studies involving this strain and ATCC 35185.}, } @article {pmid42300931, year = {2026}, author = {Medouni-Haroune, L and Medouni-Adrar, S and Messaoudene, L and Negrichi, S and Bouiche, C and Sahraoui-Remini, Y and Allam, A and Meghlaoui, Z and Mouhoubi, K and Abbou, A and Brahimi, N and Mellal, MK and Sari, Z and Madani, K}, title = {Animal-based diets and the human gut microbiota: an integrative review combining metagenomic profiling and graphical synthesis of diet-microbiota associations.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo00371k}, pmid = {42300931}, issn = {2042-650X}, abstract = {This review examines the relationships between animal-based diets, gut microbiota architecture, and human health by integrating insights from metagenomic studies and literature-based graphical representations. The gut microbiota is a complex microbial ecosystem, whose organization is closely linked to intestinal homeostasis and host health. Drawing on published metagenomic datasets, the review synthesizes patterns of dominant microbial groups and their organization within the gut, providing a framework for interpreting diet-related microbial variations across different geographic and cultural contexts. Evidence from the literature on animal-derived foods is integrated through graphical visualization to illustrate associations between specific foods and gut microbial taxa. These visualizations highlight distinct association patterns and microbial responses to various animal-based dietary components. The review discusses these patterns in relation to intestinal health, disease susceptibility, and potential dietary interventions. Overall, this work provides a structured, integrative perspective on the impact of animal-based diets on gut microbiota architecture, emphasizing the relevance of combining metagenomic insights with literature-based synthesis to inform nutritional science and public health strategies.}, } @article {pmid42301021, year = {2026}, author = {Echeverry-Pérez, JS and Castelli, M and Muñoz-Leal, S and Nava, S and Sassera, D and Sánchez-Vialas, A and Olmeda, AS and Valcárcel, F and Uribe, JE}, title = {Genomic evolution of Francisella: metabolic innovation, endosymbiotic transitions to ticks, and biogeographic history.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evag135}, pmid = {42301021}, issn = {1759-6653}, abstract = {Ticks (Ixodida) are the second most important vectors of infectious diseases in vertebrates, after mosquitoes. Beyond vector roles, they maintain mutualistic associations with bacteria, including endosymbionts that provide essential B vitamins lacking in their blood-based diet. The most extensively studied endosymbionts belong to the genera Coxiella, Midichloria, and Francisella. The genus Francisella encompasses endosymbionts (FE), pathogens (FP), opportunistic pathogens (FO) and free-living environmental strains (FL), making it a powerful system for evolutionary and comparative genomic analyses. In this study, total DNA from six adult female ticks of the genera Hyalomma and Amblyomma was sequenced to generate new FE genomes. Seven deeply sequenced public metagenomes were also assembled, yielding 71 Francisella and three Allofrancisella strains. This dataset supported phylogenomic reconstruction and comparison of genomic features, including vitamin biosynthesis and virulence pathways, with a focus on transitions to tick endosymbiosis. A densely sampled MLST phylogeny was constructed to explore biogeographic patterns. Our results show that, except for FE, no ecological trait is monophyletic, supporting an origin of Francisella diversity from free-living ancestors. Biogeography suggests Palearctic and Afrotropical FE strains are derived and may involve horizontal transfers. Francisella comparative genomics reveals two contrasting profiles: environmental generalists and host-restricted specialists. These findings reinforce the role of tick FEs as nutritional mutualists, retaining key pathways such as riboflavin, shikimate, and biotin biosynthesis. In contrast, virulence is not ancestrally conserved but an innovation in pathogenic lineages, largely degraded in tick FEs. These results advance understanding of endosymbiont evolution and provide genomic insights with potential for disease control.}, } @article {pmid42301089, year = {2026}, author = {Wang, H and Liang, Y and Wang, Z and Zhang, Y and Tu, W and Zhou, J and Diao, Y and Pei, H and Huang, J and Zhou, X and Tan, Y}, title = {Dietary High Fiber and N-Carbamylglutamate Enhance Sow Reproductive Performance via Modulating Lactobacilli, Lipid Metabolites, and the PI3K-Akt Signaling Pathway.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {12}, pages = {e72059}, doi = {10.1096/fj.202601343R}, pmid = {42301089}, issn = {1530-6860}, support = {2025M780240//China Postdoctoral Science Foundation/ ; 2023ZD04046//Biological Breeding-National Science and Technology Major Project/ ; 2025(05)//Livestock and Poultry Breeding and Healthy Farming Technology/ ; }, mesh = {Animals ; *Glutamates/pharmacology/administration & dosage ; Female ; *Lactobacillus/drug effects/metabolism ; Signal Transduction/drug effects ; Swine ; *Proto-Oncogene Proteins c-akt/metabolism ; *Reproduction/drug effects ; *Dietary Fiber/pharmacology/administration & dosage ; *Phosphatidylinositol 3-Kinases/metabolism ; *Lipid Metabolism/drug effects ; Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; }, abstract = {The aim of this study was to investigate the combined effects of a high-fiber diet supplemented with N-carbamylglutamate (NCG) (H + N) on the gut microbiota, metabolites, and transcriptome in Landrace × Yorkshire sows using a multi-omics approach. Sows were allocated to four groups in a 2 × 2 design: Low-fiber or high-fiber diets, each with or without 0.05% NCG supplementation. The H + N treatment significantly increased litter weight at weaning. Metagenomic analysis revealed H + N significantly altered gut microbiota composition and function, particularly enriching Lactobacillus at multiple taxonomic levels from order to species (including Lactobacillus sp. 910 589 175). Plasma metabolomics identified two key lipid mediators, L-α-glycerylphosphorylcholine and taurocholic acid, whose abundances were significantly elevated by H + N and positively correlated with the enriched Lactobacillus. Transcriptomic profiling showed activation of the PI3K-Akt signaling pathway in response to H + N, which was associated with observed improvement in litter weight at weaning. Collectively, the multi-omics study uncovered a novel synergistic axis wherein H + N modulated the gut microbiome (specifically Lactobacillus enrichment), which in turn shaped the lipid metabolome to activate the PI3K-Akt pathway, ultimately enhancing sow reproductive efficiency.}, } @article {pmid42301310, year = {2026}, author = {Cosoveanu, A and González-Carracedo, MA and Sopena Lasala, J and Pérez Pérez, JA and Cabrera, R}, title = {Shaping Fungal Communities in Cenchrus setaceus: Host Condition and Habitat Filtering.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02805-3}, pmid = {42301310}, issn = {1432-184X}, abstract = {We investigated the leaf-associated fungal communities of Cenchrus setaceus across a host condition gradient (high- vs. low-condition plants) and environmental zones (coast vs. hill; trade-wind exposure) on Tenerife (TF) and La Palma (LP). We hypothesized that community assembly reflects both host-driven deterministic filtering and abiotic promotion of richness in favourable environments via two mechanisms: (i) high-condition plants promote stable, guild-structured communities; (ii) humid, topographically buffered zones enhance fungal richness, especially for endophytes and saprotrophs. Nanopore sequencing and functional guild annotation revealed island- and zone-specific fungal assemblages. In TF, low-condition plants were associated with genera linked to stressed or exposed conditions whereas high-condition plants, especially in humid northern hills, supported more recurrent yeast-like and niche-associated taxa. In LP, high-condition plants in eastern hill zones were associated with distinct taxa, while drier western coastal low-condition plants were enriched in stress-related fungi. Fungal genera richness (Hill0) was consistently higher in low-condition plants (TF: 146 vs. 95; LP: 94 vs. 76; p < 0.05), while Shannon diversity diverged: greater in high-condition plants on LP (3.29 vs. 2.98), but lower on TF (3.10 vs. 3.28; p < 0.05). Community structure was shaped primarily by host condition in TF (PERMANOVA R[2] = 8.6%, p < 0.05), and by zone in LP (R[2] = 15.0%, p < 0.05). On TF, low-condition plants hosted significantly higher richness of saprotrophic, endophytic and plant-pathogenic genera (all p ≤ 0.001), whereas in LP zone × condition effects shaped guild richness patterns, with saprotroph richness increasing 2.66-fold in high condition plants from eastern hills relative to the eastern coast. Overall, high-condition plants supported less diverse but compositionally more stable fungal communities, while favourable environments enhanced guild richness independently of host condition.}, } @article {pmid42301501, year = {2026}, author = {Öz, M and Üstüner, E}, title = {Omics technologies in aquafeed: unlocking the black box towards systems biology.}, journal = {Functional & integrative genomics}, volume = {26}, number = {1}, pages = {}, pmid = {42301501}, issn = {1438-7948}, mesh = {Animals ; *Systems Biology/methods ; *Aquaculture/methods ; Multiomics ; Metabolomics ; *Fishes/genetics/metabolism/growth & development ; Animal Feed ; Proteomics/methods ; Nutrigenomics ; }, abstract = {The aquaculture industry is undergoing a critical transition from marine-based to plant-based and novel protein sources. However, the physiological impacts of these dietary shifts remain largely obscured when evaluated solely by traditional performance metrics such as Feed Conversion Ratio (FCR) and Specific Growth Rate (SGR). This 'Black Box' approach fails to detect sub-clinical metabolic disorders, gut dysbiosis, and molecular stress responses until phenotypic losses occur. This review provides a comprehensive synthesis of how omics technologies - nutrigenomics, proteomics, metabolomics, and metagenomics - are elucidating the molecular mechanisms underlying fish nutrition. We examine the capacity of transcriptomics to identify early markers of soybean meal-induced enteritis and the role of proteomics in assessing muscle quality beyond mere gene expression. Furthermore, we highlight the integration of these layers into a 'Systems Biology' approach, utilizing multi-omics and bioinformatics to unravel the complex diet-microbiota-host axis. Finally, the review discusses the transition towards 'Precision Aquafeed.' It identifies the current challenges in cost, data standardization, and bioinformatics that must be overcome to implement these high-throughput tools in commercial feed formulation.}, } @article {pmid42301503, year = {2026}, author = {Bao, W and Li, X and Pan, H and Gao, Y and Zhao, L and Liu, J and Wang, S and Zhang, Y}, title = {Detoxification mechanisms of black soldier fly larvae against microcystin-LR.}, journal = {Functional & integrative genomics}, volume = {26}, number = {1}, pages = {}, pmid = {42301503}, issn = {1438-7948}, mesh = {Animals ; *Microcystins/toxicity/metabolism ; Marine Toxins ; Larva/microbiology/metabolism/growth & development/drug effects/genetics ; *Gastrointestinal Microbiome/drug effects ; Oxidative Stress ; Inactivation, Metabolic ; *Simuliidae/microbiology/metabolism/genetics/growth & development/drug effects ; }, abstract = {This study aimed to elucidate the detoxification mechanisms of black soldier fly larvae (BSFL) against microcystin-LR (MC-LR). Using concentration-gradient exposure (0 - 400 µg/L) and integrated metagenomic and transcriptomic analyses, we investigated the growth responses, gut microbiota alterations, and synergistic detoxification mechanisms of BSFL. The results revealed that the growth performance of BSFL was not significantly affected even at high MC-LR concentrations (400 µg/L). However, significant alterations occurred in the gut microbial composition, with increased relative abundances of Actinobacteria and Firmicutes, along with increased species richness and diversity, which correlated with increasing exposure concentrations. Functional analysis revealed that functions related to carbohydrate metabolism, energy metabolism, and substrate transport were significantly enriched in the exposed groups. Transcriptomic data further indicated that MC-LR induced intestinal oxidative stress, with significant upregulation of antioxidant-related genes (superoxide dismutase, isocitrate dehydrogenase, and peroxiredoxin 6) as well as key xenobiotic metabolism genes (carboxylesterase, glutathione S-transferase, and UDP-glucuronosyltransferase). Additionally, heat shock proteins and the Toll signaling pathway were activated. We speculate that BSFL maintains gut microbial homeostasis against MC-LR toxicity through the coordinated regulation of gut microbial communities, host antioxidant systems, xenobiotic metabolism pathways, and immune responses, providing a theoretical foundation for safe resource utilization of cyanobacteria.}, } @article {pmid42301563, year = {2026}, author = {Xiao, Q and Chen, B and Xu, Z and Cui, Z}, title = {Endophthalmitis caused by Shinella species: the first case report.}, journal = {Journal of ophthalmic inflammation and infection}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12348-026-00610-0}, pmid = {42301563}, issn = {1869-5760}, abstract = {BACKGROUND: Endophthalmitis is a severe intraocular infection associated with potentially devastating visual outcomes. Shinella, a Gram-negative bacillus commonly found in water and soil, has never been reported as a cause of human disease.

CASE PRESENTATION: A 49-year-old female farmer presented with a 7-day history of vision loss, ocular irritation, and ophthalmalgia in her right eye. She had been previously misdiagnosed and treated with high-dose systemic corticosteroids at another institution. She underwent emergent pars plana vitrectomy. Vitreous samples were analyzed using conventional culture and metagenomic next-generation sequencing (mNGS), which identified Shinella species as the predominant pathogen. Intravitreal amikacin and systemic ceftazidime were initiated on postoperative day 3 after culture confirmed Gram-negative bacilli. Two weeks of targeted antibiotic therapy resulted in complete resolution of intraocular inflammation and near-full visual recovery.

CONCLUSION: To our knowledge, this is the first reported case of intraocular infection caused by Shinella species. This case highlights Shinella as a potential ocular pathogen and demonstrates the utility of pars plana vitrectomy combined with mNGS for diagnosing atypical intraocular infections.}, } @article {pmid42302013, year = {2026}, author = {Nayak, AR and Shukla, J and Kulkarni, S and Biswas, R and Kurkure, N and Kaore, M and Chaudhari, S and Bajpai, U and Kannan, K and Sivanesan, S and Sontakke, SD and Husain, A and Kulurkar, PM and Bafna, A and Kashyap, RS}, title = {Study protocol on antimicrobial resistance burden, transmission dynamics, and therapeutic bacteriophages in livestock and exposed farming populations in Nagpur, India: An integrated One Health approach.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0350919}, pmid = {42302013}, issn = {1932-6203}, mesh = {Animals ; India/epidemiology ; Humans ; *Bacteriophages/isolation & purification/physiology ; *One Health ; *Livestock/microbiology/virology ; Anti-Bacterial Agents/pharmacology ; Longitudinal Studies ; Prospective Studies ; Drug Resistance, Multiple, Bacterial ; *Drug Resistance, Bacterial ; }, abstract = {The rise in antimicrobial resistance (AMR) is a severe public health threat worldwide. India bears a disproportionately heavy burden of this problem due to ample antimicrobial usage in both humans and animals and scarce integrated surveillance. Since humans, animals, and environmental reservoirs which can harbour resistant microorganisms interact very closely on farms livestock, these are considered critical hotspots for the emergence and dissemination of antimicrobial-resistant bacteria and resistance genes. This work presents a 36-month prospective longitudinal observational study protocol aimed at quantifying the burden and characterizing the transmission dynamics of a selected set of key bacteria, that are clinically significant and hence, pathogenic-Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa-alongside their AMRprofiles in livestock, farm-exposed human populations, and environmental reservoirs in Nagpur, India, within the framework of One Health. Seasonal sampling of milk, animal faeces, human stool, soil, wastewater, drinking water, and animal feed will be carried out on dairy farms located in urban, peri-urban, and rural areas. Pathogens will be isolated using standard microbiological techniques and characterized based on antimicrobial susceptibility by employing VITEK®2 and disc diffusion methods. At the same time, bacteriophages against multidrug-resistant isolates will be isolated, purified, and characterized through plaque assays, host-range analysis, electron microscopy, and whole-genome sequencing for their therapeutic potential evaluation. Additionally, metagenomic next-generation sequencing will be utilized on a select number of samples to comprehensively characterize the resistomes and diversity of phages. The research will provide detailed longitudinal data on the frequency and spread of AMR among human, animal, and environmental compartments, create a biobank of AMR isolates and lytic bacteriophages, and offer genomic clues to delineate phage-based treatments and well-informed mitigation strategies of AMR within the framework of One Health in India. The results will be made public through peer-reviewed articles, presentations at scientific meetings, and deposition of sequence data in open-access databases.}, } @article {pmid42302279, year = {2026}, author = {Ascandari, A and Aminu, S and Benhida, R and Rachid, D}, title = {From association to causation: a decision-aware framework for reproducible biomarker discovery and precision intervention design in the human gut microbiome.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {3}, pages = {}, pmid = {42302279}, issn = {1477-4054}, support = {//University Mohammed VI Polytechnic (UM6P), Morocco/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Biomarkers ; *Colorectal Neoplasms/microbiology/genetics ; Machine Learning ; *Precision Medicine ; Causality ; Mendelian Randomization Analysis ; Metagenomics ; }, abstract = {Human gut microbiome research has generated many disease associations, yet few translate into clinical applications. A central obstacle is not a lack of data, but the limited integration of causal reasoning, as most studies report correlations without establishing directionality, confounding control, or mechanistic evidence. We propose a unified causal inference framework that integrates directed acyclic graphs, Mendelian randomization, double machine learning, mediation analysis, and tests of causal reversibility into a single decision-aware workflow. Unlike prior applications of these tools in isolation, our framework explicitly separates assumption mapping, causal identification, effect estimation, and mechanistic interpretation, introducing "assumption guardrails" that constrain interpretation at each stage and prevent overinterpretation of observational findings. Using a colorectal cancer case study with public metagenomic data, we demonstrate how the framework operates under real-world constraints, transforming observational associations into testable, mechanism-based hypotheses. The contribution is architectural in that it organizes existing tools into a disciplined, integrated pipeline that clarifies the strength of evidence at each stage. This operational blueprint provides a reproducible path from correlation to causation in microbiome research and toward precision interventions.}, } @article {pmid42302398, year = {2026}, author = {Xie, S and Ding, L and Liu, L and Ong, YS and Li, J and Zhu, Z}, title = {NanoSimFormer: an end-to-end Transformer-based nanopore signal simulator with basecaller guidance.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag402}, pmid = {42302398}, issn = {1367-4811}, abstract = {MOTIVATION: High-fidelity simulation of nanopore sequencing signals is critical for rigorous benchmarking and validation of the nanopore signal processing pipeline. However, existing signal simulators often fail to capture the non-linear dynamics of nanopore current signals, relying on static pore models or lacking optimization objectives tied to basecalling, resulting in synthetic signals with low basecalling accuracy and fidelity.

RESULTS: We introduce NanoSimFormer, an end-to-end Transformer-based signal simulator that integrates basecaller guidance during training to generate high-fidelity nanopore signals. NanoSimFormer achieves a median basecalling accuracy exceeding 99% and Q-scores above 22.8 for Oxford Nanopore Technologies' latest DNA R10.4.1 and direct RNA sequencing, closely mirroring real experimental baselines. It faithfully recapitulates experimental variant calling performance across the five human samples, achieving F1-scores of 0.9953-0.9973 and 0.7862-0.8612 for single-nucleotide polymorphisms and small indels detections, respectively. Compared with previous simulators, NanoSimFormer also substantially reduces false positives in homopolymer and short tandem repeat regions. NanoSimFormer-derived reads enable high-quality de novo bacterial assembly with consensus error rates below one mismatch per 100 kbp and maintain high correlations with experimental abundance in metagenomic and transcriptomic datasets.

NanoSimFormer is freely available on GitHub at: https://github.com/BioinfoSZU/NanoSimFormer.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid42302503, year = {2026}, author = {Chen, Y and Yoo, S and Ahn, S and Imran, HZB and Reyes, YA and Nguyen, DV and Soltani, T and Wu, D}, title = {Mesospace-domain biochar regulates electron transfer to enhance elemental sulfur-driven autotrophic denitrification for low-carbon mariculture wastewater treatment.}, journal = {Water research}, volume = {303}, number = {}, pages = {126268}, doi = {10.1016/j.watres.2026.126268}, pmid = {42302503}, issn = {1879-2448}, abstract = {Elemental sulfur-driven autotrophic denitrification (S[0]AD) offers a promising approach for nitrate removal from recirculating aquaculture system (RAS) wastewater. However, it is constrained by the low bioavailability and restricted electron-donating kinetics of elemental sulfur (S[0]). This study developed an enhanced S[0]AD system based on mesospace-domain biochar-embedded hydrogel scaffolds (S[0]AD-BCgel) that modulated electron transfer to promote denitrification and enabled sulfur recovery. Biochar (pyrolyzed at 800 °C; charBC800) increased denitrification efficiency and kinetics by 1.5-fold and 18.1-fold, respectively, compared to the biochar-free control. The improved S[0]AD was attributed to its three synergistic roles in regulating electron transfer: (i) a biopseudocapacitor with abundant quinone functionalities and high electron exchange capacity that facilitated electron relaying; (ii) a bioconductor with graphite-like structures that stimulated interfacial electron transfer; and (iii) a biomodulator that stimulated intracellular electron transfer and promoted extracellular electron transfer in extracellular polymeric substances by enriching cytochrome c and flavin-like compounds. These coordinated properties optimized S[0] utilization and interspecific microbial interactions. Metagenome-assembled genomes (MAGs) further unveiled a shift in the denitrifying microbiota toward modularized consortia characterized by robust metabolic cross-feeding, underpinning improved S[0]AD stability. Moreover, spent hydrogels after S° consumption enable in-situ and ex-situ recovery of biogenic sulfur, supporting material reusability. These findings shed light on the mechanisms by which immobilized biochar regulated electron transfer and microbial interactions during S[0]AD within hydrogel matrices, providing valuable references for sustainable mariculture wastewater treatment and resource recovery.}, } @article {pmid42302690, year = {2026}, author = {Li, X and Wen, S and Yu, C and Zhang, J and Xu, W and Yue, Z and Zhang, J}, title = {Dynamic evolution of the antibiotic resistome and mobilome on the microplastics of hospital wastewater.}, journal = {Journal of environmental management}, volume = {412}, number = {}, pages = {130243}, doi = {10.1016/j.jenvman.2026.130243}, pmid = {42302690}, issn = {1095-8630}, abstract = {Antimicrobial resistance is a major global health threat. Hospital wastewater serves as a significant reservoir for both microplastics (MPs) and antibiotic resistance genes (ARGs). MPs have recently been recognized not only as persistent pollutants but also as novel ecological niches for microbial colonization. However, the underlying mechanisms and key biological carriers driving MPs - mediated antimicrobial resistance transmission in hospital wastewater remain unclear. Here, we quantified the occurrence and characteristics of MPs in hospital wastewater and combined an incubation experiment with metagenomic sequencing to resolve the temporal dynamics of ARGs, mobile genetic elements (MGEs), and virulence factors (VFs) on MPs surfaces. MPs reached an abundance of 9.5 particles/L, with polyethylene (PE) dominating. Across the 28-day colonization period, with samples collected at 7, 14, 21, and 28 days, 68 ARGs, 443 MGEs and 414 VFs were detected, along with 129 prophage, highlighting the potential for enhanced horizontal gene transfer (HGT) in the plastisphere. We further reconstructed 360 metagenome-assembled genome (MAGs) spanning 16 phyla, and identified Pseudomonadota and Bacteroidota as core hosts of ARGs on MPs. Variance partitioning analysis revealed that MGEs were the major drivers of ARGs variation, independently explaining 44.4% of the dynamics. Our findings provide new insights into the ecological processes of antibiotic resistome of the MPs in the hospital wastewater.}, } @article {pmid42302785, year = {2026}, author = {Zhou, Q and Lu, Y and Wang, L and Zhou, W and Oba, H and Zhou, Y and Shen, M and Qu, X and De Souza, C and Rayner, A and Chen, Y and Cheng, TY and Ling, Z and Li, L and Liu, C and Voigt, AY and Xiong, R and Oh, J and Spakowicz, D and Dravillas, C and Tian, AW and Nicolls, MR and Huynh, AT and Chen, X and Hu, J and He, M and He, F and Snyder, MP and Yang, J and Zhou, X}, title = {Power and sample-size estimation in human microbiome research.}, journal = {Med (New York, N.Y.)}, volume = {}, number = {}, pages = {101174}, doi = {10.1016/j.medj.2026.101174}, pmid = {42302785}, issn = {2666-6340}, abstract = {Human microbiome research has become pivotal in advancing our understanding of complex diseases such as diabetes, inflammatory bowel disease, and cancer. Much of this work relies on comparing microbial communities across health and disease states, or case-control cohorts, using high-throughput metagenomic sequencing. Yet the very nature of sequencing-derived microbiome data makes robust cohort design and power-based sample-size estimation unusually difficult. Unlike other omics, microbiome profiles are compositional, sparse, and often zero inflated, properties that complicate statistical modeling and inflate sample-size requirements. These challenges are further compounded by the diversity of analytical frameworks-ranging from diversity indices to causal inference-each built on different statistical assumptions and optimized for a distinct research hypothesis. This review synthesizes current approaches around the study design and sample-size estimation in microbiome research, aiming to provide clinicians and researchers with practical guidance for navigating the statistical complexities unique to this field.}, } @article {pmid42302870, year = {2026}, author = {Zhao, J and Wang, J and Li, S and Lu, Q and Zhang, P and Qi, Y and Xu, X and Fan, J and Chen, C and Zhang, W}, title = {Chlorella pyrenoidosa reduces fecal heavy metal concentrations and antibiotic resistance gene abundance in lambs by modulating the gastrointestinal microbiota.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135186}, doi = {10.1016/j.biortech.2026.135186}, pmid = {42302870}, issn = {1873-2976}, abstract = {Using feed additives and their residues leads to the accumulation of heavy metals and antibiotics in the feces of fattening sheep, thereby posing a threat to the surrounding soil and ecological cycle. Chlorella, a novel feed raw material or additive widely applied in aquaculture, has the potential to mitigate such ecological risks. In this study, we investigated the potential of Chlorella pyrenoidosa as a dietary supplement for fattening lambs to mitigate multi-pollutant emissions from manure via gastrointestinal microbiome modulation. The results demonstrated that dietary supplementation with 3% Chlorella pyrenoidosa (W3) markedly reduced fecal concentrations of several heavy metals (Fe, Cu, Zn, Cr, As, Pb) and total phosphorus, while shifting phosphorus speciation toward more stable forms. Metagenomic analysis revealed that W3 reshaped the metabolic functional profile of the gastrointestinal microbiota and drove the succession of key microbial taxa, particularly promoting the proliferation of Clostridium and other genera in feces. Furthermore, Chlorella pyrenoidosa reduced the abundance of high-risk antibiotic resistance genes (ARGs, e.g., macB). It simplified the ARG-metal resistance gene co-occurrence network and was associated with an attenuated potential for vertical transmission of resistance genes along the digestive tract. Structural equation modeling further confirmed that pollutant reduction was closely associated with the functional remodeling of the microbiome. Thus, this study suggests that Chlorella pyrenoidosa may mitigate the environmental risks associated with heavy metals, bioavailable phosphorus, and ARGs in manure by regulating the gastrointestinal microbial ecosystem. This provides a novel strategy and theoretical basis for reducing source pollution in animal husbandry.}, } @article {pmid42302872, year = {2026}, author = {Wang, Y and Kang, Y and Dong, J and Cheng, C and Wu, H and Guo, Z and Zhang, J}, title = {Iron-based anodes facilitate concurrent mercury removal and bioenergy generation in constructed wetland-microbial fuel cells.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135193}, doi = {10.1016/j.biortech.2026.135193}, pmid = {42302872}, issn = {1873-2976}, abstract = {Constructed wetland-microbial fuel cell (CW-MFC) is a promising technology for wastewater treatment with concurrent resource and energy recovery. However, its power generation capacity and mercury (Hg) removal efficiency are significantly limited by the insufficient electron transfer of anode materials. In this study, CW-MFCs were developed using zero-valent iron and siderite as anode materials. The incorporation of iron-based substrates significantly enhanced Hg removal, with total Hg removal efficiencies increasing by 22.9 % and 18.4 %, respectively, compared to conventional CW-MFCs. The integration of iron-based materials increased the availability of organic/inorganic electron donors by 9.1-350.0 %, thereby enhancing power generation performance by 17.9-34.9 %. This enhancement promoted the reduction of Hg(II) and inhibited the formation of methylmercury. Additionally, the electricity generated by the MFC facilitated Fe(III)/ Fe(II) redox cycling, which supported continuous corrosion and electron release from the iron anode. Metagenomic and electrochemical analyses demonstrated that the use of iron-based materials in CW-MFCs improved both extracellular and intracellular electron transfer efficiencies, and strengthened the synergistic interaction between the iron-based anode and electroactive bacteria. The genes that related to Hg(II) reduction, including merA, were also improved. Generally, this study highlights the potential of iron-based anodes to enhance Hg removal and power generation in CW-MFCs, providing a sustainable and energy-recovering strategy for wastewater treatment.}, } @article {pmid42304204, year = {2026}, author = {Ai, X and Ren, Z and Liu, C and Zhang, C and Li, H and Ding, H and Yu, Y and Luo, W and Bi, Y}, title = {Unveiling microbial communities and biogeochemical cycles in Antarctic colored snow.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05306-y}, pmid = {42304204}, issn = {1471-2180}, support = {2022YFC2807605//National Key Research and Development Program of China/ ; KP202101//the Key Laboratory of Polar Science, MNR, Polar Research Institute of China/ ; MEEST-2022-03//the MNR Key Laboratory of Marine Eco-Environmental Science and Technology, China/ ; 91851201//National Natural Science Foundation of China/ ; 31971477//National Natural Science Foundation of China/ ; }, abstract = {Snow cover, the extensive terrestrial habitat in Antarctica, sometimes exhibits vivid coloration, yet the structure and function of its microbial communities remain poorly characterized. Using metagenomic sequencing of red snow (RS) and green snow (GS) from the Fildes Peninsula, we found that bacterial, eukaryotic, and archaeal relative abundances were 85.82%, 13.52% and 0.16%, respectively. β-Diversity differed significantly between RS and GS across these three domains (P < 0.05). Dominant bacterial phyla included Bacteroidota (RS: 62.61%; GS: 38.72%) and Pseudomonadota (RS: 32.80%; GS: 54.10%). Among eukaryotes, Chlorophyta (RS: 58.10%; GS: 52.98%) and Basidiomycota (RS: 14.80%; GS: 8.08%) were prevalent. Nanobdellota dominated archaea, with lower abundance in RS than GS. In the algal community, Sanguina, Gonium and Chloromonas were significantly enriched in red snow, while Chlorella and Micractinium were enriched in green snow (P < 0.05). Marker genes associated with carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycles were identified in green and red snow. Aerobic respiration and phosphate regulation were significantly enriched in red snow, while CO oxidation, fermentation, and denitrification were significantly enriched in green snow. Key microbial genera associated with these functional pathways also varied. In the denitrification of red snow, Stutzerimonas was the most abundant genus, while Janthinobacterium was abundant in green snow. Nitrification-related genes were detected only in red snow based on the present metagenomic data. The network of the red snow microbial community was potentially more complex and resistant based on topology, which not only benefited its own long-term survival but might also have potentially influenced the positive feedback effect of snowmelt by maintaining a low-albedo snow surface. This provided an ecological implication under climate warming: the expansion of red snow patches showed the potential to the increase nitrate runoff export, which would affect nitrogen nutrient levels in coastal Antarctic waters. Overall, this study used metagenomics to compare the multidomain (bacteria, archaea and eukaryotes) composition and diversity between red snow and green snow, and directly linked key microbial taxa with functional genes of biogeochemical cycles. This study provided new insights into the biological characteristics and functional potential of Antarctic colored snow.}, } @article {pmid42304206, year = {2026}, author = {Pfeifer, D and Graf, M and Rurik, C}, title = {Genestrip: exact and efficient read classification for selected groups of organisms.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {42304206}, issn = {1471-2105}, mesh = {*Metagenomics/methods ; Databases, Genetic ; *Software ; }, abstract = {BACKGROUND: The consumption of main memory resources is a significant burden in k-mer-based metagenomic analysis when creating related databases but also when performing (unique) k-mer-counting and read classification. Genestrip addresses this issue by focusing on small but freely configurable groups of organisms. Regarding the selected organisms, Genestrip produces k-mer databases and results comparable to those of KrakenUniq but at a fraction of its required memory resources. Our tool ensures that during database generation, the most suitable lowest common ancestor taxon is assigned for each stored k-mer by also considering genomes of organisms whose k-mers are not included in the database. This enables read analysis with high precision and recall for the organisms of interest.

RESULTS: We assess the correctness, usefulness and performance of Genestrip in different contexts and show that it indeed ascertains high quality read classifications for organisms whose genomes are included in a corresponding database. Our example databases comprise millions to a few billions of k-mers covering a dozen to a few thousands of species and lend themselves to usage in tick surveillance, medical diagnostics or agriculture. All databases were generated on a regular PC within hours, and related analysis performance was competitive to highly favorable. The deliberate focus on a particular set of genera or species allows for more genomes to be included from related organisms while the resulting databases remain small. Since k-mer compression becomes unnecessary, false positives emerging from related information loss are entirely avoided. We exemplify that such small but deep databases tend to improve recall during read classification while sustaining high precision.

CONCLUSIONS: Due to Genestrip's particular way of updating the k-mers' lowest common ancestor taxa, both database creation and fastq file analysis can be realized with little memory and with favorable runtimes as well as high classification quality. So both, database creation and read classification may be performed even on regular PCs. Genestrip's qualities empower users to flexibly design, build and use small k-mer databases for their own needs with potentially deep genomic coverage.}, } @article {pmid42304260, year = {2026}, author = {Yang, X and Jing, S and Li, S and Zhang, Y and Dong, L and Zou, T}, title = {Chronic non-bacterial osteomyelitis presenting as fever of unknown origin in a child: a diagnostic pitfall.}, journal = {BMC pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12887-026-07002-2}, pmid = {42304260}, issn = {1471-2431}, abstract = {BACKGROUND: Chronic non-bacterial osteomyelitis (CNO), also referred to as chronic recurrent multifocal osteomyelitis (CRMO), is a rare autoinflammatory bone disorder in children and adolescents. Bone pain is the most common presenting symptom, whereas prolonged recurrent fever of unknown origin is uncommon and may mimic infection or malignancy, leading to extensive diagnostic evaluations, including invasive procedures.

CASE PRESENTATION: We report a 12-year-old girl who presented with recurrent fever as the predominant symptom, accompanied by delayed and intermittent musculoskeletal pain. Extensive infectious, rheumatologic, and oncologic investigations, including repeated cultures, metagenomic next-generation sequencing, and bone marrow examination, were unrevealing. Magnetic resonance imaging demonstrated multifocal bone marrow edema, and positron emission tomography-computed tomography showed multifocal FDG-avid skeletal lesions, with a maximum SUV of 6.85 among the focal skeletal lesions, raising concern for malignancy. Histopathological examination of a femoral bone biopsy revealed lymphoplasmacytic infiltration with focal fibrosis and no evidence of infection, granulomatous inflammation, necrosis, or malignancy. Based on the clinical course, imaging findings, exclusion of infection and malignancy, and histopathological findings, a diagnosis of CNO/CRMO was established. The patient improved after stepwise treatment with naproxen, methotrexate, and prednisone.

CONCLUSION: This case illustrates an uncommon fever-dominant presentation of pediatric CNO/CRMO with multifocal skeletal lesions mimicking malignancy. CNO/CRMO should be considered in children with fever of unknown origin accompanied by delayed musculoskeletal symptoms or multifocal bone marrow lesions. In typical cases, biopsy may be avoided when clinical and imaging findings are characteristic; however, in atypical presentations with systemic symptoms and malignancy-like imaging findings, bone biopsy may remain necessary to exclude infection and neoplastic disease.}, } @article {pmid42304541, year = {2026}, author = {Dutta, R and Obayomi, O and Yosef, AF and Ghazaryan, L and Chalifa-Caspi, V and Lapidot, M and Gillor, O}, title = {A cooperative cobalamide biosynthesis guild in the endosphere of the edible aquatic plant Wolffia globosa Mankai.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00917-4}, pmid = {42304541}, issn = {2524-6372}, support = {16-38-0038//Ministry of Agriculture and Rural Development/ ; }, abstract = {BACKGROUND: Cobalamin (vitamin B12) is synthesized only by certain bacteria and archaea and is rarely found in plant-derived foods because plants neither synthesize nor require this cofactor. The edible duckweed Wolffia globosa Mankai is unusual in containing bioavailable cobalamin, suggesting a microbial origin. However, how cobalamin biosynthetic capacity is organized within angiosperm-associated microbiomes remains largely unresolved. Here, we investigated bacterial community structure and cobamide biosynthetic potential across the cultivation medium, plant surface, and internal tissues of Mankai to determine how cobalamin production is maintained in this aquatic plant microbiome.

RESULTS: Bacterial communities differed significantly among compartments, with the endosphere forming a low-diversity, host-filtered microbiome enriched in specialized taxa. Genome-resolved metagenomics showed that only a minority of endophytic bacteria encoded near-complete cobamide biosynthesis pathways consistent with de novo synthesis. In contrast, many co-occurring taxa lacked multiple biosynthetic steps but were enriched in genes associated with cobamide precursor salvage and remodeling. Network analysis identified putative producer taxa as highly connected hubs linked to salvager populations, consistent with metabolite cross-feeding. Comparative genomic analysis demonstrated reduced cobamide biosynthetic gene complements in endophytic genomes relative to closely related free-living strains, supporting adaptive pathway reduction in the host-associated niche.

CONCLUSIONS: Cobalamin production in the Mankai endosphere appears to arise from a metabolically interdependent bacterial consortium rather than from single autonomous producers. These findings identify cooperative micronutrient biosynthesis as an organizing principle in plant-associated microbiomes and position Mankai as a tractable model for studying cobamide-mediated microbial cooperation in aquatic crops. Understanding these interactions may support microbiome-informed strategies to stabilize micronutrient production and functional resilience in controlled aquatic plant cultivation systems.}, } @article {pmid42305251, year = {2026}, author = {Zicos, MH and Barnes, I and Frantz, L and Brace, S}, title = {Megaherbivore coprolite DNA: yields and comparison of three ancient DNA extraction protocols on coprolites of giant ground sloth Mylodon darwinii.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21009}, pmid = {42305251}, issn = {2167-8359}, mesh = {Animals ; *DNA, Ancient/isolation & purification/analysis ; *Sloths/genetics ; }, abstract = {Coprolites offer rich potential for palaeodietary studies as snapshots of past dietary behaviour and environment. They require adapted laboratory methods to retrieve the DNA of the depositor, its microbiome, diet and environmental taxa. Here we compare the performance of three common ancient DNA (aDNA) extraction methods to recover metagenomes from coprolites of Darwin's ground sloth Mylodon darwinii from Cueva del Milodón (Chile). The Qiagen PowerSoil Kit outperformed the other two methods in terms of DNA recovery and library complexity, but the communities inferred from the DNA extracted by the three methods were similar. We were able to recover signatures of local Patagonian flora, as well as sloth mitochondrial genomes, confirming the taxonomic identity of the coprolite depositors.}, } @article {pmid42305671, year = {2026}, author = {Wu, C and Lou, Y and Wang, L and Wang, F and Wang, X and Liu, Y and Uwaremwe, C and Li, Z and Zhang, Z and Zhu, Y and Su, X and Tian, Y}, title = {Biocontrol mechanisms of two Paenibacillus strains against Astragalus membranaceus root rot and their effects on soil microecological structure.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1827299}, pmid = {42305671}, issn = {1664-302X}, abstract = {Astragalus membranaceus is an important medicinal herb in China, yet its yield and quality are severely constrained by root rot disease. In this study, two efficient antagonistic strains, HQ-1 and HQT-2, were isolated and identified as Paenibacillus polymyxa and Paenibacillus terrae, respectively. Both strains exhibited multiple plant growth-promoting traits and strong inhibitory activity against Fusarium solani (syn. Neocosmospora solani) GF-3. In vitro assays confirmed that their sterile fermentation filtrates effectively inhibited pathogen growth and damaged fungal hyphae. GFP labeling further verified their colonization potential on plant roots, while greenhouse experiments indicated preventive efficacies of 86.046% for HQ-1 and 80.619% for HQT-2. In addition, they significantly promoted the growth of A. membranaceus. Metagenomic analysis showed that biocontrol bacterium-treated soils had significantly increased relative abundance of beneficial microorganisms, alongside a reduction in phytopathogenic taxa. Notably, despite the scarcity of biocontrol reports for P. terrae, our study introduces strains HQ-1 and HQT-2 as highly effective, multifunctional resources for sustainable control of A. membranaceus root rot. This study provides much-needed systematic evidence on the efficacy of P. terrae in biocontrol, thereby addressing a notable lack of comprehensive data in the current literature.}, } @article {pmid42306533, year = {2026}, author = {Zhang, S and Li, L and Niu, Z and Liu, M and Mao, J and Min, J and Xu, S and Li, R and Zhang, H and Yin, J and Wu, X}, title = {A large-scale retrospective analysis reveals the fungal pathogen spectrum across diverse clinical specimens using metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779223}, pmid = {42306533}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; Middle Aged ; *Metagenomics/methods ; *Fungi/genetics/classification/isolation & purification/pathogenicity ; Aged ; Adult ; Child ; Adolescent ; Young Adult ; *Mycoses/microbiology/diagnosis ; *Invasive Fungal Infections/microbiology/diagnosis ; Child, Preschool ; Aged, 80 and over ; Infant ; }, abstract = {INTRODUCTION: Early diagnosis of invasive fungal diseases (IFD) remains a major clinical challenge due to pathogen diversity and nonspecific symptoms. This study used metagenomic next-generation sequencing (mNGS) technology to comprehensively characterize fungal profiles across various clinical specimens and the demographic characteristics (sex and age) of the patient population. The results provide laboratory evidence to support the diagnosis and treatment of fungal infections.

METHODS: A total of 11,161 mNGS reports from clinical specimens collected at the Renmin Hospital of Wuhan University between March 2022 to August 2024 were retrospectively analyzed. Fungal spectra and patient demographics were comprehensively profiled and compared across different specimen types.

RESULTS: The highest fungal detection rate was observed in bronchoalveolar lavage fluid (36.85%, 1,985/5,387), followed by urine (22.76%, 264/1,160), blood (13.38%, 380/2,840), pleural and peritoneal fluid (12.91%, 174/1,348), cerebrospinal fluid (CSF) (13.82%, 17/123), and wound exudates (12.87%, 39/303). Candida species were the most frequently detected fungi across all specimen types except CSF, wherein Aspergillus predominated. Overall fungal detection rates were significantly higher in male patients than in female patients (26.76% vs. 23.84%, P < 0.01) and in individuals aged > 60 years compared with those aged ≤ 60 years (33.04% vs. 20.02%, P < 0.001), although this trend varied by specimen type. Multivariate logistic regression analysis confirmed that male sex (adjusted odds ratio [aOR]=0.893,95% confidence interval: 0.824-0.967, P = 0.006) and advanced age (≥80 years: aOR=14.77,95% confidence interval: 12.08-18.06, compared with minors) were independent risk factors for fungal detection. Among fungal-positive specimens, 68.28% (1,952/2,859) were co-detected with bacteria, and 15.63% (447/2,859) showed polyfungal detection (≥ 2 fungal species).

CONCLUSION: In conclusion, our findings highlight the predominance of Candida and Aspergillus, identify elderly male patients as a high-risk population, and underscore the high frequency of bacterial-fungal co-detection. Overall, Clinicians should combine mNGS results with imaging, conventional fungal tests (G/GM assays, culture), and clinical presentation for a more accurate diagnosis of IFD.}, } @article {pmid42306745, year = {2026}, author = {Hang, M and Liu, Y and Shen, X and Zhao, Y and Xu, Y and Gong, X and Xu, L and Li, N and Dong, L}, title = {The clinical and translational perspectives on the lung microbiome in interstitial lung diseases: a bibliometric review.}, journal = {Journal of thoracic disease}, volume = {18}, number = {5}, pages = {478}, pmid = {42306745}, issn = {2072-1439}, abstract = {BACKGROUND: Increasing evidence suggests that microbiota plays important roles in the pathogenesis and progression of interstitial lung diseases (ILDs). However, the global research landscape and emerging trends in this field remain insufficiently characterized. This study aimed to systematically characterize the research landscape, evolving hotspots, and future trends in the field of host microbiota and ILDs using bibliometric and visualization approaches, and to further explore the progress of related clinical studies.

METHODS: Publications up to November 8, 2025 were retrieved from the Web of Science Core Collection. Concurrently, clinical trials within the same timeframe were extracted from PubMed to assess advancements in the field. Bibliometric and visual analyses were conducted using VOSviewer, CiteSpace, SCImago Graphica, and Microsoft Excel.

RESULTS: A total of 295 publications were included, showing a marked increase in research output since 2012. China and the United States were the leading contributors, with the United States demonstrating higher academic impact and stronger international collaboration. Core institutions and authors were mainly concentrated in North America and Europe. Keyword analysis revealed a clear evolution of research focus, shifting from early exposure-related studies and hypersensitivity pneumonitis to lung microbiome dysbiosis, the gut-lung axis, and metagenomic approaches. Recent hotspots emphasize microbiome-based clinical applications, with increasing attention to host-microbiome interactions and immune regulatory mechanisms.

CONCLUSIONS: Research on microbiota and ILDs has expanded rapidly and shows increasing interdisciplinary integration. Future studies should enhance international collaboration, clarify underlying mechanisms, and promote clinical translation of microbiome-based biomarkers and personalized therapeutic strategies.}, } @article {pmid42306944, year = {2026}, author = {Abaeva, IS and Pestova, TV and Hellen, CUT}, title = {Genetic mechanisms underlying the structural elaboration and dissemination of viral internal ribosomal entry sites.}, journal = {Nucleic acids research}, volume = {54}, number = {11}, pages = {}, pmid = {42306944}, issn = {1362-4962}, support = {R01 GM097014/NH/NIH HHS/United States ; R21 AI188505/NH/NIH HHS/United States ; R35 GM122602/NH/NIH HHS/United States ; }, mesh = {*Internal Ribosome Entry Sites ; *RNA, Viral/chemistry/metabolism ; Nucleic Acid Conformation ; Ribosomes/metabolism ; *Dicistroviridae/genetics ; Genome, Viral ; Base Sequence ; *Peptide Chain Initiation, Translational ; }, abstract = {Viral internal ribosomal entry sites (IRESs) are highly structured cis-acting RNAs that mediate end-independent initiation of translation. Their origin remains obscure. The simplest IRESs (type 6) occur in the intergenic region of Dicistroviridae genomes (order Picornavirales), consist of two pseudoknots, and initiate translation by factor-independent binding to ribosomes. Larger variants contain a third pseudoknot that modifies the mechanism of IRES function by engaging with the ribosomal head and promoting binding to the ribosomal aminoacyl site. Metagenomic analyses undertaken to identify structurally distinct type 6 IRESs identified subsets ranging from ∼120-260 nt in length. They differ by the cumulative addition of structural elements, suggesting an accretion mechanism for the structural elaboration of IRESs. Insertions occurred at specific loci, possibly reflecting non-templated nucleotide insertion during replication, and form additional subdomains. Biochemical analysis showed that these novel classes of type 6 IRES all bound directly to the ribosomal peptidyl site. Identification of chimeric IRESs implicates recombinational exchange of domains as a second mechanism for the diversification of IRES structure. Recombination likely also accounts for the presence of type 6 IRESs at the 5'-end of dicistrovirus-like genomes and in families other than Dicistroviridae, including Marnaviridae (order Picornavirales) and Tombusviridae (order Tolivirales).}, } @article {pmid42306954, year = {2026}, author = {Lee, D and Norton, NJ and Dale, AP}, title = {Harnessing next-generation microbial diagnostics to optimize infection management in immunocompromised hosts.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, pmid = {42306954}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: Conventional microbiological tests have limitations in the microbial diagnosis of immunocompromised patients. Next-generation sequencing (NGS) technologies have the potential to overcome some of these challenges by enabling rapid, comprehensive, and hypothesis-free pathogen detection, potentially improving the speed and accuracy of microbial diagnosis and subsequent clinical outcomes. This review summarizes current evidence for the use of NGS technologies in immunocompromised populations, highlights areas of demonstrated clinical impact, and identifies key priorities for broader clinical integration.

RECENT FINDINGS: Case reports and series have demonstrated the utility of NGS in diagnosing unusual or atypical infections amongst immunocompromised patients that were initially missed by conventional methods. Retrospective observational studies indicate that NGS can achieve higher sensitivity and greater pathogen detection rates than conventional diagnostics, although performance may be limited for certain pathogens, such as Aspergillus and Mycobacterial species. The clinical impact of NGS-guided interventions varies, reflecting both differences in study design and challenges in interpreting metagenomic data.

SUMMARY: NGS technologies have the potential to enhance microbial diagnosis in immunocompromised patients, particularly in complex, polymicrobial, or atypical infections where conventional methods fail. However, widespread clinical adoption is limited by high costs, complex workflows, and the need for advanced bioinformatics infrastructure and expertise. Further research is required to define clinical impact, cost-effectiveness, and to standardize workflows and guide optimal time for implementation, in order to inform evidence-based integration of NGS into routine clinical practice.}, } @article {pmid42307633, year = {2026}, author = {Carasso, S and Kasher-Dvora, M and Gefen, T and Geva-Zatorsky, N}, title = {Phase variation-mediated bacterial functional plasticity as a lens for understanding microbe‒host interactions.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2687913}, doi = {10.1080/19490976.2026.2687913}, pmid = {42307633}, issn = {1949-0984}, mesh = {Humans ; *Host Microbial Interactions ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/physiology ; *Bacterial Physiological Phenomena ; Animals ; }, abstract = {The human gut microbiome represents a dynamic microbial ecosystem profoundly influencing host physiology, immune development, and disease susceptibility. While metagenomic approaches have advanced our understanding of microbial composition and functional potential, they remain insufficient to capture the real-time molecular events governing host‒microbe interactions. Taxonomic abundance and genomic content alone do not reflect active gene expression or phenotypic output, and functional roles cannot be reliably inferred from phylogenetic identity, given the substantial heterogeneity observed even within species. Central to bridging this gap is the concept of bacterial functional plasticity, with a focus on phase-mediated functional plasticity, the intrinsic capacity of microbes to rapidly remodel their activity and phenotype in response to environmental and host-derived cues. This review highlights phase variation as a prominent and evolutionarily conserved mechanism underlying plasticity, encompassing DNA inversions, short-sequence repeat modifications, and broader structural genomic variation. Emerging evidence demonstrates not only the prevalence of phase-variable mechanisms across diverse gut taxa but also their significant regulatory, ecological, and immunological consequences. These findings reframe the microbiome from a static consortium of species to a functionally dynamic system capable of rapid rewiring in response to environmental pressures. By integrating genomic, ecological, and host-response data, this review lays the groundwork for mechanistic frameworks that could explain how flexible microbial strategies influence bacterial behavior and host outcomes. Moving beyond cataloging microbial composition toward deciphering the logic of functional adaptation will be essential for translating microbiome research into predictive, diagnostic, and therapeutic applications.}, } @article {pmid42307846, year = {2026}, author = {Gomes, RF and García, GJY and Cardoso, MS and Dutra, JDCF and de Abreu Waldow, V and Akamine, RN and de Sousa, MP and Groposo, C and Brenig, B and Figueiredo, H and de Carvalho Azevedo, VA and Góes-Neto, A}, title = {Metagenomics and metatranscriptomics of prokaryotic and fungal microbiomes in produced water associated with petroleum degradation and pipeline corrosion from an oil terminal in Brazil.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42307846}, issn = {1573-0972}, mesh = {*Fungi/genetics/classification/metabolism/isolation & purification ; Brazil ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Archaea/genetics/classification/metabolism/isolation & purification ; *Petroleum/metabolism/microbiology ; *Metagenomics ; Biodegradation, Environmental ; Corrosion ; Oil and Gas Fields/microbiology ; *Microbiota/genetics ; *Water Microbiology ; Hydrocarbons/metabolism ; Phylogeny ; }, abstract = {The prokaryotic microbial communities involved in hydrocarbon degradation and associated with oil pipeline corrosion have been extensively studied. Nonetheless, fungi can perform significant metabolic activities in these environments. Studies evaluating metabolically active microbial communities in oil reservoirs are limited. Our study investigated the total/DNA and active/RNA communities of Archaea, Bacteria, and Fungi in produced water samples from an onshore terminal in Brazil. DNA and RNA were sequenced using the Illumina HiSeq 2500 platform, and the meta-omics sequences were analyzed. Shannon alpha diversity (taxonomic and functional) revealed that total communities were more diverse than metabolically active ones, with Bacteria showing higher diversity than Archaea and Fungi. The bacterial genera Syntrophotalea (sulfur reducer) and Pseudodesulfovibrio (sulfate reducer) were most prominent in total communities, while Halanaerobium (acid producing) dominated active communities. These results confirm the presence of Microbially Influenced Corrosion (MIC); however, the aprAB and dsrABC genes showed very low expression. Methanogenic Archaea Methanocalculus, Methanoplanus, and Methanothrix were frequent in both total and active communities, and mcrABDG genes were significantly expressed in metatranscriptomic sequences. Fungal genera Absidia, Penicillium, and Rhizopus were dominant in DNA samples, whereas Saccharomycodes, Pichia, Coemansia, and Schizosaccharomyces dominated RNA samples. These fungi can remediate environments contaminated with recalcitrant hydrocarbons. Despite the limited information obtained from fungal functional profile, an in-depth investigation of their activities and interrelation with Archaea and Bacteria in oil reservoirs is crucial for monitoring and mitigating oil biodegradation and pipeline biocorrosion processes.}, } @article {pmid42307995, year = {2026}, author = {Laiton, L and Acevedo, FE}, title = {Gut microbiome of the grape berry moth, Paralobesia viteana (Lepidoptera: Tortricidae) larvae through the grape ripening process revealed by high-throughput 16S and 18S rRNA sequencing.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, pmid = {42307995}, issn = {2057-5858}, mesh = {Animals ; *Vitis/parasitology/growth & development/microbiology ; RNA, Ribosomal, 16S/genetics ; Larva/microbiology ; RNA, Ribosomal, 18S/genetics ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; *Moths/microbiology ; Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Fungi/classification/genetics/isolation & purification ; }, abstract = {The grape berry moth (GBM) Paralobesia viteana (Lepidoptera: Tortricidae) is an important pest of grapes in eastern North America. The larvae damage grape clusters by direct feeding and by increasing susceptibility to fungal and bacterial pathogens. In this study, we sequenced the V3-V4 region of the 16S rRNA gene and the V4 region of the 18S rRNA gene to characterize the composition and diversity of GBM larval gut bacterial and fungal communities when fed on immature and mature 'Concord' grapes. The data were analysed with QIIME 2, and downstream analyses included taxonomic composition, differential abundance, phylogenetic, functional and alpha/beta diversity analyses. While overall bacterial community diversity did not differ significantly between treatments, differential abundance analysis identified specific bacterial taxa enriched in each larval group. Ninety-three per cent of the bacterial communities belonged to the phylum Proteobacteria, and some may play roles in amino acid and carbohydrate metabolism in the insect gut. Analyses of the 18S rRNA region showed significant taxon-level compositional differences in fungal communities between larvae grown on grapes at different ripening stages. Ascomycota was the dominant phylum (98%) present in the guts of larvae fed on mature grapes, while larvae fed on immature grapes mainly contained fungi within the Cryptomycota (51%). Larvae fed on ripe grapes had a 10-fold higher fungal abundance and were enriched in Saccharomycetales yeasts. Several of the identified microbial taxa in larval guts are commonly found in grapes, which suggests they might be transient insect residents that are ingested with the diet. In conclusion, diet strongly shaped GBM gut-associated fungal communities; specific bacterial taxa also differed between larval groups despite similar overall bacterial diversity. These results contribute to basic knowledge of gut-associated microbes in fruit-feeding insects.}, } @article {pmid42308045, year = {2026}, author = {Cornman, A and Tranzillo, M and Zulaybar, NG and Bouzit, I and Hwang, Y}, title = {Linear-time prediction of proteome-scale microbial protein interactions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {25}, pages = {e2610619123}, doi = {10.1073/pnas.2610619123}, pmid = {42308045}, issn = {1091-6490}, support = {GBMF13344//Gordon and Betty Moore Foundation (GBMF)/ ; G-24-67500//Schmidt Futures (Schmidt Futures Projects, LLC)/ ; }, mesh = {*Proteome/metabolism/genetics ; *Bacterial Proteins/metabolism/genetics ; *Protein Interaction Mapping/methods ; Prediction Algorithms ; Computational Biology/methods ; Protein Interaction Maps ; }, abstract = {Protein-protein interactions (PPIs) underpin biological function, yet proteome-scale interaction prediction remains bottlenecked by the quadratic computational complexity of all-vs.-all pairwise comparisons. Here, we present FlashPPI, a contrastive learning framework, grounded in residue-level interactions, that enables linear-time prediction of physical protein interfaces across a microbial proteome. By leveraging a genomic language model that captures cross-protein coevolutionary signals from metagenomic sequences, FlashPPI aligns interacting partners in a shared latent space. We demonstrate a four-fold performance increase over existing sequence-based methods, while reducing proteome-wide screening time from days to minutes. Crucially, FlashPPI achieves comparable screening performance to state-of-the-art structure-folding models at a fraction of the computational cost. Finally, we integrate FlashPPI into an interactive web platform that combines predicted networks with functional annotations and genomic context, making proteome-wide network analysis rapid and accessible for microbial discovery.}, } @article {pmid42308105, year = {2026}, author = {Zuffa, S and Allaband, C and Charron-Lamoureux, V and Caraballo-Rodriguez, AM and Patan, A and Mohanty, I and Agongo, J and Bostick, JW and Connerly, TJ and Thron, T and Needam, BD and de Castro Fonseca, M and Benitez, RS and Hansen, L and Tubb, H and Cao, J and Kalecký, K and Bottiglieri, T and MahmoudianDehkordi, S and Schimmel, L and Kueider-Paisley, A and Graham, SF and Siegel, D and Wang, M and Knight, R and Kaddurah-Daouk, R and Dorrestein, PC and Mazmanian, SK and , }, title = {A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models.}, journal = {Cell reports}, volume = {45}, number = {6}, pages = {117499}, doi = {10.1016/j.celrep.2026.117499}, pmid = {42308105}, issn = {2211-1247}, abstract = {The etiology of Alzheimer's disease (AD) remains unclear but is likely driven by gene-environment interactions. We present a multi-organ untargeted metabolomics atlas (n = 2,271) paired with metagenomics data (n = 666) from two AD transgenic mouse models (3xTg and 5xFAD) under colonized and germ-free conditions. Systems-level analyses revealed clusters of dysregulated molecules across tissues, including carnitines, bile acids, B vitamins, neurotransmitters, and N-acyl lipids. Metabolic shifts were associated with the depletion of Akkermansia muciniphila and enrichment of Mucispirillum schaedleri in the 3xTg model. We identify previously unexplored carnitines linked to microbial metabolism of phenylalanine. Using tissueMASST-a mass spectrometry search tool we developed to translate animal-model findings into a human clinical context-we trace phenylacetyl-carnitine in human plasma and serum samples (n = 1,470) from independent cohorts, revealing associations with aging, cognitive impairment, and diminished memory performance. This public resource and associated tools will aid future research in AD etiology.}, } @article {pmid42308119, year = {2026}, author = {Holman, DB and Gzyl, KE and Kommadath, A and Määttänen, P}, title = {Multi-omic characterization of the sow colostrum and milk microbiome and proteome.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, pmid = {42308119}, issn = {2057-5858}, mesh = {Animals ; *Colostrum/microbiology ; *Milk/microbiology ; Female ; *Proteome/genetics ; Multiomics ; *Microbiota/genetics ; Swine ; *Bacteria/classification/isolation & purification/genetics ; Metagenomics/methods ; Proteomics ; }, abstract = {Sow colostrum and milk provide essential nutrients, immune protection and one of the earliest microbial exposures for piglets. However, the microbial composition, functional potential and host interactions of these mammary secretions remain poorly characterized. Here, we combined culturomics, metagenomics and proteomics to comprehensively characterize the microbiome and proteome of sow colostrum and milk collected at farrowing and at 7 and 21 days postpartum. We recovered 132 bacterial isolates representing at least 42 species, including 15 putatively novel taxa. These isolates included both potentially pathogenic species, such as Sarcina perfringens and Streptococcus suis, and potentially beneficial bacterial species like Lactobacillus amylovorus and Lactiplantibacillus plantarum. The microbial composition and functional potential shifted significantly as the milk matured, with L. amylovorus, Limosilactobacillus reuteri and Rothia spp. among the most relatively abundant taxa. Several antimicrobial resistance genes, including erm(C), tet(K), tet(M), lnu(A), poxtA and fexB, were identified on contigs encoding plasmid replicons in the isolates, indicating potential for horizontal gene transfer. Functional annotation of isolate genomes indicated broad carbohydrate-active enzyme (CAZyme) repertoires, including β-galactosidase-associated families and other CAZyme families consistent with potential milk oligosaccharide utilization. The colostrum and milk proteome also shifted during lactation, reflecting declining immune-related proteins and increasing metabolic and structural proteins. Correlations between specific microbial taxa and host proteins, including Rothia spp. and immune proteins or glycoproteins, suggested potential host-microbe interactions during lactation. Together, these findings provide a multi-omic perspective on how mammary microbiome dynamics and host responses during lactation may influence neonatal microbial colonization and health.}, } @article {pmid42308338, year = {2026}, author = {Ong, CJN and Nazari, R and Cabuhat, KSP and Ogaya, JB and Ahmed, MM and Shomuyiwa, DO and Musa, SS and Daberechi, OJ and Abdi, YH and Dulay, RMR and Lucero-Prisno, DE}, title = {The mobile resistome in the water-soil-air nexus: horizontal gene transfer and environmental dissemination of antimicrobial resistance genes.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag064}, pmid = {42308338}, issn = {1574-6941}, abstract = {The rapid emergence and global dissemination of antimicrobial resistance pose a serious threat to public health, environmental sustainability, and economic development. Central to this crisis is the resistome, defined as the collection of all antimicrobial resistance genes present in pathogenic and non-pathogenic microorganisms across clinical, agricultural, and natural ecosystems. The environmental resistome plays a crucial role in the evolution and transmission of resistance, serving as both a reservoir and a conduit for ARG exchange through horizontal gene transfer. This review provides a comprehensive overview of the structure, diversity, and dynamics of the resistome, with emphasis on the interconnected water-soil-air continuum. Key mechanisms driving resistome dissemination, including mobile genetic elements such as plasmids, integrons, transposons, and bacteriophages, are discussed alongside the major routes of gene transfer, conjugation, transformation, and transduction. The review highlights anthropogenic drivers that intensify resistome expansion, including antibiotic misuse, wastewater discharge, agricultural runoff, and exposure to heavy metals, pesticides, and disinfectants, which promote co-selection. Advances in resistome profiling approaches, such as quantitative PCR, metagenomics, long-read sequencing, and functional metagenomics, are critically evaluated for their capacity to resolve ARG diversity, mobility, and host associations.}, } @article {pmid42308739, year = {2026}, author = {Tabish, RW and Lin, Y and Rochell, SJ and Pacheco, WJ and Bailey, MA and Dozier, WA and Hoerr, FJ and Robinson, K and Hauck, R}, title = {Jejunal histopathology, metagenome, and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107215}, doi = {10.1016/j.psj.2026.107215}, pmid = {42308739}, issn = {1525-3171}, abstract = {This study investigated the efficacy of various dietary fiber sources and combinations in mitigating subclinical enteric infection in broilers. Using a randomized complete block design, 2,160 d-old YP x Ross 708 male broilers were assigned to eight treatments. These included an unchallenged control and a challenged control, followed by six dietary treatments applied to challenged broilers. The dietary treatments consisted of fiber supplementation with oat hulls (OH) or soy hulls (SH), either alone or in combination with wheat middlings (WM) or sugar beet pulp (SBP). Birds were challenged with Eimeria spp. followed by Clostridium perfringens, and a multi-omics approach was employed to analyze jejunal histopathology, microbiome, and host mucosal transcriptome. While the enteric challenge induced significant histopathological changes, fiber combinations including OH-WM and OH-SBP significantly (P < 0.05) reduced cumulative pathology scores. The challenge caused a shift toward Lactobacillus crispatus dominance in the microbiome. Each fiber source altered the microbiome distinctively: OH increased Romboutsia sp., OH-SBP enriched beneficial Limosilactobacillus spp., and SH combinations enhanced butyrate-producing Dysosmobacter welbionis. Transcriptome analysis revealed that fiber supplementation suppressed inflammatory pathways while upregulating cell cycle progression and DNA repair pathways. Integration of bacteriome with host gene expression data revealed coordinated associations, including a link between Glutamicibacter protophormiae, Spirosoma, Eggerthella, and Blautia through host genes APOB, DSEL, and ENPP7, indicating a correlation of fiber-degrading bacteria with host lipid metabolism and extracellular matrix remodeling. These findings suggest that combining insoluble and soluble fibers may create a more resilient gut environment against enteric challenges through complementary mechanisms, with OH based combinations notably exhibiting reduced pathology, stronger anti-inflammatory response and suppression of opportunistic species.}, } @article {pmid42308920, year = {2026}, author = {Xu, Z and Zhu, W and Xia, Q and Huang, W and Chi, Y and Qi, H and Chan, OYP and Ching, JY and Chan, FK and Chan, NN and Ng, SC}, title = {Synbiotics and antioxidants synergistically attenuate disease progression in metabolic dysfunction-associated steatotic liver disease.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {201}, number = {}, pages = {119656}, doi = {10.1016/j.biopha.2026.119656}, pmid = {42308920}, issn = {1950-6007}, abstract = {BACKGROUND & AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) is linked to gut dysbiosis, highlighting gut microbiome modulation as a promising therapeutic strategy. This study investigated the synergistic effects of synbiotics and antioxidants in MASLD.

METHODS: We evaluated the effects of synbiotics, antioxidants, and their combination (SLD07) on metabolic and histopathological parameters and energy balance (Promethion system) in high-fat diet-fed mice. Plasma metabolome and faecal microbiome were analysed. In a 3-month pilot study of patients with MASLD (n = 27), we examined the safety and efficacy of SLD07 (20 billion CFU/day), with microbiome alterations assessed by metagenomic sequencing.

RESULTS: In mice, SLD07 significantly attenuated metabolic and hepatic parameters, including body weight gain, white adipose tissue, serum triglycerides, low-density lipoprotein, liver histology (p < 0.05), and increased the respiratory exchange ratio (p < 0.001). Synbiotics enhanced glucose tolerance and insulin sensitivity (p < 0.05), while antioxidants primarily reduced adipose tissue (p < 0.05). Liver tissue MDA levels were reduced only in the combination group, whereas GSSG levels were reduced in the combination and antioxidants alone groups (p < 0.05). Liver transcriptomics revealed that all treatments reversed HFD-upregulated inflammation and oxidative pathways, with the combination showing the broadest effect. Gut microbiota was mainly modulated by synbiotics, while systemic metabolome changes were driven by antioxidants. In the clinical pilot study, treatment reduced liver fat and stiffness (p < 0.01), increased Bifidobacterium, and upregulated the L-glutamine pathway, with no serious adverse events.

CONCLUSION: This integrated translational investigation demonstrates that the synbiotic-antioxidant combination alleviates MASLD through dual modulation of gut microbiota and systemic oxidative stress.}, } @article {pmid42309017, year = {2026}, author = {Yang, X and Liu, W and Mao, Y and Wang, H}, title = {Correlation analysis of lead stress-induced alterations in root metabolome and rhizosphere microbiome of Cuminum cyminum L.}, journal = {Ecotoxicology and environmental safety}, volume = {320}, number = {}, pages = {120390}, doi = {10.1016/j.ecoenv.2026.120390}, pmid = {42309017}, issn = {1090-2414}, abstract = {Lead (Pb) contamination in agricultural soils poses serious threats to crop production and food safety. Cuminum cyminum L. is an important spice crop widely cultivated in arid regions, but its rhizosphere responses to Pb stress remain poorly understood. Here we conducted a field plot experiment with four Pb treatment levels (0, 400, 800, and 1200 mg/kg) and employed an integrated approach combining soil physicochemical and enzymatic analyses, metagenomics, and root metabolomics to characterize the rhizosphere of C. cyminum after 40 days of Pb exposure. Pb significantly decreased soil pH, organic matter, nitrogen availability, and available phosphorus and potassium, while altering soil enzyme activities by suppressing urease and acid phosphatase and enhancing catalase activity. Pb stress reshaped rhizosphere microbial communities by increasing microbial richness at low and moderate Pb levels but reducing community evenness under high Pb stress. Metal-tolerant taxa, including Sphingomonas, Arenimonas, and Gemmatimonas, were selectively enriched. Functional analyses revealed a broad enhancement of microbial metabolic potential, particularly in amino acid, carbohydrate, and energy metabolism pathways. Concurrently, Pb exposure correlated with extensive root metabolic reprogramming, characterized by accumulation of amino acids, organic acids, and flavonoids. The random forest results indicated that soil physicochemical properties had a stronger correlation with plant growth than root metabolites or rhizosphere microorganisms under Pb stress conditions. Overall, this study reveals a coordinated rhizosphere strategy of C. cyminum to Pb stress, providing new insights into heavy metal adaptation mechanisms in spice crops and informing sustainable cultivation in Pb-contaminated soils.}, } @article {pmid42309163, year = {2026}, author = {Sutthiboonyapan, P and Jungpraditphol, I and Krasaesin, A and Khamwachirapitak, C and Choi, Y and Porntaveetus, T and Wiriyakijja, P}, title = {Supragingival Plaque Microbiome Composition Associated with Oral Lichen Planus Activity and Desquamative Gingivitis Severity: An Exploratory, Cross-Sectional, Shotgun Metagenomic Study.}, journal = {European journal of dentistry}, volume = {}, number = {}, pages = {}, doi = {10.1055/s-0046-1824444}, pmid = {42309163}, issn = {1305-7456}, abstract = {OBJECTIVES: The microbial contribution to desquamative gingivitis (DG), a frequent and debilitating form of immune-mediated oral lichen planus (OLP), remains undefined. This study employed shotgun metagenomic sequencing to investigate the role of the oral microbiome in DG site involvement and severity, as well as OLP disease activity.

MATERIALS AND METHODS: In this exploratory, cross-sectional study, supragingival plaque samples were collected from nine OLP patients at desquamative gingivitis-affected sites (DG sites), sites not affected by desquamative gingivitis (non-DG sites), and pooled full-mouth samples. Shotgun metagenomic sequencing was performed to reveal oral microbial profiles and their functional pathways. Disease severity was assessed using the Oral Lichen Planus Disease Activity Scale (OLP-DAS) and the Desquamative Gingivitis Clinical Score (DGCS).

STATISTICAL ANALYSIS: Associations between microbial profiles and disease severity were assessed using Spearman's correlation. Microbial and functional pathway profiles were compared between DG and non-DG sites using the paired Wilcoxon signed-rank test. A p-value <0.05 was considered statistically significant.

RESULTS: Significant differences in microbial composition between DG and non-DG sites were identified, including 6 genera and 17 species (p < 0.05). Several taxa showed notable correlations with disease severity (r ≥ 0.7), according to DGCS, with 10 genera and 16 species positively associated with DGCS, and 5 genera and 8 species associated with OLP-DAS. Notably, the fructan biosynthesis pathway showed a significant inverse correlation with DG severity (r = - 0.70, p < 0.05) and was linked to Actinomyces sp. oral taxon 448, which was enriched in DG sites. This suggested that increasing disease severity may be associated with reduced microbial polysaccharide-production potential.

CONCLUSIONS: The DG microbiome shows distinct functional and taxonomic changes. Fructan biosynthesis was more abundant in DG sites than in non-DG sites, but showed an inverse correlation with DG severity, highlighting candidate biomarkers and potential therapeutic targets.}, } @article {pmid42309238, year = {2026}, author = {R, K and Chandra, A and Pal, S and Tiwari, H and Shekhar, A and Agarwal, R}, title = {Microbial Dysbiosis in Oral Potentially Malignant Disorders: A Systematic Review.}, journal = {Journal of stomatology, oral and maxillofacial surgery}, volume = {}, number = {}, pages = {102876}, doi = {10.1016/j.jormas.2026.102876}, pmid = {42309238}, issn = {2468-7855}, abstract = {BACKGROUND: Oral potentially malignant disorders (OPMDs) including oral leukoplakia (OLK), proliferative verrucous leukoplakia (PVL), and oral verrucous hyperplasia (OVH) pose variable malignant transformation risk to oral squamous cell carcinoma (OSCC), yet the role of microbial dysbiosis in their progression remains ambiguous.

OBJECTIVES: To elucidate microbial shifts in OPMDs, their association with dysplasia progression and malignant transformation, highlighting prospects for early detection and risk stratification.

MATERIAL AND METHODS: A comprehensive literature search was conducted across scientific databases up to May 2025. Studies investigating microbial dysbiosis in OLK, PVL, or OVH using 16S rRNA sequencing, metagenomic, or transcriptomic analyses were included. Risk of bias was assessed using the modified Newcastle-Ottawa scale.

RESULTS: OPMDs showed inconsistent alpha diversity and distinct beta diversity compared to controls. Microbial composition differed by lesion type: OLK was enriched with Fusobacterium periodonticum, Porphyromonas pasteri, Streptococcus, and Haemophilus; PVL with Campylobacter concisus, Leptotrichia, and Haemophilus parainfluenzae; and OVH with Porphyromonas gingivalis, Tannerella forsythia, and Saccharibacteria TM7. High-risk OLK showed reduced diversity and enrichment of Fusobacterium nucleatum, Parvimonas, and Streptococcus infantis. Malignant transformation revealed lesion-specific shifts, including increased Fusobacterium, Capnocytophaga and Porphyromonas in OLK-OSCC, while Neisseria was specifically enriched in progressive OLK lesions, Treponema and Campylobacter in PVL-OSCC, and Capnocytophaga sputigena and Prevotella oris in OVH-OSCC.

CONCLUSION: This review highlights the pivotal role of microbial dysbiosis in the evolution of OPMDs to malignancy. Distinct microbial signatures across OLK, PVL, and OVH may serve as biomarkers for disease stratification and early detection of high-risk lesions.}, } @article {pmid42309478, year = {2026}, author = {Maya, MA and Raboni, SM and Giamberardino, HIG and Nogueira, MB and Giamberardino, ALG and Ferreira, LH and Torrecilha, VT and Pereira, LA and Usuga, J and Aristizabal-Valencia, M and Vasquez, A and Berg, MG and Rebolledo, PA and Averhoff, F and Cloherty, GA and Hernandez-Ortiz, JP and Osorio, JE}, title = {Clinical and Genomic Characterization of Pediatric Adenovirus-Associated Severe Acute Respiratory Infection: A Binational Study from Brazil and Colombia, 2022-2023.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108893}, doi = {10.1016/j.ijid.2026.108893}, pmid = {42309478}, issn = {1878-3511}, abstract = {BACKGROUND: Human adenovirus (HAdV) is detected in fewer than 10% of hospitalized children with acute respiratory infections, yet several regions reported unusual increases in 2021-2022. We investigated an HAdV outbreak detected through surveillance in Curitiba, Brazil, and Antioquia, Colombia, comparing clinical and genomic characteristics before and during the outbreak.

METHODS: We conducted a multicenter observational study of HAdV-associated severe acute respiratory infection in hospitalized children. Respiratory samples collected between February 2022 and April 2023 underwent metagenomic sequencing and hexon gene analysis. Clinical and phylogenetic analyses evaluated viral dynamics and genetic diversity.

RESULTS: A HAdV outbreak occurred in both regions during late 2022. HAdV-C predominated before the outbreak, whereas HAdV-B3 became the dominant genotype at both sites during the outbreak. During the outbreak, bronchiolitis/asthma exacerbation was most common in Antioquia, whereas pneumonia predominated in Curitiba. Phylogenetic analysis of the hexon gene identified two distinct HAdV-B3 clades that diverged from a shared ancestor but expanded independently in Brazil and Colombia.

CONCLUSION: Following relaxation of non-pharmacological measures, both regions experienced a substantial rise in HAdV-B3-associated disease. Despite increased case numbers, clinical patterns remained stable within sites but differed between regions. Integrated genomic and clinical surveillance provides important insights into adenovirus lineage expansion and outbreak dynamics.}, } @article {pmid42309606, year = {2026}, author = {Silverstein, J and Chapman, A}, title = {Recovery and analysis of ancient DNA: challenges, methods, and applications in forensic and archaeological science.}, journal = {Journal, genetic engineering & biotechnology}, volume = {24}, number = {2}, pages = {100702}, pmid = {42309606}, issn = {2090-5920}, abstract = {Ancient DNA (aDNA) research has revolutionised archaeology and forensic science by enabling genomic recovery from highly degraded remains. This review explores the biochemical and environmental factors influencing aDNA preservation, alongside methodological advances that have improved data yield and authenticity. Techniques such as next-generation sequencing (NGS), single-stranded library preparation, and hybridisation capture have transformed the field, allowing recovery from ultrashort fragments and challenging contexts such as warm climates. Authentication strategies-including cytosine deamination profiling, fragment length analysis, and rigorous contamination controls-remain essential to ensure reliability. Applications of aDNA extend beyond ancestry reconstruction and population genetics to include forensic identification, kinship analysis, and pathogen detection. Lessons from forensic genetics, such as stringent validation and contamination mitigation, have informed best practices in archaeological contexts. However, ethical considerations are central to both domains. Issues of Indigenous data sovereignty, consent, repatriation, and culturally sensitive interpretation demand transparent, community-led research frameworks. These principles align with international agreements such as the Nagoya Protocol and emerging guidelines for equitable benefit-sharing. Despite significant progress, challenges persist, including geographic sampling bias, interpretive uncertainty, and the need for interdisciplinary integration. Future directions emphasise long-read sequencing, metagenomic approaches, and artificial intelligence-driven analytics, alongside robust ethical governance. By combining technological innovation with culturally responsible practices, aDNA research continues to advance our understanding of human history while reinforcing the importance of ethical stewardship in forensic and archaeological science.}, } @article {pmid42309718, year = {2026}, author = {Sakiyama, Y}, title = {[Metagenomic analysis for central nervous system infections: clinical utility and future directions].}, journal = {Rinsho shinkeigaku = Clinical neurology}, volume = {}, number = {}, pages = {}, doi = {10.5692/clinicalneurol.cn-002248}, pmid = {42309718}, issn = {1882-0654}, abstract = {Encephalitis and meningitis are neurological emergencies in which delayed diagnosis may lead to severe neurological sequelae, necessitating accurate and rapid etiological identification. In recent years, metagenomic next-generation sequencing (mNGS), which enables comprehensive analysis of microbial genomes without prespecified hypotheses, has attracted increasing attention. Its clinical application in neuroinfectious diseases has contributed to improved diagnostic yield and the detection of rare pathogens. In particular, mNGS has been shown to be useful in clinically challenging situations such as culture-negative cases, anaerobic infections, mixed infections, and immunocompromised hosts. However, the technology also has inherent limitations, including enormous data volume, challenges in interpreting pathogenic relevance, limited turnaround time, high cost, and a lack of standardized analytical pipelines. Thus, although mNGS represents a valuable complementary tool to conventional diagnostic methods, it is not universally applicable, and its results must be carefully interpreted within appropriate clinical contexts.}, } @article {pmid42311379, year = {2026}, author = {Saito, Y and Sato, S and Sasanami, Y and Yamashita, T and Yamada, M}, title = {Heterologous expression and structural characterization of polyamide 4-degrading enzyme from a soil bacterium.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1811100}, pmid = {42311379}, issn = {1664-302X}, abstract = {Polyamide 4 (PA4) is a bio-based plastic with thermal stability, excellent mechanical properties, and good biodegradability in various environments. To understand the biodegradation of PA4 under natural environments, PA4-degrading microorganisms and enzymes have been investigated. Although our previous research identified the amino acid sequence and predicted the three-dimensional (3D) structure of a PA4-degrading enzyme from a marine environment (Nyl4A pa), those of an enzyme from terrestrial environments have remained unidentified. In this study, we identified the PA4-degrading enzyme gene (nyl4Apx) from the PA4-degrading soil bacterium Pseudoxanthomonas sp. TN-N1. In addition, nyl4Apx was successfully expressed in Escherichia coli BL21(DE3) and Brevibacillus choshinensis HPD31-SP3. The PA4-degrading activity of the enzyme secreted by recombinant B. choshinensis HPD31-SP3 reached 68.8 Δ655 nm/h/100 mL broth, representing a 2.4-fold increase compared with that produced by recombinant E. coli BL21(DE3). Based on a homology search using the amino acid sequence and predicted 3D structure of the enzyme, Nyl4A px was predicted to be composed of a substrate-binding domain, a middle domain, and a catalytic domain. Among these domains, the substrate-binding and catalytic domains of Nyl4A px are sequentially and structurally similar to those of Nyl4A pa . Furthermore, putative homologs of Nyl4A px and Nyl4A pa were found in marine-associated environmental metagenomes through BLAST searches. To our knowledge, this is the first report describing the structural properties of a PA4-degrading enzyme from a soil bacterium.}, } @article {pmid42311675, year = {2026}, author = {Zhang, H and Fan, B and Ma, R and Jiang, R and Qin, Z and Qu, X and Wang, J and Xue, J and Wang, C and Liu, X and Guo, L}, title = {Gut microbiota and sepsis-associated acute kidney injury: a narrative review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1724266}, pmid = {42311675}, issn = {1664-3224}, mesh = {Humans ; *Acute Kidney Injury/microbiology/etiology/therapy/immunology ; *Sepsis/complications/microbiology/immunology ; Animals ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Intestinal Barrier Function ; Signal Transduction ; }, abstract = {BACKGROUND: Sepsis-associated acute kidney injury (SA-AKI) carries high morbidity and mortality, yet its pathogenesis remains incompletely understood. Emerging evidence underscores the gut-kidney axis as a critical pathway in SA-AKI development.

OBJECTIVE: This review aims to synthesize current knowledge on how sepsis-driven gut dysbiosis compromises intestinal barrier integrity and contributes to SA-AKI, and to explore potential therapeutic strategies targeting the gut microbiota.

METHODS: A comprehensive literature search was conducted in PubMed, Web of Science, and Scopus databases for publications between 2005 and 2026. Studies focusing on gut-kidney crosstalk mechanisms in sepsis/AKI were included. Key findings from human and animal studies were summarized.

RESULTS: Sepsis induces marked gut dysbiosis characterized by loss of microbial diversity and expansion of pathobionts. This dysbiosis compromises intestinal barrier integrity, facilitating translocation of bacterial products such as lipopolysaccharide (LPS). Upon entering circulation, these mediators activate systemic inflammation and renal signaling cascades, including the Toll-like receptor 4 (TLR4)/nuclear factor-kappa B (NF-κB) pathway, leading to tubular injury and impaired renal function. Recent human metagenomic studies have identified specific microbial signatures associated with AKI, such as increased Clostridium asparagiforme and decreased Roseburia spp., alongside elevated uremic toxin-producing bacteria like Gordonibacter pamelaeae. Additionally, gut-derived metabolites including indoxyl sulfate, p-cresol sulfate, and trimethylamine N-oxide (TMAO) have been implicated in promoting renal inflammation and fibrosis. Importantly, renal dysfunction further disrupts gut homeostasis, establishing a pathological gut-kidney feedback loop. Targeting the gut-kidney axis via fecal microbiota transplantation, probiotic supplementation, or short-chain fatty acid administration may offer novel therapeutic avenues.

CONCLUSIONS: Sepsis induces gut microbiota dysregulation play an important role in the development of SA-AKI. The intestine-kidney crosstalk may provide a basis for the treatment of sepsis-induced organ injury and also provide new ideas for the treatment of SA-AKI.}, } @article {pmid42311883, year = {2026}, author = {Tan, S and Liao, Q and Wen, Y and Zhu, Y}, title = {Case Report: Invasive pulmonary aspergillosis caused by Aspergillus lentulus in a boy with chronic granulomatous disease.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1813957}, pmid = {42311883}, issn = {2296-858X}, abstract = {Aspergillus lentulus is a slow-growing and drug-resistant fungus, which has been primarily reported in adults, usually immunocompromised ones, suffering from invasive pulmonary aspergillosis (IPA). This condition is rare in children. Here, we report a case of invasive pulmonary aspergillosis due to Aspergillus lentulus in a boy with no history of recurrent infections who presented with a prolonged fever of unknown origin. Based on chest CT scan findings showing typical halo signs, a fungal infection was strongly suspected. Empirical antifungal therapy was initiated at early admission but failed to resolve the persistent fever in this case. The causative pathogen was confirmed by blood metagenomic next-generation sequencing (mNGS). Subsequent genetic analysis identified a pathogenic mutation in the X-linked CYBB gene, confirming chronic granulomatous disease (CGD). Eventually, following a combination therapy of voriconazole and micafungin, the boy became afebrile and was discharged, pending hematopoietic stem cell transplantation (HSCT). To our knowledge, no previous cases of Aspergillus lentulus infection in children with CGD have been reported in the literature. This case underscores the critical importance of identifying the causative microorganism. It also highlights the value of emerging detection methods, such as mNGS. At present, there is no consensus for the optimal antifungal regimen against pediatric Aspergillus lentulus infections. Clinical improvement was achieved in this patient following combination therapy with voriconazole and micafungin, offering a practical therapeutic reference for managing this refractory fungal infection.}, } @article {pmid42312035, year = {2026}, author = {Radzieta, M and Malone, M and Schwarzer, S and Bergamin, E and Whitely, G and Jensen, S}, title = {Anaerobe-associated microbial shifts at infection onset in diabetes-related foot ulcers revealed by longitudinal metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1812721}, pmid = {42312035}, issn = {2235-2988}, mesh = {Humans ; *Diabetic Foot/microbiology ; *Metagenomics/methods ; *Bacteria, Anaerobic/classification/genetics/isolation & purification ; *Microbiota ; Longitudinal Studies ; Male ; Female ; Aged ; Middle Aged ; Metagenome ; }, abstract = {INTRODUCTION: Diabetes-related foot infections (DRFIs) are a major cause of hospitalisation and carry a significantly increased risk of lower extremity amputation. To date there is a lack of longitudinal studies examining within-patient microbiome dynamics during the transition from non-infected to infected diabetes-related foot ulcers (DRFUs).

METHODS: We used shotgun metagenomic sequencing to longitudinally profile the wound microbiome of 6 patients with DRFUs who developed clinical infections, utilising taxonomic profiling, metagenome assembly and binning and strain level analysis to characterise within-patient microbial shifts.

RESULTS: DRFUs with no signs of clinical infection were colonised by virulent pathogens including Staphylococcus aureus, Streptococcus agalactiae, Enterococcus faecalis, Enterobacter hormaechei and Pseudomonas aeruginosa. In most patients, infection onset was associated with a decrease in pathogen abundance and a significant increase in obligate anaerobes including Prevotella spp, Peptoniphilus spp, Porphyromonas spp and Anaerococcus spp.

CONCLUSION: These findings highlight the potential importance of anaerobes and hypoxia in DRFIs and may support monitoring of tissue oxygen saturation as a predictor of infection onset.}, } @article {pmid42312150, year = {2026}, author = {Sabogal-Rodriguez, D and Caro-Quintero, A}, title = {PopMAG: a Nextflow pipeline for population genetics analysis based on metagenome-assembled genomes.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag150}, pmid = {42312150}, issn = {2635-0041}, abstract = {MOTIVATION: Metagenome-assembled genomes (MAGs) are routinely recovered from metagenomic studies, yet the population genetic information embedded within these datasets remains largely underutilized. Analyzing within-species genetic variation can reveal adaptive evolution, selection pressures, and ecological dynamics that are hidden when MAGs are treated as homogeneous entities. Existing tools address individual analysis steps in isolation, requiring manual integration and creating barriers for researchers without extensive bioinformatics expertise.

RESULTS: Here we present PopMAG, a Nextflow pipeline and interactive Shiny application that automates population genetics analysis of MAGs. PopMAG integrates quality control, community profiling, competitive read mapping, functional annotation, and microdiversity estimation into a single reproducible workflow. The pipeline calculates key population genetics metrics including nucleotide diversity (π), p N / p S ratios, fixation index (F S T), Levins' index and SNVs counts with results consolidated into an interactive visualization platform for metadata-driven exploration. We demonstrate PopMAG's utility through analysis of longitudinal cystic fibrosis lung metagenomes, where we identify patterns consistent with antibiotic-driven selection in Pseudomonas aeruginosa efflux pump genes coinciding with treatment intervention.

PopMAG and corresponding documentation are publicly available at https://github.com/daasabogalro/PopMAG.}, } @article {pmid42312179, year = {2026}, author = {Chen, X and Xue, CX and Wang, J and Wang, S and Su, M and Liu, R and Zhu, XY and Liu, J and Yao, P and Fu, L and Yang, Z and Greening, C and Todd, JD and Zhang, XH}, title = {Metagenomic expansion of Joyebacterota identifies Cavimicrobium, a dominant sulfide-producing lineage in anoxic marine ecosystems.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag137}, pmid = {42312179}, issn = {2730-6151}, abstract = {Extreme anoxic environments are hotspots of sulfur cycling and harbor numerous novel uncharacterized microbial lineages. Although the phylum Joyebacterota was recently proposed, its internal phylogenetic architecture and evolutionary adaptations remain poorly understood. Here, we significantly expand the genomic diversity and metabolic framework of this phylum by integrating recovered metagenome-assembled genomes, and propose a novel genus, Cavimicrobium. Phylogenomic analysis placed Cavimicrobium as a distinct clade and further divided into four species-level subgroups associated with diverse anoxic sources, including sediments from the Salton Sea, the Eastern Gotland Basin, and the anoxic waters of the Sansha Yongle Blue Hole (SYBH). Unlike previous broad surveys, our study revealed that this lineage evolved from a facultatively anaerobic ancestor and underwent adaptive gene gain and loss through phylogenetic reconstruction. Genomic evidence suggested that this lineage harbored a previously overlooked anaerobic sulfite reduction (asrABC) pathway that likely mediating thiosulfate uptake and conversion to sulfite and sulfide. Notably, Cavimicrobium was particularly abundant in the anoxic waters of SYBH, comprising up to one-third of the bacterial community in particle-associated fraction below 100 m, where it is likely a major contributor to sulfide accumulation. Analysis of MAGs and global amplicon datasets revealed that Cavimicrobium is widespread across anoxic environments, comprising up to 0.32% of the bacterial community in 354 200 publicly available 16S rRNA gene amplicon samples. Together, these findings reveal a new lineage dominant in certain anoxic environments where they are likely important mediators of sulfur cycling, and broaden our understanding of biogeochemical potential of Joyebacterota.}, } @article {pmid42312182, year = {2026}, author = {Wang, Z and Zhu, Y and Liu, X and Li, Z and Bai, J and Zou, M and Zhang, C and Liu, Y and Li, F and He, K}, title = {iSymBase: an integrative functional-genomic platform for ecological exploration of insect symbionts.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag128}, pmid = {42312182}, issn = {2730-6151}, abstract = {Insect symbionts play essential roles in host biology, influencing nutrition, immunity, reproduction, and environmental adaptation, ultimately shaping insect physiology, ecology, and evolution. With the rapid growth of functional and genomic datasets on insect symbionts, there remains a critical need for a dedicated platform to systematically compile, organize, and analyze these datasets from an integrative ecological perspective. Here, we developed an insect Symbiont database, named as iSymBase, by manually curating functional records and genomic datasets of insect symbionts from published academic literature. Currently, iSymBase contains over 2657 insect symbiont functional records spanning 795 host species, along with 1494 metagenomes, 14 992 amplicon datasets, and standardized genome and gene catalogs, providing a comprehensive resource for ecological and comparative insect symbiont researches. iSymBase offers standardized query functionalities, such as data browsing, keyword associative search, sequence alignment, data download, and submission. Beyond conventional database functionalities, iSymBase provides several innovative tools: insect-symbiont interaction network for host-symbiont ecological relationships, a batch annotation tool for detecting ecologically functional symbionts from microbiome profiles, and an artificial intelligence (AI)-powered chatbot iSymSeek designed to assist researchers with related knowledge queries. Taken together, iSymBase will serve as an open-access and continually updated platform for storing, querying, and analyzing insect symbiont data, supporting ecological exploration of host-symbiont interactions, symbiont functional diversity, and microbiome-driven adaptation. Database URL: http://symbiont.insect-genome.com/.}, } @article {pmid42312183, year = {2026}, author = {Zheng, YL and Guo, YS and Ren, XY and Wang, YF and Cui, HL and Zhang, LM and Ding, LJ and Zhu, YG}, title = {Unveiling the role of soil microorganisms in indicating paddy soil health via metagenomics combined with machine learning.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag133}, pmid = {42312183}, issn = {2730-6151}, abstract = {The soil microbiome performs various ecological functions, making it a potentially vital component of soil health assessment; however, the indicator taxa of soil health remain unidentified. This study explored these taxa in paddy soils of the black soil region in Northeast China. First, the soil health index (SHI) was evaluated using representative physicochemical and biological parameters, revealing that approximately one-third of the soils had a low health level. A Random Forest model was then developed based on microbial species' relative abundance to predict the SHI, achieving an R [2] value greater than 0.6. Based on the SHapley Additive exPlanations values of this model, 40 microbial species were identified as potential indicator taxa of soil health, with 39 of these taxa occurring in more than 50% of the samples. Specifically, paddy soils with more abundant carbon (C)- and nitrogen (N)-fixing bacteria exhibited higher soil organic matter and total N contents, along with higher health levels. Conversely, soils rich in denitrifying bacteria exhibited lower SHI values because of increased N loss. Furthermore, C-fixing, N-fixing, and denitrifying genes showed functional relationships with the corresponding soil properties and SHI. In addition, halophilic, halotolerant, and eutrophic bacteria indicated soil health by reflecting salinity and nutrient status. The potential of these indicator taxa was validated at multidecadal and regional spatial scales. These results highlight the practical value of such indicator taxa, which elucidate the ecological processes associated with soil health and respond predictably to changes in soil health, thereby serving as rapid diagnostic tools for assessing soil health.}, } @article {pmid42312244, year = {2026}, author = {Heidrich, V and Fackelmann, G and Ricci, L and Spadazzi, R and Baldanzi, G and Punčochář, M and Catassi, G and Marchi, P and Modesto, M and Piccinno, G and Porcari, S and Rondinella, D and Asnicar, F and Valles-Colomer, M and Mattarelli, P and Ianiro, G and Segata, N}, title = {Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals.}, journal = {Cell press blue}, volume = {1}, number = {3}, pages = {None}, pmid = {42312244}, issn = {3051-3839}, abstract = {Interpersonal strain transmission shapes the human microbiome, yet a comparative understanding of the transmission dynamics across body sites is lacking. We analyzed 1,644 paired oral and fecal metagenomes to investigate microbiome transmission among healthy cohabitants and intra-individual oral-gut overlap. Cohabitants shared significantly more oral and gut strains than non-cohabitants. Romantic partners exhibited the highest oral strain-sharing rates, exceeding their gut strain sharing. Higher oral transmissibility was associated with increased longitudinal strain replacement, while the most transmissible gut species were linked to poorer cardiometabolic health. Within individuals, 74.5% of cases of species detected in both sites involved the same strains, primarily related to abundant oral species such as Streptococcus salivarius, suggesting saliva-mediated transmission. Conversely, Bifidobacterium longum strains never overlapped between sites, with the recently proposed B. longum subsp. nexti uniquely colonizing the oral cavity. These findings extend our understanding of microbiome spread and its potential consequences for human health.}, } @article {pmid42312840, year = {2026}, author = {Peterson, LF and Wang, J and Gow, NAR and LeibundGut-Landmann, S and Brewer, MG}, title = {Influence of fungi on epithelial homeostasis and role in inflammatory diseases.}, journal = {Clinical microbiology reviews}, volume = {}, number = {}, pages = {e0031925}, doi = {10.1128/cmr.00319-25}, pmid = {42312840}, issn = {1098-6618}, abstract = {SUMMARYThe skin harbors a diverse fungal community that contributes to both epidermal homeostasis and inflammatory disease. Historically, studies of cutaneous fungi focused primarily on opportunistic infections in immunocompromised hosts. Advances in sequencing technologies and metagenomic analyses have revealed that commensal yeasts of the skin microbiome likely influence host physiology and cutaneous disease severity. In this review, we summarize the current knowledge of host-fungal interactions at the skin epithelium, with particular emphasis on the yeast genera Malassezia and Candida. We discuss how fungal colonization shapes epidermal biology through direct interactions with keratinocytes and immune cells, highlighting fungal virulence factors such as secreted proteases and candidalysin, as well as host-sensing pathways. We further examine how these interactions contribute to inflammatory skin diseases, particularly atopic dermatitis and psoriasis, and how fungi participate in polymicrobial networks with bacteria and viruses to alter susceptibility to infection. Finally, we discuss how emerging therapeutic strategies change the fungal composition on skin. These advances suggest the importance of fungi as active regulators of skin immunity and emphasize key knowledge gaps that need to be addressed in future studies to better understand how they contribute to cutaneous diseases.}, } @article {pmid42312855, year = {2026}, author = {Lim, SJ and Thompson, LR and Goodwin, K}, title = {Metagenomic analysis of water column samples collected from Green Canyon 233 prior to the Deepwater Horizon incident.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0079926}, doi = {10.1128/aem.00799-26}, pmid = {42312855}, issn = {1098-5336}, abstract = {UNLABELLED: The Gulf of Mexico/Gulf of America provides ecosystem services derived from marine biodiversity and oil and gas resources. Threats posed by unintended releases of oil and gas can be attenuated by microbial processes, necessitating the documentation of baseline microbial diversity to better understand spill dynamics and to inform bioremediation strategies. Here, we analyze metagenomic sequencing of 10 water column samples collected from the Green Canyon 233 (GC233) lease block near the mussel-fringed brine lake, Brine Pool NR-1. Bioinformatics processing produced 60 bacterial metagenome-assembled genomes (MAGs), 11 archaeal MAGs, 149 microbial taxa predicted from assembled full-length small subunit (SSU) rRNA genes, and 389 microbial genera predicted from single-copy marker genes. Abundant taxa classified from these analyses included archaeal Nitrosopumilaceae, Nitrosopelagicus, and Thalassarchaeaceae and the bacterial taxa Pelagibacteraceae and SAR324. The MAGs revealed genes that degrade gaseous and non-gaseous hydrocarbons, including methane, other alkanes, and aromatic compounds. These samples were collected in 2009, fortuitously prior to the 2010 Deepwater Horizon (DWH) oil spill. Therefore, we searched for members of the rare biosphere that dominated the DWH plume during the early phase of microbial succession. Sequences related to Bermanella spp. were not detected initially. The search was expanded by mapping reads from ours and an additional 55 metagenomic libraries to two Bermanella MAGs. Read recruitment to Bermanella sp913054445 enriched in DWH plume samples was low (<1%) for our samples, those collected after the spill, and most experimental samples compared to samples collected outside (3%) and inside the DWH plume (19%-23%) during the spill.

IMPORTANCE: Microbes execute oil spill biodegradation through complex interactions involving whole microbiome communities by harnessing genes distributed across multiple taxa. Therefore, metagenomic data sets provide taxonomic and functional annotations to aid in understanding spill dynamics. Although the Deepwater Horizon oil spill provided opportunities to observe ecosystem recovery, data about the microbiome prior to the spill are scarce and limited to amplicon sequencing. Our metagenomic libraries, although not derived from the same lease block as the blowout, contribute linkages between microbial taxonomy and function in an area of active oil and gas production. This analysis can aid microbial indicator development, machine learning, and modeling efforts to bioremediate hydrocarbon influxes in marine environments.}, } @article {pmid42313157, year = {2026}, author = {Cardenas Alegria, OV and Torres, MC and Breyer, GM and Rebelatto, R and Wuaden, CR and Pastore, J and Lazzarotti, M and Ramos, RTJ and Dorn, M and Kich, JD and Siqueira, FM}, title = {Dynamics of Bacterial Communities and Resistomes Across Swine Waste Stabilization Ponds and Fertilized Soils.}, journal = {Current microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {42313157}, issn = {1432-0991}, mesh = {Animals ; Swine ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Soil Microbiology ; *Manure/microbiology ; *Drug Resistance, Bacterial/genetics ; *Ponds/microbiology ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; Fertilizers/analysis ; Soil/chemistry ; Metagenomics ; Genes, Bacterial ; *Microbiota ; }, abstract = {The environmental dissemination of antimicrobial resistance (AMR) through livestock waste represents a growing concern for human, environmental, and animal health. This study investigated how swine waste stabilization ponds (WSPs), and subsequent manure application to agricultural soils, influence bacterial community structure, antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs). Using shotgun metagenomics, we analyzed 80 samples from 20 swine farms, including waste collected before and after WSP treatment and soils with and without a history of manure application. Distinct microbial profiles were observed between waste and soil environments. Waste samples were dominated by Bacillota, Bacteroidota, and Pseudomonadota, whereas soils were enriched in Actinomycetota, particularly Streptomyces. WSP significantly reduced microbial diversity and caused shifts toward stress-tolerant taxa, indicating selective pressures during the process. Manure-fertilized soils exhibited altered community composition and enrichment of clinically relevant ARGs, including the fluoroquinolone resistance gene adeF. Waste management practices influenced resistome composition, with treated waste showing increased relative abundance of macrolide resistance genes (ermB and mefA). In soils, ARG profiles were associated with distinct MGE patterns, suggesting environment-specific mechanisms of gene mobility. Phage-associated elements were more prevalent in waste samples, whereas transposons were more prominent in soils, where ARG-MGE co-occurrence patterns indicated potential for horizontal gene transfer. Overall, our findings demonstrate that WSP management and soil application of swine manure shape both microbial communities and resistome configurations. These results underscore the importance of integrating waste treatment strategies into AMR surveillance frameworks and support a One Health approach to mitigate its dissemination in agroecosystems.}, } @article {pmid42313166, year = {2026}, author = {Taguchi, R and Ebihara, A and Tsunematsu, Y and Jeelani, G and Suzuki, R and Nozaki, T and Suenaga, K and Iwasaki, A}, title = {Discovery, Genome-Guided Structure Elucidation, and Total Synthesis of Terukufazoline A, a Macrocyclic Docosapeptide, from a Marine Cyanobacterium.}, journal = {Journal of the American Chemical Society}, volume = {}, number = {}, pages = {}, doi = {10.1021/jacs.6c06625}, pmid = {42313166}, issn = {1520-5126}, abstract = {The structure elucidation of large molecules remains a central challenge in natural products chemistry. This challenge has been addressed through spectroscopic methods as well as degradative and synthetic approaches, which have provided effective solutions. Recent advances in genome analysis have enabled an orthogonal approach to structure elucidation based on biosynthetic gene information. In this study, we report the structure elucidation of an unprecedentedly large cyanobactin, terukufazoline A (1), through integration of spectroscopic analysis, metagenome-guided biosynthetic information, chemical degradation, and total synthesis. Terukufazolines A (1) and B (2) were discovered from an undescribed marine cyanobacterium, and the intractable NMR and tandem MS data for 1 prompted us to incorporate biosynthetic gene information. Metagenomic analysis identified the cyanobactin biosynthetic gene cluster, whose core peptide sequence enabled the assignment of the amino acid sequence of 1. The absolute configuration was established by degradation-based analyses, and the proposed structures were verified by convergent total syntheses of 1 and 2.}, } @article {pmid42313402, year = {2026}, author = {Louine, M and Dandekar, R and Reddy, SP and Karalius, MC and Waldrop, G and Wang, S and Gakuru, J and Kimuda, S and Mugabi, T and Musubire, AK and Kagimu, E and Abassi, M and Kabahubya, M and Williams, DA and Phan, HV and Dai, B and Zia, M and Zorn, KC and Fouassier, C and Gerungan, C and Marra, PS and Skipper, CP and Bahr, NC and Langelier, CR and Creswell, FV and Boulware, DR and Meya, DB and Wilson, MR}, title = {Cerebrospinal fluid transcriptional immune pathways linked to survival in HIV-associated tuberculous meningitis.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag313}, pmid = {42313402}, issn = {1537-6613}, abstract = {BACKGROUND: TB meningitis (TBM) has up to 50% mortality in people living with HIV. We investigated differences in cerebrospinal fluid (CSF) host immune responses associated with short-term mortality.

METHODS: We enrolled a prospective cohort of adults with definite, probable and possible HIV-related TBM in Kampala, Uganda. Metagenomic next-generation sequencing (mNGS) of bulk CSF RNA was used to detect co-infecting or alternate CNS pathogens and refine cohort diagnosis. Host transcriptomic profiles from the refined cohort were then compared between 14-day survivors and non-survivors.

RESULTS: CSF mNGS reclassified or excluded 14% of participants based on pathogen detection, yielding 110 participants for transcriptomic analysis, of whom 23% (n=25) died within 14 days. More than 2000 genes were differentially expressed in the CSF based on 14-day mortality (adjusted p-value <0.05). Survivors upregulated T-cell receptor signaling (LCK, FYN, LAT), T-cell survival and differentiation (IL7, CD27, IL12RB1), B-cell receptor signaling (CD81, PLCG2, TNFRSF13C), cytotoxic lymphocyte and NK cell genes (KLRD1, ULBP1), TNF signaling, and class I MHC antigen processing pathways, while downregulating neutrophil chemoattractant CXCL1 and classical complement genes C4A and C4B. Unsupervised clustering identified a hypoinflammatory subgroup with significantly elevated mortality.

CONCLUSIONS: Short-term TBM survival was associated with upregulation of adaptive immunity - including T-cell, B-cell, NK cell, and cytotoxic lymphocyte signaling - alongside TNF signaling and IFN-γ-driven class I MHC antigen processing pathways, with concurrent restraint of complement and neutrophil pathways. This supports investigation of targeted immunomodulatory agents that preserve protective responses while selectively dampening injurious innate pathways, rather than broad immunosuppression with corticosteroids.}, } @article {pmid42313512, year = {2026}, author = {Han, M and Zhao, H and Lai, J and Zhao, S and Dong, B and Xi, H}, title = {Succession and Functional Adaptation of Bacterial and Fungal Communities in Biological Soil Crusts Responding to Uranium Stress.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70359}, doi = {10.1111/1462-2920.70359}, pmid = {42313512}, issn = {1462-2920}, support = {22106182//National Natural Science Foundation of China/ ; 2022YFC3702500//National Key Research and Development Program of China/ ; SKLNBC2023-03//State Key Laboratory of NBC Protection for Civilian/ ; }, mesh = {*Uranium/metabolism ; *Soil Microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Fungi/metabolism/classification/genetics ; Adaptation, Physiological ; Biodegradation, Environmental ; *Soil Pollutants, Radioactive/metabolism ; *Microbiota ; Stress, Physiological ; }, abstract = {Uranium (U) mining causes severe radioactive contamination threatening ecosystems. Biological soil crusts (BSCs), as pioneer communities in degraded habitats, show strong heavy metal accumulation potential, yet their adaptive mechanisms under U stress remain unclear. In this study, BSCs from a uranium tailings dam in Hunan Province were exposed to simulated U stress. Results showed that BSCs exhibited exceptionally high U accumulation capacity (up to 4131 mg/kg), and effectively immobilised U by converting it into residual and organic-bound fractions (collectively > 70%) via carboxyl complexation and microbial mineralisation, thus significantly reducing environmental mobility. U stress caused damage to the photosynthetic and antioxidant systems of the BSCs. Microbial community complexity decreased, with tolerant taxa including Proteobacteria and Bacilli significantly enriched. Metagenomics revealed distinct cross-kingdom functional adaptation strategies: bacteria upregulated energy metabolism and acetaldehyde metabolism to facilitate efflux detoxification, while fungi strengthened lipid homeostasis and antioxidant metabolism. Several U-tolerant strains (Bacillus, Aspergillus and Penicillium) closely associated with U immobilisation were further isolated and verified. This study systematically reveals the synergistic tolerance mechanisms of BSCs under U stress and provides key microbial resources and theoretical support for the in situ bioremediation of U-contaminated sites.}, } @article {pmid42313858, year = {2026}, author = {Meijer, S and Hugerth, LW and Nouri, M and Erlandsson, L and Lavasani, S and Hansson, SR}, title = {Comparative analysis of gut microbiome alterations in early- and late-onset preeclampsia: A case control study.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0348943}, pmid = {42313858}, issn = {1932-6203}, mesh = {Humans ; Female ; Pregnancy ; *Pre-Eclampsia/microbiology ; Case-Control Studies ; *Gastrointestinal Microbiome ; Adult ; Dysbiosis/microbiology ; Metagenomics ; Bacteria/classification/genetics ; }, abstract = {Preeclampsia (PE) is a complication during pregnancy characterized by hypertension, organ damage, and systemic inflammation. Increasing evidence suggests that the gut microbiome may play a role in the pathophysiology of PE. However, previous studies on the gut microbiome have generally overlooked the distinction between subgroups of PE, although clinical manifestations may differ. Also, most studies have not used deep sequencing techniques. Therefore, this study aimed to explore further potential differences in gut dysbiosis in different PE subgroups compared to controls using shotgun metagenomics. We studied the bacterial gut microbiome using shotgun metagenomic sequencing in 37 pregnant patients in the third trimester from a Swedish cohort, separating patients according to subtype (healthy controls N = 21, late-onset PE N = 8, early-onset PE N = 8). Differential relative abundances and alpha diversity were evaluated using Wilcoxon rank sum test, and beta diversity was evaluated using PERMANOVA. Multiple linear regression was used to study associations between gut microbiome composition differences and clinical parameters. Late-onset PE and early-onset PE were both associated with significantly different beta diversity compared to controls. Differences remained significant after adjusting for age, and were not affected by gestational age, BMI or parity. Alpha diversity was lower in late-onset PE compared to controls. While no significant differences in taxonomic abundances were seen after correcting for multiple testing, several interesting leads were identified, including a higher abundance of genus Blautia in late-onset PE, and lower abundance of Coprococcus catus and unclassified Lachnospiraceae in early-onset PE. Functional analysis did not reveal any significant differences after false discovery rate (FDR) correction. In conclusion, our results showed subgroup-specific gut microbiome differences in PE with more pronounced associations in late-onset PE, despite limited power due to the observational design and small cohort. Accordingly, our results highlight the importance of subgroup analysis when studying PE.}, } @article {pmid42314068, year = {2026}, author = {Lytras, S and Ghafari, M and Grove, J}, title = {Studying the Deep Evolution of Viruses in the Era of Artificial Intelligence Structure Prediction.}, journal = {Annual review of virology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-virology-100424-122154}, pmid = {42314068}, issn = {2327-0578}, abstract = {High mutation rates erode viral sequence similarity, obscuring deep evolutionary history. While protein structure is far more conserved than sequence, its use in evolutionary studies has historically been bottlenecked by experimental determination. The recent revolution in artificial intelligence (AI) structure prediction has fundamentally changed this, enabling the rapid generation of millions of viral protein structures. This review examines the effect of AI-based protein structure prediction methods on our understanding of deep viral evolution. We describe the strengths and limitations of protein structure prediction and consider the questions it can be used to address: illuminating viral dark matter in metagenomic datasets, resolving high-level taxonomy for orphan lineages, and inferring function for divergent proteins. Furthermore, we assess the emerging field of structural phylogenetics, exploring the theoretical and practical challenges of integrating structure and sequence to reconstruct ancient evolutionary events. We conclude that despite remaining challenges, systematic structure prediction will extend our exploration of deep evolution across the virosphere.}, } @article {pmid42314322, year = {2026}, author = {Zhang, P and Zhu, Y and Wang, Z and Yu, P and Xue, B and Wang, L and Hu, R and Zou, H and Jiang, Y and Xiao, J and Tan, C and Wu, F and Peng, Q}, title = {Initial exploration of the health effects on Qinghai-Tibetan Plateau yaks following short-term exposure to polystyrene microplastics: Analysis of rumen microbiota, host metabolism, antioxidant function and inflammatory responses.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142707}, doi = {10.1016/j.jhazmat.2026.142707}, pmid = {42314322}, issn = {1873-3336}, abstract = {Microplastics (MPs) are ubiquitous across environments including the Qinghai-Tibet Plateau. Most existing MPs studies focus on aquatic animals and rodents, while MPs influences on yaks (Bos grunniens) remain poorly understood. Using yaks as animal models, we combined metagenomics and metabolomics to explore short-term polystyrene-MPs (PS-MPs) impacts on ruminal microbiota, metabolism, antioxidant capacity and inflammation. Seven-day PS-MPs exposure reshaped rumen microbiota and elevated β-diversity. Four KEGG pathways (peptidoglycan synthesis, vitamin B6/riboflavin metabolism, terpenoid backbone biosynthesis) were enriched alongside altered extracellular polysaccharides composition. Serum metabolomics revealed elevated L-glutamine and indole-3-propionic acid, coupled with reduced 2-C-methyl-D-erythritol 2,4-cyclodiphosphate and indole-3-lactic acid post-exposure. Urinary metabolomics revealed decreased D-erythrose 4-phosphate, dimethyl allyl pyrophosphate, and 2-C-methyl-D-erythritol 2,4-cyclodiphosphate, collectively indicating inhibited terpenoid backbone biosynthesis in yaks. Additionally, PS-MPs triggered inflammatory responses, evidenced by elevated levels of pro-inflammatory cytokines (interferon-γ, interleukin-1β, interleukin-6, interleukin-17, interleukin-22, tumor necrosis factor-α, transforming growth factor-α), yet antioxidant function indexes (total antioxidant capacity, superoxide dismutase, glutathione peroxidase, catalase and malondialdehyde) showed no significant changes. Multi-omics suggested Prevotella ruminicola may help resist PS-MPs invasion. In summary, rumen microbes may alleviate PS-MPs adverse effects, explaining yaks' mild responses to short-term PS-MPs exposure. Long-term MPs effects, tissue deposition and related molecular mechanisms warrant further study.}, } @article {pmid42315104, year = {2026}, author = {Itoh, H and Mise, K and Kuniyasu, M and Wasai-Hara, S and Ushijima, N}, title = {Isolation and global occurrence of nitrogen-fixing Acidobacteriota in soil environments.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag157}, pmid = {42315104}, issn = {1751-7370}, abstract = {Acidobacteriota, one of the most abundant and ubiquitous bacterial phyla in soils, are well recognized for their role in carbon cycling. In contrast, their roles in soil nitrogen cycling remain largely unexplored, although recent metagenome-assembled genome (MAG) analyses suggest that Acidobacteriota may harbor genes involved in nitrogen cycling. Here, we provide culture-based evidence of diazotrophy within this phylum and demonstrate the widespread occurrence of nitrogen-fixing Acidobacteriota across diverse soil types. From grassland and agricultural soils, we isolated five Acidobacteriota strains representing novel taxonomic lineages, four of which harbor functional nitrogenase (nif) gene clusters. These strains were capable of fixing atmospheric nitrogen in vitro and/or in soil microcosms, as evidenced by acetylene reduction, N2-dependent growth, transcription of nif genes, incorporation of 15N into biomass and soil, and inhibition of nitrogenase activity by ammonium. Furthermore, global-scale meta-analysis of soil metagenomes revealed that nif-harboring Acidobacteriota are widely distributed and locally dominant across soil types. These results demonstrate the nitrogen-fixing capability of Acidobacteriota at the organismal level, complementing MAG-based inferences, and underscore their adaptive capacity in nitrogen-limited environments and their potential contribution to terrestrial nitrogen fixation. We also propose novel taxa within the class Terriglobia of the phylum Acidobacteriota, including diazotrophic strains, comprising one novel family, three novel genera, and four novel species: Koromonadaceae fam. nov., Koromonas soli gen. nov., sp. nov., Koromonas humicola sp. nov., Oryzophilus luti gen. nov., sp. nov., and Humiphilus diazotrophicus gen. nov., sp. nov.}, } @article {pmid42315187, year = {2026}, author = {Benga, L and Rehm, A and Gougoula, C and Bischoff, S and Janssen, S}, title = {Is the Microbial Status an Extrinsic, Intrinsic, or Intermediate Influence on Experimental Animals?.}, journal = {Journal of the American Association for Laboratory Animal Science : JAALAS}, volume = {}, number = {}, pages = {1-4}, doi = {10.30802/AALAS-JAALAS-26-036}, pmid = {42315187}, issn = {2769-6677}, abstract = {Living entities, inlcuding laboratory animals, are composed of the host and its associated microbial communities and defined as holobionts. The host genotype and its microbiome drive together as a metagenome, the holobiont phenotype, with the microbiome itself as a well-recognized source of phenotypic variation. Multiple environmental (diet, light/dark cycles, etc.) as well as host-related factors (genotype, maternal effect, etc.) not only influence the animal experimental phenotype but also contribute to the shaping of the microbiome, raising the question of whether the microbiome of experimental animals represents an extrinsic, intrinsic, or intermediate influence. Currently, there is sufficient evidence that microbial communities at different body sites are shaped by distinct endogenous and exogenous factors, indicating that the host does not leave its microbial status to chance but instead actively modulates it through host-specific mechanisms, despite extrinsic influences. This leads to a microbiome that reflects a 'fingerprint' of its own endogenous and exogenous influences. This suggests that the microbiome of experimental animals is an intermediate factor with both intrinsic and extrinsic components and underscores the importance of refining the selection of the appropriate metagenome for each specific rodent experiment.}, } @article {pmid42315257, year = {2026}, author = {Cramer, C and Marshall, IPG and Abramson, MJ and Jõgi, NO and Khomich, M and Peddada, SD and Skottvoll, BS and Schlünssen, V and Bertelsen, RJ}, title = {Role of oral bacteria composition and functional gene profiles in respiratory diseases.}, journal = {BMJ open respiratory research}, volume = {13}, number = {1}, pages = {}, doi = {10.1136/bmjresp-2025-003938}, pmid = {42315257}, issn = {2052-4439}, mesh = {Humans ; Female ; Male ; *Microbiota/genetics ; Cross-Sectional Studies ; *Asthma/microbiology ; *Mouth/microbiology ; Adult ; Middle Aged ; *Rhinosinusitis/microbiology ; Norway/epidemiology ; Australia/epidemiology ; Estonia/epidemiology ; Nitric Oxide ; Fractional Exhaled Nitric Oxide Testing ; *Bacteria/isolation & purification/genetics ; Chronic Disease ; Spirometry ; }, abstract = {INTRODUCTION: The oral microbiome has been shown to be associated with respiratory health, primarily in adult case studies or among children. This relationship has been scarcely investigated in adult population-based cohorts.

OBJECTIVES: To investigate the association between oral microbiome and respiratory health, more specifically asthma, chronic rhinosinusitis (CRS), lung function and fractional exhaled nitric oxide (FeNO) in a population-based cross-continental multicentre study among adults.

METHODS: Subgingival samples from 355 adult European Community Respiratory Health Survey participants from Norway, Australia and Estonia underwent metagenomic sequencing. Respiratory disease was defined from questionnaires and sensitisation from specific immunoglobulin E (IgE)/skin prick tests. Spirometry and FeNO were measured. The associations between alpha diversity and disease status were evaluated in cross-sectional analyses using logistic regression adjusting for sex, smoking and study centre. Differential abundance analyses were performed using analysis of compositions of microbiomes with bias correction.

RESULTS: Alpha diversity differed by study centre and sensitisation status and was associated with non-allergic CRS (richness: 1.12, 95% CI 1.03 to 1.22). A similar though not statistically significant pattern was seen for forced vital capacity (FVC) below the lower limit of normal (LLN). Lachnospiraceae and Xanthomonas were more abundant in the oral microbiome of non-asthmatics and individuals without CRS, respectively, as compared with asthmatics and CRS patients. Several functional genes (1477-3391) and genera (54-98) were only present in the non-case groups, whereas individuals with affected respiratory health had 0-74 unique functional genes, but no unique genera present only in their respective groups.

CONCLUSION: Increased alpha diversity was associated with non-allergic CRS and a similar trend was seen for FVC below LLN. Bacterial composition and functional profiles of the oral microbiome differed by respiratory health status. This study is novel in exploring functional gene profiling in relation to asthma and FeNO.}, } @article {pmid42315409, year = {2026}, author = {Urvoy, M and Baumgart, L and Howard-Varona, C and Sullivan, MB}, title = {Beyond AMGs: Phage-encoded transcription and sigma factors as understudied virocell reprogramming tools.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.05.019}, pmid = {42315409}, issn = {1878-4380}, abstract = {Phages, the most abundant biological entities on Earth, infect bacteria and reprogram them into 'virocells' with altered physiology and ecology. While metagenomic studies have largely inferred reprogramming through virus-encoded auxiliary metabolic genes (AMGs), phages can reprogram cells through many other tools. In this review, we explore how phage-encoded, host-acting transcription and sigma factors (TSFs) reshape host transcriptional networks beyond simply regulating phage replication. We synthesize emerging genomic evidence for TSF prevalence in phages, mechanistic insights into how host-acting TSFs might influence ecologically relevant cellular functions, and highlight recent experimental and bioinformatic advances that make TSFs particularly tractable for large-scale bioinformatic studies. Together, we position TSFs as AMG-complementary mechanisms of viral reprogramming, tractable for metagenomic inferences, with potential cellular- and ecosystem-level consequences that can power translational applications.}, } @article {pmid42315843, year = {2026}, author = {Hounmanou, YMG and Gussin, GM and Conlan, S and Singh, RD and Deming, C and Proctor, DM and Teixeira, M and Earl, AM and Worby, CJ and Kong, HH and Huang, SS and Segre, JA}, title = {Strain sharing and persistence of microbial pathogens colonizing the skin of residents in a regional nursing home network.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74611-x}, pmid = {42315843}, issn = {2041-1723}, support = {ZIA-HG200382-14//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; }, abstract = {Antimicrobial resistance (AMR) is a health threat disproportionately affecting nursing home (NH) residents. Surveillance and infection control in NHs are restricted to nares or perirectal cultures, overlooking skin colonization and multidrug-resistant organisms (MDROs) not recovered by selective media. Here, within the PROTECT trial NCT03118232, we show, that NH residents' skin serves as a reservoir of transmissible MDROs. We analyzed 207 groin and axilla swabs from 38 residents across 15 California NHs using metagenomics, culturing, and genome sequencing. Culture detected MDROs in 10 of 38 residents (26.3%), including 4 (10.5%) with ESBL-producing Escherichia coli sequence type (ST)131/ST648 and 7 (18.4%) with methicillin-resistant Staphylococcus aureus. Skin microbiome analysis by metagenome-assembled genomes identified broader MDRO colonization, including 27 (71.1%) with E. coli ST93, 14 (36.8%) with Staphylococcus epidermidis ST2, 16 (42.1%) with Proteus mirabilis, 7 (18.4%) with Providencia stuartii, 7 (18.4%) with Enterococcus faecalis, and 5 (13.2%) with Pseudomonas aeruginosa. Colonization persisted after bathing. Clonal E. coli ST93 was shared by 27 residents across 9 facilities, and 5 resident pairs carried clonally related strains of ≥2 MDRO species, suggesting polymicrobial transmission. We confirmed skin as a reservoir of MDROs, utilizing metagenomics to detect colonization and transmission pathways, supporting AMR surveillance in long-term care.}, } @article {pmid42315898, year = {2026}, author = {Mishra, S and Mutnuri, S}, title = {Exploring biohydrogen producing potential of Arctic ice and water through metagenomics and dark fermentation kinetics.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-57926-z}, pmid = {42315898}, issn = {2045-2322}, abstract = {Cryospheric ecosystems in the high Arctic harbor largely unexplored microbiomes with significant biotechnological potential. The present study evaluates the biohydrogen production capabilities of the indigenous microbiome of Ny-Ålesund, Svalbard, using glacial ice and surface water samples. Dark fermentation batch assays were performed at 4 °C and 20 °C with 2-bromoethanesulfonate (BES), a methanogenic inhibitor, to track the succession of metabolic and taxonomic diversity. Metagenomic and functional analyses revealed that under 20 °C and BES conditions, psychrotolerant microbial communities maximize biohydrogen production to 85% of the total biogas produced, with an acetate-dominant fermentation pathway, as inferred from volatile fatty acid (VFA) analysis. This evolves into a highly coordinated system utilizing a coupled Rnf-nitrogenase route alongside Formate Hydrogenlyase and [FeFe]-hydrogenase pathways. Kinetic modelling using the Modified Gompertz equation, along with Q10 temperature-sensitivity indices, demonstrated a very high latent catalytic potential in these cold-adapted microbiomes. This study indicates that Arctic microbiomes are highly elastic thermodynamically and could serve as highly efficient, manipulatable biocatalysts for the environmental recovery of bioenergy through engineered low-temperature systems.}, } @article {pmid42316154, year = {2026}, author = {Seo, E and Kim, SH and Kwak, MJ and Hwang, JK and Mustafa, G and Chang, YS and Hoh, JK and Jeon, BH and Park, HK and Kim, Y}, title = {Gut dysbiosis associated with neonatal respiratory distress syndrome and biological plausibility of disease-specific probiotic intervention: a translational study.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08462-x}, pmid = {42316154}, issn = {1479-5876}, support = {202400000002957//College of Medicine, Hanyang University/ ; RS-2023-00255939//Korea Institute of Energy Technology Evaluation and Planning/ ; NSIT; RS-2025-16068814//National Research Foundation of Korea/ ; }, abstract = {BACKGROUND: Neonatal respiratory distress syndrome (RDS) is among the most prevalent morbidities in late preterm and term infants. Although the gut-lung axis has been implicated in neonatal respiratory disease, the relationship between RDS and early gut microbiome composition remains poorly characterized. This study aimed to characterize gut microbiome alterations associated with RDS and surfactant replacement therapy (SRT), and to evaluate the biological plausibility of a disease-specific probiotic intervention.

METHODS: Two complementary cohorts were prospectively enrolled. In the clinical observational cohort (n = 45), fecal samples collected within 48 h of birth were analyzed by Nanopore 16S rRNA sequencing across three groups: infants without RDS (control group, n = 25), infants with RDS who did not receive SRT (RDS(S-) group, n = 7), and infants with RDS who received SRT (RDS(S+) group, n = 13). In the probiotic discovery cohort (n = 40), gut microbiota of infants without RDS (CON group, n = 17) and infants with RDS (RDS group, n = 23) were characterized by metagenomic sequencing and culturomics. Candidate probiotic strains were evaluated in a fermenter for intestinal microbiota model (FIMM) and a fecal microbiota transplantation (FMT) mouse model.

RESULTS: The RDS(S-) group exhibited depletion of beneficial taxa including Bifidobacterium and Lacticaseibacillus and enrichment of opportunistic pathogens including Enterococcus and Staphylococcus. Following SRT, gut microbial profiles partially shifted toward those of the control group. Limosilactobacillus fermentum SLAM_LAF05 and Bifidobacterium longum SLAM_BIL02 were identified as CON-enriched candidate probiotic strains through direct microbiome comparison and selected based on superior acid and bile tolerance and adhesion capacity. In the FIMM model, probiotic supplementation increased microbial diversity and suppressed opportunistic pathogens. In the FMT mouse model, probiotic supplementation was associated with upregulation of ZO-1, MUC2, and Reg3g, reduction of fecal calprotectin, and restoration of serum IgG levels.

CONCLUSIONS: This study provides an early translational characterization of RDS-associated gut dysbiosis and its partial resolution following SRT, and establishes proof-of-concept for a disease-specific probiotic approach. These findings offer a new perspective on the interplay between gut microbial dynamics and the early postnatal respiratory course, and provide a basis for future investigations into microbiota-targeted strategies in neonates with RDS.}, } @article {pmid42316249, year = {2026}, author = {Li, R and He, X and Chen, Z and Shao, J and Feng, J and Wan, L and Zhang, M and Yang, J and Tong, Y and Dong, B and Huang, C and Qiu, H and Cai, Y and Niu, J and Xu, X and Song, X and Ma, J and Ge, H and Zhou, K}, title = {Microbial DNA analysis of paired blood-bronchoalveolar lavage fluid in post-HSCT patients with pneumonia implying application conditions of blood as a surrogate in pathogen detection.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03779-z}, pmid = {42316249}, issn = {1465-993X}, support = {82341114//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Blood testing aids pneumonia diagnosis, but its effectiveness varies. Given the invasiveness of bronchoalveolar lavage fluid (BALF) sampling versus blood testing's simplicity, this study investigates when blood can reliably substitute for BALF in detecting microbial presence, especially for pathogens.

RESULTS: Metagenomic sequencing was performed on paired BALF-blood samples from 21 post-HSCT immunocompromised (ICP) and 21 immunocompetent (ICT) patients. The ICP cohort was expanded to 62 for biomarker validation. Host responses were profiled via metatranscriptomics (30 BALF samples). Microbial alpha and beta diversity differed significantly between blood and BALF in ICP, but not ICT, patients. ICP patients' BALF contained a greater diversity and abundance of microbes. A higher proportion of microbial DNA sequences in ICP patients' blood was also present in their BALF, suggesting a potentially more permeable alveolar-capillary barrier. Related genes (e.g., NABA CORE MATRISOME, extracellular matrix organization, cell-cell adhesion) were downregulated. Upregulated pathways like VEGFA-VEGFR2 signaling and Rho GTPases suggested increased vascular permeability. In ICP patients, 419 microbial sequences in blood indicated their presence in the lower respiratory tract with > 70% certainty.

CONCLUSION: Host immune status significantly influences blood-BALF microbial diversity differences. Shared blood-BALF microbial DNA sequences show potential for aiding pneumonia pathogen diagnosis, offering a novel biomarker identification approach.}, } @article {pmid42316284, year = {2026}, author = {Wang, X and Cheng, L and Yin, K and Wang, B and Yan, X and Chen, S}, title = {Chronic proton pump inhibitor exposure aggravates intestinal injury by impairing intestinal stem cell self-renewal through the microbiota-7-ketolithocholic acid Axis.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08448-9}, pmid = {42316284}, issn = {1479-5876}, abstract = {BACKGROUND: Long-term proton pump inhibitor (PPI) use is associated with increased intestinal disease risk, but its damaging mechanisms remain unclear.

METHODS: Mice were administered rabeprazole (Rab) for 4 weeks before dextran sulfate sodium (DSS) or ionizing radiation (IR) injury. We employed RNA sequencing, metabolomics, and metagenomics, evaluated intestinal stem cell (ISC) function, and used organoids for validation.

RESULTS: Long-term Rab induced small intestinal mucosal injury and exacerbated DSS/IR-induced damage, manifesting as crypt/villus atrophy and reduced ISC numbers. Mechanistically, Rab downregulated the Wnt pathway and impaired mucosal defense and regeneration. Microbiota involvement was indicated by fecal transplantation. Integrated metagenomic and metabolomic analyses revealed that Rab induced intestinal dysbiosis and reduced ileal bile acids, particularly 7-ketolithocholic acid (7KLCA) and chenodeoxycholic acid (CDCA). Faecalibaculum rodentium supplementation restored ISC self-renewal by converting CDCA to 7KLCA. In vitro, 7KLCA activated Wnt signaling to rescue Rab-induced stem cell impairment. In vivo, both 7KLCA and Gly-β-MCA (intestinal FXR antagonists) suppressed the FXR-FGF15 axis, restored the expression of hepatic bile acid synthesis enzymes, and promoted epithelial repair, thereby mitigating DSS-induced injury.

CONCLUSIONS: Chronic PPI use impairs ISC self-renewal by disrupting the microbiota-7KLCA-Wnt axis. F. rodentium or 7KLCA supplementation ameliorates PPI-induced effects, highlighting a microbe-metabolite axis as a pivotal mechanism and potential therapies for PPI-associated intestinal damage.}, } @article {pmid42316350, year = {2026}, author = {Zhao, J and Su, Q and Wang, S and Li, Q and Chen, L and Kang, X and Xu, Q and Liu, C and Zhao, H}, title = {Differentiating hemorrhagic shock and organophosphate poisoning through integrated skin microbiome-metabolome signatures.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05276-1}, pmid = {42316350}, issn = {1471-2180}, support = {2024B04J0022//Guangzhou Science and technology planning project/ ; 82371901//National Natural Science Foundation of China/ ; 2023JC36//Grant-in Aids for Scientific Research from Ministry of Public Security of the People's Republic of China/ ; }, abstract = {Accurate determination of cause of death and estimation of postmortem interval (PMI) are critical yet challenging tasks in forensic science, particularly in cases with rapid demise and absence of obvious morphological abnormalities. We employed an integrative multi-omics approach to characterize postmortem microbial succession and metabolic alterations on facial skin in mouse models of hemorrhagic shock (HS) and organophosphorus poisoning (OP) across three decomposition stages: bloating (2 days), active decay (8 days), and advanced decay (16 days). Metagenomic profiling revealed significantly reduced α-diversity in HS compared with OP throughout all stages (p < 0.001), accompanied by stage-dependent compositional shifts, including early enrichment of Firmicutes in HS and Proteobacteria in OP. A total of 237 differential taxa were identified, with Providencia and Morganella predominating in OP, whereas Staphylococcus and Corynebacterium dominated bloating stage of HS. Untargeted metabolomics uncovered distinct cause-of-death-linked metabolites, notably elevated 2'-deoxycytidine-5'-diphosphate in early OP and persistent cholic acid/cholate accumulation in HS at later PMI. Functional analysis highlighted histidine and phosphate/phosphonate metabolism as key discriminatory pathways, exhibiting stage-specific oscillations and strong correlations with characteristic taxa. These findings demonstrate that skin-based metagenomic-metabolomic integration provides robust, mechanistically informed biomarkers for both PMI estimation and cause-of-death differentiation, offering a minimally invasive and temporally dynamic tool for forensic investigations.}, } @article {pmid42316926, year = {2026}, author = {Goldsworthy, A and Olsen, M and Obonyo, NG and Jones, P and McKirdy, S and Senok, A and Alghafri, R and Ghemrawi, R and Almheiri, R and Tronstad, O and Suen, JY and Fraser, JF and Tajouri, L}, title = {Hospital-Associated Antimicrobial Resistant Bacteria on 95 Mobile Phones: An International Metagenomic "Phonome" Analysis.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70321}, pmid = {42316926}, issn = {2045-8827}, mesh = {*Bacteria/genetics/drug effects/isolation & purification/classification/pathogenicity ; Metagenomics ; *Cell Phone ; *Drug Resistance, Bacterial/genetics ; Humans ; *Cross Infection/microbiology/epidemiology ; Bacteriophages/genetics/isolation & purification ; *Fomites/microbiology ; Anti-Bacterial Agents/pharmacology ; Hospitals ; High-Throughput Nucleotide Sequencing ; Virulence Factors/genetics ; }, abstract = {Antimicrobial resistant healthcare-associated infections present an increasing threat to public safety and the sustainability of healthcare systems around the world. Mobile phones have been highlighted as a fomite that negates hand hygiene and contributes to the dissemination of pathogenic microorganisms in healthcare settings. The objective of the current stidy was to investigate the presence of bacteria, antimicrobial resistance and virulence genes associated with high morbidity on 95 mobile phones within healthcare settings. Next-Generation Metagenomic Sequencing was undertaken and FastQ files were subsequently analyzed within COSMOSid to enable taxonomic identification. Antibiotic resistant genes, virulence genes and bacteriophages were co-located with bacteria associated with the highest global mortality. Antibiotic resistant genes were manually annotated and cross referenced with the Comprehensive Antibiotic Resistance Database (CARD) to identify gene-drug interactions. On average, mobile phones were identified to be contaminated with 3.62 of the top 10 highest mortality-causing bacteria and 2.49 ESKAPE pathogens. A total of 262 unique ARGs, 448 unique VFGs, and 314 bacteriophages were identified. Mobile phones within healthcare settings harbor pathogens alongside genes associated with increased virulence and antimicrobial resistance. Additionally, mobile phones, known to be infrequently sanitized, may increase antimicrobial resistance by providing a contaminated platform which facilitates continued horizontal genetic transfer.}, } @article {pmid42316995, year = {2026}, author = {Gu, Y and Li, L and Zhang, H and Ye, T and Zhu, Q and Zhao, X and Xie, K and Ge, R and Han, J and Qin, Y}, title = {Dietary purple sweet potato anthocyanin extracts attenuate intestinal barrier decline in naturally aged mice via the microbiota-autophagy-stem cell axis.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo00039h}, pmid = {42316995}, issn = {2042-650X}, abstract = {Age-related deterioration of the intestinal epithelial barrier exacerbates systemic metabolic and functional decline, highlighting the gut as a key target for dietary interventions in healthy aging. Here, using naturally aged mice and intestinal organoids, we demonstrate that supplementation with purple sweet potato anthocyanins (PSPAs) alleviates systemic aging phenotypes, including impaired motor coordination, hepatic lipid dysregulation, insulin resistance, and cellular senescence, while concurrently restoring intestinal barrier integrity. PSPAs enhanced tight junction protein expression and epithelial architecture, independently of inflammation resolution, and promoted the proliferative and differentiation capacity of intestinal stem cells (ISCs). Metagenomic profiling revealed that PSPAs remodeled aging-associated gut microbiota composition and functions. Fecal microbiota transplantation established the causal contribution of microbiota remodeling to ISC rejuvenation, while luminal content-organoid assays confirmed the role of microbial metabolites. Integrative metabolomics identified metabolic changes linked to autophagy-related processes, including altered SCFA profiles, while transcriptomic analysis highlighted PI3K-AKT signaling as a major pathway associated with microbial and metabolic remodeling. Collectively, this multi-omics study establishes a mechanistic framework in which PSPAs alleviate aging-associated barrier decline through a "microbiota-autophagy-stem cell" axis, providing important insights into polyphenol-based strategies for gut-centered healthy aging.}, } @article {pmid42317351, year = {2026}, author = {Lou, Y and Ma, D and Gan, Q and Xu, X and Xiao, Y and Wang, J and Li, Z and Zhang, T and Qi, L and Feng, S}, title = {Inflammatory protein mediators linking gut microbiota to degenerative lumbar spine disorders: cross-disease genetic evidence.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1855966}, pmid = {42317351}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Intervertebral Disc Degeneration/genetics/microbiology/immunology/metabolism ; Humans ; *Lumbar Vertebrae/pathology ; Rats ; Mendelian Randomization Analysis ; *Inflammation Mediators/metabolism ; *Spondylolisthesis/genetics/microbiology ; Biomarkers ; *Spinal Stenosis/genetics/microbiology ; Disease Models, Animal ; }, abstract = {BACKGROUND: Degenerative lumbar spine disorders (DLSD), including intervertebral disc disorders (IDD), degenerative spondylolisthesis, and lumbar spinal stenosis (LSS), are major contributors to low back pain and disability. Associations among gut microbiota (GM), inflammatory proteins, and DLSD have been demonstrated in prior studies. Yet, two key questions persist: whether specific circulating inflammatory proteins (IPs) mediate this association, and whether such mediation is shared across different diseases.

METHODS: We performed two-sample Mendelian randomization (MR) to evaluate causal associations among 473 GM taxa, 91 circulating IPs, and three DLSD outcomes using FinnGen R12 summary statistics. Causal estimates were obtained using inverse-variance weighted MR with complementary sensitivity analyses, pleiotropy and heterogeneity testing, and bidirectional MR. Two-step MR mediation was applied to quantify indirect effects of GM through IPs. Experimental validation was performed using rat models, with qPCR and ELISA assessing inflammatory markers in lumbar tissues and metagenomic sequencing evaluating gut microbiota profiles.

RESULTS: Genetically predicted GM taxa were associated with LSS (28 taxa), spondylolisthesis (20 taxa), and IDD (41 taxa). IP MR identified risk-increasing associations for LSS (4E-BP1 and interleukin-4), spondylolisthesis (CXCL1, CXCL5, FGF-5, IL-15RA, and IL-4) and IDD (IL-20RA and IL-6), while IL-18 showed a protective association with IDD that remained robust after multiple-testing correction. Mediation analyses identified 13 genetically supported putative GM-IPs-DLSD pathways, highlighting convergent mediators including PD-L1 for spondylolisthesis and IL-6 and IL-18 for IDD, with mediation proportions ranging from 7.55% to 13.22% across key pathways. Experimental results showed inflammatory activation and gut microbiota alterations in disease models, with partial concordance with the MR findings.

CONCLUSIONS: These findings support a genetically determined microbiota-inflammation axis in DLSD. Furthermore, they identify circulating inflammatory proteins as mediators to prioritize mechanistic studies and guide translational follow-up research.}, } @article {pmid42317755, year = {2026}, author = {Rout, AK and Tripathy, PS and Rout, SS and Kumar, N and Parida, SN and Panda, A and Suman, D and Tyagi, A and Behera, BK and Pandey, PK}, title = {Metagenomic insights into microbial diversity, xenobiotic and plastic-degrading enzymes in sediments of river Yamuna at Agra.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1828736}, pmid = {42317755}, issn = {1664-302X}, abstract = {The river Yamuna is one of the most polluted rivers in India and is heavily impacted by urban, industrial, and agricultural inputs. In this study, shotgun metagenomics was used to investigate microbial diversity and functional potential in sediments from three locations: Balkeshwar Shivpuri Agra (BSA), Taj Ganj Yamuna (TGY), and Yamuna Expressway Agra (YEA). A total of 38.3-46.5 million reads per sample were generated, yielding 3.08-5.54 million predicted ORFs. Taxonomic profiling revealed that BSA exhibited higher microbial diversity, with a more even distribution of dominant taxa compared to TGY and YEA. Functional analysis indicated that core metabolic pathways (e.g., glycolysis and TCA cycle) were more abundant in BSA, whereas pathways related to aromatic compound degradation were relatively enriched in TGY. Plastic-degrading enzyme homologs were detected across all sites, with the strongest signals associated with biodegradable polymers such as polyhydroxyalkanoates (PHA), polyhydroxybutyrate (PHB), and polyethylene glycol (PEG). The normalized abundances of PHA-associated enzymes were approximately 60-75% higher in YEA compared to BSA and TGY, while homologs linked to recalcitrant plastics such as polyethylene (PE) and low-density polyethylene (LDPE) were detected at low levels across all sites (< 10-15%). Similarly, xenobiotic degradation pathways, including chlorocyclohexane and chlorobenzene degradation, showed relatively higher abundance in YEA, whereas bisphenol degradation was more prominent in BSA. Overall, the results indicate that sediment microbial communities along the river Yamuna harbor diverse metabolic capabilities and functional potential for pollutant degradation, with site-specific variations driven by local environmental conditions.}, } @article {pmid42317759, year = {2026}, author = {Jiya, N and Sha, SP and Khudai, W and Yadav, S and Sasane, R and Sah, SP and Ghatani, K and Sharma, A}, title = {Distinct bacterial and fungal communities linked to functional potential in fermented fish and vegetables.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1850075}, pmid = {42317759}, issn = {1664-302X}, abstract = {INTRODUCTION: Traditional fermented foods constitute a vital component of ethnic community diets; consequently, characterizing their specific food microbiome is essential for elucidating their nutritional, functional and health related attributes.

METHODS: In this study, targeted metagenomics was employed to investigate the bacterial and fungal compositions of fermented fish and vegetables from North Bengal, India. The functional predictions of the fermented food microbiomes was performed using PICRUSt2.

RESULTS AND DISCUSSION: High throughput sequencing of 16S rRNA and ITS genes revealed substantial differences in the diversity indices amongst the fermented fishes and vegetables. Fish samples were dominated by Pseudomonadota (23.05%), whereas vegetables were enriched in Bacillota (32.17%), with Psychrobacter and Aliivibrio prevalent in fishes and lactic acid bacteria including Levilactobacillus, Paucilactobacillus and Pediococcus dominant in vegetables. The fungal genera Bisifusarium belonging to Ascomycota and Cystobasidium affiliated to Basidiomycota, were abundant in the fermented fishes and vegetables, respectively. Functional predictions of bacterial and fungal communities revealed enhanced carbohydrate metabolism, biosynthesis pathways related to vitamins, short-chain fatty acids, organic acids, proteolytic enzymes and compounds contributing to organoleptic attributes in these fermented foods. The assessment of microbial communities associated with the traditionally fermented foods of North Bengal revealed the key microbial taxa involved in the fermentation process and their nutritional properties.}, } @article {pmid42317762, year = {2026}, author = {Joshi, G and Rani, S and Bharti, D and Panda, N and Chavan, P and Mathpal, S and Ramaiah, S and Anbarasu, A}, title = {The role of the gut microbiome in antibiotic-driven antimicrobial resistance.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1856738}, pmid = {42317762}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) is one of the most pressing threats to global health system. The human gut harbors a complex microbial ecosystem coordinated through mechanisms of metabolic interdependence. The gut microbiota plays a vital role in normal growth and physiological processes of the human body. It serves both as a target of antibiotic-mediated disruption and as a reservoir for the propagation of antimicrobial resistance genes. Although antibiotics remain indispensable for the treatment of bacterial infections, their broad ecological impact on the gut microbiota can undermine the microbial balance that protects the host against pathogen invasion and metabolic dysfunction. The gut microbiome also functions as a reservoir of antimicrobial resistance genes collectively termed the "resistome," which can be mobilised and transferred between commensal and pathogenic bacteria via horizontal gene transfer mechanisms such as conjugation, transformation, and transduction. This review examines the composition and functions of the human gut microbiota, the mechanism of antibiotic-induced gut dysbiosis, and the role of host factors like age, genetics, diet and immune status, on microbiome dynamics and AMR development. We further evaluate emerging methods for resistome characterisation, which include PCR, next-generation sequencing, functional metagenomics and artificial intelligence-driven tools. Finally, we discuss microbiome-targeted therapeutic strategies such as faecal microbiota transplantation (FMT), phage therapy, CRISPR-based therapies, and antimicrobial peptides for combating AMR and restoring gut microbial homeostasis. Overall, this review highlights that maintaining and re-establishing the integrity of the gut microbiome should be considered a fundamental component of antimicrobial stewardship strategies aimed at controlling AMR worldwide.}, } @article {pmid42318385, year = {2026}, author = {Fu, J and Qi, Y and Zhan, J and Su, L and Gao, Y and Zhou, Q and Zhang, Y}, title = {Clinical effects of Yiqi-Yangyin-Huoxue granules in the management of type 2 diabetes mellitus and early vascular aging: a randomized, double-blind, placebo-controlled trial protocol.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1768610}, pmid = {42318385}, issn = {2296-858X}, abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) has become a major global public health challenge, affecting more than 500 million adults worldwide. Early vascular aging (EVA) is one of the key pathological changes for diabetic vascular complications. However, targeted and effective therapeutic strategies remain limited. Based on our previous research and clinical experience, we developed a granulated natural herbal formulation, Yiqi-Yangyin-Huoxue (YQYYHX). This trial aims to evaluate the clinical efficacy and safety of YQYYHX in patients with T2DM and EVA, and to preliminarily explore its potential mechanisms.

METHODS: This is a single-center, randomized, double-blind, placebo-controlled, parallel-group clinical trial. It will enroll 120 participants with T2DM and EVA, who will be randomized in a 1:1 allocation ratio to two groups. In addition to standard therapy, the treatment group will receive the YQYYHX granules, while the control group will receive a matched placebo. Based on mass spectrometry analysis, daidzin, salvianolic acid L, and oleamide were identified as the compounds with the largest peak area in YQYYHX. After a 12-week intervention, brachial-ankle pulse wave velocity (baPWV) is planned to be assessed as the primary outcome. Secondary outcomes are expected to include the ankle-brachial index, blood glucose levels, lipid profiles, inflammatory cytokines, 6-min walk test and questionnaires. Safety will be evaluated using liver transaminases, serum creatinine, and related indicators. Serum and fecal samples will be collected before and after treatment. The serum will be used for metabolomic and proteomic sequencing analysis, and feces will be used for metagenomic sequencing. Electronic case report forms are generated within the clinical record system, ensuring that all follow-up information is traceable. Subsequently, the data will be entered into a specific electronic data capture, and the data administrator will verify it.

RESULTS: The recruitment began on March 27, 2025 and is expected to end on December 31, 2026. As of March 10, 2026, 72 participants have been enrolled.

CONCLUSION: This rigorously designed trial is expected to generate reliable evidence. As a complementary and alternative therapeutic option, YQYYHX has the potential to benefit patients with T2DM and EVA.

CLINICAL TRIAL REGISTRATION: This trial has been registered with the International Traditional Medicine Clinical Trial Registry Platform (http://itmctr.ccebtcm.org.cn/, ITMCTR2024000388).}, } @article {pmid42318413, year = {2026}, author = {Hu, Z and Hou, L and Huang, A}, title = {Case Report: Methylprednisolone-induced pheochromocytoma crisis resulting in cardiac arrest.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1779740}, pmid = {42318413}, issn = {2296-858X}, abstract = {Pheochromocytoma crisis, a rare yet life-threatening endocrine emergency, is characterized by acute hemodynamic instability that can lead to severe cardiovascular collapse, including cardiac arrest. Systemic glucocorticoid administration has been shown to trigger such crises in patients with pheochromocytoma. This report describes a 38-year-old female who developed symptoms including chest tightness, dyspnea, and vomiting shortly after receiving a methylprednisolone injection for urticaria, suggesting a possible association between glucocorticoid administration and the subsequent crisis. On admission, she suffered cardiac arrest and was managed with extracorporeal membrane oxygenation (ECMO). Coronary angiography, blood microbial RNA analysis, and metagenomic testing revealed no abnormalities. Despite comprehensive pharmacological treatment, the patient's symptoms persisted, with recurrent ventricular fibrillation detected on electrocardiogram, prompting further investigations. A computed tomography (CT) scan identified an adrenal mass, and biochemical tests confirmed the diagnosis of pheochromocytoma. Following successful laparoscopic adrenalectomy, the patient experienced significant clinical improvement. This case demonstrates the potential for methylprednisolone to trigger or contribute to a pheochromocytoma crisis. However, it is important to acknowledge that other concurrent factors, such as use of medication, systemic inflammatory response, and physiological stress of resuscitative interventions, may have also played a role. The challenges posed by the diagnosis of this condition underscore the need for caution when administering glucocorticoids to patients with suspected pheochromocytoma.}, } @article {pmid42319209, year = {2026}, author = {Parsons, DAJ and Vos, RA and Price, BW}, title = {BeeGees: A High-Throughput Protein-Coding DNA Barcode Recovery Pipeline Tailored for Genome Skims of Museum Specimens.}, journal = {Molecular ecology resources}, volume = {26}, number = {5}, pages = {e70170}, pmid = {42319209}, issn = {1755-0998}, support = {101059492//European Commission/ ; 22.00173//Swiss State Secretariat for Education, Research and Innovation/ ; 24.00054//Swiss State Secretariat for Education, Research and Innovation/ ; //UK Research and Innovation/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Museums ; Animals ; *High-Throughput Nucleotide Sequencing/methods ; *Computational Biology/methods ; Workflow ; *Metagenomics/methods ; }, abstract = {Natural history collections are unparalleled archives of global biodiversity, yet most specimens remain molecularly uncharacterised due to the technical challenges of historical DNA (hDNA), including degradation, low endogenous content and contamination. Genome skimming offers a scalable alternative to PCR-based barcoding, but existing bioinformatic workflows are not optimised for the heterogeneous, metagenomic nature of museum-derived data. Here we present BeeGees (Barcode Extraction and Evaluation from Genome Skims), a high-performance computing (HPC) integrated, Snakemake-based workflow designed for protein-guided recovery and validation of mitochondrial and plastid barcode genes from degraded short-read genome sequences. BeeGees integrates dual read pre-processing, systematic per-sample parameter sweeps, sequential consensus cleaning to remove contaminant sequences and rigorous structural and taxonomic validation against curated reference databases. We benchmarked BeeGees on 1518 museum specimen-derived genome skims spanning eight phyla. The workflow completed in approximately 120 h (< 5 min per sample) on HPC infrastructure. When excluding sequencing failures (< 1 M reads), validated COI barcodes were recovered for 73.2% of specimens (1050/1435). Barcode recovery success was influenced by endogenous content, preservation quality and parameter choice rather than raw read count alone, highlighting the importance of systematic parameter optimisation. Sequential consensus cleaning eliminated ambiguous bases and reduced chimeric artefacts, proving essential for robust museomic analyses. BeeGees provides a reproducible, scalable framework for high-throughput barcode recovery and biodiversity genomics and reference gap-filling initiatives from natural history collections. The BeeGees pipeline is available at: https://github.com/bge-barcoding/BeeGees/.}, } @article {pmid42319454, year = {2026}, author = {Xie, M and Jie, Y}, title = {From Health to Disease: A Comprehensive Review of Ocular Surface Microbiota and Detection Methods in Dry Eye.}, journal = {Current microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {42319454}, issn = {1432-0991}, support = {82371022//the National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Microbiota ; *Dry Eye Syndromes/microbiology/diagnosis ; Bacteria/genetics/classification/isolation & purification ; *Eye/microbiology ; Fungi/isolation & purification/genetics/classification ; Tears/microbiology ; }, abstract = {Dry eye disease (DED) is a prevalent and multifactorial condition that significantly impacts the ocular surface, characterized by symptoms of discomfort, visual disturbance, and tear film instability. Recent research has increasingly focused on the ocular surface microbiome (OSM) and its potential role in the pathogenesis and progression of DED. The OSM consists of a diverse community of microorganisms, including bacteria, fungi, and viruses, that interact with the host to maintain ocular surface health. Dysbiosis, or the imbalance of these microbial communities, has been linked to various ocular surface disorders, including DED. This review comprehensively summarizes the current understanding of the differences in OSM between healthy individuals and patients with different types of DED, such as aqueous-deficient dry eye, evaporative dry eye, and DED associated with autoimmune conditions. Additionally, it explores the detection methods used to study the OSM, highlighting the strengths and limitations of culture-based approaches, 16 S rRNA sequencing, metagenomic shotgun sequencing, and emerging technologies like 2bRAD-M. The review also outlines future research directions, emphasizing the need for advanced multi-omics approaches, personalized microbiome-based therapies, and longitudinal studies to further elucidate the role of the OSM in DED. By enhancing our understanding of the OSM composition and function, these insights may lead to innovative diagnostic and therapeutic strategies for managing DED.}, } @article {pmid42319554, year = {2026}, author = {Wang, Q and Xiao, H and Liu, W and Dang, X and Bai, Y and Xiao, R and Tong, L and Wang, Y and Li, M and Wang, S and Pu, S and Pei, D and Zhang, D and Wang, X and Hu, G and Guo, J and Jin, X and Qin, L and Zhang, C and Li, Y and Zhang, T and Yang, J and Wang, Q and Sun, H}, title = {Fusobacterium varium Exacerbates Neutrophil-driven Intestinal Inflammation Associated with Succinate-SUCNR1-NF-κB Signaling.}, journal = {Inflammation}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10753-026-02547-x}, pmid = {42319554}, issn = {1573-2576}, support = {24ZDNA003//Gansu Provincial Major Science and Technology Special Project Plan/ ; 82572004//National Natural Science Foundation of China/ ; lzujbky-2023-eyt04//Fundamental Research Funds for the Central Universities/ ; 25YFFA067//Key Research and Development Program of Gansu Province/ ; 2023RCXM65//Gansu Province key talent project/ ; 2021-RC-115//Lanzhou Talent Innovation and Entrepreneurship Project/ ; yjrckyqdj-2020-01, yjrckyqdj-2022-01//Talent Introduction Plan of the Second Hospital of Lanzhou University/ ; }, abstract = {Disruption of gut microbial homeostasis is a hallmark of ulcerative colitis (UC), yet the specific pathobionts and effector molecules driving mucosal inflammation remain unclear. In this study, metagenomic sequencing of fecal samples from 37 patients with UC and 30 healthy controls was performed to identify differentially enriched bacterial species. Fusobacterium varium (F. varium) was found to be significantly enriched in patients with UC and was therefore selected for further functional investigation. Germ-free mice colonized with F. varium developed more severe dextran sulfate sodium (DSS)-induced colitis, accompanied by enhanced mucosal inflammation. In addition, F. varium culture supernatants increased NF-κB reporter activity and inflammatory signaling at the protein level. Bioactivity-guided fractionation combined with mass spectrometry identified succinate as a major candidate bacterial-derived bioactive metabolite. Succinate exacerbated colonic inflammation in vivo and promoted neutrophil recruitment, whereas inhibition of CXCR2 signaling reduced neutrophil infiltration and alleviated disease severity. In vitro experiments further demonstrated that succinate activated NF-κB signaling in HL-60-derived neutrophils through succinate receptor 1 (SUCNR1) and induced the production of inflammatory mediators, including CXCL8. Collectively, these findings support a role for F. varium in exacerbating intestinal inflammation under colitic conditions, at least in part through succinate-associated neutrophil recruitment.}, } @article {pmid42319773, year = {2026}, author = {Ali, H and Rieuwpassa, IE and Hamrun, N and Marlina, E and Yulianty, R and Akbar, FH and Siti Hartina Dewang, DA}, title = {Longitudinal effects of antiretroviral therapy on the oral microbiota in people living with HIV: A systematic review.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {}, doi = {10.1556/030.2026.02910}, pmid = {42319773}, issn = {1588-2640}, abstract = {People living with HIV frequently experience oral microbial dysbiosis, contributing to oral disease burden and reduced quality of life. Although antiretroviral therapy (ART) effectively suppresses viral replication and promotes immune recovery, its longitudinal effects on the oral microbiota remain incompletely understood. This systematic review aimed to evaluate longitudinal changes in oral microbiota composition and diversity in people living with HIV before and after ART initiation. A systematic review was conducted in accordance with PRISMA guidelines and registered in PROSPERO (CRD420251164326). Electronic searches were performed in PubMed, ScienceDirect, Wiley Online Library, DOAJ, and Google Scholar for studies published between 2015 and 2024. Eligible studies included longitudinal human studies reporting pre- and post-ART oral microbiota data using 16S rRNA gene sequencing or metagenomic approaches. Methodological quality was assessed using Joanna Briggs Institute critical appraisal tools. Due to substantial heterogeneity, findings were synthesized narratively. Six longitudinal studies met the inclusion criteria. ART was associated with partial and non-uniform modulation of the oral microbiota. Changes in beta diversity and selective taxonomic shifts were commonly reported, whereas changes in alpha diversity were inconsistent. Taxonomic alterations were more evident at the genus level, while several dominant oral genera remained stable before and after ART. Evidence linking oral microbiota changes with immune recovery was limited. Longitudinal evidence indicates that ART induces selective and heterogeneous changes in the oral microbiota without consistent normalization toward a non-HIV microbial profile, underscoring the importance of integrating oral health into long-term HIV care.}, } @article {pmid42320204, year = {2026}, author = {Ma, S and Cao, M and Wang, F and Geng, H and Xu, Q and Gao, Z and Li, J and Russel, M and Sun, K}, title = {DOM-microbe interactions shape carbon storage strategies in rhizosphere and detritus-rich wetland soils.}, journal = {Journal of environmental management}, volume = {412}, number = {}, pages = {130250}, doi = {10.1016/j.jenvman.2026.130250}, pmid = {42320204}, issn = {1095-8630}, abstract = {Wetland macrophytes are associated with carbon storage through photosynthetic CO2 uptake and interactions with microbes. Rhizodeposition and detritus accumulation represent two key pathways examined in this study. However, how dissolved organic matter (DOM) interacts with microbial carbon storage remains incompletely understood. Here, we investigated links between DOM characteristics and microbial carbon transformation pathways in Wuchang Lake using FT-ICR-MS, metagenomics, and geochemical analyses. Macrophyte presence was associated with a higher relative abundance of genes related to microbial carbon storage potential compared to macrophyte-free areas. Microbial taxa and carbon transformation strategies varied between rhizosphere and detritus-enriched soils and were associated with differences in DOM properties. In the rhizosphere, DOM with low H/C ratios (<1.5) and high number of transformations (>10) was associated with taxa linked to biomass degradation. In detritus-enriched soils, DOM with higher H/C ratios and lower carbon-to-phosphorus ratios (C:P) was associated with higher relative abundance of genes related to intracellular carbon storage, while genes associated with CO2 and CH4 production showed lower relative abundance. These communities also showed higher relative abundance of CO2 fixation genes. Overall, DOM molecular characteristics were associated with niche-specific microbial carbon transformation patterns, providing a conceptual framework for wetland carbon dynamics.}, } @article {pmid42320375, year = {2026}, author = {Srisakvarangkool, W and Rosyidah, A and Yasawong, M and Suriyachadkun, C and Pitiwittayakul, N and Ganta, P and Tanasupawat, S and Nantapong, N}, title = {Comparative genomics and taxonomic characterization of Streptomyces diversicolor sp. nov.: a novel species exhibiting intraspecific genomic divergence and biotechnological potential.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126737}, doi = {10.1016/j.syapm.2026.126737}, pmid = {42320375}, issn = {1618-0984}, abstract = {Two actinomycete strains, designated SSUT88A[T] and SSUT88R, were isolated from distinct soil samples in Nakhon Ratchasima, Thailand. While both belong the genus Streptomyces, they exhibited phenotypic divergence; strain SSUT88A[T] produced yellowish-white mycelia with potent antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), whereas SSUT88R produced red colonies with limited inhibitory effects. Genomic analyses confirmed the isolates are conspecific, sharing high ANI (99.99%) and dDDH (99.6%) values, yet exhibiting genomic divergence; the 11.2 Mb genome of SSUT88A[T] exceeded the 8.3 Mb genome of SSUT88R. Comparative genome mining revealed this variation extended to secondary metabolism, as SSUT88A[T] encoded a more diverse biosynthetic potential. Furthermore, ANI and dDDH values against the closest phylogenomic neighbors were below species thresholds (79.69-87.55% and 25.7-30.2%, respectively), supporting their classification as a novel species. Metagenomic screening using IMNGS and Branchwater revealed a predominantly terrestrial distribution. While the broader lineage appeared ecologically versatile, high-confidence conspecific populations (cANI ≥0.97) were restricted to soil and rhizosphere habitats, with evidence of regional persistence in Thailand. Chemotaxonomic characteristics including ll-diaminopimelic acid, MK-9(H8) and whole-cell sugars contained ribose, mannose, and glucose. The polar lipid profile included phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, and an unidentified glycolipid. Major fatty acids included iso-C16:0, anteiso-C15:0, anteiso-C17:0 and iso-C15:0. Based on this polyphasic evidence, strains SSUT88A[T] and SSUT88R are proposed to represent a novel species, for which the name Streptomyces diversicolor sp. nov. is proposed. The type strain is SSUT88A[T] (InaCC A1220[T] = TISTR 10074[T]). Strain SSUT88R is deposited as InaCC A1221 = TISTR 10075.}, } @article {pmid42320776, year = {2026}, author = {Cho, MS and Lee, IS and Kim, J and Park, JW and Kim, J and Ko, SJ}, title = {Multi-herb formulations modulating gut microbiota: A systematic review and data-driven analysis.}, journal = {Journal of ethnopharmacology}, volume = {370}, number = {}, pages = {122082}, doi = {10.1016/j.jep.2026.122082}, pmid = {42320776}, issn = {1872-7573}, abstract = {Multi-herb formulations, characterized by their complex synergistic compositions, are widely used in traditional medicine to modulate the gut microbiota. However, identifying reproducible herb-microbiota associations across disparate clinical settings remains a significant methodological challenge.

AIM OF THE STUDY: This study aims to systematically synthesize human clinical evidence to map the modulation patterns of multi-herb formulations on the gut microbiota and to identify the herbal components associated with reported directional microbial shifts.

MATERIALS AND METHODS: We conducted a systematic review and data-driven analysis of 29 clinical trials involving 954 participants in multi-herb formulation groups. To integrate findings from heterogeneous clinical settings, we employed a binarization strategy focused on statistically significant directional shifts (+1 for increase, -1 for decrease). An extreme gradient boosting (XGBoost) learning framework combined with SHapley Additive exPlanations (SHAP) was used to deconstruct these formulations and explore the predictive importance of individual constituents. To ensure the highest level of scientific integrity and prevent data leakage, the model's generalizability was rigorously validated using Leave-One-Study-Out (LOSO) cross-validation at the independent study level.

RESULTS: The LOSO validation yielded a mean accuracy of 0.84 and a macro F1-score of 0.42, indicating limited but informative cross-study pattern recognition despite the inherent heterogeneity of clinical data. Our analysis identified recurrent directional associations: formulas containing Scutellaria baicalensis Georgi were associated with reported reductions in genus-level taxa such as Escherichia-Shigella within neuropsychiatric disease contexts. Formulas containing Zingiber officinale Roscoe were associated with reported increases and decreases in selected genus-level taxa across heterogeneous disease contexts.

CONCLUSIONS: This study provides a comprehensive, evidence-based map of how multi-herb formulations modulate the human gut microbiota. By prioritizing rigorous validation and accounting for the complexity of synergistic preparations, we have identified hypothesis-generating patterns that transcend individual study variations. These findings provide a realistic foundation for future high-resolution metagenomic research and the development of standardized ethnopharmacological therapies.}, } @article {pmid42320811, year = {2026}, author = {Wang, Y and Wu, X and Deng, H and Yan, G and Xu, Z and Zhu, L}, title = {A high-molecular-weight polysaccharide from Polygonatum sibiricum inhibits distant tumor growth associated with gut microbiota remodeling and synergizes with αPD-1 therapy.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {153116}, doi = {10.1016/j.ijbiomac.2026.153116}, pmid = {42320811}, issn = {1879-0003}, abstract = {BACKGROUND: Defined polysaccharide fractions can reshape the gut microbiome and influence systemic antitumor immunity. We investigated whether an operationally defined high-molecular-weight Polygonatum sibiricum polysaccharide fraction (PSP-H) enriched by 100 kDa ultrafiltration suppresses growth of subcutaneous MC38 tumors via microbiota-dependent mechanisms and potentiates anti-PD-1 therapy.

MATERIALS AND METHODS: PSP-H was isolated by cascade ultrafiltration and compared with a total polysaccharide extract (PSP-T) and lower-MW fractions. We profiled fecal metagenomes, serum metabolites, tumor molecular readouts (immunoblotting; HDAC activity), and immunity. Fecal microbiota transplantation (FMT) tested the microbiota dependence and sufficiency of PSP-H-remodeled communities to transfer the immunometabolic phenotype. Combination with anti-PD-1 (RMP1-14) was evaluated.

RESULTS: PSP-H showed minimal direct cytotoxicity while suppressing tumor growth, selectively enriching butyrate-producing taxa (e.g., Lachnospiraceae) and elevating serum butyrate and inosine, with TNF-α reduced. In vitro, butyrate enhanced T-cell IFN-γ/IL-2/granzyme-B, inhibited tumor HDAC activity, and counteracted IFN-γ-induced PD-L1; in vivo, PSP-H created a T-cell-activating milieu with adaptive STAT1/PD-L1 up-regulation. FMT recapitulated the key metabolite/cytokine signature. PSP-H + anti-PD-1 synergistically increased intratumoral CD8[+] T cells and yielded superior tumor control versus monotherapy.

CONCLUSION: PSP-H is a defined microbiota-modulating adjuvant that engages a microbiome-butyrate-immune axis to restrain subcutaneous tumors and sensitizes them to PD-1 blockade by converting systemic immunity while inducing targetable adaptive resistance.}, } @article {pmid42321256, year = {2026}, author = {Zhao, Y and Wang, Y and Bai, S and Tan, J and Niu, H and Zhang, A and Guo, G and Fang, L and Jiang, L}, title = {Reprogramming hydrogen metabolism for methane mitigation in dairy cows: mechanistic insights from polyphenols using meta-omics approaches.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01068-7}, pmid = {42321256}, issn = {2055-5008}, support = {JR25027//Beijing High-Level Innovation and Entrepreneurship Talent Program-Basic Research Talent Project/ ; 2023YFD1301801//National Key R&D Program of China/ ; BAIC05-2025//Beijing Livestock Industry Innovation Team/ ; }, abstract = {Enteric methane emissions from ruminants contribute significantly to agricultural greenhouse gases. Plant-derived phytochemicals such as grape seed proanthocyanidins (GSP) are promising natural antimethanogenic feed additives, yet their modes of action remain incompletely understood. This study aimed to comprehensively elucidate the microbiological and functional mechanisms underlying phytochemical-induced methane mitigation using integrative meta-omics. Both in vivo and in vitro experiments demonstrated that GSP supplementation significantly reduced methane emissions; in lactating dairy cows, GSP decreased methane emission intensity by 16.5% (g/kg energy-corrected milk). Metagenomic and metatranscriptomic analyses revealed a reprogramming of microbial communities, with decreased abundance and transcriptional activity of methanogenic archaea (e.g., Methanobrevibacter) and enhanced activity of alternative hydrogenotrophic bacteria (Selenomonas, Veillonella, Sharpea). Functionally, GSP elevated expression of genes involved in reductive acetogenesis (e.g., acsB), nitrate ammonification (narG, nrfA), and sulfate reduction (dsrA), thereby redirecting hydrogen flux away from methanogenesis. These shifts were accompanied by increased microbial carbohydrate metabolism and antioxidative responses. Our findings provide the first meta-omics-based mechanistic framework for understanding methanogenesis suppression by phytochemicals in ruminants. GSP modulates microbial composition and function to reroute reductant flows and suppress archaeal methanogenesis through enhanced bacterial electron sinks. This work highlights the potential of polyphenols to modulate the rumen microbiome for sustainable methane mitigation, supporting the development of next-generation feed additives.}, } @article {pmid42321634, year = {2026}, author = {Pandey, S and Parmar, B and Gupta, A and Singh, A and Chauhan, A and Huang, KW and Karan, R}, title = {Eco-technological potential of salinity-driven functional specialization in Indian solar salterns revealed by integrated culturomics and whole-metagenome profiling.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05253-8}, pmid = {42321634}, issn = {1471-2180}, support = {RFS #5974//King Abdullah University of Science and Technology/ ; IoE/2024-25/12/FRP and IoE/2025-26/12/FRP//University of Delhi/ ; }, abstract = {Solar salterns are environmentally stable yet biologically extreme ecosystems that serve as vital models for understanding and managing hypersaline environments, including industrial saline effluents. Despite their ecological and biotechnological significance, Indian solar salterns remain functionally underexplored. In this study, we integrated culture-dependent isolation with whole-metagenome sequencing to investigate microbial community assembly, functional specialization, and eco-technological potential across four geographically distinct Indian salterns.Physicochemical analyses revealed pronounced spatial variation in salinity, pH, and electrical conductivity, which together strongly structured microbial communities. Metagenomic sequencing generated between 4.84 and 8.68 Gb of raw data across individual site, yielding between 429,420 and 669,991 predicted genes in high-salinity locations. Taxonomic reconstruction demonstrated archaeal dominance at extreme salinity, particularly among Euryarchaeota, whereas comparatively moderate salinity sites supported more balanced bacterial-archaeal assemblages. Alpha diversity patterns indicated higher richness in Tamil Nadu and Rajasthan, while Gujarat exhibited reduced evenness consistent with environmental filtering.Culture-dependent approaches recovered 42 halophilic and polyextremophilic isolates, primarily affiliated with Halobacteriaceae and Bacillaceae, complementing the broad taxonomic detection of these lineages inferred from metagenomic data. Functional annotation revealed extensive enrichment of genes involved in ion transport, energy production, osmoprotectant biosynthesis, and DNA repair, reflecting an adaptive mechanism critical for survival in high-salinity industrial processes. Amino acid metabolism genes exceeded 25,000 hits in selected sites, and replication and repair genes reached 32,554 in Gujarat, indicating heightened stress-response activity. Secondary metabolite biosynthetic gene clusters, including pathways for novel antimicrobial peptides, terpene, ribosomally synthesized and post-translationally modified peptide-like, and type III polyketide synthase pathways, were widely distributed, offering new biological control mechanisms for environments impaired by stress. Antimicrobial resistance signatures were limited and unevenly distributed across sites.These findings demonstrate that salinity acts as a dominant ecological filter driving both taxonomic composition and functional specialization in Indian solar salterns. By linking environmental gradients to adaptive genomic traits, this study establishes a functional baseline for hypersaline ecosystems.}, } @article {pmid42321797, year = {2026}, author = {Igriczi, B and Zsiborás, L and Albert, E and Német, Z and Balka, G and Dénes, L}, title = {High genetic diversity of porcine rotavirus A, B, and C in Hungary with putative novel VP4 genotypes.}, journal = {BMC veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12917-026-05649-8}, pmid = {42321797}, issn = {1746-6148}, abstract = {BACKGROUND: Rotaviruses (RVs) are important enteric pathogens of swine, contributing significantly to neonatal and post-weaning diarrhea worldwide. Although rotavirus A (RVA) is the best characterized species, much less is known about the epidemiology and genetic diversity of RVB and RVC, especially in Central Europe. This study aimed to investigate the presence and genetic diversity of RVA, RVB, and RVC in diarrheic piglets in Hungary using Nanopore third-generation sequencing.

RESULTS: A total of 77 fecal swab samples collected from diarrheic piglets across 19 swine farms were analyzed. All three RV species were detected, RVA and RVC were each identified in 54.5% of samples, while 40.3% was RVB positive. Coinfections involving multiple RV species were frequent, highlighting the complex etiology of piglet diarrhea. Altogether, 8 RVA, 3 RVB, and 4 RVC full-genome sequences, comprising all 11 segments, were identified. Genotyping of RVA strains revealed multiple G/P genotype combinations, with G9P[23] being the most prevalent. Whole-genome analysis demonstrated a Wa-like genomic backbone of porcine origin. In RVB, three complete VP4 sequences were obtained that could not be assigned to any known P genotype, suggesting the presence of a novel lineage. Hungarian RVC strains showed high genetic diversity, including five distinct G genotypes and one potential novel P genotype, underlining evolutionary diversity of porcine RVs.

CONCLUSIONS: This study provides a comprehensive molecular characterization of RVA, RVB, and RVC circulating in Hungarian pig populations. The high prevalence of coinfections and the detection of genetically diverse and potentially novel strains emphasize the complexity of RV epidemiology in swine. These findings highlight the need for continued surveillance to better understand their role in pig health and zoonotic risk.}, } @article {pmid42321844, year = {2026}, author = {Li, Y and Chen, Q and Bin, X and Xu, S and Ma, H}, title = {Bronchoalveolar lavage microbiota signatures and stage-associated alterations in early-stage and advanced-stage non-small cell lung cancer: a pilot study.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08501-7}, pmid = {42321844}, issn = {1479-5876}, support = {2023YXZX17//Tianjin Municipal Education Commission/ ; TJYXZDXK-3-032C//National Key Clinical Specialty Discipline Construction Program of China/ ; }, abstract = {OBJECTIVES: The aims of this study were to characterize the microbial flora in the bronchoalveolar lavage fluid (BALF) of patients with early-stage (stage I, II, IIIA) and advanced-stage (stage IIIB, IIIC, IV) non-small cell lung cancer (NSCLC), and to explore the associations between microbial flora and lung cancer stage.

METHODS: We collected BALF from NSCLC patients (early-stage group 26 cases; advanced-stage group 31 cases). Absolute quantitative metagenomic sequencing was performed to identify differential taxa, genes, and enriched pathways. Flow cytometry was used to profile T cell subsets. We correlated the microbial species with immune cell and gene expression. Receiver operating characteristic (ROC) curve analysis was performed to assess the ability of differential taxa to distinguish advanced-stage from early-stage NSCLC.

RESULTS: Dokdonia (q = 0.040, LDA = 5.704) and Cocleimonas (q = 0.026, LDA = 5.329) were enriched in the early-stage group, whereas Barnesiella (q = 0.046, LDA = 4.784), Pedobacter (q = 0.040, LDA = 4.913) and unclassified Bacteroides (q = 0.046, LDA = 4.932) were significantly enriched in the advanced-stage group. The microbial genes gmhD (q < 0.001, LDA = 3.926), rfaD (q < 0.001, LDA = 3.918), nudF (q = 0.004, LDA = 4.283) and sfsA (q = 0.004, LDA = 3.915) were expressed remarkably in the advanced-stage group. The advanced-stage group exhibited altered T cell subset distributions, including a higher proportion of CD8⁺ T lymphocytes (q < 0.001), whereas it showed a lower proportion of CD4⁺ T cells and a decreased CD4/CD8 ratio (q < 0.001; q < 0.001). Bifidobacterium was negatively associated with the CD4/CD8 ratio (q = 0.015) and positively significant correlated with the genes which enriched in the advanced-stage group.

CONCLUSIONS: This study delineated the microbial structure and function of early-stage and advanced-stage of NSCLC. We identified discriminating taxa, genes, and pathways linked to cancer progression, characterized the T cell subset distributions in the advanced-stage of NSCLC. Bifidobacterium abundance was associated with altered T cell subset distributions and stage-related microbial genes, providing hypotheses for future mechanistic studies on microbiota-driven NSCLC progression.}, } @article {pmid42322841, year = {2026}, author = {Wang, L and Li, X and Cao, Y and Meng, F and Xu, J and Hao, J}, title = {Microbial adaptation to benzethonium chloride exerts a double‑edged sword effect on long‑term sludge anaerobic fermentation: Volatile fatty acids promotion and antibiotic resistance genes propagation.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142682}, doi = {10.1016/j.jhazmat.2026.142682}, pmid = {42322841}, issn = {1873-3336}, abstract = {The widespread use of benzethonium chloride (BZC) leads to its significant input into wastewater treatment and then accumulation in waste activated sludge (WAS). However, the long-term consequences of BZC accumulation in WAS anaerobic fermentation still remain unexplored. This study established a continuous fermentation system with stepwise increase and decrease in BZC content to simulate fluctuating pollutant levels. The concentration-dependent effects of BZC on acidogenic fermentation were displayed: low-to-medium-level BZC (10-100 mg/L) inhibited volatile fatty acids (VFAs) production from the baseline of 1150 mg COD/L to approximately 800 mg COD/L, whereas high-level BZC (1000 mg/L) increased VFAs production to 1800 mg COD/L, representing an absolute increase of 650 mg COD/L (70% relative to control) and facilitated the solubilization of organic substrates. Molecular docking modelling showed that BZC could bind with extracellular polymeric substances (EPS) and enzyme. Microbial community analysis showed that the resilience of fermentation system was maintained mainly by the functionally redundant rare subcommunity, whereas the enrichment of specific fermentative bacteria (e.g., Proteiniclasticum) contributed directly to the enhanced VFAs production. Based on metagenomic data, BZC stress activated microbial quorum sensing (QS) response and this QS-mediated adaptation strategy increased the relative abundance of related genes for hydrolysis, transport, and VFAs biosynthesis. Critically, this adaptive success carried a hidden cost, i.e., persistently enriching high-risk antibiotic resistance genes (e.g., bacA, mepA, vanY) (20% relative to the control) and activating mobile genetic elements. These findings reveal a trade-off between the increased VFAs production and environmental resistance propagation during the BZC affected sludge anaerobic fermentation.}, } @article {pmid42323142, year = {2026}, author = {Yang, J and Zhu, D and Liu, R and Shi, L and Dai, X}, title = {Excessive biomass retention decouples ammonia-oxidizer abundance and activity in sidestream partial nitritation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135208}, doi = {10.1016/j.biortech.2026.135208}, pmid = {42323142}, issn = {1873-2976}, abstract = {Partial nitritation (PN) underpins two-stage anaerobic ammonium oxidation-based nitrogen removal, but biomass management in sidestream PN reactors remains largely empirical. This study tested three PN sequencing batch reactors maintained at contrasting biomass-retention states (2, 4, and 6 g L[-1] MLSS) under stepwise loading. Among the tested conditions, the intermediate-biomass reactor showed the most favorable performance, shortening recovery periods by 40.0-67.0% and reaching the highest apparent stable nitrogen loading rate of 2.30 g N L[-1] d[-1]. Metagenomic analysis linked this response to more deterministic community assembly and stronger species-level dominance of Nitrosomonas stercoris, whereas the low- and high-biomass states showed greater stochasticity and enrichment of heterotrophic or stress-tolerant taxa. Metatranscriptomics further showed that the intermediate-biomass state maintained the strongest ammonia oxidizing bacteria (AOB)-centred transcriptional configuration, together with peak expression of amoABC and hao, and higher AMO and HAO levels. This state was also associated with higher expression of Calvin-Benson-Bassham cycle and electron transport genes, indicating stronger coupling among ammonia oxidation, energy metabolism, and autotrophic carbon fixation. By contrast, the high-biomass reactor retained nitrifier-related potential, but this potential was not converted into proportional transcriptional or functional output. It showed weakened AOB-centered dominance and a broader reduction in chemolithoautotrophic functional expression. These findings reveal abundance-activity decoupling under excessive biomass retention and show that PN control should move beyond biomass concentration alone. A more informative operational perspective is the loading-to-biomass state, which helps indicate whether retained biomass is translated into active nitritation function.}, } @article {pmid42323145, year = {2026}, author = {Zhang, S and Lv, H and Cui, B and Zhou, D}, title = {Low-substrate nitrogen drives functional succession toward a cooperative Candidatus Brocadia consortium in anammox systems.}, journal = {Bioresource technology}, volume = {459}, number = {}, pages = {135206}, doi = {10.1016/j.biortech.2026.135206}, pmid = {42323145}, issn = {1873-2976}, abstract = {Mainstream anammox treatment is promising but limited by slow acclimation and unstable performance under low nitrogen. Community succession is often observed, but it is usually explained by kinetic differences among anammox bacteria, which cannot fully account for competitive outcomes. Here, we operated an anammox biofilter under sustained low‑nitrogen stress and combined metagenomics, metatranscriptomics, co‑occurrence networks, and SMETANA to identify ecological adaptation mechanisms. During early acclimation, Ca. Kuenenia reduced the expression of costly biosynthetic pathways, including aromatic amino acid synthesis by 25.6%-38.8%. In contrast, Ca. Brocadia showed broad transcriptional activation, with anammox genes upregulated by ∼18-fold. During long-term operation, the community shifted to a multispecies Ca. Brocadia assemblage characterized by complementary model-inferred auxotrophies, stronger positive associations around the dominant Brocadia species (68.0%), and lower predicted metabolic resource overlap than that observed in the high-nitrogen system (0.66 ± 0.12 vs. 0.77 ± 0.10). Ultimately, Ca. Brocadia replaced Ca. Kuenenia as the dominant functional lineage, increasing from 1.0% to 44.7% in relative abundance and contributing 71.5% of total transcriptional activity. These findings suggest that low-nitrogen stress favors a metabolically complementary and potentially cooperative Ca. Brocadia assemblage rather than a single superior competitor, offering ecological guidance for stabilizing anammox processes in low-strength wastewater.}, } @article {pmid42323301, year = {2026}, author = {Li, C and Feng, Y and Sáez-Sandino, T and Xiong, C and Eldridge, DJ and Gross, N and Le Bagousse-Pinguet, Y and Ochoa, V and Gozalo, B and Guirado, E and Zhou, G and García-Gómez, M and Valencia, E and Berdugo, M and Asensio, S and Martínez-Valderrama, J and Mendoza, BJ and Berhe, AA and Cutler, NA and Abades, S and Alcántara, J and Alfaro, F and Arroyo, AI and Barrett, M and Bastida, F and Blaum, N and Boldgiv, B and Bowker, M and Branquinho, C and Hart, SC and Deák, B and Durán, J and Espinosa, CI and Fajardo, A and Fraser, LH and Gallardo, A and García Velázquez, L and Geissler, K and Grebenc, T and Gusman Moltanvan, E and Kindermann, L and Köbel, M and Laanisto, L and le Roux, PC and Liancourt, P and Liang, J and Linstädter, A and Louw, MA and Macek, P and Maggs-Kölling, G and Makhalanyane, TP and Manzaneda, AJ and Marais, E and Montesinos, D and Mora, JP and Moreno, G and Muñoz-Rojas, M and Mussery, A and Unuk Nahberger, T and Nair, GR and Neuhauser, S and Plaza, C and Pueyo, Y and Rey, PJ and Rey, A and de Los Ríos, A and Rodríguez, A and Rodriguez Lozano, B and Roman, R and C Ruppert, J and Salah, A and Serôdio, J and Siles, JA and Singh, J and Travers, S and Undrakhbold, S and Valkó, O and Vivas, M and Wang, L and Williams, MA and Zaady, E and Maestre, FT and Singh, BK and Delgado-Baquerizo, M}, title = {Aridity-related differences in soil elemental ratios reshape microbial functional traits across global biomes.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73215-9}, pmid = {42323301}, issn = {2041-1723}, support = {42577352//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42407401//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Aridity alters soil carbon (C), nitrogen (N) and phosphorus (P) stoichiometry, yet the implications of these processes for soil microbial functional traits and potentials at the genomic level remain poorly synthesized. Here we combine measurements of soil C, N and P pools and ratios with shotgun metagenomes from 200 natural ecosystems spanning major biomes worldwide. Across sites, increased aridity is associated with lower soil C:N and N:P (and C:P) ratios and with a coordinated shift in microbial functional potential. Genes linked to catabolic resource acquisition-including carbohydrate-active enzymes and pathways for degradation of plant litter and organophosphorus compounds-are declined as C becomes relatively scarce. In contrast, genes supporting anabolic investment in growth and drought resistance, such as RNA transcription, protein synthesis and intracellular transport, are increased. These patterns indicate that aridity-related change in soil elemental ratios is coupled to a broad shift from catabolic to anabolic strategies in soil microbiomes. By linking soil elemental ratios to microbial functional traits across biomes, our study provides a framework for anticipating how climate-driven drying may reorganize microbial metabolism with consequences for carbon and nutrient cycling.}, } @article {pmid42323352, year = {2026}, author = {Kane, Y and Ma, Y and Yan, B and Zhao, X and Ge, T and Li, Y and Cao, L and Zhang, M and Pei, Y and Wan, Z and Zhang, T and Zhang, C}, title = {Investigating the human anellome across the lifespan reveals sex-specific biphasic trajectories.}, journal = {npj aging}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41514-026-00412-7}, pmid = {42323352}, issn = {2731-6068}, support = {BJWS2025082//Shanghai Eastern Talent Plan/ ; 32441099//National Natural Science Foundation of China/ ; }, abstract = {Anelloviruses dominate the human plasma virome, yet their lifespan dynamics and relationships with the immune system are unclear. We integrated metagenomics with cytokines, HERV-K, and CMV profiling across 405 individuals (0-100 years) and found that prevalence, abundance, and diversity varied non-linearly with age and by sex. Alphatorqueviruses accumulated progressively with age, while betatorqueviruses and gammatorqueviruses displayed biphasic, female-specific patterns. Alphatorquevirus species diversity had significant inflection points at ages 54-58 years in females. We identified a stable core of 12 age-uniform species, with their abundance trajectories diverging significantly by sex. Male bias in anellovirus metrics widened with age, and community dispersion reversed across lifespan. CMV IgG titers correlated significantly with anellovirus genus richness. In young adult females, anellovirus ORF1 was associated with IL-1β. These findings suggest altered anellovirus ecology as a correlate of age-related immune changes, positioning these viruses as strong indicators of immune status and offering new perspectives on age-modulated host-virus dynamics.}, } @article {pmid42323440, year = {2026}, author = {Carboni, S and Macfarland, C and Cheves Hernandez, S and Buret, AG and Kutz, S and Melin, AD}, title = {Ecological and methodological insights from genetic and coprological profiling of gastrointestinal communities in wild howler monkeys.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-57628-6}, pmid = {42323440}, issn = {2045-2322}, support = {RGPIN-2017-03782//Natural Sciences and Engineering Research Council of Canada/ ; 950-231257//Canada Foundation for Innovation and Canada Research Chairs/ ; }, abstract = {The gastrointestinal tract hosts a complex community of microorganisms and helminth parasites that collectively contribute to host health and fitness. Analysis of these communities provides insight into diverse aspects of host dietary ecology, immunity, nutrition, and host-parasite interactions. However, research methodologies, such as sample preservation and sequencing approach, can influence how we understand and characterize these features. Here, we profiled the gastrointestinal microbial and helminth communities in different groups of wild Costa Rican mantled howler monkeys (Alouatta palliata palliata). We compared samples stored in ethanol versus directly flash frozen, and contrasted conclusions drawn from 16S versus shotgun sequencing approaches. Bacterial, archaeal, and eukaryotic taxa associated with the digestion of plant material dominated the GI communities. Storage and sequencing methods influenced microbial profiles: ethanol-stored samples exhibited higher diversity than frozen samples, and 16S sequencing detected lower diversity than shotgun. Helminths were detected via coprological microscopy in 71% of individuals, whereas metagenomic detection was inconsistent. This study provides new data on the microorganisms and their putative digestive functions in the gut of a folivorous primate, and highlights the pros and cons of different methodological choices when profiling host-microbiome and host-parasite interactions.}, } @article {pmid42323523, year = {2026}, author = {Hatwar, N and Qureshi, A}, title = {Microbial Community and Enzymes for Biodeterioration of PVC Plastic Buried in Soil and Compost Environment.}, journal = {Current microbiology}, volume = {83}, number = {8}, pages = {}, pmid = {42323523}, issn = {1432-0991}, support = {UGC August 2021-Grant Number -191620062301//UGC/ ; }, mesh = {*Polyvinyl Chloride/metabolism/chemistry ; Biodegradation, Environmental ; *Soil Microbiology ; *Bacteria/classification/genetics/metabolism/enzymology/isolation & purification ; Composting ; *Microbiota ; Soil/chemistry ; *Plastics/metabolism ; }, abstract = {Polyvinyl chloride (PVC) plastic films accumulate in the environment and cause ecological damage due to their persistent, high-density polymeric nature. To mitigate PVC pollution, a sustainable bioremediation approach needs to be designed. Biodegradation of PVC using pure bacterial cultures has been reported as a sustainable option. However, PVC biodegradation studies in the presence of a soil/compost indigenous microbiome have not been conducted. In the present study, attempts have been made to understand and show the biodeterioration and biodegradation of PVC under soil and compost burial conditions. The study revealed that the PVC films, when buried under soil and compost at different conditions (ambient, sun-exposed, and 37 °C conditions), resulted in gravimetric weight loss with CO2 release. Under soil burial at 37 °C, PVC films showed 13.32 ± 0.10% weight reduction with 9.9 ± 0.9% CO2 evolution in 90 days, whereas compost conditions resulted in 6.89 ± 0.11% weight reduction. Another unique feature of the study is the metagenomic profiling of PVC buried soil/compost microbiomes, which revealed Proteobacteria and Actinobacteria as dominant phyla with Bacillus, Staphylococcus, Streptomyces, Arthrobacter, and Exiguobacterium as predominant genera. Also, the bioinformatics analysis revealed that these microbes possess potential metabolic capability associated with PVC biodeterioration and biodegradation (laccases, peroxidases, and oxidoreductases). Overall, the novelty reflects integrating metagenomic, spectroscopic, and morphological characterization of buried PVC plastic and linking microbial community dynamics with their enzymatic machinery and physico-chemical transformations of PVC. These multi-analytical approaches provided mechanistic evidence that the soil/compost microbial community initiates the PVC biodegradation process, offering a scientific basis for designing sustainable plastic waste management and remediation practices.}, } @article {pmid42323568, year = {2026}, author = {Alves, CPP and Pinto, OHB and Pappas, GJ and Mota, SS and Rahlff, J and Krüger, RH}, title = {Taxonomic and functional diversity of the microbiome associated with the freshwater sponge Metania sp. (Haplosclerida: Metaniidae) from the Brazilian Cerrado, a metagenomic approach.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42323568}, issn = {1471-2180}, mesh = {Animals ; Brazil ; *Porifera/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Fresh Water/microbiology ; *Archaea/classification/genetics/isolation & purification ; Symbiosis ; Phylogeny ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Sponges, the oldest metazoans on the planet, have an evolutionary history shaped by symbiotic associations with microorganisms. Although well studied in marine sponges, these associations are poorly understood in freshwater species. This study explored the taxonomic diversity and functional potential of the microbiome of the freshwater sponge Metania sp. and its distinction from the surrounding water, using a metagenomic approach. The samples were collected in the Brazilian Cerrado.

RESULTS: Taxonomic assignment identified 17 phyla, including bacterial and archaeal, with 19 sequence variants successfully assigned to the species level. Bacteria comprised 16 phyla, with a predominance of Pseudomonadota, Actinomycetota, and Bacteroidota in both microbiomes. The sponge microbiome is distinct from the water microbiome (PERMANOVA; F = 21.6, p = 0.04), sharing only 27% of the identified taxa. Functional prediction resulted in 7,201 KEGG Orthologs (KOs), assigned to 117 significantly enriched metabolic pathways. Although 95 pathways are shared, differential abundance analysis identified 1,024 KOs more abundant in the sponge microbiome and 1,275 in the water. The presence of bacterial defense systems such as CRISPR-Cas in the sponge microbiome suggests a crucial role in protecting against phages while maintaining symbiosis. In contrast, the water microbiota is enriched with pathways linked to environmental adaptation, such as secondary metabolite biosynthesis and pollutant degradation. Although the water microbiome harbored 1.3 times more biosynthetic gene clusters (BGCs), the sponge microbiome also demonstrated biotechnological potential for producing secondary metabolites, especially antimicrobial.

CONCLUSIONS: These findings demonstrate that the freshwater sponge Metania sp. hosts a complex and functionally specialized microbial community that plays fundamental roles in adaptation, nutrition, and defense, highlighting the critical importance of symbiotic associations for the host.}, } @article {pmid42323877, year = {2026}, author = {Gagniuc, PA and Gagniuc, E}, title = {The sequence alignment problem: boundary conditions as the unifying principle.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {3}, pages = {}, pmid = {42323877}, issn = {1477-4054}, mesh = {Algorithms ; *Sequence Alignment/methods/statistics & numerical data ; Humans ; }, abstract = {Sequence alignment provides a formal framework for comparison of biological sequences through score maximization over matches, mismatches, and insertion-deletion events. Classical formulations distinguish between global alignment, which enforces end-to-end correspondence through fixed boundary conditions, and local alignment, which extracts high-scoring subsequences without global consistency. Both paradigms arise from the same dynamic programing (DP) recurrences, shaped by substitution matrices and gap-penalty models that approximate molecular evolution. Canonical algorithms such as Needleman-Wunsch and Smith-Waterman establish the foundations of exact alignment, while later extensions introduce affine and convex gap costs, statistical score distributions, and probabilistic significance models. Modern work builds on these principles through bit-parallel techniques, band-restricted computation, cache-aware layouts, single instruction, multiple data and graphics processing unit parallelism, hardware accelerators, and index-assisted heuristics that enable large-scale genomic analysis. Sequence alignment underpins applications ranging from whole-genome comparison and metagenomics to protein annotation, variant detection, human leukocyte antigen typing, and microbial surveillance. Persistent challenges include scalability to ultra-long sequences, faithful models of complex mutation processes, avoidance of parameter bias, and formal limits on exact subquadratic solutions. Emerging directions emphasize adaptive data-driven scoring, hybrid global-local formulations, privacy-preserving computation, and real-time or incremental alignment. These developments reaffirm sequence alignment as a closely related DP framework shaped primarily by boundary conditions rather than distinct paradigms.}, } @article {pmid42324063, year = {2026}, author = {Stancheva, R and Valadez-Cano, C and Van Aken, B and Selckmann, GM and Lawrence, J and Cahoon, AB}, title = {Limnofasciculus delicatus (Coleofasciculaceae, Coleofasciculales), a Novel Mat-Forming Cyanobacterium From Shenandoah River, Virginia, USA.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70377}, doi = {10.1111/1758-2229.70377}, pmid = {42324063}, issn = {1758-2229}, support = {//4-VA, A Collaborative Partnership for Advancing the Commonwealth of Virginia/ ; //Virginia Interstate Commission on The Potomac River Basin/ ; //VA Department of Environmental Quality/ ; 2222322//United States National Science Foundation/ ; }, mesh = {Phylogeny ; *Cyanobacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Virginia ; *Rivers/microbiology ; Genome, Bacterial ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {Benthic cyanobacterial mats in flowing waters are complex communities typically composed of taxa from the orders Coleofasciculales and Oscillatoriales, many of which have unresolved taxonomic positions and poorly characterized toxic potential. We collected field mats of a benthic non-heterocytous filamentous cyanobacterium from the North and South Forks of the Shenandoah River in Northern Virginia (USA) that were dominated by a novel morphotype. Whole-genome and 16S rRNA gene phylogenetic analyses placed this cyanobacterium within the recently described genus Limnofasciculus (Coleofasciculaceae). Genome-based species delimitation metrics fell below accepted thresholds for bacterial species delineation relative to Limnofasciculus baicalensis, the only formally described species in the genus to date, supporting recognition of the cyanobacterium from Shenandoah River as a distinct species. Furthermore, the two Limnofasciculus species exhibited marked structural differences in the Box B helix of the 16S-23S ITS region. Comparative genomic analyses revealed a genome size similar to L. baicalensis and a conserved core gene repertoire alongside substantial divergence in biosynthetic gene cluster composition. Neither species contains biosynthetic gene clusters associated with the production of known cyanotoxins. Based on morphological, phylogenetic and genomic evidence, we describe Limnofasciculus delicatus sp. nov., supported by light microscopy and whole-genome characterization.}, } @article {pmid42324270, year = {2026}, author = {Ma, Y and Yang, M and Xu, A and Zhao, X and Dong, X and Li, W and Tu, H and Guo, Y and Song, Z and Wu, X}, title = {Characterization of gut microbiome signatures in metabolic dysfunction associated steatotic liver disease.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01059-8}, pmid = {42324270}, issn = {2055-5008}, support = {K20230085//Healthy Zhejiang One Million People Cohort/ ; 2020E10004//Zhejiang Key Laboratory of Intelligent Preventive Medicine/ ; 2019R01007//the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2020C03002//Cancer Center, Zhejiang University and Key Research and Development Program of Zhejiang Province/ ; }, abstract = {This cross-sectional study compared the gut microbiota between metabolic dysfunction associated steatotic liver disease (MASLD) patients and healthy controls. A total of 1401 participants, including 392 MASLD patients and 1009 healthy controls, were enrolled from one project site of the Healthy Zhejiang One Million People Cohort (HOPE) between January 2022 and June 2023. Shotgun metagenomic sequencing was conducted to compare the composition and functional profiles of the gut microbiome between MASLD patients and healthy controls. Compared to the control group, MASLD patients exhibited significant alterations in both alpha and beta diversity, along with reduced connectivity and robustness of the gut microbial network. We identified significant changes in the abundance of 12 microbial strains between the two groups with two strains (t_SGB4749 and t_SGB4753) enriched and ten strains depleted in MASLD patients. In comparison to the control group, MASLD patients demonstrated distinct differences in the genomic potential related to increased glycolysis, decreased pyruvate metabolism, and elevated lipopolysaccharide (LPS) biosynthesis in both metagenomic functional profiling and single-strain genome analysis. These findings suggest that alterations in specific microbial strains and metabolic pathways may contribute to MASLD pathogenesis.}, } @article {pmid42324618, year = {2026}, author = {Hernandez, JB and Abiodun, M and Hayer, SS and Dickson, T and Ayayee, P and Clayton, JB}, title = {Mapping the metagenomic landscape: combined shotgun sequencing and quantitative PCR to profile gut metagenome-assembled genomes in marmosets following treatment with a broad-spectrum antibiotic cocktail.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2687925}, doi = {10.1080/19490976.2026.2687925}, pmid = {42324618}, issn = {1949-0984}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Metagenome/drug effects ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Gastrointestinal Microbiome/drug effects/genetics ; *Callithrix/microbiology ; Metagenomics ; Shotgun Sequencing ; Real-Time Polymerase Chain Reaction ; Genome, Bacterial ; Feces/microbiology ; }, abstract = {Broad-spectrum antibiotics are invaluable tools for treating pathogenic infections, but their sustained use can contribute to changes in gut microbiome membership and the emergence of antimicrobial resistance. While these unintended side effects are independently well documented, the relationship between them has seldom been investigated. To address this, we quantified the effects of 28-d antibiotic cocktail exposure on metagenome-assembled genomes and antibiotic resistance genes in common marmosets using a custom whole-genome shotgun sequencing pipeline and quantitative polymerase chain reaction assays. We observed contrasting genus-level reductions in Bifidobacterium abundance and Fusobacterium growth, both during antibiotic treatment and a 2-week post-treatment period. Total bacterial abundance was not significantly affected by antibiotics, likely due to the presence of antibiotic-resistant opportunists. Genes for vancomycin resistance and multidrug efflux pumps were identified in metagenome-assembled genomes of an unclassified Sarcina sp. and Escherichia coli, respectively, and were accompanied by increased abundance of these species during treatment. Additionally, we detected 11 dysregulated metagenomic pathways related to carbohydrate metabolism, including 2 pathways relevant to short-chain fatty acid production, following antibiotic exposure. This study provides insights into the species-dependent emergence of antimicrobial resistance mechanisms in non-human primates following antibiotic exposure that could be relevant for antibiotic therapies and resistance management.}, } @article {pmid42324716, year = {2026}, author = {Niloy, RK and Jewel, NA and Karim, D and Rolin, MH and Khan, T and Akter, A and Mondal, SI}, title = {Human Gut Phageome Analysis Uncovers Thousands of Highly Modular Endolysins.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70344}, doi = {10.1002/mbo3.70344}, pmid = {42324716}, issn = {2045-8827}, support = {LS/2022/1/05//SUST Research Center/ ; 37.01.0000.073.04.030.23.2134//University Grants Commission of Bangladesh/ ; }, mesh = {Humans ; *Bacteriophages/genetics/enzymology/classification/isolation & purification ; *Endopeptidases/genetics/chemistry/metabolism ; *Gastrointestinal Tract/virology/microbiology ; Genome, Viral ; Bacteria/virology ; Metagenome ; Metagenomics ; }, abstract = {The escalating threat of antimicrobial resistance has renewed global interest in bacteriophages as precise and powerful tools for controlling bacterial populations in the human gut. These viruses owe much of their antibacterial potential to phage-encoded endolysins, enzymes capable of rapidly degrading bacterial cell walls with high specificity and low potential for resistance development. Despite their therapeutic promise, the overall composition of the gut phageome and the structural modularity of its endolysins remain poorly understood. In this study, we performed a large-scale analysis of 9141 human gut metagenomic samples from 34 independent studies. Using standardized workflows for assembly, genome clustering, host prediction, and protein domain annotation, we reconstructed 15,267 phage genomes and identified 3794 corresponding endolysins. The recovered genomes showed substantial variation in size and coding density, with an average GC content of 43%. Host prediction indicated that most phages targeted bacterial members of the phyla Bacillota (41%) and Bacteroidota (23%). Endolysin sequences grouped into 296 protein families and displayed striking domain modularity. Catalytic domains such as Amidase_2 and Glyco_hydro_25 frequently co-occurred with cell wall-binding motifs including LysM and CW_7. Remarkably, one endolysin contained 15 distinct domains, the highest natural domain diversity reported to date. Collectively, this study represents the most comprehensive characterization of the human gut phageome and its encoded endolysins to date. The exceptional modular diversity uncovered highlights the gut phageome as a rich reservoir of endolysin variants, providing a strong foundation for developing next-generation therapeutics against multidrug-resistant bacterial pathogens.}, } @article {pmid42324848, year = {2026}, author = {Santos-Perdomo, I and Salces-Castellano, A and Moraza, ML and Mateos, E and Muñoz-Barrera, A and González-Montelongo, R and Suárez, D and Vega-Pita, N and Falcón-López, L and Lorenzo-Salazar, JM and Flores, C and Arribas, P and Andújar, C}, title = {Integrating Megabarcoding and Metabarcoding to Unlock Diversity and Distribution Data Shortfalls in Dark Taxa.}, journal = {Molecular ecology resources}, volume = {26}, number = {5}, pages = {e70166}, doi = {10.1111/1755-0998.70166}, pmid = {42324848}, issn = {1755-0998}, support = {CGL2015-74178-JIN//Agencia Estatal de Investigación/ ; PID2021-126883NA-I00//Agencia Estatal de Investigación/ ; PID2022-143291NB-I00//Agencia Estatal de Investigación/ ; RYC2020-029196-I//Agencia Estatal de Investigación/ ; RYC2021-034291-I//Agencia Estatal de Investigación/ ; TESIS2022010039//Agencia Canaria de Investigación, Innovación y Sociedad de la Información/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Biodiversity ; Spain ; Phylogeography ; High-Throughput Nucleotide Sequencing/methods ; Genetic Variation ; *Metagenomics/methods ; Soil ; }, abstract = {Persistent biodiversity data shortfalls undermine our capacity to detect species, map their distributions and characterize their spatial genetic structure, limiting robust biogeographic analyses and the development of effective conservation strategies. This particularly affects hyperdiverse invertebrate groups where hidden diversity remains largely undocumented. This study develops and demonstrates the potential of an integrated high-throughput sequencing (HTS) framework to improve the representation of hidden diversity in regional species inventories and to help close critical gaps in our understanding of species distributions and genetic diversity from a conservation biogeography perspective. Focusing on the Canary Islands (Spain), the workflow combines megabarcoding of more than 4000 mesofauna specimens to generate a curated species-level molecular reference library with community DNA metabarcoding of 168 soil samples. This approach enables consistent taxonomic assignment across insular landscapes and increases the spatial and genetic resolution of occurrence data. We identified 145 species of mites and springtails, including 49 species newly recorded for the archipelago and numerous genetically distinct lineages likely representing undescribed taxa, highlighting all the biodiversity that remains to be described. Integration of the barcode library with metabarcoding data produced 1440 species occurrences, revealing extensive distributional gaps, multiple range expansions and strong within-island phylogeographic structuring, indicating prevalent diversification at fine spatial scales. These results highlight a deep, taxonomically broad underestimation of soil biodiversity and demonstrate that this integrative approach provides a transferable model for advancing the biogeography, evolutionary understanding and conservation of dark and cryptic taxa across broad taxonomic and conservation-relevant contexts.}, } @article {pmid42324919, year = {2026}, author = {Zhang, H and Xie, H and Liu, J and Xue, Y and Fan, Y and Chen, M and Wang, R and Zhao, Q}, title = {Dynamic CSF metagenomic next-generation sequencing to guide duration of therapy in Listeria monocytogenes ventriculitis: a multi-modal strategy with intraventricular gentamicin and neurosurgical intervention.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {81}, number = {7}, pages = {}, doi = {10.1093/jac/dkag184}, pmid = {42324919}, issn = {1460-2091}, support = {2023ZD0506502//National Science and Technology Major Project/ ; Z155080000004//National Key Clinical Specialist Construction Project/ ; }, } @article {pmid42325417, year = {2026}, author = {Zhang, X and Yang, X and Hu, J and Zhang, W and Shen, W}, title = {Treatment of brain abscess rupturing into ventricle: a case report and literature review.}, journal = {Frontiers in surgery}, volume = {13}, number = {}, pages = {1782105}, pmid = {42325417}, issn = {2296-875X}, abstract = {Brain abscess is a focal intraparenchymal infection. Brain abscess breaking into ventricles is a potentially fatal complication of brain abscess, which can lead to sudden deterioration of neurological function. Its incidence rate is 0.3%-35.0%, and the mortality rate is 84.0%-100.0%. This paper reports a case of a 50-year-old male patient who had previously undergone intracranial hematoma evacuation and skull fixation for traumatic brain injury. He was admitted to the hospital with dizziness for 20 days and bradyphrenia for 4 days. After admission, enhanced computerized tomography(CT) and magnetic resonance imaging(MRI) indicated a left frontal lobe brain abscess. During empirical treatment with ceftriaxone and metronidazole, the abscess ruptured into the ventricle, leading to ventriculitis. Bilateral external ventricular drainage (EVD) combined with ventricular lavage was performed using stereotactic technology. Metagenomic next-generation sequencing (mNGS) of the pus identified the infecting bacteria as Parvimonas micra and Fusobacterium. According to clinical guidelines, the anti-infective regimen was adjusted, short-term low-dose methylprednisolone was used, and combined with hyperbaric oxygen therapy. The patient recovered and was discharged. This paper emphasizes that timely identification of brain abscess rupture leading to ventriculitis, adoption of bilateral external ventricular drainage combined with ventricular lavage, determination of abscess pathogens using mNGS technology, and selection of sensitive antibacterial drugs can improve the cure rate of ventriculitis.}, } @article {pmid42325651, year = {2026}, author = {Mourad, A and Lupu, DS and Richey, M and Steven, P and Fowler, VG and Perkins, B and Holland, TL and Bergin, SP}, title = {Timing of Bronchoscopy and Plasma Microbial Cell-Free DNA Sequencing in Immunocompromised Host Pneumonia.}, journal = {Open forum infectious diseases}, volume = {13}, number = {6}, pages = {ofag361}, pmid = {42325651}, issn = {2328-8957}, abstract = {BACKGROUND: Immunocompromised patients are at high risk of pneumonia, with associated poor outcomes. Rapid microbiologic diagnosis is crucial, yet diagnostic yields vary widely. We evaluated the variability in diagnostic yield of usual care testing and plasma microbial cell-free DNA (mcfDNA) sequencing in the prospective observational Pneumonia in the Immunocompromised-Use of the Karius Test for the Detection of Undiagnosed Pathogens (PICKUP) study, specifically focusing on timing of testing relative to the onset of pneumonia.

METHODS: In this exploratory analysis, patient characteristics, variability in diagnostic yield, and the timing of bronchoscopy and mcfDNA sequencing from date of first abnormal imaging associated with suspected pneumonia were evaluated across enrolling sites.

RESULTS: A total of 222 patients from 10 enrolling sites were analyzed. Usual care diagnostic yield varied across sites (range, 7.7%-57.7%). Patient characteristics did not differ between sites, and median time from abnormal imaging to bronchoscopy was not different across sites (3 days [IQR, 3]). Diagnostic yield of bronchoscopy was significantly higher when performed ≤3 days (early) from abnormal imaging (38.5% [52/135]) versus >3 days (delayed) (21.8% [19/87]) (difference, 16.7% [95% CI, 2.5%-28.3%]; P = .009). Adding mcfDNA sequencing to usual care testing increased overall diagnostic yield by 7.9% for patients undergoing early bronchoscopy, and by 16.3% for delayed bronchoscopy.

CONCLUSIONS: Early bronchoscopy enhances diagnostic yield in immunocompromised patients with suspected pneumonia. Irrespective of timing, plasma mcfDNA sequencing increases overall diagnostic yield in this clinical scenario. These findings underscore the importance of prompt diagnostic strategies in this patient population.}, } @article {pmid42325854, year = {2025}, author = {Fan, L and Guan, J and Feng, L and Wang, Y and Zeng, H and Zhu, Y and Li, H and Chen, Q and Li, L and Qian, J and Liu, L and Li, Y}, title = {A patient with long-term diabetes dies following infection with Francisella novicida in Guangdong province, China: a case report.}, journal = {Infectious diseases & immunity}, volume = {5}, number = {1}, pages = {68-71}, pmid = {42325854}, issn = {2693-8839}, abstract = {The rarity of Francisella novicida infection in humans is well-known, and the F. novicida cases occur in immunocompromised patients or those with underlying health problems. Herein, we report the case of a patient with long-term diabetes who died following F. novicida infection that caused multiple organ failure, although F. novicida was effectively eliminated using antimicrobial therapy. Microbiological confirmation of F. novicida infection relies on metagenomic next-generation sequencing (mNGS) and pdpD-2 gene-specific identification. This study highlights the importance of early pathogen diagnosis in severely infected patients, particularly in cases of F. novicida, and indicates that mNGS is a useful tool for early diagnosis.}, } @article {pmid42326050, year = {2026}, author = {He, F and Yang, Y and Ma, D and Liu, P}, title = {Disseminated Cryptococcosis in a Non-HIV Patient: Diagnostic Value of Integrating mNGS, Culture, and Antigen Testing.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {597466}, pmid = {42326050}, issn = {1178-6973}, abstract = {Cryptococcus neoformans is an opportunistic fungal pathogen most commonly observed in individuals with human immunodeficiency virus (HIV) infection. Disseminated infections involving multiple organs, such as lungs, bloodstream, urinary tract, pleural cavity and central nervous system, are uncommon in patients without HIV. This work describes the case of a 72-year-old man who developed high fever and increased inflammatory markers after coronary artery bypass surgery. C. neoformans (8 sequence reads) was initially detected by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and was subsequently isolated from blood, urine and pleural effusion culture. Additionally, the cerebrospinal fluid tested positive for cryptococcal capsular polysaccharide antigen (CrAg), confirming disseminated infection involving multiple anatomical sites. The patient received liposomal amphotericin B combined with flucytosine antifungal treatment, which led to improvement in inflammatory parameters; however, the patient developed secondary multiorgan failure due to the severity of the illness. After 98 days of hospitalization, the patient was eventually discharged. This case highlights the diagnostic challenges of disseminated cryptococcosis in non-HIV hosts, particularly when involving atypical sites such as the urinary tract and pleural cavity. The integration of conventional microbiological methods, CrAg testing, and mNGS facilitated early diagnosis and enabled timely, standardized antifungal therapy.}, } @article {pmid42326398, year = {2026}, author = {Zhao, S and Peng, S and Li, H and Yang, G and Gao, X and Xu, K and Shi, L and Yu, H and Qiao, S}, title = {An approach for diagnosis of diarrhea in neonatal piglets based on the core gut microbiota and machine learning.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1852304}, pmid = {42326398}, issn = {1664-302X}, abstract = {Diarrheal diseases, such as yellow dysentery and white dysentery caused by pathogens or viruses, in newborn piglets lead to substantial economic losses in the swine industry worldwide. Gut microbiota dysbiosis is frequently observed in diarrheic piglets and is thought to play a role in disease pathogenesis, although causal relationships remain to be established. However, developing reliable microbiome-based diagnostic tools still poses a significant challenge. This study aimed to develop a diagnostic model for piglet diarrhea by integrating core microbiota analysis with machine learning. Fecal samples from diarrheic and healthy piglets were subjected to metagenomic sequencing to characterize archaeal, bacterial, and fungal communities. We identified diarrhea-associated bacterial biomarkers via LEfSe, DESeq2, and microbial cooccurrence network analysis. These microbial features were used to construct and compare multiple machine learning classifiers. Our results revealed significant disparities in the structure and diversity of the gut microbiota between diarrheic and healthy piglets, with the bacterial community showing the most notable changes. Among the models developed, the decision tree classifier based on bacterial genus-level features achieved the highest prediction accuracy of 91.18%. Furthermore, a simplified model utilizing a panel of 18 core bacterial genera also demonstrated high efficacy, with a support vector machine model achieving 88.24% accuracy. In independent validation using our internal dataset, the random forest model exhibited the best generalizability and stability. This study establishes a robust, microbiota-based diagnostic model for diarrhea in neonatal piglets, highlighting the potential of machine learning in leveraging microbiome data for disease classification and health management in livestock production.}, } @article {pmid42326408, year = {2026}, author = {Cha, J and Yang, J and Zhang, Z and Qian, L and Yang, F and Li, S and Li, J and Jian, Z and Cheng, W}, title = {Comparative metagenomic analysis of gut microbiomes in Yunnan ponies and Dutch warmblood horses.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1807081}, pmid = {42326408}, issn = {1664-302X}, abstract = {INTRODUCTION: The Yunnan pony is an officially protected pony breed in China. However, its gut microbiome characteristics remain largely unexplored. This study aimed to compare the gut microbiome and antibiotic resistance genes (ARGs) profiles between Yunnan ponies and Dutch warmblood horses.

METHODOLOGY: A total of 14 fresh fecal samples were collected from Yunnan ponies and Dutch warmblood horses. Metagenomic sequencing was employed to comprehensively analyze and compare the gut microbial composition, function, and ARGs profiles between the two breeds.

RESULTS: The results showed no significant differences between the two breeds in core phylum composition or overall microbial diversity. A total of 146 bacterial genera were identified with significant differences at the genus level. Functional analysis revealed that the gut microbiota of Yunnan ponies was significantly enriched in pathways related to carbohydrate metabolism and pectin degradation, which are involved in basic energy acquisition. In contrast, Dutch warmblood horses were more enriched in host immune interaction pathways such as Toll-like receptor signaling. Analysis of ARGs indicated that while there was no difference in the overall diversity of ARGs between the two groups. Their association networks with specific bacterial hosts were markedly distinct, and the dominant ARG subtypes differed.

DISCUSSION: This study provides a descriptive characterization of the gut microbiome of Yunnan ponies, offering baseline data for future research on the conservation of this genetic resource and its health management in breeding.}, } @article {pmid42326413, year = {2026}, author = {Peng, C and Delle Grazie, G and Ghanbari, M and May, A and Abeel, T}, title = {Antibiotic growth promoter and phytogenic feed additive consistently alter microbial community structure in chicken cecum.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1702973}, pmid = {42326413}, issn = {1664-302X}, abstract = {BACKGROUND: Efforts to replace antibiotic growth promoters (AGPs) in livestock are often hindered by a limited mechanistic understanding of how sub-therapeutic antibiotic doses enhance animal growth. Since AGP concentrations are typically too low to directly suppress pathogens, their effects on the gut microbiome, particularly its ecological dynamics, warrant closer investigation. A critical but underexplored dimension is how these additives influence the structure and stability of microbial communities as interconnected ecosystems.

METHODS: We conducted a comparative network-based analysis to examine the effects of zinc-bactracin, a commonly used AGP, and Digestarom[®], an alternative phytogenic feed additive (PFA) on cecal microbiome dynamics in broiler chickens. Using metagenomic data from a repeated cross-sectional randomized controlled trial of 96 broiler chickens assigned to three dietary groups: Basal (Control), AGP and PFA, we constructed microbial co-occurrence networks using Spearman's correlation for birds raised on basal, AGP-, or PFA-supplemented diets at key developmental stages (Day 3, 14, 21, and 35). We assessed changes in network topology, modular organization and node centrality. We evaluated whether the network-prioritized keystone taxa could discriminate among diets using a Random Forest classifier.

RESULTS: Compared to the Control group, both AGP and PFA treatments induced consistent shifts in network topology, including reduced connectivity, increased modularity, increased percentage of positive interactions, enhanced mucosa connectivity, and improved structural robustness over experiment time. Overall, these treatment-induced changes were more pronounced under AGP than under PFA. Despite these changes, we identified conserved subgraphs with stable interconnections across diets and time points during the experiment. The node centrality analysis revealed condition-specific keystone taxa, but Linear Discriminant Analysis (LDA) and Random Forest (RF) struggled to accurately differentiate between diets using their abundance, particularly between PFA and the two other groups.

CONCLUSION: Our findings reveal that feed additives can reshape gut microbial dynamics without producing marked compositional shifts. The consistent network-level changes observed for both AGP and PFA highlight the value of ecological network analysis in uncovering microbial community responses. These insights improve our understanding of cecal microbiome responses in chickens, highlight potential modes of action of AGPs, and offer a comparative framework for assessing the microbial impacts of alternative feed additives.}, } @article {pmid42326425, year = {2026}, author = {Wang, X and Yang, N and Hu, Y and Wang, X and Wu, Y and Zhang, A and Wang, Y}, title = {Vegetation restoration restructures soil sulfur allocation and sulfur-cycling functional potential in the Mu Us Sandy Land.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1845938}, pmid = {42326425}, issn = {1664-302X}, abstract = {Vegetation restoration in semi-arid sandy ecosystems can alter soil sulfur cycling not only through changes in sulfur stocks, but also through shifts in the partitioning between organic sulfur and sulfate and their microbial regulation. Here, we investigated soil sulfur pool allocation and sulfur-cycling functional potential along a five-stage vegetation restoration gradient in the Mu Us Sandy Land by integrating sulfur fraction measurements with metagenomic analyses. Vegetation restoration markedly reshaped the soil physicochemical and microbial context, as reflected by lower pH and higher TN, microbial biomass carbon, and enzyme activity in restored soils. In contrast, sulfur pools responded asynchronously: total sulfur and organic sulfur declined substantially from bare sandy land to restored vegetation types, whereas sulfate showed a weaker and comparatively more stable response. At the functional level, dominant sulfur-cycling genes were generally more abundant in bare sandy land, declined across restored vegetation types, and showed only partial recovery in forestland, indicating that restoration reorganized sulfur-cycling functional composition rather than uniformly enhancing sulfur-cycling potential. Taxonomically, dominant sulfur-cycling genes were consistently affiliated mainly with Actinomycetota and Pseudomonadota, but restored vegetation types exhibited more partitioned host compositions, with greater contributions from Acidobacteriota, Chloroflexota, and, for some genes, Thermoproteota. MAG-based analyses further showed that key sulfur-cycling genes were phylogenetically widespread but unevenly distributed across specific host lineages. Co-variation and Mantel analyses showed that sulfur-cycling genes formed coordinated functional modules and were most strongly associated with soil sulfur pools and fractions. Overall, vegetation restoration in the Mu Us Sandy Land primarily reshaped sulfur allocation and sulfur-cycling functional potential rather than promoting simple sulfur accumulation. These findings highlight that sulfur recovery in sandy drylands is better characterized by pool reallocation and functional reorganization.}, } @article {pmid42326426, year = {2026}, author = {Nelon, JN and Eltaher, SS and Abdelhamid, AG}, title = {Shotgun metagenomic and phenotypic characterization of indigenous lactic acid bacteria from raw milk artisanal cheeses: metagenomic functional insight and starter culture traits.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1820264}, pmid = {42326426}, issn = {1664-302X}, abstract = {The diversity of commercial starter cultures of lactic acid bacteria (LAB) used in fermented dairy products is limited. This has created strong demand to discover novel starter culture strains to develop unique products with appealing sensory characteristics. The current study used an integrated shotgun metagenomic and culture-based pipeline to (a) define taxonomic composition and functional potential of selected artisanal raw milk cheese microbiomes and (b) isolate and evaluate native LAB strains as potential starter cultures. Five artisanal cheeses (brie, bleu, plain gouda, mustard seed gouda, and nettle gouda) were analyzed. Shotgun metagenomics profiled the cheese microbiomes and revealed a high abundance of Lactococcus cremoris and Lactococcus lactis in gouda cheeses, whereas brie cheese contained high abundances of L. lactis and Streptococcus thermophilus. Functional profiling of metagenome-assembled genomes recovered from cheese microbiomes identified abundant pathways linked to carbon utilization, energy metabolism, and organic nitrogen metabolism. In parallel, 12 LAB isolates were recovered from all cheeses, of which five strains were classified taxonomically as L. lactis using whole genome sequencing. These five L. lactis strains displayed desirable milk and cream fermentation properties, achieving coagulation within 6 h, with final pH values of 4.5. The resulting fermented products contained 2.9%-4.2% protein content, displayed a relative increase in long-chain fatty acids, and a relative decrease in short-chain fatty acids compared to unfermented controls. The current study links cheese metagenome functional potential to dairy adaptation and identifies indigenous L. lactis strains as promising candidates for novel starter cultures in fermented dairy products.}, } @article {pmid42326431, year = {2026}, author = {Mei, X and Wu, W and Fang, N and Guo, Y and Dai, X}, title = {Sludge compost: a double-edged sword for depleted soil restoration revealed by integrated multi-omics analysis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1731456}, pmid = {42326431}, issn = {1664-302X}, abstract = {The prospective use of sludge compost for restoring depleted soils requires balancing its agronomic benefits against potential ecological risks. This study employed an integrated metagenomic and metabolomic approach to evaluate the dose-dependent effects of sludge compost on soil properties, maize growth, and rhizosphere microbial communities. Results showed that moderate compost application (≤15% w/w) enhanced soil nutrient availability, promoted root development, and enriched beneficial microbial taxa (Streptomyces, Mesorhizobium, Flavisolibacter), while upregulating plant stress-response metabolites (terpenoids, flavonoids). Conversely, excessive application (>20%) induced salinity stress, impaired root growth, and altered the microbial community, favoring thermophilic and xenobiotic-metabolizing taxa. Critically, high application rates led to the accumulation of residual pharmaceuticals (anti-neoplastic and anti-epileptic agents) and pesticides (insecticides and rodenticides), which correlated with the enrichment of microbial pathways associated with human diseases, highlighting a significant ecological risk. In addition, root integrity was the primary determinant of a sustainable plant-microbe feedback loop. These findings underscore the necessity for tailored application strategies to harness the soil-restorative potential of sludge compost while mitigating contaminant-driven risks, providing a framework for its safe use in sustainable agriculture.}, } @article {pmid42326513, year = {2026}, author = {Knight, R and Khatib, L and Patel, L and MahmoudianDehkordi, S and Labus, J and Agongo, J and Borkowski, K and Ambre, M and Brydges, C and Schimmel, L and Blach, C and Consortium, AGMP and Karu, N and Taylor, M and Diaz, E and Brosch, J and Bendlin, B and Swerdlow, R and Henderson, V and Chen, D and Saykin, A and Craft, S and Brewer, J and Wisniewski, T and Roberson, E and Dorrestein, PC and Kaddurah-Daouk, R}, title = {Interconnected influences of diet, gut microbiome, and metabolome on cognition across three metabolomics platforms.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9917711/v1}, pmid = {42326513}, issn = {2693-5015}, abstract = {Cognitive impairment is increasing with global aging, yet mechanisms linking diet, the gut microbiome, and metabolism to cognitive function remain unclear. To investigate a diet-microbiome-metabolome axis associated with cognition, we integrated fecal metagenomics, diet, and multi-platform plasma metabolomics in 505 older adults from four ADRCs. Several microbes broadly associated with circulating metabolites were also linked to multiple measures of cognitive performance. These taxa exhibited coordinated metabolic signatures, with cognition-positive microbes associated with antioxidant, lipid, and microbial-host co-metabolites, and microbes negatively associated with cognition were linked to inflammatory and aromatic amino acid-derived metabolites. Dietary patterns, particularly the Healthy Eating Index Greens and Beans component, were associated with microbial composition and metabolomic structure. Mediation analyses supported a diet-microbe-metabolite-cognition pathway, while metabolites remained associated with cognition after accounting for microbial features. These findings highlight the metabolome as a central integrator of diet, microbial activity, and cognitive function.}, } @article {pmid42326540, year = {2026}, author = {Yang, J and Nie, D and Zhang, Y and Li, C}, title = {Exploratory Pilot Multi-Omics Profiling of Gut Microbiota and Metabolic Features in Patients with Prolactinoma.}, journal = {Cancer management and research}, volume = {18}, number = {}, pages = {608026}, pmid = {42326540}, issn = {1179-1322}, abstract = {BACKGROUND: Growing evidence suggests a potential role of the gut microbiota in pituitary neuroendocrine tumors (PitNETs). This exploratory study focused on prolactinoma, the most prevalent PitNET subtype, to preliminarily characterize gut microbial and metabolic features associated with the disease.

MATERIALS AND METHODS: Fecal samples were collected from five patients with hyperprolactinemic prolactinoma and five patients with nonfunctioning (NF) PitNETs. Exploratory metagenomic and metabolomic analyses were performed to profile gut microbiota composition and metabolic alterations.

RESULTS: Compared with NF PitNET controls, prolactinoma patients showed distinct trends in gut microbial composition, including increased abundances of Bacteroides and Eubacterium and decreased abundances of Blautia and Clostridium. Metabolomic profiling identified differential metabolic features, including elevated fatty acid esters of hydroxy fatty acids (FAHFAs) and palmitoleic acid, which were mainly associated with glucose and lipid metabolism pathways.

CONCLUSION: This pilot multi-omics analysis provides preliminary evidence of altered gut microbiome-metabolite profiles in prolactinoma. These findings are hypothesis-generating and may support further investigation of gut-pituitary axis interactions in larger, well-powered cohorts.}, } @article {pmid42326568, year = {2026}, author = {Stacul, A and Valido, E and Nyfeler, N and Bertolo, A and Zeh, RM and Fontana, AO and Pannek, J and Krebs, J and Leichtle, A and Glisic, M and Stoyanov, J}, title = {Precision Rehabilitation in Spinal Cord Injury: A Systematic Review of Omics Applications for Intervention Monitoring in Spinal Cord Injury.}, journal = {Archives of rehabilitation research and clinical translation}, volume = {8}, number = {2}, pages = {100598}, pmid = {42326568}, issn = {2590-1095}, abstract = {OBJECTIVE: To systematically evaluate the application and utility of omics technologies, high-throughput methods measuring the complete or targeted set of molecules inside a biological system at a certain timepoint, in monitoring and optimizing rehabilitation interventions in traumatic spinal cord injury.

DATA SOURCES: Embase, Medline/Ovid, and Web of Science were searched from inception to November 27, 2024.

STUDY SELECTION: Eligible studies included adults (≥18 years) with spinal cord injury undergoing rehabilitation interventions assessed using omics technologies (genomics, epigenomics, transcriptomics, proteomics, metabolomics, or metagenomics).

DATA EXTRACTION: Following PRISMA guidelines, independent screening, data extraction, and risk of bias (RoB) assessment (National Institutes of Health Quality Assessment Tools) were performed by 2 investigators. Based on RoB assessment, studies were classified from level 1 (most reliable) to level 4 (least reliable).

DATA SYNTHESIS: Twenty-three trials were included: 8 randomized controlled trials, 5 non-randomized controlled trials, and 10 pre-post trials. Twenty-two studies (96%) exhibit a moderate RoB due to small sample size and heterogeneity. Omics technologies were primarily applied to exercise and electrical muscle stimulation interventions (65%), followed by hormonal and cellular therapies (22%), and diet (13%). Transcriptomic analyses revealed consistent molecular adaptations, including increased mitochondrial biogenesis (proliferator-activated receptor gamma coactivator 1-alpha) and reduced muscle atrophy gene expression (myostatin), correlating with enhanced insulin sensitivity and improved aerobic capacity. Metagenomics consistently identified microbiome shifts, such as decreased inflammatory taxa and increased beneficial taxa, associated with improved metabolic profiles and bowel function. Proteomics and metabolomics highlighted systemic changes related to neurorecovery, immune modulation, and sperm motility, linking molecular signatures directly to clinical outcomes.

CONCLUSIONS: Omics technologies enable early identification of molecular alterations. However, given small sample sizes and heterogeneity of the current studies, these findings should be interpreted with caution. Gradual integration of omics, particularly epigenomics which may capture long-term, injury-related changes holds promise for developing personalized rehabilitation protocols and monitoring clinical progression in spinal cord injury.}, } @article {pmid42326740, year = {2026}, author = {Avina-Bravo, EG and García-Lorenzo, I and Alfaro-Ponce, M and Breton-Deval, L}, title = {Machine learning-based classification of COVID-19 severity using respiratory microbiome profiles from shotgun metagenomic sequencing.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1801685}, pmid = {42326740}, issn = {2673-7647}, abstract = {Accurate clinical triage is critical for optimizing decision-making and resource allocation during infectious disease outbreaks such as COVID-19. In this study, we present an AI-driven decision-support tool for the triage of COVID-19 patients based on respiratory microbiome profiles derived from shotgun metagenomic sequencing. We analyzed 477 shotgun respiratory metagenomes from three independent public cohorts and generated genus-level taxonomic profiles, which were integrated with minimal clinical metadata (age, sex, and antibiotic exposure) to train supervised machine-learning models, including Random Forest, Support Vector Machine, and XGBoost. Model performance was evaluated using standard classification metrics, cross-validation, and particle swarm optimization for hyperparameter tuning. Across cohorts, we observed a consistent transition from microbiomes dominated by commensal taxa to dysbiotic states enriched in opportunistic and clinically relevant genera, particularly Acinetobacter and Staphylococcus, in severe and deceased patients. Among the evaluated models, XGBoost consistently achieved the best performance, reaching up to 96.1% accuracy, 97.6% F1-score, and 98.2% ROC-AUC in individual cohorts. When trained on the integrated dataset, XGBoost maintained robust performance (95.1% accuracy, 97.2% F1-score, 94.3% ROC-AUC) and demonstrated greater stability and lower variance compared to alternative models. Feature-importance analyses identified a compact and interpretable set of recurrent microbial predictors, and reduced-feature models retained substantial discriminative power when augmented with key clinical variables. These results support the respiratory microbiome as a valuable source of information for outcome-oriented clinical triage and position microbiome-informed machine learning as a scalable and interpretable decision-support approach for managing COVID-19 and future infectious disease scenarios.}, } @article {pmid42326837, year = {2026}, author = {Virwani, PD and Qian, G and Cheung, CN and Pijarnvanit, TKKTS and Hsu, MSS and Chow, YH and Tang, LK and Tse, YH and Xian, JW and Lam, SS and Lee, CPI and Lo, CCW and Liu, RKC and Ho, TL and Chow, BY and Leung, KS and Lo, EKK and Yuen, MF and Leung, SY and Hung, IF and Louie, JCY and Teo, KC and El-Nezami, H and Ho, JWK and Lau, KK}, title = {Associations between gut microbiome and 24-hour blood pressure variability: a cross-sectional study highlighting sex differences and potential therapeutic targets.}, journal = {Gut microbiome (Cambridge, England)}, volume = {7}, number = {}, pages = {e9}, pmid = {42326837}, issn = {2632-2897}, abstract = {Blood pressure (BP) variability is an independent risk factor for cardiovascular disease. Gut microbiome (GM) regulates BP, but its association with BP variability remains unclear. We examined the association of GM, determined by stool shotgun metagenomic sequencing, with 24-hour BP average real variability (ARV) assessed by ambulatory BP monitoring in 235 community-dwelling adults from Hong Kong (111 men and 124 women, mean age 54 ± 6 years) using covariate-adjusted statistical models. The GM alpha diversity was negatively associated with systolic BP (SBP) ARV in the full cohort, driven by women. In men, beta diversity of both GM species and function was associated with SBP ARV, while Bacteroides nordii and the steroid hormone biosynthesis pathway had a positive association with SBP ARV. Bacteroides nordii emerged as the key species driving the significant positive association of steroid hormone biosynthesis and other pro-pathogenic pathways with SBP ARV, including lipopolysaccharide biosynthesis, phenylalanine, and sulfur metabolism in men, warranting further investigation for its causal role. We demonstrated distinct signatures of GM dysbiosis, composition, and function with minimal overlap between men and women with increased 24-hour SBP variability. Our work suggests that sex differences should be an important consideration in mechanistic and therapeutic investigations of GM-mediated BP variability.}, } @article {pmid42327082, year = {2026}, author = {Loya, O and Villarreal, ES and Carneiro, A and Agarwal, S and Fraidenburg, D and Sun, J and de Jesus Perez, V and Lahm, T and Oliveira, SD}, title = {Sex-linked Lung Estrobolome May Contribute to Pulmonary Hypertension Penetrance of Bmpr2 R899X Mutation via an ET-1 [high] Endoregulatory Macrophage Phenotype.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.08.729693}, pmid = {42327082}, issn = {2692-8205}, abstract = {Mutations in the bone morphogenetic protein receptor 2 (BMPR2) are a major genetic driver of pulmonary arterial hypertension (PAH), yet their penetrance is strikingly sex-biased: females are disproportionately affected, while males experience poorer outcomes. While hormonal and chromosomal factors have been implicated, the biological basis for this disparity remains not fully understood. Here, we investigated the role of the lung microbiome in sex-linked PAH pathogenesis. We hypothesized that increased BMPR2 mutation penetrance in females is partly driven by the accumulation of potent vasoactive molecules, such as endothelin-1 (ET-1), in response to lung microbiome dysbiosis. Using humanized Bmpr2 [+/R899X] mice, we integrate lung metagenomics with basic functional immune profiling to show that females develop a distinct microbiome profile, characterized by increased microbial-derived lipopolysaccharide (LPS), potentially fueling the pathogenic effects of the estrogen metabolite 16α-hydroxyestrone (16α-OHE). These signals converge on macrophages, where co-exposure led to a hyperactivated state characterized by enhanced phagocytosis and ET-1 secretion. Tissue-level analyses confirmed immune cell infiltration and spatial association with elevated ET-1, providing evidence that these factors may contribute to the onset of sex-linked PAH. Taken together, these findings identify a previously unrecognized microbiome-estrogen-immune axis that amplifies BMPR2 dysfunction and provides a mechanistic basis for female-biased disease penetrance.}, } @article {pmid42327127, year = {2026}, author = {Troman, L and Kim, J and Rose, JJA and Johnson, M and Banfield, JF and Petrovski, S and Ghosal, D}, title = {A Novel Pilus System in Candidate Phyla Radiation Bacteria.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.03.709456}, pmid = {42327127}, issn = {2692-8205}, abstract = {The Candidate Phyla Radiation (CPR) represents a bacterial superphylum estimated to include between 15-50% of all bacterial species, yet CPR bacteria remain challenging to culture and have been primarily identified through metagenomic approaches. Candidatus Mycosynbacter amalyticus is a parasitic CPR bacterium that specifically targets Gordonia amarae , an actinobacterium with a hydrophobic, mycolic acid-rich cell envelope. Previous cryo-electron tomography indicated that Ca . M. amalyticus assembles thin extracellular filaments that are important for host interaction, yet their molecular identity remains unknown. Here, we applied single-particle cryo-electron microscopy to determine high-resolution structures of these filaments (2.8 and 3.6 Å), enabling the unambiguous identification of two previously uncharacterized pilins from the experimental density maps. These pilins, designated PamA and PamB, assemble into unique helical filaments distinct from all previously characterized filaments in both domain architecture and assembly mechanism. Despite low sequence identity, both PamA and PamB share conserved structural principles, including Ig-like folds and donor-strand exchange-mediated assembly. Phylogenetic analysis indicates that Pam pilins are exclusive to CPR bacteria, with homologues distributed predominantly across the classes Saccharimonadia and Microgenomatia. Analysis of the conserved pam operon identifies putative chaperones (PamC and PamD) and assembly factors structurally homologous to chaperone-usher pili components, suggesting an analogous but distinct assembly pathway. These findings expand the known diversity of bacterial pilus systems and demonstrate the power of structural approaches for characterizing uncharacterized proteins encoded within CPR genomes.}, } @article {pmid42327471, year = {2026}, author = {Li, YM and He, FF and Donge-Liu, and Bin-Xu, and Shuyi-Li, }, title = {Multi-Omic Profiling of Gut Microbiota and Fecal Metabolites in Patients With Polycystic Ovary Syndrome: A Cross-Sectional Study.}, journal = {Health science reports}, volume = {9}, number = {6}, pages = {e72593}, pmid = {42327471}, issn = {2398-8835}, abstract = {BACKGROUND AND AIM: Intestinal flora composition in polycystic ovary syndrome (PCOS) varies, and the relationship between intestinal flora, fecal metabolites, clinical characteristics, and PCOS pathogenesis remains unclear. This study aimed to elucidate the gut microbiota characteristics of patients with PCOS, focusing on changes in normal-weight individuals, to provide new insights into its pathogenesis.

METHODS: We combined 16S rRNA gene sequencing re-analysis with metagenomics and metabolomics to investigate gut microbiota and fecal metabolome alterations in PCOS. We re-analyzed our previous data on normal-weight women with PCOS (PCOS, n = 24; healthy controls [HC], n = 12) and the public databases (PCOS, n = 98; HC, n = 71) to further investigate the structure and function of the PCOS intestinal flora. Subsequently, from our previous study samples, we selected 10 patients residing in the Kaifu district, and their fecal samples (normal-weight PCOS group, n = 6; HC group, n = 4) were analyzed using metagenomic sequencing and non-targeted fecal metabolomics. Finally, the correlations among intestinal flora, fecal metabolites, and clinical indicators were evaluated.

RESULTS: Based on the 16S rRNA data reanalysis, there were no significant differences in beta and alpha diversity between PCOS and normal controls. However, the PCOS group displayed a significantly higher relative abundance of Ruminococcus, Lachnospiraceae, and Escherichia-Shigella (p < 0.05) but a significantly lower relative abundance of Prevotella (p < 0.05) compared with the HC group. Subsequent metagenomics and metabolomics analyses revealed functional alterations, particularly in pathways related to secondary bile acid and lipid metabolism. Furthermore, Ruminococcus and Roseburia were positively correlated with Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) and negatively correlated with high-density lipoprotein (HDL) in patients with normal-weight PCOS.

CONCLUSIONS: This study highlights gut microbial dysbiosis as a key feature of PCOS. Reanalysis of 16S rRNA data revealed specific taxonomic shifts without altering overall diversity, notably an enrichment of Ruminococcus and a depletion of Prevotella. Furthermore, our metagenomics study identified functional reprogramming in pathways related to secondary bile acid and lipid metabolism. Crucially, even in normal-weight PCOS patients, these microbial alterations significantly correlated with adverse metabolic profiles (heightened insulin resistance and lower HDL levels), highlighting the microbiome as a potential therapeutic target.

ETHICAL REVIEW NO: CHiECRT1900028223.}, } @article {pmid42327525, year = {2026}, author = {Maity, H and Hiwale, K and Meshram, S and Shishodiya, M and Pratyeke Maraskolhe, D and Narang, P}, title = {Zoonotic Nontuberculous Mycobacteria: Transmission Pathways, Laboratory Diagnosis, Detection Methodologies, and One Health Priorities.}, journal = {Infectious diseases & clinical microbiology}, volume = {8}, number = {3}, pages = {232-252}, pmid = {42327525}, issn = {2667-646X}, abstract = {Nontuberculous mycobacteria (NTM) are an ecologically diverse group of environmental mycobacteria that are increasingly recognized as an important cause of human and animal disease. While most infections arise from environmental exposure, evidence from outbreak reports and genomic epidemiology suggests animal- associated and device-associated transmission pathways that intersect with human occupational and clinical risk. This review synthesizes current knowledge on zoonotic and animal-associated NTM, including recent taxonomy updates driven by genomic approaches, major reservoirs (including aquaculture, livestock, wildlife, and engineered water systems), as well as clinical and veterinary manifestations, and operational laboratory approaches for detection and characterization. We present a tiered diagnostic framework, ranging from microscopy and culture to targeted polymerase chain reaction (PCR), whole-genome sequencing, and emerging metagenomic and artificial intelligence (AI)-based pipelines, and we discuss biosafety considerations, reporting standards, and One Health surveillance priorities. Key research gaps include distinguishing true animal-to-human transmission from shared-source exposure, harmonizing One Health metadata and antimicrobial resistance (AMR) surveillance, and validating climate-sensitive predictive models. We propose practical, resource-adaptive recommendations for surveillance, laboratory workflows, and outbreak response. A coordinated global investment in integrated One Health genomic surveillance, harmonized metadata standards, and capacity building is urgently required to detect, attribute, and mitigate zoonotic NTM threats.}, } @article {pmid42327630, year = {2026}, author = {Katarzyna, BS and Danuta, CL and Wiktoria, K and Małgorzata, T and Natalia, K and Dominika, MM and Karina, R and Joanna, P and Karina, K and Barbara, G and Danuta, LK and Helena, G and Wiśniewska, M and Karolina, SŻ and Stachowska, E}, title = {The impact of freeze-dried food on gut microbiota composition: a preliminary study.}, journal = {Current research in food science}, volume = {13}, number = {}, pages = {101470}, pmid = {42327630}, issn = {2665-9271}, abstract = {Freeze-dried food is widely used during space expeditions or flights. However, evidence on how this affects the gut microbiota is limited. This study aimed to assess changes in the composition of gut microbiota in volunteers subjected to a 14-day stay in a controlled space-analogue habitat. Five adults provided stool samples at baseline and after two weeks. Meals were freeze-dried and standardized for portion size and composition. Meals were served according to a daily schedule with no additional snacks allowed. Coffee and tea were permitted. Compliance was monitored by returning and verifying the packaging. Bacterial community profiles were assessed using shallow shotgun metagenomics and analyzed using paired statistical methods, including alpha diversity indices and beta diversity ordination with permutation-based testing. Differential abundance analyses were performed to identify taxa showing trends toward change during the intervention. Overall gut bacterial diversity and community structure were essentially stable over 14 days among all participants. No statistically significant changes in alpha diversity were observed, and global beta diversity patterns did not indicate a consistent separation of the entire community between baseline and day 14. Exploratory analyses suggested small changes within individuals in the relative abundance of selected taxa; however, inter-individual variability prevailed, and the small sample size limited statistical power. It appears that a diet consisting entirely of freeze-dried foods, consumed for 14 days, did not significantly affect the overall diversity of the gut microbiota or the structure of its communities. However, these studies are preliminary in nature and provide hypotheses for use in larger, controlled studies aimed at elucidating the microbiome's response to dietary regimens based on freeze-dried products.}, } @article {pmid42328576, year = {2026}, author = {Wu, Y and Gao, Y and Fang, Z and Huang, W and Guo, F}, title = {Time-dependent microbiology of peripancreatic drainage fluid in severe acute pancreatitis: a prospective real-world observational study using metagenomic sequencing and culture.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1795250}, pmid = {42328576}, issn = {2296-858X}, abstract = {OBJECTIVE: The microbiological characteristics of peripancreatic collections in severe acute pancreatitis (SAP) evolve over time, yet prospective data linking pathogen detection to disease timing and first intervention remain limited.

METHODS: This prospective single-center observational study enrolled 20 patients with SAP undergoing first-time percutaneous catheter drainage (PCD) for suspected infected pancreatic necrosis (IPN). Peripancreatic drainage fluid samples were simultaneously analyzed by conventional microbiological culture and metagenomic next-generation sequencing (mNGS). Microbiological positivity rates were compared according to time from disease onset (≤14 vs. >14 days).

RESULTS: Overall, mNGS was positive in 9/20 cases (45.0%) and conventional culture in 6/20 cases (30.0%). When stratified by time from disease onset, microbiological positivity was low within 14 days (mNGS: 1/7, 14.3%; culture: 1/7, 14.3%), but increased in patients undergoing drainage beyond 14 days (mNGS: 8/13, 61.5%; culture: 5/13, 38.5%). mNGS identified a broader spectrum of pathogens, particularly polymicrobial, anaerobic, and fungal organisms. Enterococcus species and Klebsiella pneumoniae were the most frequently detected pathogens.

CONCLUSION: In this prospective observational cohort, peripancreatic collections were predominantly culture- and mNGS-negative during the early phase of SAP, supporting the concept that early necrosis is commonly sterile. In later stages, mNGS provides complementary microbiological information beyond conventional culture. These findings offer descriptive real-world evidence on the time-dependent microbiology of suspected IPN and may inform future studies on optimized diagnostic and antimicrobial strategies.}, } @article {pmid42328632, year = {2026}, author = {Alnasser, SM and Ravikumar, S and Jayaraman, S and Selvaraj, D and Gunasekaran, V}, title = {Modulatory effect of porous silicon water-formulated catechin on gut microbiome in chronic unpredictable mild stress-induced dementia in a rat model.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1778580}, pmid = {42328632}, issn = {1663-9812}, abstract = {Stress-induced dysbiosis exacerbates mental health by modulating the nervous system and gut permeability. In this study, we investigate the therapeutic potential of porous silicon water-mixed catechin in alleviating chronic stress-induced dementia in rats. In a 28-day study, chronic unpredictable mild stress (CUMS)-induced rats were treated with Lactobacillus acidophilus (2.5 × 10^9 CFU, p.o), porous silicon water (7 mg/kg, p.o), catechin (30 mg/kg, p.o), and porous silicon water-mixed catechin (PSC) (7 mg and 30 mg/kg, p.o). The effect of porous silicon water-mixed catechin was evaluated through behavioral studies, plasma acetylcholinesterase activity, plasma glutamate, brain reactive oxygen species (ROS), brain endogenous anti-oxidant enzymes, metagenomics analysis, and histological examination of the prefrontal cortex and hippocampus. Administration of PSC significantly improved spatial learning and memory by reducing escape latency time and increased exploratory behavior in the open platform. PSC significantly inhibited acetylcholinesterase enzyme activity and restored endogenous antioxidants such as superoxide dismutase (SOD), catalase (CAT), and glutathione reductase (GSH) while reducing lipid peroxidation (LPO) compared to the CUMS group. In addition, PSC decreased the brain ROS levels, as determined by a fluorescence assay, and reduced plasma glutamate levels. 16S rRNA V3-V4 metagenomic analysis revealed a significant increase in microbial diversity (Shannon index: 7.52), microbial richness (Chao1 index: 1059.41), β-diversity index, and overall taxonomic abundance in treated rats. CUMS-induced morphological alterations in the hippocampus and prefrontal cortex were significantly improved following PSC administration. In the present study, Pearson correlation coefficient (r) demonstrates an association between gut microbial abundance and AChE activity. Hence, it has been concluded that PSC treatment may significantly modulate the gut microbiome and improve cognition in chronic unpredictable mild stress-induced dementia.}, } @article {pmid42328867, year = {2026}, author = {Wang, Y and Sheng, P and Wang, S and Zhong, X and Cao, H and Li, D and Yan, J and Yang, J and Wang, Y and Peng, J and Sun, F and Wang, S and Feng, Y and Sun, J and Zhang, F}, title = {Gut microbiota translocation contributes to early islet apoptosis in streptozotocin-induced diabetes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0017226}, doi = {10.1128/msystems.00172-26}, pmid = {42328867}, issn = {2379-5077}, abstract = {Dysbiosis of the gut microbiota and impaired intestinal barrier are associated with diabetes development. The translocation of gut microbiota induced by streptozotocin (STZ) has been confirmed to damage pancreatic islets. However, it remains uncertain whether dysregulated gut microbiota plays an essential role in the translocation leading to pancreatic injury. In specific pathogen-free (SPF) and germ-free (GF) mice treated with STZ, we measured glucose metabolism levels, pancreatic islet damage, intestinal barrier integrity, and bacterial content in the pancreas to investigate the role of gut microbiota translocation in diabetes development. Shotgun metagenomic sequencing was used to analyze the impact of STZ on gut microbiota structure and function. Fecal microbiota transplantation was performed to explore if gut microbiota translocation depends on STZ-induced structural dysregulation. STZ induced intestinal damage in SPF mice, resulting in gut microbiota translocation to the pancreas, pancreatic apoptosis, and dysregulated glucose metabolism. Despite inherent intestinal barrier damage, absence of pancreatic apoptosis in GF mice further indicates that gut microbiota translocation is an essential prerequisite for STZ-induced pancreatic islet apoptosis. STZ significantly altered mouse gut microbiota composition and function. Transplantation of fecal microbiota from STZ-treated or saline-treated mice into STZ-induced GF mice also resulted in microbial translocation and pancreas apoptosis. Apoptosis of β cells in STZ-treated mice results from gut microbiota translocating to the pancreas through impaired intestinal barrier caused by STZ treatment independent of alterations in the gut microbial community.IMPORTANCEIn our study, the apoptosis of β cells in STZ-treated mice is the result of the translocation of gut microbiota to the pancreas through the impaired intestinal barrier induced by STZ, independent of alterations in the gut microbiota. These findings proposed the potential role of compounds in impairing the intestinal barrier integrity, promoting microbiota migration and finally damaging pancreatic islets.}, } @article {pmid42328985, year = {2026}, author = {Pallotti, S and Nigro, ME and Albini, E and Russo, E and Carpi, FM and Falconi, M and Torbidoni-Baldassari, B and Giuliodori, AM and Petrelli, D and Beccacece, L and Pezzotti, G and Magistrali, CF and Massacci, FR and Napolioni, V}, title = {Long-read metagenomics reveals stable resistome and microbiome in treated Italian slaughterhouse wastewater: a preliminary study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0156226}, doi = {10.1128/spectrum.01562-26}, pmid = {42328985}, issn = {2165-0497}, abstract = {Antimicrobial resistance (AMR) poses a major threat to global health, and food production environments are increasingly recognized as potential reservoirs and dissemination points for resistant bacteria and antimicrobial resistance genes (ARGs). Slaughterhouse wastewater contains complex microbial communities originating from multiple animal sources and processing activities, yet the effectiveness of current treatment processes in mitigating microbiological and resistome-associated risks remains poorly understood. In this study, we applied high-throughput long-read metagenomic sequencing to characterize microbial community composition and resistome profiles in wastewater samples collected before and after physicochemical treatment from four Italian slaughterhouses. Taxonomic profiling revealed a diverse microbiome dominated by Bacillota and Pseudomonadota, along with DNA assigned to potentially clinically relevant taxa, including members of the ESKAPE group. Resistome analysis identified 96 ARGs conferring resistance to 16 antimicrobial classes. Comparative analyses of pre- and post-treatment samples showed no significant changes in microbial community structure, alpha- and beta-diversity metrics, or ARG profiles. These findings indicate that the applied coagulation-flocculation-based treatment has limited effects on the relative composition of the wastewater microbiome and resistome, as detected by shotgun metagenomics. Our results suggest that slaughterhouse wastewater may act as a persistent environmental reservoir of antimicrobial resistance determinants and highlight the need for enhanced treatment strategies and resistome-oriented surveillance within a One Health framework. Given the limited sample size and the preliminary nature of this investigation, these findings should be interpreted as exploratory and hypothesis-generating, rather than broadly generalizable.IMPORTANCEAntimicrobial resistance is a growing global health concern that extends beyond clinical settings into agricultural and environmental systems. Slaughterhouses represent critical interfaces where microbial communities from livestock, processing environments, and wastewater converge, creating opportunities for the persistence and dissemination of antimicrobial resistance genes. Despite the widespread use of physicochemical treatments to reduce organic load and suspended solids in slaughterhouse wastewater, their impact on microbial communities and resistome remains poorly characterized. By applying long-read metagenomic sequencing, this study provides a comprehensive characterization of the microbiome and resistome in slaughterhouse wastewater before and after treatment. Our findings show that commonly applied coagulation-flocculation treatments do not substantially alter the relative structure of microbial communities or the diversity of resistance genes. These results highlight the potential role of slaughterhouse wastewater as an environmental reservoir for antimicrobial resistance and emphasize the need for improved treatment technologies and systematic surveillance strategies to mitigate the environmental dissemination of resistance determinants in line with the One Health approach.}, } @article {pmid42329047, year = {2026}, author = {Villanelo, SAR and Vestergaard, SZ and Liu, L and Yang, Y and Pedersen, IS and Nielsen, PH and Dueholm, MKD}, title = {Application of antibiotics for the selective isolation of previously uncultured species from activated sludge.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0147726}, doi = {10.1128/spectrum.01477-26}, pmid = {42329047}, issn = {2165-0497}, abstract = {The microbial communities in activated sludge (AS) drive pollutant degradation and nutrient transformation into biomass and gaseous products, while also enabling resource recovery processes. In these systems, microorganisms grow as flocs, whose aggregation properties are essential for retaining active biomass while producing a clarified effluent. Understanding the microbial composition of AS and the functions of individual taxa is crucial for improving wastewater treatment practices and developing new treatment technologies. Although DNA-based studies have identified abundant taxa and inferred their metabolic roles, many of these organisms remain uncultured, limiting experimental validation of genome-based predictions. Here, we investigated whether antibiotics can transiently reduce community complexity and alleviate competitive exclusion during cultivation, thereby facilitating isolation of previously uncultured activated sludge bacteria. Dispersed single cells from AS were cultivated on agarose plates containing filter-sterilized AS fluid and 1 of 11 antibiotics at three concentrations. Full-length 16S rRNA gene amplicon sequencing indicated that antibiotics reduced microbial diversity and altered community composition in an antibiotic- and concentration-dependent manner. Two antibiotic conditions were selected for pure-culture isolation, resulting in 74 isolates that represented 28 different species based on genomic average nucleotide identity. These include 13 putatively novel species based on GTDB classification, and 19 species belonging to nine globally abundant AS core genera. Although several isolates belonged to genera with cultured representatives, they likely represent distinct species with potentially different ecological functions and physiological traits. These findings demonstrate that antibiotics can function as ecological selectors during cultivation and aid the targeted isolation of ecosystem-relevant activated sludge bacteria.IMPORTANCEBiological wastewater treatment relies on diverse microbial communities to degrade pollutants and drive nutrient transformations. Understanding the physiology and metabolism of these microorganisms is essential for improving the efficiency and cost-effectiveness of treatment processes. Much of our current knowledge is derived from 16S rRNA gene amplicon sequencing and metagenomic analyses. However, validating these sequencing- and genome-based insights requires bacterial species as pure cultures, and only a limited number of taxa common in wastewater treatment plants are currently available in culture. Here, we present an isolation strategy that uses antibiotics as a selective pressure to reduce microbial complexity and alleviate competitive exclusion during cultivation, while full-length 16S rRNA gene amplicon sequencing is used to monitor enrichment and guide targeted isolation, thereby facilitating the recovery of process-relevant activated sludge bacteria, including potentially uncultured taxa. These isolates can serve as model organisms for experimental validation of genome-based predictions.}, } @article {pmid42329229, year = {2026}, author = {Yao, C and Wang, Y and Zhou, J and Liu, B and Qi, L and Wang, B and Chen, F and Hou, L and Liu, M and Zheng, Y}, title = {Acidification Dominates over Hypoxia in Controlling Estuarine Nitrogen Removal Dynamics under Coupled Stressors.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c02533}, pmid = {42329229}, issn = {1520-5851}, abstract = {As critical transitional zones between land and sea, estuaries are confronting the dual threats of increasing acidification and hypoxia driven by human activities and climate change. However, the combined effects of these stressors on estuarine nitrogen removal processes remain poorly understood. In this study, using stable-isotope tracing and molecular techniques in the Yangtze estuary, we found that hypoxia promoted N removal, yet concurrent acidification can override this effect, leading to net inhibition and a consequent reduction in estuarine nitrogen removal capacity. However, in seasonally hypoxic zones, these combined stressors generally enhanced nitrogen removal rates (by up to 34.4%), which suggests a degree of resilience under such perturbations. Nevertheless, the concurrent acidification-hypoxia in seasonally hypoxic areas stimulated N2O emissions (8.5-44.4%), which may intensify climate forcing and thereby further exacerbate these environmental stressors. Metagenomic and quantitative PCR analyses corroborated these response patterns, revealing coordinated changes in the abundance and expression of key nitrogen-removal genes, as well as divergent microbial response strategies and niche differentiation under acidification-hypoxia stress. This study elucidates the previously overlooked interactive effects of acidification and hypoxia on estuarine nitrogen removal, providing a mechanistic basis for refining biogeochemical models to improve the reliability of simulations under multiple stressors.}, } @article {pmid42329244, year = {2026}, author = {Gallichan, S and Mäklin, T and Picton-Barlow, E and McKeown, C and Forrest, S and Corander, J and Moore, M and Feasey, NA and Heinz, E and Graf, FE and Lewis, JM}, title = {A more complete picture: capturing single nucleotide variant diversity in extended-spectrum beta-lactamase producing Escherichia coli using post-enrichment metagenomics.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, doi = {10.1099/mgen.0.001757}, pmid = {42329244}, issn = {2057-5858}, mesh = {*Escherichia coli/genetics/enzymology/isolation & purification ; *beta-Lactamases/genetics/metabolism ; *Metagenomics/methods ; *Polymorphism, Single Nucleotide ; Humans ; Escherichia coli Infections/microbiology/transmission ; Feces/microbiology ; Genome, Bacterial ; Whole Genome Sequencing ; Metagenome ; }, abstract = {Inferring transmission relies on accurately distinguishing between isolates from the same source and those from different sources, and high-quality genomic data are frequently used to model transmission scenarios. The post-enrichment metagenome sequencing (pe-MGS) method uses a sequencing approach to analyse the diversity of a target pathogen enriched by pre-culturing and has been effectively used to analyse the transmission of nosocomial infections. However, a direct comparison of single nucleotide variant (SNV) call accuracy, cost and feasibility between single-colony whole-genome sequence (sc-WGS) data and pe-MGS for an antimicrobial resistant bacteria of clinical importance, extended-spectrum beta-lactamase producing Escherichia coli (ESBL-EC), is required for implementation in large-scale clinical studies. A spiked stool sample and rectal swabs from six study participants were pre-enriched in buffered peptone water and cultured on MacConkey agar with 1 mg l[-1] cefotaxime. Seven single colonies were picked, and the remaining biomass of all colonies was collected from each plate, sequenced and analysed using the mSWEEP/mGEMS pipeline. We created a custom SNV calling workflow that allows heterozygous SNVs in a bacterial population and found that the choice of reference changed the number of measurable SNV distances between the sc-WGS and pe-MGS. Using our custom workflow with a core-gene reference captured 99% of all the SNV calls from multiple sc-WGS data in the pe-MGS data of the same culture. The plate sweep method offers a feasible, cost-effective alternative to multiple single colony picks for describing within-host ESBL-EC diversity. The workflow we developed allows for effective SNV calling from pe-MGS data that were comparable to SNV calls from multiple sc-WGS data from the same sample.}, } @article {pmid42330062, year = {2026}, author = {Mason, CJ and Weaver, M and Kissinger, KR and Johnson, MA and Copeland, DC and Anderson, KE and Geib, SM}, title = {Applying PCR cycle autonormalization to PacBio full-length 16S rRNA library preparations: impacts on error rates and sequence distributions.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0029526}, doi = {10.1128/msphere.00295-26}, pmid = {42330062}, issn = {2379-5042}, abstract = {The bacterial 16S rRNA gene is widely used to characterize host-associated and environmental microbiomes, most commonly through sequencing short hypervariable regions. Recent improvements in PacBio sequencing chemistry and concatenation approaches can now enable high-throughput, full-length 16S rRNA gene sequencing with high accuracy and depth. However, errors introduced during library preparation remain a major limitation, particularly during PCR amplification of full-length amplicons, where error accumulation may be elevated due to longer sequence lengths. These challenges are amplified when samples vary widely in microbial biomass, making it difficult to select a single optimal number of PCR cycles. Here, we evaluated PCR cycle autonormalization for PacBio Kinnex full-length 16S rRNA gene sequencing across seven agriculturally relevant specimen types. We compared conventional fixed-cycle PCR protocols (20, 24, and 30 cycles) with an autonormalization approach in which individual reactions were terminated during exponential amplification based on real-time fluorescence thresholds. Under the workflow tested here, autonormalized libraries generally retained a high proportion of sequences following denoising and chimera removal, exhibited low residual error rates (<0.005%), and yielded relatively even read distributions across heterogeneous sample inputs. Overamplified reactions (30 cycles) showed elevated residual error rates and greater sequence loss, particularly in samples with higher microbial biodiversity, whereas low-cycle libraries produced more variable read output among specimens. Importantly, the PCR protocol had relatively minor effects on overall community composition compared with specimen type. These results support PCR cycle autonormalization as a useful workflow strategy for heterogeneous full-length 16S library preparation, while also highlighting the importance of library design, pooling strategy, and downstream processing in shaping technical outcomes.IMPORTANCEAmplicon-based sequencing of the 16S rRNA gene is a foundational tool in microbiome research, yet PCR amplification remains a major source of library-preparation error. This challenge is magnified for full-length 16S rRNA sequencing and for workflows that process specimen types with widely varying microbial biomass. Selecting a single PCR cycle number can underamplify low-biomass samples or overamplify high-titer samples, increasing artifacts and sequence loss during downstream processing. Here, we show that PCR cycle autonormalization can be integrated into a PacBio full-length 16S rRNA workflow and, under the conditions tested, provides low residual error rates and relatively even sample representation across heterogeneous inputs. Autonormalization also enables blind pooling of amplicons without post-PCR quantification or equimolar normalization, reducing hands-on time and sample loss. These benefits make cycle autonormalization particularly valuable for high-throughput and production-scale library preparation applications handling diverse specimen types.}, } @article {pmid42330763, year = {2026}, author = {Goel, A and Ncho, CM and Jeong, CM and Gupta, V and Jung, JY and Ha, SY and Yang, JK and Choi, YH}, title = {Dietary polyphenols from shredded, steam-exploded pine particles mitigate the adverse effects of heat stress in broiler chickens.}, journal = {Poultry science}, volume = {105}, number = {10}, pages = {107298}, doi = {10.1016/j.psj.2026.107298}, pmid = {42330763}, issn = {1525-3171}, abstract = {The current study investigated the impact of supplementing polyphenols extracted from shredded, steam-exploded pine particles (PSPP) on the performance, gene expression, and gut metagenome of broilers exposed to cyclic heat stress (CHS). A total of 216 chickens were distributed into a 2 (temperature) by 3 (diets) design, with each treatment consisting of six replicates of six chickens. Specifically, chickens were fed diets containing 0% PSPP, 0.5% PSPP, and 1% PSPP and exposed to two temperature conditions: CHS (31°C) and Thermoneutral (NT, 21°C). The CHS was conducted for 6 hours every day for 7 consecutive days. Final body weight, average daily gain, and average daily feed intake (ADFI) were decreased, while feed conversion ratio and rectal temperature were increased in heat-exposed chickens. Dietary PSPP supplementation enhanced ADFI. The weight of the liver, bursa, and length of the jejunum and ileum were decreased in heat-exposed chickens. Plasma cholesterol was increased, and triglycerides were decreased in heat-exposed chickens. After heat exposure, gene expression of ZO1, ZO2, GLP2, NOX1, SOD, GPX, HSP70, HSP90, NRF2, TLR2, and TLR4 increased in the jejunum. GLP2 gene expression was similar in 1%PSPP exposed to HS in comparison to the entire NT-exposed chickens. Concerning microbiota analysis, alpha diversity indices, such as Shannon and Gini-Simpson, were increased following CHS exposure. Beta diversity, measured through unweighted and weighted UniFrac distances, showed temperature, dose, and interaction effects. The relative abundance of the phylum Candidatus Melainabacteria was increased, while Tenericutes populations were decreased in heat-exposed chickens. Furthermore, a total of thirty genera were identified as microbial biomarkers of CHS. Interestingly, the relative abundance of five pathogenic bacterial genera was found to be decreased in the 0.5%PSPP treatment. Overall, CHS negatively influences growth performance, modulates the expression of the gut antioxidant-related genes, and favors the colonization of pathogenic bacteria. However, 0.5% PSPP may mitigate CHS by reducing pathogen colonization in the gut of broilers.}, } @article {pmid42330797, year = {2026}, author = {Gebert, JT and Huleatt, EM and Scribano, FJ and Eledge, MR and Dorn, LE and Hasmi, SK and Hyser, JM}, title = {High-throughput quantitation of pathogen-induced calcium signals captured through live-cell fluorescence microscopy.}, journal = {Cell calcium}, volume = {136}, number = {}, pages = {103160}, doi = {10.1016/j.ceca.2026.103160}, pmid = {42330797}, issn = {1532-1991}, abstract = {Many intracellular pathogens manipulate host cell calcium to facilitate their survival and replication. Live-cell microscopy using fluorescent calcium indicators has become an indispensable tool for characterizing the mechanisms underlying both homeostatic and pathogen-induced cellular calcium dynamics, but such imaging must be coupled with robust quantitative analysis. Further, calcium imaging is most powerful when paired with reductive studies targeting calcium-modulating proteins. The lack of specific inhibitors or agonists to directly target most pathogen-induced calcium signals precludes many of the approaches that have allowed for robust characterization of major eukaryotic cell calcium signaling mechanisms, such as ER Ca[2+] release by inositol triphosphate receptors. Given this, we sought to develop quantitative imaging pipelines tailored for the characterization of pathogen-induced calcium signals. Using rotavirus as a prototypical calcium-modulating pathogen, we developed and optimized a suite of computational tools for automated quantitation of both intra- and inter-cellular calcium signals detected via live-cell imaging of infected epithelial monolayers expressing genetically encoded calcium indicators. Using recombinant strains of rotavirus that express fluorescent markers, we developed a system that allows for automated detection of rotavirus-infected cells and normalization of signals to infectivity. All tools were built in ImageJ, making them freely available and adaptable across operating systems and microscope setups. These tools required minimal active time from the user and allowed for the extraction of signal parameters previously unquantifiable, increasing the speed and breadth of characterization.}, } @article {pmid42330834, year = {2026}, author = {Cabrera, C and Carrión, N and Mateo, D and Heredia, L and Pino, M and Galvez, S and Forcadell-Ferreres, E and Vicens, P and Torrente, M}, title = {Shotgun metagenomic profiling of the gut microbiota in Parkinson's disease dementia and dementia with Lewy bodies.}, journal = {Parkinsonism & related disorders}, volume = {149}, number = {}, pages = {108400}, doi = {10.1016/j.parkreldis.2026.108400}, pmid = {42330834}, issn = {1873-5126}, abstract = {BACKGROUND: Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are related α-synucleinopathies that share Lewy pathology, but they differ clinically. Increasing evidence links gut microbiota (GMB) dysbiosis and microbially derived metabolites to Parkinsonian disorders yet reported associations remain heterogeneous across cohorts and the Lewy body dementia syndromes are comparatively under characterized. This study integrated clinical characterization and GMB profiling in Parkinson's disease dementia (PDD), DLB, and healthy controls (HC) to identify shared and syndrome specific features, and to relate these patterns to cognitive, neuropsychiatric, and functional outcomes.

METHODS: The present cross-sectional case-control study in Spain included 76 adults aged 60 to 85 years (HC = 38, PDD = 27, DLB = 11). Stool samples underwent shotgun metagenomic sequencing, with species-level taxonomic profiling using Kraken2. Community diversity was assessed using observed species and Chao1 richness, Shannon alpha diversity, and Bray-Curtis dissimilarity for beta diversity. LEfSe and multivariate linear modeling with MaAsLin2 were performed to identify GMB species associated with PDD and DLB and their clinical correlates.

RESULTS: PDD showed higher richness compared with HC. Shannon alpha diversity did not differ between groups. Bray-Curtis differed by separation of HC from both PDD and DLB, with no significant difference between Lewy body dementia syndromes. LEfSe identified 19 significantly differential taxa. Furthermore, several taxa showed significant multivariable associations with clinical outcomes.

CONCLUSIONS: PDD and DLB shared a broadly similar GMB alteration away from HC, with multivariable associations between several taxa and clinical outcomes. Longitudinal and functional studies are needed to clarify causality and biomarker potential.}, } @article {pmid42330882, year = {2026}, author = {Li, X and Wang, W and Liu, Y and Xu, Z and Wang, M and Zhao, J and Hua, Y}, title = {Role of nitrate-dependent Fe(II)-oxidizing bacteria in coupling nitrogen and phosphorus cycling in nearshore sediments of shallow lakes.}, journal = {Water research}, volume = {304}, number = {}, pages = {126323}, doi = {10.1016/j.watres.2026.126323}, pmid = {42330882}, issn = {1879-2448}, abstract = {The nearshore shallow-water zones of lakes serve as critical interfaces for the interception and transformation of land-derived nitrogen and phosphorus pollutants. Nitrate-dependent Fe(II)-oxidizing bacteria (NDFOB) may promote the formation of Fe(III) (hydr)oxides through nitrate reduction and Fe(II) oxidation, thereby potentially enhancing the adsorption of phosphorus in pore water and coupling of nitrogen removal and phosphorus immobilization; however, their ecological role in shallow lakes remains poorly understood. This study focused on six shallow lakes, analyzing the relationships between most probable number (MPN) counts of NDFOB, nitrogen, iron, and phosphorus contents, and using metagenomic techniques to explore their associations with functional genes involved in nitrogen, iron, and phosphorus cycling. The results showed that the number and spatial distribution of NDFOB were associated with lake trophic status. In moderately eutrophic lakes, elevated nitrogen loads were correlated with NDFOB enrichment possibly due to the provision of abundant electron acceptors (NO3[-]) for nitrate-dependent Fe(II) oxidation, and NDFOB number was positively correlated with nitrogen concentrations and negatively correlated with phosphorus content in pore water. Meanwhile, it was also associated with relative abundances of iron reduction-related genes and the presence of iron oxidation-associated genes. Network analysis further provided statistical clues for putative functional links between the ferrous iron oxidation process linked to NDFOB genera (e.g., Aquabacterium) and iron reduction, denitrification, and organic phosphorus mineralization. This study highlights the potential role of NDFOB in intercepting nitrogen and phosphorus within nearshore sediments and provides a microbial perspective for mitigating the risk of internal phosphorus release in shallow lakes.}, } @article {pmid42330901, year = {2026}, author = {Barbe, V and Saint-Picq, C and Odobel, C and Hingant, M and Pujo-Pay, M and Cruaud, C and Petit, JL and Fischer, C and Boulard, Y and Cébron, A and Ter Halle, A and Eyheraguibel, B and Lemechko, P and Bruzaud, S and Ghiglione, JF}, title = {Unveiling plastic biodegradation pathways through [13]C-DNA stable isotope probing and metagenomics.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142755}, doi = {10.1016/j.jhazmat.2026.142755}, pmid = {42330901}, issn = {1873-3336}, abstract = {Polyhydroxyalkanoates (PHAs) are promising biobased and biodegradable alternatives to conventional plastics, yet their degradation mechanisms and the diversity of microorganisms involved remain poorly characterized in marine ecosystems. Here, we used [13]C-labeled poly(3-hydroxybutyrate) (PHB) and combined DNA-stable isotope probing (DNA-SIP) with metagenomic to identify and functionally characterize active PHB-degrading bacteria in seawater. We identified three metagenome-assembled genomes (MAGs) affiliated with the genus Agarilytica that exhibited an exceptional expansion of preficted extracellular short-chain-length PHA depolymerase genes (ephaZscl) with up to 14 copies per genome, far exceeding the one-to-two copies typically reported. Comparative genomic and structural analyses revealed gene duplication and fusion events, given rise to tandem or chimeric depolymerases that may enhance catalytic diversity and substrate accessibility. Three-dimensional structural modeling confirmed that these fusion proteins retained functional catalytic domains with potential cooperative or independent activity. Such genomic redundancy and structural diversification likely confer an adaptive advantage for PHB biodegradation in marine environment. Collectively, our findings provide new insights into the ecological and evolutionary strategies of marine PHB degraders and highlight the power of DNA-SIP metagenomic for elucidating active plastic biodegradation pathways under natural conditions.}, } @article {pmid42331262, year = {2026}, author = {He, G and Guo, X and Lu, W and Zou, Y and Zheng, J and Han, X and Hong, Y and Wei, R}, title = {Molecular features of external Auditory Canal cholesteatoma by microbial metagenomic sequencing.}, journal = {Genomics}, volume = {}, number = {}, pages = {111282}, doi = {10.1016/j.ygeno.2026.111282}, pmid = {42331262}, issn = {1089-8646}, abstract = {OBJECTIVE: External auditory canal cholesteatoma (EACC), a rare destructive benign lesion, causes significant hearing loss, recurrent infections, and impaired quality of life. We characterized its microbial profiles to explore associations with disease progression.

METHODS: Cholesteatoma tissues from surgically treated EACC patients (2021-2022) underwent metagenomic sequencing (Illumina MiSeq). Taxonomic composition, functional genes, and antimicrobial resistance (AMR) profiles were systematically analyzed.

RESULTS: We identified 4377 core genes revealing abundance correlations. Dominant taxa included Firmicutes (42.1%), Proteobacteria (28.6%), and Actinobacteria (19.3%), with enriched Staphylococcus (32.4%) and Corynebacterium (21.7%). Hierarchical clustering and PCA/NMDS confirmed significant taxonomic divergence. AMR profiling detected multidrug-resistant genotypes (e.g., blaTEM, mecA).

CONCLUSION: This study defines EACC's microbial complexity and its pathogenic role, advocating microbiome-targeted strategies to mitigate infections.}, } @article {pmid42331273, year = {2026}, author = {Chen, D and Wang, Y and Cao, A and Hou, Y and Kong, F and Shi, J and Wang, S}, title = {Manganese-based activated carbon composites promote nitrogen removal in low temperature constructed wetlands via enhanced extracellular electron transfer.}, journal = {Environmental research}, volume = {}, number = {}, pages = {125092}, doi = {10.1016/j.envres.2026.125092}, pmid = {42331273}, issn = {1096-0953}, abstract = {Constructed wetlands (CWs) provide cost effective, nature based wastewater treatment but suffer performance losses at low temperatures. We tested granular activated carbon-supported manganese composites (MnX-GAC; X = Fe or Zn) positioned within CWs to enhance microbial extracellular electron transfer (EET). MnX-GAC increased electron acceptors/donors, strengthened EET activity, and improved nitrogen removal while mitigating temperature impacts. At 15°C, the MnX-GAC system (CW6) raised ammonium (NH4[+]-N) removal by 31.0% versus CW1. Although CW6 generated more CO2 due to intensified carbon mineralization, it effectively suppressed the emissions of potent greenhouse gases (N2O and CH4) and achieved the lowest GWP per unit of nitrogen removed of 4.53 mg CO2-eq/mg N. Metagenomics showed the enrichment of key functional taxa (e.g., Chloroflexota, Thermodesulfobacteriota, and Bacteroidota) and the upregulation of nitrogen metabolism genes and carbon metabolism genes, alongside increases in electron-transport chain and mediator genes, collectively facilitated electron production and utilization. These changes indicate that MnX-GAC enhances EET mediated pathways to sustain nitrogen removal under low temperature. Overall, MnX-GAC offers a practical strategy to overcome low-temperature limitations in CWs, delivering higher nitrogen removal and lower life-cycle climate impacts.}, } @article {pmid42331805, year = {2026}, author = {Shan, Z and Chen, Y and Chen, F and Zhang, Y and Chen, H and Wang, Z and Wang, X and Zhong, J and Wong, IN and Chen, J and Li, X and Lin, Z and Purcell, R and Guo, Y and Li, X and Li, X}, title = {Dietary yacon concentrate reshapes microbial-metabolite crosstalk to inhibit colorectal cancer.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00931-3}, pmid = {42331805}, issn = {2396-8370}, support = {82203520//National Natural Science Foundation of China/ ; 82203264//National Natural Science Foundation of China/ ; SHAX-LC-202332//Shanghai Anti-Cancer Association "Soar" Program/ ; }, abstract = {Yacon concentrate, which is rich in fructan, phenolic compounds, and flavonoids, exhibits notable nutritional and antioxidant properties. This study explored the potential of New Zealand yacon concentrate to modulate the gut microbiota and host metabolism, alleviate inflammation, and enhance antitumor immunity. The anti-inflammatory and antitumor effects of yacon concentrate were evaluated in mouse models of dextran sulfate sodium (DSS)-induced colitis and colorectal cancer (CRC). Ex vivo gut chemostat model experiments were performed to assess the impact of yacon concentrate on human gut microbiota remodeling. The gut microbiota composition was then analyzed via metagenomic sequencing, and metabolomic profiling was conducted to identify the key bioactive metabolites. Yacon concentrate significantly ameliorated DSS-induced colitis by reducing weight loss, lowering the disease activity index scores, and alleviating colonic shortening in mice. In CRC models, yacon concentrate markedly suppressed tumor growth, reduced tumor incidence, and decreased tumor burden. Microbiota derived from the chemostat after yacon supplementation not only enriched beneficial bacteria and inhibited the growth of immunotherapy-resistant bacteria but also enhanced energy and short-chain fatty acid metabolism. Moreover, transplantation of this microbiota into mice significantly improved the tumor microenvironment and inhibited tumor growth. Collectively, these findings indicate that yacon concentrate is associated with changes in the gut microbiota and metabolomic profiles, supporting a potential link between yacon intake and modulation of the gut microbiota-metabolome axis. These observations provide a rationale for further mechanistic and interventional studies evaluating yacon concentrate as a dietary strategy for colitis prevention and CRC prevention, and as an adjunctive treatment.}, } @article {pmid42331835, year = {2026}, author = {Yan, X and Shan, Z and Zhao, Y and Wu, W and Tao, Z and Yang, C and Wang, Y and Zhang, Y and Wang, Y and Zhang, C}, title = {Multi-omics insights into floral-fruity aroma formation during Pu'er tea fermentation inoculated with a synthetic fungal community.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00945-x}, pmid = {42331835}, issn = {2396-8370}, support = {202101BA070001-239//Yunnan provincial science and technology department science and technology project/ ; CXTD020//Pu'er tea science and technology research innovation team/ ; FWCY-ZNT2025021//Yunnan province higher education institutions science and technology projects for key industries/ ; 32360771//National natural science foundation of China/ ; 2020XJGH08//Yunnan provincial university center for Pu'er tea processing, key scientific research project of Pu'er university/ ; 2023PEXYCXTD001//Pu'er university outstanding innovation team/ ; 2024J1099//Yunnan provincial education department project/ ; }, abstract = {Pu'er tea fermentation relies on complex microbial activities. This study explored aroma formation in ripe Pu'er tea inoculated with a synthetic fungal consortium using a multi-omics approach across six sampling stages. Sensory evaluation, physicochemical analysis, volatile profiling (HS-SPME-GC×GC-TOFMS), non-volatile metabolomics (UHPLC-Q-Exactive/MS), and metagenomic sequencing were integrated. Inoculation was associated with a distinct floral-fruity aroma. Combined ROAV and VIP analyses identified four volatile compounds, namely phenylethyl alcohol, trans-β-ionone, geraniol, and 1-octen-3-ol, as potentially important aroma-active contributors. Among them, phenylethyl alcohol, trans-β-ionone, and geraniol might play a major role in the floral-fruity character, and their accumulation appeared associated with tea moisture content. Nonanal exhibited a high ROAV but a low VIP value. Non-targeted metabolomics revealed 154 significantly altered metabolites, 38 of which were associated with these volatile compounds. Metagenomic analysis indicated substantial shifts in microbial community structure and function, correlated with physicochemical parameters and volatile profiles. Random forest modeling identified Sphingomonas, Rothia, and Bacteroides as potentially involved in aroma formation. These findings provide insights into the metabolic and microbial dynamics underlying floral-fruity aroma development, offering a scientific basis for tailored starter culture design.}, } @article {pmid41928235, year = {2026}, author = {Arzu, JL and Fleury, ES and Cecil, KM and Chen, A and Lanphear, BP and Yolton, K and Buckley, JP and Braun, JM and Laue, HE}, title = {Associations of the gut microbiome and cardiometabolic risk in adolescence: the HOME study.}, journal = {BMC medical genomics}, volume = {19}, number = {1}, pages = {}, pmid = {41928235}, issn = {1755-8794}, support = {K99 ES034086/ES/NIEHS NIH HHS/United States ; R00 ES034086/ES/NIEHS NIH HHS/United States ; R01 ES027224/ES/NIEHS NIH HHS/United States ; }, abstract = {BACKGROUND: Alterations to the gut microbiome have been linked to cardiometabolic disease, like type 2 diabetes and hypertension, in adults, but few studies have investigated these associations in adolescents. We examined the relation between the gut microbiome and cardiometabolic risk in adolescence and determined whether sex and race/ethnicity modified these associations. METHODS: In 144 adolescents (age range: 11–14 years) from the Health Outcomes and Measures of the Environment (HOME) Study, we quantified gut microbiome alpha diversity using the Shannon index and species’ relative abundances (i.e., centered log-ratio normalized abundances) in stool DNA that underwent metagenomic sequencing. We assessed adolescent cardiometabolic risk using a cardiometabolic risk summary score, its individual components (i.e., visceral fat, leptin to adiponectin ratio, HOMA-IR, triglyceride to high-density lipoprotein cholesterol ratio, and systolic blood pressure), as well as total cholesterol and hemoglobin A1c. We used linear regression models to estimate covariate-adjusted cross-sectional associations of the Shannon diversity index and species’ relative abundances with cardiometabolic risk, and examine differences in these associations by sex and race/ethnicity. At the species level, the false discovery rate (FDR) correction, with q-value < 0.20, was considered statistically significant. RESULTS: Among all adolescents, a higher Shannon diversity index was associated with lower systolic blood pressure [β: -0.18 (95% CI: -0.35, -0.01)] in covariate-adjusted models. However, the associations of the Shannon diversity index with cardiometabolic risk did not differ significantly by sex or race/ethnicity. Although associations of the relative abundances of species, prevalent in at least 10% of samples, with cardiometabolic risk were not statistically significant tamong all adolescents after correcting for multiple comparisons (qFDR ≥ 0.20), sex modified the association of the relative abundance of Ruminococcus lactaris with HOMA-IR (qinteraction = 0.151), with positive association among females [β: 2.05 (95% CI: 0.93, 3.17), q = 0.155] and suggestive negative association among males [β: -0.84 (95% CI: -1.59, -0.09), q = 0.983]. Associations of the relative abundances of Streptococcus parasanguinis (qinteraction = 0.097), Enterocloster SGB14313 (qinteraction = 0.097), and Alistipes ihumii (qinteraction = 0.097) with total cholesterol also differed between female and male adolescents. We observed differences between adolescents of non-Hispanic black and non-Hispanic white race/ethnicity in the association of the relative abundance of Lachnospira pectinoschiza (qinteraction = 0.028) with total cholesterol. CONCLUSIONS: Our findings suggest that the gut microbiome is associated with cardiometabolic risk in adolescence in a sex-specific manner, and may differ by race and ethnicity.}, } @article {pmid41928361, year = {2026}, author = {Heng, YC and Chua, JHX and Silvaraju, S and Fan, H and Low, A and Lim, ACH and Chen, B and Mane, L and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Seedorf, H and Lim, KJ and Kittelmann, S}, title = {Metagenomic insights into the global wild boar faecal microbiome reveal novel taxa and carbohydrate degraders distinguishing wild and domesticated Sus.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41928361}, issn = {2049-2618}, support = {Project number CRG/2022/008319//Anusandhan National Research Foundation (ANRF), DST, Government of India/ ; FDS2223MONIELLO - CUP J83C22000160007//Fondazione di Sardegna, Italy/ ; University Research Fund 2020//University of Sassari/ ; WIL@NUS Corporate Laboratory, Singapore//Wilmar International/ ; }, mesh = {Animals ; *Feces/microbiology ; *Sus scrofa/microbiology ; *Metagenomics/methods ; Swine/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Dietary Fiber/metabolism ; Carbohydrate Metabolism ; Sequence Analysis, DNA ; Diet ; Animals, Wild/microbiology ; Phylogeny ; }, abstract = {BACKGROUND: The inclusion of fibre in domestic pig diets is favourable from a digestive health, environmental, and socio-economic perspective. Unlike the highly optimized formulated diets of domestic pigs, wild boars feed opportunistically, consuming a broad range of foods that consist predominantly of plant materials. Consequently, the intestinal microbiota of wild boars is thought to be adapted to a versatile, fibre-rich diet and may represent a valuable source of probiotics for enhancing fibre degradation. However, comprehensive studies characterizing the wild boar gut microbiome, particularly its community structure and carbohydrate utilization potential, and comparison to that of domestic pigs are still lacking.

RESULTS: We collected 89 faecal samples from wild boars across four countries and analysed them primarily using metagenomic sequencing. De novo assembly yielded 3,288 high- and medium-quality metagenome-assembled genomes (MAGs) representing 968 distinct species, of which 538 were previously unknown. Incorporating these MAGs enabled robust microbiome comparisons with 125 previously published samples largely from domestic pigs, which revealed significant structural and functional differences. These differences resolved into two community types, determined not by host species but by diet and lifestyle: C1 comprising 81% of samples from free-ranging, foraging wild boars and C2 consisting of 93% of samples from captive, fed domestic pigs. The lower alpha-diversity observed in C1 likely reflected the impact of highly fluctuating dietary resources and environmental conditions, resulting in dominance of fewer resilient or adaptable taxa. Nevertheless, both community types maintained substantial carbohydrate utilization potential: while C2 exhibited a higher relative abundance of CAZyme[sub] genes associated with a broader range of carbohydrate substrate (CHO) classes, C1 was enriched in individual species that were generally richer in CAZyme[sub] genes and CHO classes. To leverage this potential, we curated a catalogue of carbohydrate degraders from both community types and identified 47 highly versatile species, with several novel species amongst them.

CONCLUSIONS: This study uncovered the previously untapped microbial diversity in the wild boar faecal microbiome and demonstrated that the faecal microbiome of Sus is primarily shaped by diet and lifestyle. The two community types identified, which differed both structurally and functionally, represent alternative states of microbiome homeostasis in wild versus domesticated Sus populations. The curated catalogue of carbohydrate degraders provides a valuable resource to guide tailored probiotic supplementation during dietary transitions to novel fibrous feedstocks. Video Abstract.}, } @article {pmid41928791, year = {2026}, author = {Sommer, AJ and Auch, B and Khoruts, A and Bajaj, JS}, title = {Proximity-ligation metagenomics reveals disease-specific mobilome dynamics in disrupted gut ecosystems.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41928791}, issn = {2693-5015}, abstract = {Distinct ecological pressures shape accumulation of antimicrobial resistance and virulence genes in the gut microbiome. Using proximity ligation shotgun metagenomics to resolve host-mobilome relationships, we analyzed microbiomes from two patient cohorts: recurrent Clostridioides difficile infection (rCDI) and cirrhosis. While rCDI reflects antibiotic-driven disruption, cirrhosis-driven microbiome changes result from altered gut physiology. We found increased chromosomal determinants of antibiotic resistance in both, but plasmid-mediated amplification was more evident in rCDI.}, } @article {pmid41929040, year = {2026}, author = {Patabandige, DLJ and John, J and Ortiz, M and Campbell, BJ}, title = {Environmental Gradients Shape the Hydrocarbon-Degrading Microbiome in Two Mid Atlantic Bays.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.25.714183}, pmid = {41929040}, issn = {2692-8205}, abstract = {UNLABELLED: Hydrocarbons are recalcitrant organic matter that are released into the environment via natural and anthropogenic activities. We hypothesized that abiotic and biotic factors, including salinity, temperature, seasonality, microbial interactions, and functional redundancy, influence the abundance and activity of potential hydrocarbon degraders in the Delaware and Chesapeake Bays. We identified key genes in hydrocarbon degradation pathways in metagenomes, metatranscriptomes, and metagenome assembled genomes (MAGs) from these estuaries. Aerobic aromatic and alkane degradation pathways predominated in both estuaries, with higher gene abundances observed in low-salinity spring and summer samples. Hydrocarbon degrading MAG abundance were significantly structured by salinity, temperature, nitrate, and silicate concentrations. Metatranscriptomic analyses revealed consistently higher expression of aerobic alkane and aromatic degradation genes in the Delaware compared to the Chesapeake Bay, with the highest occurring under low-salinity spring conditions in the former. Catechol degradation pathways exhibited high functional redundancy, whereas the naphthalene degradation pathway showed restricted distribution. Co-expression analysis revealed that Burkholderiales displayed condition dependent metabolic coupling while Pseudomonadales integrated hydrocarbon degradation with fermentation and central metabolism, demonstrating complementary strategies that support multi-scale ecosystem resilience. In conclusion, environmental gradients and taxon-specific metabolic strategies together govern hydrocarbon degradation potential in these estuaries, with implications for predicting ecosystem responses to hydrocarbon inputs under changing conditions.

IMPORTANCE: Coastal estuaries are among the most contaminated aquatic environments on Earth, receiving continuous hydrocarbon inputs from industrial activity, urban runoff, and natural sources. Microorganisms are the primary agents of hydrocarbon breakdown in these systems yet predicting when and where this capacity is active and how resilient it is to environmental change remains a major challenge. Using paired genomic and transcriptomic data from microbial genomes across two major mid-Atlantic estuaries, we show that hydrocarbon degradation capacity is not uniformly distributed but is instead shaped by salinity, nutrients, and seasonality in pathway-specific ways. Critically, dominant degrader taxa employ fundamentally different metabolic strategies to sustain this function across fluctuating conditions, providing a form of community-level insurance against environmental disturbance. These findings advance our ability to predict microbial hydrocarbon degradation in coastal systems and inform nature-based approaches to bioremediation under increasing climate and anthropogenic pressures.}, } @article {pmid41929113, year = {2026}, author = {Wang, S and Guitor, AK and Valentin-Alvarado, LE and Garner, R and Zhang, P and Yan, M and Shi, LD and Schoelmerich, MC and Steininger, HM and Portik, DM and Zhang, S and Wilkinson, JE and Lynch, S and Morowitz, MJ and Hess, M and Diamond, S and Banfield, JF and Sachdeva, R}, title = {Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.27.714056}, pmid = {41929113}, issn = {2692-8205}, abstract = {DNA modification is central to microbial defense against extrachromosomal genetic elements (ECEs), consequently ECEs tend to adopt their host's modification patterns. Shared ECE-host modification patterns enable linking ECEs to their hosts, but modification detection tools are designed for single genomes and are ineffective at metagenome scale. Here, we present MODIFI, software for detecting DNA modifications in metagenomes. MODIFI assumes that each k-mer in a metagenome is mostly unmodified and calculates background signal levels for that k-mer from PacBio HiFi reads, eliminating the need for matched control experiments. MODIFI ECE-host linkages were validated using >1,000 isolate and mock microbiome datasets. Illustrating the approach, we identified 315 strain-resolved, non-redundant ECE-host linkages in environmental and human metagenomes. In infant gut microbiomes, a chromosomal inversion in Enterococcus faecalis alters host and associated plasmid methylation motifs simultaneously. Overall, MODIFI solves a major bottleneck in DNA modification analysis and provides a foundational tool for understanding microbial epigenomics.}, } @article {pmid41929272, year = {2026}, author = {Biesheuvel, MM and Barkema, HW and Morley, PS and Pinnell, LJ and Doster, E and Valeris-Chacin, R}, title = {In silico performance of a targeted enriched metagenomics approach to infer Mycoplasma bovis strains in milk.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1770245}, pmid = {41929272}, issn = {2297-1769}, abstract = {Strain variation plays a key role in the microbial epidemiology of Mycoplasma bovis, yet its true diversity remains incompletely characterized, partly due to limitations of culture-based methods. This study evaluated the in silico suitability of a targeted enrichment (TE) shotgun sequencing approach to detect and classify M. bovis strains in milk metagenomic samples. As a proof of concept, the accuracy of this approach was assessed using milk-derived M. bovis strains. A total of 620 M. bovis whole-genome sequences were downloaded from NCBI, of which 162 (26.1%) originated from milk samples. Genomes were grouped into Genomically Clustered Sequence Variants (GSVs) using MashTree and TreeCluster to enable strain-level classification. To simulate TE sequencing data, genomes from different milk-associated GSVs were randomly selected and fragmented in silico into 150-bp reads. Mock milk samples were generated by sampling reads with replacement from these genomes. Sequencing depth was modeled using a Poisson distribution, while mixed-strain DNA samples were simulated by including 1, 3, 6, or 9 GSVs per sample. Enrichment proportions were set at 0.3, 0.5, 0.7, and 0.9. Two classification tools, Kraken2 and Themisto/mSWEEP, were evaluated for their ability to detect and classify the simulated TE reads. Themisto/mSWEEP consistently outperformed Kraken2, achieving an average read classification accuracy of 84.9% compared with 1.4% for Kraken2. Sensitivity for Themisto/mSWEEP was 100% with a single spiked GSV and declined slightly to 97.0% with nine GSVs, whereas Kraken2 achieved sensitivities of only 17.3% and 4.7%, respectively. Positive predictive value (PPV) showed a similar pattern: 98% for Themisto/mSWEEP vs. 4.7% for Kraken2 with a single GSV, and 65.5% vs. 10% with nine GSVs. While Kraken2's PPV increased slightly with additional GSVs, Themisto/mSWEEP's PPV decreased. Both methods maintained high specificity and negative predictive value (>91%) across all scenarios. Enrichment proportion had no measurable effect on performance. Overall, Themisto/mSWEEP demonstrated superior accuracy for GSV-level identification of M. bovis strains. Enrichment to at least 30% of total reads was sufficient to recover strain-level data. Further work is needed to assess the biological relevance and practical applications of these genomic clusters.}, } @article {pmid41929449, year = {2026}, author = {Røsland, A and Amin, H and Lie, SA and Malinovschi, A and Bunæs, DF and Bertelsen, RJ}, title = {Effect of periodontal therapy on the oral microbiome and lung function: an intervention study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1725666}, pmid = {41929449}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; *Periodontitis/therapy/microbiology ; Longitudinal Studies ; Male ; *Mouth/microbiology ; Female ; Middle Aged ; *Lung/physiology ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Adult ; Dental Plaque/microbiology ; Respiratory Function Tests ; }, abstract = {INTRODUCTION: The oral cavity harbors over 700 bacterial species, and disruption of this balance can lead to periodontitis, which has been linked to systemic conditions including respiratory disease.

METHODS: In this longitudinal clinical trial, 57 never-smoking adults with stage I-II periodontitis underwent full-mouth periodontal disinfection. Airway resistance and subgingival plaque sampling (analyzed by shotgun metagenomics) was measured at baseline and six weeks after therapy.

RESULTS: Periodontal treatment significantly improved clinical periodontal parameters, and was associated with reductions in airway resistance. Microbiome analysis showed a shift from periodontitis-associated taxa, including Prevotella, Porphyromonas, and Tannerella, toward health-associated species such as Actinomyces oris, and Rothia dentocariosa. Higher airway resistance was associated with a greater relative abundance of periodontitis-associated bacteria.

DISCUSSION: Together, findings suggest that periodontal therapy promotes a healthier oral microbiome and is associated with improved lung function in non-smokers with no prior lung disease.}, } @article {pmid41929455, year = {2026}, author = {Geng, Y and Yuan, Y and Lin, X and Wei, J and Zhang, Q and Mao, X and Zhang, X and Zhang, X and Zhang, Y and Zhao, J and Guo, F and Zheng, P}, title = {Distinct characteristics on mixed infection of SARS-CoV-2 variants and other respiratory pathogens among patients with acute COVID-19 in central China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1653022}, pmid = {41929455}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/virology/epidemiology/microbiology ; China/epidemiology ; *Coinfection/microbiology/virology/epidemiology ; Female ; *SARS-CoV-2/genetics/isolation & purification ; Male ; Middle Aged ; Aged ; Adult ; Risk Factors ; Mycoplasma pneumoniae/isolation & purification/genetics ; High-Throughput Nucleotide Sequencing ; Severity of Illness Index ; Pneumonia, Mycoplasma/epidemiology ; }, abstract = {BACKGROUND: Reports on mixed infection with different severe acute respiratory syndrome coronavirus 2 variants and other respiratory pathogens in patients with acute coronavirus disease in China remain scarce. In this study, we analyzed the clinical characteristics of mixed infections involving different severe acute respiratory syndrome coronavirus 2 variants and other respiratory pathogens in patients with acute coronavirus disease in central China.

METHODS: Nested polymerase chain reactions and metagenomic next-generation sequencing were employed to identify severe acute respiratory syndrome coronavirus 2 variants. Clinical data, including hospitalization days, severity classification, outcomes, and laboratory data, were collected and analyzed.

RESULTS: Seven patients had mixed infections with different severe acute respiratory syndrome coronavirus 2 variants in samples collected on different dates. Overall, 54.6% (83/152) of patients had co-existing respiratory pathogen infection. The most common co-existing respiratory pathogen was Mycoplasma pneumoniae. Longer hospital stays, intensive care unit admission, and prolonged duration from admission to positive severe acute respiratory syndrome coronavirus 2 sample detection were independent risk factors for acute coronavirus disease infection with different respiratory pathogens. Severity classification, mixed infection, cerebral fraction, and fever were independent risk factors for failed treatment. Early detection of white blood cell count, procalcitonin, and D-dimer concentrations can help predict mixed respiratory infections and treatment outcomes.

CONCLUSIONS: The phenomenon of mixed infection with different variants in patients with coronavirus disease may have been underestimated. Therefore, active surveillance of severe acute respiratory syndrome coronavirus 2 variants should be performed in older patients with comorbidities.}, } @article {pmid41929479, year = {2026}, author = {Pan, Y and Li, B and Liu, L and Wang, Z and Liu, X}, title = {Gut dysbiosis induces the development of asthenozoospermia through butanoate metabolism.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1760881}, pmid = {41929479}, issn = {1664-3224}, mesh = {Male ; Humans ; *Asthenozoospermia/metabolism/etiology/microbiology ; *Dysbiosis/complications/metabolism/microbiology ; Animals ; Mice ; *Gastrointestinal Microbiome ; *Butyrates/metabolism ; Adult ; Fecal Microbiota Transplantation ; Case-Control Studies ; Sperm Motility ; Metabolomics ; Spermatozoa ; }, abstract = {BACKGROUND: Asthenozoospermia is a leading cause of male infertility with a rising incidence. While gut dysbiosis is implicated in metabolic disease, its role in asthenozoospermia pathogenesis remains unclear.

MATERIALS AND METHODS: We conducted a case-control study comparing the fecal microbiomes of men with isolated asthenozoospermia (n=60) and healthy controls (n=60) using shotgun metagenomic sequencing. Causality was assessed by fecal microbiota transplantation (FMT) from patients or controls into germ-free male mice. Metabolic perturbations were profiled by untargeted serum metabolomics and targeted short-chain fatty acid (SCFA) quantification in humans, alongside untargeted testicular metabolomics and serum SCFAs in recipient mice.

RESULTS: Metagenomic analysis (LEfSe) identified species-level differences, with marked depletion of butyrate-producing taxa in asthenozoospermia, most notably the prototypical butyrate producer Faecalibacterium prausnitzii. The relative abundance of F. prausnitzii was significantly positively correlated with sperm motility and progressive motility, linking gut composition to sperm quality in asthenozoospermia. Untargeted serum metabolomics identified 39 differential metabolites; KEGG enrichment prioritized butanoate metabolism. Targeted SCFA profiling confirmed significantly lower serum butyrate in asthenozoospermia versus controls. In germ-free males, FMT with patient-derived microbiota reduced sperm motility and progressive motility and induced histopathological abnormalities, including decreased interstitial Leydig cells, loss and atrophy of select intratubular cells, and an increased proportion of abnormal seminiferous tubules. Following patient FMT, recipient mice exhibited significantly reduced serum butyrate; testicular metabolomics revealed distinct profiles with 140 key differential metabolites, again implicating butanoate metabolism. Mechanistically, reduced F. prausnitzii-derived butyrate might impair Leydig cell steroidogenesis via disrupted PPAR signaling.

CONCLUSIONS: Asthenozoospermia is associated with gut dysbiosis characterized by loss of butyrate-producing bacteria, systemic and testicular disturbances in butyrate metabolism, and microbiota-mediated transmission of impaired sperm quality. These findings implicate the gut-testis axis in asthenozoospermia pathogenesis and nominate butyrate metabolism as a potential therapeutic target.}, } @article {pmid41929693, year = {2026}, author = {Xue, H and Zhang, M and Tang, Y and Huang, W and Yu, X and Zhang, J and Pan, M and Liu, Z}, title = {Integrated metagenomic and metabolomic profiling of spontaneous preterm birth in Chinese women.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1729476}, pmid = {41929693}, issn = {1664-302X}, abstract = {BACKGROUND: Spontaneous preterm birth (sPTB) remains a major cause of neonatal morbidity and mortality. We used integrated metagenomics and untargeted metabolomics to identify vaginal microbial and host metabolic signatures associated with sPTB in Chinese women.

METHODS: Vaginal swabs (sPTB, n = 37; term, n = 62) and available maternal plasma were profiled by shotgun metagenomic sequencing and UHPLC-HRMS metabolomics. Group differences in microbial diversity/taxa and metabolite features were evaluated, followed by pathway enrichment and microbiome-metabolome correlation analyses.

RESULTS: Compared with term controls, sPTB was characterized by reduced Lactobacillus dominance, higher vaginal microbial alpha diversity (p < 0.05), and distinct community structure (PERMANOVA p < 0.001). Metabolomic profiles of plasma and vaginal fluid differentiated sPTB from term pregnancy and highlighted decreased pantothenic acid and increased 4-pyridoxic acid, together with lipid and amino-acid perturbations. Pantothenic acid showed good discrimination (AUC = 0.82), and a multi-metabolite model improved classification (AUROC = 0.9544). KEGG analysis implicated vitamin B6 metabolism, pantothenate/CoA biosynthesis, and glycerophospholipid metabolism. Microbiome-metabolome integration dentified exploratory an sPTB-associated pattern in which Lactobacillus (e.g., L. crispatus) was positively correlated with pantothenic acid, while dysbiosis-/pathogen-associated taxa (including C. trachomatis) correlated with 4-pyridoxic acid.

CONCLUSION: sPTB in this Chinese cohort is associated with concurrent vaginal dysbiosis and systemic/local metabolic disturbances, supporting integrated microbiome-metabolite markers for risk stratification and potential preventive targets.}, } @article {pmid41929767, year = {2026}, author = {Peng, W and Yang, W and Ma, L and Wang, Q and Yang, R and Ji, A and She, M and Wang, T and Gong, W and Yan, L}, title = {Flower vinegar prepared from Yunnan large-leaved tea tree prevents high-fat diet-induced obesity in mice by regulating gut microbiota.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1749951}, pmid = {41929767}, issn = {2296-861X}, abstract = {Obesity and its metabolic complications are major public health concerns. The gut microbiota plays a pivotal role in regulating host adiposity. Fermented products from Camellia sinensisvar. Assamica (Yunnan large-leaved tea) flowers, a novel food ingredient, may offer therapeutic potential, but their effects on obesity and gut microbiota remain unexplored. We investigated the anti-obesity effects of vinegar fermented from Camellia sinensisvar. Assamica flowers (TTFV) in a high-fat diet (HFD)-induced obese mouse model. Body weight, glucose and lipid metabolism, hepatic injury, steatosis, inflammation, and oxidative stress were assessed. Metabolomic analysis and metagenomic sequencing of gut microbiota were performed. Key metabolic pathways were analyzed. TTFV supplementation significantly attenuated HFD-induced body weight gain, improved glucose and lipid profiles, alleviated hepatic steatosis and injury, and reduced systemic inflammation and oxidative stress. TTFV modulated host metabolite profiles and related metabolic pathways. Crucially, TTFV reshaped the gut microbiota structure: it increased the relative abundance of Bacteroidota and decreased the Firmicutes/Bacteroidota ratio at the phylum level. At the family level, it promoted beneficial bacteria (Oscillospiraceae, Eubacteriaceae) and suppressed potentially harmful ones (Erysipelotrichaceae). Metabolic pathway analysis indicated TTFV's positive role in maintaining cellular homeostasis and regulating metabolic disturbances. Our findings demonstrate that TTFV exerts protective effects against HFD-induced obesity in mice. These benefits are closely associated with the remodeling of gut microbiota composition and the modulation of key metabolic pathways. This study is the first to report the anti-obesity potential and microbiota-regulating effects of TTFV, suggesting its promise as a functional food ingredient for promoting intestinal health and mitigating obesity-related metabolic disorders.}, } @article {pmid41929953, year = {2026}, author = {Oso, TA and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Ayelaagbe, OB and Talabi, OA and Adewole, PD and Anorue, CO and Ahmed, MM and Talabi, OT and Ogaya, JB and Lucero-Prisno, DE}, title = {Microbiome alterations in Alzheimer's disease: A systematic review of current evidence and global perspectives.}, journal = {Journal of Alzheimer's disease reports}, volume = {10}, number = {}, pages = {25424823261436287}, pmid = {41929953}, issn = {2542-4823}, abstract = {BACKGROUND: Growing evidence implicates the gut-brain axis in Alzheimer's disease (AD), with gut microbiome dysbiosis proposed to modulate neuroinflammation, amyloid pathology, and cognitive decline.

OBJECTIVE: To systematically synthesize human studies (2021-2025) profiling gut microbiomes in AD; identify consistent taxonomic and functional signatures; map geographic study distribution; and highlight translational gaps.

METHODS: A PRISMA-compliant systematic review of human studies using 16S rRNA, metagenomics, metatranscriptomics, or fecal microbiota transplantation (FMT)/probiotic designs was conducted. Two reviewers screened studies and assessed quality using Joanna Briggs Institute tools. Owing to heterogeneity, findings were narratively synthesized across microbiome diversity, taxonomy, function, metabolism, oral-brain links, causality, interventions, and predictive analyses.

RESULTS: Thirty-seven studies, mainly from Asia with some from Europe, North America, and Africa, revealed consistent gut dysbiosis in AD. Findings show reduced alpha-diversity, loss of short-chain fatty acid-producing bacteria (e.g., Faecalibacterium prausnitzii, Bifidobacterium), and enrichment of pro-inflammatory taxa (Escherichia/Shigella, Proteobacteria). Functional analyses indicate reduced butyrate synthesis, disrupted lipid and tryptophan-kynurenine metabolism, and links with apolipoprotein epsilon (ε4) gene and cognition. Limited causal evidence arises from Mendelian randomization and small FMT trials, with randomized, longitudinal confirmation still needed.

CONCLUSIONS: Current evidence suggests a biologically plausible association between gut microbiota and AD pathogenesis, positioning microbiome-derived biomarkers and interventions as promising but still exploratory avenues. Harmonized, longitudinal, multi-omic, and geographically inclusive studies are urgently needed to clarify causal mechanisms and translate these correlational findings into validated diagnostics and therapeutics.}, } @article {pmid41930262, year = {2025}, author = {Bertoldi, S and Klaes, S and Claus, S and Marsans, A and Heipieper, HJ and Eberlein, C}, title = {Cross-feeding drives degradation of phthalate ester plasticizers in a bacterial consortium.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1757196}, pmid = {41930262}, issn = {1664-302X}, abstract = {Reports of plastic pollution across diverse ecosystems continue to emphasize the environmental risks associated with the increasing consumption of synthetic polymers. Plastics frequently contain additives such as phthalic acid esters, which are extensively employed as plasticizers to enhance flexibility in plastic materials and as constituents of numerous consumer products. These compounds are not chemically bound to polymers, allowing them to leach into the environment and have been implicated as potential endocrine disruptors in animals. In the present study, the bacterial degradation of selected phthalate esters was examined, with diethyl phthalate (DEP) utilized as a model compound. A bacterial consortium capable of degrading DEP was enriched from a biofilm of a polyurethane tubing. The consortium was capable to mineralize DEP as the sole carbon and energy source at concentrations of up to 4 mM, whereas concentrations above 6 mM inhibited its activity due to DEP toxicity. This degradation was only possible by the whole consortium and not by single isolates. The degradation of DEP as well as the timely occurrence of monoethyl phthalate as degradation intermediate was confirmed by UPLC analysis. Metagenomic sequencing identified the consortium as comprising a Microbacterium sp. strain and two Pseudomonas spp. Metaproteomic analyses of the consortium, performed under varying time points and carbon sources and integrated with complementary growth experiments, facilitated the reconstruction of the degradation pathway and the identification of putative enzymes involved in DEP metabolism. Microbacterium sp. DEP1M initiated the degradation by hydrolysis of DEP into ethanol and monoethyl phthalate, which is then taken up by the cells and further metabolized to ethanol and phthalate. The latter is subsequently oxidized by a dioxygenase and further transformed to the central intermediate 3,4-dihydroxybenzoic acid (protocatechuate). Protocatechuate is then exclusively degraded via the ortho cleavage pathway. Notably, the distribution of enzymatic functions among different community members strongly supports the occurrence of microbial cross-feeding, indicating that DEP mineralization is a cooperative process within the consortium.}, } @article {pmid41930266, year = {2026}, author = {Marter, P and Brinkmann, H and Freese, HM and Ringel, V and Bunk, B and Jarek, M and Koblížek, M and Wagner-Döbler, I and Petersen, J}, title = {The microbiome of marine mat-forming cyanobacteria-a microcosm of taxonomic novelty and phototrophic diversity.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag041}, pmid = {41930266}, issn = {2730-6151}, abstract = {Intertidal biological mats are highly dynamic ecosystems typically dominated by filamentous cyanobacteria of the genus Coleofasciculus. These primary producers play important roles in primary production, biogeochemical cycling, and coastal protection. 16S rRNA gene profiling of non-axenic cultures has recently revealed an astonishing wealth of associated bacteria. We analyzed the microbiomes of 14 non-axenic Coleofasciculus cultures from nine globally distributed marine sampling sites, representing seven distinct phylogenomic lineages. Metagenome sequencing and binning resulted in 320 metagenome-assembled genomes (MAGs) representing a broad spectrum of "uncultivated" bacterial diversity mostly belonging to Pseudomonadota, Bacteroidota and Planctomycetota. Marinovum algicola, and Roseitalea porphyridii were found in 12 of the microbiomes studied, making them the most common housemates. The complex microbiome of Coleofasciculus sp. WW12 contained seven Planctomycetota MAGs from so far undescribed species, representing inter alia a new family in the order Phycisphaerales and an MAG from a deeply branching sister lineage of all cultivated planctomycetes. The discovery of 36 proteobacterial MAGs with photosynthesis gene clusters (PGCs) and 32 MAGs with proteorhodopsin or xanthorhodopsin operons documented the coexistence with many photoheterotrophic bacteria, indicating that the cyanosphere is a hotspot of phototrophic life. The presence of a PGC-containing Myxococcales MAG (Candidatus Photomyxococcus marinus) is of special interest because it paves the way to investigate photosynthesis in Deltaproteobacteria. In a Mediterranean Coleofasciculus culture, three alphaproteobacterial MAGs were found that have both a xanthorhodopsin operon and the PGC, suggesting that dual phototrophy is not restricted to alpine lakes or glaciers, and can also be found in marine habitats.}, } @article {pmid41930333, year = {2026}, author = {Tan, H and Ding, Y and Gu, Z and Wang, X and Wang, J and Wei, T and Zhang, X and Pan, L and Shi, Y and Chang, S and Guo, C and Weng, J and Zheng, X and Yue, T}, title = {Microbiome-Based Clustering Identifies Glycemic Control-Related Subtypes in Youth With Recent-Onset Type 1 Diabetes.}, journal = {MedComm}, volume = {7}, number = {4}, pages = {e70705}, pmid = {41930333}, issn = {2688-2663}, abstract = {Type 1 diabetes (T1D) in children exhibits substantial heterogeneity in glycemic control, yet the biological mechanisms underlying this variation remain unclear. We aimed to explore endotype heterogeneity in youth with recent-onset T1D using unsupervised clustering based on multi-omics data, and to identify associated molecular signatures and underlying mechanisms. In a discovery cohort of 69 children and adolescents with recent-onset T1D, unsupervised clustering of fecal metagenomic profiles revealed two robust subgroups distinguished by hemoglobin A1c (HbA1c) levels. The High-HbA1c group was enriched in Bacteroidota, while the Low-HbA1c group was enriched in Firmicutes and certain Bacteroides species (Bacteroides ovatus, Bacteroides xylanisolvens, Bacteroides nordii, and Bacteroides cellulosilyticus). Metabolomics revealed significant enrichment of tryptophan-derived metabolites in the Low-HbA1c group. Bacteroides species signatures are positively correlated with tryptophan metabolite skatole. In an independent validation cohort, Bacteroides signatures discriminated individuals with good versus poor glycemic control (AUC = 0.854). Similar microbial patterns were observed in healthy children stratified by glycemic risk, indicating broader relevance of these signatures. Together, microbiome-based clustering identified glycemic control-related subtypes in T1D youth and suggested a potential role of Bacteroides and skatole in glycemic control. Mechanistic studies are warranted to confirm its role as a glycemic control-related endotype with distinct pathophysiology.}, } @article {pmid41930475, year = {2026}, author = {Tan, Y and Zou, D and Ni, C and Zeng, Q and Li, M}, title = {From Field Metagenomes to Mutant Genomes: Coevolution of Cyanophages and Synechococcus in Estuarine Ecosystems.}, journal = {Environmental science & technology}, volume = {60}, number = {14}, pages = {10789-10803}, doi = {10.1021/acs.est.5c12277}, pmid = {41930475}, issn = {1520-5851}, mesh = {*Synechococcus/genetics ; Estuaries ; *Bacteriophages/genetics ; Mutation ; *Metagenome ; Ecosystem ; }, abstract = {Picocyanobacteria, represented by Prochlorococcus and Synechococcus, are major photosynthetic organisms in aquatic ecosystems, and their viruses (cyanophages) significantly impact cyanobacterial ecology and evolution. Here, we combined metagenomics of Synechococcus communities along four representative estuaries in China and whole-genome analyses of laboratory-evolved Synechococcus mutants to link viral diversity to host adaptation and evolution. We assembled 83 cyanophage genomes (mainly cyanomyoviruses), with expanded auxiliary metabolic genes encoding glycosyltransferases and radical S-adenosyl methionine proteins involved in amino acid and lipopolysaccharide metabolism. Metagenome-assembled cyanobacterial genomes revealed mutations predominantly in membrane-associated functions linked to phage infection. In parallel, we identified genetic pathways conferring phage resistance in 18 evolved Synechococcus mutant strains that are resistant to phage infection. Notably, mutations in carbohydrate (rfbA) and photosynthetic energy transfer (cpeT) of Synechococcus mutants recurred in both cultured isolates and recovered metagenomes. These results indicate that cyanophages in estuaries leverage broader metabolic toolkits, while Synechococcus repeatedly evolves resistance. Together, these findings outline a reciprocal adaptive landscape that helps explain the persistence and turnover of picocyanobacterial populations in estuarine environments.}, } @article {pmid41930516, year = {2026}, author = {Wang, W and Li, M and Liu, X and Li, Y and Yang, K and Tuovinen, OH and Wang, H}, title = {Anaerobic antimony oxidation by mine groundwater bacteria: The energy-detoxification trade off governed by carbon source and Sb concentration.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141926}, doi = {10.1016/j.jhazmat.2026.141926}, pmid = {41930516}, issn = {1873-3336}, mesh = {*Antimony/metabolism ; Oxidation-Reduction ; *Groundwater/microbiology/chemistry ; *Carbon/metabolism ; Mining ; *Bacteria/metabolism/genetics ; *Water Pollutants, Chemical/metabolism ; Anaerobiosis ; }, abstract = {Microorganisms drive anaerobic antimony (Sb) oxidation and detoxification in groundwater, how carbon source (organic vs. inorganic) regulates this process and shapes microbial adaptive strategies remains unclear. To fill this knowledge gap, microcosms were conducted with groundwater from Xikuangshan mining-area, integrating with hydrochemistry, genes quantification, and metagenomics. The results demonstrated efficient anaerobic Sb(III) oxidation coupled with NO3[-] reduction, regulated synergistically by Sb concentration and carbon sources. The concentration of 0.5 mM Sb(III) served as a critical threshold that triggered changes in bacterial diversity, composition, and Sb(III)-oxidation behavior. Below this, NaHCO3 promoted higher oxidation rates (P < 0.05), linked to enrichment of Hydrogenophaga, Aquabacterium, Acidovorax, and aioA genes (Sb-oxidizing gene). Above 0.7 mM Sb(III), Na-lactate activated aioA and narrowed the rate gap, accompanied by increases in both abundance and niche of Dechloromonas. In addition, elevated Sb stress reshaped the metabolic networks across microcosms. The communities prioritized energy allocation to nitrogen fixation (nifH) with multiple benefits over redundant carbon fixation (cbbL). This research expands the known range of Sb and carbon drive microbial metabolic remodeling, advancing our predictive understanding of Sb biogeochemical cycling in contaminated aquifers.}, } @article {pmid41930813, year = {2026}, author = {Liu, J and Mai, Y and Xie, Y and Zhou, X and Ye, Y and Jiang, D and He, L and Ye, Z and Li, D and Xia, C and Su, J and Huang, S}, title = {Dehydroandrographolide succinate alleviates ulcerative colitis via regulating RAB9A/NF-κB axis-mediated macrophage polarization and remodeling the gut microbiota.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158039}, doi = {10.1016/j.phymed.2026.158039}, pmid = {41930813}, issn = {1618-095X}, mesh = {Animals ; *Colitis, Ulcerative/drug therapy/chemically induced ; *NF-kappa B/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Macrophages/drug effects/metabolism ; *Diterpenes/pharmacology ; Humans ; Mice ; Male ; *Anti-Inflammatory Agents/pharmacology ; Mice, Inbred C57BL ; Disease Models, Animal ; Cytokines/metabolism ; Signal Transduction/drug effects ; Dextran Sulfate ; Colon/drug effects ; Andrographis/chemistry ; }, abstract = {BACKGROUND: Dehydroandrographolide succinate (DAS), isolated from Andrographis paniculata, exhibits potent anti-inflammatory activity, yet its therapeutic potential and precise mechanism in ulcerative colitis (UC) remain unexplored.

PURPOSE: This study aims to investigate the efficacy and molecular basis that is responsible for the amelioration of DAS against UC.

METHODS: Effect of DAS against colitis was studied in a DSS-induced colitis model, and the critical role of macrophage was verified by the macrophage depletion and adoptive macrophage transfer (AMT) model. The anti-inflammation activity of DAS was investigated in the LPS/IFN-γ-stimulated THP-1-derived macrophage model in vitro, followed by DARTS, CETSA, molecular docking/dynamics, and transcriptomics to elucidate the underlying mechanism. The effect of DAS on gut microbiota was analyzed with metagenomic sequencing.

RESULTS: DAS attenuated the colitis features, including weight loss, diarrhea, rectal bleeding, and colon shortening, together with reduced inflammatory infiltrates and restored crypt architecture. DAS down-regulated pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and up-regulated anti-inflammatory mediators (IL-10, IL-13), meanwhile restoring tight-junction proteins (ZO-1, Occludin) and goblet-cell mucins. Macrophage depletion abolished DAS's benefit, while AMT with DAS-treated macrophages relieved the colitis features, confirming the macrophage-dependency of DAS. Transcriptomics and the following verification revealed that the anti-inflammatory activity of DAS mainly relied on the NF-κB signaling pathway by suppressing p65 phosphorylation and downstream targets. DAS inhibited M1 polarization and protected epithelial monolayers from macrophage-mediated damage. Moreover, DAS exhibited high-affinity binding to RAB9A, and RAB9A knockdown abolished DAS-mediated suppression of TLR4/NF-κB signaling pathway in macrophages. Metagenomic analysis revealed that DAS treatment enriched Lachnospiraceae bacterium, Duncaniella freteri, Lachnospiraceae bacterium 10-1, Bacterium 1XD8-76, Schaedlerella arabinosiphila, while depleted Muribaculaceae bacterium, Bacteroides intestinalis and Clostridiaceae bacterium. Functional gene profiling indicated that DAS upregulated genes related to butyrate metabolism, amino sugar and nucleotide sugar metabolism, and starch and sucrose metabolism.

CONCLUSION: DAS alleviates DSS-colitis by targeting RAB9A to block the NF-κB signaling pathway-driven M1 macrophage polarization, and is accompanied by gut microbiota remodeling, highlighting the promising application of DAS against UC.}, } @article {pmid41931872, year = {2026}, author = {Ren, Z and Wen, Y and Ma, Y and Li, M and Wang, L and Yu, R and Wu, L}, title = {Species-specific salinity adaptation mechanisms drive niche partitioning of nitrite-dependent anaerobic methane oxidation bacteria in a natural wetland gradient.}, journal = {Water research}, volume = {298}, number = {}, pages = {125791}, doi = {10.1016/j.watres.2026.125791}, pmid = {41931872}, issn = {1879-2448}, mesh = {*Wetlands ; Salinity ; *Methane/metabolism ; Oxidation-Reduction ; *Nitrites/metabolism ; Anaerobiosis ; Species Specificity ; Adaptation, Physiological ; }, abstract = {Nitrite-dependent anaerobic methane oxidation (N-DAMO) is a key process regulating methane emissions from wetland ecosystems. However, the species-specific mechanisms that enable N-DAMO bacteria to adapt and occupy distinct niches along environmental gradients (such as salinity) remain largely unknown. This makes it difficult to predict the ecological function of these bacteria. In this study, the structure, functional diversity, and species-specific salinity adaptation mechanisms of N-DAMO bacterial community in the Ulansuhai Wetland along a natural salinity gradient were investigated. An integrated approach combining metagenomic sequencing, isotopic tracer experiment, quantitative PCR, and biogeochemical measurements was employed for this research. The results show that salinity significantly reshaped the community structure and diversity of N-DAMO bacteria, while their potential activity remained functionally stable. This functional resilience was underpinned by distinct niche partitioning among four dominant species of Candidatus Methylomirabilis, species. Each species exhibited unique genomic potential for exopolysaccharide biosynthesis, osmoregulation, and stress response. Furthermore, the N-DAMO process constituted a significant methane sink, representing 39.5% of the observed anaerobic methane oxidation activity. Path analysis further explained that salinity regulated N-DAMO bacterial communities directly and through indirect pathways mediated by soil carbon and nitrogen pools. This research provides the first mechanistic framework linking species-specific genomic traits of N-DAMO bacteria to salinity adaptation and niche partitioning. The study offers novel insights for predicting wetland methane emissions.}, } @article {pmid41931886, year = {2026}, author = {Xiao, S and Han, Z and Tang, Y and Wu, X and Huang, J and Zeng, W}, title = {Dual roles of tetracycline-degrading bacteria in pollutant detoxification and resistome reshaping under tetracycline-copper co-contamination.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141951}, doi = {10.1016/j.jhazmat.2026.141951}, pmid = {41931886}, issn = {1873-3336}, mesh = {*Copper/metabolism/toxicity ; *Tetracycline/metabolism ; *Soil Pollutants/metabolism/toxicity ; Biodegradation, Environmental ; *Anti-Bacterial Agents/metabolism ; Soil Microbiology ; *Bacteria/metabolism/genetics ; }, abstract = {Combined contamination of soils with antibiotics and heavy metals represents a growing environmental challenge, yet remediation strategies addressing their synergistic toxicity remain limited. In this study, the bioremediation potential of a tetracycline-degrading bacterial consortium (Raoultella sp. XY-1 and Pandoraea sp. XY-2) was evaluated in tetracycline-copper (TC-Cu) co-contaminated soils by integrating chemical, biological, and ecological assessments. Soil column experiments demonstrated that bioaugmentation significantly enhanced TC degradation (48.57-53.71% after 90 days) compared to uninoculated controls (<12%), while simultaneously reducing copper bioavailability by shifting acid-extractable and reducible fractions toward more stable oxidizable forms. Inoculation further alleviated the strong inhibition of soil enzymatic activities (sucrase, urease, phosphatase), reflecting improved soil functional recovery. Metagenomic sequencing revealed that TC-Cu co-contamination reshaped microbial community composition, particularly increasing the relative abundance of Actinomycetota and Campylobacterota. Bioaugmentation further facilitated the establishment of Raoultella and indirectly stimulated indigenous resistant taxa through community interactions. Correlation network analysis further revealed that Raoultella was a highly connected genus in co-occurrence networks of antibiotic resistance gene (ARG)- and metal resistance gene (MRG)-hosting genera. LC-MS detection of intermediate products during TC microbial degradation proposed three microbial degradation pathways and inferred microbial resistance mechanisms under TC-Cu coexistence. Collectively, these findings highlight that TC-degrading bacteria not only reduce pollutant toxicity but also reshape microbial and genetic landscapes in co-contaminated soils, potentially suppressing the diffusion risk of resistance genes at low TC-Cu level. This work provides novel insights into the ecological trade-offs of bioremediation and supports the development of targeted, sustainable strategies for complex antibiotic-metal pollution scenarios.}, } @article {pmid41931897, year = {2026}, author = {Zhang, K and Chang, S and Zhu, Y and Shang, H and Fu, Q and Tu, X and Yu, Y and Feng, Y}, title = {Metagenomic analysis of urban water systems uncovers the interplay between antibiotic resistance genes and microbial communities in response to PFAS contamination.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141890}, doi = {10.1016/j.jhazmat.2026.141890}, pmid = {41931897}, issn = {1873-3336}, mesh = {*Water Pollutants, Chemical/analysis/toxicity ; *Drug Resistance, Microbial/genetics ; Metagenomics ; Wastewater/microbiology/analysis ; *Fluorocarbons/analysis/toxicity ; RNA, Ribosomal, 16S/genetics ; *Genes, Bacterial ; *Microbiota/drug effects/genetics ; Water Microbiology ; Bacteria/genetics ; }, abstract = {Urban water systems (UWS) are facing the severe challenge of coexisting emerging contaminants per- and polyfluoroalkyl substances (PFAS) and antibiotic resistance genes (ARGs). Herein, we analyze 15 PFAS at all key nodes within the UWS and the manufacturing plant park (MPP) in industrial clusters. Meanwhile, 16S rRNA and metagenomic approach were employed to annotate microbial community and ARGs, investigating their response to PFAS contamination. Fifteen PFAS were detected in MPP wastewater with total concentrations ranging from 30.28 to 3738.51 (557.68 ± 1072.03) ng/L, with short-chain accounting for 63.5%. Wastewater treatment plant (WWTP) serves as both sink and source of PFAS, with a negative average removal efficiency (mean = -158.6%) ultimately contributing to the prevalence of PFAS in the drinking water treatment plants (DWTPs) and tap water (17.64 -84.72, 36.06 ± 18.52 ng/L). 1141 ARGs subtypes were identified by metagenomic with significant differences in relative abundance between different nodes samples (p = 0.00). Additionally, the co-occurrence network revealed 14 genera may as potential hosts for 25 ARGs subtypes. However, significant differences in microbial diversity and abundance were observed at different nodes samples (R = 0.408, p = 0.00), with PFAS reducing microbial community diversity, particularly in river system (R = 0.723, p = 0.00). Finally, the structural equation modeling (SEM) revealed that PFAS exerted the greatest negative contribution to ARGs profiles (total effect = -1.39) through synergistic effects involving direct negative impacts on microbial diversity (-0.679) and mobile genetic elements (MGEs) (-0.121). This suggests that PFAS may influence the ARGs profiles by synergistically inhibiting gene-level transfer mediated by MGEs within potential host microbial. Additionally, physicochemical parameters (0.42), nutrient levels (-0.29), and ion concentrations (0.06) were also minor drivers of ARGs profiles.}, } @article {pmid41932005, year = {2026}, author = {Parente, E and Pietrafesa, R and De Filippis, F and De Vivo, A and Labella, MG and Hidalgo, M and Lavanga, E and Ricciardi, A}, title = {A survey of bacterial and fungal communities of table olives.}, journal = {International journal of food microbiology}, volume = {455}, number = {}, pages = {111759}, doi = {10.1016/j.ijfoodmicro.2026.111759}, pmid = {41932005}, issn = {1879-3460}, mesh = {*Olea/microbiology ; Fermentation ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/isolation & purification/genetics ; *Food Microbiology ; *Microbiota ; Fermented Foods/microbiology ; Italy ; }, abstract = {Table olives are produced from a large number of olive varieties subjected to different trade preparations, resulting in a highly heterogeneous family of fermented foods. To characterise the diversity of bacterial and fungal communities and its relationship with variety, ripeness, and trade preparation, we surveyed 363 samples from 40 producers across 6 countries, combining physicochemical measurements, viable counts, and amplicon-based metagenomics. This is the largest survey of table olive microbial communities to date and includes the first culture-independent characterisation of microbial communities for several Italian PDO and non-PDO varieties, most notably Oliva di Gaeta. The contrast between alkali-treated and naturally fermented olives was the dominant structuring factor, with HALAB (Halophilic and Alkalophilic Lactic Acid Bacteria) and other halophiles enriched in alkali-treated varieties and a diverse array of Lactobacillaceae and Pseudomonadota characterising naturally fermented olives. Despite these consistent signals, striking variability was observed within the same variety and even within the same producer, driven by stochastic colonization events, house microbiota, and the widespread use of small fermentation vessels. This variability obscured variety-specific microbial signatures and prevented reliable discrimination of Italian PDO varieties from similar non-PDO counterparts using amplicon-based approaches. The ecological and taxonomic complexity documented here, encompassing bacterial and fungal genera with largely untapped starter and flavour potential, provides the foundation for the development of variety-specific microbiome-based starter cultures.}, } @article {pmid41932427, year = {2026}, author = {Bao, C and Ren, Y and Tang, C and Su, Y and Yue, H and Chen, X}, title = {Viral isolation and genomic characteristics of the first bovine parainfluenza virus type 3 isolated from water buffaloes (Bubalus bubalis) in China.}, journal = {Veterinary journal (London, England : 1997)}, volume = {317}, number = {}, pages = {106655}, doi = {10.1016/j.tvjl.2026.106655}, pmid = {41932427}, issn = {1532-2971}, mesh = {Animals ; *Buffaloes/virology ; *Parainfluenza Virus 3, Bovine/genetics/isolation & purification ; China ; Phylogeny ; *Respirovirus Infections/veterinary/virology ; *Genome, Viral ; Microscopy, Electron, Transmission/veterinary ; }, abstract = {Bovine parainfluenza virus type 3 (BPIV3) is an important pathogen associated with bovine respiratory disease. In this study, we report the isolation and genomic characterization of BPIV3 from a water buffalo with respiratory symptoms in China. Virus isolation was performed using susceptible cell cultures, followed by identification via RT-qPCR, transmission electron microscopy, and indirect immunofluorescence. Metagenomic sequencing of the near-complete genome showed that the isolate shared 89.9%-91.1% nucleotide identity with BPIV3 genotype A strains. Notably, several distinct mutations were identified in the structural protein genes, and phylogenetic analysis demonstrated that the isolate formed a separate cluster within genotype A, suggesting that it may represent a novel subtype within this genotype. To our knowledge, this is the first report describing the isolation and genomic characterization of BPIV3 from water buffaloes in China. These findings provide baseline molecular data for further studies on the genetic diversity and evolution of BPIV3.}, } @article {pmid41932524, year = {2026}, author = {Qian, J and Li, X and Xu, X and Zhang, D and Xiang, G and Wang, Z and Zhang, Z and Liu, M and Hao, W and Wu, D}, title = {Thiosulfate-Driven redox buffering enables efficient nitrogen removal and norfloxacin degradation in mixed denitrifying systems.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134550}, doi = {10.1016/j.biortech.2026.134550}, pmid = {41932524}, issn = {1873-2976}, mesh = {*Norfloxacin/metabolism/isolation & purification ; *Denitrification/drug effects ; Oxidation-Reduction ; *Thiosulfates/pharmacology/chemistry ; *Nitrogen/isolation & purification ; Biodegradation, Environmental/drug effects ; Bioreactors/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Wastewaters often contain both conventional pollutants and recalcitrant antibiotics, posing challenges to biological treatment. This study investigated a mixed autotrophic-heterotrophic denitrification system driven by sodium acetate and sodium thiosulfate for simultaneous nitrate and norfloxacin removal. A sequencing batch reactor was operated in four stages, culminating in norfloxacin exposure (0.5 mg/L). Results showed stable nitrogen removal (>95%) and norfloxacin degradation (>90%) under sustained antibiotic stress. Batch tests confirmed that the co-presence of thiosulfate and acetate enhanced norfloxacin biodegradation via co-metabolic pathways, with negligible abiotic removal. Three-dimensional excitation-emission matrix spectroscopy revealed a shift toward humic-like extracellular polymeric substances under norfloxacin, supporting biofilm integrity. 16S rRNA sequencing and metagenomics indicated dynamic microbial restructuring, with persistent core taxa (Thauera, Desulfofustis) and enrichment of stress-tolerant groups (norank_o_SJA-15). Functional analysis showed upregulation of carbon metabolism (pta, ackA), denitrification (nirS, nosZ), and sulfur oxidation (SUOX, SoxX, SoxA) genes, alongside oxidative stress mitigation genes (catB, gst) and xenobiotic degradation genes (HGD, E1.13.11.4). Antibiotic resistance gene profiles shifted toward multidrug (>29%), peptide resistance (14.0%→15.4%), and glycopeptide resistance (7.0%→9.4%), dominated by multidrug efflux and target alteration mechanisms, enabling community resilience while minimizing energetically costly defenses. This work elucidates the synergistic roles of dual electron donors in pollutant co-removal and stress mitigation, offering a robust, sustainable strategy for treating antibiotic-laden wastewater.}, } @article {pmid41932525, year = {2026}, author = {Liu, Q and Wei, S and Li, Y and Yu, X and Zhang, Z and Li, J}, title = {Synthetic microbial community drive methane oxidation coupled to Cr(VI) reduction via division of labor and extracellular electron transfer.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134546}, doi = {10.1016/j.biortech.2026.134546}, pmid = {41932525}, issn = {1873-2976}, mesh = {Oxidation-Reduction ; *Chromium/metabolism ; *Methane/metabolism ; Electron Transport ; Biodegradation, Environmental ; *Microbial Consortia/physiology ; }, abstract = {While methane oxidation coupled to Cr(VI) reduction has been widely investigated, the functional specialization and division of labor within microbial consortia remain insufficiently understood. In this study, a synthetic microbial community (SynCom) was constructed by controlling methane concentration and chromium load. The maximum Cr(VI) removal load of this system reached 20.63 mg/L/d. The metagenomic assembly genome analysis showed that under hypoxic conditions, Methylocystis (6.30%) was the core microorganism driving methane oxidation. It achieved extracellular electron transfer (EET) through multiheme c-type cytochromes and conductive pili, or jointly with dominant genera such as Hyphomicrobium and Thiobacillus, to couple methane oxidation with Cr(VI) reduction. Integrated multi-omics revealed significant enrichment of differentially expressed proteins involved in quorum sensing and methane metabolism, along with elevated expression of ABC transporter substrate-binding protein and porin. The primary metabolites included N-Methyl-L-Proline, L-Histidine, and Hypaphorin, with L-Glutamine serving as a central node connecting the highest number of pathways in the metabolic network. The inhibition experiments confirmed that inhibiting the methane oxidation would directly reduce the efficiency of Cr(VI) reduction. This study revealed the microbial division of labor and the microscopic process of EET driven by aerobic methanotrophs under hypoxic conditions, and expanded its application potential in bioremediation from the perspective of SynCom. It could be a scientific foundation for pollution control technologies of methane-based biotransformation and utilization.}, } @article {pmid41932647, year = {2026}, author = {Wang, DY and Wang, YW and Yu, KC and Yang, X and Ma, J and Li, BH and Peng, YL and Deng, XY and Chen, ZX and Wang, L}, title = {Probiotic potential of Parabacteroides johnsonii in mitigating age-related ovarian functional decline.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2026.03.023}, pmid = {41932647}, issn = {1673-8527}, abstract = {The gut microbiota is increasingly recognized as a regulator of reproductive health, yet its role in ovarian aging remains unclear. Here, we combine Mendelian randomization (MR) analysis with experimental validation to investigate the causal relationship between gut microbiota and ovarian aging. MR analysis identifies four microbial taxa significantly associated with age at natural menopause. In mouse models, germ-free mice exhibit accelerated ovarian functional decline, including reduced ovarian reserve and impaired folliculogenesis. Fecal microbiota transplantation (FMT) from young donors alleviates ovarian aging phenotypes, whereas FMT from aged donors exacerbates functional decline. Metagenomic analysis reveals species-level differences between young and ovarian-aging mice, with Parabacteroides johnsonii (P. johnsonii) enriched in young mice. Administration of P. johnsonii to middle-aged mice improves ovarian reserve, reduces follicular atresia, enhances granulosa cell proliferation, and decreases systemic inflammation. These findings highlight a causal role of the gut microbiota in ovarian aging and support microbiota-targeted interventions as a potential strategy to preserve ovarian function.}, } @article {pmid41932883, year = {2026}, author = {Silva, RMB and Slyvka, A and Lee, YJ and Guan, C and Lund, SR and Raleigh, EA and Skowronek, K and Kuska, MS and Bochtler, M and Weigele, PR}, title = {A single viral enzyme drives tRNA-dependent hypermodification of DNA at adenine.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41932883}, issn = {2041-1723}, support = {FNP, POIR.04.04.00-00-5D81/17-00//Fundacja na rzecz Nauki Polskiej (Foundation for Polish Science)/ ; }, mesh = {*Adenine/metabolism/chemistry ; *RNA, Transfer/metabolism ; *Bacteriophage mu/enzymology/genetics ; *Viral Proteins/metabolism/genetics/chemistry ; *DNA, Viral/metabolism/chemistry/genetics ; *Deoxyadenosines/biosynthesis/chemistry/metabolism ; Models, Molecular ; }, abstract = {Nucleic acid modifying enzymes drive diverse defense and counter-defense measures in the evolutionary arms race between viruses and their cellular hosts. Abundant and widespread bacterial viruses (bacteriophage or phage) encode for biosynthetic pathways that install elaborate DNA hypermodifications which protect their genomic DNA from host endonucleases. Here, we establish the molecular basis for the multistep biosynthesis of 6-aminocarboxymethyl-2'-deoxyadenosine (6-NcmdA), a nucleobase hypermodification found in the virion DNA of bacteriophage Mu that leads to restriction evasion in the context of phage-host conflicts. In the first step, we show that Mu-encoded Mom enzyme catalyzes the formation of 6-NcmdA by transferring glycine from charged tRNA[Gly] to the N6 position of adenine within double-stranded DNA. We uncover a second step where the glycyl-dA intermediate undergoes an on-base rearrangement to form 6-NcmdA. Examination of the proposed reaction pathways by quantum chemical calculations confirms the instability of acyl exocyclic groups at N6-adenine and reveals an energetically favorable orientation of 6-NcmdA that restores canonical base pairing. An X-ray structure confirms Mom is a member of the GNAT superfamily and suggests binding sites for both tRNA and DNA. Guided by the Mom structure and patterns of sequence conservation across metagenomic space, we show residues R111 and S124 are essential for catalysis. This work demonstrates that the Mom enzyme defines a new category of acetyltransferases utilizing charged tRNA to modify DNA.}, } @article {pmid41932890, year = {2026}, author = {Zhao, L and Zheng, J and Shen, Y and Xu, X and Liu, X and Yu, J and Li, J and Yang, B and Chen, L and Wang, F and Liu, S and Peng, X and Du, J and Dong, R}, title = {Composite polyphenols mitigate microplastic exposure-related immune disturbances: a two-phase population trial.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71167-8}, pmid = {41932890}, issn = {2041-1723}, abstract = {Microplastics (MPs) are widespread, making it urgent to elucidate their toxicity and identify intervention strategies. Here, we designed a two-phase population trial, comprising a baseline pilot population (n = 151) and a 28-day randomized, double-blind, placebo-controlled trial (n = 98). Primary outcomes include fecal MP concentration and blood parameters (complete blood count, glycemic and lipid, and cytokines), with exploratory outcomes comprising fecal metagenomics and plasma metabolomics. The median MP concentration in 151 participants' fecal samples is 158.28 μg/g dry weight, correlating with levels of 7 inflammatory indexes, 4 cytokines, and 2 lipid indicators. Composite polyphenols (CP) significantly reduced plasma levels of IL-1β (P = 0.045, effect sizes = -0.463), IL-6 (P = 0.023, effect sizes = -0.576) and IL-8 (P = 0.022, effect sizes = -0.529). 507 differentially expressed microbiotas (DEMs; P < 0.05) and 144 significantly different metabolites (SDMs; P-FDR < 0.25, VIP ≥ 1) are observed between the high and low MP exposure groups; 108 DEMs and 85 SDMs are identified following CP intervention. Notably, CP could mitigate the pro-inflammatory effects of high MP exposure by modulating gut microbiota and up-regulating glycerophospholipid metabolism and arginine biosynthesis. The gut bacteria Staphylococcus and the plasma metabolite PC (22:5/0:0) are identified as potential mediators in this protective effect. Trial registration: ClinicalTrials.gov: NCT06437119.}, } @article {pmid41932913, year = {2026}, author = {Barbour, A and Bendayan, Y and Marks, C and Choi, YHK and Oveisi, M and Callaghan, M and Sun, C and Zargaran, S and Xia, M and Wood, D and Smith, L and McLean, JS and Mazzulli, T and Glogauer, M}, title = {Phosphorylated lantibiotics-producing commensals integrate into the human oral microbiome to suppress pathogens and promote microbiome homeostasis.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41932913}, issn = {2055-5008}, mesh = {Humans ; *Microbiota ; *Bacteriocins/pharmacology/metabolism/biosynthesis ; Homeostasis ; *Mouth/microbiology ; Phosphorylation ; Streptococcus salivarius/metabolism/genetics ; *Anti-Bacterial Agents/pharmacology ; Enterococcus faecium/drug effects ; Porphyromonas gingivalis/drug effects ; Biofilms/drug effects ; Streptococcus pneumoniae/drug effects ; Metagenomics ; Symbiosis ; Antimicrobial Peptides ; }, abstract = {Commensal bacteria produce antimicrobial peptides (AMPs) to maintain microbiome homeostasis, yet the traits underlying this resilience and their translation into biotherapeutics remain understudied. Phosphorylated lantibiotics (pLANs) are a recently identified class of ribosomally synthesized and post-translationally modified peptides (RiPPs), with dual antimicrobial and pro-immune activities. In this manuscript, we explore the potential of commensals' pLANs biosynthesis as a mechanism for pathogen suppression and microbiome homeostasis. Subgingival metagenomics revealed that oral health correlates with Streptococcus salivarius enrichment and an increased prevalence of streptococcal RiPP biosynthetic gene clusters. Guided by these associations, we screened 80 S. salivarius isolates, identifying a small subset producing pLANs with potent activity against Porphyromonas gingivalis, vancomycin-resistant Enterococcus faecium, and multidrug-resistant Streptococcus pneumoniae. A representative lead strain, SALI-10, exhibited robust epithelial adhesion and a sorbitol-driven metabolic adaptation that enhances pLANs expression. In human-derived dysbiotic biofilms, SALI-10 stably engrafted, suppressed periopathogens, reduced antibiotic-resistance genes, and enriched acid-buffering pathways. In a first-in-human feasibility trial, daily oral administration of SALI-10 for one week yielded increased pLANs signals, pathogen depletion, and reduced oral neutrophil counts. Ultimately, pLANs-producing S. salivarius acts as a precision commensal to restore ecological balance, defining a mechanistically grounded and microbiota-mediated strategy to prevent oral and respiratory infections.}, } @article {pmid41933095, year = {2026}, author = {Fu, Z and Sun, Y and Yao, H and Liu, Q and Zhang, Q and Hu, J and Zhou, Y and Jiang, N and Ai, J and Jin, J and Zhang, W}, title = {A diagnostic model based on pulmonary microbiota and host gene expression to distinguish colonization from pneumonia.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41933095}, issn = {2045-2322}, mesh = {Humans ; *Microbiota/genetics ; *Pneumonia/microbiology/diagnosis/genetics ; *Lung/microbiology ; Metagenomics ; Gene Expression Profiling ; Male ; Female ; Multiomics ; Prospective Studies ; Sputum/microbiology ; Transcriptome ; High-Throughput Nucleotide Sequencing ; }, abstract = {Pneumonia remains a leading cause of global mortality. Conventional diagnostic approaches frequently fail to distinguish microbial colonization from true infection in the lower respiratory tract, complicating clinical decision-making and contributing to antibiotic overuse. Improved diagnostic strategies are urgently needed. In this prospective, single-center study, deep sputum specimens were collected from patients with respiratory colonization (n = 17) and infectious pneumonia (n = 27) admitted to the neurosurgical ICU of Huashan Hospital. Metagenomic next-generation sequencing (mNGS) and metatranscriptomic profiling were performed to characterize both the pulmonary microbiota and the host immune response. These features were subsequently integrated to construct a diagnostic model. Microbial community profiling revealed reduced alpha diversity and enrichment of metabolically active pathogenic taxa in the infection group, consistent with a dysbiotic state permissive to invasion. In contrast, the colonization group demonstrated a more balanced microbial ecosystem. Transcriptomic analyses identified 2232 differentially expressed host genes between the two groups. The colonization group showed marked activation of the Wnt, MAPK, chemokine, and focal adhesion pathways, which are functionally implicated in epithelial barrier maintenance and early immune homeostasis. A multi-omics diagnostic model incorporating seven gene features (ANKRD52, ZC3HAV1L, SERPINE3, CDPF1, ZNF720, TAGLN3, and LRRC15) achieved a discrimination between colonization and infection (AUC = 0.951 in the training cohort; 0.875 in the validation set). By jointly analyzing the pulmonary microbiome and host transcriptome, this study provides insight into host-microbe interactions distinguishing colonization from infection and presents a predictive model with potential clinical relevance.}, } @article {pmid41933201, year = {2026}, author = {Prasoodanan Pk, V and Maistrenko, OM and Fullam, A and Mende, DR and Kartal, E and Coelho, LP and Spang, A and Bork, P and Schmidt, TSB}, title = {Unbinned contigs expand known diversity in the global microbiome.}, journal = {Nature microbiology}, volume = {11}, number = {5}, pages = {1437-1449}, pmid = {41933201}, issn = {2058-5276}, support = {12/RC/2273-P2 (APC Microbiome)//Science Foundation Ireland (SFI)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; FT230100724//Department of Education and Training | Australian Research Council (ARC)/ ; }, mesh = {*Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Metagenome ; Phylogeny ; Genetic Variation ; *Biodiversity ; Soil Microbiology ; }, abstract = {The ongoing census of microbial life is hampered by disparate sampling across Earth's habitats, challenges in isolating uncultivated organisms, limited resolution in taxonomic marker gene amplicons and incomplete recovery of metagenome-assembled genomes. Here we quantify discoverable Bacterial and Archaeal diversity in a comprehensive, curated cross-habitat dataset of 92,187 publicly available metagenomes. Clustering 502 million sequences of 130 marker genes, we predict ~705,000 Bacterial and ~27,000 Archaeal species-level clades, the vast majority of which were hidden among unbinned contigs. We estimate that ten and 145 previously undescribed Archaeal and Bacterial phyla, respectively, are discoverable in this dataset. We identify soils and aquatic environments as hotspots of discoverable lineages, but predict that undescribed taxa remain abundant across all habitats. Finally, we show that prokaryotic diversity appears to arise within common evolutionary patterns, as clade size distributions follow power laws, consistently across the Tree of Life.}, } @article {pmid41933302, year = {2026}, author = {Wu, L and Pu, J and Xi, X and Bao, Y and Luo, L}, title = {Streptomyces morookaense spinal suppurative infection: a case report.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41933302}, issn = {1471-2334}, support = {2025M781412//The China Postdoctoral Science Foundation/ ; }, mesh = {Humans ; Female ; Aged ; *Streptomyces/isolation & purification/genetics ; Anti-Bacterial Agents/therapeutic use ; Magnetic Resonance Imaging ; Thoracic Vertebrae/microbiology/diagnostic imaging/pathology ; Tomography, X-Ray Computed ; Suppuration/microbiology ; }, abstract = {PURPOSE: Streptomyces species are ubiquitous soil actinomycetes and a major source of antibiotics, but invasive human infection with spinal involvement is exceedingly rare and may mimic tuberculous or fungal spondylodiscitis. We report a thoracic suppurative vertebral infection caused by Streptomyces morookaense and highlight an integrated diagnostic approach.

METHODS: A 66-year-old woman with no known immunodeficiency developed progressive thoracic back pain one month after severe trauma with open wounds. CT/MRI showed osteolytic endplate destruction at T3-T4 with paravertebral abscess formation. Fluoroscopy-guided percutaneous biopsy of the T4 vertebral body was performed for histopathology, culture, and metagenomic next-generation sequencing (mNGS).

RESULTS: Histopathology demonstrated fibrinous exudate, necrosis, and inflammatory granulation tissue with fragmented trabeculae, without granuloma or caseous necrosis; acid-fast staining was negative. Vertebral tissue culture grew Streptomyces spp, and mNGS identified high-abundance sequences matching S. morookaense. Intravenous piperacillin/tazobactam led to rapid pain relief and normalization of inflammatory markers within one week, and no recurrence was observed during follow-up.

CONCLUSION: This case suggests that Streptomyces morookaense has the potential to involve the thoracic spine in immunocompetent individuals. For unexplained spinal infections with negative routine tests, percutaneous vertebral sampling with integrated interpretation of pathology, culture, and mNGS can improve detection of rare pathogens and help avoid inappropriate empirical therapy.}, } @article {pmid41933424, year = {2026}, author = {Zhao, Y and Wang, Z and Fan, D and Zhang, J and Tu, Y and Diao, Q and Cui, K}, title = {Gut microbiota-driven IL-17/PPAR axis mediates epigallocatechin-induced intestinal repair in weaned lambs.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41933424}, issn = {1674-9782}, support = {2024YFD1300204//National Key Research and Development Program of China/ ; 32172764//National Natural Science Foundation of China/ ; 25036//Agricultural Science Technology Project of Shijiazhuang/ ; }, abstract = {BACKGROUND: Early weaning is a key strategy to improve lamb production efficiency; however, it inevitably compromises intestinal barrier integrity and function. This study aimed to investigate the effects of epigallocatechin (EGC) on growth performance and intestinal barrier function in weaned lambs, using metagenomics, metabolomics, and intestinal transcriptomics to elucidate the underlying mechanisms.

RESULTS: Weaning induced oxidative stress, inflammation, and metabolic disruptions in the jejunum. Supplementation with 12.5 mg/kg EGC (LE) significantly improved growth performance, reduced diarrhea incidence (P < 0.05), enhanced mucosal antioxidant capacity (P < 0.001), and strengthened anti-inflammatory ability (P < 0.001). Metagenomic analysis showed that the LE intervention enriched Ruminococcus spp. and reduced the abundance of Slackia. This microbial shift was associated with elevated luminal concentrations of valeric acid and microbial metabolites derived from EGC. Transcriptomic profiling revealed that the intervention upregulated the PPAR signaling pathway, which supports nutrient metabolism and barrier repair. Concurrently, it attenuated aberrant IL-17 signaling and promoted the restoration of mucosal immune homeostasis, indicating a resolution of excessive inflammatory responses.

CONCLUSIONS: Supplementation with 12.5 mg/kg EGC alleviates weaning stress by fostering a beneficial gut microbiota and promoting the production of specific metabolites. These changes reactivate PPAR mediated epithelial repair and dampen pathological immune activation. Low-dose EGC is an effective nutritional strategy to improve intestinal health and growth in weaned ruminants.}, } @article {pmid41933601, year = {2026}, author = {Chen, J and Yan, Y and Xie, K and Gao, M and Ma, Y}, title = {Effect of delivery mode and temperature control of microbial consortium-based compound enzyme on anaerobic digestion of food waste: Decipherment from engineering and energy angles.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134536}, doi = {10.1016/j.biortech.2026.134536}, pmid = {41933601}, issn = {1873-2976}, mesh = {Food Loss and Waste ; Methane/biosynthesis ; *Temperature ; Anaerobiosis ; Hydrolysis ; *Microbial Consortia/physiology ; Archaea/metabolism ; Bioreactors/microbiology ; Bacteria/metabolism ; *Refuse Disposal/methods ; }, abstract = {Microbial consortium-based compound enzyme (MCE) has been developed as an alternative to commercial enzyme for food waste (FW) decomposition, yet how to deliver it to anaerobic digestion (AD) system for maximum energy recovery remains unclear. This study systematically compared the simultaneous hydrolysis and AD (Sim mode), as well as separate hydrolysis and AD (Sep mode) at mesophilic and thermophilic temperatures, and dissected their influencing mechanisms on methane production from FW. Results showed that Sep mode and mesophilic temperature were the optimal conditions for methane production, where over 70% of soluble COD and 96% of soluble carbohydrate were consumed within 1 d, and the highest cumulative methane yield reached 507.32 mL/g VS. Dynamics of microbial communities revealed that temperature exerted greater influence on bacterial and archaeal succession than delivery modes, and mesophilic temperature-driven transition from hydrogenotrophic archaea to acetotrophic archaea was a key factor in enhancing methane production. Metagenomic analysis further elucidated that key metabolic functions were temperature-dependent, and Methanothrix was identified as the dominant contributor to these metabolic functions. Moreover, energy balance unveiled that Sep mode respectively increased net energy recovery (ΔEtotal) and energy ratio (Er) by 68.33% and 25.90%, achieving concurrent maximization of quantity and efficiency of energy recovery.}, } @article {pmid41933710, year = {2026}, author = {Huang, S and Zhang, S and Chen, Y and Su, X and Lu, X and Song, X and Li, W and Guo, Z and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Wang, X and Shan, T and Zhang, W}, title = {Viral metagenomic analysis of CRESS-DNA viruses in six wild herbivorous mammal species from the Qinghai-Tibet plateau.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {140}, number = {}, pages = {105932}, doi = {10.1016/j.meegid.2026.105932}, pmid = {41933710}, issn = {1567-7257}, mesh = {Animals ; *DNA Viruses/genetics/classification/isolation & purification ; *Metagenomics/methods ; Tibet ; Phylogeny ; Genome, Viral ; *Mammals/virology ; Metagenome ; Virome ; }, abstract = {As natural reservoirs for diverse viruses, mammals harbor complex and highly diverse viral communities. The Qinghai-Tibet Plateau, recognized as the "Third Pole" of Earth, exerts substantial evolutionary pressure on virions through its extreme environmental conditions characterized by high altitude, hypoxia, intense ultraviolet radiation, and dramatic diurnal temperature variation. Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses represent a ubiquitous group of small viruses that play crucial roles in maintaining global ecological equilibrium. Through viral metagenomic analysis of 741 fresh fecal samples collected from six wild herbivorous mammal species across three geographical regions of the Qinghai-Tibet Plateau, we systematically characterized their virome composition, revealing distinct interspecies variations in viral community structure. Focusing on CRESS-DNA viruses, we identified 180 complete viral sequences containing intact replication-associated protein (Rep) genes, including: Circoviridae (2 sequences, 1 novel), Genomoviridae (48 sequences, 38 novel), Smacoviridae (106 sequences, 103 novel), and Unclassified CRESS-DNA viruses (24 sequences, 20 novel), collectively representing an 86% discovery rate of novel viral virus. These viral sequences exhibited remarkable genetic divergence, with the majority (73%) failing to cluster within established taxonomic units, suggesting the plateau may constitute an evolutionary hotspot for novel CRESS-DNA viruses. Our findings not only expand current understanding of CRESS-DNA viral diversity but also indicate potential long-term symbiotic virus-host relationships rather than purely pathogenic interactions in this extreme ecosystem. Notably, high viral detection rates in species such as the Pseudois nayaur suggest their potential role as key transmission vectors. These discoveries provide novel insights into virus-host coevolution mechanisms under extreme environmental conditions and establish a scientific foundation for early warning systems of viral transmission risks in high-altitude ecosystems.}, } @article {pmid41933826, year = {2026}, author = {Ma, J and Zhang, H and Liang, S and Feng, X and Xia, Z and Li, H and Zou, S and Li, D}, title = {The health threat of wild animals by Rank I ARGs from habitat soils: Metagenomic and metabolomic evidence.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {398}, number = {}, pages = {128041}, doi = {10.1016/j.envpol.2026.128041}, pmid = {41933826}, issn = {1873-6424}, mesh = {Animals ; *Animals, Wild ; *Soil Microbiology ; Ecosystem ; *Drug Resistance, Microbial/genetics ; Metagenomics ; Soil/chemistry ; Metabolomics ; Colobinae ; Bacteria/genetics ; }, abstract = {Human disturbance (HD) leads to the enrichment of antibiotic resistance genes (ARGs), posing a threat to the health of wild animals. However, not all ARGs necessarily endanger wild animals' health. Therefore, this study used the golden snub-nosed monkeys (Rhinopithecus roxellana) as a sentinel species, and employed metagenomics to investigate the impact of high-risk ARGs (Rank Ⅰ ARGs) from habitats on wild animals' health. Subsequently, we studied the expression of metabolites within the metabolic network harboring homologous functional genes based on metabolomics. The results indicated that only 0.034% of ARGs in the habitat soils were classified as Rank I ARGs. HD not only increased the accessibility, mobility, pathogenicity and availability of Rank I ARGs in the soils of wild animals' habitats, thereby elevating the health risks to wild animals. Especially, the energy metabolism and carbohydrate metabolism functions of the gut microbiome were disrupted in wild animals. Multiple factors influence the health of wild animals posed by Rank I ARGs under HD: primarily, the strong correlation between ARGs and MGEs; the indirect impact of the content of AP in the soil; the increased proportion of the host bacteria Enterobacter; and the rise in the potential host bacteria of Rank I ARGs. We suggested that the use of aminoglycoside, glycopeptide, and peptide antibiotics should be strictly controlled in nature reserves, coupled with enhanced monitoring of soil nutrients, particularly available phosphorus.}, } @article {pmid41934012, year = {2026}, author = {Moraïs, S and Mizrahi, I}, title = {Micro-scale spatial metagenomics opens a new era in microbiome ecology.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.03.005}, pmid = {41934012}, issn = {1878-4380}, abstract = {Understanding microbial communities requires moving beyond 2D representations toward a holistic view that couples 3D spatial organization with ecological function, integrating microbial inventories, genes, expression profiles, and interactions at scales and dimensions in which microbial life unfolds. In this opinion article, we synthesize recent findings and emerging approaches that enable the investigation of microbial interactions within their native 3D context. We propose conceptual frameworks for integrating spatial-functional information into comprehensive ecological maps, providing new avenues to interpret microbial interactions and to test ecological theory in situ. Together, these insights outline a new ecological paradigm for microbiome research and highlight how spatially resolved understanding can be harnessed to interpret and ultimately guide the modulation of microbial interactions and ecosystem function in natural settings.}, } @article {pmid41934196, year = {2026}, author = {Alvarez-Sala, A and Jiménez-Hernández, N and Artacho, A and Ruiz-Pérez, S and Pascual, EC and Pons, J and Sorlí, JV and Corella, D and Gosalbes, MJ}, title = {Multi-Omic Insights Into Mediterranean Diet-Associated Microbiota.}, journal = {Molecular nutrition & food research}, volume = {70}, number = {7}, pages = {e70450}, pmid = {41934196}, issn = {1613-4133}, support = {UGP-19-038//FISABIO/ ; UGP-21-205//FISABIO/ ; CIAICO/2022/27//Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital/ ; Prometeo2021/021//Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital/ ; CB06/03/0035//CIBEROBN/ ; }, mesh = {Humans ; *Diet, Mediterranean ; Multiomics ; Metagenomics ; *Microbiota ; Feces/microbiology ; Bacteria/genetics/classification ; Male ; Adult ; Fungi/genetics/classification ; Female ; }, abstract = {This study aimed to evaluate the gut microbiota and mycobiota composition, depending on the Mediterranean diet (MD) adherence, using metataxonomics. Combining metagenomics and metatranscriptomics, we also investigate the gene expression level in the bacterial community. Two groups of healthy subjects greatly differing in adherence were selected. Significant differences in microbiota composition were observed between individuals with high adherence (HAMD; mean 10.5 +/- 0.9 points) and low adherence (LAMD; 5.23 +/- 83 points). Notably, the olive oil, vegetable, and fruit consumption presented an important discriminant power between groups. Saccharomyces, Penicillium, and Candida were the most abundant genera. Mycobiota richness was higher in LAMD than in HAMD. Aspergillus was identified as a biomarker for LAMD, whereas Yarrowia, a potential probiotic, was a biomarker for HAMD. Metatranscriptomics indicated that Bacillota was the most metabolically active phylum in the gut microbiota. The low-abundant genus, Methanobrevibacter, showed high transcriptional activity, contributing to the crucial methanogenesis process. Gene expression analyses further highlighted functional differences. Overall, HAMD microbiota presented increased metabolic activity, protein synthesis, and cellular mobility. Overexpression of flagellin and urease genes may enhance immune response in HAMD. Further metatranscriptomic studies are necessary to deepen our understanding of intestinal microbiota transcriptional programs and their interactions with the diet and human health.}, } @article {pmid41934511, year = {2026}, author = {Kumar, KS and Jeyabal, J and Yagoo, A and Vilvest, J and Vaishnika, AM}, title = {Dietary chitosan enhances gut microbial diversity and modulates beneficial and pathogenic communities in Channa striata fingerlings.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {5}, pages = {}, pmid = {41934511}, issn = {1572-9699}, mesh = {Animals ; *Chitosan/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/drug effects/isolation & purification ; Dietary Supplements ; Biodiversity ; Diet ; Prebiotics ; *Fishes/microbiology ; }, abstract = {Dietary modulation of the gut microbiome is a promising approach for improving fish health and sustainability in aquaculture. Chitosan, a biopolymer derived from Artemia shells, has gained attention as a functional prebiotic feed additive due to its antimicrobial and immunomodulatory properties. The effects of dietary chitosan on gut microbial diversity and community composition were evaluated in Channa striata (murrel) fingerlings. Fish were fed three experimental diets: a basal diet (Exp-1), a black soldier fly larvae (BSFL)-based control diet (in which BSFL meal was used as a primary protein ingredient, with its nutritional composition considered during formulation), and a chitosan-supplemented diet (Exp-2). Gut microbiota were characterized using high-throughput 16S rRNA gene sequencing, and microbial diversity, composition, and interaction networks were analyzed. Alpha diversity analysis demonstrated that the chitosan-based diet significantly enhanced microbial richness (Chao1 = 531.62) and promoted a more balanced gut microbial structure compared to the basal diet, which showed reduced diversity and relative dominance of certain taxa previously reported to include opportunistic species. Chitosan supplementation enriched genera such as Lactobacillus, Bacteroides, and Alloprevotella, along with members of Muribaculaceae, which are commonly associated in the literature with functions such as polysaccharide degradation and short-chain fatty acid production, although functional roles cannot be conclusively assigned at the genus level. In contrast, the basal diet group showed a higher abundance of taxa including Plesiomonas and Clostridium sensu stricto, which have been reported in some contexts to include opportunistic strains. Network analysis further revealed stronger clustering and connectivity among microbial taxa under chitosan supplementation, suggesting improved microbial stability. Overall, dietary chitosan appears to influence gut microbial composition and diversity, suggesting a possible role in influencing gut microbial balance. These findings highlight its possible application as a sustainable feed additive in aquaculture, although further functional validation is required.}, } @article {pmid41934651, year = {2026}, author = {Zhang, N and Li, L and Chen, F and Kang, X and Liu, L and Kuang, D}, title = {Rapid Cavitary Pneumonia and Reversible Hepatic Injury in Burkholderia pseudomallei ST271 Infection.}, journal = {The American journal of case reports}, volume = {27}, number = {}, pages = {e951729}, pmid = {41934651}, issn = {1941-5923}, mesh = {Humans ; Male ; *Melioidosis/diagnosis/complications/drug therapy ; Middle Aged ; *Burkholderia pseudomallei/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; *Pneumonia, Bacterial/microbiology/diagnosis/drug therapy ; *Liver Diseases/microbiology/diagnosis ; Tomography, X-Ray Computed ; }, abstract = {BACKGROUND Burkholderia pseudomallei is the causative agent of melioidosis, an infectious disease endemic to tropical and subtropical regions that displays highly variable clinical presentations, ranging from localized abscesses to severe septicemia. Sequence type (ST) 271 has been rarely reported; data concerning its clinical and epidemiological characteristics remain limited. This report describes a rare case of ST271 infection presenting with rapidly progressive cavitary pneumonia and reversible hepatic injury. CASE REPORT A previously healthy 50-year-old male construction worker from Haikou, China, presented with a 2-week history of intermittent fever, hemoptysis, and persistent cough. Chest computed tomography revealed a thick-walled cavitary mass in the right upper lobe. Laboratory findings demonstrated substantially elevated liver enzymes, indicating acute hepatic injury. Metagenomic sequencing of bronchoalveolar lavage fluid identified B. pseudomallei, and whole-genome sequencing classified the isolate as ST271. The strain was sensitive to imipenem, ceftazidime, and trimethoprim-sulfamethoxazole; preliminary in vitro bacteriophage susceptibility also was observed. After initiation of intravenous ceftazidime followed by oral trimethoprim-sulfamethoxazole, the patient showed rapid clinical improvement that included robust resolution of the pulmonary lesion and normalization of liver enzymes, consistent with reversible hepatic injury. CONCLUSIONS This case highlights the aggressive clinical course of the rare B. pseudomallei ST271 strain, characterized by rapidly progressive cavitary pneumonia and concurrent hepatic injury in an immunocompetent host. Early identification using sequencing techniques facilitated timely targeted therapy and a favorable recovery. The observed in vitro phage susceptibility may provide preliminary insight for future research into alternative management strategies for resistant strains.}, } @article {pmid41934839, year = {2026}, author = {Dong, C and Sun, L and Liu, Z and Sun, C and Pan, D and Zhu, L and Hu, B}, title = {Seafood resistome across trophic levels: Tissue patterns, drivers, and potential dietary exposure.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141959}, doi = {10.1016/j.jhazmat.2026.141959}, pmid = {41934839}, issn = {1873-3336}, mesh = {*Seafood/microbiology/analysis ; Animals ; *Dietary Exposure ; Food Chain ; *Drug Resistance, Microbial/genetics ; Metagenome ; Genes, Bacterial ; Humans ; }, abstract = {Antibiotic resistance genes (ARGs) are recognized as emerging contaminants relevant to human exposure. They are widespread in seafood, but their distribution across trophic levels and tissues remains unclear. We analyzed 43 metagenomes covering five marine trophic levels, from seawater plankton to obligate piscivores, and examined muscle, gill, and viscera samples. Multidrug, tetracycline, bacitracin, and β-lactam genes together accounted for about 70% of total relative ARG abundance. ARG richness, diversity, and abundance increased with trophic level. In higher trophic taxa, edible muscle contributed a larger share of the total ARG signal, indicating greater relevance to dietary exposure. Procrustes and variation partitioning showed that ARG composition was mainly associated with microbial community structure and mobile genetic elements (MGEs). Contig analysis further showed co-occurrence of ARGs and MGE markers, suggesting mobility potential. A composite risk index that integrates abundance, mobility proxies, and host or pathogen association also increased with trophic position. These results show clear trophic and tissue patterns of ARGs in marine foods and support priority monitoring of high trophic taxa, edible tissues, microbiome and MGE features along seafood supply chains.}, } @article {pmid41934858, year = {2026}, author = {Chen, Z and Zheng, M and He, J and Ye, C and Zheng, W and Liang, Y and Yu, X and Guo, F}, title = {Trait-mediated restructuring of gut microbiota under chlorinated drinking water exposure.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141965}, doi = {10.1016/j.jhazmat.2026.141965}, pmid = {41934858}, issn = {1873-3336}, mesh = {*Drinking Water ; Animals ; *Chlorine/toxicity ; Halogenation ; *Gastrointestinal Microbiome/drug effects ; Humans ; Mice ; Bacteria/genetics/drug effects ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Chlorine residuals in drinking water are environmentally relevant oxidants regulated within distribution systems and ingested during routine consumption. Here, we use longitudinal, within-subject designs in humans (0.5 mg/L chlorine exposure) and a parallel mouse model (10 mg/L) to assess the ecological impact of chlorine residuals on gut microbiota under realistic conditions. Crucially, overall diversity, total bacterial biomass, antibiotic resistance genes, and phage communities remained largely unaffected. However, we report a lineage-independent de-dominance effect, where initially dominant taxa decline following exposure. Genome-resolution analysis reveals that microbes with larger genomes and functional enrichment in energy metabolism and membrane biogenesis are more likely to increase, enabling accurate prediction of microbial responses to chlorination. These patterns can be interpreted within the Competitor-Stress-tolerator-Ruderal life-history framework, in which disturbance of chlorine residuals transiently reduces the advantage of competitive dominant taxa and favors stress-tolerant taxa. Our findings demonstrate that chlorination residuals act as subtle, trait-mediated ecological stressors in the gut microbiome, producing selective yet predictable shifts. These insights frame chlorine residuals as hazardous environmental agents and inform microbiome-aware optimization of water disinfection and residual control.}, } @article {pmid41935036, year = {2026}, author = {Larsson, DGJ and Flach, CF and Kristiansson, E}, title = {Antibiotic resistance gene analyses in microbial communities: challenges and opportunities.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41935036}, issn = {2041-1723}, support = {2022-00945//Vetenskapsrådet (Swedish Research Council)/ ; }, abstract = {Culture-independent antibiotic resistance gene analyses enable broad explorations of microbial communities but often fail to link such genes to bacterial hosts and genetic contexts. This makes assessing prevalence of resistant pathogens and likelihood of further transmission or resistance evolution uncertain.}, } @article {pmid41935109, year = {2026}, author = {Zhang, M and Luo, K and Liu, D and Li, Y and Liu, Q and Li, J}, title = {The influence of human activities on the microbial community structure and function of a karst cave in southwest China.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41935109}, issn = {2045-2322}, support = {52560012//National Natural Science Foundation of China/ ; [2024]2-38//Science and Technology Plan Project of Guiyang City/ ; Qiankehe Chengguo [2025] Zhongda 103//Guizhou Provincial Science and Technology Achievement Transformation Plan Project/ ; }, mesh = {*Caves/microbiology ; China ; Humans ; Geologic Sediments/microbiology ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; *Human Activities ; Nitrogen/metabolism ; Phosphorus/metabolism ; Metagenomics ; }, abstract = {With human activities like exploration, geological investigation and tourism, the structure and function of karst cave microbial communities are prone to change. In this study, sediments from seven different spots in the Dushan Tian Cave in Guizhou Province, China were collected. And the structure and potential key metabolic functions of the microbial community were analyzed through metagenomics. The results showed that the structure of the microbial communities was associated with human-impacted environmental factors. Total phosphorus and Sulfide might promote the growth of Gemmatimonadetes_bacterium. However, Sulfide and organic matter might inhibit the growth of Gemmatimonadetes, Gemmatimonadetes_bacterium, Acidobacteria and Candidatus_Rokubacteria. Human activities triggered ecological effects. In terms of the abundance, denitrification genes increased but ammonia oxidation genes decreased in nitrogen metabolism, suggested there was an increasing trend in the potential of denitrification function. The sulfur metabolic potentials mainly involved assimilatory sulfate reduction where sulfates might be accumulated. The potential of carbon metabolism showed a trend towards the decomposition of exogenous carbon. The methane potential had changed. This study revealed the impact of human activities on cave microorganisms and clarified the response mechanism of cave microorganisms under human interference. It provided an important reference for the ecological protection and development and utilization of karst caves.}, } @article {pmid41935274, year = {2026}, author = {Dastjerdi, A and Davies, H and Abu Oun, M and Navickaite, I and Karuna, S and Nevel, M and Comin, A and Williamson, S}, title = {Virome of post-weaned diarrhoeic pigs and healthy cohorts in England.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {41935274}, issn = {1743-422X}, mesh = {Animals ; Swine ; England/epidemiology ; *Diarrhea/veterinary/virology/epidemiology ; *Swine Diseases/virology/epidemiology ; *Virome ; Feces/virology ; *Viruses/classification/isolation & purification/genetics ; Weaning ; Metagenomics ; Gastrointestinal Tract/virology ; Phylogeny ; *Virus Diseases/veterinary/virology ; }, abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a disease syndrome that negatively impacts pig health, welfare and productivity. PWD typically occurs within two weeks of weaning and coincides with significant physiological changes, including villus atrophy and increased crypt depth in the gastrointestinal (GI) tract. The GI microbiome of healthy pigs is a complex ecosystem of commensal microorganisms. Disruption of the natural integrity of the GI tract has been associated with increased colonization by both viral and bacterial pathogens.

METHODS: In this study, metagenomic sequencing was used to assess the presence, load, and diversity of viruses in the GI tracts of PWD-affected pigs and age-matched healthy (AMH) cohorts on commercial pig farms in England. In addition, the viromes of archived faecal samples from post-weaned pigs between four and six weeks of age, collected from diagnosis-not-reached (DNR) and diagnosis-reached (DR) enteric cases were investigated through sequencing.

RESULTS: Viruses belonging to at least ten virus families were identified in both PWD and AMH pigs including astrovirus, enterovirus, kobuvirus, smacovirus, picobirnavirus, sapovirus, parvovirus, posavirus, teschovirus, sapelovirus, rotavirus, torovirus, anellovirus and adenovirus. Co-infection with four viruses, astrovirus, enterovirus, kobuvirus and smacovirus was detected in all samples from PWD and AMH pigs. No sequence reads matching porcine coronaviruses, porcine reproductive and respiratory disease virus, porcine circoviruses, swine influenza virus, atypical porcine pestivirus or porcine teschovirus-1 were detected in either PWD or AMH faecal samples. Metagenomic analysis also identified several viruses with a higher virus load in PWD cases (astro, entero, sapelo, sapo, posa, adeno and toro-viruses), but the differences from those in AMH cases were not statistically significant. No viruses were detected in samples from archived DNR and DR cases that were not found in the PWD and AMH pigs.

CONCLUSIONS: This study revealed the complexity of the virus element in the enteric microbiome in the post-weaned pigs. The role of the viruses detected and their interplay with the host and other bacterial or viral flora in inducing PWD, however, remains unclear and warrants further studies.}, } @article {pmid41935328, year = {2026}, author = {Li, XX and Li, BY and Fu, GW and Zhao, H and Li, J and Zhou, YH and Zhang, X and Zhao, YC}, title = {Clinical impact of metagenomic next-generation sequencing on pathogen detection and outcomes in non-immunocompromised patients with severe pneumonia supported by veno-venous extracorporeal membrane oxygenation.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41935328}, issn = {1471-2334}, abstract = {BACKGROUND: Timely pathogen identification is crucial for guiding antimicrobial therapy in severe pneumonia requiring veno-venous extracorporeal membrane oxygenation (vv-ECMO). Compared with slow and often insensitive conventional culture, metagenomic next-generation sequencing (mNGS) enables more rapid and comprehensive pathogen detection and may improve clinical management. This study aimed to evaluate the clinical impact of mNGS compared with conventional culture in non-immunocompromised patients undergoing vv-ECMO for severe pneumonia. METHODS: The retrospective study explored non-immunocompromised patients with severe pneumonia who received vv-ECMO support between January 2017 and June 2023. A total of 151 patients were categorized into the mNGS group and the non-mNGS group, based on whether they underwent mNGS testing. Furthermore, they were stratified into the Death group and Survive group according to their survival status at day 30. Demographics, laboratory test results, pathogens, antibiotic treatment, and clinical outcomes data were recorded and analyzed. RESULTS: The positivity rate identified through the mNGS method (73.3%) was notably higher than that obtained through conventional culture (43.1%, P < 0.001). mNGS exhibited superior capabilities in identifying co-infections compared to conventional culture (70.9% vs. 30.1%, P < 0.001). Furthermore, the 30-day mortality rate within the mNGS group demonstrated a significant decrease compared to the no-mNGS group (P = 0.045). Additionally, Kaplan-Meier survival analysis yielded comparable outcomes in both groups (P = 0.035). Factors protecting against adverse outcomes encompassed prolonged hospital stay time, extended ECMO duration, lower Acute Physiology and Chronic Health Evaluation II (APACHE II) scores, successful ECMO weaning, and the application of mNGS. Antibiotic adjustments were implemented in 29 patients (58%) in the mNGS group and 39 patients (38.6%) in the no-mNGS group, with a markedly higher adjustment ratio in the former, demonstrating statistical significance (P = 0.024). Following adjustment of the treatment plan, the mNGS group demonstrated reduced APACHE II scores compared to the no-mNGS group after 5 days of treatment (P = 0.006). CONCLUSIONS: The mNGS technique, with its superior pathogen detection rate, emerges as a promising tool for microbiological diagnosis and antibiotic management, ultimately contributing to enhanced patient outcomes.}, } @article {pmid41935339, year = {2026}, author = {Castaldi, V and Wicaksono, WA and Criscuolo, MC and Gualtieri, L and Langella, E and Di Lelio, I and Monti, SM and De Filippis, F and Berg, G and Rao, R}, title = {Prosystemin-derived signals: bridging leaf microbiome dynamics and defense activation.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41935339}, issn = {2524-6372}, abstract = {BACKGROUND: Plant-derived peptides can act as resistance inducers and represent promising tools for sustainable crop protection. Despite growing interest and application, their broader effects on plant-associated microbiomes remain insufficiently characterized. Here, we investigated the impact of an immunomodulatory peptide derived from the tomato defense protein Prosystemin on the tomato phyllosphere microbiome and leaf volatilome.

RESULTS: The peptide was applied as a foliar spray at biweekly intervals from planting to two months post-germination to approximate common agricultural practices. Shotgun metagenomic sequencing combined with qPCR revealed abundant bacterial communities (up to 4.6 log10 bacterial 16S rRNA gene copies) dominated by Actino-, Alphaproteo- and Gammaproteobacteria across all samples. Peptide treatment was associated with a significant shift in community structure, characterized by reduced alpha diversity and increased microbial associations. Several genera, including Acinetobacter, Sphingobium, Sphingomonas, Brevundimonas, and Massilia, increased in relative abundance following treatment. Functional profiling indicated rearrangements in gene categories related to stress response and metabolic adaptation. Notably, volatilome analysis further revealed elevated monoterpene emissions in peptide treated plants, consistent with activation of defense-associated metabolism. Members of the Sphingomonadaceae family, particularly Sphingobium yanoikuyae, appear well suited to persist under peptide-associated conditions and may therefore contribute to the observed community restructuring, although causal mechanisms remain to be tested.

CONCLUSION: Beyond its established role in protecting tomato against pests and necrotrophic fungi, the Prosystemin-derived peptide provides an opportunity to investigate peptide-triggered plant responses and their interactions with the plant microbiota.}, } @article {pmid41935438, year = {2026}, author = {Bai, Y and Zhao, J and Wang, Z and Zheng, J and Zhu, X and Shao, Y and Zhang, X}, title = {A case of Rickettsia felis caused pneumonia and diagnosed by clinical analysis and Targeted Next-Generation Sequencing (tNGS) using Bronchoalveolar Lavage Fluid (BALF): A case report and literature review.}, journal = {Journal of infection and public health}, volume = {19}, number = {5}, pages = {103217}, doi = {10.1016/j.jiph.2026.103217}, pmid = {41935438}, issn = {1876-035X}, mesh = {Male ; Humans ; *Rickettsia felis/genetics/isolation & purification ; *Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Animals ; *Rickettsia Infections/diagnosis/drug therapy/microbiology/veterinary ; Anti-Bacterial Agents/therapeutic use ; Cats ; High-Throughput Nucleotide Sequencing ; Tomography, X-Ray Computed ; *Pneumonia, Bacterial/diagnosis/microbiology/drug therapy/veterinary ; }, abstract = {Feline rickettsia pneumonia is a rare lung disease caused by feline R. felis infection, which is mainly transmitted by feline fleas. A 57-year-old male patient was hospitalized with pain in the back of the sternum. Chest CT showed bilateral diffuse interstitial lung disease with multiple nodules. After the empirical anti-infection treatment was ineffective, the second-generation meta-genome sequencing (mNGS) of bronchoalveolar lavage (BALF) was diagnosed as feline rickettsia infection. In terms of treatment, inject tegacycline intravenously and then sequentially take minocycline. The patient's symptoms were relieved quickly, and the imaging improved significantly. This report summarizes the clinical and imaging characteristics and diagnosis and treatment experience of the case, aiming to provide reference for the early identification and treatment of such rare infections.}, } @article {pmid41935631, year = {2026}, author = {Keller, MI and de Zawadzki, A and Thiele, M and Suvitaival, T and Sulek, K and Kuhn, M and Schudoma, C and Podlesny, D and Nishijima, S and Fullam, A and Kim, CY and Niu, L and Wretlind, A and Hansen, JK and Israelsen, M and Johansen, S and Akanni, W and Hazenbrink, D and Juel, HB and Mann, M and Hansen, T and Krag, A and Bork, P and Legido-Quigley, C and , }, title = {Alcohol-related liver disease disrupts bile acid homeostasis and gut microbial bile acid metabolism.}, journal = {JHEP reports : innovation in hepatology}, volume = {8}, number = {7}, pages = {101848}, pmid = {41935631}, issn = {2589-5559}, abstract = {BACKGROUND & AIMS: Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-related deaths worldwide. Bile acids (BAs) regulate liver and gut function, but their homeostasis becomes disrupted in ALD. Gut microbes transform primary BAs to secondary BAs, which are reabsorbed via enterohepatic circulation, but BA metabolism during ALD progression remains poorly understood.

METHODS: We investigated BA homeostasis in a cross-sectional ALD cohort (n = 462), alongside matched healthy controls (n = 148), and validated key findings in two independent ALD cohorts (n = 34 and n = 52). We integrated BA concentrations, measured by targeted mass spectrometry in feces and plasma, with liver proteomics and gut microbiome profiles from metagenomic and metatranscriptomic sequencing.

RESULTS: Advanced fibrosis states were associated with decreased hepatic BA synthesis, impaired hepatic BA uptake from blood but with increased levels of primary and secondary BAs in plasma (inprimis, taurocholic acid: F = 69.9, p = 8.6e-66) and feces (inprimis, cholic acid: F = 5.5, p = 1.4e-4). The abundance of microbial secondary BA dehydroxylation and epimerization pathways in the gut microbiome community increased with disease severity. Genes encoding the oxidation arm in the multistep dehydroxylation pathway (including baiB) increased, whereas those in the reduction arm (baiN) were depleted. In patients with ALD, we suggest Eggerthella lenta, Mediterraneibacter torques, and Bacteroides thetaiotaomicron as relevant microbes for BA metabolism.

CONCLUSION: Fibrotic ALD is characterized by disrupted primary BA synthesis and hepatic uptake, leading to hepatotoxic BA accumulation in the gut and blood circulation. Altered microbial secondary BA metabolism reflects a functional shift in the gut microbiome throughout the fibrosis stages. Our findings highlight the gut-liver axis as an important factor influencing ALD progression, even in early, asymptomatic fibrosis stages.

IMPACT AND IMPLICATIONS: This study shows that integrating different omics approaches provides insight into metabolic disruptions across the gut-liver axis that drive ALD progression. Additionally, our study identifies specific bacterial species influencing BA concentrations in ALD using data from human fecal metagenomics and metatranscriptomics. These findings could inform the design of future therapeutic targets focusing on either the liver or the gut for treating ALD.}, } @article {pmid41935814, year = {2026}, author = {Sambucci, KM and Samaš, P and Ssebide, B and Petrželková, KJ and Okello, RO and Nizeyimana, F and Bukamba, N and Smiley-Evans, T and Gilardi, K and Pafčo, B and Červená, B}, title = {Shifts in strongylid communities associated with chronic wasting in mountain gorillas.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {104848}, doi = {10.1016/j.ijpara.2026.104848}, pmid = {41935814}, issn = {1879-0135}, abstract = {Host-parasite relationships are typically maintained in a dynamic equilibrium, but disruptions to this balance can lead to clinical disease and population-level health impacts. Chronic wasting, characterized by chronic loss of body condition, alopecia, a browning hair coat and pot belly, is an emerging health concern in mountain gorillas of Bwindi Impenetrable National Park, Uganda. Deworming of suspected cases has led to marked short-term health improvements, implicating intestinal helminths. To investigate, we analysed faecal samples from human-habituated gorillas collected in 2018 and 2021, and unhabituated gorillas in 2018, using high-throughput sequencing of strongylid nematodes (ITS-2) and gut bacteria (16S). Strongylid community composition varied with chronic wasting occurrence, with Oesophagostomum emerging as a key taxon driving this difference, while bacterial communities remained relatively stable. Strongylid diversity increased between 2018 and 2021, and habituated gorillas exhibited reduced strongylid genetic diversity, higher relative abundance of Oesophagostomum and lower relative abundance of Murshidia compared to unhabituated gorillas. These results suggest that a higher abundance of Oesophagostomum is associated with chronic wasting in mountain gorillas due to either a causative association or other genetic, immunological or environmental causes allowing Oesophagostomum, a common member of the gut eukaryote community of the Bwindi gorillas, to overpopulate.}, } @article {pmid41935918, year = {2026}, author = {Lazarevic, V and Ruppé, E and Schrenzel, J}, title = {10th International Conference on Clinical Metagenomics (ICCMg10): meeting report.}, journal = {Trends in microbiology}, volume = {34}, number = {5}, pages = {449-453}, doi = {10.1016/j.tim.2026.03.008}, pmid = {41935918}, issn = {1878-4380}, mesh = {*Metagenomics/methods ; Humans ; Computational Biology/methods ; }, abstract = {The 10th International Conference on Clinical Metagenomics (ICCMg10) brought together clinicians, microbiologists, bioinformaticians, and industry partners to review progress and challenges in translating metagenomics into routine clinical practice. Discussions focused on advances in sequencing technologies, automation, clinically oriented workflows, and computational and reporting strategies. Clinical sessions addressed diagnostic implementation across infectious syndromes, including respiratory, prosthetic joint, bloodstream, and deep-seated infections, with attention to cell-free DNA assays, long-read sequencing, and antimicrobial resistance detection. Broader applications of metagenomics, spanning microbiota research and environmental systems, reflected the expanding scope of the field. Overall, ICCMg10 underscored the importance of multidisciplinary collaboration, harmonized practices, and clinically meaningful interpretation to support the broader implementation of clinical metagenomics.}, } @article {pmid41936200, year = {2026}, author = {Uematsu, S}, title = {Programming systemic and mucosal immunity through co-adjuvant-based prime-boost vaccination.}, journal = {Current opinion in virology}, volume = {76}, number = {}, pages = {101525}, doi = {10.1016/j.coviro.2026.101525}, pmid = {41936200}, issn = {1879-6265}, abstract = {The development of effective mucosal vaccines has been limited by the limited availability of mucosal adjuvant approaches with established clinical track records and an incomplete understanding of how systemic and mucosal immunity are coordinated. Recent studies indicate that the priming phase of vaccination plays a decisive role in programming the quality, durability, and anatomical distribution of subsequent immune responses. This review discusses emerging evidence that co-adjuvant-based priming strategies can establish long-lasting immune programs that enable adjuvant-free mucosal boosting. Focusing on the combination of CpG DNA and curdlan as a prototypical example, this review highlights how coordinated activation of innate immune receptors during priming imprints dendritic cells, B cells, and T cells to support robust mucosal IgA and tissue-resident immunity. This review further discusses translational advances demonstrating that this immune programming paradigm can be maintained using translationally oriented formulations designed with clinical development in mind and validated in non-human primates. Independent studies using mRNA and protein-based vaccines support the general principle that the quality of priming, rather than the boosting modality, determines successful mucosal immunity. Together, these findings redefine vaccine adjuvants as tools for immune programming and provide a conceptual framework for next-generation vaccine design.}, } @article {pmid41936930, year = {2026}, author = {Zhou, Z and Song, Y and Zhou, Y}, title = {Metagenomic next-generation sequencing profiling of primary versus iatrogenic osteoarticular infections: Unveiling distinct pathogen spectra and diagnostic implications.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {168}, number = {}, pages = {108688}, doi = {10.1016/j.ijid.2026.108688}, pmid = {41936930}, issn = {1878-3511}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Male ; Iatrogenic Disease ; Retrospective Studies ; Middle Aged ; Aged ; Staphylococcus aureus/genetics/isolation & purification ; Osteomyelitis/microbiology/diagnosis ; *Bacteria/genetics/isolation & purification/classification ; Aged, 80 and over ; Coinfection/microbiology/diagnosis ; Osteoarthritis/microbiology/diagnosis ; Staphylococcal Infections/diagnosis/microbiology ; }, abstract = {OBJECTIVE: To evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) versus microbial culture in primary osteoarticular infection (POI) and iatrogenic osteoarticular infection (IOI), and to analyze pathogen spectrum differences and clinical implications.

METHODS: Ninety-two patients with confirmed osteoarticular infection (POI, n = 42; IOI, n = 50) were retrospectively analyzed. All specimens were tested using both mNGS and conventional culture. The pathogen detection rates, pathogen spectrum composition, detection of mixed infections, and concordance of results between the two methods were compared.

RESULTS: mNGS demonstrated a significantly higher overall detection rate than culture (72.83% vs 43.48%; P < 0.001), particularly in IOI (78.00% vs 34.00%; P < 0.001). Pathogen profiling showed predominance of Staphylococcus aureus in POI, whereas IOI exhibited greater microbial diversity with increased detection of Staphylococcus epidermidis (31.03%) and anaerobes (13.79%). Polymicrobial infections were more frequently identified by mNGS (14.13% vs 4.35% by culture; P = 0.024), primarily in the IOI group. Concordance between mNGS and culture was substantial in POI (κ = 0.66; 95% CI: 0.42-0.89) but only slight in IOI (κ = 0.12; 95% CI: -0.12 to 0.35), largely attributable to the high rate of mNGS-exclusive positives in IOI (48.00%).

CONCLUSION: mNGS improves pathogen detection in osteoarticular infections, especially in IOI where it identifies complex and polymicrobial infections more effectively than culture, providing critical support for guiding antimicrobial therapy.}, } @article {pmid41936935, year = {2026}, author = {Wang, J and Bi, Y and Fu, Z and Qiao, H and Liu, F}, title = {Harvesting reed (Phragmites australis) for wetland nitrogen removal: Productivity, microbial communities, and underlying mechanisms.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134553}, doi = {10.1016/j.biortech.2026.134553}, pmid = {41936935}, issn = {1873-2976}, mesh = {*Wetlands ; *Nitrogen/isolation & purification/metabolism ; *Poaceae/growth & development/metabolism ; Biomass ; Biodegradation, Environmental ; Bacteria/metabolism ; Nitrates ; }, abstract = {Non-point source nitrogen (N) pollution is a primary driver of aquatic eutrophication. While reed (Phragmites australis) wetlands effectively intercept N, the optimal harvesting strategy for maximizing N removal while maintaining ecosystem function remains unclear. This study investigated the effects of different harvesting frequencies on N removal, plant productivity, and associated microbial mechanisms in wetland microcosms over a three-year period. Four treatments were evaluated: unplanted control (CK), planted with no harvest (T0), annual harvest (T1), and biennial harvest (T2). Results demonstrated that all planted treatments significantly enhanced N removal compared to CK. Although not statistically significant among planted groups, T1 consistently achieved the highest average removal efficiencies for total nitrogen, ammonium-nitrogen, and nitrate-nitrogen. Furthermore, T1 produced the greatest aboveground biomass, facilitating the largest export of N and other nutrients. Metagenomic analysis revealed that reed planting shifted the microbial community, suppressing Cyanobacteria (e.g., Stanieria) and Nitrospirota (e.g., Nitrospira F), while enriching Proteobacteria and Chloroflexota. These compositional changes were coupled with a functional shift that key dissimilatory pathways (denitrification and dissimilatory nitrate reduction) were upregulated, while assimilatory nitrate reduction was suppressed. Additionally, annual harvesting fostered a more complex and stable microbial co-occurrence network. Structural equation modeling indicated that harvesting enhanced N removal primarily through plant-microbe interactions, with increased plant N accumulation promoting microbial N-functional gene abundance, and ultimately driving N removal. Overall, annual harvesting optimally coupled high biomass production with microbial N removal, presenting a sustainable management strategy for wetlands that balances water purification with resource recovery.}, } @article {pmid41936957, year = {2026}, author = {Ghaly, TM and Shah, BS and Coleman, NV and Elbourne, LDH and Le Roux, JJ and Gillings, MR and Paulsen, IT and Tetu, SG}, title = {Agriculture alters protein evolution of respiratory nitrate reductase in soil bacteria at a global scale.}, journal = {Environmental research}, volume = {300}, number = {}, pages = {124428}, doi = {10.1016/j.envres.2026.124428}, pmid = {41936957}, issn = {1096-0953}, mesh = {Soil Microbiology ; *Nitrate Reductase/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism ; Agriculture ; Evolution, Molecular ; }, abstract = {Humans are a major evolutionary force, yet our impacts on the evolution of Earth's microbiomes and their biogeochemical processes remain poorly understood. Notably, the overlooked potential for the intensive use of agricultural fertiliser to drive evolutionary changes in soil nutrient cycling genes warrants urgent attention. Here, analysing >2500 soil metagenomes from across the globe, we identify increased rates of diversifying positive selection on genes involved in the reduction of nitrate (a key component of nitrogen fertilisers) in agricultural, but not natural land systems. Altered selection on genes encoding the respiratory nitrate reductase (Nar) were specific to Burkholderiales, a major group of denitrifying bacteria. Nar protein regions under positive selection flanked the enzyme's substrate channel, favouring smaller amino acids, likely resulting in the widening of the channel entrance. We present a novel hypothesis that this channel widening could increase rates of substrate turnover, which we propose would be evolutionarily advantageous under excess nitrate availability, ultimately enhancing growth rates despite potential enzymatic trade-offs. As Burkholderiales are dominant nitrate reducers globally, such evolutionary consequences of agriculture on this lineage could have cascading environmental impacts, including increased nitrous oxide emissions. These findings indicate that anthropogenic selection might be altering protein-level evolution of vital microbial biogeochemical processes.}, } @article {pmid41937023, year = {2026}, author = {Field, CM and Keller, PM and Schultheiss, E and Gewitsch, B and Wiemer, DF and Schawaller, M and Halfter, M and Frickmann, H}, title = {Potential impact of antimalarial chemoprophylaxis with doxycycline on antimicrobial resistance genes in the enteric microbiome of deployed German soldiers - a case-control-study.}, journal = {Travel medicine and infectious disease}, volume = {71}, number = {}, pages = {102978}, doi = {10.1016/j.tmaid.2026.102978}, pmid = {41937023}, issn = {1873-0442}, mesh = {*Doxycycline/therapeutic use/pharmacology ; Humans ; *Military Personnel ; *Antimalarials/therapeutic use ; Case-Control Studies ; Male ; Germany ; *Gastrointestinal Microbiome/drug effects/genetics ; Adult ; Anti-Bacterial Agents ; *Drug Resistance, Bacterial/genetics ; Young Adult ; Feces/microbiology ; Female ; Malaria/prevention & control ; *Drug Resistance, Microbial/genetics ; Metagenomics ; }, abstract = {BACKGROUND: Antimalarial chemoprophylaxis with doxycycline is taken by German soldiers on tropical deployments. In a case-control-assessment, diagnostic metagenomics was applied to comparatively assess antimicrobial resistance genes in enteric microbiomes of soldiers with and without medical history of doxycycline-based antimalarial chemoprophylaxis on deployment.

METHODS: Two groups of 26 military deployment returnees, each either exposed or non-exposed to antimalarial chemoprophylaxis with doxycycline, were matched by deployment site and period, age and sex in declining order of prioritization. Metagenomic analysis of stool samples was applied to detect resistance gene sequences within the sample materials.

RESULTS: In total, 3770 different antibiotic resistance genes were detected across all samples. No significant differences were found in the frequency of antibiotic resistance genes in each sample compared between the doxycycline group and the control group. Approximately one third of metagenomically assembled genomes could be identified taxonomically at the species level (32.2%) and over half at the genus level (53.9%). The overall distribution of ABR genes at the species level showed that Escherichia coli was host for over a quarter of detected genes - 1021 genes in only 42 identified genomes. Hosts with the next highest number of ABR genes were Escherichia marmotae (156 genes), Staphylococcus aureus (85 genes), Klebsiella michiganensis (63 genes) and Leclercia adecarboxylata (62 genes).

CONCLUSIONS: The study suggests - if any - only a low impact of doxycycline intake during military deployments on the enteric resistome of soldiers at post-deployment assessments. Reasons for Escherichia's high ABR gene load remain to be investigated.}, } @article {pmid41937144, year = {2026}, author = {Bočaj, V and Pongrac, P and Likar, M}, title = {Microbial functional traits in the hyperaccumulating Noccaea praecox rhizobiome are metal-dependent and host-driven.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41937144}, issn = {2524-6372}, support = {P1-0212//The Slovenian Research and Innovation Agency/ ; }, abstract = {BACKGROUND: Noccaea praecox is a zinc (Zn), cadmium (Cd), and lead (Pb) hyperaccumulating plant native to the Italian peninsula and Western Balkans, where it occurs naturally in both metalliferous and non-metalliferous soils. In the present study, we investigated the effects of soil metal concentrations and the plant host on microbial functional traits, specifically the resistome (i.e., microbial functions associated with metal tolerance and resistance) in two soil compartments: the roots and rhizosphere of N. praecox. For this, we collected four plants from each metalliferous and non-metalliferous site and used a metagenomic sequencing approach to characterise microbial functions from paired root and rhizosphere samples, with three root samples per site obtained due to limited biomass, and four rhizosphere samples.

RESULTS: The compartment was the primary driver of the general microbial functional structure. By contrast, the soil metal concentrations and root compartment significantly shaped the microbial resistome. Functions associated with the cobalt-zinc-cadmium efflux system and copper-transporting P-type ATPase V were significantly enriched at the metalliferous compared to the non-metalliferous site, with log2 fold change being 2.62 and 1.72, respectively. Transporters associated with manganese/iron and cobalt/nickel were shaped by the host, regardless of soil metal levels, consistent with host-mediated filtering of microbial functions. Notably, several Zn transporter-related microbial functions associated with the ZIP family were more abundant in the rhizosphere, potentially supporting the plant's high Zn demand.

CONCLUSION: Overall, our results demonstrate that both environmental conditions and plant host play interactive roles in shaping the microbial functional potential, with the host sometimes exerting a stronger influence than soil metal content. The enrichment of Zn transporters (Zrt-/Irt-like proteins) in the rhizosphere of the Zn-hyperaccumulating N. praecox suggests a specific microbial adaptation that may facilitate Zn uptake. These findings provide new insight into the functional dynamics of plant-microbe interactions that support the N. praecox lifestyle.}, } @article {pmid41937169, year = {2026}, author = {Mullin, CE and Louca, S}, title = {Effects of heat-assisted sample desiccation on microbiome surveys.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41937169}, issn = {2524-6372}, abstract = {Sample preservation remains a challenge in microbiome surveys, particularly in remote areas. Drying samples eliminates the need for cold chains and preservatives, but sophisticated desiccation tools such as lyophilization are impractical in the field. Further, the effects of sample drying on modern analyses, such as gene-centric metagenomics and metagenome-assembled genome (MAG) recovery, remain poorly understood. Here we explore heat-assisted sample desiccation followed by storage at room temperature as a cost-effective and practical solution in the field. We assess its effects relative to freezing on typical metagenomic and 16 S rRNA amplicon sequence analyses of bacterial and archaeal communities, using 60 samples from 6 different source materials (soils from 3 locations, feces from 3 animals). We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG recovery, as well as impacts on inferred microbial community composition. We find that, while desiccation had a significant negative impact on multiple metrics related to DNA extraction success, its impacts on downstream metrics such as OTU richness, Shannon diversity, gene annotation and MAG recovery were more nuanced and often insignificant. Further, while the preservation method had a significant influence on the inferred microbial community composition, samples from different source materials (e.g., soils from different locations, or feces from different individuals) remained clearly distinguishable. We conclude that heat-assisted desiccation can be a viable sample preservation method for microbiome studies, when a high consistency with frozen samples is not a requirement.}, } @article {pmid41937465, year = {2026}, author = {Do, TT and Le, VV and Nguyen, LTT and Nguyen, TTK and Vu, NTH and Trinh, HN and Lee, SA and Ngo, CC and Phi, QT}, title = {Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2508050}, pmid = {41937465}, issn = {1738-8872}, mesh = {*Petroleum/metabolism/microbiology ; Biodegradation, Environmental ; Soil Microbiology ; *Salinity ; *Bacteria/genetics/metabolism/classification/isolation & purification/growth & development ; *Metagenomics ; Soil Pollutants/metabolism ; Hydrocarbons/metabolism ; Culture Media/chemistry ; Phylogeny ; Metagenome ; Metabolic Networks and Pathways ; }, abstract = {Soil salinization and crude oil contamination are critical global threats to ecosystems, agriculture, and human health. Bioremediation is widely recognized as a cost-effective and eco-friendly strategy for removing petroleum pollutants from soil. In this study, we investigated salinity-driven bacterial community dynamics collected from crude oil-contaminated soil in Cam Ranh Bay, Khanh Hoa, over a 21-day enrichment cultivation, using shotgun metagenomic and culture-based approaches. The enrichment cultivation was performed in Bushnell-Haas mineral salts (BHMS) medium supplemented with 5% (v/v) crude oil-diesel mixture (5:95) and 1.5% NaCl. Shotgun metagenomic analysis revealed that after 21 days of enrichment, the relative abundance of crude oil-degrading genera increased markedly in the enriched samples compared to the native samples-for example, Pseudomonas rose from 0.44% to 3.51%, Gordonia from 0.03% to 78.68%, and Achromobacter from 0.03% to 3.77%. Functional analysis further identified metabolic pathways, including hydrocarbon degradation, osmoprotection, and heavy metal detoxification. In addition, 36 representative bacterial strains were isolated from the enriched cultures, predominantly belonging to the genera Pseudomonas, Bacillus, Stenotrophomonas, and Achromobacter. All isolates were able to degrade crude oil under salinity stress conditions of up to 4%. Notably, Rhodococcus sp. KH5 and Gordonia sp. KH53 maintained consistently high degradation efficiencies across 0-4% salinity, ranging from 17.67-35.00% and 28.67-36%, respectively. Overall, our findings demonstrate that saline enrichment shifts the bacterial community toward halotolerant hydrocarbon and crude oil degraders.}, } @article {pmid41937665, year = {2026}, author = {Sizikova, TE and Lebedev, VN and Borisevich, SV}, title = {The Mengla virus (Filoviridae: Dianlovirus).}, journal = {Voprosy virusologii}, volume = {71}, number = {1}, pages = {7-12}, doi = {10.36233/0507-4088-356}, pmid = {41937665}, issn = {2411-2097}, mesh = {Animals ; *Chiroptera/virology ; *Filoviridae/genetics/classification/pathogenicity/isolation & purification ; *Filoviridae Infections/virology/epidemiology/genetics ; *Genome, Viral ; Phylogeny ; Humans ; Genetic Variation ; Asia, Southeastern/epidemiology ; }, abstract = {INTRODUCTION: Filoviruses associated with various species of pteropodid bats (Chiroptera: Pteropodidae) are traditionally regarded as potential causative agents of hemorrhagic fevers with epidemic potential. The known agents of Ebola and Marburg fevers periodically cause sporadic cases and epidemic outbreaks in African countries. Recent discoveries of novel filoviruses associated with pteropodid bats in South and Southeast Asia highlight the necessity to investigate their genetic diversity and pathogenic potential. The aim of this study was to investigate the genetic diversity and pathogenic potential of new filoviruses associated with bats, based on literature data.

MATERIALS AND METHODS: This review is based on an analysis of published literature describing the detection and molecular characterization of novel filoviruses identified in different geographic regions, with a particular focus on filoviruses associated with pteropodid bats in South and Southeast Asia. The analyzed studies include data on virus discovery, genome organization, taxonomic classification, and experimental assessment of biological properties.

RESULTS: Several novel filoviruses have been identified by metagenomic RNA sequencing of tissues from pteropodid bats captured in South and Southeast Asia. Among them, Mengla virus was detected in tissues of pteropodid bats (Rousettus spp.) captured in Mengla County, Yunnan Province, People's Republic of China. Owing to a high level of genetic divergence, Mengla virus was classified as a representative of a new genus, Dianlovirus, within the family Filoviridae. Although a live isolate of Mengla virus has not yet been obtained, experimental studies using chimeric minigenome systems and virus-like particles suggest that the virus may exhibit tropism for tissues of various vertebrate hosts, including humans.

CONCLUSION: Members of the family Filoviridae are widely distributed within the geographic range of their natural reservoir-pteropodid bats-across South and Southeast Asia, including viruses evolutionarily related to Ebola and Marburg viruses. Although human disease caused by Mengla virus and other recently discovered filoviruses has not been documented, the potential for cross-species transmission and the emergence of novel filovirus infections in endemic regions remains.}, } @article {pmid41937718, year = {2026}, author = {Chen, X and Xie, M and Feng, J and Zou, J and Shi, J and Xie, X}, title = {From Diet to Resistome: Habitat Fragmentation Rewires Gut Microbiomes To Elevate Antibiotic Resistance Gene Enrichment in a Horseshoe Crab Sentinel.}, journal = {Environmental science & technology}, volume = {60}, number = {19}, pages = {14120-14136}, doi = {10.1021/acs.est.5c17817}, pmid = {41937718}, issn = {1520-5851}, mesh = {Animals ; Ecosystem ; *Gastrointestinal Microbiome ; *Horseshoe Crabs/microbiology ; *Drug Resistance, Microbial/genetics ; Diet ; }, abstract = {Habitat fragmentation may amplify antibiotic resistance genes (ARGs), yet the ecological pathways linking landscape patterns to host resistomes in intertidal systems remain unclear. Macrobenthic organisms as potential reservoirs and dispersal nodes are ideal models. Focusing on the horseshoe crab (Tachypleus tridentatus), a food web hub and habitat indicator, we integrated landscape metrics, metagenomics, and path modeling (PLS-PM) to examine, across fragmented habitats, links among sediment physicochemistry, larval diet, gut microbiota, mobile genetic elements (MGEs), and ARGs. Results revealed that more fragmented habitats promoted individuals with higher ARG abundance and diversity, alongside stronger MGE enrichment and increased ARG-MGE co-occurrence, indicating enhanced mobility potential. Fragmentation also coincided with greater dietary diversity but higher among-individual convergence, selective assembly of gut microbiota with higher diversity, and tight ARG-MGE association. PLS-PM supported a diet-gut microbiota-MGE-ARG cascade, while the direct effects of sediment chemistry were not significant. Attributing ARG hosts at the MAG level, Enterobacteriaceae and Vibrionaceae dominated ARG abundance and enrichment, indicating lineage selectivity. Multidrug and polymyxin resistance was most prominent. These findings identify key AMR risk pathways and inform priority interventions for T. tridentatus and habitat conservation. The developed assessment framework is scalable and offers a paradigm for One Health management in mudflat systems.}, } @article {pmid41937905, year = {2026}, author = {Cheng, Y and Peng, L and Liu, D and Zhong, L and Liu, Y and Yang, T}, title = {Case Report: A rare culprit of severe pulmonary infection in children: prevotella.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1782202}, pmid = {41937905}, issn = {2296-2360}, abstract = {BACKGROUND: To characterize the clinical features, diagnostic pitfalls, and treatment of severe pediatric pulmonary infection caused by Prevotella species.

METHODS: We retrospectively reviewed clinical data, the diagnostic workflow, antimicrobial regimens, and outcomes of two children with severe Prevotella pulmonary infection.

RESULTS: Case 1 was an 11-year-old boy with necrotizing pneumonia, and Case 2 was a 13-year-old boy with retained foreign-body aspiration. Both patients responded poorly to initial cephalosporin-based therapy. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BAL) fluid identified Prevotella nanceiensis (sequence count 299,022; relative abundance 92.24%) and Prevotella oralis (210,449; 67.98%) within 24 h, whereas anaerobic culture (Case 1) became positive after 4 days. Based on mNGS results antibiotics were adjusted to metronidazole plus a carbapenem (meropenem for Case 1; imipenem-cilastatin for Case 2), and both children received adjunctive pulmonary rehabilitation before discharge. They subsequently recovered and were discharged.

CONCLUSION: Severe Prevotella pulmonary infection in children has non-specific manifestations and may respond poorly to conventional beta-lactam therapy, leading to delayed diagnosis. mNGS enables rapid pathogen identification and supports targeted anti-anaerobic treatment. For severe or complicated cases refractory to empirical therapy, metronidazole combined with a carbapenem may be an effective option.}, } @article {pmid41937991, year = {2026}, author = {Halphen, J and Ahmadzade, M and Mankidy, B and Berenji, A and Ghasemi-Rad, M}, title = {Letter to the Editor: Evidence for a two-step species-level pulmonary nocardiosis diagnostic approach.}, journal = {World journal of radiology}, volume = {18}, number = {3}, pages = {118126}, pmid = {41937991}, issn = {1949-8470}, abstract = {Pulmonary nocardiosis, a rare and diagnostically challenging infection, usually presents with heterogeneous radiographic findings, compounded by the low sensitivity of traditional confirmatory cultures. In their most recent work, Wang et al analyzed 102 patients with pulmonary nocardiosis to address these concerns, investigating species-characteristic imaging patterns, pathological associations, and the role of metagenomic next-generation sequencing (mNGS) in the diagnostic approach. High-resolution computed tomography (CT) in adult patients with pulmonary infections caused by Nocardia wallacei was demonstrated to have a sensitive (85.71%) and specific (83.34%) presentation of bronchopneumonia in relation to the five Nocardia species in the sample with CT data. The authors also compared traditional cultures to mNGS, finding that traditional cultures and mNGS were concordantly positive in only 3.3% of cases. This letter supports a combined radiologic and molecular diagnostic approach, enabling earlier and more accurate species identification in pulmonary nocardiosis, thereby informing treatment decisions, and enhancing epidemiologic understanding.}, } @article {pmid41938562, year = {2026}, author = {Ye, B and Liu, R and Li, R and Roduan, MRM and Noor, WSAWM and Sairi, F}, title = {Comparative gut microbiome composition and predicted microbial functions in captive and free-range yaks (Bos grunniens).}, journal = {Veterinary world}, volume = {19}, number = {2}, pages = {864-876}, pmid = {41938562}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: The gut microbiota is essential for nutrient digestion, immune function, and environmental adaptation in ruminants, particularly high-altitude species like yaks (Bos grunniens). Different husbandry practices (captive vs. free-range) can potentially alter the microbial communities and affect the yak health. However, comparative data on how these systems affect yak gut microbiomes remain limited, with most studies focusing on taxonomy rather than functional implications. This study aimed to compare gut microbiome composition, diversity, and predicted functional profiles between captive (CY) and free-range (FY) yaks using a 16S rRNA gene metabarcoding approach.

MATERIALS AND METHODS: Fecal samples were collected from healthy ~2-year-old yaks (n=5 CY, n=5 FY) in Litang County, Ganzi Prefecture, Sichuan, China, during summer. DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced on Illumina NovaSeq 6000. Bioinformatic analyses included quality filtering, Operational taxonomic units (OTU) clustering (97% similarity), taxonomic annotation (SILVA database), α- and β-diversity analysis. The microbial function was predicted using PICRUSt2 (KEGG pathways), BugBase (community phenotypes), and FAPROTAX (ecological functions). Statistical comparisan used Welch's t-tests, Wilcoxon rank-sum tests, principal coordinates analysis (PCoA), and Analysis of similarities (ANOSIM) with significance set at p < 0.05.

RESULTS: α-Diversity indices (e.g., Shannon p = 0.5476) showed no significant differences between CY and FY. However, β-diversity revealed distinct community structures (PCoA: PC1 30.52%, PC2 12.25%; ANOSIM R = 0.976, p = 0.007), with FY samples more homogeneous. At the genus level, CY were enriched in Ruminococcaceae bacterium UCG-005, Streptococcus, Escherichia-Shigella, Treponema, Christensenellaceae R-7, and Clostridium sensu stricto 1 (many fermentative or potentially opportunistic). FY showed higher abundances of Bacillus, Arthrobacter, Rhodococcus, Candidatus Saccharimonas, Prevotellaceae UCG-001, and Paenibacillus. Predicted functions indicated FY had greater capacities for carbohydrate/amino acid metabolism, DNA repair, fatty acid biosynthesis, and vitamin B pathways, while CY favored fermentation and reductive acetogenesis. BugBase highlighted higher anaerobic phenotypes in CY.

CONCLUSION: Husbandry practices profoundly influence yak gut microbiome structure and inferred metabolic potential, with free-range systems promoting, homogeneous communities suited to natural high-fiber diets while captive systems promotes fermentative and opportunistic shifts. These microbiome differences suggest opportunities for probiotic interventions to enhance yak health, productivity, and sustainability in high-altitude pastoral systems. Future metagenomic and metabolomic validation is needed.}, } @article {pmid41938867, year = {2026}, author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R}, title = {Discovery of a novel orthototivirus-like virus in patients with vulvovaginal candidiasis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779554}, pmid = {41938867}, issn = {2235-2988}, mesh = {Humans ; Female ; Phylogeny ; Genome, Viral ; *Candidiasis, Vulvovaginal/virology/microbiology ; Vagina/virology ; Sequence Analysis, DNA ; RNA-Dependent RNA Polymerase/genetics ; Capsid Proteins/genetics ; RNA, Viral/genetics ; Metagenomics ; *Double Stranded RNA Viruses/isolation & purification/genetics/classification ; }, abstract = {INTRODUCTION: Vulvovaginal candidiasis (VVC) is a common fungal infection affecting women worldwide. Although the vaginal microbiome has been extensively studied, the diversity of viruses present in the vaginal microenvironment remains poorly characterized.

METHODS: Vaginal swab samples from patients diagnosed with VVC were subjected to viral metagenomic sequencing using an Illumina NovaSeq platform. Viral contigs were assembled, annotated, and screened against public databases. Genome organization, pairwise sequence identity, and phylogenetic relationships were analyzed to determine the evolutionary position of the detected virus.

RESULTS: Here, we identified a novel double-stranded RNA virus, tentatively named Vaginal-associated orthototivirus-like 1 (VAOTV-1), in vaginal swab samples from patients with vulvovaginal candidiasis. VAOTV-1 was represented by a partial genome sequence of 4,332 bp, encoding a complete RNA-dependent RNA polymerase (RdRp; 729 amino acids) and a partial capsid protein (CP; 532 amino acids). The encoded RdRp protein shared a maximum amino acid sequence identity of 47.43% with Totiviridae sp. isolate 22AP502 (GenBank accession no. XTJ93729.1), reported from Bandicota indica. In contrast, the CP showed no significant similarity to any sequences currently available in public databases, and BLASTn searches against the NCBI nucleotide database did not yield any significant matches. Phylogenetic analysis, together with the relatively low amino acid sequence identity to known members of the genus Totivirus within the family Orthototiviridae, suggests that VAOTV-1 represents a distinct and highly divergent orthototivirus-like lineage.

DISCUSSION: These findings indicate that VAOTV-1 represents a highly divergent orthototivirus-like virus and expands the known diversity of totiviruses detected in human-associated mucosal environments. This discovery highlights previously unrecognized viral diversity in the vaginal virome and provides new insights into viruses associated with vulvovaginal candidiasis.}, } @article {pmid41939082, year = {2026}, author = {Turner, ML and Nguyen, MT and Kung, Y and Doan, T and Seitzman, GD}, title = {Rhizopus angle abscess, scleritis and endophthalmitis following Kahook Dual Blade goniotomy and phacoemulsification.}, journal = {American journal of ophthalmology case reports}, volume = {42}, number = {}, pages = {102572}, pmid = {41939082}, issn = {2451-9936}, abstract = {PURPOSE: To describe a rare case of Rhizopus angle abscess progressing to scleritis and endophthalmitis after routine cataract surgery with Kahook Dual Blade (KDB) goniotomy in an immunocompetent patient.

OBSERVATION: A 79-year-old male developed hyphema and anterior chamber fibrin three days after uncomplicated phacoemulsification with KDB. Despite intravitreal vancomycin and ceftazidime, inflammation worsened, and by postoperative day nine vision was count fingers with intraocular pressure of 29 mmHg. Slit-lamp exam showed an inferonasal corneal infiltrate with a purulent angle abscess at the goniotomy site and dense vitritis. Intravitreal and oral voriconazole were started for presumed fungal infection. Standard cultures and PCR were negative, but metagenomic RNA deep sequencing of aqueous fluid detected Rhizopus stolonifer. After two months of systemic and intravitreal voriconazole, the infection resolved and visual acuity improved to 20/70, leaving localized limbal thinning.

CONCLUSION AND IMPORTANCE: This case illustrates that Rhizopus angle abscess can occur in an immunocompetent host following anterior segment surgery and may masquerade as bacterial endophthalmitis. Early suspicion of fungal infection and use of metagenomic deep sequencing were critical for diagnosis and successful treatment, emphasizing the need to consider invasive fungal pathogens and advanced molecular diagnostics in culture-negative postoperative ocular infections.}, } @article {pmid41939697, year = {2026}, author = {Bagul, SY and S, S and Saran, PL and Khadke, GN and Das, M}, title = {Deciphering genotype and geography dependent microbiome composition and its role in disease suppression in Ashwagandha.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786817}, pmid = {41939697}, issn = {1664-302X}, abstract = {Ashwagandha, Withania somnifera (L.) Dunal is a perennial evergreen shrub widely used to treat mental health disorders and physical debility, and to enhance overall physiological function. Variations in genotype and geographic origin significantly influence rhizospheric microbial communities by altering soil physicochemical properties. This study applied shotgun metagenomic sequencing to investigate microbial community shifts in the rhizosphere of Nagori Ashwagandha (RN) from Rajasthan, Vallabh Ashwagandha-1 (GV) from Gujarat, and Nagori Ashwagandha from Rajasthan cultivated in Gujarat (GN). Fusarium wilt incidence was 67%, affecting the roots, which represent the most economically important part of ashwagandha. Taxonomic analysis identified Actinomycetota (46-60%) and Pseudomonadota (35-42%) as the predominant phyla, with Nocardioides (3.1-8.8%), Streptomyces (4.5-6.5%), and Bradyrhizobium (1-1.6%) as dominant genera across all groups in metagenomic analysis. Alpha-diversity analysis revealed higher species richness and Simpson's index in the GV group compared to the GN and RN groups. Beta-diversity assessment using Bray-Curtis distances showed partial clustering of GN and RN relative to GV in principal coordinate analysis and hierarchical dendrograms. Functional profiling based on KEGG annotation indicated that core metabolic and cellular pathways predominated across all genotypes, with no significant differences in Tier 1 and Tier 2 functional categories. To our knowledge, this represents the first shotgun metagenomic analysis of ashwagandha. Culturomics analysis yielded seventeen isolates from two rhizospheric locations; among these, Bacillus subtilis DMA1 exhibited the highest mycelial inhibition against Fusarium solani (64%), with a germination rate of 98%, root length of 2.1 cm, shoot length of 1.3 cm, seed vigor index of 333.2, and maximum fresh biomass of 1.12 g. Co-inoculation with F. solani and Bacillus subtilis DMA1 in pot trials significantly increased root length (20.1 cm), shoot length (39.5 cm), root girth (14.9 mm), and total biomass (51.1 g) compared to control and Fusarium-only treatments. These findings indicate that Bacillus subtilis DMA1 reduced wilt incidence by 70% and enhanced plant growth under pathogen-stress conditions.}, } @article {pmid41939705, year = {2026}, author = {Rey-Mariño, A and Ruiz-Ruiz, S and Jiménez-Hernández, N and Pons, X and Artacho, A and Codoñer-Franch, P and Francino, MP}, title = {Patterns of gut microbiome composition, function and dynamics in toddlers, adolescents and adults over a three-year period.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1768977}, pmid = {41939705}, issn = {1664-302X}, abstract = {Despite their relevance, studies of the long-term stability of the gut microbiome are rare due to the difficulty in following the same individual through long periods of time, particularly during childhood and adolescence. Here, we have been able to analyze microbiome stability throughout a 3-year period in toddlers, adolescents, and adults of the same population, at the levels of taxonomic composition and functional profile. Our analyses show that stability is lower at taxonomical than at functional level in all three age groups, indicating the existence of functional redundancy through time. Considering the entire period of sampling, toddlers were significantly more unstable than the other two groups at the level of taxonomic composition. However, local analyses revealed that low stability for both composition and function was restricted to the time period between 20 and 24 months of age, whereas after this point stability levels in toddlers were similar to those of adolescents and adults. Although the microbiome stabilized at around two years of age in terms of large-scale, rapid changes in diversity, composition, and functional profile, further changes did occur both before and after adolescence. Therefore, adolescence remains a transitional period, in which the abundances of some taxa and functions still differ from adult levels. These include, among others, Bifidobacterium, Streptococcus, Bacteroides fragilis and several members of the Lachnospiraceae, as well as various functions related to energy metabolism. Overall, our results pinpoint the two-years mark as a point of significant stabilization for the gut microbiome, without precluding the further occurrence of important changes in the relative abundance of specific taxa and gene functions both before and after adolescence.}, } @article {pmid41939707, year = {2026}, author = {Li, X and Jin, S and Hu, H and Lan, Y and Ni, B and Su, J and Luo, S and Tan, L and Zhang, Y and Huang, H and Xu, Y and Yang, J and Zhou, C and Chen, K and Li, S and Liang, B and Bai, S and Zhang, K and Pan, H and Dong, X and Yan, D}, title = {Feeding Diqing Tibetan pigs with 50% of soybean meal replaced by walnut meal can reduce subcutaneous fat deposition and promote intramuscular fat accumulation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1794046}, pmid = {41939707}, issn = {1664-302X}, abstract = {BACKGROUND: Protein feed resource shortage is a major constraint to the sustainable development of the livestock industry and a bottleneck problem hindering the growth of the Tibetan pig industry in China's Qinghai-Tibet Plateau region. Walnut meal, rich in protein, holds promise as a substitute for soybean meal. However, the effects and underlying mechanisms of walnut meal substitution on Tibetan pigs in Diqing remain unclear.

RESULTS: The study showed that substituting 50% of soybean meal with walnut meal in the diet of Diqing Tibetan pigs significantly reduced backfat thickness and increased intramuscular fat content (P < 0.05). Integrated multi-omics analyses, including metagenomics, transcriptomics, and lipidomics, revealed that walnut meal substitution significantly reduced the abundance of Clostridium butyricum in the cecum of Diqing Tibetan pigs. The reduction in Clostridium butyricum was linked to the lipolytic capacity of subcutaneous adipose tissue, potentially facilitating the breakdown of triglycerides into free fatty acids (FFAs), which are then released into the bloodstream. When these free fatty acids are transported to muscle tissue, the muscle exhibited inhibited oxidative metabolism (e.g., a decrease in acylcarnitine metabolites), while showing an upregulation in the expression of genes related to adipocyte differentiation (e.g., MEDAG, VDR) and triglyceride synthesis (e.g., PPARGC1A, ANGPTL4). Ultimately, these processes may contribute to the synthesis and storage of triglycerides in muscle, thereby facilitating intramuscular fat deposition.

CONCLUSION: This study reveals that walnut meal can serve as a substitute for soybean meal, and a 50% substitution ratio is conducive to intramuscular fat deposition in Diqing Tibetan pigs. The findings provide valuable insights for the development and application of unconventional protein feed resources, and offer new perspectives for the production of marbled pork.}, } @article {pmid41939710, year = {2026}, author = {Alibrandi, A and Plewka, J and di Primio, R and Bartholomäus, A and Vuillemin, A and Probst, AJ and Kallmeyer, J}, title = {Microbial diversity and community shifts in a petroleum reservoir under production: effects of water breakthrough and anthropogenic alterations.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1741638}, pmid = {41939710}, issn = {1664-302X}, abstract = {Subsurface petroleum reservoirs host indigenous microorganisms that survive extreme conditions and long-term isolation. Microbial activity in these environments can contribute to adverse effects such as oil biodegradation and reservoir souring. Unlike the broader deep biosphere, oil reservoirs are frequently subjected to anthropogenic disturbances, particularly during production, when processes like water injection introduce external microbes and electron acceptors. In this study, we investigated microbial diversity, community structure, and the impact of water breakthrough using 16S rRNA gene and metagenomic sequencing of produced fluids, production water, and injection water samples from the Edvard Grieg oil reservoir offshore Norway. We found clear regional heterogeneity in community composition, characterized by overall low diversity, dominated by thermophilic, anaerobic, and halotolerant taxa. The southern region (wells A13, A17, A18, and A19) exhibited lower diversity, while the microbial community composition of well A07 showed a distinct signature. The prevailing genera included the strictly anaerobic bacterium Thermoanaerobacter and the hyperthermophilic archaeon Thermococcus. Water breakthrough triggered shifts in community structure, not because of widespread replacement by injected microbes, but due to the increase in sulfate-reducing bacteria. Comparison between sequence data from production fluids and water samples allowed the identification of microbial signatures that can act as cost-effective tools for monitoring oil reservoir processes and integrity.}, } @article {pmid41939717, year = {2026}, author = {Navarro-Nieva, A and Martínez-Checa, F and Delgado, R and Párraga, J and Francino, MP and Jiménez-Hernández, N and Del Moral, A}, title = {Airborne microorganisms in muddy rain: microbe-mineral interactions and their ecosystem impact.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1772201}, pmid = {41939717}, issn = {1664-302X}, abstract = {The Sahara Desert and the Sahel region in North Africa contribute approximately 50-70% of global atmospheric dust emissions. Microorganisms can attach to dust particles and be dispersed into exogenous environments, being subsequently deposited by gravitational sedimentation (dry deposition) or through aqueous precipitation (wet deposition) also known as muddy rain. In the present work, five muddy rain samples were collected in Granada (Spain) during different episodes in 2021-2022. The SEM-EDX study demonstrated a high content of fine clay particles which may facilitate the atmospheric transport of microorganisms. The colonization of strategic microsites and the formation of mineral aggregates might be possible mineral-bacteria interactions. According to metagenomic analysis, Pseudomonadota (64%), Bacteroidota (13%), and Bacillota (6%) were the main phyla. At the genus level, extremophiles, plant-beneficial bacteria, and others involved in soil biogeochemical cycles have been described. Fourteen cultivable microorganisms were isolated and identified by means of 16S rRNA sequencing. Members of the phyla Pseudomonadota, Bacillota, Actinomycetota and Bacteroidota have been found. Among the isolates, Stenotrophomonas rhizophila and Brevundimonas bullata potentially exert beneficial effects at the ecosystem level. In general, muddy rain facilitates the transport and dispersal of microorganisms from different environments, with a potential positive influence on soils and vegetation in terrestrial ecosystems.}, } @article {pmid41940150, year = {2026}, author = {Luo, H and Wang, Y and Hou, H and Yang, J and Liu, YX}, title = {Advances and applications in sequencing-based pathogen surveillance.}, journal = {aBIOTECH}, volume = {7}, number = {1}, pages = {100004}, pmid = {41940150}, issn = {2662-1738}, abstract = {The ongoing emergence of infectious diseases necessitates cutting-edge diagnostic methodologies. Traditional diagnostic methods are constrained by limited range, lengthy processing times, and inadequate sensitivity. High-throughput sequencing technologies, particularly multiplex polymerase chain reaction (PCR)-based targeted sequencing, have emerged as transformative tools for pathogen detection, offering enhanced sensitivity, specificity, and cost efficiency. However, challenges in primer design, such as dimerization and bias, limit the effectiveness of these approaches. This review explores advances in sequencing technologies, emphasizing the roles of culturomics, metagenomics, and metatranscriptomics in pathogen discovery. We spotlight innovative strategies for error-tolerant primer design that address existing limitations by balancing coverage and specificity, thereby optimizing the multiplex PCR process. Furthermore, integration of artificial intelligence enhances the precision and scalability of sequencing, enabling real-time diagnostics. Collectively, these advances offer promising pathways to bolster global health, food security, and ecological resilience through robust and sustainable pathogen-detection systems.}, } @article {pmid41940273, year = {2026}, author = {Huang, F and Shi, X and Chen, P and Hu, Q and Zhao, Y and Chen, Z and Ma, W and Tan, Q and Feng, X and Zhang, X}, title = {Dietary drivers of gut microbiota diversity and function in wildlife of Wolong Nature Reserve: a metagenomic study.}, journal = {Current zoology}, volume = {72}, number = {1}, pages = {14-29}, pmid = {41940273}, issn = {1674-5507}, abstract = {While diet is known to regulate the composition, function, and diversity of the human gut microbiome, its effects on wildlife remain understudied. Here, noninvasive sampling methods were first used to conduct metagenomic analyses of the gut microbiomes of 10 protected wild animals in the Wolong Nature Reserve. There were significant differences in microbiota composition and function between herbivores and carnivores. Herbivores exhibited higher microbial diversity and evenness (Shannon and Pielou indices), with Bacillota and Acinetobacter predominating, whereas carnivores were enriched in Pseudomonadota and Escherichia. Cellulose-degrading bacterium Ruminococcus champanellensis was abundant in herbivores, while Rhodococcus and Pediococcus, which were associated with toxin degradation and pathogen inhibition, were more prevalent in carnivores. Carnivores showed higher lipid metabolism and protein degradation, as evidenced by the enrichment of leucyl aminopeptidase and oligopeptidase B, while herbivores demonstrated superior cellulose and starch digestion, characterized by the enrichment of cellulose 1,4-beta-cellobiosidase. Stochastic processes shaped gut microbiome assembly, especially in herbivores. Potential health risks from pathogens such as Escherichia and Listeria were identified, and Escherichia abundance was positively correlated with niche width. Furthermore, the findings suggest that high-altitude environments may promote the persistence and spread of pathogens. Overall, our findings underscore the intricate linkages between diet, gut microbiota composition, assembly processes, and host ecology in protected wildlife, address a key knowledge gap, and provide important theoretical and practical insights for ecological conservation, species restoration, and environmental management.}, } @article {pmid41940285, year = {2025}, author = {Jeong, GH and Lim, KS}, title = {Exploring the potential of salivary small RNAs as non-invasive biomarkers in pigs.}, journal = {Journal of animal science and technology}, volume = {67}, number = {6}, pages = {1207-1214}, pmid = {41940285}, issn = {2055-0391}, abstract = {Saliva, a non-invasive potential source of circulating microRNAs (miRNAs) and microbiomes, is not well described in pigs. Salivary miRNA expression profiles and the functional significance in pigs were investigated in this study. Saliva samples were extracted from adult female pigs, and small RNA sequencing revealed 26 known and 223 novel miRNAs. The large number of novel miRNAs also demonstrates the differences between salivary miRNAs in pigs and other biological samples. Functional analysis of miRNA target genes indicated enrichments in molecular functions related to transcription regulator activity, cytoskeleton organization, and protein binding, suggesting roles for this interaction in gene expression and physiological control. Moreover, metagenomic analysis revealed microbial sequences representing around 39% of the total reads, with Corynebacterium genus, an important member of the oral microbiota, being the most prevalent. Combining miRNA with microbiome data indicates that porcine saliva is rich in molecular information that will be useful for salivary health monitoring and microbiome studies. This study underscores the potential of salivary miRNAs as biomarkers for physiological processes and microbiome interactions in pigs, paving the way for further research into their diagnostic and monitoring applications.}, } @article {pmid41940335, year = {2026}, author = {Buysse, M and Ballinger, MJ and Bruley, M and Amoros, J and Grillet, J and Farassat, N and Serr, A and Lagrèze, WA and Wennerås, C and Grankvist, A and Schön, T and Berglund, J and Bell-Sakyi, L and Sprong, H and Duron, O}, title = {A human-associated Spiroplasma ixodetis lineage responsible for infantile cataracts and adult febrile illness.}, journal = {iScience}, volume = {29}, number = {4}, pages = {115233}, pmid = {41940335}, issn = {2589-0042}, abstract = {Bacteria of the Spiroplasma ixodetis clade are well characterized as reproductive parasites and defensive endosymbionts of arthropods. Nevertheless, clinical evidence indicates that they can also infect humans, causing neonatal ocular disease and acute febrile illness in adults. Using metagenomic assembly and phylogenomic analyses of Spiroplasma ixodetis-related human infections (SiRHIs), combined with a systematic meta-analysis of public datasets, we identified 25 human cases across ten European countries. Despite the frequent detection of multiple S. ixodetis strains in ticks, our data provide no evidence implicating tick-associated strains in human infections. Instead, SiRHI constitute a distinct monophyletic lineage within the S. ixodetis clade, consistent with a shared evolutionary origin with arthropod-associated relatives. Notably, SiRHI genomes harbor horizontally acquired chaperone genes absent from most arthropod-associated Spiroplasma, while retaining conserved effector genes typical of endosymbionts, suggesting the preservation of ancestral symbiotic traits alongside newly acquired molecular adaptations.}, } @article {pmid41940665, year = {2026}, author = {Huang, C and Feng, Q and Yu, B and Zou, H and Cai, Y and Liu, J and Li, D and Zhang, H and Zou, X}, title = {Diabetes affects the composition of the respiratory tract microbiome and transcriptome in patients with viral pneumonia.}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0191125}, pmid = {41940665}, issn = {2165-0497}, abstract = {UNLABELLED: Research shows that patients with viral pneumonia complicated by diabetes have a worse prognosis and higher mortality. Our study aimed to assess the effect of diabetes on respiratory tract microbes and the transcriptome in patients with viral pneumonia. We included 76 subjects from China-Japan Friendship Hospital, including 16 healthy people, 17 patients with viral pneumonia and diabetes (VD), and 43 patients with viral pneumonia without diabetes (VP). We collected their sputum samples for both metagenomic and 16S rRNA sequencing and collected blood samples for RNA sequencing. In transcriptome analysis, the VD group downregulated the expression of PTCH1 and upregulated the expression of ANK1, RBM38, BPGM, CRYM, TAL1, and HBD. The differential pathways are mainly reflected in the formation, development, and maintenance of red blood cells, the activity of immunoglobulins, and the membrane transport and transportation of substances. There is a significant difference in microbial diversity between the two groups. Both analysis methods demonstrate a significant increase in the abundance of g__Treponema, s__Treponema_denticola, and s__Campylobacter_rectus in the VP group. The host genes AGAP1, RNF182, and ANKRD9 are particularly closely associated with microorganisms. Our results suggest that diabetes may inhibit the expression of genes related to immune regulation, energy metabolism, and oxygen utilization in patients with viral pneumonia. Meanwhile, we predict that VD may be associated with a decrease in microbial diversity and a decline in microbial functions in cellular processes, environmental adaptation, metabolism, and genetic activity. These abnormalities can worsen the course of viral pneumonia and affect the prognosis of patients.

IMPORTANCE: We used 16S rRNA and metagenome sequencing to analyze the respiratory microbial composition of patients with viral pneumonia complicated by diabetes (VD) and patients with viral pneumonia without diabetes (VP) and used transcriptome sequencing to compare the gene expression of patients in VD, VP, and healthy people. Our results indicate significant differences in gene expression and respiratory microbiota profiles between VD and VP. VD may inhibit the immune regulatory response and affect cell energy metabolism and oxygen transport and utilization by regulating related gene pathways. The abundance of Treponema denticola in the VP group was significantly higher than that in the VD group. We predicted that the functions of differential microorganisms may be related to cellular processes, environmental information processing, genetic information processing, human diseases, and metabolism. This study found characteristic biomarkers related to viral pneumonia with diabetes, providing a new strategy for further research and clinical treatment.}, } @article {pmid41940696, year = {2026}, author = {Li, Y and Zhang, H and Xiang, B and Zhang, Y and Zhang, M}, title = {Enhanced microbiota-derived mucinases in colorectal cancer patients revealed by gut metagenome probing coupled with functional validation.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0190325}, pmid = {41940696}, issn = {1098-5336}, support = {21TQ1400210//the Shanghai Pilot Program for Basic Research-Shanghai Jiao Tong University/ ; 32071271//National Natural Science Foundation of China/ ; 32371332//National Natural Science Foundation of China/ ; 92478203//National Natural Science Foundation of China/ ; IPP30140//College Student Innovation and Practice Program of Shanghai Jiao Tong University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metagenome ; *Colorectal Neoplasms/microbiology ; *Bacteria/enzymology/genetics/classification/isolation & purification ; *Polysaccharide-Lyases/genetics/metabolism ; Mucins/metabolism ; Female ; Male ; *Bacterial Proteins/genetics/metabolism ; }, abstract = {Mucinases produced by the gut microbiota play a dual role in regulating the integrity and renewal of the mucus layer, which is essential for maintaining gut homeostasis and human health. In this study, we constructed protein hidden Markov models based on 11 known mucinases and used them to systematically identify mucinase sequences from gut metagenome-assembled genomes derived from 80 colorectal cancer (CRC) patients and 86 healthy (Healthy) subjects. A total of 1,869 mucinases were detected, widely distributed across the studied cohorts, with the majority originating from Bacteroides, Phocaeicola, and Akkermansia species. Further analysis identified 42 mucinases that differed significantly in abundance between the two groups, all of which were enriched in CRC patients. Taxonomic attribution revealed that, in CRC patients, these mucinases were primarily derived from Bacteroides (36.0%), Phocaeicola (30.6%), Akkermansia (8.8%), Alistipes (8.6%), and Escherichia (6.4%), whereas in Healthy subjects, they mainly originated from Bacteroides (26.1%), Akkermansia (22.7%), and Phocaeicola (20.3%), with a notably higher proportion from Akkermansia. Among the 42 mucinases, WL42 and LLN1 exhibited significantly higher abundance levels compared to the others. Phylogenetic and predicted structural analyses suggested that these two mucinases belonged to the M60 and M98 families, respectively. Functional validation through co-incubation experiments demonstrated that both mucinases could cleave the glycosylated MUC1 and MUC2 substrates, but not the corresponding non-glycosylated proteins. These findings confirm the feasibility of discovering novel mucinases directly from gut metagenomic data and provide insights into their potential roles in health and disease.IMPORTANCEOur study established a feasible bioinformatics pipeline for the systematic identification of microbial mucinases within the gut microbiome, providing a methodological foundation for large-scale mining of functionally active mucin-degrading enzymes. We identified 42 mucinases significantly enriched in CRC patients, suggesting their potential involvement in CRC pathogenesis. Among them, two mucinases were experimentally validated for their ability to degrade mucin, offering direct functional evidence of their capacity to disrupt the mucosal barrier. Genus-level metagenomic profiling further identified Bacteroides, Phocaeicola, and Akkermansia as major mucinase-producing genera. Maintaining the secretory balance of these mucinase-producing bacteria might be crucial for ameliorating intestinal barrier dysfunction in CRC patients. The findings of this study offer critical insights into the microbial origins and potential mechanistic contributions of mucinases in colorectal cancer, underscoring their relevance in mucus barrier breakdown and disease progression.}, } @article {pmid41940802, year = {2026}, author = {Yersin, S and Gody, JC and Mazel, F and Djimbele, E and Nigateloum, SN and Gondje, BP and Vondo, SS and Kaleb Jephté Estimé, K and Raub, A and Teo, Y and Djorie, SG and Kapel, N and Sansonetti, PJ and Vonaesch, P and , }, title = {Strain-level translocation and enrichment dynamics of oral bacteria in the lower gastrointestinal tract of stunted children.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2653550}, doi = {10.1080/19490976.2026.2653550}, pmid = {41940802}, issn = {1949-0984}, mesh = {Humans ; *Mouth/microbiology ; *Bacteria/classification/isolation & purification/genetics ; Child, Preschool ; Saliva/microbiology ; Feces/microbiology ; *Growth Disorders/microbiology ; Male ; Cross-Sectional Studies ; Central African Republic ; Female ; Infant ; *Bacterial Translocation ; *Gastrointestinal Tract/microbiology ; *Gastrointestinal Microbiome ; }, abstract = {Emerging evidence suggests that ectopic colonization of oral bacteria in the lower digestive tract may exacerbate gastrointestinal disorders. Nevertheless, it remains unclear whether bacteria of oral origin are continuously translocating from the oral cavity to the lower gastrointestinal tract or are locally adapted and persist in their respective niches. We investigated strain translocation dynamics in 44 healthy and stunted children from Bangui, Central African Republic. Using cross-sectional shotgun metagenomic sequencing of saliva, gastric, duodenal, and fecal samples, and isolation and whole-genome sequencing of 87 Streptococcus salivarius isolates, we showed the translocation of members of the genera Streptococcus, Veillonella, Rothia, and Haemophilus. Fecal isolates were more closely related to oral isolates from the same individuals than to those from other individuals. Additionally, saliva showed higher S. salivarius nucleotide diversity compared to other compartments, which is consistent with frequent intraindividual translocations from the oral cavity to the lower gastrointestinal tract. Finally, we showed that overrepresentation of oral bacteria in the duodenum of stunted children is related to increased biomass, while in the colon, it is linked to depletion of overall biomass, including in butyrate-producing strains. Our study quantifies dynamics of oral-to-gut translocation and enrichment of oral taxa, providing key insights into microbiota disruption in stunted children.}, } @article {pmid41940852, year = {2026}, author = {Jin, Z and Yuan, Q and Wang, J and Liao, H and Bol, R and Wu, D and Wu, Q and Tang, Y and Guo, W and Liu, Y and Chen, J}, title = {Recycling of Sedimentary Phosphorus Pools in Two Yunnan-Guizhou Plateau Lakes, Southwest China.}, journal = {Environmental science & technology}, volume = {60}, number = {15}, pages = {11519-11528}, doi = {10.1021/acs.est.6c00162}, pmid = {41940852}, issn = {1520-5851}, mesh = {*Geologic Sediments/chemistry ; *Lakes ; China ; *Phosphorus ; Oxygen Isotopes ; Phosphates ; }, abstract = {Applying phosphate oxygen isotopes (δ[18]OP) to identify sediment phosphorus (P) sources and its recycling is still challenging due to poor understanding in δ[18]OP variations of sediment P pools and their driving mechanisms. Here, we analyzed the δ[18]OP in inorganic P (Pi) pools of sediment cores and varied P sources from Lake Dianchi and Lake Erhai in the Yunnan-Guizhou Plateau, Southwest China. The δ[18]OP values of sediment detrital Pi (Det-Pi, nonbioavailable P) were consistent with those of watershed soils (within ∼0.4-0.6‰), indicating that the δ[18]OP of sediment Det-Pi inherits the δ[18]OP of soil Det-Pi. The δ[18]OP values of aluminum-bound Pi (Al-Pi) and authigenic Pi (Auth-Pi) in sediment were close to or within the δ[18]OP equilibrium (δ[18]OP-eq) ranges, implying oxygen isotopic exchange equilibrium between phosphate and ambient water prior to the formation of sediment Al-Pi and Auth-Pi. However, the δ[18]OP of iron oxide-bound Pi (Fe-Pi) in sediment was lighter (∼3‰) than δ[18]OP-eq, retaining the negative isotopic signal of organic P (Po) remineralization. Furthermore, [31]P NMR and metagenomic analysis indicated that microbial-mediated Po mineralization and Pi recycling are the driving factors for δ[18]OP changes in sediment Fe-Pi, Al-Pi, and Auth-Pi. These integrated insights deepen our understanding of the biogeochemical cycling for sedimentary P.}, } @article {pmid41940893, year = {2026}, author = {Liao, Y and Wang, B and Li, Y and Ni, W and Li, X and Hu, S}, title = {Establishment of the chromid database and analysis of evolutionary research.}, journal = {Molecular genetics and genomics : MGG}, volume = {301}, number = {1}, pages = {}, pmid = {41940893}, issn = {1617-4623}, mesh = {*Evolution, Molecular ; Phylogeny ; *Genome, Bacterial/genetics ; *Databases, Genetic ; *Bacteria/genetics ; *Replicon/genetics ; Metagenomics/methods ; Computational Biology/methods ; Polymorphism, Single Nucleotide ; }, abstract = {In bacterial multireplicon genomes, in addition to the main chromosome, there is a widespread class of secondary replicons with a distinct evolutionary status known as chromids. These elements possess plasmid-like replication and partitioning systems, while their nucleotide composition and gene functions are highly similar to those of the main chromosome. Therefore, chromids are considered to play important roles in the evolution of bacterial genome architecture and in environmental adaptation. With advances in long-read sequencing technologies and breakthroughs in bioinformatics methods, metagenomic data resources have been greatly expanded. Using our previously developed automated tool, "Chromid-Finder", we systematically identified and collected chromid sequences from large-scale metagenomic assemblies. These data were then uniformly curated, classified, and centrally managed to construct a public database platform dedicated to chromids-Chromid Database. On this basis, we conducted comprehensive analyses of the evolutionary and genetic characteristics of chromids. Phylogenetic analyses revealed the overall evolutionary landscape of chromids. Variation analyses showed that SNP distributions on chromids exhibit clear and well-organized patterns, depicting a dynamic population that is continuously adapting to the environment through fine-scale sequence tuning and non-coding regulatory mechanisms. Structural variation analyses further identified several hotspot regions significantly enriched in key genes related to metabolic functions, nutrient acquisition, and antibiotic resistance. The distribution patterns of recombination events suggest that their occurrence is likely driven primarily by non-phylogenetic factors such as environmental conditions and ecological niches. In addition, systematic quantification of heritable mobile genetic elements indicated that the number of integrative and conjugative elements (ICEs) largely determines the overall mobile element burden within chromids.}, } @article {pmid41941835, year = {2026}, author = {Hennen, J and Ifrach, J and Morse, C and Charcos, I and Godil, SS and Mossop, CM}, title = {First reported case of Lawsonella clevelandensis brain abscess in the setting of invasive cutaneous squamous cell carcinoma identified via bedside stereotactic aspiration: illustrative case.}, journal = {Journal of neurosurgery. Case lessons}, volume = {11}, number = {14}, pages = {}, pmid = {41941835}, issn = {2694-1902}, abstract = {BACKGROUND: Brain abscesses associated with malignant skull base invasion pose unique diagnostic and management challenges for neurosurgeons, particularly when routine cultures remain negative. The authors report the first documented intracranial infection caused by Lawsonella clevelandensis, a recently described anaerobe that mimics Nocardia or Mycobacterium sp., diagnosed using bedside stereotactic biopsy as well as metagenomic next-generation sequencing.

OBSERVATIONS: A 74-year-old woman with recurrent, locally invasive facial squamous cell carcinoma presented with recent-onset shaking of her lower extremity and a large right frontal mass extending through the calvarium and orbit. Imaging revealed ring-enhancing lesions consistent with abscess. Bedside stereotactic biopsy and drainage were performed, and metagenomic sequencing identified L. clevelandensis. Antibiotics were narrowed to ceftriaxone and metronidazole, stabilizing her condition, although repeat drainage was required for radiographic progression. She subsequently underwent multidisciplinary skull base resection and reconstruction, with operative cultures isolating Enterococcus faecium but no further Lawsonella sp.

LESSONS: This case represents the first documented intracranial L. clevelandensis infection and demonstrates the diagnostic value of molecular sequencing in culture-negative brain abscesses. It also highlights bedside stereotactic biopsy and drainage as a safe, minimally invasive strategy for managing intracranial infection in medically complex patients. https://thejns.org/doi/10.3171/CASE25887.}, } @article {pmid41942049, year = {2026}, author = {Chen, W and Zhang, Y and Tian, Y and Dai, W and Huang, D and Zhao, Z and Henawy, AR and Shao, Z and Cai, M and Huang, F and Zheng, L and Cheng, W and Zhang, J}, title = {Multi-cycle application of Virgibacillus dokdonensis induces a root-knot nematode-suppressive soil via specifically recruiting functional Pseudomonas.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.04.004}, pmid = {41942049}, issn = {2090-1224}, abstract = {INTRODUCTION: Inducing the development of disease-suppressive soils against root-knot nematodes (RKNs) represents a sustainable strategy for reducing pesticide dependence, with microbial management serving as a core approach. However, the formation mechanisms, key microbial drivers, and functional stability of RKN disease suppressive soil remain poorly understood.

OBJECTIVES: This study aimed to elucidate the ecological mechanisms underlying soil microbiome-mediated suppressiveness against RKNs induced by multi-cycle application of the deep-sea biocontrol bacterium Virgibacillus dokdonensis MCCC 1A00493.

METHODS: Using a three-cycle consecutive microcosm experiment, we tracked RKN disease incidence and soil microbial community dynamics. We combined microbiome sequencing with functional assays to identify key functional taxa, and constructed synthetic microbial communities (SynComs) to validate their synergistic suppression with V. dokdonensis.

RESULTS: Continuous application of V. dokdonensis significantly reduced RKN disease, with the control efficacy reaching 37.86%, 51.11%, and 65.85% over three cropping cycles. This suppressiveness was achieved through direct antagonism and the reshaping of the soil bacterial community, which involved the successful colonization of V. dokdonensis and specific enrichment of indigenous functional Pseudomonas. Metagenomic analysis indicated a significant upregulation of bacterial chemotaxis genes. Further chemotaxis assays confirmed that the fermentation supernatant of V. dokdonensis specifically attracts high-nematicidal Pseudomonas, achieving a relative chemotaxis index reaching 3.0 to 9.1. Based on this, we constructed synthetic communities of functional Pseudomonas with varying complexity levels. Among them, a simplified SynComV1, consisting of Pseudomonas monteilii, P. parafulva, P. fulva, P. plecoglossicida, and P. putida, exhibited the greatest disease suppression, reaching 48.38%. Notably, co-application of V. dokdonensis and SynComV1 demonstrated significant synergistic effects, enhancing the control efficacy to 58.33%.

CONCLUSIONS: Overall, this study revealed that multi-cycle application of V. dokdonensis induces a RKN-suppressive soil by specifically recruiting indigenous high-nematicidal Pseudomonas to synergistically suppress RKN disease. These findings provide a practical strategy for developing efficient and sustainable technologies for RKN management.}, } @article {pmid41942192, year = {2026}, author = {Xia, Y and Kuda, T and Zhou, Q and He, Q}, title = {Bidirectional modulation of microbial communities by tea polyphenols and gallic acid enhances quality in dry fermented sausages.}, journal = {Food research international (Ottawa, Ont.)}, volume = {233}, number = {Pt 1}, pages = {118924}, doi = {10.1016/j.foodres.2026.118924}, pmid = {41942192}, issn = {1873-7145}, mesh = {*Gallic Acid/pharmacology ; *Meat Products/microbiology/analysis ; *Polyphenols/pharmacology ; Fermentation ; *Tea/chemistry ; *Food Microbiology ; Animals ; Antioxidants/pharmacology ; *Microbiota/drug effects ; Metabolomics ; Food, Processed ; Biogenic Amines/analysis ; Swine ; }, abstract = {Tea polyphenols (TP) and its primary component gallic acid (GA) possess antibacterial and antioxidant properties, serving as natural additives to enhance the safety and quality of fermented meat products. This study investigated the bidirectional regulatory effects of TP and GA on microbial dynamics and quality attributes in dry fermented sausages. TP (1-4 mg/mL) enhanced the growth of Lactiplantibacillus plantarum while inhibiting Staphylococcus aureus and Escherichia coli, promoting lactic acid bacteria (LAB) dominance and reducing spoilage and pathogenic bacteria. Sausages treated with TP showed reduced levels of biogenic amines (291.06 vs. 376.22 mg/kg) and NDMA (0.86 vs. 1.32 μg/kg), improved texture (hardness and springiness), and better color stability, all without affecting sensory acceptability. Metabolomic and metagenomic analyses suggested that GA enriched beneficial Lactococcus garvieae and suppressed spoilage-associated Enterococcus faecalis and Citrobacter freundii. Besides, it promoted the microbial-mediated production of key antioxidant metabolites and flavor enhancers (e.g., purpurogallin, sesamol). These results indicated that TP and GA could serve as multifunctional additives that enhance fermentation efficiency, microbial safety, and sensory quality by precisely regulating microbial communities and their metabolic functions.}, } @article {pmid41942205, year = {2026}, author = {Zhang, F and Wang, X and Wang, J and Fan, X and Kong, Y and Li, X and Zeng, X and Li, H and Liu, W and Zhang, A and Song, D and Gong, H}, title = {Revealing the microbial diversity and functional annotation during postharvest storage of sweet cherry using metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {233}, number = {Pt 1}, pages = {118955}, doi = {10.1016/j.foodres.2026.118955}, pmid = {41942205}, issn = {1873-7145}, mesh = {*Metagenomics/methods ; *Prunus avium/microbiology ; *Food Storage/methods ; *Microbiota/genetics ; *Food Microbiology ; *Bacteria/classification/genetics ; *Fruit/microbiology ; }, abstract = {This study aimed to investigate the dynamic changes in the quality characteristics, microbial community diversity, functional annotation and metabolic pathways of sweet cherries stored at 25 °C for 0, 1, 3, 5 or 7 days. The results showed that the quality characteristics of sweet cherries gradually deteriorated with increasing storage time, and the abundance of Proteobacteria increased gradually. Mucoromycota appeared on D3 group, which may be one of the main microbial groups causing sweet cherry rot. In addition, 3D principal coordinate analysis showed that the species composition of sweet cherries stored for 1 day and fresh cherries was highly similar. The results of the Bray-Curtis distance analysis indicate a significant trend towards separation in species composition from the third day of storage. Moreover, KEGG annotations of metabolites and enzymes suggest that glycolysis and pyruvate metabolism are important in the storage of sweet cherries. Meanwhile, the pathway diagram shows that the main substances maintaining the pathway are pyruvate kinase and pyruvate dehydrogenase, which are detected in groups D5 and D7 groups. This study examines the changes in microbial communities and functional annotations that occur during the storage of sweet cherries after harvest. This provides a theoretical basis for developing new, efficient antibacterial agents for storing sweet cherries.}, } @article {pmid41942425, year = {2026}, author = {Peña-Valencia, MF and Robaina-Estévez, S and Custer, GF and Turak, O and Sierra, F and Mendes, LW and Rubiano-Labrador, C and Gutiérrez, J and Vaksmaa, A and Dini-Andreote, F and Rosado, AS and Reyes, A and Jiménez, DJ}, title = {Lignocellulose-mediated selection of potential halophilic PET-degrading enzymes from mangrove soil.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41942425}, issn = {2041-1723}, mesh = {*Lignin/metabolism ; *Soil Microbiology ; *Polyethylene Terephthalates/metabolism ; Phylogeny ; Bacteria/genetics/enzymology/classification ; Seawater ; Soil/chemistry ; Archaea/genetics/enzymology ; Metagenomics ; Salinity ; }, abstract = {Mangroves are ecosystems located at land-sea transition zones, where they are continuously exposed to plant biomass and plastic pollution. Their soils harbor extensive microbial diversity with potential for discovering polymer-degrading enzymes. Here, we perform a microcosm experiment to examine how mangrove soil microbial communities respond to inputs of lignocellulose or polyethylene terephthalate (PET) in the presence and absence of seawater, and to explore the selection of putative PET-active enzymes (PETases) using gene- and genome-resolved metagenomics. Incubation conditions lead to a gradual increase in salinity, resulting in the enrichment of halophilic taxa, including spore-forming bacteria and archaeal species, particularly in seawater-depleted treatments. Lignocellulose input is the primary driver of soil microbial community restructuring, followed by seawater presence. In dry, lignocellulose-amended microcosms (L treatment), microbial diversity is significantly reduced, while lignocellulolytic taxa within the phyla Bacillota and Actinomycetota are enriched. Twelve potential PETases are identified in the L treatment, sharing >70% sequence similarity with known PETases, and three are predicted to be thermostable. Two putative PETases from Microbulbifer species display distinct sequence and structural features, thereby expanding the currently limited PETase sequence landscape. This study demonstrates that perturbing environmental microbiomes with plant-derived polymers represents a promising strategy for capturing novel PETases.}, } @article {pmid41942854, year = {2026}, author = {Salengros, A and Dechamps, E and Meunier, L and George, IF}, title = {Uncovering the ecophysiological potential of Motilimonas through genomic profiling analysis.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41942854}, issn = {1471-2164}, abstract = {BACKGROUND: The Motilimonas genus was proposed in 2017 and presently include three recognized species isolated from various environments. This genus is still poorly characterized, and its ability to degrade chitin has recently been reported. A genomic profiling analysis was conducted on the seven Motilimonas genomes (family Psychromonadaceae) available in the NCBI database.

RESULTS: The phylogenetic study suggests that Motilimonas sp. E26, Motilimonas sp. 1_MG-2023 G1M02 and Motilimonas sp. Spo1_1 could form a new clade distinct from other already existing clades within the Motilimonas genus (i.e. M. cestriensis, M. pumila and M. eburnea). The genomic features of all Motilimonas genomes are consistent with a moderately copiotrophic lifestyle. For instance, they encode proteins involved in chemotaxis, motility, type IV pili biosynthesis, sugar phosphotransferase systems (PTS) and chitin degradation. Additional shared traits include aerobic respiration, a preference for sugars over organic acids as carbon sources, the use of a “compatible solute” strategy to tolerate osmotic stress in saline environments, and, except for M. cestriensis MKS20[T], the ability to perform nitrate reduction. Furthermore, all Motilimonas genomes encode a diversity of secretion systems. For example, each genome contains one or several complete type I secretion systems (T1SS), one complete T2SS, and four genomes (Motilimonas sp. Spo1_1, M. sp. E26, M. sp. 1_MG-2023 G1M02 and Motilimonas sp. KMU-193) harbor a complete type VI secretion system (T6SS). Notably, only M. pumila PLHSC7-2[T] possesses genes encoding a complete type III secretion system (T3SS).

CONCLUSIONS: These findings provide new insights into the ecological versatility and adaptive strategies of the Motilimonas genus. The next step will involve genome-resolved analyses of metagenomic datasets with the objective to investigate the functional ecology of Motilimonas in a broader range of environments contributing to the better understanding of their ecological distribution.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12781-0.}, } @article {pmid41942856, year = {2026}, author = {Liu, SW and Wang, XX and Xian, LY and Zou, DW and Huang, YF and He, XL and He, F and Wang, XT}, title = {Metagenomic analysis of intestinal microbiota characteristic differences between patients with ankylosing spondylitis and healthy individuals.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41942856}, issn = {1471-2180}, support = {2023JH2/101700219//Liaoning Province Science and Technology Plan Joint Project (Applied Basic Research Project)/ ; }, abstract = {BACKGROUND: To explore the differences in intestinal microbiota between patients with ankylosing spondylitis (AS) and healthy individuals (HC) in terms of genetic, species composition, and functional levels, and to reveal the role of intestinal microorganisms in the pathogenesis of AS.

METHODS: This study selected 17 AS patients (AS group) and 17 healthy subjects (HC group) from the Affiliated Hospital of Liaoning University of Traditional Chinese Medicine between August to October 2024. Basic clinical data, as well as the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Visual Analogue Scale (VAS) score, of the AS group, were collected. Fresh fecal samples were also collected for metagenomic sequencing. Differences in microbiota were analyzed using methods including Alpha diversity analysis, species abundance analysis, Principal Coordinates Analysis (PCoA), Non-metric Multidimensional Scaling (NMDS), DESeq2 analysis, Linear Discriminant Analysis Effect Size (LEfSe), and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation.

RESULTS: The number of unique genes in the AS group (566,526) was higher than that in the HC group (406,609). At the species level, there were no significant differences in Alpha diversity or the overall microbial structure (revealed by PCoA and NMDS) between the two groups (p > 0.05). However, significant differences in abundance were observed at the family, genus, and species levels. DESeq2 identified a total of 43 differential species, among which 22 species had increased abundance and 21 species had decreased abundance in the AS group. LEfSe analysis showed that the HC group had 16 dominant bacterial species, while the AS group had only Neoporus faecalis as the dominant species. There were differences in KEGG Level 3 functional pathways between the two groups, but no statistically significant difference was found in the overall functional structure (p = 0.698). Functional enrichment analysis revealed that AS-specific genes were primarily enriched in neurodegenerative disease pathways, protein processing in the endoplasmic reticulum, and autophagy-related pathways, with substantial contributions from genera including Bacteroides, Streptococcus, Eubacterium, and Faecalibacterium. However, neither individual differential species nor their functional pathways showed significant correlations with clinical disease activity scores (BASDAI and VAS)。.

CONCLUSION: The studies indicated that although there was no significant difference in the overall diversity of intestinal microbiota between AS patients and healthy individuals, there were obvious distinctions in genetic composition, specific bacterial species, and functional pathways, suggesting that intestinal microorganisms may be involved in the pathogenesis of AS.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04996-8.}, } @article {pmid41942925, year = {2026}, author = {Maimaitiming, A}, title = {Metagenomic next-generation sequencing (mNGS) for severe cat bite infections with negative aerobic culture: a single-center retrospective study in a rabies vaccination center.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41942925}, issn = {1471-2334}, abstract = {BACKGROUND: Cat bite infections are common emergency settings and are characterized by small, deep puncture wounds that readily form an anaerobic microenvironment, leading to a high incidence of anaerobic bacterial infections. Conventional aerobic bacterial culture has extremely low detection efficiency for such infections and is prone to false-negative results and delayed treatment. As a designated regional rabies vaccination and treatment center, our hospital manages refractory and severe animal bite cases referred from primary medical institutions, with an annual volume of approximately 3000 animal bite consultations. METHODS: Clinical data were retrospectively collected for 17 patients with cat bite infections (13 mild, 4 severe) and negative traditional aerobic bacterial cultures admitted to the Emergency Department of our hospital from May 2025 to January 2026. All patients were treated with emergency debridement and empirical antibiotic therapy. For the 4 severe patients with no improvement after conventional treatment, metagenomic next-generation sequencing (mNGS) was recommended for etiological detection, with only 1 patient consenting to external testing at Beijing You’an Hospital due to economic constraints. RESULTS: All 17 patients had deep puncture wounds (depth > 0.5 cm), and the aerobic bacterial culture results were all negative after 72 h of incubation. In the single severe patient who underwent mNGS testing within 24 h of sample collection, multiple anaerobic or facultative anaerobic pathogens were identified (no viral, fungal or parasitic pathogens detected), with the specific species and their relative abundances shown in Table 1. The dominant pathogen was Bacteroides pyogenes (67.5%), followed by other oral anaerobes, including Fusobacterium russii and Porphyromonas gulae; the classic cat bite pathogen Pasteurella multocida (1.5%) was also detected in this mixed infection. The relative abundance distribution of all identified pathogens is presented in Figure 1, and the genome coverage plots for the key pathogenic bacteria are shown in Figure 2. The 4 severe patients all achieved effective infection control after adjustment based on antibiotic regimens with reference to the mNGS results. The average treatment cycle of 4 severe patients was 14.5 ± 2.3 days, and that of 13 mild patients was 18.7 ± 3.1 days; no statistical analysis was performed due to the small sample size. CONCLUSION: In this small single-center retrospective study, aerobic culture was negative in all 17 cat bite infection cases. In the single tested severe patient, mNGS identified multiple anaerobic and facultative anaerobic pathogens and facilitated targeted antibiotic adjustment, suggesting that mNGS may serve as a potential supplementary diagnostic tool for severe culture-negative cat bite infections in emergency settings. Given the limited sample size and the fact that only one mNGS test was performed, no broad conclusions can be drawn regarding the generalizability of mNGS. Regional rabies vaccination and treatment centers should establish standardized debridement procedures, strengthen physician‒patient risk communication, and improve the referral system to reduce the risk of severe complications and medical disputes. CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid41943157, year = {2026}, author = {Bruna, P and Barra, PJ and García, M and Liachko, I and de la Luz Mora, M and Dutilh, BE and Abanto, M}, title = {Unraveling plasmid contributions to phosphorus acquisition in soil microbiomes.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41943157}, issn = {2524-6372}, support = {2023-21230832//Agencia Nacional de Investigación y Desarrollo/ ; FONDECYT Regular 1241293//Agencia Nacional de Investigación y Desarrollo/ ; 1230084//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; FONDECYT Regular 1251164//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; Consolidator grant 865694/ERC_/European Research Council/International ; }, abstract = {BACKGROUND: Phosphorus (P) is a fundamental macronutrient for plant and microbial growth, but its availability in soils is often constrained by strong interactions with minerals and organic matter. While the role of bacteriophages in P cycling has gained attention, plasmids remain comparatively underexplored despite their central role in horizontal gene transfer. This study aimed to investigate the occurrence, diversity, and ecological relevance of plasmid-borne genes involved in P acquisition across soils with contrasting P availability.

RESULTS: Using curated plasmid databases and soil metagenomes from diverse biomes, we identified a broad repertoire of plasmid-encoded P-acquisition genes. These genes encompassed regulatory pathways, transport systems, organic P mineralization, and inorganic P solubilization. Regulatory and transporter genes were the most abundant categories, with phoB, phoP, and ugpC among the most frequently detected. When additional analyses were performed using habitat-specific P classifications and continuous P gradients, these associations appeared weak and were not significant after multiple-testing correction. These results suggest that plasmid-encoded P-acquisition genes are broadly distributed across environments rather than tightly constrained by measured soil P levels, while taxonomic assignment revealed that Pseudomonadota were the predominant plasmid hosts, followed by Bacillota and Actinobacteriota, suggesting broad host diversity.

CONCLUSIONS: This study provides a genomic overview of plasmid-borne genes associated with P acquisition in soils. Our results show that these genes are widespread across plasmids from diverse environments and host taxa, suggesting that the soil mobilome may represent an important reservoir of functions related to microbial P metabolism. While the presence and relative abundance of these genes indicate their potential ecological relevance, functional expression and ecological impact remain to be experimentally validated. These findings expand current knowledge of plasmid contributions to nutrient cycling and highlight the mobilome as a potential target for future studies aiming to better understand microbial strategies for P acquisition in soil ecosystems.}, } @article {pmid41943240, year = {2026}, author = {Zhu, W and Qian, J and Peng, M and Li, Y and Hu, J}, title = {Post-COVID-19 Area Postrema Syndrome With SARS-CoV-2 in CSF: A Dual-Case Report and Review of the Literature.}, journal = {Immunity, inflammation and disease}, volume = {14}, number = {4}, pages = {e70421}, pmid = {41943240}, issn = {2050-4527}, support = {ZDXM2024003//Wenshan Prefecture People's Hospital 2024 Annual Internal Scientific Research Key Projects/ ; }, mesh = {Humans ; Female ; *COVID-19/complications/cerebrospinal fluid ; *SARS-CoV-2 ; *Area Postrema/pathology/virology ; Middle Aged ; Betacoronavirus ; Magnetic Resonance Imaging ; *Neuromyelitis Optica/cerebrospinal fluid ; Immunoglobulin G/cerebrospinal fluid ; Aquaporin 4/immunology ; Autoantibodies/cerebrospinal fluid ; Adult ; }, abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a rare autoimmune astrocytopathy characterized by inflammatory demyelinating lesions in the central nervous system. Area postrema syndrome (APS), marked by intractable nausea, vomiting, and hiccups, is a recognized but less common initial manifestation. Post-infectious autoimmunity triggered by SARS-CoV-2 has been increasingly associated with NMOSD pathogenesis; however, the clinical significance of direct viral neuroinvasion and its relationship to divergent patient outcomes remains poorly understood.

METHODS: We report two female patients who developed isolated APS shortly after COVID-19 infection. Both patients underwent comprehensive neurological evaluation, including brain and spinal magnetic resonance imaging (MRI), cerebrospinal fluid (CSF) analysis with metagenomic next-generation sequencing (mNGS), and serological testing for aquaporin-4 immunoglobulin G (AQP4-IgG), myelin oligodendrocyte glycoprotein immunoglobulin G (MOG-IgG), and glial fibrillary acidic protein immunoglobulin G (GFAP-IgG) using cell-based assays. Clinical outcomes were compared in the context of antibody serostatus and treatment strategies. A review of the relevant literature on post-COVID NMOSD was also performed.

RESULTS: Both patients presented with intractable vomiting and hiccups following SARS-CoV-2 infection, and MRI demonstrated isolated T2/FLAIR hyperintense lesions in the dorsal medulla consistent with area postrema involvement. SARS-CoV-2 RNA sequences were detected in the CSF of both patients via mNGS, suggesting direct viral neuroinvasion or blood-brain barrier compromise. Despite similar initial presentations, their outcomes diverged dramatically. Patient 1 was AQP4-IgG negative, responded well to immunotherapy with intravenous immunoglobulin and corticosteroids followed by mycophenolate mofetil maintenance, and remained relapse-free at 12-month follow-up with significant lesion regression on MRI. Patient 2 was AQP4-IgG positive in both serum and CSF, and despite acute treatment, experienced a fatal relapse 6 months later with longitudinally extensive transverse myelitis while on low-dose prednisone monotherapy.

CONCLUSIONS: Isolated APS may represent an important yet under-recognized manifestation of post-COVID-19 autoimmune neuroinflammation. Detection of SARS-CoV-2 in CSF supports a role for direct viral neuroinvasion as a localized inflammatory stimulus. AQP4-IgG serostatus serves as a critical prognostic determinant: seronegativity is associated with a benign, monophasic course, whereas seropositivity mandates prompt initiation of potent immunosuppressive therapy to prevent devastating relapses. Clinicians should maintain a high index of suspicion for NMOSD in patients with unexplained persistent vomiting following COVID-19, and perform urgent neuroimaging and antibody testing for early risk stratification.}, } @article {pmid41943413, year = {2026}, author = {Liu, F and Xie, F and Zhong, Q and Lin, X and Yang, Q and Li, Y and Huang, C and Huang, Q and Xu, L and Zhong, J}, title = {Application Value of Metagenomic Next-Generation Sequencing Using Bronchoalveolar Lavage Fluid and Blood Samples in Patients with Severe Pneumonia Complicated with Bloodstream Infection.}, journal = {Polish journal of microbiology}, volume = {75}, number = {1}, pages = {75-83}, pmid = {41943413}, issn = {2544-4646}, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Retrospective Studies ; *Pneumonia/microbiology/blood/complications ; Male ; Bacteria/isolation & purification/genetics/classification ; Aged ; Middle Aged ; Fungi/isolation & purification/genetics/classification ; Sensitivity and Specificity ; }, abstract = {This study was designed to systematically evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) using blood and bronchoalveolar lavage fluid (BALF) samples in patients with severe pneumonia complicated by bloodstream infections. A retrospective analysis of 30 patients with severe pneumonia-bloodstream infection admitted to our hospital from January 2018 to December 2022 was conducted, and the potential pathogens in both BALF and blood samples were simultaneously detected by conventional microbial examination (traditional group) and mNGS tests (mNGS group), comparing the differences in pathogen species and detection rates between the two methods. There was no significant difference in the positivity of pathogen detection in BALF and blood samples using mNGS (p = 0.492). The proportion of bacteria (p = 0.005) and fungi (p = 0.037) detected by BALF mNGS was higher than that by blood mNGS, but there was no significant difference in the proportion of viruses (p = 0.121). In addition, the positive rate of pathogen detection by mNGS in BALF and blood samples was significantly higher than that by traditional methods (p < 0.01). BALF mNGS demonstrated superior diagnostic sensitivity for bacterial and fungal pathogen detection compared to blood mNGS and conventional culture methods. Notably, blood specimens retained distinct advantages in identifying specific viral infections. Future prospective studies with larger sample sizes are warranted to validate these findings.}, } @article {pmid41943678, year = {2026}, author = {Zhou, G and Chen, L and Ma, L and Liu, J and Feng, B and Zhang, C and Ma, D and Zhang, H and Liang, Y and Zhang, J}, title = {Sodicity Thresholds Alter Biodiversity-Multifunctionality Relationships Through Fungal Dominance and Microbial Trait-Based Strategies.}, journal = {Global change biology}, volume = {32}, number = {4}, pages = {e70843}, doi = {10.1111/gcb.70843}, pmid = {41943678}, issn = {1365-2486}, support = {42277336//National Natural Science Foundation of China/ ; 42425703//National Natural Science Foundation of China/ ; BK20221561//Natural Science Foundation of Jiangsu Province/ ; CX(24)1003//Jiangsu Agricultural Science and Technology Innovation Fund/ ; NMKJXM202401-01//Key Special Projects of the "Science and Technology Revitalizing Inner Mongolia" Action Fund/ ; CARS-03//China Agriculture Research System/ ; CARS-52//China Agriculture Research System/ ; //Chinese Academy of Sciences/ ; }, mesh = {*Soil Microbiology ; *Biodiversity ; *Fungi/physiology ; *Soil/chemistry ; China ; Ecosystem ; *Sodium/analysis ; }, abstract = {Increasing soil sodicity represents a critical threat to global agroecosystem health, but how exchangeable sodium percentage (ESP) modulates relationships between biodiversity and ecosystem multifunctionality (BEF) is unresolved. We surveyed 378 soil samples from 189 paired saline-sodic lands and adjacent farmlands across four major saline-sodic regions of China spanning ~2000 km. Random forest models demonstrated that ESP emerged as the primary abiotic predictor of soil multifunctionality, defining sharp thresholds ~13% for cropped systems and ~44% for natural saline-sodic habitats beyond which BEF relationships undergo fundamental reorganization. These breaks coincide with significant shifts toward fungal dominance within microbial communities. Notably, under hyper-sodic conditions, fungal diversity emerges as essential for sustaining ecosystem functions. Metagenomic and trait-based analyses further characterized three functional dimensions of microbial trait-based strategies-environmental responsiveness, metabolic capacity, and nutrient recycling. We then mechanistically linked microbial life-history strategies to soil multifunctionality. Our results showed that in farmland soils, nutrient recycling was positively associated with multifunctionality, whereas metabolic capacity was negatively correlated with multifunctionality, and in saline-sodic soils metabolic capacity exhibited a positive association with multifunctionality. Collectively, this study establishes ESP as a key regulator of BEF relationships and microbial eco-evolutionary adaptations, providing mechanistic insights for managing saline-sodic soils under escalating climate change.}, } @article {pmid41944124, year = {2026}, author = {Cai, S and Li, E and Sun, T and Huang, A and Zhang, Y and Xiong, X and Cheng, B and Chai, H and Zhang, J and Zhang, J and Hu, C and Zhang, W}, title = {Amine-Containing Micropollutants Exposure Reshapes Sludge Anaerobic Digestion via Enzymatic Inhibition and Stress-Mediated Alteration of Methanogenic Pathways.}, journal = {Environmental science & technology}, volume = {60}, number = {21}, pages = {15124-15138}, doi = {10.1021/acs.est.5c10074}, pmid = {41944124}, issn = {1520-5851}, mesh = {*Anaerobiosis/drug effects ; *Methane/metabolism ; *Amines/metabolism/toxicity ; *Sewage/analysis/microbiology ; Stress, Physiological/physiology ; Acetate Kinase/metabolism ; Methanobacterium/physiology ; *Water Pollutants, Chemical/toxicity ; Water Purification ; Wastewater/chemistry/microbiology ; Waste Disposal, Fluid/methods ; }, abstract = {Amine-containing micropollutants (AMPs), a class of structurally diverse polar compounds characterized by one or more amine functional groups, are frequently detected in wastewater sludge. However, the anaerobic transformation of these compounds and their impacts on microbial metabolism during anaerobic digestion (AD) remain poorly understood. In this work, six representative AMPs were selected to cover 16 structurally diverse primary, secondary, tertiary amine, and quaternary ammonium functionalities. α-C hydroxylation and N-acetylation were identified as the dominant initial reactions among the detected transformation products (TP), collectively accounting for 42.6% of all identified TPs. Furthermore, compound-specific differences in metabolic disturbance were observed. Quaternary ammonium compounds, N-dodecyl-N-benzyl-N,N-dimethylammonium chloride (DDBAC) and N,N-Didodecyl-N,N-dimethylammonium chloride (DDDAC) markedly reduced acetate kinase activity by 10.69 and 14.28%, respectively, and resulted in methane production yield reductions of 88.97 and 88.19%. The genome-centric metagenome revealed that exposure to AMPs prompted the reassembly of the microbial community, altered its functional attributes, and disturbed interspecies cross-feeding interactions. Specifically, AMPs triggered a shift in the methanogenic consortium from mixotrophic Methanosarcina flavescens to hydrogenotrophic Methanobacterium sp., owing to the latter's metabolic versatility, vigorous proliferation, and superior energy conservation. These findings indicated that the chemical properties of amine functional groups have effects on anaerobic biotransformation pathways and microbial energy metabolism, providing mechanistic insight into AMPs toxicity and guiding mitigation strategies to enhance the stability and resilience of full-scale AD systems.}, } @article {pmid41944276, year = {2026}, author = {Feng, Z and Lu, JN and Wang, G and Li, M and Chen, D and Chen, C and Jiang, Y and Yu, H and Chao, Y and Tang, YT and Jin, C and Baker, AJM and Morel, JL and Xu, Z and Wang, S and Qiu, R}, title = {Beyond Metal(loid) Immobilization: Redox-Stratified Biocrusts Shield Humid Mining Regions.}, journal = {Environmental science & technology}, volume = {60}, number = {20}, pages = {14507-14521}, doi = {10.1021/acs.est.5c13821}, pmid = {41944276}, issn = {1520-5851}, mesh = {*Mining ; Oxidation-Reduction ; Metals ; Soil Microbiology ; Humidity ; Soil ; }, abstract = {Biological soil crusts (biocrusts) develop vertical redox-microbial-nutrient stratification that regulates hydrological and elemental cycles and contributes to ecological restoration in extreme environments, including mining regions. However, the roles of this heterogeneity in metal(loid) immobilization remain unclear, particularly in humid regions, where pronounced redox and microbial stratification may foster unrecognized stabilization mechanisms. We integrated physicochemical characterization with bioinformatic analysis to reveal stratified microbial communities and metabolic potentials in humid tailings biocrusts. Biocrusts exhibited stratified functionality through the upper photoautotrophic layer (PL) and the lower heterotrophic layer (HL). In the PL, Cyanobacteria and SWB02 formed a self-reinforcing oxygen barrier through clay-silt enrichment (2.8-fold higher than bare tailings sand) and extracellular polysaccharide accumulation (18-fold), which swelled upon hydration to physically hinder oxygen infiltration, confining Gammaproteobacteria-associated iron-manganese oxide immobilization to this layer. Beneath this barrier, the HL harbored sulfidogenic potential through microbes enriched in hydB (17.4-fold) and phsC (3.4-fold) genes, including Bacteroidota and Desulfobacterota, supporting a potential mechanism for metal(loid) sequestration via sulfide formation in underlying tailings, where sulfur occurred exclusively as sulfides at 5 cm depth. This barrier-mediated effect may outweigh metal(loid) immobilization within biocrusts. Our findings elucidate biocrust-mediated protection against metal(loid)s and provide theoretical support for remediation in humid mining regions.}, } @article {pmid41944309, year = {2026}, author = {Wang, Z and Zhang, J and Lu, H and Ni, J and Yang, S and Shi, Y and Zhang, S and Zhang, P and Liu, L}, title = {Gemella morbillorum Promotes Colorectal Carcinogenesis: LPBDCP-Mediated Invasion Activates Ras Signaling and Destabilizes p53.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {34}, pages = {e17245}, doi = {10.1002/advs.202517245}, pmid = {41944309}, issn = {2198-3844}, support = {82473713//National Natural Science Foundation of China/ ; 82173602//National Natural Science Foundation of China/ ; }, mesh = {*Colorectal Neoplasms/microbiology/metabolism/genetics/pathology ; Animals ; Humans ; *Tumor Suppressor Protein p53/metabolism/genetics ; Mice ; Signal Transduction ; *Carcinogenesis/genetics/metabolism ; *ras Proteins/metabolism/genetics ; }, abstract = {Gut microbiota dysbiosis promotes colorectal cancer (CRC) tumorigenesis. A global fecal metagenomic analysis identified Gemella morbillorum as a key contributor to the CRC-associated microbiota. Fluorescence in situ hybridization revealed that Gemella morbillorum is enriched in CRC tumor tissues compared to adjacent normal tissues. In vitro and in vivo experiments elucidated the oncogenic effects of Gemella morbillorum on human CRC cell lines and mouse models. Multimodal imaging shows that Gemella morbillorum can internalize into host cells. RNA sequencing, co-immunoprecipitation, and mass spectrometry identified that Gemella morbillorum invades host cells via interaction between its LysM peptidoglycan-binding domain protein (LPBDCP) and host cell surface transmembrane protein TMEM140. This invasion triggers Ca[2] [+] influx, downregulates RASA4, and activates the PI3K-AKT-NF-κB and RAF-MEK-ERK signaling pathways. Following invasion, Gemella morbillorum secretes NAD-dependent protein deacetylase (NDPD), which induces p53 deacetylation and degradation. Collectively, these events accelerate cell proliferation, shorten the cell cycle, and inhibit apoptosis, thereby promoting malignant transformation. Genetic knockout of LPBDCP or TMEM140 effectively inhibits bacterial invasion and abrogates the oncogenic effects of Gemella morbillorum. In tumor-bearing mice, knockout of LPBDCP or NDPD eliminates the tumor-promoting effects of Gemella morbillorum. These results underscore Gemella morbillorum's role in CRC and pinpoint potential intervention targets.}, } @article {pmid41944841, year = {2026}, author = {Tom, A and Kurian, PS and Philip, S and Mathew, D and Vijayaraghavan, R and Sumbula, V and Varkey, ME}, title = {Exploratory profiling of microbial communities associated with tapping panel dryness in Hevea brasiliensis.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41944841}, issn = {1432-072X}, abstract = {Tapping Panel Dryness (TPD) is a complex physiological disorder in Hevea brasiliensis that leads to the cessation of latex flow, causing significant economic loss, yet its underlying cause remains unclear. Anatomical investigation of bark samples collected from TPD-affected samples exhibited deformed latex vessels, blocked sieve tubes, and DNA-containing bodies within phloem elements. Metagenomic profiling indicated largely similar microbial composition and diversity between healthy and TPD-affected bark samples, except for the presence of low-abundance taxa such as phytoplasma only in affected samples. However, predicted metabolic pathways differed significantly between healthy and TPD samples. The combined anatomical, cytological, and molecular evidences in the current study supports the potential involvement of a biotic factor in the etiology of TPD.}, } @article {pmid41946009, year = {2026}, author = {Sutaoney, P and Singh, P and Malakar, S and Arsi, L and Ghosh, P}, title = {Microbial lipases: Catalyzing sustainable solutions for industrial innovations.}, journal = {Enzyme and microbial technology}, volume = {198}, number = {}, pages = {110869}, doi = {10.1016/j.enzmictec.2026.110869}, pmid = {41946009}, issn = {1879-0909}, mesh = {*Lipase/metabolism/chemistry/genetics ; *Bacteria/enzymology/genetics ; *Fungi/enzymology ; Biocatalysis ; Substrate Specificity ; Protein Engineering ; Biotechnology ; *Bacterial Proteins/metabolism/chemistry/genetics ; Industrial Microbiology ; Enzyme Stability ; }, abstract = {Microbial lipases are multifaceted biological catalyst that have surfaced as a key driver in various industries and are both eco-friendly and cost efficient.In large scale applications, lipases produced from bacteria, fungi and yeasts function better than their equivalents generated from plants and animals due to their wide substrate specificity, catalytic efficacy and stability under physicochemical circumstances. Recent developments in microbial lipase research, including sources, screening techniques, assay procedures, production methods, purification tactics, and biochemical characterisation, are critically examined in this review.The structural and mechanistic elements that control lipase function-such as lid domains, interfacial activation, and catalytic triads-are given special attention since they all have an impact on the stability, specificity, and industrial performance of the enzyme.Large-scale screening is done to check for the production of lipase in Bacillus sp., Achromobacter sp., Alcaligenes sp., Arthrobacter sp., Pseudomonas sp., and Penicillium sp. Additionally, the combination of synthetic biology, metagenomics, CRISPR-Cas technologies, enzyme engineering, and AI-assisted modelling is emphasized as a revolutionary strategy for identifying and customizing lipases with desired characteristics, including extreme environment microbes and application-specific variants.The review also highlights the growing industrial uses of microbial lipases in the bio-fuel, food and beverage, detergent, textile, leather, pharmaceutical, and medical industries, highlighting their contribution to the development of economically feasible and ecologically safe bioprocesses. All things considered, microbial lipases are an important biotechnological tool for developing sustainable industrial innovation and green chemistry.}, } @article {pmid41946242, year = {2026}, author = {Yang, Y and Wang, Y and Li, J and Long, Y and Xiao, X and Fang, C and Hu, L}, title = {Temperature-dependent demethylation of methylarsenic by methanogens: Linking carbon metabolism to arsenic speciation in landfills.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141986}, doi = {10.1016/j.jhazmat.2026.141986}, pmid = {41946242}, issn = {1873-3336}, mesh = {Temperature ; Waste Disposal Facilities ; Demethylation ; *Methane/metabolism ; *Arsenic/metabolism ; *Cacodylic Acid/metabolism ; *Carbon/metabolism ; *Water Pollutants, Chemical/metabolism ; *Arsenicals/metabolism ; }, abstract = {The environmental risk posed by arsenic (As) in landfills, driven by its high concentrations and mobility, is a significant concern. While inorganic arsenate [As(V)] and arsenite [As(III)] are dominant, the microbial-mediated conversion of these inorganic species into less toxic methylated arsenicals (MAs) is a key attenuation pathway. However, the reverse process-the demethylation of MAs back to more toxic inorganic forms-and its microbial drivers in landfills are not well understood. The availability of substrates and temperature are important growth factors and environmental factors that affect the activity and community structure of MA. This study investigated the demethylation of dimethylarsinic acid (DMAs) by methanogenic communities enriched from the leachate saturated zone (LSZ) under different thermal fields (15℃, 35℃, 55℃). We found that methylotrophic methanogens were the primary agents of DMAs demethylation, with the highest efficiency observed at mesophilic temperature (35℃), followed by thermophilic (55℃) and psychrophilic (15℃) conditions. Interestingly, methane (CH4) release exhibited a distinct trend (55℃ > 35℃ > 15℃), indicating an inconsistency between methanogenic activity and MAs demethylation efficiency at higher temperatures. A partial least squares path model (PLS-PM) revealed that both the abundance of methanogenic functional genes and CH4 release had a significant negative effect on As species (path coefficients of -0.615 and -0.376, respectively). Metagenomic analysis identified Methanosarcina as the dominant methylotrophic genus at 35℃, while Methanosarcina thermophila and JAULTD01 sp. were key drivers at 55℃. Our findings demonstrate that methanogens dynamically couple carbon metabolism to As speciation, and this coupling can be reshaped by temperature-mediated shifts in the dominant methanogens and their functional genes distribution.}, } @article {pmid41946252, year = {2026}, author = {Deng, B and Ren, ZH and Ren, CY and Zhao, HP}, title = {Inhibiting Cr(VI)-mediated ARG dissemination in wastewater: Synthetic antioxidant-, extracellular polymeric substance-, and nuclease-producing microbiome targeting ROS, MGEs, and ARG-MRG co-occurrence.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141985}, doi = {10.1016/j.jhazmat.2026.141985}, pmid = {41946252}, issn = {1873-3336}, mesh = {*Chromium/toxicity ; *Wastewater/microbiology ; Reactive Oxygen Species/metabolism ; Extracellular Polymeric Substance Matrix/metabolism ; *Antioxidants/pharmacology ; *Microbiota/drug effects ; *Water Pollutants, Chemical/toxicity ; Plasmids ; Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; }, abstract = {Heavy metals (HMs) trigger the sustained enrichment and dissemination of antibiotic resistance genes (ARGs) by exerting selective pressure, and there is an urgent need for effective and environmentally friendly control strategies. Herein, we found that long-term (180 d) hexavalent chromium [Cr(VI)] stress (10 mg/L) could facilitate the enrichment of multidrug-resistant plasmids (e.g., blaTEM and sul1) and significantly increase (p < 0.05) the conjugative transfer frequency. Subsequently, we constructed a synthetic carotenoid- and extracellular nuclease gene exeM-producing microbiome centered on Deinococcus radiodurans R1, which synthesizes and secretes extracellular polymeric substances (EPS) via the Wzx/Wzy-dependent pathway, thereby alleviating environmental oxidative stress by adsorbing Cr(VI) (over 85%) and scavenging ROS (approximately 18-26-fold). qPCR results demonstrated that the synthetic microbiome effectively reduced ARG abundances, along with the mobile genetic elements traG and intI1 (by more than one order of magnitude, MGEs) and the metal resistance gene chrA (by more than two orders of magnitude, MRG). Electron microscopy and metagenomic analysis demonstrated that the synthetic microbiome could further reduce the co-occurrence of ARGs and MRGs (e.g., tetA, chrA, and chrB) by impairing plasmid integrity and preserving cell membrane integrity (ompC, oprC, plsB, and fabR), thus inhibiting horizontal gene transfer. In addition, it reduced the abundance of Pseudomonadota (the host harboring ARGs and MGEs, p < 0.05) by 33-48%. This study provides a sustainable bioremediation strategy for controlling the dissemination of ARGs in heavy metal-polluted wastewater.}, } @article {pmid41946403, year = {2026}, author = {Bamanu, B and Liu, Y and Wan, H and Tian, Z and Zhao, Y}, title = {Deciphering β-lactam stress response in anammox systems: Off-target enzyme binding, electron transfer compensation and microbial collaboration.}, journal = {Bioresource technology}, volume = {452}, number = {}, pages = {134561}, doi = {10.1016/j.biortech.2026.134561}, pmid = {41946403}, issn = {1873-2976}, mesh = {Ammonium Compounds ; Oxidation-Reduction ; *Cephalexin/toxicity ; *Bioreactors ; *Microbial Consortia/drug effects ; Molecular Docking Simulation ; Stress, Physiological ; *Water Purification ; *Water Pollutants, Chemical/toxicity ; }, abstract = {The prevalence of antibiotics in pharmaceutical and municipal wastewater poses a critical threat to biological wastewater treatment, especially the anaerobic ammonium oxidation (anammox) process. This study investigated the inhibitory mechanism of cephalexin (CFX), a β-lactam antibiotic, on anammox performance. Exposure to 100 mg/L CFX reduced nitrogen removal efficiency to 48.5% and suppressed specific anammox activity and heme c content, while lower concentrations (≤10 mg/L) caused no significant inhibition. Molecular docking indicated strong binding affinities of CFX toward key functional enzymes, including nitrite reductase and hydrazine synthase, with binding energies of -7.6 and -7.4 kcal/mol, respectively, suggesting off-target enzyme interference rather than direct β-lactam-specific inhibition. The system showed reversible inhibition with multi-level adaptation, including enhanced extracellular polymeric substances secretion, strengthened antioxidant defense, elevated electron transport activity, and microbial community restructuring. Metagenomic analysis revealed enrichment of β-lactamase, efflux pump, and antioxidant-related genes during recovery, supporting detoxification and adaptive resistance. These insights establish a mechanistic framework for designing resilient anammox systems capable of recovering from β-lactam antibiotic shocks in practical wastewater treatment applications.}, } @article {pmid41946559, year = {2026}, author = {Campo-Beamud, C and Adan Ruiz, A and Bastante Quijano, J and Campo Beamud, E and Gómez-Romero, FJ and Fernández Ruíz, AJ and Copete, S}, title = {Publicly available multimodal large language models for ocular surface infections: benchmarking against corneal specialists in triage, diagnosis and treatment.}, journal = {The British journal of ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1136/bjo-2025-328867}, pmid = {41946559}, issn = {1468-2079}, abstract = {BACKGROUND/AIMS: Ocular surface infections remain a major cause of visual loss worldwide, yet diagnosis often relies on slow or insensitive microbiological techniques. Artificial intelligence may complement emerging molecular tools by supporting rapid triage and diagnostic reasoning. This study benchmarked publicly available multimodal large language models (LLMs) against corneal specialists for the diagnosis, treatment and urgency triage of infectious keratitis and conjunctivitis.

METHODS: A single-centre diagnostic-accuracy study included 60 microbiologically confirmed infectious keratitis and conjunctivitis cases, each comprising a slit-lamp photograph and a paired clinical vignette. Six multimodal LLMs (GPT-4o, GPT-5, Gemini, Claude, Perplexity and Grok) were evaluated for diagnosis, treatment and urgency triage under three input conditions (image-only, text-only and image+text). Outputs were compared with two corneal specialists.

RESULTS: LLM performance depended strongly on input modality. Image-only accuracy was lowest (best GPT-5, 61.4%; κ=0.38) with frequent misclassification of fungal and Acanthamoeba keratitis and hallucinations confined to this setting. Text input improved results (GPT-5, 83.3%; κ=0.78), though accuracy remained below specialists (87-90%; κ≈0.8). Combined image+text achieved near-human accuracy without consistently surpassing corneal specialists (Perplexity 96.7%; κ=0.95; GPT-5 91.7%; κ=0.87). Treatment accuracy remained lower (81-85% vs 90-98%), while urgency triage matched experts in multimodal input.

CONCLUSION: Publicly accessible multimodal LLMs can approach expert-level performance in diagnosis and triage when provided with clinical context and slit-lamp images. Gaps in therapeutic reasoning and rare pathogen recognition underscore the need for targeted refinement and validation. These models may complement specialist care, supporting rapid triage and integration with molecular or metagenomic diagnostics, especially in resource-limited settings.}, } @article {pmid41947210, year = {2026}, author = {Tang, G and Zhang, C and Zhang, X and Liu, H and Suen, G and Yao, J and Zhang, J}, title = {Multi-omics revealed the effects of rumen to blood path on early lactation performance in transition dairy cows.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41947210}, issn = {2049-2618}, support = {2023YFE0111800//National Key Research and Development Program of China/ ; 2024-JSGG-021//the National Center of Technology Innovation for Dairy/ ; 2024BBF01006//Key Research and Development Project of Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology ; Female ; *Lactation/physiology ; Milk/chemistry/metabolism ; Multiomics ; Metagenomics/methods ; Postpartum Period ; Prevotella/isolation & purification/genetics ; Fatty Acids, Volatile/metabolism ; Methanobrevibacter/genetics/isolation & purification ; Metabolomics ; Succinivibrionaceae/isolation & purification/genetics ; Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The transition period is vitally important to the life cycle of dairy cows. However, the function of the microbiota during both pre- and post-partum and their relationship with ruminal, plasma, and milk metabolites still require systematic investigation. To address this, the 7 highest- and 7 lowest-performing animals among a cohort of 100 dairy cows were selected based on their postpartum energy-corrected milk yield. Rumen fluid and plasma samples were collected during both pre- and post-partum periods, whereas milk samples were obtained postpartum. Shotgun metagenomics of rumen contents in addition to metabolomics of rumen, plasma, and milk samples were performed to evaluate the associations between ruminal microbes and early lactation performance in transition dairy cows.

RESULTS: Compared with prepartum cows, postpartum high-yield cows had greater concentrations of ruminal volatile fatty acids and plasma total bile acid. Moreover, plasma urea nitrogen and most amino acids, peptides, and their derivatives in plasma and milk were increased in postpartum high-yield cows, relative to postpartum low-yield cows. Metagenomic analysis revealed that the relative abundances of several species within the Prevotella, Succinimonas, Succinatimonas, and Methanosphaera increased, while other bacteria belong to Alistipes and Bacteroides, and archaeal Methanobrevibacter species decreased in postpartum cows, particularly in postpartum high-yield cows. Co-occurrence network and correlation analysis suggested that Prevotella and Succinatimonas were negatively correlated to Alistipes, Bacteroides, and Methanobrevibacter, potentially contributing to the nutritionally efficient phenotype of postpartum high-yield cows. A metabolic pathway analysis of our metagenomic data revealed that postpartum high-yield cows possessed more microbial genes involved in starch utilization and amino acid synthesis, while a wide range of microbial genes involved in cellulose utilization, acetogenesis, and amino acid degradation were found in prepartum cows with low-yield in postpartum. A structural equation model analysis showed that the increased relative abundances of Prevotella tf.2-5 and Succinatimonas CAG_777 were related to greater concentrations of plasma chenodeoxycholic acid glycine conjugate, milk 5-Methoxytryptophan, and energy-corrected milk yield. Finally, pan-genomic analysis confirmed that Alistipes, Bacteroides, and Methanobrevibacter possess genetic conservation of both hydrogenases and dehydrogenases, which may contribute to energy loss in the rumen via hydrogen dissipation.

CONCLUSION: In summary, our findings provide a fundamental understanding of how microbiome-dependent mechanisms contribute to early lactation performance in dairy cows during the transition period. The increased abundance of Prevotella, Succinimonas, and Succinatimonas in postpartum cows suggest that they are important microbes during the transition period and may help in coping with metabolic challenges, while improving nutrient utilization efficiency during this period. Our study underscores the importance of the ruminal microbiome during the transition period and highlights the need for rumen-based nutritional intervention strategies to improve production efficiency in ruminants. Video Abstract.}, } @article {pmid41947478, year = {2026}, author = {Yang, X and Zhu, C and Liu, B and Yang, P and Cao, Z and Liang, J and Hu, J and Yu, Q and Zhong, Y and Du, W and Chow, J and Yan, S and Liu, H and Li, L and Wang, T and Gu, Y and Ma, G}, title = {Astragaloside IV Exhibited Antidiabetic Effects by Improving Glucose Metabolism, Repairing Damaged Gut Barrier and Regulating Intestinal Microbiota.}, journal = {Phytotherapy research : PTR}, volume = {}, number = {}, pages = {}, doi = {10.1002/ptr.70205}, pmid = {41947478}, issn = {1099-1573}, support = {81374051//National Natural Science Foundation of China/ ; 81873078//National Natural Science Foundation of China/ ; 82074109//National Natural Science Foundation of China/ ; 82374133//National Natural Science Foundation of China/ ; }, abstract = {Astragaloside IV (AS-IV), a main active ingredient derived from Astragali Radix, displays a favorable effect in treating type 2 diabetes mellitus (T2DM). This study was aimed to figure out its antidiabetic mechanisms. The db/db mice were treated with AS-IV, and the metabolism phenotype and epithelial barrier permeability were tested. Trans-epithelial resistance assay was performed in Caco-2 cells. Metagenomic sequencing was used to determine the gut microbiota composition and function. The content of short-chain fatty acid (SCFA) in feces was determined using Agilent 8890-5977B GC-MS. Despite increasing mice body weight, AS-IV significantly reduced hyperglycemia in the db/db mice, decreased the ratio of liver weight/body weight, alleviated hepatic total cholesterol and triglyceride levels. AS-IV reduced inflammation through suppressing pro-inflammatory genes (Il1b, Tnf, Ccl2) and elevating anti-inflammatory genes (Il10, Il4, Il13, Il33) in the colonic epithelium. AS-IV also reversed the increased intestinal permeability and decreased expression of tight junction (TJ) proteins Claudin-1, ZO-1 in the db/db mice and Claudin-1, Occludin in Caco-2 cells. Additionally, metagenomic sequencing showed AS-IV altered composition and function of gut microbiota. The 80 species of gut microbiota were markedly changed, e.g., boosting of Alistipes spp. and Prevotella copri, decreasing of relative abundance of Ruminococcus gnavus and Enterocloster bolteae. AS-IV upregulated the SCFA related pathway, increased the content of SCFA, upregulated the transcription levels of SCFA receptors (i.e., GPR41, GPR43 and GPR109a), thereby improved glucose metabolism in the db/db mice. These findings demonstrate that AS-IV exhibited favorable antidiabetic effects by improving glucose metabolism and altering intestinal microbiota symbiosis via repairing the damaged gut barrier. This study will provide valuable reference for the development of new antidiabetic drugs and medication of T2DM.}, } @article {pmid41947790, year = {2026}, author = {Sun, W and Li, Y and Su, J and Mao, S and Yang, S and Zhu, Y and Liu, Y and Ma, J and You, W and Zhang, Y and Guo, H and Xing, G and Li, S and Yan, Q and Ma, X}, title = {Multi-kingdom metagenomic characterization of the gut bacteriome, mycobiome, and virome in chronic functional constipation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1744020}, pmid = {41947790}, issn = {2235-2988}, mesh = {Humans ; *Virome/genetics ; Metagenomics ; Feces/microbiology/virology ; *Fungi/classification/genetics/isolation & purification ; *Constipation/microbiology/virology ; Bacteria/classification/genetics/isolation & purification ; *Mycobiome/genetics ; *Gastrointestinal Microbiome/genetics ; Dysbiosis/microbiology ; Metagenome ; Female ; Chronic Disease ; Viruses/classification/genetics/isolation & purification ; Shotgun Sequencing ; }, abstract = {BACKGROUND: Chronic functional constipation (CFC) is a common gastrointestinal disorder increasingly linked to gut microbiome dysbiosis. However, multi-kingdom metagenomic characterization of bacterial, fungal, and viral communities in CFC remains limited.

METHODS: Fecal samples from 53 CFC patients and 48 healthy controls were analyzed using whole-metagenome shotgun sequencing. Microbial composition, function, cross-kingdom interactions, and diagnostic potential were evaluated using diversity analyses, KEGG annotation, network analysis, and random forest modeling.

RESULTS: Compared with healthy controls, CFC patients exhibited marked alterations across multiple microbial kingdoms. The gut bacteriome showed significant community-structure shifts despite comparable α-diversity, characterized by depletion of health-associated Firmicutes (e.g., Faecalibacterium and Roseburia) and enrichment of Proteobacteria (e.g., Klebsiella). The mycobiome displayed selective changes in diversity and composition, with several potentially pathogenic fungal taxa enriched in CFC (e.g., Fusarium sp. c181). In the virome, community composition differed significantly between groups, with higher viral richness in CFC and widespread depletion of diverse bacteriophages in CFC patients. Functional profiling suggested feature-level functional differences without a clear global shift, including reduced carbohydrate transport and utilization pathways and relatively higher abundance of stress-response and metabolic adaptation modules in CFC. Cross-kingdom network analysis demonstrated substantially denser microbial interactions in CFC, dominated by viral associations, with Faecalibacterium prausnitzii and Faecalibacterium_SGB15346 acting as central hubs. Machine-learning models showed strong discriminatory power for CFC classification based on bacterial and viral features, whereas fungal features contributed less.

CONCLUSIONS: CFC is associated with coordinated multi-kingdom gut microbiome dysbiosis involving bacteria, fungi, and viruses, accompanied by functional shifts and intensified cross-kingdom interactions. Bacterial and viral signatures show strong potential as microbiome-based biomarkers for CFC, highlighting the importance of integrating multi-kingdom analyses to better understand disease-associated gut ecosystem alterations.}, } @article {pmid41948038, year = {2026}, author = {Howells, AEG and Santana, M and Cook, EM and Orrill, B and Boyer, G and Debes, RV and Fecteau, KM and Colman, DR and Boyd, ES and Shock, EL}, title = {Pushing the upper temperature limit of methanotrophy in continental hydrothermal ecosystems, active biological methane oxidation in hot springs of Yellowstone National Park.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1736896}, pmid = {41948038}, issn = {1664-302X}, abstract = {Methane oxidation in terrestrial geothermal systems is an understudied process contributing to carbon cycling in extreme environments. We combined geochemical analyses, 16S rRNA gene amplicon sequencing, shotgun metagenome sequencing, and [14]CH4 microcosm assays across 61 Yellowstone hot springs spanning pH 1.9-9.0 and temperatures of 28.6-92.2 °C to survey hydrothermal systems for methanotrophy. Bacterial aerobic methanotroph phylotypes were detected at multiple sites, including Verrucomicrobia (order S-BQ2-57) and Alphaproteobacteria, with the family Methylocystaceae having the highest relative abundance among bacterial methanotroph phylotypes. No known archaeal anaerobic methanotrophs were observed. Biological methane oxidation was widespread, occurring at 14 of 17 experimental sites under both ambient and air-amended conditions. Rates were highest at CH4-rich, NH3-poor sites dominated by bacterial methanotrophs, consistent with energy supply predictions integrating CH4/O2 and CH4/NH3 concentration ratios. Conversely, NH3-rich, energy-rich sites exhibited lower methane oxidation rates (MOR) and were dominated by archaeal ammonia oxidizers, primarily Candidatus Nitrosocaldus, suggesting chemical competitive inhibition of NH3 on methanotrophy. Remarkably, significant methane oxidation occurred at eight sites where no known methanotrophs were detected, including a site at 89.9 °C-well above the previously reported upper growth temperature limit for methanotrophs from continental geothermal and hydrothermal systems-pointing to uncharacterized thermophilic lineages. These results suggest that biological methane oxidation in Yellowstone hot springs is influenced by the interplay of substrate availability and energy supply. By linking energy supply calculations with microbial distributions, we identify both known methanotrophs (Verrucomicrobia, Alphaproteobacteria) and archaeal ammonia oxidizers as potential active contributors, while highlighting the potential for novel thermophilic lineages, thereby expanding the ecological and thermal boundaries of methane oxidation in extreme terrestrial ecosystems.}, } @article {pmid41948759, year = {2026}, author = {Zhu, G and Zou, Z and Fang, Z and Xu, B}, title = {Rare but Critical: Severe Tropheryma Whipplei Pneumonia-Induced Cardiopulmonary Failure in a Young Immunocompromised Adult-A Case Report and Literature Review.}, journal = {Clinical case reports}, volume = {14}, number = {4}, pages = {e72448}, pmid = {41948759}, issn = {2050-0904}, abstract = {Tropheryma whipplei, traditionally linked to classic Whipple's disease with gastrointestinal involvement, is increasingly recognized as a cause of pneumonia. Reports of T. whipplei-associated pneumonia progressing to respiratory failure with concurrent acute cardiac failure remain extremely rare. A 38-year-old man with poorly controlled diabetes presented to the emergency department with acute chest tightness, dyspnea, and impaired consciousness. Laboratory findings indicated type II respiratory failure and elevated inflammatory markers. Imaging revealed scattered patchy hazy opacities and increased density bilaterally, prompting emergent intubation and transfer to the intensive care unit. Despite empirical antibiotics for severe pneumonia, he developed acute cardiac failure on day 3, manifesting as bloody sputum and diffuse moist rales with rhonchi on auscultation, alongside an LVEF of 49% and a markedly elevated serum BNP level of 3100 pg/mL. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid detected abundant T. whipplei sequences. He was administered targeted therapy with meropenem, supported by mechanical ventilation, diuresis, and glycemic control. Cardiopulmonary function improved, and he was discharged on oral doxycycline plus hydroxychloroquine. Follow-up endoscopy and biopsy showed no gastrointestinal involvement (Periodic Acid-Schiff negative), restored cardiac function (LVEF 58.6%), and no recurrence. This case underscores T. whipplei as a potential cause of isolated pneumonia with cardiopulmonary failure in functionally immunocompromised hosts and highlights the critical role of mNGS in guiding timely targeted therapy to improve outcomes.}, } @article {pmid41949195, year = {2026}, author = {Saini, G and Yadav, R and Bagga, R and Sharma, N and Sethi, S}, title = {Cervicovaginal microbiota in female sex workers with bacterial vaginosis: A metagenomic perspective.}, journal = {Indian journal of dermatology, venereology and leprology}, volume = {}, number = {}, pages = {1-3}, doi = {10.25259/IJDVL_1199_2025}, pmid = {41949195}, issn = {0973-3922}, } @article {pmid41949263, year = {2026}, author = {Marriott, L and Martinez-Lopez, A and Liga, A and Horiba, K and Warr, A and Phulusa, JN and Kumar, RS and Carey, L and Ito, Y and Parcell, BJ and Leslie, NR and Feasey, NA and Jacob, ST and Rylance, J and Kersaudy-Kerhoas, M}, title = {An automated and portable platform for rapid cell-free DNA isolation and its application in microbial DNA metagenomic sequencing from human blood samples.}, journal = {Lab on a chip}, volume = {26}, number = {9}, pages = {2849-2860}, doi = {10.1039/d5lc00876j}, pmid = {41949263}, issn = {1473-0189}, mesh = {Humans ; *Cell-Free Nucleic Acids/blood/isolation & purification/genetics ; *DNA, Bacterial/blood/genetics/isolation & purification ; Automation ; *Metagenomics/instrumentation ; *Sequence Analysis, DNA/instrumentation ; Rapid Diagnostic Tests ; }, abstract = {The prompt identification of pathogens in human circulation in a clinically deployable format remains an unmet clinical need. The established test for infection diagnostics remains blood culture, which typically takes 2-4 days and is positive in less than 15% of cases, with many prevalent pathogens difficult or impossible to culture. While microbial cfDNA in blood could facilitate the diagnosis of sepsis, febrile and infectious conditions, sample preparation for cell-free DNA (cfDNA) analysis in decentralised settings presents challenges due to its complexity and the low concentration and fragmented nature of cfDNA in blood plasma. We developed a portable and automated platform and a consumable (CNASafe) for cfDNA isolation from human plasma samples. The platform-device performance was evaluated by comparing relative cfDNA yield against a reference (QIAGEN QIAamp Circulating Nucleic Acid Kit). cfDNA eluates from ten non-cultured blood samples from hospital patients were sequenced on a nanopore sequencer, and results compared to blood cultures. Extraction of cfDNA using the CNASafe device was completed in 40 minutes, compared to the 1 hour 15 min reference protocol. The device achieved an average relative cfDNA recovery of 100.5% over 333 unique extractions encompassing all parameter variations, demonstrating a performance equivalent to the reference kit. From the patient samples, a sufficient quantity of microbial cfDNA was extracted to either identify pathogens missed by blood cultures or confirm negative cultures. The CNASafe platform and real-time nanopore sequencing offer a promising solution for the rapid deployment of metagenomic diagnostics, enabling pathogen identification within a few hours in decentralised clinical environments.}, } @article {pmid41949675, year = {2026}, author = {Chen, Y and Sun, N and Gan, B and He, Y and Luo, J and Pan, K and Zeng, Y and Jing, B and Zeng, D and Ni, X}, title = {Targeting Bifidobacterium animalis alleviates high-fluoride exposure-induced kidney injury in mice.}, journal = {AMB Express}, volume = {16}, number = {1}, pages = {}, pmid = {41949675}, issn = {2191-0855}, support = {2025YFHZ0278//Sichuan Science and Technology Program/ ; }, abstract = {In areas with high fluoride concentrations in drinking water, residents may consume excessive fluoride, which may increase the risk of renal impairment. Although accumulating evidence suggests that probiotics may exert renoprotective effects, support for probiotic interventions against fluoride-associated renal injury remains limited, and the effects appear to be strain dependent. In a prolonged exposure model, mice received sodium fluoride in drinking water (25 or 50 ppm) for 56 weeks, after which renal function was assessed and metagenomic profiling was performed. Mice exposed to varying fluoride concentrations developed renal injury, and the relative abundance of Bifidobacterium animalis was significantly correlated with markers of renal function. A short-term fluoride-exposure model (sodium fluoride, 24 mg/kg/day for 8 weeks, by gavage) was used to evaluate the renal protective effect of Bifidobacterium animalis GY007. Supplementation with GY007 significantly reduced renal injury markers, including β2-microglobulin (β2-MG) and lipocalin 2 (LCN2). GY007 reduced pro-inflammatory cytokines interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α), increased anti-inflammatory interleukin-10 (IL-10), and alleviated oxidative stress. Transmission electron microscopy (TEM) analysis indicated that GY007 improved mitochondrial morphology in damaged renal tissue. Further analyses showed that GY007 improved mitochondrial membrane potential, attenuated the upregulation of dynamin-related protein 1 (Drp1) and fission 1 (Fis1), and normalized altered mitochondrial DNA (mtDNA) copy number. The mRNA levels of mtDNA-encoded genes (mtND3, mtCO2, and mtcyb) and the nuclear-encoded gene Sdhb were altered. Kidney metabolomic analysis revealed metabolic alterations associated with GY007 supplementation in fluoride-exposed mice, identifying eight significantly altered metabolites. This study provides evidence supporting the development of probiotic interventions to mitigate fluoride-associated renal injury in settings with elevated fluoride concentrations in drinking water.}, } @article {pmid41949810, year = {2026}, author = {Adolph, JE and Pentek, C and Bauch, T and Held, C and Brenner, T and Felderhoff-Müser, U and Grumaz, S and Horvatek, P and Steindor, M and Asar, L and Voigt, S and Dziobaka, J and Dohna-Schwake, C and Goretzki, SC}, title = {Next-generation sequencing of cell-free microbial DNA in blood samples of critically ill children: a single-center experience.}, journal = {Molecular and cellular pediatrics}, volume = {13}, number = {1}, pages = {}, pmid = {41949810}, issn = {2194-7791}, abstract = {BACKGROUND: Rapid and accurate pathogen detection is critical for optimizing outcomes in pediatric sepsis. Next-generation sequencing (NGS) of cell-free DNA (cfDNA) from blood enables culture-independent identification of microbial DNA from bacteria, viruses, fungi, and parasites. We evaluated the diagnostic yield and clinical impact of cfDNA-based NGS in critically ill and predominantly immunocompromised pediatric patients (≤ 18 years) with suspected infection. This retrospective single-center study included pediatric patients who underwent plasma cfDNA-NGS at a tertiary care hospital in Germany. Following computational removal of human DNA, remaining sequences were aligned to curated microbial reference databases. Diagnostic performance was compared with blood cultures and viral PCR, and clinical relevance was assessed by pediatric infectious disease specialists.

RESULTS: 111 tests in 78 pediatric patients, mostly with systemic inflammatory response syndrome of unknown etiology, were performed. Overall, 61 tests (54.5%) were positive for pathogenic cfDNA. Compared with conventional microbiological diagnostics, NGS demonstrated a sensitivity of 64.7% and specificity of 88.2% when blood cultures and viral PCR served as the reference standard. NGS identified additional pathogens in a substantial proportion (41.1%) of cases that remained negative by standard testing. Of those pathogens only found by NGS, over 60% were deemed clinically relevant. In 14.8% of positive NGS results, a pathogen-specific therapy was started, while 40.2% of tests led to a discontinuation of therapy (51.0% of negative tests). Out of all positive NGS, 38 (62.3%) were classified as clinically relevant. NGS testing also detected rare infections with fungi and parasites in four cases each.

CONCLUSION: Detection of pathogenic cfDNA through NGS from blood shows promising results as an additional diagnostic tool in critically ill pediatric patients with suspected infections. Clinical utility is currently still limited by its high cost, undetermined diagnostic validity and limitations in testing for resistances and restricted availability of raw sequencing data due to data-protection constraints.}, } @article {pmid41949970, year = {2025}, author = {Lerhzouli, H and Al Ibrahmi, B and Khal-Layoun, S and Bour, A}, title = {New therapeutic approaches based on modulation of the intestinal microbiota to correct dysbiosis in patients with type 2 diabetes.}, journal = {La Tunisie medicale}, volume = {103}, number = {11}, pages = {1707-1717}, doi = {10.62438/tunismed.v103i11.6101}, pmid = {41949970}, issn = {2724-7031}, mesh = {Humans ; *Diabetes Mellitus, Type 2/complications/therapy/microbiology ; *Dysbiosis/therapy/etiology/microbiology ; Probiotics/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome/physiology/drug effects ; Prebiotics/administration & dosage ; Diet, Mediterranean ; }, abstract = {Type 2 diabetes is a chronic disease characterized by insulin resistance and reduced insulin production in pancreatic cells. Conventional treatment of type 2 diabetes relies on hypoglycemic drugs, physical activity and a balanced low-carbohydrate diet, but with technological advances in metagenomics and metabolomics researchers have developed new therapeutic approaches aimed to modulate, the gut microbiota to correct the dysbiosis confirmed in people with type 2 diabetes. This literature review provides an update on therapies aimed to modulate the gut microbiota to correct dysbiosis in type 2 diabetics and summarizes the latest advances in this field.}, } @article {pmid41950191, year = {2026}, author = {Kador, SM and Shila, JF and Afrin, S and Jannat, J and Islam, KT and Rubaiyat, RN and Bhuiyan, MIU and Chakrovarty, T and Hasan, MS and Sakib, N and Rahman, MS and Islam, OK and Islam, MT}, title = {Microbial diversity, functional genomics and antibiotic resistance in integrated chicken and fish farming systems of Bangladesh.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0344367}, pmid = {41950191}, issn = {1932-6203}, mesh = {Animals ; *Chickens/microbiology ; Bangladesh ; RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Aquaculture ; Anti-Bacterial Agents/pharmacology ; Genomics ; *Drug Resistance, Bacterial ; Metagenomics ; Biodiversity ; }, abstract = {The integrated chicken and fish farming system in Bangladesh is widely practiced for its resource efficiency, yet its microbial structure, functional potential, and associated antimicrobial resistance risks remain poorly understood. This study investigated microbial communities, metabolic functions, and antimicrobial resistance profiles across multiple components of integrated farming systems, including chicken gut, chicken droppings, feed, fish intestine, and pond sediment. Microbial profiling was performed using 16S ribosomal ribonucleic acid (rRNA) gene sequencing, functional metagenomic prediction, and culture-based isolation, complemented by antimicrobial susceptibility testing. A total of 2,838 operational taxonomic units were identified, with bacteria constituting the vast majority of detected microorganisms. Microbial community composition was strongly shaped by sample type, reflecting distinct ecological niches within the farming system. Chicken gut samples were dominated by Firmicutes, feed samples by Cyanobacteria, and sediment samples exhibited the highest microbial diversity, including taxa involved in biogeochemical cycling. Functional analysis revealed that pathways related to amino acid and carbohydrate metabolism were most abundant across all samples, while sediment and feed were enriched in pathways associated with xenobiotic degradation, suggesting a role in environmental detoxification. Culture-based methods isolated clinically relevant bacteria, including Escherichia coli and Proteus mirabilis, although metagenomic analysis indicated that these organisms represented only a minor fraction of the overall microbial community. Antimicrobial susceptibility testing demonstrated notable resistance, particularly to tetracyclines and fluoroquinolones. Metagenomic analysis further identified multiple antimicrobial resistance genes, with several showing strong associations with specific bacterial genera. This study provides the first comprehensive characterization of microbial diversity, functional capacity, and antimicrobial resistance within integrated chicken and fish farming systems in Bangladesh, highlighting potential environmental reservoirs of resistance and underscoring the need for improved management strategies to enhance sustainability and reduce public health risks.}, } @article {pmid41950533, year = {2026}, author = {Cai, X and Yao, Y and Zheng, Y and Zhao, X}, title = {Multi-omics gut microbiome signatures for treat-to-target management in inflammatory bowel disease.}, journal = {Microbiological research}, volume = {309}, number = {}, pages = {128511}, doi = {10.1016/j.micres.2026.128511}, pmid = {41950533}, issn = {1618-0623}, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/therapy/drug therapy ; Multiomics ; *Gastrointestinal Microbiome/genetics ; Drug Monitoring/methods ; Dysbiosis/microbiology ; Feces/microbiology ; Metagenomics ; Metabolomics ; Proteomics ; }, abstract = {Inflammatory bowel disease (IBD) care now relies on an expanding portfolio of biologics and small molecules, yet symptom-driven phenotyping often misses molecular endotypes, contributing to primary non-response and loss of response. This review examines how gut microbiota-centered multi-omics can be translated into decision support within treat-to-target (T2T) management and therapeutic drug monitoring (TDM). We synthesize evidence from stool and mucosal metagenomics/metatranscriptomics, virome and bacteriophage signals, metabolomics, blood proteomics, and host transcriptomic/epigenomic and genetic layers, emphasizing analytical validity, external validation, calibration, and action-linked thresholds. Longitudinal data indicate that IBD-associated dysbiosis is predominantly functional and time-varying, enabling applications in diagnosis, prognosis, therapy-response prediction, and monitoring of inflammatory burden and remission depth. However, many reported predictors show limited transportability due to pre-analytical variation, batch effects, endpoint heterogeneity, and confounding by diet, antibiotics, and prior therapies. We propose a pragmatic, tiered workflow: deploy minimal, interpretable signatures at baseline and early induction, and interpret outputs alongside fecal calprotectin/CRP, endoscopy or imaging when indicated, and drug exposure/anti-drug antibodies to distinguish underexposure and immunogenicity from true mechanistic non-response, guiding dose optimization versus mechanism switching. Digital/remote monitoring can operationalize iterative reassessment while reserving deeper omics for decision-critical checkpoints. Overall, the microbiome is best framed as an actionable layer within a multi-signal IBD management system rather than a standalone biomarker; translation will depend on standardization, workflow integration, prospective validation, and demonstrated clinical and economic value.}, } @article {pmid41950684, year = {2026}, author = {Cao, S and Liu, X and Tao, Y and Ren, J and Zhou, Z and Du, R}, title = {EPS-mediated mineralization drives granule densification and enhances denitratation-anammox coupling under alkaline conditions.}, journal = {Water research}, volume = {299}, number = {}, pages = {125888}, doi = {10.1016/j.watres.2026.125888}, pmid = {41950684}, issn = {1879-2448}, mesh = {Bioreactors/microbiology ; Hydrogen-Ion Concentration ; Nitrogen/metabolism ; *Extracellular Polymeric Substance Matrix/chemistry/metabolism ; *Denitrification ; Sewage/microbiology/chemistry ; *Waste Disposal, Fluid/methods ; Nitrates/metabolism ; }, abstract = {The granular-based CANDAN (Complete Ammonium and Nitrate removal via Denitratation-Anammox over Nitrite) process offers a promising low-carbon and high-rate strategy for nitrogen removal; yet the mechanisms by which alkaline conditions regulate granule structure and functional coupling remain insufficiently understood. Here, a 9-L sequencing batch reactor (SBR) was operated for 130 days with stepwise pH elevation from 7.31 ± 0.03 to 8.52 ± 0.08 to elucidate alkaline condition-driven structural and functional adaptations in CANDAN granules. Moderate alkaline conditions significantly improved nitrogen removal, with total nitrogen removal efficiency increasing to 91.4 ± 0.1 %, accompanied by pronounced improvement in sludge settleability (sludge volume index after 30 min of settling, SVI30, decreased from 76.4 to 19.4 mL g[-1] SS) and stabilization of dominant granule sizes at 0.5-1 mm, accounting for approximately 69.8 % of the total granules, indicating progressive granule densification. Mineralogical analyses revealed that hydroxyapatite dominated the inorganic matrix, with co-precipitation of calcium carbonate (CaCO3) and transient magnesium ammonium phosphate formation reinforcing granule structure. Elevated pH also remodeled extracellular polymeric substances (EPS), increasing loosely bound EPS, raising the protein-to-polysaccharide ratio, and enriching tryptophan-like proteins that facilitated EPS-mediated mineral nucleation. Metagenomic analysis revealed streamlined carbon metabolism and enrichment of key nitrogen-cycling genes (napA, nosZ, hzsA), while downregulation of Ca[2+], Mg[2+], and phosphate transport genes favored extracellular mineral accumulation. Overall, moderately alkaline conditions drive EPS-mediated mineralization that densifies granules and stabilizes Denitratation-Anammox coupling, providing mechanistic insight for optimizing low-carbon nitrogen removal under alkaline wastewater conditions.}, } @article {pmid41950685, year = {2026}, author = {Zuo, Z and Xing, Y and Qiao, L and Yang, S and Ren, D and Guo, M and Liu, Y and Huang, X}, title = {Unveiling in-pipe carbon-sulfur transformation and microbial function during urine transport for centralized management.}, journal = {Water research}, volume = {299}, number = {}, pages = {125840}, doi = {10.1016/j.watres.2026.125840}, pmid = {41950685}, issn = {1879-2448}, mesh = {Bioreactors/microbiology ; *Carbon/metabolism ; *Sulfur/metabolism ; *Urine/chemistry ; Sewage/microbiology ; Bacteria/metabolism ; Waste Disposal, Fluid ; }, abstract = {Source-separated urine collection and centralized nutrient recovery at city-scale hold great potential for advancing sustainable resource management. As the critical link between urine collection systems and nutrient recovery facilities, urine-transporting sewer systems have recently been incorporated into life cycle assessments (LCA), yet their potential for biochemical transformations has not been explored. Here, for the first time, we experimentally unveil key pollutant transformations and microbial functions in a urine-fed bioreactor (representing urine transport), with a sewage-fed bioreactor serving as a control. Major urine nutrients (N, P, and K) remained largely stable during transport, whereas organic carbon and sulfate decreased markedly. Methane production was negligible over 160 days, while sulfide production initially declined but fully recovered by day 80, accompanied by elevated microbial activity and substantial sulfide accumulation in sediments. Microbial community analyses revealed that urine exposure reduced community richness and led to a pronounced community, with methanogenic archaea strongly inhibited and sulfate-reducing bacteria (SRB) becoming dominant under prolonged urine stress. A Desulfomicrobium-like SRB species was progressively enriched (∼35% of total metagenome-assembled genomes (MAGs)) and likely responsible for the sulfide rebound. Spatial heterogeneity of microbial communities in sediments further explains depth-specific sulfide accumulation. Overall, this study provides important insights into carbon-sulfur transformations and microbial adaptation in urine transport systems, informing improved system design, operation, and further LCA.}, } @article {pmid41950966, year = {2026}, author = {Yan, S and Han, Q and Chen, L and Jin, D and Lu, Y and Zhou, J and Zhang, X}, title = {Simultaneous removal of Se(IV) and Cr(VI) from acidic wastewater using a Se(IV)-reducing internal circulation reactor: performance and microbial resistance mechanisms.}, journal = {Bioresource technology}, volume = {452}, number = {}, pages = {134537}, doi = {10.1016/j.biortech.2026.134537}, pmid = {41950966}, issn = {1873-2976}, mesh = {*Chromium/isolation & purification ; *Wastewater/chemistry ; Hydrogen-Ion Concentration ; *Bioreactors/microbiology ; *Selenium/isolation & purification ; *Water Purification/methods/instrumentation ; *Water Pollutants, Chemical/isolation & purification ; Oxidation-Reduction ; Biodegradation, Environmental ; Bacteria/metabolism ; Sewage/microbiology ; }, abstract = {Acidic wastewater contaminated with selenite (Se(IV)) and chromate (Cr(VI)) poses elevated environmental risks due to the combined toxicity of metal(liod) and acidity. Metal(loid)-resistant consortia, such as Se(IV)-reducing sludge (SeRS), provide a promising strategy for treating such wastewater by converting Se(IV) and Cr(VI) into less toxic Se(0) and Cr(III), respectively. In this study, an internal circulation (IC) reactor packed with SeRS and granular activated carbon was constructed to evaluate its performance in treating such wastewater. In the absence of Cr(VI), the reactor achieved Se(IV) removal efficiencies of 94.6-98.5% at influent pH values of 4.5-8.0 and Se(IV) concentrations of 1-3 mM. At an optimal pH 5.5, nearly complete removal of both oxyanions was achieved at Se(IV)/Cr(VI) molar ratios of 5.2-10.4. Alkalinity generated from acetate oxidation buffered the influent acidity at influent pH values of 4.5-5.5, thereby sustaining microbial activity. Cr(VI) stress selectively enriched Brucella, Trichlorobacter, and Seleniivibrio for Cr(VI) reduction, while Pseudomonas accounted for Se(IV) and Cr(VI) reduction. Integrated extracellular polymeric substances (EPS), glutathione reductase (GOR), and metagenomic analyses revealed that microbial resistance to Cr(VI) stress likely relied on intracellular glutathione-related detoxification, enzymatic Se(IV)/Cr(VI) reduction and antioxidant defenses, while extracellular EPS protection declined. Overall, it was demonstrated that the developed IC reactor process enabled robust and efficient removal of both Se(IV) and Cr(VI) from acidic wastewater.}, } @article {pmid41951175, year = {2026}, author = {Rana, N and Tiewsoh, K and Ray, P and Angrup, A}, title = {Automating Microbial Community Analysis (AMCA): Development and application of an amplicon based graphical pipeline in patients with Chronic Kidney Disease.}, journal = {Indian journal of medical microbiology}, volume = {61}, number = {}, pages = {101110}, doi = {10.1016/j.ijmmb.2026.101110}, pmid = {41951175}, issn = {1998-3646}, mesh = {Humans ; *Renal Insufficiency, Chronic/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Workflow ; Phylogeny ; Computational Biology/methods ; Bacteria/classification/genetics ; Software ; }, abstract = {INTRODUCTION: Amplicon sequencing is a targeted approach used to assess the diversity of microbial communities by amplifying and sequencing a specific genetic locus from DNA. QIIME2 is one of the most prevalent methods for metagenomics analysis due to its plugin-based design wherein distinct modules can be utilized to perform specific functions. However, QIIME2 data input, and plugin utilization is cumbersome to navigate. Previous amplicon pipelines also lack host depletion and statistical biomarker identification modules from upstream and downstream analysis.

METHODS: To this effect, we assembled a simple and customizable Zenity based GUI workflow for analysing amplicon data with Automating Microbial Community Analysis (AMCA). The analysis integrates key attributes of amplicon analysis: host depletion with Bowtie2 and biomarker prediction by LEfSe. The bash-based analysis guides and allows the user to select filtering parameters based on intermediate results while minimizing the need to navigate command-based plugins.

RESULTS: The outputs from the AMCA workflow include the filtered and host-depleted raw sequencing data, taxonomic abundances, alpha and beta diversity indices, alpha rarefaction analysis, phylogenetic tree (rooted and unrooted) and significant features which explain key microbial differences between conditions/classes of the experiment. The implementation of the designed workflow has been tested on a pilot study based on amplicon sequencing in 100 samples from patients of Chronic Kidney Disease and healthy controls. The exploratory LEfSE analysis revealed key taxa Streptococcus, Bacteroides and Faecalibacterium to vary between disease and control conditions. The source code related to the analysis can be assessed from the Github repository at https://github.com/Nitika-Rana/AMCA.

CONCLUSION: The study delivers an efficient, user-friendly, and customizable workflow for amplicon analysis, simplifying QIIME2 execution while enabling host depletion and biomarker characterization.}, } @article {pmid41951362, year = {2026}, author = {Kariya, E and Tirard-Collet, P and Boulagnon-Rombi, C and Destras, G and Wallon, M and Menotti, J and Lapendry, A and Kaidi, N and Rabodonirina, M and Lievre, L and Depaquit, J and Villena, I and Trecourt, A and Huguenin, A}, title = {Integrated histomolecular diagnosis of mesenteric anisakiasis.}, journal = {Journal of clinical pathology}, volume = {79}, number = {6}, pages = {427-430}, doi = {10.1136/jcp-2026-210635}, pmid = {41951362}, issn = {1472-4146}, mesh = {Humans ; Female ; Middle Aged ; *Anisakiasis/diagnosis/parasitology/pathology/surgery ; Animals ; *Anisakis/genetics/isolation & purification ; *Mesentery/parasitology/pathology ; Metagenomics ; *Mesenteric Ischemia/parasitology/surgery/diagnosis ; Larva ; }, abstract = {A 49-year-old woman was admitted with gastrointestinal symptoms and imaging consistent with duodeno-ileitis. Her clinical course was complicated by mesenteric ischaemia, requiring resection of a 45-cm ileal segment. A pre-adult Anisakis spp. larva was identified within a mesenteric nodule through an innovative diagnostic approach combining histopathological analysis with shotgun metagenomic analysis.}, } @article {pmid41951635, year = {2026}, author = {Heng, YC and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Kittelmann, S}, title = {Metagenome-assembled genomes, and gene and protein catalogues from the global wild boar faecal microbiome.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41951635}, issn = {2052-4463}, mesh = {Animals ; *Feces/microbiology ; *Metagenome ; *Sus scrofa/microbiology ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; Archaea/genetics/classification ; Bacteria/genetics/classification ; }, abstract = {Prophylactic antibiotic use in pig farming has contributed to the rise of antimicrobial resistance, spurring interest in probiotics to enhance pig gut health and immunity. Wild relatives of domestic pigs may harbour beneficial microbes, yet their gut microbiomes remain underexplored. In this study, we reconstructed 3,288 metagenome-assembled genomes (MAGs) from 89 wild boar faecal samples collected across four countries, all meeting at least MIMAG medium-quality standard (≥50% completeness, <10% contamination). These MAGs represented 968 distinct species, including 956 bacterial species from 113 families and 419 genera, and 12 archaeal species from 2 families and 7 genera, with half classified as novel. In addition, we also constructed catalogues of genes and proteins from the wild boar faecal metagenomes. Notably, most species (58%), genes and proteins (85%) identified in the wild boar faecal microbiomes were absent from equivalent catalogues of domestic pigs. Our catalogues highlight wild boars as a reservoir of previously untapped microbial resources for microbiome research and the exploration of biotechnological applications including probiotics.}, } @article {pmid41951715, year = {2026}, author = {Wang, H and Wu, SH and Zhang, K and Chen, KH and Vilgalys, R and Liao, HL}, title = {Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41951715}, issn = {2399-3642}, mesh = {*Mycobiome/genetics ; Transcriptome ; Metagenome ; *Fungi/classification/genetics ; *Metagenomics/methods ; Genetic Markers ; }, abstract = {Profiling the taxonomic and functional composition of mycobiome using metagenomic and metatranscriptomic sequencing is advancing our understanding of fungal functions in ecosystems. However, the sensitivity and accuracy of mycobiome classification using genome- or core protein-based approaches, is limited by the availability of reference genomes and the resolution of sequence databases. To address this, we propose the MicroFisher, a novel tool to identify taxonomically useful reads from metagenomic or metatranscriptomic data, enabling taxonomic identification of community members based on multiple hypervariable markers. We applied MicroFisher to profile the simulated fungal communities to assess the performance of the developed tool, and found higher performance in fungal prediction and abundance estimation compared to existing tools. In addition, we also used metagenomes from forest soil and metatranscriptomes of root eukaryotic microbes to test our method and found that MicroFisher provided more accurate profiling of environmental microbiomes compared to other classification tools. MicroFisher leverages high-resolution hypervariable marker gene databases and weighted integration algorithms to deliver more accurate fungal community classification compared to existing state-of-the-art tools. Additionally, it enables the detection of rare taxa, which is challenging with other available tools. Thus, MicroFisher serves as a novel pipeline for classification of fungal communities from metagenomes and metatranscriptomes.}, } @article {pmid41951791, year = {2026}, author = {Somerville, TF and Kaye, SB}, title = {Comment on: 'Metagenomic next-generation sequencing: a game changer in the diagnosis of unique intraocular infections'.}, journal = {Eye (London, England)}, volume = {40}, number = {9}, pages = {1421}, pmid = {41951791}, issn = {1476-5454}, } @article {pmid41951875, year = {2026}, author = {Wang, Y and Li, Y and Fang, J and Huang, Z and Zhang, C and Xu, B}, title = {A Novel Broad pH-Adaptive Bile Salt Hydrolase from Nomascus concolor Fecal Microbial Metagenome Facilitates the Cholesterol-Lowering Ability of Escherichia coli Nissle 1917.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41951875}, issn = {1867-1314}, support = {32360034//National Natural Science Foundation of China/ ; }, abstract = {High serum cholesterol levels are among the key risk factors for atherosclerosis cardiovascular disease. The utilization of probiotics to lower cholesterol is a relatively safe and efficient therapy, and the bile salt hydrolase gene serves a key function in this process. We aim to identify novel bile salt hydrolase genes from the wild western black crested gibbon (Nomascus concolor) faecal metagenome. Additionally, we intend to develop a new generation of probiotics with cholesterol-lowering properties. Our study amplified and heterologously expressed novel bile salt hydrolases from the faecal metagenome of western black crested gibbons and investigated their enzymatic properties. The recombinant probiotic was constructed using Escherichia coli Nissle 1917 (EcN), and its physiological characteristics and cholesterol-lowering ability were evaluated. We screened uncharacterized bile salt hydrolase genes (NCbsh3 and NCbsh5) from Eubacterium and Roseburia. NCbsh3 exhibited broad pH adaptability and stability; its optimal pH range was 4–7, and the relative enzyme activity was maintained at 80% after 60 min at pH 3–9. The recombinant probiotic EcN/NCbsh3 was constructed, and its bile salt tolerance and cholesterol-lowering ability significantly increased (P < 0.05). These results indicated that NCbsh3 may adapt to the complex pH environment of the intestine and that the NCbsh3 gene is expected to increase the colonization capacity of the EcN strain in the gastrointestinal tract and reduce host serum cholesterol levels. EcN/NCbsh3 has favourable application potential and may contribute positively to the treatment of diseases caused by bile acid metabolism disorders.}, } @article {pmid41952168, year = {2026}, author = {Shen, Y and Qu, S}, title = {Ganciclovir for severe neonatal varicella pneumonia when acyclovir is unavailable: a case report.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {41952168}, issn = {1743-422X}, mesh = {Humans ; Female ; *Antiviral Agents/therapeutic use/administration & dosage ; *Ganciclovir/therapeutic use/administration & dosage ; Infant, Newborn ; *Pneumonia, Viral/drug therapy/diagnosis ; Herpesvirus 3, Human/isolation & purification/genetics ; *Chickenpox/drug therapy/diagnosis ; Treatment Outcome ; Acyclovir/therapeutic use ; Pregnancy ; DNA, Viral/blood ; }, abstract = {BACKGROUND: Perinatal varicella is a rare and severe condition with a high mortality rate, particularly when it leads to complications such as pneumonia in neonates. Acyclovir is the standard treatment for varicella-zoster virus (VZV) infections; however, limited options exist when it is unavailable. This case report describes the successful treatment of neonatal varicella pneumonia with ganciclovir and provides insights into its potential as an alternative therapy. A female Asian neonate was admitted to our hospital on the 9th day of life with a rash, fever, and respiratory distress. Her mother developed varicella at 39 weeks of pregnancy, four days before delivery. The infant was diagnosed with VZV pneumonia based on clinical presentation and confirmed by detection of VZV DNA in blood(metagenomic next-generation sequencing detected 109,491 sequences with 100% relative abundance and 99% confidence).

INTERVENTION: Ganciclovir 5 mg/kg every 12 h for 8 days; intravenous immunoglobulin 400 mg/kg once daily for 3 days.

OUTCOME: The infant was successfully weaned off mechanical ventilation, with normalized blood gas parameters (PaO₂/FiO₂ ratio 346) and inflammatory markers (CRP decreased from 29.44 mg/L to 2.87 mg/L). She was discharged home with stable breathing and crusted skin lesions. Telephone follow-up at 2 and 4 weeks post-discharge confirmed the infant remained well with no respiratory symptoms or developmental concerns.

CONCLUSION: Ganciclovir may serve as a life-saving alternative for severe neonatal VZV pneumonia when acyclovir is unavailable. This case highlights the need for further research to establish its safety, optimal dosing, and efficacy in this population.}, } @article {pmid41953110, year = {2026}, author = {Craddock, HA and Motro, Y and Winner, KM and Lotem-Michaeli, Y and Segal, E and Godneva, A and Grinstein, D and Moran-Gilad, J}, title = {Metagenomic analysis of antimicrobial resistance genes in domestic canines.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101380}, pmid = {41953110}, issn = {2352-7714}, abstract = {A One Health approach is critical to addressing the spread of antimicrobial resistance (AMR). A key source of AMR in humans is companion animals, particularly canines. Recent investigation has shown that the canine fecal microbiome is rich in antimicrobial resistant genes (ARGs), yet few studies have studied the resistome of working canines. Our objective was to investigate the resistome of canines to elucidate associations between various exposures and demographic factors and ARG carriage. We performed resistome and microbiome analyses on previously-generated metagenomic sequence data from 126 Israeli working canines and 147 global canines. We found that the canine microbiome and resistome varied significantly with country of origin, and the resistome varied significantly with gastrointestinal disease state, canine job type, and microbiome composition. Tetracycline resistant genes were the most dominant across all canines. Extended-spectrum beta lactamase (ESBL) genes were observed in up to 33% of canines. Genes of concern, including potential carbapenemases (blaOXA-181 and blaOXA-347) and colistin resistance genes (mcr-10) were infrequently observed. The Inc family of plasmids, typically associated with ESBL genes, were frequently detected. Altogether our research suggests that canines, including working dogs, are a potential source of ARGs and plasmids which carry ARGs. Importantly, the abundance and identity of these ARGs is associated with various potentially modifiable factors such as microbiome composition. As canines are an important human exposure within the One Health paradigm, future work is necessary to understand the risk and transmission dynamics of ARGs between humans and their companion canines.}, } @article {pmid41953529, year = {2026}, author = {Brown, JR and Ross, CS and Worth, A and Merve, A and Storey, N and Hacohen, Y and Mankad, K and Kaliakatsos, M and Shendi, HM and Atkinson, L and Gilmour, K and Hatcher, J and Lennon, A and Bamford, A and Kusters, M and Elfeky, R and Núñe, A and Brown, IH and Reid, SM and Cooper, J and Byrne, AMP and James, J and Lean, FZ and Banyard, AC and Breuer, J}, title = {Identifying virulent avian paramyxovirus type-1: A paediatric case of progressive encephalitis diagnosed by clinical metagenomics with case series review.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02555}, pmid = {41953529}, issn = {2214-2509}, abstract = {BACKGROUND: Immunocompromised patients presenting with encephalitis can present a diagnostic conundrum as infection can be caused by a broad range of pathogens, many of which are not detected by standard of care testing pathways. Untargeted metagenomics has proven utility in the diagnosis of such infections, particularly for immunocompromised patients.

METHODS: An immunosuppressed adolescent presented with idiopathic progressive muscle weakness resulting in respiratory failure, 16 years after haematopoeitic stem cell transplant for familial haemophagocytic lymphohistiocytosis type 5. Clinical and radiological findings suggested a diagnosis of isolated central nervous system haemophagocytic lymphohistiocytosis, however the patient demonstrated no improvement on immunosuppressive therapy. Untargeted metagenomics was performed on brain biopsy tissue.

RESULTS: Clinical metagenomics detected avian paramyxovirus 1 (APMV-1) in the brain tissue 12 days after biopsy, confirmed by targeted PCR and immunohistochemistry. The metagenomics results guided treatment; immunosuppression was stopped and medication with potential activity against RNA viruses started. The patient died 8 months after symptom onset.

CONCLUSIONS: We describe the third published case of fatal encephalitis caused by APMV-1, detectable only in brain parenchyma and only by clinical metagenomics, demonstrating the utility of brain biopsy and metagenomics when investigating encephalitis in immunocompromised patients. Case series review suggests profoundly immunocompromised patients are at risk of severe infection caused by AMPV-1.}, } @article {pmid41953658, year = {2026}, author = {Song, J and Li, Y and Wang, L and Zhang, J and Shi, C and Zhong, L and Liu, C and Song, M and Yu, X and Zhang, W and Wen, P}, title = {Comparative study of the physicochemical properties, volatile compounds, and bacterial microbiota in commercial and traditional yak yogurt from the Qinghai-Tibet plateau.}, journal = {Food chemistry: X}, volume = {35}, number = {}, pages = {103771}, pmid = {41953658}, issn = {2590-1575}, abstract = {This study aimed to elucidate differences between the commercial starter culture (CK) and traditional starters from different Tibetan regions (Gannan (GN), Qinghai (QH), Tibet (XZ)) in fermenting yak yogurt by physicochemical properties, flavor, and bacterial community. Results indicated acidity, proline, arginine, alanine, and C6:0 contents were significantly higher in the traditional starter culture than CK (P < 0.05). Gas chromatography-ion mobility spectrometry analysis found the traditional starter culture group was dominated by alcohols and esters, whereas CK exhibited richer ketones. Metagenomic analysis revealed Lactobacillus delbrueckii (49.56% in XZ, 24.86% in GN) and Streptococcus spp. (18.30% in CK, 17.21% in QH) as the dominant. Moreover, pH and titratable acidity were primary factors affecting microbial diversity. Meanwhile, glutamic acid modulated ester biosynthesis like ethyl acetate, while C16:0 fatty acids inhibited off-odor ketones such as 2-pentanone. This study offers valuable insights into developing specialized fermentation agents and standardizing the quality of yak yogurt.}, } @article {pmid41953764, year = {2026}, author = {Ivan, FX and Versi, A and Tiew, PY and Abdel-Aziz, MI and Kermani, NZ and Maitland-Van Der Zee, AH and Howarth, P and Koh, MS and Adcock, IM and Chotirmall, SH and Chung, KF}, title = {Multidrug-resistant Haemophilus influenzae cluster of severe asthma from sputum bacteriome-resistome.}, journal = {ERJ open research}, volume = {12}, number = {2}, pages = {}, pmid = {41953764}, issn = {2312-0541}, abstract = {BACKGROUND: Severe asthma encompasses heterogeneous inflammatory phenotypes and airway bacteriome diversity but the state of its airway resistome remains understudied. We therefore evaluated the link between the airway microbiome and the antibiotic-resistant genes by determining the clusters from a bacteriome-resistome integration from sputum samples of patients with severe asthma.

METHODS: Induced sputum samples from severe asthma (SA; n=96), mild-moderate asthma (MMA; n=23) and healthy controls (HCs; n=23) in the European U-BIOPRED asthma cohort were metagenomically sequenced. Respiratory bacteriome was evaluated by taxonomical and functional classification. The comprehensive antibiotic resistance database was used to determine airway resistome and Similarity Network Fusion to cluster integratively the bacteriome-resistome.

RESULTS: More multidrug-resistance genes were present in SA compared with MMA and HCs with the hmrM, encoded in Haemophilus influenzae chromosome, being highest. Two of the three defined clusters were dominated by commensals with resistance genes from different classes but different in α- and β-diversities. The third cluster was dominated by multidrug-resistant H. influenzae, with SA characteristics of increased asthma duration, reduced pulmonary macrophages and decreased lung function. It had the highest signature expression of neutrophil activation, NETosis and of interleukin (IL)-5, IL-6, IL-13, IL-17 and IL-33 signalling pathways. These clusters were reproduced in an Asian-Singapore SA cohort including the multidrug-resistant H. influenzae cluster, but with an additional cluster of multidrug-resistant Pseudomonas aeruginosa.

CONCLUSION: The demonstration of U-BIOPRED multiresistant H. Influenzae and of Asian-Singapore multiresistant P. aeruginosa clusters highlights the potential importance of antibiotic-resistant genes in driving severe asthma.}, } @article {pmid41954112, year = {2026}, author = {Banerjee, M and Lahiri, A and Basak, S and DAS, S and Mukhopadhyay, S and Banerjee, R and Basak, K}, title = {StaLAENet: A stacked LSTM-nested deep-autoencoder network for identification of antimicrobial resistance of nosocomial pathogens.}, journal = {Journal of biosciences}, volume = {51}, number = {}, pages = {}, pmid = {41954112}, issn = {0973-7138}, mesh = {Autoencoder ; Humans ; Long Short Term Memory ; *Cross Infection/microbiology/drug therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Algorithms ; *Drug Resistance, Bacterial/genetics ; Enterococcus faecium/pathogenicity/genetics/drug effects ; Deep Learning ; }, abstract = {As various technological innovations are assisting medical science in a considerable way, rendering a significant leap towards 'lab-to-land' delivery, in a similar vein, algorithm development and concomitant framework-based approaches help the field to enrich its patient care. Although antimicrobial drugs revolutionized this particular area, antimicrobial resistance is a pressing global health concern as microbial strains are becoming resistant to conventional antibiotics, undermining the efficacy of these drugs and leading to increased illness and healthcare costs. To tackle this menace, apart from technological innovations such as diagnostic kits, an informatics-based framework approach is the call of the day. Despite the emergence of several computational approaches, they lack in generalization, scope, and scalability. Here, we have developed a novel framework StaLAENet (stacked LSTM-nested deep-autoencoder network) to predict antibiotic-resistant gene drug classes targeting ESKAPE pathogens. This framework comprises two modules: a feature representation module comprising a stacked LSTM-nested deep autoencoder and a classification module that leverages a dense network using latent features. StaLAENet demonstrated an efficient performance - accuracy: 0.938±0.043, specificity: 0.888±0.061, precision: 0.912±0.020, and recall: 0.881±0.021 - for Enterococcus faecium using 4-mer data, with similar results for other organisms using various k-mer data. Comparative analysis confirmed its superiority over existing pipelines. Further, independent evaluation with non-redundant sequences (sourced from another database) and with a metagenomic dataset highlighted its generalizability, robustness, and capability to analyze complex microbial communities. StaLAENet can offer a robust solution for combating AMR, enabling an efficient way of antimicrobial stewardship and patient care.}, } @article {pmid41954388, year = {2026}, author = {Zhao, P and Liu, H and Dong, J and Su, H and Jin, Q and Yang, F}, title = {From hepatitis misdiagnosis to zoonotic false alarms: a metagenomic blacklist framework for the parvo-like hybrid viral group.}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0015726}, pmid = {41954388}, issn = {2165-0497}, } @article {pmid41954393, year = {2026}, author = {Shukla, N and Budhbhatti, U and Puvar, A and Raval, I and Pandit, R and Chavda, P and Chauhan, A and Jhala, D and Shah, D and Shah, T and Raval, J and Prajapati, H and Patel, N and Upadhyay, K and Joshi, M and Patel, AK and Bondre, V and Kumar, N and Joshi, C}, title = {Genomic and evolutionary characterization of Chandipura virus: a cause of the 2024 outbreak in Gujarat, India.}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0157825}, pmid = {41954393}, issn = {2165-0497}, abstract = {UNLABELLED: Acute encephalitis syndrome (AES) caused by Chandipura virus (CHPV) is a rapidly progressive and often fatal neurological illness predominantly affecting children in India. However, limited research on CHPV disease progression and viral genomics has hindered a comprehensive understanding of its transmission dynamics and evolutionary behavior. CHPV is endemic in India, with previous outbreaks (2003-2004) reported case fatality rates (CFRs) ranging from 56% to 75%. In the current (2024) outbreak, the CFR declined to 46%, with an overall test-positivity rate of 18.6%, possibly reflecting improvements in supportive care. Despite advances in genomics and sequencing technologies, only a limited number of CHPV genomes are publicly available. To address this gap, we performed whole-genome sequencing of CHPV isolated from a pediatric patient aged 12 years from Patan, Gujarat. Comparative genomic analysis with previously reported Indian strain revealed approximately 293 mutations, including 24 non-synonymous. The estimated evolutionary rate of CHPV was ~1.62 × 10[-2] substitutions/site/year. Furthermore, the selective pressure analysis showed that, despite the virus being under strong purifying (negative) selection, several non-synonymous changes were identified. Nonetheless, as the present analysis is based on the single genome, further sequencing, validation, and broader comparative analysis are required to draw a definitive inference. However, these findings suggest that even under purifying selection pressure, CHPV retains the ability to infect and cause severe disease in children. This highlights the continued need to investigate virus-host interactions, particularly host immune responses, to better understand CHPV pathogenesis and its ability to cause disease in children.

IMPORTANCE: Chandipura virus (CHPV) is an etiological agent of acute encephalitis syndrome (AES) in children, characterized by rapid neurological decline; yet the viral and host factors governing its neuropathogenesis and sudden outbreak dynamics remain poorly defined. Despite minimal genomic variation indicative of strong purifying selection, which supports the continued efficacy of existing molecular diagnostics and candidate therapeutics, CHPV re-emerges unpredictably in human populations, as exemplified by the 2024 AES cluster in Gujarat. This outbreak underscores the importance of continuous genomic surveillance to elucidate viral behavior and immune-evasion mechanisms. Moreover, it highlights the utility of both amplicon-based and metagenomic next-generation sequencing approaches for future CHPV detection and comprehensive genome characterization.}, } @article {pmid41954722, year = {2026}, author = {Kruis, T and Wassermann, M and Graf, B and Lührig, K and Menzel, P and Schwarzer, R and Ziegler, J and Isner, C}, title = {Correction: Unmasking the mimic: vertebral alveolar echinococcosis diagnosed by metagenomic next‑generation sequencing.}, journal = {Infection}, volume = {}, number = {}, pages = {}, doi = {10.1007/s15010-026-02771-5}, pmid = {41954722}, issn = {1439-0973}, } @article {pmid41954798, year = {2026}, author = {Liu, P and Zhang, J and Liu, X and Li, B and Peng, Y and Li, B and Lyu, X and Tan, L and Guo, Z and Li, Z and Hu, M}, title = {Metagenomic next-generation sequencing for comprehensive pathogen detection in intraocular infection.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41954798}, issn = {1435-4373}, support = {Grant No.2023XQLH173//Central Universities of Central South University/ ; No. 82102499//National Natural Science Foundation of China/ ; No. 82270658//National Natural Science Foundation of China/ ; No. 2021JJ40840//the Hunan Natural Science Foundation/ ; No.202211003513//Scientific Research Project for Hunan Health Commission/ ; }, } @article {pmid41954996, year = {2026}, author = {Prabhu, A and Rinke, C}, title = {ICTV Virus Taxonomy Profile: Krittikaviridae 2026.}, journal = {The Journal of general virology}, volume = {107}, number = {4}, pages = {}, doi = {10.1099/jgv.0.002239}, pmid = {41954996}, issn = {1465-2099}, mesh = {Genome, Viral ; Phylogeny ; Virion/ultrastructure/genetics ; *Archaeal Viruses/classification/genetics/isolation & purification/ultrastructure ; Virus Replication ; DNA, Viral/genetics ; *DNA Viruses/classification/genetics/isolation & purification ; *Archaea/virology ; }, abstract = {The family Krittikaviridae includes dsDNA viruses associated with the marine archaeal lineage Poseidoniales. These viruses have been identified through metagenomic analysis of brackish estuarine samples and are closely related to other 'magroviruses'. The family belongs to the order Magrovirales and includes the genus Velanvirus and the species Velanvirus brisbanense. Viruses in the family have a genome of about 80 kbp that includes modules for DNA replication and virion morphogenesis. Krittikavirids are predicted to form virions with an icosahedral capsid and helical tail, characteristic of viruses belonging to the class Caudoviricetes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Krittikaviridae, which is available at ictv.global/report/krittikaviridae.}, } @article {pmid41955630, year = {2026}, author = {Wu, Z and Chen, H and Yao, Y and Wu, J and Li, H and Wang, W and Jiang, Q and Li, P and Zhou, H}, title = {Clinical evaluation of probe capture based targeted next generation sequencing for pulmonary infection in immunocompromised patients: a cross-sectional diagnostic accuracy study.}, journal = {Infectious diseases (London, England)}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/23744235.2026.2654559}, pmid = {41955630}, issn = {2374-4243}, abstract = {BACKGROUND: Timely aetiological diagnosis of pulmonary infection in immunocompromised patients (ICPs) remains challenging because clinical presentations may be atypical and conventional microbiological tests (CMTs) have limited sensitivity. Probe capture based targeted next generation sequencing (ptNGS) has emerged as a potential alternative to metagenomic next generation sequencing (mNGS), but its clinical performance in this population remains incompletely defined.

METHODS: In this cross-sectional diagnostic accuracy study, immunocompromised adults undergoing bronchoalveolar lavage for suspected pulmonary infection were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using CMTs, mNGS, and ptNGS. Composite clinical adjudication served as the reference standard. Diagnostic performance was compared at the case level, and pulmonary microbiota characteristics were explored.

RESULTS: Among 78 enrolled patients, 60 were classified as having pulmonary infection. Causative pathogens were identified in 52 cases, and fungal pathogens, particularly Pneumocystis jirovecii, were the most frequently detected. At the case level, ptNGS and mNGS demonstrated higher sensitivity than CMTs (80.0% vs 80.0% vs 26.7%) and showed high concordance in microorganisms identified (91.7%). Specificity was 72.2% for CMTs, compared with 44.4% for mNGS and 38.9% for ptNGS. Positive sequencing results were also observed in patients without pulmonary infection (n = 18), predominantly involving viral or opportunistic microorganisms. Microbiota analysis of 65 samples revealed reduced microbial alpha diversity and altered community composition in patients with pulmonary infection.

CONCLUSIONS: In ICPs with suspected pulmonary infection, ptNGS substantially increases pathogen detection compared with CMTs and demonstrates diagnostic performance comparable to mNGS. Sequencing results require careful clinical interpretation, given the difficulty in distinguishing infection from colonisation in respiratory specimens. Exploratory microbiota analyses suggest infection associated alterations in lung microbial ecology that warrant further validation.}, } @article {pmid41955710, year = {2026}, author = {Sahu, TK and Rathored, J and Patil, P}, title = {Tri-layer microbiology for LMIC Hospitals: linking syndromic panels with reflex culture and targeted sequencing for real world care - a narrative review.}, journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases}, volume = {30}, number = {3}, pages = {105808}, pmid = {41955710}, issn = {1678-4391}, mesh = {Humans ; Antimicrobial Stewardship ; *High-Throughput Nucleotide Sequencing/methods ; Molecular Diagnostic Techniques/methods ; Resource-Limited Settings ; }, abstract = {Rapid, syndromic molecular panels and high throughput sequencing have transformed the diagnostic landscape for sepsis, respiratory, gastrointestinal, and central nervous system infections, but their value in routine practice depends on how they are integrated with conventional microbiology and antimicrobial stewardship. This review synthesises recent high-quality evidence to propose a pragmatic three-tier hybrid framework. Tier 1 comprises syndrome specific rapid panels that provide organism and selected resistance markers within hours, primarily to accelerate early escalation or de-escalation rather than to replace culture. Tier 2 positions reflex culture and targeted adjunct tests as the non-negotiable specificity anchor, confirming molecular hits, distinguishing infection from colonisation or contamination, generating phenotypic susceptibility data and supplying isolates for infection prevention and public health surveillance. Tier 3 reserves targeted or metagenomic sequencing for a small, clinically critical subset of high suspicion, panel negative and culture negative cases, where additional breadth can realistically change management. Across sepsis/BSI, pneumonia, gastrointestinal infection and CNS disease, available data indicate that clinical benefit is driven less by any individual technology and more by disciplined implementation: clear indications, explicit reflex rules, close linkage to antimicrobial stewardship and systematic audit of key performance indicators such as time-to-targeted therapy, spectrum of antimicrobial use and cost per additional actionable diagnosis. The proposed tiered, syndrome wise algorithms provide a transferable conceptual scaffold that can be adapted to local resources, allowing laboratories in both high and low resource settings to introduce advanced diagnostics without abandoning culture-based anchors or stewardship accountability.}, } @article {pmid41955799, year = {2026}, author = {Chen, Y and Zhuo, G and Liu, C and Zheng, Y and Guo, S and Lu, X and Zhen, G}, title = {Efficient cadmium removal and immobilization from acid mine drainage by composite sulfate-reducing consortia: Mechanistic insights from EPS characterization, key enzyme activities, and metagenomics.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141956}, doi = {10.1016/j.jhazmat.2026.141956}, pmid = {41955799}, issn = {1873-3336}, mesh = {*Cadmium/metabolism ; Mining ; *Sulfates/metabolism ; Biodegradation, Environmental ; Metagenomics ; Bioreactors ; *Water Pollutants, Chemical/metabolism ; Bacteria/metabolism/genetics ; Sewage/microbiology ; Microbial Consortia ; Oxidation-Reduction ; Wastewater ; }, abstract = {Bioremediation has gained increasing attention for remediating heavy-metal wastewater from mining activities, such as acid mine drainage (AMD). Cadmium (Cd) is of special concern due to its high mobility, bioaccumulation, and highly toxic with stringent discharge limits, yet community- and metabolism-level mechanisms that sustain remediation under metal stress remain insufficiently understood. Here, three lab-scale up-flow anaerobic sludge bed (UASB) reactors enriched with sulfate-reducing bacteria (SRB) were established with inocula containing 100% sludge, 75% sludge + 25% soil, and 50% sludge + 50% soil to evaluate Cd removal performance and microbial adaptation. All reactors achieved ≥ 97.5% Cd removal, with effluent Cd consistently below detection, demonstrating effective immobilization under tested conditions. Sequestration in the bottom layer helped maintain a more favorable metabolic environment in the upper zone. Integrated analyses of extracellular polymeric substances (EPS), enzyme activities, and metagenomic revealed inoculum-dependent trade-offs: moderate soil addition enhanced recovery resilience, whereas the pure-sludge inoculum retained stronger sulfur-cycling potential than soil-derived communities. Metagenomic profiling supported distinct roles of dissimilatory sulfate reduction in sulfide generation and metal sulfide precipitation and assimilatory sulfur pathways in cellular sulfur demand and stress buffering. Notably, direct interspecies electron transfer/extracellular electron transfer (DIET/EET) associated genes and electron-transport indicators were enriched in reactors with superior recovery, supporting an inferred sulfate reduction-DIET (SR-DIET) synergy whereby coupled sulfur cycling and enhanced interspecies/extracellular electron exchange may facilitate energy restoration and sustained Cd immobilization. These findings advance mechanistic understanding of SRB-based treatment and inform engineering of resilient anaerobic consortia for mine-impacted and industrial effluents.}, } @article {pmid41955854, year = {2026}, author = {Luo, M and Fan, J and Wang, X and Ge, Y and Feng, D and Cao, S and Wang, J and Deng, H and Luo, J and Zhao, Y and Ge, C and Bu, H}, title = {Microplastics drive the reconfiguration of microbial sulfur cycling pathways in seagrass bed sediments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {398}, number = {}, pages = {128089}, doi = {10.1016/j.envpol.2026.128089}, pmid = {41955854}, issn = {1873-6424}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Sulfur/metabolism ; *Microplastics/analysis ; Bacteria/metabolism ; *Water Pollutants, Chemical/analysis ; }, abstract = {Microplastics (MPs) pollution threatens marine biogeochemical cycles, but its impact on the sediment sulfur cycle remains unclear. A 112-day microcosm incubation experiment was conducted to investigate the effects of three common MPs, polylactic acid (PLA), polyethylene (PE), and polystyrene (PS), on sulfur speciation, microbial communities, and functional genes in seagrass bed sediments using integrated amplicon sequencing and metagenomics. MPs significantly altered sediment sulfur speciation, with PLA inducing the strongest shifts, including 111.2% accumulation of total inorganic sulfate (TIS) and a 163.3% increase in TIS/Sulfide ratios, indicative of enhanced sulfur oxidation, while PE and PS promoted sustained sulfide accumulation. Distinct polymer-specific changes in sulfur-cycling bacteria communities were observed, with PLA suppressing the dominant Bradymonas (31.3% decrease) while enriching heterotrophic Sulfitobacter (26.5% increase), PE driving a transition towards autotrophic pathways with Thiohalomonas increasing by 272.8%, and PS selectively enriching generalist sulfur-oxidizing genera such as Roseovarius and Methyloceanibacter. Metagenomic analysis highlighted a shift from assimilatory biosynthetic pathways to dissimilatory energy-generating processes. These findings suggest that MPs intensify sulfide stress and disrupt sulfur metabolism, thereby reducing sediment biogeochemical stability and potentially impairing carbon burial and ecosystem resilience. These results provide critical insights into the ecological consequences of MP exposure on biogeochemical cycles in seagrass bed sediments.}, } @article {pmid41955934, year = {2026}, author = {Cornu Hewitt, B and Odendaal, ML and de Rooij, MMT and Bossers, A and Franz, E and Bogaert, D and Smit, LAM}, title = {Impacts of inhaled exposures on the upper respiratory tract microbiome: a systematic review.}, journal = {The Science of the total environment}, volume = {1030}, number = {}, pages = {181776}, doi = {10.1016/j.scitotenv.2026.181776}, pmid = {41955934}, issn = {1879-1026}, mesh = {Humans ; *Microbiota ; *Respiratory System/microbiology ; *Inhalation Exposure/adverse effects ; *Air Pollutants/adverse effects ; }, abstract = {BACKGROUND: Inhaled exposures can substantially affect human health. The upper respiratory tract (URT) microbiome forms a critical first point of interaction with inhaled agents (e.g. air pollutants and chemicals), yet its response to most inhaled exposures remains poorly characterised beyond the well-studied effects of tobacco smoking.

METHODS: We systematically reviewed research articles from 2005 to 2024 investigating the effects of inhaled exposures on the human URT microbiome, using sequencing-based approaches. Database searches in PubMed, Scopus, and EMBASE yielded 5263 unique publications. Following screening using ASReview, 66 studies met inclusion criteria, covering four exposure domains: urban outdoor, rural outdoor, household indoor, and occupational settings.

RESULTS: Inhaled exposures were consistently associated with alterations in the URT microbiome, often differing by anatomical niche (e.g. nasal, nasopharynx, oral, oropharynx). Outdoor air pollution and urbanisation were linked to reduced microbial diversity and depletion of commensals, whereas green space and agricultural exposures were associated with higher diversity, enrichment of health-associated taxa, and introduction of animal- and soil-associated microbes. Findings for other exposures (e.g. indoor pollutants, pesticides) were more heterogeneous.

CONCLUSIONS: Overall, the URT microbiome remains understudied as a mediator of respiratory health effects related to inhaled exposures, while methodological heterogeneity complicates comparability across studies. Future research should prioritise benchmarked protocols, longitudinal designs, and functional analyses (e.g. metagenomics) to clarify how inhaled exposures alter microbial activity, resilience, ecological interactions, and host outcomes. This synthesis highlights the need for integrated environmental health approaches and for assessing the long-term consequences of inhaled exposures.}, } @article {pmid41955982, year = {2026}, author = {Besharati Fard, M and Guo, H and De Vrieze, J and Wu, D}, title = {Chronic ciprofloxacin exposure reduces anaerobic digestibility of waste microalgal-bacterial aerobic granular sludge: Metagenomics and metatranscriptomics overview.}, journal = {Water research}, volume = {299}, number = {}, pages = {125876}, doi = {10.1016/j.watres.2026.125876}, pmid = {41955982}, issn = {1879-2448}, mesh = {*Ciprofloxacin/pharmacology ; *Sewage/microbiology ; Anaerobiosis ; *Microalgae/metabolism ; Bioreactors ; Methane/metabolism ; Metagenomics ; Anti-Bacterial Agents ; Waste Disposal, Fluid ; }, abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) is a promising wastewater treatment technology, but its long-term sustainability depends on whether its waste biomass (WMB-AGS) can be effectively stabilized through anaerobic digestion, particularly under antibiotic stress. Here, we compared the digestibility and ciprofloxacin response of WMB-AGS and conventional waste activated sludge (WAS) using 21-day biochemical methane potential (BMP) tests, 3-day hydrolysis-acidogenesis assays, and 90-day semi-continuous digesters, supported by enzyme activity, extracellular polymeric substances (EPS) characterization, and multi-omics profiling. The WAS produced substantially higher methane yields (302 ± 7 mL CH4/g VS) than WMB-AGS (62 ± 4 mL CH4/g VS), confirming the superior digestibility of WAS. Ciprofloxacin effects were exposure-regime dependent, a single initial dose up to 1000 µg/L did not affect methane production in BMP assays. However, continuous ciprofloxacin exposure in semi-continuous digesters significantly reduced daily biogas production, from 114 ± 9 to 96 ± 6 mL/day in WAS and from 23 ± 1 to 15 ± 2 mL/day in WMB-AGS. During the hydrolysis-acidogenesis, ciprofloxacin promoted volatile fatty acid accumulation and inhibited key hydrolytic, acidogenic, and methanogenic enzymes. Biotransformation was the dominant ciprofloxacin removal mechanism. The EPS acted as an initial protective interface but also contributed to hydrolysis limitation. Multi-omics analyses showed that chronic ciprofloxacin exposure did not suppress core methanogenesis genes, but reconfigured upstream electron-transfer and methyl-transfer functions, with enrichment of Corynebacterium and Methanobacterium. Overall, WMB-AGS is inherently less digestible than WAS. These findings highlight the need to consider substrate-specific matrix effects and long-term antibiotic pressure when evaluating the downstream anaerobic valorization.}, } @article {pmid41955988, year = {2026}, author = {Wang, X and Xue, T and Li, J and Zhang, C and Hao, G and Xing, Y and Tao, R and Guo, L and Zhang, H and Chai, S and Zheng, L}, title = {Novel photoelectron-driven nitrate reduction in anammox granules using photosensitive semiconductor iron mineral for wastewater treatment.}, journal = {Water research}, volume = {299}, number = {}, pages = {125862}, doi = {10.1016/j.watres.2026.125862}, pmid = {41955988}, issn = {1879-2448}, mesh = {Oxidation-Reduction ; *Nitrates/chemistry ; Wastewater ; Semiconductors ; Iron/chemistry ; Electrons ; Ferric Compounds/chemistry ; }, abstract = {The accumulation of nitrate byproducts and limited electron availability fundamentally constrain the efficacy of anaerobic ammonium oxidation (anammox) processes. While iron minerals regulate electron transfer, their potential to drive anammox via semiconductive photoexcitation remains underexplored. Here, we establish a novel "Photo-Chemo-Bio" strategy to overcome these thermodynamic bottlenecks using light-excited hematite (α-Fe2O3). Among tested minerals, hematite exhibited superior band-structure suitability, achieving a 3.65-fold photocurrent enhancement (4.06 μA·cm[-2]) upon bio-hybridization, facilitated by the active recruitment of photo-electrons via upregulated outer-membrane c-type cytochromes. Crucially, this photo-enhanced electron supply boosted the total nitrogen removal rate by 27.4% while suppressing nitrate yield by 42.8%. Kinetic analysis revealed a precise metabolic decoupling: solar irradiation did not accelerate ammonia oxidation but specifically diverted electron flow toward nitrate reduction pathways. Genome-resolved metagenomics unraveled the molecular basis of this synergy, identifying a "hardwired" cooperative network: flanking Desulfobacillus-like species, characterized by a specific metabolic truncation (absence of nor genes), act as obligate "net NO providers" to fuel the anammox core; concurrently, heterotrophic Casimicrobiaceae unexpectedly encode Photosystem II (psbA), functioning as auxiliary "energy antennas" to harvest photons. These findings demonstrate how mineral-microbe hybrids can orchestrate electron flux to close the nitrogen loop, offering a sustainable, carbon-free strategy for high-efficiency wastewater treatment.}, } @article {pmid41956026, year = {2026}, author = {Sorgato, AC and Kim, B and Papillon, J and Nivala, J and Silveira, DD and Lapolli, FR and Forquet, N}, title = {Microbial fuel cells inoculated with French vertical flow treatment wetland sludge: A step towards clogging biodetector development.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {171}, number = {}, pages = {109297}, doi = {10.1016/j.bioelechem.2026.109297}, pmid = {41956026}, issn = {1878-562X}, mesh = {*Bioelectric Energy Sources/microbiology ; *Wetlands ; *Sewage/microbiology ; Biofilms ; Electrodes ; Bacteria/genetics/metabolism ; France ; }, abstract = {Clogging is considered an operational challenge in French vertical flow treatment wetlands (VFTWs), causing hydraulics and aeration problems. The available monitoring methods are labor intensive. Microbial fuel cells (MFCs) have emerged as real-time biosensors, including for treatment wetlands (TW) systems. In this study, French VFTW sludge was investigated as inoculum in MFCs, to assessing its adaptation into electrochemical environment as a step for clogging MFC-based biodetector implementation in such systems. The results show that the inoculum was successfully adapted, with stable current generation at 0.4 mA. The electrochemical impedance spectroscopy (EIS) demonstrated the establishment of a biofilm with electroactive characteristics and non-limiting anode. Metagenomic analysis showed that the French VFTW harbor electroactive species, and the MFC created a selective pressure on the VFTW sludge inoculum and significantly shaped the microbial community and function, stimulating the enrichment of electroactive bacteria (EAB), such Geobacterales (4.11% to 5.83%), with potential expression of cytochrome-c for extracellular electron transference (EET). This study illustrates the feasibility of developing electroactive biofilms from French VFTW and suggests its use as an inoculum, improving the integration of TW-MFC systems. Considering these results, the well-adapted anodic biofilm could enable the detection of aeration limitations via cathodic reactions in future studies.}, } @article {pmid41956515, year = {2026}, author = {Rober, AR and Reese, LC and Brown, SP and McMahon, KD and Louca, S and Cieslik, J and Kane, ES and Turetsky, MR and Wyatt, KH}, title = {Hydrologic History Regulates Microbial Biofilm Diversity and Ecosystem Function.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70300}, pmid = {41956515}, issn = {1462-2920}, support = {MCB-2514370//National Science Foundation/ ; DEB-2141285//National Science Foundation/ ; DEB LTREB-2011286//National Science Foundation/ ; DEB LTREB-2011257//National Science Foundation/ ; DEB-1636476//National Science Foundation/ ; RJVA-PNW-01-JV-11261952-231//Pacific Northwest Research Station/ ; //USDA Forest Service/ ; }, mesh = {*Biofilms/growth & development ; *Ecosystem ; Bacteria/genetics/classification/isolation & purification ; *Fungi/genetics/classification/physiology ; *Biodiversity ; Cyanobacteria/genetics/physiology/classification ; Droughts ; Floods ; Groundwater/microbiology/chemistry ; Hydrology ; }, abstract = {Aquatic biofilms are an understudied component of northern peatlands and are expected to play a more prominent role in ecosystem processes in areas where aquatic habitat is expanding. The goal of this study was to investigate how hydrologic history influences biofilm diversity and functional genes. This study was conducted in a long-term water table manipulation that simulates drought (lowered water table treatment) and flooding (raised water table treatment) conditions relative to a control treatment (no manipulation). We used a combination of metabarcoding and metagenomic approaches to (1) examine the diversity of eukaryotic algae, cyanobacteria, bacteria and fungi within the biofilm and (2) identify functional genes associated with alternating wet-dry transitional states. Historical flooding, but not drought, led to broad changes in composition and functional genes, especially those associated with carbon metabolism and nitrogen cycling. Differences were related to changes in relative abundance rather than the presence/absence of individual taxa or genes. Hydrologic history influenced community diversity by reducing interspecific competition or by alleviating resource limitation. These findings show that hydrologic history regulates species membership of the community (and thereby associated genes) but differences in water chemistry and interspecific interactions alter the relative abundance of species and their functional potential.}, } @article {pmid41956535, year = {2026}, author = {Cui, T and Huang, M}, title = {Tuberculous Peritonitis Diagnosed by Metagenomic Next-Generation Sequencing Progressing to Fatal Encapsulating Peritoneal Sclerosis in a Peritoneal Dialysis Patient: A Case Report.}, journal = {Seminars in dialysis}, volume = {39}, number = {1-2}, pages = {53-56}, doi = {10.1111/sdi.70022}, pmid = {41956535}, issn = {1525-139X}, support = {SZSM202411016//Sanming Project of Medicine in Shenzhen/ ; }, mesh = {Humans ; Female ; *Peritonitis, Tuberculous/diagnosis/complications ; *Peritoneal Dialysis/adverse effects ; Adult ; *Peritoneal Fibrosis/etiology/diagnosis/microbiology ; Fatal Outcome ; *Kidney Failure, Chronic/therapy/diagnosis ; *High-Throughput Nucleotide Sequencing/methods ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *Metagenomics/methods ; }, abstract = {A 40-year-old woman on peritoneal dialysis for 3 years presented with febrile peritonitis. Metagenomic next-generation sequencing (mNGS) confirmed Mycobacterium tuberculosis complex in ascitic fluid, leading to prompt anti-tuberculosis therapy. She initially improved but developed ultrafiltration failure 15 months later and transitioned to hemodialysis. At 18 months, she developed bowel obstruction, bloody ascites, and characteristic imaging and laparoscopic findings of encapsulating peritoneal sclerosis (EPS). Despite supportive care, she deteriorated and died 30 months after tuberculosis peritonitis diagnosis. This case highlights that mNGS enables rapid diagnosis of tuberculous peritonitis when conventional tests are inconclusive, and that tuberculosis peritonitis may serve as a potent inflammatory trigger for EPS even after peritoneal dialysis cessation. Early recognition and timely intervention may improve outcomes.}, } @article {pmid41956809, year = {2026}, author = {Li, X and Xie, M and Kang, JX and Chen, Y and Han, J and Chen, Y and Chen, Q and Yu, T and Liu, S and Ouyang, Z and Sun, Q and Li, K and Zhang, S and She, J and Yu, J}, title = {Bifidobacterium catenulatum boosts anti-PD-1 efficacy in microsatellite stable colorectal cancer via activating CD8[+] T cells.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-336025}, pmid = {41956809}, issn = {1468-3288}, abstract = {BACKGROUND: Certain gut bacteria are associated with improved responses to immunotherapy.

OBJECTIVE: We aim to identify bacteria that inhibit colorectal cancer (CRC) progression and enhance immunotherapy efficacy.

DESIGN: The abundance of bacteria in CRC patients was evaluated in our in-house cohorts and validated in published datasets. The effect of candidate bacterium with anti-PD-1 therapy was determined in two syngeneic mouse models of MC38 (microsatellite instability-high) and CT26 (microsatellite stable, MSS), transgenic Apc [min/+] mice and azoxymethane/dextran sulfate sodium (AOM/DSS)-induced CRC tumourigenesis model. Immune landscape changes were identified by multicolour flow cytometry and immunohistochemistry staining. Metabolomic profiling was performed on stool, serum and tumour tissues.

RESULTS: Bifidobacterium catenulatum was significantly depleted in stool samples of 110 CRC patients compared with 112 healthy controls, which was further validated in 3 published metagenomic datasets comprising 198 CRC patients and 176 normal subjects. Oral administration of B. catenulatum inhibited tumour growths in multiple CRC models including MC38 and CT26 syngeneic models, Apc[min/+] mice and AOM/DSS-induced CRC. Notably, B. catenulatum synergised with anti-PD-1 therapy through enhancing intratumoural CD8[+] T cell infiltration in MSS CRC models of Apc[min/+] mice and CT26 allografts. B. catenulatum-derived acetate was identified as the functional metabolite. Mechanistically, acetate directly bound to MCT-4 in CD8[+] T cells and activated mitogen-activated protein kinase signalling. Pharmacological and genetic MCT4 ablation abolished acetate-mediated CD8[+] T cell activation in vitro.

CONCLUSION: B. catenulatum suppresses colorectal tumourigenesis through generating acetate, which also improves anti-PD-1 efficacy through activating CD8[+] T cells in MSS CRC. B. catenulatum is a potential adjuvant to improve immunotherapy against CRC.}, } @article {pmid41957175, year = {2026}, author = {Yang, S and Wang, X and Duan, J and Yang, S and He, J and Fang, C and Zhao, N and Huang, Y}, title = {Effects of replacing chemical fertilizer with organic fertilizer on organic carbon mineralization and carbon cycle functional genes in yellow soil.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41957175}, issn = {2045-2322}, support = {2022YFD1901500, 2022YFD1901505//National Key R&D Program Project/ ; ZSYS[2025]035//Guizhou Key Laboratory of Cultivated Land Quality (Qian Ke He Platform)/ ; grant number BQW[2024]009//Construction of High Quality and Efficient Mechanized Scientific and Technological Innovation Talent Team of Characteristic Coarse Cereals in Guizhou Province/ ; }, mesh = {*Soil/chemistry ; *Fertilizers/analysis ; *Carbon/metabolism/chemistry ; Soil Microbiology ; *Carbon Cycle/genetics ; Nitrogen ; Phosphorus ; Metagenomics ; }, abstract = {Fertilization-mediated soil organic carbon (SOC) mineralization is a key process in agroecosystem carbon cycling, yet the microbial mechanisms involved under different fertilization regimes remain unclear. This study, based on a three-year field experiment in acidic yellow soil (Ultisol) in Guizhou, integrated SOC mineralization incubation and metagenomic sequencing to compare SOC mineralization and functional gene profiles under no fertilization (CK), chemical fertilizer alone (NP), and replacing chemical fertilizer with 50% or 100% organic fertilizer (1/2NPM and M). Fertilization significantly increased cumulative mineralized SOC (Ct) (p < 0.05); NP showed high mineralization, whereas organic-fertilizer replacement reduced the cumulative mineralization ratio (Ct/SOC). Metagenomic analysis indicated NP did not substantially alter carbon-cycling genes but lowered the C/N ratio, increasing microbial diversity and driving "carbon-compensation" mineralization. Conversely, 1/2NPM and M improved soil pH, available phosphorus (AP), and nitrate nitrogen (NO3[-]-N), reshaped microbial community structure, up-regulated carbon-fixation genes (korA, facA, coxS), and suppressed carbon-degradation genes (pel, chi), enhancing carbon sequestration capacity. Partial least squares path modeling confirmed a "stoichiometry-community diversity" cascade significantly regulated SOC mineralization (p < 0.01), with organic-fertilizer replacement shifting functional profiles from carbon degradation to carbon fixation.}, } @article {pmid41957291, year = {2026}, author = {Yang, M and Fang, J and Liao, Q}, title = {Comment on: "Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens"-a call to disentangle clostridium scindens' bile acid metabolism from glucocorticoid modulation in SLE pathogenesis.}, journal = {Clinical rheumatology}, volume = {}, number = {}, pages = {}, pmid = {41957291}, issn = {1434-9949}, } @article {pmid41957365, year = {2026}, author = {Kan, J and Spotton, K and Morales-Amador, A and Hernandez, Y and Burian, J and Panfil, C and Ternei, MA and Boer, RE and Bhattacharjee, A and Brady, SF}, title = {Mode of action guided metagenomic natural product discovery reveals convergent evolution of a ClpP-targeting motif.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41957365}, issn = {2041-1723}, support = {R35 GM122559/GM/NIGMS NIH HHS/United States ; T32 GM136640/GM/NIGMS NIH HHS/United States ; R35GM122559//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; NIH T32 GM136640//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, mesh = {*Endopeptidase Clp/metabolism/genetics/chemistry ; *Biological Products/chemistry/metabolism/pharmacology ; Multigene Family ; Anti-Bacterial Agents/pharmacology/chemistry ; *Bacterial Proteins/metabolism/genetics ; *Metagenome ; Computational Biology ; Phenylalanine/analogs & derivatives/chemistry ; }, abstract = {The discovery of natural products with specific modes of action from metagenomes remains challenging. Here, we present resistance-CONKAT-seq, a pipeline that links biosynthetic gene clusters (BGCs) to self-resistance genes, enabling identification of metabolites with desired molecular targets. Using clpP-directed resistance-CONKAT-seq, we identify the calprotamides, which activate native ClpP and enhance its activity. Cryo-EM and bioinformatic analyses reveal that the calprotamides' medium-chain N-acylphenylalanine substructure is a convergently evolved ClpP-targeting motif and identify additional BGCs predicted to encode this moiety, including some with co-localized clp genes. The synthesis of structures bioinformatically inspired by two such clp-linked BGCs, desmethyl jomthonic acid C and tuscamide, reveals that both enhance ClpP activity. Extending our bioinformatically guided synthesis study to additional BGCs lacking nearby clp genes shows that ClpP activity enhancement correlated with antibacterial activity, with the strongest enhancers exhibiting narrow-spectrum antibiotic activity. These findings establish N-acylphenylalanine as a previously unrecognized but common natural motif for targeting ClpP, which should help guide the discovery of both natural and synthetic ClpP modulators for antibiotic and anticancer development. Resistance-CONKAT-seq offers a scalable method for exploring biosynthetic dark matter for metabolites with desired modes of action.}, } @article {pmid41957864, year = {2026}, author = {Mawarda, PC and Speksnijder, A and Krijger, D and Berkhout, J and Hoogenboom, A and Duijker, DA and Khoiri, AN and Kraaijeveld, K and Stech, M and Wittink, F}, title = {Functional redundancy and stability support the resilience of the Evernia prunastri holobiont under urbanization.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41957864}, issn = {2524-6372}, support = {NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: Lichens are now recognized as holobionts comprising a mycobiont, photobiont, and diverse microbiomes, yet the functional roles of these additional microbial partners remain poorly characterized, especially under urbanization. Here, we used the epiphytic lichen Evernia prunastri from urban and natural areas to test the hypothesis that its resilience to urbanization is underpinned by functional stability and redundancy within its multi-kingdom consortium.

RESULTS: Using an integrated approach of amplicon and shotgun metagenomic sequencing, we found that the bacterial community structure and the functional potential of the mycobiont, bacteria, and fungi remained stable despite urbanization, highlighting stability and resistance to urban environmental stress. Furthermore, by focusing on symbiosis-related functions, we found that each partner shows tendencies toward certain roles, yet we discovered broad functional overlap, suggesting microbial contributions that buffer the symbiosis. Finally, we found that E. prunastri and its microbiome harbors diverse biosynthetic gene clusters with predicted ecological functions relevant for the symbiosis, spanning photoprotection, oxidative stress mitigation, nutrient acquisition, defense, and chemical communication.

CONCLUSIONS: Our study provides unprecedented genomic evidence that lichen resilience is an emergent property of the integrated holobiont, where functional complementarity and redundancy among diverse symbiotic partners maintain stability under urban environmental conditions.}, } @article {pmid41957950, year = {2026}, author = {van der Heijden, M and Clubb, JHA and Erawijantari, PP and Ronkainen, A and Arias, V and Jirovec, E and Kudling, T and Pakola, SA and Ojala, N and Haybout, L and Basnet, S and Grönberg-Vähä-Koskela, S and Karoliina Raatikainen, S and Hemminki, O and Kanerva, A and Quixabeira, DCA and Cervera-Carrascon, V and Manuel Dos Santos, J and Lahti, L and Hemminki, A}, title = {Alistipes and Eggerthella shape the response to oncolytic adenovirus therapy in mice and humans through short-chain fatty acid metabolism.}, journal = {Oncoimmunology}, volume = {15}, number = {1}, pages = {2656514}, doi = {10.1080/2162402X.2026.2656514}, pmid = {41957950}, issn = {2162-402X}, mesh = {Animals ; Humans ; Mice ; *Oncolytic Virotherapy/methods ; *Adenoviridae/genetics ; *Oncolytic Viruses/genetics ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Female ; *Actinobacteria/genetics/metabolism ; Feces/microbiology ; *Neoplasms/therapy ; Male ; }, abstract = {Accumulating evidence implicates the microbiome as an important determinant of clinical outcomes in cancer therapies; however, the role of the microbiome in oncolytic virus therapy remains largely unexplored. We investigated the gut microbiome of cancer patients following treatment with the oncolytic adenovirus igrelimogene litadenorepvec (Ad5/3-E2F-d24-hTNF-IRES-hIL2; TILT-123). Baseline fecal samples from phase I clinical trials (NCT04695327 and NCT05271318) were analyzed using shotgun metagenomic sequencing and compared to treatment outcomes. A higher relative abundance of Alistipes was observed in patients with treatment benefit, while elevated Eggerthella was observed with reduced benefit. These associations were validated in a preclinical mouse model where administration of Alistipes shahii improved the efficacy of adenovirus therapy. In addition, enrichment analysis in patient samples showed a positive correlation between higher relative abundance of Alistipes and elevated short-chain fatty acids in both feces and serum, which in turn revealed higher circulating neutrophil counts. Finally, in a case study, we observed that adenovirus treatment resulted in increased Alistipes relative abundance and reduced Eggerthella relative abundance, indicating that adenovirus therapy may beneficially modulate the microbiome. Overall, our findings reveal a novel association between Alistipes, Eggerthella, and the therapeutic response to oncolytic adenovirus therapy, highlighting their potential as biomarkers or targets for microbiome-based interventions such as pre-, pro-, or postbiotics.}, } @article {pmid41958036, year = {2026}, author = {Shin, H and Jeon, MK and Hur, HG}, title = {A Cautionary Case for Host Assignment Based on Broad Environmental blaOXA Carriers.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70327}, pmid = {41958036}, issn = {1758-2229}, support = {RS-2023-NR076613//National Research Foundation of Korea/ ; }, mesh = {*beta-Lactamases/genetics ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification/enzymology/drug effects ; Anti-Bacterial Agents/pharmacology ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Metagenome ; *Bacterial Proteins/genetics ; }, abstract = {Metagenomic analyses rely heavily on contig assembly and reference databases, which can introduce substantial bias when predicting the hosts of antibiotic resistance genes (ARGs) in complex environmental microbiomes. Reference-based metagenomic pipelines assign ARGs mostly to clinically important pathogens because publicly available genomic repositories are dominated by clinically relevant isolates. Motivated by this limitation, we investigated whether metagenomic inferences accurately reflect the true bacterial hosts of ARGs in a wastewater treatment plant, also integrating culture-based validation. Metagenomic screening suggested that ARGs (blaOXA) were primarily associated with clinical taxa. In contrast, culture-based screening identified a wider host distribution of blaOXA genes. Our results imply that environmental bacteria, rather than clinically important taxa, are also hosts of blaOXA genes. Phenotypic testing showed elevated cephalosporin minimal but no carbapenem resistance, consistent with the nature of carbapenem-hydrolysing class D β-lactamases. Our findings reveal that reliance on reference-based metagenomic host prediction can underestimate the diversity of environmental ARG reservoirs. This integrated approach highlights the need for cautious interpretation of metagenomic host assignments and the importance of coupling metagenomic pipelines with culture-dependent validation when assessing ARG ecology in the natural environments.}, } @article {pmid41958322, year = {2026}, author = {Yang, D and Bao, C and Xia, Y and Ling, Y and Zhang, F and Ji, R and Zhong, J and Zhang, T and Tian, H and Xu, X and Sun, B}, title = {Insights Into Variations in the Gut Virome of Tibetan Macaques (Macaca thibetana) Across Wild, Captive, and Semi-Provisioned Environments.}, journal = {American journal of primatology}, volume = {88}, number = {4}, pages = {e70148}, doi = {10.1002/ajp.70148}, pmid = {41958322}, issn = {1098-2345}, support = {32171488//National Natural Science Foundation of China/ ; 32300400//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Virome ; *Macaca/virology/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Tibet ; Animals, Wild/virology ; Animals, Zoo/virology ; }, abstract = {Viruses are integral components of the mammalian gut ecosystem, playing crucial roles in regulating the gut microbiome and maintaining host health. However, the impact of human activity on the gut virome of mammals remains poorly understood. This study investigated the gut viromes of Tibetan macaques (Macaca thibetana), a primate species endemic to China, under three distinct human-influenced environments (wild, semi-provisioned, and captive) using metagenomic sequencing. Our results revealed that semi-provisioned macaques supported the highest viral diversity, while captive and wild groups exhibited lower diversity, with distinct functional shifts among groups. Furthermore, the co-variation and highly coupled KEGG functional profiles between viral and bacterial communities suggest they function as an integrated synergistic network, where changes in one directly impact the metabolic output of the other. Co-occurrence network analysis further demonstrated that the virus-bacterium interaction network in the captive group was the most fragile, with a structure indicative of a high risk of micro-ecosystem imbalance. Microbial system imbalance is characterized by alterations in both community composition and function, resulting in diminished resilience and stability, which may ultimately compromise host intestinal health. Our results demonstrate that captivity and provisioning drive divergence in the Tibetan macaque gut virome. The fragile, skewed networks in captive individuals highlight a potential cost to microbial health, which may underlie broader health and adaptation risks such as heightened pathogen susceptibility and diminished capacity to cope with environmental perturbations. Thus, monitoring the virome offers a novel early-warning system, informing strategies to enhance welfare and conservation outcomes.}, } @article {pmid41958469, year = {2026}, author = {Voigt, RM and Chaudhary, A and Naqib, A and Engen, PA and Adnan, D and Dhana, K and Green, SJ and Villanueva, M and Agarwal, P and Barnes, LL and Sacks, F and Keshavarzian, A}, title = {Weight loss and metabolic improvements dominate the microbiome response in the MIND diet intervention: a randomized controlled trial.}, journal = {Alzheimer's & dementia (New York, N. Y.)}, volume = {12}, number = {2}, pages = {e70239}, pmid = {41958469}, issn = {2352-8737}, abstract = {INTRODUCTION: Observational studies link the MIND diet to reduced risk of Alzheimer's disease (AD) and slower cognitive decline. However, a recent randomized controlled trial found no differential cognitive benefit of the MIND diet over a control diet in the context of shared caloric restriction. Given that both groups achieved significant weight loss and metabolic improvements, this study aimed to disentangle the impact of the MIND diet and host metabolic improvements on the intestinal microbiome.

METHODS: A subset of participants (n = 213) from the MIND trial were analyzed in this study. Clinical data and stool samples were collected at baseline, Year 1, Year 2, and Year 3, and longitudinal changes in microbiome composition were assessed via shotgun metagenomics.

RESULTS: Both groups exhibited significant, transient microbiome remodeling at Year 1 (the period of most active weight loss). The control group demonstrated a broad range of altered metabolic pathways, whereas the MIND diet group showed only one, suggesting a functional buffering effect of the MIND diet. Prospective modeling independent of diet group revealed that a poorer cognitive trajectory was significantly associated with increased inositol degradation (PWY-7237) and purine nucleotide salvage (PWY66-409); conversely, a better cognitive trajectory was associated with increased degradation of deoxy sugars (FUC-RHAMCAT-PWY).

DISCUSSION: Caloric restriction, weight loss, and host metabolic improvement are the dominant factors shaping the intestinal microbiome, overshadowing diet-specific taxonomic shifts. The MIND diet appeared to provide a modest stabilizing effect on the microbial functional profile against perturbations during active weight loss; however, these dietary associations did not persist in covariate-adjusted models, suggesting that host metabolic improvements remained the primary driver of functional shifts.}, } @article {pmid41958710, year = {2026}, author = {Nakamichi, K and Manandhar, A and Shrestha, S and Sundararajan, M and Poudel, MP and Karmacharya, BM and Bade, A and Banjara, P and Shrestha, A and Sandt, A and Turski, G and Buhr, ED and Chowdhary, A and Van Gelder, RN}, title = {Association of Seasonal Hyperacute Panuveitis Syndrome with S. pneumoniae Endophthalmitis.}, journal = {Ophthalmology science}, volume = {6}, number = {5}, pages = {101128}, pmid = {41958710}, issn = {2666-9145}, abstract = {PURPOSE: To identify potential infectious agents in cases of seasonal hyperacute panuveitis syndrome (SHAPU) from vitreous biopsies of patients with this disorder.

DESIGN: A retrospective cohort analysis.

SUBJECTS: Vitreous biopsies were obtained during the course of care from 53 subjects with SHAPU.

METHODS: DNA extraction and whole genome shotgun sequencing was performed using Oxford Nanopore long read sequencing. Sequences were matched against microbial and human databases. Visual outcomes at presentation and at 6 months were recorded.

MAIN OUTCOME MEASURES: Identification and characterization of metagenomic sequences in vitreous isolates from subjects with SHAPU.

RESULTS: Adequate DNA for sequencing was obtained from 32 SHAPU subjects. Fifteen samples yielded bacteria on culture, with 14 S. pneumoniae and 1 S. aureus isolate recovered. Bacterial DNA was detected by whole genome sequencing in 29 of 32 cases. S. pneumoniae was the predominant organism recovered. Bacterial genomic loads ranged up to 10 000 bacteria/human cell, indicating active infection. No pathogens were detected in control samples. Reconstruction of bacterial genome was possible in 7 SHAPU cases and indicated diverse S. pneumoniae subtypes associated with individual cases. Sufficient DNA remained for analysis of torque teno virus by qualitative polymerase chain reaction in 17 cases, of which 13 were positive. Visual outcomes were mixed, with 7 patients having hypotonous eyes at 6 months, but 8 patients having better than 20/200 vision. No relationship could be discerned between presenting bacterial load and visual outcome.

CONCLUSIONS: The majority of SHAPU cases show molecular evidence for concurrent S. pneumoniae infection. Good visual results are possible in treating SHAPU as endophthalmitis.

FINANCIAL DISCLOSURES: The authors have no proprietary or commercial interest in any materials discussed in this article.}, } @article {pmid41959051, year = {2026}, author = {Weng, Y and Moyne, O and Walker, C and Haddad, E and Lieng, C and Chin, L and Rahman, G and McDonald, D and Knight, R and Zengler, K}, title = {A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling (metaRibo-Seq) data.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959051}, issn = {2692-8205}, abstract = {Metaribosome profiling (metaRibo-Seq) enables genome-wide measurement of translation across complex microbial communities by sequencing ribosome-protected mRNA fragments, but the short length of these footprints creates substantial nonspecific mapping against large reference genome collections, leading to spurious taxonomic and functional assignments. Here we present MOPP (Multi-Omics Processing Pipeline), a modular reference-based workflow that denoises metaRibo-Seq data by leveraging matched metagenomic coverage breadth to identify genomes likely to be truly present in a sample before aligning metatranslatomic and optional metatranscriptomic reads. MOPP generates taxon-by-gene count tables across genomic, transcriptional and translational layers, enabling integrated downstream analyses of microbial function. We evaluated MOPP using a defined 79-member synthetic human gut community profiled by metagenomics and metaRibo-Seq. Coverage breadth filtering markedly improved detection accuracy relative to a standard baseline workflow, with performance remaining robust across a broad intermediate threshold range and peaking at 92-95% coverage breadth. At a 92% threshold, MOPP reduced the number of distinct detected operational genomic units by 99.4% while retaining 87.8% of aligned metaRibo-Seq reads on average, and increased the F1 score from 0.02 to 0.61. Residual false positives were predominantly attributable to genomes with extremely high nucleotide similarity to true community members, whereas false negatives were enriched among low-abundance taxa, indicating that remaining errors are driven primarily by biological similarity and detection limits rather than widespread nonspecific mapping. Together, these results establish MOPP as a high-throughput workflow for robust processing of metaRibo-Seq in the context of matched metagenomics and position it as a scalable framework for integrated taxonomic and functional analysis of microbial communities across genomic, transcriptional and translational layers.}, } @article {pmid41959053, year = {2026}, author = {Midani, FS and Lee, DH and Moon, Y and Seale, M and Horvath, TD and Ardis, AK and Cantú, J and Coles, E and Pizzini, JD and Zhu, D and Dooling, SW and Ahern, GJ and Ardis, CK and Beckford, A and Ruggiero, NM and Shin, J and Joos, R and Stanton, C and Ross, RP and Dai, DLY and Mandhane, PJ and Petersen, C and Turvey, SE and Kiely, ME and Murray, DM and Costa-Mattioli, M and Tolias, KF and Britton, RA and Danhof, HA}, title = {Infant gut microbiomes contribute to metabolic states that impact brain function.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959053}, issn = {2692-8205}, abstract = {Alterations in the gut microbiome are associated with neurodevelopmental disorders, but causal mechanisms and therapeutic strategies remain undefined. Here, we demonstrate that human infant microbiomes isolated during the first six months of life drive behavioral impairments in mice and that microbiota-based interventions restore mice to normal behavior. Early-life microbiomes from twelve infants who later exhibited cognitive deficits at 2 years old (low-scoring) transferred adverse metabolic, brain, and behavioral phenotypes to mice, in contrast to microbiomes from twenty-three cognitively typical or high-scoring infants. Deficits in mice were rescued by fecal microbiota transplant from high-scoring infants or a rationally designed consortium that promoted amino acid levels. We confirmed lower fecal amino acid concentrations in low-scoring infants and replicated the association between early-life microbiome composition and cognitive outcomes in a second geographically independent infant cohort. Altogether, we discovered an early-life microbiome-mediated metabolic state causally linked to cognitive deficits and amenable to microbial intervention.}, } @article {pmid41959121, year = {2026}, author = {Solomon, Z and Eno, M and Thompson, SC and Rager, SL and Jin, JC and Zeng, MY and Keerthy, D and Worgall, S and Johnson, EL and Heras, A}, title = {Increased S. epidermidis in the airway-gut microbiome of infants with bronchopulmonary dysplasia.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959121}, issn = {2692-8205}, abstract = {RATIONALE: Bronchopulmonary dysplasia (BPD), the lung disease associated with premature birth, is a significant health problem, often with long-term respiratory consequences. Recent research has highlighted the potential role of the lung and gut microbiome in the development and progression of BPD, yet it is unclear what aspects of the microbiome may contribute to BPD susceptibility.

OBJECTIVES: To comprehensively characterize the lung and gut microbiomes of preterm infants and identify shared microbial taxa that are associated with BPD development.

METHODS: Tracheal aspirate and stool samples were collected from 39 premature infants over the first month of life. To assess the taxonomic microbial composition of the lung and gut, samples were analyzed using shotgun metagenomic sequencing. BPD classification was determined using the National Institute of Child Health and Human Development severity-based definition at 36 weeks postmenstrual age.

MEASUREMENTS AND MAIN RESULTS: Microbial communities of the lung and gut were significantly different between infants who went on to develop BPD and those who did not, with an enrichment of skin-associated microbial genera such as Staphylococcus, Corynebacterium, and Cutibacterium in infants who developed BPD. Specifically, Staphylococcus epidermidis was enriched in premature infants who developed BPD and was the most prominent species shared between lung and gut communities. Temporal changes in gut microbial communities co-occurred with feeding practices and antibiotic exposure, suggesting an influence of external factors on microbiome composition.

CONCLUSIONS: Our findings provide evidence that certain microbial colonization patterns among premature infants are closely associated with the pathogenesis and progression of BPD.}, } @article {pmid41959210, year = {2026}, author = {Muller, E and Baum, S and Borenstein, E}, title = {MAAMOUL: Metabolic network-based discovery of microbiome-metabolome shifts in disease.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959210}, issn = {2692-8205}, abstract = {MOTIVATION: A central goal in human gut microbiome research is to identify disease-associated functional shifts, an objective increasingly pursued through metagenomic and metabolomic assays. However, common differential abundance analyses of genes or metabolites often yield long and difficult-to-interpret feature lists. Aggregating features into predefined pathways can improve interpretability but relies on fixed pathway boundaries that may not reflect context-specific functional changes. Moreover, even when paired metagenomic-metabolomic data are available, they are often analyzed separately or linked only through simple statistical associations.

RESULTS: We introduce MAAMOUL, a knowledge-based computational framework that integrates metagenomic and metabolomic data to identify disease-associated, data-driven microbial metabolic modules. Leveraging prior knowledge of bacterial metabolism, MAAMOUL maps disease-association scores onto a global microbiome-wide metabolic network and identifies custom modules enriched for altered genes and metabolites. Applying MAAMOUL to inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) datasets revealed significant disease-associated modules not detected by conventional pathway-level analysis. In IBD, modules reflected disrupted sulfur and aromatic amino acid metabolism and enhanced microbial nucleotide salvage, whereas in IBS they linked purine and nicotinate/nicotinamide metabolism. These results demonstrate that network-guided multi-omic integration can uncover coherent functional shifts in the gut microbiome overlooked by single-omic or purely statistical approaches.

AVAILABILITY: MAAMOUL is available as an R package at https://github.com/borenstein-lab/MAAMOUL.}, } @article {pmid41959308, year = {2026}, author = {Sakdinan, B and Sinha, A and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ}, title = {Species-specific prophage induction by ciprofloxacin in human gut metagenomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959308}, issn = {2692-8205}, abstract = {Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction and whether it is associated with antibiotic exposure. Across two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in specific bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut.}, } @article {pmid41959338, year = {2026}, author = {Kramer, AM and Zhang, A and Ayala, N and de Sanctis, B and Karim, L and Hinrichs, AS and Walia, S and Turakhia, Y and Corbett-Detig, R}, title = {Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959338}, issn = {2692-8205}, abstract = {Pangenomes capture population-level variation but remain computationally challenging at scale. We present Panmap, a tool that leverages evolutionary structure to place, align, and genotype sequencing reads against mutation-annotated pangenomes containing up to millions of genomes. Panmap introduces a phylogenetically compressed k-mer index that stores only sequence differences along branches, enabling efficient comparison of reads to both sampled genomes and inferred ancestors. This approach reduces index size by up to 600-fold and construction time by over three orders of magnitude relative to existing tools. Panmap places a 100× coverage SARS-CoV-2 sample onto 20,000 genomes in 0.4 seconds and onto 8 million genomes in under two minutes. Furthermore, it enables accurate haplotype identification and abundance estimation in metagenomic samples and sensitive placement of ancient environmental DNA without prior alignment. Our approach makes large-scale pangenomes directly amenable to read mapping, genome assembly, alignment-free phylogenetic placement, and metagenomic analysis.}, } @article {pmid41959403, year = {2026}, author = {Maier, J and Gin, C and Rabasco, J and Bass, A and Spencer, W and Duerkop, BA and Callahan, B and Kleiner, M}, title = {TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959403}, issn = {2692-8205}, support = {R01 AI171046/AI/NIAID NIH HHS/United States ; R35 GM138362/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Transduction is a form of horizontal gene transfer in which bacterial DNA is packaged and transferred by virus-like particles (VLPs). Transductomics is a sequencing-based method used to detect DNA carried by VLPs. During transductomics analysis, reads from a sample's ultra-purified VLPs are mapped to metagenomic contigs assembled from the same sample's whole-community. The read mapping produces coverage patterns that require a time-consuming manual inspection and classification process which makes the method's use unfeasible for datasets with many samples.

RESULTS: We developed a novel algorithm, TrIdent (Transduction Identification), that uses pattern-matching to automate the transductomics data analysis and that is available as an R package (https://jlmaier12.github.io/TrIdent/). There is no software equivalent to TrIdent so we compared TrIdent's classifications of transductomics datasets to classifications made by human classifiers. TrIdent's classifications were generally comparable to the manual classifications on a previously generated, manually classified transductomics dataset. When applied to newly generated transductomics data from the murine microbiota, TrIdent agreed with two independent human classifiers as much as the two independent human classifications agreed with each other. TrIdent classified transductomics datasets in a fraction of the time needed by human classifiers, and the classifications produced by TrIdent are fully reproducible. We used TrIdent to explore three murine gut transductomes and found that bacterial DNA associated with the Oscillospiraceae and Turicibacteraceae families was highly enriched in the DNA packaged by VLPs as compared to the whole community metagenomes.

CONCLUSIONS: The TrIdent software is a more accessible, more efficient, and more reproducible alternative to the manual inspection of read coverage patterns previously required for transductomics data analysis. To demonstrate the application of TrIdent, we analyzed transductomics datasets from murine fecal pellets and showed that specific low abundance bacterial families appear to be heavily involved in transduction.}, } @article {pmid41959459, year = {2026}, author = {Kim, M and Ardell, SM and Kryazhimskiy, S}, title = {Module-Selection Balance in the Evolution of Modular Organisms.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959459}, issn = {2692-8205}, abstract = {The architecture of the genotype-phenotype-fitness map (GPFM) is a key determinant of evolutionary dynamics. One salient feature of biological GPFMs is variational modularity, where each mutation affects only a small subset of functional traits. Variational modularity may constrain the dynamics of trait evolution, but these constraints are not well understood. Here, we use several extensions of the Fisher's geometric model with two functional traits to investigate these constrains. We find that on GPFMs with universal pleiotropy, populations evolve along the fitness gradient, which implies that the trait under stronger selection is optimized exponentially faster than the trait under weaker selection. In contrast, on modular GPFMs, populations approach a quasi-steady state that we term a "module-selection balance" where both traits improve at the same rate and their ratio remains constant. We demonstrate that the existence of a module-selection balance is robust with respect to the details of evolutionary dynamics and GPFMs themselves, as long as they are variationally modular. Our theory predicts that variationally modular organisms should exhibit stereotypical bi-phasic dynamics of genome evolution, especially in the strong clonal interference regime, and we find support for this prediction in metagenomic data from Lenski's long-term evolution experiment in bacterium Escherichia coli. We propose that module-selection balance is an inherent feature of variationally modular GPFMs, which imposes an important constraint on long-term trait evolution.}, } @article {pmid41959466, year = {2026}, author = {Sapoval, N and Treangen, TJ and Nakhleh, L}, title = {Leveraging spectrum of graph sheaf Laplacian as a genome-architecture-aware measure of microbiome diversity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959466}, issn = {2692-8205}, abstract = {MOTIVATION: Measures of microbial diversity that can be derived directly from metagenomic sequencing data offer a valuable summary view of the underlying complex systems. Prior work has shown that both taxonomic composition and abundances that are captured by standard diversity measures (e.g., Shannon entropy), and structural variation within the metagenome due to gene duplications, losses and horizontal transfers (HGT), can correlate with the host's health. However, there are no diversity measures available that simultaneously account for the genome architecture and taxonomic composition within the sample. Thus, in this work we propose the spectral energy of a graph sheaf Laplacian as such a measure, and justify its applicability through a simulation study and analysis of biological data.

RESULTS: First, we describe a theoretical framework that allows us to combine the features of genome graphs with the taxonomic data. Then, we explore the sensitivity of the proposed diversity measure to genome rearrangements and HGT events in a simulation study. Finally, we explore applicability of our proposed measure to characterization of diversity of human gut metagenomes. We find our proposed measure to offer better discrimination between healthy controls and inflammatory bowel disease (IBD) patients' samples (n = 403) in the cohorts analyzed.

https://github.com/nsapoval/bd-gsl.}, } @article {pmid41959535, year = {2026}, author = {Xue, J and Allaband, C and Zuffa, S and Zhou, D and Poulsen, O and Meadows, J and McDonald, D and Ambre, M and Ackermann, G and Birmingham, A and Cao, J and Mohanty, I and Dorrestein, PC and Knight, R and Haddad, GG}, title = {Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.31.715631}, pmid = {41959535}, issn = {2692-8205}, abstract = {Intermittent hypoxia and hypercapnia (IHC), a hallmark of obstructive sleep apnea (OSA), accelerates atherosclerosis, yet the underlying mechanisms remain unclear. The gut microbiota and metabolites, specifically bile acids, change with IHC and thus the bile acid receptor farnesoid X receptor (FXR) might mediate IHC-induced atherosclerosis. In this study, ApoE [-/-] and ApoE [-/-] FXR [-/-] mice were exposed to IHC or room air and fed with a high-fat, high-cholesterol diet for 10 weeks. Markers of atherosclerosis, fecal microbiome, and metabolome were then examined via Sudan IV staining, absolute abundance shotgun metagenomics, and untargeted liquid chromatography tandem mass spectrometry (LC-MS/MS). IHC markedly increased aortic atherosclerosis in ApoE [-/-] mice, an increase that was abolished by FXR deficiency. In addition, IHC reshaped gut microbial composition, promoting enrichment of bile acid-modifying taxa and increasing levels of microbial hydroxysteroid dehydrogenase (hsdh). The bile acid pool was also remodeled and associated with aortic atherosclerosis via FXR-dependent metabolic signals in ApoE [-/-] mice. Knockout of FXR disrupted microbiome shift under IHC and uncoupled microbial bile acid metabolism from vascular lesion development, thereby protecting against aortic atherosclerosis. These findings show that FXR has a central role in linking IHC, microbial bile acid metabolism, and cardiovascular pathology.}, } @article {pmid41959658, year = {2026}, author = {Funauchi, A and Hashimoto, K and Fukushima, K and Matsumoto, Y and Hamada, N and Hara, R and Niitsu, T and Nii, T and Matsuki, T and Tsujino, K and Miki, K and Kumanogoh, A and Nakamura, S and Kida, H}, title = {Gastric Aspirate Isolate Demonstrates Strain-Level Concordance With Sputum Isolate in Nontuberculous Mycobacterial Pulmonary Disease.}, journal = {Open forum infectious diseases}, volume = {13}, number = {4}, pages = {ofag175}, pmid = {41959658}, issn = {2328-8957}, abstract = {The nontuberculous mycobacteria (NTM) isolated from gastric aspirate have demonstrated >85% strain concordance with those from the sputum, suggesting that they originate from the lungs rather than the environment. Gastric aspirate, although not yet internationally recognized, may be a useful supplementary specimen for diagnosing NTM pulmonary disease.}, } @article {pmid41960427, year = {2026}, author = {Nuanmuang, N and Leekitcharoenphon, P and Njage, PMK and Jirakkakul, J and Dulsawat, S and Tachaleat, A and Svendsen, CA and Møller, FD and Otani, S and Cheevadhanarak, S and Aarestrup, FM}, title = {Comparative resistome from toilet waste in three different income areas, Bangkok, Thailand.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1790551}, pmid = {41960427}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) is a significant public health threat and is associated with millions of deaths worldwide each year. Besides antimicrobial usage, different socioeconomic factors have recently gained attention as being associated with increased AMR. Bangkok, a city with diverse income levels, provided a unique setting for this study, which aimed to explore the possible within-city association between income-level areas and the diversity and abundance of AMR. Twenty-seven toilet waste samples were collected from nine different sites (low-, middle-, and high-income) during March-April 2023, and metagenomic sequencing was performed. The sequencing data were quality checked, and sequences that passed quality control were mapped to antimicrobial, metal, and disinfectant resistance gene databases as well as bacterial taxonomy databases. We observed higher antibiotic resistance genes (ARGs), metal resistance, and disinfectant resistance abundance (fragments per kilobase per million mapped reads, FPKM) in low-income groups compared to middle- and high-income groups. This included both acquired ARGs and presumed intrinsic ARGs, including genes associated with completely novel antibiotics that have so far only been identified through functional cloning. Significant differences in individual ARGs were also observed between sites. Our study highlights the relative abundance of ARGs across different income groups, emphasizing how the development of resistance mechanisms revealed through metagenomic analysis can serve as a valuable tool for city-level surveillance of AMR from toilet waste, particularly in low-income settings.}, } @article {pmid41960429, year = {2026}, author = {Freund, L and Topacio, TM and Miao, Y and Porter, WC and Swenson, M and Maltz, M and Botthoff, J and Aronson, EL}, title = {Weather conditions structure the taxonomic and functional diversity of the aeolian dust microbiome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1691133}, pmid = {41960429}, issn = {1664-302X}, abstract = {INTRODUCTION: The aeolian dust microbiome is composed of uniquely adapted microorganisms that can withstand the harsh conditions of the atmosphere. Specific microbial taxa and survival strategies have been observed in dust microbiomes from around the world, yet the environmental processes that select for microbial composition and function are poorly understood.

METHODS: Here we explore the taxonomic and functional diversity of the aeolian dust microbiome from sites around the Salton Sea, a hypersaline lake in Southern California, and how dust sources and weather influenced the microbiome. Dust samples were collected from four locations around the Salton Sea in the summer and fall of 2020 and 2021, and 16S (V3-V4) rRNA amplicon sequencing and shotgun metagenomic sequencing was used to characterize the aeolian dust microbiome.

RESULTS: We observed significant differences in microbial composition between sites, and we were able to identify 13 microbial genera that were members of the core dust microbiome across samples. We also found that genes involved in sporulation, UV-radiation resistance, thermal resistance, osmotic stress resistance, quorum sensing, and antibiotic resistance were shared across the aeolian dust metagenomes. Lastly, local wind conditions and estimated dust source surface categories were significant predictors of the microbial adaptations we found in the aeolian dust metagenomes.

DISCUSSION: Our results demonstrate the ability of airborne dust microorganisms to readily adapt to their harsh environment and highlight the survival mechanisms that allow them to disperse across broad distances, thus posing a potential health risk to exposed communities.}, } @article {pmid41960438, year = {2026}, author = {Zhao, Z and Xiang, L and Liu, Y and Xu, S and Chen, Y and Yu, M}, title = {Rare fungal keratitis caused by plant pathogens: report of two cases and review of the literature.}, journal = {Frontiers in fungal biology}, volume = {7}, number = {}, pages = {1785252}, pmid = {41960438}, issn = {2673-6128}, abstract = {Macrophomina phaseolina and Colletotrichum fructicola are notable plant pathogens, yet cases of keratitis from these fungi are rarely reported. Limited awareness of this keratitis etiology among ophthalmic professionals reduces the likelihood of accurate diagnosis and timely treatment. This report aims to improve the understanding of these rare infections in eye care. We present two cases of keratitis: one caused by M. phaseolina and another by C. fructicola, both of whom experienced a complicated treatment course. Traditional fungal exams yielded negative results, which limited disease identification and focused therapy. To determine the cause, we used metagenomic next-generation sequencing (mNGS) on clinical samples obtained from corneal scrapings. The mNGS report was received during therapy and quickly identified the pathogen. Based on this, we looked for treatment regimens for this kind of infection in previous literature, altered and implemented appropriate antifungal drug therapy, and the patient's condition improved. We review the literature from 1970 to 2025 on M. phaseolina and Colletotrichum spp. keratitis. We identified 10 cases of M. phaseolina keratitis from four studies and 72 cases of Colletotrichum spp. keratitis, including five of C. fructicola, in 43 articles. Misdiagnosis was common due to limited clinical and microbiologic suspicion. The rise of infections by rare pathogens highlights diagnostic challenges. Traditional methods often delay accurate diagnosis, while mNGS enables rapid identification of pathogen, crucial for effective treatment and vision preservation.}, } @article {pmid41960830, year = {2026}, author = {Sun, S and Zhou, Y and Deng, F and Meng, Y and Zhu, X and Wang, H and Wei, D}, title = {Engineering an l-Threonine Aldolase from Staphylococcus epidermidis for Enhanced Diastereoselectivity in the Synthesis of a Chloramphenicol Intermediate.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {15}, pages = {12271-12279}, doi = {10.1021/acs.jafc.6c01578}, pmid = {41960830}, issn = {1520-5118}, mesh = {*Chloramphenicol/chemistry/metabolism ; Stereoisomerism ; *Staphylococcus epidermidis/enzymology/genetics/chemistry ; *Bacterial Proteins/genetics/metabolism/chemistry ; *Glycine Hydroxymethyltransferase/genetics/chemistry/metabolism ; Biocatalysis ; Protein Engineering ; Substrate Specificity ; }, abstract = {l-Threonine aldolase (LTA) is an attractive biocatalyst for the synthesis of l-syn-p-nitrophenylserine (l-syn-1b), a key intermediate in chloramphenicol synthesis. However, low diastereoselectivity has limited its broader application in stereospecific C-C bond formation. To overcome this limitation, a metagenomic library constructed from non-natural amino acid-enriched environments was screened, leading to the identification of an LTA from Staphylococcus epidermidis (SeLTA) that exhibits the highest diastereoselectivity toward l-syn-1b among naturally occurring LTAs reported to date. To further enhance its diastereoselectivity, structural comparison, alanine scanning, and tunnel analysis were employed to identify hotspots that modulate the diastereoselectivity of SeLTA. Subsequent saturation mutagenesis and iterative saturation mutagenesis at these positions yielded the quadruple variant A176G/Y202S/N7C/F129E (Mut4), which increased the diastereoselectivity from 32.5%syn to 92.7%syn. Furthermore, Mut4 exhibits markedly improved diastereoselectivity toward para- and meta-substituted benzaldehyde derivatives. Molecular dynamics (MD) simulations further elucidated the molecular basis underlying the enhanced diastereoselectivity of Mut4. This study provides a potential biocatalyst for the sustainable and efficient synthesis of a chloramphenicol intermediate.}, } @article {pmid41961352, year = {2026}, author = {Cao, XY and Tian, JJ and Zhang, W and Chen, CL and Ma, H}, title = {Puerarin Alleviates Depression via Integrated Regulation of TLR4/MyD88/NF-κB Signaling and Gut Microbiota-Metabolic Axis.}, journal = {Neurochemical research}, volume = {51}, number = {2}, pages = {}, pmid = {41961352}, issn = {1573-6903}, abstract = {Depression is a highly prevalent mental disorder in which dysfunction of the gut microbiota is implicated as a significant factor in its pathogenesis. Puerarin has been suggested to alleviate depression via the microbe-gut-brain axis (MGBA), although the precise mechanisms remain elusive. This study aimed to elucidate the association between the antidepressant effects of puerarin and its role in regulating intestinal flora imbalance and inhibiting subsequent activation of the LPS/TLR4 inflammatory pathway from metabolomics and metagenomics perspectives. A rat model of depression was established using a 6-week chronic unpredictable mild stress (CUMS) protocol. Depressive-like behaviors were assessed through the sucrose preference test (SPT), forced swim test (FST), and open field test (OFT). Inflammatory cytokines (TNF-α, IL-1β, IL-6), LPS, corticosterone, and 5-HT were measured via ELISA. Hippocampal and colonic protein expression of TLR4, MyD88, IκBα, and NF-κB was analyzed by western blot. Colon tissue integrity was evaluated using H&E staining, PAS staining, and transmission electron microscopy. Immunofluorescence was employed to detect Iba-1+ microglia, TLR4+ cells, and ZO-1 expression. Fecal metabolomics and metagenomics were conducted to identify differential metabolites and microbial composition, followed by KEGG and KO enrichment analyses to predict relevant pathways. Spearman correlation analysis was used to explore relationships among gut microbiota, metabolites, and behavioral indices. Puerarin markedly ameliorated depression-like behaviors in CUMS rats. Concurrently, puerarin inhibited the LPS/TLR4 signaling pathway and its downstream pro-inflammatory mediators in both the hippocampus and colon, resulting in a significant reduction in inflammatory responses across these regions, as well as in the serum. Metagenomic sequencing revealed that puerarin suppressed inflammation-associated bacteria, enhanced the abundance of Firmicutes, and induced alterations in the microbial community structure and composition. Metabolomic analysis demonstrated that puerarin could counteract dysregulated fecal metabolism, identifying 17 metabolites as potential key mediators in restoring metabolic homeostasis in CUMS rats. These biomarkers were implicated in several metabolic pathways, including Aminoacyl-tRNA biosynthesis, Pyrimidine metabolism, Alanine, Aspartate, and Glutamate metabolism. Puerarin may exert its antidepressant effects by modulating the gut microbial structure and metabolite profiles, thereby alleviating inflammatory stress in the colon, bloodstream, and hippocampus, potentially through inhibition of the LPS/TLR4 signaling pathway.}, } @article {pmid41961522, year = {2026}, author = {Song, W and Li, M and Yue, X and Meng, Y and Xie, Y and Zhang, Y and Hu, Y and Zheng, Y and Yue, X}, title = {Microbial succession and metabolic mechanisms driving flavor evolution in Northeast Chinese dajiang: a comprehensive review integrating insights from East Asian fermented soybean pastes.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-22}, doi = {10.1080/10408398.2026.2644602}, pmid = {41961522}, issn = {1549-7852}, abstract = {This review systematically explores the spatiotemporal microbial succession and flavor evolution during the fermentation of northeast Chinese soybean paste (dajiang), with a focus on the jiangpei (solid-state starter) and jianglao (brine fermentation) stages. By integrating metagenomic, metabolomic, and sensory data, this review synthesizes evidence linking microbial community dynamics-featuring Lactobacillus spp., Zygosaccharomyces rouxii, and Aspergillus oryzae-to the biosynthesis of key flavor compounds. These include umami amino acids (e.g., glutamic acid, 1.5-2.0 g/kg), fruity esters (e.g., ethyl acetate, 124.67 μg/kg), and phenolic antioxidants. Cross-feeding interactions (e.g., yeast utilization of lactic acid for ester synthesis) and environmental stressors (12%-18% NaCl, 25 °C-30 °C) are shown to enhance flavor complexity by modulating metabolic pathways like amino acid degradation and lipid β-oxidation. Unlike prior studies focusing on fragmented fermentation stages, this review systematically addresses the full fermentation continuum, highlighting how aerobic-to-anaerobic transitions drive functional metabolite accumulation. The review concludes by outlining a roadmap to modernize dajiang production through standardized quality control, precision flavor modulation, and traditional process optimization, enabled by culturomics/MAGs, multi-omics integration, and AI-assisted fermentation monitoring and control.}, } @article {pmid41961886, year = {2026}, author = {Cosma, BM and Pillay, S and Calderón-Franco, D and Abeel, T}, title = {Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0345919}, pmid = {41961886}, issn = {1932-6203}, mesh = {*Computational Biology/methods ; Machine Learning ; *Models, Biological ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Imbalances in the gut microbiome have been linked to conditions such as inflammatory bowel disease, diabetes, and cancer. While metagenomics and amplicon sequencing are commonly used to study the microbiome, they do not capture all layers of microbial functions. Other meta-omics data can provide more insights, but these are more costly and laborious to procure. The growing availability of paired meta-omics data offers an opportunity to develop machine learning models that can infer connections between metagenomics data and other forms of meta-omics data, enabling the prediction of these other forms of meta-omics data from metagenomics. We evaluated several machine learning models for predicting meta-omics features from various meta-omics inputs. Simpler architectures such as elastic net regression and random forests generated reliable predictions of transcript and metabolite abundances, with correlations of up to 0.77 and 0.74, respectively, but predicting protein profiles was more challenging. We also identified a core set of well-predicted features for each meta-omics output type, and showed that multi-output regression neural networks performed similarly when trained using fewer output features. Lastly, our experiments demonstrated that predicted features can be used for the downstream task of inflammatory bowel disease classification, with performance comparable to that of experimental data.}, } @article {pmid41962241, year = {2026}, author = {Lin, Z and Pang, S and Xu, T and Zhou, YL and Zhang, C and Qian, PY and Zhang, S}, title = {Marine plastisphere expands the ecological niche and evolutionary dynamics of nrfA-dependent nitrite ammonifying bacteria.}, journal = {Water research}, volume = {299}, number = {}, pages = {125879}, doi = {10.1016/j.watres.2026.125879}, pmid = {41962241}, issn = {1879-2448}, mesh = {*Bacteria/metabolism/genetics ; *Nitrites/metabolism ; Seawater/microbiology ; Biofilms ; Phylogeny ; Ecosystem ; }, abstract = {The marine plastisphere affects nitrogen cycling processes, but its role in nrfA-dependent nitrite ammonification, a critical phase of dissimilatory nitrate reduction to ammonium (DNRA) with important implications for nitrogen retention and greenhouse gas dynamics, remains unexplored. In this study, we analyzed 269 plastisphere metagenomes and eight metatranscriptomes from global public datasets. The plastisphere contained elevated nrfA levels compared to seawater, and nrfA transcripts were consistently detected. A total of 285 putative nrfA-dependent nitrite ammonifying bacteria were identified, including 156 novel genera. Most plastisphere MAGs overlapped with other examined marine biofilms, whereas 109 MAGs were uniquely detected in plastisphere samples within the analyzed comparative datasets. Functional studies revealed diverse electron-donor utilization strategies supporting DNRA in plastisphere microorganisms. Evolutionary analyses showed that nrfA genes were distributed across different phyla through horizontal gene transfer, whereas purifying selection limited sequence divergence. These findings highlight a previously underappreciated genetic and transcriptional potential for DNRA in plastic-associated biofilms at the particle scale, with implications for nitrogen retention within plastisphere microhabitats.}, } @article {pmid41962374, year = {2026}, author = {Zhou, LT and He, DH and Li, J and He, RX and Ma, SJ and Gong, GY and Zou, XS and Li, S and Zhou, YF and Hu, WJ}, title = {Dynamics and drivers of last-resort antibiotic resistance genes during pilot-scale aerobic fermentation of municipal sludge and subsequent bok choy pot trials.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141891}, doi = {10.1016/j.jhazmat.2026.141891}, pmid = {41962374}, issn = {1873-3336}, mesh = {*Sewage/microbiology ; Fermentation ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Aerobiosis ; Anti-Bacterial Agents/metabolism ; Pilot Projects ; }, abstract = {Sludge from wastewater treatment plants may exacerbate environmental dissemination of last-resort antibiotic resistance genes (LARGs) when applied to land. However, LARG behavior during aerobic sludge fermentation and subsequent soil-plant transfer remains poorly understood. This study specifically targeted LARGs beyond common ARGs and coupled pilot-scale fermentation with bok choy cultivation to resolve their dynamics and compartmentalization. Using metagenomic sequencing with correlation and network analyses, we identified environmental drivers and inferred potential hosts. Optimized fermentation conditions (maintaining >50 °C for 10 days) reduced moisture to 30%, lowered the C/N ratio to 24.7, and achieved germination indices of 85%-90%. Fermentation promoted microbial succession, enhanced metal passivation and organic matter humification, and reduced antibiotic and ARG abundance, with total antibiotic degradation reaching 49.19% in the thermophilic phase. LARG abundance increased by 47.6% in the mesophilic phase due to cell lysis and MGE release, then declined by 9.7% in the thermophilic phase and 47.8% during maturation. Although fermentation stabilized sludge, specific genes (e.g., KPC-22 and poxtA) rebounded, driven by horizontal gene transfer and physicochemical changes. Subsequent planting demonstrated that a 10%-15% sludge application rate optimized bok choy agronomic performance and improved soil antibiotic degradation. Across soil, rhizosphere, and phyllosphere, LARGs exhibited distinct compartmentalization patterns. Network analysis further indicated that LARGs were primarily associated with indigenous soil taxa (e.g., Streptomyces) rather than potential pathogens (e.g., Klebsiella). Consequently, the impact on the core transmission network was minor, suggesting that appropriately fermented sludge application presents a controllable ecological risk and supports its safe utilization under the studied conditions.}, } @article {pmid41963033, year = {2026}, author = {Tzora, A and Nikolaou, K and Lagkouvardos, I and Voidarou, C and Intze, E and Fotou, K and Skoufos, I}, title = {A novel classification system based on cheese microbial profiles for the assessment of cheese typicity.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105049}, doi = {10.1016/j.fm.2026.105049}, pmid = {41963033}, issn = {1095-9998}, mesh = {*Cheese/microbiology/classification ; Animals ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Food Microbiology ; Milk/microbiology ; High-Throughput Nucleotide Sequencing ; Greece ; }, abstract = {Cheese typicity reflects the unique characteristics influenced by raw ingredients, traditional tools employed, environmental and production conditions, the cheese-making process and the specific geographical region of origin. In the present study, the typicity of Greek cheeses was studied and compared with cheeses from various countries worldwide, based on microbiota profiles. The dataset included publicly available and 63 newly generated sequences, totaling 322 cheese samples, derived from seven different countries. The analysis incorporated next generation sequencing (NGS) technology, with Illumina sequencing of the 16S rRNA gene hypervariable regions V3-V4, followed by a standardized analytical pipeline process. Through de novo clustering, four main Cheese Microbial Profiles (CMP) - clusters and nine sub-clusters were identified. Core microbiota was identified within sub-clusters. The dominant bacterial genera were Lactobacillus in CMP1, Lactococcus in CMP2 and CMP3, and Streptococcus in CMP4. Distinct cheese types exhibited a statistically significant tendency for specific microbial profiles within clusters. However, no clear signatures of geographic origin were detected, nor were associations found between microbial communities and cheese production parameters such as cheese type, milk source, starter culture addition or milk pasteurization. Additionally, we developed a novel model capable of accurately classifying new cheese samples into clusters and sub-clusters, based on their bacterial ecological community structure. Our findings could support future initiatives, especially when combined with multi-omic approaches, to better identify cheese typicity, verify authenticity, potentially trace geographical origin, and ultimately enhance the quality and safety of cheeses.}, } @article {pmid41963036, year = {2026}, author = {Hou, J and Li, Y and Liu, M and Li, L and Chen, H and An, Y and Xu, H and Yao, Y}, title = {Antibiotic resistance genes (ARGs) in rice: Source attribution and putative mobility patterns.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105055}, doi = {10.1016/j.fm.2026.105055}, pmid = {41963036}, issn = {1095-9998}, mesh = {*Oryza/microbiology/genetics ; *Bacteria/genetics/isolation & purification/classification/drug effects ; Seeds/microbiology ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; Phylogeny ; Microbiota ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Soil Microbiology ; }, abstract = {Rice grains can harbor antibiotic resistance genes (ARGs), yet the relative roles of seed-associated and environmental reservoirs remain unclear. We used shotgun metagenomics on rice tissues (grain, seed, leaf, stem, root) and surrounding matrices (bulk/rhizosphere soil, irrigation water, rainwater, PM10). In total, 1019 ARG subtypes were detected; grains contained 395, the largely overlapping with seeds (290) and environmental samples (322). FEAST source tracking revealed contrasting attribution patterns: seed sources explained nearly half of the grain microbiome (average contribution 49.49%) versus 8.45% from environmental sources, whereas environmental sources contributed more strongly to the grain resistome (20.68%). 747 metagenome-assembled genomes (MAGs) were reconstructed, including 275 ARG-carrying MAGs. Phylogenetic screening identified 39 near-identical (≥99%) ARG linkages across samples, operationally classified by host consistency (same vs different predicted hosts) into 11 putative VGT-like and 28 putative HGT-like patterns. For example, blaGOB-50 in grains and seeds shared near-identical sequences within Elizabethkingia anopheles (VGT-like), while APH(9)-Ic in grains (Burkholderia) matched PM10 (Comamonas), consistent with an HGT-like linkage. In selected cases, ARG-MGE co-localization (e.g., umuC, cca) further supported mobility interpretations. Together, these results indicate seedborne signatures in the grain microbiome but comparatively stronger environmental association for the grain resistome, informing efforts to trace ARG reservoirs in rice systems.}, } @article {pmid41963043, year = {2026}, author = {Liu, G and Zhong, J and Yang, D and Zeng, Y and Cao, R and He, S and Bai, W and Qu, C}, title = {The mechanisms underlying ester enhancement and higher alcohol reduction in Chi-flavor base liquor brewing via Limosilactobacillus fermentum fortification: A multi-omics investigation.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105070}, doi = {10.1016/j.fm.2026.105070}, pmid = {41963043}, issn = {1095-9998}, mesh = {Fermentation ; *Esters/metabolism/analysis ; *Alcoholic Beverages/microbiology/analysis ; *Ethanol/metabolism/analysis ; Flavoring Agents/metabolism ; Multiomics ; Taste ; Lactates/metabolism/analysis ; Saccharomyces cerevisiae/metabolism/genetics ; *Alcohols/metabolism/analysis ; Food Microbiology ; *Lactobacillaceae/metabolism/genetics ; }, abstract = {Chi-flavor Baijiu is a unique liquor in the Pearl River Delta region. Ethyl lactate is the key flavor with low content in base liquor, affecting qualities of Chi-flavor Baijiu. To address this issue, Limosilactobacillus fermentum Y8 (Y8) isolated from sour mash, was used to fortify the fermentation. Results showed that contents of ethyl acetate and ethyl lactate reached to 663.55 mg/L and 604.25 mg/L, increased by 334.97% and 331.26%, respectively, with that of ethanol unchanged and main higher alcohols reduced significantly. Metagenomic analysis revealed that Lactiplantibacillus, Limosilactobacillus, Pediococcus, Levilactobacillus, and Lactobacillus were the top five abundance species. Metatranscriptomic data indicated that Saccharomyces cerevisiae, Lactobacillus brevis and L. fermentum were the dominant active species, the succession of which was significantly influenced by Y8 addition. Correlation analysis revealed that L. fermentum was positively related to reducing sugar, total acid and esters, while negatively to higher alcohols. Based on metatranscriptomic analysis, a new pathway for lactate synthesis from lactaldehyde was found with Y8 fortification, along with acyl-CoA thioester hydrolase gene ybgC upregulated significantly, providing more precursors for ester synthesis. At the same time, enzymes related to ester synthesis were upregulated with that of higher alcohols downregulated. Collectively, Y8 fortification could affect the succession of microbiota and promote the synthesis of ester precursors and ester synthesis pathway, and decrease higher alcohols synthesis pathway. This study not only provides a strain to fortify Chi-Flavor Baijiu brewing with improved qualities but also reveals mechanisms of flavor modulation and microbial community succession during the brewing process.}, } @article {pmid41963048, year = {2026}, author = {Diaz, M and Wilson, N and Ponsero, AJ and Seecharran, T and Som, N and Al-Khanaq, H and Gutiérrez, AV and Gilmour, M}, title = {Microbial community succession and functional potential during processing and storage of cooked ham assessed by shotgun metagenomics.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105075}, doi = {10.1016/j.fm.2026.105075}, pmid = {41963048}, issn = {1095-9998}, mesh = {Animals ; *Meat Products/microbiology/analysis ; Metagenomics ; Swine ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Food, Processed ; *Microbiota ; Cooking ; Food Microbiology ; Food Storage ; Food Handling ; }, abstract = {Wet-cured ham is a ready-to-eat meat product in which microbial communities contribute to desired product characteristics related to product quality, while also presenting as a spoilage risk. Microorganisms are introduced early during the live brining of raw meat, with the brine representing a long-standing, complex and active culture that influences nitrate generation, preservation, and flavour development. To support quality control and identify early indicators of spoilage, this study investigated taxonomic and functional microbiome changes across production stages, from brining and cooking to cold storage, slicing, and packaging under modified atmosphere. Using metagenomics, we characterised microbial community composition and functional profiles across 67 samples from raw ingredients, intermediate production steps, and final products. Microbial communities differed significantly between stages, despite sharing a related taxonomic structure. Brining markedly reduced diversity, and cooking further decreased richness and evenness. A set of 28 taxa was consistently detected across stages, though their relative abundance varied. Latilactobacillus curvatus was abundant prior to cooking but declined sharply afterwards, while Arthrobacter rhombi, initially rare, became dominant in the cooked product. During chilled storage, microbial succession continued, with some taxa re-emerging after being nearly eliminated by cooking. Functional gene profiling revealed distinct metabolic pathway shifts across stages, particularly involving respiration, amino acid metabolism, and fermentation. These findings provide a detailed baseline of microbial and functional dynamics in the production and storage of wet-cured ham. The results offer a foundation for spoilage risk assessment and contribute to the development of microbiological monitoring strategies to support product safety and shelf-life management.}, } @article {pmid41963049, year = {2026}, author = {Zhai, WT and Zhao, H and Chai, LJ and Zhang, W and Zhang, XJ and Lu, ZM and Gao, CQ and Si, GR and Zhang, WQ and Wang, ST and Shen, CH and Xu, ZH}, title = {Microbial and environmental determinants of 1-propanol biosynthesis in Jiang-flavor Baijiu fermentation.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105076}, doi = {10.1016/j.fm.2026.105076}, pmid = {41963049}, issn = {1095-9998}, mesh = {Fermentation ; *1-Propanol/metabolism/analysis ; *Flavoring Agents/metabolism ; *Wine/microbiology/analysis ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics ; *Yeasts/metabolism/genetics/classification ; Temperature ; Food Microbiology ; }, abstract = {1-Propanol is a crucial flavor compound in Jiang-flavor Baijiu, yet the key microbial pathways and environmental factors controlling its synthesis have not been systematically investigated. Using an integrated approach of metagenomics and culture-dependent techniques, this study identified the key microbes, pathways, and factors controlling 1-propanol synthesis. The highest 1-propanol level was detected in first-round base Baijiu, with rapid accumulation during early pit fermentation. Metagenomics revealed the propanoate pathway as the dominant route, primarily contributed by Limosilactobacillus, while Pichia and Saccharomyces were key providers of pyruvate decarboxylase in the citramalate and threonine pathways. Pure-culture validation confirmed that L. panis MR32 predominantly utilizes 1,2-propanediol as the precursor, while yeasts such as P. kudriavzevii 2J2 and S. cerevisiae LB7A prefer the 2-ketobutyrate pathway. Environmental tests revealed optimal 1-propanol production by L. panis MR32 at pH 5.5 and increasing yields with temperature (25-45 °C). In contrast, most yeasts produced the most 1-propanol at 30 °C, beyond which yields declined, with only P. kudriavzevii 2J2 and I. orientalis IO tolerating high lactic acid. Our findings clarify the microbial division of labor and environmental drivers of 1-propanol formation, enabling targeted fermentation control.}, } @article {pmid41963512, year = {2026}, author = {Matoba, R and Iijima, H and Sakamoto, Y and Kawabata, R and Ishiguro, A and Akamaru, Y and Kito, Y and Aizawa, M and Matsuyama, J and Takahashi, M and Makiyama, A and Suzuki, T and Tsuda, M and Yasui, H and Hihara, J and Okuda, H and Kawada, J and Yoshioka, T and Kawakami, H and Eguchi Nakajima, T and Muro, K and Ichikawa, W and Fujii, M and Sunakawa, Y}, title = {Metabolic and functional pathways of gut microbiota in patients with gastric cancer.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41963512}, issn = {2045-2322}, mesh = {Humans ; *Stomach Neoplasms/microbiology/metabolism/pathology ; Male ; Aged ; *Gastrointestinal Microbiome ; Female ; *Metabolic Networks and Pathways ; Metagenome ; Middle Aged ; Bacteria/genetics/classification ; Aged, 80 and over ; Metagenomics ; }, abstract = {We analysed the differences in bacterial composition between 475 Japanese patients with advanced gastric cancer (median age, 70 years; median BMI 20.0) and 106 healthy individuals using a comprehensive metagenome shotgun analysis. Among the patients with advanced gastric cancer, 71% were male, 37% had relapsed, and 55.5% previously underwent gastrectomy. Bifidobacterium, Anaerostipes, and Parabacteroides were predominant in healthy individuals, whereas Streptococcus, Lactobacillus, and Odoribacter were predominant in patients with advanced gastric cancer. Additionally, Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that butanoate and pyruvate metabolism was enriched in healthy individuals, whereas factors, such as ABC transporters and ribosomes, were enriched in patients with advanced gastric cancer. Cluster analysis broadly classified patients with advanced gastric cancer and healthy individuals into two clusters; however, clustering using pathway data more clearly classified patients with advanced gastric cancer and healthy individuals than clustering using flora analysis. Moreover, healthy individuals showed higher bacterial flora diversity than those with advanced gastric cancer. Although the dataset we used was limited and may be difficult to generalise, we identified some molecular characteristics and functional pathways of the microbial genera within the intestines of patients with advanced gastric cancer.}, } @article {pmid41963805, year = {2026}, author = {Roslan, MF and Saad, MFM and Pau, SSN and Basir, S and Aziz, H and Akbar, MA and Bunawan, H}, title = {Bacterial community profiling of Malaysian drinking water reservoirs using metagenomic amplicon sequencing.}, journal = {BMC genomic data}, volume = {27}, number = {1}, pages = {}, pmid = {41963805}, issn = {2730-6844}, abstract = {OBJECTIVES: Microbial communities in freshwater are pivotal for driving nutrient transformation, bioremediation, and maintaining the health balance of these ecosystems. However, microbial communities in freshwater ecosystems may undergo rapid shifts in composition in response to environmental changes. In some cases, these shifts may signal ecological imbalance. In the tropics like Malaysia, high humidity coupled with high temperatures and seasonal rainfalls creates an even hotter and highly variable environmental conditions that promote microbial proliferation and increase the risk of introducing potentially pathogenic microorganisms from surrounding anthropogenic sources via surface runoff. The current study offers a comprehensive characterisation of bacterial community composition in Malaysian freshwater drinking reservoirs using high throughput 16 S rRNA gene amplicon sequencing. This approach enables bacterial community profiling and supports initial microbial risk assessment in these vital freshwater ecosystems. DATA DESCRIPTION: State Authorities permitted the collection of water samples from eight freshwater reservoirs within Peninsular Malaysia’s protective zones. The 16 S rRNA gene’s V3-V4 hypervariable region was amplified for next generation sequencing. Raw DNA sequence data in FASTQ format were quality-filtered, adapter-trimmed and processed using a QIIME v1.9.1 based pipeline that integrated standard bioinformatics tools for OTU clustering and taxonomic assignment. Utilising R v3.3.1, statistical analyses and data visualisations were performed on this dataset. Characterising the community structure of bacteria in these important freshwater ecosystems is the first step to working with this dataset.}, } @article {pmid41963968, year = {2026}, author = {Zhou, N and Liu, J and Zhang, X and Xiao, G and Zhang, M}, title = {Vitamin K2 emerges as the key mediator: Cetobacterium somerae ZNN-1 increases muscle protein deposition and improves liver health in Nile tilapia (Oreochromis niloticus).}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41963968}, issn = {1674-9782}, support = {32373145//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Cetobacterium somerae (C. somerae) is a common indigenous bacterium in the intestine of freshwater fish. Studies have shown that it has the potential to promote protein deposition, but the underlying mechanisms remain unclear.

RESULTS: Nile tilapia were fed with C. somerae ZNN-1 (10[8] CFU/g feed), which significantly increased the carcass ratio, reduced the hepatosomatic index, and decreased whole-body lipid content. Supplementation of C. somerae ZNN-1 significantly increased the crude protein content in muscle, promoted glucose uptake and utilization in muscle tissue, and activated the phosphorylation of S6K/S6 in muscle tissue. C. somerae ZNN-1 supplementation significantly decreased hepatic total lipid, triglyceride, and free fatty acid contents. Further analysis revealed that C. somerae ZNN-1 supplementation markedly activated the phosphorylation of hepatic AMPK and upregulated the expression of genes involved in hepatic lipolysis and fatty acid β-oxidation. Integrated serum metabolomic, bacterial genomic, and gut metagenomic analyses revealed that C. somerae ZNN-1 synthesized chorismate (CHA), which serves as a precursor for gut microbiota to produce vitamin K2 (VK2). In vitro experiments demonstrated that VK2 activated the S6K/S6 pathway to promote protein synthesis, while stimulating AMPK phosphorylation and activating lipid catabolism to reduce fat accumulation.

CONCLUSIONS: These findings provide a theoretical basis for the application of C. somerae ZNN-1 in enhancing edible protein content and reducing fat deposition of aquatic animals.}, } @article {pmid41964024, year = {2026}, author = {Sosef, NP and Boxman, ILA and Dirks, RAM}, title = {Evaluation of two virome probe hybridization capture panels for food safety surveillance.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {41964024}, issn = {1743-422X}, support = {WOT Food Safety Enforcement 002//Dutch Food and Consumer Product Safety Authority/ ; }, mesh = {*Nucleic Acid Hybridization/methods ; *Food Safety/methods ; Animals ; Humans ; Ostreidae/virology ; *Virome ; Norovirus/genetics/isolation & purification ; Food Microbiology ; *Viruses/genetics/isolation & purification/classification ; }, abstract = {In recent years, viromics has received growing attention for viral disease surveillance. This study set out to compare the VirCapSeq-VERT panel and the Comprehensive Viral Research Panel (CVR Panel) for probe hybridization capture of viral nucleic acids in oyster extracts, a main vehicle for the transmission of foodborne viruses. Using ten-fold serial dilutions of human norovirus (hNoV) GI.2 and GII.4 spike-in oyster extracts, both hybridization capture panels achieved detection levels down to 14 genome copies (gc) for hNoV GI.2 and 5 gc for hNoV GII.4. For hNoV GI.2, a genome coverage of ≥ 95% was achieved at 59 gc using the CVR Panel, whereas 724 gc were required for a similar coverage using VirCapSeq-VERT. For hNoV GII.4, a genome coverage of ≥ 97% was achieved at 87 gc with either panel. Next, the hybridization capture performance was compared for a mixture of various foodborne viruses (hNoV GI.2, hNoV GI.3, hNoV GII.4, hepatitis A virus and hepatitis E virus) in the absence of matrix and in the presence of oyster matrix. Sensitive detection of all added viruses was observed at low input levels (less than 200 gc/constructed library) in oyster extract. Taken together, the CVR Panel seems as good as, or slightly more sensitive than, VirCapSeq-VERT for the viruses tested. The availability of various viral enrichment panels, together with foreseen improvements regarding the cost-effectiveness and accessibility, is poised to facilitate broad hazard assessment and genomic profiling techniques in food virology, thereby enhancing food safety and improving early warning.}, } @article {pmid41964077, year = {2026}, author = {Hernandez, LK and DiDonato, N and Pasa-Tolic, L and Chuckran, PF and Firestone, MK and Sieradzki, ET and Yuan, MM and Estera-Molina, K and Kimbrel, J and Dijkstra, P and Banfield, JF and Pett-Ridge, J and Blazewicz, SJ}, title = {Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41964077}, issn = {2049-2618}, support = {DE-SC0020163//U.S. DOE Biological and Environmental Research Award/ ; SCW1589//U.S. DOE Biological and Environmental Research Award/ ; SCW1632//U.S. DOE Office of Biological and Environmental Research Genomic Science Program/ ; }, mesh = {*Soil Microbiology ; California ; *Carbon/analysis/metabolism ; *Grassland ; *Soil/chemistry ; *Rain ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/growth & development/metabolism ; Seasons ; *Microbiota ; Carbon Dioxide/analysis/metabolism ; Carbon Cycle ; Metagenome ; }, abstract = {BACKGROUND: Changes in global patterns can leave a lasting legacy in semiarid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn-a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H2[18]O and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux, measured microbial growth and mortality via quantitative [18]O stable isotope probing and 16S rRNA gene amplicon sequencing, and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes.

RESULTS: We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by ~1 order of magnitude, yielding decreased community growth efficiency (CGE = new biomass growth/respiration), and microbial mortality declined by ~2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover); this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth.

CONCLUSIONS: Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting without a concurrent reduction in CO2 emissions. This shift results in persistently lower CGE, which has the potential to increase soil carbon loss as CO2. If such conditions are maintained over multiple years, these changes could reshape soil organic carbon stocks and alter the balance of grassland ecosystems under future climate scenarios. While our data suggest that sustained reductions in CGE may drive SOC decline, the magnitude and persistence of these effects depend on long-term environmental dynamics and warrant further investigation. Video Abstract.}, } @article {pmid41964107, year = {2026}, author = {Zhang, Z and Chen, C and Zhang, M and Zhu, J and Xu, X and Wang, Z and Zhou, L and Wu, C and Zong, M and Yin, T and Cao, Z and Gao, A and Zhang, C and Su, T and Jiang, L and Zhou, W and Zhou, W and Zhou, Y and Wang, J and Ning, G and Jiang, Y and Liu, R and Wang, W}, title = {Gut microbiota signatures in primary aldosteronism and functional identification of an aldosterone-degrading gut bacterium.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2657047}, pmid = {41964107}, issn = {1949-0984}, mesh = {Humans ; *Aldosterone/metabolism/blood ; *Hyperaldosteronism/microbiology/metabolism ; *Gastrointestinal Microbiome ; Animals ; Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; Mice ; Ruminococcus/metabolism/isolation & purification/genetics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Eubacteriales/metabolism/isolation & purification/genetics ; Essential Hypertension/microbiology ; Blood Pressure ; }, abstract = {Primary aldosteronism (PA), a major cause of secondary hypertension, is characterized by autonomous aldosterone overproduction. Although the gut microbiota is closely linked to blood pressure regulation, its role in PA remains unclear. We performed metagenomic sequencing on fecal samples from 13 patients with essential hypertension (EH), 57 with unilateral PA (UPA), and 51 with bilateral PA (BPA). Despite comparable overall microbial diversity, gut microbial compositional differences were observed among EH and PA subtypes, particularly at finer taxonomic levels. We next identified 39 microbial species that were positively associated with plasma aldosterone concentration (PAC), and 29 that were negatively associated. In the co-abundance network, Ruminococcus gnavus emerged as one of the top three central nodes and was negatively correlated with PAC. Functionally, R. gnavus efficiently degraded aldosterone and multiple natural steroid hormones in vitro, and aldosterone degradation was accompanied by the generation of 3α,5β-tetrahydroaldosterone. R. gnavus-colonized germ-free mice showed reduced fecal aldosterone levels and downregulated expression of aldosterone downstream genes in the intestine. In an aldosterone infusion model, R. gnavus similarly decreased fecal aldosterone and improved systolic blood pressure (SBP) and serum potassium. Logistic regression further revealed that the presence of R. gnavus was associated with lower odds of having a historical highest SBP ≥ 160 mmHg in patients with PA. Collectively, this study reveals different gut microbial signatures in PA and highlights the aldosterone-metabolizing capacity and blood pressure regulation of R. gnavus. These findings advance our understanding of gut microbiota-steroid hormone interactions in PA and provide a basis for exploring microbiota-based stratification and intervention strategies in steroid hormone-related conditions.}, } @article {pmid41964456, year = {2026}, author = {Lefebvre, CS and Salmona, M and Hamane, S and Dellière, S and Charlier, V and Huguenin, A and Bonnal, C and Legoff, J and Feghoul, L and Dutkiewicz, M and Caméléna, F and Berçot, B and Charvet, E and Battistella, M and Alanio, A and Ghelfenstein-Ferreira, T}, title = {Shotgun metagenomic sequencing improves cross-kingdom diagnosis of mycetoma.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {}, number = {}, pages = {}, doi = {10.1111/jdv.70450}, pmid = {41964456}, issn = {1468-3083}, } @article {pmid41964564, year = {2026}, author = {Zhao, S and Lin, S and Chen, M and Yan, J and Yang, D and Guo, F and Qu, H and Chen, Y}, title = {Iron-Cycling-Constructed Wetland-Microbial Fuel Cell-Enhanced Removal of Sartans: The Overlooked Singlet Oxygen and Functional Microorganisms.}, journal = {Environmental science & technology}, volume = {60}, number = {16}, pages = {12539-12550}, doi = {10.1021/acs.est.6c00492}, pmid = {41964564}, issn = {1520-5851}, mesh = {*Wetlands ; *Bioelectric Energy Sources ; Iron ; Singlet Oxygen ; }, abstract = {The global challenge of population aging has led to an increase in the utilization of cardiovascular drugs such as sartans, which are frequently detected in aquatic environments and necessitate advanced treatment. Current sartan removal technologies are limited by their requirement for strict reaction conditions and the potential formation of toxic byproducts. This study presents a novel iron-cycling-constructed wetland-microbial fuel cell (Fe-CWMFC) that combines biotic and abiotic processes to effectively degrade sartans (94.4 ± 3.5%-95.9% ± 3.3%). Mass balance analysis revealed that direct microbial degradation pathways made the highest contribution (40.7-44.5%), followed by ROS-driven degradation (20.3-21.8%), substrate adsorption (26.1-29.7%), and plant uptake (2.3-2.5%). Iron cycling enhanced ROS-driven degradation, with 11.3-13.3% derived from biotic [1]O2 and 7.0-9.3% derived from abiotic [1]O2. Metagenomic binning analysis identified 60 MAGs (e.g., Thiobacillus, Nitrosomonas) with sartan degradation potential, which harbor genes encoding functional enzymes (e.g., decarboxylase, dehydroxylase, and demethylase). By combining biodegradation and ROS-driven degradation to target functional groups (e.g., -COOH, -OH, and -CH3) in sartans, the toxicity was significantly reduced. This research enhances our understanding of the combined role of ROS and microorganisms in micropollutant removal and highlights Fe-CWMFC as a high-efficiency, sustainable, and low-toxicity treatment technology for complex environmental applications.}, } @article {pmid41964658, year = {2026}, author = {Liu, H and Wang, C and Huang, Z and Wang, J and Cai, F and Tian, C and Feng, J and Shen, J and Wang, X}, title = {Progressive Decomposition of Algal Organic Matter Decouples Nitrogen Transformations in Lake Sediments: Evidence from Short-Term Incubation.}, journal = {Environmental science & technology}, volume = {60}, number = {16}, pages = {12158-12169}, doi = {10.1021/acs.est.5c08386}, pmid = {41964658}, issn = {1520-5851}, mesh = {Lakes ; *Nitrogen ; Geologic Sediments ; Nitrification ; Eutrophication ; }, abstract = {Against the backdrop of global lake eutrophication, algal bloom decay is increasingly affecting ecosystems. Algal organic matter (AOM), a natural complex mixture, undergoes multiple release and transformation stages, yet its composition and pathways remain unclear. This study used spectroscopic, mass spectrometric, and metagenomic analyses to monitor a time-compressed algal decay experiment. Results showed that AOM release and transformation can be divided into three stages. Within 1 day, labile AOM consisting mainly of proteins (8.36%), lipids (8.22%), and unsaturated carbohydrates (7.72%) was rapidly released, reshaping nitrogen (N) cycling. Its high bioavailability promoted sediment mineralization and a positive priming effect, while anaerobic conditions reduced nitrification and denitrification rates by 88.7% and 34.5%. Within 3-7 days, semilabile AOM rich in tannins (19.2%) and carbohydrates (9.41%) was gradually decomposed, maintaining anaerobic conditions. The imbalance of excessive NH4[+] and depleted NO3[-] led to the decoupling of nitrification-denitrification. After 7 days, humic-like AOM dominated by lignins (56.8%) prevailed, reducing oxygen consumption and enabling rapid recovery of nitrification and slow rebound of denitrification. These findings clarify the phased transformations of AOM and their microbial interactions, providing mechanistic insights into the short-term fluctuations of lake water quality and microbial processes during bloom decay.}, } @article {pmid41965517, year = {2026}, author = {Han, J and Zhou, X and Guo, M and Zhang, C and Liu, C and Cai, L and Zhao, H}, title = {Intestinal dysbiosis associates with silica-induced pulmonary fibrosis in mice via arginine and tryptophan pathways.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41965517}, issn = {1471-2180}, support = {2025QN03136//Natural Science Foundation of Inner Mongolia/ ; 2025MS03093//Natural Science Foundation of Inner Mongolia/ ; 62231013//National Natural Science Foundation of China/ ; 62261043//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Silicon Dioxide/adverse effects/toxicity ; *Arginine/metabolism ; Mice ; *Pulmonary Fibrosis/chemically induced/metabolism/microbiology ; *Dysbiosis/microbiology/metabolism ; Disease Models, Animal ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome ; Cytokines/metabolism ; Mice, Inbred C57BL ; Male ; Lung/pathology ; Akkermansia ; }, abstract = {BACKGROUND: Pulmonary fibrosis (PF) is a life-threatening interstitial lung disease with a lack of effective therapeutic approaches. Silicosis is a subtype of PF that is specifically caused by the inhalation of crystalline silica particles. In recent years, the gut-lung axis has been shown to be involved in the occurrence and progression of various respiratory diseases. However, the involvement and specific mechanism of action of the gut microbiome in silica-induced PF remain to be elucidated. Therefore, we established a silica-induced PF murine model using an inhalation exposure system, and combined gut metagenomic and untargeted metabolomics data to correlate microbial and metabolic changes with profibrotic cytokine levels.

RESULTS: In mice exposed to silica dust for 64 days and 128 days, Akkermansia muciniphila and Staphylococcus lentus were significantly enriched, whereas the abundance of Lactobacillus murinus was notably reduced. Relevant network analysis revealed that these gut microbiota changes were highly correlated with metabolic disorders of tryptophan and arginine. Moreover, changes in the gut microbiome composition corresponded with the fluctuations in the levels of profibrotic cytokines, including transforming growth factor-beta, tumor necrosis factor-alpha, fibroblast growth factor, and hydroxyproline.

CONCLUSION: We successfully established a murine model of PF induced by silica inhalation. Our results suggest that Lactobacillus murinus, Akkermansia muciniphila, and Staphylococcus lentus are key microorganisms involved in the development of silica-induced PF, while the arginine and tryptophan metabolic pathways serve as key regulatory pathways in the gut-lung axis contributing to disease development.}, } @article {pmid41965542, year = {2026}, author = {Priya, S and Sridhar, SB and Shareef, J and Wadhwa, T and Balusamy, B and Meenakshi, DU and Sundram, S and Malviya, R}, title = {Epidemiology, diagnosis and emerging therapies for Lyme disease of the Northern Hemisphere.}, journal = {International journal of emergency medicine}, volume = {19}, number = {1}, pages = {}, pmid = {41965542}, issn = {1865-1372}, abstract = {BACKGROUND: Lyme disease is the most widespread tick-borne infection in the Northern Hemisphere and is challenging to diagnose and treat due to its changing clinical presentation, antigenic variation, tissue tropism, and the expanding distribution of vectors. This review includes ecology, pathogenesis, diagnostics, treatment, post-treatment, prevention, and novel translational approaches. METHODS: A literature review was conducted to include literature published between January 2000 and March 2026 in PubMed/MEDLINE, Scopus, and Web of Science, with landmark studies used where applicable. Original research, clinical trials, systematic reviews, and major public health reports were prioritised. RESULTS: Two-tier serology is the most common diagnostic technique, but it has limited sensitivity in early infection and does not distinguish between active and past infection. Culture and PCR are only useful in a few instances. The use of new technologies such as multiomics biomarkers, metagenomics, T-cell assays, and AI-enhanced diagnostics is promising but has not yet been tested in a prospective multicentre study. Most of the early and disseminated disease can be treated with standard antibiotics, whereas the long-term therapy of PTLD is not justified and can cause more adverse effects. These preventive and curative advancements involve VLA15 vaccination, anti-tick and reservoir-specific approaches, microbiome-engineered vectors, and anti-persister/ biofilm. CONCLUSION: Lyme disease requires combined prevention, improved diagnostics, enhanced biomarker research, and well-designed PTLD trials. The short-term benefits will be based on the optimisation of existing diagnostics and vector control, and the long-term benefits will be based on rigorous validation of vaccines, biomarkers, and specific therapies.}, } @article {pmid41965741, year = {2026}, author = {Khangarot, R and Kumari, V and Mishra, R and Singh, A}, title = {Artificial intelligence in microbiology: implications for metagenomics, diagnostics, and AMR surveillance.}, journal = {Biomedical engineering online}, volume = {25}, number = {1}, pages = {}, pmid = {41965741}, issn = {1475-925X}, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; Humans ; *Drug Resistance, Microbial/genetics ; *Microbiology ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Artificial intelligence (AI) is now a key player in modern microbiology, as it enables high-resolution analyses of genomic, metagenomic, and clinical data for the monitoring of infectious disease and antimicrobial resistance (AMR). Considerable advancements in deep learning, transformer-based sequence models, graph neural networks, and multimodal architectures have greatly improved microbial classification accuracy, antibiotic resistance gene (ARG) detection, and resistance prediction. Taking metagenomic sequencing into consideration, these advancements have contributed to the development of sensitive, scalable, and non-invasive methods to profile microbiomes, determine novel resistance, and monitor AMR trends at the population level. This review summarizes recent advances in AI-aided microbiology, with a particular emphasis on AMR surveillance. Specific topics include deep learning frameworks for ARG annotation, emerging approaches to identifying new resistance genes, and multimodal applications (genomic and clinical metadata) aimed at improving phenotype prediction. The role of metagenome-assembled genomes (MAGs) to enhance AMR surveillance efforts is noted, along with their noted limitations relative to isolate genomes. The discussion includes the examination of explainable AI (XAI) techniques including SHAP, attention mechanism approaches, and gradient-based attribution approaches, with the aim of increasing transparency and clinical explainability. We also cover potential applications including AI-enabled non-invasive fecal microbiome diagnostics, laboratory automation, and environmental surveillance. While there has been significant progress, unresolved issues exist relating to dataset variations, liability of models to datasets, interpretability, and regulatory approval. Overcoming these barriers, however, will require standardized frameworks for these workflows, privacy-preserving federated learning methods, and interpretable AI frameworks for clinical and public health tools. AI could fundamentally change AMR surveillance by allowing for earlier resistance detection, advanced risk assessment recommendation, and improved monitoring strategies globally.}, } @article {pmid41965996, year = {2026}, author = {Wang, C and Shen, J and Liu, H and Huang, Z and Wang, J and Tian, C and Cai, F and Feng, J and Sha, F and Wang, X}, title = {DNRA dominates over denitrification during algal blooms in a mesotrophic lake: Implications for nitrogen retention and eutrophication risk.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129621}, doi = {10.1016/j.jenvman.2026.129621}, pmid = {41965996}, issn = {1095-8630}, mesh = {*Lakes/microbiology/chemistry ; *Eutrophication ; *Denitrification ; *Nitrogen ; Nitrates ; }, abstract = {Nitrogen (N) overloading threatens global lake ecosystems. However, how algal blooms affect the N balance in mesotrophic lakes by shaping N-cycling biogeographic patterns remains a critical knowledge gap. This study systematically elucidated N cycling patterns and microbial mechanisms driving N retention during algal blooms in Erhai Lake by integrating field monitoring,[15]N isotope pairing technique ([15]N-IPT), and absolute quantitative metagenomics. Results revealed that algal blooms shaped a N-cycling functional pattern in Erhai Lake characterized by organic degradation and synthesis (ODAS) dominance and dissimilatory nitrate reduction (DNR) as a key process. Notably, algal blooms disrupted traditional nitrification-denitrification coupling, shifting N cycling towards a retention mode dominated by dissimilatory nitrate reduction to ammonium (DNRA). Sedimentary DNRA contributed 69% (14.69 ± 5.57 μmol N L[-1] h[-1]) of total dissimilatory nitrate reduction (DNR) process, supported by significantly elevated NrfA (602.49 ± 121.04 μmol d[-1] g[-1]) and NirBD (361.29 ± 138.39 μmol d[-1] g[-1]) enzyme activities. Partial Least Squares Path Modeling (PLS-PM) identified the nitrogen retention index (NRI) as co-regulated by water depth and algal-mediated microbial activity/rates. High-NRI sediments were dominated by Bacteroidota (mainly orders Marinilabiliales and families Prolixibacteraceae) and Myxococcota (primarily families Anaeromyxobacteraceae), while low-NRI sediments were characterized by enrichment of Pseudomonadota (Thioalkalivibrio nitratireducens and Gallionellaceae) and Campylobacterota (Campylobacter sp. BCW_8712). DNRA outcompeted denitrification, diverting nitrate to ammonium rather than N2 gas and resulting in an internal N loading that was an order of magnitude higher than external inputs. This work challenges the denitrification-centric paradigm, revealing the microbial mechanisms of endogenous N accumulation under algal bloom conditions and providing a theoretical basis for the management of plateau lakes.}, } @article {pmid41966291, year = {2026}, author = {Ashango, ZA and Seyum, EG and Nwogha, JS}, title = {Integrating metagenomics into legume breeding: A breeder-centered roadmap from core microbiomes to precision inoculation.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {141}, number = {}, pages = {105941}, doi = {10.1016/j.meegid.2026.105941}, pmid = {41966291}, issn = {1567-7257}, mesh = {*Metagenomics/methods ; *Fabaceae/microbiology/genetics ; *Plant Breeding/methods ; *Microbiota ; }, abstract = {Metagenomics, culture-independent profiling of genetic material recovered from environmental samples, provides a powerful route to characterize microbial communities associated with legumes and to translate their functional potential into breeding targets that enhance resilience and productivity. Across analyses of rhizosphere, endosphere, and seed microbiomes, repeated studies consistently identify a conserved set of microbial functions linked to nutrient cycling, responses to abiotic and biotic stress, and biological control of pathogens, thereby offering mechanistic support that community-level functional capacities can shape host outcomes, including seedling vigor, nutrient-use efficiency, and stress tolerance. To move from descriptive discovery to actionable breeding, three complementary translational strategies have emerged: (i) synthetic microbial communities (SynComs) engineered to deliver targeted metabolic functions while enabling rigorous assessment of community stability and functional consistency; (ii) predictive model systems that integrate metagenomic features with phenotypic measurements to prioritize candidate taxa or functions for subsequent validation; and (iii) precision inoculation approaches that deploy validated microbes or consortia in agronomic settings to test whether metagenome-inferred functions confer robust performance under field-relevant conditions. A critical appraisal of metagenomic, multi-omics, and translational studies indicates that functional-phenotypic mappings are promising, yet substantial barriers continue to constrain reproducibility and scalability, including heterogeneity in sampling and experimental design, biases introduced by DNA extraction and sequencing, variability across bioinformatics workflows and reference databases, and overarching biosafety and regulatory constraints that can obscure true biological signals and weaken the reliability of functional inferences intended to guide selection decisions. To mainstream metagenomics in conventional legume breeding, we propose a breeders' roadmap centered on coordinated standardization and decision-ready analytics, encompassing standardized metagenomics-compatible sampling and sequencing platforms, harmonized computational frameworks and metabolic inference tools to ensure comparable functional calls, high-throughput phenotyping protocols aligned to microbiome-sensitive host traits, and selection frameworks that explicitly incorporate microbiome-oriented decision rules rather than treating microbial signals as ancillary. Finally, integrating machine learning with multi-omics datasets alongside precision delivery systems offers a practical route to generate actionable holobiont-level selection indices, and, when coupled with clearly defined translational pipelines and methodological standardization, metagenomics can broaden breeding gains beyond those achievable using host genomics alone, enabling more reliable, function-driven microbiome-assisted improvement of legume performance.}, } @article {pmid41966300, year = {2026}, author = {Bojko, J and Abd-Alla, A}, title = {'Invertebrate-virome sequence detection: implications for invertebrate products trading and regulations' - An editorial for the special issue.}, journal = {Journal of invertebrate pathology}, volume = {217}, number = {}, pages = {108623}, doi = {10.1016/j.jip.2026.108623}, pmid = {41966300}, issn = {1096-0805}, mesh = {Animals ; *Invertebrates/virology ; *Virome ; *Viruses/genetics ; }, abstract = {Invertebrates can be infected by many viruses that may either cause disease (invertebrate‑pathogenic viruses) or be transmitted to vertebrates or plants. Viral infections may occur in natural invertebrate populations as well as in mass‑reared colonies. The significant recent advances in genome‑sequencing technologies have provided fast and relatively inexpensive tools for detecting invertebrate viruses in both wild and mass‑rearing settings, even at very low levels. The presence of such viruses raises important questions regarding the impact of covert infections on invertebrate health, sanitation, and overall colony performance. The articles in this special issue address viral sequence detection, viral sequence diversity, the impact of viruses on invertebrates, and the relationship between food and feed, and policy.}, } @article {pmid41966314, year = {2026}, author = {Liu, S and Qin, Y and Ni, H and Hou, QY and Xu, C and Leng, X and Li, XM and Yang, MT and Tang, LY and Sun, YZ and Zhao, Q and Ni, HB and Zhang, XX and Jiang, J and Yang, LH and Ma, H}, title = {Genomic characterization, antimicrobial resistance and virulence profiles of Klebsiella pneumoniae isolated from mink in Northern China.}, journal = {Microbial pathogenesis}, volume = {216}, number = {}, pages = {108485}, doi = {10.1016/j.micpath.2026.108485}, pmid = {41966314}, issn = {1096-1208}, mesh = {Animals ; *Klebsiella pneumoniae/genetics/drug effects/pathogenicity/isolation & purification ; China/epidemiology ; Anti-Bacterial Agents/pharmacology ; *Mink/microbiology ; Virulence/genetics ; *Klebsiella Infections/veterinary/microbiology/epidemiology ; Virulence Factors/genetics ; *Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; *Genome, Bacterial/genetics ; Feces/microbiology ; Plasmids/genetics ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Genomics ; Interspersed Repetitive Sequences ; }, abstract = {Klebsiella pneumoniae is an important opportunistic pathogen of One Health concern, and its multidrug-resistant (MDR) and hypervirulent strains pose serious threats to public health. However, the epidemiological characteristics, antimicrobial resistance profiles, and virulence potential of K. pneumoniae circulating in farmed minks remain poorly understood. In this study, we integrated phenotypic antimicrobial susceptibility testing, whole-genome sequencing, and metagenomic analysis to investigate the epidemiology, resistance determinants, and virulence characteristics of K. pneumoniae isolated from farmed minks in northern China. A total of 41 K. pneumoniae strains from 325 fecal samples (isolation rate: 12.62%), including three hypervirulent strains. All isolates exhibited multidrug resistance, with complete resistance to florfenicol, azithromycin, and sulfisoxazole, but remained highly susceptible to carbapenems and polymyxin B. Whole-genome sequencing revealed that the isolates harbored 241 antibiotic resistance genes (ARGs), including ESBL-associated genes and the plasmid-mediated mcr-1.1, along with 7111 virulence factor genes (VFGs) and 135 mobile genetic elements (MGEs). Metagenomic analysis further revealed a complex resistome and virulome, with 7259 ARGs and 6701 virulence-related genes identified across samples. Antibiotic target alteration and efflux were the dominant resistance mechanisms, while effector delivery systems, metabolic functions, and adherence were the major virulence categories. MGEs were abundant, especially transposases, indicating active genetic mobility within the microbial community. Overall, this study provides a comprehensive characterization of antimicrobial resistance and virulence features of mink-derived K. pneumoniae and highlights the potential role of farmed minks as reservoirs of multidrug-resistant bacteria within the One Health framework, offering important insights for antimicrobial resistance surveillance and public health risk assessment.}, } @article {pmid41966472, year = {2026}, author = {Merkhan, K and Chaudhry, AS}, title = {Phytogenic feed additives mitigate in vitro methanogenesis and alter microbial community and functional pathways in the dairy cow rumen.}, journal = {Anaerobe}, volume = {98}, number = {}, pages = {103046}, doi = {10.1016/j.anaerobe.2026.103046}, pmid = {41966472}, issn = {1095-8274}, mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle ; *Methane/metabolism/biosynthesis ; Fermentation ; *Animal Feed/analysis ; *Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; Archaea/metabolism ; Bacteria/classification/genetics/metabolism ; *Food Additives ; }, abstract = {OBJECTIVES: Using phytogenic feed additives (PFA) could be a promising strategy for mitigating enteric methane (CH4) emissions from ruminants. This study aimed to evaluate the efficacy of specific phytogenic additives on rumen fermentation, methanogenesis, microbial community, and functional pathways.

METHODS: This 2 x 4 x 3 factorial study was conducted using an in vitro rumen fermentation system for a period of 72 h. Treatments included two silage-to-concentrate ratios (60:40 and 40:60), four PFA (great burnet leaves, GBL; oregano leaves, OL; cumin seeds, CS; and garlic bulbs, GB), and three inclusion levels (0, 10, and 20 g kg[-1] DM) for each PFA.

RESULTS: The GB addition proved the most potent anti-methanogenic additive, reducing CH4 by up to 32.8% at 20 g kg[-1] DM, followed by GBL with a 28.5% reduction at 10 g kg[-1] DM, without impairing total volatile fatty acid production. Methane suppression was associated with a lower acetate-to-propionate ratio, decreased abundance of methanogenic archaea (particularly Methanobrevibacter), and reduced expression of the key methanogenesis gene mcrA and fmdB. While GB exhibited a strong anti-protozoal effect, OL effectively reduced ruminal ammonia concentrations. Additionally, metagenomic analysis identified Porcincola was among the core and most abundant genera in our bovine rumen dataset.

CONCLUSION: Optimising the inclusion of specific phytogenic additives can selectively manipulate the rumen microbiome, concurrently reduce methane production and influence nitrogen metabolism. Further research is warranted to evaluate potential synergistic interactions among these additives to enhance fermentation efficiency of ruminant diets.}, } @article {pmid41966559, year = {2026}, author = {Jordán, M and Bustos-Caparros, E and Gago, JF and Zhang, Z and Tian, Z and Singleton, DR and Rossello-Mora, R and Grifoll, M and Vila, J}, title = {Unraveling acridine degradation mechanisms in PAH-contaminated soils using DNA-SIP combined with metagenomics and soil transcriptomics.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {142004}, doi = {10.1016/j.jhazmat.2026.142004}, pmid = {41966559}, issn = {1873-3336}, mesh = {*Soil Pollutants/metabolism ; *Soil Microbiology ; Biodegradation, Environmental ; Metagenomics ; *Polycyclic Aromatic Hydrocarbons/metabolism ; *Acridines/metabolism ; RNA, Ribosomal, 16S/genetics ; Transcriptome ; Sphingomonadaceae/genetics/metabolism ; }, abstract = {Polycyclic aromatic nitrogen heterocycles (PANHs), also known as azaarenes, are common co-contaminants at sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Recent non-target analysis of PAH-contaminated soil samples has revealed an unexpected abundance and diversity of PANHs, with acridine standing out as a predominant compound within this group. Despite its known toxicity and prevalence in contaminated soils, the microbial communities and biochemical mechanisms responsible for acridine degradation remain poorly understood. We conducted DNA-stable isotope probing (DNA-SIP) using newly synthesized uniformly labeled [13]C-acridine to comprehensively assess the bacterial taxa and functional genes involved in acridine biodegradation in a creosote-contaminated soil. Metagenomic analysis of [13]C-enriched DNA from soil incubations identified a member of the genus Sphingobium as the primary acridine degrader. Transcriptomic analysis based on its 16S rRNA gene expression demonstrated a strong correlation with acridine removal from the soil. Shotgun metagenomic sequencing enabled the reconstruction of one metagenome-assembled genome (MAG). Functional annotation of this MAG revealed five gene clusters potentially involved in acridine biodegradation, and their actual contribution was assessed by gene expression analysis in soil incubations. Based on these findings, we reconstructed the metabolic pathway for putative acridine degradation in PAH-contaminated soil.}, } @article {pmid41966829, year = {2026}, author = {Tóth, AG and Paholcsek, M and Solymosi, N and Stágel, A and Gömbös, P and Posta, K and Lakatos, I and Nagy, SÁ and Ferenczi, S and Szőke, Z}, title = {Protocol for the assessment of the impact of mycotoxins and glyphosate residues on the gut microbiome and resistome of European fallow deer.}, journal = {STAR protocols}, volume = {7}, number = {2}, pages = {104498}, pmid = {41966829}, issn = {2666-1667}, abstract = {Here, we present a protocol to describe the bacteriome of the intestinal content of toxin-exposed fallow deer. We describe steps for measuring fecal mycotoxin (deoxynivalenol, zearalenone, fumonisin B1, and aflatoxin B1) levels using liquid chromatography-mass spectrometry, as well as serum glyphosate. We then detail a short-read shotgun DNA sequencing-based bioinformatic pipeline for the toxin level-associated analysis of the bacteriome and resistome and the construction of metagenome-assembled bacterial genomes. This protocol has potential applications in further toxin level-associated metagenome studies. For complete details on the use and execution of this protocol, please refer to Tóth et al.[1].}, } @article {pmid41967167, year = {2026}, author = {Okoye, CO and Okoye, KC and Ezenwanne, BC and Olalowo, OO and Andong, FA and Echude, D and Chukwudozie, KI and Emencheta, SC and Ezeonyejiaku, CD and Ikele, CB}, title = {Microbiome and multi-omics insights into sustainable aquaculture: A triennial systematic review.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {59}, number = {}, pages = {101830}, doi = {10.1016/j.cbd.2026.101830}, pmid = {41967167}, issn = {1878-0407}, mesh = {Animals ; *Aquaculture/methods ; Metabolomics ; *Microbiota ; *Multiomics ; }, abstract = {Aquaculture is the fastest-growing food production sector, yet intensive practices drive disease outbreaks, antibiotic resistance, and environmental degradation, threatening long-term sustainability. The aquaculture microbiome, encompassing host-associated and environmental microbial communities, regulates nutrient cycling, pathogen suppression, immunity, and overall system resilience. This triennial systematic review (2023-2025), conducted according to PRISMA guidelines, synthesized 19 highly relevant peer-reviewed studies that applied multi-omics approaches (metagenomics, transcriptomics, metabolomics, SNP genotyping, and their integration) to aquaculture microbiomes across shrimp, finfish, and hybrid species. The studies collectively revealed diverse host-microbe-metabolite interactions underpinning growth, immunity, and disease resistance, with representative examples including microbial-metabolite-host signaling axes and microbiome-mediated immune modulation, as seen in Salinivibrio-AMP-mTOR axis, EHP-resistant shrimp via metabolic reprogramming and stable microbiota, and Bacillus-mediated diglyceride production. Beneficial taxa such as Cetobacterium and Salinivibrio, heritable microbiome traits, and sustainable interventions including insect-meal feeds, phytogenic additives, and organic copper consistently improved growth, immunity, and microbial stability while reducing dysbiosis under stress. Environmental stressors and pathogens induced reproducible shifts in microbial diversity, functional pathways, and host metabolism. These findings demonstrate that multi-omics integration is transforming aquaculture into a precision discipline, enabling microbiome-informed selective breeding, targeted probiotics, and environmentally sound nutrition. To translate these insights into practice, future research must emphasize functional validation, machine learning-driven predictive models, and ecosystem-level assessments to achieve resilient, antibiotic-reduced, and sustainable aquaculture systems.}, } @article {pmid41967206, year = {2026}, author = {Moletta-Denat, M and Azam, O and Pourcher, AM and Manno, M and Zennaro, B and Bonin, E and Bonnafous, A and Chenon, P and Leboucher, A and Alvarez-Fraga, L and Godon, JJ and Wéry, N}, title = {Fate of pathogenic bacteria in five full-scale biogas plants monitored using cultivation, dPCR, and shotgun metagenomics: Insights from each approach.}, journal = {Waste management (New York, N.Y.)}, volume = {218}, number = {}, pages = {115505}, doi = {10.1016/j.wasman.2026.115505}, pmid = {41967206}, issn = {1879-2456}, mesh = {*Metagenomics/methods ; *Biofuels/microbiology ; Polymerase Chain Reaction/methods ; *Bacteria/isolation & purification/genetics ; Shotgun Sequencing ; }, abstract = {Current global standards for quantification of pathogenic or indicator bacteria in biogas plants primarily rely on culture-based methods using specific media. However, molecular techniques such as quantitative PCR, digital PCR (dPCR), and shotgun metagenomics are increasingly employed in research and may offer more effective pathogen monitoring for industrial applications. This study analyzed samples from five full-scale biogas plants using traditional culture-based methods, dPCR and shotgun metagenomics to monitor indicator bacteria (Escherichia coli, Enterococcus spp. and Clostridium perfringens) and pathogenic species (Salmonella enterica, Listeria monocytogenes, Staphylococcus aureus and Clostridium botulinum). The DNA extraction protocol was optimized to achieve quantification limits of 1.1 copies of gene g[-1] wet weight, compatible with regulatory thresholds. Comparing the three methods revealed that shotgun metagenomics detected a greater diversity of pathogenic species in biowaste, including S. aureus and C. botulinum. Acidophilic conditions in hydrolysis tank effectively hygienized the biowaste. In contrast, the four agricultural biogas plants showed limited effect on the three indicator bacteria, as indicated by dPCR. This study demonstrates, for the first time, the added value of combining dPCR and shotgun metagenomics to assess pathogen dynamics in biogas plants. Together, these methods provide a more comprehensive and specific view of microbial contaminants, as illustrated by the detection of Enterococcus cecorum in digestates.}, } @article {pmid41967340, year = {2026}, author = {Li, M and Yao, K and Harindintwali, JD and Qian, M and Wu, N and Kan, Y and Song, Z and Xiao, X and Liu, P and Zhao, Y}, title = {Alkali-organic synergy rewires microbial acid tolerance to restore nitrogen cycling in acidic soils.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129619}, doi = {10.1016/j.jenvman.2026.129619}, pmid = {41967340}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Nitrogen Cycle ; Hydrogen-Ion Concentration ; Nitrogen ; Manure ; Alkalies ; }, abstract = {Soil acidification in global croplands is intensifying, yet the microbial mechanisms by which amendments restore soil nitrogen (N) cycling remain poorly understood. Here, we used a decade-long field experiment in strongly acidic soils to elucidate how alkali slag and organic manure, alone and in combination, regulate acid-tolerant microbial functions and N transformation processes. By integrating soil physicochemical analyses, 16 S rRNA gene sequencing, and shotgun metagenomics, we show that the combined application of organic manure and alkali slag (OM + AS) most effectively increased soil pH (from 4.18 to 5.42) and reduced inorganic N accumulation relative to single amendments (Ammonium nitrogen, nitrate nitrogen, and total organic nitrogen decreased by 15.66 mg/kg, 12.56 mg/kg, and 46.09 mg/kg respectively). Metagenomic profiling revealed that OM + AS consistently up-regulated acid-tolerance pathways (proton pump increased by 6.12%, alkali production increased by 9.75%, acid consumption increased by 5.12%) together with key N cycling genes, with the strongest enhancement observed for nitrification (increased by 84.54%). Network analysis demonstrated significant positive co-occurrence between acid-tolerance and nitrification genes across the microbial community. Correspondingly, bacterial taxa harboring these functions, including Sphingomonas and Nitrospira, were most abundant under OM + AS. We propose that alkali slag and organic manure act synergistically to elevate soil pH, relieve acid stress on microbes, and promote a community with dual capacities for acid tolerance and active N transformation. These findings mechanistically link soil acidity amelioration with enhanced microbial-mediated N cycling and offer a functional basis for designing targeted soil remediation strategies.}, } @article {pmid41967439, year = {2026}, author = {Tang, C and Wan, C and Gan, J and He, Z and Wei, C and Tan, H and Wu, R and Yu, F and Li, Y}, title = {Rhizosphere phosphorus and iron cycling accelerates manganese phytoextraction by Polygonum lapathifolium.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {142033}, doi = {10.1016/j.jhazmat.2026.142033}, pmid = {41967439}, issn = {1873-3336}, mesh = {*Rhizosphere ; Biodegradation, Environmental ; *Iron/metabolism ; *Phosphorus/metabolism ; *Manganese/metabolism ; *Soil Pollutants/metabolism ; *Polygonum/metabolism/growth & development ; Enterobacter/metabolism ; }, abstract = {Manganese (Mn) contamination in mining soils poses persistent ecological risks due to its high mobility and potential accumulation in plants. Although exogenous microbial inoculation is increasingly used to improve phytoremediation, the mechanisms by which it regulates rhizosphere phosphorus (P) and iron (Fe) cycling, and thereby influences Mn bioavailability, remain poorly understood. We hypothesized that Enterobacter sp. inoculation would enhance Mn phytoextraction by stimulating rhizosphere P activation and Fe speciation transformation, thereby promoting nutrient acquisition and Mn mobilization. To test this hypothesis, we investigated the effects of Enterobacter sp. inoculation on rhizosphere P/Fe fractions, functional genes, and Mn phytoextraction. Enterobacter sp. significantly decreased rhizosphere soil pH and enhanced P-releasing enzyme activities, increasing available P by 26.7% under the C1.0 (3.8 ×10[7] CFU·g[-1] (soil)) treatment compared with the control (p < 0.05). Concurrently, Fe(II) and amorphous Fe increased by 11.9% and 15.1%, respectively (p < 0.05), indicating enhanced Fe transformation in the rhizosphere. These shifts facilitated plant P and Fe acquisition, promoted biomass production, enhanced Mn phytoextraction in Polygonum lapathifolium L. by strengthening rhizosphere redox conditions and mineral interfacial processes. Metagenomic analysis revealed that Enterobacter sp. inoculation increased the functional potential of genes related to P activation (e.g., gcd, phnP) and Fe biosynthesis/uptake (e.g., hemH, pchB), mainly associated with Pseudomonadota and Actinomycetota. Partial least squares path modeling further confirmed positive associations among P/Fe cycling genes, rhizosphere P/Fe fractions, enzymatic activities, and plant growth. Overall, microbial inoculation enhanced Mn phytoremediation by coordinating rhizosphere nutrient cycling processes, providing a promising strategy for the remediation of HMs-contaminated mining soils.}, } @article {pmid41967476, year = {2026}, author = {Wang, H and Di, D and Du, S and Tateno, R and Peñuelas, J and Migliavacca, M and Chen, Q and Guan, J and Song, Y and Shi, W}, title = {Plant functional trait differentiation and microbial life-history strategy shifts drive soil respiration under long-term forest restoration.}, journal = {Tree physiology}, volume = {46}, number = {5}, pages = {}, doi = {10.1093/treephys/tpag042}, pmid = {41967476}, issn = {1758-4469}, mesh = {*Soil Microbiology ; *Forests ; *Soil/chemistry ; China ; *Trees/physiology ; }, abstract = {Soil respiration (Rs) represents a major carbon (C) flux linking plant productivity with microbial decomposition; however, the mechanisms by which contrasting forest restoration pathways regulate Rs and its components remain insufficiently understood. We conducted a 6-year field observation (2017-2022) across abandoned farmland (AF), Quercus liaotungensis Koidz. forest (QF), and Robinia pseudoacacia L. plantation (RP) on the Loess Plateau, China, integrating measurements of Rs, autotrophic (Ra), heterotrophic (Rh), plant functional traits, soil physicochemical properties and microbial C metabolic potential. Afforestation significantly increased Rs, with a stronger enhancement observed in QF than in RP. Although Ra did not differ significantly between the two forest types, Rh accounted for ~70% of Rs and primarily explained the significant differences in Rs between restoration pathways. Elevated Rh in QF was strongly associated with greater abundances of microbial functional genes involved in the degradation of C substrates. Integrated analyses further revealed that differentiation in plant functional traits between QF (conservative strategy) and RP (acquisitive strategy) indirectly amplified Rh contributions to Rs by reshaping soil substrate availability and coordinating shifts in microbial life-history strategies. Collectively, our findings identify plant functional trait differentiation as a key driver of long-term Rs dynamics, mediated by shifts in microbial life-history strategies.}, } @article {pmid41967488, year = {2026}, author = {Du, M and Xue, P and Minasny, B and Jang, HJ and McBratney, A}, title = {Macroecological processes impact Australian soil resistomes and climatically stable regions with anthropogenic activities serve as ARG hotspots.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41967488}, issn = {1751-7370}, support = {4-H4T0RYS//Department of Agriculture, Fisheries, and Forestry, Australian Government/ ; }, mesh = {*Soil Microbiology ; Australia ; Climate ; *Soil/chemistry ; *Anthropogenic Effects ; Metagenomics ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; }, abstract = {Soil antibiotic resistance genes (ARGs) pose a global health threat, but a critical knowledge gap remains regarding how macro-scale pedoclimatic constraints interact with land-use intensification to determine the spatial distribution of the soil resistome. To address this, we conducted a continental-scale survey of Australian topsoils and used metagenomic analysis to reveal the hierarchy of drivers shaping soil resistome. Machine learning was applied to predict the spatial ARG distribution across Australia. We found that, at the continental scale, climatic variability acts as the dominant filter on ARG distribution, overriding local soil properties and human disturbance. Unexpectedly, climatically stable regions, characterized by sandy and low-carbon soils in Southwestern Australia, emerged as ARG hotspots. We also demonstrated that anthropogenic land use amplifies ARG abundance within these climatically stable regions. Furthermore, spatial modelling revealed distinct geographical patterns: although total ARG abundance was enriched in coastal regions, specific resistance mechanisms showed unique distributions. As a continental-scale investigation of soil ARGs in Australia, this study provides a framework to identify high-risk regions where lower climatic variability and intensive farming interact to enhance antimicrobial resistance.}, } @article {pmid41968394, year = {2026}, author = {Zhao, B and Yang, X and Feng, K and Wang, J and Liu, M and Wang, Y and Wang, D and Peng, X and He, Q and Lu, Y and Waseem, H and Wang, S and Deng, Y}, title = {Phylogenetic assembly of methanogenesis regulates methane yield in food-waste anaerobic digestion.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41968394}, issn = {1751-7370}, support = {42277104//National Nature Science Foundation of China/ ; 42577132//National Nature Science Foundation of China/ ; 2019YFC1905001//National Key Research and Development Program of China/ ; }, mesh = {*Methane/metabolism/biosynthesis ; *Phylogeny ; Anaerobiosis ; China ; Food Loss and Waste ; Biofuels ; *Archaea/classification/genetics/metabolism ; }, abstract = {Anaerobic digestion (AD) of food waste (FW) is a key waste-to-energy strategy, yet daily biogas yield is often challenging to sustain, partly due to a limited understanding of the internal methanogens and their functional divergence. Here, we investigated seven full-scale mesophilic FW-AD systems distributed across China along a broad latitudinal gradient (>2800 km), linking methane production variations (0.38-2.11 m3/m3•d-1) with the phylogenetic distributions of methanogens and their methanogenic genes. We found that hydrogenotrophic and aceticlastic pathways were ubiquitous, whereas methylotrophic methanogenesis showed regional enrichment in warmer regions, reflecting persistent influences of climate-associated upstream conditions on downstream methanogenic communities. Gene-level phylogeny of methanogenesis-related alleles, rather than species-level phylogeny, closely tracked biogas yield variation (Mantel's P < .05) and showed consistently stronger associations than gene-level compositions (mean standardized total effect: 0.491 vs. 0.298, P < .01). Higher methane yields (1.61 vs. 0.61 m3/m3•d-1 in high- vs. low-performing systems, P < .01) were significantly associated with reduced Faith's phylogenetic diversity (1.82 vs. 2.30, P < .01) and tighter clustering (mean pairwise phylogenetic distance: 0.25 vs. 0.30, P < .01) of methanogenic gene variants, suggesting that phylogenetic coherence may reflect ecological filtering favoring efficient methanogenesis, albeit at the expense of functional redundancy. These findings highlight gene-level trait phylogeny as a potential proxy for functional robustness, offering a framework for ecological design of AD microbiomes.}, } @article {pmid41968748, year = {2026}, author = {Hilpert, K}, title = {Peptidomics: A New Dimension in Microbiome Research.}, journal = {Protein and peptide letters}, volume = {33}, number = {2}, pages = {488-496}, doi = {10.2174/0109298665436241260327111926}, pmid = {41968748}, issn = {1875-5305}, mesh = {Humans ; *Proteomics/methods ; *Peptides/metabolism/chemistry ; *Gastrointestinal Microbiome ; *Microbiota ; Multiomics ; }, abstract = {The human gut microbiome is now recognised as a major determinant of health, with roles extending beyond digestion to influence neurodegeneration, metabolism, immunity, and pharmacological responses. Clinical studies link microbial imbalances to Alzheimer's disease, Parkinson's disease, depression, and cardiovascular disorders, yet the underlying mechanisms remain only partly understood. Methodological advances have progressively deepened our insight. DNA-based sequencing (metagenomics) catalogues microbial genes but reveals only potential functions. RNA-based sequencing (metatranscriptomics) highlights active gene expression, but instability of transcripts and poor correlation with protein activity limit its predictive value. Metabolomics measures small-molecule end products, providing direct evidence of microbial biochemistry and identifying disease-linked metabolites such as urolithin A, trimethylamine N-oxide, and equol. These approaches together have transformed microbiome science, but they remain incomplete. A critical and underutilised dimension is peptidomics: the systematic analysis of endogenous peptides in the gut and circulation. Enabled by peptide-enriching, protease-inhibiting workflows and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS), peptidomics directly captures unstable signaling peptides and proteolytic fragments that are often invisible to conventional proteomics. Coupled with emerging gut-specific peptide databases, such as MetaPep, and Artificial Intelligence (AI) assisted de novo sequencing and spectral prediction for non-human peptides, this provides a concrete technical route to reading out the functional peptide layer of the microbiome. Peptidomics can capture functional signals of host-microbiome interaction, reveal context-specific biomarkers, and provide mechanistic insight into disease. Recent studies demonstrate that peptide-level resolution uncovers microbial contributions to gut inflammation, modulates the gut-brain axis, and enables peptide-based disease stratification in conditions such as inflammatory bowel disease. However, despite these promising examples, peptidomics remains largely absent from mainstream microbiome research. Integrating peptidomics with existing genomic, transcriptomic, and metabolomic approaches will generate a more complete and functional picture of the microbiome. This shift will accelerate biomarker discovery, refine diagnostics, and expand the search for peptide-based therapeutics, positioning peptidomics as an essential next step in microbiome science.}, } @article {pmid41969349, year = {2026}, author = {Cheng, L and Wang, J and Sun, J and Xu, S and Zhao, G and Li, M}, title = {Integrated multi-omics of the ruminal microbiome and host metabolome reveals compensatory growth in response to dietary energy restriction and re-alimentation in growing beef bulls.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {25}, number = {}, pages = {265-281}, pmid = {41969349}, issn = {2405-6383}, abstract = {Understanding the mechanisms of dietary energy on compensatory growth in beef cattle is crucial for improving feed efficiency and mitigating the environmental footprint of beef production. The objectives of the study were to investigate the effects of dietary energy restriction and subsequent re-alimentation on growth performance, nutrient digestibility, ruminal microbiome, plasma metabolites, and nitrogen metabolism in growing beef bulls. Twelve 6-8-month-old Simmental crossbred bulls (initial body weight: 226 ± 24 kg) were randomly allocated to two groups (n = 6 per group): the dietary energy restriction group (REC) was fed a diet containing 9.25 MJ/kg metabolizable energy (ME) for 4 weeks (energy restriction period), followed by a 2-week re-alimentation period with a 10.29 MJ/kg ME diet, while the control group (CON) was fed the 10.29 MJ/kg ME diet consistently throughout the experimental period. Dietary energy restriction significantly decreased body weight and average daily gain (ADG) compared to CON (P < 0.05). However, no significant differences were observed by the end of the re-alimentation period (P > 0.05), demonstrating successful compensatory growth through dietary energy modulation. Ruminal propionate, total volatile fatty acids, ammonium nitrogen, and microbial crude protein (MCP) concentrations significantly decreased in the energy restriction treatment compared to CON (P < 0.05), but MCP exceeded the levels in CON after dietary energy re-alimentation (P < 0.05). Energy restriction also significantly increased urinary nitrogen excretion (P = 0.002), driven by imbalanced amino acid metabolism and significantly increased urinary urea (P = 0.038), which significantly reduced protein synthesis and nitrogen retention (P = 0.017). Metagenomics analysis revealed that energy restriction significantly increased the relative abundances of Limosilactobacillus, Enterococcus, and Aliarcobacter (P < 0.05), while decreasing those of Gemmatirosa and Mesorhizobium (P < 0.05). Dietary energy re-alimentation significantly increased the relative abundance of Gramella, Acetobacter, Phaeobacter, and Flammeovirga (P < 0.05). These bacteria are associated with pathways related to amination, transamination, and microbial protein synthesis. Integrated multi-omics revealed shifts in the ruminal microbiome and host metabolome, particularly in pathways related to ruminal urea hydrolysis, biosynthesis of glutamate, glutamine, and alanine, and post-absorptive amino acid metabolism, which collectively enhanced protein synthesis and compensatory growth. These findings establish a practical feeding strategy to optimize feed efficiency and enhance compensatory growth in beef bulls via short-term dietary energy manipulation.}, } @article {pmid41969354, year = {2026}, author = {Dayan, J and De Cesare, A and Soglia, F and Zampiga, M and Indio, V and Antenucci, EL and Petracci, M and Sirri, F}, title = {Nutritional alternatives to commercial lipid sources: Impact of the dietary inclusion of black soldier fly (Hermetia illucens) larvae oil on broiler chicken productivity, breast meat quality traits and caeca microbiome.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {25}, number = {}, pages = {255-264}, pmid = {41969354}, issn = {2405-6383}, abstract = {Protein production from poultry, particularly broiler chickens, is considered a key component of future global food security, due to its relatively high sustainability. However, the use of resources such as soybean oil remains a concern. Black soldier fly (Hermetia illucens [HI]) larvae oil represents a promising alternative due to a relatively rapid rearing cycle and ability to utilize organic waste as growth substrates. This study investigated how replacing a commercial lipid source such as soybean oil, with HI larvae oil affects broiler growth performance, meat quality traits, fatty acid (FA) profile, and caeca microbiome. A total of 552 one-d-old male Ross 308 broilers, with equal initial weights (48.89 ± 0.18 g; P = 0.597), were allocated to three dietary treatments with 8 replicate pens per group (23 birds/pen). All birds received the same commercial basal diet, formulated to be isoenergetic and with the same amino acid profile, differing only in the source of the supplemented oil: 100% soybean oil group (CON), 50% soybean oil + 50% HI larvae oil group (MIX), or 100% HI larvae oil group (HIO). Growth performance parameters were recorded at the end of each feeding phase (14, 28, and 42 d). At slaughter (42 d), 10 breasts (pectoralis-major muscle) and thighs (extensor-iliotibialis muscle) samples per group were collected for meat quality assessment, and caecal content samples were obtained from 8 birds/group for microbiome analysis. Growth performance metrics showed an improvement in feed conversion ratio during the starter phase for HI larvae oil-fed groups (1.54 vs. 1.45 vs. 1.46 for CON, MIX, and HIO, respectively; P < 0.001) and comparable performance across the trial. Meat quality traits remained within commercially acceptable ranges, with minimal effects observed, apart from variations in breast fillet redness and thigh protein oxidation. FA analysis indicated higher levels of saturated FAs in the HI groups, with a concurrent reduction in omega (n)-6 levels and a more balanced n-6 to n-3 ratio (16.47 vs. 15.18 vs. 11.60 for CON, MIX, and HIO, respectively; P < 0.001). The caecal microbiome revealed stable diversity across groups, with only minor shifts in relative abundance. Overall, the findings showed that HI larvae oil is an effective alternative to conventional vegetable lipid sources in poultry nutrition, with added potential to enhance growth performance during the early growth stages.}, } @article {pmid41969371, year = {2026}, author = {Ramos Peña, DE and Boussetta-Charfi, O and Antezack, A and Amroune, N and Colson, P and Monnet-Corti, V and Saia, RS and Guillemot, J and Pozzetto, B and Pillet, S and La Scola, B and Bourlet, T and Fragoso Motta, AC}, title = {Interplay Between Oral Microbiota and Mouth Health in People Living With HIV Under Antiretroviral Therapy With or Without Periodontitis.}, journal = {International journal of dentistry}, volume = {2026}, number = {}, pages = {8794149}, pmid = {41969371}, issn = {1687-8728}, abstract = {People living with HIV (PLWH) in combined antiretroviral therapy (cART) face microbiota shifts linked to immune status, ART regimen, and periodontal diseases, which are capable of inducing local and systemic inflammation. This study aimed to analyze the oral microbial community composition in PLWH under cART with (n = 24) or without (n = 25) periodontitis using shotgun metagenomic sequence analysis, and describe the interaction between bacterial species, clinical and immunological parameters, and the response to nonsurgical periodontal therapy (NSPT). Saliva samples were collected at baseline for both groups, and 30 days after NSPT for the periodontitis group. Within the periodontitis group, all periodontal parameters presented highly significant improvement after NSPT when compared to baseline. The gingival microbiota did not differ significantly between patients with periodontitis and controls; however, a wider range of bacterial species was found in the microbiota of the periodontitis group compared to the control group, while post-treatment the periodontitis group presented an alpha diversity intermediate between the two former groups. Regarding the distribution of the different bacterial species, Porphyromonas gingivalis was found significantly enriched in the periodontitis group, along with different Treponema sp., Fretibacterium fastidiosum, Campylobacter rectus, Bacteroides zoogleoformans, Tannerella forsythia, and Porphyromonas endodontalis. Correlations between seven inflammatory markers and seven periodontitis-related bacterial taxa were found for saliva in the group of periodontitis patients, which was not the case in controls; interestingly, the profiles after NSPT showed intermediate results. By contrast to saliva, the inflammatory markers of periodontitis patients showed no marked differences in blood plasma, except for TNF-alpha and partly IL-4. In view of the fact that oral microbial imbalance may contribute not only to local disease but also to systemic immune activation in the course of HIV-1 infection, reinforcing the importance of maintaining periodontal health represents a part not to be neglected for an optimal management of PLWH.}, } @article {pmid41969565, year = {2026}, author = {Kavagutti, VS and Beavogui, A and Wiart, N and Wincker, P and Oliveira, PH}, title = {Defensomes, counter-defensomes, and the remodeling of microbial communities.}, journal = {PNAS nexus}, volume = {5}, number = {4}, pages = {pgag073}, pmid = {41969565}, issn = {2752-6542}, abstract = {Bacteria and mobile genetic elements (MGEs) have coevolved for billions of years in an enduring evolutionary arms race, leading to the emergence and diversification of a vast arsenal of defense and counter-defense systems. In the last recent years, high-throughput screening methods and genome-resolved metagenomics have markedly enhanced our understanding of the diversity and abundance of immune systems across cultured and uncultured microorganisms. This fueled subsequent interest in better understanding the dynamic tri-kingdom interplay between bacteria, bacteriophages, and eukaryotic cells, and led to renewed efforts to improve alternative antibacterial phage-based therapies. Here, we discuss the evolutionary and ecological dynamics underlying the bacteria-MGE arms race, recent findings on bacterial defensomes, MGE counter-defensomes, holodefensomes, and their key role in the development of microbiome-targeted therapies. To this end, we argue why and how highly conserved anti-MGE defense systems should be prioritized as promising targets for the development of next-generation bacterial inhibitors with broad biomedical relevance, supported by a comprehensive analysis of their distribution and diversity across bacteria.}, } @article {pmid41969652, year = {2026}, author = {Zhang, H and Zhang, L and Yang, B and Gao, C and Liu, H and Zhang, Y and Chen, X}, title = {Correction: Metagenomic and metatranscriptomic profiling of bronchoalveolar lavage fluid identifies microbial and host biomarkers of drug-resistant tuberculosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1826950}, doi = {10.3389/fcimb.2026.1826950}, pmid = {41969652}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1726935.].}, } @article {pmid41969653, year = {2026}, author = {Dai, Z and Hu, Y and Tai, A and Lu, Y and Hu, S and Pan, J and Xiao, Y and Ma, X and Fu, Q and Zhao, H and Su, Z and Tong, P and Hao, Z and Yao, G and Wang, J}, title = {Characterization of a Klebsiella pneumoniae mutant strain wGF 1-2 with attenuated virulence, altered morphology, and reduced biofilm formation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1761564}, pmid = {41969653}, issn = {2235-2988}, mesh = {Animals ; *Klebsiella pneumoniae/genetics/virology/pathogenicity/physiology/growth & development ; *Biofilms/growth & development ; Virulence ; Klebsiella Infections/microbiology/pathology ; Mice ; Disease Models, Animal ; Multiomics ; Gene Expression Profiling ; Host-Pathogen Interactions ; Bacteriophages ; Proteomics ; Mutation ; Female ; Proteome/analysis ; Survival Analysis ; Virulence Factors ; }, abstract = {INTRODUCTION: The global rise of antimicrobial resistance has positioned multidrug-resistant Klebsiella pneumoniae as a critical health threat, necessitating alternative therapeutic strategies such as phage therapy. However, the long-term evolutionary consequences of phage-bacteria interactions remain poorly understood. This study characterizes a unique attenuated mutant, wGF 1-2, derived from a hypervirulent K. pneumoniae strain (GF) during phage isolation efforts.

METHODS: The wGF 1-2 mutant was serendipitously isolated during attempts to obtain lytic phages against the parental GF strain. We performed an integrated multi-omics and phenotypic characterization, including genomic sequencing, proteomic profiling, and transcriptomic analysis. Host-pathogen interactions were assessed using a murine infection model (evaluating survival and tissue colonization), and the impact on the gut microbiota was analyzed via metagenomics.

RESULTS: Compared to the parental strain, wGF 1-2 exhibited a significant reduction in biofilm formation and distinct morphological alterations. In a murine model, the mutant was avirulent, resulting in 100% survival even at a high challenge dose (10⁶ CFU), with minimal tissue colonization. Multi-omics analysis revealed extensive genomic structural variations (81 insertions and 64 deletions). Proteomic shifts included the downregulation of proteins involved in metal ion binding and metabolic pathways. Furthermore, infection with wGF 1-2 led to host inflammatory suppression and a restructuring of the gut microbiota characterized by an increase in beneficial Bacteroidota.

DISCUSSION: This study provides a comprehensive characterization of an attenuated K. pneumoniae mutant, wGF 1-2. The extensive genomic and phenotypic alterations observed highlight the significant evolutionary potential of bacterial pathogens during phage interactions. These findings underscore the necessity of thorough safety assessments, including evolutionary risk evaluations, for the future development of phage-based therapies.}, } @article {pmid41970373, year = {2026}, author = {Duan, Y and Wang, L and Cui, H and Fang, Z and Lu, Y and Sun, Z}, title = {The effect of elastic-band resistance training on fecal microbiota and derived metabolites of aged individuals with possible sarcopenia.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1762454}, pmid = {41970373}, issn = {2296-858X}, abstract = {BACKGROUND: Individuals with possible sarcopenia exhibit altered microbiota profiles and poor intestinal metabolism. Exercise training is linked to changes in gut microbiota and has been proposed to enhance the quality of aging skeletal muscle.

AIMS: In older adults with possible sarcopenia, the study aimed to determine if elastic-band resistance training modulates gut microbiota and its generated metabolites and investigate the underlying relationships with physical function.

METHODS: Thirty-one volunteers with possible sarcopenia were randomly assigned to either the control group (CG, n = 17) or the intervention group (RG, n = 14), which underwent 24 weeks of elastic-band resistance training. Physical function, body composition, and blood and fecal samples were collected from each patient at baseline and 24 weeks. Enzyme-linked immunosorbent assay (ELISA) was used to evaluate protein metabolism regulatory factors, targeted metabolomics was used to quantify short-chain fatty acid (SCFA) levels, and metagenomic sequencing was used to analyze the composition of the fecal microbiota.

RESULTS: The gait speed (GS), arm curl test (ACT), 2-min step test (2MST), and timed up-and-go test (TUGT) all showed notable improvements in the RG. The RG also showed lower serum levels of tumor necrosis factor-α (TNF-α) and higher plasma concentrations of acetate and propionate. Following the intervention, the RG displayed decreased abundances of Eisenbergiella and Eggerthella and increased abundances of the genus Bacillus. Eggerthella abundance was inversely connected with 2MST performance, whereas the change in propionate level was positively correlated with 2MST, TUGT, GS, and appendicular skeletal muscle index (ASMI).

CONCLUSION: The elastic-band resistance training effectively improved physical function, modulates gut microbiota and SCFAs. The results revealed the physiological mechanisms by which gut microbiota and SCFAs regulate aging muscle health, providing scientific support for possible sarcopenia prevention and treatment via gut-muscle axis bidirectional crosstalk.

CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn/index.html.}, } @article {pmid41971320, year = {2026}, author = {Wu, Y and Deng, L and He, X and Zhou, D and Ling, S and He, M and Wang, Q and Wang, C and Wang, M and Wu, H and Li, L and Li, D and Yun, L}, title = {Intestinal microbiome gone native: gut microbiome shift and resistome diversity in first homecoming giant panda family.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1737792}, pmid = {41971320}, issn = {1664-302X}, abstract = {INTRODUCTION: The world-famous giant pandas (Ailuropoda melanoleuca) often travel abroad for public exhibitions and international scientific cooperations. Previous research has reported alternations in the gut microbiome structure and enrichment of gut antibiotic-resistant genes (ARGs) in human international travelers, the latter of which is harmful to native residents and the environment. The microbiome and ARGs of these animal travelers, however, have not yet been investigated, even though they often interact with local keepers, visitors, and other pandas.

METHODS: In this study, we have clarified the dynamic microbiome composition and snapshot of ARGs (resistome) of the first panda family returning from overseas. Fecal samples were gathered for high-throughput sequencing for both amplicon and metagenomics sequencing, which were collected on the first day of their quarantine (Admission stage) and 3 days after the quarantine (Release stage). Feces from two native captive pandas were used as controls.

RESULTS AND DISCUSSION: The predominant Escherichia-Shigella proportion in the mother and father pandas decreased from 79.02 and 47.46% to 57.03 and 33.77%, while the Streptococcus abundance increased from 0.27 and 12.44% to 29.47 and 54.59%. The main genus of child pandas, Weissella, decreased from 45.24 to 0.02% after quarantine, and the Streptococcus ratio increased from 11.89 to 43.82%. Significant richness and bacterial diversities were found in these samples. The main ARG types are multidrug and polymyxin; the latter being an uncommon ARG in native pandas. Consequently, to protect local ecosystems from the introduction of novel ARGs, waste from translocated giant pandas should be managed under strict biosecurity protocols.}, } @article {pmid41971325, year = {2026}, author = {Qi, L and Kang, H and Li, X and Wang, L and Lin, Y and Zhan, M and Zeng, F and Xiao, Z and Liu, X and Chen, Z and Liu, L}, title = {Multi-omics profiling implicates gut microbiota-sphingolipid interplay in the neuroprotective effects of semaglutide on diabetic cognitive impairment.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1705784}, pmid = {41971325}, issn = {1664-302X}, abstract = {BACKGROUND: The gut microbiome is a critical regulator of host health, but how it mediates the therapeutic effects of drugs targeting neurodegenerative diseases like diabetic cognitive impairment (DCI) is unclear. Here, we investigated whether the neuroprotective effects of the GLP-1 agonist semaglutide (SE) are linked to its modulation of the gut-brain axis.

METHODS: We used an integrative multi-omics approach in a mouse model of DCI. We combined fecal shotgun metagenomics and targeted bile acid profiling with cerebral proteomics and metabolomics to characterize the gut-brain crosstalk following a 12-week SE treatment. Animal behavior, neuronal survival and synaptic integrity were assessed to confirm therapeutic efficacy.

RESULTS: SE treatment reversed cognitive deficits, rescued hippocampal neuronal loss, and restored synaptic integrity in diabetic mice. At the ecosystem level, metagenomics revealed that SE treatment profoundly remodeled the gut microbiota, enhancing microbial α-diversity, enriched beneficial genera (Bacteroides, Barnesiella), and depleted the pro-inflammatory genus Desulfovibrio. This microbial shift was associated with normalized fecal and cerebral bile acid profiles. Mechanistically, our analysis implicated a dysregulated sphingolipid pathway in the DCI brain, characterized by the upregulation of the transporter ATP-binding cassette transporter A2 (ABCA2) and the enzymes sphingosine-1-phosphate phosphatase 1 (SGPP1) and ceramide synthase 2 (CERS2). SE treatment dynamically modulated this pathway: it downregulated ABCA2 in a potentially weight-independent manner and SGPP1 in a weight-dependent fashion, linked to the normalization of cerebral bile acid profiles. In contrast, CERS2, a robust marker of disease severity, was not altered by SE.

CONCLUSION: Our study uncovers a novel "gut microbiota-bile acid-sphingolipid" axis in DCI and suggests that SE acts via a dual mechanism. It drives a weight-dependent restoration of the gut-brain axis, normalizing microbial and bile acid profiles to regulate SGPP1, while also exerting weight-independent effects, potentially through direct modulation of targets like ABCA2. This work highlights the gut microbiome as a key component in the therapeutic action of SE and reveals the multifaceted nature of its neuroprotective effects.}, } @article {pmid41971343, year = {2026}, author = {Qiao, YC and Jiang, XX and Zhan, JP and Cheng, XH and Liu, F and Zhang, WS and He, GP and Peng, JZ and Wu, YJ and Yang, SG}, title = {Correction: Effects of different mulching practices on soil microbial community structure, function, and interaction networks in a chieh-qua cultivation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1832275}, doi = {10.3389/fmicb.2026.1832275}, pmid = {41971343}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1691984.].}, } @article {pmid41971525, year = {2026}, author = {Adekoya, AE and Boggs, TE and Ibberson, CB}, title = {Revealing community dynamics in polymicrobial infections through a quantitative framework.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag061}, pmid = {41971525}, issn = {2730-6151}, abstract = {Laboratory models provide tractable, reproducible systems that have long served as foundational tools in microbiology. However, the extent to which these models accurately mimic the biological environments they represent remains poorly understood. A quantitative framework was recently introduced to assess how well laboratory models capture microbial physiology in situ. However, applications of this framework have been limited to characterizing the physiology of a single species in human infections, leaving a gap in our understanding of overall microbial community physiology in polymicrobial contexts. Here, we extended this framework to evaluate the accuracy of laboratory model systems in capturing community-level functions in polymicrobial infection. As a proof of concept, we applied the extended framework to a polymicrobial model of human chronic wound (CW) infection. CWs harbor metabolically diverse bacterial species that engage in a range of microbe-microbe interactions, ultimately impacting community dynamics and disease progression. However, studies on the mechanistic drivers of chronic wound infection have relied on single species or pairwise approaches. Here, we demonstrate that our adapted framework can be used to develop accurate polymicrobial models. Further, we demonstrate that this extended framework can evaluate the occurrence of known microbe-microbe interactions. Building on our prior work in large-scale metagenomic and metatranscriptomic analysis, we propose a highly accurate 6-member synthetic bacterial community model i.e. representative of the taxonomic and functional complexity of human CW infections. This approach will support the development of ecologically relevant polymicrobial models and better treatment strategies.}, } @article {pmid41971531, year = {2026}, author = {Zhang, W and Han, N and Zhang, T and Qiang, Y and Peng, X and Li, X and Kan, B}, title = {Dynamic change patterns of the human gut microbiota-fluctuation, loss-acquisition, and turnover-and their underlying causes.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag046}, pmid = {41971531}, issn = {2730-6151}, abstract = {The temporal dynamics of the gut microbiome are critical to human health, yet their patterns and underlying drivers remain poorly characterized at a monthly resolution and strain level. This knowledge gap limits the development of targeted microbiome interventions. Here, we integrate longitudinal analyses across three human cohorts-a cross-sectional cohort (n = 190), an intensive 52-month time series (n = 7), and a paired 6-month cohort (n = 43)-together with a humanized mouse model under antibiotic perturbation. Using shotgun metagenomics (516 samples), we resolve microbial dynamics at species and strain resolution. We identify three distinct modes of temporal variation: relative abundance fluctuations, species loss-acquisition events, and strain turnover. Strain turnover contributes substantially to the dynamic reservoir of functional genes, including those associated with virulence and antibiotic resistance. These dynamics are influenced by antibiotic exposure and microbial interspecies interactions. Our work provides a month-scale atlas of gut microbiome variation, revealing widespread transient colonization and strain-level plasticity, thereby offering a refined framework for understanding microbiome stability and personalized microbial ecology.}, } @article {pmid41971738, year = {2026}, author = {Ji, HL and Liu, CH and Nie, CX and Luo, JF and Li, XR and Fu, AS and Ge, YL}, title = {Metagenomic next-generation sequencing unveils invasive aspergillosis masquerading as miliary tuberculosis in a neutropenic leukemia patient: a case report.}, journal = {Frontiers in fungal biology}, volume = {7}, number = {}, pages = {1751760}, pmid = {41971738}, issn = {2673-6128}, abstract = {BACKGROUND: Empirical anti-tuberculosis therapy is a common strategy when patients with acute leukemia chemotherapy-induced neutropenia develop diffuse pulmonary small nodular and subsolid lesions. However, the absence of pathogenetic verification may lead to catastrophic consequences.

METHODS: Following negative conventional microbiological cultures (bronchoalveolar lavage bacterial culture, Gram/Gram-negative test) and ineffective anti-infective therapy, a second bronchoscopy revealed caseous obstructive lesions in the right upper lobe bronchus. Metagenomic Next-Generation Sequencing (mNGS) analysis of lavage fluid ultimately confirmed invasive pulmonary fungal disease.

RESULTS: The mNGS analysis of the bronchoalveolar lavage fluid (BALF) reported 6,750 Aspergillus fumigatus sequences, 43 Aspergillus complex sequences, and 81 Candida albicans sequences (considered airway colonization with no pathogenic significance), confirming probable invasive pulmonary aspergillosis (IPA) in line with the 2023 revised EORTC/MSGERC consensus criteria for invasive fungal diseases. Following discontinuation of anti-tuberculosis therapy, targeted antifungal treatment with amphotericin B (40 mg daily) was initiated. Post-treatment, the patient's temperature normalized. Follow-up CT demonstrated improved absorption of lesions in the left lung and right lower lobe, with stable cavitary nodules in the right upper lobe.

CONCLUSION: This case demonstrates that invasive pulmonary fungal infection can perfectly mimic the typical radiographic features of hematogenous disseminated pulmonary tuberculosis, including diffuse small nodular and subsolid lesions with a miliary distribution pattern predominantly in the upper lobes and extrapulmonary manifestations such as erythema nodosum. For unexplained pulmonary infections in immunocompromised hosts where conventional diagnosis and empirical treatment fail, the timely application of bronchoscopy combined with mNGS technology represents a critical breakthrough for achieving precise diagnosis.}, } @article {pmid41971837, year = {2026}, author = {Du, S and Lin, D and Zhang, TL and Chu, HY and Zhu, D}, title = {Earthworm gut's potential positive impact on carbon cycle by influencing carbohydrate metabolism and microbial genome size.}, journal = {Fundamental research}, volume = {6}, number = {2}, pages = {837-846}, pmid = {41971837}, issn = {2667-3258}, abstract = {The earthworm microbiome significantly impacts global soil ecosystems. This study explores how earthworm gut eukaryome (fungi and protists) and functional genes respond to land use and climatic factors. Over 150 earthworm-soil sample pairs were collected from arable and forest ecosystems across China. High-throughput and shotgun metagenomic sequencing revealed lower fungal, protistan, and CAZyme gene diversities in the earthworm gut than in the soil (0.77-fold, 0.19-fold, and 0.74-fold compared to the soil, respectively), but higher proportions of parasitic protists (3.78-fold compared to the soil) and carbohydrate metabolism genes involved in glycosyl transfer (1.41-fold compared to the soil). Arable systems showed higher abundances of functional genes associated with carbon fixation, nitrification, phosphorus dissolution, and sulfite reduction compared to forest systems. This study highlights the associations between earthworm gut microeukaryotes and functional genes especially glycosyl transferases involved in carbohydrate biosynthesis. Furthermore, larger microbial genomes were found in the earthworm gut compared to the soil, which may harbor more functional genes involved in cellular processes, carbohydrate binding, and glycosyl transfer. These findings suggest that earthworm gut microeukaryotes may have a positive impact on their average genome sizes and carbohydrate metabolism within the carbon cycle. This study contributes to advancing our understanding of the functionality of microeukaryotes in the earthworm gut, especially for the carbon cycle.}, } @article {pmid41971922, year = {2026}, author = {Zhu, W and Li, Y and Xu, Q and Lin, D and Zhou, T and Yang, F and Shi, M}, title = {Late-onset fungal infection of the bronchial stump post-lung resection: a report of two rare cases of Aspergillus flavus and mixed Candida/Cryptococcus coinfection diagnosed via metagenomic next-generation sequencing.}, journal = {AME case reports}, volume = {10}, number = {}, pages = {63}, pmid = {41971922}, issn = {2523-1995}, abstract = {BACKGROUND: Fungal infection of the bronchial stump is rare, characterized by insidious clinical manifestations and often misdiagnosed as bacterial infection or tumor recurrence. Most reported cases involve Aspergillus fumigatus, with Aspergillus flavus encountered far less frequently. Importantly, fungal colonization of the bronchial stump by Cryptococcus species has not been previously documented, nor has a mixed infection involving Cryptococcus and other fungi at this site. These rare presentations highlight diagnostic blind spots in postoperative airway management and underscore the need for heightened clinical awareness.

CASE DESCRIPTION: Case 1: A 53-year-old man underwent left upper lobectomy for adenocarcinoma four years prior. In 2024, he presented with hoarseness and chest tightness. Positron emission tomography-computed tomography (PET-CT) revealed a metabolically active soft-tissue nodule adjacent to the surgical suture line. Bronchoscopic biopsy combined with metagenomic next-generation sequencing (mNGS) confirmed the diagnosis of bronchial stump aspergillosis (BSA). The patient received posaconazole therapy for 7 months. Case 2: A 77-year-old woman underwent right lower lobectomy for adenocarcinoma six years earlier. In 2025, she developed cough with sputum production. CT demonstrated bilateral pneumonia with focal consolidation/atelectasis and bilateral pleural effusions. Bronchoscopy and mNGS identified a mixed infection with Candida albicans and Cryptococcus neoformans at the bronchial stump. Following treatment with caspofungin and fluconazole, her clinical symptoms improved, and follow-up CT imaging showed resolution of inflammatory changes.

CONCLUSIONS: Although fungal infection of the bronchial stump is rare, it warrants early consideration when post-lobectomy patients develop persistent symptoms unresponsive to antibiotics. Early radiological clues-such as unexpected metabolic activity around suture granulomas or localized nodular thickening at the stump-should prompt further evaluation. When conventional cultures remain negative and clinical deterioration continues, early initiation of mNGS can facilitate timely pathogen identification and guide targeted antifungal therapy.}, } @article {pmid41972094, year = {2026}, author = {Yoshioka, I and Hayashi, C and Endo, Y and Sawada, A and Mori, Y and Ban, S and Yaguchi, T}, title = {Detection of fungal contamination on museum books stored under controlled environmental conditions: A discrepancy between culture-based and metagenomic analysis approaches.}, journal = {Mycoscience}, volume = {67}, number = {1}, pages = {20-26}, pmid = {41972094}, issn = {1618-2545}, abstract = {Mold contamination in library and museum collections poses risks to both cultural heritage and human health. This study examined fungal flora on books stored under controlled environmental conditions (temperature <20 °C, relative humidity <50%) in The University Museum, The University of Tokyo. Both culture-dependent methods and DNA-based metabarcoding targeting the internal transcribed spacer 2 region were used. DNA analysis revealed that Aspergillus halophilicus accounted for over 90% of the sequences from six books. In contrast, culture-based methods using standard media (e.g., PDA, DG18, M40Y) primarily isolated species such as Aspergillus, Penicillium, and Cladosporium, but not A. halophilicus. However, cultivation on CzA supplemented with 70% sucrose at lower temperatures enabled successful isolation of A. halophilicus from one sample. The strain was identified based on morphological features and β-tubulin gene analysis. These findings demonstrate a notable discrepancy between molecular and culture-based results, underscoring the limitations of conventional media for detecting xerophilic fungi in dry environments. The study suggests that desiccation-tolerant species like A. halophilicus can thrive even under strict storage controls and may evade standard integrated pest management (IPM) protocols. To better assess fungal risks in preservation settings, combining improved media with DNA-based methods is essential.}, } @article {pmid41972101, year = {2026}, author = {Tong, W and Qiao, L and Yang, Y and Li, X and Zhang, Y and Huang, Z and Luo, H and Zhao, L and Zhang, S}, title = {Cross-kingdom metabolic cooperation drives vanillic acid biosynthesis: A spatiotemporal dissection of microbial functional networks in solid-state fermentation.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101394}, pmid = {41972101}, issn = {2665-9271}, abstract = {Microbial self-organization into spatiotemporally structured consortia is key to metabolic specialization in natural environments, yet the principles governing this process in food fermentation are poorly understood. Here, we elucidate how cross-kingdom microbial cooperation drives the biosynthesis of vanillic acid (VA), a critical flavor and bioactive phenolic compound, during the solid-state fermentation of strong-flavor baijiu (SFB). Integrated metagenomic and network analyses across stratified pit layers and fermentation stages revealed a defined three-phase succession model. Early phase (D0-D12) was dominated by filamentous fungi (Aspergillus, Paecilomyces) in upper layers, initiating starch hydrolysis and phenylpropane precursor synthesis (e.g., contributing 22.6% to phenylalanine ammonia-lyase). A transitional bacterial-fungal consortium (Pichia, Klebsiella) then mediated intermediate conversion (D12-D45), with enzymatic hotspots shifting downward. The maturation phase (D45-D85) was defined by the dominance of acidophilic Acetilactobacillus (>80% relative abundance) in the lower layer, which executed the final synthesis steps (contributing 31.5% to caffeic acid O-methyltransferase) and concurrently suppressed vanillic acid degradation via downregulation of vanillate O-demethylase. Network analysis confirmed a spatial metabolic division of labor: fungi specialized in upper-layer lignin deconstruction, while bacteria dominated the completion of phenylpropanoid pathways in the lower layer. Critically, peak VA accumulation (0.375 mg/L at D45) coincided with synchronized enzyme expression across layers, demonstrating active metabolic coordination rather than passive environmental filtering. Our findings establish that functional succession and spatial compartmentalization are fundamental ecological principles enabling efficient biosynthesis in solid-state fermentation, demonstrating that flavor outcomes can be programmed through targeted microbial consortium design.}, } @article {pmid41972180, year = {2026}, author = {Zhai, Y and Yu, M and Cheng, L and Liu, X and Yan, J}, title = {Orientia tsutsugamushi and Epstein-Barr Virus coinfection presenting with transient fluctuating hearing loss: a case report.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1750100}, pmid = {41972180}, issn = {1664-3224}, mesh = {Humans ; Female ; Middle Aged ; *Scrub Typhus/complications/diagnosis/drug therapy/microbiology ; *Coinfection ; *Orientia tsutsugamushi ; *Epstein-Barr Virus Infections/complications/diagnosis/drug therapy ; *Herpesvirus 4, Human ; *Hearing Loss/diagnosis/etiology ; }, abstract = {Scrub typhus, caused by the obligate intracellular bacterium Orientia tsutsugamushi(O. tsutsugamushi), is an acute febrile illness. While neurological complications are known, hearing loss is an uncommon manifestation, and coinfection with Epstein-Barr virus(EBV) presents unique diagnostic and pathophysiological challenges. A 58-year-old woman presented with a 5-day history of high fever, severe headache, and constitutional symptoms. She reported transient, fluctuating bilateral hearing loss. Examination revealed characteristic eschars on her legs. Laboratory findings indicated hepatic impairment and systemic inflammation. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid detected O. tsutsugamushi and EBV. EBV serology profile (VCA-IgG+, VCA-IgM-, EBNA-IgG+) suggested viral reactivation. The patient failed to respond to initial beta-lactam antibiotic therapy but showed rapid and complete resolution of symptoms, including hearing loss, after initiation of doxycycline. At the 1-month and 3-month follow-up, audiological assessment confirmed normal hearing. This case highlights a rare presentation of scrub typhus with EBV coinfection involving fluctuating hearing loss. The dramatic response to doxycycline suggests this auditory symptom may be a reversible, immune-mediated complication of O. tsutsugamushi infection. Physicians should be aware of this potential manifestation in endemic areas. The immunological interplay between these pathogens warrants further investigation.}, } @article {pmid41972428, year = {2026}, author = {Wang, YF and Wang, YN and Lin, D and Xu, JY and Qi, FY and Cui, HL and Lu, HJ and Qiao, M and Topp, E and Zhu, D and Rillig, MC and Zhu, YG}, title = {Diversity of Pharmaceuticals Enhances Antibiotic Resistance in the Invertebrate Gut via Biofilm-Mediated Mechanisms.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e18849}, doi = {10.1002/advs.202518849}, pmid = {41972428}, issn = {2198-3844}, support = {42307169//National Natural Science Foundation of China/ ; 42577136//National Natural Science Foundation of China/ ; U25A20803//National Natural Science Foundation of China/ ; 2023J02031//Fujian Provincial Natural Science Foundation of China/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; 2023321//Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; }, abstract = {The environmental accumulation of non-antibiotic pharmaceuticals is an emerging driver of antibiotic resistance. While individual compounds are known to shape the soil resistome, and contaminant diversity also plays a role, the impact of pharmaceutical diversity on the gut resistome of soil invertebrates remains unclear. Here, we combined metagenomics and metaproteomics to examine the collembolan gut and soil resistome across a gradient of pharmaceutical diversity under diurnal warming. Increasing pharmaceutical diversity at a constant total concentration significantly enriched antibiotic resistance genes (ARGs) in the gut microbiome, with no comparable effect in surrounding soils. This enrichment was mainly driven by multidrug resistance associated with efflux activity and biofilm-related processes, accompanied by increases in ARG-carrying taxa such as Gordonia and Ochrobactrum. Notably, Ochrobactrum encoded biofilm-related aryl polyene pathways. In vitro experiments confirmed that biofilm formation promotes resistance through coordinated cellular responses. Metaproteomic data indicated that Ochrobactrum initiates early biofilm formation by recruiting extracellular matrix producers such as Bacillus and Pseudomonas. Diurnal warming modulated these responses, indicating an interaction between chemical diversity and climate stress. These findings identify pharmaceutical diversity as an independent driver of ARG enrichment in host-associated microbiomes and establish chemical complexity as a key factor in assessing the ecological risks of pharmaceutical pollution.}, } @article {pmid41972755, year = {2026}, author = {Langenfeld, K and Arts, P and Monahan, A and Criswell, A and Wigginton, KR and Duhaime, MB}, title = {Novel machine learning-based approach to identify viral biomarkers of human respiratory emissions from oral and nasal metagenomes.}, journal = {mSphere}, volume = {11}, number = {5}, pages = {e0011326}, pmid = {41972755}, issn = {2379-5042}, support = {//Flu Lab/ ; }, mesh = {Humans ; *Machine Learning ; *Biomarkers/analysis ; *Metagenome ; *Mouth/virology/microbiology ; *Viruses/genetics/isolation & purification/classification ; *Environmental Monitoring/methods ; Microbiota ; *Nose/virology ; Saliva/virology ; Metagenomics ; }, abstract = {Humans spend approximately 90% of their lives in built environments, making virus transmission indoors a key determinant of health. Environmental sampling of respiratory viral pathogens is often challenging because of frequent non-detect measurements. Non-detect measurements do not differentiate between samples containing low or no pathogens from samples that simply lack respiratory expulsions altogether. This ambiguity can be resolved by scanning samples for a biomarker of human respiratory emissions. To do so, reliable biomarkers for environmental monitoring need to be identified. Ideal biomarkers are prevalent across individuals, abundant, and unique to the human respiratory tract. Here, we present a new machine learning-based approach to query for suitable biomarker candidates from publicly available metagenomes and apply it to identify viral biomarkers of healthy oral and nasal microbiomes. Twelve viral biomarker candidates were selected from 1,232 curated viral operational taxonomic units. The viral biomarker candidates had as much as 63% prevalence across respiratory metagenomes, and prevalence was further increased to 77%-81% by combining two or three biomarkers. Real-time PCR confirmed that these viral biomarkers were prevalent and abundant in nasal swabs and saliva samples. Notably, top candidate biomarkers remained stable and detectable through multiple lab purification steps, increasing confidence in their viral origins and demonstrating their suitability for environmental monitoring. These findings demonstrate that existing metagenomes can be used to identify effective biomarker candidates for environmental sampling.IMPORTANCEDeveloping non-pharmaceutical interventions to reduce virus transmission indoors relies on robust environmental monitoring methods. Monitoring viral pathogens is challenging because of frequent non-detect measurements that introduce uncertainty. For instance, a non-detect measurement could indicate either the absence of the pathogen or simply the lack of human respiratory activity and, thus, exposure. To aid in distinguishing these scenarios, this study identifies viruses from the human respiratory tract using publicly available sequencing data that can be incorporated into environmental monitoring as biomarkers of human respiratory activity. These viral biomarkers will improve indoor monitoring to help enact interventions to mitigate virus transmission. Furthermore, our approach to identify biomarkers from existing metagenomes can be adapted for future biomarker identification in any system.}, } @article {pmid41972785, year = {2026}, author = {He, X and Liu, J and Cheng, H and Zhu, X and Lin, H and Li, D-W and Yang, Y and Liu, R and Song, D and Zheng, Y and Lea-Smith, DJ and Pedentchouk, N and Todd, JD and Zhao, M and Zhang, X-H}, title = {Metabolically diverse microorganisms mediating hydrocarbon cycling in the subseafloor sediment of the Challenger Deep.}, journal = {mBio}, volume = {17}, number = {5}, pages = {e0394325}, pmid = {41972785}, issn = {2150-7511}, support = {2025YFF0516900, 2025YFF0516903//National Key Research and Development Program of China/ ; LSKJ202203206//Scientific and Technological Innovation Project of Laoshan Laboratory/ ; 32370118//National Natural Science Foundation of China/ ; ZR2022YQ38, ZR2024JQ006//Natural Science Foundation of Shandong Province/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; NE/X014428//Natural Environmental Research Council, United Kingdom/ ; }, mesh = {*Geologic Sediments/microbiology ; *Hydrocarbons/metabolism ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Phylogeny ; Seawater/microbiology ; Metagenomics ; Metagenome ; }, abstract = {Hadal subseafloor sediments host abundant and active microbial biosphere with considerable heterotrophic activity. However, carbon and nutrient cycling processes and mechanisms driven by hadal subsurface microorganisms remain poorly understood. Using culture-dependent and culture-independent methods, we characterized the diversity, metabolism, and vertical dynamics of hydrocarbon-degrading (HYD) bacteria in a subsurface sediment core (MT20-750, ~750 cm below seafloor [cmbsf]) collected from the Challenger Deep (10,816 m below sea level) in the Mariana Trench. The sediment core contained high concentrations of mid- and long-chain n-alkanes (310-8,724 ng/g), although no
IMPORTANCE: Fly larvae are expected to play an important role in future food and feed production through the conversion of low-value biomass into high-quality protein. The gut microorganisms of fly larvae are expected to play an important role in bioconversion and could potentially be manipulated to improve biomass conversion. In this study, the importance of the gut bacteria of house fly larvae for bioconversion was investigated by metagenomic sequencing, which provided information on the bacterial abundance and potential functional roles in the larval gut. The results reveal that the functional potential of gut bacteria is affected by larval feed and correlates with larval performance, highlighting the importance of the gut microbiome for efficient biomass conversion.}, } @article {pmid41973723, year = {2026}, author = {Denison, ER and Hillary, LS and Bolanos, HA and Anagu, HI and Emerson, JB}, title = {DNA Viral Size Fraction Metagenomics for Human Stool Samples.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {229}, pages = {}, doi = {10.3791/70187}, pmid = {41973723}, issn = {1940-087X}, support = {U01 DE034198/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Feces/virology ; *DNA, Viral/genetics/isolation & purification/chemistry ; *Metagenomics/methods ; *DNA Viruses/genetics/isolation & purification ; }, abstract = {Understanding the healthy human virosphere (the viral component of the microbiome) requires accurate measurements of viral community composition across a diverse range of viral types. Building on prior experience with soil viral community ecology methods, here we demonstrate a series of laboratory approaches for enriching and extracting DNA from extracellular DNA viruses in human stool samples. A working primary protocol is presented, along with options for deviations at different steps. The general approach involves adding a liquid buffer (default: protein-enhanced phosphate buffered saline, PPBS) to facilitate removal of free viral particles from the stool matrix, centrifugation to separate the liquid fraction containing viral particles, filtration (default: 0.2 µm pore size) to remove most cells, concentration of viral particles (default: ultracentrifugation), removal of free nucleic acids with nucleases prior to virion lysis, and then DNA extraction for sequencing. Alternative techniques, including different buffers, filter sizes, and concentration methods, are also noted. Overall, multiple options for generating high-quality viromic DNA for sequencing are offered. Rather than tailoring the approach to specific equipment and resources, the protocol's flexibility should make it broadly applicable across labs with varying standard molecular biology equipment.}, } @article {pmid41974680, year = {2026}, author = {Valverde, G and Sarhan, MS and Cook, R and Rota-Stabelli, O and Adriaenssens, EM and Zink, A and Maixner, F}, title = {An ancient genome of Streptococcus pyogenes from a pre-Columbian Bolivian mummy.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41974680}, issn = {2041-1723}, mesh = {*Streptococcus pyogenes/genetics/isolation & purification/classification/pathogenicity ; Humans ; *Genome, Bacterial/genetics ; Phylogeny ; *Mummies/microbiology ; Bolivia ; DNA, Mitochondrial/genetics ; *Streptococcal Infections/microbiology/history ; Bayes Theorem ; }, abstract = {Streptococcus pyogenes, or Group A Streptococcus (GAS), is a human pathogen responsible for a range of diseases, from mild infections to severe illnesses. Despite its significance in modern clinical settings, little is known about the pathogen's evolutionary history or its presence in ancient human populations. Here, we present genomic evidence of S. pyogenes in the pre-Columbian Americas. We analysed a tooth from a naturally mummified individual dating to the Late Intermediate Period (1283-1383 cal AD), housed in the National Museum of Archeology (MUNARQ) in La Paz, Bolivia. Mitochondrial DNA analysis confirmed the host's Native American ancestry. Shotgun metagenomic sequencing and de-novo assembly enabled the near-complete reconstruction of an ancient S. pyogenes genome displaying close similarity to contemporary strains linked to pharyngitis. The genome contains core virulence genes, but prophages lack streptococcal pyrogenic exotoxins. Phylogenetic analyses place the strain at the base of modern S. pyogenes diversity, and Bayesian analyses indicate that most extant lineages diversified globally within the past ~5,500 years. Our results push back the confirmed presence of S. pyogenes in the Americas by several centuries and suggest that the pathogen circulated among Indigenous populations prior to the European contact.}, } @article {pmid41974697, year = {2026}, author = {Espinosa, CA and Njunge, JM and Tickell, KD and Diallo, AH and Sayeem Bin Shahid, ASM and Gazi, MA and Kazi, Z and Yoshioka, E and Tigoi, C and Mburu, M and Ngari, M and Ngao, N and Omer, E and Gumbi, W and Gichuki, BM and Mitchel, A and Williams, J and Gogain, J and Janjic, N and Mandal, R and Jenkins, B and Browne, HP and Shao, Y and Rozday, T and Stares, MD and Dawson, NJR and Berson, E and Chang, A and Kim, Y and Mataraso, SJ and Shu, CH and Phongpreecha, T and Xue, L and Saleem, A and Singa, B and Ahmed, T and Voskuijl, WP and Wishart, DS and Houpt, ER and Liu, J and Ali, A and Mupere, E and Chisti, MJ and Bandsma, RHJ and Lawley, TD and Koulman, A and Lancioni, CL and Aghaeepour, N and Berkley, JA and Walson, JL and , }, title = {Multiomics characterization of acute child illness and mortality in Africa and South Asia.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41974697}, issn = {2041-1723}, mesh = {Humans ; Multiomics ; Child, Preschool ; Infant ; Female ; Male ; Biomarkers/blood ; Asia, Southern ; Acute Disease/mortality ; Child ; Feces/microbiology ; Proteomics ; Metagenomics ; Africa South of the Sahara/epidemiology ; Metabolomics ; *Child Mortality ; }, abstract = {Childhood illnesses from infectious diseases in low- and middle-income countries contribute substantially to the global under-five mortality. Many hospitalized children experience incomplete recovery, readmission, and post-discharge mortality despite guideline-directed care. However, targeted interventions remain elusive due to limited understanding of underlying mechanisms. In this work, we employ multiomic profiling and multivariate modeling to investigate biological drivers of inpatient and post-discharge mortality in 3,101 acutely ill children across nine sites in sub-Saharan Africa and South Asia. In a nested case-cohort (N = 1008), we generate plasma proteomics, serum metabolomics and lipidomics, stool metagenomics, and fecal pathogen data at admission and discharge. Additionally, we profile 270 geographically matched community children for biological baselines. We identify a generalizable mortality signature marked by immune, inflammatory, and metabolic dysregulation with gut dysbiosis. We show that mortality-associated signals persist from admission through discharge, indicating unresolved disease and that malnourished children show greater baseline perturbations, explaining elevated risk. We also find some children with low clinical severity display high predicted mortality risk from targeted biomarkers. Finally, we distill predictive models to a clinically feasible biomarker panel and validate our findings in an independent cohort (N = 100). By linking inpatient and post-discharge mortality to specific biological mechanisms, our findings highlight why current care can fail and demonstrate how biomarker-guided risk stratification can identify vulnerable children currently missed by clinical assessments, enabling targeted interventions to reduce mortality in low- and middle-income countries.}, } @article {pmid41974712, year = {2026}, author = {Zhao, N and Geng, P and Jimenez, D and Garcia, AC and Six, N and LaPlante, CI and Perez, AG and Silverman, GJ and Morel, L and Ge, Y}, title = {Multiomics-guided discovery of protective microbiome signatures in lupus-prone mice treated with Faecalibacterium prausnitzii.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41974712}, issn = {2041-1723}, support = {R21 AI180737/AI/NIAID NIH HHS/United States ; R01AI143313//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {Animals ; Humans ; Male ; Mice ; Disease Models, Animal ; *Dysbiosis/diet therapy/immunology/microbiology ; *Faecalibacterium prausnitzii/physiology ; Feces/microbiology ; *Gastrointestinal Microbiome/immunology/genetics ; *Lupus Erythematosus, Systemic/diet therapy/immunology/microbiology ; Metabolomics ; Metagenome ; Mice, Inbred C57BL ; Multiomics ; *Probiotics/administration & dosage ; T-Lymphocytes, Regulatory/immunology ; Th17 Cells/immunology ; }, abstract = {Gut microbiome dysbiosis has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). However, microbiota-targeted therapeutic strategies have been lacking. Here, we report the potential of Faecalibacterium prausnitzii (strain UT1) to ameliorate gut dysbiosis and alleviate disease progression in the B6.Sle1.Yaa male mouse model of SLE. Fecal metagenomes of patients with SLE shifted carbohydrate catabolism from dietary fibers to host glycans, coinciding with depletion of F. prausnitzii. Oral administration of UT1 partially reversed lupus-associated microbiome alterations and rescued carbohydrate metabolic deficiency in lupus-prone mice. Using correlative metatranscriptomics and metabolomics, we observed restricted expression of bacterial genes related to mucin degradation, elevated pentose phosphate pathway and bile acid-modifying activities, and redirected tryptophan catabolism toward indoleacetic and indoleacrylic acids. Further host cell profiling showed that UT1 rebalanced colonic regulatory T (Treg) and T helper 17 (Th17) cell responses, suppressed systemic autoimmune activation and autoantibody production, and reduced renal pathology. Thus, our findings identify SLE-associated active microbiome signatures and provide a probiotic candidate for the treatment of lupus disease.}, } @article {pmid41975031, year = {2026}, author = {Sepulveda, BJ and González-Recio, O and Chamberlain, AJ and Xiang, R and Cocks, BG and Wang, J and Prowse-Wilkins, CP and Marett, LC and Williams, SRO and Jacobs, JL and García-Rodríguez, A and Jiménez-Montero, JA and Pryce, JE}, title = {Reliable enteric methane prediction from the cattle (Bos taurus) rumen microbiome.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41975031}, issn = {2399-3642}, support = {DairyBio//Dairy Australia/ ; }, mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology ; *Methane/metabolism ; Metagenome ; *Gastrointestinal Microbiome ; *Microbiota ; Australia ; }, abstract = {The production of methane, a potent greenhouse gas, by ruminants during feed digestion is designated enteric methane emissions (EME) and is mainly produced by the rumen microbiome. Reliably recording EME in large populations is currently cost-prohibitive, hampering farming decisions aimed at reducing EME. Here, we perform comprehensive analyses on host genetics, KEGG orthology groups (KOs) from the rumen metagenome, and EME of more than 800 cows from Australia and Spain. We report that the rumen microbiome explains up to 34% of the EME variance, and when combined with the host genome, the variance explained is up to 59% with prediction accuracies of up to 0.40. The results support a recursive model, where both the host genome and rumen metagenome explain EME. The isometric log-ratio transformation of KOs may potentially better capture relationships between host genetics and the rumen microbiome than the centered log-ratio transformation, and BayesR yielded slightly higher microbe‑explained EME variance than best linear unbiased prediction. A forward simulation estimated to reach 90% of EME prediction accuracy with 6,000 animals with rumen microbiomes and host genomes, which could open opportunities for developing strategies to reduce EME. Our study contributes to the foundation for reducing EME, supporting global warming mitigation.}, } @article {pmid41975041, year = {2026}, author = {Stepanyan, A and Kotsafti, A and Rosato, A and Castagliuolo, I and Scarpa, M and Scarpa, M and , }, title = {Gut microbiota-associated predictors as biomarkers of neoadjuvant treatment response in rectal cancer-a systematic review.}, journal = {British journal of cancer}, volume = {135}, number = {1}, pages = {139-151}, pmid = {41975041}, issn = {1532-1827}, support = {IG 2019 - ID. 23381//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; }, mesh = {Humans ; *Rectal Neoplasms/microbiology/therapy ; *Neoadjuvant Therapy/methods ; *Gastrointestinal Microbiome ; *Biomarkers, Tumor ; Treatment Outcome ; }, abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a modulator of cancer therapy outcomes and a potential predictive biomarker. This systematic review synthesizes current evidence on microbial biomarkers associated with neoadjuvant treatment (NT) response in rectal cancer (RC).

METHODS: PubMed, Embase, and Ovid Medline databases were searched through March 2025. Eligible studies included RC patients treated with NT with baseline microbial analysis stratified by treatment response. Two reviewers independently performed screening, data extraction, and quality assessment (NIH and STORMS tools). Due to substantial heterogeneity, a structured qualitative synthesis without meta-analysis was conducted following SWiM guidelines, using a direction-of-effect vote-counting approach.

RESULTS: Sixteen observational studies (842 patients) were included, covering chemoradiotherapy (nCRT), total neoadjuvant therapy, chemotherapy, and immunochemoradiotherapy. Microbiota composition was investigated by 16S rRNA sequencing, metagenomics, or metatranscriptomics on fecal or tissue samples. While microbial diversity showed inconsistent associations, specific taxa -notably Bacteroides, Fusobacterium and Akkermansia- emerged as recurrent biomarkers of poor response to nCRT. Twelve predictive models reported AUROC values from 0.73 to 0.97, with limited external validation.

CONCLUSIONS: Specific microbial taxa show a consistent association with nCRT resistance across independent cohorts. However, methodological heterogeneity and limited reproducibility warrant standardized prospective validation before clinical implementation.

PROSPERO: CRD42023433704.}, } @article {pmid41975095, year = {2026}, author = {Guan, K and Ocampo, RF and Matheus Carnevali, PB and Castelle, CJ and Gonzalez-Osorio, L and Castanzo, DT and Thomas, NC and Brothers, M and Dangerfield, TL and Hooper, MM and West, MS and Appleby, NM and Krudop, I and Lamothe, RC and Aliaga Goltsman, DS and Alexander, LM and Butterfield, CN and Johnson, KA and Brown, CT and Taylor, DW}, title = {Comparative characterization of Cas12f orthologs reveals mechanistic features underlying enhanced genome editing efficiency.}, journal = {Nature structural & molecular biology}, volume = {33}, number = {5}, pages = {756-767}, pmid = {41975095}, issn = {1545-9985}, support = {R35 GM138348/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *CRISPR-Cas Systems ; *CRISPR-Associated Proteins/chemistry/genetics/metabolism ; RNA, Guide, CRISPR-Cas Systems/metabolism/genetics/chemistry ; Models, Molecular ; R-Loop Structures ; HEK293 Cells ; }, abstract = {Miniature CRISPR-Cas12f nucleases are attractive candidates for therapeutic genome editing because of their compact size and compatibility with adeno-associated virus (AAV) delivery. However, editing efficiencies in mammalian cells are lower than those of larger systems. The extensive phylogenetic diversity of Cas12f suggests unexplored mechanistic variation with the potential for optimization. Here we identify and characterize a naturally occurring Cas12f ortholog discovered through metagenomics, Alistipes sp. Cas12f (Al3Cas12f), which supports robust genome editing in human cells. Through structural, biochemical and kinetic analyses, we compare Al3Cas12f to two recently described orthologs, Oscillibacter sp. Cas12f and Ruminiclostridium herbifermentans Cas12f. These orthologs present divergent architectures and regulatory features governing protospacer-adjacent motif recognition, guide RNA (gRNA) binding, dimerization and DNA cleavage. Notably, Al3Cas12f achieves efficient R-loop formation through a stable dimer interface and a naturally optimized gRNA. Leveraging these structural insights, we generate an engineered Al3Cas12f variant (RKK) that increases editing and improves activity across several tested genomic loci. By overcoming locus-dependent variability and an apparent potency threshold, this engineered compact editor seems to expand the feasibility of low-dose, AAV-compatible therapeutic genome editing. Our results elucidate mechanistic determinants of Cas12f activity and offer a framework for engineering compact genome editors that may bear therapeutic potential.}, } @article {pmid41975182, year = {2026}, author = {Kleinbölting, N and Fiore, A and Cangioli, L and Visca, A and Huang, L and Hett, J and Costanzo, M and Sevi, F and Tabacchioni, S and Aprea, G and Mengoni, A and Pihlanto, A and Neuhoff, D and Sczyrba, A and Schlüter, A and Bevivino, A}, title = {Impact of microbial consortia and fertilization regimes on the soil microbiome in maize field trials.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41975182}, issn = {2045-2322}, support = {818431//Horizon 2020 Framework Programme/ ; }, mesh = {*Zea mays/microbiology/growth & development ; *Soil Microbiology ; *Fertilizers ; *Microbiota ; *Microbial Consortia ; Rhizosphere ; Bacteria/classification/genetics ; Biodiversity ; Soil/chemistry ; }, abstract = {Beneficial microbial consortia provide an eco-friendly alternative to conventional inorganic fertilizers and can serve as a complementary management tool for enhancing soil fertility and crop productivity. This study aimed to assess the impact of microbial consortia application on the indigenous maize rhizosphere microbiome under different fertilization regimes in organically managed fields in Germany. Three experimental microbial consortia (MC_B, MC_C, MC_C_AMF) and one commercial product (Micosat F) were tested in combination with three fertilization levels (unfertilized, 110 kg nitrogen ha[- 1], and 200 kg nitrogen ha[- 1]) in a split plot design. The diversity, composition and functional potential of the maize rhizosphere microbiome were analyzed at different maize growth stages. Fertilization levels exerted a stronger influence than microbial consortia, significantly shaping community composition and functional traits of the indigenous soil microbiome. Increasing fertilization intensity altered the abundance of specific plant growth-promoting (PGP)-determinants, either stimulating or suppressing potential PGP bacteria. In contrast, microbial consortia application did not impact PGP-associated abundance profiles. Overall, the results indicate that multifunctional microbial consortia can act as effective biofertilizers in sustainable maize cultivation without compromising resident microbiome diversity, thereby reducing long-term ecological risks on natural biodiversity.}, } @article {pmid41975253, year = {2026}, author = {Aquino, CI and La Vecchia, M and Pasolli, E and Sala, G and Ligori, A and Boldorini, R and Ferrante, D and Dianzani, I and Aspesi, A and Surico, D and Remorgida, V}, title = {Decoding the microbial landscape of endometrial cancer: a case-control study.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41975253}, issn = {1471-2180}, support = {IG 2021-ID. 25886//Associazione Italiana per la Ricerca sul Cancro/ ; }, abstract = {BACKGROUND: The human microbiome plays an emerging role in cancer biology, yet its contribution to endometrial cancer (EC) remains poorly defined. This study investigates the microbial composition of the vaginal, rectal, and endometrial sites in women with and without EC, aiming to uncover microbial signatures associated with the disease.

RESULTS: We performed shotgun metagenomic sequencing on vaginal, rectal, and endometrial samples from 25 patients with EC and 27 control women undergoing hysterectomy for benign conditions. Vaginal and rectal swabs were collected before surgery, while endometrial swabs were obtained post-hysterectomy using a sterile brushing technique to prevent cross-contamination. Vaginal microbiota in patients with EC showed significantly higher microbial diversity and distinct community composition compared to controls. These differences remained significant after adjusting for age and body mass index. Several bacterial species, including Peptococcus niger, Anaerococcus murdochii, Mobiluncus, Porphyromonas, and Prevotella, were more abundant in the vaginal microbiota of patients with cancer. In contrast, Lactobacillus spp. were more abundant in vaginal and rectal samples of control subjects.

CONCLUSIONS: This work represents one of the few studies to comprehensively examine the relationship between the vaginal, rectal, and endometrial microbiomes in the context of EC, suggesting a potential role for microbial imbalance in disease development. The findings underscore the importance of site-specific microbial analyses in gynecologic oncology and support further investigation into the microbiome as a possible biomarker for early detection and a target for preventive strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05017-4.}, } @article {pmid41975257, year = {2026}, author = {Tang, Z and Zhuang, D and Duan, X and Gong, Q and Tian, C and Jiang, P and Yu, J and Li, F and Zhao, F and Shi, G and Yang, H and Du, Q and Li, T and Ye, Z and Zhang, Z}, title = {MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {41975257}, issn = {1471-2105}, abstract = {BACKGROUND: Network analysis is a fundamental tool for elucidating microbial interactions, which are crucial for understanding the mechanisms that shape ecosystem structure and function. However, aggregated co-abundance/co-occurrence network approaches that infer pairwise relationships among biological entities from large sample collections often overlook sample-specific interaction patterns. To address this limitation, we developed MicroSSNet, an R package designed for analyzing microbial networks, including both aggregated and single-sample networks. RESULTS: We designed MicroSSNet primarily to fill the current gap in bioinformatics tools for constructing single-sample networks (SSNs) from microbiome data, and we evaluated both the performance and limitations of ssPCC-based SSNs using simulated and real datasets. Through Monte Carlo simulations, we assessed the statistical behavior of ssPCC and highlighted scenarios in which ssPCC is less powerful. We then applied MicroSSNet to two distinct datasets: a human gut metagenomic dataset and a soil 16S rRNA gene dataset. In the human gut dataset, SSNs revealed unique edges not detected in the aggregated network. In the soil dataset, SSN features showed some predictive value for group classification. However, SSN-derived patterns should be interpreted cautiously, as they may not exclusively reflect true interaction changes. MicroSSNet additionally implements a full aggregated-network workflow, including bipartite networks and extensive topological property analysis. CONCLUSIONS: Together, MicroSSNet offers a framework for constructing and analyzing both single-sample and aggregated microbial networks. In this work, we also highlight the potential and limitations of single-sample network approaches, supporting their application as exploratory tools in microbiome research across individual and population levels. The package is freely available on GitHub (https://github.com/TangZecheng622/MicroSSNet).}, } @article {pmid41975274, year = {2026}, author = {Nikolaidis, M and Hu, C and Juran, BD and McCauley, BM and Schlicht, EM and Bianchi, JK and Ali, AH and Tragaki, V and Atkinson, EJ and Johnson, S and Mars, RA and Eaton, JE and Carey, EJ and Franke, A and Schramm, C and Kashyap, PC and Go, YM and Tran, V and Teeny, S and Jones, DP and Grant, CW and Athreya, AP and Miller, GW and LaRusso, NF and Gores, GJ and Karlsen, TH and Hov, JR and Amoutzias, GD and Lazaridis, KN}, title = {Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2655793}, pmid = {41975274}, issn = {1949-0984}, support = {RC2 DK118619/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Metabolome ; Female ; Male ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; Middle Aged ; *Liver Cirrhosis, Biliary/microbiology/metabolism ; *Cholangitis, Sclerosing/microbiology/metabolism ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Adult ; Metagenome ; Aged ; Metabolomics ; }, abstract = {Primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC) are rare, idiopathic, chronic cholestatic liver diseases that respond differently to limited medical therapies and often lead to liver transplantation. We examined the compositional and functional differences in the gut microbiome, mycobiome, and metabolome of these diseases to better understand their impact on pathogenesis and outcomes. Stool sample metagenomes and metabolomes from patients with PSC (n = 245), PBC (n = 280) and matched controls (n = 245 and n = 278, respectively) were analyzed by shotgun sequencing and ultrahigh-resolution mass spectrometry. Comparisons were conducted with covariate-adjusted linear models. The gut microbiomes of patients with PSC and PBC were characterized by reduced diversity and increased abundance of pathobionts and virulence factors, coupled with altered microbial metabolism, including a reduction of short-chain fatty acids and B-vitamins. Untargeted stool metabolomics supported these results. Patients were stratified into groups using their microbial signatures, and each group had distinct patterns of microbiome-related changes. Cox regression analysis revealed that pathogenic microbial species were predictive of hepatic decompensation, whereas beneficial species had a protective effect. Based on previous groundwork and our new results, microbiome-based interventions such as probiotics, short-chain fatty acid supplementation, and phage therapy represent promising therapeutic options for cholestatic liver diseases.}, } @article {pmid41975427, year = {2026}, author = {Zhang, Z and Bai, J and Liu, Y and Wang, J and Lv, Z and Tang, L and Wang, R and Gao, L and Liu, C and Lu, S and Fu, X and Ni, J and Wan, P}, title = {Effects of synthetic breast milk on the gut metagenome and whole blood transcriptome in lambs.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {41975427}, issn = {1746-6148}, support = {NYHXGG.2023AA206-3//Agricultural GG Project of Xinjiang Production and Construction Corps/ ; 2025AB5012//Tacheng Talents Project/ ; 2025AA01504//Project of Major Science and Technology Project of the Corps/ ; 2022TSYCCX0124//Young Science and Technology Top Talent Program of Tianshan Talent Training Program in Xinjiang Province/ ; XJARS-09-26//Xinjiang Agriculture Research System/ ; CARS-39-07//China Agriculture Research System/ ; }, abstract = {Early postnatal nutrition is crucial for the growth and development of lambs, and artificial milk formulas are widely used as alternatives to breast milk in intensive sheep production. However, the molecular and microbial mechanisms underlying the differences between breast milk and formula feeding remain unclear. This study aimed to compare the fecal metagenomic and whole blood transcriptomic profiles of lambs fed breast milk (BF group) and commercial formula (FF group) from 4 to 45 days of age, to provide a theoretical basis for optimizing formula compositions. A total of 6 lambs were randomly divided into two groups (n = 3 per group), with body weight and body dimensions measured at 45 days of age, followed by fecal metagenomic sequencing and whole blood transcriptomic sequencing. The results showed that BF lambs had significantly higher body weight, body length, heart girth, and chest width than FF lambs. Metagenomic analysis revealed that at the phylum level, Bacteroidetes was enriched in FF lambs, whereas Firmicutes predominated in BF lambs. Differential abundance was also observed at the genus level (higher Desulfovibrio in FF lambs) and the pathway level, with BF lambs enriched in quorum sensing and FF lambs showing higher abundances of pathways related to ubiquinone and other terpenoid-quinone biosynthesis. Moreover, transcriptomic analysis identified 3290 differentially expressed genes (DEGs) between the two groups, with DEGs mainly enriched in metabolic pathways, mTOR signaling pathway, osteoclast differentiation, B cell receptor signaling pathway and MAPK signaling pathway. Collectively, compared with FF, BF enhanced lamb growth, optimized gut microbiome structure and modulated blood transcriptomic profiles related to metabolism, signaling and immunity. These findings highlight the key microbial taxa and functional pathways modulated by breastfeeding, providing valuable insights for the development of more effective milk formula alternatives.}, } @article {pmid41975703, year = {2026}, author = {Rong, R and Long, Y and Li, Y and Lin, L and Yang, J and Hu, Z and Liu, D and Chen, P}, title = {Metagenomic and Targeted Next-Generation Sequencing in Infectious Disease Diagnostics: Current Applications, Challenges, and Future Perspectives.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {7}, pages = {}, pmid = {41975703}, issn = {2075-4418}, support = {2024ZD0533100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2024ZD0533106//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; P12220011-230148//Undergraduate teachingquality and teaching reform licensing project SYSU/ ; }, abstract = {Metagenomic and targeted next-generation sequencing (NGS) technologies are rapidly transforming diagnosis and management for infectious diseases. This review comprehensively examines the current applications of metagenomic NGS (mNGS) and targeted NGS (tNGS) in clinical microbiology, highlighting their roles in pathogen detection, antimicrobial resistance profiling, virulence characterization, and outbreak investigation-particularly in complex cases such as pneumonia, critical illness with pulmonary infections, and pediatric acute respiratory illnesses. We discuss the diagnostic performance, advantages, and limitations of these approaches, including challenges related to sensitivity, specificity, standardization, bioinformatic complexity, and cost-effectiveness. Furthermore, we explore emerging opportunities for integrating NGS-based surveillance with public health strategies, such as wastewater epidemiology, to monitor healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) at the population level. Finally, we outline key steps needed to translate these powerful genomic tools from research settings into routine clinical and public health practice.}, } @article {pmid41975975, year = {2026}, author = {Szala, Ł and Staninska-Pięta, J and Piotrowska-Cyplik, A}, title = {Microbiome of Bovine Milk and Factors Influencing Its Composition.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {7}, pages = {}, pmid = {41975975}, issn = {2076-2615}, support = {MEiN/2023/DPI/2870//Ministry of Science and Higher Education/ ; }, abstract = {The bovine milk microbiome is a complex and dynamic microbial ecosystem, comprising both commensal and pathogenic bacteria. Its composition is shaped by endogenous factors, including udder physiology, lactation stage, and health status, particularly mastitis, as well as by exogenous factors, such as housing conditions, farm infrastructure, milking practices, and post-milking processing. Mastitis not only alters milk quality but also induces persistent dysbiosis that may persist even after clinical recovery, highlighting the need for continuous microbiome monitoring to ensure milk safety. Advances in molecular and metagenomic techniques have enabled the detection of microbial taxa that are difficult to identify using traditional culture-based methods. However, challenges remain due to low microbial biomass, reagent contamination, and the inability to distinguish live from dead bacteria, all of which complicate accurate characterization. Environmental contamination from skin, air, and equipment, along with microbial shifts during transport, storage, pasteurization, and product separation, further modulate microbial communities. While mastitis-related changes in milk microbiota have been extensively studied, the effects of other bovine diseases and systemic health conditions remain largely unexplored, constituting a critical knowledge gap. Understanding the factors that shape milk microbial communities is essential for ensuring dairy product safety, optimizing herd management, and developing microbiome-based innovations in milk production.}, } @article {pmid41976452, year = {2026}, author = {Li, X and Li, Y and Li, Q and Jin, Y and Chen, Y}, title = {Rumen Metagenomic and Muscle Metabolomic Characterization of Meat Quality in Duolang Sheep at Different Ages.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {41976452}, issn = {2304-8158}, support = {2022TSYCLJ0014//Program for Science and Technology Innovation Talents/ ; 2023B02015//Key Research and Development Program Project of Xinjiang Uygur Autonomous Region/ ; }, abstract = {This study aimed to investigate the changes in the meat quality characteristics of Duolang sheep using rumen metagenomic and muscle metabolomic analyses across different age groups. A total of 24 three-month-old male Duolang sheep were selected and reared, and samples of longissimus thoracis muscle and rumen contents were collected at 4, 6, and 8 months of age to evaluate meat quality, metabolites, rumen metagenome, and volatile fatty acids (VFAs). The results indicated that the lightness (L*45min) and yellowness (b*45min) of the longissimus thoracis muscle at 45 min post-slaughter were significantly higher at 4 and 6 months than at 8 months of age (p < 0.05). In terms of ruminal VFAs, butyrate concentration was significantly higher at 6 months than at 4 months (p < 0.05), and valerate concentration exhibited a quadratic relationship with age (p = 0.02). With increasing age, the relative abundances of Prevotella and Fibrobacter increased, whereas those of Methanobrevibacter and Bacteroides decreased (p < 0.05), leading to shifts in functional pathways related to amino acid, lipid, and carbohydrate and energy metabolism. Untargeted metabolomics revealed that muscle betaine and inosine peaked at 4 months of age, whereas L-arginine, L-proline, and inosinic acid were most abundant at 6 months of age (p < 0.05). Correlation analysis revealed that the b*45min was positively associated with ruminal concentrations of propionate, butyrate, and valerate, as well as with the relative abundances of key Selenomonadales taxa (p < 0.05). Inosinic acid exhibited a positive correlation with the abundance of the genus Sodaliphilus and ruminal butyrate concentration (p < 0.05), while Sodaliphilus abundance was negatively correlated with inosine (p < 0.05). In summary, this study demonstrates that age-related variations in the meat quality of Duolang sheep are closely associated with rumen microbial ecology and muscle metabolites, offering novel insights into the molecular mechanisms underlying meat quality formation and identifying potential biomarkers.}, } @article {pmid41976454, year = {2026}, author = {Olupot, CK and Sheehan, O and Kampff, Z and McDonnell, B and Woods, DF and Lugli, GA and Ventura, M and Reen, FJ and Sinderen, DV and Mahony, J}, title = {Raw Milk Cheese Microbiomes: A Paradigm for Interactions of Lactic Acid Bacteria in Food Ecosystems.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {41976454}, issn = {2304-8158}, abstract = {While industrial-scale dairy fermentations often employ pasteurized milk as the substrate, many farmhouse and traditional production practices apply raw milk derived from a variety of mammals. Certain artisanal production systems rely on the autochthonous microbiota of the milk, fermentation vessels, equipment and/or environment to initiate milk coagulation. While the technological properties of lactic acid bacteria associated with dairy fermentations are well described, their interactions with other organisms during fermentation and cheese ripening are poorly investigated. This study presents an overview of the microbial ecology of raw and pasteurized milk used in the production of Irish farmhouse cheeses using metagenomic and culture-based approaches. Metagenomic analysis of four raw milk-derived cheeses established the dominant presence of either lactococci or Streptococcus spp. and with a secondary population of various lactobacilli. Interestingly, the Brie sample was also demonstrated to possess significant proportion of Hafnia spp. This was corroborated in culture-based analysis where Hafnia isolates were also identified. Furthermore, we report on the motility phenotype, lactose utilization ability and metabolic products of isolates of Hafnia paralvei and Hafnia alvei, and determine that these strains could grow in a non-antagonistic manner on plates with strains of Lactococcus lactis and Streptococcus thermophilus. As artisanal and farmhouse production systems are often associated with protected or regionally significant products, it is essential to develop a clear understanding of the microbial communities within and the complex relationships between the community members.}, } @article {pmid41976504, year = {2026}, author = {Buranavanitvong, N and Thanthithum, C and Kanyakam, K and Azzout-Marniche, D and Jouan-Rimbaud Bouveresse, D and Chotechuang, N and Prakitchaiwattana, C}, title = {Diet-Associated Gut Bacterial Microbiota and Metabolome Signatures Linked to Fermented Food Intake in Healthy Postmenopausal Women.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {41976504}, issn = {2304-8158}, support = {FOOD_FF_68_290_2300_073//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; GCUGR1125671022D//the 90th Anniversary of Chulalongkorn University Scholarship under the Ratchadapisek Somphot Endowment Fund/ ; NA//the Second Century Fund (C2F), Chulalongkorn University/ ; }, abstract = {Long-term adherence to plant-based diets can modify gut bacterial microbiota composition and metabolite profiles, which may be particularly relevant for postmenopausal women who frequently adopt such diets and experience age-related changes in nutrient absorption and metabolism. Fermented foods, commonly consumed in vegetarian diets, enhance dietary diversity and nutritional quality. This study compared gut bacterial microbiota and fecal metabolomes between vegetarians (VGs) and omnivores (OMs) and evaluated the contribution of fermented food intake. Thirty-two healthy postmenopausal Thai women (>55 years; 16 VGs, 16 OMs) were enrolled. Gut bacterial microbiota and fecal metabolites were analyzed using 16S rRNA metagenomic and untargeted [1]H-NMR metabolomics. The five most frequently consumed fermented foods were microbiologically characterized. Fermented food consumption was found to be significantly different between groups. OM participants reported infrequent consumption (<10% per week), whereas VG participants consumed fermented foods daily, often in multiple forms (>60% of weekly meals). VG participants exhibited enrichment of Prevotella, Faecalibacterium, and Blautia, while OM participants showed higher abundances of Bacteroides and Escherichia-Shigella. LEfSe identified Weissella as a bacterial taxon associated with the VG group. Functional prediction and metabolomic analyses indicated enhanced carbohydrate fermentation and increased short-chain fatty acid (SCFA) production in VGs, whereas OM profiles reflected greater protein catabolism. Fermented foods consumed by VGs shared microbial biomarkers with the VG gut bacterial microbiota and were rich in SCFAs and essential amino acids, supporting their potential role as microbial and metabolic contributors within the gut ecosystem and nutritional adequacy in postmenopausal vegetarians.}, } @article {pmid41977149, year = {2026}, author = {Liszkowska-Walisiak, W and Motyl, I and Płacheta-Kwiatkowska, B and Wlaźlak, M and Ruman, T and Nizioł, J and Wilkowska, A and Maher, A and Berłowska, J}, title = {Apple Pomace Fermented with Non-Saccharomyces Yeast as a Factor Modulating Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {27}, number = {7}, pages = {}, pmid = {41977149}, issn = {1422-0067}, mesh = {*Malus/chemistry/microbiology/metabolism ; *Fermentation ; *Gastrointestinal Microbiome ; Humans ; *Yeasts/metabolism ; Fatty Acids, Volatile/metabolism ; Fruit ; Bacteria/classification/genetics ; }, abstract = {The valorisation of agro-industrial by-products through fermentation offers an opportunity to develop functional ingredients with targeted effects on gut microbiota. This study evaluates the impact of apple pomace fermented at a low temperature (15 °C) by cold-adapted yeast on the structure and metabolic activity of human gut microbiota, simulated using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]). The fermented apple pomace preparation was characterised by high stability under gastrointestinal conditions, supporting its potential applicability as a functional food ingredient. Supplementation with fermented apple pomace induced distinct changes in the composition and activity of gut microbiota compared to the non-fermented substrate, including increased abundance of the genera Akkermansia, Coriobacteriaceae, and Parabacteroides, and reduced abundance of Bifidobacterium, Klebsiella, Serratia, and Raoultella. The fermented preparation was associated with reduced accumulation of metabolites typically linked to proteolytic fermentation and a more stable metabolic profile throughout the supplementation and washout phases. Short-chain fatty acid analysis indicated that fermentation influenced both the quantity and proportional balance of microbial fermentation products, promoting profiles closer to physiological reference ranges. Overall, fermentation of apple pomace at 15 °C enhanced its functional properties and modulated gut microbiota metabolism in a manner consistent with improved ecosystem stability. These findings highlight the potential of fermented fruit by-products as sustainable ingredients for dietary strategies aiming to support gut microbial functionality.}, } @article {pmid41977414, year = {2026}, author = {Wang, C and Hou, L and Wang, Y and Gao, G and Geng, Y and Pan, J}, title = {Preliminary Study on the Synergistic Degradation Mechanism of the Microbial Community on the Wood of the Dingtao M2 Tomb.}, journal = {International journal of molecular sciences}, volume = {27}, number = {7}, pages = {}, pmid = {41977414}, issn = {1422-0067}, support = {2024YFF0907700//National Key R&D Program of China/ ; N/A//Fundamental Research Funds for the Central Universities/ ; N/A//Preservation Research Center of the Mausoleum of the Dingtao King/ ; }, mesh = {*Wood/microbiology/metabolism ; *Penicillium/metabolism/genetics/isolation & purification ; *Microbiota ; Lignin/metabolism ; Biodegradation, Environmental ; }, abstract = {According to our investigation carried out in July 2023, the wood of the Western Han Dynasty Dingtao M2 Tomb, stored in the preservation room, exhibited signs of microbial degradation. Our metagenomic analysis first revealed Penicillium as the dominant genus on the end of the wrapped wood. Furthermore, functional annotations demonstrated that the resident microbial community possessed cellulolytic and ligninolytic capabilities. Targeted metabolomic analysis evaluated the degradation capacity of Penicillium charlesii DTP_1, a strain isolated from the wrapped wood. We hypothesize that DTP_1 provides an acidic microenvironment via the production of organic acids; the functional microbial community then decomposes lignin into small metabolites via enzymatic action, and these products are then utilized by the microbial community, including DTP_1. Finally, we verified that liquid cinnamaldehyde and volatile gaseous allicin and carvacrol exhibit better inhibitory efficacy. Nevertheless, further optimization of plant-derived agents and application methods are still required. This study proposes a putative mechanism underlying the degradation of the Dingtao M2 Tomb wood by the microbial community, thereby providing theoretical support for the conservation of wooden cultural heritage and relics.}, } @article {pmid41978025, year = {2026}, author = {De Nat, M and Boscolo, S and Gallo, SP and Nanni, L and Fusaro, D}, title = {Ensemble Deep Learning Models on Raw DNA Sequences for Viral Genome Identification in Human Samples.}, journal = {Sensors (Basel, Switzerland)}, volume = {26}, number = {7}, pages = {}, pmid = {41978025}, issn = {1424-8220}, mesh = {Humans ; *Deep Learning ; *Genome, Viral/genetics ; Convolutional Neural Networks ; Neural Networks, Computer ; Metagenomics/methods ; *Sequence Analysis, DNA/methods ; DNA, Viral/genetics ; Ensemble Learning ; }, abstract = {Detecting highly divergent or previously unknown viruses is a critical bottleneck in clinical diagnostics and pathogen surveillance. While alignment-based methods often fail to classify sequences lacking homology to known references, deep learning offers a powerful alternative for signal extraction from 'viral dark matter.' In this work, we present a high-performance ensemble of deep convolutional neural networks specifically designed to identify viral contigs in complex human metagenomic datasets. Our framework processes sequences acquired from high-throughput biological sensors and integrates complementary architectures to capture both local motifs and global genomic signatures. The proposed ensemble achieves state-of-the-art performance, reaching an AUROC of 0.939 on 300 bp contigs and significantly outperforming existing models such as transformer-based approaches, ViraMiner, and DeepVirFinder. Crucially, our results demonstrate high robustness to data degradation, maintaining stable predictive power even with a 10% random nucleotide substitution rate, a common challenge in degraded clinical samples. Furthermore, the model generalizes to 'unseen' viral families not present during training, demonstrating its utility for emerging threat detection. To ensure full reproducibility and facilitate further research in clinical sensing, the complete code and datasets are publicly available on Github.}, } @article {pmid41979145, year = {2026}, author = {Alderete, TL and Holzhausen, EA and Liang, D and Jones, RB and Lurmann, F and Goran, MI and Chang, HH and Sarnat, JA}, title = {Early-Life Air Pollution Exposure Is Associated with the Infant Gut Microbiome and Fecal Metabolome in the First Two Years of Life.}, journal = {Research report (Health Effects Institute)}, volume = {2026}, number = {237}, pages = {1-58}, pmid = {41979145}, issn = {1041-5505}, mesh = {Humans ; Female ; Infant ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Metabolome/drug effects ; Male ; *Air Pollution/adverse effects/analysis ; *Environmental Exposure/adverse effects/analysis ; *Air Pollutants/adverse effects/analysis ; Pregnancy ; California ; Particulate Matter/analysis/adverse effects ; Prenatal Exposure Delayed Effects ; Infant, Newborn ; }, abstract = {INTRODUCTION: Obesity is a major public health concern because it increases the risk of numerous diseases, including cardiovascular disease and type 2 diabetes. Ambient and near-roadway air pollution has been associated with childhood obesity risk, independent of diet and physical activity. However, the biological mechanisms underlying these relationships remain unclear. Based on our previous work and existing literature, we hypothesized that exposure to air pollutants alters the developing infant gut microbiome and fecal metabolome, with implications for childhood obesity risk. In this study, we aimed to determine whether prenatal or early-life exposure to ambient air pollution and near-roadway air pollution is associated with the gut microbiome and fecal metabolome during the first 2 years of life.

METHODS: Our analysis had two components, both of which examined participants from the Southern California Mother's Milk Study, a Latino cohort in which we collected detailed information regarding maternal and child health during the first 24 months of life. Residential-based estimates of exposure to ambient particulate matter (particulate matter ≤2.5 µm and ≤10 µm in aerodynamic diameter: PM2.5 and PM10, respectively), nitrogen dioxide (NO2), and ozone (O3), as well as near-roadway air pollution (NOx), were modeled using residential address histories. High-throughput metagenomics and metabolomics were performed on stool samples collected at 1, 6, 12, 18, and 24 months of age. Overall, our sample included 207 unique individuals with gut microbiome data and 127 unique individuals with fecal metabolomics data. In the first analysis component, we examined the cross-sectional associations of pre- and postnatal exposure to ambient and near-roadway pollutants with the infant gut microbiome and fecal metabolome at 1, 6, 12, 18, and 24 months of age. In the second analysis component, we examined the longitudinal associations of pre- and postnatal exposure to air pollutants with the trajectory of the developing infant gut microbiome and fecal metabolome.

RESULTS: Our findings indicate that exposure to air pollutants during prenatal and postnatal periods is associated with significant changes in the developing gut microbiome and its metabolic output, as evidenced by perturbations in the fecal metabolome. These molecular alterations were evident in both cross-sectional and longitudinal analyses. The results suggest that early-life exposure to air pollution can disrupt the developmental trajectory of the gut microbiome, potentially leading to changes with substantial health implications. These findings underscore the importance of mitigating air pollution exposure during critical developmental periods to protect and promote gut health and overall well-being in infants.

CONCLUSIONS: We identified gut microbes and fecal metabolites associated with early-life exposure to air pollution. Many of these markers of gut bacterial composition and function have been linked to childhood obesity. These findings contribute to our understanding of mechanisms underlying the obesogenic effects of air pollutants in early life. Future work in this cohort will include integrated mixture and multi-omics analyses to explore the joint impact of air pollution exposure on the gut microbiome and fecal metabolome.}, } @article {pmid41979617, year = {2026}, author = {Li, G and Dan, N and Lu, T}, title = {Two Cases of Severe Chlamydia psittaci Pneumonia with Respiratory Failure and Literature Review.}, journal = {Clinical laboratory}, volume = {72}, number = {4}, pages = {}, doi = {10.7754/Clin.Lab.2025.250675}, pmid = {41979617}, issn = {1433-6510}, mesh = {Humans ; *Chlamydophila psittaci/genetics/isolation & purification ; *Psittacosis/diagnosis/microbiology/drug therapy/complications ; *Respiratory Insufficiency/microbiology/diagnosis/etiology ; Male ; *Chlamydial Pneumonia/diagnosis/microbiology/drug therapy/complications ; Middle Aged ; Female ; Anti-Bacterial Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; *Pneumonia, Bacterial/microbiology/diagnosis/drug therapy ; Treatment Outcome ; Metagenomics/methods ; }, abstract = {BACKGROUND: Chlamydia psittaci pneumonia is a zoonotic disease with non-specific clinical manifestations, often leading to delayed diagnosis. Metagenomic next-generation sequencing (mNGS) can help us identify pathogens in a timely manner and quickly adjust treatment strategies.

METHODS: We reported two cases of severe Chlamydia psittaci pneumonia with respiratory failure and reviewed relevant literature.

RESULTS: Both patients were diagnosed with Chlamydia psittaci infection through mNGS after routine pathogen testing failed. After using Omadacycline based treatment, the patients' clinical and radiological characteristics improved significantly and were successfully cured.

CONCLUSIONS: For patients infected with Chlamydia psittaci pneumonia, timely identification of the pathogen is crucial. mNGS can quickly detect Chlamydia psittaci in critically ill patients, guide clinical timely targeted treatment, and improve patient symptoms.}, } @article {pmid41979623, year = {2026}, author = {Xie, BX and Chen, Y and Tan, YR and Jiang, T and Huang, MH and Zhu, YM and Chen, S}, title = {Challenges in the Diagnosis of Hematogenous Disseminated Pulmonary Tuberculosis with Multiple Organ Involvement.}, journal = {Clinical laboratory}, volume = {72}, number = {4}, pages = {}, doi = {10.7754/Clin.Lab.2025.250640}, pmid = {41979623}, issn = {1433-6510}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Pericardial Effusion/microbiology ; Tomography, X-Ray Computed ; Male ; *Tuberculosis, Miliary/diagnosis/microbiology ; High-Throughput Nucleotide Sequencing ; Ascitic Fluid/microbiology ; }, abstract = {BACKGROUND: Tuberculosis is a public health problem worldwide, and China is a high-burden country. Hematogenous disseminated pulmonary tuberculosis is one of the most serious forms of tuberculosis, and diagnosing hematogenous pulmonary tuberculosis is a challenge, even for the most experienced clinicians, who may also feel perplexed. We report a case of hematogenous disseminated tuberculosis involving multiple organs that was initially misdiagnosed as metastatic malignancy. The diagnosis was finally confirmed by metagenomic Next-Generation Sequencing (m-NGS) of peritoneal and pericardial effusions, which detected Mycobacterium tuberculosis complex.

METHODS: Appropriate laboratory tests, m-NGS, Chest and abdominal CT, Pericardiocentesis, and Peritoneal puncture.

RESULTS: Chest and abdominal CT showed diffuse nodules in both lungs, pericardial effusion, bilateral pleural effusion, and abdominal pelvic effusion. Tuberculosis bacillus antibody was negative, erythrocyte sedimentation rate increased to 42 mm/H, and the carcinoembryonic antigen (CEA) increased to 7.1 ng/mL, peritoneal effusion adenosine deaminase increased to 65.17 U/L, pericardial effusion adenosine deaminase increased to 142.39 U/L. m-NGS of pericardial effusion and peritoneal effusion detected 886,963 M. tuberculosis complex.

CONCLUSIONS: Miliary tuberculosis is a severe and rare form of tuberculosis. Delayed diagnosis may be the most important factor leading to death from miliary tuberculosis. We report a case where Mycobacterium tuberculosis was identified through mNGS of pericardial and peritoneal effusions, enabling rapid diagnosis of disseminated tuberculosis. This case provides a new approach for the rapid diagnosis of disseminated tuberculosis.}, } @article {pmid41980062, year = {2026}, author = {Zhan, J and Yang, W and Guo, J and Yu, Y and Lai, S and Liu, X and Zhou, S}, title = {Iron plaques as terminal electron acceptors optimize clostridial fermentation and nitrogen fixation in rice rhizospheres.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41980062}, issn = {1751-7370}, support = {//Project of Fujian Provincial Department of Education/ ; //Project of Fujian Provincial Department of Science and Technology of China/ ; //National Natural Science Foundation of China/ ; //National Science Fund for Distinguished Young Scholars of China/ ; }, mesh = {*Oryza/microbiology ; *Nitrogen Fixation ; *Fermentation ; *Rhizosphere ; *Iron/metabolism ; *Clostridium/metabolism/genetics ; Oxidation-Reduction ; Plant Roots/microbiology ; Soil Microbiology ; Electron Transport ; Nitrogen/metabolism ; }, abstract = {Fermentative Clostridium species associated with rice roots can contribute substantially to biological nitrogen fixation (BNF) in anoxic paddy soils, yet whether their BNF is regulated by the redox chemistry of rhizosphere remains unclear. Here, we show that iron plaques on rice roots function as terminal electron acceptors that reprogram Clostridium fermentation and thereby enhance BNF. In nitrogen-fixation microcosms, Clostridium sensu stricto I was selectively enriched under plaque-associated Fe(III)-reducing conditions, coinciding with elevated nitrogen fixation. Metabolomic profiling coupled with metabolic flux analysis revealed that Fe(III) reduction redirects a portion of carbon and electron flow from low-energy-yield solventogenesis toward high-energy-yield acidogenesis. This shift increases cellular ATP generation and expands the reductant pool, thereby benefiting the energetic and reductant demands of nitrogenase. Integrated transcriptomic and metagenomic analyses further identified NosR, a flavin mononucleotide-binding protein that is upregulated during Fe(III) reduction and may facilitate electron delivery to plaque-associated Fe(III). Our findings establish a mechanism in which iron plaque reduction optimizes fermentation for BNF, providing fundamental insights into coupled Fe-N cycling in rice rhizospheres and suggesting potential strategies for sustainable nitrogen management in flooded agroecosystems.}, } @article {pmid41980294, year = {2026}, author = {Paulí, S and Rosell-Díaz, M and Moreno-Navarrete, JM and Pons Tamarit, J and Pérez-Brocal, V and Moya, A and Puig, J and Garre-Olmo, J and Ramos, R and Fernández-Real, JM and Mayneris-Perxachs, J}, title = {Glucose metabolism's impact on Blastocystis presence in the human gut.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {61}, number = {}, pages = {106647}, doi = {10.1016/j.clnu.2026.106647}, pmid = {41980294}, issn = {1532-1983}, mesh = {Humans ; *Blastocystis/isolation & purification ; *Gastrointestinal Microbiome/physiology ; Female ; *Glucose/metabolism ; Feces/microbiology/parasitology ; Metformin/therapeutic use/pharmacology ; Diabetes Mellitus, Type 2/drug therapy/metabolism/microbiology ; Male ; Blastocystis Infections/metabolism ; Middle Aged ; Adult ; }, abstract = {BACKGROUND AND AIMS: The role of Blastocystis spp. parasite in human health remains debated. Recent literature associates it with a healthy gut and lifestyle. Evidence suggests that Blastocystis spp. could enhance glucose homeostasis, although Blastocystis spp. is considered to be epiphenomena for a lifestyle. Moreover, some subtypes seem to have a beneficial impact while others would hinder the host's health. Here, we explore the complex link between Blastocystis spp. and glucose metabolism parameters.

METHODS: We explored shotgun metagenomic profiles of the gut microbiota from fecal samples associated with glucose metabolism parameters in 4 independent cohorts (CGM, n = 65; IMAGEOMICS, n = 1030; PECT, n = 841 and MEIFLO, n = 22), using microbiome compositional analysis methodology. We leverage data from MEIFLO, a recent clinical trial conducted in patients recently diagnosed with type 2 diabetes (T2D), to investigate how metformin-induced improvement in glucose metabolism influences gut microbiota composition, using Linear Models for Differential Abundance. We studied possible associations of Blastocystis spp. with leukocyte telomere length.

RESULTS: We confirmed and extended the relationship between glucose homeostasis and Blastocystis spp. and subtypes ST1 and ST4, showing its association with glucose and insulin levels in all cohorts. Importantly, we observed that glucose homeostasis may shape Blastocystis spp. abundance in the gut, rather than the reverse, based on clinical trial data showing that metformin (not placebo) increased Blastocystis spp. in recently diagnosed T2D patients. We identify Blastocystis as one of the microbial genera most strongly and directly associated with telomere length in the IMAGEOMICS cohort.

CONCLUSIONS: The direct relation between Blastocystis and telomere length aligns with the observed inverse associations of glucose levels with telomere length, and glucose levels with Blastocystis. We propose that Blastocystis may be associated with healthy glucose metabolism as an outcome and potentially serve as an indicator of improved metabolic health.}, } @article {pmid41980639, year = {2026}, author = {Li, R and Li, S and Yan, Y and Xie, Y and Liu, L and Zhao, J and Zhang, J and Cai, Z and Huang, X}, title = {Reductive soil disinfestation and hydrothermal biochar regulate antibiotic resistance mechanisms by reshaping soil bacterial functional traits and interaction patterns.}, journal = {Bioresource technology}, volume = {452}, number = {}, pages = {134622}, doi = {10.1016/j.biortech.2026.134622}, pmid = {41980639}, issn = {1873-2976}, mesh = {*Soil Microbiology ; *Charcoal/pharmacology/chemistry ; *Bacteria/drug effects/genetics/metabolism ; *Drug Resistance, Microbial/genetics ; *Soil/chemistry ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The health risk posed by antibiotic resistance genes (ARGs) in agricultural soils has become a growing concern. However, a systematic understanding of how microbial life history strategies, functional traits, and community interactions jointly shape ARG dynamics remains lacking. This knowledge gap not only constrains our ability to elucidate the evolutionary mechanisms underlying microbial resistance but also hampers the precise prediction and effective management of soil ARG risks. Here, we established distinct soil habitats through diverse soil managements, including control (CK), reductive soil disinfestation (RSD), and RSD combined with hydrothermal biochar application (HCR), to investigate how microbial traits and interactions shape ARG resistance mechanisms using metagenomic analyses. Our results showed that RSD and HCR treatments significantly reduced the overall abundance and ecological risk of ARGs compared to CK. In CK soils, microbial communities characterized by intensive interactions, high metabolic activity, and rapid growth efficiency promoted the enrichment of ARGs conferring resistance via antibiotic target alteration, protection, or replacement. In contrast, RSD/HCR treatments favored slow-growing, functionally complex, and competition-dominated communities, which were enriched in ARGs associated with antibiotic efflux mechanisms. Moreover, ARGs exhibited pronounced co-occurrence patterns with antimicrobial biosynthetic gene clusters in highly competitive environments. Collectively, this study reveals the selective responses of ARG resistance mechanisms to distinct microbial ecological strategies and provides new insights for the precise management of environmental antibiotic resistance risks.}, } @article {pmid41980640, year = {2026}, author = {Yang, H and Peng, N and Fan, Y and Huang, J and Zhang, J and Li, L and Ding, J and Tang, Z and Song, J and Liu, D and Hu, R and He, Z and Wang, C}, title = {Genome-Resolved insights into significance of DNRA Microbes in N2O production during manure composting.}, journal = {Bioresource technology}, volume = {453}, number = {}, pages = {134617}, doi = {10.1016/j.biortech.2026.134617}, pmid = {41980640}, issn = {1873-2976}, mesh = {*Nitrous Oxide/metabolism ; *Composting ; *Manure/microbiology ; Denitrification ; Nitrates/metabolism ; Ammonium Compounds/metabolism ; *Bacteria/genetics/metabolism ; *Genome, Bacterial ; }, abstract = {Nitrous oxide (N2O) production during manure composting has traditionally been attributed primarily to heterotrophic denitrification (HD), while the roles of alternative pathways remain poorly resolved. Using time-resolved multi-omics across 37 samples from various manure sources, our study investigated the transcriptional landscape of N2O-producing pathways during composting. Microorganisms associated with dissimilatory nitrate reduction to ammonium (DNRA), including Fermentimonas and JAHWKS01 lineages, accounted for 21.2-33.1% of N2O-producing gene expression-comparable to HD-revealing DNRA as a previously underappreciated source. DNRA-associated gene expression was regulated by viral factors, predominantly through lytic Caudoviricetes phages. Expanding our analysis to 174 public metagenomic datasets revealed that DNRA-derived N2O-producing gene abundance peaked under static and hyperthermophilic conditions, highlighting aeration and temperature as critical mitigation controls. Furthermore, our study identified a substantial proportion of microorganisms harboring both DNRA and HD pathways. These findings refine mechanistic understanding of composting N2O emissions and inform multi-pathway mitigation strategies.}, } @article {pmid41980647, year = {2026}, author = {Song, M and Jiang, L and Lin, Z and Li, J and Luo, C and Qiu, R}, title = {Size-dependent effect of microplastics on sulfamethoxazole degraders in soil as revealed by integration of SIP and metagenomics.}, journal = {Bioresource technology}, volume = {452}, number = {}, pages = {134620}, doi = {10.1016/j.biortech.2026.134620}, pmid = {41980647}, issn = {1873-2976}, mesh = {*Sulfamethoxazole/metabolism ; *Soil Microbiology ; Biodegradation, Environmental/drug effects ; *Metagenomics/methods ; *Microplastics/chemistry ; *Bacteria/metabolism/genetics ; *Particle Size ; *Soil/chemistry ; }, abstract = {Microbes related to antibiotic degradation in situ in agricultural soil with MPs and their response to different sizes of MPs are ambiguity. This study investigated the microbes participating in antibiotic degradation in soils with 4.5 mm and 0.1 mm MPs by using DNA-SIP with metagenomics, Raman-activated cell sorting (RACS) with sulfamethoxazole (SMX) and polyethylene as the model compound and MPs. The 4.5 mm MPs enhanced SMX degradation by promoting diversity and abundance of degraders benefiting from improved soil properties, relation between degraders and SMX, and bacteria with positive co-occurrence relationship with degraders. The 0.1 mm MPs inhibited SMX degradation by decreasing diversity, abundance of degraders, and intensifying bacteria mutually exclusive with degraders due to harsher soil conditions. Furthermore, DNA-SIP-RACS successfully acquired cells of SIP-identified putative degraders, and directly linked SMX degradation potential with metC1, metF1and luxS1, proving possibility of applying this approach in antibiotic-degrading microbes in soil.}, } @article {pmid41980652, year = {2026}, author = {Back, JP and Klain, V and Pintro, VO and Lopes, FC and Marques, AL and Kray, J and Beys-da-Silva, WO and Santi, L and Schrank, A and Mayer, FQ and Vainstein, MH}, title = {Viral Diversity of Coastal Restinga Soils From Southern Brazil.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70343}, pmid = {41980652}, issn = {1758-2229}, support = {441167/2023-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 382064/2025-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 383394/2024-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 314485/2021-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 305705/2025-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 303971/2025-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 313620/2021-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 303945/2025-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Brazil ; *Soil Microbiology ; *Viruses/classification/genetics/isolation & purification ; *Biodiversity ; Metagenomics ; Phylogeny ; }, abstract = {Coastal ecotones are highly dynamic environments for viral studies due to their extreme abiotic conditions, transitional nature between marine and terrestrial domains and high biodiversity. In Brazil, the Restinga is a coastal ecotone along the shoreline, characterized by nutrient-poor sandy soils, high salinity, strong winds and intense solar radiation, hosting poorly explored microbial communities essential for ecological balance. This exploratory study provides a preliminary characterization of viral diversity across three Restinga localities in southern Brazil (Imbé, Cidreira and Mostardas) using metagenomics. We identified 261 viral families, 2023 genera and 6064 species, with 'Unknown' representing 44%-46% of families and ~9% of genera. Among known taxa, Mimiviridae was most frequent (15%-16%), followed by Phycodnaviridae (9%), Peduoviridae (5%) and Kyanoviridae (4%-5%). Genera such as Tupanvirus and Fadolivirus were abundant (~5%), with Fadolivirus algeromassiliense and Donellivirus gee among the most frequent species. Although alpha diversity and composition did not differ significantly among sites, landscape features influenced viral communities. Viral richness and abundance increased with urban land cover and isolation but decreased with Restinga cover and patch fragmentation.}, } @article {pmid41980940, year = {2026}, author = {Lu, Z and Li, R and Zhou, K and Li, S and Sun, S and Liu, J and Zhao, L and Chen, S and Liu, K and Yuan, X and Shao, Z}, title = {Tick-vectored mobilization of antibiotic resistance genes: transboundary dissemination across wildlife-livestock-vector-environment interfaces.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41980940}, issn = {2055-5008}, support = {2024SF-YBXM-289//Key Research and Development Projects of Shaanxi Province/ ; 82473689//National Natural Science Foundation of China/ ; 82273689//National Natural Science Foundation of China/ ; WW25Z01SF027//Wuwei City Science and Technology Plan Project/ ; }, mesh = {Animals ; *Ticks/microbiology ; Gene Transfer, Horizontal ; Metagenomics/methods ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Metagenome ; Sheep/microbiology ; Soil Microbiology ; Marmota/microbiology ; *Livestock/microbiology ; *Animals, Wild/microbiology ; Microbiota ; *Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial ; Caves/microbiology ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging as critical environmental contaminants across diverse ecological interfaces. To dissect evidence of microbiome and resistome in the different interconnected interfaces of ecotone, we conducted a field investigation of the microbiome and resistome of marmots, along with coexisting domestic sheep, ticks and their cave soils within the same ecological habitat. We used shotgun metagenomics with metagenome-assembled genomes (MAGs), species-resolved binning, ARG identification, source-tracker analyses, and horizontal gene transfer (HGT) network analysis to examine potential cross-interface dissemination. The composition of the mammalian gut microbiome was primarily comprised of Firmicutes, while ticks and soils exhibited distinct clusters that were predominantly dominated by Proteobacteria. The observed resistance mechanisms manifested niche-specific patterns, with target alteration predominating in mammals, whereas ticks exhibited elevated antibiotic inactivation/efflux strategies, and soils prioritized efflux mechanisms. Metagenomic assembly from these four groups yielded 5339 metagenome-assembled genomes (MAGs), of which 1481 met medium- or high-quality standards. Ticks exhibited 72% species similarity and 52% ARG concordance with marmots, while soils conserved 32% ARGs and >86% toxin genes with mammals. Our findings demonstrate that the transboundary dissemination of ARGs across different ecological interfaces, necessitates integrated surveillance of antimicrobial resistance at ecological boundaries to mitigate public health risks.}, } @article {pmid41980943, year = {2026}, author = {Kim, J and Kim, N and Cha, JH and Ma, J and Lee, I}, title = {Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41980943}, issn = {2041-1723}, support = {2022R1A2C1092062//National Research Foundation of Korea (NRF)/ ; RS-2025-18362970//National Research Foundation of Korea (NRF)/ ; 2022M3A9F3016364//National Research Foundation of Korea (NRF)/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Metagenome/genetics ; *Benchmarking ; Neural Networks, Computer ; Sequence Analysis, DNA ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {Metagenomic binning is essential for reconstructing prokaryotic genomes from metagenomic samples. We benchmarked various binning tools using Critical Assessment of Metagenome Interpretation (CAMI)-simulated, custom-simulated, and real metagenomic datasets, primarily focusing on short-read sequencing data. Our analysis highlights critical factors influencing binning efficacy: (i) Sequencing depth and taxonomic complexity strongly impact binning performance, while CAMI-simulated benchmarking datasets exhibit substantially lower complexity than human gut and environmental metagenomes, (ii) Chimeric genome rates vary widely across tools, (iii) Multi-sample binning is most effective with about 20 samples, as using too few or too many samples can reduce its benefits, and (iv) Binning efficacy was lower for single-end sequencing samples due to reduced contig quality and assembly fragmentation. Neural network-based tools consistently outperformed others in genome recovery from both real samples and simulated samples with realistic taxonomic complexity, though at higher computational cost. By integrating and refining genome bins from the top three binning tools, we recovered >30% more high-quality genomes than previous methods. This study provides practical guidance for improving metagenomic binning to facilitate the reconstruction of prokaryotic genomes.}, } @article {pmid41980953, year = {2026}, author = {Luo, E and Pham, ND and Rogers, TJ and Sheam, MM and Benner, BE and Vallino, JJ and Trubl, G and Huber, JA}, title = {Quantitative stable isotope probing (qSIP)-informed metagenomics identifies viruses infecting chemoautotrophs.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41980953}, issn = {2041-1723}, mesh = {*Metagenomics/methods ; Carbon Isotopes ; Isotope Labeling/methods ; Carbon Cycle ; *Viruses/genetics ; }, abstract = {Aquatic environments absorb ~2.5 gigatonnes of atmospheric carbon each year[1], more than the carbon stored in the atmosphere, soils, and all biomass combined. Primary producers transform this dissolved inorganic carbon into biomass that can subsequently flow into other trophic levels, or be released back into the environment through viral lysis. While there is substantial knowledge about the diversity and activity of viruses infecting photoautotrophic primary producers and the ecosystem impact, little is known about viruses infecting chemoautotrophs, representing a gap in our understanding of key processes driving microbial carbon cycling. Here, we combine metagenomics with quantitative [12/13]C stable isotopic probing (qSIP) mesocosm experiments in a marine-derived meromictic pond to quantify population-specific isotopic enrichment, identify key chemoautotrophic primary producers, and virus-host dynamics. Isotopically enriched carbon is tracked from the genomes of chemoautotrophs to putative viruses, showing that active populations of hydrogen/sulfur-oxidizing chemoautotrophs (Thiomicrorhabdus, Hydrogenovibrio, Sulfurimonas, Sulfurovum) are targeted by viruses. This work provides the foundation for revealing the diversity and activity of viruses infecting globally-widespread chemoautotrophs. Our study sheds light on trophic interactions that impact microbial carbon cycling in aphotic environments and builds toward biogeochemical models that incorporate viral impacts on chemoautotrophic microbial communities.}, } @article {pmid41981035, year = {2026}, author = {Faber, Q and Baker, CCM and West, JR and Doherty, SJ and Ernakovich, JG and Barbato, RA}, title = {Antimicrobial resistance varies with warming in active layer soil and permafrost.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41981035}, issn = {2045-2322}, support = {PE 0602144A Program "Defense Resiliency Platform Against Extreme Cold Weather"//United States Department of Defense/ ; }, abstract = {UNLABELLED: Although antimicrobial resistance is a contemporary public health concern, antimicrobial resistance genes (ARGs) have existed long before human use of antimicrobials, and recent attention has focused on whether permafrost thaw could release ARGs as the resistome shifts. We present a metagenomic analysis of permafrost samples from four sites in Alaska and Sweden, thawed under laboratory conditions. We used ABRicate, an alignment-based tool, and DeepARG, a deep learning tool, to identify ARGs, assessed their abundances under experimental thaw, measured taxonomic shifts, and examined metagenome-assembled genomes (MAGs) carrying ARGs. ARG abundance varied with depth, with some permafrost containing more ARGs than the seasonally thawed active layer. ARG abundance increased with soil carbon and decreased with pH across sites, suggesting site-specific influences. The majority of 164 high-quality MAGs contained ARGs, including 80 out of 105 species identified. This included bacteria from nine phyla, demonstrating widespread distribution across microbial taxa. Laboratory thaw experiments revealed that ARG abundances did not change significantly in two of the sites, but declined with thaw in the remaining two sites. Together, these findings demonstrate that ARGs are consistently present in permafrost microbiomes across multiple sites, but relative abundances generally do not increase during thaw. While ARGs that persist may pose potential risks, our results suggest that permafrost thaw may not substantially elevate environmental or public health risks.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-46295-2.}, } @article {pmid41981202, year = {2026}, author = {Benedicenti, O and Strand, DA and Mohammad, SN and Gulla, S and Amundsen, MM and Sindre, H and Vrålstad, T}, title = {Integrated approaches for pathogen monitoring and shotgun metagenomic analysis in Atlantic salmon farming.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41981202}, issn = {2045-2322}, support = {328724//Norges Forskningsråd/ ; 101136346//European Commission/ ; 901674//Fiskeri - og havbruksnæringens forskningsfond/ ; }, mesh = {Animals ; *Salmo salar/microbiology/virology ; *Metagenomics/methods ; *Aquaculture/methods ; Shotgun Sequencing ; Metagenome ; *Fish Diseases/virology/microbiology ; Seawater/microbiology/virology ; Workflow ; }, abstract = {Specific tools for detecting waterborne pathogens are essential for limiting disease spread in aquaculture. We evaluated a field-deployable workflow combining filtration of eDNA/eRNA with targeted (RT-)qPCR and complementary shotgun metagenomics to monitor pathogens and microbial community dynamics in a single-farm study following one Atlantic salmon production cohort from hatchery to slaughter. The primary aim was to assess workflow feasibility and performance under real farm conditions, while secondarily examining whether metagenomic profiles could contextualise microbial shifts associated with pathogen presence. ISAV was consistently detected in hatchery water at ~ 4 × 10[3]-9 × 10[3] copies/L, whereas PRV1 was detected only inside sea pens from August onward (~ 4 × 10[2]-1.5 × 10[4] copies/L) and increased by more than two orders of magnitude after wellboat delousing. Shotgun metagenomics yielded a median of ~ 1.5 × 10[5] reads per sample (mean read length ~ 2.5 kb; N50 > 2 kb), enabling broad taxonomic screening. PRV1-positive seawater samples showed modest decreases in richness and shifts in viral taxa, though patterns were subtle and should be interpreted cautiously given low pathogen loads. The workflow was practical for trained farm personnel, and this integrated approach offers a scalable system for routine pathogen surveillance and supports earlier, evidence-based biosecurity actions, providing broader microbial information than qPCR alone.}, } @article {pmid41981426, year = {2026}, author = {Muzhabaier, K and Li, Y and Wang, F and Guo, X and Chen, Q and Zhang, X and Cao, L}, title = {[Differential analysis of gut microbiome in patients with periprosthetic joint infection, aseptic failure, and osteoarthritis].}, journal = {Zhongguo xiu fu chong jian wai ke za zhi = Zhongguo xiufu chongjian waike zazhi = Chinese journal of reparative and reconstructive surgery}, volume = {40}, number = {4}, pages = {548-556}, pmid = {41981426}, issn = {1002-1892}, mesh = {Humans ; Female ; Male ; *Prosthesis-Related Infections/microbiology ; *Gastrointestinal Microbiome ; *Osteoarthritis/microbiology/surgery ; Aged ; *Dysbiosis/microbiology ; Middle Aged ; Arthroplasty, Replacement, Hip/adverse effects ; *Prosthesis Failure ; Arthroplasty, Replacement, Knee/adverse effects ; Feces/microbiology ; Bacteria/isolation & purification/classification ; }, abstract = {OBJECTIVE: To explore the differences in gut microbiota diversity and structural characteristics among patients with periprosthetic joint infection (PJI), aseptic failure (AF), and osteoarthritis (OA), and to analyze the association between gut microbiota dysbiosis and the occurrence of PJI, thereby providing a new theoretical basis for elucidating the pathogenesis and treatment strategies of PJI in clinical practice.

METHODS: The study enrolled patients with PJI and AF admitted between February 2024 and December 2024, as well as OA patients admitted in February 2024. A total of 52 PJI patients, 19 AF patients, and 29 OA patients who met the selection criteria were included in the analysis. Significant differences were observed among the three groups in terms of gender, age, surgical site, preoperative C-reactive protein levels, and erythrocyte sedimentation rate (P<0.05), while no significant difference was found in American Society of Anesthesiologists (ASA) classification and body mass index (P>0.05). Among the PJI patients, infection staging was as follows: 9 cases in the acute phase, 28 cases in the delayed phase, and 15 cases in the chronic phase; 23 cases were accompanied by sinus tract formation. Fecal samples were collected at different time points: for the PJI group, samples were obtained preoperatively and on postoperative days (7±1) and (14±1); for the AF group, preoperatively and on postoperative day (7±1); and for the OA group, preoperatively only. Metagenomics next-generation sequencing were employed to analyze gut microbiota α-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) and differential bacterial genera (screened using the LEfSe algorithm).

RESULTS: Analysis of gut microbiota diversity showed that the preoperative α-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) in the PJI group were significantly lower than those in AF group and OA group (P<0.05). Compared with the AF group on postoperative day (7±1), the α-diversity indices in the PJI group on postoperative day (7±1) were lower, but the difference was not significant (P>0.05); by postoperative day (14±1), these indices further decreased, and the difference was significant (P<0.05). In the PJI group, no significant difference was observed in any of the indices across different time points postoperatively (P>0.05). Analysis of gut microbiota structural characteristics revealed that the PJI group exhibited characteristic dysbiosis both before and after operation. Preoperatively, the PJI group was characterized by enrichment of Pseudomonadota (relative abundance 13.19%), Enterobacteriaceae (Escherichia 3.26%, Klebsiella 1.90%), and opportunistic pathogens such as Enterococcus faecium (0.43%), while the relative abundances of Firmicutes (51.83%) and Bifidobacterium (0.24%) decreased. Postoperatively, the α-diversity in the PJI group further declined, with increased relative abundances of Escherichia and Klebsiella, and the relative abundance of Firmicutes decreased to 40.24%. LEfSe analysis of preoperative gut microbiota composition between the PJI group and AF group indicated that the AF group was predominated by Firmicutes, Bifidobacterium, and Roseburia preoperatively, with greater postoperative microbial stability compared to the PJI group.

CONCLUSION: Patients with PJI exhibited a gut microbiota profile characterized by reduced diversity and enrichment of opportunistic pathogens. Postoperative antibiotic treatment further aggravated this dysbiosis, providing new clinical insights into the role of gut microbiota imbalance in the pathogenesis and progression of PJI.}, } @article {pmid41981555, year = {2026}, author = {Bangera, SR and Subbiah, R and Govindaraj, S and Ibegbu, C and Reznik, D and Read, TD and Hartman, TJ and Paul, S and Torres-Patarroyo, N and Lymon, KJ and Ciers-Davis, NA and Nguyen, ML and Bruner, DW and Flowers, L and Velu, V and Xiao, C}, title = {Characterizing Oral Microbiome and Periodontal Disease in Oral HPV-Positive (COMP-HPV) individuals with HIV: an observational longitudinal study protocol.}, journal = {BMC oral health}, volume = {26}, number = {1}, pages = {}, pmid = {41981555}, issn = {1472-6831}, support = {P51 OD011132/CD/ODCDC CDC HHS/United States ; R01 DE032243/DE/NIDCR NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; R01 CA285198/CA/NCI NIH HHS/United States ; P51 OD011132/CD/ODCDC CDC HHS/United States ; R01 DE032243/DE/NIDCR NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; R01 CA285198/CA/NCI NIH HHS/United States ; }, abstract = {BACKGROUND: Human papillomavirus (HPV) is a major cause of oropharyngeal and other cancers, occurs more frequently among people with HIV (PWH). Despite antiretroviral therapy, HPV-related cancer incidence remains elevated in this group. Oral dysbiosis in PWH may impair mucosal immunity, promoting HPV persistence and inflammation. Periodontal disease, frequently observed in PWH, further contributes to microbial imbalance and immune dysregulation, increasing susceptibility to oral HPV infection. This study investigates the relationship among oral microbiome composition, periodontal disease and oral HPV infection behavior in PWH, considering immunologic and social determinants of health.

METHODS: The characterizing oral microbiome and periodontal disease in oral HPV-positive individuals (COMP-HPV), an observational longitudinal study will enroll 500 PWH and follow them up for two years. Oral rinse for HPV testing and periodontal assessment will be collected every six months; saliva for inflammatory markers, oral rinse for microbiome and oral cytobrush for immunological profiling will be collected annually. Immune profiling will include high-dimensional flow cytometry and 10X RNA-sequencing to characterize innate and adaptive immune subsets, with emphasis on HLA-DR–positive populations, enabling evaluation of oral immune modulation during HPV infection. The study has four specific aims such as to examine associations between oral microbiome composition (16S and metagenomics) and oral HPV infection, including prevalence, incidence, persistence, and clearance; to assess the impact of periodontal disease on oral HPV infection and investigate whether the oral microbiome mediates this relationship; to determine how oral microbiome composition influences immunological responses in HPV-positive PWH and to evaluate the role of social determinants on oral microbiome composition and HPV infection. Data from this longitudinal study will be used to understand the natural history of oral HPV infection, the interplay with periodontal disease, microbial alterations, and immunological changes, providing evidence to guide interventions for reducing HPV-associated disease in PWH.

TRIAL REGISTRATION NUMBER: Not applicable.

DISCUSSION: The COMP-HPV study aims to contribute to the body of research designed to investigate mechanisms underlying oral HPV infection among PWH to improve immune responses to reduce HPV infection and relevant carcinoma.}, } @article {pmid41981681, year = {2026}, author = {Brachmann, S and Kiesewetter, KN and Liddicoat, C and Wallace, KJ and Breed, MF and Eisenhauer, N and Barnes, AD}, title = {Urban forest restoration enhances soil microbial functional potential and functional insurance via shifts in β-diversity.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41981681}, issn = {2524-6372}, support = {UOWX2101//Ministry of Business, Innovation and Employment/ ; }, abstract = {BACKGROUND: Forest restoration has primarily been evaluated through changes in aboveground communities, while belowground microbial communities-critical drivers of ecosystem functions-remain less understood. Moreover, studies of soil microbes have focused largely on community structure, which does not necessarily reflect the recovery of functional capacity and stability.

METHODS: To determine how forest restoration affects microbial community structure and function and how microbial diversity relates to ecosystem multifunctional potential and stability, we analysed soil microbial communities from 79 urban forest restoration sites across New Zealand, spanning 0-63 years since initial plantings. Shotgun metagenomic sequencing was used to characterize taxonomic composition and functional potential, with diversity quantified using alpha and beta metrics. To evaluate links between diversity and ecosystem function, we assessed ecosystem multifunctional potential (EMF) which describes the ecosystem's capacity to simultaneously provide multiple functions, and we developed a novel functional insurance (FI) index grounded in ecological theory as an indicator of functional stability and resilience. To calculate FI in microbial systems from sequencing data, we quantified functional overlap by estimating over 250 million species-function correlations per sample.

RESULTS: Contrary to our expectations, only beta diversity, not alpha diversity, was positively associated with EMF and FI, indicating that community composition and dissimilarity rather than species richness underpins microbial functional capacity and stability. EMF and FI were positively correlated, showing that high functional diversity and functional overlap can co-occur in microbial systems. In addition, archaeal turnover increased with closing forest canopies, contributing to higher EMF and FI, while bacterial turnover was only weakly associated with restoration parameters. Notably, restoration time did not play a role in shaping microbial diversity, EMF and FI.

CONCLUSIONS: Our findings demonstrate that microbial compositional turnover, rather than increases in species richness, are critical for restoring soil ecosystem functions. Incorporating microbial functional metrics like the FI index into restoration frameworks that recognise both above and belowground dynamics could promote resilient and multifunctional urban forests.}, } @article {pmid41981684, year = {2026}, author = {Clough, J and Mikac, KM}, title = {Metagenomic profiling of bacterial and fungal microbiota and putative pathogens of southern greater gliders (Petauroides volans).}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41981684}, issn = {2524-4671}, abstract = {BACKGROUND: The microbiome is significant for conservation biology and should be considered in threatened species management programs. Commensal microbes contribute important functions for host health, while pathogenic microbes can negatively impact the host, leading to morbidity, mortality, and population declines. Shotgun metagenomics, involving the agnostic sequencing of all DNA within a sample, has utility for simultaneous microbial community profiling and pathogen detection. Herein, we used shotgun metagenomics to profile the faecal bacteriome and mycobiome of the southern greater glider (Petauroides volans), an endangered Australian marsupial, and identify putative pathogens that could represent threats to population health. RESULTS: We analysed faecal samples collected from wild southern greater gliders (n = 48) across southeastern New South Wales, Australia. Geographic location had significant effects on both bacterial and fungal community composition. The bacteriome was dominated by Firmicutes, Proteobacteria and Bacteroidetes, with 58 core bacterial species shared among all locations. The mycobiome was dominated by the Ascomycetes, with 261 core fungal species shared among all locations. Geographic location was associated with significant differences in bacterial and fungal microbiota abundance but not host sex or weight. We identified 18 bacterial pathogens and 41 fungal pathogens of veterinary interest, ranging from low prevalence to ubiquitous. Bacteroides fragilis was associated with shifts in the Firmicutes:Bacteroidetes ratio, and therefore, potential dysbiosis. CONCLUSIONS: Geographic location is a key determinant of faecal microbial community structure and abundance in southern greater gliders. Core communities of faecal bacteria and fungi are conserved within and among populations. Southern greater gliders carry genetic material from a variety of putative bacterial and fungal pathogens. These microbes may present threats to the health of greater gliders, their possum relatives, or other animals in Australian forest ecosystems. Scientists and natural resource managers should consider the holobiont, rather than just the individual, when planning for conservation management actions such as translocation.}, } @article {pmid41981860, year = {2026}, author = {Liu, B and Yang, J and Wang, J and Zhang, J and Wang, L and Qu, B and Guo, L and Zhang, X and Yang, X and Jiang, Y}, title = {Application of Whole-Genome Sequencing and Metagenomic Sequencing in Microbial Analysis of Milk Powder and Its Processing Environment: Current Findings and Challenges.}, journal = {Comprehensive reviews in food science and food safety}, volume = {25}, number = {3}, pages = {e70478}, doi = {10.1111/1541-4337.70478}, pmid = {41981860}, issn = {1541-4337}, support = {//Danone Asia-Pacific Management Co. Ltd./ ; }, mesh = {Animals ; *Milk/microbiology ; *Whole Genome Sequencing ; *Metagenomics ; *Food Microbiology ; }, abstract = {As dairy enterprises increasingly focus on microbial contamination, traditional detection technologies are gradually showing limitations in terms of detection capability, accurate source tracking, and rapid response, especially when dealing with microbial communities in complex processing environments. Fortunately, whole-genome sequencing (WGS) and metagenomic sequencing provide innovative alternative solutions. These technologies significantly improve the detection of harmful microbes by offering strain-level resolution, detecting low-abundance organisms, and uncovering previously undetectable microbes. This review discusses the application of WGS and metagenomic sequencing in microbial monitoring, contamination source tracking, and quality control across the entire milk powder production chain. In particular, it highlights the progress made in microbial typing and source tracking, as well as in the detection of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). This review also compares microbial control standards for milk powder and its processing environment across different countries and international organizations, providing a regulatory perspective. Furthermore, the integration of emerging technologies is also discussed, particularly machine learning (ML) and deep learning (DL). Artificial intelligence (AI) enables more efficient, predictive, and accurate microbial monitoring, improving contamination control and contributing to safer and higher-quality milk powder production processes. This review provides critical insights that contribute to improving microbial safety management and control strategies in milk powder production.}, } @article {pmid41982876, year = {2026}, author = {Ren, J and Lan, Z and Wang, C and Zhu, J and Li, M and Xu, J and Lu, Y and Tu, J and Zhang, X and Boskovic, L and Huang, J and Hu, X}, title = {Metagenomic next-generation sequencing and conventional microbiology for microbial profiling in biliary tract infections: a comparative study with clinical stratification.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1799474}, pmid = {41982876}, issn = {1664-302X}, } @article {pmid41982885, year = {2026}, author = {Santiago-Rodriguez, TM and Toranzos, GA}, title = {Editorial: Advances in phage applications: deciphering phage biological and ecological mechanisms through metagenomics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1822387}, doi = {10.3389/fmicb.2026.1822387}, pmid = {41982885}, issn = {1664-302X}, } @article {pmid41982959, year = {2026}, author = {Zhang, K and Zheng, J and Wei, A and Qin, M and Zhu, G}, title = {Pulmonary infection caused by Tropheryma whipplei in a child before hematopoietic stem cell transplantation: a case report.}, journal = {Translational pediatrics}, volume = {15}, number = {3}, pages = {91}, pmid = {41982959}, issn = {2224-4344}, abstract = {BACKGROUND: Tropheryma whipplei (TW) triggers Whipple's disease (WD), a rare, chronic multisystemic infection with heterogeneous clinical presentations that can be easily overlooked, particularly Whipple's pneumonia. The advent of metagenomic next-generation sequencing (mNGS) technology applied to bronchoalveolar lavage fluid (BALF) analysis has enabled the identification of an increasing number of patients with acute pneumonia due to TW. Most reports describe symptomatic middle-aged males with cough, while asymptomatic pediatric cases remain exceptionally rare. Without adequate antibiotic therapy, WD is invariably fatal, especially in patients undergoing hematopoietic stem cell transplantation (HSCT). There is no established consensus on the optimal treatment regimen or duration, particularly for pediatric patients.

CASE DESCRIPTION: An 8-year-old boy with primary immunodeficiency due to a genetic mutation presented without respiratory symptoms. Yet, high-resolution computed tomography (HRCT) revealed nodular lesions. Initially misdiagnosed as a fungal infection, subsequent mNGS analysis of BALF identified TW as the sole pathogen, leading to a diagnosis of TW-associated pneumonia. Following a combined anti-infective therapy regimen, the patient successfully underwent the myeloablative conditioning (MAC) regimen. Neutrophil and platelet engraftment occurred promptly, with no severe transplant-related complications.

CONCLUSIONS: This retrospective analysis describes a clinical scenario involving a pediatric patient who exhibited no respiratory symptoms prior to transplantation but showed characteristic nodular lesions on imaging studies, ultimately confirming acute pneumonia caused by TW. Under a combination anti-infection regimen consisting of intravenous ceftriaxone, oral doxycycline, and oral hydroxychloroquine, the child tolerated the MAC regimen well. Neutrophil and platelet engraftment proceeded without delay, and follow-up imaging confirmed complete resolution of the pulmonary lesions.}, } @article {pmid41983569, year = {2026}, author = {Vogel, MA and Machairas, F and Ferchiou, S and Osvatic, J and Alzubaidy, H and Séneca, J and Hausmann, B and Klun, K and Petersen, JM}, title = {Symbiont diversity within Loripes orbiculatus and the case for multiple hosts.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41983569}, issn = {1751-7370}, support = {//WWTF Vienna Research Grant/ ; //ERC Starting Grant EvoLucin and ERC Consolidator Grant SeaSym/ ; 10.55776/COE7//Austrian Science Fund/ ; PCEGP3_181272//Swiss National Science Foundation Eccellenza/ ; 51NF40_180575//Swiss National Science Foundation National Center of Competence in Research Microbiomes/ ; 51N40_225148//Swiss National Science Foundation National Center of Competence in Research Microbiomes/ ; }, mesh = {Animals ; *Symbiosis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Sequence Analysis, DNA ; *Bivalvia/microbiology ; DNA, Bacterial/genetics/chemistry ; *Biodiversity ; Plant Roots/microbiology ; DNA, Ribosomal/genetics/chemistry ; }, abstract = {Seagrasses support immense biodiversity and are critical for maintaining coastal ecosystem health. These foundation species benefit from a "three-way" facultative relationship with one of the common inhabitants of seagrass meadows, lucinid bivalves, which host specific bacterial Candidatus Thiodiazotropha symbionts. Relatives of the bivalve symbionts have been detected on seagrass roots, raising the possibility that these symbionts may colonize both animals and plants; however, no study has yet compared bivalve- and seagrass-associated symbionts at the same site and time. Our combination of 16S ribosomal RNA (rRNA) gene amplicon and metagenome sequencing revealed a greater diversity than was previously observed within both lucinid bivalves and on seagrass roots from the Adriatic Sea and resulted in the closed genome of one prominent symbiont species. We show that two of the Ca. Thiodiazotropha ASVs found on seagrass roots are identical to those found in bivalve hosts at the same site. This suggests that symbiont sharing may occur in the seagrass habitat between these two host species, which has important evolutionary and ecological implications for both hosts and symbionts.}, } @article {pmid41983714, year = {2026}, author = {Viguier, C and Mansuy, JM and Martin-Blondel, G}, title = {Recent advances in flavivirus encephalitis.}, journal = {Current opinion in infectious diseases}, volume = {39}, number = {3}, pages = {189-200}, pmid = {41983714}, issn = {1473-6527}, mesh = {Humans ; *Flavivirus Infections/diagnosis/therapy/prevention & control ; *Flavivirus ; *Encephalitis, Viral/diagnosis/therapy/prevention & control ; Biomarkers ; Prognosis ; }, abstract = {PURPOSE OF REVIEW: Flaviviruses are an increasing public health concern, responsible for a broad spectrum of human disease ranging from asymptomatic or mild febrile illness to severe neuroinvasive infections such as encephalitis. Flavivirus encephalitis is associated with substantial mortality and long-term neurological sequelae, yet no specific antiviral therapy is currently available. Diagnosis remains challenging because of transient viremia and serological cross-reactivity, and preventive strategies are unevenly implemented. This review summarizes recent advances in the diagnosis, prognostic assessment, treatment, and prevention of flavivirus-associated encephalitis.

RECENT FINDINGS: Recent studies have reshaped diagnostic strategies through improved viral detection, including multimatrix molecular testing and metagenomic approaches, alongside better characterization of host-response markers in cerebrospinal fluid. Recent work has substantially refined understanding of host susceptibility, highlighting preexisting antitype I interferon autoantibodies as a major driver of severe disease across neurotropic flaviviruses, and identifying several biomarkers with potential prognostic value. Neuroimaging work has refined MRI pattern recognition across flaviviral encephalitis, with limited but evolving prognostic implications. While management remains largely supportive, the therapeutic pipeline is increasingly diverse, with growing interest in host-directed strategies.

SUMMARY: Flavivirus encephalitis represents a major clinical challenge driven by host vulnerability, diagnostic complexity, and the absence of validated therapies. Integrating recent advances in diagnostics, risk stratification, and prevention is essential, while ongoing therapeutic development offers cautious optimism for future management.}, } @article {pmid41983840, year = {2026}, author = {Ibadullayeva, A and Khamzina, A and Smagulov, D and Khamzin, K}, title = {An overview of the livestock microbiome: sheep, horses, cattle, camels, and chickens.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {86}, number = {}, pages = {e299936}, doi = {10.1590/1519-6984.299936}, pmid = {41983840}, issn = {1678-4375}, mesh = {Animals ; Camelus/microbiology ; *Microbiota/genetics ; Cattle/microbiology ; Chickens/microbiology ; Sheep/microbiology ; Horses/microbiology ; *Livestock/microbiology ; RNA, Ribosomal, 16S ; }, abstract = {The animal microbiome plays a crucial role in determining the health, productivity, and welfare of livestock species, including sheep, horses, cattle, camel, and chicken. These animal species were selected due to the high consumption of their products in Kazakhstan. Enhancing their productivity, while maintaining the safety and quality of meat and milk derived from them, represents a pressing research priority. This review article includes current research on the composition, diversity, and purposes of the microbiota found within different organ systems of these species. This study focuses on recent advancements in sequencing technology, including metagenomics, 16S rRNA sequencing, and multiomic methods, to combine data on microbial diversity, composition, and functionality within the gastrointestinal tract and other organs. The key findings show differences in microbial communities associated with breed, age, and diet, the impact of microbiota on methane emissions and feed efficiency in ruminants, and the possibility of using microbiome management techniques (e.g., probiotics, prebiotics, and feed additives) to enhance livestock production. The microbiome influences various species, extending its effects beyond digestion and immunity to reproductive health and behavior. Despite advancements, translating microbiome data into actionable interventions is interfered by variability resulting from genetic, environmental, and management factors. Integrating microbiome research more closely with animal genetics and livestock production methods could lead to innovative approaches for improving the health, efficiency, and welfare of farm animals, ultimately supporting sustainable livestock farming practices.}, } @article {pmid41983925, year = {2026}, author = {El Zibaoui, R and Venkatesan, A}, title = {An update on infectious encephalitis: from epidemiology to management.}, journal = {Current opinion in infectious diseases}, volume = {39}, number = {3}, pages = {208-217}, pmid = {41983925}, issn = {1473-6527}, mesh = {Humans ; *Infectious Encephalitis/epidemiology/diagnosis/therapy/virology ; Animals ; Antiviral Agents/therapeutic use ; Communicable Diseases, Emerging/epidemiology/diagnosis ; Global Health ; Arboviruses ; }, abstract = {PURPOSE OF REVIEW: Infectious encephalitis (IE) is a serious neurological condition that poses a major global health threat. This review summarizes emerging pathogens, particularly arboviruses, updated diagnostic strategies, and evolving treatment approaches, emphasizing ongoing gaps in diagnosis and management.

RECENT FINDINGS: Established arboviruses such as West Nile virus, Japanese encephalitis virus, Powassan virus, and Eastern Equine virus have regained attention due to their geographic expansion and the appearance of distinct genotypes. In parallel, increasing reports of encephalitis by newly emerging pathogens such as Oropouche virus and scrub typhus speak to the evolving nature of the epidemiology of IE. Advances in diagnostics, including multiplex PCR and metagenomic next-generation sequencing, have enhanced the breadth and accuracy of pathogen identification. As treatment options remain scarce, the role of immunomodulatory agents and novel antiviral molecules in the management of IE is actively being investigated.

SUMMARY: The emergence of novel and reemerging pathogens highlights the need for rapid, accurate diagnostics. Advanced molecular techniques and the identification of novel therapeutic targets have the potential to change the landscape of IE. However, strengthening surveillance and vaccination strategies, along with ongoing efforts in vaccine development, remain crucial for optimizing patient outcomes, increasing public health preparedness, and mitigating future outbreaks.}, } @article {pmid41984378, year = {2026}, author = {Tao, X and Du, Z and Wang, X and Lv, L and Zhang, G and Liang, J and Zou, W}, title = {Volatile Fatty Acid Production from Baijiu Distillers' Grains Via Anaerobic Fermentation with Rumen Microbes: Performance and Mechanism.}, journal = {Applied biochemistry and biotechnology}, volume = {198}, number = {7}, pages = {5192-5211}, pmid = {41984378}, issn = {1559-0291}, support = {52400160//National Natural Science Foundation of China/ ; 52360020//National Natural Science Foundation of China/ ; E2024202030//Natural Science Foundation of Hebei Province/ ; RKJH[2025]26//Renhuai Municipal Science and Technology Program/ ; Qiankehe Jichu QN [2025] 292//Youth Science and Technology Talent Project of the Guizhou Provincial Basic Research Program/ ; }, } @article {pmid41984912, year = {2026}, author = {Fri, J and Njanje, I and Mahopo, TC and Mavhandu-Ramarumo, LG and Bessong, PO and , }, title = {The Gut Bacterial Resistome in the First Two Years of Life: Protocol for a Longitudinal Observational Birth Cohort Study.}, journal = {JMIR research protocols}, volume = {15}, number = {}, pages = {e86058}, pmid = {41984912}, issn = {1929-0748}, mesh = {Humans ; Longitudinal Studies ; Female ; Birth Cohort ; Prospective Studies ; Infant, Newborn ; Infant ; *Gastrointestinal Microbiome/drug effects ; South Africa ; *Drug Resistance, Bacterial ; Risk Factors ; Male ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global health threat that increases the burden of infectious diseases and disproportionately affects communities of low socioeconomic status. Despite the call for community-level AMR data, prospective studies from rural sub-Saharan African communities to inform appropriate targeted interventions remain scarce. Given the role of enteric bacteria in AMR transmission dynamics, there is a need to understand the timing, risk factors, and ecological drivers of gut resistome acquisition and development during infancy.

OBJECTIVE: This study aimed to characterize the temporal dynamics of enteric bacterial resistomes during the first 2 years of life and to identify drivers of AMR acquisition and development in a community-based, prospective, observational birth cohort study in a rural South African community.

METHODS: The study aims to enroll 200 newborns and their mothers within 17 days post partum. Data on key exposures and variables include sociodemographics; perinatal and anthropometrics; feeding practices and dietary exposures; illness, medication, and vaccination history; breast milk metabolomic profiles; household socioeconomic status; maternal psychosocial and behavioral factors; hygiene and sanitation practices; and environmental exposures including hydro-meteorological variables, in-house livestock and pets, and drinking water quality. Biological samples include stools from monthly collections and diarrhea episodes for metagenomic analysis and breast milk for metabolomics. Planned analyses include assessing the infant microbiome and resistome structure (diversity, abundance, and composition) across time points and modeling associations between risk factors and AMR outcomes. Additionally, a cross-sectional community survey on knowledge, attitudes, and practices regarding antimicrobial use is conducted to inform knowledge translation through responsive dialogues, thereby developing ethnographically relevant packages for community-level AMR stewardship.

RESULTS: Participant identification and enrollment began in August 2023. By October 2025, 167 newborns had been enrolled, with 20 having completed the 24-month follow-up. The characteristics of the enrolled participants are presented in this protocol.

CONCLUSIONS: This study will offer a unique opportunity to generate longitudinal resistome data from a rural sub-Saharan African setting. The study is expected to contribute knowledge on the microbiome and resistome structure dynamics and trajectories associated with key risk factors of acquisition and development. In addition, co-produced ethnographically tailored educational packages, informed by knowledge, attitudes, and practices and bacterial resistome data, will drive sustainable community-centered AMR awareness interventions.}, } @article {pmid41985067, year = {2026}, author = {Sarmah, MP and Zoramthara, K and Manngaihsiam, R and Boro, HH and Baraka, AGA and Saeed, AL and Gurusubramanian, G and Kharat, KR}, title = {Microbiome Simplification During Metamorphosis in Larva and Adults of Armigeres subalbatus (Coquillett, 1898) (Culicidae) Revealed by Shotgun Metagenomics.}, journal = {Archives of insect biochemistry and physiology}, volume = {121}, number = {4}, pages = {e70159}, doi = {10.1002/arch.70159}, pmid = {41985067}, issn = {1520-6327}, support = {EM/Dev/11/SG/01993/2024//Indian Council of Medical Research/ ; DST/INSPIRE Fellowship/[IF240039]//Department of Science & Technology, New Delhi, India (INSPIRE-JRF)/ ; }, mesh = {Animals ; Larva/microbiology/growth & development ; Metagenomics ; *Microbiota ; *Metamorphosis, Biological ; *Culicidae/microbiology/growth & development ; Bacteria/classification/genetics ; }, abstract = {Armigeres subalbatus is medically significant vector for filarial worms and the Japanese encephalitis virus. Shotgun metagenomic sequencing was employed to investigate the bacterial communities in A. subalbatus mosquitoes. The diversity metrics (Shannon H', Simpson 1-D, Berger-Parker) were calculated for larval and adult stages. De novo assembly and binning were used to recover metagenome-assembled genomes (MAGs) with > 82% completeness and < 4% contamination. Functional profiling assessed gene expression via transcripts per million (TPM) and clusters of orthologous groups (COG) categories. Larval microbiomes showed high alpha diversity (Shannon H' ≈ 1.336 ± 0.163, Simpson 1-D = 0.684 ± 0.046), dominated by Gammaproteobacteria (Aeromonas, Morganella, and Yersinia) and Bacteroidota, with persistent Shewanella and Acinetobacter. Adult microbiomes exhibited low diversity (Shannon H' = 0.637 ± 0.100, Berger-Parker = 0.682 ± 0.026), near-monoculture dominated by Aeromonas hydrophila, alongside low-abundance Stenotrophomonas, Pseudomonas, and Microbacterium. Six high-quality MAGs were recovered: larval (Bacteroidota, Shewanella, and Acinetobacter); adult (Acinetobacter, Stenotrophomonas, and Shewanella), confirming persistence of Shewanella and Acinetobacter, absence of Bacteroidota, and emergence of Stenotrophomonas in adults. Adult microbiomes displayed metabolic hyperactivity, with 1.5-4 times higher transcriptional output across COG categories compared to larvae. Chemotaxis [Methyl-accepting chemotaxis protein (MCP), K03406: ~6000 TPM in adults vs. < 1000 TPM in larvae] and ABC transporters (PF00005: > 10,000 TPM in adults) dominated adults, while larval expression was balanced among housekeeping functions. The microbiome undergoes significant restructuring during mosquito development, shifting from diverse larval communities to metabolically active, low-diversity adult assemblages. Recovered MAGs provide a genomic basis for future studies on mosquito microbiota dynamics and functions.}, } @article {pmid41985316, year = {2026}, author = {Ariaee, A and Hunter, A and Wignall, A and Bremmell, K and Prestidge, C and Joyce, P}, title = {Spray dried inulin-montmorillonite hybrids alleviate high-fat diet-induced inflammatory and metabolic dysregulation in rats.}, journal = {Biomaterials advances}, volume = {185}, number = {}, pages = {214878}, doi = {10.1016/j.bioadv.2026.214878}, pmid = {41985316}, issn = {2772-9508}, mesh = {Animals ; *Inulin/chemistry/pharmacology ; *Diet, High-Fat/adverse effects ; *Bentonite/chemistry/pharmacology ; Rats ; Male ; *Inflammation/metabolism/drug therapy/chemically induced ; Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; Lipid Metabolism/drug effects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Metabolic dysregulation is strongly associated with excessive dietary lipid absorption and gut microbiota imbalances under high-fat diet (HFD) conditions. This study evaluates a spray-dried inulin-montmorillonite (INU-MMT) hybrid designed to simultaneously restrict intestinal lipid digestion and modulate gut microbiota composition. In simulated intestinal digestion, INU-MMT maintained the strong lipid-inhibitory effect of montmorillonite, reducing free fatty acid release by 2.8-fold compared to HFD conditions, while exhibiting improved dispersion stability attributed to INU's ability to reduce clay platelet aggregation. In a 21-day HFD-fed rat model, INU-MMT supplementation (1 g/kg/day) attenuated cumulative weight gain by 4.7% compared to the HFD control, exceeding reductions with INU (2.0%) and MMT (1.5%) alone. 16S rRNA gene sequencing of fecal samples revealed improved gut microbial diversity (Simpson's index, p = 0.0161) and uniquely enriched health-associated taxa including Akkermansiaceae (2.5-fold), Eggerthellaceae (7.7-fold), Ruminococcaceae (3.5-fold), and Peptostreptococcaceae (8-fold). Beta diversity analysis highlighted that INU-MMT induced a distinct microbial composition from INU, suggesting the complimentary effects of the hybrid promote a more widespread microbial change than prebiotic alone. Predictive metagenomic analysis using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) software demonstrated a 98% reduction in microbial triacylglycerol lipase abundance, consistent with the observed in vitro lipolysis suppression. These findings demonstrate that the INU-MMT hybrid preserves MMT's restriction of lipid digestion while delivering INU's prebiotic benefits, producing additive effects in diet-induced weight gain and microbiota modulation. The multifunctional nature of this spray-dried hybrid highlights its potential as a dietary strategy for metabolic dysregulation.}, } @article {pmid41985330, year = {2026}, author = {Kwiendacz, H and Cembrowska-Lech, D and Skonieczna-Żydecka, K and Klimontowicz, K and Podsiadło, K and Wierzbicka-Woś, A and Styburski, D and Kaczmarczyk, M and Gumprecht, J and Łoniewski, I and Nabrdalik, K}, title = {Multi-strain probiotic enhances metformin tolerance by modulating gut microbiome and bile acid pathways: Insight from multi-omics post-hoc analysis (ProGasMet trial).}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {198}, number = {}, pages = {119370}, doi = {10.1016/j.biopha.2026.119370}, pmid = {41985330}, issn = {1950-6007}, mesh = {*Metformin/adverse effects ; Humans ; *Bile Acids and Salts/metabolism ; *Probiotics/therapeutic use/administration & dosage ; Multiomics ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; *Hypoglycemic Agents/adverse effects ; Metabolomics ; Feces/microbiology ; Diabetes Mellitus, Type 2/drug therapy ; Male ; Female ; }, abstract = {BACKGROUND: Metformin is the cornerstone therapy for type 2 diabetes, but gastrointestinal intolerance commonly limits dose escalation and long-term adherence. In the ProGasMet trial, multi-strain probiotic supplementation improved metformin tolerability. However, the underlying microbiome-metabolome mechanisms remain unclear.

METHODS AND ANALYSIS: We performed an exploratory multi-omics analysis using Period 1 of a randomized, double-blind, placebo-controlled trial. Participants with metformin intolerance received a multi-strain probiotic or placebo for 12 weeks. Paired stool samples collected at baseline and end of treatment were available from 34 participants (68 samples). We integrated shotgun metagenomic species profiles, predicted gut metabolic modules, and untargeted faecal LC-MS metabolomics using multi-block sparse PLS (DIABLO), complemented by longitudinal covariate-adjusted feature-level analyses and associations with gastrointestinal symptom burden (QACSMI and a simplified GI score).

RESULTS: In multi-omics integration at 12 weeks, bile acid-related metabolites were among the strongest contributors to group separation, with hyodeoxycholic acid and related compounds enriched in the probiotic arm. Global biodiversity and community-wide turnover did not differ between groups. Feature-level analyses suggested modest, directionally coherent changes in selected taxa, functional modules, and metabolites. Higher hyodeoxycholic acid concentrations were associated with lower gastrointestinal symptom burden in probiotic-treated participants, a pattern not observed under placebo.

CONCLUSION: Probiotic supplementation may be associated with coordinated microbiome-metabolome shifts in metformin-intolerant type 2 diabetes, highlighting bile acid remodelling, particularly hyodeoxycholic acid, as a plausible candidate for improved tolerability. These results support prioritising secondary bile acid-microbiome pathways for confirmation in larger trials incorporating targeted bile acid quantification and causal modelling.}, } @article {pmid41985671, year = {2026}, author = {Wang, Y and Liu, X and Li, Z and Kang, A and Bai, Y and Wang, Y and Liu, Y and Zhang, C and Yang, J and Cai, Q and Feng, Y and Yi, H and Zhang, M and Zhang, F and Liu, H and Xu, C}, title = {Oligofructose alleviates hyperandrogenism in polycystic ovary syndrome through gut microbiota-derived bile acids.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.04.036}, pmid = {41985671}, issn = {2090-1224}, abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is a common endocrine disorder in reproductive-age women, characterized by hyperandrogenism and metabolic dysfunction. Dietary interventions are recommended as one of the first-line therapies. Oligofructose (OFS), a prebiotic fiber, has demonstrated clinical benefits in PCOS; however, its underlying mechanism remains unclear.

OBJECTIVES: To determine whether OFS alleviates PCOS-like phenotypes through bile acid-dependent mechanisms and to identify downstream ovarian steroidogenic responses.

METHODS: Letrozole-induced PCOS-like mice received OFS supplementation. Microbiota dependence was assessed using antibiotic depletion and fecal microbiota transplantation. Bile acid involvement was evaluated using cholestyramine. Gut microbial composition and function were profiled by 16S rRNA and metagenomic sequencing, and bile acids were quantified by UHPLC-MS/MS. Ovarian transcriptomics, ex vivo ovarian explants, and primary granulosa cells were used to examine steroidogenic changes, with pharmacological inhibition applied to assess TGR5-related signaling.

RESULTS: OFS improved reproductive and metabolic abnormalities in PCOS-like mice. These benefits were abolished by microbiota depletion and bile acid sequestration, indicating microbiota- and bile acid-dependent effects. OFS was associated with increased circulating hyodeoxycholic acid (HDCA), which negatively correlated with serum testosterone. HDCA supplementation partially reproduced endocrine improvements under microbiota-depleted conditions. Ovarian transcriptomic and functional analyses demonstrated enhanced aromatization following OFS treatment. In ex vivo ovarian explants and primary granulosa cells, HDCA increased estradiol production, reduced testosterone, and upregulated CYP19A1 (encoding aromatase). Under androgen stimulation, pharmacological inhibition of TGR5 attenuated HDCA-associated increases in estradiol and aromatase activity, supporting involvement of TGR5-related signaling.

CONCLUSION: OFS alleviates PCOS-like phenotypes in a microbiota- and bile acid-dependent manner and enhances ovarian aromatization. These findings move beyond descriptive bile acid alterations in PCOS by providing functional evidence that dietary fiber-induced bile acid remodeling is associated with modulation of ovarian steroidogenic regulation.}, } @article {pmid41986005, year = {2026}, author = {Ansari, A and Shete, O and Ghosh, TS}, title = {Artificial intelligence in microbial metagenomics.}, journal = {Progress in molecular biology and translational science}, volume = {221}, number = {}, pages = {255-276}, doi = {10.1016/bs.pmbts.2026.01.009}, pmid = {41986005}, issn = {1878-0814}, mesh = {*Metagenomics ; *Artificial Intelligence ; Machine Learning ; Humans ; *Microbiota/genetics ; }, abstract = {Rapid advancements in genomic sequencing technologies and similar technological advancements in the area of accessing, isolating, extracting and functional probing of microbes residing in diverse environments has resulted in a deluge of microbiome sequencing and microbial genomic sequencing data. Concomitant developments in the area of data science, specifically in the domains of advanced statistics, and artificial intelligence (AI) can facilitate mining this data to answer complex biological questions and developing translational applications in diverse areas, ranging from health-care to industrial microbiology. For most researchers, information on which AI tools address specific biological questions is scattered across disparate sources. In this chapter, we explore the various applications of AI-based methodologies (using case-studies) in answering different biological questions using microbial genomics and metagenomic data. We also discuss different AI and machine-learning (ML) based approaches to integrate metagenomic data with other "omics" data. Finally, we highlight both challenges and possibilities with this rapidly progressing field.}, } @article {pmid41986051, year = {2026}, author = {}, title = {Correction to 'Clinical Value of Metagenomic Next-Generation Sequencing in Early Diagnosis of Peritoneal Dialysis-Associated Peritonitis: A Randomised Controlled Observational Trial'.}, journal = {Nephrology (Carlton, Vic.)}, volume = {31}, number = {4}, pages = {e70203}, doi = {10.1111/nep.70203}, pmid = {41986051}, issn = {1440-1797}, } @article {pmid41986587, year = {2026}, author = {Ishibashi, N and Akase, Y and Ito, A and Kishimoto, K and Watanabe, S and Yokoyama, H and Mekata, T}, title = {Genome characterization and environmental DNA-based detection of a novel adenovirus from red seabream (Pagrus major).}, journal = {Archives of virology}, volume = {171}, number = {5}, pages = {}, pmid = {41986587}, issn = {1432-8798}, support = {25K09243//JSPS KAKENHI/ ; }, abstract = {A novel piscine adenovirus, Pagrus major adenovirus 1 (PmAdV-1), was identified in red seabream (Pagrus major) by metagenomic sequencing. The 29,519 bp genome encodes 22 predicted open reading frames and exhibits a unique organization, with the fiber gene positioned upstream of the conserved adenovirus gene cluster. Phylogenetic analyses indicate that PmAdV-1 forms a sister lineage to red-eared slider adenovirus 1 within a clade of fish and reptilian adenoviruses, but its assignment to the genus Testadenovirus remains uncertain. A virus-specific qPCR assay was developed to monitor PmAdV-1 in environmental DNA from rearing seawater. Viral loads transiently increased in some juvenile tanks without marked mortality. These findings expand current knowledge of fish adenovirus diversity.}, } @article {pmid41986605, year = {2026}, author = {Sumithra, TG and Gayathri, S and Mannur, VS and Neethu, N and Ratheesh Kumar, R and Nair, AV and Ratheesh, L and Zainul Abid, PM and Sundari, BKR and Dharani, G and Krupesha Sharma, SR}, title = {Bathymetry and environmental features govern the microbial communities in mesopelagic sediments of the Lakshadweep Islands of India.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41986605}, issn = {2045-2322}, support = {Deep-sea Metagenomics for enhanced next-generation bioethanol production' under Deep Ocean Mission (DOM) [MoES/PAMC/DOM/176/2023 (E-14624)]//Ministry of Earth Sciences/ ; }, abstract = {UNLABELLED: Mesopelagic sediments represent a critical yet understudied component of marine ecosystems, where environmental gradients strongly influence microbial community structure and function. This study profiles prokaryotic and fungal communities in the sediments along a bathymetric transect (500–1000 m) on the upper continental slope of the Lakshadweep Sea to identify community assembly processes and environmental drivers. Mesopelagic sediments supported diverse prokaryotic and fungal assemblages, with prokaryotes exhibiting higher α-diversity indices than fungi, indicating differential ecological adaptation of prokaryotic and fungal groups. Bacteria dominated over Archaea, with Firmicutes, Chloroflexi, Bacteroidota, Proteobacteria, and Desulfobacterota as the major prokaryotic phyla. Ascomycota and Basidiomycota were the major fungi. Diversity varied significantly (p ≤ 0.05) with depth, and most microbes were habitat specialists, indicating strong vertical structuring. The FEAST analysis revealed a limited proportional contribution of microbial communities in deeper sediments from 500 m. Beta nearest taxon index analysis suggested a dominant role of deterministic processes in governing the microbial community assembly. Canonical correspondence analysis identified temperature and DO as key drivers of prokaryotes, and nitrogen and temperature for fungi. Depth was significantly correlated (p ≤ 0.05) with the relative abundance of certain microbial taxa, including a decline in bacterial abundance and an increase in archaeal abundance, as well as positive associations with Dadabacteria, Halobacterota, and Chytridiomycota. This first study from the Lakshadweep Sea provides new insights into tropical mesopelagic sediment microbial diversity and community assembly, highlighting bathymetric and environmental controls that shape the prokaryotic and fungal communities.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-48651-8.}, } @article {pmid41986657, year = {2026}, author = {Luchen, CC and Piedade, GJ and Chibuye, M and Simuyandi, M and Chisenga, CC and Chilengi, R and Bosomprah, S and Schultsz, C and Mende, DR and Harris, VC}, title = {Distinct infant resistome trajectories shaped by country income and geography revealed through global metagenomics reanalysis.}, journal = {npj antimicrobials and resistance}, volume = {4}, number = {1}, pages = {}, pmid = {41986657}, issn = {2731-8745}, support = {2023159//Amsterdam University Medical Center Amsterdam Public Health Research Institute/ ; LSHM23007//Track-AMR/ ; LSHM23007//Track-AMR/ ; 09150161810022//Netherlands Organisation for Health Research and Development (ZonMw) VENI/ ; 219775/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; LSHM21033//Co-funding by PPP Allowance awarded by Health~Holland, Top Sector Life Sciences & Health GLORIA/ ; AI173360/NH/NIH HHS/United States ; }, abstract = {Antimicrobial resistance (AMR) costs lives, diminishes antimicrobial effectiveness and increases health care costs. We conducted a re-analysis of pooled fecal metagenomes from individual participants to characterise AMR gene (ARG) distributions in 0-2 year-old healthy infants across income and geography. From 2275 screened studies, we included nine datasets and 1944 fecal metagenomes. Resistome gene identifier (RGI) was used to identify ARGs, and gut microbiomes were profiled using Sylph. We assessed associations between ARGs, Escherichia coli abundance, and national-level indicators. In the first 3 months of life, ARG abundance patterns were not significantly different across income groups; however, by 6 months of age, infants in LICs had higher ARG abundance, associated with increased E. coli carriage. Caesarean section rates, antibiotic use, and income inequality positively correlated with ARG abundance in younger infants; physician density negatively correlated with ARG abundance in older children. These descriptive age- and context-specific associations may inform interventions to mitigate the carriage and spread of ARGs and the rise of AMR in vulnerable pediatric populations.}, } @article {pmid41986663, year = {2026}, author = {Luiken, REC and Prinsen, H and Dasari, SN and Zweerus, H and Timmerman, AJ and Speksnijder, DC and Dohmen, W and Wagenaar, JA and Heederik, DJJ and Zomer, AL}, title = {Changes in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions.}, journal = {npj antimicrobials and resistance}, volume = {4}, number = {1}, pages = {}, pmid = {41986663}, issn = {2731-8745}, abstract = {The use of antimicrobials in livestock farming drives selection and dissemination of antimicrobial resistance (AMR), prompting implementation of veterinary stewardship programs to reduce antimicrobial usage (AMU). We evaluated changes in AMR on 45 Dutch pig farms before and after tailored, coaching-based interventions using phenotypic testing of Escherichia coli and metagenomic profiling of pooled faeces. Post-weaning pig farms, including nursery and fattening units, entered the intervention in a stepped-wedge design, with intervention periods ranging from 10 to 27 months. Across farms, AMU and abundances of several antimicrobial resistance gene classes declined over time, alongside reductions in overall resistome levels. Proportions of phenotypic AMR in E. coli were more variable, although decreased AMU was associated with lower resistance for specific antimicrobial classes, such as tetracyclines and beta-lactams. While longer follow-up is required to fully assess long-term impacts, these findings indicate that veterinary antimicrobial stewardship programs can yield measurable short-term reductions in AMR at farm level.}, } @article {pmid41986664, year = {2026}, author = {Frey, B and Varliero, G and Rüthi, J and Alekseev, I and Qi, W and Povazhnyi, V and Zemlianskii, V and Stierli, B and Ermokhina, K and Schaepman-Strub, G and Cuartero, J}, title = {Metagenomic insights into viral and microbial genes of Russian High-Arctic soil microbiomes.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41986664}, issn = {2399-3642}, mesh = {*Soil Microbiology ; *Microbiota/genetics ; Arctic Regions ; *Metagenomics ; *Metagenome ; Russia ; *Bacteria/genetics ; *Genes, Microbial ; }, abstract = {High-Arctic soils are extreme ecosystems where microbial and viral roles remain poorly studied. Climate-driven vegetation expansion may alter these environments, but its impact is unknown. We generate a shotgun metagenomic database from four High-Arctic islands, comparing vegetated and unvegetated sites at two depths (0-2 cm and 30-50 cm). We analyse the functional gene potential, including biosynthetic gene clusters (BGCs) and antibiotic resistance genes (ARGs) in metagenome-assembled genomes (MAGs), and assess viral diversity. Vegetated soils at 30-50 cm were enriched in genes for carbon/nitrogen cycling, energy production, and carbohydrate metabolism, indicating enhanced nutrient inputs. Conversely, unvegetated soils show higher BGC and ARG richness, reflecting microbial competition under nutrient limitation. Viral richness decreases in surface vegetated soils, while diversity and giant virus (Nucleocytoviricota) abundance increase with depth. These findings reveal how vegetation and soil depth modulate microbiomes and viromes, critical for predicting ecosystem trajectories in a warming world.}, } @article {pmid41986859, year = {2026}, author = {Iñiguez-Luna, MI and Gómez-Godínez, LJ and Cadena-Zamudio, JD and Cadena-Zamudio, DA and Aguirre-Noyola, JL and Barrera-Guzmán, LA}, title = {Omics Sciences: Driving the Conservation and Characterization of Plant Genetic Resources.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3011}, number = {}, pages = {345-364}, pmid = {41986859}, issn = {1940-6029}, mesh = {Multiomics/methods ; *Genomics/methods ; Metabolomics/methods ; *Plants/genetics/metabolism ; Crops, Agricultural/genetics ; Genome, Plant ; Proteomics/methods ; *Conservation of Natural Resources/methods ; Computational Biology/methods ; Biodiversity ; Plant Breeding/methods ; }, abstract = {Omics sciences have revolutionized the conservation and characterization of plant genetic resources by enabling a comprehensive understanding of genetic diversity, molecular mechanisms, and adaptive traits. Advances in genomics, transcriptomics, proteomics, metabolomics, and metagenomics have facilitated the identification of genes and metabolic pathways associated with stress tolerance, nutritional value, and agronomic performance. These technologies have enhanced the efficiency of germplasm banks by improving genetic resource characterization, optimizing conservation strategies, and accelerating breeding programs for climate-resilient crops. Additionally, omics approaches contribute to biodiversity conservation by revealing evolutionary relationships, ecosystem dynamics, and the functional roles of microbial communities in plant health. The integration of multi-omics data with bioinformatics and artificial intelligence further enhances predictive capabilities, enabling targeted conservation and breeding efforts. This review highlights the pivotal role of omics sciences in securing plant genetic resources for sustainable agriculture and global food security.}, } @article {pmid41987827, year = {2026}, author = {Bornbusch, SL and Thacher, PR and Francisque, M and DeCandia, AL and Bortner, R and Garelle, D and Kendrick, EL and Maslanka, MT and Muletz-Wolz, CR}, title = {How "pro" are probiotics for wildlife species? Novel data, lack of evidence, and future directions.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag036}, pmid = {41987827}, issn = {2730-6151}, abstract = {Treatments that aim to purposefully manipulate host-associated microbiomes are now prevalent in human and animal medicine. Probiotics that contain live bacteria are purported to improve microbiome function and host health. Although research is advancing, commercial probiotic development has outpaced empirical study of probiotic efficacy. Probiotics are widely used in ex-situ wildlife care despite a lack of empirical study or support. We interrogate the relevance of commercial probiotics in ex-situ wildlife by (a) sequencing the composition of commercial probiotics used to treat wildlife, (b) comparing the probiotic sequences to data on the microbiomes of >900 animal species, and (c) characterizing the effects of a commercial probiotic on probiotic colonization, prevalence of a potential enteric pathogen (Clostridium perfringens), and metagenomic function in endangered black-footed ferrets (Mustela nigripes). We found mislabeling and potential contaminants in probiotics marketed for a range of species. The probiotic bacteria were rare or absent in published animal microbiomes. In black-footed ferrets, probiotic treatment induced minimal probiotic colonization, negligible functional change, and limited influence on the potential enteric pathogen. Given our findings, which reiterate concerns about the efficacy of commercial probiotics across human and animal sectors, greater effort must be put towards identifying species-specific probiotic candidates and studying alternative microbial therapies for wildlife under human care.}, } @article {pmid41987902, year = {2026}, author = {De, R and Kanungo, S and Mukhopadhyay, AK and Dutta, S}, title = {Comparative metagenomic analysis of diarrheal and non-diarrheal gut microbiome delineating the identification of prospective prognostic markers and probiotics to protect from diarrhea: a brief report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1729497}, pmid = {41987902}, issn = {2235-2988}, mesh = {Humans ; *Diarrhea/microbiology/prevention & control/diagnosis ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Feces/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; Female ; *Probiotics/therapeutic use ; Pilot Projects ; Male ; Prognosis ; *Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Prospective Studies ; DNA, Bacterial/genetics/chemistry ; Metagenome ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {INTRODUCTION: Diarrhea is a leading contributor of mortality globally. To mitigate its disease burden, improved prognosis and alternative therapeutic approaches must be deployed. A cross-sectional gut microbiome analysis of 23 non-diarrheal and 5 diarrheal fecal samples was conducted with the aim of meeting the WHO's GAPPD (Global Action Plan for Pneumonia and Diarrhea) goals.

HYPOTHESIS: Next-generation sequencing is a potent tool being increasingly used for epidemiological surveillance. It can help in the comparison of the structural diversity of the gut microbiome between diarrheal and non-diarrheal samples, thereby aiding in the identification of prospective prognostic and therapeutic candidates.

AIM: The pilot study was designed to identify prospective taxa that were comparatively enriched in non-diarrheal samples and to predict gut microbial community interactions.

METHODOLOGY: 16S rRNA amplicon sequencing and subsequent analysis were undertaken for taxonomic profiling and abundance interpretation of OTUs.

RESULTS: Significant differences between the two groups with respect to structural composition was revealed. Firmicutes was the most abundant phylum in the majority of the samples. The B/F ratio was consistently <1 in all diarrheal samples. A significant difference in the mean B/F ratio of the two groups was found. Proteobacteria was significantly more abundant in the diarrheal group. On the other hand, Prevotellaceae was the most abundant family in non-diarrheal samples and was suppressed significantly in diarrheal samples. Streptococcaceae was the most abundant family in 60% of diarrheal samples; where Streptococcaceae was suppressed, Bacteroideaceae and Nocardiaceae were the most abundant. In non-diarrheal samples, where Streptococcaceae was almost completely suppressed, Bifidobacteriaceae was the most abundant and significantly suppressed other families. A negative correlation was observed between Prevotellaceae and Bacteroideaceae in the non-diarrheal group. Prevotella copri was the most abundant species in 70% of non-diarrheal samples and was significantly suppressed in diarrheal samples. Proteus mirabilis was identified in all the non-diarrheal samples, while they were absent in diarrheal samples.

CONCLUSION: The OTUs associated with diarrheal dysbiosis can serve as prognostic markers. To our knowledge, this is the first report on the comparative analysis of diarrheal and non-diarrheal microbiome, distinctly addressing the gut microbiome dysbiosis from the context that can lead to the development of prognostic markers and probiotics to protect the endemic population from diarrhea and help in achieving Sustainable Development Goals 2 and 3.}, } @article {pmid41988145, year = {2026}, author = {Liu, L and Wang, L and Zhang, P and Gan, M and Liujiang, R and Cheng, G and Ge, M}, title = {Neonatal herpes simplex virus encephalitis: a single-center retrospective study of 14 cases.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1740937}, pmid = {41988145}, issn = {2296-2360}, abstract = {BACKGROUND: This single-center retrospective study aims to analyze the clinical characteristics, treatment strategies, and outcome at discharge of neonatal-onset herpes simplex virus encephalitis (NHSE).

METHODS: We conducted a single-center retrospective case review of infants diagnosed with NHSE at the Children's Hospital of Fudan University between February 1, 2016, and February 1, 2024. Clinical data, including demographics, clinical symptoms, laboratory findings, neuroimaging results, treatment regimens, and outcomes at discharge, were collected and analyzed.

RESULTS: A total of 14 infants with NHSE (7 males, 7 females) were identified at our center, with a median age at diagnosis of 26 days (range: 7-51 days). Initial symptoms predominantly included fever and seizures, with neurological involvement (e.g., seizures, lethargy, irritability or altered mental states) in 13 cases. Physical examinations, such as bulging anterior fontanel, were noted. Herpes simplex virus (HSV)-DNA was detected in 13 cases (6 HSV-1, 7 HSV-2) through cerebrospinal fluid (CSF) polymerase chain reaction (PCR) or metagenomic testing. Among these, 9 cases were identified via CSF-PCR, with 7 testing positive on the initial examination and 2 on repeated testing. Notably, 6 cases were diagnosed using metagenomic next-generation sequencing (mNGS), all of which yielded positive results on the first test. Ten out of the 12 children often exhibited temporal lobe spikes on video electroencephalograms (VEEGs). Early magnetic resonance imaging (MRI) revealed cytotoxic edema, progressing to multicystic encephalomalacia. All received acyclovir antiviral treatment. Seven discontinued treatments, one was referred for ocular lesions, and six improved and were discharged.

CONCLUSIONS: In this single-center cohort, NHSE often presents with nonspecific fever and seizures, with late onset and absent indicative rashes, complicating early diagnosis. For newborns suspected of having NHSE, early CSF HSV-DNA testing and prompt antiviral treatment are essential to improve outcomes. Metagenomic sequencing is especially valuable for accurate, rapid diagnosis when conventional methods fail.}, } @article {pmid41989131, year = {2026}, author = {Schön, ME and Schvarcz, CR and Malkewitz, SV and Hinner, FC and Koslová, A and Mersdorf, U and Schimm, F and Rickert, S and Pozhydaieva, N and McBeain, K and Hackl, T and Schneider, AC and Barenhoff, K and Höfer, K and Edwards, KF and Steward, GF and Fischer, MG}, title = {Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41989131}, issn = {1751-7370}, support = {24-10280I//Czech Science Foundation/ ; 464500427//SPP 2330/ ; //Max Planck Society/ ; }, mesh = {*Giant Viruses/genetics/classification/isolation & purification ; Genome, Viral ; *Genetic Variation ; Hawaii ; Phylogeny ; *Cercozoa/virology ; DNA Methylation ; DNA, Viral/genetics ; }, abstract = {Giant DNA viruses are ubiquitous among unicellular eukaryotes and occur in marine, freshwater, and terrestrial environments. Despite intense metagenomic data mining, their strain-level diversity remains largely unexplored. Here we introduce a model system comprising four isolates of a giant virus called ChlorV, which infects marine microalgae of the class Chlorarachniophyceae (Rhizaria) from station ALOHA, Hawai'i. The ChlorV genomes are 469 kbp to 493 kbp long and encode approximately 400 proteins, at least 106 of which are present in purified virions. Although the four viral genomes are highly syntenic, they differ by several insertions and deletions that often encode methyltransferases. We found that some of these methyltransferase genes correlated with specific DNA methylation patterns in the same ChlorV strain. Our study describes the first giant viruses infecting the eukaryotic supergroup Rhizaria and demonstrates how viral strain-level variation in gene content and epigenetic features may affect eco-evolutionary processes in marine microalgae.}, } @article {pmid41989380, year = {2026}, author = {Hontelez, S and Guthrie, M and Stobernack, T and van Baarlen, P and Rousseau, C and Boks, MP and Pereira, RR and Boekhorst, J and Kleerebezem, M}, title = {Microbiome signatures correlate with diet-mediated ADHD symptom reduction.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2659400}, pmid = {41989380}, issn = {1949-0984}, mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology/metabolism ; Child ; Male ; *Gastrointestinal Microbiome ; Feces/microbiology ; Multiomics ; Diet ; *Bacteria/classification/genetics/isolation & purification ; Female ; }, abstract = {Attention-deficit hyperactivity disorder (ADHD) is one of the most common childhood neuropsychiatric conditions. Both (epi)genetic and environmental factors are suggested to contribute to the etiology of ADHD. In the last decade, nutrition has received considerable attention as a potential environmental factor triggering ADHD behavior, particularly applying a few-foods diet (FFD) has been shown to elicit considerable behavioral improvements. These studies are observational rather than investigating underlying molecular mechanisms. The present study included 79 children (boys aged 8-10) with ADHD following a progressive, i.e., increasingly restrictive, FFD diet for 5 weeks. Minimally invasive samples (feces, urine, blood, and buccal swabs) were collected before and after the intervention to obtain a multi-omics perspective of the dietary responses in the participating children. For 63% of the participating children, a more than 40% behavior score improvement was observed, with an average improvement of 73%. The strength of diet-induced changes in ADHD symptoms among children was significantly associated with the gut microbiome composition, particularly when analyzing species-stratified abundance profiles of previously characterized gut-brain modules in the fecal metagenomic data. While integrative multi-omics analysis did not identify composite signatures linked to symptom changes, the strongest multi-omics signal confirmed compliance with the dietary intervention. Our findings implicate a role of the gut microbiome and its metabolic capacity to communicate with the central nervous system in children with food-associated ADHD.}, } @article {pmid41989870, year = {2026}, author = {Zhu, YC and Deng, Y and Zeng, JQ}, title = {Effects of concurrent Helicobacter pylori infection and small intestinal bacterial overgrowth on the gut microbiota and metabolic profiles: A multi-omics study.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {73}, number = {2}, pages = {201-210}, doi = {10.1556/030.2026.02894}, pmid = {41989870}, issn = {1588-2640}, mesh = {Humans ; *Helicobacter Infections/microbiology/metabolism/complications ; Female ; *Helicobacter pylori/physiology ; *Intestine, Small/microbiology ; *Gastrointestinal Microbiome ; Male ; Multiomics ; Feces/microbiology ; *Metabolome ; Middle Aged ; Adult ; *Bacteria/classification/growth & development/genetics/isolation & purification/metabolism ; Aged ; }, abstract = {This study investigated the synergistic effects of Helicobacter pylori (Hp) infection and small intestinal bacterial overgrowth (SIBO) on the gut microbiota structure and metabolic profiles and elucidate the underlying pathophysiological mechanisms. Forty-two patients with gastrointestinal symptoms were recruited and assigned to group A (Hp+ SIBO+), B (Hp+ SIBO-), C (Hp- SIBO+), or D (Hp- SIBO-) based on their Hp infection and SIBO status. Fecal samples were collected for metagenomic sequencing and untargeted metabolomic analysis. The associations between microbiota and metabolites were evaluated using alpha/beta diversity analysis, differential species screening, metabolite identification, and Procrustes/Spearman correlation analysis. Neither Hp infection nor SIBO significantly altered the alpha or beta diversity of the gut microbiota (both P > 0.05). However, specific shifts in microbial abundance were observed. Specifically, the abundance of short-chain fatty acid-producing bacteria such as Megamonas was significantly decreased in the SIBO+ groups. Metabolomic analysis revealed significant enrichment of inflammatory metabolites (e.g., prostaglandin derivatives) in group A, disordered bile acid conjugates (e.g., chenodeoxycholylisoleucine) and nucleotide metabolism in SIBO+ groups, and abnormal lipid/carbohydrate metabolism pathways in Hp+ groups. Multi-omics integration analysis indicated a strong coupling between the microbial structure and metabolic profiles (Procrustes analysis, P < 0.05). In group A, the abundance of Faecalibacterium and Hominenteromicrobium was negatively correlated with bile acid levels, suggesting impaired bile acid transformation. Hp infection and SIBO might synergistically exacerbate gut ecological and metabolic disorders by reshaping specific microbiota and metabolic networks (enhanced inflammatory response, disrupted bile acid circulation). Their co-occurrence produces additive effects, which could explain the aggravated clinical symptoms. This study provides a theoretical basis for interventions targeting microbiota-metabolite interactions, such as probiotics and bile acid modulators.}, } @article {pmid41990029, year = {2026}, author = {Sun, Y and Zhang, M and Wang, X and Huang, X and Yu, Y and Pan, H and Li, H and Shi, L and Yang, W and Zhang, C and Ding, B and Liu, X and Li, J and Qian, C and Cheng, B and Zhang, C and Ran, J and Li, M}, title = {Gut Microbiota of Gray Snub-Nosed Monkeys: Adaptation to Seasonal Variations Through Energy Compensation and Thermogenesis.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.70092}, pmid = {41990029}, issn = {1749-4877}, support = {32330015//National Natural Science Foundation of China/ ; 32070404//National Natural Science Foundation of China/ ; QLKH [2023] 11//Guizhou Forestry Administration Scientific Research Project/ ; QLKH [2025] 11//Guizhou Forestry Administration Scientific Research Project/ ; //Investigation of Nationally Protected Wildlife Species in Tongren Region/ ; GZKPC-2025-01//Guizhou Province/ ; QCZH [2023]82//Protection and Restoration of Forests and Grasslands in 2024 from the Central Finance/ ; [2023]188//Guizhou Science and Technology Support Plan Project/ ; QKHFQ [2023]009//Construction of Capacity for Ecosystem Optimization and Innovation in Key Ecological Zones of Guizhou Province/ ; YWZ[2024]005//Construction of Capacity for Ecosystem Optimization and Innovation in Key Ecological Zones of Guizhou Province/ ; QKHPT[2021]5625//Guizhou Outstanding Young Scientist Program/ ; QJJ[2024]337//Natural Science Research Projects of the Education Department of Guizhou Province/ ; [2022]031//Guizhou Provincial Department of Education/ ; 2024BS011//Doctoral Program of the Science Research Foundation of Guizhou Education University/ ; 2024BS006//Doctoral Program of the Science Research Foundation of Guizhou Education University/ ; }, abstract = {As an extremely endangered species, the gray snub-nosed monkey (Rhinopithecus brelichi) relies on its gut microbiota for adaptation to environmental changes, particularly in coping with fluctuations in energy and nutrient availability. In this study, we employed metagenomic, metatranscriptomic, and widely targeted metabolomic analyses to characterize the gut microbiota of gray snub-nosed monkeys. Based on metagenome-assembled genomes (MAGs), we recovered 1229 non-redundant MAGs. Among them, a total of 103 MAGs exhibited significant seasonal variation, primarily belonging to the phyla Bacillota_A, Bacteroidota, and Bacillota_I. During winter, metagenomic results indicated that the gut microbiota exhibited an enhanced capacity to produce energy substrates such as amino acids, short-chain fatty acids, pyruvate, and acetyl-CoA, with increased conversion of these substrates. Metatranscriptomic analysis further confirmed that key carbon cycle-related genes and metabolic pathways were significantly upregulated in winter. Additionally, metabolite analysis indicated significantly lower levels of amino acids in winter fecal samples, suggesting that gray snub-nosed monkeys efficiently absorb and utilize metabolites, with the gut microbiota likely contributing to energy compensation. Notably, the gut microbiota may also synergistically support the host's non-shivering thermogenesis, helping maintain physiological functions in extreme cold conditions. This study elucidates the cooperative role of the gut microbiota in helping gray snub-nosed monkeys adapt to seasonal environmental fluctuations, providing new insights into how gut microbiota optimize winter energy utilization-an understanding with important implications for the conservation of endangered wildlife.}, } @article {pmid41990134, year = {2026}, author = {Chen, X and Wang, Y and Feng, J and Chen, H and Yao, B and Li, F and Yang, Q and Qu, J}, title = {Hypobaric hypoxia affects gut microbiota of rats through affected community assembly, reduced network resilience, and metabolic reprogramming.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {5}, pages = {}, pmid = {41990134}, issn = {1574-6941}, support = {32471603//National Natural Science Foundation of China/ ; XZ202601ZY0248//Key Research and Development Program of Xizang Autonomous Region/ ; 2024-TG16//Central Financial Funds for Forestry and Grassland Reform and Development in 2024/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Rats ; *Hypoxia/microbiology ; Male ; *Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Metabolic Reprogramming ; Altitude ; Metagenomics ; }, abstract = {In host-microbe interactions, host diet and environmental stress are key driving factors shaping the gut microbiota. Although previous studies have shown that hypoxia affects the structure and function of the gut microbiota in rodents, most have relied on 16S rRNA gene sequencing and lacked analysis of community assembly mechanisms, co-occurrence networks, and functional pathways. Here, we used metagenomic next-generation sequencing (mNGS) to examine the gut microbiota of rats exposed to hypobaric hypoxia (WH, simulated 6000 m altitude) compared to WL group (2100 m altitude). Hypoxia significantly altered β-diversity of gut microbiota, but did not affect its α-diversity. Community assembly was primarily governed by stochastic processes, with hypoxia stress reducing their impact. Microbial co-occurrence networks were dominated by positive correlations, although network resilience and stability declined under hypoxia. Helicobacter and Eubacterium were identified as high-abundance differentiating genera, and Akkermansia muciniphila was significantly enriched in WH group. Functional analysis revealed alterations in pathways related to protein synthesis and carbohydrate metabolism, suggesting that hypoxia may affect nutrient utilization by the host. Overall, these findings provide a comprehensive view of how hypoxic stress reshapes the gut microbiota of rats, offering new insights into microbial dynamics under environmental stress.}, } @article {pmid41990403, year = {2026}, author = {Zhao, J and Li, T and Huang, H and Servellita, V and Sotomayor-Gonzalez, A and Yakovleva, O and Wang, X and Ragupathy, V and Biswas, S and Barilko, P and Sun, E and Huynh, S and Hunsicker, M and DeQuach, J and Morales, JD and Highbarger, H and Dewar, RL and Porth, C and Denny, TN and McGivern, DR and Chiu, CY and Hewlett, I}, title = {Development and genomic characterization of a diverse HIV-1 variant reference panel for nucleic acid-based testing.}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {184}, number = {}, pages = {105941}, pmid = {41990403}, issn = {1873-5967}, support = {75N91019D00024/CA/NCI NIH HHS/United States ; FD999999/ImFDA/Intramural FDA HHS/United States ; U01 FD005978/FD/FDA HHS/United States ; }, mesh = {Humans ; *HIV-1/genetics/isolation & purification/classification ; *HIV Infections/virology/diagnosis ; *Genetic Variation ; *Genome, Viral ; Viral Load ; RNA, Viral/genetics ; Cameroon ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Reference Standards ; }, abstract = {BACKGROUND: The high worldwide genetic diversity of HIV poses significant challenges for its detection and diagnosis by nucleic acid testing (NAT). Well-characterized reference panels are important for evaluating the analytical performance of HIV tests.

OBJECTIVE: To develop a reference panel for HIV NAT that reflects the genetic diversity of circulating strains.

STUDY DESIGN: HIV was cultured from blood specimens collected from blood donor and clinical sites in Cameroon. Metagenomic next-generation sequencing in combination with spiked primer enrichment along with Sanger sequencing were used to sequence 101 cultured HIV-1 samples representing 59 strains. To establish an HIV-1 variant reference panel, a diverse subset of cultured viruses was analyzed in multiple laboratories with different assays to determine consensus viral loads.

RESULTS: Near full-length HIV-1 genomes, with an average of 9589 base pairs (bp), were recovered from 37 (62.7%) of the 59 strains. The whole genome sequences of 28 strains exhibited more than 95% similarity to our previously reported genomes obtained by Sanger sequencing. An HIV variant reference panel for NAT comprising 18 diverse HIV-1 strains was developed. The panel included four subtypes, four circulating recombinant forms, and eight unique recombinant forms. Strains were prepared at low (n = 18, 2.53 log10 copies/mL), medium (n = 18, 3.61 log10 copies/mL), and high viral loads (n = 15, 4.66 log10 copies/mL), yielding 51 panel members in total.

CONCLUSION: This diverse HIV reference panel can be used to evaluate the performance of HIV NAT and is available upon request to developers and manufacturers of HIV tests.}, } @article {pmid41990622, year = {2026}, author = {Liu, L and Wang, C and Qi, WK and Zhang, SJ and Li, YY and Peng, Y}, title = {Mechanisms of aerobic simultaneous nitrogen removal under low COD/N conditions: Diffusion-reaction coupling and particle size effects via self-recirculating microgranular system.}, journal = {Water research}, volume = {300}, number = {}, pages = {125937}, doi = {10.1016/j.watres.2026.125937}, pmid = {41990622}, issn = {1879-2448}, mesh = {*Nitrogen ; Particle Size ; Bioreactors ; Biological Oxygen Demand Analysis ; *Waste Disposal, Fluid/methods ; Nitrification ; Sewage ; Aerobiosis ; Denitrification ; Diffusion ; Wastewater ; }, abstract = {Nitrogen removal from ammonium-rich, carbon-limited wastewater remains constrained in continuous-flow microgranular sludge systems. In this study, a three-stage up-flow self-recirculating microgranular sludge reactor was developed to investigate nitrogen removal mechanisms under low chemical oxygen demand to nitrogen ratios (COD/N < 2.5) and high influent total nitrogen (TN > 400 mg/L). During long-term operation, the system achieved stable removal efficiencies of ammonium (98%), TN (94%), and COD (95%). Under ammonium stress, particle size decreased to a mean diameter of 249.2 μm, forming stable, non-flocculent microaggregates. Microgranules < 0.2 mm exhibited pronounced simultaneous partial nitrification-denitrification (SPND) and simultaneous nitrification-denitrification (SND) activities under aerobic conditions. Simultaneous nitrogen removal (SNR) activity peaked at 0.52 g TN/(g VSS·d) at a DO of 2 mg/L. In contrast, microgranules > 0.2 mm primarily followed SND-dominated pathways. Their SNR activity increased with DO and reached a maximum of 0.46 g TN/(g VSS·d). Microbial community and metagenomic analyses revealed a redox-stratified functional structural organization. Rubrivivax (11.5%) dominated the surface layer, likely linking organic matter degradation with nitrogen oxide reduction. Hyphomicrobium (11.9%) was enriched in intermediate layers and was associated with SND. In the core, the co-enrichment of Hyphomicrobium (7.2%) and Methylotenera (6.1%) supported the coupling of SND and SPND processes. These findings provide a basis for improving nitrogen removal from ammonium-rich, carbon-limited wastewater.}, } @article {pmid41990624, year = {2026}, author = {Wang, G and Yang, F and Xu, S and Lin, D and Yang, R and Yan, P and Chen, Y and Fang, F and Guo, J}, title = {Microbial niches and metabolism drive spatial heterogeneity of hydroxyapatite precipitation in aerobic granular sludge.}, journal = {Water research}, volume = {300}, number = {}, pages = {125923}, doi = {10.1016/j.watres.2026.125923}, pmid = {41990624}, issn = {1879-2448}, mesh = {*Sewage/microbiology/chemistry ; *Durapatite/chemistry ; Aerobiosis ; Bioreactors ; Phosphorus ; Chemical Precipitation ; Phosphates ; Waste Disposal, Fluid ; }, abstract = {Biologically induced phosphate precipitation (BIPP) in aerobic granular sludge (AGS) provides a promising approach to address phosphorus removal instability and granule structural fragility in practical applications. However, the roles of microbial communities, ecological niches, and metabolic activities in driving phosphate precipitation and shaping its spatial distribution within AGS remain underexplored. This study systematically investigates AGS physicochemical properties, reactor performance, phosphorus speciation, precipitation composition and distribution, microbial community structure, and metabolic activity using sodium propionate (RP) and sodium acetate (RA) as sole carbon sources. The findings reveal for the first time the mechanisms by which microbial communities, ecological niches, and metabolic functions regulate phosphate precipitation and determine its spatial heterogeneity. BIPP contributes 22.6% and 60.1% of total phosphorus removal in RP and RA, respectively, thereby enhancing phosphorus removal efficiency and granule structural stability. Multi-scale analyses-including Standards, Measurements and Testing, Raman spectroscopy, X-ray diffraction, scanning electron microscopy-energy dispersive X-ray spectroscopy, and micro-computed tomography-reveal that hydroxyapatite (HAP) predominantly accumulates in the outer region of RP granules but in the inner region of RA granules. Periodic water quality variations, fluorescence in situ hybridization, granule-stratified sequencing, and metagenomic analyses indicate that the spatial heterogeneity of HAP is driven by the ecological niche separation and metabolic activities of polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). In RP granules, PAO‑driven anaerobic phosphate release creates a high‑phosphate microenvironment, which promotes HAP formation in the granule outer region. In RA, GAO‑mediated endogenous denitrification increases local pH, thereby inducing HAP precipitation in the granule interior. Overall, this study elucidates the mechanisms underlying the spatial heterogeneity of phosphate precipitation in AGS from the perspectives of microbial community structure, ecological niches, and metabolic pathways. These findings provide guidance for optimizing AGS systems to achieve efficient phosphorus removal and stable operation.}, } @article {pmid41990657, year = {2026}, author = {Ye, YQ and Lin, D and Shen, LQ and Wu, D and Li, Y and Wang, YF and Zhu, D}, title = {Viral communities as mirrors and vectors: Tracing antibiotic resistome distribution and dissemination across diverse habitats in Macao.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {142056}, doi = {10.1016/j.jhazmat.2026.142056}, pmid = {41990657}, issn = {1873-3336}, mesh = {*Drug Resistance, Microbial/genetics ; Ecosystem ; Macau ; Sewage/virology ; Soil Microbiology ; Geologic Sediments/virology ; *Viruses/genetics ; *Virome ; }, abstract = {Virus-mediated transmission of antibiotic resistance genes (ARGs) is increasingly recognized as a significant threat to global human health. However, the role of viral communities in ARGs dissemination across highly urbanized coastal regions containing with diverse habitats remains poorly understood. Here, we conducted shotgun metagenomic analyses on 49 samples collected from four habitats (urban sewage, soil, sediment, and coastal water) in Macao China, to characterize their viral communities and resistome profiles. We identified 23,579 viral operational taxonomic units (vOTUs) and 965 ARGs subtypes across these habitats. Viral community composition and total ARGs profiles exhibited system-scale spatial concordance, with a distance-decay trend, together with a positive association between viral ARGs and total ARGs abundance. Approximately 62.80% of ARGs subtypes were shared among habitats, suggesting a high degree of compositional overlap in resistome profiles among habitats. Urban sewage and coastal waters showed enriched viral abundance and ARGs diversity, with high-risk ARGs in sewage being 10.3- and 24.7-fold greater than in soils and sediments. High-risk ARGs (e.g., macB, udg) showed co-occurrence with virulence factor genes (VFGs) on viral contigs, and prophages were identified within Pseudomonadota and Bacteroidota, the dominant groups for phages and ARGs. The co-occurrence of ARGs and auxiliary metabolic genes (AMGs) within these hosts suggests that phages may facilitate the propagation of ARGs while enhancing host adaptability, thereby promoting their enrichment. By integrating multi-habitat analyses in human-impacted coastal regions, this study highlights the potential role of viruses in ARGs dissemination and informs resistome surveillance.}, } @article {pmid41991090, year = {2026}, author = {Lee, JS and Jeon, YJ and Kim, TH and Khan, W and Yun, YM}, title = {Multiscale destabilization of anaerobic digestion by chloramphenicol: Divergence between methanogen detectability and methane recovery.}, journal = {Bioresource technology}, volume = {453}, number = {}, pages = {134635}, doi = {10.1016/j.biortech.2026.134635}, pmid = {41991090}, issn = {1873-2976}, mesh = {*Methane/biosynthesis/metabolism ; *Chloramphenicol/pharmacology ; Anaerobiosis/drug effects ; Biomass ; Kinetics ; }, abstract = {Antibiotic residues in livestock waste streams can affect anaerobic digestion (AD), yet their functional impact on microbial viability and metabolic pathways remains unclear. This study evaluated concentration-dependent effects of chloramphenicol (CAP) by integrating process kinetics, cellular integrity, dissolved-phase responses, and functional gene profiles. Methane yield was maintained at ≤ 50 mg/L CAP but declined sharply at higher concentrations, reaching near-complete inhibition at 1,000 mg/L. Estimated inhibition thresholds were derived as IC30 = 285 mg/L, IC60 = 535 mg/L, and IC90 = 852 mg/L from the fitted concentration-response relationship. Severe inhibition coincided with residual organic acid accumulation, pH decline, and enrichment of propionate and butyrate fractions with undetectable acetate. Flow cytometry revealed a marked CAP-dependent decline in intact biomass, with live-cell (P2) counts decreasing from 4.8 × 10[6] cells/mL in the control to 1.0 × 10[5] cells/mL at 1,000 mg/L, accompanied by increased forward- (FSC-A) and side-scatter (SSC-A) area indicative of structural stress. Fluorescence excitation-emission matrix (FEEM) analysis showed concentration-dependent enrichment of soluble microbial products (SMPs) fluorescence, and inoculum-only incubation confirmed biomass-associated solubilization under CAP exposure. Although methanogens remained numerically detectable (76.0% vs. 81.1%), key genes related to cofactor synthesis and electron transfer (comD, frhB, fwdA/fwdC, mcr) declined substantially at 1,000 mg/L. These convergent signals were consistent with multiscale destabilization. Given that microbial activity was not directly measured, the observed discrepancy between methanogen detectability and methane recovery should be interpreted as indicative of a potential functional imbalance rather than definitive evidence of functional decoupling.}, } @article {pmid41991504, year = {2026}, author = {Elhani, I and Bredon, M and Enea, D and Desmons, A and Arrive, L and Bazille, C and Lefevre, A and Aouba, A and Bigot, A and de Moreuil, C and Alonso, I and Blasco, H and Creusot, L and Dupuy, C and Emond, P and Krasniqi, P and Lamaziere, A and Oeuvray, C and Rainteau, D and Svrcek, M and Rolhion, N and Sokol, H and Georgin-Lavialle, S}, title = {Functional changes in the gut microbiota are associated with the intestinal phenotype in A20 haploinsufficiency.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {37}, number = {4}, pages = {e70343}, pmid = {41991504}, issn = {1399-3038}, support = {//snfmi-remi/ ; //fai2r/ ; }, mesh = {Humans ; Female ; Haploinsufficiency ; Male ; *Gastrointestinal Microbiome ; *Tumor Necrosis Factor alpha-Induced Protein 3/genetics ; Phenotype ; Child ; Liver/pathology ; Adolescent ; Feces/microbiology ; *Inflammatory Bowel Diseases/genetics/microbiology ; Liver Diseases/genetics ; Child, Preschool ; Ruminococcus ; *Intestines ; *Autoimmune Diseases/genetics/microbiology ; Eubacteriales ; }, abstract = {BACKGROUND: A20 haploinsufficiency (HA20) is an autoinflammatory disease driven by pathogenic variants in TNFAIP3, which plays a crucial role in regulating immune responses. The clinical manifestations of HA20 resemble those of inflammatory bowel disease (IBD), with prominent gastrointestinal (GI) involvement. Given the well-established association between gut microbiota alterations and IBD, this study aimed to describe the GI involvement of HA20 patients and to investigate their fecal microbiota using shotgun sequencing and metabolomics.

METHODS: This study included 16 HA20 patients and 22 healthy age and sex-matched controls. GI clinical phenotype, liver imaging, and liver and GI tissue histology were assessed. Shotgun metagenomic sequencing was performed on fecal DNA. Fecal metabolomic profiling of bile acids, short-chain fatty acids (SCFAs), and tryptophan metabolites was performed.

RESULTS: Liver imaging revealed chronic liver disease in 3/5 patients, showing as liver dysmorphia and portal hypertension. Histological analysis showed lymphoplasmocytic infiltrate of the GI tract and the liver. The fecal microbiota of HA20 patients was characterized by marked alterations, including a reduction in microbial diversity and an increase in the pro-inflammatory bacterium Ruminococcus gnavus. Microbial bile acid deconjugation and desulfation were impaired. Additionally, tryptophan metabolism was altered, with a shift towards the kynurenine pathway.

CONCLUSION: Our results show that HA20 is associated with gut microbiota alterations and significant disruptions in metabolic pathways, particularly involving bile acids. These alterations could contribute to the chronic inflammation observed in HA20. These findings highlight the role of the gut-liver axis and of mucosal barrier dysfunction in HA20.}, } @article {pmid41991788, year = {2026}, author = {Imran, H and Nouha, F and Wael, T and Haroun, BA and Wissal, M and Thouraya, BH and Darine, T}, title = {Mesorhizobium inoculation and Water-nitrogen regimes enhance Potato-chickpea intercropping performance and Rhizosphere microbiome diversity.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {5}, pages = {}, pmid = {41991788}, issn = {1573-0972}, abstract = {Increasing water scarcity poses significant threats to crop production and agricultural sustainability. Water deficit and the environmental impacts of synthetic nitrogen fertilization necessitate the development of sustainable cropping systems that enhance resource use efficiency while mitigating climate and economic risks. This study investigates the effects of Mesorhizobium ciceri inoculation (CMG6 strain (SI-DP 40653)), varying water–nitrogen regimes, and a potato-chickpea intercropping system (IC) on plant performance, metabolic responses, rhizospheric microbial diversity. Field trials, located in northeastern Tunisia, showed that IC combined with efficient M. ciceri inoculation significantly outperformed sole cropping (SC) across all physiological parameters. Under standard conditions, this synergy bolstered chickpea biomass and photosynthetic capacity. Notably, under reduced nitrogen input, inoculated intercropping (IC) boosted chickpea shoot biomass by more than twofold compared with sole cropping (SC). Intercropping also improved drought resilience, reducing stress-induced metabolic decline by approximately 40% relative to monocropping systems. Secondary metabolite production was stimulated, with higher accumulation of polyphenols and tannins observed particularly under reduced nitrogen conditions in inoculated systems. Additionally, intercropping improved potato productivity under low-nitrogen conditions while maintaining stable yields under drought stress. Metagenomic analysis showed that water stress accounted for approximately 22% of microbial community variation. However, intercropping and inoculation reshaped rhizosphere communities by enhancing the abundance and diversity of beneficial bacterial groups, particularly Bacilli, and buffering drought-induced shifts. These results emphasized the synergistic benefits of IC and Rhizobium inoculation in improving crop productivity, stress resilience, and soil health while reducing reliance on synthetic inputs.}, } @article {pmid41991911, year = {2026}, author = {Liu, Y and Huang, P and Zhang, C and Dong, Q and Wang, X and Tian, F and Zhao, J and Sun, Z and Chen, L and Chen, W and Zhai, Q}, title = {A microbiome catalog of Chinese traditional artisanal cheeses provides insights into functional and microbial diversity.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41991911}, issn = {2041-1723}, support = {32425044//China National Funds for Distinguished Young Scientists/ ; 2022YFD2100703//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; }, mesh = {*Cheese/microbiology ; *Microbiota/genetics ; China ; Animals ; Fermentation ; Metagenome ; Food Microbiology ; Polymorphism, Single Nucleotide ; Lactobacillus helveticus/genetics ; Phylogeny ; Metagenomics ; Biodiversity ; beta-Galactosidase/metabolism ; }, abstract = {Cheese has been consumed globally over millennia and serves as a natural reservoir of diverse microorganisms. Chinese traditional cheeses rely on natural fermentation and have unique physiochemical and microbial characteristics compared to European cheeses. However, there is a major knowledge gap in the understanding of Chinese cheese microbiome. Here, we present a curated Cheese microbiome catalog (cCMC) consisting of 3327 high-quality metagenome-assembled genomes, recovered from metagenomic sequencing of 235 Chinese cheese samples covering all traditional artisanal cheese-producing regions in China, together with 198 publicly available non-Chinese cheese metagenomic datasets. This catalog represents 395 nonredundant species spanning 50 families, including 85 putative novel species. We identified six lactic acid bacteria species enriched in Chinese cheeses, and confirmed that the unique presence of Acetobacteraceae contributes to improving the nutritional quality of Chinese cheese. A total of 8851 biosynthetic gene clusters were detected from cCMC, with over 57% classified as novel. We demonstrated that SNP-level variations among different Lactobacillus helveticus strains are associated with differences in β-galactosidase thermostability. Using the cCMC database, we developed a synthetic microbial community as the starter culture for Qula, a yak milk-based Chinese cheese produced by the Tibetans. Overall, the cCMC provides a comprehensive resource of cheese to enable future attempts on large-scale industrial production of naturally fermented cheeses with distinctive ethnic features.}, } @article {pmid41992382, year = {2026}, author = {Cuteri, V and Preziuso, S and Li, Y and Laus, F}, title = {Fecal virome at the human-animal interface: a one health perspective on an uncharted frontier.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41992382}, issn = {2524-4671}, abstract = {The exponential growth of the human population and associated intensifications in animal farming, pet ownership, and habitat anthropisation have dramatically increased human-animal interactions. Global livestock production now exceeds 24 billion animals annually, and pet ownership has risen to over 70% of households in many developed nations, creating unprecedented interfaces for viral exchange. This heightened contact has multiplied opportunities for zoonotic and reverse-zoonotic transmission, as tragically exemplified by the SARS-CoV-2 pandemic. The fecal virome—defined as the totality of viral nucleic acids in the gastrointestinal tract—represents a crucial, yet largely unexplored, pathway for such exchanges. While the bacterial microbiome’s role is increasingly recognized, the virome’s composition, dynamics, and transmissibility between co-habiting humans and animals remain poorly characterized. This review compiles current evidence on the fecal virome of key domestic animals (equines, livestock, pets) and their human contacts under the “One Health” framework. We critically evaluate methodological approaches—from targeted PCR to viral metagenomics—and highlight the discovery of novel viruses and identification of zoonotic agents through metagenomic approaches. Critically, we identify significant knowledge gaps, including the absence of definitive evidence for contemporary cross-species transmission versus shared ancestry or convergent evolution. We propose a strategic research agenda focused on longitudinal studies of human-animal cohorts, standardized metagenomic methodologies, and functional analyses of the virome. Elucidating the fecal virome at this interface is paramount for developing proactive surveillance strategies to predict and prevent the next emerging viral disease.}, } @article {pmid41992389, year = {2026}, author = {Gu, S and Jiang, C and Zhang, P and Luo, S and Gong, Y and Feng, W and Xiong, J and Zhang, J and Chen, K and Ning, K and Miao, W}, title = {Unraveling the colonization process of microeukaryotic communities on artificial micro-ecological islands.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41992389}, issn = {2524-6372}, support = {2022FY100400//the Science & Technology Fundamental Resources Investigation Program/ ; 2022xjkk0204//the Third Xinjiang Scientific Expedition Program/ ; U22A20454//the National Natural Science Foundation of China/ ; SNJNP2022008//the Background Resources Survey in Shennongjia National Park/ ; SNJGKL2022008//the Open Project Fund of Hubei Provincial Key Laboratory for Conservation Biology of Shennongjia Snub-nosed Monkeys/ ; }, abstract = {BACKGROUND: Micro-ecological islands provide unique habitats for microbes and play a crucial role in the functioning of aquatic ecosystems. Microbes settle on these micro-ecological islands, forming distinct microbial communities. Previous studies have provided some understanding of the colonization processes and regulatory mechanisms of protozoa in microbial communities. However, these islands are also subject to colonization by a variety of microbes beyond protozoa, and comprehensive cross-kingdom studies and their potential mechanisms remain largely unexplored.

RESULTS: Using polyurethane foam units (PFU) to simulate micro-ecological islands, we studied the colonization dynamics of microbes in two distinct aquatic ecosystems, the Yangtze River and East Lake. Over 10-day colonization survey was conducted, we applied eDNA-PFU technology combined with metagenomic sequencing to comprehensively identify species present in the microbial communities, including bacteria, fungi, flagellates, protozoa, and metazoa. We found that microeukaryotes, rather than prokaryotes, were the primary colonizers in these two aquatic ecosystems. Our study reveals a colonization process of microeukaryotes in PFUs, profoundly influenced by their motility modes. Additionally, we propose a hypothetical food web framework within micro-ecological islands that maintains community stability, representing the most fundamental biological interactions.

CONCLUSIONS: Overall, this study enriches our understanding of micro-ecological islands and provides deeper insights into the colonization processes and regulatory mechanisms of microbial communities. It highlights the practical significance of micro-ecological islands in biological resource management, environmental protection, and biodiversity conservation.}, } @article {pmid41993122, year = {2026}, author = {Saez-Torillo, SN and Danielsson, R and Nguyen, TQ and Lima, J and Cleveland, MA and Roehe, R and Martínez-Álvaro, M}, title = {Predicting beef diet nutritional composition and intake from rumen metagenomic profiles.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {25}, number = {}, pages = {297-309}, pmid = {41993122}, issn = {2405-6383}, abstract = {Knowledge of diet composition and intake levels in beef cattle is valuable for post hoc feed traceability and for more accurate modelling of the diet impact on methane emissions and performance traits. However, a direct measure of this information can be costly and labour-intensive and is not always feasible. In this study, rumen metagenomic data combined with machine learning algorithms were used to predict diet type, nutritional composition, and intake levels. An external validation to assess the generalizability of the models was also performed. Rumen samples were collected from 142 animals belonging to two breeds, Luing (n = 70) and Charolais crossbred (n = 72), with 425.6 ± 43.5 d old and 461.9 ± 70.2 kg body weight. The animals participated in a 56-d feeding trial and were assigned to diets differing in forage-to-concentrate ratio, with 72 animals receiving a concentrate-based diet and 70 receiving a forage-based diet. Liquid ruminal contents were collected immediately postmortem and subsequently subjected to metagenomic sequencing. Based on these sequences, the relative abundance of microbial genes (MGs), microbial genera (MTs), and phyla were determined. The log-ratio between the abundances of Verrucomicrobia and Chlorobi discriminated diet type with an average classification accuracy of 0.86 ± 0.05, while using the log-ratio transformed abundances of 4769 MTs and MGs as predictors reached 0.90 ± 0.05. All this microbiome information was used in a random forest model to predict continuous values for nutritional diet components starch, crude protein, neutral and acid detergent fibre, and metabolizable and gross energy with external validation prediction accuracy values between 0.77 and 0.83. Microbiome features important for prediction of diet components such as fibre and starch included Mitsuokella, Selenomonas, and MGs involved in flagellar assembly and aminoacyl-tRNA biosynthesis. Microbiome data were more informative for predicting the feed composition than the amount of feed consumed, which reached a prediction accuracy of 0.27 ± 0.12 for dry matter intake (DMI). However, microbiome data can still be used as a screening tool to classify DMI into low, medium, or high with a classification accuracy of 0.74. Incorporating dietary information into linear phenotypic and genetic models to predict methane production (MP) and DMI reduced root mean square error (RMSE) by 26.9% and 9.6%, respectively, in the phenotypic model. In the genetic model, only MP showed a reduction in RMSE, with a 31% improvement. These findings highlight rumen microbiome data as a valuable tool for the post hoc prediction of feed composition in beef cattle.}, } @article {pmid41993390, year = {2026}, author = {Hutchinson, NT and Ye, N and Jennings, M and Fang, C and Qi, N and Li, J}, title = {Engineered Lactate Catabolizing Probiotics Reveal Timescale Dependent Microbiome-Host Metabolic Coupling.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41993390}, issn = {2692-8205}, abstract = {The exchange of lactate, a metabolic substrate and regulator, between the gut lumen and systemic circulation for use in host and microbial processes is well documented, but tools capable of uncovering whether this process influences host metabolic status across acute and chronic contexts are lacking. In our prior work, we engineered probiotic Bacillus subtilis PY79 to produce lactate oxidase (LOX) intracellularly, allowing it to rapidly convert intestinal lactate to pyruvate. Following oral administration, LOX reduced systemic lactate concentrations at rest and under challenge conditions, providing a platform for investigating lactate's influence on host metabolism and microbiota. In the present work, we demonstrate that acute LOX administration effectively rewired microbiota function and host energy balance, as revealed by 16S sequencing and indirect calorimetry. In silico microbial community modeling via MICOM and metagenomic inference via PICRUSt2 suggested that acute shunting of lactate to pyruvate induced microbiota remodeling towards anabolic processes, reflected by increased flux of pyruvate, acetate, and formate, alongside moderate to large increases (Cohen's d = 0.60-1.00) in pathways for fructan degradation, B-vitamin biosynthesis, and lipid synthesis. These anabolic shifts temporally aligned with transient increases in host energy expenditure (β = 1.08, p<0.05) via glucose oxidation (β = 0.01, p<0.05), hinting at functional coupling between microbial biosynthesis and host energy balance via lactate exchange. Of note, acute LOX administration also improved thermoregulation and survival following LPS-induced sepsis, demonstrating functional relevance of these metabolic effects during acute inflammatory challenge. To assess chronic effects, we administered LOX for 6 weeks during diet-induced obesity. LOX treatment persistently reduced blood lactate. However, this chronic lactate reduction did not curtail the progression of diet-induced obesity or induce sustained modulation of host energy expenditure. This disconnect between acute and chronic findings suggests that gut-centric lactate conversion affects energy balance through microbiome and/or host-dependent mechanisms, but cannot override homeostatic forces in the long term to produce clinical benefit during chronic disease. Our results validate LOX probiotics as a tool for acute metabolic augmentation, and highlight a clear homeostatic limit to gut-centric therapies. This platform may enable targeted design of probiotic interventions matched to therapeutic timescale and inform synbiotic formulations that overcome homeostatic compensation.}, } @article {pmid41993414, year = {2026}, author = {Liu, S and Mehta, P}, title = {Ecology of metagenomes: incorporating genotype-to-phenotype maps into ecological models.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41993414}, issn = {2692-8205}, abstract = {A major theoretical problem in community ecology is to understand how genes, organisms, and environments combine to shape the structure and diversity of ecological communities. However, most classic ecological models work entirely with phenotypic parameters, neglecting the central role played by genes. This limitation is particularly acute in microbial ecology, where the widespread use of sequencing technologies allows researchers to directly measure the genomic and metagenomic properties of communities. Here, we bridge this gap by incorporating genotype-to-phenotype maps into classical ecological models, including the generalized Lotka-Volterra model (GLV) and consumer resource models (CRMs). We focus on the case where genotype-to-phenotype maps are linear, which provides a tractable yet powerful framework for analyzing complex traits. Even in this simple setting, the resulting ecological dynamics give rise to novel gene-level ecological dynamics that can be recast entirely in terms of genes, allowing us to develop an ecology of metagenomes. We find that ecological interactions between genes lead to pervasive "metagenomic hitchhiking" - low-fitness genes can survive in the ecosystem because they are integrated into genomes of high-fitness species. We also show that phylogenetic relationships between species mold the ability of closely related strains to stably coexist in complex communities. This highlights how lineage structure and competitive interactions jointly shape community composition. Our framework provides a principled foundation for interpreting metagenomic data through the lens of ecological theory.}, } @article {pmid41993507, year = {2026}, author = {Coleman, I and Ma, J and Qian, G and Jiang, Y and Brown Kav, A and Korem, T}, title = {End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41993507}, issn = {2692-8205}, abstract = {The generation of Metagenome Assembled Genomes (MAGs) has become a standard and basic step in the analysis of metagenomic data. This multi-step process, which includes assembly, binning, refinement, and quality control, has many alternative approaches, algorithms, and parameters. Determining the ideal approach for a given ecosystem and study, or highlighting algorithmic gaps in need of additional research and development, requires rigorous benchmarking. We present MAG-E (MAG pipeline Evaluator), a generalizable and expandable framework for end-to-end evaluation of entire MAG pipelines: from assembly, through binning, to quality control and filtering. MAG-E relies on simulations that are built to match an ecosystem of interest and provide a ground truth for accurate evaluation. To demonstrate the capabilities of MAG-E, we benchmark two assemblers, six binning algorithms, three binning modes, and three quality control and refinement methods in the context of the human gut microbiome. Our findings offer multiple insights into optimal MAG generation in this context. We find that metaSPAdes consistently outperforms MEGAHIT in terms of recall (completeness), and that COMEBin overall outperforms alternative binning algorithms, but has lower precision than SemiBin2. While multi-sample binning results in higher precision, as previously shown, single-sample binning has higher recall and leads to better overall performance with modern binners. Binning refinement, which combines bins from multiple different algorithms, leads to reduced performance. We further show that CheckM2 systematically overestimates completeness and underestimates contamination, and that this is partially ameliorated when using GUNC. Finally, we analyze performance at the contig level, and demonstrate that binning algorithms systematically underperform for prophages and fail to bin contigs that are shared between genomes. Overall, MAG-E offers deep insights into successes and gaps in this important analytic process.}, } @article {pmid41993555, year = {2026}, author = {Herzog, HM and Fang, C and Lam, L and Jin, K and Zamarioli, A and Dinh, E and Gupta, CL and Sharma, A and Moody, T and Pierce, JL and Hohl, MS and Takimoto, SW and Lyalina, S and Wentworth, KL and Yu, K and Lu, VF and Mamikunian, I and Hunt, NK and Lynch, S and Pollard, KS and Hernandez, CJ and Perrien, DS and Hsiao, EC}, title = {Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1[R206H]-driven heterotopic ossification.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41993555}, issn = {2692-8205}, abstract = {Inflammatory diseases cause significant morbidity and mortality, but their pathobiology is often difficult to dissect due to complex genetic-environmental interactions. Genetic forms of heterotopic ossification, such as fibrodysplasia ossificans progressiva (FOP), reduce genetic variability, allowing careful dissection of non-genetic drivers of inflammation. While >95% of FOP patients harbor the ACVR1 [R206H] mutation, patients exhibit significant variability in disease progression, suggesting a role of environmental drivers. Here, we identify the gut microbiome as a regulator of inflammation-driven HO in FOP. Metagenomic profiling of cohabitating FOP/unaffected sibling pairs revealed a pathogenic gut microbiome profile in FOP patients (Bray-Curtis, p < 0.05). In Pdgfrα-Cre/Acvr1 [R206H] (FOP) mice, gut microbiome ablation by antibiotics reduced spontaneous HO formation (47.4% reduction, p < 0.05) and reduced plasma IL-1 pathway activity. IL-1β blockade in FOP mice suppressed trauma-induced HO formation. These findings identify a gut microbiome-IL-1-HO axis with modifiable targets for developing treatments for HO and related inflammatory conditions.}, } @article {pmid41993727, year = {2026}, author = {Sun, Y and Qiu, JW and Chen, C and Martín-Durán, JM and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the tubeworm, Lamellibrachia columna Southward, 1991 (Sabellida: Siboglinidae).}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {127}, pmid = {41993727}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Lamellibrachia columna (tubeworm; Annelida; Polychaeta; Sabellida; Siboglinidae). The genome sequence has a total length of 879.73 megabases. Most of the assembly (99.96%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.78 kilobases. Gene annotation of this assembly by Ensembl identified 21 983 protein-coding genes.}, } @article {pmid41993799, year = {2026}, author = {Yue, XL and Wu, YH and Zheng, DQ and Sun, C and Xu, L and Cui, L and Xu, XW}, title = {[13]C-labeled single-cell Raman sorting reveals sulfur-driven dark carbon fixation in coastal sediments.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag073}, pmid = {41993799}, issn = {2730-6151}, abstract = {Chemoautotrophs drive carbon fixation in coastal sediments, but most of them remain uncultured with poorly characterized in situ activities. In this study, a cultivation-independent single-cell approach combining Raman spectroscopy with [13]C-stable isotope probing was developed to enable direct identification of active chemoautotrophs in coastal sediments using function-specific spectral biomarkers, targeted metagenomic sequencing and pure culture verification. [13]C-induced shifts in cytochrome c (749, 1129, 1312, 1589 cm[-1]) and phenylalanine (1002 cm[-1]) Raman bands were systematically evaluated and applied as functional biomarkers through investigations of both representative chemoautotrophic strains and environmental samples. The combined analysis of targeted sorting of active chemoautotrophic cells and metagenomic sequencing revealed dominant species and a complete Calvin-Benson-Bassham (CBB) cycle pathway in sulfur-oxidizing guilds. Remarkably, a novel sulfur-oxidizing chemoautotroph, Guyparkeria sp. TX1, which showed ≥99% gene sequence similarity to contigs recovered from sorted-cell metagenomes, was isolated from enrichment cultures. Its significant carbon fixation capacity provided experimental validation for the effectiveness of Raman-based in situ functional screening. This study establishes Raman-based functional biomarkers applicable to chemoautotrophic carbon fixation, enabling in situ mapping of microbial carbon fluxes. By integrating single-cell phenotypic activity with genomic potential, this work advances the mechanistic understanding of sulfur-driven dark carbon fixation, which sustains coastal blue carbon ecosystems as a keystone process.}, } @article {pmid41993915, year = {2026}, author = {Hoedt, EC and Burns, GL and Hedley, KE and Waller, S and Sanchez, TC and Chisolm, O and MacCallum, H and Richardson, S and Suthers, B and Pepper, E and Keely, S and Talley, NJ}, title = {Shared functional microbiome signatures in Parkinson's disease and constipation predominate irritable bowel syndrome despite taxonomic divergence.}, journal = {Brain, behavior, & immunity - health}, volume = {53}, number = {}, pages = {101218}, pmid = {41993915}, issn = {2666-3546}, abstract = {BACKGROUND: Gastrointestinal dysfunction, including constipation, is a common non-motor feature of Parkinson's disease (PD) and often precedes motor symptoms. The gut microbiome interacts with the host through neural, hormonal, and immune pathways, yet whether constipation represents a cause or consequence of PD remains unclear. Therefore, we aimed to interrogate the associations between microbiome and immune alterations in relation to constipation to provide novel insight into microbiome-gut-brain axis mechanisms in PD.

METHODS: We analysed peripheral blood mononuclear cells (PBMCs) for circulating gut-homing T cell populations and used shotgun metagenomics to profile the stool microbiome composition and functional capacity in PD patients (n = 18), healthy controls (n = 21), and individuals with constipation-predominant irritable bowel syndrome (IBS-C; n = 8). Associations between immune markers and microbial taxa were assessed, and functional pathway differences were evaluated.

RESULTS: Circulating gut-homing T cell frequencies did not differ significantly between PD and controls, but constipated PD patients showed a trend toward increased circulating gut-homing T cells. Microbiome beta-diversity analyses revealed distinct taxonomic shifts in PD and IBS-C, while functional capacity was largely conserved. Of the differential functional pathways tryptophan biosynthesis, polyamine production, and vitamin B metabolism, processes critical for neurotransmitter synthesis, epithelial integrity, and neuroimmune regulation were reduced in PD compared to IBS-C.

CONCLUSION: Our findings highlight unique microbial and immune signatures in PD, partially overlapping with IBS-C, and underscore the importance of microbial metabolic pathways in gut-brain axis disorders. Collectively our findings suggest a contribution to dopaminergic dysfunction, neuroinflammation, and impaired gut motility. Future longitudinal studies are needed to clarify causal relationships and inform targeted interventions for PD-related gastrointestinal dysfunction.}, } @article {pmid41993958, year = {2026}, author = {Meng, H and Zhao, S and Jin, H and Zhang, H and Li, Q and Zhang, L and Hu, J and Kong, F and Du, X and Li, Q and Ajwad Rahim, M and Xu, L and Xue, Y}, title = {Unveiling the Role of Rumen Microbiome in Modulating Intramuscular Fat Deposition of Pingliang Red Cattle.}, journal = {Food science & nutrition}, volume = {14}, number = {4}, pages = {e71681}, pmid = {41993958}, issn = {2048-7177}, abstract = {Pingliang Red cattle is renowned for its tender meat and symmetrical intramuscular fat (IMF) deposition. Rumen microbiota are crucial for energy metabolism and nutrient acquisition in cattle, significantly influencing IMF deposition. Therefore, this study aimed to explore how rumen microbiota impact IMF deposition in Pingliang Red cattle. 34 castrated Pingliang Red cattle were subjected to the same management for 2 months, followed by centralized and unified slaughtering. Based on the measured IMF content in the longissimus dorsi, 18 cattle were selected and divided into a high-intramuscular-fat group (HIMF, n = 9) and a low-intramuscular-fat group (LIMF, n = 9). Rumen fluid was subsequently collected for metagenomic sequencing. Results showed significant differences in taxonomic abundance at both the genus and species levels, the relative abundance of carbohydrate-active enzyme (CAZy) families, and functional profiles (p < 0.05). Specific rumen microbes, such as Limosilactobacillus panis (AUC = 0.765) and Fibrobacter succinogenes (AUC = 0.753), served as potential biomarkers for HIMF deposition in Pingliang Red cattle. With the exception of Bacillus, Fibrobacter succinogenes, Limosilactobacillus panis, Prevotella intermedia, and Streptomyces exhibited positive correlations with IMF content. Functional analysis based on KEGG orthology (KO) indicated that specific enzymes promote IMF deposition by regulating the metabolism of short-chain fatty acids (SCFAs), long-chain fatty acids (LCFAs), and lipopolysaccharides, as well as insulin signaling. These findings provide a theoretical reference for regulating rumen microbial communities to improve IMF deposition.}, } @article {pmid41994130, year = {2026}, author = {Khan, D and Espinoza, JL and Tientcheu, PE and Otchere, ID and Mohammed, NI and Worwui, A and Nicol, MP and Kwambana-Adams, B and Antonio, M and Dupont, CL}, title = {Shotgun metagenomic profiling of bacterial microbiomes, metagenome-assembled genomes and antimicrobial resistance in respiratory and blood samples from Gambian children with pneumonia.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41994130}, issn = {2693-5015}, support = {R01 AI170111/AI/NIAID NIH HHS/United States ; }, abstract = {Pneumonia is a leading cause of morbidity and mortality in children, with bacterial pathogens being important etiologic agents. Most microbiome studies in pneumonia use technologies with limited taxonomical resolution and few include lung aspirate or blood samples. In this study, we assessed the microbial communities of the nasopharynx, nasopharynx/oropharynx, induced sputum, lung aspirate and blood, and recovered metagenome-assembled genomes from the same sites using shotgun metagenomics sequencing of samples from children with severe and very severe pneumonia in The Gambia. Our data show that Proteobacteria and Firmicutes were the most common phyla across the body sites, and this was largely driven by S. pneumoniae, H. influenzae/aegyptius and M. catarrhalis. Furthermore, we observed species overlap of blood and respiratory samples with average Jaccard similarity index values ranging from 34% to 58%. We recovered 60 medium and 35 high-quality MAGs in these niches including 11 S. pneumoniae, 10 H. influenzae strains and a limosilactobacillus with less than 95% Average Nucleotide Identity to any known species in GTDB-TK. We also showed that the resistomes in our MAGs were highly species specific with more than 70% of the detected AMR genes found exclusively in a single species.}, } @article {pmid41994193, year = {2026}, author = {Jiang, T and Yan, F and Liu, B and Li, Q and Wang, K and Ru, X and Hao, Y and Guan, Y and Wang, Y}, title = {Intraventricular hemorrhage, suspected EBV reactivation, and TBA-positive epilepsy after deep cervical lymphovenous anastomosis in Alzheimer's disease: a case report.}, journal = {Frontiers in aging neuroscience}, volume = {18}, number = {}, pages = {1791011}, pmid = {41994193}, issn = {1663-4365}, abstract = {Lymphovenous anastomosis (LVA) is emerging as a potential surgical intervention to ameliorate cervical lymphatic outflow and enhance glymphatic clearance in Alzheimer's disease (AD). However, the spectrum of neurological sequelae associated with this procedure remains poorly characterized. We report the case of a 67-years-old male with amyloid PET-confirmed AD who underwent bilateral deep cervical LVA. Twenty-three days postoperatively, he presented with high-grade fever and altered consciousness. Head CT revealed acute hemorrhage in the posterior horn of the left lateral ventricle (∼2 mL). Cerebrospinal fluid (CSF) analysis demonstrated lymphocytic pleocytosis and significantly elevated protein levels; the fluid was uniformly bloody, confirming intraventricular hemorrhage. Plasma metagenomic next-generation sequencing (mNGS) identified Epstein-Barr virus (EBV), with serology supporting reactivation. Following antiviral and empirical antibiotic therapy, the patient's condition stabilized, and the hemorrhage resolved. Four months postoperatively, he developed new-onset generalized seizures. Despite negative results from a conventional autoimmune encephalitis antibody panel in both serum and CSF, a tissue-based assay (TBA) proved positive in both samples. Seizures were successfully controlled with levetiracetam. This case suggests a potential association between invasive lymphatic procedures and a hemorrhage-infection-immune cascade in highly vulnerable AD patients with preexisting metabolic and neurodegenerative risk factors.}, } @article {pmid41994268, year = {2026}, author = {Zhang, F and Chen, J and Yuan, Y and Chen, J and Jiang, W and Xiang, W and Wang, N and Wu, Z and Fan, S and Zhang, K and Ma, Y and Liu, T and Zhang, J and Yu, Q and Zhang, J}, title = {The enhancing therapeutic effect of neonatal jaundice by bifidobacterium through regulating inflammation and gut microbiota in combination with phototherapy-a randomized controlled trial.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1761245}, pmid = {41994268}, issn = {1664-302X}, abstract = {BACKGROUND: Hyperbilirubinemia is among the most common conditions in neonates, and phototherapy is currently the most widely used treatment. However, it can induce side effects such as skin rashes, diarrhea, and gut microbiota dysbiosis, particularly affecting Bifidobacterium levels. This study aimed to investigate whether the supplementation of Bifidobacterium can alleviate dysbiosis and improve clinical outcomes in jaundiced neonates.

METHODS: A total of 79 jaundiced neonates were enrolled and divided into four groups: Phototherapy Control, M-16V, Bb-12, and the combined M-16V+Bb-12 group. Probiotics were administered until 30 days post-discharge, and neurodevelopment was assessed at 1.5-2 years using the Griffith Development Scales. Fecal samples collected before, during, and after treatment were analyzed using metagenomic sequencing and non-targeted metabolomics.

RESULTS: Probiotic supplementation significantly increased daily defecation frequency, accelerated the reduction rate of transcutaneous bilirubin, and shortened hospital stays. Griffith scores indicated that Bb-12 supplementation improved scores in personal-social and performance domains. Metagenomic analysis revealed significant differences in beta diversity between the control and probiotic groups; specifically, M-16V and combined supplementation increased the abundance of Bifidobacterium breve. Pathway enrichment analysis showed up-regulation of pyrimidine-containing compound metabolic processes, intramolecular transferase activity, and DNA conformation change. Metabolomics further demonstrated that combined supplementation elevated levels of 5-methyltetrahydrofolate (linked to DNA synthesis), benzoic acid and indoleacetic acid (linked to growth and development), and the anti-inflammatory metabolite indole-3-lactic acid.

DISCUSSION: For neonates receiving phototherapy, the addition of M-16 V + Bb-12 probiotics can improve the diversity of microflora, reduce the fixed value of harmful bacteria in the intestine, and enhance the excretion of bilirubin from the intestine, to improve the inflammatory damage and microbiota disorder caused by phototherapy, and achieve the effect of clinically improving jaundice, reducing bilirubin, shortening the length of hospitalization, and promoting neurodevelopment. It provides a safer and more effective treatment for neonatal jaundice.}, } @article {pmid41994275, year = {2026}, author = {Yu, T and Yu, Y and Zhao, J and Li, H and Lu, H and Li, Y and Peng, Y and Wang, S and Wei, W and Cheng, X}, title = {Qifuyin improves physiological frailty by regulating the intestinal flora in 3xTg-AD mice.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1753643}, pmid = {41994275}, issn = {1664-302X}, abstract = {OBJECTIVE: Alzheimer's disease (AD) is often accompanied by motor dysfunction, impaired limb strength, and gut microbiota disturbances. This study aimed to evaluate the effects of Qifuyin (QFY), a traditional Chinese medicine formula, on motor deficits, limb strength, aging, and gut microbiota composition in 3xTg-AD mice, a widely used model of AD.

METHODS: Male and female 3xTg-AD mice were administered QFY at low, medium, or high doses. Motor function was assessed using grip strength and rotarod tests. Aging was evaluated through aging scores. Gut microbiota composition was analyzed at the phylum, family, genus, and species levels. Functional profiling of microbiota was performed using KEGG, eggNOG, and carbohydrate-active enzyme (CAZyme) databases. Pearson correlation analyses were conducted to explore relationships between microbiota composition and motor performance.

RESULTS: QFY treatment significantly improved both absolute and normalized grip strength in male and female 3xTg-AD mice. Similarly, motor coordination, as assessed by latency to fall on the rotarod, was significantly enhanced in the groups of QFY. Aging scores were significantly reduced after the treatment of QFY. Microbiome analysis revealed that QFY treatment restored species diversity and improved the overall composition of gut microbiota, with significant increases in Muribaculaceae and decreases in Alcaligenaceae, Rhodanobacteraceae, and Spirochaetaceae. Principal component analysis (PCA) indicated that the gut microbiota composition of the QFY group resembled that of the control (Con) group. Functional analyses showed that treatment of QFY restored microbial pathways related to metabolism and genetic information processing, with significant correlations between microbial alterations and improved motor outcomes. Additionally, QFY modulated the abundance of key carbohydrate-active enzymes, including GH43 and GH35, which were positively correlated with grip strength and rotarod performance.

CONCLUSION: Qifuyin improves motor function, reduces aging-related deficits, and restores gut microbiota homeostasis in 3xTg-AD mice. These findings suggest that QFY may offer therapeutic potential for addressing frailty and motor dysfunction in AD, in association with alterations in gut microbiota composition and predicted microbial functions.}, } @article {pmid41994276, year = {2026}, author = {Xian, J and Li, Y and Feng, Z and Jin, Y and Cai, T and Cao, M and Cao, Y}, title = {High-fat diet-driven gut microbial sphingolipid metabolic reprogramming is associated with stress susceptibility in CUMS rats.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1802003}, pmid = {41994276}, issn = {1664-302X}, abstract = {The escalating comorbidity between depression and metabolic syndromes induced by a high-fat diet (HFD) poses a substantial social and economic burden on society. However, the precise molecular mechanisms by which a HFD qualitatively alters the basal pathophysiology of chronic unpredictable mild stress (CUMS) remain unclear. In this study, the differential roles of microbial and metabolic pathways in the onset and exacerbation of depression were investigated using CUMS rat models fed a normal diet (ND-CUMS) or HFD (HFD-CUMS). Our findings indicated that HFD intervention showed a trend toward aggravating depressive behaviors and resulted in significantly more severe neuronal injury in the hippocampus relative to the ND-CUMS group. Notably, integrated multi-omics (metagenome and metabolome) analysis revealed a crucial pathway divergence: basal CUMS depression was strongly associated with the dysregulation of glycerophospholipid metabolism, linked to microbiota such as Bacteroides thetaiotaomicron and Terrisporobacter glycolicus, while HFD triggered a predominant disruption of the sphingolipid metabolism pathway. Exploratory mediation analysis suggested that a sphingolipid-related signature that may statistically connect HFD-associated microbial shifts with neural injury and behavioral readouts. Therefore, our findings reveal a distinct mechanistic shift underpinning metabolic-comorbid depression. HFD does not merely exacerbate stress-induced depression but fundamentally transitions the underlying pathology from glycerophospholipid to sphingolipid signaling, highlighting the potential of targeting specific lipid metabolic reprogramming as a promising therapeutic strategy for combating metabolic-comorbid depression.}, } @article {pmid41994278, year = {2026}, author = {Dang, M and Tang, Y and Chen, J and Xie, W and Zhong, Y and Yu, B and Zhang, E and Wang, Z}, title = {Rhizospheric soil microbial community structure and metabolic characteristics of wild Cymbidium mastersii at different altitudes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1720137}, pmid = {41994278}, issn = {1664-302X}, abstract = {INTRODUCTION: Cymbidium mastersii, a perennial orchid of high ornamental value, faces severe survival challenges due to extremely low natural seed germination rates (<15%), habitat degradation, and illegal harvesting. It is listed as a Category II Nationally Protected Plant Species in China.

METHODS: We examined the rhizosphere microbial communities and metabolomes of C. mastersii across elevation gradients. We investigated the rhizospheric soil microbial community composition and metabolic characteristics of C. mastersii across different elevations.

RESULTS: The dominant bacterial phylum was Pseudomonadota, with relative abundances of 38.22% (CmL, low elevation), 36.91% (CmM, mid-elevation), and 62.54% (CmH, high elevation). While the dominant bacterial genera varied significantly with elevation, taxonomic richness exhibited a consistent decline with increasing altitude (p < 0.05, linear regression), indicating altitudinal filtering of microbial diversity. LC-MS/MS metabolomic profiling identified 1,516 metabolites, predominantly enriched in lipid and lipid-like molecules, carbohydrates and derivatives, and aromatic compounds. Functional contribution analysis revealed Bradyrhizobium as the most influential taxon (10% variance explained), displaying a nonlinear elevational response. Correlation analysis of differential metabolites confirmed significant species-metabolite correlations (P < 0.05, R > 0.7). Our findings underscore the critical role of trophic interactions in shaping rhizosphere community assembly in alpine plants, thereby contributing to the broader understanding of microbial biogeography along elevational gradients.

DISCUSSION: This study not only confirms that the altitudinal gradient serves as a key environmental filter shaping the rhizosphere microecology of C. mastersii, but more importantly, by integrating metagenomic and metabolomic approaches, we systematically reveal for the first time that altitude differentially selects for microbial taxa with specific functions, ultimately driving the restructuring of the rhizosphere metabolic environment. Moving beyond mere community description, our work aims to elucidate the underlying pathways responsible for these shifts and their potential functional implications for host plant adaptation.}, } @article {pmid41994292, year = {2026}, author = {Sun, M and Lei, Z and Li, B and Gao, SH and Fan, L}, title = {Virus-encoded metabolism may support environmental stress adaptation of microbial hosts in an estuarine hypoxic zone.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1785655}, pmid = {41994292}, issn = {1664-302X}, abstract = {Hypoxic zones in estuaries threaten the ecological balance and the productivity in coastal areas. However, it is poorly understood how viruses regulate metabolic processes of their microbial hosts to adapt to the hypoxic environment, and consequently impact the biogeochemical cycles in hypoxic zones. In this study, the diversity and functional potentials of the bacterial, archaeal and viral communities of a hypoxic zone at the Pearl River Estuary was characterized along with local environmental factors, with a particular focus on viral auxiliary metabolic genes (AMGs). The viral community derived from the virion fraction and the cellular fraction of the seawater were distinctly different, with the cellular fraction generating fewer unique viruses, but more types of AMGs. Overall, more AMGs were identified in samples with higher dissolved oxygen levels. Globally conserved AMGs were infrequently observed in the current samples, suggesting a certain level of adaptation of AMGs to the local environment. There were strong correlations in abundances among cyanobacteria, cyanophages, and photosynthesis AMGs, suggesting potential viral participation in estuarine primary production. Many AMGs involved in nutrient limitation endurance were found, potentially assisting their host with phosphorus, iron and B family vitamin shortages. Although putative hosts were predicted for the viruses, the functionality of their AMGs appears to be a better predictor of their distribution than the hosts they infect. Our study provides a functional insight into the viral community in poorly researched estuarine hypoxic zones, and sheds light on the potential interactions of viruses with their microbial hosts for co-adaptation to this unique environment.}, } @article {pmid41994309, year = {2026}, author = {Sarkar, P and Sarkar, S and Unnisa, M and Singh, AP and Inavolu, P and Rughwani, H and Jakkampudi, A and Jaggaiahgari, S and Reddy, DN and Talukdar, R}, title = {The Jejunal Microbiota in Patients With Chronic Pancreatitis: Results From a Pilot Study.}, journal = {Gastro hep advances}, volume = {5}, number = {5}, pages = {100907}, pmid = {41994309}, issn = {2772-5723}, abstract = {BACKGROUND AND AIMS: Chronic pancreatitis (CP) is associated with several systemic metabolic abnormalities including diabetes. While the colonic microbiota and its association with diabetes in CP have been reported, the specific composition of the small intestinal microbiota and its function in CP remains poorly understood. In this pilot study, we primarily aimed to characterize the jejunal microbiota in patients with CP and explore potential associations with diabetes.

METHODS: Jejunal aspirates were collected in a RNAlater-containing sterile container from 29 patients with CP and 10 controls. The samples were then snap lysed followed by metagenomic DNA extraction. Next-generation sequencing was performed for the variable region 3-4 of the 16SrDNA in Illumina MiSeq. After quality control, microbial profiling and functional analysis were conducted using standard bioinformatics pipelines. We also evaluated tight junction integrity in jejunal biopsy samples using immunofluorescence. Furthermore, we assessed for plasma and stool metabolites.

RESULTS: Patients with CP exhibited higher abundances of Prevotella vespertina, Prevotella oris, and Prevotella salivae, while controls demonstrated higher abundances of Prevotella scopos, Veillonella, Rothia, and Lachnospiraceae. Immunofluorescence showed decreased expression of the tight junction protein occludin in the jejunal mucosa of CP diabetic (CPD) patients compared to endoscopic controls (EC) (p.corr. CPD-EC = 0.012). No differences were seen between CP nondiabetic and endoscopic controls, and between the CP subgroups (CPND-EC = 0.29 and CPD-CPND = 1 respectively). Overall, there were significant plasma metabolomic abnormalities in patients with CP and a trend toward reduction of butyrate in the stool samples of the CP patients with diabetes.

CONCLUSION: Our observations suggest alterations in the jejunal microbiota and mucosal barrier function in CP. These were associated with lower fecal butyrate. This may contribute to the pathogenesis of associated metabolic complications in CP. Further large-scale longitudinal and mechanistic studies are needed to validate our findings.}, } @article {pmid41994369, year = {2026}, author = {Bao, Q and Zhang, X and Guo, J}, title = {Enterovirus D68 and mycobacterial coinfection: case report.}, journal = {Therapeutic advances in infectious disease}, volume = {13}, number = {}, pages = {20499361261432918}, pmid = {41994369}, issn = {2049-9361}, abstract = {The threat of viral epidemics to long-standing diseases, such as mycobacterial infection, is constantly evolving. Enterovirus D68 (EV-D68) is an emerging cause of respiratory infection and has raised great interest since its first outbreak in 2014. Very few studies have been done to describe the clinical aspects of the coinfection of EV-D68 and mycobacteria, so this study was conducted to help round out the understanding of this coinfection pattern. We observed three adult cases of EV-D68 and mycobacteria, who were admitted to the first affiliated hospital of Zhejiang University in August/September 2024. Only one case had a definite past history of immunodeficient disease and received long-term corticosteroid treatment, and the other two were previously healthy. The diagnoses of EV-D68 and mycobacterial infection were all simultaneously confirmed through the metagenomic Next-Generation Sequencing in bronchoalveolar lavage fluid specimens. All three patients were presented with severe respiratory symptoms, such as fever, cough, dyspnea and tachypnea, without any manifestations of central nervous system involvement. The radiological findings in chest CT scans varied from patchy opacity to massive consolidation. The individualized anti-mycobacterium treatment showed little therapeutic effect, while the improvement of symptoms and pulmonary lesions in chest CT was observed after starting or intensifying the administration of corticosteroid. All patients had a marked clinical improvement when discharged from hospital, and it took about 6-9 months for the lung lesions of mycobacterial infections to nearly resolve. These cases illustrate the potential for EV-D68 coinfection to exacerbate pulmonary inflammation in patients with mycobacterial disease, highlighting the need for vigilance regarding possible viral coinfections in settings with a high tuberculosis burden, such as China.}, } @article {pmid41994453, year = {2026}, author = {Zhang, W and Zhang, K and Liao, Y and Yang, Z and Xia, Z and Ke, X and Zhang, D and Chen, J and Wu, H and Hong, Y and Wang, H and Liu, Z and Suo, L and Zhang, Y and Zhang, C}, title = {Characterization of the aqueous humor microbiome in Posner-Schlossman syndrome: an exploratory metagenomic sequencing study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1780981}, pmid = {41994453}, issn = {2296-858X}, abstract = {OBJECTIVE: This study aims to characterize the aqueous humor (AH) microbiome in Posner-Schlossman syndrome (PSS) patients and evaluate its potential as a diagnostic and therapeutic target.

METHODS: Metagenomic next-generation sequencing (mNGS) was performed on 59 AH samples from patients diagnosed with PSS (n = 28) and myopia patients who underwent intraocular lens (ICL) implantation (n = 31). Taxonomic profiling and diversity analyses were conducted to characterize the microbial communities. Interactions among microbial community members were evaluated using correlation analyses.

RESULTS: Key findings revealed that intraocular microbiomes existed in both normal and diseased eyes; however, PSS patients exhibited lower microbial diversity (Shannon index, p = 0.066; Simpson index, p = 0.065) and distinct community structures (PERMANOVA, p = 0.05). Disease-specific microbial signatures were identified: Paeniglutamicibacter was uniquely enriched in the PSS group, whereas Escherichia coli dominated in the ICL group. Moreover, ecological network analysis demonstrated contrasting interaction patterns. The microbiomes in the PSS group formed stable, tightly connected networks with balanced positive/negative correlations, whereas those in the ICL group exhibited antagonistic relationships, suggesting competitive exclusion. These results challenge the traditional view of ocular sterility and reveal dynamic microbiome shifts associated with PSS pathogenesis. The enrichment of Paeniglutamicibacter in PSS may represent an associated microbial signature that could potentially reflect compensatory responses to chronic inflammation, although experimental validation is needed to confirm this hypothesis.

CONCLUSION: Our study provides preliminary evidence supporting the concept of intraocular microbiome dysbiosis in PSS, which requires validation in future studies. These findings suggest that potential microbial biomarkers warrant further investigation for their diagnostic and therapeutic implications.}, } @article {pmid41994458, year = {2026}, author = {Jiang, L and Ye, T and Cai, H and He, F}, title = {Case Report: A rare case of Pneumocystis jirovecii infection with left hydropneumothorax following immunotherapy for stage IVB clear cell renal cell carcinoma.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1784855}, pmid = {41994458}, issn = {2296-858X}, abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) is an opportunistic infection that predominantly affects immunocompromised individuals, most commonly HIV-infected patients with significantly reduced CD4+lymphocyte counts, and is associated with high clinical mortality. Currently, there are few reports of pneumothorax secondary to PJP, and most cases occur in HIV-infected populations. However, PJP complicated by hydropneumothorax in cancer patients receiving immunotherapy is exceedingly rare, with limited reports in the literature. To our knowledge, this article reports a rare clinical case of Pneumocystis jirovecii infection complicated by left-sided hydropneumothorax in a patient with stage IVB clear cell renal cell carcinoma after immunotherapy, aiming to provide valuable insights for the early diagnosis and management of PJP and its complications in cancer patients undergoing immunotherapy.

CASE: A 57-year-old male patient had previously undergone surgical treatment for left renal clear cell carcinoma, and developed recurrent metastases to the descending colon, liver, and upper pole of the left kidney after surgery, with a clinical stage of T4NxM1 stage IVB. After receiving targeted combination immunotherapy with sequential PD-1 inhibitors (toripalimab) plus anti-angiogenic agents (sunitinib, axitinib)-a regimen that enhances anti-tumor immunity but may disrupt pulmonary immune homeostasis-the patient gradually developed progressive dyspnea, chest tightness, hypoxemia, and anuria. Multiple auxiliary examinations were performed clinically, including chest X-ray, bronchoalveolar lavage, and metagenomic sequencing of pathogenic microorganisms. Based on the above examination results, the final diagnosis was Pneumocystis jirovecii pneumonia complicated by left-sided hydropneumothorax.

CONCLUSION: Although PJP complicated by hydropneumothorax after immunotherapy is rare, it should be considered as a possible etiology when cancer patients develop progressive dyspnea with difficulty maintaining oxygen saturation after receiving immune checkpoint inhibitor-based therapy, particularly in the context of immune checkpoint inhibitor use. While biomarkers for predicting immunotherapy efficacy and irAEs are well-studied, the identification of specific biomarkers for predicting opportunistic infections like PJP in this context remains an area of active research.}, } @article {pmid41994961, year = {2026}, author = {Sun, QG and Zang, D and Xin, Y and Cui, J and Han, X and Chen, J}, title = {Multi-omics Analysis Reveals the Correlation of Gut Microbiota and Metabolites With Thalidomide Treatment for Chemotherapy-Induced Nausea and Vomiting in Small Cell Lung Cancer.}, journal = {Biotechnology journal}, volume = {21}, number = {4}, pages = {e70228}, pmid = {41994961}, issn = {1860-7314}, support = {82203056//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Thalidomide/therapeutic use/pharmacology ; *Small Cell Lung Carcinoma/drug therapy/microbiology/metabolism ; *Lung Neoplasms/drug therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Multiomics ; *Nausea/chemically induced/drug therapy/microbiology ; *Vomiting/chemically induced/drug therapy/microbiology ; Male ; Female ; Middle Aged ; Aged ; Metabolome/drug effects ; Metabolomics ; Antineoplastic Agents/adverse effects/therapeutic use ; }, abstract = {Small cell lung cancer (SCLC) is a highly aggressive malignancy, and chemotherapy frequently causes nausea and vomiting, which can impair treatment tolerance. Because thalidomide (THD) has shown potential clinical benefit in alleviating nausea and anorexia, we investigated whether its effects might be associated with changes in gut microbial composition and metabolite profiles. Fecal samples were collected from patients with SCLC and categorized into THD-treated and control groups. Metagenomic sequencing and nontargeted metabolomic profiling were performed to characterize microbial composition and metabolic signatures. THD treatment was also associated with higher microbial alpha diversity and increased abundance of genera such as Eubacterium and Prevotella. Metabolomic analysis identified several differential metabolites, including hydrogenated MDI, becocalcidiol, β-octylglucoside, and azelaic acid. Collectively, these findings suggest that the gut microbiota-metabolite axis may be associated with the potential effects of THD on CINV and anorexia in patients with SCLC. The identified microbial taxa and metabolites may serve as candidate biomarkers or potential therapeutic targets, although further validation in larger studies is necessary.}, } @article {pmid41995327, year = {2026}, author = {Chen, Y and Tang, X and Lu, S and Guo, L and Wang, L and Min, L and Niu, T and Zhou, Y}, title = {The diagnostic and prognostic utility of blood metagenomic next-generation sequencing for invasive pulmonary aspergillosis.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0338425}, pmid = {41995327}, issn = {2165-0497}, support = {2022YFC2406804//National Key Research and Development Program of China/ ; 82370192, U24A20680//National Natural Science Foundation of China/ ; GYYX24003//1.3.5 Project of High Altitude Medicine/ ; 82402588//National Natural Science Foundation of China/ ; 2024NSFSC1746//Natural Science Foundation of Sichuan Province/ ; 2025M772028//China Postdoctoral Science Foundation/ ; GZB20230475//the Postdoctoral Fellowship Program of China Postdoctoral Science Foundation/ ; 2024J0304//the Scientific Research Fund of Yunnan Provincial Department of Education/ ; 202401AY070001-295//the Kunming Medical Joint Special Project of Yunnan Provincial Science and Technology Plan Project/ ; }, mesh = {Humans ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology/blood/mortality ; Prognosis ; Retrospective Studies ; Female ; Biomarkers/blood ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Metagenomics/methods ; Middle Aged ; Galactose/analogs & derivatives ; beta-Glucans/blood ; Mannans/blood ; Aged ; *Aspergillus/genetics/isolation & purification ; ROC Curve ; Coinfection/microbiology/diagnosis ; Proteoglycans ; }, abstract = {UNLABELLED: Differentiating invasive pulmonary aspergillosis (IPA) from colonization in patients with Aspergillus-positive blood metagenomic next-generation sequencing (mNGS) remains a clinical challenge. This study aims to evaluate the diagnostic and prognostic value of blood mNGS-derived fungal load (reads per million [RPM]) and two key serological biomarkers (galactomannan [GM] and 1,3-β-D-glucan [BDG]) in distinguishing these two entities. This retrospective study enrolled 95 patients with Aspergillus detected by blood mNGS, stratified into infection (n = 60) and colonization (n = 35) groups using modified EORTC/MSGERC criteria. We analyzed clinical characteristics, co-infection spectra, and serological biomarkers (GM and BDG). Diagnostic performance was evaluated via receiver operating characteristic (ROC) analysis, and prognostic factors for 28-day mortality were identified using least absolute shrinkage and selection operator-Cox regression. Distinct co-infection patterns were observed between groups: the infection group was dominated by polymicrobial co-infections, including clinically significant pathogens such as Acinetobacter baumannii, Klebsiella pneumoniae, Mucor spp., and Human cytomegalovirus; in contrast, the colonization group primarily featured single viral co-infections. While mNGS effectively detected Aspergillus, RPM alone showed limited ability to discriminate infection from colonization, with area under the curves (AUCs) ranging from 0.406 to 0.657 across patient groups. The optimal RPM cutoff varied substantially by immune status, being highest in immunocompetent patients (RPM cutoff: 1.77). Diagnostic performance significantly improved when RPM was integrated with GM (AUC up to 0.900 at a cutoff of 0.36 optical density index) or BDG (AUC up to 0.881 pg/mL), particularly in immunocompetent individuals. RPM also correlated with albumin, hemoglobin, platelet counts, and lymphocyte counts (all P < 0.05). Multivariate analysis identified reversed halo sign (hazard ratio [HR] = 2.143), decreased ratio of partial pressure of arterial oxygen to fraction of inspired oxygen (PaO2/FiO2; HR = 1.361), and elevated lactate dehydrogenase (HR = 1.055) as independent predictors of 28-day mortality. Blood mNGS demonstrates high sensitivity for detecting Aspergillus but requires integration with serological biomarkers to differentiate IPA from colonization. The RPM can offer prognostic utility. A multimodal strategy is crucial for early diagnosis and improving outcomes in high-risk patients.

IMPORTANCE: First large-scale validation of blood mNGS for invasive pulmonary aspergillosis diagnosis-this study represents the first sizable cohort systematically evaluating blood metagenomic next-generation sequencing (mNGS) for distinguishing invasive pulmonary aspergillosis from colonization, addressing a critical gap in non-invasive diagnostic approaches for critically ill patients. Comprehensive Aspergillus co-infection profiling-we identified distinct co-infection patterns, with the infection group showing significantly higher rates of polymicrobial infections, providing crucial insights into co-infection dynamics in Aspergillosis. Optimized diagnostic integration strategy-our findings demonstrate that while mNGS-derived reads per million alone show limited diagnostic value, their integration with serological biomarkers significantly improves performance, establishing a clinically relevant multimodal diagnostic framework. Robust prognostic stratification model-through least absolute shrinkage and selection operator-Cox regression, we established a validated prognostic model identifying reversed halo sign, decreased PaO2/FiO2, and elevated lactate dehydrogenase as independent predictors of 28-day mortality, providing clinically actionable tools for risk stratification.}, } @article {pmid41995478, year = {2026}, author = {Conley, TE and Duncan, A and Modasia, A and Ford, AC and Pritchard, DM and Hildebrand, F and Warren, FJ and Spiller, R and Probert, CS}, title = {The Emerging Short Chain Fatty Acid Enriched Metabotype in Irritable Bowel Syndrome and Its Potential Clinical Relevance.}, journal = {Alimentary pharmacology & therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1111/apt.70677}, pmid = {41995478}, issn = {1365-2036}, abstract = {BACKGROUND: Metabolomic analysis in irritable bowel syndrome (IBS) has identified metabotypes enriched in faecal short-chain fatty acids (SCFAs), but it remains unclear whether this reflects rapid colonic transit or if these metabolites actively contribute to pathophysiology.

AIMS: We aimed to determine whether an SCFA metabotype could be identified within a cohort of patients with moderate-severe IBS-D and assess whether this metabotype associated with greater clinical severity, alterations in gut transit time and specific microbiome features.

METHODS: This was a post hoc cross-sectional exploratory analysis of baseline data from the multicentre, randomised, placebo-controlled trial of ondansetron in IBS-D (TRITON: ISRCTN17508514). Faecal volatile organic compounds were profiled by GC-MS. The microbiome was characterised by whole-genome shotgun metagenomic sequencing. Unsupervised hierarchical clustering was used to identify an SCFA-enriched metabotype and non-negative matrix factorisation (NMF) enabled the derivation of complementary metabosignatures by assessing continuous gradients in metabolite composition.

RESULTS: A SCFA-enriched metabotype was identified in 20/63 participants (31.7%). This metabotype was associated with more severe abdominal pain, urgency, increased stool frequency and faster whole-gut transit. NMF identified three metabosignatures: S3 was typified by a high proportion of SCFAs and captured the SCFA-enriched metabotype, while S1 and S2 corresponded to the non-SCFA ("Other") metabotype. SCFA relative abundance positively correlated with symptom severity and inversely correlated with transit time. The Other metabotype and S1/S2 signatures were enriched in taxa linked to slower transit, whereas S3 showed no overlapping taxa with the SCFA metabotype.

CONCLUSION: A faecal metabotype enriched in SCFAs associated with an IBS-D phenotype characterised by pain, urgency, rapid transit and higher stool frequency.}, } @article {pmid41995796, year = {2026}, author = {Vial, M and Costil, K and Agogué, J and Eustache, S and Heighton, S and Gissat, L and Gueuné, H and Caplat, C}, title = {Spatial and temporal variability of biofouling communities during early development in three French harbors of the English Channel.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {5}, pages = {}, pmid = {41995796}, issn = {1573-2959}, mesh = {*Biofouling/statistics & numerical data ; France ; Biofilms/growth & development ; *Environmental Monitoring ; Seawater/microbiology/chemistry ; Aquatic Organisms ; }, abstract = {Biofouling, the colonization of submerged surfaces by marine organisms, causes major economic losses in maritime activities. Although non-biocidal surface coatings are promoted as environmentally friendly antifouling solutions, the respective roles of surface properties and environmental conditions in shaping biofouling stages remain unclear. We hypothesized that coating surface properties primarily control early biofilm formation, whereas local environmental conditions govern subsequent macrofouling development. To test this hypothesis, we studied biofouling on two non-biocidal coatings - an anticorrosion epoxy and a fluoropolymer foul-release coating (FRC) - immersed under static conditions in three French harbors along the English Channel during the spring bloom. Early biofilm formation was assessed after 2 weeks in April, May, and June 2023 using chlorophyll a and the carbohydrate/protein ratio of extracellular polymeric substances (EPS). Macrofouling development over 3 months was evaluated through biomass, surface coverage rate, taxonomic composition, and microorganism abundances. Metagenomic analyses complemented the visual observations in Cherbourg during April and May 2023. The FRC showed a higher EPS carbohydrate/protein ratio, indicating greater resistance to initial microbial colonization, but exhibited significantly lower macrofouling intensity than the epoxy. This decoupling supports the hypothesis that surface properties and settlement processes operate at different spatial and temporal scales. Spatial variability in biofouling patterns may largely be associated with differences in nutrient availability and anthropogenic pressure. These findings demonstrate that early biofilm metrics alone cannot predict long-term fouling and highlight that antifouling performance depends on both material properties and environmental context. Integrating surface physicochemistry with site-specific ecological drivers can improve both coating design and antifouling evaluation strategies.}, } @article {pmid41996042, year = {2026}, author = {Myoung, K and Kim, S and Choi, EJ and Kim, HJ and Baek, HS and Park, WS and Hwang, JS}, title = {Integrated analysis of age-related microbiome and metabolites reveals youth-associated metabolites in young Korean women's skin.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41996042}, issn = {1618-1905}, abstract = {Alterations in the composition and functional potential of the skin microbiome are closely associated with aging. Nevertheless, integrative analyses that concurrently examine microbial composition, functional gene profiles, and skin surface metabolomics remain limited, particularly among Asian populations. In this study, we performed a comprehensive multi-omics analysis integrating skin microbiome and surface metabolomic data from Korean women to explore metabolites associated with youthful skin state. Twenty-three healthy female participants in their 20s and 60s were recruited. Skin physiological parameters were assessed, and microbiome and metabolite samples were collected from the cheek area. Unsupervised clustering of microbiome functional profiles revealed three microbial community patterns that were not strictly aligned with chronological age. Based on these patterns, samples were grouped into three functional groups. The cluster enriched in participants in their 20s showed higher relative abundance of Cutibacterium and enrichment of microbial pathways related to carbohydrate and energy metabolism. Metabolomic profiling showed that phenyllactic acid (PLA) and hydroxyphenyllactic acid were more abundant in participants in their 20s and in the functionally young cluster. These metabolite patterns were accompanied by higher abundance of genes associated with phenylalanine metabolism. In vitro experiments further showed that PLA increased procollagen production and reduced the secretion of collagen-degrading enzymes in human dermal fibroblasts under inflammatory conditions. Together, these findings suggest links between microbiome functional profiles, phenylalanine-related metabolites, and skin physiology. This study provides an integrated view of microbiome-metabolite relationships in Korean skin and identifies PLA as a candidate metabolite associated with youthful skin environments.}, } @article {pmid41996045, year = {2026}, author = {Mohanty, A and Pavan-Kumar, A and Chaudhari, A and Kumari, K and Kumar, P and Maurye, P}, title = {Comparative performance of traditional and commercial DNA extraction methods for fish gut microbiota analysis.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {41996045}, issn = {1573-4978}, support = {FBT-PB1-01//Indian Council of Agricultural Research/ ; }, abstract = {BACKGROUND: The symbiotic relationship between gut microbiota and their fish hosts has fuelled extensive research into microbial distribution besides their active role in host body metabolisms and paving the way for the sustainable aquaculture. This study aims to optimize and evaluate DNA extraction techniques for characterizing the gut microbiota of fish with diverse feeding habits: Hilsa (planktivorous), Catla (zooplankton feeder), Rohu (herbivorous), and Mrigal (illiophagus). METHODS AND RESULTS: Microbial genomic DNA was extracted using five traditional methods—PLICKS A, B, C, and CTAB (Methods D and E)—and three commercial kits (MN® Microbial, MN® Soil, and MN® Faecal), each with modifications. The efficacy of these methods was assessed based on DNA yield (traditional: 74–3070 ng/µL; commercial: 8.8–224 ng/µL), purity (traditional: A260/280: 1.38–1.92, A260/230: 1.03–2.21; commercial: A260/280: 1.30–3.25, A260/230: 0.5–2.0), and successful PCR amplification, a key step for downstream 16 S rRNA gene sequencing. Among traditional methods, PLICKS A (Catla), PLICKS C (Hilsa), CTAB (Mrigal and Catla), and PLICKS B (Catla, Rohu, Hilsa, Mrigal) delivered the highest DNA recovery (342–2080 ng/µL) and purity across different species. Similarly, among commercial kits, the MN® Microbial Modified Kit (Catla, Hilsa), MN® Soil Kit (Hilsa), MN® Soil Modified Kit (Catla, Rohu), MN® Faecal Kit (Catla), and MN® Modified Faecal Kit excelled, achieving optimal DNA recovery (108–224 ng/µL) and purity across various feeding habits. Overall, among traditional methods, PLICKS B proved to be the most effective, delivering high DNA yields (342–2080 ng/µL) with excellent purity (A260/280: 1.77–1.92; A260/230: 1.67–2.21) and enabling successful PCR amplification across fish species with diverse feeding habits. Similarly, among commercial kits, the MN Modified Faecal Kit achieved the highest DNA recovery (108–224 ng/µL) and purity (A260/280: 1.74–1.90; A260/230: 1.78–2.01), consistently supporting reliable amplification. CONCLUSIONS: These findings highlight effective DNA extraction methods tailored to fish with different feeding habits. Careful selection and optimization of extraction protocols are therefore essential for the accurate characterization of fish gut microbiota.}, } @article {pmid41996243, year = {2026}, author = {Lin, D and Ma, QX and Ye, YQ and Wanek, W and Gregory, AS and Jones, DL and Graham, DW and Zhu, D and Penuelas, J and Zhu, YG}, title = {Nutrient balance regulates soil microbial health under long-term fertilization.}, journal = {Cell reports}, volume = {45}, number = {4}, pages = {117274}, pmid = {41996243}, issn = {2211-1247}, abstract = {Fertilizer application in intensive agriculture critically influences microbial communities. It is still unclear how long-term input of different nutrients shapes microbial eco-evolutionary strategies and ecological functions. Through 180-year-old field fertilization experiment, alongside microbial culturing, pot experiments, and comprehensive metagenomic data analysis, we show that exclusive fertilization with inorganic chemicals causes carbon-nitrogen imbalances that increase microbial resource competition and antibiotic resistance gene (ARG) levels. Viruses further amplify this expansion through "piggyback the winner" strategy. The imbalanced use of nitrogen in chemical fertilizers disrupt ecological niche connections, leading to an increase in virulent viruses and reducing microbial nutrient cycling capacity. In contrast, more balanced nutrient supplies from organic fertilization reduced microbial competition and promoted microbial growth. However, responsible antibiotic use in livestock is essential to maximizing these benefits. Our research provides insights into enhancing agricultural sustainability through the management of soil nutrient conditions.}, } @article {pmid41996362, year = {2026}, author = {Buni, D and Kovács, ÁB and Wehmann, E and Grózner, D and Bányai, K and Nagy, EZ and Bradbury, J and Bottinelli, M and Stefani, E and Catania, S and Lysnyansky, I and Kovács, L and Gyuranecz, M and Kreizinger, Z}, title = {Identification and detection of genetic markers associated with antimicrobial susceptibility and evaluation of efflux pump mechanisms in Mycoplasma iowae.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0347345}, pmid = {41996362}, issn = {1932-6203}, mesh = {Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; Genetic Markers ; *Drug Resistance, Bacterial/genetics ; *Bacterial Proteins/genetics/metabolism ; *Membrane Transport Proteins/genetics/metabolism ; }, abstract = {Mycoplasma iowae is an economically significant pathogen that causes reduced hatchability, late embryo mortality and leg deformities, chondrodystrophy and skeletal lesions in poults. While prevention is essential in the control of infection, the appropriate administration of antibiotics may reduce economic losses during outbreaks. As a first step in the exploration of antimicrobial resistance mechanisms in M. iowae, target modification and efflux pump activity were examined in the present study. Point mutations were analyzed in previously described antibiotic binding sites in the whole genome sequences of 99 M. iowae strains. Mismatch amplification mutation assays (MAMAs) were designed and validated for the differentiation of mutations corresponding to elevated minimum inhibitory concentration (MIC) values for fluoroquinolones. Broth microdilution assays were performed to evaluate the effect of efflux pump inhibitors. In the presence of orthovanadate (OV), MIC values were significantly lower than in the absence of OV for spiramycin, tilmicosin, tylosin and oxytetracycline, which may indicate the presence of an active efflux system in M. iowae. Putative promoter regions of efflux-related genes were predicted and characterized. Genetic mutations, previously described in other bacteria, were described to be associated with elevated fluoroquinolone, macrolide and lincomycin MICs in M. iowae, although certain resistant phenotypes remained unexplained, promoting future examinations for deeper insights. The developed MAMAs may support rapid identification of M. iowae strains with elevated MIC values for fluoroquinolones. The better understanding of the efflux pump mechanisms enables the development of alternative methods for the support of therapy against this pathogen.}, } @article {pmid41996550, year = {2026}, author = {Bechtner, J and Hosek, J and Schwab, C}, title = {Fecal Material of Captive Wild Animals as Source of CAZymes With Application Potential.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {27}, number = {8}, pages = {e70315}, pmid = {41996550}, issn = {1439-7633}, support = {grant NNF22OC0079746//Novo Nordisk Fonden/ ; grant AU FF-F-2020-7//Aarhus Universitets Forskningsfond/ ; }, mesh = {Animals ; *Feces/microbiology ; *Animals, Wild/microbiology ; Polysaccharides/metabolism ; Metagenome ; *Glycoside Hydrolases/metabolism ; }, abstract = {Gastrointestinal systems of mammals and birds host taxonomically complex and functionally diverse microbial communities. Microbial activities contribute to community functioning and interaction with the host but can also be exploited as a source of novel enzymes or other industrially relevant microbial traits. With the overall goal to identify new resources for carbohydrate-active enzymes (CAZymes), we bioprospected fecal microbial communities of the little-explored source of captive wild animals. Using dbcan3, we identified a CAZyome dominated by glycosyl hydrolases (GHs) specialized in degrading oligo- and polysaccharides with much lower diversity and abundance of glycosyl transferases, carboxyl esterases, polysaccharide lyases, and redox enzymes with auxiliary activity. CAZyome profiles differed between animals depending on gut physiology and diet. Crude cell extracts conferred hydrolytic activity against compositionally and structurally diverse polysaccharides and nitrophenyl-sugar analogs. We identified five candidate GH68 and GH70 enzymes with the potential to produce oligo- and polysaccharides from sucrose, highlighting that fecal metagenomes are a source of rare CAZymes with industrial relevance. Taken together, we exemplify the functional potential captive wild animal fecal microbiota and suggest such a gene pool as a largely untapped resource for the discovery of novel biotechnological applications.}, } @article {pmid41996772, year = {2026}, author = {Haydar, MS and Alzate Zuluaga, MY and Astolfi, S and Del Buono, D and Cesco, S and Pii, Y}, title = {Nanoparticle-rhizosphere crosstalk: Insights into transformation, microbial interaction, plant uptake and translocation.}, journal = {Chemosphere}, volume = {403}, number = {}, pages = {144936}, doi = {10.1016/j.chemosphere.2026.144936}, pmid = {41996772}, issn = {1879-1298}, mesh = {*Rhizosphere ; *Nanoparticles/metabolism/chemistry ; *Soil Microbiology ; *Soil Pollutants/metabolism ; Plant Roots/metabolism/microbiology ; *Plants/metabolism ; Biological Transport ; Soil/chemistry ; }, abstract = {For soil-applied engineered nanomaterials, the rhizosphere is the critical frontline zone where they encounter crop roots, microbes, and soil, determining their agronomic potential and environmental risks. Within this dynamic interface, nanoparticles (NPs), depending on their surface chemistry, particle size, properties, and composition, undergo physicochemical and biological transformations that govern their stability, dissolution, mobility, availability, and ecotoxicological outcomes. This review synthesizes current mechanistic evidence linking root exudation patterns, microbial activity, and soil physico-chemical conditions to NPs aggregation, dissolution, redox conversions, and eco-/bio-corona formation. Microbial extracellular polymeric substances, low-molecular-weight metabolites, siderophores, and biofilms further reshape particle speciation, modulating ion release, immobilization, nutrient availability, and potential toxicity to soil biota and crops. Once inside roots, nanoparticles follow multiple uptake routes, including apoplastic diffusion, endocytosis, plasmodesmata-mediated transport, and vascular translocation, while undergoing in-planta transformations into ionic or ligand-bound forms with distinct physiological and agronomical consequences. These processes are strongly context-dependent, shaped by plant species, development stage, NPs concentration, and soil-climate conditions, and mediated by a tripartite molecular dialogue among NPs, microbes, and plant signalling pathways that regulate root system architecture, rhizosphere microbial recruitment, and nutrient acquisition efficiency. Advances in high-resolution and multi-omics tools-such as synchrotron-based spectroscopy, single-particle ICP-MS, NanoSIMS, stable-isotopic tracers, and metagenomics are offering new insights into these interactions under realistic agricultural scenarios. We propose an integrated agroecological framework linking rhizospheric NPs transformations to plant uptake and responses, emphasizing the need for standardized exposure metrics, realistic concentrations, and long-term field trials for safe and sustainable nanotechnology use in agriculture.}, } @article {pmid41996801, year = {2026}, author = {Chen, Y and Sun, Y and Yang, Y and Hu, S and Cui, K and Zhu, C and Fu, XZ and Li, CX and Jiang, P and Huang, Q}, title = {Differential distribution characteristics of heavy metal resistance genes and driving mechanisms of heavy metal speciation in river-lake system sediments.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142080}, doi = {10.1016/j.jhazmat.2026.142080}, pmid = {41996801}, issn = {1873-3336}, mesh = {*Metals, Heavy/analysis/toxicity ; *Geologic Sediments/chemistry/analysis ; Rivers/chemistry ; *Water Pollutants, Chemical/analysis/chemistry ; Lakes/chemistry ; Seasons ; Environmental Monitoring ; }, abstract = {River-lake systems are critical zones for heavy metal biogeochemical cycling, yet the mechanisms linking heavy metal pollution to heavy metal resistance genes (MRGs) across hydrological gradients remain elusive. This study selected the Chaohu Lake Basin as a representative river-lake system to investigate the distribution characteristics of MRGs and their driving mechanisms on heavy metal speciation. Based on metagenomic sequencing and ICP-MS analysis of 78 sediment samples collected in wet and dry seasons, we found that the resistome was dominated by multi-metal, Cu, and As resistance genes, with the arsenic resistance gene pstA identified as a consistent network hub. MRGs diversity and network complexity exhibited significant seasonal depletion and spatial heterogeneity along the river-lake gradient. Heavy metals were predominantly fractionated into the stable residual phase; however, the river-lake gradient significantly influenced the spatial distribution of bioavailable fractions. Crucially, Structural Equation Modeling (SEM) revealed a seasonal shift in the regulatory mechanisms controlling heavy metal speciation. In the wet season, the river-lake system operated under a "biologically mediated" mode, where MRGs directly facilitated the mobilization of the reducible fraction. In the dry season, it shifted to a "physicochemically driven" mode, governed primarily by basic physicochemical factors. These findings highlighted that seasonal dynamics and the river-lake gradient jointly coordinated heavy metal fate through a complex interplay of biotic and abiotic factors, providing molecular-level insights for pollution management in continuous aquatic systems.}, } @article {pmid41996860, year = {2026}, author = {Ji, Z and Fu, Z and Miao, L and Hang, D and Gu, A}, title = {Relationship between pesticide exposure, gut microbiota, and hypertension.}, journal = {Environment international}, volume = {211}, number = {}, pages = {110250}, doi = {10.1016/j.envint.2026.110250}, pmid = {41996860}, issn = {1873-6750}, mesh = {Humans ; *Hypertension/epidemiology ; *Pesticides/blood/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Environmental Exposure/statistics & numerical data ; China/epidemiology ; Adult ; Male ; Female ; }, abstract = {BACKGROUND: Both pesticide exposure and gut dysbiosis have been independently linked to an elevated risk of hypertension. However, the extent of interaction between these two factors remains poorly characterized in human populations.

METHODS: In a population-based study involving 218 adults from Jiangsu Province, China, we quantified pesticides in serum using LC-MS/MS and analyzed the gut microbiome via metagenomic sequencing. An environmental risk score (ERS) was created to represent pesticide exposure. We also used Mendelian randomization (MR) to identify causal gut microbial genera, multivariable regression for associations, and mediation analysis for potential pathways. Machine learning models were applied to differentiate hypertensive from non-hypertensive individuals based on a combined set of features.

RESULTS: Fourteen pesticides, notably bentazone and perfluorohexanesulfonate, were significantly associated with increased hypertension risk, and the ERS based on these pesticides further corroborated this association. Additionally, the overall microbiota composition was significantly associated with both pesticide exposure and hypertension status. Observational and MR analyses consistently identified branches of Clostridium as potentially contributors to hypertension risk. An interaction was observed between pesticide exposure and specific bacterial taxa. Specifically, high ERS combined with high Catenibacterium (both defined using a median split) abundance increased hypertension risk nearly fourfold. A neural network model achieved the best differentiation performance (AUC = 0.897) for hypertension.

CONCLUSIONS: Exposure to specific pesticides, particularly bentazone, is associated with increased hypertension risk. This relationship is influenced by interactions with gut bacteria and partially mediated through alterations in the gut microbiota. These findings highlight the role of environmental chemicals and the gut microbiome in the development of hypertension.}, } @article {pmid41997101, year = {2026}, author = {Liu, W and Yang, Y and Bian, J and Li, X and Lu, Z}, title = {Niche adaptation of marine heterotrophic nitrification-aerobic denitrification bacterium in mariculture wastewater treatment: Synergistic mechanism of nitrogen removal and sulfamethoxazole biotransformation.}, journal = {Water research}, volume = {300}, number = {}, pages = {125914}, doi = {10.1016/j.watres.2026.125914}, pmid = {41997101}, issn = {1879-2448}, mesh = {Denitrification ; Nitrification ; *Sulfamethoxazole/metabolism ; *Wastewater ; Nitrogen/metabolism ; Heterotrophic Processes ; Biotransformation ; }, abstract = {Efficient removal of nitrogen from mariculture wastewater (MW) by marine heterotrophic nitrification-aerobic denitrification (MHNAD) bacteria is an innovative approach to overcoming salt inhibition. However, their performance and survival strategies under long-term antibiotics exposure in real wastewater conditions remain elusive, limiting practical implementation. Here, a bench-scale biofloc-biological aerated filter (BF-BAF) system treating real MW was operated for 100 days. Under long-term exposure to sulfamethoxazole (SMX) (1.3 ± 0.4 mg/L), the stabilized nitrogen removal system achieved removal efficiencies of 97.2 ± 2.5 % and 91.6 ± 4.1 % for NH4[+]-N and SMX, respectively. MHNAD bacteria, dominated by Marinobacter and Celeribacter, were enriched (2.3-67.7 %) and identified as habitat-specific genera, while the growth of Nitrosomonas (0.02-0.04 %)-the sole ammonia-oxidizing bacteria (AOB) detected-was severely inhibited. Metagenomic analysis revealed upregulation of nitrogen assimilation (glnA and nasA) and denitrification genes (nirK and norC), driving niche differentiation. A novel MHNAD strain, Marinobacter sp. LAN01, was isolated from the settleable bioflocs. Multi-omics analysis indicated that LAN01 adapts to SMX stress by reallocating intracellular resources via NH4[+]-N assimilation (glnA-driven) and facilitates SMX degradation via N-acetylation, S-N bond cleavage, and hydrolysis. Nucleotide metabolism was downregulated to suppress DNA synthesis, thereby reducing the accumulation and transfer of sulfonamide resistance genes (sul1 and sul2). Overall, this works revealed the mechanism of synergistic nitrogen removal and antibiotic degradation, and highlighted the long-term application potential of BFT, paving the way for sustainable MW treatment.}, } @article {pmid41997104, year = {2026}, author = {Zhang, X and Weng, S and Zhen, Z and Tang, Z and Huang, X}, title = {Phage predation mitigates the spread of antibiotic resistance in anaerobic digestion under shortened solid retention times.}, journal = {Water research}, volume = {300}, number = {}, pages = {125921}, doi = {10.1016/j.watres.2026.125921}, pmid = {41997104}, issn = {1879-2448}, mesh = {*Drug Resistance, Microbial/genetics ; Anaerobiosis/physiology ; *Waste Disposal, Fluid/methods ; Anti-Bacterial Agents/pharmacology ; *Bacteriophages/physiology ; Water Purification/methods ; Sewage/microbiology/virology ; }, abstract = {Optimizing anaerobic digestion (AD) via shortening solid retention time (SRT) enhances methane recovery, yet the mechanistic impact of SRT reduction on antimicrobial resistance (AMR) dissemination remains underexplored. Herein, we employed metagenomics to investigate how reduced SRTs (from 60 to 5 days) regulated the dynamics of antibiotic resistance genes (ARGs) mediated by pathogenic hosts, plasmids, and phages in mesophilic and thermophilic AD systems. Shortened SRTs elevated ARG abundance by 5.9-388% under mesophilic conditions, driven by the SRT-elicited niche expansion of antibiotic-resistant bacteria (ARB) and the persistent dominance of ESKAPE pathogen Enterobacter hormaechei, the latter intrinsically harbored and transmitted high-risk ARGs (aadA, sul1, and qacEdelta1) via multi-resistant plasmids. Notably, plasmid-mediated and cross-phylum transmission substantially enhanced ARG mobility. Contrastingly, thermophilic conditions eliminated ARGs by 17.0-57.1% under shortened SRTs, driven by thermophilic ARB niche differentiation. Crucially, both homology search and phage-host prediction indicated the lack of ARGs matching between phages and hosts under reduced SRTs, denoting a negligible contribution of transduction to horizontal ARG transfer. The dominance of lytic phages (85.3%), intensified lytic phage-host interactions, and heightened abundance of lytic phages lysing ARB collectively imposed potent phage top-down control over ARG hosts, with the lytic phage predation on ARB being validated by laboratory assays. We also identified 9 high-risk digestate ARG biomarkers (ANT(6)-Ia, aadA, ermA, mel, qacEdelta1, sul1, tet44, tetM, tetQ) by integrating criteria of prevalence, gene mobility, clinical relevance, and host pathogenicity to inform monitoring. Overall, this study underlined the significance of phage predation in mitigating ARG propagation under shortened SRTs, informing the development of novel AMR control strategies in AD practices.}, } @article {pmid41997155, year = {2026}, author = {Yang, W and Lee, YJ and Silva, RMB and DeLiberto, A and Yancey, CE and McCallum, D and Buss, JA and Moncion, R and Ong, JL and Mabuchi, M and Hough, DM and Weigele, PR and Ettwiller, LM}, title = {The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.}, journal = {Molecular cell}, volume = {86}, number = {9}, pages = {1598-1613.e11}, doi = {10.1016/j.molcel.2026.03.027}, pmid = {41997155}, issn = {1097-4164}, mesh = {*5-Methylcytosine/metabolism ; *DNA Methylation ; Cytosine/metabolism ; Substrate Specificity ; Deamination ; High-Throughput Nucleotide Sequencing ; *Viral Proteins/genetics/metabolism ; Sequence Analysis, DNA/methods ; DNA, Single-Stranded/genetics/metabolism ; }, abstract = {Mining phages for new enzymatic activities continues to be important for the development of new tools for biotechnology. In this study, we used MetaGPA-a method linking genotype to phenotype in metagenomic data-to identify deoxycytidine deaminases, a protein family highly associated with cytosine modifications in metaviromes. Unexpectedly, a subset of these deaminases exhibited a preference for 5-methylcytosine (5mC) over cytosine (C) in both mononucleotide and single-stranded DNA substrates. In a methylome-sequencing workflow, deamination of 5mC by these enzymes enabled direct conversion of methylated cytosine while completely eliminating any background deamination of unmodified cytosine. This direct conversion allows for precise identification of methylated sites at single-base resolution with unmatched sensitivity enabling broad applications for the simultaneous sequencing of genome and methylome.}, } @article {pmid41997245, year = {2026}, author = {Wang, X and Wang, X and Ai, S and Wu, F and Xi, J and Li, J and Liu, Z}, title = {Harnessing native microbes: Intermittent aeration for bioremediation of phenolic compounds contaminated freshwater.}, journal = {Bioresource technology}, volume = {453}, number = {}, pages = {134641}, doi = {10.1016/j.biortech.2026.134641}, pmid = {41997245}, issn = {1873-2976}, mesh = {Biodegradation, Environmental ; *Phenols/metabolism/isolation & purification ; *Fresh Water/chemistry/microbiology ; *Water Pollutants, Chemical/metabolism/isolation & purification ; *Bacteria/metabolism/genetics ; Oxygen ; }, abstract = {Phenolic pollutants pose persistent risks to freshwater ecosystems due to their toxicity, structural diversity, and resistance to biodegradation. This study investigated microbial community dynamics, gene-level adaptation, and biostimulation strategies for phenolic removal using native microbial community. Metagenome analyses revealed marked taxonomic shifts under phenolic stress, with engineered systems favoring modular cooperative degradation, whereas the natural community relied on dominance of stress-resistant taxa and inter-phylum horizontal gene transfer (HGT). Functional profiling identified 28 candidate KEGG Orthologs (KOs), including oxidative, ring-cleaving, and energy-support genes, enriched across core degraders such as Pseudomonas, Sphingobium, and Bordetella. Biostimulation assays demonstrated oxygen availability as the primary limiting factor: intermittent aeration (IA) enhanced phenolic degradation by 29%, while IA combined with activated carbon (IA + AC) achieved up to 75% improvement, especially for complex compounds like bisphenol A (BPA) and nitrophenol. Predictive modeling based on KO abundance and stimulation methods (R[2] = 0.75-0.88) successfully predicted degradation performance across 50 natural samples. While IA + AC provided the most consistent improvement, 15 communities achieved comparable efficiencies under IA alone, highlighting context-dependent biodegradation capacities linked to HGT and metabolic pathway diversity. These findings establish a scalable predictive framework and emphasize the importance of tailoring biostimulation strategies to native microbial capacities, offering a practical route for in situ bioremediation of phenol-contaminated freshwater systems.}, } @article {pmid41998153, year = {2026}, author = {Li, S and Zhu, D and Saha, K and Kundu, BB and Sonkusale, S and Britton, RA and Ajo-Franklin, CM}, title = {Synthetic microbial co-cultures for modular bioelectronic sensing in diverse environments.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41998153}, issn = {1546-1696}, support = {W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; R01 AI173318/AI/NIAID NIH HHS/United States ; R01 AI173318/AI/NIAID NIH HHS/United States ; }, abstract = {Whole-cell bioelectronic sensors are particularly well-suited for environmental and health monitoring as they can be integrated into compact electronic devices for field deployment over extended periods. However, current engineering strategies lack modularity, are limited to a few microbial chassis and depend on specialized instruments for signal detection. We present the electroactive co-culture sensing system (e[-]COSENS), a plug-and-play system for whole-cell bioelectronic sensor development. Here a 'sender' bacterium produces electron mediators in response to analytes and a 'receiver' bacterium utilizes the electron mediators to generate electrical signals via extracellular electron transfer. Modularly swapping the sender bacterium and its associated genetic sensing elements achieved bioelectronic sensing of metals, small molecules and peptides in distinct environments, such as urban waterways, milk, saliva and microbial communities. We designed a centimeter-sized bioelectronic device for portable signal readout using a household digital multimeter. The e[-]COSENS system simplifies the whole-cell bioelectronic sensor design and expands the potential of bioelectronic sensor applications.}, } @article {pmid41998361, year = {2026}, author = {Thiyagarasaiyar, K and Paul, D and Kerttula, J and Keski-Karhu, M and Soosaar, K and Mander, Ü and Hallin, S and Machacova, K and Pumpanen, J and Siljanen, HMP}, title = {Genetic Potential for N2O Metabolism in Tree Tissues: Insights From Nitrogen Cycling Gene Prevalence and nosZ Diversity Across Tree Species.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41998361}, issn = {1432-184X}, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas, and microorganisms play a crucial role in its metabolism. While N2O cycling among soil microorganisms is well studied, there is a major knowledge gap regarding the distribution and diversity of these microorganisms within tree ecosystems. In this study, we aimed to comprehensively assess the potential for nitrogen (N) cycling and the diversity of N2O-reducing microorganisms in shoots (leaves and terminal branches) and wood cores of four tree species — European beech (Fagus sylvatica), European hornbeam (Carpinus betulus), birch (Betula pendula and Betula pubescens) and Norway spruce (Picea abies). We assessed N2O exchange through shoot incubation experiments and measured internal N2O concentrations in stem wood. Inorganic N species were studied as indicators of microbial transformation, and a targeted metagenomic approach was used to determine the relative abundance of N-cycling genes and nosZ clade I and II diversity. Our study revealed that hornbeam shoots showed potential N2O emissions (0.002–0.007 ng N2O g[-1] FW h[-1]), while beech shoots indicated N2O consumption (-0.001 to -0.017 ng N2O g[-1] FW h[-1]). Birch had internal stem wood N2O concentration of + 150.39 ppb, and beech − 9.74 ppb when compared to the ambient concentration. Targeted metagenomic analysis revealed the presence of key nitrification and denitrification genes in both tissue types. In particular, nosZ genes were detected in shoots (0 to 26.48 per 100,000 reads) and in wood cores (0 to 31.95 per 100,000 reads), with clade I dominating over clade II and Rhizobiales prevalent within clade I. Overall, our findings show that internal tree tissues harbour distinct N‑cycling microbial assemblages dominated by nosZ clade I, suggesting that trees may function as localized N2O sinks or sources depending on tissue type and microbial composition.}, } @article {pmid41998362, year = {2026}, author = {Parida, D and Dhali, SL and Bala, K and Nogueira, R}, title = {Early microbial colonization study of daily-use plastics exposed to river water.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {5}, pages = {}, pmid = {41998362}, issn = {1573-0972}, abstract = {In rivers, microorganisms colonize plastic surfaces, initiating processes that can lead to their microbial decomposition. Our study investigates the bacterial community composition and diversity on the surfaces of plastics used daily, such as polyethylene terephthalate (PET) and low-density polyethylene (LDPE), which were exposed to river water from the Aller and Fusche rivers. Glass was used for comparison purposes. 16s rRNA sequencing revealed that the type of surface and the native microbial community in the river water, including the water quality, significantly influenced biofilm community assembly. River water samples, especially from the Fusche site, supported the highest microbial richness, while plastic exhibited moderate diversity, and glass beads hosted the lowest richness and diversity. Proteobacteria and Bacteroidetes dominated across all samples, with notable enrichment of functionally relevant families such as Rhodobacteraceae and Comamonadaceae. Ecologically relevant genera such as Flavobacterium, Hydrogenophaga, Rhodoferax, Sediminibacterium, and Rhodobacter dominated across samples. Alpha diversity reflected the richness of taxa within each sample, while beta diversity revealed distinct clustering based on both plastic type and site, indicating the influence of ecological pressure and niche partitioning. These findings highlight the capacity of plastic surfaces to harbour diverse and specialised bacterial assemblages, with implications for biogeochemical cycling, pollutant interactions, and potential microbial degradation pathways. This work contributes to deciphering the ecological roles of biofilms in freshwater plastisphere micro-environments and underscores the importance of material-specific microbial dynamics in assessing environmental risks.}, } @article {pmid41998666, year = {2026}, author = {Yang, F and Du, Y and Ji, J and Zhang, P}, title = {Eosinophilic granulomatous inflammation and multi-organ involvement probable caused by Paragonimus heterotremus infection in a pediatric patient: a rare case report.}, journal = {BMC pediatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41998666}, issn = {1471-2431}, abstract = {BACKGROUND: Paragonimus heterotremus is a parasitic flatworm endemic to Southeast Asia that causes pulmonary and extrapulmonary infections. While more common in adults, pediatric cases are rare and often present atypically, posing diagnostic challenges. Eosinophilic granulomatous inflammation due to parasitic infection is especially difficult to identify in children.

CASE PRESENTATION: A 9-year-old female child initially exhibited subcutaneous swelling and notable peripheral blood eosinophilia, resulting in two hospital stays without a conclusive diagnosis. Upon admission to our center, laboratory results showed increased white blood cell count, hemoglobin, platelets, and persistent eosinophilia, along with a significantly increased total IgE levels. Imaging revealed granulomatous inflammation in the skin and lungs with mild pleural effusion. Despite negative parasitic serology, a newly developed umbilical mass during hospitalization was surgically excised. Anatomopathological examination and metagenomic next-generation sequencing (mNGS) supported a probable diagnosis of P. heterotremus infection.

CONCLUSIONS: This case highlights the diagnostic challenges of pediatric eosinophilic granulomatous inflammation due to rare parasitic infections, particularly in non-endemic areas. It highlights the need for heightened clinical awareness, thorough evaluation, and advanced diagnostic tools for timely and accurate identification of uncommon parasitic diseases in children.}, } @article {pmid41998767, year = {2026}, author = {Rungrojn, A and Chaisiri, K and Thaipadungpanit, J and Batty, EM and Blacksell, SD}, title = {Bacterial communities in Thai ticks: revealing geographical and methodological gaps in surveillance-a 25-year scoping review.}, journal = {Tropical medicine and health}, volume = {54}, number = {1}, pages = {}, pmid = {41998767}, issn = {1348-8945}, support = {JCPET02//Royal Society of Tropical Medicine and Hygiene/ ; 220211/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Ticks serve as key vectors for a diverse range of bacterial pathogens that affect humans and animals worldwide. In Thailand, a comprehensive understanding of tick-associated bacterial diversity remains limited. This scoping review synthesises published data on tick-borne bacteria across Thailand from 2001 to 2025, focusing on bacterial diversity, host-vector associations, geographic distribution, and molecular detection methods. Literature searches in NCBI, Embase, and Web of Science identified 402 studies (272 after duplicate removal), of which 39 met the inclusion criteria. Ticks were collected from animals, humans, and the environment across four zoogeographical regions. Rhipicephalus, Haemaphysalis, Dermacentor, and Amblyomma were the most commonly studied genera. Eighteen bacterial genera, including both pathogens and endosymbionts, were identified, with Coxiella-like endosymbionts, Rickettsia, Anaplasma, and Ehrlichia being the predominant genera. Rhipicephalus ticks exhibited the highest bacterial diversity, while Rickettsia spp. were the most frequently detected pathogens. Conventional PCR remained the principal diagnostic method, with limited application of quantitative and metagenomic sequencing approaches. Geographic analysis revealed that most studies were concentrated in the Northern Peninsular and Central Peninsular regions, while the Continental section of the Indo-Chinese Mainland and Korat Plateau zones were under-represented, which may limit the accuracy of regional risk assessments, as surveillance gaps can underestimate both the diversity and prevalence of pathogenic organisms in these areas. This review emphasises the intricate nature of tick-host-pathogen interactions and highlights the importance of implementing standardised genomic surveillance nationwide within a One Health framework. The findings reveal key gaps in current surveillance efforts and advocate for incorporating genomic tick monitoring into Thailand's national One Health strategies to improve zoonotic disease preparedness.}, } @article {pmid41998770, year = {2026}, author = {Ng, DZW and Yap, GC and Tay, CJX and Huang, CH and Zhao, S and Low, A and Tham, EH and Loo, EXL and Shek, LP and Goh, A and Chong, KW and Goh, SH and Cheng, ZR and Van Bever, HPS and Teoh, OH and Lee, YS and Yap, F and Tan, KH and Chong, YS and Chan, SY and Eriksson, JG and Godfrey, KM and Lay, C and Knol, J and Schuster, SC and Lai, JS and Chong, MF and Lee, JWJ and Lee, BW and Chan, ECY and Ta, LDH}, title = {Maternal-prenatal gut microbiome-systemic metabolome perturbations and TH2-skewed immunity link to offspring gut microbiome disruption and atopic dermatitis susceptibility.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {41998770}, issn = {1756-994X}, support = {NIHR Senior Investigator (NF-SI-0515-10042) and NIHR Southampton Biomedical Research Centre (NIHR203319)//National Institute for Health and Care Research/ ; MOH-000532//Singapore Ministry of Health's National Medical Research Council Clinician Scientist - Individual Research Grant/ ; MC_UU_12011/4/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: Emerging evidence suggests that maternal-prenatal gut microbiome disturbances shape offspring allergic outcomes through modulation of the in utero immune environment. Yet, no comprehensive clinical studies in human mother–offspring dyads have deconvoluted the maternal-prenatal gut microbiome and systemic immune-metabolome signatures underlying offspring allergic predisposition. METHODS: We performed a longitudinal nested case–control study involving 128 well-characterized mother–offspring dyads from defined cases (offspring with atopic dermatitis (AD); n = 64) and controls (offspring without AD; n = 64). Maternal stool and blood samples were collected at multiple time points during gestation for multi-omic profiling. Structural and functional gut microbiome composition was characterized via metagenomic sequencing, while systemic metabolome and serum immune milieu were profiled using targeted plasma metabolomics and Olink proximity extension assays, respectively. In offspring early-life, stool samples were collected longitudinally up to 6 months of age for gut microbiome and metabolome analyses. RESULTS: Mothers of AD infants exhibited longitudinal enrichments of gut Klebsiella pneumoniae, Roseburia intestinalis, Clostridioides difficile and Bilophila sp. 4_1_30, alongside depletions in gut Clostridium sp. CAG:678, Romboutsia timonensis, Akkermansia muciniphila, Blautia hansenii and Alistipes ihumii during pregnancy. These taxonomic shifts were associated with systemic metabolomic alterations, including elevated branched-chain amino acids and immune-related metabolites (e.g., creatine, ornithine), and a concurrent pro-inflammatory TH2-skewed immunological milieu marked by increased interleukin-4 (IL-4) and IL-5 and decreased CXCL11. In early life, AD infants harbored a dysbiotic gut microbiome characterized by persistent enrichments of potentially pathogenic Escherichia coli and K. pneumoniae, along with depletion of short chain fatty acid-producing Bacteroides species and beneficial colonizers. Integrated multi-omic analyses across the prenatal-postnatal axis indicated that the impaired establishment of gut microbiome in AD infants may, in part, be attributed to the (1) potential transmission of maternally originated Klebsiella and (2) immunomodulatory effects of a maternal-prenatal pro-inflammatory, TH2-skewed milieu during gestation. CONCLUSIONS: Our study uncovers a distinct maternal-prenatal gut microbiome and systemic metabolome–immune signature that predisposes offspring to AD by disrupting early-life gut microbial establishment. These findings highlight the gestational period as a critical window for preventive strategies targeting the maternal microbiome or systemic immune-metabolic axes to mitigate allergic disease susceptibility in offspring. TRIAL REGISTRATION: This study is registered at ClinicalTrials.gov (NCT 03531658).}, } @article {pmid41998806, year = {2026}, author = {Tang, R and Wang, J and Zhang, Z and Li, Y and Lan, Y and Fan, Z}, title = {Temporal Shifts in Gut Microbiota and Host Immunity During Chronic Diarrhea in an Infant Rhesus Macaque: A Longitudinal Case Study Based on Multi-Omics.}, journal = {Journal of medical primatology}, volume = {55}, number = {3}, pages = {e70074}, doi = {10.1111/jmp.70074}, pmid = {41998806}, issn = {1600-0684}, support = {2023NSFSC1935//Sichuan Province Science and Technology Support Program/ ; 32370450//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Diarrhea/veterinary/microbiology/immunology/drug therapy ; *Macaca mulatta/immunology/microbiology ; Longitudinal Studies ; *Monkey Diseases/immunology/microbiology ; *Gastrointestinal Microbiome ; Multiomics ; Anti-Bacterial Agents/therapeutic use ; Feces/microbiology ; Chronic Disease/veterinary ; Male ; }, abstract = {Diarrhea remains a major health challenge in captive rhesus macaques (RMs; Macaca mulatta), particularly among infants, yet the dynamic interplay between gut microbiota and host immune responses during disease progression remains poorly understood. Here, we conducted a longitudinal multi-omics study on a captive infant RM, analyzing 25 fecal metagenomes and 18 blood transcriptomes across diarrheal, antibiotic treatment, and recovery phases. Our results demonstrated that disease state was the primary driver of gut microbiota variation. The diarrheal phase was characterized by a significant reduction in microbial α-diversity and marked expansion of multidrug-resistant Enterobacteriaceae, including Escherichia, Shigella, and Salmonella, accompanied by severe depletion of probiotic genera such as Lactobacillus and Bifidobacterium. Correspondingly, antibiotic resistance genes targeting fluoroquinolones and cephalosporins accumulated substantially during diarrhea, explaining the limited efficacy of empirical antibiotic therapy. Blood transcriptome analysis revealed heightened innate immune activation, evidenced by upregulation of interferon-related genes, alongside suppression of adaptive immune pathways including interleukin-5 signaling. Integrated correlation analysis uncovered synchronized host-microbiome interactions, with inflammatory gene expression positively associated with opportunistic pathogens and negatively correlated with beneficial commensals. Clinical recovery coincided with re-establishment of probiotic populations, reduction in resistance gene burden, and normalization of immune function. These findings demonstrate that infant macaque diarrhea profoundly disrupts both gut microbial ecology and systemic immunity, supporting management strategies that prioritize targeted antimicrobial intervention and microbiome restoration over prolonged empirical antibiotic use in captive primates.}, } @article {pmid41999333, year = {2026}, author = {Tang, X and Lu, SY and Huang, JH and Cheng, ZW and Ke, YC and Ai, CF and Liu, C and Liao, HP and Zhou, SG}, title = {Phage-Encoded Metabolic Bypass Drives Herbicide Resistance in Soil Microbiomes.}, journal = {Environmental science & technology}, volume = {60}, number = {17}, pages = {12853-12867}, doi = {10.1021/acs.est.6c02641}, pmid = {41999333}, issn = {1520-5851}, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteriophages ; *Herbicide Resistance ; Herbicides ; }, abstract = {Phages reshape microbial community functions through auxiliary metabolic genes (AMGs) and are increasingly recognized as active drivers of microbial adaptation. Although herbicides such as glufosinate significantly inhibit soil microbes, these communities exhibit striking resilience; however, the role of phages in facilitating this rapid adaptation remains poorly understood. Here, we dissect the temporal dynamics (days 0, 15, 30, and 60) of phage-host interactions under two contrasting stressors: the microbially toxic glufosinate and the nontoxic dicamba. We find that glufosinate transiently suppresses microbial diversity, followed by a robust recovery on day 60. This successional shift coincides with an elevated proportion of putative temperate phages (74.1%) and a strategic attenuation of bacterial antiviral systems, signaling a transition from antagonistic predation to mutualistic lysogeny. Metagenomic analyses across 23 regions in China corroborate that this temperate phage recruitment is a generalized response to field-relevant glufosinate exposure. Selection for temperate phage infections arises from asymmetric fitness costs (burdening virulent phage-susceptible hosts) and prophage integration of AMGs like gdhA. Specifically, coevolution assays reveal that glufosinate selectively penalizes virulent phage-sensitive hosts, favoring the recruitment of temperate phage infections. Furthermore, in vitro validation confirms that phage-encoded gdhA provides a compensatory metabolic bypass for ammonia detoxification, directly mitigating herbicide toxicity. Collectively, these findings delineate a phage-mediated mechanism for herbicide resistance evolution in soil microbiomes, emphasizing the need for a microbiome-informed agrochemical design to manage long-term ecological resilience.}, } @article {pmid42000179, year = {2026}, author = {Iakovides, IC and Vasileiadis, S and Christou, A and Karaolia, P and Mina, T and Rocha, J and Duan, Y and Beretsou, VG and Gallois, N and Changey, F and Michael, C and Coelho, LP and Manaia, CM and Merlin, C and Fatta-Kassinos, D}, title = {Storage and soil depth, in addition to wastewater treatment, govern microbiota, and mobile genetic element and antibiotic resistance markers during reclaimed water irrigation.}, journal = {Water research}, volume = {300}, number = {}, pages = {125889}, doi = {10.1016/j.watres.2026.125889}, pmid = {42000179}, issn = {1879-2448}, mesh = {*Microbiota ; *Agricultural Irrigation ; Soil/chemistry ; *Wastewater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Drug Resistance, Microbial/genetics ; Soil Microbiology ; Bacteria/genetics ; Water Purification ; }, abstract = {Reclaimed water (RW) offers a sustainable solution for agricultural irrigation and freshwater conservation, but its microbial and chemical composition, shaped by treatment and storage processes, requires careful consideration for environmental and public health impacts. This study compared two RW types (conventional activated sludge with sand filtration and chlorination - CAS + SFC-RW - and membrane bioreactor - MBR-RW) with a tube well (TW) water control. The goal was to assess how storage influences the microbial composition, key antibiotic resistance and mobilome genes, and RW the impact on irrigated lysimeter soils during lettuce cultivation. Total bacteria were profiled using 16S rRNA gene sequencing and ddPCR, while antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were quantified by ddPCR and analysed by metagenomics. Initial RW samples had 1-1.5 orders of magnitude more 16S rRNA copies compared with the control, with significantly different bacterial and ARG/MGE profiles. Actinomycetota dominated CAS + SFC-RW, Bacteroidota the MBR-RW, and Pseudomonadota the TW water. Class 1 integrons and Tn916/Tn1545 were more abundant in CAS + SFC-RW compared with the MBR-RW. Storage reduced these differences toward convergence with the TW water profile, with putative pathogenic taxa, however, being more recalcitrant to change. RW irrigation altered soil bacterial composition, with MBR-RW having a greater impact as declared by the enhanced presence of Bacteroidota in the receiving soils. The RW influence was inversely related with vertical distance of the irrigation point, while the lettuce crop presence showed minimal/no impact. These results highlight the need for careful management of RW treatment and storage to ensure safe, resilient agricultural practices.}, } @article {pmid42000463, year = {2026}, author = {Devika, NT and Jayaraman, K and Nadimuthu, S and Nathamuni, SP and Sreya, PS and Jangam, AK and Katneni, VK}, title = {Gut microbial restructuring in white spot syndrome virus-infected Penaeus vannamei: Insights from long-read metagenomics.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {59}, number = {}, pages = {101834}, doi = {10.1016/j.cbd.2026.101834}, pmid = {42000463}, issn = {1878-0407}, mesh = {Animals ; *Penaeidae/virology/microbiology ; *White spot syndrome virus 1/physiology ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; }, abstract = {Microbial community restructuring following White Spot Syndrome Virus (WSSV) infection is a critical determinant in modulating the disease progression in Penaeus vannamei. In this study, full-length 16S rRNA sequencing (V1-V9) was employed to delineate the microbial shifts in healthy and WSSV-infected shrimp. The analysis revealed a pronounced reduction in Firmicutes in the WSSV-infected shrimp, a dysbiosis signature reported in WSSV-associated amplicon studies. With the advantage of full-length sequencing, this study achieved species-level resolution, identifying Vibrio alginolyticus (a known pathogen) alongside putative beneficial taxa such as Ruegeria conchae, R. arenilitoris, Demequina litorisediminis, and D.globuliformis, which were not captured in earlier amplicon-based studies. Diversity analysis demonstrated that, rather than loss of species, substantial restructuring in the form of abundance was observed between healthy and WSSV-infected shrimp, while the overall evenness of the community remained stable. Concurrently, WSSV-infection has triggered an increased abundance of core opportunistic pathogens, namely, Photobacterium damselae and V. alginolyticus, which clustered distinctly from putative beneficial taxa such as Ruegeria and Demequina species, reflecting a clear microbial imbalance. Collectively, these findings demonstrated that mortality in WSSV-infected shrimp is associated with dysbiosis characterized by a depletion of beneficial taxa and concomitant abundance of opportunistic pathogens. These insights provide a basis for developing targeted probiotic or therapeutic strategies to mitigate pathogen overgrowth.}, } @article {pmid42000510, year = {2026}, author = {Yu, Z and Song, S and Deng, W and Zhou, X and Wang, Y and Zhou, S}, title = {Metagenomics insights into humification improvement and antimicrobial resistance reduction during hyperthermophilic coupled with electric field composting process.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142094}, doi = {10.1016/j.jhazmat.2026.142094}, pmid = {42000510}, issn = {1873-3336}, mesh = {*Composting/methods ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Manure/microbiology ; *Humic Substances/analysis ; Animals ; Microbiota ; Soil Microbiology ; Bacteria/genetics ; }, abstract = {Compared to conventional thermophilic composting, hyperthermophilic composting elevates fermentation temperature and electric field composting facilitates oxygen transfer, with both strategies promoting humification and reshaping the microbial community structure. This study coupled hyperthermophilic composting with electric field composting (HEC) to further enhance livestock manure humification while suppressing antimicrobial resistance. A composting strategy consisting of 12-day hyperthermophilic pretreatment and 28-day electric field composting was implemented. Integrating analyses of the humification process, metagenomics, metabolic pathways, and key microbiota linked to humification and antimicrobial resistance, this study indicated that HEC strategy triggered an initial hyperthermophilic surge and sustained thermophilic, with potential enhancement of aerobic metabolic activity under the applied electric field, thereby driving microbial succession from Proteobacteria to Firmicutes and Actinobacteria. The favorable conditions and microbiota shift enhanced metabolic activity, accelerated transformation of organic substrates, and increased aromatic precursor accumulation, resulting in a 2.5-fold increase in humic acid carbon compared with conventional thermophilic composting. Meanwhile, HEC reduced antibiotic resistance genes (ARGs) abundance and diversity by suppressing resistance-associated microbiota, particularly Proteobacteria and Bacteroidetes, which predominantly harbor antibiotic efflux genes (e.g., adeF). The attenuation of ARGs abundance and diversity reached 66.1% and 74.2%, respectively, compared with 43.3% and 48.8% in conventional thermophilic composting after 40d fermentation, and meanwhile, dominant humus-forming microbiota were relatively less associated with ARGs. This study elucidated the mechanisms underlying enhanced humification and ARG mitigation during the HEC process, thereby offering an effective strategy for resource recovery from livestock manure.}, } @article {pmid42000517, year = {2026}, author = {Han, W and Liu, Y and Liang, X and Liu, J and Jiang, Q and Zhang, C and Zhang, Y}, title = {A Trojan Horse in the soil: Tetracycline hijacks plant organellar ribosomes to stunt growth and unbalance the rhizosphere microecology.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {141792}, doi = {10.1016/j.jhazmat.2026.141792}, pmid = {42000517}, issn = {1873-3336}, mesh = {*Tetracycline/toxicity ; *Rhizosphere ; *Ribosomes/drug effects/metabolism ; *Anti-Bacterial Agents/toxicity ; Soil Microbiology ; RNA, Ribosomal/metabolism/drug effects ; *Glycine max/drug effects/growth & development/metabolism ; *Soil Pollutants/toxicity ; Photosynthesis/drug effects ; Soil/chemistry ; Chloroplasts/drug effects ; }, abstract = {Tetracycline, a widely used antibiotic, accumulates in agricultural soils and poses significant risks to crop development and soil health. This study elucidates novel mechanisms of TC phytotoxicity by demonstrating its specific binding to the structurally conserved A-site of ribosomal small subunit RNA (SSU rRNA) in plant mitochondria and chloroplasts-organelles of prokaryotic origin. Through integrated physiological, transcriptomic, and structural analyses, we show that TC disrupts ribosomal function, induces oxidative stress, and impairs photosynthesis and antioxidant defense in soybean, and unbalances the SSU/LSU (ribosomal large subunit RNA) rRNA ratio. We further developed a comprehensive Ecological Risk Index (ERI) framework that integrates soil physicochemical properties, enzyme activities, microbial metabolism, and community structure to evaluate soil microecological shifts under TC stress. Metagenomic analysis uncovered functional adaptations in microbial nitrogen/phosphorus cycling and emphasized the role of multidrug resistance genes-rather than tetracycline-specific resistance-via mobile genetic elements, including those from ssDNA viruses. Our findings provide unprecedented insights into the evolutionary conservation of ribosomal targets of antibiotics and establish a holistic framework for assessing the ecological impact of antibiotic residues in agroecosystems.}, } @article {pmid42000556, year = {2026}, author = {Snipen, L and Stoeck, T and Angell, IL and Philip, M and Pettersen, R and Majaneva, S and Ray, JL and Stokkan, M and Keeley, N and Rudi, K}, title = {Predicting sediment ecological state from metagenomes shows equal performance for taxonomic and functional features.}, journal = {Marine environmental research}, volume = {218}, number = {}, pages = {108055}, doi = {10.1016/j.marenvres.2026.108055}, pmid = {42000556}, issn = {1879-0291}, mesh = {*Geologic Sediments/microbiology ; *Metagenome ; *Environmental Monitoring/methods ; Norway ; Iceland ; Animals ; *Microbiota ; }, abstract = {The use of environmental microbial DNA to monitor the ecological state in seafloor sediments has many advantages and efforts are being made to find reliable biomarkers from DNA-based taxonomic profiles. However, the taxonomic composition of microbial communities can vary over time and space, while their functional characteristics typically remain consistent. Furthermore, functionality may better capture the breadth of biological complexity. Therefore, we here tested whether functional attributes of microbial communities serve as more reliable indicators of environmental quality than their taxonomic composition. To test this, we analyzed a set of Metagenome-Assembled-Genomes (MAGs) from 41 different coastal locations in Norway and Iceland, characterized by environmental impact gradients resulting from salmon aquaculture. Functional and taxonomic features extracted from these MAGs were then used to predict the ecological state of the corresponding sample sites using several supervised machine learning models and stratified feature selection. Our findings indicate that both taxonomic and functional features demonstrated comparable effectiveness in predicting environmental quality. This outcome has direct relevance for eDNA-based regulatory compliance monitoring. However, the functional insights derived from the most significant functional features identified by machine learning models remain essential for deepening our understanding of the ecological processes underpinning practical biomonitoring tools.}, } @article {pmid42000565, year = {2026}, author = {Wan, X and Zhan, J and Chen, Z and Wu, B}, title = {Ventilation-driven microbial and antimicrobial resistance divergence in intensive poultry houses and the associated public health risks.}, journal = {Research in veterinary science}, volume = {206}, number = {}, pages = {106196}, doi = {10.1016/j.rvsc.2026.106196}, pmid = {42000565}, issn = {1532-2661}, mesh = {Animals ; *Chickens ; *Housing, Animal ; *Drug Resistance, Bacterial/genetics ; *Ventilation ; Public Health ; *Drug Resistance, Microbial/genetics ; *Air Microbiology ; Bacteria/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Ventilation strategies in intensive poultry production systems play a critical role in shaping airborne microbial communities and the dissemination of antibiotic resistance, with potential implications for environmental and public health. In this study, bioaerosols from closed (mechanically ventilated) and open (naturally ventilated) chicken houses were systematically characterized using high-throughput metagenomic sequencing to compare microbial community composition and antibiotic resistance gene (ARG) profiles under contrasting ventilation regimes. Open chicken houses exhibited significantly higher microbial diversity (P < 0.05), reflecting increased environmental microbial inputs, while the relative abundance of the potentially antibiotic-resistant pathogen Staphylococcus aureus was also elevated. In contrast, closed chicken houses facilitated the accumulation of a core microbial community, including potential pathogens such as Helicobacter pullorum and Clostridium perfringens. Closed chicken houses showed a greater enrichment of macrolide resistance genes. In addition, the overall abundance of ARGs, expressed as ARG copies per 16S rRNA gene, was significantly higher in closed houses than in open houses (P < 0.05). Although total ARG abundance was lower in open chicken houses, the proportion of contigs harboring both ARGs and mobile genetic elements (MGEs) was significantly higher (P < 0.05), indicating increased potential for horizontal gene transfer. These findings reveal differences in microbial diversity and associated health risks between different poultry production systems and underscore the importance of optimizing ventilation strategies to control pathogen transmission and the spread of antibiotic resistance.}, } @article {pmid42000726, year = {2026}, author = {Zhou, X and Zhou, D and Pu, Y and Kim, H and Sun, Z and Qi, W and Jin, J and Zhang, W and Xia, M and Wang, C and Hong, S and Nguyen, LH and Jiao, N and Zheng, Y and Liu, T}, title = {Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42000726}, issn = {2041-1723}, mesh = {Humans ; *Bacteriophages/genetics/physiology ; Feces/microbiology/chemistry ; *Fatty Liver/microbiology/metabolism/virology ; *Gastrointestinal Microbiome/genetics/physiology ; Ruminococcus/virology/metabolism/genetics ; Metagenomics ; Faecalibacterium prausnitzii/metabolism/genetics/virology ; Bile Acids and Salts/metabolism ; Dysbiosis/microbiology ; *Bacteria/metabolism/genetics ; Metabolomics ; Female ; Male ; Case-Control Studies ; Eubacteriales ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly linked to gut microbial dysbiosis, but most studies have focused on bacteria, neglecting viruses and fungi, and their interactions. Here we show that MASLD is characterized by coordinated disruption of bacterial, viral and fungal communities and by a disturbed phage-bacteria-metabolite axis associated with disease-related bile acid changes. Integrating shotgun metagenomics, fungal ITS2 sequencing, fecal metabolomics and clinical profiling in 210 patients with MASLD and 210 age- and gender-matched healthy controls, we find reduced microbial diversity and extensive remodeling of cross-kingdom ecological networks in MASLD. Ruminococcus gnavus emerges as an enriched central hub, while Faecalibacterium prausnitzii and its associated bacteriophages are depleted. Phage-host analyses further reveal reduced lytic activity against R. gnavus and loss of sulfur amino acid metabolism-related auxiliary metabolic genes, which may impair F. prausnitzii fitness. Diminished phage control may facilitate R. gnavus expansion, alongside increased fecal isodeoxycholic acid, a secondary bile acid implicated in hepatic steatosis. A diagnostic classifier integrating bacterial and viral features with clinical parameters distinguish MASLD from controls in our cohort and maintain predictive performance in two external datasets. Together, these findings uncover a disrupted phage-bacteria-metabolite axis in MASLD and provide a multi-kingdom framework for non-invasive biomarker discovery and microbiome-targeted therapies.}, } @article {pmid42001033, year = {2026}, author = {Galgano, S}, title = {Genomica: linear mixed model based, multiple hypothesis testing corrected, ortholog functional enrichment analysis.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {42001033}, issn = {1471-2105}, mesh = {*Software ; Linear Models ; *Metagenomics/methods ; Genomics/methods ; }, abstract = {BACKGROUND: The analysis of ortholog genes derived from metagenomic experiments provides an invaluable opportunity to assess the functional role of microbial communities towards, for example, antimicrobial resistance or biochemical pathways under different experimental conditions. Nevertheless, the integration of the statistical analysis of these complex data sets and the enrichment of the derived significantly differential abundant orthologs is not currently facilitated by existing software. Genomica is an R package that, with minimal input from the user, allows to perform a double-step analysis of functional orthologs from the KEGG Orthology. The pipeline is carried out via combining false discovery rate corrected linear mixed models to functional enrichment analysis through integrating established R pipelines (i.e., lme4 and MicrobiomeProfiler).

RESULTS: Only two data frames are needed as input to run Genomica, which contain data and metadata, respectively. The fast pipeline integrated within the function Genomica allows to analyze 4000 orthologs in circa 3 min. The outputs are collected in a single directory, containing publication-ready results from the linear mixed model and from the enrichment analysis. The Benjamini & Hochberg correction is applied to the results from the linear mixed model, therefore only P adjusted significant comparisons are further included in the enrichment analysis.

CONCLUSIONS: Genomica is a simple-to-use R package to analyze complex datasets, integrating a well-founded statistical analysis, accounting for the calculation of the type I error under repeated testing, with the enrichment analysis of the significantly differential abundant orthologs across experimental conditions, all with minimal input from the user.}, } @article {pmid42001152, year = {2026}, author = {Leroy, M and Cyriaque, V and Rattei, T and Laurion, I and Comte, J}, title = {Microbiome and plasmidome shifts drive carbon, nitrogen, and greenhouse gas dynamics within transitioning permafrost.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {42001152}, issn = {2524-6372}, support = {2021-PR-284297//Fonds de recherche du Québec - Nature et technologie/ ; RGPIN-2020-06876//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; RGPIN-2020-06874//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; 2021-PR-284297//Fonds de recherche du Québec - Nature et technologies/ ; }, abstract = {Thermokarst lakes contribute to greenhouse gas emissions but often experience constraints on available nitrogen. However, the interactions between carbon and nitrogen cycles in these systems, especially along the terrestrial-aquatic continuum, remain poorly understood. The increased soil-water connectivity in those systems affects organic matter processing, nutrient availability, and microbial transport. In Nunavik (Quebec, Canada), we sampled along a transect from a palsa (permafrost remnant) through an emerging thermokarst lake to peatland soils and mature lake. Using hybrid metagenome co-assemblies with gene-, plasmid-, and genome-centric approaches, we explored key biogeochemical cycles and the role of plasmids in microbial adaptation along the transect. Gene annotation, metagenome-assembled genome (MAG) reconstruction, and network analysis revealed a shift from potential for anaerobic ammonium oxidation (anammox) in palsa and emerging lake to potential for nitrification in mature lake. Potential for methanogenesis transitions from hydrogenotrophic in the palsa to methylotrophic in lakes, likely driven by a bacterial consortium degrading aromatic, peat-derived compounds. Sediments may support methane production via both hydrogenotrophic and acetoclastic potential for methanogenesis, partially fueled by the action of polysaccharide lyases. Anaerobic methane oxidation (AOM) potential seems important in both peat and the mature lake; and can be coupled with nitrification and sulfate-reducing partners through extracellular electron transfer, with cytochromes playing a central role. Notably, plasmidome shifts preceded metagenomic changes, especially in genes related to carbon and methane cycling, suggesting a role for plasmids in microbial adaptation to permafrost thaw. These findings highlight the complex microbial and plasmid dynamics that drive carbon, nitrogen, and greenhouse gas cycles in permafrost ecosystems.}, } @article {pmid42001834, year = {2026}, author = {Ma, Z and Gao, L and Hou, W and Wu, J and Wen, X and Zhang, Y and Dong, N and Dou, X and Shan, A}, title = {(-)-Epigallocatechin-3-gallate alleviates diarrhea in piglets by suppressing the NMU-NMUR1-ILC2 axis and modulating microbiota-associated energy metabolism.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158119}, doi = {10.1016/j.phymed.2026.158119}, pmid = {42001834}, issn = {1618-095X}, mesh = {Animals ; *Catechin/analogs & derivatives/pharmacology ; *Diarrhea/drug therapy/microbiology/veterinary ; Swine ; *Energy Metabolism/drug effects ; *Gastrointestinal Microbiome/drug effects ; Lymphocytes/drug effects/metabolism ; Escherichia coli ; Escherichia coli Infections ; }, abstract = {BACKGROUND: Bacterial diarrhea is considered a global health crisis, accounting for approximately 20 % of deaths related to colorectal cancer. (-)-Epigallocatechin 3-gallate (EGCG), one of the most abundant plant-derived polyphenols in the human diet, has shown promise in managing gastrointestinal disorders. But, the systemic evidence for EGCG in alleviating the progression of diarrhea and the mechanisms involved remain unclear.

OBJECTIVES: This study aims to determine whether EGCG confers diarrhea resistance in piglets under Escherichia coli (E. coli) and what the fundamental mechanisms involved are.

METHODS: Weaned piglets were used to create a E. coli-induced intestinal disorder-diarrhea susceptibility model. Piglets were supplemented with EGCG to identify diarrhea rate and activity of enteric nervous system (ENS). The interaction between the neuromedin U receptor 1 (NMUR1) and typeⅡinnate lymphoid cells (ILC2) was analyzed using RNA sequencing (RNA-seq) and fluorescence colocalization techniques. Metagenomic and metabolomic analyses were further performed to assess the involvement of NMUR1 and the underlying mechanisms of beneficial microbes enriched by EGCG. The effects of beneficial microbes in treating intestinal morphology were investigated through histopathology, Scanning electron microscopy (SEM) and ELISA analysis methods.

RESULTS: EGCG reduced diarrhea rate in piglets by inhibiting the NMU-NMUR1-ILC2 pathway, ameliorating gut microbiota structure, and stimulating intestinal barrier. Apparently, the enteric nerve-microbial axis is linked with EGCG conferring diarrhea resistance in piglets. Mechanistically, EGCG suppressed the NMU-NMUR1-ILC2 axis to reduce the secretion of inflammatory cytokines (TNF-α, IL-6, and IL-8), while concurrently increasing the abundance of beneficial gut microbes and altering signature microbial community functions (energy metabolism pathways); accordingly, EGCG maintained the energy supply balance in gut epithelial cells and promoted the activity of goblet cell and Paneth cell by activating the AMP-activated protein kinase (AMPK)-sirtuin 1 (Sirt1) signaling pathway.

CONCLUSION: EGCG confers diarrhea resistance in E. coli piglets by maintaining intestinal mucosal barrier via the enteric nerve-microbial axis; thus, this study provides a potential prevention strategy for young mammals at risk of diarrhea.}, } @article {pmid42002156, year = {2026}, author = {Jeon, J and Nguyen, HT and Yeo, G and Lee, C and Cho, SK and Oh, S}, title = {Integrating metagenomics and explainable artificial intelligence for modeling of food waste treatment using full-scale anaerobic digestion.}, journal = {Bioresource technology}, volume = {453}, number = {}, pages = {134649}, doi = {10.1016/j.biortech.2026.134649}, pmid = {42002156}, issn = {1873-2976}, mesh = {*Artificial Intelligence ; Anaerobiosis ; Food Loss and Waste ; Methane/biosynthesis ; *Metagenomics/methods ; Random Forest ; Data Analytics ; }, abstract = {Anaerobic digestion (AD), a biochemical process that can convert food waste (FW) into methane, offers great promise as a sustainable form of energy production. While several attempts have been made to optimize AD systems using various mathematical models, more precise modeling approaches that fully consider the complexity of the AD process are required, leading to the adoption of artificial intelligence (AI) as a suitable alternative to numerical modeling. In line with this, the present study tested 11 AI-based models on their prediction of the methane yield for a full-scale AD process using FW as a feedstock. The models incorporated operational parameters, environmental conditions, and microbial information to improve their predictive performance. Although a one-dimensional convolutional neural network (1D-CNN) was the most precise, random forest regression (RFR) was selected as the optimal model for further analysis due to its superior interpretability and stability. Explainable AI (XAI) was then used to determine the most important input features contributing to the predictions of the optimal AI model, thus allowing for detailed model interpretation. Methanothrix was identified as a key predictor of methane yield, and metagenomic analysis provided independent genome-level evidence broadly consistent with the XAI results. Overall, this study proposes a novel approach to the interpretation and optimization of AD performance, rather than focusing only on enhancing the predictive performance of a discrete model.}, } @article {pmid42002296, year = {2026}, author = {Yang, X and Zhang, L and Zhou, S and Wang, Z and Lv, Q and Zhao, M and Wang, C}, title = {Mechanisms Underlying Bioactive Compounds Decline in Medicinal Blaps rhynchopetera During Artificial Rearing.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70304}, doi = {10.1111/1462-2920.70304}, pmid = {42002296}, issn = {1462-2920}, support = {2022YFC2602500//National Key Research and Development Program of China/ ; JiaoWaiSiYa[2020]619//Lancang-Mekong Cooperation Special Fund Projects/ ; SAJC202402//Chinese Academy of Sciences/ ; 2025YKZY002//Yunnan Characteristic Plant Extraction Laboratory/ ; 202449CE340005//Yunnan Provincial Science and Technology Department/ ; 202305AH340007//Yunnan Provincial Science and Technology Department/ ; }, mesh = {Animals ; *Coleoptera/microbiology/metabolism/growth & development/chemistry ; *Gastrointestinal Microbiome ; Metabolome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; }, abstract = {Artificial rearing is essential for sustainable utilization of medicinal insects, yet its impact on bioactive compound production remains poorly understood. Here we provide preliminary evidence that rearing of the medicinal beetle Blaps rhynchopetera reshapes its gut microbiota and metabolome, beyond mere environmental effects. Metabolomic analysis revealed 727 significantly altered metabolites, with 436 compounds, many linked to analgesic and anti-inflammatory activities, markedly reduced under rearing. Network pharmacology analysis suggested that this metabolic remodelling alters the overall regulatory landscape, with reduced network complexity compared to wild counterparts. Metagenomic profiling uncovered a decline in Pseudomonadota, a phylum positively correlated with multiple bioactive metabolites. Preliminary reintroduction of four Pseudomonadota strains suggested their potential involvement in terpenoid backbone biosynthesis, a key pathway for natural product synthesis. These findings reveal an intrinsic trade-off between rearing-driven microbial homogenization and preservation of medicinal potency, highlighting the need for microbiome-informed rearing strategies.}, } @article {pmid42002357, year = {2026}, author = {Li, Z and Li, Z and Chu, L and Hu, S and Xue, C and Lin, H and Luo, Y and Zhang, Y and Zhang, J and Wang, Z}, title = {A novel Curcuma wenyujin-derived fructan modulates gut microbiota and metabolic pathways to ameliorate DSS-induced colitis.}, journal = {Carbohydrate polymers}, volume = {382}, number = {}, pages = {125292}, doi = {10.1016/j.carbpol.2026.125292}, pmid = {42002357}, issn = {1879-1344}, mesh = {Animals ; *Curcuma/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Fructans/pharmacology/chemistry/therapeutic use/isolation & purification ; Mice ; Dextran Sulfate ; Male ; *Colitis/chemically induced/drug therapy/metabolism ; Mice, Inbred C57BL ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism ; Metabolic Networks and Pathways/drug effects ; Colon/drug effects/pathology ; Dysbiosis/drug therapy ; Disease Models, Animal ; }, abstract = {Ulcerative colitis (UC) involves epithelial barrier breakdown, dysregulated mucosal immunity, and dysbiosis of the gut microbiota (GM). Given the biotherapeutic potential of dietary fructans, this study aimed to isolate a neutral fructan (CWP-W-1) from Curcuma wenyujin and to characterize its chemical structure and anti-colitis effects. CWP-W-1 was purified by DEAE-Sepharose and gel-filtration chromatography. Its structure was established using HPGPC, monosaccharide profiling, FT-IR, GC-MS, and NMR. In a DSS-induced UC mouse model, CWP-W-1 treatment alleviated disease severity and weight loss, decreased the disease activity index and rectal bleeding, prevented colon shortening, and restored histological architecture, with increased goblet cells and mucin staining. Metagenomic sequencing showed that CWP-W-1 mitigated DSS-associated dysbiosis, recovering α-diversity and shifting β-diversity toward healthy controls, with decreases in Proteobacteria and enrichment of beneficial taxa. Metabolite analyses indicated that CWP-W-1 increased short-chain fatty acids (SCFAs) and remodeled the tryptophan metabolic pathway, shifting the pro-inflammatory kynurenine bias toward indole-derived aryl hydrocarbon receptor (AhR) ligands, consistent with epithelial barrier support and immune homeostasis. Collectively, these results demonstrated that CWP-W-1 was a structurally defined fructan with significant therapeutic potential for UC through coordinated modulation of barrier function, mucosal immunity, and the gut microbiota.}, } @article {pmid42002784, year = {2026}, author = {Liu, T and Fan, S and Li, J and Wang, T and Zhang, J and Wang, C}, title = {Curcumin modulates hepatic pyroptosis-autophagy crosstalk induced by aflatoxin B1 via rumen microbiota-blood-liver axis.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42002784}, issn = {2049-2618}, support = {2023YFD1301005//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Aflatoxin B1/toxicity ; *Curcumin/pharmacology/administration & dosage ; *Rumen/microbiology/drug effects ; *Liver/drug effects/metabolism ; Sheep ; *Autophagy/drug effects ; *Pyroptosis/drug effects ; *Gastrointestinal Microbiome/drug effects ; Aflatoxin Poisoning ; }, abstract = {BACKGROUND: Aflatoxins, fungal secondary metabolites from Aspergillus species, primarily causes liver and gastrointestinal damage in ruminant. Curcumin, a plant polyphenol, has been shown to possess both anti-inflammatory and antioxidant properties, in addition to regulatory effects on gut microbiota. However, research on curcumin's impact against AFB1 toxicity in ruminants is limited. This study aims to elucidate whether AFB1 induces hepatic pyroptosis and autophagy in ruminants via the rumen microbiota-blood-liver axis and the regulatory role of curcumin. The experimental design involves the administration of AFB1 and curcumin to sheep, followed by a comprehensive observation of alterations in rumen microbiota, barrier function, and the occurrence of hepatic pyroptosis and autophagy, with the aim of elucidating the mechanism of curcumin in ameliorating AFB1-induced liver injury in sheep.

RESULTS: In the experimental setup, 800 mg/kg dry matter (DM) curcumin was administered as a dietary supplement to alleviate the adverse effects of AFB1 (500 μg/kg DM) on the rumen and liver of sheep. AFB1 suppressed NH3-N and VFAs production, whereas curcumin improved VFA generation and fermentation efficiency. Curcumin mitigated AFB1-induced rumen barrier impairment by upregulating tight junction proteins (ZO-1, Occludin, Claudin-1) and reducing LPS levels, which was consistent with metagenomic data showing amelioration of microbiota dysbiosis and reduced lysis of Gram-negative bacteria. At hepatic level, curcumin downregulated the principal mediators of the TLR4-NF-κB-NLRP3 signaling pathway (TLR4, p65, and NLRP3), attenuating pyroptosis and reducing serum AST, ALT, and LDH concentrations, while reversing inflammatory infiltration and hepatic cord disruption. Furthermore, curcumin restored autophagic flux by increasing the LC3-II/LC3-I ratio and decreasing p62 accumulation, counteracting AFB1-induced autophagy inhibition.

CONCLUSIONS: Curcumin counteracts AFB1-induced rumen-liver axis dysfunction. It works by stabilizing the microbiota, maintaining barrier integrity, and dually regulating pyroptosis and autophagy. Video Abstract.}, } @article {pmid42002835, year = {2026}, author = {Morineau, N and Tessoulin, B and Guimard, T and Papin, M and Roquilly, A and Le Gouill, S and Montassier, E}, title = {Longitudinal gut microbiome dynamics are associated with clinical outcome and toxicity during ibrutinib therapy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2659397}, pmid = {42002835}, issn = {1949-0984}, mesh = {Humans ; *Adenine/analogs & derivatives/adverse effects/therapeutic use ; *Piperidines/adverse effects/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Male ; Female ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification/drug effects/metabolism ; Treatment Outcome ; *Pyrimidines/adverse effects/therapeutic use ; *Antineoplastic Agents/adverse effects/therapeutic use ; Middle Aged ; Diarrhea/chemically induced ; Aged ; *Pyrazoles/adverse effects/therapeutic use ; Metagenomics ; }, abstract = {Accumulating evidence indicates that the gut microbiome influences therapeutic efficacy and toxicity across cancer treatments; however, its longitudinal dynamics during targeted therapies remain poorly characterized. Here, we performed whole-genome shotgun metagenomic sequencing of 291 longitudinal stool samples collected over one year from 30 patients with hematologic malignancies treated with ibrutinib. Overall gut microbial diversity remained stable at the population level but exhibited markedly divergent temporal trajectories according to clinical outcome, with progressive recovery in responders and blunted or delayed restoration in non-responders. Longitudinal modeling revealed distinct species- and pathway-level microbial dynamics between patients with treatment response or nonresponse, including enrichment of saccharolytic, short-chain fatty acid-associated taxa and metabolic pathways in responders, and expansion of bile acid-modifying, proteolytic, and inflammation-associated microbial features in non-responders. Functional profiling further demonstrated opposing temporal trends in pathways related to carbohydrate fermentation, amino-acid metabolism, and secondary bile acid synthesis. In addition, both baseline microbiome composition and longitudinal remodeling were associated with the development of ibrutinib-associated diarrhea. Together, these findings reveal coordinated, outcome-specific remodeling of the gut microbiome during ibrutinib therapy and highlight longitudinal microbiome trajectories, rather than static baseline features, as potential biomarkers of treatment response and toxicity, as well as targets for microbiome-directed interventions. In conclusion, our findings highlight a potential role of gut microbiome dynamics in modulating response to BTK inhibition and support the need for larger, prospective studies to validate these observations.}, } @article {pmid42003340, year = {2026}, author = {Tong, Y and Marcelino, VR and Turnbull, R and Verbruggen, H}, title = {ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70143}, pmid = {42003340}, issn = {1755-0998}, support = {2023.06155//Fundação para a Ciência e a Tecnologia/ ; DE220100965//Australian Research Council/ ; RYC2023-042907-I//Ministerio de Ciencia e Innovación/ ; //The University of Melbourne's Research Computing Services/ ; }, mesh = {*Genome, Plastid ; *Metagenomics/methods ; *Computational Biology/methods ; Software ; *Eukaryota/genetics/classification ; }, abstract = {Genome-resolved metagenomics has contributed greatly to discovering prokaryotic genomes. When applied to microscopic eukaryotes (protists), challenges such as the high number of introns and repeat regions found in nuclear genomes have hampered the mining and discovery of novel protistan lineages. Organellar genomes are simpler, smaller, have higher abundance than their nuclear counterparts and contain valuable phylogenetic information, but are yet to be widely used to identify new protist lineages from metagenomes. Here we present "ChloroScan", a new bioinformatics pipeline to extract eukaryotic plastid genomes from metagenomes. It incorporates a deep learning contig classifier to identify putative plastid contigs and an automated binning module to recover bins with guidance from a curated marker gene database. Additionally, ChloroScan summarizes the results in different user-friendly formats, including annotated coding sequences and proteins for each bin. We show that ChloroScan recovers more high-quality plastid bins than MetaBAT2 for simulated metagenomes. The practical utility of ChloroScan is illustrated by recovering 16 medium to high-quality metagenome assembled genomes (MAGs) from four protist-size-fraction metagenomes, with several bins showing high taxonomic novelty. The ChloroScan code (v0.1.7) is available at https://github.com/Andyargueasae/chloroscan/tree/release_v0.1.7 under Apache-2.0 licence.}, } @article {pmid42003642, year = {2026}, author = {Krausfeldt, LE and Subramanian, P and Doan, D and McCauley, K and Dolan, M and Hurt, DE}, title = {DiscoVir: an automated, web-based pipeline for viral metagenomics.}, journal = {Microbiology resource announcements}, volume = {15}, number = {5}, pages = {e0008526}, pmid = {42003642}, issn = {2576-098X}, abstract = {DiscoVir is an automated pipeline for viral metagenomics available in National Institute of Allergy and Infectious Diseases (NIAID)'s free web application for microbiome analysis, Nephele. DiscoVir makes viral discovery, taxonomic and functional annotation, host predictions, and diversity analyses of the virome easily accessible to researchers at all levels of expertise.}, } @article {pmid42003644, year = {2026}, author = {Iizuka, R and Moriya, T and Oshima, T and Uemura, S and Yohda, M}, title = {Amplicon sequence collection of putative polyethylene terephthalate hydrolases from two different composts in Japan.}, journal = {Microbiology resource announcements}, volume = {15}, number = {5}, pages = {e0017326}, pmid = {42003644}, issn = {2576-098X}, support = {22K05310//Japan Society for the Promotion of Science/ ; 25K08915//Japan Society for the Promotion of Science/ ; G-2021-3-047//Institute for Fermentation, Osaka/ ; JPMJCR2231//Japan Science and Technology Agency/ ; //Mitsui Chemicals, inc./ ; }, abstract = {We report a collection of amplicon sequences of putative polyethylene terephthalate (PET) hydrolases from two different composts in Japan. Employing previously designed degenerate primers, we identified 31 and 22 sequences from industrial and agricultural composts, respectively, confirming the presence of highly homologous PET hydrolase genes across different compost environments.}, } @article {pmid42003651, year = {2026}, author = {Kocakahya, İ and Şahin, G and Büyükkahraman, E and Arıkan, M}, title = {Metagenome-assembled genomes from urban pigeon feces in Istanbul, Türkiye.}, journal = {Microbiology resource announcements}, volume = {15}, number = {5}, pages = {e0140525}, pmid = {42003651}, issn = {2576-098X}, support = {1919B012420662//Scientific and Technological Research Council of Turkey/ ; 41481//Scientific Research Coordination Unit of Istanbul University/ ; }, abstract = {We report herein about 101 metagenome-assembled genomes (MAGs) obtained from pigeon fecal samples collected in 2025 from the Beyazıt, Kadıköy, and Beşiktaş squares of Istanbul. The MAGs were predominantly composed of members of the phyla Firmicutes, Actinobacteria, and Proteobacteria, with a lower representation of Campylobacterota and Patescibacteriota.}, } @article {pmid42004019, year = {2026}, author = {Yuan, G and Zhu, X and Zhang, L and Wang, X and Wang, Y and Guo, D and Zhang, T and Wang, G and Wang, N}, title = {Shading affects the nitrogen cycling process and plant nitrogen uptake by altering the rhizosphere microbial community.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1780344}, pmid = {42004019}, issn = {1664-462X}, abstract = {Plants adapt to environmental changes by affecting the rhizosphere environment and microbial pathways. Shading affects nitrogen absorption and accumulation in plants by directly or indirectly altering the light intensity. However, the effects this has on the rhizosphere micro-environment and especially the microbial community are not fully understood. Utilizing non-targeted metabolomics and metagenomics, we investigated the changes in the microbial community structure in the cigar tobacco rhizosphere and the nitrogen cycling process and its relationship with nitrogen absorption by the plants under artificial shading conditions. Shading significantly increased the rhizosphere soil organic carbon, hydrolyzable nitrogen, ammonium nitrogen, nitrate nitrogen, and nitrogen contents in tobacco plants. Metabolomics revealed that shading significantly affected the arginine biosynthesis pathway in the rhizosphere soil, with the expression levels of L-oxornithine, citrulline and L-arginine significantly increasing. Metagenomics analysis indicated that shading significantly altered the rhizosphere microbial community structure and the nitrogen cycling process. The abundances of organic nitrogen-decomposition (gdh A, ansB) and nitrification genes (amoA_B, amoB_B, amoC_B, hao) significantly increased. Flavobacterium and Stenotrophomonas may play important roles in the nitrogen cycle in the rhizosphere. Correlation analysis indicated that Flavobacterium and Stenotrophomonas were significantly positively correlated with L-glutamic acid, L-ornithine and L-arginine (p < 0.05). These results reveal the biological mechanism by which shading affects nitrogen absorption in crops via changes in the rhizosphere microbial community and the nitrogen cycling process, providing a scientific foundation for guiding nutrient management strategies in shaded cultivation.}, } @article {pmid42004152, year = {2026}, author = {You, G and Wang, S and Hua, Y and Su, J and Yang, Y and Shi, B and Cen, S}, title = {A four-year misdiagnosis of spinal Burkholderia pseudomallei infection: A case report and literature review.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02558}, pmid = {42004152}, issn = {2214-2509}, abstract = {Melioidosis, traditionally an endemic disease, is increasingly reported in non-endemic regions. Its causative pathogen, Burkholderia pseudomallei, exhibits distinct characteristics from common pathogens but is prone to misdiagnosis due to clinical overlap with other infections. Despite advances in diagnostics, metagenomic next-generation sequencing (mNGS) has not been featured in case reports. We present a case of melioidosis, misdiagnosed for four years, where mNGS proved pivotal for definitive diagnosis. Based on our findings and literature review, we advocate for mNGS in melioidosis diagnosis. Furthermore, we identify subtle distinctions between melioidosis and tuberculosis amidst their similarities and propose integrating these features into a differential diagnostic framework.}, } @article {pmid42004164, year = {2026}, author = {Chong, KL and Liew, KJ and Salleh, FM and Chong, CS}, title = {Metagenomic insights into mangrove lignocellulolytic bacteria and functional analysis of a glucose-tolerant GH 1 β-glucosidase.}, journal = {3 Biotech}, volume = {16}, number = {5}, pages = {163}, pmid = {42004164}, issn = {2190-572X}, abstract = {UNLABELLED: Mangrove ecosystems contain abundant lignocellulosic biomass and mangrove microorganisms that are capable of degrading plant polymers. In this study, a shotgun metagenomic approach was employed to explore the bacterial communities from Tanjung Piai National Park, Malaysia and their genes involved in lignocellulosic biomass degradation. A total of 148 of carbohydrate active enzymes (CAZy) genes spanning GH, CE, and AA families were identified with lignocellulolytic abilities. These enzymes included 20 cellulases, 46 hemicellulases, and 82 lignin-modifying enzymes. Approximately 89.19% of these genes were found from underexplored bacterial lineages. A set of lignocellulolytic genes derived from diverse bacterial taxa highlighted the synergistic action of mangrove bacteria in lignocellulose degradation. To validate the functionality of these genetic resources, one of the genes (BGL3_GH1) encoding a β-glucosidase was selected for expression and characterisation. The recombinant enzyme showed optimal activity at 60 ℃ and pH 7, retained up to 75% activity at 10% (w/v) NaCl. The enzyme exhibited a 1.6 to 2.1-fold in enzyme activity with glucose concentration up to 2 M. In a two-step saccharification assay using sugarcane bagasse, supplementation with recombinant BGL3_GH1 enhanced the saccharification yield (0.0674 g g[- 1] biomass) compared with treatments using commercial cellulase or recombinant BGL3_GH1 alone. These findings reveal the functional diversity of lignocellulose-degrading genes in mangrove bacteria and identify recombinant BGL3_GH1 as a potential enzyme candidate for biomass conversion application.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04788-x.}, } @article {pmid42004407, year = {2026}, author = {Chu, D and Liu, N and Liu, Q and Li, X and Yang, H and Zhu, N and Liu, Z and Wang, R and Yuan, S and Fu, H}, title = {Diet-Driven Divergence in Gut Microbiota Variation Between Two Sympatric Gerbil Species.}, journal = {Ecology and evolution}, volume = {16}, number = {}, pages = {e73367}, pmid = {42004407}, issn = {2045-7758}, abstract = {Gut microbiota provide various benefits to their mammalian hosts; however, knowledge regarding interspecific differences in gut microecology remains limited. This study employed 16S rRNA sequencing combined with metagenomic functional prediction (potential functions or functional potential) to conduct a comparative analysis of the gut microbial composition and functional adaptability of two sympatrically distributed gerbil species with distinct diets: the herbivorous Rhombomys opimus (RO) and the omnivorous Meriones meridianus (MM). The results revealed that the omnivorous MM exhibited a level of gut microbial alpha diversity comparable to that of the herbivorous RO, whereas RO showed significant enrichment of norank_f__Muribaculaceae, a taxon associated with fiber degradation, and demonstrated higher abundance of genes related to complex fiber degradation. Notably, bacterial genera significantly enriched in the gut of MM, such as Lachnospiraceae_NK4A136_group and Desulfovibrio, may play important roles in maintaining gut health and enhancing chitin degradation efficiency. Furthermore, the abundance of genes related to monosaccharide and chitin degradation was significantly higher in MM than in RO. Functional network analysis indicated that the cellulose degradation gene networks in both gerbil species were predominantly synergistic, but the synergistic effect was stronger in RO than in MM (ratios of positive to negative correlation edges: 2.44: 1.59). Further analysis revealed that the monosaccharide and chitin degradation gene networks in MM both exhibited synergistic interaction patterns (ratios of positive to negative correlation edges: 1.69 and 2.95, respectively), whereas these two networks in RO were primarily antagonistic (ratios of positive to negative correlation edges: 0.831 and 0.73, respectively). This suggests that the gut microbiota of RO are more conducive to digesting complex plant fibers, while those of MM are better adapted for digesting starch and chitin. This differentiation in gut microbiota optimizes the utilization of different food resources by the two species, thereby promoting their sympatric coexistence. This study enhances our understanding of the adaptive mechanisms of gut microecology in rodents with different diets and provides an important foundation for further research on the microbial ecology of wild rodents and the mechanisms underlying sympatric species coexistence.}, } @article {pmid42004633, year = {2026}, author = {Monjardino, P and Azevedo, AR and Mendonça, D and Pozsgai, G and Borges, PAV and Frias, J and Toubarro, D}, title = {Metagenomic survey of fungal communities in compost from dairy plant wastewater sludge and garden trimmings.}, journal = {Biodiversity data journal}, volume = {14}, number = {}, pages = {e174893}, pmid = {42004633}, issn = {1314-2828}, abstract = {BACKGROUND: Composting converts organic residues into stable organic matter and nutrients under aerobic conditions, improving soil properties and microbiome balance, while mitigating environmental impacts. Although microbiomes of various compost types have been studied, information is still fragmented and often not tailored to specific raw material combinations. In particular, little is known about the fungal communities involved in composting dairy plant wastewater sludge mixed with garden trimmings. This data paper contributes to filling that gap by providing a comprehensive taxonomic inventory.

NEW INFORMATION: We provide a fungus-focused dataset from 18 compost samples generated from a 1:1 (w/w) mix of garden trimmings and dairy plant wastewater sludge, collected at three process stages (thermophilic start/end; mid-cooling and maturation) under two turning regimes. Shotgun metagenomes were taxonomically annotated against NCBI taxonomy (accessed 19 Feb 2025). Only Fungi were detected within Eukarya, spanning nine phyla; Ascomycota (60.8%), Mucoromycota (17.76%), Basidiomycota (8.50%) and Chytridiomycota (7.21%) comprised 94.27% of the taxonomic features. We report 417 genera (13 >1% relative abundance each); top: Aspergillus (17.93%), Rhizopus (8.61%), Chaetomium (4.83%), Aureobasidium (3.09%), Madurella (2.85%), Paramicrosporidium (2.71%), Rhizophagus (1.88%), Rasamsonia (1.81%), Hyaloraphidium (1.39%), Thermochaetoides (1.31%), Talaromyces (1.19%), Trichoderma (1.15%), Podospora (1.06%) comprised 49.81% of the taxonomic feature abundance. Overall 663 taxa were identified (578 species, 416 genera, 230 families, 106 orders, 48 classes and 9 phyla). The dataset (DwCA; 663 occurrences) is intended to serve as a reference for compost mycobiomes and will be available via GBIF (DOI 10.15468/nmpzwr).}, } @article {pmid42004896, year = {2026}, author = {Pourghasem, M and Tabatabaii, SA and Modarresi, SZ and Jafari Nodoushan, A and Fadavi, N and Soflaee, M and Hosseini Vajari, A and Khazaii, F and Shahhosseini, B and Fakhimi Derakhshan, K and Sadat Mansouri, S}, title = {Fungal Infections in Pediatric Patients With Hematologic Malignancies and Stem Cell Transplantation: Impact on the Upper and Lower Respiratory Systems.}, journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2026}, number = {}, pages = {8766717}, pmid = {42004896}, issn = {1712-9532}, abstract = {Invasive fungal infections (IFIs) are a leading cause of morbidity and mortality in children with hematological malignancies as well as those undergoing hematopoietic stem cell transplantation (HSCT). Extreme immunological dysregulation secondary to severe neutropenia, T-cell lymphopenia, graft-versus-host disease (GVHD), intensive chemotherapy regimens, and conditioning therapy for HSCT, as well as primary immunodeficiencies (PIDs), render these patients highly susceptible to both opportunistic and pathogenic fungal infections. Despite advances in antifungal drugs and diagnostic tools, it is very difficult in these children to provide timely diagnosis and optimal management of IFIs because of the nonspecific clinical manifestations, the invasiveness of present diagnostic modalities in pediatric patients, and biomarker kinetics differences in various pediatric age groups, along with a lack of incorporation of immunological-pharmacological maturity-associated variability in the existing scoring systems borrowed from adults. This narrative review provides a comprehensive and contemporary assessment of the epidemiology, host-related risk factors, clinical presentations, diagnostic criteria, and management practices for IFIs in children with hematological malignancies and following HSCT. It also highlights the role of EORTC/MSGERC criteria in defining IFIs as probable, proven, and possible infections and explores the sensitivity and specificity of noninvasive methods such as the galactomannan index, polymerase chain reaction (PCR), ß-D-glucan assay, high-resolution CT scans (HRCTs), and the latest approaches including next-generation sequencing (NGS) and metagenomics. This review points out significant gaps in pediatric research studies and supports efforts to optimize healthcare use with risk-prediction models rather than just relying on current algorithms.}, } @article {pmid42005541, year = {2026}, author = {Naitchede, LHS and Ihearahu, OC and Saha, K and Igwe, DO and Yan, J and Osano, AA and Ray, S and Ude, G}, title = {Microbial community characterization in semi-hydroponic systems of Starbor kale (Brassica oleracea L.) grown under normal gravity and simulated microgravity.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100592}, pmid = {42005541}, issn = {2666-5174}, abstract = {Kale is a member of the Brassicaceae family and contains a range of beneficial compounds. Given the global context of climate change, various vegetable production systems using advanced technologies, such as hydroponics, are being explored to alleviate food insecurity. Herein, we characterized the comprehensive microbial community associated with Starbor kale cultivation systems under normal gravity and simulated microgravity in coco coir, representing an innovative approach compared to previous studies. The kale seedlings were planted in growth vessels set into custom 2D clinostats and placed in a CONVIRON growth chamber for 43 days. The microbial DNA from coco-coir and root samples of grown kale was extracted and subjected to shotgun metagenomic sequencing. Comparisons between components revealed a higher abundance of bacteria in the soilless, while the kale roots were dominated by Eukaryota and archaea. The phyla Pseudomonadota and Actinomycetota were highly prevalent across all samples, with relatively high abundance in the coco coir samples from horizontal clinostats (HCR) under simulated gravity and from rotating vertical clinostats (VCR). The HCR group was associated with the highest number of biomarkers (28). Both CAZymes, glycoside hydrolases and carbohydrate esterases, exhibited higher relative abundances in the coco coir samples under normal gravity, whereas carbohydrate-binding modules were more abundant in HCR and VCR. The root samples showed much higher abundances of polysaccharide lyases (ranging from 0.00088 to 0.00097) and carbohydrate esterases (ranging from 0.030 to 0.033). The top four prevalent antibiotic resistance genes were adeF, vanY, vanT, and qacG. The findings of this investigation are crucial for the cultivation of kale and leafy green agriculture in hydroponic systems.}, } @article {pmid42005844, year = {2026}, author = {Ibañez-Lligoña, M and Colomer-Castell, S and Campos, C and González-Camuesco, Á and Llauradó, A and Garcia-Larroy, J and Sánchez-Tejerina, D and Rando-Segura, A and Andrés, C and Esperalba, J and Nadal, P and Ferrer, R and Cortese, MF and Tabernero, D and Gregori, J and Riveiro-Barciela, M and Ruiz-Cobo, JC and Ruiz, A and Del Barco, E and Buti, M and Goya, M and Antón, A and Cano, A and Juntas-Morales, R and Quer, J}, title = {Unveiling pathogens and contaminants: refining metagenomics for clinical diagnostics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786985}, pmid = {42005844}, issn = {1664-302X}, abstract = {INTRODUCTION: Shotgun metagenomic sequencing (mNGS), an untargeted approach that sequences all nucleic acids in a sample, has emerged as a powerful tool for pathogen detection and genome characterization. However, its implementation in clinical diagnostics remains limited due to technical challenges such as contamination and reduces sensitivity, especially in low-biomass samples.

METHODS: We applied mNGS to 144 clinical samples representing chronic infections, acute infections, and respiratory co-infections. To address contamination, we established a framework integrating negative controls, lab-specific contaminant watchlists, and computational filtering. Viral detection performance and genome recovery were assessed across sample types and viral loads.

RESULTS: Viral load was shown to be the primary determinant of sensitivity, with reliable recovery achieved only at higher titers. Our framework substantially improved contamination management, reducing false-positive signals and enhancing viral genome recovery. mNGS enabled the detection of clinically relevant co-infections and refined viral classification beyond targeted diagnostics, while also revealing the substantial risk of spurious detections in the absence of contamination-aware workflows.

DISCUSSION: These findings define practical sensitivity thresholds for clinical mNGS and underscore the need for contamination-aware workflows, particularly for low-biomass samples, while providing an open-source contaminants watchlist that enhances reliability and utility of clinical metagenomics.}, } @article {pmid42005864, year = {2025}, author = {Steindler, L and Durán Canché, MA and Ilan, M and Bar-Shalom, R and Lopez, JV and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the marine sponge Diacarnus erythraeanus Kelly-Borges & Vacelet, 1995, and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {466}, pmid = {42005864}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Diacarnus erythraeanus (sponge; Porifera; Demospongiae; Poecilosclerida; Podospongiidae). The genome sequence has a total length of 140.86 megabases. Most of the assembly (98.57%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.34 kilobases in length. Sixty-four binned genomes were generated from the metagenome assembly, of which 46 were classified as high-quality metagenome assembled genomes (MAGs). The microbial signature is typical of HMA sponges, including the Pseudomonadota, Chloroflexota and Acidobacteriota as dominant phyla and several candidate phyla (Poribacteria, Binatota, Latescibacterota) as well as the archaeal clade Nitrosopumilaceae in lower abundance.}, } @article {pmid42005923, year = {2026}, author = {Lafon, T and Weingart, M and Vaidie, J and Calfee, CS and Jacob, ST and Freund, Y and Shapiro, NI and Barraud, O and Monneret, G and van der Poll, T and Fromage, Y and François, B}, title = {Challenges in early detection and prognostication of sepsis: new approaches from the emergency department and intensive care unit.}, journal = {EClinicalMedicine}, volume = {94}, number = {}, pages = {103864}, pmid = {42005923}, issn = {2589-5370}, abstract = {In this narrative review, we aimed to provide a comprehensive overview of emerging diagnostic strategies and precision medicine approaches in sepsis, while explicitly acknowledging the heterogeneity of clinical contexts. In the Emergency Department (ED), timely recognition of infection and sepsis represents one of the most frequent and challenging tasks, which may delay management directly increasing morbidity and mortality. Even if very popular and widely used, traditional scores and routine biomarkers remain of limited interest to confirm diagnosis and predict deterioration. Nevertheless, emerging point-of-care tools hold promise such as "real-time microbiology", bedside immune profiling, and echocardiography for on-time hemodynamic phenotyping. More advanced strategies, such as omics technologies and transcriptomic signatures, offer deeper biological precision, while machine learning and artificial intelligence can integrate high-dimensional ED data to anticipate deterioration and capture the dynamic evolution of sepsis subphenotypes. Many of these tools are already feasible at the bedside and only await integration into routine ED workflows. Embedding them within dedicated sepsis pathways and multidisciplinary teams could optimize global patient care and accelerate the transition toward precision medicine in acute sepsis. Sustainable improvements in sepsis outcomes will most likely not come from isolated devices but from their integration into coordinated and sepsis-specific pathways.}, } @article {pmid42006114, year = {2025}, author = {Dorobantu, S and Grigorescu, A and Fratea, A and Mirauta, B and Neghina, A and Bica, G and Neacsu, A and Dumitrescu, F and Streata, I and Netea, M and Riza, AL}, title = {Strength of Omics in Uncovering Sepsis Mechanisms-A Perspective.}, journal = {Current health sciences journal}, volume = {51}, number = {4}, pages = {425-436}, pmid = {42006114}, issn = {2067-0656}, abstract = {BACKGROUND: Sepsis is a significant life-threatening condition due to a dysregulated response to infection. Large datasets yield unprecedented views and transformative insights into processes through various computational frameworks. Our aim was to highlight significant contributions from genomics, transcriptomics, proteomics in the field of sepsis, as modeled from human data. We are showcasing key findings in each omics that have improved the understanding of sepsis pathophysiology, while presenting a perspective from the group's own contribution to the field.

DISCUSSION AND CONCLUSIONS: Each of the presented omics has advanced our mechanistic understanding on sepsis pathogenicity, biomarker identification for diagnosis, prognosis, and molecular stratification purposes. Multi-omics sepsis research shows strong input from genomics, transcriptomics, proteomics. These have revealed mechanistic links and produce robust endotypes but faces challenges on the path to clinical integration. Integrative sepsis studies combine large-scale omics, paired sampling, and computational multi-omics frameworks to link molecular layers to phenotype. Addressing gaps in standardization, and age/ethnicity representation could yield actionable biomarkers, stratified therapies and improved outcomes.}, } @article {pmid42006125, year = {2026}, author = {Azuma, N and Wada, N and Aoki, R and Sampei, M and Mawatari, T and Saito, Y}, title = {Administration of bifidobacteria and dietary fiber improves cognitive function by increasing short-chain fatty acid-producing bacteria and reducing inflammation.}, journal = {Bioscience of microbiota, food and health}, volume = {45}, number = {2}, pages = {139-148}, pmid = {42006125}, issn = {2186-6953}, abstract = {Bifidobacterium animalis subsp. lactis GCL2505 (GCL2505), commercially known as the "BifiX" strain in Japan, reaches the intestine alive, proliferates after a single intake, and is associated with several positive health effects. A randomized, double-blind, placebo-controlled, parallel-group clinical trial of this probiotic strain in combination with inulin (a prebiotic) reported an improvement of cognitive function in the elderly. In the present study, a follow-up analysis was performed to elucidate the underlying mechanism, using a multi-omics approach that integrated a high-throughput assay of blood inflammatory markers and metagenomic analysis of the fecal bacterial composition. After probiotic and prebiotic administration, short-chain fatty acid producers such as Faecalibacterium and Bifidobacterium were increased in the gut. Moreover, in the subgroup with greater improvement in cognitive function scores, the levels of inflammatory markers were decreased. Subgroup analysis revealed that the improvement of cognitive function was associated with a reduction of inflammation and an increase of Faecalibacterium. These results suggest that GCL2505 and inulin can improve cognitive function by alleviating inflammation via an increase of short-chain fatty acid-producing bacteria, which appears to elevate levels of short-chain fatty acids, particularly acetate and butyrate, in the gut. The present results contribute to a deeper comprehension of the gut-brain axis and propose new avenues for potential therapeutic intervention in cognitive disorders.}, } @article {pmid42006869, year = {2026}, author = {Li, Y and Zhu, H and Zhan, Z and Li, G and Zhou, Q and Zheng, C and Huang, F}, title = {Clinical features and prognostic factors of Chlamydia psittaci pneumonia: a retrospective study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1804156}, pmid = {42006869}, issn = {2296-858X}, abstract = {BACKGROUND: Chlamydia psittaci pneumonia (CPP) is frequently misdiagnosed and can progress to severe illness. A deeper understanding of its clinical and imaging features is crucial for early detection and effective treatment.

METHODS: This retrospective study analyzed 74 patients diagnosed with CPP via metagenomic (mNGS) and targeted next-generation sequencing (tNGS) between January 2022 and September 2025. Patients were categorized into severe (n = 21) and non-severe (n = 53) groups based on established criteria for severe community-acquired pneumonia. Data on demographics, clinical manifestations, laboratory findings, and imaging characteristics were collected and compared.

RESULTS: The cohort had a median age of 60 years, with a male predominance (62.2%). A history of poultry/bird exposure was reported by 87.8% of participants. Common symptoms included fever (94.6%), cough (63.5%), and fatigue (29.7%), with no significant differences between groups. Hospitalization was significantly longer in the severe group (12.95 ± 6.08 days) than in the non-severe group (8.13 ± 3.30 days) (p < 0.001). Chest CT revealed consolidation and ground-glass opacities in all patients. Pleural effusion was significantly more common in the severe group (76.2% vs. 45.3%, p = 0.016), as was bilateral lung involvement (52.4% vs. 22.6%, p = 0.013). Multivariate analysis identified elevated D-dimer (OR = 2.737, p = 0.007) and reduced lymphocyte percentage (L%) (OR = 0.813, p = 0.026) as independent predictors of severe disease. ROC curve analysis showed an AUC of 0.765 for D-dimer and 0.739 for L% reduction. Following tetracycline or quinolone therapy, 94.6% of patients recovered, with an overall mortality rate of 5.4%.

CONCLUSION: Severe CPP is associated with prolonged hospitalization, bilateral pulmonary infiltrates, and pleural effusion. D-dimer and lymphocyte percentage are valuable prognostic indicators for disease severity. Early targeted antibiotic therapy is effective, but timely respiratory support is critical for severe cases.}, } @article {pmid42006894, year = {2026}, author = {Cui, T and Huang, M}, title = {Case Report: A case of refractory tuberculous peritonitis mimicking and complicating suspected encapsulating peritoneal sclerosis in a long-term peritoneal dialysis patient.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1777805}, pmid = {42006894}, issn = {2296-858X}, abstract = {BACKGROUND: Tuberculous peritonitis (TBP) is a rare but severe complication in peritoneal dialysis (PD) patients, often presenting with non-specific symptoms. Its diagnosis is particularly challenging in patients with pre-existing or co-existing peritoneal pathology, such as changes suggestive of encapsulating peritoneal sclerosis (EPS).

CASE PRESENTATION: A 59-year-old male on PD for 14 years with no prior history of peritonitis presented with recurrent abdominal pain, fever, and cloudy effluent, following a recent episode of Staphylococcus caprae peritonitis. Initial contrast-enhanced computed tomography (CT) revealed diffuse peritoneal thickening, omental "caking," and localized ascites, raising strong suspicion for EPS. However, the patient's condition relapsed despite broad-spectrum antibiotic therapy. Metagenomic next-generation sequencing (mNGS) of peritoneal fluid definitively identified Mycobacterium tuberculosis complex. The diagnosis was thus revised to TBP manifesting with secondary peritoneal inflammatory changes mimicking EPS. Management involved laparoscopic PD catheter removal, transition to hemodialysis, and initiation of a renal-adjusted anti-tuberculous regimen (levofloxacin and linezolid), leading to gradual clinical and biochemical improvement.

CONCLUSION: This case highlights that TBP can clinically and radiologically mimic EPS in long-term PD patients, leading to diagnostic delay. High clinical suspicion and the utilization of advanced molecular diagnostics like mNGS are crucial for accurate diagnosis. Catheter removal combined with appropriate anti-tuberculous therapy forms the cornerstone of management in such complex scenarios.}, } @article {pmid42007374, year = {2026}, author = {Jeong, UJ and Ali, M and Park, YJ and You, JS and Yoon, SS}, title = {A responder-informed gut microbial consortium enhances anti-PD-1 efficacy in a mouse cancer model.}, journal = {Microbiome research reports}, volume = {5}, number = {1}, pages = {2}, pmid = {42007374}, issn = {2771-5965}, abstract = {Aim: Immune checkpoint inhibitors (ICIs), particularly anti-programmed cell death protein 1 (PD-1) therapy, have improved cancer treatment outcomes, yet durable benefit is achieved in only a subset of patients. Growing evidence implicates the gut microbiome as a modulator of ICI responsiveness, but defined and experimentally validated microbial strategies remain limited. This study aimed to identify responder-associated gut microbes and to evaluate a defined bacterial consortium for enhancing PD-1 blockade efficacy. Methods: Publicly available shotgun metagenomic datasets from anti-PD-1-treated cancer patients were re-analyzed to compare gut microbiome profiles between responders and non-responders. Bacterial taxa reproducibly enriched in responders were selected based on consistency across analytical criteria and cultivability and assembled into a four-strain consortium (UJ-04). The immune-adjuvant potential of UJ-04, alone or combined with anti-PD-1 therapy, was evaluated in a B16-F10 melanoma mouse model, with tumor growth and immune responses assessed by flow cytometry. Results: Metagenomic re-analysis identified four commensal bacterial taxa consistently enriched in responder patients, forming the defined UJ-04 consortium. While UJ-04 alone showed minimal antitumor activity, combination treatment with anti-PD-1 significantly enhanced tumor growth inhibition compared with anti-PD-1 monotherapy. This effect was accompanied by increased intratumoral CD8[+] T cells and natural killer cells, with concordant immune trends in peripheral compartments. Conclusion: A responder-informed, defined microbial consortium functionally translates clinical microbiome associations into in vivo validation and enhances PD-1 blockade efficacy by modulating host antitumor immunity. These findings support defined bacterial consortia as microbiome-based immunomodulatory adjuncts for immunotherapy.}, } @article {pmid42007699, year = {2026}, author = {Carroll, AC and Hinz, A and Hicks, AMA and Khov, E and Van Bakel, T and Doukhanine, E and Fralick, M and Nott, C and Kassen, R and Thampi, N and Hug, LA and MacFadden, D and Wong, A}, title = {Targeted metatranscriptomic detection of viruses from floors for simultaneous evaluation of respiratory disease burden and viral variant identification.}, journal = {mSphere}, volume = {11}, number = {5}, pages = {e0008626}, pmid = {42007699}, issn = {2379-5042}, mesh = {Humans ; *SARS-CoV-2/genetics/isolation & purification ; *Metagenomics/methods ; *COVID-19/epidemiology/virology ; Influenza A virus/genetics/isolation & purification ; Canada/epidemiology ; *Viruses/genetics/isolation & purification/classification ; Respiratory Syncytial Virus Infections/epidemiology ; }, abstract = {UNLABELLED: Built environment surveillance is a proven approach for tracking disease burden of some viruses within hospitals and long-term care facilities. However, studies in clinical settings are lacking for simultaneously surveying targets in a built environment using targeted metatranscriptomics. We swabbed six discrete floor locations within an acute care center's emergency department (ED) in Ottawa, Canada, and sequenced cDNA using a 132 viral taxa panel, identifying viral burden across sampling locations and time. The determined SARS-CoV-2 variant profile across time was matched to provincial variant prevalence. The correlation between metatranscriptomic read abundances and reported cases of influenza A, SARS-CoV-2, and RSV was assessed. We quantified these via qPCR and assessed the correlation of Cq versus metatranscriptomic reads for these viruses. We sequenced a median of 1,302,882 reads per sample from 38 floor swabs collected during peak respiratory viral season (November 2022-February 2023). Diversity of viral communities varied significantly across locations in the ED. SARS-CoV-2 variant abundance shifts matched the changing infection landscape concurrently reported in Ontario. Relationships between targeted metatranscriptomic read ratios and clinical burden were not statistically significant, although we found modest correspondence between qPCR signal and read depth for RSV and SARS-CoV-2. This approach characterized the viral communities and the within-species diversity within an ED. Correlating sequencing-derived data with disease burden for three key respiratory viruses was inconsistent, with the exception of significant correlation between metatranscriptomic reads and Cq data for SARS-CoV-2. We were able to recover the distribution of clinically reported SARS-CoV-2 variants from the floor swab data.

IMPORTANCE: Environmental surveillance is useful for estimating the disease burden for certain viruses. qPCR is commonly used for surveillance of wastewater and built environments, including during the COVID-19 pandemic, but single, multiplexed reaction targets are limited. Targeted metagenomic or metatranscriptomic approaches can accurately quantify microbial populations of interest in an environment, reduce off-target sequencing, and evaluate a broader number of targets than qPCR assays. Here, we assessed the capacity of a targeted viral metatranscriptomic panel to correlate viral abundance in the hospital built environment with key pathogens of interest, including influenza A, RSV, and SARS-CoV-2. Our results suggest that targeted metatranscriptomics may identify viral communities in healthcare facilities, including strain-level detection capability. However, this approach must be validated for its effectiveness in viral surveillance that accurately reflects disease burden. This work contributes to a growing toolkit for pathogen surveillance, a critical endeavor to safeguard against outbreaks of known and emerging pathogens.}, } @article {pmid42007817, year = {2026}, author = {Chen, M and Kang, Y and Cheng, M and Li, X and Keng, J and Zhao, P and Sui, H and Dong, J and Sun, L and Liu, B and Hu, Y and Jiang, J and Yang, F}, title = {Co-circulation of multiple arboviruses in acute febrile patients in Yunnan, China, identified by metagenomic sequencing.}, journal = {Journal of clinical microbiology}, volume = {64}, number = {5}, pages = {e0167025}, pmid = {42007817}, issn = {1098-660X}, support = {2021-I2M-1-038//CAMS Innovation Fund for Medical Sciences/ ; }, mesh = {Humans ; China/epidemiology ; Phylogeny ; Metagenomics ; Chikungunya virus/genetics/isolation & purification ; Female ; *Coinfection/epidemiology/virology ; Male ; Dengue Virus/genetics/isolation & purification ; *Arboviruses/genetics/classification/isolation & purification ; Adult ; Disease Outbreaks ; Zika Virus/genetics/isolation & purification ; *Arbovirus Infections/epidemiology/virology ; *Fever/virology/epidemiology ; Chikungunya Fever/epidemiology ; Middle Aged ; Zika Virus Infection/epidemiology ; Adolescent ; Dengue/epidemiology ; Young Adult ; }, abstract = {UNLABELLED: Arboviruses such as dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV) are transmitted by Aedes mosquitoes and mainly circulate in tropical and subtropical regions. With global warming, their geographic range is expanding, increasing their threat to public health. Yunnan Province, China, bordering Southeast Asia, is a hotspot for viral importation due to intensive cross-border mobility. However, systematic surveillance for these arboviruses among acute febrile patients remains insufficient. We performed metagenomic sequencing on serum specimens from 990 acute febrile patients at the China-Myanmar border between 2017 and 2023. The pathogens were confirmed by PCR and viral isolation. Phylogenetic and spatiotemporal analyses were used to infer viral origins and transmission dynamics. In this study, a CHIKV outbreak was confirmed in 2019, with strains closely related to those from Myanmar and Thailand. Four DENV serotypes 1-4 were identified, with the predominant serotype varying annually. ZIKV was detected and closely related to strains from Myanmar. Co-infections were identified, including one case each of CHIKV with DENV-1, CHIKV with DENV-3, CHIKV with ZIKV, and DENV-1 with DENV-2. Bayesian spatiotemporal analysis of CHIKV reconstructed global transmission routes, indicating that the 2019 outbreak in China likely originated in India and spread sequentially through Bangladesh, Thailand, and Myanmar. In addition, we also detected enterovirus, hepatitis virus, Saffold virus, and rhinovirus. This study reveals a comprehensive spectrum of pathogens, including the co-circulation of DENV, CHIKV, and ZIKV, and underscores the potential risk of arbovirus importation into China, highlighting the need for strengthened border surveillance.

IMPORTANCE: Arboviruses, including dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV), are expanding their range and threatening global public health. Yunnan, situated along the China-Southeast Asia border, is highly susceptible to viral introduction. By applying viral metagenomic sequencing to acute febrile patients, this study uncovered a comprehensive spectrum of pathogens and the co-circulation of DENV, CHIKV, and ZIKV. Phylogenetic analyses revealed that arboviruses were closely related to strains from Myanmar and Thailand, indicating possible frequent cross-border viral introductions. Meanwhile, we reconstructed the global transmission pathways of CHIKV through Bayesian spatiotemporal analysis, providing valuable insights for regional prevention and control of arboviruses. These findings demonstrate that Yunnan serves as a critical interface for viral importation and underscore the urgent need to strengthen border surveillance and early warning systems to mitigate the spread of arboviruses.}, } @article {pmid42008001, year = {2026}, author = {Hu, C and Yu, J and Chu, T and Wang, Q and Chen, L and Yu, Y and Wang, Y}, title = {Uncovering novel virophages and giant viruses in high-altitude Lake Namtso: diversity and evolution of host-virus-virophage tripartite interaction systems.}, journal = {Archives of microbiology}, volume = {208}, number = {7}, pages = {}, pmid = {42008001}, issn = {1432-072X}, abstract = {Virophages are small double-stranded DNA viruses that parasitize giant viruses, modulating virus–host interactions and influencing microbial community dynamics. Despite their ecological significance, virophages and giant viruses remain poorly studied in extreme environments. Here, we present the first metagenomic survey of virophage and giant virus diversity in Lake Namtso, a high-altitude saline lake on the Tibetan Plateau. Metagenomic assembly and phylogenomic analyses uncovered 93 virophage major capsid protein sequences spanning seven established families, alongside numerous unclassified lineages. Two nearly complete virophage genomes were reconstructed: Namtso Virophage 1 (NMV1), which encodes both replication- and integration-associated genes and likely represents a novel family, and Namtso Virophage 2 (NMV2), affiliated with Omnilimnoviroviridae but distinguished by duplicated protease genes and dual DNA methyltransferases. Parallel analyses identified over 18,000 giant virus marker genes, with DNA PolB affiliated to Imitervirales, Pimascovirales, Asfuvirales, Algavirales, and Chitovirales, as well as divergent lineages representing potential novel Nucleocytoplasmic large DNA viruses (NCLDVs). Homologous protein analysis and tetranucleotide clustering suggest extensive host–virus–virophage interactions. These findings significantly expand the known diversity and genomic repertoire of virophages and giant viruses, highlight their ecological roles in sustaining microbial resilience, and provide new insights into viral evolution and adaptation in extreme high-altitude ecosystems.}, } @article {pmid42008944, year = {2026}, author = {Liu, J and Li, Y and Wang, H and Wang, L and Wu, G and Zhao, B}, title = {Biphasic dynamics of N-nitrosodimethylamine precursors in effluent-receiving rivers: Insights from multi-omics into microbial nitrogen metabolism regulation.}, journal = {Water research}, volume = {300}, number = {}, pages = {125933}, doi = {10.1016/j.watres.2026.125933}, pmid = {42008944}, issn = {1879-2448}, mesh = {*Rivers/chemistry ; *Dimethylnitrosamine ; Multiomics ; *Nitrogen/metabolism ; Wastewater ; Water Pollutants, Chemical ; }, abstract = {Wastewater effluent introduces substantial dissolved organic nitrogen into rivers, thereby increasing the risk of carcinogenic N-nitrosodimethylamine (NDMA) formation from its precursors. However, the microbial metabolic mechanisms governing dynamics of these precursors along receiving rivers remain unclear. Here, through a 21-day time-series incubation of sediments from upstream, outfall, and downstream areas of a representative wastewater treatment plant, combined with multi-omics analyses i.e., 16S rRNA gene sequencing, metagenomics, and metabolomics, the transformation of precursors and microbially mediated nitrogen metabolism were elucidated. A biphasic pattern of NDMA precursors measured as formation potential (FP) was observed during incubation, characterized by a rapid formation from days 0 to 3 followed by a remarkable degradation until day 7 and subsequent stabilization. Nitrate peaked paralleling NDMA FP, with nitrite accumulation following the onset of precursors degradation. Multi-omics analysis revealed that this turnover was driven by strong functional coupling between key nitrogen-cycling taxa and specific metabolites, particularly short-chain peptides. Community structure in the early phase was dominated by r‑strategists e.g., Bacillota, which promoted organic nitrogen degradation and nitrification, resulting in the accumulation of NDMA precursors. As anoxia developed, the community shifted toward K‑strategists such as Pseudomonadota and Chloroflexota, which likely degraded precursors through co-metabolism and consumption of ammonia source. Metabolomics revealed the conversion of precursors into short-chain peptides and amino acid analogues. Notably, effluent exposure established a functionally specialized legacy effect in downstream sediments, stabilizing into a microbial metabolic hotspot with a peak NDMA FP of 1285 ng/L, 158% and 80.7% higher than those in the upstream and outfall area, respectively. This study establishes a mechanistic framework for evaluating the transformation and risk of NDMA precursors in river systems, with direct implications for monitoring strategies and designing of the wastewater outfall location.}, } @article {pmid42010118, year = {2026}, author = {Menozzi, E and Ren, Y and Geiger, M and Macnaughtan, J and Avenali, M and Toffoli, M and Gilles, M and Calabrese, R and Mitrotti, P and Gallo, L and Famechon, A and Del Pozo, SL and Mezabrovschi, R and Koletsi, S and Loefflad, N and Yalkic, S and Limbachiya, N and Clasen, F and Yildirim, S and Shoaie, S and Blottière, H and Morabito, C and David, A and Quinquis, B and Pons, N and Le Chatelier, E and Valzania, F and Cavallieri, F and Fioravanti, V and Toschi, G and Blandini, F and Almeida, M and Ehrlich, SD and Meslier, V and Schapira, AHV}, title = {Microbiome signature of Parkinson's disease in healthy and genetically at-risk individuals.}, journal = {Nature medicine}, volume = {32}, number = {6}, pages = {2096-2106}, pmid = {42010118}, issn = {1546-170X}, support = {MR/T046007/1//EU Joint Programme - Neurodegenerative Disease Research (Programi i Përbashkët i BE-së për Kërkimet mbi Sëmundjet Neuro-degjeneruese)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; }, mesh = {Humans ; *Parkinson Disease/microbiology/genetics ; Female ; Male ; *Genetic Predisposition to Disease ; *Gastrointestinal Microbiome/genetics ; Aged ; Middle Aged ; Feces/microbiology ; *Glucosylceramidase/genetics ; Risk Factors ; Case-Control Studies ; *Microbiota/genetics ; Metagenomics ; Disease Progression ; }, abstract = {Parkinson's disease (PD) is a major cause of disability. GBA1 variants are the most common genetic risk factor for PD and increase the risk up to 30-fold. Why only approximately 20% of GBA1 variant carriers develop PD remains unknown. Here, by combining clinical and fecal metagenomics data from 271 patients with PD, from 43 carriers of GBA1 variants not manifesting PD symptoms (GBA-NMC) and from 150 healthy controls, and using an innovative microbiome analysis, combining differential abundance of species and coherence of differential abundance variation between the groups as assessed by Cliff's delta (δ), we show that the composition of a large component of the gut microbiome (approximately 25%) in GBA-NMC is intermediate between healthy controls and patients with PD. This component is strongly correlated with disease progression in patients and prodromal symptoms suggestive of future development of PD in both GBA-NMC and healthy individuals. We found microbiome alterations similar to those described here in three independent cohorts from the United States, Korea and Turkey, totaling 638 patients with PD and 319 healthy controls, and we conclude that gut microbiome alterations can identify both genetically and non-genetically at-risk individuals in the general population who may be progressing toward PD, thus serving as an early marker of disease development in the premanifest phase.}, } @article {pmid42010313, year = {2026}, author = {Qi, YL and Zou, DY and Hou, JJ and Zhang, ZF and Du, H and Feng, XY and Pan, YP and Zhang, CJ and Liu, Y and Li, M}, title = {A seven-year metagenomic genome catalogue of mangrove and mudflat sediments from the Futian Reserve, China.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {42010313}, issn = {2052-4463}, support = {42430707//National Natural Science Foundation of China/ ; 32370055//National Natural Science Foundation of China/ ; 32225003, 32393970, 92251306//National Natural Science Foundation of China/ ; JCYJ20230808105711023//General Program supported by Shenzhen Natural Science Foundation in Basic Research Fund/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; 2022B002//Shenzhen University 2035 Program for Excellent Research/ ; 2024T001//Shenzhen University Special Funding Initiative/ ; }, mesh = {China ; *Wetlands ; Archaea/genetics/classification ; *Geologic Sediments/microbiology ; *Metagenome ; Phylogeny ; Bacteria/genetics/classification ; Metagenomics ; }, abstract = {Mangrove wetlands are ecologically and biogeochemically important "blue-carbon" ecosystems, yet long-term genomic resources for their microbial communities remain scarce. Here we present a seven-year (2017-2023) metagenomic dataset from the Futian Mangrove National Nature Reserve, China, comprising 65 sediment samples collected from paired habitats (mangrove forest and adjacent mudflat) across multiple depths. Sequencing produced ~5.3 Tbp of data, from which 6,922 metagenome-assembled genomes (MAGs) were reconstructed and dereplicated into 3,404 representative genomes (336 Archaea and 3,068 Bacteria). Quality control ensured that all genomes achieved medium- or high-quality standards, with assembly statistics and read recruitment rates supporting robustness and representativeness. Taxonomic annotation revealed broad phylogenetic diversity spanning 13 archaeal and 69 bacterial phyla, with many lineages lacking formal nomenclature and representing potential novel taxa. All raw sequences, genome assemblies, and detailed metadata have been deposited in public repositories, providing a standardized, time-resolved resource for comparative genomics, microbial ecology, and ecosystem restoration studies in coastal wetlands.}, } @article {pmid42010457, year = {2026}, author = {Guo, J and Liang, C and Cairang, L and Si, L and Yan, J and Liu, D}, title = {Metagenomics reveals gut microbial differences and ecological adaptation in plateau zokor (Eospalax baileyi) populations.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42010457}, issn = {1471-2180}, support = {LHZX-2023-02//Sanjiangyuan National Park Joint Grant from the Chinese Academy of Sciences and the People's Government of Qinghai Province/ ; }, abstract = {UNLABELLED: Nine geographically distinct populations of plateau zokors (Eospalax baileyi) from Qinghai Province were selected for metagenomic analysis to investigate the composition of gut microbial communities among different populations. The results showed that the core gut microbiota of plateau zokors from different geographic populations was dominated by Firmicutes, Bacteroidetes, and Proteobacteria, with significant differences in community composition among populations. Alpha diversity analysis revealed marked variation in gut microbial diversity and richness across the different geographic populations. Functional prediction further demonstrated significant differences in multiple metabolic pathways, including carbohydrate metabolism, amino acid metabolism, replication and repair, and membrane transport. Notably, carbohydrate-active enzymes associated with the degradation of cellulose, hemicellulose, and lignin exhibited significant differences among populations. In addition, correlation analyses between environmental factors and the gut microbiota indicated that environmental variables such as altitude, annual precipitation, and isothermality had significant effects on gut microbial community structure. Regression analysis between genetic and geographic distances showed that genetic distance among plateau zokor populations increased with increasing geographic distance. Overall, these results suggest that geographic isolation and environmental heterogeneity may jointly drive the differentiation of gut microbial communities in plateau zokors. This study provides microbiological evidence and theoretical support for understanding the ecological adaptation of plateau zokors and offers a scientific basis for the integrated management of grassland rodent pests.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05069-6.}, } @article {pmid42010622, year = {2026}, author = {Goldstein, C and Lavy, I and Sun, T and Ennis, D and Shreffler, WG and Yuan, Q and Virkud, YV and Martin, VM and Yassour, M}, title = {Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {42010622}, issn = {1756-994X}, support = {1685-3680//Gerber Foundation/ ; 230465//Demarest Lloyd Jr Foundation/ ; 229711//the Food Allergy Science Initiative/ ; K23AI151555//National Institute of Allergy and Infectious Diseases of the US/ ; K23AI130408//Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity/ ; }, abstract = {BACKGROUND: The complex relationship between the gut microbiome and immune system development during infancy is considered a key factor in the rising rates of pediatric allergic diseases. Food protein-induced allergic proctocolitis (AP), the earliest identified form of non-IgE-mediated food allergy in infants, occurs at the mucosal surface where dietary proteins, intestinal microbes, and immune cells directly interact, and increases the risk for life threatening IgE-mediated food allergy, making it an important model for understanding early food allergic disease development. The question of how specific microbial compositions and functional pathways contribute to AP development and progression remains poorly understood. METHODS: We performed metagenomic sequencing on 740 longitudinal stool samples from 163 infants (84 with AP, 79 without AP) enrolled in the prospective GMAP cohort. Taxonomic profiling, functional pathway analysis, strain-level characterization, and machine learning-based classification were applied to identify microbial differences across disease stages. RESULTS: Here we show that infants with AP exhibit different microbial compositions, characterized by enrichment of Escherichia coli and Bifidobacterium bifidum during early life, including pre-symptomatic stages, while species like Bifidobacterium breve and Klebsiella species are more abundant in infants without AP. These findings suggest the presence of microbial signatures that may be detectable before clinical symptoms emerge, and demonstrate that strain-level differences within E. coli populations may represent AP-associated lineages with distinct gene content profiles that were not previously recognized. For example, biofilm formation and cell adhesion genes in E. coli were particularly enriched in AP-associated clades. Short chain fatty acid (SCFA) and other functional pathways were also associated with AP, including reduced SCFA production during the symptomatic phase, and then a potentially compensatory increased production following AP resolution. CONCLUSIONS: Our results provide the first comprehensive strain-level characterization of the gut microbiome in AP, and functional implications, and generate new hypotheses to be tested regarding candidate microbial features associated with AP for future biomarker discovery and/or intervention targets. This work advances our understanding of how specific microbial taxa and functional pathways may contribute to non-IgE-mediated food allergies and opens new avenues for microbiome-targeted therapeutic approaches as well as novel prevention targets for IgE-mediated food allergies.}, } @article {pmid42010710, year = {2026}, author = {Long, L and An, Y and Zhu, LT and Xu, XL and Lin, JJ and Xu, WJ and Chen, JY and Liu, FY and Liu, XY and Huang, Q}, title = {Unveiling microbial risks in Chinese household dust: a comprehensive analysis from absolute abundance to virulence unit.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42010710}, issn = {2049-2618}, support = {(42177362)//National Natural Science Foundation of China/ ; (2025J02030, 2025J01256)//Fujian Provincial Natural Science Foundation of China/ ; (NO. NBSDC-DB-21)//National Basic Science Data Center "Environment Health DataBase"/ ; }, mesh = {Child ; Humans ; Air Pollution, Indoor/analysis ; *Bacteria/genetics/classification/isolation & purification/pathogenicity ; China ; *Dust/analysis ; Family Characteristics ; *Fungi/genetics/isolation & purification/classification/pathogenicity ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: People spend the majority of their lives indoors, yet the risk and virulence potential of household microbiota remain largely unexplored, particularly in developing countries.

RESULTS: Here, we conducted a nationwide survey on both dust samples and health information across 118 Chinese households. The microbiota composition and its functional units were analyzed using absolute 16S rRNA/ITS sequencing, metagenomics, and metaproteomics. Cross-domain network analysis of the core microbial communities revealed robust co-occurrence patterns in household dust. The mean absolute abundance of potentially pathogenic bacteria and fungi in households was 2.39 × 10[5] and 2.83 × 10[6] DNA copies/g dust. The potentially pathogenic community was primarily influenced by latitude, relative humidity, and average temperature. Although total absolute abundance was substantially lower in urban areas, the relative abundance of potentially pathogenic bacteria was markedly higher compared to rural environments. While urban-rural differences existed, the underlying statistical drivers were the environmental variables. The absolute abundance of potential pathogens was significantly associated with the prevalence of rhinitis, wheeze, and dermatitis in 266 participants. Children were identified as the highest-risk group from inhalation exposure of average daily dose. A total of 170 bacterial, 223 fungal virulence factors (VFs), and 370 antibiotic resistance genes (ARGs) were detected in dust and dust extracellular vesicle (EV)-associated DNA. EV-associated cargoes contributed 47.13% to the bacterial VF profiles, 11.90% to fungal VF profiles, and 44.45% to ARG profiles. Metaproteomic analysis confirmed the presence of VF profiles in dust EVs, which was further verified by curated proteomics data from 35 household pathogens.

CONCLUSIONS: This study provides a comprehensive, quantitative framework linking indoor microbial exposure to health risks, highlighting EVs as a non-negligible, novel, extracellular mechanistic pathway for health impact in household environments. Video Abstract.}, } @article {pmid42010711, year = {2026}, author = {You, C and Zhang, W and Guan, Y and Liang, Q and Nong, C and Yang, T and Li, M and Banerjee, S and Zhou, X and Wang, X and Xu, Y and Shen, Q and Wei, Z}, title = {Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42010711}, issn = {2049-2618}, support = {2022YFC3501501//National Key Research and Development Program of China/ ; KJYQ2025034, KJYQ2024039//Fundamental Research Funds for the Central Universities/ ; BK20240194//the Natural Science Foundation of Jiangsu Province/ ; }, mesh = {*Rhizosphere ; *Plant Roots/microbiology ; Streptomyces/genetics/metabolism/isolation & purification ; *Metabolome ; Soil Microbiology ; Fusarium/isolation & purification ; *Microbiota ; *Plants, Medicinal/microbiology ; *Angelica sinensis/microbiology/metabolism ; *Plant Diseases/microbiology ; Metagenomics/methods ; }, abstract = {BACKGROUND: The rhizosphere-associated microbiota plays a crucial role in plant responses to disease stress. Plant secondary metabolites are recognized as crucial mediators in the assembly of rhizosphere microbial communities, particularly by enhancing the colonization of beneficial microorganisms. Despite this recognized importance, a deeper understanding of how such metabolome-driven microbiome assembly specifically determines plant resistance against soil-borne diseases is still lacking.

RESULTS: Here, we focused on the widely planted medicinal plant Angelica sinensis and demonstrated that root rot-diseased rhizosphere soils (DRS) exhibited a higher relative abundance of Fusarium and a lower relative abundance of Streptomyces compared to healthy rhizosphere soils (HRS). Shotgun metagenomic sequencing revealed that metabolism-associated genes, particularly those related to steroid degradation, are significantly enriched in HRS samples. Subsequent genome and functional gene analysis of Streptomyces revealed that the steroid degradation-related genes are associated with rhizosphere colonization in hosts. Rhizosphere Streptomyces S15 directly antagonized Fusarium and enhanced the root resistance of A. sinensis. Comparative metabolomics showed that A. sinensis plants from HRS secreted more lipid and lipid-like molecules than those from DRS, especially sterol lipids and long-chain fatty acids, which promoted the growth of Streptomyces S15 isolates. Transcriptome analysis validated that the lipid hormones are essential for sporulation, biofilm formation, and streptomycin biosynthesis of S15 strain. Finally, exogenous application of synbiotics (lipid prebiotics and S15) to A. sinensis resulted in the enrichment of S15-homologous Streptomyces amplicon sequence variant (ASV), further establishing beneficial bacterial communities in Fusarium-stressed rhizospheres.

CONCLUSIONS: Our study proposes that A. sinensis recruits steroid-metabolizing Streptomyces species by exuding key lipid compounds (i.e., methyl jasmonate and brassinolide) to combat Fusarium root rot. This study provides novel insights into using functional synbiotics as a promising strategy for manipulating plant-microbiome interactions to promote sustainable agriculture. Video Abstract.}, } @article {pmid42010713, year = {2026}, author = {Tang, J and Wang, L and Yang, Z and Song, Y and Wu, S and Liang, Q and Li, Z and Zhou, S and Xiong, H and Chen, D and Li, J and Li, F}, title = {Gut microbiota induces dysspermatogenesis via microbial-derived phenylacetylglycine in Ggt1-deficient mice.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42010713}, issn = {2049-2618}, support = {32272874//National Natural Science Foundation of China/ ; 2021YFF1000601//National Key R&D Program of China/ ; 2662025DKPY008//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; Male ; Mice ; STAT5 Transcription Factor/metabolism ; *Gastrointestinal Microbiome/physiology ; Mice, Knockout ; *Spermatogenesis ; *gamma-Glutamyltransferase/genetics/deficiency/metabolism ; *Infertility, Male/microbiology/metabolism ; *Dysbiosis/microbiology ; STAT3 Transcription Factor/metabolism ; Fecal Microbiota Transplantation ; Testis/metabolism ; Signal Transduction ; *Glycine/analogs & derivatives/metabolism ; Phenylacetates/metabolism ; Suppressor of Cytokine Signaling 3 Protein ; }, abstract = {BACKGROUND: Male infertility represents a global health concern, with emerging evidence linking gut microbiota dysbiosis to dysspermatogenesis and subfertility. However, the molecular mediators and regulatory mechanisms by which gut microbiota influences testicular functions remain poorly defined.

RESULTS: This study demonstrates that male gamma-glutamyl transferase 1-deletion (Ggt1[-/-]) mice exhibits infertility phenotypes, including reduced germ and testicular Leydig cell numbers, increased rates of abnormal sperm, and altered reproductive hormone levels. Metabolomic analysis reveals elevated levels of the gut microbial-derived metabolite phenylacetylglycine (PAGly) in serum and testes of Ggt1[-/-] mice, with in vivo injection experiments indicating its role in impairing spermatogenesis. Moreover, blocking PAGly effectively restores the impaired spermatogenesis in Ggt1[-/-] mice. Fecal metagenomic and metabolomic analyses show that gut microbiota in Ggt1[-/-] mice induces elevation of phenylacetic acid, a precursor metabolite of PAGly. Strikingly, fecal microbiota transplantation from Ggt1[-/-] mice (Ggt1[-/-]-FMT) recapitulates the infertility phenotypes including reduced germ cells and increased rates of abnormal sperm. Mechanistically, integrated CUT&Tag and ATAC-Seq analyses reveal that transcription factor STAT5B occupies regulatory elements near Klk1b transcription start sites (TSS), confirming that transcription factor STAT5B directly regulates Klk1b gene transcription. Concretely, PAGly activates β2-adrenergic receptor (β2AR) on Leydig cells, triggering STAT3 phosphorylation, subsequent SOCS3 upregulation, and STAT5B phosphorylation suppression; p-STAT5B with transcriptional activation function is reduced, then Klk1b gene transcription is compromised, and therefore spermatogenesis is disrupted.

CONCLUSION: Ggt1 deletion-induced gut microbiota dysbiosis disrupts spermatogenesis via β2AR-STAT3-SOCS3-STAT5B-Klk1bs signaling pathway. Specifically, PAGly-induced β2AR activation promotes STAT3 phosphorylation, which induces SOCS3 to suppress p-STAT5B dependent Klk1bs transcription. This mechanism underscores the critical role of gut-derived metabolites in regulating testicular function and identifies potential targets for microbiota-modulated male infertility. Video Abstract.}, } @article {pmid42010746, year = {2026}, author = {Yun, CS and Kim, JK and Kwon, H and Her, M and Moon, JS}, title = {Metagenomic 16S rRNA amplicon and shotgun sequencing in investigation of granulomatous lesions in layer chickens: a case report.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42010746}, issn = {2524-4671}, abstract = {BACKGROUND: Granuloma lesions in poultry are a frequent pathological finding, representing a chronic inflammatory response to persistent infectious agents, most commonly bacteria or fungi. Accurate differentiation of the underlying cause requires additional diagnostic tests, such as acid-fast staining, fungal culture, or bacterial isolation and genetic identification. However, the pathogens often remain undetermined when conventional detection methods fail. The present case aimed to investigated granulomatous disease in multiple organs of layer chickens by applying metagenomic 16S rRNA amplicon and metagenomic shotgun sequencing. CASE PRESENTATION: A total of 35 deaths occurred in a flock of layer chickens, accompanied by a decrease in daily feed intake from 144 g to 104 g. Six carcasses from 38-weeks-old layer chickens were submitted for disease diagnosis. During necropsy, granuloma/neoplastic lesions were observed in the liver, ovary, proventriculus, pancreas and kidney. Histopathological examination revealed compartmentalized infiltration of lymphocytes and multinucleated giant cells in liver, ovary, proventriculus, pancreas and renal parenchyma. While Escherichia coli was isolated from the oviduct, no viral agents (IBV, CIAV, MDV, ALV, REV, or HEV) were detected by RT-PCR. Notably, some of the initial metagenomic shotgun results were recognized as different taxa due to the misclassification of certain reads. Following a re-analysis of these shotgun reads against the nucleotide database, both metagenomic 16S rRNA amplicon and metagenomic shotgun sequencing identified E. coli as the dominant species in liver samples. CONCLUSION: The present case indicates that E. coli may contribute to granuloma lesions in layer chickens. While 16S rRNA amplicon sequencing provided more reliable bacterial identification for diagnostic purposes, metagenomic shotgun sequencing offers complementary insight by detecting broader microbial communities. Therefore, integrating both approaches alongside conventional diagnosis may improve the accuracy of diagnosis for granulomatous diseases in poultry.}, } @article {pmid42010766, year = {2026}, author = {Combs, D and Landeros, K and Garza, K and Azari, H and Abdelrahman, M and Albracht-Schulte, K}, title = {Exercise intensity as a modulator of gut microbiota and host metabolic health in obesity.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2661415}, pmid = {42010766}, issn = {1949-0984}, mesh = {Humans ; *Obesity/metabolism/microbiology/therapy ; Animals ; *Gastrointestinal Microbiome/physiology ; *Exercise/physiology ; Fatty Acids, Volatile/metabolism ; Bacteria/classification/metabolism/genetics/isolation & purification ; }, abstract = {The gut microbiome is shaped by complex interactions among host, environmental, and lifestyle factors, with exercise emerging as a reported modulator. Growing evidence suggests that exercise intensity, ranging from low to high, can differentially influence gut microbial composition, diversity, and functional outputs relevant to metabolic health. This narrative review synthesizes current findings examining intensity-dependent microbial adaptations in the context of obesity. Across animal models (n = 17) and limited human studies (n = 5), moderate-intensity training (MIT) and high-intensity interval training (HIIT) produce the most consistent microbiota shifts, while low-intensity training (LIT) exerts minimal effects. Reported taxa associated with beneficial outcomes consistent across animal and human investigations include Akkermansia (G), and Christensenellaceae (F). Mechanistically, intensity-dependent alterations in microbial communities may influence obesity-related pathways through modulation of short-chain fatty acid (SCFA) and bile acid metabolism, gut barrier integrity, endotoxemia, and inflammatory signaling. HIIT and MIT are linked to improved expression of tight junction proteins (ZO-1, Claudin, Occludin), reducing circulating lipopolysaccharide (LPS), and increasing SCFA-producing taxa; thus, supporting a role for the gut microbiome in mediating exercise-induced metabolic benefits. However, inconsistent findings between species, interindividual variability, and considerable heterogeneity in exercise intervention duration across both animal (4-16 weeks) and human (3-12 weeks) studies, as well as limited longitudinal human studies, underscore the need for deeper mechanistic investigations. Future research should employ metagenomic and metatranscriptomic profiling, integrate sex- and diet-stratified longitudinal designs, and clarify causal links between exercise-responsive taxa, microbial metabolites, and host physiology. Collectively, these data highlight exercise intensity as a key determinant of gut microbiome dynamics and reinforce the need for integrative, translational approaches to define its therapeutic potential for obesity and metabolic disorders.}, } @article {pmid42010993, year = {2026}, author = {Wu, Y and Guo, X and Wang, X and Guo, F}, title = {Fatal Non-Hepatic Hyperammonemia Post-Glofitamab: Ureaplasma and Genetic Susceptibility: A Case Report.}, journal = {Immunity, inflammation and disease}, volume = {14}, number = {4}, pages = {e70443}, pmid = {42010993}, issn = {2050-4527}, mesh = {Humans ; Male ; Middle Aged ; *Hyperammonemia/etiology/chemically induced/diagnosis/genetics ; Fatal Outcome ; Genetic Predisposition to Disease ; *Ureaplasma Infections ; *Lymphoma, Large B-Cell, Diffuse/drug therapy ; *Antineoplastic Agents, Immunological/adverse effects ; }, abstract = {BACKGROUND: Although primarily reported in solid organ transplant recipients and patients undergoing chimeric antigen receptor T-cell immunotherapy (CAR-T), non-hepatic hyperammonemia (NHHA) is a rare but lethal complication in the broader context of post- chemo-immunotherapy hematologic malignancies. It often presents with unexplained encephalopathy that mimics primary central nervous system (CNS) progression, leading to diagnostic delays. With the expanding use of bispecific antibodies (e.g., glofitamab), the etiology of NHHA, particularly the complex interplay between opportunistic infections and potential metabolic susceptibility, remains poorly understood.

CASE PRESENTATION: We report a fatal case of NHHA in a 58-year-old male with diffuse large B-cell lymphoma (DLBCL) following glofitamab-based chemo-immunotherapy. The patient developed sudden onset altered mental status with extreme hyperammonemia (peak blood ammonia 638.9 µmol/L) despite preserved liver function. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified Ureaplasma urealyticum. Furthermore, post-mortem whole-exome sequencing (WES) identified a heterozygous variant of SLC25A13 (NM_014251.3:c.2 T > C). As biochemical confirmation of citrin deficiency was not available, the clinical significance of this variant remains uncertain, though it may represent a contributory metabolic susceptibility factor. Despite aggressive ammonia-lowering strategies, including continuous renal replacement therapy (CRRT) and targeted antibiotics, the patient succumbed to fulminant cerebral edema.

CONCLUSION: This case highlights the Ureaplasma urealyticum infection as a critical precipitant of fatal NHHA following glofitamab therapy, occurring in the background of possible genetic metabolic susceptibility (an unverified heterozygous SLC25A13 variant of uncertain functional significance). These findings underscore the critical need for early blood ammonia monitoring and rapid mNGS screening in immunocompromised patients with unexplained encephalopathy. We propose a structured diagnostic algorithm to expedite the recognition and management of this reversible yet life-threatening condition.}, } @article {pmid42011017, year = {2026}, author = {Sadia, H and Amin, A and Ahmed, I}, title = {Metagenomic and Phenotypic Insights Into Biofilm-Forming Pathogens in Patients With Nosocomial Sepsis.}, journal = {BioMed research international}, volume = {2026}, number = {1}, pages = {e8989667}, pmid = {42011017}, issn = {2314-6141}, mesh = {*Biofilms/growth & development ; Humans ; *Metagenomics ; *Sepsis/microbiology/genetics ; *Cross Infection/microbiology/genetics ; RNA, Ribosomal, 16S/genetics ; Phenotype ; *Bacteria/genetics/pathogenicity/classification ; }, abstract = {Biofilm-related infections significantly contribute to bacterial diseases, with estimates suggesting that at least 80% of such infections are associated with biofilms. These infections often involve opportunistic pathogens, which not only influence the type of infection but also impact the microenvironment by interacting with other polymicrobial pathogens, thereby altering microbial diversity within the infection site. The present study was designed to assess potential changes in bacterial communities across various infection types. The 50 samples were collected and pooled from different anatomical locations: II-H1 (calf), ul-H2 (thighs), ft-H3 (upper leg), ct-H4 (chest), and Ca-H5 (catheter). The 16S rDNA sequencing was performed on 10 representative samples using the Sanger method to identify bacterial taxa, whereas the metagenomic analysis was conducted on the Illumina MiSeq platform (Illumina, Inc., San Diego, California). Sanger sequencing identifying several bacterial strains including Bacterium MS-AsIII-61, Bacterium HB33-1, Mammaliicoccus sciuri SSB38, multiple Staphylococcus species (S. aureus DA101 and S8, Staphylococcus sp. C0021-01R and TSA25S, S. cohnii FC2265, and S. saprophyticus A), and Enterobacter hormaechei D15. The metagenomics analysis revealed variations and diversity in the different location across the organ by relative abundance of 5 bacterial phyla and 38 species. The Proteobacteria phylum was the most abundant phylum across all sites, with the highest prevalence observed in Ca-H5, followed by ul-H2, ct-H4, II-H1, and ft-H3 in the decreasing order. In contrast, the Bacteroidetes phylum exhibited the highest abundance in ft-H3. Catheter-associated infections (Ca-H5 site) show a homogeneous ARG profile, dominated by genes supporting biofilm formation and persistence. MSA samples reflect diversity in methicillin and multidrug resistance genes, consistent with surgical-site and opportunistic infections. Trypto samples may represent an environmental or experimental condition leading to alternative ARG expression, highlighting site- or condition-specific variations. The different virulence factor responsible for the boost in the establishment of biofilms in these pathogens includes, surface adhesion proteins, increasing resilience to environmental, efflux pumps, quorum-sensing regulators, stresses, and antibiotic treatments. The study demonstrates the dynamic nature and impact of biofilm-related infections at anatomical sites. It also focused on biofilm-associated infections at surgical sites, their progression into chronic conditions, and the corresponding treatment patterns. The integration of metagenomic analysis with phenotypic studies provided deeper insights into the roles of key genes and their mechanisms in biofilm formation.}, } @article {pmid42011181, year = {2026}, author = {Li, Z and Zhang, Y and Xu, H and Wang, D and Yuan, L and Su, N and Lu, H and Li, W}, title = {Prosthetic Joint Infection Caused by Staphylococcus argenteus: mNGS-Guided Diagnosis and Whole-Genome Characterization of an ST2250 Strain.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {594406}, pmid = {42011181}, issn = {1178-6973}, abstract = {BACKGROUND: Staphylococcus argenteus, a member of the Staphylococcus aureus complex, has increasingly been recognized as a human pathogen but is frequently misidentified as S. aureus in routine clinical laboratories. Reports of prosthetic joint infection (PJI) caused by this species remain rare.

METHODS: We describe a case of delayed-onset PJI in a 71-year-old woman following total knee arthroplasty. Repeated conventional cultures were negative after empirical vancomycin therapy. Metagenomic next-generation sequencing (mNGS) of wound exudate detected S. argenteus, which guided extended culture and subsequent isolation of low-abundance colonies. Species identification was confirmed by whole-genome sequencing (WGS), multilocus sequence typing (MLST), and reinterpretation of MALDI-TOF MS results. Antimicrobial susceptibility testing (AST) was performed and compared with WGS-based resistance prediction. Phylogenetic analysis was conducted using 452 publicly available S. argenteus genomes.

AIM: This study aimed to describe the clinical diagnosis, microbiological identification, and genomic characterization of a Staphylococcus argenteus strain causing prosthetic joint infection.

RESULTS: The isolate was identified as sequence type ST2250 and lacked the staphyloxanthin operon, consistent with the non-pigmented phenotype. WGS and phenotypic AST showed 100% concordance across 11 clinically relevant antibiotics. Phylogenomic analysis revealed that the strain clustered closely with Southeast Asian lineages. Following targeted therapy with intravenous vancomycin and surgical wound management, the patient showed rapid clinical improvement with resolution of local inflammation and complete wound healing.

CONCLUSION: This is the first confirmed case of S. argenteus PJI in Suzhou, China. The case highlights the diagnostic value of mNGS in culture-negative PJI, the importance of molecular tools for correctly differentiating S. argenteus from S. aureus, and the potential of WGS to support resistance prediction for rare staphylococcal pathogens.}, } @article {pmid42011762, year = {2026}, author = {Lu, J and Wang, HN and Wang, CM and Xu, J and Ikechukwu, CK and Li, W and Ning, SY and Wu, P and Liu, YW and Shen, Q and Ji, LK and Wang, XC and Yang, SX and Zhou, CL and Wang, XL and Zhang, W and Shan, TL}, title = {Comparison of gut viromes across captive mammals reveals extensive genetic diversity in bacteriophage dark matter and mammalian viruses.}, journal = {Zoological research}, volume = {47}, number = {2}, pages = {606-620}, doi = {10.24272/j.issn.2095-8137.2025.134}, pmid = {42011762}, issn = {2095-8137}, mesh = {Animals ; *Genetic Variation ; *Virome ; *Bacteriophages/genetics/classification ; *Mammals/virology ; *Animals, Zoo/virology ; Phylogeny ; *Viruses/genetics/classification ; }, abstract = {Comprehensive characterization of mammalian gut viromes is essential for early detection of commensal and potentially zoonotic viruses and for reducing the risk of cross-species transmission. Viral metagenomics was applied to profile gut viral communities from zoo mammals maintained across multiple zoological institutions in China. Viral communities differed markedly among host dietary guilds, with herbivores exhibiting the highest viral species diversity. In total, 1 027 viral sequences representing five major viral groups were recovered, including multiple mammal-associated astroviruses, picornaviruses, and parvoviruses with potential infectivity. Phylogenetic reconstruction based on viral hallmark genes demonstrated extensive genomic diversification across recovered lineages. Hosts for most microviruses were predicted to belong to the bacterial family Bacteroidaceae. In addition, 10 previously unreported crAss-like phages were identified in mammalian samples and showed close evolutionary relationships with proposed crAssphages from the human gut virome. Antibiotic resistance genes identified in the mammalian gut viromes primarily belonged to tetracyclines. These findings substantially expand current understanding of viral community structure in captive animals in China and provide a foundation for proactive surveillance frameworks targeting emerging mammalian viruses with zoonotic potential.}, } @article {pmid42011768, year = {2026}, author = {Oba, S and Okuno, K and Watanabe, S and Yamamoto, Y and Takaoka, A and Hanaoka, M and Yamauchi, S and Kagawa, H and Tokunaga, M and Ban, D and Kinugasa, Y}, title = {Intratumoral fungal burden of Candida tropicalis as a novel prognostic biomarker for recurrence and mortality in colorectal cancer.}, journal = {Cancer}, volume = {132}, number = {8}, pages = {e70408}, pmid = {42011768}, issn = {1097-0142}, support = {JP23K19499//Japan Society for the Promotion of Science/ ; JP24K18571//Japan Society for the Promotion of Science/ ; 2023DI008//Kobayashi Foundation for Cancer Research/ ; }, mesh = {Humans ; *Candida tropicalis/isolation & purification/genetics ; *Colorectal Neoplasms/microbiology/mortality/pathology ; Prognosis ; *Neoplasm Recurrence, Local/microbiology/pathology ; Male ; Female ; Middle Aged ; Aged ; Biomarkers, Tumor ; }, abstract = {BACKGROUND: The crucial role of gut fungus dysbiosis in the carcinogenesis and progression of colorectal cancer (CRC) has recently garnered increasing attention. In this study, the potential role of Candida tropicalis, commensal gut fungi, in predicting CRC prognosis was investigated.

METHODS: A total of 304 frozen surgical cancer tissue specimens were obtained from patients with CRC and evaluated the intratumoral C. tropicalis burden using quantitative polymerase chain reaction assays. Mycobial composition and diversity analyses were performed by analyzing publicly available metagenomic datasets.

RESULTS: Metagenomic dataset analysis revealed significant differences in fungal composition and diversity of Candida species among adjacent normal and CRC tissues. The 5-year recurrence-free survival and disease-specific survival rates were significantly worse in patients with a high intratumoral C. tropicalis burden than in those with a low burden (78.0% vs. 86.6%; p = .03 and 88.9% vs. 98.0%; p < .01, respectively). Furthermore, multivariate Cox regression analysis revealed that increased intratumoral C. tropicalis burden was a significant independent predictor for recurrence-free survival (hazard ratio [HR]: 1.92; 95% CI, 1.08-3.44; p = .03) and disease-specific survival (HR: 4.29; 95% CI, 1.36-13.5; p = .03).

CONCLUSIONS: These results have demonstrated, possibly for the first time, the potential of intratumoral C. tropicalis burden as a novel prognostic biomarker for recurrence and mortality in patients with CRC.}, } @article {pmid42012066, year = {2026}, author = {Guo, R and Gao, J and Zhang, C and Chang, Z and Sun, Y}, title = {Multi-Omics Analysis Reveals Coordinated Adaptations in Genes, Metabolism, and Gut Microbiota Underpinning Herbivory in Lordiphosa Flies.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.70110}, pmid = {42012066}, issn = {1749-4877}, support = {202401BC070011//Yunnan Fundamental Research Projects/ ; 32060112//Natural Science Foundation of China/ ; }, abstract = {Herbivorous insects are among the most ecologically successful animal groups. However, the adaptive mechanisms that allow them to exploit plant hosts, which are often nutrient-poor (low in simple sugars, high in structural carbohydrates) and defended by toxic secondary metabolites, are not fully resolved. Here, we investigated the evolutionary basis of herbivory in Lordiphosa clarofinis, a drosophilid species feeding on living plant tissues, using multi-omics approaches. Behavioral experiments revealed a strong oviposition preference for Galinsoga parviflora (a host rich in secondary metabolites), accompanied by elevated expression of chemosensory genes linked to host discrimination. Comparative genomic analyses revealed lineage-specific expansions of gene families associated with detoxification (e.g., cytochrome P450s) and carbohydrate metabolism, alongside positive selection on genes involved in fatty acid utilization and glycogen synthesis. Transcriptomic data showed differential expression of energy metabolism pathways in response to low-sugar plant diets, with upregulation of genes linked to lipid oxidation and gluconeogenesis. Metagenomic profiling of gut microbiota identified key taxa (e.g., Bacteroidetes) capable of degrading plant polysaccharides and synthesizing essential vitamins, potentially complementing host nutritional intake. Our results demonstrate that herbivory in L. clarofinis is associated with coordinated genomic, transcriptional, and microbial changes, rather than being attributable to a single adaptive mechanism. This study highlights how multi-level biological features covary with plant-based feeding and provides a framework for investigating the complex evolutionary and ecological correlates of herbivory in insects.}, } @article {pmid42012165, year = {2026}, author = {Werner, A and Chibani, CM and Schmitz, RA}, title = {Navigating prokaryotic viral genome analysis from metagenomic data.}, journal = {mSystems}, volume = {11}, number = {5}, pages = {e0124925}, pmid = {42012165}, issn = {2379-5077}, support = {031B0851B//Bundesministerium für Bildung und Forschung/ ; SCHM1052/26-1, SCHM1052/26-2//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Metagenomics/methods ; *Genome, Viral ; Archaea/virology ; *Archaeal Viruses/genetics ; Bacteria/virology ; Computational Biology/methods ; *DNA Viruses/genetics ; }, abstract = {Viruses play crucial roles in microbial ecosystems, yet viromic analysis remains challenging due to the field's complexity and rapid evolution. This minireview supports non-specialists through the evolving landscape of viromics, focusing on the analysis of bacterial and archaeal DNA viruses from metagenomic data. We address major challenges, including viral diversity, methodological biases, and the overwhelming array of available tools and pipelines. While describing a typical viromic workflow, we provide users with background information for each of the steps from data acquisition, preprocessing, and quality control to viral characterization and common downstream analyses. The included references and resources will provide users with the information needed to confidently start their own virome analysis.}, } @article {pmid42012213, year = {2026}, author = {Couto-Rodriguez, M and Danko, DC and Wells, HL and Rey, S and Jirau Serrano, X and Fidler, G and Papciak, J and Combs, PF and Plourde, A and Augenbraun, M and Mason, CE and Otto, C and O'Hara, NB and Nagy-Szakal, D}, title = {Analytical validation of a highly accurate and reliable next-generation sequencing-based urine assay.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0202625}, pmid = {42012213}, issn = {2165-0497}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Urinary Tract Infections/microbiology/diagnosis/urine ; *Bacteria/genetics/isolation & purification/classification ; Sensitivity and Specificity ; Metagenomics/methods ; *Urine/microbiology ; }, abstract = {Urinary tract infections (UTIs) are diagnosed based on symptoms and confirmed by urine culture, despite its limitations in sensitivity. False-negative cultures can lead to inappropriate antimicrobial use or urosepsis in high-risk patients. Next-generation sequencing (NGS)-based metagenomics offers a comprehensive and precise alternative but is rarely applied clinically. We developed and validated BIOTIA-ID, a clinical-grade NGS-based diagnostic pipeline for pathogen detection in urine. Remnant clinical and spiked urine samples underwent extraction, metagenomic library preparation, and Illumina NextSeq 550 sequencing. We trained and applied a bioinformatic pipeline that uses machine learning to identify pathogens and resistance markers. BIOTIA-DX was intentionally designed and trained to increase stringency and reduce false positive detection of urogenital commensals or opportunistic microbes present at colonization levels. Internal controls ensured standardized, high-stringency results. The assay was validated on 1,470 urine specimens evaluating over 14.5k analytes. The clinical validation achieved a 97.2% sensitivity and 99.6% specificity with a limit of detection (LoD) of <15,000 CFU/mL for most bacterial species and <5,000 CFU/mL for fungal species. Discordant results were reconciled by target-specific qPCR or 16S Sanger sequencing, and 87% of the NGS results were concordant with the comparator. A subset of 332 clinical specimens was tested and validated for antimicrobial resistance (AMR). sul and blaSHV genes were commonly associated with Escherichia coli and Klebsiella pneumoniae, while cfxA was found in Prevotella and Pseudomonas spp. detected by BIOTIA-ID. Overall, these data demonstrate that BIOTIA-ID is a comprehensive, highly accurate end-to-end diagnostic assay with notable advantages over current culture-based diagnostics.IMPORTANCEUrinary tract infections (UTIs) are among the most common infections, yet current diagnostic methods, including urine culture, often fail to detect pathogens accurately, leading to delayed treatment and inappropriate antimicrobial use. Clinical metagenomics offers a powerful alternative, especially in complicated cases. BIOTIA-ID is a validated, clinical-grade next-generation sequencing (NGS)-based assay that provides highly accurate pathogen identification and antimicrobial resistance profiling. By incorporating machine learning and stringent quality controls, BIOTIA-ID minimizes false positives and enhances diagnostic precision. Our study demonstrates its superior performance over culture, with potential to improve UTI diagnostics, guide targeted therapy, and support antimicrobial stewardship. The implementation of urine metagenomic diagnostics could support recurrent and complicated UTI patient management, providing a more reliable alternative to traditional methods.}, } @article {pmid42012671, year = {2026}, author = {Noronha, JM and Hudson, SB and Sharma, G and Ghadi, SC}, title = {Correction to: Metagenomic Insights into Viral Diversity from an Underexplored Khazan Creek and a Tropical Freshwater Lake.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, doi = {10.1007/s00284-026-04870-w}, pmid = {42012671}, issn = {1432-0991}, } @article {pmid42012700, year = {2026}, author = {Chen, J and Xi, M and Hu, W and He, R and Zhang, W and Zhang, Y and Chen, X and Chen, J}, title = {Adult Onset of MSMD Caused by IL-12Rβ1 Variants: Report of a Young Woman with NTM Infection Lacking Bacille Calmette-Guérin (BCG)-induced Diseases.}, journal = {Journal of clinical immunology}, volume = {46}, number = {1}, pages = {}, pmid = {42012700}, issn = {1573-2592}, support = {23141901900//the Shanghai Science and Technology Innovation Action Plan，experimental animal research project/ ; 23PJD073//the Shanghai Pujiang Program/ ; ynms202306//Basic Research Project of the Sixth People's Hospital of Shanghai/ ; }, abstract = {Mendelian susceptibility to mycobacterial disease (MSMD) is characterized by increased susceptibility to infections caused by weakly virulent mycobacteria (such as nontuberculous mycobacteria (NTM) or the Bacillus Calmette–Guérin (BCG) vaccine) in otherwise healthy individuals. In this study, we described a 29-year-old patient with MSMD due to NTM infection identified using metagenomic next-generation sequencing (mNGS) testing. The patient showed a poor response to standard antimycobacterial treatment. Therefore, we performed whole-exome sequencing (WES) and identified three heterozygous variants in IL-12Rβ1 (Ala131Thr, Arg323* and Arg561*). The two deleterious IL-12RB1 variants, Arg323* and Arg561*,were shown to be in trans (paternal and maternal, respectively). Further investigation revealed that two of these variants (Arg323* and Arg561*) could affect the binding between IL-12Rβ1 and IL-12Rβ2, leading to a weakened response of CD4+ T cells to stimulation with IL-12 plus tuberculosis antigen (TbAg), with reduced expression levels of IFN-γ and its downstream target p-STAT4. However, these variants did not affect the CD4+ T-cell response to glucan stimulation, as the three heterozygous variant loci do not interfere with the aggregation of IL-12Rβ1 and IL-23R. This autosomal recessive, partial IL-12Rβ1 deficiency ultimately resulted in the patient developing disseminated NTM infection. In clinical treatment, we combined IFN-γ with standard antimycobacterial therapy. The patient showed only a partial response to therapy. Therefore, as detection techniques continue to advance, it is important for clinicians to increase their understanding of MSMD to enable faster and more accurate diagnosis and treatment.}, } @article {pmid42012708, year = {2026}, author = {Kværner, AS and Birkeland, E and Avershina, E and Botteri, E and Bucher-Johannessen, C and Knudsen, MD and Hjartåker, A and Page, CM and Hov, JR and Song, M and Randel, KR and Hoff, G and Rounge, TB and Berstad, P}, title = {Alcohol consumption and colorectal carcinogenesis: an exploration of the gut microbial pathway as a potential mediator.}, journal = {European journal of nutrition}, volume = {65}, number = {4}, pages = {}, pmid = {42012708}, issn = {1436-6215}, abstract = {BACKGROUND: Alcohol consumption is one of the major risk factors of colorectal cancer (CRC), yet the mechanisms underlying this relationship, particularly the role of gut microbes, are not fully understood.

OBJECTIVE: To study associations of alcohol intake with the gut microbiome and colorectal lesions among CRC screening participants. Of particular interest was the potential role of gut microbes in mediating the association between alcohol intake and colorectal lesions.

METHODS: Screening participants with a positive faecal immunochemical test at ages 55–77 were eligible for the CRCbiome study. Alcohol intake was assessed using a validated, semi-quantitative food frequency questionnaire and linked with shotgun metagenome based gut microbial profiles to study associations with screen-detected colorectal lesions. The potential role of alcohol-associated gut microbes in mediating the association between alcohol intake and colorectal lesions was examined using causal mediation analysis.

RESULTS: Of 1468 participants with dietary data, 414 were diagnosed with advanced lesions. Alcohol intake was positively associated with advanced lesions in a dose-dependent manner (ptrend = 0.008), with odds ratio of 1.09 (95% confidence interval, 1.00, 1.19) per 10 g/day increase. Compared to non-consumers, those consuming alcohol were characterized by a distinct microbial profile, manifested as modest, but consistent, shifts in α- and β-diversity, and differentially abundant bacteria. A causal mediation analysis showed that 12% of the association between alcohol intake and advanced lesions was mediated by alcohol-associated gut bacteria.

CONCLUSION: Alcohol consumption was associated with a distinct microbial profile, which partly explained the association between alcohol intake and advanced colorectal lesions. Trial registration: The BCSN is registered at clinicaltrials.gov (National clinical trial (NCT) no. 01538550).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00394-026-03960-6.}, } @article {pmid42012901, year = {2026}, author = {Bellanco, A and Yépez-Notario, C and Lozano, M and Martínez-Cuesta, MC and Requena, T}, title = {Human Gut Microbiome Can Degrade the Sweetener Acesulfame K with Potential Damaging Effects in the Intestinal Barrier Function.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {17}, pages = {13990-13997}, pmid = {42012901}, issn = {1520-5118}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Sweetening Agents/metabolism ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Thiazines/metabolism ; Intestinal Barrier Function ; Caco-2 Cells ; Butyrates/metabolism ; Child ; }, abstract = {Acesulfame K (Ace-K) is a commonly consumed sweetener, although knowledge about the Ace-K-gut microbiota interaction remains limited. This study evaluates dose-dependent effects of Ace-K on metataxonomics, metagenomics, and metabolic activity of children gut microbiota developed in a dynamic gut simulator. An Ace-K-dose dependent increase in Anaerostipes, Coprococcus, Subdoligranulum, Blautia, Sutterella wadsworthensis, Alistipes, and Bacteroides thetaiotaomicron was observed. Butyrate showed a dose-response increase that correlated with Ace-K consumption, suggesting its microbial metabolism. Increasing bacterial taxa showed sulfatase and amidase activities potentially capable of degrading Ace-K, releasing sulfamate and acetoacetate, which species such as Anaerostipes hadrus and Intestinimonas can metabolize to produce butyrate via the butanoyl-CoA pathway. Furthermore, the Ace-K-microbiome interaction led to a dose-dependent decrease in Caco-2 epithelial integrity, possibly due to the release of sulfated metabolites. This study provides evidence of the potential risk of Ace-K consumption based on its metabolism by the human gut microbiome.}, } @article {pmid42013836, year = {2026}, author = {Steinberg, R and Pust, MM and Arias-Rojas, A and Pishchany, G and Ramsey, KA and Kieninger, E and Moeller, A and Casaulta, C and Hilty, M and Latzin, P and , and , and Korten, I and Xavier, RJ}, title = {An infant nasal microbial gene atlas uncovers intervention-driven microbiome shifts and salt-resistant pathogen expansion.}, journal = {Cell host & microbe}, volume = {34}, number = {5}, pages = {925-941.e6}, doi = {10.1016/j.chom.2026.03.019}, pmid = {42013836}, issn = {1934-6069}, mesh = {Humans ; *Microbiota/genetics/drug effects ; Infant ; Haemophilus influenzae/genetics/growth & development/drug effects ; *Cystic Fibrosis/microbiology/therapy ; Metagenomics ; *Nose/microbiology ; Metagenome ; Bacteria/genetics/classification/isolation & purification ; Saline Solution, Hypertonic/pharmacology ; }, abstract = {Functional studies of how early-life interventions shape the airway microbiome remain scarce. Here, we performed metagenomic sequencing of 704 longitudinal nasal swabs from infants with and without cystic fibrosis (CF) to construct and characterize a non-redundant gene atlas of the infant nasal microbiome. We aimed to determine how the nasal microbiome is perturbed by early therapies, as CF is commonly treated with inhaled hypertonic saline to improve mucociliary clearance. We found functional and compositional microbiome changes linked to inhalation therapy, including an expansion of salt-associated transporter genes and a community shift toward CF-associated microbial opportunists, including Haemophilus influenzae and fungi, carrying the identified salt-associated transporter genes with high sequence and structural identity. Hypertonic, compared with isotonic, saline accelerates H. influenzae growth and induces efflux pumps linked to antibiotic tolerance in vitro. This study establishes a reference framework for functional airway microbiome research, enabling the examination of therapeutic perturbations and their impact on microbial adaptation.}, } @article {pmid42013844, year = {2026}, author = {Bargheet, A and Bø, GH and Hetland, MAK and Justine, M and Moyo, SJ and Löhr, IH and Blomberg, B and Langeland, N and Klingenberg, C and Pettersen, VK}, title = {Metabolic reprogramming of the infant gut by bifidobacteria-based probiotics drives exclusion of antibiotic-resistant pathobionts.}, journal = {Cell reports. Medicine}, volume = {7}, number = {5}, pages = {102752}, pmid = {42013844}, issn = {2666-3791}, mesh = {Humans ; *Probiotics/pharmacology/administration & dosage ; *Bifidobacterium/metabolism/drug effects/physiology ; Infant ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Metabolome ; *Drug Resistance, Bacterial ; *Drug Resistance, Microbial ; Male ; Female ; Infant, Newborn ; }, abstract = {Early-life probiotics that strengthen gut resilience in infants are a promising strategy to combat the global emergency of antibiotic resistance. Still, their effects on antibiotic-resistant opportunistic pathogens, i.e., pathobionts, remain unclear. We evaluate the effects of probiotic supplementation in 152 full-term Tanzanian infants enrolled in the ProRIDE trial. Oral probiotics during the first 4 weeks of life increase gut colonization by Bifidobacterium species, while suppressing pathobionts, including extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E). Integrated metagenomics and metabolomics show that probiotics reduce resistome load and mobilome richness at 6 weeks, accompanied by concurrent shifts in the fecal metabolome. Specifically, the intervention increases lactate and pyruvate and reduces cross-feeding pathways that lead to propionate and butyrate, which partly explains the reduction in ESBL-E carriage. Our study documents putative pathways by which probiotic-driven Bifidobacterium colonization modulates the infant gut toward a lower level of antibiotic resistance.}, } @article {pmid42013850, year = {2026}, author = {Qin, Y and Zhang, YX and Liu, LP and Xie, YH and Ma, XY and Hao, Y and Zhao, LC and Dong, JJ and He, Y and Sun, K and Zhong, H and Zhu, S and Liu, M and Fang, JY and Zhou, CB}, title = {Distinct signatures in the human gut and oral microbiomes of gastric cancer.}, journal = {Cell reports. Medicine}, volume = {7}, number = {5}, pages = {102761}, pmid = {42013850}, issn = {2666-3791}, mesh = {Humans ; *Stomach Neoplasms/microbiology ; Saliva/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; Feces/microbiology ; *Mouth/microbiology ; Male ; Metagenome ; Middle Aged ; *Microbiota ; Dysbiosis/microbiology ; Aged ; }, abstract = {Microbiome dysbiosis is increasingly recognized as a hallmark of gastric cancer (GC). Here, we analyzed gut and oral shotgun metagenomic data from 317 individuals across two independent cohorts, with validation in a Harbin cohort. We identify 20 oral-gut shared species enriched in the gut of GC, predominantly lactic acid bacteria (LAB). While most gut microbial markers are abundant in saliva, none are significantly altered in GC. Strain-level analysis of 87 matched saliva-stool metagenomes confirms oral-gut transmission of Streptococcus species. GC-enriched LAB form robust co-abundance networks in oral and gut microbiomes, suggesting synergistic interactions. Functional analysis reveals enriched lactate fermentation pathways in GC stool, aligning with LAB dominance and previous findings on gastric microbiota. Moreover, microbiome-based classifiers achieve high predictive accuracy (area under receiver operating characteristic curve [AUROC] = 0.85 for stool, 0.87 for saliva) for GC diagnosis, highlighting translational potential. Collectively, these findings underscore the critical role of the oral-gut microbiome axis in GC.}, } @article {pmid42013936, year = {2026}, author = {Nie, Z and Wang, Y and Ya, T and Dang, T and Wang, X and Liu, C and Hu, Z and Wang, X}, title = {Rapid recovery from starvation stress in low-temperature anammox system: extracellular polymeric substances protection and dissimilatory nitrate reduction to ammonium synergistically promote nitrogen metabolism recovery.}, journal = {Bioresource technology}, volume = {453}, number = {}, pages = {134677}, doi = {10.1016/j.biortech.2026.134677}, pmid = {42013936}, issn = {1873-2976}, mesh = {*Nitrogen/metabolism ; *Nitrates/metabolism ; Bacteria/metabolism/genetics ; *Ammonium Compounds/metabolism ; Oxidation-Reduction ; *Stress, Physiological ; *Cold Temperature ; *Extracellular Polymeric Substance Matrix/metabolism ; }, abstract = {Understanding the response of the anammox system to starvation disturbances under low-temperature conditions is of great importance. In this study, we explored the performance, microbial community structure, and microbial metabolic in a low-temperature anammox system following a 15-day starvation period with the aim of identifying their response and recovery mechanisms after starvation stress. It was found that the low-temperature anammox system was able to regain its initial performance within 5 days. After system stabilization, the total nitrogen removal efficiency increased from 85% to 88%. The upregulation of hydrazine synthase (hzs) and hydrazine dehydrogenase (hdh) genes involved in anammox process was identified as part of a response mechanism of anammox bacteria. During the starvation period, the increased secretion of extracellular polymeric substances (EPS) served as a protective mechanism. Additionally, the synergistic interaction between dissimilatory nitrate reduction to ammonium (DNRA) bacteria and anammox bacteria contributed to the enhancement of nitrogen removal efficiency. The EPS-mediated synergistic interaction between anammox bacteria and heterotrophic bacteria was conducive to the survival of microorganisms during starvation and their prompt recovery upon the restoration of substrate supply.}, } @article {pmid42013937, year = {2026}, author = {Zhu, Y and Hou, Q and Hu, F and Zhuang, G and Ma, A}, title = {Functional activators-facilitated FeS transformation enhances petroleum hydrocarbon degradation by promoting functional microbial proliferation.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134631}, doi = {10.1016/j.biortech.2026.134631}, pmid = {42013937}, issn = {1873-2976}, mesh = {*Petroleum/metabolism ; Biodegradation, Environmental/drug effects ; *Hydrocarbons/metabolism ; *Ferrous Compounds/metabolism ; *Bacteria/metabolism/growth & development ; Reactive Oxygen Species/metabolism ; }, abstract = {Bioremediation of total petroleum hydrocarbon (TPH)-contaminated sites often faces a major challenge in sulfur-rich environments, where ferrous sulfide (FeS) immobilizes pollutants and sharply reduces their bioavailability, thereby stalling remediation. This study demonstrates that the bottleneck can be overcome by applying a composite functional activator to induce a targeted shift of the site microenvironment. The activator first selectively suppresses competing iron- and sulfur-reducing bacteria, reducing their relative abundance by 92%, thereby shifting the microbial community structure. Concurrently, a controlled decrease in local pH converts FeS from a pollutant sink into an active catalyst. The transformed FeS then activates molecular oxygen (O2) to generate reactive oxygen species (•OH and SO4[•-]), which chemically mobilize and pre-oxidize TPH, producing a "priming effect". This priming effect subsequently restructures the indigenous microbial community. Consequently, under optimized niche conditions and increased nutrient availability, TPH-degrading Bacillus populations expand significantly in the remediation environment: their relative abundance increases by 57%, and their niche breadth widens by 34%. Metagenomic analysis confirms upregulation of genes related to pollutant degradation, substance transport, and energy metabolism, strengthening the metabolic network. Ultimately, the integrated chemical-biological process achieves 90% TPH degradation. This study realizes the functional shift of FeS from remediation barrier to degradation booster, offering an innovative chemo-biological synergistic strategy and engineering paradigm for long-term stable remediation of TPH-contaminated sites.}, } @article {pmid42014006, year = {2026}, author = {Liu, H and Luo, J and Yang, Y and Yang, R and Li, W}, title = {Spleen metabolomics coupled with gut microbiome analysis to elucidate the immunomodulatory mechanisms of longan polysaccharides against cyclophosphamide-induced immunosuppression in mice.}, journal = {International journal of biological macromolecules}, volume = {362}, number = {}, pages = {152109}, doi = {10.1016/j.ijbiomac.2026.152109}, pmid = {42014006}, issn = {1879-0003}, mesh = {Animals ; *Spleen/metabolism/drug effects/immunology ; *Polysaccharides/pharmacology ; *Cyclophosphamide/adverse effects/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Metabolomics/methods ; Cytokines/metabolism ; Immunosuppression Therapy ; Male ; *Immunologic Factors/pharmacology ; *Metabolome/drug effects ; Immunosuppressive Agents ; }, abstract = {Longan polysaccharide (LP) has exhibited excellent immunomodulatory activities by modifying gut microbiota but the specific regulatory mechanism remains unclear. Therefore, spleen metabolomics and metagenomic sequencing of gut microbiota were combined to investigate the immunomodulatory mechanism of LP in cyclophosphamide (CPA)-induced immunosuppressed mice with an intact and antibiotic-depleted microbiota. The results indicated that LP significantly restored thymic and splenic indices, increased lymphocyte proliferation, and mitigated damage to immune organs. LP up-regulated the ratio of CD4[+]/CD8[+] in the mouse spleen to modulated cytokine secretion, thereby increasing serum concentrations of IFN-γ, TNF-α, IL-12, and IL-6. The metabolomic analysis indicated that LP alleviated CPA-induced splenic disturbance by coordinately improving amino acid metabolism, unsaturated fatty acid metabolism, and pyrimidine metabolism. Furthermore, LP significantly reshaped the CPA-induced gut microbiota imbalance, particularly by increasing the relative abundance of unclassified_f__Muribaculaceae and Bacteroides. However, antibiotic intervention almost offset the LP-mediated alleviation of immunosuppression. Our findings provide novel insights into the mechanisms underlying the immunosuppression-alleviating effects of natural polysaccharides.}, } @article {pmid42014453, year = {2026}, author = {Treichel, NS and Pauvert, C and Séneca, J and Pjevac, P and Berry, D and Penders, J and Hitch, TCA and Clavel, T}, title = {Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis.}, journal = {Nature microbiology}, volume = {11}, number = {5}, pages = {1233-1244}, pmid = {42014453}, issn = {2058-5276}, support = {460129525//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 445552570//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 10.55776/DOC69//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 10.55776/COE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, mesh = {*Metagenomics/methods/standards ; *Shotgun Sequencing ; *Bacteria/genetics/classification ; *Benchmarking ; Computational Biology/methods ; Metagenome ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Shotgun metagenomics can provide both taxonomic and functional insights, but benchmarking is necessary to determine the sequencing depth appropriate for specific analyses. Here we used complex mixtures of DNA from cultured bacteria and analysed taxonomic composition, strain-level resolution and functional profiles at up to 11 sequencing depths (0.1-50.0 Gb). Reference-based analysis provided accurate strain-level taxonomy at 0.5-1.0 Gb. By contrast, de novo metagenome-assembled genome (MAG) reconstruction required deep sequencing (>10 Gb), and even MAGs deemed high quality by standard metrics were chimeric, with 54.5-81.8% accurately representing original strains, depending on the bioinformatic approach. Functionally, 2 Gb provided reliable insights at the pathway level for each of the mock communities tested, but sufficient proteome coverage was achieved only at or above 10 Gb. Library preparation and host DNA contamination were identified as confounders in shallow metagenomic analysis. This analysis highlights the potential and limitations of shallow metagenomics and provides guidance to accurately capture strain-level diversity using MAGs.}, } @article {pmid42014512, year = {2026}, author = {Vijayasimha, M and Srikanth, M and Trivedi, NS}, title = {From Diagnostic Accuracy to Decision-Grade Respiratory Nanopore Metagenomics: Minimum Standards, Stewardship Endpoints, and Equitable Implementation.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {42014512}, issn = {1432-0991}, } @article {pmid42014682, year = {2026}, author = {Lee, EM and McNulty, NP and Hibberd, MC and Cheng, J and Ahsan, K and Chang, HW and Cohen, BA and Gordon, JI}, title = {Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42014682}, issn = {2041-1723}, support = {F30 DK142304/DK/NIDDK NIH HHS/United States ; DK30292//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; }, mesh = {Humans ; Animals ; Mice ; Metagenome/genetics ; *Microbiota/genetics ; *Transcriptome ; *Gene Expression Profiling/methods ; Bacteria/genetics/classification ; *Metagenomics/methods ; Germ-Free Life ; }, abstract = {Metatranscriptomic (MTX) sequencing quantifies gene expression from the collective genomes of microbial communities (microbiomes), enabling assessment of functional activity rather than functional potential. While differential expression testing is essential for RNA-sequencing analysis, current metatranscriptomic approaches have only been benchmarked on simulated data, resulting in a lack of standard practices for analysis of real datasets. Here, we use mock communities (defined mixtures of microbial cells with known properties) to quantitatively assess robustness and susceptibility of current approaches to various confounders including organisms' low relative abundance, differential abundance, low prevalence, global transcriptional output changes, and compositional effects. We show that no current method is robust to all confounders and method performance on simulated data does not generalize to real datasets. We then apply the same approaches to MTX datasets generated from gnotobiotic mice colonized with defined consortia of human bacterial strains and show that the method nominated by the mock community comparisons successfully inferred cross-feeding dynamics that were subsequently validated in vitro. Finally, using metagenome-assembled genomes from a human clinical study, we leverage genome-level sequencing depth and detection of genes to exclude low information samples on a per-organism basis to overcome confounding low prevalence and enhance differential expression inference. We conclude that MTX benchmarking on real, non-simulated datasets can and should guide choice of methods and their implementation, enabling inference and validation of microbial metabolic strategies and interactions in vivo.}, } @article {pmid42014730, year = {2026}, author = {Wang, Y and Yu, P and Huang, ES and Lu, DC and Zhang, W}, title = {Decoding a Microbial Community for Healthy Kelp: 403 MAGs from the World's Largest Kelp Farming Region.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {42014730}, issn = {2052-4463}, support = {2023-004//2023 Weihai Key Postdoctoral Research Funding Program/ ; }, mesh = {*Kelp/microbiology ; Aquaculture ; *Microbiota ; *Metagenome ; Phylogeny ; Bacteria/classification/genetics ; Archaea/genetics/classification ; }, abstract = {Kelp is economically and ecologically significant, with its organic nutrient-rich aquaculture water harboring diverse microbial communities that critically influence kelp health and productivity. To characterize these communities, we collected ten water samples from major kelp farming areas and reconstructed 403 medium- to high-quality Metagenome-Assembled Genomes (MAGs). Of these, 110 (27.3%) met high-quality criteria (completeness >90%, contamination <5%). Phylogenomic analysis classified these MAGs into 21 archaeal and 382 bacterial species across 19 phyla, with Pseudomonadota (n = 217), Bacteroidota (n = 74), and Patescibacteria (n = 24) as the dominant groups. UpSet plot analysis revealed the presence of a core set of 30 MAGs across all sampling sites. Notably, diseased samples exhibited a marked increase in Pseudomonadota MAGs, suggesting their potential as biomarkers for disease monitoring. Together, these findings provide foundational insights into the microbial ecology of kelp aquaculture systems, supporting improved disease management and sustainable practices.}, } @article {pmid42014993, year = {2026}, author = {Dong, X and Yi, J and Wang, Y and Zhou, A and Zhang, J and Shi, L and Wang, C}, title = {Multi-omics integration analyses reveal microbiome and metabolome features in pregnant sow diarrhea induced by porcine epidemic diarrhea virus.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42014993}, issn = {1471-2180}, abstract = {UNLABELLED: Gut microbial dysbiosis and its derived-metabolites changes have been evidenced to participant in diarrhea piglets; little is known underlying the crosstalk between gut microbiota and metabolites in pregnant sow diarrhea induced with PEDV. In this study, we performed fecal metagenomic and metabolomic profiling in diarrheic pregnant sows infected with PEDV to evaluate the functional characteristics of gut microbiota and metabolites. Microbiome analysis revealed the alterations in composition and diversity of gut microbiota in diarrheic pregnant sows compared with non-diarrheic. The relative abundances of the genera Prevotella, Treponema and Bacteroides were significantly lower and the abundant of Lactobacillus and Ruminococcus were increased in diarrheic pregnant sows. In addition, we found that the increase of Ruminococcus_sp_CAG563, Mycoplasma_sp_CAG472, Prevotella_sp_CAG520, Candidatus_Melainabacteria_bacterium and Eubacterium_coprostanoligenes was the important characteristics in diarrheic pregnant sows. In addition, metabolomic analysis showed a distinct metabolic profile in diarrheic pregnant sows infected with PEDV and the differential metabolites were associated with secondary bile acid biosynthesis, protein digestion and absorption, amino acid biosynthesis. Moreover, our multi-omics data integration analysis indicated that the significant dominant bacteria in diarrheic pregnant sows were positively correlated with 5-aminovaleric acid, pantothenate, 8,4-oxyneolignan-4-xyloside and xanthine, while the predominant coexistence of Treponema, Bacteroides, and Fibrobacter promoted the production of dodecanedioic acid, sesamol and sebacic acid in non-diarrheic pregnant sows infected with PEDV. Taken together, our findings revealed the dynamic changes in the microbiota and metabolites of diarrheic pregnant sows during PEDV infection, identifying microbiota‑derived metabolites associated with host resistance, providing novel insight into the host–gut microbiota interaction.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05043-2.}, } @article {pmid42015023, year = {2026}, author = {Peng, Z and He, H and Zhou, S and Qiao, L and Wang, Q and Li, M and Zhao, Y}, title = {Rhino-orbito-cerebral Rhizopus delemar infection in a patient with anti-melanoma differentiation-associated-5-positive dermatomyositis diagnosed by metagenomic next-generation sequencing: a case report.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {42015023}, issn = {1471-2334}, abstract = {BACKGROUND: Rhino-orbito-cerebral mucormycosis, caused by pathogens such as Rhizopus delemar, is a life-threatening opportunistic infection primarily affecting immunosuppressed individuals. Anti-melanoma differentiation-associated protein 5-positive dermatomyositis (MDA5+ DM) is a distinct subtype of DM associated with interstitial lung disease (ILD) and high mortality. Fungal co-infections in anti-MDA5+ DM, particularly mucormycosis, are rarely reported. CASE PRESENTATION: We report a case of rhino-orbito-cerebral mucormycosis caused by Rhizopus delemar in a patient with anti-MDA5+ DM. The patient was receiving high-dose glucocorticoids and immunosuppressive therapy for rapidly progressive ILD, and later she developed progressive neurological symptoms, palatal ulceration with black eschar, and periorbital swelling. Metagenomic next-generation sequencing (mNGS) of blood subsequently identified Rhizopus delemar, and the diagnosis was further supported by cerebrospinal fluid mNGS. Antifungal therapy was adjusted promptly after pathogen identification. Despite aggressive treatment, the infection progressed rapidly with central nervous system involvement. CONCLUSIONS: This case highlights the heightened susceptibility to invasive mucormycosis in patients with anti-MDA5+ DM, likely exacerbated by immunosuppressive therapy. Early diagnosis using mNGS and prompt initiation of targeted antifungal therapy are critical in managing such co-infections. Clinicians should maintain a high index of suspicion for invasive fungal infections in immunosuppressed anti-MDA5+ DM patients presenting with non-specific neurological or sinus symptoms.}, } @article {pmid42015434, year = {2026}, author = {Wang, S and Deng, F}, title = {Clinical Features and Coinfection Factors of Severe Community-Acquired Pneumonia with <em>Mycoplasma Pneumoniae</em> in Children.}, journal = {Journal of the College of Physicians and Surgeons--Pakistan : JCPSP}, volume = {36}, number = {4}, pages = {483-488}, doi = {10.29271/jcpsp.2026.04.483}, pmid = {42015434}, issn = {1681-7168}, mesh = {Humans ; Male ; *Community-Acquired Pneumonia/microbiology ; Female ; *Coinfection/microbiology/epidemiology/diagnosis ; Retrospective Studies ; Child, Preschool ; Child ; *Pneumonia, Mycoplasma/diagnosis/epidemiology/microbiology ; *Mycoplasma pneumoniae/isolation & purification ; China/epidemiology ; *Community-Acquired Infections/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Adolescent ; Infant ; }, abstract = {OBJECTIVE: To characterise the clinical features of children with severe community-acquired pneumonia (CAP) associated with Mycoplasma pneumoniae (Mp) infection and to identify factors influencing polymicrobial coinfections.

STUDY DESIGN: A descriptive study. Place and Duration of the Study: Department of Internal Medicine, Anhui Provincial Children's Hospital, Anhui, China, from January to December 2023.

METHODOLOGY: A retrospective cohort study was conducted on 207 hospitalised children aged <16 years with confirmed CAP who underwent BALF testing due to severe symptoms, antibiotic-unresponsive fever, or unclear aetiology. Those with chronic comorbidities were excluded. BALF pathogens were detected via multiplex PCR and metagenomic next-generation sequencing (mNGS). Patients were divided into Mp mono-infection and coinfection groups; demographic, clinical, and laboratory data were compared, and logistic regression analysis was performed to identify factors associated with coinfection.

RESULTS: The coinfection group was significantly younger (4.12 ± 2.83 vs. 6.56 ± 2.47 years, p = 0.013) and had longer hospital stays (11.21 ± 4.26 vs. 9.90 ± 3.68 days, p = 0.049) than the mono-infection group. Inflammatory markers differed significantly: the coinfection group had higher IL-6 (28.64 ± 8.03 vs. 15.86 ± 14.21 pg/mL, p <0.001), but lower IL-2R (1774.15 ± 104.18 vs. 2157.39 ± 382.76 U/mL, p <0.001) and ESR (30.31 ± 14.79 vs. 40.08 ± 13.66 mm/h, p <0.001). Logistic regression confirmed IL-6 (p <0.001), IL-2R (p <0.001), and complications (p = 0.0281) as independent factors associated with coinfections, while chest CT findings showed no correlation (p >0.05).

CONCLUSION: Younger age, elevated IL-6 levels, reduced IL-2R levels, and the presence of complications are closely correlated with polymicrobial coinfections in children with severe Mp-associated CAP.

KEY WORDS: Pneumonia, Mycoplasma pneumoniae, Paediatrics, Coinfection, Metagenomic sequencing, Clinical characteristics.}, } @article {pmid42015472, year = {2026}, author = {Song, M and Zhang, Z and Huang, H and Zou, Z and Wen, S and Cui, Y and Liu, S}, title = {Spinal Tuberculosis Diagnosed by Metagenomics Capture (MetaCAP) in a Patient Undergoing Maintenance Hemodialysis: A Case Report.}, journal = {The American journal of case reports}, volume = {27}, number = {}, pages = {e951840}, pmid = {42015472}, issn = {1941-5923}, mesh = {Humans ; Female ; Middle Aged ; *Tuberculosis, Spinal/diagnosis ; *Renal Dialysis ; *Metagenomics/methods ; *Kidney Failure, Chronic/therapy/complications ; *Mycobacterium tuberculosis/genetics/isolation & purification ; Antitubercular Agents/therapeutic use ; }, abstract = {BACKGROUND Spinal tuberculosis is difficult to diagnose in patients undergoing maintenance hemodialysis (MHD) because of immunosuppression, atypical clinical manifestations, and the limited sensitivity of conventional microbiological assays. Rapid and accurate pathogen identification is essential to distinguish spinal tuberculosis from other causes of vertebral destruction, including metastatic malignancy and bacterial spondylitis. This report aims to illustrate the diagnostic value of capture-based targeted sequencing for detecting Mycobacterium tuberculosis in extrapulmonary infection when routine tests and metagenomic next-generation sequencing (mNGS) yield inconclusive or misleading results. CASE REPORT A 64-year-old woman with end-stage renal disease secondary to IgA nephropathy, receiving long-term MHD, presented with progressive low back pain. Imaging revealed multilevel vertebral involvement with pathological fractures, raising suspicion of metastatic disease or infectious spondylitis. Histopathological examination demonstrated granulomatous inflammation, while acid-fast staining and routine cultures were negative. Initial mNGS of spinal tissue identified Staphylococcus aureus, leading to targeted antibacterial therapy. Although inflammatory markers declined, the patient's symptoms worsened and pancytopenia developed. Subsequent analysis of spinal pus using metagenomic capture (MetaCAP)-based targeted sequencing detected the Mycobacterium tuberculosis complex with high confidence. Anti-tuberculosis therapy was promptly initiated, resulting in rapid clinical improvement and radiological resolution. CONCLUSIONS This case shows the limitations of conventional microbiological methods and unbiased mNGS in diagnosing extrapulmonary tuberculosis in immunocompromised patients. Capture-based targeted sequencing offers enhanced sensitivity for Mycobacterium tuberculosis detection and may facilitate timely diagnosis and appropriate treatment of spinal tuberculosis in patients undergoing MHD.}, } @article {pmid42016528, year = {2026}, author = {Xu, H and Guo, J and Chen, C and Pang, Z and Zhang, G and Zhang, W and Kan, H and Shao, X}, title = {Metagenomics reveals the functional profiles of soil microorganisms and nutrient cycling under long-term grass vegetation cropping.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100583}, pmid = {42016528}, issn = {2666-5174}, abstract = {Soil microbes are crucial for biogeochemical cycles and their functional potential is greatly affected by ecosystem management. Yet, how does grass vegetation affect the composition of soil microbial communities and the abundance of key nutrient-cycling functional genes? In this study, based on an experimental plot built for 7 years, the long - term influence of two grass vegetation types (Carex breviculmis and Festuca arundinacea Schreb) on soil microbial community structure and C, N, P, and S cycles were explored by metagenomics. The results showed that both plants significantly increased the diversity and richness of soil bacteria and fungi, and the abundance of Pseudomonadota and Ascomycota in Carex breviculmis increased significantly, while those of Actinomycetota and Mucoromycota decreased. Microbial network analysis shows that Carex breviculmis forms a highly modular, low - complexity microbial interaction network, indicating specialized and stable microbial community functions. Conversely, Festuca arundinacea Schreb has a more complex and less modular network, suggesting enhanced microbial interactions. Carex breviculmis significantly increased the abundance of genes related to carbon fixation (fumA/B, pps, ppc) and phosphorus mineralization (phoR/P/B, phnF/P), and also enhanced soil denitrification potential. In contrast, Festuca arundinacea Schreb showed a enrichment of soil nitrogen fixation genes (nifh). Additionally, growing Carex breviculmis and Festuca arundinacea Schreb induced the growth of sulfur - oxidizing bacteria (e.g., Thiobacillus), enriching the abundance of sulfur - metabolism - related genes (apr, sox). Genes related to microbial C, N, P, and S cycles are positively correlated with soil pH, available P, and alkali-hydrolyzed nitrogen. Overall, this study reveals how different grass vegetation types regulate microbial community structure and functional gene abundance to drive nutrient cycling differentiation in grassland ecosystems, thereby providing a theoretical basis for optimizing grass vegetation configuration in managed and restored grasslands to enhance soil ecological functions.}, } @article {pmid42016568, year = {2026}, author = {Liu, L and Xu, C and Liu, Y and Yang, J and Ye, Y and Yao, Z and Lin, D and Qiu, H and Ruan, D and Qiu, Y and Wang, S and Lin, M and Zhang, Z and Huang, S and Meng, F and Zheng, E and Cai, G and Wu, Z and Wu, JJ}, title = {Restoring low-fiber diets-induced Lachnospiraceae bacterium loss partially recovers fiber digestion and immune function in mammals.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101401}, pmid = {42016568}, issn = {2665-9271}, abstract = {Mammals rely on their gut microbiota to degrade cellulose, the major component of dietary fiber. Westernized populations harbor a depleted microbiome with reduced fiber-digesting capacity and impaired immune regulation due to prolonged consumption of low-fiber diets. Comparable patterns are evident in other mammals, including Western commercial pigs raised on high-energy, low-fiber diets, exhibiting reduced diversity and abundance of fiber-degrading bacteria. In contrast, semi-free-ranging Chinese indigenous pigs consuming fiber-rich diets retain a more diverse and functionally resilient microbiota, reflecting divergent trajectories of host-microbiota co-evolution. However, the specific cellulose-degrading species lost and strategies to restore these functions remain unclear in mammals. By analyzing 473 human stool metagenomes spanning non-westernized and westernized diets, together with 251 fecal 16S rRNA datasets and 95 metagenomes from Western commercial pigs, Chinese indigenous pigs, and their crossbred progeny, we identified the Lachnospiraceae bacterium as a key symbiont enriched in non-westernized guts. This bacterium possesses an extensive Carbohydrate-Active Enzymes repertoire conferring strong fiber-degrading capacity. Notably, low-fiber diets leave a genetic signature on this keystone gut symbiont, which cannot be reversed by short-term dietary interventions alone. Reintroduction of Lachnospiraceae bacterium to germ-free mice improved feed efficiency and increased acetic acid production. Intestinal transcriptomics and peripheral blood flow cytometry revealed that it activates a broad adaptive immune response, promoting CD4[+] T cell accumulation, B cell activation, and anti-inflammatory cytokine induction. Reintroduction of this bacterium also alleviated dextran sodium sulfate-induced colitis. These findings highlight the preclinical functional potential of this Lachnospiraceae bacterium in mitigating low-fiber diets-induced dysfunction in mammals.}, } @article {pmid42016597, year = {2026}, author = {Srinivas, M and O'Sullivan, O and Cotter, PD and van Sinderen, D and Kenny, JG}, title = {Investigating the role of bacterial raw milk community members in chlorate reduction.}, journal = {Access microbiology}, volume = {8}, number = {4}, pages = {}, pmid = {42016597}, issn = {2516-8290}, abstract = {Chlorine-based detergents, used in the dairy industry for cleaning, often degrade into chlorate, contaminating milk and dairy products. Consumption of chlorate has been linked to thyroid dysfunction in adults and impaired neurological development in infants. Despite the ban on chlorine-based detergents in Ireland since 2021, chlorate contamination remains a problem in the dairy supply chain. A recent study identified chlorate-reducing bacteria naturally present in raw milk, highlighting their potential for mitigating chlorate. In this study, shotgun metagenomic sequencing was applied to determine the effects of chlorate concentration and incubation conditions on the raw milk microbiome, specifically focusing on chlorate-reducing bacteria within the community. Chlorate-spiked milk samples from different farms showed reductions in chlorate levels over time, from day 10 onwards when stored at 4 °C and after 24 h when incubated at 25 °C. Pseudomonas and Lactococcus were observed as the most dominant taxa in raw milk samples stored at 4 °C and 25 °C, respectively. High abundances of ydeP and narG genes were observed for 4 °C samples and were attributed to Pseudomonas and various low-abundance genera, respectively. High abundances of the napA gene were noted in 25 °C samples and were attributed to the Lactococcus genus. Overall, this study highlights the presence of naturally occurring chlorate-reducing bacteria as part of the raw milk microbiome and identifies multiple genes linked to various pathways potentially involved in chlorate reduction. Furthermore, incomplete pathways potentially involved in chlorate reduction were found, suggesting metabolic cross-feeding and underscoring the community roles bacteria play in chlorate reduction in raw milk. Additionally, a few previously uncharacterized genes, such as ydeP, belonging to the DMSO reductase gene family were identified at high abundances in samples that showed chlorate reduction, emphasizing the need for further biochemical characterization of these genes to better understand the pathways involved in chlorate reduction in milk.}, } @article {pmid42016660, year = {2026}, author = {Qu, Y and Liu, Y and Zhou, X and Xu, P and Wang, L}, title = {Polymicrobial Pasteurella multocida-Anaerobic Coinfection Followhing a Cat Bite: Limb Salvage Through Metagenomic Next-Generation Sequencing-Guided Diagnosis and Multidisciplinary Management.}, journal = {Clinical case reports}, volume = {14}, number = {3}, pages = {e72304}, pmid = {42016660}, issn = {2050-0904}, abstract = {Successful management of a Pasteurella multocida and polymicrobial infection following a cat bite on the left leg entailed debridement, split-thickness skin grafting with vacuum-sealing drainage, and targeted antibiotic treatment. This approach enabled successful incorporation of the skin graft, preserving the limb and eliminating the necessity for amputation.}, } @article {pmid42016731, year = {2026}, author = {Chen, G and Tang, S and Wang, H and Liang, Z and Lv, X and Han, J and Ni, L}, title = {Integration of volatile flavor metabolomics and metagenomics reveals microbial-enzymatic pathways governing key aromatic volatile compound biosynthesis in Hongqujiu fermentation.}, journal = {Food chemistry: X}, volume = {35}, number = {}, pages = {103811}, pmid = {42016731}, issn = {2590-1575}, abstract = {The anabolic pathways of key volatile flavor compounds (VFCs) in Hongqujiu (HQJ) remain insufficiently elucidated. In this study, dynamic changes in volatile flavor profiles and microbial communities throughout HQJ brewing, were systematically investigated using an integrated multi-omics strategy combining metabolomics, flavoromics and metagenomics. The results demonstrated that the ethanol content, titratable acidity, amino nitrogen and higher alcohols increased progressively throughout fermentation. Quantitative flavor metabolomic profiling identified 18 key VFCs, maining comprising ethyl esters, acetate esters and higher alcohols. Metagenomic sequencing revealed that Weissella, Lactobacillus, Saccharomyces, Aspergillus, Talaromyces and Monascus were the predominant microbal genera throughout HQJ fermentation. Functional gene annotation further indicated that key enzymes involved in flavor metabolism are primarily associated with Lactobacillus, Aspergillus, Talaromyces, Saccharomyces, Cyberlindnera and Monascus. Overall, this study elucidates the microbial-enzymatic basis of VFC biosynthesis and establishes a comprehensive flavor metabolic framework for HQJ fermentation, providing a theoretical foundation for aroma quality improvement.}, } @article {pmid42016742, year = {2026}, author = {Funada Barbosa, MR and Ramos, EDSF and Villanova, F and Oliveira Silva, RL and Garcia, SC and de Araújo, RS and Mendes-Correa, MC and Tozetto-Mendoza, TR and Zhang, W and Pandey, RP and Luchs, A and Sato, MIZ and da Costa, AC and Leal, E}, title = {Exploring the Genomics of Marnaviridae Family: Identification, Characterization, and Taxonomic Implications.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {7188239}, pmid = {42016742}, issn = {1687-918X}, abstract = {In this study, we characterized sequences similar to Marnaviridae obtained from water samples in the state of São Paulo, Brazil. Sixteen complete or nearly complete genomes were determined, all of them positive-sense single-stranded RNA, with lengths between 7074 and 10,198 base pairs, containing one or two open reading frames (ORFs). The amino acid sequences derived from the ORFs showed similarity and protein domains typical of the Marnaviridae family. Phylogenetic analysis based on RNA-dependent RNA polymerase (RdRp) revealed clusters closely related to viruses that have not yet been classified by the International Committee on Taxonomy of Viruses (ICTV). Some sequences showed proximity to established genera such as Salicharnavirus, Locarnavirus, and Labynarvirus, while others formed three distinct clades, suggesting the presence of new genera. Furthermore, one sequence displayed an RdRp identity of less than 90% and a capsid identity of less than 75%, indicating that it represents a novel species related to Marnaviridae. These findings expand current knowledge of Marnaviridae diversity, contributing to a better understanding of evolutionary relationships and emphasizing the need for taxonomic reorganization.}, } @article {pmid42016964, year = {2026}, author = {Sun, X and Peng, Y and Hao, X and Dong, R and Wang, Z and Wang, L and Wang, C and Wu, X and Chen, Z and Zhang, W and Tang, X}, title = {Safeguarding a Flagship Species: Integrated Surveillance of Cross-Species Pathogen Transmission in Giant Panda Ecosystems.}, journal = {Ecology and evolution}, volume = {16}, number = {3}, pages = {e73260}, pmid = {42016964}, issn = {2045-7758}, abstract = {Emerging infectious diseases, driven by increasing interactions among humans, wildlife, and livestock, pose an escalating threat to global health, biodiversity, and economies. As a flagship endangered species, the giant panda (Ailuropoda melanoleuca) plays a pivotal role in biodiversity conservation in China. This review synthesizes current knowledge on pathogens threatening giant panda health, including viruses, bacteria, and parasites alongside their potential transmission pathways within nature reserves. We emphasize the roles of domesticated animals, sympatric wildlife, and ectoparasites as reservoir hosts or vectors. Special focus is placed on cross-species transmission dynamics and the critical need for integrated monitoring systems utilizing metagenomics and viromics. We propose a framework for establishing early warning systems and surveillance networks at the domestic-wild animal interface to enhance pathogen detection, disease prevention, and biodiversity conservation.}, } @article {pmid42016980, year = {2026}, author = {De Panis, D and Priotto, O and Padró, J}, title = {Mitogenomic and Metabarcoding Resources for the Study and Conservation of Keystone Neotropical Raptors.}, journal = {Ecology and evolution}, volume = {16}, number = {3}, pages = {e73262}, pmid = {42016980}, issn = {2045-7758}, abstract = {Neotropical raptors are among the most threatened birds, facing increasing extinction risks due to habitat loss and human persecution. Despite their importance for ecosystem stability, basic data on their distribution, abundance, and genetic diversity remain scarce. To address these gaps, we assembled and annotated the mitochondrial genomes of nine high-priority raptors from the Neotropics, including the threatened Chaco Eagle (Buteogallus coronatus), Black-and-Chestnut Eagle (Spizaetus isidori), Rufous-tailed Hawk (Buteo ventralis), and Harpy Eagle (Harpia harpyja), as well as the Near Threatened Orange-breasted Falcon (Falco deiroleucus), Crested Eagle (Morphnus guianensis), Ornate Hawk-Eagle (Spizaetus ornatus), Plumbeous Hawk (Cryptoleucopteryx plumbea), and Solitary Eagle (Buteogallus solitarius). Mitogenome sizes ranged from 17,848 to 20,449 bp, with consistent gene content and a Control Region architecture common in Falconidae and Accipitridae. Phylogenetic analyses provided strong support for most relationships, highlighting the value of mitogenomic data for phylogeographic studies. We further designed metabarcoding primers for environmental DNA applications. Primers targeting the 12S rRNA gene and a mini-barcode for the Harpy Eagle's Control Region showed high resolution using short, conserved sequences ideal for combining degraded DNA with next-generation sequencing. Our study provides essential molecular tools for monitoring and protecting these ecologically vital yet threatened raptors across the Americas.}, } @article {pmid42017035, year = {2026}, author = {Yang, Y and Ren, Y and Ma, T and An, J and Jin, S and Dong, Y}, title = {Research advances in the role of circulating microorganisms in gastrointestinal tumors (Review).}, journal = {Molecular and clinical oncology}, volume = {24}, number = {6}, pages = {40}, pmid = {42017035}, issn = {2049-9469}, abstract = {Gastrointestinal tumors are common malignant tumors of the digestive system, which globally threaten human health. Notably, it has been discovered that blood and other circulating body fluids are not completely sterile; instead, they harbor complex and dynamic microbial DNA and signatures [circulating microorganisms (CM)]. These microorganisms primarily originate from the microbial translocation (including bacterial fragments, DNA and metabolites) through a compromised intestinal barrier, and are closely associated with the initiation and progression of gastrointestinal tumors, thus providing novel perspectives for early tumor diagnosis and prognosis. Although there is currently no evidence that CM can directly cause cancer, their metabolites and exosomes may contribute to tumor microenvironment remodeling. On one hand, they activate pattern recognition and inflammatory signaling pathways, such as Toll-like receptor/signal transducer and activator of transcription, potentially inducing and maintaining low-grade chronic inflammation. On the other hand, they may facilitate immune evasion, potentially promoting the 'inflammation-cancer' transition. With the development of metagenomic technologies and the maturation of next-generation high-throughput sequencing technologies, CM have shown potential as liquid biopsy biomarkers for the early diagnosis of gastrointestinal tumors. Interventions targeting specific CMs have also shown prospects for enhancing efficacy in early clinical trials. However, the field still faces numerous challenges, including insufficient depth of mechanistic validation and a lack of standardized detection protocols. Future efforts should aim to conduct further systematic research to clarify the biological functions and clinical translational value of CM in gastrointestinal tumors.}, } @article {pmid42017731, year = {2026}, author = {Su, DM and Ni, T and Yu, XL}, title = {Invasive streptococcus pneumoniae infection in the hip joint and thigh muscle group of an adult diagnosed by Q-mNGS: a case report.}, journal = {JPMA. The Journal of the Pakistan Medical Association}, volume = {76}, number = {3}, pages = {451-454}, doi = {10.47391/JPMA.22494}, pmid = {42017731}, issn = {0030-9982}, mesh = {Humans ; Male ; Adult ; *Hip Joint/microbiology/diagnostic imaging ; Thigh ; *Abscess/microbiology/therapy/diagnosis ; *Pneumococcal Infections/diagnosis/therapy/complications ; *Streptococcus pneumoniae/isolation & purification/genetics ; *Soft Tissue Infections/microbiology/therapy/diagnosis ; *Arthritis, Infectious/therapy/microbiology/diagnosis ; Debridement ; Anti-Bacterial Agents/therapeutic use ; Drainage ; *Myositis/therapy/microbiology ; }, abstract = {Joint infections and myositis due to S. pneumoniae are rare. We report the case of a young adult male presenting with right hip joint infection complicated by thigh muscle abscess, successfully treated by surgical debridement, drainage tube placement, and aggressive antimicrobial therapy. A 38-year-old male presented with right buttock and thigh swelling, pain, night sweats, and limited mobility for 45 days. Imaging examination indicated soft tissue infection around the right hip joint with abscess formation. Quantitative meta-genomic next-generation sequencing (Q-mNGS) of joint fluid confirmed S. pneumoniae as the pathogen. Surgical intervention was performed due to lack of significant improvement after six days of anti-inflammatory therapy. The patient recovered well post-operatively and was discharged with medication after a total hospital stay of 31 days. This case highlights the importance of considering S. pneumoniae as a potential pathogen in joint and soft tissue infections in adults.}, } @article {pmid42018084, year = {2026}, author = {Han, D and Pan, X and Pan, F and Han, B and Wu, Q and Zhou, Y and Liu, H and Xu, H and Sun, W and Cheng, H and Liu, W and Wan, R and Weng, W and Zhang, H}, title = {Translating Host-Derived Signals from Cerebrospinal Fluid Metagenomic Sequencing into a Diagnostic Tool for Autoimmune Encephalitis in Children.}, journal = {Journal of clinical immunology}, volume = {46}, number = {1}, pages = {}, pmid = {42018084}, issn = {1573-2592}, support = {82471882//National Natural Science Foundation of China/ ; 21ZR1452900//Natural Science Foundation of Shanghai Municipality/ ; GWVI-3//Three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai (2023-2025)/ ; shslczdzk06902//Shanghai Municipal Key Specialty/ ; }, abstract = {BACKGROUND: The rapid differentiation between autoimmune and infectious encephalitis in children is a critical clinical decision that dramatically impacts treatment and outcome. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) is a powerful but often underutilized tool, as its host-derived RNA component is typically discarded. We hypothesized that this host response data could be translated into a diagnostic tool for autoimmune encephalitis (AE). METHODS: We enrolled 180 pediatric patients with suspected encephalitis to evaluate the clinical performance of CSF mNGS against conventional methods. Host transcriptomic analysis was performed on CSF cells from 88 patients (autoimmune, bacterial, and viral encephalitis). A novel biomarker was validated using RT-qPCR in an independent cohort, and its functional role was investigated in neuronal cultures challenged with NMDAR1 antibodies. A diagnostic model was developed and validated. RESULTS: mNGS demonstrated a significantly higher pathogen detection rate than conventional methods (29.4% vs. 16.7%). Host transcriptomic profiling revealed that AE shared a hyperinflammatory signature with viral encephalitis but was uniquely associated with dysregulation of receptor tyrosine kinase and heme signaling pathways. Furthermore, memory B cells and activated mast cells were specifically elevated in AE. We identified and validated RAD54B as a novel biomarker specifically upregulated in AE. Functionally, RAD54B upregulation protected neurons from DNA damage stress induced by NMDAR1 antibodies. A multi-gene diagnostic model based on host-response genes robustly differentiated AE from infectious encephalitis (AUC > 0.923) in a validation set. CONCLUSIONS: We present a validated translational pipeline that repurposes routine CSF mNGS data into a dual-purpose diagnostic tool. By leveraging the host RNA data inherent in CSF mNGS, clinicians can now simultaneously investigate infectious and autoimmune etiologies in a single, rapid test. This strategy has the immediate potential to reduce diagnostic delay, guide timely therapy, and improve outcomes in children with encephalitis.}, } @article {pmid42018438, year = {2026}, author = {Sun, X and Jiang, X and Zhang, L and Li, M}, title = {Extensive individual and microorganism-specific circadian oscillations of the upper respiratory tract microbiome.}, journal = {Cell reports}, volume = {45}, number = {5}, pages = {117284}, doi = {10.1016/j.celrep.2026.117284}, pmid = {42018438}, issn = {2211-1247}, mesh = {Humans ; *Circadian Rhythm/physiology ; *Microbiota/genetics ; Female ; Adult ; Male ; *Oropharynx/microbiology ; *Respiratory System/microbiology ; }, abstract = {The upper respiratory tract microbiome (URM) influences host susceptibility and respiratory disease outcomes, but its normal temporal dynamics remain poorly understood. We conducted temporal metagenomic profiling of the URM by collecting oropharyngeal swabs from 22 healthy adults at 4-h intervals over 48 h. We identify significant 24-h cyclic variations in microbial composition and biomass, with two predominant oscillation patterns: "evening-peak" and "morning-peak" patterns. Temporal variation introduces substantial shifts in microbial profiles, leading to false positives in differential analyses. Microbial rhythmicity is linked to phenotypic traits such as oxygen and nutrient requirements. Nonetheless, rhythmic patterns differ across individuals, and regression analysis reveals that host identity contributes more substantially to microbial rhythmicity than species identity. Functional pathway analysis based on metagenomic sequencing data shows similar circadian fluctuations. Additionally, although anatomically adjacent, the oral cavity and oropharynx exhibit divergent rhythmic behaviors, highlighting local environmental influences on microbial rhythmicity. These findings reveal previously unrecognized temporal dynamics of the URM and provide a temporal framework for more accurate biomarker discovery.}, } @article {pmid42018637, year = {2026}, author = {Reynolds, RC and Weiss, ACB and James, CC and Kojima, CY and Weissman, JL and Thrash, JC and Levine, NM}, title = {Defining metabolic niches for marine microbial heterotrophs.}, journal = {Science advances}, volume = {12}, number = {17}, pages = {eadz0537}, pmid = {42018637}, issn = {2375-2548}, mesh = {Ecosystem ; *Heterotrophic Processes ; Phytoplankton/metabolism ; Carbon Cycle ; *Microbiota ; *Seawater/microbiology ; Oceans and Seas ; *Aquatic Organisms/metabolism ; Biomass ; Metagenomics ; }, abstract = {Ocean microbial communities are made up of thousands of diverse taxa whose metabolic demands set the rates of both biomass production and degradation. Thus, these microscopic organisms play a critical role in ecosystem dynamics, global carbon cycling, and climate. While we have frameworks for relating phytoplankton diversity to rates of carbon fixation, our knowledge of how variations in heterotrophic microbial populations drive changes in carbon cycling is in its infancy. Here, we leverage global metagenomic datasets and metabolic models to identify a set of metabolic niches with distinct growth strategies. These groupings provide a simplifying framework for describing microbial communities in different oceanographic regions and for understanding how heterotrophic microbial populations function. This framework, predicated directly on metabolic capability rather than taxonomy, will enable us to tractably link heterotrophic diversity directly to biogeochemical rates in large scale ecosystem models.}, } @article {pmid42019101, year = {2026}, author = {Ramírez-Arenas, PJ and López-Cortés, A and Martínez-Mercado, MA}, title = {Novel Methanosarcinaceae species Methanohalophilus methylutens sp. nov., Methanolobus methylotrophicus sp. nov., and Methanococcoides guerreronegronense sp. nov. from Guerrero Negro hypersaline microbial mats in accordance with the SeqCode.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {3}, pages = {126716}, doi = {10.1016/j.syapm.2026.126716}, pmid = {42019101}, issn = {1618-0984}, mesh = {*Methanosarcinaceae/classification/genetics/isolation & purification ; *Phylogeny ; DNA, Archaeal/genetics ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S/genetics ; Methane/metabolism ; Genome, Archaeal/genetics ; Metagenome ; }, abstract = {The Methanosarcinaceae family is the most versatile among methanogenic archaea, utilizing a wide variety of substrates for methanogenesis. It includes all known halophilic, methylotrophic methanogens. Despite evidence of their presence and even dominance over other methanogenic taxa in Guerrero Negro hypersaline microbial mats, no archaeal species have been cultured or described to date. Consequently, a significant gap remains in our understanding of their metabolic potential and diversity. In this study, seven high-quality metagenome-assembled genomes (MAGs) affiliated with the Methanosarcinaceae family were reconstructed. Three MAGs (E22BA4_117[TS], E22_A5_bin58[TS], and E22bin_1538[TS]) serve as the nomenclatural type for the novel proposed species Methanohalophilus methylutens, Methanolobus methylotrophicus, and Methanococcoides guerreronegronense, according to the SeqCode rules and representing the first Methanosarcinaceae species described from microbial mats of Guerrero Negro. Based on genomic content and phylogenetic features, we infer that these MAGs are cytochrome-containing methanogens supported by the presence of core methanogenesis genes (fwd/fmd, ftr, mch, mtd, mer, mtr and mcr). They exhibit distinct metabolic strategies: E22BA4_117[TS] is a generalist with broad substrate versatility, E22_A5_bin58[TS] is an expanded methylotrophic specialist, and E22bin_1538[TS] is a narrow-range methylotroph. All three MAGs encode the complete set of genes for the methylotrophic pathway, multiple Na[+]/H[+] antiporters and both transport and biosynthesis genes for compatible solutes, collectively indicative of their adaptations to hypersaline conditions. These novel species enrich the phylogenomic resolution of Methanosarcinaceae and expand current understanding of the diversity and ecological relevance of these methanogenic archaea in hypersaline ecosystems, while providing genomic evidence that clarifies their metabolic potential and adaptations.}, } @article {pmid42019198, year = {2026}, author = {Zhang, C and Geng, H and Li, X and Dai, X and Xu, Y}, title = {Magnetically controlled non-conductive microbial carrier-mediated anaerobic digestion of sewage sludge.}, journal = {Water research}, volume = {300}, number = {}, pages = {125963}, doi = {10.1016/j.watres.2026.125963}, pmid = {42019198}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; Anaerobiosis ; Methane/metabolism ; Bioreactors/microbiology ; Microspheres ; *Waste Disposal, Fluid/methods ; Biofuels ; }, abstract = {Magnetic porous microspheres (MPMs) have been used to enhance the anaerobic digestion (AD) of sludge. However, the feasibility of using MPMs as magnetically controlled microbial carriers in long-term AD remains unclear. Herein, without replenishment of MPMs, the methanogenic performance, main physicochemical properties of sludge and methanogenic metabolomics in 150-day MPM-mediated AD were comprehensively investigated. A substantial highly active anaerobes were found to adhere to MPMs, which maintained strong magnetic controllability and structural stability and significantly enhanced methane production (P < 0.001) and the methane proportion in biogas (P < 0.05) from AD at different hydraulic retention times (HRTs). The significant positive correlations between the interfacial Lewis acid-base (AB) interaction (R[2] > 0.79, P < 0.01) and daily methane production (R[2] > 0.52, P < 0.01) with water-mediated proton-coupled electron transfer (PCET) indicate that MPM-enhanced AB interactions can accelerate electron transfer by promoting proton movement in interfacial water molecules, thus enhancing methanogenesis during AD. Statistical analyses of variations in activities or contents of key bioenergetic substances on and within anaerobic cell membranes in AD confirmed this observation and simultaneously indicated that MPMs significantly enhanced the bioenergetics of CO2-reduction methanogenesis by promoting intracellular water-mediated PCET. Microbial community changes show that during the AD under different HRTs, MPMs significantly enriched bacteria capable of decomposing complex organics into acetate and hydrogen in an attached state, as well as free acetotrophic methanogens and attached hydrogenotrophic and hydrogen-dependent methylotrophic methanogens, thereby optimising the spatial distribution of methanogenic consortia. Metagenomics and genome-centric metagenomic analyses confirmed that MPMs significantly enhanced the hydrogen-dependent methanogenesis pathways of the attached methanogenic consortia and promoted energy-conserving metabolic cooperation between free and attached methanogenic consortia, reducing resource competition. Basic economic and environmental analyses revealed that the annual economic benefit increased by 112.2% and carbon emissions decreased by approximately 1.34 × 10[5] tons CO2/year with MPM-mediated AD relative to conventional AD. These findings can provide an important reference for the development of exogenous material-mediated AD technology.}, } @article {pmid42019199, year = {2026}, author = {Liu, S and Wei, W and Wang, C and Ni, BJ and Zhu, S}, title = {Persulfate-driven sludge biorefinery toward value-added medium-chain fatty acids.}, journal = {Water research}, volume = {300}, number = {}, pages = {125935}, doi = {10.1016/j.watres.2026.125935}, pmid = {42019199}, issn = {1879-2448}, mesh = {*Sewage/chemistry ; *Fatty Acids ; Biofuels ; Fermentation ; Waste Disposal, Fluid ; }, abstract = {Transforming waste activated sludge (WAS) into high-value biofuels is a key pathway toward sustainable waste management and carbon neutrality, yet the recalcitrance of extracellular polymeric substances (EPS) and microbial cell walls severely limits medium-chain fatty acids (MCFAs) production during anaerobic fermentation. Here, we propose a persulfate (PDS)-based pretreatment strategy that enhances MCFAs synthesis by driving sludge disintegration and substrate transformation. Treatment with 7.5 mM PDS increased MCFAs yield by ∼50%, reaching 13,341.4 mg COD/L. Mechanistic investigations reveal that SO4·[-] and ·OH radicals preferentially degrade tightly bound EPS, reducing protein and polysaccharide content by 38% and 46%, respectively, and increasing soluble chemical oxygen demand (SCOD) 5.05-fold. This transformation produces nitrogen-rich, low-molecular-weight dissolved organic matter (DOM). The resulting DOM exhibited high H/C ratios, low O/C ratios, and low aromaticity indices (AImod), significantly enhancing its bioavailability during anaerobic fermentation. Integrated metagenomic functional annotation and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) revealed that EPS-derived DOM reshaped the microbial metabolic network, stimulating glycolysis, amino acid metabolism, and carbon chain elongation. Moreover, the formation of unsaturated and aromatic-like fermentation products indicated enhanced DOM humification, which facilitated carbon chain elongation and microbial metabolic activity. Life cycle assessment and techno-economic analysis confirmed the environmental sustainability and economic feasibility of this radical-driven strategy. By elucidating the radical-EPS-DOM-metabolism cascade, this study provides mechanism-guided strategies for efficient sludge biorefinery, advancing the field from empirical operation toward targeted, high-efficiency design.}, } @article {pmid42019232, year = {2026}, author = {Xu, B and Zhou, H and Xu, S and Wang, R and Xu, Q and Wu, X and Mu, D and Li, X}, title = {AI-2-mediated quorum sensing marks the ecological transition from collective cooperation to individual survival during Daqu storage.}, journal = {International journal of food microbiology}, volume = {456}, number = {}, pages = {111785}, doi = {10.1016/j.ijfoodmicro.2026.111785}, pmid = {42019232}, issn = {1879-3460}, mesh = {*Quorum Sensing ; *Homoserine/analogs & derivatives/metabolism ; *Lactones/metabolism ; Bacterial Proteins/metabolism/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Fermentation ; *Food Storage ; *Microbiota ; Food Microbiology ; Carbon-Sulfur Lyases/metabolism/genetics ; }, abstract = {Quorum sensing (QS) is a central system reflecting microbial collective behavior; however, its role in shaping functional microbial communities within complex solid-state fermentation matrices such as Daqu remains insufficiently understood. Here, we integrated amplicon sequencing, metagenomics, proteomics, and metabolomics to investigate autoinducer-2 (AI-2)-mediated quorum sensing dynamics during Daqu storage. Storage induced a directional succession of the microbial community, revealing two distinct ecological stages. The rapid adjustment stage (0-2 months) was characterized by strong homogeneous selection and rapid species turnover, whereas the slow stabilization stage (3-9 months) was dominated by gradual shifts in microbial relative abundances. Notably, the LuxS/AI-2 pathway, the only QS system detected during Daqu storage, declined rapidly and then stabilized, coinciding with the transition between the two ecological stages. During the early stage, the core QS protein LuxS was tightly associated with the dominant taxon Lactobacillaceae and the methyl donor S-adenosylmethionine, forming a synergistic functional module. In contrast, during the late stage, LuxS became decoupled from stress-tolerant taxa and showed weakened associations with resistance-related metabolic networks. This shift was accompanied by a metabolic transition, with carbon flux gradually redirected from active glycolysis toward the pentose phosphate pathway and amino acid biosynthesis during later stages. Collectively, these findings demonstrate that temporal modulation of the LuxS/AI-2 quorum sensing system represents a critical regulatory node reflecting the transition of the Daqu microbial community from cooperative growth to stress-resilient survival, ultimately shaping metabolic phenotypes and ecosystem functions during storage.}, } @article {pmid42019335, year = {2026}, author = {Sabatino, R and Pulina, S and Sbaffi, T and Kamburska, L and Titocci, J and Cherchi, M and Pittalis, C and Piscia, R and Vaccarelli, I and Rosati, I and Padedda, BM and Allemanno, F and Casiddu, P and Di Cesare, A}, title = {Lakes and lagoons used for drinking water supply and fisheries as sources of potentially pathogenic bacteria and antimicrobial resistance.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129718}, doi = {10.1016/j.jenvman.2026.129718}, pmid = {42019335}, issn = {1095-8630}, mesh = {*Drinking Water/microbiology ; *Lakes/microbiology ; *Fisheries ; *Bacteria ; RNA, Ribosomal, 16S/genetics ; Water Supply ; Water Quality ; }, abstract = {Drinking water supplies and water basins used for fisheries represent two essential water sources for humans. Despite the growing accessibility of metagenomic approaches, their routine use for water quality monitoring is still limited. Many key water resources have yet to be fully characterized in terms of microbiome, pathobiome, and antimicrobial resistome. In this study, surface water samples were collected over one year from the artificial Lake Bidighinzu (drinking water supply) and the coastal lagoon Cabras (fisheries) located in the western Mediterranean area. Samples were analyzed for physical and chemical properties, and 16S rRNA gene amplicon and shotgun sequencing were used to characterize bacterial communities, pathobiomes, and antimicrobial resistomes. Physical and chemical properties were generally similar between sites, except for higher salinity in Cabras Lagoon. In Cabras Lagoon, richness of the bacterial community and pathobiome was generally higher in the largest trophic fraction (>20 μm), while in both sites the abundance of potentially pathogenic bacteria (PPB) increased at this fraction. PPB, including ESKAPE pathogens, were more abundant in Lake Bidighinzu. The overall antimicrobial resistome was similar across sites, with high-risk antimicrobial resistance genes (ARGs) such as emrB prevalent. Lake Bidighinzu also had more contigs where ARGs co-occurred with mobile genetic elements. This study highlights microbiological risks in two aquatic systems, particularly Lake Bidighinzu, and underscores the need to integrate metagenomic approaches, possibly with cultivation-based methods, to monitor water quality and assess health risks in drinking water supplies and fisheries.}, } @article {pmid42019341, year = {2026}, author = {Zhao, Y and Chen, Y and Dang, Z and Li, K and Zhu, Y and Xu, C and Wan, X and Jia, B and Cao, G and Shen, Q and Zhao, Z}, title = {Metagenomic and transcriptomic insights into microbial activity maintenance strategies in a pilot-scale biosorption-biodegradation system for in situ sewer overflow treatment.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129750}, doi = {10.1016/j.jenvman.2026.129750}, pmid = {42019341}, issn = {1095-8630}, mesh = {*Sewage ; Biodegradation, Environmental ; *Waste Disposal, Fluid ; Transcriptome ; Metagenomics ; }, abstract = {Sewer overflow is a widely recognized issue in urban water environment pollution. Traditional in situ treatment technologies based on filtration and flocculation often fail to remove soluble pollutants effectively. Conventional in situ biological systems also struggle to maintain activity under fluctuating and nutrient-imbalanced influent conditions. Here, a compact in situ biological treatment process based on biosorption-biodegradation technology with a shortened hydraulic retention time (HRT) is proposed. During a 180-day pilot-scale experiment integrating ballasted flocculation, the system achieved average removal efficiencies of 75-94% for CODCr, NH4[+]-N, TP, BOD5, and SS. Effluent concentrations met Chinese surface water quality standards. The system maintained stable performance during wet weather events and after multiple dry periods of up to 30 days, demonstrating effective microbial activity maintenance. Based on the metagenomic and transcriptomic analyses, this stability is potentially related to nutrient supplementation through carbon metabolism of mixotrophic organisms and pollutant adsorption by biosorption sludge. Additionally, the reduced HRT prevents endogenous respiration and sludge degradation. The compact biosorption-biodegradation process offers an efficient and space-saving strategy for maintaining microbial activity during dry periods. It provides a promising solution for mitigating sewer overflow pollution in high-density urban areas.}, } @article {pmid42019423, year = {2026}, author = {Xu, C and Feng, Y and He, S and Wu, M and Hu, S}, title = {Mining of FDRs-carrying microbes involved in aflatoxin B1 degradation.}, journal = {Food chemistry}, volume = {515}, number = {}, pages = {149316}, doi = {10.1016/j.foodchem.2026.149316}, pmid = {42019423}, issn = {1873-7072}, mesh = {*Aflatoxin B1/metabolism ; Biotransformation ; *Bacterial Proteins/metabolism/genetics ; *Mycobacterium/metabolism/genetics/isolation & purification/classification/enzymology ; *Oxidoreductases/metabolism/genetics ; Biodegradation, Environmental ; Animal Feed/microbiology/analysis ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Phylogeny ; }, abstract = {Aflatoxin B1 (AFB1), a potent hepatocarcinogenic mycotoxin commonly found in food and feed, poses significant threats to food safety and public health. Microbes reduce AFB1 via biotransformation, so mining degrading strains is key. In this study, a novel AFB1 degrader, Mycobacterium sp. strain HM-7, was isolated from an AFB1-degrading bacterial consortium (designated A-2). Genomic analysis of the reconstructed metagenome-assembled genome (MAG) 12 and strain HM-7 revealed six putative F420H2-dependent reductases (FDRs), which are essential for the biotransformation of AFB1. When strain HM-7 was applied to animal feed, it achieved a significant reduction in AFB1 levels. Furthermore, bioinformatics mining based on the Genome Taxonomy Database (GTDB) identified a wide diversity of FDRs-carrying microbes involved in AFB1 degradation, mainly those belonging to the phylum Actinomycetota, highlighting their potential for bioremediation applications. This study provides valuable insights into the diversity of FDRs-carrying microbes involved in AFB1 degradation.}, } @article {pmid42019451, year = {2026}, author = {Wei, ZW and Li, HQ and Wang, XH and Yang, XR and Su, JQ}, title = {Non-biodegradable microplastics amplify antibiotic resistance and pathogen spread in bay plastisphere.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142147}, doi = {10.1016/j.jhazmat.2026.142147}, pmid = {42019451}, issn = {1873-3336}, mesh = {*Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; *Bacteria/genetics/drug effects ; Humans ; Virulence Factors/genetics ; }, abstract = {Microplastics (MPs) serve as reservoirs that facilitate the dissemination of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs), posing significant threats to public health. However, quantitative evaluations of high-risk ARGs in the plastisphere and comprehensive assessments of their associated health implications are still scarce. In this study, we employed in-situ incubation combined with high-throughput quantitative PCR and metagenomic sequencing to systematically compare the prevalence of ARGs, virulence factor genes (VFGs), mobile genetic elements (MGEs), and HBPs between biodegradable and non-biodegradable MPs. Our findings revealed a marked enrichment of ARGs, VFGs, MGEs, and HBPs in non-biodegradable MPs (polypropylene, polyethylene, and polystyrene) relative to the biodegradable MPs (polyhydroxyalkanoates, polylactic acid, and polybutylene adipate terephthalate). Furthermore, an integrated risk assessment combining high-risk ARGs quantification with a Projection Pursuit Regression model revealed significantly elevated microbial risks associated with non-biodegradable MPs. Taxonomic analysis further indicated that Pseudomonas and Aeromonas act as key HBP vectors carrying ARGs and VFGs in the plastisphere, underscoring their role in facilitating the spread of antimicrobial resistance and virulence. These results highlight how plastic properties mediate microbial colonization patterns under complex field conditions, providing a robust framework for environmental risk evaluation and the targeted management of plastic-associated biological hazards.}, } @article {pmid42019469, year = {2026}, author = {Peng, F and Zeng, YY and Chang, L and Huang, YX and Deng, JT and Liu, YX and He, X and Song, ZH}, title = {Gut microbiota-derived taurolithocholic acid modulates myofiber-type switching via p38 MAPK/PGC-1α signaling underlying breed differences between Arbor Acres and Taoyuan chickens.}, journal = {Poultry science}, volume = {105}, number = {7}, pages = {106914}, pmid = {42019469}, issn = {1525-3171}, mesh = {Animals ; *Chickens/genetics/growth & development/physiology/microbiology ; *Gastrointestinal Microbiome/physiology ; Signal Transduction ; *Taurine/metabolism/analogs & derivatives ; p38 Mitogen-Activated Protein Kinases/metabolism/genetics ; *Avian Proteins/metabolism/genetics ; *Muscle Fibers, Skeletal/physiology ; Pectoralis Muscles/growth & development/physiology ; Male ; *Muscle Development ; }, abstract = {It is well-established that the gut microbiota plays a crucial role in skeletal muscle development and homeostasis. However, the contribution of the gut microbiome to the distinct meat quality phenotypes observed between fast-growing commercial broilers and slow-growing local chicken breeds remains poorly understood. Therefore, this study aims to elucidate how the gut microbiota modulates pectoral muscle development by comparing muscle growth phenotypes and gut microbiome dynamics across these breeds. Using the fast-growing commercial Arbor Acres (AA) broiler and the slow-growing local breed Taoyuan (TY) chicken as models, we investigated how breed-specific gut microbiota modulate pectoral muscle fiber composition. AA broilers exhibited faster muscle growth but lower oxidative type I fiber proportion than TY chickens. While small intestinal microbiota succession was similar, cecal communities diverged markedly between breeds. Integrated metagenomic sequencing and metabolomics revealed that cecal Phocaeicola dorei abundance was strongly correlated with serum taurolithocholic acid (TLCA) levels and type I fiber content, especially in TY chickens, which prompted the selection of TLCA for functional validation. Reciprocal intestinal microbiota transplantation (IMT) shifted recipient muscle fiber phenotypes toward those of donors, confirming a causal role of the cecal microbiota. Furthermore, in vitro assays using AA-derived myoblasts demonstrated that TLCA promotes mitochondrial biogenesis and type I fiber formation by enhancing p38 MAPK phosphorylation and PGC-1α activation; this effect was abolished by the p38 inhibitor SB203580. Our study demonstrated that gut microbiota-derived TLCA modulates muscle fiber type transformation via the p38 MAPK/PGC-1α signaling pathway. This finding reveals an intricate mechanism whereby the gut microbiota regulates host muscle development through a metabolite-signaling axis, providing critical insights into the gut microbe-myofiber relationship.}, } @article {pmid42019695, year = {2026}, author = {Liu, X and Wang, H and Zhou, S and Xie, Y and Wang, J and Wang, X and Xu, S and Wang, L and Jiang, C and Zhuang, X}, title = {Nanobubbles drive advanced anaerobic treatment of swine wastewater for efficient methane recovery: Performance gains and multi-pathway enhancement.}, journal = {Bioresource technology}, volume = {453}, number = {}, pages = {134692}, doi = {10.1016/j.biortech.2026.134692}, pmid = {42019695}, issn = {1873-2976}, mesh = {Animals ; *Methane/isolation & purification/biosynthesis ; Anaerobiosis ; *Wastewater/chemistry/microbiology ; Swine ; *Water Purification/methods ; Oxygen ; }, abstract = {Swine wastewater contains recoverable energy, but anaerobic digestion is often limited by complex organics and slow hydrolysis. To overcome this limitation, this study introduced nanobubble technology using three gas media (air, O2, and O3) and systematically studied their effects on methane recovery during the anaerobic digestion of swine wastewater. Batch experiments showed that O3 nanobubbles achieved the strongest enhancement, increasing cumulative methane production by 87.5% compared with the control. This improvement may result from the strong oxidative capacity of O3 nanobubbles to degrade recalcitrant organics, as indicated by the second methane production peak observed only in the O3 nanobubbles. In contrast, O2 nanobubbles provided the weakest improvement, potentially because excess dissolved oxygen stimulated facultative aerobic respiration, converting substrates to CO2 and lowering availability for methanogenesis. Further analysis revealed that all nanobubble treatments accelerated volatile fatty acid turnover and enriched key hydrolytic and acidogenic microbes, particularly under O3 nanobubbles. The enrichment of Methanothrix and downregulation of the energy-intensive PilA gene suggest promoted electron transfer. Negatively charged nanobubbles may act as abiotic mediators that facilitate direct interspecies electron transfer. Metabolic analysis indicated enhanced hydrogenotrophic, methylotrophic, and acetoclastic methanogenesis, implying strengthened synergy among pathways. Overall, O3 nanobubbles show promise for resource recovery from organic waste.}, } @article {pmid42019770, year = {2026}, author = {Xie, M and Kong, L and Hou, L and Chen, Y and Hou, J}, title = {Atopic dermatitis: Multi-omics insights into microbiota-driven modulation of the gut-skin axis.}, journal = {Microbial pathogenesis}, volume = {216}, number = {}, pages = {108504}, doi = {10.1016/j.micpath.2026.108504}, pmid = {42019770}, issn = {1096-1208}, mesh = {Humans ; *Dermatitis, Atopic/microbiology/therapy/genetics/immunology ; Multiomics ; *Gastrointestinal Microbiome/physiology ; *Skin/microbiology/pathology ; Fecal Microbiota Transplantation ; Animals ; Metagenomics ; Fatty Acids, Volatile/metabolism ; Metabolomics ; Receptors, Aryl Hydrocarbon/metabolism ; Skin Microbiome ; }, abstract = {Atopic dermatitis (AD) is a heterogeneous inflammatory skin disease resulting from complex interactions among host genetics, immune dysregulation, and microbial imbalance. Recent advances in multi-omics technologies have revealed distinct AD endotypes characterized by specific genetic variants, microbial enterotypes, and metabolite profiles. Emerging evidence highlights the gut-skin axis as an important regulatory pathway, in which alterations in gut microbiota influence the production of key microbial metabolites, including short-chain fatty acids (SCFAs) and tryptophan-derived aryl hydrocarbon receptor (AHR) ligands, thereby modulating Th2-dominant inflammatory responses. Integrated analyses combining metagenomics, metabolomics, and single-cell transcriptomics have further identified endotype-specific signatures, such as Bacteroides-enriched profiles associated with lipopolysaccharide-driven inflammation and Prevotella-dominant clusters linked to enhanced AHR activation and epithelial barrier repair. These findings provide a basis for precision stratification and the development of targeted therapeutic strategies, including genotype-guided biologics, microbiota modulation, engineered probiotics, phage therapy, and fecal microbiota transplantation. This review summarizes current evidence integrating host genetics, microbiota networks, and multi-omics biomarkers to provide a comprehensive framework for understanding AD endotypes and to highlight potential avenues for precision diagnosis and targeted interventions.}, } @article {pmid42020064, year = {2026}, author = {Peters, BA}, title = {Evidence grows for the gut-kidney axis, but questions still remain.}, journal = {Kidney international}, volume = {109}, number = {5}, pages = {832-834}, doi = {10.1016/j.kint.2026.02.015}, pmid = {42020064}, issn = {1523-1755}, mesh = {Humans ; *Kidney/physiology/microbiology ; *Gastrointestinal Microbiome ; Metabolomics ; Metagenomics ; *Kidney Diseases/microbiology ; }, abstract = {Lin et al. presented the largest cross-sectional study to date on the gut microbiome and kidney health. Their use of a vast sample size, discovery and validation approach, shotgun metagenomics, and integration with serum metabolomics represents a significant advance. In this commentary, we place these new findings into context with prior research and highlight the need for studies with a prospective design to identify true temporal relationships of the gut microbiome with kidney health.}, } @article {pmid42020421, year = {2026}, author = {Shahzadi, I and Xue, W and Ubaid Ullah, H and Maddamsetti, R and You, L and Wang, T}, title = {Integrating theory and machine learning to reveal determinants of plasmid copy number.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42020421}, issn = {2041-1723}, support = {12401660//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470701//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Plasmids are extrachromosomal mobile genetic elements whose copy numbers (PCNs) critically influence microbial evolution, antibiotic resistance and pathogenicity. Despite their importance and immense diversity, the ecological, evolutionary and molecular factors determining PCN remain poorly understood. Here, we present a theoretical model to explain the empirical power-law relationship between plasmid size and copy number, one of the fundamental quantitative principles governing PCN control. However, this relationship alone has limited predictive power. To improve PCN prediction, we introduce a data-driven approach incorporating diverse features. Trained and tested on 11,051 plasmids, our machine learning model achieves significantly enhanced accuracy, with plasmid-encoded protein domains emerging as key predictors. Applying this framework, we conduct a large-scale analysis of PCN distributions across hundreds of thousands of metagenomic plasmids (IMG/PR database) and tens of thousands of clinical isolates, revealing putative niche specific taxonomic PCN hotspots and hypothesis-generating ecological trends. These results provide valuable insights into plasmid ecology, antibiotic resistance genes (ARGs) surveillance and shed lights on the gut plasmidome, a "dark matter" in human microbiome.}, } @article {pmid42020426, year = {2026}, author = {Seki, D and Pollak, S and Kujawska, M and Kiu, R and Acuna-Gonzalez, A and Crouch, LI and Bakshani, CR and Chivers, PT and Mommers, M and van Best, N and Penders, J and Hall, LJ}, title = {Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42020426}, issn = {2041-1723}, support = {220876/Z/20/Z//Wellcome Trust (Wellcome)/ ; }, mesh = {Humans ; *Milk, Human/chemistry/metabolism ; *Escherichia coli/genetics/metabolism/growth & development/physiology ; *Oligosaccharides/metabolism ; *Bifidobacterium bifidum/genetics/physiology/metabolism/growth & development ; *Symbiosis ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/physiology ; Trisaccharides/metabolism ; Infant ; Infant, Newborn ; Breast Feeding ; }, abstract = {Infant gut microbiota development involves frequent colonization by Enterobacteriaceae, particularly Escherichia coli, yet their ecological role in healthy infants is unclear. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed infants (n = 41) and related mothers (n = 30) using shotgun metagenomics and novel computational approaches. Strain-resolved profiling indicates that Bifidobacterium species are frequently shared within families, whereas E. coli derive from external sources, but often persist within individuals. Despite differing ecological strategies, these genera co-exist and share evolutionary adaptations related to lactose acquisition in the infant gut. In vitro, we demonstrate that interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner, facilitating cooperative degradation of 2'-fucosyllactose, the predominant human milk oligosaccharide. In turn, the liberated monosaccharides sustain E. coli growth, highlighting a cooperative cross-feeding interaction that may contribute to regulating E. coli abundance within the infant host.}, } @article {pmid42020430, year = {2026}, author = {Zhou, L and Li, D and Huang, Y and Kang, J and Lu, Y and Zhang, L and Liu, SQ}, title = {Lactiplantibacillus plantarum-mediated modulation of volatile flavor and quality in low-salt spontaneously fermented yellow capsicum sauce.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00854-z}, pmid = {42020430}, issn = {2396-8370}, support = {32302036//National Natural Science Foundation of China/ ; NHXXRCXM202312//'Nan Hai Xin Xing' Science and Technology Innovation Talent Platform Project Funding of Hainan Province, China/ ; 202407560053//China Scholarship Council/ ; KYQD(ZR)-21122//Scientific Research Foundation of Hainan University, China/ ; }, abstract = {Yellow capsicum sauce (YCS) is a special fermented condiment in Hainan province, China, and its fermentation typically occurs in a high-salt environment. In this study, the effects of different salt contents (5, 10, 15, and 20%, w/w) on microbial communities and volatile flavor profiles in YCS were systematically investigated by metagenomic approach and HS-SPME-GC-MS. The results revealed that Lactiplantibacillus (54.66%) was the dominant genus in low-salt samples (SF5), while its abundance was less than 6% in higher salinity levels (SF15 and SF20). A total of 48 volatile flavor compounds (VFCs) were detected in the naturally fermented YCS, with alcohols and esters being the primary VFCs. Low-salt fermentation facilitated the accumulation of VFCs, and the total VFCs content in SF5 was the highest. Aroma compounds showed a strong correlation with Lactiplantibacillus plantarum. To further validate the findings, L. plantarum MA1 isolated from SF5 was inoculated into the low-salt YCS substrate for bioaugmented fermentation. This strain significantly increased key aroma components, such as cis-3-hexenyl isovalerate, hexyl 3-methylbutanoate, and ethyl acetate. Moreover, it significantly increased the lactic acid content while reducing the nitrite content, thereby more effectively preserving the fresh yellow color of capsicum sauce and the stability of its spiciness.}, } @article {pmid42020464, year = {2026}, author = {Bergo, NM and Peres, FV and Vieira, DC and Modolon, F and Moreira, JCF and Lizárraga, RGM and Romano, RG and Bendia, AG and Lemos, LN and de Moura Emilio, A and Amendola, AM and Castano, DCD and Chuqui, MG and Paula, FS and Brandão, WSG and Fonseca, G and Vasconcelos, ATR and Jonck, CR and Moreira, DL and Brandini, FP and Pellizari, VH}, title = {Microbial signatures define the ecosystem functions of the pelagic microbiome in a basin-scale, Southwest Atlantic Ocean.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42020464}, issn = {2045-2322}, support = {5850.0109317.18.9 and 21167-2//Petróleo Brasileiro S.A. (PETROBRAS)/ ; E-26/201.046/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Atlantic Ocean ; *Microbiota/genetics ; *Ecosystem ; Metagenomics/methods ; *Seawater/microbiology ; *Bacteria/genetics/classification ; Metagenome ; Water Microbiology ; }, abstract = {The pelagic environment represents a mosaic of biogeographical domains shaped by regional oceanographic processes. Here, a coastal-to-open ocean microbiome investigation was conducted from 64 water samples of the Santos Basin (SB), located in the subtropical South Atlantic Ocean. We combined shotgun metagenomics with a hybrid machine learning workflow to investigate the taxonomic diversity, community structure, and ecosystem functions of pelagic microbiomes. The workflow integrated self-organizing maps (unsupervised) for pattern discovery and Random Forest (supervised) for predictive modeling. Unsupervised machine learning revealed a clear spatial and vertical (light-driven) distribution, with indicator taxa reflecting biogeochemical patterns consistent with global surveys. Supervised learning identified phosphate, salinity, and nitrate, influenced by local upwelling and La Plata River plume, as the primary environmental drivers of microbial community structure. In terms of functionality, the SB microbiome displayed depth- and region-specific patterns: photoautotrophs and nitrogen fixers dominated photic waters (with differences between coastal and oceanic stations), whereas chemolithoautotrophs and mixotrophs prevailed in the aphotic zone. Notably, nitrification signatures were more frequent in northern mesopelagic communities, while sulfur-oxidation pathways were enriched toward the south. Genes for CO bio-oxidation and dimethylsulfoniopropionate (DMSP) degradation were present across all depths. Furthermore, potential non-cyanobacterial diazotrophs were detected in the deep waters, underscoring previous underappreciated to nitrogen cycling. Our findings indicated that the Santos Basin hosts a functionally diverse microbiome including putative novel lineages. The taxonomic and functional patterns observed in the SB might provide insights into potential ecological responses to shifts in nutrient dynamics and physical processes. This investigation provides an ecogenomic baseline for understanding the microbial ecosystem services in subtropical oceans and reveals the potential of machine learning to uncover ecological patterns in underexplored marine regions.}, } @article {pmid42020676, year = {2026}, author = {Purohit, HV and Chakraborty, J and Kothari, RK and Bhatt, AR}, title = {Gene Exchange Mechanisms in Natural and Engineered Probiotics Within the Human Gut Implications for Antibiotic Resistance and Metabolic Modulation.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42020676}, issn = {1867-1314}, abstract = {The human gut microbiome is a dynamic and densely populated ecosystem where microbial gene exchange plays a central role in shaping both ecological interactions and host physiology. This review critically examines the mechanisms and implications of horizontal gene transfer (HGT) among natural and engineered probiotics within the human gut, with a specific focus on antibiotic resistance dissemination and metabolic modulation. We provide an in-depth analysis of the molecular pathways of conjugation, transformation, and transduction under anaerobic gut conditions, highlighting their roles in the spread of mobile genetic elements, including antibiotic resistance genes (ARGs) and functional metabolic traits. Special emphasis is placed on the dual nature of gene exchange: while beneficial traits such as vitamin biosynthesis and polysaccharide degradation can be horizontally acquired to enhance probiotic efficacy and host-microbe symbiosis, the uncontrolled dissemination of ARGs or synthetic constructs poses significant clinical and ecological risks. Through a synthesis of recent findings from metagenomics, microbial ecology, and synthetic biology, we explore how natural probiotics may act as reservoirs of ARGs, and how engineered strains—if not properly contained—may contribute to genetic instability in the gut. We also evaluate current containment strategies such as chromosomal integration, kill switches, auxotrophy, and orthogonal circuit design to limit horizontal spread, alongside emerging tools for in situ gene transfer monitoring. Finally, we discuss regulatory challenges and propose a context-dependent risk assessment framework in which the consequences of probiotic gene exchange are determined by cargo properties, host ecological niche, gut inflammatory status, and biocontainment design.}, } @article {pmid42020750, year = {2026}, author = {Grieshop, MP and Behr, AA and Bowden, S and Lin, JD and Molari, M and Reynolds, GZ and Brooks, EF and Doyle, B and Moore, AA and Rodriguez-Nava, G and Salinas, JL and Banaei, N and Bhatt, AS}, title = {Transposable elements are driving rapid adaptation of Enterococcus faecium.}, journal = {Nature}, volume = {653}, number = {8116}, pages = {1139-1147}, pmid = {42020750}, issn = {1476-4687}, mesh = {*Enterococcus faecium/genetics/pathogenicity/isolation & purification ; *DNA Transposable Elements/genetics ; Humans ; Genome, Bacterial/genetics ; *Adaptation, Physiological/genetics ; Metagenome/genetics ; Promoter Regions, Genetic/genetics ; Feces/microbiology ; }, abstract = {Bacterial pathogens adapt rapidly to clinical and within-host selective pressures[1]. Insertion sequences (IS) are transposable elements that can contribute to pathogenic adaptation[2], but their activity and consequences in contemporary clinical populations are not well characterized. Here, combining large-scale genomic surveys with long-read sequencing of clinical isolates and longitudinal gut metagenomes, we quantify pathogen IS dynamics from global patterns to within-host evolution. Across 19,485 publicly available high-contiguity ESKAPEE pathogen genomes, Enterococcus faecium genomes are the most IS dense, dominated by replicative ISL3 family elements, which have proliferated in clinical lineages over the past 30 years. We find extensive chromosomal structural variation, largely involving ISL3, within a new single-hospital collection of bloodstream isolates. Long-read metagenomic sequencing of 28 longitudinal stool samples from 12 haematopoietic cell transplantation (HCT) recipients demonstrates within-host IS dynamics and their regulatory consequences. In one patient, an ISL3 insertion upstream of a folate transporter formed a strong promoter, increasing transcription and improving relative fitness under folate limitation. Enhanced folate scavenging may enable E. faecium to thrive in the setting of microbiome collapse, which is common in HCT and other critically ill patients[3]. Together, these results show that a recent ISL3 expansion is driving rapid evolution in healthcare-associated E. faecium, with consequences for its metabolic fitness that may help explain its increasing clinical burden. Several other pathogens also show elevated IS loads in our survey, which suggests that IS expansion-mediated evolution might be more broadly relevant.}, } @article {pmid42020953, year = {2026}, author = {Flatau, R and Bickley, CD and Altamia, MA and Gasser, MT and Distel, DL}, title = {Metabolic potential structures gill symbiont communities in two common shipworm species.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42020953}, issn = {1751-7370}, mesh = {Animals ; *Symbiosis ; *Gills/microbiology ; Phylogeny ; *Bivalvia/microbiology ; *Bacteria/genetics/classification/metabolism/enzymology ; Metagenome ; Sequence Analysis, DNA ; }, abstract = {Shipworms (Bivalvia: Teredinidae) are the most prolific wood consumers in marine environments. These wormlike marine bivalves digest wood using carbohydrate-active enzymes (CAZymes) produced by intracellular bacterial endosymbionts housed within their gills. Although several shipworm species are known to host multiple co-occurring symbiont species, the factors that influence symbiont community assembly, including the phylogenetic identity and metabolic capabilities of the symbionts, remain poorly understood. We sequenced gill symbiont metagenomes from multiple specimens of two shipworm species, Teredo bartschi (22 specimens) and Lyrodus pedicellatus (14 specimens), which have sympatric distribution in the wild, and which were reared together in laboratory co-culture. From these metagenomes, we assembled 90 metagenome-assembled genomes representing seven distinct symbiont species. The metagenome of each host specimen contained between one and five symbiont species, with each including at least one nitrogen-fixing symbiont. Six of the seven identified symbiont species were found in both host species, demonstrating a lack of host species specificity in these symbioses. We identified patterns of symbiont occurrence and co-occurrence in these two hosts and used these patterns to constrain the core set of CAZyme and nitrogen-fixation gene classes necessary to support host survival. Our results indicate that, in these two host species, symbiont community composition reflects the symbionts' capabilities for carbohydrate degradation and nitrogen fixation, rather than strict species-specific mechanisms of host and symbiont sorting.}, } @article {pmid42021075, year = {2026}, author = {Ishikawa, R and Nakamura, M and Sakurai, A and Nakayama-Imaohji, H and Kuwahara, T and Ichimura-Shimizu, M and Shishibori, M and Kataoka, K}, title = {Influences of ampicillin exposure in early life on the murine gut microbiota and steatotic liver disease associated with western diet.}, journal = {The journal of medical investigation : JMI}, volume = {73}, number = {1.2}, pages = {186-207}, doi = {10.2152/jmi.73.186}, pmid = {42021075}, issn = {1349-6867}, mesh = {Animals ; *Ampicillin/adverse effects ; *Diet, Western/adverse effects ; Female ; *Fatty Liver/etiology ; Mice, Inbred C57BL ; Mice ; *Anti-Bacterial Agents/adverse effects ; *Gastrointestinal Microbiome/drug effects ; Dysbiosis ; Male ; Feces/microbiology ; }, abstract = {Dysbiosis of gut microbiota is one of the important factors associated with metabolic dysfunction-associated steatotic liver disease (MASLD). Antibiotic use, especially in early life, could profoundly disrupt an establishing process of stable gut microbiota, and the influence on gut environment may persist throughout life. In this study, we examined effects of ampicillin exposure (AMP) in early life on the temporal changes of fecal microbiota and severity of MASLD in western diet-fed C57BL/6J mice. Histological evaluation of MASLD showed that steatosis in female mice and lobular inflammation was significantly influenced with AMP, and that NAS (MASLD activity score constituting from score of steatosis, lobular inflammation, and ballooning degeneration) tended to be high in female of AMP-treated group. 16S metagenome analyses of fecal microbiota showed significant decrease of α-diversity and remarkable shift to normally minor bacterial species at 4 weeks of age in AMP-treated mice, and the influence was continuously observed even after finishing the western diet feeding period. α-Diversity at 4weeks of age negatively correlated with combined scores of steatohepatitis and fibrosis. These results suggest that AMP in early life induced dysbiosis of gut microbiota and could promote the development of western diet-associated steatotic liver disease. J. Med. Invest. 73 : 186-207, February, 2026.}, } @article {pmid42021418, year = {2026}, author = {Ravi, A and Shestivska, V and Thiago Dobbler, P and Sechovcová, H and Maixnerová, M and Semerád, J and Nehasilová, A and Vadroňová, M and Odriozola, I and Šubrtová Salmonová, H and Větrovský, T and Musilová, Š and Cajthaml, T and Pěchoučková, E and Nemec, A and Kyselková, M}, title = {Cattle feces are a reservoir of diverse Acinetobacter species with potential to spread antibiotic resistance genes.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42021418}, issn = {2524-4671}, abstract = {BACKGROUND: Antibiotic resistance poses a major threat to human health, with antibiotic use in livestock contributing to the selection and spread of resistance genes. The genus Acinetobacter includes human- and animal-associated species capable of acquiring resistance, yet their diversity and resistance potential in livestock remain far less explored than in humans. In this study, we investigated Acinetobacter in cattle feces from 28 Czech farms with contrasting antibiotic use, aiming to assess species composition, resistance profiles, and the potential for resistance dissemination. We applied an integrative approach combining strain isolation and characterization, enrichment cultures, metabarcoding, and shotgun metagenomics.

RESULTS: Cattle feces harbored diverse Acinetobacter species with A. indicus and A. pseudolwoffii being the core species based on both isolated strains and metabarcoding, while A. baumannii was less common. Acinetobacter species occurrence determined by metabarcoding was driven by multiple factors, including production type, herd size, and per-head antibiotic use, while their abundance was mostly influenced by sample type (higher in feces from the farm floor than in rectal samples) and production type (higher in dairy than in beef cattle). Remarkably, 37% of the 284 isolated strains could not be assigned to validly named species and represent at least 19 putative novel species. Decreased susceptibility due to acquired resistance was observed in 57 strains; notably, A. indicus and A. pseudolwoffii from antibiotic-using farms were less susceptible to streptomycin than those from antibiotic-free farms. Shotgun metagenomics revealed a greater richness of acquired resistance genes in antibiotic-using farms, including the clinically relevant carbapenemase gene blaOXA-58. This gene was located on putative plasmid contigs alongside streptomycin resistance determinants strA-strB, suggesting horizontal dissemination under streptomycin selection pressure. Strain analysis confirmed the co-localization of blaOXA-58 and strA-strB on a large plasmid in A. pseudolwoffii.

CONCLUSIONS: Despite relatively strict regulations, Czech cattle farms constitute a reservoir of antibiotic-resistant Acinetobacter carrying mobile resistance genes of clinical concern. Commonly applied antibiotics likely co-select for such genes, posing an ongoing public health risk. Our findings reveal an unexpectedly high diversity of Acinetobacter spp. in cattle, highlighting the research bias toward human-associated species and underscoring the need for integrated One Health monitoring approaches.}, } @article {pmid42021724, year = {2026}, author = {Batra, N and Rout, PR and Dey, P}, title = {Modulation and adaptation of gut microbial metabolic functions under probiotic and postbiotic treatment using a novel in vitro anaerobic pseudo-colon system.}, journal = {Food & function}, volume = {17}, number = {9}, pages = {4245-4261}, doi = {10.1039/d5fo04976h}, pmid = {42021724}, issn = {2042-650X}, mesh = {*Probiotics/pharmacology ; Humans ; *Butyrates/pharmacology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Bacteria/classification/genetics/metabolism/isolation & purification ; Lactiplantibacillus plantarum/physiology ; Anaerobiosis ; *Colon/microbiology/metabolism ; Amino Acids/metabolism ; }, abstract = {Probiotic and postbiotic compounds found in food influence gut microbiota to attenuate chronic metabolic diseases; however, the underlying mechanisms are not yet fully understood. This study employed a customized in vitro anaerobic pseudo-colon system (AMMR) to evaluate the impacts of Lactiplantibacillus plantarum (probiotic) and butyrate (postbiotic) on gut microbial composition and functionality, using human fecal samples. Metagenomic (16S rRNA) profiling and untargeted metabolomic (GC-MS) analysis were conducted after 48 h treatments. The results showed that butyrate supplementation markedly enhanced microbial diversity, inhibited opportunistic pathobionts (e.g., Enterococcus and Klebsiella), and selectively enriched butyrate producers (e.g., Lachnoclostridium), while diminishing the Firmicutes : Bacteroidetes ratio. It increased indole levels metabolically and redirected pathways towards amino acid synthesis and energy metabolism, while suppressing fatty acid formation. In contrast, L. plantarum exhibited modest alterations in microbial diversity while enhancing Bacteroides and Klebsiella and preserving elevated Enterococcus levels. It elevated saturated fatty acids (octanoic/capric acid) and enhanced amino acid catabolic pathways (valine/leucine) and redox regulators (taurine metabolism). Correlation analysis revealed that butyrate was associated with fiber-degrading microbes, whereas L. plantarum was associated with lactic acid bacteria, suggesting distinct ecological niches and interaction patterns. These findings collectively indicate that butyrate and L. plantarum elicit complementary microbial alterations, i.e., butyrate directly transforms the microbial structure and metabolism towards an anti-inflammatory phenotype, while L. plantarum largely influences via metabolic byproducts and niche adjustment. The complementary actions highlight the therapeutic potential of integrated probiotic-postbiotic approaches for the enhancement of gut health.}, } @article {pmid42021875, year = {2026}, author = {Li, H and Song, Z and Zhao, Y and Li, M}, title = {[Advances in the Application of Artificial Intelligence in Clinical Microbiological Testing].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {2}, pages = {313-318}, pmid = {42021875}, issn = {1672-173X}, mesh = {*Artificial Intelligence ; Humans ; *Microbiological Techniques/methods ; Algorithms ; Machine Learning ; }, abstract = {Traditional microbiological detection methods have inherent limitations in detection speed, sensitivity, and specificity, making them increasingly unable to meet growing clinical demands. In recent years, artificial intelligence (AI) has been rapidly integrated into clinical microbiological testing, with numerous studies demonstrating its significant potential to enhance pathogen identification, predict antimicrobial susceptibility testing, and advance laboratory automation. This article systematically reviews classical AI algorithms and their latest advancements in this field. For visual data applications, deep learning-based models are used to automatically analyze microscopy images or colony morphology, significantly improving recognition efficiency and diagnostic accuracy. For non-visual data, AI has achieved breakthroughs in analyzing multi-omics data such as genomics, transcriptomics, and metagenomics, and is widely used for rapid pathogen identification and prediction of antimicrobial resistance. Despite its promising prospects, the application of AI in clinical microbiological testing remains in the early stages of transitioning from scientific research to clinical practice. This paper further discusses the key challenges and opportunities encountered during this technological translation, aiming to help clinical professionals comprehensively understand the current status, future trends, and potential impact of AI in this field, thereby promoting its development into reliable and scalable routine diagnostic methods.}, } @article {pmid42021890, year = {2026}, author = {Zhang, W and Zhong, S and Lu, S and Xiao, X and Xie, Y}, title = {[Diagnostic Performance of Metagenomic Next-Generation Sequencing for Mucormycosis: A Retrospective Cohort Study].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {2}, pages = {411-418}, pmid = {42021890}, issn = {1672-173X}, mesh = {*Mucormycosis/diagnosis/microbiology ; Humans ; Retrospective Studies ; *Mucorales/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Male ; Sensitivity and Specificity ; ROC Curve ; Middle Aged ; Adult ; }, abstract = {OBJECTIVE: Mucormycosis is a life-threatening invasive fungal infection with high mortality, yet traditional diagnostic methods are limited by low positivity rates. This study aims to evaluate the diagnostic performance and clinical utility of metagenomic next-generation sequencing (mNGS) in mucormycosis.

METHODS: A retrospective analysis was conducted on 135 patients with mNGS results positive for Mucorales fungi at West China Hospital of Sichuan University from November 1, 2022, to October 31, 2024. Based on comprehensive clinical diagnostic criteria (including proven and probable cases), patients were classified into a confirmed mucormycosis group and a non-mucormycosis group. Receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic performance of normalized read counts (lgRPM) from different specimen types. Fungal species distribution and laboratory parameters were compared between the two groups.

RESULTS: Among the 135 patients with positive mNGS results for Mucorales, 100 (74.1%) were ultimately diagnosed with mucormycosis. ROC curve analysis revealed that the diagnostic performance of mNGS varied by specimen type. For blood specimens, the area under the curve (AUC) was 0.772, with a specificity of 87.5% at the optimal cutoff value of 0.11 RPM. For bronchoalveolar lavage fluid specimens, the AUC was 0.717, with a sensitivity of 76.5% at the optimal cutoff value of 0.02 RPM. Combined analysis of all specimens showed that at the optimal cutoff value of 0.08 RPM (approximately 8 reads/100M), the sensitivity and specificity were 62.0% and 71.4%, respectively. Species distribution analysis showed that the proportions of Cunninghamella elegans (11.0% vs. 2.9%) and Rhizomucor pusillus (9.0% vs. 2.9%) were significantly higher in the confirmed group than in the non-mucormycosis group (P < 0.05). Levels of C-reactive protein and interleukin-6 were also significantly higher in the confirmed group (P < 0.05). Notably, all seven renal perfusion fluid samples yielded false-positive mNGS results.

CONCLUSION: mNGS technology can effectively improve the diagnostic yield for mucormycosis. However, results should be interpreted in conjunction with specimen type, read count, and clinical characteristics. BALF specimens offer high sensitivity, making them suitable for screening, while blood specimens demonstrate high specificity, making them valuable for confirmation. Positive results from low-biomass samples such as renal perfusion fluid warrant caution against false positivity. Fungal species identification and inflammatory markers may serve as adjunctive evidence for clinical diagnosis.}, } @article {pmid42022012, year = {2026}, author = {Conrad, RE and Rodriguez-R, LM and Lindner, BG and Gerhardt, K and Konstantinidis, KT}, title = {An ANIr-based methodology to determine if two sequence-discrete populations are identical and identify cosmopolitan prokaryotic populations.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag068}, pmid = {42022012}, issn = {2730-6151}, abstract = {Although sequence-discrete species appear to dominate microbial communities, readily distinguishing between distinct populations of a species recovered from different short-read metagenomic samples is challenging due to technical limitations associated with read length. To close this gap, we developed a novel algorithm to evaluate which reads in a metagenome belong to a target population based on the distribution of sequence identities of reads aligned to a reference sequence, which are filtered using a Kernel density estimation (KDE) as a flexible alternative to the commonly used static 95% nucleotide identity cutoff. Subsequently, we employed the average nucleotide identity of reads (ANIr) aligning above the KDE threshold, and resampling techniques for estimating the confidence intervals of ANIr values, to quantify intrapopulation sequence diversity and compare populations across globally representative marine samples. Most populations showed high ANIr in only a few samples at similar depths and decreased ANIr and increased gene-content difference between samples where a closely related population is detected (e.g. same 95% ANI-based species). Accordingly, ANIr correlated with the physical distance between the samples, and only a few truly cosmopolitan populations were identified. Among the latter, Alteromonas macleodii [97% average amino-acid identity (AAI) to the type genome] and Prochlorococcus marinus (79% AAI) showed high relative abundance in both surface (0-200 m) and deep (>1000 m) samples. These results suggest that microbial communities under different environmental conditions share very few identical and abundant populations and provide a highly needed methodology to track such populations over space and time, in marine or other habitats.}, } @article {pmid42022013, year = {2026}, author = {Franco, MEE and Singer, E and Roux, S and Meredith, LK and U'Ren, JM}, title = {Genomic and metagenomic survey of microbial carbonic anhydrase genes reveals novel clades, high diversity, and biome specificity.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag054}, pmid = {42022013}, issn = {2730-6151}, abstract = {Carbonic anhydrase (CA) enzymes catalyze the interconversion of carbon dioxide and bicarbonate with an efficiency exceeded only by superoxide dismutase. CA enzymes have evolved convergently in phylogenetically distant organisms, forming eight structurally unrelated classes that share physiological functions involved in photosynthesis, respiration, pH homeostasis, CO2 transport, and carbonyl sulfide hydrolysis that play central roles in medicine and the environment. Here, we leverage the recent surge in publicly available genomes and metagenomes to re-examine our understanding of the abundance, diversity, and phylogenetic relationships of the three major CA classes in Bacteria/Archaea and microbial Eukaryotes (Fungi, algae). We recovered a total of 57 218 α-, β-, and γ-CA sequences from 24 184 metagenomes and genomes, including the first putative α-CA from an archaeal species. CA sequences formed 3859 protein clusters (1188 with three or more sequences). Sequences within a cluster were typically taxonomically conserved only at higher levels (i.e. Superkingdom, Phylum). When viewed within a phylogenetic framework, the majority of subclades for each CA class contained CAs representing multiple Superkingdoms, although numerous novel β-CA clades appear unique to Fungi. Queries of CA Hidden Markov models against all public metagenome and metatranscriptome datasets revealed that CA is a ubiquitous enzyme present in virtually all sampled environments. However, CA clusters that were taxonomically conserved also appeared more environment-specific, which may explain high CA diversity. This work represents an important contribution to our understanding of the evolution, diversity, and environmental distribution of an enzyme that is key to life and has broad environmental and industrial applications.}, } @article {pmid42022196, year = {2026}, author = {Yan, Z and Xie, J and Jin, L and He, T and Zhang, X and Li, X}, title = {Steam Cooking Methods Promote the Transfer of Viable Antibiotic-Resistant Pathogens from Water into Air.}, journal = {Environment & health (Washington, D.C.)}, volume = {4}, number = {4}, pages = {730-741}, pmid = {42022196}, issn = {2833-8278}, abstract = {Steam cooking is an ancient and widely used method for sterilizing water and food globally. However, its effectiveness may be compromised by the ubiquitous presence of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in these media. Here, we combined metagenomic sequencing, quantitative PCR analysis, plate culture, and Sanger sequencing to examine the effects of steam cooking on the profiles of antibiotic resistance in cooked fish, tap water, and indoor air in real cooking environments (i.e., a canteen and a home kitchen) and a laboratory chamber. We found that while steam cooking eliminated over 92.0% of bacteria and ARGs in both tap water and fish, it significantly increased the absolute abundance of bacteria and ARGs in indoor fine particulate matter (PM2.5) across all settings. Tap water was identified as the primary contributor to the increase, transferring 14.6% of bacteria and 33.2% of ARGs into indoor PM2.5 during steam cooking. This process also elevated the relative abundance of certain putative human pathogens in indoor PM2.5, containing ARGs and heat shock proteins and mainly originating from tap water. To test if these transferred ARGs hosts were viable, we conducted plate culture experiments and identified a viable heat-resistant ARB, Bacillus cereus, transferred from water to indoor PM2.5 via water vapor. Our results highlight the cross-medium transport of ARB and ARGs via steam cooking and underscore the potential microbial safety issues to cooking personnel through inhalational exposure.}, } @article {pmid42022320, year = {2026}, author = {Zhang, W and Huang, R and Yuan, J}, title = {Case Report: HHV8-positive multicentric Castleman disease in an HIV-positive patient :diagnostic challenges arising from atypical histology and the role of metagenomic sequencing.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1779973}, pmid = {42022320}, issn = {2234-943X}, abstract = {BACKGROUND: Multicentric Castleman disease (MCD), especially the HHV8-positive subtype, is a rare lymphoproliferative disorder that presents considerable diagnostic and therapeutic difficulties, particularly among HIV-positive patients. The co-occurrence of other infections, such as syphilis, may further complicate its clinical picture and management.

CASE DESCRIPTION: A 65-year-old man with well-controlled HIV presented with persistent fever, fatigue, and disseminated lymphadenopathy,. Through histopathological examination, molecular testing (including mNGS for HHV8), and PET-CT imaging, HHV8-positive MCD was diagnosed, along with latent syphilis. The patient was successfully treated with R-VP16 (rituximab and etoposide) for MCD and benzathine penicillin for syphilis, showing a positive clinical response. Throughout 36 months of continuous monitoring, the patient has maintained sustained complete remission with no evidence of disease recurrence.

CONCLUSION: This case underscores the importance of considering HHV8-driven lymphoproliferative disorders in HIV patients with unexplained lymphadenopathy and systemic symptoms, particularly in HHV8-endemic regions. It also highlights the essential roles of advanced diagnostics and multidisciplinary management in such complex presentations. The favorable outcome demonstrates the effectiveness of timely and targeted treatment, though long-term follow-up remains necessary due to the potential for relapse or progression.}, } @article {pmid42022392, year = {2026}, author = {Abedien, ZU and Lean, IJ and Djordjevic, SP and Hick, PM and Westman, ME and Mckay-Demeler, J and Webster, J and Brito, BP}, title = {Next-generation detection in bovine respiratory and enteric diseases: metagenomic and amplicon sequencing insights into microbial diversity.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1788101}, pmid = {42022392}, issn = {2297-1769}, abstract = {Respiratory and enteric diseases are major contributors to morbidity, mortality, and economic loss in cattle production, with significant implications for animal welfare, particularly in calves. Traditional diagnostic approaches have laid the foundation for pathogen detection in cattle, providing essential tools for disease surveillance and control. However, their targeted nature limits the capacity to identify unexpected, novel, or polymicrobial infections that often underlie complex respiratory and enteric syndromes. Recent advances in molecular technologies, particularly amplicon sequencing (metataxonomics), metagenomics, and metatranscriptomics, enable untargeted, high-resolution profiling of microbial communities directly from clinical samples, offering transformative potential for research and diagnostics. This review synthesises current applications of these approaches in bovine respiratory and enteric disease research, highlighting key findings across virology, bacteriology, and parasitology. Collectively, these studies have expanded the catalogue of the microbial diversity, yet their interpretation remains challenged by the still-evolving understanding of microbial contributions to pathogenesis. Progress toward clinical integration is further hindered by the need for methodological standardisation, validation, and improved interpretive frameworks. Looking ahead, advancing these technologies will require harmonised protocols, integration of multi-omics datasets, and robust experimental and epidemiological studies to establish causal links between microbial signatures and disease outcomes. By bridging discovery and application, these approaches hold the potential to enhance diagnostic accuracy, strengthen surveillance, and support sustainable cattle production systems. As these technologies continue to evolve, they are likely to play an increasingly central role in bovine disease research and diagnostics.}, } @article {pmid42022531, year = {2026}, author = {Wang, Y and Fu, J and Zhan, J and Liang, Y and Chen, R and Su, L and Zhou, Q and Zhang, Y and Cong, W and Xu, F}, title = {Panax ginseng-Polygonum cuspidatum is beneficial for alleviating atherosclerosis in ApoE[-/-] mice by modulating the composition of gut microbiota and related metabolites.}, journal = {Frontiers in cardiovascular medicine}, volume = {13}, number = {}, pages = {1773819}, pmid = {42022531}, issn = {2297-055X}, abstract = {BACKGROUND: Atherosclerosis (AS) is a central pathological driver underlying most cardiovascular diseases. Gut microbiota and related metabolites participate in regulating atherosclerosis. Panax ginseng and Polygonum cuspidatum (GP) herb pair has traditionally been used for cardiovascular diseases. Some active compounds in GP have shown anti-atherosclerotic effects and the effects of GP still needs more evidence-based supports. Therefore, this study aims to investigate the potential effects of GP on atherosclerosis and explore the underlying mechanisms.

METHODS: Fifty C57BL/6J ApoE[-/-] mice were randomly assigned to five groups: model, statin, low-dose GP, medium-dose GP and high-dose GP. They were fed a high-fat diet (HFD) to induce atherosclerosis. Ten wild-type C57BL/6J mice were given chow diet and served as controls. After 12-week intervention, their aortic tissues were collected for Oil Red O staining, colon tissues for Alcian staining and immunofluorescence, and serum samples for measurement of lipid levels and inflammatory cytokines. Then, their fecal DNA was extracted for metagenomic sequencing, while cecum and ileocecal valves were for untargeted metabolomics. Finally, fecal microbiota transplantation was performed to assess the contribution of gut microbiota to observed effects. Twenty additional ApoE[-/-] mice were randomized to two groups: FMT-Mod and FMT-GPH, given feces from the model or high-dose GP group.

RESULTS: Atherosclerotic plaques accumulated in the aorta and aortic sinus after HFD, while statin and high-dose GP alleviated this burden. TC, TG, LDL-C, MCP-1, MCP-3 and IL-2 showed significant increase after HFD, while statin and GP decreased LDL-C, MCP-1 and MCP-3. The goblet cells, ZO-1 and Occludin decreased after HFD, while statin and GP increased them, indicating that the intestinal barrier integrity was improved. Additionally, the composition of gut microbiota was modulated by GP. Some candidate taxa were identified, such as Bifidobacteriales, Bacteroidetes and Escherichia coli. Twenty-two metabolites were differentially abundant among the control, model and GP groups. Nineteen of them were modulated by HFD and reversed by GP, including 1-methylnicotinamide, dopamine and lysoPA (0:0/18:0). Mice given fecal transplants from the high-dose GP group showed less aortic plaques, lower levels of some lipid and inflammatory cytokines, more goblet cells, more expression of ZO-1 and Occludin, and more 1-methylnicotinamide than those given fecal transplants from the model group.

CONCLUSION: This study suggests that GP is beneficial for alleviating atherosclerosis in HFD-induced ApoE[-/-] mice, potentially by modulating the composition of gut microbiota and related metabolites.}, } @article {pmid42022543, year = {2026}, author = {Yang, P and Meng, Y and Ma, Y and Xu, M and Zhang, X}, title = {Fermented cotton stalks preserve colonic epithelial integrity in Hu sheep via the microbiota-metabolite-NF-κB/MLCK axis and mitigate the adverse effects of direct feeding.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1777023}, pmid = {42022543}, issn = {2296-861X}, abstract = {BACKGROUND: This study aimed to compare three cotton-stalk processing strategies-grinding (FS), steam explosion (PH), and microbial fermentation (FJ)-and to clarify whether fermented cotton stalks preserve colonic epithelial integrity through a microbiota-metabolite-NF‑κB/MLCK axis in Hu sheep.

METHODS: Fifteen clinically healthy Hu sheep (26.7 ± 1.76 kg body weight; 115 ± 4 days of age) were used after a 14‑day adaptation period and randomly assigned to one of three diets (n = 5 per treatment) containing 40% processed cotton stalks (FS, PH, or FJ) for 8 weeks.

RESULTS: PH and FJ increased final body weight compared with FS, and average daily gain increased progressively from FS to PH to FJ (206.07, 282.50, and 322.14 g/d, respectively; p < 0.05). Colonic fermentation profiles were markedly improved by FJ, evidenced by lower pH, ammonia nitrogen, free gossypol, and acetate (p < 0.05), alongside higher total VFAs with elevated propionate and butyrate (p < 0.05), whereas LPS was not different among treatments (p > 0.05). Histology and scanning electron microscopy indicated that FJ maintained intact crypt architecture and epithelial surface continuity, while FS exhibited epithelial detachment and surface erosion. Metagenomic analysis revealed distinct community structures among groups, with FJ showing higher richness and enrichment of taxa associated with carbohydrate utilization and butyrate‑producing guilds (e.g., Lachnospiraceae‑related genera such as Anaerostipes, Blautia, and Coprococcus). Consistently, FJ suppressed colonic mucosal inflammation, as reflected by reduced IL‑1β, IL‑6, IL‑8, and TNF-α at both mRNA and protein levels (p < 0.05). Mechanistically, FJ attenuated NF‑κB activation and downstream MLCK signaling, shown by decreased p‑p65/p65, p‑IκB/IκB, MLCK abundance, and p‑MLC/MLC ratio (p < 0.05), while upregulating tight‑junction proteins (ZO‑1, occludin, claudin‑1, and claudin‑4; (p < 0.05).

CONCLUSION: Fermentation‑based processing of cotton stalks enhanced growth performance and promoted a favorable hindgut fermentation and microbial-metabolic milieu, thereby reinforcing colonic barrier integrity via inhibition of NF‑κB/MLCK‑associated inflammatory signaling, supporting fermented cotton stalk as a practical strategy to valorize cotton residues for ruminant feeding while mitigating gossypol‑related hindgut stress.}, } @article {pmid42022809, year = {2026}, author = {Tian, YP and Li, QH and Li, YM and Zhao, JY and Wei, XX and Wang, JY and Zhou, YL and Yang, SB and Li, W and Guo, P and Wang, LX and Dai, TT and Hu, SF and Zhong, ZQ and Xie, YM and Lv, ZH}, title = {Gut microbiota and metabolome signatures in preterm infants with high versus low risk for neurodevelopmental impairment: a prospective, matched, longitudinal multi-omics study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1799859}, pmid = {42022809}, issn = {2235-2988}, mesh = {Humans ; Prospective Studies ; Multiomics ; Longitudinal Studies ; *Gastrointestinal Microbiome ; *Metabolome ; Female ; *Infant, Premature ; Male ; Infant, Newborn ; Feces/microbiology ; Infant ; *Neurodevelopmental Disorders/microbiology ; Metagenomics ; Biomarkers ; Metabolomics ; Dysbiosis/microbiology ; }, abstract = {Preterm birth is a leading global cause of neurodevelopmental impairment (NDI), yet early predictive biomarkers remain elusive. The gut microbiome, developing in parallel with the brain and communicating via the microbiota-gut-brain axis, holds potential as a source of such biomarkers. However, specific longitudinal multi-omics signatures predictive of NDI risk in preterm infants are poorly defined. We conducted a prospective, matched, longitudinal study of 60 preterm infants, classified at 3 months corrected age (CA) into high-risk (HR, n=30) or low-risk (LR, n=30) groups for NDI based on combined motor (TIMP) and neurological (GMs) assessments. Fecal samples from birth (meconium) and 3 months CA underwent shotgun metagenomic sequencing and untargeted metabolomics. Groups were rigorously matched for gestational age, birth weight, sex, and clinical exposures. While α- and β-diversity did not differ between groups, profound taxonomic and functional divergence emerged. At 3 months CA, the LR gut was enriched with Akkermansia muciniphila, whereas the HR gut was dominated by Klebsiella variicola. Functional metagenomics revealed a dysbiotic HR trajectory, enriching pathways for bacterial virulence, stress response, and-notably-multiple pathways annotated for human neurodegenerative diseases, contrasting with LR expansion of core biosynthesis. Metabolomics confirmed a dysfunctional HR state, showing impaired amino acid metabolism and aberrant neuroactive pathway enrichment. Critically, meconium features correlated with 3-month neurobehavioral scores, demonstrating ultra-early predictive potential. Integrated networks at 3 months directly linked Akkermansia muciniphila and co-varying glycerophospholipids to superior neurodevelopmental scores, forming a beneficial "Akkermansia-lipid" axis, while Klebsiella variicola and triterpenoids formed a dysbiotic hub. Our study defines a high-risk gut ecosystem trajectory in preterm infants, characterized by early commensal depletion, pathobiont expansion, and a functional shift towards inflammation and neuroinflammation. These signatures offer novel targets for early risk prediction and microbiome-targeted interventions.}, } @article {pmid42022943, year = {2026}, author = {Fu, F and Zhang, C and Xu, Z and Ji, P and Zhang, Z}, title = {Gastric Microbiome Alterations in Sepsis-Related Gastrointestinal Bleeding: Two Case Reports and Literature Review.}, journal = {JGH open : an open access journal of gastroenterology and hepatology}, volume = {10}, number = {3}, pages = {e70318}, pmid = {42022943}, issn = {2397-9070}, abstract = {Sepsis, characterized by life-threatening organ dysfunction resulting from an uncontrolled response to infection, can impact various systems of the body, including the digestive system. Prior research has identified sepsis as a significant risk factor for gastrointestinal bleeding. However, there is limited reporting on the gastric microecology of individuals with sepsis complicated by gastrointestinal bleeding. This paper presents the cases of two patients, shedding light on this issue. The first case was a 29-year-old female who developed sepsis during perioperative liver transplantation, while the second case features a 34-year-old female with acute pancreatitis complicated by septic shock. Both patients underwent gastroscopy following gastrointestinal bleeding, revealing evident gastric mucosal injuries. Notably, the second patient exhibited suppurative gastritis. Metagenomic Next-Generation Sequencing (NGS) of gastric juice from these two patients unveiled microecological alterations in the stomach. The sequencing results indicated a substantial presence of pathogenic sequences, underscoring the role of direct gastric mucosal injury due to infection as a significant contributor to gastrointestinal bleeding. This study not only introduces a novel approach to pinpointing the causes of gastrointestinal bleeding in sepsis but also provides valuable insights for clinical diagnosis and treatment.}, } @article {pmid42022944, year = {2026}, author = {Zhao, Z and Ling, J and Chen, J}, title = {Oral Microbiome and Constipation: A Causal Link Revealed by Mendelian Randomization.}, journal = {JGH open : an open access journal of gastroenterology and hepatology}, volume = {10}, number = {3}, pages = {e70390}, pmid = {42022944}, issn = {2397-9070}, abstract = {BACKGROUND: Constipation affects approximately 15.3% of the global population. While the gut microbiome's role in constipation has been studied, the causal relationship between the oral microbiome and constipation remains unexplored.

METHODS: We utilized Mendelian randomization (MR) and large-scale GWAS data to investigate the causal relationship between the oral microbiome and constipation. Oral microbiome data were sourced from a metagenome-wide association study (mgGWAS) on 2984 individuals, while constipation GWAS data came from 176 629 samples in the Japan Biobank. Statistical methods included inverse variance-weighted (IVW) analysis, weighted median, and MR-Egger regression.

RESULTS: The MR analysis revealed significant associations between specific oral microbiome and constipation. Treponema denticola, found in saliva, was positively associated with an increased risk of constipation (OR = 3.961, 95% CI = 1.085-14.453, p = 0.037). Conversely, certain bacteria like Pauljensenia sp000308055 showed protective effects (OR = 0.409, 95% CI = 0.167-0.999, p = 0.0496). In the tongue coating, Neisseria sicca exhibited a significant positive association with constipation (OR = 4.864, 95% CI = 1.293-18.302, p = 0.019), while Aggregatibacter segnis demonstrated a protective effect (OR = 0.400, 95% CI = 0.188-0.854, p = 0.018).

CONCLUSION: This study is the first to explore the potential causal relationship between oral microbiome and constipation. The findings suggest that specific oral bacteria may influence the risk of constipation, highlighting the need for further research to validate these relationships and understand the mechanisms involved. Moreover, the study underscores the importance of considering both oral and gut microbiome in the context of gastrointestinal health and disease management.}, } @article {pmid42023092, year = {2026}, author = {Li, X and Chen, D and Xiao, Y and Lei, Z and Yang, X and Zhang, Y and Li, L and Zheng, Y and Zhang, Y and Huang, Z and Lin, B}, title = {Metagenomic next-generation sequencing improves diagnosis of Talaromyces marneffei and mixed infections in HIV/AIDS patients: a retrospective study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1800314}, pmid = {42023092}, issn = {2296-858X}, abstract = {BACKGROUND: Opportunistic infections remain a leading cause of morbidity in people living with HIV (PLWH). Talaromyces marneffei (T. marneffei) accounts for up to 15% of HIV-related hospitalizations in endemic regions. Metagenomic next-generation sequencing (mNGS) offers rapid pathogen detection; however, its utility in diagnosing HIV-associated coinfections is uncertain.

METHODS: This retrospective study enrolled 56 hospitalized PLWH with coinfections at the Third Affiliated Hospital of Sun Yat-sen University from March 2022 to October 2024. All patients underwent pathogen detection using both mNGS and CTM, with their diagnostic performance compared. Clinical data, treatment adjustments, and outcomes were analyzed.

RESULTS: mNGS demonstrated significantly higher detection rate (84.4%, 54/64; 95% CI: 73.1-92.2%) than CTM (28.1%, 18/64; 95% CI: 17.6-40.8%; p < 0.0001), especially for T. marneffei detection (100% vs. 45.5%, p < 0.0001). mNGS identified T. marneffei in 39.3% (n = 22/56) of patients, including two rare cases (urinary and intracranial infections) missed by CTM. mNGS revealed mixed infections in 82.1% (46/56) of patients, substantially higher than the 5.4% detected by CTM. Notably, mNGS-guided therapy adjustments occurred in 74.1% of cases, compared with 22.2% for CTM (p < 0.001), correlating with clinical improvement in 90% (36/40) of adjusted regimens.

CONCLUSION: Our data demonstrated that mNGS had a higher positive detection rate than CTM for detecting coinfections among PLWH, especially for T. marneffei and mixed infections. These results highlight the clinical value of mNGS as a complementary tool for pathogen identification in this vulnerable population.}, } @article {pmid42023515, year = {2026}, author = {Shang, J and Peng, C and Guan, J and Cai, D and Wang, D and Sun, Y}, title = {PhaBOX2: an enhanced web server for discovering and analyzing viral contigs in metagenomic data.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkag382}, pmid = {42023515}, issn = {1362-4962}, support = {//Hong Kong Research Grants Council/ ; 11209823//General Research Fund/ ; //City University of Hong Kong/ ; 9667256//Institute of Digital Medicine/ ; 9678241//Institute of Digital Medicine/ ; }, abstract = {Metagenomic sequencing has transformed virus discovery; however, downstream bioinformatic analyses for viral identification, classification, and host prediction remain fragmented across multiple tools. Here, we present PhaBOX2, a major upgrade that extends the platform from a specialized bacteriophage identification tool to a comprehensive and integrated suite for viral sequence analysis. PhaBOX2 broadens its detection, taxonomic, and host prediction scope beyond phages to enable the characterization of archaeal and eukaryotic viruses. The updated workflow incorporates rigorous quality control and quantitative analyses, automatically removes host contamination, clusters sequences into viral operational taxonomic units, and performs phylogenetic analysis based on marker genes. In contrast to traditional "black-box" deep learning approaches, PhaBOX2 combines alignment-based strategies with machine-learning models under a "glass-box" design philosophy, providing interpretable intermediate evidence alongside final predictions to improve transparency and biological interpretability. Powered by a dedicated high-performance computing infrastructure, the server delivers a fully automated, end-to-end workflow, while achieving an ~80% reduction in processing time. PhaBOX2 thus provides a robust and user-friendly ecosystem for viral metagenomic analysis and is freely available at https://phage.ee.cityu.edu.hk/.}, } @article {pmid42023591, year = {2026}, author = {Lei, P and Qi, Z and Ma, Q and Zhao, B and Wen, B and Jiang, W and Xi, W and Liu, Y and Xun, Y and Zhang, S and Wang, Y and Guo, Y and Wang, W and Ma, X and Jia, M and Fan, Y}, title = {Gut microbiota reshapes host energy metabolism to modulate depressive behaviors.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2662556}, pmid = {42023591}, issn = {1949-0984}, mesh = {Humans ; Animals ; *Energy Metabolism ; *Major Depressive Disorder/metabolism/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; Fecal Microbiota Transplantation ; Male ; Female ; Mice ; Bacteria/classification/genetics/isolation & purification/metabolism ; Adult ; Middle Aged ; Multiomics ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {Disturbances in energy metabolism are a key pathophysiological feature of major depressive disorder (MDD). The gut microbiota, as a critical regulator of host metabolism, may influence systemic energy homeostasis and contribute to depression. To investigate this, we performed a multi-omics analysis integrating targeted metabolomics and shotgun metagenomics on samples from 100 MDD patients and 68 healthy controls. MDD patients exhibited significant disruptions in central energy pathways (glycolysis, TCA cycle, and ornithine cycle), which correlated with symptom severity and cognitive impairment. We identified 36 bacterial species whose abundances were linked to mitochondrial fatty acid synthesis, ketogenesis, and amino acid metabolism, and were associated with altered levels of core metabolites like lactate and L-glutamic acid. Mediation analysis established a "gut microbiota-energy metabolites-depressive phenotype" axis, where metabolites mediated the effects of specific bacteria (e.g., Dorea_formicigenerans) on symptoms. To validate causality, we used a chronic social defeat stress mouse model with simultaneous autologous fecal microbiota transplantation (FMT). FMT effectively reshaped the gut microbiota, ameliorated depression-like behaviors, and reversed the stress-induced shift toward anaerobic glycolysis in serum and the central nervous system. Critically, FMT restored mitochondrial morphology and structural integrity in the prefrontal cortex and hippocampus, renormalizing the relationship between metabolism and behavior. Our findings elucidate the gut microbiota's role in MDD pathogenesis via host energy metabolism regulation and posit early autologous FMT as a novel strategy to correct central energy imbalances.}, } @article {pmid42023670, year = {2026}, author = {Santillan, E and Neshat, SA and Wuertz, S}, title = {Predicting microbial community responses to disturbance using genome-resolved trait-based life-history strategies.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42023670}, issn = {1751-7370}, mesh = {RNA, Ribosomal, 16S/genetics ; Metagenomics ; Bioreactors/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Wastewater/microbiology/chemistry ; Biomass ; Life History Traits ; Ecosystem ; }, abstract = {Understanding how microbial communities respond to disturbance remains a fundamental question in ecology, with broad implications for biodiversity, ecosystem function, and biotechnology. Trait-based approaches offer general rules to predict community responses by linking ecological strategies to measurable traits. Whereas life-history strategy frameworks such as the competitor-ruderal-stress-tolerant (CSR) model are well established in plant and animal ecology, their application to microbial communities has been limited. Here, we experimentally tested how microbial communities shift across a gradient of disturbance frequency in replicated bioreactors treating synthetic wastewater. We applied six conditions by doubling the organic loading rate at different frequencies, from undisturbed to press disturbance, and monitored changes over 42 days using genome-resolved metagenomics, 16S rRNA gene sequencing, biomass quantification, and effluent chemistry. By integrating ordination, network analysis, and machine learning, we identified emergent community-level life-history strategies, with competitor-dominated communities under undisturbed conditions, ruderal-associated strategies at intermediate disturbance frequencies, and stress-tolerant strategies under sustained high-frequency (press) disturbance. These strategies were reflected in functional trade-offs, shifts in community composition, and genomic trait distributions. A simulation-based approach was used to generate a CSR classification of metagenome-assembled genomes, which was consistent with patterns observed in other microbial ecosystems. Our results demonstrate that life-history frameworks can capture predictable microbial dynamics across disturbance regimes. This approach provides a unifying tool for linking microbial structure, function, and traits across scales, helping to reconcile ecological theory with microbial resource management in natural and engineered ecosystems.}, } @article {pmid42023843, year = {2026}, author = {Olagoke, O and Zheng, X and Chung, S and Mengistie, HD and Asfaha, K and Read, TD and Dean, D}, title = {Phylogenetic diversity, functional pathways, and network interactions of ocular chlamydia-like organisms (CLOs) in trachoma-endemic Ethiopia.}, journal = {mBio}, volume = {17}, number = {5}, pages = {e0053426}, pmid = {42023843}, issn = {2150-7511}, support = {R01 AI158527/AI/NIAID NIH HHS/United States ; }, mesh = {Ethiopia/epidemiology ; Humans ; *Trachoma/microbiology/epidemiology ; Female ; *Phylogeny ; Male ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Adult ; Adolescent ; Child ; Middle Aged ; Young Adult ; Child, Preschool ; Infant ; Eye/microbiology ; Metagenomics ; Aged ; }, abstract = {Trachoma is the leading infectious cause of blindness worldwide and classically attributed to Chlamydia trachomatis (Ct). However, other members of the phylum Chlamydiae, particularly environmental chlamydia-like organisms (CLOs), may modulate ocular ecology and influence disease outcomes. Here, we investigated CLO distribution, phylogeny, and microbiome associations among 1,059 individuals from trachoma-endemic communities in Ethiopia using targeted 16S rRNA sequencing and metagenomic shotgun sequencing. CLOs were detected in 249 (23.3%) participants of all ages and sexes and were significantly less likely to be associated with Ct or trachomatous scarring (TS) and trichiasis (TT). Phylogenetic analyses revealed extensive CLO diversity with six novel phylotypes, the most abundant of which was ancestral to Sorochlamydiaceae-a family linking pathogenic Chlamydiaceae, which includes the genus Chlamydia, and symbionts of protists. CLO-positive microbiomes exhibited significantly greater species richness and evenness with distinct differences in community composition relative to CLO-negative microbiomes. These effects were most pronounced among males and older adults. Functional profiling revealed widespread depletion of biosynthetic and metabolic pathways in CLO-positive microbiomes, particularly in participants with TS/TT, suggesting reduced community biosynthetic capacity and niche modification. Species interaction network analyses demonstrated substantial reorganization of microbial associations in the presence of CLOs with increased connectivity and centrality compared to CLO-negative networks. These findings identify CLOs as prevalent, phylogenetically diverse, and ecologically influential members of the microbiome. Their inverse association with Ct and TS/TT underscores the importance of considering intracellular symbionts beyond Ct in understanding conjunctival microbial ecology, resilience, and trachoma pathogenesis and for designing novel control strategies.IMPORTANCETrachoma caused by Chlamydia trachomatis (Ct) remains the leading infectious cause of blindness globally. While control efforts focus exclusively on Ct, other members of the phylum Chlamydiae, such as chlamydia-like organisms (CLOs), inhabit mucosal surfaces but remain understudied in the eye. Using targeted 16S rRNA and metagenomic shotgun sequencing of conjunctival samples from villagers in trachoma-endemic Ethiopia, CLOs were prevalent (23.3%; 249/1,059), phylogenetically diverse, including novel Chlamydiae phylotypes, and inversely associated with both Ct infection and severe scarring disease. CLO microbiomes had increased microbial diversity, altered community composition, depleted metabolic pathway abundance, and reorganized species interaction networks compared to CLO-negative microbiomes. These findings challenge the singular focus on Ct in trachoma control and research and suggest that CLOs represent ecologically significant members of the conjunctival microbiome. Further research on their interactions with ocular microbial communities could reveal new insights into trachoma pathogenesis and inform more holistic approaches to disease control.}, } @article {pmid42023878, year = {2026}, author = {Conte, CA and Rivarola, M and Gonzalez, S and Milla, FH and Soria, C and Giardini, MC and Segura, DF and Handler, AM and Bourtzis, K and Ragoussis, J and Lanzavecchia, SB}, title = {De novo whole-genome assembly of the Wolbachia sp. endosymbiont from Anastrepha fraterculus using long- and short-read metagenomic data.}, journal = {Microbiology resource announcements}, volume = {15}, number = {6}, pages = {e0042526}, pmid = {42023878}, issn = {2576-098X}, abstract = {A whole-genome assembly and annotation of Wolbachia sp. infecting Anastrepha fraterculus sp. 1 were generated by a metagenomic analysis of sequencing reads from a host genome project. This study contributes to the characterization of this endosymbiotic bacterium and provides valuable insights for research on host-symbiont interactions and pest management strategies.}, } @article {pmid42024170, year = {2026}, author = {Jiang, L and Tang, Y and Xu, L and Wei, Y and Liu, M and Che, X and Xin, R and Zhu, Y}, title = {Microbiome in adult severe caries and cross-kingdom biofilms validation.}, journal = {Clinical oral investigations}, volume = {30}, number = {5}, pages = {}, pmid = {42024170}, issn = {1436-3771}, support = {ZDXX25182//Nanjing Medical Science and Technique Development Foundation/ ; ZKX23053//Nanjing Medical Science and Technique Development Foundation/ ; 0224C010//High-Level Hospital Construction Project of Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University/ ; }, mesh = {Humans ; *Biofilms ; *Microbiota ; *Dental Caries/microbiology ; Adult ; Microscopy, Electron, Scanning ; Microscopy, Confocal ; Candida albicans ; Streptococcus mutans ; Female ; Male ; Saliva/microbiology ; }, abstract = {OBJECTIVES: Adult severe caries (ASC) is a form of rampant caries that develops in adulthood, causing severe impairment of oral function and reducing quality of life. However, the pathogenic mechanism of ASC remains unclear. This study aimed to identify the core microbiota in patients with ASC and preliminarily investigate the microbial interactions and pathogenicity of key ASC-associated core microorganisms.

MATERIALS AND METHODS: Saliva samples were collected from 7 adult patients with severe caries and 6 caries-free volunteers for metagenomic analysis. Based on microbiome profiling results, an in vitro cross-kingdom biofilm model composed of Streptococcus mutans (S. mutans), Candida albicans (C. albicans) and Veillonella parvula (V. parvula) was established to simulate a high caries-risk microenvironment. Scanning electron microscopy (SEM), crystal violet (CV) staining, and live/dead bacterial staining were used to evaluate biofilm formation. Acid production assays, acid stress challenge tests, confocal laser scanning microscopy (CLSM) and qRT-PCR were performed to analyze the acidogenicity and synthesis of extracellular polysaccharides (EPS). Additionally, atomic force microscopy (AFM) was used to assess the surface roughness of demineralized dentin slices.

RESULTS: Metagenomic analysis revealed significant enrichment of C. albicans and V. parvula in the saliva of patients with high caries susceptibility. The in vitro cultured cross-kingdom biofilms exhibited enhanced growth and EPS synthesis compared with single-species S. mutans biofilms. Moreover, cross-kingdom biofilms significantly increased surface roughness of demineralized samples, with a stronger effect than single- and dual-species biofilms.

CONCLUSIONS: Colonization by C. albicans and V. parvula increases biofilm biomass, enhances microbial survival under stress, and elevates biofilm virulence, which induces demineralization of dentin slices in vitro.

CLINICAL RELEVANCE: This study demonstrates that the interspecies interactions among caries-related microorganisms in ASC patients confer enhanced virulence and cariogenicity, providing novel insights for the investigation and prevention of high caries susceptibility.}, } @article {pmid42025071, year = {2026}, author = {Waseem, H and Feng, K and Zhao, B and Yang, X and Liu, M and Wang, J and Li, J and He, Q and Wang, S and Lu, Y and Örmeci, B and Deng, Y}, title = {Diversity and geographic distribution of antibiotic resistance in food waste anaerobic digestion systems.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142168}, doi = {10.1016/j.jhazmat.2026.142168}, pmid = {42025071}, issn = {1873-3336}, mesh = {Food Loss and Waste ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; China ; *Sewage/microbiology ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Antibiotic resistance genes (ARGs) present in food waste pose a significant environmental and public health challenge, with anaerobic digestion emerging as a promising technology to reduce ARG abundance during waste treatment. In this study, we analyzed the resistomes in 64 anaerobic digestion sludge samples from seven full-scale food waste treatment facilities representing seven Chinese provinces. Across all facilities, a small core set of glycopeptide (van clusters), β-lactamase, aminoglycoside, and macrolide-lincosamide-streptogramin genes accounted for most ARG abundance (70.3%), marking them as critical targets for monitoring and post-treatment at high-risk sites such as Wenzhou. Resistome composition differed significantly among facilities and exhibited moderate correlation with bacterial taxonomic composition, with Firmicutes (Bacillota), Chloroflexota, and Proteobacteria as the major carriers associated with multiple resistance classes. ARG abundance was positively correlated with mobile genetic elements (r = 0.54, p < 0.0001), driven by integrases, transposases, and Tn916. Horizontal gene transfer was largely constrained within phylogenetic boundaries, particularly within Firmicutes (66.67%), limiting cross-phyla ARG dissemination. Resistome variation was driven predominantly by deterministic processes.; these deterministic filters together with regional differences in food-waste composition and MGEs, collectively select for a glycopeptide-dominated, Firmicutes-anchored resistome that is distinct from those in activated sludge and manure digesters.}, } @article {pmid42025084, year = {2026}, author = {Xu, GL and Tan, S and Hu, Y and Cheng, M and Hou, J and Cui, HL}, title = {Five novel Haloarchaeobius species from coastal tidal flats and saline-alkali soil in China using integrated culture-dependent and culture-independent approaches.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {3}, pages = {126718}, doi = {10.1016/j.syapm.2026.126718}, pmid = {42025084}, issn = {1618-0984}, mesh = {China ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Sequence Analysis, DNA ; DNA, Archaeal/genetics ; Soil/chemistry ; Seashore ; Nucleic Acid Hybridization ; *Halobacteriaceae/classification/genetics/isolation & purification ; Sodium Chloride ; Metagenomics ; Base Composition ; }, abstract = {Six novel halophilic archaeal strains, DFWS5[T], DT45[T], DYHT-AS-18[T], HRN-SO-5[T], TZWSO28, and TZWWS8[T] were isolated from tidal flats and saline-alkali soil collected from the eastern coastal region of China. Amplicon sequencing and metagenomic analyses indicated that these strains were present at low abundance in their original habitats, with only three strains detected by culture-independent approaches. These six strains constituted an independent clade alongside members of the genus Haloarchaeobius based on the 16S rRNA gene phylogeny. Except for the comparison between strains DYHT-AS-18[T] and TZWSO28, the average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values among these strains and existing members of the genus Haloarchaeobius were 76.60-89.50%, 21.00-38.50%, and 67.99-88.76%, respectively, below the proposed thresholds for species delineation. In contrast, these three values between strains DYHT-AS-18[T] and TZWSO28 were 97.36%, 76.30%, and 97.25%, respectively, exceeding the proposed thresholds. Phylogenomic analysis revealed that the six strains clustered with members of the genus Haloarchaeobius, but formed distinct branches separate from the current species. The optimal growth conditions for these six strains in terms of NaCl, MgCl2, temperature, and pH were 0.9-4.8 M, 0-1 M, 20-50 °C, and 5.0-9.5, respectively. According to phenotypic differences in nutrition and biochemical activity, these six strains can be distinguished from their related species. On the basis of polyphasic taxonomic evidence, five novel species within the genus Haloarchaeobius are proposed to accommodate strains DFWS5[T], DT45[T], DYHT-AS-18[T], HRN-SO-5[T], TZWSO28, and TZWWS8[T], respectively.}, } @article {pmid42025086, year = {2026}, author = {Islam, A and Han, Z and Rana, ML and Qiao, W and Guruge, SK and Zhang, Y and Yang, M}, title = {Removal of protozoa, opportunistic pathogens with virulence factors in swine manure using anaerobic digestion: Full-scale investigation and lab-scale optimization.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129728}, doi = {10.1016/j.jenvman.2026.129728}, pmid = {42025086}, issn = {1095-8630}, mesh = {Animals ; *Manure/parasitology/microbiology ; Swine ; *Virulence Factors ; Phylogeny ; Anaerobiosis ; Giardia/isolation & purification ; Cryptosporidium/isolation & purification ; Cryptosporidium parvum/isolation & purification ; }, abstract = {Swine manure serves as a significant reservoir of zoonotic protozoa and opportunistic pathogens, posing environmental and public health risks when inadequately treated. In this study, multiple molecular approaches, including quantitative PCR, nested PCR with gp60-based phylogenetic analysis, virulence factor profiling, and metagenome-assembled genome (MAG) reconstruction, were employed to investigate the abundance, diversity, and treatment responses of Cryptosporidium, Giardia, twelve opportunistic pathogens, and associated virulence factors (VFs) in swine manure. Three full-scale anaerobic digestion (AD) systems were investigated, and thermophilic and hyperthermophilic pretreatments were applied to lab-scale AD systems to evaluate the efficiency of biological risk control. Cryptosporidium parvum was identified as the dominant species, with subtype IIaA17G4R1 and related zoonotic subtypes detected in both lab-scale and full-scale samples. Phylogenetic clustering of swine-derived sequences with human and cattle isolates indicates a potential risk of zoonotic transmission through manure-associated environmental contamination. In lab-scale AD, a significant reduction in Cryptosporidium, particularly under hyperthermophilic conditions, was observed, while Giardia was undetectable in both influent and effluent samples. In full-scale systems, persistence of Escherichia coli, Clostridium perfringens, Enterococcus, Salmonella, and multiple VFs was confirmed in the effluents. The hyperthermophilic-mesophilic (70 °C-37 °C) lab-scale treatments achieved a substantial reduction in overall pathogen abundance from 3.40 × 10[8] to 1.21 × 10[8] copies/g dry weight and in virulence gene loads from 5.24 to 2.35 copies/cell (P < 0.001), along with the significant removal of pathogenic MAGs such as Enterococcus, Escherichia, Pseudomonas, and Streptococcus. These findings demonstrate the effectiveness of AD for reducing microbial risks and underscore the potential of thermophilic phase digestion as a scalable, biologically effective method for reducing microbial risks associated with livestock manure reuse.}, } @article {pmid42025876, year = {2026}, author = {Stamatopoulou, P and Scarborough, MJ}, title = {Impacts of organic loading rate fluctuations and division of labor on sugar-based chain elongation revealed through metatranscriptomics.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134687}, doi = {10.1016/j.biortech.2026.134687}, pmid = {42025876}, issn = {1873-2976}, mesh = {Bioreactors/microbiology ; Caproates/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/metabolism/genetics ; *Metagenomics ; Glucose/metabolism ; *Gene Expression Profiling ; *Sugars/metabolism ; *Transcriptome ; }, abstract = {Medium-chain carboxylates (MCCs) can be produced using open, mixed cultures of microorganisms in a process termed "chain elongation." Chain elongating bacteria can increase ATP yield by producing six-carbon caproate rather than four-carbon butyrate. Therefore, requiring chain elongating bacteria to maximize ATP yield for cell synthesis may be a way to increase production of the more valuable caproate. To test this, duplicate bioreactors were operated, and the impact of organic loading rate (OLR) fluctuations were assessed with glucose and xylose as substrates in media that did not include amino acids, vitamins, or other growth factors. Increasing the OLR did not reliably improve caproate production despite several known caproate-producing bacteria being present. 16S rRNA gene amplicon sequencing and shotgun metagenomics revealed that the same chain-elongating and sugar-degrading species were enriched in both bioreactors, including members of the Caproiciproducens, Caproicibacter, Olegusella, and Tractidigestivibacter genera. Further, metatranscriptomic results suggest a distinct division of labor associated with critical growth factors, including amino acids, folate, and pantothenate. This division of labor, while potentially beneficial to the microbial community, may result in low caproate production.}, } @article {pmid42026082, year = {2026}, author = {Human, ZR and Štursová, M and Odriozola, I and Větrovský, T and Howe, A and Navrátilová, D and López-Mondéjar, R and Žifčáková, L and Brabcová, V and Mundra, S and Thoen, E and Morgado, L and Fiore-Donno, AM and Bonkowski, M and Adamczyk, B and Kohout, P and Lipton, MS and Calhoun, S and LaButti, K and Lipzen, A and Keymanesh, K and Tejomurthula, S and Pennacchio, C and Grigoriev, IV and Martin, F and Kauserud, H and Baldrian, P}, title = {Seasonality of composition, genomic potential and activity of coniferous forest soil microbiomes.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07163-w}, pmid = {42026082}, issn = {2052-4463}, support = {240859//Norges Forskningsråd (Research Council of Norway)/ ; }, abstract = {Coniferous forest soils represent a globally important carbon sink, where the microbiome is essential for carbon flux between tree roots, rhizosphere, litter and soil. Soil habitats, such as roots, rhizosphere, bulk soil and litter differ in physicochemical properties and composition of highly specialized microbial communities, whose activity reflects the seasonality of temperature and tree activity of these mid- to high-latitude biomes. Here we present a multi-omic dataset encompassing 160 samples collected from four coniferous forest soil habitats in the Czech Republic and Norway, sampled in early summer, late summer, early winter and late winter that characterize the composition, genomic potential and activity of tree roots and microbiome. For each sample, we provide metabarcoding-based composition of bacterial, fungal and eukaryotic communities, results of shotgun DNA sequencing (metagenomes) and shotgun RNA sequencing (metatranscriptomes) illustrating the functional potential and activity within habitats. This dataset enables analyses of the temporal variation of taxonomic composition, functional potential and transcription across seasons in a temperate and boreal coniferous forest.}, } @article {pmid42026126, year = {2026}, author = {Miravet-Verde, S and Cacace, E and Mores, CR and Rutschmann, C and Lin, CW and Ruscheweyh, HJ and Cuénod, A and Barazzone, EC and Marrec, E and Vershynina, K and Schumann, R and Bower, DJ and Schubert, M and Egli, A and Fiebig, T and Slack, E and Sunagawa, S and Keys, TG}, title = {In silico typing maps the natural diversity of Escherichia coli transporter-dependent capsules.}, journal = {Nature microbiology}, volume = {11}, number = {5}, pages = {1217-1232}, pmid = {42026126}, issn = {2058-5276}, support = {51NF40_225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; CRSK- 3_228959//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 117.143 IP-LS//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; LT0050/2023-L//Human Frontier Science Program (HFSP)/ ; FN24-0000000703//Novartis Stiftung für Medizinisch-Biologische Forschung (Novartis Foundation for Medical-Biological Research)/ ; 865730//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Escherichia coli/genetics/classification/metabolism ; *Bacterial Capsules/genetics/classification/metabolism/chemistry ; *Serotyping/methods ; Genome, Bacterial ; Computer Simulation ; *Membrane Transport Proteins/metabolism/genetics ; *Escherichia coli Proteins/genetics/metabolism ; Genetic Variation ; Hidden Markov Models ; Genotype ; }, abstract = {Serotyping identifies bacterial variants based on surface antigens, traditionally using antibody-based assays, but has been increasingly replaced by in silico methods that infer serotypes from genomic sequences for faster, scalable and more reproducible analyses. However, traditional Escherichia coli capsule serotyping has largely fallen out of use since the 1990s, leaving gaps in our knowledge of capsule genetics, diversity, distribution and epidemiology. As capsules influence bacterial interactions with phages, host immune systems and the environment, this gap limits our understanding of E. coli ecology and pathogenicity as well as vaccine and diagnostic development. Here we established a definitive genotype-serotype map for 35 serologically identified and structurally characterized transporter-dependent capsules. We then surveyed 37,723 E. coli genomes, cataloguing 85 transporter-dependent capsule types (K-types), including 55 types that were not part of the reference collection. We leveraged this catalogue to develop a hidden Markov model-based in silico serotyping tool, kTYPr, and applied it to curated sets of 24,015 E. coli genomes and 2,762 metagenome-assembled genomes spanning diverse environmental and clinical sources. We found previously uncharacterized K-types enriched in undersampled environments and associated with E. coli disease. This study expands our understanding of E. coli surface structures, supporting efforts for precision targeting with phage therapy or vaccines.}, } @article {pmid42026467, year = {2026}, author = {Luo, C and Yao, H and Xian, Y and Yang, T and Xiao, X and Ying, L and Xu, J and Luo, X and Qiu, D and Liu, Y and Liu, B and Li, F}, title = {Functional remodeling of the gut microbiome and metabolome in primary idiopathic male infertility.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42026467}, issn = {1471-2180}, support = {2024NSFSC0647//Sichuan Provincial Science and Technology Support Program/ ; 24SYJS01//Health Commission of Sichuan Province Medical Science and Technology Program/ ; SCU2025J4183//the Fundamental Research Funds for the Central Universities/ ; }, abstract = {BACKGROUND: Primary idiopathic male infertility (PIMI) is a complex condition with unclear biological mechanisms. Increasing evidence indicates that gut microbiome-derived functional and metabolic alterations can influence host physiological processes, yet microbiome-associated functional changes in PIMI remain poorly characterized.

METHODS: In this case–control study, fecal shotgun metagenomics and untargeted liquid chromatography-tandem mass spectrometry (LC–MS/MS) metabolomics were performed in 19 men with PIMI and 12 fertile controls, alongside computer-assisted semen analysis. The study workflow integrated differential analyses, correlation analyses among key microbial species, metabolites, and clinical traits, and Random Forest modeling to derive a microbial-metabolic panel.

RESULTS: Compared with fertile controls, infertile men exhibited selective functional remodeling of gut microbial pathways and fecal metabolic profiles, accompanied by reduced sperm concentration and progressive motility and increased round cell counts. Although overall microbial diversity was broadly comparable between groups, 23 differentially abundant species and 53 altered Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified by metagenomic profiling. Untargeted metabolomics annotated 4,434 metabolites and identified 780 differential metabolites, with enrichment of 29 KEGG pathways. Eight key microbial species and eight key metabolites mapped to sperm- and testis-related pathways showed coordinated correlations with semen parameters. An integrated Random Forest model incorporating microbial and metabolic features demonstrated robust discrimination between infertile and fertile men, with optimal performance achieved using six top-ranked features.

CONCLUSIONS: PIMI is associated with selective gut microbial functional shifts and fecal metabolic disturbances that correlate with semen quality. Multi-omics integration highlights coordinated microbiome-metabolome alterations, providing insights into host-associated microbial functional dysregulation in male infertility.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05064-x.}, } @article {pmid42026490, year = {2026}, author = {Pan, J and Kong, H and Liang, M and Fang, X}, title = {Pneumonia caused by co-infection with Mycobacterium tuberculosis and Pneumocystis jirovecii leading to acute respiratory distress syndrome in an HIV-negative immunocompromised patient: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {42026490}, issn = {1471-2334}, abstract = {BACKGROUND: Pulmonary tuberculosis (PTB) and Pneumocystis jirovecii pneumonia (PJP) often occur in immunosuppressed populations, particularly in individuals with human immunodeficiency virus (HIV) infection. However, co-infection with these two pathogens resulting in acute respiratory distress syndrome (ARDS) has been less frequently reported, especially in HIV-negative patients. CASE PRESENTATION: We report the case of a 68-year-old immunosuppressed male patient with pneumonia caused by co-infection with Mycobacterium tuberculosis and Pneumocystis jirovecii, leading to ARDS, who was successfully treated. Following a definitive diagnosis of pemphigus vulgaris and 3 months of glucocorticoid and immunosuppressive therapy, the patient had a sudden onset of fever and dyspnea. He was admitted to the respiratory department of a general hospital with a diagnosis of severe community-acquired pneumonia. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid detected the presence of M.tuberculosis and P. jirovecii. Owing to the suspected contagious nature of tuberculosis, he was transferred to the tuberculosis department of our hospital. The patient developed severe respiratory distress; chest computed tomography (CT) revealed cavitary lesions and progressive pulmonary exudative changes, and arterial blood gas analysis demonstrated hypoxic respiratory failure. Because of limited respiratory support resources in the tuberculosis department, the patient was then transferred to the Respiratory Intensive Care Unit for endotracheal intubation and invasive mechanical ventilation. The patient received high positive end-expiratory pressure respiratory support therapy and restrictive fluid management strategies. Clindamycin combined with caspofungin was administered for PJP because of a suspected sulfonamide allergy, while standard first-line anti-tuberculosis therapy was initiated concurrently. The patient showed progressive clinical improvement and was successfully extubated on day 7 after intubation. At one-month follow-up, he had recovered well, and chest CT demonstrated substantial resolution of pulmonary lesions. CONCLUSION: The successful management of this patient was attributed to timely etiological diagnosis, targeted anti-infective therapy, effective supportive respiratory care, and fluid management. This case highlights the importance of heightened vigilance and prompt, comprehensive treatment in immunosuppressed patients with severe pneumonia, particularly in non-HIV individuals.}, } @article {pmid42026803, year = {2026}, author = {Zhang, F and Hu, K and Sun, C and Chen, R and Ni, G and Liu, X and Wei, L and Su, R}, title = {Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2662690}, pmid = {42026803}, issn = {1949-0984}, mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; *Neoplasms/drug therapy/microbiology/immunology ; *Gastrointestinal Microbiome/genetics/drug effects ; Biomarkers, Tumor/genetics ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Deep Learning ; }, abstract = {Targeting programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) with immune checkpoint inhibitors (ICIs) has improved survival across multiple cancer types, but the variability in patient response highlights the need for better predictive biomarkers. Existing studies rely on taxonomic abundance derived from reference genome databases, limiting the discovery and functional interpretation of uncharacterized microbes. Here, we integrated metagenomic data from multiple ICI-treated cohorts spanning diverse cancer types and geographic regions and developed a deep learning model, named BioP-VAE, that incorporates biological prior knowledge via protein sequence embeddings and uses gene-level microbial abundance features as input. Gene-level microbial abundance outperformed taxonomy abundance in predicting both ICI response and 12-month progression-free survival (PFS). In patients receiving combination immune checkpoint blockade (CICB), BioP-VAE achieved a mean AUC of 0.89 in intracohort and 0.88 in cross-cohort evaluation. Notably, in the monotherapy-treated intracohorts, BioP-VAE achieved a mean AUC of 0.97. Feature attribution analysis revealed key microbial genes. Additionally, we identified distinct predictive microbial signatures via age-stratified analysis, suggesting that host age may modulate microbiome‒immune interactions. Importantly, this is the first large-scale study to evaluate gene-level microbial abundance features for ICI response prediction across multiple cancer types by deep learning. Our findings demonstrate that incorporating biological prior knowledge into deep learning models can improve the discovery of microbial biomarkers that can be generalized across cancer types and treatment settings, offering a novel strategy for patient stratification in immunotherapy.}, } @article {pmid42027256, year = {2026}, author = {Lu, S and Xia, Y and Sun, Q and Sun, Y and Chen, R and Jin, H and Zhang, J and Liu, W and Huang, J}, title = {Characterization of the Gut Virome in Patients with Inflammatory Bowel Disease and Non-Alcoholic Fatty Liver Disease.}, journal = {Journal of inflammation research}, volume = {19}, number = {}, pages = {581751}, pmid = {42027256}, issn = {1178-7031}, abstract = {OBJECTIVE: The dysbiosis of the gut microbiota is a well-known correlate in the pathogenesis of inflammatory bowel disease (IBD). However, the microbiome characteristics of patients with IBD who also have non-alcoholic fatty liver disease (NAFLD) are understudied, particularly the potential pathogenic mechanisms of the gut virome.

MATERIALS AND METHODS: In this study, we conducted a comprehensive gut virome correlation study, along with serum metabolomics analysis, by performing virus-like particle (VLP) and metagenomic sequencing on fecal samples from patients with inflammatory bowel disease and non-alcoholic fatty liver disease (IBD-NAFLD) and NAFLD (MASLD) controls without gastrointestinal diseases.

RESULTS: The results showed that changes in the fecal virome were associated with IBD-NAFLD (MASLD), particularly with an increase in the abundance of Caudovirales in IBD-NAFLD (MASLD) patients. Subsequent analysis of the gut virome identified Bacteroides as the top predicted host for the viruses. Additionally, we identified the pathways involved in all differential metabolites through KEGG annotation analysis, with the highest correlation being the galactose metabolism pathway.

CONCLUSION: In conclusion, by using a customized integrated gut virome catalog tailored for IBD, we revealed the fundamental changes in the gut virome of IBD-NAFLD (MASLD) patients. This study is the first to uncover the specificity of the gut virome in IBD-NAFLD (MASLD) patients and predict Bacteroides as a potential host, suggesting a microbial signature primarily influenced by intestinal inflammation.}, } @article {pmid42027295, year = {2026}, author = {Sangodkar, N and Gonsalves, MJ and Nazareth, DR}, title = {Methanotrophy dominated symbiosis in novel species Gigantidas niobengalensis from the cold seeps of Krishna-Godavari basin.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag014}, pmid = {42027295}, issn = {2633-6685}, abstract = {Bathymodiolus mussels, which are prominent invertebrates at cold seeps and hydrothermal vents, are known for hosting symbiotic microbes within their gills. In this study, the microbial communities associated with the gills of novel bathymodioline mussel Gigantidas niobengalensis from an active cold seep site of Krishna-Godavari (K-G) basin was investigated by 16S rRNA amplicon sequencing. The average abundance of culturable methanotrophs in the gill tissues was 3.4 ± 0.9 × 10[4] CFU g[-1] with average methane oxidation rates of 1.71 ± 0.04 to 1.89 ± 0.02 µM g[-1] d[-1] under aerobic and 1.86 ± 0.001 to 1.98 ± 0.005 µM g[-1] d[-1] under anaerobic conditions. Metagenomic analysis revealed dominance of methanotrophs within the microbial communities comprising of >55% bacterial and >28% archaeal methanotrophs; with phyla Proteobacteria, Firmicutes, Bacteroidetes, Verrucomicrobia, Actinobacteria, Euryarchaeota, and Crenarcheaota being prevalent. Functional classification highlighted methane metabolism (20%) and carbon fixation (22%) as major energy metabolism pathways. This study represents the first metagenomic characterization of gill-associated symbionts in the novel cold seep mussel G. niobengalensis from the Indian Ocean. The findings fill a knowledge gap on chemosynthetic symbioses in Indian cold seep ecosystems and provide insights into metabolic adaptation of G. niobengalensis in the cold seep ecosystem.}, } @article {pmid42027454, year = {2026}, author = {Chen, X and Gong, L and Lu, Y and Liu, W and Liu, F and Li, Q and Wang, L and Qiu, L and Zhang, D and Ye, X}, title = {Epidemiological characteristics and environmental surveillance of human psittacosis in Lishui City, Zhejiang Province, China (2021-2024).}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1769696}, pmid = {42027454}, issn = {1664-302X}, abstract = {INTRODUCTION: Psittacosis, caused by Chlamydia psittaci, is an underdiagnosed zoonosis that can lead to severe pneumonia and fatal outcomes. In China, traditional poultry farming poses substantial risks for avian-to-human transmission, yet comprehensive epidemiological evidence is scarce. To address this gap, we aimed to define the local epidemiology, risk factors, and environmental reservoirs of human psittacosis in Lishui City, Zhejiang Province.

METHODS: We conducted a multi-source epidemiological study (2021-2024) integrating surveillance data, clinical records, contact investigations, and environmental sampling. Cases were confirmed by quantitative polymerase chain reaction (qPCR) or metagenomic next-generation sequencing (mNGS).

RESULTS: We identified 28 laboratory-confirmed cases, showing annual fluctuations in reported case numbers. Infections, mostly confirmed by mNGS, were predominantly sporadic among elderly agricultural workers (mean age 62.6 years), with 96.4% reporting recent poultry exposure. All patients presented with pneumonia; 64.3% developed severe disease, resulting in three deaths. The median diagnostic delay-from symptom onset to diagnosis-was 12 days. A household cluster of three cases was detected; however, no secondary transmission occurred among 205 close contacts outside the household. C. psittaci DNA was detected in 14.79% (21/142) of environmental samples, with the highest number of cases detected in duck manure samples, with the highest positive rate (26.7%). Phylogenetic analysis of 20 ompA gene sequences revealed a predominantly genotype A and the waterfowl-TW genotype, which are closely related to strains from southern China.

DISCUSSION: Psittacosis in Lishui presents as a sporadic but clinically severe disease in older rural residents. The high frequency of severe pneumonia and prolonged diagnostic delay underscores an urgent need to improve clinical suspicion and access to molecular diagnostics. Detection of C. psittaci nucleic acid in environmental samples suggests possible environmental contamination; however, viability and transmissibility were not assessed.}, } @article {pmid42027830, year = {2026}, author = {Chen, L and Ding, Y and Liu, Y and Xie, Q and Hu, J and Wang, M and Zeng, X and Zou, D}, title = {Case Report: Ultrasound guided puncture for type 2 diabetes mellitus combined with psoas abscess-a report of two cases.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1773238}, pmid = {42027830}, issn = {2296-858X}, abstract = {BACKGROUND: Psoas abscess (PA) is a rare infectious disease, with type 2 diabetes mellitus (T2DM) serving as a significant risk factor. The combination of metagenomic next-generation sequencing (mNGS) and ultrasound offers innovative approaches for the rapid and precise treatment of PA.

CASE PRESENTATION: Case 1: A 77-year-old woman presented with lumbar pain was initially misdiagnosed with lumbar disc herniation based on CT scan. Subsequent CT scan and ultrasound-guided puncture confirmed a left lumbar PA. mNGS detected the presence of Streptococcus agalactiae, which was negative on conventional culture. The patient was successfully treated with vancomycin for 5 weeks, with no recurrence at 3-year follow-up. Case 2: A 56-year-old woman with a 10-year history of T2DM presented with poor appetite and fatigue. CT imaging identified a left lumbar PA along with perirenal infection. Pus from ultrasound-guided puncture for conventional culture and mNGS detected the presence of Staphylococcus aureus. Treatment with oxacillin and vancomycin led to clinical resolution. The follow-up CT scan in 2024 indicated complete resorption of the lesion.

CONCLUSION: mNGS combined with ultrasound-guided puncture overcomes conventional culture limitations. This approach suggests clinical feasibility.}, } @article {pmid42028026, year = {2026}, author = {Heinzelmann, D and Reuss, F and Zeh, N and Nilson, R and Walker, E and Fieder, J and Lindner, B and Renner, B and Schulz, P and Fischer, S and Schmidt, M}, title = {Discovery of a chimeric transposase-transposon system for advanced genome engineering.}, journal = {iScience}, volume = {29}, number = {5}, pages = {115548}, pmid = {42028026}, issn = {2589-0042}, abstract = {Transposases have transformed genetic engineering, yet functional systems remain scarce. In response, an unknown transposase system from Acyrthosiphon pisum was identified by metagenomic screening. Through systematic optimization, we enhanced nuclear localization, transposon architecture, and created a hyperactive transposase variant to boost efficiency. Intriguingly, the combined application of the newly discovered transposase with inverted terminal repeat sequences from a related pea aphid species, Aphis craccivora, further enhanced transposition activity, resulting in the first chimeric transposase system reported so far. We investigated the genomic integration events following transposition in mammalian cells to understand the underlying mechanisms and optimize the efficiency of transgene integration. This optimized system can expedite the generation of recombinant protein-producing Chinese Hamster Ovary (CHO) cell lines, even surpassing the hyperactive piggyBac system with regard to cell-specific productivity. These findings introduce a significant addition to the field of semi-targeted transgene integration technologies, offering substantial potential for enhancing biologics manufacturing.}, } @article {pmid42028145, year = {2026}, author = {Chen, Y and Zhang, L and Wang, T and Pan, X and Chen, D and Liu, J}, title = {Characteristics of CD4[+]T-cell reduction and pulmonary infections in critically ill immunocompromised patients.}, journal = {Journal of intensive medicine}, volume = {6}, number = {2}, pages = {157-165}, pmid = {42028145}, issn = {2667-100X}, abstract = {BACKGROUND: The CD4[+]T-cell count is a key indicator for evaluating immunosuppression. Infections significantly influence the survival and prognosis of critically ill patients. This study aims to systematically evaluate the association between reduced CD4[+] T-cell counts and lung infections in immunosuppressed ICU patients, offering clinical evidence to guide the management of lung infections in this population.

METHODS: This retrospective, single-center study included 40 immunocompromised patients admitted to the ICU from January 1, 2021, to June 30, 2023. All participants underwent metagenomic next-generation sequencing. Patients with suspected lung infections based on their CD4[+]T-cell counts were divided into mild (350/µL
RESULTS: Amang these forty immunosuppressed patients, 8 were assigned to the mild group, 16 to the moderate group, and 16 to the severe group. Streptococcus pneumoniae was almost all distributed in moderate patients (75.0%), while severe patients had a higher proportion of fungi detected (25.7%). Respiratory microbiome analysis identified Acinetobacter baumannii, Human alphaherpesvirus 1, and Klebsiella pneumoniae as the most abundant species. Although no significant difference in the alpha diversity index was found among the groups, index values were lower in the severe group than in the moderate group. Beta diversity analysis showed that the microbial community structure did not significantly differ among the three groups. A total of 27 microbial markers were obtained, with multiple streptococcal species showing enrichment in moderate group and Candida tropicalis in severe group. By day 28, four patients (50.0%) in the mild group had died compared with six (37.5%) in the moderate group and nine (56.3%) in the severe group. There were no significant difference in the duration of ICU or hospital stays.

CONCLUSIONS: This study on ICU-admitted immunocompromised patients identified the prevalent pathogens and microbiome features associated with pulmonary infections, as well as their relationship with CD4[+]T-cell depletion. These findings are valuable for optimizing clinical diagnosis and treatment strategies and may contribute to improving patient outcomes.}, } @article {pmid42028191, year = {2026}, author = {Hariharamohan, M and Chindarkar, M and Swain, HS and Rajesh, N and Rajesh, V}, title = {Integrating physicochemical and microbial characterization of red rice broth fermented over an 18-hour period augmented with metagenomic and metabolomic approaches.}, journal = {RSC advances}, volume = {16}, number = {23}, pages = {21129-21141}, pmid = {42028191}, issn = {2046-2069}, abstract = {Fermentation enhances the nutritional properties of foods. Fermented water of Kerala red rice (Oryza sativa L. subsp. indica), traditionally consumed in South India remains underexplored scientifically. This study characterizes the nutritional, microbial, and metabolite profiles of Kerala red rice water (broth) after 18 hours of natural fermentation using biochemical assays, shotgun whole-genome metagenomic sequencing (Illumina NovaSeq X Plus), untargeted gas chromatography-mass spectrometry (GC-MS) metabolomics, and a phytase-mediated mineral release assay. Fermentation enhanced nutritional quality with increase in carbohydrates by 22.7%, protein by 163.52%, and free amino acids by 35.47% compared to unfermented controls. Phytase activity rose from negligible levels to 0.12 U mL[-1]. Metagenomics identified 50 taxa, dominated by Proteobacteria (59.63%) and Firmicutes (40.12%), with ∼34% of the community carrying phytase-encoding genes. Dominant genera included Pantoea, Saccharibacillus, and Bacillus. Fermentation also enhanced mineral release, with calcium, iron, and zinc in the fermented rice water showing increases of approximately 1190%, 566%, and 93%, respectively, relative to unfermented controls over a 360 min in vitro digestion period. These findings provide the first integrated insight bridging traditional dietary practice with modern analytical science.}, } @article {pmid42028978, year = {2026}, author = {Xiao, L and Liu, J and Noyce, GL and Lee, J and Duarte, CM and Zhou, M and Luo, M and Sun, R and Dang, R and Zhou, L and Zhang, L and Fu, C and Tan, Y and Yu, J and Han, G}, title = {Microbial Responses to Warming Reduce Deep Blue Carbon Storage.}, journal = {Global change biology}, volume = {32}, number = {4}, pages = {e70883}, doi = {10.1111/gcb.70883}, pmid = {42028978}, issn = {1365-2486}, support = {U2106209//National Natural Science Foundation of China/ ; 42077025//National Natural Science Foundation of China/ ; 42277236//National Natural Science Foundation of China/ ; 42071126//National Natural Science Foundation of China/ ; 2021213//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; XDA23050202//Strategic Priority Research Program of Chinese Academy/ ; YICE3510303//Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences/ ; }, mesh = {*Soil Microbiology ; *Carbon Cycle ; *Carbon/metabolism ; Soil/chemistry ; *Carbon Sequestration ; Wetlands ; *Climate Change ; *Global Warming ; }, abstract = {Coastal wetlands are critical blue carbon reservoirs, yet the depth-resolved impacts of warming on belowground carbon dynamics remain poorly understood. Over the course of an 8-year in situ experiment, we investigated plant-derived carbon inputs, soil carbon losses via respiration, and microbially mediated carbon fixation across a 60 cm soil profile under a projected 2°C atmospheric warming scenario. Plant carbon fixation (above- and belowground net primary productivity) and soil respiration exhibited synchronized responses to warming, with an initial increase, followed by a decline in the mid-term, and no significant response in the later stages. Soil and microbial respiration stabilized after prolonged exposure to elevated temperatures, as these processes were constrained by substrate availability. In contrast, phospholipid fatty acid profiling, amino sugar biomarkers, and metagenome-assembled genomes consistently indicated a greater than one-third reduction in microbial carbon fixation within subsoils (40-60 cm). Our fully factorial, depth-stratified warming design reveals the particular vulnerability of deep soil microbial carbon retention to long-term climate warming, independent of shifts in plant input or respiratory carbon loss. This work highlights underappreciated pathways influencing soil blue carbon dynamics in a changing world.}, } @article {pmid42028995, year = {2026}, author = {Liu, M and Du, M and Xi, Z and Tastambek, KT and Bao, Y and Song, X and Zhou, A and Wang, Y}, title = {Bacillus aerius synergizes with coal gangue to enhance Medicago sativa growth via soil microbiome and gene regulation.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0026826}, pmid = {42028995}, issn = {1098-5336}, mesh = {*Medicago sativa/growth & development/microbiology ; *Soil Microbiology ; *Microbiota ; *Bacillus/physiology ; Soil/chemistry ; *Coal ; Gene Expression Regulation, Bacterial ; }, abstract = {UNLABELLED: The extensive accumulation of coal gangue poses significant environmental threats through water contamination, soil degradation, and atmospheric pollution, necessitating the urgent development of ecological utilization strategies. This study elucidates the mechanistic basis by which the thermophilic bacterium Bacillus aerius (B. aerius) enhances plant growth in coal gangue-amended sandy soils. Through integrated analysis of nutrient dynamics, phytohormonal activities, soil enzymatic profiles, and metagenomic functional profiling, we demonstrate significant synergy between coal gangue and B. aerius. When applied together in sandy soils, the germination rate, plant height, root length, and fresh biomass of Medicago sativa (alfalfa) increased by 1.18-2.06 times. The levels of soil nitrogen, phosphorus, and potassium also significantly increased, resulting in notable improvements in soil fertility. The bacterial treatment enhanced the activities of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and various soil enzyme activities while also optimizing the microbial community structure and increasing the abundance of beneficial bacteria, including Bacillus. Metagenomic analysis revealed the upregulation of growth-promoting genes such as acdS, nifK, and phnG, which collectively drive plant growth through multiple pathways, including enhanced soil nutrient availability, hormone regulation, soil enzyme activities, and nutrient cycling. Collectively, this work deciphers molecular-scale bacteria-gangue synergism, providing a theoretical foundation for sustainable coal gangue utilization and ecological restoration of degraded soils.

IMPORTANCE: The accumulation of coal gangue poses significant environmental challenges, necessitating the development of eco-friendly utilization strategies. This study demonstrates that the thermophilic bacterium Bacillus aerius acts synergistically with coal gangue to promote alfalfa growth in sandy soils while improving soil fertility. The combined treatment enhanced plant morphological traits, soil nutrient availability, beneficial microbial communities, and associated biological activities, with these effects supported by molecular evidence. As the first study to verify this growth-promoting mechanism, our findings address a critical knowledge gap and provide a theoretical foundation for the sustainable utilization of coal gangue in the ecological restoration of degraded soils.}, } @article {pmid42029028, year = {2026}, author = {Valdez-Nuñez, LF and Chávez, IJ and Sekerci, F and Ayala-Muñoz, D and Straub, D and Kappler, A and Fischer, S and Mansor, M}, title = {Desulfosporosinus and Acididesulfobacillus dominate an acidophilic sulfate-reducing bacteria consortium during acid mine drainage bioremediation.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0030826}, pmid = {42029028}, issn = {1098-5336}, support = {37/1027-1//Deutsche Forschungsgemeinschaft/ ; 503493769//Deutsche Forschungsgemeinschaft/ ; PE501078509-2022-PROCIENCIA//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; }, mesh = {Biodegradation, Environmental ; Mining ; *Sulfates/metabolism ; Hydrogen-Ion Concentration ; *Microbial Consortia ; Peru ; Oxidation-Reduction ; Acids/metabolism ; }, abstract = {Acid mine drainage (AMD) is an environmental threat due to its low pH and high metal content. Biological treatment of AMD using acidophilic sulfate-reducing bacteria (aSRB) represents a potential solution for this problem, but their substrate specificity and low tolerance to extreme acidity (pH ≤3.0) and toxic metals limit their application. Here, we used an indigenous aSRB-containing consortium to remove metals and neutralize a synthetic AMD (sAMD) system starting at pH 2.9. The consortium was enriched from acidic sediments of an abandoned mine tunnel in Peru. A bioremediation experiment (pH 2.9) was set up with Fe[2+] (40.25 mM), Al[3+] (5.39 mM), and Zn[2+] (3.97 mM) as the main dissolved metals. Glycerol and yeast extract were used as carbon sources. Physicochemical parameters, mineral formation, microbial communities, and dissolved metals were monitored for 160-200 days. At the end of the incubation, the final pH reached 6.1 and 100% of Zn[2+], >99% of Fe[2+], and >94% of Al[3+] were removed by the aSRB consortium as X-ray diffraction-amorphous minerals. The aSRB Desulfosporosinus and Acididesulfobacillus dominated the bioremediation experiment. Two high-quality metagenome-assembled genomes taxonomically affiliated to the aforementioned aSRB showed metabolic potential related to sulfur compounds reduction as well as to organic carbon degradation (e.g., glycerol and acetate). Differences related to carbon degradation during AMD bioremediation suggest a synergy between Acididesulfobacillus and Desulfosporosinus, thus avoiding toxic waste product accumulation. Overall, we obtained a novel aSRB-containing microbial consortium that can be used for acidity neutralization and metal removal, suitable for more robust AMD treatment technologies.IMPORTANCEAcid mine drainage (AMD) remains one of the biggest environmental challenges of the mining industry. Treatment technologies based on the application of microbial consortia are gaining popularity, taking advantage of synergistic interactions between different species to widen substrate specificity and to limit toxicity. Our research work here shows two acidophilic sulfate-reducing bacteria, Desulfosporosinus and Acididesulfobacillus, working together in AMD bioremediation. Desulfosporosinus initiated sulfate reduction at pH ~3.0 with glycerol as the carbon source and acetate as the waste product. Once pH rose to ~4.0, Acididesulfobacillus continued with sulfate reduction with acetate as a carbon source, thus avoiding acetate accumulation and cell toxicity. In the end, this synergistic interaction neutralized acidic pH and removed metals to a great extent, making it suitable for biological treatment of AMD.}, } @article {pmid42029155, year = {2026}, author = {Perlas, A and Reska, T and Sánchez-Cano, A and Mejías-Molina, C and Gygax, D and Martínez-Puchol, S and Rusiñol, M and Eger, E and Schaufler, K and Höfle, U and Croville, G and Le Loc'h, G and Guérin, J-L and Urban, L}, title = {Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0254325}, pmid = {42029155}, issn = {1098-5336}, support = {2824HS010//German One Health Platform Pilot Project/ ; PID2020-114060RR-C32//MCIN/AEI/10.13039/501100011033/ ; }, mesh = {*Wetlands ; Animals ; Birds ; Humans ; Host Tropism ; *Water Microbiology ; *Bacteria/genetics/isolation & purification/drug effects ; Influenza A virus/genetics/isolation & purification ; Metagenomics ; Ecosystem ; Viruses/isolation & purification/genetics ; }, abstract = {UNLABELLED: Wetland ecosystems provide interfaces for the transmission of microbial pathogens and antimicrobial resistances (AMR) between migratory birds, wild and domestic animals, and human populations. The efficient surveillance of wetlands is, however, challenging, since the typically low concentration of pathogens requires the sampling of large volumes of water and subsequent targeted detection, which is inherently limited to a few pathogens or AMR genes of interest. Here, we present a holistic, accessible, and cost-efficient framework to characterize the pathogen and resistance load of water sources together with their potential associated hosts by combining passive water sampling through torpedo-shaped devices with nanopore sequencing technology. We used this framework to characterize anthropogenically influenced and natural wetland ecosystems along the East Atlantic Flyway, where we obtained robust assessments of the microbial communities from long-read metagenomic and RNA virome data and showed that anthropogenically impacted wetland ecosystems consistently exhibited higher relative abundances of pathogens and AMR genes. By focusing on avian influenza viruses (AIV), we finally highlight the additional need for targeted screening and whole-genome sequencing of pathogens of interest; we detected and characterized AIV at a third of the monitored sites and used environmental DNA to explore potential animal hosts to better understand the role of wetland ecosystems as One Health interfaces, where the health of animals, humans, and the environment are interconnected and pathogen transmission can occur across these domains.

IMPORTANCE: Wetlands connect wildlife, livestock, and people, making them key places to watch for pathogens and antibiotic resistance. Yet potentially harmful microbes are easy to miss in water because they represent only a small fraction of the abundant microbial life in water, making them hard to detect. We paired 3D-printed passive torpedo-shaped samplers with a portable genetic sequencer to analyze all microbes captured. We deployed this approach at 12 wetlands in Germany, France, and Spain. It revealed local microbial communities, identified disease-causing bacteria, and linked many antibiotic resistance genes to likely bacterial hosts. By comparing locations, we observed that sites near cities, farms, or wastewater had higher levels of pathogens and resistance than protected natural sites. Our analysis also recovered all viruses present, including those from mammals, birds, fish, insects, and plants. We also specifically looked for the virus that causes avian flu, found it at several sites, and classified it as low pathogenicity. Because our method is non-invasive to wildlife, affordable, and practical to deploy, it can provide early warnings to conservation and public health agencies and guide action where risks are present.}, } @article {pmid42029954, year = {2026}, author = {Gao, J and Li, HL and Li, MS and Shao, ZJ and Yang, ZF and Li, CJ and Zhang, ZX and Zhu, D and Lv, ZH and Song, RH and Li, JL and Hu, W and Yin, YR}, title = {Cloning, heterologous expression, and characterization of a metagenome-derived GH10 xylanase with salt and alkali tolerance from Xinjiang saline-alkali soil.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {5}, pages = {}, pmid = {42029954}, issn = {1572-9699}, support = {YWLCYXZX2023300075//the Yunnan Provincial Clinical Medical Center for Emergency Traumatic Diseases/ ; 32560004//the National Natural Science Foundation of China Regional Program/ ; }, mesh = {Cloning, Molecular ; *Metagenome ; *Soil Microbiology ; *Endo-1,4-beta Xylanases/genetics/metabolism/chemistry ; Hydrogen-Ion Concentration ; Enzyme Stability ; Alkalies ; China ; Soil/chemistry ; Salt Tolerance ; Recombinant Proteins/genetics/metabolism/chemistry ; Temperature ; Xylans/metabolism ; Escherichia coli/genetics/metabolism ; Amino Acid Sequence ; Substrate Specificity ; Sodium Chloride ; }, abstract = {Xylanases are widely used in baking, seafood processing, and paper production, but their performance is often compromised under high-salt, acidic, or alkaline conditions, limiting broader industrial deployment. Identifying robust xylanases from saline-alkali environments is therefore of practical importance. Here, we report a GH10 xylanase gene, XynE102, mined from a saline-alkali soil metagenome from Karamay, Xinjiang. The deduced amino acid sequence shares 69.17% identity with a xylanase from Cellvibrionaceae bacterium (GenBank accession HEY7885703.1). XynE102 was cloned and heterologously expressed in Escherichia coli, and the recombinant enzyme was purified by Ni-NTA affinity chromatography. Using beechwood xylan as substrate, XynE102 exhibited optimal activity at 50 °C and pH 7.0. It retained ≥ 50% relative activity between 30 and 55 °C and pH 5.6-8.6, and ≥ 75% activity in 2.0 M NaCl. Notably, after preincubation at 40 °C for 60 and 120 min, its activity increased to 130% and 165% of the initial value, respectively. Following 24 h preincubation at pH 7-10, residual activity remained ≥ 80%, indicating pronounced alkaline stability. At 1 mM, Mn[2+], Co[2+], and Fe[3+] activated the enzyme, whereas Mg[2+], Cu[2+], and Cd[2+] inhibited it; 1% SDS had no measurable effect. XynE102 primarily hydrolyzed xylan to xylobiose and xylotetraose. It also hydrolyzed alkali-treated corn stalk and hot-water-pretreated wheat bran, yielding reducing sugar concentrations of 5.44 mM and 4.18 mM, respectively, after 24 h. Taken together, these results indicate that XynE102 is a neutral-pH xylanase with notable salt and alkali tolerance, supporting its potential for prebiotic XOS production and food-processing applications under moderate temperature conditions.}, } @article {pmid42030718, year = {2026}, author = {Chen, L and Zhong, J and Deng, N and Lin, H and Zhang, L}, title = {Spatiotemporal patterns of arsenic and its microbial arsenic transformation in the Pearl River Estuary.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142145}, doi = {10.1016/j.jhazmat.2026.142145}, pmid = {42030718}, issn = {1873-3336}, mesh = {*Arsenic/analysis/metabolism ; *Estuaries ; *Water Pollutants, Chemical/analysis/metabolism ; Rivers/chemistry/microbiology ; Geologic Sediments/chemistry ; China ; Bacteria/metabolism/genetics ; Seasons ; Metagenome ; Microbiota ; }, abstract = {Estuarine ecosystems are critical zones for arsenic (As) biogeochemical cycling, yet the spatiotemporal distribution and microbial transformation mechanisms of As in these dynamic environments remain poorly understood. This study integrated geochemical analyses with metagenomic and metatranscriptomic approaches to investigate As distribution and microbial transformation mechanisms in Pearl River Estuary (PRE). Our results revealed distinct spatiotemporal patterns of As in the PRE. As in sediment were significantly higher in the western region and exhibited a clear decreasing gradient from upstream to downstream. As(V) was the dominant species in both sediments and water, while organic As remained below detection limits. Seasonally, As concentrations peaked in winter and spring. Microbial community analysis showed that highly diverse microbial taxa capable of transforming As were detected, with Proteobacteria identified as the dominant phylum. Among key functional genes, arsM exhibited the highest abundance and transcription level, indicating substantial methylation potential throughout the estuary. Notably, metagenome-assembled genome (MAG) analysis uncovered a previously undocumented metabolic transition along the estuarine gradient, shifting from As(V) reduction coupled with methylation and efflux in upstream to As(III) oxidation with a more diversified strategy in mid-downstream. This systematic study clarified the distribution and microbial transformation mechanisms of As in the PRE, advancing our understanding of As biogeochemical cycling in estuarine ecosystems.}, } @article {pmid42030844, year = {2026}, author = {Zhao, H and Che, W and Tan, X and Shen, Y and Xu, Y and Man, Y}, title = {Distribution characteristics and potential microbial degradation mechanisms of microplastics in oyster aquaculture areas of southern China.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142136}, doi = {10.1016/j.jhazmat.2026.142136}, pmid = {42030844}, issn = {1873-3336}, mesh = {*Microplastics/metabolism/analysis ; *Aquaculture ; Animals ; China ; *Water Pollutants, Chemical/analysis/metabolism ; Biodegradation, Environmental ; *Ostreidae ; *Bacteria/metabolism/genetics ; Seawater ; Environmental Monitoring ; Geologic Sediments/microbiology ; }, abstract = {Microplastic (MP) pollution in coastal aquaculture is a growing environmental and public health concern. Despite increasing reports, the cross-regional and cross-media pollution patterns, ecological risks, and microbial degradation potentials in aquaculture ecosystems remain poorly understood. We investigated oyster farming systems in South China: Zhanjiang Bay (ZJB, semi-enclosed) and Xuwen (XW, open coast). MP abundances ranged from 20 to 54 items/L in seawater and 950-6483 items/kg in sediment, with particles < 50 μm and granular shapes dominant in both media, as determined by Laser Direct Infrared Imaging. MP spatial patterns differed markedly between regions; XW exhibited higher seawater MP levels attributed to larger farming scales, whereas ZJB showed greater sediment MP accumulation owing to weaker water exchange and a longer farming history. Source apportionment identified aquaculture facilities as the primary source (44.86%). Notably, while the overall pollution load was relatively low, the potential ecological risk index reached 866.51 (classified as "dangerous"), driven predominantly by highly toxic polymers such as polyurethane (PU) and polyvinyl chloride (PVC). The distribution of plastic-degrading genes (PDGs) and their host microbial communities was primarily determined by these aquaculture facilities and the environmental medium (sediment vs. seawater), rather than by localized water-quality conditions. Metagenomic analysis identified sediments as key metabolic hotspots, harboring diverse functional genes involved in polyethylene β-oxidation, polystyrene aromatic ring cleavage, and PU hydrolysis. These findings bridge the gap in understanding MP dynamics between diverse aquaculture habitats and highlight the potential of indigenous microbes in natural attenuation, providing critical insights for MP risk management.}, } @article {pmid42030878, year = {2026}, author = {Saini, K and Prajapati, A and Kumar, SS and Kumar, V and Bajar, S}, title = {Performance assessment of sulfate-reducing bacterial consortium for the treatment of real landfill leachate under anaerobic conditions.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129743}, doi = {10.1016/j.jenvman.2026.129743}, pmid = {42030878}, issn = {1095-8630}, mesh = {*Water Pollutants, Chemical/metabolism ; *Sulfates/metabolism ; Biodegradation, Environmental ; Anaerobiosis ; Bacteria/metabolism ; RNA, Ribosomal, 16S ; Metals, Heavy/metabolism ; Biological Oxygen Demand Analysis ; Waste Disposal, Fluid/methods ; }, abstract = {Landfill leachate contains complex organic pollutants, ammonia, sulfate, and toxic metals, posing major environmental challenges. This study evaluated a sulfate-reducing bacterial (SRB) consortium isolated from electroplating wastewater for the treatment of real landfill leachate under anaerobic conditions. Physicochemical characterization revealed a Leachate Pollution Index (LPI) of 63.16, confirming the high hazardous nature of the leachate. The acclimatized SRB consortium exhibited strong metabolic activity and rapidly degraded pollutants. Within 10 days of treatment, the system achieved 82.84% removal of chemical oxygen demand (COD) and 97.83% removal of biochemical oxygen demand (BOD5), demonstrating efficient biodegradation of both biodegradable and persistent organic compounds. The concentrations of heavy metals were reduced to below the detection limit (BDL), primarily due to sulfide-mediated precipitation. Thus, SRB provide dual benefits of organic degradation and metal detoxification. Metagenomic profiling (16S rRNA sequencing) revealed dominant sulfate-reducing species, including Desulfovibrio vulgaris, Desulfotomaculum nigrificans, Desulfobulbus propionicus, and Desulfosporosinus orientis. Kyoto Encyclopedia of Genes and Genomes (KEGG) based functional annotation was performed to elucidate the metabolic potential of the SRB consortium. Scanning electron microscopy (SEM) analysis before and after treatment confirmed microbial colonization and sulfide-mediated metal precipitation. Overall, SRB-based anaerobic processes demonstrate significant potential as a sustainable and efficient treatment for high-strength landfill leachate with strong potential for scale-up and integration into waste management systems. Although the treated effluent did not meet CPCB (India) and EPA COD discharge standards, this bioremediation approach provides a cost-effective alternative to conventional physicochemical treatments. Further optimization of operational parameters and microbial activity could enhance treatment efficiency and facilitate regulatory compliance.}, } @article {pmid42030912, year = {2026}, author = {Hua, Y and Xu, X and Chen, Y and Li, Y and Dai, X}, title = {Making waves: Wastewater sludge holds untapped antimicrobial potential.}, journal = {Water research}, volume = {300}, number = {}, pages = {125989}, doi = {10.1016/j.watres.2026.125989}, pmid = {42030912}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Wastewater ; *Anti-Infective Agents ; Antimicrobial Peptides ; Waste Disposal, Fluid ; }, abstract = {Wastewater treatment plants are widely recognized as critical nodes in the environmental dissemination and control of antimicrobial resistance (AMR). This risk-focused view is warranted, but incomplete. Wastewater sludge is one of the largest engineered and repeatedly accessible microbiomes on Earth, continuously shaped by diverse microbial inputs and exposure to antimicrobial compounds and other stressors. These conditions may also harbor underexplored antimicrobial functions. Here we propose framing sludge as a dual-function node within AMR stewardship: a resource for routine surveillance and risk management, and a source material for an offline, containment-first workflow to identify antimicrobial candidates, particularly antimicrobial peptides. We summarize recent advances in metagenomics and machine-learning-enabled peptide prioritization and outline an evidence ladder that links sequence signals to functional validation. A central principle is to decouple discovery from plant operations and to apply explicit decision gates early in the pipeline, including cross-resistance screening and resistance-evolution assays, to prevent inadvertently increasing selection pressure or AMR risks. Finally, we call for shared benchmarks to improve comparability across studies, including curated datasets, standardized validation panels, and routine reporting of negative findings and resistance-related outcomes. Together, these steps can help translate sludge-enabled discovery into environmentally responsible innovation aligned with AMR stewardship.}, } @article {pmid42030968, year = {2026}, author = {Brown, JR and Chiu, CY and López-Labrador, FX and de Vries, JJC}, title = {The impact of clinical metagenomic testing on patient management: facts versus fantasy.}, journal = {The Lancet. Infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/S1473-3099(26)00106-4}, pmid = {42030968}, issn = {1474-4457}, abstract = {Clinical metagenomic testing by agnostic, unbiased next-generation sequencing is a diagnostic approach with the broad-based capacity to detect all known and novel pathogens in a single assay. After the discovery of this potentially transformative method decades ago, the availability of clinical metagenomic testing in the daily practice of the infectious disease specialist is accelerating. Prospective metagenomic studies have supplemented the substantial existing body of retrospective, exploratory literature, and these reports offer us a glimpse into the real-world use of clinical metagenomic testing for the diagnosis of infections in patients. In this Review, we examine the evidence collected from the prospective reports published to date, focusing on their impact on patient management, treatment, and outcomes.}, } @article {pmid42031746, year = {2026}, author = {Yang, Y and Zhang, H and Herbold, CW and Huang, Y and Wang, R and Liu, J and Zhang, D and Ou, J and Zheng, F and Mao, C and Huang, J and Yu, Y and He, J and He, Z and Yan, Q}, title = {Trophic status strongly regulates nitrous oxide but not methane production in global freshwater lake sediments.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42031746}, issn = {2041-1723}, support = {92051120//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32030015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470097//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100086//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Nitrous Oxide/metabolism/analysis ; *Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; *Methane/metabolism ; Denitrification ; Nitrification ; Eutrophication ; Greenhouse Gases/metabolism ; }, abstract = {Freshwater lakes are globally significant sources of potent greenhouse gases (GHGs), but how their GHGs emissions respond to changing nutrient levels remains unclear. Here, we demonstrated that nitrous oxide (N2O) production pathways in lake sediments are tightly linked to trophic state, whereas methane (CH4) production appears to be multifactorial Through global metagenomics and controlled batch experiments. In eutrophic sediments, N2O is efficiently removed through complete denitrification, with nitrification serving as the main production pathway, whereas oligotrophic sediments produce N2O primarily via incomplete denitrification. By simulating nutrient transitions using an innovative cross-inoculation experiment, we further revealed that lake sediments systematically shift between these N2O production pathways as their trophic state changes, from denitrification-driven to nitrification-dominated during eutrophication, with the inverse pattern during oligotrophication. Consequently, N2O emissions can be effectively mitigated by inhibiting nitrification in eutrophic lakes and restricting incomplete denitrification in oligotrophic ones. Our findings establish trophic status as a key driver of N2O production sources in lake sediments.}, } @article {pmid42031750, year = {2026}, author = {Hallgren, J and Dharamshi, JE and Rodríguez-Gijón, A and Nuy, J and Garcia, SL and Jonas, K}, title = {Addendum: Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42031750}, issn = {2041-1723}, } @article {pmid42032005, year = {2026}, author = {Gladkikh, AS and Naydenov, DD and Sharova, AA and Popova, MR and Arbuzova, TV and Klyuchnikova, EO and Sbarzaglia, VA and Gibitova, EA and Forghani, M and Tokarevich, NK and Lunina, GA and Ramsay, ES and Dedkov, VG}, title = {Metaviromic analysis of Ixodes ticks in Northwestern Russia reveals high viral diversity and novel RNA virus lineages.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42032005}, issn = {2045-2322}, support = {N. 24-45-20005//RSF grant/ ; }, mesh = {Animals ; *Ixodes/virology ; Russia ; Phylogeny ; *RNA Viruses/genetics/classification/isolation & purification ; *Genome, Viral ; *Virome/genetics ; Genetic Variation ; }, abstract = {Ticks of the genus Ixodes are recognized as important vectors of a wide range of viral pathogens with potential implications for public and veterinary health. Recent advances in metagenomic sequencing have uncovered an unprecedented diversity within tick-associated viromes, yet much of the global tick metavirome remains unexplored, particularly in vast and ecologically diverse regions such as Northwestern Russia. In this study, we present a comprehensive metaviromic and phylogenetic characterization of viruses detected in Ixodes persulcatus and Ixodes ricinus ticks collected from five regions in Northwestern Russia between 2021 and 2023. Using high-throughput RNA sequencing, we identified viral sequences representing families Nairoviridae, Partitiviridae, Phenuiviridae, Flaviviridae, Chuviridae, and Narnaviridae, Orthototiviridae. Putative novel viral lineages were identified. Phylogenetic analyses revealed strong geographic structuring of some viral lineages. This suggests either the presence of local genotypes, or underrepresentation of Eurasian tick-associated viromes, in current databases. In addition to TBEV, other viruses previously associated with human illness were detected in ticks in Northwestern Russia (Beiji nairovirus, Mukawa virus). Our findings provide the first high-resolution snapshot of the tick virome in Northwestern Russia. They emphasize the importance of continued viral surveillance in underrepresented biogeographic zones. These data contribute to the growing global virome map and may inform the development of region-specific vector-borne disease countermeasures.}, } @article {pmid42032049, year = {2026}, author = {Zhang, X and Li, W and Wu, H and Cai, T and Chen, H and Zeng, S}, title = {Enhanced pathogen identification in fungal endophthalmitis by metagenomic next-generation sequencing: a retrospective clinical evaluation.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42032049}, issn = {2045-2322}, support = {LHGJ20220091//Henan Province Medical Science and Technology Key Project/ ; 2023A1515012220//Guangdong Basic and Applied Basic Research Foundation/ ; 2024ZDJS120//Guangdong Province Research Capability Improvement Project for Key Construction Disciplines/ ; 2025XSJ013；2024XK003；2021BQ011//Nanfang College Guangzhou/ ; }, mesh = {*Endophthalmitis/microbiology/diagnosis ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; *Eye Infections, Fungal/microbiology/diagnosis ; Aqueous Humor/microbiology ; Vitreous Body/microbiology ; *Fungi/genetics/isolation & purification/classification ; Aspergillus flavus/genetics ; }, abstract = {Fungal endophthalmitis (FE) is a vision-threatening emergency that requires rapid pathogen identification. Conventional microbial culture demonstrates limited sensitivity in FE, warranting improved diagnostic approaches. We evaluated the detection performance of unbiased metagenomic next-generation sequencing (mNGS) in 31 clinically diagnosed FE cases, including 16 vitreous humor (VH) and 15 aqueous humor (AH) specimens. mNGS showed a positivity rate of 90.3% (28/31, 95% CI: 74.2%-98%), outperforming culture (9.1%, 2/22, 95% CI: 1.1%-29.2%). The positivity rates were 100% for endogenous FE and 85% for exogenous FE, while VH and AH specimens achieved 100% and 80% positivity, respectively. mNGS identified polymicrobial infections in 5 exogenous cases, and a total of 15 fungal species across 9 genera, dominated by Aspergillus flavus, Candida albicans, and Aspergillus niger. Candida albicans and Aspergillus flavus were the predominant pathogens in endogenous and exogenous FE, respectively. Notably, mNGS enabled detection of rare fungal species including Aspergillus niger, Aspergillus welwitschiae, Fusarium oxysporum, Memnoniella echinata, Rhizopus oryzae, Rhizopus microsporus, Chaetomium globosum, and Debaryomyces fabryi. Sequencing results were supported or supplemented by culture, beta-D-glucan, and galactomannan testing in selected cases. Among mNGS-positive cases, 82.1% (23/28) experienced clinical management changes guided by fungal identification. We further propose a laboratory workflow integrating mNGS with conventional assays, tailored to the obtained specimen volume of intraocular fluids.}, } @article {pmid42032279, year = {2026}, author = {Ducarmon, QR and Karcher, N and Giri, S and Tytgat, HLP and Delannoy-Bruno, O and Pekel, S and Springer, F and Wörz, P and Schudoma, C and Typas, A and Zeller, G}, title = {Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires.}, journal = {Nature microbiology}, volume = {11}, number = {6}, pages = {1739-1753}, pmid = {42032279}, issn = {2058-5276}, support = {LUMC Fellowship//Leids Universitair Medisch Centrum (Leiden University Medical Center)/ ; 395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01KD2102A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; }, mesh = {Humans ; Metagenome ; *Gastrointestinal Microbiome/genetics ; *Bacteria/enzymology/genetics/classification ; *Metagenomics/methods ; Colorectal Neoplasms/microbiology ; Substrate Specificity ; Carbohydrate Metabolism ; Mucins/metabolism ; }, abstract = {Carbohydrate-active enzymes (CAZymes) are crucial for digesting glycans, but tools for CAZyme profiling and interpretation of substrate preferences in microbiome data are lacking. Here we develop a CAZyme profiler called Cayman (Carbohydrate Active Enzymes Profiling of Metagenomes) and a hierarchical substrate annotation scheme for use with genomic or shotgun metagenomic datasets. Using these tools, we systematically surveyed CAZymes in human gut microorganisms (n = 107,683 genomes) and identified several putative mucin-foraging bacteria, including Hungatella and Eisenbergiella species, which were confirmed experimentally. We compared CAZymes in gut metagenomes (n = 3,960) from high-income settings versus low- and middle-income settings and found that low- and middle-income setting metagenomes are enriched in fibre-degrading CAZymes, while CAZyme richness is generally higher in high-income setting metagenomes. Additional analysis (n = 1,998) indicated that metagenomes of individuals with colorectal cancer are depleted in fibre-targeting and enriched in glycosaminoglycan-targeting CAZymes. Finally, we inferred CAZyme substrates from genomic co-localization of CAZyme domains. Cayman is broadly applicable and freely available from https://github.com/zellerlab/cayman .}, } @article {pmid42032281, year = {2026}, author = {Tonkin-Hill, G and Shao, Y and Zarebski, AE and Mallawaarachchi, S and Xie, O and Mäklin, T and Thorpe, HA and Davies, MR and Bentley, SD and Lawley, TD and Corander, J}, title = {Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.}, journal = {Nature microbiology}, volume = {11}, number = {6}, pages = {1626-1638}, pmid = {42032281}, issn = {2058-5276}, support = {2025515//Department of Health | National Health and Medical Research Council (NHMRC)/ ; DE240100316//Department of Education and Training | Australian Research Council (ARC)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; }, mesh = {Humans ; *Metagenomics/methods ; Algorithms ; Polymorphism, Single Nucleotide ; Streptococcus pneumoniae/genetics ; Plasmodium falciparum/genetics ; Feces/microbiology ; COVID-19/transmission ; Malaria, Falciparum/transmission ; Gastrointestinal Microbiome/genetics ; Metagenome ; Infant ; High-Throughput Nucleotide Sequencing ; }, abstract = {Coexisting strains of the same species within metagenomic data pose a substantial challenge to inferring transmission of pathogenic and commensal microbes. Here we present TRAnsmission Clustering of Strains (TRACS), a highly accurate algorithm for estimating genetic distances between strains at the level of individual single nucleotide polymorphisms, which is robust to intra-species diversity within the host. Analysis of faecal microbiota transplantation datasets and extensive simulations demonstrates that TRACS outperforms existing methods. We use TRACS to infer transmission networks in patients colonized with multiple strains, including severe acute respiratory syndrome coronavirus 2 amplicon sequencing data, deep population sequencing data of Streptococcus pneumoniae and single-cell genome sequencing data from patients infected with Plasmodium falciparum. Applying TRACS to gut metagenomic samples from a mother-infant cohort revealed species-specific transmission rates and identified increased the persistence of Bifidobacterium breve in infants, a finding previously missed owing to the presence of multiple strains. Our study shows that TRACS can be used across microbial kingdoms to uncover strain dynamics.}, } @article {pmid42032282, year = {2026}, author = {}, title = {Benchmarking shotgun metagenomics.}, journal = {Nature microbiology}, volume = {11}, number = {5}, pages = {1149-1150}, pmid = {42032282}, issn = {2058-5276}, } @article {pmid42032888, year = {2026}, author = {Wu, S and Wang, Y and Li, H and Fang, X and Guo, J and Luo, X and Li, M and Song, F and Tan, Q and Deng, X and Xiao, S and Liu, H and Hu, C and Pan, Z}, title = {Rhizosphere microbiome influences fruit quality in citrus.}, journal = {The New phytologist}, volume = {250}, number = {6}, pages = {3914-3931}, doi = {10.1111/nph.71159}, pmid = {42032888}, issn = {1469-8137}, support = {2023YFD2300603//The National Key Research and Development Program of China/ ; 2017YFD0202001//The National Key Research and Development Program of China/ ; 2019YFD1000103//The National Key Research and Development Program of China/ ; }, mesh = {*Rhizosphere ; *Microbiota/genetics ; *Fruit/microbiology ; *Citrus/microbiology ; Iron/metabolism ; Bacteria/genetics/metabolism ; Siderophores/metabolism ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {Fruit quality is shaped by both crop genetics and cultivation environments, with soil conditions driving rhizosphere microbiome assembly. While rhizosphere microbes are known to enhance nutrient utilization and plant metabolism, their direct contribution to fruit quality regulation remains poorly understood. In this study, we demonstrate that the Satsuma mandarin (Citrus unshiu Marc.) and Navel orange (Citrus sinensis L. Osbeck) rhizosphere microbiome influence fruit sugar concentration, a key determinant of fruit quality. The rhizosphere core microbiota and soil mineral nutrients were positively correlated with fruit quality indices. Fruit quality-correlated bacterial operational taxonomic units (OTUs) explained an average of 32.6% of the observed variation in quality parameters. Inoculation with three bacterial strains (affiliated with Burkholderia, Pseudomonas, Rhizobium) and two bacterial consortia significantly increased fruit sugar concentrations. Metagenomic analysis linked sugar-associated microbes to iron (Fe) utilization, revealing genomic enrichment of siderophore biosynthesis gene clusters. Consistently, the selected bacterial strains exhibited siderophore secretion capabilities, increased leaf Fe content by 23.3-47.8% in citrus rootstock. Further field application of chelated-Fe fertilizer also increased fruit sugar concentration. Collectively, our results revealed an influence of the rhizosphere microbiome on fruit quality that is related to Fe acquisition optimization and subsequent sugar accumulation in citrus.}, } @article {pmid42032992, year = {2025}, author = {Huang, Z and Wei, J and Luo, J and Pan, X and Wei, C and Zhou, Y and Xiao, S and Xu, N and Zhong, Y and Luo, M}, title = {[Comparison of 16S rRNA gene hypervariable regions V3-V4 and V4 sequencing results of gut microbiota in obese children with non-alcoholic fatty liver disease].}, journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences}, volume = {50}, number = {12}, pages = {2312-2324}, pmid = {42032992}, issn = {1672-7347}, support = {2022JJ40668//the Natural Science Foundation of Hunan Province/ ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology ; *RNA, Ribosomal, 16S/genetics ; Child ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Feces/microbiology ; *Pediatric Obesity/microbiology/complications ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: 16S rRNA gene sequencing is an important method for studying microbial structure in samples. However, whether selecting different hypervariable regions for sequencing in the same sample affects the results remains unclear. This study aims to compare the sequencing results of 16S rRNA gene hypervariable regions V3 to V4 and V4 in children with obesity-related non-alcoholic fatty liver disease (NAFLD), and to provide evidence for scientifically evaluating gut microbiota detection results in obese children with NAFLD.

METHODS: Obese children with NAFLD and children with simple obesity who visited Hunan Children's Hospital between January 2019 and September 2021 were selected as study subjects. Fecal samples were collected, and total DNA was extracted. After PCR amplification of the gut microbiota V3 to V4 region and V4 region, sequencing was performed. α-diversity, β-diversity, and microbial community structure differences between the 2 hypervariable regions were compared. Seven samples were selected for metagenomic sequencing as the gold standard to evaluate the performance of V3 to V4 and V4 region sequencing.

RESULTS: A total of 145 participants were included, including 92 in the case group and 53 in the control group. The number of operational taxonomic units (OTUs) obtained by V3 to V4 sequencing (16 977) was higher than that obtained by V4 sequencing (3 362). α-diversity analysis showed that in the overall population, the Shannon index (5.49±1.11) and Chao1 index (1 843.04±580.78) in the V3 to V4 region were higher than the Shannon index (4.98±0.65) and Chao1 index (379.59±47.27) in the V4 region (all P<0.001). β-diversity analysis showed overall differences in microbial community structure between the V3 to V4 and V4 regions, and the intergroup differences were greater than the intragroup differences (P<0.05). Welch's t-test results showed that in the overall population, the numbers of differential taxa detected by V3 to V4 and V4 sequencing at the phylum, class, order, family, and genus levels were 2, 9, 35, 33, and 72, respectively; in the case group, the numbers were 1, 9, 32, 35, and 66; and in the control group, the numbers were 0, 7, 27, 21, and 0. Linear discriminant analysis effect size (LEfSe) analysis showed that V3 to V4 sequencing identified 29 differential taxa between the case group and control group, whereas V4 sequencing identified 7 differential taxa. Sensitivity analysis showed that the Shannon index obtained by V3 to V4 sequencing (5.41±1.62) was not significantly different from that of metagenomic sequencing (6.39±0.42) (P=0.169), while the Chao1 index (1 889.92±781.73) was lower than that of metagenomic sequencing (3 092.71±505.89), with a statistically significant difference (P<0.01). The Shannon index and Chao1 index obtained by V4 sequencing were both lower than those of metagenomic sequencing, with statistically significant differences (4.89±0.94 vs 6.39±0.42, 362.41±35.22 vs 3 092.71±505.89, respectively, both P<0.01).

CONCLUSIONS: Sequencing of the V3 to V4 and V4 regions of the 16S rRNA gene affects the results of gut microbiota structure analysis in obese children. The V3 to V4 region is more likely to detect differential taxa between case and control groups and provides a more accurate estimation of α-diversity. It may therefore be considered a preferred region for gut microbiota sequencing in children with NAFLD. However, there is currently no unified standard for selecting V regions in 16S rRNA gene sequencing, and the detection region and method should be selected comprehensively according to research objectives and sample characteristics.}, } @article {pmid42033828, year = {2026}, author = {Liu, X and Li, N and Wu, WM and Ambrosini, R and Zhong, B and Mei, X and Liu, R and Zhou, L and Yi, S and He, Y}, title = {Freeze-thaw aging and microbial colonization converts microplastics into nitrogen cycling hotspots.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142170}, doi = {10.1016/j.jhazmat.2026.142170}, pmid = {42033828}, issn = {1873-3336}, mesh = {*Microplastics/metabolism/chemistry ; *Freezing ; *Nitrogen Cycle ; *Nitrogen/metabolism ; Bacteria/metabolism/genetics ; }, abstract = {As global warming intensifies, the frequency of freeze-thaw events increases, significantly impacting microbial metabolism and biogeochemical cycling. However, the synergistic effects of freeze-thaw cycles (FTCs) and pervasive microplastics (MPs) on microbial community assembly and nitrogen cycling remain poorly understood. Here, we conducted a microcosm experiment integrating metagenomic and random forest model to elucidate the co-regulatory mechanisms of FTCs and MPs on plastisphere microbial communities and nitrogen metabolism. Results revealed that FTCs accelerated the environmental aging of MPs, inducing surface cracking and oxidation, thereby creating microenvironments favorable for microbial colonization. In the experimental microcosms, the combined effects of FTCs and presence of MPs increased microbial richness and diversity, promoted community differentiation between sediment and plastisphere, and increased microbial niche specialization. Functional analyses showed that FTCs induced a functional reconfiguration of the plastisphere nitrogen metabolism, with a selective enrichment of key enzyme genes, such as nitrite reductase, which may enhance nitrite redox activity and N2O emission capacity. In the plastisphere, the contribution of Acinetobacter to nitrogen cycling increased, whereas Nitrospira declined, possibly due to oxygen limitation. Overall, our findings suggested that FTCs may facilitate transformation of MPs from inert pollutants into potentially metabolically active microhabitats, providing critical insights for assessing emerging pollutants and climate change.}, } @article {pmid42033834, year = {2026}, author = {Su, S and Lin, M and Li, K and Lin, J and Chen, Z}, title = {Soil aggregates as functional units for cadmium sequestration: Differential regulation by nitrogen enrichment and labile carbon inputs.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142196}, doi = {10.1016/j.jhazmat.2026.142196}, pmid = {42033834}, issn = {1873-3336}, mesh = {*Cadmium/chemistry ; *Nitrogen/chemistry ; *Soil Pollutants/chemistry ; *Carbon/chemistry ; *Soil/chemistry ; Soil Microbiology ; Glucose/chemistry ; }, abstract = {While cadmium (Cd) speciation in soil is known to control its environmental risk, how nitrogen (N) enrichment and labile organic carbon (LOC) inputs redistribute Cd fractions within soil aggregates remains unclear. This study examined how ammonium enrichment (AT), nitrate enrichment (NT), and glucose input (CT) altered carbonate-bound Cd (CB-Cd) and organic matter-bound Cd (OM-Cd) within soil aggregates. Both N enrichment and glucose input enhanced CB-Cd formation, with CT increasing CB-Cd by 39.19% via stimulated microbial activity and carbonate precipitation. Different sources of enriched N regulated OM-Cd, with AT decreasing OM-Cd by 15.55%, and NT increasing OM-Cd by 24.61%. This was attributed to competitive adsorption and suppressed microbial decomposition of recalcitrant organic matter. Aggregate hierarchy was also crucial in determining Cd speciation, where macroaggregates, with higher LOC and genes involved in carbonate precipitation, favored CB-Cd partitioning, whereas microaggregates, with greater surface area and enriched alkyl/aromatic C, served as the major OM-Cd sink. Microbial community analysis revealed that glucose reshaped communities, enriching r-strategists like Amycolatopsis and Trichoderma, which were positively correlated with CB-Cd and OM-Cd. Metagenomic data indicated that glucose stimulated genes for labile C degradation, reinforcing CB-Cd formation, while N addition suppressed C-degradation genes. Random forest and PLS path models identified alkyl C, O-alkyl C, and polysaccharide derivatives as primary SOC components regulating CB-Cd, while alkyl C, phenolic, and aromatic compounds regulating OM-Cd. These findings reveal a mechanism for stabilizing Cd in less bioavailable fractions via SOC and N management, leveraging soil aggregates' role in long-term metal sequestration.}, } @article {pmid42033969, year = {2026}, author = {Tian, J and Wang, L and Wang, Y and Zheng, M and Sun, C}, title = {Distribution characteristics of emerging contaminants and microbial communities in Bohai Sea sediments.}, journal = {Marine environmental research}, volume = {219}, number = {}, pages = {108068}, doi = {10.1016/j.marenvres.2026.108068}, pmid = {42033969}, issn = {1879-0291}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Water Pollutants, Chemical/analysis ; China ; *Environmental Monitoring ; *Microbiota ; Bacteria ; }, abstract = {As a semi-enclosed marginal sea in China, the Bohai Sea has long been influenced by substantial pollutant inputs from surrounding rivers, making it an important region for investigating the distribution patterns of pollutants and microbial communities. In this study, the concentrations of emerging contaminants (ECs) in 19 sediment samples were determined, and metagenomic sequencing was employed to systematically analyze the structure and functional characteristics of microbial communities. The results showed that the detected ECs included synthetic musks (SMs, 7.96-22.85 ng/g dw), dominated by tonalide (AHTN) and galaxolide (HHCB); organophosphate esters (OPEs, not detected-282.27 ng/g dw), were not detected in most samples, but relatively high concentrations were observed at the NS-33 station; and polyhalogenated carbazoles (PHCZs, 0.70-4.36 ng/g dw), with 3,6-dichlorocarbazole (36-CCZ) constituting 61.87% of PHCZs. The microbial community was dominated by Proteobacteria (68.36%). Further network analysis indicated significant correlations between PHCZs and nitrogen metabolism genes, suggesting that PHCZs may inhibit nitrogen fixation and nitrification, while enhancing denitrification. Overall, this study reveals the distribution patterns of ECs and microbial communities in Bohai Sea sediments and their potential associations, providing insights into their interactions in coastal ecosystems.}, } @article {pmid42033990, year = {2026}, author = {Wu, Q and You, J and Li, D and Tang, S and Wu, S and Wang, Q and Teng, W}, title = {Oxygen vacancy-rich nanosystems eradicate stubborn periodontal biofilms by synergistic EPS degradation, metabolic activation and microbiome restoration.}, journal = {Biomaterials}, volume = {333}, number = {}, pages = {124234}, doi = {10.1016/j.biomaterials.2026.124234}, pmid = {42033990}, issn = {1878-5905}, mesh = {*Biofilms/drug effects ; Molybdenum/chemistry ; *Oxygen/chemistry ; *Periodontitis/microbiology/drug therapy/therapy ; *Microbiota/drug effects ; Humans ; Indocyanine Green/chemistry/pharmacology ; Animals ; *Nanoparticles/chemistry ; Photochemotherapy ; Photosensitizing Agents/chemistry/pharmacology ; Reactive Oxygen Species/metabolism ; }, abstract = {Periodontitis-associated biofilms pose a severe public health threat due to a dual defense mechanism. This involves a protective physical matrix barrier and biological interference from persistent bacteria and microbial dysbiosis. Current strategies often fail to penetrate deeply, eradicate dormant persisters and resolve microbial dysbiosis, leading to biofilm resistance and disease recurrence. In this study, we develop a multifunctional nanoplatform combining photothermal, photodynamic therapy and peroxidase-like catalysis to execute a sequential strategy. This system integrates molybdenum oxide nanodots rich in oxygen vacancy (MoO3-x) with the photosensitizer indocyanine green (ICG). It exhibits improved optical and enzymatic performance due to the introduced oxygen vacancies. Upon irradiation, the system produces localized hyperthermia and ROS storms to destabilize the biofilm matrix and promote ultrasmall nanodots penetration. The thermal and oxidative stress increase membrane permeability and reactivate metabolism of dormant persisters. Metagenomic analyses confirms that MoO3-x/ICG-treated biofilms show decreased abundance of key persistence-related genes and great enrichment in metabolic pathways. Additionally, the platform exhibits therapeutic effects and a successful shift towards a healthier oral microbiota in periodontitis model. Overall, MoO3-x/ICG demonstrates excellent biofilm eradication and successfully prevents biofilm regrowth or secondary infection. This work targets the entire biofilm lifecycle and presents a nanoplatform for long-term management of periodontal infections.}, } @article {pmid42034087, year = {2026}, author = {Liao, S and Lin, X and Wang, X and Lin, J and Lu, Y and Deng, W and He, Q and Chi, Y and Xu, Z}, title = {Insights into the salt-dependent mechanisms of physicochemical changes, microbial succession, and biogenic amine formation during Doubanjiang fermentation.}, journal = {Food chemistry}, volume = {516}, number = {}, pages = {149287}, doi = {10.1016/j.foodchem.2026.149287}, pmid = {42034087}, issn = {1873-7072}, mesh = {*Biogenic Amines/metabolism ; Fermentation ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Sodium Chloride/metabolism/analysis ; *Wine/microbiology/analysis ; Microbiota ; }, abstract = {Excessive biogenic amine formation is a major safety concern in salt-reduced Doubanjiang fermentation. This study compared high- (12%), medium- (9%), and low-salt (6%) systems to elucidate physicochemical dynamics, microbial succession, and mechanisms promoting biogenic amine accumulation. Salt reduction accelerated acidification and proteolysis, with the low-salt system showing the highest total acidity (0.73 g/100 g) and free amino acids (2684.86 mg/100 g), accompanied by excessive biogenic amine accumulation (1456.95 mg/kg). Microbial communities responded strongly to salinity, with Weissella and Bacillus dominating under low-salt conditions, whereas Tetragenococcus and Millerozyma prevailed at higher salinities. Metagenomic and culturomic analyses further identified key functional strains associated with biogenic amine metabolism. Microbially driven acid accumulation and increased amino acid availability, together with activation of decarboxylases induced by acid stress, jointly promoted biogenic amine formation in the low-salt system. These findings clarify salt-dependent mechanisms of biogenic amine formation and provide guidance for designing safe reduced-salt fermentation strategies.}, } @article {pmid42034426, year = {2026}, author = {Zhou, N and Wei, R and Yang, S and Hu, F and Feng, Y and Zheng, H}, title = {Antibiotic resistance gene profiles in the gut microbiomes of Apis cerana, Apis mellifera, and Bombus terrestris.}, journal = {Pesticide biochemistry and physiology}, volume = {220}, number = {}, pages = {107059}, doi = {10.1016/j.pestbp.2026.107059}, pmid = {42034426}, issn = {1095-9939}, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Bacteria/genetics/drug effects ; Metagenome ; Interspersed Repetitive Sequences ; }, abstract = {The gut microbiota of honeybees has been increasingly recognized as a reservoir of antibiotic resistance genes (ARGs). However, comprehensive comparisons of ARG profiles between honeybees and bumblebees inhabiting the same environments are limited. Moreover, the diversity of mobile genetic elements (MGEs) in bee gut microbiomes and their potential role in mediating the horizontal transfer of ARGs have not yet been fully elucidated. In this study, metagenomic sequencing of 48 gut samples from farmed Apis mellifera, Apis cerana, and Bombus terrestris across four regions in China revealed 127 ARG subtypes, which collectively conferred resistance to nine major antibiotic classes. We found that A. mellifera, which carried the highest load of ARGs, concurrently harbored the greatest abundance of MGEs among the three species. Although ARG abundance varied significantly by region, no consistent geographical pattern emerged across the bee species. Importantly, strong positive correlations were detected between the abundances of ARGs and MGEs, particularly between the insertion sequence gene Tn3 and plasmid gene IncQ1. Metagenome-assembled genome analyses further confirmed the co-occurrence of ARGs (sul2, aph(3″)-Ib, and aph(6)-Id) with MGEs (Tn3 and IncQ1) across the three bee species, providing direct evidence that horizontal gene transfer mediated by MGEs contributes to the dissemination of ARGs within bee gut microbiomes. Overall, these findings highlight the critical role of the bee microbiome as a reservoir for ARGs and as a bioindicator for environmental pollutants, providing important insights into the mechanisms of ARG dissemination in ecosystems.}, } @article {pmid42034448, year = {2026}, author = {Zhang, Y and Zhao, L and Zhang, P and Yang, Y and Wang, A and Xue, C and Yao, Y and Zhang, J and Zhao, M}, title = {Paenibacillus polymyxa EP-4 can effectively control southern corn leaf blight and affect the selectivity of Spodoptera frugiperda to corn.}, journal = {Pesticide biochemistry and physiology}, volume = {220}, number = {}, pages = {107047}, doi = {10.1016/j.pestbp.2026.107047}, pmid = {42034448}, issn = {1095-9939}, mesh = {Animals ; *Zea mays/microbiology/parasitology ; *Spodoptera/physiology ; *Paenibacillus polymyxa/physiology ; *Plant Diseases/microbiology/prevention & control ; *Pest Control, Biological/methods ; *Ascomycota/physiology ; }, abstract = {Southern corn leaf blight (SCLB) and Spodoptera frugiperda pose serious threats to corn yield. In recent years, an increasing number of studies have investigated biological control agents to control plant diseases and insect pests. However, research on the use of one biocontrol bacterium to control plant diseases and insect pests simultaneously is very limited. In this study, the bacterium EP-4, which can significantly inhibit the growth of Bipolaris maydis, was identified as Paenibacillus polymyxa. EP-4 metabolites inhibited hyphal growth, caused hyphal deformities, significantly reduced the spore germination of B. maydis, and damaged cell membranes, leading to DNA leakage. In the greenhouse, EP-4 significantly reduced the disease index of SCLB and the feeding and oviposition preferences of S. frugiperda to corn. Metabolite analysis revealed that inoculation with B. maydis and S. frugiperda after EP-4 pretreatment affected the production of corn resistance-related substances such as brassinolide, quercetin, 2-undecanone and naringin. Metagenomic analysis revealed that EP-4 pretreatment and subsequent inoculation with pests and diseases could induce the recruitment of Pseudomonas, Burkholderia, Azotobacter and Mesorhizobium in corn. EP-4 could significantly reduce the occurrence of SCLB and significantly affect the feeding and oviposition of S. frugiperda on corn. The mechanism of action of EP-4 on pests and diseases has been shown to differ. This strain has great application potential in corn.}, } @article {pmid42034850, year = {2026}, author = {Gupta, E and Sharma, S and Dash, PK and Parida, M}, title = {Metagenomic profiling unveils the viral diversity in field-collected Aedes larvae from Central India employing nanopore sequencing.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42034850}, issn = {2045-2322}, abstract = {UNLABELLED: Several arboviruses including Dengue, Chikungunya, Zika, West Nile and Japanese encephalitis viruses are emerging and re-emerging in many parts of the world over last two decades. Thus, environmental surveillance of the mosquito borne viruses employing latest next generation sequencing technology could enhance our comprehension about an impending outbreak, thereby, providing opportunity for timely intervention. In this study, Aedes larvae were collected from different locations of Gwalior, Central India, cultured and grown to adult and were screened utilizing metagenomic workflow in Oxford Nanopore platform. The results produced sufficient and valuable insights through demonstration of divergence of these mosquitoes’ virome. Viral families associated with Myoviridae, Mimiviridae, Iridoviridae, Bunyaviridae, Flaviviridae, Mesonivirdae etc. were prevailing across the pools, varying in relative abundance. Viruses like Betabaculovirus, Mimivirus, Shamonda virus were reported in most pools in high abundance. Viral analysis leads to Phasi Charoen-like virus (PCLV), Nam Dinh virus (NDiV), Hubei mosquito virus (HMV), Wenzhou sobemo-like virus 4 (WSLV) findings across samples. This work reports the first successful metagenomic profiling of field-collected mosquitoes from Gwalior, Central India. Consequently, this technique might be employed to wide spectrum investigation of field mosquitoes, aiding in public health awareness about currently circulating viruses as a preparedness against future epidemic.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-49112-y.}, } @article {pmid42034975, year = {2026}, author = {Wang, H and Chen, Z and Qi, L and Wang, Z and Xu, D and Mao, Y and Shen, Z and Chen, K}, title = {Metagenomic profiling of Poa alpigena rhizosphere and bulk soil microbiomes across differing land-use contexts in the Qinghai lake alpine wetland.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04999-5}, pmid = {42034975}, issn = {1471-2180}, support = {This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T).//This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T)./ ; }, } @article {pmid42034994, year = {2026}, author = {Chen, Y and Bao, R and Jin, W and Yin, X and Qin, L and Pan, J and Yao, Y and Shen, J and Fang, T and Ma, Y and Zhou, C and Miao, Q and Hu, B}, title = {Metagenomic and genomic characterization of extrapulmonary Mycobacterium abscessus infections: a comparative cohort study.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {42034994}, issn = {1471-2334}, support = {SHDC22024315//Shanghai Shen Kang Hospital Development Center/ ; }, abstract = {INTRODUCTION: The incidence of Mycobacterium abscessus complex (MABC) infections is rising, becoming a major pathogen of nontuberculous mycobacteria responsible for pulmonary disease (PD) and extrapulmonary disease (ED). However, studies on the clinical characteristics of MABC-ED remain limited. METHODS: A 7-year retrospective analysis was conducted on MABC-ED cases at Zhongshan Hospital in Shanghai, China. We analyzed predisposing factors, clinical features, metagenomic sequencing (MS) results, drug susceptibility testing (DST), and genomic characteristics of MABC-ED patients, comparing the data with those of PD cases. RESULTS: Among 17 MABC-ED patients, 15 had predisposing risk factors and underlying conditions, with 2 of 3 patients with rheumatic disease showing poor prognosis. The diagnostic performance of metagenomic sequencing for MABC-ED was comparable to that for MABC-PD. However, MABC-ED samples exhibited distinct microbiome features and a more diverse mycobacterial community structure compared to PD. Resistance rates among extrapulmonary MABC isolates were observed as follows: 0% (amikacin), 20% (macrolides), 30% (linezolid), and 40% (cefoxitin). One case showed paradoxical results between erm (41) T28 sequevar and susceptibility phenotype. Genomic analysis revealed no specific dominant circulating clones (DCC) for MABC-ED isolates. CONCLUSION: MABC-ED patients commonly present with risk factors and underlying diseases. Metagenomic sequencing diagnosis of MABC-ED poses challenges, and DST and whole genome sequencing data indicate diversity among MABC-ED isolates. Our study provides detailed data on MABC-ED, contributing to a better understanding of its disease characteristics.}, } @article {pmid42035444, year = {2026}, author = {Lopez, C and Banker, A and Venkatasamy, V and Garcia, J and Mattiazzi, A and Eidam, L and Preczewski, L and Anjan, S and Nasrallah, A and Vianna, R and Morsi, M and Natori, Y}, title = {Diagnosing Hyperammonemia Syndrome in Non-Lung Solid Organ Transplant Recipients With Metagenomic Next-Generation Sequencing: Utility and Limitations From Two Clinical Cases.}, journal = {Clinical transplantation}, volume = {40}, number = {4}, pages = {e70550}, doi = {10.1111/ctr.70550}, pmid = {42035444}, issn = {1399-0012}, } @article {pmid42035799, year = {2026}, author = {Chen, S and Zhu, B and Lu, X and Huang, Y and Wang, S and Wang, W and Chen, G and Wu, X and Zhou, J and Wu, F and Wu, K}, title = {Integrative multi-kingdom gut microbiome analysis uncovers clinical signatures of major depressive disorder.}, journal = {Journal of affective disorders}, volume = {408}, number = {}, pages = {121858}, doi = {10.1016/j.jad.2026.121858}, pmid = {42035799}, issn = {1573-2517}, mesh = {Humans ; *Major Depressive Disorder/microbiology/psychology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Young Adult ; Adult ; Metagenomics ; Machine Learning ; Case-Control Studies ; }, abstract = {BACKGROUND: Accumulating evidence indicates that gut microbiome is significantly altered in major depressive disorder (MDD). However, most studies have focused on bacteria, while the functional and ecological contributions of eukaryotes, archaea, and viruses in MDD remain poorly understood.

METHODS: Fecal samples were collected from 121 first-episode, drug-naïve young adults with MDD and 117 healthy controls (HC) with matched demographic characteristics for shotgun metagenomic sequencing. Clinical data included the Hamilton Depression Scale (HAMD) and the MATRICS Consensus Cognitive Battery (MCCB). We systematically explored the multi-kingdom gut microbiome, functional genes, and metabolic pathways in MDD and their clinical associations, further assessing their diagnostic potential via machine learning.

RESULTS: MDD patients showed significant alterations in multi-kingdom microbiota diversity, accompanied by coordinated diversity relationships across microbial kingdoms relative to HC. In addition, we further identified 19 bacterial, 16 eukaryotic, 15 archaeal, and 10 viral species, as well as 22 functional genes and 32 metabolic pathways, that differed between groups. Importantly, five bacterial and four viral species were significantly associated with cognitive function, such as a positive correlation between Bifidobacterium pseudocatenulatum and attention/vigilance in MDD. Finally, validation demonstrated that a Random Forest model integrating multi-kingdom microbiota and functional features achieved superior diagnostic performance, significantly outperforming models based solely on bacterial features.

CONCLUSION: This study revealed extensive multi-kingdom microbial dysbiosis in MDD, providing deeper insight into disease-associated ecological disruption and highlighting the potential of microbial markers for enhancing clinical auxiliary diagnosis.}, } @article {pmid42035921, year = {2026}, author = {Liu, H and Xie, B and Zhuo, H and He, B and Dai, J and Zhou, Z and Shen, G and Chen, B and Tang, J and Ren, H and Jiang, X}, title = {Molecular traces of microbial cross-kingdom migration: from the gut ecosystem to the intervertebral disc microenvironment.}, journal = {The spine journal : official journal of the North American Spine Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.spinee.2026.04.027}, pmid = {42035921}, issn = {1878-1632}, abstract = {BACKGROUND CONTEXT: Low back pain is a leading cause of disability worldwide, and lumbar intervertebral disc degeneration (IVDD) is strongly associated with its development. Recent studies have shown that the gut microbiota (GM) and its metabolites may be involved in the occurrence and development of IVDD through the gut-disc axis. However, the key microbes mediating this process and their specific molecular mechanisms remain unclear.

PURPOSE: This study aimed to identify the gut microbes that play a key role in the progression of IVDD using multiomics approaches and clarify the specific mechanisms by which these microbes participate in IVDD by regulating host cell functions.

STUDY DESIGN/SETTING: A single center, prospective cross-sectional study.

PATIENT SAMPLE: We prospectively included 113 patients who underwent surgical treatment for symptomatic lumbar degenerative diseases from May 2022 to May 2023, and their degenerated lumbar intervertebral disc (IVD) tissues as well as paired feces samples were collected.

OUTCOME MEASURES: Metagenomic next-generation sequencing (mNGS), modified Pfirrmann typing, Single-cell RNA sequencing (scRNA-seq), Bulk RNA sequencing (Bulk RNA-seq).

METHODS: Clinical IVD samples and paired fecal samples were prospectively collected and subjected to multiomics bioinformatics analysis. mNGS was used to analyze the microbial composition in IVD and paired fecal samples. scRNA-seq was employed to resolve the cellular heterogeneity of IVD tissues. Bulk RNA-seq was utilized to identify the characteristics of host response genes related to microbial exposure. Subsequent AUCell scoring was performed to evaluate the abundance of microbes in cell subsets. The CellChat algorithm was applied to analyze the microbe-mediated intercellular communication network of host cells.

RESULTS: The raw detection rate of mNGS in IVD tissues was 100%, with a positive rate of 60.2% (68/113) after excluding background bacteria. A total of 505 genera and 1,528 microbial species were detected, with dominant species including Stutzerimonas stutzeri and Moraxella osloensis. The mNGS detection rate in fecal samples was 100% (322 genera and 789 species), among which Phocaeicola vulgatus (PV) was a dominant species. A total of 7 bacterial species shared by GM and IVD were identified; however, only the relative abundances of PV and Bacteroides thetaiotaomicron (BT) increased gradually with the severity of IVDD. Single-cell RNA-seq identified 10 cell clusters, annotated as chondrocytes, macrophages, fibroblasts, and endothelial cells, with the proportions of the latter 3 nonchondrocyte populations being significantly higher in the severe IVDD group. Chondrocytes were further divided into subsets. Subsets MDC1 and MDC5 were related to mild degeneration with high expression of ACAN and SOX9, whereas SDC2, SDC3, SDC4, SDC6, and SDC7 were related to severe degeneration. AUCell scoring revealed that PV showed a significantly higher abundance in these pathological subsets, while BT was evenly distributed. Furthermore, chondrocytes with high PV abundance significantly upregulated matrix degradation genes including MMP13 and COL1A1, as well as cell adhesion genes such as POSTN and SPARC. These upregulated genes were significantly enriched in LPS-associated inflammatory cascades, extracellular matrix degradation, and metabolic reprogramming pathways. Crucially, LPS signaling genes including TLR4, MYD88, NFKB1, and RELA were upregulated in chondrocytes with high PV abundance, while short-chain fatty acid receptor genes were minimally expressed with no significant group differences. Finally, CellChat analysis revealed that high PV abundance amplified the communication between chondrocytes and macrophages, fibroblasts, and endothelial cells, which was mediated by the CXCL pathway for immune recruitment, the VEGF and ANGPT pathways for angiogenesis, and the TGF-β pathway for pro-fibrotic remodeling.

CONCLUSION: This study suggests that gut-derived PV may activate the inflammatory response of chondrocytes through the LPS-mediated TLR4-MYD88 signaling axis and reshape the intercellular communication network, thereby potentially contributing to the process of IVDD. These findings provide novel mechanistic insights into the gut-disc axis theory and offer new perspectives on IVDD therapeutic strategies targeting microbe-host interactions.}, } @article {pmid42036057, year = {2026}, author = {Stem, AD and Alayyoub, M and Aalizadeh, R and Nikolopoulou, V and Lisgara, A and Shvartsman, A and Anitha, M and Patterson, A and Coble, R and Rushing, B and Sumner, S and Vasiliou, V}, title = {Integrated Multi-Omics Reveals Synergistic Hepatotoxicity of Ethanol and PFOS Co-Exposure.}, journal = {Chemico-biological interactions}, volume = {434}, number = {}, pages = {112101}, doi = {10.1016/j.cbi.2026.112101}, pmid = {42036057}, issn = {1872-7786}, mesh = {Animals ; *Ethanol/toxicity ; *Alkanesulfonic Acids/toxicity ; *Fluorocarbons/toxicity ; *Liver/drug effects/metabolism/pathology ; Multiomics ; Mice ; Male ; Mice, Inbred C57BL ; Metabolomics ; Lipidomics ; }, abstract = {Alcohol-associated liver disease (ALD) and exposure to per- and polyfluoroalkyl substances (PFAS) share key mechanisms of hepatotoxicity, yet their combined effects remain poorly characterized. We evaluated the impact of concurrent ethanol and perfluorooctanesulfonic acid (PFOS) exposure using a murine Lieber-DeCarli model characterized via multi-omic, spatial lipidomic, and metagenomic analyses. Exposure to PFOS resulted in rapid weight loss, while co-exposure led to decreased survival and pronounced hepatomegaly exceeding the effects of either exposure alone despite reduced cumulative ethanol intake. Histological analysis revealed enhanced hepatocellular injury with combined macrovesicular and microvesicular steatosis, consistent with impaired lipid handling and mitochondrial dysfunction. Transcriptomic and metabolomic profiling demonstrated disruption of xenobiotic metabolism, fatty acid β-oxidation, mitochondrial function, and bile acid transport, with PFOS acting as a dominant driver of metabolic stress and ethanol amplifying injury-related responses. Spatial lipidomics revealed hepatocyte-scale remodeling of membrane phospholipids, characterized by increased phosphatidic acid and depletion of phosphatidylinositol and phosphatidylserine under PFOS-containing conditions. Plasma metabolomics indicated systemic metabolic disturbance, including altered amino acid and redox pathways and depletion of microbiome-derived indole metabolites. Metagenomic analysis revealed reduced bacterial load and severe dysbiosis characterized by loss of commensal anaerobes, expansion of opportunistic taxa, and decreased microbial biosynthetic capacity. These findings indicate that PFOS increases susceptibility to alcohol-induced liver injury potentially through coordinated disruption of hepatic metabolism and gut-liver crosstalk, highlighting environmental PFAS exposure as a potential modifier of ALD severity.}, } @article {pmid42036452, year = {2026}, author = {Byun, HR and Ji, SR and Frank, LE and Kipp, EJ and Larsen, PA and Chae, JS}, title = {Application of nanopore adaptive sampling for metagenomic detection of tick-borne RNA viruses.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42036452}, issn = {2045-2322}, support = {550-20250009//Seoul National University/ ; }, mesh = {Animals ; *Metagenomics/methods ; Phylogeny ; Genome, Viral ; RNA, Viral/genetics ; *RNA Viruses/genetics/isolation & purification/classification ; *Nanopores ; *Haemaphysalis longicornis/virology ; *Ticks/virology ; Republic of Korea ; *Nanopore Sequencing/methods ; }, abstract = {Nanopore sequencing is a powerful tool for real-time pathogen detection and genomic characterization; however, its application to individual ticks is limited by abundant host-derived nucleic acids and low viral RNA levels. In this study, we applied nanopore adaptive sampling (NAS) to sequence viral RNA from individual Haemaphysalis (H.) ticks collected in the Republic of Korea (ROK). By combining NAS with long-read sequencing, high-resolution genome assembly can be achieved from samples containing low-abundance viral RNA and relatively short complementary DNA (cDNA) fragments generated during library preparation. These results indicate that NAS remains effective under suboptimal fragment-size conditions and improves genome assembly compared to conventional nanopore workflows. Phylogenetic analyses revealed that the detected Dabieshan tick virus (DTV) sequences were clustered with isolates from China and Japan, suggesting regional circulation facilitated by the widespread distribution of H. longicornis. Unlike previous studies relying on pooled samples without selective sequencing, NAS allowed high-resolution viral genome assembly from single ticks. These findings confirm the presence and genotypes of DTV for the first time in the ROK and demonstrate NAS as a practical, scalable approach for tick-borne RNA virus surveillance in single ticks, improving genomic assembly and supporting the monitoring of emerging tick-borne viruses in endemic regions.}, } @article {pmid42036496, year = {2026}, author = {Tow, WK and Teh, CSJ and Ooi, CW and Lee, RFS and Krishnasamy, M and Palanisamy, UD and Sundralingam, U}, title = {Metagenomic insights into urolithin formation from rambutan rind extract by rat faecal-derived microbiome.}, journal = {Applied microbiology and biotechnology}, volume = {110}, number = {1}, pages = {}, pmid = {42036496}, issn = {1432-0614}, mesh = {Animals ; *Coumarins/metabolism ; *Feces/microbiology ; Rats, Sprague-Dawley ; Rats ; Hydrolyzable Tannins/metabolism ; *Plant Extracts/metabolism ; Ellagic Acid/metabolism ; Metagenomics ; Fermentation ; Male ; *Gastrointestinal Microbiome ; *Bacteria/metabolism/genetics/classification ; *Sapindaceae/chemistry ; }, abstract = {Ellagitannins and ellagic acid are microbially converted into urolithins, metabolites associated with antioxidant, anti-inflammatory, and mitochondrial-related activities. Although several human-derived urolithin-producing strains and their associated enzymes have recently been characterised, the diversity of microbial strategies across host systems remains poorly understood. This study investigated urolithin production in the Sprague-Dawley rat faecal-derived microbial communities supplemented with rambutan rind extract, an ellagitannin-rich agricultural by-product containing 35-40% geraniin. Rambutan rind extract supplementation was associated with reduced isobutyric acid levels at study endpoint. Ex vivo anaerobic fermentation of hydrolysed rambutan rind extract (113 µM ellagic acid equivalent) resulted in the formation of urolithin C (9.4 ± 0.6 µM) and Isourolithin A (12.5 ± 0.6 µM) by day 9. Shotgun metagenomics analysis revealed very low relative abundance of Actinobacteria (< 0.009%), despite this phylum encompassing most previously characterised urolithin-producing taxa. Canonical ellagic acid degradation genes and the MetaCyc EA degradation pathway were not detected. Comparative pathway analysis indicated overlap in general metabolic pathways with Ellagibacter isourolithinifaciens DSM 104140[T] reflecting shared metabolic frameworks rather than conserved urolithin biosynthetic pathways, with highly divergent homologues (Eadh1, Eadh2, Eadh3, and Ucdh). Together, these findings demonstrate that rambutan rind extract can support urolithin formation in rat faecal-derived microbial consortia and highlight functional associations consistent with alternative or yet-uncharacterised microbial strategies for ellagitannin biotransformation. These findings support a discovery-driven framework for investigating urolithin biotransformation in non-human gut microbiomes using ellagitannin-rich agricultural substrates. KEY POINTS: • Rambutan rind extract supports urolithin formation in rat-derived gut microbiota. • Substrate concentration influences urolithin production under ex vivo conditions. • Rat gut microbiota shows homologues' divergence in urolithin-associated proteins.}, } @article {pmid42036837, year = {2026}, author = {Yancey, CE and Brumfield, KD and Buss, JA and Colwell, RR and Ettwiller, L}, title = {A Bait-and-Switch Strategy Links Phenotypes to Genes Coding for Polymer-Degrading Enzymes in Intact Microbiomes.}, journal = {Microbial biotechnology}, volume = {19}, number = {4}, pages = {e70359}, pmid = {42036837}, issn = {1751-7915}, support = {//New England Biolabs/ ; OCE1839171//National Science Foundation/ ; CCF1918749//National Science Foundation/ ; CBET1751854//National Science Foundation/ ; R01ES030317A/ES/NIEHS NIH HHS/United States ; 80NSSC20K0814/NASA/NASA/United States ; 80NSSC22K1044/NASA/NASA/United States ; }, mesh = {*Microbiota/genetics ; Phenotype ; Soil Microbiology ; Chitin/metabolism ; *Chitinases/genetics/metabolism ; *Bacteria/enzymology/genetics/classification ; }, abstract = {Natural microbial communities, with their vast diversity and complexity, are among the richest sources of untapped novel enzymes. Identifying novel enzymes can be challenging because microbiomes often lack clear, measurable phenotypes, unlike laboratory cultures where enzymatic activity can be linked to genetic elements. These constraints have left much of the functional diversity within microbiomes inaccessible to enzyme discovery efforts. Here, we present a genotype/phenotype association framework directly on microbial communities for enzyme discovery. For this, we developed a 'bait-and-switch' treatment strategy that generates measurable dual phenotypes directly within intact microbiomes. Using soil microbiomes as a test system, we applied chitin-rich compost as 'bait' to enrich chitin-degrading organisms, followed by glucose addition to functionally 'switch' the community. This treatment produced a distinct phenotypic signature: prevalence of known chitin degradation genes increases during the bait phase, and their transcripts are rapidly downregulated during the switch phase. By performing hypothesis-free association analysis of protein domains with this dual phenotype, we identified the glycoside hydrolase 18 as the most significantly associated protein domain. Experimental validation confirmed chitinase activity in 63% of tested enzymes, including candidates from unculturable bacteria and those with previously uncharacterized domain architectures. This species-independent, reference-free approach to discover novel enzymes has broad applications in microbiome engineering, biopolymer processing and systems biology, offering a generalizable strategy for functional gene discovery in complex microbial systems.}, } @article {pmid42037322, year = {2026}, author = {Thouvenot, K and Serrat, F and Lenclume, V and Doussiet, E and Belda, E and Taïlé, J and Alili, R and Rondeau, P and Clément, K and Meilhac, O and Le Moullec, N and Gonthier, MP}, title = {Periodontitis in Patients With Severe Obesity: From the Oral and Gut Microbiota Dysregulation to the Visceral Adipose Tissue Inflammatory and Metabolic Disorders.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {9}, pages = {e71828}, pmid = {42037322}, issn = {1530-6860}, support = {APIDOM-BACTERIOB//CHU de La Réunion/ ; //Institut National de la Santé et de la Recherche Médicale (Inserm)/ ; //University of La Réunion/ ; }, mesh = {Humans ; *Periodontitis/microbiology/metabolism/complications/pathology ; Female ; Male ; *Intra-Abdominal Fat/metabolism/pathology/microbiology ; Middle Aged ; Adult ; *Gastrointestinal Microbiome ; *Obesity, Morbid/microbiology/complications/metabolism ; *Inflammation/microbiology/pathology/metabolism ; *Metabolic Diseases/microbiology/metabolism/pathology ; Porphyromonas gingivalis ; Dysbiosis/microbiology ; *Mouth/microbiology ; }, abstract = {During periodontitis, pathogenic oral bacteria like Porphyromonas gingivalis may exert systemic effects directly by translocating into the bloodstream and indirectly by deregulating the gut microbiota, aggravating obesity-related complications. This study aimed to evaluate the links between the periodontal infection, the oral and gut microbiota composition, and the inflammatory and metabolic profile during obesity. Thirty-nine patients suffering from severe obesity, with (n = 23) or without (n = 16) periodontitis, were enrolled. We examined the subgingival microbiota composition, periodontal status and salivary inflammatory response. The fecal microbiota composition was assessed by metagenomic analysis. Inflammatory and metabolic markers were measured in the plasma and epiploon visceral adipose tissue collected during bariatric surgery. Results show that patients with periodontitis exhibited an oral microbiota dysbiosis characterized by an increased abundance of bacteria from the red and orange complexes, worsened periodontal parameters (plaque index, bleeding index, gingival recession, probing depth and clinical attachment level), and higher IL-6 salivary levels. In fecal samples of patients with periodontitis, a higher proportion of the Proteobacteria phylum and changes in functional profile of bacteria were detected. Periodontitis was also linked to higher circulating concentrations of anti-P. gingivalis IgG, total cholesterol and lipoprotein (a). Moreover, periodontitis was associated with an enhanced production of TLR2, MyD88 and TGFβ, as well as higher activities of SOD and catalase antioxidant enzymes in the adipose tissue. Overall, these findings demonstrate that during obesity, the periodontal infection correlates with deregulated oral and gut microbiota composition, higher levels of pro-inflammatory mediators, and altered markers of oxidative stress and lipid metabolism.}, } @article {pmid42037351, year = {2026}, author = {Chakraborty, S and Mukherjee, D and Sar, P}, title = {Genome-resolved insights into arsenic-impacted paddy soil and microcosm-derived microbiomes from West Bengal, India.}, journal = {Microbiology resource announcements}, volume = {15}, number = {6}, pages = {e0005926}, pmid = {42037351}, issn = {2576-098X}, abstract = {This study reports 32 metagenome-assembled genomes (MAGs) reconstructed from arsenic (As)-impacted paddy soils of West Bengal, India, and microcosms from these soil samples. These MAGs, represented by 10 bacterial and 2 archaeal phyla, provided critical insights into the metabolic and biogeochemical potential of microbiomes in a highly As-impacted agroecosystem.}, } @article {pmid42037384, year = {2026}, author = {Yang, K and King, S and Marshak, A and D'Mello-Guyett, L and Grignard, L and Knee, J and Wong, G and Zhao, L and Lamaka, NG and Save, D and Gose, M and Myers, A and Trehan, I and Cumming, O and Stobaugh, H and Schwartz, DJ}, title = {Gut microbiome associations with acute malnutrition relapse in South Sudan.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0358725}, pmid = {42037384}, issn = {2165-0497}, support = {K08 AI159384/AI/NIAID NIH HHS/United States ; K08AI159384/NH/NIH HHS/United States ; }, mesh = {Humans ; *Severe Acute Malnutrition/microbiology ; South Sudan ; Recurrence ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Infant ; Child, Preschool ; }, abstract = {Severe acute malnutrition (SAM) is a leading cause of childhood morbidity and mortality that is defined by anthropometric measurements, weight-for-height z score, and mid-upper arm circumference (MUAC) falling significantly below healthy standards. While treatments for SAM and our understanding of this disease have advanced, children experiencing SAM frequently relapse to acute malnutrition (AM) following anthropometric recovery. Little is known about the contribution of the gut microbiome to AM relapse. We hypothesized that features of the gut microbiome, including microbial composition, antimicrobial resistance gene carriage, and predicted microbial functional pathways, of children discharged from treatment for uncomplicated SAM in South Sudan, may be associated with AM relapse at 1-month follow-up. Overall, broad microbiome profiles at discharge were not associated with AM relapse. We evaluated the associations of microbiome features with AM relapse 1-month post-recovery using mixed linear effect models. We identified associations between higher MUAC, which may be a proxy for future health trajectories, and increased Sutterella wadsworthensis and trimethoprim-resistant dihydrofolate reductase antimicrobial resistance genes. These findings suggest that the gut microbiome at discharge of children treated for uncomplicated SAM has limited predictive value as a standalone diagnostic tool for identifying relapse risk at 1 month.IMPORTANCESevere acute malnutrition (SAM) is a devastating illness that impacts the morbidity and mortality of millions of children worldwide. Community-based management of acute malnutrition (CMAM) is the standard of care in South Sudan and many other low-resource settings for children presenting with SAM. Despite this intervention, children treated for SAM under CMAM frequently relapse to acute malnutrition (AM) following treatment. With advancements in our understanding of malnutrition, there has been a strong and growing interest in developing microbiome-based strategies to treat, prevent, and predict relapse to AM following treatment for SAM. Our work characterizes gut microbiome features of children from a geographic area that is traditionally underrepresented in gut microbiome research and shows that in isolation, a child's gut microbiome at discharge likely holds low predictive value for relapse to AM post-CMAM treatment; however, we identified key microbes and microbial features meriting further research.}, } @article {pmid42037401, year = {2026}, author = {Wu, Q and Wu, D and Wang, J and Wang, H and Peng, J and Zhao, Y and Chen, J and Yuan, Q}, title = {Lytic viruses drive the decrease in polyphosphate-accumulating and phosphate-solubilizing potential of microbial communities with increasing reservoir age.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {5}, pages = {e0248125}, pmid = {42037401}, issn = {1098-5336}, mesh = {*Polyphosphates/metabolism ; *Phosphates/metabolism ; *Microbiota ; *Bacteria/metabolism/genetics ; Geologic Sediments/microbiology/virology ; China ; *Viruses/genetics/metabolism ; Phosphorus/metabolism ; Rivers/microbiology/virology ; }, abstract = {River damming often leads to significant phosphorus enrichment in reservoir sediments and increases the risk of eutrophication with reservoir age. Microorganisms mediate critical steps of phosphorus cycling in ecosystems, and viruses are recognized as key regulators of microbial community structure and function. However, their influence on phosphorus-cycling microorganisms (PCMs) in freshwater environments remains poorly understood. In this study, surface sediment samples were collected from nine reservoirs (12-59 years old) of southwest China and analyzed using metagenomic and metatranscriptomic approaches to profile both PCMs and viral communities. The results demonstrated that the diversity of lytic viruses was the primary factor governing both shifts in the community stability of PCMs and the restructuring of P-cycling gene patterns with increasing reservoir age. Specifically, viral lysis reduced the relative abundance of dominant PCMs, thereby enhancing community diversity and stability. Concurrently, viral activity diminished PCMs' functional potential for phosphate solubilization and polyphosphate accumulation, while stimulating high-affinity inorganic phosphate (Pi) transport. Furthermore, viruses encoded auxiliary metabolic genes (AMGs) related to phosphate solubilization, mineralization, accumulation, and transport, underscoring the viral role in regulating phosphorus retention and release. Compared to polyphosphate-accumulating microorganisms, phosphate-solubilizing microorganisms may be more susceptible to viral infection. Additionally, viral activity was associated with an increase in the relative abundance of Cyanobacteria. Taken together, our results suggest viruses are key regulators of PCMs, highlighting that they should be incorporated into future strategies for assessing and mitigating reservoir eutrophication.IMPORTANCESediment microorganisms are regarded as the engine for endogenous phosphorus release in reservoirs. Therefore, understanding their dynamics and key driving factors is essential for effective eutrophication mitigation. Viral lysis and virus-encoded auxiliary metabolic genes (AMGs) may constitute a critical yet understudied mechanism influencing microbial phosphorus cycling. Our study provides unique, time-series-based mechanistic insights into how viral activity, in the context of large-scale artificial projects (river damming), restructures microbial phosphorus cycling and its potential ecological effects over decades.}, } @article {pmid42037579, year = {2026}, author = {Virtuoso, FAS and Boekhorst, J and van Ravenstein, S and Schouten, D and Juanpere-Borràs, M and Broekhuis, F and Vissia, S and Mazebedi, R and Araldi, A and van Langevelde, F}, title = {DIY: A Practical Field-to-Sequencer Workflow for Metabarcoding the Diet of Terrestrial Carnivore Species.}, journal = {Molecular ecology resources}, volume = {26}, number = {4}, pages = {e70144}, pmid = {42037579}, issn = {1755-0998}, support = {//Wageningen University and Research/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Feces/chemistry ; *Diet ; *Carnivora/physiology/classification ; Workflow ; *Metagenomics/methods ; }, abstract = {Metabarcoding of faecal samples is a powerful, non-invasive approach for investigating the feeding ecology of carnivores, revealing prey diversity and unexpected dietary components with greater resolution than traditional methods. However, the approach remains technically demanding, as challenges and potential biases arise at every stage, from scat collection and DNA extraction to primer selection, sequencing, and data interpretation. Methodological details for these steps are often scattered across studies, limiting reproducibility and accessibility for ecologists. Here, we present a comprehensive field-to-sequencer workflow for dietary metabarcoding of terrestrial carnivores using Oxford Nanopore Technologies (ONT), covering all stages from sample collection to ecological interpretation. Drawing on field-collected scats of brown (Parahyaena brunnea) and spotted hyenas (Crocuta crocuta) across arid and semi-arid savannas in Botswana, we illustrate practical decisions, technical considerations, and common pitfalls encountered throughout the process. By integrating field, laboratory, and bioinformatic components into a single, accessible framework, this paper provides a pragmatic reference for ecologists aiming to design robust, transparent, and comparable studies of carnivore diet composition.}, } @article {pmid42038227, year = {2026}, author = {Fu, L and Zhang, Y and Wang, L and Li, X}, title = {Primary amoebic meningoencephalitis caused by Naegleria fowleri in a 6-year-old girl: case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1801355}, pmid = {42038227}, issn = {2296-2360}, abstract = {BACKGROUND: Primary amoebic meningoencephalitis (PAM) is caused by Naegleria fowleri, a rare but highly fatal central nervous system infection with a mortality rate exceeding 95%. Early diagnosis is challenging due to the close similarity of its clinical manifestations and cerebrospinal fluid (CSF) findings to those of acute bacterial meningitis. Metagenomic next-generation sequencing (mNGS) has become a vital tool for identifying rare or unexpected pathogens.

CASE PRESENTATION: A previously healthy 6-year-old girl was admitted with fever, vomiting, and headache of 1 day's duration. Six days before symptom onset, she had played in natural freshwater bodies. After admission, she developed persistent high fever and rapidly progressive altered mental status, followed by two episodes of generalized tonic-clonic seizures, hemoptysis, acute respiratory failure, and circulatory shock. Initial cranial magnetic resonance imaging showed no abnormalities. CSF analysis revealed marked inflammatory changes: a white blood cell count of 3,072 × 10[6]/L, markedly elevated protein (3,667.6 mg/L), and significantly decreased glucose (0.08 mmol/L). Despite administration of broad-spectrum antibiotics, glucocorticoids, osmotherapy, and comprehensive intensive care unit management, the patient died approximately 11 h after admission following three cardiac arrests. Two days postmortem, CSF mNGS confirmed infection with Naegleria fowleri (copy number 3 × 10[5] copies/mL), establishing the diagnosis of PAM.

CONCLUSIONS: This pediatric case serves as a warning that PAM should be considered in children with a history of freshwater exposure and rapidly progressive meningoencephalitis, even when early imaging is normal and CSF findings resemble bacterial meningitis. Early lumbar puncture, rapid molecular diagnostics, and heightened clinician vigilance are critical for the timely initiation of targeted therapy.}, } @article {pmid42038247, year = {2026}, author = {Li, X and Jiang, Y and Dai, R and Yang, Y and Wang, W}, title = {Rickettsia felis meningoencephalitis in a child: a case report and literature review.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1763281}, pmid = {42038247}, issn = {2296-2360}, abstract = {Rickettsia felis (R. felis) infection occasionally invades the central nervous system, causing encephalitis or meningoencephalitis. Although the disease typically presents as mild to moderate illness, delayed diagnosis and treatment may increase the risk of adverse prognosis in pediatric patients. This article reports a case of R. felis meningoencephalitis in a child diagnosed by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid. mNGS analysis detected high-confidence R. felis-specific sequences, and potential background microbial contamination was effectively excluded through a bioinformatics pipeline, thereby providing critical evidence for etiological confirmation. Due to insufficient clinical awareness, limited pathogen detection methods, and the self-limiting nature of the disease, R. felis infection is prone to missed diagnosis and misdiagnosis in febrile children. The clinical manifestations are nonspecific; even with central nervous system involvement, routine laboratory tests are unlikely to suggest the microbial etiology, contributing to the underrecognition and underreporting of pediatric R. felis meningoencephalitis. Therefore, enhancing diagnostic awareness and achieving early precise diagnosis and treatment may help shorten the disease course and improve patient outcomes.}, } @article {pmid42038299, year = {2026}, author = {Liu, HJ and Wang, LF and Li, XY and Li, L}, title = {Toxicity-guided dose modification for disseminated Nocardia farcinica brain abscess in a patient with pneumoconiosis: a brief research report.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1805920}, pmid = {42038299}, issn = {1663-9812}, abstract = {BACKGROUND: Optimal antimicrobial strategies for disseminated nocardiosis with central nervous system (CNS) involvement remain poorly defined, particularly regarding trimethoprim-sulfamethoxazole (TMP-SMX) dosing in immunocompromised patients with severe drug intolerance.

METHODS: This observational case study analyzed the clinical course and pharmacological management of a 55-year-old male gold miner with pneumoconiosis and chronic corticosteroid use who developed Nocardia farcinica brain abscess. Diagnosis was established via metagenomic next-generation sequencing (mNGS) and phenotypic culture. An individualized antimicrobial regimen was designed based on toxicity monitoring.

RESULTS: Diagnosis of N. farcinica was confirmed by mNGS within 48 h. The patient initially failed empirical meropenem but responded to combination therapy with imipenem, amikacin, and TMP-SMX. Due to grade III gastrointestinal toxicity (CTCAE v5.0), TMP-SMX was de-escalated from 15 mg·kg[-1]·d[-1]-11.25 mg·kg[-1]·d[-1], with maintenance at 7.5 mg·kg[-1]·d[-1]. Clinical improvement was observed at Day 120, though durable cure remains unconfirmed.

CONCLUSION: In extreme circumstances of severe dose-limiting toxicity, temporary TMP-SMX dose reduction with intensive monitoring may be feasible as a bridge to complete guideline-concordant therapy, though this approach falls below current recommendations and requires robust therapeutic drug monitoring. Species-directed antimicrobial selection and early molecular diagnosis facilitated initial clinical resolution in this high-risk immunocompromised host.}, } @article {pmid42038409, year = {2026}, author = {Nousias, O and Duffy, FG and Duffy, IJ and McCauley, M and Whilde, J and Duffy, DJ}, title = {Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.}, journal = {NAR genomics and bioinformatics}, volume = {8}, number = {2}, pages = {lqag040}, pmid = {42038409}, issn = {2631-9268}, mesh = {Animals ; *Biodiversity ; *Rivers/microbiology ; *Metagenomics/methods ; *Environmental Monitoring/methods ; Shotgun Sequencing ; Humans ; DNA, Environmental ; *Nanopore Sequencing/methods ; Metagenome ; Animals, Wild/genetics ; }, abstract = {As the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to accurately understand the current state of natural habitats and their constituent species. We assess the feasibility of a single assay: long-read shotgun metagenomic sequencing of environmental DNA (eDNA), to monitor species from across the tree of life, from viruses to complex multicellular organisms, across a representative Irish river system (Avoca River, Co. Wicklow). We conducted aquatic eDNA sampling and long-read shotgun metagenomic sequencing from a mountain tributary through to the sea. This approach could detect and quantify organismal DNA present in environmental samples, from microbes (including DNA viruses) to mammals. Rather than the traditional siloing of microbial and multicellular studies of DNA recovered from environmental samples, simultaneously considering viruses, microbes, and eukaryotes (animals, plants, and fungi) can provide deeper insights. This single assay can simultaneously quantify differences in DNA abundance for a broad range of species and pathogens across sites and sample types, enabling wide-ranging biodiversity assessments. This included human, wildlife, plant, and microbial pathogens and parasites with health, agricultural, and economic importance. The environmental genomic data enabled animal phylogeny and transmissible cancer analysis (blue mussel, Mytilus edulis) even from natural complex community settings. Oxford Nanopore sequencing provides a quantitative approach for river biodiversity, pollution, and environmental health monitoring. Long-read shotgun metagenomic sequencing of environmental samples offers the means to assess whole ecosystems and the ecological, trophic, and host-pathogen interactions occurring within them.}, } @article {pmid42038418, year = {2026}, author = {Vlasovets, O and Schaipp, F and Simpson, L and Bolyen, E and Caporaso, JG and Müller, CL}, title = {Sparse regression, classification, and microbial network estimation in QIIME 2 with q2-classo and q2-gglasso.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {42038418}, issn = {2331-8422}, abstract = {MOTIVATION: Statistical analysis of microbial count data derived from 16S rRNA or metagenomics sequencing poses unique challenges due to the sparse, compositional, and high-dimensional nature of the data. While QIIME 2 already provides many tools for data pre-processing and analysis, plugins for statistical regression, classification, and microbial network estimation tailored to compositional count data are relatively scarce.

RESULTS: We present q2-classo and q2-gglasso, two novel QIIME 2 plugins that implement penalized regression, classification, and graphical modeling approaches for microbial compositional data. q2-classo enables the prediction of a continuous or binary outcome of interest using compositional microbiome data as predictors. Both sparse log-contrast regression and classification, as well as tree-aggregated log-contrast models are available. q2-gglasso enables the estimation of taxon-taxon association networks through sparse graphical model estimation, such as, e.g., the SPIEC-EASI framework, as well as adaptive and latent graphical models. The latent model can decompose taxon-taxon associations into a sparse direct interaction matrix and a latent (low-rank) matrix which enables robust principal component embedding of a data set. Within the QIIME 2 ecosystem we demonstrate their application on the Atacama soil microbiome dataset, illustrating robust model selection, classification, and microbial network estimation with covariates and latent factors.

AVAILABILITY: The software is freely available under the BSD-3-Clause License. Source code is available at https://github.com/bio-datascience/q2-gglasso and https://github.com/bio-datascience/q2-classo-latest, with installation through QIIME 2 and Docker.

CONTACT: oleg.vlasovets@helmholtz-munich.de.}, } @article {pmid42038553, year = {2026}, author = {Rodríguez-Rodríguez, Y and Disla, AMM and Ortega, MER and Gandini, G and Tejada-Tejada, P and Guevara, MÁ and Franco, EF and Dantas, CWD and Ramos, RT and Jáuregui-Haza, UJ}, title = {Microbial Profiling and Biosafety Assessment of a Sargassum-Based Liquid Biofertilizer Using 16S rRNA Metagenomics.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {3219583}, pmid = {42038553}, issn = {1687-918X}, abstract = {Sargassum seaweed is increasingly abundant in the Caribbean, creating ecological disruption but also providing biomass for agricultural inputs. This study compares the microbial diversity and safety of a Sargassum-based liquid biofertilizer (SBLB-INTEC) with those of a conventional product (LB-BANELINO) using 16S rRNA amplicon sequencing, rather than culture-dependent methods. Both formulations contained key nutrients (K, Ca, and Mg) and low levels of heavy metals. They harbored dense but relatively simple bacterial communities dominated by Firmicutes, particularly Bacilli, with Proteobacteria and other phyla at lower abundances. Staphylococcus (Staphylococcaceae) was highly abundant in both products, while SBLB-INTEC showed a somewhat more balanced community, including Delftia and other Comamonadaceae. Shannon diversity tended to be higher in SBLB-INTEC, but differences in alpha- and beta-diversity between formulations were not statistically significant. Because 16S data cannot distinguish viable from nonviable cells or resolve strain-level pathogenicity, these results do not prove the absence of pathogens; instead, they provide a genus-level baseline to guide targeted culture, qPCR, and functional assays. Overall, the combination of a favorable chemical profile and microbial groups commonly associated with nutrient cycling and plant-associated functions suggests that SBLB-INTEC could become a valuable component of integrated nutrient management in tropical agriculture, offering hope for a more sustainable future pending confirmatory plant-response and biosafety studies. We recommend integrating these microbial data into a national biofertilizer monitoring framework, combining metagenomic surveys with targeted qPCR and resistance gene screening.}, } @article {pmid42038636, year = {2026}, author = {Ryder, JH and Turbett, SE}, title = {Mindful diagnostics: a central nervous system infection case study.}, journal = {Antimicrobial stewardship & healthcare epidemiology : ASHE}, volume = {6}, number = {1}, pages = {e96}, pmid = {42038636}, issn = {2732-494X}, abstract = {A clinical case is presented to discuss a framework for use of advanced diagnostics for central nervous system infections. Advantages, limitations, and diagnostic stewardship strategies are discussed for each modality: multiplex molecular meningitis/encephalitis panel, plasma microbial cell-free DNA sequencing, and cerebrospinal fluid metagenomic next generation sequencing.}, } @article {pmid42039195, year = {2026}, author = {Liu, Y and Liao, X and Chen, Q and Wang, H and Dai, H}, title = {What is the impact of the virome and mycobiome on female reproductive tract health? A systematic scoping review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1749584}, pmid = {42039195}, issn = {1664-3224}, mesh = {Humans ; Female ; *Vaginosis, Bacterial/microbiology/virology ; *Virome ; *Mycobiome ; *Genitalia, Female/microbiology/virology ; Microbiota ; Papillomavirus Infections/microbiology/virology ; *Reproductive Health ; Vagina/microbiology/virology ; }, abstract = {BACKGROUND: Traditional research on the female reproductive tract (FRT) microbiome has focused on the dominance of bacteria, particularly Lactobacillus, as a marker of health. This bacteriocentric paradigm, however, cannot fully explain clinical enigmas like the high recurrence of bacterial vaginosis (BV) or the persistence of HPV infection. This review introduces a new pan-microbiome framework that highlights the overlooked roles of the virome and mycobiome as the ecosystem's neglected components.

METHODS: We conducted a systematic scoping review following the PRISMA-ScR guidelines. We searched PubMed, Embase, and Web of Science databases for studies published up to October 2025. Inclusion criteria focused on original research and metagenomic studies examining the female reproductive tract (FRT) virome, mycobiome, and bacteriome, specifically their interactions and clinical associations with bacterial vaginosis (BV) and HPV persistence. Data were extracted and synthesized to evaluate the pan-microbiome framework.

RESULTS: The virome and mycobiome, despite their low biomass, are increasingly recognized as potential ecosystem modulators. Bacteriophages, for instance, are proposed to act as community "modulators," either through lytic cycles that maintain bacterial diversity or lysogenic cycles that may contribute to stabilizing pathogenic biofilms in dysbiosis like BV by introducing virulence genes. Similarly, fungi like Candida can transition from harmless commensals to pathogens when the protective bacterial balance is disturbed.

CONCLUSION: FRT health is an emergent property of the complex interactions among bacteria, viruses, and fungi. A comprehensive understanding requires a pan-microbiome perspective. Future therapeutic strategies should move beyond a "one-bug, one-drug" approach toward "ecosystem restoration," using targeted methods like phage therapy or vaginal microbiota transplantation to attempt to restore the balance of the entire microbial community.}, } @article {pmid42039480, year = {2026}, author = {Liu, J and De Paolis Kaluza, MC and Bromberg, Y}, title = {16S rRNA sequence captures microbial functional potential.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42039480}, issn = {2692-8205}, abstract = {16S rRNA amplicon sequencing is widely used for microbiome profiling, but most methods rely on reference databases of characterized organisms, limiting its accuracy in function prediction for underrepresented environments. We discovered that 16S rRNA k-mer composition carries substantial functional signal: (i) whole-genome k-mer profiles predict genome-encoded functions, and (ii) 16S rRNA k-mer profiles reflect their source genome's composition. Building on these relationships, we developed embeRNA, a neural network framework that predicts functions directly from 16S rRNA k-mer embeddings without requiring taxonomy assignment or phylogenetic placement. embeRNA outputs per-function probability scores, enabling users to tune decision thresholds to balance precision and recall or account for community novelty. In a stringent "novel microbes" benchmark - where all test sequences shared <97% identity with training data - embeRNA outperformed reference-based methods, particularly for hard-to-label functions. Applied to soil metagenomes with paired 16S and whole metagenome shotgun sequencing (WMS) data, embeRNA recovered most WMS-inferred functions and produced abundance profiles strongly correlated with WMS results, attaining better performance than a reference-based approach. Our findings demonstrate that 16S rRNA directly captures functional potential, and 16S amplicon sequencing data can complement WMS-based inference to broaden functional characterization of microbiomes, especially in understudied environments.}, } @article {pmid42039609, year = {2026}, author = {Maldonado-Pereira, L and Mutawi, TM and Singh, A and Sanderson, BJ and Rekowski, MJ and Barnaba, C and Medina Meza, IG}, title = {Dietary Oxysterols Reprogram Hepatic Lipid Metabolism and Reshape the Gut Metabolome-Microbiome Interface.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42039609}, issn = {2692-8205}, abstract = {Dietary oxysterols are biologically active cholesterol oxidation products ubiquitous in Western diets, yet their systemic effects on host metabolism and the gut microbiome remain largely unexplored. Here, we employed an integrated multi-omics approach - shotgun metagenomics, quantitative proteomics, untargeted metabolomics, and bulk RNA-seq - to characterize the impact of DOxS exposure on the gut-liver axis in rats fed a Western diet (WD vs. WD-DOxS). Hepatic proteomics revealed near-complete suppression of the mevalonate/cholesterol biosynthesis pathway, particularly in males, while de novo lipogenesis enzymes (Scd1, Fasn, Plin2) were paradoxically upregulated, consistent with dual oxysterol signaling through SREBP inhibition and LXR activation. Bile acid synthesis was concurrently suppressed, confirmed by metabolomics. Strikingly, RNA-seq across liver, heart, and brain detected virtually no differentially expressed genes, establishing that DOxS act predominantly through post-transcriptional mechanisms. In the gut, DOxS increased microbial α-diversity while depleting Limosilactobacillus reuteri, with concomitant loss of the barrier-protective metabolite 3-indoleacrylic acid. Tissue-specific responses were widespread, with liver and colon frequently mounting opposing metabolic and immune responses to the same dietary challenge. Cross-omics integration revealed convergent microbiome-metabolite axes connecting microbial remodeling to both hepatic lipid reprogramming and colonic barrier disruption. These findings reposition dietary oxysterols from food-quality markers to active modulators of the gut-liver axis, with implications for metabolic disease and intestinal barrier integrity.}, } @article {pmid42039751, year = {2026}, author = {Chen, XG and Zhou, L and Duan, K and Shi, SY and Subi, A and Sun, HW and Lu, YM and Hu, L and Yang, ZT}, title = {Integrative analysis of pathogen detection, antimicrobial resistance, virulence, and host response in severe infections using metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1786413}, pmid = {42039751}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Retrospective Studies ; Male ; Virulence Factors/genetics ; Female ; Middle Aged ; Virulence/genetics ; Aged ; Intensive Care Units ; *Bacteria/genetics/drug effects/pathogenicity/isolation & purification/classification ; *Drug Resistance, Bacterial/genetics ; *Bacterial Infections/microbiology/diagnosis ; *Host-Pathogen Interactions ; Anti-Bacterial Agents/pharmacology ; Adult ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) offers unbiased pathogen detection. However, its integrative value in simultaneously revealing resistance, virulence, and host-response interplay in Intensive Care Unit(ICU)-infected patients remains underexplored.

METHODS: In this retrospective cohort study of 156 ICU-infected patients, we compared the diagnostic performance of mNGS against conventional microbiological testing (CMT). We analyzed mNGS-derived antibiotic resistance genes (ARGs) and virulence factors (VFs) and correlated them with host immune-inflammatory markers and clinical outcomes.

RESULTS: mNGS demonstrated a significantly higher positive detection rate (89.7% vs. 67.3%, P < 0.001) and clinical concordance (75.6% vs. 35.9%, P < 0.001) than CMT. It revealed a high mixed-infection rate (72.1%). ARGs were detected in 49.0% of bacterial infections, predominantly β-lactamase genes, showing 72.0% concordance with phenotypic susceptibility. Key VFs (e.g., rmpA in K. pneumoniae) were identified. Based on mNGS results, 47.4% of patients had their antimicrobial therapy adjusted.

CONCLUSION: mNGS provides a comprehensive diagnostic tool by integrating pathogen identification, resistance and virulence profiling, and host-response context, enabling more precise and timely management of ICU-infected patients.}, } @article {pmid42039753, year = {2026}, author = {Li, X and Fang, J and Li, D and Cai, B and Yin, J and Zheng, Y and Yin, G}, title = {Performance evaluation of mNGS in pathogen diagnosis of skin and soft tissue infections and its optimization effect on antibiotic decision-making.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1771148}, pmid = {42039753}, issn = {2235-2988}, mesh = {Humans ; *Soft Tissue Infections/diagnosis/microbiology/drug therapy ; *Anti-Bacterial Agents/therapeutic use ; Retrospective Studies ; Female ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/isolation & purification/classification/drug effects ; Male ; *Metagenomics/methods ; Middle Aged ; Antimicrobial Stewardship ; Aged ; *Skin Diseases, Bacterial/diagnosis/microbiology/drug therapy ; }, abstract = {BACKGROUND: Skin and soft tissue infections (SSTIs), often caused by polymicrobial pathogens, pose diagnostic challenges due to the limitations of conventional methods, including low sensitivity and prolonged turnaround time. This diagnostic gap has perpetuated empirical antibiotic use in clinical practice. Metagenomic next-generation sequencing (mNGS), with its unbiased pathogen detection capability, offers a transformative approach for rapid and precise microbial identification in SSTIs.

OBJECTIVE: To evaluate the clinical utility of mNGS compared to conventional microbiological testing in guiding antibiotic stewardship for complex SSTIs.

METHODS: A retrospective cohort study was conducted at the First Affiliated Hospital of Zhengzhou University from April 2023 to May 2025, enrolling 69 patients with clinically diagnosed complex SSTIs. All patients underwent concurrent mNGS testing, conventional bacterial culture, and pathological examination. The diagnostic performance of mNGS was systematically compared with culture methods, with emphasis on culture-negative cases and polymicrobial infections. The impact of mNGS-guided antibiotic adjustments was assessed.

RESULTS: mNGS demonstrated significantly higher pathogen detection rates than conventional culture (P < 0.001), with a concordance of 37.5% between the two methods. Among 24 culture-negative patients, mNGS identified pathogens in 20 cases (83.3% detection rate). For polymicrobial infections (n = 20), culture detected pathogens in only 2 cases, whereas mNGS successfully identified multiple pathogens in the majority. Antibiotic therapy was adjusted based on mNGS results in 11.9% (8/69) of patients.

CONCLUSION: mNGS substantially improves pathogen detection in complex SSTIs compared to conventional methods. Beyond diagnostic accuracy, its clinical value lies in enabling targeted antibiotic therapy, thereby optimizing antimicrobial stewardship and potentially reducing healthcare costs.}, } @article {pmid42039757, year = {2026}, author = {Wu, Y and Zhang, J and Su, W and Zhang, Z}, title = {Global epidemiology of tick-borne Alpharhabdovirinae: a meta-analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1791903}, pmid = {42039757}, issn = {2235-2988}, mesh = {Animals ; Phylogeny ; *Rhabdoviridae/classification/genetics/isolation & purification ; *Ticks/virology ; Humans ; *Rhabdoviridae Infections/epidemiology/virology ; *Tick-Borne Diseases/epidemiology/virology ; }, abstract = {INTRODUCTION: The Alpharhabdovirinae subfamily of the family Rhabdoviridae encompasses a diverse and expanding group of tick-borne viruses, some of which pose potential risks as emerging human pathogens. Despite increasing detection through metagenomic surveillance, the global diversity, phylogenetic relationships, and taxonomic framework of tick-borne Alpharhabdovirinae (TBA) remain poorly characterized.

METHODS: This study conducted a comprehensive meta-analysis of all publicly available TBA sequences based on phylogenetic analysis of five structural proteins (N, P, M, G, L), combined with host associations and geographic distributions.

RESULTS: 345 TBA strains were classified into 12 distinct phylogenetic clusters, each exhibiting unique evolutionary and ecological characteristics. These clusters include: (1) seven species-level lineages within the genus Alpharicinrhavirus, predominantly associated with Hyalomma and Haemaphysalis ticks across Eurasia; (2) a cluster related to Manly virus, widely distributed in Amblyomma, Haemaphysalis, and Rhipicephalus ticks acrossAustralia and China, exhibiting additional protein-coding genes of unknown function; (3) the genus Ledantevirus (21 species), characterized by broad host tropism including bats, rodents, and humans, with some members displaying phosphoprotein phylogenetic anomalies suggestive of recombination; (4) the genus Lostrhavirus, together with Tongliao Rhabd tick virus 1, forming a cluster associated with Hyalomma and Amblyomma ticks; (5) a Mononegavirus cluster comprising Alpharicinrhavirus heilongjiang, Alpharicinrhavirus skanevik (Norway mononegavirus 1), and Mononegavirales sp. specifically associated with Ixodesticks in Eurasia; and (6) one clusters with incomplete protein repertoires and uncertain taxonomic positions, including Tahe rhabdovirus 3 and Yanbian Rhabd tick virus 1 which lacks phosphoprotein entirely. This study provide a refined phylogenetic framework for TBA viruses, clarify their evolutionary relationships, and highlight critical knowledge gaps, including numerous uncharacterized hypothetical proteins and incomplete genomes that warrant further investigation.

DISCUSSION: This study underscores the importance of enhanced global surveillance and genomic characterization to assess the emergence potential and public health threat posed by this diverse group of tick-borne viruses.}, } @article {pmid42039802, year = {2026}, author = {Adhikary, K and Selim, S and Sarkar, R and Ganguly, K and Das, J and Almuhayawi, MS and Alruhaili, MH and Gattan, HS and Karak, P}, title = {Synthetic microbiomes in bioengineered rhizospheres: new frontiers for climate-resilient agriculture.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1780132}, pmid = {42039802}, issn = {1664-302X}, abstract = {Climate change poses significant threats to global agricultural productivity, necessitating innovative strategies to ensure food security and ecological sustainability. One promising avenue lies in the deliberate design and deployment of synthetic microbiomes and engineered rhizospheres to enhance plant resilience under environmental stress. This review places particular emphasis on multi-kingdom microbial interactions including bacteria, fungi, protists, and archaea and their potential for tailored, stress-specific applications within engineered rhizosphere systems. By integrating knowledge from microbial ecology, genomics, and systems biology, researchers have begun to unravel the complex interactions between plants and their associated microbial communities. Engineered microbial assemblies tailored to specific host plants and environmental conditions have shown potential in stabilizing crop performance during drought, salinity, and nutrient limitations. Moreover, the manipulation of root exudation patterns and soil physicochemical properties can be harnessed to recruit beneficial microbes and suppress harmful ones. The review also examines the role of synthetic biology tools, such as CRISPR-based genome editing and metabolic pathway engineering, in optimizing microbial traits for enhanced plant support. However, knowledge gaps remain in understanding multi-kingdom dynamics, optimizing SynComs for specific environmental contexts, and translating laboratory successes to reliable, field-scale applications. Additionally, advances in high-throughput screening, machine learning, and metagenomic profiling are accelerating the identification of key microbial taxa and functions relevant to plant health. Despite these promising developments, challenges remain in scaling these approaches for field applications and ensuring their ecological safety and consistency. This review explores the need for interdisciplinary efforts to translate laboratory insights into field-ready technologies, ultimately contributing to the development of climate-resilient and sustainable agricultural systems.}, } @article {pmid42039826, year = {2026}, author = {Gini, C and Tiezzi, F and Jiang, J and Byrd, MH and Wen, H and Johnson, JS and Brito, LF and van Vliet, S and Maltecca, C}, title = {Data-driven enterosignatures link gut microbiome reorganization to heat stress responses in lactating sows.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1797687}, pmid = {42039826}, issn = {1664-302X}, abstract = {BACKGROUND: Heat stress (HS) can disrupt the gut microbiome, yet most livestock studies rely on taxonomic summaries that overlook the ecological structure of microbial communities. Enterosignatures (ES) as latent, co-occurring microbial assemblages learned from metagenomic data, offer a framework to capture these dynamics but have scarcely been applied in livestock HS research.

METHODS: Shotgun metagenomes were obtained from 25 lactating sows, belonging to two genetic lines (TOL, n = 13; SEN, n = 12), which were divergently selected based on genomic breeding values (GEBVs) for heat tolerance, and exposed to HS conditions. Results were decomposed using non-negative matrix factorization (NMF), yielding 8 taxonomic (T-ES) and 5 functional (F-ES) subcommunities. Functional profiles (based on KEGG Orthology, KOs) were mapped to metagenome-assembled genomes (MAGs) to integrate metabolic attributes within each ES.

RESULTS: Temporal shifts dominated T-ES variation, with limited genetic-line effects. T-ES 1 (p = 5.42 × 10[-4], Cohen's d = 0.723) and T-ES 7 (p = 0.007, Cohen's d = 0.303) showed increases from day 4 to day 14. Despite modest overall genetic line effects, TOL animals progressively transitioned toward phylogenetically diverse and balanced communities, whereas SEN animals shifted toward imbalanced states characterized by enrichment of taxa with pathobiont potential or single-taxon dominance. Other T-ES displayed small to moderate effects, and T-ES 8 showed a potentially noteworthy genetic line-specific effect size at late lactation (Cohen's d = 0.960; 95% CI: -1.80 to -0.10), though omnibus tests were non-significant (p = 0.757), and the wide confidence interval underscores substantial uncertainty at this sample size. No F-ES reached statistical significance (p > 0.05); moderate effect sizes (up to d = 0.638) suggest possible functional restructuring warranting investigation in larger cohorts.

CONCLUSION: This work presents the first use of ES to track microbiome responses to HS in lactating sows. ES revealed latent taxonomic and functional subcommunities with clear temporal reorganization, offering insights not detectable with standard clustering or diversity metrics. Although genetic-line effects were modest, several ES showed biologically relevant shifts, supporting ES as a hypothesis-generating exploratory framework for linking microbial ecology to physiological adaptation under HS conditions, while warranting validation in larger, controlled trials.}, } @article {pmid42039832, year = {2026}, author = {Sola, L and Candeliere, F and Busi, E and Raimondi, S and Amaretti, A and Rossi, M}, title = {A genomic atlas of gut clostridia: phylogeny, butyrate, and propionate production.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1761627}, pmid = {42039832}, issn = {1664-302X}, abstract = {INTRODUCTION: Clostridia is a major microbial class in the human gut, crucial for fermenting undigested carbohydrates and proteins, which produce short-chain fatty acids essential for gut health and immune balance. This study revised the taxonomic classification and phylogeny of all the species of intestinal Clostridia catalogued in the Unified Human Gastrointestinal Genome database using a whole-genome approach and assessed butyrate and propionate producing species.

METHODS: A total of 1,897 Clostridia species, including those with recognised binomial nomenclature and those lacking formal taxonomic classification, were retrieved and reclassified using GTDB-Tk. Their phylogeny was determined by identifying, concatenating, and aligning the 120 ubiquitous single-copy proteins defined in the GTDB. Average amino acid identity (AAI), percentage of conserved proteins (POCP), and phylogenetic relationships were used to organize the species into genera and families. The presence of enzymes belonging to the biosynthetic pathways for butyrate and propionate production was investigated in all genomes with the tool GapSeq.

RESULTS: Reclassification of the genomes resulted in 404 recognised species and 1,493 species lacking formal taxonomic classification. Oscillospirales and Lachnospirales encompassed most of the species. The pathways leading to butyrate and propionate production were analyzed in their entirety, revealing 519 species as potential butyrate producers, 257 as potential propionate producers and 77 capable of producing both. To assess the abundance of each species, 151 faecal metagenomes of healthy subjects were profiled, indicating that butyrate producing Clostridia accounted on average for 28.0% of each microbiome.

CONCLUSIONS: This study offers a comprehensive overview of intestinal Clostridia diversity, emphasising their role in gut ecosystems and their potential for butyrate and propionate production.}, } @article {pmid42040306, year = {2026}, author = {Yang, R and Zhu, J and Zhang, Y and Liu, Y and Li, Z and Zhang, H and Li, Q and Wang, X and Chen, X and Chen, D and Liu, Q}, title = {Organic amendments boost maize yield (Zea mays L.) in karst soils via a hierarchical process driven by soil phosphorus enhancement and microbial-mediated nutrient cycling.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1782544}, pmid = {42040306}, issn = {1664-462X}, abstract = {INTRODUCTION: Sustainable food production in fragile karst landscapes requires moving beyond input-intensive agriculture.

METHODS: This study investigated how long-term organic amendments affected maize yield, using a 15-year field trial on karst yellow soil. Integrating soil analysis, metagenomics, and causal modeling, revealed that adding farmyard manure or bio-organic fertilizer to mineral NPK increased yield by 12.08% and 11.48%, respectively, and improved key soil properties, most notably available phosphorus.

RESULTS: Organic inputs shifted the soil microbiome toward copiotrophic taxa and enriched genes for organic matter decomposition and phosphorus mobilization. However, statistical modeling revealed that these biological changes did not directly drive yield. Instead, the primary pathway was hierarchical: amendments first enhanced the soil's chemical habitat, which then directly boosted crop growth while simultaneously shaping the microbial community and its functional potential. The interaction of soil, microbes, and genes together explained 81% of the yield variation.

DISCUSSION: Our findings demonstrate that in phosphorus-limited karst soils, organic amendments act foremost as soil conditioners. Microbial processes, though crucial, are secondary mediators that translate improved soil conditions into efficient nutrient cycling. Therefore, sustainable intensification in these vulnerable agroecosystems should prioritize managing soil health over directly targeting microbial processes.}, } @article {pmid42040505, year = {2026}, author = {Collado, C and Romero-Tena, P and Wegener, G and Elvert, M and Menapace, W and Laso-Pérez, R}, title = {Anaerobic oxidation of methane supports a minimal microbial community in a subsurface biofilm at Ginsburg mud volcano.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag072}, pmid = {42040505}, issn = {2730-6151}, abstract = {Deep marine sediments generate large amounts of methane, but most of this gas is consumed by the anaerobic oxidation of methane (AOM) mediated by microscopic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). In this study, we investigated the AOM within a sulfate-methane transition zone (SMTZ) at a depth of ~9.6 m at the rim of the Ginsburg mud volcano in the Gulf of Cádiz. The SMTZ is supplied with sulfate from both overlying seawater and an underlying evaporitic deposit, and it coincides with a fracture zone that hosts a visible biofilm. Here, carbon dioxide shows the strongest [13]C-depletion, indicating intense methane consumption. Metagenomic and lipid biomarker analysis of the biofilm revealed an exceptionally simple microbial community dominated by ANME-1b archaea (63%), which predominantly produce strongly [13]C-depleted glycerol dialkyl glycerol tetraethers and, to a lesser extent, the less common macrocyclic archaeols. The putative partner bacterium Seep-SRB1c (Desulfobacterota) is less abundant (9%). Additionally, the biofilm contained five low-abundance heterotrophs that likely rely on biomass or metabolites released from the ANME-SRB consortium. Our study highlights the presence of active methanotrophic biofilms in subsurface sediments and suggests that these communities may play an overlooked role in mitigating seafloor methane emissions.}, } @article {pmid42040506, year = {2026}, author = {Zhang, T and Pan, J and Palomo, A and Ouyang, Z and Wen, X and Li, J and Wang, C and Zheng, M}, title = {Unique characteristics of acid-tolerant comammox bacteria revealed by multi-omics analyses.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag070}, pmid = {42040506}, issn = {2730-6151}, abstract = {Complete ammonia oxidation (comammox) is a critical biogeochemical process in the nitrogen cycle. In this study, we utilized comammox Nitrospira to convert urine wastewater into ammonium nitrate by operating a laboratory-scale membrane bioreactor at pH 3 ~ 4. During the process, the acid-tolerant comammox Nitrospira was highly enriched. The metagenomic and metatranscriptomic analyses were applied to reveal its unique characteristics. Comparative genomic analysis among previously reported comammox Nitrospira demonstrated that this species was phylogenetically novel, named Candidatus Nitrospira aciditolerans. Key mechanisms were further identified to enable this species to thrive in acidic environments. These include active proton efflux, regulation of proton consumption, inhibition of proton influx, and cellular strategies for acid stress management and repair. Remarkably, different from other comammox Nitrospira and acid-tolerant ammonia-oxidizing bacteria (AOB), Candidatus Nitrospira aciditolerans possesses highly expressed V-type ATPases that are typically associated with acidophilic ammonia-oxidizing archaea (AOA). This may indicate an ecologically significant role for comammox bacteria and AOA in co-maintaining ammonia oxidation activity in low pH environments. Kinetic characterization revealed an apparent ammonium half-saturation coefficient K m of 0.50 ± 0.05 μM NH3 and an apparent ammonium inhibition constant K i of 241.43 ± 45.64 μM NH3. The enrichment culture demonstrated optimal ammonia oxidation activity at neutral pH but maintained functionality across a broader pH range between 4 and 8. Like other nitrifying bacteria, this comammox culture was sensitive to temperature and salinity changes. The findings enhance our understanding of the nitrogen cycle under acidic conditions and also present opportunities for engineering applications of acid-tolerant ammonia oxidizers.}, } @article {pmid42040549, year = {2026}, author = {Chen, Q and Yang, Z and Ren, D and Bao, C and Zhao, Y and Shi, Z}, title = {Case Report: Pulmonary tuberculosis with pneumocystis jirovecii colonization in a non-HIV patient: a cautionary tale on interpreting mNGS results.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1782843}, pmid = {42040549}, issn = {2296-858X}, abstract = {The diagnosis and treatment process of this case highlights that mNGS, as a powerful pathogen detection tool, provides a rapid method for the early detection of Pneumocystis jirovecii. However, mNGS testing of lavage specimens alone cannot distinguish between colonization and infection by the pathogen, particularly when a high number of sequences are present. Clinicians should therefore interpret laboratory results with caution to avoid unnecessary treatment that may cause adverse effects to the patient. CT scans offer strong evidence for differentiating between Pneumocystis jirovecii infection and/or Mycobacterium tuberculosis infection. Performing a biopsy at the site of infection, collecting pathological samples, and submitting them for mNGS testing can further assist clinicians in making a definitive diagnosis.}, } @article {pmid42040584, year = {2026}, author = {Li, CB and Tang, S and Wen, Y}, title = {Case Report: The complete radiological resolution of diffuse cholangitis in a HIV-positive patient with cryptosporidium infection after anti-retroviral therapy.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1686336}, pmid = {42040584}, issn = {2296-858X}, abstract = {We present a case of an HIV-positive patient with AIDS cholangiopathy secondary to Cryptosporidium infection. Imaging examination showed intrahepatic and extrahepatic cholangitis without papillary stenosis and extrahepatic bile duct strictures, indicating mild bile duct disease. However, it failed to obtain positive results in fecal microscopy examinations. Alternatively, metagenomic next-generation sequencing (mNGS) of a blood sample identified Cryptosporidium infection. The diagnostic power of mNGS is highly sensitive and can simultaneously identify various pathogens. To avoid irreversible damage to the biliary system, the rapid initiation of anti-HIV therapy restored the function of the immune system and led to the clinical resolution of cryptosporidiosis.}, } @article {pmid42040837, year = {2026}, author = {Sander, MM and Stoof-Leichsenring, KR and Liu, S and Shen, W and Lisovski, S and Herzschuh, U}, title = {Sedimentary Metagenomics Reveal Avian Community Transitions From the Last Glacial Maximum to the Holocene.}, journal = {Ecology and evolution}, volume = {16}, number = {4}, pages = {e72064}, pmid = {42040837}, issn = {2045-7758}, abstract = {The transition from the Last Glacial to the Holocene was marked by significant warming. This forced a compositional turnover of terrestrial plant and mammal communities discovered by diverse palaeoecological techniques. In this study, we analysed ancient environmental DNA with shotgun metagenomics from eight lake sediment cores, collected in northern Eurasia and Alaska, to elucidate the relationship of past bird communities and vegetation structure across the last 21,000 years. We leveraged all DNA reads assigned to the class 'Aves' to characterise the compositional changes of the bird community. The dominance of chicken birds (Galliformes, mainly ptarmigans) during the Last Glacial Maximum turned into a higher taxonomic bird diversity with increased numbers of songbird, raptor and waterfowl abundances and genera. This went along with the late glacial loss of the steppe-tundra and the increase of shrub and tree cover. Compared to the northern boreal areas, vegetation and bird communities were more stable in the northern tundra sites, where open landscapes prevailed throughout. Metagenomics significantly contribute to the reconstruction of past avian community changes and thus have high potential to support the predictions of distribution changes in the course of future ecosystem change.}, } @article {pmid42041249, year = {2026}, author = {Marroquin, SM and Cohen, S and Neely, MN and Doran, KS}, title = {Akkermansia muciniphila impacts group B Streptococcus vaginal colonization.}, journal = {mBio}, volume = {17}, number = {6}, pages = {e0286825}, pmid = {42041249}, issn = {2150-7511}, support = {F32 AI186285/AI/NIAID NIH HHS/United States ; L40 HD116358/HD/NICHD NIH HHS/United States ; R01 AI153332/AI/NIAID NIH HHS/United States ; R21 AI186346/AI/NIAID NIH HHS/United States ; R01AI153332,R21AI186346//National Institute of Allergy and Infectious Diseases/ ; F32AI186285//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Female ; *Streptococcus agalactiae/genetics/growth & development/physiology ; *Vagina/microbiology ; Humans ; *Streptococcal Infections/microbiology ; Pregnancy ; Epithelial Cells/microbiology ; Animals ; Bacterial Adhesion ; Microbiota ; Akkermansia ; Mice ; }, abstract = {Streptococcus agalactiae, or group B Streptococcus (GBS), is an opportunistic pathogen that asymptomatically colonizes the vaginal tract of up to 30% of healthy individuals. However, during pregnancy, it is associated with adverse pregnancy outcomes, and GBS can be transmitted to the fetus in utero or the newborn during vaginal birth, resulting in invasive neonatal disease. Previously, we identified that Akkermansia muciniphila increases GBS vaginal persistence in a cohort of human vaginal microbiome samples collected throughout pregnancy and promotes GBS vaginal colonization in a murine model. However, the mechanisms responsible for these observations are unknown. Here, we analyze additional vaginal shotgun metagenomic data sets and show that across independent studies with diverse populations, A. muciniphila-positive samples had higher GBS abundance. We determined that A. muciniphila aggregates with human vaginal isolates of GBS across all serotypes and promotes GBS attachment to human vaginal epithelial cells (hVECs). RNA-sequencing analysis reveals that A. muciniphila changed the expression of 281 unique GBS genes during hVEC co-colonization, many of which are involved in cell wall/membrane/envelope biogenesis. We demonstrate the importance of the GBS capsule and pili for direct interaction with A. muciniphila and increased attachment to hVECs, respectively. Lastly, we found that A. muciniphila promoted GBS aggregation in the murine vaginal lumen and that continual treatment with A. muciniphila reduced GBS vaginal persistence. Our results provide mechanistic insights and further evidence of the impact of A. muciniphila on GBS vaginal colonization and also demonstrate a beneficial potential of A. muciniphila treatment in the vaginal environment.IMPORTANCEGroup B Streptococcus (GBS) is a frequent colonizer of the vaginal tract of healthy people; however, during pregnancy, maternal colonization is associated with adverse pregnancy outcomes. GBS is a leading cause of neonatal sepsis and meningitis, with transmission to neonates occurring either during vaginal delivery or through ascension into the uterus during pregnancy. The influence of the vaginal microbiota on GBS pathogenesis remains greatly underappreciated. We have found that GBS is associated with the mucin-degrading intestinal commensal Akkermansia muciniphila, a newly identified colonizer of the vaginal tract. Our research identifies the mechanistic impact of this commensal organism on GBS aggregation, cell adherence, and gene expression, as well as its therapeutic potential during GBS vaginal colonization. Unraveling relationships between GBS and the vaginal microbiota will improve maternal-fetal health and may facilitate the development of alternative methods to reduce GBS in utero complications and neonatal disease.}, } @article {pmid42041251, year = {2026}, author = {Gador-Whyte, AP and Sherry, NL and Brischetto, A and Andersson, P and Bond, KA and van Hal, SJ and Harris, PNA and Howden, BP and , }, title = {Implementation of pathogen genomics in clinical microbiology laboratories.}, journal = {Clinical microbiology reviews}, volume = {39}, number = {2}, pages = {e0017725}, pmid = {42041251}, issn = {1098-6618}, support = {FSPGN00049//Australian Government Medical Research Future Fund/ ; GNT1196103//National Health and Medical Research Council/ ; GNT2033851//National Health and Medical Research Council/ ; GNT2033803//National Health and Medical Research Council/ ; }, mesh = {Humans ; *Genomics/methods ; *Laboratories, Clinical ; Metagenomics/methods ; Whole Genome Sequencing ; }, abstract = {SUMMARYPathogen genomics, including whole-genome sequencing (WGS) and clinical metagenomics, is a transformative technology increasingly being implemented in clinical microbiology, including in hospital laboratories. Pathogen genomics can improve the control of healthcare-associated infections, provide rapid infection diagnosis, and could enable replacement of laborious microbiology tests. To date, real-world implementation of pathogen genome sequencing has primarily been limited to public health laboratories, but sequencing in the clinical microbiology setting has the potential to provide advantages, including turnaround time and ability to focus on local priorities. In this review, we consider the factors that represent barriers to, and potential enablers of, the implementation of pathogen genomics in clinical microbiology, including the availability of funding and genomics-trained staff. We outline key use cases and implementation models of pathogen genomics in clinical microbiology and suggest a broad framework for labs commencing sequencing. Finally, we consider future opportunities, including direct-from-specimen sequencing, the role of machine learning in genomics analysis, and the application of pathogen genomics to clinical decision support.}, } @article {pmid42041878, year = {2026}, author = {Carlone, J and Ribeiro, ÁCDS and Parisi, A and Giampaoli, S and Fasano, A}, title = {Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.}, journal = {Biology}, volume = {15}, number = {8}, pages = {}, pmid = {42041878}, issn = {2079-7737}, support = {P30 DK040561/DK/NIDDK NIH HHS/United States ; }, abstract = {The growing interest in the role of the gut microbiome in athletic performance has led to the application of various sequencing technologies in this field. This review critically examines the sequencing methodologies used in microbiome studies on physical performance and sport, comparing their advantages, limitations, and applicability. In particular, the focus is on 16S metabarcoding and shotgun metagenomics, evaluating how these methodological approaches influence the interpretation of results in sports contexts. Close attention is directed toward technical challenges, methodological biases, and future perspectives, including emerging technologies and multi-omics approaches. This review aims to bridge the gap between methodological rigor and sports-specific applicability, providing evidence-based methodological guidance to support researchers in designing robust athlete microbiome studies and translating sequencing-derived findings into concrete applications for performance and sports health.}, } @article {pmid42041929, year = {2026}, author = {Ma, Y and Hu, Y and Zhang, J and Sun, Q and Wang, H and Liu, X and Tian, W and Wang, W and Ma, X and Shao, D and Liu, K and Li, B and Qiu, Y and Ma, Z and Li, Z and Wei, J}, title = {The Gut Microbiome and Metabolome of Domestic Cats Were Altered by the Oral Administration of Complex Probiotics.}, journal = {Biology}, volume = {15}, number = {8}, pages = {}, pmid = {42041929}, issn = {2079-7737}, abstract = {Probiotics are commonly applied to maintain the balance of gut microbiota and regulate the intestinal metabolic function of companion animals. In the present study, complex probiotics (Bacillus coagulans SNZ-1969, Bacillus subtilis, and Bacillus licheniformis) were added into the basal diet of domestic cats to investigate their influence on the intestinal microbiome and metabolic characteristics. Results revealed that the alpha diversity of the gut microbiota in the probiotic group was enhanced when compared to the control group. The beta diversity of the gut microbiota was also altered by the oral consumption of the complex probiotics. Compared to the control group, the relative abundance of beneficial microbes (such as Clostridium, Bacteroides, Phocaeicola, and Ruminococcus) in the probiotic group was enhanced, while the relative abundance of opportunistic pathogens (such as Escherichia, Gallibacter, Corynebacterium) was decreased. Additionally, the intestinal metabolic characteristics of domestic cats were also changed. The metabolomic analysis identified 408 differential metabolites between the two groups, and the KEGG function pathway analysis proved that the dominant pathway related to the differential metabolites were the amino acid metabolism, lipid metabolism, carbohydrate metabolism, energy metabolism, endocrine system, digestive system, immune system, and other metabolic pathways. Spearman's correlation analysis revealed that the beneficial microbes had positive correlations with the differential metabolites. In conclusion, the current study demonstrated that oral administration of complex probiotics could regulate overall health and well-being in domestic cats through modulating the gut microbiome and metabolic characteristics.}, } @article {pmid42043232, year = {2026}, author = {Geng, M and Wang, X and Huang, X and Li, Y and Wei, Y and Cai, Y and Li, J and Jiang, C and Wu, W and Liu, S and Guo, N and Zhang, X and Wu, W and Han, G and Han, X and Liu, T and Li, Q and Wang, S}, title = {Metatranscriptomic Analysis of Tick Virome Diversity in Hebei Province, China.}, journal = {Viruses}, volume = {18}, number = {4}, pages = {}, pmid = {42043232}, issn = {1999-4915}, support = {ZDGWNLJS25-25//Surveillance and Early Warning Technologies for Unknown and Emerging Pathogens/ ; 20260864//Hebei Provincial Medical Science Research Project/ ; }, mesh = {Animals ; China ; Phylogeny ; *Virome ; Haemaphysalis longicornis/virology ; *Ticks/virology ; Genome, Viral ; Dermacentor/virology ; *RNA Viruses/genetics/classification/isolation & purification ; Metagenomics ; Genetic Variation ; Transcriptome ; }, abstract = {Ticks serve as primary vectors for a wide array of RNA viruses, yet the diversity and distribution of tick-associated RNA viruses remain incompletely characterized in Hebei province. To address this gap, we conducted a systematic metatranscriptomic investigation of 986 ticks representing six species, collected from the diverse ecological landscapes of Hebei Province in northern China. Our analysis recovered 25 complete or near-complete viral genomes spanning 12 families, including Phenuiviridae, Flaviviridae, and Nairoviridae. Of critical public health significance, we identified Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) in both Haemaphysalis longicornis and Dermacentor nuttalli. Phylogenetic reconstruction revealed marked geographic stratification where strains from the coastal plains clustered with the dominant Genotype F, while those from the mountainous north formed a characteristic and divergent lineage phylogenetically linked to isolates from Inner Mongolia. Furthermore, a novel viral agent provisionally named Zhangjiakou Hepacivirus was discovered in Haemaphysalis japonica. This virus shared less than 80% nucleotide identity with the rodent-associated Hepacivirus P, consistent with a rodent origin and possible cross-species transmission. Collectively, these findings reveal descriptive variation associated with vector identity, physiological status, and ecological context in shaping viral evolution and underscore the need for continuous metagenomic surveillance to mitigate emerging tick-borne disease risks within a One Health framework.}, } @article {pmid42043279, year = {2026}, author = {Rūmnieks, J and Baltā, I and Šišovs, M and Tārs, K}, title = {ssRNA bacteriophage metagenomes reveal a diverse set of novel protein families.}, journal = {Protein science : a publication of the Protein Society}, volume = {35}, number = {5}, pages = {e70582}, pmid = {42043279}, issn = {1469-896X}, support = {5.2.1.1.i.0/2/24/I/CFLA/001//European Commission/ ; }, mesh = {Open Reading Frames ; *Viral Proteins/genetics/chemistry/metabolism ; *Genome, Viral ; *Metagenome ; *Bacteriophages/genetics ; *RNA, Viral/genetics ; }, abstract = {The bacteriophages with single-stranded RNA (ssRNA) genomes (class Leviviricetes) are among the simplest known viruses that encode only three core proteins: a receptor-binding protein, a capsid protein, and an RNA-dependent RNA polymerase. The number of isolated ssRNA phages has remained very low, but the accumulating RNA metagenome data have uncovered a large variety of these viruses in many environments. Besides the core proteins, many of these genomes putatively encode additional proteins, which up to now have remained uncharacterized. We looked for non-conserved open reading frames (ORFs) in Leviviricetes sequences from the IMG/VR virus metagenome database and used sequence- and structure-based clustering to organize them into similarity groups. Potential ORFs were found throughout the ssRNA phage genomes but almost exclusively on the positive-sense RNA strand, suggestive of their protein-coding potential. The prevalence of the non-conserved ORFs varied in various phage lineages, and their distribution among different genome positions was markedly uneven. Most of the identified ORFs encode all-α proteins, a portion of which contain transmembrane segments that resemble a group of known ssRNA phage lysis proteins, while many others represent previously uncharacterized families of globular or semi-globular α-helical proteins. We additionally uncovered a major class of globular α/β proteins and experimentally determined the structure of a representative protein of this group. These results pave the way for further functional studies of novel ssRNA phage proteins for a better understanding of this diverse virus group.}, } @article {pmid42043563, year = {2026}, author = {Chatterjee, S and Dutta, S and Ghosh, J and Saha, S and Mondal, M and Sarkar, J and Mondal, N and Ghosh, W}, title = {Warming responses, antibiosis potentials, and ecological implications of cryo-adapted copiotrophs from a Trans-Himalayan lake-desert ecosystem.}, journal = {Archives of microbiology}, volume = {208}, number = {7}, pages = {}, pmid = {42043563}, issn = {1432-072X}, support = {Intramural Faculty Grant//Bose Institute/ ; }, abstract = {A Trans-Himalayan lake-desert ecosystem was explored for the low-to-high temperature adaptations of copiotrophic psychrophiles having potentials for substantive carbon remineralization under natural and/or anthropogenically-influenced conditions of high organic matter delivery to the environment. Overall 27 bacterial species were isolated from the brackish-water and sediment-surface of Tso Moriri (a massive lake on the Changthang plateau that remains frozen for approximately one third of the year), and the fine talus covering a lake-side rocky mountain. In Luria broth (LB), all isolates grew at 4 °C and 15 °C; at -10 °C, 13 could grow while others remained only metabolically-active. Catabolizing different complex-organic-compounds, all isolates achieved considerable growth at 4 °C; 20 accomplished low growth at -10 °C. LB-based growth dwindled with rising temperature: 23, 11, and none of the isolates grew at 28 °C, 37 °C, and 42 °C respectively. In agar-overlay assays, most actinobacterial isolates inhibited other mesophilic bacteria. The isolates’ genomes, and their habitats’ metagenomes, encompassed diverse genes for extreme-temperature adaptation, carbohydrate catabolism, antibiosis and antibiotic-resistance. All in-vitro findings collectively engender the following hypothesis, via contextual inferences pending field-study-based validations. Warming-induced cessation of organotrophic growth, within high-altitude cryospheres, would curb the production of simple-fatty-acids, CO2 and N2O. Short-supply of acetate and CO2 would, in turn, cut-back methanogenesis. Such negative-feedback control of greenhouse gas production at the micro-habitat level can add-up in the biome-scale to mitigate broader environmental warming; it, however, endangers the ecosystem from thermally-better-adapted foreign microbes that can usher positive-feedback cycles of warming. In the latter scenario, antibiosis potentials of native actinobacteria become pivotal to microbiome protection.}, } @article {pmid42043697, year = {2026}, author = {Lomelí-Álvarez, MF and Escamilla-Montes, R and Diarte-Plata, G and Guo, X and Fierro-Coronado, JA and Rubio-Luque, AM and Vega-Carranza, AS and González, AL}, title = {Dietary and water probiotics enhance immunity, modulate microbiota, and increase survival of Penaeus vannamei challenged with V. parahaemolyticus.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {42043697}, issn = {1678-4405}, abstract = {This study evaluated the effects of Bacillus licheniformis and Pediococcus pentosaceus administered in both culture water and feed to Penaeus vannamei over a 47-day experiment. Treatments in triplicate were as follows: (I) Commercial Feed (CF); (II) CF + P. pentosaceus in the water (3 × 10[6] CFU/L); (III) CF + B. licheniformis in the water (3 × 10[6] CFU/L); (IV) P. pentosaceus in fermented feed (51 × 10[5] CFU/g); (V) B. licheniformis in fermented feed (147 × 10[6] CFU/g); (VI) Mix of P. pentosaceus (140 × 10[5] CFU/g) + B. licheniformis (180 × 10[5] CFU/g) in fermented feed + Mix of P. pentosaceus + B. licheniformis (3 × 10[6] CFU/L) in the water. Growth, immune effectors (phenoloxidase and superoxide anion), and gut bacterial profiles via 16S metagenomic sequencing were assessed. Survival was determined after a challenge with Vibrio parahaemolyticus. Probiotics did not affect growth. Only B. licheniformis in water and fermented feed elicited a significant immunostimulatory response, increasing superoxide anion production and phenoloxidase activity, respectively. Probiotic administration also modulated the gut microbiota, significantly increasing the relative abundance of beneficial genera like Ruegeria and Haloferula. Measures of both alpha and beta diversity indicated a significant restructuring of the microbial community in response to probiotics. Most major bacterial groups showed predominantly positive intra-group interactions, while Psychromonadaceae solely exhibited negative interactions with other families. Shrimp survival was significantly higher in shrimp treated with probiotics, excluding treatment II. These results demonstrate that probiotics strengthen innate immunity and improves disease resistance in shrimp by enhancing immunocompetence and enriching beneficial gut microbes, offering a viable strategy for sustainable aquaculture health management.}, } @article {pmid42044527, year = {2026}, author = {Rabasco, JT and Bolyen, E and Caporaso, JG and Sapers, H and Callahan, BJ}, title = {Identify contaminants with decontam on the QIIME 2 Framework.}, journal = {Microbiology resource announcements}, volume = {15}, number = {6}, pages = {e0126125}, pmid = {42044527}, issn = {2576-098X}, support = {EEC-2133504//National Science Foundation/ ; R35GM133745/NH/NIH HHS/United States ; 1U24CA248454/NH/NIH HHS/United States ; }, abstract = {Here, we present the integration of the decontam method for contaminant identification and a supplemental approach for identifying the source of contaminants in sequencing data within the QIIME 2 Framework for microbiome data science. We demonstrate its use in a tutorial based on the QIIME 2 "Moving Pictures Tutorial" data.}, } @article {pmid42044543, year = {2026}, author = {Zhang, X and Chen, J and Li, Y and Tang, R and Zhu, T and Yuan, Y}, title = {Aerobic biodegradation of acesulfame by sediment-enriched microbial consortia: Kinetics, pathway, and microbial mechanism.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129734}, doi = {10.1016/j.jenvman.2026.129734}, pmid = {42044543}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; *Microbial Consortia ; Geologic Sediments/microbiology ; Kinetics ; Aerobiosis ; *Thiazines/metabolism ; }, abstract = {Artificial sweetener acesulfame (ACE), an emerging pollutant frequently detected in aquatic environments, exhibits potential ecological toxicity and risk accumulation effects. However, its environmental fate and microbial degradation mechanisms within sedimentary environments remain inadequately characterized. Herein, we established a sediment-based microcosm system to quantitatively characterize the degradation kinetics of ACE, track associated shifts in microbial community structure and function, and decipher the underlying molecular mechanisms. The results showed that successive enrichment cycles significantly augment the aerobic biodegradation of ACE by sediment microbial communities. Under aerobic conditions, the degradation rate constant increased from 0.58 to 3.60 d[-1] following enrichment, significantly exceeding the rate under the anoxic conditions. Metagenomic analysis revealed that ACE treatment reshaped the microbial community structure, with Pseudomonadota remaining the dominant phylum (60.2-65.8%). Genes encoding ACE-degrading sulfatase and amidase were linked to Chelatococcus and Devosia, both of which showed dramatic enrichment in treated samples, underscoring their critical contribution to ACE degradation. A two-step hydrolytic pathway for ACE degradation via sulfonate ester and amide bond hydrolysis was elucidated through combined product analysis. This biodegradation process coincided with significant changes in the abundance of genes governing carbon, nitrogen, and sulfur metabolism, reflecting a functional restructuring of the microbial community. Toxicity assessment indicated that most transformation products exhibited lower toxicity than the parent compound, suggesting an overall reduction in environmental risk. These findings elucidate the microbial degradation mechanisms of ACE, facilitating the assessment of its environmental risks and the development of effective bioremediation strategies.}, } @article {pmid42044779, year = {2026}, author = {Zhang, Y and Zeng, M and Guo, P and Zhang, Z and Chen, X and Li, X and Hao, F and Jiao, X and Wu, Y and Feng, W and Zheng, X}, title = {Effects of Rehmannia glutinosa Libosch. Rhizome water extract and Rehmapicrogenin on pulmonary hypertension: Multi-omics insights into epidermal growth factor receptor/pyruvate kinase M2 pathway and metabolic regulation.}, journal = {Journal of ethnopharmacology}, volume = {367}, number = {}, pages = {121775}, doi = {10.1016/j.jep.2026.121775}, pmid = {42044779}, issn = {1872-7573}, mesh = {Animals ; ErbB Receptors/metabolism ; *Rehmannia/chemistry ; Mice ; *Hypertension, Pulmonary/drug therapy/metabolism ; Male ; *Plant Extracts/pharmacology/therapeutic use ; Mice, Inbred C57BL ; *Pyruvate Kinase/metabolism ; Disease Models, Animal ; Myocytes, Smooth Muscle/drug effects ; Signal Transduction/drug effects ; Cell Proliferation/drug effects ; *Drugs, Chinese Herbal/pharmacology ; Multiomics ; }, abstract = {Rehmannia glutinosa Libosch. (RG), as one of the 'Four Famous Chinese Medicinal Herbs', has a long history of medicinal use and is classified as belonging to the meridians of the heart, liver, and kidney. RG has the effects of clearing heat and cooling blood, nourishing yin, and generating fluids. Pulmonary hypertension (PH) is a cardiovascular disease, and its pathogenesis can be summarized as 'yin deficiency', 'blood stasis', and 'qi deficiency'. The efficacy of RG is highly compatible with this disease, and the compounds isolated from RG can significantly inhibit the proliferation of pulmonary arterial smooth muscle cells (PASMCs). However, the mechanism by which it intervenes in PH remains unclear.

OBJECTIVE: In this study, the mechanisms and active components of RG were investigated for treating PH by using multi-omics analysis and surface plasmon resonance (SPR) technology, providing experimental support for clinical application.

METHODS: A PH mouse model was established through 5 weeks of hypoxia, with RG administration starting in week four. Cardiorespiratory function was evaluated after treatment. The therapeutic targets of RG were identified via 16S rDNA sequencing, metagenomics, and metabolomics. SPR ligand fishing was performed to isolate rehmapicrogenin (Reh), an RG-derived compound that targets the epidermal growth factor receptor (EGFR). The effects and mechanisms of Reh were assessed by measuring cardiac and pulmonary function, oxidative stress, apoptosis, immune cell activity, and glycolysis. An in vitro model of hypoxia-induced PASMCs proliferation was used to validate Reh's mechanism with an EGFR agonist (NSC).

RESULTS: RG extracts improved cardiorespiratory function and regulated gut microbiota, correcting the Firmicutes/Bacteroidetes (F/B) ratio in PH mice. RG also mitigated metabolic disturbances and inhibited glycolysis through pyruvate kinase M2 (PKM2) regulation, as confirmed using immunofluorescence analysis, western blotting, and PCR. SPR identified Reh as the active ingredient, which improved cardiorespiratory function, reduced oxidative stress and apoptosis, and suppressed EGFR and PKM2 expression and glycolysis. In vitro, Reh inhibited PASMC migration and proliferation, alleviated oxidative stress, and reduced mitochondrial damage. These effects were reversed upon NSC addition, confirming the role of EGFR in the mechanism.

CONCLUSION: RG and its active compound Reh mitigate hypoxia-induced PH by targeting the EGFR/PKM2 pathway, reducing glycolysis, and regulating gut microbiota dysbiosis.}, } @article {pmid42044791, year = {2026}, author = {Dai, Y and Li, J and Wang, X and Xia, F and Zheng, J and Shen, C}, title = {Synergistic mechanisms of bacteria and fungi in the biodegradation of Benzo[a]pyrene: Insights from metagenomic and metabolomic analyses.}, journal = {Environmental research}, volume = {301}, number = {}, pages = {124602}, doi = {10.1016/j.envres.2026.124602}, pmid = {42044791}, issn = {1096-0953}, mesh = {*Benzo(a)pyrene/metabolism ; Biodegradation, Environmental ; Soil Microbiology ; *Soil Pollutants/metabolism ; Metagenomics ; *Fungi/metabolism ; *Bacteria/metabolism ; Metabolomics ; *Ascomycota/metabolism ; *Pseudomonas/metabolism ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are pervasive organic pollutants, with benzo[a]pyrene (BaP), a prominent heavy-weight PAH, drawing considerable attention due to its high toxicity and resistance to degradation. While both bacteria and fungi have been demonstrated to effectively remediate BaP, their synergistic mechanisms remain poorly understood. In this study, we employed Pseudomonas nicosulfuronedens DY-8 (bacterium) and Arthrinium acutiapicum DL-5 (fungus) to explore the mechanisms underlying PAH bioaugmentation using metagenomic and metabolomic approaches. Although both strains individually enhanced BaP degradation, their combined application significantly reduced BaP residuals. qPCR analysis revealed that the bacteria promote BaP dissipation by stimulating the abundance of PAH-RHD GP genes in the soil. Correlations between metabolite abundance, enriched microbial populations, functional gene abundance, and fungal growth suggest that fungi enhance the growth of indigenous bacteria, further boosting the degradation of BaP metabolites. Additionally, the synergistic treatment of bacteria and fungi further altered the diversity of soil functional microorganisms, metabolic products, and functional genes. These findings provide insights into potential synergistic mechanisms by which bacterial-fungal interactions drive the degradation of high-molecular-weight PAHs, underscoring the potential of microbial consortia in the bioremediation of persistent organic pollutants in soil environments.}, } @article {pmid42044793, year = {2026}, author = {Zhou, Y and Hu, X and Du, L and Gu, Y and Li, J and Jia, M and Zhang, G and Wang, Y}, title = {Antibiotic resistance genes across divergent wetland types: Profiles, driving mechanisms, and risk assessment.}, journal = {Environmental research}, volume = {302}, number = {}, pages = {124601}, doi = {10.1016/j.envres.2026.124601}, pmid = {42044793}, issn = {1096-0953}, mesh = {*Wetlands ; *Drug Resistance, Microbial/genetics ; Risk Assessment ; Soil Microbiology ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; }, abstract = {Wetlands are critical reservoirs and hotspots of antibiotic resistance genes (ARGs). Metagenomic sequencing was employed to profile the ARG and mobile genetic element (MGE) abundance and diversity in coastal (B), constructed (R), and swampy (W) wetlands. In total, 560 ARGs were detected across all sites, primarily conferring resistance to cephalosporins and tetracyclines, with antibiotic efflux being the dominant mechanism of resistance. ARG richness was significantly higher in wetlands R and W than in wetland B (p < 0.001). Non-metric multidimensional scaling (NMDS) further indicated significant differences in ARG β-diversity among the wetlands. Pseudomonadota were identified as the primary hosts of both ARGs and MGEs. Soil salinity and Cr content were the key environmental factors regulating ARG profiles, with salinity exhibiting the broadest influence and linearly correlating with multiple ARG types. In addition, plasmid and insertion sequence (IS) richness positively correlated with ARG richness, showing the strongest explanatory power for ARG richness variation. Risk assessment revealed that rank I and II ARGs were significantly enriched in wetland W (p < 0.05), whereas rank IV ARGs were dominant across most sites. This study demonstrated that soil physicochemical properties, plasmids, and ISs jointly and differentially shaped ARG abundance and diversity in wetlands, accompanied by an assessment of their risk. These findings support the development of targeted strategies to mitigate ARG dissemination in wetland ecosystems.}, } @article {pmid42044853, year = {2026}, author = {Weng, H and Wang, H and Zhang, Q and Li, X and Zhang, L and Peng, Y}, title = {Enrichment of comammox Nitrospira with urea: comparative genomics reveals divergent urea response mechanisms among ammonia-oxidizing microorganisms.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134722}, doi = {10.1016/j.biortech.2026.134722}, pmid = {42044853}, issn = {1873-2976}, mesh = {*Urea/metabolism ; *Ammonia/metabolism ; *Genomics/methods ; Nitrification ; *Bacteria/metabolism/genetics ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Genome, Bacterial ; }, abstract = {Urea is a major nitrogen form in natural and engineered ecosystems, yet the traits driving niche partitioning among nitrifiers during urea nitrification remain poorly understood. In this work, a stable urea nitrification microbial community was successfully established over prolonged cultivation characterized using 16S rRNA gene amplicon sequencing, qPCR and genome-resolved metagenomics coupled with comparative genomics. A clade A comammox Nitrospira closely related to Candidatus Nitrospira nitrosa became dominant (OTU330, 13.9%) and yielded the most abundant nitrifier metagenome-assembled genome (MAG). Genomes indicate comammox Nitrospira couples ATP-dependent urea ABC uptake to a streamlined urease-only module characterized by slow substrate turnover, whereas Nitrosomonas relies on passive urea channels and redundant urease/urea-amidolyase pathways, enabling rapid urea metabolism. These contrasting urea acquisition strategies suggest an affinity-capacity trade-off that underpins niche partitioning in urea-fed, oligotrophic nitrifying systems and provide targets for enhancing urea-based wastewater treatment processes.}, } @article {pmid42045408, year = {2026}, author = {Kutuzova, S and Piera Líndez, P and Danielsen, LS and Nielsen, KN and Olsen, NS and Riber, L and Gobbi, A and Forero-Junco, LM and Erdmann Dougherty, P and Westergaard, JC and Browne, PD and Christensen, S and Hestbjerg Hansen, L and Nielsen, M and Nybo Andersen, J and Rasmussen, S}, title = {Improving metagenome binning by integrating intrinsic features and taxonomy.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {42045408}, issn = {1546-1696}, support = {NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21SA0072102//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 7076-00129B//Innovationsfonden (Innovation Fund Denmark)/ ; }, abstract = {A common procedure for studying the microbiome is binning the sequenced contigs into metagenome-assembled genomes. State-of-the-art binning methods use coabundance and sequence-based motifs such as tetranucleotide frequencies, whereas taxonomic labels derived from alignment based classification have not been widely used. Here we propose TaxVAMB, a metagenome binning tool based on semisupervised bimodal variational autoencoders, combining tetranucleotide frequencies and contig coabundances with taxonomic information. TaxVAMB outperformed all other binners on CAMI2 human microbiome datasets, returning on average 29% more high-quality assemblies than the next best binner, and performed on par with the best binners on short-read datasets. On a human gut long-read dataset, TaxVAMB recovered 29% more high-quality bins. In a typical single-sample setup, TaxVAMB on average returns 83% more high-quality bins compared to VAMB. Lastly, TaxVAMB binned incomplete genomes better than any other tool, returning on average 300% more high-quality bins of incomplete genomes than the next best binner.}, } @article {pmid42045553, year = {2026}, author = {Wei, D and Xing, C and Zeng, S and Hou, D and Deng, Z and Long, X and Wang, H and Zhou, R and Yu, L and Shu, N and Tao, Z and Zhou, X and Weng, S and He, J and Huang, Z}, title = {The crayfish-rice coculture model contributes to regulating the soil fertility of rice fields and maintaining the stability of soil microbial community composition and function.}, journal = {Advanced biotechnology}, volume = {4}, number = {2}, pages = {}, pmid = {42045553}, issn = {2948-2801}, support = {2023YFD2401705//National Key Research and Development Program of China/ ; 2024YFD2401202//National Key Research and Development Program of China/ ; AA23062047//Earmarked Fund for CARS-48-20; Guangxi Science and Technology Major Special Project/ ; SML2021SP203//Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; }, abstract = {Rice-fish coculture represents a classic sustainable agricultural paradigm; however, the microecological mechanisms underlying its capacity to maintain soil fertility and microbial community stability remain poorly understood. We conducted a 13-month field experiment comparing three cultivation systems:crayfish-rice coculture (CRCE), crayfish-waterweed coculture (CWCE), and rice monoculture (RME)-by integrating physicochemical analysis, 16S rRNA sequencing, metagenomics, microbial network analysis, and null model simulations. Our results demonstrated that coculture systems, particularly CRCE, enhanced soil fertility through carbon sequestration (total carbon: 25.0-45.0 mg/g; total organic carbon: 15.0-35.0 mg/g) and sustained redox homeostasis (consistently low oxidation-reduction potential: - 150 to - 50 mV), in stark contrast to the extreme redox fluctuations observed in RME. These stable edaphic conditions imposed deterministic selection on microbial communities (homogeneous selection contribution: 30%-50% in CRCE vs. 10%-20% in RME), shifting community assembly from stochastic drift dominance toward predictable succession. This assembly shift enriched functionally coupled keystone taxa, including iron reducers (Geobacter), sulfur oxidizers (Sulfuricurvum), and nitrifiers (Nitrospira), which formed ecological networks characterized by 98.6% positive interactions and enhanced functional gene repertoires associated with carbon, nitrogen, and sulfur biogeochemical cycles. Metagenomic analysis corroborated these findings, revealing enrichment of functional genes involved in polymer degradation, nitrification, and sulfate reduction in CRCE, supporting enhanced nutrient cycling capacity. We establish a hierarchical causal pathway in which bioturbation-induced environmental stabilization drives deterministic community assembly, which in turn promotes keystone taxon enrichment and functional integration. This framework provides a mechanistic explanation for how crayfish-rice coculture regulates soil fertility and sustains microbial community compositional and functional stability in anthropogenically designed agricultural ecosystems.}, } @article {pmid42045683, year = {2026}, author = {Boppana, LKT and Bag, R}, title = {Metagenomic Microbial Next-Generation Gene Sequencing as a Noninvasive Diagnostic Tool in Adult Lung Transplantation: A Retrospective Case Series.}, journal = {Lung}, volume = {204}, number = {1}, pages = {}, pmid = {42045683}, issn = {1432-1750}, } @article {pmid42045813, year = {2026}, author = {Lindstrøm, JC and Gjerdrum, HSV and Brynildsrud, OB and Tannæs, TM and Kristoffersen, AB and Ricanek, P and Leegaard, TM and Bjørnholt, JV and Jørgensen, SB and Tunsjø, HS and Olbjørn, C and Detlie, TE and Jahnsen, J and Kristensen, VA and Høivik, ML and Hov, JR and Moen, AE and , }, title = {Exploring alterations in the gut resistome in medically treated inflammatory bowel disease patients.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42045813}, issn = {1471-2180}, abstract = {INTRODUCTION: The members of the human gut microbiota contain a large diversity of genes, including antimicrobial resistance genes (ARGs) known as the gut resistome. The resistome is susceptible to alterations when compositional changes occur in the fecal and gut microbiome. Medical treatment may affect members of the gut microbiota. This study hypothesizes that medication used by patients with inflammatory bowel disease (IBD) leads to an increased prevalence and diversity of ARGs in the gut and a corresponding change in the taxonomic composition of the fecal microbiome.

METHODS: Fecal samples from 16 Crohn’s Disease (CD) and 16 Ulcerative Colitis (UC) patients, and 13 symptomatic controls (patients experiencing gastrointestinal symptoms, but with no endoscopic or histologic signs of IBD at inclusion, and no evidence of IBD during follow-up, were classified as symptomatic non-IBD controls) were subjected to metagenomic sequencing. The samples were collected before initiation of IBD medication, and after one year of treatment. Patients were treated with 5- Amino Salicylic Acid, Biological treatment, and Corticosteroids, or a combination of the three. Resistance Gene Identifier Comprehensive Antibiotic Resistance Database (RGI CARD) and regression modelling were used to analyze the abundance and diversity changes in the ARGs and the taxonomy.

RESULTS: We found significant associations with medicine use and abundance changes for eight resistance genes (Antibiotic Resistance Ontology (ARO) terms), four AMR gene families and 14 AMR drug classes. The use of 5-ASA was associated with abundance changes for the efflux pump efpA. This medication was also associated with significant changes in the “pyrazinamide resistant rpsA” gene family and with six drug classes (cephamycin, diaminopyrimidine, mupirocin, penem, pyrazinamide and rifamycin). Biological treatment was associated with changes in abundance of five drug classes (Zoliflodacin, lincosamide, macrolide, streptogramin and tetracycline). Corticosteroids were associated with changes in the ARO terms sul2, OXA beta-lactamase AMR gene family, and three drug classes (carbapenem, glycylcycline, and triclosan).

CONCLUSIONS: All IBD medication groups were found to be associated with significant abundance changes within the fecal resistome between inclusion and follow-up time points, where corticosteroid treatment resulted in less resistance in the microbiota compared to in the persons not treated with corticosteroids (either 5-Aminosalicylic Acid or Biological treatments).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05101-9.}, } @article {pmid42046064, year = {2026}, author = {Tang, S and Cai, L and Hao, Y and Jiang, Q and Luan, X and Fang, X and Li, Z and Zhu, J}, title = {SCFAs inhibited NETosis to alleviate lung inflammation in COPD: a potential role for GPR43.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03688-1}, pmid = {42046064}, issn = {1465-993X}, support = {82575021//the National Natural Science Foundation of China/ ; 2408085MH230//Anhui Provincial Natural Science Foundation/ ; 2022AH020044//the Science Fund for Distinguished Young Scholars in Universities of Anhui Province/ ; 2024AKLCMF04//the Foundation of Anhui Provincial Key Laboratory of Chinese Medicinal Formula/ ; }, abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide, and poses a significant socioeconomic burden attributable to its high mortality and morbidity. Short-chain fatty acids (SCFAs), as the key metabolites produced by gut microbiota, have been considered to be involved in the regulation of pulmonary inflammation. However, the underlying bridging mechanisms through the gut-lung axis remain elusive. METHODS: To delineate cellular heterogeneity during COPD progression, we profiled lung tissues from rats at distinct stages (Days 0, 7, 14, and 28) using scRNA-seq, followed by bulk transcriptomic analysis to pinpoint critical dysregulated pathways. Gas chromatography-mass spectrometry (GC-MS) was employed to quantify the differential SCFA levels. The protective effects of SCFAs against pulmonary inflammation in COPD were evaluated via pulmonary function testing, HE staining, and ELISA. Flow cytometry, Western blotting, immunofluorescence and scanning electron microscopy were employed to explore the mechanism of SCFAs regulating neutrophil extracellular trap (NET) formation in vitro and in vivo. Finally, metagenomic sequencing was applied to investigate the impact of SCFAs on gut microbial communities. RESULTS: ScRNA-seq demonstrated the intense immune activation during the progress of COPD, characterized by neutrophil accumulation exceeding 50% of cellular composition on the 14th day in the lung tissue. Transcriptomic analysis further pinpointed neutrophil-driven NETosis as the key pathogenic pathway. The results of GC-MS showed the significant downregulation of SCFAs represented by acetic acid and propionic acid in COPD. Exogenous supplementation with SCFAs (acetic acid and propionic acid) activated the key receptor GPR43, suppressed the expression of NETs marker proteins (NE, MPO, and CitH3) and attenuated inflammatory cytokine levels in COPD rats. Rescue experiments with NETs inducers/inhibitors and GPR43 agonists/antagonists further elucidated the regulatory mechanisms of SCFAs/GPR43 axis in COPD inflammation. Furthermore, metagenomic sequencing revealed that SCFAs reshaped the intestinal flora in COPD by enriching the abundance of beneficial bacteria. CONCLUSION: As one of the key receptors for gut microbiota-derived SCFAs, GPR43 may be involved in the process by which SCFAs alleviate pulmonary inflammation in COPD through regulating NET formation. These findings provide valuable experimental evidence for promoting the clinical translation of therapeutic strategies characterized by gut microbiota and their metabolites.}, } @article {pmid42046358, year = {2026}, author = {Chen, K and Huang, L}, title = {[Metagenomic next - generation sequencing for diagnosis of infection of unknown origin in intensive care units: a bibliometric analysis].}, journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control}, volume = {38}, number = {1}, pages = {79-83}, doi = {10.16250/j.32.1915.2026077}, pmid = {42046358}, issn = {1005-6661}, mesh = {*Bibliometrics ; *High-Throughput Nucleotide Sequencing/methods ; *Intensive Care Units ; Humans ; *Metagenomics/methods ; }, abstract = {OBJECTIVE: To investigate the scientific outputs of metagenomic next-generation sequencing (mNGS) for diagnosis of infection of unknown origin in intensive care units (ICUs), and to decipher the latest advances, frontier trends and spatiotemporal evolution of research hotpots in mNGS for diagnosis of infection of unknown origin in ICUs.

METHODS: Publications pertaining to the application of mNGS in diagnosis of infection of unknown origin in ICUs were retrieved from Web of Science Core Collection (WOSCC) from January 1, 2015 to December 31, 2024. The software Scimago Graphica 1.0.30 was employed to generate the network maps of collaboration relationships between countries, international collaborative relationships, author collaborations, institutional collaborative relationships, and a heatmap of journals, and the software VOSviewer 1.6.18 was used to create a heatmap of keywords, and maps of keyword co-occurrence clustering and keyword clustering timelines. In addition, the keyword burst map was created using the software CiteSpace 6.3.R3.

RESULTS: A total of 1 707 publications were included in the final analysis, and the number of publications appeared an overall tendency towards a rise from 2015 to 2024, with the largest number of publications seen in 2024 (545 publications). The largest number of publications was recorded in China (1 390 publications), followed by in USA (190 publications) and United Kingdom (31 publications), and China led the global research in this field, with 81% of global related researches linked with China. Frontiers in Cellular and Infection and Microbiology published the largest number of articles (212 publications, 12.42%), and Joseph Derisi was the most productive author (33 publications). Author collaborations occurred within groups; however, there was a lack of close inter-group collaborations, with University of California, San Francisco and Chan Zuckerberg Biohub-based group seen as the largest collaborative group. High-frequency co-occurrence keywords included mNGS, infection, diagnosis, case report, community-acquired pneumonia and bronchoalveolar lavage fluid, and the 100 most common high-frequency co-occurrence keywords were assigned into four clusters. Keyword clustering timeline analysis revealed that the research hotspots in this field shifted from virus sequencing and sequence alignment to severe pulmonary infections, and keyword burst analysis showed identification, mNGS and virus as top three keywords with the highest burst intensity.

CONCLUSIONS: mNGS was mainly used for identification of viruses among patients with infections of unknown origins in ICUs from 2015 to 2024, and future research priority shifted to pathogen detection for severe pulmonary infections.}, } @article {pmid42046871, year = {2026}, author = {Yang, Y and Tan, X and Zhang, Z and Liang, L and Wu, Z and He, J and Wang, Y and Dong, M and Zheng, J and Zhang, H and Feng, S and Cheng, W and Cui, B and Wei, H and Li, Q}, title = {Metagenomic sequencing reveals high reproducibility of human donor microbiota transplanted into germ-free mice via lower gut route.}, journal = {Journal of Zhejiang University. Science. B}, volume = {27}, number = {4}, pages = {375-389}, pmid = {42046871}, issn = {1862-1783}, support = {2021YFA0805904//the National Key Research and Development Program of China/ ; }, mesh = {Animals ; Humans ; Mice ; Germ-Free Life ; *Gastrointestinal Microbiome/genetics ; *Fecal Microbiota Transplantation/methods ; *Metagenomics ; *Metagenome ; Reproducibility of Results ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Male ; Mice, Inbred C57BL ; }, abstract = {Human flora-associated (HFA) mice are often used to simulate the structure of human intestinal microbiota and to study the causal relationships between diseases and gut microbiota. However, several factors affect the colonization efficiency of human microbiota in germ-free (GF) mice, and the differential effects of gavage and lower gut transplantation on colonization are still unclear. In this study, we explored the reproducibility of the recipient-to-donor gut microbiota community structure and function under different transplantation routes and the differences in microbial colonization between recipients via gavage transplantation (GT_mice group) and lower gut transplantation (LGT_mice group). High-throughput sequencing of the metagenome was performed on the feces of each subject, and the composition of microbiome of each group was analyzed. As expected, the introduction of human fecal microbiota into GF mice via lower gut transplantation had a high transfer efficiency, which was evident from the similar species community structure to that of the donor (Adonis R[2]=0.713 960 for LGT_mice group‒donor group; Adonis R[2]=0.774 095 for GT_mice group‒donor group) and a higher bacterial colonization rate. The findings provide unique insights into improving the accuracy of constructing humanized microbiota transplantation models, aiding our understanding of the relationships between the human gut microbiota and disease.}, } @article {pmid42047611, year = {2026}, author = {Capone, K and Kuller, J and Durand, DJ and Tierney, NK and Lund, C}, title = {Exploration of Changes in the Human Skin Microbiome by Mode of Birth and Following First Bath.}, journal = {Pediatric dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/pde.70219}, pmid = {42047611}, issn = {1525-1470}, support = {UL1 TR000004/TR/NCATS NIH HHS/United States ; //Johnson & Johnson Consumer Inc./ ; }, abstract = {BACKGROUND/OBJECTIVES: Microbes colonize the skin soon after birth, and the skin microbiome changes over time. However, the effects of bathing and hygiene products on the infant skin microbiome are not well studied. This randomized, single-center trial analyzed the skin microbiome in neonates born vaginally or via cesarean section (c-section), before and after their first bath with or without a mild baby cleanser.

METHODS: One hundred healthy full-term neonates were randomized to baths with water alone or with mild baby cleanser, stratified by delivery mode. Volar forearm swabs of neonates (before and after first bath) and their mothers were analyzed by 16S rRNA metagenomic sequencing.

RESULTS: At birth, neonates born vaginally had greater overall richness of the skin microbiome versus those born via c-section. Vaginally delivered neonates had similar species richness as their mothers, while neonates delivered via c-section had much lower species richness. Shannon diversity was similar regardless of birth mode, but community structure varied. Species richness was similar before and after bath in vaginally delivered neonates, but those born via c-section had higher species richness after their first bath and showed larger changes in community structures, compared with the vaginal group. Whether water alone or baby cleanser was used for the first bath did not greatly affect skin microbiome composition.

CONCLUSIONS: The mode of birth had the largest effect on the skin microbiome composition, richness, and structure. Neonates born via c-section showed the largest post-bath changes in the skin microbiome, while the use of water or baby cleanser had little effect.}, } @article {pmid42047812, year = {2026}, author = {Zhu, R and Zhang, J and Shen, HL}, title = {Hip joint infection by Prevotella denticola in rheumatoid arthritis : A case diagnosed with metagenomic sequencing.}, journal = {Wiener klinische Wochenschrift}, volume = {}, number = {}, pages = {}, pmid = {42047812}, issn = {1613-7671}, abstract = {BACKGROUND: Infection, as a complication of rheumatoid arthritis (RA), has attracted increasing attention from rheumatologists. Here, we present the first case of RA with hip joint infection, which was driven by infection with Prevotella denticola. Anaerobic bacterial infection was identified by metagenomic next-generation sequencing (mNGS).

METHODS: We describe the case of a 56-year-old woman with a history of RA who was admitted for intense hip joint pain and intermittent fever following long-term oral glucocorticoid (GC) treatment.

RESULTS: Although blood and hip joint effusion cultures for aerobic and anaerobic organisms were negative, we considered the possibility of a clinical diagnosis of hip joint infection; therefore, empirical antibiotic treatment was initiated but it was ineffective in this case. Prevotella denticola was identified by mNGS from the hip joint effusion obtained via ultrasound-guided puncture and the organism was resistant to the initial antimicrobial treatment. Finally, the adjustment of antimicrobial treatment led to successful treatment.

CONCLUSION: Patients with RA have a significantly greater risk of infections than the general population; however, Prevotella denticola infection of the hip joint has not been previously reported. The combination of ultrasound-guided puncture and mNGS to accurately recognize and treat joint infection in patients with RA in a timely manner is necessary to prevent the development of complications, a strategy worthy of further clinical application.}, } @article {pmid42048337, year = {2026}, author = {Bernal Hernández, N and Rodríguez Cabal, HA and Pino, NJ and Ramírez Restrepo, S and Múnera Porras, LM}, title = {Metagenomic and taxonomic profiling of phyllosphere bacteria from Mangifera indica in response to urban air pollutants in Medellín, Colombia.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0347959}, pmid = {42048337}, issn = {1932-6203}, mesh = {Colombia ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Metagenomics/methods ; *Mangifera/microbiology ; *Air Pollutants/metabolism ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Phylogeny ; }, abstract = {Urban trees and their phyllosphere-associated microbiota constitute a promising nature-based solution for mitigating urban air pollution. In this study, we characterized the taxonomic composition, diversity patterns, and functional potential of bacterial communities inhabiting the phyllosphere of Mangifera indica in two urban sites of Medellín, Colombia, with contrasting pollution levels and across two time points, analyzing a total of 12 samples. We integrated 16S rRNA gene amplicon sequencing, performed on the Illumina MiSeq platform, with shotgun metagenomic sequencing generated on the Illumina NovaSeq 6000 platform to assess community structure and the presence of genes involved in the degradation of airborne organic pollutants. Bacterial assemblages were dominated by Pseudomonadota (Proteobacteria), Actinomycetota, and Bacteroidota, with genera such as Methylobacterium, Pseudomonas, and Serratia consistently prevalent. Alpha diversity was higher in the highly polluted downtown, while beta diversity was shaped primarily by temporal variation. Functional annotation of metagenome-assembled genomes (MAGs) uncovered genes encoding complete aromatic hydrocarbon degradation pathways, including naphthalene, toluene, xylenes, and benzoate. Both ortho- and meta-cleavage routes for catechol degradation were detected, with temporal shifts in pathway dominance linked to changes in the abundance of key degraders taxa. These results reflect genetic potential for xenobiotic degradation within the M. indica phyllosphere microbiota, modulated by environmental conditions. Our findings highlight the ecological role of phyllosphere bacteria as contributors of inferred functional capacity relevant to atmospheric bioremediation and supports their integration into microbiome-informed green infrastructure strategies.}, } @article {pmid42048878, year = {2026}, author = {Shi, W and Qin, Y and Li, W and Xu, J and Xu, H and Liu, Y}, title = {The dual role of phosphorus regeneration in controlling arsenic speciation: Iron-reducing bacteria in a seasonally ice-covered lake.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142206}, doi = {10.1016/j.jhazmat.2026.142206}, pmid = {42048878}, issn = {1873-3336}, mesh = {*Phosphorus/metabolism/chemistry ; *Lakes/microbiology/chemistry ; *Arsenic/chemistry/metabolism ; *Iron/metabolism ; Seasons ; *Bacteria/metabolism/genetics ; *Water Pollutants, Chemical/metabolism/chemistry ; Oxidation-Reduction ; Ice Cover ; Geologic Sediments/microbiology/chemistry ; }, abstract = {While the reductive dissolution of iron (hydro)oxides by dissimilatory iron‑reducing bacteria (DFeRB) can mobilize sediment bound arsenic (As), the role of concomitant phosphorus (P) regeneration in actively governing As speciation transformation, rather than mere release, remains mechanistically unclear, especially under seasonally contrasting redox regimes of ice-covered lakes. This study demonstrated that DFeRB mediated P regeneration exerts a dual, season‑dependent control over As speciation in lacustrine sediments. Through microcosm experiments simulating ice‑bound and summer periods, combined with sequential extraction, X‑ray diffraction, metagenomics, and structural equation modeling (SEM), and partial least-squares path modeling (PLS-PM), resolved that regenerated P not only promote As desorption via competitive adsorption but also redirect a substantial speciation of released As into a stable, pyrite‑coprecipitated pool (As‑S7). This sequestration pathway was particularly pronounced under ice‑bound anoxia, where DFeRB sustained a low‑rate, long‑duration reduction mode, as evidenced by persistent iron‑reduction gene (K02650, K17230) abundance and delayed As(III) peak release. SEM/PLS-PM quantified the seasonal shift in dominant mechanisms: summer release was driven by intensive P competition (including organic phosphorus), whereas ice‑bound conditions favored Fe‑S‑As co‑precipitation, effectively coupling prolonged microbial iron reduction to long‑term As immobilization. These findings establish P regeneration as a decisive switch between As mobility and stability in anaerobic sediments and define the seasonal microbial‑mineral feedbacks that modulate this switch. This work provides a predictive basis for assessing As fate in seasonally stratified water bodies under changing climatic conditions and a process-based basis for risk assessment and eutrophication management.}, } @article {pmid42049031, year = {2026}, author = {Wong, O and Zheng, Z and Wang, M and Cao, A and Chan, FKL and Ng, SC and Su, Q}, title = {Microbiome biomarkers in autism spectrum disorder: Toward prediction, diagnosis, and prognosis.}, journal = {Cell reports. Medicine}, volume = {7}, number = {5}, pages = {102780}, pmid = {42049031}, issn = {2666-3791}, mesh = {Humans ; *Autism Spectrum Disorder/diagnosis/microbiology ; *Biomarkers/metabolism ; Prognosis ; *Gastrointestinal Microbiome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Autism spectrum disorder (ASD) is a heterogeneous condition that lacks objective diagnostic biomarkers, often resulting in delayed intervention. Evidence increasingly links gut microbiota dysregulation to ASD pathophysiology via the microbiota-gut-brain axis, suggesting plausible translational applications. This review outlines mechanistic insights from preclinical and clinical studies to illustrate how microbial disturbances affect neurodevelopment. It examines the evolution of biomarker research from early 16S rRNA sequencing to advanced shotgun metagenomics incorporating functional integration, multi-omics, and genomic variants. Such advancements enhance diagnostic accuracy and generalizability. Although clinical causal evidence remains indirect, these microbial signatures show potential for early diagnosis, presymptomatic risk prediction, and tailored therapies. Key challenges include prospective validation in diverse cohorts, specificity testing against comorbidities, and addressing clinical heterogeneity. By summarizing methodological gaps and providing future guidance, this review aims to bridge mechanistic research and clinical practice to improve outcomes across the spectrum.}, } @article {pmid42049067, year = {2026}, author = {Khandelwal, S and Mishra, A and Pandey, SK}, title = {Integrating microbial bioremediation, multi-omics, and emerging technologies for polycyclic aromatic hydrocarbon (PAHs) detoxification.}, journal = {Journal of microbiological methods}, volume = {245}, number = {}, pages = {107519}, doi = {10.1016/j.mimet.2026.107519}, pmid = {42049067}, issn = {1872-8359}, mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism/toxicity ; *Biodegradation, Environmental ; Bacteria/metabolism/genetics ; Multiomics ; *Environmental Pollutants/metabolism ; Fungi/metabolism/genetics ; Genomics/methods ; Archaea/metabolism/genetics ; Metagenomics/methods ; }, abstract = {Environmental organic pollutants, identified as Polycyclic Aromatic Hydrocarbons (PAHs), are widespread and toxic. These hydrocarbons are commonly produced by industrial activities, burning fossil fuels, and crude oil discharges. Their high hydrophobicity, tendency to bioaccumulate, and mutagenic, carcinogenic, teratogenic, and genotoxic properties lead to significant environmental and human health risks. Additionally, their low bioavailability and chemical stability complicate PAHs remediation. In recent years, various methods have been explored to reduce their impact, including conventional physical and chemical treatments; however, these often face issues such as inadequate removal, high costs, lengthy processes, and environmental concerns. Bioremediation has emerged as a promising, environmentally friendly solution. This approach involves microorganisms such as bacteria, fungi, algae, and archaea utilizing specific enzymatic pathways-like dioxygenases, monooxygenases, peroxidases, and laccases-to transform PAHs into less toxic substances. Advances in genomics and metagenomics have identified key catabolic genes (e.g., nah, Phn, nid, pah) and regulatory mechanisms that enhance microbial resistance in PAH-contaminated environments. Since PAHs' low bioavailability and solubility often limit bioremediation alone, integrated strategies are gaining prominence. In-situ and ex-situ methods-including bioaugmentation, bio-stimulation, composting, and phytoremediation-boost microbial degradation of PAHs. Furthermore, advanced technologies such as multi-omics platforms, CRISPR-based genetic engineering, and artificial intelligence (AI) are transforming the field by enabling the development of targeted microbial strains, improving bioremediation efficiency, and creating predictive models. This review offers a recent, comprehensive outline by unifying PAHs toxicity, microbial degradation, traditional remediation, and advanced biotechnological tools into a single framework. A comprehensive and recent update of microbial and biotechnological approaches for sustainable PAHs bioremediation is offered by this review.}, } @article {pmid42049248, year = {2026}, author = {Jose, A and Apewokin, S and Ollberding, NJ and Duan, Q and Trannguyen, J and Prisco, SZ and Thenappan, T and Hemnes, AR and Elwing, JM}, title = {Lactobacillus Is Associated With Disease in Pulmonary Arterial Hypertension: A Prospective Cohort Study.}, journal = {Comprehensive Physiology}, volume = {16}, number = {3}, pages = {e70161}, pmid = {42049248}, issn = {2040-4603}, support = {K23HL16497/HL/NHLBI NIH HHS/United States ; HL168166/HL/NHLBI NIH HHS/United States ; 23CDA1049093//American Heart Association/ ; 2022 Research Award//Team Phenomenal Hope/ ; }, mesh = {Humans ; Prospective Studies ; Male ; *Lactobacillus/physiology ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; *Hypertension, Pulmonary/microbiology ; Adult ; *Pulmonary Arterial Hypertension/microbiology/physiopathology ; Hemodynamics ; }, abstract = {BACKGROUND: Gut dysbiosis and gut-derived metabolites have been linked to pulmonary arterial hypertension. However, associations between specific microbes, and corresponding metabolites, with pulmonary arterial hypertension disease severity is limited.

METHODS: This was a prospective cohort study of patients with pulmonary arterial hypertension undergoing right heart catheterization, with pulmonary artery blood subject to nuclear magnetic resonance metabolomics, and simultaneous stool sample shotgun metagenomics. Validation of metabolite levels with disease severity was done in an independent cohort of pulmonary arterial hypertension patients with blood samples from right heart catheterization testing.

RESULTS: The presence of Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients was associated with less severe pulmonary hemodynamics and echocardiographic right ventricular dysfunction. Higher threonine levels were associated with more favorable pulmonary hemodynamic characteristics in both prospective and independent validation cohorts of pulmonary arterial hypertension patients.

CONCLUSIONS: Detectable Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients are associated with more favorable pulmonary hemodynamic and right ventricular characteristics. Circulating gut-derived metabolites may also be involved. Further investigation into the relationship between gut microbial Lactobacillus, circulating metabolites, disease severity, and clinical outcomes in pulmonary arterial hypertension may be warranted.}, } @article {pmid42049488, year = {2026}, author = {Lan, K and Bai, D and Yuan, L and Luo, H and Jin, J and Li, SC and Wu, LF and Sun, XS and Liu, SL and Chen, QY and Mai, HQ and Liu, YX and Tang, LQ}, title = {Metagenomic identification of gut microbiome signatures for accurate diagnosis and prognostic prediction of Epstein-Barr virus-associated nasopharyngeal carcinoma.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2026-338223}, pmid = {42049488}, issn = {1468-3288}, abstract = {BACKGROUND: Nasopharyngeal carcinoma (NPC) is strongly associated with Epstein-Barr virus (EBV) infection. The gut microbiome can influence outcomes of viral infections but the potential links among the gut microbiome, EBV infection and NPC remain unclear.

OBJECTIVE: To characterise gut microbiome alterations in EBV-associated NPC, evaluate microbiome-based diagnostic performance (alone and in combination with EBV markers), and explore associations between microbial features, EBV DNA burden, prognosis and the tumour microenvironment.

DESIGN: We conducted a large-scale shotgun metagenomic study including 516 patients with EBV-associated NPC and 263 healthy controls. Microbiome dysbiosis, functional pathways and associations with plasma EBV DNA were assessed. Species-level markers were used to build a random forest classifier for NPC diagnosis, and performance was evaluated alone and in combination with EBV-specific markers. Survival analyses were performed to identify microbial features associated with NPC-related mortality and relationships with an immune-suppressive tumour microenvironment were explored.

RESULTS: NPC was characterised by gut microbiome dysbiosis, including depletion of short-chain fatty acid-producing species and reduced butanoate metabolism, which were significantly associated with plasma EBV DNA. A random forest classifier based on species-level markers distinguished NPC from controls with an area under the curve (AUC) of 0.917; performance improved to an AUC of 0.984 when combined with EBV-specific markers. Specific microbial species were associated with NPC-related mortality and prognostic microbial features were linked to an immune-suppressive tumour microenvironment.

CONCLUSION: EBV-associated NPC is associated with distinct gut microbiome and functional alterations that correlate with plasma EBV DNA. Microbial markers show strong diagnostic potential, particularly when integrated with EBV-specific markers, and prognostic microbial features may be linked to an immune-suppressive tumour microenvironment, supporting a potential role of the gut microbiome in NPC tumourigenesis.}, } @article {pmid42049592, year = {2026}, author = {Pailhoriès, H and Velo-Suarez, L and Moalic, Y and Alcoforado-Diniz, J and Gouriou, S and Bessou, A and Cambau, E and Burgel, PR and Herrmann, JL and Héry-Arnaud, G and , }, title = {A disrupted microbial network and an ecological shift towards anaerobes in NTM-infected cystic fibrosis patients.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2026.04.005}, pmid = {42049592}, issn = {1873-5010}, abstract = {Nontuberculous mycobacteria (NTM) are increasingly recognized as opportunistic pathogens in people with cystic fibrosis (pwCF), but the ecological factors shaping their presence remain poorly understood. This study characterized the airway microbiota associated with NTM-positive culture using 16S rRNA gene sequencing of sputum from 108 pwCF (36 NTM-positive and 72 NTM-negative), matched by age, sex at birth, and CFTR genotype. Analyses integrated diversity metrics, differential-abundance modeling, multivariate regression, and microbial network inference, while accounting for Pseudomonas aeruginosa colonization. NTM-positive individuals exhibited slightly higher α-diversity and enrichment in strictly anaerobic taxa such as Alloprevotella tannerae, Stomatobaculum spp., and Prevotella nanceiensis, alongside reduced network connectivity. P. aeruginosa remained the dominant ecological driver, strongly reducing community diversity and structure. Partial Least Squares regression revealed that CFTR modulators (lumacaftor/ivacaftor) use and lung function (FEV1%) were associated with distinct, commensal-enriched communities. In contrast, NTM status was associated with a distinct axis, indicating an independent ecological niche. Overall, NTM-positive cultures were associated with an anaerobe-enriched but less structured microbiota, likely reflecting localized hypoxia and biofilm-associated microenvironments rather than a direct effect of disease severity or modulator therapy. These findings highlight the role of airway microecology in NTM presence and provide a framework for understanding host-microbe interactions in chronic CF airway infections.}, } @article {pmid42049781, year = {2026}, author = {Manohar, CS and Ghose, M and Parab, AS}, title = {Integrated metagenomic analysis of bacteriomes associated with beach-cast seaweeds reveals metabolic potential for biotechnological and environmental applications.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46393-1}, pmid = {42049781}, issn = {2045-2322}, support = {MLP2019//Council of Scientific and Industrial Research, India/ ; }, } @article {pmid42050358, year = {2026}, author = {Zhu, F and Wang, T and Wang, Z and Shan, Y and Ren, P and Bie, X and Wang, D and Gao, Z and Guan, Q and Ge, L and Chen, Y}, title = {Bacillus cereus T146 Enhances Wheat Salt Tolerance by Restructuring the Rhizosphere Microbiome and Activating TaPIN1-Dependent Auxin Transport.}, journal = {Plant, cell & environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70567}, pmid = {42050358}, issn = {1365-3040}, support = {2024CXPT072//Key R&D Program of Shandong Province/ ; ZR2025QC186//Shandong Provincial Natural Science Foundation/ ; ZR2023QC067//Shandong Provincial Natural Science Foundation/ ; }, abstract = {Salinity stress disrupts rhizosphere homoeostasis and inhibits root development. Although PGPR are known to alleviate such stress, critical knowledge gaps remain regarding the specific mechanisms by which they enhance tolerance under moderate to high salinity, particularly within the wheat rhizosphere -root interface. Here, we show that Bacillus cereus T146, isolated from saline-alkali soil, enhances wheat salt tolerance through two integrated mechanisms. Metagenomic and culturomic analyses further revealed that T146 enriches IAA-producing Pseudomonas in the rhizosphere, and co-inoculation experiments demonstrated that these recruited bacteria contribute synergistically to salt tolerance. On the host side, transcriptomic and cell biological analyses demonstrated that T146 reactivates salt-suppressed auxin pathways. Specifically, inoculation upregulates key regulators of lateral root development (PLT3, PLT7, GLV6) and increases PIN1, PIN2, and PIN3 abundance, leading to elevated auxin accumulation as indicated by DR5::GFP signals. Importantly, silencing TaPIN1 largely compromised T146-induced tolerance and transcriptional reprogramming, demonstrating a functional interplay between microbiome modulation and host hormonal regulation. These results reveal that T146 synergistically promotes salinity resilience by coordinating rhizosphere microbiome remodelling with auxin-mediated root development, offering a mechanistic framework for microbiome-based strategies to improve crop stress tolerance.}, } @article {pmid42050656, year = {2026}, author = {Zakharevich, N and Strokach, A and Shitikov, E and Klimina, K}, title = {Correction: Bacteriophages in gut metagenomes: from analysis to application.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {42050656}, issn = {1743-422X}, } @article {pmid42050727, year = {2026}, author = {Ivanova, M and Svensmark, B and Bruun Jensen, EE and Aarestrup, FM and Vigre, H and Otani, S}, title = {Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42050727}, issn = {2524-4671}, abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) remains a major cause of morbidity in pig production and is commonly associated with enterotoxigenic Escherichia coli (ETEC). Conventional diagnostics rely on culturing and targeted qPCR, which provide limited resolution of pathogen diversity, virulence and antimicrobial resistance. Here, we evaluated Oxford Nanopore Technologies (ONT) metagenomic sequencing as a diagnostic tool for direct detection of pathogens, virulence factors and antimicrobial resistance genes (ARGs) from diarrhoeal pig faeces.

RESULTS: Twenty-six diarrhoeal and six healthy pig faecal samples were analysed using culture, qPCR and ONT metagenomics with both high-output and rapid workflows. Culturing recovered 26 haemolytic E. coli and nine Clostridium perfringens isolates. PromethION metagenomics detected a significantly higher diversity of bacterial species, virulence factors and ARGs compared with GridION. Direct read mapping achieved 71–96% genome coverage for six E. coli isolates. Fourteen high- and medium-quality E. coli metagenome-assembled genomes (MAGs) were reconstructed, of which seven clustered closely with corresponding cultured isolates. All virulence factors detected in isolates were captured by metagenomics, while metagenomics identified additional fimbrial and enterotoxin genes not recovered by culture. Metagenomic ARG profiling identified resistance to 16 antibiotic classes, compared to eight classes in cultured isolates. No ESBL, carbapenemase or mcr genes were detected.

CONCLUSIONS: Long-read ONT metagenomics enables culture-independent, strain-resolved characterisation of the pig gut microbiome during PWD, capturing pathogen diversity together with virulence and antimicrobial resistance profiles. This approach reveals within-sample strain heterogeneity and functional potential that are not resolved by conventional culturing, supporting its value for studying microbial ecology and dysbiosis in diseased animal microbiomes.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00577-2.}, } @article {pmid42050730, year = {2026}, author = {Seppey, M and Benavides, A and Berkeley, MR and Manni, M and Zdobnov, EM}, title = {LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools.}, journal = {Genome biology}, volume = {27}, number = {1}, pages = {}, pmid = {42050730}, issn = {1474-760X}, support = {ESKAS No. 2022.0531//Federal Commission for Scholarships for Foreign Students for the Swiss Government Excellence Scholarship/ ; 310030_189062//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Metagenomics/methods ; Benchmarking ; *RNA, Ribosomal, 16S/genetics ; *Software ; }, abstract = {Metagenomics enables culture-independent investigation of microbial communities without prior knowledge of sample composition. However, sequence analysis is complex, and many computational strategies exist. Selecting among them is challenging, and novel tools face visibility issues. Here, we present LEMMIv2, an updated platform for continuous benchmarking of metagenomic profilers, providing developers with impartial benchmarks and offering users a catalogue of evaluated tools. New features include support for alternative taxonomies and long-read applications, and a standalone pipeline for local benchmarking. We also extend the approach to 16S amplicon profiling with LEMMI16S, which evaluates methods across several reference databases.}, } @article {pmid42051014, year = {2026}, author = {Memon, FU and Ahmad, S and Mo, Q and Liu, S and Xie, X and Nabi, F and Huang, Z and Tettamanti, G and Tian, L}, title = {Probiotic-based fermentation of watermelon waste: Effects on bioconversion efficiency, microbial shifts, and expression profiles of black soldier fly larvae.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70280}, pmid = {42051014}, issn = {1744-7917}, support = {//Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology/ ; //Special Project of Guangxi Collaborative Innovation Center of Modern Sericulture and Silk/ ; //Natural Science Foundation of Guangdong Province/ ; }, abstract = {Insects such as black soldier fly larvae (Hermetia illucens, BSFL) are efficient bioconverters whose growth and physiological performance are strongly influenced by diet composition, gut microbiota, and the molecular regulation. This study investigated how a probiotic-based fermentation strategy modulates larval physiology, microbiome dynamics, and gene expression when BSFL are reared on fermented watermelon waste. Watermelon waste was fermented for 14 d using a consortium of Bacillus subtilis, Enterococcus faecalis, and Aspergillus oryzae, resulting in a nutritionally enhanced substrate. BSFL fed on fermented diet exhibited significantly increased growth performance, biomass yield, and nutritional content of the insect biomass. Metagenomic analysis revealed marked enrichment of gut microbes belonging to genera known to include beneficial and commensal species (Enterococcus, Vagococcus, Carnobacterium, Tetragenococcus, and Blautia) along with a reduction in genera containing species previously associated with opportunistic or pathogenic traits (Mycobacterium, Pseudomonas, Morganella, Pedobacter, and Serpula), indicating diet-induced modulation of host-microbe interactions. Transcriptomic profiling highlighted an upregulation of key genes involved in growth and development (CK1, HIB, and PDK1), protein and fat biosynthesis (DVL, GSK3, and Lpin), and immune defense (PGRP-SA, Spz, Toll, and Cactus). Functional enrichment analysis further confirmed their participation in critical signaling pathways, including Hedgehog, Wnt, mTOR, Toll and Imd, and MAPK. Overall, this study demonstrates that probiotic fermentation improves nutrient utilization, regulates host-microbe interactions, and activates molecular pathways associated with growth and immune resilience in BSFL, providing new insights into the physiological and molecular basis of dietary adaptation in insects.}, } @article {pmid42051699, year = {2026}, author = {Du, Y and Guo, Z and Yao, D and Wang, Y}, title = {Hemophagocytic lymphohistiocytosis secondary to Pneumocystis jirovecii pneumonia: a rare case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1795567}, pmid = {42051699}, issn = {2296-858X}, abstract = {Hemophagocytic lymphohistiocytosis (HLH) secondary to Pneumocystis jirovecii pneumonia (PJP) is extremely rare in children. We present the case of a 10-year-old girl with a history of idiopathic thrombocytopenic purpura (ITP) on long-term oral prednisone, who was admitted for progressive fever, cough, and dyspnea. Metagenomic next-generation sequencing of blood and bronchoalveolar lavage fluid confirmed PJP. Despite targeted antifungal therapy and respiratory support, she developed persistent high-grade fever, pancytopenia, hyperferritinemia, hypofibrinogenemia, and hemophagocytosis on bone marrow aspirate by day 10, meeting diagnostic criteria for HLH. Genetic testing was declined by the parents. Management included dexamethasone, continuous renal replacement therapy, and plasmapheresis. Unfortunately, her condition deteriorated, and she was discharged upon parental request on day 22, succumbing on the same day. To our knowledge, this is the first reported pediatric case of HLH secondary to PJP in China. This case highlights that in children with PJP-especially those on immunosuppressive therapy-the development of persistent fever and cytopenia should prompt immediate evaluation for secondary HLH to enable timely intervention.}, } @article {pmid42052210, year = {2026}, author = {Qu, HL and Li, JN and Gao, Y and Xu, XM and Zhang, XB and Yang, SD}, title = {From microscopy to antimicrobial decisions: a clinically grounded roadmap for critical care infectious diseases.}, journal = {Frontiers in artificial intelligence}, volume = {9}, number = {}, pages = {1807400}, pmid = {42052210}, issn = {2624-8212}, abstract = {In the intensive care unit (ICU), antibiotics often begin under extreme uncertainty. Fever, leukocytosis, hypotension, and organ dysfunction may signal bacterial infection, but the same findings are common with aspiration, post-operative inflammation, drug reactions, or sterile systemic inflammation. Cultures take time and their yield falls after antibiotics. Rapid molecular tests and metagenomics can add actionable information, but they also raise the burden of interpreting complex results. Microscopy is one of the few inputs that can shift management within minutes to hours: Gram-stain patterns from positive blood-culture bottles, respiratory specimens, cerebrospinal fluid, and wound material can reshape initial coverage and support early de-escalation when negative. Tissue and cytology help distinguish invasion from key mimics. The gap is consistency-reads vary across observers, workflows differ, and results do not always translate into reliable bedside actions. This review focuses on infectious-disease artificial intelligence (AI) as ICU bedside decision support, rather than as a survey of models. Using ICU sepsis as the primary use case-and neurocritical care as a challenging setting where sedation, brain injury, and noninfectious inflammation often mimic infection-we separate evidence into pathogen signals and host-response signals. We then map both streams to six decisions over the first 72 hours: start now versus pause, choose initial spectrum, reassess and narrow, escalate diagnostics and source control, act on high-risk resistance or invasive pathogens, and stop safely. We summarize where AI is most credible today (Gram-stain assistance, culture-plate triage, urine-culture screening, infection-focused digital pathology, host-response classifiers, and selected metagenomics) and what makes outputs actionable: calibrated probabilities, explicit confidence with safe deferral when uncertain, validation across hospitals and instruments, and endpoints tied to stewardship and safety (time to appropriate therapy, antibiotic days, de-escalation within 72 hours, missed bacteremia). Evidence was updated through February 28, 2026.}, } @article {pmid42052392, year = {2026}, author = {Suenaga, H and Fujihara, H}, title = {Molecular basis for adaptive evolution of aromatic degradation enzymes in bacteria revealed by metagenomics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1795400}, pmid = {42052392}, issn = {1664-302X}, abstract = {Aromatic hydrocarbons, including persistent polycyclic aromatic hydrocarbons (PAHs), impose strong selective pressures that drive the adaptive evolution of bacterial degradation systems. Metagenomic studies have revealed extensive diversification of key catabolic enzymes, such as ring-hydroxylating and ring-cleavage dioxygenases, through the accumulation of single-nucleotide polymorphisms (SNPs) and structural modifications that increase substrate range and enhance catalytic efficiency in polluted environments. These findings demonstrate that gene mutations that change enzyme properties collectively shape the evolution of aromatic-degrading bacteria. Metagenomics is powerful tools for elucidating these evolutionary processes and advancing applications in bioremediation and industrial biocatalysis.}, } @article {pmid42052398, year = {2026}, author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC and Arsenault, RJ}, title = {Capturing the fungal diversity in manure, lagoons, troughs, and flies at a commercial dairy.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1794875}, pmid = {42052398}, issn = {1664-302X}, abstract = {The microbiomes within dairy facilities that could serve as reservoirs for beneficial and pathogenic fungi have not been extensively explored. Though fungi can cause food safety and animal health issues, they also represent species contributing to bovine digestion and environmental nutrient cycling. This study investigated whether fungal communities from specific elements at a working dairy differed between cross-vent or flow-through, free stall barn management systems and defined the possible pathogen locations. Shotgun metagenomics was carried out on manure, lagoons, troughs, and fly samples from the barns. The diversity of species was not significantly affected by management systems, except between lagoon communities. Flies carried the highest number of unique fungal species and the most abundant potential mammalian pathogens, but there was a lack of overlapping pathogen profiles between flies and the other dairy components. Thus, it remains unclear whether the species are being efficiently exchanged between these different components of the dairy environment, mechanically or biologically. Manure harbored the most opportunistic pathogenic species, lagoons harbored the most plant pathogens and beneficial species, and troughs had the most innocuous or understudied species. The results allow dairy managers to consider advantageous management systems and focus on fungal mitigation efforts at appropriate locations within the dairy.}, } @article {pmid42052556, year = {2026}, author = {Chu, T and Liu, J and Zhang, Y and Yang, K and Li, S and Yan, Q and Li, Y}, title = {Metagenome-based virome analysis identifies the oral viral signatures for periodontitis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2662091}, pmid = {42052556}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontitis (PD) is a chronic infectious disease driven by bacterial biofilms, yet the oral virome's role in pathogenesis remains poorly understood.

OBJECTIVE: This cross-cohort meta-analysis aims to define PD-associated viral signatures, characterize predicted virus-host interactions, and evaluate the diagnostic potential of viral biomarkers.

METHODS: We integrated 89 saliva (44 PD, 45 healthy) and 86 subgingival plaque (48 PD, 38 healthy) metagenomes from six public cohorts for a unified virome analysis.

RESULTS: We identified 156 viral operational taxonomic units (vOTUs) significantly associated with PD (105 in saliva, 66 in subgingival plaque and 15 shared). PD-enriched vOTUs were predicted to target periodontal pathogens including Porphyromonas gingivalis, whereas Streptococcus-targeting phages were decreased. PD-associated vOTUs harbored diverse bacterial defense and anti-defense systems, with those enriched in PD overrepresenting lysozyme and replication-associated genes. Diagnostic models based on key viral markers achieved robust performance, with AUCs of 0.95 (saliva) and 0.92 (subgingival plaque) for classifying PD.

CONCLUSION: This study delineates a distinct oral virome profile in PD, highlights predicted virus-host interactions, and underscores the potential of viral biomarkers for PD diagnosis,providing a basis for future investigations into viral ecology and phage-based interventions.}, } @article {pmid42052831, year = {2026}, author = {Li, Y and Gao, H and Liao, Z and Chen, Z and Song, Z and Xiong, W and Dai, Y and Li, W and Luan, S}, title = {Metagenomic Analysis Reveals Gut Microbiota Features in Membranous Nephropathy.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {31}, number = {4}, pages = {48982}, doi = {10.31083/FBL48982}, pmid = {42052831}, issn = {2768-6698}, support = {JCYJ20240813153002004//Shenzhen Foundation of Science and Technology/ ; JCYJ20250604191024032//Shenzhen Foundation of Science and Technology/ ; 2025A1515012512//Guangdong Basic and Applied Basic Research Foundation/ ; 2022041//Shenzhen Longhua District Healthcare Institutions Scientific Research Project/ ; //Key Medical Discipline Construction Fund of Shenzhen Longhua District/ ; JZ2025107//Guangdong Yiyang Healthcare Charity Foundation/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Glomerulonephritis, Membranous/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; *Bacteria/genetics/classification ; Case-Control Studies ; }, abstract = {BACKGROUND: Membranous nephropathy (MN) is one of the most common forms of primary glomerulonephritis worldwide and is closely associated with immune dysregulation. Increasing evidence suggests that the gut microbiota plays a critical role in regulating renal disease through the gut-renal axis. However, the use of metagenomic sequencing to analyze changes in the gut microbiota in patients with MN has not yet been reported.

METHODS: This study employed a metagenomic approach to comprehensively analyze the gut microbiota in patients with MN (n = 10) and normal controls (NCs; n = 10). Shotgun metagenomic sequencing was performed on fecal samples. Microbial diversity, taxonomic composition, and functional pathways were assessed, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. In addition, correlations between gut microbial characteristics and clinical indicators were also evaluated.

RESULTS: The gut microbial community in the MN group showed distinct differences from the control group, particularly with an increased abundance in phylum: Proteobacteria, Firmicutes_C, and Cyanobacteria; the genera Dialister, Selenomonadales, Clostridium, Bacillus, Megamonas, Romboutsia, and Inesitibacter; the species Bilophila_wadsworthia, Enterococcus_C, Megamonas funiformis, and Clostridium_perfringens. Furthermore, Bacillus_A showed a significant positive correlation with both serum creatinine and the protein-to-creatinine ratio. Conversely, higher levels of Victivallis were associated with lower blood urea nitrogen, while increased Fusicatenibacter was correlated with lower phospholipase A2 receptor levels. KEGG analysis indicated that the MN gut microbiota was enriched for pathways related to tryptophan metabolism, oxidative phosphorylation, and pathogenic Escherichia coli infection. Additionally, receiver operating characteristic analysis revealed that a four-genus model comprising enriched Dialister, Enterococcus_C, and Clostridium_P, and reduced Fusicatenibacter yielded an area under the curve of 0.90 ± 0.12, suggesting promising discriminatory potential that warrants further validation.

CONCLUSION: These findings demonstrate alterations in the composition and functional potential of the gut microbiota in patients with MN compared with the control group. Given the cross-sectional design of this study, these observations should be interpreted as associative, and further studies are required to validate these findings and explore any associated biological relevance.}, } @article {pmid42053312, year = {2026}, author = {Chung, B and Wang, S and Hao, Z and Allison, SD and Malik, AA}, title = {Plant litter chemistry and associated changes in microbial decomposition under drought.}, journal = {mBio}, volume = {17}, number = {6}, pages = {e0043826}, pmid = {42053312}, issn = {2150-7511}, support = {DE-SC0016410 and DE-SC0020382//US Department of Energy Genomic Science Program/ ; DE-AC02-05CH11231//US Department of Energy Genomic Science Program/ ; }, mesh = {*Droughts ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification ; Fungi/metabolism/genetics ; Ecosystem ; Metagenomics ; *Plants/chemistry ; Poaceae/chemistry ; *Soil/chemistry ; }, abstract = {UNLABELLED: Drought has consequences for microbial decomposition rates, including indirect effects through changes in plant litter chemistry. Here, we studied the impact of a decade-long drought on plant litter chemistry and microbial decomposition traits in a semi-arid ecosystem during an 18-month litter bag experiment. We investigated litter sourced from four conditions: grass and shrub vegetation under ambient and reduced precipitation. We hypothesized that litter chemistry drives microbial decomposition capabilities and enzyme activity due to vegetation differences and drought effects on litter chemistry. We found that carbohydrate-rich grass litter had a higher abundance of decomposition genes detected using metagenomics and enzyme activity than more recalcitrant shrub litter, which was richer in lignin and lipids; these patterns were related to substrate supply. Drought decreased some carbohydrate fractions in grass litter but did not change the lignin fraction in grass and shrub litter, suggesting that drought does not make litter more recalcitrant. Most decomposition genes and enzyme activities were not significantly affected by drought, thereby maintaining decomposition rates. Microbial community succession patterns-decreasing fungal abundance and increasing bacterial abundance with time-corresponded with decreasing chitin gene abundance and increasing peptidoglycan gene abundance over time, indicating microbial necromass recycling. We demonstrate minimal litter chemistry-mediated effects of drought but show significant changes in community composition and their decomposition capabilities over time, highlighting that complex microbial-chemical interactions under climate change can influence ecosystem-scale processes.

IMPORTANCE: Climate change is causing more severe and frequent droughts in semi-arid ecosystems, affecting soil microbes breaking down plant litter. Our research focuses on understanding the less studied pathway of drought impact on microbes via changes in plant litter chemistry. Drought can alter the plant litter chemistry by changing the composition and physiology of plants, which can alter microbial decomposition and ecosystem-level carbon cycling. We investigated litter decomposition traits of microbial communities in grass and shrub litter under long-term drought. There were significant changes in litter chemistry under drought but no increase in lignin fraction. Despite this, microbial communities maintained their decomposition capabilities under drought, highlighting the ability of microbes to adapt and continue functioning. We also demonstrate unique microbial community succession patterns and dead biomass recycling, which can have implications for carbon cycling rates in the ecosystem. This study sheds light on the complex microbial interactions that affect ecosystem functioning under climate change.}, } @article {pmid42053608, year = {2026}, author = {Çağatay, NS and Dageri, A and Saruhan, I and Tuncer, C and Guz, N}, title = {Diversity and Composition of the Microbiome Associated with Adult of the Green Shield Bug Palomena prasina (Hemiptera: Pentatomidae).}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {42053608}, issn = {1432-184X}, support = {Project number: 116O328//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; }, abstract = {UNLABELLED: Hazelnut is a major export commodity for Türkiye, the world’s leading producer, yet pest pressure in hazelnut orchards has caused substantial quantitative and qualitative yield losses in recent years. Among emerging pests, the green shield bug (GSB) Palomena prasina (Hemiptera: Pentatomidae) has become a key threat due to direct feeding on developing fruits. Despite its increasing economic relevance, the microbial community associated with P. prasina remains poorly characterized. Here, we present the first comprehensive analysis of the bacterial community associated with P. prasina using 16 S rRNA gene metabarcoding combined with prevalence screening and phylogenetic analyses. A total of 36 bacterial taxa were detected across sampled populations, with Pantoea and Sodalis identified as the dominant genera. Bacterial diversity did not differ significantly between sexes or among geographic locations, indicating a relatively stable microbial community. Prevalence analyses revealed that Pantoea spp. were present in all examined individuals, whereas Sodalis spp. showed variable infection frequencies among populations. Phylogenetic reconstruction indicated contrasting evolutionary patterns between these dominant taxa, with Pantoea lineages displaying a polyphyletic structure suggestive of repeated environmental acquisition, while Sodalis sequences formed a more cohesive, host-associated lineage consistent with a facultative symbiotic lifestyle. Overall, these findings improve our understanding of stink bug-microbe associations and provide an ecological framework for future studies exploring symbiont-based pest management strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02779-2.}, } @article {pmid42053852, year = {2026}, author = {Peng, Q and Lin, Y}, title = {A case report of infective endocarditis caused by Mycoplasma pneumoniae in a child.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42053852}, issn = {1435-4373}, abstract = {OBJECTIVE: This study aimed to investigate the clinical features and management strategies for infective endocarditis(IE) caused by Mycoplasma pneumoniae(M. pneumoniae) in children, in order to enhance understanding of this rare extrapulmonary complication of M. pneumoniae infection and provide clinical insights for its diagnosis and treatment.

METHODS: We retrospectively analyzed the clinical data and management process of a pediatric patient diagnosed with IE who was admitted to our hospital in September 2025.

RESULTS: A 9-year-old male patient was admitted with initial symptoms of fever and cough and was diagnosed with M. pneumoniae pneumonia. Subsequently, prompted by the detection of a faint blowing murmur on auscultation, transthoracic echocardiography was performed, which revealed a vegetation in the right ventricle. Empirical antibiotic treatment with doxycycline combined with vancomycin and ceftriaxone was initiated. M. pneumoniae was detected in two blood specimens using metagenomic next-generation sequencing (mNGS), while all three conventional blood cultures remained negative. Treatment was subsequently adjusted to doxycycline monotherapy. On hospital day 11, follow-up echocardiography examination showed resolution of the vegetative, with no evidence of thromboembolic events. After discharge, the patient continued oral doxycycline for a total treatment duration of 4 weeks. Follow-up revealed good recovery.

CONCLUSIONS: M. pneumoniae pneumonia in children may be complicated by IE. Antimicrobial agents should be guided by regional antimicrobial resistance patterns and resistance gene testing. The addition of anti-inflammatory and anticoagulant therapies should be considered when clinically indicated. mNGS is a valuable diagnostic tool for identifying pathogens in cases of blood culture-negative IE.}, } @article {pmid42054100, year = {2026}, author = {Mellor, SA and Bloomfield, SJ and Palau, R and Savva, GM and Wain, J and Mather, AE}, title = {Metagenomic analysis of UK retail foods finds limited evidence for associations between food production method and antimicrobial resistance gene burden.}, journal = {Microbial genomics}, volume = {12}, number = {4}, pages = {}, pmid = {42054100}, issn = {2057-5858}, mesh = {Animals ; *Metagenomics/methods ; *Food Microbiology ; Chickens/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Drug Resistance, Bacterial/genetics ; *Meat/microbiology ; Cattle ; Sheep ; Salmon/microbiology ; United Kingdom ; Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; Swine ; }, abstract = {Food is produced by a range of methods including extensive (organic and free range), intensive (conventional) and wild-caught production systems. Antimicrobial use varies between different food production systems, which may affect the microbial populations as well as the prevalence and diversity of antimicrobial resistance genes (ARGs) found on food at retail. In this study, shotgun metagenomics was used to investigate the microbial and ARG composition of 25 pork, 33 beef, 33 lamb, 60 chicken, 31 salmon and 41 leafy green samples collected in Norfolk, England, and labelled as extensive, wild caught or intensive. Food microbiomes consisted predominantly of spoilage-associated organisms including Pseudomonas, Lactococcus and Psychrobacter. Significant differences in bacterial diversity were found between intensive and extensive systems on chicken, and 22 differentially abundant genera were identified between production systems across beef, chicken and salmon. Genes conferring resistance to tetracyclines and beta-lactams comprised the majority of the food resistome across all commodities. Across most measures used to compare food resistomes between production methods, no significant differences were detected, except on chicken and salmon where differences in beta-diversity between production methods were detected, albeit with low effect sizes. Overall, these results suggest that differently produced foods, at least when tested at retail and in this region, may present a similar risk of antimicrobial resistance across the commodities investigated within this study. However, specific associations were identified with the microbial composition across chicken, beef and salmon, suggesting that production method may drive some variation in the microbial population structure on food products. Additional work at the farm or food processing levels is required to identify the drivers of these differences between production systems.}, } @article {pmid42054312, year = {2026}, author = {Revel, J and Leroy, J and Delbecq, S and Constant, O and Henry Marty, F and Naili, C and Barthès, A and Nagy, A and Schmidt-Chanasit, J and Cadar, D and Abd Rahaman, NY and Lajoix, AD and Desmetz, C and Simonin, Y}, title = {Differential properties of NS1 glycoproteins in West Nile and Usutu viruses.}, journal = {Emerging microbes & infections}, volume = {15}, number = {1}, pages = {2667565}, pmid = {42054312}, issn = {2222-1751}, mesh = {Animals ; *West Nile virus/genetics/metabolism/chemistry/pathogenicity ; *Viral Nonstructural Proteins/metabolism/genetics/chemistry/blood ; Humans ; *West Nile Fever/virology ; *Flavivirus/genetics/metabolism ; Mice ; Blood-Brain Barrier/virology ; *Flavivirus Infections/virology ; Endothelial Cells/virology ; Mosquito-Borne Diseases ; Female ; Brain/virology ; }, abstract = {West Nile virus (WNV) and Usutu virus (USUV) are neurotropic orthoflaviviruses of the Flaviviridae family, transmitted primarily by Culex mosquitoes and maintained in enzootic cycles involving birds. While WNV is a well-established human pathogen causing hundreds of neuroinvasive cases annually in Europe, USUV has emerged more recently, with fewer documented human infections but increasing evidence of neurovirulence. The viral nonstructural protein 1 (NS1) plays a central role in orthoflavivirus pathogenesis by modulating host immune responses, disrupting endothelial barrier integrity, and facilitating viral dissemination. However, the functional and biochemical properties of NS1 from WNV and USUV remain poorly characterized. We combined in vitro, in vivo, and clinical approaches to compare NS1 secretion, stability, and its impact on blood-brain barrier. Our results show that WNV NS1 is secreted at significantly higher levels, exhibits greater thermal stability, and disrupts brain endothelial barrier integrity in vitro. In contrast, USUV NS1 is secreted less efficiently, is slightly less stable, and does not compromise blood-brain barrier integrity, despite inducing distinct transcriptional responses in brain endothelial cells. In mice, WNV infection led to higher serum NS1 levels and stronger systemic inflammation than USUV. Clinically, WNV NS1 was detected mainly in patients with neurological symptoms, whereas USUV NS1 remained undetectable in all cases. Altogether, these findings reveal differential NS1 properties between these closely related viruses, with key implications for orthoflavivirus diagnosis and neurovirulence mechanisms.}, } @article {pmid42054365, year = {2026}, author = {Santos-Júnior, CD and Escobar, MC and Huber, P and Niño-Garcia, JP and Cardona, GI and Costa-Pereira, R and Sarmento, H}, title = {Resource availability structures microbial competition through genomic niche partitioning.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {18}, pages = {e2526391123}, pmid = {42054365}, issn = {1091-6490}, support = {862923//EC | Horizon 2020 Framework Programme (H2020)/ ; 304655/2025-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 22/15842-6//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 23/02850-3//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 20/11953-2//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2025hsqd014//Hubei Hongshan Laboratory/ ; }, mesh = {*Metagenome ; Humans ; Phylogeny ; Ecosystem ; *Microbiota/genetics ; Bacteria/genetics/classification ; Biodiversity ; Metagenomics ; Soil Microbiology ; Genomics ; }, abstract = {Microbial competition for scarce resources shapes biodiversity patterns and ecosystem function across global biomes, yet quantifying this process from genomic data has remained elusive. Here, we introduce CaCo, a scalable metric that transforms metagenomic carbohydrate-active enzyme profiles into precise measures of niche overlap and competition potential (Resource Partitioning Score, RPS). Analyzing 14,691 high-quality metagenome-assembled genomes spanning Ocean, freshwater, soil, and human gut microbiomes, we reveal a striking macroecological pattern: Niche overlap increases from partitioned specialists in oligotrophic oceans to overlapping generalists in carbon-rich environments, including the human gut. This gradient aligns with classic niche theory, as phylogenetic signals indicate that closely related taxa may compete most intensely. Multitiered validation, spanning BIOLOG phenotypes, synthetic cocultures, and interaction gradients, confirms CaCo's predictive power and captures competitive exclusion. CaCo bridges genomic potential and ecological reality, providing niche-breadth metrics and enabling testable predictions of how resource availability shapes microbial competition and community structure.}, } @article {pmid42054706, year = {2026}, author = {Vilaseca, A and Toledano, M and Flanagan, EP}, title = {Complexities in evaluation and management of infectious myelopathies.}, journal = {Current opinion in infectious diseases}, volume = {39}, number = {3}, pages = {227-239}, doi = {10.1097/QCO.0000000000001204}, pmid = {42054706}, issn = {1473-6527}, mesh = {Humans ; Myelitis/diagnosis/virology ; *COVID-19/complications/epidemiology ; *Spinal Cord Diseases/diagnosis/virology ; SARS-CoV-2 ; Magnetic Resonance Imaging ; Neuromuscular Diseases ; Central Nervous System Viral Diseases ; }, abstract = {PURPOSE OF REVIEW: To review recent advances in infectious myelopathies and integrate them into a practical, syndrome-based approach that supports early recognition, guides testing, and avoids pitfalls.

RECENT FINDINGS: Advances in MRI pattern recognition and pathogen-specific diagnostics have refined the evaluation of infectious myelopathies, with strategies tailored to geographic epidemiology, host susceptibility, and distinction from immune-mediated causes. During the COVID-19 pandemic, SARS-CoV-2-associated myelopathy emerged as a rare para- or postinfectious cause of myelitis. The pandemic coincided with a decline in enterovirus outbreaks and acute flaccid myelitis, which are now re-emerging, underscoring the importance of epidemiologic surveillance. Metagenomic next-generation sequencing is useful in suspected infectious myelopathy because it can identify unexpected pathogens from cerebrospinal fluid, but its imperfect sensitivity and contamination risk mean it should complement rather than replace conventional testing. Growing recognition of compartmentalized central nervous system inflammation and cerebrospinal fluid viral escape in HIV myelopathy has shifted management toward antiretroviral resistance patterns and treatment optimization. Therapeutic advances remain limited and largely pathogen-specific, although targeted approaches such as mogamulizumab for HTLV-1-associated myelopathy are promising.

SUMMARY: Recent progress in infectious myelopathies has been driven by improved pathogen detection and more tailored diagnostic strategies, although treatment advances are beginning to emerge.}, } @article {pmid42055201, year = {2026}, author = {Lu, L and Pan, C and Fu, L and Zhao, L and Wang, HY and Yao, W and Yang, M}, title = {Subchronic exposure to environmental levels of fluoxetine disturbs gut microbiota-mediated intestinal barrier homeostasis and triggers delayed feeding response in zebrafish (Danio rerio).}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {306}, number = {}, pages = {110551}, doi = {10.1016/j.cbpc.2026.110551}, pmid = {42055201}, issn = {1532-0456}, mesh = {Animals ; *Fluoxetine/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Zebrafish/physiology ; Female ; *Water Pollutants, Chemical/toxicity ; *Feeding Behavior/drug effects ; *Selective Serotonin Reuptake Inhibitors/toxicity ; Homeostasis/drug effects ; Intestinal Barrier Function/drug effects ; Intestines/drug effects ; Oxidative Stress/drug effects ; }, abstract = {Fluoxetine (FLX), a selective serotonin reuptake inhibitor, is frequently detected in aquatic environments because of its widespread use and inefficient removal by sewage treatment. Long-term FLX residues may induce chronic effects in non-target aquatic organisms. The intestine is a key metabolic and immune organ in fish, and may be affected by prolonged FLX exposure. However, studies on FLX-induced intestinal toxicity and its underlying molecular mechanisms are scarce. In the present study, adult female zebrafish were exposed to environmentally relevant FLX concentrations for 28 days, and subchronic toxic effects were assessed using an integrated approach combining physio-biochemical, behavioral, pathological, and multi-omics analyses. The results showed that the 28-day FLX exposure reduced the adult fish condition factor and altered feeding behavior. Notably, maternal FLX increased F1 offspring mortality and decreased the hatching rate, body length, and heart rate. In FLX-exposed adult intestines, goblet cell villus height was reduced and oxidative stress was induced, and transcriptome analysis revealed differentially expressed genes enriched in metabolism, neurodegenerative disease, and circadian rhythm pathways. Additionally, 16S rRNA and metagenomic sequencing showed FLX decreased gut microbiota α-diversity, altered community composition and assembly process, and enhanced antibiotic resistance genes. These findings highlight the dual threats of pharmaceutical pollution to ecological and public health, and provide support for the formulation of environmental and health protection measures.}, } @article {pmid42055262, year = {2026}, author = {Trinh, HP and Lee, SH and Park, HD}, title = {Mitigating nitrite stress and restoring functional redundancy in anammox reactor via acetate-driven DNRA-anammox coupling.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134732}, doi = {10.1016/j.biortech.2026.134732}, pmid = {42055262}, issn = {1873-2976}, mesh = {*Bioreactors/microbiology ; *Nitrites/metabolism ; *Acetates/metabolism ; *Ammonium Compounds/metabolism ; Oxidation-Reduction ; Bacteria/metabolism ; Nitrogen ; Nitrates/metabolism ; }, abstract = {Frequent fluctuations in nitrite concentrations and unstable control of partial nitritation often lead to excessive NO2[-] accumulation, resulting in performance deterioration in anammox-based systems. To address this challenge, an anammox reactor was operated for 180 days to investigate the inhibitory effects of elevated NO2[-]/NH4[+]ratios on anammox activity and to evaluate the effectiveness of external carbon supplementation in promoting dissimilatory nitrate reduction to ammonium (DNRA)-related pathways that contribute to NO2[-] reduction. Increasing NO2[-]/NH4[+]ratio from 1.3 to 3.0 decreased the nitrogen removal efficiency from 96.7% to 26.6%, reduced the relative abundance of anammox bacteria (Ca. Kuenenia and Ca. Jettenia) from 41.5% to 7.0% and promoted Nitrospira to 7.7%. In contrast, acetate supplementation at a C/N ratio of 0.2 suppressed Nitrospira to 0.2% and enhanced the abundance of anammox and DNRA-performing bacteria (e.g., Fimbriimonadaceae, Mycobacterium, Anaerolineales, Caldilineaceae, and Ignavibacteriaceae) to 31.2% and 15.7%, respectively. Metagenome-assembled genome analysis confirmed the enrichment of functional genes associated with anammox (hzsABC and hdh) and DNRA metabolism (nirBD and nrfAH), corresponding to the recovery of nitrogen removal efficiency to 82.3%. Quantitative microbial network analysis further revealed that functional redundancy index declined from 0.56 to 0.42 under nitrite stress but recovered to 0.53 following acetate supplementation, indicating the restoration of a functionally buffered microbial community. Overall, these results demonstrate that low-level acetate supplementation (C/N = 0.2) effectively stimulated DNRA-mediated NO2[-] reduction to NH4[+] by DNRA-performing bacteria, thereby supporting anammox activity and providing an energy-efficient strategy to mitigate NO2[-] accumulation and stabilize nitrogen removal in anammox-based systems.}, } @article {pmid42055314, year = {2026}, author = {Zhang, Y and Xia, J and Qiu, Z and Tian, S and Wang, J and Ren, X and Chen, M}, title = {Successful treatment of balamuthia mandrillaris amebic encephalitis diagnosed by MetaCAP in China: A case report and review of 25 survival cases.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {168}, number = {}, pages = {108745}, doi = {10.1016/j.ijid.2026.108745}, pmid = {42055314}, issn = {1878-3511}, mesh = {Humans ; Male ; Middle Aged ; *Amebiasis/drug therapy/diagnosis/parasitology ; *Balamuthia mandrillaris/genetics/isolation & purification ; *Central Nervous System Protozoal Infections/drug therapy/diagnosis ; China ; *Encephalitis/drug therapy/parasitology/diagnosis ; *Infectious Encephalitis/drug therapy/diagnosis/parasitology ; Metagenomics/methods ; Sulfasalazine/therapeutic use ; Treatment Outcome ; Case Reports as Topic ; }, abstract = {Balamuthia mandrillaris, a free-living amoeba, can cause Balamuthia amebic encephalitis (BAE), a rare and often fatal cerebral infection. The reported mortality rate is >90%, largely attributable to the absence of specific clinical manifestations, sensitive diagnostic methods, and effective therapeutic interventions. We herein describe a middle-aged, male patient diagnosed with BAE using Metagenomic Capture sequencing (MetaCAP) who achieved full recovery following early medical therapy without neurosurgical treatment. Our findings indicate that MetaCAP serves as a rapid and sensitive diagnostic approach, and sulfasalazine may confer a potential anti-inflammatory benefit in the management of BAE. In addition, we reviewed 25 survival cases of BAE reported in the PubMed database up to now.}, } @article {pmid42055803, year = {2026}, author = {Auwal, AM and Matthews, R and Cook, C and Sargent, B and Easton, A and Ray, STJ and Ellul, MA and Michael, BD}, title = {Suspected encephalitis in adults.}, journal = {Practical neurology}, volume = {}, number = {}, pages = {}, doi = {10.1136/pn-2024-004299}, pmid = {42055803}, issn = {1474-7766}, abstract = {'Query encephalitis' is one of the most common reasons for inpatient neurology referral in the context of an acutely confused patient. Growing evidence suggests that time to treatment is a key determinant of outcome in both infectious and autoimmune encephalitis; hence, these two causes should be considered simultaneously at presentation. However, under-recognition and the existence of several mimics make a rapid diagnosis of encephalitis challenging. Appreciation of clinical syndromes can guide aetiological investigation and consequent treatment. In this article, we discuss clinical phenotypes associated with both infectious and autoimmune encephalitis, as well as a systematic approach to their investigation and up-to-date treatment strategies. We also highlight ongoing areas of research, such as metagenomics and therapeutic trials.}, } @article {pmid42056322, year = {2026}, author = {Thakkar, S and Rathour, R and Rana, SS and Samant, S and Kikani, BA and Madamwar, D and Desai, C}, title = {Biochar-augmented microaerophilic fixed-film bioreactor integrated with an aerobic membrane bioreactor effectively reduces persistent, mobile chemicals in the CETP effluent treatment.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {5}, pages = {}, pmid = {42056322}, issn = {1573-0972}, support = {File No. GSBTM/JD(R&D)/662/2022-23/00292469//Gujarat State Biotechnology Mission (GSBTM), Department of Science and Technology, Government of Gujarat/ ; }, mesh = {*Bioreactors/microbiology ; *Charcoal/chemistry ; Bacteria/classification/metabolism/genetics ; *Water Pollutants, Chemical/metabolism ; Aerobiosis ; *Waste Disposal, Fluid/methods ; Biodegradation, Environmental ; *Water Purification/methods ; Membranes, Artificial ; }, abstract = {Different classes of chemical compounds including persistent, mobile chemicals (PMCs) often bypass the conventional treatment processes of common effluent treatment plants (CETPs), resulting in their unmonitored release into aquatic environments. In this study, an integrated treatment system comprising a microaerophilic fixed-film bioreactor (MFB) and an aerobic membrane bioreactor (Ae-MBR) was engineered to treat secondary CETP effluent. Two types of packing materials in the engineered MFBs were evaluated: one with wood charcoal (C-MFB) and another with 30% (w/w) biochar-augmented charcoal (BAC-MFB). The BAC-MFB showed better treatment efficiency, achieving 69.17% colour (Pt-Co units) removal and 93.01% COD removal at an optimal 3d hydraulic retention time (HRT). Integration with Ae-MBR further enhanced the treatment, achieving > 95% COD and > 94% colour removal, with an overall > 85% reduction in total number of parent chemical compounds and a specific > 83% reduction in PMCs from CETP effluent. At 3d HRT, bacterial community analysis revealed dominance of Campylobacterota and Bacillota in BAC-MFB under microaerophilic conditions, whereas Bacillota dominated in the Ae-MBR under aerobic conditions. The predicted metagenome analysis revealed significant enrichment of benzoate and aminobenzoate degradation pathways in the integrated system. While the BAC-MFB treatment alone achieved sufficient COD removal, its integration with Ae-MBR markedly enhanced the reduction in overall chemical complexity including PMCs from the CETP effluent. This study demonstrates that the engineered hybrid BAC-MFB-Ae-MBR system is a sustainable solution for the treatment of industrial CETP effluents.}, } @article {pmid42056687, year = {2026}, author = {Wedell, E and Shen, C and Warnow, T}, title = {Phylogenetic Placement Using SCAMPP and Batch-SCAMPP.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2981}, number = {}, pages = {37-52}, pmid = {42056687}, issn = {1940-6029}, mesh = {*Phylogeny ; *Metagenomics/methods ; *Software ; Likelihood Functions ; Algorithms ; Sequence Analysis, DNA/methods ; *Computational Biology/methods ; }, abstract = {Phylogenetic placement is the problem of adding sequences to an existing phylogenetic tree. While many techniques have been developed for this problem, methods based on optimizing maximum likelihood, such as pplacer and EPA-ng, have been shown to provide the highest accuracy. Unfortunately, these methods are limited to at most moderately large placement trees due to their design. SCAMPP and Batch-SCAMPP are two methods that have been developed to improve the scalability of both pplacer and EPA-ng to very large trees, while maintaining high accuracy. Here, we describe these methods and show how to use them in two applications: metagenomics, including taxon identification and abundance profiling, and incrementally growing large trees. SCAMPP and Batch-SCAMPP are available in open-source form on GitHub and PyPI.}, } @article {pmid42056742, year = {2026}, author = {Zhang, X and Li, Q and Yang, H and Li, H and Hu, C}, title = {Active responses of cyanobacterial crusts directly exposed to the extreme stratospheric environment.}, journal = {Life sciences in space research}, volume = {50}, number = {}, pages = {133-145}, doi = {10.1016/j.lssr.2026.01.001}, pmid = {42056742}, issn = {2214-5532}, mesh = {*Cyanobacteria/physiology/metabolism ; *Extraterrestrial Environment ; Mars ; Exobiology ; *Extreme Environments ; Indoles ; Phenols ; }, abstract = {The stratosphere's highly hostile environment offers a unique and relatively accessible setting to evaluate extremophilic adaptation for extraterrestrial colonization. The accelerating pace of the Martian project has underscored the need for a better understanding of the synergistic responses of microbial communities in Mars-like habitats. Here, we loaded the cyanobacterial crust, a model system with multiple trophic levels, onto a balloon-borne astrobiology platform for a direct-exposure experiment in the stratosphere, aligned with the ground-control and indoor-simulated groups. After short-term in-situ exposure, we performed multi-omics analyses to delineate alterations in community composition and the community-level metabolic response. We observed a significant shift in the community composition of active members, with the relative abundance of photoautotrophs (except Scytonema) declining while that of chemotrophs increased. However, we demonstrated the unique thriving of the cyanobacterial genus Scytonema, attributed to its synthesis of the anti-ultraviolet compound scytonemin, its diverse material, and its energy acquisition. Meanwhile, the distinct metabolic profiles exhibited by various species and their interspecies metabolic interactions synergistically facilitated the retention of organic carbon and nitrogen, ultimately sustaining the stability of the biocrust community. Our study underscores the adaptive resilience of cyanobacterial crusts under stratospheric stresses. Notably, the robustness of Scytonema, particularly its unique survival capabilities, highlights its potential for extraterrestrial applications.}, } @article {pmid42056812, year = {2026}, author = {Fu, Y and Zhuang, H and Shi, J}, title = {Reshaping of the electron transport chain and carbon metabolism by low-loading Fe3O4@PU for enhanced phenolic compounds degradation in an algal-bacterial biofilm system.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142207}, doi = {10.1016/j.jhazmat.2026.142207}, pmid = {42056812}, issn = {1873-3336}, mesh = {*Biofilms ; Electron Transport ; *Carbon/metabolism ; Bioreactors ; *Water Pollutants, Chemical/metabolism/chemistry ; *Phenols/metabolism ; Biodegradation, Environmental ; *Polyurethanes/chemistry ; Bacteria/metabolism ; *Ferric Compounds/chemistry ; Wastewater ; Waste Disposal, Fluid/methods ; }, abstract = {While previous algal-bacterial biofilm systems without magnetite have shown limited resilience to high concentration phenolic compounds, this study demonstrates that introducing low loading (5%) nano-Fe3O4 substantially enhances degradation stability by optimizing electron transfer pathways. Four algal-bacterial reactors with varying Fe3O4 loadings (5-50%) were constructed using polyurethane carriers to treat phenolic wastewater under increasing total phenol (TPh) concentrations (50-300 mg/L). The 5% loading reactor (R1) demonstrated outstanding performance, achieving > 80% TPh removal and approximately 76% COD removal even at the highest loading. Compared to without magnetite systems, R1 achieved 13-15% higher TPh degradation at 300 mg/L. R1 also exhibited the highest electron transfer system activity (0.487 μg O2·gVSS[-1]·h[-1]) and cytochrome c content (72.12 mg/g VSS), indicating that Fe3O4 serves as an electron shuttle, compensating for endogenous electron carrier limitations. Metagenomic analysis revealed that the enhanced performance stemmed from robust carbohydrate metabolism, particularly the upregulation of key glycolytic enzymes (pfkA) and glycogen degrading enzymes (GH13), ensuring efficient NADH/ATP production. This metabolic advantage supplied reducing power to the Fe3O4 optimized electron transport chain, synchronizing electron generation with respiratory utilization. These findings demonstrate that low-dose Fe3O4 optimizes natural electron transfer pathways by coupling metabolic flux with respiratory chain activity, offering a cost effective strategy for treating high strength industrial wastewater.}, } @article {pmid42057016, year = {2026}, author = {Chen, H and Shi, X and Huang, Z and Li, X and Zhou, Y and Tan, D and Xie, Z and Wu, X and Zhou, M and Hong, D}, title = {Co-occurrence of viral encephalitis and autoimmune encephalitis: overlapping peaks encephalitis or coincidence condition?.}, journal = {BMC neurology}, volume = {26}, number = {1}, pages = {}, pmid = {42057016}, issn = {1471-2377}, support = {No.82101419//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Many studies have shown that autoimmune encephalitis (AE) can occur after viral encephalitis. However, no reports have focused on the interval between viral infection peaks and probable AE peaks. OBJECTIVES: To assess the possibility that viral infection and neuronal autoantibodies are concomitantly present within a 72-hour interval in patients diagnosed with encephalitis. METHODS: We retrospectively analyzed encephalitis patients admitted to our institution between 2018 and 2025. The inclusion criteria were as follows: the interval from the initial onset of symptoms to serum and cerebrospinal fluid (CSF) sampling was less than 72 h, with concomitant detection of viral central nervous system (CNS) infection and neuronal autoantibodies. Viral detection was performed using metagenomic next-generation sequencing (mNGS), whereas neuronal autoantibodies were measured by cytometric bead array (CBA). RESULTS: Among 347 patients with encephalitis, fifteen patients had concomitant detection of viral central nervous system (CNS) infection and neuronal autoantibodies within 72 h after the initial onset of symptoms.These fifteen patients presented with prominent clinical manifestations including headache, seizures, psychosis and memory disorders. Cerebrospinal fluid (CSF) analysis revealed features consistent with aseptic or viral encephalitis. A variety of neuronal autoantibodies were identified, namely NMDA-R-IgG, CASPR2-IgG, LGI1-IgG, LON5-IgG, GFAP-IgG, GAD65-IgG and mGluR5-IgG.Metagenomic next-generation sequencing (mNGS) assays demonstrated that 5 patients were infected with Human Herpesvirus Type 1 (HSV-1) and 10 patients with Epstein-Barr Virus (EBV). CONCLUSIONS: The concomitant detection of viral infection and neuronal autoantibodies in serum or cerebrospinal fluid (CSF) within a short time window (≤ 72 h) after the initial onset of symptoms was defined in this study as Overlapping Peak Encephalitis (OPE) or coincidence condition, which suggests that it represents a distinct clinical entity. This finding underscores the importance of simultaneously performing both metagenomic next-generation sequencing (mNGS) and neuronal autoantibody assays in patients with suspected viral encephalitis. Early identification of such comorbid conditions is of paramount importance; timely diagnosis combined with antiviral therapy and immunomodulatory intervention may significantly improve clinical outcomes.}, } @article {pmid42057074, year = {2026}, author = {de Oliveira, LG and Lopes Mechler-Dreibi, M and Storino, GY and Moreira Petri, FA and Carvalho Abreu Fantini, M and Silva Martins, T}, title = {Respiratory microbiota dynamics in piglets under nanotechnology-based and conventional vaccination protocols against Mycoplasma hyopneumoniae.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {42057074}, issn = {1746-6148}, mesh = {Animals ; *Microbiota ; Swine ; *Mycoplasma hyopneumoniae/immunology ; *Pneumonia of Swine, Mycoplasmal/prevention & control/microbiology ; *Bacterial Vaccines/administration & dosage/immunology ; *Vaccination/veterinary/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Nanotechnology ; Female ; RNA, Ribosomal, 16S/genetics ; Administration, Oral ; }, abstract = {Mycoplasma hyopneumoniae is a key pathogen in porcine enzootic pneumonia (PEP) and plays an important role in the porcine respiratory disease complex (PRDC). Understanding how vaccination strategies relate to the respiratory microbiota in piglets may provide insights into host-microbiota interactions and vaccine performance. This study evaluated the temporal dynamics of the respiratory microbiota in piglets subjected to different vaccination protocols, including a nanotechnology-based oral vaccine formulated with mesoporous silica (SBA-15), alone or combined with a commercial vaccine, on the respiratory microbiota of piglets. Forty-eight piglets from M. hyopneumoniae-free sows were divided into four experimental groups receiving different vaccination protocols: CV + SBA received the pure silica-based adjuvant (SBA-15) orally and a commercial vaccine at 24 days of life; OV3 + CV received an oral vaccine (OV) at 3 days and an intramuscular commercial vaccine at 24 days; CV received only the intramuscular commercial vaccine at 24 days; and OV + CV received both the oral and commercial vaccines at 24 days. Microbiota composition was assessed at 3, 41, and 71 days of life using 16S rRNA gene sequencing from nasal swabs and bronchoalveolar lavage fluid (BALF). Significant differences in nasal microbiota diversity were observed at early life stages. At D3, CV exhibited the highest diversity, while OV3 + CV had the lowest (Shannon index, p < 0.05 between CV and OV3 + CV). At D41, microbiota differences between groups had diminished, with only OV + CV showing higher richness compared with OV3 + CV (Chao1 index, p < 0.05). At D71, no significant differences were observed in overall diversity or bacterial composition among groups. As no treatment had been administered prior to sampling, these differences likely reflect baseline variability between groups. Additionally, no consistent associations were detected between microbiota diversity patterns and vaccination outcomes assessed by lung lesion scores and bacterial DNA load. These findings indicate that early-life differences in nasal microbiota were observed, but these were not sustained over time, and the respiratory microbiota converged toward a more stable community structure regardless of vaccination protocol.}, } @article {pmid42057154, year = {2026}, author = {Mahmud, MR and Uddin, MK and Kareljärvi, P and Jalasvuori, M and Peräkylä, J and Eklund, T and Biström, M and Hasan, S and Vatanen, T and Kiljunen, S and Oliviero, C}, title = {Impact of phage therapy in post-weaning piglets challenged with ETEC strain in a controlled minitrial.}, journal = {Porcine health management}, volume = {12}, number = {1}, pages = {}, pmid = {42057154}, issn = {2055-5660}, abstract = {Enterotoxigenic Escherichia coli (ETEC) is a pathogen responsible for post-weaning diarrhea (PWD) in piglets, which results in economic losses in pig production. The rise of antibiotic-resistant ETEC strains together with restrictions on addition of zinc oxide in pig feed require alternative management approaches. Our research examines bacteriophage therapy as a solution to control ETEC infections in newly weaned piglets. A cocktail of phages targeting a strain of ETEC F4LT1ST2 was identified and subsequently multiplicated in laboratory. We conducted a trial including nine piglets divided into three groups. The negative control group was exposed to the phage cocktail by administration with the bedding material (saw dust) on the floor of their pen. The treatment group was exposed to the ETEC strain and to the phage cocktail, and the positive control group was exposed to the ETEC strain only. Shotgun metagenomic sequencing was performed on fecal samples to characterize bacterial and phage dynamics. Throughout a 10-day period we monitored daily the rectal temperature and the diarrheal score of piglets. Subsequently we evaluated phage and bacterial counts in fecal samples to determine phage therapy effect on gut microbiota dynamics and piglet health. The PHAGE+ETEC group showed 19.2% lower cumulative diarrhea burden (p = 0.044) and 61.9% higher average daily gain (p = 0.065). Rectal temperature correlated significantly with diarrhea severity (per-piglet Spearman's ρ = 0.727, p = 0.027). Alpha diversity did not differ between treatment groups across timepoints, suggesting that phage administration did not cause major shifts in microbial diversity. Metagenomic analyses showed significant reduction of E. coli abundance in PHAGE+ETEC group compared to PHAGE groups (p = 0.009). Consistent with these observations, plaque assay results confirmed active phage-bacteria interactions: no plaque formation was detected in the feces of the ETEC-only group, whereas the PHAGE+ETEC group showed phage replication, reaching 10[6] PFU/ml. This pilot study highlights the potential of phage therapy as an alternative to antibiotics for ETEC infections in piglets. Additional research with larger pig population and longer duration is required to confirm these findings and develop optimal phage application methods for swine production.}, } @article {pmid42057164, year = {2026}, author = {Cabello, AM and Salles, S and Domínguez-Huerta, G and Capo, E and Camarena-Gómez, MT and García-Gómez, C and Sánchez, A and Mangot, JF and Cerezo, I and Bautista, R and Pérez, P and García, R and Ruiz, JM and Mercado, JM and Ferrera, I}, title = {Environmental disturbances and cyanobacterial traits shape prokaryotic dynamics in a eutrophic Mediterranean coastal lagoon.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00893-9}, pmid = {42057164}, issn = {2524-6372}, abstract = {BACKGROUND: Coastal ecosystems face increasing threats from eutrophication, driven by excess nutrient inputs that lead to ecosystem-disruptive algal blooms (EDABs). The Mar Menor coastal lagoon, located in the south-eastern Iberian Peninsula, has experienced severe ecological disruption since 2015, beginning with a Synechococcus‑dominated cyanobacterial bloom and followed by major shifts in eukaryotic phytoplankton composition. However, the mechanisms that affect phytoplankton dynamics in this coastal environment remain unknown. Here, we investigate the spatiotemporal dynamics of prokaryotic communities in the lagoon after the initial Synechococcus bloom using three years of 16S rRNA gene sequencing data and evaluate how environmental factors shape these patterns. In addition, we examine the fine‑scale diversity and dynamics of Synechococcus variants through metagenomics (petB gene) and use genome‑resolved analyses to identify functional traits associated with their succession in the lagoon. Finally, to investigate the role of biotic interactions in regulating cyanobacterial growth, we examine the temporal dynamics of cyanophages.

RESULTS: Microbial communities in the waters of the Mar Menor responded rapidly and consistently to short‑term environmental fluctuations and showed a weak seasonal signal in alpha and beta diversity. Prokaryotic assemblages associated with two deoxygenation events following extreme weather conditions (intense rainfall in autumn 2019 and unusually high temperatures in summer 2021) illustrated how episodic disturbances can drive substantial shifts in microbial composition; notably, Synechococcus became particularly prevalent after the intense rainfall event. Fine‑scale analyses of 16S rRNA and petB gene variants revealed that a restricted set of Synechococcus lineages dominated throughout the study period. Comparative genomic analyses of these cyanobacterial populations highlighted distinct functional repertoires, including genes involved in osmoprotectant biosynthesis, diverse toxin-antitoxin systems, herbicide resistance, and multiple viral defense mechanisms, present only in specific variants. Finally, temporal analyses of viral assemblages indicated that cyanophages played a key role in modulating Synechococcus population dynamics.

CONCLUSIONS: The temporal dynamics of prokaryotic communities in the Mar Menor indicate that the lagoon remains in an altered, non‑equilibrium state, likely sustained by recurrent anthropogenic and climatic pressures. The contrasting microbial responses observed during two different deoxygenation events underscore the ecosystem's complexity. This study highlights the importance of incorporating microbial community analyses into long‑term monitoring of threatened coastal systems, and the power of comparative genomics for identifying functional traits that enable cyanobacterial proliferation in disturbed ecosystems.}, } @article {pmid42057198, year = {2026}, author = {Dikareva, E and van Best, N and Bervoets, L and West, CE and Rossel, C and Driessen, C and Mommers, M and Penders, J}, title = {The impact of the COVID-19 pandemic and associated lifestyle changes on early-life microbiome development.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {42057198}, issn = {1756-994X}, support = {2021-01637//Vetenskapsrådet/ ; 967569//Västerbotten Läns Landsting/ ; 529051010//The Netherlands Organization for Health Research and Development (ZonMw) through the European Union Joint Programming Initiative-A Healthy Diet for a Healthy Life/ ; 09150162410022/ZONMW_/ZonMw/Netherlands ; }, mesh = {Humans ; *COVID-19/epidemiology/microbiology ; *Life Style ; Infant ; SARS-CoV-2 ; *Gastrointestinal Microbiome ; Pandemics ; Feces/microbiology ; Metagenome ; Male ; Female ; Longitudinal Studies ; Hygiene ; }, abstract = {BACKGROUND: The COVID-19 pandemic triggered rapid, population-wide behavioral and environmental changes, offering a unique natural experiment to study how early-life microbiome development responds to abrupt shifts in social and hygiene-related exposures.

METHODS: Using longitudinal data from 139 infants in the Dutch LucKi Gut study, we compared gut microbiome development in fecal samples collected before and during the pandemic. Whole metagenome sequencing of 808 stool samples was performed across nine time points in the first 14 months of life. An exposure index (EI) capturing variation in household-level pandemic-related behaviors was constructed for the 36 infants with samples collected during the COVID-pandemic to quantify variations in social distancing, lifestyle and hygiene measures.

RESULTS: Microbial richness and diversity increased with age, following established developmental trajectories. However, from 6 months onward, the COVID-19 pandemic independently shaped gut microbial composition, explaining up to 2.7% of variation by 11 months of age (Q-value = 0.006). Forty-four species were differentially abundant in pandemic-era samples, including depletion of Gordonibacter pamelaeae and several Actinomyces species. Notably, greater environmental exposure (higher EI scores) was associated with lower abundance of G. pamelaeae, a microbe implicated in bile acid and immunomodulatory metabolism.

CONCLUSIONS: This is the first longitudinal whole-genome sequencing study to demonstrate that pandemic-related behavioral changes measurably altered infant gut microbiota maturation. These findings highlight the sensitivity of microbiome development to societal-level environmental disruptions and suggest that early-life microbial exposures, modulated by hygiene and social behavior, may carry long-term implications for child health.}, } @article {pmid42057295, year = {2026}, author = {Klaps, J and Lemey, P and Bletsa, M and , and Kafetzopoulou, LE}, title = {nf-core/viralmetagenome: A novel pipeline for untargeted viral genome reconstruction.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {5}, pages = {}, pmid = {42057295}, issn = {1367-4811}, support = {511260616//German Research Foundation [Deutsche Forschungsgemeinschaft/ ; G005323N//Research Foundation-Flanders/ ; G051322N//Research Foundation-Flanders/ ; 1SH2V24N//Research Foundation-Flanders/ ; 12X9222N//Research Foundation-Flanders/ ; }, mesh = {*Genome, Viral ; *Metagenomics/methods ; *Software ; Humans ; High-Throughput Nucleotide Sequencing ; }, abstract = {MOTIVATION: Reconstructing eukaryotic viral genomes from metagenomic data is challenging due to their extensive diversity and potential genome segmentation. Current approaches often rely on labor-intensive manual curation for reference selection and scaffolding, limiting scalability for large studies or rapid outbreak response. We address the critical need for an automated, scalable pipeline for efficient viral metagenomic analysis without manual intervention.

RESULTS: We present nf-core/viralmetagenome, a comprehensive Nextflow pipeline for the untargeted reconstruction and variant analysis of eukaryotic DNA and RNA viruses from short-read metagenomic or hybridisation capture enriched samples. The pipeline automates the entire process from read preprocessing to consensus generation, integrating multiple de novo assemblers, automated reference selection, and iterative consensus refinement. It features robust quality control, extensive documentation, and seamless portability via Docker and Singularity. We validated the pipeline on diverse simulated and real datasets, demonstrating its ability to recover high-quality genomes from complex metagenomic samples and resolve co-infections, making it a powerful tool for viral surveillance.

AVAILABILITY: nf-core/viralmetagenome is freely available at https://github.com/nf-core/viralmetagenome with comprehensive documentation at https://nf-co.re/viralmetagenome. Archival code repository snapshots are published at zenodo with doi: https://doi.org/10.5281/zenodo.17524074.}, } @article {pmid42057740, year = {2026}, author = {Wang, JL and Huang, SY and Chen, ZT and Zhou, Y and Kuzyakov, Y and Chen, JH and Ma, XM}, title = {Functional Resistance of Microbiome to Differently Charged Nanoplastics in Rhizosphere Hotspots Soil.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {18}, pages = {14335-14347}, doi = {10.1021/acs.jafc.5c17636}, pmid = {42057740}, issn = {1520-5118}, mesh = {Rhizosphere ; Soil Microbiology ; Zea mays/growth & development/microbiology/metabolism/drug effects ; *Microbiota/drug effects ; Bacteria/genetics/isolation & purification/drug effects/classification/metabolism ; Soil/chemistry ; *Soil Pollutants/chemistry/pharmacology/toxicity ; *Plastics/chemistry ; }, abstract = {Nanoplastics (NPs) pose greater soil ecological risks than microplastics due to their surface charge-dependent uptake, transport, and accumulation in plants. However, how differently charged NPs affect maize growth and microbial functional resistance in rhizosphere hotspots remains unclear. Here, we investigated the effect of positively (PS-NH2) and negatively (PS-SO3H) charged NPs on maize growth, enzyme activities and gene abundance, microbial resistance, and functional properties in acidic soil using soil zymography, 16S rRNA sequencing, and metagenomics. PS-NH2 showed stronger inhibitory effects on maize growth than PS-SO3H, mainly through reducing microbial diversity and weakening N and P cycling-related enzyme activities and resistance. Conversely, PS-SO3H maintained higher microbial resistance. Functional hotspots microbial species (particularly in Actinobacteria) alleviated NPs toxicity by accelerating N and P cycling to meet the demand for nutrients limiting maize growth. This study provides a mechanistic basis for assessing soil NPs risk with implications for agricultural sustainability and food safety.}, } @article {pmid42057783, year = {2026}, author = {Harshvardhan, and Kaur, M and Grover, V and Pinnaka, AK and Korpole, S}, title = {Metagenomic insights into oral microbiota dynamics in diabetic and non-diabetic periodontal disease: a pilot study.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1799124}, pmid = {42057783}, issn = {1664-302X}, abstract = {INTRODUCTION: Subgingival microbial dysbiosis is one of the key reasons behind periodontitis, a chronic inflammatory disease, which is further get severe in the presence of type 2 diabetes mellitus (T2D). Although changes in taxonomic composition have been well established, the functional interactions and metagenomic profiles across different stages of the disease remain unclear.

METHODS: A shotgun metagenomic analysis was performed on subgingival dental plaque samples from 16 individuals, divided into healthy, staged periodontitis, and diabetic periodontitis groups. Group-wise DNA pooling was done for maximum DNA yield. Further, Alpha/beta diversity, taxonomic profiling, pathogen-probiotic ratios, and metabolic pathway abundance were analyzed and studied.

RESULTS: The healthy group showed the highest alpha diversity, especially in the core biosynthetic pathways. On the other hand, the earlier stages of periodontitis showed a unique community structure and the lowest alpha diversity. Early periodontitis also showed the highest abundance of commensals like Actinomyces and Bifidobacterium, along with increased UMP/guanosine and L-arginine biosynthesis pathways. The advanced periodontitis group had an increase of red complex bacteria and loss of probiotics. An increase of the degradative pathways, such as L-histidine degradation, had also been observed in this stage. The diabetic periodontitis group had a distinct microbial profile that included Capnocytophaga and a considerable metabolic shift toward lipid metabolism and glycolysis, with higher overall microbial diversity than the other periodontitis groups.

CONCLUSION: The results clearly show that the subgingival microbial and functional patterns are different across the stages of the disease and metabolic status, which can be developed for underscoring the importance of targeting early metabolic shifts to prevent dysbiosis.}, } @article {pmid42057917, year = {2026}, author = {Szentiványi, T and Bruszniczky, B and Biró, Z and Katona, K and Klein, Á and Bende, A and Bánáti, L and Vass, G and Lehotzky, P and Kovács, D and Földvári, G and Csivincsik, Á and Nagy, G and Nagy, RR and Miklós, M and Szabadi, KL and Szabó, ÉS and Garamszegi, LZ}, title = {Unwelcome guests: Nematodes of zoonotic and animal health importance in native and invasive carnivores of Hungary.}, journal = {Current research in parasitology & vector-borne diseases}, volume = {9}, number = {}, pages = {100380}, pmid = {42057917}, issn = {2667-114X}, abstract = {Wild carnivores are important reservoirs of parasitic nematodes, several of which have veterinary and zoonotic significance. In Europe, the role of invasive carnivores in parasite circulation remains poorly understood. Here, we screened 371 individuals of six wild carnivore species from Hungary (red foxes, badgers, golden jackals, raccoons, raccoon dogs, and beech martens), using molecular markers (cox1 and S12), and detected five nematode parasites: Dirofilaria immitis, Crenosoma vulpis, Angiostrongylus vasorum, Thelazia callipaeda, and Spirocerca lupi. The highest prevalence was observed in badgers (32.0%) and red foxes (15.7%), while invasive raccoons also showed a relatively high infection rate (13.2%). Dirofilaria immitis was one of the most common nematode species detected: it was found in four host species, including the first confirmed cases in Hungarian badgers and invasive raccoons, extending the known host range of this parasite in central Europe. Importantly, T. callipaeda was recorded in red foxes and an invasive raccoon dog, representing the first invasive host records of this zoonotic eyeworm in Hungary. Crenosoma vulpis was identified in raccoons, suggesting invasive species may act as incidental carriers of endemic parasites. Both C. vulpis and D. immitis showed low host specificity. These findings indicate that invasive carnivores, particularly raccoons, may harbour unexpectedly high prevalence and play a greater role in local parasite networks than previously assumed. Our results highlight the epidemiological significance of both native and invasive carnivores in sustaining nematodes of zoonotic and veterinary importance in central Europe, stressing the need for continued surveillance in wild carnivores.}, } @article {pmid42058175, year = {2026}, author = {Zhong, H and Sun, C and Lu, Y and Cai, X and Cao, M and Wang, L and Feng, C and Song, M and Sun, W and Shi, M and Tao, Y and Zhou, J and Chen, C and Lu, X and Li, Y and Ni, Y and Cai, Y and Zhong, J and Li, Y and Wu, W and Shi, Y and Wang, M and Su, X}, title = {The clinical value of metagenomic next generation sequencing in the diagnosis of non-neutropenic invasive pulmonary aspergillosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1731736}, pmid = {42058175}, issn = {2235-2988}, mesh = {Humans ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Sputum/microbiology ; Male ; Sensitivity and Specificity ; Middle Aged ; *Aspergillus/genetics/isolation & purification/classification ; Adult ; Galactose/analogs & derivatives ; Aged ; Mannans/analysis/blood ; }, abstract = {BACKGROUND: This study aims to explore the performance of metagenomic next generation sequencing (mNGS) in the diagnosis of non-neutropenic invasive pulmonary aspergillosis (IPA) and its clinical application value.

METHODS: This multi-center study enrolled 293 suspected IPA patients who conducted mNGS from October 2020 to February 2024. These cases were classified into IPA group and non-IPA group according to IPA diagnostic criteria. We analyzed the diagnostic value of mNGS by comparing with sputum culture, BALF culture, serum and BALF GM test.

RESULTS: A total of 118 IPA patients (4 proven/113 probable/1 possible diagnosis) were included in our study. The most common Aspergillus species was A. fumigatus (63.4%), followed by A. flavus (23.2%), A. oryzae (7.1%), A. niger (3.6%) and A. terreus (2.7%). The sensitivity of bronchoalveolar lavage fluid (BALF) mNGS was significantly higher than BALF culture (81.9% vs. 27.0%, p<0.001) and BALF galactomannan (GM) (81.9% vs. 55.8% (GM≥1.0 cutoff value), p<0.001). The specificity of BALF mNGS was 92.2%, which was similar with BALF culture (98.5%) and BALF GM (94.7%). The combination of BALF mNGS and GM could increase the sensitivity to 88.7%, and had great negative predictive value (NPV, 92.3%). The sensitivity of blood mNGS was significantly higher than serum GM (58.8% vs. 16.7%, p<0.001). And the sensitivity of sputum mNGS was 66.7%, which was significantly higher than sputum culture (30.0%, p=0.025).

CONCLUSION: mNGS demonstrated significant diagnostic value for IPA, exhibiting significantly higher sensitivity compared to current conventional microbiological tests while maintaining equivalent specificity. The combination of BALF mNGS with GM performed great sensitivity and negative predictive value. BALF specimens seemed to be superior to blood and sputum samples. However, for patients unable to undergo bronchoscopy, sputum and blood mNGS were still superior to other methods.}, } @article {pmid42058649, year = {2026}, author = {Kwarteng, A and Amedorme, D and Addy, HPK and Amewu, EKA and Osei-Poku, P and Larbi, A}, title = {Brukina in Focus: A Narrative Review on Metagenomic Approaches to Fermentation and Food Safety.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {6677609}, pmid = {42058649}, issn = {1687-918X}, abstract = {Brukina, a traditional fermented beverage smoothie made from milk and millet, is popular in Ghana and other West African countries due to its tasty flavor, high nutritional content, and affordability. Despite its widespread consumption, the nature of its production through artisanal fermentation processes presents concerns regarding microbial consistency, nutritional optimization, and food safety. This literature review explores the potential of metagenomic approaches to uncover microbial diversity, functional capacity, and safety profiles of Brukina. By integrating insights from amplicon-targeted and shotgun whole-genome sequencing studies on fermented foods, we highlight how next-generation sequencing technologies can characterize lactic acid bacteria, yeast, and other microorganisms that drive fermentation. Additionally, we discuss how metagenomics can identify functional genes influencing carbohydrate metabolism, flavor and aroma generation, and production of antimicrobial resistance compounds. Thus, metagenomics provides a powerful framework for assessing public health risks and nutritional benefits. Bioinformatic tools have also been highlighted, and their relevant application in analyzing sequenced data to achieve taxonomic classification, identification of biochemical pathways, and functional profiling of microbial ecology of fermented foods. This review outlines key research gaps and recommends future directions, including starter culture development, standardization of Brukina production, multi-omics integration in metagenomics, and microbiome-informed food safety standards. Metagenomic profiling of Brukina holds promise for improving product quality, consumer safety, and scientific understanding of traditional fermented foods. By tackling the challenges raised, metagenomic techniques can be extremely helpful in maximizing Brukina fermentation, guaranteeing food safety, and maintaining the customs that give this product its distinctive character.}, } @article {pmid42058681, year = {2026}, author = {Budai, M and Rák, G and Wenner, B and Móré, A and Bancsik, B and Nagy, B and Kovács, G and Szabolcs, M and Ladnyik, Z and Molnár, C and Guller, ZE and Lengyel, A and Vadász, C and Mizsei, E}, title = {The Influence of Plant Species Composition on an Endangered Grassland Specialist Reptile, the Hungarian Meadow Viper.}, journal = {Ecology and evolution}, volume = {16}, number = {}, pages = {e73579}, pmid = {42058681}, issn = {2045-7758}, abstract = {The Hungarian meadow viper (Vipera ursinii rakosiensis) is one of the most threatened vertebrates in Hungary, whose populations are not growing significantly despite enormous conservation efforts. Previous studies suggested an influence of vertical vegetation structure on habitat use, while the role of horizontal vegetation structure is still poorly understood. In the present study, we used vegetation survey data to investigate the effects of variables related to the horizontal structure and functional composition of vegetation on the occupancy and density of the Hungarian meadow viper. During a spring survey period, we collected viper occurrence data in 59 sampling quadrats alongside plant community samples, then used single-season occupancy models and N-mixture models for analysis. After model selection, the best models included the moisture-related vegetation gradient, species richness, graminoid-forb ratio, and height of plants as explanatory variables for both occupancy and density. Wetter meadows with fewer plant species, a higher graminoid/forb ratio, and habitats with characteristically lower-growing plant species were more probable to be used by the vipers. Our results suggest that the horizontal structure of the vegetation influences the habitat use of vipers and also draw attention to the threats posed by more frequent droughts and heatwaves.}, } @article {pmid42059272, year = {2026}, author = {Damian, R and Katarzyna, J and Sebastian, W and Piotr, J and Joanna, G and Małgorzata, C and Monika, H and Edyta, K}, title = {Native Aquatic Plastispheres in a River-Wastewater Catchment: Carbapenem-Resistant Bacteria Isolation and Microscopy-Based Structural Analysis.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70312}, doi = {10.1111/1462-2920.70312}, pmid = {42059272}, issn = {1462-2920}, support = {2021/43/B/ST10/01076//Narodowe Centrum Nauki/ ; }, mesh = {*Rivers/microbiology ; *Biofilms/growth & development ; *Wastewater/microbiology ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/isolation & purification/drug effects/genetics/classification ; Drug Resistance, Bacterial ; Plastics ; *Carbapenem-Resistant Enterobacteriaceae/isolation & purification ; }, abstract = {Plastispheres, microbial biofilms formed on plastic surfaces, are increasingly recognised as ecological niches capable of transporting pollutants and antibiotic-resistant microorganisms. However, mechanistic insights into antimicrobial resistance (AMR) dynamics in natural plastispheres remain limited, particularly for priority pathogens such as carbapenem-resistant Enterobacterales (CRE). Here, we evaluated plastispheres as environmental reservoirs and vectors of carbapenem-resistant bacteria, comparing wastewater (secondary settling tanks, representing the final stage before environmental discharge) and riverine environments. Using a combined SEM-CFM approach, we resolved plastic surface topography and the spatial organisation of biofilm-associated bacteria. Although CRE were not detected, carbapenem-resistant bacteria constituted a stable fraction of heterotrophic communities in both environments and were primarily associated with intrinsic resistance mechanisms. Carbapenem-resistant isolates included Aeromonas spp. (blaCphA), Stenotrophomonas maltophilia (blaL1), and Pseudomonas putida (efflux-based resistance). Microscopy revealed dense bacterial clusters on plastic surfaces, suggesting microenvironments that may facilitate cell-cell interactions, including horizontal gene transfer. These findings highlight plastispheres not only as vectors of AMR but also as potential evolutionary hotspots shaping resistance persistence and dissemination in aquatic systems. Future integrating metagenomic and genomic data on resistance gene mobility with spatially resolved microbial community structure will provide critical insights into the mechanisms and risks of AMR dissemination in plastisphere environments.}, } @article {pmid42059388, year = {2026}, author = {Mejia, ME and Bowman, S and Lee, J and El-Halwagi, A and Ferguson, K and Maliekel, M and Zhou, Y and Serchejian, C and Robertson, CM and Ballard, MB and Lu, LB and Khan, S and Oladunjoye, OO and Huang, S and Agarwal, SK and Patras, KA}, title = {A cross-sectional analysis of the vaginal microenvironment in rheumatoid arthritis.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0360225}, pmid = {42059388}, issn = {2165-0497}, support = {AI157981/NH/NIH HHS/United States ; AI167538/NH/NIH HHS/United States ; DK128053/NH/NIH HHS/United States ; GM136554/NH/NIH HHS/United States ; NGP10103//Burroughs Wellcome Fund/ ; //Baylor College of Medicine/ ; }, mesh = {Humans ; Female ; *Arthritis, Rheumatoid/microbiology/immunology ; *Vagina/microbiology/immunology ; Adult ; Middle Aged ; Cross-Sectional Studies ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Cytokines ; *Bacteria/classification/genetics/isolation & purification ; Adolescent ; Young Adult ; Rheumatoid Factor ; C-Reactive Protein/analysis ; Anti-Citrullinated Protein Antibodies/analysis ; }, abstract = {The human microbiota is implicated in the development and progression of rheumatoid arthritis (RA). Given the increased RA burden in women and well-known correlations between the vaginal microbiota and local inflammation, we seek to understand the vaginal microenvironment in the context of RA pathology. Self-collected vaginal swabs and questionnaires on dietary, menstrual, and health information were obtained from 36 RA and 50 demographically-matched control women, 18-63 years of age. Medication regimen, along with disease activity and severity, was captured for the RA cohort. Vaginal swabs were subjected to long-read 16S rRNA gene sequencing, multiplex cytokine analyses, and quantification of rheumatoid factor, C-reactive protein, and anti-citrullinated protein antibodies (ACPAs). Vaginal microbial richness and Peptoniphilus and Prevotella, among other rare taxa, were elevated in RA versus control samples. Vaginal interleukin (IL)-18 and epidermeal growth factor (EGF) levels were increased in the RA group; IL-18 correlated with multiple microbial features, whereas EGF levels were not associated with bacterial composition or other host factors. When faceted by diet and menopausal status, several immune markers were increased in the RA vaginal environment. Vaginal ACPAs were higher in the RA group and positively correlated with Streptococcus and multiple vaginal inflammatory cytokines. We describe vaginal microbial and immunological differences in women with RA, particularly when accounting for diet and menopausal status, and disease activity and severity. This work opens a new avenue in the multidisciplinary approach to RA patient care.IMPORTANCERheumatoid arthritis (RA) is a debilitating autoimmune disease that disproportionately impacts women. Although it is widely recognized that microbial factors can trigger or aggravate RA symptoms and alter disease progression, it is unknown whether RA impacts the microbiota and immune responses within the vaginal tract. In this study, we compare the vaginal microbial communities and immune (cytokine) profiles in women with RA and healthy controls. Within RA patients, we also evaluate how these factors relate to clinical RA symptoms, RA biomarkers, and RA-related medications. Overall, we found that RA was associated with increased microbial diversity and multiple inflammatory markers, some of which were also associated with RA biomarkers and disease activity. These findings suggest that the vaginal tract may be an additional tissue impacted by RA disease, and further research is needed to understand mechanisms and potential for therapeutic intervention.}, } @article {pmid42059394, year = {2026}, author = {Murphy, MM and Pinnell, LJ and Doster, E and Wolfe, CA and Baker, LA and Machado, VS and Morley, PS}, title = {Early-life development of the microbiome and resistome in antibiotic-naïve dairy calves.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0251025}, pmid = {42059394}, issn = {2165-0497}, support = {AP19VSCEAH00C014//U.S. Department of Agriculture/ ; //Texas A&M University/ ; }, mesh = {Animals ; Cattle/microbiology ; Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Female ; *Gastrointestinal Microbiome/drug effects ; Weaning ; *Drug Resistance, Bacterial ; Texas ; Dairying ; *Microbiota/drug effects ; }, abstract = {This study aimed to characterize early-life changes in the fecal microbiome and resistome of calves. Fecal samples were collected from 49 Holstein heifers born and raised at a large organic dairy in Texas without antimicrobial drug exposures. Samples were collected from five age groups: early pre-weaning at 2-3 days old (Pre 1), late pre-weaning at 5 weeks old (Pre 2), prior to weaning at 12-13 weeks old (Pre 3), post-weaning in group hutches at 12-13 weeks old (Post 1), and later post-weaning at 13-14 weeks old (Post 2). Fecal samples were analyzed using 16S rRNA gene sequencing to characterize microbial communities and target-enriched shotgun sequencing to characterize antimicrobial resistance genes in the resistome. Richness of microbial communities increased as calves aged through the Pre 1, 2, and 3 samplings, before plateauing in the Post 1 and 2 groups. Diversity also increased in the Pre 1 and 2 groups, remaining similar thereafter. In contrast, resistome richness and diversity decreased during early life and then stabilized at around 5 weeks of age (Pre 2). Changes in microbial community structures were dramatic during the first 12 weeks, largely due to a significant decrease in the relative abundance (RA) of Pseudomonadota (Proteobacteria) and an increase in the RA of Bacillota (Firmicutes) and Bacteroidota. The resistome changed with an increased RA of tetracycline resistance genes, while drug and biocide resistance genes decreased. The apparent stabilization of microbial community features after 12 weeks of age may reflect a period when gut microbiome structure begins to establish greater stability.IMPORTANCEEarly-life development of the gut microbiome can have lasting effects on animal health, immune maturation, and productivity. Using 16S rRNA gene sequencing together with target-enriched metagenomic sequencing, we provide an in-depth characterization of the fecal microbiome and resistome of antibiotic-naïve dairy calves during early life. We demonstrate that microbiome diversity increased with age while resistome diversity decreased, revealing distinct temporal trajectories and suggesting ecological succession as a potential driver of resistance gene dynamics independent of antimicrobial drug exposure. Major resistome features appeared to stabilize earlier than overall microbiome structure, highlighting critical windows in early development when resistance gene composition may be most dynamic. These findings establish an important baseline for interpreting microbiome-resistome interactions and for evaluating how management practices and antimicrobial exposures may influence calf health and antimicrobial resistance ecology in dairy production systems.}, } @article {pmid42059571, year = {2026}, author = {Čepić, A and Rausch, P and Geese, T and Dempfle, A and Grassl, GA and Baines, JF}, title = {Host genetics shapes the recovery of the gut microbiome after antibiotic treatment: the role of the blood group related B4galnt2 gene.}, journal = {mSystems}, volume = {11}, number = {5}, pages = {e0164025}, pmid = {42059571}, issn = {2379-5077}, support = {EXC 2167/2 - 390884018//Deutsche Forschungsgemeinschaft/ ; 237291755//Deutsche Forschungsgemeinschaft/ ; FOR 5042 - 426660215//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; *Anti-Bacterial Agents/pharmacology ; Mice ; Streptomycin/pharmacology ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/genetics/microbiology ; Mice, Knockout ; Male ; Mice, Inbred C57BL ; Metagenomics ; }, abstract = {UNLABELLED: The intestinal microbiota is integral to host health, metabolism, and colonization resistance. Antibiotics can disrupt microbial homeostasis, leading to dysbiosis and altered colonization resistance. While antibiotic-induced microbiota disruption is well-documented, less is known about how host genetics shapes post-antibiotic recovery. Here, we investigate the impact of B4galnt2, a blood-group-related glycosyltransferase gene, on microbiota recovery following antibiotic treatment. Using a longitudinal, multi-omic approach-including 16S rRNA gene sequencing, metagenomics, and metatranscriptomics-we compare the microbiota dynamics of B4galnt2[+/-] and B4galnt2[-/-] mice after treatment with streptomycin, kanamycin, and vancomycin. Our findings reveal that B4galnt2[-/-] mice exhibit faster recovery of microbial diversity and composition following streptomycin treatment compared to their B4galnt2[+/-] counterparts. This accelerated recovery is associated with higher relative abundance of taxa such as Blautia, Dorea, and other Lachnospiraceae, and increased expression of motility-related genes, and differential regulation of antibiotic resistance genes (ARGs), including the aminoglycoside nucleotidyltransferase genes aadA and aadE. Genotype-dependent differences in recovery were most pronounced following streptomycin and were not consistently observed with kanamycin or vancomycin, indicating an antibiotic-by-genotype interaction shaped by the B4galnt2-associated microbiota. These results underscore the role of host genetics in shaping microbiota response and recovery following antibiotic exposure. By demonstrating the interplay between glycosylation-mediated microbiota composition, antibiotic response, and microbial recovery, our study may provide insights into the potential for personalized approaches to mitigate dysbiosis-related health outcomes.

IMPORTANCE: Antibiotic treatments disrupt the gut microbiome, often leading to long-term alterations that potentially affect host health. While much is known about how antibiotics cause microbial dysbiosis, little is understood about the factors that could influence the speed of microbial community recovery, such as host genetic differences. Using a mouse model, this study reveals that genetic variation at the blood group-related B4galnt2 gene significantly alters recovery after streptomycin treatment. Mice lacking intestinal B4galnt2 expression recover faster, with distinct changes in microbial composition, activity, and antibiotic resistance gene expression. These findings highlight how a single host gene can shape microbiota dynamics following antibiotic-induced disruption. The work emphasizes the importance of considering host genetic factors when predicting microbiome responses to antibiotics and suggests potential for genotype-guided strategies to reduce the adverse effects of microbiome-targeted therapies.}, } @article {pmid42059572, year = {2026}, author = {Zhang, J and Wang, X and Wang, D and Zheng, Z and Wang, H and Ma, L}, title = {Advances and future directions in identifying specific taxa from microbial meta-omics data: from pipeline to deep learning.}, journal = {mSystems}, volume = {11}, number = {5}, pages = {e0080025}, pmid = {42059572}, issn = {2379-5077}, support = {42577239, 42277193//National Natural Science Foundation of China/ ; MEER-2024-10//Open Fund of Key Laboratory of Mine Ecological Effects and Systematic Restoration, Ministry of Natural Resources/ ; }, mesh = {*Deep Learning ; *Microbiota/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; Ecosystem ; }, abstract = {Molecular profiling enabled by meta-omics technologies has significantly expanded our knowledge of microbial catalog across diverse environments. Increasing attention has now been focused on identifying ecologically significant taxa, particularly keystone that stabilize communities, rare taxa that underpin functional redundancy, and indicators that reflect environmental gradients. However, current pipeline methods remain limited in deciphering complex ecological relationships and modeling the evolution of community dynamics. As a transformative computational tool, deep learning (DL) offers novel strategies to address these challenges through autonomous feature extraction, nonlinear interaction modeling, and integration of multi-modal data sets. Nevertheless, there are still obstacles to the widespread adoption of DL for collaborative identification of specific microbial taxa, primarily including the intrinsic heterogeneity and imbalance of data sets, the difficulty of model generalization across diverse ecosystems, and the limited ecological interpretability of model outputs. This review summarizes existing research advances and proposes to build a unified DL framework for multi-modal data, exploring its implementation pathways, challenges, and potential coping strategies. The envisioned framework establishes a multi-task learning architecture for unified identification of keystone, rare, and indicator taxa, incorporating domain knowledge through ecological constraint layers and explainable AI modules, while providing flexible implementation pathways for heterogeneous data integration and model customization across microbial ecosystems. This framework has the potential to form a closed-loop verification in combination with synthetic microbial community experiments, reshape the paradigm of microbial community research, and promote the transition from empirical classification to mechanistic ecological cognition.}, } @article {pmid42059616, year = {2026}, author = {Moidu Jameela, R and Kedare, MM and Khan, R and Dhankad, N and Sinha, RK and Zade, A and Shah, S and Chatterjee, A}, title = {Whole genome sequence of Tsukamurella tyrosinosolvens extracted from metagenome of human pleural fluid enriched in Mycobacteria Growth Indicator Tube.}, journal = {Microbiology resource announcements}, volume = {15}, number = {6}, pages = {e0151825}, pmid = {42059616}, issn = {2576-098X}, abstract = {Misdiagnosis of emerging pathogen Tsukamurella tyrosinosolvens is common due to phenotypic similarity with Mycobacterium tuberculosis (MTB). We report a high-quality, near-complete genome of T. tyrosinosolvens from pleural fluid enriched in Mycobacteria Growth Indicator Tube. The genome of this clinically successful strain can be studied to understand pathogenesis and diagnostic challenges.}, } @article {pmid42059625, year = {2026}, author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Spatial ecology of the Capnocytophaga genus in the human oral cavity.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0362625}, pmid = {42059625}, issn = {2165-0497}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; T90 DE026110/DE/NIDCR NIH HHS/United States ; R01 DE03013, R01 DE022586, 2R01 DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Capnocytophaga/genetics/classification/isolation & purification/physiology ; *Mouth/microbiology ; Microbiota ; Phylogeny ; Dental Plaque/microbiology ; Genome, Bacterial ; Metagenomics ; Metagenome ; }, abstract = {UNLABELLED: The human oral microbiome, a complex ecosystem of niche-specific communities influenced by local ecological factors, plays a critical role in health and disease. Capnocytophaga species are prevalent in the human mouth, often abundant in dental plaque and linked to both commensalism and pathogenicity, motivating a detailed study of their ecological and functional diversity. This study employs metapangenomics to reveal Capnocytophaga strain-level distributions and functional adaptations across distinct sites in the human oral cavity. Pangenomic, phylogenetic, and average nucleotide identity analyses enabled classification of unnamed genomes and identified 13 groups, of which 8 include validly named species, and the remainder are named using Human Microbial Taxon (HMT) designations in the Human Oral Microbiome Database (HOMD; https://www.homd.org/). Mapping metagenomic reads to the pangenome revealed a strong preference of most Capnocytophaga genomes for dental plaque (both supra- and subgingival), yet identified strain-level variants of C. sputigena, C. gingivalis, C. granulosa, and C. leadbetteri detected more often on the tongue. Among dental plaque-abundant taxa, functional analyses uncovered two clades: one with cbb3-type cytochrome oxidase that is tied to enhanced denitrification and could help the organism adapt to hypoxic zones, and another with bd-type ubiquinol oxidase, more suited to aerobic metabolism. Carbohydrate and amino acid metabolism pathways also differed between these clades. These findings identify metabolic adaptations that may underlie sub-specialization within the plaque habitat and highlight the strain-level diversity of Capnocytophaga, including low-prevalence strains that are preferentially detected in sites outside the primary plaque habitat of this taxon.

IMPORTANCE: Understanding the ecological roles of Capnocytophaga in the oral microbiome is critical for deciphering its contributions to health and disease, including periodontal and systemic infections. This metapangenomics study reveals a pronounced specialization by Capnocytophaga to dental plaque (including supragingival, subgingival, and periodontal pockets) and identifies metabolic adaptations, such as distinct respiratory, carbohydrate, and amino acid pathways, that may drive niche-specific survival. These findings support the site-specialist hypothesis and enhance our understanding of oral microbial community structure, laying a foundation for future research into microbial interactions and targeted therapies for oral health.}, } @article {pmid42059663, year = {2026}, author = {Liu, C and Mao, Z and Yu, F and Ni, J and Bao, J and Qu, W and Huang, M and Shen, Y and Zheng, S and Chen, Y}, title = {Integrative multi-omics analysis reveals microbiota alterations and clinical indicators predictive of pulmonary fibrosis progression following SARS-CoV-2 infection.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {2}, pages = {}, pmid = {42059663}, issn = {1477-4054}, support = {82300005//National Natural Science Foundation of China/ ; 82072377//National Natural Science Foundation of China/ ; 81971919//National Natural Science Foundation of China/ ; LR23H200002//Zhejiang Provincial Natural Science Foundation/ ; }, mesh = {Humans ; *COVID-19/complications/virology/microbiology ; Male ; *SARS-CoV-2 ; Female ; Middle Aged ; Disease Progression ; *Pulmonary Fibrosis/microbiology/etiology/virology/pathology ; *Microbiota ; Aged ; Gastrointestinal Microbiome ; Bronchoalveolar Lavage Fluid/microbiology ; Transcriptome ; Metagenomics ; Multiomics ; }, abstract = {Pulmonary fibrosis (PF) following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a life-threatening complication. Despite growing concerns about PF after SARS-CoV-2 infection, early recognition remains challenging. Additionally, the role of changes in respiratory and intestinal microbiota in PF progression remains insufficiently understood. To address this gap, this study uses a multi-omics approach to analyze microbiota and clinical changes in PF patients following SARS-CoV-2 infection, developing a predictive model for PF progression with risk stratification to enable early interventions and improve outcomes. A total of 68 patients with confirmed SARS-CoV-2 infection were included in the study, divided into two subgroups: patients with PF (COVID-PF) and patients without PF (COVID-non PF). Metagenomic sequencing of bronchoalveolar lavage fluid (BALF) and fecal specimens was performed to profile respiratory and intestinal microbiota. Peripheral blood mononuclear cells (PBMCs) were collected for transcriptome sequencing. A random forest classifier was developed to predict PF risk based on integrated respiratory-intestinal microbiota profiles as well as clinical indicators. Our findings suggest that there are significant differences in the respiratory and intestinal microbiota between COVID-non PF and COVID-PF patients. Transcriptomic analysis of PBMCs revealed significant activation of immunomodulatory pathways associated with PF development. The machine learning model further allowed early PF risk stratification, demonstrating that changes in both microbiomes, along with clinical indicators, can predict the progression and prognosis of PF. Overall, these results offer new insights into disease and suggest options for early detection and personalized treatment strategies for PF in SARS-CoV-2-infected patients.}, } @article {pmid42059780, year = {2026}, author = {Wolfe, BE}, title = {Metagenomes enriched with Virgibacillus are associated with a pink paste defect in an unpasteurized blue cheese.}, journal = {Microbiology resource announcements}, volume = {15}, number = {6}, pages = {e0002726}, pmid = {42059780}, issn = {2576-098X}, abstract = {Shotgun metagenomes were used to identify microbes associated with a pink discoloration of an unpasteurized blue cheese made in the United States. Taxonomic assessments of individual reads and metagenome-assembled genomes revealed that the genus Virgibacillus was present in the pink paste, but not in unaffected paste.}, } @article {pmid42059891, year = {2026}, author = {Pang, H and Peng, B and Yan, X and Wang, J and Lu, Y and Yuan, X and Zhang, Y and Zhang, L and Huang, J and Zhang, Y and Yang, R and Ma, X and Wang, X and Fan, C and Zhang, L and Song, W and Cheng, Y and Liang, S and Wang, Y and Zheng, W and Li, G}, title = {Pregnancy-induced hypertension are preceded by prenatal perturbations of the gut microbiome and metabolome.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00018-026-06221-1}, pmid = {42059891}, issn = {1420-9071}, support = {2024ZD0532100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; No. Lingjunrencai-02-02//High-level construction project of public health technical personnel in Beijing Municipal Health System/ ; }, abstract = {Pregnancy-induced hypertension (PIH) is a major cause of maternal and perinatal morbidity. However, the longitudinal dynamics of the gut microbiome before clinical onset remain poorly characterized. This nested case-control study within a prospective pregnancy cohort included 75 women who developed PIH and 195 matched controls. Fecal samples collected at early and mid-pregnancy underwent shotgun metagenomic sequencing, integrated with nontargeted plasma metabolomics and clinical data. Compared with healthy pregnancies, women who developed PIH exhibited altered gestational microbiome progression. This was characterized by a persistent enrichment of Bacteroides stercoris and Bacteroides eggerthii. Microbial pathways including amino acid biosynthesis and 2-oxocarboxylic acid metabolism were perturbed before diagnosis, with Bacteroides stercoris as a key contributor. Co-occurrence networks revealed Bacteroides-driven ecological restructuring. Plasma metabolomics identified stage-specific host disturbances. In early pregnancy, glycolytic intermediates were elevated, whereas in mid-pregnancy, bile acid and arachidonic acid metabolism were dysregulated. Notably, these changes included increased cholic acid and decreased pro-resolving mediators such as 15(R)-Lipoxin A4 (15-R-LxA4). These metabolic shifts correlated with microbial features, suggesting microbiota-linked vascular and inflammatory regulation prior to PIH diagnosis. In conclusion, impaired microbiome remodeling and associated metabolic disturbances precede the onset of PIH and may contribute to its development, although causal relationships require further investigation.}, } @article {pmid42060200, year = {2024}, author = {Demirci, T}, title = {Highlighting the Microbial Community of Kuflu Cheese, an Artisanal Turkish Mold-Ripened Variety, by High-Throughput Sequencing.}, journal = {Food science of animal resources}, volume = {44}, number = {2}, pages = {390-407}, doi = {10.5851/kosfa.2023.e59}, pmid = {42060200}, issn = {2636-0780}, abstract = {Kuflu cheese, a popular variety of traditional Turkish mold-ripened cheeses, is characterized by its semi-hard texture and blue-green color. It is important to elucidate the microbiota of Kuflu cheese produced from raw milk to standardize and sustain its sensory properties. This study aimed to examine the bacteria, yeasts, and filamentous mold communities in Kuflu cheese using high-throughput amplicon sequencing based on 16S and ITS2 regions. Lactococcus, Streptococcus, and Staphylococcus were the most dominant bacterial genera while Bifidobacterium genus was found to be remarkably high in some Kuflu cheese samples. Penicillium genus dominated the filamentous mold biota while the yeasts with the highest relative abundances were detected as Debaryomyces, Pichia, and Candida. The genera Virgibacillus and Paraliobacillus, which were not previously reported for mold-ripened cheeses, were detected at high relative abundances in some Kuflu cheese samples. None of the genera that include important food pathogens like Salmonella, Campylobacter, Listeria were detected in the samples. This is the first experiment in which the microbiota of Kuflu cheeses were evaluated with a metagenomic approach. This study provided an opportunity to evaluate Kuflu cheese, which was previously examined for fungal composition, in terms of both pathogenic and beneficial bacteria.}, } @article {pmid42060748, year = {2026}, author = {Xie, F and Jiang, C and Li, Z and Feng, J and Yan, X and Hu, C and He, J and Chai, X and Huang, Z and Xu, Q and Wang, Y and Xiao, Y and Chen, K and Qin, W and Xiao, Y and Zhang, J and Wang, G and Jin, W and Guo, K and Lin, L and Liu, Y and Gao, X and Zheng, L and Shu, X and Wang, R and Wang, M and Si, H and Du, R and Zhu, W and Guan, LL and Wang, W and Qiu, Q and Mao, S and Xiong, J and Miao, W}, title = {Rumen ciliates modulate methane emissions in ruminants.}, journal = {Science (New York, N.Y.)}, volume = {392}, number = {6797}, pages = {eadv4244}, doi = {10.1126/science.adv4244}, pmid = {42060748}, issn = {1095-9203}, mesh = {Animals ; Cattle/microbiology ; Female ; *Ciliophora/classification/genetics/metabolism ; *Greenhouse Gases/metabolism ; Hydrogen/metabolism ; Hydrogenase/metabolism/genetics ; Metagenome ; *Methane/biosynthesis/metabolism ; Oxygen/metabolism ; *Rumen/microbiology ; *Genome, Microbial ; }, abstract = {Rumen ciliates are major contributors to enteric methane emissions from ruminant animals, yet the underlying mechanisms remain poorly understood. We present a catalog of 450 rumen ciliate genomes, with 87% newly generated. Using this resource, we quantified methane emissions from 100 cows and analyzed 1877 rumen metagenomic and metatranscriptomic datasets, which revealed correlations among ciliate abundance, methanogen abundance, and methane emissions. We further demonstrated that taxon-specific effects of rumen ciliates on methane production arise from a single-membrane, hydrogen-producing organelle called the hydrogenobody (HB), which is distinct from canonical hydrogenosomes in other protists. HBs are positioned near ciliary basal bodies and harbor specific hydrogenases and oxygen reductases. We found that Vestibuliferida ciliates, which have more abundant HBs than do Entodiniomorphida, exhibit enhanced hydrogen production and oxygen-scavenging capacity, thereby strongly promoting methanogenesis.}, } @article {pmid42060822, year = {2026}, author = {Poretsky, RS and Dhiman, VK and Hendricks, DL and Lin, CY and Sanchez Gonzalez, D and Greenwald, S and Owens, SM and Williams, CH and Leslie, MT and Bemis, K and Frias, M and Kaufman, JT and O'Connor, DH and Johnson, MC}, title = {Detection of a Single Measles Infection Using Untargeted Ultra-Deep Metagenomic Sequencing of Wastewater in Cook County, Illinois.}, journal = {NEJM evidence}, volume = {5}, number = {6}, pages = {EVIDpha2600079}, doi = {10.1056/EVIDpha2600079}, pmid = {42060822}, issn = {2766-5526}, mesh = {Humans ; Illinois ; *Wastewater/virology ; *Measles virus/genetics/isolation & purification ; *Measles/diagnosis ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; }, abstract = {AbstractMeasles is a contagious, vaccine-preventable viral disease that can be shed into wastewater by infected individuals. In September 2025, as part of an ongoing, nontargeted, ultra-deep metagenomic sequencing effort of wastewater in Cook County, Illinois, we detected measles reads from a facility serving more than 1 million people. Out of more than 900 million reads sequenced from wastewater collected on September 14, 2025, 43 matched measles virus genotype B3. Subsequent genomic analysis linked these reads to a confirmed measles infection that was present in the community on that day, demonstrating that untargeted metagenomics appeared to detect a single measles infection in a large municipal wastewater stream.}, } @article {pmid42060994, year = {2026}, author = {Huang, D and Sun, X and Lin, W and Lan, X and Tan, Z and Ren, Y and Huang, Y and Cao, Y and Sun, W}, title = {Hydrogen oxidation coupled to dissimilatory arsenate reduction: A potentially widespread pathway associated with arsenic mobility in anoxic sediments.}, journal = {Water research}, volume = {301}, number = {}, pages = {125984}, doi = {10.1016/j.watres.2026.125984}, pmid = {42060994}, issn = {1879-2448}, mesh = {Oxidation-Reduction ; *Hydrogen/metabolism/chemistry ; *Arsenates/metabolism ; *Geologic Sediments/microbiology/chemistry ; *Arsenic/metabolism ; Water Pollutants, Chemical/metabolism ; Anaerobiosis ; Phylogeny ; Bacteria/metabolism/genetics ; }, abstract = {In aquatic environments, the arsenic (As) mobilization from anoxic sediments is an important process affecting water quality and associated health risks, as sediment-bound As can serve as a persistent secondary source to overlying waters and groundwater systems. Dissimilatory arsenate reduction (DAsR) is a key microbial process releasing dissolved As(III), yet the role of inorganic electron donors in this pathway remains poorly constrained. Although hydrogen (H2) is thermodynamically favorable for arsenate respiration, its role in arsenate reduction in natural sediments remains insufficiently resolved. In this study, hydrogen oxidation coupled to arsenate reduction (HOAsR) was investigated using sediments from an As-contaminated, mining-impacted river system. Microcosm incubations showed that H2 amendment stimulated As(V) reduction under anoxic conditions. DNA-stable isotope probing combined with metagenomics identified Sulfuritalea, Dechloromonas, and a Moorellia-related lineage as putative HOAsR-associated populations. Corresponding metagenome-assembled genomes encoded both H2 uptake [NiFe]-hydrogenases and the dissimilatory arsenate reductase gene (arrA). Comparative genome analysis further revealed that ∼75% of arrA-containing genomes harbor H2 uptake [NiFe]-hydrogenases, suggesting that H2 oxidation represents a phylogenetically widespread metabolic trait among DAsR bacteria. Analysis of public riverine metagenomes further indicated that HOAsR-associated genetic configurations are broadly distributed across sediment microbial communities. Together, these results indicated that HOAsR is a biologically plausible and geographically widespread potential pathway contributing to arsenic mobilization in anoxic sediments.}, } @article {pmid42061080, year = {2026}, author = {Chen, C and Hao, H and Hao, R and Yu, N and Li, X}, title = {Microbial driving mechanisms of sludge reduction in modular wastewater treatment systems under surplus aeration regulation.}, journal = {Journal of environmental management}, volume = {406}, number = {}, pages = {129816}, doi = {10.1016/j.jenvman.2026.129816}, pmid = {42061080}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; *Wastewater/microbiology ; *Waste Disposal, Fluid/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The treatment and disposal of residual sludge pose a critical bottleneck to the sustainable development of wastewater treatment plants (WWTPs). Modular wastewater treatment systems have garnered significant interest due to their high efficiency and operational flexibility, making them well-suited for small-scale community applications. This study aims to investigate the microbial driving mechanisms underlying sludge reduction in such field-based systems under surplus aeration regulation. By comparing treatment performance, microbial community structure, and metabolic functions between the Surplus Aeration (SA) group and the Conventional (Conv.) group-coupling 16S rRNA high-throughput sequencing and metagenomic analysis -the microbiological basis of sludge reduction was systematically elucidated. Results demonstrated that the SA group achieved a 63.7% reduction in residual sludge while maintaining compliant effluent quality (GB 18918-2002), with COD and NH4[+]-N removal rates both reaching more than 85%. 16S rRNA profiles indicated higher alpha diversity in the SA group and clear community separation from the Conv. group (PERMANOVA, p < 0.001). The SA group was enriched in taxa with documented extracellular polymeric substance (EPS) degradation potential, including Saccharimonadales, Saprospiraceae, and Caldilineaceae, whereas the Conv. group showed relatively higher abundance of taxa often associated with proliferation and EPS production (e.g., OLB17, Acinetobacter). Metagenomic functional annotation suggested higher representation of genes and pathways related to carbohydrate processing and energy metabolism in the SA group. As these omics results primarily reflect functional potential rather than confirmed in situ activity, we present a conceptual mechanism in which surplus aeration improves DO distribution and substrate utilization in the field system, thereby favoring EPS breakdown and energy-use efficiency-consistent with the observed reduction in sludge yield.}, } @article {pmid42061404, year = {2026}, author = {Su, Q and Chen, S and Lau, LH and Lui, RN and Wang, Y and Xu, Z and Cheung, CP and Ching, JYL and Shen, X and Peng, Y and Tun, HM and Ianiro, G and Rubin, D and Chang, EB and Chan, FKL and Ng, SC}, title = {Artificial intelligence-driven donor-recipient gut microbiome matching for optimized fecal microbiota transplantation.}, journal = {Cell reports}, volume = {45}, number = {5}, pages = {117301}, doi = {10.1016/j.celrep.2026.117301}, pmid = {42061404}, issn = {2211-1247}, mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; *Artificial Intelligence ; *Gastrointestinal Microbiome/genetics ; *Tissue Donors ; Female ; Metagenome ; Male ; }, abstract = {Fecal microbiota transplantation (FMT) has emerged as a promising therapy for gastrointestinal diseases, yet its clinical efficacy remains individually variable. Here, we analyze multi-kingdom and functional profiles in pre- and post-FMT metagenomes from 515 FMTs across 30 cohorts and 12 diseases, in which 94 metagenomes from 44 FMTs are newly collected. We reveal a robust association between clinical efficacy and post-FMT microbiome convergence of recipients toward donors, across diseases. To predict post-FMT microbial convergence, we develop MOZAIC (Microbiome Matching Optimization via Artificial Intelligence), a framework that integrates multi-dimensional donor-recipient microbiota features. MOZAIC achieves an average area under the curve (AUC) of 0.88 and accuracy/recall >0.80 in forecasting microbiome convergence, with 78.7% accuracy in predicting clinical outcomes, and retrospectively simulates a 1.44-fold improvement (from 49.4% to 71.0%) in clinical response rates over baseline. This study establishes microbiome convergence as a key mediator of FMT and provides a scalable tool for precision matching in microbiota-based therapies.}, } @article {pmid42061651, year = {2026}, author = {Neuhaus, S and Tausch, SH and Gulich, K and Körber, N and Grützke, J and Hensel, A and Dahouk, SA and Dieckmann, R}, title = {Kitchen Sponges as Reservoirs of Foodborne Pathogens: Microbial Growth Dynamics, Surface Cross-Contamination, and Hygiene Implications.}, journal = {Journal of food protection}, volume = {89}, number = {6}, pages = {100794}, doi = {10.1016/j.jfp.2026.100794}, pmid = {42061651}, issn = {1944-9097}, mesh = {Staphylococcus aureus/growth & development ; Humans ; Colony Count, Microbial ; Salmonella enteritidis/growth & development ; Escherichia coli/growth & development ; Food Contamination/analysis ; Food Microbiology ; Hygiene ; }, abstract = {Foodborne pathogens pose a persistent risk to public health, with domestic environments representing a major but often underestimated source of contamination. In this study, we investigated the survival, proliferation, and transfer potential of Salmonella Enteritidis, Escherichia coli, and Staphylococcus aureus in kitchen sponges harboring an established core microbiota. Using culture-based, metagenomic, and fluorescence in situ hybridization approaches in combination with confocal laser scanning microscopy, we examined pathogen persistence, desiccation tolerance, cross-contamination potential, and spatial microbial organization over 14 days. All three pathogens persisted within the sponge matrix for at least 2 weeks, even at very low initial populations (approximately 2,5 log10 colony-forming units (CFU) per sponge section). Escherichia coli and Salmonella Enteritidis rapidly established stable populations reaching approximately 9 log CFU per sponge section, whereas S. aureus showed limited growth of approximately 4 log CFU per sponge section, indicating species-specific interactions with the resident microbiota. Notably, pathogen populations remained stable after 3 days of desiccation, confirming the role of sponges as long-term microbial reservoirs. Contact between colonized sponges and surfaces under mild pressure resulted in transfer of up to 5 log CFU to contacted surfaces, highlighting realistic domestic transmission pathways. Sensory changes such as odor or discoloration were not correlated with microbial load, indicating that visual assessment is unreliable for sponge replacement decisions. These results underscore the role of kitchen sponges as critical microbial reservoirs in households and emphasize the need for regular sponge replacement or the use of alternative cleaning utensils. The standardized sponge model developed in this study provides a valuable platform for evaluating sanitation strategies and for understanding microbial interactions relevant to domestic hygiene and public health.}, } @article {pmid42061790, year = {2026}, author = {Zhang, Y and Zhang, G and Liang, J and Chang, J and Zhang, P and Fang, W and Wang, Q}, title = {Regulation of greenhouse gas emissions and carbon sequestration in wetland by submerged plant mowing time and potential mechanisms.}, journal = {Environmental research}, volume = {302}, number = {}, pages = {124621}, doi = {10.1016/j.envres.2026.124621}, pmid = {42061790}, issn = {1096-0953}, mesh = {*Wetlands ; *Greenhouse Gases/analysis/metabolism ; *Carbon Sequestration ; Methane/metabolism/analysis ; *Magnoliopsida/metabolism/physiology ; Carbon Dioxide/metabolism/analysis ; Nitrous Oxide/metabolism/analysis ; }, abstract = {Mowing is an important submerged plant growth management measure to maintain the balance of inland wetland ecosystems. However, systematic studies on plant mowing time affecting wetland greenhouse gas (GHG) emissions and carbon sequestration remain scarce. In this research a pilot-scale wetland system was established to investigate the effects of submerged plant Ceratophyllum demersum L. mowing time on GHG emissions and carbon sequestration, and metagenomic techniques were employed to explore the functional microorganisms and genes for carbon and nitrogen cycling in wetland. The results showed that C. demersum L. mowing resulted in CO2 flux reduction of 55.76%-79.34%, CH4 flux reduction of 83.54%-99.48%, and N2O flux reduction of 75.80%-82.88%. The optimal plant mowing time was July, achieving abetter trade-off between carbon sequestration and carbon emissions. The C. demersum L. biomass showed obvious temporal dynamics, with the highest biomass for mowing in July, increasing by 12.12% compared with that of control. However, plant mowing slightly reduced the water purification capacity. Microbial analysis revealed that plant mowing downregulated the expression of key functional genes (mcrA, pmoA, norB, nosZ) and decreased the abundance of methanogens and denitrifying bacteria, explaining the reduction in CH4 and N2O fluxes. These findings provide a scientific basis for wetland plant growth management. Future research should explore long-term field validation and effects of environmental variables.}, } @article {pmid42062403, year = {2026}, author = {Radwan, HM and El Menofy, NG and Tharwat, EK and Mysara, M and Radwan, SMR}, title = {Metagenomic profiling of microbial communities and the resistome within Egyptian hospital wastewater and tap water.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42062403}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; Egypt ; *Metagenomics/methods ; Hospitals ; *Drinking Water/microbiology ; Humans ; *Microbiota/genetics ; Water Microbiology ; *Metagenome ; *Bacteria/genetics/classification/drug effects ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Antimicrobial resistance (AMR) is a worldwide health concern that compromises the successful treatment of a growing array of infectious diseases, particularly in low- and middle-income countries. AMR is exaggerated by the spread of antimicrobial resistance genes (ARGs) across humans, animals, and environmental reservoirs like water and soil. Hospital wastewater (HWW) is the main source of antimicrobial resistance in the environment. The current study used high throughput metagenomic nanopore sequencing to investigate the microbial abundance and ARGs associated with both HWW and tap water in five different hospitals in Cairo, Egypt. The bacterial community composition of the HWW microbiome identified 25 taxonomic families. The most abundant genera in HWW were Acinetobacter (6%) and Propioniciclav (5%) out of 101 unique genera while, the most abundant in tap water were Enterococcus (53%), Escherichia (15%), and Francisella (14%) out of 89 unique genera. Alpha diversity analysis revealed significantly greater microbial diversity in the HWW samples than in the tap water samples (P value > 0.05), moreover beta diversity analysis revealed a significant difference in the microbial community composition between the tap water and HWW samples (P value > 0.05) using Chao metric for richness estimation and Shannon metric for richness and evenness estimation. Total ARG analysis revealed absence of ARGs in tap water using the three databases, while comparable levels of ARGs were detected in HWW across the five hospitals. In total, 45, 28, and 28 ARG subtypes were identified in the HWW samples using ResFinder, CARD, and the NCBI AMRFinderPlus databases, respectively. The most abundant AMR mechanisms among the five hospitals were linked to the inhibition of protein synthesis. Using the ResFinder database, streptogramin resistance genes were most prevalent in Hospitals 1 and 5 (15% and 40%, respectively); using CARD, aminoglycoside, lincosamide, and macrolide resistance genes were most predominant (relative abundances 35-60%). Using NCBI AMRFinderPlus, streptomycin, tetracycline, and macrolide resistance genes were most prevalent (relative abundances 30.1-60%). Detection of plasmid replicons in HWW identified 39 different plasmid-associated replication genes via the PlasmidFinder database. The Col440l-1, colRNAI-1 and Col440ll-1 plasmid replicons were the most detected across the five hospitals with relative abundances of 16.6%, 10.9% and 9.6%, respectively. This study revealed different microbial communities among HWW and tap water in addition to the widespread occurrence of ARGs and AMR encoding plasmid replicons in the HWW in the five different hospitals in Cairo, Egypt indicating a significant risk associated with HWW, necessitating the implementation of preventative measures to avert their environmental diffusion. To our knowledge, this is one of the first Egyptian studies to apply Oxford Nanopore long-read metagenomic sequencing for simultaneous profiling of microbial communities and the resistome in HWW and tap water, using three ARG databases across five hospitals in two seasons.}, } @article {pmid42062603, year = {2026}, author = {Xu, T and Yang, Y and Zhu, R and Lin, W and Li, J and Zheng, Y and Zhang, P and Zhang, G and Zhao, G and Jiao, N}, title = {DeepSeMS: revealing the hidden biosynthetic potential of the global ocean microbiome with a large language model.}, journal = {Nature computational science}, volume = {}, number = {}, pages = {}, pmid = {42062603}, issn = {2662-8457}, support = {32470098//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82170542//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92451303//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Microbial-derived secondary metabolites (SMs) hold great therapeutic potential but are predominantly discovered from cultured species, representing only a fraction of microbial biodiversity. Advances in metagenomics have unveiled reservoirs of biosynthetic gene clusters (BGCs), but translating genomic sequences into precise chemical structures remains challenging owing to the structural complexity of cryptic BGCs and the context-dependent substrate tolerance and cross-reactivity of modular biosynthetic domains. Here we present DeepSeMS, a transformer-based large language model that accurately predicts secondary metabolite chemical structures from BGC sequences. By encoding biosynthetic genes as functional domains and leveraging a feature-aligned data augmentation, DeepSeMS outperformed existing methods and successfully generated chemically valid predictions for 96.38% of cryptic BGCs. Applying DeepSeMS to a global ocean metagenome, we characterized over 60,000 secondary metabolites, revealing chemical diversity, ecological specificity and considerable biomedical potential, especially as antibiotics. This study underscores the capability of deep learning-driven approaches in revealing hidden biosynthetic potential of Earth's largest, yet largely unexplored, microbial ecosystem.}, } @article {pmid42062664, year = {2026}, author = {Kieliszek, M}, title = {Selenium: From Redox Signaling to Interactions with the Gut Microbiome.}, journal = {Biological trace element research}, volume = {}, number = {}, pages = {}, pmid = {42062664}, issn = {1559-0720}, abstract = {Selenium is an element that plays a crucial role in the proper functioning of the body. It is a component of selenoproteins, which exhibit strong antioxidant properties. This allows it to neutralize reactive oxygen species and protect cells from oxidative stress. It also plays a crucial role in supporting the proper functioning of the immune system. In this context, particular importance is attributed to its influence on the Th1/Th2 immune response and the activity of T lymphocytes and NK cells. There is a mutual relationship between selenium and the intestinal microbiota. Microorganisms in the gastrointestinal tract participate in the accumulation, transformation, and differentiation of selenium's chemical forms. These processes influence selenium's bioavailability and its activity in the host organism. The development of metagenomic methods has enabled the identification of specific selenium-dependent metabolic pathways within the microbiome. This represents an important research direction in the development of this field of biotechnology. In turn, appropriate selenium levels and selenoprotein activity influence the composition of the intestinal microbiota and the metabolite profile it produces. It is worth emphasizing that in the context of the development of microbiome engineering, there are also emerging concepts of designing probiotics capable of controlled selenium biotransformation. The beneficial properties of selenium for organisms depend on its appropriate chemical form and dose. It is worth noting that selenium deficiency can impair the antioxidant system, leading to a redox imbalance. Such processes can weaken the integrity of the intestinal barrier, leading to the development of various gastrointestinal diseases. Therefore, the interaction with intestinal microflora is such a crucial element of selenium's action. Microorganisms inhabiting the digestive tract participate in the processes of accumulation and transformation of various chemical forms of this element. These biochemical properties of microorganisms are crucial for the bioavailability of selenium in the human body. Therefore, the appropriate form of selenium is crucial for the proper functioning of the intestinal barrier. This article discusses the importance of selenium in redox processes and in the function of the gut microbiota. It highlights the potential role of this element in the prevention and treatment of gastrointestinal diseases. Future research should focus on further understanding these interactions and developing targeted approaches that utilize selenium-dependent pathways to restore intestinal homeostasis.}, } @article {pmid42062918, year = {2026}, author = {Guo, P and Zhang, S and Huang, Z and Zhu, J and Zhang, W}, title = {Potential drug-drug interactions and 30-day mortality in ICU patients with bloodstream infection: a single-center retrospective study.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13426-z}, pmid = {42062918}, issn = {1471-2334}, abstract = {BACKGROUND: Patients in intensive care units (ICUs) with bloodstream infection (BSI) commonly receive multiple antimicrobials and supportive drugs, which increases the likelihood of potential drug-drug interactions (pDDIs). Evidence focused specifically on ICU patients with BSI remains limited.

OBJECTIVES: To describe the prevalence and severity of pDDIs in ICU patients with BSI and to examine whether pDDI exposure was associated with 30-day mortality.

METHODS: We performed a single-center retrospective cohort study of 90 adult ICU patients with an index episode of BSI between January 2019 and December 2024. Time zero was defined as the sampling time of the first qualifying positive blood culture or a clinically accepted positive blood metagenomic next-generation sequencing result for the index episode. Medication administration records, rather than prescription orders alone, were used for pDDI ascertainment. pDDIs were screened with the Micromedex Drug Interactions database (Merative, web-based version updated daily; accessed January 15, 2025). Exposure was defined within a fixed 48-hour window after time zero; a pDDI required actual administration of both interacting agents within the same 24-hour period during this window. Severity was standardized as mild, moderate, or severe. The primary outcome was 30-day all-cause in-hospital mortality. Because only 18 deaths occurred, the primary multivariable model included any pDDI exposure and SOFA score.

RESULTS: Seventy of 90 patients (77.8%) had at least one pDDI within the fixed exposure window. Based on the highest patient-level severity, 13/70 (18.6%) had mild, 22/70 (31.4%) moderate, and 35/70 (50.0%) severe pDDIs. The most frequent combinations were vancomycin plus amikacin (18/90, 20.0%) and piperacillin/tazobactam plus vancomycin (15/90, 16.7%). The clinical consequences listed for common pairs were reference-predicted interaction consequences rather than adjudicated observed toxicities. In the parsimonious multivariable model, any pDDI exposure was associated with higher observed 30-day mortality (adjusted OR 4.23, 95% CI 1.27-14.09; P = 0.02), and each 1-point increase in SOFA score was also associated with mortality (adjusted OR 1.32, 95% CI 1.07-1.64; P = 0.01).

CONCLUSIONS: pDDIs were common in this ICU BSI cohort and were associated with higher observed 30-day mortality. These findings should be interpreted cautiously given the retrospective single-center design, limited event count, residual confounding, and incomplete control of time-dependent exposure. Structured pDDI screening may still support medication safety in critically ill patients.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid42063196, year = {2026}, author = {Liu, Z and Meng, C and Shen, J and Wang, H and Guo, J and Zhao, J and Mu, C and Zhu, W}, title = {Dietary regulation on gut resistome linked with microbial amino acid metabolism in pigs.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42063196}, issn = {2524-4671}, support = {National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; }, abstract = {Dietary protein plays a crucial role in shaping the gut microbiome and modulating intestinal amino acid metabolism. Gut microbiome is recognized as a reservoir for carrying antimicrobial resistance genes. However, the relationship between amino acids metabolism and antibiotic resistome remains poorly understood. Here, a pig model was used to study this relationship by comparing the impact of dietary casein hydrolysate diet with those of an intact casein diet. Metabolomics analysis revealed that casein hydrolysate supplementation primarily altered amino acid metabolism, characterized by significantly reduced levels of several amino acids, including tyrosine and glutamine, accompanied by increased levels of amino acid–derived metabolites. Metagenomics analyses indicated that these metabolic shifts were closely associated with microbial changes in the gut, particularly the genera Escherichia and Bifidobacterium. Consistently, microbial genes related to amino acid transport and metabolism exhibited higher abundances. Notably, the abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were significantly enriched in response to casein hydrolysate supplementation. Integrated metabolome–resistome correlation analyses revealed significant associations between multiple amino acids, including tyrosine and glutamine, and distinct ARG subtypes, indicating a tight coupling between amino acid metabolism and antibiotic resistance potential. Metagenomics binning and assembly further resolved the taxonomic origins of these functional traits. Specifically, in Escherichia fergusonii and Bifidobacterium thermophilum, genes related to amino acid metabolism, ARGs, and MGEs were co-localized on the same contigs with close genomic proximity. Together, these findings highlight a strong link between microbial amino acid metabolism and the resistome, suggesting that dietary casein hydrolysate reshapes both microbial metabolic functions and antibiotic resistance potential within the intestinal ecosystem.}, } @article {pmid42063256, year = {2026}, author = {Liu, Y and Wu, J and Yang, Y and He, Y and Zhou, R and Li, Y and Sun, J and Gong, M and Mei, X and Li, Y and Huang, H and Du, F and Deng, W and Ye, C and He, X and Li, L and Hao, J and Yang, M and Zhu, Y and Zhu, S}, title = {Decoupling the "attract-and-kill" strategy: Independent zoospore attraction and ROS-executed killing synergistically drive disease-suppressive intercropping.}, journal = {Plant communications}, volume = {}, number = {}, pages = {101876}, doi = {10.1016/j.xplc.2026.101876}, pmid = {42063256}, issn = {2590-3462}, abstract = {Soilborne Phytophthora diseases pose a major threat to agricultural sustainability. However, how nonhost roots disrupt the transmission of soilborne Phytophthora pathogens without relying solely on classical antimicrobial exudates remains poorly understood. Through a decade-long field study, we demonstrate that strip intercropping can sustainably suppress disease incidence by up to 46.85% by leveraging nonhost roots as ecological barriers that intercept zoospore transmission. Moving beyond the conventional focus on antimicrobial exudates, we resolve the "attract-and-kill" strategy into two discrete functions: a broad-spectrum attraction function widespread among nonhost plants (13 of 15 genera), which alone reduces disease incidence by 9.2%-24.4%, and a specialized killing function restricted to a few species, such as garlic, in which elevated concentrations of sulfur compounds at the root interface induce cystospore rupture and inhibit germination, delivering 42.9%-49.3% field suppression. The synergy between universal attraction and targeted killing enhances disease suppression at the rhizosphere interface. Mechanistically, killing is executed through a conserved reactive oxygen species-programmed cell death (ROS-PCD) pathway, with pathogen sensitivity determined by intrinsic redox-buffering capacity. Metagenomic profiling further revealed that garlic roots and sulfur compounds are associated with the enrichment of genes involved in microbial motility and apoptosis-related pathways, adding a complementary mechanistic layer to the attract-and-kill framework. We thus propose this ecology-based, two-component strategy for sustainable Phytophthora management in diversified cropping systems.}, } @article {pmid42063433, year = {2026}, author = {Chen, L and Li, J and Liu, X and Chen, X and Li, H and Xie, D and Chen, Y and Yuan, J and Tao, E}, title = {Case Report: Beyond commensal: Staphylococcus epidermidis as a novel cause of NARDS.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1631683}, pmid = {42063433}, issn = {2296-2360}, abstract = {Staphylococcus epidermidis (S. epidermidis), usually a harmless skin bacterium, can become an opportunistic pathogen in newborns, particularly those with risk factors like premature membrane rupture. Although it commonly causes late-onset sepsis, its association with neonatal acute respiratory distress syndrome (NARDS) is rare. This report describes a unique case of NARDS in a full-term newborn caused by S. epidermidis. The infant, born via cesarean at 40 2/7 weeks with a 30.5-hour membrane rupture, developed severe respiratory failure shortly after birth, necessitating mechanical ventilation. Initial treatment with penicillin and cefotaxime was ineffective, and by day 3, the infant's condition worsened, showing respiratory distress, petechial rashes, and high inflammatory markers. Treatment was changed to vancomycin and meropenem, with the addition of intravenous immunoglobulin and two doses of pulmonary surfactant. Metagenomic next-generation sequencing (mNGS) confirmed S. epidermidis in the airway secretions. The patient was discharged after 19 days with a diagnosis of NARDS, intrauterine infectious pneumonia, neonatal air leak syndrome, type II respiratory failure, neonatal sepsis, and congenital heart defects. In conclusion, S. epidermidis is a novel pathogen capable of causing NARDS in high-risk infants with prolonged membrane rupture. The proposed mechanisms-including surfactant dysfunction and biofilm-associated virulence-are supported by experimental literature and are consistent with the clinical phenotype observed in our patient, though direct confirmation requires further study. Notably, skin symptoms like erythematous rash and petechiae may indicate invasive S. epidermidis infection, especially in cases of respiratory distress with skin symptoms following premature rupture of membranes. Moreover, mNGS is vital for pathogen identification when traditional cultures fail.}, } @article {pmid42063498, year = {2026}, author = {Xiang, L and Wang, X and Wen, M and Wang, X and Zhang, Y and Tian, W and Liu, M and Zhang, W}, title = {Metagenomic insights into the rhizosphere microbiome dysbiosis associated with tobacco bacterial wilt.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809980}, pmid = {42063498}, issn = {1664-302X}, abstract = {Tobacco bacterial wilt, caused by Ralstonia solanacearum, threatens global tobacco production. While the rhizosphere microbiome defends against soil-borne pathogens, mechanisms underlying how bacterial wilt reshapes microbial community structure, function, and ecological interactions remain poorly understood. Here, we employed metagenomic sequencing to investigate taxonomic and functional alterations in the rhizosphere microbiome of symptomatic (S) and asymptomatic (A) tobacco plants across two locations (Fenggang and Bozhou), establishing four groups: FA, FS, BA, and BS. Quality control of sequencing data showed no technical bias between groups (p > 0.05). Contrary to the paradigm that pathogen invasion reduced microbial diversity, alpha diversity analysis revealed higher species richness (Sobs) in symptomatic soils, whereas community evenness (Shannon and Simpson indices) remained unchanged, suggesting selective reshuffling rather than microbiome collapse. Beta-diversity analysis revealed significant compositional shifts associated with disease status (PERMANOVA, R [2] = 0.713, p = 0.001), with symptomatic communities displaying greater heterogeneity. Taxonomic profiling revealed consistent enrichment of the pathogen R. solanacearum and opportunistic bacteria (including Stenotrophomonas and Pseudomonas) in symptomatic rhizospheres, concomitant with depletion of putative beneficial taxa (Candidatus_Solibacter, Luteitalea, and Metarhizium). Functional annotation indicated a metabolic shift from homeostatic maintenance to stress adaptation and pathogenicity. Symptomatic soils exhibited significant enrichment of virulence factors, including motility and secretion system genes, microbial defense mechanism genes (COG), and antibiotic resistance genes (CARD). Additionally, increased abundance of carbohydrate-active enzymes (CAZy)-particularly glycoside hydrolases-suggested intensive nutrient acquisition from decaying tissues. Co-occurrence network analysis revealed that asymptomatic communities formed denser, competition-driven networks characterized by a higher proportion of negative correlations. Disease destabilized these networks by reducing connectivity and, crucially, rewired interactions of R. solanacearum from negative to positive associations with taxa such as Sphingobium, thereby reflecting erosion of competitive constraints and pathogen incorporation into cooperative networks. Our findings revealed that bacterial wilt drove multi-layered dysbiosis, encompassing pathogen-driven taxonomic selection, functional shifts toward stress adaptation and intensified competition, and collapse of stable antagonistic networks associated with plant health. This study provided mechanistic insights into microbiome-mediated disease progression and identified specific microbial taxa and network properties as candidate targets for ecological disease management and early diagnostic indicators.}, } @article {pmid42063509, year = {2026}, author = {González de Figueras, C and Gómez, S and Lamprecht-Grandío, M and Mirete, S and Díaz-Rullo, J and Martínez-Rodríguez, P and Sánchez-Costa, M and González-Pastor, JE}, title = {Enhancing UV-C and perchlorate resistance in Arabidopsis thaliana through the introduction of microbial genes from hypersaline environment.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1789302}, pmid = {42063509}, issn = {1664-302X}, abstract = {Ultraviolet (UV) radiation reaching the Earth's surface affects all living organisms. Recent reports show a trend of increasing exposure levels due to stratospheric ozone depletion and contamination. UV-B radiation (280-315 nm), previously largely absorbed by the ozone layer, now reaches the surface in higher doses, posing a particular threat to plants, which are sessile organisms and cannot escape adverse conditions. The intrinsic protective and repair mechanisms in plants may be insufficient to counteract this increase, potentially impacting crop productivity, distribution, and quality, with serious implications for agriculture and ecological stability. This study aims to enhance plant resistance to UV radiation by introducing genes derived from extremophilic microorganism, which have previously shown to confer UV-protective effects in UV resistance to a radiation-sensitive Escherichia coli strain (recA mutant). Extremophile microorganisms have been discovered in high-irradiation environments, such as hypersaline lakes, where survival relies on unique genetic adaptations. In our laboratory, four genes were selected from metagenomic libraries derived from high-altitude hypersaline lakes in Argentina (Diamante and Ojo Seco, at 4,589 m and 3,200 m respectively) and from the Es Trenc salt flat (Mallorca, Spain). Based on these promising results, the genes were introduced into Arabidopsis thaliana to evaluate their potential to enhance UV-B tolerance in plants. The selected genes included one encoding a TATA-box binding protein, and three hypothetical proteins. Each gene was independently transformed into Arabidopsis thaliana lines and subjected to UV-B and UV-C irradiation (4.5 kJ·m[-2]), with UV-C (100-280 nm) ultimately chosen for its higher damaging potential to test the limits of plant tolerance. Additionally, cross-resistance was evaluated using sodium perchlorate, a common soil contaminant and oxidative stressor. Plants were exposed to concentrations between 3.67 and 7.34 g/L, exceeding those used in previous studies. As a result, the plants obtained were more resistant to UV radiation and were also capable of growing in environments containing higher levels of perchlorate in the growth medium. Thus, the expression of these genes in the plant appears to contribute to enhanced stress resistance.}, } @article {pmid42063777, year = {2026}, author = {Zhu, M and Sun, C and Zhang, Y and Na, Y and Wang, Y and Zhao, Q and Gu, Y}, title = {Blepharitis driven by microbiome dysbiosis and Demodex infestation: possible pathogenic mechanisms.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1801375}, pmid = {42063777}, issn = {2296-858X}, abstract = {Blepharitis is a chronic inflammation of the eyelid margin that is mediated by the immune system. It is one of the common ocular surface diseases and often leads to serious sequelae that threaten vision, such as dry eye syndrome due to insufficient tear secretion, corneal neovascularization, and stubborn chalazion. Elucidating its precise etiology is therefore imperative. Emerging high-throughput sequencing and metagenomic analyses have unveiled a quantitative and qualitative disruption of the periocular microbiome (dysbiosis), characterized by the expansion of specific bacterial species such as Staphylococcus aureus, coupled with episodic blooms of Demodex. These perturbations are no longer considered epiphenomena. In this review, we reveal the possible mechanisms of the role of blepharitis and microbiota dysbiosis.}, } @article {pmid42063778, year = {2026}, author = {Wu, S and Wu, M and Li, W and Zhang, C and Bi, Y and Fan, Y and Xu, Y and He, D}, title = {Case Report: Diagnosis of leptospirosis presenting as aseptic meningitis using metagenomics CAPture sequencing.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1734396}, pmid = {42063778}, issn = {2296-858X}, abstract = {BACKGROUND: Leptospirosis is a globally prevalent zoonotic disease caused by pathogenic Leptospira species. The manifestation of leptospirosis can range widely, from being asymptomatic to causing severe multi-organ failure with a high mortality rate. It is uncommon for leptospirosis to present primarily with neurological complications. In this context, we discuss a notable case of Leptospira borgpetersenii infection manifesting as aseptic meningitis in China.

CASE PRESENTATION: In this study, we describe a primary case of neuroleptospirosis leading to symptomatic aseptic meningitis following exposure to Leptospira borgpetersenii. Initially managed for viral meningitis, the diagnosis of leptospirosis was subsequently confirmed through cerebrospinal fluid (CSF) analysis using metagenomic next-generation sequencing (mNGS) and Metagenomics CAPture Sequencing (MetaCAP), both of which identified Leptospira borgpetersenii. Following a course of antibiotics and methylprednisolone therapy, the patient fully recovered.

CONCLUSION: This case underscores the importance of considering leptospirosis in differential diagnoses for aseptic meningitis, especially in individuals with occupational risks related to water or animal exposure. MetaCAP's extensive coverage, sensitivity, and early pathogen detection capabilities can significantly enhance patient outcomes.}, } @article {pmid42063908, year = {2026}, author = {Kateete, DP and Lubega, C and Nasinghe, E and Mbabazi, M and Galiwango, R and Jjingo, D}, title = {Gut microbial profiles of COVID-19 patients in Uganda.}, journal = {African health sciences}, volume = {26}, number = {1}, pages = {1-15}, pmid = {42063908}, issn = {1729-0503}, mesh = {Humans ; *COVID-19/microbiology/epidemiology ; Uganda/epidemiology ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; Middle Aged ; SARS-CoV-2 ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Bacteria/isolation & purification/genetics ; }, abstract = {BACKGROUND: The role of the microbiome in COVID-19 outcomes remains an area of exploration. We comprehensively explored the gut microbiome of Ugandan COVID-19 patients and inferred potential implications.

METHODS: Stool and demographic data were collected from 100 COVID-19 confirmed cases at the covid isolation and treatment centers in Kampala during the first and second waves of the pandemic in Uganda (2020 and 2021, respectively). 16S rRNA sequencing was performed on the DNA extracted from stool, followed by bioinformatics analysis. Machine-learning techniques were used to determine microbes that were associated with disease severity.

RESULTS: We observed differences in microbial composition between COVID-19 patients and healthy controls. Pathogenic bacteria such as Klebsiella oxytoca, Salmonella enterica and Serratia marcescens had an increased presence in COVID-19 disease states, especially severe cases. Additionally, there was an increase in opportunistic pathogens like Enterococcus species, along with a decrease in beneficial microbes, such as Alphaproteobacteria, when comparing mild and severe cases. Machine-learning identified age and microbes like Ruminococcaceae, Bacilli, Enterobacteriales, porphyromonadaceae and Prevotella copri as predictive of severity.

CONCLUSION: The microbiome likely plays a role in the dynamics of SARS-CoV-2 infection in Ugandan patients. The shift in abundance of specific microbes can moderately predict severity of COVID-19 in this population.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid42064023, year = {2026}, author = {Liu, Y and Wang, W and Peng, Y and Feng, L and Li, C and Zhang, Z and Zhao, J and Yang, C and Mu, T and Wang, J and Li, C and Yang, C}, title = {Sources of Microbial and Organic Contaminants in the Production of Soybean Whey Protein for Feed and Potential Food Applications.}, journal = {Food science & nutrition}, volume = {14}, number = {5}, pages = {e71709}, pmid = {42064023}, issn = {2048-7177}, abstract = {Soybean whey wastewater (SWW), a rich source of soybean whey protein (SWP), is prone to microbial rancidity, posing environmental and resource challenges. This study explores the causes of rancidity-characterized by a pungent, sour, and putrid odor-in the effluents of sealed buffer tank during SWP recovery via pneumatic flotation. Metagenome, bacterial diversity, and HPLC analyses showed the obligate anaerobe Megasphaera spp. dominated rancid effluents (up to 44% abundance), consumed lactate (decreasing from 10.2 g/L in influent to 2.7 g/L in effluent), and produced malodorous propionate and butyrate (up to 3.6 and 4.3 g/L, respectively). Three mitigation strategies were assessed: (1) full-scale high-throughput aeration-likely effective but energy- and cost-intensive; (2) local aeration-low-cost but weakly inhibitory; and (3) microbial intervention using the probiotic Enterococcus faecium LBSW, which colonizes the buffer tank, with localized aeration used only if microbial control fails. Strategy (3) was adopted for its energy and cost efficiency, successfully reducing pollution and supporting SWP recovery. Although the biosafety of E. faecium LBSW in food applications requires caution, the recovered SWP is primarily intended for animal feed, and subsequent high-temperature drying and sterilization (> 120°C) also offer potential for food-grade use.}, } @article {pmid42064333, year = {2026}, author = {Reider, KE and Fannin, C and Hannah, KA and Gelona, AR and Anderson, C and Barnard-Kubow, K and Enke, RA}, title = {16S rRNA amplicon metabarcoding dataset from a retreating glacier forefield in the high tropical andes.}, journal = {Data in brief}, volume = {66}, number = {}, pages = {112758}, pmid = {42064333}, issn = {2352-3409}, abstract = {Glaciers are retreating rapidly worldwide, particularly at high elevations, changing the environments and habitats of microorganisms, plants, and animals drastically and leaving behind nutrient-poor sediment. We sought to explore seasonal, elevational, and soil age differences in microbial community diversity found in moraine deposits exposed by recent deglaciation and previously exposed during the Little Ice Age in the Cordillera Vilcanota of southeastern Peru. In the wet and dry seasons of 2023, JMU students and other researchers collected soil samples from 35 sites across a 2.5 square kilometer range in the Andes mountains. Each sample was assigned to the season collected, elevation of collection, and age of exposure. Total DNA was extracted from samples and the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq platform. The data were then processed and analyzed using the QIIME2 bioinformatics pipeline. This dataset will be useful to the field for studying ecological community and ecosystem formation in glacier forefields emerging from climate change.}, } @article {pmid42064443, year = {2026}, author = {Niyomvong, N and Wongsorn, D and Pitiwittayakul, N}, title = {Metagenomics of a Photo-Fermentative Bacterial Solution and Its Effect on the Growth And Yield of Mini Green Cos Lettuce.}, journal = {Tropical life sciences research}, volume = {37}, number = {1}, pages = {85-108}, pmid = {42064443}, issn = {1985-3718}, abstract = {Photosynthetic bacteria (PSB) are widely utilised in agriculture to enhance plant growth and crop quality by improving nutrient uptake and phytohormone production. This study aimed to analyse the metagenomic composition of a photo-fermentative bacterial solution derived from fermentation and assess its effects on the growth and yield of Mini Green Cos lettuce. Metagenomic analysis revealed that Bacteroidota (38%) was the most abundant phylum, followed by Proteobacteria (23%), Thermotogota (17%) and Firmicutes (15%). Within Proteobacteria, Alphaproteobacteria was dominant followed by Gammaproteobacteria. At the genus level, Petrimonas (22%), uncultured clones belonging to family Petrotogaceae (17%), Rhodopseudomonas (11%), Rubrivivax (6%), and an unidentified genus from Lentimicrobiaceae (4%) were the most prevalent. These findings highlight the microbial diversity of PSB solution, suggesting its potential role in plant growth promotion. A plant growth experiment was conducted using a Completely Randomised Design (CRD) with four treatments: control (T1), chemical fertiliser (T2), undiluted PSB solution (T3) and PSB solution diluted at a 1:1 ratio (T4), with 10 replicates per treatment. Among all treatments, lettuce irrigated with undiluted PSB solution (T3) exhibited the highest growth rate, yield and total chlorophyll content. However, its performance was not significantly different from that of the chemical fertiliser treatment (T2). These results suggest that PSB can effectively promote plant growth and yield, yielding results comparable to chemical fertilisers. Therefore, photo-fermentative bacterial solutions offer a sustainable and eco-friendly alternative to chemical fertilisers, supporting environmentally conscious agricultural practices.}, } @article {pmid42065019, year = {2026}, author = {Behera, S and Gupta, S and Kale, A and Yadav, A and Rao, GP}, title = {Draft genome of a 'Candidatus Phytoplasma trifolii' -related strain BLL-Delhi associated with brinjal little leaf disease.}, journal = {3 Biotech}, volume = {16}, number = {5}, pages = {173}, pmid = {42065019}, issn = {2190-572X}, abstract = {The draft genome sequence of the brinjal little leaf (BLL) phytoplasma strain BLL-Delhi, related to 'Candidatus Phytoplasma trifolii' (16SrVI group), was recovered using a metagenome-resolved assembly strategy from Illumina HiSeq data. The genome comprises 476,098 bp assembled into 12 contigs, with a G+C content of 21.86%, encoding 421 predicted protein-coding sequences, 27 tRNAs, one tmRNA and one additional non-coding RNA, and shows 94% completeness. Genome annotation revealed a reduced yet functionally coherent gene repertoire, including putative effector-like proteins and genes associated with mobile genetic elements. This genome provides a resource for high-resolution taxonomic placement, comparative genomics within the 16SrVI phytoplasma group, and genome-based diagnostics for brinjal little leaf disease.}, } @article {pmid42065375, year = {2026}, author = {Ding, SC and Yu, J and Liao, T and Ahmann, L and Yao, Y and Ho, C and Wang, L and Pinsky, BA and Gu, W}, title = {Adapting clinical chemistry plasma as a source for liquid biopsies.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, pmid = {42065375}, issn = {2050-084X}, support = {CA230156//NIH Office of the Director/ ; CAMS//Burroughs Wellcome Fund/ ; }, mesh = {Humans ; *Cell-Free Nucleic Acids/blood ; Liquid Biopsy/methods ; *Plasma/chemistry ; *Blood Specimen Collection/methods ; *Specimen Handling/methods ; }, abstract = {Circulating cell-free DNA (cfDNA) is valuable for molecular testing, but typically requires specialized collection tubes or immediate processing. We investigated whether residual plasma from heparin separators, routinely used in clinical chemistry, could serve as an accessible and underused source for cfDNA. We analyzed matched plasma samples from healthy volunteers in two experiments: an immediate-processing comparison across EDTA, Streck, and heparin separator tubes (n=5), and a clinical-handling simulation comparing EDTA and heparin separator tubes under delayed processing at room temperature or 4°C (n=6). We also analyzed matched plasma samples from viral PCR-positive patients in a hospital cohort (n=38). Whole-genome sequencing and enriched methylation sequencing were performed to assess concordance across metagenomics, copy number, methylation, and fragmentomic features. Under immediate processing, heparin separator plasma showed high concordance with EDTA and Streck plasma for methylation patterns (Spearman's ρ=0.65-0.70) and fragmentation features. In the Hospital Cohort, heparin separator plasma showed strong concordance with matched EDTA plasma for viral detection (Spearman's ρ=0.95), copy number alteration profiling (Spearman's ρ=0.72-0.96), and methylation patterns (Spearman's ρ=0.50-0.83). These findings support the feasibility of using refrigerated, promptly processed residual plasma from routine clinical chemistry as a supplementary source for cfDNA biobanking and molecular analyses.}, } @article {pmid42066399, year = {2026}, author = {Yang, X and Chen, M and Song, B and Liu, T and Zhao, YG and He, Q and Chen, Y}, title = {Micro(nano)plastics reshape constructed wetlands: Linking biofilm succession's role to key biogenic substance transformation.}, journal = {Water research}, volume = {301}, number = {}, pages = {126024}, doi = {10.1016/j.watres.2026.126024}, pmid = {42066399}, issn = {1879-2448}, mesh = {*Biofilms ; *Wetlands ; *Plastics ; Microplastics ; }, abstract = {Constructed wetlands (CWs) are increasingly recognized as terminal sinks for micro- and nanoplastics (MNPs), yet how chronic MNPs accumulation reshapes biofilm-mediated biogenic substance transformation remains poorly understood. Here, using a 300-day CW experiment integrating process analysis, biofilm microstructure characterization, and metagenomics, we demonstrate that plastic particle size acts as a decisive ecological switch governing biofilm succession and multi-element cycling. Long-term microplastics (MPs) exposure unexpectedly enhanced denitrification and sulfate reduction, whereas nanoplastics (NPs) persistently suppressed carbon, nitrogen, phosphorus, and sulfur transformations. Mechanistic analyses reveal that these divergent outcomes arise not from direct metabolic toxicity but from size-dependent reorganization of biofilm architecture, regulatory gene networks, and microbial cooperation. MPs promoted extracellular polymeric substance synthesis, reinforced anaerobic redox stratification, and strengthened electron-transfer-driven microbial clustering, while NPs disrupted biofilm integrity, downregulated succession-related genes, and fragmented functional interactions. This study challenges the prevailing assumption that MNPs accumulation uniformly degrades treatment performance and establishes a mechanistic framework linking particle size, biofilm succession, and ecosystem functioning. Our findings provide new insights into the long-term ecological effects of emerging particulate pollutants and offer guidance for designing resilient biofilm-based treatment systems under increasing plastic pressure.}, } @article {pmid42066496, year = {2026}, author = {Río-López, R and Vourlaki, IT and Clavell-Sansalvador, A and Valdés, A and Padilla, L and García-Gil, LJ and Xifró, X and Ballester, M and Quintanilla, R and Ochoteco-Asensio, J and Prenafeta-Boldú, FX and Dalmau, A and Ramayo-Caldas, Y}, title = {Integrative metagenomic and metabolomic profiling identifies faecal biomarkers of prolonged social stress in pigs.}, journal = {Animal : an international journal of animal bioscience}, volume = {20}, number = {5}, pages = {101823}, doi = {10.1016/j.animal.2026.101823}, pmid = {42066496}, issn = {1751-732X}, mesh = {Animals ; Biomarkers/analysis ; *Feces/chemistry/microbiology ; Metabolomics ; *Stress, Psychological/metabolism ; *Gastrointestinal Microbiome ; Metagenomics ; Swine ; *Metabolome ; Male ; *Sus scrofa/physiology ; }, abstract = {Stressors significantly impact human and animal health, increasing the risk of physical and mental disorders, in part by affecting the gut-brain axis. Although a link between stress, alterations in gut microbial composition, and the serum metabolite profile has already been established in humans, multiomics studies integrating the faecal microbiome and untargeted metabolomics remain unavailable. The objectives of the present study were twofold: first, to identify microbial and metabolic signatures associated with prolonged stress, and second, to evaluate the potential of integrative multiomics approaches to predict key metabolites and discover non-invasive faecal biomarkers of stress in pigs (n = 60). Gut microbial profiles were obtained by shotgun metagenomic sequencing, while faecal metabolites were analysed by untargeted reverse-phase liquid chromatography quadrupole time of flight mass spectrometry, followed by partial least squares discriminant analysis. Metabolite prediction from microbial features was performed using the machine learning method based on neural ordinary differential equations. Eleven discriminant metabolites were identified. In the control group, neurotransmitters such as serotonin and metabolites such as 2-acetamidophenol and sinapine (which possess anti-inflammatory and antioxidant properties) were the most prominent. Conversely, the stressed group exhibited elevated levels of xanthosine, pyrimidine bases (thymine and uracil), n-octadecylamine, and N-α-acetyl-L-lysine. N-octadecylamine (r = 0.37) showed a positive, and serotonin (r = -0.32) a negative correlation with hair cortisol. The results revealed interspecific interactions that modulated microbial and metabolic shifts between the control and stressed pig groups. Feature selection further identified 64 microbial genes that improved classification accuracy between control and stressed pigs to 91.06% and enhanced the prediction of key metabolites, including serotonin and xanthosine. Overall, this integrative multiomics framework elucidates complex microbiome-metabolite interactions and identifies non-invasive biomarkers of prolonged stress-induced metabolic dysregulation, providing valuable insights for animal welfare and translational human health research.}, } @article {pmid42066541, year = {2026}, author = {Li, L and Chi, Y and Kong, Y and Zheng, D and Shi, Z and Kang, X}, title = {Rapid species-level discrimination of pulmonary TB and NTM by metagenomic next-generation sequencing with concurrent respiratory microbiome profiling.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {1}, pages = {117442}, doi = {10.1016/j.diagmicrobio.2026.117442}, pmid = {42066541}, issn = {1879-0070}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Male ; Middle Aged ; Female ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Aged ; *Nontuberculous Mycobacteria/genetics/isolation & purification/classification ; Adult ; *Mycobacterium tuberculosis/genetics/isolation & purification/classification ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Aged, 80 and over ; }, abstract = {INTRODUCTION: Rapid discrimination between Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) remains clinically challenging, especially when conventional microbiological evidence is limited. Whether metagenomic next-generation sequencing (mNGS) can provide rapid species-level identification while simultaneously characterizing the respiratory microbiome remains to be systematically evaluated.

METHODS: Bronchoalveolar lavage fluid from 74 retrospectively enrolled patients with clinically diagnosed pulmonary mycobacterial disease (62 TB, 12 NTM-pulmonary disease (NTM-PD)) was analyzed by mNGS. Conventional test results were extracted from medical records. A supplementary assessment excluding mNGS from diagnostic review was additionally performed to reduce potential incorporation bias. Microbial diversity and between-group differences in the respiratory microbiota were evaluated.

RESULTS: In the clinically diagnosed cohort, mNGS was positive in 61/62 TB cases (98.4%) and 12/12 NTM-PD cases (100%). Mycobacterial cultures were negative in all tested patients in routine clinical practice. By comparison, AFB (8.82%, 3/34), T-SPOT.TB (71.43%, 10/14), and Xpert MTB/RIF (69.23%, 9/13) showed lower positivity among tested patients. In the supplementary assessment, 45/46 independently classified TB cases were mNGS-positive (97.8%). mNGS additionally detected non-mycobacterial pathogens in 62.16% (46/74) of patients, facilitating recognition of polymicrobial infection. Microbiome analysis revealed that the TB group showed relatively higher abundance of Streptococcus parasanguinis besides MTB, whereas NTM group was relatively enriched in opportunistic pathogens including Pseudomonas aeruginosa and Stenotrophomonas maltophilia.

CONCLUSION: In this retrospective real-world cohort, mNGS achieved rapid species-level discrimination of MTB and NTM with high positive detection rates, and simultaneously provided clinically relevant microbiome information, supporting its value as an adjunctive diagnostic tool for pulmonary mycobacterial infection.}, } @article {pmid42066584, year = {2026}, author = {Xu, Q and Wang, Q and Hou, D and Zhang, F and Zhang, C and Qi, B and Wei, M and Chen, J and Zha, Q and Qin, H and Song, Y and Wu, X}, title = {Cryptococcal pneumonia susceptibility in immunocompetent patients: Role of pseudomonas aeruginosa via IL-2/IL-12/IL-17 pathways.}, journal = {Journal of infection and public health}, volume = {19}, number = {6}, pages = {103230}, doi = {10.1016/j.jiph.2026.103230}, pmid = {42066584}, issn = {1876-035X}, mesh = {Adult ; Pseudomonas aeruginosa/immunology ; *Pseudomonas Infections/immunology/microbiology ; Cryptococcosis/immunology/microbiology ; *Immunocompetence ; *Immunocompromised Host/immunology ; Interleukin-17/immunology/metabolism ; Bronchoalveolar Lavage Fluid/microbiology ; Interleukin-12/immunology/metabolism ; Interleukin-2/immunology/metabolism ; }, abstract = {BACKGROUND: While pulmonary cryptococcosis affects immunocompromised patients, it also occurs in immunocompetent individuals. However, underlying mechanisms contributing to susceptibility in immunocompetent patients remain poorly understood.

METHODS: We enrolled 43 patients with pulmonary cryptococcosis, including 19 apparently immunocompetent patients (ICPC) and 24 immunocompromised patients (IMCPC), compared with community-acquired pneumonia (CAP) controls. Bronchoalveolar lavage fluid (BLAF) microbiota composition was analyzed using metagenomic next-generation sequencing. Peripheral blood immune parameters were measured, and correlation analyses were performed to identify potential associations. Publicly available single-cell transcriptomic datasets were analyzed to explore immune pathway alterations associated with chronic Pseudomonas infection.

RESULTS: ICPC patients were predominantly male, less likely to present with fever, and showed normal inflammatory markers compared to CAP controls. Despite normal reference ranges, ICPC patients demonstrated significantly reduced CD4⁺ T lymphocyte percentages，accompanied by elevated IL-2 and reduced IL-12p70 and IL-17A levels. BALF analysis revealed a significant enrichment of nonfermenting gram-negative bacteria: Ralstonia, Sphingomonas, Acinetobacter, Stenotrophomonas, Burkholderi and Pseudomonas, in ICPC patients，whereas no such alterations were observed in the IMCPC group. Correlation analyses demonstrated inverse relationships between the relative abundances of Stenotrophomonas and Pseudomonas abundance and CD4 + T lymphocyte percentages and CD4 + /CD8 + ratios. Furthermore, single-cell transcriptomic analysis of chronic Pseudomonas infection showed enrichment of IL-2 signaling genes and suppression of IL-12 and IL-17A signaling pathways.

CONCLUSIONS: ICPC patients exhibit decreased peripheral CD4 + T lymphocyte percentage with elevated IL-2 and reduced IL-12p70/IL-17A levels. The observed enrichment of specific bacterial taxa, particularly Pseudomonas species, and its inverse correlation with immune parameters suggest potential microbiome-immune interactions that may contribute to cryptococcal susceptibility.}, } @article {pmid42066983, year = {2026}, author = {Rajabal, V and Ghaly, TM and Colombi, E and Russell, DH and Sia, C and Shah, B and McPherson, VJ and Qi, Q and Coleman, NV and Gillings, MR and Tetu, SG}, title = {Discovery of novel antimicrobial resistance genes: Integrons as a high-throughput gene capture and functional screening platform.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {400}, number = {}, pages = {128228}, doi = {10.1016/j.envpol.2026.128228}, pmid = {42066983}, issn = {1873-6424}, mesh = {*Integrons/genetics ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Genes, Bacterial ; High-Throughput Screening Assays ; }, abstract = {Integrons are genetic elements that drive bacterial adaptation by capturing and expressing mobile gene cassettes. They play a key role in dissemination of antimicrobial resistance (AMR) genes, particularly in Gram-negative bacteria. In addition to known AMR determinants, integron gene cassettes carry a vast reservoir of novel genes whose functions are largely uncharacterised, making it difficult to assess their full contribution to the resistome. Contributing to this are limitations in current sequence-based prediction methods which often lack the ability to identify unknown AMR or other adaptive genes with novel mechanisms. To address this, we developed a high-throughput gene cassette capture system that utilises site-specific recombination activity of integrons and a counter selection strategy to capture and express gene cassettes from metagenomes. Coupling this platform with a functional screening approach allowed us to rapidly assay large libraries of environmental gene cassettes. Using this system, we recovered previously unknown AMR determinants while also providing insights into the prevalence of known clinical AMR genes in a range of environmental samples, including food and fertiliser. Here we provide experimental data on multiple novel bleomycin resistance genes and a stress response gene conferring gentamicin and tobramycin resistance. Our sequence analysis of the captured library also highlighted the diversity of the environmental cassette pool, with 656 unique cassettes recovered, the majority of which encoded proteins with unknown functions. The cassette capture system is a powerful tool for accessing hidden elements of the resistome and discovering novel adaptive genes that may go undetected using current sequence-based approaches.}, } @article {pmid42067165, year = {2026}, author = {Zong, K and Zhang, T and Li, Y and Ji, M and Lu, J and Guo, Y and Zhao, C and Lv, J and Kong, Q and Wang, Q and Zhang, J}, title = {Mechanism of magnetite coupled microbial enhancement in mariculture wastewater treatment: Dual edged role of magnetite.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134749}, doi = {10.1016/j.biortech.2026.134749}, pmid = {42067165}, issn = {1873-2976}, mesh = {*Wastewater/microbiology/chemistry ; *Ferrosoferric Oxide/chemistry/pharmacology ; Nitrogen/isolation & purification ; Phosphorus/isolation & purification ; Wetlands ; *Aquaculture ; *Water Purification/methods ; Biodegradation, Environmental ; Biological Oxygen Demand Analysis ; }, abstract = {Marine aquaculture wastewater treatment faces dual challenges of microbial inhibition and greenhouse gas (GHG) emissions under saline stress. This study investigates the synergistic effects of submicron magnetite and intertidal microorganisms on treatment efficiency in constructed wetlands (CWs). Three CWs were designed: "Mag" (magnetite composite microorganisms), "IWS" (microorganisms only) and "CK" (control). Nutrient removal and GHG emissions were evaluated, and microbial mechanisms under saline conditions were explored via metagenomics. Mag achieved the highest removal efficiencies for NH4[+]-N, total nitrogen (TN), COD, and total phosphorus (TP), with TP removal 20.1% and 43.7% higher than in IWS and CK, respectively. Biological iron redox cycling on magnetite surfaces continuously generated reactive sites that enhanced nutrient adsorption and forms conductive pathways that facilitate direct interspecies electron transfer through the upregulation of pilA and cytochrome c, thereby promoting the transformation of aqueous organic pollutants into inorganic gaseous products. IWS promoted sulfur-driven autotrophic denitrification, effectively removing nitrogen and suppressing CH4 through competition between sulfur oxidizers and methanogens. Plant uptake also contributed to high TN and TP removal with low GHG emissions. CK exhibited dominant glycolytic activity with energy directed toward osmotic regulation, resulting in low contaminant removal and high GHG emissions. This study offers practical guidance for balancing nutrient removal efficiency with reduced GHG emissions in the treatment of saline wastewater.}, } @article {pmid42067590, year = {2026}, author = {Alasadi, GJ and Khakvar, R and Zirak, L}, title = {Metagenomic detection of novel bacterial combinations associated with citrus decline in Iraq.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-51185-8}, pmid = {42067590}, issn = {2045-2322}, abstract = {Citrus decline diseases pose significant threats to global fruit production, with complex bacterial pathogen interactions remaining poorly understood. In Iraq's Karbala governorate, severe citrus decline has affected orange orchards for 25 years, causing tree mortality within 3-5 years and substantial economic losses. PCR screening was performed on 75 symptomatic orange trees to detect phloem-limited bacterial pathogens, followed by whole-genome metagenomics on three selected PCR-positive samples to characterize associated microbial communities. Raw NGS reads from these three samples were quality-filtered, then MetaPhlAn2 was used to map reads to a curated marker database and identify bacterial, archaeal, viral, and eukaryotic taxa. The analysis revealed complex mixed infections involving three major plant bacterial pathogens: whereas PCR assays identified Candidatus Phytoplasma citri in 13.3% of the 75 samples, two additional phloem-limited pathogens, Ca. Liberibacter asiaticus and Spiroplasma sp., were exclusively detected via metagenomic sequencing across the three analyzed samples. Trimmed reads were assembled into contigs and analyzed phylogenomically against a global reference dataset. Genome assemblies yielded three for Ca. P. citri (576,881 bp, 424,689 bp, and 72,017 bp) and one each for Ca. L. asiaticus (1,151,288 bp) and Spiroplasma sp. (1,833,004 bp). These findings should be considered exploratory given the limited metagenomic sample size (n = 3); independent validation using targeted molecular approaches is required to confirm the presence of Ca. L. asiaticus and Spiroplasma sp. This is the first report documenting the metagenomic detection and characterization of a mixed infection involving Ca. Phytoplasma citri, Ca. Liberibacter asiaticus, and Spiroplasma sp. associated with citrus decline in Iraq. These findings provide crucial insights into pathogen populations and characterization and inform targeted management strategies for emerging bacterial diseases in Iraqi agricultural systems.}, } @article {pmid42067625, year = {2026}, author = {Liu, X and Zhang, H and Wang, YZ and Tu, X and Wen, J and Lei, S and Liu, N and Wei, X and Li, C and Li, Y and Liu, B and Feng, YQ and Zhu, QF and Liu, X and Ning, K}, title = {Sulfated bile acid produced by a human gut commensal alleviates paediatric sepsis in mice.}, journal = {Nature microbiology}, volume = {11}, number = {6}, pages = {1495-1510}, pmid = {42067625}, issn = {2058-5276}, support = {2023YFA1800900, 2018YFC0910502//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2022FYC3400800//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 32071465, 31871334, 31671374//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22361132526, 22274119, 22474101//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Child ; Female ; Humans ; Male ; Mice ; *Deoxycholic Acid/analogs & derivatives/metabolism/pharmacology/therapeutic use ; Disease Models, Animal ; *Enterococcus/metabolism ; *Gastrointestinal Microbiome ; *Intestinal Barrier Function/drug effects ; Metabolomics ; *Sepsis/microbiology/drug therapy/metabolism ; Case-Control Studies ; }, abstract = {Gut microbiota and bile acids have been reported to affect sepsis progression, but the underlying mechanisms remain largely unknown. Here we investigated gut microbiota-bile acid interplay in two paediatric sepsis cohorts. Integration of bile acid-targeted metabolomics with gut metagenome data from paediatric sepsis patients identified deoxycholic acid 3-sulfate (DCA-3S) as significantly associated with paediatric sepsis progression. In vitro and in vivo experiments identified Enterococcus raffinosus as the primary producer of DCA-3S, contributing at least 80% of its total production, challenging the conventional notion of hepato-centric bile acid sulfation pathways. Intervention experiments in mouse and intestinal organoid models revealed that DCA-3S administration effectively alleviated sepsis by improving intestinal barrier function and attenuating inflammatory response. Collectively, our findings highlight a previously unrecognized microbial contribution to bile acid sulfation and position DCA-3S as a promising diagnostic and therapeutic biomarker for paediatric sepsis.}, } @article {pmid42067917, year = {2026}, author = {Fang, Q and Huang, S and Zhang, C and Li, M and Ye, Z and Guo, H and Xiao, M and Wang, S and Yu, L and Zhang, H and Zhao, J and Tian, F and Chen, W and Zhai, Q}, title = {Capsaicin ameliorates glycemic levels via gut microbiota-derived 5-aminolevulinic acid in mice.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42067917}, issn = {2049-2618}, support = {BX20250339//Postdoctoral Fellowship Program and China Postdoctoral Science Foundation/ ; U23A20259//National Natural Science Foundation of China/ ; JUSRP622013//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Capsaicin/pharmacology ; Fecal Microbiota Transplantation ; *Aminolevulinic Acid/metabolism ; Male ; TRPV Cation Channels/genetics/metabolism ; Bacteria/classification/metabolism/genetics ; *Blood Glucose/drug effects ; Mice, Inbred C57BL ; Metagenomics ; Metabolomics ; Specific Pathogen-Free Organisms ; }, abstract = {BACKGROUND: Capsaicin, a natural alkaloid in chili peppers, regulates glycemic levels; however, its mechanisms and therapeutic potential remain unclear. This study aimed to elucidate the role of gut microbiota and their metabolites in mediating capsaicin's glycemic regulatory effects. We conducted experiments in specific pathogen-free (SPF) and germ-free (GF) mice, transient receptor potential vanilloid 1 (TRPV1) receptor ablation studies, and fecal microbiota transplantation (FMT) to demonstrate the involvement of gut microbiota in capsaicin-mediated glycemic control. Metagenomics and metabolomics analyses were employed to identify key microbial strains and metabolic pathways. Keystone strains and metabolites were supplemented in GF mice without capsaicin intervention to validate their effects on glycemic regulation. In vitro co-culture experiments were performed to investigate the mutualistic relationships among keystone strains under capsaicin treatment.

RESULTS: Gut microbiota constitute an important component of capsaicin-mediated glycemic regulation, acting in concert with but not solely dependent on TRPV1 signaling. Gut microbiota altered by capsaicin promote the production of 5-aminolevulinic acid (5-ALA), which contributes to heme synthesis and enhances glycemic control. Supplementation with Akkermansia muciniphila, Ligilactobacillus murinus, or 5-ALA in GF mice recapitulates the glycemic benefits of capsaicin. Furthermore, capsaicin enriches Akkermansia muciniphila, which in turn supports the growth of Ligilactobacillus murinus.

CONCLUSION: Capsaicin-induced changes in the gut microbiota promote 5-ALA synthesis, leading to improved glycemic control. These findings suggest that dietary or probiotic interventions targeting gut microbiota, particularly Akkermansia muciniphila and 5-ALA, may offer promising strategies for managing glycemic disorders, including type 2 diabetes (T2D). Video Abstract.}, } @article {pmid42068031, year = {2026}, author = {Chen, S and Feng, H and Wang, Y and Huang, J and Xu, S and Gong, Y and Liu, X and Ouyang, Y and Ye, Q and Zheng, D and Sun, K and Wang, A and Chen, Y}, title = {Intestinal epithelial Syndecan-1 maintains mucosal homeostasis in inflammatory bowel disease by enhancing Faecalibacterium prausnitzii biofilm formation.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2665870}, pmid = {42068031}, issn = {1949-0984}, mesh = {Animals ; *Syndecan-1/genetics/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Mice ; *Intestinal Mucosa/microbiology/metabolism ; Gastrointestinal Microbiome ; *Biofilms/growth & development ; Mice, Knockout ; Humans ; *Faecalibacterium prausnitzii/physiology/genetics/growth & development ; Mice, Inbred C57BL ; Homeostasis ; Disease Models, Animal ; Dextran Sulfate ; Colitis/microbiology/chemically induced ; Male ; Fecal Microbiota Transplantation ; }, abstract = {Despite the rising global incidence of inflammatory bowel disease (IBD), curative therapies remain unavailable. While our previous work implicated the intestinal proteoglycan Syndecan-1 (SDC1) in IBD-associated barrier dysfunction and inflammation, the underlying mechanism was unclear. This study aimed to elucidate how SDC1 maintains intestinal barrier integrity through interactions with the gut microbiome. In DSS-induced colitis, global knockout of Sdc1 (Sdc1[-/-]) exhibited exacerbated inflammatory infiltration and greater impairment of barrier structure and function than wild-type (WT). Formation of intestinal organoids was independent of genotype, indicating that Sdc1[-/-] does not impair barrier function via disrupting epithelial development. The heightened colitis susceptibility in Sdc1[-/-] mice was abolished in the antibiotic-treated pseudo-germ-free models, and transmissible to WT mice via fecal microbiota transplantation. Similar results were reproduced in a germ-free mouse model. Metagenomic sequencing identified Faecalibacterium prausnitzii as the most significantly depleted species upon Sdc1 knockout. In vitro, SDC1-attached glycosaminoglycans (heparan sulfate (HS) and chondroitin sulfate (CS)) but not the SDC1 core protein promoted F. prausnitzii growth. Prokaryotic transcriptome profiling indicated that HS/CS induces cobalamin biosynthesis in F. prausnitzii. The critical role of cobalamin as a mediator was confirmed, as its synthetic inhibition significantly diminished the growth-promoting effect of HS/CS. Mechanism studies showed that HS/CS enhanced biofilm formation in F. prausnitzii, thereby facilitating cobalamin biosynthesis. Oral administration of HS ameliorated DSS-induced colitis and promoted mucosal colonization of F. prausnitzii, independent of the host genotype. Finally, human IBD biopsies revealed a positive correlation between epithelial SDC1 and mucosal F. prausnitzii, as well as an inverse correlation with bacterial translocation and the number of LPS‑positive cells. Our study elucidates a novel mechanism in which the glycosaminoglycan chains of SDC1 promote F. prausnitzii colonization and growth through enhanced biofilm formation and cobalamin synthesis, thereby highlighting the therapeutic potential of HS for IBD and offering a new basis for host-directed microbiota regulation.}, } @article {pmid42068598, year = {2026}, author = {Xu, M and Cheng, K and Cai, Z and Chen, G and Zhou, J}, title = {Metagenomic and metatranscriptomic insights into Ruegeria profundi-driven protective responses in coral holobionts against Vibrio coralliilyticus infection.}, journal = {Microbiological research}, volume = {309}, number = {}, pages = {128530}, doi = {10.1016/j.micres.2026.128530}, pmid = {42068598}, issn = {1618-0623}, mesh = {Animals ; *Anthozoa/microbiology/genetics ; *Vibrio/pathogenicity/genetics ; Metagenomics ; Symbiosis ; *Rhodobacteraceae/genetics/physiology ; Coral Reefs ; Gene Expression Profiling ; Transcriptome ; Virulence/genetics ; Microbiota ; Microalgae/genetics ; Photosynthesis/genetics ; Vibrio Infections ; }, abstract = {In the context of climate-driven coral reef degradation, opportunistic pathogens such as Vibrio coralliilyticus are emerging as significant secondary threats, acting in synergy with thermal stress to accelerate coral bleaching and mortality. In this study, we investigated the role of Ruegeria profundi in mitigating V. coralliilyticus-induced bleaching. Specifically, the responses of coral holobiont members to pathogenic and probiotic influences were evaluated using metagenomics and metatranscriptomics. We found that the presence of V. coralliilyticus enhanced the metabolic potential of the coral-associated bacterial community, particularly regarding carbohydrate utilization and virulence. Conversely, R. profundi reduced the relative abundance of pathogenic Vibrio species by over 50% and broadly suppressed the expression of virulence genes within the coral-associated bacterial community, including a > 2-fold downregulation of genes involved in quorum sensing and flagellar assembly. Transcriptomic data indicated that immune-related genes in the host were upregulated, whereas photosynthesis-related genes in photosymbiotic microalgae were downregulated in response to V. coralliilyticus infection. R. profundi significantly promoted apoptosis resistance and antimicrobial peptide activity in the host and enhanced photosynthesis in photosymbiotic microalgae (p < 0.05). Furthermore, R. profundi significantly suppressed virulence gene expression in the coral-associated bacterial community (p < 0.05). Collectively, our results indicated that R. profundi orchestrates a tripartite defense mechanism involving the coral host, its associated bacterial community, and symbiotic microalgae, effectively mitigating pathogen-induced dysbiosis and bleaching. These findings have promising implications for microbiome-based strategies in coral reef restoration.}, } @article {pmid42068877, year = {2026}, author = {Liao, W and Gao, J and Zhang, J and Wu, Y and Jiang, Y and Liu, H and Chen, S and Xiu, L and Zhong, G}, title = {Haizao Yuhu Decoction alleviates goiter via the gut-thyroid axis: Microbiota-derived SCFAs promote hormone synthesis and restore apoptosis.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {156}, number = {}, pages = {158256}, doi = {10.1016/j.phymed.2026.158256}, pmid = {42068877}, issn = {1618-095X}, mesh = {Animals ; *Apoptosis/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology ; *Thyroid Gland/drug effects/metabolism ; Male ; Rats ; *Goiter/drug therapy/chemically induced/metabolism ; *Fatty Acids, Volatile/metabolism ; Rats, Sprague-Dawley ; Fecal Microbiota Transplantation ; Propylthiouracil ; Thyroid Hormones/biosynthesis ; Disease Models, Animal ; }, abstract = {BACKGROUND AND PURPOSE: Haizao Yuhu Decoction (HYD) is a classic Traditional Chinese Medicine for goiter, but its mechanism related to the "gut-thyroid axis" remains unknown. This study investigates whether HYD treats goiter via this axis and elucidates the underlying mechanisms.

METHODS: A rat goiter model was induced with propylthiouracil (PTU), followed by two weeks of HYD treatment. Gut microbiota was analyzed by metagenomic sequencing; fecal and serum short-chain fatty acids (SCFAs) were quantified by targeted LC-MS/MS analysis. Thyroid function was assessed via iodine content and hormone levels. Key proteins in hormone synthesis and apoptosis were evaluated by Western blot and immunohistochemistry. Fecal microbiota transplantation (FMT) supported microbiota causality.

RESULTS: HYD alleviated goiter and hypothyroidism. It restored gut microbiota diversity and enriched SCFA-producing bacteria (e.g., Bifidobacterium pseudolongum), coincident with increased SCFAs including butyrate. These SCFA changes correlated with reduced HDAC1/2/3/8 in thyroid tissue, consistent with enhanced histone acetylation, and were accompanied by upregulation of NIS, TG, TPO, and DUOX2. Concurrently, elevated SCFAs were associated with AKT/Mdm2 pathway inhibition, p53 stabilization, downstream activation of P21 and Caspase-3, and suppression of Bcl-2, supporting a model of promoted thyroid cell apoptosis. FMT supported that HYD-modulated microbiota alone reproduced these effects.

CONCLUSION: HYD alleviates PTU-induced goiter in rats in a manner associated with gut microbiota remodeling and increased SCFA production, which correlate with enhanced thyroid hormone synthesis and restored apoptosis-a relationship supported by FMT experiments. However, direct interactions between HYD and PTU cannot be fully excluded. These findings are consistent with a model in which HYD acts through the gut-thyroid axis, providing mechanistic insights into its therapeutic effects.}, } @article {pmid42069091, year = {2026}, author = {Jin, H and Meng, L and Yulug, B and Altay, O and Li, X and Cankaya, S and Hanoglu, L and Ji, B and Coskun, E and Idil, E and Nogaylar, R and Oktem, EO and Sayman, D and Karaca, R and Ozsimsek, A and Shoaie, S and Turkez, H and Nielsen, J and Borén, J and Zhang, C and Uhlén, M and Mardinoglu, A}, title = {Machine learning based multi-omics analysis reveals key molecular determinants of Parkinson's disease severity.}, journal = {Neurobiology of disease}, volume = {225}, number = {}, pages = {107424}, doi = {10.1016/j.nbd.2026.107424}, pmid = {42069091}, issn = {1095-953X}, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; Biomarkers/metabolism/blood ; *Machine Learning ; Metabolomics/methods ; Multiomics ; *Parkinson Disease/metabolism/diagnosis/genetics ; *Predictive Learning Models ; Proteomics ; Severity of Illness Index ; }, abstract = {While single-omics analyses of Parkinson's Disease (PD) have demonstrated their ability in revealing the underlying molecular mechanisms, they often fail to provide a comprehensive view of the complete disease mechanisms. In this study, we leveraged multi-omics data from 64 heterogeneous, well-phenotyped PD patients, generated plasma metabolomics data and Olink proteomics data together with the gut and saliva metagenomics data, and investigated the altered molecular mechanisms and their interactions in association with the severity of motor function disorders in PD patients. Based on our multi-omics approach, we identified a panel of 58 biomarkers comprising one clinical variable, 10 proteins, and 17 metabolites from plasma, 26 gut species, and 4 saliva species for PD severity. These biomarkers exhibited superior predictive performance for assessing PD severity compared to those derived from single-omics datasets. The predictive power of our machine learning models based on these biomarkers was validated using additional multi-omics data from the same group of PD patients after a 3-month follow-up. The contribution of each omics dataset was evaluated by both supervised and unsupervised machine learning approaches, highlighting the importance of plasma metabolomics in disease stratification. Our study unveiled disease-related molecular alterations across multiple omics datasets, offering potential diagnostic and therapeutic insights for PD. Moreover, it underpinned the significance of employing multi-omics analyses when studying complex diseases like PD.}, } @article {pmid42069117, year = {2026}, author = {Makowska-Zawierucha, N and Trzebny, A and Mokracka, J and Bradley, JA}, title = {The high Arctic resistome: stress-response genes, virulence determinants, and microbial populations in human-impacted environments of Spitsbergen.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {402}, number = {}, pages = {128242}, doi = {10.1016/j.envpol.2026.128242}, pmid = {42069117}, issn = {1873-6424}, mesh = {Arctic Regions ; Humans ; Drug Resistance, Microbial/genetics ; *Bacteria/genetics ; Virulence/genetics ; *Environmental Monitoring ; Estuaries ; Sewage/microbiology ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Microbiota ; Metagenome ; Stress, Physiological/genetics ; Genes, Bacterial ; }, abstract = {The high Arctic, particularly Spitsbergen, faces the combined challenges of climate change and other anthropogenic pressures - including waste and contaminant release from human activity - that influence microbial populations and the spread of antimicrobial resistance (AMR). This study presents a snapshot analysis of metagenomes from various environments across Spitsbergen, including untreated and treated wastewater outflows, fjords, and glacial ice cores, to explore the abundance of stress-response genes, including antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs), and virulence genes (VGs), alongside the compositions of the associated bacterial populations. We reveal varying levels of stress-response genes and VGs in environments exposed to differing levels of human influence. ARGs and MRGs dominate in raw sewage, while VGs are more prevalent in fjord waters receiving both raw sewage and effluent, indicating that specific environmental conditions favor different resistance and virulence traits. We detected high abundance of ARGs and VGs downstream of both untreated and treated wastewater. Our analyses indicate the presence of bacterial populations with resistance and virulence traits - including Enterobacteriaceae, Enterococcaceae, Bacillaceae, and Staphylococcaceae - in downstream ecosystems. While we do not directly assess effects on human health or ecosystem function, these observations point to potential ecological impacts in Arctic environments and highlight the importance of continued monitoring to understand and manage the possible effects of human activities and climate change.}, } @article {pmid42069315, year = {2026}, author = {Wu, G and Du, J and Li, H and Dong, Y and Wang, Q and Hu, F and Ji, J}, title = {Synergistic integration of sustainable wastewater treatment and agricultural waste valorization: Rapid in-situ enrichment of anammox bacteria via corncob biocarriers.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134769}, doi = {10.1016/j.biortech.2026.134769}, pmid = {42069315}, issn = {1873-2976}, mesh = {*Wastewater/microbiology/chemistry ; Biofilms ; Nitrogen/isolation & purification/metabolism ; *Bacteria/metabolism ; *Agriculture ; *Water Purification/methods ; Oxidation-Reduction ; }, abstract = {The slow proliferation of anammox bacteria (AnAOB) limits the large-scale application of anammox technology in mainstream wastewater treatment. Here, an innovative strategy was proposed in which agricultural waste corncob was utilized as biocarriers for the rapid enrichment of AnAOB. This study systematically validated the feasibility of using corncob as biocarriers to enhance the self-enrichment of AnAOB. Results showed that corncob addition shortened the anammox startup time by approximately 64.0% and increased total inorganic nitrogen (TIN) removal efficiency by 28.4%. The anammox activity of the corncob biofilm and flocs was 3.2- and 1.1-fold higher, respectively, than that of the control. The microbial community analysis indicated that corncob biofilm harbored the highest relative abundance of AnAOB (23.9%). Within the corncob biofilm, lignocellulolytic microbes degraded macromolecular organics to provide electron donors for denitrifiers, which facilitated nitrogen metabolic couplingbetween denitrifiers and AnAOB, therebyestablishing favorable microenvironment for the enrichment of AnAOB. Furthermore, metagenomic revealed NO cross-feeding between AnAOB and their symbionts further offered an ideal niche for AnAOB. Concurrently, the upregulation of key carbon metabolism genes indicated heightened microbial activity within the biofilm, while quorum sensing (QS) mechanisms also played a significant role in maintaining the dynamic stability of microbial community. This work established a natural and highly efficient pathway for the self-enrichment of AnAOB, simultaneously providing a synergistic solution for agricultural wastes (AWs) valorization, advanced wastewater nitrogen removal, and carbon neutrality, demonstrating broad application prospects and significant ecological value.}, } @article {pmid42069316, year = {2026}, author = {Zhao, X and Tian, X and Zhang, H and Dang, Y and Ma, J}, title = {Metagenomic understanding of the performance enhancement in anaerobic digestion by granular activated carbon coupled with riboflavin under high organic loading.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134752}, doi = {10.1016/j.biortech.2026.134752}, pmid = {42069316}, issn = {1873-2976}, mesh = {Anaerobiosis/drug effects ; *Riboflavin/pharmacology ; *Metagenomics/methods ; Bioreactors/microbiology ; Methane/metabolism ; Fatty Acids, Volatile/metabolism ; *Charcoal/chemistry ; Biological Oxygen Demand Analysis ; *Metagenome ; }, abstract = {Anaerobic digestion (AD) often suffers operation failure from ammonia inhibition and volatile fatty acids (VFAs) accumulation under high organic loading rates (OLRs). To overcome these limitations, this study employed granular activated carbon coupled with riboflavin (RFGAC) by stimulating direct interspecies electron transfer (DIET). A semi-continuous AD experiment was conducted for 145 days with OLRs ranging from 2.25 to 11.25 kg COD/(m[3]·d). The results showed that the RFGAC group achieved the highest methane content of 78%, and maintained a COD removal rate above 95%, outperforming the GAC group and the control. At an OLR of 6.75 kg COD/(m[3]·d), the control collapsed due to severe acidification when the pH dropped lower than 6.5, while the RFGAC group stably operated with effluent COD of 2200-5300 mg/L and seldom VFAs accumulation. Microbial community analysis revealed that RFGAC selectively shifted microbial community composition especially at high OLR, promoting Methanosarcina to form a synergistic consortium. The Pearson correlation analysis of digestion performance and metagenome revealed that Methanosarcina had a stronger correlation with methanogenesis than Methanothrix, which was enriched in the presence of GAC alone. Metabolic pathway analysis confirmed key DIET-related functional genes, hdrA2 and methyl transfer-associated mtrH, were respectively upregulated by 7-fold and 5-fold. This study offers a viable strategy to improve chicken manure AD, and provides deep mechanistic insights on RFGAC modulation of microbial community succession and functional gene expression.}, } @article {pmid42069539, year = {2026}, author = {Hagenbeek, A and Masukagami, Y and Palanichamy, P and Husnik, F}, title = {Genome-resolved metagenomics reveals unexpected diversity and host range of Candidatus Lariskella (Rickettsiales: Midichloriaceae).}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12881-x}, pmid = {42069539}, issn = {1471-2164}, support = {RGEC29/2024;DOI:https://doi.org/10.52044/HFSP.RGEC292024.pc.gr.194160//Human Frontier Science Program/ ; }, abstract = {The intracellular endosymbiont Candidatus Lariskella (Alphaproteobacteria, Candidatus Midichloriaceae) has been found across a wide diversity of terrestrial arthropods, including ticks, true bugs, beetles, fleas, wasps and moths. Despite its prevalence, little is known about the biology of Ca. Lariskella, nor do we grasp the full extent of its host range. Here, we report the first known occurrence of Ca. Lariskella infecting a population of free-living marine nematodes (Enoplida, Thoracostomopsideae). This novel nematode-infecting Ca. Lariskella was found to be closely related to insect-infecting strains, despite the drastic shift in both host taxonomy and habitat. TEM and FISH microscopy showed Ca. Lariskella is localized within both the nematode somatic cells and developing oocytes, confirming its status as a nematode endosymbiont and strongly suggesting maternal transmission. This finding led us to reassess the host range of Ca. Lariskella. We screened the SRA database for Ca. Lariskella sequences and performed genome-resolved metagenomics on SRA entries positive for Ca. Lariskella. We recovered 16 novel Ca. Lariskella metagenome-assembled genomes from SRA entries, including from novel hosts such as ants and treehoppers. However, we did not encounter further instances of Ca. Lariskella within nematodes or marine invertebrates, which we attribute to the relatively poor sampling of these groups. Overall, our findings illustrate the ability of Ca. Lariskella to infect both arthropods and nematodes as well as hosts from both terrestrial and marine environments.}, } @article {pmid42069617, year = {2026}, author = {Yuan, H and Song, Y and Nie, L and Yang, Z and Yang, L and Yang, K and Yang, Y and Li, W and Wang, X and Zhang, XX and Hua, Y and Yuan, ZG}, title = {The gut metabolite arachidonic acid alleviates intestinal injury induced by a Toxoplasma gondii strain isolated from a wild rodent.}, journal = {Parasites & vectors}, volume = {19}, number = {1}, pages = {}, pmid = {42069617}, issn = {1756-3305}, support = {2025A1515012622//Natural Science Foundation of Guangdong Province/ ; }, mesh = {Animals ; *Toxoplasma/isolation & purification/pathogenicity/genetics ; *Arachidonic Acid/metabolism/pharmacology ; *Toxoplasmosis, Animal/parasitology/pathology ; Mice, Inbred C57BL ; Mice ; Gastrointestinal Microbiome ; *Intestines/pathology/parasitology ; Female ; Virulence ; Animals, Wild/parasitology ; }, abstract = {BACKGROUND: Wild isolates of Toxoplasma gondii may exhibit different virulence characteristics and host adaptability compared with those of laboratory strains. In this study, we isolated a novel rodent-derived T. gondii strain, denoted TgRodGz1, and evaluated its pathogenic features.

METHODS: TgRodGz1 was isolated from T. gondii-positive wild rodents in Guangdong Province and compared with the RH and Me49 strains in C57BL/6 mice. Virulence and intestinal injury were evaluated by survival analysis, brain cyst quantification, histopathology, tight junction assessment and qPCR. Gut microbiota and metabolic alterations were analyzed by metagenomic sequencing and LC-MS/MS-based metabolomics.

RESULTS: Compared with theT. gondii laboratory strains RH and Me49, TgRodGz1 was associated with more pronounced intestinal injury, including villus atrophy, barrier disruption and downregulation of tight junction proteins and increased gut permeability and inflammation. Metagenomic analysis revealed significant intestinal flora dysbiosis, with a marked reduction in beneficial bacteria and expansion of pathogenic bacteria. Metabolomic analysis revealed suppression of arachidonic acid (ARA) metabolism during TgRodGz1 infection. Supplementation with ARA did not directly inhibit parasite growth but significantly alleviated intestinal lesions, reduced brain cyst burden and attenuated inflammatory responses, including microglial activation.

CONCLUSIONS: These findings suggest that TgRodGz1 represents a distinct T. gondii genotype associated with pronounced intestinal pathology and suggest that ARA supplementation may alleviate intestinal and neuroinflammatory changes associated with T. gondii infection.}, } @article {pmid42069941, year = {2026}, author = {Singh, A and Bhattacharjee, S and Singh, Y and Kostova, I}, title = {Parabiotics as Next-Generation Microbiome Therapeutics: Insights into Mechanisms, Evidence, and Therapeutic Potential.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {42069941}, issn = {1432-0991}, mesh = {Humans ; *Prebiotics/administration & dosage ; Animals ; *Gastrointestinal Microbiome/drug effects ; Probiotics ; *Microbiota ; }, abstract = {Parabiotics (also termed paraprobiotics) are defined as non-viable microbial cells or their components, including peptidoglycans, teichoic acids, surface proteins, that confer health benefits without requiring viability which distinguishes them from traditional probiotics. Their non-viable nature eliminates risks such as microbial translocation, bacteremia, and sepsis, making them suitable for vulnerable populations including immunocompromised, critically ill, paediatric and elderly individuals. In addition, parabiotic exhibit improved thermal stability, extended shelf life, and easier incorporation into functional foods, nutraceuticals, and pharmaceutical formulations without cold-chain requirements. Mechanistically, parabiotics retain immunomodulatory, anti-inflammatory and have barrier-enhancing activities through interactions with host pattern recognition receptors, including Toll-like receptors, modulation of cytokine responses, and reinforcement of gut epithelial integrity. Preclinical and clinical studies support their therapeutic potential such as in case of heat-killed Lactobacillus acidophilus LB (L. acidophilus) has shown efficiency in managing acute paediatric diarrhoea, while heat-inactivated Lacticaseibacillus paracasei PS23 (Lcb. paracasei) has demonstrated improvements in muscle strength and inflammatory markers, including reduced C-reactive protein and interleukin-6 and increased interlukin-10 in elderly individuals. Similarly, inactivated Lactiplantibacillus plantarum (Lpb. plantarum) and Bifidobacterium strains have been associated with benefits in irritable bowel syndrome, atopic dermatitis, respiratory infections, visceral fat reduction, and antibiotic-associated dysbiosis. Synergistic combinations with prebiotics, postbiotics and related bioactives further enhance therapeutic outcomes in inflammatory, metabolic and infectious conditions. Advances in metagenomics, next-generation sequencing, proteomics, metabolomics, CRISPR-Cas systems, and synthetic biology are accelerating strain characterization, functional evaluation, and scalable production. Despite ongoing challenges in standardization and regulated harmonization, parabiotics represent a safe and effective approach for microbiome-targeted interventions. This review synthesizes current evidence on their therapeutic applications, technological advancements, and translational potential, highlighting their role in precision health and next-generation functional nutrition.}, } @article {pmid42070641, year = {2026}, author = {Wu, M and Liao, H and Luo, Y and Yao, Y and Yang, D and Hu, Z and Gao, L and Xia, X}, title = {Moisture transfer-driven quality enhancement in solid-state fermented Daqu: Synergistic effects of microbial community adaptation and functional enzyme metabolism.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134771}, doi = {10.1016/j.biortech.2026.134771}, pmid = {42070641}, issn = {1873-2976}, mesh = {*Fermentation ; *Water/metabolism ; *Microbiota ; alpha-Amylases/metabolism ; }, abstract = {Solid-state fermented Daqu exhibits a typical heterogeneous structure, where moisture regulates the microbial activity by driving gas diffusion in the pores and nutrient enrichment, playing a crucial role in the quality of the final product. However, there is a lack of clarity regarding how moisture transfer affects Daqu microbial assembly and metabolic flux. This study pioneered a real-time controllable fermentation platform, employing stoichiometry, nuclear magnetic resonance, and metagenomics to investigate microbial saccharifying metabolic functions under moisture transfer regulation. Comparing representative low (LM: 34%, 36%) and high (HM: 38%, 40%) moisture groups, we found that porosity exhibited a strong positive correlation with water activity (coefficient > 0.9, p < 0.01), serving as the primary physicochemical contributor governing moisture transfer priority. Furthermore, steady-state mass transfer in the HM group (≥ 38%) enhanced the transfer rate from free water (T23) to capillary water (T22: 10-100 ms), shaping a saccharifying functional microbial community dominated by Rhizopus and Bacillus. Weighted network and functional gene predictions indicated that this process strengthened the substrate preference of core microorganisms toward starch, significantly reinforcing the metabolic synergy between glucoamylase and α-amylase. Conversely, transient mass transfer in the LM group (< 38%) triggered microbial functional differentiation, promoting the redistribution of non-starch polysaccharide hydrolases. Our research revealed the effects of moisture transfer on nutrient availability, microbial adaptation, and metabolic functions in stack-fermented Daqu. This work ensures Daqu stability and presents novel strategies to optimize solid-state fermentation efficiency through moisture-driven microbial metabolic trade-offs.}, } @article {pmid42070688, year = {2026}, author = {Shurigin, V and Lu, X and Khan, AR and Muhammad, M and Ullah, I and Egamberdieva, D and Yu, Y and Li, L}, title = {Unveiling the plant growth-promoting and antifungal potential of Melissa officinalis endophytes: The integrative culture-dependent and metagenomic approaches.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {369}, number = {}, pages = {113182}, doi = {10.1016/j.plantsci.2026.113182}, pmid = {42070688}, issn = {1873-2259}, mesh = {*Endophytes/physiology/genetics ; *Melissa/microbiology/growth & development ; *Antifungal Agents/metabolism ; Metagenomics ; *Plant Growth Regulators/metabolism ; Fusarium ; Bacteria/genetics ; Microbiota ; }, abstract = {Endophytic bacteria play a central role in plant health, yet their diversity and functions in medicinal plants remain poorly characterized. In this study, we integrated high-throughput sequencing, culture-based isolation, functional assays, and greenhouse validation to characterize the endophytic microbiome of Melissa officinalis L. High-throughput sequencing revealed 347 species with strong tissue-specific structuring. Paucibacter and Pseudomonas genera related to phylum Pseudomonadota dominated in all plant tissues. Nineteen culture-dependent strains representing Pseudomonas, Microbacterium, Plantibacter, Agreia, and Kocuria demonstrated various plant growth-promoting traits, including phosphate solubilization, nitrogen fixation, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, indole-related compounds (IRC) production, siderophore secretion, and hydrolytic enzyme activities (chitinase, protease, and lipase). Pseudomonas fluorescens XIEG-4RS14 showed antifungal activity against Fusarium graminearum (50%) and F. moniliforme (37%), P. marginalis XIEG-4RS15 showed 100 and 62%, P. baetica XIEG-4RS18 showed 28 and 42%, P. fluorescens XIEG-4RS32 showed 45 and 39%, and P. rhodesiae XIEG-4RS37 showed 58 and 27% respectively. Greenhouse assays demonstrated that strains Pseudomonas fluorescens XIEG-4RS14, P. fluorescens XIEG-4RS32, P. taetrolens XIEG-4RS19, and P. poae XIEG-4RS27 increased wheat root and shoot dry weight by up to 113 and 60% respectively. These findings revealed that M. officinalis harbors highly cooperative and functionally effective endophytes with strong potential as next-generation bioinoculants for sustainable crop production.}, } @article {pmid42070841, year = {2026}, author = {Li, S and Yan, X and Ndayishimiye, JC and Smirnov, A and Tsyganov, AN and Nassonova, E and Mazei, NG and Mazei, YA and Yang, J}, title = {Urban park metagenomics highlights sediments as a potential hotspot for CH4 and N2O emission across diverse habitats.}, journal = {Journal of environmental sciences (China)}, volume = {164}, number = {}, pages = {481-491}, doi = {10.1016/j.jes.2025.07.053}, pmid = {42070841}, issn = {1001-0742}, mesh = {*Methane/analysis ; Metagenomics ; *Geologic Sediments/microbiology/chemistry ; Parks, Recreational ; *Nitrous Oxide/analysis ; Ecosystem ; *Environmental Monitoring ; *Air Pollutants/analysis ; Greenhouse Gases/analysis ; Microbiota ; }, abstract = {Urban areas contribute the vast majority of greenhouse gas (GHG) emissions, and urban greenspaces, including urban parks, are being established to promote environmental health by mitigating GHG emissions. However, the diversity of CH4 and N2O cycling genes and microbiomes in urban park ecosystems remains poorly understood. Here, we sampled five types of habitats in subtropical urban parks, including moss, sediment, soil, tree hole, and water, to explore the microbial communities and microbially mediated CH4 and N2O cycling processes using metagenomic sequencing. We found strongly positive biodiversity-ecosystem-functioning (BEF) relationships in nitrogen cycling functions, as well as in CH4 cycling, except in sediment, indicating the microbial community in the sediment had reached function saturation for CH4 cycling. CH4 cycling was driven by a few specific microbial genera, whereas many microorganisms participated in the denitrification process. Microbes in sediment exhibited the highest CH4 and N2O metabolic potential among the five habitats, especially for methanogenesis and N2O production processes. Significant positive correlations were observed between the mcrA and N2O cycling genes, suggesting methanogenesis could be coupled with denitrification. Environmental factors, such as dissolved oxygen, total nitrogen, and total carbon greatly affected microbial community composition and functional gene families. These results highlight that pond sediments are an overlooked potential source of CH4 and N2O emissions, which may undermine the role of urban greenspace in reducing GHG emissions. Reducing nitrogen pollution and eutrophication is recommended to mitigate CH4 and N2O emissions from pond sediments in urban environments.}, } @article {pmid42070844, year = {2026}, author = {Wu, C and Wu, Y and Pan, J and Lv, Y and Li, W and Hu, M and Wang, J and Su, S and Zou, Q and Xue, S}, title = {Evolution and role of manganese-transforming bacterial microorganisms during natural manganese-tailing succession.}, journal = {Journal of environmental sciences (China)}, volume = {164}, number = {}, pages = {516-525}, doi = {10.1016/j.jes.2026.01.018}, pmid = {42070844}, issn = {1001-0742}, mesh = {*Manganese/metabolism ; *Bacteria/metabolism ; Biodegradation, Environmental ; *Soil Microbiology ; *Soil Pollutants/metabolism ; Mining ; }, abstract = {The natural succession of tailings is critical for reducing their adverse environmental impacts. However, the current knowledge of the Mn-transforming microorganisms involved in the natural vegetation succession of Mn tailings is very limited. This study reveals for the first time the evolution of Mn-transforming microorganisms during vegetation succession in Mn tailing. The results revealed that the amount of reducible Mn increased during the succession process (divided into nake-land, bryophyte, herb and woody-plant stages), which is the most important geochemical property driving bacterial community diversity. Metagenomic functional profile analysis revealed that the abundance of genes involved in nutrient uptake, metal tolerance, and metal detoxification increased during succession. A total of 51 metagenome-assembled genomes (MAGs) were reconstructed, in which 6 encoding multicopper oxidase (cotA)-containing MAGs were identified. The relative abundance of these cotA-containing MAGs first increased but then decreased during succession. Notably, genes associated with carbon fixation and denitrification were also identified in these cotA-containing MAGs, indicating their roles in coupling the cycling of manganese, carbon and nitrogen. These results suggest that Mn(II)- oxidizing bacteria could be crucial for lowering Mn toxicity, obtaining nutrients, and potentially contributing to the ecological succession of Mn tailings. The investigation of Mn-transforming microorganisms (cotA-MAGs) has also contributed to understanding the succession mechanisms and restoration of Mn tailing ecosystems.}, } @article {pmid42070845, year = {2026}, author = {Yan, S and Li, R and Shen, X and Zhu, Y and Li, Y and Xu, M and Xie, S}, title = {Unveiling the role of bacterial communities in carbon fixation of mangrove wetlands: Insights into the redox potential and biogeochemical interactions.}, journal = {Journal of environmental sciences (China)}, volume = {164}, number = {}, pages = {526-537}, doi = {10.1016/j.jes.2025.08.024}, pmid = {42070845}, issn = {1001-0742}, mesh = {*Wetlands ; *Carbon Cycle ; Oxidation-Reduction ; *Soil Microbiology ; *Bacteria/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Mangrove wetlands are crucial for carbon sequestration, however, the contributions of bacterial carbon fixation in these ecosystems are often overlooked, and the predominant pathways remains unknown. This gap seriously hinders the understanding and precise assessment of carbon sequestration. This study systematically investigates the pathways, rates, and influential factors of bacterial carbon fixation in mangrove wetlands, utilizing soils from various tidal zones and depths. Through an integrated approach that combines in situ metagenome sequencing, [13]CO2 tagging experiment, functional gene abundance measurement, and 16S rRNA sequencing, we provide the first evidence that the reverse tricarboxylic acid cycle is the predominant pathway for carbon (C) fixation in mangrove soils. The mangrove ecosystem was identified as a significant hotspot for bacterial carbon fixation, with rates in topsoil ranging from 15 to 63 mmol C/(m[2]·day), significantly influenced by environmental variables such as oxidation-reduction potential, and ammonium and nitrate concentrations. In deep soils, high carbon fixation rates were detected in low tidal zones but not in middle and high tidal zones, which did not align with the abundance of carbon fixation functional genes. Notably, we found a strong correlation between carbon fixation rates and nitrogen metabolism processes, underscoring the ecological interactions between these biogeochemical cycles. These findings greatly enhance our understanding of microbial contributions to carbon cycling in mangrove ecosystems and offer novel insights into blue carbon sequestration and the management of coastal wetlands under varying environmental conditions.}, } @article {pmid42070879, year = {2026}, author = {Xin, Y and Liu, L and Chen, SH and Zhao, QB and Zheng, YM}, title = {Enhancing urban river self-purification through riverbed substrates configuration: A nature-based solution for nutrient removal and restoration planning.}, journal = {Journal of environmental sciences (China)}, volume = {164}, number = {}, pages = {95-108}, doi = {10.1016/j.jes.2026.01.038}, pmid = {42070879}, issn = {1001-0742}, mesh = {*Rivers/chemistry ; *Water Pollutants, Chemical/analysis ; Nitrogen/analysis ; *Environmental Restoration and Remediation/methods ; Nutrients ; Phosphorus/analysis ; }, abstract = {Appropriate riverbed substrates, as nature-based engineering components, are critical for enhancing nutrient mitigation and ecosystem sustainability in urban rivers. However, their role in regulating hydrologically mediated nutrient fluxes and biofilm functions remains unclear, limiting substrate-optimized design for urban river restoration. This study integrated machine learning modeling, scenario simulations, and metagenomic analysis to quantify substrate-driven interfacial nutrient removal efficiencies and uncover microbial regulation mechanisms. A back propagation neural network could accurately predict interfacial ammonium and total organic carbon removal efficiencies (RMSE: 0.59-6.92 mg/(L·h·m[2]), R[2]: 0.66-0.97), with retention time, temperature, dissolved oxygen, and nutrient load identified as key predictors. Building upon the model-predicted scenario results, analysis of similarity tests confirmed that substrate type significantly influenced interfacial nutrient removal efficiencies (R > 0.05, P < 0.001). Scoring metrics demonstrated fine sand (1295) and gravel (1281) gained higher total scores than other substrates (1110-1182), indicating higher interfacial nutrient removal capacities. Metagenomic analyses revealed that these differences were driven by divergence in microbial functional potential. Substrate type selectively enriched functional genes related to nitrogen and carbon cycling (R > 0.18, P < 0.05), with gravel microcosms showing significantly higher gene abundance (8.00 × 10[-4]-2.08 × 10[-3]), despite similar community compositions governed by stochastic assembly (R[2] > 0.84). Topological analysis revealed that redundancy of functional gene network significantly influenced ammonium removal efficiency (P < 0.05), with fine sand and gravel enhancing ammonium removal, while lower clustering coefficients in artificial filler and gravel microcosms significantly promoted total organic carbon removal. This study suggested that fine sand and gravel should be more effective riverbed substrates for enhancing interfacial nutrient removal in urban river restoration.}, } @article {pmid42071059, year = {2026}, author = {Gajjar, K and Panchal, D and Chaudhary, M and Raval, I and Chaudhary, D and Patel, CK and Bagatharia, S and Joshi, C and Patel, A and Dharajiya, D}, title = {Multi-omics characterization of microbial and metabolite profiles of Jeevamrit and Ghanjeevamrit cow-based bioformulations used in sustainable agriculture.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-50831-5}, pmid = {42071059}, issn = {2045-2322}, support = {GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; }, abstract = {Jeevamrit (JV) and Ghanjeevamrit (GH) are traditional cow-based bioformulations used in natural farming practices, and this study provides a comprehensive characterization of their microbial profiles via 16 S rRNA amplicon metagenomics and metabolite profiles via GC-MS and LC-MS analysis, with two different groups of samples: experimental preparation (EP) and farmer preparation (FP). JV and GH harbored diverse and functionally rich microbial communities, including Lactiplantibacillus, Arcobacter, Comamonas, Planifilum, Pseudomonas, Gp6, etc., associated with nutrient cycling, microbial activity, and plant growth promotion. Untargeted metabolomics revealed ~ 222 (GC-MS) and ~ 1049 (LC-MS) metabolites in Jeevamrit and ~ 96 (GC-MS) and ~ 1208 (LC-MS) metabolites in Ghanjeevamrit. These metabolites were primarily classified as organoheterocyclic compounds, organic acids, lipids, benzenoids, and organic oxygen/nitrogen compounds, and are functionally associated with nutrient solubilization, microbial metabolism, regulation of plant growth, and enhancement of stress tolerance. Multi-omics analysis revealed a clear separation of EP and FP groups with high inter-omics correlations (Jeevamrit up to r = 0.92; Ghanjeevamrit up to r = 0.91). Jeevamrit exhibited dense connectivity with predominance of positive microbial-metabolite associations, while Ghanjeevamrit displayed fewer and more balanced positive and negative correlations. Overall, the study demonstrates that Jeevamrit and Ghanjeevamrit are microbially diverse and metabolically rich bioformulations, reinforcing their roles in enhancing soil health and plant growth. Future works on strain-level diversity, functional pathways analysis, and field trials across different crops and soil types are needed for the standardization and optimization of natural farming inputs.}, } @article {pmid42071227, year = {2026}, author = {Guo, S and Cao, M and Wu, J and Ma, W and Liang, D and Xie, H and Xie, Y and Luo, Z and Lai, P and Liu, D and Zeng, W and Zheng, J and Xing, M and Yin, X and Xia, M and He, Z}, title = {Parvimonas micra promotes carcinogenesis of colorectal cancer through phenyllactic acid-induced DNA damage.}, journal = {Clinical and translational medicine}, volume = {16}, number = {5}, pages = {e70667}, pmid = {42071227}, issn = {2001-1326}, support = {2022YFA1304000//National Key R&D Program of China/ ; 2024B1111150001//Guangdong S&T Program/ ; //National Key Clinical Discipline/ ; U21A20344//National Natural Science Foundation of China/ ; 82273346//National Natural Science Foundation of China/ ; 2020B1111170004//Guangdong Provincial Clinical Research Center for Digestive Diseases/ ; 2021B1212040017//Science and Technology Program of Guangdong Province, China/ ; 2024A04J4086//Science and Technology Program of Guangdong Province, China/ ; B2302036//Shenzhen Medical Research Special Fund Project Target disease/ ; 2023WST03//Key Laboratory Start-Up Project (Sixth Affiliated Hospital of Sun Yat-Sen University)/ ; }, mesh = {*Colorectal Neoplasms/microbiology/genetics/pathology/etiology ; Humans ; Animals ; *DNA Damage/drug effects ; Mice ; Male ; *Lactates/metabolism/adverse effects ; Gastrointestinal Microbiome ; *Carcinogenesis ; Female ; Feces/microbiology ; Middle Aged ; }, abstract = {Recent studies have demonstrated the significance of gut microbiota in the colorectal cancer (CRC) pathogenesis. But their role in carcinogenesis remains to be established. Thus, we established a clinical cohort and the faecal samples from CRC and healthy control were collected. Our metagenomic analysis found that the presence of Parvimonas micra exhibited the most significant relationship with the occurrence of CRC. Increased colonisation of P. micra in CRC was validated with analysis of 1379 faecal metagenomes from eight public cohorts. Untargeted metabolomics subsequently identified an accumulation of phenyllactic acid (PLA) in faecal samples from CRC patients. Higher concentration of PLA was detected in the supernatant from our isolated P. micra. Whole-genome sequencing confirmed that a series of genes associated with PLA biosynthesis such as pdhD were observed in the P. micra genome. Importantly, both P. micra and PLA-induced carcinogenesis in Apc[Min/+] and azoxymethane/dextran sulphate sodium salt mice model. The roles of P. micra and PLA in CRC development were associated with DNA damage. Engineered Escherichia coli BL21 that encoded the heterologous pdhD from P. micra could also induce DNA damage. Mechanically, PLA-induced DNA damage and CRC carcinogenesis were significantly alleviated in Ahr[-/-] mice. Aryl hydrocarbon receptor (AHR) inhibitor exhibited a therapeutic potential to reduce mice carcinogenesis. These findings established the role of P. micra and its metabolite, therefore providing diagnostic and therapeutic targets for treating CRC.}, } @article {pmid42071909, year = {2026}, author = {Corrigan, A and Stockdale, S and Mackenzie, AM and Wilkinson, RG and Warren, H and Taylor-Pickard, J and Murphy, R}, title = {Rumen Microbiome Development in Lambs Following Maternal and Early-Life Prebiotic Mannan-Rich Fraction (MRF) Supplementation.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {8}, pages = {}, pmid = {42071909}, issn = {2076-2615}, support = {NA//Alltech (Ireland)/ ; }, abstract = {The early-life rumen microbiome is highly dynamic, shaped by dietary transitions and maternal influences. Several dietary additives have been studied during the pre- and post-weaning periods to improve animal welfare, growth performance, and farming efficiencies. This study investigated microbial community assembly and growth performance of lambs provided with a mannan-rich fraction (MRF) supplement, either through maternal supplementation, directly, or via a combination of both. Using metagenomic sequencing and gas chromatography, we found differences in rumen microbial alpha and beta diversity related to both sampling time point and MRF supplementation (p < 0.05). At week 8, lamb microbiomes showed greater variance in their Shannon alpha diversity, with direct MRF supplementation only to the lamb resulting in a significantly greater diversity (p < 0.05). At week 20, combined maternal and lamb supplementation resulted in the highest Shannon diversity and was different compared to all other groups (p < 0.05). Beta diversity analyses combined with differential abundance analyses revealed that microbial community structures are driven by both diet and time, with maternal MRF supplementation associated with enrichment of taxa involved in carbohydrate fermentation and succinate metabolism, including Succiniclasticum ruminis, Succinovibrio dextrinosolvens, and Fibrobacter succinogenes. Generalized linear modeling identified significant associations between microbial alpha diversity metrics and total volatile fatty acids in lambs, particularly butyrate and valerate. Furthermore, at week 8, there was a significant positive correlation between alpha diversity metrics and propionate and valerate. In this study, lambs receiving MRF through maternal and direct supplementation had the highest growth performance, measured as the median average daily gains (kg) and final weights (kg) of lambs. These findings suggest that MRF supplementation, especially when provided both maternally and directly, may influence the lamb rumen microbiome and alter its metabolic potential with potential implications for optimizing early-life nutrition strategies in ruminant production systems.}, } @article {pmid42072313, year = {2026}, author = {Alamri, A and Almutairi, AK and AlSinan, F and Alramadhan, A and Aldehalan, F and Almutairi, H and Alghuraybi, M and AlHarbi, NM and Alghannam, SF and Alotaibi, SS and AlOmary, M and AlKhater, S}, title = {Functional and Resistome Profiling of Paediatric Airway Microbiota in Asthma Using Shotgun Metagenomics.}, journal = {Biomedicines}, volume = {14}, number = {4}, pages = {}, pmid = {42072313}, issn = {2227-9059}, support = {IF-2020-016-CAMS//This work was funded by the Deputyship for Research & Innovation, Ministry of Education in Saudi Arabia (IF-2020-016-CAMS) and approved by the deanship of scientific research (DSR) at Imam Abdulrahman bin Faisal University (IAU)./ ; }, abstract = {Background/Objectives: Asthma affects millions of patients worldwide and impacts their quality of life, particularly among children. Colonisation or an imbalance within natural resident microbiota may drive inflammatory responses in asthma; antibiotic resistance genes (ARGs) have also been investigated in asthma microbiome studies. However, research on the association between airway microbiota and ARGs remains limited. Therefore, we elucidated functional-level characterisation at the level of ARGs, virulence factors, and active pathways among a paediatric asthma cohort relative to a healthy control. Methods: Overall, 29 children with asthma and 20 control subjects were enrolled, and 3 swabs (2 nasal and 1 oropharyngeal) were obtained from each participant. Genomic DNA was extracted and sent for shotgun sequencing, after which bioinformatic analysis was conducted to remove human reads and analyse the microbiota pattern in the samples. The abundance of antibiotic resistance genes was evaluated along with the distribution of virulence genetic markers. Functional investigation of the most prevalent metabolic pathways was also performed. Results: Upper airway microbiome functional capacity varied by anatomical location, with oropharyngeal communities exhibiting greater metabolic breadth than nasal communities, suggesting the sample source to be the dominant factor shaping gene content, pathway profiles, and community structure. Asthma-related functional differences were modest, and no biological pathways remained significant following false discovery rate correction. Enrichment of antimicrobial resistance genes was observed, particularly those conferring resistance to β-lactams, macrolides, and tetracyclines. Conclusions: Different anatomical niches exhibit differential activities, and further exploration in this direction could aid in the development of diagnostic and therapeutic biomarkers for asthma.}, } @article {pmid42073328, year = {2026}, author = {Indio, V and Mekonnen, YT and Oliveri, C and Rubboli, S and Candela, M and Seguino, A and Serraino, A and De Cesare, A}, title = {Reducing Antimicrobial Resistance in Poultry Carcasses Extends Beyond Farm-Level Interventions.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {8}, pages = {}, pmid = {42073328}, issn = {2304-8158}, support = {Horizon 2020 "Controlling Microbiomes Circulations for Better Food Systems" (CIRCLES) no. 818290.//European Union/ ; }, abstract = {The aim of this study was to assess how raising chickens without the use of antimicrobials affects the microbiome of poultry carcasses. A total of 151 caeca and neck skin samples from chickens raised without antimicrobials were collected in the same slaughterhouse and submitted to shotgun metagenomic sequencing. Caeca were dominated by Bacillota and Bacteroidota, while carcasses by Pseudomonadota. The caeca microbiome was enriched in genes related to a proliferating and metabolically active microbial community. Carcass-associated microbiomes were enriched in functional genes linked to adaptation to nutritionally limited and oxidative environments. A significantly higher cumulative antimicrobial resistance gene abundance was detected in carcasses compared to caeca. Specifically, carcasses exhibited approximately 1.5 times more AMR genes, reflecting an increase of nearly 49%. While caeca showed enrichment of resistance determinants associated with Gram-positive anaerobic gut commensals, carcasses were characterized by a predominance of multidrug efflux systems and clinically relevant β-lactam resistance genes, commonly associated with environmental and opportunistic Gram-negative bacteria. In carcasses, carbapenem-associated genes, such as OXA-58-like and CphA, were detected. However, these genes have not been associated with carbapenemase-producing Enterobacterales. Overall, the findings of this study indicate that reducing antimicrobial resistance in food animal production systems extends beyond farm-level intervention. At present, the benefits of the interventions aimed at reducing antimicrobial resistance at farm level seem to be compromised during the post-harvest stages.}, } @article {pmid42073366, year = {2026}, author = {Brasileiro, CG and Moreno, MTDC and Santos, EO and Saranraj, P and Cardoso, AM and Vieira, JMBD}, title = {Assessing Food Safety Risks in Homemade Fermented Beverages: A Case Study with Quinoa Rejuvelac.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {4}, pages = {}, pmid = {42073366}, issn = {2075-1729}, support = {E2023//FAPERJ, CNPq, and CAPES/ ; }, abstract = {Spontaneous fermentation processes can promote uncontrolled microbial growth and increase the risk of foodborne contamination, making the characterization of artisanal beverages essential for consumer safety. This study investigated the microbial composition of quinoa-based rejuvelac, a homemade fermented drink often perceived as a functional food, with the objective of identifying potential microbiological hazards associated with its preparation. High-throughput sequencing of the 16S rRNA V3-V4 region was combined with shotgun metagenomics to profile bacterial communities and recover metagenome-assembled genomes. The analysis revealed a strong dominance of Pseudomonadales, mainly Pseudomonas, Acinetobacter, Enterobacter and Burkholderiales, while lactic acid bacteria typically responsible for stable and safe fermentations were not detected. Shotgun metagenomics recovered medium- to high-quality genomes from Burkholderiaceae and Clostridiales, supporting the overrepresentation of non-beneficial taxa and indicating deviations from expected fermentation microbiota. These results show that the spontaneous preparation of rejuvelac may favor bacterial groups associated with environmental contamination rather than fermentative pathways, underscoring the importance of hygiene practices, controlled starter cultures and monitoring strategies to mitigate microbiological risk. The study highlights the need for improved safety standards in artisanal fermented foods to prevent unintended microbial contamination and protect consumers.}, } @article {pmid42073451, year = {2026}, author = {Cerreto, M and Maestri, M and Pallozzi, M and Cerrito, L and Stella, L and Ianiro, G and Gasbarrini, A and Ponziani, FR}, title = {Gut Microbiota Biomarkers in Patients with Hepatocellular Carcinoma in the Era of Immune Checkpoint Inhibitors.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {4}, pages = {}, pmid = {42073451}, issn = {2075-1729}, abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized the therapeutic landscape for hepatocellular carcinoma (HCC); however, a considerable proportion of patients do not achieve durable clinical benefits. This highlights the need for reliable predictive biomarkers, which are currently lacking. The accumulated evidence supports a relevant role of the gut-liver axis in modulating immunotherapy outcomes, and several studies have identified distinct microbial features associated with either responders or non-responders. Responders to immunotherapy frequently present with higher microbial diversity and enrichment of beneficial taxa, whereas the expansion of pro-inflammatory and pathogenic bacteria has been associated with primary resistance and increased treatment-related toxicity in non-responders. However, the available findings remain heterogeneous across cohorts, likely owing to differences in geography, diet, liver disease etiology, treatment regimens, and microbiome analytical methods. Machine-learning models integrating metagenomic and metabolomic data have shown encouraging results in defining microbial signatures associated with treatment outcomes, although variability among cohorts currently limits their clinical applicability and generalizability. Beyond microbial taxonomic composition, microbiota-derived metabolites-such as short-chain fatty acids, bile acids, inosine, and tryptophan catabolites-appear to play a crucial role in shaping the tumor microenvironment and host immune responses, thus representing additional candidate biomarkers, also due to the relative ease of their measurement. Finally, microbiota-targeted interventions are emerging as potential strategies to enhance immunotherapy efficacy. Overall, the gut microbiome and its metabolic activity represent promising tools, albeit still under investigation, for patient stratification and personalized management in HCC treated with ICIs. Therefore, this review aims to summarize and critically discuss the current evidence on gut microbiota-derived biomarkers of response and resistance to ICIs in HCC, with particular focus on microbial composition, microbiota-related metabolites, and emerging microbiome-based therapeutic strategies. This narrative review provides an updated overview of the role of gut microbiota as both a biomarker and a therapeutic target in patients with hepatocellular carcinoma (HCC) receiving immune checkpoint inhibitor (ICI) therapy.}, } @article {pmid42073497, year = {2026}, author = {Carraturo, F and Salamone, M and Annunziata, M and Di Brizzi, EV and Giorgio, CM and Petrillo, A and Fedi, L and Maione, A and Guida, M and Galdiero, E}, title = {Preliminary Characterization of Skin Microbiota and Mycobiota in Atopic Dermatitis by Metagenomic and Culture-Based Analyses.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {4}, pages = {}, pmid = {42073497}, issn = {2075-1729}, support = {PRIN2022//European Union-Next Generation EU location/ ; 2022HC3FRM//Serum metabolomics in atopic dermatitis (MetabAD)/ ; }, abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease influenced by several factors, including immune system imbalance, impairment of the epidermal barrier, and alterations in the composition of the gut and skin bacterial and fungal microbiota. This study combines metagenomic sequencing and culture-based methods to explore the impact of probiotic supplementation on the cutaneous microbiota and mycobiota of AD patients. Twenty-five adults diagnosed with AD were enrolled, and skin swabs were analyzed to characterize microbial diversity and load. Culturomic analyses identified 42 bacterial and 6 fungal species, confirming Staphylococcus aureus and Candida parapsilosis as predominant taxa. High-throughput sequencing revealed Staphylococcus spp. and Malassezia spp. as dominant genera, with notable interindividual variability. While probiotic use did not significantly influence bacterial diversity, it was associated with higher richness and evenness in fungal communities, as shown by alpha and beta diversity metrics. Malassezia restricta was more prevalent among probiotic users, whereas Candida parapsilosis and Rhodotorula mucilaginosa were enriched in non-users. These findings indicate an association between probiotic use and differences in the composition and diversity of the skin mycobiota compared with the bacterial microbiota, suggesting that fungal communities may be more responsive to probiotic-associated factors. Integrating metagenomic and culturomic approaches offers valuable insights into the complex interactions among host factors, microbial communities, and probiotic use in AD, paving the way for targeted microbiome-based therapeutic strategies.}, } @article {pmid42073729, year = {2026}, author = {Ren, L and Zhang, X and Xu, X and Qin, Q and Fan, H and Wang, Z and Wang, W}, title = {Enhancing Duck Manure Anaerobic Digestion with Hydrochar: Exploring Green Material Potential via Bidirectional AD-HTC Coupling.}, journal = {Materials (Basel, Switzerland)}, volume = {19}, number = {8}, pages = {}, pmid = {42073729}, issn = {1996-1944}, support = {Grant No. 52300163//National Natural Science Foundation of China/ ; Grant No. ZR2024QE099//Shandong Provincial Natural Science Foundation/ ; }, abstract = {The efficient resource utilization of duck manure and agricultural/forestry wastes (AFW) plays a significant role in environmental protection and promoting the sustainable development of the economy and society. This study examined the effects of hydrochar derived from AFW in the anaerobic digestion (AD) process, determining the optimal addition ratio. This research systematically investigated the impact of hydrochar on methane yield, as well as changes of short-chain fatty acids, microbial community dynamics, and metabolic pathways during AD of duck manure. The underlying mechanisms were clarified by metagenomic and metabolomic analyses. This experiment used duck manure as substrate and added hydrochar of four different dosage levels. Laboratory batch tests ran for 32 days at 37 ± 0.5 °C, with three parallel samples for each group. The results indicated that hydrochar additive significantly improved methane yield (p < 0.05), with a maximum increase of 27.13% at an optimal dosage of 10.91 g·L[-1]. This amendment enhanced the abundance of Firmicutes, Bacteroidota, Chloroflexota, Halobacteriota, and Methanosarcina significantly. Compared to the control group, the abundances of functional genes involved in hydrolysis, acidogenesis, and acetogenesis pathways increased by 28-254% in the optimal treatment group, with methanogenesis-related genes showing a 16-155% enhancement (p < 0.05).}, } @article {pmid42074337, year = {2026}, author = {Liu, X and Chen, Y and Zhou, X and Xiao, Y and Yuan, X and Su, N and Chen, C and Yan, Q and Chen, X}, title = {Bacillus subtilis and Trichoderma harzianum Reshape Rhizosphere Microbiome and Reprogram Root Transcriptome to Promote Mungbean Growth Under Continuous-Cropping Conditions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {8}, pages = {}, pmid = {42074337}, issn = {1422-0067}, support = {2025YFE0121200//National Key R&D Program of China/ ; CARS-08//China Agriculture Research System of MOF and MARA-Food Legumes/ ; JBGS[2021]004//Jiangsu Seed Industry Revitalization Project/ ; }, mesh = {*Bacillus subtilis/physiology ; *Rhizosphere ; *Vigna/growth & development/microbiology/genetics ; *Plant Roots/microbiology/genetics/growth & development ; *Transcriptome ; *Microbiota ; Soil Microbiology ; Metagenomics ; *Hypocreales/physiology ; Gene Expression Profiling ; }, abstract = {Mungbean (Vigna radiata) is an important cash crop, yet the production is significantly compromised by continuous cropping. Beneficial microbial inoculation offers a promising strategy to alleviate the stresses through rhizosphere modulation and host physiological reprogramming. This study evaluated the efficacy of two biological control agents, Bacillus subtilis (B. subtilis) and Trichoderma harzianum (T. harzianum), in promoting mungbean growth under continuous-cropping conditions. Both individual applications of B. subtilis and T. harzianum significantly improved plant biomass, root system architecture, and yield. Combined metagenomic and transcriptomic analyses were conducted to unravel the underlying mechanisms. According to metagenomic analysis, both B. subtilis and T. harzianum were responsible for significant changes in beta diversity without significantly affecting the alpha diversity of the rhizosphere microbial community. T. harzianum recruited Chitinophagaceae unclassified, Abditibacterium, Hydrogenophilaceae unclassified, Methylophilaceae unclassified, and Chimaeribacter, while Bs recruited Candidatus Saccharibacteria unclassified. Transcriptomic analysis indicated that T. harzianum induced more extensive transcriptional reprogramming than B. subtilis. The enrichment analysis revealed both shared and distinct responses triggered by the two treatments. These findings suggest that B. subtilis and T. harzianum alleviate continuous-cropping stress through distinct yet complementary mechanisms involving rhizosphere microbiome modulation and mungbean transcriptional reprogramming. This study provides a sustainable strategy for legume cultivation.}, } @article {pmid42075183, year = {2026}, author = {van Essen, RRT and Kaur, J and Li, T and Sawbridge, TI}, title = {Isolation of N-Fixing Bacteria from Warm-Season Pasture Grasses and the Evaluation of Nitrogen Effects on the Bacterial Communities Present in Cenchrus clandestinus.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, pmid = {42075183}, issn = {2076-2607}, support = {DB F.2//DairyBio 21-26, Future Forages Program/ ; }, abstract = {Nitrogen is essential for plant growth. Reliance on synthetic nitrogen fertilisers, however, is costly and contributes to soil degradation. Utilising nitrogen-fixing bacteria as biofertilisers may offer a sustainable alternative, reducing fertiliser costs and environmental impact. In this study, we attempted to isolate nitrogen-fixing bacteria from 14 seed batches of warm-season pasture grasses and successfully isolated bacteria from three of these batches. Whole genome sequencing confirmed the presence of the nif operon within all three isolates. Two seed batches of Cenchrus clandestinus (Hochst. ex Chiov.) Morrone from which nif-containing bacteria were isolated, along with two 'nif'-negative C. clandestinus seed batches, were used in nitrogen-limiting growth assays. This was done to evaluate the effect of the presence of seed-associated nitrogen-fixing bacteria within a seed batch on nitrogen-limited plant growth and the associated plant microbiome composition, using 16S amplicon sequencing of root and shoot samples. Initial plant growth assays revealed significantly reduced root length between plants grown from seed batches harbouring nitrogen-fixing bacteria and those without, under limiting nitrogen availability, but no resulting shoot biomass reduction was observed. The plant microbiomes of these nif-positive seed batches were also statistically similar to each other, compared to the nif-negative seed batch plants. Plant microbiomes of all four C. clandestinus seed batches were significantly different from their original seed microbiomes, showing shifts in community composition. This study demonstrates the presence of potential nitrogen-fixing bacteria associated with warm-season pasture grass seeds at low abundance and reveals differences in plant-associated bacterial community composition between seed batches harbouring and lacking these bacteria.}, } @article {pmid42075229, year = {2026}, author = {Lai, R and Wang, Z and Liu, P and Tong, J and Ahmed, Z and Cui, R and Gu, Y and Luo, G}, title = {Environmental Altitude and Host Genetics Shape Divergent Microbiota and a Conserved Resistome in Porcine Intestinal Niches.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, pmid = {42075229}, issn = {2076-2607}, support = {Grant No. RQD2025005//Southwest Minzu University Research Startup Funds/ ; 32472888//National Natural Science Foundation of China/ ; XZ202501ZY0147//Science and Technology Projects of Xizang Autonomous Region/ ; 2024YFHZ0373//Sichuan Science and Technology Program/ ; sccxtd-2026-08//Program for Pig Industry Technology System Innovation Team of Sichuan Province/ ; 2024MS150//he Sichuan Provincial Administration of Traditional Chinese Medicine Science and Technology Research Special Project/ ; }, abstract = {Environmental stressors and host genetics influence gut microbiota and antimicrobial resistance, but their combined effects across intestinal niches remain poorly unexplored. We conducted a metagenomic analysis of 60 jejunal and cecal samples from 30 native Chinese pigs across three altitudes (500 m, 1400 m, and 3850 m). The aim was to disentangle the interactive impacts of altitude, breed, and intestinal site on microbiome structure and antibiotic resistome dynamics. The cecal microbiota was taxonomically conserved and strongly associated with breed. Conversely, while jejunal communities exhibited structural variations among the sampled cohorts, differences in alpha diversity (Shannon index, p < 0.01) appeared to be primarily associated with breed differences rather than an independent altitudinal effect. High-altitude Tibetan pigs showed an enrichment of Bifidobacterium and Pseudomonas, which may be linked to hypoxia adaptation. Despite a shared core resistome (88 ARG types), the cecum harbored significantly higher ARG abundance than the jejunum within-breed comparisons of Tibetan pigs across altitudes; this revealed stable ARG profiles (p > 0.05) suggesting that, although some descriptive differences were observed, the independent effect of altitude weakens when the genetic effect is taken into account. Furthermore, carbohydrate-active enzymes (e.g., CBM13, GH33) correlated positively with ARG abundance. In conclusion, the jejunum appears to act as an environmentally responsive niche, while the cecum exhibits a higher ARG abundance that is closely associated with the host breed.}, } @article {pmid42075233, year = {2026}, author = {Mousa, WK and AlShami, R and Ghemrawi, R}, title = {Shared Microbial Blueprints Underlying Symbiotic Plasticity in Desert Plant Endophytes.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, pmid = {42075233}, issn = {2076-2607}, support = {SWARD-F23-020.//Sandooq Al Watan/ ; }, abstract = {The desert ecosystem harbors a resilient microbial community that sustains plant life under extreme stress. Understanding the endophytic microbiota of desert flora provides key insights into how these microorganisms enable plant survival and maintain ecological balance in arid landscapes. To date, the endophytic bacterial communities of dominant desert plants in the Arabian Peninsula have not been comprehensively characterized. Here, we investigated the endophytic microbiota of five co-adapted desert species, namely, Schweinfurthia papilionacea, Sesuvium verrucosum, Ochtocloa compressa, Helianthemum nummularium, and Convolvulus arvensis. These plants coexist in hyper-arid habitats and exhibit exceptional tolerance to drought, salinity, and nutrient scarcity. We hypothesized that, despite their phylogenetic divergence, these plants host functionally convergent microbial communities shaped by desert selection pressures. Using 16S rRNA gene amplicon sequencing, we obtained 3.4 million high-quality reads from 25 samples. Clustering at 97% similarity revealed 35 phyla and 17 dominant genera, highlighting notable microbial richness and ecological complexity. Alpha-diversity indices showed comparable species richness across hosts, while beta-diversity indicated community differentiation driven by environmental filtering. The dominant phyla included Pseudomonadota, Actinomycetota, Cyanobacteriota, and Bacillota, reflecting microbial adaptation to extreme desert conditions. Functional pathway prediction revealed enrichment of genes associated with DNA repair and protein turnover, suggesting metabolic flexibility and enhanced survival under stress. Overall, this study provides a comparative metagenomic insight into the endophytic bacterial communities of five desert plant species, uncovering a consistent pattern of functional convergence across diverse hosts. The findings suggest the presence of shared functional traits among the endophytic microbiota examined here, offering preliminary evidence for microbial contributions to plant resilience in arid environments.}, } @article {pmid42075236, year = {2026}, author = {Wang, Z and Ma, C and Huang, H and Ke, S and Lv, J and Hu, J and Wang, S and Bao, Z}, title = {Holo-2bRAD: A Hologenomic Method for High-Resolution Analysis of Coral Microbiomes During Bleaching.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, pmid = {42075236}, issn = {2076-2607}, support = {2025B1111180001//Guangdong S&T Program/ ; 2025A04J3824//GCI Science & Technology (China)/ ; SOLZSKY2025013//Department of Science and Technology of Hainan Province/ ; }, abstract = {Coral reefs are biodiversity hotspots increasingly threatened by climate-induced bleaching, yet profiling the coral holobiont-the host and its associated microbiota-remains technically challenging due to high host-DNA contamination (often >95%) and the lack of comprehensive reference databases. Here, we present holo-2bRAD, a type IIB restriction site-associated DNA sequencing approach. This method, strategically integrated with a meticulously curated hologenome database (comprising 404,946 microbial genomes and 56 coral-derived metagenome-assembled genomes), effectively overcomes overwhelming host contamination (~99%). We demonstrate its exceptional species specificity (99.92%) in profiling Galaxea fascicularis (Linnaeus, 1767; Order Scleractinia, Family Euphylliidae) holobionts across bleaching severities, thereby validating its technical feasibility. Leveraging this high-resolution tool, our hologenome analysis revealed significant restructuring of coral-associated microbiota during bleaching, where microbial shifts (e.g., depletion of beneficial Thermoanaerobacterium thermosaccharolyticum and enrichment of stress-responsive bacteria) correlated more strongly with bleaching phenotypes than host genetic variation. By providing cost-effective, multi-domain hologenome profiling at unprecedented resolution, holo-2bRAD offers a practical tool for investigating holobiont dynamics and developing microbiome-informed coral conservation strategies.}, } @article {pmid42075252, year = {2026}, author = {Amin, H and Šantl-Temkiv, T and Finster, K and Schlünssen, V and Sigsgaard, T and Wouters, IM and Sørensen, MT and Malinovschi, A and Thorarinsdottir, H and Bertelsen, RJ}, title = {Airborne Movement of Antibiotic Resistance Genes Between Livestock Stables and Farmers' Homes.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, pmid = {42075252}, issn = {2076-2607}, support = {TMS2021TMT03//Trond Mohn stiftelse/ ; No. 137087//NordForsk/ ; }, abstract = {Antibiotic resistance genes (ARGs) are prevalent in livestock environments due to antimicrobial use, yet their airborne dispersal into human-occupied indoor spaces remains poorly characterized. We investigated whether airborne ARGs disperse from livestock stables into farmers' homes and surrounding outdoor environments. Electrostatic dust collectors were deployed in paired pig and cow stables and their associated homes in Jutland, Denmark, to collect settled airborne dust. Pooled samples were analyzed using shotgun metagenomic sequencing. ARG dispersal patterns were assessed using FEAST source tracking and ecological similarity metrics, including shared ARG ratios and Jaccard indices. Pig production systems exhibited higher antibiotic use and stronger resistome continuity with farmers' homes than cow systems, reflected by greater FEAST contributions (P = 0.029) and Jaccard similarity (P = 0.029). Beta-diversity analysis supported higher compositional similarity between pig stables and homes (PERMANOVA R[2] = 0.23, p = 0.052), whereas cow environments showed greater divergence (R[2] = 0.41, P = 0.035). Across environments, tetracycline, macrolide-lincosamide-streptogramin B, and aminoglycoside resistance genes dominated, consistent with livestock-specific antibiotic use patterns. Supplementary indoor-outdoor comparisons across cow, pig, and chicken stables (from an independent 2024 sampling campaign not directly comparable to the 2008 EDC-based survey) revealed contrasting dispersal dynamics, with higher bacterial species spillover from cow stables but stronger ARG overlap from pig stables. Collectively, these findings are consistent with airborne ARG connectivity across occupational and environmental interfaces and support consideration of air as a potential pathway in One Health AMR surveillance.}, } @article {pmid42075269, year = {2026}, author = {Yang, J and Yue, Y and Li, X and Lv, R}, title = {Dynamics of Microbial Carbon Metabolism During Vegetation Restoration in Sandy Ecosystems.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, pmid = {42075269}, issn = {2076-2607}, support = {2024B04031-2//Research and Development of Efficient Utilization Technology for Brackish Water in Desert Photovoltaic Power Stations/ ; 2024AAC03102//Natural Science Foundation of Ningxia/ ; }, abstract = {Understanding the succession of soil microbial carbon metabolism functions is crucial for elucidating carbon cycling mechanisms during ecosystem restoration in sandy lands. Soils were collected from Caragana korshinskii shrubland sites across a restoration chronosequence (0, 10, 30, 50, and 70 years) in the Mu Us Sandy Land. Biolog carbon source utilization analysis and metagenomic sequencing were employed to characterize the successional patterns of microbial carbon metabolism functions-a shift in carbon metabolism strategies from acquisition to conservation, and a transition in functional diversity from generalism to specialization. The results indicated that microbial communities exhibited two associated successional shifts in functional characteristics: carbon source utilization tended to transition from simple to complex substrates, while functional gene expression showed a progressive shift from broad multi-pathway patterns toward pathway-specific specialization. AWCD values increased continuously with restoration duration, and carbon source utilization patterns diverged significantly around 30 years. Early-stage sites (0-30 years) primarily utilized simple carbon sources, whereas late-stage sites (50-70 years) shifted toward more complex and diverse substrates. Principal component analysis revealed that 27 carbon sources contributed 91.3% of the variance to PC1. Microbial community structure succession revealed that Actinobacteria peaked at 10 years (43.63%), Proteobacteria peaked at 30 years (45.66%), and taxa such as Bacilli and Solirubrobacter dominated at 50-70 years. Carbon metabolism pathways exhibited stage-specific succession: glycolysis and the ED pathway were active in early stages, acetate metabolism dominated with the 3HB cycle peaking in intermediate stages, and the CBB cycle increased in later stages while methane metabolism shifted from high to low contribution. These two associated successional shifts occurred along the same restoration chronosequence, with the progressive transition in substrate utilization accompanying the development of specialist functional characteristics. These findings provide insights into the successional dynamics of microbial carbon metabolism during vegetation restoration, offering a microbiological basis for optimizing ecological restoration practices and enhancing soil carbon sequestration in sandy lands.}, } @article {pmid42075270, year = {2026}, author = {Oladipo, P and Kade, A and Onohuean, H and Ram, JL}, title = {From Cryptic Clade to Emerging Pathogen: Exploring the Evolutionary Divergence and Clinical Relevance of Escherichia marmotae.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, pmid = {42075270}, issn = {2076-2607}, abstract = {The Escherichia genus includes both commensal and pathogenic species and is characterized by its diversity and adaptability to the mammalian gut and other environments. Among these species, E. coli has facilitated many scientific advances as a model organism. Recently, a new member of the Escherichia genus, Escherichia marmotae, has been described as a phylogenetically distinct clade that shows the greatest genetic divergence from E. coli. This review explores E. marmotae, its cryptic evolution, distinct characteristics, and ecological niches. E. marmotae has recently gained scientific prominence due to its association with animal feces, environmental occurrence, human clinical samples, and emerging as a potential pathogen. While its pathogenicity remains understudied, growing evidence from clinical, environmental, and animal sources suggests the need for heightened surveillance. This review highlights current knowledge gaps, underscores the need for improved diagnostic tools, and proposes future research directions to elucidate the clinical and ecological implications of this emerging pathogen.}, } @article {pmid42075274, year = {2026}, author = {Chen, L and Chen, Y and Peng, Q and Zhou, D and Feng, S}, title = {Metagenomics and Metagenome-Assembled Genomes Analysis of Highland Barley Baijiu Daqu.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, pmid = {42075274}, issn = {2076-2607}, abstract = {Highland barley Baijiu is a kind of fermented liquor with national characteristics produced in the Qinghai-Tibet Plateau, and its quality largely depends on the highland barley Baijiu Daqu (HBQ). HBQ contains abundant microbial resources and embedded unknown genomes that have not yet been decoded. In order to deeply understand the key contribution of microorganisms in HBQ, this study analyzed the microbial community structure of HBQ, inferred predicted functions and recovered high-quality metagenome-assembled genomes (MAGs) based on Metagenomics. The results indicated that Pantoea agglomerans was the most abundant species in HBQ, followed by Lichtheimia ramosa, Pichia kudriavzevii, Saccharomycopsis fibuligera and Wickerhamomyces anomalus. The predictive function of the HBQ was focused on annotating carbohydrate metabolism and amino acid metabolism. Meanwhile, six high-quality MAG strains were recovered and identified as Unclassified Kroppenstedtia, Erwinia persicina, Leuconostoc citreum, Saccharopolyspora rectivirgula, Levilactobacillus brevis, and Pantoea agglomerans. Genome annotation of the recovered genomes showed eggNOG predicted function as well as primary and secondary metabolites. The metabolic network diagram of the functional microorganisms in HBQ related to flavor compounds was also predicted. The results can help to understand the formation mechanism of flavor profiles in highland barley Baijiu.}, } @article {pmid42075297, year = {2026}, author = {Li, X and Qin, Z and Wang, H and Tao, X and Xia, J and Zhao, Y and Yi, P and Ma, Y and Wang, X and Ma, X and Li, N and Zhong, Q and Yao, G}, title = {Seasonal Dynamics of Skin Microbiota and Metabolites in Transhumant-Grazed Altay Sheep.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, pmid = {42075297}, issn = {2076-2607}, support = {2022TSYCJC0026//the "Tianshan Talent" Youth Science and Technology Top Talent Project of Xinjiang Uygur Autonomous Region/ ; }, abstract = {To explore the seasonal variation patterns of the skin microecology of Altay sheep under transhumant grazing conditions, skin swabs were collected from 60 free-grazing Altay sheep at seasonal transition nodes in the Altay region. Metagenomic sequencing combined with untargeted metabolomics was used to characterize their bacterial community structure, functional pathways, and metabolite profiles. The results showed that the skin microecology of Altay sheep presented obvious seasonal variation patterns. In spring, 35 of the 39 highly abundant bacteria were environmentally derived, five proliferation-related pathways were significantly enriched, and the levels of five metabolites associated with microbial community regulation and skin barrier defense were elevated. In summer, the abundance of three skin symbiotic bacteria increased, the activities of eight pathways mainly related to biofilm formation were significantly enhanced, and the contents of five metabolites primarily associated with membrane lipid homeostasis and selective bacteriostasis increased. In autumn, the abundances of nine radiation-resistant and cold-tolerant strains increased, together with the elevated abundance of two opportunistic pathogens; five repair-related pathways were active, and the levels of four anti-inflammatory and repair-associated metabolites were synchronously increased. In winter, the abundance of two cold-tolerant strains increased, the activities of pathways related to nitrogen metabolism and energy synthesis were enhanced, and one lignan compound was identified as the key metabolite. These findings elucidate the seasonal dynamic patterns of the skin microecology of Altay sheep and provide a theoretical basis for research on the adaptive mechanisms and seasonal health management of Altay sheep and other sheep in alpine regions.}, } @article {pmid42075311, year = {2026}, author = {Cruells, A and Eguren, C and Robainas Barcia, A and Martínez, H and Sharaf, M and Ruiz, C and Sánchez-Baos, A and Carrón, N and Bou, L and Pérez, M and De Lucas, R and Guerra-Tapia, A}, title = {Shotgun Metagenomic Characterization of Acne Microbiota Before and After Treatment with a Topical Biotechnological Phytocomplex: Understanding Skin Dysbiosis.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, pmid = {42075311}, issn = {2076-2607}, abstract = {This study assessed the impact of a topical phytocomplex on the acne skin microbiota, encompassing bacterial, fungal, and phage communities. Skin samples obtained from participants exhibiting a positive response to the treatment were analyzed using high-throughput sequencing and bioinformatic approaches including taxonomic profiling, metagenome assembly, functional annotation, and phage identification. Results showed that after treatment, microbial diversity increased, reflecting a more balanced microbial composition. Cutibacterium acnes levels were reduced, particularly virulent IA1/IA2 phylotypes, whereas non-pathogenic or unclassified strains increased. Opportunistic pathogens such as Klebsiella pneumoniae were no longer detected, and beneficial genera including Psychrobacter and Dermabacter were enriched. Functional analysis showed reduced virulence- and biofilm-related pathways, alongside enhanced tryptophan metabolism, SCFA production, lipid synthesis, and riboflavin and folate biosynthesis. Fungal populations, dominated by Malassezia, became more evenly distributed, with notable post-treatment reductions in M. arunalokei, Exophiala spinifera, and Wickerhamomyces anomalus. Phage populations mirrored bacterial changes, with enrichment of Cutibacterium-associated phages post-treatment. These findings demonstrate that the phytocomplex promotes functional rebalancing of the skin microbiota by reducing pathogenic features while maintaining ecosystem stability. The inhibition of quorum sensing, potentially mediated by N-acyl-homoserine lactone acetylation, emerged from metabolic pathway annotation as a hypothetic key mechanism impairing bacterial communication and virulence associated with acne vulgaris.}, } @article {pmid42075321, year = {2026}, author = {Wang, W and Wang, Z and Zhang, P and Zhang, J}, title = {Environmental Regulation of Gut Microbial Networks Links to Growth Variation in Schizopygopsis younghusbandi Across Contrasting Aquaculture Systems.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, pmid = {42075321}, issn = {2076-2607}, support = {XZ202501JD0019; XZ202402ZD0005; XZ202401ZY0059//Science and Technology Program of Tibet Autonomous Region/ ; XZ202501JD0019//the Base and Talent Program Projects of Science and Technology Program of Tibet Autonomous Region/ ; 42371170//National Natural Science Foundation of China/ ; //the Agricultural and Animal Husbandry Science and Technology Innovation Project/ ; }, abstract = {Schizopygopsis younghusbandi is an endemic and economically important fish in the Qinghai-Xizang Plateau, but its aquaculture is limited by harsh environmental conditions and incomplete understanding of host-microbiome-environment interactions. This study applied metagenomic sequencing to examine how different culture environments affect growth, water microbial communities, and gut microbiome network stability. Three-year-old juveniles (initial body weight 50.57 ± 1.88 g) were reared for 90 days in five systems: conventional pond (P), wetland (WL), concrete tank (G), river (R), and recirculating aquaculture system (RC). No significant differences in initial body weight or length were observed among groups (p > 0.05). Fish in the RC system achieved the highest final body weight, weight gain rate, and specific growth rate (p < 0.05), while survival rates were highest in the river and RC groups and lowest in ponds (p < 0.05). Microbial diversity and community composition differed significantly among culture modes, with bacterial and protozoan communities showing the strongest environmental responsiveness. Co-occurrence network analyses revealed that RC and G systems exhibited higher network complexity, density, and proportion of positive correlations, reflecting enhanced microbial interaction and ecological stability, whereas the WL system showed reduced network connectivity. Correlation analysis indicated that bacterial abundance was positively associated with total nitrogen, total phosphorus, and dissolved oxygen (p < 0.05), highlighting environmental regulation of microbial assemblages. Overall, the aquaculture environment shapes gut microbial networks, which closely relate to growth performance. Recirculating aquaculture systems can mitigate growth limitations in plateau fish by stabilizing the environment and reinforcing gut microbial communities, providing a sustainable strategy for high-altitude aquaculture development.}, } @article {pmid42075340, year = {2026}, author = {Cheng, L and Shen, Q and Wang, Y}, title = {Root-Zone Nitrogen Fertilization Increases Oilseed Rape Yield: Reprogramming Rhizosphere N-Cycling and Strengthening Soil-Plant Coupling.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {8}, pages = {}, pmid = {42075340}, issn = {2223-7747}, support = {2024J0487//Scientific Research Fund Project of the Education Department of Yunnan Province/ ; 202304BQ040005//Project of Science and Technology Department of Yunnan Province/ ; }, abstract = {Root-zone nitrogen fertilization (RZF) can increase crop N uptake and yield, yet the underlying rhizosphere N-cycling functional mechanisms remain insufficiently resolved. In a field experiment with winter oilseed rape (Brassica napus L.), RZF was compared with conventional fertilization (CF) under the same N input rates, alongside a zero-N control (N0). Compared with CF, RZF significantly increased seed yield (by 0.44 t ha[-1]) and aboveground N uptake (by 20.45 kg ha[-1]), while simultaneously enriching rhizosphere mineral N pools (NH4[+]-N and NO3[-]-N by 54.50% and 56.02%, respectively). Shotgun metagenomics revealed that RZF reprogrammed rhizosphere N-cycling functional potential, characterized by enhanced nitrogen fixation, reduced nitrification and denitrification, and a tendency toward increased assimilatory nitrate reduction. These module-level shifts were supported by concordant changes in key functional genes, indicating greater genetic potential for N retention and assimilation (nifD, glnA, gltB, nasA, napB, nrfA) and reduced potential for nitrification- and denitrification-driven N losses (amoB/C, narI, nirK, norB). Taxonomic composition analysis showed enrichment of Bradyrhizobium and suppression of key nitrifier taxa (Nitrosospira and a Nitrososphaeraceae-affiliated taxon) under RZF. Rhizosphere pH exhibited the strongest Mantel correlation with multiple N-cycling modules, and rhizosphere available N (AN; sum of NH4[+]-N and NO3[-]-N) was positively associated with plant N traits and yield. Structural equation modeling supported a pathway in which a functional balance index (retention/assimilation vs. loss/oxidation) increased AN (0.22), and AN strongly promoted yield (0.90). Collectively, these results elucidate a rhizosphere-centered mechanism whereby localized N placement strengthens soil-plant N coupling and enhances crop productivity through reprogramming microbial N-cycling functional potentials, positioning rhizosphere N processes as a key mechanistic bridge for microbiome-informed optimization of root-zone fertilization.}, } @article {pmid42075353, year = {2026}, author = {Aleynova, OA and Ananev, AA and Nityagovsky, NN and Suprun, AR and Beresh, AA and Dubrovina, AS and Kiselev, KV}, title = {Ability of Different Bacteria from Grapevine to Colonize Arabidopsis thaliana Plants.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {8}, pages = {}, pmid = {42075353}, issn = {2223-7747}, support = {22-74-10001-П//the Russian Science Foundation/ ; }, abstract = {This study investigates the impact of inoculating seeds with bacterial endophytes isolated from Vitis amurensis Rupr. on endophytic community composition in Arabidopsis thaliana (L.) Heynh. Ten bacterial isolates of the genera Agrobacterium, Bacillus, Curtobacterium, Erwinia, Frondihabitans, Gordonia, Pantoea, Pseudomonas, Sphingomonas, and Xanthomonas were applied to seeds and some visible phenotypic effects were observed on plant growth after two weeks. High-throughput sequencing of 16S rRNA revealed that the native endophytic microbiome of A. thaliana was dominated by Gammaproteobacteria, Actinomycetes, Bacteroidia, and Alphaproteobacteria. The key families were Microscillaceae, Chitinophagaceae, Rhizobiaceae, Rhodanobacteraceae, Nocardioi-daceae, Nocardiaceae, Xanthomonadaceae, Devosiaceae, Microbacteriaceae, Crocinitomi-caceae, Pseudomonadaceae, Solimonadaceae, Comamonadaceae, Caulobacteraceae, and Micrococcaceae. Arabidopsis seed inoculation with Agrobacterium sp. R8SCh-B12, Curtobacterium sp. P7SA-B3, and Gordonia aichiensis P6PL2 significantly reduced alpha diversity (Shannon index) and altered beta diversity relative to controls, indicating strong community restructuring. These three isolates, along with Pseudomonas sp. R8SCh-B2, Sphingomonas sp. RA62c-B5, Xanthomonas sp. R7SCh-B6, and Bacillus velezensis AMR25, successfully colonized the plant tissues, as evidenced by significant increases in genus-specific amplicon sequence variants, ASVs (up to 17,820-fold for Curtobacterium sp. ASV33). In contrast, Pantoea sp. P7SCH-B5, Erwinia sp. R8SCh-B3, and Frondihabitans sp. RA62c-B2 failed to colonize A. thaliana, despite being applied to the seeds, suggesting the existence of mechanisms restraining colonization. These findings demonstrate that only a subset of grapevine-derived endophytes can effectively colonize A. thaliana, and that successful colonization correlates with significant shifts in the native microbiome, even in the absence of overt phenotypic changes. This emphasizes the importance of strain-specific compatibility in plant-endophyte interactions. Thus, we report the first descriptions of several novel endophytes that colonized Arabidopsis plants and establish a convenient model to investigate plant-bacterial interactions.}, } @article {pmid42076876, year = {2026}, author = {Krupa, Ł and Schmarz, GP and Staroń, R and Schmidt, HH and Rehner, J and Becker, SL and Krawczyk, M}, title = {Metagenomic profiling of bile in malignant cholestasis: Analysis of samples collected during EUS-guided biliary drainage.}, journal = {European journal of clinical investigation}, volume = {56}, number = {5}, pages = {e70200}, doi = {10.1111/eci.70200}, pmid = {42076876}, issn = {1365-2362}, support = {Precision-BTC-Network CA22125//European Cooperation in Science and Technology/ ; //Saarland University and the UdS-HIPS TANDEM initiative/ ; 469073465//Deutsche Forschungsgemeinschaft/ ; 2022-784-024//European Union Horizon 2020 Transcan project/ ; 2024-040//Dr. Rolf M. Schwiete Stiftung/ ; }, } @article {pmid42076937, year = {2026}, author = {Lundtorp-Olsen, CM and Andersen, SVR and Massarenti, L and Gürsoy, M and Splunter, AV and Bikker, FJ and Gursoy, UK and Markvart, M and Damgaard, C and Belstrøm, D}, title = {Probiotics Augment the Effect of Non-Surgical Periodontal Treatment-A Randomised, Double-Blinded, Placebo-Controlled Trial.}, journal = {Journal of clinical periodontology}, volume = {53}, number = {7}, pages = {1016-1030}, pmid = {42076937}, issn = {1600-051X}, support = {1044-00093B//Innovationsfonden/ ; //Archer Daniels Midland/ ; }, mesh = {Humans ; *Probiotics/therapeutic use ; Double-Blind Method ; Female ; Selenomonas ; Saliva/microbiology/chemistry ; Adult ; Middle Aged ; Male ; Fusobacterium nucleatum/isolation & purification ; Treponema ; Lacticaseibacillus rhamnosus ; Placebos ; Follow-Up Studies ; *Chronic Periodontitis/therapy/microbiology ; Periodontal Index ; Periodontal Pocket/therapy/microbiology ; Gingival Hemorrhage/therapy ; }, abstract = {AIM: To determine the effect of probiotic lozenges containing Lacticaseibacillus rhamnosus PB01, Latilactobacillus curvatus EB10 and xylitol after non-surgical periodontal treatment (NSPT) on changes in microbial composition. The secondary aims were to assess the clinical and immunological impact of probiotic consumption.

MATERIALS AND METHODS: Eighty adults with stage II or III periodontitis were enrolled and received NSPT at baseline, followed by a 12-week consumption of probiotics or placebo. Microbial sampling and clinical examination were performed at baseline, Week 6 and Week 12. The subgingival microbiota was analysed using 16S sequencing, the salivary microbiota by metagenomic sequencing and selected cytokines and proteases in saliva by bead-based immunoassay.

RESULTS: Sixty-one participants completed the trial (probiotics n = 32, placebo n = 29). At Week 12, Treponema socranskii , Selenomonas sputigena , Dialister pneumosintes , Dialister invisus , Anaeroglobus geminatus and Fusobacterium nucleatum were significantly associated with the placebo group, while Streptococcus sanguinis , Neisseria elongata and Neisseria oralis were associated with the probiotic group. Bleeding on probing percentage (BoP%) and number of periodontal pockets (PPD) ≥ 5 mm decreased significantly more in the probiotic group compared to the placebo group (p < 0.05).

CONCLUSION: The tested probiotic supplement resulted in an additional short-term decrease in periodontitis-associated species along with greater improvements in BoP% and PPD ≥ 5 mm 12 weeks post-NSPT, compared to the placebo group.}, } @article {pmid42077846, year = {2026}, author = {Pinheiro, GL and Lin, NJ and Parratt, KH and Hines, I and Hack, HR and Servetas, SL and Iyer, H and Da Silva, SM}, title = {The Integration of Focused Ultrasonication, ddPCR, and Flow Cytometry Effectively Estimates Genome Copies per Cell and Enhances DNA Extraction Efficiency in Escherichia coli Samples.}, journal = {ACS omega}, volume = {11}, number = {16}, pages = {23885-23899}, pmid = {42077846}, issn = {2470-1343}, abstract = {Microbiology researchers rely on nucleic acid measurement techniques, such as the quantitative polymerase chain reaction (qPCR) and DNA sequencing, to address diverse scientific and practical challenges. These applications range from detecting microbial contaminants in regenerative medicine and biotherapeutic products to advancing waste remediation, pathogen detection, biosurveillance, and microbiome studies. A critical step in these techniques is DNA extraction, which involves breaking cells to release their DNA as the required input for downstream analyses. The efficiency of this process, known as DNA extraction efficiency (DEE), directly impacts the accuracy of quantitative measurements and, therefore, the interpretation of results. Unfortunately, most DNA extraction methods suffer from suboptimal efficiency that varies across microbial strains, potentially leading to inaccurate results. In this paper, we present a highly efficient DNA extraction protocol leveraging adaptive focused acoustics (AFA) technology to achieve a balance between cell lysis and DNA integrity. Using Escherichia coli as the model organism, the protocol delivers nearly 100% DEE, setting a benchmark for performance. A key innovation in this protocol is the integration of focused ultrasonication, droplet digital polymerase chain reaction (ddPCR), and flow cytometry to estimate genome copies and the corrected DNA extraction efficiency (cDEE), which accounts for the number of genome copies. The proposed protocol addresses the need for an accurate assessment of DEE and DNA quantification, as demonstrated here with E. coli, for various DNA-based techniques, including metagenomic analysis of complex microbial communities and the development of new DNA extraction protocols. This novel protocol addresses a longstanding limitation in microbiological research and has the potential to significantly enhance accuracy and reproducibility across various applications. While there is significant potential for applying this approach, the authors acknowledge that further studies using microorganisms with thicker cell walls will enhance the utility of this framework. However, the knowledge generated in this study can be readily applied and tailored to the specific objectives of individual research groups.}, } @article {pmid42078366, year = {2026}, author = {Sy, M and Ndiaye, T and Thakur, R and Gaye, A and Levine, ZC and Ngom, B and Bellavia, KL and Firer, D and Toure, M and Ndiaye, IM and Diedhiou, Y and Mbaye, AM and Gomis, JF and DeRuff, KC and Deme, AB and Ndiaye, M and Badiane, AS and Paye, MF and Sabeti, PC and Ndiaye, D and Siddle, KJ}, title = {Oral and plasma microbiome in the context of acute febrile illness.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {42078366}, abstract = {Emerging infectious diseases and antimicrobial resistance (AMR) have surfaced as two major public health threats over the past two decades. Consequently, integrative surveillance systems capable of detecting both emerging pathogens and resistance-carrying bacteria are crucial. With advances in next-generation sequencing, simultaneous detection of pathogens and AMR is increasingly feasible. In this study, we used short-read metatranscriptomics complemented by total 16S rRNA metagenomic long-read sequencing to analyze paired oral and plasma samples from a cohort of febrile individuals at two locations in Senegal. Oral microbiomes differed in community composition between locations, and reduced diversity and richness were significantly associated with high fever. We identified at least one known pathogen in 15.33 % (23/150) of samples, with Borrelia crocidurae as the most frequently detected pathogen. We detected both pathogenic and non-pathogenic viruses in oral (10/72) and plasma (09/78) samples. Finally, we observed a high frequency of genes associated with resistance and virulence: 10% of samples expressed at least one AMR gene (ARG), and 24% expressed virulence factor genes. Resistance to widely used beta-lactam antibiotics was the most prevalent. Our findings provide critical data on oral and plasma microbiomes in the context of acute febrile illness in Senegal while expanding understanding of circulating ARGs.}, } @article {pmid42078431, year = {2026}, author = {Tang, J and Luo, Z and Li, Y and Jiang, W and Weng, Y and Zhang, G and Li, C and Liu, Y and Sun, X and Chen, L}, title = {Invasive pericardial and pulmonary aspergillosis by uncommon Aspergillus species in anti-interferon-γ autoantibody-associated immunodeficiency: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1760017}, pmid = {42078431}, issn = {2296-858X}, abstract = {This case report describes a 51-year-old female patient who presented with dyspnea and was diagnosed with invasive aspergillosis affecting the pericardium and lungs, secondary to immunodeficiency syndrome caused by anti-interferon-γ autoantibodies. Diagnosis was established by pericardial tissue metagenomic next-generation sequencing (mNGS) identifying Aspergillus udagawae and serum anti-interferon-γ autoantibody testing (titer 1:2,500). Despite sequential antifungal therapy with voriconazole, isavuconazole, and amphotericin B, the patient developed progressive multifocal infection, including an abdominal wall abscess and mediastinal infection caused by Aspergillus siamensis, and ultimately died of multiple organ failure. This case highlights the diagnostic challenges and poor prognosis associated with this rare immunodeficiency syndrome and emphasizes the importance of early recognition, precise pathogen identification, and consideration of immunomodulatory therapy.}, } @article {pmid42078521, year = {2026}, author = {Meng, T and Shi, J and Zhang, X and Zhao, X and Liu, Y and Rong, M and Chen, L and Dai, Y and Wei, S and Liu, J and Lu, Z}, title = {Mechanistic insights into nitrogen fertilizer regulation of carbon-nitrogen cycling and greenhouse gas emissions: a metagenomics-based investigation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1808047}, pmid = {42078521}, issn = {1664-302X}, abstract = {Nitrogen (N) fertilizer application can regulate the structure of soil microbial community and influence the abundance of functional genes involved in carbon (C) and N cycling, thereby affecting greenhouse gas (GHG) emissions. This study was conducted in 2023-2024, setting up six nitrogen application rates: N0 (0 kg·ha[-1]), N120 (0 kg·ha[-1]), N180 (0 kg·ha[-1]), N240 (0 kg·ha[-1]), N300 (0 kg·ha[-1]), and N360 (0 kg·ha[-1]). Using 16S amplicon sequencing technology and metagenomic sequencing, the study analyzed the abundance of carbon and nitrogen cycling functional genes. Combined with measurements of CH4, N2O, and CO2 emission fluxes, the research elucidated the mechanism by which nitrogen fertilizer regulates microbial modulation of greenhouse gas emissions. The results indicated that nitrogen application significantly increased greenhouse gas (CH4, N2O, CO2) emissions, with the highest emissions observed under the N300 treatment. Nitrogen application regulated soil nutrients, increasing soil total nitrogen, nitrate nitrogen, and microbial biomass carbon content. Reasonable nitrogen application (N240) increased bacterial α-diversity (Shannon index, Chao index, PD index) in the soil by 10.82, 14.65, and 1.92%, respectively, compared to N0. It also increased the abundance of dominant nitrogen-fixing bacterial phyla, including Actinobacteria, Proteobacteria, and Nitrospirota. Furthermore, it regulated the abundance of microbial-mediated functional genes involved in dissimilatory nitrate reduction (nirB), assimilatory nitrate reduction (nasA), denitrification (narG, narH, nirS), nitrification (norC, nxrA, nxrB, hao, amoC), as well as those in the carbon cycle related to methane metabolism (pmoA, pmoC, mttC), carbon fixation (por/nifj, rbcl/cbbl), and hydrogenotrophic methanogenesis (mch, hdrA, frdE). This regulation further modulated greenhouse gas emissions. Therefore, this study clarifies the microbe-associated mechanisms underlying the N fertilizer-driven coupling of C and N cycles with GHG emissions through an integrated analysis of microbial diversity and metagenomics. Furthermore, it offers new insights for sustainable N fertilizer management and emission mitigation strategies in agricultural systems.}, } @article {pmid42078528, year = {2026}, author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R and Han, Y}, title = {Identification of novel CRESS-DNA viruses in the human vaginal microbiome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1790643}, pmid = {42078528}, issn = {1664-302X}, abstract = {INTRODUCTION: Circular replication-associated protein (Rep)-encoding single-stranded DNA (CRESS-DNA) viruses are widely distributed across diverse hosts and environments, yet their diversity within the human vaginal virome remains poorly characterized. This study aimed to investigate the presence, diversity, and evolutionary relationships of CRESS-DNA viruses in the human vaginal niche.

METHODS: Viral metagenomic sequencing was performed on 24 pooled vaginal swab libraries derived from women with and without vaginitis. After host sequence removal and quality control, de novo assembly and viral identification were conducted. Candidate viral genomes were curated based on genomic features, followed by functional annotation, phylogenetic analysis using Rep protein sequences, and genome-wide pairwise nucleotide identity comparisons.

RESULTS: A total of five CRESS-DNA viral genomes were identified, including four complete and one nearly complete circular genomes. All genomes exhibited canonical architectures, encoding Rep and Cap proteins and containing conserved HUH endonuclease and superfamily 3 helicase motifs. Phylogenetic analysis placed these viruses within the orders Rohanvirales, Ringavirales, Cirlivirales, and Cremevirales, representing multiple distinct evolutionary lineages. Genome-wide pairwise identity analysis showed that all identified viruses fell below established species- and genus-level thresholds, indicating that they represent novel taxa. Comparative analyses further revealed substantial divergence from known environmental and vertebrate-associated viruses.

DISCUSSION: These findings expand the known diversity of CRESS-DNA viruses in the human vaginal virome and highlight their broad evolutionary diversity. The detected viruses likely represent diverse ecological origins rather than stable host-specific infections, and no clear association with vaginitis was observed. This study provides new insights into the evolutionary landscape of CRESS-DNA viruses in the human reproductive tract and underscores the need for further investigation into their biological roles and potential health implications.}, } @article {pmid42078532, year = {2026}, author = {Padmanabhan, C and Puig, A}, title = {Editorial: Metagenomic insights into microbial communities in fruits and vegetable plants.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1844864}, pmid = {42078532}, issn = {1664-302X}, } @article {pmid42078537, year = {2026}, author = {Shen, T and Zhou, Y and Gao, J and Xiong, X and Chen, C}, title = {Gut microbiota regulates growth retardation in pigs through their metabolites of taurine and butyric acids.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1811659}, pmid = {42078537}, issn = {1664-302X}, abstract = {Growth retardation of piglets has always been observed in current pig production system. Here we defined these pigs as stunted pigs. Stunted pigs show normal feed intake, but exhibit extremely slow growth speed. This brings a big economic loss to pig industry. Many factors can lead to growth retardation, including gut microbiota which has been reported to play important roles in growth retardation of children. However, whether and which gut microbial taxa are associated with growth retardation of piglets are largely unknown. Here we used 16S rRNA gene and shotgun metagenomic sequencing to identify bacterial taxa associated with growth retardation in 126 pigs including stunted pigs and their pairwise littermates showing normal growth. We identified several Clostridium spp. significantly enriched in the gut of normal growing pigs, including Clostridium symbiosum which was the key biomarker distinguishing stunted pigs and normal growing pigs, while several Bacteroides spp. had higher abundances in stunted pigs. Clostridium spp. was significantly associated with the shifts of functional capacities of the gut microbiome between normal and stunted pigs, e.g., biosynthesis of unsaturated fatty acids. Untargeted serum metabolome analysis found that normal growing pigs had higher concentration of taurine in serum. Increased concentration of serum taurine was associated with increased abundance of Clostridium symbiosum. Furthermore, all metabolites having higher abundances in normal growing pigs were enriched in the pathway of taurine and hypotaurine metabolism. Short-chain fatty acids (SCFAs) analysis identified butyric acid having higher concentration in feces of normal growing pigs in both discovery and validation cohorts, and the changes in the abundances of Clostridium symbiosum was correlated with the shifts of the concentrations of fecal SCFAs. These results suggested that Clostridium spp., especially Clostridium symbiosum improved pig growth by increasing the concentrations of serum taurine and fecal butyric acid, and was an important biomarker associated with pig growth. This study provided important insights into the effect of the gut microbiome on pig growth retardation.}, } @article {pmid42078542, year = {2026}, author = {Mao, Y and Lv, Q and Chen, S and Wang, L and Li, K and Xie, Z and Yin, F and Xu, L and Wang, Q and Zhao, C}, title = {Case Report: An imported severe case of paediatric scrub typhus with Karp B subgenotype in non-endemic Northern China, Beijing.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1733143}, pmid = {42078542}, issn = {2296-2360}, abstract = {Scrub typhus, a zoonosis caused by Orientia tsutsugamushi (O. tsutsugamushi), remains a significant public health threat in the Asia-Pacific region. This disease is transmitted through the bite of infected trombiculid mite larvae (chiggers) and typically manifests as acute undifferentiated fever during the early stage. Despite the availability of targeted antibiotic therapies, delayed diagnosis frequently leads to severe complications and fatal outcomes. Here, we report a severe imported paediatric case in Beijing, a city in China's temperate zone, involving a 12-year-old girl with a recent travel history to Yunnan Province. The patient presented with fever, characteristic eschar, regional lymphadenopathy, and septic shock, ultimately progressing to multiorgan dysfunction syndrome. Whole-genome metagenomic next-generation sequencing (mNGS) of blood, cerebrospinal fluid (CSF), and sputum samples revealed O. tsutsugamushi with high sequence read counts, whereas blood cultures remained negative for other bacterial pathogens. Subsequent PCR amplification and Sanger sequencing confirmed the mNGS findings. Phylogenetic analysis of the TSA56 gene classified the strain within the Karp cluster. Serological analysis revealed the presence of O. tsutsugamushi-specific IgM and IgG antibodies. This severe paediatric case highlights the importance of considering travel-associated scrub typhus in the differential diagnosis of febrile illnesses in non-endemic regions. This is particularly relevant for patients with a history of insect bites in areas known to be endemic for O. tsutsugamushi.}, } @article {pmid42079098, year = {2026}, author = {Wucher, BR and Pardo-De la Hoz, CJ and Stamper, I and Sharma, S and Kaune, D and Bendale, P and Peled, J and Xavier, JB}, title = {Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42079098}, issn = {2692-8205}, abstract = {The gut microbiota contains trillions of bacteria essential to health, but also harbors potential pathogens. The phylum Pseudomonadota, which includes Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa, typically composes <1% of the microbiota but causes disproportionate numbers of gut-borne bloodstream infections. Identifying the ecological dependencies that enable Pseudomonadota to cause gut-borne disease is important for human health. Here, we studied microbiota dynamics in patients undergoing allogeneic hematopoietic cell transplantation (allo-HCT) to find that microbiota compositions permissive to Pseudomonadota had, following antibiotic prophylaxis, high levels of Bacteroides-a major reservoir of polysaccharide utilization loci (PULs). We tested the causality of this clinical association in a mouse co-colonization model and discovered that Bacteroides fragilis promotes Pseudomonas gut colonization and survival to ciprofloxacin, a drug commonly used as prophylactic in allo-HCT. In vitro experiments revealed a general mechanism by which diverse Pseudomonadota species depend on Bacteroides polysaccharide breakdown to grow better, form more biofilm, and survive ciprofloxacin treatment under anaerobic conditions, a type of ecological dependency termed metabiosis. Guided by this insight, we used metagenomics to identify the PUL-encoded functions underlying the metabiotic potential of a patient's microbiota and establish a link to gut-derived Gram-negative bacteremia in allo-HCT. Together, our findings translate mechanistically based microbiome ecology into a clinically actionable framework for early risk stratification and intervention.}, } @article {pmid42079121, year = {2026}, author = {Qian, K and Abhyankar, V and Keo, D and Zarceno, P and Toy, T and Eskin, E and Arboleda, VA}, title = {Systematic evaluation of 24 extraction and library preparation combinations for metagenomic sequencing of SARS-CoV-2 in saliva.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42079121}, issn = {2692-8205}, abstract = {Sequencing the respiratory tract transcriptome has the potential to provide insights into infectious pathogens and the host's immune response. While DNA-based sequencing is more standard in clinical laboratories due to its stability, RNA assays offer unique advantages. RNA reflects dynamic physiological changes, and for RNA viruses, viral RNA particles directly represent copies of the viral genome, enabling greater diagnostic sensitivity. However, RNA's susceptibility to degradation remains a significant challenge, particularly in RNase-rich specimens like saliva. To address this, we conducted a systematic, combinatorial evaluation of 24 distinct mNGS workflows, crossing eight nucleic acid extraction methods with three RNA-Seq library preparation protocols. Remnant saliva samples (n = 6) were pooled and spiked with MS2 phage as a control. The SARS-CoV-2 virus was spiked into half of the samples, which were extracted using the eight different extraction methods (n = 3) and compared using RNA Integrity Number equivalent (RINe) scores and RNA concentration. The extracted RNA was then processed across the three library construction methods and subjected to short-read sequencing to assess all 24 combinations head-to-head. We compared methods based on viral read recovery and found that RINe and concentration did not correlate with viral detection. The Zymo Quick-RNA Magbead kit and the Tecan Revelo RNA-Seq High-Sensitivity RNA library kit were the extraction and library-preparation kits that yielded the most SARS-CoV-2 reads, respectively. Importantly, our combinatorial analysis revealed that any small variability attributable to different nucleic acid extraction methods was heavily overshadowed by differences in quality attributable to the RNA-Seq library preparation methods. These findings challenge the reliance on conventional RNA quality metrics for clinical metagenomics and underscore the need to redefine extraction quality standards for mNGS applications.}, } @article {pmid42079283, year = {2026}, author = {Brenner, E and Vang, C and Johnson, C and Ravi, J}, title = {Genotype-phenotype modeling of light ecotypes in Prochlorococcus reveals genomic signatures of ecotypic divergence.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42079283}, issn = {2692-8205}, support = {T15 LM009451/LM/NLM NIH HHS/United States ; }, abstract = {Prochlorococcus species are the most abundant marine photosynthetic bacteria. Despite broadly shared phenotypic traits and marine habitats, they exhibit remarkable genomic diversity. We ask what genomic signatures underlie its ecotypic divergence into high- and low-light adapted lineages, and whether these signatures can still be recovered from incomplete assemblies. From ~1,000 publicly available Prochlorococcus genomes, we focused on those with information on their light adaptation ecotype (high-light/low-light), phylogenetic clades, and depth of isolation. Across these divisions, we calculated average nucleotide identity and constructed pangenomes to assess cyanobacterial core genes vs. those that separate ecotypes. Despite scant conservation, we observe a sharp taxon separation by light ecotypes. Classical machine learning models trained to predict ecotype achieve near-perfect binary classification accuracy even when predicting on partial genomes (Matthews Correlation Coefficient = 0.86 - 1.00), while regression models trained to predict the depth of isolation performed poorly, with high root mean square error values (37.6 - 42.0m). For ecotype prediction, we analyzed top gene features across model runs and classes; these features included photosynthesis-associated genes and pathways, as well as many novel markers of unknown function. When separating ecotypes further by previously described phylogenetic clades, genomic content and composition show even clearer separation among clades, supporting the taxonomic breadth of the Prochlorococcus collective. These results emphasize the genomic specialization underlying ecotypic divergence and support the utility of ML approaches for cyanobacterial ecotype prediction from metagenomic data. Expanded sampling will yield novel clade-specific biology. All data, models, and results are available on GitHub: https://github.com/JRaviLab/cyano_adaptation.}, } @article {pmid42079297, year = {2026}, author = {Cornman-Homonoff, J and Rajendran, KM and Kolandaivelu, S and Coon, SD and Kupec, JT and Wang, L and Hu, G and Jala, VR and Sandle, GI and Rajendran, VM}, title = {Dietary Sodium Restriction Reprograms Gut Microbial Fermentation and Reduces Host Energy Harvest.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.20.719706}, pmid = {42079297}, issn = {2692-8205}, abstract = {Diet is a major determinant of gut microbiome structure and function, yet the role of dietary electrolytes-particularly sodium-remains poorly defined. Here, we identify dietary sodium availability as a key regulator of gut microbial fermentation and host energy harvest. Using a controlled sodium-sufficient versus sodium-deprived dietary intervention in rats, we integrated shotgun metagenomic sequencing, functional pathway analysis, targeted short-chain fatty acid (SCFA) quantification, and host physiological phenotyping. Sodium deprivation induced a coordinated restructuring of the gut microbiome, characterized by depletion of classical saccharolytic Firmicutes, including multiple Lactobacillus species, and enrichment of stress-tolerant, metabolically flexible taxa. Functional profiling revealed a shift away from growth-associated metabolic programs toward stress-adaptive and nutrient-scavenging pathways. Consistent with these changes, fecal concentrations of key SCFAs-including acetate, butyrate, hexanoate, and valerate-were significantly reduced, indicating impaired microbial fermentative capacity. These microbiome-level alterations translated into measurable host phenotypes, including reduced cecal mass and attenuated weight gain, consistent with decreased microbial energy harvest. Together, these findings establish a functional link between luminal sodium availability, microbial metabolic efficiency, and host energy balance, extending the framework of diet-microbiome interactions beyond macronutrients to include dietary electrolytes. This work identifies sodium as a previously underappreciated ecological constraint shaping gut microbial metabolism and suggests that modulation of dietary sodium intake may influence host metabolic outcomes through microbiome-mediated mechanisms.}, } @article {pmid42079427, year = {2026}, author = {Xolalpa-Aroche, A and Contreras-Peruyero, H and Delgado-Suárez, EJ and Hernández-Mena, DI and Moguel-Chin, WI and Rivero-Cruz, JF and Velarde, RA and Ortiz-Vázquez, E and Rivero-Cruz, BE and Lovaco-Flores, JA and Rodríguez Orduña, L and Licona-Cassani, C and Barona-Gómez, F and Sélem-Mojica, N}, title = {Genome-resolved metagenomics reveals a phylogenetically cohesive Acetilactobacillus-like species complex dominating stingless bee pot honey.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag063}, pmid = {42079427}, issn = {2730-6151}, abstract = {Pot honey, the honey produced by stingless bees, is valued for its antimicrobial capacity, which may be influenced by its microbial content. While Lactobacillaceae species are commonly associated with honeybees and honey microbiomes, most studies have focused on Apis mellifera, leaving pot honey microbial diversity largely unexplored. We present the first pot honey shotgun metagenomic analysis from bee species Melipona beecheii and Scaptotrigona mexicana. We reconstructed 24 metagenome-assembled genomes (MAGs), 15 of which lacked close matches to any described species, showing [Formula: see text]81% Average Nucleotide Identity (ANI) to available reference genomes. Phylogenetic analyses resolved these MAGs into four well-defined clades (intraclade ANI [Formula: see text], interclade ANI [Formula: see text]), consistent with four novel species within the family Lactobacillaceae. GTDB-Tk classification placed MAG clades 1 and 2 closest to Nicoliella, and clades 3 and 4 closest to Acetilactobacillus. We validated the presence of these lineages in honey by sequencing three isolates that clustered within MAG clade 2. Aminoacid similarity (AAI/cAAI) indicates the presence of two genus-level lineages: one occupying a transitional genomic space near Nicoliella, and a second representing an undescribed genus. The genomic similarity of our MAGs and isolates to those from pot honey or larval food in Malaysia, Brazil, and Australia suggests these taxa are closely associated with stingless bees and may contribute to honey properties. By reducing the genomic underrepresentation of evolutionarily divergent sister clades related to Nicoliella and Acetilactobacillus, our genome-resolved analyses reveal a globally distributed, phylogenetically cohesive Lactobacillaceae species complex dominating pot honey.}, } @article {pmid42079429, year = {2026}, author = {Christensen, R and Wang, YHD and Arnoldini, M and Cremer, J}, title = {Abundance-weighted pathway mapping demonstrates family-level structure of butyrate and propionate production across the human gut microbiome.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag075}, pmid = {42079429}, issn = {2730-6151}, abstract = {Fermentation products released by bacteria in the large intestine, such as butyrate and propionate, play central roles in host physiology and health. While the metabolic pathways producing these short-chain fatty acids (SCFAs) are well-characterized, less is known about their relative prevalence across hosts and gut conditions. Here, we introduce a genome-resolved, abundance-weighted bioinformatics framework that integrates pathway-based gene identification with extensive literature validation to systematically quantify the potential for butyrate and propionate production across bacterial species and human gut microbiomes. By comparing pathway predictions against over 700 experimentally characterized strains, we demonstrate high concordance with reported metabolic phenotypes, validating our approach beyond prior purely computational studies. Weighted by species abundance across ~18 000 metagenomic samples, we find that dominant gut taxa disproportionately drive SCFA production, with butyrate pathways enriched in Bacillota and propionate pathways in Bacteroidota. This abundance-weighted analysis reveals that pathway presence is well conserved at the family level, highlighting the ecological relevance of dominant taxa for community-level fermentation potential. Our results further show pronounced inter-individual variation and associations with age, birthing method, and inflammatory bowel disease, emphasizing how shifts in microbiota composition influence SCFA availability. By combining pathway-level resolution, abundance-weighted inference, and literature-based validation, our framework provides a robust, scalable approach to link microbial functional potential with host-relevant outcomes.}, } @article {pmid42079433, year = {2026}, author = {Batilong, LS and Traifalgar, RFM and Del Castillo, CS and Jore, KAG and Fantonalgo, IRL and Huervana, FH and Javellana, TF and Pagapulan, MJBB and Failaman, AN and Gayosa, VED}, title = {Gut-Derived Lactic Acid Bacteria, Pediococcus pentosaceus, Enhances Growth Performance and Resistance to Pathogenic Vibrio harveyi of Hatchery-Bred Milkfish (Chanos chanos) in Nursery Culture.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {6489487}, pmid = {42079433}, issn = {1687-918X}, abstract = {Hatchery-bred milkfish (Chanos chanos) fry continue to face stocking challenges due to inferior growth performance and reduced resilience compared with wild-caught fry. Recent metagenomic studies have shown that wild fry harbor a higher relative abundance of bacterial taxa belonging to the phylum Bacillota. These include lactic acid bacteria (LAB), which are widely recognized for their probiotic potential in aquaculture. Building on this metagenomic insight, the present study adopted a targeted approach to isolate LAB with anti-Vibrio activity and evaluate its probiotic potential in hatchery-bred C. chanos nursery culture. Screening identified Pediococcus pentosaceus HLAB22 as a promising LAB candidate, which was subsequently assessed through in vivo probiotic trials. Probiotic supplementation significantly improved growth performance, survival, and reduced the incidence of opercular deformities in early juveniles. The most pronounced effects observed at 10[6] CFU, followed by 10[3] CFU g[-1] feed compared with the control group. Gut colonization experiment demonstrated that dietary supplementation with P. pentosaceus HLAB22 at 10[6] CFU g[-1] feed enabled intestinal colonization within 12 days. This also resulted in near-complete suppression of Vibrio populations, supporting the significant decrease in water and C. chanos gut Vibrio load during the feeding trial. Furthermore, during immersion challenge with pathogenic V. harveyi, the in vitro anti-Vibrio activity of P. pentosaceus HLAB22 was translated into enhanced in vivo protection, yielding a survival rate of 83.33% in treated fish compared with 33.33% in the control group. Collectively, these findings indicate that oral application of P. pentosaceus HLAB22 at 10[6] CFU g[-1] feed is an effective strategy for promoting growth and enhancing resilience in C. chanos nursery culture. This study supports the use of targeted, host-associated probiotics to improve the performance of hatchery-bred milkfish fry and mitigate key challenges in nursery production systems.}, } @article {pmid42079444, year = {2026}, author = {Fang, T and Yuan, F and Chen, Y and Li, N and Zhang, Y and Liu, H and Liu, X and Miao, Q and Hu, B}, title = {Emerging role of metagenomic next-generation sequencing in infectious disease diagnostics: Clinical integration and future directions.}, journal = {mLife}, volume = {5}, number = {2}, pages = {148-163}, pmid = {42079444}, issn = {2770-100X}, abstract = {Infectious disease diagnostics has been transformed by metagenomic next-generation sequencing (mNGS), an unbiased approach that detects bacteria, viruses, fungi, and parasites in a single assay. By sequencing all nucleic acids in a sample, mNGS overcomes the narrow detection scope and slow turnaround of conventional tests, substantially improving pathogen detection. In conditions such as meningitis/encephalitis, sepsis, and pneumonia, mNGS frequently identifies etiologies missed by routine diagnostic tests, thereby facilitating earlier pathogen-directed therapy and, in selected settings, improving clinical management and outcomes. This approach is particularly valuable for immunocompromised, pediatric, and intensive care unit (ICU) patients with atypical infections. Currently, clinical mNGS workflows primarily rely on short-read sequencing platforms (e.g., Illumina), whereas long-read platforms (e.g., Nanopore, PacBio) offer advantages for rapid or high-resolution applications. Optimized bioinformatics and stringent quality control are essential for reliable results. Beyond clinical diagnostics, mNGS provides valuable genetic data on antimicrobial resistance (AMR) and pathogen phylogeny, supporting public health and outbreak surveillance (e.g., wastewater monitoring and variant tracking). Current challenges include distinguishing colonization from infection, interpreting sequencing data quantitatively, and reducing cost and turnaround time. Looking ahead, emerging strategies such as targeted panels, rapid automated workflows, and host‑response integration are expected to further shorten time‑to‑result and improve diagnostic specificity. Parallel progress in ethical and regulatory frameworks remains essential to ensure responsible implementation. To support clinical adoption, a standardized framework for clinical interpretation of mNGS results, together with associated training, has been developed and implemented. Overall, mNGS is likely to become an increasingly important component of infectious disease diagnostics, with ongoing innovations expected to broaden its clinical and epidemiological impact.}, } @article {pmid42079557, year = {2026}, author = {Kujala, K and Kinnunen, V}, title = {Lactic acid bacteria dominate urban Bokashi: a participatory, culture-independent pilot study of microbial diversity and functional potential in household-scale food waste fermentation.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag018}, pmid = {42079557}, issn = {2633-6685}, abstract = {In recent years, concerns over declining biodiversity in urban spaces have increased. Urban Bokashi composting (i.e. microaerobic or anaerobic fermentation of food waste indoors) has been suggested as a possibility to promote microbial diversity in the domestic environment. However, studies on microbial communities in household-scale Bokashi and their potential impacts on health and environment are lacking. Thus, the present pilot study investigated microbial communities in different stages of the Bokashi composting process in collaboration with six Bokashi practitioners by looking into physicochemical characteristics as well as microbial community composition (16S amplicon sequencing, 34 samples) and functional potential (shotgun metagenome sequencing, 11 samples). The collective results indicate that i) microbial communities in Bokashi compost differed between stages, but also between households, ii) microbial communities were dominated by lactic acid bacteria like Lentilactobacillus or Lacticaseibacillus, iii) metabolic pathways for the production of diverse organic acids were detected, iv) application of Bokashi ferment or leachate to soil can supply nutrients and organic acids to promote plant growth but does not substantially affect soil microbial community composition, and v) potentially pathogenic organisms were detected in extremely low abundances. Thus, urban Bokashi is likely not associated with increased health risks and positive impacts are feasible.}, } @article {pmid42079638, year = {2026}, author = {Han, X and Zang, D and Lin, M and Yin, Y and Liu, D and Sun, Q and Chen, J}, title = {Dynamic changes in gut microbiota and metabolites in advanced lung cancer patients with immune-related adverse events.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1731931}, pmid = {42079638}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; Male ; Female ; Middle Aged ; *Lung Neoplasms/drug therapy/immunology/metabolism ; Aged ; *Immune Checkpoint Inhibitors/adverse effects ; *Metabolome ; Metabolomics/methods ; *Drug-Related Side Effects and Adverse Reactions/metabolism/etiology ; Feces/microbiology ; }, abstract = {BACKGROUND: Immune-related adverse events (irAEs) represent an urgent clinical challenge. Although accumulating evidence suggests that irAEs are associated with the gut microbiota and its metabolites, our understanding of the dynamic alterations in the gut microbiota and related metabolic profiles throughout the onset and progression of irAEs remains limited.

METHODS: A total of 48 fecal samples were collected from 32 lung cancer patients treated with immune checkpoint inhibitors, including 16 patients who developed irAEs and 16 who did not. Fecal samples were collected at baseline and, in patients with irAEs, at the time of irAEs onset. Metagenomic sequencing and untargeted metabolomics analyses were performed to identify baseline differences in gut microbiota and metabolites, characterize longitudinal dynamic changes in gut microbiota and metabolite profiles in patients with irAEs, and construct a machine learning based random forest model to predict the occurrence of irAEs.

RESULTS: There were baseline differences in microbial communities and metabolites between the two groups. In the non-irAEs group, Phocaeicola coprocola was enriched and Micrococales decreased. At baseline, viomycin was positively correlated with irAEs, while metabolites such as calcitriol and L-isoleucine were negatively correlated with irAEs. The roles of valine, leucine and isoleucine metabolism and vitamin B6 metabolism pathways were downregulated in the irAEs group. Compared to baseline, there were significant changes in gut microbiota and metabolites during the onset of irAEs, and the abundance of Veillonella increased during irAEs onset. Dynamic monitoring of metabolic changes in irAEs revealed decreased levels of trypsin butylester, BQ 123, DL-o-tyrosine, and nicotinamide-beta-riboside during irAEs attacks. Lysine degradation, arachidonic acid metabolism, folate biosynthesis, nicotinate and nicotinamide metabolism, and C5-branched dibasic acid metabolism were downregulated during the progression of irAEs. A model for predicting the occurrence of irAEs based on differential microbiota and metabolites was constructed, and after robust validation, the model showed good performance and excellent discriminative power.

CONCLUSIONS: The occurrence and development of irAEs are associated with the composition of the gut microbiota and metabolites, as well as their dynamic changes over time. These findings highlight the potential of gut microbiota and metabolites as biomarkers for predicting the occurrence and progression of irAEs.}, } @article {pmid42080299, year = {2026}, author = {Li, Z and Ren, M and Hu, A and Meng, F and Wang, J}, title = {Depth Stratification Shapes Viral Diversity, Interactions, and Metabolic Potential in a Deep Freshwater Lake.}, journal = {Molecular ecology}, volume = {35}, number = {9}, pages = {e70367}, doi = {10.1111/mec.70367}, pmid = {42080299}, issn = {1365-294X}, support = {U24A20578//National Natural Science Foundation of China/ ; 42507557//National Natural Science Foundation of China/ ; 42372353//National Natural Science Foundation of China/ ; BK20240111//Basic Research Program of Jiangsu Province/ ; }, mesh = {*Lakes/virology/microbiology ; *Viruses/genetics/classification ; Metagenomics ; Fresh Water/virology ; Microbiota/genetics ; Ecosystem ; Geologic Sediments/virology ; Biodiversity ; Metagenome ; }, abstract = {Deep freshwater lakes exhibit distinct microbial community stratification across depth gradients, which plays important roles in biogeochemical cycling and ecosystem stability. As crucial regulators of microbiome composition and function, viruses may play key ecological roles in these stratified systems, yet their distribution patterns and ecological significance in deep-lake surface sediments remain poorly understood. Here, we assessed viral community dynamics and functional potential across the entire water depth gradient (0-155 m) of Fuxian Lake using metagenomics from 44 surface sediment samples. A total of 11,523 viral OTUs were recovered, with only 18% annotated to the family level and approximately 93% classified as putatively lytic. Viral communities showed systematic depth-related shifts across multiple dimensions. Specifically, alpha diversity, community turnover, and stochastic assembly processes increased significantly with water depth, accompanied by enhanced lytic virus dominance and larger genome sizes. Predicted virus-host association networks transitioned from highly connected and generalized at shallow depths to increasingly sparse and specialized at greater depths. Virus-encoded auxiliary metabolic genes showed significantly increasing abundance with water depth, along with functional shifts from host defense to enhanced biosynthesis and energy metabolism, especially regarding carbon fixation and organic matter degradation. Collectively, these results highlight the importance of water depth gradients in structuring viral communities within surface sediments and expand our understanding of viral ecological functions in deep lake ecosystems.}, } @article {pmid42080548, year = {2026}, author = {Zhang, X and Zhong, A and Liu, Y and Zou, J and Gu, M and Zhu, X and Xu, H and Yin, S}, title = {Chronic intermittent hypoxia exacerbates hepatic steatosis in a microbiota-dependent manner in lean mice.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0016326}, doi = {10.1128/msystems.00163-26}, pmid = {42080548}, issn = {2379-5077}, abstract = {Chronic intermittent hypoxia (CIH), a hallmark pathological feature of obstructive sleep apnea (OSA), is extensively linked to hepatic steatosis in high-fat-diet-induced mice. However, the association between CIH and hepatic steatosis in lean mice, as well as the potential involvement of gut microbiota-related mechanisms, remains poorly understood. Four hundred participants in the Shanghai Sleep Health Study were included to assess the association between apnea-hypopnea index (AHI) and hepatic steatosis index (HSI). To characterize CIH-associated phenotypes and explore microbiota-related alterations in lean mice, liver histology, inflammatory cytokine profiling, metagenomic sequencing with antibiotic intervention, plasma untargeted metabolomics, and liver transcriptomics were performed. As a result, AHI was positively associated with HSI in non-obese participants. In lean mice, 16-week CIH alone induced hepatic steatosis and inflammation, accompanied by significant alterations in gut microbiota composition. Antibiotic treatment attenuated hepatic steatosis and inflammation in 16-week CIH-exposed mice. Metagenomic analysis revealed CIH-associated depletion of Bacteroides uniformis, which was reversed by antibiotic treatment. Plasma metabolomic profiling identified deoxycholic acid as a metabolite exhibiting opposite, phenotype-aligned alterations between CIH and CIH plus antibiotic groups and showing the strongest correlation with Bacteroides uniformis abundance. In parallel, liver transcriptomics revealed coordinated alterations in bile acid-related metabolic pathways and PPAR signaling consistent with CIH-induced and antibiotic-sensitive metabolic remodeling. Together, these findings indicate that prolonged CIH exposure induces hepatic lipid accumulation in lean mice and is associated with coordinated, antibiotic-sensitive alterations in gut microbiota composition, bile acid metabolism, and hepatic transcriptional programs, suggesting a potential involvement of gut microbiota-bile acid-liver interactions in CIH-associated hepatic steatosis.IMPORTANCEObstructive sleep apnea (OSA) is increasingly recognized as a contributor to metabolic dysfunction, yet its role in hepatic steatosis independent of obesity remains incompletely understood. This study shows that chronic intermittent hypoxia (CIH), a defining pathological feature of OSA, is sufficient to induce hepatic steatosis and inflammation in lean mice, independent of dietary manipulation. These findings broaden current understanding of OSA-associated liver disease beyond the context of obesity and metabolic syndrome. By integrating metagenomic sequencing, plasma metabolomics, and liver transcriptomics, this work highlights coordinated alterations in gut microbial composition, bile acid profiles, and hepatic lipid-related transcriptional programs associated with CIH exposure. Depletion of Bacteroides uniformis and elevation of deoxycholic acid were linked to CIH-induced hepatic phenotypes and were sensitive to antibiotic intervention, supporting a contributory role of gut microbiota-bile acid interactions in this process. Together, these findings underscore the potential importance of gut microbiota-host metabolic crosstalk in OSA-associated hepatic steatosis and suggest that microbiota- or bile acid-targeted strategies may warrant further investigation as adjunctive approaches for risk stratification and therapeutic intervention in OSA-related liver disease.}, } @article {pmid42080847, year = {2026}, author = {Terzi, I and Akinosoglou, K}, title = {More Detection, Better Decisions? Rethinking Pathogen-Driven Therapy in Diabetic Foot Infections.}, journal = {The international journal of lower extremity wounds}, volume = {}, number = {}, pages = {15347346261447707}, doi = {10.1177/15347346261447707}, pmid = {42080847}, issn = {1552-6941}, abstract = {Pathogen-driven therapy is central to the management of diabetic foot infections (DFIs), where antimicrobial selection relies on microbiological identification. Over the past decade, diagnostic capabilities have expanded from conventional cultures to high-resolution molecular sequencing, substantially increasing pathogen detection. Whether this expansion translates into better therapeutic decisions, however, remains uncertain. This narrative review examines the roles and limitations of culture-based methods, antimicrobial susceptibility testing, targeted polymerase chain reaction panels, 16S rRNA gene sequencing, and shotgun metagenomics in DFIs. Culture remains the cornerstone of pathogen-directed therapy because it identifies viable organisms and provides phenotypic susceptibility data that inform antibiotic selection and de-escalation. Molecular techniques broaden detection and reveal polymicrobial complexity and resistance genes, yet increased analytical sensitivity does not consistently clarify pathogen prioritization, distinguish colonization from infection, or improve patient-centered outcomes. Intensified diagnostic strategies often lead to antimicrobial modification without clear gains in healing or cost-effectiveness. These findings underscore a persistent interpretative gap: detection capacity has advanced more rapidly than frameworks linking microbiological data to meaningful therapeutic action. Microbiology is indispensable but insufficient in isolation. Improved outcomes will depend less on detecting additional organisms and more on integrating microbiological findings with surgical management, vascular status, and multidisciplinary care.}, } @article {pmid42081091, year = {2026}, author = {Gui, C and Li, J and Wang, Q and Chen, L and Shao, Q}, title = {Robot-Assisted Incision and Drainage for a Polymicrobial Brain Abscess.}, journal = {The Journal of craniofacial surgery}, volume = {}, number = {}, pages = {}, doi = {10.1097/SCS.0000000000012848}, pmid = {42081091}, issn = {1536-3732}, abstract = {OBJECTIVE: To evaluate the clinical utility of robot-assisted incision and drainage in the management of a polymicrobial brain abscess located in the central region.

METHODS: We retrospectively analyzed a case of polymicrobial odontogenic brain abscess in a 71-year-old male who presented with stroke-like symptoms. The patient was admitted due to progressive right-sided weakness, initially mimicking an acute ischemic stroke. Gadolinium-enhanced T1-weighted magnetic resonance imaging (MRI) revealed ring-enhancing lesions in the left precentral gyrus and the right temporal lobe, with corresponding high signal on diffusion-weighted imaging (DWI), highly suggestive of a brain abscess. Following empirical antibiotic therapy (vancomycin and meropenem), the patient clinically deteriorated, and a repeat MRI demonstrated enlargement of the left central abscess. During the Remebot robotic navigation, the abscess was incised and drained, yielding thick, yellowish-white purulent material. Postoperative metagenomic next-generation sequencing (mNGS) of the pus identified a polymicrobial infection comprising Fusobacterium nucleatum, Streptococcus constellatus, Parvimonas micra, and Porphyromonas gingivalis.

RESULTS: Based on the microbiological findings, the antibiotic regimen was tailored to a triple combination of vancomycin, meropenem, and metronidazole for 2 weeks, followed by vancomycin plus meropenem for an additional 4 weeks, complemented by rehabilitation and hyperbaric oxygen therapy. The patient demonstrated remarkable neurological recovery. One month post-surgery, right limb muscle strength had returned to grade 5, with only mild residual impairment in fine-motor coordination of the right hand. Three-month follow-up MRI revealed complete resolution of the previously observed intracranial ring-enhancing lesions.

CONCLUSION: For eloquent-area brain abscesses that progress despite medical management, robot-assisted incision and drainage offers a safe, precise, and efficacious minimally invasive surgical option. Integration of mNGS technology for pathogen identification enables targeted antimicrobial therapy, a pivotal step toward achieving favorable outcomes in complex infections.}, } @article {pmid42081443, year = {2026}, author = {Reddy, SP and Morgenroth-Rebin, J and Wang, S and Wilson, MR}, title = {Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Detection of Central Nervous System Pathogens.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {230}, pages = {}, doi = {10.3791/70075}, pmid = {42081443}, issn = {1940-087X}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Central Nervous System Infections/cerebrospinal fluid/microbiology ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has emerged as a powerful tool for unbiased pathogen detection and host transcriptional profiling in clinical and research settings. While its utility in diagnosing central nervous system (CNS) infections is increasingly recognized, cerebrospinal fluid (CSF) samples pose unique challenges due to low nucleic acid abundance and susceptibility to degradation. This study presents an optimized research-based protocol for Illumina sequencing platforms tailored to CSF mNGS, spanning sample handling, nucleic acid extraction, library preparation, sequencing, and bioinformatic analysis. Quality control approaches adaptable to both high and low-resource settings are also provided, including alternatives to capillary electrophoresis. This study demonstrates the protocol's robustness through two representative cohorts: a high-depth, NovaSeq-based workflow and a cost-conscious NextSeq-based workflow. Across these cohorts, pathogens were detected in over 50% of cases, underscoring the method's diagnostic potential even with resource-constrained adaptations. This protocol facilitates reproducible CSF mNGS, providing a foundation for diverse applications in neuroinfectious disease research and diagnostics.}, } @article {pmid42081609, year = {2026}, author = {Wang, Y and Zhang, B and Shen, C and Cao, M and Wang, N and Chen, T and He, G and Sun, G and Li, C and Li, Y and Yin, X and Sun, Y and Li, C and Zhou, X}, title = {N-Carbamoylglutamate enhances bull spermatogenesis via Paraprevotella-mediated vitamin B6 biosynthesis in rumen microbiota.}, journal = {Reproduction (Cambridge, England)}, volume = {171}, number = {5}, pages = {}, doi = {10.1093/reprod/xaag049}, pmid = {42081609}, issn = {1741-7899}, support = {CARS-36//The China Agriculture Research System of MOF and MARA/ ; 20240303081NC//The key Research and Development Program of Jilin Province/ ; XZ202401ZY0053//The key Research and Development Project of Tibet Autonomous Region/ ; }, mesh = {Animals ; Male ; *Spermatogenesis/drug effects ; Cattle ; *Rumen/microbiology/drug effects/metabolism ; *Glutamates/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Vitamin B 6/biosynthesis ; Mice ; }, abstract = {In brief: Emerging evidence suggests that gut microbial metabolites can influence male fertility, but how rumen microbiota regulate spermatogenesis in ruminants remains unclear. This study demonstrates that N-carbamoylglutamate promotes bull spermatogenesis through a rumen microbiota-vitamin B6 axis associated with Paraprevotella. Abstract: N-Carbamoylglutamate (NCG), a functional analog of the arginine precursor, shows strong potential in enhancing spermatogenesis in bulls. In this study, dietary NCG supplementation significantly increased sperm density and motility in XiangXi yellow bulls, the local beef cattle. Metagenomic and serum metabolomic analyses revealed that NCG altered the composition of rumen microbiota, notably increasing the abundance of Paraprevotella and elevating serum vitamin B6 levels (p < 0 .05), suggesting a possible microbiota-associated metabolic modulation underlying its reproductive benefits. To explore this mechanism, a busulfan-induced mouse model of impaired spermatogenesis was established. Mice received transplants of either rumen microbiota from NCG-treated bulls or the differential genus Paraprevotella. Both treatments alleviated reproductive damage and increased vitamin B6 levels in serum and testis. Mechanistic investigation indicated that Paraprevotella was associated with upregulated expression of 3-phosphoserine aminotransferase, a key enzyme involved in vitamin B6 biosynthesis. Subsequent vitamin B6 supplementation experiments showed increased testicular glutathione levels and reduced thiobarbituric acid-reactive substances level (expressed as MDA equivalents). These experiments supported a contributory role of vitamin B6 in promoting spermatogenesis, including increased sperm count and enhanced expression of spermatogenic cell markers. In summary, this study demonstrated that NCG enhanced spermatogenesis in bulls by reshaping the rumen microbiota, particularly through enrichment of Paraprevotella, which was associated with increased systemic vitamin B6 levels and contributed to reproductive improvement. These findings provide further insights into the application of NCG in improving fertility in ruminants.}, } @article {pmid42082028, year = {2026}, author = {Zhang, Q and Hu, Y and Wang, G and Kong, L and Xu, Z and Ma, X and Chen, R}, title = {Deciphering the impact of chlortetracycline on methanogenesis, microbial properties and antibiotic resistance genes in an anaerobic ceramic membrane bioreactor treating swine wastewater.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134760}, doi = {10.1016/j.biortech.2026.134760}, pmid = {42082028}, issn = {1873-2976}, mesh = {Animals ; *Methane/biosynthesis/metabolism ; *Bioreactors/microbiology ; *Wastewater/microbiology ; Swine ; *Ceramics/chemistry ; *Chlortetracycline/pharmacology ; Anaerobiosis/drug effects ; *Drug Resistance, Microbial/genetics/drug effects ; *Membranes, Artificial ; Biodegradation, Environmental ; *Water Purification/methods ; }, abstract = {The presence of chlortetracycline (CTC) in swine wastewater poses a threat to anaerobic treatment and ecological safety. This study investigated the concentration-dependent effects of CTC on methanogenesis, microbial properties, and antibiotic resistance genes in an anaerobic ceramic membrane bioreactor (AnCMBR). Batch assays identified a biological inhibition threshold at 50 mg/L CTC. During long-term operation, CTC at 10 mg/L (after a brief adaptation) increased methane yield by 28%, while 50 mg/L CTC inhibited methanogenesis and reduced COD removal from 97% to 86%. High-level CTC raised antibiotic resistance gene abundance and decreased acute toxicity removal from 68% to 46%. Biodegradation dominated CTC removal, but its contribution declined from 42% to 19% as CTC increased, lowering overall removal from 60% to 30%. Metagenomic analysis revealed that low-level CTC upregulated hydrolysis/fermentation-related genes (e.g., enolase, phosphoglycerate mutase, pyruvate kinase), enhancing substrate supply for methanogenesis. In contrast, high-level CTC markedly enriched Spirochaetes (from 3% to 66%), suppressed key methanogenic genes involved in methyl-CoM reductase and downstream acetyl-CoA metabolism, while preserving acetoclastic pathway genes (acsS1.2, ackA, pta), collectively shifting the pathway toward acetoclastic methanogenesis. Notably, the AnCMBR maintained stable filtration performance, with the transmembrane pressure remaining below 6.5 kPa over 160 days. These findings demonstrate that low CTC levels can be tolerated after acclimation, whereas high CTC stress severely impairs methanogenesis, detoxification, and biosafety.}, } @article {pmid42082029, year = {2026}, author = {Hou, Y and Ren, B and Song, J and Li, P and Xue, Z and Zhao, Y and Dzakpasu, M}, title = {Antibiotics removal and nutrient transformation in constructed wetlands using novel aluminum Sludge-Derived Substrates.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134779}, doi = {10.1016/j.biortech.2026.134779}, pmid = {42082029}, issn = {1873-2976}, mesh = {*Anti-Bacterial Agents/isolation & purification ; *Wetlands ; *Sewage/chemistry ; *Aluminum/chemistry ; Biological Oxygen Demand Analysis ; Water Pollutants, Chemical/isolation & purification ; Biodegradation, Environmental ; Nitrogen/isolation & purification ; *Nutrients/isolation & purification ; Phosphorus/isolation & purification ; Water Purification/methods ; Norfloxacin/isolation & purification ; }, abstract = {The widespread use and environmental persistence of norfloxacin (NOR) and sulfamerazine (SMR) have raised concerns over their impacts on aquatic systems and biological nutrient removal. Constructed wetlands (CWs) offer a sustainable, low-cost approach for antibiotic abatement, yet the mechanisms by which NOR and SMR influence microbial nutrient transformation in CWs remain unclear. Here, alum sludge was repurposed as a novel substrate (NALS) in vertical flow CWs, providing a dual pathway for valorizing waste while targeting simultaneous antibiotic and nutrient removal. The systems effectively removed both NOR and SMR (70-77%) under environmentally relevant concentrations (3 and 10 mg/L) and maintained robust nutrient elimination, with COD removal of 75-81%, TP > 90%, and peak NH4[+]-N and NO3[-]-N removals of 93% and 88%, respectively. High antibiotic levels inhibited COD and TP removal, whereas low concentrations stimulated TP removal. Notably, elevated NOR impaired NH4[+]-N and TN removal, while SMR showed negligible effects on ammonium dynamics. Metagenomic analysis revealed that both antibiotics distinctly suppressed microbial communities across taxonomic levels and disrupted functional genes related to nitrification, denitrification, and nitrogen fixation. This work demonstrates the efficacy of NALS-based CWs in co-removing antibiotics and nutrients, while offering mechanistic insights into how antibiotic exposure reshapes microbial structure and function-advancing the design of sustainable treatment systems for antibiotic-laden wastewater.}, } @article {pmid42082030, year = {2026}, author = {Li, D and Zhao, Z and Li, H}, title = {Achieving nitrogen removal in the integrated upper fixed-biofilm activated sludge reactor without recirculation: Differential protein and metagenomic analysis.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134774}, doi = {10.1016/j.biortech.2026.134774}, pmid = {42082030}, issn = {1873-2976}, mesh = {*Nitrogen/isolation & purification/metabolism ; *Sewage/microbiology ; *Bioreactors/microbiology ; *Biofilms ; Biological Oxygen Demand Analysis ; *Metagenomics/methods ; Water Purification/methods ; Oxygen ; Wastewater ; Bacteria/metabolism/genetics ; }, abstract = {The Integrated Fixed-film Activated Sludge (IFAS) system emerges as an advanced nitrogen removal technology, particularly effective for treating high-nitrogen wastewater due to its sophisticated configuration. This research introduces an enhanced Integrated Upper Fixed-film Activated Sludge (IUFAS) reactor featuring a two-stage series design. By strategically positioning carrier media in the upper compartment and implementing controlled influent distribution with aeration in the lower section, the system achieves functional compartmentalization within a single reactor without liquid and sludge recirculation. Experimental results under influent conditions of chemical oxygen demand/total nitrogen (C/N) ratio (4 ∼ 5) and hydraulic retention time (10 h) confirmed effective nitrogen removal, evidenced by effluent total nitrogen consistently below 7 mg N/L and removal efficiency exceeding 87%. Notably, the optimized IUFAS configuration achieved functional zoning by establishing a pronounced dissolved oxygen gradient between the upper (0.1 ∼ 0.7 mg/L) and bottom compartments (0.3 ∼ 3.6 mg/L). This oxygen stratification facilitated distinct nitrogen removal pathways, including stable anaerobic ammonium oxidation (Anammox) as evidenced by successful Candidatus Brocadia enrichment in the secondary reactor's upper zone. Microbial analysis further indicated potential modulation of electron flow by sulfate-reducing bacteria and sulfur-driven denitrifying bacteria, whose synergistic activity optimized electron transfer pathways and enhanced denitrification efficiency. Additionally, microalgae reduced aeration demand, lowering energy consumption. These findings propose novel strategies for optimizing carbon source allocation in nitrogen removal processes, supporting the development of energy-efficient wastewater treatment systems.}, } @article {pmid42082383, year = {2026}, author = {Asthana, S and Bhat, AD and Mahadevan, G and Kothegala, L and Negi, S and Yadav, S and Sudhakaran, A and Roy, A and Makwana, M and Patel, R and Rao B, H and George, CE and Gayen, S and Shukla, S and Jhunjhunwala, S and Sen, P and Kaur, P and Bhat, R and Saini, DK and , and , }, title = {The BHARAT study: a multi-modal, multi-omics investigation of aging signatures in the Indian population.}, journal = {Aging}, volume = {18}, number = {1}, pages = {380-396}, doi = {10.18632/aging.206373}, pmid = {42082383}, issn = {1945-4589}, mesh = {*Aging ; *Multiomics ; India ; Cross-Sectional Studies ; Humans ; Male ; Female ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged ; Rural Population ; Urban Population ; Longevity ; Research Design ; Biomarkers ; Biological Specimen Banks ; }, abstract = {India is undergoing a rapid demographic transition, with its elderly population projected to exceed 347 million by 2050. Although aging is the primary risk factor for multiple chronic diseases, most biological age (BA) models have been developed for Western populations, with limited applicability to Indian demographics. The BHARAT study (Biomarkers of Healthy Aging, Resilience, Adversity, and Transitions) aims to develop and validate composite signatures of aging in the Indian population by integrating multi-omics, biochemical, clinical, and lifestyle data. The BHARAT study is a multi-center, cross-sectional observational study designed using a hub-and-spoke model, with the Indian Institute of Science (IISc) serving as the central hub for omics analyses, biobanking, and data integration. Participants are stratified into five age groups (18-29, 30-44, 45-59, 60-74, ≥75 years) with balanced rural-urban and gender representation. The study primarily includes healthy participants, excluding those with chronic diseases that are not resolved by medication. Data collection encompasses comprehensive clinical and cognitive assessments, lifestyle and quality-of-life questionnaires, and biological sampling (including blood, urine, stool, cheek swabs, and hair). Multi-omics profiling spans epigenomics, proteomics, metabolomics, lipidomics, metagenomics, and immune phenotyping, integrating untargeted discovery-based Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) with targeted assays under harmonized protocols and quality-controlled biobanking standards. As the first large-scale, discovery-driven aging cohort in India, BHARAT will generate population-specific reference datasets, (re)train and calibrate biological clocks, develop a data-driven framework for organ-specific clocks, and identify biomarkers of physiological resilience and decline. Given that presently this study is cross-sectional in design, it will help establish a scalable framework for subsequent longitudinal and translational research to develop context-specific diagnostics, predictive models, and therapeutic targets for healthy aging in India.}, } @article {pmid42082531, year = {2026}, author = {An, K and Wang, D and Qu, Y and Yu, H and Liang, H and Mao, Z and Xue, Z and Li, J}, title = {Branched-chain amino acids ameliorate CD4[+] T-cell-associated gut immune inflammation in Parkinson's disease.}, journal = {NPJ Parkinson's disease}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41531-026-01375-y}, pmid = {42082531}, issn = {2373-8057}, support = {81901303//National Natural Scientific Foundation of China/ ; 82471273//National Natural Scientific Foundation of China/ ; 82301621//National Natural Scientific Foundation of China/ ; }, abstract = {Previous studies have shown that alterations in the gut microbiota and its derived metabolites, branched-chain amino acids (BCAAs), are correlated with T-cell-associated immune imbalance and Parkinson's disease (PD). However, the associations among BCAAs, gastrointestinal dysfunction and T-cell-related gut inflammation remain unclear. This study showed that the constipation symptoms in the PD mice persisted after chronic MPTP treatment. An imbalance in the CD4[+] T-cell subtypes was observed in the colonic lamina propria (cLP), mesenteric lymph nodes (mLNs), and spleen. Metagenomic and metabolomic analyses showed that microbial dysbiosis promoted BCAA degradation rather than biosynthesis, and reduced BCAA levels were confirmed in the serum. BCAA supplementation alleviated constipation symptoms and increased Th1 and Th17 cell infiltration in the cLP, mLNs and spleen were significantly attenuated after BCAA treatment. This study highlights the therapeutic value of BCAAs in mitigating gut immune inflammation-associated constipation symptoms in PD.}, } @article {pmid42082533, year = {2026}, author = {Tamang, S and Sherpa, MT and Najar, IN and Kumar, S and Das, S and Sharma, P and Das, N and Chowdhury, R and Thaosen, R and Ranjan, RK and Pandey, P and Thakur, N}, title = {Metagenomic analysis of bacterial diversity, antibiotic resistance, and functional profiles in the ice core samples from two glaciers of Sikkim Himalaya.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42082533}, issn = {2045-2322}, support = {BT/PR41644/NER/95/1718/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {*Ice Cover/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Metagenomics/methods ; Sikkim ; Biodiversity ; *Drug Resistance, Microbial/genetics ; *Metagenome ; Microbiota ; }, abstract = {Glaciers cover a substantial portion of the world and are home to various biological populations. The Himalayas constitute the largest glaciated region outside the poles; hence, they are regarded as "The Third Pole" of the World. There are around 84 glaciers in the Teesta basin (Sikkim Himalaya). There is substantially less data available on the microbial diversity embedded in the glacial ice core samples of the Sikkim Himalaya, as well as their physico-chemistry and potential geomorphological hazards related to their retreat or decrease in snow-line cover. The present study aims to evaluate the microbial diversity in the glacier ice core region and the study area; therefore, two glaciers in the Sikkim Himalaya were chosen: Frey-Peak and Rathong Glacier. The bacterial diversity analysis reveals the prevalence of various phyla, including Pseudomonadota, Actinomycetota, Bacillota, and Bacteroidota. The random forest model reveals the significant contributions of various elements, including Na, Mg, K, Ca, and Zn, to the alpha diversity of the studied glaciers. Among physicochemical parameters, pH was found to contribute the most in shaping bacterial diversity. Cluster of Orthologous Groups (COG) analysis underscored a predominance of genes associated with amino acids (23.5%), carbohydrates (18.93%), lipids (10.88%), energy (17.26%), coenzymes (9.38%), and ion transport/metabolism (14.71%). KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology (KO) analysis revealed the presence of 4,915 to 96,954 genes. Interestingly, the metagenomic analysis revealed the presence of specific species of Bradyrhizobium, Beijerinckia, Burkholderia, and Corynebacterium, which are associated with nitrogen metabolism, suggesting their potential involvement in biogeochemical processes. Additionally, a total of 59 to 419 bacterial genes related to sulphur metabolism were deduced through the KEGG functional analysis. The study detected the presence of various antibiotic resistance genes corresponding to different classes of antibiotics, including aminoglycoside, tetracycline, fluoroquinolone, macrolide, and erythromycin. Network analysis reveals that antibiotic resistance genes primarily interact with the phyla Pseudomonadota, Bacillota, and Actinomycetota. The melting of glaciers, a significant effect of climate change, may release contaminants, antibiotic resistance genes, and pathogenic bacteria into free-flowing rivers, potentially impacting human health.}, } @article {pmid42082982, year = {2026}, author = {Li, J and Guo, S and Yu, H and Hong, X and Nie, J and Sun, H}, title = {Thyroid functional state-dependent dysbiosis of gut microbiota in Hashimoto's thyroiditis: a cross-sectional metagenomic profiling study.}, journal = {Thyroid research}, volume = {19}, number = {1}, pages = {}, pmid = {42082982}, issn = {1756-6614}, abstract = {BACKGROUND: Hashimoto's thyroiditis (HT) is a prevalent autoimmune thyroid disease (AITD) closely linked to genetic predisposition and environmental factors. Gut microbiota dysbiosis has recently been implicated as a critical contributor to AITDs' pathogenesis. Our study aims to systematically investigate the dynamic alterations in gut microbial communities under varying thyroid functional statuses and elucidate their underlying mechanisms.

METHODS: 67 HT patients with varying thyroid functional statuses and 23 healthy controls were enrolled. Fecal 16 S rDNA sequencing and analyses (alpha diversity, LEfSe, correlation, functional pathways) assessed microbiota-thyroid function links.

RESULTS: HT patients with hypo/hyperthyroidism had lower gut microbiota richness than euthyroid patients (more reduced in hyperthyroidism). The hyperthyroid group exhibited enrichment of Fusobacterium, the hypothyroid group was dominated by Clostridium sensu stricto_1, and the euthyroid group showed a predominance of short-chain fatty acid (SCFA)-producing bacteria (e.g., Lactobacillus). Clostridium sensu stricto_1 positively correlated with TPO-Ab levels but negatively correlated with FT3.Pro-inflammatory genera(e.g., Escherichia-Shigella, Streptococcus) demonstrated negative correlations with FT3.Functional prediction analysis revealed potential associations with L-tyrosine degradation in the hyperthyroid group, reduced proportions of bile acid metabolism pathways in the hypothyroid group, and enriched proportions of fatty acid metabolism pathways in the euthyroid group.

CONCLUSIONS: This study revealed that gut microbiota dysbiosis is closely associated with thyroid functional statuses in HT. Specific bacterial genera, such as Clostridium sensu stricto_1 and Fusobacterium, may contribute to immune regulation and disease progression. The dynamic alterations in gut microbial profiles provide potential biomarkers for precision diagnosis and treatment of HT.}, } @article {pmid42083021, year = {2026}, author = {Han, Y and Cui, J and Huang, X and Guo, P and Yang, S}, title = {Microbial inoculants with straw mediate degradation-level-specific changes in soil carbon cycling genes and microbial community.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00898-4}, pmid = {42083021}, issn = {2524-6372}, support = {2022YFD1500600//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Enhancing soil organic carbon (SOC) sequestration in degraded lands is critical for climate mitigation and sustainable agriculture. While straw amendment combined with microbial inoculants holds great promise, the underlying mechanisms governing its impact on soil microbiome and carbon cycling genes remain poorly understood.

RESULTS: Here, we employed metagenomic sequencing to analyze responses in soil carbon (C) cycling genes, microbial community structure, and functional profiles across three degradation levels (severely, moderately, and non-degraded) of cinnamon soils under straw application alone or in combination with microbial inoculants. Results showed that both straw and straw-microbial inoculants treatments significantly improved soil properties, with improvements in available nitrogen and microbial biomass carbon (severe degradation), SOC (moderate degradation), and available nutrients (non-degradation). The combined application notably reshaped microbial communities by enhancing bacterial alpha diversity while reducing fungal diversity, and strengthened the relationship of relevant key soil C genes in severely degraded soils. Soil pH exhibited significant positive correlations with soil C cycling genes. Key bacterial genera (Sphingomonas, Bradyrhizobium) showed strong associations with ABC transporters and glycoside hydrolases, and fungal genus (Chaetomium) linked to pyruvate and purine metabolism. Importantly, we observed degradation-level specificity: straw addition significantly increased the abundance of the amylase gene K01214 (encoding α-amylase for starch hydrolysis) in severely degraded soils, whereas the straw-inoculant combination enriched the chitinase gene K01207 (encoding chitinase for chitin hydrolysis) in moderately degraded soils.

CONCLUSIONS: Accordingly, we propose targeted application of straw with a customized chitinolytic-cellulolytic synthetic microbial community (1-5% of straw mass) to restore carbon cycling functions in degraded soils, while adopting optimized agronomic management to preserve microbiome stability in non-degraded soils. Our findings provide novel insights into microbial-mediated carbon cycling and a foundation for targeted soil restoration.}, } @article {pmid42083059, year = {2026}, author = {Diop, K and Benlaïfaoui, M and Hunter, S and Méndez-Salazar, EO and Hakozaki, T and Richard, C and Prifti, DK and Kourtian, S and Proulx-Rocray, F and Naimi, S and Ponce, M and Messaoudene, M and Cauchois, F and Belkaid, W and Bataille, V and Lee, K and Mihalcioiu, C and Watson, IR and Elkrief, A and Routy, B}, title = {Metagenomics and culturomics reveal the dual role of the gut microbiome in the development of immune-related toxicities and the efficacy of immune checkpoint inhibitors in cancer.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02419-4}, pmid = {42083059}, issn = {2049-2618}, support = {284894//Fonds de recherche du Québec/ ; }, abstract = {BACKGROUND: Despite their major impact on cancer treatment, immune checkpoint inhibitors (ICI) are frequently associated with immune-related adverse events (irAE). Growing evidence suggests that the occurrence of irAE may be correlated with enhanced ICI efficacy, although the underlying mechanisms remain unknown. Most studies investigating the role of the gut microbiome in oncology have relied on sequencing approaches, particularly shotgun metagenomics. Although microbiome profiling revealed strong associations between specific bacterial taxa and clinical outcomes, it has limitations, including an inability to detect low-abundance bacteria and to recover live cultivable bacteria. To overcome these limitations, we combined shotgun metagenomics and culturomics on fecal samples collected from patients with melanoma and non-small cell lung cancer (NSCLC), at baseline and at the onset of immune related (ir)-colitis.

RESULTS: We first validated across three independent cohorts of 589 patients with melanoma or NSCLC treated with ICI that grade ≥ 2 irAE were associated with significantly longer overall survival (OS) and progression-free survival (PFS). Complementary analysis using shotgun metagenomics and culturomics revealed that patients who developed grade ≥ 2 irAE had a lower alpha diversity compared to those who did not develop grade ≥ 2 irAE. Metagenomics results showed enrichment of Ruminococcus gnavus and Streptococcus vestibularis at baseline in grade ≥ 2 irAE patients, while Clostridium paraputrificum and Streptococcus spp. were isolated by culturomics from baseline stool samples from ir-colitis patients. Longitudinal analysis of paired stool samples revealed a shift in microbiome composition with enrichment of Paraclostridium bifermentans and Clostridium paraputrificum, lower lipopolysaccharide and higher flagellin concentrations at baseline compared with the time of ir-colitis. Fecal microbiome transplantation from a patient with ir-colitis into mice induced surrogate markers of colonic inflammation and enhanced the anti-tumor activity of combined anti-PD-1/CTLA-4. P. bifermentans isolated from this patient sample demonstrated direct epithelial barrier disruption in Caco-2 monolayers, characterized by decreased ZO-1 and Occludin immunofluorescence signal and increased TNF-α and IL-1β expression. Moreover, in the dextran sodium sulfate (DSS) colitis model, P. bifermentans worsened weight loss. In a separate tumor model, it amplified the anti-tumor effect of dual ICI. This beneficial effect was also maintained after treatment with P. bifermentans < 3 kDa filtered supernatant.

CONCLUSION: Altogether, our results suggest that P. bifermentans promotes subclinical colitis while increasing the efficacy of dual ICI. This provides a potential microbiome-derived link between irAE and improved anti-tumor responses. Video Abstract.}, } @article {pmid42083116, year = {2026}, author = {Onohuean, FE and Onohuean, M and Olot, H and Onohuean, H}, title = {Poor Glycemic Control in East Africa: Prevalence, Risk Factors and Public Health Implications in Diabetes Management.}, journal = {Endocrinology, diabetes & metabolism}, volume = {9}, number = {3}, pages = {e70233}, pmid = {42083116}, issn = {2398-9238}, mesh = {Humans ; *Glycemic Control/statistics & numerical data ; Africa, Eastern/epidemiology ; Risk Factors ; Prevalence ; *Public Health ; *Diabetes Mellitus/epidemiology/therapy/blood ; Cross-Sectional Studies ; Blood Glucose/analysis ; Glycated Hemoglobin/analysis ; *Diabetes Mellitus, Type 2/epidemiology/blood/therapy ; }, abstract = {BACKGROUND: Diabetes mellitus remains a major public health concern in East Africa, and poor glycaemic control continues to drive avoidable complications, deaths and pressure on already stretched health systems.

OBJECTIVE: To estimate the prevalence of poor glycemic control and describe the main factors associated with it among people living with diabetes in East Africa.

METHODS: This review synthesized evidence from observational studies, cross-sectional surveys and regional health databases identified through PubMed, Scopus and Web of Science, following PRISMA guidance. Sociodemographic, clinical and behavioural indicators were examined to identify common patterns and predictors of poor glycaemic control. The review also considered how measurement approaches shaped reported estimates.

RESULTS: Fifty records were identified across PubMed (10), Scopus (23) and Web of Science (17). After screening, 37 records were eligible for full-text review, and 15 studies met the inclusion criteria for evidence synthesis. Across the region, poor glycemic control was consistently high, ranging from 60% to 85%. Most studies were facility-based and cross-sectional. Glycemic control was assessed mainly using HbA1c, commonly defined as ≥ 7% or > 7.5%, and less frequently by fasting blood glucose, typically ≥ 7.2 mmol/L or > 130 mg/dL. Type 2 diabetes was the dominant population studied, with fewer mixed cohorts and only one study focused on type 1 diabetes. Factors repeatedly linked to poor control included older age, longer duration of diabetes, poor medication adherence, limited access to care, low health literacy, inadequate diabetes education, insulin use, comorbidities, diabetic complications, unhealthy diet, physical inactivity, sedentary behaviour, substance use and limited self-management support.

CONCLUSION: Poor glycemic control is alarmingly common among people with diabetes in East Africa and reflects intertwined clinical, behavioural and health-system challenges. Region-specific strategies are needed to strengthen primary care, improve diabetes education, expand affordable monitoring and treatment and enhance surveillance to guide policy and resource allocation.}, } @article {pmid42083299, year = {2026}, author = {Qin, R and Wang, C and Cong, M and Tian, L and Li, N}, title = {Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pneumonia in Patients With Cancer.}, journal = {Cancer medicine}, volume = {15}, number = {5}, pages = {e71915}, pmid = {42083299}, issn = {2045-7634}, support = {JYKY2024-0050409022//Beijing Vlove Charity Foundation/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Retrospective Studies ; *Neoplasms/complications ; Aged ; *Pneumonia/diagnosis/microbiology ; Sputum/microbiology ; Adult ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: With the development of new sequencing technologies, metagenomic next-generation sequencing (mNGS) has become a diagnostic tool for respiratory tract infections. Patients with cancer may develop pneumonia caused by infections or antitumor therapy. Therefore, pneumonia in patients with cancer is more complex than that in healthy individuals. Currently, few reports are available on the use of mNGS for diagnosing pneumonia in patients with cancer.

METHODS: In this retrospective study, 14 patients with cancer diagnosed with pneumonia in March 2023 were enrolled from the Emergency Department of the Chinese Academy of Medical Sciences Cancer Hospital. Sputum samples from the patients were examined using conventional tests and mNGS to identify pathogens. The mNGS and conventional test results were compared to assess the diagnostic yield in patients with cancer.

RESULTS: The overall pathogen detection rate of mNGS was 64.29% (9/14), with corresponding diagnostic sensitivity, specificity, false-negative rate and false-positive rate of 90.00%, 25.00%, 10.00% and 75.00%, respectively. Among 13 paired sputum specimens, mNGS exhibited a numerically higher pathogen detection rate (61.54%, 8/13) than conventional diagnostic assays (38.46%, 5/13). McNemar's paired chi-square test demonstrated no statistically significant difference between the two detection methods (p = 0.37), and Kappa concordance analysis generated a coefficient of 0.27 (p = 0.23), suggesting poor inter-method consistency. Compared with conventional tests, mNGS detected additional pathogens in 8 specimens and identified a greater number of pathogens in 9/14 (64%) samples. Moreover, mNGS results led to diagnostic revisions and subsequent antimicrobial therapy adjustments in 64% (9/14) of enrolled patients. Additionally, mNGS detected antibiotic resistance genes in five patients, which provided guidance for antibiotic selection.

CONCLUSIONS: Metagenomic next-generation sequencing (mNGS) showed potential value in pathogen detection, as it appeared to identify pathogens more rapidly and comprehensively than conventional methods. It may provide auxiliary support for the diagnosis and treatment of pneumonia in this vulnerable population.}, } @article {pmid42083599, year = {2026}, author = {Kozlova, AS and Zgoda, AV and Petushkova, NA and Bolochenkov, NA and Zgoda, VG and Salnitska, MA and Kazakov, DV and Lisitsa, AV}, title = {The Microbiomic Metaproteome of the Taiga Tick Ixodes persulcatus from the Tyumen Region.}, journal = {Acta naturae}, volume = {18}, number = {1}, pages = {55-63}, pmid = {42083599}, issn = {2075-8251}, abstract = {Metagenomic studies have revealed the taxonomic composition of the taiga tick (Ixodes persulca tus) microbiome, whereas metaproteomic data has provided information on the biochemically active fraction of the microbial community residing in the tick. The aim of this study was to characterize the biological pro cesses taking place within the microbiome of the taiga tick I. persulcatus using a metaproteomic approach. To expand the range of identifiable proteins, we used two trypsin concentrations in sample preparation for mass spectrometric analysis. The metaproteomes of unfed female and male ticks were analyzed, which ena bled identification of protein products encoded by 2,100 genes from microorganisms belonging to 203 bacteri al and fungal species. Increased abundance of proteins associated with Ascomycota fungi, particularly abun dant in females, were detected. Proteins from the pathogenic Rickettsia and Borrelia species were identified. These findings enable a transition from a taxonomic metagenomic description to a functional analysis of the microbial consortium role in the physiology of the vector tick, particularly given the identified microbiota differences related to the tick sex.}, } @article {pmid42084116, year = {2026}, author = {Qi, J and Liang, C and Zhang, C and Wang, M and Wei, G and Jiao, S}, title = {Intensifying Aridity Undermines the Role of Soil Biodiversity in Supporting Ecosystem Stability.}, journal = {Global change biology}, volume = {32}, number = {5}, pages = {e70903}, doi = {10.1111/gcb.70903}, pmid = {42084116}, issn = {1365-2486}, support = {42477129//National Science Foundation of China/ ; JYB2025XDXM706//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; }, mesh = {*Biodiversity ; *Soil Microbiology ; *Climate Change ; China ; *Soil/chemistry ; *Ecosystem ; *Desert Climate ; }, abstract = {Biodiversity is widely recognized for enhancing ecosystem stability, yet its contribution is highly sensitive to climate change. However, whether and how climatic factors, particularly aridity, modulate the role of soil biodiversity in stabilizing ecosystems remains poorly understood. Here, we integrated a comprehensive soil survey of 265 dryland agricultural fields along a 3800 km east-west transect in China with a global meta-dataset encompassing 996 sites across six continents. Our analysis revealed a positive association between soil biodiversity and ecosystem stability, quantified using 11-year Normalized Difference Vegetation Index (NDVI) data (2012-2022). Critically, both our field data and global synthesis revealed that increasing aridity significantly weakened this biodiversity-stability relationship. The decline in soil microbial network complexity with increasing aridity partially explains this decoupling. Metagenomic analyses further showed that as aridity increased, microbial life history strategies shifted toward greater investment in stress tolerance at the expense of growth yield and resource acquisition. Together, our findings represent a substantial advance in revealing how intensifying aridity undermines the role of soil biodiversity in supporting ecosystem stability, and highlight the importance of microbial network complexity and life history strategies as key predictors of biodiversity-stability relationships under global change.}, } @article {pmid42084385, year = {2026}, author = {Rodríguez, P and Simon, SA and Probst, AJ and Magnabosco, C}, title = {Depth-associated selection and drift shape persistent microbial populations in Holocene lake sediments.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0150025}, doi = {10.1128/msystems.01500-25}, pmid = {42084385}, issn = {2379-5077}, abstract = {Cosmopolitan microbial lineages are found in anoxic sediments worldwide, but the details about their ecology and evolution remain underexplored. In this study, we identified persistent populations from these cosmopolitan lineages belonging to Planctomycetes, Chloroflexi Atribacteria, and Candidatus Bathyarchaeia from an ~8,000-year sedimentary sequence. To investigate the genomic variations within these persistent populations, a pangenome of each population was constructed using all non-redundant metagenome-assembled genomes (MAGs) recovered from the sedimentary sequence and was screened for enriched functional genes, single-nucleotide polymorphism (SNP) density, dN/DS ratios, and pseudogene content. Our results show that the majority of persistent populations studied possess large variable genomes enriched for energy conservation and transcriptional regulation functions with increasing depth, whereas Planctomycetes retain a highly conserved, SNP-poor core genome. Analysis of SNPs across depths indicates progressive isolation with burial, while a subset of core genes shows signatures of positive selection. Collectively, the data support depth-associated selection acting alongside drift across Lake Cadagno's persistent sedimentary lineages.IMPORTANCEThroughout the subsurface, multiple examples of "evolutionary stasis" have been reported in microbial lineages that exhibit lower rates of metabolic activity and cellular turnover. This study uses an ~8,000-year sedimentary record of Lake Cadagno to evaluate how persistent populations of cosmopolitan bacteria and archaea have changed with burial and identifies signals of progressive genetic isolation along with positive selection of population-specific subsets of core genes with depth. Together, these changes show that Lake Cadagno's persistent populations are not in stasis but diverge over time and burial.}, } @article {pmid42084478, year = {2026}, author = {Wang, C and Dou, P and Wang, Y and Li, X and Zhang, Y and Ma, X}, title = {A wolf in sheep's clothing: An unusual zoonotic pathogen in peritoneal dialysis effluent and an important diagnostic strategy.}, journal = {Peritoneal dialysis international : journal of the International Society for Peritoneal Dialysis}, volume = {}, number = {}, pages = {8968608261448060}, doi = {10.1177/08968608261448060}, pmid = {42084478}, issn = {1718-4304}, abstract = {Brucellosis is an infectious disease characterized by a natural foci, caused by Brucella, a genus of Gram-negative bacilli known for its obligate aerobic growth and capability for intracellular parasitism. This pathogen can be transmitted zoonotically between animals and humans. Due to its mechanism of intracellular survival, monotherapy with a single antibiotic often proves ineffective in eradicating Brucella. Therefore, clinical management necessitates the implementation of multidrug combination therapy alongside extended therapeutic regimens to achieve optimal bacteriological clearance. Conventional diagnostic methods, such as bacterial culture and serological testing, are frequently hindered by the fastidious growth requirements of the pathogen and the risk of false-positive serological cross-reactivity. These limitations may result in delayed diagnosis or unnecessary interventions. Recent advancements in molecular biology-particularly genomic analysis technologies-have revolutionized pathogen detection by facilitating rapid and precise identification of elusive pathogens. This study reports the first documented case of refractory peritoneal dialysis-associated peritonitis caused by Brucella diagnosed via metagenomic next-generation sequencing (mNGS). By employing mNGS to identify the pathogen, we summarize the clinical characteristics of this case and highlight the diagnostic advantages of this technology. Our findings aim to guide clinicians in selecting appropriate diagnostic approaches for similar cases, avoiding unnecessary delays and optimizing resource utilization in clinical practice.}, } @article {pmid42084497, year = {2026}, author = {Leech, J and Obafemi, YD and Breselge, S and Aremu, T and Obadina, AO and Itohan, ME and Ezekiel, CN and Parkouda, C and Tankoano, A and Traoré, K and Banwo, K and Kunadu, AP and Madilo, FK and Sanni, AI and Ogunremi, OR and Onipede, G and Odeny, DA and Otieno, C and Claesson, MJ and Cotter, PD}, title = {Characterizing microbiomes of African fermented foods in a global context.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {5}, pages = {}, pmid = {42084497}, issn = {1465-2080}, mesh = {*Fermented Foods/microbiology ; *Microbiota/genetics ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Food Microbiology ; Metagenome ; Fermentation ; Africa ; Kenya ; Burkina Faso ; Ghana ; }, abstract = {Fermentation plays a vital role globally, shaping traditional diets and enhancing food preservation, nutrition and flavour. With over 5,000 varieties of fermented foods globally, the microbiomes of many of these have yet to be explored, particularly with respect to those produced in some regions of Africa. To begin to address this knowledge gap, we conducted a shotgun metagenomics-based analysis of 91 fermented foods produced in Burkina Faso, Ghana, Kenya and Nigeria and compared them to a larger, global curated Food Metagenomic Database (cFMD). As for other studies of fermented food microbiomes in general, the substrate that was fermented emerged as the primary determinant of microbial beta diversity within the current African dataset and between the broader cFMD dataset. However, it was notable that the newly studied samples showed a small but statistically significant geographic signal. The African samples also displayed more alpha diversity than the global dataset, with cassava-, seed- and grain-based samples having the highest alpha diversity among the African foods. We also characterized the functional and antimicrobial profiles of all food-derived metagenome-assembled genomes (MAGs), noting the prevalence of pathways associated with carbohydrate metabolism across both African and non-African MAGs and an absence of known antimicrobial resistance genes in numerous genera. These findings not only expand our fundamental understanding of Africa's under-studied fermented food microbiomes but also lay the foundation for starter culture development tailored to local substrates and conditions, fostering opportunities to enhance product safety, quality and scalability while retaining key characteristics associated with the original, artisanal product.}, } @article {pmid42084683, year = {2026}, author = {Maurya, S and Shukla, AK and Reddy, B and Singh, AK and Singh, VK and Tripathi, M}, title = {Metagenomic insights into microbial community, antibiotic resistance genes, and virulence factor in Saryu River water, India.}, journal = {Environmental science and pollution research international}, volume = {33}, number = {16}, pages = {7765-7777}, pmid = {42084683}, issn = {1614-7499}, mesh = {*Rivers/microbiology ; India ; Virulence Factors/genetics ; *Drug Resistance, Microbial/genetics ; Metagenomics ; Bacteria/genetics ; Anti-Bacterial Agents ; Water Microbiology ; }, abstract = {A river confluence is an important ecosystem to investigate the microbial community and functional profile. Even after the enormous applications of trace elements and antibiotics, their release into the environment causes pollution and selective pressure that facilitate the proliferation and dissemination of resistance genes against antibiotics, metals and biocides among bacterial communities. Metagenomic exploration plays a pivotal role in deciphering riverine ecosystems and offers valuable insights for the mitigation of pollution and the dissemination of resistance genes. Monitoring microbial diversity could aid in identifying various prokaryotes, pathogens, and pollutants, including dyes and their associated resistance genes. Therefore, we aimed to elucidate the occurrence of resistance genes and virulence factors in the microbial community of Saryu River water using high-throughput metagenomics coupled with bioinformatic analyses. The highly dominant antibiotic resistance gene (ARG) types identified were rifampin, tetracycline, macrolide, polymyxin and rifampicin multidrug/efflux. ARGs such as rpoB2, Txr, adeF, tetB(P), and acrB were found to be abundant in Saryu River water. Among the detected MRG subtypes, namely, ruvB and arsB, the most abundant are in water. Further, the biocides against which the resistance was identified were ethidium bromide, triclosan, sodium dodecyl sulfate, etc. Among the virulence factors, tufa, htpB (adherence), Gmd (immune-modulation), cheD (motility), and clpV1 (effector-delivery-system) were found to be highly prevalent. Taxonomic classification revealed that Cyanobateriota, followed by Pseudomonadota (Proteobacteria) and Bacteroidota were the dominant phyla in the river water. Microcystis was the most dominant genus, followed by Desulfomicrobium and Dechloromonas. The present study shows that antibiotics and metals are the major sources of resistance genes development and dissemination in the environment.. Further, this is a preliminary study based on a single composite sample, representing a "snapshot" at a specific time and location. The present study highlights the persistence of ARGs, MRGs, biocides, and virulence factors in Saryu River water and provides valuable baseline data for risk assessment.}, } @article {pmid42084764, year = {2026}, author = {Joshi, G and Khannam, KS}, title = {Marine microbiomes and their expanding role in biotechnological potential: a systematic review.}, journal = {Archives of microbiology}, volume = {208}, number = {7}, pages = {}, pmid = {42084764}, issn = {1432-072X}, mesh = {*Microbiota ; *Biotechnology ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Ecosystem ; Biodegradation, Environmental ; }, abstract = {Marine bacteria are present almost everywhere in the ocean environment and are essential to many biogeochemical processes. The perspectives of ecologists and evolutionary biologists on the significance of microbes in ecosystem function are shifting as a result of exploring the marine microbiomes. This is especially true in ocean habitats, where microbes comprise the bulk of the biomass and are responsible for the majority of the planet's key biogeochemical cycles, including those that influence the global climate. Emerging research suggests that many ecosystem services provided by coastal marine environments depend on intricate interactions between groups of microbes and the environment or their hosts. The structure, variety, and functional capability of marine microbial populations have been revealed on a global scale thanks to recent developments in molecular ecology techniques. Over-recent-decades, industrialization and urbanization have led to widespread contamination of oceans. These contaminants accumulate in seawater and sediments, particularly in coastal areas, posing risks to marine ecosystems and human health. Marine microorganisms possess diverse catalytic abilities and extreme environmental tolerance, making them suitable for bioremediation of toxins. Effective-degradation of pollutants often depends on syntrophic-interactions within microbial communities, highlighting the importance of understanding their collaboration and communication for marine resource management. Here, we assess the current level of knowledge about marine microbiome research and highlight key issues within this developing field of study. The review aims to enhance understanding of marine microbiome's roles and potential uses in biogeochemical analysis, biotechnology, and environmental remediation, which could support sustainable and circular business models for future generations.}, } @article {pmid42085791, year = {2026}, author = {Besharati Fard, M and Ahmadi, N and Chen, Y and How, SW and De Vrieze, J and Wu, D}, title = {Tetracycline and ciprofloxacin reduce nitrification and denitrification activity and alter microbial community composition and activity in microalgal-bacterial aerobic granular sludge.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142255}, doi = {10.1016/j.jhazmat.2026.142255}, pmid = {42085791}, issn = {1873-3336}, mesh = {*Ciprofloxacin/pharmacology ; *Tetracycline/pharmacology ; *Sewage/microbiology ; Nitrification/drug effects ; Denitrification/drug effects ; Bioreactors/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Microalgae/metabolism/drug effects ; *Water Pollutants, Chemical/metabolism ; Aerobiosis ; *Microbiota/drug effects ; Bacteria/metabolism/drug effects ; Waste Disposal, Fluid/methods ; Biological Oxygen Demand Analysis ; }, abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) systems offer promising potential for wastewater treatment under chemical stress. However, their performance in the presence of antibiotics remains poorly understood. This study evaluated the response of MB-AGS to 1000 µg/L of tetracycline and ciprofloxacin in two separate bioreactors operated under alternating dark (60 min) and light (170 min) cycles at 20 °C. Chemical oxygen demand (COD) removal remained stable at 90 ± 4% (tetracycline) and 91 ± 6% (ciprofloxacin) over 80 days, suggesting that COD conversion was not impacted by antibiotic exposure. However, phosphate removal declined from ∼63% (antibiotic-free bioreactors) to 45 ± 6% (under tetracycline exposure) and 38 ± 8% (under ciprofloxacin exposure) after addition of antibiotics. Ciprofloxacin inhibited nitrification (declined to ∼50% NH4[+] removal), associated with reduced abundance of Nitrosomonas, while tetracycline impacted denitrification, evidenced by a lower Thauera abundance. Despite these impacts, the system removed 88.3 ± 5.6% of tetracycline and 69.5 ± 12.4% of ciprofloxacin, primarily through biosorption (for both antibiotics were more than 80%). Extracellular polymeric substances content increased by ∼19% under antibiotics exposure. Metagenomic analysis indicated changes in microbial community composition and function, while the overall antibiotic resistance gene profile remained relatively stable despite dynamic changes in individual resistance genes under antibiotic exposure. These findings demonstrate the strong potential of MB-AGS systems for effective organic carbon removal, while also highlighting opportunities to further enhance nutrient removal and mitigate antibiotic resistance genes under antibiotic stress.}, } @article {pmid42085838, year = {2026}, author = {ElHefnawi, M and Amin, DH and Elfiky, AM and Tamam, FMM and Elabiad, MA and Zada, S and Abu-Shahba, N}, title = {From culture to metagenomics: A paradigm shift in diagnosing infective endocarditis.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {1}, pages = {117449}, doi = {10.1016/j.diagmicrobio.2026.117449}, pmid = {42085838}, issn = {1879-0070}, mesh = {Humans ; *Metagenomics/methods ; *Endocarditis/diagnosis/microbiology ; Blood Culture/methods ; Bacteria/genetics/isolation & purification ; Molecular Diagnostic Techniques/methods ; Biofilms/growth & development ; }, abstract = {Infective endocarditis (IE) is a severe disease that damages heart valves and can lead to major complications, including heart failure, embolic events, and stroke. It is the third most common fatal infection worldwide. This review examines the clinical burden of IE, its microbial causes, and the ongoing challenges in diagnosis. Particular attention is given to the limitations of traditional blood cultures, especially in detecting culture-negative and fastidious organisms, and to the emerging role of metagenomic approaches. A comprehensive review of the literature was conducted, focusing on diagnostic methods such as blood cultures, molecular assays, and metagenomic sequencing. The role of bacterial biofilms in treatment failure and antibiotic resistance was also explored. Metagenomics, especially cell-free metagenomic DNA (cf-mDNA), shows promise as a non-invasive diagnostic tool that can overcome culture-based limitations. However, standardized protocols and prospective studies are needed to validate its routine clinical application in IE diagnosis and management.}, } @article {pmid42085875, year = {2026}, author = {Amin, H and Šantl-Temkiv, T and M Wouters, I and Johannesen, A and Sigsgaard, T and Schlünssen, V and Malinovschi, A and Thorarinsdottir, H and Bertelsen, RJ}, title = {Urban indoor airborne antibiotic resistance genes: Role of antibiotic use and outdoor air pollution.}, journal = {The Science of the total environment}, volume = {1034}, number = {}, pages = {181854}, doi = {10.1016/j.scitotenv.2026.181854}, pmid = {42085875}, issn = {1879-1026}, mesh = {*Drug Resistance, Microbial/genetics ; *Air Microbiology ; *Environmental Monitoring ; *Anti-Bacterial Agents/analysis ; *Air Pollution, Indoor/analysis/statistics & numerical data ; Cities ; *Air Pollutants/analysis ; Air Pollution/statistics & numerical data ; Dust/analysis ; }, abstract = {Antibiotic resistance genes (ARGs) in airborne dust represent an emerging concern for public health, particularly in indoor environments where human exposure is prolonged. While external environmental pressures are known to shape the abundance and diversity of microorganisms in indoor dust, their role in ARG dynamics remains underexplored. This study assessed the temporal and spatial patterns of airborne ARGs in indoor dust across four Nordic cities (Aarhus, Bergen, Reykjavik, and Uppsala) using electrostatic dust collectors (EDCs) in the same households at two time points: 2012 and 2022. Shotgun metagenomic sequencing was performed to profile ARGs. National antibiotic consumption data were obtained from the European Surveillance of Antimicrobial Consumption (ESAC-Net), outdoor air pollution data (PM2.5 and PM10) from the Copernicus Atmosphere Monitoring Service (CAMS), and meteorological parameters from the NASA POWER database. Beta diversity analysis revealed city-specific differences in ARG composition (PERMANOVA, R[2] = 0.18, P = 0.03), but no consistent temporal shift over the 10-year period. Macrolide, tetracycline, and aminoglycoside resistance genes were among the most abundant and persistent classes. A previously undetected macrolide resistance sequence was identified across all cities in 2022. Although national antibiotic consumption declined, cross-sectional correlations between national antibiotic consumption and ARG abundance strengthened from 2012 (Spearman's ρ = 0.25) to 2022 (ρ = 0.37), suggesting sustained ARG presence despite reduced antibiotic consumption. Several ARG classes showed associations with outdoor particulate matter, and these relationships were influenced by local meteorological conditions. For example, higher absolute humidity was associated with a weaker relationship between PM and polymyxin resistance genes, whereas stronger wind speeds were associated with stronger relationships between PM and Sulfonamide resistance genes. These findings highlight the complex environmental interplay between antibiotic consumption, air pollution, meteorological factors, and ARG dynamics in indoor air, emphasizing the need for integrated environmental and AMR surveillance, especially in the context of climate change.}, } @article {pmid42085931, year = {2026}, author = {Wang, Z and Wang, Y and Peters, BA and Post, WS and Brown, TT and Palella, FJ and Rinaldo, CR and Witt, MD and Gange, SJ and Kuniholm, MH and Sha, BE and Chichetto, NE and Clish, CB and Gerszten, RE and Hodis, HN and Sharma, A and Anastos, K and Burk, RD and Kaplan, RC and Qi, Q and Hanna, DB}, title = {Multi-omics analysis of the gut microbiome and carotid artery atherosclerosis in men with and without HIV.}, journal = {EBioMedicine}, volume = {127}, number = {}, pages = {106281}, pmid = {42085931}, issn = {2352-3964}, support = {K01 HL169019/HL/NHLBI NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *HIV Infections/complications/microbiology ; *Carotid Artery Diseases/etiology/metabolism/microbiology/complications/diagnosis ; Middle Aged ; Biomarkers ; Aged ; *Metabolomics/methods ; Metagenomics/methods ; Adult ; Plaque, Atherosclerotic ; Metabolome ; Multiomics ; }, abstract = {BACKGROUND: How gut microbiota alterations may contribute to host inflammation and metabolomic profiles affecting atherosclerosis is not fully elucidated, especially in the context of HIV.

METHODS: We examined associations between gut microbial features (measured by shotgun metagenomics) and subclinical carotid atherosclerosis, as assessed by high-resolution B-mode ultrasound, in 359 men from the MACS/WIHS Combined Cohort Study. We measured 822 plasma metabolites using LC-MS/MS, and up to 2866 circulating proteins by the Olink Explore 3072/384 platform (with a primary focus on 617 proteins related to inflammation and immune function).

FINDINGS: Carotid artery plaque was detected in 115/359 men (32%). Adlercreutzia equolifaciens and Eubacterium sp3131 were associated with lower odds of plaque (OR [95% CI] = 0.57 [0.43, 0.77], 0.84 [0.76, 0.93], respectively), while Coprococcus sp13142 was associated with higher odds of plaque (OR [95% CI] = 1.14 [1.06, 1.23]). Results were consistent in men both with and without HIV. A. equolifaciens was positively correlated with HDL cholesterol and inversely correlated with systolic blood pressure. These plaque-associated microbial species were also associated with a range of circulating metabolites and inflammatory proteins. For example, A. equolifaciens positively correlated with the metabolites palmitoyl-EA and mesobilirubinogen, and inversely correlated with the pro-inflammatory chemokine CXCL9, the immune regulator CD160, and IL-24.

INTERPRETATION: We identified gut microbial features associated with carotid artery atherosclerosis, consistent across HIV status; these associations were partially explained by specific microbiota-related metabolites and inflammatory markers. If validated, these findings suggest gut microbiota-related targets for CVD prevention.

FUNDING: The study was funded by the National Heart, Lung, and Blood Institute (U01HL146204-04S1, K01HL169019).}, } @article {pmid42086548, year = {2026}, author = {Lu, M and Jiao, JJ and Luo, X and Feng, X and Liang, W and Yu, S and Qi, Y and Wang, Z and Li, H and Li, M}, title = {Microbial drivers of ammonium accumulation in Holocene sediments of the Pearl River Delta.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72058-8}, pmid = {42086548}, issn = {2041-1723}, support = {32225003, 32393970, 32393971, 92251306//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42407109//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42130702//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Elevated ammonium concentrations in deltaic groundwater pose a widespread environmental challenge, yet the microbial mechanisms linking depositional history to ammonium dynamics remain poorly understood. The Pearl River Delta, with the highest naturally occurring groundwater ammonium concentrations documented globally, provides a unique natural system to investigate these processes. Here, by integrating geochemical and metagenomic data, we show that fermentation-related genes are the most prevalent across all depositional zones, suggesting fermentation as the potential primary pathway for ammonium production, with the functional potential declining as sedimentary organic matter becomes increasingly recalcitrant with sediment age. Secondary mechanisms shift from nitrate reduction to nitrite ammonification across terrestrial-to-marine-dominated zones, reflecting salinity-driven metabolic partitioning. Notably, the marine-derived genus Brevirhabdus emerges as a key taxon linking depositional history to present-day biogeochemistry, demonstrating remarkable metabolic versatility. These findings demonstrate that paleo-depositional and hydrogeological evolution fundamentally shape microbial landscapes and dictate groundwater quality in deltaic systems worldwide.}, } @article {pmid42086631, year = {2026}, author = {Moon, K and Kang, I and Cho, JC}, title = {Virome datasets and viral metagenome-assembled genomes from aquaculture-impacted freshwater environments.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07383-0}, pmid = {42086631}, issn = {2052-4463}, support = {NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; NA//Hankuk University of Foreign Studies (HUFS)/ ; }, abstract = {Bacteriophages in natural environments play a critical role in microbial ecology by regulating bacterial populations, mediating nutrient cycling, and facilitating horizontal gene transfer. Aquaculture operations, particularly inland fish farms, are major sources of anthropogenic influence on freshwater ecosystems. Here, we present three viral metagenomic datasets derived from freshwater samples collected at an inland aquaculture effluent site and adjacent upstream and downstream locations along the Sung-am River in Jincheon County, South Korea. The datasets were generated using the Illumina HiSeq X sequencing platform, yielding approximately 10.0-11.2 Gbp per sample. Quality assessments confirmed minimal bacterial contamination, with negligible proportions of rRNA and bacterial marker genes. Assembly using metaSPAdes and MEGAHIT, application of Phables to resolve high-quality phage genomes (viral metagenome-assembled genomes; vMAGs), viral identification with VirSorter2, and clustering using Vclust, resulted in 2,837-3,156 virus operational taxonomic units (vOTUs; ≥10 kb) per sample. Each vOTU sequence is analyzed for taxonomic assignment and putative host prediction. These datasets provide a valuable resource for further studies on viral diversity and microbial ecology in freshwater ecosystems affected by aquaculture.}, } @article {pmid42086823, year = {2026}, author = {Ismaeil, M and Saeed, AM and Donia, SA and El-Sayed, WS}, title = {Predictive functional profiling of 16S rRNA genes amplicons reveals bioremediation and sulfur metabolism capacity in thermophilic hot spring bacteriomes.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42086823}, issn = {2045-2322}, mesh = {*Hot Springs/microbiology ; *Sulfur/metabolism ; *RNA, Ribosomal, 16S/genetics ; Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; Microbiota ; Phylogeny ; Soil Microbiology ; Hot Temperature ; Proteobacteria/genetics/metabolism ; }, abstract = {Thermophilic hot springs host highly specialized microbial communities critical for biogeochemical cycling and novel biotechnological applications. This study investigated the structure of the bacterial communities (bacteriomes) and predicted functional potential related to bioremediation and sulfur metabolism across three geochemically diverse soil sites within the Pharaoh's Bath Hot Springs ecosystem in South Sinai, Egypt. These sites were categorized by distinct thermal profiles: 70 °C (HS1), 75 °C (HS2), and 80 °C (HS3). Using 16 S rRNA gene amplicon sequencing and PICRUSt functional prediction, sequence analysis via the EzBioCloud server revealed that the HS2 site harbored the highest evenness and overall microbial diversity. Taxonomically, the HS1 and HS3 sites were dominated by Proteobacteria; in contrast, the HS2 site exhibited a more diverse profile, characterized by a reduced Proteobacteria presence and a high abundance of Rhodothermaeota. Predictive functional profiling identified 13 genes associated with biodegradation pathways (e.g., catechol and xylene degradation), suggesting an intrinsic genetic capacity to degrade complex aromatics and halogenated compounds across these thermal gradients. Regarding sulfur metabolism, functional predictions indicated that the HS2 site possessed the highest potential for dissimilatory sulfate reduction. Meanwhile, the HS1 site specialized in assimilatory sulfate reduction and, alongside the HS2 site, demonstrated a higher predicted capacity for sulfide oxidation. The distribution of heat-response genes varied by location: HspQ and Hsp33 were most prominent at the HS1 site, while HSP20 and DnaK reached their maximum abundance at the HS2 site. Overall, this study demonstrates the substantial intrinsic bioremediation potential of the studied bacteriomes and provides a predictive framework for understanding microbial functional potential in this system, with future studies offering opportunities to refine in situ functional validation and application.}, } @article {pmid42087721, year = {2026}, author = {Pan, W and Tang, S and Wanek, W and Luo, Z and Chen, J and Yang, Y and Ge, T and Marsden, KA and Liang, G and Chadwick, DR and Chen, X and Gregory, AS and Wu, L and Liang, Y and Jones, DL and Ma, Q}, title = {Microbial Community Traits and Necromass Dynamics Shape Soil Carbon Accumulation.}, journal = {Global change biology}, volume = {32}, number = {5}, pages = {e70906}, doi = {10.1111/gcb.70906}, pmid = {42087721}, issn = {1365-2486}, support = {U24A20575//National Natural Science Foundation of China/ ; 32573140//National Natural Science Foundation of China/ ; 32402680//National Natural Science Foundation of China/ ; 2024M752818//China Postdoctoral Science Foundation/ ; 2026SNJF084//San Nong Jiu Fang Technology Cooperation Program of Zhejiang Province/ ; 2025SNJF025//San Nong Jiu Fang Technology Cooperation Program of Zhejiang Province/ ; 202303AC100013//Yunnan Key Research and Development Program/ ; 05//Smart Fertilization Project/ ; BBS/E/RH/23NB0007//UK Research and Innovation Biotechnology and Biological Sciences Research Council/ ; //Lawes Agricultural Trust/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism/analysis ; Fertilizers/analysis ; *Microbiota ; *Carbon Sequestration ; }, abstract = {Soil organic carbon (SOC) sequestration is vital for food security and climate mitigation. However, its long-term response to fertilisation remains unclear. Using the 180-year Broadbalk Experiment (the world's longest-running fertilisation trial; Rothamsted, UK), combined with [14]C labelling and metagenomics, we identified fundamentally distinct mechanisms of SOC accumulation: a microbially mediated dual pathway under organic fertilisation versus a resource-limited pathway under inorganic fertilisation. Sustained organic inputs matched inorganic fertilisers in maintaining crop yields while increasing total SOC by 160% (relative to a no-fertilisation control), far exceeding the 26% gain under inorganic fertilisation. Mechanistically, the continuous supply of labile organic matter provided an energetic surplus, allowing copiotrophic microbial communities with high carbon use efficiency to reduce investment in energy-intensive enzyme synthesis. This metabolic efficiency facilitated a dual-pathway expansion, elevating dynamic particulate organic carbon (POC) from 1.4 to 7.5 g kg[-1], while microbial assimilation and necromass accumulation concurrently increased mineral-associated organic carbon (MAOC) from 6.8 to 21.5 g kg[-1]. Conversely, inorganic fertilisation induced an oligotrophic 'mining' strategy, in which microorganisms upregulated the degradation of complex organic matter under carbon-limited conditions, restricting sustained SOC accumulation primarily to the MAOC pool. A global meta-analysis of field experiments (0-120 years) corroborated these temporal trajectories across diverse soil types, showing that SOC under organic fertilisation increases in a time-dependent manner, reaching a 77% gain after 80 years (three-fold greater than under inorganic inputs). Overall, organic fertilisation enhances total SOC via POC and MAOC accumulation, whereas inorganic fertilisation mainly increases MAOC. Long-term SOC persistence depends not only on carbon inputs, but also on microbial community traits and necromass dynamics, suggesting that aligning nutrient inputs with these biological mechanisms is critical for sustainable carbon sequestration.}, } @article {pmid42088021, year = {2026}, author = {Wang, A and Wang, Q and Zhang, T and Qi, G and Ren, W and Tian, W and Chen, J}, title = {Integrated multi-omics profiling reveals phenotype- and tissue-specific host-microbiota interactions in paired tumor and peritumoral tissues of advanced gastric cancer patients from Northwest China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1763765}, pmid = {42088021}, issn = {2235-2988}, mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology/genetics ; China ; Female ; Male ; Middle Aged ; Gene Expression Profiling ; Gastric Mucosa/microbiology/pathology ; Aged ; Phenotype ; *Host Microbial Interactions/genetics ; Metagenomics ; *Microbiota ; Transcriptome ; Adult ; Helicobacter Infections/microbiology ; *Gastrointestinal Microbiome ; Helicobacter pylori ; Multiomics ; }, abstract = {BACKGROUND: Advanced gastric cancer (AGC) exhibits a high incidence in Northwest China, largely attributed to region-specific dietary patterns and environmental exposures. Its pathogenesis involves complex host-microbiota crosstalk, which has not yet been comprehensively elucidated through integrated multi-omics approaches. Herein, we employed trasncriptomic and shotgun metagenomic sequencing on paired tumoral and peritumoal mucosal tissues from 88 AGC patients in Northwest China. Our aim was to systematically characterize host gene expression profiles, the composition and functional potential of the gastric mucosal microbiota, and their intricate interrelationships.

RESULTS: Transcriptomic profiling clearly distinguished tumoral from peritumoral regions (PERMANOVA, R[2] = 0.24, P = 0.0001), with 8870 differentially expressed genes (DEGs) identified between the two tissue types. Tumor tissues harbored 8377 up-regulated DEG, which were enriched in extracellular matrix (ECM) organization, cell cycle regulation, signaling transduction, and inflammatory pathways (e.g., PI3K-Akt, IL-17 signaling). In contrast, peritumoral tissues showed 493 up-regulated DEGs primarily associated with metabolic processes. Host gene expression was significantly modulated by Lauren classification in tumoral mucosa (P = 0.025) and by Helicobacter pylori (Hp) infection in peritumoral tissues (P = 0.0424). Hp-infected tissues exhibited 65 up-regulated DEGs linked to transcriptional misregulation in cancer, inflammation, immune activation and mitochondrial pathways. Lauren subtypes displayed distinct transcriptomic signatures: intestinal-type AGC was enriched in metabolic processes, diffuse-type in immune and signal transduction pathways, and mixed-type in Ras/MAPK/ErbB and NF-κB signaling pathways. Correlation analysis between the 8870 DEGs and seven differentially abundant bacterial species (e.g., Serratia surfactantfaciens, Pseudomonas protegens, Prevotella jejuni, and Streptococcus infantis) revealed 13199 significant correlations. Among these, S. surfactantfaciens and P. protegens exhibited the strongest connectivity with host genes. Functionally, the correlated DEGs were involved in ECM structure, cell cycle progression, immune and inflammatory responses, cellular proliferation and differentiation, and metabolic processes.

CONCLUSIONS: Our findings demonstrated phenotype- and tissue-specific regulation of host gene expression in AGC and revealed extensive host-microbe interactions. This work fills a critical gap in multi-omics research on AGC in the Northwest Chinese population and suggests potential diagnostic and therapeutic targets for AGC.}, } @article {pmid42088457, year = {2026}, author = {Li, P and Kahsen, J and Olsson-Francis, K and Green, SJ}, title = {Using Carrier DNA in Ultra-Low Input Library Preparations for Next-Generation Sequencing.}, journal = {Journal of biomolecular techniques : JBT}, volume = {37}, number = {1}, pages = {18-26}, pmid = {42088457}, issn = {1943-4731}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Gene Library ; *DNA/genetics ; Polymerase Chain Reaction/methods ; *Metagenomics/methods ; Metagenome/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The purpose of this study was to evaluate the use of carrier DNA (i.e., exogenous DNA spike-in) for shotgun metagenome sequencing of ultra-low levels (less than 50 picograms) of metagenomic DNA. The study hypothesized that carrier DNA would improve the robustness of library preparation for samples with DNA concentrations that are below detection by providing a tangible amount of known DNA thereby bringing total DNA concentrations closer to recommended input ranges for metagenomic library kits. The study employed adaptive polymerase chain reaction (PCR) cycling using an iconPCR instrument (N6tec) to allow dynamic thermocycling until a sufficient library for sequencing was amplified, regardless of the input DNA concentration. Libraries were sequenced and mapped in order to reference genomes of Lambda and mock community organisms, and outcome measures included total reads, on-target reads, evenness of coverage across 10 organisms within each mock community, and PCR duplication rate. The study demonstrated that libraries can be prepared down to 50 fg of input DNA, but there is a strong correlation between input DNA concentration and PCR duplication rate. The utility of spiking in carrier DNA is equivocal as it has mild negative impacts on the observed distribution of mock communities and serves as a loss of sequencing output. Although the loss of sequencing capacity due to carrier DNA can be partially offset by a reduced loss of data from PCR duplication, carrier DNA spike-in is not recommended for routine library preparation of ultra-low input samples. Adaptive cycling allows for appropriate cycling conditions when input DNA concentrations are below detection.}, } @article {pmid42089121, year = {2026}, author = {Bhagat, S and Kushwaha, S and Singh, S}, title = {Targeted Gut Delivery of Zn, Cu, and Mn Nanominerals Alleviates Oxidative Stress by Activating Endogenous SOD Enzymes.}, journal = {Advanced healthcare materials}, volume = {15}, number = {23}, pages = {e71209}, doi = {10.1002/adhm.71209}, pmid = {42089121}, issn = {2192-2659}, support = {C0046//National Institute of Animal Biotechnology, Hyderabad/ ; }, mesh = {Animals ; *Oxidative Stress/drug effects ; *Superoxide Dismutase/metabolism ; *Copper/pharmacology/chemistry/administration & dosage ; *Zinc/pharmacology/chemistry ; *Manganese/pharmacology/chemistry/administration & dosage ; Rats ; Antioxidants/chemistry/pharmacology ; Male ; Rats, Sprague-Dawley ; *Minerals/pharmacology/chemistry/administration & dosage ; Cell Line ; }, abstract = {Trace minerals such as Zn, Cu, and Mn are essential for maintaining cellular redox balance as cofactors of key antioxidant enzymes, including SOD1 and SOD2. However, their oral supplementation is often limited by poor stability in the acidic gastric environment and low intestinal absorption. Here, we report the synthesis of methionine-coated-ZnO (Met-ZnO), ascorbic acid-coated Cu2O (AA-Cu2O), and dextran-coated MnO2 (Dex-MnO2) nanominerals, followed by encapsulation into pH-responsive microcapsules (NMs-MCap) for targeted intestinal delivery. The nanomineral mixture demonstrated strong antioxidant activity at physiological pH by scavenging superoxide radicals, hydrogen peroxide, and ABTS[•+] radicals. In intestinal epithelial (IEC-6) cells, nanominerals significantly alleviated BSO-induced oxidative stress, reducing apoptosis, necrosis, and intracellular ROS accumulation. Oral administration of NMs-MCap in Zn, Cu, and Mn-deficient rats elevated mineral levels in blood and liver, mitigated BSO-induced oxidative damage, reduced lipid peroxidation and pro-inflammatory cytokines, and preserved tissue architecture. Importantly, oral supplementation restored SOD1 and SOD2 expression in key organs, supporting enhanced endogenous antioxidant defense. Metagenomic analysis revealed that mineral deficiency, combined with oxidative stress, caused gut dysbiosis, reducing beneficial taxa and enriching opportunistic ones. Nanomineral supplementation restored microbial balance, increased SCFA-producing bacteria, and improved antioxidant and metal-handling functions, establishing NMs-MCap as a safe, targeted antioxidant strategy supporting host health.}, } @article {pmid42089290, year = {2026}, author = {Banday, MM and Banday, S and Rahman, M and Harrison, AO and Singh, N and Moore, RM and Khan, MM and Shankar, S and Goda, Y and Coppolino, A and Movval, N and Stutts, S and Woolley, A and Dishaw, L and Goldberg, H and Mebratu, Y and Polson, SW and Patel, KN and Gaggar, A and Hayes, D and Krishnamoorthy, N and Gewurz, BE and Washko, G and Tesfaigzi, Y and Rehman, R and Sharma, NS}, title = {Anellovirus-Mediated Interferon Dysregulation Enhances Virus-Induced Lung Injury.}, journal = {American journal of respiratory cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajrcmb/aanag048}, pmid = {42089290}, issn = {1535-4989}, support = {R01 AI148180/AI/NIAID NIH HHS/United States ; R01 HL161620/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: The lung virome (LV) and its interactions with the host-immune system leading to allograft injury after lung transplantation are not well characterized.

METHODS: Shotgun metagenomics and qPCR was performed on a multicenter BAL/serum cohort from lung transplant recipients (LTRs). Viral constructs from betatorquevirus clade and group 2 TTVs were transfected in primary bronchial epithelial cells (PBECs) or airways of C57BL/6 mice with and without exposure to Influenza A (IAV) or RSV.

RESULTS: LV in LTRs was dominated by viruses from the family Anelloviridae. CLAD LV was characterized by the enrichment of betatorquevirus clade (BTV). Validation in an independent cohort confirmed BTV abundance in CLAD BAL, serum and lung tissues. BTV ORF1 protein (kV1) suppressed PBEC IFNα and IFNγ responses by preventing intranuclear STAT translocation. Co-culture of IAV or RSV in kV1 transfected PBECs significantly augmented replication of RSV and IAV and increased cellular injury. Likewise, in-vivo transfection of kV1 increased replication and lung injury associated with IAV.

CONCLUSION: Our work illuminates a novel virus-associated dysregulation of host interferon responses that promote lung injury associated with respiratory viral infections and, in part, explain differential host responses to viral infections after lung transplantation.}, } @article {pmid42089622, year = {2026}, author = {Mustajab, M and Basler, N and De Smet, L and de Graaf, DC and Matthijnssens, J}, title = {Coding-complete genome sequence of a divergent black queen cell virus strain identified from honeybees (Apis mellifera) in Romania.}, journal = {Microbiology resource announcements}, volume = {15}, number = {6}, pages = {e0012226}, pmid = {42089622}, issn = {2576-098X}, support = {955974//H2020 Marie Skłodowska-Curie Actions/ ; 817622//Horizon 2020 Framework Programme/ ; G049521N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {We report the 8,451-nt coding-complete genome sequence of a divergent black queen cell virus strain (BQCV-Ro). This strain was identified via retrospective analyses of metagenomic virome data of Apis mellifera samples from Europe. The genome assembly is supported by extensive read mapping, with 100% horizontal coverage and a mean sequencing depth of ~38,171×. and shares 94.3% identity with the BQCV Yeongdeok isolate.}, } @article {pmid42090957, year = {2026}, author = {Kämpfer, P and Lipski, A and Lawrence, KS and Olive, WR and Newman, MM and McInroy, JA and Viver, T}, title = {Pseudomonas corni sp. nov., Pseudomonas oplopanacis sp. nov., Pseudomonas salicis sp. nov., Pseudomonas rosaeacicularis sp. nov., Pseudomonas artemisiae sp. nov., Pseudomonas imperatae sp. nov. and Zestomonas ipomoeae sp. nov., isolated from rhizospheres showing plant growth promoting potential.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126719}, doi = {10.1016/j.syapm.2026.126719}, pmid = {42090957}, issn = {1618-0984}, abstract = {Several bacterial strains affiliated with the genera Pseudomonas and Zestomonas were isolated from rhizosphere samples and screened for plant growth-promoting (PGP) traits. Nine strains were analyzed polyphasically, showing ANI and dDDH values below or near species thresholds, together with phenotypic and biochemical traits supporting their differentiation. Genomic analyses revealed a repertoire of PGP-associated functions, including vitamin and cofactor biosynthesis (riboflavin, cobalamin, and thiamin), and high-affinity nutrient acquisition systems as phosphate transporters and phosphonate utilization. All strains encoded traits relevant to the rhizosphere inferred from genome annotation, including genes involved in auxin and cytokinin biosynthesis, oxidative stress tolerance, dissimilatory nitrate reduction, sulfur assimilation, and siderophore production. Metagenomic screening showed that most species are globally distributed across plant-associated, soil, freshwater, and animal-associated habitats. Based on phylogenetic, genomic, and phenotypic evidence, the strains represent seven novel species: Pseudomonas rosaeacicularis sp. nov., with AK-381[T] as the type strain (= LMG 34445[T] = CCM 9596[T]); Pseudomonas corni sp. nov., with AK-10[T] as the type strain (= CCM 9599[T] = LMG 34325[T]); Pseudomonas oplopanacis sp. nov., with AK-188[T] as the type strain (= CCM 9593[T] = LMG 34326[T]); Pseudomonas salicis sp. nov., with AK-309[T] as the type strain (= CCM 9595[T] = LMG 34328[T]); Pseudomonas artemisiae sp. nov., with DT-100[T] as the type strain (= LMG 32880[T] = DSM 115114[T] = CCM 9281[T]); Pseudomonas imperatae sp. nov., with ST-212[T] as the type strain (CCM 9594[T] = LMG 34330[T]); and Zestomonas ipomoeae sp. nov., with ST-55[T] as the type strain (LMG 32881[T] = CCM 9283[T] = DSM 115239[T]).}, } @article {pmid42091967, year = {2026}, author = {Vinayagam, S and Bhowmick, IP and Rajendran, D and Arumugam, DK and Sekar, K and Renu, K and Kaur, H and Sattu, K}, title = {Genetic diversity and gut microbiome of Anopheles mosquitoes in Tamil Nadu by using COI DNA barcoding and 16S rRNA metagenomics.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-48529-9}, pmid = {42091967}, issn = {2045-2322}, support = {NER/85/2022-ECD-I//ICMR- Adhoc/ ; }, abstract = {Anopheles mosquitoes transmit infections to humans. Identifying the right mosquito species is crucial for vector control evaluation. This study uses COI gene DNA barcoding and 16S rRNA metagenomics to show the genetic diversity and gut microbial profile of undiscovered mosquito species. Three genera were found, including eight morphologically different Anopheles mosquitoes, and six mosquito species were molecularly validated, including An. moghulensis. The analysis of genetic diversity indicated that there is a state of balanced natural selection present. The species An. maculatus s.s. and An. stephensi exhibited nearly identical mutations, while An. moghulensis demonstrated evidence of purifying selection within the studied population. The gut microbiomes of An. moghulensis (149,377 reads), An. maculatus (51,016 reads), and An. dravidicus (33,126 reads) mosquitoes were also revealed. Afipia felis and Prevotella copri were the leading bacterial species, followed by other phyla including Proteobacteriota, Spirochaetes, and Firmicuteota. In An. moghulensis, alpha diversity assessments of Chao I incidence were dominating, whereas Shannon index was plentiful in An. maculatus s.s. mosquitoes. The mosquito's distinct bacterial species and shared microbial community are shown in the Venn diagram. These results suggest that the discovered bacterial taxa might be exploited to create vector control techniques for vector-borne illnesses.}, } @article {pmid42092044, year = {2026}, author = {Loukas, A and Kalaentzis, K and Venetsianou, NK and Damianou, C and Paragkamian, S and Lagani, V and Jensen, LJ and Pafilis, E}, title = {CCMRI: a classification and curated database of climate change-related microbiome studies.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-51914-z}, pmid = {42092044}, issn = {2045-2322}, support = {2772//Hellenic Foundation for Research and Innovation/ ; }, abstract = {Climate Change (CC) is reshaping all ecosystem processes and structures. Microbial data provide valuable insights into how microbial processes contribute to CC and how CC, in turn, alters microbial communities. However, the growing volume of environmental genomics data makes identifying CC-related records challenging. The Climate Change Metagenomic Record Index (CCMRI) has been developed to harvest metagenomic/microbiome records pertaining to CC and to provide researchers with a curated database of CC-related microbiome studies (https://ccmri.hcmr.gr). To guide interpretation, the database's 169 metagenomic studies have been labelled according to their relation to CC as CC-caused, CC-causing, and CC-mitigating. They have also been annotated with the CC phenomena they explore, like methane production, temperature rise, permafrost thawing, greenhouse gas emission, methanotrophy, and ocean acidification. To ease navigation, they have also been classified according to their biome as aquatic, terrestrial, host-associated, and engineered. The CCMRI database was initially constructed through manual curation of all aquatic and terrestrial studies in the MGnify resource. It was then expanded with the help of the CCMRI curation-assistant system. This leveraged Large Language Models to scan the remaining MGnify studies, filtered them for relevance, and proposed candidates for inclusion. With a recall greater than 90%, the system achieved high accuracy in identifying CC-related studies. The final decisions on CC-relatedness and categorization were performed by a human curator. This approach combines the efficiency of automation with human oversight and greatly reduces the curation effort, ensuring sustainability and scalability.}, } @article {pmid42092708, year = {2026}, author = {Ye, Y and Miao, H and Fang, W and Ni, J and Yang, K and Gu, P and Ren, X and Zhang, Z}, title = {Deciphering dual effects of humic substrates on anaerobic ammonium oxidation: from metabolic facilitation to systemic nitrogen flux interference.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134791}, doi = {10.1016/j.biortech.2026.134791}, pmid = {42092708}, issn = {1873-2976}, mesh = {*Humic Substances ; *Nitrogen/metabolism/isolation & purification ; *Ammonium Compounds/metabolism ; Oxidation-Reduction ; Anaerobiosis ; Bioreactors/microbiology ; Benzopyrans ; }, abstract = {Anaerobic Ammonium Oxidation (Anammox) is a promising strategy for nitrogen removal from landfill leachate due to its energy efficiency and independence from external carbon sources. However, continuous changes in recalcitrant organic compounds (i.e., fulvic acid (FA) and humic acid (HA)) at different landfill stages have potential effect on stability of anammox process. The present study systematically investigated the successive change of FA/HA concentrations and ratio that induced by different landfill age on anammox process in a laboratory-scale moving bed biofilm reactor operated over 200 days. Results showed a distinct dual-effect transition of FA and HA on the anammox process. 50-100 mg/L FA significantly improved nitrogen removal, achieving a peak total nitrogen removal efficiency (TNRE) of 91%. In contrast, the introduction of HA (100-200 mg/L) triggered a decline in TNRE to 80% and caused substantial nitrate (NO3[-]-N) accumulation. Microbial analysis revealed that FA-driven carbon abundance stimulated Candidatus Kuenenia and DNRA-functional Paracoccus and Bacillus, whereas HA suppressed DNRA bacteria in favor of nitrification. Metagenomic analysis showed that the electron shuttle and carbon source characteristics of FA enriched the relative abundance of energy metabolism genes (i.e., F-type ATPase) and quorum sensing genes (i.e., lamB), accelerating the anammox and denitrification process. However, HA interfered with the nitrogen metabolic flux via suppressing denitrification process (i.e., napA/B and nirS) and promoting nitrification genes (i.e., amoA and nxrA/B), leading to the accumulation of NO3[-]-N. These findings provide a mechanistic basis for optimizing anammox processes under varying humic substance conditions in landfill leachate treatment.}, } @article {pmid42092716, year = {2026}, author = {Chai, Z and Chen, H and Cui, J and Song, C and Zheng, Y and Li, Y and Gao, T and Zheng, M}, title = {Micromolar chlorate sensitivity of wastewater-associated comammox Nitrospira: Endogenous toxification mechanism and implications for nitrification management.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134789}, doi = {10.1016/j.biortech.2026.134789}, pmid = {42092716}, issn = {1873-2976}, mesh = {*Nitrification/drug effects ; *Wastewater/microbiology ; Ammonia/metabolism ; Oxidation-Reduction/drug effects ; *Chlorates/pharmacology/toxicity ; Nitrites/metabolism ; *Bacteria/metabolism/drug effects ; }, abstract = {Chlorate (ClO3[-]) is widely employed as a specific inhibitor of nitrite-oxidizing bacteria (NOB) to differentiate the contributions of ammonia-oxidizing microorganisms (AOMs). However, the discovery of completed ammonia oxidizing (comammox) Nitrospira, which performs both ammonia and nitrite oxidation, challenges the assumed specificity of chlorate, raising the question of whether it also inadvertently inhibits the ammonia oxidation activity of comammox Nitrospira, potentially leading to an underestimation of total ammonia oxidation activity in mixed communities. This study investigates the inhibitory kinetics and mechanisms of chlorate on wastewater-associated comammox Nitrospira. Batch assays revealed that comammox ammonia oxidation was hypersensitive to chlorate, with a half-maximal inhibitory concentration (IC50) of 9.11 µM, orders of magnitude lower than canonical NOB inhibition levels. Metabolic assays showed that 10 μM chlorate reduced ammonia oxidation activity to 49.1% during exposure, with recovery requiring multiple cultivation cycles. Integrated metagenomic and meta-transcriptomic analyses uncovered an endogenous toxification mechanism: chlorate is reduced by nitrite oxidoreductase (NXR) to cytotoxic chlorite, which triggers the upregulation of chlorite dismutase (CLD) and reactive chlorine species (RCS) defense genes, ultimately leading to metabolic arrest. This study confirms the inhibitory effect of chlorate on comammox Nitrospira and deciphers its RCS-mediated mechanism, emphasizing the need for caution when using chlorate-based assays to assess ammonia oxidation activity and providing a theoretical basis for selectively suppressing comammox Nitrospira in WWTPs.}, } @article {pmid42092717, year = {2026}, author = {Fu, D and Ma, H and Zhang, J and Wang, H and Wu, Y and Ge, L and Fan, C and Wu, S and Zhang, S and Gao, H and Chen, Z}, title = {Interplay of quorum-sensing signals (homoserine lactone/penicillic acid) and nitrate in regulating microbial processes: As(III) immobilization, CH4 and N2O emission in constructed wetlands.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134788}, doi = {10.1016/j.biortech.2026.134788}, pmid = {42092717}, issn = {1873-2976}, mesh = {*Quorum Sensing/drug effects ; *Nitrates/metabolism/pharmacology ; *Wetlands ; *4-Butyrolactone/analogs & derivatives/metabolism ; *Methane/metabolism ; *Nitrous Oxide/metabolism ; Biodegradation, Environmental ; }, abstract = {The concurrent mitigation of arsenic (As) pollution and greenhouse gas (GHG) emissions in constructed wetlands represents a significant challenge, largely due to the complex interactions within microbial-driven elemental cycles. This study investigated the regulatory roles of distinct quorum-sensing (QS) signals, i.e., C4-homoserine lactone (C4-HSL, a promoter) and penicillic acid (PA, a quencher), in concert with nitrate on the microbial-mediated transformation of As and GHGs (CH4 and N2O) in flooded paddy soil microcosms. The results revealed that the nitrate + C4-HSL treatment concurrently enhanced As(III) immobilization (increased by 8%) while suppressing CH4 and N2O emissions (by 7% and 56%) over a 24-day incubation period, compared to nitrate alone. Conversely, the nitrate + PA treatment inhibited As(III) oxidation (∼17.6 µM residual As(III) leaching) and promoted the accumulation of GHGs (increasing CH4 and N2O emissions by 8% and 77%). Mechanistically, C4-HSL activated the complete QS signaling network under nitrate amendment. This activation led to the enrichment of key functional microbial consortia (e.g., Pseudogulbenkiania, Streptomyces and Alicyclobacillus), an increase in relative abundance of critical metabolic genes (e.g., aox, pmo, nosZ, cpaF, tadA and cco), stimulated the secretion of protein-rich extracellular polymeric substances, and enhanced overall electron transfer system activity. These coordinated changes fostered coupled biogeochemical processes such as Fe(II)/Mn(II)-coupled denitrification and denitrifying AOM. In contrast, PA disrupted native QS communication, suppressed the aforementioned functional microbial groups and altered biofilm composition. Overall, the application of specific QS signals with nitrate exhibits the potential to directionally steer microbial community function, thereby highlighting a promising microbial-level strategy for the co-management of As and GHGs in engineered wetland systems.}, } @article {pmid42092753, year = {2026}, author = {Palanisamy, M and Babalola, OO and Ramalingam, S}, title = {Shotgun metagenomic dataset of leaf endophytic microbiome of the garden sage (Salvia officinalis L.).}, journal = {BMC genomic data}, volume = {27}, number = {1}, pages = {}, pmid = {42092753}, issn = {2730-6844}, support = {CMRG2400927//Chief Minister`s Research Grant (CMRG), Government of Tamil Nadu, India/ ; }, mesh = {*Salvia officinalis/microbiology ; *Plant Leaves/microbiology ; *Metagenomics ; *Endophytes/genetics/classification ; *Microbiota ; *Metagenome ; Bacteria/genetics/classification ; Fungi/genetics ; }, abstract = {OBJECTIVES: Garden sage (Salvia officinalis L.) is a traditional medicinal plant known for its rich bioactive secondary metabolites. However, there is limited information about the diversity of endophytic microbial communities, including bacteria, fungi, archaea, and viruses. Therefore, the study employs shotgun metagenomics to generate and make publicly available a dataset representing the leaf endophytic microbiome of Salvia officinalis.

DATA DESCRIPTION: Metagenomic DNA was extracted from leaves of S. officinalis collected as three biological replicates and sequenced using the Illumina NovaSeq X platform. Host-derived and contaminant sequences were removed by mapping reads to the S. officinalis reference genome using BWA-MEM. The resulting high-quality FASTQ files were analyzed to characterize the taxonomic composition of the endophytic microbiome using Kraken2-based classification.}, } @article {pmid42093069, year = {2026}, author = {Yuan, J and Li, J and Jin, L and Ye, J and Zhang, Z}, title = {Human herpesvirus-6B infection leading to hemophagocytic lymphohistiocytosis in an adult: a case report.}, journal = {Journal of medical case reports}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13256-026-06071-2}, pmid = {42093069}, issn = {1752-1947}, abstract = {BACKGROUND: Hemophagocytic lymphohistiocytosis (HLH) secondary to human herpesvirus-6B (HHV-6B) infection is rare in immunocompetent adults.

CASE PRESENTATION: We report the case of a 43-year-old East Asian (Chinese) woman who developed HLH, presenting with persistent fever, jaundice, and cytopenias. Metagenomic next-generation sequencing (mNGS) identified HHV-6B in both peripheral blood and liver tissue, thereby establishing the etiologic diagnosis. Prompt initiation of antiviral therapy with ganciclovir, combined with corticosteroids and intravenous immunoglobulin, resulted in rapid clinical remission.

CONCLUSIONS: This case highlights the critical importance of early pathogen identification using mNGS and timely immunomodulatory treatment for improving outcomes in adult patients with virus-associated HLH.}, } @article {pmid42093272, year = {2026}, author = {Li, C and Zhang, X and Yang, Y and Zeng, H and Shi, Y and Zhang, J and Liu, L and Zhu, C and Zhang, Z and Li, C and Wang, X and Bai, X and Deng, H and Li, Q}, title = {Bifidobacterium animalis suppresses melanoma progression and activates anti-tumor immunity by inhibiting YAP1 expression in CD8+ T cells.}, journal = {Cancer biology & medicine}, volume = {23}, number = {5}, pages = {737-754}, pmid = {42093272}, issn = {2095-3941}, support = {82403246//National Natural Science Foundation of China/ ; 2025A04J4030//Guangzhou Science and Technology Project/ ; }, mesh = {Animals ; *CD8-Positive T-Lymphocytes/immunology/metabolism/drug effects ; Mice ; YAP-Signaling Proteins ; Humans ; *Bifidobacterium animalis/immunology ; *Melanoma, Experimental/immunology/pathology ; *Probiotics/pharmacology ; Mice, Inbred C57BL ; Cell Proliferation ; Disease Progression ; Cell Line, Tumor ; Gastrointestinal Microbiome ; *Transcription Factors/metabolism ; }, abstract = {OBJECTIVE: The probiotic, Bifidobacterium animalis, (B. animalis) is known to provide health benefits in humans. This study investigated the role of B. animalis in suppressing malignant melanoma progression and modulating tumor immunity.

METHODS: Bifidobacterium spp. were isolated from human faeces and verified by whole-genome sequencing. The anti-tumor effects were assessed in B16-F10 melanoma cells. B. animalis efficacy was further evaluated in a syngeneic murine model. Immune profiling was performed with flow cytometry and CD8[+] T cell dependency was tested with antibody depletion. Functional metabolites were analyzed by liquid chromatography-mass spectrometry (LC-MS). Transcriptome sequencing elucidated the YAP1 mechanism in CD8[+] T cells. Gut microbiota composition was assessed via shotgun metagenomic sequencing.

RESULTS: Among the selected Bifidobacterium spp., B. animalis and its conditioned medium effectively inhibited melanoma cell proliferation. Oral administration of B. animalis significantly reduced the growth of B16-F10 allografts, accompanied by an increase in tumor-infiltrating effector T cells. The bioactive component of B. animalis was identified as a < 3-kDa non-protein fraction containing mannose, which phenocopied the anti-tumor and immunostimulatory effects of B. animalis. Microbiota profiling revealed probiotic enrichment in mannose-treated mice. CD8[+] T cell depletion abrogated mannose efficacy. Combination therapy with B. animalis and anti-PD-1 synergistically enhanced tumor control and T cell activation. Mechanistically, the bioactive fraction and mannose downregulated YAP1 expression in CD8[+] T cells.

CONCLUSIONS: B. animalis suppresses melanoma tumorigenesis in mice by restoring gut microbiota and secreting functional mannose. Mannose enhances anti-PD-1 efficacy by inhibiting YAP1 expression in CD8[+] T cells, thereby improving effector function. B. animalis may serve as a preventive measure for melanoma management.}, } @article {pmid42093327, year = {2026}, author = {Wang, S and Li, S and Lyu, H and Zhi, W and Dang, Z and Guo, R and Zhu, X and Ji, G}, title = {Quantifying the Contribution of Cryptic Sulfide-Driven Autotrophic Denitrification to N2O Production in a Seasonally Hypoxic River-Reservoir System.}, journal = {Environmental science & technology}, volume = {60}, number = {19}, pages = {14011-14022}, doi = {10.1021/acs.est.6c03313}, pmid = {42093327}, issn = {1520-5851}, mesh = {*Denitrification ; *Nitrous Oxide ; Rivers ; Autotrophic Processes ; Sulfides ; Thiobacillus ; Seasons ; }, abstract = {Sulfur-autotrophic denitrification (S-ADN) has been frequently reported in inland waters, yet its quantitative contribution to nitrous oxide (N2O) productions remains poorly constrained. By combining field sampling, enrichment cultures, stable isotopes, and metagenomic analysis, we quantified S-ADN-derived N2O productions in an oligotrophic river-reservoir system and validated the universality of our approach across diverse aquatic ecosystems. A Thiobacillus-dominated S-ADN enrichment culture was successfully established over 218 days of continuous supplementation with reduced sulfur compounds, yielding critical isotopic signatures for source partitioning (δ[15]N[Bulk], average N isotopic composition; δ[18]O; and δ[15]N[SP], site preference). Then, the multi-isotope Bayesian model revealed that S-ADN (14.8%) and nitrifier denitrification (NDN, 21.1%) rapidly occupied the ecological niche of heterotrophic denitrification (HDN, 8.6%) to total microbial N2O sources under organic carbon-limited conditions. The cryptic sulfur cycle supplies a considerable pool of electron donors for S-ADN under low-sulfide conditions. Autotrophic denitrifiers (e.g., Thiobacillus, Sulfuritalea) exhibited significant synergistic interactions with ammonia-oxidizing archaea (AOA, Nitrosarchaeum), while ammonia-oxidizing bacteria (AOB, Nitrosomonas) and nitrite-oxidizing bacteria (NOB, Nitrospira) jointly completed nitrification─with Nitrosomonas further competing for nitrite to drive NDN. This study advances the quantitative assessment of S-ADN's role in N2O production and provides novel insights into microbial community interactions in oligotrophic aquatic systems.}, } @article {pmid42093770, year = {2026}, author = {Niu, S and Guo, L and Li, Z and Liu, Y and Zhao, L}, title = {Clinical utility of metagenomic next-generation sequencing in the diagnosis of severe influenza complicated by invasive pulmonary aspergillosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1746504}, pmid = {42093770}, issn = {2235-2988}, mesh = {Humans ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology/complications ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Influenza, Human/complications/diagnosis ; Retrospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Sensitivity and Specificity ; *Metagenomics/methods ; Mannans/blood ; Galactose/analogs & derivatives ; Aged ; ROC Curve ; Adult ; China ; }, abstract = {OBJECTIVE: The incidence and mortality of severe influenza complicated by invasive pulmonary aspergillosis (IPA) have risen markedly in recent years. This study aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) for detecting IPA in patients with severe influenza.

METHODS: Severe influenza patients with suspected of having IPA admitted to Xinxiang Central Hospital, Henan Province, China, from March 2020 to September 2025 were retrospectively enrolled. Bronchoalveolar lavage fluid (BALF) and blood were collected for fungal culture, galactomannan (GM) assay, and mNGS. Final classification into IPA and non-IPA groups was based on composite clinical and microbiological criteria. Sensitivity, specificity, and receiver operating characteristic curves were used to compare the diagnostic performance of the three methods.

RESULTS: Comparison with traditional fungal culture and GM testing, mNGS provided significantly faster results. Among 189 patients suspected of severe influenza-associated IPA, mNGS demonstrated a sensitivity of 72.1% and a specificity of 80.2%. Its sensitivity was higher than that of fungal culture (28.6%), serum GM testing (37.6%), and BALF GM testing (44.1%); however, its specificity was slightly lower than that of fungal culture (89.5%), serum GM testing (84.3%), and BALF GM testing (81.3%). The area under the ROC curve (AUC) for mNGS was 0.76, which is higher than that for BALF GM testing (0.63), serum GM testing (0.61), and fungal culture (0.59). The combined diagnostic approach yielded an AUC of 0.83.

CONCLUSION: mNGS offers a rapid, sensitive and accurate solution for invasive pulmonary aspergillosis in severe influenza patients. It outperforms conventional fungal culture and galactomannan assays. Integrating mNGS with traditional diagnostic methods could substantially improve early detection and overall yield of IPA.}, } @article {pmid42094492, year = {2026}, author = {Shan, Y and Pucci, N and Berns, C and Hoogendijk, R and Beijnvoort, M and Li, S and Sánchez-Cano, A and Kramer, G and Du, W and Mende, DR and Jan van Dijk, AD and Wortel, M and Zhang, J}, title = {A bifidobacterial enzyme orchestrates ecology and function of infant gut bacterial community.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42094492}, issn = {2692-8205}, abstract = {Human milk oligosaccharides (HMOs) are abundant and structurally diverse glycans that shape the development of infant gut microbiota. Yet, how individual HMOs and bacterial genes drive the community assembly remain elusive. Here, we reconstructed an eight-member infant Bacterial Community (iBaCo) from representing dominant taxa in human infant feces. When individual HMOs were the sole carbohydrate source, they showed deterministic effects on the iBaCo composition and metabolic output. Notably, the tetramer HMO lacto-N-tetraose (LNT), in spite of its identical monomer composition as lacto-N-neotetraose (LNnT), showed a strong effect on maintaining Bifidobacterium breve abundance in iBaCo, whereas LNnT did not. Monoculture growth profiling, proteomics, enzymatic kinetic assay, and molecular docking revealed that β-galactosidase D4BMY8 and the relevant downstream pathways are induced by LNT and that D4BMY8 has substrate preference on LNT over LNnT, enabling a faster growth of Bi. breve and accumulation of acetate and lactate in LNT compared to LNnT. Metabolic flux analysis indicated that the substrate-preference of β-galactosidase D4BMY8 drives the skewed energy cost toward lactate/acetate metabolic output. Finally, the D4BMY8-encoding gene lacZ5 is widely spread in all isolated Bi. breve genomes, but divergently distributed in infant metagenome-assembled Bi. breve genomes. Together, we demonstrated that a single enzyme-substrate interaction could orchestrate the composition and metabolic function of an infant bacterial community, which may contribute to the assembly of dynamic infant gut microbiota. Our integrative approach provides a mechanistic framework for understanding the interaction between diet, microbial community, and infant gut health.}, } @article {pmid42094499, year = {2026}, author = {Majidian, S and Chalco, A and Zheng, X and Webby, RJ and Bowman, AS and Poulson, RL and Nemeth, NM and Sedlazeck, FJ and Agustinho, DP}, title = {Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42094499}, issn = {2692-8205}, abstract = {Phylogenomic surveillance is limited not by sequencing throughput, but by the difficulty of converting heterogeneous raw data into reliable evolutionary inference, particularly for low-titer and contaminated viral field samples. Here we present Omni2Tree, an assembly-free framework that reconstructs viral phylogenies directly from raw sequencing reads and generates easily shareable interactive reports and genome-wide entropy profiles to identify diversification. In H5N1 benchmark analyses, Omni2Tree maintained accurate placement and topological stability even under low coverage, unlike assembly or reference based methods. Omni2Tree generated an annotated phylogeny for 64-sample H5N1 field surveillance dataset from the eastern USA in under 3 hours. Omni2Tree recovered known phylogenetic structure and key variability insights across 1,328 hepatitis C virus and 707 human cytomegalovirus datasets, and resolved co-infecting respiratory viruses in clinical metagenomic samples. By enabling direct analysis from raw reads, Omni2Tree supports faster, more portable, and more decentralized phylogenomic surveillance across outbreak, clinical, and resource-limited settings.}, } @article {pmid42094537, year = {2026}, author = {Debray, R and Dickson, CC and Webb, SE and Ferretti, P and Meloimet, A and Gilbert, J and Alberts, SC and Blekhman, R and Archie, EA and Tung, J}, title = {Social microbiome transmission predicts microbial specialization and host lifespan in a wild primate.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42094537}, issn = {2692-8205}, abstract = {Social interactions are proposed to provide reliable routes for microbial transmission between animals, facilitating animal-microbiome co-evolution. However, microbiome transmission remains challenging to measure in wild populations. Here we combine behavioral observations of wild baboons with repeated strain-resolved metagenomic profiling to identify individual gut microbial species that follow a dominant mode of social transmission. In an 18-year metagenomic time series from the same population, baboons with higher levels of socially transmitted species lived longer than those with lower levels of socially transmitted species. Socially transmitted species were also more stable and persistent within baboons, yet had narrower host ranges outside of baboons. Thus, social transmission is not only detectable in free-living primates, but may play a special role in both host and microbial fitness.}, } @article {pmid42094770, year = {2026}, author = {Tekere, M and Kalu, CM}, title = {Relative abundance of heavy metal resistance genes of three drinking water treatment plants unveiled through shotgun metagenomics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1822428}, pmid = {42094770}, issn = {1664-302X}, abstract = {INTRODUCTION: The occurrence and abundance of heavy metal resistance genes (HMRGs) in drinking water treatment plants (DWTPs) and the stages at which they occur are a global challenge due to the risk of consuming contaminated water.

METHODS: The present study identified HMRGs associated with raw water sources, treatment stages (disinfection and filtration), final treated water, and produced sludge in three DWTPs across three provinces (Gauteng, Limpopo, and Mpumalanga) in South Africa, using a shotgun metagenomic approach.

RESULTS: In total, five classes of heavy metals (copper, arsenic, mercury, chromate, silver) and 50 resistance genes were identified across the three DWTPs. Most of the genes were obtained from the disinfection stages of the DWTPs.

DISCUSSION: This genomic dataset provides valuable information on the impact of disinfection stages on the relative abundance of HMRGs in drinking water treatment processes. Additionally, the transfer of genes into the final treated water consumed by the populace is a significant human health concern.}, } @article {pmid42094845, year = {2026}, author = {Olson, N and Thystrup, CAN and Smith, F and Mucache, H and Fafetine, J and Saíde, J and Mondlane-Milisse, A and Brito, DRA and Jesser, KJ and Brown, J and Hald, T and Freeman, M and Levy, K and Nadimpalli, ML}, title = {Strain-level analyses of public sequencing data to characterize Escherichia coli strain sharing between children and chickens in Mozambique.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101429}, pmid = {42094845}, issn = {2352-7714}, abstract = {Escherichia coli causes diarrhea in children and can be transmitted from animals. Characterizing the scope of human-animal strain sharing is crucial for assessing potential health risks; however, conventional methods that assess single isolates are resource-intensive and lack sensitivity. Strain-level metagenomic analyses can reveal within-host strain diversity and between-host strain sharing. In this study, we aimed to determine whether E. coli strains we previously detected among chickens in Mozambique might pose meaningful risks to local children. To achieve this, we compared E. coli strains in chicken metagenomes to E. coli strains reported by others in children's stool in the same community during the same period (2014-2022) using the Strain Genome Explorer toolkit. At least one E. coli strain was shared between 37/23,937 (0.15%) chicken-human pairs. This approach represents a novel method for assessing the scope of bacterial strain sharing between human and animal populations within a community.}, } @article {pmid42094906, year = {2026}, author = {Zeng, Q and Xie, L and Dai, W and Xu, F and Dai, Y}, title = {Extracorporeal Membrane Oxygenation Haemoperfusion for Leptospirosis Pulmonary Hemorrhagic Disease: Report of 1 Case.}, journal = {Respirology case reports}, volume = {14}, number = {}, pages = {e70565}, pmid = {42094906}, issn = {2051-3380}, abstract = {Severe pulmonary leptospirosis (SPFL), characterized by diffuse alveolar haemorrhage (DAH) and acute respiratory distress syndrome (ARDS), carries a high mortality, often due to diagnostic delays and complex management. We report a case of a 42-year-old male with outdoor occupational exposure who presented with fever and hemoptysis, rapidly progressing to severe respiratory failure and thrombocytopenia. Chest imaging confirmed DAH/ARDS. For refractory hypoxemia, veno-venous extracorporeal membrane oxygenation (VV-ECMO) was initiated without systemic anticoagulation due to active pulmonary haemorrhage. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid rapidly identified Leptospira interrogans, enabling targeted antimicrobial therapy alongside multidisciplinary support. The patient gradually improved, was successfully weaned from ECMO and ventilator support, and was discharged without residual organ dysfunction. This case demonstrates that early application of anticoagulation-free VV-ECMO combined with mNGS-based rapid diagnosis and multidisciplinary care can improve outcomes in SPFL, highlighting the importance of considering this diagnosis in febrile patients with DAH and environmental exposure.}, } @article {pmid42094994, year = {2026}, author = {Vasselin, A and Scavazzin, V and Talarmin, JP and Lamoureux, C and Pérès, M and Le Bars, H and Fangous, MS and Beauruelle, C and Ansart, S and Héry-Arnaud, G}, title = {Granulicatella adiacens infective endocarditis in pregnancy: diagnostic contribution of metagenomic sequencing-a case report.}, journal = {ASM case reports}, volume = {2}, number = {3}, pages = {}, pmid = {42094994}, issn = {2996-2684}, abstract = {BACKGROUND: Granulicatella adiacens is a fastidious Gram-positive coccus and is a rare but recognized cause of infective endocarditis. Infective endocarditis during pregnancy is uncommon but carries substantial maternal and fetal risk. Plasma metagenomic analysis of microbial cell-free DNA has emerged as a complementary diagnostic tool in culture-negative infections.

CASE SUMMARY: We describe a 35-year-old pregnant woman with known mitral valve prolapse who presented at 21 weeks of gestation with an acute ischemic stroke. Initial etiological work-up, including transesophageal echocardiography, was unremarkable. Ten days later, she re-presented with left-arm pain and neurologic symptoms. Repeat echocardiography revealed multiple mitral vegetations compatible with infective endocarditis. Despite multiple sets of prolonged-incubation blood cultures and extensive serological testing, all microbiological investigations remained negative. Empirical intravenous ceftriaxone was initiated based on the working diagnosis of HACEK endocarditis. A plasma metagenomic cell-free DNA test ultimately identified G. adiacens, which was suspected to have entered the body through dental treatment received a few weeks earlier. Ceftriaxone was continued given the favorable clinical response, with vegetation resolution, troponin decline, and uncomplicated term delivery of a healthy infant.

CONCLUSION: This case illustrates the diagnostic challenges of culture-negative infective endocarditis in pregnancy and underscores the value of plasma microbial cell-free DNA sequencing as a complementary tool when conventional methods fail. It also emphasizes the need to repeat echocardiography when clinical suspicion remains high and raises the question of antibiotic prophylaxis for high-risk dental procedures in pregnant women with underlying valvular heart disease.}, } @article {pmid42095002, year = {2026}, author = {de Araújo Butarelli, AC and Peres, FV and Pellizari, VH and Bendia, AG}, title = {Hot life in Antarctica: a novel metabolically versatile Pyrodictiaceae genus thriving at a volcanic-cryosphere-marine interface.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag080}, pmid = {42095002}, issn = {2730-6151}, abstract = {Deception Island fumaroles in Antarctica represent rare environments where extreme heat intersects with cryospheric and marine conditions, creating remarkable environmental gradients. From the near-boiling sediments, we reconstructed a high-quality metagenome-assembled genome affiliated with the Pyrodictiaceae. Phylogenomic analyses revealed that this genome, proposed to represent Ca. Pyroantarcticum pellizari, forms a distinct lineage separated from known genera in the family. Functional annotation uncovered a versatile metabolic repertoire, including pathways for sulfur and nitrogen cycling, peptide and amino acid transport, and mixotrophic energy conservation. Stress-response systems such as reverse gyrase, thermosome, and small heat-shock proteins were complemented by lineage-specific genes related to membrane stability, metal detoxification, and Pyrodictiaceae-specific cannulae. These adaptations likely support survival under sharp temperature gradients, hydrogen sulfide emissions, and high metal concentrations at the volcanic-cryosphere-marine interface. Our findings expand the phylogenetic and ecological scope of Pyrodictiaceae, highlighting Antarctic marine volcanoes as unique refuges for hyperthermophiles and as valuable models for investigating life's habitability under extreme temperatures.}, } @article {pmid42095017, year = {2026}, author = {An, QT and Li, W and Ren, Y and Liu, X and Yao, L and Li, Y and Zhao, X and Zhang, Y and Feng, P and Du, X}, title = {A comparative study of gut microbiota and metabolites in Tibetan sheep during cold and warm seasons.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1768985}, pmid = {42095017}, issn = {2297-1769}, abstract = {Tibetan sheep, a vital livestock species adapted to the extreme hypoxia, low temperatures, and intense radiation of the Qinghai-Tibet Plateau, rely on gastrointestinal microbiota for ecological balance and host nutrition, metabolism, and immunity. However, the possible associations of gut microbiota and metabolites with seasonal phenology remain unclear. Integrating biochemical, metagenomic, and metabolomic analyses, this study investigated seasonal variations in serum indices, microbial communities, and metabolites to inform enhanced breeding strategies. Analysis of forage nutritional composition showed that warm-season forages had significantly higher concentrations of dry matter (DM), crude protein (CP), and ether extract (EE) (p < 0.01), whereas cold-season forages were characterized by significantly greater levels of neutral detergent fiber (NDF) and acid detergent fiber (ADF) (p < 0.01). Correspondingly, serum analysis revealed significantly higher warm-season concentrations of alanine aminotransferase, total cholesterol, creatinine, and urea nitrogen compared with the cold season (p < 0.01). Gut microbiota composition shifted seasonally, with Bacteroides dominating in warm seasons and Bacillus predominating in cold seasons. Functional metagenomics indicated cold-season enrichment in pathways related to carbon metabolism, ABC transporters, aminoacyl-tRNA biosynthesis, pyruvate metabolism, DNA replication, and methane metabolism (p < 0.01). Metabolomics identified elevated warm-season microbial metabolites (His-Met, leucylleucine, luteolin 7-glucoside, ursolic acid; p < 0.05) and higher cold-season compounds (melatonin, glabrol, prostaglandin E2; p < 0.05), with KEGG enrichment linking these to steroid hormone biosynthesis, fatty acid metabolism, bile acid synthesis, and propanoate pathways. These findings suggest possible associations between seasonal extremes and: (1) modulation of nutrient metabolism (e.g., secondary bile acids and short-chain fatty acids); (2) activation of stress-response pathways (e.g., pentose phosphate pathway, ABC transporters, and DNA replication); and (3) immune regulation mediated by bioactive metabolites. Cold-season enrichment in DNA repair and energy-production pathways may be associated with responses to oxidative stress, whereas warm-season shifts in lipid metabolism are consistent with increased nutrient availability. Fluctuations in key metabolites-such as elevated melatonin in cold seasons and elevated ursolic acid in warm seasons-likely reflect adaptations related to thermoregulation and antioxidant defense. This work provides foundational insights into microbiota-host interactions under extreme environmental conditions, supporting the optimization of supplementation, probiotic use, and sustainable husbandry on the Qinghai-Tibet Plateau.}, } @article {pmid42095439, year = {2026}, author = {Williams, TGS and Umpleby, H and Fisayo, T and Rampling, T and Houlihan, CF}, title = {Clinician perspectives on patient consent for metagenomic next-generation sequencing of blood samples for the diagnosis of infection in clinical practice.}, journal = {Journal of medical microbiology}, volume = {75}, number = {5}, pages = {}, pmid = {42095439}, issn = {1473-5644}, mesh = {Humans ; *Metagenomics ; *High-Throughput Nucleotide Sequencing ; *Informed Consent ; Surveys and Questionnaires ; United Kingdom ; *Communicable Diseases/diagnosis/blood ; }, abstract = {Introduction. Pathogen diagnostics based on metagenomic next-generation sequencing (mNGS) are now in clinical use. mNGS can identify unexpected pathogens or organisms of unclear significance and generate human genomic data. Given these features, it has been suggested that patients should provide specific informed consent for mNGS.Gap Statement. There is limited published guidance on the appropriate form of consent for clinical infectious disease mNGS to guide clinical implementation and current practice varies.Aim. To inform a pilot of mNGS for returning travellers delivered at a reference laboratory for use by specialist infection clinicians, we sought clinician perspectives on the form of consent required for mNGS and the information patients require to make an informed decision.Methodology. A national survey of infection specialists provided clinicians' opinions.Results. If consent for an infection screen including blood-borne virus testing had already been provided, only a minority of surveyed clinicians (22 out of 124, 18%) thought that mNGS should be discussed before it was performed on pre-existing blood samples.Conclusion. Most of the UK infection clinicians surveyed did not think that mNGS of blood from returning travellers required discussion before being performed when patients had already consented for infection diagnostics to find the cause of their illness. However, clinicians felt that patients should be aware of the potential for additional testing and wanted information on mNGS to be readily available.With the increasing availability of clinical infectious disease mNGS, engagement of non-specialist clinicians and patients is required to confirm the generalizability of these perspectives. The model of consent used for clinical infectious disease mNGS should be ethically adequate in addition to being acceptable to patients and clinicians.}, } @article {pmid42095681, year = {2026}, author = {Muthamilselvi Sivabalan, SK and Vijayakumar, V and Sengupta, P and Palmal, S and Krishnamurthi, S and Kumar Singh, N and Kyrpides, NC and Raman, K and Venkateswaran, K}, title = {Unveiling hidden microbial diversity in Mars 2020 mission assembly cleanrooms with molecular insights into the persistence and perseverance of novel species defying metagenome sequencing.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0127325}, pmid = {42095681}, issn = {2165-0497}, support = {Mars Program 2016//Jet Propulsion Laboratory/ ; PM research Fellowship//Ministry of Education, India/ ; DE-AC02-05CH11231//United States Department of Energy/ ; }, mesh = {Mars ; *Bacteria/genetics/classification/isolation & purification ; *Metagenome ; Whole Genome Sequencing ; Space Flight ; Biodiversity ; Genome, Bacterial ; Environment, Controlled ; Phylogeny ; Spacecraft ; }, abstract = {NASA cleanrooms, which are critical for assembling space mission components, are maintained under stringent decontamination protocols to minimize biological contamination. These environments are characterized by nutrient-poor and oligotrophic conditions, leading to low microbial loads. Despite extensive cleaning, oligotrophs capable of surviving in such conditions continue to persist, often remaining undetected due to their low abundance, resistance to environmental stresses, and difficulties in biomolecule extraction. Even with shotgun metagenome sequencing technologies, these microbes may go undetected or be underrepresented due to their robust cell walls and the absence of reference genomes in publicly available databases. Over a 6-month study of Mars 2020 mission cleanrooms, 182 bacterial strains belonging to 19 families were identified using a whole-genome sequencing (WGS) approach. Among these, 14 novel Gram-positive species were discovered, including eight spore formers. Though the novel species comprised only 0.001% of the sequencing data, their successful cultivation allowed for functional characterization. Through WGS data mining, genomic traits associated with resilience in extreme conditions were revealed. These species were found to be involved in nitrogen cycling, carbohydrate metabolism, and radiation resistance, traits essential for survival in extreme environments. Furthermore, 12 biosynthetic gene clusters were identified, including those linked to ectoine and [Formula: see text]-poly-L-lysine production, suggesting potential biotechnological applications. These findings highlight the hidden microbial diversity within cleanrooms and emphasize the necessity of advanced detection strategies. A better understanding of these microbes will provide insights into extremophiles with applications in biotechnology, medical research, and life support systems for future space exploration missions.IMPORTANCEDespite strict decontamination protocols, NASA cleanrooms harbor low-biomass microbial communities adapted to nutrient-poor environments. These oligotrophic microbes often go undetected in shotgun metagenomics methods due to their low abundance, resistance to lysis, and lack of reference genomes. Standard shotgun metagenome sequencing methods fail to retrieve them, as dominant microbial DNA overshadows rare species. Over 6 months of monitoring Mars 2020 mission cleanrooms, 182 bacterial strains from 19 families were identified, including 14 novel Gram-positive species, 8 of which were spore formers. Though present at 0.001% abundance in sequencing data, we successfully cultured them, enabling functional characterization. These microbes exhibited roles in nitrogen cycling, carbohydrate metabolism, and radiation resistance, with 12 biosynthetic gene clusters linked to ectoine and [Formula: see text]-poly-L-lysine production. These findings highlight the previously underestimated microbial diversity in cleanrooms and emphasize the need for advanced detection strategies to explore extremophiles with applications in biotechnology and space exploration.}, } @article {pmid42096004, year = {2026}, author = {Huang, YJ and Shen, ZQ and Hu, DP and Huang, YY and Chen, GY and Lin, Y and Hu, BM and Yuan, XX and Deng, GP and Li, X}, title = {Multi-Omics Analysis Reveals Inflammatory Activation and Maternal-Fetal Interface Remodeling in Spontaneous Abortion.}, journal = {Current medical science}, volume = {}, number = {}, pages = {}, pmid = {42096004}, issn = {2523-899X}, abstract = {BACKGROUND: Spontaneous abortion (SA) is a common adverse outcome of early pregnancy, yet its underlying pathophysiological mechanisms remain incompletely understood. Accumulating evidence suggests that dysregulated inflammatory responses at the maternal-fetal interface play a critical role in pregnancy loss. However, the potential associations between alterations in gut microbiota, metabolic disturbances, and localized decidual inflammation in patients with SA have not been systematically characterized.

METHODS: Women with SA (n = 30) and those with normal early pregnancy (NP, n = 28) were enrolled in this study. Proinflammatory cytokines were quantified in decidual tissue homogenates, and histopathological and molecular analyses were performed to evaluate inflammatory activation at the maternal-fetal interface. The gut microbiota composition was profiled using shotgun metagenomic sequencing, while metabolic alterations in the feces were assessed by untargeted metabolomics. Integrated multi-omics analyses were conducted to explore associations among gut microbial dysbiosis, metabolic perturbations, decidual inflammatory signaling, and molecular alterations.

RESULTS: Compared with those from the NP group, the decidual tissues from the SA group exhibited significantly elevated levels of IL-1β and TNF-α (1.49-fold and 1.51-fold, both P < 0.0001), accompanied by pronounced histopathological abnormalities. Enhanced activation of the NF-κB signaling pathway was observed at the maternal-fetal interface in SA patients. Metagenomic analyses revealed distinct differences in the gut microbiota composition and community structure between the two groups, with differentially abundant bacterial taxa identified (LDA score > 2.0). Consistent with these findings, fecal metabolomic profiling clearly revealed differences between SA and NP patients, with differentially abundant metabolites (VIP > 1.0, adjusted P < 0.05) predominantly enriched in lipid metabolism, amino acid metabolism, and immune-related pathways. In addition, the expression of leucine-rich repeat-containing G protein-coupled receptor 6 was significantly upregulated (P < 0.0001) in the decidual tissue of SA patients.

CONCLUSIONS: These findings indicate that SA is associated with localized inflammatory activation at the maternal-fetal interface, dysregulation of decidual molecular activity, gut microbiota dysbiosis, and metabolic perturbations. Integrated multi-omics analyses suggest potential interactions among these factors that may be linked to decidual dysfunction during early pregnancy, providing new insights into the complex pathophysiology of SA.}, } @article {pmid42096148, year = {2026}, author = {Zhu, D and Wang, S and Sun, X and Britton, RA}, title = {CRISPR-AsCas12a and dAsCas12a-Mediated Gene Knockout and Knockdown in Clostridioides difficile.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3046}, number = {}, pages = {47-55}, pmid = {42096148}, issn = {1940-6029}, mesh = {*Clostridioides difficile/drug effects/genetics/pathogenicity ; *Gene Knockout Techniques ; *Gene Knockdown Techniques ; Bacterial Proteins ; Endodeoxyribonucleases ; CRISPR-Associated Proteins ; *CRISPR-Cas Systems ; *Gene Editing/methods ; Acidaminococcus/enzymology ; Virulence/genetics ; *Drug Resistance, Bacterial/genetics ; *Host-Pathogen Interactions/genetics ; }, abstract = {Clostridioides difficile (C. difficile) is a leading cause of antibiotic-associated diarrhea and severe colitis, yet its genetic manipulation has long been constrained by low DNA transfer efficiency and limited recombination systems. Recent advances in CRISPR-based technologies have revolutionized the genetic toolkit for this pathogen, enabling precise genome editing and transcriptional regulation. Among CRISPR nucleases, Cas12a offers distinct advantages over Cas9 for bacterial applications, including a smaller size, T-rich PAM recognition, single-crRNA requirement, and reduced toxicity, which enhances conjugation efficiency in genetically recalcitrant organisms. AsCas12a-based platforms have enabled large fragment deletions, multiplex editing, and rapid generation of marker-free mutants in C. difficile. Complementing these nuclease-active systems, nuclease-deactivated variants (dCas9 or dAsCas12a) support CRISPR interference (CRISPRi)-a reversible, tunable approach for transcriptional repression without altering genomic sequences. Compared to traditional mutagenesis, CRISPRi greatly accelerates functional genomics by enabling high-throughput screening and drug target discovery. Together, our lab has independently developed CRISPR-AsCas12a-mediated genome editing and dAsCas12a-based CRISPRi tools, providing complementary strategies to overcome longstanding genetic barriers in C. difficile. These tools open new avenues for system-level interrogation of virulence, antibiotic resistance, and host-pathogen interactions.}, } @article {pmid42096157, year = {2026}, author = {Pizzini, J and McCullough, HC and Sidner, BS and Britton, RA and Piepenbrink, KH and Auchtung, JM}, title = {An In Vitro Model for Studying Interactions Between Gastrointestinal Microbes and Planktonic and Sessile Clostridioides difficile Populations.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3046}, number = {}, pages = {171-187}, pmid = {42096157}, issn = {1940-6029}, mesh = {*Clostridioides difficile/physiology ; *Gastrointestinal Microbiome ; Humans ; Mucins/metabolism/chemistry ; Bacterial Adhesion ; Bioreactors/microbiology ; *Plankton ; Intestinal Mucosa/microbiology ; Hydrogels/chemistry ; Biofilms/growth & development ; }, abstract = {Interactions between Clostridioides difficile, the gastrointestinal microbiota, and the host mucosal epithelium play important roles in governing the ability of C. difficile to colonize and cause disease. Several in vitro tools have been developed to investigate C. difficile physiology in the presence of microbial communities. In this chapter, we describe a model for studying C. difficile-mucin interactions in the presence of a complex microbiota using continuous flow bioreactors. This model can facilitate mechanistic studies of specific microbes and mucin structures important for C. difficile colonization, complementing findings from animal models. The approach presented here builds upon the preceding chapter's protocol for generating mucin hydrogels on glass slides and extends it to examine C. difficile adhesion to mucosal surfaces.}, } @article {pmid42096470, year = {2026}, author = {Hardick, J and Anantharam, R and Lu, J and Salzberg, SL and Rothman, RE and Fenstermacher, KZJ and Pekosz, A and Onzia, A and Nakiyingi, L and Manabe, YC and Kandathil, AJ}, title = {Comparison of unbiased metagenomic next generation sequencing to targeted multiplex diagnostic assays for the detection of respiratory viruses.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0347750}, pmid = {42096470}, issn = {1932-6203}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Respiratory Tract Infections/virology/diagnosis ; Male ; Female ; Adult ; Nasopharynx/virology ; Middle Aged ; Multiplex Polymerase Chain Reaction/methods ; SARS-CoV-2/genetics/isolation & purification ; *RNA Viruses/genetics/isolation & purification ; Aged ; Child, Preschool ; Adolescent ; Child ; Young Adult ; }, abstract = {OBJECTIVES: Accurate diagnosis of existing and emerging respiratory pathogens is important. We evaluated the capability of unbiased metagenomic next generation sequencing (mNGS) to identify pathogenic RNA viruses from two cohorts of nasopharyngeal (NP) swabs previously tested by commercial multiplex respiratory diagnostics.

METHODS: NP swabs (N = 100) in viral transport media (VTM) were assessed using mNGS for this study. Cohort 1 (N = 52) consisted of symptomatic individuals who tested negative for SARS-CoV-2, influenza A/B, and RSV by the Xpert Xpress CoV-2/Flu/RSV Plus multiplex respiratory virus panel and were tested by mNGS for undetected pathogens. Cohort 2 (N = 48) included symptomatic individuals who were positive (N = 26) or negative (N = 22) by the ePlex RP2 multiplex respiratory pathogen panel. Samples were positive for influenza A (N = 8), rhinovirus/enterovirus (N = 5), RSV (N = 4), adenovirus (N = 3), parainfluenza (N = 2), seasonal coronaviruses (N = 2), and human metapneumovirus (N = 1), as well as a rhinovirus/enterovirus/human metapneumovirus co-infected sample (N = 1). mNGS results were compared with ePlex RP2 findings, and symptomatic negative samples were evaluated for additional pathogen detection.

RESULTS: Cohort 1 contained 8% (4/52) viral and 19% (10/52) bacterial reads. In cohort 2, positive concordance between ePlex RP2 and mNGS was 31% (8/26). mNGS did not identify any viral reads in ePlex RP2-negative samples. However, it detected other microbial reads, such as Acanthamoeba castellanii, in 21% (10/48) of samples.

CONCLUSION: In this study, targeted multiplex amplification methods demonstrated better overall sensitivity in NPs of symptomatic respiratory individuals than mNGS. Other mNGS approaches may produce different results. This study suggests that mNGS may offer adjunctive information, including the detection of rare pathogens, which may be helpful in some clinical contexts.}, } @article {pmid42096522, year = {2026}, author = {Zhao, D and Zhang, C and Li, M and Li, H and Su, S and Zhang, X}, title = {Characteristics of carbon-fixing microbial communities and pathways across different aquatic systems in the Tianjin Binhai region.}, journal = {Journal of applied microbiology}, volume = {137}, number = {5}, pages = {}, doi = {10.1093/jambio/lxag112}, pmid = {42096522}, issn = {1365-2672}, support = {25JCZDJC00400//Tianjin Natural Science Foundation/ ; 42102299//National Natural Science Foundation of China/ ; }, mesh = {*Carbon Cycle ; *Archaea/metabolism/genetics/classification/isolation & purification ; *Bacteria/metabolism/genetics/classification ; China ; *Groundwater/microbiology ; *Water Microbiology ; Rivers/microbiology ; Microbiota ; Metagenomics ; Carbon/metabolism ; }, abstract = {AIMS: Microbial carbon fixation is central to carbon cycling and carbon sink functioning in coastal aquatic ecosystems. Although carbon fixation pathways have been increasingly investigated across diverse aquatic environments, comparative evidence remains limited for hydrologically connected yet hydrochemically contrasting coastal groundwater and surface water systems. This study aimed to compare carbon-fixation-associated microbial communities and major carbon fixation pathways across groundwater, river water, and reservoir water in the Tianjin coastal region.

METHODS AND RESULTS: We integrated metagenomic sequencing with hydrochemical analyses to characterize carbon-fixation-associated microbial communities and six representative carbon fixation pathways. Surface waters were dominated by bacteria and showed relatively stable community composition, whereas groundwater communities comprised both bacteria and archaea and displayed pronounced spatial heterogeneity. The Calvin-Benson-Bassham cycle was prevalent across all water types, and the reductive tricarboxylic acid (rTCA) cycle was also widely distributed. Groundwater showed higher contributions of the Wood-Ljungdahl pathway, the archaeal 3-hydroxypropionate/4-hydroxybutyrate and dicarboxylate/4-hydroxybutyrate cycles, together with the rTCA cycle, indicating coexisting carbon fixation strategies. Pathway abundance and module completeness further suggested differences in pathway integrity among water types. Total dissolved solids, HCO3⁻, CO32⁻, and dissolved organic carbon were key correlates of carbon fixation gene distribution.

CONCLUSIONS: Carbon-fixation-associated microbial communities, pathway distributions, and pathway integrity differed markedly between coastal groundwater and surface waters. Groundwater exhibited enhanced non-CBB cycle potentials and more diversified carbon fixation strategies, highlighting the importance of groundwater processes in evaluating carbon sequestration potential and carbon cycling in hydrochemically heterogeneous coastal aquatic systems.}, } @article {pmid42096753, year = {2026}, author = {Jin, B and Bai, Z and Yan, Y and He, H and Du, J and Xu, Y and Wang, L and Ji, J}, title = {Antibiotic-driven mechanisms in endogenous partial denitrification (EPD): Nitrite accumulation, microbial adaptation, functional gene responses and resistance gene proliferation.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142257}, doi = {10.1016/j.jhazmat.2026.142257}, pmid = {42096753}, issn = {1873-3336}, mesh = {*Denitrification/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Nitrites/metabolism ; Sulfamethoxazole/pharmacology ; *Water Pollutants, Chemical/metabolism ; Sulfadiazine/pharmacology ; Tetracycline/pharmacology ; Adaptation, Physiological ; *Bacteria/genetics/metabolism/drug effects ; Biodegradation, Environmental ; Drug Resistance, Bacterial/genetics ; Biological Oxygen Demand Analysis ; }, abstract = {The mechanisms by which antibiotics affect Endogenous Partial Denitrification (EPD) systems remain unclear. This study investigated the relationships between antibiotic type and pollutant removal, along with the underlying microbial metabolic mechanisms in an EPD system exposed to three antibiotics. The results showed that sulfadiazine (SD) and sulfamethoxazole (SMZ) exhibited higher chemical oxygen demand removal efficiency than tetracycline (TC). In the SD system, NO3[-]-N removal was 84.13%, whereas other systems achieved 97%, which was associated with a higher abundance of the n arG and nirS. Proteobacteria and Chloroflexi demonstrated strong adaptability to the antibiotics. TC inhibited the tricarboxylic acid cycle and organic matter degradation may be related to the reduced mdh. SD induced microorganisms to convert carbon sources into polyhydroxybutyrate instead of utilizing them directly, while SMZ optimized nitrogen metabolism by increasing the abundance of nirS and nirK, leading to higher NO2[-]-N accumulation in these two EPD systems. SD stress reduced the abundance of ppk2/ppx gene, inhibited the energy production and internal carbon reserve of denitrifying polyphosphate-accumulating organisms in anaerobic stage. Although the microorganisms had stronger phosphorus uptake potential by up-regulating ppk1 gene, the lack of ATP necessary to drive this process eventually led to the reduction of PO4[3] [-]-P removal ability. The abundance of resistance genes peaked in the SD system, significantly increasing the risk of antibiotic resistance. This study deciphers the metabolic mechanisms of the EPD system in response to three types of antibiotics and provides a scientific basis for its application in environments with fluctuating antibiotic stress.}, } @article {pmid42096819, year = {2026}, author = {Kumar, K and Dutta, P}, title = {Integration of mass spectrometry and molecular biotechnology to study bioaerosols.}, journal = {Chemosphere}, volume = {405}, number = {}, pages = {144949}, doi = {10.1016/j.chemosphere.2026.144949}, pmid = {42096819}, issn = {1879-1298}, mesh = {Aerosols/analysis ; *Mass Spectrometry/methods ; *Environmental Monitoring/methods ; *Biotechnology/methods ; Humans ; *Air Pollutants/analysis ; Metabolomics ; *Air Microbiology ; }, abstract = {Conventional culture-based and microscopic approaches yield limited information about the diversity, content, and real-time behaviour of biological aerosols. In recent years, mass spectrometry (MS) and molecular biotechnology have evolved as powerful and complementary analytical methods for detecting, identifying, and characterising air biological particles. This study critically reviews recent improvements in MS-based techniques for analysing bioaerosol chemical markers, proteins, metabolites, and toxins, including MALDI-TOF MS, GC-MS, LC-MS/MS, and real-time aerosol mass spectrometry. In parallel, contemporary advances in molecular biotechnology, including as PCR-based assays, metagenomics, and MS-driven proteomics and metabolomics, are described, with a focus on atmospheric applications. Special emphasis is placed on integrated analytical workflows that combine MS with molecular techniques to improve specificity, sensitivity, and source attribution. The current issues of low biomass concentrations, sampling artefacts, data interpretation, and standardisation are discussed, and future perspectives on portable MS systems, multi-omics integration, and AI-assisted data processing are presented. This study offers a thorough analytical chemistry viewpoint on next-generation methodologies for monitoring bioaerosols and promotes the development of enhanced instruments for assessing air quality and protecting human health.}, } @article {pmid42097292, year = {2026}, author = {Hennecart, B and Belda, E and de Lahondès, R and Zucker, JD and Prifti, E}, title = {StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {5}, pages = {}, pmid = {42097292}, issn = {1367-4811}, support = {//Paris Île-de-France Region/ ; //French ANR/ ; ANR-24-PESA-0010//JEMINI/ ; }, mesh = {*Metagenomics/methods ; *Software ; *Metagenome ; Workflow ; Reproducibility of Results ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA/methods ; }, abstract = {SUMMARY: Metagenomic workflows involve complex multi-step analyses, from quality control and assembly to binning, annotation, and strain-level profiling. Few existing metagenomic pipelines achieve the combination of flexibility, reproducibility, and hybrid assembly support within a unified workflow. We present StrainMake, a Snakemake-based workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data. StrainMake integrates widely used tools across all major steps-quality control, assembly, binning, dereplication, taxonomic and functional annotation-while also providing non-redundant gene catalogues, community-scale metabolic models, and strain-level microdiversity metrics. The modular design enables the use of alternative tools, scalable execution on HPC systems, and full reproducibility through Snakemake and Conda.

RESULTS: Applied to the CAMI II strain-madness dataset, StrainMake produced high-quality assemblies and metagenome-assembled genomes (MAGs), while enabling strain-resolved comparisons across samples. Hybrid assemblies improved contiguity, whereas short-read assemblies offered faster runtimes, illustrating the workflow's benchmarking capacity.

StrainMake is open source and available at https://github.com/UMMISCO/strainmake, together with comprehensive documentation. Generated data are deposited in Zenodo (doi: 10.5281/zenodo.16950162).}, } @article {pmid42097342, year = {2026}, author = {Yin, D and Chen, M and Chen, X and Feng, Y and Zhou, X and Guan, Y and Zhang, Y and Bai, S and Li, L and Ouyang, H and Cheng, J and Zhu, W}, title = {Integrative multi-omics reveals that Pueraria thomsonii Radix alleviates dyslipidemia by remodeling gut microbiota and regulating arachidonic acid metabolism.}, journal = {Journal of ethnopharmacology}, volume = {368}, number = {}, pages = {121816}, doi = {10.1016/j.jep.2026.121816}, pmid = {42097342}, issn = {1872-7573}, mesh = {Animals ; *Dyslipidemias/drug therapy/metabolism ; *Gastrointestinal Microbiome/drug effects ; Male ; Multiomics ; *Pueraria/chemistry ; *Arachidonic Acid/metabolism ; Diet, High-Fat ; Rats, Sprague-Dawley ; Rats ; Humans ; Liver/drug effects/pathology/metabolism ; Metabolomics ; *Drugs, Chinese Herbal/pharmacology ; *Plant Extracts/pharmacology ; Lipid Metabolism/drug effects ; }, abstract = {Pueraria thomsonii Radix (PTR, "Fen-ge") is a food-medicine herb widely used in China for metabolic complaints. Its putative lipid-modulating effects are supported by traditional practice, but the molecular basis remains incompletely understood.

AIM OF THE STUDY: To elucidate the active constituents and mechanisms by which PTR mitigates dyslipidemia.

MATERIALS AND METHODS: Chemical profiling and plasma exposure of PTR constituents were characterized by UPLC-Q-TOF-MS/MS. A high-fat-diet rat model was used to assess pharmacodynamic endpoints including serum lipid panel, hepatic histopathology, liver injury markers and inflammatory cytokines. Untargeted plasma metabolomics was performed in rats and patients; rat fecal 16S rRNA gene sequencing and hepatic transcriptomics complemented mechanism inference. Multivariate models were cross-validated and FDR-controlled; pathway and multi-omics correlation analyses integrated metabolite-microbe-gene relationships.

RESULTS: PTR significantly ameliorated dyslipidemia in high-fat diet-fed rats, as evidenced by improved serum lipid profiles, reduced ALT/AST levels, and alleviated hepatic steatosis and inflammation in histopathological examination. Integrated metabolomic analysis across rats and patients revealed that the restored metabolic pathways were primarily concentrated in arachidonic acid and unsaturated fatty acid metabolism. Gut microbiota analysis indicated that PTR remodeled microbial taxa correlated with arachidonic acid-related lipid metabolism. Meanwhile, hepatic transcriptomics data showed that differentially expressed genes were functionally enriched in biological processes such as lipid oxidation and were bioinformatically linked to the AMPK signaling pathway.

CONCLUSIONS: PTR may ameliorate dyslipidemia through coordinated modulation of the gut microbiota and arachidonic acid metabolic network. Based on integrated omics analysis, the hepatic AMPK signaling pathway may potentially be involved in this regulatory process; however, its direct mechanistic role requires further experimental validation. Future investigations employing targeted lipid-omics, protein phosphorylation assays, and microbiota-transfer experiments are warranted to elucidate the causal relationships.}, } @article {pmid42097354, year = {2026}, author = {Kaliappa, GD and Palanisamy, H and Vidyalakshmi, S}, title = {Integrative machine learning models to unravel gut microbial dysbiosis and functional disruption in polycystic ovary syndrome.}, journal = {F&S science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.xfss.2026.04.005}, pmid = {42097354}, issn = {2666-335X}, abstract = {OBJECTIVE: To study gut microbial diversity and metabolic pathway disruptions in women with PolyCystic Ovary Syndrome (PCOS) compared with healthy controls, and to evaluate the diagnostic potential of microbiome-driven machine learning models.

DESIGN: Case-controlled metagenomic data analysis SUBJECTS: Gut metagenomic data from women diagnosed with PCOS and age-matched healthy female controls EXPOSURE: Presence of PCOS MAIN OUTCOME MEASURES: The primary outcome measures will include gut microbial alpha and beta diversity indices, microbial taxon abundance, functional pathway profiles, predicted metabolite levels, microbe-functional pathway-metabolite interaction networks, and the diagnostic accuracy of microbiome-based machine learning models.

RESULTS: Alpha and beta diversity analyses revealed marked gut microbial dysbiosis in women with PCOS, despite comparable species richness to healthy controls. Differential abundance analysis identified 41 significantly altered microbial species, including enrichment of proinflammatory taxa, such as Bacteroides vulgatus and Ruminococcus gnavus, and depletion of beneficial commensals, including Roseburia hominis and Prevotella copri. These compositional shifts indicate a proinflammatory microbial community structure in PCOS. Functional profiling demonstrated the upregulation of pathways involved in nucleotide turnover, lipid and carbohydrate metabolism, and neurotransmitter synthesis, potentially contributing to metabolic and neuroendocrine disruption. Network analysis revealed fragmented and unstable microbial-metabolite associations in PCOS compared with cohesive networks in controls. Microbiome-based machine learning models achieved a diagnostic accuracy of 84.25% (area under the curve 0.93), underscoring their predictive potential.

CONCLUSION: The gut microbiome in PCOS is characterized by a proinflammatory community structure and disrupted metabolic pathways. These findings demonstrate the diagnostic potential of microbiome-based models and underscore the gut microbiome as a promising target for therapeutic interventions in the management of PCOS.}, } @article {pmid42097759, year = {2026}, author = {Li, Z and Zhang, Q and Wang, H and Zhang, Z and Liu, J and Li, L and Lin, Y and Wang, Y and Yin, C and Wang, W and Shen, F and Han, Z and Hao, S and Cong, P and Tian, T and Liu, Q and Chen, X and Zhan, H and Peng, T and Yu, X and Pu, X and Lian, X and Wang, T}, title = {Diagnostic Value of Metagenomic Next-Generation Sequencing for Suspected Native Spinal Brucella Infection: A Multicenter Study.}, journal = {Neurospine}, volume = {23}, number = {2}, pages = {487-499}, pmid = {42097759}, issn = {2586-6583}, support = {2023YFC2812004//National Key Research and Development Program/ ; 24-4-4-zrjj-154-jch//Qingdao Natural Science Foundation/ ; //Qingdao City Healthcare Key Discipline Construction Project/ ; 2023TSGC051l//Technological Innovation Capability Improvement Project/ ; ZR2024MH251//Shandong Provincial Natural Science Foundation General Project/ ; 202404070869//Shandong Province Medical and Health Science Project/ ; }, abstract = {OBJECTIVE: The aim is to study the diagnostic positive rates of metagenomic next-generation sequencing (mNGS), microbial culture, and serologic testing in suspected native spinal brucellosis, and to evaluate the clinical value of their combined application.

METHODS: In this multicenter, retrospective observational study, 128 patients with suspected native spinal brucellosis from 6 medical centers (February 2020 to February 2025) were enrolled. Specimens from infection sites were subjected to microbial culture, mNGS, and serological testing (agglutination test).

RESULTS: Of the 128 patients with suspected native spinal Brucella infections, 118 patients were diagnosed with Brucella spondylitis. Among the 118 confirmed Brucella spondylitis cases, mNGS demonstrated a positivity rate of 92.37% (109 of 118), significantly higher than that of culture (26.27%, 31 of 118) and agglutination test (83.05%, 98 of 118). In the 87 culture-negative samples, mNGS detected Brucella in 91.95% (80 of 87), compared to 82.76% (72 of 87) by agglutination test. mNGS confirmed Brucella infection in all 16 cases that were agglutination test negative. mNGS combined with agglutination tests can effectively complement each other, improving the sensitivity of diagnosis and thereby minimizing missed diagnoses to the greatest extent. Among the 10 nonbrucellar spinal pathologies, agglutination test showed a high false-positive rate of 90% (9 of 10), whereas mNGS had a 10% (1 of 10) false-positive rate. Therefore, the agglutination test has a relatively high rate of false positives.

CONCLUSION: mNGS detection represents an effective adjunct to microbial culture and the agglutination test. The concurrent use of all 3 methods enhances diagnostic accuracy and reduces the likelihood of missed and incorrect diagnoses, significantly improving patient prognosis and guiding personalized clinical treatment.}, } @article {pmid42098163, year = {2026}, author = {Weng, Y and He, S and Luo, Z and Sun, J and Cheng, Q and Chen, Y and Tong, H}, title = {Keystone microbial taxa in the formation of stale aroma during pile fermentation of ripened Pu-erh tea.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00794-8}, pmid = {42098163}, issn = {2396-8370}, support = {CYB23127//Chongqing Graduate Student Research Innovation Project/ ; 2024J1110//Yunnan Provincial Department of Education/ ; 32272764//National Natural Science Foundation of China/ ; }, abstract = {Ripened Pu-erh tea is prized for its distinctive stale aroma. Methoxy-phenolic compounds, key contributors to this aroma, are produced during pile fermentation; however, the specific microorganisms responsible for their synthesis remain unclear. In this study, we identified the dominant taxa (Aspergillus luchuensis, A. fumigatus, Staphylococcus gallinarum, and S. kloosii) during pile fermentation through morphological analysis and metagenomic profiling. Gas Chromatography-Mass Spectrometry (GC-MS) analysis demonstrated the pivotal role of methoxy-phenolic compounds in the stale aroma. Moreover, using a metagenomic-based Weighted Gene Co-expression Network Analysis (WGCNA) combined with bivariate correlation network analysis, we identified key microbial taxa (Trichomonascus ciferrii, Heyndrickxia coagulans and Enterococcus sp.) involved in the generation of these compounds. Finally, we found that solid-state fermentation involving both dominant and keystone microbial taxa produced the highest levels of methoxy-phenolic compounds. Our findings reveal an inconsistency between dominant high-abundance taxa and keystone microbial taxa responsible for methoxy-phenolic compound synthesis during pile fermentation.}, } @article {pmid42098310, year = {2026}, author = {Li, W and Ni, P and Xu, J and Zhao, X and Dou, A and Wang, Y and Peng, L and Huang, S and Chen, Y and Shi, Q and Xie, Y and Zhang, W and Pan, S and Zhou, C}, title = {HIV-driven virome dysbiosis unveils distinct virome features and inter-viral correlations in blood and respiratory niches.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10221-z}, pmid = {42098310}, issn = {2399-3642}, support = {No. 82550118//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {While systemic immune dysregulation is well-documented in HIV infection, its impact on blood and respiratory tract viromes remains poorly understood. This study characterizes HIV-associated alterations in viral communities and examines their clinical relevance. Using viral metagenomics, we compare 203 ART-treated HIV-positive individuals and 120 healthy controls. HIV infection significantly restructures the blood virome, shifting from bacteriophage dominance (96.2% in controls) to eukaryotic virus predominance (69.1%). Increased alpha diversity, significant β-diversity divergence, and heightened dispersion heterogeneity are observed in HIV cases. Consistent enrichment of Flaviviridae, Parvoviridae, and Anelloviridae is detected. Throat viromes maintain phage dominance (>90%) but exhibit strain-level diversification, including Microviridae proliferation. Network analysis reveals Retroviridae-Anelloviridae co-dynamics (r = +0.562) and identifies Picobirnaviridae as a key interactor. Functional analysis shows enriched viral replication and host modulation genes. Compartment-specific disruption patterns nominate Pegivirus C, parvovirus B19, and Anelloviruses as potential biomarkers. Cross-kingdom viral interactions suggest novel mechanisms influencing disease progression and support future virome-targeting adjunct therapies.}, } @article {pmid42098386, year = {2026}, author = {Wei, X and Bashir, K and Tian, X and Farooq, A and Olimi, E and Cernava, T and Zhang, L and Yu, X and Chen, Q and Penttinen, P and Gu, Y}, title = {Microplastic and lead shift microbiomes enriching viral auxiliary metabolic genes for potential polylactic acid degradation.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10162-7}, pmid = {42098386}, issn = {2399-3642}, support = {41201256//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Biodegradable microplastics and heavy metals increasingly co-occur in soils through plastic mulching, organic amendments, and legacy metal contamination. Yet, their combined effects on soil-plant-microbiota interactions remain unclear, particularly for the virus. Here we evaluated the impacts of bio-MPs, polylactic acid (PLA), lead (Pb), and their combination on buckwheat and rhizosphere bacterial-viral communities. Co-contamination reduced soil pH and nutrient availability, increased Pb accumulation in plant tissues and suppressed buckwheat growth. Metagenomic analyses revealed that both bacterial and viral communities were altered under Pb-containing treatments. Bacterial genes associated with carbon and phosphorus metabolism were suppressed, while viral auxiliary metabolic genes (AMGs) related to carbon utilization were enriched, especially carbohydrate esterases that hydrolyze PLA ester bonds. A putative AMG-associated carbohydrate esterase gene (P9222_28545) was identified and the esterase activity confirmed via heterologous expression in E. coli. These findings highlight a potential role of viruses in mediating microplastic degradation in soils.}, } @article {pmid42098439, year = {2026}, author = {Prendergast, PJ and Bishop, HV and Herbold, CW and Verdu, EF and Dobson, RCJ and Day, AS and Ogilvie, OJ}, title = {Comprehensive cross-cohort analysis reveals global gut microbiome signatures of celiac disease.}, journal = {Communications medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s43856-026-01627-1}, pmid = {42098439}, issn = {2730-664X}, abstract = {BACKGROUND: Celiac disease affects ~1-2% of people and remains incurable, requiring lifelong dietary restriction. The gut microbiome is thought to contribute to the development and progression of celiac disease. However, findings across previous studies are fragmented, making it difficult to understand exactly how the gut microbiome is involved.

METHODS: We integrate over 900 samples from global datasets spanning different disease stages (before onset, during active disease, and after treatment), body sites, and research methods. Datasets produced using both 16S rRNA gene sequencing and shotgun metagenomics profile the gut microbiome. Alpha and beta diversity analyses and differential abundance testing identify consistent changes in bacterial communities linked to celiac disease. Machine learning tests how well microbiome data predicts disease status.

RESULTS: Here, we show that celiac disease is not marked by large changes in gut microbiome diversity. Instead, there are subtle, consistent changes in specific bacteria, including a reduction in beneficial butyrate producers (Faecalibacterium, Prevotella, Agathobacter, Gemmiger), changes in mucin-associated microbes (Akkermansia muciniphila), and an increase in potentially harmful bacteria (Helicobacter, Campylobacter, Haemophilus parainfluenzae). These changes are seen before and during active disease and persist on a gluten-free diet. Microbiome-based disease prediction is moderately accurate for active disease and weaker for prospective performance, likely constrained by training data.

CONCLUSIONS: Our findings suggest that celiac disease is linked to specific changes in gut bacteria that are not fully resolved by diet alone. Future treatments may need to focus on restoring healthy gut bacteria, not just avoiding gluten, to better manage the disease.}, } @article {pmid42098757, year = {2026}, author = {Jiang, X and Zhang, C and Zhang, Y and Li, J and Ren, J and Wang, J and Hou, X and Zhang, Z and Wu, S and Yao, J}, title = {Multi-omics analysis of soy isoflavone-induced responses in rumen fermentation, endocrine status and milk production in cows with varying milk yields.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42098757}, issn = {1674-9782}, support = {2024-KFKT-011//the National Center of Technology Innovation for Dairy/ ; 32272829//National Natural Science Foundation of China/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; }, abstract = {BACKGROUND: Improving milk yield and feed efficiency is pivotal for climate-smart dairy systems, as rumen mediated fermentation governs energy and nitrogen utilization and thereby greenhouse-gas emission intensity. Soybean isoflavones (SIF) may modulate rumen fermentation, yet their effects on rumen function, microbiome features, host endocrine/metabolic responses, and lactation performance-particularly across cows with divergent milk-yield phenotypes-remain unclear.

RESULTS: Fifty‑six lactating Holstein cows (28 high‑yield cows, HY; 28 low‑yield cows, LY) were divided into two categories by milk yield. Within each yield category, cows were randomly assigned to one of two dietary treatments: a basal diet (Control) or the basal diet supplemented with SIF at 0.01% of dry matter. This yielded a 2 × 2 factorial design with four experimental groups (n = 14 per group): high‑yield control (HCON), high‑yield SIF (HSIF), low‑yield control (LCON), and low‑yield SIF (LSIF). SIF increased milk yield by 8.75% and improved fat-corrected milk (+ 7.20%), dry matter intake (+ 3.20%), and feed efficiency (+ 3.26%), with larger gains in HY cows (milk yield + 8.89%; feed efficiency + 4.55%). Rumen fermentation shifted toward a more energetically favorable profile, with lower acetate (- 2.70%), higher propionate (+ 4.55%), and a reduced acetate-to-propionate ratio (- 7.02%), accompanied by increased microbial crude protein (+ 21.53%) without changes in pH or NH3-N. SIF altered endocrine status irrespective of phenotype, increasing estradiol and progesterone while decreasing prolactin and growth hormone, and reduced blood ALP, lactate, and triglycerides. Metagenomics indicated phenotype-dependent microbial and functional responses to SIF: HY cows showed enrichment of taxa (e.g., Caudoviricetes sp., Eubacterium sp., and Butyrivibrio sp.) associated with amino-acid, cofactor metabolism and propionate pathways, whereas LY cows exhibited enrichment of Prevotella sp. and Bacteroides sp. with functions favoring carbohydrate degradation. The HCON group exhibited greater abundances of Prevotella sp. and Hallella spp. with enhanced carbohydrate degradation functions, whereas the LCON group was enriched in Ruminococcus sp. and Methanobrevibacter sp., associated with methane metabolism.

CONCLUSIONS: In conclusion, this study highlights the potential of SIF supplementation to improve lactation efficiency, modulate rumen microecology and endocrine function in dairy cows. These findings establish a theoretical framework for achieving efficient and precise feeding management on large-scale dairy farms.}, } @article {pmid42098796, year = {2026}, author = {Monteleone, E and Cianci, MA and Albano, A and Loperfido, F and Griffante, G and Brasi, L and Borella, F and Gallio, N and Preti, M and Marchi, A and Gardella, B and Molineris, I and Donati, G and Proserpio, V}, title = {Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42098796}, issn = {2049-2618}, support = {IG 2023 - Id. 28831//Fondazione AIRC per la ricerca sul cancro ETS/ ; MFAG 2023 - ID. 29203//Fondazione AIRC per la ricerca sul cancro ETS/ ; CRT 2023 RF = 106089 / 2023.1841//Fondazione CRT/ ; COD. 2022CLTAYH//Ministero dell'Università e della Ricerca/ ; 2025.0983//Compagnia di San Paolo/ ; }, mesh = {Humans ; Female ; *Microbiota/genetics ; *Vulva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; *RNA, Messenger/genetics ; Vagina/microbiology ; *Host Microbial Interactions/genetics ; *RNA-Seq/methods ; Transcriptome ; }, abstract = {BACKGROUND: To describe both host gene expression and microbiome composition in a single sample, parallel experimental and computational workflows (mRNA-sequencing and either 16S rRNA gene or metagenomics) have been traditionally applied. The vulvar milieu represents an area of emerging research for its role in health and disease. Located at the interface between the vagina and the perineum, the vulvar microbiome displays an intermediate signature, with influx from both ecosystems.

RESULTS: Following validation of the reliability of poly(A)-enriched mRNA-sequencing in reconstructing the microbiota composition using both a quantitative microbial standard (mock) and metagenomic analysis, we analyze a full cohort of 30 healthy vulvar samples. Crucially, the analysis of the entire cohort relies solely on mRNA-sequencing without the use of parallel DNA metagenomics. This unified approach allows us to analyze not only the vulvar cell transcriptome, but also the composition and dynamics of microbial communities, including the microbial gene expression signatures. This three-level analysis (host-mRNA, individual bacterial species, bacterial gene pathways) on the very same specimens further enables a gene-level exploration of host-microbe molecular crosstalk. Using this unified framework, we reveal marked heterogeneity and high inter-individual variability in the vulvar microbiota, identifying community state types that mirror those described in the vagina. Importantly, we show that distinct microbial configurations are associated with specific host transcriptional programs: Lactobacillus crispatus correlates with epithelial differentiation and barrier integrity, whereas communities enriched in Gardnerella vaginalis, or other taxa associated with dysbiosis, exhibit transcriptional signatures linked to inflammation. Interestingly, Lactobacillus gasseri, which has been associated with lower protection, shows an intermediate effect on vulvar cells.

CONCLUSIONS: Beyond providing new biological insights into an understudied anatomical niche, our study introduces a broadly applicable strategy with substantial impact for the field. With tens of thousands of human RNA-seq datasets already available in public repositories, our approach enables retrospective extraction of microbiome information and host-microbe interaction signals from existing transcriptomic data, without the need for additional sequencing or specialized microbiome protocols. This unlocks a powerful and cost-effective opportunity to revisit archived RNA-seq studies across tissues, diseases, and low-biomass environments, revealing previously inaccessible layers of host-microbiome crosstalk and maximizing the scientific value of published data. Video Abstract.}, } @article {pmid42098851, year = {2026}, author = {Dong, J and Cao, Y and Chen, X and Xie, T and Zhang, X and Zhao, Q and Shi, C and Miao, Q and Xu, Z and Yan, L and Dong, L}, title = {Buyang Huanwu Decoction promotes neurorepair after spinal cord injury through a Lactobacillus johnsonii-indole-3-lactic acid-AhR-PI3K/Akt axis.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {}, pmid = {42098851}, issn = {1749-8546}, support = {YSJ2025009//Postgraduate Research & Practice Innovation Program of Yan'an University/ ; 22XYJ0002//Xi'an Innovation Capability Strong Foundation Plan - Medical Research Project/ ; 2025PT-01//Platform Construction Project of Shaanxi Province's Health and Wellness Scientific Research and Innovation Capacity Enhancement Program/ ; }, abstract = {BACKGROUND: Spinal cord injury (SCI) induces gut microbiota dysbiosis, which significantly affects recovery. Buyang Huanwu Decoction (BHD), a traditional Chinese medicine formula, has shown therapeutic effects on SCI. Although BHD is known to modulate gut microbiota, whether its benefits are mediated through the gut-spinal cord axis remains unclear.

METHODS: A rat SCI model was established. BHD was administered orally, and fecal microbiota transplantation (FMT) from BHD-treated rats (BHD-FMT) was performed to assess neuroprotective and gut-protective effects. Behavioral testing, histology, and immunofluorescence evaluated motor recovery, inflammation, and neuroregeneration. Gut microbiota profiling was performed using 16S rDNA sequencing and metagenomics, while targeted metabolomics quantified tryptophan metabolites. Transcriptomics validated key pathways, and a microbiota-metabolite-signaling network was constructed.

RESULTS: BHD significantly improved motor function, reduced spinal inflammation, and promoted neuronal survival and axonal regeneration. It restored gut function, reduced colonic inflammation, and enhanced ZO-1 and Occludin expression, which were further confirmed by FMT. BHD-FMT reshaped the gut microbiota and enriched Lactobacillus johnsonii, which correlated positively with recovery. Metabolomics showed increased tryptophan metabolites, including indole-3-lactic acid (ILA) and indole-3-propionic acid (IPA), with ILA strongly associated with functional improvement. Transcriptomic analysis and Western blot validation demonstrated that BHD-FMT activated the AhR-PI3K/Akt pathway, which was suppressed by an AhR antagonist.

CONCLUSION: BHD promotes neuroregeneration after SCI by reshaping gut microbiota and enhancing tryptophan metabolism, potentially exerting its effects through the L. johnsonii-ILA-AhR-PI3K/Akt network. These findings reveal a gut-spinal cord axis-mediated mechanism of BHD and highlight microecological targets for SCI therapy.}, } @article {pmid42098871, year = {2026}, author = {Biswas, P and Ahmed, S and Mondal, S and Oladokun, S and Gundogdu, O and Mallick, AI}, title = {Recombinant LAB vector-based multicomponent vaccine against Campylobacter jejuni potentially promoting a healthier microbial balance in the poultry gut.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02421-w}, pmid = {42098871}, issn = {2049-2618}, support = {BB/Y007115/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; P409/2023-24//BactiVac, University of Birmingham, UK/ ; IC-12047(12)/2/2024-BP-IUCA//Indo-UK (DBT-BBSRC)/ ; }, abstract = {BACKGROUND: Diarrheal diseases remain the second leading cause of preventable death globally, particularly among children under the age of 5 in developing countries, accounting for an estimated 2-3 million deaths annually. Among bacterial pathogens causing diarrheal illness, Campylobacter jejuni (C. jejuni) remains a major contributor, particularly in low- and middle-income countries (LMICs). As a common gut pathogen, C. jejuni expresses several secretory or surface-expressed colonization proteins (SECPs), namely haemolysin co-regulated protein (Hcp), valine glycine repeats G (VgrG), Campylobacter adhesion to fibronectin (CadF), fibronectin-like protein A (FlpA), and jejuni lipoprotein A (JlpA). Most of these proteins play pivotal roles in bacterial self-survival, host-cell adhesion, and invasion of avian and non-avian hosts. To minimize C. jejuni adhesion and subsequent colonization in the avian gut, we explored the potential of a multicomponent mucosal vaccine composed of CadF, Hcp, and JlpA protein of C. jejuni.

RESULTS: For this purpose, we bioengineered a food-grade Lactic Acid-producing Bacterium, Lactococcus lactis (L. lactis), to express three key immunogenic subunits of C. jejuni, CadF, Hcp, and JlpA. Utilizing this live vector-based multicomponent mucosal vaccine platform, we investigated the immunoprotective potential of these antigens in chickens. Since the particular strain of L. lactis is non-colonizing, we used chitosan, a natural mucoadhesive, biodegradable polymer, to microencapsulate the engineered bacteria and increase their gut retention time for optimal interaction with local immune cells. Our in vivo immunization study demonstrated that oral administration of this multicomponent vaccine formulation elicited a strong local antibody response (sIgA) (p < 0.0001) and upregulated key pro-inflammatory cytokines, leading to robust mucosal immune protection (~ 1.54 log10 reduction) against the cecal colonization of C. jejuni. Beyond targeting C. jejuni, we hypothesized that the vaccine may influence the overall gut microbiota, potentially promoting a healthier microbial balance in the poultry gut. To this end, gut metagenomic analysis of vaccinated birds revealed a marked reduction in the phylum Campylobacterota (~ 2-fold), accompanied by increased abundance of the phyla Bacteroidota, as part of a beneficial microbial community.

CONCLUSIONS: Together, this study underscores the potential of a live vector-based, multicomponent mucosal vaccine as a promising, cost-effective strategy to reduce the cecal load of C. jejuni, potentially limiting the risk of foodborne transmission in poultry production systems.}, } @article {pmid42098876, year = {2026}, author = {Liu, Z and Guo, Y and Xiao, L and Guo, J and Chen, Y and Wang, H and Nan, X and Zhou, M and Zhang, F and He, Y and Yu, Z and Wang, R and Ren, Z and Wu, J and Wang, M and Tang, X and Xiong, B}, title = {Proanthocyanidins inhibit methane emissions by interacting with methyl-coenzyme M reductase and reshaping rumen microbiome function.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42098876}, issn = {2049-2618}, support = {2023YFD2000703//National Key R&D Program of China/ ; 2023YFD2000701//National Key R&D Program of China/ ; 32525054//National Natural Science Foundation of China/ ; CAAS-CSSAE-202402//Innovation Program of Chinese Academy of Agricultural Sciences/ ; 2022YFD1301100//Integrated Demonstration of Scalable and Efficient Healthy Breeding for Cattle and Sheep/ ; }, mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism ; Cattle ; *Proanthocyanidins/pharmacology/metabolism ; Female ; *Oxidoreductases/metabolism ; Fermentation ; *Gastrointestinal Microbiome/drug effects ; Molecular Docking Simulation ; Dietary Supplements ; Lactation ; }, abstract = {BACKGROUND: Enteric methane (CH4) emissions from ruminants are a major source of agricultural greenhouse gases and represent an energy loss to the host. Methyl-coenzyme M reductase (MCR) is the terminal enzyme in methanogenesis and represents a key target for CH4 mitigation. This study integrated computational screening, in vitro fermentation, and in vivo experiments to identify plant-derived compounds capable of reducing enteric CH4.

RESULTS: Molecular docking of 3,900 phytochemicals identified proanthocyanidins (PAC) as top candidate, exhibiting strong predicted affinity to the MCR active site (-8.150 kcal/mol). In vitro rumen fermentation assays showed that PAC supplementation reduced CH4 production by 22% while increasing dry matter degradability. In lactating dairy cows, dietary PAC supplementation (10 or 20 g/kg dry matter) decreased daily CH4 emissions by ~ 8%, and improved ruminal nitrogen utilization without affecting milk yield or ruminal volatile fatty acid production. Amplicon sequencing and metagenomic analyses revealed PAC supplementation shifts in rumen microbial community, characterized by increased relative abundance of Bacteroidota taxa and a decreased relative abundance of methanogenesis-related genes. Functional genes associated with carbohydrate, lipid, and nitrogen turnover were more abundant, indicating potential improvements in nutrient utilization. Consistent with these changes, untargeted metabolomics likewise identified shifts in metabolite profiles that may associated with alternative routes for utilizing reducing equivalents.

CONCLUSIONS: This study provides integrated computational, microbial, and physiological evidence that PAC supplementation can reduce enteric CH4 emissions in lactating dairy cows, inducing rumen microbial and functional shifts and improving nitrogen utilization. These findings support the potential of PAC as a natural approach to lowering CH4 emissions and advancing sustainable dairy production. Video Abstract.}, } @article {pmid42099457, year = {2026}, author = {Liu, Y and Zhang, Z and Wu, G and Li, B and Wang, L and Wang, J and Wei, Z and Wang, Z and Yang, J and Zhang, K and Zhang, T and Tao, X and Chen, T and Fan, J and Zhou, J and Yang, X and Zhao, L and Wei, Y}, title = {Two stable gut microbiome guilds predict liver tumor class and treatment responses.}, journal = {iMeta}, volume = {5}, number = {2}, pages = {e70123}, pmid = {42099457}, issn = {2770-596X}, abstract = {Gut microbiome alterations are increasingly associated with hepatocellular carcinoma (HCC), highlighting the gut-liver axis as a key contributor to tumor progression and prognosis. Taxon-based HCC microbiome studies have shown limited reproducibility because they are affected by database dependency, taxonomic ambiguity, and overlooked ecological interactions. The Two Competing Guilds (TCG) model, based on stable gut microbiome interactions, provides a structurally grounded framework for robust, generalizable biomarkers. Using shotgun metagenomic data from a newly recruited cohort of 120 surgically resectable HCC cases and 76 benign liver tumor controls, we constructed co-abundance networks to identify stably correlated genome pairs and assembled a hepatic cancer-TCG (HCC-TCG) model composed of 142 genomes. Functionally, one Guild had more genes for butyrate production from carbohydrate fermentation while the other Guild was enriched in genes for virulence factors and antibiotic resistance, highlighting its potential proinflammatory roles. Classifiers trained on the abundance profiles of HCC-TCG genomes successfully distinguished HCC from benign liver tumors (area under the receiver operating characteristic, AUROC = 0.70) and from colorectal liver metastases (CRLM) (AUROC = 0.78). In an external validation cohort, the model further discriminated against HCC from intrahepatic cholangiocarcinoma (iCCA) (AUROC = 0.72), and from healthy controls (AUROC = 0.79-0.85), demonstrating its broad applicability for tumor stratification across clinical contexts. Moreover, HCC-TCG profiles predicted post-resection recurrence risk and response to adjuvant therapies (AUROC up to 0.83). Importantly, external validation in two independent cohorts of advanced HCC patients treated with PD-1/PD-L1 inhibitors demonstrated consistent predictive performance (AUROC = 0.64-0.73), confirming the model's generalizability in nonsurgical and immunotherapy contexts. This genome-specific, ecologically structured, and database-independent framework identifies a conserved Guild-based microbiome signature for HCC. Our findings demonstrate that a fixed genome-resolved ecological structure retains transferable discriminatory signal across clinical contexts. The HCC-TCG framework provides a genome-specific, interaction-based foundation for future development of non-invasive microbiome stratification strategies requiring prospective validation.}, } @article {pmid42099461, year = {2026}, author = {Wu, R and Wen, T and Shang, N and Xie, P and Wang, Z and Li, H and Li, S and Zhang, D}, title = {Chondroitin sulfate restores muscle mass via gut-muscle axis remodeling through sugar-bile acid metabolism reprogramming.}, journal = {iMeta}, volume = {5}, number = {2}, pages = {e70118}, pmid = {42099461}, issn = {2770-596X}, abstract = {Glucocorticoid-induced myopathy is characterized by progressive muscle atrophy and impaired regeneration, yet effective microbiota-oriented interventions for preserving muscle homeostasis remain largely unexplored. Here, we demonstrate that dietary chondroitin sulfate (DCS) restores muscle mass and function through a microbiota-dependent gut-muscle metabolic axis. DCS failed to confer protection in germ-free or antibiotic-treated mice, establishing gut microbiota as a prerequisite for its efficacy. Microbiota transplantation and mono-colonization experiments identified Lactobacillus johnsonii Z-RW as a functionally relevant mediator capable of recapitulating muscle protection under controlled microbial conditions. Integrated metagenomic, metabolomic, and proteomic analyses revealed coordinated reprogramming of intestinal sugar utilization and bile acid metabolism following DCS administration. Notably, DCS promoted bile acid deconjugation and enrichment of secondary bile acids, coinciding with restoration of muscle regenerative and energetic programs, including upregulation of NMRK2, PAX7, and SIRT1. Metabolite supplementation further implicated bile acids as candidate mediators linking microbial metabolism to muscle phenotypes. To quantitatively integrate these shifts, we introduce the sugar-bile acid ratio as a systems-level descriptor of microbiota-driven metabolic remodeling. Our findings delineate a microbiota-dependent metabolic framework through which a functional polysaccharide reshapes intestinal biochemistry to influence distal muscle physiology. This work highlights bile acid-associated signaling as a central relay within the gut-muscle axis and provides a conceptual foundation for microbiota-targeted strategies to mitigate muscle wasting.}, } @article {pmid42099660, year = {2026}, author = {Leal, F and Filho, RM and Inoue, LT and Heidrich, V and Dos Santos, EX and Bastos, DA and Camargo, AA and Jardim, DLF}, title = {Urinary microbiota diversity and composition in patients with advanced renal cell cancer.}, journal = {BJUI compass}, volume = {7}, number = {5}, pages = {e70186}, pmid = {42099660}, issn = {2688-4526}, abstract = {OBJECTIVES: This study aims to investigate the role of urinary microbiota in renal cell carcinoma; we analysed urinary microbiota in kidney cancer patients and explored its potential role as biomarker.

SUBJECTS AND METHODS: Samples were collected from 49 males (28 patients planned to undergo systemic therapy and 21 healthy volunteers). Two samples were collected from each patient, one prior to treatment and one after 8 to 12 weeks of systemic therapy. Microbiota was analysed by 16S rRNA sequencing. Microbiota diversity, taxonomic composition and relative abundance were compared between groups and longitudinal samples.

RESULTS: Amplicon sequence variant (ASV) richness was higher in renal cancer patients (p = 0.042) than controls. Beta diversity also differed between patients and controls by means of Jaccard (p = 0.001), Bray-Curtis (p = 0.008), and nonweighted UniFrac metrics (p = 0.001). Acetobacter, Lacticaseibacillus, Alloscardovia, Brevibacterium and the family Propicionibactericeae had higher relative abundance in cancer patients, while Prevotella, Microbacterium and Sphingomonas were more abundant in controls. Beta diversity differed between pretreatment and posttreatment samples (p = 0.008). After systemic treatment, we found an increased relative abundance for Prevotella, Rothia, Bradyrhizobium, Methylobacterium/Methylobrum, Porphiromonas and Fusobacterium and a decreased one for the Burkeholderia-Caballeronia-Paraburkholderia group. Higher ASV richness was predictive of poor prognosis for RCC patients (p = 0.043) but not of treatment response.

CONCLUSIONS: Urinary microbiota in patients with renal cell carcinoma differed from controls. Changes in microbiota composition were observed after systemic treatment. Urinary microbiota should be further investigated as a potential biomarker in renal cell carcinoma.}, } @article {pmid42100218, year = {2026}, author = {Hussain, N and Muccee, F and Mirza, AF and Ashraf, NM and Al Haddad, AHI}, title = {Genomic insights into Solea solea gut-borne Enterococcus faecalis for the development of new probiotics in aquaculture.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1778532}, pmid = {42100218}, issn = {2297-1769}, abstract = {Dietary manipulations using probiotics may contribute to the sustainable development of aquaculture. For probiotic applications, their traits, safety profiles, and functional characteristics should be explored. Whole genome sequencing (WGS) can be an informative tool in this regard. We initiated this study to obtain genomic insights into S. solea gut-associated bacteria. Bacteria (n = 20) exhibiting probiotic characteristics were subjected to DNA extraction. A mixture comprising equimolar concentrations of each bacterial DNA was prepared and analyzed through WGS. BV-BRC, metaSPAdes, MetaBAT2, DAS Tool, and PATRIC were used for taxonomic profiling, metagenome assembly, genome binning, comprehensive genome annotation, and subsystem analysis, respectively. For tree construction, MUSCLE and RaxML were employed. Fourteen bins comprising Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota were generated. Among these, the bin comprising the genome of Enterococcus faecium was selected. Its genome comprises 129 contigs with 2,944 coding sequences (CDSs). Genes associated with metabolism, protein processing, stress response, defense and virulence, cellular processes, and cell envelope were identified. Pathways identified included fatty acid and ketone body biosynthesis, glycerolipid and glycerophospholipid metabolism, linoleic acid metabolism, and self-defense mechanisms. This study confirmed the probiotic efficiencies of E. faecium. Hence, this bacterium might be employed as a fish feed supplement in aquaculture.}, } @article {pmid42100351, year = {2026}, author = {Hu, Y and Yan, X and Gao, F and Xu, D and Yang, Y and Cheng, J and Chen, S and Cui, Z}, title = {Probiotic-driven microbiome remodeling is associated with coordinated immune and metabolic responses, improving growth and disease resistance in farmed tongue sole (Cynoglossus semilaevis).}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100600}, pmid = {42100351}, issn = {2666-5174}, abstract = {In flatfish aquaculture, labour-intensive tank cleaning represents a major operational challenge, limiting sustainability due to its high labour requirements and associated costs. We tested a new semi-closed recirculating aquaculture system (RAS) protocol for Cynoglossus semilaevis (tongue sole), replacing manual cleaning with post-feeding water exchange (80% drained) and probiotic application. Compared with control groups, the probiotic-water exchange protocol significantly improved growth (+0.18%/day) and survival (+7.9%), while shifting the gut microbiota from a Vibrio-dominated configuration to a Photobacterium-dominated one. Metagenomics revealed that Photobacterium damselae became the predominant taxon (86%) in the probiotic group, accompanied by the enrichment of quorum sensing pathways, CAZymes (CEs, AAs), and nutrient metabolism functions. Histological examination showed improvements in the intestinal muscular layer and villi structure. Multi-tissue transcriptomics identified systemic changes in immune and metabolic pathways, including activation of intestinal immune networks (IgA production, NF-κB signaling) and antimicrobial peptide genes. Liver, gill, and skin transcriptomes revealed enhanced DNA repair, cytokine signaling, and barrier pathways. JAK-STAT pathway was also activated, linking microbial metabolite sensing to growth promotion (stat5b, igf2bp3). The probiotic-integrated protocol modifies the gut microbiome by shifting microbial composition through changes in competitive interactions and microbial signaling pathways. It also improves the intestinal wall, overall immunity, and nutrient absorption. These findings provide insights into the microbiome-host interaction under probiotic treatment and suggest that this strategy may offer potential benefits under farm conditions, but further studies are needed to validate its safety and ecological implications.}, } @article {pmid42100652, year = {2026}, author = {Luo, J and Feng, Y and Chen, J and Xu, N and Zhang, G and Ni, J and Li, C}, title = {Functional metagenomic reconstruction of microbial pathways altered by probiotic supplementation in liver failure.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1799729}, pmid = {42100652}, issn = {2235-2988}, mesh = {Animals ; *Probiotics/administration & dosage ; Rats, Wistar ; Male ; Metagenomics ; Rats ; Feces/microbiology/chemistry ; Disease Models, Animal ; *Gastrointestinal Microbiome ; *Liver Failure ; Cytokines ; Ammonia/blood ; Dysbiosis ; Galactosamine ; }, abstract = {INTRODUCTION: Liver failure is a severe condition marked by circulatory failure, systemic inflammation, and gut microbial dysbiosis. This dysbiosis worsens liver damage by reducing beneficial metabolites and increasing harmful products. This study investigates the effects of probiotics on gut microbial functional pathways in liver failure. The aim is to link microbial metabolic reprogramming with host biochemical, inflammatory, and gut barrier responses through functional metagenomic reconstruction.

METHODS: Acute liver failure was induced in male Wistar rats using D-galactosamine (700 mg/kg) and lipopolysaccharide (10 μg/kg). Probiotic treatment began 24 hours after induction and was administered daily for 14 consecutive days before euthanasia. Two doses were used: low (1×10⁸ CFU/day) and high (1×10⁹ CFU/day). Fecal samples underwent shotgun metagenomic sequencing, followed by functional pathway reconstruction. These predictions were validated using metabolite profiling, quantitative PCR of microbial genes, intestinal barrier assays, and immune cell cytokine analysis. Host phenotypic markers were correlated with microbial pathways.

RESULTS AND DISCUSSION: Liver failure significantly elevated serum ALT (42.6±6.8 to 512.4±48.9 U/L), AST (78.3±9.5 to 684.7±62.1 U/L), and plasma ammonia (38.9±5.2 to 128.6±14.3 μmol/L). Probiotic supplementation showed a dose-dependent improvement. ALT dropped to 382.7±41.6 U/L (low dose) and 248.9±32.4 U/L (high dose). Ammonia levels decreased to 86.4±9.7 μmol/L and 59.8±7.6 μmol/L, respectively. Metagenomic analysis revealed a 1.7- and 2.6-fold increase in short-chain fatty acid (SCFA) biosynthesis pathways and a 38% and 61% decrease in urease-associated nitrogen metabolism. These changes were confirmed by higher fecal SCFAs (31.8±4.2 to 63.9±6.4 mM), lower ammonia (8.9±1.1 to 3.7±0.5 mM), improved intestinal barrier integrity (TEER: 462±38 to 721±44 Ω·cm²), and reduced TNF-α (214.6±22.8 to 74.9±12.3 pg/mL). Probiotic supplementation significantly reprogrammed the gut microbiome in liver failure. This highlights its potential as a therapeutic modulator of the gut-liver axis.}, } @article {pmid42100656, year = {2026}, author = {Li, T and Liu, J and Wang, X}, title = {Diagnostic performance and clinical utility of metagenomic next-generation sequencing in suspected pulmonary infections: a comparative study stratified by immune status.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1812778}, pmid = {42100656}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Adult ; *Respiratory Tract Infections/diagnosis/microbiology/immunology ; Sensitivity and Specificity ; Bacteria/genetics/isolation & purification/classification ; Fungi/genetics/isolation & purification/classification ; Aged, 80 and over ; Molecular Diagnostic Techniques/methods ; }, abstract = {BACKGROUND: Pulmonary infections represent a significant global health concern, contributing substantially to morbidity and mortality worldwide. Metagenomic next-generation sequencing (mNGS) represents an advanced, comprehensive, and unbiased diagnostic approach for pathogen identification, effectively overcoming many limitations inherent in conventional diagnostic methods. This study aimed to systematically evaluate the clinical performance of mNGS in the etiological diagnosis of pulmonary infections, with a particular emphasis on its utility across diverse immune statuses.

METHODS: This retrospective study included 136 patients with suspected pulmonary infections admitted to the Department of Respiratory Medicine at Shandong Provincial Hospital from June 2023 to April 2025. Bronchoalveolar lavage fluid (BALF) samples were collected from all patients and concurrently subjected to mNGS and conventional microbiological testing (CMT). The pathogen detection spectrum and diagnostic performance of mNGS were systematically compared against those of CMT.

RESULTS: mNGS exhibited a significantly higher overall pathogen detection rate compared to CMT (77.2% vs. 50.0%, P < 0.001). Regarding the pathogen spectrum, mNGS identified a broader array of microorganisms, encompassing 19 bacterial, 9 fungal, and 2 mycobacterial species, in contrast to the 11 bacterial, 5 fungal, and 1 mycobacterial species detected by CMT. Diagnostic performance analysis further revealed that mNGS sensitivity was significantly superior to that of CMT (74.6% vs. 46.7%, P < 0.001). Furthermore, mNGS demonstrated a distinct advantage in detecting mixed infections, with a detection rate of 19.1%, significantly exceeding that of CMT (8.8%, P < 0.05). Subgroup analysis indicated a significantly higher incidence of mixed infections in immunocompromised patients compared to immunocompetent patients (35.1% vs. 13.1%, P < 0.05). Additionally, immunocompromised patients were more frequently subjected to adjustments in antimicrobial therapy guided by mNGS results (56.8% vs. 35.4%, χ² = 5.094, P < 0.05).

CONCLUSIONS: In conclusion, mNGS offers superior sensitivity and broader pathogen coverage for the etiological diagnosis of pulmonary infections compared to conventional microbiological testing. Its enhanced capability to detect mixed infections significantly improves diagnostic accuracy in immunocompromised patients and effectively facilitates the dynamic optimization of antimicrobial therapy. Serving as a powerful complement to traditional diagnostic methods, mNGS holds particular value for the rapid diagnosis of complex and immunosuppression-associated pulmonary infections.}, } @article {pmid42100705, year = {2026}, author = {Li, J and Liu, M and Yang, C and Fan, Z and Su, J and Hu, Y and Yang, Y and Li, J and Pu, Y and Ma, E and Deng, X and Sun, J}, title = {Preceding crops may reduce denitrification potential and enhance ammonium assimilation pathways.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1808894}, pmid = {42100705}, issn = {1664-302X}, abstract = {BACKGROUND: Soil microorganisms are pivotal to nitrogen (N) cycling in croplands, yet how preceding crops modulate their functional profiles remains unclear.

OBJECTIVE: This field study aimed to quantify the effects of barley (BT) and rapeseed (RT) preceding crops (vs. no preceding crop, CK) on soil microbial functions and N-metabolic pathways in tobacco fields.

RESULTS: High-throughput metagenomics revealed that BT and RT significantly increased soil microbial richness (Chao1 index) compared to CK. At the genus level, CK contained 64% and 24% fewer unique taxa than BT and RT, respectively. While the top five KEGG functional pathways (e.g., Metabolic pathways, Biosynthesis of secondary metabolites) were conserved across treatments, their relative abundances differed. Critically, preceding crops reduced soil denitrification rates and increased glutamine dehydrogenase activity. Redundancy analysis confirmed that ammonium-N concentration was the key edaphic factor strongly correlated with microbial community structure and function (P < 0.01).

CONCLUSION: Our findings demonstrate that barley and rapeseed preceding crops enhance microbial richness and activity, thereby inhibiting denitrification and promoting N fixation via altered ammonium-N dynamics.}, } @article {pmid42100978, year = {2026}, author = {Ranade, AV and Hegde, PS and Agni, MB and Rai, P and Upadhyay, SS and Aravind, A and Keshava Prasad, TS and Gowda, KMD}, title = {Cardiometabolomic signatures and gut microbiota dynamics in perinatally undernourished F1 offspring: Decoding the metabolic footprint.}, journal = {Journal of biosciences}, volume = {51}, number = {}, pages = {}, pmid = {42100978}, issn = {0973-7138}, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; Female ; Rats ; Pregnancy ; Rats, Wistar ; *Malnutrition/metabolism/microbiology ; Docosahexaenoic Acids/administration & dosage/pharmacology ; Metabolome ; Fetal Development ; Male ; Metabolomics ; Maternal Nutritional Physiological Phenomena ; Dietary Supplements ; *Prenatal Exposure Delayed Effects/metabolism ; Xanthophylls ; }, abstract = {The Developmental Origins of Health and Disease (DOHaD) hypothesis asserts that detrimental prenatal conditions, such as dietary deficiencies, may lead to enduring health consequences. Perinatal undernutrition, an important concern during fetal development, may affect growth and metabolic programming, resulting in lasting health implications. Maternal nutrition is crucial in modulating fetal endocrine systems and metabolic functions, influencing the development, blood circulation, and nutrient absorption. The present study examines the impact of perinatal undernutrition on the composition of gut microbiota and metabolite levels in offspring of undernourished dams, using an Albino Wistar rat model. Furthermore, we investigated the combined impact of astaxanthin (AsX) and docosahexaenoic acid (DHA) supplementation on cardiometabolic outcomes in these progenies. Astaxanthin, a powerful antioxidant, and DHA, an omega-3 fatty acid, have shown the ability to favorably alter the gut flora and metabolic pathways. The direct influence of AsX on gut microbiota remains unexplored, whereas DHA's role in fostering beneficial microbes and regulating metabolite production is well documented. The current study used metabolomics and metagenomics to investigate the intricate relationship between metabolites and gut microbiota in health and disease, offering insights into fetal programming and possible strategies to improve offspring health. The results highlight the need to address perinatal undernutrition and enhance gut health through targeted dietary interventions to improve long-term health outcomes.}, } @article {pmid42100992, year = {2026}, author = {Xu, X and Chen, D and Luo, N and Zhang, W and Lou, L}, title = {Metagenomic next-generation sequencing for pathology-suspected fungal infections at rare anatomical sites: a case series.}, journal = {Future science OA}, volume = {12}, number = {1}, pages = {2669032}, pmid = {42100992}, issn = {2056-5623}, abstract = {OBJECTIVE: Histopathology for suspected fungal infections lacks species-level identification and is prone to morphological mimics. The utility of metagenomic next-generation sequencing (mNGS) at rare anatomical sites is underexplored.

METHODS: We retrospectively analyzed 10 cases with histopathology suggestive of fungal infection at rare sites (brain, cardiac valve, bone, etc.). All underwent mNGS testing on formalin-fixed paraffin-embedded samples.

RESULTS: mNGS detected fungal DNA in 8/10 cases (80%), providing species-level identification (e.g., Cryptococcus, Candida, Fusarium, Rhizopus, Histoplasma). Polymicrobial infections were identified in 70%. mNGS corrected two misdiagnoses: one confirmed neurocysticercosis; another revealed only bacteria in a suspected fungal lesion. Antimicrobial resistance genes (ErmB) were identified in two cases.

CONCLUSION: mNGS enhances diagnostic precision at rare sites by enabling species identification, uncovering polymicrobial infections, and correcting morphological misdiagnoses, supporting targeted therapy.}, } @article {pmid42101034, year = {2026}, author = {Walker, JR and Bachand, PT and Turner, JW and Labonté, JM}, title = {Viral Assemblages of a Hypersaline Estuary Show Divergent Responses to Freshwater and Temperature Disturbances.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70354}, pmid = {42101034}, issn = {1758-2229}, support = {NA19NOS4190106//Texas General Land Office/ ; }, mesh = {*Estuaries ; *Fresh Water/chemistry/microbiology/virology ; Salinity ; *Viruses/genetics/classification/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; Temperature ; Metagenomics ; Ecosystem ; }, abstract = {Hypersaline environments harbor extremely dense bacterial and viral populations unique from other aquatic ecosystems. Changes to the hydrologic cycle and anthropogenic disturbances have the potential to alter these poorly described communities. Here, we aimed to assess the variation within the viral and bacterial communities of one of the world's largest hypersaline estuaries over 13 months. Using metagenomics, we identified viruses associated with two different salinity regimes, and we showed how viruses responded to pulse disturbances including freshwater inundation and freeze events. We identified 17, 324 viral species, of which 12,132 were found in only one of the salinity regimes. Our results demonstrate a potential association between freshwater pulses throughout June 2021 and shifts in viral community composition. Freeze events showed a greater propensity to alter the auxiliary metabolic genes (AMGs), or genes carried by viruses to alter host metabolism during infection. Viruses associated with low temperatures led to higher incidences of AMGs associated with sulfur cycling and oxidative phosphorylation as opposed to photosynthesis with freshwater inundation and no extreme weather. The contrasting responses to different pulse disturbances make evident the need to better understand how different types of disturbances alter viral communities and their potential to modulate important biogeochemical cycles.}, } @article {pmid42101202, year = {2026}, author = {Yashar, M and Thigale, UY and Karakus, S}, title = {Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment.}, journal = {Current opinion in ophthalmology}, volume = {37}, number = {4}, pages = {299-307}, doi = {10.1097/ICU.0000000000001228}, pmid = {42101202}, issn = {1531-7021}, mesh = {Humans ; *Microbiota/physiology ; *Eye Infections, Bacterial/microbiology ; }, abstract = {PURPOSE OF REVIEW: Growing use of sequencing technologies has accelerated investigation of the ocular surface microbiome, yet this environment is characterized by extremely low microbial biomass, complicating data interpretation. This review assesses current evidence linking microbial communities to ocular surface disease, discusses methodological and biological factors influencing interpretation of microbiome-disease associations, and proposes a framework in which microbial roles may be considered as drivers, modifiers, or markers.

RECENT FINDINGS: Studies across multiple ocular surface diseases report alterations in microbial composition, including reduced α-diversity and shifts in dominant taxa. Genera such as Staphylococcus , Corynebacterium , and Cutibacterium are frequently reported as resident members of the ocular surface microbiome, although their abundance varies across individuals and sampling sites. Across diseases, microbial patterns often overlap and remain inconsistent between studies. Emerging mechanistic evidence has identified specific microbial products, such as lipoteichoic acid, that promote ocular surface inflammation through defined signaling pathways, providing initial support for a potential driver or modifier role. In low-biomass environments such as the ocular surface, contamination, host DNA predominance, and methodological variability can strongly influence detected microbial signals.

SUMMARY: Interpretation of ocular surface microbiome data remains inherently challenging in this low-biomass context. However, the emergence of mechanistic studies suggests a transition from purely associative observations toward functional and translational investigation. Future studies should be designed to better define microbial roles by integrating standardized methodologies with multiomics approaches and detailed clinical phenotyping. Until such evidence emerges, microbiome research is best viewed as advancing biological insight rather than informing clinical decision-making.}, } @article {pmid42101460, year = {2026}, author = {Colmant, AMG and Parry, RH and Charrel, R and Coutard, B}, title = {Benchmarks for taxonomic classification of jingmenviruses and closely related viruses using newly identified genomic sequences.}, journal = {The Journal of general virology}, volume = {107}, number = {5}, pages = {}, pmid = {42101460}, issn = {1465-2099}, mesh = {*Genome, Viral ; Phylogeny ; *Flaviviridae/classification/genetics/isolation & purification ; Genomics ; Metagenomics ; }, abstract = {Jingmenviruses are a group of viruses related to orthoflaviviruses characterized by a segmented genome and multipartite organization that have been detected worldwide in a wide range of hosts. With the growing number of new jingmenvirus sequences identified in metagenomics data, it can be difficult to assess whether a new sequence is associated with a new virus species or with a strain of an existing species. The ICTV is about to ratify the reclassification of the Flaviviridae family, recognizing segmented viruses previously designated jingmenviruses as part of that family and proposing two genera to classify them: Jingmenvirus and Guaicovirus. These proposals do not include clear criteria to classify jingmenviruses and related sequences into species or genera. In order to determine such criteria, we generated a large sequence database from published and newly assembled sequences. Indeed, we screened public raw sequencing data from studies that did not search for or report jingmenvirus or related sequences, looking for new strains of previously described viruses. We then performed multiple sequence alignments and used the inferred percentage identity values to determine demarcation criteria based on the distribution of evolutionary distances upon pairwise comparisons. We report the identification of almost 60 libraries containing jingmenvirus and related sequences, in a wide range of sample types and geographical locations. Using these data and published sequences, we have determined that to be classified as a virus species, at least four segments are required, on which eight cut-off values in percentage identity (nucleotide and amino acid) are used for demarcation. The use of these criteria would enhance consistency in jingmenvirus taxonomy and provide a standardized framework for comparative genomics studies of these viruses, as they are still under-characterized.}, } @article {pmid42101522, year = {2026}, author = {Yuan, C and Zhang, T and Huo, J and Liang, W and Wang, L}, title = {Comparative analysis of next-generation versus third-generation sequencing for pathogen detection in clinical samples: a diagnostic accuracy study.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42101522}, issn = {1573-0972}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Prospective Studies ; *Communicable Diseases/diagnosis/microbiology ; *Bacteria/genetics/isolation & purification/classification ; Viruses/genetics/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Fungi/genetics/isolation & purification ; *Molecular Diagnostic Techniques/methods ; }, abstract = {BACKGROUND: The rapid and accurate identification of pathogens is crucial for clinical management of infectious diseases. While Next-generation sequencing (NGS) has transformed pathogen detection, Third-generation sequencing (TGS) offers advantages in real-time analysis and long-read capabilities. This study comprehensively compares the diagnostic performance of NGS and TGS across diverse clinical samples.

METHODS: We conducted a prospective diagnostic accuracy study involving 105 clinical samples (58 bronchoalveolar lavage fluid, 28 whole blood, 19 other body fluids) from patients with suspected infections. All samples were analyzed using both NGS (BGI platform) and TGS (Nanopore platform). Diagnostic performance was evaluated against a composite reference standard incorporating clinical diagnosis, microbiological culture, and laboratory findings.

RESULTS: NGS demonstrated significantly higher sensitivity compared to TGS (95.9% vs. 82.4%, p < 0.001), while TGS showed superior specificity (87.1% vs. 64.5%, p = 0.012). The overall agreement between platforms was 85.7% (Kappa = 0.702). NGS exhibited particular advantages in viral detection (32 vs. 8 detections, p < 0.001) and fungal identification (28 vs. 18 detections, p = 0.023), whereas both technologies showed comparable bacterial detection capabilities. The area under the ROC curve was 0.92 for NGS and 0.85 for TGS. Turnaround time was significantly shorter for TGS (median 8 h vs. 30 h, p < 0.001).

CONCLUSION: NGS and TGS demonstrate complementary strengths in clinical pathogen detection. NGS offers superior sensitivity and enhanced detection of viral and fungal pathogens, making it suitable for comprehensive diagnostic evaluation. TGS provides rapid results with higher specificity, advantageous for time-critical clinical decisions. A combined or scenario-specific approach may optimize pathogen detection in clinical practice.}, } @article {pmid42101699, year = {2026}, author = {Bharsakale, RD and Gubyad, MG and Jagannadham, PTK and Kokane, SB and Warghane, AJ and Kokane, AD and Ghosh, DK}, title = {Draft genome sequence CR-NGP1 strain of 'Candidatus Liberibacter asiaticus' (CLas) from the host Citrus reticulata (Nagpur mandarin) from Central India.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42101699}, issn = {1573-0972}, support = {Grant No. F.No. 16-11/PP/ICAR-CRP/25-26//ICAR- Consortium Research Platform on Vaccine and Diagnostics/ ; }, mesh = {*Citrus/microbiology ; India ; *Genome, Bacterial ; *Plant Diseases/microbiology ; *Rhizobiaceae/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Whole Genome Sequencing ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Base Composition ; Liberibacter ; }, abstract = {Huanglongbing (HLB, 'Candidatus Liberibacter asiaticus') is one of the most devastating pathogens in citrus domain. Here, we present the nearly complete genome sequence of a CR-NGP1 strain obtained a from symptomatic Nagpur Mandarin (Citrus reticulata) tree in the Nagpur region of Central India. High-throughput sequencing on the Illumina NovaSeq 6000 platform generated ~ 85.7 million paired-end reads, 63.5 million paired-end reads and 14.8 million paired-end reads for sample CLas_001, CLas_002 and CLas_003 each with 150 bp read length, respectively. Two assembly strategies were used: (i) reference-based assembly with SPAdes produced a draft genome of ~ 1.19 Mb with assembly comprised 149 contigs, with an N50 of 14,173 bp, longest contig of 39,711 bp, and an overall GC content of 36.27%. (ii) KBase CONCOCT binning v1.1 applied to all 3 samples produced a nearly complete CR-NGP1 genome of ~ 1,156,009 bases with assembly of 93 contig, with an N50 of 17,668 bp, a longest contig of 39,711 bp, and an overall GC content of 36.4%. This resource of a CLas genome from Central India provides important insights to understand genetic diversity of CLas strains and will facilitate comparative genomics and epidemiological studies of Huanglongbing.}, } @article {pmid42101805, year = {2026}, author = {Li, Q and Yang, X and Zhu, H and Yang, S and Yin, G}, title = {A rare case of long-standing lupus vulgaris with psoriasiform manifestations diagnosed by mNGS: a case report.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42101805}, issn = {1435-4373}, abstract = {This report describes a rare case of lupus vulgaris mimicking psoriasis, undiagnosed for over 40 years. Conventional diagnostics, including histopathology and mycobacterial culture, failed to yield a definitive diagnosis. Ultimately, metagenomic next-generation sequencing (mNGS) of the skin tissue detected the Mycobacterium tuberculosis complex, confirming the infection. The patient showed marked clinical improvement following two months of dual-drug anti-tuberculosis therapy. This case highlights the clinical utility of mNGS for diagnosing atypical, long-standing cutaneous tuberculosis when conventional methods are negative, thereby preventing prolonged misdiagnosis and ensuring timely treatment.}, } @article {pmid42102564, year = {2026}, author = {Long, Z and Zhang, B and Bing, H and Wu, Y}, title = {Identifying microbial candidates for assisted phytoremediation through long-term microbial succession and functional gene shifts across a 50-year chronosequence of vanadium-titanium magnetite tailings.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142304}, doi = {10.1016/j.jhazmat.2026.142304}, pmid = {42102564}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; *Vanadium/metabolism ; *Soil Microbiology ; *Titanium ; *Soil Pollutants/metabolism ; Mining ; *Bacteria/genetics/metabolism ; *Microbiota ; }, abstract = {Soil microorganisms are central to vegetation restoration in metalliferous wastes. However, within mine tailings restoration chronosequences, particularly those enriched with vanadium (V), the long-term successional dynamics of microbial communities, their functional potentials, and the functional partitioning between key microbial taxa and lower-abundance microbial lineages remain poorly understood. Here, we utilized metagenomic sequencing across a 50-year restoration chronosequence to investigate changes in the microbial community and functional genes related to plant growth-promotion (phosphorus, nitrogen, and iron acquisition) and V tolerance/bioreduction. The results demonstrated significant shifts in the microbial community after five years of restoration. At the phylum level, Actinobacteria, Acidobacteria, Pseudomonadota, and Gemmatimonadota were dominant. In early stages (< 15 years), nitrogen and phosphorus acquisition genes (e.g., nif, fix, phoD) were 1.3-2.5 times more prevalent than in later stages, whereas functional genes associated with V (e.g., napA, narG, nirS) increased 1.5- to 2-fold over time. Vanadium and nitrogen were the primary environmental factors regulating both community structure and the relative abundance of critical functional genes. Keystone taxa possessed more nitrogen and phosphorus acquisition genes (65% and 45%, respectively), while metagenome-assembled genomes (MAGs) were enriched in genes related to siderophore biosynthesis (71%) and denitrification (potential V bioreduction) (65%). Based on functional gene profiles, Bradyrhizobium, Allosphingosinicella, Baekduia, Sphingomicrobium, and Hylemonella were identified as promising microbial candidates for enhancing restoration in V-contaminated sites. This study enables the development of targeted microbial consortia to mitigate nutrient deficiency and V toxicity, directly informing the design of more efficient, stage-specific phytoremediation strategies in V-rich tailings.}, } @article {pmid42102590, year = {2026}, author = {Feng, R and Wang, X and Zhang, X and Li, L and Gao, X and Li, J and Kang, J and Yu, X and Jia, S and Zheng, G and Shi, P}, title = {Hidden antibiotic resistance risks and key drivers during tertiary wastewater treatment deciphered by an integrated metagenomic framework.}, journal = {Environment international}, volume = {212}, number = {}, pages = {110281}, doi = {10.1016/j.envint.2026.110281}, pmid = {42102590}, issn = {1873-6750}, mesh = {*Wastewater/microbiology ; *Drug Resistance, Microbial/genetics ; Metagenomics ; *Waste Disposal, Fluid/methods ; Genes, Bacterial ; Bacteria/genetics ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents ; }, abstract = {Potential high-risk antibiotic resistance genes (ARGs) were considered as higher public health threats in wastewater treatment systems. While tertiary wastewater treatment processes (TWTPs) effectively remove conventional and emerging pollutants, their impact on ARGs with potential higher risk remains unclear. In this study, metagenomic assembly and binning were applied to profile potential-risk ARGs and identify key factors shaping their distribution during TWTPs. Results showed that potential-risk ARGs accounted for 34.32 ± 1.98% to 59.71 ± 1.55% of total ARGs, indicating their widespread persistence. Notably, DB significantly increased the relative abundance of potential-risk ARGs, particularly those conferring resistance to multidrug, bacitracin, and aminoglycoside. In parallel, DB treatment elevated the abundance of mobile genetic elements (MGEs), primarily transposase-related. DB treatment facilitated the co-occurrence of potential-risk ARGs and MGEs, especially multidrug and transposase/recombinase. Key bacterial hosts carrying potential-risk ARGs, such as Pseudomonas and Acinetobacter, were highly enriched after DB treatment, contributing substantially to the proliferation of these ARGs. In contrast, UV disinfection and CW treatment continuously reduced the abundance and risk levels of potential-risk ARGs, highlighting their complementary roles in mitigating antibiotic resistance risks during TWTPs. Variation partitioning analysis showed that bacterial community composition explained 36.15% of the variation in potential-risk ARG profiles, underscoring its primary role in ARG dynamics. Overall, this study provides genome-resolved insights into the hidden risks of ARGs and key drivers during TWTPs, highlights the necessity of optimizing operational parameters to mitigate antibiotic resistance dissemination.}, } @article {pmid42102689, year = {2026}, author = {Wang, W and Jiang, H and Liang, C and Yang, Y and She, D and Cheng, G and Wang, H}, title = {Soil functional carbon fraction accrual in temperate forests is linked to understory herbs, soil nutrients and microbial alterations.}, journal = {Journal of environmental management}, volume = {407}, number = {}, pages = {129886}, doi = {10.1016/j.jenvman.2026.129886}, pmid = {42102689}, issn = {1095-8630}, mesh = {*Forests ; *Soil/chemistry ; *Carbon ; Nitrogen ; *Soil Microbiology ; China ; Trees ; }, abstract = {Enhancing stable soil organic carbon (SOC) storage is vital for climate change mitigation. This study challenges the tree-centric paradigm in forest carbon management by investigating the relative roles of trees and understory herbs in driving SOC sequestration in temperate forests of Northeast China. Analyzing 720 soil samples from a 7.2 ha experimental forest, we measured oxidizable SOC fractions and tested the hypothesis that the understory herb layer is a primary driver of SOC accrual, mediated by soil properties and microbial communities. Results strongly supported our hypotheses. Plots with dense, tall herbs exhibited significantly higher levels of active and passive carbon fractions (increases of 7%-16%, amplified to 21%-45% when accounting for soil nutrients, physiochemistry, and water-holding capacity), whereas tree size showed no significant effect. Soil nitrogen was the strongest predictor of SOC variation. Herbs intensified the positive SOC-nitrogen relationship and were positively associated with beneficial soil conditions (e.g., near-neutral pH), contrary to the weak or negative correlations observed for trees. Structural equation modeling revealed that herbs exerted significant direct and indirect positive effects on carbon fractions, while the effects of trees were nonsignificant. Metagenomic analysis identified two contrasting microbial phyla groups: "positive-SOC" phyla (e.g., Thaumarchaeota, Planctomycetes) associated with herbs and high SOC, and "negative-SOC" phyla (e.g., Chloroflexi, Gemmatimonadetes). These findings underscore the critical, underappreciated role of the understory herb layer in SOC sequestration, mediated through soil nutrient enhancement, soil acidity, water retention, and shifts in microbial communities. Forest management strategies aiming to maximize carbon storage should prioritize herb layer conservation alongside tree layer considerations.}, } @article {pmid42102934, year = {2026}, author = {Chen, Y and Li, Y and Cheng, S and Ma, Y and Zhang, Y and Zhang, W and Xu, X and Liu, Z and Duan, X and Duan, H and Zhou, A and Li, X and Makinia, J}, title = {Brief aerobic pretreatment for stabilizing long-term caproate production from food waste via fungi-bacteria chain-elongating consortia.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134810}, doi = {10.1016/j.biortech.2026.134810}, pmid = {42102934}, issn = {1873-2976}, mesh = {Aerobiosis ; *Bacteria/metabolism ; *Fungi/metabolism ; *Food ; *Microbial Consortia ; *Waste Products/analysis ; Carboxylic Acids/metabolism ; Bioreactors/microbiology ; Food Loss and Waste ; }, abstract = {Recovery of medium-chain carboxylic acids (MCCA) from food waste is constrained by low efficiency and instability. This study validated a short-term aerobic pretreatment (AP) strategy to enhance fungi-bacteria synergy. In batch tests, AP (0.2 vvm) achieved optimal caproate titers of 22.32 ± 1.56 g COD/L. The pretreatment enriched ethanol-producing yeasts and lactate-producing bacteria, establishing a robust co-electron donor pool. Metagenomic analysis revealed that this synergy suppressed the competing tricarboxylic acid cycle, redirecting carbon flux towards reverse β-oxidation (RBO) pathway and providing essential precursors for Clostridium_sensu_stricto_12. In a 134-day semi-continuous operation, AP sustained high titers (17.2-22.1 g COD/L) through a specialized guild dominated by the Ruminococcaceae bacterium BL-6, avoiding the systemic performance deterioration observed in controls. Life cycle assessment (LCA) confirmed a >60% carbon footprint reduction compared to conventional routes. Short-term aerobic pretreatment effectively regulates microbial succession to stabilize low-carbon MCCA production from food waste.}, } @article {pmid42102935, year = {2026}, author = {Li, J and Wu, Y and Li, X and Gao, R and Chen, X and Zhang, S and Zhang, J and Zhang, L and Zhang, S and Peng, Y}, title = {Partial Denitrification-Mediated anammox Evolution in anoxic Compartments: Deciphering metabolic activity and microbial community.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134812}, doi = {10.1016/j.biortech.2026.134812}, pmid = {42102935}, issn = {1873-2976}, mesh = {*Denitrification ; Bioreactors/microbiology ; Biofilms ; Wastewater/microbiology ; Nitrogen/isolation & purification/metabolism ; Anaerobiosis ; *Ammonium Compounds/metabolism ; Oxidation-Reduction ; Water Purification/methods ; Bacteria/metabolism ; Nitrates/metabolism ; }, abstract = {The integration of partial denitrification (PD, NO3[-]→NO2[-]) with anaerobic ammonium oxidation (Anammox) in anoxic biofilm systems presents a transformative approach for enhanced nitrogen removal from municipal wastewater. Through a 7-month comparative analysis of spatially stratified anoxic zones in an anaerobic-anoxic-oxic bioreactor treating real wastewater (NH4[+]: 47.6 ± 4.7 mg N/L; COD: 154.8 ± 29.6 mg/L), this study achieved 71.8 ± 5.8% total nitrogen removal (effluent TN: 12.9 ± 3.9 mg N/L), aiming to propose optimization frameworks targeting biofilm carrier deployment in the anoxic zone. Test results showed that functional dominance partitioning emerged as a key determinant: the first anoxic zone (A1) exhibited peak anammox activity (0.034 kg N/m[3]/d) via rapid acetate-driven nitrate reduction, while the third zone (A3) sustained maximum Ca. Brocadia abundance (1.7%). Metagenomic sequencing further revealed that the highest ratio of NO3[-] reductase gene (narG) to NO2[-] reductase genes (nirS, nirK) was 2.06 in A3 compared to 1.39-1.68 in the other biofilms, indicating a stronger ability to supply NO2[-] to anammox. Carbon metabolic gene distribution revealed A1's acetate/glucose preference versus A3's endogenous metabolism dominance (elevated TCA cycle genes). This study proposes an innovative biofilm management framework for energy-efficient municipal wastewater treatment: front-positioned carriers maximize anammox nitrogen removal under moderate carbon-to-nitrogen ratios (3-5), while rear-positioned units secure anammox biomass retention during carbon surges.}, } @article {pmid42102938, year = {2026}, author = {Wu, Y and Yang, X and Deng, Y and Zhao, S and Wang, D and Zhang, W}, title = {Performance of microbial deodorization on anaerobically digested biosolids and odor rebound under rewetting conditions.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134809}, doi = {10.1016/j.biortech.2026.134809}, pmid = {42102938}, issn = {1873-2976}, mesh = {*Odorants/analysis ; Anaerobiosis ; *Sewage/microbiology ; Ammonia ; Bacteria/metabolism/genetics ; Volatile Organic Compounds/analysis ; Nitrogen ; }, abstract = {Odor control is a critical bottleneck in the quality upgrade of anaerobically digested biosolids for land application. The efficacy of microbial deodorization on biosolids has been scarcely evaluated and the mechanisms behind remain unclear. This study applied a sensory-instrumental combined analysis approach to evaluate the deodorization efficiency of two microbial agents on biosolids and odor recurrence upon rewetting. Results show that treatment with microbial agent could reduce the odor intensity and mitigate ammonia emission, yet it failed to completely eliminate the odor. The volatile profile of biosolids is complex, including various N-, S-, O-containing organic and inorganic compounds that collectively contribute to the malodor of biosolids. Rewetting of biosolids induced a rapid odor rebound to varying degrees depending on the maturity of biosolids. Deodorization treatment enhanced the solubility, transformation of biosolids organic matter and increased the humic-like characteristics of WEOM and reshaped the bacterial community showing enrichment of functional taxa (e.g., Actinobacteriota and Chloroflexi). Metagenomic analysis revealed that the key nitrogen-cycling genes (ureC, narG) were suppressed, thereby limiting the generation of NH3 and other related odorants. These findings elucidate a mechanistic linkage between microbial dynamics and the odor generation potential of biosolids, and highlight the critical role of moisture management in governing odor generation and post-deodorization biological stability of biosolids.}, } @article {pmid42102997, year = {2026}, author = {Li, Y and Yu, T and Li, Z and Peng, J and Jiang, Y and Wang, Q and Xie, S}, title = {From high-to low-risk resistomes: Dynamic shifts in antibiotic resistance during biofilm development in a full-scale biological activated carbon fluidized bed.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {400}, number = {}, pages = {128291}, doi = {10.1016/j.envpol.2026.128291}, pmid = {42102997}, issn = {1873-6424}, mesh = {*Biofilms/growth & development ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; Bioreactors/microbiology ; Drinking Water/microbiology ; Charcoal ; Water Purification/methods ; }, abstract = {Antibiotic resistance genes (ARGs) in drinking water bioreactor biofilms pose significant public health risks, yet existing studies focus on mature biological activated carbon (BAC) biofilms, overlooking the early colonization stage critical for ARG origin and dissemination. This gap hinders understanding of ARG dynamics and resistance mechanisms during drinking water BAC biofilm development. Using metagenomics, we first systematically investigated ARG risk dynamics in a full-scale biological activated carbon fluidized bed (BACFB)-a state-of-the-art drinking water technology-across operational days 7-187. Microbial communities and ARG profiles clustered distinctively into early (days 7-37) and late (days 82-187) stages. Upon biofilm stabilization, total ARG abundance significantly decreased (P < 0.05), with high-mobility/high-risk ARGs (sulfonamide-, florfenicol-, aminoglycoside-type) replaced by low-mobility types (rifamycin-, fosfomycin-type). These shifts were correlated with reduced abundance of Pseudomonadota (P < 0.05), increasing trends in the abundance of Bacillota and Actinomycetota (P < 0.1), and decreased abundance of mobile genetic elements, particularly plasmids (P < 0.01). Pathogenic ARGs shifted from aminoglycoside/tetracycline to rifamycin, with Bacillus thuringiensis/Streptococcus pneumoniae (rphB-carrying) as key late-stage risks. Rank I/II and emerging ARGs (mcr, tet(X)) also declined. Our findings uncover the dynamics of ARG risks during BAC biofilm development and highlight the underlying ecological drivers, providing a robust scientific basis for targeted risk mitigation in drinking water treatment systems.}, } @article {pmid42103024, year = {2026}, author = {Zhang, T and Li, S and Wu, Y and Leung, J and Jiang, H and Xu, Z and Ng, SC and Kwok, T}, title = {Gut microbial signatures for aging-related sarcopenia and dietary links among community-dwelling old-old adults: A metagenomic study.}, journal = {Experimental gerontology}, volume = {220}, number = {}, pages = {113161}, doi = {10.1016/j.exger.2026.113161}, pmid = {42103024}, issn = {1873-6815}, mesh = {*Sarcopenia/microbiology/epidemiology ; Humans ; Female ; Male ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; *Aging/physiology ; Aged, 80 and over ; *Diet ; Metagenomics ; Longitudinal Studies ; Independent Living ; }, abstract = {BACKGROUND AND OBJECTIVES: Sarcopenia, characterized by progressive loss of muscle mass, strength and function, poses a major aging-related health challenge. While a gut-muscle axis is implicated, microbiota-sarcopenia associations in the old-old (≥80 years) remain unexplored.

METHODS: This cross-sectional analysis included 315 community-dwelling adults aged ≥80 years from a longitudinal cohort at the 20-year follow-up timepoint, of whom 180 met the inclusion criteria. Gut microbiota was profiled by shotgun metagenomic sequencing alongside sarcopenia assessment. Microbial taxa associated with sarcopenia were identified using MaAsLin2, and dietary associations were assessed by partial Spearman correlation.

RESULTS: The prevalence of sarcopenia in this old-old cohort (mean age 86.8 ± 4.3 years) was 51.7%. Sarcopenic individuals showed lower nutrition scores, reduced microbial richness and altered β-diversity (all P < 0.05). Multivariable analysis identified six differentially abundant species associated with sarcopenia (FDR < 0.10), including two positively associated (Ruthenibacterium lactatiformans and Catenibacillus scindens), and four negatively associated (Phascolarctobacterium faecium, Pyramidobacter piscolens, Lacrimispora saccharolytica and Limosilactobacillus mucosae). Random forest and LEfSe analysis validated R. lactatiformans and P. faecium as the most discriminative signatures for sarcopenia. After adjusting for obesity, these signatures remained significant (P < 0.05). These alterations were linked to functional dysregulation, including increased purine degradation and reduced biotin biosynthesis potential. R. lactatiformans abundance negatively correlated with dietary maltose intake (P < 0.05).

CONCLUSION: In old-old adults, we identified distinct gut microbiota signatures associated with sarcopenia. R. lactatiformans and P. faecium emerged as candidate features. The dietary-microbiota correlations suggest potential nutrition strategies. These findings provide a basis for exploring microbiota-based approaches in advanced aging.}, } @article {pmid42103277, year = {2026}, author = {Yan, J and Jin, N and Xu, C and Wu, H and Jiang, Q and Liu, H and Yuan, J and Yin, D and Lin, F and Wang, R and Liang, Y and Feng, Y and Lan, Y and Lin, X and Wang, Y and Zhang, N and Dai, L and Li, T and Dong, S and Cheng, L and Sun, X}, title = {Multi-omics landscape and machine learning predictors of acute and chronic coronary syndrome diagnosis in young patients.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.05.015}, pmid = {42103277}, issn = {2090-1224}, abstract = {BACKGROUND: Acute coronary syndrome (ACS) is a leading global cause of death, and its incidence is increasingly rising in young adults, who exhibit distinct clinical characteristics from elderly patients. However, multi-omics studies focusing specifically on young coronary heart disease (CHD) patients remain scarce, hindering precise diagnosis and mechanism exploration.

METHODS: Here, we enrolled 206 young chest pain patients (18-45 years old), including 122 ACS patients, 38 chronic coronary syndrome (CCS) patients, and 46 individuals with healthy coronary arteries (NC). We performed integrated analyses of peripheral blood mononuclear cell transcriptomics, serum metabolomics, stool metabolomics, and gut microbiome metagenomics to characterize CHD subtypes and develop targeted diagnostic tools.

RESULTS: Our results showed that single omics layers had limited ability to distinguish CHD subtypes, while multi-omics integration significantly improved diagnostic efficacy. We identified unique molecular signatures for different subtypes: STEMI was associated with abnormal amino acid and carbohydrate metabolism, CCS was dominated by amino acid metabolism disturbances, and both STEMI and ACS showed enriched inflammation-related pathways. Novel biomarkers including p-chlorobenzene sulfonamide, cotinine, and the gut bacterium Streptococcus parasanguinis were identified, with Streptococcus parasanguinis validated as an atherogenic pathogen in a murine model. We constructed three multi-omics fusion diagnostic models (ACS vs. NACS, CCS vs. NC, STEMI vs. NSTE-ACS) with AUC values of 0.99, 0.95, and 0.96, respectively, and integrated them into a comprehensive diagnostic pipeline. Furthermore, multi-omics functional analysis unraveled a synergistic "microbiota-metabolism-immunity" regulatory network underlying CHD subtypes, linked to disordered amino acid and carbohydrate metabolism and aberrant inflammatory activation.

CONCLUSION: This study provides a systematic molecular landscape of young CHD, a high-precision diagnostic strategy, and novel targets for mechanism research and targeted intervention, addressing the unmet clinical need for precise management of young CHD patients.}, } @article {pmid42103708, year = {2026}, author = {Basler, N and De Smet, L and Bouras, G and Swinnen, J and Pranga, K and Brussaard, CPD and Vandamme, P and de Graaf, DC and Matthijnssens, J}, title = {The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72757-2}, pmid = {42103708}, issn = {2041-1723}, support = {955974//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 817622//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; H2020//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, abstract = {Honey bees (Apis mellifera) contribute to crop production and floral biodiversity via pollination, but their health is increasingly challenged by stressors including pathogens, parasites and agricultural practices. Although the honey bee gut microbiome is relatively simple, its phages are not well studied. Here, we conducted a metagenomic study, providing a comprehensive catalogue of honey bee gut phages from 450 virus-enriched samples from 63 hives, across eight European countries, three seasons and three gut sections. We describe a diverse phageome including many phages that appear to belong to novel taxa, as well as a core set of 97 highly prevalent phages. In addition, we identify potential auxiliary metabolic genes, such as a sulfur metabolism gene carried by phages that are predominantly temperate and likely infect mutualistic honey bee core bacteria. This gene is associated with land use around the sampled hives, indicating complex ecological interactions in the tripartite system of the honey bee, its microbiota and the phages therein.}, } @article {pmid42103726, year = {2026}, author = {Goulet, L and Plaza Oñate, F and Famechon, A and Quinquis, B and Belda, E and Prifti, E and Le Chatelier, E and Gautreau, G}, title = {CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72637-9}, pmid = {42103726}, issn = {2041-1723}, support = {ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {Metagenomic sequencing provides insights into microbial communities, but it can be compromised by technical biases, including cross-sample contamination. This phenomenon arises when microbial content is inadvertently exchanged among concurrently processed samples, distorting microbial profiles and compromising the reliability of metagenomic data and downstream analyses. Existing detection methods rely on negative controls, which are insufficiently used and do not detect cross-contamination within non-control samples. Meanwhile, strain-level bioinformatics approaches do not distinguish contamination from natural strain sharing and lack sensitivity. To fill this gap, we introduce CroCoDeEL, a decision-support tool for detecting and quantifying cross-sample contamination. Leveraging linear modeling and a pre-trained supervised model, CroCoDeEL identifies specific contamination patterns in species abundance profiles. It requires no negative controls or prior knowledge of sample processing positions, offering improved accuracy and versatility. Benchmarks across three public datasets demonstrate that CroCoDeEL can detect contaminated samples and identify their contamination sources, even at low rates (<0.1%), provided sufficient sequencing depth. Application of CroCoDeEL to several existing studies reveals previously undetected contamination.}, } @article {pmid42103925, year = {2026}, author = {Anil, and Ramesh, KB and Gouda, MNR and Subramanian, S}, title = {Microbial zonation and functional roles in the gut of white grub (Maladera insanabilis) larvae.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-52250-y}, pmid = {42103925}, issn = {2045-2322}, abstract = {Maladera insanabilis, a widespread and destructive agricultural pest in India, thrives in nitrogen-deficient subsoil environments due to its dependency on gut bacteria. In particular, the hindgut is an anaerobic fermentation chamber, supporting microbial-driven nitrogen transformations essential for larval development. Despite its ecological significance, detailed studies exploring gut bacterial diversity and functional role in M. insanabilis are lacking. This study integrates metagenomics, culture-based techniques, enzymatic assays, and gene expression analyses to characterize the nitrogen-cycling potential of gut microbiota along the different gut compartments. The culture-based analysis isolated 16 aerobic and 8 anaerobic bacterial strains, predominantly from Bacillota and Pseudomonadota. High-throughput 16 S rRNA Illumina sequencing revealed 134 shared amplicon sequence variants (ASVs), with distinct bacterial assemblages, Burkholderia and Pseudomonas in the foregut, Paenibacillus in the midgut, and anaerobic genera such as Bacteroides and Desulfovibrio dominating the hindgut. Functional annotation using the KEGG database indicated that anaerobic gut bacteria are actively involved in nitrification, denitrification, and nitrogen fixation. The Enzyme assays confirmed high nitrate and nitrite reductase activity, with Burkholderia contaminans and Bacillus cepacia showing the highest activities. Michaelis-Menten kinetics and Lineweaver-Burk analysis (R[2] = 0.9871) showed a higher capacity (Vmax) for nitrate and nitrite reduction; a small Km indicates a high affinity for nitrate and nitrite. Gene expression studies viz., hzo, nifH, amx, nirS, and nirK revealed a significantly high expression level in the hindgut, especially under vermicompost treatment. This study provides the first comprehensive insight into nitrogen-cycling gut bacteria in M. insanabilis, highlighting their role in host nutrition and nitrogen transformation. These findings lay a foundation for future microbiome-targeted pest control strategies aimed at disrupting nutrient acquisition in soil-dwelling grubs.}, } @article {pmid42103932, year = {2026}, author = {Wang, F and Zeng, W and Zhang, Z and Li, N and Cui, Z and Bai, J and Yan, J and Zhang, Y and Miao, Y and Gu, L and Xiong, B}, title = {Gut microbiota-modulated glutamic acid rejuvenates the quality of oocytes deteriorated by advanced reproductive age.}, journal = {EMBO molecular medicine}, volume = {18}, number = {6}, pages = {2404-2435}, pmid = {42103932}, issn = {1757-4684}, support = {2023YFD1300502//MOST | National Key Research and Development Program of China (NKPs)/ ; BYSYSZKF2023029//State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital/ ; KYCX25_1007//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; }, mesh = {Animals ; *Oocytes/physiology/drug effects/metabolism/cytology ; Female ; *Glutamic Acid/metabolism ; *Gastrointestinal Microbiome ; Mice ; Fecal Microbiota Transplantation ; Aging ; Metabolome ; Fertility ; }, abstract = {The gut microbiota plays a vital role in maintaining the physiological function of host health and the pathogenesis of various diseases. However, its relationship with maternal age-associated decline in oocyte quality remains elusive. Here, we report that establishment of gut microbiota from young donors in aged mice by fecal microbiota transplantation (FMT) is an effective method to rejuvenate the quality of maternally aged oocytes. Specifically, young gut microbiota promoted the ovulation and maturation of aged oocytes, and inhibited occurrence of cytoplasm fragmentation and spindle/chromosome abnormalities, hence enhancing the oocyte quality and female fertility. By integrating metagenome and untargeted metabolome of intestinal digesta, as well as targeted metabolome of ovaries and micro-transcriptome of oocytes, we identified that Bacteroides_caecimuris-modulated glutamic acid levels mediated the restorative effects of young gut microbiota on the aged oocytes through strengthening the mitochondria function. In addition, we demonstrated that in vivo supplementation of glutamic acid also enhanced the quality of aged oocytes, and the improvement of oocyte quality by glutamic acid was conserved across species. Altogether, our findings highlight the importance of gut microbiota in the oocyte aging and provide potential improvement strategies for age-related decline in oocyte quality and female fertility.}, } @article {pmid42104156, year = {2026}, author = {Minnaar, LS and Inokuma, K and Hasunuma, T and den Haan, R}, title = {Engineering natural Saccharomyces cerevisiae isolates for enhanced one-step cellulosic ethanol production.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-026-13830-0}, pmid = {42104156}, issn = {1432-0614}, abstract = {Engineering yeast strains for use as chassis organisms in second-generation (2G) bioethanol is a promising strategy to improve process economics. Natural isolates of Saccharomyces cerevisiae offer strain backgrounds with greater genetic diversity and enhanced robustness, with the potential for improved heterologous protein production capabilities. In this study, heterologous cellulase production using different expression strategies was evaluated in various process-relevant conditions. Enhanced cellulolytic activity was clearly demonstrated in a cell-tethered enzyme system, compared to a free enzyme system, across identical strain backgrounds. Superior secretory capacity was obtained for YI59_V2 for all individual enzymes across all process-relevant conditions tested. In addition, this strain exhibited improved hydrolysis efficiency and ethanol production from crystalline cellulose, achieving ~10 g/L after 96 h (~88% of the maximum theoretical yield) without the need for exogenous cellulase supplementation. Interestingly, enhanced strain robustness against process-relevant, secretion, and cell wall stresses was also observed in transformants with cell-tethered cellulase systems compared to those with free enzyme systems. This study highlights that the expression design strategy for cellulase-encoding genes in this natural isolate was pivotal for increasing protein titres and for influencing strain robustness. Strains exhibiting elevated cellulase activity and increased robustness represent a key step toward the industrial deployment of consolidated bioprocessing (CBP). KEY POINTS: • Cell-tethered expression greatly boosted cellulase activity and cellulose breakdown. • YI59_V2 yielded ~ 10 g/L ethanol from crystalline cellulose without added enzymes. • Tethered enzymes reshaped cell walls and altered stress tolerance.}, } @article {pmid42104260, year = {2026}, author = {Nguyen, TT and Steen, IH and Bøe, MH and Otterlei, M and Stokke, R}, title = {Arctic deep-sea hydrothermal microbiomes as a natural niche for novel antimicrobial peptides.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05098-1}, pmid = {42104260}, issn = {1471-2180}, abstract = {BACKGROUND: The escalating threat of antimicrobial resistance (AMR) has created an urgent need for new antimicrobial agents. Antimicrobial peptides (AMPs) are promising alternatives to conventional antibiotics due to their broad-spectrum activity and reduced risk of resistance development. While most AMP discovery efforts have focused on terrestrial microbes, extreme environments remain largely untapped. Deep-sea hydrothermal vent biofilms, such as those from the Arctic Mid-Ocean Ridges (AMOR), are unique ecosystems characterized by high pressure, temperature gradients, and chemical extremes. These conditions select for microorganisms with specialized adaptations, including the production of bioactive compounds that confer survival advantages. Such peptides may exhibit enhanced stability and novel mechanisms of action, making hydrothermal biofilms an exceptional resource for next-generation antimicrobials.

RESULTS: Using metagenomic and metatranscriptomic datasets from nine recently published AMOR biofilms, we predicted 961 AMP sequences with Macrel, of which 873 were unique and showed no identity to entries in the Antimicrobial Peptide Database (APD). AMPs were distributed across 51 microbial phyla, including underrepresented archaeal groups such as Asgardarchaeota, Nanoarchaeota, and Micrarchaeota. Transcriptomic profiling detected AMP expression in 25 phyla, including low-abundance candidate taxa, highlighting active AMP production. In silico minimum inhibitory concentration (MIC) prediction using APEX 1.1 suggested that 16.7% of AMPs may inhibit at least one clinically relevant pathogen, with Acinetobacter baumannii emerging as the most susceptible. Four peptides were synthesized for experimental validation; AMP OLKFNNDA_52_10 exhibited moderate in vitro activity against Staphylococcus aureus and weak activity against Escherichia coli, while showing low cytotoxicity toward human HEK293 cells. Other tested peptides displayed weak or no activity, underscoring discrepancies between computational predictions and biological outcomes.

CONCLUSIONS: Our study reveals extensive taxonomic and structural diversity of AMPs in Arctic hydrothermal vent biofilms and identifies novel candidates withbioactive potential. These findings emphasize the importance of integrating metagenomics, transcriptomics, machine learning, and experimental validation to uncover bioactive compounds from underexplored microbial ecosystems. Overall, AMOR biofilms represent a rich and untapped source of AMPs, offering new opportunities for antimicrobial drug discovery in the fight against AMR.}, } @article {pmid42104558, year = {2026}, author = {Luo, X and Lei, Z and Fang, D and Chen, H and Qian, L and Jin, C and Wang, X and Liu, X and Liu, H and Wang, Y}, title = {Integrated multi-omics decipher the complex nodule microbiota and distinct Frankiaceae symbiotic traits in wild actinorhizal plants.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71234}, pmid = {42104558}, issn = {1469-8137}, support = {32300265//Young Scientists Fund of the National Natural Science Foundation of China/ ; }, abstract = {Actinorhizal plants are ecologically important pioneer species in temperate regions, capable of nitrogen-fixing root nodule symbiosis with Frankiaceae bacteria. Despite their significance within the nitrogen-fixing clades (NFC), multi-omics studies of actinorhizal symbiosis remain scarce. We profiled prokaryotic communities in the rhizosphere, root, and/or nodule compartments from five phylogenetically representative actinorhizal species, three legumes, and four nonnodulated NFC species using 16S rDNA sequencing. Transcriptomic and metagenomic analyses were performed on actinorhizal roots and nodules, respectively. Metagenome-assembled genomes revealed four novel Frankiaceae species. Frankiae relative abundance levels in nodules were generally lower than rhizobia in legumes. Actinorhizal nodules harbour diverse bacterial taxa, which exhibit predominantly positive interactions, with Frankiae forming a tightly interacting subgroup. Actinorhizal plants engage actively with soil microbiota, recruiting a specific rhizosphere community enriched with beneficial microbes, including ammonia-oxidising archaea. Many symbiotic mechanisms in nodulating host plants are conserved and derived from pre-existing molecular modules. Our analysis suggests the phosphoinositide signalling likely functions in actinorhizal symbiotic signal transduction. However, Frankiae exhibit fundamentally different symbiotic functional characteristics compared to rhizobia, reflecting less intimate symbiosis, which might favour the life-history strategies of temperate perennial actinorhizal plants.}, } @article {pmid42104576, year = {2026}, author = {Ii C, JF and Vidal, MJS and Dela Cruz, FSE and Tantengco, OAG and Menon, R}, title = {The Microbiome Signature of the Placenta and its Role in Spontaneous Preterm Birth: A Systematic Review and 16S rRNA Re-Analysis.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {95}, number = {5}, pages = {e70246}, doi = {10.1111/aji.70246}, pmid = {42104576}, issn = {1600-0897}, mesh = {Humans ; Female ; Pregnancy ; *Placenta/microbiology ; *Premature Birth/microbiology/immunology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; }, abstract = {PROBLEM: The advent of high-throughput 16S rRNA sequencing has enabled deeper insights into microbial communities associated with adverse pregnancy outcomes, including spontaneous preterm birth (sPTB). While microbial dysbiosis in the cervicovaginal and oral-gut microbiomes has been implicated in sPTB, the existence of a placental microbiome remains contentious. Traditional paradigms of a "sterile womb" have been challenged by studies suggesting a low-biomass microbial community in the placenta, though recent evidence disputes this claim, attributing findings to contamination or transient microbial DNA signals.

METHOD: This study systematically reviewed placental microbiome studies employing 16S rRNA sequencing and re-analyzed publicly available datasets to determine microbial signatures in term and preterm placentas. Following a comprehensive search of three databases and stringent inclusion criteria, seven studies were included. The risk of bias was assessed using a modified Joanna-Briggs tool, revealing moderate-to-low risk across studies. Methodological heterogeneity, including differences in contamination controls, sequencing regions, and analytical platforms, was a significant limitation.

RESULTS: A re-analysis of sequencing data showed no consistent microbiome signature distinguishing the term from preterm placentas. Beta diversity analysis revealed no group clustering, while alpha diversity indices showed comparable species richness. Bacterial DNA in placental tissues was primarily attributed to contamination from the urogenital tract or laboratory processes.

CONCLUSION: Findings underscore the importance of robust contamination control and standardized protocols in low-biomass microbiome research. Future studies should employ advanced techniques, such as metagenomics and fluorescence in situ hybridization, to evaluate the functional relevance of microbial communities in the placenta, as well as rule out microbial DNA deposited in the placenta through circulating bacterial extracellular vesicles (EVs).}, } @article {pmid42104663, year = {2026}, author = {Yang, KL and Zhai, JN and Ye, JW and Zhang, XN and Wei, QC and Wang, H and Wang, HM and Chu, LL and Yang, J}, title = {Dysbiosis of Gut Archaea is Associated with Obesity and Could be Recovered after Bariatric Surgery.}, journal = {Biomedical and environmental sciences : BES}, volume = {39}, number = {4}, pages = {437-446}, doi = {10.3967/bes2026.019}, pmid = {42104663}, issn = {2214-0190}, mesh = {Humans ; *Bariatric Surgery ; *Gastrointestinal Microbiome ; *Obesity/microbiology/surgery ; Male ; Female ; *Archaea/physiology/genetics/classification ; Adult ; Middle Aged ; *Dysbiosis/microbiology ; }, abstract = {OBJECTIVE: Obesity is closely associated with an altered gut microbiota; however, the role of archaea in obesity remains unknown. We aimed to delineate the alterations in gut archaea in obese subjects and explore the changes in bariatric surgery-associated gut archaeal composition.

METHODS: Metagenomic sequencing data from 191 obese subjects and 184 lean controls were retrieved from three public cohorts. Of these, 23 obese patients who underwent bariatric surgery were followed up for 3 months.

RESULTS: The gut archaea of obese subjects showed significantly lower Shannon diversity index than those of lean controls. Principal component analysis of the gut archaea revealed distinct clusters in obese subjects and lean controls. A model using the 20 top archaeal genera discriminated obese from lean controls with an area under the receiver operating characteristic curve (AUC) of 0.79, 0.83, and 0.86 in three cohorts. Ecological analysis showed decreased trans-kingdom correlations between archaea and bacteria in obese subjects compared to those in lean controls, with partial restoration observed after bariatric surgery.

CONCLUSION: This is the first study to demonstrate that obesity is characterized by gut archaeal dysbiosis across multiple cohorts. Bariatric surgery-induced weight loss is associated with significant changes in the gut archaea.}, } @article {pmid42104937, year = {2026}, author = {Kang, X and Hu, L and Song, J and Zhang, Z and Li, Y and Zhang, Q and Luo, C and Pang, Y and Guo, P and Yue, B and Li, P and Fan, Z}, title = {Snake Gut Microbiota as a Source of Anti-Inflammatory Probiotics: Isolation and Functional Characterization of Two Novel Strains.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.70118}, pmid = {42104937}, issn = {1749-4877}, support = {2023NSFSC1935//Sichuan Science and Technology Program/ ; }, abstract = {The intestinal microbiome is fundamental to host physiological homeostasis, while deviations from its balanced state have been linked to inflammatory bowel diseases (IBD). To address the limitations of conventional antibiotic therapies, this study explored snake gut microbiota as a novel source of anti-inflammatory probiotics. We explored the gut microbiota of five snake species (Deinagkistrodon acutus, Trimerodytes annularis, Trimerodytes percarinatus, Lycodon rufozonatus, and Trimeresurus stejnegeri) through metagenomic sequencing. Community composition analysis revealed that the phylum-level composition was mainly Proteobacteria, Bacteroidetes, Actinomycetota, and Firmicutes. We further detected some potential probiotic species, such as Enterococcus, Lactobacillus, and Limosilactobacillus. From 196 isolated strains, Lactobacillus johnsonii DA0116 and Limosilactobacillus reuteri DA0218 were selected through rigorous safety and functional assessments, including acid/bile tolerance, pathogen inhibition, and adhesion capacity. In a DSS-induced murine colitis model, both strains significantly reduced disease activity index (DAI), pro-inflammatory cytokines (TNF-α, IL-6, and IL-8), and restored gut microbiota diversity. Additionally, whole-genome analysis identified bacteriocin synthesis clusters (gassericin-S/T) and carbohydrate metabolism genes, explaining their antimicrobial and immunomodulatory properties. This study not only emphasizes the untapped latent value of reptilian gut microbiota for probiotic discovery but also provides two candidate strains with therapeutic promise for IBD and functional food applications.}, } @article {pmid42105239, year = {2026}, author = {Minich, JJ}, title = {Protocol for high-throughput processing of fecal samples for long-read metagenomic sequencing using PacBio HiFi or Oxford Nanopore Technologies.}, journal = {STAR protocols}, volume = {7}, number = {2}, pages = {104526}, pmid = {42105239}, issn = {2666-1667}, abstract = {Long-read sequencing, whether using PacBio (PB) or Oxford Nanopore Technologies (ONT), requires high-molecular-weight (HMW) DNA at high purity and free of contaminants. Here, we present a protocol for high-throughput processing of fecal samples for long-read metagenomic sequencing. We describe steps for microbial inactivation, nucleic acid stabilization, and HMW DNA extraction. We then detail procedures for DNA cleanup, shearing, library preparation, and DNA sequencing. For complete details on the use and execution of this protocol, please refer to Minich et al.[1].}, } @article {pmid42105544, year = {2026}, author = {Li, T and Feng, K and Wang, S and Du, X and Li, J and Gu, S and Zhao, B and Yang, X and Peng, X and He, Q and Wang, Y and Wang, D and Wang, J and Wang, Z and Liu, M and Xiao, J and Men, J and Jin, D and Zhang, J and Deng, Y}, title = {Integrating digital PCR and metagenomics to quantify potential soilborne bacterial pathogens in urban ecosystem.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142312}, doi = {10.1016/j.jhazmat.2026.142312}, pmid = {42105544}, issn = {1873-3336}, mesh = {*Soil Microbiology ; Polymerase Chain Reaction/methods ; Ecosystem ; *Metagenomics ; *Bacteria/genetics/isolation & purification ; Humans ; Beijing ; }, abstract = {Understanding the environmental occurrence patterns of soilborne pathogens is essential for public health, yet a comprehensive and accurate assessment remains challenging. This study presents an innovative technical framework integrating metagenomic pathogen screening with quantitative validation using chip-based digital PCR (dPCR) targeting the overall bacteria community as well as three dominant species-Ralstonia pickettii, Saccharomonospora viridis, and Gordonia terrae. This approach enabled a comprehensive quantification of potential human-, plant-, and zoonotic pathogens and elucidation of their environmental drivers across urban soil habitats in Beijing. Farmland and hospital greenspaces exhibited higher potential pathogen richness (15.55 ± 5.87 and 10.70 ± 4.52) and abundance (22,475.52 ± 15,559.92 and 26,217.62 ± 19,299.90 copies g[-1] soil) compared with forests and campus greenspaces. The composition of potential pathogens varied among habitats, with farmlands containing the highest number of unique species, and four taxa were detected across all habitats, showing strong adaptive capacity. Pathogen diversity was positively correlated with total and available phosphorus and with total bacterial α- and β-diversity, while negatively associated with soil organic carbon, reflecting limited pathogen inputs in carbon-rich forest soils and the key role of phosphorus in pathogen enrichment. Climatic and soil physicochemical factors indirectly influenced pathogen diversity by modulating bacterial communities, whereas human activities directly increased pathogen abundance. Molecular ecological network analysis demonstrated that 81% of the associations between pathogenic and non-pathogenic taxa were significantly negative, suggesting competitive exclusion as a key regulatory mechanism. Collectively, these findings provide a precise monitoring framework and new insights into cross-species interactions, contributing to improved risk assessment and One Health strategies for the prevention of soilborne diseases.}, } @article {pmid42105734, year = {2026}, author = {Zhang, J and Zeng, W and Meng, Q and Gong, Q and Lu, Y and Bi, Z and Peng, Y}, title = {Efficient amino acid capture from sludge fermentation by Tetrasphaera enhances simultaneous nitrification, endogenous denitrification and phosphorus removal.}, journal = {Water research}, volume = {301}, number = {}, pages = {126061}, doi = {10.1016/j.watres.2026.126061}, pmid = {42105734}, issn = {1879-2448}, mesh = {*Sewage ; *Phosphorus/metabolism ; Fermentation ; *Amino Acids/metabolism ; Denitrification ; Nitrification ; Nitrogen ; Bioreactors ; Wastewater ; }, abstract = {The simultaneous nitrification endogenous denitrification and phosphorus removal (SNDPR) process shows great potential for carbon, nitrogen, and phosphorus removal. However, its application is challenged by limited carbon availability and the strong reliance of glycogen-accumulating organisms (GAOs) and traditional polyphosphate-accumulating organisms (PAOs) on volatile fatty acids. This study first established a fermentative PAO Tetrasphaera-dominated SNDPR coupled with in-situ sludge fermentation process, achieving stable and efficient nitrogen (95.7 ± 0.6%) and phosphorus (92.6 ± 1.6%) removal using complex organics (e.g., amino acids and proteins) from wastewater and sludge as carbon sources. Extending the anaerobic duration (from 5 h to 17 h) regulated the phosphorus removal and fermentation capacity of Tetrasphaera, promoting its dominance at the genomic (10.89%), transcriptional (6.24%), and translational (24.0%) levels. For phosphorus removal, the denitrifying phosphorus removal (DPR) rate using nitrite increased from 0.98 ± 0.05 mgN/gVSS·h at 5 h to 2.70 ± 0.07 mgN/gVSS·h at 17 h, shifting the system from aerobic phosphorus uptake dominance to a cooperative pattern with DPR, effectively lowering carbon demand. For fermentation, metagenomic analysis revealed that efficient amino acid capture by Tetrasphaera facilitated the retention of substantial sludge hydrolysates for intracellular amino acid storage, improving nutrient removal and mitigating NH4[+]-N and PO4[3-]-P release. Additionally, anammox bacteria (Candidatus Brocadia, 2.67%) self-enriched and synergistically contributed to nitrogen removal. Overall, this study provides new insights into the metabolic shift between fermentation and phosphorus removal in Tetrasphaera, demonstrating the feasibility of stable and efficient carbon, nitrogen and phosphorus removal by the SNDPR process in VFA-limited wastewater.}, } @article {pmid42106331, year = {2026}, author = {Davin, ME and Ortís Sunyer, J and Delgado, LF and Tavis, SL and Lowndes, T and Zafar, Z and Caussin, J and Halder, R and Hickl, O and Laczny, CC and Hanslian, E and Koppold, DA and Rajput-Khokhar, A and Steckhan, N and Schade, S and Schneider, J and Mollenhauer, B and Michalsen, A and May, P and Hettich, RL and Wilmes, P}, title = {High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72762-5}, pmid = {42106331}, issn = {2041-1723}, support = {863664//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Graduate Research Fellowship Program//National Science Foundation (NSF)/ ; }, abstract = {Small open reading frames (smORFs), which encode proteins under 100 amino acids, represent an underexplored dimension of the human gut microbiome, despite growing evidence of their essential biological roles. Due to small size and poor annotation, smORFs are typically excluded from metagenomic/metaproteomic analyses. Here, we present a high-resolution multi-omic workflow that integrates smORF prediction into metaproteome searches and enables ultra-deep detection of smORF-encoded proteins (SEPs), without experimental size-based enrichment, utilizing state-of-the-art mass spectrometry instrumentation. Applied to human gut microbiomes, this approach resulted in the largest number of detected SEPs to date, allowing identification of over 25,000 SEPs in the metaproteome, alongside the measurements of the larger proteins. Our multi-omics integrative strategy is critical for advancing human metaproteome research. It also provides a generalizable strategy for comprehensive SEP discovery across diverse microbial ecosystems greatly expanding the previously hidden proteomic landscape.}, } @article {pmid42106335, year = {2026}, author = {Xue, H and Godneva, A and Tang, F and Li, H and Li, Y and Hu, M and Li, R and Su, J and Segal, E and Razzak, I}, title = {Population-scale characterization of the oral microbiome and associations with metabolic health.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72748-3}, pmid = {42106335}, issn = {2041-1723}, abstract = {The oral microbiome may capture system-specific information about host metabolic health, yet large-scale, multi-system evidence remains scarce. We analyzed 9,431 participants in the Human Phenotype Project (HPP), integrating buccal-swab oral whole metagenome profiles with 44 metabolic measures spanning liver ultrasound, continuous glucose monitoring (CGM), and dual energy X ray absorptiometry (DXA). Here we show that using a microbiome-wide association study (MWAS) framework, we constructed a multilayer map across strains, gene families and pathways, revealing widespread associations: 213 strains, 124,603 gene families and 299 pathways were significantly associated with metabolic measures. Prioritizing the strongest and cross-phenotype signals, we identified multiple oral features with most significant associations to metabolic health. For example, acyl carrier protein (ACP) was associated with lower liver inflammation and reduced adiposity, whereas polyamine biosynthesis and ceramide α oxidation tracked higher glucose variability and adverse liver and adiposity phenotypes. Leveraging these MWAS-derived signals, we trained disease classification models using phenotype-selected oral features, which outperformed full-feature oral models across six metabolic diseases. These association signals were also robust in oral-health sensitivity analyses in HPP, and key BMI and waist-circumference associations directionally replicated at the genus level in an independent cohort (n = 20, 293). Together, these findings provide a population-scale oral-metabolic association map and highlight the potential of oral microbial markers as non-invasive tools for metabolic risk stratification.}, } @article {pmid42106361, year = {2026}, author = {Sun, Y and Wu, S and Wu, Z and Zhu, W and Gao, H and Xing, J and Zhao, J and Fan, X and Su, X}, title = {Instance-based transfer learning enables cross-cohort early detection of colorectal cancer.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01001-y}, pmid = {42106361}, issn = {2055-5008}, support = {2021YFF0704500//National Key Research and Development Program of China/ ; 20251ZDYF020482//Innovation Yongjiang 2035 Key R&D Programme/ ; }, abstract = {Colorectal cancer (CRC) continues to be a major global public health challenge. Extensive research has underscored the critical role of the gut microbiome for diagnostics of CRC. However, early-stage prediction of CRC, particularly at the precancerous adenomas (ADA) stage, remains challenging due to the instability of microbial features across cohorts. In this study, we conducted a systematic analysis of 2053 gut metagenomes from 14 globally-sampled public cohorts and a newly recruited cohort. Despite substantial regional and cohort-level heterogeneity in microbiome composition, we elucidated that the consistent differences between groups in microbial signatures provide the fundamental basis for CRC detection. These patterns enabled robust performance in both inter-cohort and independent validations using an optimized bioinformatics framework. In contrast, such basis was lacking in ADA-associated microbial markers, limiting the generalizability of early detection models. To address this, we developed an instance-based transfer learning approach, Meta-iTL, which effectively leveraged knowledge from existing datasets to detect CRC risk at the ADA stage in the newly recruited cohort. Thus, Meta-iTL overcomes challenges posed by cohort-specific variability and limited data availability and advances the application of non-invasive approaches for the early screening and prevention of CRC.}, } @article {pmid42106412, year = {2026}, author = {Guo, L and Holyoak, GR and DeSilva, U}, title = {Insights from healthy mares reveal that mammalian uteri harbor a diverse virome.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-49532-w}, pmid = {42106412}, issn = {2045-2322}, abstract = {The Earth's estimated 10[31] virions, primarily phages, significantly impact microbial ecosystems. Despite their abundance, viromes remain relatively understudied-particularly in domestic animals. While recent studies have described a dynamic commensal microbiome in mammalian uteri, no research has yet characterized the commensal virome in a mammalian uterus. In this study, we report for the first time the presence of a sparse, but diverse native virome in the equine uterus. The resulting virome database consists of 513 non-redundant viral genomes (> 2 kb). Taxonomic annotations revealed the prevalence of taxadominated by the genera Gammaretrovirus, Mamastrovirus, Sapovirus and Rosenblumvirus. Notably, 75% of the assembled genomes represented novel species. Phylogenetic analysis revealed distinct clades suggesting unexplored viral diversity within the uterine environment. Furthermore, bacterial hosts for equine uterine phages were predicted, aligning with previous studies' findings. Most notably, the study identified antibiotic resistance genes within the virome, hinting at potential gene transfer mechanisms between bacteria and viruses. This study establishes the first uterine virome of any mammal, shedding light on a previously unexplored domain. The findings highlight the potential for phage therapy in reproductive infectious diseases and the importance of understanding the maternal gestational environment. Moreover, the study emphasizes the need for further research to expand the uterine virome databases and deepen our understanding of uterine microbiome and its implications for animal and human health.}, } @article {pmid42106682, year = {2026}, author = {Wang, Y and Ma, Y and Yi, J and Li, X and Shao, Y and Cao, L}, title = {A case report of post-arthroscopic knee infection caused by Capnocytophaga sputigena in an anemic patient.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13507-z}, pmid = {42106682}, issn = {1471-2334}, support = {23ZR1480300//Science and Technology Innovation Action Program of the Shanghai Science and Technology Commission/ ; }, abstract = {BACKGROUND: Capnocytophaga sputigena (C. sputigena), a species of bacteria resident in the human oral cavity. Here, to the best of our knowledge, this is the first reported case of a post-arthroscopic knee infection caused by this organism in an anemic patient. We described the clinical characteristics, therapeutic intervention and outcome associated with knee joint infection induced by this bacterium. Furthermore, the treatment approaches and challenges in managing this particular pathogen were explored.

CASE PRESENTATION: A 58-year-old female patient presented with a knee infection following arthroscopy, caused by C. sputigena. The species C. sputigena was confirmed on the basis of the results of the joint fluid culture and metagenomics next-generation sequencing (mNGS). The infection was treated with arthroscopic debridement, in addition to intravenous and intra-articular meropenem irrigation. The initial therapy with meropenem resulted in clinical improvement, and was subsequently de-escalated to amoxicillin-clavulanate potassium. Following a period of observation, the patient was discharged, as her condition was stable.

CONCLUSIONS: The case of a post-arthroscopic knee infection caused by C. sputigena in an anemic patient resulted in surgeons developing a more profound clinical understanding of infections induced by the bacterium. The combination of arthroscopic debridement with meropenem therapy (subsequently followed by de-escalation to amoxicillin-clavulanate potassium) yielded favourable clinical outcomes, thereby establishing a practical reference point for the management and prognosis of such infections.}, } @article {pmid42106812, year = {2026}, author = {Ottesen, A and Kocurek, B and Mammel, MK and Charles, SJ and Dietrich, J and Pauley, S and Cole, SD and Rankin, S and Ceric, O}, title = {Breaking the culture habit: Complementing culture-based veterinary diagnostics with metagenomic data -A case study of feline and canine skin infections.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {42106812}, issn = {1746-6148}, mesh = {Animals ; Dogs ; Cats ; *Cat Diseases/microbiology/diagnosis ; *Dog Diseases/microbiology/diagnosis ; Metagenomics ; Microbial Sensitivity Tests/veterinary ; Anti-Bacterial Agents/pharmacology ; Skin/microbiology ; }, abstract = {BACKGROUND: Skin infections have been described as the primary cause for veterinary small animal practice visits, frequently requiring topical and systemic antibiotics. These infections often represent secondary complications of underlying pathologies, that can lead to recurrent infections and multiple antibiotic exposures. This creates selection pressure toward antibiotic resistance at the intersection of skin, bloodstream, and shared human-animal environments. This case study integrates Veterinary Diagnostic Laboratory (VDL) aerobic culture results with metagenomic (MGX) data to evaluate the combined utility of these approaches in advancing One Health veterinary diagnostics. Simultaneous reporting of culture-recovered pathogens alongside infection microbiomes and resistomes could strengthen pathogen epidemiology, illuminate polymicrobial etiologies, and inform antimicrobial stewardship.

RESULTS: One feline and eight canine skin swabs were analyzed with aerobic culture and traditional antimicrobial susceptibility testing (AST) and compared with MGX profiles. VDL aerobic culture and AST identified Staphylococcus aureus, S. pseudintermedius, S. schleiferi, methicillin resistant (MR) S. schleiferi (MRSS), MR S. pseudintermedius (MRSP) and Pseudomonas aeruginosa. MGX data detected the identical bacterial pathogens and identified methicillin resistance genes (mecA, mecI, mecR1) in samples where AST had confirmed MRSP and MRSS. MGX data also detected mec genes in samples without culture confirmed MR phenotypes as well as describing multi-domain microbiota (bacteria, fungi, protists, viruses, phages), antimicrobial resistance genes (ARGs), plasmids, and metabolic features associated with the skin infection samples.

CONCLUSIONS: MGX data detected the identical VDL recovered pathogens and genes that confer the AMR phenotypes recovered by VDL AST. MGX data also detected additional uncultured pathogens, ARGs, multi-domain microbiota, mobile AMR elements, and metabolic features. Future applications for these methods used simultaneously could support monitoring programs, advance pathogen epidemiology, inform treatment strategy, advance judicious antimicrobial administration, and provide data for machine learning (ML) models to improve precision veterinary diagnosis and treatment.}, } @article {pmid42106836, year = {2026}, author = {Navazesh, SE and Ter Horst, A and Wen, W and Liu, Y and Kiang, D and Li, Z and Yu, A and Brown, CT and Ji, P}, title = {Dietary iron and metal-based growth promoters differentially modulate the gut resistome and Escherichia coli virulome in weaned pigs.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42106836}, issn = {1674-9782}, support = {NNFSA210073688//Novo Nordisk Foundation/ ; NNFSA210073688//Novo Nordisk Fonden/ ; }, abstract = {BACKGROUND: High levels of zinc oxide (ZnO) and copper sulfate are widely used as alternative growth promoters in postweaning pig diet. However, excessive exposure to these metals may drive co-selection for heavy metal (HMR) and antibiotic resistance (AMR). Nursery diets also contain abundant iron to offset the low bioavailability of plant-derived iron, yet how dietary iron influence gut dysbiosis and microbial resistance in postweaning pigs remains unclear. This exploratory study examined the effects of dietary iron and metal-based growth promoters on the fecal resistome of postweaning pigs using shotgun metagenomics and whole-genome sequencing (WGS).

METHODS: Fifty weanling pigs were stratified and randomly assigned to five dietary treatments for 24 d. Experimental diets included a control diet (Con) containing 25, 139, and 141 mg/kg of Cu, Fe, and Zn, respectively, a low-iron diet (LFe, 19 mg Fe/kg), a high-iron diet (HFe, 1,219 mg Fe/kg), a high-copper diet (HCu, 257 mg Cu/kg), and a high-zinc diet (HZn, 2,631 mg Zn/kg, including 2,490 mg Zn/kg from ZnO). All pigs were orally administered with F18 enterotoxigenic Escherichia coli (ETEC) on d 13-16. Metagenome sequencing were performed on d 24 fecal DNA (n = 24) to identify HMR genes (BacMet Predicted database) and AMR genes (CARD database). Functional annotation was performed using HUMAnN3. Whole genome sequencing (WGS) was conducted on 120 E. coli isolates from fecal cultures on d 1, 12, and 24, and AMR and virulence genes were identified from contig assemblies using ABRicate.

RESULTS: Dietary metal treatments significantly altered β-diversity of HMR genes compared with Con, with HZn differing from both HCu and LFe (P < 0.05). Fecal iron levels correlated with sodB (ρ = 0.64, P = 0.075), an iron-containing superoxide dismutase, while fecal copper levels correlated with pcoC (ρ = 0.66, P = 0.075), a plasmid-mediated copper resistance gene. Across metagenomes, 172 AMR genes were identified, dominated by glycopeptide and tetracycline resistance. While dietary iron had minimal effects on fecal AMR profile, HZn induced the largest shifts in resistome, including increases of ant(9)-la, conferring aminoglycoside resistance on mobile genetic elements, and adeF, encoding a multidrug efflux pump (P < 0.05). Functional profiling revealed enrichment of carbohydrate metabolism pathways in HZn group (P < 0.05). WGS of E. coli isolates showed distinct AMR profiles under HZn on d 24 and distinct virulence profile under LFe on d 12, exhibiting increased prevalence of exotoxin and T3SS genes (P < 0.05).

CONCLUSION: Dietary iron restriction enhanced E. coli virulence genes, whereas excessive ZnO induced the most pronounced changes in the gut resistome and microbial metabolism, highlighting a risk for AMR co-selection and marked influence on gut microbiota.}, } @article {pmid42107247, year = {2026}, author = {Tan, T and Hu, T and Chen, B and Kuang, W and Yu, H and Xie, Y and Zhang, Z and Wang, H and Deng, Z and Zhang, C}, title = {Boosting anaerobic reductive dehalogenation with natural protein amendments to unlock cryptic organohalide-reducing bacteria.}, journal = {Marine environmental research}, volume = {219}, number = {}, pages = {108100}, doi = {10.1016/j.marenvres.2026.108100}, pmid = {42107247}, issn = {1879-0291}, mesh = {Halogenation ; Geologic Sediments/microbiology ; *Bacteria/metabolism ; Biodegradation, Environmental ; Tetrachloroethylene/metabolism ; Anaerobiosis ; *Water Pollutants, Chemical/metabolism ; Oxidation-Reduction ; Serum Albumin, Bovine/metabolism ; Phenols ; }, abstract = {Deep-sea sediments host a rich yet largely unexplored reservoir of microorganisms capable of reductive dehalogenation. However, the activity of dehalogenating consortia is often limited even under carbon-rich conditions, impeding the identification of key functional players. In this study, we report that the addition of natural protein materials can dramatically stimulate reductive dehalogenation in an enrichment culture derived from deep-sea cold seep sediments. This stimulatory effect was clearly demonstrated by supplementation with bovine serum albumin (BSA), which significantly enhanced the degradation rates of 2,4,6-tribromophenol (2,4,6-TBP) and tetrachloroethene (PCE). Integrated metagenomic and metatranscriptomic analyses revealed that two candidate novel clostridial lineages-Romboutsia and Oxobacteraceae-present in BSA-amended cultures harbored distinct reductive dehalogenase (RDase) genes. Romboutsia harbored three RDase genes, with one being upregulated during the degradation of 2,4,6-TBP intermediates and another specifically responding to PCE, suggesting a substrate-dependent regulatory strategy. Oxobacteraceae encoded a cytosolic RDase that was highly expressed during 2,4,6-TBP transformation. Metabolic reconstruction further indicated that both lineages could utilize BSA-derived amino acids for growth. This work establishes an effective biostimulation strategy to activate dehalogenation in deep-sea microbial communities and expands the known diversity and functional versatility of candidate organohalide-reducing bacteria.}, } @article {pmid42107339, year = {2026}, author = {Zhang, X and Lu, J and Bao, Q and Xu, K}, title = {Renal mucormycosis caused by Apophysomyces species: case report and literature review.}, journal = {Journal de mycologie medicale}, volume = {36}, number = {2}, pages = {101627}, doi = {10.1016/j.mycmed.2026.101627}, pmid = {42107339}, issn = {1773-0449}, mesh = {Humans ; *Mucormycosis/diagnosis/microbiology/drug therapy ; Male ; Middle Aged ; *Mucorales/isolation & purification/genetics ; *Kidney Diseases/microbiology/diagnosis ; Antifungal Agents/therapeutic use ; Fatal Outcome ; Immunocompromised Host ; }, abstract = {INTRODUCTION: Mucormycosis represents an uncommon yet aggressive and life-threatening fungal infection, typically occurring in immunocompromised individuals. Unlike most Mucorales infections, Apophysomyces frequently infects otherwise healthy hosts, raising significant clinical concern. Alarmingly its atypical manifestation, necrotizing fasciitis, is often misdiagnosed as a bacterial infection due to overlapping clinical features.

CLINICAL CASE: Herein we present a case of Apophysomyces infection in kidney in an immunocompetent 52-year-old man, whose condition deteriorated swiftly, leading to failure of several organs, culminating in death. All laboratory results, including serological assays and microbial cultures from blood, respiratory secretions, urine, and stool, showed no abnormalities. The diagnosis was confirmed through metagenomic next-generation sequencing (mNGS) which was highlighted as valuable for early diagnosis. We conducted a literature review of 13 cases previously reported from 1994 to 2025, implying a higher prevalence among immunocompetent individuals. Patients of Indian constituted the majority across all reported cases. PCR, fungal culture and histopathological examination served as the primary diagnostic methods. Systemic antifungal agents were administered to 13 individuals, while surgical intervention was performed in 8 cases. Complete recovery was achieved in 7 patients.

CONCLUSIONS: Therefore our report highlights Apophysomyces variabilis as a novel pathogen of clinical importance in China, emphasizing that mortality rates escalate substantially without timely detection and appropriate management.}, } @article {pmid42107405, year = {2026}, author = {Guo, Y and Zhou, W and Dong, M and Qiu, W and Gao, X and Ahmad, T and Farid, B and Lyu, W and Sun, L}, title = {Root-secreted aminosalicylic acid and 4,6-dioxoheptanoic acid: Dual roles in enhancing 4-nonylphenol bioavailability and regulating rhizospheric microbiota community.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142282}, doi = {10.1016/j.jhazmat.2026.142282}, pmid = {42107405}, issn = {1873-3336}, mesh = {*Plant Roots/metabolism ; *Aminosalicylic Acids/analysis/metabolism ; *Heptanoates/analysis/metabolism ; *Phenols/metabolism/toxicity ; *Rhizosphere ; Soil Microbiology ; *Soil Pollutants/metabolism/toxicity ; Microbiota/drug effects/physiology ; Biodegradation, Environmental ; Astragalus Plant/metabolism/microbiology ; *Plant Exudates/metabolism ; }, abstract = {Root exudates and rhizospheric microorganisms are key drivers of organic pollutant degradation in soil. However, the mechanisms underlying their coordinated effects are not yet fully understood. This paper analyzes the changes in the composition of Astragalus sinicus root exudates induced by 4-nonylphenol (4-NP) exposure and investigates the effects of key exudate components on 4-NP sorption-desorption, rhizospheric degradation, and soil microbial community. Metabolomic analysis indicated significant alterations in profile composition induced by 4-NP exposure, with organic acids representing the major responsive category. Specifically, aminosalicylic acid and 4,6-dioxoheptanoic acid-two pivotal organic acids-markedly enhanced 4-NP desorption from soil at a concentration of 50 μmol/L. Their addition reduced the desorption coefficient by 6.4-fold and 3.2-fold, respectively, compared to the control. A pot experiment further validated that application of the two organic acids significantly increased rhizospheric dissipation of 4-NP by 20.0-23.0% compared to soils planted with A. sinicus alone. Metagenomic analysis demonstrated that the key root exudates selectively enriched pollutant-degrading microorganisms (Pseudoxanthomonas sp. A, Cupriavidus, Rhodococcus, and Penicillium), and increased the abundance of functional genes (Cox1, ligB, ligI, and pcaF) and pathways associated with xenobiotic biodegradation. These findings indicate that specific root exudates enhance microbial degradation capacity by improving 4-NP bioavailability, providing a mechanistic basis for the targeted optimization of phytoremediation strategies for 4-NP-contaminated soils.}, } @article {pmid42107727, year = {2026}, author = {Ramesh, K and Chellam, PV}, title = {Comparative genomic surveillance of fluoroquinolone resistance markers across major riverine hotspots by leveraging public metagenomes.}, journal = {International journal of antimicrobial agents}, volume = {67}, number = {8}, pages = {107839}, doi = {10.1016/j.ijantimicag.2026.107839}, pmid = {42107727}, issn = {1872-7913}, abstract = {OBJECTIVE: The global surge in fluoroquinolone resistance (FQR) underscores the urgent need for robust environmental surveillance. From a One Health perspective, rivers serve as critical conduits and hotspots for antimicrobial resistance (AMR) dissemination.

METHODS: To address this issue, we conducted a systematic metagenomic surveillance of FQR across spatially prioritized freshwater ecosystems using distribution data of five major markers (gyr, par, qnr, aac, and qep) retrieved from the National Center for Biotechnology Information Pathogen Detection Isolate Browser.

RESULTS: Among 164 riverine metagenomic datasets, 31 high-quality datasets from the Mississippi, Yukon, Saint Lawrence, Yangtze, and Pearl Rivers were analysed. FQR genes were detected in 12 datasets, with normalized abundances ranging from 0.01 to 1.22 copies per bacterial cell. Plasmid-mediated qnrS2 and efflux pump genes (qepA2 and AbaQ) emerged as the most prevalent determinants. Multivariate analyses revealed river-specific clustering patterns and strong correlations with metal resistance genes, highlighting co-selection pressures. The predominance of conjugative mobile genetic elements indicated an elevated potential for horizontal gene transfer. Taxonomic profiling further revealed enrichment of clinically important and World Health Organization priority pathogens. Community structure analyses (permutational multivariate analysis, R² = 0.7598, P = 0.003) confirmed significant microbial variations across rivers.

CONCLUSIONS: Collectively, this integrative approach identifies environmental reservoirs of FQR genes, supporting river-based AMR surveillance. These insights are pivotal for shaping evidence-driven mitigation strategies and informing both national and global AMR policies.}, } @article {pmid42107869, year = {2026}, author = {Wang, L and Lin, F and Ye, Y and Li, S and Pan, Z and Wu, Y and Gao, Y and Zhu, L and Wang, J and Wang, J}, title = {Humic substances with different molecular weights independently increased antibiotic resistance in agricultural soils contaminated with sulfamethazine.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {401}, number = {}, pages = {128302}, doi = {10.1016/j.envpol.2026.128302}, pmid = {42107869}, issn = {1873-6424}, mesh = {*Humic Substances/analysis ; *Sulfamethazine/analysis ; *Soil Pollutants/analysis ; *Soil Microbiology ; Agriculture ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Anti-Bacterial Agents ; Molecular Weight ; }, abstract = {Humic substances (HS) are known to enhance soil structure, but their effects on the antibiotic resistance distribution in agricultural soils, especially under sulfonamide contamination, remain poorly understood. This study employed an indoor soil microcosm experiment combined with metagenomic sequencing to examine the effects of high molecular weight humic acid (HA) and low molecular weight fulvic acid (FA) on the dynamics of the antibiotic resistance in sulfamethazine (SM2) contaminated agricultural soil, with the aim of identifying key driving factors. The results revealed that both HA and FA, especially at 1 g/kg, increased the total abundance of antibiotic resistance genes (ARGs), including dominant genes, such as Sul1, Cmx, VanR, Sul2 and FloR. Additionally, HS application led to increased abundance of mobile genetic elements (MGEs) and potential ARG hosts, such as Actinobacteria. Notably, HA inhibited the growth of cultivable sulfonamide-resistant bacteria (SRB), while FA promoted their growth. However, the antibiotic resistance ratio of cultivable bacteria remained relatively high under both HS treatments, consistent with the elevated ARG abundance. This may be attributed to the enhanced competitiveness of Pseudomonas within the SRB community under HS exposure. Variance partitioning analysis (VPA) indicated that MGEs and microbial communities jointly contributed to ARG variation and were closely associated with the antibiotic resistome. This study provides new insights into the ecological risks associated with HS application in agricultural soils.}, } @article {pmid42107880, year = {2026}, author = {Yao, L and Shen, L and Liu, X and Fu, J and Pan, D}, title = {Ventriculo-Abdominal Subcutaneous Tunneled External Drainage as a Transition Therapy to Reduce Shunt Failure Rate in Post-Infection Hydrocephalus Patients: A Single-Center Retrospective Cohort Study.}, journal = {World neurosurgery}, volume = {212}, number = {}, pages = {125037}, doi = {10.1016/j.wneu.2026.125037}, pmid = {42107880}, issn = {1878-8769}, abstract = {OBJECTIVE: Assess the clinical efficacy of Ventriculo-Abdominal Subcutaneous Tunneled External Drainage (VASTED) as a transition treatment before ventriculoperitoneal shunt (VPS) in the management of postinfectious hydrocephalus (PIH).

METHODS: This study enrolled 384 patients who developed PIH after craniotomy. Following external ventricular drainage and combined intravenous antibiotic therapy, patients underwent VASTED as a transitional treatment measure before definitive VPS placement when they achieved 3 consecutive negative cerebrospinal fluid bacterial cultures within 2 weeks and no pathogen detection by metagenomic next-generation sequencing. The primary endpoint of the study was the shunt failure rate after 1 year of follow-up, with infection and catheter blockage as the evaluation criteria.

RESULTS: A total of 378 cases underwent VPS surgery, with 6 cases refusing or abandoning treatment. During a 1-year follow-up period, 9 shunt failures occurred (2.38%, 95% confidence interval: 0.43-3.05). Among these, 5 failures were infection-related (1.3%) and 4 were due to pure mechanical obstruction (1.1%). The shortest duration of VASTED was 14 days, while the longest was 387 days, with a median drainage time of 69 days (95% confidence interval: 28-112 days).

CONCLUSIONS: In patients with PIH, implementing VASTED as a transitional surgical treatment approach is closely associated with an extremely low 1-year failure rate of VPS. This transitional strategy can significantly reduce the high failure rate following VPS.}, } @article {pmid42108251, year = {2026}, author = {Yin, M and Chen, X and Lu, R and Dong, Y and Luo, W and Tang, Z and Zeng, M and Xu, Y and Qing, Y and Xi, C and Feng, X and Guo, H and Mo, S and Luo, J}, title = {Diversity of fecal viromes and zoonotic risk assessment in captive wild felids using viral metagenomics.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-52077-7}, pmid = {42108251}, issn = {2045-2322}, support = {(Grant No. HX2023115P).//This research was supported by the grant for "Metagenomic Analysis of Viruses Carried by Amur Tigers and Leopards" (Grant No. HX2023115P)./ ; }, abstract = {Emerging viral diseases-particularly zoonotic pathogens-affect the health and conservation of endangered felids, including Panthera tigris altaica (Amur tiger) and Panthera pardus (leopard). To address this challenge, we employed a viromics approach to investigate the diversity of the fecal virome in wild felids and assess its zoonotic potential. Using in-depth metagenomic sequencing and analysis of fecal samples from captive wild felids housed in a wildlife institution, this study characterized the enteric virome and evaluated associated risks. A total of 18 viral families and 48 viral genera were identified. The DNA virus community exhibited stability in abundance and composition, dominated by the phyla Heunggongvirae and Bamfordvirae. Within Heunggongvirae, the class Caudoviricetes was the core component, with its abundance aligning with the intestinal bacterial community, suggesting a potential role of these bacteriophages in regulating microbial ecology. Additionally, sequences of the family Poxviridae, homologous to Variola virus (VARV), were detected. In contrast, the RNA virus community displayed higher diversity and variability, with the order Ortervirales as the predominant group. Sequences highly homologous to feline leukemia virus (FeLV) were repeatedly identified, suggesting potential latent infections. The detection of sequences related to rare environmental viruses, such as Casadabanvirus, highlights the potential risk of cross-species virus transmission under captive conditions. Stability analysis revealed that dominant DNA virus groups exhibited low abundance variability across samples. In contrast, unclassified RNA viral taxa showed higher abundance variability. KEGG functional annotation mapped DNA viral contigs primarily to microbial metabolic modules. Conversely, RNA assemblies extensively mapped to eukaryotic pathways (e.g., arachidonic acid and energy metabolism); due to the total nucleic acid extraction methodology, these mappings primarily reflect co-extracted host transcriptomic background rather than viral-encoded functions, providing an indirect snapshot of the concurrent enteric microenvironment. These baseline data delineate the virome structure in captive environments and provide practical targets for zoological biosecurity and proactive veterinary surveillance.}, } @article {pmid42108276, year = {2026}, author = {Saha, PK and Sar, P and Sarkar, S and Mukherjee, D and Kazy, SK}, title = {Deep subsurface rock-hosted chemolithotrophic bacterial communities exhibited differential CO2 assimilation and bioconversion potential under varying oxygen level.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-51641-5}, pmid = {42108276}, issn = {2045-2322}, support = {MoES/P.O.(Seismo)/1(383)/2020 dated February 10, 2022//Ministry of Earth Sciences (MoES), Government of India/ ; }, abstract = {Deep continental subsurface hosts diverse microbial ecosystems that are primarily driven by chemolithoautotrophy. In this study, we investigated deep continental igneous rock-hosted bacterial populations enriched under microoxic (ME) and anoxic (AE) conditions. Metataxonomic, metagenomics and metabolomics approaches, along with physiological analyses, were performed to elucidate community composition, CO2 utilization and possible bioconversion potential of subsurface rock enrichment cultures under chemolithoautotrophic conditions. Following prolonged incubation, ME enrichments resulted in higher microbial growth with greater species diversity than the AE cultures. Ralstonia and unclassified Comamonadaceae were predominant in both the enrichment conditions. On the other hand, Cellulomonas, Phenylobacterium, Deinococcus, Desulfurispora, etc. were relatively abundant in ME, and Solimonas, Curvibacter, Caulobacter, Novosphingobium, Anaeromyxobacter, unclassified Clostridia, etc. were abundant in AE communities. CO2/H2 utilization and organic acids production were greater in ME enrichments. Shotgun metagenomics and predictive metabolic profiling revealed CBB cycle as the predominant carbon fixation pathway in ME, whereas WL pathway was prominent in AE. Genes for hydrogen, sulfur, and nitrogen metabolisms were observed in both the enrichment cultures. HRLC-MS based untargeted metabolomics indicated the presence of valuable metabolites (organic acids, osmolytes, lipids/amides) in rock cultures, reflecting the potential of deep subsurface microorganisms for CO2 utilization and possible bioconversion to valuable biomolecules.}, } @article {pmid42108288, year = {2026}, author = {Yan, C and Zhang, F and Long, C and Yin, Y and Wang, L}, title = {A Brief Review of Microbial Omics: Methods and Perspectives.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {1-20}, pmid = {42108288}, issn = {1940-6029}, mesh = {*Genomics/methods ; *Metabolomics/methods ; *Proteomics/methods ; *Microbiota/genetics ; *Computational Biology/methods ; Single-Cell Analysis/methods ; Artificial Intelligence ; Transcriptome ; Metagenomics/methods ; }, abstract = {Microbial omics has progressed from isolated genomic analyses into a comprehensive, integrated multi-omics framework, profoundly advancing our understanding of microbial complexity and functionality. This mini-review systematically outlines the core technologies within microbial omics-including genomics, transcriptomics, proteomics, and metabolomics-by introducing their fundamental principles, common experimental workflows, and state-of-the-art bioinformatic strategies. We particularly highlight the emergence of single-cell microbial omics as a transformative methodology that resolves molecular and functional heterogeneity within communities, enabling the identification of rare taxa, strain-level microdiversity, and specialized functional roles that are obscured in bulk analyses. Furthermore, we discuss how artificial intelligence (AI)-driven tools are revolutionizing the interpretation of high-dimensional omics data, uncovering latent biological patterns, improving predictive modeling of microbial behavior, and facilitating the translation of microbiome insights into clinical and environmental applications. The review concludes by comparing the strengths, limitations, and optimal use cases of each omics layer and single-cell approach while also addressing ongoing technical challenges and future directions in the field.}, } @article {pmid42108290, year = {2026}, author = {Li, B and Xu, J and Zhao, T and Yang, X and Yin, Q and Zou, Y}, title = {Metagenomic Data Preprocessing and Quality Control.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {43-61}, pmid = {42108290}, issn = {1940-6029}, mesh = {*Metagenomics/methods/standards ; Quality Control ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Software ; Workflow ; *Metagenome ; *Computational Biology/methods ; }, abstract = {Accurate metagenomic analysis relies on clean and well-processed sequencing reads. This chapter presents a concise four-step workflow for preprocessing: raw data assessment, adapter and quality filtering, host DNA removal, and final clean-read evaluation. By standardizing these essential procedures, researchers can minimize contamination, reduce technical bias, and ensure reliable inputs for assembly and downstream metagenomic analyses.}, } @article {pmid42108291, year = {2026}, author = {Li, B and Yang, X and Zhao, T and Xu, J and Meng, Q and Yin, Q and Zou, Y}, title = {Metagenomic Assembly and Gene Prediction.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {63-89}, pmid = {42108291}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Metagenome ; *Computational Biology/methods ; Molecular Sequence Annotation ; Contig Mapping/methods ; Software ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomic assembly and gene prediction connect quality-controlled reads to downstream microbiome analyses. This chapter outlines core assembly strategies, including per-sample versus co-assembly and short-read versus hybrid approaches, and highlights key parameters and metrics for evaluating assembly quality. Gene prediction from contigs and the construction of nonredundant gene catalogs are introduced as fundamental steps for representing community coding potential. The resulting contigs and gene sets provide essential input for metagenome-assembled genome (MAG) reconstruction, as well as taxonomic and functional annotation in subsequent chapters.}, } @article {pmid42108292, year = {2026}, author = {Guo, JX and Gao, YZ}, title = {Absolute Quantification of Bacteria in the Microbiome and Its Application.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {91-103}, pmid = {42108292}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; *Bacteria/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {The advent of genomics and deep sequencing technologies has facilitated the development of absolute quantification techniques, which offer researchers more objective and precise sequencing outcomes. Unlike traditional relative quantification methods, which provide comparative data, absolute quantification delivers definitive measurements of genes or taxa. This analytical approach mitigates the potential for extraneous influences when comparing disparate samples, thereby reducing analytical errors. The implementation of absolute quantification techniques enhances our comprehension of microbial community structures, ecological dynamics, and their associations with host health or disease conditions. This chapter emphasizes a straightforward and broadly applicable method for genomic quantification, which necessitates the incorporation of a specified amount of internal standard DNA into the samples, eliminating the need for subsequent adjustments during library construction and sequencing. By assessing the proportion of internal standard DNA across various samples, sequencing data can be transformed into absolute quantification metrics. The internal standard method for absolute quantification is versatile and can be effectively utilized across multiple domains, including disease diagnosis, microbial ecology research, the fermentation industry, and environmental monitoring. Overall, absolute quantification methods furnish a more accurate and holistic perspective for microbiome research.}, } @article {pmid42108294, year = {2026}, author = {Xia, H and Zhou, C and Fu, B and Han, H}, title = {Unlocking Enzyme Discovery: Leveraging Multi-Omics, Machine Learning, and De Novo Design.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {117-146}, pmid = {42108294}, issn = {1940-6029}, mesh = {*Machine Learning ; *Proteomics/methods ; Metagenomics/methods ; *Enzymes/genetics/metabolism/chemistry ; Lignin/metabolism ; Genomics/methods ; Multiomics ; }, abstract = {Enzymes are fundamental protein catalysts essential to life processes and widely applied in industrial and healthcare sectors. However, the broader application of natural enzymes is constrained by their inherent catalytic limitations, and traditional discovery methods such as microbial enrichment are often slow and low-throughput. Driven by advances in multi-omics and artificial intelligence, a range of novel screening strategies has been developed, enabling significant enhancements in both catalytic efficiency and stability of enzymes. This chapter assesses high-throughput approaches, such as metagenomics, metaproteomics, machine learning, and de novo design, comparing their respective advantages and limitations for enzyme discovery. Furthermore, we discuss the application potential of lignocellulose-degrading and plastic-degrading enzymes in biomass conversion and plastic waste recycling.}, } @article {pmid42108295, year = {2026}, author = {Peng, B and Chang, X}, title = {Omics Approaches to Unraveling the Complexity of the Gut-Lung Axis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {147-164}, pmid = {42108295}, issn = {1940-6029}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Lung/metabolism ; *Metabolomics/methods ; Lung Diseases/metabolism/microbiology ; Metagenomics/methods ; Dysbiosis ; Animals ; *Genomics/methods ; Proteomics/methods ; }, abstract = {The complex, bidirectional communication between the gut and the lungs, known as the "gut-lung axis," profoundly influences host immune homeostasis and the pathogenesis of respiratory diseases. In recent years, multi-omics approaches, including metagenomics, metabolomics, and metatranscriptomics, have emerged as the core driving force for unraveling the complexity of this interorgan cross talk network. This review aims to systematically summarize the current omics-based evidence in the field of the gut-lung axis. We highlight key communication mechanisms discovered through multi-omics integration, particularly how gut microbiota-derived metabolites, exemplified by short-chain fatty acids (SCFAs), mediate distal immune regulation. Concurrently, we consolidate omics evidence from the contexts of respiratory infectious diseases, chronic lung disorders, and aging, systematically delineating the impact of gut dysbiosis on pulmonary pathophysiology via the gut-lung axis and emphasizing the feasibility of disease management in patients with lung diseases by modulating the gut microbiota. Although omics technologies have significantly advanced our understanding of this field, the challenge of effectively integrating vast, heterogeneous data and transitioning from "correlation" to "causation" remains a primary hurdle. By reviewing and discussing the current omics evidence in the gut-lung axis, this paper aims to provide new perspectives for future mechanistic explorations and clinical translation strategies.}, } @article {pmid42109826, year = {2026}, author = {Sun, A and Jin, SL and Liu, JG}, title = {A practical guide for characterization of novel CRISPR-Cas systems with Pro-CRISPR factors.}, journal = {Biophysics reports}, volume = {12}, number = {2}, pages = {85-99}, pmid = {42109826}, issn = {2364-3420}, abstract = {The emergence of advanced genome editing technologies has revolutionized research in life sciences, offering an unprecedented way to uncover unknown biological functions and innovative therapeutic strategies. Among all genome editing tools, CRISPR-Cas-based technologies play a pivotal role in this revolution, particularly Class 2 effectors such as Cas9 and Cas12, owing to their high efficacy and ease of programmability. With the advancements in genome sequencing and metagenomics, an increasing number of novel CRISPR-Cas systems have been discovered, including those found in extreme environments and viruses. Furthermore, recent studies have revealed an unexpected role of non-Cas accessory genes, such as the Tn7-like transposon and Pro-CRISPR factors (Pcr), in conferring additional functionalities to the CRISPR system, providing new insights into the understanding of CRISPR-mediated bacterial immunity and advancing the development of genome editing technologies. Therefore, it is essential to develop comprehensive methods for characterizing the Cas proteins and Pro-CRISPR factors with a growing diversity. In this protocol, we provide a method encompassing protein purification, biochemical characterization, validation of protein-protein interactions, and preliminary in vivo functional assays in bacteria for Cas nuclease and its associated Pro-CRISPR factor. We hope this protocol will not only assist in the characterization of the CRISPR-Cas system, but also provide valuable guidance for the characterization of other nucleases or nucleic acid modification systems.}, } @article {pmid42109869, year = {2026}, author = {Gao, Y and Zhu, T and Jiang, Y and Tian, F and Li, Y and Liu, W and Xu, S and Tong, Y and Qin, Z and Hu, F}, title = {Genomic characterization of two duck-origin picornaviruses with seven putative 2A peptides.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1753959}, pmid = {42109869}, issn = {2297-1769}, abstract = {INTRODUCTION: The Picornaviridae family is a large group of viruses comprising 68 genera. Duck-origin picornaviruses are categorized into four genera, however, the taxonomic status of some recently identified strains remains to be determined.

METHODS: In this study, two virus strains isolated from breeding ducks experiencing reduced egg production were identified and characterized through viral metagenomic analysis.

RESULTS: Two viral strains (NC0246 and PX0394) exhibiting the typical picornavirus-like genomic structure were identified and characterized. Notably, both strains exhibit extended 2A sequences that each possesses seven distinct 2A polypeptides considered rare in Picornaviridae family. Specifically, NC0246 exhibits a deletion of 73 amino acids (aa) in the region corresponding to 2A4-2A5 when compared to PX0394 indicating the genetic diversity of picornaviruses. Homology analysis revealed that the P1 region of NC0246 was most closely related to duck aalivirus A1, with aa identity of 37.37%. Conversely, the P1 region of PX0394 was most closely related to duck egg-reducing syndrome virus (DERSV), with aa identity of 64.44%. Furthermore, the 2C and 3D proteins of NC0246 and PX0394 was most closely related to DERSV. Phylogenetic analyses indicate that NC0246 and PX0394 form a sister clade to DERSV and duck aalivirus A1 and display marked heterogeneity in the P1 protein. While NC0246 and PX0394 branch nearest to DERSV and duck aalivirus A1, duck hepatitis A virus types 1 and 3, sharing secondary homology, occupy a separate lineage.

CONCLUSION: Two picornaviruses were identified and characterized from breeding ducks that exhibited decreased egg production. Through genomic structure and homology analysis, these viruses were most closely related to DERSV and duck aalivirus A1. NC0246, PX0394, and the previously reported DERSV show a close evolutionary relationship with the genus Aalivirus based on genomic and phylogenetic analyses, suggesting a potential affiliation with this genus.}, } @article {pmid42110882, year = {2026}, author = {Mayne, R and Smith, DB and Brown, K and Chen, YP and Firth, AE and Katayama, K and Knowles, NJ and Simmonds, P}, title = {Comprehensive hallmark gene sequence, genomic and structural analysis clarifies new and established taxa within the Picornavirales.}, journal = {Virus evolution}, volume = {12}, number = {1}, pages = {veag023}, pmid = {42110882}, issn = {2057-1577}, abstract = {The order Picornavirales is a group of highly diverse RNA viruses that includes many pathogens of significance to human and veterinary health, agriculture, and the wider environment. However, the wide range of viruses assigned to the order, together with their genomic variability, and the recent description of numerous 'picorna-like' viruses derived from metagenomic analyses of environmental samples, challenge the established taxonomic classification of members of the order and the criteria for their classification. Here, we combine the existing gold standard, hallmark RNA-directed RNA-polymerase (RdRP) gene sequence-based analysis with helicase sequence-based phylogeny, RdRP structural prediction through the use of ColabFold and Fold Tree, and analysis of coding-complete genomes using GRAViTy-V2, to genetically classify 525 picornaviral genomes and recently described 'picorna-like' viruses. All analyses were conducted with a bespoke, fully automated pipeline for retrieval of genome sequences, domain prediction and extraction, phylogenetic analysis, and output conditioning, which is available as open-source software. Our results reveal broad support for established families as well as for 6 novel families, and 32 new genera. In instances where inconsistencies were found between classification methods, we demonstrate how examination of the pipeline's output may be used to reconcile differences with respect to the genomic features quantified by the analysis. Automated multimodal taxonomic analysis may save significant resources over manual methods and better define demarcation criteria for families and genera.}, } @article {pmid42111070, year = {2026}, author = {Zurdo-López, M and Sagredo Del Rio, M and Cháfer Rudilla, M and Ibarra, A and Doncel-Pérez, E}, title = {Microbiota and Guillain-Barré syndrome: role of microbial metabolites, biomarkers, and emerging therapeutic strategies.}, journal = {Frontiers in neurology}, volume = {17}, number = {}, pages = {1815899}, pmid = {42111070}, issn = {1664-2295}, abstract = {Guillain-Barré syndrome (GBS) is an acute autoimmune polyradiculoneuropathy that follows infection and is characterized by immune-mediated demyelination or axonal injury of the peripheral nervous system. While established triggers such as Campylobacter jejuni are well recognized, increasing evidence implicates the gut microbiota as a key modulator of immune responses relevant to GBS pathogenesis. The intestinal microbiota produces a diverse array of bioactive metabolites, including short-chain fatty acids (SCFAs), tryptophan-derived indoles, and neurotransmitter-like molecules, which influence immune tolerance, gut barrier integrity, and neuroinflammatory signaling. SCFAs, particularly butyrate, exert anti-inflammatory effects and support epithelial and blood-nerve barrier function. Microbial tryptophan metabolites regulate astrocyte and microglial activity via aryl hydrocarbon receptor (AHR) signaling, thereby restraining central and peripheral neuroinflammation. In contrast, dysbiosis-associated metabolites such as lipopolysaccharide (LPS) may enhance systemic inflammation, disrupt immune tolerance, and promote autoantibody production through mechanisms including molecular mimicry. Studies suggest that specific microbial taxa and metabolite signatures may serve as diagnostic or prognostic biomarkers in GBS, offering insights into disease susceptibility and progression. Microbiota-targeted therapeutic strategies are emerging as promising adjuncts to immunotherapy. Probiotics and prebiotics may restore beneficial microbial communities and rebalance immunoregulatory metabolite production, while host-directed metabolic interventions such as creatine supplementation may further support mitochondrial function, immunometabolic homeostasis, and neuroprotection. Fecal microbiota transplantation (FMT), though still experimental in GBS, has shown benefit in related neuroinflammatory disorders by reestablishing eubiosis and dampening immune activation. Future studies integrating metagenomic, metabolomic, and immunologic profiling in well-characterized GBS cohorts are essential to validate these findings and advance personalized microbiota-based interventions.}, } @article {pmid42111291, year = {2026}, author = {Marcos, S and Odriozola, I and Aizpurua, O and Eisenhofer, R and Mak, SST and Martin-Bideguren, G and Kale, V and Baldi, G and Richardson, LJ and Finn, RD and Tarradas, J and Estonba, A and Gilbert, MTP and Alberdi, A}, title = {Functional gut microbiota dynamics of generalist and specialist bacteria in association with chicken growth.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag091}, pmid = {42111291}, issn = {2730-6151}, abstract = {The early-life development of the gut microbiome in broiler chickens is a dynamic ecological process with significant implications for host physiology and productivity. Using 388 genome-resolved metagenomic and 61 metatranscriptomic samples across two replicated trials, we analysed the compositional and functional succession of the caecal microbiome in chickens from hatching to slaughter age. We reconstructed 822 bacterial genomes and distilled gene annotations into comprehensive metabolic traits that captured the functional capacities of each genome. We observed that the increase in microbial diversity with chicken age was accompanied by a decline in community-level average metabolic capacity, driven by a shift from metabolically versatile generalists (Lachnospiraceae) to hitherto uncultured, genome-reduced specialists (RF39, RF32, and UBA1242). However, the specific identity of the dominant genome-reduced specialists varied among individuals, resulting in contrasting associations with host body weight. At slaughter age, only 10 UBA660 (RF39) bacteria were positively associated with body weight, while other genome-reduced lineages, such as UBA1242 (Christensenellales), were among 190 negatively associated bacteria. Gene expression analyses revealed that despite their reduced functional repertoire, UBA660 exhibited greater metabolic activity than UBA1242, particularly in the production of two key metabolites for host nutrition and intestinal homeostasis: the essential amino acid lysine and the signaling molecule indole-3-acetate. These findings provide new insights into the functional ecology of the chicken gut microbiome and highlight the relevance of cultivation approaches to retrieve underexplored and uncultured bacterial taxa, which could open new avenues for microbiome-based strategies aimed at improving poultry growth and health in intensive production systems.}, } @article {pmid42111294, year = {2026}, author = {Yergaliyev, T and Enokela, SO and Eberhardt, G and Flisikowski, K and Hornburg, SC and Reyer, H and Tetens, J and Wimmers, K and Zentek, J and Camarinha-Silva, A}, title = {Toward reproducible pig gut microbiome profiling through standardized methodologies.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag097}, pmid = {42111294}, issn = {2730-6151}, abstract = {Reproducible microbiome profiling is essential for linking microbial communities to host health, yet methodological variation continues to undermine reproducibility across studies. This problem is acute in pig microbiome research, where no standardized DNA extraction protocols exist despite the species' importance in agriculture and biomedicine. Here, we benchmark how 12 widely used extraction kits influence microbiome outcomes in 16S rRNA gene amplicon sequencing and shotgun metagenomics of pig fecal samples. We demonstrate that extraction choice biases 16S rRNA gene datasets, affecting DNA yield, diversity, community composition, and spike-in recovery, whereas metagenomic taxonomy and functional profiles are comparatively robust. Kit-dependent recovery of Gram-positive versus Gram-negative taxa revealed systematic biases with direct consequences for biological interpretation. By integrating spike-in controls, taxonomic resolution, and metagenome-assembled genomes, we establish a framework for evaluating DNA extraction methods in animal microbiome research. Our findings demonstrate that 16S rRNA gene amplicon sequencing is more susceptible to extraction-driven artifacts than metagenomics, highlighting the need for standardized protocols to ensure reproducibility and comparability across pig microbiome studies. Moreover, while shotgun metagenomics was comparatively robust to DNA extraction choice, the number of assembled good-quality metagenome-assembled genomes recovered was strongly dependent on the extraction kit selection.}, } @article {pmid42111296, year = {2026}, author = {De Chiara, L and Doughty, R and Estévez-Gómez, N and Gallego-García, P and Alvariño, P and Díez-Martín, A and Dávila Piñón, P and Treangen, TJ and Cubiella, J and Posada, D}, title = {A comparison of methods for the optimal recovery of the human fecal virome.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag090}, pmid = {42111296}, issn = {2730-6151}, abstract = {Human virome research is gaining increasing attention as viruses are recognized as critical modulators of microbial communities and human health. Viral metagenomics, however, faces unique challenges, including the low abundance and diversity of viruses in biological samples, the absence of universal marker genes, and biases introduced by experimental protocols. While various virome protocols have been benchmarked using viral particles or nucleic acids from mock communities, these approaches often fail to capture the complexity and heterogeneity of natural viromes. In this study, we systematically evaluated modifications to key methodological steps in the metagenomic analysis of human fecal samples, including viral enrichment, nucleic acid extraction, genome amplification, and library preparation. Using gold-standard bioinformatic approaches on sequencing datasets generated after amplification, we assessed the impact of these modifications on relative viral taxonomic assignment, contig quality, richness, diversity, and inferred genome structure. Our findings reveal striking trade-offs between recovery of viral genomes and retention of nonviral sequences, demonstrating how methodological choices can shape the inferred virome composition. Based on these observations, we propose an optimized protocol that enhances viral genome recovery while reducing contamination from nonviral sequences. This refined workflow provides a more robust and reliable framework for gut virome studies, paving the way for a deeper exploration of the role of viruses in human health and microbial ecosystems.}, } @article {pmid42111477, year = {2025}, author = {Gudenkauf, JC and Wagstaff, E and Arneson, EJ and Gill, C and Gillman, AN and Haim, H and Tan, CS}, title = {Successful Recovery from Meningoencephalitis Associated with Archetype-like JC Virus in a Lung Transplant Recipient: Case Report and Review of the Literature.}, journal = {Annals of clinical case reports}, volume = {10}, number = {1}, pages = {}, pmid = {42111477}, issn = {2474-1655}, support = {R01 AI170205/AI/NIAID NIH HHS/United States ; }, abstract = {Meningoencephalitis due to JC polyomavirus (JCV) is rare and delays in diagnosis could lead to potentially fatal outcomes in immunosuppressed patients. We present a case of an HIV-negative lung transplant recipient who presented with neurological deficits, including aphasia and right-sided weakness. Brain imaging lacked demyelination usually diagnostic of progressive multifocal leukoencephalopathy (PML), the disease most often associated with JC virus, however cerebrospinal fluid (CSF) metagenomic analysis confirmed a high JC viral load, suggestive of JCV-associated meningoencephalitis. After reducing immunosuppression, the patient showed significant neurological improvement within three months and full recovery by 6 months. The JCV genome sequenced from patient's plasma and CSF were identical and resembled the "nonpathogenic" archetype in the non-coding region but shared homology in the coding region with the classically-considered neurotropic strains detected in those with PML. These findings suggest that mutations in the virus's noncoding region are not necessary for neuropathogenesis. We also review other cases of JCV-associated meningitis and encephalitis, which, in contrast to our case, were all fatal. Clinicians should consider JCV testing in immunosuppressed patients with encephalopathy and focal neurological deficits, even in the absence of significant brain radiographic abnormalities.}, } @article {pmid42111802, year = {2026}, author = {Belkina, DD and Vinogradova, SV}, title = {Plant virome analysis by high-throughput sequencing: concepts and approaches.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {30}, number = {2}, pages = {311-320}, doi = {10.18699/vjgb-26-35}, pmid = {42111802}, issn = {2500-0462}, abstract = {The metagenomic approach based on high-throughput sequencing is becoming increasingly prevalent for the detection of viral infections in plants. This method allows us to study the species composition of viruses associated with the plant, including novel species, describe their population genetic structure, and develop genetic test systems for routine diagnostics. A metagenomic approach to phytosanitary monitoring can help to determine the cause of unknown plant diseases, which is particularly important for preventing the spread of pathogens, such as viruses. Furthermore, as it is impossible to eliminate plant viruses in field conditions, comprehensive diagnostics using high-throughput sequencing is becoming an effective tool for complying with quarantine regulations on the import of foreign material, as well as for producing high-quality local planting material. High-throughput sequencing is becoming more affordable every year, with both the instrumentation and analytical capacity improving. This review summarizes key approaches to analyzing plant virome using high-throughput sequencing. The analysis process, from sample collection to bioinformatic data processing, validation and interpretation, is described in detail. The features of sequencing platforms and the factors affecting sequencing quality, including contamination, are discussed. Three complementary approaches to processing bioinformatic data are described: mapping reads to reference viral sequences; assembling and annotating contigs; taxonomic classification of reads without assembly. The importance of carefully interpreting the results is emphasized, considering the bioinformatic analysis and the validation by molecular genetic methods. This review will be useful for both researchers and specialists who have no experience with high-throughput sequencing, and those who have used this method for other applications.}, } @article {pmid42111813, year = {2026}, author = {Mubaraki, FA}, title = {From sequencing to intelligence: how AI is transforming metagenomics.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21137}, pmid = {42111813}, issn = {2167-8359}, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Machine Learning ; Deep Learning ; Metagenome ; }, abstract = {Microbial communities are critical in advancing human health. Metagenomics is a technique that analyzes these communities and allows for investigating their composition and functions. Metagenomic shotgun sequencing enables to capture all of the genetic material in environmental samples, such as water, soil, or the human gut. Despite this advantage, one of the main challenges of this technique is the assembling and interpreting of its data, as it produces many short, fragmented reads. Though long-read technologies may change this in the future, artificial intelligence (AI), machine learning (ML) and data science (DS) offer a powerful solution now, enabling scientists to efficiently process and analyze these large and complex datasets. This review explores the latest advancements in AI and ML applications across the metagenomic pipeline. First, it examines the impact of deep learning (DL) on next-generation sequencing, particularly for long-read technologies. Then, it discusses how ML is automating and improving quality control processes, as well as the use of AI applications in metagenome-assembled genome (MAG) assembly, with a focus on contig binning. Finally, this article looks at how AI and ML can improve predictive modeling for phenotype prediction.}, } @article {pmid42112348, year = {2026}, author = {Hua, M and Luo, J and Li, P and Zhang, Y and Zhang, X and Wu, Y and Dong, H}, title = {The microbiota-systemic lupus erythematosus axis: mechanisms, diagnostics, and therapeutic frontiers.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1782828}, pmid = {42112348}, issn = {1664-3224}, mesh = {*Dysbiosis/immunology/therapy ; *Microbiota ; *Lupus Erythematosus, Systemic/diagnosis/immunology/microbiology/therapy ; Humans ; Animals ; Molecular Mimicry ; Autoimmunity ; }, abstract = {Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease in which host-microbiota crosstalk plays a pivotal role in immune dysregulation. Recent metagenomic studies have revealed that disease-specific dysbiosis--characterized by the expansion of pathobionts and depletion of immunoregulatory commensals--occurs across the gut, oral cavity, skin, and genital tract. Integrative multi-omics analyses have identified three mechanistic pathways linking microbial imbalance to autoimmunity: (1) microbial peptides trigger molecular mimicry and epitope spreading, activating autoreactive lymphocytes: (2) microbial metabolites disrupt redox homeostasis, impair epithelial barriers, and skew the AhR-mediated Th17/Treg balance; and (3) dysbiosis alters epigenetic regulation by inhibiting DNA methyltransferases, leading to hypomethylation of SLE-risk genes. Translational studies have shown that microbiome-targeted interventions, including probiotics, prebiotics, fecal microbiota transplantation, and even B cell-depleting chimeric antigen receptor T-cell (CAR-T) therapy, can restore microbial balance, reduce autoantibody levels, and modulate the gut-immune axis. Furthermore, microbial signatures are emerging as potential biomarkers for disease activity and treatment response. Despite this promise, challenges remain, such as the impact of immunosuppressants on the microbiota, spatial heterogeneity in host-microbe interactions, and limitations in causal inference. Looking forward, integrating single-cell metagenomics, microbiota-directed diets, and engineered microbial consortia may pave the way for personalized microbiome-based therapies. Reframing SLE as a "meta-organismal imbalance" positions microbial ecology at the forefront of precision medicine.}, } @article {pmid42112399, year = {2026}, author = {Wang, Y and Dong, W and Qin, J}, title = {Fatal AA-like bone marrow failure and invasive pulmonary aspergillosis after long-term pembrolizumab in squamous NSCLC: a case report.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1800904}, pmid = {42112399}, issn = {1664-3224}, mesh = {Humans ; Male ; Middle Aged ; *Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use ; *Carcinoma, Non-Small-Cell Lung/drug therapy/complications ; *Lung Neoplasms/drug therapy/complications ; *Invasive Pulmonary Aspergillosis/etiology/diagnosis ; *Anemia, Aplastic/chemically induced/diagnosis/etiology ; Fatal Outcome ; *Immune Checkpoint Inhibitors/adverse effects ; *Antineoplastic Agents, Immunological/adverse effects ; }, abstract = {Immune checkpoint inhibitors (ICIs) such as pembrolizumab have substantially improved outcomes in advanced non-small cell lung cancer (NSCLC), including squamous histology, but prolonged exposure may be complicated by immune-related adverse events (irAEs) and opportunistic infections. We report a 58-year-old man with advanced squamous NSCLC who achieved durable tumor control after six cycles of pembrolizumab plus platinum-based chemotherapy, followed by pembrolizumab maintenance monotherapy (18 cycles). During the later course, he developed severe bacterial pneumonia, invasive pulmonary aspergillosis (IPA), and subsequent aplastic anemia (AA)-like bone marrow failure. Despite systemic antifungal therapy and supportive measures, he experienced progressive pancytopenia complicated by massive hemoptysis and ultimately died. This case underscores the dual nature of ICIs: while providing meaningful and sustained antitumor benefit, they may rarely precipitate life-threatening hematologic toxicity and facilitate severe opportunistic infections in a complex immunologic milieu. Close surveillance of blood counts and infectious complications is warranted during long-term ICI therapy; unexplained cytopenias or new/worsening radiologic abnormalities should prompt early bone marrow evaluation and comprehensive microbiologic work-up. Metagenomic next-generation sequencing (mNGS) may offer useful adjunctive evidence in diagnostically challenging infections, particularly when invasive sampling is not feasible, but results should be interpreted in conjunction with clinical and radiologic context within a multidisciplinary framework.}, } @article {pmid42112463, year = {2026}, author = {Guo, L and Luo, X and Luo, M and Zhang, M and Wang, B and Fu, Y and Wu, X and Yu, Y and Bai, L and Xu, Z}, title = {Diagnosis and treatment of a patient with mediastinal infection caused by Emergomyces orientalis and Mycobacterium fortuitum.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1778930}, pmid = {42112463}, issn = {2235-2988}, mesh = {Humans ; Female ; Young Adult ; *Mycobacterium Infections, Nontuberculous/diagnosis/drug therapy/microbiology ; *Coinfection/diagnosis/microbiology/drug therapy ; *Mycobacterium fortuitum/isolation & purification/genetics ; Antifungal Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; Tomography, X-Ray Computed ; *Mediastinum/microbiology/pathology/diagnostic imaging ; Amphotericin B/therapeutic use ; China ; Treatment Outcome ; *Eurotiales/isolation & purification ; }, abstract = {BACKGROUND: Emergomycosis, an emerging dimorphic fungal infection caused by Emergomyces species, primarily affects immunocompromised individuals. Emergomyces orientalis has been reported in China, including rare cases in immunocompetent individuals. Diagnosis remains challenging due to the lack of typical clinical manifestations and radiological features. Co-infection with other pathogens further complicates management, with no prior global reports of concurrent E. orientalis and non-tuberculous mycobacterial (NTM) infections.

CASE PRESENTATION: A 21-year-old immunocompetent woman with occupational exposure to soil presented with cough, fever, and a mediastinal mass on chest CT. The initial biopsy specimens revealed granulomatous inflammation and yeast-like fungi. Metagenomic next-generation sequencing (mNGS) of endobronchial ultrasound (EBUS)-guided specimens confirmed E. orientalis (40 reads). Liposomal amphotericin B induction therapy initially relieved the symptoms. However, recurrence prompted repeat mNGS, which revealed elevated Mycobacterium fortuitum loads (791 reads). Combined with the patient's history of soil exposure, a diagnosis of mediastinal E. orientalis with M. fortuitum co-infection was established based on the clinical presentation, the chest CT findings, histopathological observations of yeast-like fungi, the mNGS results, and the therapeutic response. Following confirmation of the co-infection, tailored adjustments to the antimicrobial regimen led to successful clinical management.

CONCLUSION: To the best of our knowledge, this is the first study in which E. orientalis and M. fortuitum were documented to coexist in the mediastinum. The dual pathogens were identified through a combination of EBUS-guided biopsy and mNGS. Accurate pathogen identification followed by tailored, pathogen-directed therapy is essential for the effective management of an E. orientalis and M. fortuitum mixed infection.}, } @article {pmid42112573, year = {2026}, author = {Liborio, MP and Peri, AM and Harris, PNA}, title = {Evaluating emerging molecular diagnostics for severe infections in neutropenic patients with hematological malignancies.}, journal = {Expert review of molecular diagnostics}, volume = {26}, number = {4}, pages = {345-361}, doi = {10.1080/14737159.2026.2667917}, pmid = {42112573}, issn = {1744-8352}, mesh = {Humans ; *Hematologic Neoplasms/complications ; *Molecular Diagnostic Techniques/methods ; *Neutropenia/complications/etiology/diagnosis ; High-Throughput Nucleotide Sequencing ; *Pathology, Molecular/methods ; }, abstract = {INTRODUCTION: Neutropenia significantly increases infection risk in hematologic malignancies. Clinical signs are often subtle and fever may be the only indicator. Molecular diagnostic methods promise faster, more sensitive pathogen detection compared to conventional methods, aiming to improve timely and appropriate therapy.

AREAS COVERED: This review summarizes emerging molecular diagnostics for severe infections in neutropenic hematological malignancies, focusing on microbiological performance and, where available, clinical impact. We conducted a search in PubMed and Embase using subject headings: 'molecular diagnosis,' 'neutropenic,' 'infections,' 'hematological malignancies,' supplemented by information from manufacturers of commercial assays. The technologies reviewed include multiplex polymerase chain reaction, microarray-based assays, metagenomic and targeted next-generation sequencing, host transcriptomics, and methods for diagnosing invasive fungal infections. For each, we describe key characteristics, diagnostic performance, and clinical utility when reported.

EXPERT OPINION: Emerging molecular diagnostics shorten time to pathogen and resistance identification and broaden detection of organisms in febrile neutropenic patients with hematological malignancies. These methods are best integrated as complements to culture-based methods within centers with antimicrobial stewardship programs, where they inform earlier targeted therapy and rational de-escalation. Priority actions include prospective trials powered for measuring clinical outcomes and economic endpoints, with standardized workflows, reporting, and quality assurance to enable clinical implementation.}, } @article {pmid42112737, year = {2026}, author = {Ji, G and Duan, J}, title = {Pharmacist-driven optimization of presumptive psittacosis management: a case report of rapid clinical resolution.}, journal = {Journal of infection in developing countries}, volume = {20}, number = {4}, pages = {596-600}, doi = {10.3855/jidc.22259}, pmid = {42112737}, issn = {1972-2680}, mesh = {Humans ; Female ; Middle Aged ; *Psittacosis/drug therapy/diagnosis ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; Chlamydophila psittaci/isolation & purification ; Community-Acquired Infections/drug therapy/diagnosis/microbiology ; Animals ; }, abstract = {INTRODUCTION: Chlamydia psittaci has a high incidence of pneumonia after infection, but clinical diagnosis still faces challenges due to the lack of specific clinical manifestations and low positive rates in routine testing.

CASE PRESENTATION: A 60-year-old female patient with community-acquired pneumonia (CAP) failed to respond to initial intravenous antimicrobial therapy with cefmetazole/ciprofloxacin followed by piperacillin-tazobactam/levofloxacin, exhibiting persistent fever and worsening symptoms. Serial laboratory testing revealed progressive elevation of inflammatory markers, with C-reactive protein (CRP) rising from 110.2 to 120.9 mg/L and procalcitonin (PCT) from 1.37 to 2.15 ng/mL. Essential bronchoscopic examination and metagenomic next-generation sequencing (mNGS) could not be performed due to patient refusal, creating a diagnostic deadlock. The clinical pharmacist identified avian exposure during medication rounds, enabling presumptive diagnosis of psittacosis. Immediate pharmacist-initiated interventions included discontinuation of levofloxacin and commencement of targeted oral minocycline therapy. Clinical resolution occurred within 48 hours with defervescence and symptomatic improvement. Subsequent minocycline-induced nausea and diarrhea were effectively managed through pharmacist-instructed co-administration with food. Continuous clinical improvement facilitated discharge on oral minocycline, with follow-up imaging confirming complete resolution of pulmonary infiltrates.

CONCLUSIONS: This case underscores the value of pharmacist-led pharmaceutical assessment in uncovering atypical infection etiologies and guiding targeted antimicrobial therapy.}, } @article {pmid42112819, year = {2026}, author = {Wei, X and Song, W and Li, S}, title = {Seasonal variations drive microbial community structure and nitrogen cycling in sediments of tributary pumping station forebays.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0304725}, pmid = {42112819}, issn = {2165-0497}, support = {B240201187//Fundamental Research Funds for the Central Universities/ ; 52100175//National Natural Science Foundation of China/ ; }, mesh = {Seasons ; *Nitrogen Cycle ; *Geologic Sediments/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology/chemistry ; *Microbiota/genetics ; Denitrification ; Metagenomics ; }, abstract = {Discharge from tributary pumping stations often impacts mainstream water quality, yet microbial communities and nitrogen metabolism in pumping station forebays remain poorly understood. Therefore, this study investigated the microbial community structure and nitrogen cycling mechanisms in sediments of tributary pumping station forebays within the Qinhuai River Basin using 16S rRNA and metagenomic sequencing. Results showed significant seasonal variations in the diversity and structure of sediment microbial communities, with higher diversity in spring than in winter. Genes associated with denitrification (e.g., narG, nirS, and nosZ) showed the highest abundance, suggesting that denitrification may be a key nitrogen transformation pathway. Co-occurrence network analysis revealed tighter associations between microbial taxa and nitrogen-cycling genes in spring, indicating more complex potential interactions during this season. The shift of network hubs across seasons suggested a seasonal succession of potential core functions related to nitrogen cycling. Redundancy analysis revealed that nitrate nitrogen (NO3[-]-N), water temperature (WT), and ammonium nitrogen (NH4[+]-N) were the factors most strongly associated with microbial community variation, with WT showing the strongest association with functional gene distribution. Partial least squares path modeling revealed that seasonal variation had a significant positive association with denitrification gene abundance and a significant negative association with genes related to assimilatory nitrate reduction to ammonium and anaerobic ammonium oxidation. These findings improve our understanding of microbially mediated nitrogen cycling in pumping station forebays and provide a scientific basis for water quality management in river networks influenced by pumping station drainage.IMPORTANCEThis study is important because it reveals that pumping stations, which are key infrastructure in managed river systems, are not just hydraulic structures but dynamic bioreactors where microbial communities actively transform nitrogen. By demonstrating seasonal variations in microbial diversity and revealing a high denitrification potential, the research provides a mechanistic understanding of how nitrogen pollution is naturally mitigated in these engineered environments. Crucially, it pinpoints temperature as a primary regulator of these microbial functions. These insights allow water managers to proactively optimize pumping operations and design interventions that harness microbial activity, ultimately protecting downstream water quality from nutrient pollution in a changing climate.}, } @article {pmid42112890, year = {2026}, author = {Sorokin, DY and Khot, V and Merkel, AY and Mosier, D and Bale, NJ and Koenen, M and Strous, M}, title = {Physiology, functional genomics, and proteomics of Verruconatronum alginivorum gen. nov., sp. nov., the first isolated haloalkaliphile within Verrucomicrobiota, representing a new family, Verruconatronumaceae fam. nov.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {6}, pages = {e0047526}, pmid = {42112890}, issn = {1098-5336}, support = {25-14-00272//Russian Science Foundation/ ; CRC-2020-00257//Canada Research Chairs/ ; }, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; Lakes/microbiology ; Genomics ; *Verrucomicrobia/genetics/classification/isolation & purification/physiology/metabolism ; Proteomics ; Alginates/metabolism ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Despite the successful cultivation of many microbes from rich bacterial communities inhabiting alkaline soda lakes, members of the bacterial phylum Verrucomicrobiota have so far been detected only through metagenomics. Here, we used alginate as a selective substrate to enrich and isolate two strains of haloalkaliphilic Verrucomicrobiota. The isolates share identical 16S rRNA gene sequences representing a new genus lineage, and, together with other metagenome assembled genomes, a new family within Opitutales. Cells of strains AB-alg1[T] (from soda lakes) and AB-alg4 (from soda solonchak soils) are small and motile cocci forming submerged colonies in soft alginate agar. They are saccharolytic heterotrophs growing aerobically on polysaccharides (alginate, starch, and inulin) and sugars (glucose, fructose, mannose, sucrose, melezitose, maltose, and cellobiose). They also grow anaerobically by fermentation of alginate and D-mannose and by coupling incomplete denitrification to oxidation of alginate. Both isolates are obligately alkaliphilic and moderately salt-tolerant. The dominant membrane phospholipids include phosphatidylcholines and diphosphatidylglycerols (cardiolipins). The genome of AB-alg1[T] features polysaccharide lyases of the PL6, 7, 15, 17, 38, and 39 families for depolymerization of alginate. Based on distinct phenotype and phylogeny, we propose classification of strains AB-alg1[T] (JCM 35393[T]=UQM 41574[T]) and AB-alg4 as Verruconatronum alginivorum gen. nov., sp. nov. within a new family Verruconatronumaceae.IMPORTANCEAlkaline soda lakes and soils are extreme habitats dominated by obligate haloalkaliphic prokaryotes, some of which can produce alkali- and salt-stable polysaccharide-degrading exoenzymes useful for industrial and domestic applications. However, so far, little was known about the microbial potential for mineralization of acidic polysaccharides, such as alginate, in these habitats. The described isolates are the first representatives of a new family within the phylum Verrucomicrobiota specializing in the degradation of alginate and related polysaccharides. We present the key enzymatic machinery for alginate breakdown. These enzymes are high-pH tolerant and have potential for industry applications, for example, in washing powders and biomass waste recycling. Furthermore, the new family is one of the most abundant taxa in alkaline environments, and these environments are not known to harbor signature alginate producing biota, such as brown algae. This way, our study opens a new window on polysaccharide turnover in alkaline environments.}, } @article {pmid42112913, year = {2026}, author = {Krupovic, M and Koonin, EV}, title = {Organization and evolution of the virosphere and the replicator space.}, journal = {Comptes rendus biologies}, volume = {349}, number = {}, pages = {35-75}, doi = {10.5802/crbiol.193}, pmid = {42112913}, issn = {1768-3238}, mesh = {*Viruses/genetics ; *Biological Evolution ; Animals ; Virus Replication ; Humans ; Virion/genetics ; Genome, Viral ; }, abstract = {Viruses are obligate symbionts of cellular life forms that can replicate only within host cells and typically form virions (virus particles) to spread among host organisms. Virions numerically dominate the biosphere, exceeding the number of cells several-fold, and also comprise the main reservoir of genetic diversity on earth. Nearly all organisms host multiple, diverse viruses. Unlike cellular organisms, viruses have genomes (genetic information carriers incorporated into virions) that consist of all forms of RNA and DNA, suggesting an evolutionary connection between extant viruses and the primordial replicator pool. Lately, extensive mining of metagenomes and metatranscriptomes has dramatically expanded the world of viruses (virosphere), revealing an unsuspected and unprecedented diversity. Viruses share no universal genes and have multiple origins. However, about 15 viral hallmark genes each bring together multiple, diverse groups of viruses, and many other genes are shared within such groups. Evolution of viruses is inextricably intertwined with the evolution of their hosts. A key aspect of virus-host coevolution is the arms race resulting in accelerated evolution on both sides, especially of host defenses and viral counter-defenses. A complementary, prominent feature of this coevolution is exaptation, whereby viral genes are coopted by the hosts for antiviral defense and other roles, and conversely, viruses capture host genes for diverse functions in virus replication, virion morphogenesis and virus-host interaction. In this review, we attempt a synthesis of the current understanding of the global organization of the virosphere, the major trends and events in the evolution of viruses, and the high-level taxonomy of viruses.}, } @article {pmid42113294, year = {2026}, author = {Cortez-Cervantes, J and Carrillo-Reyes, J and Cervantes-Avilés, P and Moreno-Andrade, I}, title = {A statistical framework for identifying microbial indicators of ammonia-induced process instability in food waste anaerobic digestion.}, journal = {Bioprocess and biosystems engineering}, volume = {}, number = {}, pages = {}, pmid = {42113294}, issn = {1615-7605}, support = {IN104825//DGAPA-UNAM PAPIIT/ ; IN105025//DGAPA-UNAM PAPIIT/ ; 2022 Core Lab Genomics Tec-BASE Seed Fund//Instituto Tecnológico y de Estudios Superiores de Monterrey/ ; }, abstract = {Ammonia is an essential nutrient for anaerobic digestion (AD) but becomes inhibitory at elevated concentrations, leading to process instability. Although numerous microbial taxa and functional genes have been proposed as indicators of ammonia stress, most lack systematic validation across defined inhibitory thresholds. In this study, batch anaerobic digestion assays were conducted under increasing total ammonia nitrogen concentrations to experimentally characterize ammonia-induced inhibition. Methane yields obtained from batch tests were fitted using a Hill model to define non-inhibitory, inhibitory, and minimum inhibitory ammonia levels. Shotgun metagenomic sequencing was applied to samples representative of each inhibition level, and a statistical framework integrating differential abundance analysis, network topology, redundancy analysis, and metabolic relevance was used to identify robust microbial indicators. Key taxa, including Anaerolinea, Methanomassiliicoccus, and Syntrophobacter, along with functional genes involved in acetate and propionate metabolism (e.g., acs and fhs), showed consistent and threshold-dependent responses to ammonia stress. These microbial indicators provide mechanistic insight into ammonia-induced AD instability and offer a promising basis for early-warning monitoring and microbial management strategies to improve the operational stability of anaerobic digesters treating food waste.}, } @article {pmid42113401, year = {2026}, author = {Bhattacharjee, A and Singh, AK}, title = {Ecological and genomic insights into Bacillus altitudinis as a potential indicator of resistance genes in soil antimicrobial resistance pools.}, journal = {Environmental science and pollution research international}, volume = {33}, number = {16}, pages = {7996-8011}, pmid = {42113401}, issn = {1614-7499}, support = {OLP-2035//CSIR/ ; OLP-2081//CSIR/ ; OLP-2503A//CSIR/ ; GPP-0423//DST-ANRF/ ; }, mesh = {*Soil Microbiology ; *Bacillus/genetics ; Anti-Bacterial Agents/pharmacology ; Soil ; Animals ; India ; Poultry ; Microbial Sensitivity Tests ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Soil associated with intensive poultry farming serves as a seminal reservoir of antimicrobial resistance genes. This study employed an integrated approach that combined metagenomics, phenotypic analysis, and whole-genome sequencing to investigate the soil resistome of poultry farms in the Jorhat district, Northeast India, and to evaluate Bacillus altitudinis as an environmental potential indicator for antimicrobial resistance. Metagenomic analysis of poultry-affected soil revealed a diverse array of resistance genes, including 753 unique resistance ontologies related to β-lactam, glycopeptide, macrolide, aminoglycoside, chloramphenicol, and colistin resistance. Culture-based testing of soil and fecal isolates (400 isolates) showed high resistance rates to colistin and ciprofloxacin (~60%), as well as notable resistance to erythromycin and kanamycin, indicating strong antibiotic selection pressures in these ecosystems. Among multidrug-resistant strains, B. altitudinis S2 was particularly notable, exhibiting high minimum inhibitory concentrations for last-line antibiotics such as vancomycin (>50 µg/mL), colistin (>50 µg/mL), and fourth-generation cephalosporins. It also demonstrated multidrug β-lactam resistance supported by synergistic inhibitors. Whole-genome sequencing (3.7 Mb) uncovered a complex antimicrobial resistance gene (ARG) profile, including vanZ, mcr-1, catA, mph, aph, and oxa-type β-lactamase genes, alongside multiple SMR, MATE, and RND efflux mechanisms. Many of these genes were located within genomic islands, prophage traces, and mobile genetic elements, strongly indicating horizontal gene transfer from various bacteria, including gut-associated enterococci. The genome also contained genes for resistance to heavy metals and oxidative stress, suggesting co-selection processes that sustain ARGs in soil. The study tries to show B. altitudinis as a crucial environmental indicator for ARGs, serving a genetic bridge between poultry gut microbiota and soil antimicrobial resistance pools, highlighting its significance for One Health antimicrobial resistance surveillance.}, } @article {pmid42113811, year = {2026}, author = {Mussa, AJ and Ruboha, JO and Kabota, SA and Martin, MJ and Mwatawala, MW}, title = {Elevation and land use shape soil entomopathogenic fungal communities in the Uluguru mountains, Tanzania: Insights from metagenomic and culture-based approaches.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0348781}, pmid = {42113811}, issn = {1932-6203}, mesh = {Tanzania ; *Soil Microbiology ; Animals ; *Fungi/genetics/classification/isolation & purification ; *Altitude ; Biodiversity ; Soil/chemistry ; Metagenomics/methods ; *Mycobiome ; }, abstract = {BACKGROUND: Soil-borne entomopathogenic fungi (EPFs) support ecological regulation of pests, yet their distribution across tropical mountain agroecosystems is poorly characterized. The study conducted between April and December 2024, evaluated diversity and distribution of soil EPF along the Uluguru Mountains slopes in Morogoro, Tanzania.

METHODS: Twenty-four soil samples were collected from cultivated and fallow soils at low (518 m), medium (1100 m), and high (1700 m) elevations on the Uluguru slopes (Morogoro, Tanzania). Amplicon sequencing of the ITS region profiled fungal communities, and selective isolation with ITS barcoding confirmed cultivable taxa. Diversity indices, Bray-Curtis dissimilarity, Principal Coordinate Analysis (PCoA), and PERMANOVA evaluated patterns across elevation and land use.

RESULTS: Fourteen EPF species in 12 genera were detected, dominated by Ophiocordycipitaceae (56.1%) and Clavicipitaceae (37.8%). Purpureocillium lilacinum, Metarhizium anisopliae, Clonostachys rosea, and Pochonia chlamydosporia were widespread. Cultivated soils at medium- and high elevations showed greater richness and diversity (1.37 and 1.57) than fallows (0.64 and 0.48) respectively, while high-altitude fallows were strongly dominated by Metapochonia suchlasporia. Community composition clustered by land use, with elevation as a secondary driver (PERMANOVA p = 0.06). Selected P. lilacinum and C. rosea species caused 10-50% mortality of Spodoptera frugiperda larvae in preliminary laboratory assays.

CONCLUSIONS: Elevation and land use jointly structure EPF communities in the Uluguru Mountains. Some taxa showed preliminary pathogenicity in laboratory assays, indicating potential for future evaluation as biological control agents in smallholder farming systems. Public deposition of sequencing reads will facilitate reuse and benchmarking.}, } @article {pmid42113832, year = {2026}, author = {Cai, Y and Wei, Y and Du, G and Zhang, X and Wang, Z and Wang, Z and Han, Z and Zhang, Y and Xu, Y and Han, X and Li, J and Li, Q}, title = {Identification and genetic characterization of a distinct genotype of Puumala orthohantavirus in Hebei Province, China.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {5}, pages = {e0014250}, pmid = {42113832}, issn = {1935-2735}, mesh = {China/epidemiology ; Animals ; Phylogeny ; *Genotype ; Genome, Viral ; *Puumala virus/genetics/classification/isolation & purification ; Arvicolinae/virology ; Rodentia/virology ; RNA, Viral/genetics ; *Rodent Diseases/virology/epidemiology ; }, abstract = {Orthohantavirus infections pose a significant threat to human health, while numerous orthohantaviruses have been identified, suspected viral infections remain undiagnosed in the world, which highlights the need for further identification and characterization of viruses circulating in humans and host animals. In this study, viral metagenomics was utilized to investigate orthohantaviruses present in tissue samples collected from rodents trapped at the Bashang Grassland of Hebei Province, China. A total of 145 wild rodents belonging to six species were captured in the study area, and 725 tissue samples (lung, liver, kidney, spleen, gut) were collected in 2024. A Puumala orthohantavirus (PUUV), named Guyuan strain, was identified in Myodes rufocanus, with a positive rate of 0.69%. The complete genomic sequences of the L, M, and S segments were obtained and confirmed by Sanger sequencing. Phylogenetic analysis of these genomic sequences with those of other orthohantavirus species showed that the L, M, and S segments clustered with PUUV genomic sequences, while sharing a nucleotide sequence similarity of 81.2%, 80.2%, and 84.3% with previously characterized reference viral strains Kitahiyama128L, Tobetsu_04, and Baltic/205 Cg, respectively. Amino acid homology analysis demonstrated that the sequences exhibited the highest identity to PUUV Hokkaido strain at a level of 95.4%, 94.6%, and 97.0% respectively. Viral particles were observed in lung and kidney tissues using transmission electron microscopy, and viral protein antigen was detected in viral RNA-positive lung, liver, and kidney tissues through immunofluorescence assay with antibodies against the PUUV nucleocapsid protein, thereby confirming the virus's multiorgan tropism. The results demonstrated that a distinct genotype of PUUV was circulating in rodents in the study areas, which may have implications for zoonotic transmission surveillance and public health management in Hebei Province.}, } @article {pmid42114216, year = {2026}, author = {Que, H and Jiang, X and Wu, X and Li, S}, title = {Construction of a "three-stage and four-level" evaluation system for cerebrospinal fluid pathogens based on mNGS: insights from a case of co-detection of Cryptococcus and Epstein-barr virus.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {1}, pages = {117457}, doi = {10.1016/j.diagmicrobio.2026.117457}, pmid = {42114216}, issn = {1879-0070}, mesh = {Humans ; *Cryptococcus/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; *Herpesvirus 4, Human/genetics/isolation & purification ; *Epstein-Barr Virus Infections/diagnosis/cerebrospinal fluid/virology ; *Cerebrospinal Fluid/virology/microbiology ; *Coinfection/diagnosis/microbiology/virology ; Male ; *Metagenomics/methods ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) has brought about a revolutionary change in the diagnosis of central nervous system (CNS) infections. Nevertheless, the interpretation of results with multiple detected pathogens still poses a substantial clinical challenge.

AIM: A preliminary exploration of the application value of the developed "Three-Stage, Four-Level" assessment system in interpreting mNGS cerebrospinal fluid test reports.

METHODS: Based on a systematic review of relevant domestic and international literature, combined with practical experience in the field, a multi-dimensional "Three-Stage, Four-Level" evaluation system centered on a clinical-microbiological evidence chain was constructed. This study explores the application value of the system through a case of mNGS detection for co-preservation of Cryptococcus and Epstein-Barr virus (EBV) in cerebrospinal fluid (CSF).

RESULTS: The system effectively integrated multi-source information, facilitating a precise and stratified interpretation of CSF mNGS results. It successfully differentiated Cryptococcus as the pathogenic agent and EBV as a latent pathogen. Consequently, early antifungal therapy was initiated, resulting in a gradual improvement of symptoms and a favorable prognosis.

CONCLUSION: This case initially demonstrates that the "Three-Stage,Four-Level "evaluation system provides a standardized and operational framework for interpreting mNGS cerebrospinal fluid multiplex pathogen detection results, showing preliminary value in precisely distinguishing pathogen types; however, further validation with larger sample sizes is warranted.}, } @article {pmid42114574, year = {2026}, author = {Li, X and Cheng, S and Wang, X and Gu, X and Xu, X and Duan, X and Xue, G and Oleskowicz-Popiel, P and Xu, J and Liu, B and Liu, Z and Zhou, A and Makinia, J}, title = {Intrinsic waste component synergy: calcium-rich eggshell waste modulates fungal-bacterial microbiome toward selectively medium-chain fatty acid production.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134795}, doi = {10.1016/j.biortech.2026.134795}, pmid = {42114574}, issn = {1873-2976}, mesh = {*Fatty Acids/biosynthesis ; *Microbiota/drug effects ; Animals ; *Egg Shell/chemistry ; *Fungi/metabolism ; *Bacteria/metabolism ; *Calcium ; Ethanol/metabolism ; *Waste Products/analysis ; Caproates ; }, abstract = {The valorization of waste streams into medium-chain fatty acids (MCFAs) through fungi-bacteria synergy is often hindered by substrate competition and distinct ecological niches. This study demonstrates that eggshell waste acts as a bioregulator to optimize this interaction for caproate production. At a 20 g/L dosage, eggshells facilitated high caproate production (22.3 ± 1.3 gCOD/L) driven by in-situ ethanol supply (11.3 ± 1.9 gCOD/L). The amendment established stable micro-niches, significantly enriching yeasts (Wickerhamomyces, Candida, and Issatchenkia, 69.2%) and chain-elongating bacteria (CEB, Caproiciproducens, and Clostridium_sensu_stricto_12, 10.2%), while metagenomics confirmed upregulated glycolysis and reverse β-oxidation pathways. Additionally, yeast synergy with CEB via ethanol cross-feeding in a sugar-rich environment can be disrupted under the sugar-depleted phase. The coculture experiments unveiled that 8 g/L Ca[2+] alleviates fungi-bacteria conflict and promotes CEB functionality. This study presents a waste valorization strategy, leveraging intrinsic waste synergies to optimize fungal-bacterial interactions and drive endogenous ethanol-based caproate production.}, } @article {pmid42114636, year = {2026}, author = {Zou, G and Zou, N and Tang, Y and Wang, Q and Xiao, H and Chen, Q and Liu, Z and Wang, K and Yang, F and Zhao, H and Qin, Y and Du, A and Chen, Y}, title = {Tire wear particles induce a functional trade-off in bioretention systems: Coupled effects on nitrogen removal and greenhouse gas emissions.}, journal = {Environmental research}, volume = {303}, number = {Pt 1}, pages = {124722}, doi = {10.1016/j.envres.2026.124722}, pmid = {42114636}, issn = {1096-0953}, mesh = {*Nitrogen/analysis ; *Greenhouse Gases/analysis ; *Air Pollutants/analysis ; }, abstract = {Bioretention systems are widely adopted nature-based solutions (NbS) for mitigating urban stormwater pollution, yet their long-term functional stability is increasingly undermined by the accumulation of tire wear particles (TWPs). This study moves beyond descriptive performance assessment to investigate the underlying biogeochemical mechanisms governing the response of bioretention media to dynamic TWP stress (0, 1, 10, and 100 mgL[-1]). Our results reveal a sophisticated functional trade-off induced by TWPs: although nitrogen removal efficiency was significantly compromised-with NH4[+]-N and total nitrogen (TN) removal rates decreasing by up to 14.64% and 11.02%, respectively-the system's net global warming potential was concurrently mitigated, achieving a 7.41-61.26% reduction in CO2-equivalent emissions. Mechanistically, partial least squares path modeling (PLS-PM) identified that TWPs trigger a metabolic bottleneck in the nitrogen cycle. The accumulation of TWPs significantly inhibited hydroxylamine oxidoreductase (HAO) and hydroxylamine reductase (HyR) activities (path coefficient: -0.742, p < 0.01) and suppressed the abundance of nitrifying bacteria (e.g., Nitrospira). Crucially, metagenomic insights demonstrated that TWPs redirected the nitrogen flux by upregulating the nrfA gene, thereby facilitating dissimilatory nitrate reduction to ammonium (DNRA) as an alternative pathway. These findings demonstrate that high TWP levels impair nitrogen removal through multi-interface synergy, highlighting potential ecological risks. This study provides a novel predictive framework for managing emerging microplastic pollutants in green infrastructure, offering actionable insights for optimizing the multifunctional ecosystem services of urban NbS under anthropogenic stress.}, } @article {pmid42114650, year = {2026}, author = {Yang, J and Zhang, Z and Li, G and Yan, K and Song, Y and Zhang, J and Guo, Q and Zha, S and Sun, P and Zhang, X and Xia, Z and Yao, Z and Feng, X and Liang, J}, title = {Virus-associated immune dysregulation presenting as facial granulomatous dermatitis in DiGeorge syndrome: A case series.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {169}, number = {}, pages = {108776}, doi = {10.1016/j.ijid.2026.108776}, pmid = {42114650}, issn = {1878-3511}, mesh = {Humans ; *DiGeorge Syndrome/complications/immunology/virology ; Male ; Female ; *Dermatitis/virology/diagnosis/immunology ; *Granuloma/virology ; Child, Preschool ; Herpesvirus 4, Human/isolation & purification/genetics ; Infant ; *Epstein-Barr Virus Infections/immunology/complications/diagnosis ; Skin/pathology/virology ; DNA, Viral/blood ; }, abstract = {Chronic granulomatous dermatitis in children with inborn errors of immunity poses diagnostic challenges, particularly when persistent viral detection coexists with impaired T-cell surveillance. We report two children with 22q11.2 deletion syndrome who developed chronic facial granulomatous dermatitis in the setting of T-cell immunodeficiency and EBV detection. Both patients had persistent facial plaques refractory to conventional antimicrobial or anti-inflammatory treatment, elevated EBV DNA in blood and granulomatous lymphohistiocytic infiltrates on skin biopsy. Tissue mNGS identified EBV in lesional specimens. In patient 1, EBER positivity and a restricted/skewed TRB repertoire provided stronger support for local EBV-associated immune dysregulation. In patient 2, EBV was detected by mNGS, but EBER staining was negative, additional microorganisms were identified, and TRB findings were more consistent with reactive or oligoclonal expansion, making causal attribution less certain. Rubella virus-associated granuloma, a key differential diagnosis in immunodeficient children, was not supported by lesion-directed testing. These cases highlight chronic granulomatous dermatitis as a possible manifestation of virus-associated immune dysregulation in DiGeorge syndrome and emphasize that mNGS results require careful integration with tissue localization, histopathology, clonality assessment, and immune context.}, } @article {pmid42114714, year = {2026}, author = {Zhang, D and Yan, Z and Liang, J and Zhong, J and Liu, Y and Li, S and Wang, L and Gong, F and Hu, N and Ding, D and Yu, H}, title = {Uranium-induced differentiation in metabolic responses and functional potential of nitrogen-cycling microorganisms across different soil types.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {401}, number = {}, pages = {128317}, doi = {10.1016/j.envpol.2026.128317}, pmid = {42114714}, issn = {1873-6424}, mesh = {*Soil Microbiology ; *Uranium ; Soil/chemistry ; *Nitrogen Cycle ; Nitrogen/metabolism ; Bacteria/metabolism ; Forests ; Grassland ; }, abstract = {Uranium (U) contamination poses a severe ecological risk by disrupting key biogenic element cycles, particularly nitrogen (N) transformation. However, the extent to which intrinsic soil heterogeneity shapes the functional adaptation of N cycling microorganisms to U stress remains poorly understood. This study investigated soil microcosms with metagenomic analysis to unravel the structural and functional differentiation of N cycling communities across forest (FT), grassland (GL), and farmland (FL) soils. Our results indicated that U contamination exerted significant selective pressure, leading to distinct functional differentiation in N cycling processes (R[2] = 0.56) which was primarily shaped by land-use legacy (R[2] = 0.62). Driven by this U-induced pressure, the three soils diverged into unique N cycling adaptive strategies. Specifically, U stress shifted the FT towards a strategy of energetic autonomy, enriching robust nitrate reduction coupled with a metabolic repertoire associated with U(VI) resistance and transformation potential. In the GL, U exposure shaped a complex, self-sustaining co-occurrence network associated with potential functional stability, characterized by cross-pathway complementation among N fixation, nitrification, and anammox. Conversely, U contamination drove the FL into a maladaptive simplification, where the reduction of functional redundancy and the dominance of a single nitrification pathway led to heightened vulnerability. Collectively, this study demonstrates that U stress acts as a selective filter that amplifies pre-existing soil driven discrepancies, driving soil microbial communities onto distinct functional potential trajectories. These findings emphasize the necessity of developing differentiated risk management strategies based on the specific N cycling resilience of various soil types.}, } @article {pmid42114750, year = {2026}, author = {Saedi, N and Zhang, S and Sahana, G and Villumsen, TM and Stephansen, RB and Lund, MS and Cai, Z and Karaman, E}, title = {Comparison of 16S rRNA Sequencing and Shotgun Metagenome Sequencing for Estimating Genotypic and Phenotypic Parameters of Enteric Methane Emission in Dairy Cattle.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-28157}, pmid = {42114750}, issn = {1525-3198}, abstract = {Methane emissions from ruminants significantly contribute to greenhouse gases, making it crucial for sustainable livestock breeding to understand how both genetic and microbial factors influence methane production. We compared the heritability and microbiability for enteric methane in cows using microbial features derived from 16S rRNA amplicon data and shotgun metagenomics data, together with genome-wide marker data. The features derived from 16S rRNA data were 16s genus (16s-G), 16s species (16s-S), 16s Predicted microbial genes (16s-PMG) and 16s Predicted metabolic pathways (16s-PMP). The features derived from metagenomics data were metagenomic species (M-S) and metagenomic genus (M-G) considering 3 different databases (MGnify, GTDB, and NCBI). The heritability of methane ranged from 0.08 to 0.14. The 16s-G explained 28% of phenotypic variation in methane, and contributed the most to the heritability estimate for methane among other features. For the same feature data sets, we estimated the heritability of each microbial feature. Most microbial features had low heritability, while a subset had high values (up to 0.8). The highest heritabilities were observed for M-S MGnify feature RUG592 sp902767285 (0.95) and M-G NCBI genus feature Leadbettera (0.98). We found that the microbiota in the rumen is primarily determined by environmental factors, whereas host genetics has a significant impact on the abundance of certain functionally important microbes. To the best of our knowledge, this study presents the first comparison of methane heritability in dairy cattle incorporating microbial data (1) from multiple techniques such as 16S rRNA amplicon sequencing and shotgun metagenomic sequencing, and (2) from multiple levels of microbial features such as 16s-G, 16s-S, 16s-PMG, 16s-PMP, and M-S and M-G. Our results highlight heritable microbial species/genus as potential targets for microbiome-informed breeding strategies to reduce methane emissions in dairy cattle.}, } @article {pmid42115187, year = {2026}, author = {Zhang, J and Chen, F and Xu, X and Zhang, L and Zhang, L and Qin, B and Li, K and Liu, Q and Hou, H and Li, Y and Liu, C and Li, Y and Shi, J and Teng, T and Wang, C and Zhou, X}, title = {Gut microbiota dysbiosis drives depression-like behavior in adolescent rats via lysine-regulated mTOR autophagy pathway.}, journal = {Translational psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41398-026-04095-2}, pmid = {42115187}, issn = {2158-3188}, abstract = {The prevalence of major depressive disorder (MDD) is increasing globally, particularly among adolescents. Although gut-brain axis dysfunction has been implicated in adolescent depression, the mechanisms by which gut microbiota dysbiosis drives depressive behaviors and potential antidepressant targets remain unclear. In this study, fecal microbiota transplantation (FMT) was performed from either healthy controls (HCs) or adolescents with MDD into antibiotic-treated adolescent rats. FMT from MDD adolescents induced depressive-like behaviors in recipient rats. Metagenomic sequencing revealed that FMT from MDD adolescents led to alterations in gut microbiota in recipient rats. While qPCR, Western blotting, immunofluorescence, and transmission electron microscopy (TEM) confirmed that these rats exhibited prefrontal cortex (PFC) autophagy hyperactivation, evidenced by a reduction in SQSTM1/p62 levels, an elevation in the LC3-II/LC3-I ratio, upregulated Beclin1, and increased numbers of autolysosomes. Similar autophagy-related transcriptional changes were observed in peripheral blood from MDD adolescents. Furthermore, ELISA showed reduced plasma lysine levels in MDD adolescents and decreased lysine concentrations in the PFC of FMT-MDD rats. The antidepressant effect of lysine and its interaction with autophagy were explored in a chronic unpredictable mild stress (CUMS) rat model with or without rapamycin (the autophagy activator, RAPA). Lysine supplementation alleviated depressive-like behaviors and suppressed PFC autophagy hyperactivation, while these effects were abolished by RAPA co-treatment. These findings reveal lysine deficiency as a metabolic bridge between gut microbiota imbalance and neuronal autophagy dysregulation, suggesting a gut microbiota-lysine-autophagy axis as an innovative mechanism and therapeutic focus for adolescent depression.}, } @article {pmid42115271, year = {2026}, author = {Li, Z and Zhang, Q and Yang, J and Lei, R and Lu, W}, title = {Altered gut microbiota and metabolites in children with non-organic anorexia: a multi-omics integration study.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-52084-8}, pmid = {42115271}, issn = {2045-2322}, support = {S2024106612441//Provincial-level College Students' Innovation and Entrepreneurship Project of Zunyi Medical University/ ; S2024106612258//Provincial-level College Students' Innovation and Entrepreneurship Project of Zunyi Medical University/ ; Basic of QKh-ZK [2024] General 312//Science and Technology Department of Guizhou Province/ ; gzwkj2025-401//Science and Technology Fund Project of Guizhou Provincial Health Commission/ ; }, abstract = {Gut microbiota alterations have been linked to childhood eating disorders, but the functional and metabolic changes in non-organic anorexia (NOA) remain poorly understood. This study aimed to characterize the gut microbial composition, function, and metabolic profiles in children with NOA using an integrated multi-omics approach. A case-control study was conducted involving 88 children aged 1-5 years (48 NOA, 40 healthy controls). Gut microbiota composition was assessed via 16S rRNA gene sequencing of all fecal samples. Subsequently, the five most representative samples from each group were selected for deep shotgun metagenomic sequencing and liquid chromatography-mass spectrometry (LC-MS) based non-targeted metabolomics. NOA children showed significantly higher microbial richness and diversity (Chao1, Shannon; P < 0.001). The NOA group had elevated Firmicutes, Bacteroidota, Bacteroides, Faecalibacterium, Subdoligranulum, and Roseburia, but reduced Actobacteriota, Bifidobacterium, and Enterococcus. Metagenomics revealed downregulated riboflavin metabolism and upregulated fat digestion/absorption pathways in NOA (P < 0.05). Metabolomics identified 26 differential fecal metabolites, including decreased L-carnitine derivatives and elevated tyramine glucuronide involved in bile secretion. These metabolites were significantly correlated with altered bacterial genera. Our integrated multi-omics analysis demonstrates that NOA in children is associated with a specific gut ecosystem characterized by altered microbiota structure, perturbed microbial metabolic functions (particularly riboflavin metabolism), and corresponding host-microbiota co-metabolic disturbances. These findings provide novel evidence for the disrupted "microbiota-metabolite" axis in NOA, offering new mechanistic insights.}, } @article {pmid42115921, year = {2026}, author = {Bulfoni, M and De Martino, M and Gualandi, N and Marzinotto, S and Vesca, G and Krpan, B and Marcon, B and Bertoni, M and Tascini, C and Pipan, C and Curcio, F}, title = {Gut microbiota profiling of the population residing in Friuli-Venezia Giulia through next-generation sequencing.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05117-1}, pmid = {42115921}, issn = {1471-2180}, abstract = {The gut microbiota is an ecological community of symbiotic and commensal microorganisms that play crucial roles in nutrient metabolism, maintaining the structural integrity of the intestinal mucosal barrier, immunomodulation, and pathogen protection. The composition of the gut microbiota varies with age, ethnicity, lifestyle, and dietary habits. Given the microbiota's growing role as a modulator of various physiological and pathological conditions, our study aimed to investigate the genetic profile of the microbiome individuals residing in the Friuli-Venezia Giulia region. We analyzed fecal swab samples from 109 individuals belonging to a general population cohort. The hypervariable V3-V4 regions of bacterial 16 S rRNA were analyzed using Next Generation Sequencing (NGS) on the MiSeq system (Illumina). The relative abundance of phyla, classes, orders, families, and species was defined using the BaseSpace 16s metagenomics app (Illumina). Firmicutes was the most represented phylum (51.1%), followed by Bacteroidetes (38.3%) and Actinobacteria (3%). At the class level, Clostridia (45.2%) and Bacteroidia (37.7%) were predominant, while Clostridiales (46.9%), Bacteroidales (26.6%), and Anaeroplasmatales (12.6%) were notable orders. Lachnospiraceae (21.9%) and Ruminococcaceae (16.2%) were the most frequent families, with Faecalibacterium prausnitzii (10.3%), Bacteroides vulgatus (4.6%), and Bacteroides dorei (3.5%) being prominent species. Each participant's taxa were analyzed to identify genera associated with alterations in gut microbial composition. Significant associations emerged between specific taxa of microorganisms and age, gender, anti-inflammatory drugs, tobacco consumption, and allergies. This study provides valuable insights into gut microbiota composition in a population-based cohort. The characterization of the microbiota in the Friuli-Venezia Giulia (FVG) region lays the foundation for future research into regional variations in microbiota composition and its impact on health.}, } @article {pmid42116123, year = {2026}, author = {Zhou, J and Cheng, H and Zhang, Y and Liu, T and Chen, X and Lea-Smith, DJ and Todd, JD and Liu, J and He, X and Liu, R and Zhang, XH}, title = {Vertical distribution and metabolic diversity of autotrophic microbes in the deep sediment of the challenger deep.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00908-5}, pmid = {42116123}, issn = {2524-6372}, support = {BB/Y008332/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NE/X014428//Natural Environmental Research Council/ ; NE/P012671//Natural Environmental Research Council/ ; RPG-2020-413//Leverhulme Trust/ ; ZR2024JQ006//Natural Science Foundation of Shandong Province/ ; 32370118//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2025YFF0516900&2025YFF0516903//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Carbon fixation in marine ecosystems is a vital process that contributes to climate regulation, with ocean sediments playing a critical role in carbon sequestration. This process is driven by chemolithoautotrophy in marine sediments, fueled by reduced compounds, such as those containing nitrogen and sulfur. However, the vertical distribution of microbial autotrophs and their energy coupling systems remain poorly understood in many sediments. In this study, we investigated a 750 cm sediment core from the Challenger Deep, the deepest point on Earth, which harbors abundant and diverse microbes under extreme conditions.

RESULTS: To explore the autotrophic characteristics across redox conditions in this core, we characterized the microbial community, metagenome, and metagenome-assembled genomes (MAGs), and their potential for carbon fixation processes and associated energy metabolism. The Wood-Ljungdahl (WL) pathway, primarily driven by Planctomycetota and Aerophobota, and the reverse oxidative TCA (roTCA) cycle, primarily driven by Bacteroidota and Gemmatimonadota, were the dominant predicted carbon fixation pathways, with hydrogen as the primary energy source, coupled to nitrogen and sulfur metabolism. Notably, the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle, mediated by Nitrososphaeria, showed the highest abundance in the oxidized environment (15-27 cm below the seafloor), where ammonia oxidation likely served as the primary energy source. Gammaproteobacteria were predicted to utilise sulfur oxidation, whereas Alphaproteobacteria and Chloroflexota used hydrogen to drive the Calvin-Benson-Bassham (CBB), reductive glycine pathway (rGly) in Alphaproteobacteria and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB) in Chloroflexota, respectively. The abundance of carbon fixation, and nitrogen, sulfur and hydrogen cycling functional genes were significantly correlated with environmental factors (NH4[+] and SiO3[2-]) based on Pearson's correlation analysis.

CONCLUSION: This study reveals the vertical distribution of microbial carbon fixation potential and diversity in sediments driven by redox conditions, highlights the crucial role of hydrogen as an energy source, and provides new insights for optimizing global deep-sea carbon cycle models. Collectively, these findings extend the redox tower theory by revealing a hadal-sediment specific distribution of autotrophic genes, characterized by persistent enrichment of energetically efficient pathways and dominant hydrogen-based energy coupling across deep sediment layers.}, } @article {pmid42116193, year = {2026}, author = {Tamang, A and Kumar, A and Thakur, A and Kumar, R and Kumar, D and Hallan, V and Pandey, SS}, title = {Unravelling the fungal endomicrobiome of Picrorhiza kurrooa for increasing in-planta picroside biosynthesis using endophytic Trichoderma harzianum PKRF1.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00909-4}, pmid = {42116193}, issn = {2524-6372}, support = {MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; }, abstract = {BACKGROUND: Endophytic fungi form an integral part of plant microbiomes, influencing host physiology, stress resilience, and secondary metabolism. While next-generation sequencing (NGS) has greatly advanced the identification of endophytes, it often falls short of assigning functional roles, necessitating integration with culture-based approaches for downstream applications. Picrorhiza kurrooa, a critically endangered Himalayan medicinal herb valued for its hepatoprotective picrosides, suffers from reduced metabolite content in tissue culture-derived plants, likely due to microbiome loss in the course of aseptic in-vitro practices. Moreover, the diversity and functional role of fungal endomicrobiome in P. kurrooa remain unexplored.

METHODS: Internal transcribed spacer (ITS)-based amplicon sequencing was performed to assess and compare the endophytic fungal communities of wild-type (Wt) and in-vitro propagated (Tc) P. kurrooa. Fungal taxa unique to Wt-plants were identified and cross-referenced with culturable isolates. A dominant isolate present only in Wt-plants, Trichoderma harzianum PKRF1, was reintroduced into Tc-plants to evaluate its effect on plant growth and picroside biosynthesis. Whole-genome sequencing and comparative genomics of PKRF1 were also conducted to elucidate its functional capabilities and possible candidates for its endophytic nature.

RESULTS: Metagenomic analysis revealed a significant reduction in fungal diversity in Tc plants, with several taxa, including Trichoderma, Cyphellophora, and Preussia, exclusively associated with Wt-plants. Inoculation of Tc-plants with PKRF1 led to successful root colonization, enhanced photosynthetic efficiency, biomass, and significantly higher levels of picrosides. Transcript profiling confirmed upregulation of key biosynthetic genes. Genomic analysis of PKRF1 revealed genes associated with multiple plant-beneficial traits, including nutrient acquisition, phytohormone production, stress tolerance, plant colonization, and competitive interactions, distinguishing it from non-endophytic Trichoderma isolates.

CONCLUSIONS: These findings provide the first comprehensive insight into changes in endophytic fungal diversity of P. kurrooa associated with in-vitro cultivation. Furthermore, the application of cultivated endophytes from wild plants demonstrated the potential to restore microbial functions lost during in-vitro propagation and enhance secondary metabolite production in cultivated plants. Overall, this approach offers a promising strategy to integrate metagenomic information into beneficial plant-microbe interactions for practical applications.}, } @article {pmid42116465, year = {2026}, author = {Ozaki, GEDN and Maciel, ESO and Souza, BP and da Silva-Padilha, MP and Santos, NMMO and Oliveira, JCS and Souza, VB and Tulini, FL}, title = {Development and characterization of seriguela (Spondias purpurea) water kefir: metagenomic insights and functional potential of a spray-dried probiotic powder.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119194}, doi = {10.1016/j.foodres.2026.119194}, pmid = {42116465}, issn = {1873-7145}, mesh = {*Kefir/microbiology/analysis ; *Probiotics/analysis ; Powders ; Fermentation ; *Metagenomics ; *Spray Drying ; Food Microbiology ; Hydrogen-Ion Concentration ; Antioxidants/analysis ; Fruit/chemistry/microbiology ; Bacteria/classification/genetics ; }, abstract = {Water kefir is a fermented probiotic beverage suitable for those with lactose intolerance, dairy allergies, or vegan diets. Adding fruits during fermentation can modulate microbial dynamics, sensory attributes, and biochemical composition, thereby enhancing functional properties. In this context, Spondias purpurea (seriguela), a bioactive-rich fruit native to the Americas, represents a promising yet underexplored substrate for the development of functional beverages. Therefore, this study investigated the composition of seriguela and its application in water kefir production, followed by physicochemical and metagenomic characterization and the evaluation of spray-dried formulations. Seriguela fruits exhibited an acidic pH (3.63), the presence of coumarins, steroids, and tannins, and remarkable antioxidant activity. Seriguela-flavored kefir maintained microbial levels comparable to those of traditional kefir (7.1 and 6.8 log CFU/mL for bacteria and yeasts, respectively), promoting a predominance of Komagataeibacter saccharivorans, Acetobacter aceti, A. lovaniensis, Liquorilactobacillus mali, Clostridium pasteurianum, and yeasts from the Saccharomyces genus. This change in the microbiota of seriguela-flavored kefir indicates a more homogeneous fermentation with pronounced acetic characteristics and probiotic potential. Furthermore, the spray-dried kefir demonstrated good physical properties, remarkable resistance under simulated gastrointestinal conditions, and moderate stability during refrigerated storage throughout 30 days (75.7% and 82.9% of survival for bacteria and yeasts, respectively, enumerated on De Man, Rogosa & Sharpe agar and potato dextrose agar), highlighting its potential as a stable probiotic product. Overall, these results demonstrate the suitability of seriguela as a functional ingredient in water kefir and confirm spray-drying as a viable strategy for producing stable fermented powders with potential health-promoting properties.}, } @article {pmid42116469, year = {2026}, author = {Liu, D and Li, J and Zhang, J and Zhang, C}, title = {CO2-modified atmosphere improves the flavor quality of low-salt Xuecai by regulating microbial communities and metabolic functions.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119201}, doi = {10.1016/j.foodres.2026.119201}, pmid = {42116469}, issn = {1873-7145}, mesh = {*Carbon Dioxide/chemistry ; *Taste ; *Microbiota ; *Vegetables/microbiology/metabolism/chemistry ; *Food Microbiology ; *Atmosphere ; Biogenic Amines/analysis/metabolism ; Food Handling/methods ; Volatile Organic Compounds/analysis ; }, abstract = {Low-salt pickled vegetables are often limited by their poor flavor and the accumulation of biogenic amines (BAs). In the present study, the effects of CO2-modified atmosphere (CMA) technology on the dynamics of flavor compounds, microbial communities, and metabolic functions in low-salt Xuecai during pickling were investigated. In comparison with low-salt pickling under natural air conditions, a CMA effectively prevented excessive acidification, enriched volatile metabolites (e.g., isothiocyanates, alcohols, and esters), and minimized the accumulation of bitter-tasting amino acids, resulting in pickled vegetables with excellent flavor quality. Moreover, a CMA significantly inhibited the formation of BAs compared to low-salt natural pickling (P < 0.05; 46.71 vs. 114.29 mg/kg after 90 days of pickling), thereby enhancing the safety of low-salt Xuecai. In addition, metagenomic analysis showed that using a CMA for low-salt Xuecai production inhibited halophilic and spoilage microorganisms while enriching Lactobacillus-related populations. Metabolic pathway analysis revealed that the expression levels of the tricarboxylic acid cycle, amino acid metabolism, and genes encoding enzymes (i.e., amino acid decarboxylases, amine deiminases, and amine synthases) related to BA production were lower under a CMA. This, in turn, improved the flavor quality and inhibited the generation of BAs in low-salt Xuecai. Our study offers an alternative method for developing low-salt fermented foods.}, } @article {pmid42116470, year = {2026}, author = {Wang, L and Zhu, N and Cai, F and Lin, X and Lai, C and Hu, H and Tao, Q and Song, J and Dai, W and Jia, X and Zhang, W}, title = {Fructooligosaccharides alleviate early-life antibiotic-exposed food allergy via the Indole-3-propionic acid-AhR-Nrf2 Axis: A multi-omics prospective cohort study.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119200}, doi = {10.1016/j.foodres.2026.119200}, pmid = {42116470}, issn = {1873-7145}, mesh = {*NF-E2-Related Factor 2/metabolism ; Animals ; *Indoles/metabolism ; *Oligosaccharides/pharmacology ; Gastrointestinal Microbiome/drug effects ; Mice ; *Propionates/metabolism ; *Food Hypersensitivity/prevention & control/etiology/metabolism/drug therapy ; *Receptors, Aryl Hydrocarbon/metabolism ; *Anti-Bacterial Agents/adverse effects ; Humans ; Male ; Female ; Prospective Studies ; Dysbiosis/chemically induced ; Oxidative Stress/drug effects ; Multiomics ; }, abstract = {BACKGROUND: Gut microbiota is critical in food allergy (FA) development. While early-life antibiotics increase FA risk, the mechanism is unclear, and current treatments cannot correct underlying immune defects.

OBJECTIVE: To investigate how early-life antibiotics exacerbate FA and whether fructo-oligosaccharides (FOS) can restore gut-immune balance.

METHODS: We linked early-life antibiotic use to gut dysbiosis and metabolites in a birth cohor, modeled mechanisms and FOS intervention in antibiotic-exposed FA mice, and validated FOS efficacy in a pediatric trial.

RESULTS: Early-life antibiotics caused persistent gut dysbiosis (notably Lactobacillus depletion) and disrupted tryptophan metabolism, ultimately resulting in oxidative stress, barrier damage, and T-cell imbalance. FOS restored Lactobacillus and the tryptophan metabolite indole-3-propionic acid (IPA). IPA alleviates mitochondrial dysfunction and reactive oxygen species accumulation via activation of the aryl hydrocarbon receptor (AhR)-nuclear factor erythroid 2-related factor 2 (Nrf2)-heme oxygenase-1 (HO-1) antioxidant pathway, and enhances intestinal barrier integrity, ultimately rebalancing T-cell homeostasis and attenuating FA. In a pediatric trial, metagenomic sequencing revealed that FOS enriches both Lactobacillus johnsonii and Clostridium sporogenes, synergistically promoting IPA production-which correlates with reduced SCORAD scores and improved weight gain.

CONCLUSIONS: Early-life antibiotics cause lasting disruptions in gut microbiota and metabolism that worsen FA. FOS mitigates FA by boosting microbiota-derived IPA to activate the protective AhR-Nrf2-HO-1 pathway, highlighting its therapeutic potential for FA, particularly in patients with prior antibiotic exposure.}, } @article {pmid42116511, year = {2026}, author = {Xu, H and Kong, W and Tang, Q and Fan, K and Liu, M and Mo, K and Xu, Z and Zhang, W}, title = {Analysis of microbiome succession and metabolome dynamics in Jiupei during Chinese strong-flavor Baijiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119274}, doi = {10.1016/j.foodres.2026.119274}, pmid = {42116511}, issn = {1873-7145}, mesh = {*Fermentation ; *Microbiota ; *Metabolome ; Food Microbiology ; Taste ; Volatile Organic Compounds/analysis ; Bacteria/metabolism/classification/genetics ; *Wine/microbiology/analysis ; Fungi/metabolism/classification ; Metabolomics ; Flavoring Agents ; China ; }, abstract = {Microbial successions during Jiupei fermentation are critical for the flavor synthesis of strong-flavor Baijiu, but their dynamics and associated metabolites across different vertical Jiupei layers have not yet been characterized in detail. This study employed metagenomic sequencing combined with metabolomic techniques to investigate the complex relationship between microbial succession and metabolite formation in Jiupei of strong-favor Baijiu fermentation. Results demonstrated that a total of 2940 compounds were identified and classified into 13 classes; of which over 94.7% of amino acids and derivatives, 57.5% of organic acids, and certain sugar alcohols increased during fermentation, whereas more than 81.8% of flavonoids decreased, particularly in the lower Jiupei layer. The volatile compounds, including ethyl caproate and ethyl lactate, showed a significant increase. Meanwhile, microbial diversity and richness dropped sharply from day 0 to day 30, with a recovery by day 60 in the middle and lower layers. The early stage of fermentation is characterized by the fungi Paecilomyces variotii, Lichtheimia ramosa, Rhizopus arrhizus, and Aspergillus chevalieri, as well as the bacteria Saccharopolyspora rectivirgula, Lactiplantibacillus plantarum, Leuconostoc citreum, and Weissella confusa, which secrete amylases and glycosylases to hydrolyze starch into sugars via enrichment of carbohydrate-related pathways, such as starch and sucrose metabolism, glycolysis/gluconeogenesis, and fructose and mannose metabolism. Acetilactobacillus jinshanensis, Lentilactobacillus diolivorans, and Philodulcilactobacillus myokoensis sharply increased in the later stage of fermentation, alongside enriched pathways for fatty acid and secondary metabolite biosynthesis. Acetilactobacillus jinshanensis ‌might synergistically accumulate characteristic flavor compounds through transferase and ligase reactions. These findings reveal the stage-specific microbial metabolic characteristics and synergistic mechanisms in flavor formation, providing a scientific basis for optimizing Baijiu fermentation processes to enhance Baijiu quality.}, } @article {pmid42116518, year = {2026}, author = {Zhou, H and Xu, B and Zhang, L and Yan, L and Wang, R and Xu, Q and Jiang, C and Chen, A and Wu, X and Li, X}, title = {Ecological dominance and genomic features of bacterial generalists during pit fermentation of three distinct baijiu types in Anhui Province.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119296}, doi = {10.1016/j.foodres.2026.119296}, pmid = {42116518}, issn = {1873-7145}, mesh = {*Fermentation ; China ; *Food Microbiology ; *Bacteria/genetics/classification/metabolism ; *Wine/microbiology/analysis ; Lactobacillus/genetics/metabolism ; }, abstract = {Microbial generalists are pivotal for maintaining the stability of fermentation systems, yet their distribution across different Baijiu types remains poorly understood. This study identified generalists and specialists during the pit fermentation of strong-flavor, jian-flavor, and sesame-flavor Baijiu in Anhui Province, and further elucidated their genomic features. Results showed that bacterial communities in all three types are dominated by generalists, whereas fungal communities depend more on diverse specialists. Bacterial generalists were represented by OTUs classified as Acetilactobacillus, Lactobacillus, and Limosilactobacillus. Targeted removal of these generalists increased the robustness of time-series networks, as they correlated negatively with most other taxa and were strongly linked to physicochemical properties. The major species belonging to bacterial generalists included Acetilactobacillus jinshanensis, Lactobacillus acetotolerans, and Limosilactobacillus pontis. These generalists possessed specialized genomic features for niche dominance, characterized by: (i) a low-acquisition, high-growth life history strategy (A/Y < 1); (ii) a preference for sugar metabolism (SAP >0); (iii) a complete multi-layered defense system conferring tolerance to acid and ethanol; and (iv) a streamlined (< 2 Mb) and non-redundant (lacking the TCA cycle) genome that minimizes regulatory burden. This study provides a systematic analysis of generalists across distinct Baijiu types in Anhui Province, offering a theoretical framework for understanding the rules of microbial assembly in the brewing process.}, } @article {pmid42116534, year = {2026}, author = {Veyrenche, N and Boluda, S and Pérot, P and Malissin, I and Leruez-Ville, M and Jamet, A and Ferroni, A and Regnault, B and Salmona, M and Feghoul, L and Robert-Capraro, L and Leroux, A and Grasland, B and Niqueux, E and Briand, FX and Plu, I and Seilhean, D and Megarbane, B and Fourgeaud, J and Dheilly, NM}, title = {One Health Investigation into Fatal Encephalitis Caused by Pigeon Paramyxovirus Type 1, France.}, journal = {Emerging infectious diseases}, volume = {32}, number = {5}, pages = {753}, pmid = {42116534}, issn = {1080-6059}, mesh = {Humans ; France/epidemiology ; *Newcastle disease virus/genetics/classification/isolation & purification ; Fatal Outcome ; *Newcastle Disease/virology/diagnosis/epidemiology ; Animals ; Male ; Phylogeny ; Columbidae/virology ; *Encephalitis, Viral/diagnosis/virology/epidemiology ; }, abstract = {Pigeon paramyxovirus type 1 (PPMV-1) is a genotype of avian paramyxovirus type 1 that uses species of the family Columbidae as reservoir species. We report fatal PPMV-1 encephalitis in a human without immunosuppression or travel history outside metropolitan France. Postmortem analyses revealed PPMV-1 in tissues, underscoring that physicians should consider this potential diagnosis.}, } @article {pmid42116592, year = {2026}, author = {Andreani, J and Boschi, C and Decoppet, A and Delerce, J and Penant, G and Karadeniz, A and Grimaldier, C and Jardot, P and Zangoli, L and Mandy, M and Vigroux, N and Polesso, F and Edouard, S and Cano, P and Lagier, JC and La Scola, B and Colson, P}, title = {Severe Respiratory Illness and Death Associated with Outbreak of Human Rhinovirus B14 among Older Adults, France, 2024.}, journal = {Emerging infectious diseases}, volume = {32}, number = {5}, pages = {768-773}, pmid = {42116592}, issn = {1080-6059}, mesh = {Humans ; France/epidemiology ; *Rhinovirus/genetics/classification/isolation & purification ; *Disease Outbreaks ; *Picornaviridae Infections/epidemiology/virology/mortality ; Aged ; Male ; Female ; Aged, 80 and over ; *Respiratory Tract Infections/epidemiology/virology/mortality ; Phylogeny ; Genome, Viral ; }, abstract = {We investigated an outbreak of unknown respiratory disease and 8 deaths among older adults in a long-term care facility in France. We identified human rhinovirus (HRV) by quantitative PCR and HRV-B14 by metagenomics. We obtained 5 HRV-B14 genomes that diverged from 5 publicly available genomes. Real-time metagenomics could enable rapid clinical diagnoses.}, } @article {pmid42116727, year = {2026}, author = {Kutter, JS and Cuevas-Lobato, O and Fernandez-Pacheco-Gonzalez-Echavarri, BE and Moreno-Gomila, C and Garcia-Ibañez, N and Camacho, J and Ruiz-Pedro, E and Cabrerizo, M and Alós, JI and Diez-Fuertes, F and Fernandez-Garcia, MD}, title = {Unraveling the Transmission Dynamics of a Novel Norovirus GII.17[P17] Lineage During Two Consecutive Outbreaks in a Spanish Hospital.}, journal = {Journal of medical virology}, volume = {98}, number = {5}, pages = {e70966}, pmid = {42116727}, issn = {1096-9071}, support = {PI23CIII-00009//Instituto de Salud Carlos III/ ; }, mesh = {Humans ; *Caliciviridae Infections/epidemiology/transmission/virology ; *Norovirus/genetics/classification/isolation & purification ; *Disease Outbreaks ; Spain/epidemiology ; Phylogeny ; *Cross Infection/epidemiology/virology/transmission ; Feces/virology ; *Genotype ; Male ; Female ; Middle Aged ; Adult ; Molecular Epidemiology ; Aged ; Hospitals ; High-Throughput Nucleotide Sequencing ; *Gastroenteritis/epidemiology/virology ; Young Adult ; Genome, Viral ; }, abstract = {Norovirus outbreaks in healthcare settings pose significant challenges to infection prevention and control (IPC). To prevent and control such outbreaks efficiently, identifying sources and transmission clusters (TCs) is crucial but often limited by traditional outbreak investigations. Here, we examined two consecutive hospital norovirus outbreaks employing a genomic epidemiology approach to elucidate transmission dynamics and guide IPC strategies. Stool samples of 54 symptomatic patients were analyzed with different diagnostic methods, and 26 norovirus-positive samples underwent metagenomic next-generation sequencing (mNGS) for phylodynamic and phylogenetic analyses. All infections belonged to the novel GII.17[P17] lineage, circulating globally since 2023/2024. LiquidArray® outperformed fluorescence immunoassay (FIA, 28.6%) and RT-PCR (85.7%) with FIA's low sensitivity leading to missed cases highlighting the need for molecular confirmation for accurate outbreak management. Genomic analysis revealed multiple introductions, with two TCs identified in Outbreak-1 and one in Outbreak-2, as well as inter-hospital-unit spread. Reconstruction of transmission trees indicated sustained person-to-person spread with 0-3 unobserved intermediate cases in both outbreaks. Identical sequences in patients without clear epidemiological links suggested possible fomite transmission. These analyses provided key insights into infection sources and TCs that would have remained unknown using epidemiological investigations alone, supporting more targeted IPC resource allocation and intervention strategies.}, } @article {pmid42116832, year = {2026}, author = {Dawson, MN and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the moon jellyfish, Aurelia sp. 4 Dawson et al. 2005 (Semaeostomeae: Ulmaridae) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {189}, pmid = {42116832}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Aurelia sp. 4 Dawson et al., 2005 (moon jellyfish; Cnidaria; Scyphozoa; Semaeostomeae; Ulmaridae). The genome sequence has a total length of 462.10 megabases. Most of the assembly (99.99%) is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.88 kilobases. From the metagenome data, we recovered 3 bins, of which 2 were high-quality MAGs.}, } @article {pmid42116847, year = {2026}, author = {Williams, NLR and Bei, Q and Raut, Y and Fuhrman, JA}, title = {Converting relative amplicon abundances to absolute abundances via flow cytometry: metagenomic validation and application to long ocean transects.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag081}, pmid = {42116847}, issn = {2730-6151}, abstract = {With microbes critical for ocean ecological and biogeochemical processes, we need to understand their abundance and diversity distributions. While traditional amplicon sequencing provides only relative abundance data, and the strongly preferred absolute abundances can be determined from samples spiked with internal standards, few oceanographic studies with absolute abundances exist. However, many have flow cytometry (FCM) data that should allow us to retrospectively "anchor" the relative abundances into absolute abundances. We tested this hypothesis with data from the 29th Atlantic Meridional Transect (AMT29) cruise where we had FCM of Synechococcus and Prochlorococcus, amplicons corrected with internal standards, and absolute cell count estimates from single copy recA and radA metagenomics. Anchoring the AMT29 amplicon data with Synechococcus FCM (used because phycoerythrin in Synechococcus is reliably detected by FCM in surface waters) yielded results strongly correlated with amplicon data corrected with internal standards (Pearson's r = 0.94, slope = 0.73), FCM (r = 0.80, slope = 0.43), and recA-based genome counts (Pearson's r = 0.94, slope = 0.62). Seeing this method worked reasonably well, we then generated estimates of absolute rRNA gene abundances from the Global rRNA Universal Metabarcoding of Plankton (GRUMP) transects that had FCM data (Pacific ~65 N to ~40S). These FCM-anchored gene copy estimates also showed strong correlations to FCM data (i.e. anchor with Synechococcus and predict Prochlorococcus), with r values ranging from 0.48-0.86. While the results are clearly only reasonable estimates, we believe the approach has the potential to significantly enhance the value of amplicon data which have accompanying FCM data.}, } @article {pmid42117813, year = {2026}, author = {Qi, W and Lü, L and Huang, K and Qi, J and Li, M and Shi, M and Wang, H}, title = {Effects of Rotary Tillage and Fertilization on Chemical Properties and Microbial Communities of Soil Under Continuous Morchella Mushroom Cultivation.}, journal = {Biology}, volume = {15}, number = {9}, pages = {}, pmid = {42117813}, issn = {2079-7737}, support = {2024XTCX0403//Liaoning Academy of Agricultural Sciences Collaborative Innovation Project/ ; 2026NYGG010//Key Core Technology Research and Development in Shaanxi Province Agriculture/ ; }, abstract = {The severe continuous cropping obstacles in Morchella cultivation, driven primarily by soil microecological imbalance, critically constrain the sustainable development of the industry. To address this challenge, this study evaluated the efficacy of rotary tillage, calcium cyanamide (CaCN2), and organic fertilizer, applied individually and in combination, in mitigating these obstacles and explored the underlying microbial mechanisms. The soil was treated on 5 August 2024, and soil samples were collected on 5 October 2024. Four treatments were established: continuous cropping control (CK), rotary tillage (XGX), rotary tillage combined with calcium cyanamide (MPD), and rotary tillage combined with calcium cyanamide and organic fertilizer (MPX). Soil chemical properties were analyzed in conjunction with metagenomic sequencing to characterize the responses of soil properties and microbial communities, including both eukaryotic and bacterial taxa. The results indicated that the MPD treatment showed a relatively pronounced effect in enhancing key soil fertility indicators, including soil organic matter (OM), total nitrogen (TN), available nitrogen (AN), available potassium (AK), and total phosphorus (TP). All amendments significantly altered microbial community structures. Specifically, the integrated MPX treatment effectively reduced the relative abundance of the pathogenic fungus Olpidium while maintaining higher overall microbial diversity. It also significantly promoted the abundance of Morchella itself and beneficial bacterial phyla such as Actinomycetota and Pseudomonadota. Redundancy analysis identified AN and AK as the primary drivers of eukaryotic community variation, whereas Availa-ble phosphorus (AP) and potential of hydrogen (pH) were the key factors shaping the bacterial community. The results indicated that MPD was the showed relatively pronounced effectiveness in rapidly improving soil fertility and suppressing pathogenic fungi. In contrast, MPX showed relatively better performance in optimizing microbial community structure, enhancing microbial diversity, and strengthening overall ecological stability. These two treatments exhibited distinct advantages in soil chemical improvement and microbial community regulation, respectively, thereby providing alternative practical strategies and a theoretical basis for the ecological management of continuous-cropping obstacles in Morchella cultivation. It should be noted that this study did not include treatments with calcium cyanamide alone, organic fertilizer alone, or their combined application without rotary tillage. This is primarily because rotary tillage is a standard land preparation practice in Morchella cultivation, and the use of soil amendments without accompanying tillage is rarely adopted under practical production conditions.}, } @article {pmid42118424, year = {2026}, author = {Devi, P and Nath, SK and Barua, B and Saha, T}, title = {Big data and artificial intelligence in animal nutrition: a new era of precision feeding.}, journal = {Tropical animal health and production}, volume = {58}, number = {4}, pages = {}, pmid = {42118424}, issn = {1573-7438}, mesh = {Animals ; *Big Data ; *Artificial Intelligence ; *Animal Feed/analysis ; *Animal Husbandry/methods ; *Animal Nutritional Physiological Phenomena ; *Livestock/physiology ; Dairying/methods ; }, abstract = {The convergence of Big Data and Artificial Intelligence (AI) is redefining animal nutrition by enabling precision feeding systems that are individualized, data-driven, and sustainability-oriented. This review synthesizes recent advances in multi-omics technologies, sensor-based monitoring, and machine learning applications across feed formulation, health surveillance, and production optimization. Precision feeding in pigs has been shown to reduce production costs by more than 8%, decrease protein and phosphorus intake by approximately 25%, lower nutrient excretion by up to 40%, and reduce greenhouse gas (GHGs) emissions by 6%, while maintaining or improving performance. In dairy systems, precision feed management strategies have achieved approximately 9.7% lower dietary crude protein levels, 14% reductions in manure nitrogen excretion, and annual net income gains of USD 137 per cow. AI-driven models have enhanced prediction of milk yield, feed conversion ratio (R[2] = 0.74), and residual feed intake (R[2] = 0.76), while enabling 96.26% accuracy in detecting microplastics in poultry feed. Integration of genomic, phenotypic, and sensor-derived datasets supports real-time monitoring, with wearable and IoT technologies transforming livestock management through continuous tracking of feeding behavior, emissions, and welfare indicators. Despite significant progress, current systems remain constrained by data heterogeneity, limited interoperability, and insufficient prescriptive decision-support frameworks. This article identifies methodological, technological, and adoption-related gaps, while highlighting future directions including nutrigenomics- and metagenomics-informed diet design, adaptive precision nutrition, and cost-effective solutions for smallholder systems. Collectively, these innovations establish Big Data and AI-enabled precision nutrition as a cornerstone of sustainable livestock production, advancing food security, climate resilience, and ethical animal management.}, } @article {pmid42118429, year = {2026}, author = {Tekin, B and Gurbanov, R}, title = {Taxonomic and functional remodeling of the gut microbiota during aging and implications for microbiota-derived biomarkers.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42118429}, issn = {1573-0972}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Aging/physiology ; Biomarkers/analysis ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Animals ; Host Microbial Interactions ; Fatty Acids, Volatile/metabolism ; }, abstract = {The gut microbiota represents a complex microbial ecosystem that contributes to host metabolic regulation, immune homeostasis, and intestinal barrier function. Across the lifespan, gut microbial communities exhibit marked taxonomic and functional variation driven by environmental exposures, dietary patterns, medication use, and age-associated immune alterations. These differences are closely linked to chronic inflammatory states and immune dysregulation that accompany aging. This review synthesizes current evidence on age-associated differences in gut microbiota composition and functional capacity, with a focus on microbial traits and metabolic pathways relevant to host-microbe interactions. Pathological aging is frequently associated with reduced microbial diversity, loss of short-chain fatty acid-producing commensal bacteria, and enrichment of opportunistic or pro-inflammatory taxa. In contrast, healthy aging and longevity are commonly associated with more stable, resilient, and metabolically adaptable microbial communities. At the functional level, recurrent alterations in short-chain fatty acid biosynthesis, bile acid transformation, and tryptophan- and choline-related metabolic pathways define conserved features across aging-associated microbial profiles. Across neurodegenerative, metabolic, and cardiovascular conditions, overlapping taxonomic and functional patterns indicate shared microbiota-associated signatures linked to inflammatory states. Advances in metagenomic sequencing, functional annotation, and microbiome-focused biotechnological approaches now enable integrated analysis of microbial structure and metabolic potential. These developments provide a robust framework for identifying reproducible microbiome-based indicators relevant to aging-associated physiological changes and for translating microbiome research into biotechnology-driven applications.}, } @article {pmid42119030, year = {2026}, author = {Yu, J and Tang, SN and Lee, PKH}, title = {Host-linked virome assembly and turnover predict bacterial community structure in wastewater treatment systems.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {42119030}, issn = {1751-7370}, support = {//TAL Apparel Limited/ ; 9231297//City University of Hong Kong/ ; }, mesh = {*Bacteria/virology/genetics/classification ; *Wastewater/microbiology/virology ; *Virome ; Sewage/virology/microbiology ; Metagenomics ; Bioreactors/virology/microbiology ; Water Purification ; *Microbiota ; *Host Microbial Interactions ; Ecosystem ; }, abstract = {Viruses play crucial roles in bacterial ecology and evolution through virus-host interactions; however, their distribution, assembly mechanisms, and temporal turnover remain underexplored in engineered ecosystems. In the present study, we used activated sludge (AS) and anaerobic treatment (AT) reactors from four full-scale industrial textile wastewater treatment plants as model ecosystems, integrating metagenomics, macroecological modeling, and deep learning to characterize viral structure, dynamics, and host interactions. A total of 1046 and 1386 high-quality viral operational taxonomic units were recovered from AS and AT systems, respectively, and most were affiliated with Caudoviricetes. Viral composition and genetic microdiversity were highly plant-specific and shaped by environmental selection and host interactions. Lognormal species abundance distributions and deviations from neutral expectations indicated deterministic assembly. Virulent viruses exhibited faster temporal turnover than temperate viruses. Viral co-occurrence networks showed strong plant-specific modularity and greater temporal stability than bacterial networks, suggesting that they play a stabilizing role in community dynamics. Tight virus-host abundance coupling and gene-level signatures of host-linked selection indicated ongoing coevolutionary interactions. A deep learning model accurately predicted bacterial community dynamics from viral composition at both the taxon and sample levels, highlighting the ecological relevance of viral signatures. Together, these findings reveal dynamic, plant-specific viromes tightly coupled to bacterial communities and highlight viral signatures as potential indicators for monitoring engineered ecosystems. Incorporating viral ecology into microbial management could enhance the stability, resilience, and functional performance of engineered ecosystems.}, } @article {pmid42119140, year = {2026}, author = {Bao, Y and Ho, YW and Shen, Z and Lam, EY and Fang, JKH and Leung, KMY and Lee, PKH}, title = {Seasonal Divergence between Microbiomes on Microplastics and Natural Particles Increases with Rising Water Temperatures in Urban Rivers.}, journal = {Environmental science & technology}, volume = {60}, number = {20}, pages = {14712-14725}, doi = {10.1021/acs.est.5c13903}, pmid = {42119140}, issn = {1520-5851}, mesh = {*Rivers/microbiology ; *Microbiota ; *Microplastics ; Seasons ; Temperature ; }, abstract = {The "plastisphere," which comprises microplastics (MPs)-associated microbial communities, is an emerging component of urban river ecosystems. However, its seasonal dynamics remain poorly understood, especially compared with microbiomes on natural particles (NPs). We therefore conducted a year-long metagenomic study at 15 sites across 10 major urban rivers in Hong Kong to compare MP- and NP-associated microbiomes across four seasons. Representative high-quality metagenome-assembled genomes revealed significant seasonal variations in both taxonomic and functional compositions across particle types, with water temperature identified as the primary environmental driver. As temperatures increased, both MP and NP microbiomes exhibited increased taxonomic and functional diversity but reduced functional redundancy and network stability. Compared to NPs, MP microbiomes exhibited higher taxonomic and functional turnover, more complex and connected cooccurrence networks, and distinct taxonomic and functional traits along the temperature gradient. In MP microbiomes, warmer conditions were associated with a higher abundance of pollutant-degrading and putatively virulent taxa (particularly from Firmicutes and Actinobacteria), along with enhanced biosynthetic functions and increased potential microbial sharing and horizontal gene transfer with surrounding aquatic microbiomes. These findings highlight the temperature-dependent ecological impacts of MP microbiomes and underscore the need to consider climatic factors when assessing the long-term ecological risks of MPs in urban riverine ecosystems.}, } @article {pmid42119184, year = {2026}, author = {Pilliol, V and Beye, M and Boualam, MA and Tellissi, L and Slimani, A and Drancourt, M and Aboudharam, G and Tassery, H and Grine, G and Terrer, E}, title = {Evidence of a millennia-old association between a methanogenic archaeon and a bacterium in dental calculus: A re-analysis of ancient and modern metagenomic datasets.}, journal = {Archives of oral biology}, volume = {188}, number = {}, pages = {106622}, doi = {10.1016/j.archoralbio.2026.106622}, pmid = {42119184}, issn = {1879-1506}, mesh = {*Dental Calculus/microbiology ; *Methanobrevibacter/genetics/isolation & purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Humans ; }, abstract = {OBJECTIVES: Granehäll et al. (2021) identified TS-2 as an unknown Methanobrevibacter lineage abundant in ancient dental calculus, less prevalent in modern samples, and not linked to any cultivated representative. We aimed (i) to determine whether TS-2 corresponds to the cultivated oral archaeon Methanobrevibacter massiliense using genome-based species delineation, and (ii) to assess the antiquity of the association between M. massiliense and Pyramidobacter piscolens in ancient and modern dental calculus.

DESIGN: This fully in silico study combined comparative genomics with re-analysis of 97 ancient and modern dental calculus metagenomic datasets. Species-level relationships were assessed using average nucleotide identity, digital DNA-DNA hybridization, and 16S rRNA phylogeny. Metagenomic associations were examined using Kraken2-based taxonomic profiling, with Methanobrevibacter sp. YE315 as a proxy because M. massiliense was absent from the classifier database, and direct competitive read mapping to M. massiliense. Associations with P. piscolens were evaluated using Spearman correlation and negative binomial regression.

RESULTS: Comparative genomics supported TS-2 and M. massiliense as the same species-level taxon, with > 95% average nucleotide identity and > 90% digital DNA-DNA hybridization. In metagenomic analyses, the YE315 proxy was positively associated with P. piscolens in Kraken2 Spearman analysis (ρ = 0.3506, q = 0.0026), and mapped M. massiliense reproduced this pattern (ρ = 0.2939, q = 0.0153). Negative binomial models showed concordant but weaker support, whereas the signal for M. oralis was less consistent.

CONCLUSION: These results identify M. massiliense as the cultivated representative of TS-2 and support an ancient, recurrent association between M. massiliense and P. piscolens in dental calculus.}, } @article {pmid42119293, year = {2026}, author = {Li, H and Xu, Y and Lin, T and Hu, C and Yang, Z and Su, H}, title = {Overwintering waterbirds are important reservoirs for the spread of antibiotic resistance genes (ARGs): Shared patterns at the waterbird-environment interface and the risk of horizontal transfer.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142298}, doi = {10.1016/j.jhazmat.2026.142298}, pmid = {42119293}, issn = {1873-3336}, mesh = {Animals ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Birds/microbiology ; Seasons ; *Genes, Bacterial ; China ; Wetlands ; Ecosystem ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The global spread of antibiotic resistance genes (ARGs) has become a critical challenge to public health. Long-distance migratory waterbirds are recognized as important biological vectors in the transregional spread of ARGs. However, the sharing patterns of ARGs and the horizontal transfer risks between these birds and their habitats during the wintering period remain poorly understood. This limits a comprehensive understanding of their role in ARG transmission. This study investigated a typical wintering wetland in southwestern China along the East Asian-Australasian Flyway, using metagenomic approaches to systematically characterize the distribution patterns, sharing profiles, and horizontal transfer risks of ARGs in the guts of overwintering waterbirds and their associated aquatic and terrestrial habitats. The results show that multidrug resistance genes are the predominant type of resistance observed both in the guts of overwintering waterbirds and in their habitats. Extensive sharing of ARGs occurs between the guts of overwintering waterbirds and their habitats, with approximately 50% of the 1250 identified ARG subtypes shared by both. We detected 55 high-risk ARG subtypes belonging to 10 resistance categories. Among these, β-lactam resistance genes (e.g., blaNDM-5 and blaCTX-M-15) were the predominant types. In addition, the co-localization of ARGs with mobile genetic elements (MGEs) (e.g., transposons and plasmids) suggests that the gut of waterbirds and aquatic environments may represent potential hotspots for horizontal transfer of ARGs. This study highlights the high connectivity of ARGs between overwintering waterbirds and their habitats, offering important insights into ecological and public health risks related to ARG spread.}, } @article {pmid42119385, year = {2026}, author = {Pan, L and Huang, Y and Chen, Y and Peng, T and Yang, J and Qiu, Y and Ji, M and Wu, X}, title = {Responses of soil microbes to antimony stress and coupled nutrient cycling in karst mining areas of Southwest China.}, journal = {Ecotoxicology and environmental safety}, volume = {318}, number = {}, pages = {120248}, doi = {10.1016/j.ecoenv.2026.120248}, pmid = {42119385}, issn = {1090-2414}, mesh = {*Antimony/toxicity/analysis ; China ; *Soil Microbiology ; Mining ; *Soil Pollutants/toxicity/analysis ; *Microbiota/drug effects ; Environmental Monitoring ; Bacteria/drug effects ; Soil/chemistry ; }, abstract = {Persistent and poorly mobile heavy metals in soil present a widespread environmental challenge. Among these, antimony (Sb) is a contaminant of emerging concern whose transformation and migration in soil require further investigation to inform effective remediation strategies. Microbial processes are central to these dynamics, yet the mechanisms underlying Sb-microbe interactions remain poorly defined. In this study, we used integrated geochemical and metagenomic analyses to assess Sb contamination and microbial community responses systematically in an abandoned Sb mining area in Southwest China. The data reveal how microbial communities respond to low and moderate levels of Sb contamination. Contamination was highest in the mining area, followed by the smelting and tailings areas; the control area exhibited the lowest levels. Community structure analysis revealed significant enrichment of Thiobacillus, Geothrix, and Anaeromyxobacter in the mining area, while Nocardioides and Sphingomonas were more abundant in the smelting area. Bradyrhizobium dominated in the control area. These patterns reflect distinct microbial responses to the Sb contamination gradient. Critically, partial least squares path modeling revealed that Sb contamination did not directly affect microbial α-diversity. Instead, its influence was indirectly mediated through disruptions in sulfur cycling functions-a novel finding highlighting the indirect ecological impact of Sb. Sb, along with co-occurring copper, may drive adaptive microbial succession by interfering with sulfate respiration. This process enriches microbial groups with sulfur-cycling-related detoxification functions, resulting in simplified community structure and reduced diversity. Thus, the primary mechanism by which Sb alters microbial communities in karst soils is indirect, operating via perturbation of the sulfur cycle rather than direct toxicity. These findings offer a theoretical basis for developing targeted microbial remediation strategies and restoring ecological functions in Sb-contaminated environments by regulating key elemental cycles.}, } @article {pmid42119482, year = {2026}, author = {Paula, MPO and Varani, AM and da Silva, VLC and Roesch, LFW and Tótola, MR and Ramos, AC and Pylro, VS}, title = {Genome-resolved characterization of microbial consortia driving glyphosate degradation in soil.}, journal = {Chemosphere}, volume = {405}, number = {}, pages = {144948}, doi = {10.1016/j.chemosphere.2026.144948}, pmid = {42119482}, issn = {1879-1298}, mesh = {Glyphosate ; *Glycine/analogs & derivatives/metabolism ; *Soil Microbiology ; Biodegradation, Environmental ; *Herbicides/metabolism ; *Microbial Consortia/genetics ; *Soil Pollutants/metabolism ; Soil/chemistry ; Achromobacter/genetics/metabolism ; Serratia/genetics/metabolism ; Organophosphorus Compounds ; }, abstract = {Glyphosate is a widely used non-selective herbicide associated with ecological and human health concerns due to its environmental persistence, highlighting the need for effective remediation strategies. Among available approaches, microbial enzyme-mediated degradation represents a promising biological solution. This study aimed to enrich and characterize glyphosate-degrading microbial consortia from coffee plantation soils, validate glyphosate and aminomethylphosphonic acid (AMPA) degradation by chromatographic analyses, and integrate genome-based functional annotation with comparative structural analyses to investigate enzymatic systems involved in C-P and C-N bond cleavage. The enrichment process, followed by metataxonomic and metagenomic analyses, revealed dynamic shifts in microbial community composition. Achromobacter and Serratia were identified as key genera, harboring genetic potential for glyphosate and AMPA degradation. High-performance liquid chromatography with diode array detection confirmed efficient transformation of both compounds, with consortia Con_CC and Con_CC-G achieving the highest removal efficiencies under carbon- and phosphorus-limited conditions. Genome-based functional annotation showed that both genera encode gene clusters associated with the C-P lyase pathway, while only Achromobacter harbors the gene encoding glyphosate oxidoreductase (GOX), linked to oxidative C-N bond cleavage. Structural modeling indicated conservation of key catalytic residues in PhnJ, whereas GOX-related sequences in Serratia corresponded to partial homologs lacking a complete catalytic site. By integrating chromatographic, genomic, and structural analyses, this study provides a multi-level framework linking microbial community dynamics, functional potential, and molecular mechanisms underlying glyphosate degradation.}, } @article {pmid42119567, year = {2026}, author = {Chen, C and Xing, Y and Xing, G and Zeng, F and Zheng, N and Sha, S and Zhao, L and Zhang, Y and Ling, Y and Yao, X and Liu, C and Zhang, Y and Mei, T and Guo, R and Kang, J and Cheng, L and Fan, S and Sun, W and Li, S and Yan, Q and Yao, X and Kong, X and Ma, W}, title = {Multi-faceted characterization of the gut microbiome and metabolome in patients with primary Sjögren syndrome.}, journal = {Cell reports. Medicine}, volume = {7}, number = {5}, pages = {102777}, pmid = {42119567}, issn = {2666-3791}, mesh = {Humans ; *Sjogren's Syndrome/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; *Metabolome ; Female ; Middle Aged ; Male ; Feces/microbiology ; Adult ; Dysbiosis/microbiology ; Aged ; Case-Control Studies ; Metagenome ; }, abstract = {The gut microbiome and its metabolomic potential in primary Sjögren syndrome (pSS) remain largely unexplored. Here, we perform whole-metagenome shotgun sequencing of fecal samples from 206 pSS patients and 355 non-pSS controls, integrating compositional and functional profiling with serum and fecal metabolomes. pSS is associated with extensive multi-kingdom alterations, including 49 bacterial (e.g., Streptococcus parasanguinis, Ligilactobacillus salivarius, and Veillonella parvula), 19 fungal (notably Candida albicans), and 1,323 viral species. These signatures form robust inter-kingdom correlations and achieve high diagnostic accuracy in an independent validation cohort. Functional and metabolomic analyses reveal enrichment of toxin-related and aromatic pathways and depletion of protective metabolites in patients. pSS-enriched bacteria harbor abundant immunogenic epitopes, virulence factors, and antimicrobial resistance genes, and induce proinflammatory responses ex vivo. Together, these findings outline a multi-faceted microbial framework for pSS and suggest mechanistic links between gut dysbiosis and immune dysregulation.}, } @article {pmid42119613, year = {2026}, author = {Liu, Y and Cheng, C and Xie, H and Nie, W and Chen, Y and Yu, C and Pavlostathis, SG and Zhang, J and He, Q}, title = {New insights into nitrous oxide-driven anaerobic methane oxidation mediated by Methylococcales and Gemmatimonadales.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134844}, doi = {10.1016/j.biortech.2026.134844}, pmid = {42119613}, issn = {1873-2976}, mesh = {*Methane/metabolism ; *Nitrous Oxide/metabolism ; Oxidation-Reduction ; Anaerobiosis ; *Methylococcaceae/metabolism ; Wetlands ; }, abstract = {The simultaneous biogeochemical transformation of methane (CH4) and nitrous oxide (N2O) in anoxic environments is a recently proposed pathway for decreasing carbon emission in wetlands. However, the mechanisms underlying this coupled process have yet to be elucidated. Here, two systems with CH4 to N2O molar ratios of 1:1 (R1) and 1:2 (R2) were established. Isotopic tracing showed that the production rate of [13]CO2 in R2 consistently exceeded than that in R1, with a maximum N2O-driven AOM rate of 2.29 μmol∙g[-1]dw∙d[-1], demonstrating the superior performance of R2. Microbial community analysis revealed that Methylococcales and Rhizobiales were the dominant methanotrophs, whereas Gemmatimonadales and Sphingobacteriales represented the primary denitrifiers involved in N2O reduction. Metagenomic binning further indicated that Methylococcales and Gemmatimonadales harbor complementary genomic potentials for CH4 oxidation and N2O reduction, supporting a synergistic interaction driving N2O-dependent AOM. This cooperation appears to rely on electron transfer between the methanotrophic and denitrifiers. Collectively, these findings provide mechanistic evidence for N2O-driven AOM, advancing the understanding of coupled carbon-nitrogen transformations and offering new insights into microbial strategies for mitigating greenhouse gas emissions in wetland systems.}, } @article {pmid42119614, year = {2026}, author = {Zhang, Y and Yu, W and Chen, B and Lu, D and Guo, R and Fu, S}, title = {Harnessing microbial resource Rhodopseudomonas palustris for saline-alkaline paddy soil amelioration: key role of extracellular polymeric substances.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134777}, doi = {10.1016/j.biortech.2026.134777}, pmid = {42119614}, issn = {1873-2976}, mesh = {*Rhodopseudomonas/metabolism ; *Soil/chemistry ; *Extracellular Polymeric Substance Matrix/metabolism ; *Soil Microbiology ; Biodegradation, Environmental ; *Salinity ; Oxidation-Reduction ; Hydrogen-Ion Concentration ; *Alkalies ; Oryza ; Electric Conductivity ; }, abstract = {Bioremediation offers an eco-friendly solution for soil salinization, yet few salt-alkali-tolerant microorganisms can adapt to redox fluctuations induced by wet-dry alternation in paddy soil. Rhodopseudomonas palustris (R. palustris) holds promise for addressing this challenge, while the mechanism is still poorly understood. This study established a microcosm experiment mimicking paddy wet-dry alternation by regulating redox conditions to investigate the mechanisms of R. palustris and its extracellular polymeric substances (EPS) in soil amelioration. R. palustris adapted well to redox alternation and significantly reduced soil pH and electrical conductivity (EC) by 3-7% and 7-28%. In anaerobic phase, R. palustris secreted organic acids and promoted EPS synthesis, which directly complexed salt ions and drove soil acidification. Upon transition to aerobic conditions, it accumulated glycogen and polyhydroxyalkanoate (PHA) to sustain growth and EPS secretion. In the subsequent aerobic phase, EPS gradually transformed into amino acids, fulvic acid, and humic-like substances, as revealed by excitation-emission matrix (EEM) spectra, thereby improving soil fertility. Metagenomic analysis further revealed R. palustris and its EPS reshaped the microbial community and regulated the expression of related functional genes. Collectively, this study demonstrates R. palustris serves as an effective microbial resource for sodic-saline paddy soil amelioration, with EPS acting as a key bioactive component that drives this process toward biotechnology-driven remediation strategies.}, } @article {pmid42119617, year = {2026}, author = {Yang, C and Cao, Y and Yang, Q and Li, J and Dong, T and Liu, Y and Li, X and Liu, F}, title = {Hematite-enhanced denitrification in bioelectrochemical system at low current density: kinetics, biofilm chemistry and metagenomic mechanisms.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134852}, doi = {10.1016/j.biortech.2026.134852}, pmid = {42119617}, issn = {1873-2976}, mesh = {*Denitrification/drug effects ; *Biofilms ; *Ferric Compounds/chemistry/pharmacology ; Kinetics ; Nitrates/metabolism ; *Metagenomics/methods ; Electrodes ; *Electrochemical Techniques/methods ; *Bioelectric Energy Sources ; }, abstract = {Nitrate contamination of groundwater threatens drinking-water safety and necessitates the development of sustainable, low-energy remediation technologies. Bioelectrochemical systems (BESs) can enhance denitrification; however, their performance is constrained by low cathodic electron efficiency and ammonium accumulation. We developed a hematite-enhanced BES (HBES) and evaluated denitrification at different current densities (0-400 mA/m[2]). Hematite shifted the optimal current density from 200 to 100 mA/m[2], achieving complete nitrate removal within 72 h while suppressing ammonium formation to 0.38 ± 0.02 mg-N/L. Mechanistically, hematite improved cathodic kinetics and minimized activation losses, increased nitrate reductase activity, and promoted extracellular polymeric substance (EPS) enrichment with higher redox-active fulvic- and humic-like fractions. Community profiling revealed hematite-associated enrichment of Thauera, Acinetobacter, Hydrogenophaga, and Alishewanella, consistent with enhanced denitrification and electroactivity. Metagenomic analyses further revealed enhanced modules for sequential nitrate reduction to N2, suppression of dissimilatory nitrate reduction to ammonium (DNRA) marker genes, and elevated potentials for cytochrome-associated extracellular electron transfer (EET) and oxidative phosphorylation. Overall, hematite restructures electron-transfer networks and microbial metabolism at the mineral-biofilm-electrode interface, facilitating efficient and cleaner denitrification at relatively low current density and offering operational insights for BES-based groundwater nitrate remediation.}, } @article {pmid42119682, year = {2026}, author = {Mardirossian, JM and Abdallah, B and Douglas, GM and Barbour, J and Shapiro, BJ and El Chaar, M}, title = {Early-life acquisition of antimicrobial resistance genes and strain-level genomic concordance across maternal-infant compartments.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {142}, number = {}, pages = {105956}, doi = {10.1016/j.meegid.2026.105956}, pmid = {42119682}, issn = {1567-7257}, mesh = {Humans ; Female ; Infant, Newborn ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Milk, Human/microbiology ; Adult ; Meconium/microbiology ; Metagenomics ; Whole Genome Sequencing ; Genome, Bacterial ; Microbial Sensitivity Tests ; }, abstract = {BACKGROUND: Early-life microbial colonization and antimicrobial resistance gene (ARG) acquisition may influence long-term health outcomes. High-resolution genomic studies assessing strain-level concordance and resistome overlap across maternal-infant interfaces during the immediate postnatal period remain limited.

METHODS: We analyzed 32 healthy mother-newborn dyads in Lebanon (91 samples), including maternal colostrum and breast milk and neonatal meconium and stool. Culture-based isolation, antimicrobial susceptibility testing, shotgun metagenomics, and whole-genome sequencing were used to characterize microbial composition, resistome profiles, and strain-level relatedness.

RESULTS: Viable bacteria were recovered from 80% of meconium samples, with Escherichia coli and Enterococcus faecalis among the most frequent isolates. Whole-genome sequencing identified highly similar strains (≥99.9% average nucleotide identity) of E. coli, Klebsiella pneumoniae, and K. oxytoca across maternal and neonatal samples in six dyads. Metagenomic profiling demonstrated early acquisition of multidrug resistance genes, including blaCTX-M-15, tet(M), and oqxA/B, alongside mobile genetic elements such as IncF and Col-type plasmids. The colistin resistance gene mcr-10.1 was detected in one neonatal stool sample.

CONCLUSION: These findings demonstrate early-life resistome establishment and strain-level genomic concordance across maternal-infant compartments within the first week of life. While low-biomass samples require cautious interpretation, the observed genomic similarities and shared ARGs are consistent with potential maternal or shared environmental contributions to neonatal microbial and resistance gene acquisition, although the direction of transfer cannot be definitively established. This work underscores the importance of integrating genomic surveillance of maternal and neonatal resistomes in perinatal health research.

IMPORTANCE: This study provides high-resolution genomic insight into early-life microbial colonization and antimicrobial resistance gene acquisition by integrating culture-based microbiology, shotgun metagenomics, and whole-genome sequencing across matched maternal (colostrum, breast milk) and neonatal (meconium, stool) samples. The identification of viable bacteria and clinically relevant resistance determinants within the first week of life, including instances of strain-level genomic concordance between maternal and neonatal samples, contributes to understanding the early establishment of the neonatal resistome. While low-biomass samples require cautious interpretation, the observed genomic similarities and shared mobile genetic elements suggest potential maternal or shared environmental influences on early colonization dynamics. These findings highlight the value of considering maternal reservoirs in studies of neonatal microbial and resistance gene evolution and underscore the need for genomic surveillance of early-life resistome development in perinatal settings.}, } @article {pmid42119744, year = {2026}, author = {Mao, N and Liao, C and Hao, J and Sun, H and Zheng, Y and Yin, H and Xie, Y}, title = {Late-window oxygen pulsing unlocks lignin-carbohydrate shielding and enhances fiber deconstruction during maize stover fermentation.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134854}, doi = {10.1016/j.biortech.2026.134854}, pmid = {42119744}, issn = {1873-2976}, mesh = {*Lignin/metabolism/chemistry ; *Fermentation ; *Zea mays/metabolism/chemistry ; *Oxygen/metabolism ; Anaerobiosis ; *Carbohydrates/chemistry ; Cellulase/metabolism ; Hydrolysis ; }, abstract = {Staged aeration offers a controllable lever to relax the strict-anaerobic paradigm in lignocellulosic fermentation. We compared single-dose air injection at early, mid, and late windows with a cellulase benchmark and anaerobic control, integrating fiber fractions, fermentation products, FTIR metrics, metagenomic functional profiles (CAZy and nitrogen cycling), microbial succession, and network topology. Mid and late aeration promoted ADL reduction and fiber deconstruction, lowering acid detergent lignin and acid detergent fiber by 23-34% and 13-15% versus the control, reaching cellulase-comparable levels. Late aeration produced the strongest structural unlocking, with attenuation of carbohydrate- and lignin-aromatic FTIR regions and reduced carbonyl-associated bands, consistent with disrupted lignin shielding and improved substrate accessibility. Late aeration increased glycosyltransferases yet showed the lowest glycoside hydrolases and auxiliary activities while achieving the largest net ADL and fiber losses, indicating that accessibility rather than terminal hydrolytic potential governs deconstruction intensity. Network analysis showed reduced mean degree and K-core but higher modularity under late aeration, consistent with a more compartmentalized interaction structure and reallocated carbon use. Overall, aeration timing is a scalable, low-input lever for process design. Future work should test generality across feedstocks and develop accessibility-based monitoring and control.}, } @article {pmid42119966, year = {2026}, author = {Athira, AS and Sreejith, VN and Megha, C and Athira, PS and Reshmi, K and Murugadas, V and Joseph, TC}, title = {Metagenomic characterization of bacterial communities on beach macroplastics: Insights into antimicrobial resistance and virulence.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {405}, number = {}, pages = {128213}, doi = {10.1016/j.envpol.2026.128213}, pmid = {42119966}, issn = {1873-6424}, abstract = {Macroplastic debris in coastal environments provides stable substrates for microbial colonization, yet comparative assessments with natural substrates remain limited. This study investigated bacterial communities associated with beach macroplastics collected from four sites along the Kochi coast, Kerala, India (Fort Kochi, Cherai, Puthenthode, and Puthuvypin) during the pre-monsoon season, and compared them with those colonizing natural inanimate substrates (driftwood, seaweed, and shells). Composite sampling across multiple transects was employed, and shotgun metagenomic sequencing was used to characterize taxonomic composition, functional pathways, antimicrobial resistance genes (ARGs), and virulence factors. Across all samples, Pseudomonadota (average ∼64.8%) dominated, followed by Bacillota, Actinomycetota, and Bacteroidota. Plastic-associated communities showed greater dominance of specific genera, including Vibrio, Alteromonas, and Pseudoalteromonas, whereas natural substrates exhibited more evenly distributed taxa (Streptomyces, Marinobacter, Sulfitobacter etc). Functional annotation revealed the presence of core metabolic pathways across all samples, while xenobiotic degradation and lipid metabolism pathways were more prominently represented in plastic-associated communities, particularly at urban-influenced sites. A total of 42 ARGs belonging to eight antibiotic classes were identified, with β-lactam resistance genes constituting ∼42% of detected ARGs. Plastic-associated samples showed broader ARG profiles, including blaTEM-116, tetM, and sul1. A total of 73 virulence genes were identified, with plastic samples showing higher abundance of β-lactamase (blaTEM-116, tetM) and adhesion-associated genes (pilA, ompA). In addition, 1264-2046 virulence-related gene hits per site were detected, with consistently higher counts observed in plastic-associated communities. Overall, the findings demonstrate that macroplastics support distinct microbial assemblages and functional gene distributions compared to natural substrates, highlighting their role as microbial habitats in human-impacted coastal environments.}, } @article {pmid42120015, year = {2026}, author = {Ito, T and Li, B and Sakaguchi, T and Yagita-Sakamaki, M and Itoi, H and Murakami, M and Wu, R and Fukada, A and Motooka, D and Ogino, T and Nakamura, S and Okuzaki, D and Takeda, K and Kayama, H}, title = {The IL-10/IL-10Rα axis in fibroblasts limits large intestinal pathology by suppressing type I interferon signaling.}, journal = {International immunology}, volume = {}, number = {}, pages = {}, doi = {10.1093/intimm/dxag022}, pmid = {42120015}, issn = {1460-2377}, abstract = {Recent studies identified that the dysregulation of fibroblast activity, in addition to impairment in epithelial integrity and uncontrolled immune response, is implicated in the pathogenesis of inflammatory bowel disease (IBD). The anti-inflammatory cytokine IL-10 and its receptors IL-10Rα and IL-10Rβ have IBD-associated single nucleotide polymorphisms. In the intestine, IL-10 signaling is essential for maintaining an anti-inflammatory state of myeloid cells and inducing regulatory T cells, thereby preventing intestinal inflammation linked to IBD development. However, its impact on the physiology and pathophysiology of intestinal fibroblasts is poorly understood. Here, we show that Il10ra deficiency leads to increased expression of a subset of genes in colonic fibroblasts, most of which are associated with the type I interferon (IFN) and type II IFN signaling pathways. In addition, Pdgfra-cre; Il10raf/f mice aged 16 weeks or older develop chronic spontaneous colitis and subsequent fibrosis accompanied by enhanced infiltration of myeloid cells and effector CD4+ T cells in the lamina propria of the colon. Moreover, Pdgfra-cre; Il10raf/f mice at 12 weeks of age exhibit more severe clinical symptoms than those of Il10raf/f mice during dextran sodium sulfate-induced colitis that can be suppressed by the administration of anti-IFNAR1 antibody but not anti-IFNGR1 antibody. Therefore, inhibition of type I IFN pathway via IL-10Rα signaling in fibroblasts is one of the IL-10-dependent mechanisms underlying the prevention of large intestinal pathology.}, } @article {pmid42120057, year = {2026}, author = {Owens, LA and Berkman, LK and Pease, BS and Dunn, CD and Nielsen, CK and Groninger, JW and Bosch, K and Hudman, D and Timm, SR and Goldberg, TL}, title = {Viruses and Parasites in Swamp Rabbits (Sylvilagus aquaticus): A Baseline Survey to Aid Conservation Efforts.}, journal = {Journal of wildlife diseases}, volume = {}, number = {}, pages = {}, doi = {10.7589/JWD-D-25-00059}, pmid = {42120057}, issn = {1943-3700}, abstract = {Technical advancements have enabled the discovery of potential pathogens in an ever-broadening range of wildlife taxa. To further the scope of this body of knowledge and to inform conservation efforts, we examined potential disease agents present in swamp rabbits (Sylvilagus aquaticus) of southeastern Missouri, USA, during winter 2023. This region represents the northernmost portion of the species' range and is characterized by an intermixed landscape of preferred bottomland hardwood forest and agricultural landcover. Concerns about infectious disease threats to swamp rabbits have increased since the emergence of rabbit hemorrhagic disease, caused by rabbit hemorrhagic disease virus 2 (RHDV2; Caliciviridae, Lagovirus europaeus), that has spread to domestic, wild, and feral rabbits and hares, predominantly in the western and midwestern USA. We applied metagenomic and metabarcoding methods, designed to characterize communities of viruses and parasites, to noninvasively collected rabbit fecal samples. We identified seven viruses and eight parasite genera that probably infect mammals. Although some relatives of these agents cause disease, none are unexpected in lagomorphs, and none are considered a health concern. Notably, RHDV2 was not detected. These results provide baseline data for future conservation and management efforts, especially if RHDV2 or other pathogens become a concern for swamp rabbits.}, } @article {pmid42120383, year = {2026}, author = {Tingley, JP and Andersen, TO and Mihalynuk, LG and Xing, X and Low, KE and Whiteside, DP and Altshuler, I and Jujihara, N and Shearer, AY and Klassen, L and Serin, S and Smith, E and Reintjes, G and Patel, TR and Boraston, AB and Hagen, LH and Pope, PB and Abbott, DW}, title = {Distribution of microbial carrageenan foraging pathways reveals a widespread latent trait within the ruminant intestinal microbiome.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42120383}, issn = {2041-1723}, support = {J-002817; J-003135//Gouvernement du Canada | Agriculture and Agri-Food Canada (Agriculture et Agroalimentaire Canada)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics/physiology ; *Carrageenan/metabolism ; *Ruminants/microbiology ; Rumen/microbiology ; Glycoside Hydrolases/metabolism/genetics ; Feces/microbiology ; Bacteria/metabolism/genetics/classification/isolation & purification ; Seaweed/metabolism ; Bacteroides/metabolism/genetics/isolation & purification ; Metagenomics ; Phylogeny ; }, abstract = {Seaweeds represent a promising source of sustainable, alternative feeds for livestock. Despite their increasing popularity in agriculture, the dietary fate of seaweed polysaccharides, such as carrageenan, is unknown. Here, we apply functional microbiome analyses of ruminant gastrointestinal tract microbiomes to discover catabolic enzymes specific for carrageenan digestion from the red seaweed Mazzaella japonica. M. japonica preferentially increased Bacteroides abundance within the feces over the rumen, and bacterial isolates have the capacity to use carrageenans as a sole carbon source. We identify carrageenan-active polysaccharide utilization loci (CarPULs) and characterize recombinant GH16 subfamily 17 carrageenases, informing previously uncharacterized substrate specificities for the subfamily, and providing insights into pathway specialization of divergent CarPULs. Selective enrichment and metagenomic mining reveals that carrageenan catabolism is widespread among geographically and taxonomically distinct ruminants, suggesting it is a latent trait widely distributed in the Order Artiodactyla and carried within their microbiomes as part of the microbial "dark matter". These pathways are structurally distinct from those found in marine bacteria, highlighting a complex and ancient evolutionary history of CarPULs in ruminant microbiomes.}, } @article {pmid42120665, year = {2026}, author = {Chen, LG and Zhou, L and Wang, BW and Javed, M and Liu, YF and Yang, SZ and Gu, JD and Mu, BZ}, title = {Microbial assembly and metabolic restructuring following CO2 injection in subsurface oil reservoir.}, journal = {AMB Express}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13568-026-02066-w}, pmid = {42120665}, issn = {2191-0855}, support = {Grant No. 42473082//National Natural Science Foundation of China/ ; No. 42173076//National Natural Science Foundation of China/ ; No. 52074129//the National Natural Science Foundation of China/ ; 21ZR1417400//the Natural Science Foundation of Shanghai/ ; JKJ01231714//the Fundamental Research Funds for the Central Universities of China/ ; }, abstract = {Carbon dioxide (CO2) injection into oil reservoirs is a well-established and promising strategy for enhancing oil recovery while simultaneously sequestering carbon, whose effectiveness is increasingly recognized to be influenced by microbial-mediated mechanisms and biogeochemical processes. However, the impact of CO2-injected and storage on functional microbial communities and their metabolic potential remains poorly understood. The study employed high-throughput sequencing to analyze the composition and diversity of microbial communities in produced water from three production wells with a long-term (> 20 years) history of CO2 injection and two adjacent water-flooding ones in Xinli Oilfield, China. The results showed that CO2-injected wells had significantly higher microbial diversity and distinct metabolic potential relative to the adjacent water-flooding wells. A metabolic difference in the archaeal communities towards hydrogenotrophic and heterotrophic metabolisms, alongside an enrichment of bacterial taxa associated with sulfur and nitrogen cycling was observed. Correlation analysis revealed that microbial differentiation was strong associated with geochemical alteration (especially pH and some inorganic ions), with NH4[+] and S[2-] identified as key factors in this process. Metagenomic analysis based on high-quality metagenome-assembled genomes (MAGs) further demonstrated that CO2 injection led to a different profile of microbial metabolic functions relative to the water-flooding condition, characterized by significantly enhancing hydrogenotrophic methanogenesis, dissimilatory sulfate reduction, and denitrification, while diminishing methylotrophic methanogenesis and Wood-Ljungdahl pathway activity. These findings provide new insights into the microbial mechanisms driving carbon transformation in CO2-flooded oil reservoirs.}, } @article {pmid42120930, year = {2026}, author = {Huang, L and Zhang, X and Wu, Y and Li, H and Li, M and Shao, C and Yang, Q and Jin, G and Hu, X}, title = {The gut microbiota and metabolomics in the pathogenesis of type 2 diabetes mellitus combined with coronary atherosclerotic heart disease.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-51805-3}, pmid = {42120930}, issn = {2045-2322}, support = {Grant No.202204295107020049)//the Clinical Translation Project of Anhui Province/ ; Grant No. 2208085MH216//the Natural Science Foundation of Anhui Province/ ; Grant No. 2020byfy004//the Major Natural Science and Technology Project of Bengbu Medical Uuniversity/ ; Grant No. AHWJ2023BAc10028//The Scientific Research Program of Anhui Provincial Health Commission/ ; }, abstract = {To investigate the characteristics of intestinal bacteria and their metabolites in healthy controls (CONs) compared with individuals with type 2 diabetes mellitus (T2DM) and individuals with type 2 diabetes mellitus combined with coronary atherosclerotic heart disease (T2DM-CAD). Thirty samples were collected from 10 healthy people, 10 T2DM patients, and 10 T2DM-CAD patients. We determined the gut bacterial composition via metagenomic sequencing analysis and analyzed the gut microbes and their metabolomic changes via metabolomics. The potential key gut microbes and metabolites were explored with random forest and receiver operating characteristic (ROC) curve analyses. Finally, Spearman correlation analysis and linear regression were used to identify the correlations between the gut bacteria and metabolites. Eight gut microorganisms with diagnostic significance were screened out, including Prevotella disiens, Bacteroides sp._AM25_34, Paraprevotella clara, Bacteroides sp._CAG_875, Sutterella wadsworthensis, Prevotella sp. 885, Ruminococcus sp. AM42_11 and Anaerobutyricum hallii. Meanwhile, eight characteristic metabolites were identified, including fructose, salicyluric acid, 12-ketoLCA, pyroglutamic acid, glutamic acid, suberic acid, gallic acid and adipic acid. Additionally, the correlations between the above differential gut microbiota and characteristic metabolites were clarified. Our study revealed that gut flora such as g-Bacteroides, Alistipes_putredinis_CAG_67, and Alistipes_putredinis may be key flora, and that fructose, gallic acid, sebacic acid, and 12-ketoLCA may be key metabolites involved in the pathology of T2DM and T2DM-CAD.}, } @article {pmid42121077, year = {2026}, author = {Song, C and Li, Y and Deng, Y and He, D and Fan, X}, title = {Gut microbiota profiles associated with temporal lobe epilepsy and psychiatric comorbidities: a family-matched case-control 16S rRNA study.}, journal = {BMC neurology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12883-026-04958-7}, pmid = {42121077}, issn = {1471-2377}, abstract = {We investigated alterations in the intestinal microbiota of patients with temporal lobe epilepsy (TLE) and their associations with drug resistance and psychiatric comorbidities. Thirty TLE patients and 30 family-matched healthy controls sharing the same household diet were recruited, and fecal samples were analyzed by high-throughput 16S rDNA sequencing on the Illumina MiSeq [Formula: see text] bp platform. Differential abundance was assessed using Metastats and LEfSe with Benjamini-Hochberg false-discovery-rate correction, and independently validated using ANCOM-BC to account for the compositional nature of microbiome data. Community α- and β-diversity indices showed no significant differences between groups; however, ANCOM-BC identified species-level signatures in drug-resistant epilepsy, including significant depletion of Bacteroides plebeius and Coprococcus comes. Among psychiatric subgroups, Ruminococcus was significantly reduced in patients with comorbid depression, while Bilophila was enriched in those with comorbid anxiety and depression. Bacteroides stercoris distinguished the anxiety-plus-depression subgroup from the depression-only subgroup with robust support from both ANCOM and ANCOM-BC. Given the modest overall sample size ([Formula: see text] per arm) and small psychiatric and drug-resistance subgroups, these findings should be regarded as exploratory and hypothesis-generating associations rather than definitive biomarkers. They identify candidate microbial taxa warranting validation in larger, longitudinal cohorts combined with metagenomic and metabolomic approaches.}, } @article {pmid42121260, year = {2026}, author = {Zhou, Z and Lamanna, A and Halder, R and Pansart, E and Narayanasamy, S and Boussoufa, B and Kerkour, T and Wilmes, P and Williams, E}, title = {Integrative analysis of the mouse cecal microbiome across diet, age, and weight in the diverse BXD population.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42121260}, issn = {2049-2618}, support = {PRIDE21/16749720/NEXTIMMUNE2//Luxembourg National Research Fund/ ; }, mesh = {Animals ; *Cecum/microbiology ; Mice ; *Gastrointestinal Microbiome/genetics ; *Body Weight ; Diet, High-Fat ; Male ; Age Factors ; Diet ; Transcriptome ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Metagenomics/methods ; }, abstract = {BACKGROUND: The gut microbiota adapts to and shapes the host's metabolic state through affecting circulating metabolites and consequent gene regulatory networks, resulting in systemic influences in diverse organs via connections such as the gut-liver axis. Numerous variables such as diet, age, and host genetics modulate the composition of the gut microbiome, but their interactions and specific associative and mechanistic links to host molecular phenotypes remain incompletely unannotated. Integrated multi-omics approaches in genetically diverse populations offer an opportunity to dissect these interactions and identify predictive microbial signatures for host phenotypes, such as body weight and molecular associations with gene expression pathways in gut and liver.

RESULTS: We sequenced, aligned, and integrated the cecal metagenome, metatranscriptome, and host transcriptome from 232 mice across 175 distinct cohorts according to a low-fat chow diet (CD) or a high-fat diet (HF), four adult ages (between roughly 180 to 730 days of age), and 43 distinct genotypes (inbred BXD strains). Genetics and diet exerted the strongest influence on microbiota abundance and activity, followed by age. HF feeding significantly reduced diversity across all ages and all genotypes, altering > 300 species. Machine learning models based on microbial profiles reliably predicted body weight within dietary group (AUC = 0.84 for CD, 0.79 for HF) and chronological age (AUC = 0.84), with model performance of age prediction rising to 0.95 when integrating top microbial features with liver proteomics. Network analyses of expression data revealed links between genes, pathways, and specific microbes, including a negative association between cecal Ido1 expression and short-chain fatty acid (SCFA)-producing Lachnospiraceae, suggesting dietary fat may modulate host tryptophan metabolism through microbiota shifts.

CONCLUSIONS: Whole metagenome and metatranscriptome sequencing approaches have massively expanded the landscape of microbiome analysis compared to earlier short-read 16S analyses. The resulting datasets quantify hundreds of uniquely identifiable microbes, which can be used to create sets of highly predictive microbial biomarkers for aging and obesity. When trained on controlled mouse populations, these results demonstrate that microbiome profiling can achieve high predictive capacity (AUC = 0.95 with multi-omics integration) for complex readouts such as age and body weight (AUC = 0.84), even considering genetic and dietary variation, establishing a framework for biomarker development. While at present many bacteria are still functionally unannotated at the species level, multi-omics approaches - including gene expression from the host tissues - provide insights into the functional associations of specific taxa in the microbiome. Video Abstract.}, } @article {pmid42121284, year = {2026}, author = {Burkhart Colorado, AS and Nusbacher, NM and O'Connor, J and Marden, T and Higgins, J and Neff, CP and Fiorillo, S and Campbell, TB and Borok, M and Boyd, K and Sterrett, J and Palmer, BE and Lozupone, C}, title = {The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02410-z}, pmid = {42121284}, issn = {2049-2618}, support = {R01 DK108366/DK/NIDDK NIH HHS/United States ; T15LM009451//U.S. National Library of Medicine/ ; }, abstract = {BACKGROUND: People living with HIV (PLWH) suffer from chronic inflammation even with effective antiretroviral therapy (ART). A high-fat, low-fiber western-type diet has been linked with inflammation, in part through gut microbiome changes. In sub-Saharan Africa (SSA), a region with high HIV burden, urbanization has been linked with a shift from traditional agrarian towards westernized diets, and with changes in food security. To explore the relationship between diet, inflammation, and the gut microbiome in PLWH, we enrolled 1) ART Naïve PLWH who provided samples before and after 24 weeks of ART, 2) PLWH on ART at both timepoints and 3) HIV-seronegative controls. Individuals were evenly recruited from rural and urban Zimbabwe. Using a food frequency survey designed to measure intake of agrarian versus western-type food items in Zimbabwe, we determined how diet differs with urbanization, HIV-infection and treatment, and is related to inflammation and the gut microbiome.

RESULTS: Individuals residing in a rural area of Zimbabwe less frequently consumed high-fat, low-fiber western type food items and had lower consumption of diverse food items overall, except for sadza, a subsistence staple, processed from home-grown grains. Consumption of a more western-type diet correlated with lower CD4 + T cell percentage in untreated and treated PLWH and increased T cell exhaustion in PLWH on ART. PLWH on ART at time of enrollment also consumed diverse food items at a lower frequency and more often were underweight. Low food consumption correlated with muted improvements in T cell exhaustion after 24 weeks of ART. Individuals residing in the rural area had more Prevotella-rich/Bacteroides-poor microbiomes, but this was not significantly mediated by diet. Carbohydrate substrate degradation capabilities in the microbiome, based on predictions made using metagenomic polysaccharide utilization loci, correlated with dietary intake patterns.

CONCLUSIONS: Taken together, this work supports that consumption of more high-fat/low-fiber type food items has the potential to exacerbate HIV pathogenesis in a sub-Saharan setting where HIV burden is high and reinforces the importance of nutritional support for promoting immunologic response to ART in PLWH in SSA. Video Abstract.}, } @article {pmid42121750, year = {2026}, author = {Moharam, I and Brüggemann, J and Schmitt, F and Schade, B and Böhm, B and Kappe, E and Emmrich, F and Najar, FZ and El-Mayet, FS}, title = {Molecular Epidemiology of Enteric Viral Infections in Poultry Flocks in Southern Germany and the First Complete Genome Sequence of Avian Sicinivirus.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {9}, pages = {}, pmid = {42121750}, issn = {2076-2615}, abstract = {Enteric viral infections represent a major concern for poultry production, causing growth retardation, impaired feed conversion, and increased mortality, particularly in young birds. To investigate the involvement of RNA and DNA enteric viruses in flocks exhibiting growth problems, seven poultry farms in southern Germany, including broiler, pullet, and breeder operations, were examined for the presence of chicken astrovirus (CAstV), avian reovirus (ARV), and fowl adenovirus-1 (FAdV-1) by means of RT-PCR. All farms exhibited growth retardation, diarrhea, and enteritis-associated lesions. Histopathology revealed features of runting-stunting syndrome in most of the broiler farms and depletion of lymphatic tissue in most of the pullet farms. CAstV was detected in all flocks, ARV in six, and FAdV-1 in four farms. To further characterize the viral agents, metagenomic sequencing of cecal tonsils from one severely affected broiler flock confirmed the presence of a CAstV strain identical (100%) to CAV/Belgium/4134_001/2019. In addition, the complete genome of avian Sicinivirus was assembled for the first time in Germany, showing 96.8% nucleotide identity with a Dutch strain (Chicken/NLD/2019/V_M_056_picorna_2). These findings demonstrate the widespread circulation and co-infection of enteric viruses on German poultry farms and underline the transboundary nature of these infections, emphasizing the need for enhanced surveillance and biosecurity measures to mitigate their impact on poultry health and productivity.}, } @article {pmid42121788, year = {2026}, author = {Gao, F and Zuo, Z and Wu, Q and Xiao, H and Peng, Z and Zou, L and Jiang, G and Tian, X and Feng, Z and Xie, X and Tian, L}, title = {Analysis of Ochetobibus elongatus (Kner) Dietary Habits Based on Digestive System Morphology, Histology, and Intestinal Content Sequencing Technology.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {9}, pages = {}, pmid = {42121788}, issn = {2076-2615}, support = {HARS-07//Hunan Provincial Modern Agriculture (Aquaculture) Industry Technology System Project/ ; }, abstract = {Ochetobibus elongatus (Kner) is a migratory fish found in the Yangtze River basin and areas south of it, and listed as a critically endangered (CR) fish on the China Red List of Vertebrates. To achieve group recovery and artificial breeding, this study investigated the dietary characteristics of O. elongatus based on high-throughput sequencing of its intestinal contents, and its digestive system morphology, and its histology. Results showed that the digestive system of O. elongatus lacked a stomach and mainly consisted of the oropharynx, pharyngeal teeth, esophagus, intestine, and anus. The gut index was 0.88, with clear segmentation of the foregut, midgut, and hindgut, and the visceral mass index was 7.35%. Histological analysis of the digestive system revealed the presence of keratinized dental plates or pharyngeal teeth in the pharynx, as well as a high density of taste bud cells in the soft palate of the oral cavity. The surface layer of the intestinal villi contained numerous mucous cells, with the average number of mucous cells per villus gradually increasing from the esophagus to the hindgut, and the foregut having the longest and most abundant mucosal folds. The esophagus exhibited well-developed circular and longitudinal muscle layers, while in the hindgut, both the circular and longitudinal muscle layers were slightly thicker than those in the midgut. High-throughput sequencing of the intestinal contents of O. elongatus revealed the following phyla based on 18S V4 meta-barcoding: Chlorophyta, Diatoms, Arthropoda, Basidiomycetes, and Ascomycetes, with the genus Hypophthalmichthys and algae being the main classifications. In contrast, based on COI meta-barcoding, the study newly identified the phyla Cnidaria and Mollusca, with the genera Chlorophyta, Scenedesmus, Pectinodesmus, and zooplankton such as Pseudodiaptomus. Metagenomic sequencing revealed that the gut microbiota at the phylum level was predominantly composed of Pseudomonadota, Ascomycota, Basidiomycota, Chytridiomycota, and Bacillota, with key genera including Cetobacter, Pseudomonas, Acinetobacter, Aeromonas, and Clostridium. This study indicates that O. elongatus is an omnivore with carnivorous tendencies. Basic biological research on O. elongatus is of great significance for the restoration of the population, artificial breeding, and the development of its artificially formulated feed. It also provides important data for the formulation of biodiversity conservation measures.}, } @article {pmid42122064, year = {2026}, author = {Hussain, A and Abbas, Q and Nadeem, M and Nazar, A and Athar, A and Rahman, HUU}, title = {Meat-Borne Bacterial Pathogen Detection: Conventional, Molecular and Emerging AI-Based Strategies.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {9}, pages = {}, pmid = {42122064}, issn = {2075-4418}, abstract = {Meat serves as a prime medium for the growth of foodborne pathogens due to its rich protein content and high water activity, contributing significantly to the global burden of foodborne illnesses. This review synthesizes current advances in meat-borne bacterial pathogen detection with particular emphasis on emerging artificial intelligence (AI)-enabled applications. Major pathogens of concern, including Salmonella, Listeria monocytogenes, Escherichia coli, Campylobacter, Clostridium, and Staphylococcus aureus, are examined in relation to their relevance across the meat supply chain. Recent progress in biosensors (clustered regularly interspaced short palindromic repeats), CRISPR-based assays, isothermal amplification, and metagenomics is evaluated alongside the growing role of AI in automating signal interpretation, enhancing image-based diagnostics, and supporting early contamination prediction. AI-based systems have proved 96.4-104% recovery and 100% bacterial capture ability. Embedding AI methods in a wet lab demands technical and logical modeling, as well as learning and calibration decorum. Nonetheless, AI readiness and full-scale application for meat-borne pathogens surveillance are on the way. Furthermore, additional focus is aligned on meat-borne bacterial pathogen genomic databases, i.e., (NCBI Pathogen Detection, EnteroBase, VFDB, ComBase, and GenBank), which serve as critical training resources for AI models for outbreak tracking, virulence profiling, and antimicrobial resistance (AMR) prediction. By integrating molecular methods, genomic surveillance, and AI-driven analytics, this review presents a framework for strengthening meat safety systems. This will improve early detection capabilities and support data-driven public health interventions in the future.}, } @article {pmid42122249, year = {2026}, author = {Dragomir, RD and Saftescu, S and Sandu, DL and Dulan, A and Croitoru-Cazacu, IM and Croitoru, AE and Croitoru, VM and Vornicu, V and Nagy, DE and Perva, IT and Sirca, D and Popovici, DI}, title = {Artificial Intelligence-Guided Personalized Gut Microbiome Modulation for Persistent Secondary Gastrointestinal Symptoms in Oncology Patients: Clinical Efficacy and Biological Correlates from a Prospective Validation Study.}, journal = {Cancers}, volume = {18}, number = {9}, pages = {}, pmid = {42122249}, issn = {2072-6694}, support = {No Grant Number//Victor Babeș University of Medicine and Pharmacy Timișoara/ ; }, abstract = {Background/Objectives: Persistent gastrointestinal (GI) symptoms following oncologic treatment represent a major unmet need in survivorship care, often managed symptomatically without addressing underlying biological mechanisms. This study aimed to evaluate the clinical efficacy and biological correlates of an artificial intelligence (AI)-guided, personalized microbiome modulation strategy in oncology patients with chronic secondary GI dysfunction. Methods: We conducted a prospective, single-arm, open-label validation study including 29 adult female oncology patients with persistent GI symptoms lasting ≥3 months. Participants underwent baseline multidimensional assessment integrating shotgun metagenomic sequencing, inflammatory and nutritional biomarkers, and clinical symptom profiling. An AI-guided platform generated individualized dietary, supplement, and lifestyle recommendations. Outcomes were assessed at baseline and after a 3-month intervention, focusing on intra-individual changes in stool frequency (primary endpoint), self-reported energy, microbiome composition, and metabolic biomarkers. Paired statistical analyses, correlation testing, and multivariable regression were performed. Results: After three months, stool frequency significantly decreased (4.69 ± 2.41 to 2.07 ± 1.19 episodes/day; p < 0.0001), accompanied by a marked increase in energy levels (4.00 ± 1.04 to 7.24 ± 1.12; p < 0.0001). Microbiome analysis revealed consistent enrichment of butyrate-producing and barrier-supportive taxa, including Faecalibacterium prausnitzii, Eubacterium rectale, Roseburia intestinalis, Akkermansia muciniphila, and Bifidobacterium longum. Butyrate-related biomarkers and vitamin-associated parameters (B-complex, vitamin D) showed significant improvement, while lactate levels normalized. Changes in Bifidobacterium longum were independently associated with stool frequency reduction (β = -0.783, p = 0.0082). Conclusions: AI-guided personalized microbiome modulation was associated with significant clinical improvement and biologically coherent microbial and metabolic shifts in oncology patients with persistent GI symptoms. These findings support a precision supportive-care approach targeting microbiome restoration, warranting further validation in randomized controlled trials.}, } @article {pmid42122826, year = {2026}, author = {Pardo, JM and Suwannarach, N and Malichan, S and Cuellar, WJ and Siriwan, W}, title = {Mixed-Pathogen Infections in Vegetatively Propagated Crops: From Biological Synergism to Integrated Management.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {9}, pages = {}, pmid = {42122826}, issn = {2223-7747}, support = {000//Ministry of Higher Education, Science, Research and Innovation/ ; 000//Kasetsart University/ ; CROP-2023-157//Australian Centre for International Agricultural Research/ ; 000//National Research Council of Thailand/ ; }, abstract = {Vegetatively propagated crops, including cassava, sweet potato, banana, and potato, are susceptible to mixed-pathogen infections resulting from the continuous use of clonal planting material and infrequent seed replacement. A diverse array of viruses, bacteria, and fungi can accumulate within these materials over successive cultivation cycles, precipitating seed degeneration and complex disease syndromes that complicate diagnosis and management. Mixed infections frequently trigger synergistic interactions that exacerbate disease severity and yield losses. This review synthesizes data on mixed-pathogen complexes in vegetatively propagated crops, with particular focus on vascular and systemically colonizing pathogens and analyzing starch crops to highlight the epidemiological, biological, and ecological drivers of synergism and antagonism. Furthermore, the review examines host defense responses during coinfection, including the modulation of plant immune pathways, and evaluates how interpathogen dynamics influence pathological outcomes. Although advancements in molecular diagnostics-notably next-generation sequencing and metagenomics-have revolutionized the detection of mixed infections, they have also introduced challenges in differentiating causal agents from commensal microorganisms. Finally, we discuss the implications for integrated disease management, emphasizing clean seed systems, resistance breeding, and phenotyping strategies tailored to multipathogen environments. The dynamics of mixed infections is critical for resilient and sustainable management strategies amidst increasingly complex agricultural and climatic shifts.}, } @article {pmid42122957, year = {2026}, author = {Terry, C and Hall, LA and Halle-Smith, J and Edwards, LA and Sivakumar, S and Chapple, I and Beggs, A and Iqbal, T and Roberts, KJ}, title = {Pancreatic Cancer in the Holobiont and Therapeutic Targets: A Review.}, journal = {Journal of clinical medicine}, volume = {15}, number = {9}, pages = {}, pmid = {42122957}, issn = {2077-0383}, abstract = {Increasing evidence suggests pancreatic cancer develops within a host-microbe ecosystem in which microbial communities across anatomical niches interact with tumour biology, immune regulation, metabolism, and therapeutic response. This review examines pancreatic cancer through the lens of humans as holobionts, integrating evidence from the oral, gut, biliary, and intratumoural microbiomes. Epidemiological and sequencing studies demonstrate consistent microbial alterations across these niches in pancreatic cancer, including oral dysbiosis associated with periodontal pathogens, gut microbial shifts toward pro-inflammatory taxa, disease-specific biliary microbial signatures, and the presence of distinct intratumoural microbial communities. Mechanistic studies indicate that intestinal barrier disruption, microbial translocation, immune and metabolite signalling can influence tumour immune architecture, macrophage polarisation, T-cell infiltration, oncogenic signalling pathways, and chemotherapeutic metabolism, particularly inactivation by tumour-associated bacteria. Microbiome-driven shifts in immunometabolism can reprogramme immune-cell metabolic pathways, impairing effective T-cell activation, promoting tumour-supportive macrophage phenotypes. Emerging therapeutic strategies aim to modulate the microbiome-tumour axis, including dietary interventions, probiotics and immunonutrition, faecal microbiota transplantation, engineered microbial therapies, and microbiome-informed antibiotic strategies. While pre-clinical findings are compelling and early-phase clinical studies suggest feasibility, most evidence remains associative and heterogeneous across cohorts and methodologies. Understanding pancreatic cancer as a multi-site ecological system may help explain inter-patient variability in disease progression and treatment response. This could usher in a new era for therapeutic manipulation where future progress will depend on longitudinal, multi-omic, and interventional studies to determine whether microbiome-targeted strategies can produce clinically meaningful improvements in pancreatic cancer outcomes.}, } @article {pmid42123237, year = {2026}, author = {Liu, JW and Ma, X and Qian, YT and Wang, JW and Zhu, CY and Ma, DL}, title = {Detection of Nontuberculous Mycobacterial Skin Infection by Next-Generation Sequencing: A Pilot Study.}, journal = {Journal of clinical medicine}, volume = {15}, number = {9}, pages = {}, pmid = {42123237}, issn = {2077-0383}, support = {2022- PUMCH-161//National High Level Hospital Clinical Research Funding/ ; 3332024006//the Fundamental Research Funds for the Central Universities/ ; }, abstract = {Background: Nontuberculous mycobacteria (NTM) skin infections pose significant diagnostic challenges in clinical practice, due to nonspecific clinical/histopathological features and limitations of conventional pathogenic detection methods. Metagenomic next-generation sequencing (mNGS) offers a promising approach but requires further evaluation. Methods: A prospective pilot study at Peking Union Medical College Hospital enrolled 20 patients with cutaneous NTM infection, confirmed by positive skin culture or mNGS. All patients underwent thorough clinical assessment, skin biopsy for histopathology and culture, and mNGS testing of skin tissue. Treatment was based on identified species and disease extent. Treatment outcomes were tracked. Results: Among 20 patients (median age 45.5 years), fingers were the most common site affected (n = 10), followed by forearms (n = 7), hands (n = 4), and face (n = 4). Mycobacterium marinum was the predominant pathogen (n = 12), associated with fish bone puncture, followed by M. abscessus (n = 4). mNGS demonstrated a substantially higher positivity rate than culture (95% [19/20] vs. 30% [6/20]) and delivered results faster. Histopathology revealed granulomatous inflammation in all cases. Nineteen patients presented with non-disseminated disease; one immunocompromised patient (GATA2 deficiency) had disseminated M. abscessus infection. Treatment success was achieved in 17 patients (85%) with tailored antibiotic regimens. Adverse drug effects occurred in seven patients. Conclusions: In this pilot study of cutaneous NTM infections, mNGS enabled more rapid diagnosis relative to conventional culture. Clinical presentation and exposure history correlate with specific NTM species. Integrating mNGS with clinical assessment significantly improves diagnosis and management.}, } @article {pmid42123326, year = {2026}, author = {Zaman, S and Ali, N and Ullah, W and Taimur, N and Akbar, NU and Waheed, A and Muhammad, N and Khan, MS}, title = {Metagenomic Profiling Reveals Extensive Bacterial Diversity in Chicken Manure and Associated Contaminated Wastewater.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123326}, issn = {1422-0067}, mesh = {Animals ; Chickens/microbiology ; *Manure/microbiology ; *Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; Microbiota/genetics ; Biodiversity ; }, abstract = {Chicken manure and its potential to contaminate water systems through the dispersal of pathogenic bacteria are major concerns in environmental and public health. In this study, a metagenomic analysis was employed to systematically identify and compare bacterial assemblages in chicken manure (CM) and in a contaminated sample of chicken manure wastewater (CMW). Whole DNA was extracted from CM and CMW, followed by whole-genome shotgun sequencing; data analysis was done using online Galaxy software (ver. 26.0.1.dev1). Metagenomic analysis reveals a complex One Health challenge. Data showed that CM and CMW are different in their microbiota, as indicated by a distinct separation of beta diversity values and limited overlapping of species between sample types. In the current study, we found a greatly significant common functional set of adapted bacterial masses, including major pathogenic bacterial groups as well as opportunistic and environmental bacterial species, indicative of a direct contamination from CM and CMW. Notably, in both CM and CMW, a plethora of opportunistic, enteric, and environmental pathogens like Escherichia coli, Salmonella enterica, and Acinetobacter baumannii were found, coupled with an indication of a direct functional flow between both ecosystems as tangled reservoirs. Chicken manure samples showed differences in taxonomic composition and inferred functional profiles at the time of sampling: CM1 was pathogen-enriched, CM2 exhibited strong nitrogen-supportive metabolism, CM3 was dominated by fiber-degrading decomposers, and CM4 showed high methane-producing potential with environmental risk. Such findings underscore the raising of chickens as a potential source of harmful bacteria for the environment. It is important to note that this study represents a preliminary investigation with certain limitations, including the absence of biological replicates, lack of temporal sampling, and limited capacity to infer dynamic ecological interactions. Yet this metagenomic report is more about describing the taxonomy and functional potential of the bacteria, rather than discussing the actual ecological processes of these microorganisms in the environment. Future studies will be required to explore these aspects.}, } @article {pmid42123473, year = {2026}, author = {Cheng, R and Liu, T and Liao, C and Wu, X and Zhu, L and Zhang, S}, title = {Integrating Protein Language Models with Multimodal Embeddings to Accelerate Function Prediction of Uncharacterized Proteins.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123473}, issn = {1422-0067}, support = {No. 32401056//National Natural Science Foundation of China/ ; 2024RC3144//Hunan Province Science and Technology Innovation Program/ ; }, mesh = {*Proteins/chemistry/metabolism ; *Computational Biology/methods ; Databases, Protein ; Humans ; Molecular Sequence Annotation ; }, abstract = {Accurate prediction of protein function is fundamental to progress in biotechnology and biomedicine, yet progress remains severely hampered by the widening chasm between exponentially growing genomic data and the limited capacity for functional annotation. High-throughput sequencing and metagenomics have driven an explosion in sequence data that far outstrips experimental characterization. UniProt now contains over 203 million protein entries, of which only ~2% have been experimentally validated. This widening "sequence-function gap" exceeds the reach of traditional homology-based tools such as BLAST (v2.17.0) and HMMER (v3.2), which are inherently constrained by sequence identity thresholds. The emergence of Protein Language Models (PLMs), including ESM and ProtTrans, has introduced a transformative paradigm, thereby shifting functional inference from similarity-based retrieval to geometric reasoning within learned semantic spaces. Nevertheless, current approaches remain largely confined to unimodal or narrowly bimodal frameworks, failing to capture the inherently multidimensional determinants of enzymatic function, including active-site geometry, chemical reaction logic, and literature-embedded semantic context. This review systematically adopts a multimodal global-fusion perspective, elucidating how three-dimensional geometric features, chemical reaction semantics, and textual knowledge graphs are synergistically integrated around PLMs as a core backbone. We delineate complementary mechanisms and integration strategies that together enable fine-grained protein function annotation beyond the performance ceiling of single-sequence methods. Furthermore, we survey the translational potential of such frameworks from computational prediction to real biological applications, and critically examine persistent bottlenecks including activity cliffs, transition-state inference, and conformational dynamics. We identify the integration of physics-informed machine learning with dynamics-aware architectures as a pivotal direction toward a causal, mechanism-level understanding of protein function.}, } @article {pmid42123477, year = {2026}, author = {Baldo, E and Abeni, D and Agostini, G and Armato, U and Bauer, P and Belloni Fortina, A and Calza, A and Cervadoro, E and Chiarini, A and Ciprandi, G and Dal Prà, I and Faga, A and Farina, S and Geat, D and Giovannini, M and Girolomoni, G and Gisondi, P and Jousson, O and Manara, S and Mira, E and Nicoletti, G and Pagliarello, C and Pedron, R and Peroni, A and Rizzo, V and Segata, N and Tettamanti, G and Zanoni, M and Zumiani, G and Cristofolini, M}, title = {Clinical and Mechanistic Evidence for Comano Thermal Water: A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123477}, issn = {1422-0067}, mesh = {Humans ; *Mineral Waters/therapeutic use ; Balneology/methods ; Animals ; Skin/drug effects ; }, abstract = {Comano thermal water (CTW) is a hypotonic, bicarbonate-calcium-magnesium mineral water traditionally used to manage chronic inflammatory and relapsing skin diseases. This review summarises and discusses the available clinical, experimental, and translational evidence on CTW, with a particular focus on dermatological indications. The physicochemical properties of CTW, along with the presence of a stable, non-pathogenic microbial community, are examined in relation to their potential biological activity. Clinical studies indicate that CTW-based balneotherapy, alone or in combination with narrowband Ultraviolet B (UVB) phototherapy, is associated with improvements in disease severity, symptom burden, and quality of life in patients with psoriasis and atopic dermatitis, and has a favourable safety and tolerability profile. Experimental data further suggest that CTW may exert anti-inflammatory and immunomodulatory effects, modulate keratinocyte function, support skin barrier restoration, and influence the cutaneous microenvironment, including microbiome-related pathways. The review also outlines emerging evidence for CTW in skin regeneration and in upper airway inflammatory conditions treated via inhalation-based approaches. Overall, this review suggests that CTW may serve as a biologically active therapeutic resource, warranting further investigation as a complementary approach within integrative management strategies for inflammatory and barrier-related conditions.}, } @article {pmid42123517, year = {2026}, author = {Nguyen-DeMary, K and Vascellari, S and Mastinu, M and Melis, M and Bastiaanssen, TFS and Tomassini Barbarossa, I and Tepper, BJ}, title = {Cranberry Polyphenol Extract (CPE) Oral Rinse Improves Salivary Microbiome in 6-n-Propylthiouracil (PROP) Non-Tasters and Palatability of Aronia Juice.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, pmid = {42123517}, issn = {1422-0067}, support = {10180//United States Department of Agriculture/ ; }, mesh = {Humans ; *Saliva/microbiology/drug effects ; Female ; Male ; *Vaccinium macrocarpon/chemistry ; *Polyphenols/pharmacology/administration & dosage/chemistry ; *Microbiota/drug effects ; Adult ; Propylthiouracil ; *Plant Extracts/pharmacology/chemistry/administration & dosage ; *Photinia/chemistry ; Taste/drug effects ; *Mouthwashes/pharmacology/chemistry ; *Fruit and Vegetable Juices ; Young Adult ; }, abstract = {Sensitivity to the bitterness of 6-n-propylthiouracil (PROP) is controlled by variations in the TAS2R38 gene. This phenotype is often used as a marker for individual differences in taste perception. Previous findings show that PROP taster status is associated with differences in the salivary microbiome. It is well known that diet and environmental factors influence the risk of oral disease, but there is far less evidence showing how genetic differences play a role. Forty-seven young, healthy, PROP taster-classified adults rinsed with a cranberry polyphenol extract (CPE) oral rinse (0.75 g/L CPE powder in spring water) twice daily for 11 days. Saliva was collected pre- and post-intervention for microbiome analysis using shotgun metagenomic sequencing. At the same time points, participants evaluated two astringent juices (cranberry and aronia berry) for key attributes. At baseline, PROP taster groups differed in their salivary microbiome compositions, but post-intervention, the groups had more similar bacterial compositions. Post-intervention, non-tasters showed decreases in the relative abundance of 15 bacterial species, including a significant reduction (p = 0.037) in Eikenella corrodens, which is one bacterium, among several others, involved in oral biofilm formation. Additionally, after the intervention, sourness was reduced, and overall liking increased significantly for aronia juice. Oral dysbiosis, a risk factor for oral disease, may be controlled by bactericidal mouthwashes. Our results suggest that CPE, a natural alternative to traditional bactericidal rinses, may selectively target pathobionts while preserving salivary microbiota diversity. CPE might also provide greater benefits to non-tasters, who are at greater risk for oral disease.}, } @article {pmid42124595, year = {2026}, author = {Mejía-Pitta, A and Zhang, Z and Hossain, AA and Bartosik, K and Baca, CF and Peralta, C and Molina, H and Teplova, M and Brady, SF and Micura, R and Patel, DJ and Marraffini, LA}, title = {A 5-hydroxymethylcytosine DNA glycosylase provides defense against T-even bacteriophages.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {42124595}, issn = {2692-8205}, abstract = {The most abundant prokaryotic mechanisms of defense against phage predation involve the recognition and destruction of the infecting DNA. One method of counter-defense is the incorporation of modified nucleobases into the phage genome to avoid interaction with enzymes that target the viral DNA. T-even coliphages replace cytosine with 5-hydroxymethylcytosine (5hmC) that in some cases are further decorated with glucosyl groups. To explore the diversity of immunity genes that recognize 5hmC, we infected a library of metagenomic DNA inserts from uncultured, non-sequenced soil bacteria with a mutant T4 phage that harbored only non-glucosylated 5hmC on its genome. Bacteria that resisted infection carried a DNA glycosylase, Brig3, that specifically excises 5hmC nucleobases to generate abasic sites in the phage genome and prevent viral proliferation. The crystal structure of Brig3 bound to its substrate revealed a catalytic mechanism in which the 5hmC nucleobase is flipped out of the DNA into the active site and replaced by an asparagine residue that inserts into the double helix to contact the complementary guanosine. Brig3 is encoded within an operon that also encodes BapA, a hydrolase that removes glucosyl groups from glucosyl-5hmC present in the genome of otherwise Brig3-resistant T-even phages carrying this hypermodified base. Our results uncover a defense strategy in which the combined action of BapA and Brig3 widens the immune response to restrict the infection of T-even phages with genomes that are either partially or completely glucosylated.}, } @article {pmid42125129, year = {2026}, author = {Khantsi, M and Babalola, OO}, title = {Influence of Cowpea Plants on Soil Bacterial Community and Soil Quality: Effects of the Rhizosphere.}, journal = {Plant-environment interactions (Hoboken, N.J.)}, volume = {7}, number = {}, pages = {e70157}, pmid = {42125129}, issn = {2575-6265}, abstract = {Cowpea (Vigna Unguiculata), a vital legume for suitable agriculture and food security in sub-Saharan Africa, plays a crucial role in improving soil health through intricate plant-microbe interactions in the rhizosphere. This review synthesizes current knowledge on the microbial interactions in the rhizosphere, focusing on soil health, microbial diversity, and their contributions to nutrient cycling and plant growth. Cowpea roots foster a diverse microbial consortium, including nitrogen-fixing rhizobia, phosphate-solubilizing bacteria and organic matter decomposers, which enhance soil fertility and structure. The microbial community in the cowpea rhizosphere is shaped by complex soil physiochemical properties, such as potential of hydrogen (pH), nutrient availability, and salinity, which significantly influence plant-microbe interactions. However, contradictions persist regarding pH's effect on microbial diversity, with unresolved questions about how specific environmental conditions regulate microbial taxa. Advanced techniques, including metagenomic analyses, have provided deeper insights into the taxonomic and functional composition of rhizosphere microbiomes, uncovering both abundant and rare microbial taxa involved in these processes. Despite these advancements, gaps remain in understanding the dynamic responses of microbial communities to environmental stresses. Bridging these gaps through integrative multi-omics approaches will enable the development of microbiome-informed strategies to improve cowpea productivity and promote sustainable agricultural practices, ensuring resilience in the face of climate variability.}, } @article {pmid42125266, year = {2026}, author = {Nõlvak, H and Dang, NP and Truu, M and Peeb, A and Devarajan, AK and Petrich, C and O'Sadnick, M and Tiirik, K and Truu, J}, title = {Microbial succession and hydrocarbon-degrading potential in Arctic sea ice exposed to dispersed crude oil and chemical dispersant.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag022}, pmid = {42125266}, issn = {2633-6685}, abstract = {The increasing oil exploration and transport activities in the Arctic amplify the risk of oil spills in ice-containing marine environments. Chemical dispersants, intended to promote oil biodegradation by breaking hydrocarbons into small droplets, are potential tools in cold marine oil spill mitigation; however, their fate and effectiveness within sea ice remain uncertain. This study examined the influence of dispersed crude oil and the chemical dispersant (FinasolOSR 51) on microbial community dynamics and hydrocarbon-degrading potential compared to clean ice during an 89-day sea-ice mesocosm experiment using shotgun metagenomics and metagenome-assembled genomes. Dispersant addition markedly reshaped microbial communities in both dispersed-oil and dispersant containing ice, causing similar shifts toward psychrophilic hydrocarbon degraders such as Oleispira, Bermanella, and Pseudoalteromonas. Although aliphatic hydrocarbon degradation genes were enriched, several dominant taxa exhibited limited hydrocarbon metabolic capacity yet possessed extensive stress-response traits. Oil hydrocarbon loss in ice remained modest despite the presence of degraders, likely due to the very low microbial abundance. These findings demonstrate that dispersants can strongly shape microbial communities in Arctic sea ice, without necessarily enhancing the biodegradation of oil hydrocarbons. This highlights the need for careful evaluation of dispersants as remediation tools in ice-containing Arctic marine environments.}, } @article {pmid42125370, year = {2014}, author = {, }, title = {Schmallenberg virus: State of Art.}, journal = {EFSA journal. European Food Safety Authority}, volume = {12}, number = {5}, pages = {3681}, pmid = {42125370}, issn = {1831-4732}, abstract = {This scientific report provides an overview of all research carried out on Schmallenberg virus (SBV), reviewing the current knowledge on SBV regarding genotyping findings, susceptible species, pathogenesis, transmission routes, immunity, seroprevalence, geographical and temporal SBV spread, improved within-herd transmission model, SBV impact assessment and within-herd and regional spread models. Metagenomic analysis identified SBV as a novel orthobunyavirus emerged in 2011 and it has been detected in domestic cattle, sheep, goats and 12 wild species. Seroprevalence studies indicate that SBV has probably spread over the whole of Europe, showing high seroprevalence at national scale, while larger variability is observed at regional scales. Clinical disease frequency is low and experimental infection on pregnant ewes and cows suggest that SBV rarely induces malformations. SBV may be detected from semen with a low frequency though there is no scientific evidence of transmission through insemination. Vector competence studies suggest that Culicoides are likely to be able to transmit SBV but found no evidence that mosquitoes are likely to be able to transmit it. SBV vertical transmission has not yet been identified as a major route. SBV has successfully overwintered, despite lengthy period of minimal vector activity and duration of immunity in cattle lasts for at least one year. A farm-to-farm spread model for SBV shows a rapid spread of infection across the study region and latent period, duration of viraemia, probability of transmission from host to vector and virus replication are sufficient to account for the rapid SBV spread. The between-farm SBV transmission model indicates that the application of movement restrictions has little effect on SBV spread. An impact assessment based on limited data suggests a probable effect of SBV infection on abortion, short gestation, non-return and the number of artificial inseminations required per animal. International trade restrictions by third countries represent the main SBV impact.}, } @article {pmid42125413, year = {2026}, author = {Wang, J and Qiu, J and Zhang, C}, title = {Crusted scabies complicated by septic shock: a fatal case report with incidental detection of Sarcoptes scabiei DNA in peripheral blood.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02577}, pmid = {42125413}, issn = {2214-2509}, abstract = {Crusted scabies is a severe form of scabies characterized by massive mite burden and profound immune dysregulation. Secondary bacterial infection is common and may progress to sepsis with fatal outcomes. We report a fatal case of crusted scabies complicated by septic shock in a 58-year-old man with diabetes mellitus and chronic dermatitis. The patient presented with diffuse erythroderma, extensive hyperkeratotic crusts, and deep skin fissures, and several household members had similar pruritic skin lesions. Laboratory investigations revealed marked eosinophilia, extremely elevated serum immunoglobulin E levels, and multiorgan dysfunction. Peripheral blood metagenomic next-generation sequencing identified multiple bacterial pathogens and incidentally detected Sarcoptes scabiei DNA. Despite broad-spectrum antimicrobial therapy, antiparasitic treatment, and intensive supportive care, the patient deteriorated and died. This case highlights crusted scabies as a potentially lethal condition when complicated by severe bacterial infection and underscores the need for cautious interpretation of parasitic DNA detected in blood, particularly in non-invasive ectoparasitic diseases.}, } @article {pmid42125597, year = {2026}, author = {Pasaribu, B and Herawati, T and Purba, NP and Lewaru, MW and Sofyana, NT and Dilens, CVM and Dewanti, LP and Alina, DN and Agung, MUK}, title = {Shotgun metagenomic dataset of microbial communities in the water column of the Flores Sea, Indonesia.}, journal = {Data in brief}, volume = {66}, number = {}, pages = {112791}, pmid = {42125597}, issn = {2352-3409}, abstract = {The Flores Sea is a crucial component of the Indonesian Throughflow (ITF) pathway, which influences the transport of carbon, oxygen, and nutrients that support marine ecosystems. Here, we present the first dataset of microbial communities from the Flores Sea, Indonesia, generated using shotgun metagenomic sequencing of water column samples. Taxonomic analysis revealed that Proteobacteria (86%) was the most abundant phylum. In the dataset, the most abundant taxa identified through metagenomic analysis demonstrated Pseudoalteromonas lipolytica, Chromohalobacter salexigens, Marinobacter nauticus, Halopseudomonas aestusnigri, Pseudomonas mendocina, Flavobacterium beibuense, and Flavobacterium rakeshii, respectively. Functional annotation indicated that metabolism was major functional category in the microbial community. This metagenomic dataset provides valuable baseline information on microbial communities that may support future ocean monitoring and conservation strategies in the Flores Sea.}, } @article {pmid42125669, year = {2026}, author = {Szaraz, D and Bohm, J and Machacek, C and Salokova, G and Gachova, D and Ruzicka, F and Danek, Z and Gheit, T and Zavadil, J and Borilova Linhartova, P}, title = {Bacteriome-based oral dysbiosis index in patients with oral squamous cell carcinoma.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2668149}, pmid = {42125669}, issn = {2000-2297}, abstract = {BACKGROUND: Oral dysbiosis plays an important role in the pathogenesis of oral squamous cell carcinoma (OSCC). Our study aimed to perform a pairwise comparison of the oral microbiota, especially the bacteriome, from OSCC tumoral surface vs other oral samples and evaluate the association of a novel bacteriome-based Oral Dysbiosis Index (bbODI) with the OSCC surface.

MATERIALS AND METHODS: This pilot observational study used 84 patient-matched samples from the OSCC tumoral surface (swabs and biopsies), healthy oral mucosa (tongue and buccal swabs), and supragingival dental plaque swabs. Bacteriomes were analyzed by 16S rRNA amplicon sequencing. The presence of microscopic fungi and selected viruses was also evaluated.

RESULTS: The relative abundance of the genus Fusobacterium, the ratio of the relative abundances of gram-negative to gram-positive bacterial genera, and the bbODI on the tumour surface significantly differed from patient-matched healthy oral mucosa (both buccal and tongue swabs) and supragingival dental plaque samples. Oral candidosis was found in 25% of patients; all patients were negative for cytomegalovirus and Epstein-Barr virus.

CONCLUSIONS: Certain characteristics of the bacteriome composition of the OSCC surface differ from patient-matched samples of healthy oral mucosa and supragingival dental plaque. The proposed bbODI appears to be a promising non-invasive tool for the identification of bacteriome disruption on the OSCC surface.}, } @article {pmid42125783, year = {2026}, author = {Hu, X and Han, L and Ochoa-Hueso, R and Song, J and Yang, X and Wang, G}, title = {From Microbes to Molecules: Biodegradable Microplastics Reshape Soil Carbon Metabolism and Composition of Dissolved Organic Matter.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {20}, pages = {15958-15969}, doi = {10.1021/acs.jafc.6c01030}, pmid = {42125783}, issn = {1520-5118}, mesh = {*Carbon/metabolism/chemistry ; Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Soil/chemistry ; *Microplastics/metabolism/chemistry ; *Dissolved Organic Matter/chemistry/metabolism ; Biodegradation, Environmental ; Carbon Cycle ; *Soil Pollutants/metabolism/chemistry ; Viruses/genetics/metabolism/isolation & purification/classification ; }, abstract = {Microplastics (MPs) are ubiquitous in the environment, yet how conventional MPs (CMPs) and biodegradable MPs (BMPs) alter microbial carbon (C) metabolism and dissolved organic matter (DOM) remains unclear. Using metagenomic sequencing and Fourier transform ion cyclotron resonance mass spectrometry, we found that BMPs altered microbial C cycling profiles more profoundly than CMPs. This was driven by a significant enrichment of functional genes involved in aerobic respiration, C fixation, intracellular C decomposition, and fermentation. In addition, BMPs exerted stronger influences on prokaryotic and viral community structures than CMPs. Notably, BMPs specifically enriched unique microbial taxa and virus-host linkages carrying diverse C-cycling genes, coregulating key metabolic pathways, and promoting a "viral shuttle" mechanism that accelerated DOM turnover. These effects were mediated through enhanced accumulation of labile and recalcitrant C components in relation to fertilization regimes. These findings revealed mechanisms by which BMPs reshape soil carbon dynamics through microbial-viral interactions.}, } @article {pmid42125851, year = {2026}, author = {Fisher, CJ and Khrongsee, P and Subramaniam, K and Pushinsky, AD and Stevenson, V and Crawford, C and Goncalves, R}, title = {Acute Respiratory Distress Syndrome in a Dog With Canine Respiratory Coronavirus Infection.}, journal = {Journal of veterinary emergency and critical care (San Antonio, Tex. : 2001)}, volume = {}, number = {}, pages = {}, doi = {10.1111/vec.70113}, pmid = {42125851}, issn = {1476-4431}, abstract = {OBJECTIVE: To describe the clinical progression of acute respiratory distress syndrome (ARDS) associated with canine respiratory coronavirus and suspected aspiration in a previously healthy young dog.

CASE SUMMARY: A 1.5-year-old neutered male Rottweiler was presented for acute respiratory distress. The dog had a productive cough 2 weeks prior that was reported to have improved. While at a boarding facility, the dog developed decreased appetite and lethargy, regurgitated, and became acutely dyspneic. The dog was taken to the veterinarian on site, where thoracic radiographs revealed severe consolidation of the cranioventral lung lobes. The dog was presented to a university referral hospital approximately 12 h after regurgitation with fever, hypotension, hypoglycemia, and leukopenia, and was treated with positive pressure ventilation after failing high-flow oxygen therapy. The dog remained profoundly hypoxemic, developed acute kidney injury, and was euthanized after 24 h. Necropsy revealed diffuse alveolar damage consistent with a diagnosis of ARDS. Bacterial cultures were negative. Real-time polymerase chain reaction results from upper respiratory and fresh lung samples, as well as metagenomics analysis from a lung sample, confirmed the presence of canine respiratory coronavirus.

Canine respiratory coronavirus is primarily associated with mild upper respiratory signs and has not been previously associated with ARDS. Direct pulmonary damage from the virus, decreased mucociliary clearance secondary to viral ciliary damage followed by aspiration, and secondary pulmonary damage from systemic inflammation and coagulation disturbances are all possible in this case. The practical use of metagenomics, an emerging diagnostic screening tool that provides characterization of a virus's entire genome, is also demonstrated here. Metagenomics has not been previously described in small animal clinical medicine and may aid in surveillance of infectious canine respiratory disease and provide better understanding of the role of "milder" pathogens in patients with multifactorial respiratory failure.}, } @article {pmid42126224, year = {2026}, author = {Abuah, CY and Sipes, K and Buongiorno, J and Steen, AD and Bradley, JA and Giovannelli, D and Abramov, A and Peters, SL and Giannone, RJ and Hettich, RL and Liang, R and Boike, J and Vishnivetskaya, TA and Lloyd, KG}, title = {Capacity of Arctic fjord sediments to degrade carbohydrates from permafrost active layer.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0045626}, pmid = {42126224}, issn = {2165-0497}, support = {DESC0020369//U.S. Department of Energy/ ; FG-2015-65399//Alfred P. Sloan Foundation/ ; OCE-2145434//National Science Foundation/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Permafrost/microbiology/chemistry ; Arctic Regions ; *Bacteria/genetics/metabolism/classification/isolation & purification/enzymology ; Soil Microbiology ; Metagenome ; Estuaries ; Biodegradation, Environmental ; Microbiota ; *Carbohydrate Metabolism ; Metagenomics ; Carbohydrates/chemistry ; Soil/chemistry ; Svalbard ; }, abstract = {The degradation of organic matter (OM) by microorganisms in thawing permafrost produces greenhouse gases. Terrestrial OM is transported into fjords through hydrological runoff, but it is unclear whether the microbial mechanisms of OM degradation on land persist after soils enter marine environments, which differ greatly in conditions and microbial communities. This question is particularly relevant for low-OM soils, which dominate Arctic landscapes and are more exposed to oxidants. Here, we compared OM-degrading capacity in permafrost-affected active layer soils and adjacent fjord sediments from Kongsfjorden, Svalbard, focusing on carbohydrate-active enzymes (CAZymes), which target some of the most abundant types of organic matter in soils. Using multi-omics approaches-metagenomics, metagenome-assembled genomes (MAGs), metabolomics, metatranscriptomics, and metaproteomics-we examined CAZyme presence, distribution, and activity. Despite environmental differences, both soils and sediments harbored diverse glycoside hydrolases and polysaccharide lyases, most of which showed evidence of activity. Verrucomicrobia expressed the highest number of CAZyme transcripts, indicating that they dominated active carbohydrate degradation in fjord sediments, while Acidobacteria and Actinobacteria were more active in soils. Notably, CAZymes in fjord sediments targeted primarily soil-derived OM, and the proportions of enzymes degrading terrestrial OM, marine OM, and microbial necromass-remnants of dead microbial cells were similar across both environments. These results suggest that microbial communities in both soils and fjord sediments are equipped to degrade carbohydrates, and that burial of terrestrial-derived OM in fjord sediments may not protect it from microbial breakdown under Arctic warming.IMPORTANCEPermafrost thaw may be a critical climate feedback because microbial degradation of organic matter (OM) can release greenhouse gases. While fjords serve as major carbon burial sites, our results show that burial of terrestrial-derived OM in these sediments does not ensure protection from microbial degradation. Microbial communities in both active layer soils and fjord sediments harbor a broad arsenal of carbohydrate-active enzymes, with evidence of activity across diverse taxa. This functional continuity indicates that once terrestrial material is washed into fjords, it remains vulnerable to microbial breakdown despite different environmental conditions. Understanding these cross-system continuities in microbial function is essential for predicting the fate of OM in a rapidly warming Arctic and highlights the importance of including fjord sediments in global carbon cycle models.}, } @article {pmid42126240, year = {2026}, author = {Prakash, H and Perez, RK and Ross, M and Tisza, M and Javornik Cregeen, SJ and Deegan, J and Petrosino, JF and Boerwinkle, E and Clark, JR and Maresso, AW}, title = {Detection, persistence, and rising prevalence of oncogenic viruses revealed by wastewater metagenomics.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {6}, pages = {e0054726}, pmid = {42126240}, issn = {1098-5336}, support = {S.B. 1780//87th Texas State Legislature, 2021 Reg. Sess./ ; U19 AI157981/AI/NIAID NIH HHS/United States ; Joseph Melnick Seed Funds//Baylor College of Medicine/ ; Alkek Foundation Seed Funds//Baylor College of Medicine/ ; }, mesh = {*Metagenomics ; *Wastewater/virology ; Texas/epidemiology ; *Oncogenic Viruses/isolation & purification/genetics/classification ; Prevalence ; Humans ; Genome, Viral ; }, abstract = {Oncogenic viruses cause high-risk cancers in humans and are responsible for nearly 20% of all cancer cases worldwide. Currently, very limited data exist in the realm of wastewater-based viral epidemiology (WBE) for cancer-causing viruses, with existing studies using targeted approaches (i.e., PCR-based approaches) that lack genomic resolution. In this study, we used a hybrid-capture approach to detect, filter, and sequence all known oncogenic virus signals from wastewater samples collected over 3 years (May 2022-May 2025) in 16 Texas cities, covering nearly 25% of the state's population. Once sequenced, we used custom computational tools designed for wastewater metagenomics to assign reads into their respective virus of origin, estimate viral abundances over time, and measure genomic read coverage. Our data indicate that we successfully detected oncogenic viruses, including six known oncogenic viruses, and three suspected oncogenic viruses, across all sampling locations within Texas. We observed a gradual increase in the viral abundance of oncogenic viruses over 3 years, with distinct peaks and dips over the summer and winter months. The prevalence of high-risk viruses such as human papillomavirus (HPV) and Epstein-Barr virus (EBV) rose, with sharp increases in viral abundance observed post-2024. We also obtained nearly 100% genome coverage with viral reads captured using this hybrid-capture technique for nearly all oncogenic viruses, with resolution down to the species and type taxonomic levels in some cases, such as that of HPV. Our study showcases the utility of hybrid-capture techniques to detect and track multiple oncogenic viruses simultaneously.IMPORTANCECancer-causing viruses are of major clinical significance, responsible for nearly 20% of all recorded cancer incidences in humans worldwide. There is a need for improved detection, tracking, and control of oncogenic viruses across the globe. To our knowledge, this work is the first comprehensive WBE approach used to detect all known oncogenic viruses concurrently, demonstrating the feasibility of monitoring the presence and levels of cancer-causing viruses and enabling the possibility of public health interventions in the future. Using this method, we obtain broad genomic coverage at strong depth and specificity, coupled with consistent real-time tracking dynamics of multiple oncogenic viruses. Furthermore, we showcase the ability to identify genomic regions on viral reference genomes from which sequenced reads originate. This information can be an invaluable tool toward understanding the viral prevalence dynamics in general populations, their relationship to cancer incidences in humans, and their mechanisms of viral evolution, including mutations.}, } @article {pmid42126253, year = {2026}, author = {Hambücken, L and Sudianto, E and Verleyen, E and Saw, JH and Baurain, D and Cornet, L}, title = {An early diverging SQR enzyme in Antarctic Gloeobacterales indicates sulfide tolerance in thylakoid-lacking cyanobacteria.}, journal = {Microbiology spectrum}, volume = {14}, number = {6}, pages = {e0042326}, pmid = {42126253}, issn = {2165-0497}, support = {PDR T.0018.24//FRS-FNRS/ ; //FRS-FNRS/ ; FRIA//FRS-FNRS/ ; 2.5020.11//FRS-FNRS/ ; }, mesh = {*Sulfides/metabolism ; *Cyanobacteria/genetics/enzymology/classification/metabolism ; Phylogeny ; Photosynthesis ; *Quinone Reductases/genetics/metabolism ; Antarctic Regions ; *Thylakoids/metabolism ; *Bacterial Proteins/genetics/metabolism ; Photosystem II Protein Complex/metabolism ; }, abstract = {Oxygenic photosynthesis, which converts solar energy into carbohydrates via a linear electron transport chain and two photosystems (PSII and PSI), first appeared in cyanobacteria approximately 3.3 Ga and drove the Great Oxidation Event around 2.4 Ga. During this period, euxinic conditions-characterized by sulfidic, anoxic oceans-posed a metabolic challenge to cyanobacteria, as sulfide inhibits PSII, the reaction center responsible for water splitting. Here, we report the presence of a sulfide-quinone reductase (SQR) enzyme in Antarctic representatives of Gloeobacterales, the earliest-branching cyanobacterial lineage. Phylogenetic analyses consistently position these SQR sequences at the base of the cyanobacterial clade, likely predating the multiple lateral transfers reported for this gene in the phylum. Additional searches in metagenomic data sets indicate that such sequences are restricted to cold environments. Our findings unveil possible adaptive strategies of early cyanobacteria to cope with sulfidic stress and point to Antarctic lakes as preserved natural laboratories for investigating cyanobacterial diversification and the evolution of oxygenic photosynthesis under euxinic conditions.IMPORTANCEThe diversification of cyanobacteria during and after the Great Oxidation Event occurred in early Proterozoic oceans that were partially euxinic (anoxic and sulfidic), a condition generally considered incompatible with oxygenic photosynthesis due to photosystem II inhibition. The presence of a sulfide quinone reductase in an early diverging cyanobacterium lacking thylakoids, isolated from Antarctica, suggests that oxygenic and anoxygenic photosynthesis coexisted early on in cyanobacterial evolution. The occurrence of these organisms in Antarctic lakes under euxinic conditions offers a natural laboratory for studying the physiology and adaptation of the first oxygenic photosynthetic organisms.}, } @article {pmid42126918, year = {2026}, author = {Smith, DB and Simmonds, P and Siddell, SG}, title = {Virus taxonomy and the ICTV - 21 FAQs for the perplexed virologist.}, journal = {The Journal of general virology}, volume = {107}, number = {5}, pages = {}, pmid = {42126918}, issn = {1465-2099}, mesh = {*Viruses/classification/genetics ; *Virology ; *Classification/methods ; Terminology as Topic ; }, abstract = {Just over 125 years has passed since the 'filterable' agents of tobacco mosaic disease and foot-and-mouth disease were first described as infectious, replicating entities smaller than bacteria. Today, viruses are formally classified into more than 16,000 species ranked into genera, families and higher taxa. The development of an official virus taxonomy has been overseen by an International Committee, first constituted in 1966 and renamed as the International Committee on Taxonomy of Viruses (ICTV) in 1975. Despite the engagement of the ICTV in virus taxonomy over the last 60 years, many aspects of virus classification and nomenclature may seem odd or sometimes incomprehensible to virologists more familiar with the taxonomy of cellular organisms. Who runs the ICTV? What are virus species demarcation criteria? Why have all virus species names become binomial? How can a sequence in a metagenomic dataset be assigned to a virus species? This article attempts to answer several such questions and outlines how a large, inclusive and global community of virologists has developed new and responsive policies for virus taxonomy in a decade when the pace of virus discovery has dramatically accelerated.}, } @article {pmid42127418, year = {2026}, author = {Parizadeh, M and Laforest-Lapointe, I and Serrano-Vázquez, A and Morán-Silva, P and Rojas-Velázquez, L and Torres, J and Ximénez-García, C and Arrieta, MC}, title = {Impact of Maternal, Infant, and Household Factors on Early-life Gut Microbiome Development in a Rural Setting.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag124}, pmid = {42127418}, issn = {1751-7370}, abstract = {Early-life gut microbiome development is influenced by host, microbial, environmental, and social factors. Rural infants typically exhibit greater microbial diversity than their urban counterparts, yet microbiome maturation patterns in less industrialized settings remain underexplored. Additionally, though microbial eukaryotes are integral to gut ecology, most studies to date have focused predominantly on bacterial communities. Using shallow shotgun metagenomics and 18S rRNA gene sequencing, we characterized eukaryotic and bacterial gut microbiomes in an intensively sampled longitudinal cohort of ten infants from a rural community in Morelos, Mexico, each followed monthly from the first to the 18th month, providing an unusually detailed view of early-life microbiome development in a low-resource setting. Although both bacterial and eukaryotic alpha diversity increased over time, they showed distinct colonization trajectories. Age, delivery mode, and environmental exposures, such as animal contact and household factors, influenced bacterial and eukaryotic community compositions, as well as bacterial metabolic composition. Inter-kingdom microbial networks varied with age, with a reduction in taxonomic diversity after the first year of life. Age and mode of birth also influenced changes in the overall community structure and connectivity of microbial co-occurrence patterns, but did not impact the associations among specific microbial taxa. Functional profiling revealed that bacterial metabolic potential diversified with age, whereas the mode of birth had a minimal impact on functional variation. These findings highlight the dynamic nature of bacterial and eukaryotic microbiota in early life and underscore the need to explore how rural environmental exposures shape microbial maturation, with potential implications for immune development and long-term health.}, } @article {pmid42127818, year = {2026}, author = {Mahler, M and Yuping, L}, title = {Predicting phage anti-defenses that shoot the messenger.}, journal = {Cell host & microbe}, volume = {34}, number = {5}, pages = {811-813}, doi = {10.1016/j.chom.2026.04.014}, pmid = {42127818}, issn = {1934-6069}, mesh = {*Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; *Viral Proteins/metabolism/genetics ; Metagenomics ; Signal Transduction ; }, abstract = {Locked in a constant arms race, bacteria and their phage predators have evolved various defenses and counter-defenses. Compared to the numerous identified defenses, phage-encoded counter-defenses are understudied. In a recent Science paper, Tal et al. developed a structure-guided approach to identify phage proteins counteracting nucleotide signaling defenses using metagenomic data.}, } @article {pmid42127820, year = {2026}, author = {Bickel, S and Berg, G}, title = {Microbial diversity creates a global firewall against pathogens in soil.}, journal = {Cell host & microbe}, volume = {34}, number = {5}, pages = {817-819}, doi = {10.1016/j.chom.2026.04.016}, pmid = {42127820}, issn = {1934-6069}, mesh = {*Soil Microbiology ; Humans ; Metagenomics ; *Biodiversity ; *Bacteria/genetics/classification/isolation & purification ; Melioidosis/microbiology ; *Microbiota ; Tuberculosis/microbiology ; Soil ; Animals ; }, abstract = {Soil is a critical ecological contributor to plant and animal health. In this issue of Cell Host & Microbe, Xiong et al. use global metagenomic data to show that human pathogens linked to diseases like tuberculosis, melioidosis, and sepsis are widespread in humid and agricultural soils harboring reduced microbial diversity.}, } @article {pmid42127824, year = {2026}, author = {Bouzek, DC}, title = {What the nose knows of cystic fibrosis microbes and hypertonic saline.}, journal = {Cell host & microbe}, volume = {34}, number = {5}, pages = {827-829}, doi = {10.1016/j.chom.2026.04.017}, pmid = {42127824}, issn = {1934-6069}, mesh = {*Nasopharynx/microbiology ; Humans ; *Cystic Fibrosis/drug therapy/microbiology ; Infant ; Case-Control Studies ; *Microbiota/drug effects/genetics ; Metagenomics ; *Saline Solution, Hypertonic/administration & dosage ; Administration, Inhalation ; Nebulizers and Vaporizers ; Osmotic Pressure/drug effects ; }, abstract = {In this issue of Cell Host & Microbe, Steinberg et al.[1] present a microbial gene atlas of nasopharyngeal swabs in infants with cystic fibrosis and healthy controls using shotgun metagenomic sequencing. The impacts of clinical interventions on respiratory microbial function can be identified and experimentally validated using the atlas.}, } @article {pmid42127855, year = {2026}, author = {Mei, Z and Zhou, H and Liu, K and Gao, C and Du, H and Sheng, Z and Gong, Y}, title = {Traditional Chinese medicine improves performance and intestinal health in laying hens under acute and chronic heat stress by modulating ileal metabolic functions.}, journal = {Poultry science}, volume = {105}, number = {8}, pages = {107056}, pmid = {42127855}, issn = {1525-3171}, abstract = {Heat stress (HS) represents a significant challenge in poultry production, impairing thermoregulation, intestinal function, and productive performance. This study utilized acute (6 h) and chronic (14 d) HS models at 36°C in laying hens to characterize stage-dependent responses and evaluate the protective effects of a ten-ingredient traditional Chinese medicine (TCM) formulation. Both acute and chronic HS significantly increased rectal temperature and respiratory rate. Egg production declined by approximately 18% following acute HS and was further compromised under chronic exposure, along with reduced eggshell strength and weight. Dietary TCM supplementation (0.5%) alleviated physiological stress and partially restored laying performance, with more pronounced recovery observed under chronic HS. Serum analysis and histopathology indicated that TCM attenuated HS-induced impairment of ileal barrier function. Metabolomic profiling revealed stage-dependent responses: acute HS primarily disturbed redox balance, whereas chronic HS induced broader remodeling related to energy and nutrient utilization. TCM supplementation modulated metabolic functions to support immediate stress buffering under acute HS while stabilizing long-term energy support and intestinal capacity under chronic HS. Metagenomic analysis indicated that TCM selectively promoted microbial groups related to intestinal metabolism and nutrient utilization, aligning with metabolomic findings. Correlation analyses linked these TCM-associated microbial and metabolic signatures with improved thermoregulatory responses, oxidative status, and intestinal barrier indicators. Collectively, these results demonstrate that TCM supplementation enhances heat resilience in laying hens through stage-dependent modulation of the gut microbiota-metabolome axis, supporting its application as a nutritional strategy to maintain productivity under thermal challenge.}, } @article {pmid42127905, year = {2026}, author = {Shen, J and Sun, Z and Song, H and Pu, Y and Wang, P and Hailili, G and Huang, Y and Mei, Z and Chen, H and Huang, L and Yuan, C and Wang, X and Zheng, Y}, title = {Healthful plant-based diet, gut enterotype, and cognition in a rural Chinese elderly cohort: A longitudinal multi-omics study.}, journal = {Cell reports. Medicine}, volume = {7}, number = {6}, pages = {102797}, doi = {10.1016/j.xcrm.2026.102797}, pmid = {42127905}, issn = {2666-3791}, mesh = {Humans ; Aged ; *Cognition/physiology ; *Diet, Plant-Based ; *Gastrointestinal Microbiome/physiology/genetics ; China ; Female ; Aged, 80 and over ; Male ; Multiomics ; Longitudinal Studies ; Rural Population ; Feces/microbiology ; Metagenomics ; East Asian People ; }, abstract = {The gut microbiome may shape how diet influences cognitive aging, but population-based evidence remains limited. In 784 older adults living in rural China (70-98 years old) with fecal metagenomics and structured dietary assessment, a modified healthful plant-based diet index (mHPDI) is associated with distinct gut microbial structure and taxonomic shifts (15 species, 17 genera). Among participants with repeated cognitive measurements, higher mHPDI is associated with better global cognition, with stronger benefits in participants with non-Prevotella-dominant enterotypes (highest versus lowest tertile β = 0.34, 95% confidence interval [CI], 0.16 to 0.52) than in those with a Prevotella-dominant enterotype (0.04, -0.22 to 0.29; p interaction = 0.04). Enterotype-associated differences in microbial metabolic pathways, including preQ0 and L-isoleucine biosynthesis, parallel this heterogeneity. Moreover, 12 circulating microbiota-related metabolites (primarily amino acids and short-chain fatty acids) are linked to mHPDI. A composite score comprising these metabolites mediates 11.0% of the mHPDI-cognition association (p mediation = 0.02), with branched-chain amino acids as major contributors. These findings suggest that gut microbial context may shape diet-cognition associations.}, } @article {pmid42128151, year = {2026}, author = {Yang, F and Sui, C and Tian, H and Ao, J}, title = {Metagenomic next-generation sequencing reveals the clinicopathological features of mucormycosis.}, journal = {Microbial pathogenesis}, volume = {216}, number = {}, pages = {108553}, doi = {10.1016/j.micpath.2026.108553}, pmid = {42128151}, issn = {1096-1208}, mesh = {Humans ; *Mucormycosis/diagnosis/microbiology/pathology ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Middle Aged ; Adult ; *Metagenomics/methods ; Aged ; Adolescent ; Aged, 80 and over ; Young Adult ; Child ; Child, Preschool ; Mucor/genetics ; }, abstract = {BACKGROUND: Mucormycosis is a rare but highly lethal opportunistic infection driven by mucor fungi, which mainly affects individuals with compromised immune systems, such as diabetic patients and organ transplant recipients. This study aims to investigate the clinicopathological features of patients with mucormycosis diagnosed by metagenomic next-generation sequencing (mNGS).

METHODS: A systematic analysis was conducted in 15 cases of mucormycosis diagnosed and treated at Hunan Provincial People's Hospital between January 2019 and July 2024. Various detection methods were utilized, including hematoxylin-eosin staining, fungal fluorescence staining, fungal culture, and high-throughput mNGS technology to ensure an accurate diagnosis. Furthermore, we conducted a literature review and analyzed 311 cases of mucormycosis published in the public databases between 2021 and 2024 to assess the underlying pathological characteristics.

RESULTS: Of the 15 cases treated in our institute, ten (66.7%) were males, with a median age of 41 (range 4-78),five (33.3%) were females, with a median age of 58.5 (range 32-85). Compared to other detection methods including PAS/PASM staining, mNGS proved effective in diagnosing typical mucormycosis infections in 15 of the patients in this study. The literature review of 311 cases indicated that the lungs and bronchi were the main sites of infection, followed by the nasal cavity, brain, and skin. Diabetes emerged as the most prevalent underlying condition, present in more than 40% of cases. Other internal and immune system disorders, such as immunodeficiency disease, were also associated with an increased risk of infection.

CONCLUSIONS: MNGS is an effective diagnostic tool for mucormycosis.}, } @article {pmid42128673, year = {2026}, author = {, and , and , }, title = {[Expert consensus on laboratory identification of emerging pathogens based on metagenomic next-generation sequencing technology(2025 edition)].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {60}, number = {5}, pages = {669-684}, doi = {10.3760/cma.j.cn112150-20251117-01086}, pmid = {42128673}, issn = {0253-9624}, support = {2024ZD0532804//National Science and Technology Major Special Project for Noncommunicable Chronic Diseases/ ; 2025ZD01903400//National Science and Technology Major Special Project for Prevention and Control of New Emergencies and Major Infectious Diseases/ ; 2025-I2M-KJ-001, 2025-I2M-XHJC-004//CAMS Innovation Fund for Medical Sciences(CIFMS)/ ; }, mesh = {*High-Throughput Nucleotide Sequencing ; *Metagenomics ; Humans ; Consensus ; *Communicable Diseases, Emerging/diagnosis ; Computational Biology ; }, abstract = {Emerging pathogen infections pose a significant challenge to global public health security. Pathogen metagenomic next-generation sequencing (mNGS), characterized by its hypothesis-free, culture-independent, and unbiased nature, provides a powerful tool for the timely detection and precise identification of emerging pathogens. This consensus was jointly developed by multidisciplinary experts from clinical laboratories, infectious diseases, disease prevention and control, and other relevant fields. It aims to standardize the identification process for clinically suspected emerging pathogen infections, as well as specimen submission, technical requirements, bioinformatic analysis, and reporting and interpretation procedures for the laboratory identification of emerging pathogens using clinical mNGS technology. This framework provides systematic guidance for clinical early warning and practice.}, } @article {pmid42128675, year = {2026}, author = {Zhou, HJ and Ma, JX and Hu, JR and Han, YX and Yang, B and Zhou, ZM and Li, LL and Liu, JY and Du, XL and Cui, ZG and Kan, B}, title = {[Analysis on the epidemiological characteristics of legionnaires' disease in China based on multi-source data].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {60}, number = {5}, pages = {714-720}, doi = {10.3760/cma.j.cn112150-20260306-00178}, pmid = {42128675}, issn = {0253-9624}, support = {GZNL2024A01025//Special Project of Guangzhou National Laboratory/ ; 2022YFC2305300//National Key Research and Development Program of China/ ; }, mesh = {Humans ; China/epidemiology ; *Legionnaires' Disease/epidemiology/microbiology ; Male ; Middle Aged ; Aged ; Female ; Genotype ; High-Throughput Nucleotide Sequencing ; Legionella pneumophila ; Legionella/genetics ; Adult ; Incidence ; }, abstract = {Objective: To analyze the epidemiological characteristics of Legionnaires' disease in China based on multi-source data. Methods: Based on the metagenomic next-generation sequencing (mNGS) data of bronchoalveolar lavage specimens collected from a third-party medical testing institution from March 2024 to September 2025, this study aggregated nucleic acid detection data for multiple pathogens from the National Pathogenic Bacteria Identification Network's respiratory syndrome surveillance and conducted a meta-analysis by combining published literature. Descriptive epidemiological methods were used to analyze the demographic characteristics, spatiotemporal distribution, and Legionella species and genotype of Legionnaires' disease in China. Results: By integrating three types of data sources, a total of 1 866 Legionnaires' disease cases were included in the study. Chinese Legionnaires' disease patients were predominantly middle-aged and elderly males, accounting for 64.31% of cases. The age distribution of cases exhibited a bimodal pattern, with a significant concentration in the middle-aged and elderly population. The 60-65 age group had the highest incidence. However, in addition to the peak in the middle-aged and elderly population, there was also a peak in the 0-5 age group. The number of cases showed a peak occurring from July to August. The cases exhibited significant regional distribution disparities across the country. Legionella pneumophila infection was predominant (accounting for 95.70%), with other species including Legionella macleodii (20 cases) and Legionella longbeachae (18 cases). Among 412 samples, L. pneumophila genotypes were obtained, divided into 7 sequence types, including ST36 (n=148), ST1 (n=60), ST23 (n=58), ST51 (n=51), ST734 (n=51), ST42 (n=32), and ST47 (n=12). The distribution of STs in different geographical regions had commonalities, but there were also certain regional differences. The results of universal core genome multi-locus sequence typing showed that each ST formed relatively independent branch clusters, indicating clear genetic differentiation between different STs. The overall genetic diversity of Legionella in China was high. Conclusion: Legionella-positive cases have been detected throughout the year in China, with a wide distribution and regional differences. L. pneumophila has a high proportion and a large genetic diversity in its genome.}, } @article {pmid42128850, year = {2026}, author = {Fujii, N and Nakajima, M and Narihiro, T and Kuroda, K and Kindaichi, T}, title = {Current Understanding of Taxonomy and Ecology of the Phylum Minisyncoccota.}, journal = {Microbes and environments}, volume = {41}, number = {2}, pages = {}, doi = {10.1264/jsme2.ME25084}, pmid = {42128850}, issn = {1347-4405}, mesh = {*Bacteria/classification/genetics/isolation & purification/metabolism ; Phylogeny ; Ecosystem ; Genome, Bacterial ; }, abstract = {The phylum Minisyncoccota (formerly known as "Candidatus Patescibacteria"/candidate phyla radiation [CPR] and designated under SeqCode as Patescibacteriota) represents one of the major bacterial phyla; however, its physiological and ecological characteristics remain unclear. This review summarizes relevant studies on currently available isolate and genomic/metagenomic data, outlining the phylogenetic placement, metabolic features, host interactions, and unique genetic code usage of Minisyncoccota. Minisyncoccota play complementary and interdependent roles within microbial communities, while being restricted by incomplete metabolic capabilities that prevent independent survival. Studies on Minisyncoccota offer important insights into the diversity and evolution of uncultivated bacteria, as well as the hidden interaction networks that shape microbial ecosystems.}, } @article {pmid42129189, year = {2026}, author = {Lacruz-Pleguezuelos, B and Pérez-Cuervo, A and Coleto-Checa, D and Bazán, GX and Romero-Tapiador, S and Freixer, G and Fernández-Cabezas, J and Aguilar-Aguilar, E and Martín-Segura, A and Cárdenas-Roig, N and Carrasco-Guijarro, L and Fernández, LP and Espinosa-Salinas, I and Ramírez de Molina, A and Morales, A and Tolosana, R and Ortega-Garcia, J and Pancaldi, V and Marcos-Zambrano, LJ and Carrillo de Santa Pau, E}, title = {Network topology of the gut microbiome associates with metabolic health in obesity.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42129189}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Male ; Female ; *Obesity/microbiology/metabolism ; Middle Aged ; Cross-Sectional Studies ; Adult ; Feces/microbiology ; Metagenomics ; *Obesity, Metabolically Benign/microbiology/metabolism ; Dysbiosis/microbiology ; Phenotype ; }, abstract = {Obesity is a heterogeneous condition comprising a continuum of phenotypes with various metabolic and inflammatory profiles. Metabolically healthy obesity (MHO) identifies individuals with obesity but a relatively preserved metabolic state, although little is known about the gut microbiome features underlying this phenotype. Here, we analyzed gut microbial network structures of 931 individuals living with metabolically healthy non-obesity (MHNO), MHO, metabolically unhealthy non-obesity (MUNO), and metabolically unhealthy obesity (MUO), performing cross-sectional analyses on feces shotgun metagenomics data. Individuals with MHNO and MHO harbor more robust and functionally cohesive microbial networks, while communities from MUO and MUNO phenotypes exhibit a potentially dysbiotic state with reduced connectivity. A nutritional intervention cohort showed an improvement in network connectivity in parallel with metabolic improvements. Our findings show differences in microbial connectivity and association patterns across metabolic and obesity phenotypes, shedding light on how distinct microbial network structures may associate with host metabolic health and disease.}, } @article {pmid42129350, year = {2026}, author = {Parkin, K and Christophersen, CT and Verhasselt, V and Palmer, DJ and Cooper, MN and Prescott, SL and Silva, D and Martino, D}, title = {Chlorinated drinking water exposure enriches antimicrobial resistance pathways in the infant gut microbiome: a randomized trial.}, journal = {Communications medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s43856-026-01626-2}, pmid = {42129350}, issn = {2730-664X}, abstract = {BACKGROUND: Water chlorination is essential for controlling harmful microbes in drinking water; however, the antimicrobial effects of chlorine-based disinfectants present in tap water may influence early-life gut microbial ecology.

OBJECTIVE: To investigate the functional and compositional impact of chlorinated drinking water on the gut microbiome of infants.

DESIGN: The waTer qUality and Microbiome Study (TUMS) was an Australian-based double-blinded, randomised controlled trial. Six-month-old infants (n = 197) received either de-chlorinated drinking water via benchtop filtration (treatment, n = 99), or regular chlorinated water (control, n = 98) for twelve months. Tap water and stool samples were collected at baseline and at end of intervention. Metagenomic sequencing was used for faecal microbiome analysis. Primary outcomes were differences in gut microbiota between groups, secondary outcomes included incidence of allergic sensitization and respiratory conditions.

RESULTS: At baseline, 170 stool samples (83 control, 87 intervention) were collected, with 130 samples obtained at the end of the intervention (65 control, 65 intervention). Overall community structure was similar between groups after the intervention, including beta diversity (0.56% variance explained; p = 0.84), richness (-4.25, 95% CI; -14.85 to 6.35, p = 0.43) or Shannon Index (-0.14, 95% CI; -0.32 to 0.04, p = 0.12). The chlorinated water group showed enrichment of antibiotic resistance MetaCyc groups and pathways (adjusted p < 0.05). Stratified analysis suggested this effect was potentiated by clinical antibiotic use.

CONCLUSION: Chlorinated drinking water may enhance resistance functions in the infant gut microbiome. While remaining vital for public health, future studies should explore whether adjusting the timing or method of drinking water disinfectants into the infant diet can reduce selective pressures.

TRIAL REGISTRATION: ACTRN12619000458134; https://www.anzctr.org.au.}, } @article {pmid42129659, year = {2026}, author = {Chen, J and Li, X and Deng, Z and Ying, Y and Lu, M}, title = {Clinical characteristics of sporadic acute Q fever diagnosed by metagenomic next-generation sequencing: a retrospective analysis and literature review in China.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13477-2}, pmid = {42129659}, issn = {1471-2334}, support = {MISP-102684//MSD Investigator Initiated Studies Program Review Committee/ ; 2022YFC2303203-01//National Key Research and Development Program of China/ ; Z-2017-24-2202//Metagenomics of the Bacterial Infection and Drug Resistance Prevention of the Chinese Medical Association/ ; }, abstract = {BACKGROUND: Acute Q fever manifests sporadically in mainland China, where its clinical spectrum and optimal diagnostic strategies remain under-recognized. This study aimed to delineate the clinical phenotype and antimicrobial prescribing patterns of sporadic acute Q fever diagnosed via metagenomic next-generation sequencing (mNGS).

METHODS: We conducted a retrospective, single-center cohort study of adult patients with sporadic acute Q fever. A comprehensive literature review of all published sporadic cases across China was subsequently performed to delineate the national clinical spectrum of sporadic Q fever.

RESULTS: The cohort comprised 22 male patients (mean age 36.7±13.5 years). All patients presented with high-grade pyrexia (>39°C) accompanied by a characteristic symptom constellation of headache, fatigue, myalgia, and hepatic involvement (100%, mean ALT 122.2±56.9 U/L). Pneumonia was observed in 2 patients (2/22, 9.1%). A distinct dissociation was observed between markedly elevated C-reactive protein (mean 67.4 ± 33.6 mg/L) and normal leukocyte counts. A pooled analysis of 94 published cases and 22 consecutive patients from our center yielded 116 confirmed Q fever cases (male-to-female ratio 11.9:1, the proportion of hepatitis and pneumonia:87.9% and 24.1%) The median interval from symptom onset to pathogen confirmation was 7.8 ± 2.8 days. mNGS yielded a diagnosis in 77.5 % of 116 patients, the remaining 22.5 % were identified by PCR and antibody testing.

CONCLUSION: Acute Q fever in China predominantly affects young males, presenting as a systemic febrile illness with a distinctive hepatic phenotype (elevated liver enzymes) rather than prominent pneumonia. The clinical triad of high fever, influenza-like symptoms (headache/myalgia), and "WBC-CRP dissociation" (normal white cell count with elevated CRP) serves as a potential clinical indicator. Empiric doxycycline should be initiated promptly in suspected cases. mNGS is a valuable tool for definitive diagnosis, particularly when empiric therapy fails or in severe/complicated cases.}, } @article {pmid42129710, year = {2026}, author = {Wang, Z and Tang, J and Yang, K and Cui, Z and Li, Z}, title = {Diagnostic challenges and lessons learned of Guillain-Barré syndrome mimicking central nervous system infection - a case report.}, journal = {BMC neurology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12883-026-04942-1}, pmid = {42129710}, issn = {1471-2377}, abstract = {BACKGROUND: Guillain-Barré syndrome (GBS) is an immune-mediated disorder affecting the peripheral nervous system, often triggered by infections, vaccinations, trauma, or surgery. Typically, it presents as progressive, symmetric limb weakness with hyporeflexia. However, some GBS subtypes can present atypically with symptoms like headache, facial palsy, and confusion. These symptoms overlap significantly with central nervous system (CNS) infections, often causing diagnostic delays.

CASE PRESENTATION: A 57-year-old man was admitted with cough, sputum, and shortness of breath, having received a rabies vaccination a month earlier. He developed headache, dysphagia, progressive muscle weakness, and impaired consciousness, requiring Intensive Care Unit (ICU) transfer, endotracheal intubation, and mechanical ventilation. The initial cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) detected Pseudomonas aeruginosa (sequence count: 6094), combined with fever and a series of clinical symptoms before transfer to the ICU, CNS infection was considered. Treatment with piperacillin-tazobactam, meropenem, and ciprofloxacin yielded no improvement. Albumino-cytological dissociation in the CSF led to a neurology consultation for suspected GBS, and intravenous immunoglobulin (IVIg) therapy began. Negative CSF bacterial cultures and mNGS, along with positive anti-GT1a IgM ganglioside antibodies and electromyogram(EMG) result indicating nerve damage, confirmed the GBS diagnosis. After five days of IVIg, the patient was weaned from mechanical ventilation and showed significant neurological recovery.

CONCLUSION: The significant clinical overlap between GBS and CNS infections poses a major diagnostic and therapeutic challenge. This case highlights the importance of thorough history-taking, comprehensive neurological assessment, careful interpretation of lab results, and early neurologist involvement to minimize diagnostic delays in GBS and prevent subsequent treatment delays.}, } @article {pmid42129938, year = {2026}, author = {Zhao, L and Wu, L and Yin, S and Gao, W and Xiang, X and Xie, Y and Guo, Y and Wang, Z}, title = {Multi-omics reveals effects of several rumen bacteria on reproductive performance of sheep.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02426-5}, pmid = {42129938}, issn = {2049-2618}, support = {2025SNJF019//Three Agriculture Nine Party Science and Technology Cooperation Project/ ; 32573211//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Mounting evidence indicates that the rumen microbiota plays a crucial role in the reproductive health of sheep. However, the potential beneficial effects of rumen microbiota on lambing performance in sheep across different stages of the reproductive cycle and the precise mechanisms underlying these effects remain unclear. We aimed to elucidate the rumen microbial regulatory network underlying differences in reproductive performance in sheep by integrating multi-stage metagenomics and metabolomics.

RESULTS: No significant difference was observed in the ruminal microbial α-diversity between sheep with high and low litter size. However, significant stage-specific segregation was observed in their community structures. We identified a cohort of key species strongly associated with litter size. These included Asaia bogorensis, Methanolobus zinderi, Erwinia gerundensis, Marinobacter sp. BSs20148, and Lactobacillus amylolyticus enriched during pregnancy; Rhizobium gallicum, Aeromonas caviae, Pseudolysobacter antarcticus, Mucilaginibacter rubeus, Thermococcus paralvinellae, and Janthinobacterium svalbardensis enriched during lactation; Pseudomonas mandelii, Gordonia sp. HY186, Arachidicoccus sp. BS20, Mesotoga prima, Acidovorax ebreus, Donacia cinerea, and Salmonella enterica enriched during estrus. Host plasma metabolomics analysis further revealed an enrichment of a set of core metabolites in the blood of high-fertility sheep, including Inositol, 2-Linoleoylglycerol, lysophosphatidylcholines and neuromodulatory substances such as tyramine and sphingosine-1-phosphate. We constructed stage-specific "rumen microbe-rumen metabolite-plasma metabolite" regulatory axes. These results suggest the influence of the rumen microbiome on plasma metabolic profiles and subsequent fertility outcomes in sheep.

CONCLUSION: We elucidate the dynamic mechanism by which the rumen microbiota in high-fertility sheep is associated with superior reproductive performance through stage-adaptive community succession and functional remodeling, which in turn may modulate the host's neuroendocrine and lipid metabolic profiles. These findings provide a new perspective for understanding the regulation of fertility in ruminants and lay a theoretical foundation for improving reproductive efficiency through nutritional strategies targeting the rumen microbiota. Video Abstract.}, } @article {pmid42130304, year = {2026}, author = {Preston, S and Jones, J and Huggett, MJ and Adam, AAS and White, NE and Tan, KC and Richards, Z}, title = {Comparing Microbial Communities of Diseased and Healthy Isopora palifera Corals and Adjacent Waters at the Cocos (Keeling) Islands.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70324}, pmid = {42130304}, issn = {1462-2920}, support = {LP160101508//Australian Research Council/ ; }, mesh = {*Anthozoa/microbiology/growth & development ; Animals ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Seawater/microbiology ; Islands ; Coral Reefs ; }, abstract = {Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood. Microorganisms are integral to coral health, but the role of bacterial communities in GAs remains unclear. We investigated an outbreak of GAs in Isopora palifera at the Cocos (Keeling) Islands using 16S rRNA amplicon sequencing to compare bacterial communities of GA-affected and asymptomatic corals, surrounding water and potential pollution sources. Significant differences in bacterial beta diversity were observed across sites, with an interaction between location and coral health status. Coral and water samples hosted distinct microbial communities, but there was no evidence linking GA-affected corals to local pollution. Moreover, no consistent bacterial taxa were associated with disease, suggesting that resident microbes may not be primary drivers of GAs. However, our study does not account for transient microbes that may have initiated GAs. Our findings challenge assumptions of single-agent causality and microbial compositional homogeneity in coral diseases. This study advances understanding of microbial dynamics in coral disease ecology and underscores the importance of early-stage investigation and functional metagenomics to identify viral, fungal and microbial functional shifts in disease emergence. Studying outbreaks in minimally impacted systems offers valuable baselines for disentangling natural disease processes.}, } @article {pmid42130363, year = {2026}, author = {DU, WQ and Liu, LJ and Zhang, L and Tang, YF and Liu, LQ and Li, XF and Xiao, YY}, title = {[A case of Bartonella henselae meningitis characterized by bone marrow hemophagocytosis].}, journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics}, volume = {28}, number = {5}, pages = {618-623}, pmid = {42130363}, issn = {1008-8830}, mesh = {Humans ; Male ; Adolescent ; *Bartonella henselae ; *Cat-Scratch Disease/complications ; *Lymphohistiocytosis, Hemophagocytic/etiology ; *Bone Marrow/pathology ; *Meningitis, Bacterial ; }, abstract = {A 13-year-old boy with Bartonella henselae meningitis is reported. He presented with recurrent fever with no history of cat scratches and no lymphadenopathy. Cerebrospinal fluid analysis showed an elevated white blood cell count, and Bartonella henselae infection was confirmed by metagenomic next-generation sequencing. Bone marrow examination revealed hemophagocytosis predominantly involving nucleated erythrocytes; to our knowledge, this bone marrow morphological abnormality is the first reported worldwide in association with Bartonella henselae infection. Transient bilateral hip pain occurred during the illness and was considered infection-related joint involvement. The patient improved with treatment and had no neurological sequelae. This case expands the spectrum of clinical and bone marrow manifestations of Bartonella henselae infection and warrants vigilance for possible central nervous system and bone marrow involvement in cases of fever of infectious etiology presenting without typical lymphadenopathy.}, } @article {pmid42130962, year = {2026}, author = {Tomar, SS and Khairnar, K}, title = {Disruption in the Host-Phage Dynamics and Altered Microbial Diversity in the Upper Respiratory Tract of SARS-CoV-2-Infected Individuals.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {7}, number = {1}, pages = {9-20}, pmid = {42130962}, issn = {2641-6549}, abstract = {BACKGROUND: The upper respiratory tract (URT) is an important site for the predisposition and multiplication of the SARS-CoV-2 virus. Therefore, URT is a critical site for investigating the changes in the microbiome caused by the SARS-CoV-2 infection. This study aims to compare phageome diversity and investigate the correlation of the phageome profiles with the sample type (SARS-CoV-2 or control) to determine the nature of phage-host interactions in the human URT microbiome and to assess the effect of SARS-CoV-2 viral load on host and phage abundance.

MATERIALS AND METHODS: In this study, we have used the whole-genome shotgun metagenomic approach to investigate URT swab samples (n = 96) collected from SARS-CoV-2-positive individuals (n = 48) (nonhospitalized but symptomatic) and healthy controls (n = 48) belonging to five districts of central India.

RESULTS: The results revealed distinct phageome profiles among the groups; Detrevirus dominated the composition in the control samples, while Maxrubnervirus was dominant in SARS-CoV-2 samples. Microbial diversity analysis showed significantly higher richness in the SARS-CoV-2 group compared to controls for both bacteria (Chao1: 886.00 vs. 351.00, p < 0.0001) and phages (Chao1: 39.00 vs. 16.00, p = 0.0002). Bacterial diversity (Simpson index) was lower in the SARS-CoV-2 group (0.88 vs. 0.93, p = 0.0024), whereas phage diversity was higher in the SARS-CoV-2 group (0.86 vs. 0.79, p = 0.0384). Viral load, as reflected by cycle threshold (Ct) values, significantly influenced both bacteria (H = 6.69, p = 0.035) and phage (H = 8.97, p = 0.011) abundances. Host-phage interaction networks appeared disrupted in SARS-CoV-2 samples, with a weaker logistic model fit (R [2] = 0.7425) than controls (R [2] = 0.9265).

CONCLUSION: SARS-CoV-2 infection alters URT microbiome composition, increasing microbial diversity but disrupting host-phage dynamics. SARS-CoV-2 Viral load correlates with the shifts in microbial abundance, indicating infection-driven shifts in microbiome stability compared to healthy controls.}, } @article {pmid42131203, year = {2026}, author = {Zahra, M and Ouf, A and Azzazy, HME and Moustafa, A}, title = {Metagenomic profiling of gut microbiome signatures across liver disease stages and HCV-related hepatocellular carcinoma in Egyptian patients.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1758563}, pmid = {42131203}, issn = {1664-302X}, abstract = {INTRODUCTION: Dysbiosis in the gut microbiome, particularly concerning the synchronous crosstalk between the gut and the liver, has been associated with various diseases. This study examines the gut microbiome's role in liver diseases among Egyptian patients, with a focus on the hepatitis C virus (HCV) and hepatocellular carcinoma (HCC), both of which are highly prevalent in Egypt.

METHODS: Utilizing shotgun metagenomic sequencing, we analyzed microbial gene catalogs and taxonomic profiles from 46 Egyptian patients categorized into five groups: healthy individuals, liver disease patients of different etiologies, post-HCV, treated HCV, and HCV-HCC patients.

RESULTS: Healthy and treated HCV patients exhibited distinct microbial profiles characterized by an abundance of beneficial bacteria, Faecalibacterium and Bifidobacterium (p < 0.05), associated with anti-inflammatory short-chain fatty acid production. Conversely, liver disease and HCC patients displayed increased pathogenic bacteria, Escherichia (p < 0.05), and genes linked to inflammation and oncogenesis, including lipopolysaccharide biosynthesis.

DISCUSSION: These findings suggest a dominance of Faecalibacterium in healthy Egyptians, likely attributable to traditional dietary patterns, and cytochrome P450 genes as potential HCC biomarkers, possibly connected to aflatoxin exposure. Treated HCV patients showed significant microbiome recovery, reflecting effective antiviral therapy. These findings emphasize that Egypt-specific factors, such as persistent resistance genes post-HCV due to antibiotic use and the prominence of bile acid metabolism genes, are influenced by high HCV prevalence and environmental exposures like aflatoxins. Taken together, the results highlight the need for region-specific microbiome research priorities in Egypt and underscore how local dietary, clinical, and environmental factors may shape future objectives in understanding liver disease pathogenesis and prevention.}, } @article {pmid42131208, year = {2026}, author = {Hembram, DB and Panda, SP and Das, BK and Soren, D and Singh, NR}, title = {Microbial elicitors to metabolic reprogramming: an integrative model of plant-microbe interactions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1816468}, pmid = {42131208}, issn = {1664-302X}, abstract = {Plant growth, soil health, and crop productivity with nutritional quality can be significantly enhanced by employing microbial consortia that incorporate diverse microorganisms with complementary functions. Plants produce various types of secondary metabolites such as terpenoids, alkaloids, phenolics, essential oils, and other metabolites through various cellular mechanisms, which are often stimulated by microbial interactions. These metabolites exert beneficial effects on plants and perform multiple roles in agriculture, contributing significantly to growth and economy. This review summarizes microbial consortia-mediated enhancement of plant health and their intricate interactions with host plants. Beneficial microbes of a consortium trigger complex signaling cascades leading to a dynamic regulatory strategy through which plants enhance their secondary metabolite synthesis. Secondary messengers and hormonal cross-talk further integrate the signal to transcription factors, which play a central role in activating or repressing the key genes of the metabolic pathways. Thus, the interplay of microbial signal, secondary messengers, hormonal cross-talk, and key metabolite genes forms the basis of plant secondary metabolite biosynthesis. In addition, recent advances in systems microbiology, including metagenomics, metatranscriptomics, and metabolomics, have enabled a holistic understanding of microbial community dynamics and their collective role in regulating secondary metabolism.}, } @article {pmid42131214, year = {2026}, author = {Sudianto, E and Shlafstein, MD and Durieu, B and Harmel, M and Cornet, L and Saw, JH}, title = {Taxonomic description of cyanobacteria from extreme habitats through genome-based classification.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1824103}, pmid = {42131214}, issn = {1664-302X}, abstract = {INTRODUCTION: Cyanobacteria form a morphologically and phylogenetically diverse group of oxygenic phototrophic bacteria inhabiting a wide range of environments, including extreme habitats such as hot springs and volcanic steam vents. Many lineages, particularly those from these extreme environments, remain uncultured and are known only from metagenome-assembled genomes (MAGs), limiting their integration into formal taxonomy.

METHODS: Analysis of 46 steam vent associated samples from Hawai'i using 16S rRNA amplicon sequencing revealed that cyanobacteria dominate these communities. Gloeobacter kilaueensis dominated pit-like environments with low-light conditions, while Leptolyngbyaceae and other families are more dominant in structured soil and wall communities. We further reconstructed 38 high-quality cyanobacterial MAGs and incorporated them into a phylogenomic analysis comprising 343 cyanobacterial genomes, followed by genome-based comparisons against 9,026 reference genomes.

RESULTS: This revealed eight novel species and one novel genus spanning five orders: Chroococcidiopsidales, Leptolyngbyales, Nostocales, Oculatellales, and Oscillatoriales. Following SeqCode guidelines, we provide the first formal taxonomic descriptions of cyanobacterial MAGs and propose guidelines for integrating genome-based and cultivated material.

CONCLUSION: These findings highlight Hawaiian steam vents as hotspots of previously uncharacterized cyanobacterial diversity and underscore the importance of genome-based nomenclature.}, } @article {pmid42131265, year = {2026}, author = {Cheng, J and Ni, J and Zhao, Y and Jiang, L and Huang, Y and Zhang, Y and Yan, P and Long, Z and Fu, H and Jiang, X}, title = {The clinical utility of metagenomic next-generation sequencing in the management of fever in patients with hematological disorders.}, journal = {Nagoya journal of medical science}, volume = {88}, number = {1}, pages = {84-98}, pmid = {42131265}, issn = {2186-3326}, mesh = {Humans ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Adult ; *Metagenomics/methods ; Aged ; *Hematologic Neoplasms/complications/microbiology ; *Fever/microbiology/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Patients with hematological malignancies frequently present with severe and intricate infections that pose life-threatening risks. Conventional pathogen detection methods offer limited clinical insights and therapeutic guidance. This retrospective study evaluated the clinical application of metagenomic next-generation sequencing (mNGS) in hematologic patients who remained febrile despite prolonged antibiotic therapy, which means unresponsive to antibiotic therapy. This retrospective analysis included 204 patients with hematologic malignancies, undergoing conventional pathogen detection and peripheral blood mNGS. The cohort was stratified into neutropenia and non-neutropenia groups to compare the diagnostic and therapeutic implications of mNGS versus conventional microbiological tests (CMT). Among the 204 patients with mNGS, the overall positive detection rate was significantly higher than that of CMT (68.1% vs 30.9%, P<0.001). In both the neutropenia and non-neutropenia group, mNGS demonstrated a higher positivity rate for bacteria than for CMT (bacteria, 36.4% vs 15.6%, P<0.01). mNGS proved notably advantageous for bloodstream infections with clinically relevant drug-resistant strains, particularly in the neutropenia cohort (26.4% vs 12.5%, P<0.001). Using a composite reference standard, mNGS manifested sensitivity and specificity rates of 78.4% and 61.9%, respectively. Patients in the neutropenia group derived superior clinical benefit from mNGS, including higher diagnostic accuracy and treatment efficacy (diagnosis, 56.4% vs 40.6%, P=0.036; treatment, 49.3% vs 31.3%, P = 0.016). Additionally, the 30-days mortality rate was notably higher among mNGS-positive patients who tested compared to those who tested negative (17.3% vs 1.5%, P<0.001). mNGS demonstrated clinical relevance in patients with hematologic malignancy who received prolonged antibiotic treatment and holds promise in predicting patient survival prognosis.}, } @article {pmid42131305, year = {2026}, author = {Toto, F and Cardile, S and Scanu, M and Marzano, V and Petito, V and Masi, L and Puca, P and Giorgio, V and Alterio, T and Diamanti, A and De Angelis, P and Lopetuso, LR and Scaldaferri, F and Putignani, L and Del Chierico, F}, title = {Ecological patterns of the gut mycobiome and microbiome in ulcerative colitis across life stages.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1769892}, pmid = {42131305}, issn = {2235-2988}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/immunology ; *Mycobiome ; *Gastrointestinal Microbiome ; Adult ; Child ; Male ; Female ; *Fungi/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Young Adult ; Adolescent ; Dysbiosis/microbiology ; Metagenome ; Child, Preschool ; Age Factors ; Aged ; Feces/microbiology ; }, abstract = {INTRODUCTION: Age-related variations in the gut microbial communities may influence immune regulation and inflammatory processes in inflammatory bowel diseases (IBD). However, distinguishing age effects from differences in clinical characteristics remains challenging.

METHODS: We investigated life-stage-associated patterns of the gut microbiome and mycobiome while accounting for clinical heterogeneity between paediatric and adult ulcerative colitis (UC) populations. We analysed 73 targeted metagenomes of bacteria and 69 targeted metagenomes of fungi from 26 paediatric and 47 adult patients with UC. Microbial diversity metrics and multivariate analyses were applied to evaluate community variation, and mucosal immune markers were assessed by ELISA. Clinical variables, including disease activity, duration, and treatment exposure, were considered when interpreting age-related microbial differences.

RESULTS: Fungal communities exhibited higher richness in adults and formed distinct age-related clusters in beta-diversity analyses, whereas bacterial composition remained largely comparable across age groups. Children were enriched in inflammation-associated fungi (Saccharomycetes, Aureobasidium, Cladosporium) and depleted in taxa commonly linked to gut health (Clavispora, Vishniacozyma, Betamyces). Stratification by life stage identified young adults as displaying the most pronounced dysbiosis, characterised by Basidiomycota/Ascomycota and Firmicutes/Bacteroidota ratios, and reduced Faecalibacterium prausnitzii abundance. Age-associated immune patterns were observed, with lysozyme levels increasing across life stages, correlating with sIgA, and positively associating with F. prausnitzii, although declining with increasing disease severity.

DISCUSSION: Age-related variation was more evident in fungal than bacterial communities, suggesting that host developmental and immunological factors contribute to mycobiome configuration beyond clinical imbalance alone. Together, these findings indicate that life stage is linked to ecological variation of the gut mycobiome and mucosal immune responses in UC, while bacterial communities appear primarily shaped by disease-related factors. The transition from childhood to adulthood may represent a critical window of host-fungal interaction relevant for age-tailored microbiome-based strategies.}, } @article {pmid42131468, year = {2026}, author = {Mazibuko, X and Mtimka, S and Ngobese, LM and Mafuna, T and Simelane, MB and Yakobi, SH and Gumede, X and Pooe, OJ}, title = {Metagenomic Profiling of Taxonomic and Functional Diversity in Soil Microbial Communities at Buffelsdraai Landfill, South Africa: Implications for Bioremediation.}, journal = {Bioinformatics and biology insights}, volume = {20}, number = {}, pages = {11779322251413418}, pmid = {42131468}, issn = {1177-9322}, abstract = {Soil microbial communities in landfills play a crucial in waste degradation and pollution mitigation, yet their diversity and functionality in many regions remain underexplored. This study used shotgun metagenomic sequencing to characterise microbial communities in soil samples from the Buffelsdraai landfill waste site (samples: XM-AA, XM-BB, XM-CC, XM-DD). We identified dominant taxa, namely, Actinobacteria, Acidobacteria, and Bacteroidetes, and evaluated their taxonomic diversity and metabolic potential. Diversity indices revealed high richness in XM-AA (Shannon: 4.188), suggesting the potential of a strong waste-processing capacity, while XM-BB showed reduced diversity (Shannon: 1.453), likely due to contaminant stress (eg, nickel, cobalt). XM-CC and XM-DD exhibited moderate diversity (Shannon: 2.671-2.942) with Actinobacteria dominance (99%), suggesting adaptation to landfill conditions. Functional profiling via Kyoto Encyclopaedia of Genes and Genomes pathways highlighted carbohydrate and lipid metabolism, alongside xenobiotic biodegradation, pointing to potential for organic waste and pollutant breakdown. Physicochemical analyses detected elevated sodium (22 640 mg/kg in cell 1) and trace metals (eg, Ni: 0.1469 mg/kg), influencing microbial composition. These results emphasise microbial diversity's role in landfill soil functionality and position Actinobacteria as a bioremediation target for degrading leachate organics and immobilising metals. This study provides a baseline profile of microbial taxonomic and functional responses to landfill-associated environmental stressors in South Africa. The findings highlight the ecological roles of landfill microbial communities and their potential relevance for future bioremediation research.}, } @article {pmid42131611, year = {2026}, author = {Zhai, X and Pan, H and Zheng, J}, title = {Spinal infection caused by Coxiella burnetii and surgical treatments: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1785109}, pmid = {42131611}, issn = {2296-858X}, abstract = {Q fever is a rare global zoonosis caused by Coxiella burnetii, with bone and joint involvement being an uncommon manifestation that poses significant diagnostic challenges. This article reports a case of persistent focal spinal infection caused by C. burnetii in an elderly female without a clear epidemiological exposure history, who was initially misdiagnosed with vertebral compression fractures. The diagnosis was confirmed by third-generation nanopore-based metagenomic next-generation sequencing (mNGS), which detected 12,170 reads of C. burnetii with a relative abundance of 98.27%. The patient was initially treated with oral doxycycline (0.1 g q12h) and rifampin capsules (0.45 g daily) for 4 weeks, resulting in decreased inflammatory markers and reduced paravertebral abscess size. After clinical stabilization, surgical intervention (posterior approach T12-L1 vertebral lesion resection, intervertebral bone graft fusion, and pedicle screw rod fixation) was performed under general anaesthesia. Postoperative follow-up for 3 months showed a significant improvement in the patient's low back pain [visual analogue scale (VAS) score from 6 preoperatively to 1 at 3 months] and functional status [Oswestry Disability Index (ODI) from 65% preoperatively to 10% at 3 months], with normalized inflammatory markers and a reduced C. burnetii IgG antibody titre (from 1:256 to 1:128). Serological follow-up revealed persistent negative IgM antibodies throughout the treatment course. This case highlights the diagnostic value of third-generation mNGS for rare spinal infections caused by C. burnetii and the efficacy of a multimodal treatment approach combining targeted antimicrobial therapy and surgical intervention. The rationale for antibiotic selection and surgical management is discussed, along with the limitations of the present case and clinical insights for managing similar cases.}, } @article {pmid42132311, year = {2026}, author = {Tulloch, RL and Rojahn, J and Neaves, LE and Trujillo-González, A and Holleley, CE and Hahn, EE}, title = {Evaluating the Molecular Potential and Interpretability of DNA in Historical Spirit Collection Media.}, journal = {Molecular ecology resources}, volume = {26}, number = {4}, pages = {e70153}, pmid = {42132311}, issn = {1755-0998}, support = {//Centre for Biodiversity Analysis/ ; }, mesh = {*DNA/isolation & purification/genetics ; *Specimen Handling/methods ; Animals ; Metagenomics/methods ; DNA Barcoding, Taxonomic/methods ; Museums ; *Preservation, Biological/methods ; }, abstract = {Advancements in historical genomics increasingly leverage museum collections to study past ecosystems, species interactions and biodiversity. Formalin-fixed, ethanol-preserved specimens, once thought inaccessible to molecular analyses due to DNA degradation, are emerging as valuable genomic resources. If recoverable and reliably attributable, DNA within preservation media could provide a non-destructive alternative to conventional tissue sampling, with the potential to expand molecular access to valuable or irreplaceable specimens. We tested whether preservation media contains recoverable DNA suitable for taxonomic inference. We coupled passive adsorption and active filtration of specimen media with hot alkaline lysis DNA extraction followed by metabarcoding and shotgun metagenomics. DNA was recoverable across samples, including 41 of 61 (~67%) targets in a composite sample. However, detections were dominated by non-target taxa, indicating that preservation media retain a layered mixture of specimen-derived DNA and broader collection-level background. Detection success tracked with preservation chemistry (near-neutral pH and low residual formaldehyde) rather than specimen age. Method choice influenced detections: active filtration increased target detections but admitted more background; passive capture was sparser but more selective; shotgun sequencing retrieved broader vertebrate signals, including reptiles, but was heavily enriched for non-targets. Because both target and non-target taxa were often abundant, read-abundance cut-offs were unreliable for attribution. Spirit-media DNA is therefore best interpreted as a collection-level signal and a screening tool to identify jars with molecular potential (e.g., taxa of conservation or biosecurity interest), rather than as a definitive non-destructive proxy for specimen identity. Prioritising chemically favourable jars and implementing rigorous contamination controls should improve signal interpretability and help unlock the value of preservation media for historical genomics.}, } @article {pmid42132424, year = {2026}, author = {Bae, J and Takemura, M}, title = {Refining a giant virus lineage: a novel order unifying Mamonoviridae and "Manesviridae," unveiled by the discovery of furtivovirus.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0203125}, doi = {10.1128/jvi.02031-25}, pmid = {42132424}, issn = {1098-5514}, abstract = {UNLABELLED: The evolutionary origins and taxonomic framework of giant viruses related to the family Mamonoviridae and its relative group, including clandestinovirus, remain unclassified due to gaps in genome size and host range between these two groups. This study aimed to address this gap by integrating our newly isolated virus with publicly available metagenome-assembled genomes (MAGs) to construct a more robust phylogenetic framework. Here, we report the isolation and characterization of a new giant virus, furtivovirus, using the unicellular amoeba Vermamoeba vermiformis as a host. Furtivovirus has a genome of approximately 560 kbp and shares key features with its closest relative, clandestinovirus. Ultrastructural analysis revealed a unique host-nucleus-dependent replication strategy characterized by the breakdown of the nuclear membrane and the packaging of nascent virions directly within the nucleoplasm, distinguishing it from canonical cytoplasmic virion factories. Comprehensive phylogenetic and comparative genomic analyses of shared orthologous groups and nucleocytovirus marker proteins revealed that furtivovirus, clandestinovirus, ushikuvirus, and usurpativirus form a distinct monophyletic clade, for which we propose a new family, "Manesviridae." Further analysis using amino acid-based similarity metrics of Nucleocytoviricota viral genomes, including established MAGs, demonstrated that this new family is robustly placed as a sister group to the family Mamonoviridae. This study elucidated the evolutionary relationships between viruses with large and small genomes that possess similar virion sizes within this lineage. Based on this cumulative evidence, we propose the establishment of a new order to unify these two families, thereby expanding their diversity and clarifying the evolutionary history of this branch within Nucleocytoviricota.

IMPORTANCE: Giant viruses challenge our traditional understanding of viral evolution, raising the question of how a single related group can diverge to infect different hosts while evolving into vastly different genome sizes and replication strategies. The family Mamonoviridae and its relatives epitomize this evolutionary divergence: one group possesses massive genomes, whereas the other has genomes that are less than half their size. The discovery of furtivovirus and its unique nucleoplasm-dependent replication cycle provides a critical biological context for this genomic disparity. Through deep comparative genomic analysis, we demonstrated that these seemingly disparate lineages share a cohesive evolutionary origin that is distinct from other established orders. This finding highlights the complexity of genome evolution, demonstrating that giant viruses can expand their overall genome size to adapt to uncertain environments while reducing their core essential genes, thereby providing new insights into the evolutionary pressures that shape the diversity of the virosphere.}, } @article {pmid42132850, year = {2026}, author = {Bright, K and Dienes, B and van Dongen, B and Strashnov, I and Han, X and Aeppli, M}, title = {Emerging investigator series: metagenomic insights into microbial controls of carbon cycling in alpine soils.}, journal = {Environmental science. Processes & impacts}, volume = {}, number = {}, pages = {}, pmid = {42132850}, issn = {2050-7895}, abstract = {Alpine riparian zones span topographic gradients from wet soils on the plain near streams to drier soils on adjacent slopes. These differences in soil moisture are generally associated with shifts in the soil redox state from anoxic on the plain to oxic on the slope. In anoxic plain soils, soil organic carbon (SOC) may accumulate due to thermodynamic constraints on microbial activity. Here, we used shotgun metagenomics to examine how microbial diversity and functional potential vary across differing redox conditions on plain and slope soils in two catchments in the Swiss Alps. We complemented these analyses with soil physicochemical characteristics and information on the chemical composition of organic matter. Plain soils had higher SOC stocks and higher relative abundance of phenol compounds relative to slope soils, consistent with SOC preservation and preferential mineralisation of easily degradable organic compounds under anoxic conditions. Microbial communities in plain soils further exhibited greater taxonomic and functional diversity, including increased potential for anaerobic respiration pathways. Genes for nitrate, iron, and sulfate reduction were linked to the Chloroflexota, Acidobacteria, and Desulfobacterota phyla, respectively. Based on NMDS correlations, electron accepting capacity, calcium content, and pH shaped microbial community composition. Slope soils, by contrast, supported less diverse microbial communities, determined mainly by electron donating capacity and clay content. Our work demonstrates how soil redox conditions and microbial functional potential shape carbon cycling across landscape positions in alpine riparian zones. This mechanistic understanding is critical to anticipate changes in carbon cycling in alpine ecosystems in a changing climate.}, } @article {pmid42132937, year = {2026}, author = {Enuh, BM and Myers, KS and Bott, C and Klaus, S and McCullough, K and McIntosh, L and Beach, N and Young, M and Donohue, TJ and Noguera, DR}, title = {Metagenomes and metagenome-assembled genomes from microbial communities in a biological nutrient removal plant operated at Hamptons Road Sanitation District (HRSD) with high and low dissolved oxygen conditions.}, journal = {Microbiology resource announcements}, volume = {15}, number = {6}, pages = {e0149225}, pmid = {42132937}, issn = {2576-098X}, abstract = {Aeration is a major cost at biological nutrient removal (BNR) plants. We report on microbial communities in a pilot-scale BNR system before and after a dissolved oxygen transition from 2.5 to 0.2 mg/L implemented over 18 months. Four PacBio metagenomes and 316 metagenome-assembled genomes are announced.}, } @article {pmid42132952, year = {2026}, author = {Özel, Ş and Lauritano, D}, title = {Oral mucosal microbiome alterations in recurrent aphthous stomatitis: a systematic review of 16 S rRNA gene sequencing studies.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42132952}, issn = {1573-4978}, mesh = {Humans ; *Stomatitis, Aphthous/microbiology/genetics ; *Mouth Mucosa/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Dysbiosis/microbiology ; Case-Control Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; Recurrence ; }, abstract = {Recurrent aphthous stomatitis (RAS) is a prevalent inflammatory disorder of the oral mucosa characterized by recurrent painful ulcerations in otherwise healthy individuals. This systematic review aimed to evaluate alterations in the oral mucosal microbiome of patients with RAS based on studies using 16 S rRNA sequencing. A systematic search of PubMed, Scopus, and Web of Science was conducted on April 14, 2026. Eligible studies included human case-control investigations evaluating oral mucosal swab samples from patients with clinically diagnosed RAS and healthy controls using 16 S rRNA sequencing. Studies based solely on saliva, culture methods, PCR-only analyses, or lacking controls were excluded. Joanna Briggs Institute Critical Appraisal Checklist for Case-Control Studies was used for the evaluation of selected articles. Six studies met the inclusion criteria. Considerable heterogeneity was observed in alpha and beta diversity outcomes. Most studies reported reduced microbial richness in RAS lesions, whereas others found increased or unchanged diversity. Ulcerated sites frequently demonstrated reduced abundance of health-associated taxa such as Streptococcus and Firmicutes, with increased levels of Proteobacteria and inflammation-associated genera including Neisseria, Haemophilus, Prevotella, and Fusobacterium. Microbial alterations were most pronounced at active ulcer sites, while non-ulcerated or healed mucosa more closely resembled healthy controls. Current evidence suggests that RAS is associated with localized, site-specific microbial dysbiosis rather than generalized oral microbiome disruption. However, methodological heterogeneity and small sample sizes limit definitive conclusions. Future standardized longitudinal studies integrating functional metagenomics are warranted to clarify the role of the microbiome in RAS pathogenesis.}, } @article {pmid42133155, year = {2026}, author = {Zhang, Q and He, G and Guo, Z and He, Y and Xiong, J and He, T and Lee, SL}, title = {Comparative metagenomic and metabolomic characterization of conventionally and nitrogen-only fertilized maize soils and a forest-derived fermentation-enriched microbial community.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42133155}, issn = {1573-0972}, support = {42367039, 42267038//National Natural Science Foundation of China/ ; 2022YFD1901505//National Key Research and Development Program of China/ ; Z2024417//Guizhou Provincial Science and Technology Department/ ; Liu Jin Xiang [2024] No. 44, 202406670023//Overseas Study Program for Young Key Teachers/ ; }, mesh = {*Nitrogen/metabolism ; *Soil Microbiology ; *Zea mays/growth & development/microbiology ; Forests ; Fermentation ; Soil/chemistry ; *Metagenomics/methods ; *Fertilizers ; *Metabolomics/methods ; China ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Agriculture ; Carbon/metabolism ; }, abstract = {Long-term nitrogen-only fertilization can alter soil physicochemical properties and microbial community structure in maize fields. In this study, nitrogen-only fertilized soil (S) and conventionally fertilized soil (B) were collected from a four-year maize field trial in Anshun City, Guizhou Province, China. Meanwhile, a forest-derived microbial enrichment system (T) was prepared through fermentation using forest soil, rice bran, and molasses. Metagenomic sequencing and untargeted metabolomics were used to compare microbial, functional gene, and metabolite differences between S and B soils within the agricultural field system, and to describe the microbial community composition, functional gene profiles, and metabolite features of T as an independent reference system. The results showed that Pseudomonadota accounted for 44.33% of the microbial community in T, compared with 20.63% in S and 22.31% in B. Carbon and nitrogen metabolism-related genes, including ackA, gltB, and ureC, showed higher relative abundances in T than in S. Pathway-level annotation indicated higher representation of genes or modules related to glycolysis and nitrogen metabolism in T. Metabolomic profiling revealed distinct metabolite patterns in T, including differences in amino acids, carbohydrates, and metabolites annotated to phenylpropanoid-related pathways. Candidatus Rokubacteria also showed high relative abundance among nitrogen-metabolism-associated taxa in T. Overall, this study provides descriptive multi-omics evidence of the microbial composition, functional gene profiles, and metabolite features of a forest-derived fermentation-enriched microbial community. Because T was an artificially enriched system and was not introduced into agricultural soil, these results should be interpreted as baseline data for future controlled validation rather than direct evidence of soil remediation or functional compensation.}, } @article {pmid42133463, year = {2026}, author = {Che, J and Du, J and Piao, Y and Dong, Y and Zhang, L and Su, D and Zhang, C and Zhao, Y and Du, W and Che, N}, title = {Fungal species identification in FFPE tissues: A comparative evaluation of droplet digital PCR, ITS sequencing, and metagenomic next-generation sequencing.}, journal = {Medical mycology}, volume = {64}, number = {6}, pages = {}, doi = {10.1093/mmy/myag049}, pmid = {42133463}, issn = {1460-2709}, support = {82472378//National Natural Science Foundation of China/ ; 2025ZD01908700//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project/ ; DFL20241601//Dengfeng Talents Project of Beijing Hospitals Authority/ ; BRWE2024W042160103//Beijing Research Ward Excellence Program/ ; }, mesh = {Humans ; *Polymerase Chain Reaction/methods ; *Fungi/genetics/classification/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; Paraffin Embedding ; *Mycoses/diagnosis/microbiology ; *Metagenomics/methods ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Sequence Analysis, DNA ; Tissue Fixation ; Formaldehyde ; }, abstract = {Accurate histological diagnosis of fungal infections is challenging due to morphological similarities among fungi, which can affect treatment outcomes. This study evaluated the performance of droplet digital PCR (ddPCR), internal transcribed spacer (ITS) sequencing, and metagenomic next-generation sequencing (mNGS) using 111 formalin-fixed, paraffin-embedded tissue samples with histologically confirmed fungal infections. All three methods showed comparable detection rates for filamentous fungi (84.2%-94.7%; P = .2). For yeast-like fungi, however, mNGS demonstrated significantly higher detection (66.7%) than ddPCR (46.3%) and ITS sequencing (35.2%) (P < .01). mNGS also achieved superior genus- and species-level identification (81.1% for both) compared to ddPCR (65.8% and 64.9%) and ITS sequencing (61.3% and 50.5%) (P < .01). Additionally, mNGS identified two unusual fungi (Scedosporium apiospermum and Schizophyllum commune) previously misdiagnosed as Aspergillus. These findings support the integration of mNGS into clinical diagnostic workflows for the accurate identification of yeast-like and rare fungal pathogens, thereby enabling targeted antifungal therapy.}, } @article {pmid42133477, year = {2026}, author = {Tian, B and Liu, Y and Su, KJ and Jiang, LD and Lin, X and Qiu, C and Luo, Z and Tian, Q and Shen, J and Shen, H and Zhang, LS and Xiao, HM and Deng, HW}, title = {Gut species Porphyromonas asaccharolytica and Bacteroides fragilis are associated with whole body fat percentage.}, journal = {Journal of applied microbiology}, volume = {137}, number = {6}, pages = {}, pmid = {42133477}, issn = {1365-2672}, support = {/NH/NIH HHS/United States ; 2016YFC1201805//National Key R&D Program of China/ ; 2017YFC1001100//National Key R&D Program of China/ ; 201604020007//Science and Technology Program of Guangzhou, China/ ; 81770878//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Bacteroides fragilis/genetics/physiology/isolation & purification ; Male ; *Porphyromonas/genetics/physiology/isolation & purification ; *Obesity/microbiology ; *Adipose Tissue/metabolism ; *Gastrointestinal Microbiome ; Cohort Studies ; Middle Aged ; Metagenomics ; }, abstract = {AIMS: Obesity is linked to various adverse health effects, with body fat percentage being a key indicator of these risks. While the gut microbiota (GM) plays important roles in obesity, the specific species involved remain poorly understood. We aimed to identify gut species that may influence obesity in a cohort of US men.

METHODS AND RESULTS: We conducted a comprehensive integrative analysis using metagenomics and whole-genome sequencing data in the US cohort. MaAsLin2 was used to identify associations between GM and whole body fat percentage (PFAT). Mendelian randomization (MR) was applied to investigate potential directional relationships between GM species and PFAT, as well as possible interactions between microbial species. Porphyromonas asaccharolytica (P. asaccharolytica) was negatively associated (β = -0.181, P = 0.005) with PFAT, while Bacteroides fragilis (B. fragilis) was positively associated (β = 0.239, P = 0.001); these associations were validated in an independent Chinese cohort. MR analysis suggested that P. asaccharolytica may influence PFAT in part through its potential effect on B. fragilis abundance.

CONCLUSION: Gut species P. asaccharolytica and B. fragilis are associated with host body fat percentage and may influence obesity individually or collaboratively. The observed associations provide evidence consistent with a potential directional relationship between these species and human adiposity.}, } @article {pmid42133579, year = {2026}, author = {Lai, X and Gao, Q and Wu, L}, title = {A 56-Year-Old Male Farmer From China With Severe Fever With Thrombocytopenia Syndrome and Pulmonary Aspergillosis: A Case Report and Review of Literature.}, journal = {The American journal of case reports}, volume = {27}, number = {}, pages = {e951798}, pmid = {42133579}, issn = {1941-5923}, mesh = {Humans ; Male ; Middle Aged ; *Severe Fever with Thrombocytopenia Syndrome/diagnosis/complications ; China ; *Pulmonary Aspergillosis/diagnosis/complications ; Farmers ; COVID-19 ; Coinfection ; Aspergillus fumigatus/isolation & purification ; Antifungal Agents/therapeutic use ; }, abstract = {BACKGROUND Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne infectious disease caused by the Dabie bandavirus (commonly known as SFTS virus, or SFTSV). SFTSV-induced immunosuppression during infection renders patients highly susceptible to invasive pulmonary aspergillosis. SFTS-associated pulmonary aspergillosis (SAPA) presents major therapeutic challenges and is linked to drastically worsened outcomes, including high mortality. This report aims to highlight the diagnostic and therapeutic challenges of SAPA and emphasize the value of early diagnosis using metagenomic next-generation sequencing (mNGS). CASE REPORT We report a case of a previously healthy 56-year-old male farmer admitted with SFTS. On hospital day 3, when only mild cough had begun, mNGS of both blood and sputum concurrently detected Aspergillus fumigatus alongside SFTSV. This very early, pre-radiographic diagnosis prompted immediate targeted therapy with voriconazole and favipiravir. Despite this, imaging showed progressive pulmonary infiltrates with cavitation. The clinical course was further complicated by severe acute respiratory syndrome coronavirus 2 co-infection, but the patient recovered with intensive care and was discharged on day 24. A review of 13 literature-reported SAPA cases revealed a mortality rate of 30.77% (4/13). CONCLUSIONS SAPA is a severe, rapidly progressive complication of SFTS with high mortality, typically emerging 1-2 weeks after onset. This case highlights the importance of early diagnosis using rapid methods such as mNGS and the need for timely antifungal intervention to improve patient outcomes. Early antifungal therapy in high-risk patients is crucial.}, } @article {pmid42134120, year = {2026}, author = {Liang, W and Nong, Q and Huang, H and Huang, J and Shao, J and Wang, M and Hong, P and Liu, S and Zhou, C and Zhong, S}, title = {Correlation analysis between microbial diversity in mixed-fermented shrimp juice and the synthesis pathways of characteristic flavor compounds.}, journal = {Food chemistry}, volume = {518}, number = {}, pages = {149574}, doi = {10.1016/j.foodchem.2026.149574}, pmid = {42134120}, issn = {1873-7072}, mesh = {Animals ; Fermentation ; *Flavoring Agents/metabolism/analysis/chemistry ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Microbiota ; *Penaeidae/microbiology ; *Fermented Foods/microbiology/analysis ; Taste ; *Shellfish/microbiology/analysis ; Metagenomics ; Amino Acids/metabolism/analysis ; }, abstract = {This study elucidated flavor formation in fermented shrimp juice using metagenomics and correlation analyses. The amino acid nitrogen content peaked at 0.54 g/100 mL on the 30th day, surpassing that of traditional fish sauce. Phenolic compounds, including guaiacol and phenylacetaldehyde, were identified as key flavor contributors. The microbial community gradually developed into a stable microbiota dominated by nine genera, including Aspergillus, Lactiplantibacillus, and Meyerozyma. Metagenomic analysis demonstrated that this core microbiome governed critical metabolic pathways for carbohydrate, amino acid, and lipid metabolisms, collectively driving the efficient flavor development in the fermented product.}, } @article {pmid42134135, year = {2026}, author = {Huang, Z and Wang, J and Yang, C and Lv, Z and Wang, R}, title = {Integrated transcriptomics and metagenomics analyze the dynamic correlations between cecal mucosal tissue and cecal microbiota in Liangshan Yanying chickens during early postnatal development.}, journal = {Poultry science}, volume = {105}, number = {8}, pages = {106904}, pmid = {42134135}, issn = {1525-3171}, abstract = {Liangshan Yanying chicken, a precious indigenous Chinese breed listed in the Catalog of Livestock and Poultry Genetic Resources in China, is an economic pillar in Liangshan Yi ethnic area and critical for poverty alleviation-to-rural revitalization transition. It has excellent phenotypic traits, high nutritional value, unique flavor, and strong adaptability to 380-4500 m altitudes. However, the co-evolutionary mechanism between its cecal mucosal tissue and gut microbiota (key to intestinal homeostasis and productivity) remains unclear. We systematically investigated their dynamic crosstalk in 1-, 14-, and 28-day-old chickens (n = 10/group) using transcriptomics, metagenomics, bioinformatics, and qPCR. Cecal length increased from 3.77 cm (1 d) to 8.98 cm (28 d), with higher growth rate at 14-28 d. We identified 67 DEGs (34 upregulated immune-related, 33 downregulated development-related) and 16 dynamically changed microbial taxa. Host-microbiota crosstalk was mediated by 52 shared KEGG pathways, with 10 core genes and 13 functional taxa maintaining homeostasis via PI3K-Akt pathway. This study first reveals a "gut microbial homeostasis" model for cecal dynamic homeostasis, providing insights for local poultry intestinal health and breeding.}, } @article {pmid42134217, year = {2026}, author = {Hua, Y and Xue, Y and Li, Z and Zhang, Y and Liu, Q and Liu, L and Tang, J}, title = {Effect of microplastics on arsenic transport in shallow groundwater of coastal transition zones.}, journal = {Water research}, volume = {301}, number = {}, pages = {126097}, doi = {10.1016/j.watres.2026.126097}, pmid = {42134217}, issn = {1879-2448}, mesh = {*Groundwater/chemistry ; *Microplastics/chemistry ; *Arsenic/chemistry ; *Water Pollutants, Chemical/chemistry ; Seawater/chemistry ; Salinity ; Polyesters ; }, abstract = {Coastal transition zones (CTZs) are dynamic zones where seawater intrusion and freshwater discharge interact. Arsenic (As) is a common contaminant in these zones, however its co-transport with increasing abundance microplastics (MPs) remains unclear. In this study, saturated column experiments combined with Hydrus-1D modeling were used to investigate the co-transport of As with polystyrene (PS), polyethylene (PE), and polylactic acid (PLA). Increasing salinity inhibited As transport in the absence of MPs. Under the same salinity, MPs generally increased As breakthrough, following the order PS > PE > PLA. With salinity increased, PS maintained a slight promoting effect on As breakthrough, whereas PE and PLA exhibited reduced breakthrough under high-salinity conditions. Co-transport was most pronounced at an As:MP ratio of 1:2, although PLA showed a non-linear response and lower As mobility at 1:1. Simulated seawater intrusion indicated that ionic-strength fluctuations produced distinct release peaks. MPs further enhanced non-equilibrium As release during flushing. Metagenomic sequencing of samples from the 21-day experiment indicated that MPs altered the microbial communities and increased the relative abundance of several As-related genes (such as AS3MT and arsC), particularly in the PS treatment. These findings clarify the effects of MPs on As transport and support risk assessment for coastal groundwater systems.}, } @article {pmid42134269, year = {2026}, author = {Jiang, J and Liu, R and Shen, Y and Yin, Z and Li, Y}, title = {Mechanistic insights into antimony immobilization by sulfur-metabolizing microorganisms under alternating oxic-anoxic conditions.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142328}, doi = {10.1016/j.jhazmat.2026.142328}, pmid = {42134269}, issn = {1873-3336}, mesh = {*Antimony/metabolism/chemistry ; *Sulfur/metabolism ; Thiosulfates/metabolism/chemistry ; Oxidation-Reduction ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; Anaerobiosis ; }, abstract = {Antimony (Sb), as a toxic heavy metal(loid) element, poses potential risks to the environment and human health. The migration and transformation of Sb in the environment are closely linked to the macronutrient sulfur. However, under alternating oxic-anoxic conditions, the roles of sulfur and sulfur-metabolizing microorganisms in Sb mobility remain unclear. This study systematically investigated the role of exogenous thiosulfate (S2O3[2-]) in Sb(V) immobilization and the underlying mechanisms by integrating microcosm incubations, speciation analyses, and genome-resolved metagenomic analyses. We found that during the oxic-anoxic-oxic transition, Sb(V) was immobilized under anoxic condition and was released under oxic condition. However, thiosulfate amendment significantly inhibited Sb release through facilitating the sulfur-dependent reduction of Sb(V) to Sb(III) and formation of Sb2O3 precipitates. Complete Sb(V) immobilization was achieved within 14 days, concurrently with the oxidation of S2O3[2-] to SO4[2-], indicating thiosulfate is the primary electron donor for microbial reduction of Sb(V). Key microorganisms, including Ramlibacter (Bin.5), Thiomonas (Bin.105), and Unclassified (Bin.112 and Bin.123), which harbor antimonate/arsenate respiratory reductase gene (arrA) and sulfur oxidation pathway (Sox system), drive the sulfur-dependent Sb immobilization, as evidenced by metagenome-assembled genomes (MAGs) results. These findings enhance our understanding of the coupled cycling of Sb and S in alternating oxic-anoxic environments and provide a potential approach for Sb remediation.}, } @article {pmid42134371, year = {2026}, author = {Govender, KN and Street, TL and Sanderson, ND and Leach, L and Morgan, M and Eyre, DW}, title = {Rapid diagnosis of common, undetected, and uncultivable bloodstream infections from positive blood cultures using Oxford Nanopore sequencing: a metagenomic pipeline analysis.}, journal = {The Lancet. Microbe}, volume = {7}, number = {6}, pages = {101333}, doi = {10.1016/j.lanmic.2025.101333}, pmid = {42134371}, issn = {2666-5247}, mesh = {Humans ; *Metagenomics/methods ; *Blood Culture/methods ; Sensitivity and Specificity ; *Nanopore Sequencing/methods ; *Bacteremia/diagnosis/microbiology ; *Bacteria/genetics/isolation & purification/classification/drug effects ; Drug Resistance, Bacterial ; *Sepsis/diagnosis/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {BACKGROUND: Metagenomic sequencing can potentially transform clinical microbiology by enabling rapid pathogen identification and antimicrobial resistance (AMR) prediction in critically ill patients with bloodstream infections. However, the clinical use of metagenomic sequencing has been constrained by its speed, accuracy, and technical feasibility. Our aim was to develop and evaluate a direct-from-positive blood culture workflow using Oxford Nanopore sequencing that overcomes these limitations and delivers rapid, accurate results.

METHODS: In this metagenomic pipeline analysis, 211 positive (130 aerobic and 81 anaerobic) and 62 negative (30 aerobic and 32 anaerobic) randomly selected blood cultures were processed from Oxford University Hospitals for comparing species identification, AMR detection, and time-to-result against standard culture-based diagnostics performed by the hospital's routine microbiology laboratory. Species prediction was performed using Kraken2 with a comprehensive standard database, applying heuristic and random forest classification models. Additionally, we benchmarked AMR classification tools and databases, including ResFinder, CARD, and NCBI AMRFinderPlus.

FINDINGS: Across all samples, our method achieved 97% sensitivity and 94% specificity for species identification compared with that of routine culture and matrix-assisted laser desorption ionisation time-of-flight-based diagnostics; both sensitivity and specificity increased to 100% after adjudication of plausible additional infections. We detected 19 additional infections (13 polymicrobial, five previously unidentifiable, and one in a culture-negative sample) and delivered species identification results within 3 h 20 min (IQR 3 h 7 min-3 h 27 min), approximately 10 h earlier than routine diagnostic methods. For the ten most common clinically relevant pathogens, our method yielded AMR results 20 h earlier than current antimicrobial susceptibility testing, with an overall sensitivity of 88% and specificity of 93%. Performance varied by species. For Staphylococcus aureus, the AMR prediction sensitivity was 100% and specificity was 99%, and for Escherichia coli, the prediction sensitivity was 91% and specificity was 94%.

INTERPRETATION: These findings show that metagenomic sequencing has the potential to rapidly and comprehensively detect pathogens and AMR in bloodstream infections. Integration into clinical practice could help to close diagnostic gaps, reduce empirical antibiotic use, and enable rapid targeted treatment. Nonetheless, improvements in AMR prediction for some species and drugs, along with further multisite validation, are required before clinical implementation.

FUNDING: National Institute for Health Research (NIHR) Oxford Biomedical Research Centre.}, } @article {pmid42134579, year = {2026}, author = {Zhao, C and Hu, Z and Wang, D and Xu, M and Hao, Z and Fu, C and Zhang, J and Zhuang, L}, title = {Metagenomic insights into the enhancement of doxycycline hydrochloride removal in constructed wetlands under moderate lead stress.}, journal = {Bioresource technology}, volume = {455}, number = {}, pages = {134878}, doi = {10.1016/j.biortech.2026.134878}, pmid = {42134579}, issn = {1873-2976}, mesh = {*Doxycycline/isolation & purification ; *Wetlands ; *Lead/toxicity ; Biodegradation, Environmental/drug effects ; *Metagenomics/methods ; *Water Pollutants, Chemical/isolation & purification ; Anti-Bacterial Agents/isolation & purification ; *Stress, Physiological/drug effects ; Water Purification/methods ; }, abstract = {Constructed wetlands (CWs) serve as an important ecological barrier preventing contaminated water from entering surface waters and are frequently exposed to antibiotic-heavy metal co-contamination under real operating conditions. However, how heavy metal stress regulates antibiotic removal through microbial processes in CWs remains poorly understood. Here, CWs subjected to doxycycline hydrochloride (DOX) and lead (Pb) co-contamination were established to elucidate the effects of different Pb stress levels on DOX removal performance and the underlying microbial mechanisms. The results showed that DOX removal was maximized under moderate Pb stress (1 mg/L), reaching a highest removal efficiency of 95.8%. Consistent toxicity responses were observed, with moderate Pb exposure significantly reducing effluent biotoxicity, alleviating plant stress, and improving overall system stability. Mass balance analysis demonstrated that microbial transformation dominated DOX removal, accounting for over 79% of total removal. Metagenomic analyses further revealed the underlying microbial mechanisms, showing that moderate Pb stress reshaped microbial community structure, promoted the enrichment of key functional microorganisms, and increased the abundance of DOX degradation-related functional genes. Representative functional taxa included Sphingomonas, Propionibacterium, and Candidatus Woesearchaeota archaeon. In contrast, high Pb stress (10 mg/L) imposed strong metal toxicity that suppressed the activity and diversity of core functional microorganisms, resulting in reduced DOX degradation capacity accompanied by toxicity accumulation. Collectively, this study clarifies how heavy metal stress regulates antibiotic removal through microbial pathways in CWs, and provide a reference for understanding CWs performance under co-contamination.}, } @article {pmid42134580, year = {2026}, author = {He, J and Xiang, B and Xu, W and Pan, Z}, title = {Comparative study on microbial mechanisms of denitrification failure in AAO process and air-lift internal circulation process under ultra-low C/N ratios.}, journal = {Bioresource technology}, volume = {456}, number = {}, pages = {134881}, doi = {10.1016/j.biortech.2026.134881}, pmid = {42134580}, issn = {1873-2976}, mesh = {*Denitrification ; *Nitrogen/metabolism ; *Carbon/metabolism ; *Bioreactors/microbiology ; Anaerobiosis ; *Bacteria/metabolism/genetics ; Adenosine Triphosphate/metabolism ; *Air ; Nitrates/metabolism ; }, abstract = {Denitrification failure under low-carbon conditions limits biological nitrogen removal. This study compared the recovery performance of a conventional anaerobic-anoxic-oxic (AAO) process and an air-lift internal circulation reactor (AICR) after carbon supplementation, following long-term operation at ultra-low C/N (≈1). Batch experiments showed that the AICR initiated denitrification more rapidly than the AAO. At C/N = 7, the AICR removed 62% of nitrate nitrogen (NO3[-]-N) within 4.5 h, while the AAO removed only 43%. After 10 h, removal efficiencies reached 78% in the AICR and 69% in the AAO. The AICR also had higher adenosine triphosphate (ATP) levels and greater denitrification enzyme activities. Quantitative polymerase chain reaction (qPCR) confirmed that nirS and nosZ copy numbers in the AICR were approximately twice those in the AAO. Metagenomic analysis revealed distinct genomic architectures in the two systems. The AAO relied on a limited number of versatile strains carrying complete denitrification gene clusters. In contrast, the AICR harbored a distributed network where denitrification steps were partitioned among phylogenetically diverse and functionally specialized strains. These differences in community architecture were linked to the distinct flow regimes of the two reactors and corresponded to enhanced functional modularity and metabolic redundancy in the AICR, which contributed to its faster recovery under carbon fluctuations.}, } @article {pmid42134588, year = {2026}, author = {Chauhan, A and Santhiya, D and Sharma, JG}, title = {Microbial consortium driven degradation of mixed microplastics: systematic review on enzymes and omics-based insights.}, journal = {Bioresource technology}, volume = {456}, number = {}, pages = {134885}, doi = {10.1016/j.biortech.2026.134885}, pmid = {42134588}, issn = {1873-2976}, mesh = {Biodegradation, Environmental ; *Enzymes/metabolism ; *Microbial Consortia ; *Microplastics/metabolism ; *Multiomics ; }, abstract = {Microplastics (MPs) are among the most persistent pollutants in the environment. Mixed polymer waste further complicates the remediation due to their toxic additives and heterogenous composition. Conventional remediation methods show limited efficiency, especially for mixed MPs. As a result, biological approaches, particularly microbial consortium mediated degradation is a promising alternative. It is gaining increasing attention due to their cooperative metabolism and ability to degrade multiple polymers simultaneously. This review summarizes recent advances in consortium-based degradation of mixed MPs. It compares existing studies and identifies key challenges in translating laboratory findings to real-world. This review further discusses enzymes involved in the degradation of major polymer constituting mixed MPs. In addition, the role of multi-omics approaches like metagenomics, meta-transcriptomics, metabolomics, and integrated systems biology is also highlighted to explain microbial-metabolite interaction, functional pathways, and degradation mechanisms. Further, this review proposed future research directions focusing on green and scalable technologies. These include green biosensors for real-time monitoring, agro based aerogels and biochar for microbial immobilization, and nano-bubble assisted systems to enhance degradation under economic real-world conditions.}, } @article {pmid42134644, year = {2026}, author = {Liang, M and Wang, X and Li, J and Li, R and Peng, J and Gao, B and An, R and Chen, X and Zhang, J and Liu, X}, title = {Antibiotic-mediated gut microbiota depletion partially attenuates methamphetamine-induced reward and linoleic acid metabolic disturbance.}, journal = {Neuropharmacology}, volume = {296}, number = {}, pages = {111022}, doi = {10.1016/j.neuropharm.2026.111022}, pmid = {42134644}, issn = {1873-7064}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Methamphetamine/administration & dosage/pharmacology ; *Reward ; *Linoleic Acid/metabolism ; *Anti-Bacterial Agents/pharmacology ; Multiomics ; Male ; Animals ; Mice ; Mice, Inbred C57BL ; *Central Nervous System Stimulants/administration & dosage/pharmacology ; *Bacteria/drug effects/metabolism ; *Brain-Gut Axis/drug effects/physiology ; }, abstract = {Methamphetamine (METH) is a highly addictive psychostimulant that possesses potent toxicity to multiple organs. Emerging evidence has suggested associations between gut microbiota dysbiosis and METH-induced rewarding effects. However, the role and underlying mechanisms of gut microbiota in METH addiction remain poorly understood. Using a mouse conditioned place preference (CPP) model combined with multi-omics profiling of gut microbiota and metabolites, we first investigated how METH exposure affects gut microbiota composition. Then, antibiotic (ABX)-mediated gut microbiota depletion was conducted to explore the role of gut microbiota in the METH-induced associative memory of context-reward (METH reward) and metabolic dynamics. Furthermore, associations among gut microbiota, metabolites, and behavioral phenotypes were determined to reveal the potential key microbial taxa and metabolites in METH reward. Finally, the key metabolite was intervened to reveal the role of it in the METH reward. Our results demonstrated that repeated METH administration induced significant alterations in gut microbiota profiles. ABX-mediated microbiota depletion attenuated METH-induced rewarding effects and metabolic perturbations, especially in linoleic acid (LA) metabolism. METH exposure led to an increase in, while gut microbiota depletion rescued the activation of LA metabolism. Correlation analyses consistently demonstrated associations among specific bacterial species, LA metabolites, and CPP scores. Supplementation of LA could facilitate, while inhibition of its oxidative metabolism could attenuate the METH-induced CPP. These findings highlight LA metabolism as a potential mechanistic link between gut microbiota dysbiosis and METH reward. Future gut microbiota-targeted therapeutic interventions, particularly those modulating LA metabolism, may improve the treatment of METH use disorder.}, } @article {pmid41736110, year = {2026}, author = {Pirolo, M and Sherwani, MK and Espinosa-Gongora, C and Eriksen, EØ and Tassinato, C and Alberdi, A and Guardabassi, L}, title = {Faecal microbiome profiling uncovers putative biomarkers for piglets resilient to post-weaning diarrhoea.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41736110}, issn = {2524-4671}, abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a major health and economic concern in intensive pig production. In this study, we hypothesized that the faecal microbiome, sampled before disease onset, could provide early prognostic markers of PWD risk and applied a machine-learning framework to identify biomarkers predictive of piglet susceptibility or resilience to PWD. At two Danish commercial farms experiencing PWD outbreaks, four pens per farm were monitored for 14 days post-weaning, with daily clinical assessments and rectal swabs collected every other day. In a nested case–control design, we profiled 140 samples from 41 piglets that developed PWD and 82 samples from 16 piglets that remained healthy by 16S rRNA sequencing. Additionally, we performed shotgun metagenomics on 56 pre-diarrhoeic samples from susceptible piglets and 47 from resilient piglets. A random-forest classifier with recursive feature elimination identified metagenome-assembled genomes (MAGs) predictive of resilience or susceptibility, trained and cross-validated independently within each farm. Negative binomial zero-inflated mixed (NBZIM) models assessed associations with known PWD risk factors (e.g. birth/weaning weights, weaning age and dam parity). RESULTS: Prior to diarrhoea onset, microbial community structures differed significantly between resilient and susceptible piglets at both farms (PERMANOVA, p < 0.05). Feature-reduced models achieved high accuracy (AUC = 0.94 and 0.82 in Farm A and Farm B, respectively) and identified 10 and 13 MAGs enriched in resilient piglets, and one and two MAGs enriched in susceptible piglets from the two farms, respectively. All MAGs were farm-specific, highlighting the multifactorial aetiology of PWD. NBZIM models indicated that most predictive MAGs were independent of established PWD risk factors. Temporally, these MAGs peaked in relative abundance early after weaning (day 4 in Farm A; day 0 in Farm B). In the farm with unclear aetiology, functional analysis showed that susceptibility-associated MAGs were depleted for arginine/ornithine and vitamin (cobalamin, thiamine) biosynthesis and lactate production traits, suggesting metabolic dysbiosis. CONCLUSIONS: Our findings indicate that pre-diarrhoeic faecal microbiome signatures predict PWD risk and provide a foundation for early prognostic tools and targeted interventions, including probiotic development, to mitigate PWD and reduce reliance on antimicrobials in pig production.}, } @article {pmid41736165, year = {2026}, author = {Wei, C and Chen, Z and Wang, Y and Huang, L and Chen, C}, title = {Large-scale genomic analysis of jumbo phages: coevolution, genome architecture, and host interaction mechanisms.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41736165}, issn = {2524-4671}, support = {32272831//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Jumbo phages are phages with comparatively large genome sizes. Jumbo phages have been identified in various microbial communities. However, their diversity, genome structure, potential function, and their interactions with hosts and other phages are largely unknown due to insufficient genomic data. RESULTS: We collected 59,652,008 putative viral genomes from seven habitats by using 38 public metagenome datasets, an integrated public viral genome database (IGN), and pig gut viral genome databases. We obtained 10,754 jumbo phage genomes with sizes ranging from 200 to 831 kb. Most (94.64%) of these jumbo phage genomes were classified into Caudoviricetes, and the results have expanded the known diversity of Caudoviricetes. We found 2,389 species-like operational genome clusters that contained 3,727 (34.69%) genomes without any known viral genomes in the IGN, suggesting potential novel species-like genomes. Genome analysis suggested the potential coevolution of jumbo phages with habitat types and highlighted the utilization of alternative genetic codes and their corresponding suppressor tRNAs for recoding stop codons. CRISPR spacer analysis revealed potential bacterial or archaeal hosts of jumbo phages and uncovered competitive networks among jumbo phages. Habitat type had an important effect on the variation in phage auxiliary metabolic genes. CONCLUSIONS: This study provides an important resource and new knowledge for future studies on the interaction between jumbo phages and their bacterial or archaeal hosts.}, } @article {pmid41736367, year = {2026}, author = {Keum, HL and Sul, WJ and Kim, S and Chung, IY and Koh, A and Kim, HS}, title = {Preliminary characterization of the skin microbiota in basal cell carcinoma: An exploratory pilot study in Korean patients.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {64}, number = {2}, pages = {e2511012}, doi = {10.71150/jm.2511012}, pmid = {41736367}, issn = {1976-3794}, support = {//Incheon St. Mary's Hospital/ ; //Catholic University of Korea/ ; //National Research Foundation of Korea/ ; 2023R1A2C1007759//Ministry of Science and ICT/ ; //Korea Health Industry Development Institute/ ; RS-2023-KH-136575//Ministry of Health and Welfare/ ; RS-2025-02217860//Ministry of Health and Welfare/ ; }, mesh = {Humans ; *Basal Cell Carcinoma/microbiology/pathology ; *Skin Microbiome ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; *Skin Neoplasms/microbiology/pathology ; Republic of Korea ; Male ; Female ; Middle Aged ; *Skin/microbiology/pathology ; Aged ; *Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; *Microbiota ; Biopsy ; }, abstract = {Basal cell carcinoma (BCC) is the most common form of skin cancer, with ultraviolet radiation recognized as the primary environmental driver; however, the potential contribution of alterations in the skin microbiota remains incompletely understood, particularly in Asian populations. This exploratory pilot study describes bacterial community patterns in BCC lesions compared with contralateral clinically normal skin in 20 Korean patients. Lesional and contralateral samples were obtained using paired skin swabs and punch biopsies and analyzed by full-length 16S rRNA gene sequencing, with targeted quantitative PCR (qPCR) of the roxP antioxidant gene of Cutibacterium acnes. Given the low-biomass nature of skin samples and the exploratory design, analyses focused on descriptive trends rather than confirmatory inference. Across available samples, C. acnes was the dominant taxon, with a trend toward lower relative abundance in BCC lesions, particularly in biopsy-derived datasets. Microbial evenness appeared higher in lesions than controls. Predictive functional profiling suggested reduced representation of vitamin B6 metabolism pathways in lesions, while qPCR analysis of swab samples showed a trend toward lower roxP/16S rRNA ratios in BCC-associated microbiota. These findings should be interpreted cautiously in light of methodological constraints, including sample heterogeneity, lidocaine exposure prior to biopsy, absence of sequencing-based negative controls, and reliance on predictive functional inference. Overall, this pilot study highlights potential differences in skin bacterial community structure between BCC lesions and contralateral skin in a Korean cohort. Larger, methodologically optimized studies incorporating metagenomic and functional validation will be required to determine whether these microbiota shifts contribute to, or result from, BCC-associated changes in the cutaneous environment.}, } @article {pmid41736423, year = {2026}, author = {Dongqi, LI and Tongxing, W and Zixuan, W and Yihui, Y and Jie, LI and Jiaojiao, GU and Cuiru, LI and Aili, W and Lingling, S and Yongjie, M and Zeyu, Z and Yunlong, H and Huailin, G}, title = {Improving glucose tolerance in obese rats: the role of Jinlida granules () in gut microbiota modulation.}, journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan}, volume = {46}, number = {1}, pages = {62-72}, pmid = {41736423}, issn = {2589-451X}, support = {2017YFC700500//National Key Research and Development Program 'Modernization Research of Traditional Chinese Medicine': Cardiovascular Event Chain (Metabolic Syndrome, Atherosclerosis, Myocardial Infarction, Arrhythmia, Heart Failure)/ ; 223777155D//Key R&D Program of Hebei: Traditional Chinese Medicine Innovation Project: Clinical Research on the Treatment of Diabetes Foot with Collateral Drugs and the Mechanism of Its Influence on Collateral Vessel Reconstruction/ ; 2023179//Scientific Research Project of Hebei Provincial Administration of Traditional Chinese Medicine: Clinical Study on Jinlida Granules in Treating Intestinal Dysfunction of diabetes and Its Effect on Short Chain Fatty Acids/ ; 2018200//Scientific Research Project of Hebei Provincial Administration of Traditional Chinese Medicine: Clinical Study on Tongluo Therapy for Diabetes Foot and Its Influence on Microcirculation/ ; }, mesh = {Animals ; Rats ; *Drugs, Chinese Herbal/administration & dosage ; *Obesity/metabolism/drug therapy/microbiology/genetics ; Rats, Sprague-Dawley ; Male ; *Gastrointestinal Microbiome/drug effects ; Humans ; Diet, High-Fat/adverse effects ; Glucose Tolerance Test ; }, abstract = {OBJECTIVE: To investigate the effects of Jinlida granules (, JLD) on body weight, glucose tolerance, intestinal inflammation and barrier function in high-fat diet (HFD)-induced obese rats and explore the regulation of the gut microbiota as a potential treatment mechanism.

METHODS: Sprague-Dawley rats were divided into control, HFD, low-dose JLD (L-JLD), high-dose JLD (H-JLD), and sitagliptin groups. The rats, with the exception of those in the control group, were fed a HFD to establish an obesity model while simultaneously receiving 0.5% carboxymethyl cellulose, L-JLD, H-JLD or sitagliptin for 25 weeks. We assessed body weight, conducted oral glucose tolerance tests, and analysed faecal samples using metagenomic sequencing. Haematoxylin-eosin (HE), Masson and immunohistochemical (IHC) staining were employed to evaluate histological changes in the colon tissue. Immunofluorescence (IF) staining was used to measure the expression levels of Zonula occludens-1 (ZO-1) and Claudin-1 in colon tissue. The colon tissue was also subjected to transcriptomic evaluation.

RESULTS: JLD treatment significantly reduced body weight and enhanced glucose tolerance in obese rats. It alleviated colonic tissue damage, decreased collagen deposition, inhibited macrophage infiltration, and increased the expression of the tight junction proteins ZO-1 and Claudin-1. Metagenomic analysis revealed JLD-induced shifts in the gut microbiota composition (increasing the abundance of Turicibacter, Faecalibaculum, Coriobacteriaceae and Lactobacillus reuteri), enriching beneficial bacteria and metabolic pathways (increasing the biosynthesis of various secondary metabolites, ascorbate and aldarate metabolism, oxidative phosphorylation, C5-branched dibasic acid metabolism and beta-alanine metabolism). Transcriptomic analysis revealed downregulation of inflammatory and immune pathways (inhibition of the tumour necrosis factor signalling pathway, advanced glycation end products-receptor for advanced glycation end products signalling pathway, toll-like receptor signalling pathway, and interleukin-17 signalling pathway), suggesting a comprehensive modulatory effect of JLD on intestinal health and metabolic function.

CONCLUSIONS: JLD granules effectively improve glucose tolerance and ameliorate obesity-related intestinal dysfunctions in HFD-induced obese rats. These benefits are likely mediated through the modulation of the gut microbiota, the suppression of intestinal inflammation, the enhancement of barrier function, and the attenuation of proinflammatory pathways. Our findings offer novel insights into the therapeutic potential of JLD, emphasizing its role in integrating gut microbiota management into the treatment of metabolic disorders.}, } @article {pmid41736479, year = {2026}, author = {Kong, S and Ning, Z and Chen, Z and Zhang, M}, title = {Broad-Spectrum Co-Metabolic Substrates Enhance the Bioremediation of 1,2,3-Trichloropropane in Groundwater by a Non-Dehalogenimonas Consortium.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {98}, number = {3}, pages = {e70318}, doi = {10.1002/wer.70318}, pmid = {41736479}, issn = {1554-7531}, support = {252S7601D//Hebei Province Science and Technology Support Program/ ; 242S4201Z//Hebei Province Science and Technology Support Program/ ; }, mesh = {*Groundwater/chemistry/microbiology ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Propane/analogs & derivatives/metabolism ; *Microbial Consortia ; }, abstract = {1,2,3-Trichloropropane (TCP), a highly mobile chemical byproduct, has severely exacerbated groundwater environment deterioration. Due to the lack of effective natural attenuation pathways, TCP typically exhibits a fate of persistent retention within aquifers. To address this challenge, instead of relying on limited specific strains, this study focused on exploring broad-spectrum co-metabolic substrates to enhance the degradation efficiency of a non-Dehalogenimonas synergistic consortium optimized through long-term directed domestication. Results indicated that the average degradation rate of the domesticated consortium increased to 19.06 μmol L[-1] d[-1], achieving complete removal within 3.5 days, thereby effectively altering the environmental persistence of TCP. Microbial community and metagenomic analyses revealed that this transformation process was driven by a synergistic alliance comprising Fusibacter, Desulfovibrio, Nitratidesulfovibrio, and Parabacteroides, realized through a coupled metabolic module of "hydrogen production, cofactor synthesis, and reductive dechlorination". Crucially, the consortium demonstrated exceptional broad-spectrum adaptability to various co-metabolic substrates, where sodium acetate and lactate significantly enhanced the degradation efficiency. This study confirms that utilizing suitable co-metabolic substrates can effectively activate the non-Dehalogenimonas consortium to regulate the migration and fate of pollutants in complex groundwater environments, offering an efficient bioremediation strategy to arrest groundwater contamination.}, } @article {pmid41736790, year = {2026}, author = {Yu, S and Niu, H and Zhang, Y and Yu, L and Zhang, Q and Liu, X and Sang, Y and Wang, R and Zhang, M}, title = {Characterization of gut microbiota in patients with diabetic kidney disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1713005}, pmid = {41736790}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetic Nephropathies/microbiology ; Female ; Feces/microbiology ; Male ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; Metagenomics ; Aged ; Adult ; Disease Progression ; }, abstract = {INTRODUCTION: Diabetic kidney disease (DKD) is a major complication of diabetes mellitus (DM). Although dysbiosis of the gut microbiota in DKD has been reported, the specific microbial species associated with disease progression from DM to DKD remain insufficiently defined.

METHODS: We conducted shotgun metagenomic sequencing on fecal samples from 55 healthy participants, 47 patients with DM, and 38 patients with DKD. Gut microbiota diversity, composition, and functional pathways were compared across groups; correlations with glycemic and renal indices were evaluated.

RESULTS: Overall alpha-diversity showed no significantly difference between DKD and healthy controls; however, the simpson's index was higher in DKD than in DM (p < 0.05). There was a difference in beta-diversity between DKD and the healthy control (p = 0.002), but no significant difference was observed between the DKD and DM group. Bacteria significantly enriched in DM/DKD include Mediterraneibacter, Enterocloster, Shigella, Limosilactobacillus, and Thomasclavelia, which showed positive correlations with glycemic indicators (HbA1c, fasting blood glucose) and renal indicators (BUN, UACR). In contrast, health-enriched bacteria, Phocaeicola, Faecalibacterium, Lachnospira, Agathobacter, Odoribacter, and Paraprevotella were negatively correlated with these parameters. Functional analysis revealed that compared to the DM group, the DKD group enriched pathways related to aromatic amino acid biosynthesis (phenylalanine, tyrosine, tryptophan), biofilm formation, and lipopolysaccharide biosynthesis. Gut microbial shifts along the DM-DKD correlates with adverse glycemic and renal phenotypes, as well as functional characteristics associated with inflammation and barrier injury. These findings suggest that microbially driven metabolic and structural pathways represent potential targets for mitigating the progression of DKD.

CONCLUSION: This study elucidates the distinct characteristics of the gut microbiota in DKD patients and highlights potential microbial markers involved in the progression from DM to DKD.}, } @article {pmid41736795, year = {2026}, author = {Pan, H and Wu, L and Sheng, S}, title = {Metagenomic profiling of the gut microbiome to predict orthopedic healing responses in postmenopausal women.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1771312}, pmid = {41736795}, issn = {2235-2988}, mesh = {Humans ; Female ; *Postmenopause ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Aged ; Feces/microbiology ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; Biomarkers ; *Wound Healing ; Osteoarthritis/surgery ; }, abstract = {INTRODUCTION: Recovery following orthopedic procedures in postmenopausal women is often prolonged and more complex due to age-related physiological changes, including reduced bone mineral density, altered hormonal profiles, impaired immune regulation, and delayed tissue regeneration. Conventional recovery assessment methods such as radiographic imaging, range-of-motion evaluation, and functional mobility tests provide valuable clinical information but offer limited insight into the underlying biological processes that influence healing. Emerging evidence indicates that the gut microbiome plays a critical role in regulating inflammation, immune homeostasis, and tissue repair, highlighting its potential as a predictive biomarker for post-surgical recovery outcomes. This study investigated the association between gut microbiome dynamics and recovery following orthopedic surgery in postmenopausal women.

METHODS: Stool samples were collected from preoperative (baseline) and 6 weeks postoperative time points. Microbial profiling was performed using 16S rRNA gene sequencing on the Illumina MiSeq platform, and data processing and taxonomic analysis were conducted using QIIME2. Microbial diversity was evaluated through alpha diversity metrics to assess community richness and beta diversity to characterize compositional differences over time. Clinical recovery was assessed using radiographic imaging, the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), and the Timed Up and Go (TUG) functional mobility test. To evaluate the predictive potential of the gut microbiome, a random forest machine learning model was trained using microbial abundance data and correlated with clinical recovery outcomes.

RESULTS: The results revealed significant temporal shifts in gut microbial composition during the recovery period. Bacterial diversity varied across time points, with Firmicutes and Bacteroidetes identified as the dominant phyla. Increased abundance of these taxa was strongly associated with improved functional outcomes and faster recovery. In contrast, elevated levels of Proteobacteria and Escherichia were linked to delayed healing and poorer clinical performance. The predictive model achieved an accuracy of 85%, demonstrating the robustness of gut microbiome signatures as indicators of postoperative recovery.

DISCUSSION: Overall, this study highlights the significant influence of gut microbiome composition on orthopedic recovery in postmenopausal women. Identification of microbial biomarkers associated with favorable healing outcomes provides a foundation for developing microbiome-guided, personalized therapeutic strategies to enhance postoperative recovery and improve long-term musculoskeletal health.}, } @article {pmid41736799, year = {2026}, author = {Zhao, Q and Wang, D and Lin, H and Zhou, T and Zhang, J and Shang, J and Cai, D and Sun, Y and Hu, Z and Zhang, J}, title = {Unraveling the activity of phage-carrying antibiotic resistance genes in constructed wetlands.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1764958}, pmid = {41736799}, issn = {2235-2988}, mesh = {*Wetlands ; *Bacteriophages/genetics ; Geologic Sediments/microbiology ; *Bacteria/genetics/drug effects/virology ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Gene Expression Profiling ; Water Microbiology ; Metagenome ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Gene Transfer, Horizontal ; Plants/microbiology ; }, abstract = {Antimicrobial resistance (AMR) is a global public health challenge, and risk assessments based solely on gene abundance often underestimate the immediacy of resistance dissemination. This study presented a carrier-centric framework integrating metagenomic and metatranscriptomic profiling with deep learning-based identification of mobile genetic elements, applied to a full-scale constructed wetland (CW). CW overall reduced ARG burdens, with genomic abundance in plants, sediments, and water decreasing by 98.5%, 80.9%, and 88.8%, respectively. However, transcriptional activity showed an opposite trend, with sediments exhibiting the highest ARG expression, highlighting their pivotal role in the persistence and dissemination of resistance. In sediments, phage-mediated expression increased sharply from 4.0% to 92.5%, exceeding plasmid-associated levels by ~276-fold, revealing a low-abundance but high-activity residual risk pattern. Furthermore, 16 of the 310 recovered nonredundant MAGs were identified as phage hosts, 11 of which were potentially pathogenic, antibiotic-resistant bacteria (PARB) and were more active in sediments than in water or plants. These findings indicate that transduction within high-density, biofilm-associated niches constitutes a key terminal risk source. In addition, sediment acts as a high-risk reservoir where redox and ionic gradients, together with residual lomefloxacin and other antibiotics, enhance phage infectious activity and the accumulation of ARGs. Through cross-compartment transmission along the sediment-water interface, these phage-associated and PARB populations continuously seed the overlying water. It is recommended that ARG risk assessment shift from static abundance to an activity-aware, carrier- and host-resolved approach, prioritizing sediment-targeted transcript monitoring and phage transduction early warning to support risk mitigation in CW.}, } @article {pmid41736897, year = {2025}, author = {Badillo-Pazmay, GV and Fortunato, C and Cianfruglia, L and Novazzi, F and Spezia, PG and Rosa, L and Limongi, D and Prezioso, C and D'Argenio, V and Scudiero, O and Bevilacqua, L and Malavolta, M and Russo, P and Maggi, F and Balietti, M and Giacconi, R}, title = {The gut and circulating virome: emerging players in aging and longevity.}, journal = {Frontiers in aging}, volume = {6}, number = {}, pages = {1731621}, pmid = {41736897}, issn = {2673-6217}, abstract = {A growing body of evidence indicates that the human virome, comprising both the gut and circulating viral communities, plays a critical role in shaping host physiology across the lifespan. In the context of aging, this complex viral ecosystem is increasingly recognized as a key modulator of immune function, inflammation, and metabolic balance, with direct implications for healthspan and longevity. While much attention has traditionally focused on bacterial components of the microbiota, recent advances in metagenomics have uncovered age-related shifts in the composition and function of the virome, including expansion of specific bacteriophage families, reactivation of latent viruses, and the persistence of commensal viral pathobionts. These changes are tightly linked to immunosenescence, chronic inflammation, and neurodegeneration, hallmarks of unhealthy aging. Notably, centenarians appear to harbor a unique virome signature marked by increased viral diversity, enhanced lytic activity, and the enrichment of phage-encoded metabolic functions, suggesting a potential protective role in extreme longevity. Despite these insights, significant challenges remain in virome profiling, including technical biases, database limitations, and the vast proportion of taxonomically unassigned sequences known as "viral dark matter". This review highlights emerging data on the aging virome, underscores its relevance within the Geroscience framework, and discusses current barriers and future directions for translating virome research into clinical aging studies.}, } @article {pmid41736978, year = {2026}, author = {Ling, Y and Yang, DX and Xia, YN and Bao, CP and Zhang, F and Xu, XJ and Sun, BH}, title = {Effects of Age, Sex, and Social Network on Antibiotic Resistance Genes in the Gut Microbiome of Tibetan Macaques (Macaca thibetana).}, journal = {Ecology and evolution}, volume = {16}, number = {2}, pages = {e73137}, pmid = {41736978}, issn = {2045-7758}, abstract = {The transmission and dissemination of antibiotic resistance genes (ARGs) have increasingly drawn global attention. However, our knowledge of the antibiotic resistance gene pool in wild primates' gut microbiomes and its influencing factors remains limited. In this study, we focus on a social group of Tibetan macaques (Macaca thibetana) in Huangshan, utilizing behavioral and metagenomic data to investigate the effects of host sex, age, and social network on the ARG profiles of the gut microbiome. Our results demonstrate a high diversity of ARGs in the gut microbiota of Tibetan macaques, with multidrug, glycopeptide, and peptide resistance genes being the most prevalent. Although host age, sex, and social networks did not significantly affect the overall diversity of ARGs, these factors were significantly correlated with the relative abundance of several highly abundant ARG types, including gryB, rpoB, macB, novA, efrA, patB, Staphylococcus aureus mupA conferring mupirocin resistance, RanA, and cdeA. Further analysis revealed extensive interactions between gut bacteria and ARGs, with age emerging as a potentially key factor in this covariation process. These findings provide new insights into the formation and transmission mechanisms of antibiotic resistance in the gut microbiome of wildlife, particularly in social primates.}, } @article {pmid41737133, year = {2025}, author = {Wu, R and Zu, W and Wei, L and Wu, R and Su, S and A, R and A, T and E, N and Li, H and Hu, R and Li, L}, title = {Metagenomics and metabolomics integrated to explore the protective mechanisms of Mongolian medicine Zadi-5 in myocardial ischemic model rats.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1677322}, pmid = {41737133}, issn = {1664-302X}, abstract = {BACKGROUND: Myocardial ischemia (MI) is a pathological state of abnormal energy metabolism caused by insufficient blood and oxygen supply to the coronary arteries. The "gut-heart axis" theory plays an important role in myocardial ischemia occurrence, mechanism, prevention, and cure. Traditional Mongolian medicine posits that "internal diseases originate from gastrointestinal dysfunction," linking the intestine, a key component of the digestive system, to physiological and pathological changes in the heart. Furthermore, the traditional Mongolian clinical treatment of cardiovascular diseases includes guidelines for digestive system function corresponding to the modern concept of the gut-heart axis. Accordingly, Zadi-5, a traditional Mongolian medicine, has been used for over 200 years to prevent and treat cardiovascular diseases. However, the mechanism by which the gut microbiota and metabolism are regulated to protect an ischemic heart is unclear.

AIM: This study aimed to investigate the potential mechanism by which Zadi-5, through its interaction with the gut microbiota and metabolic pathways, alleviates myocardial ischemic injury induced by a high-fat diet and isoproterenol (ISO).

METHODS: Sprague-Dawley rats were divided into control, model, Zadi-5 high-dose, and Zadi-5 low-dose groups. All groups, except the control group, were fed a high-fat diet for 4 weeks. Subsequently, all animals received subcutaneous injections of 4 mg/kg ISO daily for 3 days to induce a myocardial infarction (MI) rat model. The pharmacological effects of Zadi-5 on MI were assessed using electrocardiography (ECG), hematoxylin-eosin (HE) staining of myocardial tissue, and serum levels of cardiac troponin T (cTn-T), creatine kinase-MB (CK-MB), lactate dehydrogenase (LDH), total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C). Furthermore, fecal metagenomics and serum untargeted metabolomics were performed to investigate the protective mechanisms of Zadi-5 against MI. Finally, MetOrigin was used to analyze the correlation between key metabolic pathways and the gut microbiota to elucidate the mechanism by which Zadi-5 protects against myocardial ischemia.

RESULTS: First, the MI rat model was successfully established by ISO, and Zadi-5 significantly preserved MI injury, according to ECG recording, index of TC, TG, LDL-C, cTn-T, LDH, CK-MB, and histopathology results. Second, Zadi-5 regulates gut microbiota diversity and abundance, as well as glutamine and glutamate metabolism. The mechanism is related to the gut microbiota phyla Actinobacteria, Firmicutes, Bacteroidetes, and Proteobacteroidetes, and classes Gammaproteobacteria, Betaproteobacteria, Bacteroidia, Actinomycetes, Clostridia, and Bacilli. Zadi-5 also regulates L-glutamic acid, L-glutamine, ornithine, and oxaceprol metabolisms.

CONCLUSION: Zadi-5 exerts cardioprotective effects in MI rats by improving dysbiosis of the gut microbiota and regulating the glutamate-glutamine metabolism pathway. This may represent only one of the complicated protective mechanisms of Zadi-5 against MI. The cardioprotective mechanisms of Zadi-5 will be explored at the molecular and cellular levels.}, } @article {pmid41737867, year = {2026}, author = {Niu, X and Yu, Q and Cao, L and Shen, W and Tian, J}, title = {Challenges in Diagnosis and Treatment of HIV-Negative Host Pulmonary Talaromyces marneffei in Non-Endemic Areas: A Case Report with a History of Pulmonary Tuberculosis.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {582375}, pmid = {41737867}, issn = {1178-6973}, abstract = {Talaromyces marneffei is an important opportunistic fungal pathogen closely related to acquired immunodeficiency syndrome (AIDS), and its infection is relatively rare in human immunodeficiency virus (HIV)-negative populations. Although HIV-related immunosuppression remains the main risk factor, the history of treated tuberculosis and subsequent structural lung damage may constitute an underrecognized predisposing condition in non-epidemic areas, especially in elderly patients. This report described a 69-year-old HIV-negative male pulmonary infection case from a non-endemic area of T. marneffei, with a history of treated pulmonary tuberculosis and residual fibrotic lesions on imaging. The patient complained of chest tightness and cough for one month and fever (temperature 38.0-38.5°C) for a week upon admission. The chest computed tomography (CT) scan observed patchy consolidation and multiple cavities in the upper lobes of both lungs, accompanied by pulmonary texture disorder and pleural adhesions and thickening. The imaging findings were difficult to distinguish from active pulmonary tuberculosis. The diagnosis of T. marneffei infection was confirmed through sputum culture, bronchoscopy sampling culture, matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), and metagenomics next-generation sequencing (mNGS). After diagnosis, the patient was given oral voriconazole 200 mg every 12 hours, resulting in gastrointestinal intolerance. Subsequently, the dosage was adjusted to 100 mg every 12 hours, and the gastrointestinal symptoms improved significantly. The patient was eventually discharged but subsequently lost to follow-up. The case emphasizes that among HIV-negative individuals in non-epidemic areas of T. marneffei, for patients with unexplained pneumonia, especially those who have a history of tuberculosis and other potential immunological impairments, the differential diagnosis approach should be broadened and modern diagnostic techniques should be actively applied. It also highlights the importance of addressing drug tolerance issues and implementing long-term follow-up management in clinical treatment.}, } @article {pmid41737956, year = {2026}, author = {Zhang, B and Wang, X and Qi, X and Zhang, L and Pei, N and Tao, Z and Liu, J}, title = {Bacterial co-detection is associated with higher multidrug-resistant Pseudomonas aeruginosa risk: insights from the MIMIC-IV database and metagenomic analysis.}, journal = {JAC-antimicrobial resistance}, volume = {8}, number = {1}, pages = {dlag023}, pmid = {41737956}, issn = {2632-1823}, abstract = {BACKGROUND: Pseudomonas aeruginosa (PA) poses a significant clinical challenge due to its high antibiotic resistance. While microbial communities aid in spreading antibiotic resistance genes (ARGs), their role in the emergence of multidrug-resistant Pseudomonas aeruginosa (MDR-PA) is unclear. This study examines the impact of bacterial interactions on MDR-PA prevalence and underlying mechanisms.

METHODS: This retrospective cohort study analysed 2965 PA-positive culture patients from the Medical Information Mart for Intensive Care IV (MIMIC-IV version 3.1) database, stratified by bacterial co-detection with PA. Propensity score matching (PSM) and logistic regression were used. Metagenomic sequencing was performed on deep endotracheal secretions from 19 PA ventilator-associated pneumonia (VAP) patients, constructing an ARGs dissemination network within the lower respiratory tract (LRT) microbiota. Comparative analysis of LRT microbiota and ARGs profiles was conducted between PA-VAP survivors and non-survivors.

RESULTS: Patients with bacterial co-detection with PA had a significantly higher MDR-PA prevalence and mortality than those with PA-only detection. Logistic regression identified bacterial co-detection as an independent risk factor for MDR-PA (adjusted OR 2.14; 95% CI 1.64-2.83, P < 0.001) and subsequent mortality (adjusted OR 1.67; 95% CI 1.30-2.14, P < 0.001). Metagenomic analysis of 19 PA-VAP cases suggested that horizontal gene transfer (HGT) may facilitate inter-species dissemination of ARGs (e.g. eptB, smeE, ANT(4')-Ia) between PA and other co-colonizing LRT microbiota. Distinct ARG profiles were observed between PA-VAP survivors and non-survivors.

CONCLUSION: Our findings indicate that bacterial co-detection with PA elevates the risk of MDR-PA and worsens clinical outcomes, potentially driven by HGT-mediated ARG exchange within the host microbiota.}, } @article {pmid41738431, year = {2026}, author = {Khade, K and Dadachanji, R and Bhonde, G and Patil, A and Bhor, VM and Mukherjee, S}, title = {Gut microbiota dysbiosis in Indian women with PCOS may be linked to metabolic and hormonal dysregulation.}, journal = {Future microbiology}, volume = {21}, number = {2}, pages = {153-165}, pmid = {41738431}, issn = {1746-0921}, mesh = {Humans ; Female ; *Polycystic Ovary Syndrome/microbiology/metabolism ; *Dysbiosis/microbiology/metabolism ; India ; *Gastrointestinal Microbiome/genetics ; Haptoglobins/analysis ; RNA, Ribosomal, 16S/genetics ; Adult ; Protein Precursors ; Hyperandrogenism/microbiology ; Feces/microbiology/chemistry ; Fatty Acids, Volatile/analysis/metabolism ; Cholera Toxin/analysis ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Young Adult ; Lipopolysaccharides/analysis ; }, abstract = {AIM: Polycystic ovary syndrome (PCOS) is a common gynecological and cardiometabolic disorder in reproductive-aged women. Recently gut microbiota alterations have been identified as key contributors to PCOS pathophysiology, but it remains understudied in Indian population.

METHODS: 16S rRNA gene amplicon sequencing using Illumina-MiSeq platform was conducted in 57 PCOS and 30 control women. Diversity indices were assessed and significantly altered taxa were identified by differential abundance tests (Wilcoxon-rank-sum test, ANCOMBC2 and LEfSe) in total and hyperandrogenism-based PCOS subgroups. We quantified levels of short-chain fatty acids (SCFAs) and gut barrier integrity marker, zonulin and LPS by HPLC and ELISA respectively.

RESULTS: Our study showed significantly altered beta diversity between PCOS and control groups, driven by hyperandrogenism. PCOS women demonstrate enrichment of Ligilactobacillus species, not previously reported to our knowledge, along with Collinsella species and markedly reduced SCFA-producing taxa, Oscillospiraceae. Additionally, levels of zonulin and fecal butyric acid, a potent SCFA, were significantly altered in PCOS women. Significantly altered taxa correlated with gonadotropin and SHBG levels and were involved in important metabolic pathways in total and PCOS subgroups.

CONCLUSION: Our study offers new insights into the mapping of gut microbiota in PCOS women from western India and implicates hyperandrogenism in driving dysbiosis.}, } @article {pmid41738442, year = {2026}, author = {Ma, X and Johnson, KB and Li, C}, title = {Copepod Grazing and Prokaryotic Decomposition Amplify the Effect of Diatom-Dinoflagellate Regime Change on Biological Carbon Pump Efficiency.}, journal = {Environmental science & technology}, volume = {60}, number = {9}, pages = {7092-7110}, doi = {10.1021/acs.est.5c11967}, pmid = {41738442}, issn = {1520-5851}, mesh = {Animals ; *Copepoda ; *Diatoms ; *Dinoflagellida ; Carbon ; Phytoplankton ; }, abstract = {Copepod fecal pellets (FPs) are an important but highly variable component of the global Biological Carbon Pump (BCP). This study decoupled and quantified how copepod grazing and prokaryotic activities affect BCP efficiency under different phytoplankton dietary regimes. With a diet of diatoms, copepod FP production rates double, FP sinking rates triple, and FP decomposition rates are significantly lower relative to those with dinoflagellate diets. When dinoflagellates are the primary producers, inefficient grazing and enhanced prokaryotic activity synergistically decrease the efficiency of FP exports to the deep ocean. This finding confirms previous observations. Opportunistic particle-attached (PA) prokaryotes are crucial for FP decomposition. Metagenomic analyses revealed that CAZymes and lysosomal enzyme abundances highly correlated with FP decomposition rates, representing important bioindicators of FP decomposition. These functional enzymes targeting phytoplankton- and copepod-intestine-derived macromolecules from the PA prokaryotic communities were key to FP decomposition. Genomic properties of the Planctomycetota revealed that strong motile ability, detoxification systems, and macromolecule degradation enzymes enabled the success of these opportunistic PA prokaryotes. Elevated temperatures amplified FP decomposition rates by enhancing enzyme abundances and especially accelerated the decomposition of FPs composed of dinoflagellates. This reduced BCP efficiency, as rapidly recycled organic materials remain in surface waters. Our findings highlight the synergistic biological activities amplifying the effects of phytoplankton composition changes on BCP efficiency. This underscores the importance of considering grazing regimes in combination with microbial dynamics in assessing ocean carbon cycling.}, } @article {pmid41738467, year = {2026}, author = {Goldsworthy, A and Olsen, M and Shiratuddin, MF and McKirdy, S and Alghafri, R and Senok, A and Alfalasi, H and Wong, KW and Tajouri, L}, title = {A Pilot Metagenomic Study Demonstrating Virtual Reality Head Mounted Displays Utilized in Medical Education Are Reservoirs of Viable Pathogenic Microbes.}, journal = {MicrobiologyOpen}, volume = {15}, number = {2}, pages = {e70255}, pmid = {41738467}, issn = {2045-8827}, support = {//Australian Government Research Training Program Scholarship/ ; }, mesh = {*Metagenomics ; Humans ; *Virtual Reality ; Pilot Projects ; *Education, Medical/methods ; *Bacteria/isolation & purification/genetics/classification ; Drug Resistance, Bacterial ; Klebsiella/isolation & purification/genetics ; Staphylococcus aureus/isolation & purification/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Virtual reality (VR) devices are increasingly being utilized within operating theaters and intensive care units where appropriate sanitation is vital to ensure that patients do not unnecessarily acquire hospital-associated infections. The morphology of VR devices in conjunction with the variety of materials and internal components provides challenges to their repurposing. This study aimed to evaluate the microorganisms remaining on VR headsets following sanitation by laboratory staff in a medical education anatomy teaching facility. The external components and internal facial interface were swabbed and separately cultured on four AGAR plates (Horse Blood, Nutrient, bile Esculin, and Mannitol Salt). Colonies were counted, sampled, pooled and subsequently processed for shotgun metagenomic sequencing. A higher number of colonies were present on surfaces closest to the eyes and facial interface compared to the external components. Metagenomic analysis identified 27 pathogenic bacteria including 4 "ESKAPE" pathogens (Enterobacter sp., Staphylococcus aureus, Klebsiella spp. and, Escherichia coli) and numerous organisms associated with ocular infections. A broad range of antimicrobial resistance genes were identified conveying resistance to Methicillin, Aminoglycosides, Macrolides, Tetracyclines, and Polymixins. Further research is required to ensure that current sanitization practices of VR head mounted displays are appropriate within high-risk hospital settings.}, } @article {pmid41738753, year = {2026}, author = {Brothwell, JA and Toh, E and Xing, Y and Dong, Q and Xu, LH and Giacani, L and Beiras, CG and Mitjà, O and Gao, X and Spinola, SM}, title = {The etiology of exudative cutaneous ulcers in a yaws-endemic community prior to receipt of antimicrobials is similar to that found in communities after mass treatment with azithromycin.}, journal = {mSphere}, volume = {11}, number = {3}, pages = {e0091925}, pmid = {41738753}, issn = {2379-5042}, support = {R01AI134727//National Institute of Allergy and Infectious Diseases/ ; ERC-2019-STG 850450//H2020 European Research Council/ ; }, mesh = {Humans ; *Azithromycin/therapeutic use/administration & dosage ; *Yaws/drug therapy/epidemiology/microbiology ; *Skin Ulcer/microbiology/etiology/epidemiology/drug therapy ; Haemophilus ducreyi/isolation & purification/genetics ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; Child, Preschool ; *Mass Drug Administration ; Treponema pallidum/isolation & purification/genetics ; Streptococcus pyogenes/isolation & purification/genetics ; Female ; Metagenomics ; Treponema ; Male ; Endemic Diseases ; }, abstract = {Mass drug administration (MDA) of azithromycin (AZ) and case finding and treatment of children with cutaneous ulcers (CUs) have been trialed as strategies to eliminate yaws. Metagenomic sequencing of CU swabs obtained from children 3 to 4 years after the initiation of a yaws elimination campaign on Lihir Island showed enrichment for Treponema pallidum subsp. pertenue (TPE), Haemophilus ducreyi (HD), Streptococcus pyogenes (SP), and several anaerobic bacteria. Whether these results were influenced by AZ pressure or are generalizable to other populations is unknown. Here, we performed quantitative PCR (qPCR) for TPE, HD, and SP DNAs and metagenomic sequencing on 260 CU specimens collected from children on New Britain Island, whose inhabitants had not received MDA of AZ. Based on qPCR results, specimens were classified as containing no pathogens, a single pathogen, or multiple pathogens. 31.9% of the specimens contained SP, 28.1% HD, and 25.4% TPE DNAs; mixed infections with two or three pathogen DNAs occurred in 16.5% of cases. No pathogen DNA was detected in 31.5% of the specimens, which were defined as idiopathic ulcers (IUs). In most categories, the same pathogen(s) used to classify the ulcers by qPCR were the most abundant taxa present in the specimens. In IU, the most abundant taxon was Arcanobacterium haemolyticum; however, its relative abundance was similar across all groups, suggesting that this organism may adapt to the CU environment rather than represent a cause of IU. These data indicate that TPE, HD, and SP are the primary causes of CU in this untreated population.IMPORTANCECutaneous ulcers (CUs) affect ~100,000 children annually in tropical regions. After mass drug administration (MDA) of azithromycin (AZ) failed to eradicate yaws, the World Health Organization proposed an integrated disease management strategy to control CU, which emphasizes identifying the causative pathogens in each population. This is critical because organisms associated with CU vary geographically, with Treponema pallidum subsp. pertenue (TPE), Haemophilus ducreyi (HD), Streptococcus pyogenes (SP), and Leishmania spp. predominating in different countries. We previously found that TPE, HD, and SP DNAs were enriched in CU specimens from children on Lihir Island in Papua New Guinea (PNG), a population heavily exposed to AZ. Here, we show that these three organisms were also the major pathogens in CU specimens from children on New Britain Island in PNG, whose population had not received MDA of AZ, suggesting that our previous findings are generalizable within PNG and not a consequence of AZ exposure.}, } @article {pmid41738755, year = {2026}, author = {Ren, X-Y and Ji, J-H and Hu, L and Bao, P and Xie, B-B and Li, S and Musat, N and Musat, F and Chen, S-C}, title = {In situ interrogation of microorganisms mediating hydrocarbon degradation.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {3}, pages = {e0259125}, pmid = {41738755}, issn = {1098-5336}, support = {226-2025-00166//Fundamental Research Funds for the Central Universities/ ; 42507165//National Natural Science Foundation of China/ ; JYB2025XDXM909//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; ZR2025MS514//Shandong Provincial Natural Science Foundation/ ; NNF22OC0071609//the Novo Nordisk Foundation through the Young Investigator Award ReFuel/ ; }, mesh = {*Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics/classification ; *Archaea/metabolism/genetics ; Oxidation-Reduction ; }, abstract = {Microbially mediated hydrocarbon biodegradation is a cornerstone of natural attenuation and engineered bioremediation, yet the in situ mechanisms and key microbial players remain incompletely resolved due to the historical reliance on cultivation-based approaches. Recent advances in cultivation-independent tools, particularly metagenomics, stable isotope probing (SIP), and single-cell techniques, now enable more effective identification of active microbial populations, their functional genes, and metabolic networks directly mediating hydrocarbon degradation in situ. These studies have unveiled a far greater phylogenetic and functional diversity than previously recognized, including the unexpected co-existence of alkane-oxidizing archaea and bacteria in similar environments. The underlying microbial actors exploit distinctive enzymes to initialize hydrocarbon oxidation under oxic and anoxic conditions and achieve complete degradation through complex ecological networks that involve cooperative and/or competitive interactions with other community members such as viruses. These findings offer better insights into the functioning of the microorganisms that control the fate of hydrocarbons in situ and, as a final outcome, help tailor bioremediation strategies for better performance.}, } @article {pmid41738843, year = {2026}, author = {Feng, T and Wu, Y and Xu, Y and Chen, WH}, title = {A comprehensive ruminant microbial catalog (CRMC) reveals convergent selection for key vitamin-synthesizing pathways and genes across ruminants and human.}, journal = {GigaScience}, volume = {15}, number = {}, pages = {}, pmid = {41738843}, issn = {2047-217X}, support = {5001170159//Provincial Departments Affiliated Universities in Hubei Province/ ; }, mesh = {Animals ; *Ruminants/microbiology ; Humans ; *Vitamins/biosynthesis ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Metagenome ; *Biosynthetic Pathways ; *Bacteria/genetics/classification/metabolism ; }, abstract = {BACKGROUND: The ruminant gastrointestinal tract (GIT) serves as a natural microbial reservoir in which vitamin-synthesizing microbes play key integrated roles in digestion, nutrient absorption, and metabolic balance; however, studies systematically elucidating their functional characteristics and ecological roles remain limited due to the lack of a large-scale reference genome catalog for ruminant gastrointestinal vitamin-synthesizing microbes. Here, based on 2,325 metagenomic samples from 8 ruminant hosts, we comprehensively reconstructed and analyzed the ruminant GIT microbiome and the distribution patterns of vitamin-synthesizing microbes.

RESULTS: We reconstructed a unified ruminant gastrointestinal microbiome catalog (CRMC) with 39,696 MAGs, achieving the highest mapping rate (~83.45%) among 2,325 metagenomic datasets, surpassing GTDB, RGMGC, and other catalogs. Across the 8 ruminant hosts, we identified a total of 17,349 vitamin-synthesizing microbes spanning 9 biosynthetic pathways (thiamine, riboflavin, niacin, pantothenate, pyridoxine, biotin, folate, cobalamin, and menaquinone). These microbes exhibited unified pathway selection patterns consistent with those in the human gut microbiome. Furthermore, within the major vitamin-synthesizing pathways commonly selected across ruminants, vitamin-synthesizing microbes displayed concentrated co-selection of specific functional gene nodes, revealing that despite taxonomic differences among gastrointestinal vitamin-synthesizing communities, they share highly convergent pathway preferences and common node-level selection patterns.

CONCLUSIONS: Together, by reconstructing the ruminant GIT microbiome reference genome catalog (CRMC), we elucidated the core microbial taxa and their functional features across ruminants, as well as the pathway preferences and distribution patterns of vitamin-synthesizing microbes. These findings provide an effective reference for advancing ruminant GIT microbiome research, offering gene co-selection insights for microbial synthetic biology design, and guiding microbiome-based interventions in ruminant systems.}, } @article {pmid41740284, year = {2026}, author = {Wang, D and Huang, N and Hou, X and Chen, L and Jiang, Y and Liu, S and Zhu, S}, title = {Inorganic nitrogen in inflowing water governs dissolved organic matter transformation regulated by sediments in recipient basin.}, journal = {Water research}, volume = {296}, number = {}, pages = {125603}, doi = {10.1016/j.watres.2026.125603}, pmid = {41740284}, issn = {1879-2448}, mesh = {*Nitrogen/chemistry ; *Geologic Sediments/chemistry ; *Dissolved Organic Matter/chemistry ; Lakes ; China ; Nitrates ; }, abstract = {Frequent Water Diversion Project significantly regulates the biogeochemical processes and water quality of surface systems, yet it remains poorly understood how recipient basin sediments respond to the inflowing water for mediating the dynamic transformation of dissolved organic matter (DOM). This study systematically conducted a long-term incubation experiment to simulate the interactions of recipient sediments of Dongping Lake, China, with the inflowing waters from different sources. Results showed the significant divergence and heterogenization in aromaticity and molecular weight of DOM in the overlying layer after a 75 day-incubation, during which sunlight irradiation and inorganic nitrogen levels were key in driving the biogeochemical transformation. Metagenomic analyses confirmed that inorganic nitrogen concentrations in the inflowing water governed microbial community succession, with Proteobacteria and Cyanobacteria sensibly responding to nitrogen level fluctuations. Further, nitrate and ammonia nitrogen influenced dissimilatory nitrate reduction activity and exerted positive feedback on the refractory carboxylic-rich alicyclic molecules (CRAM) metabolisms, thereby controlling the aromatization or humification processes of DOM. Specially, compositional characteristics of DOM were primarily determined by the abundance and activity of key functional genes, including narG, narZ, nxrA, narH, narY, nxrB, narI, and narV. This study provides new insights into the significant role of the Water Diversion Project in determining the dissolved organic carbon pool of inflowing water in recipient basins, enhancing biogeochemical understanding of its water quality responses.}, } @article {pmid41740290, year = {2026}, author = {Gong, Q and Zeng, W and Hao, X and Yuan, Z and Wen, J and Wang, X and Peng, Y}, title = {Mixotrophic partial denitrification coupled with anammox achieves robust nitrogen removal under organic-rich conditions: Insights into metabolic adaptations of sulfur-oxidizing and anammox bacteria.}, journal = {Water research}, volume = {296}, number = {}, pages = {125599}, doi = {10.1016/j.watres.2026.125599}, pmid = {41740290}, issn = {1879-2448}, mesh = {*Denitrification ; *Nitrogen/metabolism ; *Bacteria/metabolism ; *Sulfur/metabolism ; Oxidation-Reduction ; Wastewater ; Bioreactors/microbiology ; }, abstract = {Sulfur-driven partial denitrification coupled with anammox (SPDA) process is a promising sustainable nitrogen removal pathway. However, its microbial adaptability and metabolic mechanism under long-term organic-rich conditions remain poorly understood. In this study, a single-stage mixotrophic partial denitrification-anammox (MPDA) system, driven by both thiosulfate and organic carbon from real domestic wastewater, was established and operated for 292 days. The system demonstrated excellent and robust performance, achieving average ammonia and total nitrogen removal efficiencies of 93.3% and 90.9%, respectively, despite fluctuating organic loading rates (0.35-0.45 kg COD/m[3]/d). [15]N isotopic tracing revealed that the PDA processes driven by thiosulfate and organic carbon contributed 51.3% and 27.7% of nitrogen removal, respectively. DNA-SIP experiments identified key facultative mixotrophic sulfur-oxidizing bacteria (SOB) (e.g., Thiobacillus and norank_f_Hydrogenophilaceae) as primary contributors to nitrite supply. Notably, the core anammox bacteria, Candidatus Brocadia, exhibited a positive correlation with organic load and was actively labeled by organic [13]C-carbon, suggesting previously overlooked organoautotrophic activity. Metagenomic analysis revealed that Thiobacillaceae employed the Calvin cycle for carbon fixation and possessed a complete pentose phosphate pathway, while Brocadiaceae utilized the Wood-Ljungdahl pathway alongside a near-complete TCA cycle and robust glycogen metabolism to support their mixotrophic capabilities. This study provides novel insights into the metabolic plasticity and synergistic interactions between SOB and anammox bacteria, demonstrating the feasibility and mechanism of the MPDA process for efficient nitrogen removal in organic-laden wastewater.}, } @article {pmid41740355, year = {2026}, author = {Lee, J and Hong, S and Choi, J and Song, H and Han, JH and Suh, YD and Yeon, SC and Cho, S}, title = {Whole-genome shotgun metagenomics reveals environmental perturbations in the gut microbiome and resistome of wild raccoon dogs rescued at a wildlife center.}, journal = {The Science of the total environment}, volume = {1021}, number = {}, pages = {181588}, doi = {10.1016/j.scitotenv.2026.181588}, pmid = {41740355}, issn = {1879-1026}, mesh = {Animals ; *Raccoon Dogs/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Shotgun Sequencing ; *Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial ; }, abstract = {Raccoon dogs are potential vectors for the transmission of zoonotic pathogens and antimicrobial resistance, with their gut microbiome carrying genetic determinants of virulence and resistance. However, previous studies have primarily relied on traditional culture-based approaches, limiting our understanding of the entire dynamics and genetic potential of the gut microbiome in raccoon dogs. In this study, we employed both culture-dependent approach and whole-genome shotgun sequencing in raccoon dogs undergoing rehabilitation for eight weeks. We integratively assessed how rehabilitation-related environmental shifts influence the gut microbiome and resistome. Rehabilitation induced shifts in gut microbiome composition. Notably, within-group diversity decreased at week eight, indicating increased compositional similarity. Throughout rehabilitation, a total of 18 genera (e.g., Paeniclostridium, Psychrobacter) significantly increased, and 40 genera (e.g., Intestinimonas, Erysipelatoclostridium) decreased in abundance. Rehabilitation also induced shifts in the gut resistome, with reduced within-group diversity at weeks four and eight, indicating increased compositional similarity over time. Overall, 253 antimicrobial resistance genes (ARGs) present at week 0 disappeared, whereas 273 ARGs were acquired during rehabilitation. Additionally, the abundance of 15 ARGs significantly decreased and that of 33 increased, with beta-lactamases being the most common among the latter. Culture-dependent methods revealed a marked increase in bacteria resistant to third-generation cephalosporins, monobactams, and sulfonamides. Changes in microbiome composition during rehabilitation indirectly influenced the resistome and virulome through mobile genetic elements. Our findings suggest that rehabilitation-induced perturbations in the gut microbiome and resistome of raccoon dogs are likely driven by environmental shifts such as diet and habitat. These changes may affect their post-release fitness and raise concerns owing to the potential dissemination of zoonotic pathogens and antimicrobial resistance.}, } @article {pmid41740416, year = {2026}, author = {Fan, Z and Wu, J and Li, R and Li, H and Xu, Y}, title = {Co-application of organic fertilizer and biochar ameliorates the triple composite pollution of microplastics, antibiotic resistance genes, and heavy metals in soil.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141520}, doi = {10.1016/j.jhazmat.2026.141520}, pmid = {41740416}, issn = {1873-3336}, mesh = {*Metals, Heavy/analysis ; *Fertilizers ; *Soil Pollutants/analysis ; *Charcoal/chemistry ; Soil Microbiology ; *Microplastics/analysis ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Agriculture ; }, abstract = {Intensive facility agriculture is increasingly threatened by the co-occurrence of heavy metals (HMs), micro-/nano plastics (MNPs), and antibiotic resistance genes (ARGs), yet effective strategies for mitigating ternary composite pollution remain limited. Here, a five-year field trail was conducted to evaluate the imparts of different fertilization regimes on the occurrence, interaction, and mitigation of composite pollution in facility agricultural soils, with a particular attention on the co-application of biochar and organic fertilizer. The results showed that conventional fertilization exacerbated the accumulation and synergistic risks of HMs, MNPs, and ARGs, whereas its co-applied with biochar significantly reduced individual pollutant loads and lowered the comprehensive ternary pollution index by 28.0-62.2 %. Variance partitioning and structural equation modeling revealed that microbial community structure played a dominant role in regulating composite pollution, exceeding the contribution of soil physicochemical properties. The biochar-organic fertilizer amendment reshaped microbial community assembly by narrowing ecological niche breadth, enhancing community stability, which primarily drove a targeted enrichment of functional taxa (e.g. Nitrospira, Sphingopyxis, Hydrogenophaga, and Steroidobacter) involved in microplastic degradation and heavy metal immobilization, concurrently suppressing ARGs host populations. Metagenomic analyses indicated a dual-level regulation of microbial carbon metabolism. The treatment enhanced fermentation-driven, energy-efficient carbon conversion pathways in functional microbes responsible for plastic degradation and metal immobilization, while concurrently inhibiting carbon fixation-dependent metabolic functions in ARG-associated hosts, thereby reducing their ecological competitiveness. Overall, this study highlights carbon resource-driven microbial metabolic differentiation as a central mechanism for the synergistic mitigation of complex soil pollution and provides a practical fertilization strategy for sustainable pollution control in protected agricultural systems.}, } @article {pmid41740635, year = {2026}, author = {Hsu, CY and Almajidi, YQ and Abohassan, M and Gafarov, R and Basunduwah, TS and Hjazi, A and Arora, V and Nayak, PP and Shukla, SK and Jayabalan, K}, title = {Pharmacomicrobiomics in blood cancers: How the gut microbiome and its metabolites shape drug efficacy and toxicity.}, journal = {Critical reviews in oncology/hematology}, volume = {221}, number = {}, pages = {105229}, doi = {10.1016/j.critrevonc.2026.105229}, pmid = {41740635}, issn = {1879-0461}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Hematologic Neoplasms/drug therapy/metabolism/microbiology/therapy ; *Antineoplastic Agents/therapeutic use/adverse effects ; Hematopoietic Stem Cell Transplantation ; Animals ; Metabolome ; Graft vs Host Disease/etiology ; }, abstract = {Clinical management of hematologic cancers is frequently complicated by marked, unpredictable inter-patient variation in both therapeutic benefit and adverse effects. Beyond host genetics, accumulating mechanistic and translational data implicate the gut microbiota and its small-molecule metabolome as active modifiers of drug chemistry, host immune tone, and clinical outcomes. In this review we synthesize three recurring, actionable findings: (1) discrete microbial enzymes, most prominently bacterial β-glucuronidases, repeatedly re-activate hepatic drug-glucuronides in the gut and amplify local gastrointestinal toxicity (e.g., irinotecan and mycophenolate), a pathway successfully targeted in preclinical and translational studies. (2) loss of anaerobic short-chain fatty acid production, especially butyrate, is a recurrent, causal mediator of mucosal injury and aggravated graft-versus-host disease after allogeneic hematopoietic cell transplantation. (3) reduced gut microbial diversity and the depletion of key functional taxa predict worse transplant outcomes (including mortality), arguing that baseline ecosystem state is a prognostic biomarker that merits routine consideration in trial design. Building on these syntheses, we propose a compact clinical framework for hematology trials and practice: (A) baseline ecosystem phenotyping (shotgun metagenome + targeted metabolite panel including butyrate and measured bacterial β-glucuronidase activity), (B) risk-stratified interventions (enzyme-targeted inhibitors, defined consortia, or metabolite replacement for high-risk patients), and (C) embedded holo-omic endpoints to confirm on-target biochemical modulation and link molecular change to clinical benefit. Together, these elements move Pharmacomicrobiomics beyond descriptive cataloging toward mechanistic stratification and testable interventions that can reduce unexplained variability in drug response and toxicity for patients with leukemia, lymphoma and myeloma.}, } @article {pmid41740877, year = {2026}, author = {Orth, HM and Meierkord, D and Holtfreter, MC and Luedde, T and Schmidt-Chanasit, J and Feldt, T}, title = {Zika virus infection in a German traveller to the Maldives, August 2025.}, journal = {Travel medicine and infectious disease}, volume = {70}, number = {}, pages = {102960}, doi = {10.1016/j.tmaid.2026.102960}, pmid = {41740877}, issn = {1873-0442}, mesh = {Humans ; *Zika Virus Infection/diagnosis/virology/transmission ; Maldives ; *Travel ; *Zika Virus/genetics/isolation & purification ; Phylogeny ; Germany ; Female ; RNA, Viral ; Adult ; Animals ; }, abstract = {BACKGROUND: Zika virus (ZIKV) is a neurotropic flavivirus associated with generally mild disease but the risk of congenital abnormalities when contracted during pregnancy. Reports from the Maldives are rare.

METHODS: We describe a ZIKV infection in a traveller returning from the Maldives in August 2025, including clinical findings and molecular diagnostics with metagenomic sequencing and phylogenetic analysis.

RESULTS: ZIKV ribonucleic acid was detected by reverse transcription polymerase chain reaction, and sequencing identified the ZIKV Asian lineage. However, the limited sequence length precluded precise phylogenetic placement.

CONCLUSION: This case underlines the ongoing risk of ZIKV transmission in areas where compatible arthropod vectors are present. Since there is no systematic surveillance in the Maldives, the detection of ZIKV infections in returning travellers is becoming increasingly important for assessing the epidemiological situation.}, } @article {pmid41741009, year = {2026}, author = {Li, S and Yan, Q and Tong, J and Li, Y and Bai, L and Peng, Q}, title = {Distinct Defence Mechanisms of Allelopathic Rice Against Quinclorac-Susceptible and -Resistant Barnyardgrass: Involvement of Specific Metabolites and Rhizosheath Microbiota.}, journal = {Plant biotechnology journal}, volume = {24}, number = {6}, pages = {3876-3896}, pmid = {41741009}, issn = {1467-7652}, support = {U22A20461,32372564//National Natural Science Foundation of China/ ; }, mesh = {*Oryza/metabolism/microbiology/genetics/drug effects ; *Echinochloa/drug effects ; *Allelopathy ; *Herbicides/pharmacology ; Plant Roots/microbiology/metabolism ; *Microbiota ; Herbicide Resistance ; Quinolines ; }, abstract = {Allelopathic rice is increasingly recognised as a promising strategy for sustainable weed management. Resistance to the herbicide quinclorac is widespread in barnyardgrass, but it remains unclear whether allelopathic rice exerts the same defence against herbicide-susceptible and -resistant barnyardgrass. We conducted integrated transcriptomic, metabolomic, and metagenomic analyses to investigate the responses of allelopathic rice to quinclorac-susceptible (S) and -resistant barnyardgrass (R) lines. Distinct chemical strategies were identified in allelopathic rice: Terpenoids (e.g., carnosic acid, phytocassane B, and ipomeatetrahydrofuran) mainly suppressed S, while amino acids (e.g., pipecolic acid, L-glutamate, and L-histidine) were key against R. Correspondingly, terpenoid biosynthesis and nitrogen metabolism were the most enriched pathways under S and R stress, respectively. Additionally, terpenoid accumulation correlated positively with salicylic acid (SA) and jasmonic acid (JA) concentrations in roots under S. Both terpenoids and amino acids formed the stable ecological networks with rhizosheath microbiota. Functional metagenomic analysis further showed that ABC transporter and quorum sensing pathways were upregulated under S, whereas nitrogen fixation predominated under R. Notably, amino acids formed a nitrogen-related ecological network with nitrogen-metabolising microbiota, contributing to improved plant-available soil nitrogen and total nitrogen content in rice plants. Bioassays showed that exogenous pipecolic acid (≥ 40 μM) and L-histidine (80 μM) inhibited barnyardgrass seedling growth without affecting allelopathic and non-allelopathic rice. These findings demonstrate that allelopathic rice employs divergent chemical-microbial defence strategies against S and R barnyardgrass, highlight the dual role of amino acids, and provide a basis for precision weed management, particularly for herbicide-resistant weeds in paddy fields.}, } @article {pmid41741460, year = {2026}, author = {Lin, Y and Kouraki, A and Cheetham, NJ and Louca, P and Bowyer, RC and Pope, R and Asnicar, F and Zhang, X and Visconti, A and Falchi, M and Spector, TD and Segata, N and Valdes, AM and Menni, C}, title = {Gut microbiome composition and function reflect socioeconomic deprivation.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41741460}, issn = {2055-5008}, support = {MR/W026813/1 and MR/Y010175/1//UKRI/MRC grants/ ; }, abstract = {Socioeconomic status (SES) correlates with adverse health outcomes, but the underlying biological mechanisms remain unclear. We examined how area-level deprivation (Townsend Deprivation Index) influences gut microbiome composition and function and whether the gut microbiome mediates the effects of deprivation on metabolic and mental health. A total of 1390 females from TwinsUK with shotgun metagenomes were included in this study. We found that higher Townsend deprivation was associated with reduced alpha diversity (Beta [95% CI] = -1.60 [-3.00, -0.21]) and distinct microbial composition shifts (PERMANOVA P = 0.001). Twelve species and 22 functional pathways were linked to deprivation, distinguishing between deprivation groups (AUC = 0.725-0.744), with altered energy metabolism in deprived individuals. Townsend deprivation was associated with anxiety (OR [95%CI] = 1.09 [1.01, 1.18]) and diabetes (OR [95% CI] = 1.16 [1.03, 1.30]). Importantly, Intestinimonas massiliensis and Lawsonibacter sp_NSJ_51 partially mediate the effect of anxiety. Lawsonibacter sp_NSJ_51 also mediated the deprivation-diabetes association. These findings suggest that socioeconomic deprivation influences microbiome composition and function, mediating disparities in metabolic and mental health.}, } @article {pmid41741786, year = {2026}, author = {Flinn, H and Marshall, A and Holcomb, M and Burke, M and Kara, G and Cruz-Pineda, L and Soriano, S and Treangen, TJ and Villapol, S}, title = {Antibiotic-induced gut microbiome remodeling reduces neuroinflammation in traumatic brain injury.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41741786}, issn = {2399-3642}, support = {T15 LM007093/LM/NLM NIH HHS/United States ; EF-2126387//NSF | BIO | Division of Emerging Frontiers (EF)/ ; R56AG080920//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; }, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Brain Injuries, Traumatic/microbiology/complications/drug therapy ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects ; *Neuroinflammatory Diseases/microbiology/prevention & control/etiology/drug therapy ; Dysbiosis ; Mice, Inbred C57BL ; }, abstract = {Traumatic brain injury induces neuroinflammation and gut microbiome dysbiosis, yet the effects of short-term antibiotic treatment on these processes remain poorly understood. To address this, male mice received controlled brain injuries followed by a brief course of oral antibiotics. Antibiotic treatment reduced bacterial abundance in feces and altered microbial diversity, with more pronounced shifts after two injuries. Despite this disruption, antibiotic-treated mice exhibited smaller lesion volumes, reduced cell death, attenuated microglial and macrophage activation, lower pro-inflammatory cytokine levels, and decreased astrogliosis and peripheral immune cell infiltration compared with vehicle-treated mice after two injuries. In the gut, increasing injury severity was associated with villus shortening and loss of mucus-producing cells, and antibiotic treatment further modified these injury-related changes. Circulating levels of short-chain fatty acids and associated microbial metabolic functions were reduced by antibiotic exposure. In contrast, germ-free mice showed increased lesion volumes and exacerbated gliosis following brain injury. Long-read metagenomic sequencing identified Parasutterella excrementihominis and Lactobacillus johnsonii as taxa that persisted despite antibiotic treatment. Collectively, these results suggest that antibiotics can reduce brain damage after injury through mechanisms not explained by short-chain fatty acids, while also highlighting potential drawbacks of altering the gut microbiome.}, } @article {pmid41742048, year = {2026}, author = {Zhang, Y and Wangjia, P and Yang, S and Liu, P and Xu, X and Han, H}, title = {Bartonella quintana endocarditis presenting with severe coombs-positive anemia: a case report.}, journal = {BMC cardiovascular disorders}, volume = {26}, number = {1}, pages = {}, pmid = {41742048}, issn = {1471-2261}, support = {XZ202501ZR0145//Natural Science Foundation of Tibet Autonomous Region/ ; XZZR202402030(W)//Natural Science Foundation of Tibet Autonomous Region/ ; XZZR202402105(W)//Natural Science Foundation of Tibet Autonomous Region/ ; }, abstract = {BACKGROUND: Bartonella quintana is a recognized cause of blood culture-negative endocarditis, often associated with predisposing social factors or pre-existing valvulopathy. Diagnosis is challenging and relies on advanced microbiological techniques.

CASE PRESENTATION: A 17-year-old Tibetan herdsman from a high-altitude region presented with a two-week history of fever, dyspnea, and lower limb edema. He had no history of homelessness or alcoholism but lived in poor sanitary conditions. Laboratory investigations revealed severe Coombs-positive hemolytic anemia and serological markers suggestive of systemic lupus erythematosus (SLE). Transthoracic echocardiography showed vegetations on both aortic (bicuspid) and mitral valves with severe regurgitation and rapid hemodynamic progression. All blood cultures were negative. Metagenomics Next-Generation Sequencing (mNGS) of peripheral blood identified B. quintana as the causative pathogen. Antibiotic therapy was adjusted to doxycycline (9 weeks) and gentamicin (3 weeks). Concurrently, immunomodulatory therapy with methylprednisolone and intravenous immunoglobulin was administered for the hemolytic anemia. Given the severe valvular insufficiency, the patient successfully underwent urgent aortic and mitral valve replacement. His clinical condition improved significantly post-operatively.

CONCLUSION: This case highlights the diagnostic utility of mNGS in confirming B. quintana endocarditis in a culture-negative scenario, especially when clinical presentation is complicated by concomitant autoimmune features mimicking Libman-Sacks endocarditis. A treatment strategy combining targeted antibiotics for the infection and immunomodulation for the hematologic complication, followed by definitive surgery, led to a successful outcome. It underscores that B. quintana infection should be considered in patients from disadvantaged backgrounds with endocarditis, even in the absence of classic risk factors.}, } @article {pmid41742303, year = {2026}, author = {Palma, DE and Schapheer, C and Gaete, A and Aravena, P and Albarrán-Cuitiño, C and Aguado-Norese, C and González, M and Cambiazo, V}, title = {The root system of Pappostipa frigida as a hotspot of active bacterial communities in the Andean steppe of the Atacama desert.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41742303}, issn = {2524-6372}, support = {FONDECYT 1241424//ANID/ ; FONDECYT 1211893//ANID/ ; }, abstract = {BACKGROUND: In arid ecosystems, soil microorganisms experience prolonged drought and nutrient limitation, resulting in widespread dormancy and a decoupling between microbial presence and activity. The rhizosphere is a resource-rich microenvironment where plants, inputs may alleviate these constraints and regulate microbial metabolic states. However, it remains unclear whether root system effects in extreme environments reflect taxonomic turnover or the activation of dormant soil bacteria. Here, we investigated whether the rhizosphere-surrounding soil (RSS) of Pappostipa frigida, a dominant perennial grass of the Andean steppe of the Atacama Desert, reshapes soil bacterial communities primarily by promoting the activation of dormant taxa rather than by recruiting distinct bacterial populations, and how this process influences microbial diversity, activity, and functional potential.

RESULTS: We employed a combination of soil physicochemical analyses, RNA/DNA metabarcoding, shotgun metagenomic sequencing and culture-based assays to compare bulk soil (BS) and RSS bacterial communities. The active bacterial community in the RSS exhibited significantly higher diversity and Shannon index than those in BS, whereas total (DNA-based) communities showed no significant differences between soil compartments. Taxonomic structure was primarily shaped by soil compartment rather than nucleic acid type, and active bacteria in the RSS showed a stronger correlation with total bacterial populations than those in the BS. Notably, 65% of putatively dormant bacterial taxa in BS were detected as active in RSS, and 75% were recoverable in culture. Additionally, 24% were members of PGP bacterial families. Functionally, the bacterial communities of the BS were enriched in sporulation genes, whereas active bacterial communities in the RSS showed higher abundances of genes associated with osmotic stress tolerance, siderophore synthesis, and resuscitation-promoting factors.

CONCLUSIONS: Our results indicate that the root system of Pappostipa frigida functions as a localized hotspot of microbial activity in an extreme arid environment by promoting the activation of dormant members of the soil microbial seed bank rather than by recruiting distinct taxa. By integrating microbial activity, functional traits, and culturability, this study highlights the central role of plant-associated microenvironments in regulating microbial life-history strategies in drylands and provides a mechanistic framework for understanding plant-microbe interactions under chronic environmental stress.}, } @article {pmid41742321, year = {2026}, author = {Mazzoni, C and Ochana, BL and Orlanski-Meyer, E and Ben Ya'acov, A and Focht, G and Harpenas, E and Shmorak, S and Ledder, O and Lev-Tzion, R and Shemer, R and Shteyer, E and Dor, Y and Yassour, M}, title = {Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41742321}, issn = {2049-2618}, mesh = {Humans ; *Feces/microbiology/chemistry ; Child ; Female ; *Inflammatory Bowel Diseases/microbiology ; Adult ; Male ; Adolescent ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; DNA Methylation ; Young Adult ; Neutrophils ; DNA, Bacterial/genetics ; Child, Preschool ; *DNA/analysis ; Sequence Analysis, DNA/methods ; Inflammation/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Middle Aged ; Shotgun Sequencing ; }, abstract = {BACKGROUND: Feces represent a complex biological matrix that provides valuable information about intestinal physiology and gut microbial activity. Comprehensive fecal DNA sequencing is mostly utilized as a non-invasive way to profile the gut microbiome, and both clinical practice and research on inflammatory bowel diseases (IBD) would greatly benefit from accurate and non-invasive methods to monitor gut inflammation in IBD patients. In IBD, excessive immune cell recruitment and epithelial cell shedding in the gut increase the amount of human DNA in feces, making fecal DNA profiling a desirable approach to monitor gut inflammation dynamics.

METHODS: We used a combination of sequencing techniques to comprehensively characterize the fecal DNA diversity in a newly established cohort of pediatric IBD patients and controls (Pediatric cohort, N = 134 children, Israel). We performed methylation-based human cell-specific profiling together with shotgun metagenomics to characterize the human and the microbial DNA content in feces, respectively. Moreover, we included a large complementary external cohort including adult IBD patients and controls (Adult cohort, N = 689 adults, the Netherlands), not only to compare microbial patterns across the age spectrum, but also to extend our findings from the methylation-based profiling to the more broadly-available quantification of human DNA in metagenomic sequencing.

RESULTS: We found that neutrophil DNA dominates fecal human DNA content in IBD patients, and our measurements were highly correlated with fecal calprotectin levels. Combining neutrophil and other cell type DNA fractions in one metric was able to distinguish between remissive and active cases of IBD. Human reads percentage by metagenomics was well correlated with disease severity and species richness, which had distinct trends in CD and UC over time. We used a combination of species richness, human DNA percentage, and microbiome composition data to predict IBD and distinguish CD from UC in both adult and pediatric IBD cohorts.

CONCLUSIONS: The comprehensive characterization of human and microbiome fecal DNA is a useful approach to track immune response level and investigate the interaction that the immune system has with gut microbiome richness and composition over time, enriching opportunities for better disease monitoring and thus better treatment of IBD patients. Video Abstract.}, } @article {pmid41742329, year = {2026}, author = {Cai, G and Wu, Y and Chen, Z and Yang, X and Jiang, X and Wang, Q and Cai, R and Wang, H}, title = {Host-driven evolution shapes the polysaccharide utilization profiles of alga-associated Flavobacteriaceae.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41742329}, issn = {2049-2618}, support = {42476092//National Natural Science Foundation of China/ ; 42476122//National Natural Science Foundation of China/ ; 2025A1515010891//Guangdong Provincial Department of Science and Technology/ ; 2022B1515020017//Guangdong Provincial Department of Science and Technology/ ; }, mesh = {*Flavobacteriaceae/genetics/metabolism/classification/isolation & purification ; *Polysaccharides/metabolism ; Phylogeny ; Glycoside Hydrolases/genetics/metabolism ; Chlorophyta/microbiology ; *Seaweed/microbiology ; Diatoms/microbiology ; Evolution, Molecular ; Genome, Bacterial ; Rhodophyta/microbiology ; }, abstract = {BACKGROUND: Marine algae represent major producers of complex polysaccharides and serve as hosts for diverse microbial communities in the phycosphere. Flavobacteriaceae are among the key bacterial taxa involved in polysaccharide degradation and carbon remineralization in this environment. However, the extent to which algal hosts drive the divergence of polysaccharide utilization profiles in these bacteria remains unclear.

RESULTS: We conducted a genome-resolved analysis of 103 cultured Flavobacteriaceae strains isolated from red, green, and brown macroalgae, as well as from diatoms and dinoflagellates. We found that macroalga-associated strains generally harbored more abundant and diverse CAZyme-encoding genes than their microalga-associated counterparts. Moreover, strains associated with different algal phyla showed distinct metabolic specializations that aligned with the typical polysaccharides of their respective hosts, strongly supporting host-specific adaptation. In four widely distributed genera (Maribacter, Flagellimonas, Polaribacter, Winogradskyella), CAZyme profile dissimilarity and key glycoside hydrolase gene divergence exhibited phylogenetic congruence with algal host phylogeny (Mantel r up to 0.76 and 0.85, respectively), indicative of host-associated functional adaptation. Using Maribacter as a model, cultivation experiments and transcriptome characterization demonstrated that polysaccharide utilization efficiency is not solely linked to the organization of genes into polysaccharide utilization loci (PULs), but also associated with the expression dynamics of key transcription factors (TFs), particularly those from AraC and DeoR families, whose expression patterns were coordinated with laminarin degradation. Notably, these two TF families also exhibited host-associated divergence patterns similar to those of CAZyme-encoding genes. Furthermore, analysis of the Tara Oceans metagenomic data indicated that, within the AraC and DeoR families, a higher proportion of genes were positively correlated with chlorophyll a content compared to other TF families, reinforcing their specialized roles in alga-associated bacterial lifestyles.

CONCLUSIONS: Our integrative genomic and transcriptomic analyses reveal evolutionary and regulatory adaptation of marine Flavobacteriaceae to distinct algal hosts. These findings highlight algae-derived habitats as specialized niches that shape microbial metabolic potential, and suggest that carbohydrate metabolism plays a key role in host-driven bacterial evolution across global oceans. Video Abstract.}, } @article {pmid41742841, year = {2026}, author = {Wang, Y and Wu, H and Qu, M and Zhang, C and Xu, Z and Pei, Y and Zhao, C and Wang, J and Ma, S and Lyu, N and Xu, X and Bi, Y and Zhu, B and Gao, GF}, title = {A Genomic Catalog of Migratory Microbiomes from Wild Birds across China's Habitats.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {26}, pages = {e74581}, pmid = {41742841}, issn = {2198-3844}, support = {2023YFC2307101//National Key Research and Development Program of China/ ; 235200810058//Project for Young Scientists of the Joint Funds of Science and Technology Research and Development Plan of Henan Province, China/ ; 30501278//Young TopNotch Talents Foundation of Henan Agricultural University/ ; }, mesh = {Animals ; *Birds/microbiology/genetics ; China ; *Animal Migration/physiology ; *Animals, Wild/microbiology/genetics ; *Metagenome/genetics ; Ecosystem ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; *Microbiota/genetics ; }, abstract = {Migratory birds play an important role in the spread of antimicrobial resistance (AMR); however, gaps in surveillance data from vital regions along migratory flyways across China limit the detection of emergent threats. Here, we assembled 340 metagenomes from 52 bird species covering 11 provincial administrative districts in China, presenting a specialized migratory microbial genome and gene catalog to archive the genomic and functional diversity of gut microbiomes in wild birds. This comprehensive migratory bird microbial genome and gene (MBGG) catalog includes 5823 metagenome-assembled genomes (MAGs), 13 072 plasmid sequences, and 44 974 viral genomes, which represent 1709 candidate species spanning 36 phyla. The catalog also contains over 20 million non-redundant protein-encoding genes, the use of which is confirmed by the mining of 15 678 secondary metabolite biosynthetic gene clusters, 1814 known antibiotic resistance genes, and 7219 virulence factors. The number of clinically critical ARGs identified in Grus japonensis was the highest, followed by Cygnus cygnus and Sibirionetta formosa, which indicated that these species are hotspot species of clinically critical AMR dissemination. Moreover, we mapped the profile of bacterial zoonotic/opportunistic pathogens carried by wild birds and evaluated their associations with publicly available genomes. Finally, the precise migratory movements for 10 bird species using a global positioning system tracking system help to assess the movement of microorganisms and AMR risk. Collectively, this valuable resource provides the basis for the integration and unification of global wild bird microbiomes, timely sharing, and assessing the uncertainty of migratory microbiomes in the future.}, } @article {pmid41743088, year = {2026}, author = {Li, Q and Liu, S and Wang, J and Yu, L and Sun, S}, title = {Case Report: A rare case of ANCA-positive Q fever endocarditis-associated glomerulonephritis.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1701814}, pmid = {41743088}, issn = {2296-858X}, abstract = {BACKGROUND: Q fever is a zoonotic disease caused by Coxiella burnetii and is endemic worldwide. Q fever endocarditis is commonly found in adults and is rarely seen in children. Infectious endocarditis can also lead to renal damage. Here, we present a case of Q fever endocarditis-associated glomerulonephritis in a Chinese boy with positive Antiproteinase 3 antibody (PR3)-antineutrophil cytoplasmic antibody (ANCA).

CASE PRESENTATION: A 12-year-old Chinese boy presented with intermittent fever and hematuria for 2 months. He was diagnosed with Tetralogy of Fallot at birth and underwent multiple cardiac surgeries between 1 and 4 years of age. The examinations showed positive serum mycoplasma antibody and increased serum Epstein-Barr virus (EBV) DNA. However, antibiotic and antiviral treatment was not effective. PR3-ANCA antibody was positive (109.8-158.8CU), while anti-myeloperoxidase (MPO) antibody, anti-glomerular basement membrane (GBM) antibody, antinuclear antibodies (ANA), and double-stranded DNA (dsDNA) were negative. Chest CT showed bronchitis. Ophthalmic examination and ENT examinations revealed no abnormalities. Coxiella burnetii was found positive by metagenomics next generation sequencing (mNGS) and immunofluorescence assay (IFA) in the detection of pathogenic microorganisms causing bloodstream infections. Prominent vegetation was present on the pulmonary valve, as demonstrated by cardiac ultrasound. Secondary hyperplastic glomerulonephritis was considered by renal biopsy. Therefore, the final diagnosis was Q fever endocarditis-associated glomerulonephritis. Doxycycline was given to the boy orally and daily, and no fever occurred again. Sixteen months later, hematuria disappeared and PR3-ANCA remainded positive.

CONCLUSIONS: Q fever endocarditis should be considered for children presenting with chronic fever, hematuria and positive ANCAs, especially those with a history of congenital heart disease or cardiac operation. It is very helpful for the diagnosis to undergo these examinations, including mNGS, cardiac ultrasound and renal biopsy.}, } @article {pmid41743122, year = {2026}, author = {Shen, S and Ning, M and Li, M and Qian, S and Ye, X and Zhuang, Q and Wu, S and Wan, X and Dong, Z}, title = {Sevelamer inhibits the formation of cholesterol gallstones by modulating bile acid metabolism.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1737631}, pmid = {41743122}, issn = {1663-9812}, abstract = {BACKGROUND: The purpose of this study was to investigate the effect and mechanism of Sevelamer hydrochloride (Sev) on cholesterol gallstone formation via the intestinal Fxr-Fgf15 signaling pathway in a mouse model.

METHODS: A cholesterol gallstone mouse model was established. Mice were divided into groups treated with Sev, Fxr agonist, or controls. The incidence and severity of gallstones, along with liver/body weight ratio, were recorded. Total cholesterol (TC) and total bile acid (TBA) levels were measured. Biliary cholesterol supersaturation index (CSI) was calculated. Serum ALT and AST levels were quantified by ELISA. The expression of Fxr-Fgf15 pathway-related molecules and bile acid transporters were detected by RT-PCR and Western blot. Targeted bile acid metabolomics characterized ileal bile acid profiles, while metagenomics assessed gut microbiota alteration.

RESULTS: Sev treatment reduced hepatic lipid deposition, lowered biliary CSI, attenuated gallbladder wall thickening, improved liver function, and decreased TC levels. Mechanistically, Sev inhibited the intestinal Fxr-Fgf15 pathway, promoting hepatic bile acid synthesis and altering ileal bile acid composition. Fxr agonist reversed these effects, increasing Fgf15/Shp expression, suppressing bile acid synthesis, elevating CSI, and partially restoring gallstone susceptibility. Sev reshaped gut microbiota diversity, reducing Blautia and enriching Bacteroidales and Roseburia at genus level. Concurrently, Sev modulated the ileal bile acid pool, decreasing Fxr-activating bile acids and increasing Fxr-antagonizing bile acids. Microbiota-bile acid correlation analysis highlighted significant associations between specific taxa and bile acid profiles.

CONCLUSION: Sev might prevent cholesterol gallstone formation by inhibiting the intestinal Fxr-Fgf15 pathway, promoting hepatic bile acid synthesis, reducing biliary cholesterol supersaturation, and restoring gut microbiota balance.}, } @article {pmid41743140, year = {2026}, author = {Su, S and Pan, J and Wu, H and Ouyang, S and Chen, L and Zeng, Y and Deng, N}, title = {Tree species diversity promotes soil microbial carbon fixation gene abundance via nutrient-mediated interactions in subtropical forests.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1751295}, pmid = {41743140}, issn = {1664-302X}, abstract = {Soil microbial carbon (C) fixation represents a vital yet uncertain component of forest carbon cycling, and its underlying mechanisms especially depth-specific responses remain unclear. To address this, we integrated metagenomics and machine learning to examine these relationships along a tree species richness gradient (1-8 species), analyzing both topsoil (0-10 cm) and subsoil (10-20 cm). Results revealed distinct vertical stratification in soil properties and microbial carbon fixation strategies. Microbial carbon fixation gene abundance was primarily driven by soil organic carbon (SOC) and nitrate nitrogen (NO3[-]-N), exhibiting a nonlinear threshold at ~85 g kg[-1] SOC. The promoting effect of SOC peaked at moderate richness (3-5 species) but declined at higher richness. Depth-resolved analysis revealed that the Calvin cycle gene rbcL responded mainly to richness in topsoil, whereas rTCA cycle genes (korA, korC) were more sensitive in subsoil These findings demonstrate that tree diversity enhances microbial carbon fixation through nutrient-mediated mechanisms, but these effects are nonlinear, context-dependent, and depth-specific. Incorporating such complexity is essential for accurately predicting forest carbon sequestration.}, } @article {pmid41743204, year = {2026}, author = {Xu, K and Guan, P and Du, W and Zeng, H and Chen, M and Lv, Z and Liu, Y and Shao, M and Qu, B}, title = {Warming outweighs nitrogen deposition in shaping rhizosphere microbial structure involved in carbon, nitrogen, and phosphorus cycling in Ambrosia trifida.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1686326}, pmid = {41743204}, issn = {1664-462X}, abstract = {INTRODUCTION: Ambrosia trifida, a harmful invasive plant, poses significant ecological and economic threats and is expected to spread further under future warming and nitrogen deposition scenarios. According to plant-soil feedback and enhanced mutualist hypothesis, invasive plants may gain a competitive edge by recruiting specific microorganisms. However, little is known about the composition and functional potential of its rhizosphere microbiome.

METHODS: In this study, we combined metagenomics with widely targeted metabolomics to investigate the interactions between root exudates and soil microbial communities under experimental warming and nitrogen deposition.

RESULTS AND DISCUSSION: The results showed that warming and nitrogen addition together promoted biomass accumulation. And their combination enhanced soil nutrient content. Warming increased the abundance of functional genes involved in carbon fixation (e.g., acs, acsA, PCCA, MUT), whereas nitrogen addition suppressed nitrification and denitrification genes. Warming also enhanced the abundance of genes related to inorganic phosphate solubilization (ppk, ppx), phosphorus mineralization (phnPP, phnF, glpQ), and phosphorus transport (pstBC, ugpABCE). Functionally, warming increased the relative abundance of beneficial taxa such as Sphingomicrobium, Massilia, and Nocardioides, while reducing Pseudomonas, Trinickia, and Rhizomicrobium. Nitrogen deposition had a comparatively weaker effect on the functional microbial community. Correlation analysis between metabolites and functional genes suggested that alkaloids, organic acids, and phenolic compounds may be key drivers of microbial functional shifts. Overall, our findings demonstrate that warming has a greater influence than nitrogen deposition on shaping the rhizosphere soil microbial community and enhancing nutrient cycling functions, potentially increasing the risk of A. trifida invasion under future climate change.}, } @article {pmid41743327, year = {2026}, author = {Lee, SC and Tee, MZ and Shen, Z and Er, YX and Neelam, R and Cadwell, K and Segre, JA and Lim, YAL and Loke, P}, title = {Functional divergence of the gut microbiome associated with lifestyle and helminth infection in Indigenous Peninsular Malaysian.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41743327}, issn = {2693-5015}, support = {R00 AR084058/AR/NIAMS NIH HHS/United States ; }, abstract = {Gut microbiome catalogs from Indigenous Southeast Asian populations remain underrepresented. Here, we integrated metagenomic and metatranscriptomic data from Indigenous Orang Asli (OA) in Peninsular Malaysia and urban residents of Kuala Lumpur (KL), together with immune profiling, to investigate gut microbial activity and functions associated with lifestyle and helminth infection. Prevotella showed significantly higher transcriptional activity in OA, whereas Bacteroides was more active in KL, corresponding to distinct immune signatures. Microbial genome-wide association studies (mGWAS) revealed Prevotella copri_A variants were linked to lifestyle and host immunity, while Blautia strain variation was associated with helminth infection. Malaysian metagenome-assembled genomes (MAGs) uncovered 307 novel species, predominantly within Clostridia. Among these, the novel HGM13006 species were enriched with genes for starch and sucrose metabolism, and the novel Ruminococcus_D species in flagellar assembly and chemotaxis. Together, these findings provide function-level insights into gut microbiome variation associated with lifestyle and helminth infection in an indigenous population.}, } @article {pmid41743798, year = {2026}, author = {Wang, X and Ma, T and He, W and Shan, T and Zhang, G and Peng, F and Chen, L and Ma, J and Ding, C and Niu, P and Chen, T}, title = {Disrupted Tryptophan Metabolism Mediates Manganese-Induced Neurogenesis and Neuroinflammatory Impairments: Rescue by Exogenous Melatonin.}, journal = {Environment & health (Washington, D.C.)}, volume = {4}, number = {2}, pages = {275-290}, pmid = {41743798}, issn = {2833-8278}, abstract = {Manganese (Mn) is a common environmental pollutant, and excessive exposure can lead to motor dysfunction resembling Parkinson's disease. Increasing evidence suggests that Mn impairs endogenous neurogenesis and hinders neural repair. This study aims to investigate the effects of both acute and long-term Mn exposure on neurogenesis and to elucidate the underlying mechanisms. By establishing acute (7 and 14 days) and long-term (2 and 4 months) Mn exposure mouse models, we assessed neurogenesis under different exposure conditions. The mRNA sequencing, untargeted metabolomics, and metagenomics were employed to uncover the molecular pathways involved in Mn-induced neurogenesis impairment. The results revealed that early stage Mn exposure, including acute and 2 months exposure, transiently promoted neurogenesis. However, prolonged Mn accumulation in the brain led to suppressed neurogenesis, accompanied by neuroinflammation and oxidative stress, which contributed to a vicious cycle of neural damage. Multiomics analyses identified dysregulation of the tryptophan metabolic pathway as a key mechanism, with a marked reduction in melatonin levels following Mn exposure. Notably, exogenous melatonin supplementation effectively rescued Mn-induced impairments in neurogenesis, neuronal integrity, and neuroinflammation. These findings provide new insights into Mn neurotoxicity and highlight melatonin as a potential therapeutic agent for Mn-related neural damage.}, } @article {pmid41743802, year = {2026}, author = {Wei, H and Xu, Y and Jin, B and Zhao, X and Yang, X and Guan, Q and Gao, B and Zhang, Z and Sun, H and Ye, Y and Ikeda, A and Xia, Y}, title = {Population-Level Amplicon and Metagenomic Analyses Uncover Distinct Effects of Landscape-Level Pesticides on the Maternal Gut Microbiome.}, journal = {Environment & health (Washington, D.C.)}, volume = {4}, number = {2}, pages = {246-258}, pmid = {41743802}, issn = {2833-8278}, abstract = {The environment dominates over host genetics in shaping the gut microbiome, which plays a pivotal role in modulating human health. Experimental evidence supports the notion that exposure to pesticides could perturb the gut microbiome, and the toxicant-induced dysbiosis may affect host homeostasis. However, the field of human studies, especially in early life, is still in its infancy. We aimed to evaluate the effects of landscape pesticide exposure on the maternal gut microbiome. Here, we assessed the blood levels of a broad array of pesticides in 405 pregnant women. Gut microbial compositions and functional profiles were assessed by using both 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing. Microbial alpha diversity indices were regressed on host and environmental factors using linear models. Differences in overall microbial compositions were evaluated by using univariable permutational multivariate analyses of variance (PERMANOVA) with Bray-Curtis dissimilarities. All pesticides, as well as other host and environmental factors, were correlated to the gut microbiome at the phylum, genus, species, and pathway levels employing the multivariable regression models adjusted for the potential covariates, respectively. The joint effects of the mixture of pesticide exposure on the gut microbiome were investigated using quantile g-computation. Microbial ecological networks were constructed via Spearman correlations to explore species co-occurrence patterns related to pesticide exposure. Significant associations were observed between exposure to various pesticides individually or as a mixture and maternal gut microbiome features. Specific taxa and pathways were enriched or depleted in response to varying pesticide concentrations, indicating the potential exposure-response relationships. Notably, mirex exposure showed a positive correlation with both the relative abundance of Blautia_wexlerae and the sucrose biosynthesis II pathway. Microbial co-occurrence network analyses revealed marked shifts in species interactions associated with increasing levels of pesticide exposure. Mediation analyses further identified a greater number of microbial taxa, particularly Blautia_wexlerae, as significant mediators linking pesticide exposure to alterations in microbial functional pathways. Our large-scale amplicon and metagenomic analyses unraveled the extensive impacts of landscape-level pesticides on the maternal gut microbiome. Further observational and experimental research is warranted to validate our findings as well as to elucidate whether and how these microbial changes affect maternal and offspring health.}, } @article {pmid41743993, year = {2026}, author = {Li, G and Puumala, E and Zhang, Z and Rajapakse, NS and Ristagno, EH and Wolf, MJ and Rodning, AA and Simner, PJ and Gaensbauer, JT and Patel, R}, title = {Cerebrospinal Fluid Metagenomic Next-Generation Sequencing in Pediatric Central Nervous System Infection: Clinical Experience and Diagnostic Stewardship Strategies.}, journal = {Open forum infectious diseases}, volume = {13}, number = {2}, pages = {ofag054}, pmid = {41743993}, issn = {2328-8957}, abstract = {BACKGROUND: Identification of the microorganisms causing infection in children with central nervous system infection is important. Conventional cerebrospinal fluid (CSF) tests may provide limited pathogen detection. CSF metagenomic next-generation sequencing (mNGS) may provide broader pathogen detection in a single assay.

METHODS: Results of CSF mNGS testing performed at Mayo Clinic on patients and nonpatients between January 2024 and June 2025 were retrospectively analyzed. The subcohort of children treated at Mayo Clinic was analyzed to assess test performance as compared with conventional CSF diagnostics and potential clinical impact.

RESULTS: In total 134 patients (138 CSF mNGS tests) from 22 US states and 2 international sites were included. Overall positivity was 16% with viruses representing most (59%) detections. In the Mayo Clinic subcohort (n = 15), test positivity was 27%: organisms included single detections of Streptococcus mitis group and HIV type 1, as well as 2 detections of Epstein-Barr virus, all confirmed by conventional tests. Positive results were associated with CSF pleocytosis (P = .026). Higher yield was observed in participants whose care was overseen by pediatric infectious diseases (PID) specialists (P = .026) and when a specimen hold strategy was applied (P = .033). Most results (87%) did not alter antimicrobial therapy, with 2 negative results contributing to antimicrobial de-escalation.

CONCLUSIONS: CSF mNGS demonstrated higher diagnostic yield in patients whose specimens showed CSF pleocytosis and in those who had PID consultation. Diagnostic stewardship strategies were applied, including specimen hold approaches and PID consultation.}, } @article {pmid41744501, year = {2026}, author = {Whitham, JM and Goller, CC}, title = {Improving knowledge of metagenome-assembled genomes (MAGs) through bioinformatics and article annotation.}, journal = {Journal of microbiology & biology education}, volume = {27}, number = {1}, pages = {e0022625}, pmid = {41744501}, issn = {1935-7877}, support = {R25 GM130528/GM/NIGMS NIH HHS/United States ; }, abstract = {DNA from microbial communities can be sequenced and assembled to gain insight into the microbes that may be present in unique environments. Powerful computational tools, combined with more accessible sequencing technologies, have enabled metagenome-assembled genome (MAG) analysis in course-based settings. However, the computational methods and assumptions surrounding the creation of MAGs, as well as their application in understanding microbes in biomes, are often complex and intimidating to new users. The metagenomics course we designed enrolls undergraduate and graduate students in a half-semester lab experience. We hypothesized that collaborative annotation of specific bioinformatics research articles, paired with student application of tools using guided case studies on the powerful KBase bioinformatics web platform, would enhance learning of key MAG concepts. Student learning outcomes on conceptual quizzes, as well as learner perceptions of the assignment and confidence in using KBase and other bioinformatics tools, were analyzed. Assessments and surveys of student perceptions were collected over several semesters using consistent assignments, readings, and KBase narratives. Learning gains were identified for specific MAG analysis concepts and data interpretation. Nevertheless, misconceptions continue, and confidence in bioinformatics approaches varies. Additional exploration of qualitative data may suggest concepts to reinforce and resources to support learners. Combining KBase, collaborative annotation of primary literature, guided case studies, and aligned assessments effectively promotes students' conceptual and mechanistic understanding of MAGs and the assumptions underlying their creation and use.}, } @article {pmid41744504, year = {2026}, author = {Firrman, J and Liu, L and Mahalak, K and Lemons, JMS and Narrowe, A and Friedman, ES and Wu, GD and Van de Weile, T}, title = {An in vitro model of the small intestinal microbiota provides key insights into interindividual variability in structure and function.}, journal = {mSystems}, volume = {11}, number = {3}, pages = {e0137325}, pmid = {41744504}, issn = {2379-5077}, support = {P30 DK050306/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; *Intestine, Small/microbiology ; Metabolomics/methods ; Metagenomics ; *Bacteria/classification/genetics/metabolism ; }, abstract = {UNLABELLED: Although there is clear evidence demonstrating the importance of the small intestinal microbiota (SIM) for nutrient utilization within the upper gastrointestinal tract, research is limited by difficulties accessing this community in vivo. Additionally, the high level of interindividual variability in taxonomic structure, which is well documented for the SIM, raises the question of how such divergent communities fill the same physiological roles. Here, we designed and evaluated an in vitro model of the terminal ileum representative of four unique donors and utilized it to interrogate interindividual variability. Shotgun sequencing confirmed that the in vitro communities were representative of their specific inocula and composed of facultative and obligate anaerobic taxa typical of the SIM, such as Klebsiella, Escherichia, Streptococcus, and Enterococcus. Untargeted metabolomics revealed a high degree of similarity between communities in terms of which metabolites were produced. Combining metagenomics and metabolomics, a core set of genes, features, and metabolites was found shared across all communities despite the high degree of structural variability observed. These results indicated that while the taxonomic structure of the SIM was variable between individuals, there were similarities in functional outcome due to underlying gene representation in the microbiome. Moving forward, this model system may serve as a starting point to further elucidate the role of the SIM in nutrition and health.

IMPORTANCE: The small intestinal microbiota (SIM) plays a pivotal role in nutrient digestion and absorption and immune function, with researchers continuing to find connections between this community and human health. Expanding on the currently available methods within the field to study this community, here, an in vitro model of the SIM was developed and designed to mimic the terminal ileum. Metagenomic and metabolomic analysis confirmed that this model recapitulated the unique communities of four different donors while maintaining the interindividual variability canonical of the SIM. Despite variation in taxonomic structure, in-depth analysis found that there was a core set of genes shared among the four in vitro communities that correlated with a relatively consistent metabolomic signature. These significant findings provided unique insight into the relationship between structural and functional variability for the SIM and furthered the field's understanding of how such structurally variable communities have such similar physiological outcomes.}, } @article {pmid41745076, year = {2026}, author = {Murmu, M and Singh, R and Gaikwad, R and Banodkar, A and Barage, S and Sudhakara, P and Santhosh Kumar, AW}, title = {Comparative Analysis of Oral Microbiome in Indian Type 2 Diabetes Mellitus (T2DM) and Periodontitis Cohorts.}, journal = {Diseases (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {41745076}, issn = {2079-9721}, abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) and periodontitis are highly prevalent immune-inflammatory diseases that interact bidirectionally. However, how early-onset T2DM, periodontitis, and adverse lifestyle behaviors collectively remodel the gingival plaque microbiome at the ecological network level remains poorly understood in Indian populations.

METHODS: A cross-sectional 16S rRNA gene (V3-V4) sequencing study was conducted on supragingival and subgingival plaque from 60 adults (30-40 years) recruited in Mumbai. Participants were categorized as healthy (H, n = 10), periodontitis (P, n = 10), T2DM (n = 20), and T2DM with periodontitis (T2DM_P, n = 20). Comprehensive demographic, anthropometric, metabolic, periodontal, dietary, lifestyle, and oral hygiene data were collected. Sequence data were processed using QIIME2-DADA2, followed by diversity, differential abundance, and genus-level co-occurrence network analyses (Spearman |r| ≥ 0.6, FDR < 0.05; core prevalence ≥ 70%).

RESULTS: α-diversity showed no marked depletion across groups, whereas Bray-Curtis β-diversity revealed significant global separation, with maximal dissimilarity between H and T2DM_P. Healthy individuals with favorable lifestyle behaviors harbored scaffold-forming taxa such as Corynebacterium matruchotii, Lautropia mirabilis, and Capnocytophaga spp. In contrast, P and T2DM_P groups showed enrichment of proteolytic, inflammation-adapted genera including Porphyromonas, Tannerella, Treponema, Fretibacterium, Peptostreptococcus, and Selenomonas. Network analysis revealed a shift from commensal-rich modular networks to densely connected, keystone-centered disease modules.

CONCLUSION: Early-onset T2DM and periodontitis, particularly under adverse lifestyle behaviors, reorganize plaque microbial composition and interaction architecture rather than depleting diversity, highlighting plaque-based keystone taxa and networks as targets for microbiome-informed risk stratification and integrated medical-dental-lifestyle interventions.}, } @article {pmid41745125, year = {2026}, author = {Gori Savellini, G and Alessandri, G and Beligni, G and Badano, D and Fanciulli, PP and Frati, F and Cusi, MG}, title = {Metagenomic sequencing discloses the virome composition of mosquitoes and sandflies from Central-Southern Tuscany, Italy.}, journal = {Microbiology spectrum}, volume = {14}, number = {4}, pages = {e0186725}, pmid = {41745125}, issn = {2165-0497}, support = {PE00000007 CUP B63C22001400007 INF-ACT//Ministero dell'Università e della Ricerca/ ; Programma Nazionale per la Ricerca (PNR) (D.M. 737)//Ministero dell'Università e della Ricerca/ ; PRIN2022 PNRR Grant No. P2022WYNAH)//Ministero dell'Università e della Ricerca/ ; }, mesh = {Animals ; Italy ; *Virome/genetics ; Metagenomics ; Flavivirus/genetics/isolation & purification/classification ; Phlebovirus/genetics/isolation & purification/classification ; *Aedes/virology ; *Psychodidae/virology ; *Culicidae/virology ; Humans ; *Culex/virology ; Phylogeny ; }, abstract = {Mosquitoes and sandfly species are well-known vectors of viral pathogens of public health concern. However, the diversity and ecology of viruses within mosquitoes, including those responsible for clinical and sub-clinical infections in humans, remain poorly understood. In this study, we investigated the presence of phleboviruses and flaviviruses in Aedes albopictus and Culex pipiens mosquitoes, as well as Phlebotominae species, collected from the Siena and Grosseto districts (Tuscany, Italy) during the 2022-2024 summer season. Furthermore, A. albopictus and C. pipiens larvae were reared under laboratory conditions, and adults were collected for further virological analysis. Molecular investigations (reverse-transcription polymerase chain reaction [RT-PCR]) detected phleboviruses and/or flaviviruses in several batches of both field-collected and laboratory-reared flies. Notably, the highest incidence and co-circulation of both viral genera were observed in samples from the 2024 season. Furthermore, metagenomic analysis was performed on only 42 out of 67 RT-PCR-positive pools of mosquitoes and sandflies. This approach aimed to identify wild-type or recombinant viruses and assess the virome of autochthonous arthropods, contributing to knowledge on viral ecology in southern Tuscany and potential threats to humans. The resulting data revealed a wide viral community shared among mosquitoes, spanning over 30 taxonomic virus families, albeit no potential human pathogen virus was identified. Furthermore, our findings confirmed the mosquito specificity of certain endogenous arthropod viruses and provided evidence of their potential transovarial transmission in some cases. The present study provides a comprehensive analysis of the mosquitoes and sandflies virome, contributing to viral surveillance efforts and underscoring the need for enhanced monitoring of arthropod-borne pathogens.IMPORTANCEIn this study, we analyzed the co-circulating phleboviruses and flaviviruses, providing foundational data on the diversity, composition, and transmission of insect-specific and vector-borne viruses in Central-Southern Tuscany, an area increasingly exposed to arbovirus threats due to climate change and globalization. This is the first comprehensive metagenomic study to characterize the virome of Aedes albopictus, Culex pipiens, and Phlebotomine spp. in this region. Furthermore, we identified for the first time Punique virus (PUNV) in Italy, a phlebovirus with potential (though not yet confirmed) human pathogenicity.}, } @article {pmid41745296, year = {2026}, author = {Wang, Y and Insuk, C and Olson, C and Xu, J}, title = {Metagenomic and Genomic Analyses Reveal Prevalent Spread and Evolution of the Bat White-Nose Pathogen Pseudogymnoascus destructans in Western Canada.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {41745296}, issn = {2309-608X}, support = {2000803492//Environment and Climate Change Canada/ ; }, abstract = {Bats play a crucial role in the ecosystem. However, North American bat populations have experienced a dramatic decline since 2006 due to white-nose syndrome, a disease caused by Pseudogymnoascus destructans (Pd). This fungus can invade and damage the skin on bat wings and muzzles during hibernation. Since 2021, Pd has been reported at selected sites in western Canada, the region with the highest bat diversity in Canada, eliciting urgent calls for action among diverse stakeholders. Here we analyze nine metagenomes of bat guanos and wing swabs and the genomes of five Pd strains from western Canada to investigate the distribution and diversity of Pd in this region. Pd was found in all nine metagenomic samples and the metagenome sequences enabled us to identify the associated bat species. Divergence time estimates of Pd based on whole-genome sequences suggest that Pd likely entered Alberta two to five years before its first official report. Furthermore, we found evidence of abundant gene copy number variations in this species. Together, our metagenomic and genomic analyses indicate that Pd is more prevalent than currently recognized and is evolving and diversifying. Continued surveillance with more comprehensive methods is needed to accurately track its spread and facilitate timely management of white-nose syndrome in North America.}, } @article {pmid41745484, year = {2026}, author = {Serna-García, R and Lanzoni, Y and García-Depraect, O and Muñoz, R and Cantera, S}, title = {Harnessing Biogas into High-Value Chemicals: The Role of Algal-Methanotrophic Co-Cultures.}, journal = {Marine drugs}, volume = {24}, number = {2}, pages = {}, pmid = {41745484}, issn = {1660-3397}, support = {CIAPOS/2022/70//Generalitat Valenciana, Conselleria de Educación, Universidades y Empleo/ ; PID2022-139110OA-I00//Spanish Ministry of Science and Innovation/ ; UIC393, UIC 379//Regional Government of Castilla y León/ ; }, abstract = {The conversion of biogas into high-value chemicals for pharmaceutical, cosmetic, and nutraceutical markets offers an attractive alternative to conventional fossil-based production routes, enabling circular value chains with significant socio-economic impact. This study evaluated the valorization of biogas into osmolyte and carotenoid compounds with market prices ranging from 1000 to 7000 $·kg[-1]. Specifically, an algal-methanotrophic co-culture operated under saline conditions, preventing external microbial contamination and stimulating osmolytes and carotenoids, was assessed for its capacity to simultaneously remove methane (CH4) and carbon dioxide (CO2), with efficiencies of 92 and 89%, respectively. while producing ectoine, hydroxyectoine, lutein, β-carotene, and astaxanthin. Shotgun metagenomic analyses identified the key microorganisms driving the process, predominantly alkaliphilic and halophilic green algae (Chlorella, Dunaliella) and cyanobacteria (Leptolyngbya), and halotolerant methanotrophs (Methylotuvimicrobium) and methylotrophs (Methylophaga). Metagenomics further revealed the presence of key metabolisms related to C1 utilization and biosynthetic genes associated with carotenoid and osmolyte production, confirming the metabolic potential of the consortium to convert biogas-derived carbon directly into high-value compounds. Overall, these results demonstrate the feasibility of an efficient, biologically driven bio-platform capable of transforming greenhouse gas-rich waste streams into economically relevant bioactive molecules, contributing to global priorities in sustainable biomass-to-biochemical innovation.}, } @article {pmid41745624, year = {2026}, author = {Liu, Y and Diao, M and Hao, Y and Liu, Z and Ma, H and Zou, Y and Ma, L and Wang, L and Zhi, W and Yu, Q}, title = {Acute High-Intensity Noise Exposure Induces Cognitive Impairment and Arachidonic Acid Metabolism-Related Molecular Alterations in Rats: A Multi-Omics Study.}, journal = {Metabolites}, volume = {16}, number = {2}, pages = {}, pmid = {41745624}, issn = {2218-1989}, abstract = {Background: Acute high-intensity noise exposure represents a critical environmental stressor; however, its impact on brain function and the underlying mechanisms remain incompletely understood. This study aimed to investigate the effects of acute high-intensity noise exposure on cognitive function in rats, utilizing multi-omics analysis to explore potential mechanisms. Methods: Rats were exposed to acute noise at 120 dB, and brain function was evaluated using the novel object recognition (NOR) test, recordings of electroencephalographic activity, and histopathological examination. Longitudinal serum metabolomics and fecal metagenomics were performed on samples collected at 0 h, 7, 14, and 28 days post-exposure. Quantitative profiling of oxylipins and proteomics were conducted at a critical time point, followed by integrative multi-omics network analysis. Results: Acute high-intensity noise exposure significantly reduced the recognition index in the NOR test, increased theta-band power, and induced hippocampal neuronal damage. Multi-omics analyses revealed time-dependent alterations in gut microbiota and metabolic profiles, identifying day 7 as the critical response window, with arachidonic acid (AA)-derived metabolites consistently downregulated across omics layers. Integrated analysis revealed a coordinated microbiota-oxylipins-proteins network, highlighting key AA-derived oxylipins (e.g., 8-HETE, 12-HETE) that correlated with specific gut microbiota and proteins involved in lipid metabolism and inflammation. Conclusions: Acute high-intensity noise exposure induces cognitive impairment and systemic molecular disturbances. AA-centered lipid metabolism acts as a key hub linking gut microbiota dysbiosis with inflammatory and metabolic protein alterations, providing multi-omics evidence for coordinated microbiota-lipid-protein dysregulation underlying noise-induced neurobiological dysfunction.}, } @article {pmid41745919, year = {2026}, author = {Elmagzoub, WA and Weidmann, M and Elnaiem, MHE and Dennig, A and Waller, U and Bernhard, A and Junhold, J and Abd El Wahed, A and Truyen, U and Ceruti, A}, title = {Microbiome as a Tool to Monitor Aquarium Systems.}, journal = {Veterinary sciences}, volume = {13}, number = {2}, pages = {}, pmid = {41745919}, issn = {2306-7381}, abstract = {The bacterial microbiome in aquaria plays an essential role in system stability by metabolizing toxic compounds like ammonia. This study monitored microbiome changes in seven zoo aquatic systems during their first year to assess responses to external influences. Over one year (October 2021-October 2022), water and swab samples were collected from one seawater tank and six filtration systems at regular intervals. Bacterial cultivation included total bacterial counts. Metagenomic analysis was performed on samples corresponding to environmental events using Oxford Nanopore sequencing. Taxonomical analysis at the phylum and genus levels used EPI2ME software. Diversity analyses and statistical tests were performed using R. Total bacterial counts increased steadily after inoculation and stabilized by the end of the collection period. Diversity analysis revealed significant differences within and between freshwater and saltwater tanks. Each aquarium exhibited a distinct bacterial community with frequent compositional changes. Despite environmental conditions and maintenance interventions and resulting disturbances that affected the microbiome, the overall nitrifying capacity remained unaffected. Nitrifying taxa emerged as potential indicators for environmental effects. Combined with investigations of ecological function, next-generation sequencing could facilitate the development of aquarium management protocols, ultimately improving fish welfare.}, } @article {pmid41746166, year = {2026}, author = {Joshi, B and Zulk, JJ and Serchejian, C and Hameed, ZA and Larson, AB and Terwilliger, AL and Kumar, D and Mysorekar, IU and Britton, RA and Maresso, AW and Patras, KA}, title = {Bacteriophage-mediated reduction of uropathogenic E. coli from the urogenital epithelium.}, journal = {Infection and immunity}, volume = {94}, number = {4}, pages = {e0054325}, pmid = {41746166}, issn = {1098-5522}, support = {F31 DK136201/DK/NIDDK NIH HHS/United States ; F31 DK136201/NH/NIH HHS/United States ; U19 AI157981/NH/NIH HHS/United States ; Early Career Award Program//Thrasher Research Fund/ ; }, mesh = {*Uropathogenic Escherichia coli/virology ; Humans ; Female ; Animals ; *Escherichia coli Infections/therapy/microbiology ; Mice ; *Urinary Tract Infections/microbiology/therapy ; *Phage Therapy/methods ; Vagina/microbiology ; Epithelial Cells/microbiology ; *Bacteriophages/physiology ; Cell Line ; Disease Models, Animal ; }, abstract = {Urinary tract infections (UTIs), primarily caused by uropathogenic Escherichia coli (UPEC), affect millions annually. UPEC gains access to the urinary tract through mucosal reservoirs, including the vaginal tract. With rising antibiotic resistance and frequent recurrence, alternative non-antibiotic strategies like bacteriophage (phage) therapy are gaining attention. We explored the potential of a lytic phage, ΦHP3, as well as a phage cocktail to decolonize UPEC from the urogenital tract using in vitro and in vivo models. Phage demonstrated replication and lytic activity in both bacteriologic medium and simulated vaginal fluid. Pretreatment of human vaginal epithelial cells (VK2/E6E7) and bladder carcinoma cells (HTB-9) with phage reduced adhesion and invasion of UPEC compared with controls. Phage treatment was further able to reduce intracellular UPEC in VK2 cells. Notably, phage pretreatment did not impact phage-resistant UPEC strains, indicating that phage lysis was the primary driver of phenotypes. Live confocal microscopy confirmed the interaction of phage particles with UPEC and with both epithelial cell lines. In vivo, daily intravaginal ΦHP3 administration in humanized microbiota mice significantly reduced vaginal UPEC burden after 4 days. Treatment with a phage cocktail also reduced vaginal and cervical tissue burdens by day 7 post-treatment. UPEC dissemination was observed in uterine and kidney tissues, but burdens were not different between phage and mock-treated groups. In conclusion, we demonstrate that phage and phage cocktails can modestly reduce UPEC urogenital colonization, highlighting the potential of phage therapy as a viable prevention strategy for UTI.}, } @article {pmid41746975, year = {2026}, author = {Wang, G and Liu, L and Zhang, H and Mao, P and Lu, S and Zhang, X and Li, X and Song, C}, title = {Effects of tacrolimus treatment on the gut microbiota and metabolites in liver transplant recipients.}, journal = {PloS one}, volume = {21}, number = {2}, pages = {e0343817}, pmid = {41746975}, issn = {1932-6203}, mesh = {Humans ; *Tacrolimus/therapeutic use/adverse effects/pharmacology/administration & dosage ; *Liver Transplantation/adverse effects ; Female ; *Gastrointestinal Microbiome/drug effects ; Male ; *Immunosuppressive Agents/therapeutic use/adverse effects ; Middle Aged ; Feces/microbiology ; Adult ; }, abstract = {BACKGROUND: Liver transplantation (LT) is an effective treatment for patients with end-stage liver disease. In recent years, more and more evidence has supported the association between gut microbiota dysbiosis and the pathogenesis and progression of liver diseases.

METHODS: The study included 36 patients who received tacrolimus treatment after liver transplantation. Patients were stratified into subgroups according to three key variables: tacrolimus treatment duration, whole-blood tacrolimus concentration, and tacrolimus concentration-to-dose (C/D) ratio. Fecal samples and whole-blood specimens were collected from all participants. The Illumina HiSeq X platform was used to detect the gut metagenome, analyzing the composition and characteristics of the gut microbiota. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology was employed to detect metabolites of the gut microbiota, revealing their metabolic profiles.

RESULTS: As the duration of tacrolimus use increased, the diversity of the gut microbiota also increased, and the abundance of Escherichia coli_D and Bacteroides stercoris rose. Additionally, the abundance of Brunovirus and Uetakevirus tended to decrease. The abundance of gene functions related to chemical carcinogenesis and bacterial invasion of epithelial cells significantly decreased. In the gut microbiota metabolites, 16 substances like Astragaloside A and Acetyl-L-carnitine significantly increased, while 108 substances like Capsaicin and TLK significantly decreased. Within a certain range, as the concentration of tacrolimus in whole blood increased, the diversity of the gut microbiota increased. The abundance of Phocaeicola and Klebsiella increased, and the abundance of Peduovirus among viruses also rose. However, excessively high concentrations may lead to a decrease in the diversity of the gut microbiota and a decrease in the abundance of Phocaeicola. With respect to the C/D ratio, increased ratios were linked to significantly higher levels of 57 fecal metabolites (e.g., PC 34:2, 5-Methyl-2'-deoxycytidine), whereas 13 metabolites (e.g., FAHFA 2:0/16:0) showed substantial declines.

CONCLUSIONS: Tacrolimus treatment is associated with distinct alterations in gut microbiota and metabolites among LT recipients. These findings provide a preliminary framework for future investigations aimed at optimizing immunosuppressive regimens, although their clinical translational potential requires validation in larger-scale, prospective cohort studies.}, } @article {pmid41747414, year = {2026}, author = {Zhang, Q and Bao, C and Wang, K and Liu, L and Huang, H and Cai, S and Lu, H and Zheng, S and Luo, J and Kong, J}, title = {The impact of bronchiectasis on the lung microbiota of community-acquired pneumonia patients: An mNGS-based study.}, journal = {Computational biology and chemistry}, volume = {123}, number = {}, pages = {108948}, doi = {10.1016/j.compbiolchem.2026.108948}, pmid = {41747414}, issn = {1476-928X}, mesh = {Humans ; *Bronchiectasis/microbiology/complications ; *Microbiota/genetics ; *Community-Acquired Pneumonia/microbiology ; Female ; Male ; *Lung/microbiology ; Retrospective Studies ; Middle Aged ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {BACKGROUND: Changes in lung microbiota are associated with bronchiectasis and its clinical parameters. However, it is unclear whether distinct microbiota patterns reflect the characteristic lung status in bronchiectasis.

OBJECTIVE: This study aimed to identify key microbiota associated with community-acquired pneumonia (CAP) complicated with bronchiectasis and explore its relationship with clinical features.

METHODS: A single-center retrospective study enrolled 59 CAP patients who underwent bronchoscopy. Bronchoalveolar lavage samples were analyzed using metagenomic next-generation sequencing. The top 10 bacterial species and α- and β-diversity indices were compared between patients with and without bronchiectasis. Linear discriminant analysis was used to identify distinctive microbes. Spearman was used to analyze the correlation between the distinctive microbes and clinical characteristics.

RESULTS: The CAP with bronchiectasis group was dominated by Pseudomonas, while Prevotella dominated the non-bronchiectasis group. The bronchiectasis group had significantly lower α-diversity and distinct β-diversity compared to the non-bronchiectasis group. Stutzerimonas was identified as a key microbe in the bronchiectasis group, positively correlated with lymphocyte percentage and count, and negatively correlated with neutrophil percentage. Pseudomonas aeruginosa and Nocardia pneumoniae were key species in the bronchiectasis group.

CONCLUSION: The composition and diversity of lung microbiota in patients with CAP combined with bronchiectasis are significantly different. The genus Stutzerimonas can serve as a key marker to distinguish bronchiectasis from non-bronchiectasis patients to reflect the characteristic lung microbiota status. This study provides a potential basis for disease stratification and personalized management.}, } @article {pmid41747516, year = {2026}, author = {Hu, X and Yu, K and Chai, B and Tang, Q and Gao, X and Wang, J and Yan, Z and Li, Y and Zhang, L and Wang, C and Lei, X and Chen, B and He, L}, title = {Polyethylene microplastics specifically drive the dissemination of ARGs: Mechanisms involving microbial community restructuring and horizontal gene transfer.}, journal = {The Science of the total environment}, volume = {1021}, number = {}, pages = {181587}, doi = {10.1016/j.scitotenv.2026.181587}, pmid = {41747516}, issn = {1879-1026}, mesh = {*Microplastics/toxicity/analysis ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Polyethylene/toxicity ; *Water Pollutants, Chemical/toxicity/analysis ; *Microbiota/drug effects ; Lakes/microbiology ; Genes, Bacterial ; }, abstract = {As emerging contaminants, the impact of microplastics (MPs) on antibiotic resistance genes (ARGs), virulence factors (VFs), and host microbial communities in lakes remains unclear. To address this, we conducted a 28-day incubation experiment using water from Yiquan Lake, employing metagenomic sequencing to investigate the effects of different types of microplastics-polyethylene (PE), polystyrene (PS), polypropylene (PP), and a mixture (Mix), each at a concentration of 1 item/L-compared to a raw water control (RAW). Results showed significant enrichment of Proteobacteria and Bacteroidetes in PE and Mix groups. Genera such as Agrobacterium and Microbacterium increased in PE and PS groups, serving as major hosts of ARGs and VFs. Network analysis revealed positive correlations between Agrobacterium, Escherichia, and ARGs, suggesting horizontal gene transfer may facilitate the spread of resistance and virulence. Two-factor PS formed highly connected yet competitive networks, whereas Mix constructed modular and stable networks. Single-factor PE enhanced microbial connectivity but reduced ARGs connectivity, while Mix increased the modularity of both microbes and ARGs. PE elevated the abundance of ARGs, VFs, and mobile genetic elements, with multidrug resistance and efflux pumps as dominant mechanisms. Additionally, PE downregulated quorum sensing transporter genes while upregulating regulatory factors, significantly promoting RND efflux systems (AcrAB-TolC) to maintain resistome homeostasis. This study highlights the distinct environmental effects of different MPs, underscoring the need to prioritize PE-related risks in aquatic ecosystems. Improved management of plastic waste in and around lakes is recommended to mitigate MP-mediated ARG dissemination and preserve freshwater ecosystem services.}, } @article {pmid41747669, year = {2026}, author = {Lin, C and Li, J and Zhao, A and Jiang, Y and Chen, F and Chen, L and Xu, J and Zhang, W and Huang, M and Ma, D and Xu, Q and Wang, C}, title = {Effect of electric field on lactic acid and ethanol production from food waste anaerobic fermentation.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {170}, number = {}, pages = {109248}, doi = {10.1016/j.bioelechem.2026.109248}, pmid = {41747669}, issn = {1878-562X}, mesh = {*Ethanol/metabolism ; *Fermentation ; *Lactic Acid/biosynthesis/metabolism ; Food Loss and Waste ; Anaerobiosis ; *Electricity ; Temperature ; }, abstract = {Electro-fermentation (EF) enhances product yields from food waste (FW). This study investigated the coupled effects of temperature (40 or 55 °C) and electric field (0.2-1.4 V) on ethanol and lactic acid production via anaerobic fermentation (AF). Results showed that a 1.4 V field at 40 °C (G23) boosted ethanol yield by 37.1%, while a 0.2 V field at 55 °C (G3) increased lactic acid yield by 60.3%. Notably, 0.2 V at 40 °C (G14) simultaneously enhanced both products. EF accelerated hydrolysis of polysaccharides and proteins, and modulated microbial communities, enriching key functional genera (Bacillus at 55 °C; Lactobacillus/Weissella at 40 °C). Metagenomic analysis revealed upregulated genes for ethanol dehydrogenase, lactate dehydrogenase, and NADH dehydrogenase under respective optimal conditions. This work demonstrates that tailored EF conditions can steer metabolic pathways, offering an efficient strategy for dual-bioproduct recovery from FW.}, } @article {pmid41747681, year = {2026}, author = {Chen, Z and Wang, X and Xu, Y and Chen, S}, title = {Molecular mechanisms underlying the mitigation of nitrous oxide emissions by hyperthermophilic composting fertilizer.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129067}, doi = {10.1016/j.jenvman.2026.129067}, pmid = {41747681}, issn = {1095-8630}, mesh = {*Nitrous Oxide ; *Fertilizers ; Soil Microbiology ; *Composting ; Soil/chemistry ; Bacteria ; }, abstract = {Nitrous oxide (N2O) emissions associated with fertilized agricultural soils are a major source of greenhouse gases. While hyperthermophilic composting reduces N2O emissions, how its products affect the niche distribution of nitrogen (N) cycling microorganisms and regulate N2O source-sink mechanisms remains unclear, limiting its application in soil ecosystems and further technology development. To address this, we established a pot-based experiment with different organic fertilizer treatments: no fertilization (NF), hyperthermophilic composting fertilization (HTCF), and thermophilic composting fertilization (TCF). Using gas chromatography combined with metagenomic sequencing and binning approaches, we investigated the effects of HTCF on soil N2O emissions and the associated microbial mechanisms. The results showed that organic fertilization significantly altered soil properties, influencing bacterial community succession and N2O emissions. Compared to TCF (9.57 g), HTCF (14 g) increased pakchoi biomass by 47.02%. Meanwhile, HTCF (2835 mg m[-2]) reduced N2O emissions by 47.15% compared to TCF (5364 mg m[-2]). HTCF decreased the abundance of N2O-producing genes, including norB and nirK, thereby contributing to lower N2O emissions. HTCF altered microbial community structure, resulting in a greater relative abundance of obligate N2O-reducing bacteria carrying the nosZ gene, which could contribute to reduced N2O emissions. HTCF significantly enriched microorganisms such as Nostoc, Rhizobium, Mesorhizobium, and Piscinibacter, maintaining a stable soil environment and promoting the smooth progress of N fixation and nitrification. These findings elucidate microbial mechanisms underlying HTCF-induced N2O mitigation and provide a scientific basis for integrated fertilization strategies to reduce greenhouse gas emissions.}, } @article {pmid41747689, year = {2026}, author = {Zhang, F and Zhou, T and Feng, Y and Chen, Y and Zhao, Q and Han, Q and Liu, J and Zhang, D and Jiang, H and Zhang, H}, title = {Metagenomic insights into the impacts of Vulcanococcus proliferation on microbial communities in a coastal bay.}, journal = {Marine environmental research}, volume = {217}, number = {}, pages = {107939}, doi = {10.1016/j.marenvres.2026.107939}, pmid = {41747689}, issn = {1879-0291}, mesh = {*Microbiota ; Seawater/microbiology ; Metagenomics ; *Bays/microbiology ; *Metagenome ; *Enterococcaceae/physiology ; }, abstract = {Cyanobacterial blooms pose a major ecological challenge globally, with their outbreaks exerting profound effects on aquatic ecosystems. Vulcanococcus, a recently described cyanobacterial genus previously thought to be restricted to freshwater habitats, was documented in this study proliferation in seawater for the first time. Here, we reconstructed prokaryotic metagenome-assembled genomes (MAGs), including Vulcanococcus and the associated bacteria, enabling the assessment of their metabolic potential and influence of proliferation of Vulcanococcus on marine ecosystems. The proliferation of Vulcanococcus significantly altered the prokaryotic community compositions in the water, leading to a marked decline in the stability of prokaryotic co-occurrence networks. Comparative genomic analysis revealed that Vulcanococcus MAGs clustered within the freshwater Vulcanococcus clade, suggesting a possible freshwater origin. The high-quality Vulcanococcus MAG possess a complete set of urea transporter genes as well as urease genes, highlighting its potential for efficient urea utilization. The genome of Vulcanococcus encodes critical genes involved in vitamin B1 biosynthesis and is capable for de novo vitamin B12 synthesis, implying that proliferation of Vulcanococcus may serve as an important source of B vitamins for phytoplankton. Furthermore, Vulcanococcus exhibited significant correlations with eukaryotic phytoplankton, including diatoms and dinoflagellates, suggesting that Vulcanococcus may enhance B-vitamin availability for phytoplankton. Overall, these findings provide novel insights into the ecological roles and metabolic versatility of Vulcanococcus in marine environments, underscoring its potential impact on microbial community dynamics and nutrient cycling.}, } @article {pmid41747700, year = {2026}, author = {Zhang, H and Du, Y and Guan, E and Xu, X and Zhang, P and Gao, L}, title = {Microbial mechanisms of protein degradation and nicotine removal during aerobic composting of tobacco waste as the sole nitrogen source.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141461}, doi = {10.1016/j.jhazmat.2026.141461}, pmid = {41747700}, issn = {1873-3336}, mesh = {*Nicotine/metabolism ; *Composting ; *Nicotiana/metabolism/chemistry ; *Nitrogen/metabolism ; Plant Leaves/metabolism ; Aerobiosis ; Animals ; Cattle ; Biodegradation, Environmental ; Manure/microbiology ; Germination ; Fermentation ; *Plant Proteins/metabolism ; Proteolysis ; }, abstract = {The massive accumulation of tobacco waste poses threats to environment safety and human health due to its high nicotine content. While aerobic composting represents an effective strategy for managing waste biomass, its application to fresh discarded tobacco leaves remains unreported. This study pioneered the use of tobacco leaves in aerobic composting and investigated the microbial mechanisms driving substrate transformation. Waste tobacco leaves are rich in protein and can be used as the sole nitrogen source of composting. The microbiota was characterized by a higher abundance of Bacillota and Pseudomonadota, but a lower abundance of Actinomycetota, compared with that during cattle manure composting as a control. The degradation of proteins in tobacco leaves was primarily mediated by proteases (e.g., families S8, S9, M42) secreted by Bacillota. Notably, a greater abundance of S8 family proteases was induced, of which two exhibiting larger substrate cavity volumes. Nicotine content decreased rapidly during initial fermentation, achieving a removal rate exceeding 97 % and meeting European Union safety standards. This degradation was primarily driven by the pyrrolidine pathway via Stutzerimonas stutzeri and Pseudomonas sp. Seed germination and pot experiments demonstrated the superior growth promoting effects of fermented tobacco leaves over cattle manure product. These findings elucidate the microbial mechanisms of tobacco waste fermentation and provide a theoretical basis for screening efficient nicotine-degrading strains and developing value-added fermentation products.}, } @article {pmid41747725, year = {2026}, author = {Chen, K and Liu, Y and Rong, J and Dai, N and Xu, C and Li, H and Zhong, L and Wang, B and Ji, Z and Xie, S and Xu, Y and Yang, F and Wang, J and Li, D and Gu, Y and Zhou, X and Li, Y and Chen, M and Chen, Y and Li, W and Tang, Z and Cai, J and Xu, J and Xia, S and Zhan, Q and Zhou, Z}, title = {Strain-level genetic heterogeneity and colonization dynamics drive microbiome therapeutic efficacy.}, journal = {Cell host & microbe}, volume = {34}, number = {3}, pages = {393-405.e5}, doi = {10.1016/j.chom.2026.02.002}, pmid = {41747725}, issn = {1934-6069}, mesh = {*Fecal Microbiota Transplantation ; Humans ; *Genetic Heterogeneity ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology ; *Lung Neoplasms/therapy/microbiology ; *Microbiota/genetics ; Metagenome ; Treatment Outcome ; *Gastrointestinal Microbiome/genetics ; Animals ; Bacteria/classification/genetics ; }, abstract = {Fecal microbiota transplantation (FMT) has shown immunotherapeutic promise, yet its efficacy in non-small-cell lung cancer (NSCLC) remains unclear. We demonstrate that FMT improves anti-PD-1 efficacy and progression-free survival in a single-arm trial of advanced PD-L1-negative NSCLC. Analyzing over 2,000 metagenomes from diverse disease cohorts and healthy controls via a high-resolution strain-tracking framework, we reveal that phylogenetically distinct strains within identical species exert opposing therapeutic effects, resolving prior inconsistencies. We identify conserved ecological principles where engraftment relies on species-intrinsic metabolic and immune evasion traits. Crucially, successful colonization by specific beneficial strain variants correlates with positive clinical outcomes. Finally, we identify 38 priority species with robust engraftment potential and significant heterogeneity as candidates for precision therapeutics. These findings establish a strain-function-efficacy paradigm, elucidating the mechanistic basis of variable outcomes and guiding next-generation microbiome drug development.}, } @article {pmid41747730, year = {2026}, author = {Matias Rodrigues, JF and Tackmann, J and Malfertheiner, L and Patsch, D and Perez-Molphe-Montoya, E and Näpflin, N and Gaio, D and Rot, G and Danaila, M and Peluso, ME and Dmitrijeva, M and Schmidt, TSB and von Mering, C}, title = {The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems.}, journal = {Cell}, volume = {189}, number = {7}, pages = {2092-2107.e17}, doi = {10.1016/j.cell.2026.01.021}, pmid = {41747730}, issn = {1097-4172}, mesh = {*Microbiota/genetics ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Earth, Planet ; Bacteria/genetics/classification ; Metagenomics ; Phylogeny ; }, abstract = {Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the entire planet-from the deep subsurface to the mountaintops-covering a myriad of hosts, biomes, and conditions. Yet, the diversity of sequencing and processing strategies hampers universal insights. MicrobeAtlas unifies more than two million microbiome samples in a single resource, harmonized to facilitate discoveries across technologies. Communities are hierarchically quantified at adjustable small subunit rRNA marker gene resolution and feature detailed metadata, including rich geographic information. Connections to the genome, phenotype, and ecological resources enable multimodal insights. Microbial lineages can be reliably tracked across environments, including a "long tail" of rare, uncharacterized species. Recurring community structures and geographic preferences become apparent, and global, taxonomy-specific generalism trends emerge. With MicrobeAtlas (www.microbeatlas.org), known and newly described species and communities can readily be placed into their ecological context, taking full advantage of earlier work.}, } @article {pmid41747902, year = {2026}, author = {Corso, D and Melita, M and Massaccesi, N and Quero, GM and Basili, M and Di Cesare, A and Sabatino, R and Sbaffi, T and Fazi, S and Rakaj, A and Luna, GM and Amalfitano, S}, title = {Constructed wetlands for aquaculture wastewater treatment: Insights on the structural and functional shifts of the aquatic microbial community.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134278}, doi = {10.1016/j.biortech.2026.134278}, pmid = {41747902}, issn = {1873-2976}, mesh = {*Aquaculture ; *Wastewater/microbiology ; *Wetlands ; *Water Purification/methods ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Bacteria/genetics ; Animals ; *Water Microbiology ; *Microbiota ; }, abstract = {Aquaculture practices generate nutrient-rich effluents with associated microbiological hazards, such as pathogens and antimicrobial resistance genes (ARGs). Despite their growing popularity as nature-based solutions, little is known about how constructed wetlands (CWs) affect the dynamics of microbial communities at the field scale. By combining flow cytometry, 16S rRNA gene sequencing, shotgun metagenomics, and metabolic potential assays, we investigated the structural and functional responses of the aquatic microbial community following the recurrent exposure to CW-treated effluents from an intensive marine fish farm (Orbetello lagoon, Italy). While the CW promoted abundant, metabolically active, and functionally redundant microbial communities, the phylogenetic composition diverged primarily between water and sediments. Microbial profiles in CW outlet waters converged towards those of the lagoon baselines, suggesting gradual ecological recovery. The CW attenuated the occurrence of potential pathogens, such as members of the genera Francisella and Campylobacter, and acted as a buffer system in ARG dissemination, with sediments serving as reservoirs of microbial and genetic signatures. Functional profiles, dominated by chemoheterotrophy, denitrification, and sulfur respiration, remained stable across environments, reflecting microbial resilience. Our results highlight CWs as effective, field-proven solutions to mitigate aquaculture wastewater impacts while preserving core ecosystem services.}, } @article {pmid41747903, year = {2026}, author = {Li, LX and Yang, TT and Yuan, Y and Han, YL and Zhao, Q and Wang, WH and Sun, Y and Cao, XX and Jiang, XL and Li, T and Wang, X}, title = {Rapid enrichment of ternary carbon-fixing microbial consortia from anaerobic sludge via pressurized pre-autotrophic strategy for scalable microbial electrosynthesis.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134276}, doi = {10.1016/j.biortech.2026.134276}, pmid = {41747903}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Microbial Consortia/physiology ; Acetates/metabolism ; Anaerobiosis ; *Carbon Cycle ; *Autotrophic Processes ; *Carbon/metabolism ; *Pressure ; Electrodes ; Bacteria/metabolism ; *Bioelectric Energy Sources ; }, abstract = {As a promising platform for microbially catalyzed carbon capture, microbial electrosynthesis (MES) is constrained by inoculation strategies that limit carbon fixation efficiency and scalability. Mixed-culture inocula outperform pure cultures in functional redundancy and ecological resilience in large systems, but slow acclimation and erratic community composition yield inconsistent performance. Here, this study presents a pressurized pre-autotrophic (PA) strategy that rapidly enriches carbon-fixing microorganisms (CFMs) from anaerobic sludge, in comparison with direct autotrophic (DA) and electrode reversal (ER) strategies. PA increased CFM abundance to 51%, 3.5-fold higher than in DA-MES and ER-MES (both 15%). Acetate production in PA-MES reached 14.47 g·m[-2]·d[-1]. In addition to enhanced acetate productivity, PA-MES exhibited superior electrochemical performance, achieving the highest Faradaic efficiency for acetate and energy efficiency among the tested systems, together with the lowest energy consumption per unit acetate. Metagenomic analysis revealed a PA-defined core community with coordinated activation of the Wood-Ljungdahl, rTCA, and methanogenic pathways, providing redundant routes for stable CO2 fixation. By transforming mixed-culture inocula into a functionally cohesive carbon-fixing community, the PA strategy enables rapid startup and sustained carbon fixation, offering a practical framework for scalable MES.}, } @article {pmid41747907, year = {2026}, author = {Wang, Z and Hong, Y}, title = {Atmospheric and room-temperature plasma mutagenesis of microalgae for efficient swine wastewater treatment and bioresource recovery.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134287}, doi = {10.1016/j.biortech.2026.134287}, pmid = {41747907}, issn = {1873-2976}, mesh = {Animals ; *Wastewater/microbiology/chemistry ; *Microalgae/genetics/metabolism ; *Mutagenesis ; *Temperature ; *Water Purification/methods ; Nitrogen/isolation & purification ; *Plasma Gases/pharmacology ; Swine ; Chlorella/genetics/metabolism ; Phosphorus/isolation & purification ; }, abstract = {In response to the serious harm of swine wastewater (SW) and the drawbacks of existing treatment technologies, this study innovatively applies atmospheric and room-temperature plasma (ARTP) mutagenesis, followed by a four-round screening process strategy (solid actual SW (ASW) medium, growth in liquid ASW, comprehensive performance in the sterilized ASW (S-ASW), final evaluation in the unsterilized ASW (US-ASW)) to cultivate high-performance mutant microalgae for the efficient treatment of ASW without complex and expensive pretreatment or other strengthening methods. Chlorella sorokiniana HWY30-4 was eventually selected for its good adaptability and ASW treatment performance. The removal efficiencies of Chlorella sorokiniana HWY30-4 to total nitrogen (TN), NH4[+]-N, and total phosphorus (TP) for US-ASW were 60.31%, 80.07%, and 94.12%, respectively. In addition, HWY30-4 accumulated abundant high-value substances (0.06 g/L polysaccharides, 0.13 g/L proteins, and 0.23 g/L lipids) while treating US-ASW. Metagenomics revealed that the performance enhancement mechanisms mainly involve the enhanced critical metabolic pathways, alongside beneficial microbial synergies. This study offers an efficient and viable route for simultaneous ASW treatment and bioresource recovery, underscoring the potential of ARTP-based strain improvement in strengthening the microalgal performance for environmental governance.}, } @article {pmid41748019, year = {2026}, author = {Piccinno, G and Asnicar, F}, title = {Advanced computational analysis in metagenomic studies to support precision medicine.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {32}, number = {7}, pages = {1075-1080}, doi = {10.1016/j.cmi.2026.02.018}, pmid = {41748019}, issn = {1469-0691}, mesh = {Humans ; *Precision Medicine/methods ; *Metagenomics/methods ; *Computational Biology/methods ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The human microbiome has been linked to host health and is suggested to play a direct role in the onset of certain human diseases, as well as in impacting treatment efficacy. Characterizing the microbiome composition and its interaction with the host is now supported by an established, continuously improving set of bioinformatic and statistical resources that enable reproducible answers to fundamental questions about microbiome sample composition and its association with sample and host information. Extensive evidence highlighted that, in a nondiseased state, the microbiome composition is determined by multiple factors, including the acquisition of microbes at birth, lifestyle, dietary patterns, social interactions, antibiotic use, or probiotic intake, among others. In disease states, the microbiome may alter its composition and, in some cases, present specific biomarkers, as in colorectal cancer. Some microbiome components have also been associated with improved immunotherapy response in clinical oncology, suggesting a potential beneficial role for certain species and supporting the use of the microbiome as an additional therapeutic tool in these scenarios.

OBJECTIVES: This review summarizes computational approaches for microbiome characterization, highlights key findings on microbiome-disease associations, and provides a perspective on directions and open questions relevant to address in the future.

SOURCES: We selected scientific studies and reviews, published in peer-reviewed journals, based on their impact in the field and relevance to the topic of this manuscript. Literature selection was conducted by reviewing scientific publications retrieved from major scientific databases, such as PubMed, and by combining with the authors' knowledge of the literature.

CONTENT: Here we review computational approaches to characterize and model the microbiome's structure in health and disease and discuss multicohort data analysis, integration, and validation methods.

IMPLICATIONS: Improved microbiome characterization supports precision medicine by informing prevention or treatment, leveraging refined microbiome signature and modulation strategies.}, } @article {pmid41748043, year = {2026}, author = {Alvaro-Fuss, M and DeClercq, V and Blodgett, JM and Theou, O and Langille, MGI and Beiko, RG}, title = {Effect of bedrest on the human gut and oral microbiome: implications for frailty.}, journal = {Experimental gerontology}, volume = {216}, number = {}, pages = {113079}, doi = {10.1016/j.exger.2026.113079}, pmid = {41748043}, issn = {1873-6815}, mesh = {Humans ; Aged ; Female ; Male ; Middle Aged ; *Bed Rest ; *Frailty/microbiology ; *Gastrointestinal Microbiome/physiology ; *Mouth/microbiology ; Feces/microbiology ; Saliva/microbiology ; *Microbiota ; *Head-Down Tilt/physiology ; Aging/physiology ; Exercise/physiology ; Frail Elderly ; }, abstract = {The physiological effects of spaceflight resemble those of ageing and prolonged inactivity, and ground-based microgravity analogs have emerged as promising models for studying frailty. The human microbiome is increasingly recognised for its role in age-associated decline, although precise mechanisms remain unclear. Here, we evaluate the gut and oral microbiomes of twenty-two participants, aged 55-65, who were enrolled in a head-down tilt bedrest (HDBR) study, the first Canadian HDBR study conducted in an older cohort. Participants were randomly assigned to an inactivity or multi-modality exercise intervention group for fourteen days of HDBR, followed by seven days of rehabilitation and additional follow-up appointments. Gut (n = 343) and oral (n = 344) taxonomic profiles were generated using V4-V5 16S rRNA gene sequencing from fecal and salivary samples collected throughout the study. Gut functional profiles were generated using metagenomic (n = 86) data, used for pathway inference, and metabolomic (n = 83) data. Frailty was measured using a 36-item frailty index. Inactivity-associated changes to the gut microbiome during HDBR included decreasing α-diversity, decreasing Akkermansia and Lactobacillus, and increasing Bacteroides. Exercise-associated changes included increasing gut Roseburia. Both gut and oral β-diversity were associated with frailty scores and individual frailty components. We conclude that inactivity-associated changes to the human microbiome are associated with the early stages of frailty development, and that exercise may serve as an effective countermeasure against these effects. These results may inform strategies to preserve the health of both older adults facing prolonged periods of inactivity, as well as astronauts during longer space exploration missions.}, } @article {pmid41748159, year = {2026}, author = {Liu, W and Lu, Y and Ng, SC and Chan, FK and Sung, JJ and Yu, J}, title = {Bacterial genomic structural variations in children with autism serve as diagnostic biomarkers.}, journal = {Gut}, volume = {75}, number = {5}, pages = {937-948}, pmid = {41748159}, issn = {1468-3288}, mesh = {Humans ; Animals ; Child ; Mice ; Female ; Male ; Biomarkers ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Autism Spectrum Disorder/microbiology/diagnosis ; *Genome, Bacterial/genetics ; Child, Preschool ; *Bacteria/genetics ; Dysbiosis/microbiology ; Disease Models, Animal ; Metagenome ; }, abstract = {BACKGROUND: Gut microbiota dysbiosis is linked to autism spectrum disorder (ASD) in children. However, the role of bacterial genomic structural variations (SVs) in ASD remains largely unexplored.

OBJECTIVE: We aimed to identify bacterial SVs associated with ASD and explore their mechanistic role and clinical application.

DESIGN: We collected faecal metagenomes from 452 children (261 ASD, 191 neurotypical) across an in-house and seven public datasets. Using linear mixed-effects modelling, we identified ASD-associated SVs and compositional shifts and validated candidate SVs in humanised gut microbiome mice.

RESULTS: We identified 100 bacterial SVs significantly associated with ASD (p<0.05). These SVs were enriched in genes involved in critical biological processes, including ion and amino acid metabolism and bacterial growth regulation in ASD. In particular, we found important SVs in Bacteroides uniformis related to thiamine and iron metabolism. Moreover, SVs in Ruminococcus torques were associated with the MazF (endoribonuclease toxin) and MazE (antitoxin) system, a key regulator of pathobiont proliferation. Validation in humanised mouse models confirmed significant correlations between these SV signatures and ASD-like behaviours, such as reduced social interaction and increased repetitive behaviours. Both phylogeographically conserved and regionally restricted SVs showed strong associations with ASD. A diagnostic model combining nine SVs and three bacterial species achieved an area under the receiver operating characteristic curve of 81.1%, outperforming models based solely on variable SVs (79.1%), deletion SVs (75.2%) or bacterial species abundance alone (72.3%).

CONCLUSION: Our findings suggest the significant role of bacterial genomic SVs in ASD and highlight their potential as diagnostic biomarkers.}, } @article {pmid41748614, year = {2026}, author = {Ma, Z and Xu, X and Peng, W and Zhang, T and Chen, Z and Cao, S and Zhang, F and Wang, Y and Xiao, H and Zhang, Y and Liu, Z and Liu, Z and Xue, H and Long, Q and Hou, T and Wang, W and Liu, Y and Jin, Z and Zhang, M and Peng, Y and Wen, J and Gaut, B and Zhou, Y}, title = {Population genomics reveals association of transposable elements variants with climatic adaptation in wild Amur grape.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41748614}, issn = {2041-1723}, support = {32300191//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32372662//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Vitis/genetics/physiology ; Polymorphism, Single Nucleotide ; Genome, Plant/genetics ; *DNA Transposable Elements/genetics ; Climate Change ; *Adaptation, Physiological/genetics ; Genetic Variation ; Genetics, Population ; Genomics ; Metagenomics ; Plant Breeding ; *Acclimatization/genetics ; }, abstract = {Amur grape (Vitis amurensis Rupr.) is widely recognized for its cold tolerance traits and serves as a valuable genetic resource for breeding climate-resilient grape cultivars. Here, we construct a graph pangenome reference (Vampan_V1.0) and generate a variant map comprising 48,308,434 short variants and 127,094 TE-associated structural variants (TEVs) using deep resequencing data from 330 samples across 31 natural populations covering the species' distribution range. We discover a biased accumulation of SNPs around TEVs and identify 823 candidate adaptive genes associated with environmental variables. Using machine learning-based genetic offset models, we further show that putative adaptive TEVs significantly reduce genetic offsets by 7.3% to 8.2% under future climate scenarios. Our study shows the power of a graph-based pangenome to resolve complex variation and highlights the impact of TEVs on genetic diversity, local adaptation, and resilience to future climate change, providing insights into utilizing crop wild relatives in climate-resilient crop breeding.}, } @article {pmid41748627, year = {2026}, author = {Huang, Z and Petersen, JM}, title = {Recovery of metagenome-assembled genomes from Spartina alterniflora root microbiome in Fujian Province, China.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41748627}, issn = {2052-4463}, support = {2025J01967//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; }, mesh = {China ; *Metagenome ; *Plant Roots/microbiology ; *Poaceae/microbiology ; *Microbiota ; *Genome, Bacterial ; }, abstract = {The saltmarsh cordgrass Spartina alterniflora proliferates along the coast of China. Like all plants, S. alterniflora hosts a specific microbiome that plays crucial roles in sustaining plant growth and health. Till now, very few studies have investigated the root microbiome of S. alterniflora in China, where it is considered an invasive pest. Here, ~350 Gbp metagenomes of S. alterniflora were generated from 8 sampling sites in South Fujian Province, China. 798 bacterial metagenome-assembled genomes (MAGs) and 7 archaeal MAGs were obtained, which were de-replicated into 205 and 3 representative genomes at a 95% ANI cutoff. The recovered bacterial MAGs mainly belonged to Gammaproteobacteria, Alphaproteobacteria, Bacteroidia and Campylobacterota. Sedimenticolaceae were prevalent at all sampling sites, accounting for 4-30% of the corresponding MAGs. These genomic datasets provide a new resource for investigating S. alterniflora root microbiomes, particularly valuable considering current efforts to eradicate this species in China.}, } @article {pmid41749104, year = {2026}, author = {Baz, L}, title = {Functional potential of archaeal KEGG enzymes in the Moringa oleifera rhizosphere revealed by metagenomic analysis.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41749104}, issn = {1471-2164}, abstract = {BACKGROUND: Archaea are a major domain of life that inhabit diverse and often extreme environments, contributing to biogeochemical cycles and participating in nutrient cycling within plant rhizospheric soils. This study applies metagenomic whole-genome shotgun sequencing to characterize the archaeal component of the rhizospheric microbiome associated with the wild plant species Moringa oleifera in Saudi Arabia.

RESULTS: Based on KEGG-annotated enzymes, Thaumarchaeota and Euryarchaeota emerged as the predominant archaeal phyla in the rhizosphere, with higher abundance than in bulk soil. The most abundant archaeal enzymes were assigned to metabolic pathways related to nitrogen and sulfur metabolism, carbon transformations, and responses to oxidative stress, indicating a putative contribution to nutrient turnover and stress-related functions. Network analysis further identified archaeal chemotaxis-related regulators and two-component sensor kinases linked to the root–soil interface. Key enzymes detected included urease, glutamine synthetase, thiosulfate sulfurtransferase, and catalase-peroxidase.

CONCLUSIONS: These findings suggest that archaeal communities form a distinct functional module within the M. oleifera rhizosphere, potentially influencing soil nutrient dynamics and plant performance. The chief limitation is reliance on DNA-based metagenomic data from a single site and time point, without multi-omics or detailed soil characterization, restricting temporal and ecological generalization. Nonetheless, the dataset provides a genome-scale view of archaeal functional potential and offers testable directions for future experimental and process-oriented studies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12700-3.}, } @article {pmid41749291, year = {2026}, author = {Haro-Moreno, JM and Díaz-Arinero, E and Aldeguer-Riquelme, B and Rubio-Portillo, E}, title = {Effects of marine heatwaves on the dynamics of marine coastal microbial communities.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41749291}, issn = {2524-6372}, support = {CIGE/2022/21//Generalitat Valenciana/ ; }, abstract = {BACKGROUND: Climate change is projected to intensify and prolong marine heatwaves, characterized by abnormally high sea surface temperatures. These events can profoundly alter ecosystem composition and functioning, sometimes triggering mass mortality events. The Mediterranean Sea, due to its semi-enclosed nature, is particularly susceptible to warming, with future climate scenarios predicting a temperature increase of up to 3.8 °C and at least one persistent heatwave annually by 2100. Despite this vulnerability, the effects of marine heatwaves on seawater microbial and viral communities remain poorly understood.

RESULTS: Using microcosm experiments, we examined microbial and viral dynamics under control conditions (20 °C) and two simulated marine heatwaves (MHWs) (23 °C and 25 °C). By the end of the experiment, microbial assemblages in all three conditions were dominated by metagenome-assembled genomes (MAGs) that were not detected in the initial natural sample, indicating the competitive success of rare biosphere taxa over initially abundant species. Virulence factors and antibiotic resistance genes increased in relative abundance throughout the incubation, but such increase was amplified under warming conditions. Temperature also shaped viral strategies, with heatwaves showing a higher percentage of integrated lysogenic viruses compared to control samples. This trend was consistent with observations from natural samples, where lysogenic viruses peaked during warmer months.

CONCLUSIONS: The shift toward lysogeny observed under elevated temperatures may enhance horizontal gene transfer, accelerating the spread of virulence and antibiotic resistance genes. In fact, we observed an increased abundance of these genes in samples under heat stress. These processes could weaken ecosystem resilience, disrupt microbial-driven biogeochemical cycles, and amplify risks to marine and human health. Our study underscores the need to integrate microbial and viral responses into predictions of ocean functioning in a rapidly warming world.}, } @article {pmid41749306, year = {2026}, author = {Liu, Z and Liu, M and Chen, H and Li, S and Zheng, N and Xing, G and Zhang, Y and Xu, J and Li, M and Xiao, C and Lu, T and Yan, Q and Lei, Z and Feng, M and Li, Y}, title = {Distinct gut virome profiles are associated with response to anti-PD-1 therapy in non-small cell lung cancer.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41749306}, issn = {1479-5876}, abstract = {BACKGROUND: The gut microbiota is a key modulator of immune checkpoint inhibitor (ICI) efficacy, yet the contribution of the gut virome remains poorly defined, particularly in advanced non–small cell lung cancer (NSCLC). Here, we characterized the gut virome and explored its potential role in shaping response to PD-1 blockade.

METHODS: We performed metagenomic virome profiling of fecal samples from 338 advanced NSCLC patients treated with PD-1 inhibitors and evaluated model generalizability in an independent external cohort (n = 30). Viral diversity, taxonomic composition, and functional potential were analyzed. Virus–bacteria co-occurrence networks were constructed, and random forest classifiers were developed to predict treatment response.

RESULTS: Viral Shannon diversity decreased progressively with poorer clinical response, and β-diversity analyses revealed distinct virome community structures between responders (R) and non-responders (NR). Differential abundance analysis identified 194 NR-enriched vOTUs, predominantly assigned to Peduoviridae and Inoviridae, and 594 R-enriched vOTUs, mainly from Herelleviridae and Microviridae. Host prediction indicated that NR-enriched vOTUs frequently targeted bacterial genera such as Clostridium_M, Bacteroides, and Escherichia, whereas R-enriched vOTUs targeted beneficial genera such as Faecalibacterium and Roseburia. Network analyses further revealed response-specific virus–bacteria interaction modules. Functional profiling showed that NR-enriched vOTUs were associated with metabolic functions, including K01689 (eno; enolase). A virus-only random forest model outperformed a bacterium-only model in predicting response (area under the curve [AUC] = 0.768 vs. 0.664) and maintained superior performance in the external cohort (AUC = 0.742). In addition, Akkermansia muciniphila positivity was associated with a higher-diversity, responder-favorable virome configuration.

CONCLUSIONS: The gut virome undergoes marked remodeling during anti–PD-1 therapy in advanced NSCLC and displays distinct taxonomic, ecological, and functional signatures associated with clinical outcome. These findings support the gut virome as a strong predictor of ICI response and highlight its potential as both a biomarker and a therapeutic target.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07900-0.}, } @article {pmid41749685, year = {2026}, author = {Zhu, Y and Tang, Y and Qi, X and Zhu, X}, title = {Transformer Models, Graph Networks, and Generative AI in Gut Microbiome Research: A Narrative Review.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, pmid = {41749685}, issn = {2306-5354}, support = {Grant No. LCMYZHYX-KFKT202303//Open Project of the Sichuan Provincial Key Laboratory for Clinical Immunology and Translational Medicine/ ; Grant No. 2022JC03//Scientific Research Foundation of Chengdu Women's and Children's Central Hospital/ ; }, abstract = {BACKGROUND: The rapid advancement in artificial intelligence (AI) has fundamentally reshaped gut microbiome research by enabling high-resolution analysis of complex, high-dimensional microbial communities and their functional interactions with the human host.

OBJECTIVE: This narrative review aims to synthesize recent methodological advances in AI-driven gut microbiome research and to evaluate their translational relevance for therapeutic optimization, personalized nutrition, and precision medicine.

METHODS: A narrative literature review was conducted using PubMed, Google Scholar, Web of Science, and IEEE Xplore, focusing on peer-reviewed studies published between approximately 2015 and early 2025. Representative articles were selected based on relevance to AI methodologies applied to gut microbiome analysis, including machine learning, deep learning, transformer-based models, graph neural networks, generative AI, and multi-omics integration frameworks. Additional seminal studies were identified through manual screening of reference lists.

RESULTS: The reviewed literature demonstrates that AI enables robust identification of diagnostic microbial signatures, prediction of individual responses to microbiome-targeted therapies, and design of personalized nutritional and pharmacological interventions using in silico simulations and digital twin models. AI-driven multi-omics integration-encompassing metagenomics, metatranscriptomics, metabolomics, proteomics, and clinical data-has improved functional interpretation of host-microbiome interactions and enhanced predictive performance across diverse disease contexts. For example, AI-guided personalized nutrition models have achieved AUC exceeding 0.8 for predicting postprandial glycemic responses, while community-scale metabolic modeling frameworks have accurately forecast individualized short-chain fatty acid production.

CONCLUSIONS: Despite substantial progress, key challenges remain, including data heterogeneity, limited model interpretability, population bias, and barriers to clinical deployment. Future research should prioritize standardized data pipelines, explainable and privacy-preserving AI frameworks, and broader population representation. Collectively, these advances position AI as a cornerstone technology for translating gut microbiome data into actionable insights for diagnostics, therapeutics, and precision nutrition.}, } @article {pmid41750438, year = {2026}, author = {Suzhaeva, L and Egorova, S and Polev, D and Saitova, A and Starkova, D}, title = {Fluoroquinolone Resistance Patterns in Multidrug-Resistant Escherichia coli from the Gut Microbiota of Young Children.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41750438}, issn = {2079-6382}, abstract = {Background/Objectives: The high prevalence of fluoroquinolone-resistant E. coli in healthy children represents a significant public-health risk, facilitating the spread of antimicrobial resistance and increasing the potential for difficult-to-treat extraintestinal infections with severe clinical outcomes. This study aimed to investigate the prevalence of fluoroquinolone resistance in multidrug-resistant E. coli isolated from presumptively healthy children in St. Petersburg, Russia, with a particular focus on fluoroquinolone resistance determinants. Methods: Phenotypic AST was performed on 307 E. coli isolates from fecal pediatric samples, comprising 230 isolates from 2012 to 2013 and 77 isolates from 2021 to 2022. A subset (n = 47) of MDR isolates underwent whole-genome sequencing. Results: The frequency of MDR E. coli strains rose significantly from 15.7% to 32.5% over the study period. The most significant increases in resistance among E. coli strains were to third-generation cephalosporins (CTX, CTZ) and fluoroquinolones (CIP), rising fourfold over a decade. Based on phenotypic resistance profiles of MDR E. coli to quinolones, the highest resistance rates were observed for MFX (80.9%) followed by NAL (74.5%), LVX (44.7%) and CIP (40.4%). Genotypic analysis revealed distinct pathways: low-level NAL resistance required only an S83 mutation in gyrA, whereas low-level MFX resistance was predominantly conferred by a plasmid-borne qnr gene. In contrast, resistance to CIP and LVX involved at least three QRDR mutations: S83L and D87N/Y in gyrA, and S80I in parC. Notably, our study showed the predominance of the ST131 and ST38 clones in E. coli isolated from pediatric samples. Conclusions: Our findings suggest that the efficacy of moxifloxacin for empirical treatment of infections caused by MDR E. coli might be severely compromised. Overall, the current study highlights that the pediatric gut microbiota serves as a reservoir for resistant E. coli with the expansion of multidrug-resistant clones independently of direct antibiotic selection pressure.}, } @article {pmid41750446, year = {2026}, author = {Magnano San Lio, R and Maugeri, A and Barchitta, M and Favara, G and La Rosa, MC and La Mastra, C and Ferrante, M and Agodi, A}, title = {The Wastewater Resistome: A Shotgun Metagenomics Analysis of Urban Treatment Plants in Sicily.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41750446}, issn = {2079-6382}, support = {MUR-PNRR project SAMOTHRACE (ECS00000022)//European Union (NextGeneration EU)/ ; }, abstract = {Background/Objectives: Antimicrobial resistance (AMR) in wastewater represents a valuable reservoir of information for wastewater-based epidemiology (WBE) and a major environmental and public health concern, as wastewater treatment plants (WWTPs) are recognized hotspots for the accumulation and dissemination of antimicrobial resistance genes (ARGs). Within the One Health framework, and to better understand the contribution to AMR spread and the potential of metagenomic surveillance, this study aimed to characterize the taxonomic, functional, and resistome profiles of three WWTPs in Sicily, specifically those located in Catania, Giarre, and Syracuse. Methods: Sixty-nine composite influent samples were collected between February 2022 and December 2023. Shotgun metagenomic sequencing was performed on the Illumina NovaSeq platform. Bioinformatic analyses were conducted to assess microbial community composition, functional pathways, and ARG prevalence across sites. Results: Dominant genera included Aliarcobacter, Bacteroides, and Acinetobacter. Site-specific taxonomic variations reflected differences in local microbial ecology. Functional profiling revealed enrichment in membrane-associated, ribosomal, and energy metabolism pathways, consistent with the expected functional redundancy of wastewater microbiomes. Resistome analysis detected a diverse and ubiquitous array of ARGs, dominated by β-lactam and macrolide resistance genes, followed by aminoglycoside, sulphonamide, and tetracycline classes. Conclusions: These findings highlight urban wastewater as a relevant reservoir and dissemination route for AMR and support the integration of metagenomic approaches into wastewater surveillance programs. By providing region-specific, integrated taxonomic, functional, and resistome data from Sicilian WWTPs, this study contributes to the growing body of evidence supporting WBE as a valuable tool for AMR monitoring and One Health-oriented risk assessment.}, } @article {pmid41750451, year = {2026}, author = {Agga, GE and Loughrin, J}, title = {Evaluation of Anaerobic Digestion Amended with Micro-Aeration and/or Sound Treatment on the Resistome and Virulence Factor Gene Profiles in Poultry Litter.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41750451}, issn = {2079-6382}, support = {5040-12630-007-000-D//U.S. Department of Agriculture, Agricultural Research Service/ ; }, abstract = {Background: Commercial broiler farms produce a large amount of litter that must be removed. Anaerobic digestion (AD) is animal manure management technology with the added benefit of producing reusable energy. Our team previously showed that the micro-aeration and sound treatment of animal manure during AD increase biogas production. However, their influence on antimicrobial resistance genes (ARGs) and bacterial virulence factor genes (VFGs) is unknown. Therefore, the objective of this study was to evaluate the effect of AD on the resistome and VFGs in poultry litter (PL) and see if the effect is modified by micro-aeration and/or sound treatments. Methods: A field experiment was conducted in four anaerobic digesters that consisted of a control (a standard AD system with no air or sound), micro-aeration, sound, and combined micro-aeration and sound treatments. Overall, 21 samples were collected and analyzed with shotgun metagenomic sequencing. The samples included digestate samples (n = 12) from the four digesters obtained at 6 (baseline, i.e., before beginning of micro-aeration and sound treatments), 23 and 42 weeks, raw PL samples (n = 4), two disks comprised of the same wood as the bedding material, an initial digestate seed sample, and two initial week 0 mix samples. Results: Across all sequence reads (n = 3190) obtained from 21 samples, over 80% of the resistome was composed of four antimicrobial classes: macrolides-lincosamides-streptogramins, tetracyclines, aminoglycosides, and glycopeptides. While the total number of ARGs declined in the control digestor, it increased over time in micro-aerated or sound-treated digesters, and their combination greatly increased the number of ARGs detected. This is a new finding, and it clearly shows that micro-aeration, sound, and their combination treatment during the anaerobic digestion of PL enriches ARGs. In contrast, sound-treated AD by itself significantly (p = 0.035) reduced the mean total ARG abundance compared to the control. The number and abundance of ARGs detected in the initial digestate and PL were lower than those in the AD samples, indicating their enrichment during the AD process. On the other hand, although the AD samples had a lower frequency and abundance of VFGs than the PL, AD did not completely remove the VFGs, and their detection frequency increased over time. While micro-aeration increased the abundance of VFGs compared to the control, this effect was countered by its combination with sound treatment, offering a good animal manure treatment strategy to reduce bacterial VFGs. Conclusions: Although additional research may be required, it was shown that while sound treatment may enrich the occurrence of ARGs, it seems promising to reduce the abundance of ARGs and VFGs during the AD of PL. On the other hand, micro-aeration, alone or when combined with sound treatment, increases the abundance of both ARGs and VFGs. Moreover, the study showed that AD, with or without micro-aeration and sound treatment, is not effective for the complete removal of ARGs and VFGs from poultry litter. Rather, AD systems may act as a hotspot for ARGs, and post-AD treatments such as composting need to be evaluated.}, } @article {pmid41750879, year = {2026}, author = {Samantaray, P and Saha, S}, title = {Decoding the Microbial Diversity of Indian Fermented Foods: Integrating Ethnobiology, Multi-Omics and Functional Insights.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, pmid = {41750879}, issn = {2304-8158}, support = {SRMAP/URG/SEED/2023-24/049//SRM University Andhra Pradesh/ ; }, abstract = {India's diverse culinary heritage includes a wide spectrum of traditional fermented foods that harbour complex microbial communities essential for flavour development, preservation, and nutritional enhancement. These microorganisms-primarily lactic acid bacteria, yeasts, and molds-contribute functional properties that extend beyond food transformation to confer health benefits, including probiotic potential and metabolic regulation. This review integrates classical microbiological studies with modern molecular approaches such as metagenomics, metatranscriptomics, and metabolomics to elucidate the microbial diversity of Indian fermented foods. It highlights how geography, substrates, and ethnic traditions shape region-specific microbial consortia sustained through long-standing ethno-microbiological practices. Special focus is given to the glycemic modulation achieved through microbial fermentation, wherein organic acid production and resistant starch formation lower glycemic index and improve glucose metabolism. These processes, along with enhanced nutrient bioavailability, vitamin synthesis, and immunomodulation, illustrate the broader functional potential of fermentation. The review also examines interactions between food-borne microbes and the human gut microbiota, underscoring implications for personalized nutrition. Finally, it discusses modernization and commercialization strategies and outlines future directions involving multi-omics integration, indigenous starter cultures, and microbiome-based innovations to harness India's microbial heritage for improved health and sustainable food development.}, } @article {pmid41751034, year = {2026}, author = {Wang, J and Cheng, M and Huang, F and Chen, L and Xu, W and Cai, J and Chen, Z and Zhao, Y and Zhang, X}, title = {Metagenomic-Metabolomic Integration Reveals Gut Microbiota Dynamics and Metabolic Changes in Super-Geriatric Captive Giant Pandas.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, pmid = {41751034}, issn = {2076-2615}, support = {2025ZNSFSC0252//the Science and Technology Project of Sichuan Province/ ; }, abstract = {Age-related changes throughout the lifespan are known to influence gut microbiota composition, microbial functional potential, and host-associated metabolic processes. Understanding these age-related variations is important for elucidating their potential physiological implications at different life stages. However, information regarding the gut microbiome and metabolomic characteristics of super-geriatric captive giant pandas (Ailuropoda melanoleuca) remains limited. In this study, fecal samples were collected from adult and super-geriatric captive giant pandas and analyzed using metagenomic sequencing combined with untargeted metabolomics. The gut microbiota of super-geriatric individuals exhibited a marked decrease in Bacillota and an enrichment of Pseudomonadota compared with adult individuals. Functional profiling revealed age-associated shifts in microbial metabolic potential, with a transition from biosynthesis-dominated pathways toward pathways related to substrate degradation and energy utilization. Metabolomic analyses further revealed pronounced metabolic alterations in super-geriatric giant pandas, including elevated levels of unsaturated fatty acids and changes in bile acid-related metabolites. Alterations in gut microbiota composition, particularly the relative enrichment of Pseudomonadota-associated taxa, were associated with inflammation-related metabolic features. Collectively, these findings indicate coordinated changes in gut microbial composition and metabolic profiles during aging. Overall, this study characterizes age-associated alterations in gut microbiota structure and fecal metabolic signatures in super-geriatric captive giant pandas, providing a scientific basis for future studies on microbiota-metabolism interactions and for improving nutritional management and health monitoring strategies in aged individuals of this endangered species.}, } @article {pmid41751100, year = {2026}, author = {Yang, L and Xu, Z and Liu, D}, title = {The Effects of Dual-Yeast Compound Preparation on the Intestinal Health and Metabolism of Lambs.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, pmid = {41751100}, issn = {2076-2615}, support = {NDYB2022-5//Inner Mongolia Agricultural University High-level/excellent Doctoral Talent Introduction Research Project/ ; BR230118//University Basic Scientific Research Business Expenses Project-Young Teachers Research Ability Enhancement Fund Project, 2023 Financial Funds/ ; 2025MS03114//Natural Science Foundation of Inner Mongolia Autonomous Region Project/ ; SYKJZD202302//Discipline Project of College of Veterinary Medicine, Inner Mongolia Agricultural University/ ; }, abstract = {Microecological preparations exert beneficial effects on the health of young ruminant animals; however, the mechanism is unclear. As a result, the present study analyzed the effects of yeast cultures on the growth properties, microbiome, and metabolism of weaned lambs. In this study, a total of 20 weaned lambs were randomly, stochastically divided into four teams: the control group (Group A) were fed a basic diet; Group B were fed with Saccharomyces cerevisiae BC strain culture (30 g/head/d); Group C were fed with Kluyveromyces marquez XR4 strain culture (30 g/head/d); Group D were fed with a composite culture of the two yeast strains (30 g/head/d). The study lasted for 40 days, with daily records of lamb feed intake and weight. Lamb feces were collected regularly for metagenomic sequencing and metabolomics analysis. The average daily weight gain and average daily yield of Group D lambs were significantly higher than those of Group A lambs (p < 0.01). The feed utilization rate in the yeast-fed groups was considerably higher than in the control group (p < 0.05), indicating that the addition of yeast crops to lamb feed might improve lamb feed performance. Bacteroides and the mTOR signaling pathway were dramatically enriched in the intestines of weaned lambs in the yeast-culture-fed groups, and their expression levels of ketones and benzoic acid compounds were significantly upregulated. These results indicated that yeast culture had excellent effects on weaned lambs in regulating immunological functioning and the intestinal environment, protecting the enteric mucosal barrier, improving digestion and nutritional absorption, and enhancing antioxidant function. In summary, adding yeast culture to weaned lamb feed can generate a positive effect on its productivity performance and gut health. These findings provide novel insights into promoting the health of young ruminants.}, } @article {pmid41751138, year = {2026}, author = {Xu, Z and Liang, M and Li, J and Song, B and Zhang, M and Jiang, H and Chai, J and Zhao, J and Deng, F and Li, Y}, title = {16S rRNA Gene and Metagenomic Analysis Revealed an Association Between Cecal Microbiota and Pork Umami.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, pmid = {41751138}, issn = {2076-2615}, support = {2023YFE0124400//National Key Research and Development Program of China/ ; 2023B10564001//Specific University Discipline Construction Project/ ; No. 32202715//National Natural Science Foundation of China/ ; }, abstract = {Umami is a key determinant of pork flavor, but the association between the intestinal microbial community and umami differences remains unclear. Here, we used the taste-sensing electronic tongue system to divide the Duroc × Landrace × Yorkshire pigs into high, medium and low groups. We combined 16S rRNA gene and shotgun metagenomic sequencing to study the differences in the microbial community composition and functional genes. The results showed that the microorganisms in the cecum of different groups had a similar core microbial community. The Shannon diversity analysis showed that there were no significant differences among the different groups. The Bray-Curtis distance indicated that there were differences in the bacterial communities between the high umami group and the other two groups. The LEfSe analysis and Spearman correlation analysis revealed that the uncultured species CAG-632 sp900539185 maintained a high abundance in the high umami group and was significantly correlated with umami. Metagenomic functional analysis revealed distinct functional signatures among umami groups, with enrichment of genes related to carbohydrate transport and metabolism, butanoate and other short-chain fatty acid pathways, nitrogen utilisation, cell-surface structures, adhesion and RNA metabolism in high umami groups. These research findings indicate that the differences in the delicious flavor of pork are more likely to be associated with specific microbial species and the functional characteristics of the cecal microbial community, rather than the overall situation of the entire microbial community.}, } @article {pmid41751141, year = {2026}, author = {Xue, F and Zhang, F and Zhuang, Q and Jiang, L and Sun, M and Shang, J and Xiong, B}, title = {Metagenomic Insights into the Modulatory Effects of Thiamine Supplementation for Treating Subclinical Ketosis Dairy Cows.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, pmid = {41751141}, issn = {2076-2615}, support = {20242BAB20311//Natural Science Foundation Project of Jiangxi Province/ ; 2024YFD1300600//Integrated Demonstration of Intelligent Feeding and Environmental Control Technologies for Cattle and Sheep/ ; }, abstract = {(1) Background: The objective of this study was to investigate the modulatory effects of thiamine on BHBA metabolism, milk yield, and the rumen microbial ecosystem. (2) Methods: A total of 24 SCK dairy cows with similar body conditions were selected and randomly allocated to SCK (SCK) or SCK with thiamine supplement (SCKT) treatment. Twelve healthy dairy cows served as the control (CON) treatment. Milk yield, milk quality, ruminal fermentability parameters, rumen and fecal microbial communities were further measured. (3) Results: Thiamine significantly decreased BHBA content, milk CFUs, and somatic cells, while significantly increasing milk yield, milk fat, acetate, and the A/P ratio (p < 0.05). Thiamine-treated cows exhibited significantly increased ruminal and fecal Proteobacteria but significantly decreased ruminal Firmicutes (p < 0.05) as well as fecal Spirochaetes and Cyanobacteria (p < 0.05), compared with SCK cows. Functional analysis showed that differential rumen bacteria exhibited high energy metabolism, nucleotide metabolism, and glycan biosynthesis and metabolism, while the metabolism of terpenoids and polyketides were the primary functional pathways of differential fecal microbiota. (4) Conclusions: Thiamine supplementation in SCK cows effectively alleviated subclinical ketosis by reducing BHBA content, enhancing ruminal fermentability, and proliferating rumen microbial communities, leading to improved milk yield in the early-lactation period.}, } @article {pmid41752202, year = {2026}, author = {Jung, S}, title = {Microbiome-Genome Crosstalk in Colorectal Cancer: Colibactin Signatures and Fusobacterium nucleatum in Epidemiology, Driver Selection, and Translation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, pmid = {41752202}, issn = {1422-0067}, support = {RS-2022-NR069378//National Research Foundation of Korea/ ; RS-2025-18732993//National Research Foundation of Korea/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics/epidemiology ; *Fusobacterium nucleatum/genetics/physiology ; *Polyketides/metabolism ; *Peptides/metabolism ; Mutation ; *Microbiota ; }, abstract = {Colibactin, a genotoxin produced by pks[+]E. coli, imprints highly specific mutational signatures SBS88 and ID18 in colorectal cancer (CRC) and even in normal colonic crypts. Population-scale analyses show these signatures are enriched in early-onset CRC, vary geographically, and are imprinted early during tumor evolution, where probabilistic attribution indicates that colibactin contributes to a measurable fraction of APC driver mutations in colibactin-positive cancers. Beyond colibactin, Fusobacterium nucleatum exerts clade-specific effects on tumor ecology and therapy response, with data supporting both chemoresistance and sensitization to anti-PD-1 in microsatellite stable (MSS) CRC. This article covers mechanistic, genomic, and molecular epidemiology evidence, outlines analytic standards for signature detection (whole-genome sequencing (WGS)/whole-exome sequencing (WES), single-sample fitting, and limits at low mutation counts), and charts translational paths spanning noninvasive screening (stool metagenomics + mutational signatures in tissue/circulating tumor DNA (ctDNA)), risk stratification, and microbial-targeted interventions (antibiotics, phages, ClbP inhibitors). Framing microbiome-genome crosstalk as a tractable axis enables testable clinical hypotheses for precision oncology.}, } @article {pmid41752220, year = {2026}, author = {Kareem, HA and Khan, MF}, title = {Current Research Advances and Future Prospects on Microbial Consortia for Sustainable PFAS Remediation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, pmid = {41752220}, issn = {1422-0067}, support = {82930-NP//University College Dublin Internal Fund/ ; }, mesh = {Biodegradation, Environmental ; *Microbial Consortia ; *Fluorocarbons/metabolism ; *Soil Pollutants/metabolism ; Soil Microbiology ; }, abstract = {Soil contamination by per- and polyfluoroalkyl substances (PFAS) represents a pressing environmental and public health concern due to the exceptional persistence of carbon-fluorine bonds, which prevent natural attenuation and limit the effectiveness of conventional remediation. Agricultural and industrial soils serve as long-term sinks for PFAS, continuously releasing these pollutants into groundwater and facilitating their transfer through the food chain. Conventional chemical and physical remediation methods are often costly, energy-intensive, and yield incomplete removal, underscoring the need for sustainable and biologically driven alternatives. Microbial consortia have emerged as a promising solution due to their metabolic complementarities, cross-feeding interactions, and ecological resilience, which together enable PFAS transformation and partial defluorination under complex soil and subsurface conditions. Key enzymes such as oxygenases, reductive dehalogenases, and hydrolases are often operating within co-metabolic networks, which play central roles in these processes. Advances in metagenomics, CRISPR-based functional screening, and metabolic modelling are rapidly uncovering novel PFAS-degrading microbes and pathways. Integration of machine learning with multi-omics and environmental datasets further enables the prediction of degradation mechanisms, identification of keystone degraders, and rational design of synthetic consortia. Emerging sustainable strategies, including biochar- and nutrient-amended soil microcosms, plant-microbe partnerships for coupled soil-groundwater phytoremediation, and bioelectrochemical systems that offer new avenues for enhancing PFAS biodegradation in situ. This review synthesises recent research progress and provides critical perspectives on the mechanistic, ecological, and engineering dimensions of PFAS bioremediation, proposing an integrated conceptual framework linking microbial consortia dynamics, enzymatic pathways, and environmental engineering interventions to guide scalable field applications and sustainable management of PFAS-contaminated soil-groundwater ecosystems.}, } @article {pmid41752933, year = {2026}, author = {Mahbub, MH and Hase, R and Yamaguchi, N and Asai, Y and Harada, M and Ichimura, N and Hayakawa, Y and Inohana, Y and Umakoshi, Y and Yamaguchi, R and Kimura, R and Tsujimura, H and Matsumoto, M and Higashijima, F and Yoshimoto, T and Kimura, K and Hirano, T and Ohishi, K and Doi, K and Matsunaga, K and Tanabe, T}, title = {Gut Microbial Diversity and Community Structure Are Largely Similar Between Apparently Healthy Elderly Japanese Males and Females: A Shotgun Metagenomic Study.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {2}, pages = {}, pmid = {41752933}, issn = {2075-1729}, support = {21K10397//This research was supported by a joint project funded by Yamaguchi Prefecture, Yamaguchi City, Shimadzu Corporation, Kao Corporation, and Kyodo Milk Industry Co., Ltd. It was also supported by a Grant-in-Aid for Scientific Research from the Japan Society/ ; }, abstract = {Sex differences in gut microbiota may affect health and aging, but evidence in elderly populations is limited and inconsistent. This study examined sex-specific similarities and differences in gut microbiota diversity and composition among apparently healthy elderly Japanese individuals using shotgun metagenomic sequencing. A cross-sectional study was conducted in 100 community-dwelling adults aged 75-83 years (54 males, 46 females). Fecal samples underwent metagenomic sequencing. Alpha and beta diversity were assessed across six taxonomic levels, and taxonomic differences were evaluated using non-parametric tests. No significant sex differences were observed in alpha diversity indices (Shannon, Simpson, evenness, Chao1) at any taxonomic level. Beta diversity based on Bray-Curtis dissimilarity and PCoA also showed no sex-specific clustering. However, certain taxa differed in relative abundance. Males showed higher abundances of Bacteroidota (phylum), Bacteroidia and Betaproteobacteria (class), and Bacteroidales and Burkholderiales (order) (p < 0.05). No significant differences were detected at the family, genus, or species levels. Overall, gut microbial diversity and community structure were largely similar between elderly males and females, with only modest sex-associated differences at higher taxonomic levels. These findings suggest that biological sex may have a limited influence on gut microbiota composition in advanced age and provide population-level reference data for future longitudinal and interventional studies in elderly cohorts.}, } @article {pmid41753552, year = {2026}, author = {Shulga, EY and Islamov, BR and Sukhanov, AY and Frolov, M and Laikov, AV and Trachtmann, NV and Validov, SZ}, title = {Biotechnological Potential and Metabolic Diversity of Lignin-Degrading Bacteria from Decaying Tilia cordata Wood.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753552}, issn = {2076-2607}, support = {FMEG-2025-0028//The government assignment for the FRC Kazan Scientific Center of RAS/ ; }, abstract = {Lignin is a complex aromatic polymer that constitutes a major fraction of plant biomass and represents a valuable renewable carbon resource. Naturally decaying wood serves as an environmental reservoir of microorganisms capable of degrading lignin. In this study, we isolated and characterized sixteen bacterial strains from decaying Tilia cordata wood using an enrichment culture technique with lignin as the sole carbon source. Taxonomic identification via 16S rRNA gene sequencing revealed microbial diversity spanning the genera Bacillus, Pseudomonas, Stenotrophomonas, and several members of the Enterobacteriaceae family, including Raoultella terrigena isolates. Metagenomic sequencing of the wood substrate revealed an exceptionally rich and balanced bacterial community (Shannon index H' = 5.07), dominated by Streptomyces, Bradyrhizobium, Bacillus, and Pseudomonas, likely reflecting a specialized consortium adapted to lignin rich late-stage decay. Functional phenotyping demonstrated that all isolates possess ligninolytic potential, evidenced by peroxidase/laccase-type activity through methylene blue decolorization. Dynamic Light Scattering (DLS) and HPLC analyses showed that some isolates, such as Raoultella terrigena MGMM806, effectively depolymerized lignosulfonate into low molecular weight fragments (1.23 nm), while others accumulated intermediate metabolites or completely mineralized the substrate. Growth profiling on monolignol substrates revealed a broad spectrum of catabolic specialization in lignin monomer degradation. The results demonstrate a complex system of metabolic partitioning within a natural bacterial consortium. This collection represents a foundational genetic resource for developing engineered biocatalysts and synthetic microbial communities aimed at the efficient conversion of lignin into valuable aromatic compounds.}, } @article {pmid41753592, year = {2026}, author = {Özdemir, K}, title = {Characterization of a Boron-Tolerant Nocardia niigatensis Isolated from Boron-Rich Soils: Physiological, Enzymatic, and Genomic Insights.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753592}, issn = {2076-2607}, support = {BAP-19-1003-003//Bandırma Onyedi Eylül University Scientific Research Projects Coordination Unit (BAP)/ ; }, abstract = {In this study, a Nocardia niigatensis strain was isolated from boron-rich mining soils in the Bigadiç region of Türkiye and comprehensively characterized. The primary aim of this study was to isolate boron-tolerant Nocardia species and evaluate their physiological, enzymatic, and biochemical profiles. Selective isolation techniques were employed to obtain Nocardia isolates, and species-level identification was achieved using both 16S rRNA gene sequencing and MALDI-TOF MS analysis, which consistently confirmed the isolate as N. niigatensis. In addition to molecular identification, the morphological, physiological, and biochemical characteristics of the strain were extensively investigated. The strain demonstrated notable boron tolerance, exhibiting robust growth at concentrations up to 50 mM, highlighting its potential applicability in the bioremediation of boron-contaminated environments. Physiological assays further revealed moderate halotolerance and a mesophilic growth profile, with optimal growth observed at 27-37 °C. Enzymatic screening indicated positive L-glutaminase activity, an enzyme of considerable industrial relevance. Moreover, API ZYM profiling revealed a broad enzymatic spectrum, including esterases, arylamidases, phosphatases, and glucosidases, suggesting substantial metabolic versatility. Antibiotic susceptibility testing showed sensitivity to doxycycline, tobramycin, and erythromycin, whereas resistance was observed against imipenem and several β-lactam antibiotics. Metagenomic analysis of boron-rich soils from two distinct mining sites revealed marked differences in microbial community composition, with variations in Actinobacteria abundance associated with mineral type. Overall, these findings emphasize the adaptive capacity and biotechnological potential of environmental Nocardia strains inhabiting chemically stressful ecosystems, warranting further genomic and metabolomic investigations.}, } @article {pmid41753628, year = {2026}, author = {Meinen-Jochum, J and Satheesh, V and Masonbrink, RE and Rodriguez-Gallegos, J and Wright, DA and Severin, AJ and Mellata, M}, title = {Sequencing and Analysis of Chicken Segmented Filamentous Bacteria Genome Revealed Unique Avian-Specific Features.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753628}, issn = {2076-2607}, support = {20236701539078//U.S. Department of Agriculture's National Institute of Food and Agriculture/ ; }, abstract = {Segmented filamentous bacteria (SFB) are host-specific, immune-modulating microorganisms that colonize the small intestine of various vertebrate species, playing a crucial role in stimulating immune maturation during early life. Previous research on the genomes of SFB from humans, rats, and mice has revealed significant differences among SFB strains associated with various hosts, suggesting that their evolution is closely linked to their relationships with specific hosts. However, the genome of SFB from chickens has not been extensively investigated. In this study, we present the metagenomic reconstruction of an SFB genome derived from the ileum of layer Lohmann Select Leghorn (LSL) chickens. We utilized Hi-C sequencing techniques to assemble the LSL-SFB and annotate the avian SFB from both turkeys and chickens. Our reference-guided consensus assembly, followed by Hi-C scaffolding, produced a high-quality genome for LSL-SFB. Our pangenomic analysis revealed substantial conservation of core gene clusters among mammalian SFB strains, but we also identified a distinct repertoire of genes in chicken and turkey SFB. Furthermore, metabolic network analysis indicated a reduced capacity for biosynthesis, signifying an increased reliance on the host, as shown by the absence of key biosynthetic and utilization pathways. We also discovered a unique flagellin subunit (fliC-2) in chicken SFB from different genetic lines and confirmed its interaction with the chicken flagellin receptor, Toll-like receptor five. This study provides the first high-quality genome and annotation of LSL-SFB, alongside that of turkeys, offering valuable insights into the mechanisms of host specificity and adaptation. Understanding the interactions between host-specific SFB and their hosts, as well as their role in promoting immune maturation, is essential for improving intestinal health.}, } @article {pmid41753632, year = {2026}, author = {Wang, M and Tian, W and Liu, Z and Yan, D and Li, Y and Cao, A and Wang, Q and Fang, W}, title = {Differential Selection Effects of Continuous AITC Fumigation on Soil Microbial Communities and Functions and Identification of Tolerant Strains.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753632}, issn = {2076-2607}, support = {2024YFD1701900//The National Key R&D Program of China/ ; 32572893//The National Natural Science Foundation of China/ ; CAAS-CSAL-202401//The Innovation Project of the Chinese Academy of Agricultural Sciences/ ; }, abstract = {Allyl isothiocyanate (AITC) is effective as a bio-based fumigant in controlling soil-borne diseases; however, the selective pressure it exerts on soil microecology and evolutionary dynamics remains inadequately characterized. This study systematically investigated the remodeling effects of continuous AITC fumigation on soil microbial communities, functional genes, and functional strains by integrating metagenomic analysis and pure culture techniques. Results demonstrate that AITC drives directional selection from "sensitive" to "tolerant" microorganisms. Fungal communities exhibit greater cumulative damage than bacterial communities, with the proportion of significantly suppressed fungi increasing linearly from 9.3% at baseline to 35.7%. At the genus level, sensitive groups were predominantly enriched in pathogen-associated genera, e.g., Pseudomonas and Xanthomonas, whereas tolerant groups, represented by Bacillus and Streptomyces, maintained ecological dominance under continuous stress. Functionally, AITC induced differential evolution of functional gene repertoires. Nitrogen cycle genes (e.g., amoC) exhibited high negative sensitivity, with significant downregulation by 20%, whereas the TCA core module in the carbon cycle exhibited strong robustness. Virulence assays confirmed EC50 values for tolerant beneficial bacteria (Bacillus spp.) (>40 mg·L[-1]) were significantly higher than those for pathogens (1.3-7.9 mg/L). This study established a microbial "sensitive-tolerant" response framework under AITC stress, revealing the core potential of endogenous tolerant strains for the precise ecological restoration of fumigated soils.}, } @article {pmid41753645, year = {2026}, author = {Liu, M and Zhao, L and Li, T and Li, X and Jiang, H and Yang, P}, title = {Deciphering the Arterial and Venous Blood Bacterial DNA Profile: Pioneering Insights into Coronary Heart Disease Etiology and Progression.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753645}, issn = {2076-2607}, support = {2023YFC3503702//National Key Research and Development Program of China/ ; No. ZRJY2023-QM11//Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; }, abstract = {BACKGROUND: Coronary heart disease (CHD) is the leading cause of death and disability worldwide. The human microbiota, particularly gut bacteria, plays a role in the development of CHD. However, determining the contribution of gut bacteria translocation to systemic circulation in the progression of atherosclerosis remains challenging.

METHODS AND RESULTS: In this exploratory study, we conducted 16S rRNA-based metagenomic analysis to characterize systemic bacterial profiles in a cohort of 27 patients with CHD (9 with severe coronary artery stenosis and 18 with mild to moderate stenosis). We compared microbial diversity between arterial and venous blood and across different blood fractions. For the first time, we observed higher microbial diversity in plasma than in serum. We also identified differences in microbial richness among arterial whole blood, venous whole blood, arterial plasma, venous plasma, arterial serum, and venous serum, with 15, 22, 43, 10, 4, and 3 genera showing significant differences, respectively. Many of the detected blood taxa belonged to genera typically found in intestinal, oral, or skin microbiota, although their precise source cannot be determined from this study.

CONCLUSIONS: Our study provides preliminary evidence of distinct bacterial profiles between arterial and venous blood fractions in patients with CHD, as determined by 16S rRNA sequencing. These findings should be interpreted with caution given the small sample size and the absence of a healthy control group, and they warrant confirmation in larger, controlled studies.}, } @article {pmid41753646, year = {2026}, author = {Bosco, G and Vaccalluzzo, A and Russo, N and Pino, A and Caggia, C and Randazzo, CL}, title = {Effect of By-Products from Pistachio Skin on Gastrointestinal Microbiota of Healthy Lambs as Sustainable Feeding Ingredient.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753646}, issn = {2076-2607}, support = {Piano Nazionale Di Ripresa E Resilienza (PNRR) - Missione 4 Componente 2, Investimento 1.4 - D.D. 1032 17/06/2022, CN00000022//European Union Next-GenerationEU/ ; }, abstract = {Pistachio skin is a by-product that is considered a promising novel feed ingredient for ruminants; however, its role in shaping the lamb gastrointestinal tract microbiota is poorly studied. The present study aimed to investigate, through a metagenomics approach, the effects of integrating pistachio skin into the diet on the faecal and ruminal microbiota of healthy lambs. Faecal samples, collected at the beginning (d0) and 58 days after the start of the dietary treatment (d58), and ruminal samples, collected after slaughter, were subjected to Illumina MiSeq analysis of the 16S rRNA gene. The results revealed that, although temporal variations were observed, the supplementation of pistachio skin did not markedly affect the overall faecal microbiota structure. Conversely, specific rumen taxa were selectively modulated by the experimental diet. In conclusion, the use of pistachio skin as a feed ingredient can be considered a suitable and sustainable dietary strategy that modulates specific rumen microbial groups, thereby preserving the stability of the gut microbiota in lambs.}, } @article {pmid41753649, year = {2026}, author = {Feng, Y and Liu, S and Ke, H and Li, H and Zhao, H and Dang, X and Mou, C and Zhou, J and Huang, Z and Deng, Y and Li, Q}, title = {A Pseudotumorous Syndrome Associated with an As-Yet-Unidentified Eukaryotic Parasite Causing Functional Gonadal Arrest in Largefin Longbarbel Catfish (Hemibagrus macropterus).}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753649}, issn = {2076-2607}, support = {2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; }, abstract = {This study presents the first documented case of a disease syndrome in cultured largefin longbarbel catfish (Hemibagrus macropterus). The condition is characterized by massive abdominal pseudotumor formation, severe cachexia, and functional gonadal arrest. Comprehensive pathological investigation revealed that the pseudotumor was encapsulated by fibroblasts and primarily composed of host-derived, poorly differentiated hyperplastic cells, interspersed with invasive, basophilic Type III cells. These cells and associated inflammatory-fibrotic lesions were also disseminated in the gill, kidney and spleen. Systematic diagnostic approaches, including microbiology and transmission electron microscopy, found no evidence of conventional bacterial or viral pathogens. Metagenomic analysis further supported these findings and suggested a link to infection by an as-yet-unidentified eukaryotic parasite, with Microsporidia or Ichthyosporea being the primary candidates. Functional (KEGG) profiling of the pseudotumor tissue further revealed a molecular signature consistent with active cellular proliferation and metabolism. We propose that the pseudotumor acts as a metabolically active "nutrient sink," driving the systemic catabolism that underlies the severe cachexia and reproductive arrest. This work provides the first case of a eukaryotic parasite-induced pseudotumorous syndrome in fish, which represents an emerging threat to conservation aquaculture and offering novel insights into parasite-mediated host metabolic hijacking and tumor-mimicry.}, } @article {pmid41753674, year = {2026}, author = {Ece, G and Aktaş, A and Koyuncu Özyurt, Ö and Demirbakan, H and Alışkan, HE and Sağlık, İ and Zorbozan, O and Çetin Duran, A and Uğur, AR and Öcal, D and Uzunoğlu, E and Kaya, E and Mutlu Sarıgüzel, F and Bayındır, F and Yetkin, G and Altındiş, M and Yenice Aktaş, S and Kula Atik, T}, title = {Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753674}, issn = {2076-2607}, abstract = {The human microbiome is increasingly recognized as a key determinant of health and disease, yet methodological variability continues to limit reproducibility and clinical translation of findings. This review synthesizes current approaches in microbiome research, critically evaluating each step from sampling to sequencing and downstream bioinformatics. Pre-analytical factors such as sample type, collection method, preservation, and storage conditions profoundly affect microbial community profiles and remain a major source of bias. Nucleic acid extraction protocols and quality assessment strategies are discussed with emphasis on optimized lysis techniques, contamination controls, and DNA yield evaluation. Advances in sequencing technologies are highlighted, including 16S rRNA amplicon sequencing, shotgun metagenomics, third-generation long-read platforms, and emerging single-cell and minimal-input methods, each with specific advantages and limitations in taxonomic and functional resolution. Bioinformatics pipelines for taxonomic profiling, variant detection, phylogenetic inference, and functional annotation are compared, with attention to widely used reference databases such as RefSeq, GTDB, and SILVA. Integrative multi-omics approaches, including metatranscriptomics, metabolomics, and genome-scale metabolic modeling, are presented as powerful tools for linking microbial community structure to host physiology and disease mechanisms. Despite these advances, the lack of standardized workflows across pre-analytical, sequencing, and computational steps continues to hinder inter-study comparability and biomarker validation. This review aims to provide a methodological framework that highlights both strengths and limitations of current technologies while underlining the need for harmonized protocols to ensure reproducibility and accelerate the translation of microbiome research into clinical practice.}, } @article {pmid41753703, year = {2026}, author = {Zhang, L and Xu, L and Zhang, Z and Liu, Z and Chen, Y}, title = {The Remediation Mechanism of Soil Atrazine Contamination by Vermicompost: A Metagenomic Perspective.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753703}, issn = {2076-2607}, support = {XDA28110201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, abstract = {Atrazine persistence poses serious environmental threats. This study used metagenomics and qPCR to elucidate the remediation mechanism of vermicompost in atrazine degradation pathways. Seven treatments were established: unsterilized soil (CKn); sterilized soil amended with 45 (SsV1), 60 (SsV2), and 75 (SsV3) days of vermicompost; and unsterilized soil with the same vermicompost (SnV1, SnV2 and SnV3). Vermicompost significantly restructured soil microbial communities. SsV1 exhibited the highest Proteobacteria abundance (51.38%), while SsV3 markedly increased Bacteroidetes abundance (10.34%). Functional annotation revealed that vermicompost enriched carbohydrate metabolism-related COG units and upregulated CAZymes (e.g., CE1 and CE10 families), providing energy support for degrading microbial communities. Regarding metabolic pathways, SnV2 exhibited the highest atrazine degradation abundance (2.94%), significantly enriching Bauldia (4.84 RPKM) for dechlorination. During cyanuric acid ring-opening, SnV3 significantly enriched Pseudorhodoplanes (12.14 RPKM). During terminal mineralization, SsV2 increased Caenimonas abundance (15.25 RPKM) and introduced the exogenous genus Pseudorhodoplanes (7.78 RPKM). qPCR confirmed SnV2's trzN (day 20) and atzB (day 40) reached 9.03 × 10[4] and 6.95 × 10[7] copies/g, respectively. These findings indicate vermicompost accelerated atrazine mineralization by enriching degradative microbial communities and promoting key functional gene expression, with 60-day vermicompost demonstrating superior performance. This study provides a robust theoretical framework for remediating atrazine-contaminated soil by vermicompost.}, } @article {pmid41753722, year = {2026}, author = {Ayilaran, E and Kilonzo-Nthenge, A}, title = {Metagenomic Insights into Antimicrobial Resistance in Small-Scale Poultry and Cattle Farms.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753722}, issn = {2076-2607}, support = {2018-68006-28103//National Institute of Food and Agriculture/ ; Grant No. 2018-68006-28103//United States Department of Agriculture/ ; }, abstract = {Antimicrobial resistance (AMR) poses a critical challenge to global health, with food animal production systems recognized as significant reservoirs of antimicrobial-resistant bacteria. This study evaluated the prevalence and distribution of antimicrobial resistance genes (ARGs) and virulence factors (VFs) across small-scale poultry and cattle farms. A total of 468 samples (soil, feces, water, and natural land soil) were collected from four farms and analyzed using shotgun metagenomics. Proteobacteria (34.91%) were the dominant phylum across environments, followed by Cyanobacteria (15.67%), Actinobacteria (14.95%), Firmicutes (10.57%), and Bacteroidetes (8.69%). Tetracycline (33.41%) and beta-lactam (30.30%) resistance genes were the most abundant, with macrolide (9.32%) and aminoglycoside (8.39%) resistance also detected. Both tetracycline and beta-lactam resistance genes were significantly enriched across sample types (p < 0.05). The detection of diverse VFs alongside ARGs highlights the pathogenic potential of bacterial communities in these production systems. Collectively, the findings reveal that small-scale animal farms are reservoirs of AMR with implications for public health through foodborne transmission. Targeted surveillance and control measures are necessary to prevent the dissemination of ARGs into the broader food chain and to safeguard both human and animal health.}, } @article {pmid41753740, year = {2026}, author = {Machineski, GDS and Menoncin, AS and Leonardo, HCL and Colozzi Filho, A}, title = {Riparian Forest Restoration Drives the Recovery of Soil Chemistry, Microbial Community Structure, and Enzymatic Activity in the Itaipu Reservoir Protection Zone.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753740}, issn = {2076-2607}, support = {Vitorias 4500074504 Itaipu/IDR-Paraná-Fapeagro//ITAIPU Binacional Convênio/ ; }, abstract = {Riparian forests play a critical role in protecting soil and water resources and maintaining ecosystem stability. In this study, we evaluated the response of soil chemical and microbial attributes to different stages of riparian forest restoration in the protection zone of the Itaipu Reservoir (Brazil). Soil samples were collected during summer and winter from sites representing four restoration stages (initial, 3, 19, and 30 years), as well as from an adjacent agricultural field and a native forest used as reference systems. We assessed soil chemical properties, microbial biomass carbon, basal respiration, enzymatic activities, and the soil microbial community structure using 16S rRNA gene sequencing. Principal component analysis (PCA) revealed a clear restoration gradient, with older restored sites progressively converging toward the native forest condition. Soil chemical properties showed gradual recovery along the restoration trajectory, with increases in soil organic carbon, cation exchange capacity, and base saturation. In contrast, the availability of P, K, Ca, and Mg declined at early restoration stages and increased with restoration age. Microbial biomass carbon increased by approximately 60% from early restoration to native forest conditions, while metabolic quotients (qCO2) decreased, indicating greater microbial efficiency and reduced metabolic stress. Enzyme activities related to C, P, and S cycling increased by 1.5- to 3-fold with restoration age. Sequencing analyses indicated a progressive convergence of microbial community composition toward that of the native forest, driven by shifts in relative abundance and the enrichment of forest-associated taxa, such as Verrucomicrobia and Acidobacteria, at advanced restoration stages. Overall, long-term riparian forest restoration promoted substantial recovery of soil chemical fertility and microbial community structure and functioning, reinforcing the role of soil microbiota as a sensitive indicator of ecosystem resilience and restoration success.}, } @article {pmid41753762, year = {2026}, author = {Labrín-Sotomayor, NY and Becerra-Lucio, PA and Ruiz-González, H and Peña-Ramírez, YJ}, title = {Taxonomic and Functional Diversity of Leaves and Stem Endophytes of Eight Agave Species.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753762}, issn = {2076-2607}, support = {YJPR 5103711808 2024-2025 and NYLS 5103711911 research grants//El Colegio de la Frontera Sur/ ; }, abstract = {More than 63% of Mexico's territory is classified as arid or semiarid, where plants belonging to the genus Agave have evolved. Adaptation to drylands resulted from biochemical, physiological, and anatomical properties shared with other crassulacean plants; however, microbial symbionts also play critical roles in plants' growth, health, and drought tolerance. To explore endophytic communities in Agave plants, we used a shotgun metagenomic approach. The taxonomic and functional diversity of endophytes were studied in the leaves and stem organs of Agave americana, A.angustifolia, A. fourcroydes, A. karwinskii, A. potatorum, A. tequilana, A. cupreata, and A. rodacantha. The microbial community structure did not differ significantly among species, regardless of geographic origin or local environmental conditions, whereas significant differences were observed between organs. We found 4058 genera shared among organs, of which 957 genera are exclusive to the stem and 492 to the leaves. The community analysis of stems and leaves identified bacterial genera, including Acinetobacter, Klebsiella, Escherichia, Corynebacterium, and Streptomyces. Significant differences were also observed between organs in the functional annotations. The dominant functional categories were associated with cell signaling and protein metabolism in both organs.}, } @article {pmid41753775, year = {2026}, author = {Galisteo, C and Puente-Sánchez, F and de la Haba, RR and Bertilsson, S and Ventosa, A and Sánchez-Porro, C}, title = {Uncovering the Prokaryotic Diversity of Hypersaline Soils of Odiel Saltmarshes Natural Area Through Metagenome-Assembled Genomes.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753775}, issn = {2076-2607}, support = {PID2020-118136GB-I00//MCIN/AEI/10.13039/501100011033/ ; PID2023-148654NB-I00//MCIN/AEI/10.13039/501100011033/ ; 2022-04801//Swedish Research Council (Vetenskapsrådet)/ ; PRE2018-083242//Spanish Ministry of Science and Innovation/ ; }, abstract = {The hypersaline soils of the Odiel Saltmarshes Natural Area in Southwest Spain harbor highly diverse microbial communities adapted to extreme conditions. However, their genomic diversity remains largely unexplored. In addition to high salinity, these soils are contaminated with heavy metals, creating a hostile environment of great interest for studying extremophilic microorganisms and their metabolic adaptations. This study aims to characterize the uncovered prokaryotic taxa as Candidatus species inhabiting the hypersaline soils of the Odiel Saltmarshes, based on their metagenomic assembled genomic sequences. The reconstructed genomes were assessed for quality based on completeness and contamination thresholds and subsequently taxonomically classified. Comparative genomic analysis of six high-quality MAGs revealed key metabolic traits related to survival under extreme salinity and heavy metal conditions. The findings provide new insights about microbial diversity of hypersaline environments and expand the catalog of known prokaryotic genomes. Detailed characterization of six novel Candidatus taxa highlights the unique adaptations of these microorganisms, enhancing our understanding of life in extreme habitats.}, } @article {pmid41753780, year = {2026}, author = {Palanisamy, V and Bosilevac, JM and Barkhouse, DA and Velez, SE and Dass, SC}, title = {Unraveling the Coevolutionary Dynamics of Phage and Bacterial Protein Warfare Occurring in the Drains of Beef-Processing Plants.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, pmid = {41753780}, issn = {2076-2607}, support = {2020-67017-30776//USDA-NIFA/ ; }, abstract = {Phages, the most abundant entities on Earth, exhibit a complex interplay with bacteria, especially within environmental biofilms, resulting in an ecological arms race. This study investigates the interaction between phages and bacteria in the drains of beef-processing plants using high-throughput sequencing and metagenomic analysis. Metagenomic data collected from 75 drain samples from beef-processing plants were analyzed to investigate phage-bacterial interactions. First, assembled contigs were screened to identify viral sequences, which were then taxonomically annotated to determine the viral composition, including phages. Functional annotation of these viral sequences provided information about the viral genes and their roles in bacterial interactions specifically associated with attack and counterattack of bacteria. In parallel, bacterial contigs were examined to identify genes associated with antiphage defense systems, providing insights into the strategies adapted by bacteria to resist phage infection. Taxonomic annotation of viral sequences from the bulk metagenomic data revealed the presence of phages targeting Pseudomonas, Klebsiella, and Enterococcus. The higher abundance of Pseudomonas phages aligns with our previous study, where Pseudomonas was identified as the dominant bacterial genus, suggesting potential copersistence of phages and their hosts. Functional annotation of phage contigs revealed infective and lysis-related genes, highlighting their potential role in bacterial attack. Conversely, bacterial contigs encoded antiphage defense systems, including CRISPR-Cas, restriction-modification, and other defense-related genes. The study also uncovered the presence of anti-CRISPR proteins in phages, suggesting a counterattack on the bacterial defense. These findings provide evidence for phage attack, bacterial defense, and phage counterattack and may showcase the ongoing coevolutionary arms race between phages and bacteria. While this evidence looks promising, these results remain preliminary and further studies are needed to validate these findings. Still, this study provides a foundational understanding of bacteria-phage coexistence in beef-processing plant drains and paves the way for further explorations of these intricate interactions and their possible applications in controlling pathogenic microorganisms within biofilms.}, } @article {pmid41754080, year = {2026}, author = {Qin, P and Berzina, L and Geiker, NRW and Sandby, K and Krarup, T and Kristiansen, K and Magkos, F}, title = {Associations Between Gut Microbiome Enterotypes and Body Weight Change During Whole Milk Consumption.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, pmid = {41754080}, issn = {2072-6643}, support = {NA//Arla Food for Health/ ; NA//Danish Milk Levy Fund/ ; }, mesh = {Animals ; Humans ; Male ; *Milk ; *Gastrointestinal Microbiome/physiology ; *Body Weight ; *Obesity/microbiology ; Feces/microbiology/chemistry ; Adult ; Streptococcus thermophilus ; Bacteroides ; Diet ; }, abstract = {Background: Evidence is accumulating that gut bacterial communities modulate the outcome of dietary interventions. Objective: To assess how gut microbial enterotypes correlate with obesity-related outcomes during one month of whole milk consumption. Methods: This post hoc analysis used data from a previously published trial, which included a lead-in phase during which men with abdominal adiposity replaced habitual dairy product consumption with 400 g/day of whole milk for one month. We compared body weight, urinary metabolites, fecal metabolites, and gut microbiome composition and function based on shotgun metagenomic sequencing at the beginning and at the end of the lead-in phase between individuals with the two most prevalent enterotypes, the Bacteroides1 (B1) enterotype (n = 24) and the Ruminococcaceae (R) enterotype (n = 38). Results: Individuals with the B1 enterotype, but not those with the R enterotype, exhibited decreases in body weight and the relative abundance of Streptococcus thermophilus. Multiple linear regression analysis identified enterotype as a strong predictor of body weight change (p = 0.0034). In addition, urinary taurine level change was positively associated with body weight change in B1 individuals, not in R individuals. Conclusions: Our findings reveal an enterotype-specific response to an identical dietary modification, underscoring the value of integrating enterotype information into nutrition-intervention design and personalized nutrition strategies.}, } @article {pmid41754175, year = {2026}, author = {Wang, Z and Wei, J and Huang, Z and Liu, X and Li, S and Fang, Z and Hu, L and Li, R and Tao, L and Li, C and Chen, H}, title = {Metagenomics and Machine Learning Identify TMA-Producing Serratia Induced by High-Fat/Choline Diet: A Novel Obesity Target for TMA.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, pmid = {41754175}, issn = {2072-6643}, support = {2023ZYD0129//Sichuan Province Central Leading Local Science and Technology Development Special Project/ ; 2024YFD2101003//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Choline/administration & dosage/metabolism ; *Diet, High-Fat/adverse effects ; Male ; *Methylamines/metabolism ; *Machine Learning ; Mice, Inbred C57BL ; *Obesity/microbiology/metabolism/etiology ; *Metagenomics/methods ; Mice ; Gastrointestinal Microbiome ; *Serratia/metabolism/genetics ; Liver/pathology/metabolism ; Feces/microbiology/chemistry ; }, abstract = {BACKGROUND: High-fat diet-induced metabolic disorders are associated with trimethylamine (TMA)/trimethylamine N-oxide (TMAO), whose production is linked to gut microbial choline metabolism. However, changes in specific gut microbiota under a high-fat diet and the relationship between these changes and choline in TMA/TMAO production remain unclear.

METHODS: A total of 48 7-week-old male C57BL/6J mice were subjected to one-week acclimatization feeding, and then randomly divided into four groups (12 mice per group) to establish a 2 × 2 factorial design animal experiment: the control group (CON, basal diet), the choline-supplemented control group (CON + C, basal diet supplemented with 1% choline), the high-fat diet group (HF, high-fat diet), and the high-fat plus choline group (HF + C, high-fat diet supplemented with 1% choline). The experiment lasted for 9 weeks, during which dynamic monitoring of TMAO levels in mice was performed in the first 4 weeks. At the ninth week, the mice were sacrificed and samples were collected for subsequent assays, including the concentrations of TMA and TMAO in serum, colonic contents and feces; the pathological morphology of liver tissue, adipocyte staining characteristics and serum biochemical parameters; and the expression levels of key genes and proteins in liver, small intestine and colon tissues. Meanwhile, metagenomic analysis was conducted on colonic contents, combined with machine learning to predict the correlation between gut microbiota and TMA. In addition, gene cloning, multiple sequence alignment, molecular simulation and in vitro culture experiments were carried out to verify the TMA-producing function of the target strain.

RESULTS: This study elucidated that high-fat diet and high choline exert a significant interaction in TMA/TMAO production through a 2 × 2 animal experiment; meanwhile, the significantly increased TMA/TMAO levels co-induced by the two factors further exacerbate metabolic disorders. Notably, through combined metagenomics and machine learning, we identified Serratia marcescens as the primary TMA-producing microorganism under high-fat/choline diet induction. In vitro cultures simulating the intestinal environment revealed that the TMA conversion ability of Serratia marcescens is time-dependent, reaching 60 ± 2.49% after 24 h of anaerobic culture with choline chloride. Multiple sequence alignment and molecular simulation further demonstrated that the CutC enzyme of Serratia marcescens has a conserved amino acid sequence and high affinity for choline.

CONCLUSIONS: We uncovered a two-factor synergistic effect of a high-fat/choline diet on TMA/TMAO, and for the first time identified the genus Serratia as a TMA-producing bacterium. These findings provide a new potential target for intervening in metabolic disorders mediated by high-fat diet-induced TMAO elevation.}, } @article {pmid41754394, year = {2026}, author = {Rabello, E and de-Paris, F}, title = {Tuberculosis Diagnostic Methods: Clinical Applicability, Implementation Challenges, and Integrated Testing Strategies.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41754394}, issn = {2076-0817}, support = {https://ror.org/010we4y38.//This research was funded by the Fundo de Incentivo à Pesquisa e Eventos (FIPE) from the Hospital de Clínicas de Porto Alegre (HCPA) - https://ror.org/010we4y38./ ; }, mesh = {Humans ; *Tuberculosis/diagnosis/microbiology ; *Molecular Diagnostic Techniques/methods ; Nucleic Acid Amplification Techniques/methods ; *Mycobacterium tuberculosis/genetics/isolation & purification ; }, abstract = {Tuberculosis (TB) remains one of the leading causes of death from a single infectious agent worldwide, a burden further exacerbated by HIV co-infection and the increasing prevalence of drug-resistant strains. Although a wide range of laboratory diagnostic methods are currently available, their applicability, implementation, and clinical impact vary substantially across healthcare settings with different levels of complexity and resources. This review provides a comprehensive overview of the main laboratory diagnostic methods for active and latent TB, emphasizing their clinical applicability, implementation challenges, and role within integrated diagnostic strategies. Conventional approaches, such as smear microscopy and culture, are discussed alongside modern diagnostic technologies, including automated nucleic acid amplification tests (NAATs), loop-mediated isothermal amplification (LAMP), line probe assays (LPAs), next-generation sequencing (NGS), and lateral flow assays, highlighting their strengths and limitations in distinct epidemiological and operational contexts. Unlike existing WHO guidelines and prior reviews that predominantly focus on test performance and recommendation status, this review adopts an implementation-oriented perspective, critically examining diagnostic methods in light of real-world constraints, regional disparities, and evidence gaps. Particular attention is given to limitations related to laboratory infrastructure, biosafety, workforce capacity, and sustainability, as well as to under-addressed areas such as latent TB, metagenomic approaches, and the investigation of co-pathogens. By integrating WHO guidance with contextual and operational considerations, this review aims to support rational test selection and the development of flexible, integrated diagnostic workflows tailored to local health system capacity, patient populations, and clinical scenarios, thereby strengthening the effectiveness and equity of TB diagnostic strategies.}, } @article {pmid41754400, year = {2026}, author = {Wang, X and Duan, R and Ming, A and Zhang, Y and Liu, T and Wang, X and Diao, M}, title = {Age-Dependent Dynamics of the Biliary Microbiome in Children with Choledochal Cysts: Functional Remodeling Underlying Taxonomic Conservation.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41754400}, issn = {2076-0817}, mesh = {Humans ; *Choledochal Cyst/microbiology ; Child, Preschool ; Infant ; Child ; *Microbiota ; Age Factors ; Female ; Male ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Biliary Tract/microbiology ; }, abstract = {Choledochal cyst (CC), a congenital biliary anomaly, is associated with recurrent infections, chronic inflammation, and an increased risk of malignancy. Although emerging evidence implicates the biliary microbiome in disease pathophysiology, its developmental dynamics in pediatric CC remain unclear. Using deep metagenomic sequencing and comprehensive functional annotation, this study characterized age-dependent changes in the biliary microbiome of 201 pediatric CC patients stratified into infancy (<1 year), early childhood (1-5 years), and later childhood (5-12 years). We found that while the taxonomic composition and alpha diversity of the microbiota remained conserved across age groups, profound functional remodeling occurred with host development. A core set of microbial species(Bacteroidota, Actinomycetota, Bacillota, and Pseudomonadota) and functional pathways was shared across all ages; however, early childhood (1-5 years) exhibited the greatest number of unique functional genes, metabolic pathways, and carbohydrate-active enzymes, identifying this period as a critical window for microbial metabolic adaptation. Age-specific patterns were also evident in clinically relevant traits: infants (<1 year) harbored the most unique antibiotic resistance and virulence factor genes, whereas the resistome and virulome became more streamlined in older children. These findings establish a paradigm of "taxonomic conservation coupled with functional remodeling" in the CC microbiome and highlight age as a key determinant of microbial community function. This study offers novel insights into the microbial dynamics underlying CC progression and suggests potential age-specific targets for future therapeutic strategies.}, } @article {pmid41754413, year = {2026}, author = {Kibenge, F and Kibenge, M and Vargas, D and Godoy, M}, title = {Amarilloviruses of Aquatic Animals.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41754413}, issn = {2076-0817}, support = {I-11251070//FONDECYT/ ; }, mesh = {Animals ; *Aquatic Organisms/virology ; Phylogeny ; Genome, Viral ; *Flaviviridae/genetics/classification ; Host Specificity ; Fishes/virology ; }, abstract = {The family Flaviviridae has been expanded to include the highly divergent flavi-like viruses into three new families, Flaviviridae, Pestiviridae, and Hepaciviridae, in the order Amarillovirales. Classical flavivirids are small, enveloped viruses with positive-sense ssRNA genomes lacking a 3' poly(A) tail and ~9.0-13.0 kb in length, with a single open reading frame (ORF) encoding structural proteins at the N-terminus and nonstructural proteins at the C-terminus. Members infect a wide range of mammals, birds, and insects, and many are host-specific and pathogenic. Although the RNA-directed RNA polymerase (RdRP) gene sequences of the flavi-like viruses group phylogenetically with those of classical flavivirids, flavi-like viruses often encode larger polyproteins and possess substantially longer genomes of up to ~40 kb, and some have a 3' poly(A) tail. Their host range extends across the whole animal kingdom and angiosperm plants. This review describes the reported flavi-like viruses of aquatic animals, providing a meaningful update on all three new families in Amarillovirales that have been discovered using metagenomics in fish, crustaceans, mollusks, and echinoderms. These amarilloviruses include pathogenic viruses of aquatic animals, such as Cyclopterus lumpus virus (CLuV) detected in moribund lumpfish, and infectious precocity virus (IPV) found in iron prawn syndrome (IPS)-affected farmed giant freshwater prawns.}, } @article {pmid41754473, year = {2026}, author = {Vilela, C and Mendoza, L and Vilela, R and Moreira Jardilino, FD and Brilhante Bhering, CL and Moreno, A}, title = {Microbial Diversity and Composition Uncovered on Obturator Prosthesis Biofilms: Exploratory Findings from a Pilot Study.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41754473}, issn = {2076-0817}, mesh = {*Biofilms/growth & development ; Pilot Projects ; Humans ; *Palatal Obturators/microbiology ; *Microbiota ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; *Biodiversity ; Fungi/classification/genetics/isolation & purification ; Archaea/genetics/classification/isolation & purification ; Viruses/classification/genetics/isolation & purification ; }, abstract = {Microbial communities on obturator prosthesis biofilms have yet to be investigated. This pilot study explores eukaryotes, prokaryotes, and viruses present on obturator prosthesis biofilms using metagenomics. The prostheses of the selected patients (n = 3) were collected and their biofilms were physically removed. The total genomic DNA was extracted, followed by metagenomic analysis. The microbial diversity in each of the investigated biofilms was exceptionally abundant. Between 2616 to 3024 species were detected in the three biofilms. The highest percentage included prokaryotes and unclassified species, followed by low percentages of fungi, viruses, and archaea. Unusual pathogens rarely reported in oral biofilms, such as Mycobacterium and other species, were also found at very low percentages. Unigenes for functional pathways related to metabolism, cellular processes, human disease, and other microbial unigenes were abundant. In addition, unigenes for several antibiotic-resistance mechanisms were also detected. This study reveals, for the first time, that biofilm formation on obturator prostheses comprises a variety of dynamic microbial communities, suggesting a putative role in health and disease in patients following maxillofacial surgery.}, } @article {pmid41754515, year = {2026}, author = {Zaluzhnyi, V and Verhoeven, JTP and Stenson, GB and Lang, AS and Dufour, SC and Canuti, M}, title = {Characterization of a Novel, Highly Divergent Paramyxovirus Discovered in a Bearded Seal of Subarctic Canada.}, journal = {Viruses}, volume = {18}, number = {2}, pages = {}, pmid = {41754515}, issn = {1999-4915}, support = {RGPIN 2020-04131 (S.C.D.)//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Phylogeny ; Genome, Viral ; Canada ; *Paramyxoviridae/genetics/classification/isolation & purification ; *Seals, Earless/virology ; Viral Proteins/genetics ; *Paramyxoviridae Infections/veterinary/virology ; Sequence Analysis, DNA ; Arctic Regions ; }, abstract = {Seals are keystone animals in the Arctic and a valuable resource for Indigenous communities, but their virome is poorly understood. Through a preliminary investigation of the virome of seven North Atlantic bearded seals (Erignathus barbatus) from northwest Newfoundland, Canada, we discovered a new member of the Paramyxoviridae, a family including important animal pathogens. The complete coding genome sequence (15,898 nt) of the novel paramyxovirus, which we named bearded seal-associated paramyxovirus 1 (BSAPV-1), encoded five core paramyxoviral proteins-nucleoprotein, matrix, fusion, hemagglutinin-neuraminidase, and polymerase-and three proteins with no identifiable homologues that may represent the phosphoprotein, a small hydrophobic protein, and a transmembrane protein. Phylogenetic analysis, including BSAPV-1 and all 153 currently known paramyxoviral species, positioned the novel virus in a long-branched clade with Wenzhou Pacific spadenose shark paramyxovirus (Skoliovirinae, Scoliodonvirus scoliodontis), its closest relative (pairwise identity of the L protein: 30.1%). According to ICTV criteria, BSAPV-1 is likely the first member of a novel paramyxoviral subfamily. As the virus was found in combined tracheal/fecal swabs of a single animal, we could not conclude whether this is a seal virus or a virus associated with seal food. This study expands our knowledge about marine paramyxoviruses, and future studies should investigate BSAPV-1 ecology, spread, and host spectrum.}, } @article {pmid41754522, year = {2026}, author = {Atkins, H and Stegman, N and Putonti, C}, title = {Diverse Temperate Coliphages of the Urinary Tract.}, journal = {Viruses}, volume = {18}, number = {2}, pages = {}, pmid = {41754522}, issn = {1999-4915}, support = {1R15AI171873-05/NH/NIH HHS/United States ; }, mesh = {*Urinary Tract/microbiology/virology ; Humans ; Urinary Tract Infections/microbiology ; Female ; *Escherichia coli/virology ; *Coliphages/genetics/classification/isolation & purification/ultrastructure/physiology ; Genome, Viral ; Host Specificity ; Microscopy, Electron, Transmission ; Phylogeny ; Escherichia coli Infections/microbiology ; Prophages/genetics/isolation & purification/classification ; Whole Genome Sequencing ; }, abstract = {While Escherichia coli can be found in the bladders of females without lower urinary tract symptoms, its presence is often associated with urinary tract infections (UTIs). The genomic plasticity of E. coli, including urogenital strains, is largely shaped by the integration of prophages. Although genomic and metagenomic analyses of urinary E. coli and the urinary microbiome suggest that prophages are abundant, many represent uncharacterized species. Sequence analysis suggests that these prophages represent temperate phages. This study aimed to fill this gap, isolating and characterizing temperate phages from urinary E. coli strains. We assessed phage host range across a panel of urinary isolates, providing a critical first step for future work investigating their putative role in shaping E. coli populations within the urinary community. In total, 20 temperate urinary phages were evaluated. Phage morphology and genic content of these phages were determined via transmission electron microscopy (TEM) and whole-genome sequencing, respectively. Together, these analyses provide insight into the diversity, infectivity, and genomic composition of temperate coliphages from the female urinary tract.}, } @article {pmid41754608, year = {2026}, author = {Zheng, H and Shankar, A and Osis, G and Burgin, A and Sheth, M and Kiani, KG and Duong, YT and Cowan, D and Switzer, WM}, title = {Identification of Significant Genomic Changes and Compartmentalization of Simian Foamy Virus in a Human Zoonotically Infected by a Chimpanzee (Pan troglodytes troglodytes).}, journal = {Viruses}, volume = {18}, number = {2}, pages = {}, pmid = {41754608}, issn = {1999-4915}, mesh = {Animals ; *Pan troglodytes/virology ; *Simian foamy virus/genetics/classification/isolation & purification ; Humans ; *Retroviridae Infections/virology/veterinary/transmission ; *Genome, Viral ; Phylogeny ; *Zoonoses/virology ; Male ; Proviruses/genetics ; Genomics ; Viral Load ; Genetic Variation ; }, abstract = {Despite increasing reports of zoonotic simian foamy virus (SFV) infections globally, knowledge of its genetic adaptation in humans and impact on viral transmission and pathogenicity remains limited. We obtained complete SFV genomes using metagenomics analysis of viral isolates from peripheral blood lymphocytes (PBLs) and throat specimens from a worker (Case 6) and source chimpanzee (B1) that bit him. We analyzed viral diversity in three genomic regions (LTR, tas, and bet) involved in replication and latency using longitudinal specimens (PBLs, throat, saliva, urine, and semen) from Case 6 over five years, and PBLs from B1 and five additional chimpanzees over three years. Proviral loads were measured using a validated qPCR assay. Phylogenetic analysis revealed nearly identical SFV genomes in Case 6 and B1. Overall, bet sequences exhibited high genetic stability across body compartments and over time, with evidence of compartmentalization in Case 6 urine and semen specimens. G→A substitutions in GG and GA motifs in bet indicated heterogeneous APOBEC-associated editing across hosts and anatomical compartments following zoonotic transmission. Case 6 had significant deletions in the LTR region that were absent in B1 and other chimpanzees. Length variation in tas, including truncated forms, was observed across longitudinal specimens from Case 6, B1, and other chimpanzees. Proviral loads were consistently low and undetectable in most Case 6 urine specimens. Together, analysis of this SFV transmission pair identifies genomic changes likely to affect viral replication and persistence, highlighting mechanisms that may limit secondary transmission and pathogenicity of SFV in humans.}, } @article {pmid41754611, year = {2026}, author = {Anderson, M and Orf, GS and Holzmayer, V and Olivo, A and Harris, BJ and Berg, MG and Yu, G and Achari, A and Federman, S and Chiu, CY and James, L and Mampunza, S and Cloherty, GA and Rodgers, MA}, title = {Next-Generation Sequencing Reveals Continued Circulation of Rare HIV-1 Subtypes in the Democratic Republic of the Congo and Refines the Estimate of the Emergence Dates of Three Subtypes.}, journal = {Viruses}, volume = {18}, number = {2}, pages = {}, pmid = {41754611}, issn = {1999-4915}, support = {NA//Abbott/ ; }, mesh = {*HIV-1/genetics/classification ; Democratic Republic of the Congo/epidemiology ; High-Throughput Nucleotide Sequencing ; Humans ; *HIV Infections/virology/epidemiology ; Phylogeny ; Genome, Viral ; Genetic Variation ; Genotype ; }, abstract = {HIV-1 diversified for decades within the Democratic Republic of the Congo (DRC) before spreading globally in the early 1980s. Thus, the DRC is home to some of the most ancestral and diverse HIV-1 strains. Recent serosurveys conducted from 2017 to 2019 in Kinshasa, DRC, indicated high prevalence of HIV-1, yet sequence data is lacking from this period. Given the history of circulating rare HIV-1 subtypes in the DRC, a viral whole-genome sequencing study was conducted to determine current diversity in the greater Kinshasa area. Next-generation sequencing (NGS) through metagenomic and target enrichment methods was conducted on 197 specimens collected from 2017 to 2019. A large array of HIV subtypes (A, B, C, D, F1, G, H, J, and K), circulating recombinant forms (CRF01_AE, CRF02_AG, CRF05_DF, CRF11_cpx, CRF13_cpx, CRF25_cpx, CRF 45_cpx, and CRF92_C2U), unique recombinant forms, and unclassifiable sequences were observed, with many branching in basal positions within, or outside of, many subtypes on phylogenetic trees. Incorporating these new sequences into Bayesian inference of phylogeny pushes back the dates of the most recent common ancestors of HIV-1 group M and the rare subtypes G, H, and J by between 3 and 7 years each. The DRC continues to harbor diverse and rare HIV-1 subtypes that could challenge diagnostic tests, treatments, and vaccines. In addition to shifting subtype emergence dates, the sequences from our study are evidence that rare strains continue to circulate and should be regularly monitored.}, } @article {pmid41755800, year = {2026}, author = {Ding, J and Wang, M and Xu, X and Wang, D and Chen, X and Li, S and Zheng, X and Che, Y and Deng, Y and Lam, TTY and Li, L and Zhang, T}, title = {Highly Resolved Community Sewage Metagenomics Unveiling Landscape and Transmission Patterns of Antibiotic Resistome in Hong Kong Populations.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {20}, pages = {e08389}, pmid = {41755800}, issn = {2198-3844}, support = {T21-705/20-N//Theme-based Research Scheme/ ; 17202522//General Research Funds/ ; COVID1903015//Health and Medical Research Fund/ ; }, mesh = {Hong Kong ; *Sewage/microbiology ; *Metagenomics/methods ; Humans ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; }, abstract = {The increasing global burden of antimicrobial resistance (AMR) has been identified as a critical public health crisis, necessitating the development of robust, real-time surveillance frameworks to evaluate AMR dynamics. Sewage surveillance is emerging as a promising tool that utilizes sewage fingerprinting to provide comprehensive and unbiased information on antibiotic resistance genes (ARGs) within human populations. Here, we conducted a large-scale, year-long field surveillance of resistome in the community sewage using both short- and long-read metagenomic sequencing. We examined samples collected from 95 geographically distributed sites across Hong Kong, covering a population of 4.8 million residents, during summer and winter seasons. Our findings revealed distinct seasonal patterns through high-resolution resistome profiling. We found that the resistome structures shifted from the community sewage collected at sewer manholes to the influent of wastewater treatment plants (WWTPs), driven by taxonomic variation. Notably, community sewage exhibited a significantly higher similarity to the resistome of human feces than WWTP influent, which provides insights for selecting suitable sampling sites for epidemiological ARG surveillance. The application of long-read sequencing markedly enhanced our understanding of the phylogenetic diversity of ARG hosts and uncovered a broad spectrum of potentially mobile ARGs with varied genetic backgrounds. Furthermore, we observed multiple local ARG transmission patterns and subsequently evaluated their potential threats to public health based on the gene trees to inform future epidemiological control strategies. Overall, this work expands our current understanding of community sewage for population-level AMR monitoring and establishes a baseline for advancing sewage surveillance efforts to better combat AMR.}, } @article {pmid41756353, year = {2026}, author = {Martins, GL and Monteiro, GGTN and Lange, M and de Freitas, AS and do Nascimento Silva Barbosa, L and van Leeuwen, J and de Carvalho Soares, JE and Hanada, RE and Gleixner, G and Tsai, SM}, title = {Land-use intensification reshapes microbial phosphorus cycling, organic matter composition, and phosphorus fractions in Amazonian soils.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag027}, pmid = {41756353}, issn = {2730-6151}, abstract = {Soil phosphorus (P) is a limiting factor for vegetation growth in the Amazon rainforest, where plants depend on microorganisms for organic matter cycling and nutrient uptake. While forest-to-agriculture conversion fundamentally reshapes plant-microbe-soil interactions and P cycling, these dynamics are further modulated by the intensity of land management. This study examined the 30-year effects of converting a primary forest into two contrasting systems: a low-intensity agroforest and a high-intensity citrus monoculture. We investigated how microbial and low molecular weight organic compounds (LMWCs) composition interacted with soil physicochemical attributes, acid phosphatase activity, and P fractions (labile, moderately labile, non-labile, and residual). Agroforest soils retained physicochemical and enzymatic attributes similar to the primary forest, while soils of the citrus plantation showed increased P in all fractions due to mineral fertilization and reduced soil organic matter content, mainly in deeper layers. Microbial and LMWC composition patterns reflected land-use, with agroforest representing an intermediate state between primary forest and citrus monoculture. Pseudomonadota and nutrient-rich LMWC were more abundant in the agroforest, whereas Ascomycota and nutrient-poor LMWC predominated the citrus plantation. Genes related to "P acquisition" were more abundant in forest and agroforest soils, while genes related to "P-compound synthesis" were more abundant in the citrus plantation. Labile P was negatively correlated with genes related to microbial metabolism, suggesting that reduced P availability may induce a boost in microbial activity for internal P-cycling. These findings demonstrate that forest-to-agriculture conversion strongly affects microbial functions, with responses aligning with land-use intensity and LMWC resource availability. Nonetheless, microbes adapt by shifting strategies: prioritizing mineralization and solubilization or favoring biosynthesis depending on P availability.}, } @article {pmid41756416, year = {2026}, author = {Catchpole, R and McLean, J and St John, E and Reysenbach, AL and Krupovic, M and Terns, MP}, title = {CRISPR spacers reveal diverse and abundant Thermococcales viruses in hydrothermal vents.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41756416}, issn = {2693-5015}, abstract = {Viruses are the most pervasive biological entities on Earth and they profoundly shape host ecology and evolution. However, for many microbial lineages, knowledge of their viromes remains limited, especially for those inhabiting remote environments, including deep-sea ecosystems. Here, we leverage one of the most extensively cultivated and genomically characterized archaeal lineages, the Thermococcales, to identify novel viral genomes. By utilizing CRISPR spacers from isolates and spacer arrays reconstructed from metagenomes, we mined mobile genetic elements (MGEs) in 1,172 publicly available and newly sequenced hydrothermal vent metagenomic datasets. Comparative genomics and identification of viral hallmark proteins revealed 620 viral genomes across 19 taxonomic families, most of which were previously undescribed. Structural modeling of major capsid proteins (MCPs) revealed diverse virion morphotypes, including viruses with spindle-shaped, head-tailed, icosahedral, filamentous, ovoid and bacilliform virions, greatly expanding the previously limited Thermococcales virome. Family-level comparisons uncovered extensive flux of virus-encoded replication proteins that are evolutionarily and structurally distinct from host homologs, as well as dramatic variation in glycan-binding lectins suggestive of diverse infection strategies. Together, our results substantially broaden the Thermococcales virosphere and demonstrate the power of combining cultivated isolates with culture-independent, CRISPR-guided metagenomics to interrogate archaeal virus diversity and evolution.}, } @article {pmid41756466, year = {2026}, author = {Brunner, A and Mahout, M and Amoros, J and Rahmoun, M and Jarry, M and Bordenstein, SR and Bordenstein, SR and Trouche, B and Reveillaud, J}, title = {Extensive mobilome dynamics in a widespread endosymbiont: long read metagenomics reveal dimeric plasmids and highly fragmented prophages in Wolbachia from Culex pipiens.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41756466}, issn = {2693-5015}, abstract = {BACKGROUND: The obligate, intracellular bacteria Wolbachia have gained increasing interest due to their selfish modifications of host arthropod reproduction, impacts on host evolution, and utility in vector control efforts to reduce arbovirus transmission. Despite their highly reduced genomes, Wolbachia harbor a rich global mobilome that includes phages and plasmids in mosquito vectors. However, these mobile genetic elements are structurally complex, and standard genome assemblies often fail to resolve their organization and their functional relationships, leaving gaps in our understanding of how they evolve, mobilize, and influence host genomes.

RESULTS: Here, we present the first near-complete genome of Wolbachia and its mobile elements from the vector Culex pipiens molestus in Montpellier (France), reconstructed from Oxford Nanopore long read sequencing of single female ovaries without prior DNA amplification. Additional short reads from individuals of the same strain were used to assess and validate candidate mutations, particularly in repetitive regions. We report the assembly of a new dimeric form of the pWCP plasmid, providing evidence that the element is a replicating molecule and functionally active. We also observed extensive fragmentation of prophage WO regions despite long read sequencing, underscoring their structural complexity. Raw long read analyses recovered multiple alternative gene syntenies within WO regions, pointing to heterogeneous prophage architectures missed by the assembly and marked diversity of WO elements in Wolbachia of Culex pipiens (wPip) group strains.

CONCLUSIONS: Taken together, our results show the high dynamism of the endosymbiont genome that is shaped by integrated and episomal active mobile elements.}, } @article {pmid41756881, year = {2026}, author = {Krieger, M and Kerns, KA and Palmer, EA and McLean, JS and Kreth, J and Yardimci, GG and Merritt, JL}, title = {Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41756881}, issn = {2692-8205}, abstract = {BACKGROUND: Inflammatory oral diseases are associated with reproducible shifts from commensal-dominated microbiota toward pathobiont-enriched communities, yet the ecological mechanisms underlying the emergence of inflammophiles remain poorly understood. This study aims to investigate if host-derived inflammatory environments act as selective pressures that restructure microbial metabolism and community organization during disease progression.

METHODS: We performed 16S rRNA gene sequencing of patient-matched pediatric dental plaque and odontogenic abscess specimens to capture microbial community transitions across an inflammatory ecological gradient. Community ecology modeling and inferred metagenomic analyses were used to identify taxa and functional programs associated with commensal and inflammophilic states.

RESULTS: Patient-matched comparisons revealed a reproducible ecological selection gradient linking inflammatory environments to expansion of metabolically specialized inflammophiles and depletion of carbohydrate-utilizing commensals. Commensal-dominated plaque communities exhibited anabolic, carbohydrate-centered metabolic capacity, whereas abscess microbiota were enriched for catabolic metabolism, amino acid fermentation, and antimicrobial resistance, consistent with adaptation to inflammation-driven nutrient landscapes and immune pressure.

CONCLUSIONS: These findings support a model in which host inflammation drives ecological restructuring of the oral microbiome toward metabolically adapted inflammophilic communities. Defining the metabolic requirements and selective pressures governing these transitions provides a framework for microbiome-directed therapeutic strategies aimed at restoring ecological stability during inflammatory dysbiosis.}, } @article {pmid41756930, year = {2026}, author = {Yuan, L and Qin, Y and West-Roberts, J and Anantharaman, K and Wang, H and Zou, Y and Duan, Y and Camargo, AP and Koonin, EV and Chen, L}, title = {A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41756930}, issn = {2692-8205}, abstract = {Closely related prophages are frequently found in phylogenetically distant bacteria in the human gut, despite limited evidence of productive phage infections across broad host ranges. Thus, it remains unclear how the wide distribution of prophages could emerge. Here, we identify a potential mechanism of prophage dissemination. We describe two deeply diverged groups of conjugative megaplasmids (>300 kilobases) in the human gut microbiome, which we term Hodors. Hodors encode conserved replication, partitioning, and type IV secretion systems, together with a complex surface-associated gene module. A subset of Hodors harbor complete, intact prophage genomes, and closely related prophages are detected across phylogenetically distant Bacillota lineages, including both Bacilli and Clostridia. Further analysis indicates that Hodor-associated prophages can exist as extracellular particles and demonstrate their transcriptional activity. Our findings support a model in which conjugative megaplasmids act as composite mobile platforms that disseminate prophage genomes across bacterial lineages, providing a mechanistic explanation for the widespread occurrence of closely related prophages in phylogenetically distant gut bacteria and effectively decoupling lysogenic host range from infective host range.}, } @article {pmid41757006, year = {2026}, author = {Tran, HN and Kirven, KJ and Davenport, ER}, title = {SCiMS: Sex Calling in Metagenomic Sequences.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41757006}, issn = {2692-8205}, abstract = {BACKGROUND: Host sex is a critical determinant of microbial community structure, influenced by hormonal profiles, physiology, and sex-stratified behaviors. Despite its importance, sex metadata is frequently missing or mislabeled in microbiome studies. Existing genomic sex-calling tools often fail in low-host-biomass samples (e.g., stool) because they require high read depths to achieve reliability.

RESULTS: Here, we present SCiMS (Sex Calling in Metagenomic Sequences), a bioinformatic tool that leverages host-derived DNA within metagenomic datasets to accurately predict host sex, even at low host coverage. SCiMS uses sex-chromosome read density ratios within a Bayesian classifier to provide high-accuracy sex calls. In simulations, SCiMS achieves >85% accuracy with as few as 450 host reads. When applied to 1,339 samples from the Human Microbiome Project, SCiMS outperforms existing tools, showing higher accuracy and more balanced precision-recall tradeoffs across body sites. SCiMS also generalizes effectively to non-human hosts, achieving 100% accuracy in a murine dataset and outperforming alternatives in a chicken dataset with a ZW sex determination system.

CONCLUSIONS: SCiMS provides an accurate, scalable, and cross-species generalizable solution for host sex classification in metagenomic datasets, even when host DNA is minimal. By enabling the recovery of missing sex metadata, it serves as a quality-control tool for ensuring the integrity of analyses in microbiome research. SCiMS is freely available at http://github.com/davenport-lab/SCiMS.}, } @article {pmid41757095, year = {2026}, author = {Wang, F and Holmes, AJ and Browne, GV and He, X and Bockmann, MR and Davis, KM and Hughes, TE and Adler, CJ}, title = {Ecological and evolutionary dynamics of the oral microbiome across childhood.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41757095}, issn = {2692-8205}, abstract = {Childhood represents a critical period for oral microbiome development, yet evolutionary trajectories and the relative roles of host and environment remain unclear. Using a large longitudinal metagenomic dataset of 920 samples from a twin cohort spanning the first decade of life, we characterised microbial shifts and population dynamics of key bacterial groups. Microbiome diversity was initially reduced and highly heterogeneous and became increasingly complex and convergent with age. Microbial community state was associated with developmental age, environment and in late childhood was surprisingly strongly associated with host genotype. Strain-level analyses revealed species-specific temporal patterns of genetic variation particularly within Streptococcus, reflecting adaptive responses to host and environmental pressures. Fusobacterium exhibited consistently high replication rates, indicating sustained growth dynamics. Phylogenetic reconstruction further revealed host and niche specific genomic diversification of Saccharibacteria lineages. These findings establish childhood as a decisive period of oral microbial evolution and highlight the role of host-microbiome and epithelial interactions in shaping community structure, providing guidance for oral management strategies that promote lifelong oral health.}, } @article {pmid41757098, year = {2026}, author = {Duan, L and Baumgartner, WA and Wanyama, JW and Okyere, L and Alvarado, DA and Minhas, BF and Gaulke, CA}, title = {Sex-stratified Gut Microbiome Disruption is Associated with Altered Hepatic Gene Expression during Acute Azoxystrobin Exposure.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41757098}, issn = {2692-8205}, abstract = {Azoxystrobin is a widely used fungicide that has been associated with to reproductive, neurological, and developmental defects. This chemical also disrupts gut microbial communities; however, if these perturbations contribute to the harms associated with exposure to azoxystrobin, this remains unclear. In this study, we investigated the effects of acute exposure to a series of concentrations (5-500 mg/kg) of azoxystrobin on the host and gut microbiota in zebrafish. Fecal amplicon and shotgun metagenomic sequencing was integrated with liver gene expression to quantify associations between microbiome disruption azoxystrobin toxicity in the host. Azoxystrobin exposure resulted in significant alteration in microbiome composition and functional potential in a dose- and sex-dependent manner. Microbial communities in exposed animals exhibited an increased abundance of xenobiotic metabolism pathways and decreased bacterial motility and lipopolysaccharide biosynthesis pathway metabolism. At the host level, histopathology identified increased biliary proliferation, most evident in medium- and high-dose fish. We also observed hepatic transcriptional changes consistent with a stress response, including altered redox-associated genes and reduced expression of lipid and small-molecule metabolic genes, with sex-stratified differences. Importantly, alterations in host transcriptional programming correlated with the compositional changes in exposed microbiota. Together, these results suggest concurrent impacts of azoxystrobin on gut microbiota and the liver implicate the microbiome as a potential contributor to changes in liver gene expression during exposure.}, } @article {pmid41757355, year = {2025}, author = {Lai, CM and Xiao, XS and Liu, LW and Li, XL and Luo, YW and Liang, YQ and Cheng, Y and Qin, Y}, title = {The impact of nanodrugs on the metagenome of tobacco rhizosphere soil.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1715400}, pmid = {41757355}, issn = {1664-302X}, abstract = {The occurrence of tobacco diseases seriously restricts the healthy development of the tobacco industry. Soil microorganisms play an important role in regulating ecosystem functions. However, the impact of nanodrugs on the rhizosphere microbial community of tobacco and its related functions is still unclear. Therefore, this study combined field experiments to evaluate the effect of nanodrugs in reducing diseases and combined metagenomic sequencing to further explore the micro-ecological mechanism of nanodrugs in stably reducing soil biological barriers. The results show that nanodrugs can significantly improve the health level of tobacco. Metagenomic sequencing found that nanodrugs treatment increased the diversity and abundance of bacterial communities and could regulate the structure of soil microbial communities. It could selectively recruit beneficial microorganisms such as Sphingomonas, Bradyrhizobium, Pseudomonas, and Nocardioides to assist tobacco in disease control. GO function analysis showed that nanodrug treatment groups had significant enrichment of energy metabolism-related functions such as electron transfer activity, ATPase activity, and redox processes. KEGG pathway analysis showed that the relative abundance of key metabolic pathways such as fatty acid metabolism, aminoacyl-tRNA biosynthesis, ribosome, and purine metabolism was significantly increased. This study found that nanodrugs may indirectly promote plant health and alleviate tobacco diseases by shaping microbial community structure, enriching beneficial bacterial communities, and activating key metabolic pathways. These findings provide a theoretical basis for the application of NMs in the regulation of agricultural micro-ecosystems.}, } @article {pmid41757357, year = {2025}, author = {Secker, B and Nayak, A and Husain, AA and Arora, S and Nag, A and Shrivastava, SK and Singer, AC and Gomes, RL and Acheampong, E and Chidambaram, SB and Bhatnagar, T and Vetrivel, U and Kashyap, RS and Atterbury, RJ and Blanchard, AM and Monaghan, TM}, title = {Metagenomic insights into the urban-rural variation of antimicrobial resistance and pathogen reservoirs in untreated wastewater from central India.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1722229}, pmid = {41757357}, issn = {1664-302X}, abstract = {INTRODUCTION: Rapid and scalable surveillance of antimicrobial resistance (AMR) is urgently needed in resource-constrained countries where routine monitoring is limited. Wastewater-based metagenomics offers a potential solution for early detection and geographic mapping of AMR.

METHODS: We conducted a retrospective DNA shotgun metagenomic analysis of untreated wastewater collected across Nagpur, India (February-April 2021). A total of 422 grab samples were pooled into 138 composite samples from 10 urban zones and rural catchments. The bacterial microbiota and resistome were profiled, and urban-rural patterns were compared using diversity metrics and correlation analyses.

RESULTS: Across all samples, 871 bacterial genera were detected, dominated by Proteobacteria, with frequent presence of Pseudomonas, Acinetobacter, Aeromonas, Acidovorax and Bacteroides. Beta diversity revealed statistically significant but subtle urban-rural compositional shifts. Of 33 globally important pathogens examined, 13 were detected at generally low relative abundance (<1%). Vibrio cholerae appeared in one sample, while Aeromonas spp. were most prevalent. Seven pathogens occurred in ≥10% of samples, with Aeromonas, Citrobacter, and Enterobacter differing significantly between locations (p < 0.05). The resistome comprised 606 unique antimicrobial resistance genes (ARGs), dominated by drug/biocide efflux determinants, followed by macrolide-lincosamide-streptogramin B genes driven largely by 23S rRNA mutations. Carbapenemases (blaNDM, blaKPC) and colistin resistance (mcr) were detected at lower abundance. Correlation analyses linked Pseudomonas with mexEF/emhABC efflux and copBCDRS copper resistance operon, Acinetobacter with oxa and dfrA, and Aeromonas with ctx, tetA, sul1, dfrB/F, and gyrA/parC.

DISCUSSION: These findings show that wastewater metagenomics sensitively resolved clinically relevant pathogens and ARGs in an Indian urban-rural setting, capturing nuanced geographic structure. Integrating routine DNA metagenomics into One Health environmental surveillance could strengthen AMR early warning and guide interventions in resource-constrained contexts.}, } @article {pmid41757394, year = {2026}, author = {Wang, Z and Kojima, R and Kiji, R and Fujita, K and Tachibana, R and Tsuchiya, R and Uchiyama, T and Minagawa, Y and Mizuno, T and Igarashi, K and Noji, H and Kamiya, M and Urano, Y}, title = {Low-Background Cancer Imaging with a Bioorthogonal Fluorescence Probe and Engineered Reporter Enzyme Bearing a Targeting Moiety.}, journal = {Journal of the American Chemical Society}, volume = {148}, number = {11}, pages = {11492-11502}, pmid = {41757394}, issn = {1520-5126}, mesh = {*Fluorescent Dyes/chemistry/metabolism ; Humans ; Animals ; Mice ; *Glycoside Hydrolases/metabolism/chemistry/genetics ; *Optical Imaging ; Protein Engineering ; Cell Line, Tumor ; Erb-b2 Receptor Tyrosine Kinases/metabolism ; Female ; Fucose/chemistry ; }, abstract = {Combinatorial use of an antibody-reporter enzyme conjugate and a fluorescence probe activated by the enzyme is a powerful strategy for fluorescence-guided cancer surgery. However, conventional probes for typical reporter enzymes lack sufficient bioorthogonality, leading to high background signals in nontarget tissues. We screened a library of HMRef (rhodol derivative)-based fluorescence probes with various sugar moieties and found that HMRef-β-d-Fucose is bioorthogonal in mammalian systems but is activated by a metagenomic glycosidase, Td2F2. Directed evolution generated a mutant with a kcat/Km of 3.3 × 10[5]/M/sec, 7.3 times higher than wild-type Td2F2 and comparable to β-galactosidase (LacZ) with its corresponding probe. Theoretical calculation suggested the E296G mutation facilitates probe access to the enzyme's active site. In a proof-of-concept study, SKOV-3 cells, which endogenously express HER2, were visualized with minimal background in the mesentery of a mouse model using HMRef-β-d-Fucose and engineered Td2F2 conjugated or fused to a HER2-binding antibody or nanobody.}, } @article {pmid41757490, year = {2026}, author = {Wang, Y and Schleheck, D and Marinova, E and Wessels, M and Schaller, S and Anselmetti, FS and Schwalb, A and Pedersen, MW and Epp, LS}, title = {Prokaryotic assemblages recovered by sedimentary DNA record natural and human-driven disturbances over the past 13 500 years in a cultural landscape.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41757490}, issn = {1751-7370}, support = {298726046//German Research Foundation/ ; //Research Training Group R3 - Resilience of Lake Ecosystems/ ; 290492639//International Continental Scientific Drilling Program/ ; //Elite Program for Postdocs, Baden-Württemberg Foundation/ ; 57450037//German Academic Exchange Service/ ; //MEiN Programme of the University of Konstanz/ ; //Doctoral Fund of the University of Konstanz/ ; }, mesh = {*Geologic Sediments/microbiology ; *Archaea/genetics/classification/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; Humans ; Lakes/microbiology ; DNA, Bacterial/genetics ; *DNA, Ancient/analysis ; DNA, Archaeal/genetics ; Sequence Analysis, DNA ; Metagenomics ; }, abstract = {Bacteria and archaea are under-characterized in palaeoecological studies, despite their ubiquity, high diversity, and tight integration with the abiotic, biotic, and human-influenced environments. The complexity of their assemblages and difficulties in separating living- from paleo-prokaryotes render research challenging. Here, we present an ancient metagenomic time series of prokaryotes from a sediment core of Lake Constance, spanning the last 13 500 years of natural and anthropogenic impact. We mapped DNA to reference genomes and characterized the DNA damage of taxa as collectively increasing with time. By constructing co-abundance networks, we recognize major assemblage groups, containing both dead and living microbes, that show specific dynamics: short-term and often low-abundance assemblages are linked to the Pleistocene-Holocene transition, floods, and human activities. Noticeably, certain lineages harbouring microbes common in human-impacted environments expanded during the Middle Ages and Modern time. Some abundant taxa associated with various freshwater and soil environments persisted through millennia. By extricating different sources and trajectories of change, we demonstrate the power of prokaryotic sedimentary DNA in revealing nature- and human-caused long-term eco-evolutionary consequences.}, } @article {pmid41757865, year = {2026}, author = {Hu, X and Shi, Z and Gao, Y and Zheng, H and Lin, L and Chen, JP and Chen, Y and Zhang, CX and Li, Y}, title = {Characterization of the dynamic microbiome evolution across thrips species.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70265}, pmid = {41757865}, issn = {1744-7917}, support = {2023J06040//Natural Science Foundation of Fujian Province/ ; //Ningbo Yongjiang grant/ ; 32472657//National Natural Science Foundation of China/ ; 32570491//National Natural Science Foundation of China/ ; }, abstract = {The insect microbiome profoundly influences host physiology and ecology, yet its composition and evolutionary dynamics in thrips remain poorly understood. Here, we present a systematic characterization of thrips-associated microbiomes through integrated metagenomic and culture-based approaches. Our analysis reveals that thrips microbiomes are dominated by both intracellular symbionts (e.g., Wolbachia and Spiroplasma) and extracellular taxa (e.g., Serratia, Pantoea, and Acinetobacter), with species-specific compositions exhibiting frequent gains and losses of bacterial lineages. We demonstrate that thrips microbiomes exhibit low interspecific microbial sharing, forming host-specific bacterial communities with minimal overlap between species. To address methodological challenges in microbiome research, we developed a dual-sequencing framework combining short-read sequencing (for comprehensive taxonomic detection) and long-read sequencing (for genomic verification), enabling the reconstruction of high-quality metagenome-assembled genomes that validated short-read findings. Furthermore, we isolated and sequenced the complete genomes of two dominant extracellular symbionts-Pantoea dispersa and Serratia marcescens-and performed pan-genome analyses. These revealed small core gene sets and expansive accessory genomes, including host-specific functional genes (e.g., hydrolases and neurotoxic N-acetyltransferases) likely involved in host adaptation. Our study provides a foundational genomic resource and a robust analytical pipeline for dissecting thrips microbiome evolution, with implications for understanding insect-microbe interactions and symbiont-mediated adaptations.}, } @article {pmid41757890, year = {2026}, author = {Tarasov, K and Zarubin, M and Yakhnenko, A and Gangapshev, A and Kravchenko, E}, title = {Metagenomic analysis of the biofilm community at the oxic-anoxic interface of a deep-underground saline spring at the Baksan Neutrino Observatory.}, journal = {Microbiology spectrum}, volume = {14}, number = {4}, pages = {e0210325}, pmid = {41757890}, issn = {2165-0497}, support = {24-24-00003//Russian Science Foundation/ ; }, mesh = {*Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenomics ; *Archaea/genetics/classification/isolation & purification/metabolism ; *Biofilms/growth & development ; *Metagenome ; Russia ; *Microbiota/genetics ; Phylogeny ; Methane/metabolism ; }, abstract = {In this work, the first-ever metagenomic study of the microbial community from the deep-underground saline spring located at the Baksan Neutrino Observatory (BNO) (Kabardino-Balkaria, Russia) is presented. Using the metagenomic approach, we obtained 19 metagenome-assembled genomes (MAGs) attributed to the phyla Pseudomonadota (the dominant phyla), Planctomycetota, Myxococcota, Nitrospirota, Gemmatimonadota, Armatimonadota, and Cyanobacteriota. Archaea are generally absent in the metagenome. The microbial community of the Baksan Neutrino Observatory demonstrates a high metabolic diversity, including carbon dioxide-fixing, methane-oxidizing, dinitrogen-fixing, nitrate- and iron-reducing, anammox, nitrifying, and predatory bacteria. Hydrogen, methane, ammonia, and reduced iron compounds, present in the ecosystem, provide energy for primary organic production. The abundance and diversity of bacteria capable of carrying out various stages of the nitrogen cycle suggest that nitrogen compounds are of great significance for microbial community metabolism. On the basis of the Genome Taxonomy Database Toolkit classification of MAGs and comparison to the closest RefSeq genomes, we have identified six new genera, with the proposed names-"Candidatus Jinrbaksania," "Candidatus Neutrinellum," "Candidatus Jinrextremum," "Candidatus Inrsubterrania," "Candidatus Inralta," and "Candidatus Neutrinobacter." Comparative analysis with metagenomes of microbial communities from the deep underground granitic sites and karst caves reveals that the BNO microbial community represents a unique transitional ecosystem on the boundary between the deep anoxic and surface aerobic biosphere.IMPORTANCEThe deep biosphere makes up 12-20% of the Earth's biomass and is poorly studied due to its inaccessibility. To date, only a few metagenomic studies of local deep biospheres have been performed in Russia. The Baksan Neutrino Observatory (BNO) is a deep-underground laboratory, with some abandoned tunnels. One of them hosts a mineral spring saturated with volcanic gases from the peripheral magma chamber of Mount Elbrus. The metagenomic analysis of the biofilm from this mineral spring has revealed the presence of unique microbial community whose composition occupies a transitional position between deep-underground microbial communities and communities of karst caves. We believe that this study of the microbial metagenome of the saline spring of the BNO will make a valuable contribution to understanding the composition and functioning of microbial communities formed at the oxic-anoxic interface.}, } @article {pmid41757938, year = {2026}, author = {Hashimoto, K and Fukushima, K and Matsumoto, Y and Saito, H and Funauchi, A and Hamada, N and Yamauchi, J and Nitta, T and Motooka, D and Nii, T and Matsuki, T and Tsujino, K and Miki, K and Komukai, S and Kumanogoh, A and Nakamura, S and Kida, H}, title = {Comparison of culture and culture-free methods for comprehensive identification of mycobacteria: a single-center prospective study.}, journal = {Journal of clinical microbiology}, volume = {64}, number = {4}, pages = {e0112825}, pmid = {41757938}, issn = {1098-660X}, support = {//Takeda Science Foundation/ ; //Japanese Respiratory Society/ ; //Foundation of Kinoshita Memorial Enterprise/ ; //MSD Life Science Foundation/ ; //Osaka Medical Research Foundation for Intractable Diseases/ ; //Uehara Memorial Foundation/ ; 24fk0108673h0702//Japan Agency for Medical Research and Development/ ; JP21lm02007, JP223fa627002//Japan Agency for Medical Research and Development/ ; 2020B02//The Japan Intractable Diseases (Nanbyo) Research Foundation/ ; 24K11378//JSPS KAKENHI/ ; 24K18468//JSPS KAKENHI/ ; //Inamori Foundation/ ; //Senri Life Science Foundation/ ; }, mesh = {Humans ; Prospective Studies ; Sputum/microbiology ; *Nontuberculous Mycobacteria/isolation & purification/classification/genetics ; *Bacteriological Techniques/methods ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Whole Genome Sequencing ; Multilocus Sequence Typing ; Female ; Aged ; Middle Aged ; }, abstract = {The genus Mycobacterium, including Mycobacterium tuberculosis and over 200 nontuberculous mycobacteria (NTM), shows wide variability in clinical outcomes and drug susceptibility. Although culture-based identification remains the gold standard, slow mycobacterial growth delays diagnosis and treatment. In this study, we evaluated a novel culture-free method for subspecies-level identification directly from sputum. In this single-center prospective cohort study at Osaka Toneyama Medical Center, we analyzed 125 sputum samples from 115 patients with NTM pulmonary disease and 10 with non-NTM respiratory conditions. Samples were decontaminated using N-acetyl-L-cysteine-sodium hydroxide (NALC-NaOH) or succinic acid. We compared the reference culture method (mycobacterial culture plus whole-genome sequencing) and a culture-free direct target capture sequencing method. Core genome multi-locus sequence typing identified subspecies in both workflows, covering 186 mycobacterial species, including M. tuberculosis. The 115 NTM cohort specimens yielded 57 smear-positive and 93 culture-positive results. The identified subspecies included 48 Mycobacterium avium subsp. hominissuis, 22 Mycobacterium intracellulare subsp. intracellulare, 5 subsp. chimaera, 7 Mycobacterium abscessus subsp. abscessus, 5 subsp. massiliense, 1 M. tuberculosis, and 5 other NTM species. The culture-free method showed a high identification rate for smear-positive specimens (75.4%) but a low identification rate for smear-negative specimens (13.9%). NALC-NaOH pretreatment resulted in higher accuracy (90.5%) than did succinic acid pretreatment (66.7%). Thus, our culture-free subspecies-level identification method achieved high accuracy, especially in alkaline-treated smear-positive sputum samples, achieving rates above 90%. This method is recommended in clinical practice for patients who require rapid diagnosis and timely initiation of appropriate treatment, bypassing time-consuming culture steps.IMPORTANCEAccurate identification of Mycobacterium species and subspecies is crucial for effective treatment, as drug susceptibility and clinical outcomes vary significantly among them. However, conventional diagnosis relies on culture-based methods that can take several weeks, critically delaying appropriate therapy. This study validates a novel culture-free method using target capture sequencing for the comprehensive, subspecies-level identification of over 186 mycobacterial species directly from sputum specimens. Our findings revealed the high accuracy of this approach for smear-positive specimens, especially with alkaline pretreatment. This rapid method is applicable in clinical settings and enables timely and precise treatment decisions, greatly benefiting patients who require urgent intervention.}, } @article {pmid41758007, year = {2026}, author = {Nieves-Morales, R and Quiles-Pérez, CJ and Rivera-Lopez, EO and Torres-Zapata, I and Rodriguez-Ramos, J and Rios-Velazquez, C}, title = {Metagenomic libraries data sets from the hypersaline benthic microbial mats of the Fraternidad Lagoon, Puerto Rico, using an indirect DNA extraction method.}, journal = {Microbiology resource announcements}, volume = {15}, number = {4}, pages = {e0150425}, pmid = {41758007}, issn = {2576-098X}, support = {MCB-0455620//National Science Foundation/ ; }, abstract = {Microbial mats are biofilm formations that reflect early Earth ecosystems. To investigate their microbial diversity, an indirect DNA extraction method was applied to benthic ephemeral microbial mats from Fraternidad Saltern Lagoon during rainy and dry seasons. This approach yields high molecular DNA, suitable for metabolic and diversity analysis.}, } @article {pmid41758194, year = {2026}, author = {Chen, J and Wang, Y and Xu, L and Li, X and Zhao, L}, title = {Exploring the gut microbiome and metabolomic interactions of antimetabolite drugs to optimize therapy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2638009}, pmid = {41758194}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Antimetabolites/therapeutic use/pharmacology/pharmacokinetics/adverse effects ; Animals ; Metabolomics ; Dysbiosis/chemically induced/microbiology ; Neoplasms/drug therapy/microbiology ; Bacteria/metabolism/drug effects/genetics/classification ; }, abstract = {Antimetabolite drugs are cornerstones in treating various cancers and autoimmune diseases; however, their clinical utility is often hampered by systemic toxicity caused by drug-induced gut microbiota dysbiosis. Predicting patient responses remains a significant challenge. Several studies have highlighted the influence of gut microbiota on antimetabolite treatment outcomes, revealing complex bidirectional interactions between the drugs and microbial communities. This review synthesizes the effects of common antimetabolites (including 5-fluorouracil, methotrexate, gemcitabine, capecitabine, 6-mercaptopurine, and thioguanine) on gut microbial communities and outlines a framework (pharmacokinetics, endogenous metabolite production, immune modulation, and apoptotic pathway modulation) for assessing chemotherapy-microbiota interactions. Additionally, potential microbial biomarkers for predicting treatment responses and strategies for manipulating the gut microbiota to enhance therapeutic efficacy are discussed. Therefore, advances in methodologies such as metagenomics and real-time microbial monitoring will be essential for unraveling these interactions and promoting the precise application of antimetabolite drugs.}, } @article {pmid41758250, year = {2026}, author = {Kumar, A and Bandyopadhyay, TK and Das, D}, title = {Bacterial laccases for green remediation of contaminants of emerging concern: from molecular cloning to metagenomic and computational insights.}, journal = {Biodegradation}, volume = {37}, number = {2}, pages = {}, pmid = {41758250}, issn = {1572-9729}, mesh = {*Laccase/metabolism/genetics/chemistry ; Biodegradation, Environmental ; *Bacteria/enzymology/genetics ; Cloning, Molecular ; Metagenomics ; *Bacterial Proteins/metabolism/genetics/chemistry ; }, abstract = {Contaminants of emerging concern (CECs) are increasingly recognized for their persistence, widespread occurrence, and potential risks to environmental and human health. Their frequent detection in wastewater, surface water, drinking water, and food chains underscores the urgent need for sustainable remediation strategies. Laccases, versatile multicopper oxidases, have demonstrated strong potential for degrading organic pollutants through oxidative mechanisms that transform complex contaminants into less toxic products. While fungal laccases have been extensively studied, bacterial laccases are gaining attention due to their structural simplicity, stability under alkaline conditions (pH 7.5-9.0), and limited requirement for post translational modifications. Recent studies indicate that bacterial laccases can transform approximately 60-80% of industrial dyes, a major class of CECs, even in complex wastewater matrices. Despite notable progress, broader application of bacterial laccases remains constrained by limited enzyme stability under industrial operating conditions, reduced catalytic performance under high salinity, extreme pH, and mixed pollutant environments, and frequent dependence on costly redox mediators, highlighting the need for more robust enzymes and sustainable mediator alternatives. This review summarizes recent advances in bacterial laccase research, with emphasis on structural and substrate specific insights, molecular cloning, heterologous expression, and optimized purification strategies. It also highlights emerging approaches such as metagenomics and machine learning for identifying robust, thermostable, and alkali resistant bacterial laccases suitable for large scale applications. Collectively, these advances support green chemistry principles and contribute to multiple United Nations Sustainable Development Goals by enhancing wastewater treatment efficiency, reducing energy and chemical inputs, and promoting sustainable waste valorization.}, } @article {pmid41759061, year = {2026}, author = {Hong, S and Winkler, MH and Wang, ZW and Dhanasekar, A and Goel, R}, title = {Unveiling Metabolic Insights and Niche Differentiation of Microbial Communities in EBPR-Anammox Reactor through Integration of Long-Read Metagenomics and Metatranscriptomics.}, journal = {Environmental science & technology}, volume = {60}, number = {10}, pages = {7967-7982}, doi = {10.1021/acs.est.5c17958}, pmid = {41759061}, issn = {1520-5851}, mesh = {*Bioreactors/microbiology ; Metagenomics ; Phosphorus/metabolism ; Biofilms ; Sewage ; Denitrification ; }, abstract = {In this manuscript, we report niche differentiation among important groups of organisms involved in phosphorus and nitrogen cycling, and the interplay between relevant metabolic pathways carried out by these key organisms. We employed nanopore-based long-read and Illumina-based short-read sequencing techniques for metagenomics and metatranscriptomics, respectively, on samples collected from an integrated fixed film activated sludge (IFAS) bioreactor run in the conventional A[2]O mode under low dissolved oxygen (DO) conditions. Among the recovered metagenome-assembled genomes (MAGs), >90 MAGs from each community were high-quality, including 39 and 30 MAGs that were close-circularized, from the floc and biofilm communities, respectively, with no or minimal contamination. Some Candidatus Accumulibacter strains encoded for either full or partial denitrification. Ca. Accumulibacter were very efficient in aerobic and anoxic inorganic phosphorus (Pi) uptake, while the second highly enriched Ca. Accumulibacter was as competitive for denitrification metabolism. The potential of nitrous oxide (N2O) emissions in both the floc and biofilm communities was nearly 20 times higher in the aerobic zone than in the anoxic zone. As opposed to our initial hypothesis that slow growers will mostly reside in biofilms, the expression of ammonium monooxygenase (amoABC) was higher in flocs than in biofilm communities.}, } @article {pmid41759241, year = {2026}, author = {Myers, PN and van Beijsterveldt, IALP and Snowden, SG and Eriksen, C and Nielsen, HB and Hughes, IA and Ong, KK and Hokken-Koelega, ACS and Koulman, A and Brix, S}, title = {Breastfed infants receiving formula supplementation show altered lipid and gut microbiota profiles at 3 months of age.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {59}, number = {}, pages = {106602}, doi = {10.1016/j.clnu.2026.106602}, pmid = {41759241}, issn = {1532-1983}, mesh = {Humans ; *Breast Feeding ; Infant ; *Infant Formula ; Female ; *Gastrointestinal Microbiome/physiology ; Lipidomics ; *Lipids/blood ; Feces/microbiology ; Male ; *Dietary Supplements ; Infant Nutritional Physiological Phenomena ; Prospective Studies ; }, abstract = {BACKGROUND & AIMS: Exclusive breastfeeding offers numerous health benefits. Despite advancements in formula, significant differences compared with breast milk remain. We aimed to assess how milk feeding type and volume at 3 months affect the infant plasma lipidome and gut microbiota.

METHODS: Infants were classified into exclusive breastfeeding (EBF), mixed feeding (MF), or exclusive formula feeding (EFF) groups based on feeding data collected prospectively across two European cohorts (n = 519). Lipidomics and shotgun metagenomics were applied to plasma and stool samples, respectively.

RESULTS: Feeding type explained major variation in both lipidomic and microbial profiles. Plasma lipids showed distinct signatures across groups, particularly in sphingomyelins and diacylglycerols. Microbiota diversity and species richness increased with formula exposure. Formula rich in intact whey protein was linked to higher S. thermophilus abundance in the infant gut. Random forest classification of feeding type using either lipidomic or gut microbiota features achieved high discriminatory accuracy (AUROC >0.90) in training and validation datasets.

CONCLUSION: Early nutrition is a critical determinant of the lipidome and gut microbiome during the breastfeeding phase.}, } @article {pmid41759316, year = {2026}, author = {Zhang, J and Zhang, Z and Shen, Z and Yu, Z and Chen, J and Zeng, L and Li, D and Yan, X and Li, B and Wong, JWC}, title = {PDG_DB: A comprehensive database unveils environmental distribution patterns of plastic-degrading genes via large-scale multi-omic data analysis.}, journal = {Water research}, volume = {296}, number = {}, pages = {125619}, doi = {10.1016/j.watres.2026.125619}, pmid = {41759316}, issn = {1879-2448}, mesh = {*Biodegradation, Environmental ; *Plastics/analysis/metabolism ; Environmental Monitoring ; }, abstract = {Plastic pollution has become a global environmental crisis, driving urgent research into plastic-degrading enzymes for achieving efficient green transformation and recycling of plastic waste. However, current plastic-degrading gene (PDG) databases remain fragmented and incomplete. Simultaneously, research has predominantly focused on laboratory-isolated strains with the limited exploration of the vast reservoir of PDGs in environmental metagenomes. To address these limitations, we employed large-scale environmental multi-omics analysis to systematically mine and characterize PDGs across diverse ecosystems. We constructed PDG_DB (https://github.com/Z-bioinfo/PDG_DB), a comprehensive PDG database containing 341 experimentally validated sequences categorized by substrate specificity. Large-scale multi-omics analysis across environmental samples identified 7,111 PDGs (3,612 non-redundant), with polyhydroxyalkanoate (PHAs) degrading genes predominating. Molecular docking revealed that novel putative PDGs for PHA degradation exhibited stronger binding affinity compared to known PDGs, demonstrating the necessity of mining novel enzymes from environmental sources. Most PDGs were bacterial, primarily from Pseudomonadota, with the genus Pseudomonas showing the broadest degradation range. Our global analysis of 5,466 datasets revealed high PDG abundance in East Asia, North Europe, America, and the oceans. Unexpectedly, drinking water systems harbored the highest PDG abundance, challenging assumptions about plastic contamination in potable water. PDG distribution varied by environment: soil favored genes for non-biodegradable plastics, while wastewater systems preferred those for biodegradable plastics. Metatranscriptomic analysis showed the highest PDG activity in marine environments. This work provides a comprehensive resource for PDGs, revealing distinctive global distribution patterns with drinking water systems as an unexpected reservoir. PDG_DB serves as a foundational database for identifying PDGs, facilitating future environmental monitoring and biotechnology applications.}, } @article {pmid41759320, year = {2026}, author = {Yin, Y and Wu, H and French, CE and Lu, Z}, title = {Triclosan induced restructuring of microbial communities and antibiotic resistance gene dynamics in activated sludge: insights and mitigation strategies.}, journal = {Water research}, volume = {296}, number = {}, pages = {125614}, doi = {10.1016/j.watres.2026.125614}, pmid = {41759320}, issn = {1879-2448}, mesh = {*Triclosan/pharmacology ; *Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Gene Transfer, Horizontal ; *Microbiota/drug effects ; }, abstract = {The widespread presence of emerging contaminants, such as triclosan (TCS), in environmental systems raises significant concerns regarding their ecological risks, particularly the propagation of antibiotic resistance genes (ARGs). In this study, sequencing batch reactors (SBRs) were exposed to a TCS concentration gradient to simulate the accumulation of TCS in activated sludge and to elucidate its effects on microbial community structure, ARG dissemination, and horizontal gene transfer (HGT). Using a multi-omics approach that integrated 16S rRNA amplicon sequencing, short- and long-read metagenomics, and genome-scale metabolic modeling, we demonstrated that increasing TCS concentrations progressively reduced microbial diversity and stability. At lower TCS concentrations (0-1.0 mg/L), ARG-carrying bacteria were enriched, whereas at higher concentrations (10 mg/L), TCS eliminated ARG-carrying bacteria and selected for strains rich in mobile genetic element (MGE). Notably, HGT led to genome expansion of Acidomonas methanolica (from 3.75 Mb to 7.13 Mb), disrupting the microbial interaction networks within the community. Additionally, the introduction of a triclosan-degrading hydrogel-magnetic biochar-engineered strain composite mitigated the destabilizing effects of TCS stress on the microbial community, enhanced its resilience, and facilitated TCS degradation, thus reducing associated environmental risks. Our findings highlight how gradient TCS exposure reshapes microbial communities, promotes the dominance of MGE-enriched taxa, and has profound implications for the ecological and evolutionary dynamics of microbial communities in aquatic ecosystems. This study provides novel insights into the role of emerging contaminants in the propagation of resistance and microbial adaptation.}, } @article {pmid41759554, year = {2026}, author = {Dai, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Xu, H and Sun, J}, title = {Insights into antibiotic resistomes from gut metagenome-assembled genomes of the free-range pigs.}, journal = {Microbiology spectrum}, volume = {14}, number = {4}, pages = {e0240725}, pmid = {41759554}, issn = {2165-0497}, support = {24D1J01//CARS | National Swine Industry Technology System/ ; 2024M762004//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; Swine/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Metagenome ; *Gastrointestinal Microbiome/genetics/drug effects ; China ; Feces/microbiology ; Metagenomics ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; }, abstract = {The pig gut microbiome serves as a reservoir for antibiotic resistance genes (ARGs), which pose a threat to public health and environmental safety. To investigate the presence of ARGs carried by free-range pigs, which have frequent contact with humans and their environment, we characterized the resistome of the pig gut microbiome through metagenomic sequencing of fecal samples from 120 pigs across four provinces in China (Yunnan, Guizhou, Sichuan, and Jiangsu). By constructing metagenome-assembled genomes (MAGs) and gene catalogs, we explored the microbial community structure and ARG distribution. Our analysis revealed a highly diverse array of ARGs, particularly those conferring resistance to multidrug, glycopeptide, peptide, and tetracycline antibiotics. Bacillota A and Actinomycetota were the dominant phyla across samples. However, notable regional differences in microbiota composition and resistance profiles were observed. These differences were likely influenced by local farming practices and environmental conditions. Guizhou harbored 11 unique ARG types, followed by Sichuan (seven), which showed region-specific resistome signatures. Escherichia coli and other microbial taxa were closely linked with ARG abundance, suggesting potential vectors for horizontal gene transfer. Analysis of mobile genetic elements (MGEs) further supported this, revealing a strong linear correlation between MGE and ARG abundance, with transposase elements particularly associated with multidrug ARGs. These findings highlight the central role of MGEs in ARG dissemination and underscore the need for targeted strategies to curb antibiotic resistance in livestock systems. Regional variation in resistome profiles further emphasizes the influence of local agricultural practices on resistance dynamics.IMPORTANCEThe growing prevalence of antibiotic resistance poses a significant global health threat, making it imperative to trace the origins and transmission routes of ARGs. This study delivers a comprehensive genomic reference for the porcine gut microbiota and clarifies how regional farming practices shape distinct resistome profiles. Integrating these data with analyses of mobile genetic elements and microbial hosts reveals the complex interplay among host, microbiota, and environment, thereby extending current knowledge of the pig gut ecosystem. These findings provide an evidence-based foundation for targeted surveillance and intervention strategies to curb antibiotic resistance in livestock and safeguard public health.}, } @article {pmid41759557, year = {2026}, author = {Yang, W and Shi, L and Li, X and Rao, F and Luo, R and Huang, C}, title = {Alterations in the gut virome of children with allergic rhinitis: enrichment of pro-inflammatory bacteriophages and depletion of fungal viruses.}, journal = {Microbiology spectrum}, volume = {14}, number = {4}, pages = {e0327625}, pmid = {41759557}, issn = {2165-0497}, mesh = {Humans ; *Virome ; Child ; *Rhinitis, Allergic/virology/immunology/microbiology ; *Bacteriophages/genetics/isolation & purification/classification ; Female ; *Gastrointestinal Microbiome ; Metagenomics ; Feces/virology/microbiology ; Male ; *Fungal Viruses/genetics/isolation & purification/classification ; Immunoglobulin E/blood ; Bacteria/classification/genetics/isolation & purification ; Fungi/virology ; Animals ; Child, Preschool ; Allergens/immunology ; }, abstract = {This study aimed to characterize the gut virome in children with allergic rhinitis (AR) and explore its interactions with immune markers and allergens. Metagenomic sequencing was performed on fecal samples from 16 AR and 17 healthy control (HC) children. Viral genes (VGs) were identified and taxonomically annotated using BLASTP against the NCBI NR database. Virome diversity, differential abundance, and correlations with IgE were analyzed using LEfSe, random forest, and Spearman correlation. While alpha diversity did not differ, beta diversity revealed subtle compositional trends. Taranisvirus was enriched in AR and positively correlated with total IgE (ρ = 0.4647, P = 0.045). Mitovirus and Duamitovirus were depleted in AR and negatively correlated with allergens. Virus-bacteria co-occurrence network analysis revealed a reconfigured ecological interactome in AR, characterized by pro-phage-centric associations that may disrupt mucosal immune homeostasis. Random forest identified total IgE, milk, and dust mite as top discriminators. This first study of the gut virome in pediatric AR reveals a pro-inflammatory phage enrichment and protective fungal virus depletion, implicating the virome in modulating Th2 immunity. These findings suggest a potential correlation between virome alterations and allergic diseases, which may inform future research on virome-targeted interventions.IMPORTANCEAllergic rhinitis is a prevalent childhood condition with a significant impact on quality of life, yet its pathogenesis is not fully understood. While the bacterial microbiome has been studied, the role of the gut virome remains largely unexplored. Our study provides the first evidence of gut virome dysbiosis in children with allergic rhinitis. We identified specific pro-inflammatory bacteriophages that are enriched and correlated with IgE levels, as well as protective fungal viruses that are depleted. These findings offer new perspectives on allergic disease pathogenesis by suggesting a potential role of the virome in modulating host immunity. This work not only opens a new avenue for understanding the environmental and microbial drivers of allergic diseases but also suggests the potential for novel virome-based diagnostics and therapeutic strategies, such as phage therapy, which could have a broad impact on clinical practice.This study is registered with ClinicalTrials.gov as ChiCTR2400085982.}, } @article {pmid41759636, year = {2026}, author = {Liang, L and Su, S and Peng, L and Zhuang, H and Chen, Y and Cao, Y}, title = {Development of Mycobacterium tuberculosis post in vitro fertilization and embryo transfer: A case series derived from a multi-omics analysis and literature review.}, journal = {Microbial pathogenesis}, volume = {214}, number = {}, pages = {108408}, doi = {10.1016/j.micpath.2026.108408}, pmid = {41759636}, issn = {1096-1208}, mesh = {Humans ; Female ; Pregnancy ; *Fertilization in Vitro/adverse effects ; *Mycobacterium tuberculosis/genetics/isolation & purification/pathogenicity ; *Embryo Transfer/adverse effects ; Adult ; *Pregnancy Complications, Infectious/microbiology ; Multiomics ; Placenta/microbiology/pathology ; *Tuberculosis/microbiology/diagnosis ; Metagenomics ; }, abstract = {The extensive progress in assisted reproductive technology has facilitated successful pregnancies through in vitro fertilization and embryo transfer (IVF-ET) for patients facing infertility. Pregnancy induces substantial endocrine and immune alterations that may diminish immune function, consequently heightening vulnerability to Mycobacterium tuberculosis (M.tb) infection or reactivation. Hematogenous disseminated pulmonary tuberculosis (TB), tuberculous meningitis, and potential congenital TB are serious complications that may arise after IVF-ET, posing significant risks to both maternal and fetal health. The clinical manifestations of TB during pregnancy frequently coincide with non-typical pregnancy symptoms, and the nonspecific characteristics of early-stage presentations render prompt diagnosis especially difficult. The existing literature on this subject is sparse, primarily consisting of isolated case studies involving individual participants, thereby yielding insufficient data and inadequate representations to comprehensively clarify this clinical emergency. This paper presents a case series of patients with normal immune function who developed hematogenous disseminated TB, including placental and central nervous system involvement, subsequent to IVF-ET. We showcased the multi-omic findings, including metagenomic sequencing and histopathological analyses, from patients with twin and singleton pregnancies and presented an extensive literature review. Additionally, we used metagenomic next-generation sequencing (mNGS) to detect pathogenic microorganisms in blood, bronchoalveolar lavage fluid (BALF), and cerebrospinal fluid (CSF) samples. Rare histopathological findings of placental TB were also documented, providing direct pathological evidence relevant to congenital TB. These findings expand the limited clinical evidence on TB following IVF-ET and underscore the importance of heightened clinical vigilance and multimodal diagnostic strategies in this high-risk population.}, } @article {pmid41759875, year = {2026}, author = {Nuranindita, R and Natanegara, S and Wusono, AD and Amirudin, FA and Hitipeuw, D and Rahayu, AA and Daud, MM and Yuwanita, MR and Qanita, NG and Saputra, EY and Jun, H and Jeon, BY and Lee, MR and Ju, JW and Malik, MDA and Garjito, TA and Han, JH and Muh, F}, title = {Metatranscriptomic analysis of Anopheles species from Menoreh Hills endemic area in Central Java, Indonesia.}, journal = {Acta tropica}, volume = {277}, number = {}, pages = {108033}, doi = {10.1016/j.actatropica.2026.108033}, pmid = {41759875}, issn = {1873-6254}, mesh = {Animals ; *Anopheles/microbiology/virology/genetics/classification ; Indonesia ; *Microbiota ; *Mosquito Vectors/virology/microbiology ; Bacteria/classification/genetics/isolation & purification ; Gene Expression Profiling ; Transcriptome ; Metagenomics ; *Viruses/classification/genetics/isolation & purification ; }, abstract = {BACKGROUND: The mosquito microbiome plays a crucial role in vector competence and disease transmission dynamics, yet comprehensive metatranscriptomic analyses of Anopheles species microbiomes remain limited, particularly in malaria-endemic regions like the Menoreh Hills of Central Java, Indonesia. This study aimed to characterize the microbial and viral community compositions of five Anopheles species and their potential implications for vectorial capacity.

METHODS: Metatranscriptomic analysis was performed on five Anopheles species (An. barbirostris, An. flavirostris, An. kochi, An. maculatus, and An. vagus) collected from the Menoreh Hills endemic area using RNA sequencing, taxonomic classification, and functional annotation approaches.

RESULTS: Proteobacteria emerged as the dominant bacterial phylum across all species, with variations in relative abundance of other taxa. Baculoviridae emerged as the overwhelmingly dominant viral family across all species, with other families including Bunyavirales, Herpesvirales, and Nucleocytoviricota present at much lower abundances. Diversity indices revealed An. vagus with the highest microbial diversity and An. barbirostris with the lowest. Adherence-related virulence factors were predominant, particularly in An. maculatus and An. vagus, while carbohydrate-active enzymes AA1 and GT35 were abundant across all species.

CONCLUSIONS: This study examines microbiome and virome across five Anopheles species from Menoreh Hills. Betabaculovirus dominated virome, while bacterial and fungal communities showed species-specific patterns. Analyses revealed virulence differences. Study limitations include pooled samples. The results provide data for malaria research.}, } @article {pmid41760689, year = {2026}, author = {Yarlina, VP and Tandra, JL and Indiarto, R and Andoyo, R and Harlina, PW and Ubaidillah, NHN and Lani, MN}, title = {Unraveling Tempeh through omics: a scoping review of fermentation pathways and functional health benefits.}, journal = {NPJ science of food}, volume = {10}, number = {1}, pages = {}, pmid = {41760689}, issn = {2396-8370}, support = {No. 2245/UN6/N/PT.01.03/2025//Universitas Padjadjaran/ ; }, abstract = {Tempeh, a traditional Indonesian fermented soybean product, is widely recognized for its functional properties and for containing bioactive compounds produced by microbial fermentation. This study integrates recent advances in multi-omics technologies to elucidate the microbial community dynamics, enzymatic pathways, and metabolite transformation underlying Tempeh's health-promoting characteristics. A bibliometric analysis of studies published between January 2000 and August 2025, indexed in Scopus, PubMed,Web of Science, and ScienceDirect identified 36 relevant articles that met predefined inclusion criteria. Metagenomic and transcriptomic evidence highlights the important roles of Rhizopus species and associated Lactic acid bacteria in fermentation, supported by the presence of genes encoding key enzymes such as phytases, amylases, and proteases. Proteomic and peptidomic analyses have further identified bioactive short peptides exhibiting antioxidant and angiotensin-converting enzyme (ACE) inhibitory activities. Metabolomic profiling revealed elevated levels of amino acids, γ-aminobutyric acid (GABA), and isoflavone aglycones, compounds linked to various health benefits. Collectively, these multi-omics insights provide a mechanistic understanding of Tempeh's functional potential and highlight opportunities for innovation in fermentation optimization and clinical translation. Future integration of standardized fermentation protocols with targeted human studies will be essential to advance Tempeh from a traditional food to a globally recognized functional food product.}, } @article {pmid41760690, year = {2026}, author = {Sammons, SL and Kuntz, TM and DiLullo, M and Morgan, XC and Martin, A and Hughes, ME and Rahman, T and Barroso-Sousa, R and Ogayo, ER and Giordano, J and Ryan, S and Waks, AG and Schlam, I and Ligibel, J and Lin, NU and Garrido-Castro, AC and Mittendorf, EA and Tolaney, SM}, title = {The landscape of the intestinal microbiome among patients with newly diagnosed invasive breast cancer and ductal carcinoma in situ (DCIS).}, journal = {NPJ breast cancer}, volume = {12}, number = {1}, pages = {}, pmid = {41760690}, issn = {2374-4677}, support = {P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; Dana-Farber Cancer Institute project number 6395601//Massachusetts Life Sciences Center/ ; }, abstract = {The intestinal microbiome shapes immune responses and is associated with patient outcomes in cancer following immunotherapy. We evaluated differences between the intestinal microbiome profiles of patients with early-stage invasive breast cancer (BC) and ductal carcinoma in situ (DCIS) by subtype using whole genome metagenomic sequencing. There were no significant differences in microbiome composition between DCIS and invasive BC as measured by alpha diversity (p = 0.20, ANOVA) or beta diversity (p = 0.52, PERMANOVA). Within invasive BC, patients with hormone receptor-positive (HR +)/HER2 + BC differed significantly in beta diversity relative to other subtypes (p < 0.05), with differences in six species (q < 0.25). Bacteroides ovatus was significantly more abundant in patients with stage III BC vs. stage I (p = 0.0003). Functional pathway analysis using HUMAnN3 revealed stage-specific enrichment of amino acid biosynthesis and nucleotide-related pathways. Altogether, these findings highlight potential microbial signatures associated with BC subtype and stage.}, } @article {pmid41761072, year = {2026}, author = {Costa, J and Pascoal, F and Baptista, MS and Hop, H and Assmy, P and Wold, A and Magalhães, C and Duarte, P}, title = {Comparative analysis of prokaryotic communities, hydrography, and biogeochemistry in Atlantic vs non-Atlantic influenced Svalbard fjords.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41761072}, issn = {1471-2180}, abstract = {BACKGROUND: Fjords in Svalbard are undergoing significant changes due to climate warming. Those along the west coast of Spitsbergen are particularly affected by the increasing influence of “warm” Atlantic Water (AW), a process known as Atlantification. We compared Kongsfjorden, a relatively “warm” fjord on the west coast, with Rijpfjorden, a typical cold Arctic fjord on the north coast of Nordaustlandet, combining physical and biogeochemical data with 16S rRNA gene amplicon and shotgun metagenomic sequencing. We hypothesize that differences in fjords’ water masses and prokaryotic communities provide insight into the effects of Atlantification as it expands eastwards along the shelf north of Svalbard.

RESULTS: We found that warm AW dominated in Kongsfjorden, whereas Rijpfjorden was dominated by cold Arctic Water and Winter Cooled Water. Our results suggest that the Atlantic-influenced Kongsfjorden is a nutrient sink, whereas Rijpfjorden showed similar behavior only in 2016, a particularly warm year, otherwise no clear sink/source role could be identified. Analysis of 16S rRNA gene sequences revealed that Proteobacteria had higher relative abundances in Kongsfjorden while Bacteroidota dominated in Rijpfjorden. Ammonium and nitrite-oxidizing prokaryotes were most prevalent in deeper water masses of both fjords. The archaeal taxa of the ammonia-oxidizing community, mainly Nitrosopumilus and Nitrosopelagicus, were consistently more dominant than ammonium and nitrite-oxidizing bacteria. Denitrification and nitrogen fixation genes differed between the fjords, with Kongsfjorden having a higher coverage of diazotroph genes.

CONCLUSIONS: Kongsfjorden and Rijpfjorden displayed distinct hydrographic conditions, with Kongsfjorden being under a stronger influence of Atlantification. Our results suggest that warmer water masses are linked to higher nutrient uptake. The clear association between microbial communities and water masses offers insight into changes driven by Atlantification.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04821-2.}, } @article {pmid41761093, year = {2026}, author = {Qureshi, A and Wahid, A and Qazi, S and Shahzad, MK and Kiani, HM and Asif, MDA}, title = {DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {41761093}, issn = {1471-2105}, abstract = {PURPOSE: Gut microbiome dysbiosis is a critical determinant for autologous fecal microbiota transplantation (Auto-FMT) eligibility, yet current classification approaches rely predominantly on supervised learning with manually annotated sequencing labels, which are often scarce. This study proposes DynaBiome, a framework designed to predict gut dysbiosis by leveraging unsupervised learning and clinical phenotypic proxies as a scalable alternative to ground-truth genomic labeling. METHODS: Our framework employs an LSTM autoencoder architecture to capture temporal microbiome dynamics within 14-day windows. The model reconstructs normal microbiome patterns, where high reconstruction errors signal potential dysbiosis. To ensure rigorous evaluation and prevent data leakage, the dataset was partitioned via a strict patient-level split. Unsupervised anomaly signals were refined via phenotypic proxy labels (e.g., fever, neutropenia) via weak supervision, and ensemble learning methods were applied to optimize classification performance. RESULTS: The initial LSTM autoencoder successfully flagged dysbiotic sequences but required refinement to reduce false positives. Ensemble learning significantly enhanced predictive accuracy. The stacked ensemble (with Logistic Regression meta-learner) demonstrated optimal performance with an ROC AUC of 0.8908 and a Weighted F1-score of 0.7909. This approach significantly outperformed the standard One-Class SVM baseline (ROC AUC 0.6033), confirming the superiority of deep temporal modeling over static anomaly detection. Critically, the model achieved performance levels comparable to fully supervised baselines, confirming the efficacy of the proxy-label framework. CONCLUSION: Integrating unsupervised temporal feature extraction with stacked ensemble methods provides a viable framework for dysbiosis prediction. These results demonstrate that leveraging phenotypic via weak supervision can effectively approximate supervised baselines, thereby reducing the reliance on comprehensive metagenomic annotations for longitudinal patient monitoring.}, } @article {pmid41761378, year = {2026}, author = {Biggel, M and Oberhänsli, T and Kümmerlen, D and Walkenhorst, M and Stephan, R and Holinger, M}, title = {Diversity and abundance of antimicrobial resistance genes in manure from pig farms with varying antibiotic use: a long-read metagenomic sequencing approach.}, journal = {Porcine health management}, volume = {12}, number = {1}, pages = {}, pmid = {41761378}, issn = {2055-5660}, support = {04.1240.PZ//Swiss Expert Committee for Biosafety (SECB)/ ; }, abstract = {BACKGROUND: Livestock production contributes to the emergence and spread of antimicrobial resistance (AMR), with pig farming accounting for a large share of veterinary antibiotic use. Manure application to fields can release drug-resistant bacteria and AMR genes into the environment, creating potential transmission routes to humans. Mobile genetic elements such as plasmids and transposons facilitate horizontal transfer of AMR genes between bacteria, including pathogens. However, quantitative data on the manure resistome and its links to antibiotic use remain limited. Shotgun metagenomics provides broad insights into microbiota and AMR composition, with long-read sequencing offering improved resolution of the genomic context of AMR genes. Here, we applied long-read shotgun metagenomics to investigate the diversity, abundance, and mobility potential of AMR genes in 24 manure samples from 14 Swiss pig farms with documented antibiotic use. RESULTS: Across 24 manure samples, 225 distinct AMR genes were detected, with tetracycline resistance genes being most prevalent. Manure samples from farms reporting the highest recent antibiotic use contained greater AMR gene abundance and richness. Metagenomic assemblies revealed that 77% of AMR genes with resolved flanking regions were located near transposases, recombinases, integrases, or relaxases, suggesting high transfer potential. The tigecycline resistance gene tet(X6) and related variants were identified in 21 of 24 samples, frequently embedded within mobile genetic elements. Two samples contained complete gene clusters of the vancomycin resistance determinant vanB, one of which was part of the conjugative transposon Tn1549. In one sample, a single highly abundant plasmid encoding beta-lactam and aminoglycoside resistance accounted for 42% of the total AMR gene load. CONCLUSIONS: Pig manure is a reservoir of diverse and mobile AMR genes, including those conferring resistance to critically important antibiotics. Long-read metagenomics adds valuable genomic context, supporting AMR monitoring and risk assessment within a One Health framework.}, } @article {pmid41761979, year = {2026}, author = {Guo, Z and Gao, Z and Zhao, Y and Ni, X and Zhang, W and Li, L and Ren, S and Li, Q and Guo, D and Yue, L and Liu, Y and Lin, L and Fan, S and Hai, X}, title = {Administering Bifidobacterium pseudolongum With Arsenic Trioxide Attenuates Acute Promyelocytic Leukemia in Mice by Restoring Immune Microenvironment and Intestinal Homeostasis.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {31}, number = {2}, pages = {48584}, doi = {10.31083/FBL48584}, pmid = {41761979}, issn = {2768-6698}, support = {82274028//National Natural Science Foundation of China/ ; 2022ZX02C09//Heilongjiang Key R&D Program/ ; //Fundamental Research Funds for the Provincial Universities in Heilongjiang Province (2025)/ ; JJ2025PL0189//Natural Science Foundation of Heilongjiang Province/ ; 2024M10//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 2024M25//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 230000253533210000086//2025 Central Government Fiscal Subsidy Fund for Medical Care Compliance and Capacity Enhancement (Traditional Chinese Medicine Undertakings and Inheritance and Development Component)/ ; }, mesh = {*Arsenic Trioxide/pharmacology/administration & dosage/therapeutic use ; Animals ; *Leukemia, Promyelocytic, Acute/immunology/drug therapy/microbiology/therapy ; Humans ; Homeostasis/drug effects ; Mice ; *Bifidobacterium ; Gastrointestinal Microbiome/drug effects ; Intestines/drug effects/microbiology/immunology ; Dysbiosis ; *Antineoplastic Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Probiotics/administration & dosage ; Tumor Microenvironment/drug effects/immunology ; }, abstract = {OBJECTIVE: Arsenic trioxide (ATO) is a cornerstone of acute promyelocytic leukemia (APL) therapy but induces severe gut microbiota dysbiosis, limiting its efficacy and safety. This study investigated whether adjunctive Bifidobacterium pseudolongum (BP) could mitigate these adverse effects and enhance therapeutic outcomes.

METHODS: 16S rRNA gene sequencing data of gut microbiota were obtained from a cohort of 22 APL patients treated with ATO-based regimens (20 of 22 data were obtained and analysis further), accessible under BioProject ID PRJNA935705. To evaluate the within-sample microbial community richness and evenness, alpha and beta diversity indices were calculated. Using a murine APL model, we compared ATO monotherapy with ATO+BP co-treatment. Analyses included fecal metagenomic sequencing, single-cell RNA sequencing (sc-RNA-seq), flow cytometric immune profiling, and assessment of intestinal tight junction proteins (claudin-1, occludin, and ZO-1) via immunofluorescence.

RESULTS: ATO treatment significantly reduced gut microbial diversity and depleted beneficial taxa. Sc-RNA-seq data showed that ATO could orchestrate the APL immune microenvironment mainly through functional activation of CD8+ T cells and monocytes. BP supplementation restored microbial homeostasis and synergistically enhanced ATO's antileukemic effect, reducing the leukemic burden in peripheral blood by 72% and in bone marrow by 64% compared to ATO alone. Mechanistically, BP preserved intestinal barrier integrity by upregulating tight junction protein expression and modulated anti-tumor immunity, notably increasing bone marrow CD8+ T cells by 2.21-fold.

CONCLUSIONS: BP is an effective adjunct to ATO therapy, counteracting gut dysbiosis, intestinal damage, and the immune microenvironment while synergistically improving antileukemic efficacy. Targeting the gut-leukemia axis with BP represents a promising strategy for improving the precision and safety of APL treatment.}, } @article {pmid41762228, year = {2026}, author = {Liu, T and Ding, H and Lv, Z and Yan, C and Feng, S and Lu, D and Hang, F and Meng, X}, title = {Lactobacillus Taiwanensis Inhibits Gallstone Formation by Regulating Ileal Metabolism.}, journal = {Current microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {41762228}, issn = {1432-0991}, support = {82270598//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Ileum/metabolism/microbiology ; *Gallstones/prevention & control/microbiology/metabolism ; Mice, Inbred C57BL ; Mice ; *Gastrointestinal Microbiome ; Male ; *Lactobacillus/physiology ; Liver/metabolism ; }, abstract = {In recent years, gut microbiota has been recognized to participate in gallstone formation via the gut-liver axis, yet the specific changes and roles of ileal microbiota remain unclear. This study aims to investigate the effects of microbial communities in different digestive tract segments on the formation of gallstones and the underlying mechanisms. Six-week-old C57BL/6J mice were randomly divided into a lithogenic diet group and a normal diet group. Ileal and colonic contents were collected separately for metagenomic sequencing.The Lactobacillus taiwanensis gavage model was constructed to compare its effects on gallstone formation and ileal metabolism. An intraperitoneal injection model of Lipoxin A4 (LXA4) was established to investigate the mechanisms by which Lactobacillus taiwanensis and LXA4 inhibit gallstone through Western blot analysis and ELISA methods. We found that there were significant differences in the intestinal microbiota between the group with gallstone formation and the control group in the small intestine and colon. Species-level analysis indicated that the lithogenic diet reduced the abundance of Lactobacillus taiwanensis in the small intestine. When Lactobacillus taiwanensis was administered intragastrically to mice, the incidence of gallstones decreased. Through metabolomics analysis and experimental verification, we demonstrated that Lactobacillus taiwanensis could down-regulate the expression of NETs in the liver and bile by increasing the level of LXA4, thereby reducing gallstone. The ileal and colonic microbiota exert site-specific effects in gallstone formation. Lactobacillus taiwanensis may inhibit gallstone formation by regulating ileal metabolism, may contribute to prevention and treatment of gallstones.}, } @article {pmid41762314, year = {2026}, author = {Dabravolski, SA and Vatlin, AA and Pavshintsev, VV and Mitkin, NA and Maltseva, ON and Orekhov, AN}, title = {A metagenomic perspective on microbial hydrocarbon degradation: uncovering novel pathways and community dynamics.}, journal = {Environmental geochemistry and health}, volume = {48}, number = {5}, pages = {}, pmid = {41762314}, issn = {1573-2983}, support = {202760-2-000//RUDN University/ ; }, mesh = {Biodegradation, Environmental ; *Metagenomics ; *Hydrocarbons/metabolism ; Anaerobiosis ; *Bacteria/metabolism/genetics ; Petroleum/metabolism ; Microbial Consortia ; Aerobiosis ; Polycyclic Aromatic Hydrocarbons/metabolism ; }, abstract = {The microbial degradation of petroleum hydrocarbons is a fundamental biogeochemical process and a cornerstone of environmental bioremediation. While traditional culture-based studies have outlined the basic principles, the advent of metagenomics has revolutionised our understanding by revealing the full genetic and functional diversity of hydrocarbon-degrading communities in situ. This review synthesises the current state of knowledge on both aerobic and anaerobic hydrocarbon biodegradation, providing a critical comparative analysis of traditional versus multi-omics methodologies. We provide an in-depth examination of aerobic mechanisms, initiated by oxygenases (e.g., alkB, PAH-RHDα), and contrast them with the diverse array of anaerobic activation pathways, including fumarate addition (bssA) and the recently elucidated direct carboxylation pathway for polycyclic aromatic hydrocarbons (PAHs). Furthermore, we highlight groundbreaking metagenomic insights into anaerobic benzene degradation and the critical role of syntrophic networks driven by interspecies electron transfer. Finally, we present specific case studies demonstrating the translation of genomic data into practical bioremediation strategies, such as the rational design of synthetic consortia. This review charts these recent advances, highlights remaining knowledge gaps, and outlines future directions for harnessing multi-omics to translate genomic potential into effective, field-scale environmental solutions.}, } @article {pmid41762333, year = {2026}, author = {Pavan, JS and Deeksha, PM and Rajarushi, CN and Paschapur, AU and Rishika, KS and Ramakrishnan, B and Subramanian, S}, title = {Gut microbiota-mediated nitrogen recycling in the white Grub Holotrichia longipennis: A model for microbiome-targeted pest control.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {3}, pages = {}, pmid = {41762333}, issn = {1573-0972}, abstract = {White grubs, Holotrichia longipennis, are major agricultural pests that cause extensive crop damage. The gut microbiota plays a critical role in nitrogen metabolism, enabling larvae to thrive on nitrogen-poor diets. Shotgun metagenomic sequencing revealed a diverse gut microbiota dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with Enterobacter (32%), Bacillus (20%), and Rhizobium showing clear spatial variation across gut compartments. Functional annotation (FOAM, FAPROTAX) identified bacterial genes involved in uric acid degradation (puuE, allC), urea hydrolysis (ureA, ureB, ureC), and ammonia assimilation via the GS–GOGAT/GDH pathways (gdhA, glnA, glnK, gltB, gltD), whereas nitrogen fixation genes (nifH, nifK, nifD) were absent. KEGG-based quantification (FeatureCounts, HTSeq) showed significantly higher nitrogen metabolism gene abundance in the hindgut, especially gdhA, glnA, and urease genes, which was validated by qPCR with 86-fold, 108-fold, and 34-fold upregulation, respectively. Uricolytic and ammonia-tolerant bacteria (Sporosarcina, Ureaplasma, Corynebacterium, Klebsiella) were isolated and functionally characterized, confirming their active role in nitrogen recycling, with urease assays showing higher ammonia production in the hindgut (0.155 µmol NH3/min/mg protein). Importantly, antibiotic treatment caused a dose-dependent reduction in gut bacterial abundance and larval survival, demonstrating the essential role of symbionts in host physiology. This study provides the first comprehensive evidence that H. longipennis larvae depend on gut microbes for nitrogenous waste recycling and identifies gut nitrogen-cycling bacteria and their key metabolic pathways (urease and ammonia-assimilation systems) as actionable targets for microbiome-based pest control strategies.}, } @article {pmid41762461, year = {2026}, author = {Shen, S and Wang, L and An, X and Liu, H and Shi, M and Tu, Y and Ji, W and He, Z and Li, A}, title = {Basin governance coincides with lower MGE loads yet rewired ARG mobility: a hazard‑oriented, platform‑centric assessment.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141608}, doi = {10.1016/j.jhazmat.2026.141608}, pmid = {41762461}, issn = {1873-3336}, mesh = {*Rivers/microbiology ; *Genes, Bacterial ; China ; *Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Metagenomics ; Bacteria/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) serve as critical indicators for evaluating the ecological success of river restoration policies. We investigated the restructuring of the riverine resistome in the Yangtze River following the implementation of the "Ten-Year Fishing Ban" and the Yangtze River Protection Law. Using basin-wide surveys in the Jiangsu reach (2021 vs. 2023), we integrated shotgun metagenomics and RT-qPCR functional validation with a noise-filtering sampling design to assess how the removal of anthropogenic pressures reshaped resistance dissemination. Results show that policy-driven ecological recovery significantly altered microbial assembly mechanisms. While total ARG abundance declined, microbial communities shifted toward a more dispersal-dominated regime, with neutral model fits increasing from 0.817 to 0.913. Crucially, RT-qPCR analysis confirmed that the transcriptional activity of key resistance elements remained significantly elevated relative to a pristine baseline, suggesting persistent functional risks despite lower overall abundance. As localized selective pressures relaxed, the resistome transitioned toward integrated genetic platforms, evidenced by a significant rise in the mosaic index (MGI) from 12.81% to 22.50% (p < 0.05). Structural equation modeling (R2 = 0.766) identified a dominant sequential pathway from environmental co-selectors to mobile genetic elements and subsequently to ARGs, with intensified roles for integrons and insertion sequences (intI1, IS26). These findings demonstrate that policy success requires evaluation through both abundance-based and structural indicators. We propose a platform-centric surveillance framework incorporating the mosaic index as an early-warning tool for environmental agencies.}, } @article {pmid41762466, year = {2026}, author = {Ma, Q and López, MJ and Zhang, S and Jin, L and Wei, D and Yang, J and Liu, J and Ruan, Z}, title = {Carbon source-dependent activation of herbicide-mixture degradation in a synthetic microbial community enriched from black soil.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141615}, doi = {10.1016/j.jhazmat.2026.141615}, pmid = {41762466}, issn = {1873-3336}, mesh = {*Herbicides/metabolism ; *Soil Microbiology ; Biodegradation, Environmental ; *Carbon/metabolism ; *Soil Pollutants/metabolism ; *Microbial Consortia ; Sulfonylurea Compounds/metabolism ; RNA, Ribosomal, 16S/genetics ; Glucose/metabolism ; Bacteria/metabolism/genetics ; Atrazine/metabolism ; Pyridines/metabolism ; Cyclohexanones ; }, abstract = {The extensive use of herbicides in agriculture has resulted in persistent soil contamination. Although microbial degradation of single herbicides has been extensively investigated, the responses and co-metabolism of microbial consortia to complex herbicide mixtures remain unclear. This study aimed to investigate the influence of a simple carbon source (glucose) on herbicide degradation by a natural microbial consortium (NMC) and identify key degraders for constructing an efficient synthetic microbial community (SynCom). An NMC enriched from herbicide-stressed agricultural black soil in Northeast China was inoculated into mineral salt media containing a mixture of herbicides (atrazine, nicosulfuron and mesotrione) as the sole carbon/nitrogen source, without (MSM) or with glucose supplementation (GSM). Significant herbicide degradation occurred only in the GSM system, with degradation rates of 97.27% for nicosulfuron, 68.00% for mesotrione, and 22.91% for atrazine after 8 days. Integrated 16S rRNA gene sequencing and metagenomic analysis linked the glucose amendment to a specific shift in the microbial community structure and activation of central carbon metabolism (tricarboxylic acid [TCA] and glycolytic), which enhanced cellular energy supply and environmental acidification for co-metabolic degradation of herbicides. In contrast, metabolism in the MSM system was biased toward biosynthesis. Combined random forest (RF) and co-occurrence network analyses identified the Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter as the keystone taxa. Metagenomic screening showed that these taxa were enriched for functional genes associated with herbicide degradation, including atzF (allophanate hydrolase) and gst (glutathione S-transferase). A simplified four-isolate SynCom, constructed based on these functional associations, degraded the herbicide mixtures more efficiently than either the individual isolates or the NMC in the GSM system. These findings elucidate the role of labile carbon in driving the co-metabolism of complex herbicides and provide direct candidate strains and a construction strategy, facilitating practical bioremediation applications.}, } @article {pmid41762491, year = {2026}, author = {Yan, S and Li, R and Shen, X and Li, Y and Zhang, L and Xu, M and Xie, S}, title = {Redox potential drives divergent microbial carbon fixation in mangrove wetland sediments, with ammonium exerting context-dependent effects.}, journal = {Marine pollution bulletin}, volume = {227}, number = {}, pages = {119457}, doi = {10.1016/j.marpolbul.2026.119457}, pmid = {41762491}, issn = {1879-3363}, mesh = {*Wetlands ; *Geologic Sediments/microbiology/chemistry ; Oxidation-Reduction ; *Carbon Cycle ; *Ammonium Compounds ; }, abstract = {Mangrove wetlands represent dynamic coastal interfaces where redox conditions and nutrient cycling shape microbial communities and their biogeochemical functions. However, tidal-driven siltation continuously transports sediment from low- to high-tide zones, altering sediment redox potential and nutrient content. The microbial responses to these changes, particularly the response mechanisms of carbon-fixing microorganisms, remain unclear. We integrated metagenomic and metatranscriptomic sequencing with [13]C and [15]N isotope labeling to examine how oxidation-reduction potential (ORP) and ammonium (NH4[+]) availability regulate microbial assembly and metabolism in mangrove sediments. ORP emerged as the primary determinant of microbial composition and diversity, while NH4[+] exerted variable effects on microbial traits. Under high ORP, CBBL-microorganisms predominantly utilized the cmmG CO2-concentrating mechanism, and carbon fixation rates decreased with increasing NH4[+] concentration. Under low ORP, CBBM-harboring genera dominated, primarily utilizing another mechanism cmmE, while NH4[+] had little effect and total organic carbon (TOC) exerted stronger control. ORP thus acts as the dominant environmental filter, with NH4[+] selectively affecting nitrifiers and carbon-fixing taxa. This was the first study to simultaneously measure ammonia oxidation and carbon fixation rate in mangrove sediments, revealing their mechanistic coupling. This work provides new mechanistic insights into the regulation of microbial metabolic potential in mangrove ecosystems and contributes to a broader understanding of their resilience and function in coastal biogeochemical cycles under fluctuating climate and environmental conditions.}, } @article {pmid41762498, year = {2026}, author = {Jiang, PY and Tang, H and Tong, WK and Liu, J and Liu, K and Tang, W and Liu, JB and Gao, MT and Liu, N and Hu, J and Li, J}, title = {Interface modification of membrane substrates: Mitigating microbial interfacial adhesion and augmenting adsorptive capacity for seawater uranium recovery.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129080}, doi = {10.1016/j.jenvman.2026.129080}, pmid = {41762498}, issn = {1095-8630}, mesh = {*Uranium ; *Seawater/chemistry ; Adsorption ; *Membranes, Artificial ; Bacterial Adhesion ; Biofilms ; }, abstract = {Seawater is endowed with vast reserves of high-value trace metals (gold, lithium, uranium) for resource recovery. However, their extremely low concentrations entail extensive, long-duration seawater processing in membrane-based systems, leading to pronounced microbial fouling and a substantial deterioration in adsorption efficiency. Given that practical membrane modules possess a multi-component architecture, this study mitigated microbial fouling via indigo modification of membrane supporting substrates, while maintaining the structural and functional integrity of the adsorptive membrane. This approach avoids the impairment of adsorption sites and porous structures induced by direct antimicrobial modification of the membrane. Column breakthrough experiments were employed to assess the fouling characteristics and severity of membrane modules in terms of macroscopic retention and structural evolution. Before modification, the membrane module exhibited interception rates of 79.8% and 77.3% for single strains and in-situ marine microbial communities (multiple strains), respectively, which were reduced to 45.6% and 57.1% after modification. Analysis using the dual-kinetic-site attachment-detachment model demonstrated that indigo-modified substrates reduced Langmuirian attachment and ripening, while the functional complementarity within microbial communities mitigated these effects. Metagenomic analysis confirmed that the modification selectively suppressed the attachment of microorganisms with strong adhesion and biofilm-forming ability. In a 28-day adsorption validation in real seawater, the modification increased the uranium adsorption capacity from 1.05 to 2.38 mg/g, effectively attenuating the performance decline induced by microbial contamination. The spatially decoupled integration of substrate anti-adhesion and membrane adsorption offers a new paradigm for membrane module design and optimization, extending its application potential in marine uranium recovery.}, } @article {pmid41762508, year = {2026}, author = {Zhang, L and Jiang, L and Zhang, Z and Wang, Y and Yao, C and Yu, K and Tao, H and Sun, W and He, X and Gu, J and Qian, X}, title = {Unraveling metal-organic frameworks impact on resistome and virome dynamics in swine manure anaerobic digestion via metagenomic.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129121}, doi = {10.1016/j.jenvman.2026.129121}, pmid = {41762508}, issn = {1095-8630}, mesh = {Animals ; *Manure/microbiology ; Swine ; Anaerobiosis ; *Virome ; Metagenomics ; *Drug Resistance, Microbial/genetics ; }, abstract = {Livestock manure is a major hotspot of antibiotic resistance genes (ARGs). However, the efficacy and mechanisms of anaerobic digestion (AD) in reducing ARGs, along with the ecological roles and risks of viral communities, remain poorly understood. This study demonstrates that AD significantly reduces total ARG abundance and diversity, with addition of metal-organic frameworks (MOFs) further enhancing the reduction of high-risk and clinically critical ARGs. ARG abundance decline was primarily driven by core ARGs, whereas diversity reduction was mainly attributed to the depletion of rare ARGs. ARGs exhibit a broad host distribution, alongside pervasive pathogenic host species. Viral communities display high diversity and novelty, with the Drexlerviridae family as the dominant virome. Viruses exhibit strong host specificity, with Actinobacteria (47.4%) and Atribacterota (12.7%) as primary hosts. Only eight viral contigs carried ANT(6)-Ia and lsa(B), indicating limited viral contribution to ARG horizontal transfer. Viruses enhance host metabolic capabilities by introducing diverse and unique auxiliary metabolic genes (AMGs). The AD process predominantly influences viral diversity, lifestyle, and AMG carriage. Mechanistically, AD reduces ARGs via decreasing co-occurrence frequencies of ARGs and plasmids, coupled with reduced abundances of ARG-hosting. These findings provide new insights for optimizing AD processes to control the diffusion of ARGs.}, } @article {pmid41762837, year = {2026}, author = {Wang, Y and Zhang, X and Wu, Y and Sun, X and Zhang, X and Lv, J}, title = {Biodegradation pathway of organophosphate esters in sludge composting implications for environmental safety.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141622}, doi = {10.1016/j.jhazmat.2026.141622}, pmid = {41762837}, issn = {1873-3336}, mesh = {*Composting ; *Sewage/microbiology ; Biodegradation, Environmental ; *Esters/metabolism ; *Organophosphates/metabolism ; Bacteria/metabolism/genetics ; }, abstract = {Organophosphate esters (OPEs) are emerging contaminants of growing concern, and there is limited information about the bacterial transformation during sludge composting. In this study, under the stress of 100 mg/kg ∑7OPEs, three bacterial strains with degradation capabilities-Bacillus subtilis, Bacillus licheniformis, and Ralstonia pickettii-were screened and isolated, and a synthetic bacterial community (SynCom) was constructed. During 55 days sludge composting, the concentration of ∑7OPEs decreased significantly. In CK, TnBP degraded the fastest (> 90%). For the exogenous OPE-added groups strengthened with SynCom (T1B and T2B), the removal rates of TCPP and TPhP were nearly complete (> 93%). However, high concentrations of ∑7OPEs inhibited the degradation of compounds such as TCrP and EHDPP. Hydrolysis was identified as the preferentially initiated pathway for ∑7OPEs degradation during sludge composting. Functional enzyme such as phosphatase, as well as bacterial strains from the Rhodococcus and Paracoccus, synergistically participated in the degradation process. Multiple linear regression analysis confirmed that SynCom promoted ∑7OPEs removal by boosting phosphomonoesterase activity and enriching phosphatase-producing microorganisms. pH and total phosphorus (TP) emerged as critical environmental factors influencing this degradation. Composting significantly lowered OPE-associated ecological risks, ensuring the safe resource recovery of sludge. This study focused on the biological removal of OPEs during sludge composting. It first systematically evaluated the biodegradation efficiency of ∑7OPEs and clarified core metabolic pathways. Furthermore, key microbial communities and functional genes associated with ∑7OPEs degradation were identified, revealing their regulatory roles. It provides scientific support for controlling OPEs pollution and promoting sludge resource utilization.}, } @article {pmid41763050, year = {2026}, author = {Cai, F and Wang, C and Liu, H and Shen, J and Wang, J and Yang, Y and Wang, X}, title = {Partitioning dynamics and microbial responses drive the fate of polycyclic aromatic hydrocarbons in a plateau lake.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129097}, doi = {10.1016/j.jenvman.2026.129097}, pmid = {41763050}, issn = {1095-8630}, mesh = {*Polycyclic Aromatic Hydrocarbons/analysis ; *Lakes/chemistry ; China ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; Seasons ; Geologic Sediments ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are persistent organic contaminants of concern in freshwater drinking-water sources, yet their environmental fate in hydrologically dynamic plateau lakes remains poorly constrained. Here, we investigated the multi-compartment distribution, apparent particle-water partitioning, microbial functional potential, and associated ecological and human-health risks of PAHs in Erhai Lake, a large subtropical plateau lake in southwestern China. PAHs were quantified simultaneously in the dissolved, suspended particulate, and surface-sediment phases across three seasons. Dissolved low-molecular-weight PAHs dominated the water column, exhibiting pronounced seasonal variability with summer peaks (12.9-49.8 ng L[-1]) driven by intensified tourism and hydrological inputs. In contrast, high-molecular-weight PAHs preferentially accumulated in sediments, forming depositional hotspots in the southern basin. Apparent organic-carbon-normalized partition coefficients (KOC,app) revealed that suspended particulates act as dynamic regulators of PAH transport and microbial accessibility. Metagenomic analysis revealed that the distribution of PAH-degradation-related functional genes co-varied with chemical partitioning patterns, suggesting potential microbial mediation of PAH fate. Ecological and human health risk assessments, including probabilistic Monte Carlo simulations, indicated that PAH-related risks remained within a low-risk regime across all seasons. Collectively, these findings provide a mechanistic framework for understanding how partitioning and microbial metabolism jointly regulate the fate of PAHs in plateau lakes, offering critical insights for the management of sensitive freshwater resources.}, } @article {pmid41763967, year = {2026}, author = {Boix-Amorós, A and Bu, K and Blank, RB and Cantor, A and Gutiérrez-Casbas, A and Rodríguez-Lago, I and Marin-Jimenez, I and Sanz, J and Masmitja, JG and Trujillo, E and Muñoz, MC and Vivar, MLG and Carrillo, M and Hernández, MVH and Calvet, X and Salaet, MA and Romero, MI and García, AB and Pérez, S and Llorente, JFG and Gonzalez-Lama, Y and Argumánez, CM and Plaza, Z and Domínguez, M and Cañete, JD and Diaz-Gonzalez, JF and Scher, JU and Clemente, JC}, title = {Microbial signatures in psoriatic arthritis distinguish disease phenotypes and newly diagnosed inflammatory bowel disease independent of faecal calprotectin.}, journal = {Annals of the rheumatic diseases}, volume = {85}, number = {5}, pages = {806-817}, doi = {10.1016/j.ard.2026.01.018}, pmid = {41763967}, issn = {1468-2060}, mesh = {Humans ; *Leukocyte L1 Antigen Complex/analysis ; *Arthritis, Psoriatic/microbiology/immunology/diagnosis ; *Feces/chemistry/microbiology ; Female ; Male ; *Inflammatory Bowel Diseases/microbiology/diagnosis/immunology ; Phenotype ; Middle Aged ; Adult ; Biomarkers/analysis ; *Gastrointestinal Microbiome ; Cytokines/blood ; }, abstract = {OBJECTIVES: There is growing evidence of microbial involvement in immune-mediated inflammatory diseases, including psoriatic arthritis (PsA) and inflammatory bowel disease (IBD). However, it remains unclear whether different PsA phenotypes exhibit distinct microbial profiles. Furthermore, up to 4% of patients with PsA have comorbid IBD, which often remains undiagnosed. We hypothesised that the gut microbiome distinguishes PsA subphenotypes and serves as a biomarker of IBD in patients with PsA independent of faecal calprotectin (fCAL).

METHODS: We obtained samples from 192 patients with axial or peripheral PsA and no prior diagnosis of IBD enrolled in the EISER study. Patients with elevated fCAL and subclinical IBD symptoms underwent colonoscopy with intestinal biopsy. Stool samples were used to measure fCAL, and gut microbiome was characterised using shotgun metagenomics. Serum samples were used for cytokine profiling.

RESULTS: Axial PsA had lower alpha diversity and loss of several commensals compared with peripheral PsA, as well as a depletion of microbial biotin and arginine metabolism and higher levels of IL-23, IL-17F, and IL-8. Five subjects had newly diagnosed IBD which was characterised by a depletion of tryptophan and vitamin B6 metabolism. They also showed significant enrichment of several taxa compared to non-IBD and with a larger effect size than fCAL.

CONCLUSIONS: Our results identify a distinct microbiome and immune profile in axial PsA, with lower microbiome diversity, a depletion of commensals and protective microbial mechanisms, and higher levels of some proinflammatory cytokines. In patients with newly diagnosed IBD, we identified microbial taxa associated with the condition yet independent of fCAL, the current clinical standard.}, } @article {pmid41764137, year = {2026}, author = {Zhao, S and Zou, Y and Wang, Z and Ye, L and Chen, Y and Cao, Z and Xu, X and Gao, A and Ying, X and Chen, M and Qin, K and Zhang, Y and Gu, W and Wang, J and Ning, G and Wang, W and Liu, R and Jin, J and Hong, J}, title = {Gut Microbiota and Bile Acid Profiles as Predictors of PCOS Remission: Findings from a Sleeve Gastrectomy Treatment Study.}, journal = {Obesity surgery}, volume = {36}, number = {4}, pages = {1607-1620}, pmid = {41764137}, issn = {1708-0428}, abstract = {OBJECTIVE: To identify predictive biomarkers from the perspectives of gut microbiota and bile acid metabolites for polycystic ovary syndrome (PCOS) remission following metabolic bariatric surgery in patients with PCOS and obesity. METHODS: We conducted a one-year follow-up of patients with obesity and PCOS who underwent sleeve gastrectomy (SG) to assess their PCOS remission status. Metagenomics and bile acid metabolomics were performed and compared between the remission and non-remission groups to identify differential microbial species and bile acid metabolites. The associations between these biomarkers and PCOS remission was then evaluated using Generalized Estimating Equations (GEE) models and Receiver Operating Characteristic (ROC) analysis. RESULTS: SG led to marked improvements in metabolic parameters and hyperandrogenemia. These changes were accompanied by substantial shifts in the gut microbiome, which correlated with alterations in gonadal hormone levels. Based on PCOS outcomes, patients were categorized into remission and non-remission groups. The remission group showed a higher abundance of A. equolifaciens and Clostridium sp CAG 299, along with lower baseline circulating levels of ursodeoxycholic acid (UDCA). These factors were positively associated with PCOS remission. ROC analysis demonstrated that the combination of A. equolifaciens, Clostridium sp CAG 299, UDCA, and average follicle number yielded an AUC of 0.93 for predicting remission. CONCLUSION: A composite biomarker signature incorporating specific gut microbiota profiles, circulating UDCA levels, and ovarian follicle count shows strong potential as an effective predictor of PCOS remission after SG.}, } @article {pmid41764386, year = {2026}, author = {Mtetwa, HN and Amoah, ID and Mthethwa-Hlongwa, NP and Pieerneef, R and Kumari, S and Bux, F and Reddy, P}, title = {Decoding mycobacterial ecology in Sub-Saharan African wastewater: metagenomic and metatranscriptomic insights for tuberculosis surveillance.}, journal = {Journal of water and health}, volume = {24}, number = {2}, pages = {109-127}, pmid = {41764386}, issn = {1477-8920}, support = {96086//South African Medical Research Council/ ; }, mesh = {*Wastewater/microbiology ; *Mycobacterium/genetics/isolation & purification/classification ; Metagenomics ; Africa South of the Sahara/epidemiology ; *Tuberculosis/epidemiology/microbiology ; Animals ; Humans ; *Metagenome ; }, abstract = {Tuberculosis (TB) remains a major public health challenge in sub-Saharan Africa, driven by high transmission, delayed diagnosis, and limited surveillance. This study presents one of the first integrated applications of shotgun metagenomic and metatranscriptomic sequencing to investigate Mycobacterium communities in wastewater across six TB-endemic countries: Cameroon, Ghana, Kenya, Nigeria, South Africa, and Uganda. Twelve untreated and treated wastewater samples were analysed to characterise taxonomic composition, strain-level diversity, and transcriptional activity. Metagenomic analyses revealed diverse Mycobacterium communities, including M. tuberculosis, M. canettii, M. bovis, and members of the M. avium complex. Metatranscriptomic data detected MTBC-associated transcripts, indicating transcriptional activity and/or persistence of MTBC RNA signals in wastewater, with higher signal predominance in influent samples, consistent with community-level shedding. Metagenome-assembled genomes (MAGs) recovered from South Africa, Cameroon, and Uganda showed >82% completeness and included zoonotic species. MTBC strains clustered into Lineages 1, 2, 4, and 6, with animal-adapted strains linked to livestock and rodents, highlighting One Health relevance. Overall, this dual-omics approach supports wastewater-based epidemiology as a scalable tool for TB surveillance in high-burden settings.}, } @article {pmid41764388, year = {2026}, author = {Zhu, K and Amirali, A and Auch, B and Babler, KM and Biswas, P and Bowie, K and Choudhary, S and Currall, BB and Grills, GS and Healy, HG and Liachko, I and Lucaci, AG and Mason, CE and Sharkey, M and Shigeno Risse-Adams, O and Shukla, BS and Sisson, Z and Stevenson, M and Williams, SL and Zulli, A and Peccia, J and Solo-Gabriele, HM}, title = {Proof-of-concept of host attribution of antimicrobial resistance genes using wastewater Hi-C metagenome sequencing.}, journal = {Journal of water and health}, volume = {24}, number = {2}, pages = {148-159}, pmid = {41764388}, issn = {1477-8920}, support = {//4Catalyzer/ ; U01DA053941/DA/NIDA NIH HHS/United States ; P30AI073961/NH/NIH HHS/United States ; }, mesh = {*Wastewater/microbiology ; *Metagenome ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; }, abstract = {The proliferation of antimicrobial resistance genes (ARGs) poses public health risks globally, with wastewater treatment plants (WWTPs) serving as dissemination hubs for horizontal gene transfer. In this study, we evaluated the potential of applying Hi-C sequencing coupled with metagenomic bioinformatics for surveillance of ARGs and other microbial fitness traits using samples from WWTPs. Hi-C sequencing has the advantage over other molecular approaches by directly associating genes conveying fitness to their host microbe, plus to their element type (in plasmids, phages, or within the core genome of its host microbe). Results from Hi-C analyses confirm results from more laborious approaches by showing that aminoglycoside resistance is disseminated by plasmids. Mercury resistance was found in Zoogloea bacteria. Resistance genes to quaternary ammonium compounds were found within bacteriophages. Results from this study provide proof-of-concept for the potential value of Hi-C metagenome sequencing in wastewater attribution studies by illustrating the breadth of information that can be obtained about the microbial community, the exchange of genes, and their interconnections. We believe that with further development, Hi-C sequencing can be integrated into routine monitoring of wastewater for the purpose of providing near-real-time information about the dissemination of fitness traits, including ARGs.}, } @article {pmid41764528, year = {2026}, author = {Zhang, W and Su, Q and Shi, H and Sun, Y and Li, X and Li, M and Wang, H and Yu, J and Wong, N and Chan, FKL and Zhang, J and Ng, SC}, title = {Discovery and characterization of Christensenella hongkongensis as a novel bacterium in the adenoma-carcinoma progression.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41764528}, issn = {1479-5876}, abstract = {BACKGROUND: Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide and commonly starts from a pre-cancerous stage. This study aimed to identify potential fecal bacterial candidates associated with progression of CRC from the adenoma-carcinoma sequence and to explore underlying mechanisms of carcinogenesis.

METHODS: Publicly metagenomic datasets were analyzed using MaAsLin2 to identify bacterial species enriched in CRC patients compared to healthy controls. Additionally, we established a large cohort in mainland China, consisting of 686 subjects, including 285 CRC patients, 73 advanced adenoma patients (AA), 134 non-advanced adenoma patients (nAA), and 194 healthy controls (NC). Fecal samples from this cohort were analyzed by duplex quantitative polymerase chain reaction (qPCR) to validate the abundance of key bacterial candidate and its association with tumor node metastasis (TNM) stages. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic performance of Christensenella hongkongensis (C. hongkongensis) alone and in combination with fecal immunochemical test (FIT) across different CRC stages. In vitro experiments and transcriptome sequencing were performed to explore the effects of C. hongkongensis and its mechanisms in CRC progression.

RESULTS: MaAsLin2 analysis identified seven bacterial species were significantly more abundant in fecal samples of CRC patients than in healthy controls (p < 0.05). Among them, C. hongkongensis, an obligately anaerobic, catalase-positive, motile, non-sporulating, gram-positive coccobacillus was distinguished by its lowest abundance in healthy controls and significant enrichment in CRC patients. Validation in our recruited cohort showed that the abundance of C. hongkongensis progressively increased from non-advanced adenomas to advanced adenomas and CRC. For classifying AA from nAA, C. hongkongensis yielded an area under the ROC curve (AUC) of 0.60 (95% CI 0.53–0.68), with 45.2% sensitivity and 85.8% specificity. A combined model integrating C. hongkongensis abundance and FIT further improved diagnostic performance, increasing AUCs from 0.77 to 0.81 for AA vs NC (p < 0.05) and from 0.76 to 0.82 for AA vs nAA (p < 0.001). Linear regression analysis revealed a significant positive association between C. hongkongensis and TNM stages in CRC. In vitro experiments showed that C. hongkongensis promoted CRC cell proliferation, inhibited apoptosis, and enhanced the growth of patient-derived CRC organoids. RNA-seq analysis identified activation of the Wnt/β-catenin signaling pathway, which was further validated by elevated protein levels of active β-catenin, reduced phosphorylation of GSK3β, and the upregulation of downstream targets c-Jun and Cyclin-D1.

CONCLUSIONS: Our findings suggest that C. hongkongensis promotes colorectal tumorigenesis via Wnt/β-catenin activation, and highlight its potential as a novel non-invasive bacterial marker for early detection and monitoring of CRC progression.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07886-9.}, } @article {pmid41764576, year = {2026}, author = {Li, J and Ren, J and Xu, J and He, J and Xu, J and Yin, Q and Yao, J and Wu, S}, title = {Ability of the Chinese herbal residue to alleviate short-distance transportation stress in sheep through the remodeling of the rumen microbiome-metabolism axis.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41764576}, issn = {1674-9782}, support = {2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; 32573272//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; }, abstract = {BACKGROUND: Transportation is a common stressor in sheep production that is capable of inducing oxidative stress and impairing sheep health and production performance. This study aimed to investigate the alleviating effects of the traditional formula Siji Antiviral Mixture residue after water extraction, which still contains active ingredients, including fiber, polyphenols, and flavonoids, on short-distance transport stress in sheep, as well as its mechanism of action in regulating oxidative stress through the rumen microbiota‒metabolism axis.

RESULTS: Twenty first-lambing East Friesian × Hu sheep hybrids weighing 54.49 ± 7.94 kg were randomly assigned to a control group (CON, basal diet) or a Chinese herbal residue group (CMR, basal diet + 50 g/d CMR) feeding at 4 h after approximately 300 km of short-distance transport. Results indicated that 4 h of short-distance transport significantly elevated serum reactive oxygen species (ROS) levels in sheep. Supplementation with Chinese herbal medicine residues markedly reduced serum ROS and lactate dehydrogenase levels while increasing glutathione peroxidase and immunoglobulin G levels. Metagenomic results revealed significantly increased abundance of bacteria such as Selenomonas ruminantium in the rumen of the CMR group, along with substantial increases in CAZymes, including AA7, GH113, and GH84. Metabolomic analysis revealed differentially expressed metabolites in plasma and rumen fluid that were enriched in metabolic pathways such as glycerophospholipid metabolism, α-linolenic acid metabolism, and drug metabolism-cytochrome P450. Correlation network analysis further revealed that Selenomonas ruminantium was significantly negatively correlated with ROS and positively correlated with ruminal LysoPC (16:1(9Z)/0:0), plasma phosphatidylcholine, and key glycerophospholipid metabolism enzymes (e.g., EC 3.1.4.3, PLC). Glycerophospholipid metabolism exhibited synergistic regulatory interactions with arachidonic acid metabolism and drug metabolism-cytochrome P450 pathways.

CONCLUSION: This study confirmed that 4 h of short-distance transport can induce oxidative stress in sheep. Supplementing feed with Siji Antiviral Mixture herbal residue effectively alleviated transport stress and enhanced immune function. The mechanism of action involved rumen microbial conversion of the herbal residue, which substantially increased the abundance of Selenomonas ruminantium. Related metabolites then regulated host arachidonic acid metabolism and cytochrome P450 drug metabolism indirectly through the glycerophospholipid metabolic pathway and the rumen microbiota-metabolism axis, thereby synergistically exerting antioxidant effects.}, } @article {pmid41764595, year = {2026}, author = {Martínez-Murcia, A and Navarro, A and Miró-Pina, C and García-Sirera, A and Pérez, L and García-Román, V and Navarro-Gracia, JF}, title = {Early detection of nosocomial pathogens in air and surfaces using an innovative genetic approach for surveillance in healthcare settings.}, journal = {Antimicrobial resistance and infection control}, volume = {15}, number = {1}, pages = {}, pmid = {41764595}, issn = {2047-2994}, support = {INNCAD/2022/23//AVI/ ; }, abstract = {BACKGROUND: Healthcare-associated infections remain a major cause of morbidity, mortality, and financial burden worldwide, further exacerbated by the emergence of antimicrobial resistance. Environmental reservoirs of pathogens, including air and surfaces, play a critical role in nosocomial transmission. This study aimed to validate an integrated air and surface molecular surveillance system for the early detection of clinically relevant pathogens and resistance genes in hospital environments.

METHODS: Weekly air and surface samples were collected over 28 weeks from two hospitals in southeastern Spain. DNA and RNA were extracted and analysed by quantitative PCR (qPCR) targeting bacterial, fungal, and viral pathogens, as well as antimicrobial resistance genes. A subset of samples underwent shotgun metagenomic sequencing to confirm qPCR results and characterize microbial communities. Environmental findings were compared with clinical infection data from both hospitals.

RESULTS: Viral, bacterial and fungal pathogens were detected with similar patterns between air and surface samples and between hospitals. Carbapenem resistance genes showed distinct distribution profiles between hospitals. Respiratory viruses displayed strong temporal correlations with patient admissions, with viral RNA occasionally detected before clinical peaks.

CONCLUSIONS: This integrated molecular surveillance system allows sensitive detection of pathogens and resistance genes in hospital environments. Coupling air and surface sampling with qPCR provides a robust tool for identifying contamination sources and tracking temporal infection trends. Its scalability and adaptability make it suitable for implementation as an early warning system in infection prevention programmes, enhancing patient safety and supporting proactive control of nosocomial infections.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13756-026-01725-8.}, } @article {pmid41764643, year = {2026}, author = {Zeller, LM and Schorn, S and Nicolas-Asselineau, L and Zopfi, J and Ahmerkamp, S and Schubert, CJ and Lepori, F and Kuypers, MMM and Graf, JS and Milucka, J}, title = {Redox gradients define the ecological niche of ciliates with denitrifying endosymbionts in anoxic lake waters.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41764643}, issn = {1751-7370}, support = {//internal funds of Eawag/ ; //Max Planck Society/ ; }, mesh = {*Symbiosis ; *Lakes/microbiology/chemistry ; *Ciliophora/microbiology/physiology ; Nitrates/metabolism ; Oxidation-Reduction ; Switzerland ; Phylogeny ; Oxygen/metabolism ; Anaerobiosis ; Denitrification ; Sequence Analysis, DNA ; Sulfides/metabolism ; Ecosystem ; Molecular Sequence Data ; }, abstract = {Bacterial endosymbionts of the family Candidatus Azoamicaceae obligately associate with anaerobic ciliates belonging to the class Plagiopylea. The symbionts' unique role for their host involves anaerobic respiration of nitrate and generation of adenosine triphosphate (ATP), analogous to the role of mitochondria in aerobic eukaryotes. As this symbiosis remains so far uncultured, insights into its functioning have been mainly inferred from environmental metagenomes. Here, we investigated the distribution and environmental role of this symbiosis in the anoxic basins of two freshwater lakes, Zug and Lugano (Switzerland), over a course of several years. We found that the environmental niche of the ciliate host is defined by the combined effects of sulfide, oxygen, and nitrate, the latter of which is essential for the symbiont's respiratory function. Moreover, the distribution and abundance of ciliates with denitrifying endosymbionts in the water column suggest that they may substantially contribute to nitrate consumption in Lake Zug. Our microscopic analyses further demonstrated a coordinated division of the Ca. Azoamicus ciliaticola symbionts and their ciliate hosts, implying a vertical inheritance of denitrifying symbionts. These observations offer new insights into the evolution of ciliates with denitrifying endosymbionts and their ecological role in oxygen-depleted lake waters.}, } @article {pmid41764831, year = {2026}, author = {Peng, X and Zhang, L}, title = {Advances and challenges in the application of metagenomic sequencing for the diagnosis and treatment of infectious diseases: from pathogen spectrum identification to personalized antimicrobial strategies.}, journal = {Diagnostic microbiology and infectious disease}, volume = {115}, number = {2}, pages = {117321}, doi = {10.1016/j.diagmicrobio.2026.117321}, pmid = {41764831}, issn = {1879-0070}, mesh = {Humans ; *Metagenomics/methods ; *Communicable Diseases/diagnosis/drug therapy/microbiology/therapy ; *Precision Medicine/methods ; Shotgun Sequencing ; Computational Biology ; High-Throughput Nucleotide Sequencing ; }, abstract = {Infectious diseases remain a major global public health concern, demanding rapid and accurate identification of pathogens. Although conventional diagnostic methods such as culture, PCR, and immunological assays are widely used, they are limited by long processing times, narrow detection scopes, and poor capability for identifying unknown pathogens. untargeted shotgun metagenomic sequencing (mNGS), as a non-targeted, high-throughput detection technology, enables broad-spectrum identification of diverse microorganisms and functional gene annotation, making it an increasingly important complement in infectious disease diagnostics. This review summarizes the clinical value of mNGS in key scenarios such as neurological, respiratory, and bloodstream infections. It also discusses its utility in antimicrobial resistance (AMR) monitoring and personalized therapy, highlights current challenges in sensitivity, bioinformatics analysis, and result interpretation, and briefly explores future directions involving artificial intelligence (AI), multi-omics integration, and healthcare information system integration. The goal is to provide a reference for the standardized application of mNGS in infectious disease diagnosis and treatment.}, } @article {pmid41764843, year = {2026}, author = {Das, N and Pandey, P}, title = {Striking a microbial balance: Rhizoremediation of crude oil-contaminated soils suppresses resistomes and reconstructs hydrocarbon-degrading microbial networks.}, journal = {The Science of the total environment}, volume = {1022}, number = {}, pages = {181586}, doi = {10.1016/j.scitotenv.2026.181586}, pmid = {41764843}, issn = {1879-1026}, mesh = {*Soil Pollutants/metabolism/analysis ; *Biodegradation, Environmental ; *Petroleum/metabolism/analysis ; *Soil Microbiology ; *Hydrocarbons/metabolism ; Polycyclic Aromatic Hydrocarbons/metabolism ; }, abstract = {Integrated plant-microbe systems are crucial for restoring hydrocarbon- and heavy metal-contaminated soils. Here, Azadirachta indica inoculated with a hydrocarbon-degrading bacterial consortium (SynCom) was used in microcosm and field trials to remediate chronically oil-contaminated soils. SynCom treatment enhanced degradation of total petroleum hydrocarbons (TPHs) and polycyclic aromatic hydrocarbons (PAHs) up to 99%, reduced heavy metal concentrations, and neutralized soil pH, while improving organic matter, soil aggregation, and nutrient mobilization (N, P, K). Metagenomic analyses revealed a shift from Proteobacteria to Actinobacteria, with a 10-fold reduction in antibiotic resistance genes, particularly multidrug resistance and efflux pump genes. Key functional taxa (Nocardioides, Bradyrhizobium japonicum, Rhodopseudomonas) were enriched, correlating with enhanced nutrient cycling, soil enzyme activity, and hydrocarbon degradation. Functional gene profiling indicated reduced oxidative stress and ecological recovery. This study demonstrates that targeted rhizoremediation effectively detoxifies soils while mitigating ARGs dissemination, offering a sustainable One Health-aligned strategy for environmental and public health protection.}, } @article {pmid41764882, year = {2026}, author = {Huang, L and Feng, L and Sun, Y and Li, Z and Deng, L and Zhang, P and Li, X and Gao, D and Wang, Y and Deng, S and Shen, F and Fang, D}, title = {Oxygen stress drives overcompensation of carbon sources for enhanced polymer denitrification.}, journal = {Water research}, volume = {296}, number = {}, pages = {125631}, doi = {10.1016/j.watres.2026.125631}, pmid = {41764882}, issn = {1879-2448}, mesh = {*Denitrification ; *Oxygen/metabolism ; *Carbon/metabolism ; Biofilms ; Polyesters ; Nitrates ; Polymers ; }, abstract = {Dissolved oxygen (DO) is traditionally considered as a strong inhibitor of denitrification. However, its impact on polymer-based denitrification, where carbon bioavailability is rate-limiting, remains poorly understood. Here, we investigated the response of a polycaprolactone (PCL)-supported biofilm system to long-term DO stress (2-8 mg/L). Contrary to conventional expectations, elevating DO from 2 to 8 mg/L significantly accelerated nitrate removal (from 8.06 to 10.50 mg N/L) rather than suppressing it. Stoichiometric modeling and metabolomic analysis revealed an oxygen-induced carbon release mechanism, where high DO stimulated the secretion of extracellular esterases and intensified the β-oxidation pathway, increasing polymer carbon release by 17.71 mg/L. This excess carbon overcompensated for aerobic consumption, effectively alleviating electron donor limitations. Metagenomics further confirmed a structural shift towards an oxygen-tolerant consortium, with significant enrichment of dual-function genera (e.g., Pseudoxanthomonas) and enhanced coupling of respiratory chain complexes (I-III). The biofilm achieved spatial decoupling, utilizing the outer aerobic layer for rapid hydrolysis and oxygen consumption to protect the inner anoxic denitrification zone. These findings overturn the strict anoxic requirement for denitrification, providing a robust strategy for advanced nitrate removal in oxygen-fluctuating tailwaters.}, } @article {pmid41764931, year = {2026}, author = {Wang, G and Wei, J and Qiu, G and Guo, Z and Wang, W and Liu, X and Song, Y}, title = {Mechanism of activated carbon enhanced activated sludge (ACEAS) in treating recalcitrant chemical wastewater.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129058}, doi = {10.1016/j.jenvman.2026.129058}, pmid = {41764931}, issn = {1095-8630}, mesh = {*Sewage/chemistry ; *Waste Disposal, Fluid/methods ; *Wastewater/chemistry ; Nitrobenzenes ; *Charcoal/chemistry ; *Water Pollutants, Chemical ; Biological Oxygen Demand Analysis ; }, abstract = {Recalcitrant chemical accident wastewater, especially nitrobenzene-containing wastewater, has posed a significant treatment challenge due to complex hazardous compounds as well as elevated toxicity. Activated carbon combined activated sludge processes can effectively remove hazardous organic pollutants from chemical wastewater. However, the interaction mechanism between activated carbon and activated sludge remains unclear. This study proposed the activated carbon enhanced activated sludge (ACEAS) process for treating nitrobenzene-containing wastewater. Combined with material characterization and metagenomic analysis, the removal efficiency of nitrobenzene was evaluated, and the interaction mechanisms between activated carbon and activated sludge was further investigated. The key findings include: The effluent nitrobenzene concentration in conventional activated sludge (AS) process was 6.5 and 9.2 times higher than in the original ACEAS (OS) and regenerated ACEAS (RS) processes, respectively. Without activated carbon replenishment, chemical oxygen demand (COD) removal efficiency in OS and RS processes increased by 10.19%-15.86% and 11.41%-14.60%, respectively, compared to AS process during long-term operation (6-24 h). Due to the formation of biofilms on the surface of activated carbon, and the content of C-O/C=O and C-N/C=N on OS increased by 13.2% and 17.3%, respectively, compared to original activated carbon (OC). Eventually, four enhanced mechanisms of activated carbon were proposed, each contributing to distinct degradation stages in the ACEAS system. In prophase, activated carbon might reduce toxicity and improve microbial degradation capacity by adsorption. During metaphase, biofilms on activated carbon surface further diminished adsorption/desorption effect. In the telophase, microbial carrier's fixation affected strengthens, reshaping microbial community structure, functional gene expression, and metabolic pathway selection, thereby enhancing activated sludge degradation efficiency.}, } @article {pmid41764980, year = {2026}, author = {Xie, J and Hu, T and He, J and Cai, Y and Wu, Q and Li, L and Liu, H}, title = {Genome characterization and evolutionary analysis of a novel Anativirus from a wild Muscovy duck in Guangdong, China.}, journal = {Virology}, volume = {618}, number = {}, pages = {110849}, doi = {10.1016/j.virol.2026.110849}, pmid = {41764980}, issn = {1096-0341}, mesh = {Animals ; *Genome, Viral ; China ; Phylogeny ; *Ducks/virology ; *Picornaviridae Infections/veterinary/virology ; *Evolution, Molecular ; Open Reading Frames ; Sequence Analysis, DNA ; *Bird Diseases/virology ; *Picornaviridae/genetics/classification/isolation & purification ; RNA, Viral/genetics ; }, abstract = {A novel member of the genus Anativirus was identified and characterized from a naturally deceased wild Muscovy duck (Cairina moschata) collected in Maoming, Guangdong Province, China. This strain, provisionally designated Anativirus GD2411, was detected through metagenomic next-generation sequencing (mNGS), which yielded a complete genome of 8,085 nucleotides. The genome comprises a single open reading frame (nt 413-7,873) encoding the canonical picornaviral polyprotein, flanked by a 5' untranslated region (UTR; 412 nt) and a 3' UTR (209 nt) with a poly(A) tail. Whole-genome nucleotide identity analysis revealed that GD2411 clustered with duck-origin strains, sharing 88.0% identity with CH01 and 81.2% with TW90, but only 50.6% with the chicken-derived strain CHK1. High amino acid conservation was observed across functional regions, particularly in 2C (≥91.9%), 3C (≥92.4%), and 3D (≥97.0%), reflecting the preservation of RNA-dependent RNA polymerase function. Phylogenetic analyses based on complete genomes and 3D protein sequences using maximum likelihood methods consistently placed GD2411 within the duck Anativirus clade, indicating a close evolutionary relationship with TW90 and CH01. Although an experimental infection model was not established, PCR screening revealed broad gastrointestinal distribution of the virus, with the highest viral load detected in the cecum, suggesting fecal-oral transmission as a primary route. These findings provide preliminary evidence of Anativirus infection in wild Muscovy ducks in southern China, though the limited sample size precludes definitive conclusions regarding host range expansion. The highly conserved 3D region is highlighted as a potential target for antiviral therapy or vaccine development.}, } @article {pmid41765175, year = {2026}, author = {Clarke, BC and Ordinola-Zapata, R and Noblett, WC and Gould, M and Staley, C}, title = {Taxonomy and Virulence Factors in the Root Canal Microbiome: Metagenomic Insights by Lesion Size and Clinical Factors in Primary Endodontic Infections.}, journal = {Journal of endodontics}, volume = {52}, number = {6}, pages = {919-928}, doi = {10.1016/j.joen.2026.02.016}, pmid = {41765175}, issn = {1878-3554}, mesh = {Humans ; *Microbiota/genetics ; *Dental Pulp Cavity/microbiology ; *Virulence Factors/genetics ; Female ; Metagenomics ; Male ; Adult ; *Dental Pulp Diseases/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacterial Load ; }, abstract = {INTRODUCTION: This study aimed to investigate the taxonomic and functional profiles of the root canal microbiome in teeth with large versus small periapical lesions, examining the influence of clinical variables on microbial composition and functional pathways.

METHODS: Samples from 25 teeth with large (>8 mm) and 20 with small periapical lesions (<2 mm) were analyzed. Quantitative polymerase chain reaction, 16S next-generation and whole genome sequencing were used to assess microbial load, diversity, and composition. Functional predictions were performed using the Kyoto Encyclopedia of Genes and Genomes and MetaCyc databases. Alpha diversity was calculated using Shannon and Chao1 indices. Beta diversity was assessed using ANOSIM and PERMANOVA. Significant variables were explored using MaAsLin3. Kruskal-Wallis tests were used for univariate comparisons.

RESULTS: Teeth with large lesions exhibited significantly higher bacterial load (P = .011), but comparable alpha diversity and number of species per group in 16S and whole genome analysis (P > .05). Lesion size showed significance by ANOSIM (P = .04) but not in PERMANOVA (P = .36). Age was significant in both beta diversity tests, but the effect size only explained 3.6% of the variance. All clinical variables were not significant in 16S analysis for beta diversity. MetaCyc pathway analysis identified percussion sensitivity as the most influential clinical variable in both tests (ANOSIM R = 0.182, P = .012; PERMANOVA R[2] = 0.063, P = .046). MaAsLin3 modeling revealed enrichment of enzymatic pathways involved in methionine and cysteine-related metabolism.

CONCLUSIONS: Large periapical lesions contain significantly higher bacterial load, but similar diversity compared to small lesions. Functional predictions suggest bacterial metabolic activity may contribute to mechanical allodynia in endodontic infections.}, } @article {pmid41765316, year = {2026}, author = {Lyu, Y and Ye, Y and Zhang, C and Zhong, W and Zhu, L}, title = {Bisphenol A bis (diphenyl phosphate) disrupts tryptophan metabolism through microbiota dysbiosis to promote intestinal toxicity.}, journal = {Environmental research}, volume = {297}, number = {}, pages = {124140}, doi = {10.1016/j.envres.2026.124140}, pmid = {41765316}, issn = {1096-0953}, mesh = {Animals ; *Tryptophan/metabolism ; *Phenols/toxicity ; Zebrafish ; *Flame Retardants/toxicity ; *Benzhydryl Compounds/toxicity ; Bisphenol A Compounds ; *Dysbiosis/chemically induced ; *Gastrointestinal Microbiome/drug effects ; *Intestines/drug effects/microbiology ; *Organophosphates/toxicity ; *Water Pollutants, Chemical/toxicity ; Interleukin-22 ; }, abstract = {Organophosphorus flame retardants (OPFRs) are associated with intestinal injury. Bisphenol A bis(diphenyl phosphate) (BDP), an emerging OPFR that presents widely in organisms and humans, may induce intestinal toxicity, yet the effect and underlying mechanism remains unclear. In this study, zebrafish were exposed to BDP at 2, 20 and 200 μg/L for 21 days. Distinct histopathological changes in the intestine of zebrafish were observed, and the relative expressions of mucus secretion and tight junction related genes (MUC-2, Occuludin a and ZO-1) were all downregulated. Through the integrated analysis combining metabolomics and metagenomics, the results demonstrated that BDP exposure downregulated the abundances of microbiota Peptostreptococcus, Clostridium, Bombilactobacillus and Sporolactobacillus in zebrafish intestines, to depress tryptophan metabolism and eventually reduce the abundances of tryptophan metabolites. As a result, the expression of AhR, an important receptor activated by tryptophan metabolites, was inhibited to downregulate IL-22 expression, promoting intestinal toxicity. In vivo experiment with indole-3-propionic acid supplement alleviated the pathological changes, which further confirmed that BDP destroyed microbiota-tryptophan metabolism homeostasis to interfere with the AhR-IL-22 axis, eventually promoted pathological toxicity in the intestines. This study highlights vulnerability of intestines to BDP, and provides first insight into the mechanism through which BDP threats intestinal health.}, } @article {pmid41765557, year = {2026}, author = {Wang, M and Zhao, J and Gao, J and Cai, S and Gu, Y and Liu, Y and Gao, L and Xu, Y and Wu, Y and Zhou, Z and Zhang, J and Tian, W}, title = {Deciphering the potential of Bacillus cereus HS-9 in cadmium bioremediation and ensuring rice safety.}, journal = {Journal of environmental sciences (China)}, volume = {162}, number = {}, pages = {573-583}, doi = {10.1016/j.jes.2025.05.044}, pmid = {41765557}, issn = {1001-0742}, mesh = {*Oryza/growth & development ; *Bacillus cereus/metabolism/physiology ; *Cadmium/metabolism/analysis ; *Soil Pollutants/metabolism/analysis ; Biodegradation, Environmental ; Soil Microbiology ; }, abstract = {Cadmium (Cd) contamination in agricultural soils poses significant environmental and health risks due to its non-degradable and bio-magnifying nature. With the global imperative for eco-friendly Cd remediation strategies, microbial bioremediation emerges as a promising approach. Here, Bacillus cereus HS-9 was isolated from Cd-contaminated paddy soil using LB medium supplemented with 5 mg/L of Cd. HS-9 exhibited an impressive Cd removal efficiency of 95.44 % at a concentration of 5 mg/L. A rice pot experiment was conducted using Cd-contaminated soil, with HS-9 inoculation as the treatment group and non-inoculated soil as the control. The treatment group resulted in a 38.99 % reduction in soil Cd availability and a 34.33 % decrease in rice Cd content without affecting rice yield. The microbial community of the rice rhizosphere was analyzed using metagenome sequencing. The results revealed an increased abundance of czcA, frnE, and irlS genes in the soil microbiome, indicating enhanced Cd resistance and efflux capabilities. Microbial community showed significant shifts towards a beneficial microbial consortium, particularly marked by increases in Lysobacter and Sphingomonas genera which are known for their roles in heavy metal resistance and bioremediation. B. cereus HS-9 demonstrated significant potential for the bioremediation of Cd-contaminated soil. This study provides foundation for the development of microbial-based strategies for the eco-friendly remediation of heavy metal-polluted agricultural lands.}, } @article {pmid41765668, year = {2026}, author = {Nian, YP and Ning, SS and Li, SS and Yu, PB and Meng, Y and Zhao, X and Ren, RQ and Yan, J and Han, XY and Zheng, ZX and Zhang, QF and Wang, X and Zhang, Y}, title = {[Investigation and management of the first case of human infection with avian influenza A(H10N3) virus in northern China].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {47}, number = {2}, pages = {275-280}, doi = {10.3760/cma.j.cn112338-20250616-00397}, pmid = {41765668}, issn = {0254-6450}, mesh = {Humans ; China/epidemiology ; *Influenza, Human/epidemiology/virology ; *Influenza A virus/isolation & purification ; Animals ; Male ; Influenza in Birds/epidemiology ; Female ; }, abstract = {Objective: To summarize and analyze the epidemiological characteristics and field investigation of the first case of human infection with avian influenza A(H10N3) virus in northern China and to provide reference for the investigation and management of human infection with animal-derived influenza in the future. Methods: Case epidemiological investigation, identification and medical observation of co-exposed people and close contacts, and tracing investigation and analysis of infection source were carried out. Samples were collected from the case, co-exposed persons, close contacts, poultry, and the external environment. Real-time fluorescent quantitative RT-PCR was used to detect influenza A virus. The positive samples were subjected to metagenomic sequencing and compared. Results: This is the first case of human infection with the avian influenza A(H10N3) virus in northern China, and a third-party laboratory performed the detection. The patient became ill on April 13, 2025, with no history of contact with similar cases prior to symptom onset but with a history of exposure to poultry. The macrogene test of bronchoalveolar lavage fluid was positive for avian influenza A(H10N3) virus on April 28, 2025. A total of 168 samples were collected from co-exposed individuals, close contacts, poultry, and the external environment, and all were negative for avian influenza A(H10N3) virus. Metagenomic sequencing analysis showed that the sequence had high homology with the human infection case of avian influenza A(H10N3) virus reported in Guangxi Zhuang Autonomous Region in December 2024. After taking emergency measures such as medical observation of close contacts, harmless treatment of poultry in the sick home, and disinfection of suspected exposure places, no secondary cases occurred. The case was cured and discharged on May 14. Conclusions: The source of the first human case of avian influenza A(H10N3) infection in northern China remains unclear, but no human-to-human transmission has been found. It is important to improve the sensitivity of surveillance for new subtypes of animal-derived influenza viruses, such as avian influenza A(H10N3), and to strengthen joint prevention and control between health and animal husbandry departments to support scientific approaches to preventing and controlling human infection with these viruses.}, } @article {pmid41766220, year = {2026}, author = {Schwedhelm, C and Pinart, M and Forslund-Startceva, SK and Oluwagbemigun, K and Dötsch, A and Schlicht, K and Schwarz, F and Siampani, SM and Avraam, D and De Angelis, M and Bouwman, J and Brigidi, P and Caderni, G and Calabrese, FM and Cuadrat, RRC and De Filippo, C and De Filippis, F and Ercolini, D and Fabbrini, M and Laudes, M and Nöthlings, U and Özsezen, S and Sharon, I and Schulze, MB and Turroni, S and Vitali, F and Pischon, T and Nimptsch, K}, title = {Associations of Adiposity With Gut Microbiota Composition Among Adults-Results From a Federated Analysis of Individual Participant Data From Eight European Observational Studies.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {}, number = {}, pages = {e70106}, doi = {10.1111/obr.70106}, pmid = {41766220}, issn = {1467-789X}, support = {FKZ 01EA1906A//Bundesministerium für Bildung und Forschung/ ; 01EA1906B//Bundesministerium für Bildung und Forschung/ ; 01EA1906F//Bundesministerium für Bildung und Forschung/ ; BMBF//Bundesministerium für Bildung und Forschung/ ; //Fund for Scientific Research (FRS-FNRS, Belgium)/ ; //Research Foundation-Flanders (FWO, Belgium)/ ; //Institut National de la Santé et de la Recherche Médicale/ ; //Bundesministerium für Ernährung und Landwirtschaft/ ; //Ministero dell'Istruzione, dell'Università e della Ricerca/ ; //National Institute of Health Carlos III/ ; //the Netherlands Organization for Health Research and Development (ZonMw, the Netherlands)/ ; //Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie/ ; //Ministry of Science and Technology (Israel)/ ; //Formas (Sweden) and HDHL-Intimic Era-Net (EarlyFOOD)/ ; JTC-2017-7//Joint Programming Initiative a Healthy Diet for a Healthy Life-Intestinal Microbiomics (JPI HDHL-INTIMIC) Call for Joint Transnational Research Proposals on "Interrelation of the Intestinal Microbiome, Diet and Health"/ ; //European Union/ ; DZD Grant 82DZD00302//Ministerium für Ländliche Entwicklung, Umwelt und Landwirtschaft des Landes Brandenburg/ ; 442326535//National Research Data Infrastructure for Personal Health Data (NFDI4Health) by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)/ ; }, abstract = {Gut microbiota may contribute to the adiposity-associated disease risk, but human studies reported inconsistent associations of adiposity with gut microbiota composition. We examined associations of body mass index (BMI) with alpha diversity and relative microbial abundance at the phylum and genus taxonomic levels (based on 16S rRNA amplicon sequencing or metagenomics) among 7415 adults from eight European observational studies in a joint federated analysis of harmonized data using DataSHIELD. Higher BMI (per 5 kg/m[2]) was associated with lower alpha diversity (β: -0.05; 95% CI: -0.07, -0.03) and, on the phylum level, positively associated with Proteobacteria, but neither with Firmicutes nor Bacteroidetes nor their ratio, where high between-study heterogeneity was observed. On the genus level, BMI was inversely associated with the relative abundance of Faecalibacterium of the Firmicutes phylum (β: -0.11; 95% CI: -0.14, -0.07) but positively with the odds of detection of Dorea, Streptococcus, and Clostridium (all three Firmicutes) as well as Collinsella (Actinobacteria). This federated analysis of multiple studies found lower alpha diversity, alongside depleted Faecalibacterium, as well as higher odds of detection of Dorea, Streptococcus, Clostridium, and Collinsella with higher adiposity. By combining data from diverse study populations using harmonized data and statistical methods, our analysis partly overcomes sources of heterogeneity that may explain previously observed inconsistencies.}, } @article {pmid41766731, year = {2026}, author = {Peddle, SD and Cando-Dumancela, C and Costin, S and Davies, T and Doane, MP and Edwards, RA and Hodgson, RJ and Krauss, SL and Liddicoat, C and Breed, MF}, title = {Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings.}, journal = {Ecology and evolution}, volume = {16}, number = {3}, pages = {e73172}, pmid = {41766731}, issn = {2045-7758}, abstract = {Soil microbiomes are fundamental ecosystem components that are increasingly used to monitor the efficacy of restoration efforts. However, given high levels of functional redundancy among soil microbial taxa and the subsequent lack of definitive taxa-function links, taxonomic assessments (e.g., via metabarcoding) alone are limited for inferring ecological recovery. Here, we used shotgun metagenomics on soils from six post-agricultural restoration sites in southwest Western Australia to test whether soil microbial functional potential recovers following restoration plantings. We compared taxonomic and functional gene diversity and composition across degraded, passively regenerated, revegetated, and remnant land conditions. Effective number of functions (alpha diversity) did not differ across land conditions. However, functional composition (beta diversity) differed between remnant and revegetated conditions and associated with altered soil abiotic properties, especially elevated phosphorus. Remnant soils supported a greater diversity of phosphorus metabolism functions despite lower available phosphorus, indicating a microbial adaptation to nutrient limitation in phosphorus deficient soils. Rather than indicating a lack of functional recovery, these results suggest a functional response to persistent agricultural legacies that may reflect a shift toward an alternative state. Restoration interventions that aim to target the soil microbiome (e.g., soil inoculations) or directly address abiotic legacies (e.g., phosphorus mining plants) may therefore be required to facilitate recovery of the soil microbial functions and the wider ecosystem.}, } @article {pmid41767535, year = {2026}, author = {Chen, J and Yang, J and Zhang, Y}, title = {Case Report: Rare pulmonary infection and cytomegalovirus retinitis revealed a case of lymphoma.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1732360}, pmid = {41767535}, issn = {2296-858X}, abstract = {BACKGROUND: Recurrent cytomegalovirus retinitis (CMVR) and rare opportunistic pulmonary infections may be the initial manifestations of underlying immunodeficiency caused by occult hematologic malignancy. Epstein-Barr virus-positive diffuse large B-cell lymphoma, not otherwise specified (EBV[+]DLBCL-NOS) is an aggressive lymphoma associated with immune dysfunction, predisposing patients to severe opportunistic infections, including CMVR. However, pulmonary co-infection with Tropheryma whipplei and Penicillium digitatum has not been previously described as a presenting feature of EBV[+] DLBCL-NOS.

CASE: A 66-year-old male presented with blurred vision and was diagnosed with CMVR, with profoundly low CD4[+] T-cell counts (102 cells/μL) and high cytomegalovirus (CMV) DNA levels in blood and aqueous humor. He initially responded to ganciclovir, but CMVR recurred five months later, accompanied by new pulmonary nodules. Despite negative conventional microbiological tests, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified co-infection with Tropheryma whipplei and P. digitatum. Broad-spectrum antimicrobial therapy led to partial clinical improvement, but pulmonary lesions persisted. PET-CT revealed hypermetabolic lung and lymph node lesions, and subsequent lung biopsy confirmed EBV[+] DLBCL-NOS. The patient's progressive immunodeficiency, recurrent CMVR, and refractory pulmonary infection were ultimately attributed to underlying lymphoma.

CONCLUSION: This case highlights that severe, unexplained immunodeficiency with recurrent CMVR and rare opportunistic pulmonary infections should prompt a high index of suspicion for underlying hematologic malignancy. mNGS and PET-CT are critical tools in the diagnostic workup, but definitive diagnosis relies on histopathological confirmation. Early recognition of such presentations can prevent delays in diagnosing aggressive lymphomas.}, } @article {pmid41767718, year = {2026}, author = {Cao, M and Zhang, X and Huang, L}, title = {Advanced renal tuberculosis due to misdiagnosis as recurrent urinary tract infection: A case report.}, journal = {IDCases}, volume = {43}, number = {}, pages = {e02527}, pmid = {41767718}, issn = {2214-2509}, abstract = {Renal tuberculosis (RTB) lesions often initially localize to a specific part of the kidney, presenting with minimal clinical symptoms and a very slow disease progression, which makes the condition highly susceptible to misdiagnosis. We report an instructive case from the Second Affiliated Hospital of Zhejiang University School of Medicine, where a patient was ultimately diagnosed with advanced RTB after a 20-year diagnostic odyssey. The patient exhibited atypical clinical symptoms and was repeatedly diagnosed with recurrent urinary tract infection (UTI). Initial urinalysis revealed microscopic hematuria (52 RBCs/μL), pyuria (615 WBCs/μL), and 1 + proteinuria (0.7 g/L). A urine culture tested positive for Escherichia coli. Ultrasound imaging indicated a right renal calculus, and intravenous pyelography demonstrated significantly diminished right renal function. Suspicion for RTB was raised by CT findings and a positive tuberculosis infection T-cell spot (T-SPOT.TB) test. Acid-fast bacilli were consistently detected in two consecutive urine sediment examinations. The diagnosis was ultimately confirmed through metagenomic next-generation sequencing (mNGS) and postoperative pathological examination. This case underscores that the early diagnosis of RTB is challenging and requires a high index of clinical suspicion, comprehensive analysis of manifestations, and the strategic integration of modern diagnostic tools.}, } @article {pmid41767950, year = {2026}, author = {Tang, L and Luo, Z and Gao, S and Lin, Z and Sun, M and Li, R and Gao, SH and Wu, G and Li, Y and Huang, L and Fan, L}, title = {A hot origin of dissimilatory sulfite reduction catalyzed by DsrAB in the Paleoarchean Era.}, journal = {mLife}, volume = {5}, number = {1}, pages = {108-121}, pmid = {41767950}, issn = {2770-100X}, abstract = {Dissimilatory sulfite reduction (DSR) has been essential to microbial energy metabolism in the biogeochemical sulfur cycle since the Paleoarchean Era. However, due to the lack of an integrated assessment of geological record and genomic data, the evolutionary origin of DSR remains elusive in terms of time, habitat, and genetic basis. In this study, we reconstructed the evolutionary pathways and the ancestral sequences of Dsr proteins by mining metagenomes ranging from mesothermal to hyperthermal environments. A phylogenetic analysis of the key catalytic enzyme, DsrAB, and other Dsr proteins indicates that the earliest and most basic functional cascade, DsrABCNM, emerged prior to the latest common ancestor of several basal branching DsrAB clusters encoded by bacteria and archaea. Using a molecular dating strategy that calibrates the protein tree with a species tree, we predicted that the DSR originated 3.508 billion years ago (Ga). This finding strongly confirms the earliest geological evidence of DSR (~ 3.47 Ga). Further predictions from ancestral sequence reconstruction indicate that the optimal catalytic temperature of DsrA at the time of DSR origin was approximately 73°C, which is consistent with the petrographic and geochemical evidence in early Archean hydrothermal deposits. After its hot origin, DsrA diversified into subclades that adapted to various temperature levels following the Great Oxidation Event. This is exemplified by the evolution of the reductive archaeal-type DsrA. Our results synchronize the molecular ages with the geological record, which advances our understanding of the earliest DSR systems and highlights the enzymatic adaptations of microbial life in the Archean biosphere.}, } @article {pmid41768053, year = {2026}, author = {Lv, M and Tian, D and Wang, G and Hou, C and Fan, T and Li, W}, title = {Salinity gradients alter root-zone soil microbiome structure and nitrogen-related functional potential in alfalfa (Medicago sativa L.): a pot experiment.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1753229}, pmid = {41768053}, issn = {1664-462X}, abstract = {INTRODUCTION: Soil salinization constrains agricultural sustainability in arid and semi-arid regions. This study examined integrated soil-plant-microbe responses of alfalfa (Medicago sativa L.) to a salinity gradient.

METHODS: A pot experiment was conducted with control, low-, and moderate-salinity treatments. Root-zone soil and plants were sampled to measure soil EC, pH, and inorganic nitrogen forms, and to assess plant growth traits. Shotgun metagenomics was used to characterize microbial community composition and metagenome-inferred functional potential.

RESULTS: Salinity increased soil EC and pH and altered inorganic nitrogen forms, with higher NO3 [-]-N under moderate salinity and lower NH4 [+]-N under salinity compared with the control. Plant height peaked under low salinity, whereas fresh and dry biomass decreased under both salinity treatments. Microbial β-diversity differed among treatments, while α-diversity showed limited responses. Functional annotations indicated treatment-associated trends in nitrogen- and stress-related categories and KEGG level 3 pathways; however, most differences were not significant after FDR correction.

DISCUSSION: This integrative root-zone assessment links salinity-driven soil chemistry changes with alfalfa performance and suggests coordinated shifts in soil chemistry, microbiome structure, and plant growth under salinity stress.}, } @article {pmid41768378, year = {2026}, author = {Li, J and Zeng, P and Mu, X and Cai, C}, title = {Clinical Characteristics and Risk Factors Analysis of Nontuberculous Mycobacterial Pulmonary Disease Complicated with Bronchiectasis.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {483326}, pmid = {41768378}, issn = {1178-6973}, abstract = {BACKGROUND: Nontuberculous mycobacteria pulmonary disease (NTM-PD) frequently coexists with bronchiectasis. This study aimed to compare clinical profiles and identify risk factors between NTM-PD patients with/without bronchiectasis and explore differences between rapid- vs slow-growing non-tuberculous mycobacteria (NTM) species.

METHODS: A retrospective analysis was conducted on patients diagnosed with NTM-PD and admitted to Beijing Tsinghua Changgung Hospital between April 2021 and April 2025. Among 496 inpatients with pulmonary diseases who underwent metagenomic next-generation sequencing (mNGS) analysis of bronchoalveolar lavage fluid, NTM were identified in 57 patients. Ultimately, 43 of these cases were confirmed and diagnosed as having NTM-PD. Relevant clinical data were collected, and the association between each variable and adverse outcomes was assessed using univariate and multivariate logistic regression analyses.

RESULTS: Among the 43 confirmed NTM-PD patients, 24 had concurrent bronchiectasis (NTM-PD with bronchiectasis group) and 19 did not (NTM-PD group). In terms of baseline characteristics, the NTM-PD with bronchiectasis had a significantly higher proportion of females (79.17% vs 31.57%, P=0.002) and lower BMI (19.46 vs 22.46, P=0.023). Slow-growing NTM (SGM, mainly Mycobacterium avium complex [MAC]) was more common in the NTM-PD with bronchiectasis group (70.83% vs 31.58%, P=0.010); rapid-growing NTM (RGM, mainly M. abscessus) was more prevalent in the NTM-PD group (57.89% vs 20.83%, P=0.013). The positive rate of T-SPOT.TB in the NTM-PD group was higher than that in the NTM-PD with bronchiectasis group (47.37% vs 8.33%, P=0.010). Multivariate logistic regression identified female sex as an independent risk factor for NTM-PD complicated with bronchiectasis (OR=17.784, 95% CI: 1.103-286.857, P=0.042), while T-SPOT.TB was not (OR=0.047, 95% CI: 0.002-1.341, P=0.074).

CONCLUSION: Female sex is an independent risk factor for NTM-PD complicated with bronchiectasis. NTM-PD patients with bronchiectasis are more likely to be infected with SGM (especially MAC), while those without bronchiectasis tend to have RGM (especially M. abscessus) infection.}, } @article {pmid41768489, year = {2025}, author = {Raghavan, K and Dedeepiya, VD and Yamamoto, N and Ikewaki, N and Iwasaki, M and Dinassing, A and Senthilkumar, R and Preethy, S and Abraham, SJK}, title = {Randomised trial of Aureobasidium pullulans-produced beta 1,3-1,6-glucans in patients with Duchenne muscular dystrophy: favourable changes in gut microbiota and clinical outcomes indicating their potential in epigenetic manipulation.}, journal = {BMJ nutrition, prevention & health}, volume = {8}, number = {2}, pages = {e000776}, pmid = {41768489}, issn = {2516-5542}, abstract = {OBJECTIVE: Duchenne muscular dystrophy (DMD) is an X-linked neuromuscular disorder that leads to increasing muscle weakening and early death. Steroids, the standard treatment of choice in slowing down disease progression, are plagued with adverse effects. Anti-inflammatory, antifibrotic effects and enhancement of muscle regeneration biomarkers after oral consumption of Aureobasidium pullulans strain N-163-produced beta 1,3-1,6-glucan (Neu REFIX) having been demonstrated in clinical and preclinical studies of DMD; in this study, we have investigated the effects on the gut microbiome in patients with DMD.

DESIGN: Twenty-seven patients with DMD were included in the study (control (n=9), N-163 (n=18)). Whole-genome metagenomic sequencing was performed in pre-N-163 and post-N-163 intervention faecal samples of each of these participants.

RESULTS: After N-163 beta-glucan administration, the constitution of the gut microbiome in all the participants was modified to one with positive outcomes on health. There was an increase in butyrate-producing species such as Roseburia and Faecalibacterium prausnitzii. There was a decrease in harmful bacteria associated with inflammation such as enterobacteria and Alistipes.

CONCLUSION: Beneficial reconstitution of the gut microbiome after Neu REFIX beta-glucan administration and its safety have been confirmed. These outcomes correlating with the anti-inflammatory, anti-fibrotic effects along with increase in dystrophin in skeletal muscle and plasma, reported earlier make us recommend further in-depth exploration on its role in epigenetic manipulation which when found encouraging might help other genetic diseases as well.

TRIAL REGISTRATION NUMBER: CTRI/2021/05/033346.}, } @article {pmid41768492, year = {2025}, author = {Vignal, L and de Lahondès, R and Gillibert, A and Tavolacci, MP and Prifiti, E and Formstecher, E and Ribet, D and Quillard, M and Coeffier, M and Déchelotte, P}, title = {Metagenomic analysis of salivary microbiota in patients with anorexia nervosa and association with functional digestive disorders (ORMICAN pilot study).}, journal = {BMJ nutrition, prevention & health}, volume = {8}, number = {2}, pages = {e001112}, pmid = {41768492}, issn = {2516-5542}, abstract = {BACKGROUND: Patients with anorexia nervosa (AN) have intestinal dysbiosis and are frequently affected by oral and upper gastrointestinal disorders. Until now, no metagenomic sequencing data were available on oral microbiota in AN.

DESIGN: This observational study enrolled 46 patients with restrictive/purging AN and 20 controls. Salivary samples were performed after fasting. DNA of oral microbiota from salivary samples was analysed by whole genome shotgun deep sequencing. The primary objective was to compare the diversity of oral microbiota between patients with AN and healthy individuals. Secondary endpoints were to assess the associations between the diversity of oral microbiota and the severity of functional digestive disorders, between patients with a restrictive type of AN and patients with a mixed/purging type and between the diversity of oral microbiota and the severity of AN.

RESULTS: We observed not only a significant decrease in the alpha diversity of oral microbiota in AN patients (4.47 (4.05; 4.75)) versus controls (4.81 (4.68; 5.04)) (p=0.001) but also in gene richness (p=0.00023). There was no significant correlation (95% CI) between oral microbiota diversity and functional digestive disorders nor between patients with a restrictive type of AN and patients with a mixed/purging type of AN, nor between the diversity of oral microbiota and the severity of AN. In addition, we observed four bacterial taxa that were decreased in AN patients.

CONCLUSION: Our study highlights a decreased diversity of oral microbiota in AN patients. Future larger studies may help identify the prognostic and therapeutic value of oral microbiota in AN.}, } @article {pmid41768933, year = {2025}, author = {Ameer, A and Saleem, F and Keating, C and Afzal, F and Irshad, H and Ahmed, K and Sattar, S and Ijaz, UZ and Javed, S}, title = {Avian cecal microbiome response and resilience to Newcastle disease are dictated by breed background.}, journal = {Frontiers in systems biology}, volume = {5}, number = {}, pages = {1659648}, pmid = {41768933}, issn = {2674-0702}, abstract = {A wide range of viral infections threaten the long-term sustainability of poultry production. Newcastle disease (ND), caused by Newcastle disease virus (NDV), is endemic in most Asian countries, including Pakistan, causing 50%-100% mortality in young and mature chickens. Some local chicken breeds show resistance to certain diseases and have greater survival probability. The chicken gut microbiome is linked to immune response against infections and to production performance parameters. The present study aims to comprehend disease resistance patterns in multiple chicken breeds with respect to gut microbial communities. Day-old Naked Neck, Black Australorp, Rhode Island Red, white layer, and broiler chicks were raised on an antibiotic-free diet in a semi-controlled setup. Vaccinated and non-vaccinated birds were challenged with NDV. Disease onset was delayed in breeds other than broilers, in which disease symptoms appeared at day 3 post-challenge with maximum severity and mortality. Other breeds, irrespective of vaccination, survived through the challenge period. Naked Neck showed the least variation in clinical features and growth parameters. A lower diversity in broiler groups with a significant decrease after NDV challenge was revealed by 16S rRNA amplicon sequencing of cecal DNA. Furthermore, broiler cecal core microbiome membership was found to be more variable than other breeds. Moreover, differentially abundant genera were observed across treatment groups and breeds with a similar effect on the predicted metabolic pathways, indicating varied energy metabolism responses. Shotgun metagenomics revealed a higher abundance of functional genes, including antimicrobial resistance (AMR) genes, stress genes, virulence genes, and amino acid degradation genes in the broiler NDV-infected group compared to the control group. The gut microbiota in chickens affects immunity to infections, health, and productivity. Compared to broilers, local chicken breeds, specifically Naked Neck, are found to have high immune competence in resisting ND while maintaining most performance metrics. Broilers show lower alpha diversity with an unstable core microbiome. Therefore, stable core microbiome maintenance may help the birds cope with the viral infection. The results support the farming of resistant chicken breeds over broilers to reduce production losses from NDV outbreaks.}, } @article {pmid41769339, year = {2026}, author = {Wangprapa, P and Nagy-Szakal, D and Wells, HL and Fidler, G and Sangtian, M and Panmontha, W and Bunlungsup, S and Techasathit, W and Couto-Rodriguez, M and Danko, DC and Mason, CE and O'Hara, NB and Sriswasdi, S and Viangteeravat, T}, title = {Analytical validation of a metagenomic next-generation diagnostic platform for urinary tract infection in a Thai tertiary hospital setting: a BI-Biotia UTI cohort study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1751074}, pmid = {41769339}, issn = {2235-2988}, mesh = {Humans ; *Urinary Tract Infections/diagnosis/microbiology ; Tertiary Care Centers ; Thailand ; Retrospective Studies ; *Metagenomics/methods ; Female ; Sensitivity and Specificity ; *High-Throughput Nucleotide Sequencing/methods ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/isolation & purification/classification ; Male ; Middle Aged ; }, abstract = {BACKGROUND: The BIOTIA-DX platform (BDX), a commercially available clinical-grade mNGS-based test in the United States, has not been analytically validated for urinary tract infections (UTIs) in a Southeast Asian cohort, where microbial epidemiology and antimicrobial resistance (AMR) patterns differ significantly.

OBJECTIVE: Our primary objective was to evaluate the analytical performance and concordance with standard urine culture of the BIOTIA-DX platform in a Thai tertiary hospital setting, thereby assessing its transportability to a Southeast Asian population with distinct microbial epidemiology.

METHODS: We analyzed 398 retrospectively collected urine samples from patients with suspected UTI at a private hospital in Bangkok. Each sample was processed in parallel using standard-of-care urine culture and the BDX mNGS workflow. After excluding 30 samples with insufficient sequencing reads (<500 non-human reads), 368 samples (231 culture-positive, 137 culture-negative) were included. Diagnostic accuracy was assessed against culture, and genotypic AMR predictions were compared to phenotypic antimicrobial susceptibility testing (AST) N = 192.

RESULTS: The BIOTIA-DX platform demonstrated high analytical sensitivity at the sample level (98.7% [95% CI: 0.95-0.99]; 228/231 culture-positive samples detected) and organism level (94.6%; 229/242 culture-identified organisms correctly detected). Among 137 culture-negative samples, BIOTIA-DX detected microbial DNA in 98 samples (71.5%), identifying 264 organisms not detected by standard culture. These additional detections predominantly comprised anaerobic organisms (150/264, 56.8%) and fastidious species (54/264, 20.5%); however, the clinical significance of these detections (infection vs. colonization vs. contamination) could not be determined without clinical correlation. For AMR prediction, genotype-phenotype concordance rates were 94.1% for fluoroquinolone resistance in E. coli (96/102 resistant isolates correctly predicted), 91.4% for beta-lactams (106/116), 91.3% for aminoglycosides (21/23), and 81.5% for sulfamethoxazole/trimethoprim (75/92). Specificity and positive predictive value could not be calculated because organisms detected by BIOTIA-DX but not by culture could not be definitively classified as true positives or false positives without independent confirmation.

CONCLUSIONS: The BIOTIA-DX platform demonstrates robust analytical concordance with urine culture in a Thai patient population. Prospective clinical validation studies are needed to assess clinical utility and impact on patient outcomes, particularly in culture-negative and polymicrobial cases. This study represents the first analytical validation of this platform using Oxford Nanopore Technology and the first validation in Southeast Asia.}, } @article {pmid41769343, year = {2026}, author = {Yan, X and Zhang, X and Wang, L and Song, W and Qi, T and Wang, Z and Tang, Y and Sun, J and Xu, S and Yang, J and Shao, Y and Chen, Y and Wang, J and Chen, J and Zhang, R and Liu, L and Shen, Y}, title = {Gut microbiota alterations and microbial translocation in HIV/SARS-CoV-2 co-infected patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1688580}, pmid = {41769343}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/microbiology ; *Coinfection/microbiology/virology ; Female ; *HIV Infections/microbiology/complications/virology ; SARS-CoV-2 ; *Gastrointestinal Microbiome ; *Bacterial Translocation ; Male ; Feces/microbiology ; Adult ; Lipopolysaccharides/blood ; Lipopolysaccharide Receptors/blood ; Middle Aged ; Haptoglobins/analysis ; Protein Precursors/blood ; Severity of Illness Index ; Cohort Studies ; Metagenomics ; }, abstract = {OBJECTIVE: To characterize gut microbiome alterations and microbial translocation in human immunodeficiency virus (HIV)/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infected patients and identify microbial signatures associated with COVID-19 severity.

METHODS: In this cohort study, blood and fecal samples from 38 HIV/AIDS patients (20 SARS-CoV-2 co-infected [PC group]; 18 SARS-CoV-2-negative [NC group]) were analyzed. The PC group was stratified by COVID-19 severity: mild-to-moderate (PC1, n=13), severe-to-critical (PC2, n=3), and mixed infections (PC3, n=4). Serum lipopolysaccharide (LPS), soluble CD14 (sCD14), and zonulin levels were measured to assess microbial translocation and gut barrier integrity. Fecal metagenomic profiling was performed via whole-genome shotgun sequencing (Illumina NovaSeq/HiSeq).

RESULTS: Co-infected patients exhibited significantly elevated plasma LPS (78.09 vs 48.72 pg/mL, p=0.032) and sCD14 (2667 vs 1927 ng/mL, p=0.0015) compared to controls. Although no differences in α-diversity or overall taxonomic abundance were observed between the PC and NC groups, 329 PC-unique and 216 NC-unique microbial species were identified. Nine genera demonstrated diagnostic potential for co-infection [Area Under the Curve (AUC), >0.7] with Akkermansia showing the highest predictive value (AUC = 0.811). Critically, Blautia abundance was significantly reduced in severe-to-critical cases (PC2) versus mild-moderate cases (PC1, p=0.043) and controls (NC, p=0.006). Besides, our function prediction for gut microbiota suggested that SARS-CoV-2 may exacerbate lipid metabolic dysregulation in HIV-infected individuals.

CONCLUSIONS: HIV/SARS-CoV-2 co-infection is characterized by heightened microbial translocation and species-specific microbiota alterations rather than global dysbiosis. Blautia depletion may correlate with COVID-19 severity.}, } @article {pmid41769388, year = {2026}, author = {Chang, ACG and Amaral, MWW and Keepers, K and Ikudaisi, C and Greenwood, M and Li, J and Hamsher, SE and Miller, SR and Kociolek, JP}, title = {An alternative technique for organelle genome recovery in diatoms using culture-independent, minimal-cell whole genome amplification.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20767}, pmid = {41769388}, issn = {2167-8359}, mesh = {*Diatoms/genetics ; *Genome, Mitochondrial ; *Genomics/methods ; *Genome, Chloroplast ; }, abstract = {BACKGROUND: This study presents an alternative method in diatom genomics using two raphid diatoms-Campylodiscus clypeus and Plagiotropis lepidoptera-whose organellar genome characteristics have remained unexplored due to cultivation constraints. Only a small fraction of the estimated 200,000 diatom species has been cultured in the laboratory. This research showcases the use of minimal-cell genomics as a viable alternative for studying diatoms and other eukaryotic microorganisms that do not respond well to traditional laboratory culture methods.

METHODS: Initial attempts to culture C. clypeus and P. lepidoptera were unsuccessful, hindering the acquisition of genomic data. To overcome these challenges, we employed minimal-cell whole genome amplification (mcWGA) techniques for two uncultured species, followed by metagenomic sequencing and assembly. This enabled direct genomic recovery from minimally isolated and pooled cells, eliminating the need for cultivation.

RESULTS: Using mcWGA approach, we successfully obtained the complete chloroplasts and mitochondrial genomes of C. clypeus and P. lepidoptera using only 8-12 viable cells isolated from fresh environmental samples. The plastome size of C. clypeus was 143,367 bp and mitogenome size was 46,274 bp, while P. lepidoptera has plastome and mitogenome sizes of 116,161 bp and 49,356 bp, respectively. The data generated provides a valuable resource for further research, highlighting the importance of culture-independent techniques in microbial genomics.}, } @article {pmid41769651, year = {2026}, author = {Wang, L and Yu, Y and Shen, X and Li, X and Wang, D and Zhai, Y and Jiang, W and Zhao, W and Yu, Q and Liong, MT and Chen, D and Zhao, A}, title = {Bifidobacterium supplementation maintains gut microbiota stability and enhances well-being during short-term travel.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1724829}, pmid = {41769651}, issn = {2296-861X}, abstract = {BACKGROUND: International travel exposes individuals to abrupt environmental, dietary, and circadian changes that can disturb gut microbiota and overall well-being. While probiotics are known to support gastrointestinal and systemic health, their effects during short-term travel remain incompletely characterized in randomized trials.

METHODS: This randomized, double-blind, placebo-controlled study investigated whether a multi-strain Bifidobacterium probiotic could maintain gut microbiota stability and support health during a five-day trip from China to Japan. Forty healthy adults were randomly assigned to receive either probiotic (n = 22) or placebo (n = 18) daily from Day 1 to Day 4. Stool samples collected before departure (Day 0) and after return (Day 5) were analyzed by metagenomic sequencing, quantitative PCR, and fecal secretory immunoglobulin A (sIgA) assays. Participants completed validated questionnaires on gastrointestinal and respiratory symptoms, sleep quality (PSQI), anxiety (GAD-7), and well-being (WHO-5).

RESULTS: Compared with placebo, participants receiving the probiotic showed maintenance of microbial diversity (Chao1 and Fisher indices, both p = 0.044), prevented enrichment of potentially harmful taxa (Bilophila, Flavonifractor), and increased Bifidobacterium abundance. Clinically, the probiotic group reported fewer respiratory and systemic symptoms, including sore throat (p = 0.034) and fatigue (p = 0.043). Sleep quality also improved, with longer sleep duration (p = 0.023), fewer total occurrence days of PSQI >5 (p = 0.009), lower anxiety scores (p = 0.001) and higher WHO-5 well-being scores (p = 0.041). Functional profiling showed up-regulation of vitamin biosynthesis pathways (folate, biotin, retinol) and decreased antibiotic resistance gene prevalence.

CONCLUSION: Short-term probiotic administration demonstrated gut microbiota resilience and improved physiological and psychological stability during travel. Probiotics may serve as an accessible strategy to support well-being under transient environmental and lifestyle stress.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier NCT07163819.}, } @article {pmid41769655, year = {2026}, author = {Ray, S and Shankaran, P}, title = {Nutrition and the gut microbiome: a symbiotic dialogue influencing health and disease.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1761992}, pmid = {41769655}, issn = {2296-861X}, abstract = {The gut microbiome, a complex consortium of trillions of microorganisms, significantly influences human health through its metabolic activities, immune modulation, and interaction with the nervous system. Diet plays a significant role in shaping the gut microbiome, with plant-based diets promoting the colonization of beneficial bacteria and fiber fermentation, whereas meat-based diet may encourage harmful microbial shifts associated with systemic inflammation. Gut bacteria produce short-chain fatty acids (SCFAs) from dietary fibers and those are crucial for energy metabolism, intestinal integrity, and immune modulation. Certain neurotransmitters like GABA and serotonin produced by gut bacteria, play a vital role in the gut-brain axis. Dysbiosis in the gut microbiota have been linked to various psychiatric and neurological disorders like anxiety, depression, bipolar disorder, Schizophrenia, Alzheimer's and Parkinson's. Beyond neurological implications, the gut microbiota also linked to metabolic and cardiovascular diseases, including obesity, hypertension, and coronary artery disease, as well as colorectal cancer. Imbalances in bacterial ratios, such as Firmicutes to Bacteroidetes, can impact metabolism and inflammation. This review (i) elucidates the complex interplay between nutrition and the gut microbiome, emphasizing its implications for human health and disease; (ii) critically examines the methodological and analytical limitations inherent in current metagenomic studies; and (iii) proposes an integrated, multi-layered, systems-level framework for developing predictive models of host-microbe interactions and their pathological significance.}, } @article {pmid41770016, year = {2026}, author = {Silva, JM and Martins, I and Almeida, JR}, title = {HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.}, journal = {GigaScience}, volume = {15}, number = {}, pages = {}, pmid = {41770016}, issn = {2047-217X}, support = {UID/00127/2025//FCT/ ; 101081813//European Commission/ ; }, mesh = {*Metagenomics/methods ; *Software ; *Metagenome ; Humans ; *Computational Biology/methods ; }, abstract = {BACKGROUND: Reliable taxonomic classification of metagenomic sequences remains constrained by high mutation rates, fragmented assemblies, and large heterogeneous reference databases. HYMET (Hybrid Metagenomic Tool) was developed to overcome these challenges through a 2-stage hybrid design combining adaptive Mash-based screening with Minimap2 alignment and a coverage-weighted Lowest Common Ancestor classifier. Its sample-adaptive thresholds and on-the-fly reference database construction enable efficient, domain-agnostic classification while maintaining accuracy across divergent genomes.

RESULTS: Across 7 CAMI assembly datasets in contig mode, HYMET achieved a mean F1 of 83.89%, with genus-level F1 of 76.75% and species-level F1 of 60.18%, while averaging 115.93 s runtime and a mean peak memory of 6.24 GB. Performance remained stable under mutation rates up to 30% for most domains (F1 $\ge$ 0.8), with viral sequences showing the expected decline (F1 $\approx$ 0.5 at 30%). Read and contig inputs produced nearly identical results when sharing reference caches, and real-world datasets confirmed robustness with the human gut metagenome, which reproduced typical anaerobic profiles, while in the ZymoBIOMICS mock community, HYMET recovered all bacterial members; a further ground-truth evaluation on the ZymoBIOMICS Gut Microbiome Standard (D6331) yielded near-perfect genus-level concordance (Pearson $r = 0.998$, Bray-Curtis $= 0.04$) across bacteria, fungi, and archaea.

CONCLUSIONS: HYMET achieves a practical balance of accuracy, efficiency, and scalability for metagenomic classification. Its adaptive candidate selection, alignment-anchored taxonomy, and reproducible reference caching collectively enhance performance across domains. HYMET source code is fully available at https://github.com/ieeta-pt/HYMET.}, } @article {pmid41770210, year = {2026}, author = {Du, Y and Wang, Y and Sun, F}, title = {Metagenomic Hi‑C Protocols for Viral Genome Binning, Taxonomic Annotation, and Interaction Network Visualization.}, journal = {Current protocols}, volume = {6}, number = {3}, pages = {e70341}, pmid = {41770210}, issn = {2691-1299}, support = {EF-2125142//NSF/ ; }, mesh = {*Metagenomics/methods ; *Genome, Viral ; Molecular Sequence Annotation/methods ; *Viruses/genetics/classification ; Computational Biology/methods ; Metagenome ; }, abstract = {Metagenomic Hi-C (metaHi-C) links mobile genetic elements to their cellular hosts directly within complex microbial communities. Once shotgun and Hi-C libraries have been generated, however, the main challenges shift to the bioinformatics required for preprocessing, genome binning, taxonomic annotation, and network-level interpretation. Here, we present metaHi-C protocols that span from raw reads to downstream data analyses. Basic Protocol 1 describes quality control of shotgun and Hi-C reads, metagenomic assembly, Hi-C read mapping, and viral contig identification from assembled contigs. Basic Protocol 2 details the use of ViralCC to recover viral metagenome-assembled genomes (vMAGs) and infer virus-host linkages. Support Protocol 1 introduces NormCC and ImputeCC for normalization of raw Hi-C contacts and host genome binning. Support Protocols 2 and 3 describe taxonomic annotation of host MAGs with GTDB-Tk and viral bins with Virgo, respectively. Support Protocol 4 shows how to integrate these outputs in MetaHiCNet to generate cross-taxa and cross-bin Hi-C interaction networks. Together, these protocols provide a reproducible workflow for reconstructing viral and host genomes, assigning consistent taxonomies, and visualizing metaHi-C-derived virus-host interaction structure across diverse microbiomes. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preprocessing raw metagenomic Hi-C data Basic Protocol 2: Viral genome binning and virus-host interaction inference using ViralCC Support Protocol 1: Host genome binning using ImputeCC Support Protocol 2: Host MAG taxonomic annotation with GTDB‑Tk Support Protocol 3: Viral bin taxonomic annotation with Virgo Support Protocol 4: Visualization of virus-host interaction networks with MetaHiCNet.}, } @article {pmid41770401, year = {2026}, author = {Han, T and Yang, T and Liu, Y and He, Z and Hao, Y and Cao, W and Ren, J and Wang, G and Gong, C and Hou, J}, title = {Dietary supplementation with allicin enhances growth performance and antioxidant capacity, and reduces gut pathogens and antibiotic resistance genes in Trachidermus fasciatus.}, journal = {Fish physiology and biochemistry}, volume = {52}, number = {2}, pages = {}, pmid = {41770401}, issn = {1573-5168}, support = {2025JNZ-C01//the earmarked fund of Hebei Agricultural S&T Achievements Transformation/ ; 21326307D//the Key R&D Program of Hebei Province, China and the National Marine Genetic Resource Center/ ; }, mesh = {Animals ; *Sulfinic Acids/pharmacology/administration & dosage ; Disulfides ; *Antioxidants/metabolism ; *Dietary Supplements ; *Drug Resistance, Microbial/genetics ; Animal Feed/analysis ; Gastrointestinal Microbiome/drug effects ; Diet/veterinary ; *Fishes/growth & development/microbiology ; }, abstract = {Allicin, a bioactive sulfur compound from garlic known for its antimicrobial and immunomodulatory properties, was evaluated in this study for its effects on growth, antioxidant activity, gut microbiota, and antibiotic resistance genes (ARGs) in Trachidermus fasciatus. Fish were administered allicin at concentrations of 100 mg/kg, 200 mg/kg, and 300 mg/kg. The 200 mg/kg allicin group had significantly higher WGR, LGR, and SGR than the control group. Hepatic SOD and LZM activities were also higher in the 200 mg/kg group. Metagenomics showed that allicin altered the gut microbiota composition, decreased the diversity, and altered the community structure. Allicin-treated fish had significantly reduced levels of potentially damaging bacteria, including Pseudomonas and Vibrio species. The ARGs showed that genes associated with multidrug resistance, including specific subtypes, were markedly reduced in the 200 mg/kg allicin-treated fish. The control group had a markedly decreased number of genes resistant to β-lactam antibiotics. Allicin reduced the number of genes resistant to rpoB2 and mdtC, suggesting the potential for antibiotic resistance. Network analysis of co-occurrence patterns showed that genes resistant to multiple drugs, tetracyclines, and peptides were prevalent, with most possible potential host taxa belonging to Ascomycota and Firmicutes. These results indicate the importance of allicin for fish health as a sustainable alternative to antibiotic resistance and provide a viable alternative to antibiotic resistance for fish farming.}, } @article {pmid41771404, year = {2026}, author = {Zhang, C and Zheng, L and Zhang, Q and Zhang, Y and Zheng, X}, title = {Synergistic removal of methanethiol and other odorant gases by a metabolically complementary synthetic consortia isolated from food waste.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134313}, doi = {10.1016/j.biortech.2026.134313}, pmid = {41771404}, issn = {1873-2976}, mesh = {*Sulfhydryl Compounds/isolation & purification/metabolism ; *Odorants/analysis ; Food Loss and Waste ; *Gases/isolation & purification ; Biodegradation, Environmental ; Bacteria/metabolism/genetics ; *Microbial Consortia ; }, abstract = {Methanethiol (MeSH), a typical volatile sulfur compound, contributes significantly to environmental malodor and poses ecological risks. In this study, three bacterial strains capable of MeSH removal efficiencies exceeding 40% were isolated from food waste. These strains were taxonomically identified asAgrobacterium cavarae,Mycolicibacterium neoaurum, andPseudomonas qingdaonensis. Metagenomic annotation by Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that all strains possess key enzymes for the methionine and cysteine metabolism pathway, suggesting potential for MeSH degradation. In binary consortia, the combination of A. cavarae R1 and P. qingdaonensis CF (5:1 ratio) exhibited the optimal degradation performance, achieving removal efficiency of 87.2% for MeSH, 98.7% for H2S, and complete NH3 elimination (100%) after a 6-day cultivation. Among ternary consortia, the A. cavarae R1/M. neoaurum CD/ P. qingdaonensis CF combination at 3:2:1 and 3:1:2 ratios demonstrated superior removal efficiency for all three target odorants. Specifically, the 3:2:1 ratio consortium achieved 94.7% MeSH degradation, while the 3:1:2 ratio showd 91.7% NH3 removal efficiency. These results demonstrate the feasibility of using composite microbial agents for odor control in waste management systems.}, } @article {pmid41771407, year = {2026}, author = {Zhao, Y and Zhang, X and Chen, X and Zhu, Z and Jiao, P and Ma, L and Li, Y}, title = {Evidence for Propioniciclava as a novel polyphosphate-accumulating organism and construction of its metabolic profile.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134320}, doi = {10.1016/j.biortech.2026.134320}, pmid = {41771407}, issn = {1873-2976}, mesh = {*Polyphosphates/metabolism ; Bioreactors/microbiology ; Glycogen/metabolism ; Phosphorus/metabolism ; *Metabolome ; In Situ Hybridization, Fluorescence ; }, abstract = {Enhanced biological phosphorus removal (EBPR) relies on polyphosphate-accumulating organisms (PAOs). This study identifies Propioniciclava as a novel putative PAO. High phosphorus release and uptake rates were achieved in two lab-scale Propioniciclava-dominated sequencing batch reactors (SBRs), reaching up to 2.37 and 2.10 mmolP/(gVSS·h), respectively. Metabolic pathway reconstruction for Propioniciclava was based on its most abundant metagenome-assembled genome (bin70), which accounted for 28.8% in SBR1 and 45.5% in SBR2. Functional annotation of bin70 revealed genes for phosphorus and glycogen metabolism but not for polyhydroxyalkanoate synthesis, suggesting a distinct storage strategy. Fluorescence in situ hybridization combined with 4',6'-diamidino-2-phenylindole (FISH-DAPI) staining provided evidence for intracellular polyphosphate granules. Metatranscriptomic analysis further highlighted genes related to phosphorus and glycogen synthesis being actively transcribed by Propioniciclava. The enrichment of Propioniciclava was crucially dependent on glucose. These findings expand the known diversity of PAOs and elucidate the metabolic profile of Propioniciclava, enhancing our understanding of EBPR microbiology.}, } @article {pmid41771597, year = {2026}, author = {Payne, T and Shaw, A and Hanjani, LS and Homes, R and Giddens, F and Ravuri, HG and Yap, CX and Walsh, J and Kumar, V and Garton, FC and Rhee, H and Huang, A and Francis, RS and Reid, N and McAdams-DeMarco, M and Gordon, E and Midwinter, M and Hubbard, R}, title = {ReFIT study (reversing frailty in transplantation): protocol for a longitudinal study to assess clinical and biomedical changes in frailty through kidney transplantation.}, journal = {BMJ open}, volume = {16}, number = {3}, pages = {e100158}, pmid = {41771597}, issn = {2044-6055}, mesh = {Humans ; *Kidney Transplantation ; Longitudinal Studies ; *Frailty/etiology/physiopathology ; Middle Aged ; Aged ; Adult ; Female ; Male ; Research Design ; }, abstract = {INTRODUCTION: Losses of functional reserve across multiple physiological systems have been identified in frail patients, yet the exact aetiology of frailty remains unclear. Although strongly associated with chronological age, frailty often develops at a younger age in patients with organ failure. Frailty is prevalent in patients with kidney failure; however, individuals experience improvements in physical frailty measures following kidney transplantation. This makes younger patients with kidney failure a unique population for studying both the accelerated onset of frailty and its reversal. This research project aims to test the hypothesis that frailty secondary to organ failure and age-related frailty are associated with similar molecular and physiological measures.

METHODS AND ANALYSIS: This longitudinal study will recruit 150 patients in three groups. Group A (kidney transplant recipients aged ≥40 years; n=50) and Group B (patients aged ≥40 years active on the kidney transplant waitlist; n=50) will comprise younger adults with frailty from organ failure. Group C (adults aged ≥65 years (or ≥55 years for Aboriginal and Torres Strait Islander patients); n=50) will comprise older community dwellers. The primary outcome is the Frailty Index (FI). Secondary outcomes include the change in FI over time, and at baseline when considering various clinical metadata, immune parameters, kidney function and nutrition intake which will be measured at baseline and 12-month time points. Longitudinal changes in frailty will be analysed using linear mixed models with multiple testing corrections for false discovery rates.Endocrine profiles and metabolomics, measures of immune function and microcirculatory dysfunction, will be measured by liquid chromatography-mass spectrometry and/or gas chromatography-mass spectrometry. The gut microbiome will be sequenced via shotgun metagenomics (Illumina NextSeq500, 150 bp paired-end, [3]Gbp/sample). Circulating cell-free DNA/mitochondrial DNA will be quantified through droplet digital PCR. Microcirculation will be assessed via sublingual dark field videomicroscopy with glycocalyx markers measured by ELISA.

ETHICS AND DISSEMINATION: This study will be conducted with all stipulations of this protocol, and the conditions of the ethics committee approval. Ethical principles have their origin in the Declaration of Helsinki, all Australian and local regulations and in the spirit of the standard of Good Clinical Practice (as defined by the International Conference on Harmonisation). Organs/tissues will be sourced ethically and will not be sourced from executed prisoners or prisoners of conscience or other vulnerable groups.Ethics approval was received by the Metro South Health Research Ethics Committee (HREC/2023/QMS/95392) and ratified by the University of Queensland.Results will be disseminated through peer-reviewed publications, academic conferences, participant newsletters and health organisation collaboration.}, } @article {pmid41771902, year = {2026}, author = {Qian, Y and Xu, S and He, X and Lai, Y and Zhang, Y and Mo, C and Ai, P and Yang, X and Xiao, Q}, title = {Gut ecosystem dysfunction in parkinson's disease: deciphering faecal metabolome-metagenome links for novel diagnostic panels.}, journal = {NPJ Parkinson's disease}, volume = {12}, number = {1}, pages = {}, pmid = {41771902}, issn = {2373-8057}, support = {81901283//National Natural Science Foundation of China/ ; 81801254//National Natural Science Foundation of China/ ; 82171246//National Natural Science Foundation of China/ ; 22YF1440200//Shanghai Sailing Program/ ; 22QA1405700//the Shanghai Rising-Star Program/ ; 2018B030337001//Key Field Research and Development Program of Guangdong Province/ ; SHDC2020CR3012A//Clinical Research Plan of SHDC/ ; 2022YFE0210100//National Key Research and Development Program of China/ ; }, abstract = {Gut ecosystem dysfunction is implicated in Parkinson's disease (PD), but integrative faecal metabolome-metagenome links are undefined. We explored these interactions in Chinese PD patients to develop diagnostic panels. Targeted faecal metabolomics (LC‒MS/MS) was performed on 132 PD and 113 healthy controls (HCs) and shotgun metagenomics was integrated for 39 PD/HC pairs. We identified 33 significantly altered faecal metabolites in PD (FDR-P < 0.05). A novel 12-metabolite panel could distinguish PD from HCs. Multi-omic integration revealed gut ecosystem dysfunction manifests via co-disruptions in microbial genes (e.g., amino acid metabolism genes) and metabolites. Critically, a combinatorial diagnostic panel integrating faecal metabolites and microbial gene markers achieved exceptional PD detection (AUC = 0.961, 95% CI = 0.923-0.998). This study deciphers metabolome-metagenome links driving gut dysfunction in PD, identifying amino acid metabolism as a core perturbed pathway. The novel diagnostic panels provide mechanistic insights and clinical tools for PD precision diagnosis.}, } @article {pmid41771971, year = {2026}, author = {Deng, S and Wu, X and Xu, W and Wu, X and Cai, H and Wang, S and Liu, J and Cao, J}, title = {Multi-dimensional immunoprotection of Ganoderma lucidum spore oil in immunosuppressed mice via microbiome-proteome-metabolome network analysis.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41771971}, issn = {2045-2322}, support = {JCYJ20220530153201003//Science and Technology Planning Project of Shenzen Municipality/ ; GDRC202119//Natural Science Foundation of Top Talent of SZTU/ ; 82104362//National Natural Science Foundation of China/ ; 20211063010055//Research Founding of Post-doctor who came to Shenzhen/ ; SDAIT-20-05//Shandong Province Traditional Chinese Medicine Industry Project/ ; 2022ZDJS119//Guangdong Province Key Discipline Construction Research Project/ ; }, abstract = {UNLABELLED: Ganoderma lucidum has a long-standing history of use as a medicinal mushroom, with its spore oil (GLSO) extracted from broken cell walls using CO2 supercritical extraction. However, there is a notable scarcity of experimental studies on the protective effects and underlying mechanisms of GLSO on immune function impairment. The present study aims to explore the characteristics that GLSO contributes to protecting immune functions in cyclophosphamide-induced immunocompromised mice through a multi-omics analysis approach. GLSO administration significantly improved serum hemolysin levels, macrophage phagocytosis, and NK cell activity in immunosuppressed mice. Metagenomics, metabolomic, and proteomic analyses revealed that the immune protection mediated by GLSO was associated with structural rearrangements within gut microflora and shifts in microbial diversity. Specifically, there was an increase in beneficial microorganisms and a decrease in pathogenic organisms, accompanied by various alterations in metabolites and protein expressions. The identified 5 metabolites (propionic acid, beta-glycyrrhetinic acid, 3-aminosalicylic acid, creatine, and 2-phenylacetamide) and 5 proteins (Slc9a9, Blm, Hk3, AP1M2, and J chain) might serve as potential mediators of GLSO to alleviate immune dysfunction collectively caused by CYP in immunosuppressed mice.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-40137-x.}, } @article {pmid41772715, year = {2026}, author = {Merenstein, C and Litichevskiy, L and Thaiss, C and Collman, RG and Bushman, FD}, title = {Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41772715}, issn = {2049-2618}, support = {F31 HL170550/NH/NIH HHS/United States ; T32 HG000046/NH/NIH HHS/United States ; DP2 AG067492/NH/NIH HHS/United States ; U54 AG089323/NH/NIH HHS/United States ; U19 AI174998/NH/NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; *Caloric Restriction ; Genome, Viral ; *Gastrointestinal Microbiome ; Metagenome ; *Bacteria/virology/classification/genetics ; Host Specificity ; Longitudinal Studies ; Prophages/genetics/classification ; Female ; DNA, Viral/genetics ; Longevity ; }, abstract = {BACKGROUND: The majority of bacteria in the vertebrate gut harbor integrated bacterial viruses ("bacteriophages" or "phages"; integrated phage are termed "prophages"). To probe phage replication strategies in the mammalian gut microbiome, we investigated phage activity in a large longitudinal study of diversity outbred mice (913 animals) undergoing extreme dietary restriction with detailed phenotypic characterization across lifespan.

RESULTS: We assembled 54,119 candidate DNA viral genomes from 2997 longitudinal metagenomes, forming 6462 viral operational taxonomic units (vOTUs). Over 85% of vOTUs annotated as novel. Viruses annotated predominantly as prophages in the Caudoviricetes class. We detected no eukaryotic DNA viruses, and none of the strictly lytic Crassvirales order that is abundant in human gut. The most prevalent phages had the widest predicted host ranges. The relative abundance of most phages was highly correlated to that of their inferred host bacteria, suggesting quiescent prophages dominate viral metagenomes, consistent with "piggyback-the-winner" dynamics. After accounting for close phage-bacterial covariation, we did identify a subset of phages changing in relative abundance and prevalence relative to their hosts in response to dietary restriction and aging. In particular, phages with larger genomes become less common in diets with restricted calories, potentially reflecting a higher fitness cost to their host. Generalist phages were enriched for a gene encoding a single-strand DNA binding protein which is reportedly involved in DNA repair and protection from nucleases encoded by host cells. Lytic phages became more common with aging, and we observed a reduction in phage richness with age, both findings previously observed in human cohorts.

CONCLUSION: These studies enrich our understanding of DNA phage dynamics in gut while emphasizing the predominance of "piggyback-the-winner" strategies.}, } @article {pmid41772733, year = {2026}, author = {Buscaglia, M and Castillo-Inaipil, W and Schulz, F and Guajardo-Leiva, S and Iriarte, JL and Aparicio-Rizzo, P and Masotti, I and Díez, B}, title = {Unveiling the viral frontier in a warming world: temperature as a key ecological driver of viral diversity in subantarctic Chilean Patagonia fjords.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41772733}, issn = {2524-6372}, support = {21190726//ANID/ ; AUB1900003//ANID/ ; DG_06-20//INACH/ ; 151500003//ANID-FONDAP/ ; 1523A0002//ANID-FONDAP/ ; CIMAR25F//CONA-SHOA/ ; ICN2021_044//ANID - Millennium Science Initiative Program/ ; }, abstract = {BACKGROUND: The fjords of Chilean Patagonia (~ 41.5-55.9 °S) lie at the forefront of global warming, where rising temperatures threaten to disrupt microbial processes central to ocean productivity and carbon cycling. Despite their ecological relevance, the diversity and environmental drivers of viral communities, both giant viruses and prokaryotic viruses, remain poorly understood in high-latitude fjords.

RESULTS: Here, we leveraged metagenomics across a 500 km latitudinal gradient in Chilean Patagonia (4-10 °C; salinity 18-33 PSU) to decode the structure and distribution of marine viral communities. We recovered 126 giant viruses (polB sequences dereplicated at 100% average nucleotide identity) and 9213 prokaryotic viruses (viral contigs dereplicated at 95% average nucleotide identity), primarily affiliated with Prasinoviridae (proposed genus g177, order Algavirales) and Caudoviricetes, respectively. Consistent with global-scale studies, temperature emerged as the strongest driver structuring viral communities, outpacing the effects of salinity, depth, dissolved oxygen, chlorophyll-a, and geography. Viral diversity was consistently higher in the northern warmer waters (7.5-10.4 °C), while southern colder sites (4.0-7.4 °C) harbored less diverse and compositionally distinct communities. Giant viruses shift from Pandoravirales and AG_04 (Algavirales) at lower temperatures to increasing dominance of IM_01 (Imitervirales) and Prasinoviridae (AG_01) in warmer habitats. Prokaryotic virus communities also displayed strong temperature structuring, with additional influence from salinity.

CONCLUSIONS: Together, our findings underscore the environmental sensitivity of viral communities in subpolar marine systems and highlight their vulnerability to climate-driven changes. Given the critical role of viruses in microbial turnover, nutrient cycling, and ecosystem resilience, shifts in their diversity and structure may have far-reaching consequences for biogeochemical fluxes and food web dynamics in the fjords of Chilean Patagonia.}, } @article {pmid41773230, year = {2026}, author = {Li, X and Feng, Q and Yu, H}, title = {A Rare Case of Concurrent Tropheryma Whipplei and Pneumocystis Jirovecii Pneumonia in a Patient During Endocrine Therapy for Breast Cancer.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {580235}, pmid = {41773230}, issn = {1178-6973}, abstract = {Tropheryma whipplei (TW), a rare Gram-positive bacterium, is an uncommon cause of pulmonary infection, typically being reported in the context of gastrointestinal or neurological Whipple's disease. We present a case of a patient receiving endocrine therapy and ovarian suppression for breast cancer who developed a concurrent pulmonary infection with both Pneumocystis jirovecii (PJ) and TW. The diagnosis was secured through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid, which successfully identified both pathogens. Following the initiation of targeted antimicrobial therapy, the patient exhibited significant clinical and radiological improvement.}, } @article {pmid41773424, year = {2026}, author = {Valdés-Varela, L and Goyache, I and Virto, R and Sáinz, N and López-Yoldi, M and Sánchez-Vicente, A and López-Giral, N and Gil, AG and Milagro, FI and Aranaz, P}, title = {Companilactobacillus alimentarius CNTA 209 alleviates diet-induced obesity in mice through adipose tissue browning and gut barrier modulation.}, journal = {Food & function}, volume = {17}, number = {6}, pages = {2851-2870}, doi = {10.1039/d5fo04242a}, pmid = {41773424}, issn = {2042-650X}, mesh = {Animals ; *Obesity/metabolism/drug therapy ; Mice ; Mice, Inbred C57BL ; Male ; *Probiotics/pharmacology/administration & dosage ; Rats ; Diet, High-Fat/adverse effects ; *Adipose Tissue, Brown/metabolism/drug effects ; Rats, Wistar ; Gastrointestinal Microbiome/drug effects ; Intestinal Barrier Function ; Humans ; *Lactobacillaceae/physiology ; }, abstract = {The use of probiotics with health-promoting effects has emerged as a promising therapeutic strategy for managing obesity and metabolic syndrome. In this study, we characterized the probiotic properties of a novel strain, Companilactobacillus alimentarius CNTA 209, and investigated its potential anti-obesity effects and safety in rodent models. C. alimentarius exhibited sensitivity to all tested antibiotics, resistance to simulated gastric and intestinal conditions in vitro, and functional activities including β-galactosidase activity and short-chain fatty acid (SCFA) production. C. alimentarius supplementation mitigated liver damage induced by a high-fat, high-fructose diet and significantly reduced adiposity in obese C57BL/6 mice by enhancing brown adipose tissue metabolic activity. Metagenomic analysis revealed a beneficial modulation of gut microbiota composition, associated with improved intestinal barrier function. A comprehensive toxicological assessment conducted in Wistar rats confirmed the safety of the strain at a dose of 1 × 10[9] CFU per animal per day for oral administration. This study provides the first documented evidence of anti-obesity and metabolic benefits conferred by a strain of C. alimentarius, positioning CNTA 209 as a novel and safe candidate for the development of probiotic-based interventions targeting obesity and related metabolic disorders.}, } @article {pmid41773475, year = {2026}, author = {Ma, H and Dai, Y and Xu, C and Geng, H and Li, R and Wang, S and Yang, M}, title = {Correction to "Identification of Three Novel Umami Peptides from Metagenomics of Traditional Fermented Fish, Suanyu, and Receptor Binding Mechanism via the Graph Neural Network-Based Model and Molecular Dynamics Simulation".}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {9}, pages = {8027}, doi = {10.1021/acs.jafc.6c01914}, pmid = {41773475}, issn = {1520-5118}, } @article {pmid41773588, year = {2026}, author = {Sun, S and Subramaniyan, S and Ranjani, G and Cid Gomes, L and Bernin, D and Bayer, T and Bornscheuer, UT and Hakkarainen, M and Syrén, PO}, title = {Polyurethane Cascade Depolymerization by a Combination of Thermal Pretreatment and Enzymatic Hydrolysis.}, journal = {ChemSusChem}, volume = {19}, number = {5}, pages = {e202502633}, pmid = {41773588}, issn = {1864-564X}, support = {CTS 23:2626//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; 2021-02509//Svenska Forskningsrådet Formas/ ; NNF23OC0086236//Novo Nordisk Fonden/ ; NNF25OC0100562//Novo Nordisk Fonden/ ; }, mesh = {*Polyurethanes/chemistry/metabolism ; Hydrolysis ; *Polymerization ; *Carboxylic Ester Hydrolases/metabolism/chemistry ; *Temperature ; Molecular Docking Simulation ; }, abstract = {Enzymatic depolymerization of postconsumer polyurethanes (PURs) offers a promising route for sustainable plastic waste management. However, the complex chemistry of PURs containing carbamate, ether, and ester bonds poses a challenge for such a biotechnological process. Here, we explored the deconstruction of a commercial polyether-polyester-PUR through a cascade depolymerization approach, in which a low-temperature thermal pretreatment (180°C, 4 h) was combined with tandem enzymatic hydrolysis. Heat treatment modified the polymer's physicochemical properties, enabling the cutinase HiC from Humicola insolens to cause more than 8% weight loss of the treated PUR films, versus less than 2% of the untreated control after 48 h incubation. Furthermore, the addition of the metagenomic urethanase SP2 completed the one-pot enzymatic cascade, achieving not only depolymerization to the constituent monomer, 4,4'-methylenedianiline (MDA), but also a nearly 3-fold increase in MDA yield compared to using SP2 alone. Docking studies highlighted HiC's specificity toward ester bonds in the PUR polymeric units, and two HiC variants further enhanced degradation within 24 h. Altogether, this work lays the foundation for future investigation and process design for the depolymerization of polyether-polyester-PURs and related materials by cascade enzymatic reactions.}, } @article {pmid41773858, year = {2026}, author = {Vijayakumar Padmavathy, B and Shanmugavel, AK and Shanmugam, S and Narayanan, M}, title = {Dissecting the effect of single- and co-infection of TB and COVID-19 pathogens on the sputum microbiome.}, journal = {Microbiology spectrum}, volume = {14}, number = {4}, pages = {e0222025}, pmid = {41773858}, issn = {2165-0497}, support = {SB24250033CSIITM008892//Women Leading IIT Madras (WLI)/ ; SB21221740CSRBEI008892//Robert-Bosch Center for Data Science and Artificial Intelligence/ ; }, mesh = {Humans ; *Coinfection/microbiology ; *Sputum/microbiology ; *Microbiota/genetics ; *COVID-19/microbiology/complications ; SARS-CoV-2 ; *Tuberculosis/microbiology ; Female ; Male ; Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Metagenomics ; Adult ; Mycobacterium tuberculosis ; Dysbiosis/microbiology ; }, abstract = {UNLABELLED: Tuberculosis (TB) and COVID-19 are both respiratory diseases, and understanding their interaction is important for effective co-infection management. Although some studies have investigated TB and COVID-19 co-infection in terms of immune responses, microbial dysbiosis in such cases remains unexplored. In this study, we understand the interface between TB and COVID-19 by systematically inspecting the microbial composition of sputum samples collected from four groups of individuals: TB only, COVID-19 only, and both TB and COVID-19 (TBCOVID) infected patients, and uninfected group (Controls). Besides metagenomic analysis of the microbiome of these sputum samples, we also performed whole-genome sequencing analysis of a subset of TB-positive samples. Different bioinformatic analyses ensured data quality and revealed significant differences in the microbial composition between Control vs disease groups. To understand the effect of COVID-19 on TB, we compared TBCOVID vs TB samples and observed (i) higher read counts of TB-causing bacteria in the TBCOVID group, and (ii) differential abundance of several taxa, including Capnocytophaga gingivalis. Functional profiling with PICRUSt2 revealed elevated pathways, including the pulmonary surfactant lipid metabolism pathway (with a fold change of 7.46) in the TBCOVID group. Further clustering of these pathways revealed a sub-cluster of individuals with adverse treatment outcomes. Two individuals in this sub-cluster had a respiratory pathogen, Stenotrophomonas maltophilia-knowing such information on key respiratory pathogens in a patient can help personalize the patient's antibiotic regimen. Overall, our study reveals the effect of COVID-19 on the airway microbiome of TB patients and encourages the use of co-microbial/co-pathogen profiling to personalize TB treatment.

IMPORTANCE: The community of microbes in an individual's airway tract can play a complex role in respiratory diseases like tuberculosis (TB) and COVID-19. Although changes in microbial composition in TB and COVID-19 patients have been studied separately, we present a first-of-its-kind investigation of the airway-tract microbiome of individuals simultaneously infected with TB and COVID-19 pathogens. Our results highlight that co-infection with COVID-19 in TB patients alters the abundance of certain bacterial species and their related pathways. For instance, Capnocytophaga gingivalis is abundant in co-infected patients, but not in TB-only patients. This species and other differentially abundant species we identified in the co-morbid condition, if replicated in independent cohorts, can help explain how COVID-19 could exacerbate the severity of lung infection in TB patients. Our study also stimulates future longitudinal studies using expanded data sets to understand the role of concomitant pathogens and assess whether adjusting the antibiotic regimen accordingly can improve TB treatment outcomes.}, } @article {pmid41774204, year = {2026}, author = {Gulumbe, BH and Alum, EU and Abdulrahim, A and Abubakar, TM and Bagwai, MA and Ali, M}, title = {The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance.}, journal = {Current microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {41774204}, issn = {1432-0991}, mesh = {*Microbiota ; Humans ; *Bacteria/genetics/drug effects/classification ; Gene Transfer, Horizontal ; *Environmental Microbiology ; *Drug Resistance, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Ecosystem ; }, abstract = {Antimicrobial resistance (AMR) poses an escalating global health challenge with important environmental dimensions. While the environment is well known as a reservoir and conduit for antibiotic resistance genes (ARGs), the regulatory role of environmental microbiomes in modulating ARG dissemination remains inadequately studied. This review synthesizes current knowledge on how environmental microbiomes influence the spread of AMR by acting as buffers, amplifiers, or gatekeepers of ARG flow in natural and human-impacted ecosystems. We synthesize findings from metagenomic analyses, ecological experiments, and theoretical frameworks to evaluate how microbial diversity, community composition, and ecological interactions shape the persistence and horizontal transfer of ARGs in the environment. Evidence suggests that diverse and resilient microbial communities can inhibit ARG persistence and limit gene transfer, whereas environmental disturbances and biodiversity loss may facilitate ARG propagation. These dynamics highlight the importance of microbial ecosystem structure in shaping AMR trajectories. Understanding the ecological role of environmental microbiomes in AMR dissemination offers new perspectives for antimicrobial stewardship within the One Health framework. Integrating this knowledge into practical interventions, such as engineered microbial consortia and bioremediation can help manage environmental sources of resistance and strengthen global efforts against AMR.}, } @article {pmid41774281, year = {2026}, author = {Kapoor, V and Sanchez-Vicente, S and Donovan, W and Park, J and Nagapurkar, A and Gokden, A and Shrivastava, P and Horn, E and Briese, T and Lipkin, WI and Tokarz, R}, title = {Adaptation of custom capture sequencing panels to the Oxford Nanopore MinION platform.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {41774281}, issn = {1573-4978}, support = {75A50122C00012//Biomedical Advanced Research and Development Authority/ ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods/instrumentation ; *Sequence Analysis, DNA/methods ; Animals ; *Metagenomics/methods ; Nanopores ; Humans ; Sensitivity and Specificity ; Gene Library ; *Nanopore Sequencing/methods ; }, abstract = {BACKGROUND: Next generation sequencing (NGS) remains underutilized in clinical microbiology applications despite providing broad pathogen spectrum detection superior to other molecular methods. This is primarily because of lower sensitivity of metagenomic NGS (mNGS) compared to PCR, lengthy turn-around times, cost, and complexity of data analysis. Capture sequencing is a technique that can mitigate some of the limitations of mNGS. Using probes that are engineered to selectively bind and pull down desired nucleic acids, capture sequencing enriches for targets of interest and can result in up to a 10,000-fold increase in sensitivity compared to mNGS. In this study, we describe the application of capture sequencing on Oxford Nanopore Technology's portable sequencer, the MinION MK1C.

METHODS: We examined the performance of VirCapSeq-VERT and TBDCapSeq, two distinct capture sequencing assays that target vertebrate viruses and tick-borne pathogens, respectively. Both assays were originally established on the Illumina platform. To enable sequencing on the MinION instrument, we developed a modified hybrid workflow using our established library preparation and capture protocol for Illumina, followed by the addition of the ONT sequencing adaptor. In tests using contrived and clinical samples, we compared sensitivity thresholds and sequencing output, including pathogen genome coverage and relevant read counts.

RESULTS: The addition of capture enrichment to MinION NGS provided significant improvement in pathogen detection when compared to mNGS. Assessment of assay performance on pathogen-positive samples revealed equivalent sensitivity on the MinION MK1C and Illumina NextSeq. We found that the elevated read counts and sequencing depth generated by Illumina NGS were offset by the greater read length obtained on the MinION MK1C and resulted in comparable pathogen genome coverage between the two platforms.

CONCLUSION: This study demonstrates the utility for employment of VirCapSeq and TBDCapSeq on different sequencing platforms and suggest the potential of the MinION platform for broad-spectrum clinical diagnostics.}, } @article {pmid41775000, year = {2026}, author = {Mammeri, M and Obregon, D and Chevillot, A and Abuin-Denis, L and Skičková, Š and Kratou, M and Wu-Chuang, A and Maitre, A and Christine, J and Polack, B and Cabezas-Cruz, A and Adjou, KT}, title = {Yeast probiotic protects gut microbiota diversity and metabolic potential against Cryptosporidiosis-induced disruption in goat kids.}, journal = {Veterinary parasitology}, volume = {343}, number = {}, pages = {110729}, doi = {10.1016/j.vetpar.2026.110729}, pmid = {41775000}, issn = {1873-2550}, mesh = {Animals ; *Cryptosporidiosis/parasitology/microbiology ; *Probiotics/administration & dosage/pharmacology ; Goats ; Male ; *Goat Diseases/parasitology/prevention & control/microbiology ; Cryptosporidium parvum/physiology ; *Gastrointestinal Microbiome/drug effects ; *Saccharomyces cerevisiae ; Feces/parasitology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cryptosporidiosis, caused by Cryptosporidium parvum, is a major cause of enteric disease and gut microbiota disruption in neonatal ruminants. It can lead to impaired growth, increased susceptibility to pathogens, and long-term gut dysfunction. In this study, we investigated whether supplementation with a live yeast probiotic (Saccharomyces cerevisiae Sc47) could help preserve gut microbiota resilience and functional homeostasis during an experimental C. parvum oral infection in goat kids. Thirty male French Alpine goat kids were assigned to three groups: uninfected control (healthy), infected, and infected with yeast supplementation. Longitudinal 16S rRNA gene sequencing, network analysis, and functional metagenomic predictions were used to assess microbial diversity, community composition, co-occurrence patterns, and metabolic potential, with a focus on short-chain fatty acid (SCFA) biosynthesis. Infection induced marked dysbiosis, characterised by a substantial reduction in microbial richness and a widespread loss of SCFA-producing commensals and metabolic functions. In contrast, yeast supplementation significantly reduced oocyst excretion by more than 84% throughout the experiment, attenuated pathogen-induced community shifts, and maintained beneficial genera such as Butyricicoccus and members of the Oscillospiraceae family. Furthermore, network analysis revealed that probiotic treatment preserved microbial association structures and reduced community fragmentation. Consistent with these findings, functional profiling showed the retention of pathways involved in carbohydrate metabolism, amino acid biosynthesis, and SCFA production, suggesting enhanced microbiota resilience. These findings demonstrate that S. cerevisiae supplementation can mitigate infection-associated dysbiosis by controlling pathogenic overgrowth while sustaining commensal bacterial stability and functional capacity. This highlights its potential as a microbiota-targeted strategy to support gut health in neonatal ruminants.}, } @article {pmid41775040, year = {2026}, author = {Liu, T and Sun, X and Huang, D and Kong, T and Huang, W and Lin, Z and Wang, Z and Li, B and Sun, W}, title = {Differential patterns of antibiotic resistance, virulence, and dissemination risks in floating and sedimented plastispheres.}, journal = {Water research}, volume = {296}, number = {}, pages = {125644}, doi = {10.1016/j.watres.2026.125644}, pmid = {41775040}, issn = {1879-2448}, mesh = {*Geologic Sediments/microbiology ; *Drug Resistance, Microbial/genetics ; Plastics ; Virulence ; China ; Drug Resistance, Bacterial ; Rivers ; }, abstract = {The plastisphere, a unique ecological niche on plastic surfaces, enriches microbial antibiotic resistance genes (ARGs) and virulence factors (VFs), posing environmental and health risks. Although aquatic sediment is a major sink for plastic contaminants, the resistance, virulence and dissemination potentials of sedimented plastispheres remain poorly characterized compared to floating plastics. Through investigation of metagenomes from two sites in the Pearl River in China, one of the world's plastic pollution hotspots, we report that water plastisphere showed 2.4 and 3.6 times more ARG and VF genes than those in sediment plastisphere and surrounding environments, together with higher mobile genetic element (MGE) abundances and a denser ARG-VF co-occurrence network (5,879 vs. 2,874 edges; density 0.043 vs. 0.025), indicating enhanced horizontal gene transfer potential. These differences coincide with contrasting ARG/VF assembly mechanisms, with deterministic and stochastic assembly processes dominating ARG/VF profiles in water and sediment plastispheres, respectively. Genome-resolved analyses further revealed that dominant plastisphere populations harbored multiple ARGs and VFs, with 41 MAGs predicted with pathogenicity capacities, most of which belonged to the families Mycobacteriaceae, Aeromonadaceae, Moraxellaceae, and Pseudomonadaceae. Notably, these taxa have been repeatedly reported as common plastisphere members across diverse ecosystems, suggesting that elevated resistance and virulence in floating plastispheres may be a widespread phenomenon across aquatic ecosystems. Together, our findings demonstrate that floating plastics act as dynamic vectors of antimicrobial resistance and pathogenicity, as well as their dissemination potentials, highlighting water-sediment transition may reduce these ecological risks within the plastisphere.}, } @article {pmid41775186, year = {2026}, author = {Geromino, P and LeMoine, CM and Drahun, I and Cassone, BJ}, title = {Co-supplementation of a polyethylene diet for improved fitness of Galleria mellonella larvae.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141617}, doi = {10.1016/j.jhazmat.2026.141617}, pmid = {41775186}, issn = {1873-3336}, mesh = {Animals ; Larva/growth & development ; *Polyethylene ; *Moths/growth & development/physiology ; Diet ; Animal Feed ; }, abstract = {A growing number of plastivore insects have been discovered that readily consume and biodegrade various petro plastics, including LDPE. The caterpillar larvae of Galleria mellonella are capable of breaking down the polymers at expedited rates; however, feeding on LDPE as a sole nutrient source is inefficient and detrimentally impacts larval survival, growth, and development. The objective of our study was to improve fitness parameters and feeding activities of LDPE-fed larvae through the addition of various macro- and micronutrients. Each co-supplementation recovered fitness and consumption to some extent in comparison to pure LDPE; however, artificial sources produced outcomes that were well below those of the caterpillar's natural diet, regardless of the combination. Co-supplementation of LDPE, honeycomb, and corn syrup was the most successful, with larval fitness and consumption approximating their natural diet. To provide mechanistic insights into this recovery, qPCR and metagenomics analyses indicated the co-supplementation promoted greater gut bacterial abundance and species richness and evenness. In addition, GC-MS analyses identified notable differences in their fat body metabolic profiles that may contribute to slower developmental rates. We also assessed the capability of the larvae to eliminate food wastes, which showed promise and could represent a potential co-supplement source for LDPE biodegradation.}, } @article {pmid41775197, year = {2026}, author = {Lin, L and Su, Z and Yang, X and Yang, F and Zhang, L and Adyari, B and Yang, X and Liu, S and Hu, A}, title = {Impacts of tributaries and sewage effluents on antibiotic resistance genes and pathogens in an urban river.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141641}, doi = {10.1016/j.jhazmat.2026.141641}, pmid = {41775197}, issn = {1873-3336}, mesh = {*Rivers/microbiology ; *Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Environmental Monitoring ; China ; *Bacteria/genetics ; }, abstract = {The dissemination of antibiotic resistance genes (ARGs) within urban rivers presents an increasingly public health threat. This study utilized shotgun metagenomics to assess the distribution, drivers, and risks associated with ARGs and ARG-carrying pathogens (APs) in the Xiaoqing River, focusing on impacts from sewage treatment plant (STP) effluents and tributaries. Results demonstrated significantly elevated ARG and AP abundance and diversity in urban segments and STP effluents relative to upstream and downstream areas. Macrolide-lincosamide-streptogramin resistance genes dominated the urban river resistome. Tributaries were characterized by elevated concentrations of ARGs and identified as important reservoirs. STP effluents introduced APs, including Acinetobacter johnsonii, Enterobacter asburiae and Escherichia coli. Although overall ARG pollution decreased downstream, 44.8% of ARG subtypes and clinically relevant APs persisted, with downstream E. coli strains notably carrying an 8-fold higher ARG load. Mobile genetic elements showed a strong correlation with ARG propagation (R[2] > 0.60, P < 0.001), which may be facilitated by erythromycin and clarithromycin. Semi-quantitative source tracking analysis indicated that tributaries and STP effluents likely represent nonnegligible contributors to ARGs and APs in the urban river. This study demonstrates that sustained urban and tributary discharges drive resistome dissemination, posing persistent risks that require integrated riverine antimicrobial resistance management.}, } @article {pmid41775198, year = {2026}, author = {Xiao, J and Wang, Y and Chen, H and Bu, F and Xu, W and Qiu, S and Kang, Y and Wang, D and Wu, H and Hu, Z and Zhang, J and Guo, Z}, title = {Overlooked fate and associated pathogens of antimicrobial resistance in the Yellow River Delta, China.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141645}, doi = {10.1016/j.jhazmat.2026.141645}, pmid = {41775198}, issn = {1873-3336}, mesh = {*Rivers/microbiology/chemistry ; China ; Wetlands ; *Anti-Bacterial Agents/analysis/pharmacology ; Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; Geologic Sediments/chemistry ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; Water Microbiology ; }, abstract = {The spread of antibiotic resistance genes (ARGs) within terrestrial inputs and marine dispersal in estuarine deltas has posed significant environmental challenges, exacerbated by diverse microbial habitats, estuarine eutrophication, and other anthropogenic impacts. However, the precise mechanisms governing persistence and associated risks of ARGs in this region remain poorly understood. In this study, the distribution, mobility, removal and hosts of ARGs in wetlands and rivers of the Yellow River Delta (YRD) region were systematically investigated through metagenomic approaches. A total of 23 antibiotics were detected in water (0.07-4.67 ng/L) and 14 antibiotics in sediment (0.0042-0.4768 ng/g). Following wetland treatment, despite a 67.5% reduction in antibiotic concentrations, the relative abundance of antibiotic resistance genes decreased by only 7.60%, indicating substantial persistence of genetic resistance. Moreover, Proteobacteria were identified as primary hosts for ARGs. ARGs carried by resistant pathogens, especially ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), also showed a significant reduction in the abundance and diversity throughout the wetland. Notably, total nitrogen in water (Water-TN) greatest shaped the composition of the resistome and microbiome, while the presence of antibiotics exerted stronger selective pressure on ARGs in wetland than in river. Collectively, this study highlights the associated risks of ARGs in YRD, offering insights for controlling antimicrobial resistance in deltas.}, } @article {pmid41775266, year = {2026}, author = {Han, Z and Sun, Z and Zhao, Q and Du, L and Zhen, D and Liu, X and Jiang, S and Liu, YY and Zhang, J}, title = {Competition and compromise between exogenous probiotics and native microbiota.}, journal = {Cell systems}, volume = {17}, number = {3}, pages = {101516}, doi = {10.1016/j.cels.2025.101516}, pmid = {41775266}, issn = {2405-4720}, mesh = {Animals ; *Probiotics/metabolism/pharmacology ; Mice ; *Gastrointestinal Microbiome/physiology/genetics ; *Bifidobacterium animalis/genetics ; Feces/microbiology ; Inulin/metabolism ; Mice, Inbred C57BL ; }, abstract = {Probiotic interventions are effective strategies to modulate the gut microbiome, but how exogenous probiotics compete with native gut microbiota remains elusive. Here, we use a mouse model and a well-documented probiotic, Bifidobacterium animalis subsp. lactis V9 (BV9), to mechanistically investigate its competitive strategies. We perform metagenomic and whole-genome sequencing of stool samples and isolated BV9, longitudinally collected from 24 mice orally administered with BV9 and different diets. Results show that a high-fiber diet most effectively supports the colonization of BV9, where BV9 selectively competes with Parabacteroides distasonis (P. distasonis), rather than extensively with other gut bacteria. By comparing the genomic structures of BV9 and P. distasonis isolated during the washout period, we infer their co-evolution mechanisms, highlighting their competition and compromise in utilizing inulin-derived glucose. Finally, our in vitro co-culture experiments validate such competitive dynamics. This study fills a critical gap in our understanding of niche competition in colonization.}, } @article {pmid41775298, year = {2026}, author = {Luo, J and Yang, S and Feng, Q and Zou, X and Wu, Y and Wang, F}, title = {Triazine-induced extracellular polymeric substance disruption drives metabolic reprogramming and enhanced volatile fatty acid production in anaerobic sludge fermentation.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134322}, doi = {10.1016/j.biortech.2026.134322}, pmid = {41775298}, issn = {1873-2976}, mesh = {*Fatty Acids, Volatile/biosynthesis ; *Fermentation/drug effects ; *Sewage/microbiology ; Anaerobiosis/drug effects ; *Triazines/pharmacology ; *Extracellular Polymeric Substance Matrix/metabolism/drug effects ; *Metabolic Reprogramming/drug effects ; Molecular Docking Simulation ; }, abstract = {The accumulation of antimicrobial contaminants in waste-activated sludge (WAS) posed challenges to anaerobic fermentation processes, with mechanistic impacts on volatile fatty acids (VFAs) production remaining poorly understood. 1,3,5-triazine (triazine), a widely detected triazine-based antimicrobial agent, paradoxically enhanced VFAs production in a concentration-dependent manner, achieving maximum yields of 1771 mg COD/L (18.4-fold increase compared with control). Enhanced production was accompanied by a distinct metabolic shift from propionate to acetate dominance (from 38.7 to 54.3%), driven by systematic disruption of extracellular polymeric substances (EPS), especially proteins. Molecular docking revealed that triazine induced conformational instability and structural damage in proteins through hydrogen bonding and hydrophobic interactions. Meanwhile, the increase in ammonium nitrogen concentration under triazine stress provided further confirmation of the hydrolysis of proteins, providing readily fermentable substrates for VFAs production (particularly acetate). High-throughput 16S rRNA sequencing uncovered concentration-dependent microbial community restructuring, characterized by enrichment of proteolytic bacteria (Petrimonas) and acetate producers (Anaerovorax), concurrent with the suppression of methanogens. Functional metagenomic analysis using PICRUSt2 revealed upregulation of proteolytic enzymes (e.g., EC:3.4.16.4) and acetyl-CoA synthesis genes (e.g., PDHA), facilitating enhanced protein hydrolysis and acetate biosynthesis. Critically, triazine stress activated quorum sensing and two-component regulatory systems, with luxS expression increasing 5.7-fold, promoting metabolic coordination and stress resilience rather than community collapse. Partial least squares path modeling confirmed that substrate availability (λ = 0.459) served as the primary driver of VFAs accumulation, mediated by microbial community adaptation (λ = 0.560). These findings unveil how antimicrobial stress enhanced resource recovery via EPS-mediated metabolic reprogramming.}, } @article {pmid41775307, year = {2026}, author = {Li, Y and Pan, J and Li, Y and Zhao, Z and Zhang, Y}, title = {Direct interspecies electron transfer-based methanogenic aggregate: A survival strategy to overcome defensive attack from type VI secretion system during syntrophic cooperation.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134329}, doi = {10.1016/j.biortech.2026.134329}, pmid = {41775307}, issn = {1873-2976}, mesh = {Electron Transport ; *Type VI Secretion Systems/metabolism ; Sewage/microbiology ; *Methane/metabolism/biosynthesis ; Bioreactors/microbiology ; Rheology ; Hydrogen-Ion Concentration ; Temperature ; Fimbriae, Bacterial/metabolism ; Anaerobiosis ; }, abstract = {Physically tight structure of methanogenic aggregates formed by syntrophic microbes that exchange electrons via interspecies hydrogen/formate transfer (IHT/IFT) can activate defensive attack from type VI secretion system (T6SS), which has been recognized as the primary cause for poor stability. Direct interspecies electron transfer (DIET) may alleviate the technical bottleneck of proximity-triggered defensive attack from T6SS, since syntrophic microbes function long-distance electron transfer via electrically conductive pili (e-pili) or its displayed c-type cytochromes. Here, three up-flow anaerobic sludge blanket reactors, respectively with ethanol, propionate, and butyrate as a sole substrate, were used to culture DIET- and IHT/IFT-based aggregates. DIET-based aggregates were generally larger and exhibited a looser, porous structure compared to IHT/IFT-based aggregates. However, rheological behavior showed that they possessed higher rigidity and toughness, attributed to the structural support of the conductive pili network. 3D reconstruction and imaging of a single DIET-based aggregate by nano-industrial computed tomography showed that syntrophic microbes did not display a pronounced localized aggregation pattern. Conductivity-temperature/pH response showed that the DIET-based aggregates exhibited a metallic-like conductance similar to that found in e-pili. Meanwhile, the surface-enhanced Raman spectra showed that the intensities of characteristic peaks associated with c-type cytochromes in DIET-based aggregates were higher than those in IHT/IFT-based aggregates. Analysis of metagenomic and metaproteomic data showed that in DIET-based aggregates expression of key proteins of T6SS was suppressed. These results demonstrated that in DIET-based aggregates syntrophic microbes did not aggregate to form a physically tight structure, eluding defensive attack from T6SS and strengthening their stabilities.}, } @article {pmid41775707, year = {2026}, author = {Wang, J and Wang, S and Li, T and Hou, W and Deng, Y}, title = {A watershed-scale potential pathogenic bacteria dataset from the Yangtze River Basin.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41775707}, issn = {2052-4463}, support = {42277104//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Rivers/microbiology ; China ; *Bacteria/genetics/pathogenicity/classification ; *Water Microbiology ; Metagenome ; Metagenomics ; Soil Microbiology ; Geologic Sediments/microbiology ; }, abstract = {Microbial safety is fundamental to ensuring water quality, particularly in the Yangtze River Basin, China's most critical drinking water source. Despite its ecological and economic importance, the basin faces significant anthropogenic pressures, including wastewater discharge, which may elevate the risk of pathogenic contamination. However, fragmented sampling efforts and limited coverage have hindered a systematic understanding of pathogenic microbial diversity and distribution across this vast ecosystem. A novel bioinformatic pipeline leveraging Genome-Specific Markers to accurately identify and quantify potential pathogenic taxa in metagenomic data was applied to 625 publicly available metagenomes, spanning water, sediments, and riparian soils along the 6,300 km Yangtze River continuum. We reconstructed a potential pathogen catalog comprising 403 taxa, largely expanding the pathogen diversity in the large river ecosystem. We also generate the Richness distribution maps of potential pathogens for water, sediments and soils along Yangtze River. The basin-scale pathogen inventory not only establishes a baseline for potential pathogenic bacteria communities in the Yangtze Basin but also serves as a reference library for quick biosurveillance and risk management from genomic resolution.}, } @article {pmid41775798, year = {2026}, author = {Nearman, A and Lamas, ZS and Niño, EL and Fine, J and Mayack, C and Seshadri, A and Boncristiani, D and Huang, WF and Evans, JD and Chen, YP}, title = {Metagenomic and gene expression patterns in declining commercial honey bee colonies.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41775798}, issn = {2045-2322}, support = {FSA25IRA0012292//Farm Service Agency/ ; 8130-0960//Animal and Plant Health Inspection Service/ ; }, abstract = {UNLABELLED: Managed honey bee colonies (Apis mellifera) in the US continue to experience high overwinter loss rates driven by parasites, pathogens, poor nutrition, and pesticides. To mitigate these losses, inspection and monitoring are critical for identifying traits of colonies in decline and potential causal factors. In this study, we apply molecular methods to associate potential causative agents with colonies in various stages of decline. Initially, we investigated in-hive bee metagenomic RNA isolated from 15 colonies across seven managed operations in California whose adult bee and brood populations were classified as Strong, Medium, or Weak in strength. We discovered that Weak colonies harbored 2.2- and 3.6- fold more viral species than Medium and Strong colonies, respectively, as well as larger viral read pools despite similar library sizes. They also displayed higher nucleotide variation in Varroa-vectored viruses, indicating associations with high mite populations. When investigating differences in host gene expression, we discovered an upregulation of immune-related pathways in Weak colonies relative to Strong. Specifically, Weak colonies upregulated genes related to wound healing, phagocytosis, oxidative stress resistance, apoptosis, and RNA interference. Most antimicrobial peptides were upregulated in Weak colonies, although defensin1 was significantly higher in Strong colonies, along with several detoxification enzymes and the royal jelly peptide apisimin. Weak colonies also showed an upregulation of transcripts tied to abnormal protein digestion. The low levels of viral replication and fewer species of mite-vectored viruses in Strong colonies may be due to successful Varroa management. Strong colonies also displayed upregulated levels of nine different ubiquinone transcripts, arguably reflecting increasing longevity or a younger in-hive population compared to Weak colonies. Overall, these results provide a detailed account of viral metagenomics and associated host responses, providing new insights into the mechanisms underlying honey bee colony decline under comparable management conditions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42605-w.}, } @article {pmid41775849, year = {2026}, author = {Plewnia, A and Hildwein, T and Quezada Riera, AB and Terán-Valdez, A and Crawford, AJ and Heine, C and Franco-Mena, D and Székely, D and Armijos-Ojeda, D and Siavichay, FR and Arpi, JD and Salazar, J and Erens, J and Páez-Vacas, MI and Székely, P and Böning, P and Stassen, R and Carvajal-Endara, S and Lötters, S and Guayasamin, JM}, title = {Environmental DNA metabarcoding facilitates integrative conservation assessments and species rediscoveries in tropical biodiversity hotspots.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41775849}, issn = {2045-2322}, abstract = {UNLABELLED: Environmental DNA (eDNA) metabarcoding is an emerging and versatile tool in biodiversity research. With recent advances in field sampling techniques, this approach becomes increasingly suited for application in tropical ecosystems where biodiversity monitoring gaps remain significant and species detection is particularly challenging. Using amphibians as a model, we harness eDNA metabarcoding in 52 localities in the Tropical Andean biodiversity hotspot to rapidly trace elusive, threatened, or presumed extinct species as a baseline for conservation action. Metabarcoding ‘bycatch’ of non-target species further revealed specific environmental threats through the detection of invasive species and pathogens, thus facilitating integrative conservation assessments despite the incompleteness of reference data and the vast species richness hampering biodiversity assessments in complex tropical communities. Consequently, we call for more intense employment of eDNA metabarcoding in conservation to rapidly bridge critical knowledge gaps on elusive species or declining populations in tropical biodiversity hotspots.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41937-x.}, } @article {pmid41776033, year = {2026}, author = {Yu, Q and Liu, H and Shi, H and Abdrakhmanov, Y and Shen, J and Zhang, C and Dong, Z and Zong, L and Si, L and Dai, L and Li, Y}, title = {Uncovering evolutionarily remote and highly potent antimicrobial peptides with protein language models.}, journal = {Nature biomedical engineering}, volume = {}, number = {}, pages = {}, pmid = {41776033}, issn = {2157-846X}, abstract = {Identifying evolutionarily remote antimicrobial peptides (AMPs) is crucial for discovering underexplored clinical candidates to combat antibiotic resistance. Existing experimental and computational methods are limited by their reliance on sequence identity to known AMPs, missing distant homologues. Here we introduce HMD-AMP, a protein language model-based approach for AMP discovery. HMD-AMP outperforms previous methods in identifying evolutionarily distant AMPs and enables the discovery of unknown and highly potent AMPs from metagenomic data. Applied to host and gut microorganism genomes of nine mammals, HMD-AMP revealed over 37 million predicted AMPs. Of 91 high-confidence sequences experimentally validated, 74 showed strong antibacterial activity and 48 were evolutionarily remote from known AMPs. Four of these AMPs exhibited broad-spectrum antibacterial activity at low effective concentrations and showed low toxicity, with the most potent peptide demonstrating therapeutic efficacy in a mouse model of peritoneal Escherichia coli infection. This study introduces an effective strategy to uncover AMPs.}, } @article {pmid41776310, year = {2026}, author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA}, title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.}, journal = {Nature aging}, volume = {6}, number = {3}, pages = {682-702}, pmid = {41776310}, issn = {2662-8465}, support = {#00034120//Pew Charitable Trusts/ ; T32 AG052374/AG/NIA NIH HHS/United States ; No. 58-1950-7-707//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; }, mesh = {Animals ; Female ; *Ovary/physiology ; *Gastrointestinal Microbiome/physiology ; *Fecal Microbiota Transplantation ; Mice ; *Aging/physiology ; *Menopause/physiology ; Mice, Inbred C57BL ; Transcriptome ; Fertility ; }, abstract = {The decline in ovarian function with age affects fertility and is associated with increased risk of age-related diseases, including osteoporosis and dementia. Notably, earlier menopause is linked to shorter lifespan, yet the molecular mechanisms underlying ovarian aging remain poorly understood. Recent evidence suggests the gut microbiota may influence ovarian health. Here we show that ovarian aging is associated with distinct gut microbial profiles in female mice and that the gut microbiome can directly influence ovarian health. Using fecal microbiota transplantation from young or estropausal female mice, we demonstrate that heterochronic microbiota transfer remodels the ovarian transcriptome, reduces inflammation-related gene expression and induces transcriptional features consistent with ovarian rejuvenation. These molecular changes are accompanied by enhanced ovarian health and increased fertility. Integrating metagenomics-based causal mediation analyses with serum untargeted metabolomics, we identify candidate microbial species and metabolites that may contribute to the observed effects. Our findings reveal a direct link between the gut microbiota and ovarian health.}, } @article {pmid41776502, year = {2026}, author = {Tümmler, B and Schulz, A and Minso, R and Alfeis, N and Tamm, S and Rademacher, J and Ringshausen, FC}, title = {CFTR activity in nasal potential difference of adults with idiopathic bronchiectasis.}, journal = {Respiratory research}, volume = {27}, number = {1}, pages = {}, pmid = {41776502}, issn = {1465-993X}, abstract = {BACKGROUND: Multiple documented underlying etiologies may lead to bronchiectasis, but the European Bronchiectasis Registry found that in 38% of patients the cause is unknown, referred to as idiopathic. We wanted to resolve the role of CFTR dysfunction in people with idiopathic bronchiectasis by nasal potential difference (NPD) measurements. METHODS: NPD was examined in people with cystic fibrosis (CF), healthy controls, 40 people with idiopathic bronchiectasis recruited from the local outpatient clinic and in 60 people with idiopathic bronchiectasis with the suspected etiology of CF who had been referred from 2010 – 2022 to our electrophysiological laboratory to make a diagnosis by NPD. RESULTS: The unselected MHH cohort and the preselected diagnostic cohort of people with idiopathic bronchiectasis matched in their basal NPD potential with healthy controls. Conversely, after inhibition of the sodium conductance with amiloride, the distribution of the CFTR-mediated depolarization potential upon exposure to chloride-free solution and isoproterenol was in between those of healthy controls and CF patients with exocrine pancreatic insufficiency and overlapped with that of patients with exocrine pancreatic sufficiency. This intermediate phenotype was characteristic for the whole study population of 100 people with idiopathic bronchiectasis irrespectively of whether clinical features of CFTR dysfunction had been recognized before in an individual. Taking the Sermet Score that was developed to discriminate patients with CF from non-CF patients by NPD, the bronchiectasis population was significantly distinct from both healthy people and people with CF. CONCLUSIONS: A CFTR activity of the nasal surface epithelium in the lower quartile is typical for people with idiopathic bronchiectasis, but further CFTR-independent inherited susceptibilities and external insults are necessary to materialize the emergence of bronchiectasis. TRIAL REGISTRATION: Clinical trial number: not applicable.}, } @article {pmid41776697, year = {2026}, author = {Shi, X and Chen, F and Dai, M and Tang, Y and Wang, J and Lin, Y and Shi, M and Lan, T and Liu, H and Jin, X and Xiao, L and Kristiansen, K and Li, X}, title = {Comprehensive catalog of gut microbial genomes in Asian elephants: insights from shotgun metagenomics.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41776697}, issn = {2524-4671}, abstract = {BACKGROUND: The gut microbiota plays a crucial role in metabolism, immune regulation, and ecological adaptation of mammals. Although significant advancements have been made in shotgun metagenomic sequencing and the emergence of algorithms for generation of metagenome-assembled genomes (MAGs), a comprehensive investigation of the gut microbiota at the species level of wild mammals, among these the Asian elephant (Elephas maximus), is still lacking. RESULTS: Here, based on a total of 82 fresh fecal samples collected from Asian elephants residing in distinct regions of the Yunnan Province, we established a comprehensive genome catalog containing 1421 species-level genome bins (SGBs) and a gene catalog comprising 44,596,628 non-redundant genes covering the gut microbiota composition of representative Asian elephant populations. At the species level, 1368 bacteria and 53 archaea were identified, and more than 93% of the SGBs remained unclassified, indicating that there are a large number of potential new species in the Asian elephant gut microbiota. At the functional level, carbohydrate hydrolases, biosynthetic gene clusters, and metabolic pathways dominated the gut microbiome of Asian elephants. Lifestyle and migration affected the composition and functional potential of the gut microbiota of Asian elephants. A northward migration was accompanied by an increase in gut microbiota diversity, an increase in the abundance of the phylum Bacteroidota, and a decrease in the presence of potentially pathogenic genera. In contrast, a southward migration of elephant herds was accompanied by exposure to unfavorable environments, with changes in gut microbiota including increased xenobiotic degradation and metabolic capacity. CONCLUSIONS: We constructed comprehensive catalogs of gut microbial genes and genomes representative for Asian elephant populations, providing a valuable data resource for future research. Our study elucidates migration and lifestyle may modulate the composition and functionality of the gut microbiota in Asian elephants, offering critical insights for monitoring their health and enhancing conservation strategies for wild populations.}, } @article {pmid41777069, year = {2026}, author = {Zamperin, G and Palumbo, E and Castellan, M and Marciano, S and Fusaro, A and Monne, I}, title = {Metagenomic sequencing of zoonotic viruses: evaluation of a CRISPR-Cas-based rRNA depletion system.}, journal = {Veterinaria italiana}, volume = {62}, number = {2}, pages = {}, doi = {10.12834/VetIt.3908.38985.2}, pmid = {41777069}, issn = {1828-1427}, mesh = {Animals ; *CRISPR-Cas Systems ; *Metagenomics/methods ; *RNA, Ribosomal/genetics ; *Zoonoses/virology ; Genome, Viral ; RNA, Viral/genetics ; }, abstract = {Pathogen-agnostic diagnostics are crucial for the early detection of emerging viruses. Shotgun metagenomic sequencing enables unbiased detection of viral genomes but is frequently constrained by the abundance of host and microbial ribosomal RNA (rRNA), which reduces sensitivity and increases sequencing costs. CRISPR-Cas9-based rRNA depletion has emerged as an alternative to enzymatic methods; however, its performance for the characterization of zoonotic viruses across diverse animal hosts and tissues remains underexplored. We compared CRISPR-Cas9 (Jumpcode CRISPRclean™ Plus) and RNase H-based enzymatic depletion (Ribo-Zero Plus, Illumina) using 12 samples positive for rabies lyssavirus, influenza A virus, West Nile virus or norovirus, from multiple host species and tissues, including both high-quality and degraded RNA. CRISPR-Cas9 efficiently reduced rRNA content (14.5%) but recovered fewer viral reads than Ribo-Zero, which achieved up to 60.7× enrichment. Both methods produced complete viral consensus genomes when RNA quality and viral load were sufficient. However, based on the data generated here, enzymatic depletion currently remains more efficient and cost-effective for viral metagenomics. Further optimization of CRISPR-Cas9 workflows could enhance its utility for viral surveillance and diagnostics.}, } @article {pmid41777393, year = {2026}, author = {Zhang, B and Liu, Y and Zhou, D and Lv, Y and Cao, M and Li, H and Yang, Z and Liu, Z and Yin, H and Wang, X and Huang, Z and Meng, D}, title = {The role of quorum sensing in rhizosphere community regulation during bacterial wilt pathogen invasion.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1685007}, pmid = {41777393}, issn = {1664-462X}, abstract = {Bacterial wilt, caused by the soil-borne pathogen Ralstonia solanacearum is a major threat to solanaceous crops worldwide. The onset of this disease is frequently associated with disruptions in the rhizosphere microbial community. Quorum sensing (QS), a key mechanism for microbial communication, plays a critical role in regulating microbial interactions and maintaining community structure. However, whether and how QS is involved in reshaping the rhizosphere microbiome during R. Solanacearum infection remains poorly understood. In this study we compared QS-related genes, signaling pathways, and network structures in metagenomes of healthy and wilt-infected rhizospheres. The results show QS-related genes of the plant beneficial bacterial were significantly down-regulate, whereas QS-related genes of pathogenic R. Solanacearum were up-regulated in wilt-infected rhizosphere. The up-regulated QS genes of pathogens belong to eight QS signaling pathways (AI-1, GABA, PapR, NprX, Phr, cCF10, and DSF). Network analysis showed a simplified structure in the wilt-infected rhizosphere. It is also found the number of connectors in the QS gene co-occurrence network was reduced in wilt-infected rhizosphere network. This is due to the upregulation of QS system allows the pathogen to mediate the rhizosphere microbial ecology network, and leads to destabilization of rhizosphere community. These findings demonstrate that QS system contributes to bacterial wilt infection by suppressing the QS-based interactions among plant beneficial microbes, thereby triggering community function disruption.}, } @article {pmid41777539, year = {2026}, author = {Wang, M and Li, X and Liu, X and Ye, Y and Zhou, P and Liu, Y and Zhu, L and Wei, W and Li, Z and Li, Z and Wu, R and Peng, Y and Liu, Z and Lu, X and Zhao, J and Kan, B}, title = {Restaurant occupational exposure affects the profiles of oral and gut pathobiomes and resistomes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1771459}, pmid = {41777539}, issn = {1664-302X}, abstract = {INTRODUCTION: Restaurant occupational exposure refers to contact with food-processing environments, raw materials, and customers, which may influence the composition of the human microbiome. Differences and associations between human oral and gut pathobiome and their resistomes under restaurant occupational exposure remain unclear. We conducted a comprehensive metagenomic analysis of paired oral and fecal samples from Front-of-House (FOH) workers and Back-of-House (BOH) workers to elucidate the effects of occupational exposure in the restaurant environment on oral and gut pathobiome, antimicrobial resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs).

METHODS: We collected the oral and fecal samples from 35 FOH and 37 BOH workers across 24 Chinese restaurants in Zhengzhou, Henan, China. The diversity and relative abundances of microbial species, ARGs, VFs, and MGEs were compared. Clonal strains from paired oral and fecal samples were analyzed. The serovars of Salmonella were determined using the ucgMLST. Finally, we used the O2PLS method to explore relationships among ARG subtypes, bacterial communities (species-level), MGEs (subtype-level), and plasmids.

RESULTS: The gut microbiome acts as the primary reservoir, exhibiting greater alpha diversity and a higher burden of pathogens/resistomes (including high-risk Rank_I genes). In contrast, the oral microbiome was more sensitive to occupational differences. Significant beta diversity variations in microbiomes, antimicrobial resistance genes (ARGs), and virulence factors were observed exclusively in oral samples. Notably, Salmonella Typhimurium was significantly more prevalent in the oral cavity of BOH workers (R [2] = 0.032, p = 0.047), indicating their potential role as intermediaries in foodborne pathogen transmission. Strain-level analysis confirmed that clonal strains of the opportunistic pathogen and probiotics were shared between the oral cavity and the gut. O2PLS analysis identified plasmids as the main correlates of ARGs.

DISCUSSION: While the gut serves as the primary reservoir for pathogens/resistomes, restaurant occupational exposure distinctly shapes oral microbial/resistome profiles, underscoring the critical need for reinforced hygiene management, particularly for BOH workers, to mitigate pathogen and resistance transmission.}, } @article {pmid41777547, year = {2026}, author = {Maisto, L and Telegrafo, C and Rubino, F and Santamaria, M and Traka, MH and Tullo, A and Bouwman, J and Sbisà, E and Balech, B}, title = {Multifaceted human gut microbiome data associated with health and nutrition.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1722500}, pmid = {41777547}, issn = {1664-302X}, abstract = {The microbiome, also considered the hidden organ, is a fundamental ecosystem directly associated with the disease and health status of the human body. With the availability of high-throughput DNA sequencing technologies, a growing number of studies from clinical and experimental (observation and intervention) samples are constantly revealing new findings on the relationship between human organs and their microbiomes. In such a context, diet and nutrition are among the key factors influencing microbiome composition, richness, and functional behavior. In this review, we illustrate how microbiome-related data and associated metadata are in recent times scattered across primary and specialized databases with different levels of curation, annotation, and standardization, limiting, to some extent, the possibility of deep data discovery, reuse, alignment, and harmonization. Therefore, we describe the way Findable, Accessible, Interoperable, and Reusable (FAIR) data principles would enhance the onset of novel scientific hypotheses and potential microbiome-targeted therapies by improving the standardization policies in data sources. Accordingly, using advanced semantic classification and data mining technologies based on suitable and comprehensive ontologies, annotations of studies present in source databases or in scientific literature would further improve the data and metadata enrichment, integration and alignment relevant to microbiome data associated with health, disease and nutrition.}, } @article {pmid41778161, year = {2026}, author = {Wang, D and Han, J and Wang, X and Wang, J and You, C and Wu, Z}, title = {Lacticaseibacillus rhamnosus B6 alleviates metabolic dysfunction-associated fatty liver disease by suppressing intestinal LPS synthesis and regulating lipid metabolism.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1755982}, pmid = {41778161}, issn = {1664-2392}, mesh = {Animals ; *Lacticaseibacillus rhamnosus/physiology ; Mice ; *Lipid Metabolism/drug effects ; *Lipopolysaccharides/biosynthesis ; Male ; *Probiotics/pharmacology ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; *Non-alcoholic Fatty Liver Disease/metabolism/etiology ; *Metabolic Diseases/metabolism ; Liver/metabolism ; }, abstract = {INTRODUCTION: Metabolic dysfunction-associated fatty liver disease (MAFLD) has become a global epidemic with an unclear etiology and no effective therapeutic options. Disruption of the gut-liver axis driven by intestinal dysbiosis is closely implicated in MAFLD pathogenesis, making gut microbiota-targeted probiotic interventions promising preventive strategies.

METHODS: Lacticaseibacillus rhamnosus B6, a probiotic strain isolated from homemade Bulgarian fermented milk, synthesizes immunomodulatory macromolecules and regulates the intestinal flora. In the present study, we comprehensively investigated the colonization ability and MAFLD-alleviating effects of L. rhamnosus B6 in a high-fat diet (HFD)-induced murine MAFLD model using an integrated approach encompassing metagenomics, untargeted metabolomics, serum biochemical assays, and liver histopathological analysis.

RESULTS: Supplementation with L. rhamnosus B6 markedly decreased the relative abundance of Cupriavidus, Desulfovibrionaceae, and Enterobacteriacea, and inhibited the predicted lipopolysaccharide (LPS) synthesis pathway, thereby suppressing the inflammatory response. Furthermore, L. rhamnosus B6 intervention elevated unsaturated fatty acid levels by modulating lipid metabolic pathways, specifically mitochondrial β-oxidation of long-chain saturated fatty acids, α-linolenic acid, linoleic acid, and sphingolipid metabolism, while downregulating predicted myo-inositol degradation pathways, collectively contributing to MAFLD alleviation. In vitro, the metabolites of L. rhamnosus B6 exerted potent inhibitory activity against LPS-producing bacteria (e.g., Escherichia coli and Salmonella enterica).

DISCUSSION: These findings demonstrate that L. rhamnosus B6 is a promising probiotic for MAFLD alleviation via dual mechanisms of attenuating inflammation and regulating lipid metabolism. This study provides compelling evidence for the specific protective effects of L. rhamnosus B6 against MAFLD and offers a novel probiotic-based therapeutic strategy for MAFLD.}, } @article {pmid41778495, year = {2026}, author = {Lu, J and Bi, H and Zhang, R and Liu, X and Wang, B and Wu, J and Lee, JK and Kalia, VC and Gong, C}, title = {Pesticide Biodegradation Catalyzed by a Cold-Adapted Acetylxylan Esterase Identified from a Metagenome-Assembled Genome.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {10}, pages = {8187-8197}, doi = {10.1021/acs.jafc.5c13419}, pmid = {41778495}, issn = {1520-5118}, mesh = {Cold Temperature ; *Pesticides/metabolism/chemistry ; *Bacterial Proteins/metabolism/genetics/chemistry ; Biodegradation, Environmental ; *Acetylesterase/metabolism/genetics/chemistry ; Metagenome ; Pyrethrins/metabolism ; Substrate Specificity ; Enzyme Stability ; Carbaryl/metabolism/chemistry ; Malathion/metabolism ; Biocatalysis ; Hydrogen-Ion Concentration ; Escherichia coli/genetics/metabolism ; Cloning, Molecular ; }, abstract = {This study identified a putative cold-adapted acetylxylan esterase in Glutamicibacter soli Em07 via a metagenome-assembled genome. The gene encoding this enzyme was cloned and heterologously expressed in Escherichia coli. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis showed that the protein has a molecular weight of 33.24 kDa. Using 1-naphthyl acetate as a substrate, the enzyme activity was optimal at 20 °C and pH 9. Furthermore, the enzyme exhibited excellent cold adaptation, alkali resistance, and salt tolerance. It demonstrated OCP pesticide-degrading activity: 66.48% degradation of carbaryl, 92.14% of cypermethrin, and 97.78% of malathion, underscoring its strong potential in environmental remediation. Notably, this esterase emerged as the first to simultaneously possess cold adaptation, alkali resistance, and salt tolerance. These results positioned the enzyme as a promising candidate for bioremediation strategies in multiextreme environments. Further research will investigate its activity on other persistent organic pollutants.}, } @article {pmid41778780, year = {2026}, author = {Mambuque, E and Del Amo-de Palacios, A and Huete, SG and Marsh, CC and Theron, G and García-Basteiro, AL and Serrano-Villar, S}, title = {Beyond bacilli: integrating the microbiome into the TB research agenda.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2638004}, pmid = {41778780}, issn = {1949-0984}, support = {K43 TW012302/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; *Tuberculosis/microbiology/therapy/diagnosis ; Dysbiosis/microbiology ; Multiomics ; *Gastrointestinal Microbiome ; *Microbiota ; Animals ; Metabolomics ; Antitubercular Agents/therapeutic use ; Lung/microbiology ; }, abstract = {Tuberculosis (TB) remains a leading infectious killer, with growing evidence that the human microbiome-particularly in the gut and lungs-shapes susceptibility, progression, and treatment outcomes. Over the past decade, studies have reported that TB-associated dysbiosis, which is more common in the gut than in the lung, is often marked by the loss of short-chain fatty acid-producing taxa and the expansion of opportunistic microbes. However, findings are frequently confounded by diet, antibiotic exposure, comorbidities, geography, and methodological variability. Most research has relied on compositional profiling, offering limited insight into functional mechanisms. This narrative review synthesizes recent evidence, emphasizing the need to integrate multiomics approaches-metagenomics, metatranscriptomics, and metabolomics-and experimental validation to uncover causal links between microbiome alterations and TB pathogenesis or therapy response. We discuss potential clinical applications, including microbiome-based diagnostics (such as stool-based microbial or metabolite signatures for TB risk stratification), prognostic indicators (such as gut microbiome recovery predicting immune normalization during therapy), and adjunctive interventions (including microbiome-derived products to reduce drug-induced liver injury or fecal microbiota transplantation, which has been shown to be safe in people with HIV on stable ART) to mitigate drug toxicity or enhance immune recovery. Key priorities include methodological standardization, confounder control, mechanistic studies, and the inclusion of high-burden settings. By moving beyond descriptive surveys toward functional, translational research, integrating insights from different microbiome methods into TB prevention, diagnosis, and treatment could redefine the clinical research agenda and open new avenues for precision medicine in this global disease.}, } @article {pmid41778788, year = {2026}, author = {Lee, S and Kim, H-L and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Cho, J and Kim, H-N}, title = {Gut microbial community structure, metabolic signature, and resistome in dyslipidemia: implications for cardiovascular disease management.}, journal = {Microbiology spectrum}, volume = {14}, number = {4}, pages = {e0097125}, pmid = {41778788}, issn = {2165-0497}, support = {RS-2023-NR077149//National Research Foundation of Korea/ ; }, mesh = {Humans ; *Dyslipidemias/microbiology/metabolism ; *Cardiovascular Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Lipid Metabolism ; Cross-Sectional Studies ; Female ; Metagenomics ; Male ; Middle Aged ; }, abstract = {Dyslipidemia, characterized by abnormal blood lipid levels, constitutes a significant risk factor for cardiovascular disease. Emerging evidence indicates that the gut microbiota influences lipid metabolism, although findings across studies have been inconsistent. In this cross-sectional investigation, we analyzed the composition of gut microbiota, associated metabolic pathways, predicted gut metabolites, and the resistome in 1,384 participants (including 895 individuals with dyslipidemia and 489 controls) through shotgun metagenomic sequencing. Our findings demonstrated that Bacteroides caccae was enriched among dyslipidemia cases, potentially contributing to inflammation and altered lipid metabolism. Conversely, Coprococcus eutactus and Coprococcus catus, recognized producers of short-chain fatty acids (SCFAs) involved in lipid regulation, as well as Blautia obeum, known to be positively affected by SCFAs, were more prevalent in the control group. Additionally, we identified an enrichment of the gene family responsible for dTDP-beta-D-fucofuranose biosynthesis, associated with bacterial pathogenicity, in dyslipidemia cases, with Bacteroides stercoris serving as a major contributor. Dyslipidemia cases also exhibited depletion of glycogen and peptidoglycan biosynthesis pathways, which may compromise energy storage and immune function, alongside decreased levels of pseudouridine, a molecule involved in RNA metabolism. Furthermore, a marginal increase in abundance of antibiotic-resistance genes, tetQ, was observed in dyslipidemia cases, suggesting a potential link between the gut resistome and metabolic dysregulation. These results offer novel insights into the role of gut microbiota in the pathophysiology of dyslipidemia and underscore potential microbiome-targeted interventions for metabolic disease management.IMPORTANCEDyslipidemia, characterized by abnormal blood lipid levels, is a significant risk factor for cardiovascular disease. Emerging evidence suggests that the gut microbiota plays a role in lipid metabolism, although findings across studies have varied. This study analyzed the gut microbiota, metabolic pathways, predicted gut metabolites, and antimicrobial resistance genes in 1,384 participants using shotgun metagenomic sequencing. Individuals with dyslipidemia exhibited an imbalance in gut bacteria, including an increase in Bacteroides caccae, a species associated with inflammation, and a decrease in short-chain fatty acid-producing bacteria such as Coprococcus eutactus and Blautia obeum, which support metabolic health. Furthermore, we identified significant changes in microbial metabolic pathways related to energy storage and immune function, as well as an increased abundance of tetracycline resistance genes (tetQ), suggesting a potential link between dyslipidemia and antimicrobial resistance. Our study provides a comprehensive overview of dyslipidemia-associated gut microbial alterations, highlighting potential mechanistic links and therapeutic targets.}, } @article {pmid41778823, year = {2026}, author = {Shean, RC and Tardif, KD and Rangel, A and Dutrschi, J and Bogumil, D and Cruse, A and Hernandez, S and Iremadze, N and Pollock, S and Lipson, D and Bradley, BT}, title = {Evaluation of the Ultima Genomics UG 100 sequencer for low-cost, high-sensitivity metagenomic pathogen detection from cerebrospinal fluid.}, journal = {Microbiology spectrum}, volume = {14}, number = {4}, pages = {e0187425}, pmid = {41778823}, issn = {2165-0497}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods/economics/instrumentation ; *Metagenomics/methods/economics/instrumentation ; *Cerebrospinal Fluid/microbiology ; Streptococcus pneumoniae/genetics/isolation & purification ; Sensitivity and Specificity ; Haemophilus influenzae/genetics/isolation & purification ; Herpesvirus 1, Human/genetics/isolation & purification ; *Meningitis/diagnosis/microbiology/cerebrospinal fluid ; *Encephalitis/diagnosis/microbiology/cerebrospinal fluid/virology ; *Bacteria/genetics/isolation & purification/classification ; Molecular Diagnostic Techniques/methods/economics ; }, abstract = {Clinical metagenomic next-generation sequencing (mNGS) is a diagnostic tool allowing near-universal pathogen detection directly from clinical specimens. Despite promising clinical data, broad adoption of mNGS has been hindered by high cost and reduced sensitivity relative to targeted nucleic acid amplification tests (NAATs). Recently, Ultima Genomics introduced the UG 100 NGS platform which advertises 10 billion reads per $2,400 sequencing wafer. By lowering costs and improving sequencing depth, the historical value proposition of mNGS may be improved. This study evaluates the UG 100 sequencer's ability to generate reads for metagenomic pathogen detection from cerebrospinal fluid specimens. Ultima reads demonstrated 93% (26/28) positive agreement with orthogonal test results and 63% (10/16) negative agreement against a syndromic panel for meningitis and encephalitis. Near full-length genomes were recovered for three organisms (human herpesvirus-1 [HSV-1], Streptococcus pneumoniae, and Haemophilus influenzae), with the ability to detect putative antimicrobial resistance genes for H. influenzae. Recovery of Borrelia burgdorferi reads (6.1 reads per million [RPM] and 9.03 RPM) was achieved from clinical samples with late cycle threshold values (39.7 and 43.0, respectively). Limit of detection (LoD) studies demonstrated detection of HSV-1 and S. pneumoniae reads at concentrations of 50 genomes/mL each, which is below the reported LoD for the orthogonal NAATs used in this study. Reducing sequencing costs and improving the analytical sensitivity remove two major hurdles for mNGS adoption by clinical laboratories. While these results are preliminary, they demonstrate a future in which mNGS may be more widely implemented.IMPORTANCEClinical metagenomic next-generation sequencing has struggled to gain wider adoption for nearly a decade, due in part to its high cost and reduced performance versus targeted molecular assays. This study demonstrates the ability of the UG100 sequencing platform to reduce per-base metagenomic sequencing costs while producing reads that maintain high positive agreement with existing molecular assays. Further improvements to cost and analytical performance may shift clinical metagenomics from an expensive test of last resort to a front-line diagnostic for identifying infections.}, } @article {pmid41779028, year = {2026}, author = {Ladd-Wilson, SG and Fawcett, RW and Park, SY and Venkatasubrahmanyam, S and Lindner, MS and Davis, S and Spry, A and Singleton, J and Karpathy, SE and Paddock, CD}, title = {Rickettsia lanei Rickettsiosis, Oregon, USA, 2025.}, journal = {Emerging infectious diseases}, volume = {32}, number = {4}, pages = {666-668}, pmid = {41779028}, issn = {1080-6059}, mesh = {Humans ; *Rickettsia/genetics/classification/isolation & purification ; *Rickettsia Infections/microbiology/epidemiology/diagnosis ; Oregon/epidemiology ; Animals ; Rocky Mountain Spotted Fever/diagnosis/microbiology ; Metagenomics ; }, abstract = {Using metagenomic sequencing, we identified a patient infected with Rickettsia lanei who was initially diagnosed with Rocky Mountain spotted fever (RMSF), a clinically similar disease caused by infection with R. rickettsii. Our investigation highlights the importance of clinical, epidemiologic, and laboratory partnerships to leverage the discovery of novel pathogens.}, } @article {pmid41780079, year = {2026}, author = {Zhao, B and Xu, Y and Li, F and Song, S and Liu, Z and Liu, J and Liu, Z and Chen, X and Zhou, M and Zhao, L and Wang, X}, title = {Cyclosporine A ameliorates ulcerative colitis by inhibiting cellular senescence, modulating the JAK2-STAT3/NF-κB signaling pathway, and regulating the gut microbiota-metabolite axis.}, journal = {International immunopharmacology}, volume = {175}, number = {}, pages = {116452}, doi = {10.1016/j.intimp.2026.116452}, pmid = {41780079}, issn = {1878-1705}, mesh = {Animals ; *Colitis, Ulcerative/drug therapy/chemically induced/pathology/metabolism/immunology ; Janus Kinase 2/metabolism ; STAT3 Transcription Factor/metabolism ; *Cyclosporine/therapeutic use/pharmacology ; Signal Transduction/drug effects ; Cellular Senescence/drug effects ; *Gastrointestinal Microbiome/drug effects ; NF-kappa B/metabolism ; Mice ; Dextran Sulfate ; Humans ; Mice, Inbred C57BL ; *Immunosuppressive Agents/therapeutic use/pharmacology ; Male ; Disease Models, Animal ; Colon/pathology/drug effects ; }, abstract = {Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease characterized by immune dysregulation, compromised intestinal barrier integrity, and disruptions in the microbiota-metabolite axis. Current clinical management of UC remains limited, underscoring the need for novel therapeutic approaches. Cellular senescence is increasingly recognized as a significant contributor to the pathogenesis of this disease. Senescent cells promote inflammatory responses via the sustained release of pro-inflammatory mediators such as IL-6, IL-1β, and TNF-α. Conversely, persistent inflammation drives further cellular senescence, establishing a self-amplifying cycle that exacerbates disease progression. Additionally, gut microbiota dysbiosis (reduced Akkermansia abundance) and metabolic abnormalities (disrupted bile acid metabolism) may further compromise intestinal barrier integrity. Cyclosporine A (CsA), a classical immunosuppressant, has unclear mechanisms in UC, particularly regarding its potential effects on senescence and the microbiota-metabolite axis. In this investigation, using a dextran sulfate sodium (DSS)-induced UC model, we demonstrated that CsA significantly alleviated DSS-induced acute colitis in mice and senescence-associated pathological changes. Multi-omics analyses integrating network pharmacology, transcriptomics, metabolomics, and metagenomics demonstrated that CsA likely exerts its therapeutic effects through inhibition of the JAK2-STAT3/NF-κB signaling pathway. This leads to reduced release of pro-inflammatory cytokines, modulation of intestinal microbiota composition and metabolite profiles, and enhanced intestinal barrier function.These findings elucidate new mechanisms by which CsA improves DSS-induced colitis in mice through anti-senescence effects and microbiota-metabolic regulation, providing potential therapeutic targets for UC.}, } @article {pmid41780235, year = {2026}, author = {Xin, Y and Liu, LH and Liu, L and Chen, SH and Zheng, YM and Zhao, QB}, title = {Seasonal variation regulates the efficacy of phytoremediation strategies on the rhizosphere resistome in urban river ecosystems.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141647}, doi = {10.1016/j.jhazmat.2026.141647}, pmid = {41780235}, issn = {1873-3336}, mesh = {*Rhizosphere ; *Seasons ; Biodegradation, Environmental ; *Rivers/microbiology ; Ecosystem ; Bacteria/genetics/drug effects ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {Phytoremediation, as a representative nature-based solution, holds significant potential for mitigating the dissemination of antibiotic resistome in urban rivers, which is vital for safeguarding public health and aquatic ecosystems. However, the performance and mechanisms of different phytoremediation strategies (hydroponic or substrate-based strategies) in influencing the rhizosphere resistome across seasonal variation remain poorly understood. This study combined in-situ plant cultivation with metagenomic sequencing and statistical modelling to elucidate rhizosphere resistome dynamics in different phytoremediation strategies. The results showed that the phytoremediation strategies exerted limited influence on the composition and diversity of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), mobile genetic elements (MGEs), and antibiotic-resistant bacteria (ARB). Instead, the above parameters were predominantly regulated by seasonal variation and generally exhibited higher abundances during winter (4.07 ×10[-4]-2.92 ×10[-2]) than summer (3.35 ×10[-4]-2.26 ×10[-2], ANOSIM: R>0.12, P < 0.05). Nonetheless, phytoremediation strategies still led to distinct patterns for the specific resistome (P < 0.05). The relative abundance of specific VFGs was also significantly higher in the substrate-based strategy (7.21 ×10[-4]-8.82 ×10[-4]) than the hydroponic strategy (5.87 ×10[-4]-7.98 ×10[-4]), particularly during summer. The key ARB, such as those belonging to Bacteroidota, showed higher relative abundance in the hydroponic strategy (2.28 ×10[-2]-6.23 ×10[-2]) than substrate-based strategy (1.12 ×10[-2]-3.65 ×10[-2]) across seasonal variation. Mechanistically, rhizosphere exudate-derived dissolved organic matter mediated ARG dynamics by regulating bacterial communities, MGEs, and VFGs (P < 0.05). This study delineates strategy-specific controls of hydroponic and substrate-based phytoremediation on ARG dissemination across seasonal variations, delivering actionable protocols for nature-based solutions optimization in urban rivers.}, } @article {pmid41780243, year = {2026}, author = {Sun, Y and Chen, R and van den Broek, S and Wen, J and Li, Y and Zeng, X and Su, S and Garland, G}, title = {Transmission and migration of antibiotic resistance genes following agricultural fertilization in sloping croplands.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141666}, doi = {10.1016/j.jhazmat.2026.141666}, pmid = {41780243}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Fertilizers ; Agriculture ; China ; *Genes, Bacterial ; Gene Transfer, Horizontal ; Manure ; Metagenome ; Soil/chemistry ; }, abstract = {Livestock manure, a major anthropogenic source of antibiotic resistance genes (ARGs) in agricultural soils due to residual veterinary antibiotics, is commonly used as a nutrient-rich fertilizer on sloping cropland. However, the role of landscape features, particularly topographic heterogeneity in shaping ARG transmission and migration remains poorly understood. In this study, we analyzed 76 metagenomes from five environmental habitats collected along three sloping cropland routes in the Dongting Lake region of China. Soil shared 276 ARG subtypes with other habitats, indicating manure fertilization on slopes facilitates ARGs diffusion across ecosystem. ARG abundance exhibited strong spatial patterns in soil samples, associated with distance from fertilized zones and buffer strips. In fertilized highland soils, mobile genetic elements (MGEs), such as transposases and Insertion Sequence Common Region (ISCRs), were significantly correlated with ARG abundance, indicating active horizontal gene transfer. In unfertilized-lowland soils, ARG composition was primarily influenced by heavy metals, particularly arsenic and cadmium. Source-tracking analysis showed that up to 70.3% of microbes migrated downslope via gravitational runoff, facilitating long-distance ARG dispersal. Risk assessment revealed higher ecological than human health risks, with high-risk ARGs linked to crop pathogens. Our findings highlight the need for landscape-based ARG management strategies within the One Health framework.}, } @article {pmid41780383, year = {2026}, author = {Wang, X and Liu, L and Fan, W and Liu, R and Yuan, H and Li, X}, title = {Enhancing methane production in anaerobic digestion of food waste by Fe-MOF and Fe-MOF-derived carbon composites: Insights into properties, multi-omics analyses, and mechanisms.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129181}, doi = {10.1016/j.jenvman.2026.129181}, pmid = {41780383}, issn = {1095-8630}, mesh = {*Methane ; Anaerobiosis ; Food Loss and Waste ; Multiomics ; Carbon ; Iron ; }, abstract = {In this work, Fe-MOF and Fe-MOF-derived carbon composites (Fe-MDCs) derived at 300, 500, and 700 °C were first applied in anaerobic digestion to achieve efficient renewable energy production from food waste. The enhancement mechanism of methane yield was further explored using metagenomic and metaproteomic analysis. The results showed that compared with the control group, methane yield was enhanced by 9.66%-13.99%, 16.21%-23.56%, and 7.99%-19.84% in Fe-MOF, Fe-MDC-500, and Fe-MDC-700 groups, respectively. Among them, Fe-MDC-500 possessed superior electronic conductivity and a higher specific surface area, which was beneficial for improving methane production by facilitating interspecies electron transfer and providing abundant surface sites for microbial attachment. Metagenomic analysis demonstrated that the functional microorganisms, key genes related to methane metabolism, and the activity of corresponding coenzymes were increased in Fe-MOF, Fe-MDC-500, and Fe-MDC-700 groups. The poor syntrophic interaction resulted in the lowest methane yield under Fe-MOF-300 addition. Metaproteomic analysis indicated that the expressions of proteins related to quorum sensing system, transcription, and translation were also up-regulated, indicating that Fe-MDC-500 potentially promoted microbial communication among methanogenic and symbiotic microorganisms, ultimately boosting the metabolic activity of anaerobic digestion system. Meanwhile, the expressions of vital proteins involved in enzyme synthesis and catalytic bioconversion, including RNA polymerase, Ribosome, and Aminoacyl-tRNA biosynthesis, were significantly upregulated. This research clarified the mechanism of exogenous materials enhanced methane production by elucidating the key metabolic pathways and functional genes, which provided valuable insights for optimizing energy recovery system.}, } @article {pmid41780389, year = {2026}, author = {Du, Y and Zhao, S and Gao, Y and Yan, Y and Kong, Y and Meng, W and Lu, X and Zheng, S and Mu, H and Chen, X and Kong, Q}, title = {The synergistic effect of algal-bacterial granular sludge in a sequencing batch reactor with tetracycline-containing synthetic livestock and poultry breeding wastewater.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129178}, doi = {10.1016/j.jenvman.2026.129178}, pmid = {41780389}, issn = {1095-8630}, mesh = {Animals ; *Tetracycline ; *Wastewater ; *Bioreactors/microbiology ; *Sewage/microbiology ; Poultry ; Livestock ; *Waste Disposal, Fluid/methods ; Anti-Bacterial Agents ; Bacteria ; Water Pollutants, Chemical ; }, abstract = {The concentration of environmental antibiotics, along with their ecological risk, has increased due to the continuous accumulation of livestock and poultry breeding wastewater (LPBW). In this study, two sequencing batch reactors (SBRs) were established-one equipped with algal-bacterial granular sludge (ABGS) and the other with aerobic granular sludge (AGS)-to investigate the treatment performance of tetracycline containing synthetic LPBW. Pollutant removal efficiency and underlying mechanisms were determined by analyzing the physiological and biochemical properties, dynamic changes in the microbial community, and the fate of antibiotic resistance genes (ARGs). Compared to AGS, ABGS resulted in faster granulation and greater lipid production. Exposure to tetracycline significantly altered the contents of extracellular polymeric substances (EPS) and chlorophyll. During the cultivation stage, the removal efficiencies of TN and TP by ABGS were 7.01% and 1.52% higher, respectively, than those by AGS. However, after tetracycline was added, the TN and TP removal efficiencies of ABGS decreased by 0.77% and 6.91%, respectively, compared to those of AGS. The tetracycline removal efficiency of ABGS reached 86.32%, which was 4.49% greater than that of AGS. Metagenomic analysis revealed that the relative abundances of Pseudomonas and Stenotrophomonas (key tetracycline-degrading bacteria) in ABGS were 36.61% and 66.82% greater, respectively, than those in AGS. After tetracycline was added, the relative abundances of tetracycline-related ARGs (tetX and MuxB) increased by 36.01% and 61.68%, respectively, in AGS but decreased by 53.98% and 5.71%, respectively, in ABGS. In this study, ABGS exhibited outstanding performance in enhancing the removal of pollutants from tetracycline-containing synthetic LPBW in SBR systems.}, } @article {pmid41780396, year = {2026}, author = {Xia, R and Shi, T and Liu, W and Li, G and Zhi, S and Luo, W and Xu, Z}, title = {Genome-resolved metagenomic insights into cornstalks-mediated reduction of pathogens and antibiotic resistomes during passively aerated static composting of swine manure.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129185}, doi = {10.1016/j.jenvman.2026.129185}, pmid = {41780396}, issn = {1095-8630}, mesh = {*Manure/microbiology ; Animals ; *Composting ; Swine ; *Drug Resistance, Microbial/genetics ; Zea mays ; Metagenomics ; Anti-Bacterial Agents ; }, abstract = {Passively aerated static composting is widely adopted for livestock manure treatment; however, its efficacy in eliminating antibiotic resistance genes (ARGs) and pathogens is often inadequate due to ineffective oxygen diffusion to restrict organic biodegradation and thus the formation of thermophilic condition. Despite extensive research on aerobic composting, the optimal amendment strategy and mechanistic role of crop stalks in shaping ARG dynamics during passively aerated static composting of swine manure remain unclear. Here, cornstalks and swine manure were representatively selected to elucidate how their passively aerated static composting was successfully initiated to improve ARG elimination using genome-resolved metagenomics and multivariate statistical analysis. Results show that adding 10% cornstalks significantly enhanced antibiotic resistome removal by improving composting properties (e.g. moisture content and oxygen permeability) and increasing temperature (above 65 °C). This improvement effectively inactivated bacterial hosts of ARGs and restrict horizontal gene transfer (HGT). Under these conditions, cornstalk addition promoted thermal inactivation of ARG hosts (e.g. Actinomycetota), particularly pathogenic antibiotic-resistant bacteria (e.g. Corynebacterium), thereby suppressing HGT. More importantly, chromosomally encoded mobile genetic elements (rather than plasmids and viruses) dominated HGT during composting. The transfer of multidrug, bacitracin, and macrolide-lincosamide-streptogramin resistance genes was primarily facilitated by intra-phylum HGT events, particularly within Bacillota. Cornstalk addition significantly accelerated inactivation of pathogens and ARG hosts (e.g. macrolide-lincosamide-streptogramin resistant bacteria), resulting in an increased removal of over 49.0% for both. These findings provide mechanistic insights into the optimization of passively aerated static composting for safe agricultural reuse of livestock manure.}, } @article {pmid41780408, year = {2026}, author = {Wu, H and Qi, F and Huo, Y and Li, R and Ye, M and Topp, E and Qiao, M and Zhu, Y}, title = {Feed additives increase soil risk from antibiotic resistance genes via distinct horizontal gene transfer pathways.}, journal = {Environment international}, volume = {209}, number = {}, pages = {110174}, doi = {10.1016/j.envint.2026.110174}, pmid = {41780408}, issn = {1873-6750}, mesh = {*Gene Transfer, Horizontal ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Copper ; Saccharin ; *Soil Pollutants ; Animal Feed ; }, abstract = {Non-antibiotic components of feed additives can enter farmland soils via livestock manure and accumulate persistently in agroecosystems, presenting potential environmental risks. We established soil microcosms, integrated metagenomes with viromes, and applied a contig-based horizontal gene transfer (HGT)-resolution pipeline to partition vector-level contributions, to assess how saccharin, copper, and their co-contamination affect soil gene flow and health risk. Results indicate divergent vector responses under additive stress: phage-host associations increased under saccharin (82 pairs vs. control 29 pairs), whereas copper strengthened plasmid-host associations. With saccharin, phage nucleotide diversity rose while synonymous nucleotide diversity declined, consistent with stronger purifying selection atop enhanced mutation supply, whereas copper increased lysogeny. Saccharin significantly elevated HGT frequency (∼50% increase), expanded donor-recipient phylogenetic span (class-level P < 0.05), and raised the phage-mediated share (∼100% increase). Copper primarily modestly increased the plasmid-mediated contribution (Cu 2.7%, HS 1.9%). Two-factor analyses revealed a significant antagonistic interaction between saccharin and copper, reducing overall HGT across taxonomic ranks under co-exposure. Although total ARG abundance did not change significantly, the health-risk index increased under saccharin, driven by enhanced ARG-MGE co-occurrence. Under co-contamination, auxiliary metabolic genes were enriched, suggesting phage-conferred metabolic empowerment that mitigates stress, partly explaining the antagonism. Altogether, our findings reveal that feed additives reshape vector-specific gene mobility and ARG risk, and they underpin a three-tiered risk-assessment framework that progresses from mere abundance to network-structured mobility and finally to mobility drivers incorporating phylogenetic transfer distance, offering a more mechanistic basis for soil-health management.}, } @article {pmid41780450, year = {2026}, author = {Li, Z and Li, X and Jiao, B and Yang, Y and Wang, H and Gu, L and Ai, H and Cheng, H and Cheng, S}, title = {Redox oscillations in riparian zone stimulate carbon loss by enhancing microbial respiration.}, journal = {Water research}, volume = {296}, number = {}, pages = {125672}, doi = {10.1016/j.watres.2026.125672}, pmid = {41780450}, issn = {1879-2448}, mesh = {Oxidation-Reduction ; *Carbon/metabolism ; Soil Microbiology ; Iron ; }, abstract = {Redox oscillations within riparian ecosystems emerge as a critical threat to carbon sequestration, yet the mechanistic coupling between abiotic drivers and microbial metabolism remains elusive. Through controlled incubation experiments, we demonstrate that redox-oscillating conditions significantly reduce microbial carbon use efficiency (CUE), thus accelerating carbon loss compared to static oxic or anoxic conditions. Mechanistically, redox oscillations drove the cycling of iron (Fe) species, thereby reducing the amorphous Fe pool and liberating mineral-associated organic carbon (MAOC) composed of substantial biodegradable organic substrates (e.g., lipids and proteins). Concurrently, hydroxyl radicals (•OH) generated during Fe(II) oxidation depolymerize complex aromatic organic matter into labile forms. Integrated metagenomic and metabolomic analyses further demonstrated that redox oscillations significantly reshaped soil metabolite profiles and microbial community. In particular, microbial catabolic pathways such as pentose phosphate pathway and the tricarboxylic acid (TCA) cycle were activated to efficiently mineralize newly available substrate. Together, these results identify a coupled abiotic-biotic "prime and burn" mechanism in which Fe-driven substrate reorganization primes microbial differentiation toward enhanced respiration. This study highlights redox-oscillating zones as potential carbon leakage hotpots in the terrestrial carbon sink.}, } @article {pmid41780551, year = {2026}, author = {Wolf, J and Goggin, KP and Inaba, Y and Allison, KJ and Ahmed, AA and Maron, G and Ferrolino, J and Lazure, L and Kohler, C and Brenner, A and Sun, Y and Tang, L and Gonzalez-Pena, V and Rubnitz, JE and Gawad, C and Margolis, EB and Thomas, P}, title = {Predicting bloodstream infection by plasma cell-free metagenomic sequencing: a prospective cohort study.}, journal = {The Lancet. Microbe}, volume = {7}, number = {4}, pages = {101312}, pmid = {41780551}, issn = {2666-5247}, support = {P30 CA021765/CA/NCI NIH HHS/United States ; R25 CA023944/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Prospective Studies ; Female ; Sensitivity and Specificity ; Male ; Child ; Adolescent ; *Metagenomics/methods ; Child, Preschool ; *Bacteremia/diagnosis/microbiology/blood ; *Cell-Free Nucleic Acids/blood/genetics ; *Sepsis/diagnosis/microbiology/blood ; Infant ; DNA, Bacterial/blood/genetics ; Leukemia/complications ; }, abstract = {BACKGROUND: Patients receiving myelosuppressive chemotherapy or haematopoietic cell transplantation are at high risk for life-threatening bloodstream infections. A novel pre-emptive treatment paradigm guided by pathogen detection before symptoms appear might reduce this risk, but no validated screening test is available. This study evaluated the sensitivity and specificity of plasma microbial cell-free DNA metagenomic sequencing (mcfDNA-Seq) for predicting bloodstream infections in children and adolescents receiving therapy for high-risk leukaemia.

METHODS: In this prospective cohort study, between Aug 9, 2017, and Feb 28, 2022, leftover clinical plasma samples were prospectively collected up to once per day from patients who were younger than 25 years, receiving care for leukaemia at St Jude Children's Research Hospital (Memphis, TN, USA), and at high risk for life-threatening bloodstream infections. mcfDNA-Seq was used to identify pathogen DNA in blood samples obtained during the 7 days before to 1 day after bloodstream infection onset, and in control samples from the same population in the absence of fever or infection. The testing laboratory was masked to sample status. Primary outcomes were predictive sensitivity of mcfDNA-Seq for detecting the expected bloodstream infection pathogen during the 3 days preceding the day of bloodstream infection onset, with a prespecified favourable sensitivity of 50%, and predictive specificity of mcfDNA-Seq in control samples. Exploratory analyses comprised assessing sensitivity and specificity restricted to bacteria or common bloodstream infection pathogens, and after applying a data-derived DNA fragment concentration cutoff; estimating the predictive sensitivity on each of the 7 days before bloodstream infection onset; identifying clinical characteristics that affected predictive sensitivity or specificity; and examining the clinical relevance of additional organisms identified by mcfDNA-Seq during bloodstream infection episodes. Diagnostic sensitivity was also assessed on samples collected on the day of, or day after, diagnosis of bloodstream infection. This study is registered with ClinicalTrials.gov, NCT03226158.

FINDINGS: 94 evaluable bloodstream infections occurred in 60 (38%) of 158 enrolled participants; 19 episodes were previously described in the pilot phase of this study. The predictive sensitivity of mcfDNA-Seq was 51·9% (95% CI 40·5-63·1) for all bloodstream infection episodes, 53·8% (42·2-65·2) for bacterial infection only, and 51·9% (40·5-63·1) when applying a DNA fragment concentration cutoff of 140 molecules per μL. Sensitivity was lowest at day -7 and increased daily until the day of diagnosis. Diagnostic sensitivity was 81·3% (95% CI 71·0-89·1) for all bloodstream infection episodes and 83·1% (72·9-90·7) for bacterial infections only. Predictive specificity was 82·7% (95% CI 76·0-88·2), but improved to 88·9% (83·0-93·3) for common bloodstream infection pathogens, and to 93·8% (88·9-97·0) when also applying the DNA fragment concentration cutoff. Predictive sensitivity was higher in participants with acute lymphoblastic leukaemia (adjusted odds ratio [aOR] 11·1 [1·7-74·2] vs those with acute myeloid leukaemia), and it was lower in polymicrobial infections (aOR 0·0 [0·0-0·2] vs monomicrobial Gram-positive infections). Clinical false-positive results were positively associated with gastrointestinal disturbance alone (p=0·037) or combined with recent administration of high-dose cytarabine (p=0·012). Additional organisms identified by mcfDNA-Seq that were not identified by blood culture were less likely than expected organisms to have an increasing DNA concentration during the days preceding bloodstream infection diagnosis.

INTERPRETATION: mcfDNA-Seq can detect causative pathogens before the onset of some bloodstream infection episodes in profoundly immunocompromised patients. Predictive specificity might be improved by restricting results to a subgroup of relevant organisms, excluding patients with high risk of false-positive results, or applying a higher concentration cutoff. Clinical trials are needed to evaluate mcfDNA-Seq-guided pre-emptive therapy for preventing life-threatening bloodstream infections in patients with high risk.

FUNDING: The National Cancer Institute, American Lebanese Syrian Associated Charities, St Jude Children's Research Hospital, and Karius.}, } @article {pmid41781852, year = {2026}, author = {Eldridge, N and Spörri, L and Kreuzer, M and Haldimann, G and Zinkernagel, MS and Zysset-Burri, DC}, title = {Uncovering the relationship between the human ocular surface microbiome and gut microbiome.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41781852}, issn = {1471-2180}, support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; }, abstract = {BACKGROUND: The human body harbors diverse microbial communities that play essential roles in health and disease. While the gut microbiome (GM) has been extensively studied and linked to numerous systemic conditions, the ocular surface microbiome (OSM) remains less well understood due to its low microbial biomass and technical challenges in sequencing. Previous work has suggested possible connections between gut dysbiosis and ocular disease, but whether the OSM and GM are directly related remains unclear.

RESULTS: This study investigated the relationship between the ocular surface microbiome (OSM) and the gut microbiome (GM) by analysing matched samples from both niches in the same individuals. Using high-throughput sequencing, we characterised microbial composition and diversity at each niche, followed by statistical analysis to show common taxa. A Mantel test was applied to assess potential correlations between the two microbial communities. Our results revealed no significant correlation between the composition of the OSM and GM, neither in structure nor in diversity.

CONCLUSION: This study suggests that the two niches are shaped independently, likely due to their distinct environmental conditions and microbial densities. These findings highlight the uniqueness of each microbiome and underscore the need for niche specific approaches when investigating host microbiome interactions.

TRIAL REGISTRATION: ClinicalTrials.gov, TRN: NCT02438111, Registration date: 28 April 2015, and TRN: NCT 04658238, Registration date: 01 December 2020.}, } @article {pmid41781872, year = {2026}, author = {Tian, N and Liu, M and Zhao, Y and Lian, Y and Jin, M and Yang, F}, title = {Gut microbiota dysbiosis and metabolic reprogramming in pediatric migraine: a multi-omics analysis revealing diagnostic biomarkers.}, journal = {The journal of headache and pain}, volume = {27}, number = {1}, pages = {}, pmid = {41781872}, issn = {1129-2377}, support = {2022 Budget Approval No. 180 of Hebei Provincial Department of Finance//Provincial Medical Outstanding Talents Project funded by the Provincial Government in 2022/ ; Grant No. 20260868//Hebei Provincial Medical Science Research Project funded by the Health Commission of Hebei Province/ ; 2026 Hebei Provincial Introduction of Foreign Intelligence Project//Hebei Provincial Department of Science and Technology/ ; }, abstract = {BACKGROUND: Numerous studies have identified disruptions in the gut microbiota of patients with migraine, and the role of the gut–brain axis in the pathogenesis and development of migraine has been established. The incidence of migraine in children increases with age, yet the intestinal microbiota in pediatric migraine has been inadequately investigated. Therefore, we aim to investigate the composition, functional characteristics, and metabolite profiles of the gut microbiota in children with migraine. METHODS: We recruited 30 children with migraine and 30 healthy controls aged 5–14 years from Hebei Province, China, and collected 60 fresh fecal samples. Metagenomic sequencing was performed to obtain species abundance profiles and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotations of gene sequences. Non-targeted metabolomic analysis was applied to assess differential changes in gut microbiota metabolites between children with migraine and healthy controls. RESULTS: The abundance of gut microbiota species was significantly reduced in children with migraine (P = 0.001), and was associated with migraine presence (R2 = 0.051, P = 0.001). Bacteria within Pseudomonadota were significantly enriched in the gut flora of children with migraine, with Escherichia coli being the most abundant species. The propionic acid, the arginine and proline metabolism pathways were significantly upregulated in children with migraine (P < 0.05). In contrast, the porphyrin metabolism pathway, amino acid biosynthesis pathway, and arginine biosynthesis pathway were significantly down-regulated (P < 0.05). The intestinal lipopolysaccharide biosynthetic pathway showed diagnostic potential for pediatric migraine, with an Area Under the Curve (AUC) of 0.75 (95% CI: 0.63–0.87). Intestinal metabolites were also dysregulated in children with migraine; notably, Docosahexaenoyl Ethanolamide (DHEA) and kynurenic acid were significantly depleted (P < 0.05). CONCLUSION: This study revealed an association between gut microbiota and its metabolite in children with migraine, suggesting that the potential pathogenic role of gut microbiota may be mediated by the functions of Pseudomonadota and Escherichia coli and by the levels of metabolites derived from them. Furthermore, this study provides strong evidence for the diagnostic potential of kynurenic acid in pediatric migraine and supports future targeted metabolite research.}, } @article {pmid41781883, year = {2026}, author = {Xie, Y and Wang, R and Liu, X and Du, Q and Mo, S and Liu, Q and Yang, G and Fan, Z and Li, J}, title = {Metagenome-assembled genomes from the gut microbiome of spontaneous diabetic macaques provide insights into microbes associated with type 2 diabetes mellitus.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41781883}, issn = {1471-2180}, support = {32171607//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Gut microbiota plays a crucial role in type 2 diabetes mellitus (T2DM) pathogenesis. Spontaneous T2DM macaques offer a valuable model for investigating contributions of gut microbiota to T2DM pathogenesis due to physiological similarities to humans and the absence of glucose-lowering drug interference.

RESULTS: We performed de novo assembly of metagenome-assembled genomes (MAGs) to explore the diversity and function of the gut microbiome at the genome level. We obtained 317 non-redundant MAGs from fecal metagenomes of macaques and 325 MAGs from humans, 168 of which were potential novel species. Most members of Lachnospiraceae, the main carriers of carbohydrate-active enzymes (CAZymes) and virulence genes, significantly increased in the guts of T2DM macaques and unmedicated T2DM patients. Further analysis on the MAGs of Lachnospiraceae identified concordant enrichment of potential microbial signatures of T2DM, including the macaque-derived Eubacterium_Q sp900314445 (Mm_bin23) and human-derived Eubacterium_F sp003491505 (Hs_bin20) and Eubacterium ramulus (Hs_bin147). They all carried intestinal barrier-associated virulence genes and diabetes-associated hypervirulence genes, which might be associated with barrier dysfunction, inflammation, and disrupt glucose homeostasis, thereby potentially contributing to the pathogenesis of T2DM.

CONCLUSIONS: This study assembled extensive MAGs from the gut microbiome of spontaneous T2DM macaques and asymptomatic controls. Furthermore, we identified three Eubacterium genomes harboring virulence genes and diabetes-associated genes, which were significantly enriched in both T2DM macaques and T2DM humans, highlighting the potential roles of these microbes in T2DM pathogenesis. Overall, this study provides a critical foundation for elucidating gut microbiome-mediated mechanisms and developing targeted therapeutic strategies for T2DM.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04902-2.}, } @article {pmid41781897, year = {2026}, author = {Liu, D and Yu, S and Tian, X and Wang, Z and Lu, Y and Dai, Y and Hu, C and Ma, X and Mao, M and Xue, L and Yi, Z and Zhang, G and Li, S and Wang, Q and Zhang, Z and Tian, Z}, title = {Epidemiological investigation of an acute gastroenteritis outbreak associated with norovirus GΙΙ.17[P17] in a cross-border travel group - Shanghai Port, China, 2024.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41781897}, issn = {1471-2334}, support = {2024HK149//General Administration of Customs Project/ ; 2022YFC2302800//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Caliciviridae Infections/epidemiology/virology ; *Norovirus/genetics/isolation & purification/classification ; *Gastroenteritis/epidemiology/virology ; *Disease Outbreaks ; China/epidemiology ; Female ; Male ; Travel ; Adult ; Middle Aged ; Phylogeny ; }, abstract = {BACKGROUND: Norovirus is a leading cause of acute gastroenteritis and spreads efficiently in closed, mobile cohorts such as organized travel groups. This case is notable for the real-time detection and genomic confirmation of a cross-border outbreak at a port of entry, including near-identical Norovirus GΙΙ.17[P17] genomes and documented asymptomatic carriage, illustrating the practical value of integrated metagenomic surveillance in border health operations.

CASE PRESENTATION: On July 21, 2024, 26 travelers arrived at Shanghai Port after a 12-day group tour in Europe. Clinical interviews identified 15 individuals (57.7%) with diarrhea, nausea, dizziness, and abdominal pain; no hospitalizations occurred. On-site anal swab testing was negative for SARS-CoV-2, influenza A and B, Vibrio cholerae, and Escherichia coli. RT-qPCR detected Norovirus GII in 10 samples (38.5%), including two asymptomatic individuals. Metagenomic sequencing generated near-complete genomes for all RT-qPCR-positive samples, which were 99.9-100% identical and classified as Norovirus GΙΙ.17[P17], confirming a cross-border outbreak within the travel cohort. Prompt public health response measures were initiated by Shanghai Customs and CDC authorities.

CONCLUSIONS: This case demonstrates the feasibility and impact of rapid, genomically informed surveillance at the border for detecting and characterizing travel-associated enteric virus outbreaks. The findings underscore the need for robust port-of-entry monitoring, rapid diagnostics, and integrated genomic analysis to mitigate transmission in group travel settings.}, } @article {pmid41781966, year = {2026}, author = {Srivastava, AK and Mishra, P and Kumari, S and Uddin, N and Chen, S and Zhao, Y and Xie, X}, title = {Post translational modifications as biomarkers of soil microbe responses to nano-pesticides.}, journal = {Journal of nanobiotechnology}, volume = {24}, number = {1}, pages = {}, pmid = {41781966}, issn = {1477-3155}, support = {32272514//National Natural Science Foundation of China/ ; }, mesh = {*Protein Processing, Post-Translational/drug effects ; *Soil Microbiology ; Biomarkers/metabolism ; *Pesticides/toxicity ; Microbiota/drug effects ; *Nanoparticles/toxicity/chemistry ; }, abstract = {Nano-pesticides represent a significant technology advancement in modern agricultural, offering improved target specificity and reduced chemical load. However, their potential to induce subtle, sub-lethal disturbance in soil microbial function remains poorly resolved and is not adequately capture by conventional indicators such as microbial diversity, abundance, or bulk enzymatic activity. The central novelty of this review lies in proposing post-translational modifications (PTMs) as functional, early-warning biomarkers for nano-pesticide induced microbial stress, providing a molecular resolution that bridges exposure and ecological outcome. This review critically examines the current evidence on nano-pesticides-microbiome interaction and PTM-centric framework to interpret microbial responses at the protein regulation level. We highlight phosphorylation, acetylation, and ubiquitination regulate microbial stress responses, modulating detoxification enzymes, efflux pumps, and cellular signalling pathways under nanoparticle-induced stress. Unlike prior reviews that emphasize toxicity endpoints or gene-level responses, this work integrates metaproteomic evidence demonstrating PTM enrichment within stress-responsive functional protein groups across real environmental datasets, underscoring their relevance as conserved biomarkers of adaptive and maladaptive responses. By integrating metagenomics with metaproteomic and metabolomics, this review illustrates how PTM profiling enables mechanistic insight into microbial adaptation, functional impairment, and resilience under nano-pesticide pressure. Furthermore, we introduce a systems-level perspective that combines PTM data with computational modelling and AI-assisted bioinformatics to predict microbiome shifts and ecological risk, an approach not previously synthesized within the context of nano-pesticide assessment. Collectively, this review bridges nanomaterial design, microbial molecular regulation, and environmental risk evaluation, and proposes PTM-based assessment as a new paradigm for developing microbiome-safe, eco-compatible nano-pesticides and advancing molecular environmental monitoring strategies.}, } @article {pmid41782011, year = {2026}, author = {Wang, X and Tian, S and Zhang, Y and Yang, L and Hu, D and Wang, Z and Yang, X and Li, S and Wei, J and Zhou, W and Wang, S and Deng, L and Li, F and Hou, S and Li, P and Ru, J}, title = {Bacteria and phage consortia modulate cecal SCFA production and host metabolism to enhance feed efficiency in ducks.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41782011}, issn = {2049-2618}, support = {CARS-42-2//China Agriculture Research System of MOF and MARA/ ; 32341055//National Natural Science Foundation of China/ ; 273124240//Deutsche Forschungsgemeinschaft/ ; 226-2025-00030//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; *Ducks/microbiology/metabolism ; *Cecum/microbiology/metabolism ; *Fatty Acids, Volatile/metabolism/biosynthesis ; *Bacteriophages/genetics/physiology/classification ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenome ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Propionates/metabolism ; Butyrates/metabolism ; }, abstract = {BACKGROUND: The gut microbiota influences poultry health, nutrition, feed efficiency (FE), and overall productivity. However, the relationship between gut microbes, including bacteria and phages, and FE in ducks remains underexplored. To address this, we integrated cecal 16S amplicon, metagenome, microbiota-derived short-chain fatty acids (SCFAs) profiling, liver transcriptome, and serum metabolome data to illustrate the contribution of the gut microbiome (bacteria and viruses) to duck FE.

RESULTS: We reconstructed viral genomes and prokaryotic metagenome-assembled genomes (MAGs) and annotated their genes using comprehensive databases. Prokaryotic hosts of viruses were also predicted to understand virus-host dynamics within the gut ecosystem. Our results revealed that high-FE ducks have higher concentration of propionate and butyrate in cecum compared with low-FE ducks. The metagenome sequencing revealed distinct cecal microbiota profiles between two groups, with increased relative abundance of representative SCFA producers, especially Paraprevotella sp905215575 and Bacteroides sp944322345, and enhanced SCFA-biosynthesis pathways in high-FE ducks. Virome genome assembly identified two phages encoding auxiliary metabolic genes (AMGs) involved in pyruvate metabolism, enhancing nutrient availability for host bacteria to produce SCFAs (e.g., temperate phage-encoded pyruvate phosphate dikinase) or exploiting host central metabolic pathways for viral replication (e.g., lytic phage-encoded formate C-acetyltransferase). Furthermore, these representative SCFA-producing bacteria and phage consortia were associated with serum metabolites (including L-histidine and 4-hydroxydecanedioylcarnitine) linked to duck FE.

CONCLUSION: Collectively, these findings provide novel insights into the gut microbial factors regulating FE in ducks, offering potential strategies to optimize poultry nutrition and productivity. Video Abstract.}, } @article {pmid41782139, year = {2026}, author = {Mao, K and Zang, Y and Wang, C and Yang, W and Lu, G and Qiu, Q and Ouyang, K and Zhao, X and Song, X and Liang, H and Xu, L and Qu, M and Li, Y}, title = {Rumen microbiota-associated stress alleviation by creatine pyruvate in newly received cattle: a multi-omics study.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41782139}, issn = {2049-2618}, support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; No. 3230810//the National Natural Science Foundation of China/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology ; Multiomics ; *Stress, Physiological/drug effects ; Mice ; *Creatine/pharmacology/administration & dosage ; Metabolomics ; *Gastrointestinal Microbiome/drug effects ; *Pyruvic Acid/metabolism/pharmacology ; Prevotella/drug effects ; Metagenomics ; Fatty Acids, Volatile/metabolism ; }, abstract = {BACKGROUND: Stress experienced by newly received cattle is a significant challenge in the beef industry, frequently resulting in weakened immune responses and impaired growth. The rumen microbiota is essential to host health, and its imbalance can exacerbate stress. This study investigates the mechanisms by which creatine pyruvate (CrPyr) mitigates stress in newly received cattle through multi-omics approaches, including metagenomics, metabolomics, in vitro and in vivo experiments, and rumen microbiota transplantation (RMT) in mice.

RESULTS: Our results revealed that CrPyr significantly reduces stress-related hormones (cortisol and adrenocorticotropic hormone) and inflammatory markers (IL-6, IL-1β, and TNF-α), and enhanced antioxidant capacity (SOD: 57.38 versus 46.93 U/mL, P < 0.05; GSH-Px: 305.87 versus 217.07 U/mL, P < 0.05; T-AOC: 9.62 versus 7.66 U/mL, P < 0.05). Metagenomic analysis demonstrated that CrPyr increased Prevotella abundance, a key rumen bacterium involved in volatile fatty acid (VFA) production, and enriches metabolic pathways associated with energy metabolism (ATP synthesis, and pyruvate metabolism) and antioxidant defense (glutathione metabolism, FC = 1.08, P < 0.05). In vitro and in vivo experiments, as well as RMT studies in mice, further validate these findings, demonstrating that CrPyr promote VFA synthesis and increased ATP production through the electron transport phosphorylation pathway.

CONCLUSIONS: CrPyr modulates the abundance of ruminal Prevotella in transport-stressed cattle to enhance glutathione and VFA metabolism and to accelerate ATP and nucleotide synthesis, thereby alleviating stress in newly received cattle. This multimodal approach established CrPyr as an effective nutritional intervention that improves rumen function and increases livestock productivity. Video Abstract.}, } @article {pmid41782849, year = {2026}, author = {Fang, T and Hu, P and Zhang, Y and Hu, B and Miao, Q}, title = {Chronic Mycobacterium kansasii Pleural Infection Mimicking Metastatic Breast Cancer: A Seven-Year Diagnostic Odyssey and the Critical Role of Metagenomic Sequencing.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {580064}, pmid = {41782849}, issn = {1178-6973}, abstract = {INTRODUCTION: Nontuberculous mycobacteria such as Mycobacterium kansasii can mimic malignancy on imaging and pathology, leading to prolonged diagnostic uncertainty and inappropriate anticancer therapy.

CASE REPORT: A 76-year-old woman with remote right breast carcinoma (mastectomy and adjuvant therapy in 1996) had a persistent right chest-wall lesion with rib changes and encapsulated pleural effusion repeatedly interpreted as metastatic disease from 2017 to 2023, despite multiple biopsies showing only fibrous hyperplasia. In August 2024, fever and cough prompted re-evaluation. PET-CT demonstrated a hypermetabolic pleura-adjacent lesion (SUVmax 10.8) without distant metastases. Plasma metagenomic next-generation sequencing (mNGS) yielded a low-level M. kansasii signal; pleural fluid mNGS identified 146 reads (94% relative abundance), later confirmed by culture. Targeted anti-NTM therapy stabilized the infection; however, the patient developed severe varicella-zoster virus infection and cardiac complications and subsequently died. The death was attributed to these complications rather than the progression of the M. kansasii infection.

CONCLUSION: Chronic M. kansasii pleural infection can masquerade as metastatic breast cancer for years. PET-CT alone is insufficient to distinguish infection from malignancy; careful imaging review combined with unbiased mNGS can establish the diagnosis and avert unnecessary anticancer therapy. Multidisciplinary collaboration is essential for timely recognition and management.}, } @article {pmid41783251, year = {2026}, author = {Nibbering, B and Nooij, S and Harmanus, C and Sanders, IMJG and Miedema, IM and Ducarmon, QR and Vossen, RHAM and Kloet, SL and Ardis, CK and Britton, RA and Yousefi, F and Bayne, J and Charavaryamath, C and Law, A and Murphy, ML and Sponseller, B and Burrough, ER and Ramirez, A and Mooyottu, S and Opriessnig, T and Kuijper, EJ and Roestenberg, M and Smits, WK}, title = {Characterization of the clade 4 non-toxigenic C. difficile isolate L-NTCD03 carrying the cfr(B) gene.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag010}, pmid = {41783251}, issn = {2633-6685}, abstract = {Clostridioides difficile infection (CDI) is a toxin-mediated gastro-intestinal disease. Yet, C. difficile is a phylogenetically diverse species that includes many non-toxigenic strains. In general, these are understudied, despite having significant potential impact for our understanding of the colonization process and as therapeutic modalities. Here, we present an in-depth characterization-including the complete genome sequence-of the non-toxigenic C. difficile strain L-NTCD03. This strain belongs to PCR ribotype 416, clade 4 and multilocus sequence type 39. It is resistant to multiple antimicrobials, but not those used for treatment of CDI. We validated the relevance of the cfr(B) gene from this strain in antimicrobial resistance to clindamycin, linezolid, retapamulin, and streptogramin A. We found the L-NTCD03 strain to be non-toxic in various assays. Altogether, L-NTCD03 is a promising candidate for developing into a live biotherapeutic product.}, } @article {pmid41783404, year = {2026}, author = {Liu, D and Ma, Y and Ma, Q and Huang, H and Li, T and Wang, J and Zhang, J and Cheng, X and Ge, X and Chen, Y and Zhang, Y}, title = {Clinical pathogen profiles and lung microbiome features in lung infection patients and concurrent cancer: insights from metagenomics next-generation sequencing.}, journal = {Open life sciences}, volume = {21}, number = {1}, pages = {20251220}, pmid = {41783404}, issn = {2391-5412}, abstract = {Pulmonary infections in immunocompromised cancer patients present significant diagnostic and therapeutic challenges. From Dec 2021 to Aug 2023, 85 patients with pulmonary infection were enrolled and categorized into a cancer group (CP, n = 20) and a non-cancer control group (NCP, n = 18). Pathogen detection was performed using both mNGS and culture and lung microbiome analysis was conducted. mNGS demonstrated a significantly higher pathogen detection rate than culture (P < 0.0001). The CP group exhibited older age (P < 0.001), elevated neutrophil counts (NE) and higher procalcitonin (PCT) levels compared to the NCP group. Furthermore, fungal pathogens were significantly more prevalent in the CP group (P = 0.046). Both cancer status and advanced age were independent influencing factors for the detection of pulmonary fungi. Pulmonary microbiome analysis revealed no significant differences in α-diversity or β-diversity between groups. These findings indicate that mNGS offers superior sensitivity over culture. Cancer-related pulmonary infections present a distinct pathogen profile characterized by a higher prevalence of fungal pathogens. This underscores the need for enhanced clinical vigilance, especially among elderly cancer patients.}, } @article {pmid41783570, year = {2026}, author = {Lin, H and Zhu, XY and Xue, CX and Yao, P and Fu, L and Yang, Z and Zhang, XH and Moreau, JW}, title = {Metagenomics reveals diverse community of putative mercury methylators across different biogeochemical niches in Sansha Yongle blue hole.}, journal = {Marine life science & technology}, volume = {8}, number = {1}, pages = {206-220}, pmid = {41783570}, issn = {2662-1746}, abstract = {UNLABELLED: Methylmercury (MeHg) is a potent neurotoxin and bioaccumulates in food webs. Microbial transformation of inorganic mercury (Hg) produces most of the MeHg in the marine environment. The gene pair hgcAB encodes for Hg methylation, a process predominantly attributed to anaerobic bacteria. However, recent studies indicate the formation of methylmercury in low-oxygen zones within marine water columns, although the mechanisms remain poorly understood. "Blue holes" are marine sinkholes containing redox gradients stratified with depth and high microbial diversity across a range of biogeochemical cycles. Here, we present the first metagenomic analysis focused on the potential for Hg methylation in a blue hole ecosystem. Yongle Blue Hole (YBH), currently the world's deepest known blue hole, was selected as a representative site to investigate the genetic potential for Hg methylation and to explore the functional capabilities of putative Hg-methylators within this unique environment. Metagenomic analysis showed that the anoxic sulfidic deep water was likely to be a hotspot for Hg methylation, driven by abundant and diverse Deltaproteobacteria. In the suboxic intermediate layer, Nitrospina and Myxococcota dominated the Hg-methylating community. Furthermore, Hg methylators were found to have different lifestyles (free-living or particle-associated) and to occupy distinct ecological niches within the YBH. In addition, the contribution of sinking particles to Hg methylation, especially in the deep anoxic water column, was highlighted. Our study unveils the biodiversity and survival strategies of Hg methylators across distinct environments. The findings suggest that blue holes could serve as model stratified ecosystems for studying Hg methylation processes across different habitats.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00332-7.}, } @article {pmid41784027, year = {2026}, author = {Mekonnen, YT and Indio, V and Lucchi, A and Manfreda, G and Serraino, A and De Cesare, A}, title = {Detection of Chlamydia ibidis in the neck skin microbiome of broiler carcasses at the end of slaughter.}, journal = {Italian journal of food safety}, volume = {15}, number = {2}, pages = {}, pmid = {41784027}, issn = {2239-7132}, abstract = {Chlamydia is the etiological agent of chlamydiosis in wild and domestic birds, mammals, and humans. In this study, Chlamydia reads were detected in the microbiome of the neck skin of 76 broiler carcasses collected in the same slaughterhouse at the end of the chilling tunnel. The carcasses originated from four different flocks of female Ross 308, reared in two broiler houses located in Northern Italy. One flock from each poultry house was sampled in 2019, and one flock in 2023. The carcass neck skin microbiome was investigated by shotgun metagenomic sequencing. Chlamydia reads displayed a mean relative abundance of 7.38%, with significant differences between carcasses obtained from the two poultry houses, sampled at both sampling times. Chlamydia ibidis was the prevalent species among time points and poultry houses. The zoonotic potential of C. ibidis and foodborne transmission have never been demonstrated. However, it is known that the genus Chlamydia has "spore"-like extracellular forms able to survive for months outside the host. Therefore, the presence of C. ibidis reads on broiler carcasses at the end of the chilling tunnel deserves further investigation. The results of this study highlight the feasibility of microbiome investigations to detect unexpected biological hazards in foods.}, } @article {pmid41784373, year = {2026}, author = {Aizpurua, O and Martin-Bideguren, G and Gaun, N and Alberdi, A}, title = {Grass supplementation to a pellet-based diet fails to enrich gut microbiomes with wild-like functions in captive-bred hares.}, journal = {Microbiology spectrum}, volume = {14}, number = {4}, pages = {e0369125}, pmid = {41784373}, issn = {2165-0497}, support = {CF20-0460//Carlsbergfondet/ ; DNRF143//Danmarks Grundforskningsfond/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Animals, Wild/microbiology ; *Hares/microbiology/metabolism ; *Poaceae/metabolism ; *Animal Feed/analysis ; Diet ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Dietary Supplements/analysis ; Metagenome ; Metagenomics ; }, abstract = {Reintroducing captive-bred animals into the wild often faces limited success, with the underlying causes frequently unclear. One emerging hypothesis is that maladapted gut microbiota may play a significant role in these challenges. To investigate this possibility, we employed genome-resolved metagenomics to analyze the taxonomic and functional differences in the gut microbiota of 45 wild and captive European hares (Lepus europaeus), as well as to assess the impact of fresh grass supplementation to a pellet-based diet aimed at pre-adapting captive hares to wild conditions. Our analyses recovered 860 metagenome-assembled genomes, with 87% of them representing novel species. We found significant taxonomic and functional differences between the gut microbiota of wild and captive hares, notably the absence of Spirochaetota in captive animals and differences in amino acid and sugar degradation capacities. While grass supplementation induced some minor changes in the gut microbiota, it did not lead to statistically significant shifts toward a more wild-like microbial community. The increased capacity for degrading amino acids and specific sugars observed in wild hares suggests that, instead of bulk grass, dietary interventions tailored to their specific dietary preferences might be necessary for pre-adapting hare gut microbiota to wild conditions.IMPORTANCEThis study sheds light on the role of gut microbiota in the success of reintroducing captive-bred animals into the wild. By comparing the collection of 860 near-complete genomes of wild and captive European hares, we identified significant taxonomic and functional differences, including the absence of key microbial groups in captive hares. Grass supplementation to a pellet-based diet yielded limited success in restoring a microbiota similar to that of wild counterparts, highlighting the need for more tailored approaches to mimic natural diets. With 87% of recovered microbial genomes representing novel species, this research also enriches our understanding of microbial diversity in wildlife. These findings emphasize that maladapted gut microbiota may hinder the survival and adaptation of reintroduced animals, suggesting that microbiome-targeted strategies could improve conservation efforts and the success of animal rewilding programs.}, } @article {pmid41784805, year = {2026}, author = {Shen, J and Gao, J and Gao, L and Yan, D and Wang, Y and Meng, J and Li, H and Chen, D and Wu, J}, title = {Melatonin ameliorates autistic-like behaviors by restoring gut microbiota-derived tryptophan metabolites.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {83}, number = {1}, pages = {}, pmid = {41784805}, issn = {1420-9071}, support = {2023-MS-310, 2019-BS-098//Natural Science Foundation of Liaoning Province/ ; LJKQZ2021149//Scientific Research Fund of Liaoning Provincial Education Department/ ; }, abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social deficits and repetitive stereotyped behavior. Disrupted microbiota‒gut‒brain axis (MGBA) signaling contributes to the pathology of ASD and cognitive disability. Melatonin (MT), a naturally occurring compound, has shown potential in ameliorating core symptoms of ASD and mitigating gut microbiota dysbiosis, yet the underlying mechanism is poorly understood. This study aimed to investigate whether exogenous melatonin improves behavioral deficits in valproic acid (VPA)-exposed male offspring rats, and the modulation of gut microbiota-derived tryptophan metabolites. In prenatal VPA-induced model rats, microbial diversity and construction was analyzed through metagenomic sequencing, targeted-metabolomics and transcriptomics were conducted to explore related metabolic pathways and molecular profiles. We identified 7 gut bacterial genus causally associated to ASD: Faecali-bacterium, Lachnospiraceae, Ruminococcaceae, Butyricimonas, and Bacteroides exhibited protection, whereas Erysipelotrichaceae and Clostridia enhanced risk. The exacerbation of Erysipelotrichaceae and Clostridia by VPA versus restoration of Faecalibacterium, Butyricimonas, Bacteroides and Bifidobacterium by melatonin, which are known to participate in tryptophan metabolism. Correspondingly, systemic metabolomics pointed to melatonin’s restoration of tryptophan metabolic disorders (IDO1-kynurenine, TPH1/2-serotonin-melatonin, and Indole-3-propionic acid (IPA)) induced by VPA, paralleled the rectification of microglial reactivity, synaptic proteins, dendritic morphology, and hippocampal neurogenesis. These molecular profiles were further integrated by transcriptomics, highlighted tryptophan-derived neurotransmitters and neuroactive ligand-receptor interaction, contributing to enhanced social and cognitive behaviors under melatonin intervention. Based on multi-omic analysis, our findings underscore key bacteria and metabolites contributing to neurological and immune dysfunction in VPA-exposed rats, providing novel targets for possible therapeutics of melatonin.}, } @article {pmid41785052, year = {2026}, author = {Roy, P and Roy, D and Bhattacharjee, S and Ghosh, A and Saha, S}, title = {MDPD reveals specific microbial signatures in human pulmonary diseases.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {2}, pages = {}, pmid = {41785052}, issn = {1477-4054}, mesh = {Humans ; *Microbiota ; *Lung Diseases/microbiology ; Bacteria/genetics/classification ; *Databases, Factual ; }, abstract = {Pulmonary diseases are becoming a serious threat worldwide, and enormous data from different human microbiomes have been generated to understand these complex diseases. Here, we introduce Microbiome Database of Pulmonary Diseases (MDPD), an open-access, comprehensive systemic catalog of pulmonary diseases by manually curating global studies from 2012 to 2024 (13 years). We have compiled 59 362 runs from 430 BioProjects, encompassing data from 10 body sites related to 19 pulmonary diseases and healthy groups covering 278 distinct sub-groups. MDPD enables users to analyze each BioProject and customize analysis with multiple BioProjects to identify taxonomic profiles and disease group/sub-group specific microbial signatures. The re-analyzed intermediate Biological Observation Matrix files are provided for each BioProject for the accessibility of users for further applications, such as machine learning-based classification. Identified microbes (bacteria, fungi, viruses) in MDPD are annotated with several attributes, providing further insights into their disease-causing potential and specificity to certain diseases and body sites. MDPD is freely available at: https://bicresources.jcbose.ac.in/ssaha4/mdpd/.}, } @article {pmid41785249, year = {2026}, author = {Pucci, N and Kaan, AM and Ujčič-Voortman, J and Verhoeff, AP and Zaura, E and Mende, DR}, title = {Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome.}, journal = {PLoS computational biology}, volume = {22}, number = {3}, pages = {e1013185}, pmid = {41785249}, issn = {1553-7358}, mesh = {Humans ; *Mouth/microbiology ; *Microbiota/genetics/physiology ; Infant ; Female ; Metagenome/genetics ; Phylogeny ; Metagenomics ; Longitudinal Studies ; }, abstract = {Early-life oral microbiome development is a complex community assembly process that influences long-term health outcomes. Nevertheless, microbial functions and interactions driving these ecological processes remain poorly understood. In this study, we analyze oral microbiomes from a longitudinal cohort of 24 mother-infant dyads at 1 and 6 months postpartum using shotgun metagenomics. We identify two previously undescribed Streptococcus and Rothia species to be among the most prevalent, abundant and strongly co-occurring members of the oral microbiome of six-month-old infants. By leveraging metagenome-assembled genomes (MAGs) and genome-scale metabolic models (GEMS) we reveal their genomic and functional characteristics relative to other infant-associated species and predict their metabolic interactions within a network of co-occurring oral taxa. Our findings highlight unique functional features, including genes encoding adhesins and carbohydrate-active enzymes (CAZymes). Metabolic modeling identified potential exchange of key amino acids, particularly ornithine and lysine, between these species, suggesting metabolic cross-feeding interactions that may explain their co-abundance across infant oral microbiomes. Overall, this study provides key insights into the functional adaptations and microbial interactions shaping early colonization in the oral cavity, providing testable hypotheses for future experimental validation.}, } @article {pmid41785480, year = {2026}, author = {Shekarriz, S and Vigod, SN and Bianco, T and Bala, A and Hao, C and Allard, JP and Hota, S and Poutanen, S and Surette, MG and Taylor, VH}, title = {The Safety, Efficacy, and Feasibility of Fecal Microbiota Transplantation in a Population With Bipolar Disorder During Depressive Episodes: A Pilot Parallel Arm Randomized Controlled Trial: Sécurité, efficacité et faisabilité de la transplantation de microbiote fécal chez une population atteinte de troubles bipolaires, au cours d'épisodes dépressifs : essai pilote contrôlé à répartition aléatoire et à groupes parallèles.}, journal = {Canadian journal of psychiatry. Revue canadienne de psychiatrie}, volume = {}, number = {}, pages = {7067437261420877}, pmid = {41785480}, issn = {1497-0015}, abstract = {BackgroundThe gut microbiome has been proposed as a potential modifiable target to treat mental illness. This double-blind randomized control trial investigated fecal microbiota transplant (FMT) in bipolar disorder (BD) to assess efficacy, safety, and feasibility. The primary outcome evaluated the effectiveness of standard approved therapy for BD depression + FMT in individuals not responding to standard treatment, measured by change in the Montgomery-Åsberg Depression Rating Scale (MADRS) score from baseline to week 24. Secondary outcomes included FMT's impact on anxiety, global function, side-effects, and safety. The feasibility of this novel intervention was also assessed. Microbial analysis utilized whole-genome shotgun metagenomic sequencing, comparing outcomes between allogenic (donor) and autologous (participants own) FMT.MethodsA total of 35 participants (28 women and 7 men) with at least moderate depressive-phase BD (MADRS) were randomized to receive either allogenic FMT (n = 17) or autologous FMT (n = 18) via colonoscopy and were followed for 24 weeks.ResultsMADRS scores significantly improved from baseline to the last visit in both treatment arms. There was no significant difference between allogenic FMT (16.74-point improvement) and autologous FMT (15.4-point improvement) regarding clinical efficacy (t = -0.47, p-value = .64, 95% confidence interval [CI] = -7.3-4.6). Microbiota analysis showed that allogenic FMT let to a bacterial profile similar to the healthy donor and increased bacterial diversity at the 6-month mark, whereas those receiving autologous FMT did not. The intervention was well tolerated with no significant adverse events. Recruitment, randomization, and retention metrics support feasibility of a larger trial.ConclusionFeasibility and tolerability data indicate further investigation into microbial manipulation in BD is warranted. The absence of efficacy differences between the two types of FMT, despite microbial change, highlights the importance of a true placebo in future studies, as well as the importance of understanding exactly what bacteria are linked to improvements. ClinicalTrials.gov, NCT0327922.}, } @article {pmid41785576, year = {2026}, author = {Poirier, S and Rondeau-Leclaire, J and Faticov, M and Roy, A and Lajeunesse, G and Lucier, JF and Tardif, S and Kembel, SW and Ziter, C and Laprise, C and Paquette, A and Girard, C and Laforest-Lapointe, I}, title = {Season and city shape urban bioaerosol composition beyond vegetation and socioeconomic gradients.}, journal = {The Science of the total environment}, volume = {1023}, number = {}, pages = {181623}, doi = {10.1016/j.scitotenv.2026.181623}, pmid = {41785576}, issn = {1879-1026}, mesh = {Aerosols/analysis ; *Air Microbiology ; Cities ; Seasons ; *Environmental Monitoring ; *Air Pollutants/analysis ; Plants ; Socioeconomic Factors ; Fungi ; *Air Pollution/statistics & numerical data ; Canada ; }, abstract = {Urban vegetation varies with socio-economic gradients, as lower-income neighborhoods often host sparser and less diverse green spaces. This disparity may affect respiratory health by influencing exposure to bioaerosols. Understanding the characteristics of this aerobiome could help anticipate risks related to allergies and other respiratory conditions. Here, we hypothesized that urban vegetation cover and socio-economic status shape urban bioaerosol dynamics. We sampled bioaerosols at 65 sites across three Canadian cities of varying population size and density using an active air sampler over four months, and characterized their bacterial, fungal, and plant particles composition using amplicon sequencing. Seasonal alpha diversity varied significantly for fungi and plant particles. Based on beta diversity, sampling period alone explained up to 40% of plant particle, 29% of fungal, and 11% of bacterial bioaerosol composition variation. In contrast, vegetation cover explained only a minor portion of the variance in bioaerosol composition, and median household income, almost none. These findings provide a critical baseline for understanding the urban aerobiome and highlight the need to study how vegetation identity and diversity, rather than cover alone, may shape bioaerosol dynamics in cities. As cities grow and urban greening initiatives expand, demystifying the aerobiome dynamics becomes an urgent public health priority.}, } @article {pmid41785649, year = {2026}, author = {Dong, W and Ye, T and Zhang, Z and An, L and Peng, Y and Chen, Y and Zhang, Y and Ke, L and Chen, S and Zhao, S and Hu, Y}, title = {Quorum sensing-associated acid adaptation in bacterial communities during pit fermentation of sauce-flavor Baijiu.}, journal = {International journal of food microbiology}, volume = {453}, number = {}, pages = {111715}, doi = {10.1016/j.ijfoodmicro.2026.111715}, pmid = {41785649}, issn = {1879-3460}, mesh = {*Quorum Sensing ; Fermentation ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Adaptation, Physiological ; Food Microbiology ; *Fermented Foods/microbiology/analysis ; Lactic Acid/metabolism ; Microbiota ; Hydrogen-Ion Concentration ; }, abstract = {Sauce-flavor Baijiu is produced by multi-round solid-state fermentation under progressively increasing acidity, yet how bacterial communities adapt to this extreme acid stress and whether quorum sensing (QS)-associated features are involved remain unclear. Here, fermented grains from eight pit-fermentation rounds under both traditional and mechanized processes were analyzed by metagenomic sequencing and physicochemical profiling. The traditional process showed higher moisture, stronger and faster acidification, greater lactic acid accumulation, and more rapid depletion of reducing sugars and starch than the mechanized process. These conditions coincided with a sharper decline in bacterial α-diversity and convergence toward a community overwhelmingly dominated by Acetilactobacillus jinshanensis (>90%) in the traditional process, whereas the mechanized process maintained higher diversity and a multi-species core dominated by A. jinshanensis, Lactobacillus acetotolerans, Bacillus, and actinomycetes. Canonical correspondence analysis identified acidity (lactic acid) as a major environmental factor associated with these divergent trajectories. QS gene profiling revealed process-specific signatures, with the LuxS/AI-2-associated module being the most abundant QS-related feature and significantly enriched in the traditional process. Functional annotation uncovered coordinated enrichment of acid-adaptation genes (ATPF1A, clpP, ATPF1B, dnaK, and groEL) during mid-to-late stages under high acidity. Network analysis further highlighted tighter co-associations among A. jinshanensis, QS modules, and acid-adaptation genes, supporting a community-level QS-associated functional framework for ecological convergence. Collectively, this study links LuxS/AI-2-associated features to acid-adaptation capacity and A. jinshanensis dominance in high-acidity environment. These findings provide ecological insight into microbial resilience in high-acidity solid-state fermentations and offer QS-informed perspectives for future targeted validation in Baijiu production.}, } @article {pmid41786226, year = {2026}, author = {Li, Y and Wang, WJ and Zhang, S and Luo, Q and Qian, NF and Chen, DZ and Jin, RC and Feng, LJ and Yang, GF}, title = {Chaotic effects in completely autotrophic nitrogen removal over nitrite process: how minor dissolved oxygen variations reshape microbial community and functional genes to drive divergent nitrogen removal.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134333}, doi = {10.1016/j.biortech.2026.134333}, pmid = {41786226}, issn = {1873-2976}, mesh = {*Oxygen/metabolism ; *Nitrogen/isolation & purification/metabolism ; *Nitrites/metabolism ; Bioreactors/microbiology ; *Autotrophic Processes ; *Bacteria/metabolism/genetics ; *Genes, Bacterial ; Oxidation-Reduction ; }, abstract = {To elucidate how dissolved oxygen (DO) regulates nitrogen removal in the completely autotrophic nitrogen removal over nitrite (CANON) process, three continuous-flow reactors were operated under micro-aerobic conditions. Results revealed that minor DO variations (0.36-0.51 mg/L) triggered dramatic bifurcation in performance and microbial ecology, demonstrating chaotic effects characterized by nonlinear dynamics and sensitive dependence on initial conditions. A superior total nitrogen removal rate of 0.38 kg/m[3]/d and a NH4[+]-N removal efficiency of 86.7% were achieved at 0.36 mg/L DO. However, a slight increase to 0.51 mg/L DO significantly enhanced nitrite-oxidizing bacteria (NOB) activity and nitrate accumulation. Lower DO favored anammox bacteria and their essential genes (hzs/hdh), while elevated DO promoted NOB competition and oxidative stress responses, evidenced by Fe-Mn SOD gene upregulation and altered extracellular polymers composition. Our findings establish a direct link between minor DO fluctuations and macro-scale functional outcomes, providing a mechanistic framework for predicting and controlling CANON process.}, } @article {pmid41786734, year = {2026}, author = {Gao, M and Delgado-Baquerizo, M and Xiong, C and Sáez-Sandino, T and Wang, J and Liang, J and Guirado, E and Muñoz-Rojas, M and Román, R and Maestre, FT and Singh, BK}, title = {Dominance and natural suppression of bacterial plant pathogens across global soils.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41786734}, issn = {2041-1723}, support = {DP230101448//Department of Education and Training | Australian Research Council (ARC)/ ; }, mesh = {*Soil Microbiology ; Ralstonia solanacearum/genetics/isolation & purification ; *Plant Diseases/microbiology ; Streptomyces/genetics/isolation & purification ; Soil/chemistry ; Clavibacter/genetics/isolation & purification ; *Plants/microbiology ; Climate Change ; *Bacteria/genetics ; Mycorrhizae/genetics ; Metagenome ; Ecosystem ; }, abstract = {Soils are the primary environmental reservoir of plant pathogens impacting food production and ecosystem productivity worldwide. Yet, some soils can also suppress pathogens through environmental and microbial regulation. Here we integrate 1602 soil metagenomes from 59 countries with a greenhouse experiment to identify 32 dominant pathogens, including Ralstonia solanacearum, Clavibacter michiganensis, and Streptomyces europaeiscabiei. Pathogen hotspots occur primarily in warm ecosystems and agricultural soils, whereas higher soil microbial diversity, increased soil organic carbon and colder climatic conditions are associated with lower pathogen prevalence. Non-pathogenic Streptomyces spp., arbuscular mycorrhizal fungi, and biosynthetic gene clusters encoding terpenes and polyketides are associated with reduced pathogen prevalence. Predictive modelling suggests that several dominant bacterial pathogens are likely to increase in prevalence under future climate scenarios, particularly in tropical and subtropical regions. By identifying global drivers of dominant pathogens and their suppression, this study provides a foundation for improved surveillance and management of plant disease risks under climate change.}, } @article {pmid41786735, year = {2026}, author = {Wen, Y and Gao, M and Wang, Z and Liu, X and Zhang, Y and Lin, G and He, P and Yang, H and Xiao, Y and Lyu, W}, title = {Dietary copper-driven colonic dysbiosis mediates oxidative stress and butyrate deficiency to facilitate the spread of resistome in pigs.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41786735}, issn = {2055-5008}, support = {10417000025CE0615G//State Key Laboratory for Managing Biotic and Chemical Threats to the Safety of Agro-products/ ; 32372907//National Natural Science Foundation of China/ ; LR25C170001//Natural Science Foundation of Zhejiang Province/ ; }, mesh = {Animals ; *Oxidative Stress/drug effects ; Swine ; *Butyrates/metabolism ; *Copper ; *Dysbiosis/microbiology/veterinary/chemically induced ; *Colon/microbiology ; Feces/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Copper Sulfate ; Dietary Supplements ; Diet ; Drug Resistance, Bacterial ; Metagenomics/methods ; Animal Feed/analysis ; }, abstract = {Copper-induced transmission of antimicrobial resistance has been well documented in livestock farming environments, but the in vivo mechanisms driving fecal resistome development remain unclear. Here, 120 mg/kg CuSO4 and copper-peptide were supplemented to piglets, and the fecal resistome development was first analyzed by metagenomic sequencing. In this study, dietary CuSO4 drove abundant and diverse ARGs and MRGs. Following CuSO4 deprivation, ARGs and copper resistance exhibited a persistent promotion, whereas most MRGs rapidly declined. The resistance development was characterized by abundant MGEs. This phenomenon expanded the multiple-antibiotic resistance reservoir in fecal community, which was preferentially harbored by pathogens. Furthermore, dietary CuSO4 disturbed colonic homeostasis, characterized by impaired epithelial integrity and reduced butyrate-producing bacteria abundance, which coincided with an oxidative stress environment and increased prevalence of multiple-resistant pathogens, such as Escherichia coli and Enterococcus spp. In vitro validation further supported these associations, showing that butyrate supplementation and hypoxic conditions alleviated Cu[2+]-induced ROS generation and reduced the frequency of ARGs conjugative transfer. Overall, this study suggests that dietary inorganic copper may contribute to microbial disturbances linked to oxidative stress and potentially facilitate antimicrobial resistance transmission among pathogens, highlighting organic copper as a sustainable alternative for mitigating resistance risks in farmed animals.}, } @article {pmid41786764, year = {2026}, author = {Franciosa, I and Castelnuovo, G and Cantele, C and Cardenia, V and Bo, S and Ponzo, V and Goitre, I and Pontonio, E and Tortarolo, D and Verni, M and Bugianesi, E and Cordero, F and Beccuti, M and Cocolin, L and Ferrocino, I}, title = {Gut microbiome modulation by cricket, pea, and whey protein using the SHIME in vitro simulator.}, journal = {NPJ science of food}, volume = {10}, number = {1}, pages = {}, pmid = {41786764}, issn = {2396-8370}, support = {D17G22000150001//NODES funding from the MUR - M4C2 1.5 of PNRR, funded by the European Union - NextGenerationEU, Mission 4 Component 1.5 - ECS00000036/ ; }, abstract = {Entomophagy is increasingly popular, and Acheta domesticus offers an ecologically sustainable protein alternative, but the effects on the human gut microbiome need further investigation. In this study, we investigated the impact of the intake of three isolated proteins: pea (plant), whey (animal), and cricket (insect) on gut microbiome of a single-donor using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). Cricket protein intake was associated with potential beneficial taxa such as Bifidobacterium and Lactobacillus, genes related to vitamin biosynthesis and bacteriocin transport, and short and medium-chain fatty acids. Pea protein intake was associated with Faecalibacterium and Slackia, while whey protein with Butyricimonas and Lactobacillus. Metagenomic analysis revealed that pea intake led to increased lysine degradation genes, promoting SCFAs production. Each protein has its own unique characteristics that may contribute positively to gut health. Specifically, cricket protein intake appears to have beneficial effects, promoting the growth of potentially beneficial taxa and enhancing short-chain fatty acid production. The results of this study indicate that cricket protein does not exhibit any detrimental effects compared to pea and whey proteins.}, } @article {pmid41786809, year = {2026}, author = {Nagy, NA and Laczkó, L and Freytag, C and Tóth, RB and Nagy, SV and Sramkó, G and Barta, Z}, title = {Draft genomes of two Lethrus species.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41786809}, issn = {2052-4463}, mesh = {Animals ; *Coleoptera/genetics ; *Genome, Insect ; }, abstract = {The superfamily Scarabaeoidae is a species-rich and diverse group within the order Coleoptera. The members of this taxon are of interest due to the diversity of their feeding and mating behaviour, and their ecological importance. Despite the size of the superfamily, only a few genomes have been published, leaving a large gap in our understanding of the evolution of these beetles. To reduce this gap, we generated third-generation sequencing data to describe the first genome assembly of Lethrus scoparius and to improve the assembly of Lethrus apterus. The genome of L. scoparius consists of 2,873 contigs with an N50 value of 301,243 bp. BUSCO analysis revealed 98.1% complete ortholog hits in the Endopterygota ortholog database. For the L. apterus genome, we were able to assemble 886 scaffolds with an N50 value of 1,378,308 bp and a complete BUSCO hit of 96.8%. We assigned functions to 15,252 genes in L. scoparius and 15,520 in L. apterus. These genomes may contribute to understanding the evolution of the superfamily.}, } @article {pmid41786830, year = {2026}, author = {Nowak, RG and Gough, E and Holm, JH and Hu, F and Akinyombo, K and Okudo, C and Ozumba, PJ and Jonathan, EC and Tiamiyu, AB and Kokogho, A and Adebajo, SB and Shoyemi, E and Baral, SD and Lombardi, K and Peel, S and Lim, JN and Gaydos, CA and Manabe, YC and Sears, CL and Shardell, M and Ravel, J and Crowell, TA and Tuddenham, S}, title = {Metagenomic analysis reveals rectal microbiota features associated with HIV and behavioral factors in Nigerian men who have sex with men.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41786830}, issn = {2045-2322}, support = {R21 AI156765/AI/NIAID NIH HHS/United States ; U54 EB007958/EB/NIBIB NIH HHS/United States ; R01MH099001/MH/NIMH NIH HHS/United States ; R21AI156765//National Institute of Allergy and Infectious Diseases/ ; R01MH099001/MH/NIMH NIH HHS/United States ; }, abstract = {UNLABELLED: Emerging data suggest unique features characterize the rectal microbiota of men who have sex with men (MSM) and people living with HIV (PLWH). The microbiota may have important health implications in these groups, but most studies have been conducted in the United States or Europe. This study leveraged metagenomic sequencing to evaluate relationships between rectal microbiota composition and clinical, behavioral and demographic characteristics in a cohort of Nigerian MSM. PLWH with suppressed viral load had lower α-diversity (richness) compared to people without HIV (PWoH), with similar trends for PLWH with an unsuppressed viral load. Lower α-diversity (Shannon) was associated with use of petroleum jelly lubricant for anal sex. Lower relative abundance of the genus Prevotella was seen in PLWH with a suppressed viral load versus PWoH. There were differences in abundance of the top 20 taxa associated with age, HIV status (enhanced in virally suppressed PLWH versus PWoH), lubricant use, receptive anal intercourse, and condom use, suggesting multiple clinical and behavioral factors impact the rectal microbiota. Future characterization of health outcomes associated with the rectal or gut microbiota in MSM and PLWH as well as potential interventional insights will necessitate larger, dedicated studies across diverse geographic locations.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42119-5.}, } @article {pmid41787122, year = {2026}, author = {Panagiotou, K and Geesink, P and Köstlbacher, S and de Zwaan, GH and Ettema, TJG}, title = {Diversity, ecology, cell biology and evolution of the Asgard archaea.}, journal = {Nature reviews. Microbiology}, volume = {24}, number = {6}, pages = {377-391}, pmid = {41787122}, issn = {1740-1534}, mesh = {*Archaea/genetics/classification/physiology ; Phylogeny ; *Biological Evolution ; Evolution, Molecular ; Genome, Archaeal ; *Biodiversity ; Genetic Variation ; }, abstract = {The Asgard archaea are a clade of archaea that was first discovered through metagenomic surveys of marine sediments. The past decade has witnessed a substantial expansion of their genomic diversity, revealing diverse metabolic repertoires and providing insights into their ecological interactions and function. Notably, comprehensive phylogenomic analyses, together with the identification of numerous eukaryotic signature proteins in Asgard archaeal genomes, have provided compelling evidence that Asgard archaea had a central role in the emergence of eukaryotes. Studies have reported the characterization of cultured Asgard archaeal representatives, uncovering unique cell biological characteristics hinting at thus far undescribed lifestyles. Here, we review the current state of the research field focusing on these intriguing microorganisms and outline future research directions aiming to resolve their ecology, cell biology and evolution.}, } @article {pmid41787125, year = {2026}, author = {Schleper, C and Rodrigues-Oliveira, T}, title = {Asgard archaea: have we found our microbial ancestors?.}, journal = {The EMBO journal}, volume = {45}, number = {6}, pages = {1836-1851}, pmid = {41787125}, issn = {1460-2075}, support = {W1257//Austrian Science Fund (FWF)/ ; EFP 25//Austrian Science Fund (FWF)/ ; }, mesh = {*Archaea/genetics/ultrastructure ; *Biological Evolution ; Cell Cycle ; *Eukaryota ; Genome, Archaeal ; Metagenomics ; Organelle Biogenesis ; Protein Biosynthesis ; Symbiosis ; Transcription, Genetic ; }, abstract = {The discovery of Asgard archaea about a decade ago has greatly reshaped our understanding of archaeal evolution and the origin of eukaryotes. Asgards are currently thought to be the closest prokaryotic relatives of eukaryotes and to represent the archaeal host lineage that participated in the endosymbiotic event leading to the first eukaryotic cell. The presence of numerous eukaryotic signature proteins in Asgard genomes supports this view and provides important insights into the deep evolutionary roots of eukaryotic cellular complexity. However, the close relationship between archaea and eukaryotes had been observed for decades, based on features that are shared in different molecular processes. This review discusses the discovery of Asgard archaea in the broader context of archaeal molecular and cellular biology and highlights how earlier findings foreshadowed their emergence. Primarily targeted at newcomers to the field, the review provides an overview of evolutionary innovations across the Archaea domain and discusses molecular and cellular features of cultivated Asgard strains in light of previous archaeal research.}, } @article {pmid41787208, year = {2026}, author = {Fiola, TE and Rathore, RS and Akinbi, GO and Mwashote, B and Badisa, VLD and Chen, G and Ibeanusi, V}, title = {Investigation of water quality and microbial diversity in Mississippi's major land resource area.}, journal = {Environmental science and pollution research international}, volume = {33}, number = {10}, pages = {4231-4255}, pmid = {41787208}, issn = {1614-7499}, support = {NR204423XXXXC125-F1-SA1-21//U.S. Department of Agriculture/ ; TOA/PO-NO: 0000663592//U.S. Department of Energy/ ; DE-EM0005308//U.S. Department of Energy/ ; 0000005948//U.S. Department of Energy/ ; }, mesh = {Mississippi ; *Water Quality ; *Water Microbiology ; Environmental Monitoring ; Metals, Heavy/analysis ; Water Pollutants, Chemical ; Hydrogen-Ion Concentration ; }, abstract = {The purpose of this research is to assess the quality of water in the Nesbit farm, which is located in the Major Land Resource Area (MLRA) in Mississippi, United States of America. This is a land resource area that faces a high risk of nutrient runoff. This research did an in-depth analysis of the quality of water in the Nesbit farm in the MLRA in Mississippi in the United States of America. This research will help to address the problems associated with the quality of water in this region by using physicochemical analysis, microbial community analysis, water quality index analysis, and geospatial analysis. The quality of water in this region, the problems associated with the quality of water in this region, and the microbial communities for grazing land management are taken into consideration in this research. The results for water temperature were obtained as (32.23 ± 0.39 °C), slightly acidic pH values ranging from (6.23-6.52), heavy metals were below the permissible limits for water as per the World Health Organization. Total dissolved solids were in the range of (1.4-1.6 mg/L), and the levels of dissolved oxygen were low (2.49-3.45 mg/L), indicating organic enrichment. Nitrate (0.11-6.36 mg/L), phosphate (0.03-0.15 mg/L) were high in concentration. The WQI of Nesbit farm water quality was 7.35, which shows that water quality is excellent in spite of localized stressors. The principal component analysis showed that the first two components explained 85.7% of the variance, and the major contributing parameters were chloride and pH. The Pearson correlation analysis indicated that there is a positive correlation between lead, total dissolved solids, chloride, and nitrate, which could be related to runoff. The metagenomics analysis indicated that Proteobacteria (30-35%) and Bacteroidetes (13-17%) are dominant species, which could be related to low organic matter. The study has provided valuable insight into water quality for Mississippi grazing land, which could be useful for effective management and conservation of natural resources.}, } @article {pmid41787261, year = {2026}, author = {Dühr, H and Pärnänen, K and Kucháriková, N and Werner, P and Pershagen, G and Lahti, L and Alenius, H and Bergström, A and Ruuskanen, MO and Fyhrquist, N}, title = {Lifestyle associates with unique resistome and microbiome signatures in children.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41787261}, issn = {1471-2180}, abstract = {BACKGROUND: Antibiotic resistance is a global health crisis that is not solely explained by antibiotics usage. However, environmental and lifestyle contributions to antimicrobial resistance (AMR) in children are not well understood, especially compared to adults. As the gut functions as a reservoir for antibiotic resistance genes (ARGs), the aim of this study was to better understand the influence of lifestyle on the gut microbiome and resistome using shotgun-metagenomic sequencing data of Swedish children from the PARSIFAL (Prevention of Allergy Risk factors for Sensitization In children related to Farming and Anthroposophic Lifestyle) study.

RESULTS: Farm children exhibited high proportions of unique bacterial species and differentially abundant ARGs linked to the farm environment, and similar differences were found in anthroposophic children. Age, breastfeeding duration, and obesity significantly influenced the overall resistance load, independently of lifestyle. Despite limited statistical power, our findings suggest that lifestyle and environment both shape the microbiome and resistome of children.

CONCLUSIONS: This study corroborates the possible influence of the farm environment on the gut microbiome and resistome, revealing a highly individualized repertoire of low-abundance microbes and ARGs in farm children. Additionally, associations of age, obesity and the duration of exclusive breastfeeding with ARG load were found in a currently understudied age range. Overall, this study raises the need for further research on rare species and ARGs as well as their transmission dynamics in relation to the environment.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04665-2.}, } @article {pmid41787302, year = {2026}, author = {Li, Y and Liu, L and Long, M and Guan, D and Deng, W}, title = {Habitat-driven variation in gut microbiome composition and function of the pygmy grasshopper (Tetrix japonica) across diverse ecosystems in China.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41787302}, issn = {1471-2164}, support = {2023GXNSFDA026037//Natural Science Foundation of Guangxi Province,China/ ; 32360124//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The gut microbiome plays an important role in insect adaptation, yet how habitat variation shapes microbial communities in pygmy grasshoppers remains unclear. We investigated this question using Tetrix japonica, which inhabits diverse ecosystems across China and provides an ideal model to study microbiome-environment interactions. Shotgun metagenomic sequencing was performed on gut samples from six populations representing coniferous forest, broadleaf forests in Shandong and Shaanxi, grassland, shrubland, and laboratory-reared populations.

RESULTS: Microbial diversity and community composition varied significantly among habitats, with field populations exhibiting higher diversity than laboratory-reared ones. Despite environmental differences, a core microbiome comprising 1,162 shared species was consistently detected, suggesting stable symbiotic relationships. Habitat-specific microbial signatures were most evident between forest and grassland populations, with lignocellulose-degrading taxa enriched in forest habitats. Moreover, geographic separation between Shandong and Shaanxi broadleaf forests led to distinct microbial profiles despite similar vegetation. Functional analysis revealed differential enrichment of genes related to plant polymer degradation, nitrogen cycling, and secondary metabolite biosynthesis across habitats.

CONCLUSION: These findings demonstrate that both habitat conditions and geography influence gut microbiome assembly in T. japonica, with microbiome plasticity facilitating adaptation. The reduced diversity observed in laboratory populations highlights the importance of natural habitats for maintaining functional microbiome integrity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12725-8.}, } @article {pmid41788258, year = {2026}, author = {Keles, E and Celik, O}, title = {Metagenomic and microbiological analyses of historical manuscripts for bacterial community profiling and bacteria-related biodeterioration assessment.}, journal = {Microbial cell (Graz, Austria)}, volume = {13}, number = {}, pages = {117-130}, pmid = {41788258}, issn = {2311-2638}, abstract = {Bacteria are important agents in the biodeterioration of cultural heritage objects, including historical manuscripts. Characterizing bacterial communities and generating robust microbiological data has therefore become crucial for conservation and restoration strategies. In this study, we investigated the bacterial communities associated with biodeterioration in six historical manuscripts using both culture-dependent and culture-independent (Illumina MiSeq) approaches. Culture-dependent methods yielded only 16 viable and culturable isolates, highlighting the limitations of traditional techniques. In contrast, metagenomic analysis revealed a far richer and more diverse bacterial community, capturing both living and non-living microbial traces accumulated over centuries. Bacterial genera with known cellulolytic and/or proteolytic activities, such as Bacillus, Stenotrophomonas, Pseudomonas and Acinetobacter, were identified as part of a core microbiome commonly associated with paper deterioration. High abundances of gut-associated bacteria (Prevotella, Faecalibacterium, Bacteroides, Porphyromonas) and human-related taxa (Staphylococcus, Streptococcus, Cutibacterium) indicated extensive historical human handling. A notable finding was the detection of Pseudonocardia broussonetiae, an endophytic bacterium associated with paper mulberry (Broussonetia papyrifera), suggesting the possible use of this plant as a papermaking material in one manuscript. This represents an important contribution to understanding Islamic paper production. Overall, our results demonstrate that effective conservation strategies require a detailed understanding of each manuscript's microbial ecology, together with evidence of past environmental conditions, handling history, and production materials.}, } @article {pmid41788574, year = {2026}, author = {Liang, ZW and Guan, YH and Lv, Z and Yang, SC and Zhao, M and Chen, JW}, title = {Metagenomics reveals an interaction among rhizosphere microbial community, soil properties and active ingredients in a medicinal crop Panax notoginseng.}, journal = {Journal of ginseng research}, volume = {50}, number = {2}, pages = {100918}, pmid = {41788574}, issn = {1226-8453}, abstract = {BACKGROUND: This study aimed to examine the effects of intensive cultivation practices on the rhizosphere microecology of Panax notoginseng. Additionally, we sought to compare these practices with an understory cultivation model that was intended to mimic native growth conditions, with the objective of improving the quality of Radix Notoginseng.

METHODS: The total saponin and active ingredient content in both cultivation methods were quantified using high-performance liquid chromatography (HPLC). The nutrients of the rhizosphere soils associated with both cultivation methods (understory cultivated P. notoginseng rhizosphere soil [UCPS] and intensive cultivated P. notoginseng rhizosphere soil [ICPS]) were analyzed. The microbial communities present in UCPS and ICPS were characterized using metagenomic sequencing.

RESULTS: The underground biomass accounted for 71.21 % and 74.00 % of the total biomass in understory cultivated P. notoginseng (UCPn) and intensively cultivated P. notoginseng (ICPn), respectively. The total saponin content in the main root of UCPn was found to be 109.24 ± 3.40 mg/g, compared to 91.31 ± 5.82 mg/g in ICPn. The concentration of medicinal ingredients (ginsenoside Rb1 + ginsenoside Rg1 + notoginsenoside R1) in UCPn was 10.83 %, while ICPn exhibited a higher concentration of 13.39 %. Microbial biomarkers identified in UCPS include Bradyrhizobium, Pseudomonas, and Paraburkholderia, which are associated with nitrogen cycling processes. In contrast, Variovorax and Sphingobium were predominant in ICPS, contributing to phosphorus metabolism.

CONCLUSION: Rhizosphere soil microbial biomarkers influence soil carbon nutrition, which directly impacts the quality of UCPn. The quality of ICPn is primarily determined by phosphorus-related biomarkers, with indirect influences from carbon and nitrogen nutrition.}, } @article {pmid41788684, year = {2026}, author = {Cao, W and Li, R and Zhang, H and Zhang, T and Pan, H and Sun, W and Wang, L and Ke, J and Petersen, JD and Zhang, P}, title = {Exploratory multi-omics analysis of gut microbiota and fecal metabolites in relation to serum S-equol levels in older adults with osteoporosis from a tropical community: a pilot study.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1784894}, pmid = {41788684}, issn = {2296-861X}, abstract = {BACKGROUND: Osteoporosis (OP) is a multifactorial skeletal disorder influenced by host metabolism, inflammation, and gut microbiota-derived metabolites such as S-equol. However, the interplay between intestinal microbiota, S-equol production, and host metabolic profiles in OP remains incompletely understood.

OBJECTIVE: To conduct a preliminary multi-omics investigation integrating metagenomic and metabolomic analyses to identify gut microbiota and metabolite biomarkers associated with serum S-equol levels in older adults with OP.

METHODS: A cross-sectional study was conducted in 39 community-dwelling adults aged ≥50 years in Haikou, China. Participants were grouped into OP and control groups based on lumbar spine T-scores, using a cut-off value of ≤ - 2.5 to define osteoporosis. Serum biomarkers (S-equol, inflammatory cytokines, oxidative stress indicators) were assessed by ELISA. Fecal samples underwent metagenomic sequencing and untargeted metabolomics. LEfSe, Spearman correlation, machine learning, and KEGG enrichment were used to explore microbiota-metabolite-bone health axes.

RESULTS: Serum S-equol levels were significantly lower in the OP group compared to controls (3,561 ± 304 vs. 3,855 ± 469 pg/mL, p = 0.026), whereas most inflammatory markers were comparable between groups, apart from a modest increase in IL-1β in OP. Metagenomic analysis revealed a lower relative abundances of key SCFA-producing taxa in OP (e.g., Faecalibacterium prausnitzii, Roseburia hominis, Bacteroides uniformis). Metabolomic profiling identified distinct alterations in amino acid and tryptophan pathways, with KEGG analysis highlighting disruptions in glycerophospholipid, glycine-serine-threonine, and choline metabolism. Discriminative metabolites (e.g., Gln-Val-Ile-Asp., 5-oxooctanoic acid) showed diagnostic potential (AUC > 0.75). S-equol levels positively correlated with these beneficial microbes and with amino acid-related metabolites (e.g., D-tryptophan, 3-indoleacrylic acid, N-methylglutamate). Network and heatmap analyses illustrated differences in microbial-metabolite association patterns between groups.

CONCLUSION: In conclusion, low levels of serum S-equol in older adults with osteoporosis were associated with distinct changes in gut microbiota composition and fecal metabolic profiles in this pilot study.}, } @article {pmid41789009, year = {2026}, author = {Cao, HT and Sun, RJ and Qian, QY and Yang, D and Sun, YY and Zhao, LY and Zhang, GY and Zhang, MD and Gu, H and Cao, HW and Wang, B and Huang, YW and Yang, YL}, title = {Molecular characterization and evolutionary dynamics of a recombinant PDCoV strain in a swine diarrhea epidemic with SADS-CoV co-infection.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1749819}, pmid = {41789009}, issn = {2297-1769}, abstract = {Porcine deltacoronavirus (PDCoV) is an emerging enteropathogenic coronavirus that poses a significant threat to the swine industry. In this study, a novel PDCoV strain, designated PDCoV-ZJHZ2024, was identified from fecal samples of diarrheic pigs in China. Metagenomic analysis revealed co-detection of PDCoV and swine acute diarrhea syndrome coronavirus (SADS-CoV), with the microbial community predominantly composed of bacteria and characterized by abnormal enrichment of Bacillus cereus and pronounced gut microbiota dysbiosis. Genomic analyses demonstrated that PDCoV-ZJHZ2024 has undergone independent recombination events involving the ORF1b region and the spike (S) gene, accompanied by cross-regional genetic exchange, highlighting the critical role of recombination in PDCoV evolution and diversification. Codon usage analysis further indicated that codon preferences in this strain are primarily shaped by natural selection, potentially conferring enhanced translational efficiency in the host. Collectively, these findings underscore the evolutionary adaptability and transmission potential of PDCoV-ZJHZ2024 and provide new insights into PDCoV evolutionary dynamics, thereby informing future surveillance efforts and prevention strategies in swine populations.}, } @article {pmid41789433, year = {2026}, author = {Eldholm, V and Straume, D and Brynildsrud, OB}, title = {Assessing sequencing-based pathogen surveillance of a recreational swimming area in Oslo, Norway.}, journal = {Access microbiology}, volume = {8}, number = {2}, pages = {}, pmid = {41789433}, issn = {2516-8290}, abstract = {Sequencing-based surveillance can enable rapid and sensitive detection of environmental pathogens. The Oslofjord inlet is relatively narrow and is exposed to substantial human activity, including occasional wastewater contamination. Restricted water exchange also allows for occasional summer heat spells with elevated water temperatures. Thus, infections stemming from wastewater contamination and seasonal opportunistic pathogens are potential health threats to recreational users of the fjord. In this pilot study, we assess the suitability of sequencing-based surveillance for the detection of pathogens at a popular urban location for recreational water activities, employing both long- and short-read sequencing platforms, paired with selective culturing. We find both metagenomic and full-length 16S sequencing to be promising tools for surveillance of seasonal opportunistic Vibrio pathogens. Furthermore, we identified Rhodoferax abundance to be a potentially attractive indicator of sewage contamination using low to medium-depth full-length 16S sequencing. Selective plating revealed minimal abundance of culturable extended-spectrum β-lactam-resistant bacteria, of which none were detected by metagenomic sequencing. Metagenomic analyses did, however, pick up several other β-lactamases in various bacterial taxa, including some that were closely related to those identified by selective plating and sequencing.}, } @article {pmid41789894, year = {2026}, author = {Liu, M and Wang, L and Liu, J and Yuan, Q and Zhang, Y and Wu, S and Zhang, Y and Guo, R and Zhang, Y and Lu, T and Yan, Q and Li, S and Xing, G and Dong, B and Zheng, N}, title = {Gut virome and metabolic associations in patients with acute pancreatitis.}, journal = {mSystems}, volume = {11}, number = {3}, pages = {e0140025}, pmid = {41789894}, issn = {2379-5077}, mesh = {Humans ; *Pancreatitis/metabolism/virology/microbiology ; *Virome ; Female ; *Gastrointestinal Microbiome ; Male ; Acute Disease ; Middle Aged ; Adult ; Metagenomics ; Metagenome ; }, abstract = {Acute pancreatitis (AP) is a frequent inflammatory disorder with outcomes ranging from mild disease to severe forms marked by infection and organ failure. Gut microenvironment disruption and barrier dysfunction are increasingly recognized as key drivers of AP progression, yet most microbiome studies have focused on bacteria. The gut virome modulates bacterial ecology and host immune responses and remains poorly characterized in AP. We aimed to comprehensively profile virome alterations in AP and evaluate their associations with disease severity, etiology, and clinical parameters. Metagenomic sequencing data from AP patients and healthy controls (HCs) were analyzed using the viromic tools. Viral diversity, taxonomy, functional composition, and predicted viral-host linkages were profiled. Microbial-viral-metabolite networks were constructed, and classification performance was evaluated using random forest models. AP viromes exhibited significantly reduced Shannon and Simpson diversity and distinct β-diversity separation from HCs. AP-enriched phages predominantly targeted Parabacteroides, Escherichia, and Bacteroides, while HC-enriched phages were linked to SCFA-producing commensals. Functional analysis revealed enrichment of replication- and lysis-related auxiliary metabolic genes (AMGs) in AP-enriched viral operational taxonomic units (vOTUs), whereas HC-associated vOTUs carried stability-related functions. Severity- and etiology-stratified analyses indicated consistent enrichment of Peduoviridae infecting Enterobacteriaceae and higher prevalence of eukaryotic viruses in advanced stages. Network analyses revealed denser microbial-viral-metabolite interactions in AP, correlated with hepatobiliary and lipid metabolic markers. A minimal seven-virus panel achieved an AUC of 97.5% for AP classification. AP is characterized by profound gut virome remodeling reflecting disease severity and etiology, with diagnostic and mechanistic relevance for future therapeutic strategies.IMPORTANCEThis study highlights the gut virome as a previously underappreciated component of acute pancreatitis (AP)-associated dysbiosis and suggests that viral communities may influence disease severity and metabolic disturbances beyond bacterial effects alone. By demonstrating the diagnostic potential of virome-based signatures, our findings support expanding microbiome research in AP to include viral components, with implications for improved disease stratification and future therapeutic development.}, } @article {pmid41789915, year = {2026}, author = {Chen, S and Li, Y and Xue, J and Hao, Y and Shaalan, MGA and Ghallab, EHS and Guo, Z and Jin, S and Fang, Y and I M Khater, E and Li, S}, title = {Metagenomic sequencing reveals viral diversity of mosquitoes from Egypt: co-circulation of multiple insect-specific viruses.}, journal = {Microbiology spectrum}, volume = {14}, number = {4}, pages = {e0213525}, pmid = {41789915}, issn = {2165-0497}, support = {2022FY100900//Science & Technology Fundamental Resources Investigation Program/ ; 2022FY100904//Science & Technology Fundamental Resources Investigation Program/ ; 32161143036, 32311540013//National Natural Science Foundation of China-Yunnan Joint Fund/ ; ASRT/NSFC 2022-2024//Academy of Scientific Research and Technology/ ; GWVI-11.1-12//Three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai/ ; }, mesh = {Animals ; Egypt ; Phylogeny ; Metagenomics ; *Insect Viruses/genetics/classification/isolation & purification ; Genome, Viral ; *Culex/virology ; Genetic Variation ; *Mosquito Vectors/virology ; Virome ; *Culicidae/virology ; *Aedes/virology ; *Viruses/genetics/classification/isolation & purification ; Mosquito-Borne Diseases ; }, abstract = {UNLABELLED: Mosquito-borne virus surveillance is pivotal for investigating mosquito viromes, facilitating understanding of viral evolutionary histories and genetic diversity. Natural viral communities in mosquitoes include not only insect-specific viruses (ISVs) but also viruses infecting symbiotic microorganisms. In this study, a total of 654 mosquito samples-encompassing species from the Aedes and Culex genera-were collected from Egypt and subjected to metagenomic sequencing analysis. Over 130 virus species were identified, grouped into 35 families or equivalent taxonomic ranks. Detected ISVs included Culex flavivirus (CxFV), Kustavi Toti-like virus, Hanko Toti virus 5, Culex phasma-like virus (CPLV), Culex Iflavi-like virus 1, Culex Iflavi-like virus 4, Guadeloupe Culex rhabdovirus (GCRV), and Sarawak virus, confirming concurrent ISV circulation in Egyptian mosquitoes. Phylogenetic analyses of these ISVs revealed their closest evolutionary affinities to viral genome sequences originating from the Middle East, Europe, Oceania, and Asia. Specifically, Egyptian CxFV strains exhibited a closer genetic relationship with the tropical lineage within the Latin American/Caribbean/Africa genotype. Furthermore, our study uncovered 10 putative novel viruses, which are distributed across seven viral families: Amagaviridae, Chrysoviridae, Mitoviridae, Totiviridae, Virgaviridae, Narnaviridae, and Orthomyxoviridae. Collectively, our findings emphasize the necessity for more in-depth investigations into arthropod viromes-encompassing both mosquitoes and ticks-in Egypt, as well as in neighboring African and Middle Eastern countries. Such research is critical for enhancing our understanding of viral diversity and evolutionary biology, elucidating their roles in mosquito-pathogen-host interactions, and exploring their potential as biocontrol agents against vector-borne diseases of public health importance.

IMPORTANCE: Mosquito-borne viruses are estimated to cause over 100 million human infections annually, making surveillance of these pathogens increasingly crucial amid growing international travel and trade. Egypt, situated in northeastern Africa, serves as a geopolitical and geographical hub connecting Asia, Europe, and Africa-a unique location that complicates the surveillance of mosquito-borne viruses. Arboviruses persist in nature through cyclical transmission between arthropod vectors (e.g., mosquitoes, ticks, and midges) and susceptible vertebrate hosts. Despite this, systematic investigations into mosquito viromes remain relatively scarce in Egypt. The present study aimed to explore the genetic diversity and evolutionary relationships of mosquito-associated viruses in Egypt using metaviromic sequencing. Our findings significantly expand the current knowledge of both known and previously uncharacterized mosquito-associated viruses in the region, while also providing complete genome sequences of several viruses that may infect arthropods or vertebrates, and potentially interfere with the replication of pathogenic arboviruses.}, } @article {pmid41789917, year = {2026}, author = {Chen, D and Zhang, Z and Wang, S and Li, W and He, Y and Zhang, W and Sun, W and Chen, M and Zou, S and Qian, X}, title = {Differential assembly and functional roles of bacterial communities in coniferous and mixed conifer-broadleaf forest soils.}, journal = {mSphere}, volume = {11}, number = {3}, pages = {e0062725}, pmid = {41789917}, issn = {2379-5042}, support = {202510389028//Fujian Agriculture and Forestry University/ ; S202510389078//Fujian Agriculture and Forestry University/ ; }, mesh = {*Soil Microbiology ; *Forests ; *Bacteria/classification/genetics ; *Tracheophyta/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Microbiota ; Metagenomics ; DNA, Bacterial/genetics ; }, abstract = {Forest soils harbor a diverse array of bacteria that play a crucial role in nutrient cycling. However, the differential effects of coniferous versus mixed conifer-broadleaf forests on the distribution of both abundant and rare bacterial taxa remain poorly understood. In this study, we integrated 16S rRNA gene amplicon sequencing with metagenomic shotgun sequencing to conduct a comparative analysis of soil bacterial communities in a conifer plantation and an adjacent mixed conifer-broadleaf forest, specifically examining their community structure, assembly mechanisms, co-occurrence networks, and functional potential. Both abundant and rare taxa showed significant differences in community composition between the two forest types. Soil pH and organic matter content significantly influenced the total and abundant bacterial communities, while available phosphorus and potassium were key determinants of rare community composition. Co-occurrence network analysis revealed that abundant communities formed highly clustered, simplified networks, contrasting with more fragmented and keystone-rich networks in rare communities. Null model analyses indicated that community assembly was largely driven by stochastic processes, with ecological drift accounting for about 80% of the variation in total and rare communities, and dispersal limitation explaining nearly 72% of the variation in abundant communities. Functional predictions indicated that bacterial communities in mixed forests were enriched in pathways linked to glycosylation, carbohydrate degradation, and nitrogen fixation, while coniferous forests favored pathways related to autophagy, signaling, and stress responses. This study highlights the complementary roles of abundant and rare bacterial taxa in forest soil ecosystems and underscores the importance of preserving mixed forests to sustain microbial functional diversity.IMPORTANCEForest soils host a complex web of common and rare bacteria that quietly regulate nutrient cycles. By comparing pure conifer stands with mixed conifer-broadleaf forests, we found that abundant species underpin essential functions while rarer microbes fill specialized niches. Acidity and nutrients strongly influence which bacteria thrive; mixed stands favored microbes that break down carbohydrates and fix nitrogen, whereas conifer soils supported organisms adapted to stress and nutrient-poor conditions. These findings emphasize the importance of preserving diverse forest ecosystems for soil health, carbon storage, and effective forest management strategies in climate change adaptation.}, } @article {pmid41789923, year = {2026}, author = {Yao, J and Yang, C and Wang, H and Zhang, C and Meng, J}, title = {Metagenomic analysis of gut bacteria in different developmental instars of Spodoptera litura.}, journal = {Microbiology spectrum}, volume = {14}, number = {4}, pages = {e0208125}, pmid = {41789923}, issn = {2165-0497}, support = {2024XM05//Science and Technolugy Program of Guizhou Tobacco Company/ ; 110202201020(LS-04), 110202201022(LS-06)//Major Project of China National Tobacco Corporation/ ; No. 2022XM12//Zunyi Tobacco Company Program/ ; }, mesh = {Animals ; *Spodoptera/microbiology/growth & development ; Larva/microbiology/growth & development ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; *Gastrointestinal Microbiome/genetics ; Pupa/microbiology/growth & development ; Phylogeny ; Metagenome ; }, abstract = {Spodoptera litura is a globally distributed agricultural pest across Asia and Australia (EPPO database, https://gd.eppo.int/taxon/PRODLI/distribution), whose gut microbiota significantly influences host feeding, digestion, immunity, and development. We used whole metagenomic sequencing to analyze the diversity and functional roles of gut bacteria at different developmental stages (eggs, first to sixth instar larvae, pupae, and adults). Findings revealed that Pseudomonadota predominated at the phylum level, with notable differences across instars: Bacillota was dominant in young larvae, whereas Verrucomicrobiota was added in older larvae, eggs, pupae, and adults. At the genus level, Pseudomonas dominated, Enterococcus was prevalent in larvae, and Piscirickettsia was prevalent in eggs, pupae, and adults. Metagenomic analysis identified numerous carbohydrate-active enzymes (CAZy database) aiding in plant cell wall polysaccharide digestion. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated differential gene expression in metabolism and xenobiotic degradation across instars, with metabolic gene annotation levels declining as development progressed. Detoxification-related enzyme genes were predominantly expressed in early instar larvae and adults, uncovering microbial origins of these enzymes.IMPORTANCEOur study provides evidence that the gut microbiota significantly modulates the physiology of Spodoptera litura, with profound effects on its dietary habits, metabolic processes, and host fitness. Using whole metagenomic sequencing, we analyzed gut bacteria across different life stages. At the phylum level, Pseudomonadota and Bacillota were dominant, while at the genus level, Pseudomonas was the most abundant taxon. Metagenomic analysis identified enzymes aiding in plant cell wall digestion. Kyoto Encyclopedia of Genes and Genomes analysis showed varying gene expression in metabolism and detoxification, with higher expression in early instar larvae and adults. This research enhances understanding of S. litura gut microbiota-host interactions and supports novel pest control strategies targeting gut microbiota.}, } @article {pmid41789948, year = {2026}, author = {Yadav, S and Yang, T and MacLean, MA and El-Naggar, MY}, title = {Metagenome-assembled genome sequence of Candidatus Electrothrix sp. NPCB-01 from Southern California marine sediments.}, journal = {Microbiology resource announcements}, volume = {15}, number = {4}, pages = {e0002526}, pmid = {41789948}, issn = {2576-098X}, support = {8626//W. M. Keck Foundation/ ; 10148//Gordon and Betty Moore Foundation/ ; }, abstract = {Cable bacteria conduct long-distance electron transport in sediments but are not yet isolated in pure culture. We report the metagenome-assembled genome of Candidatus Electrothrix sp. NPCB-01 from Newport Bay, California. This 3.46-Mb genome encodes sulfur oxidation, nitrogen and carbon metabolism, and nickel homeostasis genes, expanding resources for these electroactive microbes.}, } @article {pmid41790075, year = {2026}, author = {Kong, C and Jin, Y and Guo, F and Yang, Y and Liu, G and Chen, Z and Li, J and Wang, Q and Ma, Y}, title = {Revealing the Antagonistic Interactions of Faecalibacterium prausnitzii and Bacteroides fragilis in Colorectal Cancer.}, journal = {Gastroenterology}, volume = {170}, number = {7}, pages = {1501-1517}, doi = {10.1053/j.gastro.2025.12.030}, pmid = {41790075}, issn = {1528-0012}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/metabolism/genetics ; Animals ; *Bacteroides fragilis/metabolism/genetics ; *Faecalibacterium prausnitzii/metabolism/genetics ; Mice ; Feces/microbiology ; Female ; Male ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; Multiomics ; Disease Progression ; Tryptophan/metabolism ; Case-Control Studies ; }, abstract = {BACKGROUND & AIMS: Maladaptation of host-microbe metabolic interactions plays a crucial role in development of colorectal cancer (CRC). However, remains a lack of comprehensive studies using multi-omics analysis to illustrate host-microbe metabolic interactions in CRC.

METHODS: We collected and analyzed 440 stool samples from a discovery cohort in Shanghai China (255 patients with CRC and 185 healthy controls). Each sample was subjected to metagenomic sequencing and nontargeted liquid chromatography mass spectrometry. Fresh-frozen specimens of tumors and matched adjacent normal mucosae were extracted from 62 patients with CRC, and whole exome sequencing and RNA sequencing were performed to explore host genomic patterns and host-microbe metabolic interactions. Finally, relationships detected in the discovery cohort were validated against independent cohorts, organoid models, and mice experiments.

RESULTS: The relationship between disrupted microbial homeostasis and CRC progression is characterized by Bacteroides fragilis enrichment and reduction of Faecalibacterium prausnitzii. F prausnitzii metabolizes tryptophan into picolinic acid (PIA) via the enzyme 2-amino-3-carboxymuconate semialdehyde decarboxylase, with PIA exerting an antagonistic effect on enterotoxigenic B fragilis-mediated tumor progression. Mechanistically, enterotoxigenic B fragilis up-regulates the expression of genes associated with poor differentiation and recurrence, namely TCERG1 and CKAP2, and PIA induces tumor cell apoptosis by down-regulating these 2 genes. Independent validation cohorts and murine models corroborated that a tryptophan-rich diet effectively elevates circulating PIA levels, suggesting its potential as an anticancer dietary intervention.

CONCLUSIONS: Our research characterized a representative microbe-metabolite-host regulatory pathway occurring in CRC, namely the F prausnitzii-PIA-TCERG1/CKAP2 axis antagonizing enterotoxigenic B fragilis-induced CRC progression. As a treatment option, we highlight the therapeutic potential inherent in a tryptophan-rich diet and in manipulating microbial composition targeting the F prausnitzii-PIA axis to prevent CRC.}, } @article {pmid41790111, year = {2026}, author = {Kumar, K}, title = {Cultivation of yet-to-be cultured microorganisms: advances, strategies, and prospects.}, journal = {Journal of applied microbiology}, volume = {137}, number = {3}, pages = {}, doi = {10.1093/jambio/lxag066}, pmid = {41790111}, issn = {1365-2672}, mesh = {Bioreactors/microbiology ; *Bacteria/growth & development/isolation & purification/genetics/metabolism ; Coculture Techniques ; Metagenomics/methods ; *Microbiological Techniques/methods ; }, abstract = {More than 99% of microorganisms in the natural environment are not readily culturable using standard laboratory techniques. These microbes can be reservoirs of novel metabolites and biomolecules having pharmaceutical applications against bacterial infections, chronic diseases, and antibiotic resistance. Given this, our work is a comprehensive synthesis of recent advances in understanding, detection, and cultivation of "yet-to-be cultured" (YTBC) microbes. We highlight physiological traits that restrict their domestication under standard laboratory conditions. Some of the factors that may influence are their metabolic dormancy, specialized nutrient demands, siderophore-mediated iron acquisition, microbial signaling, and interspecies interactions. The review discusses various strategies, such as simulated natural environments, co-culture, and advanced bioreactor systems, which can be implemented to cultivate them. We reviewed recent metagenomic approaches and single-cell isolation methods, including label-based techniques (e.g. fluorescence in situ hybridization), label-free approaches such as Raman-activated cell sorting, and high-throughput tools like flow cytometry. We also examined culture-dependent approaches, including co-cultivation with helper strains with a special emphasis on bioreactor-based systems, diffusion chamber, hollow-fiber membrane chamber, high-throughput isolation chip (iChip), and encapsulation. Overall, this review provides a roadmap to unlock the biotechnological potential of YTBC microbes by outlining new technologies, methodological trends, and important knowledge gaps.}, } @article {pmid41790499, year = {2026}, author = {Liu, G and Bai, P and Ren, M and Li, Q and Li, T}, title = {Vitamin B12-associated interactions between Mesorhizobium sp. TaiHu and Synechococcus sp. PCC 7002 revealed by multi-omics analysis.}, journal = {Microbial genomics}, volume = {12}, number = {3}, pages = {}, pmid = {41790499}, issn = {2057-5858}, mesh = {*Vitamin B 12/metabolism/biosynthesis ; *Synechococcus/genetics/metabolism/growth & development ; *Mesorhizobium/genetics/metabolism/growth & development ; Multiomics ; Microbial Consortia/genetics ; Metagenomics/methods ; Gene Expression Regulation, Bacterial ; Gene Expression Profiling ; Microbial Interactions ; Transcriptome ; }, abstract = {The marine cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) is a model organism that lacks the gene cluster required for vitamin B12 biosynthesis, necessitating cooperative interactions with other microbes. In this study, we established a synthetic microbial consortium by co-culturing Syn7002 with a bloom-forming Microcystis community, followed by purification, and subsequently investigated the interactions between Syn7002 and the associated microbial community. Electron microscopy revealed numerous rod-shaped bacteria clustered around Syn7002 cells, indicating close spatial associations between species. Metagenomic analysis showed that the early-stage community consisted mainly of Syn7002, Mesorhizobium sp. TaiHu (MesTH) and Pseudomonas sp. TaiHu (PseTH), although the abundance of PseTH declined after community stabilization. Investigation of vitamin B12 regulation between MesTH and Syn7002 through metatranscriptomic analysis revealed upregulation of nitrogen metabolism-related genes in the microbial community. Transcriptomic data further indicated that vitamin B12 biosynthesis and transport genes were significantly upregulated in MesTH. Combined with vitamin B12-positive control experiments, these results confirm potential vitamin B12 complementarity between the two strains. The results further suggest that MesTH promotes the growth of Syn7002 in the community by providing the small amount of vitamin B12 needed for its growth. These findings provide new insights into vitamin-mediated microbial interactions and reveal additional transcriptional features of the synthetic community.}, } @article {pmid41790792, year = {2026}, author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Rahman, R and Hassan, J and Islam, T and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT}, title = {Shotgun metagenomic profiling reveals Bacillus-dominated bacterial communities in urban rooftop and surface garden soils of Bangladesh.}, journal = {PloS one}, volume = {21}, number = {3}, pages = {e0344114}, pmid = {41790792}, issn = {1932-6203}, mesh = {*Soil Microbiology ; Bangladesh ; *Metagenomics/methods ; *Bacillus/genetics/classification/isolation & purification ; *Microbiota/genetics ; Gardens ; Metagenome ; Shotgun Sequencing ; Soil/chemistry ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Urban rooftop and surface garden systems play a critical role in food security in densely populated regions, yet their soil microbiomes remain understudied. To date, no baseline data exists on rooftop and surface garden soil microbiomes in Bangladesh. Understanding these communities is vital for enhancing soil health, nutrient cycling, and resilience for sustainable, climate-adapted urban agriculture. This study therefore investigated the bacterial diversity and community structure of rooftop and surface garden soils across Dhaka and Gazipur, Bangladesh. The goal was to uncover location- and garden-type-specific patterns that influence soil functionality. Using shotgun metagenomics of 27 garden soil samples (seven Dhaka rooftop [DRG], six Dhaka surface [DSG], eight Gazipur rooftop [GRG], and six Gazipur surface [GSG]), we identified 755 bacterial species dominated by Firmicutes (65-83%) and Proteobacteria (3-25%). While alpha diversity was consistent across sites (p > 0.05), beta diversity revealed distinct community structuring (p = 0.017), with surface gardens harboring greater bacterial richness (DSG:717, GSG:750 species) and elevated Bacteroidota (DSG:11.5%, GSG:2.7%) compared to rooftop soils. Strikingly, Bacillus species dominated all soils (>53% relative abundance) but exhibited location-specific distributions. DRG soils were notably enriched with B. paralicheniformis (28.3%) and B. licheniformis (25.2%). In contrast, DSG was characterized by B. cereus sensu lato (16.0%), Brevibacillus agri (12.1%), and Flavobacterium thermophilum (11.4%). GRG soils were dominated by B. cereus sensu lato (42.4%) and B. agri (11.5%). GSG soils showed diverse Bacillus species, including B. stratosphericus (14.6%), B. licheniformis (12.7%), B. safensis (9.7%), and B. altitudinis (8.8%). Of 41 detected Bacillus species, more than 58.0% were shared across gardens, yet their abundances varied with microhabitat. Moreover, KEGG profiling revealed marked functional divergence among urban garden soils. Carbohydrate metabolism dominated all sites (9.30-11.07%). DRG was uniquely enriched in photosynthesis (8.40%) and methane metabolism (8.62%), whereas DSG, GRG, and GSG showed higher oxidative phosphorylation (3.75-4.08%), two-component systems (3.24-3.73%), and biosynthetic pathways. This study unveils the ecological dominance of Bacillus species in urban agricultural soils, with location-driven compositional and functional shift. These findings are pivotal for optimizing sustainable urban agriculture in rapidly developing regions, where soil bacteriomes can be harnessed to improve crop resilience and food security.}, } @article {pmid41790828, year = {2026}, author = {Carrillo, A and Hageman, E and Chittick, L and Mackey, AI and Ndlovu, KS and Tian, F and Gilbert, NE and Muratore, D and Vik, D and LeCleir, GR and Sun, C and Jang, HB and Pavan, RR and Weitz, JS and Wilhelm, SW and Sullivan, MB}, title = {Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts.}, journal = {PLoS biology}, volume = {24}, number = {3}, pages = {e3003474}, pmid = {41790828}, issn = {1545-7885}, mesh = {Atlantic Ocean ; *Seawater/virology ; Bermuda ; Population Dynamics ; Ecosystem ; *Viruses/genetics/isolation & purification/classification ; Metagenome ; Water Microbiology ; }, abstract = {Ocean microbes contribute to biogeochemical cycles and ecosystem function, but they do so under top-down pressure imposed by viruses. While viruses are increasingly understood spatially and beginning to be incorporated into predictive modeling, high-frequency ocean virus dynamics remain understudied due to methodological challenges. Here we sampled stratified Bermuda Atlantic Time Series (BATS) waters for 112 hours at sub-daily 4- (surface) or 12- (deep chlorophyll maximum) hour intervals, purified viral particles from these samples, sequenced their metagenomes, and used the resulting data to characterize high-frequency virus community dynamics. Aggregated community diversity metrics changed with depth, but were not statistically significant temporally at a fixed location. However, finer-scale population-level analyses revealed both depth and temporal change, including physicochemical depth-driven differences and, in surface waters, thousands of viral populations that exhibited statistically significant diel rhythms. Statistical analyses revealed three main archetypes of temporal dynamics that themselves differed in abundance patterns, host predictions, viral taxonomy, and gene functions. Among these, highlights include viruses resembling an archetype with a night peaking pattern in activity that include an over-representation of viruses that putatively infect Prochlorococcus, a phototrophic cyanobacteria. Together, these efforts provide baseline community- and population-scale short-time-frame observations relevant to future climate state modeling.}, } @article {pmid41790921, year = {2026}, author = {Wang, J and Jiang, B}, title = {Utilizing metagenomic next-generation sequencing to diagnose central nervous system infections after craniotomy.}, journal = {Journal of infection in developing countries}, volume = {20}, number = {2}, pages = {263-270}, doi = {10.3855/jidc.21771}, pmid = {41790921}, issn = {1972-2680}, mesh = {Humans ; *Craniotomy/adverse effects ; Prospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Central Nervous System Infections/diagnosis/microbiology ; Female ; *Metagenomics/methods ; Male ; Middle Aged ; Adult ; Bacteria/isolation & purification/genetics/classification ; Sensitivity and Specificity ; Aged ; *Postoperative Complications/diagnosis/microbiology ; }, abstract = {INTRODUCTION: Postoperative central nervous system (CNS) infections in craniotomy patients diagnosed through clinical signs and cerebrospinal fluid (CSF) bacterial culture, pose a challenge due to the morbidity and mortality of bacterial meningitis. The objective of this study was to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in diagnosing CNS infections post craniotomy.

METHODOLOGY: A prospective study compared mNGS with traditional diagnostics from January 2021 to October 2023. Patients with suspected post-craniotomy intracranial infections were enrolled, following guidelines and regulations.

RESULTS: mNGS and traditional culture diagnosed 111 patients with suspected intracranial infections. mNGS showed higher sensitivity (62.5% vs. 25%). Traditional culture excelled in specificity and positive predictive value. Of the 18 mNGS-positive samples, 12 were culture-negative. mNGS detected pathogens such as Candida albicans (2 cases), Enterobacter cloacae (1 case), Enterococcus faecalis (1 case), Klebsiella pneumoniae (2 cases), Pseudomonas aeruginosa (1 case), Staphylococcus aureus (2 cases), Staphylococcus epidermidis (2 cases), and Streptococcus haemolyticus (1 case). Some pathogens were likely missed due to prior antibiotic use and fastidious growth requirements. Physicians adjusted treatments based on mNGS pathogen detection for culture-negative patients. Empirical therapy continued for patients with negative results until more diagnostic information was available.

CONCLUSIONS: mNGS detects post-neurosurgery CNS infections, especially hard-to-cultivate microorganisms. While mNGS has advantages, traditional culture's higher positive predictive value confirms infections and remains indispensable. Combining mNGS with traditional methods provides a comprehensive diagnostic strategy, aiding physicians in accurately identifying infections, reducing misdiagnosis, and offering personalized treatment plans to improve outcomes and quality of life.}, } @article {pmid41791253, year = {2026}, author = {Fu, CX and Cai, JJ and Liu, JL and Qiu, GY and Chen, XD and Zhang, JB and Qiao, M and Tong, WB and Guo, B}, title = {Mechanistic investigation of the associations between bacterial community composition and cadmium distribution in Zizania latifolia.}, journal = {Ecotoxicology and environmental safety}, volume = {312}, number = {}, pages = {119972}, doi = {10.1016/j.ecoenv.2026.119972}, pmid = {41791253}, issn = {1090-2414}, mesh = {*Cadmium/metabolism/analysis ; Rhizosphere ; *Bacteria/metabolism/genetics/classification ; Plant Roots/microbiology/chemistry/metabolism ; *Soil Pollutants/metabolism/analysis ; *Poaceae/microbiology/metabolism/chemistry ; Soil Microbiology ; Plant Leaves/microbiology/metabolism/chemistry ; }, abstract = {The role of bacteria in external niches regulating cadmium (Cd(II)) in plant tissues remains unclear. We explored Cd(II) profiles and identified bacterial contributors among phyllosphere, rhizoplane, and rhizosphere of four Zizania latifolia varieties through integrated metagenomic and chemical analyses. Zizania latifolia accumulated Cd(II) in leaves (0.06-0.77 mg/kg), roots (0.73-1.57 mg/kg), and rhizosphere (0.43-3.15 mg/kg), respectively. The highest enrichment coefficient (leaf-Cd(II)/soil-Cd(II)) was observed in Genotype 3 (0.6). Among top 10 genus-level bacteria, Enterococcus in phyllosphere, Streptomyces and Dechloromonas in rhizoplane, and Bradyrhizobium, Pseudolabrys, Mycobacterium, and Dechloromonas in rhizosphere were significantly related to Cd(II). Enterococcus adsorbed Cd(II) by extracellular polysaccharides and precipitated Cd(II) sulfide. Rhizoplane and rhizosphere bacteria absorbed Cd(II) by cell-surface functional groups, and fixed Cd(II) through synthesizing polyphosphate and driving Fe (II) oxidation. Additionally, 64.4%-80% of bacteria were shared between rhizoplane and rhizosphere, 5.5%-6.9% between rhizoplane and phyllosphere, and 4.4%-6.1% between rhizosphere and phyllosphere. Metagenomic analysis indicated that Cd(II) disturbed bacterial secretion system and amino acid metabolic pathways. These findings provided comprehensive insights into interrelationships between Cd(II) and bacteria in leaves, roots, and rhizosphere of Zizania latifolia, offering valuable foundations for developing targeted strategies to mitigate Cd(II) accumulation in aquatic vegetables.}, } @article {pmid41791469, year = {2026}, author = {Ma, J and Liu, J and Guo, Z and Zhu, M and Chai, Z and Jiang, F and Li, Z and Liang, Z and Jiang, Z}, title = {Characteristics of the microbial carbon pump in kelp farming areas and the impact of artificial reefs: A metagenomic and ecological perspective.}, journal = {Environmental research}, volume = {297}, number = {}, pages = {124166}, doi = {10.1016/j.envres.2026.124166}, pmid = {41791469}, issn = {1096-0953}, mesh = {Metagenomics ; *Carbon/metabolism ; *Kelp ; *Coral Reefs ; *Aquaculture ; Geologic Sediments/microbiology ; Dissolved Organic Matter/analysis ; *Carbon Cycle ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The microbial carbon pump (MCP) can transform labile dissolved organic carbon (LDOC) into recalcitrant dissolved organic carbon (RDOC), yet how sedimentary MCP efficiency is regulated by natural gradients of organic carbon input remains unclear. In this study, we investigated sediments in a kelp farming environment, leveraging the contrast between artificial reef (AR) areas and adjacent non-reef (NR) areas. We combined full-length 16S rRNA sequencing, metagenomics, and fluorescent dissolved organic matter (FDOM) characterization to compare microbial processing under these contrasting depositional regimes. Elevated LDOC inputs in the AR zones were associated with reshaped community metabolic profiles and with enhanced turnover and potential formation of RDOC. High substrate availability was linked to coordinated metabolic functional potential, in which increased genetic potential for upstream catabolism covaried with genomic features indicative of expanded acetyl-CoA supply potential. This putative metabolic overflow was more strongly associated with the mevalonate (MVA) pathway than with the alternative methylerythritol phosphate pathway, consistent with a potential routing toward isoprenoid and terpenoid backbone biosynthesis and the formation of carboxyl-rich alicyclic molecule (CRAM) precursors. Genome-resolved reconstructions further suggested metabolic complementarity among taxa, with predicted cross-feeding interactions that could help sustain carbon processing in MVA-enriched copiotrophs. Overall, humic-like FDOM signals co-vary with organic loading driven by artificial reefs, indicating that these engineering interventions serve as controllable levers, providing a scientific basis for optimizing the carbon sink function of marine ranching through strategic artificial reef deployment.}, } @article {pmid41791723, year = {2026}, author = {Raj, A and Pant, A and Kumar, A and Kumar, A and Kalamdhad, AS and Khwairakpam, M}, title = {Systems-Level Insights Into Microbial Naphthalene Biodegradation: An Integrated In Silico and Omics Perspective.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70264}, doi = {10.1111/1462-2920.70264}, pmid = {41791723}, issn = {1462-2920}, support = {IITG/R&D/IPDF/2024-25/20240815P852//Indian Institute of Technology Guwahati/ ; }, mesh = {*Naphthalenes/metabolism ; Biodegradation, Environmental ; Computer Simulation ; *Bacteria/metabolism/genetics ; Systems Biology ; *Environmental Pollutants/metabolism ; Polycyclic Aromatic Hydrocarbons/metabolism ; Metabolic Networks and Pathways ; }, abstract = {Naphthalene, a widely detected polycyclic aromatic hydrocarbon (PAH), is among the 16 priority PAHs identified as major environmental hazards due to its persistence, ubiquity, and toxicity to ecosystems and human health. Its occurrence in crude oil, combustion residues, vehicle emissions, and household products highlights the urgent need for sustainable remediation strategies. Microbial-based bioremediation stands out as an eco-friendly and cost-effective approach that harnesses the metabolic versatility of diverse microorganisms, their genes, and enzymes responsible for naphthalene degradation. Recent advances in omics technologies and high-throughput sequencing have expanded our understanding of novel microbial taxa, metabolic pathways, and stress responses under naphthalene exposure. Complementarily, computational modelling, in silico tools, machine learning, and systems biology have enabled the prediction of degradation dynamics and the design of synthetic microbial consortia optimised for field use. Despite these advances, challenges such as environmental fluctuations, co-contaminant effects, and the gap between laboratory and field outcomes remain. Overcoming these requires an integrative framework that connects microbial ecology, omics insights, and computational modelling. This review consolidates current knowledge on microbial degradation of naphthalene, emphasising key taxa, genes, and pathways, and highlights how omics, in silico tools and systems biology can drive sustainable remediation in the Anthropocene.}, } @article {pmid41791848, year = {2026}, author = {Louca, P and Manning, S and Hackney, E and Sharp, L and Hull, MA and Koo, S and Young, GR and Taylor, GS and Dunneram, Y and Mitra, S and Hampton, JS and Dobson, C and Neilson, LJ and Addison, C and El-Omar, EM and , and Stewart, CJ and Rees, CJ}, title = {Gut microbiome signatures in colorectal neoplasia: a cross-sectional study across neoplasia stages and subtypes.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337478}, pmid = {41791848}, issn = {1468-3288}, abstract = {BACKGROUND: While colorectal cancer (CRC) has been linked to the gut microbiome, it remains unclear whether specific microbial signatures are detectable in precursor lesions such as adenomatous polyps, serrated lesions or sessile serrated lesions.

OBJECTIVE: To assess gut microbiome taxonomic and functional associations with colorectal neoplasia presence, severity (non-advanced, advanced and CRC) and subtype and evaluate predictive potential in high-risk neoplasia.

DESIGN: Analysed cross-sectional stool metagenomes (pre-colonoscopy) from 1762 participants (97% White British) undergoing colonoscopy in the multicentre COLO-COHORT study. Neoplasia was classified per British Society of Gastroenterology surveillance guidelines. Linear mixed-effects models and random forest classifiers assessed taxonomic and functional associations, adjusting for dietary, clinical and lifestyle covariates.

RESULTS: Gut microbiome composition differences between individuals with and without neoplasia were statistically significant but minimal (R[2]=0.0008, p=0.03). A small number of species, including Mediterraneibacter faecis and Pseudoruminococcus massiliensis, and microbial pathways, including amino acid biosynthesis and β-lactam resistance, were modestly linked to neoplasia, particularly early lesions (q value <0.05). Associations were generally weak and attenuated after covariate adjustment. Predictive models combining the microbiome with clinical/demographic features modestly improved high-risk neoplasia classification (area under the curve=0.64 vs 0.58 for clinical/demographic features alone).

CONCLUSION: This large prospective cross-sectional study found weak and inconsistent associations between the gut microbiome and premalignant colorectal neoplasia, with no robust microbial signatures. Findings suggest that previously reported microbial shifts may emerge later in disease progression, potentially as a consequence rather than a cause of CRC. Longitudinal, multiomic studies disentangling temporal and causal pathways between the gut microbiome and neoplasia are required.}, } @article {pmid41792155, year = {2026}, author = {Benoit, G and James, R and Raguideau, S and Alabone, G and Goodall, T and Chikhi, R and Quince, C}, title = {High-quality metagenome assembly from nanopore reads with nanoMDBG.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41792155}, issn = {2041-1723}, support = {BBX011089/1,BBS/E/ER/230002C,BB/CSP1720/1,BB/X011054/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 872539, 956229, 101047160 and 101088572//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Metagenome/genetics ; *Nanopores ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *Software ; }, abstract = {Third-generation long-read sequencing technologies, significantly improve metagenome assemblies. Highly accurate PacBio HiFi reads can yield hundreds of near-complete metagenome-assembled genomes (MAGs) from a single sample. Recently, the accuracy of the more cost-effective Oxford Nanopore Technologies (ONT) platform has increased to a per-base error rate of 1-2%. However, current metagenome assemblers are optimized for HiFi and do not scale to the large data sets that ONT enables. We present nanoMDBG, an evolution of metaMDBG, which supports the latest ONT reads through an error correction pre-processing step in minimizer-space. Across a range of ONT datasets, including a large 400 Gbp soil sample, nanoMDBG reconstructs up to twice as many high-quality MAGs as the next best ONT assembler, metaFlye, while requiring a third of the CPU time and memory. Critically, the latest ONT technology can now produce comparable MAG construction results as those obtained using PacBio HiFi at the same sequencing depth.}, } @article {pmid41792508, year = {2026}, author = {Li, M and Li, Y and Li, C and Liu, A and Liu, Y and Li, Y and Xiao, J and Zhang, D and Jin, Y and Wang, G and Pang, X and Jiang, K and Yin, Y}, title = {Dynamic reorganisation of intratumoural bacterial florae during colorectal cancer progression.}, journal = {British journal of cancer}, volume = {134}, number = {9}, pages = {1261-1275}, pmid = {41792508}, issn = {1532-1827}, support = {81874235/82030081//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Colorectal Neoplasms/microbiology/pathology ; Humans ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; Animals ; *Microbiota ; Cell Movement ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) exhibits distinct bacterial community compositions compared to healthy mucosae, which intimately correlate with CRC clinical outcomes. There is a lack of explanation for the inducements of microbiota remodelling.

METHODS: FISH experiments and 16S rRNA sequencing were conducted to determine the inducements of various bacterial colonisation within tissues. Community cultivation was conducted to estimate the capacity of tumours to remodel bacterial communities. Metagenomic analyses were utilised to determine the remodelled communities of CRC with distant metastasis. Scratch tests and three-dimensional (3D) cultivation were employed to investigate the influence of specific taxa on tumour cell behaviours.

RESULTS: Colorectal tumours exhibit heterogeneous and individualised preferences in constantly remodelling intratumoural bacterial florae. Various degrees of colorectal gland differentiation within tumours cause heterogeneous intratumoural bacterial colonisation. CRC progression further alters bacterial community composition. Particularly, Prevotella is significantly enriched in the newly established communities colonising the primary foci of metastatic CRC. Furthermore, Prevotella intermedia (P. intermedia) promotes the invasion, migration, and ectopic tumorigenesis of CRC cells.

CONCLUSIONS: Individual evaluation of the preference of tumours in microbiota may pave the way to the development of CRC therapeutic strategies, and Prevotella is an emerging genus worthy of clinical attention.}, } @article {pmid41792614, year = {2026}, author = {Zhou, J and Gu, T and Zhou, J and Zeng, X and Liu, Y and Chen, F and Hu, Y and Li, S}, title = {Clostridium zhoujianii sp. nov., a novel gram-negative species isolated from bat feces and its genetic characteristics.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41792614}, issn = {1471-2180}, support = {Qiankehe Platform Talent-ZDSYS [2023] 004//Key Laboratory of Microbiol and Infectious Disease prevention &Control in Guizhou Province/ ; Guo Jikong Zong Ren Han [2024] 122//Project for Public Health Talent Cultivation of China/ ; Qiankehe [2025] 024//The local science foundation of Guizhou Province guided by the Central Committee of China/ ; }, abstract = {UNLABELLED: A strictly anaerobic, rod-shaped bacterial strain, designated LP20ᵀ, was isolated from the intestinal contents of bats collected in Qiandongnan, China. Phylogenetic analysis of the 16 S rRNA gene revealed that strain LP20ᵀ shared its highest similarity with Clostridium paraputrificum ATCC 25780ᵀ (98.10%), a value below the accepted threshold for species delineation. Whole-genome sequencing further supported its taxonomic novelty, with ANI, dDDH, and AAI values to the closest relatives all falling well below species-level cutoffs. Strain LP20ᵀ exhibited unusual Gram-stain-negative morphology, grew optimally at 30–37℃ and pH 7.0–8.0, and possessed distinctive fatty acid and polar lipid profiles, including the presence of an unidentified aminophospholipid. Phenotypic assays revealed several metabolic and enzymatic traits that differentiated LP20ᵀ from its closest phylogenetic neighbors. 16 S rRNA amplicon sequencing and metagenomic screening confirmed the presence of this species in multiple bat hosts, suggesting a wider distribution within bat gut microbiomes. Functional genomic analysis indicated enrichment of genes involved in carbohydrate metabolism and a limited antibiotic resistance profile. Based on polyphasic evidence, strain LP20ᵀ represents a novel species within the genus Clostridium, for which the name Clostridium zhoujianii sp. nov. is proposed. The type strain is LP20ᵀ (= JCM 37970ᵀ = GDMCC 1.5627ᵀ).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04884-1.}, } @article {pmid41792922, year = {2026}, author = {Mertz, CM and Mancuso, CJ and Robinson, DM and Yeboah, LD and Fogel, ML and Takacs-Vesbach, C and Newsome, SD}, title = {Microbially derived essential amino acids compensate for dietary deficiencies in an ecologically relevant mammalian host.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41792922}, issn = {1751-7370}, support = {1755402//NSF Division of Integrative Organismal Systems/ ; 1755353//NSF Division of Integrative Organismal Systems/ ; 2439853//NSF Graduate Research Fellowship Program/ ; }, mesh = {Animals ; *Peromyscus/microbiology/metabolism ; *Amino Acids, Essential/biosynthesis/metabolism ; *Gastrointestinal Microbiome ; Diet ; *Muscle, Skeletal/metabolism ; Carbon Isotopes/analysis ; *Bacteria/metabolism/classification/genetics ; Dietary Proteins/metabolism ; }, abstract = {Protein is the main structural and functional component of cells, making it crucial for the survival of all living organisms. Yet mammalian herbivores and omnivores often consume diets deficient in the amount of protein required for growth, homeostasis, and reproduction. To compensate, mammals likely rely on their gut microbiota to synthesize essential amino acids (AAESS), particularly during periods of dietary protein limitation. We quantified the contribution of microbially synthesized AAESS to skeletal muscle in captive, wild-derived deer mice (Peromyscus maniculatus) fed diets varying in macromolecular quantity and quality. Using amino acid carbon isotope (δ13C) analysis combined with genetic sequencing, we assessed the origin of AAESS incorporated into host muscle and identified gut microbial taxa with the genetic potential for AAESS biosynthesis. We estimate that up to 25% of host muscle AAESS were microbially derived, with greater microbial contributions in mice fed diets containing low protein or more complex macronutrients. Gut microbial populations with the genetic potential for AAESS biosynthesis were more abundant in mice with larger contributions of microbially-derived AAESS in their tissues. These results demonstrate the crucial and likely pervasive role the gut microbiome plays in host protein metabolism, especially in mammals facing seasonal or persistent dietary protein limitation.}, } @article {pmid41793806, year = {2026}, author = {Qi, J and Song, Y and Luo, S and Zhu, M and Fu, F and Feng, Y and Mei, W and Feng, H and Li, X and Song, C}, title = {Soil water and inorganic nitrogen contents drive soil microbial carbon fixation during wetland reclamation and restoration.}, journal = {Water research}, volume = {297}, number = {}, pages = {125666}, doi = {10.1016/j.watres.2026.125666}, pmid = {41793806}, issn = {1879-2448}, mesh = {*Wetlands ; *Carbon Cycle ; *Soil Microbiology ; *Nitrogen ; *Soil/chemistry ; Water/chemistry ; China ; }, abstract = {Wetlands are critical terrestrial carbon sinks, playing a vital role in mitigating global warming by fixing substantial atmospheric carbon dioxide. To explore how wetland reclamation and restoration affect soil microbial carbon fixation, we sampled soils from five land-use types in western Jilin Province, China: undisturbed natural reed wetland, reclaimed rice paddy and upland field, restored agricultural drainage wetland and naturally restored wetland after farmland abandonment. We analyzed the effects of wetland reclamation and restoration on microbial communities, metabolic pathways, and carbon fixation potential. Results showed Proteobacteria (31.81 %), Actinobacteria (27.08 %), and Acidobacteria (15.12 %) dominated carbon-fixing microbes, with the reductive tricarboxylic acid cycle and dicarboxylate/4-hydroxybutyrate cycle as major carbon-fixing pathways. The natural wetland had the highest carbon fixation potential, with a mean value of 1.58 mg·kg[-1] across the 0-15 cm topsoil layer and 15-30 cm subsoil layer, which was 1.30 to 4.02 times that of the reclaimed wetlands and restored wetlands. Among reclaimed sites, the rice paddy retained soil microbial community similarity to the natural wetland with complex, stable microbial networks. Compared to the naturally restored wetland, the agricultural drainage-restored wetland showed superior restoration outcomes, including microbial communities more similar to the natural wetland, higher network stability, and greater carbon fixation potential. Soil water and inorganic nitrogen contents were core drivers regulating carbon fixation via RubisCO activity and microbial metabolic pathways. This result highlights that the key to wetland restoration lies in prioritising hydrological regulation and nitrogen management, thereby enhancing microbial carbon fixation potential.}, } @article {pmid41793822, year = {2026}, author = {Li, P and Wang, Y and Bao, Z and He, X and Wang, S and Su, X and Nie, W and Xu, F and Zhou, H and Li, H and Xu, B}, title = {Metagenomics-based insights into the microbial community composition and quality characteristics development potentiality in traditional dry-cured ham.}, journal = {International journal of food microbiology}, volume = {453}, number = {}, pages = {111705}, doi = {10.1016/j.ijfoodmicro.2026.111705}, pmid = {41793822}, issn = {1879-3460}, mesh = {Animals ; *Metagenomics ; Food, Processed ; Volatile Organic Compounds/analysis ; *Meat Products/microbiology/analysis ; Swine ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; Food Microbiology ; Staphylococcus ; Peptides ; }, abstract = {The objective of this study was to elucidate the formation mechanisms of quality characteristics in traditional dry-cured ham. The microbial community composition in three types of dry-cured ham was analyzed using metagenomics technology. Volatile flavor profiles were characterized via gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS), while peptide profiles were determined using liquid chromatography-mass spectrometry (LC-MS). Based on metagenomic data, biosynthetic pathways of volatile flavor compounds and bioactive peptides in dry-cured hams were reconstructed. Key microorganisms identified include Staphylococcus equorum, Staphylococcus saprophyticus, Aspergillus glaucus, Aspergillus ruber, Debaryomyces hansenii, and Debaryomyces fabryi. Using GC-MS and GC-IMS, 25 volatile compounds were identified in dry-cured ham, with branched-chain compounds exhibiting higher odor activity values (OAVs). LC-MS analysis identified 203 microbial-derived peptide fragments, predominantly possessing angiotensin-converting enzyme (ACE) inhibitory, dipeptidyl peptidase-IV (DPP-IV) inhibitory, and antioxidant activities. Further investigation into the contribution of microbial communities to the characteristic quality attributes revealed that Staphylococcus species promote the formation of 3-methyl-butanal via branched-chain amino acid transaminase (BCAT) and 3-hydroxy-2-butanone via acetolactate synthase (ALS). With regard to functional bioactive peptides, Staphylococcus indirectly contributes to the synthesis of NPPKFD, DLEE, and KRQKYD via glutamyl endopeptidase activity. Additionally, proteins derived from Aspergillus glaucus (actin-related protein 5) and Staphylococcus equorum (chromosome segregation protein) serve as direct precursors for bioactive peptides, yielding potential sequences such as KNSKDPVSI and LEDDI. This study provides evidence indicating the role of microbial communities in shaping the quality characteristics of dry-cured ham.}, } @article {pmid41793859, year = {2026}, author = {Brito, B and Frost, M and Webster, J and To, J and Kirkland, P}, title = {Quantifying the impact of sequencing depth and reference genome choice on metatranscriptomic detection of four bovine RNA viruses.}, journal = {Research in veterinary science}, volume = {204}, number = {}, pages = {106125}, doi = {10.1016/j.rvsc.2026.106125}, pmid = {41793859}, issn = {1532-2661}, mesh = {Animals ; Cattle ; *Genome, Viral/genetics ; Coronavirus, Bovine/genetics/isolation & purification ; *RNA Viruses/genetics/isolation & purification ; Deltainfluenzavirus/genetics/isolation & purification ; Nidovirales/genetics/isolation & purification ; Diarrhea Virus 1, Bovine Viral/genetics/isolation & purification ; RNA, Viral/genetics ; *Cattle Diseases/virology/diagnosis ; Transcriptome ; }, abstract = {Metatranscriptomic sequencing enables untargeted detection of RNA viruses across clinical and environmental contexts. Evaluating this approach through metrics such as limits of detection and genome coverage, in direct comparison with established molecular tools like qRT-PCR, is essential for understanding its potential diagnostic utility. In the present study, we assessed the detection performance of metatranscriptomic sequencing for four bovine respiratory RNA viruses: Bovine coronavirus (BCoV), Bovine nidovirus (BNV), Influenza D virus (IDV), and Bovine viral diarrhea virus-1 (BVDV-1) in nasal swabs, using reference-based mapping. Sequencing depth (1, 10, and 20 million (M) reads) and reference genome choice (NCBI RefSeq and study-assembled) were systematically varied to quantify their effects on viral read recovery and genome coverage. For BNV and BCoV, sequencing at ≥10 M reads was sufficient for metatranscriptomic detection of samples that were qRT-PCR positive at high Ct values (up to 40), but recovering high genome completeness was only achieved for samples with Ct < 30. IDV detection was less sensitive: several qRT-PCR-positive samples (Ct 29.6-34.5) yielded no mapped reads even at 20 M. BVDV-1 recovery was strongly reference-dependent; mapping to study-assembled genomes markedly increased read counts and coverage compared with NCBI RefSeq, reflecting divergence between field strains and the standard reference sequence. A low number of mapped reads was observed in several qRT-PCR-negative BVDV-1 pools when using the NCBI RefSeq, consistent with potential misclassification of host-derived sequences. By quantitatively linking qRT-PCR Ct values, sequencing depth, and reference divergence, the present study outlines methodological considerations that may guide future applications of metatranscriptomics into veterinary diagnostics.}, } @article {pmid41793868, year = {2026}, author = {Wang, M and Yu, G and Zhang, Y and Ren, J and Chen, W and Li, Q and Cong, P}, title = {Seasonal dynamics and environmental regulation of pathogenic bacteria in the Weihe River Basin.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141646}, doi = {10.1016/j.jhazmat.2026.141646}, pmid = {41793868}, issn = {1873-3336}, mesh = {*Seasons ; *Rivers/microbiology ; *Water Microbiology ; *Bacteria/genetics/pathogenicity/isolation & purification ; China ; Pseudomonas aeruginosa/genetics/isolation & purification ; }, abstract = {Waterborne pathogen transmission poses a significant global environmental health risk. This study employs metagenomic sequencing combined with co-occurrence network analysis, redundancy analysis (RDA), and partial least squares path modeling (PLS-PM) to investigate the distribution and transmission risk of pathogens in the Weihe River Basin. The study identified 232 pathogenic species in the Weihe River's main and tributary waters, with core pathogens (such as Pseudomonas aeruginosa and Salmonella enterica) consistently present across all hydrological periods. RDA analysis indicated temperature, salinity, nitrate-nitrogen, and chlorophyll-a are key environmental factors driving pathogen community structure. The PLS-PM model reveals significant seasonal variations in the association patterns between mobile genetic elements (MGEs) and pathogens. During the high-water period, MGEs showed the strongest correlation with pathogens, suggesting that pathogens are the primary hosts of MGEs. MGEs-mediated horizontal gene transfer may drive pathogen dissemination during this period. During the normal-water period, MGEs primarily facilitated the transfer of virulence factors (VFs), enhancing the potential pathogenicity of pathogens. During the low-water period, environmental factors promoted the spread of MGEs while inhibiting the expression of virulence genes, leading to a reduction in pathogen virulence. Co-occurrence networks further demonstrate that during the high-water period, MGEs closely linked key VFs, such as Capsule, with enteric pathogens; network connectivity decreased significantly during the normal-water period, maintaining only limited associations; during the low-water period, functional VFs were frequently co-occurring with opportunistic pathogens. This study provides scientific evidence and management references for pathogen risk assessment and control in river basins.}, } @article {pmid41793890, year = {2026}, author = {Dong, M and Zhang, Q and Wang, Y and Wang, S and Feng, G and Qi, H}, title = {Restructuring tilth layers suppresses cotton Verticillium wilt through the niacinamide-mediated enrichment of beneficial Pseudomonas.}, journal = {Microbiological research}, volume = {307}, number = {}, pages = {128491}, doi = {10.1016/j.micres.2026.128491}, pmid = {41793890}, issn = {1618-0623}, mesh = {*Verticillium/growth & development ; *Pseudomonas/metabolism/growth & development/genetics ; Rhizosphere ; *Gossypium/microbiology ; *Niacinamide/metabolism/pharmacology ; *Plant Diseases/microbiology/prevention & control ; Soil Microbiology ; Metabolomics ; Metagenomics ; }, abstract = {Restructuring tilth layers (RTL) is an innovative tillage practice that involves the vertical exchange of topsoil and subsoil while the deeper layer is loosened, and this practice has been verified to significantly reduce the incidence of cotton Verticillium wilt. However, the ecological mechanisms underlying disease suppression remain unclear. In this study, we integrated field experiments, metagenomic sequencing, untargeted metabolomics, and functional validation to elucidate the effects of RTL on the rhizosphere ecosystem from the perspectives of microbe and metabolite interactions. RTL significantly altered the diversity and composition of the rhizosphere microbial communities and increased their network complexity and stability. Linear discriminant analysis effect size (LEfSe) revealed that RTL promoted the enrichment of beneficial taxa such as Pseudomonas, Lysobacter, and Mesorhizobium. Metabolomic profiling revealed that the abundance of niacinamide was 19.11-fold higher (P < 0.05) in the RTL rhizosphere than in the control rhizosphere. Exogenous supplementation and antagonistic assays demonstrated that niacinamide stimulated Pseudomonas enrichment and activation in the rhizosphere. Although niacinamide did not have direct antifungal activity, its coapplication with Pseudomonas reduced the disease index of Verticillium wilt by 81.89%. Overall, RTL suppresses Verticillium wilt through two pathways, by establishing a more stable and complex microbial network and regulating rhizosphere metabolite composition, particularly niacinamide accumulation, which drives the colonization and activation of defense mediated by beneficial microbes, forming an ecological defense mechanism that links metabolite signaling, microbial response, and pathogen suppression.}, } @article {pmid41793958, year = {2026}, author = {Li, X and Sun, Z and Lin, L and Deng, T and Xu, M}, title = {Attenuation of sulfamethoxazole and associated antimicrobial resistome by enriched electroactive microbial consortia.}, journal = {Environment international}, volume = {209}, number = {}, pages = {110182}, doi = {10.1016/j.envint.2026.110182}, pmid = {41793958}, issn = {1873-6750}, mesh = {*Sulfamethoxazole/metabolism ; *Microbial Consortia ; *Drug Resistance, Microbial/genetics ; Biodegradation, Environmental ; Bacteria/genetics ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/metabolism ; }, abstract = {Electroactive biofilms with the capacity of extracellular electron transfer (EET) have shown great promise for mitigating antibiotics and antibiotic resistance genes (ARGs). However, detailed interactions between antibiotics and electroactive microorganisms, along with ARGs dissemination dynamics within the electroactive consortia, remained poorly understood. In this study, stable electroactive microbial consortia were enriched, and their influences on the fates of sulfamethoxazole (SMX) and associated ARGs were systematically investigated. The results showed the enriched consortia could degrade SMX effectively within a wide concentration range through co-metabolism which was stimulated by their electrogenic respiration. Moreover, with accelerated SMX removal, the abundances of associated ARGs including sul1 and sul2 in the consortia decreased significantly due to alleviated SMX-induced selective pressure and probably weakened horizontal gene transfer mediated by mobile genetic elements (e.g., IS91 and tnpA). Degrader isolation and metagenomic analysis identified the core EET-proficient genera (e.g., Geobacter and Alcaligenes) as essential for the accelerated co-metabolism biodegradation of SMX, whereas the proliferation of other bacteria with limited or no EET capacity (e.g., Hydrogenophaga, Burkholderia, Comamonas, Desulfovibrio and Pseudomonas) was closely linked to the ARGs dissemination. This work provides a mechanistic elucidation of how electroactive microbial consortia stimulate antibiotic degradation and attenuate ARGs proliferation, offering strategic insights for risk control of the resistome during wastewater treatment.}, } @article {pmid41794383, year = {2026}, author = {Wannaiampikul, S and Lee, B and Chen, J and Prentice, KJ and Ayansola, R and Xu, A and Santosa, S and Pantopoulos, K and Sweeney, G}, title = {Integrated metabolomics and metagenomics analysis identifies a unique signature characterizing metabolic syndrome.}, journal = {The Journal of nutritional biochemistry}, volume = {154}, number = {}, pages = {110327}, doi = {10.1016/j.jnutbio.2026.110327}, pmid = {41794383}, issn = {1873-4847}, mesh = {Humans ; *Metabolic Syndrome/microbiology/metabolism/blood ; *Metagenomics/methods ; *Metabolomics/methods ; Female ; Male ; *Gastrointestinal Microbiome ; Middle Aged ; Feces/microbiology ; Multiomics ; Metabolome ; Adult ; }, abstract = {Metabolic Syndrome (MetS) presents a global health challenge, characterized by obesity, hypertension, dyslipidemia, and insulin resistance. Despite recognition of the gut microbiome's role in metabolic health, there remains an opportunity for defining association of unique microbes with clinical status. Unique genetic, dietary, and lifestyle factors may influence gut microbial composition and circulating metabolites, and consequently susceptibility to MetS. By identifying specific microbial and metabolomic signatures associated with MetS, we aim to uncover potential targets for reducing the disease burden. We correlate comprehensive clinical parameters with fecal metagenomics and untargeted serum metabolomics to delineate population-specific characteristics from 142 individuals with MetS (N=97) or control (CTRL; N=45). Microbiome species-level alpha diversity was reduced in MetS compared to CTRL. After adjustment for sex, age, BMI, and intensity of statin usage, we identified 20 MetS-related species. A co-abundant network analysis revealed Eubacterium eligens, enriched in the CTRL population, with the highest node degree. Serum metabolomics identified 106 significantly differentially regulated metabolites. N-arachidonoyl dopamine (NADA), an endocannabinoid implicated in GABAergic signaling, was the most significantly altered, enriched in CTRL and correlated with E. eligens. sPLS-DA modeling revealed that E. eligens and D. formicigenerans species cluster together with metabolites NADA and tetrahydrocorticosterone (THB), representing defining characteristics distinguishing MetS in this population. Our data reveal a distinct multi-omic signature of MetS, characterized by a significant reduction in E. eligens and D. formicigenerans abundance, and in circulating NADA and THB levels.}, } @article {pmid41794459, year = {2026}, author = {Cai, J and Huang, A and You, L and Wang, Z and Huang, C and Huang, R and Li, Y and Liang, T and Zhang, F and Wu, Q and Wang, J and Zhu, Z and Ding, Y}, title = {Neomycin-sensitive gut bacteria-derived brassicasterol mediates the anti-obesity effects of Cordyceps militaris polysaccharide.}, journal = {Food research international (Ottawa, Ont.)}, volume = {230}, number = {}, pages = {118574}, doi = {10.1016/j.foodres.2026.118574}, pmid = {41794459}, issn = {1873-7145}, mesh = {Animals ; *Cordyceps/chemistry ; Mice ; Male ; *Neomycin/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Diet, High-Fat ; Mice, Inbred C57BL ; *Obesity/drug therapy/metabolism ; *Polysaccharides/pharmacology ; *Anti-Obesity Agents/pharmacology ; Liver/metabolism ; Lipid Metabolism/drug effects ; Sterols ; }, abstract = {Diet-based modulation of the gut microbiota has emerged as a promising strategy to alleviate obesity and its related complications. Our previous study demonstrated that polysaccharide derived from Cordyceps militaris (CMP) exerts anti-obesity effects, yet the specific mechanism linking gut microbiota to its metabolic impact remains unclear. Herein, we utilized murine models with distinct gut microbial profiles created via antibiotic cocktails to investigate these mechanisms. The protective effects of CMP against high-fat diet (HFD)-induced obesity and associated metabolic disturbances were substantially impaired in mice depleted of neomycin-sensitive gut bacteria. Metagenomic analyses further established that CMP required these bacteria to restore gut microbial homeostasis. Notably, we observed that CMP elevated hepatic levels of brassicasterol in a manner dependent on neomycin-sensitive gut bacteria. Brassicasterol treatment alone replicated the anti-obesity effects of CMP, as indicated by reduced body weight gain, improved lipid and glucose metabolism, and decreased inflammation. Through transcriptomic and functional analyses, we identified hepatic Apoa4 as a key downstream effector of brassicasterol. Our results indicated that brassicasterol upregulated Apoa4, facilitating lipid transport and suppressing inflammation both in vitro and in vivo. Collectively, our findings indicate that CMP exerts its anti-obesity effects through a neomycin-sensitive gut bacteria-brassicasterol-Apoa4 pathway. This work expands the mechanistic understanding of CMP and highlights a novel microbiota-metabolite-host regulatory axis for dietary intervention in metabolic disorders.}, } @article {pmid41794462, year = {2026}, author = {Di Gianvito, P and Sáez, V and Dimopoulou, M and Papandreou, C and Francesca, N and Vrhovsek, U and Rantsiou, K and Cocolin, L and Arapitsas, P and Englezos, V}, title = {The role of mycobiome in terroir and during Muscat grapes fermentation unveiled by multi-omic analysis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {230}, number = {}, pages = {118577}, doi = {10.1016/j.foodres.2026.118577}, pmid = {41794462}, issn = {1873-7145}, mesh = {*Fermentation ; *Vitis/microbiology/metabolism ; *Wine/microbiology/analysis ; Multiomics ; Italy ; Kluyveromyces/metabolism ; *Mycobiome ; Metabolomics/methods ; Greece ; Saccharomyces cerevisiae/metabolism ; Metabolome ; Amino Acids/metabolism ; Metagenomics ; }, abstract = {The wine microbiome is a key determinant in shaping wine terroir. To date, a comprehensive understanding of how microbial signatures influence wine metabolic profile remains poorly understood. To address this, in the present study an integrated shotgun metagenomics and untargeted metabolomic approach was employed to investigate the wine metabolome and connect the composition and functions of microbiomes involved in wine fermentation of Muscat grapes harvested in Italy and Greece. Beta diversity highlighted the dissimilarity between Italian and Greek fungal terroirs. A marked reduction in diversity during fermentation underscored the dominance of the inoculated Saccharomyces cerevisiae starter culture. The LEfSe analysis revealed an enrichment of Torulaspora delbrueckii in Greek samples, while Kluyveromyces marxianus and lactis were more abundant in Italian samples. Functional analysis revealed geographic differences in nucleotide, fatty acids and lysine metabolisms. Significant shifts were observed in energy, carbohydrate, and amino acid metabolisms, reflecting terroir-specific microbial activity. The metabolomics data highlighted regional differences in oligosaccharides, glycosylated phenolics, peptide and amino acid turnover, and central redox metabolites, suggesting divergent microbial responses and metabolic trajectories shaped by terroir and fermentation conditions. Obtained results highlight the effectiveness of this multi-omics approach in identifying product-specific fungal communities and wine metabolite signatures, providing new tools that could be used to ensure wine authenticity and quality control.}, } @article {pmid41794791, year = {2026}, author = {Song, Z and Li, R and Liang, L and Zhang, M and Wang, H and Bu, H and Zhang, Y}, title = {Varicella zoster virus-related myelitis: a case series and literature review.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {41794791}, issn = {1743-422X}, support = {No. H2023206903//the National Science Foundation of Hebei Province/ ; }, mesh = {Humans ; Female ; Middle Aged ; *Myelitis/virology/drug therapy/diagnosis/pathology ; Male ; Antiviral Agents/therapeutic use ; *Herpesvirus 3, Human/genetics/isolation & purification ; Spinal Cord/pathology/virology ; *Varicella Zoster Virus Infection/drug therapy/virology ; *Herpes Zoster/drug therapy/virology ; Immunoglobulins, Intravenous/therapeutic use ; High-Throughput Nucleotide Sequencing ; }, abstract = {INTRODUCTION: Varicella zoster virus (VZV) is a human neurotropic herpesvirus that remains latent in the dorsal root ganglia and can reactivate to cause herpes zoster. In immunocompromised patients, reactivation may lead to severe neurological complications such as encephalitis, meningitis, myelitis, and neuropathy. However, varicella zoster virus-related myelitis (VZVM) is relatively rare, particularly in immunocompetent adults. The pathogenesis may involve direct viral invasion of the spinal cord parenchyma during the acute phase or a postinfectious immune-mediated inflammatory response.

CASE PRESENTATIONS: This report describes three patients with VZVM(one woman ages 49 years and two men age 60 and 56 years), none of whom presented with a typical rash. Two patients (cases 1 and 2) developed encephalomyelitis at disease onset, characterized by fever, impaired consciousness, and long-segment spinal cord lesions. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) detected VZV nucleic acid in both cases. In case 3, the patient initially developed VZVM complicated by cerebral venous sinus thrombosis. After an interval of approximately 40 days, delayed thoracic myelitis developed, and repeated CSF mNGS testing yielded negative results. All three patients received intravenous antiviral therapy; two additionally received low-dose corticosteroids combined with intravenous immunoglobulin, and one received intravenous methylprednisolone. During follow-up, one patient achieved full recovery of lower-limb motor function, whereas two patients remained paraplegic.

CONCLUSIONS: VZVM presents with diverse clinical manifestations and may occur without the typical vesicular rash. It can develop either during the initial phase of VZV infection or as a delayed complication. Early magnetic resonance imaging and CSF molecular testing support timely diagnosis. Prompt and adequate antiviral therapy combined with immunomodulatory treatment may improve neurological outcomes.}, } @article {pmid41794977, year = {2026}, author = {Yaikhan, T and Wongsurawat, T and Jenjaroenpan, P and Thaipisuttikul, I and Chayakulkeeree, M and Tribhuddarat, C and Nitayanon, P and Peizner, MT and Tansirichaiya, S and Kamolvit, W and Surachat, K}, title = {Evaluating long-read metagenomics for bloodstream infection diagnostics: a pilot study from a Thai Tertiary Hospital.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41794977}, issn = {2045-2322}, support = {B13F660074//the NSRF through the Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; MED6801076S//the National Science Research and Innovation Fund (NSRF) and Prince of Songkla University, Thailand/ ; }, abstract = {UNLABELLED: Bloodstream infections (BSIs) are life-threatening and require rapid, accurate pathogen characterization to guide antimicrobial therapy. Conventional culture-based diagnostics offer limited insight into the genetic basis of antimicrobial resistance (AMR) and virulence. In this study, we applied Oxford Nanopore Technology (ONT) metagenomic sequencing directly to 40 positive blood culture bottles collected at Siriraj Hospital, Thailand (2022 and 2025). Long-read data enabled species identification, AMR marker detection, virulence profiling, and plasmid replicon analysis. Diverse Gram-negative and Gram-positive pathogens were identified, including ESBL-producing Escherichia coli, carbapenem-resistant Klebsiella pneumoniae, Enterococcus spp., and Staphylococcus spp. Comprehensive genomic profiling revealed complex resistance mechanisms, multiple virulence factors related to adhesion, biofilm formation, and toxin production, and diverse plasmid types associated with horizontal gene transfer (HGT). This study demonstrates the value of ONT-based metagenomics as a faster workflow that is blood culture-dependent but subculture-independent, enabling species identification and AMR gene detection within 6–8 h, compared with 5–7 days for conventional methods, while supporting integrated genomic characterization for diagnostics, infection control, and regional AMR surveillance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41247-2.}, } @article {pmid41795336, year = {2026}, author = {Hao, J and Zhang, YT and Li, X and Dai, X and Xu, Y}, title = {Water-evaporation-induced efficient high-temperature aerobic fermentation of food waste.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134368}, doi = {10.1016/j.biortech.2026.134368}, pmid = {41795336}, issn = {1873-2976}, mesh = {*Fermentation ; Food Loss and Waste ; *Water/chemistry ; Aerobiosis ; *Hot Temperature ; Oxygen ; Volatilization ; }, abstract = {Aerobic fermentation is an effective approach for reducing, stabilising, and recovering resources from food waste. However, its performance is often constrained by poor oxygen transfer within the fermentation substrate. In this study, we investigated the inductive mechanism of water evaporation enhancing aerobic fermentation of food waste. It was observed that water evaporation, as the primary driving force, promoted microscale moisture redistribution and pore structure optimization, leading to an 84.8% (p < 0.01) increase in the average pore diameter and an 8.7% (p < 0.01) increase in porosity. As a result, a significant increase in the oxygen mass transfer coefficient (+250.1%) was achieved within the food waste. This improved microenvironment steered microbial community succession toward thermophilic functional groups dominated by Bacillus and Diutina, prolonging the thermophilic phase by 167% (p < 0.05) and facilitating the degradation of major organic components. Among them, the degradation rate of lipids was significantly increased by 57.1% (p < 0.01). Consequently, the humic substance content in the fermentation product increased by 18.8% (p < 0.05) and the corresponding germination index increased by 41.4% (p < 0.05). These results were further confirmed by the metagenomic analysis, which indicated that water evaporation induced the significant enrichment of functional genes associated with the tricarboxylic acid cycle and electron transport chain in the aerobic fermentation. These findings offer new mechanistic insights into leveraging microscale moisture regulation to optimize aerobic bioconversion.}, } @article {pmid41795395, year = {2026}, author = {Chen, Z and Kerfahi, D and He, X and Zhang, X and Zhang, P and Gao, G and Gao, K and Hall-Spencer, JM and Adams, JM and Lin, X}, title = {Ocean acidification reduces diatom and photosynthetic gene abundance on plastic in an coastal bay mesocosm experiment.}, journal = {Marine environmental research}, volume = {217}, number = {}, pages = {107917}, doi = {10.1016/j.marenvres.2026.107917}, pmid = {41795395}, issn = {1879-0291}, mesh = {*Ocean Acidification ; *Plastics ; *Diatoms/physiology ; *Photosynthesis/genetics ; China ; *Seawater/chemistry ; Carbon Dioxide ; *Water Pollutants, Chemical/toxicity/analysis ; Bays/chemistry ; *Environmental Monitoring ; }, abstract = {Discarded plastics are accumulating in the global ocean and posing threats to marine life. The plastisphere - the community colonizing plastic surfaces - profoundly influences the environmental behavior of plastic, affecting its degradation and entry into marine food webs. Ocean acidification (OA) due to anthropogenic CO2 emissions, is also threatening marine ecosystems, but the effect of OA on the structure and ecological functions of plastisphere communities remain poorly understood. Here, using a mesocosm experiment, we investigated the effects of OA on the plastisphere colonizing floating PET plastic bottles. The study was conducted using subtropical eutrophic coastal water from Southern China under two CO2 conditions: increased CO2 to 1000 μatm (HC) and ambient CO2 410 μatm (LC). Metagenomic sequencing of the plastic samples, after exposure for 32 days, showed striking changes in relative abundance of eukaryotes and bacteria caused by HC. There was a 75.3 % decrease in eukaryote read abundances at high CO2, most strikingly a 95.6% decrease in the relative abundance of diatoms. In addition, the relative abundance of genes involved in photosystem II light reactions and pigment synthesis decreased under high CO2 conditions. This suggests that OA could reduce the photosynthetic potential of the plastisphere. Shifts in plastisphere community structure and potentially diminished photosynthesis under OA could influence food chains within plastisphere, plastic degradation, transportation, and carbon cycling involving plastics. Overall, our results suggest that OA can alter the functional ecology of the plastisphere, with potential implications for marine biogeochemical processes and food web dynamics in subtropical eutrophic coastal water.}, } @article {pmid41795412, year = {2026}, author = {Zhang, T and Yang, L and Xie, F and Xing, M and Zhang, H and Song, X and Ai, L}, title = {Docynia delavayi (Franch.) Schneid polyphenols: Optimization of ultrasound-assisted extraction and bioactivity study.}, journal = {Ultrasonics sonochemistry}, volume = {128}, number = {}, pages = {107804}, pmid = {41795412}, issn = {1873-2828}, mesh = {*Polyphenols/pharmacology/isolation & purification/chemistry ; *Chemical Fractionation/methods ; *Ultrasonic Waves ; Antioxidants/pharmacology/isolation & purification/chemistry ; alpha-Amylases/antagonists & inhibitors ; Anti-Bacterial Agents/pharmacology/isolation & purification ; Bacteria/drug effects ; }, abstract = {Docynia delavayi is a polyphenol-rich indigenous plant from China, known for its medicinal and edible properties. However, its bioactivities have been scarcely studied. This study aimed to establish an efficient ultrasound-assisted extraction (UAE) process for isolating D. delavayi polyphenols (DDP) and to systematically assess their bioactivities. Single-factor assays combined with response surface methodology were employed to determine optimal UAE conditions for DDP: 43% ethanol, 460 W ultrasonic power, 21 mL/g liquid-to-solid ratio, and 41 min extraction. In vitro evaluation showed that DDP exhibited excellent antioxidant (DPPH radical scavenging IC50 = 3.75 μg/mL) and carbohydrate digestion enzyme (α-Glucosidase and α-Amylase) inhibitory activity. Moreover, DDP also exhibited inhibitory effects on Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Salmonella. Metagenomic analysis revealed that DDP promoted species associated with short-chain fatty acid synthesis, such as Flavonifractor plautii and Eubacterium sp., while reducing pathogenic bacteria, including Shigella sonnei and Klebsiella pneumoniae. Untargeted metabolomics analysis showed that DDP modulated the intestinal metabolic profile and enriched pathways involved in Fatty acid biosynthesis, Fatty acid metabolism, and Fatty acid elongation in mitochondria. We believe that DDP, owing to its remarkable biological activity, may exhibit significant prebiotic effects, thereby modulating the gut microbiota and metabolic network, ultimately improving host health. This study elucidated an efficient UAE process and the diverse biological activities of DDP, providing an experimental foundation for its development as a natural functional ingredient and supporting high-value utilization of medicinal and edible plant resources.}, } @article {pmid41795563, year = {2026}, author = {Chen, J and Zhou, Z and Liu, D and Yao, Y}, title = {Kaolinite-mediated dual enhancement of tetracycline degradation and methane recovery in anaerobic digestion of contaminated sludge: Microbial community reshaping and metabolic pathway regulation.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141659}, doi = {10.1016/j.jhazmat.2026.141659}, pmid = {41795563}, issn = {1873-3336}, mesh = {*Methane/metabolism ; *Sewage/microbiology ; *Kaolin/chemistry ; *Tetracycline/metabolism/chemistry ; Anaerobiosis ; Biodegradation, Environmental ; *Anti-Bacterial Agents/metabolism/chemistry ; Metabolic Networks and Pathways ; Bacteria/metabolism/genetics ; }, abstract = {Tetracycline (TC) residues in waste-activated sludge (WAS) inhibit key microbial guilds, destabilizing anaerobic digestion (AD). Conventional AD systems rarely achieve both effective antibiotic detoxification and energy recovery. This study investigates the use of kaolinite, a low-cost mineral with superior stability and surface adsorption properties compared to montmorillonite, as an additive for TC-spiked WAS treatment. At an optimal dosage of 0.2 g·L[-1] , kaolinite increased specific methane yield to 44.4 L·kg VS[-1] , a 4.0-fold enhancement over the control, while improving TC removal by 55%. LC-HRMS identified eleven TC transformation products through three main degradation pathways: hydroxylation, N-dealkylation, and ring cleavage. Metagenomic sequencing showed kaolinite selectively enriched syntrophic taxa (Anaerolinea, Hydrogenispora) and the methanogen Methanosarcina, while upregulating genes involved in extracellular electron transfer (e.g., mhcA), methanogenesis (mcrA), and antibiotic resistance/detoxification (tetW, tetX). Network analysis revealed a shift from competitive to mutualistic interactions, enhancing community resilience under TC stress. Mechanistically, kaolinite acts as a "physicochemical buffer and microbial-activity regulator", stabilizing the microenvironment and promoting efficient methanogenesis through direct interspecies electron transfer. These combined effects improve both pollutant removal and methane production, demonstrating a promising approach for optimizing AD in antibiotic-laden sludge management.}, } @article {pmid41795600, year = {2026}, author = {Fu, Z and Wang, T and Zhang, J and Wang, W and Zhang, X and Wei, K and Tahir, M and Zhong, J}, title = {Multi-Omics Reveals Phenethyl Acetate and Its Producer Lactiplantibacillus plantarum as Key Drivers of Enhanced Palatability in Alfalfa Silage.}, journal = {Microbial biotechnology}, volume = {19}, number = {3}, pages = {e70332}, pmid = {41795600}, issn = {1751-7915}, support = {32201467//National Natural Science Foundation of China/ ; XDA26040201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2025KJHZ0041//Science and Technology Program of the Inner Mongolia Autonomous Region/ ; }, mesh = {*Silage/analysis/microbiology ; *Medicago sativa/chemistry/microbiology ; Fermentation ; Amino Acids/analysis/metabolism ; *Acetates/metabolism ; Flavoring Agents/metabolism ; *Lactiplantibacillus plantarum/metabolism ; Taste ; Animals ; Phenylethyl Alcohol/analogs & derivatives ; }, abstract = {High-quality silage enhances palatability and feed intake; however, the effects of co-fermentation with flavouring agents and lactic acid bacteria (LAB) on its flavour quality, core microbiota, and taste-active amino acids remain unclear. This study investigated the effects of fermentation using Lactiplantibacillus plantarum (LP) alone or in combination with phenethyl acetate (LPP) on the flavour profile of alfalfa silage and its subsequent influence on feed intake. Both LP and LPP significantly improved fermentation quality versus control (CK), with markedly higher feed intake-LP > CK and LPP > LP. Key flavour compounds, including dimethyl trisulfide, 4-ethylphenol and β-damascenone, were significantly increased in the LP alone group. Contrarily, essential taste-related amino acids including aspartic acid, alanine, proline, histidine, isoleucine, and valine were decreased, except for arginine. These metabolic shifts collectively contributed to enhanced feed intake. The addition of LPP increased phenylethyl alcohol, benzyl alcohol and hexanal, and decreased arginine, contributing to enhanced palatability. Aryl alcohol dehydrogenase, proline aminopeptidase, histidine dehydrogenase, and branched-chain amino acid transaminase from LP played a crucial role in the formation of phenylethyl alcohol, proline, histidine and isoleucine during fermentation. These results provide insights into how LAB and flavouring agents jointly regulate flavour development in high-quality alfalfa silage.}, } @article {pmid41796197, year = {2026}, author = {Sujeeth, NK and Dharani Bommi, KB and Manojkumar, S and Angayarkanni, J and Gnanadesigan, M}, title = {Microbiome signatures of mangroves and salt marsh halophyte rhizosphere soil sediments: a metagenomic approach.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41796197}, issn = {2045-2322}, abstract = {UNLABELLED: In this research, the rhizosphere soil microbiome diversity of mangrove trees such as Avicennia marina, Ceriops tagal & Rhizophora apiculata and salt marsh halophytes Suaeda maritima, Suaeda monoica and Sesuvium portulacastrum from Karankadu mangroves of Tamil Nadu, India was investigated. The collected sample was profiled by 16S rRNA Illumina NovaSeq 6000 platform sequencing of V3–V4 amplicon region by metagenomic approach to investigate the bacterial communities related with the different mangrove species. Root-associated microbes of the mangrove trees play important roles in protecting and maintaining mangrove ecosystems. Bacteria were the most abundant domain followed by Archaea and Eukaryota; Proteobacteria, Actinobacteria, Firmicutes, Fibrobacterota, Chlorobiota, and Bacteroidota were found to be predominant phyla present in all samples; Unculturable environmental microbes were also detected, particularly abundant in S. maritima and S. monoica samples. Staphylococcus aureus, Vibrio parahaemolyticus, Klebsiella pneumoniae, Salmonella enterica, Streptomyces griseocarneus were the most abundant species observed in this study. The variations in bacterial community structure across these ecosystems may be influenced by the distinct environmental conditions of each sampled mangrove habitat. For the first time, our findings highlight the richness of microbial diversity in the Karankadu mangroves, providing essential baseline data and revealing differences between mangrove trees and halophytes. This study offers valuable insights for further investigation into the mechanisms governing rhizosphere microbiome interactions with their host environment.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42270-z.}, } @article {pmid41796297, year = {2026}, author = {Shi, K and He, Q and Wang, S and Guo, J}, title = {An adaptive weight self-distillation deep learning framework for phenotype prediction from longitudinal gut microbiome data.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41796297}, issn = {1471-2180}, support = {62562022//National Natural Science Foundation of China/ ; Guike ZY22096025//Special Funds for Guiding Local Scientific and Technological Development by the Central Government/ ; 2025JJA170175//Guangxi Natural Science Foundation/ ; Z-C20241570//Guangxi Health Commission Self-Funded Research Project/ ; }, abstract = {BACKGROUND: The gut microbiota plays a vital role in maintaining human health. In recent years, extensive researches has focused on phenotype prediction in relation to various diseases, with the gut microbiota as a key predictor. Nevertheless, most existing studies rely on single-time-point analyses, which are insufficient to capture the dynamic patterns of host states and temporal variations inherent in longitudinal data.

RESULTS: In this study, we propose a deep learning framework, AWSD-CNN-LSTM, designed to classify host phenotypes using longitudinal metagenomic data. Unlike conventional approaches that treat each time point as an independent sample, our method models the sequential samples of each individual as a whole, integrating convolutional neural network (CNN) and long short-term memory network (LSTM) to effectively capture temporal dependencies in longitudinal microbiome sequencing data. In addition, the model incorporates an adaptive point-wise self-distillation mechanism to more accurately characterize host-specific patterns. Compared with state-of-the-art methods, AWSD-CNN-LSTM demonstrates superior performance on the PROTECT, DIABIMMUNE, and Infants datasets, achieving area under the receiver operating characteristic curve (AUC) values of 0.896, 0.813, and 0.894, respectively.

CONCLUSIONS: For the task of disease phenotype classification based on temporal data, we propose a novel framework that effectively captures the characteristics of time-series data and achieves high accuracy across multiple datasets. Our approach holds promise as a potential new tool for microbial knowledge discovery.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04922-y.}, } @article {pmid41796809, year = {2026}, author = {He, J and Zhang, A and Wang, L and Ping, Q and Gao, P and Liu, Y}, title = {Aging attenuates threat: how moderate aging of microplastics suppresses antibiotic resistance gene proliferation during sludge anaerobic digestion.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134342}, doi = {10.1016/j.biortech.2026.134342}, pmid = {41796809}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; Anaerobiosis ; *Microplastics ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Microplastics (MPs) are known to promote antibiotic resistance gene (ARG) dissemination in waste activated sludge; however, most existing evidence is based on unaged MPs, and the influence of aging degree remains poorly understood. This study systematically investigated how varying aging degrees of polyethylene (PE) and polypropylene (PP) MPs modulate ARG profiles and transfer mechanisms during anaerobic digestion. The results demonstrated a non-monotonic effect of aging degree on ARG proliferation, with moderate aging of MPs showing the strongest attenuation of ARG promotion. Under moderate carbonyl indices (CI) of 0.104 for PE-MPs and 0.219 for PP-MPs, the average reduction of the most affected ARGs reached 40% and 50%, respectively, compared with the unaged MPs. Metagenomic analysis further revealed that moderate aging of MPs reduced both the abundance and diversity of ARGs stimulated by unaged MPs. Mechanistically, unaged MPs induced multiple biological responses. These included enrichment of dominant ARG-hosting genera within Proteobacteria and Chloroflexi, elevated oxidative stress, increased membrane permeability, and activation of horizontal gene transfer (HGT) pathways, including the type IV secretion system (T4SS), quorum sensing (QS), and two-component systems (TCS). Conversely, aging weakened these microbial signaling and stress responses at moderate aging degrees but led to a rebound at higher aging degrees, thereby modulating HGT potential in a non-monotonic manner. These findings indicate that aging of sludge-relevant MPs (PE and PP) fundamentally alters their ecological impact on the sludge resistome, highlighting the necessity of incorporating aging dynamics into the risk assessment of MPs in engineered ecosystems.}, } @article {pmid41797015, year = {2026}, author = {Jeon, J and Lee, DH and Kim, JH and Choi, Y and Jin, YK and Hong, JK and Lee, YM}, title = {Methanotrophic community structure and metabolic potential in the sulfate-methane transition zone of the ARAON mounds, Arctic Chukchi Sea.}, journal = {Marine environmental research}, volume = {217}, number = {}, pages = {107959}, doi = {10.1016/j.marenvres.2026.107959}, pmid = {41797015}, issn = {1879-0291}, mesh = {*Methane/metabolism ; Arctic Regions ; *Archaea/metabolism ; *Sulfates/metabolism ; Geologic Sediments/microbiology ; Seawater/microbiology ; *Microbiota ; Bacteria/metabolism ; Oceans and Seas ; Oxidation-Reduction ; }, abstract = {Anaerobic oxidation of methane (AOM) mediated by archaea is a pivotal process for methane consumption in gas seepage-associated sediments. Despite its importance in regulating methane flux, the ecological roles and metabolic potential of microbial communities involved in AOM remain poorly understood in Arctic regions. In this study, we investigated the microbial community structures and methanotrophic signatures in sediments from gas hydrate-bearing and non-gas hydrate-bearing sites in ARAON Mounds (AMs) and reference sites. Microbial communities in AMs were distinct from those in reference sites, with high relative abundances of Euryarchaeota (45.5 ± 11%), Lokiarcheota (35 ± 6.1%), and Atribacterota (50.1 ± 23.3%). Anaerobic methanotrophic archaea (ANME) showed site- and depth-specific distributions, with ANME-1a, ANME-1b, and ANME-2c predominating the sulfate-methane transition zone (SMTZ) of the gas hydrate-bearing sites, and ANME-1a prevailing at non-gas hydrate-bearing sites. Sulfate-reducing bacteria (SRB) affiliated with Seep-SRB1 co-occurred with ANME-1a and ANME-1b within the AMs. Metagenome-assembled genomes (MAGs) of ANME-1b and ANME-2c recovered from the SMTZ of the gas hydrate-bearing site (AM6) harbored key AOM-related genes, and their putative syntrophic bacterial partner, ETH-SRB1, possessed essential genes for sulfate reduction. Additionally, Lokiarchaeota and Atribacterota MAGs encoded genes involved in protein degradation, fermentation, and hydrogen metabolism, indicating their possible roles in methane cycling. Collectively, these results reveal distinct microbial assemblages and their functional genomic traits, suggesting niche specialization associated with methane oxidation potential at the SMTZ of the gas hydrate-bearing site.}, } @article {pmid41797140, year = {2026}, author = {You, G and Jin, H and Wu, M and Li, Y and You, X and Huang, C and Xu, Y and Hou, J}, title = {Insights into antibiotic resistance gene dynamics during Tanfloc-induced flocculation-storage process for cyanobacteria removal in an algae-laden drinking water source.}, journal = {Journal of environmental management}, volume = {403}, number = {}, pages = {129223}, doi = {10.1016/j.jenvman.2026.129223}, pmid = {41797140}, issn = {1095-8630}, mesh = {Flocculation ; *Drinking Water/microbiology ; *Cyanobacteria ; *Drug Resistance, Microbial/genetics ; Tannins ; }, abstract = {Tannin-based flocculants (TA) are increasingly promoted as green polymeric alternatives for cyanobacteria removal in algae-laden drinking water sources, yet their potential to influence antibiotic resistance gene (ARG) dissemination during subsequent flocculation-storage remains unclear. This study compared TA with polyaluminum chloride (PACl) to assess ARG fate in both supernatant and cyanobacteria-laden drinking water sludge throughout flocculation and 8-day storage. Results showed that TA achieved over 97% removal efficiency for both cyanobacteria and ARGs at a low dosage of 20 mg/L, outperforming PACl. Moreover, TA treatment led to markedly reduced release of microcystin-LR and dissolved organic matter (DOM) after storage. Nevertheless, elevated biomass within TA-induced flocs promoted ARG proliferation, primarily due to enhanced production of triplet-state DOM and suppression of carotenoid synthesis. Metagenomic evidence indicated elevated abundances of CAZyme genes (e.g., GH43, CE4, CE1, GH9, CE11), highlighting an increased functional potential for TA-associated polymer breakdown and consequent weakening of the floc coating after 8 days, which in turn promoted ARG escape from flocs. Meanwhile, increased motility of phycosphere-associated antibiotic-resistant bacteria (e.g., Pseudomonas) promoted ARG transfer into the supernatant, accompanied by enrichment of mobile genetic elements and virulence factor genes, which collectively amplified ecological risks. These findings underscore that ARG release and dissemination should be explicitly integrated into safety assessments of TA-based cyanobacteria control, and they provide mechanistic guidance for mitigating ARG hazards in algal-affected drinking water supplies.}, } @article {pmid41797187, year = {2026}, author = {Tang, Z and Liu, X and Yang, J and Zhang, F and Shan, X and Liu, Y and Li, F and Lu, S and Xi, B}, title = {Unraveling the redox-driven mechanisms of viral-bacterial interactions in modulating the fate of antibiotic resistance genes.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134358}, doi = {10.1016/j.biortech.2026.134358}, pmid = {41797187}, issn = {1873-2976}, mesh = {Oxidation-Reduction ; *Bacteria/genetics/virology ; *Genes, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Wetlands ; Electrodes ; Bioelectric Energy Sources/microbiology ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging contaminants in wastewater systems, where heterogeneous redox conditions regulate microbial community assembly and ARG dissemination. However, how within-system redox gradients generated by electrochemical configurations structure bacterial and viral processes and ultimately control ARG dynamics remains unclear. Here, we established a vertical-flow wetland (VW), a direct-current powered VW (DW), and a microbial fuel cell-coupled VW (MW), and performed metagenomic analyses of substrates adjacent to anodes and cathodes to resolve spatial ARG patterns and mechanisms. Across all systems, 478 ARG subtypes from 26 classes were detected, dominated by sulfonamide, multidrug, and tetracycline resistance genes. Electrochemical operation substantially reduced total ARG abundance, with inhibition efficiencies of 49% in DW and 73% in MW and suppressed high-risk genes such as sul1, sul2, tetG, and bacA. Pronounced divergence occurred between anodic and cathodic microenvironments, with ARG levels averaging 0.419 and 0.229 copies per cell, respectively. Redox differentiation reshaped ARG host composition, microbial diversity, ecological networks, virus-host interactions, and metabolic strategies. Cathodic reductive zones were enriched in viral auxiliary metabolic genes linked to folate pathways, potentially alleviating sulfamethoxazole-driven selection, whereas anodic oxidative environments favored outer-membrane porins and mobile genetic elements, coinciding with elevated ARG abundance and greater horizontal transfer potential. Collectively, these results highlight redox-driven microbial metabolism, viral auxiliary functions, and MGE-mediated mobility as key regulators of ARG fate in electrochemical wetlands and provide guidance for engineering redox-optimized systems to mitigate ARG dissemination.}, } @article {pmid41797508, year = {2026}, author = {Huang, C and Xiao, W and Zhao, J and Zhong, R and Gao, L and Ma, H and Tian, L and Yue, P and Lin, Y and He, Q and Xia, B and Yuan, J and Yang, M and Meng, W}, title = {Gut Microbiome Dysbiosis Promotes Gallstone Formation via Bile Acid Metabolic Disorder: A Multiomics Study.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {6}, pages = {e71656}, pmid = {41797508}, issn = {1530-6860}, support = {82204123//MOST | National Natural Science Foundation of China (NSFC)/ ; 82473707//MOST | National Natural Science Foundation of China (NSFC)/ ; LCYSSQ20220823091203008//Funding of Shenzhen Clinical Research Center for Gastroenterlogy (Gastrointestinal Surgery)/ ; 2022YFC2407405//MOST | National Key Research and Development Program of China (NKPs)/ ; }, mesh = {Humans ; *Bile Acids and Salts/metabolism ; *Gallstones/metabolism/microbiology/etiology/pathology ; *Dysbiosis/metabolism/microbiology/complications ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Middle Aged ; *Metabolic Diseases/metabolism/microbiology ; Adult ; Amidohydrolases/metabolism ; Case-Control Studies ; }, abstract = {Gallstone disease is a common global digestive disorder. This study intends to analyze gut microbiota-gallstone disease interactions, to inform disease mechanism and microbiota-targeted prevention and treatment strategies. Participants were recruited from health check-up populations, outpatients, and inpatients. Basic information and biological samples were collected: fecal samples for metagenomic sequencing, and serum samples for bile acid metabolism detection. A total of 62 gallstone patients and 62 healthy controls were enrolled in this study. Compared with the control group, gallstone patients exhibited increased level of bile salt hydrolase (BSH)-producing bacteria, including the genera Bacteroides, Enterococcus, Bifidobacterium, and the family Lactobacillaceae. Further KEGG analysis revealed that the significantly enriched signaling pathways in the gallstone patients were mainly related to bile acid biosynthesis, lipid and bile acid precursor metabolism. Subsequently, we found that in gallstone patients, the levels of hydrophobic bile acids, (e.g., lithocholic acid, LCA), was increased, while the levels of hydrophilic bile acids taurolithocholic acid (TLCA) were decreased. In the correlation analysis between differential bile acids and differential bacterial species, Bacteroides intestinalis was positively correlated with LCA, while Bacteroides fragilis was negatively correlated with TLCA. These results further confirm the role of BSH-active bacteria in bile acid dysregulation. This study proposes the "intestinal microbiota imbalance-bile acid metabolic disorder-gallbladder stone formation" axis, and confirms that gallstone patients exhibit intestinal dysbiosis, which leads to bile acid dysregulation. Furthermore, the accumulation of hydrophobic bile acids is identified as a key factor in gallbladder stone formation.}, } @article {pmid41797768, year = {2026}, author = {Dai, M and Pang, L and Hu, M and Meng, J and Ji, C and Sheng, L and Zhang, W}, title = {Case report: Be alert to parvovirus infection in patients with unexplained anemia after cerebral hemorrhage surgery.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1700344}, pmid = {41797768}, issn = {2296-858X}, abstract = {BACKGROUND: Human parvovirus B19 (PVB19) is a highly prevalent single-stranded DNA virus that infects a large proportion of the global population. It can involve multiple organ systems, leading to a broad spectrum of clinical manifestations. While most infections in immunocompetent individuals are mild and self-limiting, PVB19 can occasionally cause severe and diverse complications.

CASE PRESENTATION: We report a rare case of an immunocompetent patient who experienced unexplained clinical deterioration following surgical evacuation of an intracerebral hemorrhage. The patient presented with refractory anemia, impaired consciousness, fever, seizures, and progressive dysfunction of the cardiac, hepatic, and renal systems. Metagenomic next-generation sequencing revealed high levels of PVB19 DNA in the cerebrospinal fluid, blood, and pleural effusion. The patient was treated with intravenous immunoglobulin (IVIG) therapy and supportive care. Following treatment, improvements were observed in consciousness, mobility, and anemia. However, renal function failed to recover and ultimately progressed to renal failure, necessitating renal replacement therapy.

CONCLUSION: This case underscores the potential severity of PVB19 infection following cerebral hemorrhage surgery, particularly when accompanied by unexplained anemia. Accurate diagnosis requires a high index of suspicion and the use of advanced diagnostic tools. Management primarily involves IVIG therapy and supportive care. This case highlights the importance of expanding the differential diagnosis in postoperative patients presenting with unexplained anemia and multi-organ dysfunction, as early recognition of atypical infections may improve clinical outcomes.}, } @article {pmid41797781, year = {2026}, author = {Zhang, X and Li, W and Zhao, S and Han, Y and Ma, W and Jiang, Z and Ma, Y and Zhang, G and Wang, J and Jia, H and Guo, S and Cui, N}, title = {Fulminant amebic colitis complicated by appendiceal perforation and massive abdominal hemorrhage: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1760895}, pmid = {41797781}, issn = {2296-858X}, abstract = {INTRODUCTION: Fulminant amebic colitis complicated by intestinal perforation or massive intra-abdominal hemorrhage is uncommon but associated with extremely high mortality. In non-endemic regions, diagnosis is frequently delayed because early manifestations resemble bacterial appendicitis or perforated peritonitis.

CASE PRESENTATION: We report a fatal case of Entamoeba histolytica infection presenting with appendiceal perforation, septic shock, and recurrent intra-abdominal bleeding. Surgery revealed extensive transmural necrosis, deep ulcers, and exposure of submucosal vessels. Metagenomic next-generation sequencing (mNGS) of blood and peritoneal drainage fluid was performed, followed by histopathological confirmation. Despite emergent appendectomy, bowel resection, and prompt initiation of anti-amebic therapy, the patient developed refractory septic shock and recurrent intra-abdominal hemorrhage, resulting in death.

CONCLUSION: mNGS can facilitate early recognition of severe amebiasis when conventional diagnostic modalities are uncertain, particularly in non-endemic settings. Fulminant amebic colitis complicated by perforation or hemorrhage carries a poor prognosis. Timely clinical suspicion and early anti-amebic therapy are essential to improve outcomes.}, } @article {pmid41798955, year = {2026}, author = {Xiao, Y and Zhang, T and Chen, Q and Zhang, Y and Chen, B and Wang, M and Zhang, Y and Huang, M and Su, Y and Guo, J}, title = {Multi-omics analysis reveals the mechanism of verbenalin in treating gout via modulating purine metabolism, gut microbiota, and inflammatory pathways.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1761558}, pmid = {41798955}, issn = {1664-3224}, mesh = {Animals ; *Purines/metabolism ; Multiomics ; Rats ; Male ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Signal Transduction/drug effects ; *Gout/drug therapy/metabolism ; *Anti-Inflammatory Agents/pharmacology ; Metabolomics ; Inflammation/metabolism/drug therapy ; }, abstract = {BACKGROUND: Gout is a prevalent metabolic disorder characterized by hyperuricemia and inflammation. Verbenalin, an iridoid glycoside from Verbena officinalis, possesses anti-inflammatory properties; however, its therapeutic potential and underlying mechanisms in gout remain underexplored.

OBJECTIVE: This study aimed to evaluate the pharmacological effects and elucidate the molecular mechanisms of verbenalin in a rat model of gout.

METHODS: Hyperuricemia and acute gouty arthritis were induced in rats using potassium oxonate/hypoxanthine and monosodium urate, respectively. Verbenalin was administered orally for 7 days. Therapeutic efficacy was assessed via physical symptom scores (inflammation, gait, swelling), renal/hepatic function indices, and histopathology. Furthermore, a multi-omics strategy integrating transcriptomics, metagenomics, and metabolomics, combined with Western blotting, was employed to investigate the pharmacological mechanisms.

RESULTS: Verbenalin treatment significantly alleviated joint inflammation and swelling while improving gait scores. It effectively lowered serum uric acid (UA), creatinine, and BUN levels, inhibited hepatic xanthine oxidase (XOD) activity, and promoted urinary UA excretion. Histopathological damage in the joints, kidneys, and liver was markedly mitigated. Mechanistically, verbenalin downregulated the expression of urate transporters (URAT1, GLUT9) and inflammatory mediators (NLRP3, IL-1β) by inhibiting the PI3K-AKT and MAPK signaling pathways. Multi-omics analysis further revealed that verbenalin restored gut microbiota diversity and modulated purine metabolism, correlating with reduced UA levels.

CONCLUSION: These findings demonstrate that verbenalin may exert anti-gout effects through the potential synergy of modulating purine metabolism, shifting gut microbiota composition, and suppressing PI3K-AKT and MAPK inflammatory signaling pathways. This study provides a preliminary scientific basis for further investigation into verbenalin as a prospective multi-target therapeutic candidate.}, } @article {pmid41799583, year = {2026}, author = {Ofuchi, T and Hu, Q and Omachi, K and Kanemitsu, K and Otsu, H and Yonemura, Y and Tobo, T and Baba, Y and Iwatsuki, M and Mimori, K}, title = {Intratumoral Fusobacterium nucleatum Drives Cancer-Associated Fibroblasts Enrichment and Immune Exclusion in Esophageal Squamous Cell Carcinoma.}, journal = {Annals of gastroenterological surgery}, volume = {10}, number = {2}, pages = {611-620}, pmid = {41799583}, issn = {2475-0328}, abstract = {BACKGROUND: Fusobacterium nucleatum, an oral commensal bacterium, has been increasingly recognized for its oncogenic role in gastrointestinal malignancies. In esophageal squamous cell carcinoma (ESCC), F. nucleatum has been implicated in promoting tumor progression and facilitating immune evasion. However, its relationship with stromal remodeling and the tumor microenvironment (TME) remains unclear.

METHODS: We performed integrative analyses using metagenomic profiling and transcriptomic deconvolution, and histopathological assessment of 93 The Cancer Genome Atlas (TCGA)-ESCC cases and an independent cohort of 126 resected tumors. F. nucleatum status was determined by microbial abundance and quantitative Polymerase Chain Reaction (q-PCR).

RESULTS: F. nucleatum-positive tumors showed significant enrichment of TNFα/NF-κB signaling and reduced CD8[+] T cell infiltration. Stromal analysis revealed a marked increase in cancer-associated fibroblasts (CAFs) in F. nucleatum-positive tumors, confirmed by transcriptomic deconvolution and α-SMA immunohistochemistry. Notably, immunohistochemical analysis demonstrated increased nuclear localization of NF-κB p65, indicating F. nucleatum-induced NF-κB activation in tumor cells. Clinically, among elderly patients with poor performance status, the prevalence of F. nucleatum positivity was significantly higher.

CONCLUSION: F. nucleatum may contribute to the progression of ESCC by inducing NF-κB-mediated inflammatory signaling in tumor cells and promoting CAFs activation. Its presence may facilitate immune exclusion and tumor invasion through stromal remodeling. Furthermore, F. nucleatum positivity may reflect broader host vulnerability, particularly in frail elderly individuals. These findings highlight F. nucleatum as a potential biomarker of tumor immune dynamics and suggest the importance of maintaining good oral hygiene to reduce F. nucleatum colonization.}, } @article {pmid41799605, year = {2026}, author = {Suzuki, Y and Osumi, W and Taniguchi, K and Kato-Kogoe, N and Sakaguchi, S and Nakamura, S and Imai, Y and Nakano, T and Ueno, T and Lee, SW}, title = {Comparison of Pre- and Postoperative Gut Microbiota Diversity in Patients With Rectal Cancer Undergoing Stoma Creation and Closure.}, journal = {Annals of gastroenterological surgery}, volume = {10}, number = {2}, pages = {492-501}, pmid = {41799605}, issn = {2475-0328}, abstract = {AIM: To investigate the impact of temporary stoma creation and its subsequent closure on gut microbiota composition and diversity in patients undergoing rectal cancer surgery.

METHODS: Nineteen patients with primary rectal cancer who underwent curative surgery were enrolled and divided into two groups: stoma (n = 10, all underwent temporary ileostomy) and non-stoma (n = 9). Fecal samples were collected preoperatively and 6 months postoperatively. Gut microbiota composition was analyzed using 16S rRNA gene sequencing. Alpha diversity (observed operational taxonomic units and Shannon index) and beta diversity (UniFrac distances) were compared between time points. Taxonomic shift was identified using Linear discriminant analysis Effect Size (LEfSe).

RESULTS: In the stoma group, alpha diversity significantly decreased after surgery (p = 0.049), and beta diversity analyses revealed significant changes in microbial composition (PERMANOVA; unweighted p = 0.026; weighted p = 0.046). LEfSe analysis identified an increased abundance of potentially pathogenic genera (e.g., Enterococcus and Eggerthella) and a decreased abundance of short-chain fatty acid-producing genera (e.g., Megamonas and Anaerostipes). These changes persisted for at least 6 months after stoma closure. In contrast, the non-stoma group showed no significant alterations in microbial diversity or composition over time.

CONCLUSION: Temporary stoma creation in rectal cancer surgery induces persistent alterations in gut microbiota; these alterations are characterized by reduced diversity and a shift toward a dysbiotic profile with increased pathogenic and decreased beneficial taxa. These findings highlight the potential need for microbiota-targeted strategies to mitigate long-term dysbiosis in patients undergoing stoma-related procedures.}, } @article {pmid41799966, year = {2026}, author = {Habuding, X and Chen, J and Zhu, J and Wang, G and Ma, L and Abulikemu, T}, title = {Integrated metagenomic and culturomic strategies to mine and validate beneficial rhizosphere Actinobacteria from lavender.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1745076}, pmid = {41799966}, issn = {1664-462X}, abstract = {INTRODUCTION: The lavender industry faces significant constraints from soil salinization and continuous cropping obstacles. However, systematic exploration and functional analysis of beneficial rhizosphere microbial resources, particularly Actinobacteria, remain inadequate.

METHODS: To address this, we integrated metagenomic and culturomic strategies to investigate the rhizosphere and endophytic microbiomes in saline-alkaline lavender cultivation areas in Huocheng, China (soil pH ~8.04, salt ~0.074%). Metagenomic functional annotation and soil factor correlation analysis guided a subsequent culturomics approach to isolate strains. Isolates were screened for plant growth-promoting (PGP) traits, and selected strains were evaluated in pot inoculation experiments with Arabidopsis thaliana.

RESULTS: High-throughput sequencing revealed that Actinomycetota dominated the microbial communities, with Streptomyces and Nocardioides as key genera. Metagenomic analysis showed the community was enriched with functional genes related to saline-alkaline stress response, secondary metabolite synthesis, and nutrient cycling, whose distribution correlated significantly with soil pH and salinity. From this resource, 10 actinobacterial strains with multiple PGP traits (e.g., P-solubilization, siderophore production, IAA, ACC deaminase, and nitrogenase activity) were obtained. Pot experiments confirmed that these saline-alkaline-derived actinobacteria, both as single strains and as a bacterial consortium (C4 + A1), significantly promoted the growth of A. thaliana.

DISCUSSION: This study achieves a closed-loop verification from in silico functional prediction to empirical validation of beneficial strains. It provides the first systematic elucidation of the functional adaptation mechanisms of the lavender rhizosphere actinobacterial community under saline-alkaline stress and identifies elite microbial resources with both stress tolerance and PGP functions. The findings offer novel microbial agents and a theoretical foundation for developing specialized inoculants to mitigate saline-alkaline obstacles in lavender cultivation.}, } @article {pmid41800013, year = {2026}, author = {Walia, T and Srivastava, N and Shetty, RM and Rana, V}, title = {Metagenomics as an Effective Diagnostic Approach for Exploring Oral Microbial Diversity and Dental Diseases: A Narrative Review.}, journal = {International journal of clinical pediatric dentistry}, volume = {19}, number = {2}, pages = {278-284}, pmid = {41800013}, issn = {0974-7052}, abstract = {AIM AND BACKGROUND: The oral cavity harbors a diverse microbiota that significantly influences oral health and disease. Conventional microbiological techniques have limitations in detecting the full range of microbial species, particularly those that are uncultivable. Metagenomics, through culture-independent, high-throughput sequencing methods, offers a comprehensive approach to studying oral microbial diversity. This narrative review aims to evaluate the role of metagenomics in exploring the oral microbiome and its association with dental diseases.

METHODS: This review systematically synthesized current literature and research on metagenomic technologies, including 16S ribosomal RNA (rRNA) sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics, and metabolomics. It highlighted their principles, diagnostic capabilities, and limitations in analyzing microbial communities in caries, endodontic infections, and periodontitis. It also reviewed auxiliary tools such as quantitative polymerase chain reaction (qPCR), microarrays, fluorescence in situ hybridization (FISH), and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and discussed the integration of artificial intelligence (AI) in metagenomic data interpretation.

RESULTS: Metagenomic studies have expanded the scope of known microbial species involved in dental caries beyond Streptococcus mutans, highlighting the contributions of Lactobacillus, Veillonella, Actinomyces, and Candida albicans. In endodontics, resistant species such as Enterococcus faecalis, Porphyromonas endodontalis, and Fusobacterium nucleatum are implicated in persistent infections. In periodontitis, a dysbiotic microbial shift has been associated with the presence of complex microbial consortia, including red and orange complex bacteria.

CONCLUSION: Metagenomics is a powerful diagnostic tool that provides an in-depth characterization of the complex microbial ecosystem of the oral cavity. It offers diagnostic potential through early and accurate detection of pathogenic shifts, promotes personalized treatment planning, and opens avenues for the development of potential biomarkers of disease progression.

CLINICAL SIGNIFICANCE: The integration of metagenomics into dental practice can revolutionize caries risk assessment, treatment precision, and disease prevention strategies. Although challenges such as high cost, data complexity, and lack of standardization remain, ongoing advancements in sequencing technologies and bioinformatics are expected to enhance its accessibility and clinical relevance.

HOW TO CITE THIS ARTICLE: Walia T, Srivastava N, Shetty RM, et al. Metagenomics as an Effective Diagnostic Approach for Exploring Oral Microbial Diversity and Dental Diseases: A Narrative Review. Int J Clin Pediatr Dent 2026;19(2):278-284.}, } @article {pmid41800387, year = {2026}, author = {Gupta, S and Quarato, V and Lai, W and Kobel, CM and Aho, VTE and Vera-Ponce de León, A and La Rosa, SL and Sandve, SR and Pope, PB and Hvidsten, TR}, title = {OmniCorr: an R-package for visualizing putative host-microbiome interactions using multi-omics data.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag057}, pmid = {41800387}, issn = {2635-0041}, abstract = {Holo-omics leverages omics datasets to explore the interactions between hosts and their associated microbiomes. Although the generation of omics data from matching host and microbiome samples is steadily increasing, there remains a scarcity of computational tools capable of integrating and visualizing this data to facilitate the prediction and interpretation of host-microbiome interactions. We present OmniCorr, an R package designed to: (i) manage the complexity of omics data by clustering co-varying features (e.g. genes, proteins, and metabolites) into modules, (ii) visualize correlations of these modules across different omics layers, host-microbiome interfaces, and metadata, and (iii) identify statistically significant associations indicative of putative host-microbiome interactions. OmniCorr's utility is demonstrated using datasets from two systems: (i) Atlantic salmon, integrating host transcriptomics with metagenomics and metatranscriptomics to explore dietary impacts, and (ii) cattle, combining host proteomics with metaproteomics to investigate methane emission variability. Availability and implementation: OmniCorr is freely available at https://github.com/shashank-KU/OmniCorr.}, } @article {pmid41800416, year = {2026}, author = {Bustos, ML and Song, K and Brochu, HN and Zhang, Q and Iyer, LK and Icenhour, CR}, title = {Impact of non-standardized reporting on reproducibility, usability, and integration in nasopharyngeal metagenomic research: a systematic review.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1707004}, pmid = {41800416}, issn = {1664-302X}, abstract = {INTRODUCTION: The nasopharyngeal microbiome plays a critical role in respiratory health and disease and is a major focus of metagenomic research. However, inconsistent reporting practices across studies limit reproducibility, dataset usability, and cross-study integration, thereby reducing the overall scientific value of publicly available nasopharyn.

METHODS: A systematic review was conducted to evaluate the impact of non-standardized reporting on reproducibility, usability, and integration of nasopharyngeal metagenomic datasets. A total of 988 studies were screened, and 227 manuscripts met predefined inclusion and exclusion criteria for full-text review. Methodological reproducibility, metadata completeness, and compatibility between reported laboratory methods and deposited datasets were assessed. Reproducible datasets were further analyzed to evaluate the interchangeability of nasopharyngeal aspirates and nasopharyngeal swabs.

RESULTS: Only 78 studies (34%) contained methods sections sufficient for reproducibility, and of these, 33 studies (15%) provided analytically sufficient metadata to support secondary analysis. Mismatches between reported laboratory methods and deposited datasets were identified in 4% of studies. These deficiencies were primarily attributed to incomplete methodological reporting, inaccessible or insufficient metadata, and incompatible file formats. Comparative analysis of reproducible datasets demonstrated significant differences in microbial profiles between nasopharyngeal aspirates and nasopharyngeal swabs, confirming that these specimen types are not interchangeable within a study.

DISCUSSION: The findings demonstrate that inadequate reporting standards substantially impair the reproducibility, reuse, and integration of nasopharyngeal metagenomic data. The observed methodological and metadata inconsistencies limit the reliability of downstream analyses and cross-study comparisons. Standardized reporting guidelines are urgently needed to improve transparency, ensure reproducibility, and enhance the integrative potential of nasopharyngeal microbiome research. Adoption of comprehensive and consistent reporting practices would significantly strengthen the scientific rigor and utility of metagenomic studies in this field.}, } @article {pmid41800425, year = {2026}, author = {Huangfu, H and Pu, J and Jiao, M and Zhou, H and Fan, Q and Deng, H and Ling, Q and Luo, X and Xu, J}, title = {Unveiling the RNA viral diversity in three organs of the Asian house shrew (Suncus murinus) from Tropical Hainan, China: a previously underappreciated key zoonotic reservoir.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1738936}, pmid = {41800425}, issn = {1664-302X}, abstract = {Shrews represent an important reservoir of diverse human-pathogen viruses with implications for human infectious diseases. As the most populous shrew species, the Asian house shrew-Suncus murinus (Su. murinus) is widely distributed across South and Southeast Asia-particularly tropical and subtropical regions-yet its virome remains poorly studied. In this study, we collected 249 Su. murinus from 18 cities/counties (excluding Sansha) across Hainan Island and conducted RNA sequencing on gut, spleen, and lung tissues. We identified 192 RNA viruses, comprising 120 known viral species and 72 novel viruses, including key zoonotic viral families: Arenaviridae, Hantaviridae, Paramyxoviridae etc. We assembled 102 complete and nearly complete genomes. Notably, 64 known viruses exhibited cross-species transmission potential, including 57 with spillover risk and 7 human-pathogenic viruses: Mammarenavirus choriomeningitidis (LCMV), Henipavirus (HeV), Wenzhou virus (WENV), Langat virus (LGTV), Amur virus (AMRV), Influenza A virus (H1N1), and Rotavirus A (RVA). Additionally, AMRV, LGTV, and LCMV were reported here for the first time in Su. murinus based on metagenomic detection. Our phylogenetic and RT-PCR results indicate Su. murinus is a candidate reservoir for Langya-like henipavirus. Collectively, our study reveals tropical populations of Su. murinus are a previously underappreciated reservoir of viral diversity, underscoring their key role in zoonotic emergence and necessitating surveillance in tropical regions.}, } @article {pmid41800589, year = {2026}, author = {Juan, DR and Dilanaz, A and Camila, RV and Fernando, DG and Pedro, SR and Ana, MB and Ricardo, U and Barrie, JD and Mario, V and Díez, B and Matías, C and Pedro, T and Alejandra, G and Francisco, I and Raquel, Q}, title = {Microbial succession and assembly shaped by sulfur, spatial partitioning, and water flow in a volcanic acidic river of northern Patagonia.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41800589}, issn = {1751-7370}, mesh = {*Sulfur/metabolism/analysis ; *Rivers/chemistry/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Argentina ; Metagenomics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; *Archaea/classification/genetics/metabolism ; DNA, Ribosomal/genetics/chemistry ; Molecular Sequence Data ; }, abstract = {Extreme acidic environments represent natural laboratories for investigating the mechanisms of microbial community assembly, yet the ecological processes structuring these communities remain incompletely understood. Here, we investigate how spatial partitioning, hydrodynamics, and colonization history shape microbial succession in a unique sulfur-rich, acidic river of volcanic origin in northern Patagonia. We combined 16S rRNA gene profiling and shotgun metagenomics with a multi-scale experimental framework encompassing water column fractionation and colonization assays under native and controlled conditions. Microbial diversity was strongly influenced by spatial fractionation, with free-living communities exhibiting higher richness and temporal variability than particle-associated assemblages. Water flow modulated community structure, increasing evenness in free-living fractions under high-flow conditions, but had limited impact on particle-attached communities. Colonization of sulfur-beads followed a structured successional trajectory, with autotrophic sulfur oxidizers dominating early stages and heterotrophs adapted to biofilm lifestyles increasing over time. Ex situ recolonization assays revealed strong priority effects, with initial colonizers determining successional trajectories. Turnover analyses revealed that the balance among stochastic and deterministic assembly processes shifted across communities with pronounced stochasticity in the water column and flow-dependent effects in free-living communities, while biofilm associated communities on sulfur-beads exhibited stronger contribution of deterministic selection. These ecological patterns were mirrored by functional differentiation, with gene enrichment analyses revealing adaptive signatures of substrate attachment and resource acquisition. By integrating fine-scale environmental variation with colonization dynamics, this study reveals how microscale habitat structure and temporal fluxes jointly modulate microbial community assembly rules, offering a nuanced framework to dissect ecological processes in extreme systems.}, } @article {pmid41800893, year = {2026}, author = {Ge, T and Zhao, T and Ruan, Y and Ye, L and Xiao, Y and Xiao, F and Li, Y and Li, X and Wang, R and Hu, H and Lu, C and Sun, H and Zhang, C and Yu, G and Zhang, T}, title = {Dysbiosis of fecal virome in pediatric Crohn's disease and its dynamic changes during infliximab therapy.}, journal = {mSystems}, volume = {11}, number = {4}, pages = {e0148925}, pmid = {41800893}, issn = {2379-5077}, support = {8247031679//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Infliximab/therapeutic use ; *Crohn Disease/drug therapy/virology ; *Feces/virology/microbiology ; Female ; Child ; Male ; *Dysbiosis/virology/drug therapy ; *Virome/drug effects ; Adolescent ; Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Agents/therapeutic use ; }, abstract = {UNLABELLED: The gut virome is an emerging but underexplored component of the human microbiota, especially in pediatric Crohn's disease (CD). This study aimed to characterize the fecal virome in children with CD and evaluate its association with clinical response to infliximab (IFX) therapy. A total of 85 participants, including 60 pediatric CD patients and 25 healthy controls (HC), were recruited. Among the CD patients, 53 received ≥3 IFX infusions, 41 achieved remission (IFX-R), and 12 did not (IFX-NR). Viral-like particles in fecal samples were enriched and profiled by metagenomic sequencing, while bacterial communities were assessed via 16S rRNA gene sequencing. Pediatric CD patients exhibited significantly reduced viral richness and altered viral community compared to HCs. Functional analyses revealed that CD patients exhibit a shift in fecal virome function from DNA repair to viral replication and assembly. Trans-kingdom correlations were disrupted in CD, particularly between Torque teno viruses and beneficial bacteria, such as Blautia. An integrated machine learning model combining viral and bacterial markers achieved a certain level of diagnostic accuracy for pediatric CD (area under the curve [AUC] = 89.3%). IFX treatment influences the gut virome, with remission associated with higher abundances of Microviridae and Siphoviridae, while Anelloviridae, Myoviridae, and Podoviridae were enriched in IFX-NR at baseline. These findings suggest the virome as a potential biomarker for predicting clinical outcome in pediatric CD, offering a novel avenue for disease diagnosis and personalized treatment strategies.

IMPORTANCE: Crohn's disease (CD) in children poses a growing clinical challenge, with increasing incidence and variable response to biologic therapies such as infliximab (IFX). While gut bacterial dysbiosis has been extensively studied, the role of the gut virome in pediatric CD remains largely unexplored. This study provides the first longitudinal characterization of the fecal virome in children with CD undergoing IFX therapy. We reveal distinct viral community patterns, functional alterations, and virus-bacteria interactions in pediatric CD patients. Notably, integration of virome and bacteriome profiles enhances diagnostic accuracy, offering a promising avenue for predictive biomarker development. Furthermore, virome changes may be associated with the IFX treatment outcomes in children with CD. These findings highlight the gut virome as a critical but overlooked dimension of host-microbiome interactions in pediatric CD, with potential implications for personalized therapy and mechanistic understanding of treatment resistance.}, } @article {pmid41801284, year = {2026}, author = {Wang, J and Ge, H and Liu, Y and Huang, C and Zhang, L and Yu, Y and Xu, L and Fang, H}, title = {Earthworm gut microbiome promotes biodegradation of albendazole in soil.}, journal = {Crop health}, volume = {4}, number = {1}, pages = {}, pmid = {41801284}, issn = {2948-1945}, support = {2023YFD1902903//National Key Research and Development Program of China/ ; 42177252//National Natural Science Foundation of China/ ; 2023C02039-01//Leading Goose" R&D program of Zhejiang Province of China/ ; }, abstract = {The excretion of the anthelmintic drug albendazole (ALB) from treated animals into the soil, as well as its widespread application as a fungicide, poses a serious ecological risk to the soil environment. In this study, we investigated the degradation of ALB in soil and its bioaccumulation in earthworms, changes in the microbiome and degradation genes, and the effect of zinc oxide nanoparticles on the degradation and enrichment behaviors of ALB and microbial community structure and function. Our findings showed that ALB selectively enriched specific albendazole degradation genes (i.e., hmr and ami) in the earthworm, preferentially activating the pathways associated with sulfur reduction, amination of ALB sulfone, and hydroxylation of ALB. Metagenomic analysis revealed that the relative abundances of ppo, xylA, cutC, and nfsl in the earthworm gut were 0.19-52.64-fold higher in the ALB treatment than in the control, indicating their potential dominance in ALB biodegradation. Network analysis further identified potential bacterial hosts carrying biodegradation genes and albendazole degradation genes. Notably, Sphaerobacter, Saccharothrix, Actinomadura, and Nocardia were recognized as potential dual hosts of biodegradation genes and albendazole degradation genes, displaying a 0.05-1.32-fold elevation in relative abundance in ALB-treated earthworm guts compared to the control. Additionally, ZnO nanoparticles were found to reduce ALB bioaccumulation in earthworms and accelerate its dissipation in soil. These findings provide novel insights into the bioremediation mechanisms of pesticides in soil-earthworm ecosystems.}, } @article {pmid41801404, year = {2026}, author = {Petouhoff, A and Hicks, R and Husain, M and Hoyd, R and Xu, M and Dravillas, C and Patel, SH and Johns, A and Grogan, M and Li, M and Lopez, G and Miah, A and Liu, Y and Muniak, M and Schmidt, M and Das, A and Lathrop, H and Das, P and Secor, A and Haddad, T and Tinoco, G and Carbone, D and Kendra, K and Otterson, GA and Presley, CJ and Mace, T and Spakowicz, D and Owen, DH}, title = {Impact of proton pump inhibitors on immunotherapy is modulated by prior chemotherapy and linked to gut microbiome-immune cell signatures.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {75}, number = {4}, pages = {}, pmid = {41801404}, issn = {1432-0851}, support = {P30CA016058/NH/NIH HHS/United States ; UL1TR002733/TR/NCATS NIH HHS/United States ; Innovator Award 1046611//American Lung Association/ ; Research Scholar Award RSG-23-1023205//American Cancer Society/ ; }, mesh = {Humans ; *Proton Pump Inhibitors/therapeutic use/pharmacology ; Female ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; *Immunotherapy/methods ; Retrospective Studies ; *Immune Checkpoint Inhibitors/therapeutic use ; Middle Aged ; Aged ; }, abstract = {Proton pump inhibitors (PPIs) are one of the most widely used medications in the world. They have been associated with an altered microbiome, which is demonstrated to be important for immune checkpoint inhibitor (ICI) response. We sought to determine whether PPI use was associated with shorter overall survival (OS) in patients treated with ICIs, and whether these changes were associated with altered microbiomes and immune cell composition. Our retrospective study of patients with advanced cancer (n = 1078) evaluated the impact of PPI use on OS. We also analyzed stool samples from melanoma patients treated with ICIs (n = 42) and stool and blood samples from patients with non-small cell lung cancer (NSCLC) and renal cell carcinoma treated with ICIs (n = 8). With the data from our prospective study, we assessed microbiome composition from stool samples using metagenomic whole-genome shotgun; immune cell populations from blood samples were determined using CyTOF. Associations between PPI use, clinical outcomes, the microbiome, and immune cell populations were evaluated using survival analyses, diversity metrics, and multivariable models. PPI use was associated with shorter OS in patients with advanced cancers treated with ICIs, with the strongest effects seen in melanoma. PPI use was associated with worse clinical outcomes and microbiome alterations in patients with advanced cancers treated with ICIs, suggesting that its use may influence the efficacy of immunotherapy; prospective studies implicate its effect on the microbiome. These findings underscore the importance of considering the microbiome and concomitant medications when to enhance treatment response and efficacy.}, } @article {pmid41802510, year = {2026}, author = {Gou, X and Shen, Y and Liu, F and Wang, Y and Zong, Y and Qu, D and Ren Zeng, C and Nhamdriel, T and Kuang, T and Fan, G}, title = {Swertia chirayita ameliorates MAFLD by improving intestinal microenvironment and hepatic lipogenesis.}, journal = {Journal of ethnopharmacology}, volume = {364}, number = {}, pages = {121471}, doi = {10.1016/j.jep.2026.121471}, pmid = {41802510}, issn = {1872-7573}, mesh = {Animals ; *Lipogenesis/drug effects ; Male ; *Liver/drug effects/metabolism/pathology ; *Swertia/chemistry ; *Plant Extracts/pharmacology/therapeutic use ; Diet, High-Fat/adverse effects ; Rats ; Rats, Sprague-Dawley ; *Fatty Liver/drug therapy/metabolism ; Intestines/drug effects ; }, abstract = {Metabolic-associated fatty liver disease (MAFLD) is emerging as a very serious threat to human health. The search for effective remedies for MAFLD from natural herbs is gaining increasing attention. Swertia chirayita (SC) is a famous herb in China, India, and Nepal. It has long been employed within the traditional Tibetan medical system for managing hepatic disorders. Nevertheless, the therapeutic impacts and possible mechanisms of SC in the context of MAFLD are unclear.

AIM OF THE STUDY: This present investigation was designed to research the pharmacological influence and potential mechanisms of SC in MAFLD rats. We conducted a particular examination of its effects on the intestinal microenvironment and hepatic lipogenesis.

MATERIALS AND METHODS: The pharmacological effects of SC were evaluated in MAFLD rats established through a 12-week high-fat diet (HFD) feeding. After 8 weeks of SC administration, biochemical assessments were conducted for body fat, liver function, glucose metabolism, lipid parameters, and inflammatory factors. The main chemical constituents of SC and three short-chain fatty acids (SCFAs) in rat feces were quantitatively analyzed by HPLC. Furthermore, targeted metabolomics, transcriptomics, metagenomics, and Western blotting were employed to investigate possible mechanisms by which SC improves MAFLD.

RESULTS: Treatment with SC significantly ameliorated excessive fat accumulation and insulin resistance in MAFLD rats. It also improved hepatic enzyme activities (AST and ALT), several lipid metrics (TG, TC, and LDL-C), and liver histopathological changes. Moreover, SC attenuated systemic inflammation, as shown by decreased circulating IL-1β, TNF-α, LPS, and IL-6. Metagenomic profiling revealed that SC administration helped reestablish the dysregulation of multiple types of gut microbiota (bacteria, fungi, archaea, and viruses) in MAFLD rats. It improved microbial diversity, community composition, and transkingdom correlations. In addition, SC enhanced gut barrier function by raising the amount of butyric acid, acetic acid, and propionic acid and upregulating the expression of several ZO-1, occludin, and claudin-1. Liver transcriptomic analysis suggested that SC could regulate the metabolism of bile acids (BAs). Importantly, targeted metabolite analysis and western blotting demonstrated that SC improved bile acid dysfunction in MAFLD rats. In particular, SC increased TCDCA, TCA, and DCA, thereby activating the FXR/FGF15 signaling axis. This activation then controlled the production of SHP and SREBP-1c proteins in the hepatic, thereby inhibiting hepatic lipogenesis to improve MAFLD.

CONCLUSIONS: SC has shown a good therapeutic effect on MAFLD by improving intestinal microenvironment and hepatic lipogenesis. Specifically, it improves the imbalance of multiple types of gut microbiota, restores disrupted transkingdom interactions, promotes creation of beneficial SCFAs and bile acid, protects the intestinal barrier, and inhibits hepatic lipogenesis by regulating the BAs/FXR/FGF15 and SHP/SREBP-1c signaling pathways.}, } @article {pmid41802644, year = {2026}, author = {Wang, X and Feng, X and Zhou, Z and Li, M and Zhang, R}, title = {A pre-LECA origin of giant viruses as revealed by polymerase-based time tree.}, journal = {Molecular phylogenetics and evolution}, volume = {220}, number = {}, pages = {108602}, doi = {10.1016/j.ympev.2026.108602}, pmid = {41802644}, issn = {1095-9513}, mesh = {*Phylogeny ; *Giant Viruses/genetics/classification ; *DNA-Directed DNA Polymerase/genetics ; *Evolution, Molecular ; *DNA-Directed RNA Polymerases/genetics ; *Eukaryota/genetics/virology ; Sequence Analysis, DNA ; Fossils ; }, abstract = {The viral phylum Nucleocytoviricota (NCLDV) infects a wide range of eukaryotic hosts and exhibits genome complexities and virion sizes comparable to prokaryotes, blurring the boundaries between cellular life and viral entities. Despite significant advances from large-scale metagenomic surveys and identification of endogenous viral elements that expand our understanding of NCLDV's genomic diversity and host range, their evolutionary origin remains contentious. Here, we utilize DNA-directed DNA polymerase (DNAP) and RNA polymerase (RNAP), conserved markers across eukaryotes, prokaryotes, and NCLDVs, to leverage abundant eukaryotic fossils for dating the origins of NCLDVs. Phylogenetic analyses showed that NCLDV's DNAP and RNAP consistently form deep branches separate from their eukaryotic homologs. Molecular dating analyses further indicated that both DNAP and RNAP in NCLDV originated before the emergence of last eukaryotic common ancestor (LECA), findings which are robust across various dating settings. Notably, the estimated origin based on RNAP was older compared to DNAP, underscoring the need to identify additional orthologues shared with eukaryotes. Collectively, our findings represent the first attempt, to the best of our knowledge, to establish a reliable temporal framework for NCLDV evolution, supporting a pre-LECA origin of ancestral NCLDVs and suggesting a prolonged co-evolutionary history with their (proto-)eukaryotic hosts during eukaryogenesis.}, } @article {pmid41802657, year = {2026}, author = {Ma, R and Jia, B and Zhang, X and Zhao, Z and Zhao, F and Liong, MT and Ali, A and Abd Hamid, IJ and Hasan, TH and Taib, F and Sun, Z}, title = {Bifidobacterium longum subsp. infantis B8762 modulates the infant gut-lung axis via microbial and metabolic reprogramming.}, journal = {Microbial pathogenesis}, volume = {215}, number = {}, pages = {108431}, doi = {10.1016/j.micpath.2026.108431}, pmid = {41802657}, issn = {1096-1208}, mesh = {Humans ; *Probiotics/administration & dosage ; Infant ; Feces/microbiology ; *Lung/microbiology ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; *Gastrointestinal Tract/microbiology ; Female ; Male ; Metabolic Networks and Pathways ; *Bifidobacterium longum subspecies infantis ; Respiratory Tract Infections/prevention & control ; Metagenomics ; Bifidobacterium ; }, abstract = {Respiratory and gastrointestinal infections are leading causes of morbidity in children. Increasing evidence highlights the gut-lung axis as a key regulatory interface influencing infection susceptibility. Bifidobacterium longum subsp. infantis B8762 (B8762) has shown clinical efficacy in reducing such infections, but its mechanistic basis remains unclear. In a randomized, double-blind, placebo-controlled study involving 115 infants (probiotic group: n = 57, placebo group: n = 58; aged 6-12 months), fecal metagenomic sequencing was performed to assess microbial and functional changes after four weeks of B8762 supplementation (0.5 × 10[10] CFU/day). B8762 significantly altered the gut microbial structure (β-diversity, P < 0.05) without affecting α-diversity. The intervention enriched beneficial taxa including Bifidobacterium longum, Eubacterium limosum, and Roseburia hominis, while reducing potential pathogens such as Staphylococcus aureus and Candida parapsilosis (P < 0.05). Functionally, B8762 upregulated metabolic pathways involved in coenzyme A and L-tryptophan biosynthesis and enhanced predicted production of immunoregulatory metabolites including butyrate, inosine, and chenodeoxycholic acid. In summary, this study suggests that B8762 modulates the pediatric gut microbiota toward a composition and metabolic profile that supports mucosal barrier integrity and systemic immune regulation. These findings provide mechanistic insight into its protective role against respiratory and gastrointestinal infections in children, supporting its use as a targeted gut-lung axis probiotic intervention.}, } @article {pmid41803086, year = {2026}, author = {Faure, E and Pommellec, J and Noel, C and Cormier, A and Delpech, LM and Eren, AM and Fernandez-Guerra, A and Vanni, C and Fourquez, M and Houssais, MN and Guyet, U and Da Silva, C and Gavory, F and Perdereau, A and Labadie, K and Wincker, P and Poulain, J and Hassler, C and Lin, Y and Cassar, N and Maignien, L}, title = {Water mass specific genes dominate the Southern Ocean microbiome.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41803086}, issn = {2041-1723}, support = {18-CE02-0024//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; //France Génomique/ ; /SNSF_/Swiss National Science Foundation/Switzerland ; //Laboratoire d’Excellence” LabexMER/ ; }, mesh = {*Microbiota/genetics ; Oceans and Seas ; *Seawater/microbiology ; Antarctic Regions ; *Bacteria/genetics/classification ; Metagenome ; Sulfonium Compounds/metabolism ; Arctic Regions ; *Genes, Bacterial ; }, abstract = {The Southern Ocean (SO) plays a key role in regulating global biogeochemical cycles and climate, yet microbial genes sustaining its biological activity remain poorly characterized. We introduce a microbial genes collection from 218 metagenomes sampled during the Antarctic Circumnavigation Expedition, the majority of which are missing from functional databases. 38% even lack homologs in current reference marine gene catalogs, defining a singular genetic seascape. We show that SO gene assemblages exhibit a common polar signature with the Arctic Ocean while being structured by water masses at the SO-scale. We analyze genomic markers of diverse SO biomes, focusing on dimethylsulphoniopropionate (DMSP) cleavage by polar-adapted bacteria, organic matter consumption in the blooming Mertz polynya and adaptation to polar conditions in the ubiquitous bacteria Pelagibacter. Our work takes a step towards a comprehensive understanding of SO's plankton ecology and evolution, capturing the current state of the unique microbial diversity in this rapidly changing Ocean.}, } @article {pmid41803098, year = {2026}, author = {Zhu, Y and Sun, M and Chen, B and Liu, X and Yang, G and Li, X}, title = {Diagnostic Value of Cerebrospinal Fluid Metagenomics Next-generation Sequencing in Neurobrucellosis in Children: Erratum.}, journal = {The Pediatric infectious disease journal}, volume = {45}, number = {4}, pages = {384}, pmid = {41803098}, issn = {1532-0987}, } @article {pmid41803433, year = {2026}, author = {Jalal, RS and Alshehrei, FM}, title = {Rhizospheric glycosyltransferase repertoires as a resource for enabling sustainable bioprocessing and green biocatalyst discovery.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41803433}, issn = {2045-2322}, support = {UJ-25-DR-1837//University of Jeddah/ ; }, abstract = {UNLABELLED: The rhizospheric microbiomes associated with wild plant species Moringa oleifera and Abutilon fruticosum, endemic to the arid northwestern Mecca region of Saudi Arabia, represent untapped reservoirs of genetic capability with significant implications for agriculture, biotechnology, medicine, and environmental sustainability. Leveraging high-throughput metagenomic sequencing and advanced bioinformatics, this study systematically cataloged carbohydrate-active enzymes (CAZymes), with a particular focus on glycosyltransferase (GT) families, within these root-associated microbial consortia. The analysis revealed pronounced compositional divergence between rhizospheric and bulk soil microbiomes, underscoring the influence of plant species and edaphic factors in shaping niche-specific microbial assemblages and functional repertoires. The two rhizospheric microbiomes were consistently enriched in all six CAZy classes, with lineage-specific CAZymes of GT families (GT2 and GT84 in M. oleifera and GT31, GT39, and GT66 in A. fruticosum). These lineage-specific CAZymes catalyze the synthesis of structurally diverse polysaccharides, including cellulose, chitin, β-glucans, mannans, and chondroitin, thereby positioning the rhizospheric microbiomes of Moringa oleifera and Abutilon fruticosum as promising reservoirs of biocatalysts for possible future applications in industrial applications, biomedical engineering, and environmentally sustainable technologies. The evolutionary history of these enzymes in hot, oligohydric soils suggests adaptation to thermal and water-limited conditions, which may render them particularly suitable for deployment in industrial and biotechnological bioreactors. These CAZymes are predicted to be positioned as pivotal assets for sustainable bioeconomy initiatives and possible therapeutic glycoengineering.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42974-2.}, } @article {pmid41803498, year = {2026}, author = {Zhou, H and Sun, R and Nie, X and Xia, L and Dong, H and Liu, Y and Hou, S and Dong, W and Zhu, X and Yao, Y and Zhao, GP and Lu, S and Wang, Y and Yang, C}, title = {A clinic-responder-derived defined microbial consortium enhances anti-PD-1 immunotherapy efficacy in mice.}, journal = {Nature microbiology}, volume = {11}, number = {4}, pages = {993-1007}, pmid = {41803498}, issn = {2058-5276}, support = {82241228//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32230060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31925001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073152//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82241227//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82030045//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Mice ; Humans ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology ; *Immunotherapy/methods ; Fecal Microbiota Transplantation ; *Carcinoma, Non-Small-Cell Lung/therapy/immunology ; *Gastrointestinal Microbiome ; *Lung Neoplasms/therapy/immunology ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; Cell Line, Tumor ; Female ; *Immune Checkpoint Inhibitors/therapeutic use ; Mice, Inbred C57BL ; CD8-Positive T-Lymphocytes/immunology ; }, abstract = {Targeting the gut microbiota is a promising strategy to enhance the efficiency of cancer immunotherapy; however, success has been limited. Here we combined metagenomic analysis and in silico prediction to identify bacterial species associated with immunotherapy response in patients with non-small-cell lung cancer. We constructed a defined consortium (RCom) of 15 bacterial species, most of which were isolated from responder patient faeces, associated with improved clinical response to anti-programmed cell death protein 1 (PD-1) treatment. Metabolic models and in vitro experiments revealed that RCom is a stable and cooperative community, and in vivo experiments showed that RCom engrafts and produces immunomodulatory metabolites. Oral administration of RCom improved the anti-tumour activity of anti-PD-1 by increasing the intratumoural infiltration and cytotoxic function of CD8[+] T cells in syngeneic tumour models and across mice with heterogeneity in baseline gut microbiota composition. RCom supplementation also limited anti-PD-1 resistance in mice conferred by faecal microbiota transplantation from individual non-responsive patients. These findings suggest that RCom is a potential adjuvant to improve responsiveness to anti-PD-1 therapy in cancer.}, } @article {pmid41803682, year = {2026}, author = {Shen, Z and Zhang, Z and Gao, J and Chen, J and Xu, Q and Li, D and Zeng, L and Cheng, D and Wang, K and Zhang, J and Wong, JWC}, title = {Microbial succession accompanies increased antibiotic resistance risk during grass carp (Ctenopharyngodon idella) spoilage under ambient household conditions.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41803682}, issn = {1471-2180}, support = {2024A1515140076//Guangdong Basic and Applied Basic Research Foundation/ ; 22206107//National Natural Science Foundation of China/ ; 2023ZT10L060//Program for Guangdong Introducing Innovative and Entrepreneurial Teams of China/ ; 221110133//Dongguan University of Technology Top Talent Professor Start Up Fund/ ; }, mesh = {Animals ; *Carps/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/drug effects ; *Drug Resistance, Microbial/genetics ; Biogenic Amines/analysis ; *Microbiota/genetics ; Food Microbiology ; Food Safety ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Food Storage ; Food Packaging ; }, abstract = {Understanding fish spoilage mechanisms under household storage conditions is critical for food safety in regions with limited cold chain infrastructure, where ambient storage remains common practice. This study investigated the spoilage dynamics, microbial succession, and antibiotic resistance gene (ARG) proliferation in grass carp stored under simulated household conditions at 13.0 ± 3.4 °C using three packaging scenarios. The biogenic amine index (BAI) of fish exceeded 50 mg/kg within 16 h, marking early spoilage onset. After 64 h, K-values surpassed 60%, TVB-N exceeded the safety limit of 20 mg/100 g, and BAI reached over 220 mg/kg, indicating advanced spoilage. 16S rRNA amplicon sequencing demonstrated dramatic microbial community shifts from Cyanobacteriota-dominated fresh samples to Pseudomonadota-dominated spoilage communities, with Aeromonas emerging as the primary specific spoilage organism (SSO), increasing from 0.001% to 67.2% at 64 h. Pathogen abundance escalated from 0.06% to 72.2% in muscle tissues, posing substantial food safety risks. Distinct microbial community structures were observed across tissue types (muscle vs. gut) and packaging treatments, with storage time exerting the strongest selective pressure on community composition. Metagenomic analysis revealed progressive ARG enrichment, with surface samples exhibiting 2.6-fold higher total ARG abundance and 3.8-fold greater ARG type richness compared to the fresh gut baseline by 24 ~ 64 h. Rapid ARG enrichment was detected during early spoilage (24 h), representing a critical food safety concern. Notably, carbapenem resistance genes (e.g., OXA-12, cphA6) were substantially enriched, underscoring the high risk posed by these clinically relevant resistance genes. These findings demonstrate that grass carp stored under ambient household conditions maintain acceptable quality for < 16 h, necessitating immediate consumption or cold chain implementation to ensure food safety and minimize ARG dissemination.}, } @article {pmid41803729, year = {2026}, author = {Tian, J and Jiang, Y and Ye, N and Zhang, Y}, title = {A case of uveitis and retinal vasculitis induced by varicella-zoster virus: vitrectomy treatment and literature review.}, journal = {BMC ophthalmology}, volume = {26}, number = {1}, pages = {}, pmid = {41803729}, issn = {1471-2415}, support = {20260814//Medical Science Research Project of Hebei/ ; }, abstract = {BACKGROUND: Infectious uveitis can be induced by a variety of factors, including viral, bacterial, and parasitic infections, among others. Among these, viral infections are the most common cause of infectious uveitis. Traditional diagnostic methods have limited sensitivity and are often cumbersome, which restricts their ability to accurately identify the viral pathogens responsible. As a result, there is still no gold-standard diagnostic tool for detecting uveitis. With advancements in molecular diagnostic technologies, metagenomic next-generation sequencing (mNGS) has become widely used in clinical sample detection, molecular sequencing, and microbial analysis. CASE REPORT: This article reports a case of an elderly male patient who presented with a one-month history of left eye vision deterioration. The patient had a generally healthy status, with a 17-year history of hypertension, and denied any other underlying conditions. Ophthalmic examination showed planktonic cells (+++) in the anterior chamber of the left eye, partial posterior adhesion of the iris, lens opacity, visible attachment of iris pigments in front, severe vitreous opacity, visible flocculent yellow white floating material, and faintly visible optic disc structure in the fundus. These findings led to a diagnosis of left eye uveitis. Given the severity of the ocular condition, a decision was made to perform vitreous cavity puncture for smear culture and metagenomic mNGS to identify the pathogen. mNGS promptly detected 9939 sequence counts of Varicella-zoster virus (VZV), confirming the pathogen. Following the identification, Acyclovir injection is used for systemic intravenous injection and local intravitreal injection of ganciclovir injection for antiviral therapy.After two weeks of treatment, the symptoms of anterior uveitis showed some improvement, but the vitreous inflammation remained largely unchanged. Consequently, a vitreous body removal (vitrectomy) was performed, postoperative fundus examination showed the refractive interstitium is clear, and Kyrieleis plaques along the inner wall of the paraoptic artery can be seen. Postoperatively, the patient’s vision improved rapidly. Previous reports typically emphasize the importance of antiviral therapy. However, in this case, the authors discuss the use of vitrectomy in a VZV infection-induced pan-uveitis and retinal vasculitis patient, where antiviral therapy alone was insufficient, resulting in a satisfactory outcome post-surgery. CONCLUSION: Intraocular fluid metagenomic testing is an effective method for diagnosing unexplained uveitis. For patients with VZV-associated uveitis and severe vitreous opacity, early vitrectomy is an effective therapeutic approach.}, } @article {pmid41803767, year = {2026}, author = {Maeda, K and Tamura, Y and Nagai, Y and Kariya, Y and Katsuta, H and Ajiro, N and Yoshida, H and Han, Y and Hashimoto, S and Chikamatsu, K and Takaki, A and Matsumoto, Y and Fatimah, RM and Tanaka, M and Nakamura, S and Iida, T and Mitarai, S and Nagai, T}, title = {Non-tuberculous Mycobacterial pulmonary disease due to novel mycobacterium: Mycobacterium habikinoensis: a case report.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41803767}, issn = {1471-2334}, abstract = {BACKGROUND: The incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) is increasing, and the identification of new Mycobacterium species is also increasing. We describe the first case of chronic pulmonary infection caused by a novel Mycobacterium species. CASE PRESENTATION: A 66-year-old man was referred to our hospital with a several-week history of low-grade fever and productive cough. An acid-fast bacillus smear test of the sputum revealed positive. Polymerase chain reaction (PCR) for Mycobacterium intracellulare was positive; however, Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) failed to identify the strain. The isolated culture was referred for further genotypic identification and was confirmed to be a novel species. Combination therapy with clarithromycin, rifampicin, and sitafloxacin was started. Despite treatment, the patient’s condition gradually worsened during the subsequent follow-up period. CONCLUSIONS: We describe the first case of NTM-PD with a novel Mycobacterium species. Mycobacterium habikinoensis is a novel species closely related to Mycobacterium colombiense but with distinct characteristics. Further investigation is required to clarify its pathogenicity, antimicrobial susceptibility, and clinical significance in human infections.}, } @article {pmid41803907, year = {2026}, author = {Fernández-de-Bobadilla, MD and Pérez-Cobas, AE and Andremont, A and Martínez, JL and Baquero, F and Lanza, VF and Coque, TM}, title = {The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the "robust-yet-fragile" architecture of human gut microbiomes.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41803907}, issn = {2049-2618}, support = {pFIS F19/00366//Instituto de Salud Carlos III/ ; CB21/13/00084//Instituto de Salud Carlos III/ ; CC23140547//Fundación Francisco Soria Melguizo/ ; MISTAR AC21_2/00041//Joint Programming Initiative on Antimicrobial Resistance/ ; "Ayudas de atracción de talento investigador César Nombela" 2023-T1/SAL-GL28953//Comunidad de Madrid/ ; FP7#282004//European Union/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Feces/microbiology ; Metagenomics/methods ; French Guiana ; *Metals/pharmacology ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; Metagenome ; }, abstract = {BACKGROUND: Metagenomics enables detailed profiling of genes encoding antimicrobial resistance. However, most studies focus exclusively on antibiotic resistance genes (ARGs), excluding those associated with non-antibiotic antimicrobials (metals, biocides), and often rely on methods with low-sensitivity and low-specificity. Furthermore, they rarely examine populations exposed to minimal anthropogenic pollution. We analyzed fecal resistomes of 95 Wayampi individuals, an Indigenous community in remote French Guiana, using a targeted metagenomic capture platform covering 8667 genes, including ARGs, metal resistance genes (MRGs) and biocide resistance genes (BRGs) (PMID: 29335005). Resistome profiles were compared with those of Europeans to assess population-level differences.

RESULTS: ARG richness was similar between groups (259 in Wayampi vs. 264 in Europeans, 159 shared), but MRGs + BRGs gene richness was significantly higher in Wayampi (11,930 vs. 7419). Most genes appeared in a minority of individuals (mean 5% for ARGs, 2% for MRGs + BRGs), but several ARGs for tetracyclines [tet(32), tet(40), tet(O), tet(Q), tet(W), tet(X), tetAB(P)], aminoglycosides (ant6'-I, aph3-III), macrolides (ermB, ermF, mefA), and sulfonamides (sul2) were present in all individuals. Tetracycline resistance genes predominated overall, while beta-lactam resistance genes were more common in Wayampi, and genes conferring resistance to aminoglycosides, amphenicols, and folate inhibitors were more frequent in Europeans. Among MRGs, copper and arsenic resistance genes prevailed in both groups, followed by those for zinc, iron, cobalt, and nickel. Up to 76% of Wayampiis carried acquired MRGs for copper (pcoABCDRS and tcrB), silver (silACFPRS), arsenic (ars), and mercury (mer) detoxification. Shannon diversity indices were similar for ARGs, MRGs, and BRGs, but composition and evenness differed significantly. UMAP and ADONIS analyses distinguished cohorts based on ARG profiles (p < 0.001), but not on MRGs or BRGs. Correlation analysis revealed conserved gene-sharing networks and introgression of acquired ARGs and MRGs within both gut microbiomes.

CONCLUSIONS: The diverse and balanced Wayampi resistome reflects a less perturbed microbiome compared to industrialized populations, and reveals a background of "core" and "shell" acquired ARGs and MRGs, consistent with the "robust-yet-fragile" architecture of scale-free networks. The patchy yet resilient gene distribution suggests varying levels of conserved gene sharing highways among populations, likely shaped by long-term microbial-human evolution, and supports a broader view on acquired antimicrobial resistance. Video Abstract.}, } @article {pmid41803939, year = {2026}, author = {Fauszt, P and Mikolas, M and David, P and Szoke, Z and Gashi, N and Szilagyi-Tolnai, E and Szilágyi, E and Szarvas, MM and Fazekas, ME and Kun-Nemes, A and Stagel, A and Gal, F and Czegledi, L and Biro, S and Stundl, L and Remenyik, J and Paholcsek, M}, title = {Longitudinal source-sink dynamics of fecal litter and farm indoor environmental resistomes in broiler chicken and Cherry Valley ducks.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41803939}, issn = {2524-4671}, abstract = {BACKGROUND: Antimicrobial resistance is a major One Health threat, and intensive poultry systems function as amplifiers. Although broilers and ducks are reared under similarly controlled conditions, their microecologies diverge. Integrated, longitudinal source-sink analyses quantifying overlap and directional flux between host-associated and environmental resistomes remain scarce. A two-year (2022–2024), longitudinal, commercial-scale comparison was undertaken across 15 stocking cycles under harmonized husbandry in Ross 308 broiler and Cherry Valley duck. Parallel shotgun metagenomics profiled fecal litter and farm indoor environments across standardized production, with daily monitoring in one complete cycle per system; in total, 96 pooled samples were sequenced to quantify cross-compartment overlaps. RESULTS: Antibiotic resistance gene (ARG) reservoir dominance proved to be system-specific, duck systems were environment-centric, whereas broiler systems were fecal litter-centric. Although overall ARG diversity was similar between systems (broiler 2,542; duck 2,494 types), ducks exhibited greater compartmental divergence, with ~ 2.6-fold more environment-unique ARGs than paired fecal litter and 1.15-fold higher environmental richness than broilers. Compartment coupling also differed: broilers showed tighter host-environment overlap, while ducks were more partitioned. A shared environmental ARG pool (57.5%) indicated substantial cross-system exchange potential. Temporally, shared ARGs accumulated across the grow-out and peaked pre-depopulation. The distribution of significant ARG carrier species revealed asymmetric host-environment coupling: overlap across compartments was 66.67% in broilers versus 45.45% in ducks, notably. The impact of antimicrobial use was nuanced: short, targeted courses were associated with lower aaAMR burden overall Collectively, the recurrent detection of clinically consequential carriers (P. aeruginosa, E. coli, A. baumannii, S. aureus, K. pneumoniae, S. maltophilia, toxigenic Clostridium spp.) underscored One Health risks of zoonotic spillover and food-chain contamination. CONCLUSION: Reservoir behavior in intensive poultry systems should be treated as system-specific, and matrix-targeted, with biofilm and humidity management prioritized in duck operations, and litter/manure control emphasized in broilers. The finisher-depopulation window emerges as a critical intervention point, warranting intensified mitigation clean-out. Finally, mitigation should extend beyond individual farms to transport crates, vehicles, shared equipment, and supply chains.}, } @article {pmid41804366, year = {2026}, author = {Jiang, W and Luo, M and Jiang, M and Yang, J and Qin, L and Yang, Z and Xue, F and Long, Z and Zhao, L and Long, H}, title = {Clinical Features and Risk Factors for Severe Disease in 57 Cases of Chlamydia psittaci Pneumonia: A Retrospective Study.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {584050}, pmid = {41804366}, issn = {1178-6973}, abstract = {BACKGROUND: This study aimed to analyze the clinical features of Chlamydia psittaci (C. psittaci) pneumonia and identify risk factors for severe patients to facilitate early diagnosis and treatment.

METHODS: In this retrospective analysis, we collected and summarized the clinical data of 57 patients with C. psittaci pneumonia confirmed by metagenomic next-generation sequencing (mNGS) or targeted next-generation sequencing (tNGS), who were admitted to the First Affiliated Hospital of Guilin Medical University between July 2020 and August 2025. Patients were further divided into a severe group (n=23) and a non-severe group (n=34) for comparative analysis of their clinical characteristics.

RESULTS: The mean age of the patients was 58.68 ± 12.36 years. Common symptoms included fever, cough/sputum, fatigue, dyspnea, and neurological and gastrointestinal symptoms. The severe group had a significantly higher incidence of fatigue, dyspnea, and neurological and gastrointestinal manifestations. Laboratory findings revealed that most patients had normal or mildly elevated white blood cell counts with lymphopenia, alongside significantly elevated levels of C-reactive protein (CRP), procalcitonin (PCT), and erythrocyte sedimentation rate (ESR). Anemia, hypoalbuminemia, and abnormalities in liver enzymes, myocardial enzymes, and electrolytes were also commonly observed. The predominant chest computed tomography finding was consolidation, with pleural effusion present in 59.6% of all patients and occurring more frequently in the severe group. Multivariate analysis identified CRP as an independent risk factor for severe C. psittaci pneumonia, while albumin and platelet count were protective factors.

CONCLUSION: Pneumonia patients presenting with non-specific influenza-like symptoms should raise clinical suspicion for C. psittaci pneumonia. Particular vigilance for potential progression to severe disease is warranted in male patients, the elderly, those with underlying comorbidities, and individuals presenting with neurological or gastrointestinal symptoms. Elevated CRP, hypoalbuminemia, and thrombocytopenia serve as significant predictors of severe C. psittaci pneumonia.}, } @article {pmid41804595, year = {2026}, author = {Long, C and Gui, J and Wang, F and Wang, C and Zhang, L}, title = {Evaluation of the clinical application of MALDI-TOF MS for identification of difficult-to-classify nontuberculous mycobacterial strains isolated in the laboratory.}, journal = {Acta clinica Belgica}, volume = {81}, number = {3}, pages = {293-302}, doi = {10.1080/17843286.2026.2643452}, pmid = {41804595}, issn = {2295-3337}, mesh = {*Nontuberculous Mycobacteria/classification/genetics/isolation & purification ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Reference Standards ; Reagent Kits, Diagnostic/standards ; Molecular Typing/methods/standards ; Sequence Analysis, DNA/standards ; Nanopore Sequencing/methods/standards ; DNA, Bacterial/isolation & purification ; Metagenomics/methods/standards ; High-Throughput Nucleotide Sequencing/methods/standards ; China ; Humans ; }, abstract = {OBJECTIVES: This study aims to evaluate the clinical application value of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in the verification and identification of difficult-to-classify nontuberculous mycobacterial (NTM) strains.

METHODS: From December 2024 to June 2025, 106 suspected NTM isolates were collected from 10 districts in Shenzhen, China. Initial identification was performed using HRM and REBA commercial kits, with targeted nanopore sequencing and mNGS as the composite reference standard. MALDI-TOF MS was used to verify strains unresolved by the kits, and its diagnostic performance was evaluated.

RESULTS: The HRM kit demonstrated concordance with the reference standard in 98 of 106 samples (concordance rate: 89.1%), whereas the REBA kit concorded in 88 samples (concordance rate: 80.0%). The REBA kit exhibited a tendency toward misidentification of NTM species as Mycobacterium tuberculosis. When the reference results were used as a baseline with tNanopore providing parallel validation (achieving ≥95% concordance with reference results), MALDI-TOF MS demonstrated poor performance in identifying difficult-to-classify NTM strains. Specifically, MALDI-TOF MS showed poor concordance in detecting M. abscessus (Kappa = 0.244), while Mycobacterium intracellulare, Mycobacterium kansasii, and Mycobacterium gordonae demonstrated kappa values of 0.543, 0.477, and 0.483, respectively, indicating low concordance overall. Furthermore, 13 species exceeded the detection range of MALDI-TOF MS, resulting in false-positive identifications or detection failures, with Mycobacterium abscessus exhibiting the highest rate of misidentification.

CONCLUSION: The limitations of MALDI-TOF MS in verifying difficult-to-classify NTM strains have been demonstrated. The findings emphasize that PCR-based molecular detection combined with gene sequence analysis remains the most reliable methodological approach for accurately identifying challenging NTM species in clinical practice.}, } @article {pmid41804664, year = {2026}, author = {Bai, Y and Xu, Y and Wu, D and Su, Y and Zhan, M and Xie, B}, title = {The Polymer-Plastisphere-Function Nexus Links to Divergent Biodegradation of Microplastics During Composting.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70278}, doi = {10.1111/1462-2920.70278}, pmid = {41804664}, issn = {1462-2920}, support = {22276059//National Natural Science Foundation of China/ ; 2018YFC1901000//National Key Research and Development Program of China/ ; }, mesh = {Biodegradation, Environmental ; *Microplastics/metabolism ; *Composting ; *Polymers/metabolism/chemistry ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Polyesters/metabolism ; *Microbiota ; Soil Microbiology ; }, abstract = {Microplastic (MP) biodegradation is critical for mitigating plastic pollution, yet the ecological mechanisms linking polymer properties to plastisphere microbiome assembly and catalytic function remain unclear. Using thermophilic composting as an accelerated model, we reveal a fundamental dichotomy in which biodegradable MPs (BMPs: polylactic acid [PLA] > polybutylene succinate [PBS] > poly (butylene adipate-co-terephthalate) [PBAT]) undergo rapid thermophilic degradation shaped by stronger environmental filtering of diverse degraders, whereas conventional MPs (CMPs: low-density polyethylene [LDPE]) exhibit delayed degradation with greater stochastic influence. Metagenomics uncovered 489 degradative genes predominantly distributed across uncultured taxa, enabling reconstruction of polymer-specific multi-enzyme pathways, supported by isolating 32 potential degraders (31 candidate novel). PLA/PBS degradation primarily relied on thermophilic-phase PLA depolymerase and cutinase, PBAT on late-stage polyesterase and PETase, and LDPE on alkane monooxygenase and laccase. Statistical modelling showed BMP degradation strongly associated with plastisphere-physicochemical interactions (> 90% variance), whereas CMP appeared primarily constrained by material properties (e.g., degrader succession in PLA, enrichment in PBS/PBAT, and high molecular weight in LDPE). Functionally dominant degraders (1.9% of total microbes) were estimated to contribute 52.4%-80.6% of biodegradation efficiency. This work elucidates the core polymer-plastisphere-functional nexus underlying MP biodegradation during composting, providing a predictive framework and microbial resource for targeted remediation.}, } @article {pmid41804674, year = {2026}, author = {Liu, D and Luo, M and Li, M and Chen, C and Chen, S and Wu, Y and Zhang, G and Gao, Y and Hong, Y and Zhou, Q and Li, X and Zhou, S and Wu, Y and Zhao, Y and Zhang, Y and Yin, J}, title = {Dynamic interaction between Escherichia coli enterotoxins and bacteriocins.}, journal = {The FEBS journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/febs.70488}, pmid = {41804674}, issn = {1742-4658}, support = {2023YFD1401400//the National Key R&D Program of China/ ; 32471200//the National Natural Science Foundation of China/ ; kq2208167//the Natural Science Foundation of Changsha/ ; xjt [2021] 346//the postgraduate joint training base project in Hunan Province/ ; 2023JJ10029//the Natural Science Foundation for Distinguished Young Scholars of Hunan Province/ ; }, abstract = {The intestinal microbiota constitutes a crucial defense barrier against pathogenic invasion; however, the molecular mechanisms enabling pathogens to evade or modulate this defense remain poorly understood. Here, we established a coculture model combining the commensal Escherichia coli Y18J, isolated from the piglet gut, and the enterotoxigenic E. coli (ETEC) strain W25K to investigate microbe-pathogen interactions. Our findings reveal a bidirectional regulatory mechanism between Y18J and W25K mediated by bacteriocin and toxin signaling. Colicin B/M produced by Y18J upregulates the expression of heat-stable enterotoxin (ST) in W25K during the early phase of coculture, while ST suppresses colicin B/M synthesis in Y18J. At later stages, colicin B/M stimulates heat-labile enterotoxin (LT) expression, which in turn enhances colicin B/M production. Notably, LT markedly reduces intestinal colonization of W25K(ST[-]LT[+]) in murine hosts. Leveraging metagenomic and bioinformatic analyses, we further identified a Ligilactobacillus strain within the murine gut microbiota capable of producing multiple bacteriocins that effectively inhibit W25K colonization. Transcriptomic profiling of Y18J revealed glutamine synthetase as a pivotal regulator of colicin B/M-mediated antagonism. Mechanistic investigations demonstrated that ST suppresses colicin B/M expression through the cGMP signaling pathway, whereas LT enhances it via the cAMP signaling pathway. Collectively, these findings uncover a dual regulatory mechanism through which bacterial enterotoxins modulate probiotic antimicrobial activity, providing new insights into the molecular dialog between commensal and pathogenic bacteria. This study establishes a conceptual framework for developing microbiota-based strategies to prevent and control enteric infections.}, } @article {pmid41805117, year = {2026}, author = {Chen, S and Li, C and Wang, Z and Teng, Y and Ren, W and Wang, H and Ma, J and Ma, W and Luo, Y and Kuramae, EE}, title = {Specific Metabolites Modulate Core Microbes and Microbial Interactions to Drive Fomesafen Dissipation in the Soybean Rhizosphere.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {10}, pages = {8268-8283}, doi = {10.1021/acs.jafc.5c15254}, pmid = {41805117}, issn = {1520-5118}, mesh = {Soil Pollutants/chemistry/metabolism ; Microbiota ; Bacteria/chemistry/metabolism ; Rhizosphere ; Biodegradation, Environmental ; *Soil Microbiology ; *Glycine max/growth & development/metabolism/microbiology ; }, abstract = {Rhizosphere metabolites regulate organic pollutant dissipation through microbiome modulation, yet dynamic interrelationships among metabolite shifts, microbial assembly, and pollutant removal remain unclear. Using multiomics (16S rRNA sequencing, metabolomics, and metagenomics), this study deciphered the temporal dynamics of rhizosphere metabolites and microbiome during the dissipation of fomesafen in soybean pots. Fomesafen dissipation exhibited biphasic kinetics during soybean growth, with an initial rapid phase followed by prolonged stabilization, which was synchronized with time-dependent microbiome perturbations of initial enrichment and subsequent attenuation. Metabolomics revealed fomesafen-induced shifts in rhizosphere metabolites, with 2-naphthalenesulfonic acid (↓20.84%) and 2-hydroxyoctadecanoic acid (↑13.30%) exhibiting opposing effects on microbial assembly, which ultimately affect fomesafen dissipation, as outlined in our conceptual model. Microcosm experiments further demonstrated 2-naphthalenesulfonic acid enhanced while 2-hydroxyoctadecanoic acid inhibited fomesafen dissipation. Our findings highlight the significance of rhizosphere metabolite-mediated interactions between core microbes and potential fomesafen-degraders in governing fomesafen dissipation.}, } @article {pmid41805177, year = {2026}, author = {Pereira, AC and Cortez, F and Chaves, G and Nanetti, E and Leite, RB and Mendes, MC and Oliveira, I and Abreu, H and Martins, M and Keller-Costa, T and Costa, R}, title = {Thirteen metagenome-assembled genomes of Paraglaciecola chathamensis associated with the farmed red seaweeds Porphyra dioica and Porphyra umbilicalis.}, journal = {Microbiology resource announcements}, volume = {15}, number = {4}, pages = {e0149625}, pmid = {41805177}, issn = {2576-098X}, support = {C644915664-00000026//EU Next Generation Fund/ ; UIDB/04565/2020, UIDP/04565/2020, LA/P/0140/2020//Fundação para a Ciência e a Tecnologia/ ; }, abstract = {We report 13 metagenome-assembled genomes (MAGs) of Paraglaciecola chathamensis (Gammaproteobacteria) retrieved from farmed Atlantic Nori (Porphyra spp.) across several developmental stages. MAGs encode proteins involved in host-microbe interactions, nutrient acquisition, nitrogen and cofactor metabolism, stress resilience, and genome plasticity, illuminating the possible roles of Paraglaciecola in the Porphyra holobiont.}, } @article {pmid41805398, year = {2026}, author = {Bouderka, F and López-García, P and Deschamps, P and Zhou, Y and Krupovic, M and Gutiérrez-Preciado, A and Ciobanu, M and Bertolino, P and David, G and Moreira, D and Jardillier, L}, title = {Parasitic connections: a patescibacterial epibiont, its methylotrophic gammaproteobacterial host, and their phages.}, journal = {mBio}, volume = {17}, number = {4}, pages = {e0002526}, pmid = {41805398}, issn = {2150-7511}, support = {787904//H2020 European Research Council/ ; 101141745//HORIZON EUROPE European Research Council/ ; ANR-22-CE02-0012-02, ANR-23-CE02-0016-01//Agence Nationale de la Recherche/ ; }, mesh = {*Bacteriophages/genetics/physiology/classification/isolation & purification ; Phylogeny ; Host Specificity ; *Gammaproteobacteria/virology/physiology/genetics ; Sequence Analysis, DNA ; Fresh Water/microbiology ; Symbiosis ; }, abstract = {Patescibacteriota form a very diverse and widely distributed phylum of small bacteria inferred to have an episymbiotic lifestyle. However, the prevalence of this lifestyle within the phylum and its host specificity remain poorly known due to the scarcity of cultured representatives. Here, we describe a complex system consisting of a patescibacterium, its gammaproteobacterial hosts, and their respective phages based on enrichment cultures and metagenomic data from two shallow, geographically close, freshwater ecosystems. The patescibacterium Strigamonas methylophilicida sp. nov. defines a new genus within the family Absconditicoccaceae. It grows as an epibiont on cells of methanotrophic species of the gammaproteobacterial family Methylophilaceae. Strigamonas cells grow tightly attached to the host, sometimes forming stacks that connect two host cells. Despite a surprisingly large genome (1.9 Mb) compared to many other Patescibacteriota, S. methylophilicida lacks many essential biosynthetic pathways, including the complete biosynthesis of phospholipids, amino acids, and nucleic acids, implying a dependence on the host to obtain these molecules. We also identified and assembled the complete genomes of one patescibacterial phage that might represent a new virus family within the class Caudoviricetes, and two Methylophilaceae phages predicted to have head-tailed and filamentous virions, respectively. The patesciphage uses a modified genetic code similar to that of its host and encodes four tRNA genes, including the suppressor tRNA gene for the UGA stop codon, which is reassigned to glycine in many Patescibacteriota. Our results confirm a prevalent episymbiotic lifestyle in Absconditicoccaceae and further suggest a clade-specific adaptation of this patescibacterial family for gammaproteobacterial hosts.IMPORTANCEPatescibacteriota are ultra-small bacteria with reduced genomes that rely on symbiotic interactions with other prokaryotes; however, their host specificity and associated viral parasites remain poorly characterized due to limited cultured representatives. By combining targeted cultivation with genomic and microscopy analyses, we reveal previously unrecognized host lineages and expand the known viral diversity infecting this major, but still poorly known, bacterial phylum. We describe Strigamonas methylophilicida, a new patescibacterial species of the family Absconditicoccaceae that grows as an epibiont on various methylotrophic Gammaproteobacteria. This expands the host range for this family, previously found to infect only photosynthetic partners. Using enrichment cultures and metagenomics, we retrieved complete genomes of novel phages infecting S. methylophilicida and its methylotrophic hosts, including one phage that uses a modified genetic code matching that of the patescibacterium, which shows a specific viral adaptation to infect Absconditicoccaceae hosts. Our findings reveal a previously unrecognized patescibacteria-methylotrophs-phages tripartite interaction in freshwater environments, highlight the adaptations of patescibacterial phages, and shed light on the complex ecology and evolution of host-parasite-phage dynamics in understudied bacterial lineages.}, } @article {pmid41805951, year = {2026}, author = {López-Puentes, D and Ojeda-Pérez, ZZ and Arias-Moreno, DM}, title = {Metagenomic Insights into the Microbial Composition and Functional Potential of Cocoa (Theobroma Cacao L.) During Fermentation and Drying in Colombia.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41805951}, issn = {1432-184X}, abstract = {Shotgun metagenomics is an approach increasingly applied to investigate microbial succession and functional potential in complex fermented food systems, including cocoa bean fermentation. In this study, we used Illumina-based shotgun metagenomic sequencing to characterize microbial community dynamics and metabolic potential across two post-harvest cocoa processing routes (R1 and R2) in Boyacá, Colombia, encompassing both fermentation and drying stages. Cocoa beans were sampled at defined time points during fermentation and subsequent natural drying, and non-host metagenomic reads were subjected to taxonomic classification and functional annotation to assess fungi, bacteria, and viruses. A clear multi-ecological succession was observed throughout post-harvest processing. Fungal communities shifted from a yeast-dominated profile, mainly Saccharomyces and Pichia during fermentation, to the emergence of the filamentous fungus Aspergillus during drying. Bacterial populations transitioned from diverse Enterobacteriaceae in early fermentation to a near-complete dominance of Acetobacter, which persisted throughout the drying phase. Viral communities also displayed structured successional patterns, with Lambdavirus and Punavirus prevalent in early fermentation, followed by Spbetavirus, Lafunavirus, and Pemunavirus during later stages and drying. Functional analyses revealed high metabolic potential for carbohydrate, energy, and amino acid metabolism during early fermentation, followed by a marked reduction in later stages, indicating a metabolic slowdown. Core metabolic functions were retained during drying at substantially lower activity levels. This integrated metagenomic analysis links microbial structure to functional potential and provides a scientific basis for optimizing starter cultures and post-harvest processing strategies to enhance cocoa quality and safety.}, } @article {pmid41806005, year = {2026}, author = {Dong, X and Zhang, T and Tang, B and Zeng, Q and Hu, Z and Huang, P and Xiong, X and Wang, X and Dong, W and Cai, Y}, title = {Microbial and metabolic profiles in autism spectrum disorder with atopic dermatitis in children.}, journal = {AMB Express}, volume = {16}, number = {1}, pages = {}, pmid = {41806005}, issn = {2191-0855}, abstract = {Atopic dermatitis (AD), an inflammatory skin disease, exhibits increased incidence with autism spectrum disorders (ASD) in children. However, the mechanism underlying the ASD-AD comorbidity remains unclear. Here, we integrated the metagenomic and metabolomics analysis to characterize the compositions and functional profiles of gut microbiome in ASD children with AD. We found significant alteration in the composition of the intestinal microbial species between ASD-AD group and ASD group based on beta diversity analysis. LEfSe analysis showed tyzzerella_nexilis, eubacterium_sp_OM08_24 and clostridium_nexile_CAG348 were significantly increased in ASD children with AD. In addition, metabolite profiles showed that differentially expressed metabolites were mainly lipids and organic acids. Meanwhile, functional profiles showed that the pathway of cholesterol metabolism and biosynthesis of unsaturated fatty acids was abundant in ASD children with AD. Furthermore, the correlation analysis revealed that bacteroides_sp_CAG443, limosilactobacillus_mucosae had a positive correlation with traumatic acid and ricinoleic acid that were decreased in ASD-AD group, respectively. Eubacterium_ramulus and lachnospiraceae_bacterium were positively correlated with 11,14-eicosadienoic acid (EDA). Taken together, our results propose that altered gut microbiota regulates metabolites to affect the development of atopic dermatitis in ASD children.}, } @article {pmid41806446, year = {2026}, author = {Lo Giudice, A and Papale, M and Bertolino, M and Reboa, A and Rizzo, C}, title = {Diversity and ecology of the prokaryotic microbiome associated with marine sponges across Antarctica.}, journal = {The Science of the total environment}, volume = {1025}, number = {}, pages = {181655}, doi = {10.1016/j.scitotenv.2026.181655}, pmid = {41806446}, issn = {1879-1026}, mesh = {Animals ; *Porifera/microbiology ; Antarctic Regions ; *Microbiota ; Ecosystem ; *Biodiversity ; Archaea ; Bacteria/classification ; Seawater/microbiology ; }, abstract = {Antarctic sponges host diverse and functionally relevant microbial communities that play central roles in the structure and resilience of polar benthic ecosystems. This review provides a focused analysis of the prokaryotic microbiomes associated with Antarctic sponges, with an emphasis on three ecologically significant species: Mycale (Oxymycale) acerata, Dendrilla antarctica, and Hymeniacidon torquata. Drawing from recent molecular studies, we examine the composition, predicted functional potential, and environmental responsiveness of these bacterial and archaeal communities. Comparative analyses with surrounding seawater and sediments reveal both overlaps and distinct host-specific microbial signatures, suggesting that sponge-associated microbiomes are shaped by selective pressures at the host and habitat levels. A conserved microbial core appears to coexist with more variable taxa influenced by host physiology and environmental gradients. We also discuss the impact of environmental stressors on microbiome structure and stability. Functional insights from metagenomic data highlight key microbial contributions to nutrient cycling, symbiotic lifestyles, secondary metabolite and vitamin production, quorum sensing, and the biodegradation of aromatic compounds. This review critically assesses current knowledge on Antarctic sponge-associated prokaryotic microbiomes, identifying recurrent taxonomic and functional patterns and evaluating evidence for core microbial functions across species and regions. We hypothesize that, despite taxonomic variability and geographical sampling bias, Antarctic sponge microbiomes share conserved functional traits shaped by host- and environment-driven selective pressures. Although foundational knowledge has expanded, particularly for shallow-water species, significant gaps persist-especially in underexplored habitats and in linking predicted functions to ecological dynamics. We conclude by outlining research priorities, including standardized protocols, broader spatial and temporal sampling, and multi-omics integration to better understand microbiome resilience under climate-driven change.}, } @article {pmid41806753, year = {2026}, author = {Wang, R and Liu, Z and Zhang, Q and Lian, J and Meng, H}, title = {Performance of oxic/anoxic process for treating aniline wastewater and gaseous N2O emission characteristics under low dissolved oxygen conditions.}, journal = {Journal of environmental management}, volume = {403}, number = {}, pages = {129250}, doi = {10.1016/j.jenvman.2026.129250}, pmid = {41806753}, issn = {1095-8630}, mesh = {*Aniline Compounds/metabolism ; *Oxygen/chemistry ; *Wastewater/chemistry ; *Nitrous Oxide ; Bioreactors/microbiology ; *Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical ; Nitrogen ; }, abstract = {In the biological treatment of aniline wastewater, the influence mechanism of dissolved oxygen (DO) concentration on the degradation of pollutants and N2O emission remains unclear. In this study, three A/O reactors were constructed to treat aniline wastewater, with the aerobic stage was operated under distinct low DO conditions: R1 (0.2-1.0 mg/L, ultralow oxygen), R2 (0.3-1.5 mg/L, lower oxygen), and R3 (0.4-2.0 mg/L, low oxygen). The results showed that as DO concentration increased, the removal rates of aniline, COD and NH4[+]-N improved slightly, whereas TN removal rate decreased significantly. During one operating cycle, cumulative gaseous N2O emissions were lowest in R2 and highest in R3. Therefore, considering pollutants removal, N2O emission and energy conservation, the lower oxygen control strategy (0.3-1.5 mg/L) was recommended. The metagenomic data revealed the enrichment of the aniline-degrading bacteria CAADHD01, and denitrifying bacteria JABWCM01, UBA12294, and Thauera in all reactors. The metabolic pathways of aniline and nitrogen were inferred. Aniline degradation primarily occurred via the meta-cleavage pathway, and nitrogen transformation involved assimilation, nitrification, and denitrification, while nitrification was inhibited by aniline. At the lower oxygen level (R2), the abundance of hao (hydroxylamine oxidoreductase gene) was lowest, and that of nosZ (nitrous oxide reductase gene) was highest, leading to lowest N2O emission. This study provides valuable strategies for N2O reduction during the biological treatment of aniline wastewater.}, } @article {pmid41806901, year = {2026}, author = {Yin, Z and Ping, H and Li, C}, title = {Associations between antibiotic and metal resistance genes in geothermal springs.}, journal = {Environmental research}, volume = {298}, number = {}, pages = {124235}, doi = {10.1016/j.envres.2026.124235}, pmid = {41806901}, issn = {1096-0953}, mesh = {*Hot Springs/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; China ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; *Metals ; }, abstract = {Metals, particularly toxic heavy metal(loid) pollutants, have been widely reported to facilitate the co-selection of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in contaminated environments. However, in natural geogenically metal-rich systems such as geothermal springs-often considered pristine environments analogous to early Earth-the occurrence of ARGs and their associations with MRGs remain poorly understood. Here, we investigated ARGs and MRGs distribution patterns in China's largest geothermal field using metagenomic and metatranscriptomic analyses. ARGs were detected in all studied geothermal springs, with total abundances ranging from 52.80 to 668.12 TPM. Macrolide-lincosamide-streptogramin (MLS), bacitracin, and rifamycin resistance genes were the most abundant ARGs. Significant associations between ARGs and MRGs were observed across the geothermal springs, as evidenced by Mantel tests and Procrustes analysis. For instance, bacitracin (R = 0.96, P = 1.06E-05) and rifamycin (R = 0.95, P = 3.41E-05) resistance genes exhibited strong positive correlations with arsenic (As) resistance genes. Metagenome-assembled genomes (MAGs) analyses further identified putative key drivers mediating the linkage between ARGs and MRGs (e.g., Thiomonas and Tepidimonas). Metatranscriptomic data confirmed the active transcription of ARGs, MRGs, and mobile genetic elements (MGEs). Collectively, this study provides a systematic understanding of the distribution patterns of ARGs in pristine geothermal springs and highlights their associations with MRGs.}, } @article {pmid41806991, year = {2026}, author = {Martinez-Tellez, B and Schönke, M and Kovynev, A and Garcia-Dominguez, E and Ortiz-Alvarez, L and Verhoeven, A and Gacesa, R and Vich Vila, A and Ducarmon, QR and Jimenez-Pavon, D and Gomez-Cabrera, MDC and Weersma, RK and Smits, WK and Giera, M and Ruiz, JR and Rensen, PC}, title = {Roseburia inulinivorans increases muscle strength.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-336980}, pmid = {41806991}, issn = {1468-3288}, abstract = {BACKGROUND: Gut bacteria have been implicated in a wide range of health conditions, yet their potential role in preventing and treating muscle-wasting disorders remains largely unexplored.

OBJECTIVE: We aimed to investigate whether specific gut microbial species are associated with muscle strength and to explore underlying mechanisms linking the gut microbiota to muscle health.

DESIGN: We conducted metagenomic analyses in cohorts of younger and older adults extensively phenotyped for muscle strength. Associations were tested between bacterial taxa and performance measures. Causality was assessed by oral supplementation of candidate species in antibiotic-treated mice. Metabolomic profiling and muscle phenotyping were performed to elucidate mechanisms.

RESULTS: The relative abundance of Roseburia inulinivorans, but not other Roseburia species, was positively associated with multiple strength measures including handgrip, leg press and bench press in humans. Supplementation of R. inulinivorans in mice significantly enhanced forelimb grip strength, whereas other Roseburia species had no effect. Metabolomic analyses revealed that R. inulinivorans reduced amino acid concentrations in the caecum and plasma, while activating the purine and pentose phosphate pathway in muscle. These changes coincided with increased muscle fibre size and a shift from type I to type II fibres. Accordingly, we observed that the relative abundance of R. inulinivorans is lower in older adults compared with young adults.

CONCLUSION: R. inulinivorans emerges as a species-specific modulator of muscle strength, linking gut microbiota to muscle metabolism and function. These findings support its potential as a probiotic candidate for nutraceutical interventions targeting age-related muscle-wasting diseases.

TRIAL REGISTRATION NUMBER: NCT02365129.}, } @article {pmid41807455, year = {2026}, author = {Bi, D and Wu, Y and Ji, G and Zhu, X and Li, H and Xie, R and Gao, Y and Deng, Z and Han, D and Qin, H and Wei, Q}, title = {Integrating ANI and phylogenies for re-evaluation of Fusobacterium taxonomy and disease associations.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41807455}, issn = {2041-1723}, support = {82572576//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82072236//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82072634//National Natural Science Foundation of China (National Science Foundation of China)/ ; SHDC2020CR2069B//Shanghai Hospital Development Center (SHDC)/ ; }, mesh = {*Phylogeny ; *Fusobacterium/genetics/classification ; *Fusobacterium Infections/microbiology ; Humans ; Genome, Bacterial/genetics ; DNA Gyrase/genetics ; Colorectal Neoplasms/microbiology ; }, abstract = {The genus Fusobacterium encompasses significant pathogens implicated in diseases spanning from infections to cancer. However, taxonomic ambiguities persist within the genus, particularly concerning Fusobacterium nucleatum (sensu lato). Through genus-wide average nucleotide identity (ANI) and phylogenetic analyses of 540 Fusobacterium genomes, we identify an ANI gap (93.38%-93.89%) for species delineation, leading to comprehensive taxonomic revisions that resolve these ambiguities. We further establish gyrB and rpoB as high-resolution taxonomic markers with phylogenies consistently supporting the revised taxonomy. Leveraging these markers, we develop B&B, a general strategy for precise species identification without whole-genome sequencing, and validate its accuracy in clinically relevant strains. Integrating the revised taxonomy with genomic/metagenomic toolkits demonstrate broad utilities, reinterpreting key colorectal cancer-associated species. This work establishes a unified taxonomic framework and enables standardised species classification for Fusobacterium isolates and microbiomes, highlighting the genetic divergence among Fusobacterium species and providing the taxonomic precision essential for advancing Fusobacterium-related research.}, } @article {pmid41807604, year = {2026}, author = {Santacroce, M and Baranek, J and Adamski, Z and Trzebny, A and Dabert, M and Bufo, SA and Scrano, L}, title = {Prevalence of Bacillus species in the lytic cultural heritage of Santa Lucia alle Malve Rupestrian Church.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41807604}, issn = {2045-2322}, abstract = {UNLABELLED: Santa Lucia alle Malve (SLM) is a unique rupestrian heritage site, entirely carved into limestone. This monument, which was a church in the ancient settlement of Benedictine nuns over a millennium ago in southern Italy, holds exceptional value not only from an architectural and cultural perspective but also in terms of its microbial ecology. Until now, the specific microbiota of this site had remained unexplored. In this study, the bacterial community inhabiting the interior walls of Santa Lucia alle Malve was investigated using a metagenomic approach, alongside the isolation and comprehensive characterization of cultivable strains from various sampling sites. Both methodologies consistently revealed a dominance of spore-forming bacteria from the phylum Bacillota, particularly the genus Bacillus. Notably, most of the cultivable strains belonged to the Bacillus cereus sensu lato group and the Bacillus. licheniformis clade. Despite the high genetic similarity among these microorganisms, each strain exhibited a unique set of phenotypic traits, highlighting the potential complexity of the SLM metabolome. Additionally, two isolates were identified as Bacillus thuringiensis, entomopathogenic bacteria with possible applications in biological pest management. Finally, Staphylococcus warneri, a human skin commensal found in the church, suggests human influence on the microbial landscape.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41655-4.}, } @article {pmid41808169, year = {2026}, author = {Cui, T and Yang, Y and Lange, D and Wang, X and Ruan, J and Ji, J and Dang, K and Zhou, Y and Xiao, J}, title = {Gut microbiome and metabolome signatures in calcium oxalate stone recurrence: a multi-omics study.}, journal = {Microbial cell factories}, volume = {25}, number = {1}, pages = {}, pmid = {41808169}, issn = {1475-2859}, support = {20240930//Beijing Key Clinical Specialty Project/ ; BJPSTP-2024-30//Beijing Physician Scientist Training Project/ ; 82000717//National Natural Science Foundation of China/ ; QML20190106//Beijing Hospitals Authority Youth Programme/ ; }, abstract = {BACKGROUND: The incidence and recurrence rate of nephrolithiasis have been increasing annually. Recent evidence highlights a close association between the composition and function of the gut microbiome and the occurrence and recurrence of kidney stones. We performed a multi-omic study to investigate changes in gut microbiota and their metabolites during nephrolithiasis development and recurrence, and to explore the underlying molecular mechanisms. Stool samples from 37 recurrent stone patients, 38 first-episode stone patients, and 39 healthy controls were collected for 16S rDNA amplicon sequencing and liquid chromatography-mass spectrometry. Ten samples from each group were randomly selected for metagenomic sequencing.

RESULTS: Compared to incident cases, recurrent stone patients exhibited further reduced gut microbial richness and diversity, with enrichment of Enterobacterales, Pseudomonadota, Gammaproteobacteria, Enterobacteraceae, Escherichia-Shigella, and Bacillia. In the recurrent kidney stone group, 9 metabolites were upregulated and 86 downregulated, with enrichment of genes in purine and caffeine metabolism pathways. We identified 10 metabolites as recurrence biomarkers and significant correlations between Escherichia-Shigella and Asn-Tyr, Leu-Ala-Ile, Tyrosyl-Alanine, or 3'-hydroxyhexobarbital. Additionally, gender-specific gut microbiota signatures were observed. Oxalate decarboxylase and short-chain fatty acid-related enzymes decreased during stone formation but rebounded with recurrence. Caffeine and its metabolites were significantly downregulated in recurrent patients, suggesting a potential association with stone formation and recurrence that merits further investigation.

CONCLUSIONS: Our study comprehensively characterizes gut microbiome and metabolome signatures associated with nephrolithiasis recurrence. The findings reveal that recurrent nephrolithiasis is characterized by impaired gut microbial evenness, enrichment of specific taxa including Escherichia-Shigella, and dysregulated metabolic pathways such as purine metabolism and caffeine metabolism. The 10 identified metabolites show promise as potential recurrence biomarkers, with notable correlations between Escherichia-Shigella and key metabolites. These results highlight the critical association of the gut microbiome-metabolome axis with renal stone recurrence, providing novel microbial and metabolic targets for early prediction, with potential implications for prevention and personalized treatment that require further validation.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12934-026-02977-0.}, } @article {pmid41808525, year = {2026}, author = {Jiménez, DJ and Rosado, AS}, title = {Discovering PETases: An Interlink Between Engineering Enzymes and Microbiomes.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70272}, pmid = {41808525}, issn = {1462-2920}, support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; }, mesh = {*Polyethylene Terephthalates/metabolism ; *Microbiota ; *Hydrolases/metabolism/genetics ; Metagenomics ; Biodegradation, Environmental ; *Bacteria/enzymology/genetics/metabolism ; Biocatalysis ; Protein Engineering ; }, abstract = {Polyethylene terephthalate (PET), an abundant synthetic polyester, is the only plastic that has been enzymatically recycled at an industrial scale. Over the last decades, research efforts have focused on screening and engineering PET-degrading hydrolases (PETases), aiming to identify variants that can operate efficiently in both environmental and industrial settings. The detection of potential PETases from marine and terrestrial ecosystems has primarily been conducted via metagenomics using homology strategies. However, the use of benchmark PETases as references has limited the searches, narrowing the sequence landscape. Currently, there remains a need to identify efficient thermophilic, halotolerant and pH-robust PETases for the industrial biocatalysis of PET. In line with this, in this article, we discuss recent findings related to the following topics: (i) the identification of suitable ecosystems for mining PETases; (ii) the discovery of PETases via the restructuring of microbiomes; (iii) advancements in metagenomics and artificial intelligence (AI)-based approaches for the detection and ranking of PETases and (iv) the future of PET biocatalysis. Overall, we suggest that disrupting microbiomes with polyester-rich substrates, combined with innovative computational and AI-based strategies, can be an effective pathway for the discovery of PETases that can be used as scaffolds for protein engineering and biotechnological applications.}, } @article {pmid41808728, year = {2026}, author = {Pereira, MH and Tyagi, S and Mohanty, A and Garg, S and Kumar, A}, title = {Metagenomic studies reveal diverse microbial community in the developmental stages of highly adaptable malarial vector Anopheles stephensi liston.}, journal = {3 Biotech}, volume = {16}, number = {4}, pages = {124}, pmid = {41808728}, issn = {2190-572X}, abstract = {UNLABELLED: Anopheles stephensi, a highly adaptable malaria vector species, continues to expand its range from South Asia to Sub-Saharan Africa, posing a serious global public health concern. In India, it serves as the principal urban vector of both Plasmodium falciparum and P. vivax. Conventional control measures reliant on chemical insecticides have raised issues of resistance, highlighting the need for alternative strategies such as microbiota-mediated vector control. This study aimed to test the hypothesis that a subset of bacterial taxa persist across developmental stages of An. stephensi, representing potential candidates for transstadial transmission and future paratransgenic manipulation. Using both culture-based data and next-generation sequencing (NGS) approaches targeting the 16 S rRNA gene (V3-V4 region), we characterized bacterial communities from breeding water, larvae, pupae, and adult mosquitoes (male and female) collected in Goa, India. Across all developmental stages, Proteobacteria and Firmicutes were the dominant phyla, while 15 bacterial genera formed the putative core microbiome shared by ≥ 80% of stages at ≥ 0.1% abundance. Among these, Pseudomonas (adult males: 11.5%, pupae: 3.2%), Exiguobacterium, Acinetobacter, Psychrobacter, and Asticcacaulis were consistently detected, together contributing approximately 30% of total microbial composition. Alpha diversity indices indicated higher richness and evenness in pupae and adults than in larvae, suggesting microbial enrichment during metamorphosis. Beta diversity and PCoA analyses clustered pupal and adult stages distinctly from larvae and breeding water, confirming selective microbial retention through development. These findings reveal that An. stephensi harbors a stable, stage-spanning core microbiome dominated by metabolically versatile genera with potential for transstadial persistence. The dominance of Pseudomonas across life stages supports its candidacy for paratransgenic applications aimed at disrupting malaria transmission. This work provides the first integrated culture-NGS baseline of An. stephensi microbiota from India, offering essential insight for microbiome-based vector control strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04739-6.}, } @article {pmid41808765, year = {2026}, author = {Rivera-Sánchez, ES and Salinas-García, M and Viviano, E and Villaró-Cos, S and Lafarga, T}, title = {Effect of salinity on growth and microbial diversity in cultures of Scenedesmus almeriensis produced at a pilot scale.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {14}, number = {}, pages = {1753183}, pmid = {41808765}, issn = {2296-4185}, abstract = {Introduction: Freshwater scarcity represents a major constraint for the sustainable industrial-scale cultivation of microalgae. This study investigates the feasibility of producing Scenedesmus almeriensis using seawater in 3.1 m[3] tubular photobioreactors under winter-spring conditions. The appearance of algal predators represents a significant challenge in industrial facilities, and this research also explores whether seawater can serve as a strategic water source for more resilient and efficient production systems. Methods: Biomass productivity and microbial diversity were compared between freshwater and seawater-based cultures under batch and semi-continuous regimes at dilution rates of 0.1, 0.2, and 0.3 day[-1]. The production was carried out in duplicate using identical tubular photobioreactors. Analytical determinations included measuring biomass concentration, chlorophyll fluorescence, and oxygen production via photorespirometry. Microbial diversity was assessed through microscopy and metagenomic analysis (18S and 16S rDNA) to identify taxonomic classifications and potential biotic contaminants. Results and Discussion: Maximum biomass concentrations reached 0.60 and 2.15 g·L[-1] in freshwater and seawater, respectively. Production using seawater led to a higher biomass productivity (0.18 g·L[-1]·day[-1]) compared to freshwater (0.06 g·L[-1]·day[-1]) at a fixed dilution rate of 0.1 day[-1]. Seawater cultures exhibited greater stability and higher photosynthetic efficiency, with Scenedesmus dominating up to 70% of the microalgal community due to reduced contamination by zooplankton, fungi, and ciliates. In contrast, freshwater cultures were rapidly degraded by rotifers and anaerobic fungi, leading to a culture crash when dilution rates were increased. These findings highlight the potential of seawater to act as a biological barrier against contaminants while significantly reducing freshwater requirements in industrial microalgae production.}, } @article {pmid41809220, year = {2026}, author = {Wishahi, M}, title = {Gut microbiotas attributed to disorders and diseases of the gastrointestinal tract, colorectal cancer, bladder cancer: Geographical factors, inflammation, metabolic toxic.}, journal = {World journal of gastrointestinal pharmacology and therapeutics}, volume = {17}, number = {1}, pages = {115573}, pmid = {41809220}, issn = {2150-5349}, abstract = {Recently, there were several publications that attributed gut microbiota (GM) to various gastrointestinal tract functional disorders and diseases, including inflammatory bowel diseases, colon cancer, pancreatic cancer, and diverticulosis. GM is attributed to the initiation of urinary tract diseases and bladder carcinoma (BCa). The concern is whether GM is dysbiotic or protective. We explored the studies on GM contribution to colorectal cancer and BCa. Selected studies from different geographical regions on tissue samples or faecal samples from patients with colorectal cancer and controls. The results showed diverging results of microbiota abundance, genus, class, and phylum. These data indicated that other factors of environmental, diet, ethnic, and personal factors are contributors to GM in the initiation of inflammation and tumors. GM are not inhabitants in the urinary tract; it is postulated that GM attributes to BCa via the circulating metabolic toxins in the initiation of tumorigenesis and BCa.}, } @article {pmid41809269, year = {2026}, author = {Pei, J and Chen, L and Pushparaj, R and Huang, P and Pan, G and Sun, C and Gao, X and Zhang, L and Manirujjaman, M and Huang, CK and Ting, PS and Deng, Z and Chen, S and Zhang, X and Vatsalya, V and McClain, CJ and Feng, W}, title = {High-dose taurine supplementation exacerbates alcohol-associated liver disease by inducing gut microbiota dysbiosis and bile acid dysregulation in mice.}, journal = {eGastroenterology}, volume = {4}, number = {1}, pages = {e100321}, pmid = {41809269}, issn = {2976-7296}, support = {R01 AA023190/AA/NIAAA NIH HHS/United States ; R01 AA028435/AA/NIAAA NIH HHS/United States ; R01 AA030424/AA/NIAAA NIH HHS/United States ; R01 AA030756/AA/NIAAA NIH HHS/United States ; }, abstract = {BACKGROUND: β-aminoethanesulfonic acid (taurine) is a conditionally essential amino acid that plays critical roles in bile acid (BA) conjugation, antioxidative defence and metabolic regulation. Previous studies showed that faecal taurine level was reduced in patients with alcohol-associated liver disease (ALD), suggesting that taurine supplementation may have beneficial effects. This study aimed to determine whether oral taurine supplementation prevents the development of ALD in mice and to elucidate the underlying mechanisms.

METHODS: A total of 8-week-old male mice were subjected to a chronic-plus-binge ALD model. Taurine was administered orally via the diet for ten days before and during ethanol exposure. Faecal 16S ribosomal RNA metagenomic analysis, liver RNA sequencing and BA profiling were performed.

RESULTS: High-dose taurine supplementation (3 g/kg body weight/day) was associated with worsened ethanol-induced liver injury, as indicated by increased serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, hepatic steatosis, apoptosis and inflammation. At the molecular level, high-dose taurine treatment was associated with reduced Cpt1a expression, altered expression of genes involved in fatty acid β-oxidation and lipogenic gene Fasn, and decreased expression of Baat, accompanied by changes in taurine-conjugated BA profiles. These alterations were accompanied by changes in BA composition and intestinal FXR-associated gene expression. Taurine supplementation was also associated with shifts in gut microbial composition, including enrichment of hydrogen sulfide-producing bacteria, increased microbial H2S production, impaired intestinal barrier-related parameters and increased bacterial translocation to the liver, paralleling enhanced hepatic inflammatory responses. In contrast, low-dose taurine supplementation (0.2 g/kg body weight/day) was associated with improved liver phenotypes, including reduced steatosis, lower serum ALT and AST levels, decreased Fasn expression and enhanced BA conjugation. Collectively, these results indicate a dose-dependent association between taurine supplementation and ALD-related outcomes.

CONCLUSIONS: Our findings suggest that high-dose taurine supplementation is associated with unfavourable alterations in gut microbiota composition, intestinal barrier integrity, BA metabolism and hepatic taurine-related pathways in ALD, coinciding with exacerbated liver injury. In contrast, low-dose taurine supplementation was associated with improved hepatic outcomes. These results highlight the importance of dose considerations in taurine supplementation and support the concept that taurine may exert divergent effects on ALD depending on the administered dose.}, } @article {pmid41809628, year = {2026}, author = {Zhang, W and Tang, Y and Luo, R and He, J and Yan, J and Long, F and Li, L}, title = {Altitudinal changes induce responses in Coptis chinensis Franch. rhizomes: endophytic communities, metabolite types, and alkaloid contents.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1777206}, pmid = {41809628}, issn = {1664-462X}, abstract = {Coptis chinensis Franch. is a perennial medicinal plant with huge economic and social benefits, but how altitude affects the accumulation of bioactive compounds through microbial ecosystems remains unexplored. This study examined how microbial communities at different altitudes influence the bioactive components of Coptis chinensis, to help identify beneficial microorganisms for application to its rhizomes. Samples of Coptis chinensis were cultivated at four different altitudes in Shizhu, Chongqing. To characterize the phytochemical profile of Coptis chinensis, nine specific alkaloids were quantified by High Performance Liquid Chromatography (HPLC) and Ultraviolet-Visible Spectrophotometry (UV-Vis), with Liquid Chromatography-Mass Spectrometry (LC-MS) subsequently employed to characterize differential metabolite accumulation at each altitude. Microbial community structure in the rhizomes was analyzed by metagenomic sequencing. Results indicated that the contents of groenlandicine, coptisine, berberine, and total alkaloids increased with altitude, with the total alkaloid content rising from 15.97% at 907 m to 17.82% at 1698 m (P < 0.01). Analysis revealed 912 differential metabolites, with distinct accumulation patterns at different altitudes. Microbial diversity in the rhizomes also varied by altitude, with significant shifts in Mucoromycota, Pseudomonadota, Rhizophagus, and Mesorhizobium populations. Moreover, the relative abundance of these microorganisms was intricately linked to alkaloid content. High altitude significantly enhances alkaloid accumulation in C. chinensis, and this effect is primarily mediated by the enrichment of beneficial endophytes, which promote the biosynthesis of target alkaloids via optimizing nitrogen utilization and inducing the expression of key enzymes.}, } @article {pmid41809656, year = {2026}, author = {Burakova, I and Smirnova, Y and Morozova, P and Pogorelova, S and Kryukova, O and Kislova, T and Korneeva, O and Syromyatnikov, M}, title = {The effect of short-term consumption of Bifidobacterium bifidum on the gut microbiome of obese individuals.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {251}, number = {}, pages = {10894}, pmid = {41809656}, issn = {1535-3699}, mesh = {Humans ; *Bifidobacterium bifidum/physiology ; *Probiotics/administration & dosage ; *Obesity/microbiology ; High-Throughput Nucleotide Sequencing ; Dysbiosis/therapy ; Male ; }, abstract = {It is known that gut microbiota dysbiosis can lead to obesity by disrupting energy consumption and metabolism. Probiotic supplements are a potential therapeutic option for improving intestinal homeostasis. The aim of this study was to investigate the effect of a probiotic supplement containing Bifidobacterium bifidum on the intestinal microbiome of people with obesity using high-throughput sequencing on the DNBSEQ-G50 platform. The study demonstrated a positive effect of the supplement on bacterial species such as Bacteroides uniformis, Alistipes putredinis, Alistipes shahii, Dysosmobacter welbionis, and Gemmiger formicilis. Therefore, we suggest the potential use of this bacterial species in the treatment of gut microbiota dysbiosis of obese individuals.}, } @article {pmid41809703, year = {2026}, author = {Suvvari, TK and Kodakandla, R and Kandi, V}, title = {Redefining the diagnostic pathway for pulmonary nocardiosis: The imperative for early metagenomic sequencing.}, journal = {World journal of radiology}, volume = {18}, number = {2}, pages = {119080}, pmid = {41809703}, issn = {1949-8470}, abstract = {In this article, we comment on the pivotal article by Wang et al. We focus on the critical intersection of advanced imaging and molecular diagnostics highlighted by their findings. The study delineates specific high-risk computed tomography patterns, notably consolidation with nodules/cavities, particularly in immunocompromised hosts or patients with bronchiectasis, that should serve as immediate red flags for pulmonary nocardiosis. Traditionally, diagnosis has relied on slow-growing cultures, leading to dangerous therapeutic delays. This editorial argues that the presence of these defined radiologic signatures may represent an important step toward refining the diagnostic pathway for pulmonary nocardiosis. Rather than a confirmatory last resort, metagenomic next-generation sequencing should be deployed as a first-line investigative tool following high-suspicion imaging. We propose a concrete, integrated diagnostic algorithm where imaging triage triggers parallel processing with metagenomic next-generation sequencing and conventional microbiology. This synergy of morphology and metagenomics promises to expedite species-specific diagnosis, guide timely targeted therapy, and ultimately improve outcomes for patients with this challenging and often elusive infection.}, } @article {pmid41809936, year = {2026}, author = {Su, M and Luo, Y and Huan, X and Xi, C and Yang, L and Zhong, H and Liu, F and Zhang, Q and Liu, Q and Wang, X and Cao, Y and Wang, M and Ta, F and Wang, B and Ai, J and Zhao, C and Zheng, J and Luo, S}, title = {Application of Droplet Digital PCR in Sputum Samples in Myasthenia Gravis Patients with Pneumonia.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {588779}, pmid = {41809936}, issn = {1178-6973}, abstract = {BACKGROUND: Due to the rapid progression of the pneumonia in patients with Myasthenia gravis (MG), faster pathogen detection techniques are needed. The droplet digital polymerase chain reaction (ddPCR) has the ability to detect pathogens in about 3 h. Thus, this study focused on application of ddPCR in sputum samples in the MG patients with pneumonia and analyzed the association between ddPCR and other laboratory results.

METHODS: We prospectively enrolled 22 MG inpatients with pneumonia and collected 24 sputum samples. All samples were analyzed using traditional culture, ddPCR and metagenomic next-generation sequencing (mNGS) in parallel. Clinical outcomes during hospitalization were documented.

RESULTS: Among the 24 sputum samples collected from 22 MG patients, ddPCR achieved a 100% positivity rate with the identification of bacteria in all 24 samples, while mNGS also demonstrated a high detection rate, identifying bacteria in 23 of 24 samples (95.8%), and additionally detecting viral and fungal pathogens across multiple cases. In 4 patients with negative sputum culture results, pathogens were identified by both ddPCR and mNGS.

CONCLUSION: The ddPCR demonstrated rapid and sensitive identification of predefined bacterial targets and drug-resistance genes, making it suitable for initial diagnostic screening and timely clinical decision-making in MG patients with pneumonia. The speed of ddPCR detection is faster than mNGS and traditional culture, and the results are similar to mNGS and culture, with good consistency.}, } @article {pmid41809988, year = {2026}, author = {Parks, DH and Newell, RJP and Ginn, AN and Bowerman, KL and Alsheikh-Hussain, A and Fang, L and Shah, S and MacDonald, S and Wimpenny, T and Evans, P and Arias Guzman, NE and Pribyl, AL and Tyson, GW and Hugenholtz, P and Krause, L and Newcombe, J and Griffin, P and Wehrhahn, MC and Angel, NZ and Wood, DLA}, title = {Metagenomics enables parallel detection of 176 clinically relevant targets from faecal samples.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1759322}, pmid = {41809988}, issn = {2235-2988}, mesh = {Humans ; *Feces/microbiology/virology ; *Metagenomics/methods ; Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/isolation & purification ; Viruses/genetics/isolation & purification ; *Molecular Diagnostic Techniques/methods ; Virulence Factors/genetics ; Reproducibility of Results ; }, abstract = {BACKGROUND: Robust identification of pathogens is essential for managing patients with symptomatic infection, yet conventional diagnostic methods focus on a subset of the most prevalent pathogens and genes. Metagenomic next-generation sequencing (mNGS) is a powerful technology that can comprehensively and simultaneously assess a broader range of pathogens and genes in a sample. This study evaluates the clinical (22 targets), analytical (19 targets), and in silico (176 targets) performance of a faecal mNGS assay on clinically relevant bacterial, eukaryotic, viral, virulence factor (VF) and antimicrobial resistance (AMR) genes.

METHODS: Diagnostic performance was evaluated relative to conventional pathology testing using 510 clinical faecal samples from patients presenting with gastrointestinal symptoms. Contrived samples were used to assess analytical performance and establish the assay's limit of detection by adding cells to a faecal matrix. In silico faecal samples containing targets reflecting the limit of detection of the assay were used to evaluate performance across all 176 targets.

RESULTS: Clinical specificity was ≥96% (≥99% for all but Adenovirus F), and median pathogen sensitivity was 91%. VF and AMR gene detection was less sensitive (median 58.7%). The assay was highly reproducible in biological triplicates (27,656/27,808 calls concordant; 99.5%). Importantly, broad mNGS coverage increased diagnostic yield, with 256/510 (50.2%) samples containing one or more additional targets not reported by standard care, and 181/510 (35.5%) containing AMR genes, including carbapenemases. In silico benchmarking showed strong performance for all 176 targets down to analytically defined detection limits.

CONCLUSIONS: The faecal mNGS assay performed competitively with existing diagnostic techniques while substantially expanding actionable detection in a single assay. These results support stool mNGS as a high-yield second-line or syndromic test for gastrointestinal infection, enabling improved recognition of rare pathogens, co-infections, and resistance determinants.}, } @article {pmid41810030, year = {2026}, author = {Karr, AF and Ruane, R}, title = {Effects of Training Data Quality on Classifier Performance.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {41810030}, issn = {2331-8422}, abstract = {We describe extensive numerical experiments assessing and quantifying how classifier performance depends on the quality of the training data, a frequently neglected component of the analysis of classifiers. More specifically, in the scientific context of metagenomic assembly of short DNA reads into "contigs," we examine the effects of degrading the quality of the training data by multiple mechanisms, and for four classifiers-Bayes classifiers, neural nets, partition models and random forests. We investigate both individual behavior and congruence among the classifiers. We find breakdown-like behavior that holds for all four classifiers, as degradation increases and they move from being mostly correct to only coincidentally correct, because they are wrong in the same way. In the process, a picture of spatial heterogeneity emerges: as the training data move farther from analysis data, classifier decisions degenerate, the boundary becomes less dense, and congruence increases.}, } @article {pmid41810234, year = {2026}, author = {Yang, G and He, S and Wang, J and Yu, S and Zhang, S and Fan, W}, title = {Cryptococcus neoformans infection presenting as a mediastinal mass in an immunocompetent child with parrot exposure: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1771746}, pmid = {41810234}, issn = {2296-858X}, abstract = {Cryptococcus neoformans typically causes pulmonary or central nervous system (CNS) infections, but mediastinal mass as its primary manifestation is rare-especially in immunocompetent children with pet parrot exposure. This study reports a 7-year-old girl who presented with recurrent fever and a mediastinal mass secondary to Cryptococcus neoformans infection, with a 5-month history of daily contact with parrot feces. Conventional diagnostic tests (e.g., fungal culture, serology) were negative, and the diagnosis was confirmed by targeted metagenomic next-generation sequencing (tNGS) of bronchoalveolar lavage fluid (BALF). The patient received a three-phase antifungal regimen: induction with amphotericin B + flucytosine, consolidation with fluconazole, and maintenance with low-dose fluconazole. After one year of treatment, the mediastinal mass nearly resolved, and no recurrence was observed. A literature review, supplemented with specific cases of parrot-associated Cryptococcus neoformans infection, highlights that parrot exposure is an underrecognized risk factor for pediatric cryptococcosis, and tNGS significantly improves diagnostic efficiency for atypical extrapulmonary manifestations. This case emphasizes the importance of inquiring about pet bird exposure in children with unexplained mediastinal masses and fever, and supports the use of tNGS for early, non-invasive diagnosis.}, } @article {pmid41810244, year = {2026}, author = {Zhou, F and Zhang, Y and Liu, Y and Mou, Y and Chen, J}, title = {Streptococcus suis meningitis in an elderly man: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1735413}, pmid = {41810244}, issn = {2296-858X}, abstract = {BACKGROUND: Streptococcus suis is a zoonotic pathogen that resides in pigs. It can be transmitted to humans through several routes, including contact with sick or carrier pigs via broken skin or mucous membranes and consumption of undercooked pork products. Streptococcus suis often causes severe clinical symptoms such as meningitis, sepsis, and shock.

CASE PRESENTATION: A 66-years-old male butcher was admitted to the hospital with a sudden high fever and disturbance of consciousness, and he remained in a state of persistent restlessness. The neurological examination findings were as follows: he was poorly cooperative with the examinations of higher cortical functions and cranial nerves, uncooperative with the examination of limb muscle strength, and unable to cooperate with the examinations of sensation and ataxia. He presented with nuchal rigidity, with a distance of four finger breadths between the chin and chest, and Kernig's sign was positive. The patient was diagnosed with Streptococcus suis meningitis based on the results of Metagenomic Capture sequencing, cerebrospinal fluid culture, and blood culture. Considering the patient's critical condition, he had received empirical treatment with cephalosporin in the previous hospital, but the therapeutic effect was not satisfactory. Moreover, in this region, there is a phenomenon of decreased sensitivity in Streptococcus pneumoniae to penicillin and third-generation cephalosporins. Therefore, the patient received antibiotic treatment with vancomycin (1 g) intravenously every 12 h. Concurrently, he was administered mannitol to reduce intracranial pressure and ulinastatin for anti-inflammatory effects and immune enhancement. Subsequently, vancomycin 20 mg was administered by intrathecal injection. The patient's condition improved, and he was discharged from the hospital. There was no special discomfort during follow-up.

CONCLUSION: This case report describes the diagnosis and treatment process of Streptococcus suis meningitis. It proposes an antibiotic treatment plan centered on vancomycin. Intrathecal injection of antibiotics may provide an effective treatment option for severe patients and offer a treatment choice for drug-resistant bacterial infections in the central nervous system. It was also pointed out that Metagenomic Capture sequencing can reduce host gene interference and increase the detection rate of pathogens. This case aims to enhance clinicians' understanding of the disease and provide a reference for early identification and standardized treatment.}, } @article {pmid41810372, year = {2026}, author = {Ding, SC and Yu, J and Liao, T and Ahmann, LS and Yao, YY and Ho, C and Wang, L and Pinsky, BA and Gu, W}, title = {Adapting Clinical Chemistry Plasma as a Source for Liquid Biopsies.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41810372}, abstract = {BACKGROUND: Circulating cell-free DNA (cfDNA) has become a valuable analyte for molecular testing, but requires specialized collection tubes or immediate processing. We investigated the feasibility of using residual plasma from heparin separators, which are routinely used in clinical chemistry, as an accessible and underutilized source for cfDNA biobanking and testing.

METHODS: We analyzed matched plasma samples from healthy volunteers in two experiments: an immediate-processing tube comparison across EDTA, Streck, and heparin separators (n = 5) and a clinical-handling simulation that paired EDTA and heparin separator tubes and delayed processing at room temperature versus 4°C (n = 6). We also analyzed matched EDTA and heparin separator plasma samples from viral PCR-positive patients (Hospital Cohort; n =38). Whole-genome sequencing and genome-wide enriched methylation sequencing were performed to evaluate concordance across multiple benchmarks, including metagenomics, chromosomal copy number, methylome, and fragmentomics.

RESULTS: Under immediate processing, heparin separator plasma showed high concordance with EDTA and Streck plasma for methylation patterns (Spearman's ρ=0.65-0.70) and fragmentation features (n = 5). In the clinical-handling simulation, cfDNA integrity in heparin separators was comparable to that in EDTA at 4°C (n=6). In the Hospital Cohort, heparin separators showed a strong concordance with matched EDTA tubes for viral detection (n=38, Spearman's ρ=0.95), copy number alteration profiling (n=6, Spearman's ρ=0.72-0.96), and methylation patterns (n=12, Spearman's ρ=0.50-0.83).

CONCLUSION: Hospital residual plasma from routine clinical chemistry tests that are processed within a short pre-centrifugation window and refrigerated can provide a vast, untapped resource for cfDNA biobanking and potential testing.}, } @article {pmid41810379, year = {2026}, author = {Anzà, S and Rosa, BA and Herzberg, MP and Lee, G and Herzog, ED and Zhao, P and England, SK and Ndao, IM and Martin, J and Smyser, CD and Rogers, CE and Barch, DM and Hoyniak, C and McCarthy, R and Luby, J and Warner, BB and Mitreva, M}, title = {Simplifying Daily Cortisol Cycle Analysis: Validation and Benchmarking of the Cortisol Sine Score Against Cosinor and JTK_CYCLE models.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41810379}, support = {R01 MH113883/MH/NIMH NIH HHS/United States ; }, abstract = {The daily cortisol cycle is a critical indicator of hypothalamic-pituitary-adrenal (HPA) axis function. The current analytical approaches produce several outputs difficult to integrate into simple statistical models, clinical workflows, and ML/AI pipelines requiring single-value inputs. We developed the Cortisol Sine Score (CSS), a model-free scalar metric that quantifies daily cortisol exposure by computing a weighted sum of cortisol measurements across the day, using sine-transformed time-of-day weights. The CSS produces positive values for morning-dominant patterns, negative values for evening-shifted profiles, and near-zero values for flattened rhythms characteristic of chronic stress and circadian disruption. We validated the CSS performance in 3,006 samples from 501 pregnant women enrolled in the March of Dimes program, with cortisol values measured at 6 time points per day collected during the second trimester of pregnancy. The CSS showed strong correlations with observed and model-estimated amplitude and acrophase from Cosinor regression and JTK_CYCLE approaches, with excellent classifying performance (AUC=0.89, high versus low). The CSS successfully captured established associations between social disadvantage and cortisol dysregulation, and demonstrated utility in predicting gut microbiome composition in metagenomic analyses. Importantly, the CSS maintains excellent fidelity to the full 6-sample protocol with as few as 3-4 daily measurements. The 4-sample protocol achieves great performance (r = 0.952, MAE = 0.087) while reducing participant burden. The 06:00 time point was identified as essential for accurate CSS quantification. The CSS bridges the gap between circadian analysis and practical implementation by providing a simple, interpretable, and robust assessment of cortisol daily cycle in large-scale epidemiological studies, clinical screening, and biomedical sensors.}, } @article {pmid41810553, year = {2026}, author = {Boscá-Sánchez, I and Rodríguez-Díaz, J and Yebra, MJ}, title = {Sequence-Based and Functional Analysis for the Discovery of N-Glycan Degrading Glycosidases From the Microbial Metagenome of the Infant Gut.}, journal = {MicrobiologyOpen}, volume = {15}, number = {2}, pages = {e70264}, pmid = {41810553}, issn = {2045-8827}, support = {PID2023-148094OB (C21 and C22)//Ministerio de Ciencia e Innovación/ ; }, mesh = {Humans ; *Polysaccharides/metabolism ; *Metagenome ; Infant ; *Glycoside Hydrolases/metabolism/genetics ; Feces/microbiology ; *Gastrointestinal Tract/microbiology ; Substrate Specificity ; }, abstract = {The role of bacterial glycosyl hydrolases (GHs) in degrading free human milk oligosaccharides is well documented. However, their activity on glycoconjugates is less well known. Here, an in silico analysis of the metagenome of the fecal microbiome of breastfed infants was employed to identify GH2 β-galactosidases, GH20 exo-N-acetylglucosaminidases and GH18 endo-N-acetylglucosaminidases active on N-glycans. A total of nine β-galactosidases were recombinantly expressed and two of them, Gal1b and Gal99, were able to remove galactose from the G2 peptide and asialofetuin. Gal1b, Gal25, Gal37c, Gal99 and Gal296 hydrolyzed lactose and N-acetyllactosamine, indicating specificity for galactose β1,4-linked to glucose or GlcNAc. All of the exo-β-N-acetylglucosaminidases studied here (Exo10a, Exo18, Exo38, Exo39b, Exo360 and Exo399) hydrolyzed the disaccharide N-acetylglucosaminyl-β1,2-mannose, which forms part of the N-glycan structures. Exo10a, Exo38 and Exo360 hydrolyzed N-acetylglucosamine (GlcNAc) from the G2 peptide pretreated with Gal1b. Notably, Exo360 hydrolyzed GlcNAc at both the α1,3 and α1,6 branches of the G2 peptide core mannose simultaneously, whereas Exo10a showed a preference for GlcNAc at one branch. Exo38 and Exo360 also release GlcNAc from asialofetuin once galactose has been removed. The whole structures of N-glycans were liberated from glycoproteins by the action of the endo-N-acetylglucosaminidases Endo38 and Endo358. These enzymes hydrolyze the N,N'-diacetylchitobiose core of N-linked glycans of the high-mannose and non-sialylated complex types, respectively. Overall, these results provide insight into the range of glycosyl hydrolases present in the infant gut microbiota that act on glycoconjugates, which may play a role in the establishment and composition of the newborn microbiota.}, } @article {pmid41811526, year = {2026}, author = {Tammi, R and Maukonen, M and Kaartinen, NE and Koponen, K and Niiranen, T and Méric, G and Albanes, D and Eriksson, JG and Jousilahti, P and Koskinen, S and Pajari, AM and Knight, R and Havulinna, AS and Salomaa, V and Männistö, S}, title = {Interplay between colorectal cancer-related lifestyles and the gut microbiome: an exploratory analysis of metagenomic data.}, journal = {Cancer causes & control : CCC}, volume = {37}, number = {4}, pages = {}, pmid = {41811526}, issn = {1573-7225}, support = {352481//Strategic Research Council/ ; 352483//Strategic Research Council/ ; }, mesh = {Humans ; *Life Style ; Female ; *Colorectal Neoplasms/microbiology/epidemiology/etiology ; Middle Aged ; Male ; Adult ; *Gastrointestinal Microbiome/genetics ; Risk Factors ; Metagenomics/methods ; Finland/epidemiology ; Metagenome ; Diet ; }, abstract = {PURPOSE: The gut microbiome may modify the associations between lifestyle factors and colorectal cancer (CRC) risk, but their complex interplay, including the interactions between lifestyle factors, remain underexplored. We examined associations between CRC-related lifestyle patterns and gut microbiome diversity and composition in Finnish adults.

METHODS: Our data included 1,228 adults aged 25-64 years from the National FINRISK/FINDIET 2002 Study. Information on lifestyle and background factors was obtained through self-administered questionnaires. Dietary data were gathered using a 48-h dietary recall. CRC-related lifestyles were modelled using a CRC lifestyle index based on nine major risk factors for CRC. Lower index points reflected higher-risk lifestyles. The gut microbiome profiles were analyzed using shallow shotgun metagenome sequencing. Associations between the index and microbial diversity and composition were assessed using, e.g., linear regression and permutational multivariate ANOVA adjusted for relevant confounders.

RESULTS: The index explained 0.2% of the variation in microbial composition between participants (p < 0.05). Higher-risk lifestyles for CRC were associated with lower microbial diversity (β 0.037, p 0.009). Higher-risk lifestyles were also associated with a higher relative abundance of species representing primarily the family Lachnospiraceae and genera such as Dorea and Mediterraneibacter, and lower relative abundance of species within the genus Bifidobacterium (< 0.0001).

CONCLUSIONS: Participants with higher- and lower-risk lifestyles showed clear differences in their gut microbiome diversity and composition, higher-risk lifestyles being associated with potentially adverse microbial traits. These findings contribute to identifying microbial features that may characterize early stages of CRC development in individuals with high-risk lifestyles.}, } @article {pmid41811805, year = {2026}, author = {Vilkoite, I and Silamiķelis, I and Kloviņš, J and Tolmanis, I and Lejnieks, A and Runce, E and Cēbere, K and Margole, K and Sjomina, O and Silamiķele, L}, title = {Colorectal adenoma presence is associated with decreased menaquinone pathway functions in the gut microbiome of patients undergoing routine colonoscopy.}, journal = {PloS one}, volume = {21}, number = {3}, pages = {e0344050}, pmid = {41811805}, issn = {1932-6203}, mesh = {Humans ; *Adenoma/microbiology/metabolism ; *Colorectal Neoplasms/microbiology/metabolism/diagnosis ; Case-Control Studies ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Colonoscopy ; Male ; *Vitamin K 2/metabolism ; Cross-Sectional Studies ; Feces/microbiology ; Aged ; }, abstract = {BACKGROUND: Colorectal adenomas are key precancerous lesions and a major target for colorectal cancer prevention. While gut microbiome alterations are well described in colorectal cancer, microbial composition and functional capacity at the adenoma stage remain poorly understood. Emerging metagenomic data suggest early adenomas are associated with loss of microbial metabolic functions supporting epithelial and immune homeostasis.

OBJECTIVES: To investigate the association between gut microbiome composition and functional pathways and the presence of colorectal adenomas in patients undergoing routine colonoscopy.

MATERIALS AND METHODS: This cross-sectional case-control study included adult patients undergoing routine colonoscopy. Participants were enrolled based on strict inclusion and exclusion criteria to minimize confounding factors such as inflammatory bowel disease, prior colorectal surgery, and recent antibiotic or probiotic use. Fecal samples were collected prior to bowel preparation, and gut microbiome taxonomic composition and functional pathways were analyzed using shotgun metagenomic sequencing.

RESULTS: A total of 136 participants were included, of whom 56 had colorectal adenomas. Alpha diversity indices did not differ significantly between adenoma-positive and adenoma-negative groups. In contrast, beta diversity analysis revealed significant differences in overall microbial community structure. Descriptive genus-level differences suggested features of dysbiosis in adenoma-positive patients, including higher relative abundance of Bacteroides and Prevotella and lower abundance of Faecalibacterium and Anaerostipes. Differential abundance analysis identified a single species-level feature, UBA7597 sp003448195, enriched in the adenoma group. Functional profiling showed reduced microbial pathways related to menaquinone (vitamin K₂) biosynthesis, Stickland fermentation, and short-chain fatty acid (propionate) production in patients with adenomas.

CONCLUSIONS: The presence of colorectal adenomas was associated with reduced microbial metabolic functions linked to vitamin K₂ biosynthesis, amino acid fermentation, and propionate production, alongside compositional shifts toward a less functionally robust gut microbiome. These findings indicate that early colorectal neoplasia is accompanied by functional microbiome alterations that may serve as markers of adenoma-associated dysbiosis and provide insight into early metabolic changes in the colonic microenvironment.}, } @article {pmid41812751, year = {2026}, author = {Prabhakar, S and Rajeev, AC and Sankappa, NM and Harsha, R}, title = {High-throughput metagenomic profiling of functional and resistome features in estuarine microplastic microbiomes.}, journal = {Environmental research}, volume = {298}, number = {}, pages = {124159}, doi = {10.1016/j.envres.2026.124159}, pmid = {41812751}, issn = {1096-0953}, mesh = {*Estuaries ; *Microplastics/analysis ; *Microbiota ; India ; Metagenomics ; *Water Pollutants, Chemical/analysis/toxicity ; Environmental Monitoring ; High-Throughput Nucleotide Sequencing ; *Metagenome ; Bacteria/genetics ; }, abstract = {Microplastics (MPs) are now recognized as persistent pollutants in aquatic ecosystems, providing unique surfaces for microbial colonization and acting as vectors for the spread of pathogens, antibiotic resistance, and virulence factors. Estuarine systems, due to their dynamic hydrology and proximity to anthropogenic activity, are particularly vulnerable to MP accumulation and associated microbial risks. This study presents the first comprehensive metagenomic investigation of MP-associated microbial communities across five estuaries spanning the northern and southern coastal regions of Karnataka, India. MPs were isolated, characterized, and the extracted total DNA from the MPs was subjected to high-throughput sequencing and comprehensive bioinformatic analyses. Taxonomic, functional, and resistance gene profiling were performed to evaluate microbial diversity, ecological roles, and potential public health implications. The findings revealed distinct regional differences in microbial community structure and functional potential, with evidence of clinically relevant pathogens, antibiotic resistance genes, and virulence determinants within the plastisphere. These results highlight the role of MPs as reservoirs and vectors for microbial risks in estuarine ecosystems. By linking microbial diversity of MPs with environmental and anthropogenic influences, this work provides crucial baseline data for monitoring and managing estuarine health. It also underscores the urgent need for integrated strategies to mitigate plastic pollution and its cascading ecological and public health impacts.}, } @article {pmid41812803, year = {2026}, author = {Bao, Z and Ji, X and Liu, Q and Zhang, L}, title = {Light-driven N-doped carbon quantum dots facilitate microbial chain elongation: Bridging process enhancement to functional metagenomics.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134393}, doi = {10.1016/j.biortech.2026.134393}, pmid = {41812803}, issn = {1873-2976}, mesh = {*Carbon Quantum Dots ; *Light ; *Metagenomics/methods ; *Nitrogen/chemistry ; Fatty Acids/biosynthesis/metabolism ; *Carbon/chemistry ; Caproates/metabolism ; Bacillus/metabolism/genetics ; }, abstract = {Microbial chain elongation (CE) converts low-value substrates into medium-chain fatty acids (MCFAs), but its efficiency is often constrained by limited electron availability and incomplete elongation from C4 to C6 products. This study demonstrates that nitrogen-doped carbon quantum dots (NCQDs), under visible light irradiation, significantly improved CE performance and product selectivity. At 1.5 g/L NCQDs, caproate concentration increased to 3.76 g/L, representing a 276% improvement over the control, while butyrate accumulation decreased, indicating enhanced elongation toward longer-chain products. Electrochemical characterization showed that NCQDs exhibited visible light absorption, a 2.31 eV bandgap, measurable photocurrent responses, and reduced charge-transfer resistance, reflecting enhanced redox activity at the system level. Metagenomic analysis revealed increased relative abundance of Bacillus and enrichment of functional genes associated with reverse β-oxidation and fatty acid biosynthesis pathways. In addition, quorum sensing-related genes (LuxI, LuxR, RpfF) and Hnd hydrogenase-associated gene clusters were enriched, indicating enhanced functional potential for microbial coordination and redox-related metabolism. These coordinated shifts in electrochemical behavior, microbial community composition, and functional gene abundance were consistent with improved caproate production and metabolic selectivity. This work provides an effective hybrid photochemical-microbial strategy associated with enhanced MCFAs production and offers a promising approach for waste valorization into value-added biochemicals.}, } @article {pmid41812817, year = {2026}, author = {Freitas, JF and Oliveira, TT and Agnez-Lima, LF}, title = {Longitudinal wastewater metagenomics reveals distinct environmental and anthropogenic associations with resistance, virulence, and viral communities.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {397}, number = {}, pages = {127943}, doi = {10.1016/j.envpol.2026.127943}, pmid = {41812817}, issn = {1873-6424}, mesh = {*Wastewater/microbiology/virology ; *Metagenomics ; Virulence/genetics ; *Drug Resistance, Microbial/genetics ; Brazil ; Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; Viruses/genetics ; Metagenome ; Environmental Monitoring ; Virulence Factors/genetics ; Anthropogenic Effects ; Humans ; }, abstract = {Urban wastewater systems are reservoirs of antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs), increasingly recognized as emerging environmental pollutants. However, longitudinal evidence linking tourism-related human mobility to its dynamics remains limited in the Southern Hemisphere. We evaluated whether tourism seasonality, used as a proxy for transient population load, is associated with changes in the wastewater resistome, virulome, and virome in Natal (Northeast Brazil). Using year-long shotgun metagenomics (June 2021-May 2022) of 24 monthly pooled metagenomes (12 composites × 2 replicates) from three wastewater treatment plants, we observed differential enrichment patterns despite stable bacterial community composition dominated by Aliarcobacter. Redundancy analysis (RDA) demonstrated that the model for bacterial community explained 40.1% of the total variance (F = 1.79, p = 0.039), with tourism showing marginal effects. In contrast, precipitation was not significant (p = 0.262). RDA also revealed that precipitation was associated with ARG distribution (p = 0.027) and that VFG composition was associated with international tourism (p = 0.002). ARGs were more abundant during high-precipitation periods, whereas VFGs showed higher relative abundance during international tourism peaks. Metagenome-assembled genomes (n = 95) revealed 33 multidrug-resistant hosts, including understudied taxa such as Tolumonas and the family Aquaspirillaceae, harboring plasmids (e.g., IncFIB(K)). Co-occurrence networks showed that viruses were positively correlated with ARGs and negatively correlated with VFGs, except for crAssphage, which was associated with virulence traits. These findings reveal distinct environmental and human mobility factors underlying wastewater microbial dynamics. We underscore the importance of integrating longitudinal metagenomics into seasonally adjusted surveillance frameworks to mitigate antimicrobial resistance as an emerging form of environmental pollution.}, } @article {pmid41813810, year = {2026}, author = {Top, FK and Gaye, A and Boussiengui, GL and Sall, Y and Sall, NC and Camara, D and Ba, M and Ndiaye, NKD and Seye, AO and Ndiaye, NK and Diallo, B and Sagne, SN and Mbanne, M and Diagne, MM and Faye, O and Fall, G and Sow, B and Loucoubar, C and Ndiaye, EHM and Diop, B and Sall, AA and Dia, N and Faye, O and Sow, A and Faye, M}, title = {The 2024 Mpox surveillance in Senegal uncovers a large circulation of Chickenpox.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41813810}, issn = {2045-2322}, mesh = {Humans ; Senegal/epidemiology ; *Chickenpox/epidemiology/virology/diagnosis ; Male ; Female ; Adult ; Adolescent ; *Herpesvirus 3, Human/genetics/isolation & purification ; Child ; Young Adult ; Phylogeny ; Child, Preschool ; Middle Aged ; Prevalence ; Infant ; }, abstract = {During preparedness activities in Senegal to the 2024 Mpox Public Health Emergency of International Concern, a study was conducted to assess the prevalence of Varicella-Zoster virus among patients suspected of having Mpox. Samples, including skin swabs, serum, and nasopharyngeal swabs, were collected from 103 patients who presented with Mpox-like symptoms. Molecular testing via qPCR revealed that 30.1% of patients tested positive for herpesviruses, whereas no Mpox cases were detected. Common symptoms include fever, skin rash, headache, and myalgia, which closely resemble Mpox symptoms, increasing the risk of misdiagnosis. The most affected group was children under 15 years of age (50% of herpesvirus cases), followed by adults over 30 years of age (30.8%). The male/female sex ratio among herpesvirus-positive patients was 2.1, indicating a higher prevalence in males. Phylogenetic analysis of 14 newly characterized Varicella-Zoster virus genomes from metagenomic sequencing revealed that the strains circulating in Senegal were closely related to those from Guinea-Bissau, suggesting possible regional transmission. In addition, viral and bacterial coinfections were identified in Mpox-negative patients, which may have contributed to some skin lesions initially suspected to be Mpox. Our data highlight the importance of differential diagnostic testing to distinguish between Mpox and other infections, such as Chickenpox. The unexpectedly high prevalence of herpesviruses among suspected Mpox cases underscores the need for improved laboratory diagnostics, enhanced epidemiological surveillance, and targeted public health interventions to prevent misdiagnosis and improve patient management.}, } @article {pmid41813906, year = {2026}, author = {Vass, M and Abramova, A and Bengtsson-Palme, J}, title = {Antimicrobial resistance dissemination via horizontal gene transfer is constrained in stratified waters.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41813906}, issn = {2399-3642}, support = {KAW 2020.0239//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2024-05922//Vetenskapsrådet (Swedish Research Council)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Seawater/microbiology ; *Bacteria/genetics/drug effects ; *Fresh Water/microbiology ; *Drug Resistance, Microbial/genetics ; *Water Microbiology ; Ecosystem ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Metagenomics ; }, abstract = {Aquatic ecosystems are major reservoirs of antibiotic resistance genes (ARGs) and hubs for microbial interactions that can facilitate their spread through horizontal gene transfer (HGT). While mobile genetic elements (MGEs), including plasmids and viruses, are recognized as important drivers of ARG mobility, the extent to which water column stratification constrains their vertical dissemination remains unresolved. Here, we analysed depth-resolved metagenomic data from stratified freshwater and marine systems to assess the role of HGT in ARG spread. We found that ARG diversity is consistently lower in marine than freshwater environments and that only a small fraction of ARGs is mobilized by plasmids and viruses. Importantly, we detected no evidence for recent HGT-mediated dissemination of ARGs across depth layers, despite genetic compatibility among co-occurring bacteria. Instead, ARGs appear largely confined to lineage-specific inheritance and within-layer persistence. These findings suggest that stratification acts as a barrier, limiting vertical ARG transfer while promoting within-layer accumulation. Given projections of intensified and prolonged stratification under climate change, our results imply reduced vertical connectivity of ARGs in aquatic environments, with potential consequences of further mitigation in its dynamics by water stratification.}, } @article {pmid41813975, year = {2026}, author = {Telles-de-Deus, J and Claro, IM and Bertanhe, M and Whittaker, C and Port-Carvalho, M and Rocha, EC and Coletti, TM and da Silva, CAM and Valença, IN and Lima-Camara, TN and Bicudo de Paula, M and Cunha, MS and de Jesus, JG and Dos Santos Andrade, P and Cox, V and de Azevedo, NCCF and Guerra, JM and Summa, JL and Teixeira, APP and Bergo, ES and Pereira, M and Moreira, FRR and Felix, AC and de Paula, AV and de Araujo Eliodoro, RH and da Silva Lima, M and de Oliveira, FM and de Souza, VR and Franco, LAM and Nardi, MS and Sanches, TC and da Silva, ETBC and Coimbra, AAC and Dos Santos, PR and Lima de Gouveia, K and Vilela, FESP and Hill, SC and Oliveira, DAG and Piedade, HM and Guimarães-Luiz, T and Abreu, CMG and Casoni da Rocha, G and Abade, L and de Souza, WM and Lambert, B and Pereira de Souza, R and Pinter, A and Sabino, EC and Mucci, LF and Faria, NR}, title = {Evolution and spillover dynamics of yellow fever at the forest-urban interface in Brazil.}, journal = {Nature microbiology}, volume = {11}, number = {4}, pages = {877-891}, pmid = {41813975}, issn = {2058-5276}, support = {R25 AI147376/AI/NIAID NIH HHS/United States ; MR/X020258/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; 316633/Z/24/Z//Wellcome Trust (Wellcome)/ ; 226075/Z/22/Z//Wellcome Trust (Wellcome)/ ; }, mesh = {Animals ; *Yellow Fever/epidemiology/transmission/virology/veterinary ; Brazil/epidemiology ; *Yellow fever virus/genetics/classification/isolation & purification ; Forests ; Phylogeny ; Humans ; Disease Outbreaks ; Mosquito Vectors/virology ; Culicidae/virology ; Genome, Viral ; }, abstract = {Yellow fever virus (YFV) continues to threaten human and wildlife populations in the Americas, yet its transmission at the forest-urban interface remains unclear. Here we integrate ground- and canopy-level mosquito surveillance, systematic monitoring of non-human primate carcasses and viral metagenomics to describe the dynamics of a sylvatic YFV outbreak in a 186-hectare Atlantic Forest fragment embedded within metropolitan São Paulo, Brazil, between 2017 and 2018. Our analyses reveal that transmission was primarily driven by a single genetic cluster introduced during a period of high abundance of the main vector, Haemagogus leucocelaenus mosquitoes. A near-complete hepatitis A virus genome was detected in a YFV-infected howler monkey, suggesting potential co-infections at the human-wildlife interface. Phylogenetic and epidemiological modelling estimated a basic reproduction number, R0, for sylvatic yellow fever of 8.2 (95% CI 5.1-12.2), substantially higher than previous estimates for urban outbreaks. Our findings demonstrate that multisource surveillance could provide actionable early warnings in regions at risk for zoonotic spillover.}, } @article {pmid41814006, year = {2026}, author = {Baldanzi, G and Larsson, A and Sayols-Baixeras, S and Dekkers, KF and Hammar, U and Nguyen, D and Graells, T and Ahmad, S and Gazolla Volpiano, C and Meric, G and Järhult, JD and Tängdén, T and Ludvigsson, JF and Lind, L and Sundström, J and Michaëlsson, K and Ärnlöv, J and Kennedy, B and Orho-Melander, M and Fall, T}, title = {Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals.}, journal = {Nature medicine}, volume = {32}, number = {4}, pages = {1351-1361}, pmid = {41814006}, issn = {1546-170X}, support = {20230687//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2018-0343//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2023-0380//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2019-01471//Vetenskapsrådet (Swedish Research Council)/ ; 2025-02673//Vetenskapsrådet (Swedish Research Council)/ ; 2022-01460//Vetenskapsrådet (Swedish Research Council)/ ; 2020-00243//Vetenskapsrådet (Swedish Research Council)/ ; 2018-02784//Vetenskapsrådet (Swedish Research Council)/ ; Strategic Research Area Exodiab 2009-1039//Vetenskapsrådet (Swedish Research Council)/ ; 2020-00989//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; IRC-0067//Stiftelsen för Strategisk Forskning (Swedish Foundation for Strategic Research)/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/adverse effects ; *Gastrointestinal Microbiome/drug effects/genetics ; Feces/microbiology ; Female ; Clindamycin/adverse effects ; Sweden ; Metagenome/drug effects ; Male ; Penicillin V/adverse effects ; Fluoroquinolones/adverse effects ; Adult ; Floxacillin/adverse effects ; Nitrofurantoin/adverse effects ; Middle Aged ; }, abstract = {Disruptions in gut microbiome are implicated in cardiometabolic disorders and other health outcomes. Antibiotics are known gut microbiome disruptors, but their long-term consequences remain underexplored. Here we combined individual-level data from the Swedish Prescribed Drug Register with fecal metagenomes of 14,979 adults to examine the association between oral antibiotic use over 8 years and gut microbiome. In multivariable confounder-adjusted regression models, antibiotic use <1 year before fecal sampling was associated with the greatest reduction in species diversity, but significant associations were also observed for use 1-4 and 4-8 years earlier. Clindamycin, fluoroquinolones and flucloxacillin accounted for most of the associations with the abundance of individual species. Use of these antibiotics 4-8 years earlier was associated with altered abundance of 10-15% of the species studied; penicillin V, extended-spectrum penicillins and nitrofurantoin were associated with only a few species. Similar results were found comparing one antibiotic course 4-8 years before sampling versus none in the past 8 years. These findings indicate that antibiotics may have long-lasting consequences for the gut microbiome.}, } @article {pmid41814161, year = {2026}, author = {Platova, SE and Poliushkevich, LO and Starunova, ZI and Starunov, VV and Novikova, EL}, title = {Transcriptomic analysis of three annelid species: looking for markers of positional information.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41814161}, issn = {1471-2164}, support = {21-14-00304//Russian Science Foundation/ ; }, abstract = {BACKGROUND: Positional information, classically defined through morphogen gradients, underlies the establishment and maintenance of spatial coordinates in developing organisms and remains essential throughout post-embryonic growth and regeneration. Many conserved developmental regulators, including components of the Wnt, FGF, retinoid, caudal, Hox, and ParaHox pathways, continue to function after embryogenesis, supporting posterior growth, segmentation, stem cell activity, and regenerative responses. Studies across metazoans demonstrate that gradients of these factors are maintained in adult tissues and are reorganized after injury, thereby guiding correct pattern restoration. Annelids provide a powerful model for investigating post-embryonic patterning and the maintenance of positional information. They grow by adding segments from a posterior growth zone, exhibit dynamic shifts in segment position throughout life, and show diverse regenerative capacities, offering an opportunity to identify molecular correlates of these differences.

RESULTS: We generated spatially resolved transcriptomes for three annelid species with distinct regenerative potentials – Pygospio elegans, Platynereis dumerilii, and Arenicola marina. By analyzing differential gene expression across body fragments, we reconstructed expression patterns along the anterior-posterior axis and examined genes involved in organogenesis, growth zone function, and potential positional information.

CONCLUSION: This comparative transcriptomic study shows that spatial gene expression in three annelid species broadly corresponds to major anatomical territories but also reflects deeper developmental origins. The clear transcriptional differences between larval and postlarval segments in P. elegans and P. dumerilii suggest that segment ontogeny, not anatomy alone, contributes to regional molecular identity. The posterior growth zones of these two species exhibit strong activation of Wnt, cad, Hox, and GMP genes, consistent with an active stem-cell–based growth program. In contrast, the posterior region of A. marina lacks these signatures, supporting previous evidence for an inactive growth zone and the absence of posterior regeneration. Gradient-like expression of Hox, ParaHox, and Wnt genes in P. elegans and P. dumerilii indicates that these factors may encode positional information along the body axis and facilitate regeneration. Their truncated expression in A. marina likely reflects functional specialization of the adult body. Overall, our findings highlight conserved molecular systems involved in posterior growth and positional identity, while revealing species-specific modifications associated with reduced regenerative capacity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12671-5.}, } @article {pmid41814236, year = {2026}, author = {Xiao, H and Zhang, Y and Zhu, L and Guo, M and Yao, K and Dong, F and Duan, X and Liu, G}, title = {Meningitis and subdural empyema caused by group A streptococcal infection.}, journal = {BMC pediatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41814236}, issn = {1471-2431}, support = {2024-1-2092//Capital's Funds for Health Improvement and Research/ ; 2-1-2-6-15//2022 Beijing Major Epidemic Prevention and Control Specially Construction Project/ ; }, abstract = {BACKGROUND: Group A streptococcus (GAS) could lead to various disease types in children, but central nervous system (CNS) infections are uncommon. In this paper, we analyzed the clinical features of a GAS case with meningitis and subdural empyema, and characterized the GAS clone.

CASE PRESENTATION: A thirteen-year-old boy complained of fever, headache, and left hemiplegia. Physical examination also showed central facial palsy of left side. The examinations of blood and cloudy cerebrospinal fluid (CSF) showed bacterial meningitis. Blood cultures and metagenomic sequencing (mNGS) of CSF showed GAS, and GAS antigen of throat swab was positive. The first anti-streptolysin (ASO) was negative, but increased obviously after 2 weeks. The examination of emm type showed emm 12.0 isolate. The head MRI showed restricted diffusion in the right frontal lobe, subdural empyema in the right side of cerebral falx, and meningitis. The CT revealed rhinosinusitis and mastoiditis. Bacterial meningitis, subdural empyema, sepsis, and sinusitis were diagnosed, and vancomycin and ceftriaxone were given. The patient also received dexamethasone in the beginning. Gradual improvement was seen in the patient’s clinical status, laboratory parameters (blood/CSF), and radiographic manifestations.

CONCLUSIONS: The contiguous spread from rhinosinusitis could lead to meningitis and intracranial abscess in adolescent. GAS infection could be the pathogen for subdural empyema in patients with an abrupt onset of symptoms and rapidly deteriorating clinical course.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12887-026-06722-9.}, } @article {pmid41814258, year = {2026}, author = {Zhou, Y and Yu, D and Li, S and Ruan, S and Ye, J and Zhou, D and Chen, Q and Jin, J and Song, K}, title = {Case Report: diagnosis of mixed Scedosporium apiospermum infection assisted by bronchoalveolar lavage fluid morphology.}, journal = {BMC pulmonary medicine}, volume = {26}, number = {1}, pages = {}, pmid = {41814258}, issn = {1471-2466}, support = {2025HZZD01//The Construction Fund of Key Medical Disciplines of Hangzhou, Laboratory Diagnostics/ ; 2025JK256//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; }, abstract = {BACKGROUND: Scedosporium apiospermum is a highly aggressive opportunistic pathogen, widely distributed in natural environments. Infections predominantly occur in immunocompromised individuals but may also affect immunocompetent individuals with predisposing factors such as trauma, drowning, exposure to contaminated water, diabetes, or malnutrition. CASE PRESENTATION: In the reported case, morphological abnormalities were initially identified in bronchoalveolar lavage fluid (BALF). Subsequent microbial culture identification and metagenomic next-generation sequencing (mNGS) confirmed a mixed infection involving S. apiospermum. CONCLUSIONS: This case highlights the importance of improving laboratory personnel’s morphological recognition of S. apiospermum in routine examinations. The combined use of multiple diagnostic methods enhances detection rates, shortens the time to identification, ensures timely and effective treatment for patients, and ultimately reduces mortality.}, } @article {pmid41814359, year = {2026}, author = {Lai, C and Zhang, J and Xiong, Y and Wang, Y and Liu, Z and Shi, M and Ye, S and Zeng, J}, title = {Multi-omics analysis reveals the association of cesarean delivery with altered gut microbial profiles and a Th2-biased immune response in neonates.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41814359}, issn = {1479-5876}, support = {Z-A20241044//Guangxi Zhuang Autonomous Region Health Department/ ; Z20210019//Guangxi Zhuang Autonomous Region Health Department/ ; Z-A20240946//Guangxi Zhuang Autonomous Region Health Department/ ; 2024GXNSFBA010112//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; }, abstract = {BACKGROUND: The gut microbiota plays a crucial role in providing essential stimulatory signals for the development of the immune system during the early stages of life. Cesarean delivery is associated with altered vertical microbial transmission and may affect early immune priming. Currently, only a limited number of studies have investigated the interactions among gut microbiota, fecal metabolites, and immune function in neonates delivered by cesarean section, which underscores the necessity for further research.

METHODS: We performed metagenomic sequencing and untargeted metabolomics to compare the gut microbiota and fecal metabolites of neonates born through cesarean delivery (n = 18) and vaginal delivery (n = 20). RNA sequencing (RNA-Seq) was utilized to identify differentially expressed genes (DEGs) in peripheral blood mononuclear cells (PBMCs). Immune profiling involved flow cytometry analysis to determine the proportions of Th1 and Th2 cells, ELISA-based quantification of plasma IFN-γ, IL-12p70, IL-4, and IL-10, and assessment of STAT4 and STAT6 expression via ELISA and Western blot. Multi-omics integration was applied to elucidate the systemic impact of cesarean delivery on the neonatal gut microbiome, metabolome, and immune system.

RESULTS: The composition and functional features of the gut microbiota, and fecal metabolite profile, were significantly altered in Cesarean group. PBMC gene expression also showed marked differences, presenting a Th2-biased immune response and enrichment of genes associated with systemic lupus erythematosus and primary immunodeficiency. Flow cytometry and ELISA confirmed a Th1/Th2 imbalance, while Western blot revealed decreased STAT4 and increased STAT6 expression in the Cesarean group. Multi-omics analysis indicates that Bacteroides sp. is associated with alterations in fecal metabolite in neonates delivered via cesarean section. The reduced abundance of Bacteroides sp. and Bacteroides fragilis correlated with Th1/Th2 dysregulation. Additionally, gut microbiota changes were correlated with variations in the host oxidative phosphorylation pathway via fecal phosphate levels.

CONCLUSIONS: This multi-omics study reveals an association between the mode of delivery and distinct gut microbiota structure, fecal metabolite profiles, and immune development during early life. This provides a framework for investigating the potential connection between early-life immune programming and mode of delivery.

CLINICAL TRIAL NUMBER: Not applicable.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07988-4.}, } @article {pmid41814421, year = {2026}, author = {Lee, CZ and Worsley, SF and Davies, CS and Komdeur, J and Hildebrand, F and Dugdale, HL and Richardson, DS}, title = {Host immunogenetic variation and gut microbiome functionality in a wild vertebrate population.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41814421}, issn = {2049-2618}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics/immunology ; Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Animals, Wild/microbiology/immunology ; }, abstract = {BACKGROUND: The gut microbiome (GM) -important for host health and survival- is partially shaped by host immunogenetics. However, to date, no study has investigated the influence of host Major Histocompatibility Complex (MHC) genes on gut microbiome functionality in a wild population. Here we use a natural population of the Seychelles warbler (Acrocephalus sechellensis) to assess the effects of MHC genes on GM taxonomy and functionality using shotgun metagenomics.

RESULTS: Our results show that taxonomic GM composition was associated with MHC-II diversity and the presence of one specific MHC-I allele (Ase-ua 7). Specifically, MHC-II diversity was associated with decreased Lactococcus lactis and increased Staphylococcus lloydii abundance, while Ase-ua 7 was linked to reduced Enterococcus casselifavus and Gordonia sp OPL2 but increased Escherichia coli and Vulcaniibacterium thermophilum. These taxonomic changes may reflect differences in MHC-mediated microbial recognition. In contrast, functional GM composition was significantly associated with increasing individual MHC-I diversity but not MHC-II diversity. In particular, increasing MHC-I diversity was associated with an increased prevalence of microbial defence genes but a reduced prevalence of microbial metabolism genes. Analysis also revealed that functional GM networks were more fragmented in high compared to low MHC-I diversity hosts.

CONCLUSION: These results suggest that MHC variation (particularly at MHC-I) plays an important role in shaping both the taxonomy and function of the GM in wild vertebrates. In the Seychelles warbler, this results in trade-offs whereby there is an increase in microbial defence and a reduction in GM metabolic potential in individuals with higher MHC-I diversity. Thus, this work sheds light on the possible costs and benefits of maintaining a healthy microbiome, which is essential for understanding how the GM and immune system co-evolve. Video Abstract.}, } @article {pmid41814441, year = {2026}, author = {Stead, CE and Walker, L and Greco, C and Galloway, T and R Cousins, C and Nagel, F and Breitling, R and Takano, E and Björnsdóttir, SH and Nixon, SL}, title = {Exploring the biotechnological potential of terrestrial hot spring microbiomes for CO2 utilisation.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41814441}, issn = {2524-6372}, support = {ST/W002337/1//UK Space Agency/ ; RGS\R2\222350//Royal Society/ ; BB/V00560X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Terrestrial hot springs are extreme environments shaped by geothermal heat, geogenic gases and extremes of pH and temperatures. Their gas fluxes, which include CO2, CO, H2S and SO2, mirror the chemical composition of CO2-rich waste streams. Microbial communities inhabiting these environments are typically thermotolerant or thermophilic and sustained by CO2 fixation and chemolithotrophic metabolism. Such communities may therefore provide a natural starting point for developing ex-situ, consortium-based biotechnologies capable of operating under elevated temperatures and chemically harsh conditions. Here, we assess the metabolic capabilities of hot spring microbiomes systematically through a biotechnological lens.

RESULTS: We conducted comparative analysis of 73 worldwide hot spring metagenomes, spanning a wide range of environmental conditions (pH 1.5-10.0, temperatures 25-98 °C). By taking a gene-centric approach to whole communities, we show that hot spring microbiomes ubiquitously encoded carbon fixation pathways and biosynthetic genes (and gene clusters) for the synthesis of value-added products, regardless of geographical location and pH-temperature conditions. Candidate value-added products include platform chemicals such as acetone, lactic acid, and 1,2-propanediol, as well as high-value biomolecules including B vitamins and alginate.

CONCLUSIONS: This first biotechnology-focused assessment of hot spring microbiomes demonstrates that these communities encode the genomic potential to support novel, ex situ microbial platforms for upgrading CO2 and transforming chemically complex gas mixtures.

SIGNIFICANCE: Industrial CO2 waste streams pose both an environmental challenge and an unutilised resource. Harnessing microbial consortia to valorise CO2, through a circular bioeconomy, remains underexplored and could offer an alternative to energy-intensive chemical methods. By reanalysing predominantly publicly available metagenomic data, we demonstrate how hot spring microbiomes can be mined for traits pre-adapted to CO2-rich, high-temperature, and chemically extreme conditions. In doing so, we provide proof-of-concept for their future biotechnological application and establish a blueprint for other microbiome-scale bioprospecting surveys.}, } @article {pmid41814651, year = {2026}, author = {Tao, D and Xu, B and Li, S and Liu, H and Wei, Y and Cao, X and Shi, S and Wang, Y and Jiang, R and Zhang, Y and Zhao, C and Ruan, J and Fu, L and Huang, X and Li, X and Zhao, S and Xie, S}, title = {Structural mining and engineering of metagenome-derived Cas12a orthologs expands the CRISPR genome editing and multiplex diagnostics toolkit.}, journal = {Molecular therapy : the journal of the American Society of Gene Therapy}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ymthe.2026.03.011}, pmid = {41814651}, issn = {1525-0024}, abstract = {CRISPR-Cas12a is a compact, RNA-guided nuclease widely deployed in genome editing and molecular diagnostics, yet its broader utility is limited by suboptimal cis-cleavage efficiency and incompletely defined trans-cleavage behavior. To overcome these constraints, we developed an artificial intelligence-guided structural discovery pipeline powered by AlphaFold2, which identified 1,261 previously uncharacterized Cas12a orthologs. From this set, 21 structurally conserved but sequence-divergent candidates were selected for biochemical characterization. Using structure-informed engineering, we generated PcuCas12a MAX, a high-fidelity variant that achieves genome-editing efficiencies in human cells comparable to the benchmark AsCas12a Ultra while retaining robust activity in murine and porcine systems. In addition, four orthologs (LcoCas12a, FcaCas12a, EsoCas12a, and Mac2Cas12a), when paired with specifically engineered CRISPR RNAs, exhibited distinct single-stranded DNA trans-cleavage signatures. These properties enabled construction of a multiplex CRISPR sensor capable of simultaneously detecting multiple nucleic acid targets. Together, these findings expand the Cas12a endonuclease repertoire and enhance its utility in genome engineering and next-generation diagnostics.}, } @article {pmid41814700, year = {2025}, author = {Wu, D and Niu, JJ and Hu, JP and Wang, H and Kuang, HX}, title = {[Mechanism study on anti-hyperuricemic effects of Zhejiang Plantaginis Semen glycosides based on metabolomics and metagenomics].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {50}, number = {24}, pages = {6919-6927}, doi = {10.19540/j.cnki.cjcmm.20250725.705}, pmid = {41814700}, issn = {1001-5302}, mesh = {Animals ; Rats ; Male ; Metabolomics ; Rats, Sprague-Dawley ; *Hyperuricemia/drug therapy/metabolism/microbiology/genetics ; Metagenomics ; *Glycosides/administration & dosage ; *Drugs, Chinese Herbal/administration & dosage ; Uric Acid/metabolism/blood ; Liver/metabolism/drug effects ; Humans ; Kidney/drug effects/metabolism ; Bacteria/isolation & purification/genetics/classification ; }, abstract = {A rat model of hyperuricemia was established using potassium oxonate, hypoxanthine, and adenine. The anti-hyperuricemic mechanisms of Zhejiang Plantaginis Semen glycosides(ZPG) were subsequently explored utilizing metabolomics and metagenomics approaches. Forty SD rats were randomly divided into five groups: control, model, benzbromarone(20 mg·kg~(-1)), low-dose ZPG(100 mg·kg~(-1)), and high-dose ZPG(400 mg·kg~(-1)), with 8 rats in each group. Hyperuricemia was induced by continuous intragastric administration of potassium oxonate(200 mg·kg~(-1)), hypoxanthine(500 mg·kg~(-1)), and adenine(50 mg·kg~(-1)) for 21 days, while drug treatment was administered simultaneously. Serum and liver tissues were collected to measure the levels of uric acid(UA), creatinine(Cr), blood urea nitrogen(BUN), and xanthine oxidase(XOD). Renal tissues were subjected to histopathological examination. Additionally, untargeted metabolomics analysis was performed on serum samples, and fecal metagenomics sequencing was conducted to analyze the composition of the gut microbiota. The results showed that ZPG effectively reduced the levels of serum UA, Cr, and BUN in hyperuricemic rats, inhibited XOD activity in both serum and liver, alleviated renal pathological damage, and mitigated inflammatory responses. Metabolomics analysis identified 16 differential metabolites, mainly involved in lipid metabolism, purine metabolism, and amino acid metabolism pathways. The results of fecal metagenomics analysis revealed that ZPG restored the Firmicutes-to-Bacteroidetes ratio and increased the relative abundance of probiotics such as Lactobacillus＿johnsonii, Limosilactobacillus＿reuteri, and Ligilactobacillus＿murinus. In summary, ZPG effectively reduces serum UA levels, improves renal injury, and attenuates inflammatory symptoms in hyperuricemic rats. These effects may be attributed to its inhibition of XOD activity, correction of inflammatory lipid metabolism abnormalities, regulation of disordered purine metabolism, and modulation of gut microbiota structure.}, } @article {pmid41815497, year = {2026}, author = {Pan, J and Jiang, H and Luo, S and Zhang, L and Wu, G and Li, W and Cai, S and Mei, Y and Chen, X and Chen, B and Zhang, W and Tong, P and Xie, J}, title = {Identification of a novel Ungulate copiparvovirus 10 in sheep of Hami, East Xinjiang, China.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1678726}, pmid = {41815497}, issn = {2297-1769}, abstract = {Parvovirinae viruses are a subfamily of the Parvoviridae family that can infect various vertebrate hosts and cause infections ranging from asymptomatic to severe disease. This study performed a metagenomic assessment of the sheep sera virome to evaluate emerging and exotic viruses in border zones, and identified a novel copiparvovirus. The DNA of Ovine copiparvovirus (OVPV) was only observed in the serum of sheep in Dahe Town of Hami City. Furthermore, the region-dependent prevalence was 10.4% (96/807) from 2022 to 2024. The OVPV genome was 5,219 nucleotides (nt) long and shared 99.3% nt identity with two bovine parvovirus 2 SXO335parvoV2 and SXO338parvoV (GenBank accession numbers: MZ244302 and MZ244302), reported in the ticks collected from China. Comparison of NS1 protein showed that two OVPVs obtained in this study had 99.8%-99.9% amino acid homology with the tick-derived bovine parvoviruses, which had not been classified within the genus Copiparvovirus and then provisionally designated "Ungulate copiparvovirus 10," because they are far distant from other 10 species in Copiparvovirus genus with 48.5%-72.8% homology identified. Phylogenetic analysis further confirmed the classification of the OVPVs as a new species in the genus Copiparvovirus.}, } @article {pmid41816570, year = {2026}, author = {Zou, T and Zheng, J and Xie, Z and Hu, Y and Yang, X and Xue, X and Lu, L and Chen, X and Mao, S and Niu, M}, title = {Colon cancer cachexia remodels gut microbiota and metabolite profiles in a murine model.}, journal = {Journal of gastrointestinal oncology}, volume = {17}, number = {1}, pages = {13}, pmid = {41816570}, issn = {2078-6891}, abstract = {BACKGROUND: Cancer cachexia is a multifactorial syndrome involving involuntary weight loss, muscle atrophy, and systemic inflammation, contributing significantly to mortality in advanced cancers. Although gut microbiota dysbiosis has been implicated in metabolic and inflammatory disturbances relevant to cachexia, the functional metabolic consequences remain poorly understood. Using a murine model of colon carcinoma 26 (C26)-induced cachexia, we integrated metagenomic sequencing and non-targeted metabolomics to delineate cachexia-specific microbial and metabolic alterations compared to non-cachexia tumor-bearing and healthy controls.

METHODS: To investigate colon cancer cachexia-induced remodeling of the gut ecosystem, we established mouse models using cachexia-inducing and non-cachexia-inducing colon carcinoma 26 cells. Food intake, body weight, muscle and fat weight were monitored. Cecal content was collected for metagenomic sequencing and non-targeted metabolome analysis.

RESULTS: Colon cancer cachexia models were successfully established as evidenced by reduced food intake, decreased body weight, and loss of muscle and fat mass. Metagenomic sequencing revealed decreased microbial diversity and distinct structural separation in colon cancer cachexia mice, with enriched genera including Bacteroides, Phocaeicola, Escherichia, Enterobacter, Helicobacter, and Proteus, and depletion of butyrate- and bile acid-producing taxa including Alistipes, Eubacterium, Roseburia, Clostridium, and Hungatella. Functional analysis indicated significant alterations in metabolic pathways. Metabolomic profiling identified reduced levels of ursodeoxycholic acid (UDCA), hyodeoxycholic acid (HDCA), branched-chain amino acids, and bacterial amino acid metabolites (bAAms), alongside enrichment in nucleotide and steroid hormone metabolism. Correlation analyses demonstrated significant associations between specific microbial genera and altered metabolites.

CONCLUSIONS: Colon cancer cachexia remodeled the gut microbiota and metabolite landscape in a murine model. These findings suggested specific bacterial taxa and metabolites as potential biomarkers and therapeutic targets, offering new directions for the prevention and treatment of cancer cachexia. This study reveals distinct taxonomic and functional shifts in the gut microbiota alongside associated metabolic disruptions, offering new insights into cachexia pathophysiology and potential therapeutic targets.}, } @article {pmid41816693, year = {2026}, author = {Xiao, X and Niu, Q and Zhou, K and Ma, L and Zhao, Z and Zhang, J and Chu, X and Shan, G}, title = {The invasion of Euphorbia jolkinii is mediated through the regulation of nitrogen transformation by functional microbial abundance in rhizosphere soils.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1757844}, pmid = {41816693}, issn = {1664-302X}, abstract = {INTRODUCTION: Euphorbia jolkinii Boiss. is a native invasive weed. Its invasion altered microbial composition, total nitrogen (TN) and available nitrogen (AN). However, the mechanisms influencing N transformation remain unclear. Particularly, the roles of the microbiome and genes in mediating N transformations to facilitate E. jolkinii invasion remain poorly understood. Therefore, the primary objectives of this study were to evaluate how E. jolkinii invasion affects N transformation, microbial interactions, and key genes associated with AN accumulation.

METHODS: We compared three patches (non-invaded, lightly, and heavily invaded patches of E. jolkinii) by analyzing rhizosphere soils of E. jolkinii and Poa crymophila Keng. Integrating soil physicochemical indices with metagenomic sequencing, we investigated the relationships among microbial communities, gene abundance, and N transformation.

RESULTS: With E. jolkinii increasing invasion intensity, N accumulation and transformation rates were significantly reduced in the rhizosphere of P. crymophila but enhanced in that of E. jolkinii, particularly for AN. Metagenomic analysis revealed that the invasion and expansion of E. jolkinii promoted functional adaptation of the microbial community, particularly by enriching the N cycling-related genes and increasing their relative abundance in the rhizosphere soil of E. jolkinii. Moreover, it inhibited the accumulation of N transformation functional genes in the rhizosphere soil of the companion plant, P. crymophila. Structural equation modeling identified Nitrospirota, Edaphobacter, Anaeromyxobacter, and soil N transformation rates as key drivers of AN accumulation.

DISCUSSION: E. jolkinii facilitated N accumulation in its rhizosphere by modulating N-transforming microbes and key functional genes, underscoring one of its invasive advantages.}, } @article {pmid41816706, year = {2026}, author = {Tu, Y and Chen, Z and Jing, M and Tan, W and Huang, D and Xu, J and Wang, M and Li, H and Yang, Y and Liu, X and Hu, X and Pan, Y and Niu, C and Huang, Z}, title = {Supragingival Actinomyces naeslundii aggravates metabolic dysfunction-associated fatty liver disease via the oral-gut axis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2639208}, pmid = {41816706}, issn = {2000-2297}, abstract = {BACKGROUND: Metabolic dysfunction-associated fatty liver disease (MAFLD) is the most prevalent chronic liver disease but lacks effective therapies. Oral microbial dysbiosis is closely associated with metabolic dysfunction.

OBJECTIVE: This study aimed to delineate MAFLD-specific oral microbiota signatures and identify diagnostic biomarkers.

DESIGN: Supragingival plaque samples from 21 patients with MAFLD and 20 healthy individuals were subjected to metagenomic sequencing. Potential oral biomarkers were identified bioinformatically and further validated using a MAFLD mouse model.

RESULTS: Patients with MAFLD exhibited significantly reduced supragingival microbial diversity, altered composition, and enhanced consortial interactions compared to healthy individuals. Seven resident oral species were identified as candidate biomarkers. Among these, Actinomyces naeslundii was notably enriched in the oral cavity of patients with MAFLD and strongly correlated with clinical indices. In vivo experiments further demonstrated that the oral administration of A. naeslundii significantly aggravated MAFLD phenotypes and induced gut dysbiosis in mice fed a high-fat diet.

CONCLUSION: This study reveals a potential link between the oral microbiota and MAFLD. Specifically, the excessive enrichment of the oral resident bacterium A. naeslundii is associated with the MAFLD progression in mice.}, } @article {pmid41816992, year = {2026}, author = {Rao, B and Jiang, J and Zhang, R and Zhang, D and Zhang, C and Li, A and Lu, H and Zhang, H and Zhou, L and Guo, W and Wen, P and Xue, J and Pan, J and Aji, T and Lan, Z and Jiang, X and Zheng, S and Yu, Z and Ren, Z}, title = {Multicohort Validation of Gut Microbiome Signatures for Cholangiocarcinoma Diagnosis and Functional Characterization of Bifidobacterium Pseudocatenulatum.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {27}, pages = {e17658}, pmid = {41816992}, issn = {2198-3844}, support = {82470654//National Natural Science Foundation of China/ ; 232300421124//Natural Science Foundation Key Project of Henan Province/ ; 24HASTIT063//University Science and Technology Innovation Talent Support Plan of Henan Province/ ; ZYYC202301ZD//Henan Zhongyuan Medical Science and Technology Innovation and Development Foundation/ ; 2022D01C219//Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; JNL-2025007B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; }, mesh = {Humans ; *Cholangiocarcinoma/diagnosis/microbiology ; *Bile Duct Neoplasms/diagnosis/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; *Bifidobacterium ; Feces/microbiology ; Male ; Dysbiosis/microbiology ; Female ; Metagenomics ; China ; Middle Aged ; }, abstract = {Growing evidence suggests a role for the gut microbiome in progression of cholangiocarcinoma (CCA), however, its diagnostic and therapeutic potential remains incompletely characterized. Here, metagenomic sequencing was performed on fecal samples (n = 785) from individuals across East, Central, and Northwestern China. Gut microbial dysbiosis in CCA was characterized by depletion of short-chain fatty acids-producing species and enrichment of potential pathobionts (Klebsiella aerogenes, Clostridium symbiosum). Diagnostic models built using species-level markers demonstrated superior performance, compared to pathway-based models, achieving area under the curve (AUC) values of 98.63% and 99.42% in the discovery cohort, with robust cross-regional validation (AUC = 80.89% and 80.43%). The model effectively distinguished CCA from hepatocellular carcinoma (AUC = 97.86%) and liver fibrosis (AUC = 98.73%) and nonalcoholic fatty liver disease (mean AUC = 96.86%). Analysis of public datasets encompassing 6847 samples across 31 studies and 11 disease states revealed moderate disease specificity influenced by biomarker overlap across conditions. Mechanistically, depleted Bifidobacterium pseudocatenulatum suppressed CCA progression, associated with inhibition of the PI3K-AKT-mTOR pathway. Collectively, this study supports the potential of fecal metagenomic signatures as a complementary noninvasive aid for CCA detection, and provides functional evidence for a candidate protective microbe.}, } @article {pmid41816995, year = {2026}, author = {Zhao, F and Zhang, R and Wei, R and Fan, H and Hu, Y and Shi, W and Wang, J}, title = {Alternating High-Fat and Polysaccharide Diets Modulates Gut Phage-Bacterial Interplay.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {29}, pages = {e16916}, pmid = {41816995}, issn = {2198-3844}, support = {2022YFA1304102//National Key Research and Development Program of China/ ; T2341010//National Natural Science Foundation of China/ ; 32370053//National Natural Science Foundation of China/ ; //2115 Talent Development Program of China Agricultural University/ ; }, mesh = {Animals ; *Polysaccharides/pharmacology/metabolism ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome/drug effects/physiology ; *Bacteriophages/physiology/genetics ; Mice ; *Bacteria/virology ; Humans ; Metagenome ; Virome ; }, abstract = {Phages dominate the human gut virome and are known for their ability to prey on bacteria and shape microbiota. However, their response to diet has only been elucidated using small-scale studies. By integrating a massive meta-analysis of 6932 diet-associated metagenomes with a time-resolved mouse model of a high-fat diet and polysaccharide intake, the impact of diet on the gut virome and phage-bacterial interactions was systematically characterized. Diet types, particularly high-fat and polysaccharide-rich diets, exert the strongest shaping force on the gut virome, enhancing the crosstalk between phages and bacteria. High-fat diets promote changes in phage abundance across a broad taxonomic range, from 34.21% to 50.00%, drive phages of diet-associated bacteria toward a lytic lifestyle, and remarkably enrich auxiliary metabolic genes related to amino acid metabolism. Conversely, fucoidan reversed HFD-induced dysbiosis and enhanced phage-mediated horizontal gene transfer by 8.5-fold relative to the baseline. crAssphages and Parabacteroides phages may be important contributors, broadly supporting horizontal gene transfer and auxiliary metabolism or strengthening phage-host interactions in polysaccharide interventions, including fucoidan supplementation. These findings provide a comprehensive landscape of diet-driven cross-kingdom interactions and phage-mediated gene exchange in the gut, offering new insights into potential strategies for precise nutritional interventions targeting the intestinal microbiota.}, } @article {pmid41817311, year = {2026}, author = {Zhang, Q and Hu, L and Rono, JK and Li, B and Wang, S and Lyu, Y and Feng, Z}, title = {Discovery of a Novel Cellulase ZF580 From Mount Everest Metagenome Featuring a Catalytically Active DUF5916 Domain.}, journal = {Biotechnology journal}, volume = {21}, number = {3}, pages = {e70210}, doi = {10.1002/biot.70210}, pmid = {41817311}, issn = {1860-7314}, support = {32370089//National Natural Science Foundation of China/ ; MMLKF21-07//State Key Laboratory of Microbial Metabolism/ ; ALAQ202401011//Anhui Vocational College of Grain Engineering/ ; }, mesh = {*Cellulase/genetics/metabolism/chemistry ; *Metagenome/genetics ; Catalytic Domain ; Mutagenesis, Site-Directed ; Phylogeny ; Models, Molecular ; Substrate Specificity ; }, abstract = {Cellulases are crucial biocatalysts with extensive industrial applications, yet their study has been constrained by cultivation limitations of native microorganisms. Here, we report the discovery and characterization of a novel multifunctional cellulase (ZF580) from the extreme environment of Mount Everest using metagenomic approaches. Functional screening revealed ZF580's unique capacity to hydrolyze diverse substrates, including 4-nitrophenyl-β-D-glucopyranoside (pNPG), chitin, microcrystalline cellulose, and carboxymethyl cellulose sodium (CMC-Na). Phylogenetically, ZF580 forms an independent clade distinct from characterized β-glucosidases and known glycoside hydrolase (GH) families, suggesting its classification as a progenitor of a novel GH lineage. Structural modeling revealed a distinctive (β/α)8 TIM-barrel fold, diverging from canonical GH family architectures. Crucially, truncation analysis and site-directed mutagenesis identified the previously uncharacterized Domain of Unknown Function 5916 (DUF5916) as a catalytic functional region, with residue E373 serving as its essential proton donor. This study provides the first experimental evidence of DUF5916's enzymatic activity, redefining it as a novel catalytic domain. Overall, these findings suggest that ZF580 is a cellulolytic enzyme with β-glucosidase activity and that DUF5916 forms its catalytic core, offering insights that may be valuable for future studies on enzyme function and engineering.}, } @article {pmid41817429, year = {2026}, author = {Zhang, L and Yang, K and Zhang, X}, title = {Draft metagenome-assembled genome sequence of a Dehalogenimonas species from an enriched consortium for complete trichloroethylene reductive dechlorination.}, journal = {Microbiology resource announcements}, volume = {15}, number = {4}, pages = {e0131625}, pmid = {41817429}, issn = {2576-098X}, abstract = {A draft metagenome-assembled genome was recovered from an anaerobic consortium capable of complete reductive dechlorination of trichloroethene to ethene. The draft genome, assigned to a Dehalogenimonas species, is 1.84 Mb in size with a G + C content of 54.53% and encodes 33 reductive dehalogenase homologs.}, } @article {pmid41817433, year = {2026}, author = {Mounchili-Njifon, A and Heang, V and Pum, L and E Messanga, LL and Moumbeket-Yifomnjou, MH and Modiyinji, AF and Tsafack, DTT and Nzi Mbouo-Njoya, L and Lissock, SF and Mbouyap, PR and Assam Assam, JP and Karlsson, EA and Nouhin, J and Njouom, R}, title = {Characterization of near-complete human Pegivirus 2 (HPgV-2) genomes in individuals co-infected with hepatitis C virus (HCV) in Cameroon.}, journal = {Microbiology resource announcements}, volume = {15}, number = {4}, pages = {e0006926}, pmid = {41817433}, issn = {2576-098X}, abstract = {Human pegivirus (HPgV) genomes were detected in HCV-infected plasma via nanopore metagenomics. Six nearly complete HPgV-2 genomes were identified. Phylogenetic analysis confirmed HPgV-2 genotype. This study reveals co-infection dynamics, highlights viral diversity, and supports improved diagnostics.}, } @article {pmid41818685, year = {2026}, author = {Qu, Q and Jia, Y and Wang, S and Hu, K and Liu, C and Hu, X and Mu, L}, title = {Responses of Microbial Communities in River to Atmospheric Deposition.}, journal = {Environmental science & technology}, volume = {60}, number = {11}, pages = {8583-8592}, doi = {10.1021/acs.est.6c01648}, pmid = {41818685}, issn = {1520-5851}, mesh = {*Rivers/microbiology ; Bacteria ; Atmosphere ; Fungi ; *Microbiota ; }, abstract = {Atmospheric deposition threatens aquatic ecosystems, yet its effects on the microbial diversity, composition, and function in rivers remain unclear. Here, we examined the responses of microbial communities to atmospheric pollutants across 105 Chinese rivers. We found that PM2.5 and PM10 were associated with reduced bacterial and fungal diversity and richness. Structural equation modeling revealed that atmospheric deposition (e.g., PM2.5, SO2, NO2, and organic matter aerosol) was directly and indirectly associated with bacterial and fungal community composition through cascading pathways mediated by dissolved oxygen, pH, Mn, inorganic nitrogen, nitrate nitrogen, ammonium nitrogen, and chlorophyll-a. Compared with fungal communities, bacterial communities exhibited broader environmental thresholds and greater sensitivity to atmospheric pollutants. Ecological network analysis further revealed that deposition preferentially disrupted mutualistic motifs in bacterial networks but intensified competitive interactions in fungal networks. Metagenomic analysis revealed that atmospheric pollution is significantly associated with key microbial functional genes involved in carbon degradation (e.g., glucoamylase, pullulanase, and β-glucosidase), nitrogen assimilation and reduction (e.g., nifD, narB, and nirS), and sulfur reduction (e.g., sat, aprA, and dsrA) in rivers. Our findings underscore the importance of air quality mitigation in terms of protecting river ecosystem health.}, } @article {pmid41818964, year = {2026}, author = {Sun, B and Kuang, P and Cui, Y and Yang, Y and Zheng, C}, title = {Simultaneous nitrification and denitrification microbial fuel cells (SND-MFC) for nitrogen removal and bioelectricity recovery: a review of performances, mechanisms, microorganisms, and applications.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129278}, doi = {10.1016/j.jenvman.2026.129278}, pmid = {41818964}, issn = {1095-8630}, mesh = {*Bioelectric Energy Sources ; *Denitrification ; *Nitrification ; *Nitrogen ; Wastewater ; Waste Disposal, Fluid ; }, abstract = {Complex nitrogen pollution in wastewater and the rising energy consumption are calling for the development of coupled advanced technologies to simultaneously remove pollutants and recover energy. Simultaneous nitrification and denitrification microbial fuel cells (SND-MFCs) enable efficient removal of nitrogen and recovery of energy. This review systematically discusses the latest developments of SND-MFC system under different system designs, including reactor configurations, electrode materials, and critical operating parameters that govern the efficiency of the removal of nitrogen and the generation of power. Meanwhile, mechanisms are firstly analyzed from the points of reacting substances, functional zoning and distribution of electrons. This review also describes microbial synergy among nitrifiers, denitrifiers and electroactive taxa from the points of biofilm's stratification, microbial community, strain screening with metagenomic detection and electron-transfer pathways. Furthermore, characteristics of real wastewater of SND-MFC in coking, pharmaceutical, and livestock wastewater are also summarized, exhibiting comprehensive elimination of nitrogen and recovery of bioelectricity under carbon- and aeration-free conditions. Subsequent research should further optimize the performance of the system by developing intelligent strategies based upon machine learning (ML) and digital twin technologies, electrobiological communication circuits, combination of strain screening and gene editing to unlock the full-scale potential of SND-MFC technology. In addition, the transition from laboratory-scale to practical applications also faces multiple technical challenges that require attention.}, } @article {pmid41819166, year = {2026}, author = {Zhao, X and Zhang, J and Li, Y and Wang, Q and Li, J and Xia, Y and Zha, M and Chen, Y}, title = {Elucidating the microbiota-metabolite interplay in Hurood and Chula: An integrated multiomics investigation.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-28134}, pmid = {41819166}, issn = {1525-3198}, abstract = {Hurood and Chula, traditional fermented dairy products from Xilingol, China, show flavor and quality differences due to variations in production processes. Therefore, how heating and kneading affect their microbial, nonvolatile metabolite, and volatile organic compound (VOC) composition warrants exploration. In this study, shotgun metagenomic sequencing revealed the differential micro-organisms between Hurood and Chula. Ultra-performance liquid chromatography-tandem MS identified 47 differential metabolites. Among these, organic acids and their derivatives, benzene and substituted derivatives, free fatty acids (FFA), and lysophosphatidylcholines showed the highest content in Chula, whereas lactose, melibiose, and histamine were significantly enriched in Hurood, suggesting that the heating and kneading process affected galactose and histidine metabolic pathways. In contrast, headspace solid-phase microextraction GC-MS identified 4 differential VOC with elevated levels in Hurood. These compounds functioned as key aroma contributors, imparting richer and more complex aroma characteristics that included creamy, oily, fatty, caramel, coconut, woody, spice, and maple notes. Correlation analysis indicated that the differential micro-organisms were involved in metabolite dynamics and VOC accumulation and further revealed that they drove the directed accumulation of VOC through regulating FFA release and transformation and by regulating the Maillard reaction of small peptides, thereby underpinning their distinct flavor profiles. This study provides important insights into the heating- and kneading-induced formation of flavor and quality in traditional fermented dairy products from Xilingol, China, thereby facilitating the precise control of traditional processes and subsequent product quality improvement.}, } @article {pmid41819185, year = {2026}, author = {Yoshida, S and Matsumoto, Y and Kajihara, A and Funato, M and Tsuyuguchi, K and Mitarai, S and Takemoto, K and Nakamura, S}, title = {Fomite transmission of Mycobacterium abscessus between severely disabled patients.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {32}, number = {6}, pages = {1015-1019}, doi = {10.1016/j.cmi.2026.02.029}, pmid = {41819185}, issn = {1469-0691}, mesh = {Humans ; *Mycobacterium abscessus/genetics/isolation & purification/classification ; *Cross Infection/transmission/microbiology/epidemiology ; *Mycobacterium Infections, Nontuberculous/transmission/epidemiology/microbiology ; Japan/epidemiology ; *Disease Outbreaks ; *Fomites/microbiology ; Female ; Middle Aged ; }, abstract = {OBJECTIVES: We aimed to investigate a nosocomial outbreak of Mycobacterium abscessus subspecies massiliense (MAM) and to track its transmission route via genomic analyses and environmental surveys at a hospital in Osaka, Japan. The outbreak was initially detected in two patients (M1 and M2) with severe disability in 2020 and then expanded to five other patients (M3‒M7).

METHODS: The 34-month observation period was divided into three phases separated by two interventions. Mycobacterial culture screening was performed for 294 clinical and environmental samples. We confirmed that five patients (M1‒M5) had infections in phase 1 (March 2020 to July 2021) and implemented an initial intervention. In phase 2 (November 2021 to May 2022), new patients (M6 and M7) were identified, wherein an environmental survey identified MAM strains, prompting a second intervention. No patients were identified in phase 3 (September to December 2022). However, MAM was isolated from the environment during follow-up surveys. A total of 52 MAM isolates were analysed, including 11 clinical isolates (one from M1 and M2 in each phase and one each from M3-M7) and 41 environmental isolates obtained from care gloves, medical devices, and room equipment surrounding patients. We sequenced the isolate genomes and identified 15 subclone clusters with a threshold of 24.5 single-nucleotide variants (SNVs).

RESULTS: The overall SNV distribution of the clinical and environmental strains was within 61 SNVs, showing near-identical genomes. Clinical strains from patient M2 with persistent positivity were classified as the same subclone, with 0-6 SNVs. The isolate from a wagon brought into patient rooms showed the lowest number of SNVs (3-8) compared with isolates from M2. This subclone cluster, involving M2 and wagon isolates, formed the hub of the intercluster connection of 11 clusters comprising other clinical and environmental strains.

CONCLUSIONS: M. abscessus could persist in dry environments and might be indirectly transmitted via fomites.}, } @article {pmid41819201, year = {2026}, author = {Jiang, J and Wei, J and Zhang, B and Chen, Y and Wang, J and Zhang, Y and Hu, J and Dai, Q}, title = {Integrating metabolomics and metagenomics reveals potential mechanism of rice root exudates in inhibiting nitrification in coastal saline soils.}, journal = {Environmental research}, volume = {298}, number = {}, pages = {124265}, doi = {10.1016/j.envres.2026.124265}, pmid = {41819201}, issn = {1096-0953}, mesh = {*Nitrification ; *Plant Roots/metabolism/chemistry ; *Oryza/metabolism/genetics ; Metabolomics ; Metagenomics ; *Soil/chemistry ; Salinity ; *Plant Exudates/metabolism ; Soil Microbiology ; }, abstract = {Rice root exudates are known to suppress nitrification and mitigate nitrogen losses in agricultural soils; however, their specific roles in coastal saline soils remain poorly understood. Here, root exudates were collected at 6 and 10 weeks after transplanting from two genotypes (Oryza sativa L. 'Nanjing 9108' and 'Yangjing 5118') using a hydroponic system, and their effects on nitrification in coastal saline soils were investigated through microcosm experiments integrating metabolomic and metagenomic analyses. Root exudates inhibited net nitrification rate (NNR) and potential nitrification activity (PNA), with the inhibitory effect primarily dependent on genotype. The abundance of nitrification genes was not significantly altered by root exudates and was negatively correlated with PNA, suggesting that root exudates mainly inhibited heterotrophic rather than autotrophic nitrification. Root exudates at 10 weeks after transplanting significantly increased the abundance of nitrate reduction genes. Integrated analyses revealed that differential metabolites dominated by terpenoids and lipids, as well as several exudates (e.g., L-isoleucine, L-valine, and pyridoxine) that generated reducing electrons during metabolism, particularly in treatments with root exudates from Nanjing 9108, showed a negative correlation with PNA and positively correlated with the abundance of nitrate reduction genes. Furthermore, the mechanisms of NNR inhibition varied with genotype. Specifically, root exudates from Nanjing 9108 inhibit NNR synergistically by reducing heterotrophic nitrification and promoting nitrate reduction, whereas those from Yangjing 5118 inhibit NNR mainly by reducing heterotrophic nitrification. Overall, root exudates primarily enhance nitrate reduction and/or reduce PNA by creating microhabitats and generating reducing agents, which inhibit nitrate accumulation in coastal saline soils. These findings provide a scientific basis for the formulation of nitrogen management measures in coastal saline paddy fields.}, } @article {pmid41819204, year = {2026}, author = {Qi, Y and Zheng, X and He, X and Huang, K and Wang, D and Zhang, XX}, title = {Linkages between core microbiome and functional convergence during artificially selecting microbial communities for benzotriazole degradation.}, journal = {Environmental research}, volume = {298}, number = {}, pages = {124241}, doi = {10.1016/j.envres.2026.124241}, pmid = {41819204}, issn = {1096-0953}, mesh = {*Triazoles/metabolism ; Biodegradation, Environmental ; *Microbiota ; *Microbial Consortia ; *Bacteria/metabolism/genetics ; Bioreactors/microbiology ; Sewage/microbiology ; }, abstract = {The escalating prevalence of benzotriazole (BTR), an emerging refractory organic pollutant, has drawn significant attention for the development of efficient bioremediation solutions. Although the construction of microbial consortia represents a promising strategy, the intrinsic relationship between community succession and functional features during artificial selection remains poorly understood. To address this, this study engineered two distinct microbial consortia from activated sludge using a top-down selection strategy in sequencing batch reactors fed with increasing BTR concentrations. While the two consortia evolved along divergent taxonomic pathways, they exhibited remarkable functional convergence, maintaining consistently high BTR transformation (>96%) and chemical oxygen demand (>75%) removal efficiencies. This robust performance under the stringent condition of BTR as the sole carbon source highlighted their significant adaptive potential. Metagenomic analysis further attributed this functional stability to the principle of functional redundancy, wherein taxonomically distinct keystone species (e.g., Nocardioides and Methylobacterium) harbored functionally analogous gene clusters. Additionally, multiple congeneric species (e.g., MAG.480 and MAG.17) within the Bacteroidota phylum exhibited significant divergence in their degradation gene repertoires. These findings not only advance ecological understanding of microbiome-mediated BTR biodegradation but also provide a foundation for the rational design and optimization of high-performance bioremediation consortia.}, } @article {pmid41819291, year = {2026}, author = {Kalimuthu, S and Muthusamy, A}, title = {MobiRes: An integrative pipeline for resistome risk prediction through mobilome profiling.}, journal = {Journal of microbiological methods}, volume = {244}, number = {}, pages = {107448}, doi = {10.1016/j.mimet.2026.107448}, pmid = {41819291}, issn = {1872-8359}, mesh = {Humans ; *Interspersed Repetitive Sequences/genetics ; Animals ; *Bacteria/genetics/drug effects ; DNA Transposable Elements/genetics ; Plasmids/genetics ; *Metagenomics/methods ; Machine Learning ; *Computational Biology/methods ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; }, abstract = {Antimicrobial resistance (AMR) poses a significant global health challenge, with the environment serving as a crucial reservoir and conduit for resistance determinants. Although antibiotic resistance genes (ARGs) have been extensively studied in environmental contexts, systematic approaches for assessing and prioritizing the risks associated with mobile genetic elements (MGEs), such as plasmids, phages, transposons, and integrative elements (IEs), remain unclear. To address this gap, we present MobiRes, an open-source computational framework designed to predict resistome risk by integrating information from the mobilome and microbiome. The pipeline was evaluated using a wide range of publicly available metagenomic datasets spanning diverse environments, including wastewater, poultry, soil, sediments, and human fecal samples. To validate the framework, statistical analyses and machine learning models were applied to evaluate the role of MGEs in driving ARG dissemination. The pipeline identified transposons as the dominant MGE class while capturing environment-specific variation in plasmid, phage, and IE -associated ARGs. Transposon-associated ARGs showed the most consistent environmental differentiation (ANOVA p = 0.0017; Kruskal-Wallis p = 0.018), whereas plasmid and phage-associated ARGs varied moderately (p = 0.015-0.040) and IE-associated ARGs remained comparatively stable across environments (p > 0.05). The Random Forest (RF) model achieved an AUC of 0.82, and subsequent feature importance and SHapley Additive exPlanations (SHAP) analyses revealed that transposon abundance is the primary factor driving ARG dissemination across diverse environments. By integrating host, mobility, and ecological factors, MobiRes provides a scalable and One Health-oriented framework for comprehensive AMR risk assessment. This pipeline is publicly available at https://github.com/santhiyakc17/MobiRes_Pipeline.}, } @article {pmid41819657, year = {2026}, author = {Li, E and Xie, X and Zhang, Y and Yan, L and Wang, Y}, title = {Biogeochemical cycling of sulfur and iron constrains arsenic enrichment in groundwater: Microbial functionality and organic matter composition.}, journal = {Water research}, volume = {297}, number = {}, pages = {125724}, doi = {10.1016/j.watres.2026.125724}, pmid = {41819657}, issn = {1879-2448}, mesh = {*Groundwater/chemistry ; *Arsenic ; *Iron/chemistry ; *Sulfur/chemistry ; Bacteria/metabolism ; }, abstract = {Groundwater arsenic contamination is governed by the coupled iron-sulfur-arsenic biogeochemical cycle, where microbial functional genes and organic matter transformation play central roles, though regional-scale mechanisms remain unclear. This study integrates hydrogeochemistry, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), metagenomic sequencing, and metagenome-assembled genomes (MAGs) to reveal microbially driven mechanisms of arsenic migration and transformation in the Datong Basin. The results indicate distinct zonation of arsenic, sulfur, and iron speciation along the groundwater flow path. Furthermore, dissolved organic matter (DOM) dominated by carboxyl-rich alicyclic molecules (CRAM) and aromatic compounds promotes arsenic release through chelation and electron transfer. Microbial community and functional gene analyses further reveal key zonation characteristics. In the recharge zone, genera such as Acinetobacter and Hydrogenophaga were predominant, with functional genes related to arsenite oxidation (aioA, aoxB) contributing to arsenic retention. In the transition zone, sulfate-reducing bacteria including Desulfovibrio became abundant, and sulfate reduction genes (CysND, CysH, CysJI) facilitated the formation of thioarsenates, leading to arsenic release. In the discharge zone, methylotrophic genera such as Methylocystis together with methanogens were enriched. The co-occurrence of the methane metabolism gene ackA and the arsenic reduction gene arsC suggested a potential coupling between methane-related metabolism and arsenic transformation under reducing conditions. This study elucidates iron-sulfur-arsenic coupling as a key mechanism governing arsenic biogeochemical cycling, providing a theoretical biogeochemical framework for understanding regional arsenic spatial heterogeneity.}, } @article {pmid41819697, year = {2026}, author = {Ciaralli, L and Valente, T and Monfardini, E and Berto, D and Rampazzo, F and Libralato, G and Manfra, L and Piermarini, R and Silvestri, C and Radicioli, M and Gioacchini, G and Chemello, G and Trotta, E and Capó, JD and Tomassetti, P and Matiddi, M}, title = {Callinectes sapidus - coast to coast: Integrating stable isotope analysis and shotgun metagenomics to unravel trophic dynamics and microlitter ingestion across two Mediterranean sites.}, journal = {Marine pollution bulletin}, volume = {227}, number = {}, pages = {119532}, doi = {10.1016/j.marpolbul.2026.119532}, pmid = {41819697}, issn = {1879-3363}, mesh = {Animals ; Metagenomics ; Mediterranean Sea ; *Food Chain ; *Environmental Monitoring ; Carbon Isotopes/analysis ; Nitrogen Isotopes/analysis ; }, abstract = {The increasing presence of microlitter in the marine environment poses a growing threat to aquatic organisms. This study investigates microlitter ingestion and trophic ecology of Callinectes sapidus from two populations of the Mediterranean basin: the Adriatic and Tyrrhenian Seas. To disentangle potential differences in feeding strategies between the populations, we adopted an integrated framework combining stable isotope analysis with shotgun metagenomic analysis of gastrointestinal contents, thus providing a complementary view of long-term trophic position and short-term dietary composition. Gastrointestinal analysis revealed microlitter ingestion in 39% of Adriatic and 50% of Tyrrhenian individuals, with 123 particles retrieved. Fibres dominated (94.3%), though composition varied regionally: Adriatic individuals ingested mainly cellulose-based microlitter (62.5%), whereas Tyrrhenian ones mostly synthetic polymers (61.4%). Eight chemical types were identified, with cellulose, polyethylene terephthalate, and resin-based polymers most abundant. Stable isotope analysis (δ[15]N and δ[13]C) indicated distinct trophic patterns: Adriatic population had higher δ[15]N (mean ± sd: 11.50 ± 2.27‰) and less depleted δ[13]C (-16.20 ± 1.52‰) compared to the Tyrrhenian one (δ[15]N: 9.01 ± 2.27‰; δ[13]C: -18.57 ± 0.88‰), suggesting region-specific feeding strategies. Shotgun metagenomics provided complementary information on prey composition, helping to characterise the opportunistic diet of C. sapidus. Overall, these findings highlight spatial differences in microlitter exposure and trophic dynamics, likely shaped by environmental availability and feeding behaviour. By integrating microlitter ingestion, stable isotope analysis, and metagenomics, this study provides insight into how C. sapidus interacts with anthropogenic and natural resources, emphasizing the feeding flexibility underlying its invasive success in Mediterranean Sea.}, } @article {pmid41819887, year = {2026}, author = {Onohuean, H and Igere, BE and Apollo, E and Idris, SO and Olutona, GO}, title = {Meta-synthesis of research advances on drug residues associated with antihelmintic, antibiotics in livestock and poultry: Implications for public health.}, journal = {Food research international (Ottawa, Ont.)}, volume = {231}, number = {Pt 2}, pages = {118757}, doi = {10.1016/j.foodres.2026.118757}, pmid = {41819887}, issn = {1873-7145}, mesh = {Animals ; *Anti-Bacterial Agents/analysis ; *Drug Residues/analysis ; *Poultry ; *Public Health ; *Livestock ; *Anthelmintics/analysis ; *Food Contamination/analysis ; Humans ; Meat/analysis ; }, abstract = {INTRODUCTION: This meta-synthesis summarizes research advances on drug residues associated with using antihelmintic/antibiotics in poultry and livestock farming to highlight their implications on public health.

METHODS: The study applied the Preferred Reporting Items guidelines for the Systematic Reviews and Meta-Analyses (PRISMA) on diverse core databases (PubMed, Scopus, Medline and Web of Science) using the title-specific search keywords/terms.

RESULTS: Among the 176 included and eligible articles on drug residues associated with the use of antihelminthic/antibiotics in livestock and poultry farms, only 77 were meta-synthesized which revealed a poor growth rate of 1.95% within the periods. The meta-synthesis depicts the most reported pharmaceuticals, residue/metabolite to include Monensin (MON), unchanged Nicarbazin (NCZ), Doxycycline (DOX), Thiabendazole, Dimetridazole (DMZ), concentrated in meat, chicken, eggs, muscle, and liver of livestock with a concentration detected ranging from 0.01 μg/kg to 4840 μg/kg. It is important to note that the residual concentration observed was higher than major countries maximum residual limits (MRLs) for such farm products which reveals the risk of such observed values to consumers. Also, most reported method of residue detection was HPLC-MS/MS and LC-MS/MS, usually, this is due to the disease and infection threat of coccidiosis and histomoniasis in livestock production.

CONCLUSION: The relatively low annual growth rate of 1.95%indicates poor study between 2000 and 2024 which further emphasizes that the mainstream research in this regard may be neglected gradually if the trend continues, leaving the concern of drug residue unattended while the implications on public health systems remain unengaged. It also revealed high residue and risk associated with the use of antihelminthic/antibiotics in poultry/livestock farming which necessitates intentional and adroit surveillance especially in low- and middle-income nations.}, } @article {pmid41820042, year = {2026}, author = {Zhou, F and Liu, ZP and Cao, B}, title = {[Annual review of community-acquired pneumonia (CAP) 2025].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {49}, number = {3}, pages = {339-344}, doi = {10.3760/cma.j.cn112147-20251124-00741}, pmid = {41820042}, issn = {1001-0939}, support = {2024ZD0522500//Major Project of the Ministry of Science and Technology of China/ ; }, mesh = {Humans ; *Community-Acquired Pneumonia/epidemiology/drug therapy ; Anti-Bacterial Agents/therapeutic use ; Mycoplasma pneumoniae/drug effects ; Community-Acquired Infections/epidemiology ; China/epidemiology ; Macrolides ; Metapneumovirus ; Pneumonia, Mycoplasma/drug therapy/epidemiology ; }, abstract = {Community-acquired pneumonia (CAP) remains a significant global health challenge. This review summarizes the major advances in clinical research or CAP between October 1, 2024, and September 30, 2025. Given the high prevalence of macrolide-resistant Mycoplasma pneumoniae (MRMP) in China, PCR test for MRMP was recommended in pediatric patients to guide appropriate antibiotic selection. Increased attention is warranted for respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) due to their increasing prevalence and poor prognosis. PSI and CURB-65 scores remain the reliable tools for assessing the severity of CAP, while the SOFA-2 score may offer a promising approach for identifying patients requiring intensive care unit (ICU) admission. Although multiplex PCR (mPCR), targeted next-generation sequencing (tNGS), and metagenomic next-generation sequencing (mNGS) have been widely adopted in clinical practice, current evidence does not demonstrate sufficient benefits in improving patient survival or optimizing antibiotic stewardship. A rational, empirical antibiotic strategy should be individualized according to local pathogen epidemiology, risk of antimicrobial resistance and aspiration, and patient's clinical presentation. Short-course antibiotic therapy guided by "clinical stability" criteria is reliable, yet achieving stability requires more time in elderly patients and cases with comorbidities. Cefpirome and lefamulin are new antimicrobial agents on the market, but further clinical data are needed to support their use in severe cases and elderly patients. Suraxavir marboxil (GP681), a newly antiviral agent drug targeting the polymerase acidic protein of the influenza virus RNA polymerase, has recently been approved in China. Extending the administration of steroids to severe CAP without septic shock should be approached with extreme caution. High level of C-reactive protein may serve as a potential indicator for identifying cases who could benefit from steroids. In addition, RSV vaccines and monoclonal antibodies will emerge as important strategies for preventing RSV pneumonia in high-risk populations.}, } @article {pmid41820832, year = {2026}, author = {Vela-Chauvin, MG and Ramirez-Villacis, DX and Armijos, CE and Narvaez, M and Quelal-Madrid, F and Bustamante, G and Torres-Sobrevilla, C and Debut, A and Corredor, F and Calero-Cáceres, W and Machado, A and Zapata-Mena, S}, title = {Characterization and evaluation of a phage cocktail targeting Salmonella enterica in a Turkey farm.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41820832}, issn = {1471-2180}, support = {FSPI grant (Project ID 17827)//French Embassy in Ecuador/ ; Collaboration Grant (Project ID 23185)//Universidad San Francisco de Quito/ ; }, abstract = {BACKGROUND: Salmonella enterica is a major food-borne pathogen strongly associated with poultry products, causing over 150 million human infections annually despite extensive control measures. Among its serovars, S. enterica serovar Infantis is highly prevalent on poultry farms and represents an increasing food safety and public health concern. Alternative strategies to reduce Salmonella dissemination are urgently needed, and bacteriophages have emerged as promising biocontrol agents.

RESULTS: In this study, we enriched and characterized a phage cocktail recovered from wastewater and propagated with Salmonella Infantis. The cocktail underwent a comprehensive stability evaluation, including tolerance to a range of temperatures (4–50 °C), acidic conditions (loss of infectivity at pH 2 and pH 4), and oxidative stress (remaining stable after exposure to hydrogen peroxide concentrations up to 100 ppm). It demonstrated the ability to reduce preformed Salmonella biofilms by 39.9%. Genomic characterization was performed via Illumina sequencing, revealing the presence of nine phages belonging to a distinct genera (Kuttervirus, Berlinvirus, Jacunavirus, Rosemountvirus, Felixounavirus, Mooglevirus, Zindervirus, Astrithrvirus, and one unclassified). Importantly, virulence factors, antimicrobial resistance genes, or lysogenic elements were not detected in the genomes of eight of the nine phages analyzed; for one phage, incomplete genomic information prevented full assessment, supporting the genetic safety of the cocktail. Field evaluation under commercial turkey-rearing conditions showed that both control and phage treated poultry houses tested negative for Salmonella at the end of the production cycle. Therefore, treatment efficacy could not be conclusively determined. However, the study supports the feasibility and safety of applying enriched phage lysates in a commercial production setting, as phage application did not adversely affect production parameters.

CONCLUSIONS: These findings support the use of well-characterized enriched lysates, as promising candidates for biocontrol strategies to improve food safety and reduce the burden of Salmonella in poultry production systems.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04849-4.}, } @article {pmid41821123, year = {2026}, author = {Thygesen, VFDF and Farahani, MF and Nielsen, SH and Constancias, F and Givskov, M and Abranches, J and Scorrano, G and Jørkov, MLS and Ebrahimi, G and Bendezu-Sarmiento, JC and Demeter, F and Kristiansen, K and Belstrøm, D and Sikora, M}, title = {The genomic history of Streptococcus mutans from the Mesolithic until modern times.}, journal = {Genome biology}, volume = {27}, number = {1}, pages = {}, pmid = {41821123}, issn = {1474-760X}, support = {R302-2018-2155, R155-2013-16338//Lundbeck Foundation/ ; NNF18SA0035006//Novo Nordisk Foundation/ ; CF18-0024//Carlsberg Foundation/ ; DNRF94, DNRF174//Danish National Research Foundation/ ; KU2016 programme//University of Copenhagen/ ; UNS69906/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Streptococcus mutans/genetics/classification ; Humans ; Phylogeny ; *Genome, Bacterial ; DNA, Ancient/analysis ; Evolution, Molecular ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: Streptococcus mutans is a member of the human oral microbiota and is considered one of the most important cariogenic organisms. Previous studies have suggested an expansion of S. mutans populations about 10,000 years ago with the onset of agriculture, yet direct molecular evidence of its presence from ancient DNA remains sparse.

RESULTS: Here, we present population genomic analyses of 25 ancient S. mutans genomes (average read depth 0.1X - 387X) recovered from archaeological remains across Eurasia spanning ~ 8,000 years of human evolution. Recombination-corrected phylogenomic analyses using Gubbins show a star-like phylogeny indicative of an early radiation, with the ancient genomes falling within the genomic diversity of modern isolates but restricted to one of the major clades of the phylogeny (D). Analyses of genes encoding present day virulence factors reveals that the presence of the mutanobactin operon involved in oxygen tolerance is restricted to specific subclades (A & B) and absent among the ancient samples. Using the MEGAHIT assembler followed by binning of contigs with CONCOCT, we recover metagenome-assembled genomes (MAG) of 7 high-coverage ancient S. mutans strains, including a 7,500-year-old sample from an early European Neolithic farmer. Pangenome analysis with modern isolates using the anvi'o's suite revealed the presence of specific functional genes in the ancient isolates, which were lost through time.

CONCLUSIONS: Our study demonstrates that Streptococcus mutans DNA is well preserved in tooth samples from archaeological remains and show that it formed part of the human oral microbiota already before the onset of agriculture, consistent with a radiation and population expansion well before 8,000 years ago.}, } @article {pmid41821330, year = {2026}, author = {Yi, XH and Zhu, HX and He, MY and Gao, S and Li, M}, title = {Decoding Links between Gut Microbiota and Metabolic-associated Fatty Liver Disease: Meta-analysis and Mediation Study Uncover Species-specific Taxa and a Novel Bile Acid Mediator.}, journal = {Biomedical and environmental sciences : BES}, volume = {39}, number = {2}, pages = {202-214}, doi = {10.3967/bes2025.162}, pmid = {41821330}, issn = {2214-0190}, mesh = {*Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; Humans ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Fatty Liver/microbiology ; Species Specificity ; Bacteria/classification ; }, abstract = {OBJECTIVE: Previous Mendelian randomization (MR) studies have suggested an association between the gut microbiome and metabolic-associated fatty liver disease (MAFLD). However, the reliance on 16S rRNA sequencing data has led to inconsistent findings and limited species-level insights. To address this, we conducted a de novo MR analysis using species-level shotgun metagenomic data, combined it with a meta-analysis to consolidate the existing evidence, and explored metabolite-mediated pathways.

METHODS: Bidirectional MR analyses were performed between 883 gut microbiota taxa (derived from shotgun metagenomic genome-wide association study) and MAFLD. Published MR studies (up to December 1, 2024) were identified using PubMed, Embase, Web of Science, and the Cochrane Library for meta-analysis. Multivariable MR (MVMR) and mediation analyses were applied to assess the mediating effects of 1,400 blood metabolites.

RESULTS: The de novo MR identified 25 MAFLD-associated microbial taxa. Integration with 7 published studies revealed 34 causal taxa, including 10 at the species level. Among the 1,400 metabolites, 53 showed causal links with MAFLD. MVMR and mediation analyses identified deoxycholate as a mediator of the effect of Bifidobacterium on MAFLD risk (22.06% mediation proportion).

CONCLUSION: This study elucidated the connections between species-level gut microbiota and MAFLD, highlighting the interplay between microbiota, metabolites, and disease pathogenesis. These findings provide novel insights into the potential therapeutic targets for MAFLD.}, } @article {pmid41821545, year = {2025}, author = {Yun, S and Seo, Y and Yoon, Y}, title = {Prevalence of Microorganisms and Suggestion for Potential Contribution of Microorganisms to Volatile Basic Nitrogen Production in Beef at Current Purchase Stages.}, journal = {Food science of animal resources}, volume = {45}, number = {6}, pages = {1710-1723}, pmid = {41821545}, issn = {2636-0780}, abstract = {This study investigated the prevalence of microorganisms related to meat quality and analyzed volatile basic nitrogen (VBN) levels in beef samples to suggest potential bacteria that might contribute to VBN production at current purchase stages using metagenomic analysis. Seventy beef samples were analyzed for coliform, Escherichia coli, enterohemorrhagic E. coli, Listeria monocytogenes, Salmonella, Staphylococcus aureus, total aerobic bacteria (TAB), Enterobacteriaceae, lactic acid bacteria (LAB), Pseudomonas spp., yeast and molds (YM), and psychrotrophic bacteria (PB). VBN levels ranged from 0.69 to 22.51 mg%. Microbiota from three samples with the highest and three with the lowest VBN levels were analyzed. S. aureus was detected in only one sample at 1.2 Log CFU/g. The cell counts for TAB, coliform, Enterobacteriaceae, LAB, Pseudomonas spp., YM, and PB were 5.1, 1.7, 2.6, 4.2, 1.9, 2.9, and 5.4 Log CFU/g, respectively. Microbiota analysis revealed that samples with high VBN levels had high relative abundances of Lactobacillus and Leuconostoc. This study showed that these relatively abundant LAB were potential bacteria that might contribute to producing more VBN in beef at current purchase stages. However, the potential bacteria were suggested only by metagenomic analysis with a limited sample size without considering the endogenous meat enzymes. Therefore, further research is necessary to identify and isolate these bacteria with a larger sample size while excluding VBN produced by endogenous enzymes. Additionally, environmental factors not included due to the limited objective of this study could also be considered in further research with the different objectives from this study.}, } @article {pmid41821969, year = {2026}, author = {Lim, JJL and Chin, NL and Chong, CW and Ripen, AM and How, S and Teoh, SQ}, title = {Review on kefir beverages from milk and water: health benefits, processing and applications.}, journal = {Food science of animal resources}, volume = {46}, number = {1}, pages = {31}, pmid = {41821969}, issn = {2636-0780}, abstract = {Kefir is a trending and highly valued fermented beverage known for its beneficial microbes and giving a wide spectrum of health benefits. It includes milk kefir and water kefir which have gained separate attention. Although milk kefir is more heard of than water kefir, it is essential to understand both in greater details in terms of similarities and differences. The key health benefits such as probiotics, protection in the gastrointestinal tract, control of glucose level, antioxidant, antimutagenic, anticarcinogenic, regulating cholesterol, antimicrobial and improving lactose digestion are discussed and supported with recent in-vivo or in-vitro scientific evidences. This review addresses the gap of individual focus of each kefir by direct comparison of its microbial diversity, processing and physicochemical qualities. It provides updated information on lactic acid bacteria by species from advanced techniques of metagenomic analysis and also highlights the potential of kefiran, exopolysaccharides of milk kefir grains in food, biopharmaceutical and packaging industries.}, } @article {pmid41822155, year = {2026}, author = {Schmitt, MS and Lee, KK and Bunbury, F and Landsittel, JA and Vitelli, V and Kuehn, S}, title = {Learning functional groups in complex microbiomes.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {41822155}, issn = {2331-8422}, abstract = {From soil to the gut, communities composed of thousands of microbes perform functions such as carbon sequestration and immune system regulation. Here, we introduce a data-driven approach that explains how community function can be traced to just a few groups of microbes or genes. In gut communities, our neural-network based clustering algorithm correctly recovers known functional groups. In the ocean metagenome, it distills ~500 gene modules down to three sparse groups highlighting survival strategies at different depths. In soils, it distills ~4400 bacterial species into two groups that enter a mathematical model of nitrate metabolism. By combining interpretable ML with strain isolation and sequencing experiments, we connect the metabolic specialization of each group to community-wide responses to perturbations. This integrated approach yields simple structure-function maps of microbiomes, allowing the discovery of molecular mechanisms underlying human and environmental health. More broadly, we illustrate how to do function-informed dimensionality reduction in biology.}, } @article {pmid41822221, year = {2026}, author = {Donbraye, E and McLeod, L and Chai, Z and Lacoste, SR and McCarthy, EL and Hill, JE and Erickson, NEN and Links, MG and Otto, SJG and Huang, Y and Waldner, CL}, title = {Diagnostic sensitivity and specificity of metagenomic sequencing and qPCR for detection of viruses associated with bovine respiratory disease estimated using Bayesian latent class models.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1704414}, pmid = {41822221}, issn = {2297-1769}, abstract = {INTRODUCTION: Very few studies have examined the diagnostic sensitivity and specificity of currently available laboratory tests for detecting respiratory pathogens in cattle, and even fewer have examined test performance on samples from animals before the onset of clinical disease.

METHODS: In this study, Bayesian latent class modeling (BLCM) was used to assess diagnostic test performance in the absence of a gold standard on nasal swabs collected from 19 western Canadian feedlots. Viruses associated with bovine respiratory disease (BRD) were identified using qPCR from a commercial diagnostic laboratory from 760 nasal swabs collected from fall-placed calves (FPC) and yearlings (YRL) at and shortly after feedlot arrival. Using BLCM, the qPCR results were compared to previously reported matching nanopore metagenomic sequencing data for these same samples. Based on BLCM, test sensitivities and specificities were estimated for the detection of bovine coronavirus (BCoV), bovine herpesvirus type 1 (BoHV-1), bovine parainfluenza virus type 3 (BPIV-3), bovine respiratory syncytial virus (BRSV), and influenza D virus (IDV). Estimates informed by BLCM were not available for the detection of bovine viral diarrheal virus (BVDV) because qPCR did not detect this virus in any samples.

RESULTS: Diagnostic sensitivity of qPCR was higher than metagenomic sequencing for detecting BCoV (qPCR 0.90, 95% CrI 0.81-0.99; sequencing 0.35, 95% CrI 0.25-0.46) and BoHV-1 (qPCR 0.39, 95% CrI 0.19-0.99; sequencing 0.04, 95% CrI 0.01-0.15). However, the estimated diagnostic sensitivity of metagenomic sequencing was higher than qPCR for identifying BRSV (qPCR 0.32, 95% CrI 0.22-0.43; sequencing 0.60, 95% CrI 0.44-0.77). No significant difference among sensitivities was noted for the detection of BPIV-3 (qPCR 0.42, 95% CrI 0.21-0.66; sequencing 0.52, 95% CrI 0.19-0.87) and IDV (qPCR 0.65, 95% CrI 0.53-0.79; sequencing 0.60, 95% CrI 0.48-0.73). Diagnostic specificity was comparable for most viruses, except for BCoV, where metagenomic sequencing (BCoV 0.91, 95% CrI 0.88-0.95) outperformed qPCR (BCoV 0.59, 95% CrI 0.51-0.68). The specificity and sensitivity for detection of BRD-associated bacteria from the same metagenomic data were also similar to those estimated for culture and qPCR results for the same samples.

DISCUSSION: Estimated test sensitivities of both nanopore metagenomic sequencing and qPCR for the detection of BRD viruses of interest in nasal swab samples were moderate to very low for most viruses. While the tests varied in their ability to detect individual viruses, data from this study suggest nanopore metagenomic sequencing offers a potential alternative for diagnostic laboratories to identify three of six important BRD viruses as well as bacteria associated with BRD.}, } @article {pmid41822328, year = {2026}, author = {Hu, H and Cai, D and Li, J and Wang, K}, title = {Pulmonary infection by Nocardia saintgeorgesii mimicking lung cancer with concurrent pulmonary embolism in an immunocompetent host: a case highlighting the diagnostic role of mNGS.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1765925}, pmid = {41822328}, issn = {2235-2988}, mesh = {Humans ; *Nocardia Infections/diagnosis/drug therapy/microbiology ; *Nocardia/genetics/isolation & purification/classification ; *Pulmonary Embolism/diagnosis/microbiology ; Anti-Bacterial Agents/therapeutic use ; *Lung Neoplasms/diagnosis ; High-Throughput Nucleotide Sequencing ; Male ; Diagnosis, Differential ; Tomography, X-Ray Computed ; Immunocompetence ; Diagnostic Errors ; }, abstract = {BACKGROUND: Pulmonary nocardiosis presents a diagnostic challenge due to its frequent mimicry of lung cancer on imaging and the low sensitivity of conventional cultures. We report a case initially misdiagnosed as malignancy in an immunocompetent host, where metagenomic next-generation sequencing (mNGS) provided a definitive diagnosis and revealed a concurrent pulmonary embolism, suggesting a potential underrecognized association.

CASE PRESENTATION: This report describes a case of PN in an immunocompetent patient who was initially misdiagnosed with lung cancer based on imaging findings but later confirmed as pulmonary nocardiosis via mNGS. Notably, the patient also developed pulmonary embolism (PE). Empirical antibiotic therapy with piperacillin-tazobactam was initiated initially, supplemented with inhaled ipratropium bromide and expectorants to alleviate symptoms. Based on imaging findings suggestive of lung cancer, an invasive procedure was scheduled. mNGS was subsequently performed for further diagnosis. The subsequent results, along with CT scans, indicated no evidence of malignancy, leading to a consideration of Nocardia infection. The treatment regimen was then adjusted to ceftriaxone sodium combined with compound sulfamethoxazole, and the surgical schedule was canceled. The patient's condition showed significant improvement, and he was discharged without fever or dyspnea. Some literature suggests that many PN patients present with concurrent deep vein thrombosis (DVT), suggesting a potential yet underrecognized association between Nocardia infection and thrombotic events. However, this correlation has not been fully reported before.}, } @article {pmid41822329, year = {2026}, author = {Tee, KK and Xia, X}, title = {Strengthening preparedness and response to emerging henipavirus diversity.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1761347}, pmid = {41822329}, issn = {2235-2988}, mesh = {Animals ; *Henipavirus Infections/epidemiology/prevention & control/virology/diagnosis/transmission ; Humans ; *Henipavirus/classification/genetics/isolation & purification ; *Communicable Diseases, Emerging/prevention & control/epidemiology/virology/diagnosis ; Zoonoses/epidemiology/virology/prevention & control ; Nipah Virus ; Viral Zoonoses/epidemiology/prevention & control ; Disease Reservoirs/virology ; Chiroptera/virology ; }, abstract = {Henipaviruses, including the highly pathogenic Nipah virus and Hendra virus, represent a major zoonotic threat with high mortality rates and potential for human-to-human transmission. Recent discoveries of novel henipaviruses in China, Europe and other regions highlight the urgent need for enhanced surveillance in both wildlife reservoirs such as bats, shrews, rodents, and human populations, particularly in high-risk areas. Despite advancements in metagenomic sequencing, gaps in integrated surveillance, fragmented One Health implementation, and insufficient diagnostic infrastructure in large parts of the world hinder global preparedness. This paper identifies key challenges in henipavirus detection and control and proposes an operational roadmap for surveillance, diagnostics, and cross-sectoral collaboration. With the known animal hosts of henipaviruses and related henipa-like orthoparamyxoviruses now documented across more than 130 countries and territories, strengthening these capabilities is critical to preventing future epidemics and addressing the evolving threat of emerging henipavirus diversity.}, } @article {pmid41822332, year = {2026}, author = {Xu, Y and Wu, W and Dong, D and Liu, N and Liu, J and Qi, B and Gu, Q}, title = {The value of metagenomic next-generation sequencing in lower respiratory tract infections among critically ill patients in the ICU.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1746117}, pmid = {41822332}, issn = {2235-2988}, mesh = {Humans ; Intensive Care Units ; *High-Throughput Nucleotide Sequencing/methods ; Critical Illness ; *Metagenomics/methods ; *Respiratory Tract Infections/microbiology/diagnosis/virology/mortality ; Retrospective Studies ; Bacteria/genetics/classification/isolation & purification ; Female ; Male ; Sensitivity and Specificity ; Aged ; }, abstract = {Lower respiratory tract infections (LRTIs) frequently occur as a severe complication in intensive care unit (ICU) patients, substantially raising patient mortality rates and extending hospitalization periods. In this study, a retrospective cohort study of 261 suspected LRTI patients in the ICU of Nanjing Drum Tower Hospital between April 2021 and February 2024 was conducted. The results showed that metagenomic next-generation sequencing (mNGS) had a sensitivity of 80.1%, a specificity of 35%, and an accuracy of 66.3% across all samples. For pathogen detection, mNGS outperformed conventional microbiological testing (CMT) in detecting bacteria and DNA viruses, while CMT had a slight advantage in RNA virus detection, though the difference was not statistically significant (p = 0.305). When comparing microbial profiles between survival and death groups, survivors had a more diverse pathogen spectrum, particularly in bacteria and RNA viruses. There were 262 species detected in both groups, with Corynebacterium striatum being the dominant species in the survival group and Pseudomonas aeruginosa in the death group. In the 128 patients whose treatment plans were adjusted based on mNGS results, 59.4% underwent escalation, 25.8% had their medications changed, and 1.6% initiated new treatment regimens. Further follow-up revealed that mNGS - guided treatment adjustments were effective in improving clinical symptoms in 58.6% of ICU patients. A predictive model for patient outcomes was developed utilizing the random forest algorithm, achieving an area under the receiver operating characteristic curve (AUC) of 0.722.}, } @article {pmid41823069, year = {2026}, author = {Savini, F and Indio, V and Prandini, L and Tomasello, F and De Cesare, A and Oliveri, C and Seguino, A and Zanato, E and Serraino, A}, title = {Outside in: assessment of microbial composition of the crust of dry-aged beef and its relevance in relation to food business operator practices.}, journal = {Italian journal of food safety}, volume = {15}, number = {2}, pages = {}, pmid = {41823069}, issn = {2239-7132}, abstract = {Dry aging of beef has recently been defined in Delegated Regulation 2024/1141, amending Regulation 853/2005. The delegated regulation lists specific measures to be applied when processing such a product. Specifically, a point is dedicated to the crust trimming that should be carried out in a hygienic manner, since the interventions performed at the end of the process might determine contamination of the edible parts. Nevertheless, despite the punctual application of good hygiene practices (GHP) and good manufacturing practices (GMP), a certain degree of contamination with pathogenic and spoilage microorganisms of the cut portions cannot be avoided, as demonstrated by some authors reporting contamination of the inner parts of dry-aged meat. In order to investigate the level of contamination occurring in field conditions during trimming and portioning, we performed two different trials: the sterility trial with the aim of evaluating the sterility of the inner parts of beef during aging, and the contamination trial to assess the transfer of microbial populations from the outer to the inner part of the dry-aged beef. All tests were performed by means of cultural and non-cultural methods. Results of the sterility trial show that a very limited percentage of non-host DNA is present in the inner parts of the meat starting from the beginning of the test, and that the detectable DNA increases slightly during the time of aging. Besides, the contamination trial results showed that the contamination of the trimmed meat is qualitatively and quantitatively related to the contamination of the crust. As a consequence, adherence to GHP and GMP during trimming and handling of dry-aged meat according to scientific literature is crucial to avoid/minimize cross-contamination since our data clearly demonstrate that processing practices are fully reflected in the final product quality.}, } @article {pmid41823302, year = {2026}, author = {Al, KF and Jia, S and Silverman, M and Reid, G and Burton, JP and Parvathy, SN}, title = {Prebiotic modulation of FMT donor microbiota enhances MASLD-relevant taxa and functions in an in vitro gut model.}, journal = {Journal of applied microbiology}, volume = {137}, number = {4}, pages = {}, doi = {10.1093/jambio/lxag074}, pmid = {41823302}, issn = {1365-2672}, support = {//Lawson/ ; //Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Prebiotics/analysis ; Humans ; Inulin/metabolism ; *Gastrointestinal Microbiome/drug effects ; Oligosaccharides/pharmacology ; *Fecal Microbiota Transplantation ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Glucuronates ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Fatty Acids, Volatile/metabolism ; }, abstract = {AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD, formerly non-alcoholic fatty liver disease) is a prevalent and progressive condition closely linked to gut microbiota composition. Fecal microbiota transplantation (FMT) may help restore a health-associated microbiome, but its efficacy is often limited by inconsistent engraftment of beneficial taxa. Prebiotics may selectively support keystone microbes associated with reduced MASLD risk. This study evaluated two prebiotics, inulin and xylooligosaccharides (XOS), for their ability to modulate the microbiota of healthy FMT donors in an in vitro gut model, focusing on enriching beneficial taxa and functions associated with MASLD resilience.

METHODS AND RESULTS: Stool from eight clinically qualified FMT donors was cultured anaerobically for 24 h with or without prebiotics. Microbiota composition was assessed by 16S rRNA gene sequencing and short-chain fatty acid (SCFA) concentrations were measured using nuclear magnetic resonance. Functional potential was inferred using predictive metagenomic analysis. Prebiotic responses were highly donor-specific, yet both inulin and XOS consistently enriched Bifidobacterium and Bacteroides-genera associated with SCFA production and metabolic health. XOS preferentially enriched Lactobacillus and Parabacteroides, while inulin enhanced Holdemanella and Mediterraneibacter. Functional pathways relevant to MASLD pathophysiology were enriched, including carbohydrate metabolism, vitamin biosynthesis, fatty acid metabolism, and tryptophan degradation. Both prebiotics significantly increased acetate levels, while butyrate showed a donor-dependent increasing trend.

CONCLUSIONS: These findings suggest that prebiotic supplementation can selectively enrich MASLD-relevant microbial taxa and functions in donor-derived FMT material, supporting their potential as adjuvants to enhance the efficacy and disease-specificity of FMT interventions for MASLD.}, } @article {pmid41823408, year = {2026}, author = {Thorn, AV and Brinch, C and Aarestrup, FM and Munk, P}, title = {Urban sewage resistomes partially reflect clinical resistomes.}, journal = {mSystems}, volume = {11}, number = {4}, pages = {e0003126}, pmid = {41823408}, issn = {2379-5077}, support = {NNF16OC0021856//Novo Nordisk Foundation/ ; 874735//Horizon 2020 Framework Programme/ ; }, mesh = {*Sewage/microbiology ; Humans ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects/isolation & purification ; *Metagenome ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Cities ; }, abstract = {Antimicrobial resistance (AMR) poses a major global public health threat, and ongoing surveillance of antimicrobial resistance genes (ARGs) is critical to mitigate current and future risks. Sewage-based ARG surveillance is gaining traction, but insight into how it compares to surveillance by clinical bacterial isolates is limited, especially when it comes to ARG mutational variants. We compared ARGs identified in clinical bacterial isolates (n = 2,989) with those detected in sewage metagenomes (n = 468) across 33 countries. ARG variant detection data from clinical isolates and sewage metagenomes shared some regional patterns in detection, but many ARG variants were detected exclusively in either sewage metagenomes or clinical isolates. We found that across all samples, only 69% of ARG clusters detected in clinical isolates were also detected via read mapping in sewage. Some ARGs highly prevalent in clinical isolates were not detected in sewage. Among clinically widespread ARGs, prevalence varied across bacterial species and clinical isolate types depending on whether the ARGs were also detected in sewage. This could indicate that sewage surveillance is better suited for detection of clinically relevant ARGs prevalent in certain bacterial species and infection sites than others. Spearman correlation between ARG abundance in sewage and the proportion of clinical isolates from the same country with detection was 0.28 overall, with stronger correlations for certain ARGs. The results demonstrate that sewage ARG profiles correlate, to some extent, to the clinical AMR landscape, but do not capture the full spectrum of clinically relevant ARGs at currently realistic sequencing depths.IMPORTANCEAntimicrobial resistance (AMR) is a major public health threat. Surveillance of AMR is important and can be conducted via the detection of antimicrobial resistance genes (ARGs). Sewage can be used as a medium for surveillance as an alternative to analyzing individual bacterial isolates from health clinics. We compared detection in large global data collections of sewage metagenomes and clinical isolates. We found that while there were significant positive correlations between findings in sewage and clinical isolates, some widespread clinical ARGs were not detectable in sewage. This should be considered if establishing sewage surveillance systems.}, } @article {pmid41823694, year = {2026}, author = {Pessi, IS and Eronen-Rasimus, E and Näkki, P and Thomas, DN and Kaartokallio, H}, title = {Bioplastic biodegradability shapes microbial communities in a coastal brackish environment.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41823694}, issn = {1751-7370}, support = {332174//Research Councils of Finland/ ; }, mesh = {*Seawater/microbiology ; Metagenomics ; Biodegradation, Environmental ; *Bacteria/metabolism/classification/genetics ; *Microbiota ; *Biodegradable Plastics/metabolism ; Gene Expression Profiling ; *Plastics/metabolism ; Cellulose/metabolism/analogs & derivatives ; }, abstract = {Microorganisms are metabolically versatile and central to marine ecosystems, yet the potential of marine microbial communities to degrade different bioplastics and the effect of environmental factors are poorly understood. Employing multi-seasonal in situ and in vitro experiments, we assessed the biodegradation of six commonly used bio-based bioplastic materials at a coastal site in the brackish Baltic Sea and characterized the associated microbial communities using metagenomics and metatranscriptomics. Cellulose acetate (CA), polybutylene succinate (PBS), and polyhydroxybutyrate/valerate (PHB) degraded at varying rates across materials, seasons, and experimental settings, with up to 28% weight attrition after 97 weeks in situ (CA) and 56% carbon loss as CO2 after 4 weeks in vitro (PBS). The three biodegraded plastics developed similar microbial communities that differed markedly from those on the other materials (cellulose acetate propionate, polyamide, and polyethylene) and in the water column. The main microbial populations on the biodegraded plastics included aerobic and facultative anaerobic heterotrophs with a broad capacity for carbohydrate metabolism. Populations with the potential for nitrogen fixation and denitrification were more prevalent on the biodegraded plastics, suggesting that bioplastic biodegradation is constrained by and coupled to the marine nitrogen cycle. Based on the metatranscriptomic signal of key genes involved in the initial hydrolysis of CA, PBS, and PHB, we identified diverse microbial populations that can potentially drive the biodegradation of these materials in the Baltic Sea, many of which encoded the potential to degrade multiple bioplastics. We propose the term 'bioplastisphere' to denote the distinctive microbial communities associated with biodegradable plastics.}, } @article {pmid41824008, year = {2026}, author = {Wen, M and Wang, X}, title = {Diagnostic value of metagenomic next-generation sequencing on bronchoalveolar lavage fluid via radial endobronchial ultrasound for peripheral pulmonary infectious lesions: A retrospective cohort study.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {73}, number = {2}, pages = {211-222}, doi = {10.1556/030.2026.02865}, pmid = {41824008}, issn = {1588-2640}, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; Middle Aged ; Aged ; *Endosonography/methods ; Sensitivity and Specificity ; *Metagenomics/methods ; Bronchoscopy ; Adult ; *Respiratory Tract Infections/diagnosis/microbiology ; }, abstract = {The etiological diagnosis of peripheral pulmonary infectious lesions (PPILs) is challenging due to the limitations of conventional microbiological methods (CMMs). This study aimed to evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) performed on bronchoalveolar lavage fluid (BALF) obtained via radial endobronchial ultrasound (r-EBUS) for PPILs. This single-center, retrospective diagnostic accuracy study enrolled 110 patients with PPILs who underwent r-EBUS-guided BALF between January 2023 and December 2024. BALF samples were subjected to both mNGS and CMMs. The final diagnosis was established by two senior pulmonologists based on a comprehensive review of all clinical data. The diagnostic performance of mNGS and CMMs was compared against this final diagnosis. A definitive diagnosis was established in all 110 patients, with 68 cases identified as infectious lesions and 42 as non-infectious. The sensitivity of mNGS for detecting pathogens in infectious lesions was significantly higher than that of CMMs (89.7% vs. 47.1%, P < 0.001). The overall diagnostic accuracy of mNGS was also superior to CMMs (90.9% vs. 66.4%, P < 0.001). Among patients with positive mNGS results, clinical management was altered in 73.8% of cases based on the findings. mNGS uniquely identified pathogens in 31 cases that were missed by CMMs. For patients with PPILs, mNGS analysis of BALF samples obtained via r-EBUS demonstrates significantly greater diagnostic sensitivity and accuracy than conventional methods. This approach has a substantial impact on clinical decision-making, facilitating targeted antimicrobial therapy and representing a powerful tool in the diagnostic workflow for peripheral pulmonary infections.}, } @article {pmid41824271, year = {2026}, author = {Singh, K and Sambyal, D and Julka, JM}, title = {Metagenomic exploration of bacterial community shifts before, during, and after passage through earthworm Eutyphoeus waltoni.}, journal = {Biologia futura}, volume = {77}, number = {2}, pages = {387-399}, pmid = {41824271}, issn = {2676-8607}, abstract = {Understanding the transformation of soil microbial communities during their passage through the earthworm gut provides essential insights into soil health and ecosystem functioning. In this study, we employed 16S rRNA gene sequencing to investigate the bacterial community dynamics in the surrounding soil, gut, and casts of anecic earthworm Eutyphoeus waltoni, an important ecosystem engineer. This research aims to elucidate the microbial selection and transformation processes that occur as microorganisms pass through the earthworm’s alimentary canal. E. waltoni was selected for its significant role in organic matter decomposition and nutrient cycling within Indian soils. While species like Eisenia fetida and Lumbricus terrestris are well-studied, E. waltoni remains understudied despite its ecological importance. We observed notable shifts in microbial communities across the three microhabitats, primarily composed of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria. The gut environment selectively enriched Firmicutes, particularly Clostridioides, and reduced Proteobacteria. In the cast, microbial recovery was partial, with the presence of genera such as Azospira and Nitrospira, which are linked to nutrient turnover. These findings demonstrate that E. waltoni selectively restructures microbial assemblages, promoting taxa that enhance nutrient cycling and biogeochemical processes.}, } @article {pmid41824493, year = {2026}, author = {De Anda, V and Appler, KE and Aguilar-Pine, E and Aitolo, GL and Halverson, GP and Baker, BJ}, title = {The archaeal roots of eukaryotic life.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {13}, pages = {e2516062123}, pmid = {41824493}, issn = {1091-6490}, support = {73592LPI//Simons Foundation (SF)/ ; LI-SIAME-00002001//Simons Foundation (SF)/ ; }, mesh = {*Archaea/genetics/classification/metabolism ; Biological Evolution ; Phylogeny ; *Eukaryota/genetics ; *Eukaryotic Cells ; }, abstract = {Resolving the biological and geological events that led to the origin of eukaryotes is an ongoing challenge in biology. A major step in the evolution of complex cellular life was the merger between an ancestral host cell and a bacterium (that became the mitochondrion) some two billion years ago. Recently, metagenomics has enabled the reconstruction of a broad diversity of genomes, referred to as the Asgard Archaea. The Asgards are monophyletic with eukaryotes on the tree of life. Asgards have an array of genes, previously thought exclusive to eukaryotes, involved in cellular trafficking, the ubiquitin system, endosomal sorting, and cytoskeleton formation, with growing evidence demonstrating the functions of these proteins mirror those in eukaryotes. This gene repertoire suggests that these Archaea are descendants of the archaeal host from which eukaryotes evolved. Increased sampling has revealed that Asgard lineages are metabolically versatile and play key roles in various ecosystems and uncovered evolutionary transitions between Archaea and eukaryotes, such as innovations in eukaryotic defense systems. The positioning of eukaryotes in the Asgards is debated, but eukaryotes appear to branch within the Heimdallarchaeia. Lineages within this group, particularly Hodarchaeales and Kariarchaeaceae, contain a broad repertoire of eukaryote-like traits, including high-energy yielding metabolisms. Observing and studying Asgard interactions with bacterial descendants of mitochondria in a modern setting will transform our understanding of the origin of complex cellular life.}, } @article {pmid41825203, year = {2026}, author = {Fu, Q and Dai, H and Wang, J and Zheng, S and Zhou, Y and Liu, H and Xu, F and Cheng, C and Jiang, H and Qian, Y and Zhang, S and Liu, L and Zheng, H and Li, Y and Zhang, L and Chen, Y and Cheng, X and Yang, T}, title = {Multi-omics analysis of dynamic profiles in response to various nutrient loads provides novel insights into obesity.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {59}, number = {}, pages = {106607}, doi = {10.1016/j.clnu.2026.106607}, pmid = {41825203}, issn = {1532-1983}, mesh = {Humans ; *Obesity/metabolism/blood/microbiology ; Male ; Female ; Multiomics ; Postprandial Period/physiology ; Adult ; *Nutrients ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Diet ; Metabolomics ; Overweight/metabolism ; Proteomics ; Feeding Behavior/physiology ; }, abstract = {BACKGROUND& AIMS: Obesity is a global health issue driven by improper nutrient intake and metabolic dysregulation. The complexity of dietary components and the dynamic nature of postprandial metabolism limit our understanding of how different nutrient loads associated with obesity. This study aims to characterize the dynamic metabolic responses to nutrient intake using multi-omics approaches, assess the influence of dietary habits and gut microbiota, and evaluate the acute obesity-risk signature (AORS) associated with different macronutrients.

METHODS: We conducted a mixed meal tolerance test (MMTT) in 147 non-diabetic individuals (54 controls, 38 overweight, 55 obese). Blood samples were collected at multiple time points for untargeted metabolomics, lipidomics, proteomics, and hormone assays. Gut microbiota was profiled via metagenomic sequencing. A separate single macronutrient tolerance test (SMNTT) involving glucose, whey protein, butter, and olive oil was performed in 24 healthy volunteers to compare acute metabolic responses and derive an AORS based on postprandial multi-omics data.

RESULTS: Postprandial multi-omic analytes showed stronger associations with obesity indicators than fasting measures. Distinct temporal changes in metabolites, lipids, and proteins were observed across different BMI groups, with enrichment in pathways such as bile acid biosynthesis, triglyceride metabolism, and complement activation. Dietary habits and gut microbiota significantly influenced postprandial metabolic profiles, with specific metabolites and proteins mediating their effects on obesity. In SMNTT, glucose load exhibited the lowest AORS among isocaloric macronutrients (0.1082 ± 0.1917 %). Gut microbiota composition further modulated metabolic responses, with olive oil showing divergent AORS between Bacteroides- and Prevotella-dominated enterotypes (p = 0.043).

CONCLUSION: Postprandial multi-omics provides superior insights into obesity pathophysiology compared to fasting measurements. Our findings reveal that dietary habits and gut microbiota significantly influence postprandial metabolism and obesity risk, and demonstrate that different macronutrients confer distinct AORS values, which are further modified by an individual's gut microbiota composition. This underscores the potential for personalized nutritional strategies based on dynamic metabolic responses and microbial ecology.}, } @article {pmid41825216, year = {2026}, author = {Li, S and Gao, Z and Da, Y and Zhang, Y and Huang, Z and Yuan, G and Wu, C and Huang, T and Sun, Q and Zhou, G}, title = {ESKAPE pathogens contribute largely to antibiotic resistance spread via horizontal gene transfer in aquatic environments.}, journal = {Journal of contaminant hydrology}, volume = {279}, number = {}, pages = {104922}, doi = {10.1016/j.jconhyd.2026.104922}, pmid = {41825216}, issn = {1873-6009}, mesh = {*Gene Transfer, Horizontal ; *Anti-Bacterial Agents/analysis/pharmacology ; *Wastewater/microbiology ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; *Water Pollutants, Chemical/analysis ; *Water Microbiology ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The overuse of antibiotics in human healthcare, livestock, and aquaculture has led to the accumulation of antibiotic residues in aquatic environments. It promotes the dissemination of antibiotic-resistant bacteria (ARB) that pose a threat to public health. However, the mechanisms that shape antibiotic resistance gene (ARG) profiles in different water types remain poorly understood. In this study, three water types, including hospital wastewater, breeding wastewater, and natural waters, were employed. Using a combination of high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS), 16S rRNA gene sequencing, and metagenomic analysis, we found that ofloxacin in hospital wastewater posed the highest ecological risk, whereas norfloxacin and tetracycline in natural waters posed elevated health risks. Among 101 detected ARG subtypes, hospital effluents carried the highest abundances of high-risk ARGs and their host bacteria compared to breeding wastewater and natural waters. Interestingly, mobile genetic elements (MGEs) were the primary direct driver of ARG enrichment (PLS-PM path coefficient = 0.725), in contrast to the negligible contributions from typical antibiotic residues, physicochemical parameters, and microbial community structure. Furthermore, genera associated with ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) dominated the co-hosts of both ARGs and MGEs across all water types. Among these, Enterobacter spp. and Klebsiella pneumoniae were found to co-harbor the most diverse MGEs and multidrug-resistant ARGs. Consequently, this study underscores the critical role of ESKAPE pathogens in the environmental dissemination of ARGs and provides a scientific foundation for targeted antibiotic resistance control and sustainable water resource management.}, } @article {pmid41825251, year = {2026}, author = {Chang, L and Su, X and Hu, W and Fang, Y and Liu, J and Li, J and Huang, L and Shu, W}, title = {Genomic insights into adaptation and microevolution of two novel non-AOA Nitrososphaeria, Acidarchaeum fankouense and Thermosulfuris yongpingense, in acid mine drainage ecosystems.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {3}, pages = {126711}, doi = {10.1016/j.syapm.2026.126711}, pmid = {41825251}, issn = {1618-0984}, mesh = {Mining ; Phylogeny ; Ecosystem ; *Sulfolobaceae/genetics/classification/physiology ; *Genome, Archaeal/genetics ; Metagenome ; Geologic Sediments/microbiology ; *Adaptation, Physiological/genetics ; China ; *Evolution, Molecular ; Oxidation-Reduction ; Acids ; }, abstract = {The class Nitrososphaeria is best known for ammonia-oxidizing archaea (AOA), yet deeply branching non-AOA lineages remain poorly characterized, leaving a critical gap in our understanding of the group's early evolution and ecological diversification. Herein, we recovered 44 non-AOA Nitrososphaeria metagenome-assembled genomes (MAGs) from acid mine drainage (AMD) sediments in diverse metal mines, representing two novel genera within the family Thermosulfuridaceae, Acidarchaeum and Thermosulfuris. A meta-analysis of 251 AMD-associated metagenomes worldwide showed that these potentially thermophilic lineages were detected only in China and were typically rare, with localized blooms (up to ∼7.65%) at a few sites, particularly Fankou lead-zinc mine. Metabolic reconstruction suggested a facultatively anaerobic, mixotrophic lifestyle capable of CO oxidation and sulfur reduction, and extensive acid- and heavy-metal resistance mediated primarily by ether-linked archaeal lipids, ion efflux systems, and enzymatic reduction. Genus-specific traits include dissimilatory sulfate reduction in Thermosulfuris and urea utilization in Acidarchaeum, illuminating distinct ecological niches. Population-genomic analyses reveal low homologous recombination and pervasive purifying selection in these non-AOA populations, together with local relaxation of selection and elevated diversity, the former being correlated with geochemical stressors (notably copper), pointing to long-term, geochemically driven adaptation. Overall, these findings provide insights into the biodiversity, ecophysiology, and evolutionary dynamics of non-AOA Nitrososphaeria.}, } @article {pmid41825425, year = {2026}, author = {Wu, B and Zhai, Y and Li, S and Yang, Y and Cao, D and Wu, W and Yang, J and Huang, T and Zhuang, J}, title = {Oligo-cyanobacterial microalgae-bacteria granular sludge for mitigating cyanotoxin risk: Cultivation, characteristics, and formation mechanism.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129300}, doi = {10.1016/j.jenvman.2026.129300}, pmid = {41825425}, issn = {1095-8630}, mesh = {*Microalgae ; *Sewage/microbiology ; *Cyanobacteria ; }, abstract = {Microalgae-bacteria granular sludge (MBGS) is a promising technology for wastewater treatment, due to its advantage of superior nutrient removal and potential for carbon-neutrality. However, cyanobacteria, which produce cyanotoxins and raise environmental concerns, was prevalent in previously cultivated MBGS. In this study, Oocystis borgei (O.borgei), which could inhibit cyanobacteria in microalgae-bacterial mixed culture (MBMC), was added in inoculum for the oligo-cyanobacterial MBGS cultivation. Flow cytometry and 16S/18S rRNA gene sequencing showed that the abundance of cyanobacteria was maintained at consistently low levels during the cultivation of MBGS. Moreover, the cyanotoxin concentration was only 0.15 μg/g-VSS, which was significantly lower than that in MBGS cultivated with other inoculums. Using autofluorescence-based cell sorting technology (AFCS), we found that the extracellular protein (PN) content of bacteria increased remarkably in the mixed culture with O.borgei, leading to the significant increase of extracellular polymeric substances (EPS) in MBMC. In addition, metagenomic analysis revealed that the abundance of lipoprotein (LPP) directed transport ATPase gene (lolD) and lipopolysaccharide (LPS) transport gene (lptB), key genes associated with EPS secretion, was increased from 493 to 343 fragments per kilobase of transcript per million mapped reads (FPKM) in inoculum to 775 and 548 FPKM in rapid granulation period. Genomic-annotation found that the Proteobacteria, encoded the EPS-producing genes, was dominated in oligo-cyanobacterial MBGS. These results suggested that microalgae could stimulate Proteobacteria to secrete PN, promoting MBGS formation. This work provides an effective approach for oligo-cyanobacterial MBGS cultivation and deep insight into the granulation mechanism, which provides theoretical support for the engineering application of MBGS technology.}, } @article {pmid41825544, year = {2026}, author = {Li, D and Kim, S and Tang, T and Wu, S and Ma, H and Liu, Y}, title = {Thermophilic keystone taxa drive humification in coal gangue co-composting via shikimate-pathway carbon flux.}, journal = {Environmental research}, volume = {298}, number = {}, pages = {124250}, doi = {10.1016/j.envres.2026.124250}, pmid = {41825544}, issn = {1096-0953}, mesh = {*Shikimic Acid/metabolism/analogs & derivatives ; *Composting ; *Soil Microbiology ; *Carbon Cycle ; Coal ; Soil/chemistry ; *Bacteria/metabolism ; Carbon/metabolism ; }, abstract = {Co-composting of coal gangue and organic solid waste is an effective resource utilization method, but systematic understanding of the humification process in co-composting systems remains limited. The study systematically investigated the evolution of humic substances in a coal gangue co-composting system and identified the roles of thermophilic keystone taxa by machine learning models combined with metagenomic analysis in the humification process. The results indicate that maintaining the thermophilic phase is crucial for humification in the coal gangue co-composting system. Experimental groups that maintained a stable thermophilic phase achieved complete humification and produced compost that effectively promoted wheatgrass growth on sandy soil. The key thermophiles (Thermobifida, Thermopolyspora, and Planifilum) are significantly associated with humic substances and the shikimate pathway. These bacteria support the humification process by enhancing the synthetic potential of the shikimate pathway, thereby providing the necessary supply of aromatic precursor substances. This study elucidates the humification process in the coal gangue co-composting and identifies the role of key thermophiles, providing theoretical and practical guidance for the bioutilization of coal gangue and the improvement of desertified soils.}, } @article {pmid41825562, year = {2026}, author = {Li, D and Ravindran, B and Liang, J and Xu, Q and Zhang, J and Yan, X and Yuan, L and Wong, JWC}, title = {Enhancing nitrogen retention in low C/N food waste digestate composting: synergistic effects of biochar and nitrifying inoculation.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134412}, doi = {10.1016/j.biortech.2026.134412}, pmid = {41825562}, issn = {1873-2976}, mesh = {*Charcoal/chemistry/pharmacology ; *Composting/methods ; *Nitrogen/metabolism ; *Nitrification ; Food Loss and Waste ; *Carbon/analysis ; Bacteria/metabolism/genetics ; Nitrous Oxide ; Ammonia ; }, abstract = {Food waste digestate (FWD) composting at low C/N ratios is increasingly applied to enhance treatment capacity, but it is often limited by severe nitrogen (N) loss caused by excessive ammonia (NH3) volatilization, nitrous oxide (N2O) emissions, and delayed nitrification. This study evaluated the individual and combined effects of biochar and a nitrifying bacterial inoculant on N transformation, gaseous emissions, microbial community succession, and functional gene dynamics during FWD composting at an initial C/N ratio of around 15. Results showed that biochar alone reduced total N loss by 33% relative to the control, primarily by suppressing NH3 and N2O emissions through physicochemical adsorption and a higher N2O-reduction potential (e.g., increased nosZ abundance). In contrast, nitrifying inoculation alone accelerated nitrification and compost maturity, but increased N2O emissions due to enhanced nitrifier-denitrification. The combined application of biochar and nitrifiers exhibited a synergistic effect, maintaining high nitrification efficiency while mitigating N2O emissions associated with nitrifier addition. This strategy reduced NH3 emissions by 41%, reduced total N loss by 27% relative to the control, and shortened the composting period required to reach maturity by 14 days. Metagenomic and qPCR analyses revealed that nitrifying inoculation significantly increased amoA and hao abundances, whereas biochar amendment was consistently associated with higher nosZ abundance, suggesting an increased N2O reduction potential. Overall, integrating biochar with nitrifying inoculants offers a promising strategy to enhance nitrogen retention, reduce gaseous emissions, and accelerate maturity during low C/N FWD composting.}, } @article {pmid41825563, year = {2026}, author = {An, M and Yu, J and Lin, X and Lu, Y and Li, X and He, J and Zhao, G}, title = {Multi-stage synthetic microbial consortia outperform single-stage augmentation by remodeling metabolism and mediating function-stability trade-off in anaerobic digestion.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134417}, doi = {10.1016/j.biortech.2026.134417}, pmid = {41825563}, issn = {1873-2976}, mesh = {Anaerobiosis ; Methane/biosynthesis/metabolism ; Bioreactors/microbiology ; *Microbial Consortia/physiology ; Fatty Acids, Volatile/metabolism ; Food Loss and Waste ; }, abstract = {Anaerobic digestion (AD) of food waste often suffers from low methane yield and volatile fatty acids (VFAs) accumulation, primarily due to inefficiencies or imbalances within the native microbial community. To address these metabolic and ecological limitations, we constructed two synthetic microbial communities (SynComs) using a function-driven strategy: a methanogen-only consortium (SynCom-J) and a multi-stage consortium comprising hydrolytic, acidogenic, and methanogenic members (SynCom-YSJ). Both SynComs were introduced into semi-continuous reactors that already harbored a metabolically complete native microbiome, serving as bioaugmentation agents. When fed daily with partially hydrolyzed feedstock containing residual macromolecular organics and short-chain VFAs, SynCom-YSJ consistently outperformed SynCom-J during the entire hydraulic retention time. Compared to the non-bioaugmented control under identical operating conditions, SynCom-YSJ increased methane yield by 22% (vs. 8% for SynCom-J) and nearly eliminated the start-up lag phase, while both consortia reduced propionate accumulation by 1.6-fold. Successful colonization of the SynComs reshaped the AD microenvironment-characterized by elevated acetate, reduced propionate, and a moderate, non-inhibitory increase in total ammonia nitrogen-thereby imposing deterministic selection on the resident community. Metagenomic analysis revealed that SynCom-YSJ triggered broader metabolic reprogramming, upregulating genes involved in hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism, and acetoclastic/hydrogenotrophic methanogenesis. Notably, a trade-off between microbial network stability and process performance emerged: SynCom-J promoted a more robust network, whereas SynCom-YSJ formed a more complex and high-efficiency network that prioritized methane yield. This study demonstrates that coordinated multi-stage bioaugmentation optimizes methanogenesis through targeted metabolic remodeling and provides an ecology-informed design principle for engineering SynComs that balance system performance with stability. These findings highlight the potential of multi-stage bioaugmentation to enhance both functional robustness and system resilience in food waste AD.}, } @article {pmid41825740, year = {2026}, author = {Alvarado, DA and Holthaus, TA and Martell, S and Southey, NL and Atallah, M and Sarma, R and Revilla, D and Brown, M and Mehta, T and Khan, NA and Holscher, HD}, title = {Effects of Soluble Corn Fiber Consumption on Executive Functions and Gut Microbiota in Middle to Older Age Adults: A Randomized Controlled Crossover Trial.}, journal = {The Journal of nutrition}, volume = {156}, number = {5}, pages = {101473}, pmid = {41825740}, issn = {1541-6100}, mesh = {Humans ; Cross-Over Studies ; Double-Blind Method ; *Executive Function/drug effects ; *Dietary Fiber/pharmacology/administration & dosage ; *Zea mays/chemistry ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; Female ; Aged ; Male ; Feces/microbiology ; Cognition/drug effects ; Fermentation ; Cognitive Enhancement ; }, abstract = {BACKGROUND: Dietary fiber may support cognition through gastrointestinal-microbiota mechanisms, but clinical evidence is limited.

OBJECTIVES: We aimed to determine whether soluble corn fiber (SCF) improved cognition and altered fecal microbiota and fermentation end products in adults.

METHODS: In a randomized, double-blind, crossover trial, 42 healthy adults (45-75 y) consumed SCF (18 g/d) or a maltodextrin placebo control (CON: 22 g/d) for 4 wk, separated by a washout. Cognitive outcomes included executive function with event-related potentials, relational memory, neuropsychological performance, and mood. Secondary outcomes included fecal microbiota, metabolomics, and gastrointestinal tolerance. Tertiary analyses related microbial and metabolite changes to cognitive improvements using correlation, mediation, and moderation models, and explored SCF fermentation pathways with 16S-predicted functional profiling, shotgun metagenomics, and in vitro culturing.

RESULTS: SCF improved reaction times (RT) during congruent (β = -9.8 ms, 95% confidence interval (CI): -18.4, -1.2, false discovery rate (FDR) P = 0.01) and incongruent (β = -14.2 ms, 95% CI: -22.8, -5.6, FDR P = 0.003) flanker trials and increased Parabacteroides (∼4-fold, β = 1.44 log, 95% CI: 1.01, 1.88, FDR P < 0.001). At the SCF endpoint, congruent RT tended to be inversely associated with fecal acetate (ρ = -0.33) and propionate (ρ = -0.36), whereas Parabacteroides was marginally positively associated with acetate (ρ = 0.34) (all FDR P < 0.1). Moderation analyses indicated that SCF-RT relation varied by Parabacteroides magnitude change. At endpoint, SCF increased the predicted functional potential of carbohydrate-related KEGG Orthologs and pathways (FDR P < 0.05). In vitro culturing confirmed Parabacteroides distasonis ferments SCF.

CONCLUSIONS: SCF consumption improved attentional inhibition, altered the gut microbiota, and selectively enriched Parabacteroides. Although mediation analyses did not support a direct microbiota-to-cognition pathway, moderation analyses suggested that SCF-related cognitive effects may depend in part on Parabacteroides abundance. Collectively, these findings suggest that certain cognitive benefits of SCF consumption may be partly underpinned by the gut microbiota. This study was registered at clinicaltrials.gov as NCT05066425 (https://clinicaltrials.gov/study/NCT05066425).}, } @article {pmid41826827, year = {2026}, author = {Duduk, B and Galic, I and Stanojević, N and Stankovic, N and Rekanović, E}, title = {Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41826827}, issn = {1471-2180}, support = {451-03-136/2025-03/200214//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 451-03-136/2025-03/200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; }, abstract = {BACKGROUND: Phloem-sap-feeding planthopper Reptalus artemisiae is an emerging vector of rubbery taproot disease (RTD) and syndrome basses richesses (SBR) in sugar beet, diseases associated with 'Candidatus Phytoplasma solani' and 'Candidatus Arsenophonus phytopathogenicus', respectively. Despite studies on related cixiids, the microbiome of R. artemisiae remains uncharacterized. Using a PCR-free metagenomic long-read shotgun sequencing approach, this study investigates the bacterial diversity associated with R. artemisiae, and provides genomic insight into two plant pathogens 'Ca. P. solani' and 'Ca. A. phytopathogenicus'.

RESULTS: Taxonomic assignment revealed six prokaryotic taxa in R. artemisiae: two plant pathogens ('Ca. P. solani' and 'Ca. A. phytopathogenicus') and four insect endosymbionts – three primary endosymbionts ('Candidatus Vidania', 'Candidatus Purcelliella', and 'Candidatus Karelsulcia') and a secondary endosymbiont (Wolbachia). Community profiles showed a consistent presence of all four endosymbionts across five evaluated R. artemisiae individuals. Phylogenetic analyses of 16S rRNA gene sequences of primary endosymbionts confirmed strong congruence with the cytochrome oxidase subunit I phylogeny of the insect host, indicative of long coevolution and vertical transmission. In contrast, plant pathogen presence in R. artemisiae varied, with 'Ca. P. solani' and 'Ca. A. phytopathogenicus' each detected in three individuals. Genome assembly yielded a complete 774 kb circular chromosome for 'Ca. P. solani' with streamlined metabolism featuring limited biosynthetic pathways, but a full arsenal of genes related to host–pathogen interactions and pathogenicity typical for this biotrophs. The draft genome of 'Ca. A. phytopathogenicus' comprising 18 scaffolds totalling 3.11 Mb and two plasmids shows a self-sufficient metabolism with several missing metabolic modules and presence of genomic islands, virulence factors, and a dynamic mobilome indicating a bacterium in transition that is reorganizing its genetic material, possibly in response to host interactions.

CONCLUSION: These findings represent the first in-depth characterization of R. artemisiae microbiome, highlighting a stable endosymbiont consortium and variable pathogen presence that emphasize ecological complexity in vector-pathogen-endosymbiont interactions. The assembled genomes enhance the understanding of microbial ecology, pathogen adaptation and transmission, offering resources for comparative genomics and potential applications in disease management strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04915-x.}, } @article {pmid41826873, year = {2026}, author = {Wang, X and Tian, W and Tian, X and Qin, X and Ma, Y and Yang, T and Cao, S and Wu, L and Feng, H and Ma, B}, title = {Metagenomic analysis of wolfberry branch substrates under tomato cultivation without additional nitrogen fertilization.}, journal = {BMC plant biology}, volume = {26}, number = {1}, pages = {}, pmid = {41826873}, issn = {1471-2229}, support = {32160706//National Natural Science Foundation of China/ ; 2023GKLRLX09//Science and Technology Innovation Leading Talent Program of Ningxia Hui Autonomous Region/ ; }, abstract = {BACKGROUND: Under conditions without additional nitrogen fertilization, nitrogen availability in organic substrate–based horticultural systems depends largely on microbially mediated mineralization processes within the plant–substrate system. Woody agricultural wastes such as wolfberry (Lycium barbarum L.) branches contain substantial organic nitrogen pools and are increasingly used as cultivation substrates. However, how crop cultivation, particularly tomato as a representative horticultural crop, influences rhizosphere nitrogen cycling and microbial functional structure in such substrates remains poorly understood.

RESULTS: A wolfberry branch-derived organic substrate was used without additional nitrogen fertilization; nitrogen supply relied entirely on mineralization of substrate-derived organic nitrogen. Two treatments were established: tomato cultivation (NZP) and no cultivation (NZNP). Tomato cultivation significantly increased ammonium nitrogen (NH₄⁺–N), organic nitrogen, and net nitrogen mineralization rates, while suppressing nitrate (NO₃⁻–N) accumulation. Urease activity was enhanced, whereas protease and sucrase activities declined, indicating a shift away from inorganic nitrogen dependence toward sustained organic nitrogen mineralization. Metagenomic analysis indicated shifts in community functional potential, with higher relative abundances of copiotrophic taxa (e.g., Proteobacteria and Bacteroidota) and increased relative abundance of nitrogen-transforming genera such as Thauera. The relative abundances of nirA and amoA showed statistically significant differences between treatments, whereas other nitrogen-cycling genes exhibited non-significant trends. Redundancy and correlation analyses identified pH, NH₄⁺–N, and microbial biomass nitrogen as key drivers shaping microbial community structure and nitrogen cycling functions.

CONCLUSIONS: Tomato cultivation significantly altered rhizosphere microbial community structure and nitrogen cycling functional profiles in wolfberry branch substrates under conditions without additional nitrogen fertilization. The observed increase in organic nitrogen mineralization and reduced nitrate accumulation suggest a potential shift in nitrogen transformation patterns; however, these findings reflect functional potential inferred from metagenomic analysis rather than directly measured nitrogen retention processes. These findings provide mechanistic insight into plant–microbe interactions that support efficient nitrogen use in organic substrate-based horticultural systems.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-026-08573-z.}, } @article {pmid41826874, year = {2026}, author = {Wang, H and Fu, Y and Xu, H and Song, X and Huang, S and Chen, Y and Xu, J and Li, W and Zhang, J and Wu, P and Shen, Q and Yang, S and Wang, X and Liu, Y and Ji, L and Li, Y and Yang, H and Tang, J and Zhou, C and Zhang, W}, title = {Viromic profiling of amniotic fluid reveals distinct viral communities associated with maternal health status.}, journal = {BMC pregnancy and childbirth}, volume = {26}, number = {1}, pages = {}, pmid = {41826874}, issn = {1471-2393}, support = {No. 2023YFD1801300//National Key Research and Development Programs of China/ ; no. 82341106//National Natural Science Foundation of China/ ; JSYGY-1-2023-03(03)//Hospital Management Innovation Research Project of Jiangsu Provincial Hospital Association/ ; Nos. SH2023058, SH2022092 and SH2024091//Social Development Projects in Zhenjiang/ ; }, abstract = {BACKGROUND: Amniotic fluid is a critical compartment in pregnancy; however, its virome remains poorly characterized, and potential associations with maternal–fetal health are largely unexplored. This study aimed to comprehensively profile the human amniotic fluid virome and explore its association with maternal health status during pregnancy. METHODS: We performed viral metagenomic sequencing of 515 amniotic fluid samples from 515 pregnant women in Changzhou, China, including healthy pregnancies (n = 275) and pregnancies with complications (n = 240). Viral sequences were identified using a bioinformatics pipeline, and phylogenetic analyses were used to assess genetic relationships. RESULTS: We identified diverse viral sequences, including members of viral families such as Anelloviridae and Paramyxoviridae. BLAST-based nucleotide comparisons showed high nucleotide identity to previously reported viruses, indicating that many detected sequences are closely related to known viruses. Phylogenetic analyses further supported their placement within established viral taxa. Community-level analyses indicated differences in virome composition profiles between the healthy control and disease groups. CONCLUSIONS: Our findings describe a previously undercharacterized virome in human amniotic fluid. This study establishes a basis for future investigations into the origins and potential associations of these viral signatures with pregnancy health, highlighting the importance of assessing their clinical relevance for both maternal and neonatal outcomes. Because metagenomic sequencing detects viral nucleic acids, these findings do not establish viral infectivity or causality.}, } @article {pmid41826937, year = {2026}, author = {Ma, X and Zhang, R and Zuo, L and Liang, X and Geng, J and Xia, Y}, title = {When cough leads to infarction: systemic arterial embolism as a sentinel complication of insidious pulmonary mucormycosis in an immunocompetent patient.}, journal = {BMC pulmonary medicine}, volume = {26}, number = {1}, pages = {}, pmid = {41826937}, issn = {1471-2466}, support = {2024YFC2309202//National Key Research and Development Program of China/ ; 202402AA310055//Yunnan Provincial Department of Science and Technology Major Science and Technology Special Program/ ; }, abstract = {BACKGROUND: Pulmonary mucormycosis is a rapidly progressive and often fatal invasive fungal infection typically associated with immunocompromised states. However, its emergence in immunocompetent individuals is increasingly reported. This case describes an unusual presentation of pulmonary mucormycosis in an immunocompetent adult complicated by arterial embolism, a rare and life-threatening vascular manifestation. CASE PRESENTATION: We report the case of an immunocompetent adult patient presenting with persistent respiratory symptoms and radiological abnormalities. Despite the absence of conventional risk factors, the diagnosis was challenging due to nonspecific clinical features. The clinical course was further complicated by the development of an arterial embolism. The pathogen was successfully identified through metagenomic next-generation sequencing (mNGS), highlighting the utility of molecular diagnostic platforms for early detection in atypical hosts. The patient’s management required a combination of targeted antifungal therapy and intervention for the vascular complication. CONCLUSIONS: This case underscores the shifting epidemiology of mucormycosis and the necessity of maintaining a high index of clinical suspicion even in patients without apparent immunodeficiency. It emphasizes the critical role of advanced diagnostic tools like mNGS in reducing delays in intervention for a disease with mortality rates exceeding 30%–50%. Further research is required to standardize diagnostic algorithms and management strategies for pulmonary mucormycosis in immunocompetent populations.}, } @article {pmid41827056, year = {2026}, author = {Chen, X and Xu, X and Lin, Y and Shi, X and Wang, D and Zhang, T}, title = {Pilea: profiling bacterial growth dynamics from metagenomes with sketching.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41827056}, issn = {2049-2618}, support = {T21-705/20-N//University Grants Committee/ ; }, mesh = {*Bacteria/growth & development/genetics/classification ; *Metagenome ; Software ; *Metagenomics/methods ; *Computational Biology/methods ; Microbiota ; }, abstract = {BACKGROUND: Quantifying bacteria's growth rates is essential for understanding their ecological roles and for building predictive models in environmental and clinical settings. Peak-to-trough ratios (PTRs) derived from shotgun metagenomes offer a culture-independent proxy for in situ growth rates of bacterial species, yet their reliable computation remains challenging.

RESULTS: We introduce Pilea (https://github.com/xinehc/pilea), an alignment-free, sketching-based method that incorporates statistical models for robust PTR estimation. Pilea achieves speed improvements over existing methods while also enhancing accuracy, as demonstrated on both simulated and real datasets.

CONCLUSIONS: By scaling efficiently to comprehensive reference collections such as the Genome Taxonomy Database (GTDB), Pilea enables large-scale analyses of bacterial growth dynamics across biomes, unlocking new insights for ecological research. Video Abstract.}, } @article {pmid41827064, year = {2026}, author = {Yu, S and Yue, X and Yang, Q and Xu, P and Yuan, H and Tang, W and Luan, Y and Wang, Q}, title = {Omics integration reveals how the gut microbiota of Warmblood horses responds to equestrian show jumping-a short-duration, high-intensity technical exercise stress.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41827064}, issn = {2524-4671}, abstract = {BACKGROUND: Intestinal microbial homeostasis and metabolic balance play a crucial role in maintaining normal physiological function in horses. Exogenous stress involving abrupt turns and jumps during show jumping significantly impacts intestinal microbial homeostasis and metabolic balance in these animals.

RESULTS: By comparing rectal (faecal) samples from 10 Warmblood horses collected before and immediately after a show jumping competition on the same day, we observed substantial alterations in intestinal microbial homeostasis and metabolic balance post-exercise. Microbial evenness significantly increased following the competition, accompanied by enrichment of specific taxa such as Bacteroides, Ruminococcus, Prevotella, and Fibrobacter. Metabolite analysis revealed a marked decrease in antioxidant-related compounds, including orsellinic acid, 2,3-dimethyl-2-cyclohexen-1-one, and (1 R,6 R)-1,4,5,5a,6,9-hexahydrophenazine-1,6-dicarboxylate. Conversely, glucosan and thiamine pyrophosphate levels increased. Post-competition, membrane lipid metabolism pathways were significantly downregulated, while antioxidant responses and energy metabolism pathways were upregulated. Spearman correlation analysis indicated positive associations between Fibrobacter, Ruminococcus, and Prevotella with energy metabolism-related metabolites, whereas Lysinibacillus correlated positively with metabolites involved in antioxidant activity and intestinal mucosal protection.

CONCLUSION: Collectively, our findings demonstrate that show jumping induces shifts in intestinal microbial homeostasis and metabolic balance in Warmblood horses. These adaptations appear conducive to preserving epithelial integrity and enhancing energy provision to meet the demands of high-intensity exercise. This study provides novel insights into the impact of acute high-intensity exercise on equine gut microbial dynamics and metabolism, offering a theoretical basis for probiotic-based interventions to support intestinal health in sport horses.}, } @article {pmid41827072, year = {2026}, author = {Takkar, B and Maddheshiya, A and Adhikary, P and Reddy, VA and Majumder, PP and Mukherjee, S and Das, T and , }, title = {Gut microbiome changes in people with diabetic retinopathy in India. DRMS-India report # 1: operational protocol and trends from first 100 participants.}, journal = {Gut pathogens}, volume = {18}, number = {1}, pages = {}, pmid = {41827072}, issn = {1757-4749}, abstract = {BACKGROUND: Diabetic retinopathy (DR) is a common microvascular complication of diabetes mellitus (DM), and the leading cause of vision impairment and blindness. India is among the top three countries in DM prevalence, and both DM and DR are projected to rise sharply in the future. There is no accepted strategy for the prevention of DR other than DM control. Recent studies suggest that DM is associated with alterations in a core group of gut microbiota, and progression to DR may be influenced by changes within this core group, highlighting a potential link between DR and gut microbiome. We studied these changes in a protocol-driven large case-control study, the Diabetic Retinopathy Microbiome Study-India (DRMS-India: CTRI/2024/02/062511), analysed the results of the first 100 individuals, and evaluated variations in gut microbiome in DR.

METHODS: The DRMS is designed to recruit 462 people aged ≥ 30 years into three cohorts: healthy controls (HCs), DM, and DR, at 17 independent sites in India. Shotgun metagenomic sequencing of first-pass morning fecal samples is performed at a centralized laboratory and correlated with disease status, lifestyle, dietary, and systemic factors.

RESULTS: The first 100 participants included 26 HC, 33 DM, and 41 DR. The trends showed the DR group had 1, 6, and 10 unique core phyla, genera, and species, respectively. Alpha diversity was highest in the DR group; Beta diversity plots showed separate clusters of HCs and DR, with DM overlapping both. Firmicutes (highest in DR), Proteobacteria (highest in DM), Bacteroidetes, and Actinobacteria (highest in HC) were common phyla. Segatella was the most common genus, and Segatella copri was the most common species across all groups to date. Most microbial gene families were annotated to Molecular Functions (MF), and the pathways attributed to carbohydrate, amino acid, lipid, and nucleotide metabolism, indicating distinct functional adaptations in their gut microbiome.

CONCLUSION: Trends from the first 100 individuals indicate that the gut microbiome of Indians with DR exhibits discriminatory features in microbial diversity and abundance, as well as in gene families and pathways that impact host gut metabolism. Data trends from DRMS-India indicate a region-specific non-invasive biomarker that may guide preventive therapy for DR.}, } @article {pmid41827905, year = {2026}, author = {Braile, A and Bani, A and Hosseininasab, SF and Regno, ND and Orabona, N and Bove, A and Braile, M}, title = {Profiling Osteoporosis via Integrated Multi-Omics Technologies.}, journal = {Cells}, volume = {15}, number = {5}, pages = {}, pmid = {41827905}, issn = {2073-4409}, mesh = {Humans ; *Multiomics ; *Osteoporosis/metabolism/genetics ; Proteomics/methods ; Metabolomics ; Biomarkers/metabolism ; Epigenomics ; }, abstract = {BACKGROUND: Osteoporosis is a complex disorder involving bone loss and muscle degeneration. Multi-omics technologies provide novel insights into its molecular mechanisms and may support biomarker discovery, patient stratification, and therapeutic development.

OBJECTIVE: This scoping review aimed to synthesize current evidence on the application of multi-omics approaches in osteoporosis, focusing on molecular insights, methodological diversity, and translational potential.

METHODS: A literature search of PubMed, Embase, and Scopus retrieved 433 records using the keywords "osteoporosis," "osteosarcopenia," and "omics." After removing duplicates and screening titles, abstracts, and full texts, 30 studies met the inclusion criteria. Data on study populations, biological samples, multi-omics techniques, and integration methods were extracted.

RESULTS: Studies employed transcriptomics, proteomics, metabolomics, lipidomics, epigenomics, and metagenomics, often combined in multi-omics analyses with computational modeling. Key pathways included osteoclast differentiation, immune regulation, ferroptosis, and microbiome-metabolite interactions. Multi-omics integration enabled the identification of molecular subtypes, candidate biomarkers, and potential therapeutic targets. Limitations included small or single-center cohorts, heterogeneous designs, and limited validation, restricting generalizability and clinical translation.

CONCLUSIONS: Multi-omics approaches offer a powerful framework to uncover the molecular mechanisms underlying bone and muscle degeneration and to guide precision diagnostics and interventions. Future studies should prioritize large, multicenter, longitudinal designs integrating multi-omics data with clinical and functional validation to facilitate clinical application.}, } @article {pmid41828538, year = {2026}, author = {Chen, J and Xu, Y and Liu, Z}, title = {Enzymatic Synergy-Driven Biotransformation Generates a Postbiotic-Rich Functional Matrix That Reprograms Gut Microbiota Metabolic Pathways Under Stress Conditions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828538}, issn = {1422-0067}, mesh = {Animals ; Biotransformation ; *Stress, Physiological ; *Gastrointestinal Microbiome/physiology ; Fermentation ; Mice ; *Metabolic Networks and Pathways ; Metabolomics/methods ; Lactiplantibacillus plantarum/metabolism ; }, abstract = {The physiological efficacy of plant-based matrices is often limited because bioactive compounds are sequestered within complex lignocellulosic architectures, restricting their release and downstream activity. Fermentation-driven enzymatic biotransformation can overcome these structural barriers; however, the mechanisms by which fermentation-derived, non-viable functional ingredients (postbiotics) confer benefits remain incompletely defined. Here, we examined whether a postbiotic-rich, co-fermented plant matrix enhances host resilience under metabolic stress and whether such effects are accompanied by a remodeling of gut microbial functional capacity. A functional plant matrix was produced by solid-state co-fermentation using two Lactobacillus plantarum strains selected for complementary lignocellulolytic profiles. Untargeted metabolomics and deep shotgun metagenomic sequencing were integrated with a hydrocortisone-induced murine metabolic stress model to quantify substrate remodeling, host neuroendocrine/behavioral outcomes, and microbiome functional reprogramming. Co-fermentation markedly remodeled the phytochemical landscape, increasing extractable flavonoids and generating distinct metabolite clusters. In vivo, administration of the postbiotic-rich matrix partially normalized stress-responsive neuroendocrine markers (ACTH, TRH, and testosterone) and improved behavioral outcomes in open-field and forced swim assays. These systemic changes were paralleled by a coordinated shift in microbial functional potential, including the enrichment of carbohydrate-active enzyme (CAZyme) families involved in complex polysaccharide utilization (e.g., AA9, GH129, CE14) and attenuation of phosphotransferase system modules and cytochrome P450-related functions. Enzymatic synergy-driven biotransformation yields a postbiotic-rich functional matrix that is associated with a selective remodeling of gut microbiome metabolic potential under stress and concomitant improvement in host physiological resilience. This study underscores microbial functional remodeling as a critical mechanistic interface linking fermentation-modified substrates to host physiological recovery, providing a molecular framework for the development of targeted postbiotic interventions.}, } @article {pmid41828642, year = {2026}, author = {Sadurski, J and Ostrowska, M and Staniszewski, A and Waśko, A}, title = {Genomic Plasticity and Functional Reweighting Facilitate Microbial Adaptation During the Ripening of Artisanal Goat Cheese.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828642}, issn = {1422-0067}, mesh = {*Cheese/microbiology ; Animals ; Goats ; Metagenome ; *Genome, Bacterial ; *Adaptation, Physiological/genetics ; Metagenomics/methods ; Food Microbiology ; Phylogeny ; }, abstract = {This study presents a genome-resolved shotgun metagenomic analysis of artisanal raw-milk goat cheese from the Masurian region of Poland, addressing the limited understanding of strain-level diversification and functional restructuring during traditional cheese ripening. While microbial succession in cheese has been widely described, comprehensive genome-resolved analyses integrating strain-level genomic heterogeneity, pathway reweighting, and mobile genetic elements in artisanal goat cheese remain scarce. By combining taxonomic profiling with metagenome-assembled genome (MAG) reconstruction and pathway-level functional analysis, we characterised microbial succession and genome plasticity across ripening stages. Genome reconstruction yielded 37 MAGs during early ripening and 141 MAGs in mature cheese, revealing increased genome recoverability and pronounced strain-level heterogeneity within dominant taxa, including Lactiplantibacillus plantarum, Lacticaseibacillus paracasei, and Lactococcus lactis. Alpha diversity increased in mature samples, consistent with progressive community restructuring. Functional profiling demonstrated coordinated metabolic reweighting, particularly within carbohydrate metabolism, while amino acid and lipid metabolism remained proportionally stable. Genome-resolved analyses further identified tetracycline- and sulfonamide-associated resistance determinants and diverse bacteriophages targeting lactic acid bacteria, highlighting the role of mobile genetic elements in horizontal gene transfer and microevolutionary adaptation during ripening.}, } @article {pmid41828944, year = {2026}, author = {Xu, S and Zhang, B and Liang, W and Jia, M and Guo, X and Su, B and Wang, R and Pan, Y and Lin, Y and Li, X and Hu, D and Yan, D}, title = {Comparative Analysis of Gut Microbiota and Metabolome of Captive Male Malayan Pangolins with Normal and Abnormal Reproduction.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {5}, pages = {}, pmid = {41828944}, issn = {2076-2615}, support = {1(2024GXNSFBA010369);2(Forestry Science No. 202301);3(JA-23-03-01); 5(2024RT05)//1Guangxi Natural Science Foundation;2Basic Research Project of Guangxi Forestry Research Institute; 3Key Laboratory Project of Guangxi Characteristic Economic Forest Cultivation and Utilization;4Guangxi's first batch of Young Talents Support Program (Natu/ ; }, abstract = {Ex-situ conservation and captive breeding are important measures for protecting endangered species. However, captive conditions inhibit reproduction in some wild animals, especially males. Under captive conditions, which differentially expressed microbiota and metabolites significantly influence or are key to reproductive performance? This study aimed to investigate the effects of differentially expressed microbiota and metabolites on reproductive performance, including male Malayan pangolins with normal reproductive behavior (NR, with natural mating behavior) and those with abnormal reproductive behavior (AR, without natural mating behavior). Five male Malayan pangolins with normal reproductive behavior and eight with abnormal reproductive behavior were divided into NR and AR groups. Fresh fecal samples were collected for metagenomic and metabolomic analysis. The results showed that Bacillota, Pseudomonadota, Bacteroidota, Actinomycetota, and Fusobacteriota were the dominant phyla. Escherichia, Lactobacillus, Lactococcus, Limosilactobacillus, and Ligilactobacillus were the dominant genera. The abundance of Absiella, Butyribacter, and Candidatus Scatovivens in the gut of the NR group was significantly higher than in the AR group (p < 0.05), while the abundance of Clostridium, Mycoplasmopsis, and Facklamia in the gut of the AR group was significantly higher than in the NR group. A total of 94 differentially expressed metabolites were identified, with Argininosuccinic acid and Cortol significantly upregulated in the AR group, and gamma-Aminobutyric acid and gamma-Glutamylglutamic acid significantly downregulated. These microbiota and metabolites can be screened as potential key biomarkers that might influence the reproductive performance of male pangolins. These findings provide important insights into the husbandry and management of captive pangolins and other endangered wild animals.}, } @article {pmid41829143, year = {2026}, author = {Song, D and Song, L and Luo, Y and Chen, J and Zhang, C and Yang, L}, title = {Innovative Systems Biology in Baijiu Fermentation: Unveiling Omics Landscapes and Microbial Synergy.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {41829143}, issn = {2304-8158}, support = {NSFC 32460269//National Natural Science Foundation of China/ ; QianKeHeJiChu- ZD[2025]018//Guizhou Provincial Basic Research Program (Natural Science)/ ; MTXYTD202501//The Science and Technology Innovation Team of Maotai Institute/ ; mygccrc[2022]011//Research Foundation for Scientific Scholars of Moutai Institute/ ; mygccrc [2022]013//Research Foundation for Scientific Scholars of Moutai Institute/ ; mygccrc [2022]026//Research Foundation for Scientific Scholars of Moutai Institute/ ; XYNJ20240104//Moutai Institute & Guangdong Li'er'an Chemical Group Co., Ltd./ ; }, abstract = {The production of Chinese Baijiu relies on the synergistic metabolism of multi-species microbial communities in an open environment. Its intricate microbial succession and flavor formation mechanisms have long been considered complex systems that are difficult to fully deconstruct. Traditional culture-dependent techniques inherently fail to comprehensively capture the actual functional roles and dynamic regulation of "viable but non-culturable" (VBNC) microorganisms within this complex system. In recent years, the rapid advancement of multi-omics technologies has offered a novel perspective for elucidating the underlying fermentation mechanisms of Baijiu. This paper systematically reviews the recent progress in the application of metagenomics, metatranscriptomics, metaproteomics, and metabolomics in Baijiu research. Specific focus is placed on the unique contributions of these tools to resolving microbial community structural diversity, mining key functional genes and enzymes, uncovering microbial stress response mechanisms under environmental fluctuations, identifying phages and spoilage microorganisms, and tracing the metabolic pathways of flavor substances. Furthermore, the pivotal role of multi-omics integration strategies in constructing "microbe-metabolite" regulatory networks is highlighted. Finally, current challenges regarding standardization and data integration are discussed, with an outlook on leveraging omics big data to promote digital monitoring and intelligent brewing in the Baijiu industry.}, } @article {pmid41829938, year = {2026}, author = {Kroplewski, B and Przybyłowicz, KE and Sawicki, T and Przemieniecki, SW}, title = {Supplementation with Animal- and Plant-Derived Proteins Modulates the Structure and Predicted Metabolic Potential of the Gut Microbiota in Elite Football Players.}, journal = {Nutrients}, volume = {18}, number = {5}, pages = {}, pmid = {41829938}, issn = {2072-6643}, support = {MEiN/2023/DPI/2862//Minister of Science Republic of Poland/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Dietary Supplements ; Male ; Whey Proteins/administration & dosage ; Oryza ; Pea Proteins/administration & dosage ; *Plant Proteins/administration & dosage ; Young Adult ; *Athletes ; Animals ; Resistance Training ; Adult ; Bacteria/classification/metabolism ; Soccer ; RNA, Ribosomal, 16S/genetics ; *Football ; }, abstract = {BACKGROUND/OBJECTIVES: The primary outcome of this 8-week randomized, controlled, parallel trial was to assess longitudinal shifts in gut microbiota structure and predicted metabolic potential in 45 elite football players following protein supplementation.

METHODS: Participants combined resistance training with daily intake (30 g) of whey protein concentrate (WPC), pea protein isolate (PPI), rice protein isolate (RPI), or a plant-protein blend (MIX). For the acquisition of prokaryotic metataxonomic data, the V3-V8 region of the 16S rRNA gene was sequenced using Oxford Nanopore Technology (ONT). Functional potential was inferred through the MACADAM database and STAMP software. Strict dietary monitoring and gravimetric adherence checks were performed to isolate the intervention effect.

RESULTS: While microbial alpha-diversity indices (Chao1, Shannon, Simpson) remained stable across all groups, significant source-specific shifts in taxonomic structure and predicted metabolic activity were identified. Whey protein concentrate (WPC) was associated with an increase in Bacteroidetes abundance and greater balance within the microbial community structure, whereas pea protein isolate (PPI) and the MIX correlated with reduced fermentative bacteria and elevated taxa potentially involved in cadaverine biosynthesis. Rice protein isolate (RPI) supplementation was associated with a higher predicted representation of taxa involved in succinate-to-butyrate fermentation pathways. These functional markers and differential responses of selected bacterial groups to particular protein types were observed.

CONCLUSIONS: The data indicate complex interactions between supplement type, exposure duration, and microbiome response, underscoring the necessity for individualized dietary recommendations and supplementation strategies to optimize gut health and training adaptation in professional football players.}, } @article {pmid41830297, year = {2026}, author = {Chen, W and Zhang, L and Zhang, W}, title = {Integrated multi-omics elucidates the microbial-metabolite interplay governing antioxidant capacity in mung bean sour liquid.}, journal = {Journal of the science of food and agriculture}, volume = {106}, number = {8}, pages = {4978-4993}, doi = {10.1002/jsfa.70579}, pmid = {41830297}, issn = {1097-0010}, support = {262102111058//Department of Science and Technology of Henan Province, P.R. China/ ; }, mesh = {*Antioxidants/metabolism/analysis/chemistry ; Multiomics ; Fermentation ; *Fermented Foods/analysis/microbiology ; *Vigna/microbiology/metabolism/chemistry ; *Lactobacillus/metabolism/genetics ; Metabolomics ; Metagenomics ; }, abstract = {BACKGROUND: Mung bean sour liquid (MBSL) is a traditional fermented food, yet the microbial-metabolic basis of its antioxidant capacity is unclear. This study employed integrated metagenomics and metabolomics to elucidate the dynamic formation of antioxidant biomarkers during fermentation.

RESULTS: The mid-fermentation stage (6-12 h) was critical for antioxidant development, marked by peak accumulation of key biomarkers such as phenyllactic acid, epigallocatechin and catechin. Antioxidant activity [2,2-diphenyl-1-picrylhydrazyl/2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)] (DPPH/ABTS) significantly increased during this period, reaching 77.4% and 74.5% by 24 h. These changes were directly correlated with specific Lactobacillus spp. (e.g. Lactobacillus curvatus and Lactobacillus mudanjiangensis). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed stage-specific metabolic reprogramming, from early activation of amino acid/lipid metabolism to late-phase downregulation of central carbon metabolism. Correlation networks further linked these Lactobacilli to key carbohydrate-active enzymes (CAZy), such as glycoside hydrolases.

CONCLUSION: This study decipheedr the microbial-driven metabolomic remodeling that governs antioxidant capacity in MBSL, demonstrating a clear temporal alignment between key metabolite accumulation and functional enhancement. This work decodes the scientific basis of its traditional value and establishes a robust foundation for its targeted optimization and development as a health-promoting functional beverage. © 2026 Society of Chemical Industry.}, } @article {pmid41830759, year = {2026}, author = {Nasir, MM and Qayyum, H and Shuhui, S and Ali, A and Kayani, MUR}, title = {MetaBolt: A computationally efficient pipeline for the rapid recovery of metagenome-assembled genomes.}, journal = {Computational biology and chemistry}, volume = {123}, number = {}, pages = {109006}, doi = {10.1016/j.compbiolchem.2026.109006}, pmid = {41830759}, issn = {1476-928X}, mesh = {*Metagenome/genetics ; *Metagenomics ; *Software ; *Computational Biology ; Algorithms ; }, abstract = {Metagenome-resolved metagenomics refers to the recovery of metagenome-assembled genomes from the metagenomic datasets. It is a multi-step and laborious process that requires substantial computational resources and technical expertise. Though various semi-automated pipelines have been developed to automate the recovery process, high computational requirements remain a major bottleneck. Since de novo assembly is the key step that consumes higher computational time and resources, optimizing this step can address the underlying challenges. Hence, to address these limitations, we introduce MetaBolt, an automated Nextflow-based pipeline designed for the rapid recovery of metagenome-assembled genomes from short-read metagenomic datasets. Based on an empirically optimized set of k-mers for MEGAHIT-based assembly, this pipeline offers a unique solution. When tested on both real and simulated metagenomic datasets, it consistently exhibited efficient performance within reduced computational time. From gut metagenomes, MetaBolt recovered MAGs at a 2.3 and 3.8-times faster rate than nf-core/mag and MetaWRAP, respectively, while recovering ∼5% more high-quality MAGs compared to the other two pipelines. Whereas, in the case of real metagenome samples, it reduced the computational times to 2-4%, particularly for low-biomass samples. By integrating optimized assembly parameters with automated workflow management, MetaBolt lowers computational barriers to genome-resolved metagenomics without compromising output quality. MetaBolt is available on the web at https://github.com/muneebdev7/metabolt.}, } @article {pmid41830810, year = {2026}, author = {Martins, IB and Silva, JM and Almeida, JR}, title = {A systematic review and benchmarking of modern metagenomic tools for taxonomic classification.}, journal = {Computers in biology and medicine}, volume = {206}, number = {}, pages = {111600}, doi = {10.1016/j.compbiomed.2026.111600}, pmid = {41830810}, issn = {1879-0534}, mesh = {*Metagenomics/methods ; Benchmarking ; *Software ; Computational Biology/methods ; }, abstract = {Advancements in metagenomics have been driven by the continuous development of bioinformatic tools, particularly taxonomic classification software, which are central to the accurate characterization of microbial communities. However, establishing direct comparisons between these tools remains challenging due to variations in evaluation metrics, reference databases, and input data types. In this study, we present a systematic review of recently developed metagenomic taxonomic classification tools. Of the 31 identified tools, nine satisfied all functional and methodological criteria for the benchmark analysis. We evaluated their accuracy and computational performance using a standardized dataset derived from the NCBI RefSeq database. Our analysis revealed that most of these tools are domain-specific, each excelling in particular areas. Tools like TAMA, CAMITAX and PhyloFlash achieved higher accuracy for prokaryotic organisms, while ViWrap and PhaBOX achieved higher accuracy for viral classifications. SqueezeMeta achieved high F1 scores across most domains, though its assembly-based architecture limits effectiveness on highly diverse samples. MegaPath-Nano was least affected by increased mutation rates. The execution time varied widely among the tools, with domain-specific and machine learning-based tools generally being faster, while tools like BASTA had longer runtimes and lower accuracy. This review synthesizes performance results for current tools, providing an overview of their strengths and computational methodologies.}, } @article {pmid41831184, year = {2026}, author = {Rangamaran, VR and Sushmitha, TJ and Tamilmani, KK and Murugesan, H and Venkataraman, P and Arunachalam, R and Pramanik, R and Dharne, M and Gopal, D}, title = {Integrated omics analyses reveal insights into microbial dark matter associated with deep-sea water in Central Indian Ocean.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {3}, pages = {}, pmid = {41831184}, issn = {1573-0972}, support = {DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; }, abstract = {Deep-sea environments represent one of the most complex ecosystems on Earth and harbour extensive microbial dark matter (MDM) that remains poorly characterized due to limitations of culture-dependent approaches. Here, we present a pilot-scale multi-omics investigation to profile MDM from a deep-sea water sample collected at 1600 m, employing an integrated workflow that combine Illumina and Nanopore hybrid metagenomics sequencing, fluorescence-activated cell sorting-based single-cell genomics and untargeted metabolomics using LC(Orbitrap) -MS and GC-MS. Hybrid sequencing yielded metagenome-assembled genomes (MAGs) from well-reported clades Pseudomondota, Actinomycetota, and Bacteriodota. Taxonomic profiling revealed rare groups viz. Candidatus Omnitrophota, Saccharibacteria, and Abscondibacteria. A total of 150 single amplified genomes (SAGs) were generated which were found to be affiliated to MDM candidate phyla including Patescibacteria, Armatimondota, J088, and Thermoproteota. Annotation of SAGs suggested the critical role of MDM in complex carbohydrate metabolism, methyl-linked methanogenesis and methanotrophy. SAGs from potentially novel MDM exhibited a high density of Biosynthetic Gene Clusters (BGCs). Further exometabolomic analysis divulged the presence of complex fatty acid biosynthesis, polyketide synthesis and terpenoid pathway networks. This study has provided a significant pointer on applying integrated metagenome and single-cell genome-based exploration of complex microbiomes which could potentially be a precursor to high-throughput culturomics and downstream bio-prospection studies.}, } @article {pmid41831290, year = {2026}, author = {Tang, Z and Li, Y and Zhang, L and Xi, B and Tan, W and Yuan, Y}, title = {Space-for-time substitution reveals mechanisms driving heavy metal induced dynamics of antibiotic resistance genes of varying risk levels in landfill leachate.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141740}, doi = {10.1016/j.jhazmat.2026.141740}, pmid = {41831290}, issn = {1873-3336}, mesh = {*Metals, Heavy/analysis/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; *Waste Disposal Facilities ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences ; }, abstract = {Landfills are recognized as persistent reservoirs of antibiotic resistance genes (ARGs); however, the temporal dynamics of their risk profiles after closure remain poorly understood. Because long-term monitoring of ARG risks in landfill leachate is challenging, a "space-for-time" substitution was employed to characterize ARGs, metal resistance genes (MRGs), mobile genetic elements (MGEs), and microbial hosts in landfill leachate at three stages: unclosed landfills (UL), landfills closed for 1-5 years (CF), and landfills closed for more than 6 years (CS). Metagenomic analyses identified 518 ARG subtypes across 22 classes. ARG abundance peaked in the CF stage (1.28 copies/cell), significantly higher than in UL (0.292 copies/cell) and CS (0.597 copies/cell) stages (p < 0.05). Elevated concentrations of nickel, copper, and arsenic during the CF stage promoted ARG enrichment via co-selection, primarily driven by efflux pump-mediated cross-resistance and co-resistance within ARG-MRG clusters. IntI1 was strongly linked to high-risk ARGs, indicating horizontal gene transfer as a major dissemination pathway. Key bacterial hosts, including Pseudomonas spp. and Escherichia coli, harbored both ARGs and MRGs. These findings highlight the early post-closure period (1-5 years) as a critical surveillance window and support targeted monitoring of high-risk ARGs, MGEs, indicator taxa, and heavy metals to mitigate environmental dissemination of antibiotic resistance.}, } @article {pmid41831647, year = {2026}, author = {Tashiguano, VM and Sierra, K and Black, MT and Sirmon, M and Leeds, P and Jones, J and Doster, J and Smith, C and Jia, Z and Garner, L and Cho, S and Hanna, J and Trout, K and Almasri, M and Li, H and Morey, A}, title = {A Multidisciplinary Approach for Predicting the Microbiological Spoilage of Chicken Breast Fillets due to Cold-Chain Disruption.}, journal = {Journal of food protection}, volume = {89}, number = {5}, pages = {100754}, doi = {10.1016/j.jfp.2026.100754}, pmid = {41831647}, issn = {1944-9097}, mesh = {Animals ; Chickens ; Food Microbiology ; Food Storage ; Food, Processed ; Meat ; }, abstract = {Cold-chain disruptions during the storage and distribution of raw poultry can significantly reduce product shelf-life and safety. This study evaluated the effects of short-term cyclic temperature abuse (TA) on the retail shelf-life of fresh chicken breast, using a multidisciplinary approach that combined food microbiology, machine learning (ML), metagenomics, and volatile compound (VC) analysis. Boneless, skinless chicken breast trays (n = 450) were obtained from a commercial poultry processor and transported under refrigeration (4 °C) to Auburn University. In three independent trials, trays were randomly assigned to one of three treatments: (1) Control at 4 °C for 24 h; (2) TA Cycle 1: alternating 30 min at 4 °C and 1 h at 30 °C; and (3) TA Cycle 2: alternating 30 min at 4 °C and 1 h at 37 °C. TA cycles lasted 7.5 h, after which all trays were stored at 4 °C. Samples were analyzed on days 0, 2, 4, 6, and 8 for aerobic, facultative anaerobic, and lactic acid bacteria (LAB) counts, and for VCs using an electronic nose. Rinsates from Trial 3 were stored at -80 °C for metagenomic analysis. TA Cycle 2 resulted in the highest spoilage rates, followed by TA Cycle 1. A neural network model moderately predicted bacterial growth (R[2] = 0.65-0.75 for aerobic and facultative anaerobic microorganisms; lower for LAB). Metagenomics demonstrated a shift toward Pseudomonas spp. dominance under TA conditions, while control samples retained microbial diversity. These findings underscore that even short-term TA significantly alters the microbiome and accelerates spoilage in raw poultry, emphasizing the importance of cold-chain integrity. Practical Relevance. This study shows that short, high-temperature abuse events from refrigeration failure, handling delays, or other supply chain disruptions can accelerate spoilage in raw chicken. By combining rapid spoilage-detection tools with predictive models, poultry producers and retailers may better monitor these events, helping to maintain cold-chain integrity and reduce losses.}, } @article {pmid41831799, year = {2026}, author = {Qi, H and Wu, R and Liao, J and Alvarez, PJJ and Yu, P}, title = {Longitudinal multi-omics reveal phase-dependent viral adaptive strategies and functional potential during formation of algal-bacterial granular sludge.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134410}, doi = {10.1016/j.biortech.2026.134410}, pmid = {41831799}, issn = {1873-2976}, mesh = {Multiomics ; *Sewage/microbiology/virology ; *Bacteria/virology/genetics ; }, abstract = {Virus-prokaryote interactions within microbial aggregates critically influence microbiome function and stability, yet the interactive dynamics during microbial aggregation remain largely unexplored. Here, longitudinal multi-omics revealed that prokaryotic host community diversity underwent decline and subsequent recovery during algal-bacterial granular sludge (ABGS) formation from activated sludge. Declined host diversity in the collapse phase enriched for lysogenic viruses and facilitated virus-host mutualistic symbiosis, during which the proportion of lysogenic metagenome-assembled genomes (MAGs) peaked at 84% (841,649 TPM), with auxiliary metabolic genes (AMGs) primarily involved in genetic information processing and amino acid metabolism. Moreover, low host diversity increased viral microdiversity by 1.97-fold and selected for virion structure genes that were conducive to viral fitness and replication. As host diversity recovered during the recovery phase, viruses and hosts engaged in an evolutionary arms race, with both host defense systems (DS) (Spearman's Rho = 0.68, P < 0.05) and viral anti-defense systems (ADS) (Spearman's Rho = 0.51, P < 0.05) enriched along with granule maturation. Furthermore, active lysogenic infections were accompanied by the dissemination of AMGs predominantly associated with the metabolism of cofactors, vitamins, terpenoids, and polyketides. Despite their phase-dependent functional profiles, lysogenic phages with AMGs putatively enhanced the structural and functional stability of the microbiome during ABGS formation. Overall, our study unveils a phase-dependent co-evolutionary interplay between viruses and prokaryotic hosts during ABGS formation, providing insights into virus-mediated microbial structural and functional resilience in engineered ecosystems.}, } @article {pmid41831800, year = {2026}, author = {Xie, J and Zhu, W and Wang, W and Min, B and Xu, J and Xie, L}, title = {Optimizing anaerobic digestion for antibiotic degradation and antimicrobial resistance mitigation.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134409}, doi = {10.1016/j.biortech.2026.134409}, pmid = {41831800}, issn = {1873-2976}, mesh = {*Anti-Bacterial Agents/metabolism ; Lincomycin/metabolism ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; Biodegradation, Environmental ; Methane/metabolism ; Wastewater ; Glucose/metabolism ; Temperature ; Clostridium/metabolism ; }, abstract = {Anaerobic digestion (AD) is widely applied to treat antibiotic pharmaceutical wastewater for antimicrobial resistance mitigation and synchronous bio-energy recovery. However, process efficiency and risk control depend critically on operational strategies. Here, we systematically evaluated the roles of feedstock composition and digestive temperature in optimizing lincomycin-containing AD. Glucose-rich mesophilic digestion achieved superior lincomycin degradation and methane recovery compared to thermophilic and protein-rich systems. Transformation product analysis suggested that glucose-rich feedstock might facilitate the furan ring-opening step during lincomycin degradation, possibly owing to structural and metabolic similarities between glucose and lincomycin. The enrichment of lincomycin-degrading Clostridium and Methanobacterium in response to glucose-rich mesophilic condition, together with their potential syntrophic interaction, further supported the accelerated lincomycin degradation and methanation. Metagenome-assembled genome analysis revealed that protein-rich and thermophilic operation intensified the proliferation of host consortia harboring gene clusters with antibiotic resistance gene-mobile genetic element (ARG-MGE) co-occurrence, and induced putative horizontal transfer of ARG, resulting in the increased ARG abundance. ARG proliferation in thermophilic systems was associated with enrichment of lincomycin-resistant consortia (JAAYZQ01 sp034428935 and Tenuifilum sp018056955) after antibiotic exposure, which preferentially enriched under higher-temperature conditions. In contrast, glucose-rich digesters exhibited a reduced potential for horizontal gene transfer mediated by MGEs and natural conjugation. Overall, feedstock composition exerted a greater influence on antimicrobial resistance dissemination compared to temperature. Collectively, our findings provide an operational framework for sustainable treatment and valorization of antibiotic-containing wastewater.}, } @article {pmid41831863, year = {2026}, author = {Patel, SS and Shree, T and Kumar, A}, title = {Microbial consortia interactions and bioremediation of pesticides: A review on designing, mechanism and efficacy.}, journal = {Pesticide biochemistry and physiology}, volume = {219}, number = {}, pages = {106993}, doi = {10.1016/j.pestbp.2026.106993}, pmid = {41831863}, issn = {1095-9939}, mesh = {Biodegradation, Environmental ; *Pesticides/metabolism ; *Microbial Consortia ; *Soil Pollutants/metabolism ; Soil Microbiology ; }, abstract = {Ecosystems and human health are at serious risk due to the extensive application of pesticides in the agricultural system for controlling pests and diseases. The use of microbial consortia (MicroCons) has emerged as a promising solution for the remediation of pesticide-contaminated soil, offering a sustainable and eco-friendly alternative to physical and chemical methods; however, a systematic review on this aspect is still lacking. This comprehensive review provides an in-depth analysis of the current knowledge on microbial consortia-based remediation of pesticides in agricultural soil. Efficacy of single-strain vs multiple strains in MicroCons have been discussed to unravel the workload distribution between microbial strains in pesticide degradation. We also discuss the design and optimization of microbial consortia for remediation, highlighting the role of advanced tools and the mechanisms of MicroCons action. Furthermore, emerging trends and future directions in the field, including the potential of synthetic biology, machine learning (ML), and artificial intelligence (AI) are also covered. This review aims to critically expand the mechanistic understanding of how microbe-mediated remediation strategies might reduce pesticide phytotoxicity, enhance crop production in pesticide-stressed soils, and inspire future research and practices in MicroCons-based remediation to achieve the Sustainable Development Goals (SDGs).}, } @article {pmid41831922, year = {2026}, author = {Kashyap, B and Jayaraj, H and Rajpal, S and Sidiq, Z and Arora, VK}, title = {Landscape of metagenomics: fight against tuberculosis and other infectious disease in India.}, journal = {The Indian journal of tuberculosis}, volume = {73}, number = {1}, pages = {13-16}, doi = {10.1016/j.ijtb.2026.02.012}, pmid = {41831922}, issn = {0019-5707}, mesh = {Humans ; India ; *Metagenomics/methods ; *Tuberculosis/diagnosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {Metagenomics is an evolving diagnostic tool worldwide for studying microorganisms which cannot be cultured in routine laboratory settings. From Sanger sequencing to Next Generation Sequencing like Illumina, and now Oxford Nanopore sequencing has been a boon in detecting difficult-to-diagnose infectious disease conditions and delivering patient-tailored treatment. In developing countries like India, these advancements in diagnostics aid in decreasing disease burden, growing antimicrobial resistance and to study new microorganism.}, } @article {pmid41832076, year = {2026}, author = {Gundra, SR and Jiang, W and Aouida, M and Wang, Q and Kazlak, AM and Elbehery, AHA and Saleh, A and Masood, M and Ghouneimy, A and Mahfouz, M}, title = {Characterization and engineering of highly efficient Cas12j genome editors.}, journal = {Trends in biotechnology}, volume = {44}, number = {6}, pages = {1740-1765}, doi = {10.1016/j.tibtech.2026.02.001}, pmid = {41832076}, issn = {1879-3096}, mesh = {*Gene Editing/methods ; *CRISPR-Cas Systems/genetics ; Animals ; Humans ; *CRISPR-Associated Proteins/genetics/metabolism ; Protein Engineering/methods ; }, abstract = {The large size of widely used CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) enzymes limits their delivery for therapeutic applications. Cas12j nucleases offer a hypercompact alternative but show modest editing efficiency. To overcome this limitation, we identified eight novel Cas12j orthologs from viral metagenomes, which in their native form exhibit low editing activity in mammalian cells. We therefore engineered T5 exonuclease-Cas12j fusions, resulting in substantially enhanced genome-editing activity across multiple mammalian cell types, reaching levels comparable to established compact CRISPR-Cas editors. Intriguingly, robust cellular editing occurred in the presence of a previously unrecognized trinucleotide sequence context within the target DNA. Furthermore, we developed Cas12j-based adenine base editors by coupling catalytically inactive Cas12j orthologs with adenine deaminase, enabling efficient A-to-G base conversion in mammalian cells. This study expands the CRISPR toolbox by establishing engineering principles that convert compact Cas12j nucleases into efficient and modular genome-editing platforms well suited for delivery-constrained therapeutic applications.}, } @article {pmid41832122, year = {2026}, author = {Van Etten, J and Johnson, MD}, title = {The ecology of horizontal gene transfer.}, journal = {Trends in genetics : TIG}, volume = {42}, number = {6}, pages = {539-554}, doi = {10.1016/j.tig.2026.02.002}, pmid = {41832122}, issn = {0168-9525}, mesh = {*Gene Transfer, Horizontal/genetics ; *Ecology ; Animals ; Genetic Variation ; Evolution, Molecular ; DNA/genetics ; }, abstract = {Horizontal gene transfer (HGT) generates genetic variation in populations across all domains of life; however, most studies focus on individual transfers and functional information derived therefrom. This is useful but does not consider DNA transfer more broadly, that is, nongene transfers, donor-recipient dynamics, or trends and background levels that may help infer ecological information. Here, we review the mechanistic underpinnings of DNA transfer, literature from diverse fields that addresses HGT on a community basis and the associated methodological challenges, and propose a framework for conceptualizing the process of DNA transfer, highlighting DNA mobility as a feature of community ecology and DNA itself as a public good. These ideas coalesce to support DNA transfer as a fundamental ecological phenomenon that remains largely unmeasured.}, } @article {pmid41832496, year = {2026}, author = {Ali, S and Hassan, M and Essam, T and Abdelmalek, S and Al-Amry, KF}, title = {Antimicrobial resistance profiling in poultry industry: a culture-independent resistome analysis and risk factor assessment.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {41832496}, issn = {1746-6148}, abstract = {UNLABELLED: Antimicrobial resistance (AMR) is a global health crisis, often termed as the “silent pandemic”. As emphasized by the One Health framework, the food production chain, especially poultry, serves as a critical point for monitoring AMR emergence and spread. In this study, we conducted a culture-independent screening of 27 antimicrobial resistance genes (ARGs) relevant to both human and veterinary health using cloacal samples collected from 9 farms across two of Egypt’s major poultry-producing cities. Alongside ARG screening, farm-level risk and managemental factors were assessed. Results showed that broiler farms had notably higher antimicrobial usage (AMU) and ARG prevalence compared to layer farms. Genes such as sul1 and sul2, tetA and tetM were significantly more abundant in broilers (P < 0.05, Fisher's Exact Test). Beta-lactam and sulphonamide resistance genes were widespread in both production systems. Key risk factors associated with increased ARG richness included bird type, lower farm biosecurity scores, summer season, diseased birds, use of multiple antibiotic classes and absence of veterinary prescriptions. Cluster analysis revealed parC, aac (3)-1a, sul2, blaTEM, intI1, tetM, tetA, and sul1 as the most prevalent genes among the screened samples. Additionally, intI1, a known marker of horizontal transfer, was detected in 79% of the samples and significantly co-occurred with tetracycline, beta-lactam, sulphonamide, and quinolone resistance genes (P >0.05, Fisher's Exact Test). To the best of our knowledge, this is the first study in Kalyoubia and Giza, two of Egypt’s major poultry trading hubs to comprehensively assess ARGs using a rapid, culture-independent PCR-based resistome analysis, highlighting critical AMR risks and its relation to ARGs’ richness in these poultry sectors.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12917-026-05334-w.}, } @article {pmid41833387, year = {2026}, author = {Han, Z and Wang, Y and Yang, J}, title = {Physiological and biochemical changes and microbial community succession during the postharvest rot process of Stropharia rugosoannulata.}, journal = {The Journal of general and applied microbiology}, volume = {72}, number = {1}, pages = {}, doi = {10.2323/jgam.2026.03.001}, pmid = {41833387}, issn = {1349-8037}, mesh = {Metagenomics ; *Microbiota ; Superoxide Dismutase/metabolism ; Food Microbiology ; Glycosyltransferases/genetics/metabolism ; Bacteria/genetics/classification/isolation & purification ; Pseudomonas/genetics ; Malondialdehyde/metabolism ; }, abstract = {This study systematically elucidated the microbial community succession and functional gene dynamics during the postharvest spoilage process of Stropharia rugosoannulata by integrating physiological and biochemical indicators with metagenomic analysis. The experimental results demonstrated that as storage time extended, the activities of antioxidant enzymes (superoxide dismutase, peroxidase) in S. rugosoannulata significantly declined, while the content of membrane lipid peroxidation product malondialdehyde increased, leading to compromised cell membrane integrity and creating favorable conditions for microbial colonization. Metagenomic analysis revealed that during the spoilage phase (post-harvest day 14), the relative abundance of Pseudomonadota increased to 85.7%, with Pseudomonas replacing Ewingella as the absolutely dominant microbial population. Further functional gene analysis showed that the post-harvest day 14 exhibited significant enrichment of glycosyltransferases (GT0, GT1, GT2, GT4) and carbohydrate-binding modules (CBM10, CBM16, CBM50), along with pectinase (GH78), chitinase (GH19), and polysaccharide-modifying enzymes (CE4, CE11). This indicated a metabolic shift towards cell wall synthesis and substrate recognition. In contrast, the post-harvest day 7, prior to fruiting body softening, demonstrated high expression of glycoside hydrolases (GH1, GH2, GH4, GH94) and carbohydrate esterase CE8, focusing on the degradation of cellulose and starch. These findings, for the first time from a molecular ecology perspective, clarify that the essence of postharvest spoilage in S. rugosoannulata is a quality deterioration process driven by a Pseudomonas-dominated microbial community. The study provided a basis for the development of targeted antibacterial preservation strategies.}, } @article {pmid41833574, year = {2026}, author = {Saibu, S and Obayori, OS and Diagboya, PN and Oso, SO and Shedrack, AE and Agbomeji, RO and Eletu, MO and Ajibike, OR and Ishola, FM and Adimabua, RN and Oyetibo, GO}, title = {Spatial variation in bacterial community structure and pollution response in river sediment.}, journal = {Journal of contaminant hydrology}, volume = {279}, number = {}, pages = {104923}, doi = {10.1016/j.jconhyd.2026.104923}, pmid = {41833574}, issn = {1873-6009}, mesh = {*Rivers/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; *Bacteria/classification/genetics ; Polycyclic Aromatic Hydrocarbons/analysis ; *Water Pollutants, Chemical/analysis ; RNA, Ribosomal, 16S/genetics ; Environmental Monitoring ; }, abstract = {Rivers are unique ecosystems where pollution frequently occurs, altering the biogeochemical characteristics of both water bodies and sediments. However, little is known about the effects of human activities on the lower course of River Ogun. This study assessed the association between anthropogenic activities and sediment bacterial communities at the time of sampling by comparing sediment physicochemical properties and the bacterial community structures of samples. Samples were taken from four distinct sites along the lower course of the river. Bacterial community structure of these sites was investigated using the 16S rRNA gene PacBio sequencing. Total polycyclic aromatic hydrocarbons (PAHs) were lowest at Location B (6.95 mg/kg) and highest at Location A (15.6 mg/kg). The dominant bacterial phyla in the sediments were Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota. A notable abundance of Thauera was observed across all the locations, particularly at Location A, and Psychrobacter known for plastic degradation was detected exclusively at this site. Among all the sites, Location A exhibited the lowest bacterial diversity, as indicated by both species' richness and evenness, where the Thauera selenatis group and Psychrobacter maritimus were dominant. Location B exhibited the highest bacterial diversity, Location C and D displayed intermediate diversity, sharing a 40% similarity index. Environmental variables that significantly explained beta diversity patterns included pH, anthracene and fluoranthene. This study provides insights into bacterial metagenomes of a freshwater inundated with plastics, heavy metals and consortium of persistent organic compounds. The findings highlight the value of integrating metagenomic and physicochemical analyses to identify correlations that help explain the key drivers shaping ecosystem dynamics.}, } @article {pmid41833938, year = {2026}, author = {Li, D and Qu, ZS and Wang, C and Peng, ZH and Zhou, X and Cai, L}, title = {The Anna Karenina principle in the assembly of plant microbiome under pathogen stress.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41833938}, issn = {2055-5008}, support = {U24A20343//National Natural Science Foundation of China/ ; 32300009//National Natural Science Foundation of China/ ; 32330002//National Natural Science Foundation of China/ ; XDB0810000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Zea mays/microbiology ; Soil Microbiology ; Rhizosphere ; Fusarium/physiology ; *Stress, Physiological ; *Bacteria/classification/genetics/isolation & purification ; Plant Roots/microbiology ; Plant Diseases/microbiology ; Sequence Analysis, DNA ; Metagenomics/methods ; DNA, Bacterial/genetics ; Plant Stems/microbiology ; }, abstract = {The Anna Karenina Principle (AKP) posits that healthy microbiomes converge toward similar compositional states, whereas dysbiotic microbiomes diverge into distinct and system-specific configurations. Despite its broad recognition in microbiome research, systematic evidence remains scarce as to whether pathogen stress drives plant microbiome assembly in accordance with AKP. To address this knowledge gap, we examined 1,410 samples from multiple compartments (bulk soil, rhizosphere soil, roots, stems, and seeds) across a continental-scale, comparing healthy and Fusarium stalk rot-infected maize using 16S rRNA gene sequencing, complemented with metagenomic sequencing of 93 selected rhizosphere and stem samples. By integrating variations of bacterial community diversity, beta dispersion, average variation degree, and a modified stochasticity ratio, we demonstrated that pathogen-induced microbiome shifts conform to AKP predictions. Notably, AKP-conforming stochastic assembly enriched oligotrophic taxa, resulting in microbial communities with higher GC content, smaller average genome size, and reduced 16S rRNA operon copy numbers. Moreover, the selective enrichment of specific functional traits (including peptidoglycan biosynthesis and degradation, chromatin structure and dynamics, and lipid transport and metabolism) was closely associated with AKP. Our findings support AKP as a useful framework for understanding plant microbiome assembly under pathogen pressure and provide new insights into plant-microbiome-pathogen interactions.}, } @article {pmid41834217, year = {2026}, author = {Yuan, X and Gong, H and Zhang, L and Liu, Y and Zhou, M and Liu, Y and Tang, J and Pan, S and Xu, X and Wang, Y and Zhang, X and Zhang, T and Song, J}, title = {T2DM-Induced Gut Dysbiosis Exacerbates Periodontitis Through Intestinal Barrier Disruption and Redox Imbalance.}, journal = {Journal of clinical periodontology}, volume = {53}, number = {5}, pages = {821-833}, doi = {10.1111/jcpe.70116}, pmid = {41834217}, issn = {1600-051X}, support = {U22A20314//National Natural Science Foundation of China/ ; 82170968//National Natural Science Foundation of China/ ; 82301082//National Natural Science Foundation of China/ ; 2022YFC2504200//National Key Research and Development Program of China/ ; 2025MD774176//China Postdoctoral Science Foundation/ ; YXQN202401//Chongqing Youth Talent Support Program/ ; }, mesh = {Animals ; *Dysbiosis/complications ; *Periodontitis/microbiology/etiology/metabolism ; *Diabetes Mellitus, Type 2/complications ; Mice ; Mice, Inbred C57BL ; Oxidation-Reduction ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/physiology ; Intestinal Barrier Function ; Oxidative Stress ; Male ; Disease Models, Animal ; }, abstract = {AIM: To investigate the potential role and underlying mechanisms of gut microbiota in type 2 diabetes mellitus (T2DM)-exacerbated periodontitis.

MATERIALS AND METHODS: A T2DM-associated periodontitis model was established in C57BL/6 mice and analysed using multi-omics sequencing (16S rRNA, metagenomics and metabolomics). Faecal microbiota transplantation (FMT) from T2DM donors was carried out in recipient mice to investigate the impact of gut dysbiosis on periodontitis. FMT from healthy donors, supplementation of intestinal barrier protectant or the metabolite oleic acid (OA) was administered to mice with T2DM-associated gut dysbiosis to examine their ameliorative effects on periodontal damage.

RESULTS: T2DM-associated gut dysbiosis, independent of hyperglycaemia, triggered intestinal barrier disruption, which disturbed systemic redox-related metabolisms and elevated oral oxidative stress, thereby aggravating periodontitis. Restoring gut microbiota via FMT from a healthy donor or protecting the intestinal barrier ameliorated periodontitis. Exogenous supplementary metabolite OA rescued periodontal damage by activating the SIRT1/FoxO1 pathway and enhancing antioxidant enzymes in mice with T2DM-associated gut dysbiosis.

CONCLUSIONS: T2DM-induced gut dysbiosis exacerbates periodontitis through intestinal barrier disruption and redox imbalance. These findings provide new adjunctive therapeutic perspectives including microbiota restoration, intestinal barrier protection and antioxidant supplementation for managing patients with T2DM-induced periodontitis.}, } @article {pmid41834639, year = {2026}, author = {Soliman, MS and Abbas, AM and Algebaly, HF and El-Kholy, AA and Soliman, NS}, title = {Metagenomics profiling of the lower respiratory tract microbiome and relevant respiratory pathogens in pediatric intensive care unit patients: a pilot exploratory study in Egypt.}, journal = {Acute and critical care}, volume = {41}, number = {1}, pages = {136-147}, pmid = {41834639}, issn = {2586-6060}, abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) are a leading cause of mortality in children. These infections disrupt the equilibrium of lower respiratory tract (LRT) microbiota, allowing respiratory pathogens to dominate. The conventional culture method has limitations in describing complex microbiomes and may fail in the detection of respiratory pathogens. In the present study, we sought to use the advanced technology of 16S metagenomics next-generation sequencing (16SmNGS) to characterize the LRT microbiome among children with LRTIs and to identify the underlying respiratory pathogens that commonly evade detection by traditional culture.

METHODS: Twenty LRT specimens from hospitalized children with LRTIs were analyzed using 16SmNGS, as well as standard microbiological culture.

RESULTS: The 16SmNGS taxonomical analysis revealed the highest relative abundances for Streptococcus (27.7%) and Escherichia (13.3%) genera, which belong to the phyla of Firmicutes (45.4%) and Proteobacteria (45.3%), respectively. Streptococcus pneumoniae (45%), Escherichia coli (45%), Pseudomonas aeruginosa (15%), Staphylococcus aureus (10%), Acinetobacter baumannii (5%), and Haemophilus influenzae (5%) were the primary respiratory pathogens. Conventional culture failed to detect growth in 100%, 77.7%, and 55.5% of 16SmNGS-positive specimens for H. influenza, S. pneumoniae, and E. coli, respectively.

CONCLUSIONS: The 16SmNGS technique revealed a predominance of Streptococcus and Escherichia genera belonging to the phyla of Firmicutes and Proteobacteria in pediatric LRTIs. In this exploratory study, 16SmNGS was able to enhance the identification of significant respiratory pathogens, particularly those difficult to isolate in culture. However, to rule out contamination by flora, it is advisable not to interpret metagenomics results independently from culture, clinical, and radiological data. In addition, further clinical correlations are desired to reach appropriate clinical decisions.}, } @article {pmid41834860, year = {2026}, author = {Du, Y and Chen, L and Zhang, X and Zeng, J and Hu, C}, title = {Based on untargeted metabolomics and metagenomics: a study on the mechanism of Miao ethnomedicine Zingiber mioga (Thunb.) Rosc. in treating slow transit constipation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1751739}, pmid = {41834860}, issn = {1664-302X}, abstract = {INTRODUCTION: Slow transit constipation (STC) is a prevalent gastrointestinal disorder characterized by impaired intestinal motility, metabolic dysregulation, and gut microbial dysbiosis. Zingiber mioga (Thunb.) Rosc. (RH), a traditional medicinal-edible plant, is empirically used to alleviate gastrointestinal dysfunction, but its therapeutic mechanisms in STC remain unclear. Herein, we investigated the laxative efficacy and mechanism of RH in a rat STC model via integrated untargeted metabolomic and metagenomic analyses, providing experimental evidence for its clinical use.

METHODS: A rat STC model was established by intragastric loperamide hydrochloride (5 mg/kg) for 35 consecutive days. Thirty-six SD rats were randomly divided into six groups (n = 6): normal control, STC model, mosapride-positive control (2 mg/kg), and low- (1350 mg/kg), medium- (2700 mg/kg), high-dose (3400 mg/kg) RH groups, with concurrent drug intervention. Serum concentrations of SP, MTL, and GAS (key gastrointestinal motility regulators) were quantified. Colonic pathological damage was histopathologically evaluated, and intestinal propulsive rate was measured. Untargeted serum metabolomics and fecalmetagenomics identified differential metabolites and gut microbiota alterations.

RESULTS: Compared with the STC model, RH significantly reduced serum SP (intestinal motility inhibitor) and increased MTL/GAS (motility promoters). It also dose-dependently ameliorated colonic lesions and improved intestinal propulsive rate. Serum metabolomics identified 15 differential metabolites, mainly enriched in nitrogen metabolism, neuroactive ligand-receptor interaction, and amino acid metabolism. Fecal metagenomics showed RH restored the Eubacteriales/Lachnospirales ratio (a STC dysbiosis marker) and increased beneficial genera (e.g., Ruminococcus sp., Eubacterium sp.).

DISCUSSION AND CONCLUSION: Our findings show RH effectively ameliorates colonic injury and gastrointestinal motility in STC rats, associated with regulating gastrointestinal hormone secretion. Its benefits are likely mediated by improving dysregulated amino acid/nitrogen metabolism and modulating gut microbiota composition. This study provides mechanistic evidence for RH as a natural functional agent for STC management, laying a foundation for exploring its active components and clinical translation.}, } @article {pmid41834868, year = {2026}, author = {Niu, M and Pan, J and Guo, Y and Zhang, F and Guan, H and Yang, X and Li, H and Xiong, H and Zhang, Y and Chen, Y}, title = {Neonatal jaundice and the infant gut microbiome: an integrated shotgun metagenomics and bidirectional Mendelian randomization study in Xinjiang.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1761712}, pmid = {41834868}, issn = {1664-302X}, abstract = {BACKGROUND: Neonatal jaundice is a common condition, yet inter-individual variation in its onset and severity cannot be fully explained by traditional clinical risk factors. Emerging evidence suggests that the infant gut microbiome may modulate bilirubin metabolism, but its compositional and functional signatures in jaundiced neonates remain incompletely defined. This study aimed to characterize the taxonomic and functional features of the gut microbiome in neonatal pathologic jaundice and to explore potential causal links using Mendelian randomization (MR).

METHODS: We conducted a case-control study of term infants with pathologic jaundice and matched healthy controls. Stool samples were subjected to shotgun metagenomic sequencing to assess microbial diversity, taxonomic composition, functional gene repertoires, and carbohydrate-active enzyme families, and publicly available genome-wide association study summary statistics were used to perform bidirectional MR between microbiome-related traits and neonatal jaundice.

RESULTS: Alpha diversity indices did not differ significantly between groups, whereas beta diversity based on Bray-Curtis dissimilarity showed clear separation of jaundiced and control infants, indicating a restructured microbial community rather than a simple loss of richness. Jaundiced neonates exhibited increased relative abundance of Gram-negative taxa, including Escherichia coli, and reduced levels of putatively beneficial genera such as Bifidobacterium and Lactobacillus. Functionally, pathways involved in bile acid synthesis and metabolism, carbohydrate and energy metabolism, and cofactor and vitamin biosynthesis were enriched in the jaundiced group, accompanied by marked shifts in carbohydrate-active enzyme profiles. Forward MR suggested that several microbial metabolic pathways exert genetically predicted effects on jaundice risk, whereas reverse MR provided little evidence that genetic liability to jaundice substantially alters microbiome traits.

CONCLUSIONS: Neonatal pathologic jaundice is associated with distinctive compositional and functional alterations in the gut microbiome. Genetic evidence from MR supports a potential causal contribution of specific microbial pathways to jaundice risk, highlighting candidate targets for microbiome-based prevention or adjunctive therapy in early life.}, } @article {pmid41834872, year = {2026}, author = {Han, Z and Wang, H and Liu, X and Tian, Z and Gong, Q and Zhang, X and Li, X and Du, R and Hu, X and Xu, C}, title = {Cross-species transmission alert: a novel canine-raccoon dog coronavirus infecting an Amur Tiger in China.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1764349}, pmid = {41834872}, issn = {1664-302X}, abstract = {Canine coronavirus (CCoV) is an important enteric alphacoronavirus primarily affecting canids. Here, we detected canine coronavirus RNA in a captive 9-year-old Amur tiger (Panthera tigris altaica) in China. The complete viral genome was obtained using metagenomic next-generation sequencing. Phylogenetic and recombination analyses were then performed to investigate its evolutionary relationship with canine and feline coronaviruses. The identified CCoV strain clustered within established canine coronavirus lineages and showed sequence evidence of recombination involving coronavirus strains previously reported in other carnivore species. Although the detection of viral RNA alone does not establish a causal relationship between CCoV infection and disease outcome, this study provides molecular evidence that Amur tigers are susceptible to canine coronavirus infection. These findings expand the known host range of CCoV and contribute to understanding the evolution and cross-species transmission potential of coronaviruses among carnivores.}, } @article {pmid41834952, year = {2026}, author = {Tu, Y and Niu, C and Huang, Z}, title = {[Analysis of the Characteristics of the Oral Virome in Metabolic Dysfunction-Associated Fatty Liver Disease].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {1}, pages = {65-72}, pmid = {41834952}, issn = {1672-173X}, mesh = {Humans ; *Saliva/virology ; *Virome/genetics ; Female ; Male ; *Dental Plaque/virology ; *Mouth/virology ; *Fatty Liver/virology ; Case-Control Studies ; Middle Aged ; Adult ; *Non-alcoholic Fatty Liver Disease/virology ; }, abstract = {OBJECTIVE: To investigate the characteristics of salivary and supragingival plaque viromes in patients with metabolic dysfunction-associated fatty liver disease (MAFLD), and provide new insights for noninvasive oral screening and ecological intervention for MAFLD.

METHODS: This study included 21 MAFLD patients and 20 healthy controls. Saliva and supragingival plaque samples were collected, and metagenomic sequencing was used to analyze the characteristics of the oral virome.

RESULTS: The α-diversity and β-diversity of the salivary virome did not differ significantly between MAFLD patients and healthy individuals (P > 0.05). However, compared with healthy individuals, the α-diversity (Shannon index) and β-diversity (Bray-Curtis distance) of the supragingival plaque virome showed significant differences (P = 0.0303, P = 0.001). For species with a relative abundance greater than 0.1%, 14 viral species in saliva and 5 in supragingival plaque differed significantly in relative abundance between the two groups (P < 0.05), with multiple Streptococcus phages enriched in the saliva of MAFLD patients. LEfSe and random forest analyses identified potential biomarkers in saliva and supragingival plaque. Receiver operating characteristic (ROC) curve analysis showed strong diagnostic performance for these biomarkers in both saliva (area under the curve [AUC] = 0.9548, 95% CI: 0.8898-1.0000) and supragingival plaque (AUC = 0.8952, 95% CI: 0.7774-1.0000). Spearman correlation analysis revealed associations between viral species in saliva or supragingival plaque and various disease indicators (P < 0.05). Compared with healthy individuals, MAFLD patients showed higher node counts, significant relationship numbers, and average node degrees in the co-occurrence networks of salivary and supragingival plaque viromes.

CONCLUSION: Differences in the species composition and structure of the oral virome between MAFLD patients and healthy individuals suggest that oral viral species could serve as potential biomarkers for diagnosing MAFLD.}, } @article {pmid41835009, year = {2026}, author = {Kariithi, HM and Volkening, JD and Mueni, SN and Helmy, MA and Afonso, CL and Chaudhari, PP and Decanini, EL}, title = {Co-detection and genomic characterization of avian rotavirus A, avian orthoreovirus, and chicken megrivirus-C using nontargeted metagenomic surveillance in Indian broiler chickens.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1690222}, pmid = {41835009}, issn = {2235-2988}, mesh = {Animals ; Metagenomics/methods ; *Chickens/virology ; Phylogeny ; India/epidemiology ; *Poultry Diseases/virology/epidemiology ; *Genome, Viral ; *Rotavirus/genetics/isolation & purification/classification ; *Orthoreovirus, Avian/genetics/isolation & purification/classification ; *Reoviridae Infections/veterinary/virology/epidemiology ; *Rotavirus Infections/veterinary/virology/epidemiology ; Genotype ; *Coinfection/virology/veterinary ; High-Throughput Nucleotide Sequencing ; Metagenome ; Avastrovirus/genetics/isolation & purification ; *Astroviridae Infections/veterinary/virology/epidemiology ; Mamastrovirus ; }, abstract = {Nontargeted metagenomic surveillance of the poultry enteric virome reveals underrecognized threats to poultry health and productivity in intensive production systems. In South Asia, avian rotavirus A (AvRV-A) and avian orthoreovirus (ARV) are frequently detected in broilers by conventional diagnostics, whereas chicken megrivirus genotype C (ChMeV-C) is often identified through metagenomic surveillance. Often present in both clinical disease and coinfections, these viruses may impair gut function, immune responses, and growth performance, yet their genomic diversity and evolutionary dynamics in poultry remain poorly characterized. Here, we report complete genomes of AvRV-A, ARV, and ChMeV-C strains co-detected via nontargeted metagenomic next-generation sequencing (ntNGS) in a pooled cloacal sample comprising 150 commercial broiler chickens (19 and 33 days old) collected from three commercial farms in Kamrup Rural District, Assam, Northeast India. Despite routine vaccination, all three flocks experienced > 10% mortality, poor weight gain, and postmortem lesions including pale kidneys and hepatomegaly. Phylogenetic analyses revealed segmental clustering in ARV and AvRV-A consistent with reassortment-driven divergence, though not supported by detectable recombination, while ChMeV-C clustered within a distinct C1 sublineage, suggesting intercontinental lineage connectivity and highlighting the need to expand regional genomic baseline data. We also identified nonsynonymous single nucleotide polymorphisms in several key viral proteins, including RNA-dependent RNA polymerases (VP1 of AvRV-A, λB of ARV, and 3D of ChMeV-C), capsid proteins (VP2 and VP7 of AvRV-A, λA and σB of ARV, and VP0 and VP1 of ChMeV-C), and replication-associated nonstructural proteins. These findings expand the genomic baseline for poultry enteric viruses in South Asia, reveal novel polymorphic signatures, and underscore the value of ntNGS-based metagenomic surveillance in virus detection, diversity monitoring, and informing vaccine and biosecurity strategies.}, } @article {pmid41835092, year = {2026}, author = {Pérez, T and Vacelet, J and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the carnivorous sponge, Lycopodina hypogea (Vacelet & Boury-Esnault, 1996) (Poecilosclerida: Cladorhizidae) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {130}, pmid = {41835092}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Lycopodina hypogea (carnivorous sponge; Porifera; Demospongiae; Poecilosclerida; Cladorhizidae). The genome sequence has a total length of 235.10 megabases. Most of the assembly (98.85%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 31.1 kilobases. Gene annotation of this assembly by Ensembl identified 16 317 protein-coding genes. From the metagenome data we recovered 39 bins, of which 27 were high-quality MAGs, including four fully circularised genomes. The MAGs included archaea and bacteria involved in nitrification and sulfate-reduction as well as known sponge symbionts affiliated with Gammaproteobacteria (Candidatus Spongiihabitans, Porisulfidus) and Acidimicrobiales (Candidatus Poriferisodalaceae), among others.}, } @article {pmid41836173, year = {2026}, author = {Fuques, E and Massey, AL and Qureshi, F and Campos-Silva, JV and Ferreira da Silva, DJ and Peres, CA and Levi, T and Vega Thurber, RL}, title = {Large-scale metagenomic surveillance study expands the known diversity of RNA viruses in mosquito populations from the Amazon Basin.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20880}, pmid = {41836173}, issn = {2167-8359}, mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification ; Brazil ; *Metagenomics ; *Culicidae/virology ; Phylogeny ; Female ; Genome, Viral ; *Virome/genetics ; High-Throughput Nucleotide Sequencing ; *Mosquito Vectors/virology ; }, abstract = {The Amazon Basin is one of the most biologically diverse regions on Earth, yet its viral diversity remains poorly characterized. Mosquitoes are important vectors and reservoirs of RNA viruses, but little is known about the composition and structure of their viromes in remote areas of the Amazon. In this study, we performed a large-scale metagenomics survey of RNA viruses associated with mosquito populations collected from the Jurua River region in the Western Amazon Basin of Brazil. We analyzed 211 pooled samples of adult female mosquitoes collected across thirty-seven sites, representing one of the most comprehensive mosquito virome studies conducted in this region to date. Utilizing high-throughput sequencing and de novo assembly, we identified over 500 viral sequences from 18 families, including 21 complete or nearly complete genomes. Our analysis revealed 18 putative novel viral species spanning diverse families and strains of nine previously described viruses. Phylogenetic analyses also revealed undocumented diversity within several virus families, including Iflaviridae, Mesoniviridae, Phasmaviridae, Phenuiviridae, Togaviridae, and Totiviridae, encompassing both novel species and previously known viruses detected for the first time in this region. Our findings highlight the immense, yet largely unexplored, diversity of RNA viruses circulating in mosquito populations in this ecologically rich but understudied region and provide critical insights into the evolutionary dynamics of mosquito-associated viruses. By leveraging high-throughput sequencing to uncover novel viral strains, this research demonstrates the value of metagenomic approaches in expanding the known diversity, distribution, and evolutionary relationships of RNA viruses, contributing to a broader understanding of virus-mosquito interactions and genome evolution.}, } @article {pmid41836379, year = {2026}, author = {Wang, P and Pang, J and Xu, H and Wang, M and Lai, W and Hui, D and Cai, Q and Li, X and Zhu, J}, title = {Hemophagocytic lymphohistiocytosis directly triggered by peginterferon alfa-2b in a patient with chronic hepatitis B.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1760610}, pmid = {41836379}, issn = {1664-3224}, mesh = {Humans ; Male ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/chemically induced/drug therapy/etiology ; *Polyethylene Glycols/adverse effects/therapeutic use ; *Interferon alpha-2/adverse effects ; Adult ; *Hepatitis B, Chronic/drug therapy/complications ; *Antiviral Agents/adverse effects/therapeutic use ; Recombinant Proteins/adverse effects/therapeutic use ; Interferon-alpha ; }, abstract = {This case report describes a 42-year-old male with chronic hepatitis B (CHB) who developed hemophagocytic lymphohistiocytosis (HLH) following treatment with peginterferon alfa-2b (PegIFN-α-2b). The patient tolerated the initial injections well. After the 16th injection in February 2025, laboratory tests revealed cytopenia, prompting discontinuation of PegIFN-α-2b. The onset of a high-grade fever approximately three weeks after drug cessation coincided with the timeframe for the drug's clearance, suggesting a continued immunostimulatory effect. HLH was diagnosed based on hyperferritinemia (>50,000 ng/mL), elevated soluble interleukin-2 receptor (sCD25), and hemophagocytosis on bone marrow biopsy. He responded well to etoposide and dexamethasone. However, his course was complicated by sequential opportunistic infections: severe anemia due to parvovirus B19 (confirmed by plasma metagenomic next-generation sequencing, mNGS) and subsequent herpes simplex virus (HSV) encephalitis (diagnosed via CSF mNGS). Both complications were managed successfully with intravenous immunoglobulin and acyclovir, respectively. This case highlights PegIFN-α-2b as a rare direct trigger of HLH in CHB and underscores the critical risk of opportunistic infections during immunosuppressive therapy, demonstrating the pivotal role of mNGS in diagnosing elusive infections in immunocompromised hosts.}, } @article {pmid41836788, year = {2026}, author = {Cha, JH and Jeong, SA and Ye, BS and Lee, I and Jung, BY}, title = {Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2643036}, pmid = {41836788}, issn = {2000-2297}, abstract = {INTRODUCTION: Dementia poses a growing burden in the aging population, prompting the search for noninvasive biomarkers for early detection.

MATERIALS AND METHODS: We performed shotgun metagenomic sequencing of tongue-coating samples from older adults with dementia (n = 30) and cognitively healthy controls (n = 28) to identify oral microbiome signatures.

RESULTS: The analysis revealed distinct microbial compositions associated with dementia, including an enrichment of Veillonella parvula in dementia patients, whereas Lautropia dentalis was more abundant in healthy controls. We also identified functional alterations in the microbiome in the dementia group, including increased abundance of the histidine degradation and biotin biosynthesis pathways, whereas ubiquinol biosynthesis was more abundant in the healthy control group. The abundance of several microbial taxa and metabolic pathways were correlated with scores on the Korean Mini-Mental State Examination 2nd edition (K-MMSE), a clinical assessment of dementia severity. Prevotella pleuritidis, Actinomyces sp., Leptotrichia buccalis, and Leptotrichia sp. were positively correlated, whereas Oribacterium parvum was negatively associated with K-MMSE scores. Among the metabolic pathways, glutamine/glutamate biosynthesis was positively correlated with cognitive performance.

CONCLUSIONS: These results suggest that specific oral taxa and their metabolic functions are associated with cognitive status and may reflect underlying neurodegenerative processes.}, } @article {pmid41836789, year = {2026}, author = {Manzoor, M and Pussinen, PJ and Saarela, RK and Pitkälä, K and Hiltunen, K and Mäntylä, P}, title = {Denture-associated oral microbiome in dentate and edentulous older adults living in long-term care facilities.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2641915}, pmid = {41836789}, issn = {2000-2297}, abstract = {BACKGROUND: The denture-associated oral microbiome (DAOM) may act as reservoirs of pathogenic microorganisms with potential health effects.

OBJECTIVES: To characterize the compositional and functional activity of the DAOM in dentate and edentulous older adults residing in long-term care facilities (LTCFs).

METHODS: Participants (51 dentate and 56 edentulous) aged ≥64 years were recruited from the Finnish Oral Health Studies in Older Adults. Clinical oral examinations were performed, and biofilm samples for shotgun metagenomics were collected from the acrylic surface of removable dentures. Diversity indices, taxonomic composition, and functional pathways were assessed to characterize DAOM.

RESULTS: Alpha diversity was similar, whereas beta diversity showed modest differences between groups. Dentate participants had a higher abundance of Streptococcus mutans, Veillonella parvula, and Parascardovia denticolens, whereas edentulous participants were enriched with Haemophilus parainfluenzae and Propionibacterium acidifaciens. Edentulous participants had reduced microbial network stability and interconnectedness but highly active microbial metabolic functions, particularly those associated with Streptococcus pneumoniae.

CONCLUSION: Although tooth loss does not markedly alter the overall microbial diversity of DAOM, it is associated with distinct taxonomic and functional shifts. Edentulous individuals have less stable and less interconnected microbial networks alongside heightened metabolic activity, reflecting notable changes in the DAOM of older adults living in LTCFs.}, } @article {pmid41837347, year = {2026}, author = {Arnold, MJ and Bergner, LM and Malik, H and Ten Doeschate, M and Davison, NJ and Brownlow, A and Mollentze, N and Babayan, SA and Streicker, DG}, title = {Drivers of Viral Diversity and Sharing in Marine Mammals.}, journal = {Molecular ecology}, volume = {35}, number = {6}, pages = {e70294}, pmid = {41837347}, issn = {1365-294X}, support = {217221/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 218518/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; BB/V003798/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DEB 2011069/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; PLP-2020-362//Leverhulme Trust/ ; NE/X01424X/1//Natural Environment Research Council/ ; INV-003079/GATES/Gates Foundation/United States ; INV-030025/GATES/Gates Foundation/United States ; MC_UU_00034/3/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Scotland ; *Cetacea/virology ; *Caniformia/virology ; *Viruses/genetics/classification ; Phylogeny ; Biodiversity ; }, abstract = {Knowledge of viral infection in marine mammals, a group severely threatened by human activity, is largely limited to the pathology and epidemiology of few endemic viruses. The recent emergence in marine mammals of high-consequence viruses, such as H5N1 avian influenza and rabies, underscores the importance of understanding the ecology of viral transmission in these species. Metatranscriptomic approaches now enable relatively unbiased characterisation of full viral communities that can reveal ecological and evolutionary drivers of infection. We sequenced RNA from 15 marine mammal species (42 pools, 237 tissues, 128 animals) sampled in Scotland through the Scottish Marine Animal Strandings Scheme. Viral sequences were detected in 41 of 42 pools, representing more than 120 distinct viral taxonomic units (vOTUs). Virus host network analysis showed that viral communities were partly structured by host taxonomy, with clear differences between seals and cetaceans. However, vOTUs were frequently shared between species, mirroring reported ecological interactions, including cross-order sharing between seals and cetaceans. Generalised linear models showed no effect of host taxonomy on viral richness. Instead, age was the strongest predictor: juvenile pools contained roughly twice as many viral taxa as adults and more than neonates, indicating that changing population demography may impact viral transmission in marine mammals. These results provide a basis for understanding how anthropogenic stressors may exacerbate viral transmission in marine mammals and demonstrate the increasing practicality of using genomics to understand ecological and evolutionary drivers of virus infection in natural populations.}, } @article {pmid41837390, year = {2026}, author = {Abagnale, V and Palacin-Lizarbe, C and Paul, D and Kerttula, J and Ronkainen, J and Siljanen, HMP}, title = {Activity and Abundance of Nitrous Oxide Reducing Bacteria in Platismatia glauca: An Epiphytic Lichen in the Boreal Spruce Forest.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70279}, pmid = {41837390}, issn = {1462-2920}, support = {342362//Academy of Finland/ ; 346516//Academy of Finland/ ; 361980//Academy of Finland/ ; 337550//Academy of Finland/ ; 357905//Academy of Finland/ ; 359343//Academy of Finland/ ; 202400252//Maj ja Tor Nesslingin Säätio/ ; 20231200//OLVI-Säätiö/ ; }, mesh = {*Nitrous Oxide/metabolism ; *Lichens/microbiology/metabolism ; *Picea/microbiology ; Finland ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Oxidoreductases/genetics/metabolism ; Taiga ; Forests ; }, abstract = {The nitrous oxide (N2O) dynamics in boreal forests are better known at the ecosystem scale, with greater uncertainty associated with specific ecosystem compartments. We investigated the N2O dynamics of the lichen Platismatia glauca in boreal forests near Kuopio, North Savo, Finland. At the study sites, P. glauca is the most abundant lichen colonising Norway spruce (Picea abies). Despite their abundance, the contribution of epiphytic lichens like P. glauca to N2O dynamics in boreal forests has received little attention. By incubating P. glauca, we assessed the effects of moisture, temperature, and oxygen availability on its N2O dynamics. We observed net N2O consumption potential, particularly at +5°C at aerobic condition. Quantitative real-time PCR analysis targeting the N2O reductase gene fragment (nosZ) revealed that it was present and active in both in situ and incubated lichens. nosZ transcription was higher at +5°C. Clade I nosZ was dominant, with most sequences affiliated with the order Rhizobiales. We confirmed the presence of nosZ gene with targeted metagenomics sequencing. Our results demonstrate that P. glauca acts as a net consumer of N2O, with potential ranging between 0.1 and 0.4 ng N2O-N g DW[-1] h[-1] under aerobic conditions.}, } @article {pmid41837422, year = {2026}, author = {Mwasya, SK and Okanda, D and Odoyo, S and Katama, EN and Lewa, C and Lambisia, AW and Githinji, G and Agoti, CN}, title = {Eight coding-complete genomes of human metapneumovirus recovered by virus metagenomics in coastal Kenya, 2021-2024.}, journal = {Microbiology resource announcements}, volume = {15}, number = {4}, pages = {e0006526}, pmid = {41837422}, issn = {2576-098X}, abstract = {Few human metapneumovirus coding-complete genomes are available from Africa despite significance in optimizing local molecular diagnostics and global phylogeographic analysis. We report eight genomes recovered following nanopore metagenomic sequencing of samples collected in coastal Kenya (2021-2024). These fell into sub-lineages A2b/A2.2.1 (n = 3), A2c-wt/A2.2.2 (n = 4), and B1 (n = 1).}, } @article {pmid41837616, year = {2026}, author = {Fleres, G and Kline, EG and Squires, KM and Tate, T and Creager, HM and Shields, RK and Van Tyne, D}, title = {Within-patient evolution of Pseudomonas aeruginosa populations during antimicrobial treatment.}, journal = {mSphere}, volume = {11}, number = {4}, pages = {e0065625}, pmid = {41837616}, issn = {2379-5042}, support = {SCON-00006650//Cystic Fibrosis Foundation/ ; }, mesh = {*Pseudomonas aeruginosa/genetics/drug effects/classification/isolation & purification ; Humans ; *Pseudomonas Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Whole Genome Sequencing ; Mutation ; *Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; *Evolution, Molecular ; Metagenomics ; Multilocus Sequence Typing ; Genetic Variation ; }, abstract = {UNLABELLED: Multidrug-resistant (MDR) Pseudomonas aeruginosa infections pose a major challenge to effective treatment. Understanding genomic adaptations during antimicrobial therapy in patients infected with this pathogen is crucial for preventing therapeutic failure. Here, we investigated the population diversity and evolution of P. aeruginosa collected longitudinally from six patients who evolved multidrug-resistant infections. Serial clinical P. aeruginosa single-colony isolates (n = 63) and culture-enriched metagenomic population samples (n = 39) were collected and subjected to whole-genome sequencing. The resulting data were used to characterize and compare the species composition, multi-locus sequence types (STs), and resistance-associated mutations present within each sample type. Single-colony isolate sequencing showed that each patient was infected with a single P. aeruginosa strain that accumulated mutations and became increasingly more antibiotic-resistant over time. Mutations in genes associated with β-lactam resistance, including ampC, ftsI, and mexR, arose over time and corresponded with changes in antimicrobial susceptibility in single-colony isolates. Species profiling of culture-enriched metagenomic populations revealed that all samples contained P. aeruginosa, but also additional gram-negative pathogens. Metagenomic analysis of culture-enriched populations identified resistance-associated mutations at low frequency, many of which were not identified in single-colony isolates from the same sample. In some cases, resistance-associated mutations initially detected at low frequency rose to fixation after antimicrobial treatment. Overall, this study shows that population-based metagenomic sequencing effectively captures the within-patient genomic diversity of P. aeruginosa during antimicrobial therapy and could aid the detection and interpretation of resistance-associated mutations in this pathogen.

IMPORTANCE: Pseudomonas aeruginosa infections are notoriously difficult to treat and are associated with high rates of morbidity and mortality. While the genetic basis of resistance in P. aeruginosa is well documented in vitro, less is known about how resistance evolves within patients during antibiotic therapy. Standard approaches based on analysis of clonal isolates may miss within-patient diversity, potentially overlooking low-frequency mutations that contribute to treatment failure. In this study, we compared single-colony isolate whole-genome sequencing with culture-enriched metagenomic sequencing to monitor the evolution of P. aeruginosa populations in patients receiving antibiotic therapy. The culture-enriched metagenomic approach enabled the detection of emerging resistance mutations, such as low-frequency variants in ampC and ftsI, before these variants rose to fixation. It also revealed genetically resistant subpopulations missed by isolate sequencing alone. Overall, our findings highlight the value of population-based metagenomic sequencing in capturing bacterial adaptation during infection and underscore its potential to improve resistance surveillance and guide personalized antimicrobial therapy.}, } @article {pmid41837716, year = {2026}, author = {Pantiukh, K and Krigul, KL and Aasmets, O and Org, E}, title = {Metagenome-assembled genomes from a population-based cohort uncover novel gut species and within-species diversity, revealing prevalent disease associations.}, journal = {mSystems}, volume = {11}, number = {4}, pages = {e0011426}, pmid = {41837716}, issn = {2379-5077}, support = {PRG1414//Estonian Research Council Grant/ ; 3573//EMBO Installation grant/ ; 16-0125//Estonian Center of Genomics/Roadmap II/ ; }, mesh = {Humans ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Cohort Studies ; Genetic Variation ; *Bacteria/genetics/classification ; Genome, Bacterial ; }, abstract = {UNLABELLED: Metagenomic profiling has advanced the understanding of microbe-host interactions. However, widely used read-based approaches are limited by incomplete reference databases and the inability to resolve strain-level variation. Here, we present a scalable, genome-resolved framework that integrates population-specific metagenome-assembled genomes (MAGs) to discover novel species, within-species diversity, and disease associations. From 1,878 deeply sequenced samples in the Estonian Microbiome Cohort (EstMB-deep), we reconstructed 84,762 MAGs representing 2,257 species, including 353 (15.6%) previously uncharacterized species reaching up to 30% relative abundances in some individuals. We integrated these MAGs with the Unified Human Gastrointestinal Genome collection to create an expanded reference (GUTrep), enabling profiling of 2,509 EstMB individuals and testing associations with 33 prevalent diseases. Of the 25 diseases with significant associations, 8 involved newly identified species, underscoring the value of population-specific MAGs. To quantify within-species diversity, we developed the genome unit number (GUN), a novel MAG-based metric that informed within-species analyses. Based on normalized GUN, we prioritized Odoribacter splanchnicus, a prevalent species with the lowest within-species heterogeneity, yielding sufficient power for a within-species association study. We identified two dominant genome units, GU-N1 and GU-N2, with distinct gene repertoires and divergent disease associations. Notably, GU-N1 was negatively associated with gastritis, duodenitis, and hypertensive heart disease, associations undetected at the species level. Our study expands the human gut reference landscape, demonstrates the importance of population-specific MAGs for uncovering novel microbial diversity, and reveals new disease associations at the within-species level obscured at higher taxonomic levels, highlighting the need for genome-resolved approaches in microbiome research.

IMPORTANCE: Microbiome studies increasingly recognize that species-level profiles can mask critical within-species differences relevant to health and disease. However, our work shows that within-species diversity varies drastically across gut microbes, with some species exhibiting almost as many distinct within-species clusters as recovered genomes, making association studies at the within-species level essentially intractable. To address this, we introduce the genome unit number (GUN), a scalable metric for quantifying within-species structure. Using GUN, we demonstrate that only species with limited within-species diversity, such as Odoribacter splanchnicus, currently allow for robust within-species association testing. These findings emphasize the need to systematically evaluate species structure across the gut microbiome and call for the development of new computational and statistical approaches to enable meaningful within-species analyses in highly diverse species.}, } @article {pmid41838353, year = {2026}, author = {Xu, Q and Wang, M and Wang, H and Wu, Z and Li, X and Sun, J and Yang, Z and He, N and Sun, Y and Zhang, H and Zhong, Y and Xiao, L and Li, S and Zou, Y}, title = {Lactobacillus gasseri TF08-1 Alleviates DSS-Induced Acute Colitis by Protecting Intestinal Epithelial Barrier.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41838353}, issn = {1867-1314}, support = {2025YFA1310200//Ministry of Science and Technology of the People's Republic of China/ ; U25A2015//National Natural Science Foundation of China/ ; JCYJ20241202124801003//Shenzhen Municipal Government of China/ ; }, abstract = {Lactobacillus species have been extensively studied for their beneficial effects on vaginal health, but recent evidence highlights their broader therapeutic potential in gut homeostasis. Building on our prior genomic analysis of 3,324 gut bacterial strains, we selected Lactobacillus gasseri TF08-1 for inflammatory bowel disease intervention. In a DSS-induced mouse model, L. gasseri TF08-1 administration produced marked clinical improvements, including attenuated body weight loss, reduced disease activity index (DAI), and restored colon length. Histological analysis confirmed its protective effects on intestinal mucosal integrity. Additionally, L. gasseri TF08-1 alleviated systemic and colonic inflammation by regulating the expression of pro- and anti-inflammatory cytokines. Metagenomic analysis revealed that L. gasseri TF08-1 altered gut microbiota composition, increasing microbial diversity and restoring key genera associated with gut health. These results suggest that L. gasseri TF08-1 holds promise as a therapeutic candidate for inflammatory bowel disease.}, } @article {pmid41838746, year = {2026}, author = {Adachi, K and Chikaraishi, Y and Nomura, S and Goto-Inoue, N and Zaima, N and Kuriya, Y and Araki, M and Morioka, K and Yanagimoto, T and Nakaya, M and Yamamoto, J}, title = {New insights into the feeding behaviour of the Japanese squid Todarodes pacificus paralarvae, and a combined analysis of metagenome and amino acid isotope ratios.}, journal = {PloS one}, volume = {21}, number = {3}, pages = {e0340579}, pmid = {41838746}, issn = {1932-6203}, mesh = {Animals ; *Decapodiformes/physiology/genetics/microbiology ; *Metagenome ; *Feeding Behavior/physiology ; *Amino Acids/metabolism ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Nitrogen Isotopes ; Electron Transport Complex IV/genetics ; }, abstract = {The Japanese flying squid Todarodes pacificus (Ommastrephidae) is a commercially and ecologically important species; however, there remains much room for investigation in its early life phase, especially its diet in wild environments. After excising the digestive gland (cecum sac) of wild paralarvae of T. pacificus using Laser Microdissection (LMD), the dietary species were estimated via metagenomic analysis. The 16S rRNA analysis predominantly detected Burkholderiales and Xanthomonadales, regardless of mantle length (ML) of T. pacificus and capture area. COI (Cytochrome c oxidase subunit I) analysis detected in various organisms including Discosea, Arthropoda, Nemertea, Porifera, golden algae, and fungi (Ascomycota and Basidiomycota), which were found irregularly. About half of the paralarval cecum sacs were found empty during the histological analysis. We also estimated the trophic position (TP) of wild paralarvae in the same sea region via stable isotope analysis of amino acids. The TP estimated was 3.0 for all larval groups regardless of ML, suggesting that the trophic tendency of paralarvae is carnivorous, likely feeding on herbivorous organisms. Taken together, our results suggest that the paralarvae feed mostly on various kinds of living herbivorous organisms and partly on detritus.}, } @article {pmid41838875, year = {2026}, author = {Chen, Q and Zhang, B and Peng, C and Huang, J and Liu, Z and Shen, X and Jiang, C}, title = {Kun-peng enables scalable and accurate pan-domain metagenomic classification.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {2}, pages = {}, pmid = {41838875}, issn = {1477-4054}, support = {82341109//National Natural Science Foundation of China/ ; 82173645//National Natural Science Foundation of China/ ; }, mesh = {*Metagenomics/methods ; *Metagenome ; Algorithms ; Humans ; *Software ; Databases, Genetic ; *Computational Biology/methods ; }, abstract = {Comprehensive pan-domain metagenomic classification is increasingly constrained by the memory and runtime costs of building and querying the rapidly expanding reference genome space. We introduce Kun-peng, a taxonomic classifier powered by an intelligent block-partitioned database structure and optimized search strategies, enabling ultra-scalable, memory-efficient pan-domain profiling. Using the Critical Assessment of Metagenome Interpretation II benchmark, Kun-peng substantially reduces the memory usage of database-building and querying by up to 24-fold, and accelerates sample classification by up to 4.73-fold compared with Kraken2. Kun-peng achieves competitive accuracy with fewer false positives than Kraken2, Centrifuger, and even KrakenUniq, while maintaining consistently high sensitivity across diverse datasets. In a real-world evaluation of 586 metagenomic samples spanning air, water, soil, and human-associated environments, we performed classification using a 4.3 TB pan-domain database comprising 204,477 genomes, which was built by Kun-peng with only 4.1 GB peak memory. Kun-peng processed each sample in 0.2-11.2 min with 4.0-35.4 GB peak memory, corresponding to a 54-473-fold reduction in memory usage relative to Kraken2. Compared with Sylph, Kun-peng achieved up to a 46-fold speedup while requiring 21-fold less memory. Kun-peng classified 69.8%-94.3% of reads, improving coverage by 20%-60% over the standard Kraken2 database with 62,026 genomes. This improvement reflects expanded reference coverage, although a small fraction of false positives is inherent to k-mer-based methods. Overall, Kun-peng effectively eliminates the long-standing memory bottleneck in pan-domain database building and classification, enabling rapid and scalable pan-domain taxonomic analysis of complex environmental, ecological, and exposomic sequencing datasets.}, } @article {pmid41839407, year = {2026}, author = {Chen, S and Zhao, A and Zhang, W and Liu, Q and Li, D}, title = {Metabolic reprogramming disrupts the resistome-mobilome nexus and enhances bio-sanitization in synthetic microbial community-mediated composting.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134433}, doi = {10.1016/j.biortech.2026.134433}, pmid = {41839407}, issn = {1873-2976}, mesh = {*Composting/methods ; *Microbiota ; *Drug Resistance, Microbial/genetics ; Lignin/metabolism ; Bacteria/metabolism/genetics ; }, abstract = {The persistence of antibiotic resistance genes (ARGs) and pathogens during manure composting poses critical risks within the One Health framework. However, the ecological and metabolic mechanisms by which microbiome engineering disrupts the dissemination of these biohazards remain poorly understood. This study evaluated a thermophilic lignocellulose-degrading synthetic microbial community (SynCom, comprising Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum) in mitigating these risks. KEGG analysis highlighted a pivotal metabolic reprogramming from a biofilm-dependent defense-survival model to an active motility-metabolism mode, characterized by depleted lipopolysaccharide biosynthesis and enriched flagellar assembly. This metabolic shift implies a fitness cost trade-off that physically restricts horizontal gene transfer (HGT) opportunities. Metagenomic analysis showed SynCom inoculation caused a transient ARG rebound followed by profound attenuation. While thermophilic hosts temporarily enriched specific ARGs, SynCom ultimately achieved a significant reduction in multidrug resistance genes and virulence factors by intensifying thermophilic fermentation. Mantel correlation analysis revealed the SynCom-driven rapid decrease in carbon/nitrogen ratio and enhanced humification were critical environmental drivers, restricting ARGs and alleviating co-selection pressure on metal resistance genes. Network analysis demonstrated SynCom induced a structural collapse of high-risk interactomes (reducing potential host-gene associations by 26.6%), effectively disrupting ARG and mobile genetic element connections by suppressing key recombinases (XerD, IntI1) and eliminating Pseudomonadota hub hosts. Consequently, deep bio-sanitization was achieved by synchronously eliminating high-risk pathogens (e.g., Pseudomonas aeruginosa), phytopathogens, and specific virulence factors. These findings indicate that SynCom provides a robust microbiome engineering strategy to disrupt the genetic dissemination of biohazards and ensure organic fertilizer biosafety.}, } @article {pmid41839411, year = {2026}, author = {Duan, Z and Kong, X and Yue, J and Han, X and Zhu, G and Yu, H}, title = {Integrated multi-barrier attenuation of antibiotic resistance genes by self-elevating ultra-high temperature composting: Phase-resolved evidence for within-process risk reduction.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134432}, doi = {10.1016/j.biortech.2026.134432}, pmid = {41839411}, issn = {1873-2976}, mesh = {*Composting/methods ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial/genetics ; *Hot Temperature ; Temperature ; }, abstract = {The dissemination of antibiotic resistance genes (ARGs) from livestock manure poses risks to environmental and public health, while conventional composting often shows limited and inconsistent ARG attenuation. Here, we evaluated ARG and mobile genetic element (MGE) dynamics during self-elevating ultra-high temperature composting (sf-HTC) and examined phase-resolved associations among thermal conditions, microbial succession, MGE patterns, and humification indicators using metagenomics, network analysis, and structural equation modeling (SEM). Sf-HTC reduced the absolute abundance of total ARGs and MGEs by 98.86% within 28 days. High-risk ARG classes (tetracycline and sulfonamide-resistance genes) decreased by>94.3%, outperforming traditional composting (TC). The hyperthermophilic phase coincided with the largest decreases in ARGs and with enrichment of thermophilic genera (Calditerricola and Thermophilum) and increased microbial network complexity. SEM further suggested that the thermal regime, reductions in MGEs, and increased humification were major, interrelated pathways statistically associated with ARG reduction (standardized path coefficients: 0.97, -1.41, and 0.78, respectively). Sf-HTC also promoted humic acid accumulation (up to 58.9 g/kg) and more aromatic dissolved organic matter, which was consistent with enhanced immobilization potential for residual ARGs. Overall, our results support a phase-resolved "thermal-biological-chemical" multi-barrier conceptual model for ARG attenuation during sf-HTC and highlight its potential for reducing resistome burdens in agricultural organic wastes.}, } @article {pmid41839668, year = {2026}, author = {Nadeem, SA and Ali, I and Hussain, H and Ullah, I and Ali, W and Alzahrani, KJ and Ali, H and Khan, ZI and Abass, KS and Rahman, RU}, title = {Metagenomic analysis of bacterial and viral communities of Aedes aegypti and Aedes albopictus.}, journal = {Journal, genetic engineering & biotechnology}, volume = {24}, number = {1}, pages = {100643}, pmid = {41839668}, issn = {2090-5920}, abstract = {BACKGROUND: The complicated relationship between the Aedes mosquito microbiome, arbovirus transmission and essential physiological processes, is extremely important. Microbial community plays a vital role in shaping vector biology, impacting critical aspects such as parasite replication within the vector, vector longevity, and ultimately, vector competence. Understanding the composition and function of the Aedes microbiome is therefore crucial for developing novel strategies to control arboviral diseases. Therefore, we aimed to identify prevalent bacterial and viral communities in Aedes mosquitoes from Pakistan.

METHODS: Ae. aegypti and Ae. albopictus were collected and from three different regions of Khyber Pakhtoonkhwa, Punjab and federal capital Islamabad. We isolated DNA and sequenced two pools of each species and conducted metagenomic analysis, identifying a variety of bacteria and viruses.

RESULTS: We found diverse bacterial and viral communities in both studied species. In Ae. aegypti, the most abundant bacterial species was Klebsiella pneumoniae followed by Acinetobacter baylyi. Ae. albopictus presented Pseudomonas putida as the most abundant bacterial species followed by Brevundimonas diminuta. Similarly in Ae. aegypti, we found that Escherichia phage HK639 was the most abundant viral species while in Ae. albopictus, it was Lactobacillus phage 2. It is important to mention that the prevalent viruses in both Aedes species belong to the Siphoviridae genus.}, } @article {pmid41840004, year = {2026}, author = {Das, R and Tamang, B}, title = {Metagenomic insights reveal β-glucosidase-producing lactic acid bacteria from Miyamikhri with taxiphyllin degradation potential.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41840004}, issn = {2045-2322}, abstract = {UNLABELLED: “Miyamikhri,” a traditionally fermented bamboo shoot consumed by the Dimasa tribe of Assam, was investigated using a multi-omics approach integrating metagenomics, functional prediction, molecular docking, and probiotic evaluation. Samples (M1, M2, M3; pH: 4.03–4.52) showed Bacillota dominance (50.04–100%), with notable abundance of Cyanobacteria (M1: 32.72%) and Proteobacteria (M2: 28.85%). At the genus level, Lactobacillus (38.75–60.86%), Weissella, and Pediococcus were predominant. Diversity indices indicated M3 had the highest diversity species (Simpson: 0.7099; Evenness: 0.9199), while M1 showed the highest richness (Chao-1 = 6). Functionally, predictive KEGG analysis identified enrichment in metabolism (29.72%) and disease-related pathways (23.27%). Genes related to dopaminergic synapse (mao, comt, ddc, th), cyanoamino acid metabolism (bgl) and glycerolipid metabolism (mgll, gk, agpat1, lpin1) were detected. From 51 LAB isolates, eight showed high β-D-glucosidases activity (> 0.7 µg/mL pNP); Levilactobacillus brevis M12 exhibited the highest activity under optimal conditions (pH 5, 30 °C, 7% NaCl). Molecular docking revealed highest affinity of − 8.049 kcal/mol (M12) with taxiphyllin. MD simulations (100 ns) confirmed complex stability (RMSD: 0.27 ± 0.04 nm, avg. H-bonds: 6.86), and MM-PBSA calculations showed stronger binding for M12 (–190.28 kJ/mol) over L. plantarum WCFS1 (–49.16 kJ/mol).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-43021-w.}, } @article {pmid41840154, year = {2026}, author = {Garza-González, DA and Quezada-Euán, JJG and Medina-Medina, LA and Solís-Sánchez, T and O'Connor-Sánchez, A}, title = {Comparative analysis of the gut microbiota of the sympatric stingless bee species Melipona beecheii and Melipona yucatanica.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {41840154}, issn = {1678-4405}, support = {INFR2016 01-269833//Consejo Nacional de Ciencia y Tecnología/ ; CAR-21861//Universidad Autónoma de Yucatán/ ; }, abstract = {The gut microbiota of insects plays a crucial role in host health and is thought to have co-evolved with each species. In stingless bees, a general understanding of these associations has begun to emerge; however, several important knowledge gaps remain. In this study, we employed amplicon sequencing to compare the gut microbiota of individual specimens from two closely related and sympatric Neotropical stingless bee species from the Maya region, Melipona beecheii and Melipona yucatanica. Our results revealed that (i) most amplicon sequence variants (ASVs) in both species were transient; (ii) the core microbiota of these species was almost entirely distinct, sharing only one ASV out of a total of 31; and (iii) despite this divergence, all core ASVs identified in both species belonged to only four bacterial orders. This pattern suggests that, while their microbiota have differentiated at finer taxonomic scales, it likely originated from a shared ancestral community. We contextualize these findings within the current understanding of stingless bee microbiotas and highlight future directions for exploring their evolution and diversity.}, } @article {pmid41840625, year = {2026}, author = {Zhang, Y and Zhang, Q and Luo, Y and Li, X and Zhao, R and Xu, Y and Zhang, S and Bai, X and Chen, H and Li, H and Hong, Y and Xie, Z}, title = {Bifidobacterium breve inhibits colorectal cancer via extracellular vesicles containing formate acetyltransferase.}, journal = {Journal of nanobiotechnology}, volume = {24}, number = {1}, pages = {}, pmid = {41840625}, issn = {1477-3155}, support = {82574649//National Natural Science Foundation of China/ ; JCYJ20250604175304006//Shenzhen Municipal Science and Technology Innovation Council/ ; 2023B03J1382//Guangzhou Science and Technology Program/ ; 2022ZD004//Nansha Science and Technology Program/ ; }, mesh = {*Extracellular Vesicles/metabolism ; Animals ; Humans ; *Colorectal Neoplasms/pathology/microbiology/drug therapy/metabolism/therapy ; *Bifidobacterium breve/enzymology/metabolism ; Mice ; *Probiotics/pharmacology ; Apoptosis/drug effects ; *Acetyltransferases/metabolism ; Cell Line, Tumor ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is the second leading cause of cancer-related mortality worldwide. The gut microbiota exerts unique therapeutic advantages against CRC, and the probiotic Bifidobacterium breve (B. breve) has been extensively documented to suppress CRC initiation in murine models. Although the role of B. breve in CRC has been established, whether its extracellular vesicles (EVs), as key mediators of bacteria-host crosstalk, exert a functional impact remains undefined. Here, we aim to explore the therapeutic potential of B. breve-derived EVs (B.breEVs) and their active cargo, formate acetyltransferase (pflB), in CRC.

RESULTS: Integrative analysis of the curated database of human gut metagenomes cohort (GMrepo) database and an MC38 subcutaneous tumor model revealed a significant reduction of B. breve abundance in faecal samples from CRC patients and tumor-bearing mice. Administration of live B. breve or its cell-free supernatant markedly inhibited tumor growth, whereas pasteurized bacteria or GW4869-mediated EVs blockade abolished this effect, indicating that EVs are the critical effector entities. Isolated B.breEVs selectively accumulated within tumor tissue, directly triggered apoptosis of colorectal cancer cells, and elevated the proportion of IFN-γ⁺ CD8⁺ cytotoxic T lymphocytes (CTLs) in tumor while concurrently ameliorating gut microbial structure and function. Mass-spectrometric profiling identified the pflB as an important active protein within B.breEVs. Recombinant pflB selectively inhibited MC38 cell viability in vitro and significantly reduced CRC burden in vivo. RNA sequencing of tumor issue demonstrated that pflB up-regulated granzyme B, perforin1 and CTL/NK-associated transcripts, and activated the intrinsic apoptotic pathway. Immuno-combination studies further revealed that pflB plus anti-PD1 therapy markedly increased the infiltration of CD8⁺ CTL and NK cells, and enhanced their cytotoxicity compared to either monotherapy.

CONCLUSIONS: B. breve secretes pflB-loaded EVs that reshape the intestinal micro-ecology, activate CD8⁺ CTL/NK anti-tumor immunity, directly induce mitochondrial apoptosis in malignant cells, and enhance the effects of immune checkpoint blockers to overcome drug resistance, offering a precision "probiotic-EVs-active protein" triadic intervention strategy for CRC.}, } @article {pmid41840712, year = {2026}, author = {Xu, L and Liu, C and Chen, S and Mao, A and Zi, X and Li, J and Ge, X and Liu, Q and Wang, S and Li, X and Wu, Q and Wan, J and Zhang, Z and Xu, H and Li, J and Lin, Q and Cao, Z}, title = {Characterization of age-related changes in the gut microbiome and metabolome of Kunming dogs and their associations with police performance.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41840712}, issn = {2049-2618}, support = {2023YNPKLANF004//Open Foundation of the Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science/ ; YNWR-QNBJ-2018-137//Young Talent of Yunnan Xingdian Support Project for High Level Talents/ ; 202305AC160040//Yunnan Provincial Middle-Young Academic and Technical Leader Candidate/ ; }, mesh = {Animals ; Dogs/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Metabolome ; Age Factors ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Police ; Male ; Aging ; Metagenome ; Female ; Feces/microbiology ; }, abstract = {BACKGROUND: Gut microbiota plays a pivotal role in regulating the host's central nervous system (CNS) activity and behavior. However, its influence on the police performance of Kunming dogs and the underlying mechanisms remain largely unexplored. This study was the first to apply multi-omics technologies to investigate the dynamic variations in gut microbiota and their metabolic profiles across different ages of Kunming dogs. Furthermore, we systematically examined the associations between these microbial alterations and police performance metrics, providing a theoretical foundation for enhancing the working capabilities of Kunming dogs through targeted modulation of intestinal microecology.

RESULTS: The study showed that puppies, young dogs and adult dogs had significantly better police performance than elderly dogs, with young dogs exhibiting the highest scores. Analysis of 16S rRNA sequencing demonstrated that gut microbial diversity and stability were highest during the young dog stage, gradually declining with age. Metagenomic analysis revealed that the abundance of Lactobacillus acidophilus, Lactobacillus johnsonii, Limosilactobacillus reuteri, Ligilactobacillus animalis and Muribaculum gordoncarteri were strongly correlated with police performance. The results of metagenome-assembled genomes (MAGs) indicated that the above species have functional genes involved in GABAergic and glutamatergic synapse pathways. Furthermore, metabolomic analysis showed that differential metabolites were enriched in the neuroactive ligand-receptor interaction pathway, in which GABA (γ-aminobutyric acid), histamine and tyramine metabolites were positively correlated with the above species and police performance.

CONCLUSION: The species L. acidophilus, L. johnsonii, L. reuteri, L. animalis, and M. gordoncarteri, which were enriched in the gut of puppies and young Kunming dogs, may potentially influence the nervous system through the production of neurotransmitters and neuromodulators, suggesting a possible association with police performance. Video Abstract.}, } @article {pmid41840715, year = {2026}, author = {Liang, R and Liu, X and Chen, Q and Zhang, M and Xu, Y and Shi, H and Wang, S and Jing, W}, title = {Daikenchuto ameliorates dextran sulfate sodium-induced acute and chronic ulcerative colitis by regulating gut microbiota-derived indoles to activate AhR signaling.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {}, pmid = {41840715}, issn = {1749-8546}, support = {82174059//National Natural Science Foundation of China/ ; 2022SF-123//Natural Science Foundation of Shaanxi Province/ ; 2023-ZQNY-004//Outstanding Young and Middle-Aged Scientific and Technological Talents of Shaanxi Administration of Traditional Chinese Medicine/ ; 2022-SLRH-YQ-001//Shaanxi Administration of Traditional Chinese Medicine/ ; JCYJ20250604184258076//Science and Technology Planning Project of Shenzen Municipality, China/ ; }, abstract = {BACKGROUND: Ulcerative colitis (UC), a chronic-relapsing inflammatory disease with rising prevalence worldwide, is primarily driven by intestinal epithelial barrier dysfunction resulting from gut microbial dysbiosis and metabolic disturbances. Daikenchuto (DKT), a traditional Chinese medicine formulation, is commonly used for digestive disorders. Although DKT has demonstrated therapeutic potential for gut inflammation by modulating gut microbiota, its therapeutic effects on chronic ulcerative colitis (CUC) and the related mechanisms remain elusive.

METHODS: The main components of DKT were tentatively identified using ultra-performance liquid chromatography-quadrupole-time of flight-mass spectrometry (UPLC-Q-TOF-MS), and the therapeutic effects of DKT were evaluated in the mouse models of acute colitis (AC) and CUC induced using dextran sulfate sodium. The models were validated based on alterations in the disease activity index (DAI), colonic inflammatory status, and intestinal barrier integrity. The impact of DKT on the dysbiosis of gut microbiota was evaluated using the 16S rRNA gene and metagenomic sequencing. Targeted metabolomics was conducted to quantify shifts in short-chain fatty acids and tryptophan (Trp) metabolites. To further elucidate the underlying mechanisms of DKT, key pathways were analyzed using Western blotting, immunohistochemistry, and real-time quantitative polymerase chain reaction.

RESULTS: The principal constituents of DKT were tentatively identified. DKT administration significantly alleviated the symptoms of AC and CUC, reduced inflammation, and maintained intestinal barrier function. Furthermore, DKT modulated the structure and abundance of gut microbiota. Metagenomic sequencing analysis demonstrated that DKT significantly enriched the relative abundance of Ligilactobacillus murinus, Lactobacillus taiwanensis, and Lactobacillus johnsonii. Moreover, Trp metabolism and Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathways might be the therapeutic mechanisms of DKT. Targeted metabolomics confirmed that Trp/indole was the major pathway during the therapeutic process of DKT on CUC. Further mechanistic studies demonstrated that activation of the aryl hydrocarbon receptor (AhR) signaling enhanced proliferation in the colonic crypts by stimulating IL-22 secretion and promoting STAT3 phosphorylation.

CONCLUSIONS: DKT alleviated AC and CUC in mouse models by modulating gut microbiota, restoring Trp metabolism, and activating the AhR/IL-22/STAT3 signaling pathway. These findings provide a basis for the clinical application of DKT in UC patients.}, } @article {pmid41840729, year = {2026}, author = {Mori, H and Fujisawa, T and Higashi, K and Tanizawa, Y and Nakagawa, Z and Nishide, H and Fujiyoshi, M and Nakamura, Y and Uchiyama, I and Matsui, M and Yamada, T}, title = {Microbiome Datahub: an open-access platform integrating environmental metadata, taxonomy, and functional annotation for comprehensive metagenome-assembled genome datasets.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41840729}, issn = {2049-2618}, support = {JPMJND2206//Japan Science and Technology Agency/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *Metadata ; Molecular Sequence Annotation ; *Microbiota/genetics ; *Databases, Genetic ; *Bacteria/classification/genetics ; Computational Biology/methods ; Biocuration ; }, abstract = {BACKGROUND: Metagenome-assembled genomes (MAGs) provide crucial insights into the genomic diversity of uncultured microbes. However, MAG datasets deposited in public repositories such as INSDC are often difficult to reuse due to heterogeneous quality, inconsistent taxonomic and functional annotations, and insufficiently curated environmental metadata. While secondary MAG databases such as MGnify, IMG/M, and SPIRE provide standardized resources, they reconstruct MAGs de novo from public metagenomic reads and therefore do not represent the original MAGs reported in publications.

RESULTS: To address this gap, we developed Microbiome Datahub, an open-access platform that systematically aggregates and re-annotates original MAGs from INSDC. We collected 214,427 MAGs, predicted genes by DFAST, performed quality assessment with CheckM, standardized taxonomic assignments with GTDB-Tk, inferred 27 phenotypic traits using Bac2Feature, assigned proteins to MBGD ortholog clusters and KEGG Orthology IDs using PZLAST, and annotated environmental metadata with the Metagenome and Microbes Environmental Ontology. Across these MAGs, the average completeness was 80.5% and contamination 1.8%; notably, the most frequent values were >95% completeness and <1% contamination, indicating that the majority of MAGs are of high quality. Comparative analyses showed that Microbiome Datahub provides phylogenetically and environmentally diverse MAGs: while the majority originated from vertebrate gut environments, a substantial number were also recovered from other habitats such as groundwater, including nearly 10,000 MAGs from the Patescibacteria. Inference of 27 phenotypic traits, including optimum growth temperature, further revealed ecological differentiation across phyla. Protein clustering revealed 56 million identity 40% clusters, with the majority unique compared with MGnify and GlobDB, and ~19% of proteins unassigned to MBGD ortholog clusters, underscoring their novelty.

CONCLUSIONS: Microbiome Datahub integrates MAG genome sequences, gene and protein predictions, quality metrics, environmental and taxonomic annotations, ortholog cluster assignments, and phenotype predictions, all accessible via a web interface, API, and bulk downloads. By combining original MAGs with curated metadata and functional annotations, Microbiome Datahub constitutes a comprehensive and reusable resource that will accelerate microbiome and microbial genomics research. Video Abstract.}, } @article {pmid41841243, year = {2026}, author = {Sbampato, V and Khan, AA and Tsoupras, A and De Marco, G and Ceroni, D}, title = {From Culture to Sequencing: Evolving Strategies for the Diagnosis of Pediatric Spondylodiscitis.}, journal = {Orthopaedic surgery}, volume = {18}, number = {4}, pages = {607-618}, pmid = {41841243}, issn = {1757-7861}, mesh = {Humans ; *Discitis/diagnosis/microbiology ; Child ; }, abstract = {Pediatric spondylodiscitis is a rare but clinically significant infection affecting the intervertebral disc and adjacent vertebral bodies. Diagnostic delays are common due to its nonspecific presentation and the limited sensitivity of conventional microbiological methods. Early and accurate pathogen identification is essential to guide antimicrobial therapy, minimize unnecessary invasive procedures, and prevent long-term sequelae. Traditional diagnostic tools-including laboratory tests, imaging, blood cultures, biopsy, and histopathological evaluation-remain fundamental but are often insufficient, as they may yield nonspecific results or culture-negative cases, particularly after prior antibiotic exposure or infection with fastidious organisms. In recent years, molecular approaches, ranging from polymerase chain reaction assays to metagenomic next-generation sequencing, have markedly improved diagnostic accuracy. These techniques allow rapid and comprehensive pathogen detection, including atypical or previously uncultivable organisms, thereby overcoming many limitations of conventional methods. This narrative review synthesizes current evidence on pediatric spondylodiscitis, outlining its epidemiology, clinical features, and the evolving spectrum of diagnostic strategies-from conventional methods to advanced molecular and sequencing-based technologies-while discussing future directions in this challenging field.}, } @article {pmid41841491, year = {2026}, author = {Vidal, E and Phanthanourak, AL and Gharib, A and Webel, H and Assis, J and Ayala-Ruano, S and Cunha, AF and Santos, A}, title = {ABaCo: addressing heterogeneity challenges in metagenomic data integration with adversarial generative models.}, journal = {Nucleic acids research}, volume = {54}, number = {5}, pages = {}, pmid = {41841491}, issn = {1362-4962}, support = {NNF20CC0035580//Novo Nordisk Foundation/ ; Pasteur Network, Sep/2023//Calmette & Yersin PhD Grant/ ; }, mesh = {*Metagenomics/methods ; Autoencoder ; Humans ; *Software ; Microbiota/genetics ; Generative Adversarial Networks ; Algorithms ; Generative Artificial Intelligence ; Metagenome ; }, abstract = {The rapid advancement of high-throughput metagenomics has produced extensive and heterogeneous datasets with significant implications for environmental and human health. Integrating these datasets is crucial for understanding the functional roles of microbiomes and the interactions within microbial communities. However, this integration remains challenging due to technical heterogeneity and the inherent complexity of these biological systems. To address these challenges, we introduce ABaCo, a generative model that combines a variational autoencoder with an adversarial discriminator specifically designed to handle the unique characteristics of metagenomic data. Our results demonstrate that ABaCo effectively integrates metagenomic data from multiple studies, corrects technical heterogeneity, outperforms existing methods, and preserves taxonomic-level biological signals. We have developed ABaCo as an open-source, fully documented Python library to facilitate, support and enhance metagenomics research in the scientific community.}, } @article {pmid41841524, year = {2026}, author = {Akresi, JE and Do, TVT and Cui, Z and Shanmugam, NRS and Moraïs, S and Mizrahi, I and Bayer, EA and Auchtung, JM and Yin, Y}, title = {Limousia bacteria encode mucinolysome for mucin utilization in animal gut microbiomes.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2645267}, pmid = {41841524}, issn = {1949-0984}, support = {R01 GM140370/GM/NIGMS NIH HHS/United States ; R03 OD039979/OD/NIH HHS/United States ; }, mesh = {Animals ; *Mucins/metabolism ; Humans ; *Gastrointestinal Microbiome ; Metagenome ; Feces/microbiology ; Cell Cycle Proteins/metabolism ; Cohesins ; Bacterial Proteins/metabolism/genetics ; *Eubacteriales/metabolism/genetics/isolation & purification/classification ; Animals, Domestic/microbiology ; }, abstract = {Mucins create a physical barrier that protects human and animal tissues from microbial pathogens. Here, we provide evidence that mucin degradation can be mediated by unique mucinolysomes, defined as extracellular cellulosome-like multi-enzyme complexes specializing in mucin degradation. We predicted the presence of mucinolysomes across 63 metagenome-assembled genomes (MAGs) and two isolated genomes of three anaerobic species of Limousia, including seven MAGs from human gut microbiome samples from six countries. We validated that mucins can support the growth of the Limousia strain ET540 as its sole carbon source, triggering the upregulation of most mucinolysome-related genes in ET540. We modeled the mucinolysome assembly by predicting cohesin‒dockerin interactions among most of the mucinolysome proteins using AlphaFold3. We performed metagenomic read mapping of 2897 fecal samples from various human cohorts and wild/domesticated animals against Limousia MAGs. We found that Limousia has a greater abundance and prevalence in farm animals than in humans. This study characterizes and adds the Limousia bacteria as unique member to the list of human and animal gut mucin glycan-degrading bacteria. Overall, we discovered that this novel gut bacteria genus (Limousia) uses a previously unrecognized molecular mechanism for highly organized mucin glycan degradation, shedding new light on microbe‒host interactions in the gastrointestinal tracts of diverse animal hosts, including humans.}, } @article {pmid41841608, year = {2026}, author = {Farsi, DN and Cotillard, A and Wilson, B and So, D and Gibson, PS and Slater, R and Probert, C and Morris, S and Scott, SM and Quinquis, L and Pichaud, M and Shetty, S and Tap, J and Le Nevé, B and Rossi, M and Whelan, K}, title = {Gut Microbiome Composition and Function, Diet, and Clinical Factors in Relation to Fermentable Carbohydrate-Induced Bloating: A Double-Blind, Randomized, Crossover Trial.}, journal = {The American journal of gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.14309/ajg.0000000000003997}, pmid = {41841608}, issn = {1572-0241}, support = {//Danone/ ; }, abstract = {INTRODUCTION: Specific foods are associated with abdominal bloating, which can significantly affect quality of life. To identify responders to fiber-induced bloating and the mechanisms underpinning clinical and microbial responses.

METHODS: Double-blind, placebo-controlled, randomized, 2-period, 2-challenge crossover trial in 41 individuals with functional bloating. Participants were randomized to 8 g/d of fructan or α-galacto-oligosaccharides (α-GOS) for 7 days with a 21-day washout. Clinical, nutritional, microbial (shotgun sequencing, metatranscriptomics), and fermentation (short-chain fatty acids, volatile organic compounds, breath hydrogen) profiles were characterized before each challenge to identify factors predicting response and after the challenge to elucidate mechanisms underpinning food-induced bloating.

RESULTS: Thirty-nine participants completed both challenges (39 fructan, 40 α-GOS). Overall, 7 (7/39, 17.9%) participants were fructan responders and 8 (8/40, 20%) were α-GOS responders (experienced fiber-related symptom induction). Clinical metrics indicative of bloating distinguished responders and nonresponders to both challenges, including greater abdominal girth (fructan, P = 0.009; α-GOS, P = 0.030). α-GOS responders had higher breath hydrogen (H 2) prechallenge than α-GOS nonresponders (P = 0.011). Trends were identified within metagenomic and metatranscriptomic gut microbial analyses, with higher carbohydrate active enzyme (CAZyme) diversity in fructan responders (prechallenge, adjusted P -value (P adj) = 0.024; postchallenge, P adj = 0.042) and greater increase in gene expression for gamma-aminobutyric acid (GABA) degradation in α-GOS responders (P adj = 0.041).

DISCUSSION: A higher burden of GI symptoms predicts clinical response to fermentable fibers in functional bloating, while for α-GOS, higher repeated fasting breath H 2 is also a predictor. Gut microbiome function and fermentation is associated with functional bloating; however, further investigations are required to draw firm conclusions for the microbial influence in this interplay.}, } @article {pmid41841712, year = {2026}, author = {Oganesyan, EG and Zhuk, AS and Venchakova, VV and Dolgo-Saburova, YV and Zhorzh, ON and Zhang, FM and Vasilyeva, NV and Taraskina, AE}, title = {Microbiome associated with recurrent vulvovaginal candidiasis: key characteristics and potential therapeutic targets.}, journal = {Biomeditsinskaia khimiia}, volume = {72}, number = {1}, pages = {62-74}, doi = {10.18097/PBMCR1644}, pmid = {41841712}, issn = {2310-6972}, mesh = {Humans ; Female ; *Candidiasis, Vulvovaginal/microbiology ; *Microbiota ; *Vagina/microbiology ; Adult ; Case-Control Studies ; Lactobacillus/isolation & purification/genetics ; Recurrence ; Prevotella ; }, abstract = {Recurrent vulvovaginal candidiasis (RVVC) is one of the most complex forms of urogenital infection in terms of its clinical burden, impact on quality of life, and difficulty in preventing relapses. The aim of this study was to comprehensively characterize the taxonomic composition and functional potential of the vaginal microbiome associated with RVVC. This case-control study included patients with RVVC and conditionally healthy women. Vaginal samples were analyzed using shotgun metagenomic sequencing, followed by taxonomic and functional annotation of the microbiome using data quality control, taxonomic classification (Kraken2, MetaPhlAn4), and functional annotation (HUMAnN 3.9). At the community structure level, the RVVC microbiome exhibited pronounced interindividual variability and did not represent a uniform microbiota configuration. The taxonomic profile of the microbiome in RVVC was characterized by an increased relative abundance of Lactobacillus iners and anaerobic taxa (Prevotella bivia, Dialister microaerophilus), forming a compact "core" of intergroup differences. Functional analysis revealed a limited but reproducible set of metabolic pathways associated with RVVC; these included pathways of purine metabolism, central carbohydrate metabolism, and biosynthesis of cofactors and cell wall components. RVVC is associated not only with changes in the taxonomic composition of the microbiota but also with a stable reconfiguration of its functional potential. The identified shifts in metabolic pathway patterns reflect a transition of the vaginal microbial community to an alternative functional state, thus highlighting the need to develop new therapeutic strategies alternative to traditional antifungal-based approaches.}, } @article {pmid41841737, year = {2026}, author = {Cruz, MC and Ruhal, R and Lavin, J and Bridwell, S and Maghboli Balasjin, N and Raasch, B and Melton, R and Mayer, BK and Marshall, CW and Hristova, K}, title = {Acinetobacter spp. with lower susceptibility to quaternary ammonium compounds enriched in microbial communities of frequently used sinks.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {4}, pages = {e0196825}, pmid = {41841737}, issn = {1098-5336}, support = {W9132T-22-2-0001//U.S. Department of Defense/ ; }, mesh = {*Quaternary Ammonium Compounds/pharmacology ; *Acinetobacter/drug effects/genetics/isolation & purification/physiology ; *Disinfectants/pharmacology ; Biofilms/drug effects ; *Microbiota/drug effects ; Seasons ; Drug Resistance, Bacterial ; }, abstract = {Sanitary environments that undergo frequent cleaning and disinfection may harbor microbial communities with potential health risks. While biofilms in healthcare settings are well studied, comparatively less is known about sink-drain microbiomes in public and educational buildings, where hundreds of people may interact with shared sink fixtures. This study characterized the spatial and temporal heterogeneity of sink-drain biofilm microbiomes in academic buildings. We sampled 16 sinks from two buildings (four floors each, with sinks closest and furthest to the bathroom entrance), which are cleaned daily with quaternary ammonium compound (QAC) disinfectants, during periods of low and high student traffic (during and after academic breaks, respectively) across winter, spring, and summer. We observed significant spatial and temporal variations in microbial assemblages. Individual sinks accounted for 43% (PERMANOVA, P < 0.0001) of the variation in microbial communities. Microbiomes in each building were dominated by two genera, which together accounted for 30% of the community composition: Acinetobacter and Enhydrobacter (also classified as Moraxella) in the newer building, and Sphingomonas and Mycobacterium in the older building. Acinetobacter abundance varied seasonally and showed higher relative abundance during periods of high traffic. Metagenomic analysis of selected sinks revealed a high prevalence of qac genes and metagenome-assembled genomes (MAGs) harboring antimicrobial resistance genes (ARGs), including A. parvus. Notably, 34%-53% of qac genes were co-localized on contigs associated with mobile genetic elements. These findings suggest that disinfected sink drains serve as persistent reservoirs of diverse microorganisms and potentially mobile resistance elements.IMPORTANCESink drains are recognized as environmental reservoirs for multidrug-resistant bacteria and have been linked to healthcare-associated outbreaks. In public and educational buildings, these microbiomes are shaped by frequent human activity, making them potential sources of exposure and contributors to the environmental dissemination of antibiotic resistance genes. Quaternary ammonium compound (QAC) disinfectants are widely used on surfaces; however, they can select for resistant taxa and co-select for antibiotic resistance. In this study, despite routine cleaning of sink surfaces with QACs, public restroom sink drains remain colonized by resilient biofilms, posing a potential risk to multiple users. Additionally, factors such as human traffic and seasonal variation may influence drain usage and microbial community composition. Elucidating how seasonal dynamics and human activity shape sink-drain biofilms is essential for understanding their role in the environmental transmission of antimicrobial resistance and informing mitigation strategies in nonclinical settings.}, } @article {pmid41841761, year = {2026}, author = {Ward, B and Bindels, LB and Balligand, J-L and Bearzatto, B and Bommer, G and Cani, PD and De Greef, J and Dewulf, JP and Gatto, L and Haufroid, V and Jodogne, S and Kabamba, B and Pyr Dit Ruys, S and Vertommen, D and Yombi, JC and Belkhir, L and Elens, L}, title = {Association of nasopharyngeal Dolosigranulum pigrum and Corynebacterium species with post-acute sequelae of SARS-CoV-2 in a longitudinal cohort.}, journal = {Microbiology spectrum}, volume = {14}, number = {4}, pages = {e0231325}, pmid = {41841761}, issn = {2165-0497}, support = {2021-I4201010-221801//Fondation Saint Luc/ ; HC01020F//Fonds De La Recherche Scientifique - FNRS/ ; ARC 25/30-151//Fonds Spéciaux de Recherche/ ; WELBIO-CR-2022A-02P//Walloon excellence in life sciences and biotechnology/ ; EOS 40007505//Fonds De La Recherche Scientifique - FNRS/ ; FRC//Fondation Saint Luc/ ; 2021//Fonds Spéciaux de Recherche/ ; }, mesh = {Humans ; *Nasopharynx/microbiology ; Longitudinal Studies ; Microbiota ; *COVID-19/microbiology/complications ; Male ; Female ; *Corynebacterium/isolation & purification/genetics/classification ; SARS-CoV-2 ; Adult ; Middle Aged ; Post-Acute COVID-19 Syndrome ; *Actinobacteria/isolation & purification/genetics/classification ; }, abstract = {This longitudinal study investigated the differential composition of the nasopharyngeal microbiome in patients presenting different COVID-19 infectious phenotypes and its evolution during convalescence, with a focus on post-acute sequelae of SARS-CoV-2 (PASC) and its potential microbiome-related mechanisms. Microbiota composition was assessed for a cohort of healthy participants (n = 25), influenza patients (n = 24), and patients with moderate (n = 50) and severe (n = 57) COVID-19. Samples were collected at two time points: during the acute infection phase and at approximately 3-month follow-up. From collected nasopharyngeal swab samples, metagenomics using shotgun sequencing was performed and the microbiota composition was analyzed. Alpha and beta diversity analyses revealed no significant differences in overall community diversity between patient groups across visits. However, differential abundance testing identified specific species, such as Dolosigranulum pigrum and various Corynebacterium species, whose profiles correlated with PASC development. Furthermore, the analysis of microbial co-associations identifies commensal species, including D. pigrum and Corynebacterium species, which are less abundant in patients who develop PASC, consistent with a potential protective role suggested by experimental studies but not proven by our observational data. Antibiotic use was associated with lower levels of key protective taxa, which may increase susceptibility to PASC in case of superinfection. These findings highlight the potential importance of the nasopharyngeal microbiome in acute COVID-19 disease outcomes and suggest that preserving or restoring a balanced respiratory microbiome could mitigate the risk of COVID-19 persistent symptoms and PASC development. Our results may set the stage for future clinical interventions involving probiotics or microbial-derived metabolites to promote respiratory health post-COVID-19.IMPORTANCEThis study highlights the importance of bacteria naturally found in the upper respiratory tract, particularly the nasopharynx (the nasopharyngeal microbiome), in shaping how severely COVID-19 affects patients and whether they experience persistent symptoms, also called long-COVID or post-acute sequelae of SARS-CoV-2 (PASC). By examining microbiome samples from healthy people, influenza patients, and individuals with COVID-19 during acute and convalescent phases, we found that certain commensal bacteria, namely, Dolosigranulum pigrum and Corynebacterium species, were less abundant in individuals who developed long-COVID and more abundant in those who fully recovered. We also observed that antibiotic treatment was associated with lower abundances of these commensal taxa, in turn coinciding with a higher frequency of PASC. These findings suggest that the composition of the nasopharyngeal microbiome is associated with recovery trajectories after COVID-19 and motivate future research into treatments aimed toward the microbiome to improve respiratory health following infection.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT05557539.}, } @article {pmid41842581, year = {2026}, author = {Wang, X and Chen, J and Xia, J and Ma, T and Yang, W and Shan, T and He, W and Zhang, G and Xia, Z and Wang, W and Liu, Z and Zheng, Y and Nong, K and Niu, P and Chen, T}, title = {Brain-Targeted RVG-Liposomal Melatonin Ameliorates Manganese Neurotoxicity by Enhancing Neurogenesis and Modulating Systemic Amino Acid Profiles.}, journal = {Journal of pineal research}, volume = {78}, number = {2}, pages = {e70137}, doi = {10.1111/jpi.70137}, pmid = {41842581}, issn = {1600-079X}, support = {82173489//National Natural Science Foundation of China/ ; 7232234//Beijing Natural Science Foundation/ ; }, mesh = {Animals ; *Melatonin/pharmacology/administration & dosage ; Liposomes ; *Manganese/toxicity ; Mice ; *Neurogenesis/drug effects ; *Brain/metabolism/drug effects ; *Amino Acids/metabolism/blood ; Male ; Rabies virus ; *Glycoproteins/pharmacology/chemistry ; }, abstract = {Chronic manganese (Mn) exposure induces severe neurotoxicity, characterized by impaired neurogenesis and disrupted metabolic homeostasis. Although melatonin (MT) possesses established neuroprotective properties, its clinical utility is hindered by poor bioavailability and limited brain delivery. Here, we developed a brain-targeted, rabies virus glycoprotein (RVG)-modified liposomal delivery system encapsulating melatonin (MT@RVG-Lip) to enhance therapeutic efficacy. Multi-omics analyses including brain and intestinal transcriptomics, serum metabolomics, and gut metagenomics were conducted to elucidate the underlying mechanisms. MT@RVG-Lip significantly improved motor deficits and enhanced neurogenesis while reducing neuroinflammation in Mn-exposed mice. Compared with regular MT and CaNa2-EDTA, MT@RVG-Lip more effectively alleviated Mn-disrupted gene expression in neurogenesis regions, particularly genes involved in amino acid metabolism. Additionally, MT@RVG-Lip demonstrated a regulatory effect on serum amino acid profiles and intestinal transporter gene expression. Gut microbiota analysis further revealed that MT@RVG-Lip partially reversed Mn-associated dysbiosis and promoted the improvement of key amino acid-related microbiota-mediated metabolic pathways. The RVG-modified liposomal formulation conferred sustained release and improved brain-targeting capability, prolonging MT bioavailability and enhancing therapeutic outcomes. These findings provide a new mechanistic framework for MT-based interventions in neurodegenerative diseases and highlight the therapeutic potential of multifunctional delivery strategies.}, } @article {pmid41842880, year = {2026}, author = {González-Mercado, VJ and Jean Lim, S and Kumar Singh, P and Sales-Martinez, S and Fernandez-Cajavilca, M and Marrero, LM and Pedro, E and D'Eramo Melkus, G}, title = {Dietary Quality and Microbiome Profiles among Rectal Cancer Patients: A Cross-Sectional Pilot Study.}, journal = {Puerto Rico health sciences journal}, volume = {45}, number = {1}, pages = {3-10}, pmid = {41842880}, issn = {2373-6011}, support = {K23 NR020039/NR/NINR NIH HHS/United States ; P50 GM133807/GM/NIGMS NIH HHS/United States ; R21 CA288925/CA/NCI NIH HHS/United States ; U54 GM133807/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Female ; Male ; Pilot Projects ; *Rectal Neoplasms/microbiology/therapy ; Cross-Sectional Studies ; *Diet/standards ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Aged ; Feces/microbiology ; Metagenomics/methods ; }, abstract = {OBJECTIVE: Examining whether gut microbial taxa abundances and predicted functional pathways correlate with dietary quality scores at the end of neoadjuvant chemoradiotherapy (nCRT) for rectal cancer (RC); identifying differentially abundant bacterial species from the pantothenate and acetyl-coenzyme A biosynthesis pathways that differ among dietary quality groups in a subset of participants.

METHODS: RC patients (n = 30) provided stool samples for 16S rRNA gene sequencing. To validate pathway predictions from the 16S rRNA gene data, stool samples from a subset of 17 participants underwent shallow shotgun metagenomics sequencing (SMS). Dietary quality was calculated using the Prime Diet Quality Score (PDQS; 24-hour recall). 16S rRNA gene data were analyzed using QIIME2, and SMS data were analyzed using HUMAnN2.

RESULTS: At the genus level, Parvimonas, Caproiciproducens, and uncultured Eggerthellaceae abundances positively correlated (Spearman's rho = 0.36 to 0.50) with PDQS scores, whereas abundances of Prevotella, Rothia, Peptostreptococcus, Paeniclostridium, Enterococcus, and Howardella correlated negatively (Spearman's rho = -0.43 to 0.36). Predicted pathways, including those related to B-vitamin biosynthesis and enzyme cofactor biosynthesis (e.g., B5/pantothenate [phosphopantothenate biosynthesis I]), were correlated with higher PDQS scores. Mean abundances of species predicted to encode the vitamin B5-CoA pathway were greater in the high- diet-quality group.

CONCLUSION: Findings suggest important associations between the taxa abundances of gut bacteria and the abundances of predicted B-vitamin biosynthesis pathways and dietary quality at the end of nCRT. Three bacterial species encoding vitamin B5-CoA biosynthesis pathways were prominent in high-dietaryquality participants.}, } @article {pmid41843187, year = {2026}, author = {Chu, T and Wang, Q and Hu, C and Yu, J and Chen, L and Yu, Y and Wang, Y}, title = {Microalga-virus-virophage coculture reveals co-infection of multi-virophages with a giant virus.}, journal = {Archives of virology}, volume = {171}, number = {4}, pages = {}, pmid = {41843187}, issn = {1432-8798}, support = {31570112//National Natural Science Foundation of China/ ; }, mesh = {*Chlorella/virology ; Coculture Techniques ; *Giant Viruses/physiology/genetics ; *Virophages/genetics/physiology ; *Microalgae/virology ; Coinfection/virology ; Lakes/virology ; }, abstract = {Virophages parasitize the replication of co-infecting giant viruses within eukaryotic cells, forming tripartite cell-virus-virophage (CVv) systems. Tripartite interactions are well-documented in protozoa, yet comparable systems in algae remain largely unexplored at the experimental level. Here, we report an experimentally validated CVv system involving the green, single-celled microalga Chlorella sp. DSL01, Dishui Lake large algal virus 1 (DSLLAV1), and multiple Dishui Lake virophages (DSLVs). Inoculation of Chlorella sp. DSL01 at low MOI established laboratory co-cultures in which time-series PCR detected DSLLAV1 early but not after Day 10, whereas all tested virophages persisted. Metagenomic profiling of the terminal supernatant (end-point sample) indicated a virophage-dominated assemblage with DSLV3 most represented. Droplet digital PCR at discrete time points (Days 5, 10, and 15) then provided absolute counts for DSLLAV1 and DSLV1/3/7, corroborating an early DSLLAV1 peak followed by collapse and/or a delayed rise of multiple virophages coincident with host growth recovery. Nested PCR on the algal pellet detected virophages DSLV1/3/7 but not DSLLAV1. Together, these results demonstrate that Chlorella sp. DSL01 supports co-infection by DSLLAV1 and multiple virophages, establishing an experimentally validated algal CVv system and revealing multi-virophage participation in freshwater algal virus-virophage-host dynamics.}, } @article {pmid41843252, year = {2026}, author = {Xia, HL and Liang, PY and Yuan, WG and Cao, XD and Sun, Y and Jiang, JZ and Yuan, LH}, title = {PhaGCN_Cluster: A Scalable and Robust Framework for Automated Classification and Discovery of Viral Dark Matter from Metagenomes.}, journal = {Interdisciplinary sciences, computational life sciences}, volume = {}, number = {}, pages = {}, pmid = {41843252}, issn = {1867-1462}, support = {No. 2022KCXTD017//Innovation Team Project of Guangdong Universities/ ; No. 324CXTD435//Natural Science Foundation of Hainan Province/ ; No. 2023TD44//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; }, abstract = {Viruses are the most abundant biological entities on Earth, playing essential roles in shaping microbial communities, driving evolution, and maintaining ecosystem functions. Metagenomic sequencing has unveiled a vast landscape of uncharacterized viral "dark matter", comprising highly divergent sequences that elude traditional taxonomic approaches. Here, we develop PhaGCN_Cluster, a next-generation viral classification tool built upon a graph convolutional neural network (GCN) framework. By integrating protein-level sequence similarity and contig-level genomic features, PhaGCN_Cluster establishes a scalable knowledge graph-based analytical system. The optimized algorithm yields significant gains in computational efficiency, supporting accurate taxonomic assignment of up to 300,000 contigs per run. Compared with existing methods, PhaGCN_Cluster demonstrates superior classification accuracy and F1-scores, particularly under conditions of low sequence similarity, and exhibits strong robustness in detecting evolutionarily distant viruses. Notably, PhaGCN_Cluster incorporates an updated logic for assigning "_like" taxa, which enhances its capacity to accommodate novel viral groups while preserving high precision-though at the cost of a slight reduction in recall. By generating high-fidelity network graphs, PhaGCN_Cluster uncovers previously unrecognized clades and bridges evolutionary gaps between reference viruses and novel sequences, thereby providing critical insights into viral diversity and evolution. PhaGCN_Cluster represents an interpretable, efficient, and scalable solution for automated virus classification. The source code of PhaGCN_Cluster is available via https://github.com/xiahaolong/PhaGCN_Cluster .}, } @article {pmid41843710, year = {2026}, author = {Qian, C and Jeunen, GJ and Han, W and Chan, TY and Jiang, Y and Fu, W and Seymour, M}, title = {Developing and Evaluating Aquatic Passive Sampling of Environmental DNA for Microbial Community Profiling.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70121}, pmid = {41843710}, issn = {1755-0998}, support = {MCEF21003//Marine Conservation Enhancement Fund/ ; }, mesh = {*DNA, Environmental/genetics/isolation & purification ; *Metagenomics/methods ; Biodiversity ; *Specimen Handling/methods ; Bacteria/genetics/classification ; Extrachromosomal DNA ; Filtration/methods ; *Biota ; }, abstract = {Environmental DNA (eDNA) metabarcoding has transformed biodiversity monitoring across taxa from bacteria to mammals, yet sample collection remains a major bottleneck. Passive sampling via adsorption and entrapment has emerged as a promising alternative to overcome the limitations of conventional active filtration. However, the performance of passive sampling for microbial biodiversity monitoring remains unknown. Here, we developed passive sampling-based microbial community profiling by testing five submersion times and three common eDNA extraction methods in mesocosms, and comprehensively evaluated it by comparing results with active filtration in estuarine and coastal environments. We found that passive sampling for 24 h with enzymatic extraction yielded significantly more eDNA and higher biodiversity than shorter durations and mechanical extractions. Passive sampling consistently outperformed active filtration at every field site, with average increases of >100% in eDNA yields and >50% in taxonomic and phylogenetic diversities. Additionally, active filtration and passive sampling yielded significantly different prokaryotic and microeukaryotic community compositions, driven primarily by turnover rather than nestedness (on average 4-fold larger), implying that passive sampling is better suited for spatiotemporal detection than active filtration. Passive sampling showed greater sensitivity in identifying key environmental factors (3 vs. 2) and potential environmental bioindicators (40 vs. 20) compared with active filtration. Overall, this study establishes an efficient and practical passive sampling method for microbial biodiversity monitoring and environmental assessment in aquatic environments.}, } @article {pmid41843957, year = {2026}, author = {Zhu, L and Huang, C and Tian, Y and Zuo, W and Shan, G}, title = {Targeted enhancement of ammonia assimilation and microbial community metabolic synergy in chicken manure aerobic composting mediated by tricarboxylic acid cycle modulators.}, journal = {Waste management (New York, N.Y.)}, volume = {216}, number = {}, pages = {115471}, doi = {10.1016/j.wasman.2026.115471}, pmid = {41843957}, issn = {1879-2456}, mesh = {*Ammonia/metabolism ; Animals ; *Citric Acid Cycle ; *Composting/methods ; Chickens ; Nitrogen/metabolism ; Isocitrate Dehydrogenase/metabolism ; *Microbiota ; }, abstract = {Reducing nitrogen loss during composting is essential. To investigate the effects of directly modulating the tricarboxylic acid (TCA) cycle on microbial ammonia assimilation during composting, this study employed paired stable isotope labeling combined with metagenomic analysis to assess the role of the TCA cycle regulator citric acid (CA) in enhancing ammonia assimilation efficiency and regulating carbon-nitrogen metabolism within the microbial community. CA markedly reduced NH3 emissions (0.5-2265 ppm) and increased organic nitrogen retention (4.2%-17.7%), primarily through improved ammonia assimilation efficiency (0.06-0.22 mg N·kg[-1]·d[-1]) rather than weakened mineralization. Mechanistically, CA upregulated IDH1 (5.4%-18.5%) and increased IDH enzyme activity (0.35-0.66 IU/g), combined with NH3 uptake, balancing oxoglutarate and ammonium supply. Moreover, CA strengthened the glutamine synthetase-glutamate synthase (GS-GOGAT) pathway (3.4%-23.4%) and enzyme activity (0.08-0.74 IU/g), particularly in the initial and thermophilic phases. In addition, CA induced an upregulation (14.8%-28.4%) of genes encoding succinyl-CoA synthetase, providing sufficient energy to support the ammonia assimilation process. Furthermore, CA enhanced microbial diversity and metabolic cooperation while reducing competition, thereby promoting NH3 assimilation and glutamate synthesis. Inorganic and amino acid metabolism emerged as critical cooperative processes within core microbial populations.}, } @article {pmid41844593, year = {2026}, author = {Ni, N and Ding, Q and Zhang, T and Liu, C and Guo, X and Zhu, C and Wang, Q and Zhu, D and Wang, N and Luo, Y}, title = {Fragmented Microplastics Synergize with Biological Treatment To Potentiate Antibiotic Resistance Dissemination during Sewage Treatment.}, journal = {Environmental science & technology}, volume = {60}, number = {12}, pages = {9554-9564}, doi = {10.1021/acs.est.5c18221}, pmid = {41844593}, issn = {1520-5851}, mesh = {*Microplastics ; *Sewage ; *Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; }, abstract = {Wastewater treatment plants (WWTPs) are important reservoirs for antibiotic resistance genes (ARGs) and microplastics (MPs), and serve as hotspots for antibiotic resistance spread. However, actual survey data on their combined pollution along the entire sewage treatment chain remain scarce. This study integrated metagenomic sequencing and high-throughput qPCR to analyze the correlation between ARGs and MPs. The results revealed that clinically relevant and rank I high-risk intracellular antibiotic resistance genes (iARGs) were significantly enriched in the plastisphere throughout the sewage treatment process, particularly on fragmented MPs. FEAST source-tracking analysis revealed that MP-bound iARGs and extracellular ARGs in the biologically treated sewage contributed to 13-43 and 25-39% of the corresponding iARGs and eARGs detected in the effluent, respectively. Fragmented MPs also colocalized ARGs, virulence factors, and mobile genetic elements, potentially facilitating plasmid-mediated gene transfer. Acinetobacter, the primary ARG host and detected across 75 WWTPs with high ARG load, may serve as an antibiotic resistance indicator. This study highlights MP-driven ARG dissemination in WWTPs and informs resistance control strategies.}, } @article {pmid41844673, year = {2026}, author = {Singh, NK and Garg, P and Kumari, S and Banda, L and Patel, AM and Sindhuja, RH and Bhandari, Y and Khan, NA and Tandon, S and Jain, R and Rajesh, T and Qureshi, A and Vodapalli, A and Singha, B and Esari, D and Annan, MO and Nagabandi, T and Panda, A and Kapley, A and Nandicoori, VK and Mishra, RK and Sowpati, DT and Siva, AB and Tallapaka, KB}, title = {Metagenomic profiling of antimicrobial resistance in wastewater from metropolitan cities of India.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41844673}, issn = {2041-1723}, support = {2021 HTH 018//Rockefeller Foundation/ ; }, mesh = {India ; *Wastewater/microbiology ; *Metagenomics/methods ; Cities ; *Metagenome/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Interspersed Repetitive Sequences/genetics ; *Drug Resistance, Microbial/genetics ; Microbiota/genetics ; }, abstract = {Wastewater-based surveillance has emerged as a powerful tool for monitoring microbial diversity, antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). In this study, wastewater samples collected from March 2022 to March 2024 from 19 locations in four metropolitan cities of India were profiled using shotgun metagenomics. Taxonomic abundance and beta diversity analyses revealed significant differences in microbial community compositions, with city-specific clustering; suggesting distinct local environmental influences. However, such distinct clusters were not evident with the ARGs. A high proportion of potentially novel metagenome-assembled genomes (MAGs) (53-70%) were identified on reconstructing the microbial genomes from the metagenomic data. ARGs conferring resistance to antibiotics such as tetracyclines and beta-lactams showed higher association with MGEs in contrast to macrolide resistance genes. Microbial co-occurrence network analysis revealed a city-specific structure and higher contribution of ARGs from specific communities of microbes. These findings underscore the complex interplay between microbial diversity, ARG dissemination, and MGEs in wastewater environments, emphasizing the need for continued surveillance, for designing appropriate mitigation strategies towards curbing the spread of antimicrobial resistance.}, } @article {pmid41845022, year = {2026}, author = {Selvatici, S and Jin, C and Zazula, G and Hall, E and Hewitson, S and Moots, HM and Sharif, B and Ersmark, E and Parducci, L and Dalén, L and Díez-Del-Molino, D and Oteo-García, G}, title = {Genomic identification and complete mitochondrial recovery of a Late Holocene porcupine (Erethizon dorsatum) mummy from Yukon permafrost.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41845022}, issn = {2045-2322}, mesh = {*Genome, Mitochondrial ; *Porcupines/genetics ; Permafrost ; DNA, Mitochondrial/genetics ; Yukon Territory ; Phylogeny ; *Mummies ; Genomics/methods ; Animals ; Sequence Analysis, DNA ; }, abstract = {We identified a 3000-year-old specimen from the Traditional Territory of the Tr'ondëk Hwëch'in in central Yukon Territory, Canada as the first known mummified remains of an ancient North American porcupine (Erethizon dorsatum), known as "Ts'ey" in the Hän language, using genetic analysis and metagenomic validation. Our analysis of the sample yielded the first-ever complete ancient mitochondrial genome for (E. dorsatum) and only the second full mitogenome for the species. Its Holocene age is considerably younger than the Pleistocene megafauna typically recovered in the Yukon permafrost, demonstrating the potential for these deposits to preserve specimens from interglacial periods. Crucially, this finding confirms the presence of porcupines in the region 3000 years ago, in line with the hypothesis that this species only dispersed into Yukon and Alaska following the establishment of boreal forests after the Last Glacial Period.}, } @article {pmid41845390, year = {2026}, author = {Sung, H and Hyun, DW and Whon, TW and Kim, PS and Kim, HS and Lee, JY and Lee, SY and Choi, JW and Yoo, JH and Jung, MJ and Yun, JH and Lee, JY and Tak, EJ and Jeong, YS and Kim, SW and Baeg, M and Eun, YG and Lee, YC and Bae, JW}, title = {Unraveling the diagnostic and prognostic signatures of oral microbiota in head and neck cancer.}, journal = {BMC biology}, volume = {24}, number = {1}, pages = {}, pmid = {41845390}, issn = {1741-7007}, support = {RS-2020-NR049315//National Research Foundation of Korea/ ; 22213MFDS537//Ministry of Food and Drug Safety/ ; }, mesh = {Humans ; *Microbiota ; Prognosis ; *Head and Neck Neoplasms/diagnosis/microbiology ; *Mouth/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Squamous Cell Carcinoma of Head and Neck/diagnosis/microbiology ; }, abstract = {BACKGROUND: Head and neck cancer, predominantly squamous cell carcinoma, has emerged as a significant global health concern. Growing evidence has established a strong association between dysbiosis of the oral microbiota and both oral and systemic diseases. However, the association between the oral microbiota and head and neck cancer has not yet been fully described. This study aimed to investigate the distinct profiles of the oral microbiota in patients with head and neck cancer and their potential as diagnostic and prognostic biomarkers for head and neck cancer.

RESULTS: Comparative analyses revealed that compared to controls, the oral microbiota of patients with head and neck squamous cell carcinoma (HNSCC) exhibited an increased abundance of anaerobic, biofilm-forming bacteria, and potential pathogens. A machine learning model successfully differentiated HNSCC patients from controls with an area under the curve of 0.902. Key features of this model, such as Peptostreptococcus and Capnocytophaga, were found to be candidate biomarkers for HNSCC, with certain taxa, such as Abiotrophia, serving as prognostic indicators. Although pronounced differences in oral microbiota among HNSCC patients primarily resulted from inter-individual variations, distinct community types were identified, with the type dominated by Proteobacteria being associated with the lowest probability of survival.

CONCLUSIONS: Our findings indicate that the oral microbiota may predict HNSCC and may act as a therapeutic target to improve the prognosis of HNSCC. This investigation underscores the crucial role of oral microbial dysbiosis in the etiopathogenesis and clinical prognosis of HNSCC, making a case for further integrative metagenomic and clinical research.}, } @article {pmid41845399, year = {2026}, author = {Luo, J and Guo, W and Zou, S and Tan, Y and Liu, J and Song, S and Yang, H and Liang, K}, title = {Case report: thoracic syphilitic gumma masquerading as a malignant tumor in a patient with AIDS.}, journal = {AIDS research and therapy}, volume = {23}, number = {1}, pages = {}, pmid = {41845399}, issn = {1742-6405}, support = {2020-PT320-004//The Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; }, mesh = {Humans ; Diagnosis, Differential ; *Acquired Immunodeficiency Syndrome/complications ; *Syphilis/diagnosis/drug therapy/complications ; Treponema pallidum/isolation & purification ; Male ; Anti-Bacterial Agents/therapeutic use ; Immunohistochemistry ; Immunocompromised Host ; Penicillins/therapeutic use ; }, abstract = {Syphilis, a systemic infection caused by Treponema pallidum, can present with atypical and severe manifestations in people living with the human immunodeficiency virus (HIV), posing significant diagnostic challenges. We report the case of a patient with acquired immunodeficiency syndrome (AIDS) who presented with a chest wall mass. Imaging findings were initially suggestive of a malignancy. However, subsequent evaluation, guided by positive serum syphilis antibodies despite non-specific inflammatory changes on histology and a negative metagenomic next-generation sequencing (mNGS) result, led to the diagnosis of a syphilitic gumma, which was confirmed by immunohistochemical staining. The lesion entirely resolved following penicillin therapy. This case highlights a critical clinical insight: syphilis must be considered in the differential diagnosis of mass lesions in immunocompromised hosts, and immunohistochemical staining is imperative for definitive diagnosis.}, } @article {pmid41845494, year = {2026}, author = {Huang, Q and Du, D and Guo, J and Liu, J and Sun, P}, title = {Heat stress suppresses lactation through potential rumen-mammary communication mediated by extracellular vesicles: integrated analysis of microbiome, metabolome, and miRNA profiles.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41845494}, issn = {2049-2618}, support = {2022YFD1301101//National Key Research and Development Program of China/ ; CARS-37//Earmarked Fund for China Agriculture Research System/ ; Y2025YC52//Central Public-interest Scientific Institution Basal Research Fund/ ; ASTIP-IAS07//Agricultural Science and Technology Innovation Program/ ; }, mesh = {Animals ; Female ; *Rumen/microbiology/metabolism ; *Lactation/physiology ; *Extracellular Vesicles/metabolism/genetics ; Cattle ; *MicroRNAs/genetics/metabolism ; Metabolome ; *Heat-Shock Response/physiology ; Milk/metabolism/chemistry ; Multiomics ; *Mammary Glands, Animal/metabolism/physiology ; Gastrointestinal Microbiome ; Bacteria/classification/genetics/isolation & purification/metabolism ; Fermentation ; }, abstract = {BACKGROUND: Heat stress (HS) imposes significant physiological and economic challenges to dairy production, yet the integrative mechanisms linking rumen microbial dysbiosis, host metabolic disruption, and lactation suppression remain not yet fully understood. Emerging evidence suggests that extracellular vesicles (EVs) and their cargo, particularly microRNAs (miRNAs), may participate in systemic inter-organ communication under stress. This study aimed to elucidate how HS suppresses lactation through potential rumen-mammary communication mediated by EVs, using a comprehensive multi-omics approach.

RESULTS: Dairy cows exposed to HS exhibited elevated rectal temperatures and respiratory rates, accompanied by significant reductions in the yield of milk, milk fat and protein. Rumen fermentation was markedly impaired, with decreased pH, butyrate, and valerate proportions, and systemic inflammation was evidenced by increased pro-inflammatory cytokines and barrier dysfunction. Metagenomic profiling revealed that HS reshaped the rumen microbiome, significantly reducing the relative abundances of Prevotella, Bifidobacterium, and Lactobacillus species while enriching methanogenic and low-efficiency fermentative taxa. Functionally, HS enhanced microbial methane metabolism and suppressed carbohydrate degradation pathways, reducing the host's energy supply for milk synthesis. Metabolomic analyses supported this shift, with distinct metabolites significantly correlated with lactation performance. Notably, extracellular vesicle (EV)-derived miRNAs from both plasma and milk showed significant expression changes under HS conditions, predominantly targeting signaling pathways related to stress and immune responses, hormone regulation, and mammary gland development and function.

CONCLUSIONS: This study demonstrates that HS suppresses lactation through multi-level alterations in the rumen microbiome, metabolic homeostasis, and EV-derived miRNA signaling, collectively supporting the existence of a potential rumen-mammary communication axis. These findings offer novel insights into the pathogenesis of HS responses.}, } @article {pmid41845521, year = {2026}, author = {Hoepfner, C and Moreno-Perlin, T and Pérez-Llano, Y and Cardona, K and Rivera, DS and Minter, D and Guzmán, D and Batista-García, RA}, title = {Microbial diversity, metabolic specialization, and genomic novelty across polyextreme saline lakes of the Central Dry Andes.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41845521}, issn = {2524-6372}, support = {ATE240004//Agencia Nacional de Investigación y Desarrollo/ ; PT09CB001//Swedish International Development Cooperation Agency/ ; Grant 31-001//Darwin Initiative/ ; Postdoctoral fellowship grant//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; }, abstract = {The high-altitude saline lakes of the Central Dry Andes are polyextreme environments characterized by hypersalinity, high alkalinity, fluctuating redox conditions, and elevated levels of trace metals (e.g., Li, As, Mn, Mg). These conditions challenge microbial life yet select for highly specialized and functionally versatile communities. Through metagenomic analyses across four lakes (Colorada, Hedionda, Mama Khumu, and Loromayu), we identified taxonomic assemblages dominated by halophilic and halotolerant bacteria (e.g., Halomonas, Marinobacter, Rhodohalobacter), phototrophic cyanobacteria and algae (Dunaliella, Chlorella), archaeal Halobacteria (Halorubrum, Natrinema, Haloterrigena), and halotolerant fungi (Aspergillus, Penicillium). Notably, Laguna Mama Khumu exhibited the highest microbial and functional diversity, reflecting its heterogeneous salinity and richer chemical gradients, whereas the most extreme lakes (Colorada and Loromayu) harbored narrower specialized communities. Across all sites, oxidative phosphorylation dominated as the primary metabolic strategy. Additional pathways such as photosynthesis, sulfur and methane cycling were especially prominent at Mama Khumu. Patterns of carbohydrate-active enzyme (CAZyme) also diverged: Loromayu harbored abundant glycoside hydrolases, indicating strong polysaccharide degradation potential, while Mama Khumu displayed a boarder and more functionally redundant CAZyme repertoire. High-quality metagenome-assembled genomes (MAGs) uncovered novel lineages (< 95% ANI to known species) encoding key traits including energy metabolism (ATP synthase, anoxygenic photosynthesis), sulfur oxidation, arsenic resistance, and heavy-metal efflux systems. These features highlight the genomic innovation fostered by polyextreme conditions. Overall, our findings showed that within a shared scaffold of aerobic respiration and halophilic resilience, local geochemistry drives divergent taxonomic and metabolic adaptations. The Bolivian Andean saline lakes thus emerge as natural laboratories for studying microbial adaptation under multiple stressors and offer promising sources for biotechnological discovery.}, } @article {pmid41845557, year = {2026}, author = {Dormiente, A and Mancabelli, L and Ventura, M and Longhi, G and Mergoni, G and Manfredi, M}, title = {Metagenomic Evaluation of Oral Microbiota in Patients Affected by Oral Lichen Planus: A Pilot Study.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.70296}, pmid = {41845557}, issn = {1601-0825}, support = {//Bando di Ateneo per la Ricerca 2023- Azione B/ ; }, abstract = {OBJECTIVE: To characterize the oral bacterial and fungal microbiota of symptomatic oral lichen planus patients undergoing topical corticosteroid therapy and to explore microbial patterns potentially associated with subsequent oral candidiasis.

METHODS: Twelve patients with clinically and histologically confirmed OLP were enrolled. Unstimulated saliva and tongue dorsum swabs were collected at baseline and weekly for three weeks during betamethasone therapy. Bacterial communities were profiled using shallow shotgun metagenomics analyzed with METAnnotatorX2, and fungal communities through ITS sequencing and QIIME 2 workflows. Beta-diversity analyses assessed the effects of time, clinical variables, and later candidiasis development. Associations between bacterial taxa and Candida abundance were evaluated using Spearman correlations.

RESULTS: Oral candidiasis developed in three patients (25%). Microbiota composition showed marked inter-individual variability but high intra-subject stability, with no consistent shifts linked to corticosteroid therapy. Commensal taxa such as Streptococcus, Rothia, and Actinomyces were negatively associated with candidiasis and Candida abundance, whereas anaerobic species including Porphyromonas gingivalis, Prevotella multiformis, and Lachnoanaerobaculum gingivalis displayed positive correlations with fungal proliferation.

CONCLUSIONS: Despite overall stability of the oral microbiota during therapy, specific bacterial signatures were associated with subsequent Candida overgrowth. These findings suggest that cross-kingdom interactions may influence susceptibility to corticosteroid-associated candidiasis and warrant validation in larger cohorts.}, } @article {pmid41845564, year = {2026}, author = {Zhang, Y and Wang, DD}, title = {Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2644682}, pmid = {41845564}, issn = {1949-0984}, support = {K99 DK119412/DK/NIDDK NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; U54 AG089325/AG/NIA NIH HHS/United States ; RF1 AG083764/AG/NIA NIH HHS/United States ; }, mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; Humans ; Multiomics ; Metagenomics ; *Gastrointestinal Microbiome/physiology ; Animals ; Diet ; Metabolomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; }, abstract = {Type 2 diabetes (T2D) is a heterogeneous metabolic disorder in which environmental exposures interact with host biology to drive insulin resistance and progressive β-cell dysfunction. This review synthesizes recent advances showing how the gut microbiome mediates these processes across multiple levels of resolution. First, large-scale shotgun metagenomic studies consistently identify a reproducible T2D-associated signature characterized by depletion of short-chain fatty acid-producing taxa and enrichment of opportunistic, pro-inflammatory microorganisms, while highlighting the importance of controlling for major confounders such as adiposity and glucose-lowering medications. Second, functional profiling and metabolomics link microbial community shifts to coordinated pathway changes-including reduced short-chain fatty acid and secondary bile acid production and increased endotoxin- and branched-chain amino acid-related metabolism-that influence gut barrier integrity, inflammatory tone, insulin sensitivity, and pancreatic β-cell function. Third, we discuss how integrative multi-omics (metagenomics, metatranscriptomics, proteomics, and metabolomics) can connect microbial genetic potential to in vivo activity and circulating metabolites, while introducing key challenges such as temporal variability, anatomical heterogeneity, and "dark matter" in gene and metabolite annotation. Fourth, strain-resolved analyses reveal that many disease-associated functions are carried by specific lineages within species, refining microbial targets and helping explain inconsistent species-level associations. Fifth, we summarize how diet shapes microbial ecology and function-supporting microbiome-informed precision nutrition-and highlight emerging evidence beyond bacteria, including viral and fungal community components. Finally, we outline translational opportunities and evidence gaps, emphasizing the need for diverse longitudinal cohorts, mechanistic validation, and well-controlled interventional trials to evaluate microbiome-directed strategies for T2D prevention and treatment.}, } @article {pmid41846023, year = {2026}, author = {Segovia-Cruz, JA and Zárate-Romero, A and Herrera-Hernández, MM and Loza-Tavera, H and Vargas-Suárez, M and Ayala, M and Paz-González, AD and Rivera, G and Magaña-Montiel, N and Schnabel, D and Sánchez-Reyes, A}, title = {Characterization and application of two novel environmental DyP-type peroxidases as sustainable biocatalysts for textile dye treatment.}, journal = {International journal of biological macromolecules}, volume = {355}, number = {}, pages = {151457}, doi = {10.1016/j.ijbiomac.2026.151457}, pmid = {41846023}, issn = {1879-0003}, mesh = {*Coloring Agents/chemistry/metabolism ; *Peroxidases/chemistry/metabolism/genetics ; *Textiles ; Animals ; Hydrogen-Ion Concentration ; *Biocatalysis ; Biodegradation, Environmental ; Wastewater/chemistry ; Water Decolorization ; Artemia/drug effects ; }, abstract = {The environmental impact of synthetic textile dyes highlights the urgent need for sustainable wastewater treatment solutions. Here, we report the cloning, heterologous expression, purification, and characterization of two novel bacterial dye-decolorizing peroxidases (DyPs), named PbDyP and MbDyP, selected from the metagenome of the BP8 polyurethane-enriched microbial consortium, isolated from a landfill. Both enzymes showed an acidic pH optimum (4.0-4.5) and a moderate temperature preference (∼40 °C), but they differed in stability and sensitivity to hydrogen peroxide. Spectroscopic analyses confirmed their heme-binding nature, while dynamic light scattering revealed different oligomerization states. Both enzymes achieved efficient biotransformation (>80%) of representative anthraquinone, azo, phthalocyanine, sulfur, and triphenylmethane dyes, with particularly high activity toward anthraquinone Reactive Blue 19. Following enzymatic treatment, FT-IR spectroscopy revealed structural changes in diagnostic functional groups of several dyes, such as Vat Red 10, Disperse Orange 30, Direct Black 22, and Reactive Blue 19, while UPLC-MS analysis identified a lower-mass sodium 2-(3-aminobenzene-1-sulfonyl) ethyl sulfate derivative (m/z 318.31), indicating biotransformation of the parent compound. We also conducted in vitro transformation assays for bisphenols, benzenedithiols, and substituted phenols to thoroughly assess the oxidative capabilities of the DyP-type peroxidases. Toxicity tests using Artemia salina demonstrated that, although enzymatic treatment reduced toxicity in the supernatants, the precipitated fractions remained harmful, underscoring the need for integrated remediation strategies. Overall, these findings position PbDyP and MbDyP as promising candidates for eco-friendly dye degradation, providing a foundation for their potential application in industrial wastewater treatment.}, } @article {pmid41846078, year = {2026}, author = {Li, Q and Yuan, J and Sun, Y and Wang, Y and Li, Y and Ni, A and Zong, Y and Yang, H and Li, X and Huang, X and Ma, H and Chen, J}, title = {Multi-omics analysis revealed that oxidative phosphorylation contributed to the heterosis for feed efficiency in laying chickens.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106658}, pmid = {41846078}, issn = {1525-3171}, mesh = {Animals ; *Chickens/genetics/physiology/microbiology ; *Hybrid Vigor ; Female ; *Oxidative Phosphorylation ; Multiomics ; *Gastrointestinal Microbiome ; Animal Feed/analysis ; }, abstract = {Improving feed efficiency has been the top priority in animal husbandry. Host genetics and gut microbiota synergistically regulate feed efficiency in laying chicken. However, the role of gut microbiota in heterosis for feed efficiency was rarely investigated. Herein, we used multi-omics data to elucidate the regulatory mechanisms of heterosis for feed efficiency in White Leghorn, Beijing-You chicken, and their reciprocal crosses. We observed divergent heterosis for residual feed intake (RFI) between two crossbreds during the laying period from 43 to 46 weeks of age. Metagenomic analysis showed the significant difference in richness and function of cecal microbiota among crossbreds and purebreds (P < 0.05), and the differential functional pathways were mainly related to metabolism. Most microorganisms (>90 %) were non-additive in crossbreds. Weighted gene co-expression network analysis and LDA effect size analysis revealed seven non-additive RFI-associated microorganisms, such as Leyella, Paraprevotella, and Zongyangia. We also identified 544 RFI-associted metabolites, which were mainly overrepresented in glycerophospholipid metabolism and oxidative phosphorylation. Integrative analysis further revealed the interactions among non-additive microorganisms, genes, and metabolites. Specifically, the non-additive expression of Zongyangia was positively correlated with UQCR10 and Ubiquinone-1 levels within the oxidative phosphorylation pathway. These factors were negatively correlated with RFI, contributing to the RFI heterosis. Our study highlighted that key microorganisms, genes, and metabolites involved in oxidative phosphorylation interact to regulate negative heterosis for RFI in laying hens. The findings established a theoretical and practical foundation for further exploring the molecular mechanisms that drive heterosis for feed efficiency.}, } @article {pmid41846103, year = {2026}, author = {Trzos, K and Hutsch, T and Koval, A and Śmierciak, D and Machaj, G and Molano, LG and Rehner, J and Rahman, MM and Förster, MO and Bednarek, M and Yilmaz, B and Pilarczyk-Zurek, M and Surma, S and Koziel, J and Krawczyk, M and Keller, A and Becker, SL and Ylla, G and Jura, J and Kotlinowski, J}, title = {Probiotic Lactobacillus rhamnosus mitigates PBC-like features in Mcpip1-deficient mice via modulation of gut-liver crosstalk.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {1872}, number = {5}, pages = {168216}, doi = {10.1016/j.bbadis.2026.168216}, pmid = {41846103}, issn = {1879-260X}, mesh = {Animals ; *Lacticaseibacillus rhamnosus ; Mice ; *Probiotics/pharmacology ; *Liver/metabolism/pathology/drug effects ; Mice, Knockout ; Disease Models, Animal ; *Liver Cirrhosis, Biliary/pathology/microbiology/genetics/drug therapy/metabolism/therapy ; *Transcription Factors/genetics/deficiency ; *Ribonucleases/genetics/deficiency ; *Gastrointestinal Microbiome/drug effects ; Bile Acids and Salts/blood/metabolism ; }, abstract = {BACKGROUND: Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease characterized by progressive biliary destruction and cholestasis. Current therapies, including ursodeoxycholic acid (UDCA), exhibit limited efficacy in advanced disease. In this study, we investigate the therapeutic potential of microbial intervention using Lactobacillus rhamnosus (Lbr) in the Mcpip1[fl/fl]Alb[Cre] knockout mouse model of PBC, which we described previously. Knockout mice develop human PBC-like features such as bile acid dysregulation, autoantibodies, cholangiocyte hyperplasia and fibrosis.

METHODS: Six-week-old Mcpip1[fl/fl] (wild-type) and Mcpip1[fl/fl]Alb[Cre] (knockout) mice were treated with Lactobacillus rhamnosus supplementation, UDCA (15 mg/kg/day), UDCA + Lbr, and UDCA + OCA (obeticholic acid, 10 mg/kg/day) for six weeks. Treatment response was characterized by liver and gut pathology, serum biomarkers, transcriptomic profiles, and microbiome composition.

RESULTS: Treatment of Mcpip1[fl/fl]Alb[Cre] animals with Lbr decreased serum bile acids and reduced pathological cholangiocyte dysplasia in the liver, decreased leukocyte infiltration and fibrosis. RNAseq of liver tissue revealed enrichment of humoral immune responses and T cell activation pathways in knockouts, all of which were significantly attenuated by Lbr monotherapy. Gut pathology marked by increased intraepithelial lymphocyte infiltration and mucosal hypertrophy, was also normalized upon Lbr administration. Finally, probiotic treatment modulated the microbiome by increasing the Firmicutes/Bacteroidetes ratio and enriching butyrate-producing Lachnospiraceae. Administration of UDCA and UDCA+OCA had less pronounced effects: only decreased serum bile acids was detected in both groups.

CONCLUSIONS: Probiotic intervention with Lbr represents a feasible strategy to attenuate fibrotic progression in a mouse model of autoimmune cholestatic disease by modulation of the gut-microbiome-immune crosstalk.}, } @article {pmid41846126, year = {2026}, author = {Wang, X and Zhao, L and Teng, Y and Hu, W and Xu, Y and Ma, J and Song, J and Ren, W and Zhang, J and Zhu, H and Wang, X and Wang, Y and Luo, Y and Kuramae, EE}, title = {Decoding the adaptive strategies of versatile diazotrophs to multi-metal(loid) stress in mercury-mining impacted farmland soils.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141760}, doi = {10.1016/j.jhazmat.2026.141760}, pmid = {41846126}, issn = {1873-3336}, mesh = {*Soil Pollutants/toxicity/analysis ; Mining ; *Mercury/toxicity/analysis ; *Soil Microbiology ; *Metals, Heavy/toxicity/analysis ; *Nitrogen Fixation ; Farms ; Arsenic/analysis/toxicity ; Selenium/analysis ; Bacteria/metabolism/genetics ; }, abstract = {Diazotrophs are crucial for Earth's nitrogen cycle via biological nitrogen fixation, while also modulating other elemental cycles and exhibiting bioremediation potential. However, their responses to co-occurring heavy metal(loid) (HM) contaminants in polluted soils remain poorly understood. Using combined nifH (encoding nitrogenase) amplicon and metagenomic sequencing, we characterized the taxonomic structure and metabolic potential of diazotrophic community across multi-HM contamination gradients in mercury-mining impacted farmlands (paddy vs. upland). Results identified selenium (upland soils: 0-3.08 mg kg[-1]) and arsenic (paddy soils: 5.38-17.1 mg kg[-1]) as the primary HMs shaping diazotrophic diversity, whereas mercury (0.067-99.6 mg kg[-1]) showed a significant but weak correlation. Selenium and mercury correlated positively with diversity in upland soils (arsenic negatively), whereas all three HMs correlated negatively in paddy soils. Diazotrophic indicator taxa varied by HM type, yet certain taxa tolerated all three HMs simultaneously-notably Chromatiaceae/Pseudomonadaceae in upland soils and Xanthobacteraceae in paddy soils. Moreover, diazotrophs in upland soils exhibited synergistic associations with functional guilds involved in HM resistance and element cycling (e.g., carbon fixation and hydrogen metabolism), contrasting with the negative correlations in paddy soils. Metagenomic binning indicated that dominant diazotrophs were primarily aerobic heterotrophs with versatile metabolic potentials, including multi-HM resistance (e.g., arsenic/mercury reduction, efflux, and antioxidation) and energy acquisition via trace gas (CO, H2), manganese, and sulfide oxidation. These findings provide novel insights into diazotrophic adaptive strategies under multi-HM stress, advancing our understanding of their ecological and environmental functions.}, } @article {pmid41846977, year = {2026}, author = {Sharaf, H and Bobay, LM}, title = {MetaStrainer: Accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41846977}, issn = {2692-8205}, abstract = {SUMMARY: Metagenomics provides broad insights from microbial communities, but more biological relevant phenotypes are attributed to subtle changes at the strain-level rather than species. Despite development of several tools using different algorithms, resolving individual strains from short-read pair-end sequencing data remains challenging. We developed MetaStrainer, a tool capable of reconstructing strain genotypes from metagenomic data. Compared with existing approaches, MetaStrainer substantially increases genotype accuracy, correctly identifies the number of strains, and accurately estimates their relative abundances. Accuracy of reconstructed genotypes is robust to choice of mapping reference.

MetaStrainer is implemented in Python 3. Source code and instructions are available on GitHub at https://www.github.com/lbobay/MetaStrainer and on Zenodo: https://doi.org/10.5281/zenodo.17872331.}, } @article {pmid41847008, year = {2026}, author = {Yancey, CE and Brumfield, KD and Ettwiller, L and Colwell, RR}, title = {Microbial Community multi-omic analysis of marsh sediment post crustacean shell compost enrichment: pathogen emergence and community response.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41847008}, issn = {2692-8205}, abstract = {Changes in nutrient availability can rapidly alter microbial processes in natural environments, with implications in biogeochemical cycling and pathogen emergence. Short-term, functional responses of microbial communities to nutrient amendment in coastal communities remain poorly understood, particularly in temperate environments. A 48-hour microcosm pulse experiment was completed in which paired metagenomic and metatranscriptomic sequencing were employed to examine how the decomposition of chitin rich substrates, namely crab and lobster shell compost, alters salt marsh microbiome structure and function. Within 48 hours of amendment, pronounced shifts in community metabolism were observed, including increased chitin degradation and utilization, stress-response, and sporulation. These responses coincided with marked decreases in genes associated with key biogeochemical processes, including carbon fixation, sulfur oxidation and reduction, and other metabolic pathways. Shell compost addition also enriched putative pathogens and virulence-associated genes, accompanied by modest transcriptional activation, notably aerolysin A (aerA), which encodes the pore-forming exotoxin aerolysin. These results demonstrate temperate salt marsh sediment microbiomes can undergo shifts in community composition and function that is associated with chitin-rich nutrient perturbation. The sensitivity of temperate coastal systems to organic matter input and the potential for ecological and public-health relevant outcomes are underscored, notably given that chitin is among the most abundant and readily available bionutrients in aquatic ecosystems globally.}, } @article {pmid41847199, year = {2026}, author = {Ha, S and Kim, N and Song, CH}, title = {Age- and sex-dependent alterations of jejunal microbiota in Fischer 344 rats fed with a high-fructose, high-fat diet: depletion of Lactobacillus intestinalis in small bowel contents.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1779112}, pmid = {41847199}, issn = {1664-302X}, abstract = {INTRODUCTION: Our previous research demonstrated that a high-fat diet (HFD) induced jejunal inflammation and hepatic steatosis, suggesting that small bowel microbiota contribute to these pathologies. This study investigated age- and sex-specific alterations in jejunal microbiota following a high-fructose, high-fat diet (HFHFD) in F344 rats.

METHODS: Six-week-old and two-year-old rats of both sexes were fed an HFHFD for 8 weeks, after which jejunal contents were collected for metagenomic analysis. Taxonomic profiling and linear discriminant analysis were performed, and Spearman's rank correlation analysis was used to evaluate associations with jejunal inflammation and hepatic steatosis. Beta-diversity analysis was conducted to assess group separation. In vitro, HIEC-6 human intestinal epithelial cells were used to test the protective effect of Lactobacillus intestinalis under palmitic acid-induced lipotoxic stress.

RESULTS: HFHFD reduced the Firmicutes/Bacteroidetes ratio in young females and in aged rats of both sexes. Notably, Lactobacillus intestinalis-which supports barrier function-decreased in young males and aged females. In contrast, Akkermansia muciniphila increased across all HFHFD groups, particularly in young females and aged rats. Bacteroides vulgatus increased in aged HFHFD-fed rats of both sexes, while Bacteroides caccae was elevated in females across both age groups. Furthermore, the Lactobacillus reuteri group decreased only in young HFHFD rats. L. intestinalis and L. reuteri groups negatively correlated with jejunal inflammation and hepatic steatosis, whereas B. caccae and A. muciniphila showed positive correlations with both pathogenic phenotypes. Beta-diversity revealed a pronounced diet- and sex-dependent separation in young rats, which was attenuated in aged groups. In HIEC-6 cells, L. intestinalis significantly restored viability under palmitic acid-induced lipotoxic stress, though its conditioned medium did not.

DISCUSSION: Collectively, HFHFD induces age- and sex-dependent dysbiosis in the jejunum, and L. intestinalis may serve as a potential probiotic for metabolic dysfunction-associated steatotic liver disease.}, } @article {pmid41847396, year = {2026}, author = {Yan, J and Yang, H and Zhang, W and Li, Y and Yu, X and Xiong, Z and Shi, C and Hu, Y}, title = {A Case Report of Tuberculous Peritonitis with Negative GeneXpert and Positive Metagenomic Sequencing Results.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {560202}, pmid = {41847396}, issn = {1178-6973}, abstract = {A 65-year-old male patient undergoing peritoneal dialysis was diagnosed with Mycobacterium tuberculosis-related peritonitis. Initial diagnostic tests, including acid-fast smear of ascites, GeneXpert test, and Mycobacterium tuberculosis culture, yielded negative results. However, metagenomic capture sequencing (metaCAP) and metagenomic next-generation sequencing (mNGS) identified the presence of Mycobacterium tuberculosis. The patient was subsequently treated with standard anti-tuberculosis therapy, leading to clinical improvement. This case highlights the utility of advanced molecular diagnostics in identifying atypical pathogens in peritoneal dialysis-related infections.}, } @article {pmid41847603, year = {2026}, author = {Zhang, Y and Zhang, Y and Zhang, K and Wang, L and Huang, D and Zhen, F and Wang, R and An, C}, title = {Parameter-Specific Effects of Low-Intensity Transcranial Focused Ultrasound Stimulation on Depression-Like Behaviors in a CUMS Mouse Model.}, journal = {Neuropsychiatric disease and treatment}, volume = {22}, number = {}, pages = {586583}, pmid = {41847603}, issn = {1176-6328}, abstract = {PURPOSE: Depression is a multifactorial disorder involving neurotransmitter dysregulation, gut microbiota imbalance, and metabolic disturbances. Low-intensity transcranial focused ultrasound stimulation (LIFUS) holds promise for treating depression. However, the effects of different LIFUS parameter settings on depression-like behaviors, and their potential associations with gut microbiota and fecal metabolite changes, remain largely unexplored. This study aims to investigate the parameter-specific effects of LIFUS on depression-like behaviors in a chronic unpredictable mild stress (CUMS) mouse model, and to explore potential associations with changes in gut microbiota and fecal metabolites.

METHODS: To establish a depression model, C57BL/6 mice were subjected to CUMS, while a separate cohort was kept as a control (CON) group. The CUMS-exposed mice were then randomly divided into four groups: CUMSpo, LIFUS1, LIFUS2 and SHAM. Depressive-like behaviors were evaluated using the sucrose preference test (SPT) and forced swim test (FST). The levels of neurotransmitters and Fecal concentrations of metabolites were quantified using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gut microbiota composition was analyzed by metagenomic sequencing, and α-diversity was assessed using the ACE, Chao1, and Shannon indices. Histopathology was assessed via HE staining.

RESULTS: LIFUS at 1.5 kHz PRF, but not 300 Hz, significantly attenuated CUMS-induced depressive-like behaviors, evidenced by increased sucrose preference and reduced immobility time, without affecting locomotor activity. This behavioral effect was accompanied by a significant increase in cortical glutamate. LIFUS2 protocol was associated with a significant increase in tryptamine, alongside a concurrent trend towards restoring the abundance of Clostridia and enhancing gut microbiota α-diversity. HE staining confirmed protocol safety.

CONCLUSION: The antidepressant-like effects of LIFUS appear to be associated with multi-systemic alterations, including changes in cortical glutamate, modulation of the gut microbiota, and specific changes in tryptophan metabolism.}, } @article {pmid41848047, year = {2026}, author = {Xue, R and Zhang, Y and Li, H and Li, J and Ke, W and Hu, S and Li, C and Chan, FKS and Cui, L}, title = {Persistent antimicrobial resistance during soil remediation driven by residual heavy metal co-selection.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41848047}, issn = {1751-7370}, support = {2024J011016//Fujian province/ ; 22193061//Natural Science Foundation of China/ ; 42307165//Natural Science Foundation of China/ ; 2022YFF0713100//National Key Research and Development Program of China/ ; }, mesh = {*Soil Microbiology ; *Metals, Heavy/pharmacology/analysis ; *Soil Pollutants ; *Drug Resistance, Bacterial ; *Environmental Restoration and Remediation ; *Bacteria/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Selection, Genetic ; }, abstract = {Remediation of heavy metal-contaminated soil is a global priority, particularly as reclaimed land increasingly intersects with urban development and human exposure. However, the ecological consequences of soil remediation, especially its impact on antimicrobial resistance (AMR) as a global health threat, have remained poorly understood. Here, we combined single-cell Raman-D2O probing with genome-resolved metagenomics to monitor the dynamics of phenotypic and genotypic resistance to metals and antibiotics during a 120-day remediation of soils with three contamination levels from a lead-zinc smelting site. Although chemical remediation substantially reduced bioavailable metals (by 42%-65%), AMR was not diminished. Instead, both phenotypic activity and gene abundance of metal- and antibiotic-resistant microorganisms increased, resulting in a two- to three-fold increase in AMR-associated health risks. Among 76 metagenome assembled genomes (MAGs) from phenotypic resistance communities, all Cd resistance-associated MAGs harbored multidrug resistance genes, half of which were colocalized with metal resistance determinants, and their prevalence continued to rise with remediation. These findings reveal that although remediation alleviates acute metal toxicity, residual low-concentration bioavailable metals sustain evolutionary selection for resistance, highlighting a disconnect between chemical recovery and biological safety. Moreover, the improved soil nutrient and physiochemical properties of remediated soils further promoted the proliferation of antibiotic-resistant bacteria. This study offers new ecological insights into the unintended consequences of anthropogenic interventions, underscoring the need to integrate biological safety into soil health and safety assessments.}, } @article {pmid41848058, year = {2026}, author = {Calusinska, M and Herold, M and Klimek, D and Bertucci, M and Lemaigre, S and Cambier, S and Zorzan, S and Leclercq, C and Dolfing, J and Westerholm, M and Müller, B and Nasirzadeh, L and Schnürer, A and Wilmes, P and Delfosse, P and Goux, X}, title = {Phylum-wide propionate degradation and its potential connection to poly-gamma-glutamate biosynthesis in Candidatus Cloacimonadota phylum.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41848058}, issn = {1751-7370}, support = {C17/SR/11687962//FNR CORE 2017 project CLOMICS/ ; C22/SR/17271192//FNR CORE 2023 project eBioMeth/ ; }, mesh = {*Propionates/metabolism ; *Bacteria/metabolism/genetics/classification ; Anaerobiosis ; Phylogeny ; Methane/metabolism ; Metagenomics ; }, abstract = {The candidate phylum Cloacimonadota is frequently detected in anoxic environments such as anaerobic digestion (AD) reactors, hydrothermal vents, and deep-sea sediments, yet its metabolism remains poorly understood. Metagenomic evidence suggests capacities for amino acid fermentation, carbohydrate degradation, as well as a potential role in syntrophic propionate oxidation (SPO), a key bottleneck in AD. However, a complete methylmalonyl-CoA (mmc) pathway, central to SPO, has not been previously identified in Cloacimonadota genomes. Here, we report results from an acidified lab-scale anaerobic baffled reactor fed with sugar beet pulp, where an increase in the relative abundance of Cloacimonadota correlated with recovery of methanogenesis, resulting in increased methane content in the produced biogas. Metagenomic and metatranscriptomic analyses enabled metabolic reconstruction of the dominant Cloacimonadota operational taxonomic unit (OTU). Furthermore, using a curated database of 204 genome-resolved Cloacimonadota species, we characterized the phylum-level metabolic potential. Comparative genomics revealed alternative proteins, including 2-oxoglutarate:ferredoxin oxidoreductase and aspartate aminotransferase, likely to substitute for missing enzymes in the classical mmc pathway. These proteins were widely distributed and highly conserved across the analyzed Cloacimonadota genomes, suggesting that this variant of the SPO pathway could represent a phylum-specific trait. Moreover, we hypothesize that these alternative pathway steps may link propionate metabolism to protein degradation and poly-γ-glutamate biosynthesis. Network analysis identified the methanogenic archaeon Methanothrix as a potential syntrophic partner, an interaction further supported by propionate-fed enrichment cultures showing co-occurrence of Cloacimonadota and Methanothrix species. Our study sheds light on the Cloacimonadota metabolism, advancing our understanding of their ecological roles and potential for biotechnological applications.}, } @article {pmid41848770, year = {2026}, author = {Prabhu, A and Rinke, C}, title = {ICTV Virus Taxonomy Profile: Apasviridae 2026.}, journal = {The Journal of general virology}, volume = {107}, number = {3}, pages = {}, pmid = {41848770}, issn = {1465-2099}, mesh = {Genome, Viral ; *DNA Viruses/classification/genetics/ultrastructure/isolation & purification ; Phylogeny ; *Archaeal Viruses/classification/genetics ; DNA, Viral/genetics ; *Archaea/virology ; Virus Replication ; Virion/ultrastructure/genetics ; }, abstract = {The family Apasviridae includes dsDNA viruses associated with the marine archaeal lineage Poseidoniales. Members of this family have been identified using metagenomic analyses of brackish estuarine samples and are related to other 'magroviruses' infecting Poseidoniales archaea. The family belongs to the order Magrovirales and includes the genus Agnivirus and the species Agnivirus brisbanense. Viruses in the family possess a linear dsDNA genome of about 108 kbp and encode modules for DNA replication and virion morphogenesis, such as those relating to the formation of an icosahedral capsid and a helical tail, characteristic of members of the class Caudoviricetes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Apasviridae, which is available at ictv.global/report/apasviridae.}, } @article {pmid41849038, year = {2026}, author = {Biçer, Y and Sönmez, G and Turkal, G and Telli, AE and Akkurt, MY and Uçar, G}, title = {Potential use of whey in kefir production: evaluation of fermentation kinetics and microbiota.}, journal = {Food science of animal resources}, volume = {46}, number = {1}, pages = {}, pmid = {41849038}, issn = {2636-0780}, abstract = {This study was carried out on the effect of different amounts of whey on the kefir production process and the bacterial microbiota of the beverages. Fermentation was carried out by mixing commercial kefir grains with cow, sheep, and goat milk with their whey at concentrations of 0% (control group), 25%, 50%, and 75%. The bacterial microbiota in the produced beverages and the relative abundances of seven microorganisms (Lactobacillus kefiranofaciens, Lactobacillus kefiri, Lactobacillus delbrueckii, Lactococcus lactis, Streptococcus thermophilus, Leuconostoc mesenteroides, and acetic acid bacteria) were determined using metagenomic analysis targeting the V3-V4 region of 16 S rRNA gene, and quantitative polymerase chain reaction (qPCR), respectively. Lactococcus lactis and Leuconostoc mesenteroides were detected in higher abundance in whey-containing goat samples. While Lactobacillus was dominant in the cow milk samples containing 0%, 25%, and 50% whey, Enterococcus was dominant in the samples containing 75% whey. In sheep milk samples, Lactobacillus was dominant in samples with 75% and 50% whey, Lactococcus was dominant in samples with 25% whey, and Enterococcus was dominant in samples with no (0%) whey. Lactobacillus was dominant in all goat milk samples. In conclusion, high levels of lactic acid bacteria were shown to preserve their viability in the experimentally produced beverages with the addition of whey at different concentrations, and the whey could be used to produce kefir.}, } @article {pmid41849467, year = {2026}, author = {Ferreira, LDS and Silva, JFBR and Vilhena, MPSP and Alegria, OC and Ramos, RTJ and Sousa, MPA}, title = {Bacterial diversity of lowland soils under cocoa cultivation in Amazon.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {86}, number = {}, pages = {e295836}, doi = {10.1590/1519-6984.295836}, pmid = {41849467}, issn = {1678-4375}, mesh = {*Cacao/growth & development ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Brazil ; *Biodiversity ; DNA, Bacterial/genetics ; }, abstract = {This study investigated bacterial diversity in soils from six cacao-producing islands in Mocajuba, Pará, Brazil. Using next generation sequencing shotgun metagenomic DNA, we characterized the microbial composition and ecological structure of floodplain soils cultivated with Theobroma cacao. Taxonomic classification revealed a rich bacterial community encompassing 21 phyla, 54 classes, 121 orders, 240 families, 604 genera, and 2,289 species. The dominant phyla, Actinomycetota and Pseudomonadota, are known for their ecological roles in organic matter decomposition, antibiotic production, nitrogen cycling, and plant growth promotion. Alpha diversity metrics varied among samples, with P3 showing the highest species richness and P5 exhibiting the highest Shannon, Simpson, and evenness indices, suggesting a more balanced community. Beta diversity analysis based on Bray-Curtis dissimilarity under Total Sum Scaling (TSS) normalization revealed ecological gradients ranging from 0.228 to 0.527. Spatial ordination and hierarchical clustering indicated gradual shifts in community composition, supporting the concept of a compositional continuum shaped by environmental gradients. Functionally, Burkholderia lata was dominant in P1, reflecting its role in potassium solubilization, while Streptomyces species-detected in five of the six samples-contribute to biogeochemical cycling and pathogen suppression. Bradyrhizobium and Paraburkholderia, identified in P3, P5, and P6, are associated with nitrogen fixation and plant hormone regulation. These findings reveal the ecological complexity and functional potential of cacao soil microbiomes, providing insights for sustainable management of Amazonian floodplain agroecosystems.}, } @article {pmid41849523, year = {2026}, author = {Mardiyaningsih, A and Astuti, P and Widodo, W and Purwanto, P}, title = {Metagenomic analysis of Gatot, a cassava-based fermented food from Yogyakarta Indonesia: a potential source of Lactobacillaceae probiotic.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {86}, number = {}, pages = {e298140}, doi = {10.1590/1519-6984.298140}, pmid = {41849523}, issn = {1678-4375}, mesh = {*Manihot/microbiology ; Indonesia ; *Probiotics ; Metagenomics ; Food Microbiology ; *Fermented Foods/microbiology ; *Lactobacillaceae/genetics/classification/isolation & purification ; DNA, Bacterial/genetics ; Fermentation ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Gatot, a traditional Indonesian fermented food product made from cassava (Manihot utilissima), is valued for its potential health benefits and contribution towards local food security. As fermentation induces a rich microbial environment that could enhance nutritional properties and produce bioactive compounds, understanding the bacterial communities involved is fundamental for optimizing their health-promoting potential. However, the bacterial diversity of Gatot across different regions remains underexplored. This study aims to detect and identify the bacterial communities in Gatot samples, as well as to measure the differences in their abundance in Gatot from three different regions in Yogyakarta. Gatot samples were collected from Bantul, Gunungkidul, and Kulon Progo regions. Genomic DNA was extracted from the samples, and DNA concentration was measured using NanoDrop and Qubit. Libraries were then prepared with Oxford Nanopore Technology kits. For bacterial identification, the V1-V9 regions of the 16S ribosomal RNA gene were amplified using 27F and 1492R primers under specific polymerase chain reaction conditions. Sequencing was performed on a GridION platform using MinKNOW (version v24.02.16) and Dorado (version v7.3.11) for high-accuracy basecalling. Quality filtering and visualization of FASTQ files were performed using NanoPlot and NanoFilt, while taxonomic classification was referenced against the NCBI 16S RefSeq database. Data analysis was completed in Pavian and RStudio. The dominant bacterial family across all samples was the Lactobacillaceae family. However, each region exhibited unique microbial signatures at the genus level: Bantul samples were dominated by Weissella, Gunungkidul by Leuconostoc, and Kulon Progo by Lactiplantibacillus. Specific species were also predominant in each location, with Weissella confusa in Bantul, Liquorilactobacillus hordei in Gunungkidul, and Lactiplantibacillus plantarum in Kulon Progo. These regional variations highlight how location-specific bacterial communities influence the fermentation profile of Gatot, potentially affecting flavor, texture, and nutritional value. This study provides the first comprehensive metagenomic analysis of Gatot's bacterial communities across different regions, offering new insights into the influence of geographical environment on microbial composition in fermented cassava products. The findings support the potential for controlled fermentation processes tailored to local microbial ecosystems, to enhance Gatot's functionality as a health-promoting food and source of probiotic.}, } @article {pmid41850677, year = {2026}, author = {Mi, X and Liu, R and Jiang, Z and Tang, M and Yan, J and Liu, J and Li, Y and Zheng, J and Yang, W and Gong, L and Shi, J}, title = {Gut Microbiota-Derived Propionate Governs Hepatic N2 Neutrophils in Wilson's Disease.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {20}, number = {7}, pages = {101770}, pmid = {41850677}, issn = {2352-345X}, mesh = {Animals ; *Neutrophils/metabolism/immunology/drug effects ; *Hepatolenticular Degeneration/pathology/immunology/microbiology/metabolism ; *Propionates/metabolism/pharmacology ; Mice ; Mice, Knockout ; *Gastrointestinal Microbiome/immunology ; Transforming Growth Factor beta1/metabolism ; *Liver/pathology/immunology/metabolism ; Fecal Microbiota Transplantation ; Copper-Transporting ATPases/genetics ; Disease Models, Animal ; Male ; Humans ; Hydroxamic Acids ; }, abstract = {BACKGROUND & AIMS: Neutrophil functions play a pivotal role in hepatic pathogenesis. Our previous work has established that N2-polarized neutrophils promote hepatic fibrogenesis in Wilson's disease depends on hepatic transforming growth factor-β1 (TGF-β1) production. However, the regulators governing TGF-β1 production in orchestrating disease-associated N2 neutrophils remain elusive. In this study, we investigated the immunomodulatory effects of gut microbiota-derived short-chain fatty acids (SCFAs) on neutrophil polarization.

METHODS: Fecal metagenomic sequencing and short-chain fatty acid (SCFA) profiling were performed on ATP7B-knockout (ATP7B-KO) mice and their wild-type (WT) littermate controls. Fecal microbiota transplantation (FMT) experiments were conducted by transferring feces from WT mice or Akkermansia muciniphila into recipient mice. Additionally, propionate or trichostatin A (TSA) was administered to both ATP7B-KO and WT groups. Mice were assessed using histological analyses, Sirius Red staining, flow cytometry, biochemical assays, immunohistochemistry, measurement of TGF-β1 levels, immunofluorescence, and quantitative real-time polymerase chain reaction (qRT-PCR) for gene expression profiling. To elucidate the underlying molecular mechanisms, 4D label-free quantitative acetylated proteomics, site-directed mutagenesis, plasmid transfection, co-immunoprecipitation (IP), and luciferase reporter assays were employed.

RESULTS: We report that Akkermansia muciniphila was markedly reduced in the gut microbiota of mice with Wilson's disease, accompanied by decreased SCFA levels, especially propionate. Additionally, transplantation of fecal bacteria from wild-type mice or A muciniphila could promote an antifibrotic effect, elevate propionate levels, reduce TGF-β1 secretion, and decrease hepatic N2 neutrophils in mice with Wilson's disease. Moreover, administration of propionate also significantly enhanced antifibrotic immunity. Mechanistically, propionate reduced the production of TGF-β1 in hepatocytes by inhibiting histone deacetylase activity, increasing the acetylation of DNAJA3 at sites K134 and K385, thus decreasing expression of DNAJA3. Consistently, gut-derived propionate inversely correlated with hepatic injury severity in patients with Wilson's disease, which could be functionally mediated by TGF-β1.

CONCLUSIONS: Gut microbiota are pivotal for hepatic neutrophil polarization and liver fibrosis in Wilson's disease. Our findings suggest that therapeutic modulation of gut microbiota, SCFA profiles, and TGF-β1 production, particularly when combined with histone deacetylase inhibitors, may represent promising therapeutic approaches for Wilson's disease.}, } @article {pmid41850876, year = {2026}, author = {Regmi, H and Dritsoulas, A and Kamali, S and Stelinski, LL and Diepenbrock, LM and Duncan, L}, title = {Edge effects, tree cover and soil properties linked to the distribution of Diaprepes abbreviatus in a Florida citrus orchard.}, journal = {Pest management science}, volume = {82}, number = {7}, pages = {6409-6420}, doi = {10.1002/ps.70723}, pmid = {41850876}, issn = {1526-4998}, support = {CRDF22-013//Citrus Research and Development Foundation, Inc./ ; }, mesh = {Animals ; Florida ; *Citrus/growth & development ; *Weevils/physiology ; *Soil/chemistry ; *Animal Distribution ; Seasons ; Soil Microbiology ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: Diaprepes root weevil (DRW, Diaprepes abbreviatus) is a major economic pest of citrus trees in Florida and the Caribbean Basin. To identify potential drivers of local patterns of weevil abundance and tree condition, we measured relationships between DRW and edaphic properties in a Florida orchard in which half the trees were initially protected from herbivores by individual protective covers (IPCs) of fabric mesh. Weevils were monitored for 2 years in 94 plots arranged in a grid pattern. Soil samples were processed for physicochemical properties, and DNA from soil organisms was subjected to metabarcoding for ITS2 rDNA, 16S rDNA, and COI mtDNA.

RESULTS: Weevils aggregated each summer along plot boundaries adjacent to a natural area of alternate hosts, consistent with an edge-biased distribution reflecting seasonal weevil migration. Fourteen months after the covers were removed, 93% of 484 prokaryote species (dominated by Bacilli, Actinobacteria, Alphaproteobacteria, and Cyanobacteria) that were most closely associated with IPC use were less abundant beneath the trees that were formerly covered than under previously uncovered trees. Soil moisture, Paenibacillus spp. diversity, and IPCs were associated with DRW patterns and tree condition including mortality.

CONCLUSIONS: Early season, edge-biased distribution of DRW should be exploited for monitoring and management efficacy. The relationship here between tree mortality and microbiome species deficits associated with IPCs supports the need for research to resolve the role of tree covers in potential trophic cascades that affect plant health. © 2026 Society of Chemical Industry.}, } @article {pmid41850962, year = {2026}, author = {Zhao, Y and Zheng, J and Liu, Q}, title = {The diversity of emerging tick-borne viruses globally.}, journal = {Trends in parasitology}, volume = {42}, number = {4}, pages = {207-209}, doi = {10.1016/j.pt.2026.03.001}, pmid = {41850962}, issn = {1471-5007}, mesh = {Animals ; Humans ; *Tick-Borne Diseases/virology ; *Ticks/virology ; *Communicable Diseases, Emerging/virology ; *Viruses/genetics/classification ; }, abstract = {Zhang et al. provide the first global synthesis of 230 emerging tick-borne viruses, introducing a genomic model that predicts zoonotic risk. Their approach identifies 25 very-high-risk viruses and clinically validates three novel human pathogens, shifting the paradigm from reactive discovery to proactive risk assessment for global health security.}, } @article {pmid41851124, year = {2026}, author = {Luzmore, A and Grauer, J and Barber, D and Lau, P and Jorgensen, G and Jain, S and Perron, GG}, title = {Seasonal frost improves probiotic and nutrient availability in fermented vegetables.}, journal = {NPJ science of food}, volume = {10}, number = {1}, pages = {}, pmid = {41851124}, issn = {2396-8370}, abstract = {Climate-driven shifts in seasonal frost patterns raise important questions about their impact on food quality and resilience. Here, we show that a single 12-h frost event at harvest can enhance both the microbial and nutritional properties of fermented cabbage and carrots, two cold-tolerant crops widely grown in the U.S. Northeast. Using microbial amplicon and metagenomic sequencing, we found that frost exposure led to subtle but consistent changes in microbial composition, including greater abundance of cold-adapted taxa such as Leuconostoc and Debaryomyces. These changes corresponded to increased abundance of genes involved in vitamin biosynthesis, particularly menaquinone (K2), cobalamin (B12), and threonine pathways. Nutritional assays confirmed higher concentrations of vitamins A and E in frost-conditioned carrot ferments and increased vitamin K1 in cabbage. Our findings suggest that exposure to seasonal frost can enhance the health-promoting and sensory qualities of fermented vegetables, offering a novel strategy for value-added, climate-resilient food production in temperate regions.}, } @article {pmid41851512, year = {2026}, author = {Zhang, S and Yang, B and Xie, Z and Jiang, F and Liu, K}, title = {Occurrence of Antibiotics at a Typical Livestock Farm in Northwest China: Emergence Characteristics and Ecological Risk Assessment.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {116}, number = {4}, pages = {}, pmid = {41851512}, issn = {1432-0800}, support = {2024TCYCQNBS03//"Tianchi Talents" Young Doctors Recruitment Program/ ; 252102321066//Key Research & Development and Promotion of Special Project (Scientific Problem Tackling) of Henan Province/ ; }, abstract = {This study analyzed veterinary antibiotics (VAs) and resistance genes (ARGs) in manure and soil at a typcial livestock farm in Northwest China using LC-MS and metagenomics. Sulfonamides (SAs) were highest in chicken manure, while quinolones (QNs) dominated cattle manure and adjacent soil (172.784 ng g−1 total QNs). Transfer rates of QNs and tetracyclines from manure to soil exceeded 100%, indicating significant ecological risk via the food chain. Metagenomics revealed the tetracycline resistance gene tetA (58) dominated the soil ARG pool. Significant positive correlations (p < 0.05) existed between QN concentrations (including ciprofloxacin, lomefloxacin) and quinolone resistance genes (flu), and between soil tetracyclines and multidrug resistance genes (mul). Ecological risk modeling confirmed a high mixed contamination risk for QNs (RQ = 2.36 > 1).}, } @article {pmid41851530, year = {2026}, author = {Cohen, Y and Jansen, T and Onwuka, S and Elinav, E}, title = {Advances and opportunities in measuring dietary intake: from omics to AI.}, journal = {Nature metabolism}, volume = {8}, number = {4}, pages = {795-809}, pmid = {41851530}, issn = {2522-5812}, mesh = {Humans ; *Artificial Intelligence ; Proteomics ; *Eating ; *Diet ; Gastrointestinal Microbiome ; Nutrition Assessment ; }, abstract = {Accurate measurement of dietary intake remains a cornerstone challenge in optimizing the efficacy of nutritional interventions in human disease. Traditional self-reporting methods, although scalable and widely used, are prone to major bias and measurement error, thereby limiting their precision and clinical utility. In this Review, we highlight recent advances in technology-assisted food intake measurement, including image-based logging, wearable sensors and artificial intelligence (AI)-based dietary estimation, which may reduce reliance on recall and improve intake estimation. We review the emergence of non-invasive biological methodologies, such as metagenome-informed metaproteomics, in accurately enabling objective measurement of food intake and nutrient digestion and absorption in molecular resolution. We explore the possible interactions and effects of the gut microbiome in modulating such person-specific digestive and absorptive patterns and discuss challenges and prospects in the convergence of omics-based, measurement-based and AI-based dietary assessment tools into precision nutrition, in fulfilling its immense potential towards optimization of patient care.}, } @article {pmid41851880, year = {2026}, author = {Sharma, AA and Martinou, AF and Cadar, D and Omirou, M and Neira, M and Christophides, GK}, title = {Integrated vector and arbovirus surveillance in Cyprus: first reports of Usutu virus and Culex pipiens bioform diversity highlight potential for zoonotic arbovirus transmission.}, journal = {Parasites & vectors}, volume = {19}, number = {1}, pages = {}, pmid = {41851880}, issn = {1756-3305}, support = {856612//Horizon 2020/ ; }, mesh = {Animals ; Cyprus/epidemiology ; *Culex/virology/classification/genetics ; *Mosquito Vectors/virology/classification ; Mosquito-Borne Diseases ; *Flavivirus/isolation & purification/genetics ; *Arbovirus Infections/transmission/epidemiology/virology ; Zoonoses/transmission/virology ; *Arboviruses/isolation & purification/genetics ; Aedes/virology ; *Flavivirus Infections/transmission/epidemiology/virology ; Female ; Humans ; Birds/virology ; West Nile virus ; }, abstract = {BACKGROUND: Anthropogenic pressures, including urbanisation, globalisation and climate change, have facilitated an increased risk for emergence or re-emergence of mosquito-borne diseases into regions such as the Eastern Mediterranean and Middle East. Cyprus is a major stop-over site for migratory birds and has previously experienced outbreaks of West Nile virus (WNV). The island has native mosquito vector populations; however, it has also seen the recent establishment of invasive Aedes albopictus and Ae. aegypti mosquitoes. Given the dynamic climatic conditions and the shifting ecological and epidemiological landscapes in the region, the need for routine vector and pathogen surveillance has never been more critical.

METHODS: Herein, we present the results from localised adult mosquito surveillance that were conducted in two cities of Cyprus between 2019 and 2022. Mosquito taxa were identified through morphological analysis, and molecular techniques were used to further characterise the Culex pipiens bioforms. Engorged mosquito midguts were analysed to determine host blood meals. Metagenomic next-generation sequencing was employed to screen mosquito pools for arboviruses.

RESULTS: Our results provide the first report of Usutu virus in Cx. pipiens mosquitoes in Cyprus. Blood meal analysis identified multiple vertebrate hosts, including Cetti's warbler, a bird species previously reported to be seropositive for WNV on the island. Additionally, we report the presence of both Cx. pipiens pipiens and Cx. pipiens molestus, an ornithophilic and a mammophilic bioform, respectively, as well as their hybrids.

CONCLUSIONS: Our findings highlight the urgent need for enhanced mosquito surveillance strategies where mosquito populations will be regularly screened for pathogens to mitigate emerging risks of arbovirus transmission in Cyprus.}, } @article {pmid41851941, year = {2026}, author = {Shrestha, E and Katuwal, N and Sitaula, RK and Gurung, H and Shrestha, A and Karki, P and Shrestha, R}, title = {Identification of the Causative Pathogen in the 2023 Conjunctivitis Outbreak of Nepal Using Unbiased Metagenomic Next Generation Sequencing.}, journal = {Journal of Nepal Health Research Council}, volume = {23}, number = {3}, pages = {527-532}, doi = {10.33314/jnhrc.v23i03.4749}, pmid = {41851941}, issn = {1999-6217}, mesh = {Humans ; Nepal/epidemiology ; *Disease Outbreaks ; Female ; Male ; High-Throughput Nucleotide Sequencing ; Child ; Metagenomics/methods ; *Conjunctivitis/epidemiology/virology ; Adolescent ; Adult ; Child, Preschool ; *Enterovirus C, Human/isolation & purification/genetics ; Infant ; Young Adult ; Middle Aged ; }, abstract = {BACKGROUND: In mid-2023, Nepal experienced a significant outbreak of conjunctivitis, affecting over 60% of outpatients in eye hospitals and prompting school closures. The outbreak, peaking in August, predominantly impacted children and individuals with compromised immunity. Clinical manifestations included sudden-onset redness, foreign body sensation, watery discharge, and occasional lid swelling. Most cases exhibited acute haemorrhagic conjunctivitis, with management involving ocular lubricants, personal hygiene, and topical antibiotics. This case series from Himalaya Eye Hospital in Pokhara details the genomic epidemiology and clinical characteristics of conjunctivitis cases during the outbreak.

METHODS: To understand the causative agents, conjunctival swabs from patients were subjected to unbiased metagenomic next-generation sequencing (mNGS) in Illumina iSeq100 at Dhulikhel Hospital Kathmandu University Hospital Results: This case series revealed the presence of Enterovirus C (coxsackievirus strain A24) as the major pathogen responsible for the outbreak.

CONCLUSIONS: This case series contributes valuable insights into the genomic diversity of conjunctivitis-associated viruses, highlighting the potential of mNGS in enhancing diagnostic capabilities and guiding public health responses.}, } @article {pmid41852102, year = {2026}, author = {Qu, X and Liao, Y and Muthuri, CW and Winowiecki, LA and Zi, H and Zhang, Y and Li, X}, title = {Soil Functionality Undermined by Symbiotic Fungal Decline Following Forest Conversion.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70268}, doi = {10.1111/1462-2920.70268}, pmid = {41852102}, issn = {1462-2920}, support = {W2412011//National Natural Science Foundation of China/ ; 32430069//National Natural Science Foundation of China/ ; jxsq2023102214//Double Thousand Plan of Jiangxi Province/ ; }, mesh = {*Soil Microbiology ; *Forests ; *Fungi/classification/genetics/physiology ; *Symbiosis ; *Soil/chemistry ; China ; Carbon/metabolism ; Biodiversity ; Nitrogen/metabolism/analysis ; Phosphorus/metabolism/analysis ; Bacteria/classification/genetics ; Ecosystem ; }, abstract = {The conversion of native forests to other terrestrial ecosystems represents a profound form of land-use change, threatening aboveground biodiversity and biomass. However, its impact on soil ecological functions remains uncertain, particularly the regulatory role of soil microbial communities. To address this, we evaluated soil functionality related to carbon, nitrogen and phosphorus cycling by measuring nine enzyme activities in soils from native forests, plantations and croplands in subtropical China. Our results demonstrated a significant decline in soil functionality following the conversion of native forests, with the most pronounced reductions observed in croplands. This decline in soil functionality was strongly associated with a decrease in fungal richness but was independent of bacterial alpha-diversity. Specifically, the reduction in the abundance of symbiotic fungi, including key taxa such as Lactifluus and Tomentella, was identified as a primary driver of the functional impairment. Metagenomic analyses further confirmed that the loss of microbial functional genes was linked to the observed decline in soil functionality. Our findings underscore the critical role of key fungal taxa in maintaining soil processes and highlight the importance of their conservation and restoration to ensure ecosystem functionality in managed landscapes.}, } @article {pmid41852114, year = {2026}, author = {Kaneko, Y and Hino, T and Taminishi, S and Matoba, Y and Motooka, D and Hoshino, A and Matoba, S}, title = {Inhibition of N-Terminal Acetyltransferase C Mitigates Endoplasmic Reticulum Stress-Mediated Muscle Atrophy in Cancer Cachexia.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {17}, number = {2}, pages = {e70249}, pmid = {41852114}, issn = {2190-6009}, support = {22H03071//JSPS Grant-in-Aid Scientific Research/ ; 25K02651//JSPS Grant-in-Aid Scientific Research/ ; //Nakatomi Foundation/ ; }, mesh = {Animals ; *Cachexia/etiology/metabolism/pathology ; Mice ; *Endoplasmic Reticulum Stress/drug effects ; *Muscular Atrophy/etiology/metabolism/pathology ; Male ; *Neoplasms/complications ; Humans ; Disease Models, Animal ; }, abstract = {BACKGROUND: Cancer cachexia is a complex syndrome marked by weight loss and muscle wasting, significantly impacting patient quality of life and survival. Mechanistically, it is characterized by suppressed protein synthesis and enhanced muscle catabolism, with the role of endoplasmic reticulum (ER) stress and unfolded protein response (UPR) becoming increasingly evident. This study aimed to explore ER stress-tolerant factors in muscle wasting and evaluate their potential to prevent muscle loss in cancer cachexia.

METHODS: A genome-wide CRISPR screening was conducted in the context of ER stress-mediated growth inhibition of C2C12 myoblasts. The candidate genes resistant to ER stress were further evaluated in C2C12 myotubes treated with conditioned medium of Lewis lung adenocarcinoma (LLC) cells. Twelve-week-old male mice were administered LLC cells and shRNA against Naa35 via adeno-associated virus. Four weeks later, tibialis anterior (TA) muscles were analysed for muscle mass, grip strength and molecular changes with quantitative polymerase chain reaction, western blotting and histological analysis.

RESULTS: CRISPR screening identified Naa35, Naa38 and Naa30, all three components of N-terminal acetyltransferase C, as key molecules for resistance to ER stress. The atrophic muscles of mice bearing LLC demonstrated an elevation of UPR, as well as 1.64-fold upregulation of Naa35 protein (p = 0.0072). Among the three branches of the UPR, an ATF6 inhibitor, AEBSF, abolished upregulation of Naa35, Naa38 and Naa30, and an ATF6 activator, AA147, induced Naa35 expression in a dose-dependent manner (p < 0.001). In cells treated with LLC conditioned medium, Naa35 knockdown reduced the amount of cathepsin K (CTSK) protein, which subsequently resulted in the CTSK-mediated proteolysis of insulin receptor substrate 1. In LLC-bearing mice, Naa35 knockdown led to a 65.4% reduction in CTSK protein expression (p < 0.001) and preservation of the phosphorylation levels of protein kinase B (p < 0.0324) and anabolic-related S6 kinase (p < 0.0375). Concurrently, the expression of catabolism-related genes was repressed (MuRF1, p < 0.0015; MAFbx1, p < 0.0265). These alterations were associated with the restoration of TA muscle mass (2.52 ± 0.19 vs. 3.72 ± 0.45 mg/g, p = 0.0004), fibre area (1741 ± 992 vs. 2099 ± 1264 mm[2], p < 0.0001), grip strength in all four limbs (0.0328 ± 0.0076 vs. 0.0506 ± 0.0130 N/g, p = 0.0295) and wire mesh hanging time (496 ± 331 vs. 1038 ± 370 s, p = 0.0406).

CONCLUSIONS: Inhibition of N-terminal acetyltransferase C prevents ER stress-induced muscle wasting via the downregulation of CTSK and subsequent activation of the anabolic pathway. This suggests that N-terminal acetyltransferase C is a potential therapeutic target for combating muscle wasting in cancer cachexia.}, } @article {pmid41852383, year = {2025}, author = {Urrutia-Angulo, L and Lavín, JL and Oporto, B and Aduriz, G and Hurtado, A and Ocejo, M}, title = {Resistome and microbiome profiling of bovine milk following antimicrobial dry cow therapy: insights from short- and long-read metagenomic sequencing.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1672438}, pmid = {41852383}, issn = {2813-4338}, abstract = {Selective antimicrobial dry cow therapy (DCT) is implemented as part of mastitis control programs, particularly in dairy cows with recent clinical episodes or elevated somatic cell counts. In this study, we investigated the effects of the use of antimicrobials at drying-off on the milk microbiota and resistome by comparing treated (T, n=18) and untreated (NT, n=13) cows. Milk samples from all animals were analyzed using short-read Illumina shotgun sequencing and a subset of 10 samples were also subjected to long-read Oxford Nanopore Technologies (ONT) sequencing. No significant differences in microbial composition or diversity were observed between treated and untreated groups with either technique, indicating that antimicrobial DCT may not induce long-term shifts in the milk microbiota. However, cows receiving antibiotic treatment showed a higher diversity and abundance of genetic determinants of resistance (GDRs) in their milk resistome. Findings from the two sequencing platforms revealed limited concordance in antimicrobial resistance gene content, highlighting that sequencing platform and bioinformatic pipeline choices substantially influence resistome profiling outcomes. Furthermore, the high proportion of host DNA limited sequencing depth and sensitivity, underscoring the need for improved host DNA depletion or targeted enrichment strategies. This study provides insights into the biological and methodological challenges of milk resistome characterization, particularly in low-biomass, host-DNA-rich samples and demonstrates the lack of standardized analytical approaches in resistome studies. Overall, our findings support the prudent use of antibiotics and highlight the need for further longitudinal studies to clarify the temporal dynamics of antimicrobial DCT effects on the milk resistome and microbiota.}, } @article {pmid41852393, year = {2025}, author = {Wadop, YN and Muhammad, J and Bernal, R and Satizabal, CL and Beiser, A and Vasan, RS and Xavier, R and Kautz, T and Seshadri, S and Himali, JJ and Fongang, B}, title = {Adherence to Life's Essential 8 enhances gut microbiota diversity and cognitive performance.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1592023}, pmid = {41852393}, issn = {2813-4338}, abstract = {INTRODUCTION: Emerging evidence suggests a complex interplay among cardiovascular health, gut microbiome composition, and cognitive function. Life's Essential 8 (LE8), developed by the American Heart Association, includes vital metrics of cardiovascular health, such as diet, physical activity, nicotine exposure, sleep health, body mass index (BMI), blood glucose, blood lipids, and blood pressure.

METHODS: In this study, we analyzed data from 781 participants in the Framingham Heart Study (FHS) to explore the relationship between LE8 adherence, gut microbiota, and cognitive performance. Multivariable linear regression models and mediation analysis were used to investigate this relationship.

RESULTS: Participants with greater adherence to LE8 demonstrated significantly increased gut microbial diversity (α-diversity: Chao1, p = 0.0014; Shannon, p = 0.0071) and distinct microbial compositions (β-diversity: PERMANOVA p = 1e-4). Higher adherence to LE8 was related to an increased abundance of genera Barnesiella and Ruminococcus, while a reduced abundance of Clostridium was associated with higher LE8 adherence. Greater gut microbial diversity (α-diversity: Chao1, p = 0.0012; Shannon, p = 0.0066), and beneficial genera like Oscillospira correlated with better global cognitive scores (GCS). Taxonomic overlap analyses revealed microbial taxa that simultaneously influence both LE8 adherence and cognitive outcomes. Mediation analyses indicated that specific taxa, including Barnesiella and Lentisphaerae, mediated the link between LE8 adherence and cognitive performance. These taxa may serve as key modulators in the gut-brain axis, connecting cardiovascular and brain health. Conversely, higher Clostridium abundance was associated with poorer cognitive performance.

DISCUSSION: This study highlights the significance of comprehensive cardiovascular health metrics in shaping gut microbiota and enhancing cognitive resilience. Our findings underscore the therapeutic potential of targeting gut microbiota to mitigate cognitive decline, warranting further exploration through longitudinal and metagenomic studies.}, } @article {pmid41852395, year = {2025}, author = {Ortega-Reyes, D and Takeuchi, T and Ogata, Y and Iwami, T and Suda, W and Kubota, T and Kubota, N and Kadowaki, T and Tomizuka, K and Ohno, H and Horikoshi, M and Terao, C}, title = {Interplay between host genetics and gut microbiome composition in the Japanese population.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1635907}, pmid = {41852395}, issn = {2813-4338}, abstract = {BACKGROUND: Host genetics significantly influence the composition of the gut microbiota, but this relationship remains poorly understood, especially in non-European populations. This study aims to investigate the associations between host genetic variation and gut microbiome composition in the Japanese population and to assess methodological factors affecting reproducibility in microbiome research.

METHODS: We performed whole-genome sequencing on 306 Japanese individuals and obtained their gut microbiome profiles using shotgun metagenomic sequencing. Genome-wide association studies (GWAS) were conducted to identify associations between host genetic variants and the relative abundance of microbial taxa and bacterial pathways. Phenome-wide association studies (PheWAS) were performed on predicted high-impact variants. Additionally, we compared methodological approaches to assess their impact on microbiome composition and reproducibility.

RESULTS: We identified significant associations between host genetic variants and the relative abundance of one bacterial family, one genus, one species and eight bacterial pathways (p ≤ 5×10[-8]). However, none of these associations surpassed the stringent significance threshold of p ≤ 2.75×10[-11]. Notably, we were unable to replicate associations reported in prior studies, including those conducted in Japanese populations, even regarding the direction of effects. Our PheWAS analysis uncovered a frameshift variant in the OR6C1 gene (rs5798345-CA) that was significantly associated with an increased abundance of Bacteroides uniformis. Furthermore, comparative analyses highlighted that methodological differences, particularly in sample processing and DNA extraction protocols, substantially influence the observed gut microbiome composition. This variability may be a key factor contributing to the lack of reproducibility across studies.

CONCLUSION: Our findings enhance the understanding of how host genetics shape the gut microbiota in the Japanese population and underscore the importance of methodological standardization in microbiome research. The identified associations between host genetic variants and specific microbial taxa provide insights into the complex interplay between genetics and the gut microbiome. Addressing methodological discrepancies is crucial for improving reproducibility and advancing knowledge of host-microbiome interactions.}, } @article {pmid41852396, year = {2025}, author = {Zoruk, P and Morozov, M and Veselovsky, V and Strokach, A and Babenko, V and Klimina, K}, title = {Impact of DNA extraction techniques and sequencing approaches on microbial community profiling accuracy.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1688681}, pmid = {41852396}, issn = {2813-4338}, abstract = {BACKGROUND: Quality control in metagenomic data analysis is crucial for ensuring the accuracy and reliability of research results. Among the key steps in microbiome research, DNA extraction plays a critical role, as it directly determines DNA yield, integrity, and representation of microbial taxa.

RESULTS: We compared three commercial DNA extraction kits and our protocol specifically developed for the recovery of high molecular weight (HMW) DNA from complex microbial communities, using the ZymoBIOMICS Gut Microbiome Standard. The PureLin[™] Microbiome DNA Purification Kit and our custom protocol provided superior recovery of DNA from Gram-positive bacteria, while the Wizard[®] kit and our protocol yielded HMW DNA suitable for long-read Oxford Nanopore sequencing. Among sequencing approaches, metagenomic sequencing on the Illumina platform provided the most accurate representation of the reference composition. However, all methods showed limited ability to detect taxa below 0.5% of relative abundance. Additionally, taxonomic classification based on 16S rRNA gene amplicon sequencing data misclassified closely related species due to high gene homology, a limitation not observed with metagenomic approaches.

CONCLUSIONS: Our study establishes that a customized DNA extraction protocol is optimal for comprehensive microbiome studies utilizing long-read sequencing technologies. We show that metagenomic sequencing outperforms 16S rRNA gene amplicon sequencing for species-level accuracy, providing a validated benchmark for future gut microbiome research.}, } @article {pmid41852403, year = {2025}, author = {Helal, M and Bari, VK}, title = {Insights into human respiratory microbiome under dysbiosis and its analysis tool.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1549166}, pmid = {41852403}, issn = {2813-4338}, abstract = {The human respiratory tract microbiome is a multi-kingdom microbial ecology that inhabits several habitats along the respiratory tract. The respiratory tract microbiome promotes host health by strengthening the immune system and avoiding pathogen infection. The lung microbiome mostly originates in the upper respiratory tract. The balance between microbial immigration and removal determines the nature of the lung microbiome. Identification and characterization of microbial communities from airways have been made much easier by recent developments in amplicon and shotgun metagenomic sequencing and data analysis techniques. In pulmonary medicine, there is a growing interest in the respiratory microbiome, which has been linked to human health and illness. However, the primary causes of bacterial co-occurrence seem to be interactions with fungi and bacteria as well as host and environmental factors. This study focused on identifying techniques and the current understanding of the relationship between the microbiota and various lung diseases.}, } @article {pmid41852404, year = {2025}, author = {Xuan, L and Sun, X and Wang, B and Chen, F and Yi, Y and Mao, H and Wang, Y and Zhao, G and Wang, J and Zhang, Y}, title = {Cold-water immersion alleviates intestinal damage induced by exertional heat stroke via modulation of gut microbiota in rats.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1531991}, pmid = {41852404}, issn = {2813-4338}, abstract = {OBJECTIVE: The pathogenesis of exertional heatstroke (EHS) involves substantial contributions from gut microbiota and their metabolites. In this study, we assessed whether cold water immersion (CWI) mitigates EHS-induced intestinal damage via alterations in the microbiome.

METHODS: An EHS model was created with 18 Wistar rats divided into three groups, that is, the EHS group comprising rats with exertional heat stroke, the CWI group with rats with heatstroke treated with cold water immersion, and the control (CTRL) group (rats with normothermia control). Pathological changes, core temperature (Tcore), and lactic acid (Lac) and endotoxin lipopolysaccharide (LPS) levels were evaluated. Fecal samples were subjected to metagenomic shotgun sequencing and liquid chromatography-mass spectrometry for microbiota and metabolomic profiling.

RESULTS: Hematoxylin and eosin staining showed that CWI treatment significantly reduced EHS-induced intestinal congestion, edema, and necrosis compared to the EHS group. The EHS group had the highest Tcore, while the CWI group had significantly lower Tcore than the EHS group. The CWI group had significantly reduced LPS and Lac levels, similar to those observed in the CTRL group. Microbiome analysis indicated that EHS disrupted gut bacteria, with an increase in the proportion of pathogens such as Desulfovibrio fairfieldensis, Desulfamplus magnetovallimortis, and Desulfococcus oleovorans (P<0.05). CWI treatment resolved these disturbances and restored the gut microbiota to a level similar to that of the CTRL group. Metagenomic analysis showed that CWI restored gut microbiota diversity (Shannon index, P<0.05), significantly reducing the proportion of pathogenic Desulfovibrio. Metabolomic profiling identified key metabolites, such as inosine, hypoxanthine, guanosine, and taurine (Variable importance in projection>1, P<0.05 with P-values adjusted for multiple comparisons using the Benjamini-Hochberg method, FDR<0.05), differentiating between the CWI and EHS groups.

CONCLUSION: The metabolites inosine, taurine, hypoxanthine, and guanosine correlated with restored gut microbiota, reduced proportion of Desulfovibrio, and attenuated inflammation (lower LPS/Lac), suggesting that their dual role in mitigating intestinal damage. These findings underscore the therapeutic potential of CWI by modulating microbial-derived metabolites, highlighting its impact on the intestinal health of patients with EHS.}, } @article {pmid41852413, year = {2025}, author = {Guerrero-Toledo, FM and Espinosa-Solares, T and Hernández-Eugenio, G and Huber, DH}, title = {Community assembly following disturbance in batch anaerobic digesters displays highly reproducible secondary succession and a shifting stochastic-deterministic balance.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1707779}, pmid = {41852413}, issn = {2813-4338}, abstract = {The great diversity of anaerobic digestion (AD) microbiomes indicates high redundancy and flexibility in the assembly of the community. Moreover, AD microbiomes are frequently subjected to disturbances during start-up and operation that require (re)assembly. We tested the reproducibility of secondary succession and AD community assembly mechanisms using a pre-assembled microbiome that was subjected to intense disturbances. Microbiome diversity and functions were followed in replicate mesophilic batch digesters initiated with multiple stressors, including high feed-to-inoculum ratio and many foreign species. Three 10 L batch digesters were derived from a single long-term CSTR digester pre-adapted to poultry litter feedstock and operated in parallel. Physicochemical parameters (methane, acetate, propionate, butyrate, pH, N-NH3, COD) were measured. Metagenome samples were used to assess diversity and functions. Three performance phases were found along the successional gradient: (1) methane inhibition, (2) high methane production, and (3) low methane plateau. The inventory of species (>1600) remained nearly the same, however the relative abundance of species, families, and functions changed during each successional stage. Syntrophic bacteria peaked in abundance during the mid-succession, high methane stage. Succession of overall KEGG functions was highly similar although species and carbohydrate functions diverged during late succession, suggesting diversity of niche partitioning during degradation of recalcitrant organic matter. We estimated the relative contributions of stochastic and deterministic processes and found a shift in the balance during succession. Early succession was not dominated by either dispersal or selection while late succession was dominated by variable selection. In conclusion, methane production recovered following severe (non-lethal) disturbance in a pre-adapted digester microbiome through a reproducible community assembly pathway that shifted toward deterministic, variable selection over time.}, } @article {pmid41852418, year = {2025}, author = {Berdy, BM and Williams, CE and Sizova, M and Jung, D and Tandogan, N and Goluch, ED and Epstein, S}, title = {Diverse cultivation strategies are necessary to capture microbial diversity in High Arctic lake sediment.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1619859}, pmid = {41852418}, issn = {2813-4338}, abstract = {While metagenomics has revolutionized our understanding of microbial diversity and function, the cultivation of microorganisms remains indispensable for elucidating their physiological characteristics and potential biotechnological applications. Cultivation provides context to the vast metagenomic datasets and helps verify metagenome-based hypotheses on microbial interactions. The majority of microorganisms remain uncultivated, and this is particularly prominent from extreme environments such as the Arctic. Here we aimed to contribute to the growing body of work investigating microbial ecology in extreme environments by assessing the efficacy of a variety of cultivation approaches in lake sediment in the High Arctic. To try and capture the full breadth of organisms present, we used standard, in situ, and anoxic cultivation methods. We cultured a total of 1,109 microorganisms which clustered into 155 OTUs (97% rRNA gene sequence similarity), representing organisms from Proteobacteria, Actinobacteria, Bacteroidota, and Firmicutes. Importantly, no single method of cultivation proved to be sufficient to represent the cultivable organisms within the environment. Rather, each method resulted in many unique OTUs. Therefore, multiple approaches should be used in conjunction to access the bulk of microbial taxa in a given environment.}, } @article {pmid41852432, year = {2025}, author = {Mhuireach, GÁ and Collins, S and Dietz, L and Horve, PF and Laguerre, A and Northcutt, D and Stenson, J and Wymelenberg, KVD and Gall, E and Fretz, M}, title = {Effects of wetting events on mass timber surface microbial communities and VOC emissions: implications for building operation and occupant well-being.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1395519}, pmid = {41852432}, issn = {2813-4338}, abstract = {INTRODUCTION: Humans have used wood as a construction material throughout history. Currently, mass timber products, such as cross-laminated timber (CLT), are becoming more popular as a structural material, since they are renewable and have a lower carbon footprint than concrete or steel. Nonetheless, some building types, such as healthcare, veterinary, and food manufacturing, avoid using structural mass timber due to concerns about microbial growth in the event of wetting. One solution is to use protective coatings on mass timber products to increase moisture resistance, although the coatings themselves may generate concerns about volatile organic compound (VOC) emissions. Natural uncoated wood also produces VOCs, some of which may have intrinsic antimicrobial effects.

METHODS: In this study, we inoculated coated and uncoated cross- laminated timber (CLT) blocks with a mock microbial community and isolated each block within individual sealed microcosms. We characterized VOCs and surface microbial communities from the CLT blocks before, during, and after wetting periods of varying durations. VOC concentration and emission rate were analyzed with chromatography-mass spectrometry (GC-MS), while microbial community abundance, diversity, and composition were analyzed through qPCR and shotgun metagenomics.

RESULTS: VOC emissions were elevated immediately after inoculation, then decreased through the remainder of the experiment, except for a plateau during the wetting period. VOCs from uncoated CLT blocks were primarily terpenes, while coated blocks emitted VOCs associated with coatings, plastics, and industrial solvents, as well as terpenes. One VOC-acetoin (3-hydroxy, 2-butanone)-was present at high levels across all samples immediately after microbial inoculation. Bacteria comprised 99.54% of the identified microbial sequences. The plastic control microcosm (not containing a CLT block) had higher abundance of viable bacteria for the majority of the study, but there was no difference in abundance between coated and uncoated blocks. Prior to wetting periods, microbial composition was driven primarily by sampling day, whereas surface type played a larger role during and after wetting periods.}, } @article {pmid41852435, year = {2025}, author = {Trubl, G and Malard, L and Rahlff, J}, title = {Editorial: Ecology, evolution, and biodiversity of microbiomes and viromes from extreme environments.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1604002}, doi = {10.3389/frmbi.2025.1604002}, pmid = {41852435}, issn = {2813-4338}, } @article {pmid41852443, year = {2025}, author = {Palazzi, CM and Ciampaglia, G and Binato, B and Ragazzini, M and Bertuccioli, A and Cavecchia, I and Matera, M and Cazzaniga, M and Zonzini, GB and Zerbinati, N and Tanda, ML and Di Pierro, F}, title = {Position statement of the Microbiota International Clinical Society.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1657750}, pmid = {41852443}, issn = {2813-4338}, } @article {pmid41852664, year = {2026}, author = {Shibata, N and Yoshifuji, A and Oyama, E and Komatsu, M and Azegami, T and Hayashi, K and Ishii, Y and Hasegawa, N and Namkoong, H}, title = {Urinary microbiota and bacterial membrane vesicles in chronic kidney disease: contribution to antimicrobial-resistant urinary tract infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1748638}, pmid = {41852664}, issn = {2235-2988}, mesh = {Humans ; Male ; *Urinary Tract Infections/microbiology ; *Renal Insufficiency, Chronic/complications/microbiology ; *Microbiota ; *Drug Resistance, Bacterial ; RNA, Ribosomal, 16S/genetics ; *Urine/microbiology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Metagenomics ; Middle Aged ; Aged ; Microscopy, Electron, Transmission ; Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; }, abstract = {Chronic kidney disease (CKD) is associated with an increased risk of severe urinary tract infections (UTIs), particularly those caused by antimicrobial-resistant bacteria. Although urinary microbiota and bacterial membrane vesicles (BMVs) are thought to contribute to UTI pathogenesis, their roles in CKD remain insufficiently understood. In this exploratory study, urine samples were collected from 10 male patients with CKD (eGFR <45 mL/min/1.73 m[2]) and 10 male non-CKD controls (eGFR ≥60 mL/min/1.73 m[2]). Urinary microbiota and BMV fractions were isolated and analyzed to compare microbial composition and antimicrobial resistance gene (ARG) profiles, and to evaluate their potential involvement in UTI development and the emergence of antimicrobial resistance in CKD. Both fractions were subjected to shotgun metagenomic sequencing; metagenomic analysis of BMVs was performed using pooled samples within each group. In addition, BMV fractions were characterized by transmission electron microscopy and 16S rRNA gene PCR. Urinary microbiota α-diversity was significantly lower in patients with CKD than in controls (ACE index, p = 0.04). Vesicle-like structures consistent with BMVs, with diameters of 20-200 nm, were detected in urine samples from both controls and patients with CKD. Principal coordinate analysis demonstrated that BMV fractions clustered within the corresponding urinary microbiota profiles. Furthermore, multiple antimicrobial resistance genes (ARGs), including ftsI and adeF, were identified in both urinary microbiota and BMV fractions. This study provides exploratory evidence of reduced urinary microbiota α-diversity in patients with CKD and the presence of ARGs in both urinary microbiota and BMV fractions from controls and patients with CKD. These findings suggest microbiological factors that may contribute to the high incidence of antimicrobial-resistant UTIs in this population. Future validation in larger cohorts with individual-level BMV profiling will be required to determine whether analyses focusing on urinary microbiota and BMVs can contribute to a better understanding of antimicrobial-resistant UTIs and to improved infection risk assessment in patients with CKD.}, } @article {pmid41852665, year = {2026}, author = {Zhang, Y and Wang, H and Yan, R and Wang, K and Man, J and Yang, L}, title = {Research advances on the urinary microbiome in non-infectious urinary tract diseases: from community composition to clinical prospects.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1728182}, pmid = {41852665}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; *Urologic Diseases/microbiology/diagnosis ; Dysbiosis/microbiology ; Male ; *Urinary Tract/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Urine/microbiology ; }, abstract = {INTRODUCTION: With the rapid development of 16S rRNA sequencing and metagenomic technologies, the traditional concept of sterile urine has been completely overturned, and a diverse urinary microbiome has been identified even in healthy individuals. Increasing evidence indicates that dysbiosis of the urinary microbiome is closely associated with the onset and progression of various non-infectious urological diseases.

METHODS: This review systematically summarizes recent advances in the role of the urinary microbiome in non-infectious urological diseases, including bladder cancer, benign prostatic hyperplasia, prostate cancer, nephrolithiasis, interstitial cystitis/bladder pain syndrome, and urinary incontinence, with a focus on microbial dysbiosis, pathogenic mechanisms, and clinical applications.

RESULTS: Studies have shown that alterations in the composition and diversity of the urinary microbiome are closely related to chronic inflammation, immune dysregulation, metabolic disturbances, and changes in the local microenvironment. These alterations may contribute to disease pathogenesis through mechanisms such as persistent low-grade inflammation, abnormal metabolic activity, and biofilm formation. In recent years, non-invasive detection based on urinary microbial profiles has shown promising potential in the early diagnosis of bladder and prostate cancers, with some machine learning models achieving diagnostic accuracies above 80 percent. Furthermore, the urinary microbiome may influence the efficacy of immunotherapy, offering new insights for personalized precision medicine.

CONCLUSIONS: This review summarizes the mechanisms, research status, and clinical prospects of the urinary microbiome in non-infectious urological diseases, emphasizing the importance of methodological standardization and highlighting its potential applications in early screening, diagnostic stratification, and microbiome-targeted interventions.}, } @article {pmid41852689, year = {2026}, author = {Anandan, S and Ali, A and Selvarajoo, A and Supramaniam, CV}, title = {Trichoderma combined with palm kernel shell biochar promotes root health and rhizosphere biodiversity in young oil palm seedlings infected with Ganoderma boninense.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1742803}, pmid = {41852689}, issn = {2813-4338}, abstract = {Oil palm (Elaeis guineensis) contributes up to 3% of gross domestic product (GDP) in Malaysia. Long-term monoculture production reduced natural biodiversity and increased severe threat by Ganoderma boninense, a causal agent of basal stem rot (BSR) disease. BSR recorded projections of 860,610 hectares of plantations to be devastated by BSR by 2040. While disease management has prioritised good sanitation practices, Trichoderma spp. is a potential solution to combatting G. boninense. In this study, we determined the efficacy of Trichoderma spp. isolate 4A added to palm kernel shell (PKS) biochar (T-mix) to improve oil palm root health. Three-month-old seedlings were observed in control treatments, T1 to T4 and Trichoderma sp. treatments, T5 to 12 with Ganoderma added in T7,8, 11 and 12. Root development parameters such as root architecture, length, diameter, and surface area were observed every two months for six months. Root length of T5 (3.3 m) and T9 (4.4 m) was higher than no-treatment control, T1 (2.5 m) indicating Trichoderma sp. support of root health. T9 (T-mix) has significantly improved root architecture in root scan with denser and multiple root branches as while all other diseased oil palms exhibit stunted roots. The diameter of roots shows similar trend to root length of T9 roots with the highest reading at 5.4 mm. T11 showed the overall improved fungal biodiversity at 6 months post inoculation with potential disease suppressive effects against other common pathogens such as Fusarium sp. This study highlights a new perspective of Trichoderma spp. treatment with biochar to provide protection to growing young oil palm root health, beyond disease control, indicating a beneficial role for early application at seedling stage. For long term application, Trichoderma spp. combined with biochar support healthy fungal dynamics without over-dominating indigenous fungal inhabitants. This is the first study to highlight the role of combined Trichoderma spp. and biochar in influencing the root architecture and rhizosphere dynamics of a perennial oil palm at the seedling stage. Overall, this study presents an exciting opportunity to use a new Trichoderma sp.-biochar solution in the battle against G. boninense.}, } @article {pmid41852814, year = {2022}, author = {Jagadeeshwari, U and Sasikala, C and Rai, A and Indu, B and Ipsita, S and Ramana, CV}, title = {Characterization of metagenome-assembled genomes of two endo-archaea of Candida tropicalis.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1020341}, pmid = {41852814}, issn = {2813-4338}, abstract = {INTRODUCTION: Host-microbe interactions are pivotal in host biology, ecology, and evolution. Recent developments in sequencing technologies have provided newer insights into the same through the hologenome concept.

METHODS: We report here the study on metagenome-assembled genomes (MAGs) associated with Candida tropicalis (studied through shotgun metagenome sequencing), adding to the knowledge about endomicrobiomes of yeast. De novo assembly and binning recovered two partial archaeal genomes, taxonomically belonging to the phylum Asgardarchaeota.

RESULTS AND DISCUSSION: The phylogenomic analysis based on the core genes revealed that both the binned genomes cladded separately with the less studied and uncultivated 'Candidatus' superphylum, designated as Asgard archaea (the nearest known relative of eukaryotes). Between the two binned genomes, the average nucleotide index (ANI) was 71.2%. The average nucleotide identities (ANI) of the two binned genomes with 'Candidatus Heimdallarchaeota' were 60.4-61.2%. The metabolic pathways of both the binned genomes predicted genes belonging to sulfur reduction, Kreb's pathway, glycolysis, and C1 carbon metabolism. Further, both the binned genomes were predicted to support autotrophic as well as the heterotrophic mode of growth, which might probably help the host in its nutritional requirements also. Further, the genomes showed few eukaryotic signature proteins (ESPs) and SNARE proteins indicating that members of Asgardarchaeota are the closest relatives of eukaryotes. The gaps present in the metabolic potential of the MAGs obtained and the absence of a few essential pathways shows that they are probably in a symbiotic relationship with the host. The present study, reports for the first-time endosymbiosis of Asgard archaea with yeast. It also provides insights into the metabolic potential, ecology, evolutionary history, and endosymbiotic nature of the important but 160 poorly studied Asgard archaea.}, } @article {pmid41852815, year = {2022}, author = {van Belkum, A and Lisotto, P and Pirovano, W and Mongiat, S and Zorgani, A and Gempeler, M and Bongoni, R and Klaassens, E}, title = {Being friendly to the skin microbiome: Experimental assessment.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1077151}, pmid = {41852815}, issn = {2813-4338}, abstract = {Both academia and dermatological and cosmetic industries have acknowledged that healthy skin microbiota contribute to overall skin integrity and well-being. This implies that formulations developed for personal care (skin, scalp, hair etc) or (medical and cosmetic) treatment need to be compatible with microbiota conservation or possibly even improvement. The various chemical and biological components and mixtures thereof intended for direct application to the skin should not extensively affect the qualitative and quantitative composition of the skin microbiota. A compound should promote beneficial microbes and inhibit pathogens. Compounds but also final products could be considered at least theoretically "microbiome friendly" while in some cases changes to the microbiota may even be considered beneficial. An important hurdle lies in the practical and methodological approaches to be used for defining microbiota inertia of compounds and formulations. Clear guidelines for assessing microbiome friendliness are lacking. We propose three testing concepts that may help to define microbiome friendliness based on the assessment of minimal microbiota perturbation and possibly elimination of potential pathogens. Methods to prove microbiome friendliness should ultimately be based upon (metagenomic rather than amplicon-based) next generation sequencing of naive versus compound- or final product-exposed skin microbiota in vivo, but preferably also including in vitro and ex vivo pre-screening methodologies to build an understanding of their consequences. As in many domains of microbiome research, the development of experimental process controls and internal standards, which are essentially lacking to date, should be taken as a future prerequisite. There is also a requirement from regulatory agencies to define and harmonize acceptance criteria.}, } @article {pmid41852816, year = {2022}, author = {Tadmor, AD and Mahmoudabadi, G and Foley, HB and Phillips, R}, title = {Identification and spatio-temporal tracking of ubiquitous phage families in the human microbiome.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1097124}, pmid = {41852816}, issn = {2813-4338}, support = {DP1 OD000217/OD/NIH HHS/United States ; R01 GM098465/GM/NIGMS NIH HHS/United States ; }, abstract = {Viruses are a major component of the human microbiome, yet their diversity, lifestyles, spatiotemporal dynamics, and functional impact are not well understood. Elucidating the ecology of human associated phages may have a major impact on human health due to the potential ability of phages to modulate the abundance and phenotype of commensal bacteria. Analyzing 690 Human Microbiome Project metagenomes from 103 subjects sampled across up to 18 habitats, we found that despite the great interpersonal diversity observed among human viromes, humans harbor distinct phage families characterized by their shared conserved hallmark genes known as large terminase subunit (TerL) genes. Phylogenetic analysis of these phage families revealed that different habitats in the oral cavity and gut have unique phage community structures. Over a ~7-month timescale most of these phage families persisted in the oral cavity and gut, however, presence in certain oral habitats appeared to be transitory, possibly due to host migration within the oral cavity. Interestingly, certain phage families were found to be highly correlated with pathogenic, carriage and disease-related isolates, and may potentially serve as novel biomarkers for disease. Our findings shed new light on the core human virome and offer a metagenomic-independent way to probe the core virome using widely shared conserved phage markers.}, } @article {pmid41852852, year = {2026}, author = {Gusareva, ES and Vettath, VK and Gaultier, NE and Sadovoy, AV and Dacanay, JGA and Schuster, SC}, title = {Dermatophagoides pteronyssinus in ambient air bioaerosols.}, journal = {The journal of allergy and clinical immunology. Global}, volume = {5}, number = {3}, pages = {100667}, pmid = {41852852}, issn = {2772-8293}, abstract = {BACKGROUND: House dust mite (HDM) sensitization is a leading cause of allergic rhinitis and asthma worldwide, with Dermatophagoides pteronyssinus, Dermatophagoides farinae, and Blomia tropicalis being the primary allergenic species typically associated with indoor environments. Even effective multicomponent interventions creating an HDM-free indoor environment are often insufficient to prevent allergy, as HDM exposure may also occur outdoors.

OBJECTIVE: To assess the potential for outdoor HDM exposure, we applied air biomass sequencing and metagenomic techniques to detect HDM DNA in both indoor and outdoor bioaerosols, offering an alternative to conventional dust sampling methods.

METHODS: We used 2 data sets in this study: (1) a global data set comprising 1,171 outdoor air samples collected across 33 countries in open air environments and (2) a data set of indoor (n = 161) and outdoor (n = 156) air samples collected across 156 apartments from 106 locations in Singapore. All air samples were collected by drawing 24,000 to 36,000 L of air using SASS3100 air samplers; all samples were processed identically. Species-level taxonomic classification was performed using Kaiju software aligned to the National Center for Biotechnology Information nonredundant database, with a minimum threshold of 40 reads per taxon.

RESULTS: Analysis of 1,171 global outdoor air samples revealed D pteronyssinus as the most prevalent HDM species; it was detected in 208 samples, with abundance increasing from temperate toward equatorial regions. In Singaporean households, D pteronyssinus was found in 58.4% of indoor samples and 21.2% of nearby outdoor samples, with high median DNA read counts outdoors suggesting that exposure to HDM is not limited to domestic environments. B tropicalis and D farinae were also detected in Singapore, albeit at lower frequencies.

CONCLUSION: Our findings highlight the need to expand environmental allergen surveillance beyond household dust to include ambient and outdoor air, particularly in tropical climates.}, } @article {pmid41853108, year = {2026}, author = {Khan, A}, title = {Disseminated Mycobacterium intracellulare subsp. chimaera infection, undiagnosed for years, highlights the enduring clinical utility of "old school" microbiological testing and a robust differential.}, journal = {ASM case reports}, volume = {2}, number = {2}, pages = {}, pmid = {41853108}, issn = {2996-2684}, abstract = {Disseminated Mycobacterium intracellulare subsp. chimaera (MC) infections are rare, slow-progressing, and easily overlooked, particularly when a patient's history of prior cardiac surgery is not incorporated into the diagnostic evaluation. In a recent ASM Case Reports article (1:e00003-25, 2025, https://doi.org/10.1128/asmcr.00003-25), Ladines-Lim et al. describe a disseminated MC infection in a patient with prior aortic and mitral valve replacement that remained undiagnosed for over 4 years. Conventional microbiological testing was not pursued early in the course of illness because the history of cardiopulmonary bypass was not linked with the constellation of unexplained symptoms. This case urges clinicians to remain vigilant and suspect MC in patients with prior open-chest cardiac surgery who present with gradually worsening, systemic symptoms. Since 2013, global outbreaks of delayed-onset MC infections have been traced to contaminated heater cooler devices, yet many centers continue to face barriers to replacing or monitoring such equipment. A delayed diagnosis in this case was eventually established by cell-free metagenomic next-generation sequencing (cfmNGS). However, the result was not acted upon until weeks later, after central nervous system involvement. A more timely, cost-effective diagnosis might have been achieved using traditional, widely available, culture-based testing guided by a robust exposure-driven differential. Clinicians should suspect MC in patients with prior cardiac surgery-even years earlier-who develop unexplained, progressive systemic symptoms. Early suspicion and appropriate testing are critical to improved outcomes. This case shows that next-generation sequencing assays are only as useful as the clinical reasoning guiding their use. Traditional microbiological testing-when leveraged early and thoughtfully-remains an accessible cornerstone of diagnosing complex MC infections.}, } @article {pmid41853337, year = {2023}, author = {Peter, H and Michoud, G and Busi, SB and Battin, TJ}, title = {The role of phages for microdiverse bacterial communities in proglacial stream biofilms.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1279550}, pmid = {41853337}, issn = {2813-4338}, abstract = {Viruses modulate the diversity and activity of microbial communities. However, little is known about their role for the structure of stream bacterial biofilm communities. Here, we present insights into the diversity and composition of viral communities in various streams draining three proglacial floodplains in Switzerland. Proglacial streams are characterized by extreme environmental conditions, including near-freezing temperatures and ultra-oligotrophy. These conditions select for few but well-adapted bacterial clades, which dominate biofilm communities and occupy niches via microdiversification. We used metagenomic sequencing to reveal a diverse biofilm viral assemblage in these streams. Across the different floodplains and streams, viral community composition was tightly coupled to that of the bacterial hosts, which was underscored by generally high host specificity. Combining predictions of phage-host interactions with auxiliary metabolic genes (AMGs), we identify specific AMGs shared by phages infecting microdiverse clade members. Our work provides a step towards a better understanding of the complex interactions among bacteria and phages in stream biofilm communities in general and streams influenced by glacier meltwaters and characterized by microdiversity in particular.}, } @article {pmid41853339, year = {2023}, author = {Wong, MT and Nesbø, CL and Wang, W and Couturier, M and Lombard, V and Lapebie, P and Terrapon, N and Henrissat, B and Edwards, EA and Master, ER}, title = {Taxonomic composition and carbohydrate-active enzyme content in microbial enrichments from pulp mill anaerobic granules after cultivation on lignocellulosic substrates.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1094865}, pmid = {41853339}, issn = {2813-4338}, abstract = {Metagenomes of lignocellulose-degrading microbial communities are reservoirs of carbohydrate-active enzymes relevant to biomass processing. Whereas several metagenomes of natural digestive systems have been sequenced, the current study analyses metagenomes originating from an industrial anaerobic digester that processes effluent from a cellulose pulp mill. Both 16S ribosomal DNA and metagenome sequences were obtained following anaerobic cultivation of the digester inoculum on cellulose and pretreated (steam exploded) poplar wood chips. The community composition and profile of predicted carbohydrate-active enzymes were then analyzed in detail. Recognized lignocellulose degraders were abundant in the resulting cultures, including populations belonging to Clostridiales and Bacteroidales orders. Poorly defined taxonomic lineages previously identified in other lignocellulose-degrading communities were also detected, including the uncultivated Firmicutes lineage OPB54 which represented nearly 10% of the cellulose-fed enrichment even though it was not detected in the bioreactor inoculum. In total, 3580 genes encoding carbohydrate-active enzymes were identified through metagenome sequencing. Similar to earlier enrichments of animal digestive systems, the profile encoded by the bioreactor inoculum following enrichment on pretreated wood was distinguished from the cellulose counterpart by a higher occurrence of enzymes predicted to act on pectin. The majority (> 93%) of carbohydrate-active enzymes predicted to act on plant polysaccharides were identified in the metagenome assembled genomes, permitting taxonomic assignment. The taxonomic assignment revealed that only a small selection of organisms directly participates in plant polysaccharide deconstruction and supports the rest of the community.}, } @article {pmid41853340, year = {2023}, author = {Yang, Q and Wang, J and Zhang, D and Feng, H and Bozorov, TA and Yang, H and Zhang, D}, title = {Effects of multi-resistant ScALDH21 transgenic cotton on soil microbial communities.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1248384}, pmid = {41853340}, issn = {2813-4338}, abstract = {Transgenic crops are increasingly prevalent worldwide, and evaluating their impact on soil microbial communities is a critical aspect of upholding environmental safety. Our previous research demonstrated that overexpression of ScALDH21 from desiccant-tolerant moss, Syntrichia caninervis, in cotton revealed multi-resistance to drought, salt, and biotic stresses. We conducted metabarcoding using high-throughput sequencing to evaluate the effect of ScALDH21 transgenic cotton on soil microbial communities. We further conducted soil tests to analyze the chemical properties of transgenic and non-transgenic cotton, including the total content and availability of chemical elements (K, P, and N), organic matter, and pH value. Both transgenic and non-transgenic cotton fields exhibited soil pH values higher than 8. The presence of transgenic cotton significantly enhanced the availability of available K and the total content of total P in the soil. Alpha and beta diversity indices of soil microbiota showed no difference between two transgenic and non-transgenic cotton groups. Dominant clades of fungal and bacterial genera were equivalent at the phylum and genus levels in all three groups. The correlation analysis of microbial communities and soil environmental factors revealed the absence of significant differences between transgenic and non-transgenic cotton genotypes. Functional predictions of soil microbial communities indicated that microbial community function did not show significant differences between transgenic and non-transgenic cotton samples. These findings are essential for evaluating the environmental effects of transgenic crops and supporting the secure implementation of transgenic cotton.}, } @article {pmid41853343, year = {2023}, author = {Ionescu, D and Zoccarato, L and Cabello-Yeves, PJ and Tikochinski, Y}, title = {Extreme fluctuations in ambient salinity select for bacteria with a hybrid "salt-in"/"salt-out" osmoregulation strategy.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1329925}, pmid = {41853343}, issn = {2813-4338}, abstract = {Abundant microbial biofilms inhabit underwater freshwater springs of the Dead Sea. Unlike the harsh (i.e., over 35% total dissolved salts) yet stable environment of the basin, the flow rate of the springs changes with random amplitude and duration, resulting in drastic shifts in salinity, pH, and oxygen concentrations. This requires the organisms to continuously adapt to new environmental conditions. Osmotic regulation is energetically expensive; therefore, the response of the biofilm organisms to rapid and drastic changes in salinity is interesting. For this purpose, we studied the metagenome of an enrichment culture obtained from a green biofilm-covered rock positioned in a spring. We obtained metagenome-assembled genomes (MAGs) of Prosthecochloris sp. (Chlorobiales), Flexistipes sp. (Deferribacterales), Izemoplasma (Izemoplasmatales), Halomonas sp. (Oceanospirillales), and Halanaerobium (Halanaerobiales). The MAGs contain genes for both the energetically cheaper "salt-in" and more expensive "salt-out" strategies. We suggest that the dynamic response of these bacteria utilizes both osmoregulation strategies, similar to halophilic archaea. We hypothesize that the frequent, abrupt, and variable-in-intensity shifts in salinity, typical of the Dead Sea spring system, select for microorganisms with scalable adaptation strategies.}, } @article {pmid41853350, year = {2023}, author = {Oliveira, RS and Pinto, OHB and Quirino, BF and de Freitas, MAM and Thompson, FL and Thompson, C and Kruger, RH}, title = {Genome-resolved metagenomic analysis of Great Amazon Reef System sponge-associated Latescibacterota bacteria and their potential contributions to the host sponge and reef.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1206961}, pmid = {41853350}, issn = {2813-4338}, abstract = {The Great Amazon Reef System (GARS) is an extensive biogenic reef influenced by a plume layer of sediments. This creates an extreme environment where light is reduced, thus affecting physicochemical properties as well as living organisms such as sponges and their microbiomes. The sponge's microbiome has numerous ecological roles, like participation in biogeochemical cycles and host nutrition, helping the sponge thrive and contributing to the ecosystem. Also, sponges and sponge-associated microorganisms are rich sources of bioactive compounds, and their products are applied in different areas, including textile, pharmaceutical, and food industries. In this context, metagenome-assembled genomes (MAG), obtained from GARS sponges microbiota, were analyzed to predict their ecological function and were prospected for biotechnological features. Thus, in this work, tissues of GARS sponges were collected, their metagenomes were sequenced and assembled, and 1,054 MAGs were recovered. Ten of those MAGs were selected based on their taxonomic classification in the candidate phylum Latescibacterota and this group's abundance in GARS sponges. The workflow consisted of MAG's quality definition, taxonomic classification, metabolic reconstruction, and search for bioactive compounds. Metabolic reconstruction from medium to high-quality MAGs revealed genes related to degradation and synthesis pathways, indicating functions that may be performed by GARS sponge-associated Latescibacterota. Heterotrophy, a recurring attribute in Latescibacterota that might be crucial for GARS sponge holobiont nutrition, was verified by the presence of genes related to respiration and fermentation. Also, the analyzed bacteria may contribute to the host's survival in multiple ways, including host protection via defense systems; aid in nutrient consumption by breaking complex substrates and producing essential nutrients like vitamins and certain amino acids; and detoxification of mercury, arsenic, ammonia, and hydrogen sulfide. Additionally, genes linked to persistent organic pollutant degradation, including glyphosate, and biogeochemical cycles reactions, such as ammonification, sulfate reduction, thiosulfate disproportionation, phosphorus remineralization, and complex organic matter degradation, were identified, suggesting the participation of these Latescibacterota in bioremediation and nutrient cycling. Finally, the investigated MAGs contain genes for numerous bioactive compounds, including industrial enzymes, secondary metabolites, and biologically active peptides, which may have biotechnological value.}, } @article {pmid41853380, year = {2023}, author = {Galeeva, JS and Starikova, EV and Fedorov, DE and Manolov, AI and Pavlenko, AV and Konanov, DN and Krivonos, DV and Babenko, VV and Klimina, KM and Veselovsky, VA and Morozov, MD and Gafurov, IR and Gaifullina, RF and Govorun, VM and Ilina, EN}, title = {Microbial communities of the upper respiratory tract in mild and severe COVID-19 patients: a possible link with the disease course.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1067019}, pmid = {41853380}, issn = {2813-4338}, abstract = {The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, it is involved in modulating the immune response to infectious agents in the host organism, just like the intestinal microbiota. A relationship between the composition of the respiratory microbiota and the likelihood of development and the severity of COVID-19 may be assumed. In this study, we applied the 16S rRNA metagenomic sequencing to analyze the oropharyngeal swabs from 120 COVID-19 patients collected during the first and the second waves of the COVID-19 epidemic in Russia. Differential abundance analysis with respect to comorbidities suggested association of Neisseria oralis, Neisseria mucosa, unidentified Veillonella spp., Lautropia mirabilis species with more severe lung damage, and Streptococcus salivarius, Capnocytophaga sputigena and Haemophilus parahaemolyticus with a milder course of the disease. We hypothesize that the latter bacteria (or some of them) might be beneficial for the respiratory tract and might be able to alleviate the course of the COVID-19 disease.}, } @article {pmid41853383, year = {2023}, author = {Ramirez Garcia, A and Greppi, A and Constancias, F and Ruscheweyh, HJ and Gasser, J and Hurley, K and Sturla, SJ and Schwab, C and Lacroix, C}, title = {Anaerobutyricum hallii promotes the functional depletion of a food carcinogen in diverse healthy fecal microbiota.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1194516}, pmid = {41853383}, issn = {2813-4338}, abstract = {INTRODUCTION: Anaerobutyricum hallii is a human gut commensal that transforms the heterocyclic amine 2-amino-1-methyl-6-phenylimidazo [4,5-b] pyridine (PhIP), a carcinogen from cooked meat. The transformation mechanism involves the microbial production of acrolein from glycerol, and its conjugation with PhIP, thus blocking its mutagenic potential. A potential cancer prevention strategy could therefore involve supplementing complex human microbial communities with metabolically competent bacteria such as A. hallii that can deplete PhIP. However, it has not been established how the proportion of A. hallii in diverse healthy human gut microbial communities relates to functional capacity for PhIP transformation and, moreover, how supplementing microbiomes with A. hallii affects this function.

METHODS: In this study, shotgun metagenomics was used to study taxonomic profiling, the abundance of glycerol/diol dehydratase (gdh)-harboring taxa, the proportion of resident A. hallii, and the reconstruction of A. hallii population genomes in the fecal samples of 20 healthy young adult donors. Furthermore, the influence of supplementing 10[6] cells/mL of A. hallii DSM 3353 with diluted fecal microbiota was characterized.

RESULTS AND DISCUSSION: Six microbiota were assigned to Bacteroides, nine to Prevotella, and five to Ruminococcus by enterotype-associated clustering. The total number of gdh copies in the 20 fecal microbiota expressed per 10[10] bacterial cells ranged between 1.32 × 10[8] and 1.15 × 10[9]. Eighteen out of the 20 donors were dominated by A. hallii, representing between 33% and 94% of the total gdh relative abundance of the samples. The microbiota with low A. hallii abundance (i.e., with a relative abundance < 1%) transformed less PhIP than the microbiota with high A. hallii abundance (i.e., with a relative abundance > 1%). Furthermore, supplementing the low-A. hallii-abundant microbiota with glycerol significantly increased the PhIP transformation capacity after 6 h while reducing total short-chain fatty acid (SCFA) levels, which is most likely due to acrolein production. Although acetate decreased in all microbiota with glycerol and with the combination of glycerol and A. hallii, for most of the microbiomes, butyrate production increased over time. Thus, for a significant number of diverse healthy human fecal microbiomes, and especially when they have little of the taxa to start with, supplementing A. hallii increases PhIP transformation. These findings suggest the need to test in vivo whether supplementing microbiomes with A. hallii reduces PhIP exposure.}, } @article {pmid41853385, year = {2023}, author = {Leo, S and Cetiner, OF and Pittet, LF and Messina, NL and Jakob, W and Falquet, L and Curtis, N and Zimmermann, P}, title = {The association between the composition of the early-life intestinal microbiome and eczema in the first year of life.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1147082}, pmid = {41853385}, issn = {2813-4338}, abstract = {INTRODUCTION: The early-life intestinal microbiome plays a crucial role in the development and regulation of the immune system. Perturbations in its composition during this critical period have been linked to the development of allergic diseases.

OBJECTIVE: This study aimed to investigate the association between the composition of the early-life intestinal microbiome and the presence of eczema in the first year of life using shotgun metagenomic sequencing and functional analyses (metabolic pathways).

METHODS: Stool samples from 393 healthy term infants collected at 1 week of age were analyzed with shotgun metagenomic sequencing. Environmental and clinical data were prospectively collected using 3-monthly validated questionnaires. Participants were clinically assessed during study visits at 12 months of age. Eczema was diagnosed by the UK diagnostic tool and by a research nurse. Data analysis was stratified by delivery mode.

RESULTS: Eczema was diagnosed in 16.4% (60/366) of participants by nurse diagnosis. Infants born by cesarean section (CS) with nurse-diagnosed eczema had a higher relative abundance of Escherichia, Shigella, Enterobacter, and Citrobacter and a lower relative abundance of Veillonella than CS-born infants without eczema. In addition, CS-born infants without eczema had a higher abundance of genes involved in lactic fermentation. Vaginally born infants with eczema had a higher relative abundance of Bacteroides and a lower abundance of Streptococcus.

CONCLUSION: There is an association between the bacterial composition of the intestinal microbiome at 1 week of age and the presence of eczema in the first 12 months of life.}, } @article {pmid41853387, year = {2023}, author = {Rodríguez-Ramos, J and Oliverio, A and Borton, MA and Danczak, R and Mueller, BM and Schulz, H and Ellenbogen, J and Flynn, RM and Daly, RA and Schopflin, L and Shaffer, M and Goldman, A and Lewandowski, J and Stegen, JC and Wrighton, KC}, title = {Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1199766}, pmid = {41853387}, issn = {2813-4338}, abstract = {Although river ecosystems constitute a small fraction of Earth's total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.}, } @article {pmid41853501, year = {2024}, author = {Faber, Q and Davis, C and Christner, B}, title = {Metagenomic inference of microbial community composition and function in the weathering crust aquifer of a temperate glacier.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1488744}, pmid = {41853501}, issn = {2813-4338}, abstract = {Bacterial, fungal, and algal communities that colonize aquatic systems on glacial ice surfaces mediate biogeochemical reactions that alter meltwater composition and affect meltwater production and storage. In this study, we sought to improve understanding of microbial communities inhabiting the shallow aquifer that forms seasonally within the ice surface of a glacier's ablation zone (i.e., the weathering crust aquifer). Using a metagenomic approach, we compared gene contents of microbial assemblages in the weathering crust aquifer (WCA) of the Matanuska Glacier (Alaska, USA) to those recovered from supraglacial features and englacial ice. High abundances of Pseudomonadota, Cyanobacteriota, Actinomycetota, and Bacteroidota were observed across all samples, while taxa in class Gammaproteobacteria were found at significantly higher abundances in the weathering crust aquifer. The weathering crust aquifer samples also contained higher abundances of Dothideomycetes and Microbotryomyetes; fungal classes commonly observed in snow and other icy ecosystems. Phylogenetic analysis of 18S rRNA and rbcL gene sequences indicated high abundances of algae in the WCA that are closely related (> 98% and > 93% identity, respectively) to taxa of Ancylonema (Streptophyta) and Ochromonas (Ochrophyta) reported from glacial ice surfaces in Svalbard and Antarctic sea ice. Many functional gene categories (e.g., homeostasis, cellular regulation, and stress responses) were enriched in samples from the weathering crust aquifer compared to those from proximal englacial and supraglacial habitats, providing evidence for ecological specialization in the communities. The identification of phagotrophic phytoflagellate taxa and genes involved in mixotrophy implies that combined phototrophic and heterotrophic production may assist with persistence in the low light, low energy, and ephemeral conditions of the weathering crust environment. The compositional and functional differences we have documented indicate distinct microbial distributions and functional processes occur in the weathering crust aquifer environment, and we discuss how deciphering these nuances is essential for developing a more complete understanding of ecosystem biogeochemistry in supraglacial hydrological systems.}, } @article {pmid41853503, year = {2024}, author = {Greenman, N and Abdelli, LS and Hassouneh, SA and Ali, S and Johnston, C and Naser, SA and Azarian, T}, title = {Impact of propionic acid-rich diets on microbial composition of the murine gut microbiome.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1451735}, pmid = {41853503}, issn = {2813-4338}, abstract = {Propionic acid (PPA), an anti-fungal agent and common food additive, has been shown to induce atypical neurodevelopment in mice, accompanied by gastrointestinal dysfunction potentially resulting from gut dysbiosis. A putative association between dietary PPA exposure and gut dysbiosis is suggested but has not been explored directly. Here, we investigated PPA-associated alteration in gut microbial composition that may result in dysbiosis. Using long-read metagenomic sequencing, gut microbiomes of mice fed an untreated (n=9) or PPA-rich (n=13) diet were sequenced to assess differences in microbial composition and bacterial metabolic pathways. Dietary PPA was associated with an increased abundance of notable taxa, including several species of Bacteroides, Prevotella, and Ruminococcus, whose member species have previously been associated with PPA production. Microbiomes of PPA exposed mice also possessed a greater abundance of pathways related to lipid metabolism and steroid hormone biosynthesis. Our findings demonstrate PPA's effect in altering the gut microbiota and associated metabolic pathways. These observed changes highlight how preservatives listed as safe for consumption may affect gut microbiome composition with implications for one's health.}, } @article {pmid41853504, year = {2024}, author = {Muwonge, A and Gerber, PF and Wee, BA and Thomson, J and Wang, J and Halbur, PG and Opriessnig, T}, title = {Exploring the utility of bioaerosol metagenomics compared to PCRs for swine pathogen surveillance.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1439108}, pmid = {41853504}, issn = {2813-4338}, abstract = {INTRODUCTION: Pathogen introduction and transmission at the farm, regional, or national level are associated with reduced animal welfare and negative impacts on herd economics. Ongoing infectious disease surveillance, active or passive, is therefore of high importance. For optimal resolution, each pig is sampled individually, for example by collecting blood or nasal swabs. In recent years, oral fluids have become very useful for population surveillance at the pen level. Another alternative is sampling the air to capture pathogens circulating across the entire barn via bioaerosols.

OBJECTIVE: This study aimed to examine the potential utility of bioaerosol metagenomics for pathogen detection on pig farms.

METHODS: Bioaerosols via automated air sampler, and oral fluid via pen-based ropes, were collected from each of two Scottish indoor pig farms. All samples were subjected to conventional routine bacterial isolation. Total genomic nucleic acids were extracted for PCR screening for three pig DNA viruses, three bacterial Mycoplasma species and an RNA virus. Illumina shotgun metagenomic sequencing was also conducted.

RESULTS: Oral fluids contained more DNA compared to bioaerosol samples. DNA integrity exhibited limited impact on PCR or sequence yield. While Streptococcus suis could be cultured from a single oral fluid sample, reads mapped to S. suis were detectable in all metagenomic samples. Other bacterial pig pathogens, including Mycoplasma hyorhinis, M. hyopneumoniae and M. hyosynoviae, were detected in oral fluid and aerosols by PCR and metagenomics. One of the two farms was PRRSV positive, and the virus was detectable via PCR in oral fluids but not in bioaerosols. Antimicrobial resistance (AMR) gene profiles had less variation between bioaerosols and oral fluids. Some identified AMR genes had strikingly similar abundance overall.

CONCLUSION: Overall, these findings indicate that there is potential utility of bioaerosol metagenomics for pathogen surveillance on pig farms; however, more research is needed for technical and cost optimization to allow for routine pathogen detection on livestock farms.}, } @article {pmid41853506, year = {2024}, author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S}, title = {Corrigendum: A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1484878}, doi = {10.3389/frmbi.2024.1484878}, pmid = {41853506}, issn = {2813-4338}, abstract = {[This corrects the article DOI: 10.3389/frmbi.2024.1359580.].}, } @article {pmid41853507, year = {2024}, author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S}, title = {A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1359580}, pmid = {41853507}, issn = {2813-4338}, abstract = {The human gut microbiome, crucial for health, can be disrupted by antibiotic treatment, leading to various health issues and the rise of antimicrobial resistance (AMR). This study investigates the impact of a probiotic on the gut microbiome's composition and antimicrobial resistance genes (ARGs) content following antibiotic treatment. Conducted as a single-centre, double-blind, randomized, placebo-controlled trial, adults taking oral antibiotics were allocated into a probiotic or placebo group. Evaluations included viable cell enumeration and shotgun metagenomic sequencing for microbiome analysis, along with ARG assessment. The probiotic maintained the numbers of lactobacilli, significantly increased the Bacteroides population and decreased numbers of enterobacteria. The lactobacilli and enterococci numbers decreased in the placebo. The alpha diversity remained stable in the probiotic group throughout the study, but significant reductions were observed in the placebo group post antibiotic treatment. There was significant spatial separation in beta diversities between groups at the end of the study. Compared to baseline levels, there was a significant reduction in the abundance of ARGs in the probiotic group at the end of the study, while ARG abundance in the placebo group was comparable with baseline levels at the end of the study. Co-occurrence network analysis observed consistent betweenness centrality and node degree within group in the probiotic group whereas scores decreased in the placebo group. This study suggests that the probiotic may minimize the disruption of antibiotic treatment on the gut microbiome by preserving microbial diversity and reducing ARG abundance.}, } @article {pmid41853508, year = {2024}, author = {Molotzu, MR and Cabras, PA and Di Marcantonio, L and Atzeni, R and Macciotta, NPP and Canu, A}, title = {Metagenomic analysis of goat feces from Ogliastra (Sardinia, Italy).}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1474497}, pmid = {41853508}, issn = {2813-4338}, abstract = {With its constitutive and functional characteristics, the intestinal microbiota plays a crucial role in the health condition of the animals. Variations in the composition and gene expression of the intestinal microbiota are associated with the risk of the onset of various pathologies of the gastrointestinal tract and chronic inflammatory intestinal diseases. The objectives of this study were to evaluate the variability in the composition of the intestinal microbiota of goats of different breeds (Sarda, Maltese, and Alpine) farmed in different flocks of the region of Ogliastra (Sardegna, Italy) and to assess whether the type of feeding (natural pasture grazing-based versus intensive) could affect the intestinal bacterial composition. We also evaluated possible differences in the composition of the intestinal microbiota between healthy and Caprine arthritis encephalitis (CAE)-affected goats. The economic damage caused by this pathology is due to the reduction in milk production, with infected animals having greater susceptibility to contract diseases. The results of our study highlighted a statistically significant difference (P = 0.001-0.005) in the intestinal bacterial composition between the intensively managed flock and the other natural pasture-based flock.g In particular, a significantly greater abundance of Acidoaminococcaceae in the intensive flock was obgserved. Furthermore, a significantly greater abundance of Prevotellaceae was found in two localities in which, out of a total of 29 animals, only four tested negative for CAE. From these data, we deduced that the presence of Prevotellaceae can be an indication of the disease. This difference could be attributed to the farming system, the Cardedu farm being the only intensive one, and to the geographical distance of this location from the other sampling sites. Therefore, the results of the present study suggest that extensive or intensive farm management may affect the intestinal microbiota of goats.}, } @article {pmid41853526, year = {2024}, author = {Liu, S and Zhao, J and Feng, WL and Zhang, ZJ and Gu, YF and Wang, YP}, title = {Microbial community succession of cow manure and tobacco straw composting.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1301156}, pmid = {41853526}, issn = {2813-4338}, abstract = {Composting livestock manure using microorganisms is a safe and resourceful practice. The continual fluctuations in physicochemical parameters during composting are intricately linked to the composition of microbial communities. This study investigated the dynamics of microbial communities during the composting of cow manure and tobacco straw using amplicon sequencing and shotgun metagenomics. The sequencing results revealed major genera such as Sphaerobacter, Actinomadura, Thermomonospora, Flavobacterium, Bacillus, Hydrogenophaga, Pseudomonas, Lysinibacillus, Aneurinibacillus, and Azotobacter. Metagenomic analysis highlighted that the phylum Proteobacteria constituted the largest proportion. Furthermore, the presence of the genus Rhodococcus, known to cause human and animal diseases, gradually decreased over time. These findings offer initial insights into the microbial community composition and function during cow manure and tobacco straw composting.}, } @article {pmid41853529, year = {2024}, author = {Huttelmaier, S and Shuai, W and Sumner, JT and Hartmann, EM}, title = {Phage communities in household-related biofilms correlate with bacterial hosts.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1396560}, pmid = {41853529}, issn = {2813-4338}, abstract = {The average American spends 93% of their time in built environments, almost 70% of that is in their place of residence. Human health and well-being are intrinsically tied to the quality of our personal environments and the microbiomes that populate them. Conversely, the built environment microbiome is seeded, formed, and re-shaped by occupant behavior, cleaning, personal hygiene and food choices, as well as geographic location and variability in infrastructure. Here, we focus on the presence of viruses in household biofilms, specifically in showerheads and on toothbrushes. Bacteriophage, viruses that infect bacteria with high host specificity, have been shown to drive microbial community structure and function through host infection and horizontal gene transfer in environmental systems. Due to the dynamic environment, with extreme temperature changes, periods of wetting/drying and exposure to hygiene/cleaning products, in addition to low biomass and transient nature of indoor microbiomes, we hypothesize that phage host infection in these unique built environments are different from environmental biofilm interactions. We approach the hypothesis using metagenomics, querying 34 toothbrush and 92 showerhead metagenomes. Representative of biofilms in the built environment, these interfaces demonstrate distinct levels of occupant interaction. We identified 22 complete, 232 high quality, and 362 medium quality viral OTUs. Viral community richness correlated with bacterial richness but not Shannon or Simpson indices. Of quality viral OTUs with sufficient coverage (614), 532 were connected with 32 bacterial families, of which only Sphingomonadaceae, Burkholderiaceae, and Caulobacteraceae are found in both toothbrushes and showerheads. Low average nucleotide identity to reference sequences and a high proportion of open reading frames annotated as hypothetical or unknown indicate that these environments harbor many novel and uncharacterized phage. The results of this study reveal the paucity of information available on bacteriophage in indoor environments and indicate a need for more virus-focused methods for DNA extraction and specific sequencing aimed at understanding viral impact on the microbiome in the built environment.}, } @article {pmid41853533, year = {2024}, author = {Liu, Z and Shen, Y and Fu, Y and Sun, D and Li, L and Lv, Z}, title = {Association of resistome abundance with hyperuricaemia in elderly individuals: a metagenomics study.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1384703}, pmid = {41853533}, issn = {2813-4338}, abstract = {INTRODUCTION: Hyperuricaemia (HUA), one of chronic diseases, has an increased prevalence and is related to diseases such as gout, arthritis, infectious diseases, etc. Antimicrobial resistance (AMR) in the gut is considered as an atypical chronic disease, and poses risk to human health. The gut microbiome has been proved to be a reservoir for AMR and play an important role in HUA patients. The microbial characteristics of the gut in individuals with HUA have been previously explored, however, the characteristics of the resistome in individuals with HUA have remained largely unexplored.

METHODS: Thus, we investigated the landscape of the AMR in individuals with HUA and without HUA, and the potentially influential factors in a case-control study using metagenomics-based approaches.

RESULTS: We found that drinking juice and abnormal stool were risk factors associated with HUA. The taxonomic diversity of gut microbiota in individuals with HUA was lower than that in non-HUA individuals. Notably, a higher abundance and diversity of the resistome (entire antimicrobial resistance genes) was observed in individuals with HUA (median: 1.10 vs. 0.76, P = 0.039, U-test), especially in tetracycline resistance genes (median: 0.46 vs. 0.20, P < 0.001, U-test), which are associated with more complex mobile genetic elements (MGEs) in individuals with HUA. Furthermore, we found that a higher abundance of the resistome was positively correlated with uric acid (UA) levels and affected by several host-associated factors (mainly dietary habits). Specifically, pork consumption and the consumption of root and tuber vegetables were identified as contributing factors. We also found a higher abundance of virulence genes (VGs), mostly related to adherence, antimicrobial activity, competitive advantage, and exoenzymes, in the gut microbial community of individuals with HUA.

DISCUSSION: All findings revealed higher activity of the resistome and pathogenicity of the microbiota in individuals with HUA, indicating a higher health risk in the elderly HUA population.}, } @article {pmid41853535, year = {2024}, author = {Alian, OM and Brazelton, WJ and Aquino, KA and Twing, KI and Pendleton, HL and Früh-Green, G and Lang, SQ and Schrenk, MO}, title = {Microbial community differentiation in vent chimneys of the Lost City Hydrothermal Field reflects habitat heterogeneity.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1401831}, pmid = {41853535}, issn = {2813-4338}, abstract = {Oceanic hydrothermal vent systems represent some of the oldest habitats on Earth and serve as analogs for extraterrestrial environments. The Lost City Hydrothermal Field (LCHF) near the Mid-Atlantic Ridge is one such environment, and its large chimneys are unique in hosting actively venting hydrothermal fluids that are primarily controlled by serpentinization reactions in the subseafloor. Microbial communities within LCHF have been studied for insights into their functional adaptations to the warm, alkaline, and dissolved inorganic carbon-limited environment. Metagenomic and mineralogical data collected during a recent expedition to Lost City were analyzed to delineate associations between microbial populations and physical, chemical and biological characteristics of the chimneys. Bacterial 16S rRNA gene sequences show a high degree of putative microdiversity within the relatively dominant genera Desulfotomaculum, Sulfurovum, Thiomicrorhabdus, and Serpentinicella, which represent a large core of the overall LCHF vent bacterial community. This microdiversity relates to the compositional fraction of aragonite, brucite, and calcite minerals within chimney samples rather than just the composition of nearby vent fluids. Although many species are found in both chimneys and venting fluids, the overall microbial community structures in chimney biofilms remain distinct from the hydrothermal fluids that flow through them. Shotgun metagenomic analyses reveal differences among genes predicted to be involved in carbon, methane, nitrogen and sulfur cycling with respect to their correlations to the abundances of specific minerals. These data hint at microenvironmental complexity lost within standard bulk analyses. The findings of this study underscore the need to more closely examine microbe-mineral interactions in natural environments, critically informing not just population-level distributions, but also the functional underpinnings of these extremophile microbial communities.}, } @article {pmid41853539, year = {2024}, author = {Chandel, N and Gorremuchu, JP and Thakur, V}, title = {Antimicrobial resistance burden, and mechanisms of its emergence in gut microbiomes of Indian population.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1432646}, pmid = {41853539}, issn = {2813-4338}, abstract = {INTRODUCTION: The human gut microbiome harbors millions of bacterial species, including opportunistic pathogens, and this microbial community is exposed to antimicrobial agents present in food, the external environment, or drugs. Thus, it increases the risk of commensals being enriched with resistant genes, which may get even transmitted to opportunistic pathogens often with the help of mobile genetic elements. There is limited information about the current burden of resistant genes in the healthy gut microbiome of the Indian population, the latter is not only the largest in the world but is also periodically monitored for the prevalence of antibiotic resistance in clinical samples.

METHODS: We analyzed publicly available fecal whole-metagenome shotgun sequencing data from 141 samples from three healthy Indian cohorts for antimicrobial-resistance burden, and their likely transmission modes.

RESULTS: The overall resistance profile showed a higher number of resistance genes against tetracycline, glycopeptide, and aminoglycoside. Out of a total of 188 antimicrobial resistance genes identified in all cohorts, moderately to highly prevalent ones could potentially target seven of the 'reserve' group antibiotics (colistin, fosfomycin, Polymyxin). We also observed that geographical location affected the prevalence/abundance of some of the resistance genes. The higher abundance of several tetracycline and vancomycin resistance genes in tribal cohorts compared to the other two urban locations was intriguing. Species E. coli had the highest number of resistant genes, and given its relatively modest abundance in gut microbiomes can pose a risk of becoming a hub for the horizontal transfer of resistance genes to others. Lastly, a subset of the resistance genes showed association with several types of mobile genetic elements, which potentially could facilitate their transmission within the gut community.

DISCUSSION: This is a first systematic report on AMR genes in healthy gut microbiome samples from multiple locations of India. While trends for several of the prevalent AMR genes showed similarity with global data, but a few population specific trends need further attention by policy-makers. The association of AMR genes with mobile elements may pose a risk for transmission to other gut bacteria.}, } @article {pmid41853546, year = {2024}, author = {Bailey, A and Hogue, S and Pierce, CM and Paul, S and La Fuente, N and Thapa, R and Kim, Y and Robinson, LA}, title = {Metagenomic characterization of the tracheobronchial microbiome in lung cancer.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1457537}, pmid = {41853546}, issn = {2813-4338}, abstract = {BACKGROUND: The tracheobronchial and oral microbiome may be associated with lung cancer, potentially acting as predictive biomarkers. Therefore, we studied the lung and oral bacteriome and virome in non-small cell lung cancer (NSCLC) patients compared to melanoma controls to discover distinguishable features that may suggest lung cancer microbial biomarkers.

METHODS: In this pilot case-control study, we recruited ten patients with early-stage NSCLC (cases) and ten age-matched melanoma patients (controls) who both underwent tumor resection. Preoperative oral gargles were collected from both groups, who then underwent transbronchoscopic tracheal lavage after intubation. Lung tumor and adjacent non-neoplastic lung were sterilely collected after resection. Microbial DNA from all lung specimens underwent 16S rRNA gene sequencing. Lavage and gargle specimens underwent whole-genome shotgun sequencing. Microbiome metrics were calculated to compare both cohorts. T-tests and Wilcoxon rank sum tests were used to test for significant differences in alpha diversity between cohorts. PERMANOVA was used to compare beta diversity.

RESULTS: No clear differences were found in the microbial community structure of case and control gargles, but beta diversity of case and control lavages significantly differed. Two species, Granulicatella adiacens and Neisseria subflava, which are both common oral commensal organisms, appeared in much higher abundance in case versus control lavages. Case lavages also maintained higher relative abundances of other oral commensals compared to controls.

CONCLUSIONS: Lung lavages demonstrated oral microbiota enrichment in cases compared to controls, suggesting microaspiration and resultant inflammation. The oral commensals Granulicatella adiacens and Neisseria subflava were more abundant in the tracheobronchial lavages of lung cancer versus melanoma patients, implicating these microorganisms as potential lung cancer biomarkers, warranting further validation studies.}, } @article {pmid41853549, year = {2024}, author = {Mahmoudabadi, G and Homyk, K and Catching, AB and Mahmoudabadi, A and Foley, HB and Tadmor, AD and Phillips, R}, title = {Machine learning models can identify individuals based on a resident oral bacteriophage family.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1408203}, pmid = {41853549}, issn = {2813-4338}, support = {R01 GM098465/GM/NIGMS NIH HHS/United States ; R35 GM118043/GM/NIGMS NIH HHS/United States ; }, abstract = {Metagenomic studies have revolutionized the study of novel phages. However these studies trade depth of coverage for breadth. We show that the targeted sequencing of a small region of a phage terminase family can provide sufficient sequence diversity to serve as an individual-specific barcode or a "phageprint'', defined as the relative abundance profile of the variants within a terminase family. By collecting ~700 oral samples from ~100 individuals living on multiple continents, we found a consistent trend wherein each individual harbors one or two dominant variants that coexist with numerous low-abundance variants. By tracking phageprints over the span of a month across ten individuals, we observed that phageprints were generally stable, and found instances of concordant temporal fluctuations of variants shared between partners. To quantify these patterns further, we built machine learning models that, with high precision and recall, distinguished individuals even when we eliminated the most abundant variants and further downsampled phageprints to 2% of the remaining variants. Except between partners, phageprints are dissimilar between individuals, and neither country-of-residence, genetics, diet nor cohabitation seem to play a role in the relatedness of phageprints across individuals. By sampling from six different oral sites, we were able to study the impact of millimeters to a few centimeters of separation on an individual's phageprint and found that such limited spatial separation results in site-specific phageprints.}, } @article {pmid41853558, year = {2024}, author = {Pannoni, SB and Holben, WE}, title = {Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1274277}, pmid = {41853558}, issn = {2813-4338}, abstract = {Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA-simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.}, } @article {pmid41853664, year = {2026}, author = {Donbraye, E and McLeod, L and Chai, Z and Lacoste, SR and McCarthy, EL and Links, MG and Waldner, CL}, title = {Comparison of short nasal swab and deep nasopharyngeal swab sampling methods to describe BRD-associated viruses and bacteria detected using a metagenomics approach optimized for virus recovery in fall-placed beef calves shortly after feedlot arrival.}, journal = {Veterinary and animal science}, volume = {32}, number = {}, pages = {100609}, pmid = {41853664}, issn = {2451-943X}, abstract = {Short nasal swabs (SNS) have potential advantages of lower costs, collection time and training of personnel than deep nasopharyngeal swabs (DNPS) for detecting bovine respiratory disease (BRD) pathogens. This study examined differences between DNPS and SNS in BRD-associated pathogens detected using a nanopore metagenomic sequencing protocol, optimized for respiratory RNA viruses, collected from 150 calves in six feedlot pens. Short nasal swabs yielded higher viral read counts and prevalence than DNPS for BCoV (mean reads 75 versus 17; OR = 21.4, P = 0.001) and IDV (mean reads: 560 versus 192; OR = 2.60, P = 0.02). Agreement varied among viruses: IDV (κ=0.57), BRSV (κ=0.43), and BCoV at both ≥1 read (κ=0.35) and ≥30 reads (κ=0.10). No BoHV-1 and BAdV3 were detected. Mannheimia haemolytica was detected (≥14 reads) more frequently in SNS than DNPS (mean reads: 169 versus 57; OR = 5.73, P = 0.001), as was Pasteurella multocida (≥ 1 read) (mean reads: 4.0 versus 1.2; OR = 2.02, P = 0.02). Mesomycoplasma dispar was less prevalent in SNS (mean reads: 5.2 versus 29; OR = 0.27, P = 0.001). Detection of Histophilus somni, Bibersteinia trehalosi, and Mycoplasmopsis bovis did not differ between swab types. Agreement for detection of M. haemolytica (≥14 reads) was moderate (κ = 0.46, P = 0.001). For all other bacteria examined in this analysis, kappa values were very low. Short nasal swabs were a sensitive and practical alternative for BRD pathogen surveillance providing evidence of which viruses and bacteria are circulating, potentially informing vaccination and disease management.}, } @article {pmid41853712, year = {2026}, author = {Yao, J and Wang, F and Li, H and Zhang, R and Ji, G and Liu, D}, title = {Comparative analysis of microbial diversity and clinical outcomes in critically ill patients with and without malignancies: a single-center retrospective cohort study.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1777861}, pmid = {41853712}, issn = {1664-302X}, abstract = {BACKGROUND: Sepsis and septic shock are severe complications for surgical malignancy patients. Conventional diagnostics often fail to capture the complex infectome in these populations. This study aimed to characterize the distinct microbial and resistome landscapes in cancer versus non-cancer patients using multi-site metagenomic next-generation sequencing (mNGS) to support specific antimicrobial strategies.

METHODS: We conducted a single-center retrospective cohort study at the General Surgery ICU of Xuanwu Hospital, including 107 septic shock patients (52 cancer; 55 non-cancer). mNGS was performed on blood, bile, ascitic fluid, and bronchoalveolar lavage samples to identify pathogens and antibiotic resistance genes (ARGs). Findings were analyzed for their association with ICU length of stay and mortality.

RESULTS: Cancer patients were significantly older (median 68 vs. 51 years, p < 0.0001) with higher comorbidity scores (CCI: 7.0 vs. 4.0, p = 0.006). However, mNGS revealed a lower pathogen detection rate in cancer patients (53.85% vs. 85.45%, p = 0.0006) and a lower incidence of bacteremia (25.0% vs. 45.45%, p = 0.0426). Cancer patients had shorter ICU LOS (9 vs. 13 days, p = 0.0369) and antibiotic durations (7 vs. 11 days, p = 0.0368). Dominant pathogens included Klebsiella pneumoniae and Enterococcus faecium, harboring diverse ARGs across beta-lactam and aminoglycoside categories. Multivariate Cox regression identified IL-6 (p = 0.018) was significant prognostic indicators for cancer patients. We also examined the distribution of virulence factors, despite their low detection rates.

CONCLUSION: Septic shock in cancer patients exhibits a unique resistome signature and distinct prognostic drivers. The identification of microbial targets via mNGS was associated with the implementation of targeted antimicrobial strategies and inflammation monitoring. These findings suggest that mNGS provides valuable molecular insights that may support clinical management and prognostic stratification for cancer patients in the surgical ICU.}, } @article {pmid41853717, year = {2026}, author = {Matturro, B and Tucci, M and Firrincieli, A and Niccolini, L and Peña-Álvarez, V and Resitano, M and Trinchillo, M and Peláez, AI and Rossetti, S and Petruccioli, M and Viggi, CC and Aulenta, F}, title = {Multi-guild microbial cooperation sustains long-term anaerobic toluene degradation through sulfur cycling.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1773863}, pmid = {41853717}, issn = {1664-302X}, abstract = {Anaerobic degradation of aromatic hydrocarbons such as toluene plays a critical role in the natural and engineered attenuation of contaminated environments. Here, we developed and characterized a microbial consortium enriched under strictly anoxic conditions, capable of sustained toluene degradation through sulfate reduction. By integrating biodegradation kinetics, long-read 16S rRNA profiling, and genome-resolved metagenomics, we elucidated the structure and function of a multi-guild community. The consortium was co-dominated by Desulfoprunum, a sulfate-reducing bacterium (SRB), and Sulfurovum-affiliated sulfur oxidizers (~34% each), with additional members including Stenotrophomonas, Achromobacter, and Stutzerimonas. Such co-dominance appears uncommon, as sulfate-reducing enrichments are often characterized by low diversity and the predominance of a single lineage, such as Desulfobacula or Desulfosarcina in marine systems. Genome-resolved analyses recovered seven metagenome-assembled genomes (MAGs) with distinct but complementary metabolic roles. Desulfoprunum encoded the fumarate-addition pathway (bss/bbs) for anaerobic toluene activation and dissimilatory sulfate reduction (aprAB, dsrAB). In contrast, Sulfurovum and several Gammaproteobacteria encoded sulfide:quinone oxidoreductase (sqr), coupling H2S detoxification to energy conservation, while a Moranbacterales MAG carried a putative sulfhydrogenase (hydAB) potentially catalyzing elemental sulfur (S°) reduction. Additional MAGs encoded assimilatory sulfate reduction (cys), suggesting integration of sulfur into biosynthetic pathways. Together, these features are consistent with the presence of a putative distributed sulfur redox loop, in which biogenic H2S may be recycled via oxidation and reduction reactions mediated by co-occurring taxa. This sulfur loop is hypothesized to contribute to buffering sulfide toxicity and stabilize redox dynamics, thereby potentially supporting long-term toluene degradation under sulfidic conditions. Our findings highlight anaerobic degradation as a community-driven process enabled by sulfur-cycling interactions. By revealing the role of cryptic sulfur cycling in stabilizing hydrocarbon degradation, this work offers a new framework for designing bioremediation strategies in contaminated anoxic environments.}, } @article {pmid41853758, year = {2025}, author = {Song, W and Liu, S and Zang, D and Meng, W and Liu, C and Chen, J}, title = {Correlation between gut microbiota and their metabolites and the efficacy of chemotherapy combined with immunotherapy for extensive-stage small cell lung cancer.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1683347}, pmid = {41853758}, issn = {2234-943X}, abstract = {INTRODUCTION: Gut microbiota has been reported to be associated with the host's immune system and immunotherapy response, as well as immune-related adverse events (irAEs). Additionally, gut microbial metabolites have various immunomodulatory effects. Our study focused on the differences in gut microbiota and their metabolites between long progression-free survival (PFS) and short PFS in patients with small cell lung cancer before and after chemotherapy combined with immunotherapy.

METHODS: The enrolled patients collected in our department were divided into long PFS and short PFS groups according to whether the PFS was ≥6 months, and the stool samples before and after treatment were analyzed using metagenomics and metabolomics.

RESULTS: The results showed that Streptococcus (P = 0.00648), Actinomyces (P = 0.0124), and Roseburia (P = 0.0127) differed between the long and short PFS groups. In the analysis of differential metabolites, we found that indirubin-3'-monoxime (AUC 0.611), stearidonic acid (AUC 0.867), leukotriene B4 (AUC 0.844), trans-cinnamic acid (AUC 0.792), and L-tyrosine (AUC 0.751) could be used as potential biomarkers.

DISCUSSION: Gut microbiota and their metabolites hold broad prospects for translational applications in cancer clinical management, such as the development of microbial biomarkers and the modulation of microbiota to enhance the efficacy of chemotherapy and immunotherapy.}, } @article {pmid41853994, year = {2026}, author = {Yang, Q and Aghdam, R and Tran, PQ and Anantharaman, K and Solís-Lemus, C}, title = {Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70245}, pmid = {41853994}, issn = {1758-2229}, support = {506328//A Community Science Program New Investigator award/ ; //Natural Science and Engineering Research Council of Canada (NSERC)/ ; DBI-2047598//National Science Foundation/ ; DEB-2144367//National Science Foundation/ ; Hatch 1025641//USDA National Institute of Food and Agriculture/ ; //University of Wisconsin-Madison/ ; //Joint Genome Institute/ ; //Office of Science/ ; }, mesh = {*Ecosystem ; *Fresh Water/microbiology ; Metagenome ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; *Lakes/microbiology ; Transcriptome ; Water Microbiology ; }, abstract = {Freshwater lakes are dynamic ecosystems, with varying oxygen dynamics that influence microbiome structure, composition, and transcriptomic activity. In many freshwater studies, ecological function and abundance metrics are used to discover keystone species; however, it is well established that abundance does not equal activity. Despite the existence of long-term time series spanning multiple years, no previous study has looked at how microbial community and activity (metatranscriptomics) are influenced by shifting oxygen conditions across depths at the microbial network level. In this study, we leverage metagenome-assembled genomes and transcriptomic activity to identify keystone taxa in the ecosystem. Using the SPIEC-EASI and CARlasso methods, we mapped key microbial associations and used permutation-based analyses to assess the robustness of keystone identification. Our results reveal that a taxon's ecological centrality is context-dependent and that many species identified as keystone by abundance alone do not exhibit corresponding transcriptional activity. Notably, members of Bacteroidota and other lineages emerged as keystone taxa only when both abundance and activity were considered. Our study underscores the importance of combining metagenomic and metatranscriptomic approaches for accurate identification of functionally relevant keystone species in freshwater ecosystems, providing a framework for future microbial ecology studies.}, } @article {pmid41854100, year = {2026}, author = {Hu, K and Qu, Q and Ban, Z and Hu, X and Wang, A and Dong, X and Liu, C and Deng, P and Wang, R}, title = {Risks of Microplastics Shaping Viral Communities and Functions in Real Marine Environments.}, journal = {Environmental science & technology}, volume = {60}, number = {12}, pages = {9333-9344}, doi = {10.1021/acs.est.5c17054}, pmid = {41854100}, issn = {1520-5851}, mesh = {*Microplastics ; Viruses ; Seawater ; Environmental Monitoring ; }, abstract = {Microplastic (MP) pollution has become a global issue, especially in the oceans. However, the extent of changes in the ecological states of viruses that coexist with MPs and their subsequent influence on the biogeochemical cycle remain unclear. We found that the subtropical Atlantic has emerged as a viral diversity hotspot, while the hotspots of increasing viral diversity are concentrated in the South China and Eastern Archipelagic Seas, with 87.57% of the area showing increasing trends. Ignoring the effects of MPs would result in more than 15% underestimation of viral diversity in the Mediterranean region and temperate zone of the Indian Ocean, which is notably higher than the global overall underestimation of 2.4% for viral diversity. Beyond a critical MP threshold (1 × 10[4] items·km[-2], accounting for 55.26% of marine zones during 2025), a distinct positive association with marine viral diversity was observed, especially in low-diversity regions. In regions with higher MP concentrations, viral community networks exhibited higher connectivity and lower modularity, coinciding with a stronger presence of lytic bacteriophages for lysogenization. MPs emerge as significant environmental indicators linked to marine viral ecological niches and host-virus interactions. This work addresses the non-negligible role of MPs in shaping marine ecosystems by viruses.}, } @article {pmid41854101, year = {2026}, author = {Liu, Q and Wu, S and Gong, S and Su, H and Jin, Y and Chen, H and Fan, Y and Yin, R and Ren, X and Wang, J}, title = {Ecologically Informed Design of Synthetic Microbial Community Enables Robust Degradation and Engraftment for Antibiotic Removal in Wastewater.}, journal = {Environmental science & technology}, volume = {60}, number = {12}, pages = {9367-9380}, doi = {10.1021/acs.est.6c01020}, pmid = {41854101}, issn = {1520-5851}, mesh = {*Wastewater ; *Anti-Bacterial Agents ; Biodegradation, Environmental ; Sulfamethoxazole ; Water Pollutants, Chemical ; }, abstract = {Conventional biological wastewater treatment often fails to remove emerging contaminants (ECs) because specialized degraders are absent. We developed a function-ecology-integrated framework for designing synthetic microbial communities (SynComs) by combining metagenome-guided identification of degradation potential, quorum-sensing functionality screening, and keystone-based selection from genome-scale metabolic models (GSMMs). Applied to sulfamethoxazole (SMX) degradation, this approach identified five strains with stable catabolic potential and high ecological coherence. GSMM simulations predicted SynCom5 (three species) and SynCom11 (four species) would achieve the highest SMX uptake fluxes (30.7 and 31.7 mmol gDW[-1] h[-1], respectively), driven by complementary amino acid cross-feeding and a high ratio of metabolic interaction potential to resource overlap. Experimentally, both SynComs removed >90% of SMX within 72 h, with SynCom11 selected for bioaugmentation. In activated sludge microcosms, SynCom11 achieved 91.3% SMX removal over 7 days, compared to 25.8% in controls, and successfully engrafted 2 of its 4 members. This approach avoids high-concentration selective pressure, minimizing resistance risks, and demonstrates that embedding an ecologically informed design within catabolic function enables robust, scalable bioaugmentation for ECs.}, } @article {pmid41854267, year = {2026}, author = {Eisenhofer, R and Alberdi, A and Woodcroft, BJ}, title = {Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns.}, journal = {mSystems}, volume = {11}, number = {4}, pages = {e0106225}, pmid = {41854267}, issn = {2379-5077}, support = {FT210100521//Department of Education and Training/ ; DP230101171//Department of Education and Training/ ; DNRF143//Danmarks Grundforskningsfond/ ; CF20-0460//Carlsbergfondet/ ; }, mesh = {*Metagenome ; *Archaea/genetics ; *Metagenomics/methods ; *Bacteria/genetics ; *DNA, Bacterial/genetics ; *DNA, Archaeal/genetics ; Humans ; Algorithms ; Genome, Archaeal ; }, abstract = {Metagenomes often contain many reads derived from eukaryotes, but there is usually no reliable method for estimating their prevalence. This forces many analysis techniques to make the often-faulty assumption that all reads are prokaryotic. Here, we present SingleM prokaryotic_fraction (SPF), an algorithm that scalably and robustly estimates the number of bacterial and archaeal reads in a metagenome. It also estimates the average genome size of bacteria/archaea in a sample. SPF does not use eukaryotic reference genome data and can be applied to any modern Illumina metagenome. Based on SPF, we propose the domain-adjusted mapping rate (DAMR) as an improved metric to assess prokaryotic genome recovery from metagenomes. Applying SPF to 136,284 publicly available metagenomes, we report substantial variation in prokaryotic fractions and biome-specific patterns of prokaryotic abundance, providing insights into how microorganisms and eukaryotes are distributed across Earth. Finally, we show that substantial amounts of human host DNA sequence data have been deposited in public metagenome repositories, possibly counter to ethical directives that mandate screening of these reads prior to release. As the adoption of metagenomic sequencing continues to grow, we foresee SPF being a valuable tool for the appraisal of genome recovery efforts and for investigating global patterns of microorganism distribution.IMPORTANCEMetagenomics data sets capture DNA from all organisms in a sample, enabling the analysis of communities without relying on culture-based techniques. However, many samples include uncharacterized eukaryotic organisms and viral elements, meaning the proportion of bacterial and archaeal DNA is often unknown. This study presents SingleM prokaryotic_fraction (SPF), a robust and scalable method for estimating the prevalence of bacterial and archaeal DNA in metagenomes. Crucially, SPF is calculated independent of eukaryotic and viral reference genomes, which are often incomplete or unavailable. Applying SPF to over 136,000 public metagenomes uncovered substantial variability between microbial communities living in different environments. SPF also identified previously overlooked human genetic data contamination in public data sets, raising important ethical and privacy considerations. Building on SPF, we propose the domain-adjusted mapping rate (DAMR) metric, a new metric that improves genome recovery assessment by accounting for non-prokaryotic reads.}, } @article {pmid41854352, year = {2026}, author = {Joseph, J and Patnaik, SK and Abraham, D and Mathew, J and Alexander, J}, title = {Gut and oral microbiota characterized in systemic lupus erythematosus patients from India: A pilot study.}, journal = {Lupus}, volume = {35}, number = {7}, pages = {667-677}, doi = {10.1177/09612033261432163}, pmid = {41854352}, issn = {1477-0962}, mesh = {Humans ; *Lupus Erythematosus, Systemic/microbiology/immunology ; Pilot Projects ; Female ; India ; Adult ; Saliva/microbiology ; Male ; Killer Cells, Natural/immunology ; *Dysbiosis/microbiology/immunology ; *Mouth/microbiology ; Middle Aged ; *Gastrointestinal Microbiome/immunology ; Case-Control Studies ; Feces/microbiology ; *Microbiota ; Young Adult ; CD8-Positive T-Lymphocytes/immunology ; CD4-Positive T-Lymphocytes/immunology ; }, abstract = {Introduction: Systemic lupus erythematosus (SLE) is a multifaceted autoimmune disorder influenced both intrinsically by immune cell alterations, genetic factors, and the microbiome, as well as extrinsically by environmental factors. Methods: In this pilot study, we investigated the role of various peripheral immune cells (CD3[+], CD4[+], CD8[+], CD4[+]/CD8[+], CD4-/CD8-, NK cells (CD16[+]CD56[+]), and CD19[+]) and the gut and salivary microbiota in patients with SLE, comparing these factors to healthy controls. Results and Discussion: Results showed significant alterations in the proportions of CD4[+] and CD8[+] T cells in SLE patients, with an inverse correlation between these subsets. Additionally, the CD4[+] ratio was found to be elevated in SLE. CD4[+] T cells were strongly correlated with double-negative T cells, while CD8[+] T cells correlated with NK cells. Metagenomic shotgun sequencing of fecal and salivary samples revealed a disruption in the microbiome, particularly the taxa Pasteurellaceae and Veillonella, which were altered in both the gut and oral microbiomes of SLE patients. These changes suggest that there may be overlap in the composition and function of these microbial populations across different body sites. Dysbiosis was observed in both the gut and oral microbiomes of individuals with SLE, distinguishing them from healthy controls. Conclusion: Our findings highlight specific microbiome alterations in SLE patients and suggest that microbiome composition could serve as a potential exploratory tool for diagnosing and prognosticating the disease in larger, adequately powered cohorts.}, } @article {pmid41854356, year = {2026}, author = {Khadivar, H and Bui, H and Huesemann, M and Gao, S and Gerlach, R}, title = {Metagenome-assembled genome of the alkaliphilic Cyanobacterium sp. PNNL-SSL1.}, journal = {Microbiology resource announcements}, volume = {15}, number = {4}, pages = {e0139825}, pmid = {41854356}, issn = {2576-098X}, support = {DE-EE0009676, DE-EE0007004//U.S. Department of Energy/ ; 2125083, 2125748//National Science Foundation/ ; 505760//Joint Genome Institute/ ; }, abstract = {Microalgae and cyanobacteria are promising sources of fuels, chemicals, and bioproducts, but CO2 supply increases production cost. We present the metagenome-assembled genome of the alkaliphilic Cyanobacterium sp. strain PNNL-SSL1 obtained from Soap Lake (Washington, USA). PNNL-SSL1 shows strong potential for biomass production using only atmospheric CO2, reducing cultivation expenses.}, } @article {pmid41854421, year = {2026}, author = {Colina Prisco, C and Fourie, NH and Wang, Y and Steck, M and de Jesús Vega, M and Graves-Dixon, LY and Jaime-Lara, RB and Henderson, WA and Joseph, PV}, title = {Examining mRNA-miRNA Interactions and Gene Expression in Overweight and Obesity.}, journal = {Biological research for nursing}, volume = {28}, number = {3}, pages = {427-444}, doi = {10.1177/10998004261433237}, pmid = {41854421}, issn = {1552-4175}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Gene Expression ; *MicroRNAs/genetics/metabolism ; *Obesity/genetics ; *Overweight/genetics ; *RNA, Messenger/genetics/metabolism ; }, abstract = {Obesity is characterized by excess adipose tissue, metabolic imbalance, and persistent low-grade inflammation, all of which can affect brain centers and their communication with peripheral organs. The genetic basis of obesity is complex, involving genetics, metagenomics, and gene-environment interactions that impact gene expression. Micro-RNAs (miRNAs) are small, single-stranded, non-coding RNAs that post-transcriptionally regulate the translational rates of target messenger RNAs (mRNAs). Exploring miRNA-mRNA interactions in obesity offers insights into molecular processes, potential biomarkers, and therapeutic targets of this condition. The current study examined the interplay between miRNA and mRNA collected from individuals with overweight and obesity, and normal weight controls. To our knowledge, this is the first experimental attempt to construct a comprehensive dataset of miRNA-mRNA interactions in overweight and obesity. Total RNA, including miRNA, was isolated from venous blood samples collected from 95 participants. Subsequently, 100 ng of RNA from each sample was analyzed using the NanoString quantitative assay. Quantile normalization, the Bayesian-based method Combat, multi-variable linear regression, over-representation, weighted gene correlation network analyses, and functional analyses were conducted. We found an association between IQGAP1 and DAZAP2 genes and miRNA-20-a and miRNA-2113. IQGAP1 and DAZAP2 were associated with insulin signaling and energy metabolism and insulin sensitivity, respectively. We also identified a positive correlation between peripheral cortisol levels and miRNA-548 with alterations in metabolic processes and the immune system. This suggests that miRNA-mRNA interactions in overweight and obesity may impact insulin sensitivity, metabolism, and immunity, providing novel insight into miRNA-mRNA interactions in overweight and obesity. (ClinicalTrials.gov identifier #NCT00824941; https://clinicaltrials.gov/study/NCT00824941).}, } @article {pmid41854491, year = {2026}, author = {Wang, HC and Zhang, Y and Feng, R and Cai, LT and Chen, X and Hsiang, T and Wang, F}, title = {Metagenomic Analysis of Potential Pathogens and Other Microorganisms in Tobacco Leaves.}, journal = {Plant disease}, volume = {110}, number = {4}, pages = {1238-1249}, doi = {10.1094/PDIS-03-25-0520-RE}, pmid = {41854491}, issn = {0191-2917}, mesh = {*Plant Leaves/microbiology ; *Nicotiana/microbiology ; *Bacteria/genetics/isolation & purification/classification/pathogenicity ; *Plant Diseases/microbiology ; *Metagenomics ; Alternaria/genetics/isolation & purification/pathogenicity ; *Fungi/genetics/isolation & purification/pathogenicity/classification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; }, abstract = {Tobacco leaf spot is a major challenge for tobacco leaf production, and the phyllosphere of tobacco is the main habitat for many pathogens. In this study, tobacco leaves with typical symptoms were sampled, and morphological and molecular biological methods were used to identify pathogens. Illumina high-throughput sequencing and Biolog-ECO were used to investigate the composition and carbon metabolic capacity of the microorganisms in the tobacco leaves. A total of 24 fungal isolates were obtained, including one taxon each of Diaporthe, Paramyrothecium, Botrytis, Phoma, and Mortierella; six each of Fusarium and Epicoccum; four of Trichoderma; and three of Alternaria. Six genera of bacteria were isolated: Bacillus, Pantoea, Enterobacter, Pseudomonas, Prolinoborus, and Atlantibacter. Pathogenicity tests revealed that four isolates of Epicoccum and three isolates of Alternaria were pathogenic, and the leaf spot symptoms induced by coinfection with members from these two groups were similar to those observed in the field. These pathogens were identified as Epicoccum latusicollum and Alternaria alternata through multigene analysis. High-throughput sequencing analysis showed that the dominant fungi in diseased tobacco tissues were Alternaria and Epicoccum, and the dominant bacteria were Pseudomonas, Paenibacillus, and Pantoea. In carbon source utilization tests, where various carbohydrates were the main carbon sources, the utilization capacity of phyllosphere microorganisms in diseased tobacco leaves was lower than that in healthy leaves. The combined application of culture-dependent and independent methods provided comprehensive insights into plant disease diagnosis and tobacco phyllosphere microorganism community composition and metabolic function.}, } @article {pmid41854683, year = {2026}, author = {Wang, J and Shi, Y and Jia, Y and Peng, J}, title = {Effect of Diosmetin on Gut Microbiota and Serum Metabolites in Acute Pancreatitis Mice: A Metagenomic and Metabolomic Study.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {6}, pages = {e71679}, doi = {10.1096/fj.202503650RRR}, pmid = {41854683}, issn = {1530-6860}, support = {2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; 82170661//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Pancreatitis/drug therapy/metabolism/microbiology/chemically induced/blood ; Mice ; *Flavonoids/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Metabolomics/methods ; Mice, Inbred C57BL ; Metagenomics/methods ; Ceruletide/toxicity ; *Metabolome/drug effects ; Acute Disease ; Pancreas/drug effects/metabolism ; Fecal Microbiota Transplantation ; }, abstract = {Diosmetin is a bioactive flavonoid that exhibits well-documented antioxidant, anti-inflammatory, and anti-tumor properties. However, its potential to attenuate acute pancreatitis (AP) progression through gut microbiota modulation has not yet been elucidated. In this study, mice were pretreated with varying oral doses of diosmetin for 1 week before AP induction via intraperitoneal (i.p.) caerulein injections. The therapeutic efficacy and optimal dosage were determined through histopathological analysis of pancreatic tissue and serological biomarker assessment. Additionally, transcriptomic profiling and western blot were employed to elucidate the underlying signaling pathways. Furthermore, based on integrated metagenomic and metabolomic analyses, a core gut microbiota-metabolite-gene interaction network modulated by diosmetin was constructed. Finally, fecal microbiota transplantation (FMT) experiments validated the critical role of gut microbiota in the effects of diosmetin against AP. The results showed that medium-dose diosmetin treatment significantly attenuated pancreatic histopathological damage and acinar cell apoptosis in AP mice, while suppressing the activation of the MAPK inflammatory signaling pathway. Notably, diosmetin treatment was associated with restored microbial diversity, altered bacterial community structure, and changes in key metabolic pathways, reversing gut microbiota dysbiosis. Specifically, a diosmetin-responsive interaction network was constructed, highlighting associations between core bacterial taxa (Butyricimonas faecalis, Enterocloster bolteae, Roseburia intestinalis), key metabolites (3-indoleacrylic acid, 2-methoxy-4-vinylphenol, nitrite), and MAPK pathway-related genes. Finally, the protective effect of diosmetin was further substantiated by FMT, suggesting a potential role of the gut microbiota in this process. In conclusion, diosmetin ameliorated pancreatic injury in a murine model of caerulein-induced AP by modulating gut microbiota composition and associated metabolic profiles. These findings suggested that diosmetin represented a promising therapeutic option for AP, offering a scientific foundation for its clinical application and the underlying mechanisms involved.}, } @article {pmid41855720, year = {2026}, author = {Miao, H and Zeng, W and Hao, X and Gu, Y and Peng, Y}, title = {S[0]-S[2-] co-substrate system achieves efficient nitrite accumulation under high alkalinity and ultra-short HRT: Multidimensional responses and metabolic regulation mechanism.}, journal = {Water research}, volume = {297}, number = {}, pages = {125737}, doi = {10.1016/j.watres.2026.125737}, pmid = {41855720}, issn = {1879-2448}, mesh = {*Nitrites/metabolism ; Hydrogen-Ion Concentration ; *Sulfur/metabolism/chemistry ; Denitrification ; Sulfides/metabolism ; Bioreactors/microbiology ; Bacteria/metabolism/genetics ; }, abstract = {Sulfur autotrophic denitrification under highly alkaline conditions provides a novel strategy for nitrite supply, but low nitrate conversion flux often limits nitrite accumulation rate. This study proposes an element sulfur-sulfide (S[0]-S[2][-]) co-substrate enhancement strategy based on an alkaline environment. Under high pH (10) with an ultra-short hydraulic retention time (0.65 h) and low S[2][-] feeding (S[2-]/NO3[-]-N ratio of 0.17), the nitrate conversion efficiency (84.3%) was nearly 20% higher than that only at high pH conditions. Moreover, the strategy achieved an excellent nitrite accumulation efficiency of 60.6% and a rate of 1.54 kg N·m[-3]· d[-1]. Microbial physiological responses revealed that reactive oxygen species accumulation significantly inhibited microbial activity and disrupted nitrogen-sulfur metabolism at high pH. However, supplemental S[2-] promoted the ring-opening activation of S[0] to form high bioavailability polysulfide, and restored electron transfer system activity and energy metabolism. The abundance of sulfur-oxidizing genes Sox and fccAB increased by 15.7%-95.6%, ensuring robust electron flux. Under this strategy, the system exhibited an optimized metabolic trade-off that prioritized survival advantages over complete denitrification. This was achieved by prioritizing energy allocation to Na[+](K[+])/H[+] antiporters (Mrp/Pha/Kef/Trk) and glutamate synthesis to maintain cellular homeostasis. Concurrently, the increased narGHI/napAB abundance (14.6%-58.9%) and reduced nirS abundance (25.6%-41.3%) ensured a higher nitrite accumulation rate. Functional annotation further revealed that Thiobacillus (40.2%) and Pseudoxanthomonas (3.9%) served as key genera driving nitrite accumulation. This study not only proposes an efficient nitrite supply strategy for Anammox but also reveals the underlying microbial response mechanisms under high alkalinity.}, } @article {pmid41855876, year = {2026}, author = {Lou, J and Zhu, Z and Zheng, Y and Chen, J and Su, Q and Zhu, J}, title = {Response mechanism of the DAMO-associated denitrification system to oxytetracycline stress.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129409}, doi = {10.1016/j.jenvman.2026.129409}, pmid = {41855876}, issn = {1095-8630}, mesh = {*Denitrification ; *Oxytetracycline ; Anti-Bacterial Agents ; Methane/metabolism ; Oxidation-Reduction ; }, abstract = {Antibiotics and denitrifying anaerobic methane oxidation (DAMO) processes frequently coexist in natural ecosystems and wastewater treatment systems. This study investigated the performance and microbial ecology of a denitrification system coupled with Nitrite-dependent anaerobic methane oxidation (N-DAMO) under oxytetracycline (OTC) stress. Specifically, 1 mg/L OTC enhanced nitrogen removal efficiency by 15% relative to the control, whereas 10 mg/L OTC exerted a significant inhibition of 58%. The Michaelis-Menten kinetic model predicted that the system could tolerate the maximum OTC concentration of 26.76 mg/L. Mechanistically, the secretion of protein-rich extracellular polymeric substances (EPS) served as a protective barrier against toxicity. The abundance of the DAMO bacterium Candidatus Methylomirabilis correlated negatively with OTC concentration. At 1 mg/L OTC, denitrification was enhanced through the enrichment of Thauera. However, 10 mg/L OTC damaged EPS structure and suppressed microbial activity, and led to a decrease in the abundance of related functional bacteria and an increase in the abundance of antibiotic resistant bacteria such as Hyphomicrobium and Thermomonas. Metagenomic analysis revealed that denitrification genes (e.g., norB, norC) were upregulated with 1 mg/L OTC, whereas high-concentration OTC induced pronounced enrichment of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), with frequently co-localization within the same hosts. This suggests an increased potential for horizontal gene transfer (HGT) occurred within the DAMO community, which may contribute to the dissemination of ARGs. These findings provide new insights into the adaptive mechanisms of N-DAMO systems under antibiotic stress and highlight their potential for nitrogen removal in contaminated environments.}, } @article {pmid41855937, year = {2026}, author = {Jiang, L and Liang, Z and Williams, TA and Deng, Y and Yu, H and Hao, Q and Cao, J and Zhou, H and Lai, H and Chen, J and Chen, H and Zhang, C}, title = {Vertical stratification and metabolic versatility of methanogens in Haima cold seep sediments: Alkane-fueled acetoclastic methanogenesis revealed by metagenomics and experimental verification.}, journal = {Marine environmental research}, volume = {217}, number = {}, pages = {107972}, doi = {10.1016/j.marenvres.2026.107972}, pmid = {41855937}, issn = {1879-0291}, mesh = {*Geologic Sediments/microbiology ; *Alkanes/metabolism ; Metagenomics ; *Methane/metabolism ; *Archaea/metabolism/genetics ; Oxidoreductases ; }, abstract = {Cold seeps are hot spots for studying the biogeochemical processes mediated by methyl-coenzyme M reductase (MCR) containing archaea, yet these processes remain poorly understood. Here, we investigated the microbial communities in a 5-m-long sediment core encompassing sulfate-methane transition zone (SMTZ), collected from the Haima cold seep. We focused on distinct biogeochemical characteristics and metagenomics to study the vertical patterns of mcrA-containing archaea and their role in alkane metabolism. Background alkane analysis showed that long chain alkanes were dominant in the sediment core. Metagenomic and quantitative PCR (qPCR) analysis revealed that the abundance of mcrA gene within and below the SMTZ were substantially higher than those above the SMTZ. We recovered 21 mcrA-containing MAGs, 11 affiliated with Methanosarcinaceae. One MAG (CG1-BIN56) encoded complete key genes for all three methanogenic pathways. Functional gene profiles suggested that acetoclastic methanogenesis is the dominant pathway. Furthermore, a 10-month anaerobic enrichment with n-alkanes (C10/C16) using SMTZ (CG15: 350 cmbsf) inocula exhibited high degradation rate (C10: 94.2% ± 2.5%, C16: 66.8% ± 2.8%) accompanied by acetate accumulation. These findings suggest that acetate, as a likely intermediate associated with alkane degradation process, potentially fuels acetoclastic methanogenesis. This indicates a likely syntrophic interaction between alkane-degrading and methane-cycling microorganisms in cold seep sediments.}, } @article {pmid41855981, year = {2026}, author = {Ye, T and Li, P and Zhou, Z and Xiong, B and Zhao, Y and Zhao, J and Qi, J and Ma, B and Chen, Y}, title = {Enhanced pollutant removal in multi-pollutants contaminated water by bioaugmented slow filtration.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141806}, doi = {10.1016/j.jhazmat.2026.141806}, pmid = {41855981}, issn = {1873-3336}, mesh = {Filtration/methods ; *Water Pollutants, Chemical/metabolism/isolation & purification ; *Water Purification/methods ; *Bacteria/metabolism/genetics ; Biodegradation, Environmental ; Manganese/metabolism ; Oxidation-Reduction ; Oxides ; Drug Resistance, Microbial/genetics ; Trimethoprim/metabolism ; Atenolol/metabolism ; }, abstract = {Slow filtration is a low-cost and low-carbon water treatment approach, yet its broad application is limited by long start-up times and insufficient understanding of multi-pollutant removal. Here, we evaluate whether bioaugmentation with manganese-oxidizing bacteria enhances pollutant removal in water contaminated with NH4[+] -N, Mn[2+], readily biodegradable emerging contaminants (ECs, atenolol and trimethoprim), and relatively non-biodegradable ECs (carbamazepine and sulfamethoxazole). Bioaugmented filtration increased the removal rates of NH4[+]-N and Mn[2+] by 32.2% and 33.9%, respectively, during the first 10 days of the experiment. The proposed approach also demonstrated superior average removal rates (30.1%-99.6%) of four ECs compared to the filter column without QJX-1 inoculation (16.7%-99.3%). Furthermore, bioaugmented filtration effectively reduced the relative abundances of antibiotic resistance genes (ARGs) subtypes such as macB, tetA(58), and bcrA in the influent. The composition of ARGs on the filter media in both process groups is highly similar, with the relative abundance of ARGs at the top and middle of the filter column slightly higher than at the bottom. The mechanism study revealed that Mn[2+] was effectively oxidized to biological manganese oxides, which was conducive to the adsorption and oxidation of Mn[2+] and ECs. The metagenomic results confirmed the pmoC-amoC gene in Nitrospira promoted the removal of NH4[+]-N. Toxicity prediction indicated that the toxicity of most ECs intermediates was significantly lower than that of their parent compounds. The findings of this study verify the viability of employing cost-effective and few-chemical water treatment technologies to treat muti-pollutant contaminated water and guarantee the quality of drinking water.}, } @article {pmid41855987, year = {2026}, author = {Demaria, F and Suleiman, M and Bargiela, R and Ferrer, M and Hernández, SB and Núñez, AE and Petchey, OL and Corvini, PF and Junier, P}, title = {Micropollutant-driven bacterial adaptation enables resilient pharmaceuticals biodegradation at trace concentrations in biologically treated wastewater.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141801}, doi = {10.1016/j.jhazmat.2026.141801}, pmid = {41855987}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; Bioreactors/microbiology ; *Wastewater/microbiology/chemistry ; Pharmaceutical Preparations/metabolism ; *Bacteria/metabolism/genetics ; Microbial Consortia ; Waste Disposal, Fluid ; Adaptation, Physiological ; }, abstract = {Pharmaceutical residues are persistent contaminants that resist conventional wastewater treatment and can disrupt ecosystems; however, microorganisms provide a promising biobased solution to transform or mineralize these complex xenobiotics. Whether pollutant-adapted communities maintain their degradative capacity under realistic environmental conditions remains a long-standing debate in environmental biotechnology. Here, microbial consortia enriched in six membrane bioreactors under high pharmaceutical concentration (100 mg/L) retained full biodegradation capacity across a 5000-fold concentration range. After prolonged exposure to six model compounds (atenolol, caffeine, diclofenac, enalapril, ibuprofen, and paracetamol) complete removal occurred for all except diclofenac. Degradation remained efficient even at lower and environmentally relevant concentrations (1 mg/L-20 µg/L) and recovered rapidly upon re-exposure to higher loads (100 mg/L). Metagenomic profiling revealed enrichment of oxygenase-mediated catabolic pathways supporting this resilience. When transferred to a 7 liters bioreactor treating real wastewater, the adapted community removed targeted and untargeted pharmaceuticals, demonstrating robustness, scalability, and strong potential for sustainable micropollutant remediation.}, } @article {pmid41856032, year = {2026}, author = {Caetta, A and Aasen, D and Adamczyk, P and Yuan, H and Grindle, C and Schoem, S and Zhou, Y and Roberts, D and Hughes, A}, title = {Characterizing the microbiome of the middle ear using 16S RNA sequencing in pediatric patients with and without middle ear effusions requiring ventilation tubes.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {204}, number = {}, pages = {112798}, doi = {10.1016/j.ijporl.2026.112798}, pmid = {41856032}, issn = {1872-8464}, } @article {pmid41856107, year = {2026}, author = {Potloane, D and Symul, L and Ngcapu, S and Lewis, L and France, M and Vermeren, L and Elsherbini, J and Chetty, C and Mafunda, NA and Polliah, AM and Mtshali, A and Kama, A and Magini, N and Mitchev, N and Mzobe, G and Khan, A and Demidkina, BC and Goldenberg, M and Xu, J and Rutt, L and Shirtliff, B and Cook, S and Murthy, M and Hussain, F and Passmore, JS and Jaspan, HB and Kullin, B and Happel, AU and Liebenberg, L and Relman, DA and Holmes, S and Kwon, DS and Ravel, J and Mitchell, CM}, title = {VIBRANT: A phase 1 randomized trial of multi-strain vaginal L. crispatus live biotherapeutic products in people with bacterial vaginosis.}, journal = {Cell host & microbe}, volume = {34}, number = {4}, pages = {751-760.e5}, doi = {10.1016/j.chom.2026.02.016}, pmid = {41856107}, issn = {1934-6069}, mesh = {Female ; *Vaginosis, Bacterial/therapy/microbiology ; Humans ; *Lactobacillus crispatus/genetics ; Metronidazole/therapeutic use ; *Vagina/microbiology ; Adult ; *Probiotics/administration & dosage/therapeutic use ; Administration, Intravaginal ; South Africa ; United States ; Young Adult ; Treatment Outcome ; Metagenomics ; *Biological Therapy/methods ; }, abstract = {Bacterial vaginosis (BV) is characterized by high microbial diversity. High recurrence rates following antibiotics may stem from poor recolonization by protective Lactobacillus species. This phase 1 randomized trial in the United States and South Africa evaluated two vaginally delivered live biotherapeutic products (LBPs) containing multiple Lactobacillus crispatus strains. After metronidazole treatment for BV, participants received either a placebo or 3 or 7 days of active LBPs. LBP strains were detected by metagenomics in 66.1% (47/71) of participants in the active arms in the first 5 weeks. Among those, nearly half (49%, 23/47) remained colonized at 12 weeks despite the short initial treatment course. Participants were most often colonized by one of three component strains, with no geographic differences in strain colonization observed. LBPs were safe, acceptable, and well tolerated, with no serious adverse events (AEs) reported. These results provide a foundation for the development of transformational interventions aimed at optimizing the vaginal microbiome.}, } @article {pmid41856148, year = {2026}, author = {Michels, EHA and Dequin, PF and Butler, JM and Guillon, A and Evrard, B and Paling, FP and Reijnders, TDY and Schuurman, AR and van Engelen, TSR and Brands, X and Haak, BW and Bos, LDJ and Leroux, C and Giamarellos-Bourboulis, EJ and Stoker, J and Prins, JM and Faber, DR and Douma, RA and Sweeney, TE and Malhotra-Kumar, S and Kluytmans, JAJW and Scicluna, BP and Cremer, OL and Matthay, M and Calfee, C and Wiersinga, WJ and Peters-Sengers, H and van der Poll, T}, title = {Quantifying immune dysregulation in pneumonia and sepsis with a parsimonious machine-learning model: a multicohort analysis across care settings and reanalysis of a hydrocortisone randomised controlled trial.}, journal = {The Lancet. Respiratory medicine}, volume = {14}, number = {4}, pages = {327-340}, doi = {10.1016/S2213-2600(25)00429-1}, pmid = {41856148}, issn = {2213-2619}, mesh = {Humans ; *Machine Learning ; *Sepsis/immunology/drug therapy/blood ; *Hydrocortisone/therapeutic use ; Biomarkers/blood ; Female ; Male ; Middle Aged ; Community-Acquired Pneumonia/immunology ; Aged ; Severity of Illness Index ; Predictive Learning Models ; }, abstract = {BACKGROUND: Sepsis is a dysregulated host response to infection resulting in life-threatening organ failure. Although immune dysregulation is central to the sepsis definition, immunomodulation trials enrol participants based on clinical severity, not the extent of dysregulation, which could contribute to treatment heterogeneity. A pragmatic way to quantify immune dysregulation could improve prognostication, help to evaluate treatment responses, and identify individuals most likely to benefit from immunomodulation. We aimed to construct a parsimonious machine-learning tool that defines and quantifies immune dysregulation, thereby supporting biologically informed immunomodulation.

METHODS: In this multicohort analysis and reanalysis of a randomised controlled trial, the primary objective was to derive and validate a categorical and continuous immune dysregulation score that is independent of clinical presentation or outcome. We measured 35 plasma biomarkers reflecting key host response domains in individuals with community-acquired pneumonia (CAP) across different care settings (emergency department, general ward, and intensive care unit) and disease severities using data from three independent cohorts. We applied unsupervised trajectory inference analysis to identify an immune dysregulation gradient captured as discrete immune dysregulation stages (Dysregulated Immune Profile [DIP]) and a continuous score (cDIP; 0-1). We developed two parsimonious machine-learning models to predict the DIP stages and cDIP scores based on 35 biomarkers, and validated their ability to capture immune dysregulation and predict clinical outcomes in five independent cohorts. On the basis of our hypothesis that only individuals with severe immune dysregulation benefit from immunomodulation, we carried out a post-hoc analysis of a randomised trial evaluating hydrocortisone in severe CAP (CAPE COD trial, NCT02517489), assessing treatment effects across DIP stages and the cDIP continuum, and how hydrocortisone influenced dysregulation trajectories over time.

FINDINGS: We organised 398 participants with CAP along a continuum of immune dysregulation from mild to severe on the basis of 35 plasma biomarkers, yielding three dysregulation stages (DIP1-3) and a continuous score (cDIP). Clinical severity proved to be an inadequate proxy for immune dysregulation. A three-biomarker machine-learning framework (procalcitonin, soluble TREM-1, and IL-6) accurately predicted the degree of dysregulation derived from 35 biomarkers (DIP stage accuracy 91·2%; cDIP root mean square error 0·056). Although the framework was not designed for outcome prediction, increased immune dysregulation-reflected in DIP and cDIP-was associated with a gradual rise in mortality (cDIP odds ratio [OR] 1·26 [95% CI 1·13-1·40] per 10% increase, p<0·0001) and secondary infections (OR 1·50 [1·22-1·93] per 10% increase, p=0·0005), independent of clinical severity. The three-biomarker tool was validated in five external cohorts of varying infections, severities, and care settings (n=1191). Reanalysis of the CAPE COD trial showed that hydrocortisone conferred a survival benefit only in participants classified as severely dysregulated by our model (30-day mortality: DIP3 OR 0·25 [0·05-0·85], p=0·042; cDIP ≥0·63 OR 0·21 [0·10-0·72], p=0·011), accompanied by faster immune recovery (time × treatment interaction, p<0·0001). No such effect modification was observed when stratifying participants by clinical severity.

INTERPRETATION: We have provided a publicly available three-biomarker framework to determine the extent of host response dysregulation with potential value for precision-guided immunomodulatory therapy.

FUNDING: EU Horizon 2020.}, } @article {pmid41856334, year = {2026}, author = {Ma, WJ and Zhang, HM and An, ZJ and Tian, Y}, title = {Biochar enhances nitrogen removal capacity in sulfur-driven autotrophic denitrification at low temperatures: Performance evaluation, microbial structure analysis, and metabolic pathway reconstruction.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134438}, doi = {10.1016/j.biortech.2026.134438}, pmid = {41856334}, issn = {1873-2976}, mesh = {*Nitrogen/isolation & purification/metabolism ; *Denitrification/drug effects ; *Sulfur/metabolism ; *Autotrophic Processes/drug effects ; *Charcoal/pharmacology/chemistry ; *Metabolic Networks and Pathways ; Thiobacillus/metabolism ; Bacteria/metabolism/genetics ; Bioreactors/microbiology ; *Cold Temperature ; }, abstract = {Sulfur-driven autotrophic denitrification (SAD) is a low carbon-footprint wastewater treatment process, but its stable operation is hindered by low temperatures. This study found that biochar amendment enhanced the denitrification performance in the SAD process at low temperatures: at 15 °C, the biochar-amended reactor achieved 94.57% nitrogen removal efficiency (NRE); at 10 °C, the control reactor lost denitrification capacity, while the biochar reactor maintained 28.39% NRE. Mechanistic investigations revealed that biochar enhances microbial energy utilization and bioelectrochemical capacity, widens the ecological niche of sulfur-oxidizing bacteria, and enriches Thiobacillus at low temperatures. Metabolic pathway reconstruction reveals that Thiobacillus contains more genes related to nitrogen (nar, nir, nor, nos, nap, nrf, gln, glt, and gdh) and sulfur (dsr, sox, fcc, asr, soe, sat, apr) cycles. Therefore, Thiobacillus is more potent in nitrogen removal and sulfur utilization. However, Sulfurimonas possesses only one pathway for denitrification and sulfur oxidation mediated by sox enzymes. In carbon metabolism, Sulfurimonas contains genes for Calvin-Benson cycle, resulting in its potential for carbon fixation and low-temperature adaptability. Overall, this study proposes a low-carbon strategy to enhance denitrification performance at low temperatures.}, } @article {pmid41856620, year = {2026}, author = {Lan, HY and Yang, XY and Zhang, YH and Lyu, YW and Bao, LL and Yu, YY}, title = {[Study on the characteristics and differences of intestinal microbiota in children with allergic diseases].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {60}, number = {3}, pages = {346-358}, doi = {10.3760/cma.j.cn112150-20251015-00988}, pmid = {41856620}, issn = {0253-9624}, support = {GSWS2024031//Research Project of the Gusu Talent Program of Suzhou City/ ; }, mesh = {Humans ; Child, Preschool ; *Gastrointestinal Microbiome ; Case-Control Studies ; Infant ; Child ; Male ; Female ; *Hypersensitivity/microbiology ; Dermatitis, Atopic/microbiology ; Feces/microbiology ; Food Hypersensitivity/microbiology ; Rhinitis, Allergic/microbiology ; }, abstract = {Objective: Based on metagenomic sequencing technology, this study aims to investigate the characteristics and differences of the intestinal microbiota in children with different allergic diseases, providing a theoretical basis for the early prevention and treatment of allergic diseases. Methods: The study adopted a case-control research method. 214 children with allergic diseases (Group A) who visited the Suzhou Hospital Affiliated to Nanjing Medical University from March 2023 to June 2024 were selected. According to age matching, 93 healthy controls (Group H) who participated in physical examinations during the same period were also included. Fecal samples and clinical data of the subjects were collected. The subjects were grouped according to age and type of allergic disease, and the fecal samples of the subjects were analyzed using metagenomic sequencing technology to study the characteristics and differences of the gut microbiota in different groups. The subjects were divided into 0-1 year old group (A1 and H1), 1-3 year old group (A2 and H2), and≥3 year old group (A3). According to the disease type, A1 was divided into food allergy without atopic dermatitis (F1) group and food allergy with atopic dermatitis (F2) group, A2 was divided into atopic dermatitis (AD) group, allergic rhinitis (AR) group and AD with AR group. A3 was divided into AR group, AD with AR group and AR with asthma (AS) group. Results: With age increase, the number of species annotated at the genus level in the microbiota showed a gradually increasing trend. There were significant differences in the diversity and composition of the intestinal microbiota between the allergic disease group and the control group. In the diversity analysis, it was found that there were differences in species richness between group A and group H (chao index, group A: 955.2±226.1, group H: 762.3±260.9, W=5 664, P<0.000 1), and significant differences in β-diversity between group A2 and group H2, and between group A3 and group AD-AR and group AR-AS (R=0.045, P=0.018, R=0.044, P=0.011). At the species level, the allergic disease group was mainly enriched with Bifidobacterium, Enterococcus, Escherichia, Mediterraneibacter and Blautia, while the control group was mainly enriched with Bifidobacterium. By age group analysis, the relative abundance of Mediterraneibacter and Blautia in group A1 (0-1 years old) was significantly higher than that in group H1 (Mediterraneibacter: A1: 5.2±9.4, H1: 0.9±2.1, W=718, P=0.000 8; Blautia: A1: 3.5±6.0, H1: 1.3±3.2, W=701, P= 0.000 5). In group A2 (1-3 years old), the relative abundance of Bacteroides and Faecalibacterium was significantly higher than that in group H2 (Bacteroides: A2: 5.6±8.7, H2: 3.1±5.8, W=456, P=0.020 8; Faecalibacterium: A2: 2.6±2.8, H2: 1.2±1.9, W=395, P=0.002 8). In the clinical subtype analysis, the relative abundance of Blautia and Fusicatenibacter was significantly increased in AR children (Blautia: AD: 8.0±7.9, AD-AR: 13.5±8.3, AR: 20.2±7.8, H=9.300 8, P=0.009 6; Fusicatenibacter: AD: 0.5±0.9, AD-AR: 1.2±1.6, AR: 2.2±2.4, H=7.878 3, P=0.019 5), and the relative abundance of Escherichia was significantly increased in AD children (AD: 3.3±4.3, AD-AR: 1.8±4.5, AR: 0.8±2.0, H=9.476 6, P=0.008 8). In group A3 (≥3 years old), Mediterraneibacter was significantly enriched (A3: 6.3±6.9, H3: 2.9±1.9, W=571, P=0.039 7), and the relative abundance of Anaerostipes was significantly increased in AR children (AD-AR: 2.9±2.9, AR: 5.2±4.9, AR-AS: 3.2±3.5, H=7.269, P=0.026 4). Conclusion: In infancy, the species of intestinal flora gradually increase with age. There are significant differences in the composition of intestinal flora among children with different allergic diseases. Bifidobacterium, as the main dominant species in infancy, has a lower relative abundance in the allergic disease group at different ages than in the healthy control group, suggesting that the lack of Bifidobacterium may be related to the occurrence and development of allergic diseases.}, } @article {pmid41856866, year = {2026}, author = {Jelen, BI and Baker, BJ}, title = {Mapping environmental microbiomes across an entire country.}, journal = {Trends in microbiology}, volume = {34}, number = {4}, pages = {342-344}, doi = {10.1016/j.tim.2026.02.013}, pmid = {41856866}, issn = {1878-4380}, mesh = {*Microbiota ; Biodiversity ; *Bacteria/classification/genetics/isolation & purification ; Ecosystem ; Denmark ; Metagenomics ; *Environmental Microbiology ; }, abstract = {Microbial diversity underpins ecosystem function and resilience, yet large-scale spatial baselines remain rare. Singleton et al. present a Danish atlas of environmental microbiomes, revealing nationwide patterns of diversity. By emphasizing gamma diversity, they show how nitrifying communities differ in scale and composition between natural and disturbed habitats.}, } @article {pmid41857392, year = {2026}, author = {Zhai, X and Jin, J and Yu, M and Liu, R and Li, J and Liu, Y and Zhang, XH and Liu, J}, title = {Spatial Heterogeneity of Microbial Communities and Biogeochemical Function in Water Column of Site F Cold Seep, South China Sea.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41857392}, issn = {1432-184X}, support = {202172002//the Fundamental Research Funds for the Central Universities/ ; LSKJ202203206//the Science & Technology Innovation Project of Laoshan Laboratory/ ; ZR2022YQ038, ZR2024JQ006//Shandong Province Natural Science Foundation/ ; }, abstract = {Cold seep is a distinctive deep-sea environment mainly formed by methane-rich fluids leaking on the seafloor, gaps remain regarding the influence of seepage on microorganisms inhabiting water column across vertical and horizontal dimensions. Site F cold seep, located at 1,120 m depth on the northern South China Sea (SCS) slope, is one of the most active cold seeps in SCS. We performed 16S rRNA gene and metagenomic sequencing on samples collected by Niskin bottles mounted on Conductivity-Temperature-Depth profiler and Remote Operated Vehicle to analyze the structure and metabolic potentials of microbial communities throughout the water column at Site F. Microbial abundance generally decreased with depth at all sampling spots and was higher at sites adjacent to the seepage compared to those farther away, indicating a potential vertical and horizonal influence of methane seepage on water microbial community. High microbial abundance at deeper depths may attribute to a higher proportion of Gammaproteobacteria, comprised mainly of Alcanivoracaceae, Alteromonadaceae, Marinobacteraceae, methylotrophs represented by Methylophagaceae and Methylococcales (mainly Methylomonadaceae), and sulfur-oxidizing bacteria represented by SUP05 and Ectothiorhodospiraceae. Consistently, the aerobic methane oxidation gene pmoA was more prevalent in the deeper water and was found in four bacterial classes in addition to Gammaproteobacteria. Sulfur-oxidizing genes also exhibited higher abundances at depths and were primarily affiliated with Rhodobacteraceae. These microbes likely play important roles in aerobic oxidation of methane and sulfur, contributing to methane depletion during upward diffusion. By integrating sampling across vertical and horizontal dimensions, we demonstrate that seepage shapes the microbial community and biogeochemical functions in the water column at Site F.}, } @article {pmid41857415, year = {2026}, author = {}, title = {Metagenomic surveillance of zoonotic yellow fever and spillover dynamics at a forest-urban interface.}, journal = {Nature microbiology}, volume = {11}, number = {4}, pages = {847-848}, pmid = {41857415}, issn = {2058-5276}, } @article {pmid41857781, year = {2026}, author = {Alexander, JE and Appleton, C and Beatty, SSK and Brown, DC and Carvell-Miller, L and McKee, TS and Morrison, J and Patterson-Kane, JC and Reynolds, R and Wadulack, S and , }, title = {Cohort profile of the first 2,000 canine enrolees in the Mars Petcare Biobank: demographic, hematologic and serum biochemistry results from March 2022 to December 2024.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {41857781}, issn = {1746-6148}, abstract = {BACKGROUND: The MARS PETCARE BIOBANK™ (MPB) is a study recruiting pets visiting Mars Veterinary Health hospitals in the USA over a ten-year period, with the aim of analysing longitudinal data from thousands of otherwise healthy dogs and cats at their first presentation to identify novel and actionable pet health insights . The present study summarises the baseline demographic, haematologic, and serum biochemistry data recorded for the first 2000 dogs enroled in the MPB study between March 2022 and December 2024 and considers how representative they are of the general population in the United States. RESULTS: The median enrolment age was 3.0 years (0.5–10.0 yrs). The population was 52% male and 48% female with approximately 84% of the population having undergone neutering by their initial study visit. The median enrolment body weight was 20.0 kg (2.5 – 71.5 kg) and the median body condition score was 5/9 (range 3–7). One hundred and twenty eight breeds were represented and 47% of the population were described as mixed breed. The median values for all serum biochemistry and complete blood count parameters were within the applicable reference interval. For certain analytes including serum glucose, amylase, cholesterol, phosphorus, creatine phosphokinase, precision pancreatic lipase, platelet count, haematocrit, and haemoglobin more than 5% of dogs had results outside the reference intervals. On review only 0.25% of dogs were subsequently excluded from continuing the MPB study because the results were considered of clinical significance. CONCLUSIONS: The MPB aims to enable research to deliver insights applicable to the general dog population accessing primary veterinary care in the USA, and recruits accordingly. These data suggest that the first 2,000 dogs recruited in the MPB are comparable in demographics to other studies of the US population. The number of blood test results falling outside of reference intervals (up to 17% depending on analyte), for dogs deemed by veterinarians to be healthy in the context of the clinical history and examination, raises questions around the definition of health and how reference intervals are used. Data gathered during the study is expected to provide valuable information to studies pertaining to genetic, metagenomic, metabolic, dietary, and environmental risk factors associated with early signals of transition to various common diseases.}, } @article {pmid41857851, year = {2026}, author = {Yu, X and Wen, Z and Zhou, W and Zheng, Y and Chen, J and Xiao, WJ and Lin, S and Liang, H and Duan, X and Wang, W and Wu, H and Chen, X}, title = {Respiratory syndromic disease study in Shanghai community population.}, journal = {BMJ open}, volume = {16}, number = {3}, pages = {e103001}, pmid = {41857851}, issn = {2044-6055}, mesh = {Humans ; China/epidemiology ; *Respiratory Tract Infections/epidemiology/microbiology ; Female ; Prospective Studies ; Male ; Adult ; Middle Aged ; Coinfection/epidemiology/microbiology ; Child ; Incidence ; Adolescent ; Young Adult ; Seasons ; Child, Preschool ; Urban Population ; Aged ; }, abstract = {PURPOSE: This prospective community-based cohort study (Acute Respiratory Infection Epidemiological Characteristics Assessment Study (ARI-ECAS)) aims to systematically monitor acute respiratory infection (ARI) incidence, characterise multiple pathogen coinfection patterns and explore microbial landscape dynamics in Shanghai's general population. By integrating syndromic surveillance, molecular diagnostics and metagenomic sequencing, the study seeks to enhance understanding of ARI epidemiology, seasonal variation and host-pathogen interactions to inform predictive modelling and optimise public health interventions in high-density urban environments.

PARTICIPANTS: The study enrolled 15 199 permanent residents from all 16 districts of Shanghai, with baseline oropharyngeal swab samples across five representative districts (Xuhui, Jing'an, Jiading, Songjiang and Fengxian). Inclusion criteria required residency ≥6 months and consent for weekly follow-ups. Exclusion criteria addressed mobility limitations (planned relocation >6 months) and recent ARI history. Participants provided demographic, behavioural and clinical data via the Shanghai Health Cloud platform, with baseline and symptomatic-phase biological samples collected for analysis.

FINDINGS TO DATE: During the initial 8-month surveillance period (May 2024-January 2025), the ARI-ECAS cohort demonstrated critical insights into the epidemiology of acute respiratory infections in Shanghai's urban communities. Among 15 199 participants, 10.96% reported symptomatic episodes, of whom 21.43% experienced recurrent infections. Pathogen detection using targeted next-generation sequencing (tNGS) identified microbial aetiologies in 53.52% of symptomatic cases, revealing a high prevalence of coinfections: 27.96% involved dual pathogens, while 33.01% showed polymicrobial interactions (≥3 pathogens). Notably, 85.09% of symptomatic episodes were self-managed, underscoring a low healthcare-seeking rate (14.91%) consistent with patterns observed in urban China during postpandemic transitions.

FUTURE PLANS: The current phase of data collection will conclude in June 2025; however, syndromic surveillance and tNGS protocols will be sustained to capture multiyear seasonal transmission patterns. To enhance comparative rigour, future protocols will aim to collect samples from participants during asymptomatic periods in the subsequent year to serve as seasonal baseline controls. Building on this foundation, the study will integrate contact behaviour and mobility surveys to quantify parameters critical for understanding pathogen transmission dynamics (eg, household contacts and public transportation usage). Furthermore, pathogen detection and metagenomic data will be combined with transcriptomic and metabolomic profiling in selected cases to model multipathogen interaction networks and delineate host immune response pathways, thereby advancing mechanistic insights into polymicrobial cocirculation.}, } @article {pmid41857857, year = {2026}, author = {Ngoumou, GB and Ngandeu Schepanski, S and Blakeslee, SB and Diedering, A and Twal, E and Raue, SL and Schroeder, M and Wicaksono, WA and Stritter, W and Berg, G and Seifert, G}, title = {Effects of fermented versus unfermented red cabbage on symptoms, immune response, inflammatory markers and the gut microbiome in young adults with allergic rhinoconjunctivitis: a randomised controlled trial protocol.}, journal = {BMJ open}, volume = {16}, number = {3}, pages = {e115290}, pmid = {41857857}, issn = {2044-6055}, mesh = {Humans ; *Conjunctivitis, Allergic/diet therapy/immunology ; Young Adult ; Adult ; *Gastrointestinal Microbiome ; Quality of Life ; Randomized Controlled Trials as Topic ; Adolescent ; *Brassica ; Female ; Biomarkers/blood ; Male ; *Fermented Foods ; }, abstract = {INTRODUCTION: Allergic rhinoconjunctivitis (ARC) is a highly prevalent immune-mediated condition associated with substantial symptom burden, impaired quality of life and increased healthcare use. Emerging evidence highlights the role of the gut microbiome in immune regulation and allergic disease. Fermented foods may contain live microbes (when unpasteurised or uncooked) and bioactive postbiotic metabolites that can modulate immune responses. Despite growing interest in dietary strategies targeting the microbiome, no randomised controlled trial has compared fermented versus unfermented red cabbage for ARC.

METHODS AND ANALYSES: This single-centre, randomised, controlled trial with a sensory-matched, unfermented cabbage comparator investigates the effects of daily consumption of fermented red cabbage for 8 weeks compared with an unfermented red cabbage control in young adults (18-35 years) with ARC. A total of 158 participants will be randomly assigned (1:1). The primary outcome is change in Total Nose and Eye Symptom Score from baseline to week 8. Secondary outcomes include daily symptoms and medication use captured via mobile ecological momentary assessments, quality of life, psychological well-being, gastrointestinal symptoms, systemic inflammatory markers, total IgE, immune cell profile and metagenomic characterisation of stool samples. A nested qualitative component explores participants' experiences and acceptability of the intervention. Analyses will include mixed-effects models, time-series analyses incorporating daily pollen counts and comprehensive microbiome statistics. Safety outcomes and adverse events will also be assessed.

ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Charité-Universitätsmedizin Berlin (EA4/043/25) and is conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. Results will be disseminated through peer-reviewed publications, conference presentations and a lay summary provided to participants. Anonymised datasets and analysis scripts will be made available in public repositories, and metagenomic sequencing data will be deposited in an international sequence archive to ensure transparency and reproducibility.

TRIAL REGISTRATION NUMBER: DRKS00036475.}, } @article {pmid41858204, year = {2026}, author = {Chen, X and Ji, M and Yan, D and Liu, Y and Chen, Y and Dong, R and Shen, L and Takeuchi, N and Kong, W}, title = {Metabolic capacities and potential microbial interactions in red and green snow of the Antarctic Peninsula.}, journal = {The New phytologist}, volume = {250}, number = {5}, pages = {3349-3365}, doi = {10.1111/nph.71089}, pmid = {41858204}, issn = {1469-8137}, support = {32161123004//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 72574092//National Natural Science Foundation of China/ ; }, mesh = {Antarctic Regions ; *Snow/microbiology ; *Microbial Interactions ; Carbon/metabolism ; Color ; Nitrogen/metabolism ; Phosphorus/metabolism ; Bacteria/metabolism/genetics ; Sulfur/metabolism ; }, abstract = {Colored (red and green) snow is widespread in Antarctica due to climate warming. This phenomenon reduces snow albedo, accelerates snowmelt, alters microbial functions, and impacts regional geochemical cycles. Diverse microorganisms are associated with this phenomenon, yet their functions remain poorly understood. We employed metagenomic sequencing to reveal the metabolic interactions and functional specialization within microbial communities of colored snow, focusing on carbon, nitrogen, phosphorus, and sulfur metabolism. While broad metabolic profiles were similar between red and green snow, targeted analysis of specific pathways revealed significant enrichment of denitrification and organic-phosphorus mineralization genes in green snow and labile carbon degradation genes in red snow. Betaproteobacteria were dominant drivers of nitrogen, sulfur, and phosphorus transformation, while diverse eukaryotic algae and bacteria were responsible for carbon fixation. Additionally, we recovered 2257 bacteriophages, 529 algal viruses, and 2302 secondary metabolite gene clusters. Specifically, viruses encoded 126 auxiliary metabolic genes that may influence the elemental cycling of hosts, while secondary metabolites, such as pyoverdine, may assist algal iron acquisition. Our findings offer new insights into the metabolic potentials and interactions of microbial communities in Antarctic colored snow, highlighting their potential relevance to snow biogeochemical processes.}, } @article {pmid41858247, year = {2026}, author = {Groninga, J and Wittig, L and Bouderka, F and Bornemann, TLV and Lipp, JS and Schubotz, F and Keden, S and Probst, AJ and Hinrichs, KU}, title = {Novel Extended Tetraether Lipids Found in a High-CO2 Geyser.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70286}, pmid = {41858247}, issn = {1462-2920}, support = {101118631/ERC_/European Research Council/International ; }, mesh = {*Archaea/metabolism/genetics/chemistry ; *Lipids/chemistry ; *Carbon Dioxide/analysis/metabolism ; *Groundwater/microbiology/chemistry ; }, abstract = {The growing research into the archaeal lipidome has uncovered a remarkable structural diversity in isoprenoidal glycerol dialkyl glycerol tetraethers (iGDGTs) and revealed complex membrane adaptations, especially in extreme environments. We performed a comprehensive analysis of the lipidome from the subsurface aquifer of the CO2-rich, cold-water Geyser Andernach (Germany), using ultra-high-resolution mass spectrometry. We detected iGDGT-0, presumably derived from the dominant community member Candidatus Altiarchaeum, providing supporting evidence for its ability to synthesise tetraethers, as previously predicted from metagenomic data. Beyond the typical iGDGT-0 and acyclic glycerol trialkyl glycerol tetraether (iGTGT-0), we discovered novel structural derivatives, here referred to as extended iGDGTs and iGTGTs, characterised by the asymmetrical addition of up to two isoprenoid units to only one of their hydrocarbon side chains, analogous to those found in extended archaeols. The apparent absence of GDGT ring synthase A and B genes in the corresponding metagenome-assembled genome raises the possibility that the producing archaea may utilise extended iGDGTs as a membrane adaptation to cope with the nutrient-depleted conditions of the geyser environment, highlighting the adaptive flexibility of archaea to extreme physicochemical conditions.}, } @article {pmid41858251, year = {2026}, author = {Morissette, O and Côté, G and Couillard, MA and Pouliot, R and Bernatchez, L}, title = {Trait-Based Biomonitoring Using eDNA Metabarcoding to Assess Anthropogenic Disturbances on Freshwater Fish Communities.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70131}, pmid = {41858251}, issn = {1755-0998}, mesh = {Animals ; Quebec ; *DNA Barcoding, Taxonomic/methods ; *Fishes/classification/genetics ; *DNA, Environmental/genetics ; Rivers ; *Environmental Monitoring/methods ; Fresh Water ; Biodiversity ; Ecosystem ; *Biological Monitoring/methods ; *Biota ; Extrachromosomal DNA ; *Metagenomics/methods ; }, abstract = {Various anthropogenic disturbances affect the succession of aquatic habitats along dendritic river networks. Bioindicator taxa, such as fish, can be used to assess the effects of these disturbances on habitat quality. Environmental DNA (eDNA) metabarcoding offers a novel approach to complement traditional sampling and analysis of bioindicator taxa. Here, we apply a trait-based biomonitoring framework, focusing on fish tolerance to pollution, to assess habitat quality and fragmentation within two watersheds in southern Québec (Canada). We sampled 193 sites within the dendritic networks of the Châteauguay and St. François watersheds and estimated fish community tolerance indices on the basis of 12S metabarcoding. We found a significant correlation between the fish community tolerance index and environmental factors such as subwatershed land use, precipitation and elevation. We also found that river fragmentation caused by dams affected fish assemblages and native fish movement but also prevented the spread of the non-native common carp. Finally, we applied random-forest modelling to predict the tolerance of fish communities to disturbances in unsampled areas, providing a broader understanding of habitat quality within catchments. Our research highlights how eDNA metabarcoding for large-scale biomonitoring and river fragmentation studies provides a cost-effective and non-invasive method for assessing fish biodiversity and riverine ecosystem health.}, } @article {pmid41858257, year = {2026}, author = {Geerts, MM and Curto, M and Alverson, AJ and Stone, J and Gante, HF}, title = {Disentangled Assembly Graphs Reveal Hidden Eukaryotic Diversity in eDNA Metagenomic Data.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70128}, pmid = {41858257}, issn = {1755-0998}, support = {STG/21/044//KU Leuven Research Fund/ ; 11Q4724N//Fonds Wetenschappelijk Onderzoek/ ; UIDP/50027/2020//InBIO Programático FUI 2020-2023/ ; DEB-2331644//Division of Environmental Biology/ ; }, mesh = {*Metagenomics/methods ; *Diatoms/genetics/classification ; Extrachromosomal DNA/genetics ; *Computational Biology/methods ; Phylogeny ; Czech Republic ; United States ; *Biodiversity ; *DNA, Environmental/genetics ; Fresh Water ; *Eukaryota/genetics/classification ; Sequence Analysis, DNA ; }, abstract = {Genome assembly graphs contain valuable yet frequently overlooked information that can enhance assembly completeness by revealing contig connectivity. Here, we demonstrate how leveraging these information-rich structures enables the discovery of hidden microeukaryotic diversity in environmental DNA shotgun metagenomic datasets. While GetOrganelle has previously been used for organellar genome assembly from isolated tissues, we present its first application to water eDNA metagenomic data, using diatoms as an example. We tested the efficiency of this organellar genome assembly tool on three freshwater eDNA metagenomic datasets with varying diatom abundances, finding that GetOrganelle alone yields fragmented scaffolds due to mixed-species complexity. By implementing manual disentanglement of assembly graphs, we successfully recovered complete organellar genomes from these assemblies. From high-abundance bloom samples, we recovered complete plastomes of Stephanodiscus hantzschii with 99.9% pairwise identity across distant geographical locations (USA and Czech Republic). From a lower abundance non-bloom sample, we reconstructed a potentially novel Cyclotella plastome with only 94.0% identity to its closest available reference, Cyclotella atomus. Our assembly quality assessment confirmed effective manual disentanglement even at low diatom abundances. By integrating sequence similarity, gene order conservation and phylogenetic analysis, we achieved robust species-level resolution and resolved previous taxonomic uncertainties. Our findings demonstrate that mining eDNA metagenomic data with GetOrganelle reveals previously hidden microeukaryotic diversity and provides higher taxonomic resolution than traditional binning methods. This approach proves especially valuable for microeukaryotes, where reference organellar genomes remain underrepresented in existing databases.}, } @article {pmid41858380, year = {2026}, author = {Beran, P and Rost, M and Beranová, K and Kváč, M and Stehlíková, D and Udoh, OE and Jozová, E and Čurn, V}, title = {genCRC32: collision-free CRC32-based hashing of DNA sequences.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbaf315}, pmid = {41858380}, issn = {2635-0041}, abstract = {MOTIVATION: Efficient and collision-free hashing of DNA sequences is essential for accuracy and performance in bioinformatics applications such as genome assembly, sequence alignment, and metagenomic classification. Traditional hashing methods often result in collisions, impacting the precision and/or performance of downstream analyses. Thus, it is highly advantageous to have hashing functions that guarantee collision-free mappings for DNA sequences, particularly for k-mers up to length 16, where practical limits for 32-bit hashing are reached. In this study, we evaluate genCRC32 as a hashing primitive, reporting collision behavior, bucket balance, sensitivity to single-base changes, and speed to inform its potential use in downstream tools. Evaluation within specific software tools is outside the scope of this paper and is planned as future work.

RESULTS: We present genCRC32, an innovative hashing method that integrates a straightforward preprocessing step (gen32) with CRC32 hashing, specifically identifying eight CRC32 polynomials that ensure collision-free hashing for all DNA k-mers up to 16 nucleotides in length. Through extensive empirical evaluations, genCRC32 demonstrated zero collisions for these k-mers, achieving a one-to-one mapping without auxiliary data structures. Benchmark tests confirmed minimal computational overhead introduced by preprocessing, maintaining hashing performance comparable to established methods such as MurmurHash3 and xxHash32.

The source code for genCRC32 is publicly available at: https://github.com/berybox/genCRC32. The implementation is provided in Go (version 1.24) and leverages only standard libraries, ensuring portability and ease of integration into existing bioinformatics workflows.}, } @article {pmid41858392, year = {2026}, author = {Tu, W and Zeng, P and Wu, Z and Li, Z and Yu, T and Zhang, W and Chen, R and Liang, L}, title = {A case report of brain abscess caused by Nocardia cyriacigeorgica identified by metagenomic next-generation sequencing.}, journal = {World journal of emergency medicine}, volume = {17}, number = {2}, pages = {199-201}, pmid = {41858392}, issn = {1920-8642}, } @article {pmid41858535, year = {2026}, author = {Zhang, L and Chen, S and Li, H and Li, L and Liu, H}, title = {Molecular epidemiology and genomic analysis of bulbul coronavirus in Guangdong, China.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1659863}, pmid = {41858535}, issn = {2297-1769}, abstract = {INTRODUCTION: Bulbul coronavirus (BuCoV), a delta coronavirus recently identified in passerine birds, remains poorly characterized regarding its ecology and evolutionary dynamics. This study aimed to determine the prevalence of BuCoV in wild avifauna, clarify its evolutionary relationship with other delta coronaviruses, and identify genetic signatures potentially relevant to host adaptation and cross-species transmission in southern China.

METHODS: From 2023 to 2024, we conducted molecular surveillance across 12 regions in Guangdong Province, China. A total of 2,145 avian fecal samples were collected and screened for BuCoV using real-time quantitative PCR. The complete genomes of representative strains were obtained using next-generation sequencing. Subsequent analyses included phylogenetic reconstruction using maximum likelihood methods, recombination detection using RDP4 and SimPlot, and comparative amino acid analysis.

RESULTS: BuCoV was detected exclusively in Shenzhen (3/168, 1.78%), with all positive samples originating from bulbuls (Pycnonotus spp.). The Shenzhen strain GD2411 exhibited the highest nucleotide identity with BuCoV strains HKU11-796 (97.26%) and HKU11-934 (96.79%), but far lower similarity (78.9%-82.4%) to other delta coronaviruses. Phylogenetic analysis placed GD2411 in a monophyletic clade with HKU11 strains. Recombination analyses revealed mosaic structures within the spike (S) gene, involving multiple coronavirus lineages. Thirty-one amino acid substitutions were detected in the S protein, together with mutations in RdRp, 3CLpro, and nucleocapsid.

DISCUSSION: These findings suggest that BuCoV GD2411 emerged through inter-lineage recombination and is undergoing adaptive evolution, particularly in the spike protein. The detection of BuCoV exclusively in Shenzhen, a critical node in the East Asian-Australasian Flyway, suggests that migratory birds may facilitate viral dissemination. The identified mutations may affect viral replication, host adaptation, or immune evasion. These findings provide essential baseline genomic and epidemiological data critical for understanding BuCoV diversity and assessing potential zoonotic risks in southern China.}, } @article {pmid41858674, year = {2026}, author = {Zholdasbek, A and Tekebayeva, Z and Kulzhanova, K and Abzhalelov, A and Bekshin, Z and Yevneyeva, D and Saylau, M and Li, X and Tan, Z and Wang, Z and Temirkhanov, A and Nurbekova, Z}, title = {Microbiome and plant relationship: a symbiosis against phytopathogens.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1722279}, pmid = {41858674}, issn = {1664-462X}, abstract = {Phytopathogens are among the major biotic stressors limiting global crop productivity. Conventional control methods, including chemical pesticides and fungicides, have contributed to pathogen resistance, environmental pollution, and soil degradation, highlighting the need for sustainable alternatives. This review highlights innovative, eco-friendly strategies that exploit plant-microbe interactions to enhance plant health and resilience across diverse agroecosystems. Rhizosphere-, phyllosphere-, and endosphere-associated microbial assemblages contribute to plant immune enhancement through induced systemic resistance, competitive nutrient exclusion, antimicrobial metabolite production, and mycoparasitism. The review emphasizes the functional roles of beneficial microbial communities and the emerging applications of synthetic consortia and bio-organic fertilizers to improving disease suppression, nutrient use efficiency, and soil fertility. In addition, recent progress in omics-based tools and microbial formulation technologies is discussed as a key driver for translating laboratory findings into practical field applications. However, large-scale implementation remains challenged by high research costs, limited metagenomic infrastructure, and the lack of standardized microbial formulations across environments. Strengthening institutional capacity, integrating omics-based tools, and improving technology transfer will be essential to unlock the full potential of microbiome-based pathogen control. Overall, this review highlights microbiome-based interventions as a sustainable alternative to chemical-intensive plant protection strategies under changing environmental conditions.}, } @article {pmid41859061, year = {2026}, author = {Wang, Z and Yang, R and Xiao, Y and Huang, B and Yang, Z and Yang, L}, title = {Primary Cutaneous Aspergillosis Due to Aspergillus flavus in an Immunocompetent Patient.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {565781}, pmid = {41859061}, issn = {1178-6973}, abstract = {Invasive aspergillosis is a life-threatening infection caused by Aspergillus species, affecting the lungs, central nervous system, nasal and orbital regions, and skin. Primary cutaneous aspergillosis (PCA) occurs through direct skin inoculation via trauma, burns, or surgical wounds, with Aspergillus fumigatus, Aspergillus flavus, and Aspergillus niger as common causative species, and is rare in immunocompetent individuals. We report a case of PCA in a 56-year-old immunocompetent patient with facial and right ankle ulcers, persisting for two years. The patient had no history of diabetes, corticosteroid use, or immunodeficiency. Fungal culture and metagenomic next-generation sequencing (mNGS) confirmed A. flavus infection. Voriconazole therapy, surgical debridement, and specialized wound care led to the gradual healing of the ulcers. This case highlights the importance of early diagnosis and intervention to prevent infection spread and progression to systemic aspergillosis or septic shock.}, } @article {pmid41859064, year = {2026}, author = {Gu, P and An, X and Wei, Y and Xu, W and Han, Y and Gao, Q and Liu, S and Bi, Y}, title = {Elusive Diagnosis of Recurrent Subcutaneous Emphysema: Nocardia farcinica Infection in an Immunocompetent Female Patient.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {556094}, pmid = {41859064}, issn = {1178-6973}, abstract = {This case report describes an immunocompetent female with recurrent subcutaneous emphysema and refractory soft tissue infections involving multiple non-contiguous sites-bilateral breasts, chest wall, and upper limb-over seven years, consistent with disseminated nocardiosis. Initial presentations mimicked bacterial mastitis, with localized swelling, erythema, crepitus, and elevated inflammatory markers. Despite repeated incision and drainage procedures, antibiotic therapies, and bilateral mastectomies, symptoms recurred persistently. Conventional microbial cultures repeatedly failed to identify a pathogen, while metagenomic next-generation sequencing (mNGS) of a late-stage chest wall lesion ultimately revealed Nocardia farcinica, an opportunistic actinomycete with a known propensity for systemic dissemination even in immunocompetent hosts. The patient's atypical clinical course-marked by multifocal gas-forming soft tissue necrosis, chronic recurrence, and resistance to empiric treatments-underscores the diagnostic challenges posed by fastidious pathogens like Nocardia. Key lessons include the utility of mNGS in identifying culture-elusive organisms, the importance of considering nocardiosis in refractory subcutaneous infections regardless of immune status, and the necessity of prolonged, targeted antimicrobial regimens (eg, sulfonamides) combined with surgical intervention. This case highlights evolving paradigms in managing complex disseminated infections through advanced genomic diagnostics and multidisciplinary approaches.}, } @article {pmid41859067, year = {2026}, author = {Jiang, X and Wu, L and Duan, S and Bian, J and Lv, T and Zheng, L and Zhao, Y and Shen, P and He, J and Chen, Y}, title = {Long-Term Antibiotic-Driven Gut Microbiota Disruption Promotes Toxigenic Clostridioides difficile Proliferation: A Four-Year Retrospective Study of a Single ICU Patient.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {562973}, pmid = {41859067}, issn = {1178-6973}, abstract = {OBJECTIVE: This four-year longitudinal study of a single critically ill patient leverages deep temporal profiling to unravel the dynamic interplay between antibiotic pressure, gut microbiota, and Clostridioides difficile (C. difficile) colonization, providing temporal insights unattainable through cross-sectional designs.

METHODS: We performed a retrospective analysis of one critically ill patient (2015-2019). Sixty-four fecal samples were subjected to toxigenic C. difficile culture and metagenomic sequencing. To isolate short-term effects, we implemented a 7-day retrospective window, categorizing each sample based on antibiotic exposure in the preceding week: no antibiotics, monotherapy, or polypharmacy.

RESULTS: Antibiotic exposure significantly reduced microbial diversity and promoted dysbiosis. Crucially, we identified a transitional C. difficile colonization state (Tcd±) that potentially determines progression to toxigenic (Tcd+) or non-toxigenic (Tcd-) outcomes. Analysis using the 7-day window revealed that intensive antibiotic pressure was strongly associated with successional progression towards toxigenic dominance. Conversely, brief antibiotic-free intervals were linked to partial restoration of microbial network complexity and a competitive landscape favoring non-toxigenic strains.

CONCLUSION: This deep temporal profiling of a single case provides novel, hypothesis-generating insights. The identification of a transitional colonization state and the association between short-term antibiotic pressure and colonization outcomes define critical dynamics for future validation. These findings highlight the potential of longitudinal data to inform precise antibiotic stewardship strategies in high-risk, critically ill populations.}, } @article {pmid41859237, year = {2026}, author = {Xiao, Y and Zhao, R and Zhao, W and Wang, P and Xiao, X and Peng, X and Jing, H}, title = {Genomics-based insights into the expanded diversity and adaptation strategies of hadal trench anammox bacteria.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag011}, pmid = {41859237}, issn = {2730-6151}, abstract = {Anaerobic ammonium oxidation (anammox) bacteria are an important functional guild in the nitrogen cycle and contribute up to 50% of nitrogen loss in the global ocean. Hadal trenches have been recognized as a hotspot of marine biogeochemical cycles; however, the metabolic traits, ecological adaptations, and potential origins of anammox bacteria in this critical habitat remain largely unexplored. Here, we reconstructed eight anammox metagenome-assembled genomes from sediments of four hadal trenches (Diamantina, Kermadec, Mariana, and Yap), which represent four out of the five distinct anammox bacterial families (i.e. Candidatus Scalinduaceae, Ca. Anammoxibacteraceae, Ca. Subterrananammoxibiaceae, and Ca. Bathyanammoxibiaceae). The dominant trench anammox bacteria, affiliated with Ca. Scalindua, were similar to those found in shallow coastal sediments and oxygen-deficient seawaters. Beyond the core anammox metabolism, the hadal Ca. Scalindua genomes contain genes encoding cyanase and urease, indicating that they can utilize cyanate and urea besides ammonium to thrive in the hadal trenches. Compared to trench-derived Ca. Subterrananammoxibiaceae and Ca. Bathyanammoxibiaceae, ABC-type Fe[3+] transporter and sulfate transporter CysZ could help trench-derived Ca. Anammoxibacteraceae genomes to uptake Fe[3+] and synthesize sulfur-containing amino acids. Molecular clock analysis suggests that the ancestors of the hadal anammox bacterial lineages appeared on Earth 1.46-0.07 billion years ago, significantly earlier than the geological formation of the trenches. The first hadal anammox bacteria were likely derived from shallower sediments and were transported into the trenches via sediment wasting. Overall, our study reveals a remarkable diversity of hadal anammox bacteria and their origin as well as survival strategies in hadal sediments.}, } @article {pmid41859321, year = {2026}, author = {Salama, RA and Abdel Kader, RG and Wadid, NA}, title = {Artificial intelligence in combating challenges in antimicrobial resistance: a narrative review.}, journal = {Infection prevention in practice}, volume = {8}, number = {2}, pages = {100522}, pmid = {41859321}, issn = {2590-0889}, abstract = {Antimicrobial resistance (AMR) is a major global health challenge that threatens the effective prevention and treatment of infections. It arises from increasing resistance rates, limited diagnostic capacity, inappropriate antimicrobial use, and a declining pipeline of new antibiotics. These challenges highlight the need for innovative approaches to complement existing AMR control strategies. Artificial intelligence (AI) has emerged as a valuable tool to address the complexity and scale of AMR. This narrative review examines how AI can be more effectively integrated into key components of AMR management. By analysing large clinical and laboratory datasets, AI-based surveillance and predictive models enable near real-time monitoring of resistance patterns and early outbreak detection. AI-powered diagnostic tools, including image analysis and genomic methods, improve rapid pathogen identification and prediction of antimicrobial susceptibility. In clinical practice, AI-driven decision support systems strengthen antimicrobial stewardship by optimizing prescribing and monitoring antibiotic use. In addition, deep learning approaches accelerate antimicrobial drug discovery and repurposing, reducing development timelines. AI also enhances the detection and surveillance of resistance genes through genomic and metagenomic analyses across human, animal, and environmental settings. Despite its potential, AI applications in AMR face challenges related to data quality, bias, interoperability, privacy, and clinician adoption. Therefore, AI should be seen as a tool that supports, rather than replaces, existing AMR strategies. When regulated well and integrated within One Health frameworks, AI can strengthen surveillance, improve treatment decisions, and support evidence-based interventions to curb AMR.}, } @article {pmid41859442, year = {2026}, author = {Wang, Y and Zhang, L and Huang, W and Wang, N and Sun, M and Wu, L and Wang, W and Shi, C}, title = {Metagenomic analysis of the community structure and functional potential of Tamarix rhizosphere microbiomes along a soil salinity gradient.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1756020}, pmid = {41859442}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil salinization strongly shapes rhizosphere microbial communities and their functional potential in arid ecosystems. Tamarix is a key halophytic shrub in desert saline-alkali environments, yet how its rhizosphere microbiomes respond to natural salinity gradients remains insufficiently understood. Here, we compared community structure, functional potential, and potential salt-adaptation strategies across a soil salinity gradient.

METHODS: Rhizosphere soils of Tamarix were collected from four sites (S1-S4) in Xinjiang, China spanning increasing salinity. Soil physicochemical properties were measured, followed by shotgun metagenomic sequencing. Taxonomic profiles and functional annotations were generated from metagenomic data and compared among salinity groups.

RESULTS: Salinity was associated with clear shifts in community composition. Bacteria dominated at low-to-moderate salinity, whereas archaeal relative abundance increased at higher salinity, with Euryarchaeota becoming dominant in the high-salinity group. Functional profiling indicated that core metabolic pathways remained prevalent along the gradient, suggesting relative stability in overall metabolic capacity. However, higher salinity was accompanied by enrichment of functions linked to genetic information processing (e.g., translation and replication/repair) and ion transport, while lipid metabolism, cell motility, and signal transduction were reduced.

DISCUSSION: Together, these results support a salinity-driven transition in microbial functional strategy from "growth expansion" toward "homeostasis maintenance." Under high salinity, microbes appear to allocate more resources to maintaining cellular integrity and coping with stress, consistent with the observed enrichment of genetic information processing and repair-related functions. Mechanistically, the increased representation of Na[+]/H[+] antiporter systems and V/A-type ATPases in the very high salinity group suggests that energy-dependent ion homeostasis is a prominent adaptation, helping regulate intracellular ion balance and mitigate salt toxicity. In contrast, pathways for compatible solute synthesis (e.g., betaine and ectoine biosynthesis) were relatively reduced, indicating that osmoprotection may rely less on de novo solute production and more on ion regulation and maintenance processes along this gradient. Overall, the metagenomic evidence clarifies how Tamarix rhizosphere microbiomes restructure taxonomically and functionally with increasing salinity and highlights key candidate mechanisms underpinning salt-stress adaptation. These insights provide a microbial basis for understanding plant-microbe interactions in desert saline-alkali soils and may inform ecological restoration and management in salinized regions.}, } @article {pmid41859445, year = {2026}, author = {Huang, Y and Liang, Q and Shen, Y and Chen, J and Xu, W}, title = {Oral microbiome dysbiosis in autism spectrum disorder: the oral-gut-brain axis and future perspectives: a narrative review.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1783810}, pmid = {41859445}, issn = {1664-302X}, abstract = {Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a steadily increasing global prevalence, yet its etiology remains largely unclear. Emerging evidence suggests that oral microbiome dysbiosis may contribute to the pathogenesis of ASD, potentially through the oral-gut-brain axis, although the exact role and causality remain to be fully established. In this narrative review, we synthesize recent clinical and metagenomic evidence on oral microbiome alterations in ASD and critically evaluate the potential pathways through which these microbial imbalances may impact neurodevelopmental outcomes. We summarize the key host-microbe interactions, including inflammatory signaling, epithelial barrier disruption, and immune-neural crosstalk, while emphasizing that direct causal evidence is still limited. Dysbiosis in individuals with ASD is characterized by altered microbial communities, including increased Streptococcus and decreased Prevotella, which correlate with clinical symptom severity. Moreover, metagenomic profiling has indicated the presence of potential biomarkers in the oral microbiome, which may serve as promising noninvasive diagnostic tools for ASD. While the clinical applications of oral microbiome diagnostics are still in the early stages, we explore the challenges and opportunities for developing these biomarkers for risk stratification. Finally, we outline future research directions that could enhance the understanding of the oral microbiome's role in ASD and facilitate the development of personalized intervention strategies.}, } @article {pmid41859451, year = {2026}, author = {Cristofolini, M and Ronsivalle, M and Pramazzoni, M and Zaccarini, G and Pizzamiglio, V and Solieri, L}, title = {Role of microbial interactions in the impaired cultivability of thermophilic lactic acid bacteria in natural whey starter for Parmigiano Reggiano PDO cheese production.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1755652}, pmid = {41859451}, issn = {1664-302X}, abstract = {Natural whey starter (NWS) cultures play a pivotal role in the production of Parmigiano Reggiano (PR) Protected Designation of Origin (PDO) cheese; however, their microbial ecology and functional dynamics remain only partially understood. In particular, Lactobacillus delbrueckii subsp. lactis, a dominant species in type-D NWS communities, exhibits impaired cultivability that limits its isolation and characterization. Consequently, most studies have focused on strain variability within Lactobacillus helveticus, which is predominant in type-H NWS communities. In this study, we evaluated the effects of 14 different medium supplementations on the recovery and maintenance of L. delbrueckii subsp. lactis isolates from two PR NWS samples representatives of type-D and type-H communities. Although most supplementations increased lactobacilli plate counts compared with the control MRS medium, they failed to sustain cell viability during the purification for culture collection establishment. Moreover, these media altered species ratios in favor of L. helveticus, even when L. delbrueckii dominated the community according to metagenomic profiling (type-D NWS). Supplementation of MRS medium with cysteine and formic acid enabled the recovery of viable L. delbrueckii subsp. lactis isolates, accounting for 35% of the strains obtained from type-D NWS. Cross-feeding experiments further revealed that co-culturing L. delbrueckii with the formate-producing Streptococcus thermophilus significantly enhanced milk acidification compared with monocultures, indicating a beneficial metabolic interaction. In contrast, no such improvement was observed in the presence of L. helveticus, likely due to negative interactions with L. delbrueckii subsp. lactis. Accordingly, the impaired cultivability of L. delbrueckii subsp. lactis could thus be partially alleviated either in co-culture with S. thermophilus or under axenic conditions mimicking natural metabolite exchange between these species.}, } @article {pmid41860433, year = {2026}, author = {Boers, D and Chapleur, O and Andersson, AF and Schnürer, A}, title = {Comparing the performance of functional versus taxonomic metagenomics for detecting ammonia disturbances in the biogas system.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {5}, pages = {}, pmid = {41860433}, issn = {1574-6941}, support = {//Swedish University of Agricultural Sciences/ ; P2022-00552//Swedish Energy Agency/ ; 2022-06725//Swedish Research Council/ ; }, mesh = {*Ammonia/analysis/metabolism ; *Metagenomics/methods ; *Biofuels/analysis/microbiology ; *Bioreactors/microbiology ; *Bacteria/genetics/classification/metabolism ; }, abstract = {Biogas is a renewable energy source with great potential, but its production is frequently hindered by process disturbances, of which a high ammonia concentration is one common cause. It is desirable that such disturbances are found as early as possible; metagenomics data has the potential to improve this detection. This study compares functional and taxonomic aspects of metagenomics data, hypothesizing that functional data will perform better for detecting ammonia disturbances. The hypothesis was tested by metagenomic sequencing of samples from three independent studies, which followed lab-scale reactors during ammonia disturbances. The resulting sequences were used to predict genes, which were functionally and taxonomically annotated. The read counts of these features were fitted to disturbance states and ammonia concentrations of reactor samples using regularized regression, which allowed filtering out irrelevant features even with limited sample sizes. Within studies, taxonomic data had similar or better performance in detecting ammonia disturbances and in fitting ammonia concentrations. When applying trained models to other studies however, while performance was generally poor, functional models more often performed better compared to taxonomic models than the other way around. All in all, our hypothesis that functional metagenomics would outperform taxonomic metagenomics only found limited support.}, } @article {pmid41860453, year = {2026}, author = {Shen, S and Zhao, S and He, Z and An, X and Dong, J and Wang, L and Ji, W and Li, A}, title = {The Efflux-Two-Component System (TCS)-Virulence Axis Drives Resistance-Virulence Convergence in Aquatic "Superhost Precursors" under Pollution Stress.}, journal = {Environmental science & technology}, volume = {60}, number = {15}, pages = {11253-11266}, doi = {10.1021/acs.est.5c09604}, pmid = {41860453}, issn = {1520-5851}, mesh = {Virulence ; Anti-Bacterial Agents ; }, abstract = {The coexpression of antibiotic resistance and virulence traits in aquatic bacteria represents an emerging ecological and public health threat, yet the mechanisms underlying their coordinated regulation under complex environmental pressures remain unclear. In this work, we integrated metagenomic, proteomic, and metabolomic data sets from surface water samples across the Yangtze River Basin in Jiangsu Province to elucidate the drivers of resistance-virulence convergence under multipollutant stress. Among 392 multidrug-resistant (MDR; resistant to ≥3 antibiotic classes) isolates, approximately 5% were identified as "culturable superhost precursors" exhibiting pandrug-resistant (PDR; resistant to ≥10 antibiotic classes) phenotypes. Multiomics analyses indicated frequent colocalization and synchronous activation of antibiotic resistance genes (ARGs) and virulence factors (VFs) in these environmental reservoirs. Functional assays under subinhibitory antibiotic exposure demonstrated enhanced cytotoxicity and efflux activity, accompanied by the upregulation of tolC and two-component regulators evgA/evgS. Together, these results characterize a putative redox-coupled efflux-two-component system (TCS)-virulence functional axis that synchronizes adaptive gene expression under pollution stress. Crucially, our findings challenge traditional antimicrobial resistance (AMR) surveillance approaches, which rely primarily on static gene abundance metrics, by demonstrating that the dynamic regulatory activation of this axis provides a more sensitive indicator of environmental health risks. Furthermore, tolC and evgA were identified as potential transcript-level biomarkers, providing a proof of concept for environmental antimicrobial resistance early warning tools within the One Health framework.}, } @article {pmid41860568, year = {2026}, author = {Zhang, Y and Wu, Y and Li, X and Ren, T and Zhang, H and Chen, J}, title = {Klebsiella enrichment is associated with disease severity in ulcerative colitis.}, journal = {Journal of applied microbiology}, volume = {137}, number = {4}, pages = {}, doi = {10.1093/jambio/lxag079}, pmid = {41860568}, issn = {1365-2672}, mesh = {Humans ; *Colitis, Ulcerative/microbiology ; Feces/microbiology ; Prospective Studies ; *Klebsiella/isolation & purification/genetics/physiology ; Female ; Severity of Illness Index ; Male ; Adult ; Middle Aged ; *Gastrointestinal Microbiome ; Intestinal Mucosa/microbiology ; }, abstract = {BACKGROUND AND OBJECTIVE: Ulcerative colitis (UC), a chronic inflammatory bowel disease. This study uniquely undertook a parallel, severity-stratified comparison of both fecal and mucosal microbiota and metabolites in UC patients. Our objective was to identify niche-specific (fecal vs. mucosal) and severity-associated microbial and metabolic signatures, clarifying its potential clinical utility.

METHODS: A prospective cohort study (ChiCTR2300071816) enrolled 83 UC patients (≥18 years) from the First Affiliated Hospital of Nanjing Medical University and Northern Jiangsu People's Hospital (Jan 2022-Dec 2024) and 30 healthy controls. Clinical data, stool, and rectal mucosal samples were collected. Metagenomic sequencing and metabolomics were performed. Disease severity was stratified by modified Mayo score to analyze microbiota diversity, differential genera, metabolites, and enriched metabolic pathways.

RESULTS: Fecal microbiota α-diversity was significantly lower in UC vs. controls (Shannon index 4.15 vs. 5.44, P = 0.005); mucosal diversity showed no difference (P = 0.63). Beta diversity did not differ. Severe UC exhibited a non-significant decrease in α-diversity (fecal: 3.99 vs. 4.37, P = 0.14; mucosal: 3.40 vs. 3.72, P = 0.92), significantly higher fecal/mucosal Klebsiella abundance, and lower Erysipelatoclostridium and Blautia abundance vs. mild-to-moderate UC. Metabolomics identified 363 fecal differential metabolites (e.g. allopurinol, histidine), enriching tyrosine, and alanine/aspartate/glutamate metabolism pathways. Mucosal analysis revealed 127 differential metabolites (e.g. quinic acid, sphingosine), implicating sphingolipid metabolism and lysine synthesis.

CONCLUSION: UC demonstrates gut dysbiosis and metabolic disruption correlating with severity. Elevated Klebsiella abundance suggests a pathogenic role in progression. Distinct fecal and mucosal metabolic pathway alterations provide novel insights for disease classification and therapeutic targeting.}, } @article {pmid41860726, year = {2026}, author = {Stevens, KA and de Souza, JO and Li, H and Ouro-Djobo, A and Alabi, OJ and Al Rwahnih, M}, title = {Agave associated crinivirus A: a novel monopartite crinivirus homolog isolated from agave.}, journal = {Archives of virology}, volume = {171}, number = {4}, pages = {}, pmid = {41860726}, issn = {1432-8798}, abstract = {We describe the complete genome of the first monopartite and putative member of the genus Crinivirus which we propose naming agave associated crinivirus A (AaCA). AaCA was identified by high-throughput sequencing in an Agave tequilana leaf sample during a routine metagenomic screening of Agave plants from California. The 16,161 bp genome contains the protein hallmarks of the family Closteroviridae, the HSP70h and the three coat protein homologs (CPh, CP, CPm), along with the open reading frames (ORFs) unique to criniviruses. Two ORFs downstream of the CPm are unique to AaCA. The monopartite nature of the genome was verified by PCR and Sanger sequencing. Phylogenetic analysis of the HSP70h gene clusters AaCA basally with existing criniviruses.}, } @article {pmid41860897, year = {2026}, author = {Olaleye, M and O'Ferrall, AM and Goodman, RN and Kabila, DW and Peters, M and Falq, G and Samuel, J and Doyle, D and Gomez, D and Oloruntuyi, G and Isah, S and Adetunji, AS and Farley, E and Evans, NJ and Sherlock, M and Roberts, AP and Amirtharajah, M and Ainsworth, S}, title = {Shotgun metagenomic analysis of the oral microbiomes of children with noma.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {3}, pages = {e0014118}, pmid = {41860897}, issn = {1935-2735}, mesh = {Humans ; Metagenomics ; *Microbiota/genetics ; *Noma/microbiology ; *Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; Child ; Female ; Male ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; *Mouth/microbiology ; Dysbiosis/microbiology ; Treponema/genetics/isolation & purification ; Shotgun Sequencing ; Child, Preschool ; }, abstract = {Noma is a rapidly progressive orofacial gangrene that predominantly affects children living in extreme poverty. Despite its documentation since antiquity and its designation as a World Health Organisation Neglected Tropical Disease in 2023, the microbiological cause of noma remains poorly understood, with no specific organisms confidently identified as definitive aetiological agents. Here, we present the first deep shotgun metagenomic profiling of oral saliva microbiomes from 19 Nigerian children with acute noma. Our analyses of this preliminary study reveal marked microbial dysbiosis in noma microbiomes, with machine learning and multivariate statistical analyses indicating significant enrichment of Treponema, Porphyromonas, and Bacteroides, alongside depletion of Streptococcus and Rothia, as key microbial signatures of noma disease. From the dataset we recovered 40 high-quality Treponema metagenome assembled genomes (MAGs) spanning 19 species, 14 of which were novel. Notably, a novel species designated Treponema sp. A was detected in 15 of the 19 noma participants and was entirely absent from an internationally representative set of healthy saliva metagenomes. Re-analysis of previously published 16S rRNA datasets from children with noma in Niger also revealed Treponema sp. A to be highly prevalent in noma cases but extremely rare in controls. While these findings highlight Treponema, particularly Treponema sp. A, as an organism of interest and a potential contributor to noma pathogenesis, further comprehensive studies will be required to confirm this association and to clarify whether it reflects a causal role and/or is a genuine marker of noma dysbiosis. Additionally, analysis of antimicrobial resistance determinants detected in noma metagenomes revealed concerning levels of resistance to antibiotics commonly used in noma treatment, particularly β-lactams and metronidazole, especially among Prevotella spp. These findings provide the first high-resolution microbial framework for noma and offer a foundation for future research into its pathogenesis and the development of novel diagnostics, therapeutics, and preventive strategies in endemic settings.}, } @article {pmid41861238, year = {2026}, author = {Loop Yao, M and Dai, Y and Zhang, W}, title = {Natural Products from the Oral Microbiome.}, journal = {Annual review of biochemistry}, volume = {95}, number = {1}, pages = {569-593}, doi = {10.1146/annurev-biochem-051024-050248}, pmid = {41861238}, issn = {1545-4509}, abstract = {The human oral microbiome is a densely populated and chemically dynamic ecosystem where interspecies competition and cooperation shape community structure and influence host health. Metagenomic analyses reveal the immense biosynthetic potential of oral microbes to encode biosynthetic gene clusters (BGCs) and produce natural products. These metabolites are increasingly recognized as key mediators of microbial interactions, with many oral BGCs linked to health and disease. This review focuses on natural products in the oral microbiome derived from nonribosomal peptide synthetases and polyketide synthases, which are notable for their large size, modular machinery, and ecological relevance. We review the biosynthetic origins and bioactivities of these specialized metabolites in oral bacteria and discuss their biosynthetic regulation within the broader microbial community. Continued investment in whole-genome sequencing, integrative omics, and natural product discovery pipelines is essential for elucidating the microbial biochemical drivers of disease and advancing strategies to promote oral health.}, } @article {pmid41861543, year = {2026}, author = {Mohapatra, RK and Choi, Y}, title = {Exploring multi-omics approaches in anammox-based wastewater treatment processes: A review of recent applications and technological advances.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129342}, doi = {10.1016/j.jenvman.2026.129342}, pmid = {41861543}, issn = {1095-8630}, mesh = {*Wastewater ; Multiomics ; *Waste Disposal, Fluid ; Metabolomics ; Oxidation-Reduction ; Metagenomics ; }, abstract = {Anaerobic ammonium oxidation (anammox) has arisen as a sustainable and energy-efficient approach for nitrogen removal in wastewater treatment. Recently, the utilization of multi-omics approaches, mainly metagenomics, metatranscriptomics, metaproteomics, and metabolomics has risen to reveal the complexity and functionality of anammox-based systems. These integrated approaches offer a comprehensive investigation of microbial community structure, gene expression, protein function, and metabolite dynamics across diverse operating contexts. Progress in high-throughput sequencing, mass spectrometry, and bioinformatics has facilitated the discovery of novel anammox bacteria, functional genes, and metabolic pathways, resulting in vital processes such as nitrogen cycling, microbial interactions, and system resilience. Metagenomics has shown the taxonomic and functional diversity within anammox consortia, whereas metatranscriptomics and metaproteomics have elucidated active metabolic pathways and functional responses to environmental alterations. Metabolomics has furnished direct evidence of metabolic states and biomarkers for enhancing reactor health and efficacy. Researchers have begun to elucidate the intricate physiological and biochemical mechanisms that govern the stability, recovery, and effectiveness of the anammox process through the integration of multi-omics datasets. This review explores recent technological breakthroughs and cutting-edge applications of multi-omics methods in anammox-based wastewater treatment. The article summarizes the principal research findings presented by numerous researchers, providing significant insights for the strategic design and management of robust and efficient water treatment systems aimed at future environmental sustainability.}, } @article {pmid41861844, year = {2026}, author = {Tam, KK and Suster, CJE and Fong, W and Golubchik, T and Sivalingam, V and Jeoffreys, N and Tay, E and Ko, D and Wehrhahn, MC and Ginn, AN and Robson, J and Gardner, I and Papanicolas, LE and Kennedy, K and Graham, M and Tran, T and Speers, D and Cooley, L and Baird, RW and Meumann, EM and Harbidge, J and Campbell, S and Basile, K and Chen, SC and Sintchenko, V and Kok, J and Rockett, RJ}, title = {Genomic Surveillance Reveals Emergence and Spread of Macrolide-Resistant Mycoplasma pneumoniae in Australia During the 2023-2024 Epidemic.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag163}, pmid = {41861844}, issn = {1537-6613}, abstract = {BACKGROUND: The resurgence of Mycoplasma pneumoniae (MP), first reported in China in 2023 was attributed to waning post-pandemic immunity with notable increases in macrolide-resistant MP (MRMP) (>80%). In Australia, infections peaked in early 2024, particularly among children under 15. While MRMP remains low in Europe, North America, and Australia (<5%), limited routine testing and surveillance restricts understanding of resistance dynamics. As macrolides are first-line therapy in many health settings, MRMP surveillance is essential for guiding empirical treatment and stewardship.

METHODS: We applied a novel capture-based targeted metagenomic sequencing (tNGS) to PCR-positive MP specimens (n=356) from across Australia. This approach enabled whole-genome recovery and MRMP detection directly from clinical specimens, without culture. MRMP detections were benchmarked against RT-PCR and clinical data were analysed to assess associations between resistance and healthcare utilisation.

RESULTS: This is the first genomics-informed national study of MP in Australia. We recovered 124 high-quality genomes, revealing a genetically diverse population with co-circulation of P1 Type 1 (69%) and Type 2 (31%). MRMP was identified in 13% of genomes, all belonging to clades prior to 2024 had only been reported in Asia (ST3 and ST14). MRMP cases were geographically widespread, suggesting importation and local transmission. Unlike reports from China, macrolide-susceptible clades (ST3, ST7, ST17 and ST20) predominated (87%) and were associated to significant lower healthcare utilisation compared to MRMP cases.

CONCLUSION: Our findings demonstrate the utility of tNGS for genomic epidemiology and highlight the need for MRMP surveillance. Although macrolides remain effective in Australia, emerging MRMP strains require close monitoring to inform treatment guidelines and antimicrobial stewardship.}, } @article {pmid41861946, year = {2026}, author = {Wang, ST and Li, L and Yang, Q and Zhang, GF}, title = {Artificial reef age reshapes benthic microbial communities and modulates the genetic potential for nitrogen and sulfur cycling.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124314}, doi = {10.1016/j.envres.2026.124314}, pmid = {41861946}, issn = {1096-0953}, mesh = {*Sulfur/metabolism ; *Microbiota ; *Nitrogen Cycle ; *Coral Reefs ; Bacteria/genetics/metabolism ; China ; Archaea/genetics/metabolism ; *Nitrogen/metabolism ; Seawater/microbiology ; }, abstract = {Artificial reefs (ARs) are widely used to restore coastal ecosystems; however, the impact of reef age on microbial communities and their biogeochemical functions remains unknown. This study integrated metagenomic sequencing with physicochemical analysis to examine successional changes in benthic nitrogen and sulfur cycling along a chronosequence spanning from non-artificial reefs (0 years) to 14-year-old ARs in the coastal waters of the Bohai Sea, China. Our analysis revealed a systematic, time-dependent reorganization of the benthic microbiome, characterized by significant enrichment of ammonia-oxidizing archaea (Nitrososphaerota) and bacteria (Nitrospirota) in reefs older than 6 years. Conversely, taxa involved in coupled nitrate reduction and sulfur oxidation (Sulfurovum) declined significantly. Functionally, this led to a shift in genetic potential: the abundance of nitrification genes (amoB and amoC) increased, while genes associated with dissimilatory nitrate reduction (nirB and nrfA), denitrification (nosZ and napB), thiosulfate reduction (phsC and ttrB), and sulfur oxidation (sqr and sox) decreased. Genome-resolved analysis further demonstrated that these functional shifts were driven by the proliferation of nitrifiers and concurrent decline of versatile bacterial lineages. Importantly, this genomic shift was corroborated by geochemical observations of decreased ammonium and increased nitrate concentrations in both bottom seawater and sediments of ARs compared to non-artificial reefs. These results indicate that reef age reshapes benthic microbial communities and functions, favoring aerobic nitrification over anaerobic or microaerophilic nitrate reduction and sulfur metabolism. This study provides a scientific basis for AR adaptive management, underscoring the necessity of integrating microbial functional metrics into the long-term impact assessment of marine infrastructures.}, } @article {pmid41861947, year = {2026}, author = {Guo, J and Liang, X and Lei, W and Zhang, Z and Shen, Y and Han, S and Wang, H and Qian, Y and Nie, B and Wang, L and He, S}, title = {Contrasting microbial sources of soil N2O emissions revealed by metagenomics in natural and agricultural soils along the Yellow River.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124311}, doi = {10.1016/j.envres.2026.124311}, pmid = {41861947}, issn = {1096-0953}, mesh = {*Nitrous Oxide/analysis/metabolism ; *Soil Microbiology ; Metagenomics ; Denitrification ; Rivers ; Agriculture ; *Soil/chemistry ; Nitrification ; Archaea/metabolism ; Bacteria/metabolism/genetics ; China ; Environmental Monitoring ; }, abstract = {Soil nitrous oxide (N2O) emission is a potent greenhouse gas source, yet the dominant production pathway (nitrification vs. denitrification) and its microbial mechanisms in regions like the Yellow River Basin remain unclear, particularly under different land uses. In this study, we integrated qPCR quantification, metagenomic sequencing and binning, as well as microbial network analysis to investigate the dominant microbial processes and regulatory mechanisms underlying potential soil N2O production. Results showed that denitrification dominated regional potential N2O production (N2ODen, 56.71 ± 102.94 nmol/(kg·h)), significantly exceeding nitrification (N2ONif, 4.34 ± 4.27 nmol/(kg·h)). On average, both N2ODen (115.34 ± 143.60 nmol/(kg·h)) and N2ONif (5.29 ± 4.42 nmol/(kg·h)) in natural soils were higher than in cultivated soils (28.56 ± 62.52 and 3.88 ± 4.22 nmol/(kg·h), respectively). Mechanistically, natural soils were enriched with ammonia-oxidizing archaea (AOA) and incomplete denitrifiers (e.g., Acidobacteriota), which, along with a higher norB/nosZ and more stable co-occurrence network, favored N2O accumulation. In cultivated soils, microbial community stability was reduced; however, they were enriched with strong N2O reducers (e.g., Pseudomonadota, Gemmatimonadota), resulting in lower potential N2O production. Altitude, total nitrogen, and pH collectively influenced the potential N2O emission patterns by regulating functional genes and microbial metabolism. This study provides a scientific basis for regional greenhouse gas mitigation from a microbial ecology perspective.}, } @article {pmid41862052, year = {2026}, author = {Gunasekaran Rajalakshmi, S and K, RB and Viswanathan, P}, title = {Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR.}, journal = {Life sciences}, volume = {393}, number = {}, pages = {124336}, doi = {10.1016/j.lfs.2026.124336}, pmid = {41862052}, issn = {1879-0631}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Dysbiosis/microbiology/genetics ; Male ; *Metagenomics/methods ; *Diabetes Mellitus, Type 2/microbiology/complications ; *Renal Insufficiency, Chronic/microbiology ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Feces/microbiology ; Adult ; Real-Time Polymerase Chain Reaction/methods ; Diabetic Nephropathies/microbiology ; Aged ; }, abstract = {BACKGROUND: Type 2 diabetes (T2D) is a major contributor to diabetic nephropathy, the leading cause of chronic kidney disease (CKD). This study investigated gut microbial dysbiosis and composition shift among healthy individuals and diabetic patients with or without CKD using a 16S rRNA metagenomic approach, validated by qRT-PCR and clinical data integration to identify the significant key genera associated with disease progression.

METHODS: Stool samples from 22 individuals were analysed using 16S rRNA amplicon sequencing to assess gut microbiota composition. Differential abundance analysis, LEfSe, and network-based methods were employed to identify key taxa. Significant features were validated by qRT-PCR. Integrated approaches, including Pearson correlation, WGCNA, random forest, and propensity score matching, were used to associate microbial features with clinical markers. Functional enrichment of microbial pathways was predicted using PICRUSt2.

KEY FINDINGS: A total of 1409 amplicon sequence variants (ASVs) were identified. Bray-Curtis dissimilarity showed significant microbial diversity differences between disease and healthy subjects (p < 0.031). Key taxa associated with eGFR and serum creatinine (sCr) included Bacteroidetes uniformis (LFC +9), Ruminococcus (LFC +8.1), and Dialister succinatiphilus (LFC +6.7), linked to disease progression and metabolic regulation. In contrast, protective taxa such as Bifidobacterium adolescentis (LFC -9.5), Faecalibacterium prausnitzii (LFC -6.39), Collinsella, and Megasphaera elsdenii were reduced. Integration of Pearson correlation, WGCNA, propensity score matching, and random forest classification revealed microbial features associated with clinical covariates.

SIGNIFICANCE: Our findings show the gut microbiome shifts begin in diabetics without CKD conditions but become more pronounced in diabetics with CKD, with a lower ratio of beneficial bacteria, reflecting a gradual microbial imbalance along disease progression.}, } @article {pmid41862737, year = {2026}, author = {Liu, L and Yu, QQ and Zhang, YL and Zhou, JT and Jin, Y and Jiang, CH and Zhuang, S and Wei, J and Li, P and Miao, H and Zhao, YY}, title = {Renal fibrosis is induced by hyperactive Wnt/β-catenin pathway via microbial-mediated tryptophan metabolism-driven AhR signaling in rodents and humans.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {83}, number = {1}, pages = {}, pmid = {41862737}, issn = {1420-9071}, support = {82274079//National Natural Science Foundation of China/ ; 82274192//National Natural Science Foundation of China/ ; 82474062//National Natural Science Foundation of China/ ; LHZSZ25H270001//Natural Science Foundation of Zhejiang Province/ ; 2023-ZDLSF-26//Key Science and Technology Program of Shaanxi Province/ ; }, abstract = {Renal fibrosis is a common pathological endpoint in progressive chronic kidney disease (CKD). Clinical evidence indicates that a decline in renal function is more closely associated with tubulointerstitial fibrosis (TIF) than with glomerular injury. Recent advances in multi-omics technologies have provided powerful tools for uncovering unrecognized disease molecular mechanisms. Metagenomic and metabolomic analyses were performed to profile the fecal microbiota and serum metabolites, respectively, and to identify tubulointerstitial damage (TID)-related bacterial taxa and metabolites. Identified serum metabolites were also determined in healthy controls and tubulointerstitial nephropathy (TIN) patients. The expression of aryl hydrocarbon receptor (AhR) and Wnt/β-catenin signaling–related genes and proteins was evaluated in obstructed kidney of unilateral ureteral obstruction (UUO) rats and AhR shRNA-treated UUO mice as well as in 1-hydroxypyrene (HP)-stimulated HK-2 cells untreated or treated with AhR shRNA. UUO induced progressive TID and TIF in rats. Alterations in gut microbiota composition, particularly changes in Enterocloster aldenensis (E. aldenensis) and Lactobacillus acidipiscis (L. acidipiscis), were strongly correlated with TID. In parallel, microbial-derived tryptophan catabolites (MDTCs), including tryptamine, indole-3-acetic acid (IAA), indole-3-lactic acid (ILA), indole-3-propionic acid (IPA), indole-3-acrylic acid, indole-3-aldehyde (IAld), and indoxyl sulfate were strongly associated with TID severity. Linear regression analyses revealed correlation coefficients exceeding 0.80 between E. aldenensis and IAA, ILA, and IPA, and between L. acidipiscis and IAld, indicating close relationships with progressive TIF. Similarly, the changes of 14 MDTCs were further demonstrated in TIN patients and they could separate TIN patients form healthy controls. Some MDTCs showed strongly correlation with estimated glomerular filtration rate in TIN patients and high values of area under the curve, sensitivity and specificity. These microbial and metabolic alterations were accompanied by activation of the AhR–Wnt/β-catenin signaling pathway. By contrast, AhR shRNA treatment inhibited mRNA expression of AhR and its downstream target genes, including cytochrome P450 family 1 subfamily A member 1 (CYP1A1), CYP1A2, CYP1B1 and cyclooxygenase-2 accompanied by suppressing nuclear AhR localization, retarded protein expression of Wnt1, β-catenin and Twist, enhanced E. aldenensis and L. acidipiscis abundances and reversed MDTC dysregulation in UUO mice. Bioactivity-directed isolation and identification demonstrated that polyporusterone A (PPA) from Polyporus umbellatus increased abundance of E. aldenensis and L. acidipiscis and normalized dysregulated MDTCs in UUO rats. PPA treatment suppressed intrarenal AhR signaling and Wnt1/β-catenin pathway. Consistent effects were observed in HP-induced HK-2 cells treated with PPA; however, AhR knockdown partially attenuated these inhibitory effects. Taken together, this study first demonstrated that the enrichment of pathogenic bacteria and depletion of probiotics-mediated dysregulation of MDTCs is closely linked to the activation of the AhR–Wnt/β-catenin signaling axis in UUO rat model. Targeting GM may represent a promising therapeutic strategy for CKD and renal fibrosis.}, } @article {pmid41862790, year = {2026}, author = {Amir, A and Zhong, J and Yao, Y and Chen, T and Li, M and Yan, H}, title = {Seasonal diet shifts alter the gut microbiome and resistome of captive geriatric giant pandas (Ailuropoda melanoleuca).}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41862790}, issn = {1471-2180}, support = {2024CPB-B18//Chengdu Research Base of Giant Panda Breeding/ ; 2024CPB-B18//Chendu Research Base of Giant Panda Breeding/ ; }, abstract = {UNLABELLED: The nutritional changes of giant pandas (Ailuropoda melanoleuca) in response to the seasonal variations from bamboo shoots (rich in proteins) to fibrous leaves trigger significant alterations in the structure and functions of the gut microbiome. However, the effect these dietary changes have on the gut resistome, especially in older adults, is not well characterized. In this study, shotgun metagenomic sequencing and quantitative PCR (qPCR) were used to investigate the microbial composition, functional potential, and profiles of antibiotic- and metal-resistance genes (ARG and MRG) in feces of adult (n = 11) and geriatric captive pandas (n = 11) that were fed on bamboo shoots or leaves. The microbes varied considerably among diet and age groups, with diet becoming the main source of taxonomic and functional disparity (P < 0.05). Shoot-fed pandas exhibited higher alpha diversity at the genus level and distinct clustering in principal coordinate analyses, whereas leaf-fed groups showed enrichment of taxa associated with fiber degradation and stress tolerance (P < 0.05). Functional annotation of bacterial responses to diet showed changes in carbohydrate processing pathway, carbohydrate transport, and cellular process pathways by changes in the KEGG pathway (P < 0.05). Changes depending on diet were also identified with significant changes in carbohydrate-active enzyme (CAZy) family during changes in the composition of the bamboo parts. Metagenomics and qPCR revealed that several antibiotic resistance genes, such as aac(3)-Xa, bcrA, tet44, sul2 and macB, were highly interacting between diet and age and the most diverse resistome was found in geriatric pandas (P < 0.05). Correlation analysis demonstrated that there is a positive co-occurrence pattern of Enterobacteriaceae and several ARGs. Collectively, our findings demonstrate that seasonal dietary shifts and host aging jointly restructure the gut microbiome and resistome of giant pandas, suggesting diet-mediated modulation of microbial adaptation, resistance dissemination, and ecological resilience in captivity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04966-0.}, } @article {pmid41862850, year = {2026}, author = {Li, Z and Wu, C and Huang, D and Liang, Y and Zhai, Y and Mai, C and Han, Y and Tang, LA and Wang, W and Ning, C and Tan, W}, title = {Metagenomics reveals pathogenic diversity and temporal dynamics in severe pneumonia among patients in adult intensive care unit.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41862850}, issn = {1471-2334}, support = {2021YFC2300101//the National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) emerging as a standout in the clinical setting. In this study, we harnessed the power of mNGS to explore the pathogenic spectrum and temporal variations in respiratory tract specimens collected from adult patients with severe pneumonia who were admitted to the Intensive Care Units (ICUs) of two hospitals in Guangxi, China. METHODS: From December 2021 to July 2022, 44 respiratory tract samples (including sputum and bronchoalveolar lavage fluid) from 25 adult patients (comprising 18 males and 7 females) diagnosed with severe pneumonia and admitted to the ICUs of two hospitals in Guangxi. A customized mNGS detection protocol was developed and applied for analyzing the composition and temporal variations of pathogens within the respiratory tract samples. RESULTS: Among these patients, the bacteria, fungi, and viruses were markedly higher detected by mNGS compared to conventional microbial culture methods (P < 0.001). The most prevalent bacteria detected were Stenotrophomonas maltophilia (61.36%), Corynebacterium striatum (54.55%), and Escherichia coli (54.55%). The viruses with the highest detection rates were human herpesviruses(HSV-1, 31.82%;HCMV, 27.27%;HSV-2, 11.36%). The most frequently identified fungi were Candida albicans (50%) and Nakaseomyces glabratus (27.27%). Single-pathogen infections accounted for 64% (28/44) of the cases, while mixed-pathogen infections comprised 36% (16/44). Dynamic monitoring using mNGS in 8 patients uncovered diverse respiratory pathogenic spectra, with the majo Candida glabratarity of patients exhibiting dynamic changes that correlated with fluctuations in inflammatory markers such as leukocyte counts, procalcitonin levels, and C-reactive protein levels, alongside the clinical progression of the disease. CONCLUSION: mNGS exhibits superior performance in diagnosing mixed infections and real-time tracking of the pathogen spectrum, which provide a robust empirical basis for guiding clinical diagnosis and treatment strategies of patients in ICU. CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid41863347, year = {2026}, author = {Lutfi, A and Holstein, T and Andreotti, S and Muth, T}, title = {MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {5}, pages = {}, pmid = {41863347}, issn = {1367-4811}, support = {MU 4430/2-1//German Research Foundation (DFG)/ ; }, mesh = {*Software ; *Peptides/chemistry ; Algorithms ; Databases, Protein ; *Proteomics/methods ; *Sequence Analysis, Protein/methods ; }, abstract = {MOTIVATION: A central problem for metaproteomic analysis is the often-unknown taxonomic composition of the analyzed microbiomes. Using a database search, the standard approach requires prior knowledge of which proteins and taxa to include in the protein reference database or to use tailored metagenome-derived databases, which are expensive and error-prone in their generation. A possible strategy to circumvent this database search issue is de novo sequencing, where peptide sequences are directly identified from mass spectra. However, these sequences must still be mapped back to potentially extensive databases. Here, alignment-based approaches enable robust and precise results, with the potential drawback of high memory usage and long run times.

RESULTS: We present MegaPX, a software for rapidly classifying de novo peptide sequences against large protein databases. MegaPX implemented as a C++-based tool, uses an alignment-free, k-mer approach as a taxonomic classification method with the possibility of generating mutated reference databases for error-tolerant searching. It uses various algorithms, including interleaved Bloom filters, to efficiently compute approximate membership queries, ensuring fast processing times while querying and indexing large databases in a multi-indexing fashion. We demonstrate the potential of MegaPX by analyzing different samples, including metaproteomics, against extensive reference databases, highlighting its use as a fast screening tool.}, } @article {pmid41863618, year = {2026}, author = {Majumder, D and Dash, S and Bhattacharya, D and Gill, HS and Raja, V and Dewi, JR and Roy, A and Rajeev, M and Pandit, S and Sharma, S and Dwivedi, SP and Nag, M and Lahiri, D}, title = {Genetically engineered lipases: advances in expression and upscaling for industrial applications.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41863618}, issn = {1432-072X}, abstract = {Lipases are versatile enzymes with widespread industrial applications, including detergents, food processing, pharmaceuticals, biofuels, and environmental cleanup. Their ability to catalyze both hydrolytic and synthetic reactions under diverse conditions underpins their biotechnological significance. Native lipases, however, exhibit limitations such as low stability, narrow substrate spectrum, and low production yields, which limit their large-scale application. Emerging developments in genetic and protein engineering have enabled accurate modulation of enzyme properties and expression systems, offering potential solutions to overcome these challenges. This review presents an integrated view of existing strategies for designing high-performance lipases for industrial applications. It summarizes advancements from metagenomic discovery and gene optimization to expression optimization through codon improvement, promoter adjustment, signal peptide design, and chaperone-mediated folding. Protein engineering strategies, including rational design, directed evolution, and domain recombination; are addressed to enhance catalytic activity, selectivity, and thermostability. Concomitantly, breakthroughs in fermentation optimization, host metabolism engineering, and enzyme immobilization have enhanced the scalability and operational robustness of lipase manufacturing. Novel omics-driven and systems biology platforms now facilitate the rational design of microbial hosts optimized for efficient enzyme biosynthesis. Collectively, these advances outline a coherent blueprint for engineering lipases into strong, industrially applicable biocatalysts.}, } @article {pmid41863619, year = {2026}, author = {Jonathan, AR and Balasubramanian, VK and Ho, ST and Chen, YP and Khunnamwong, P and Chou, JY}, title = {Next-generation strategies for PLA degradation: microbial consortia, metagenomics, enzyme engineering and AI-guided approaches.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41863619}, issn = {1432-072X}, support = {MOST 111-2621-B-018-001 to Jui-Yu Chou//Ministry of Science and Technology, Taiwan/ ; }, mesh = {*Metagenomics ; Biodegradation, Environmental ; *Microbial Consortia ; *Polyesters/metabolism/chemistry ; Animals ; Bacteria/metabolism/genetics/classification ; Artificial Intelligence ; Fungi/metabolism/genetics ; Protein Engineering ; }, abstract = {Polylactic acid (PLA) is one of the most widely used biodegradable bioplastics; however, its slow degradation under natural conditions limits its environmental sustainability. This review summarizes recent advances in microbial and biotechnological strategies that enhance PLA biodegradation across diverse ecosystems. Emerging approaches include screening insect gut microbiota, isolating fungal species with strong adsorption or enzymatic capacities, and exploring soil, compost, and aquatic microbiomes using metagenomics and environmental DNA (eDNA) tools. Microbial consortia, thermophilic degraders, and co-culture systems are highlighted as effective solutions to overcome the intrinsic crystallinity and hydrolysis-dependent breakdown of PLA. Beyond natural systems, this review emphasizes the increasing role of synthetic biology, directed evolution, and artificial intelligence (AI) in engineering high-performance PLA-degrading enzymes. AI-driven structural prediction and machine-learning platforms offer new possibilities for designing robust depolymerases with improved specificity, thermostability, and catalytic efficiency. Collectively, these multidisciplinary strategies provide a roadmap for accelerating PLA degradation in industrial composting, wastewater treatment, and bioremediation. Future integration of ecological screening with computational enzyme engineering is expected to advance scalable and sustainable PLA waste management.}, } @article {pmid41863708, year = {2026}, author = {Mishra, AK and Verma, S and Mishra, A and Khan, G and Singh, H}, title = {Unlocking the role of microbiome through gut-skin axis to alleviate aging: current perspectives and future scope.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {41863708}, issn = {2509-2723}, abstract = {The microbiota of intestinal origin has a significant impact on the aging process, affecting skin health and overall cell longevity. Aging is marked by physiological alterations, such as enhanced oxidative stress, which is intensified by external factors like UV radiation and environmental pollution. The gut microbiota profoundly influences immune functions and results in reduced inflammation, which contributes to the anti-aging process. The present review is an attempt to showcase the current studies on the gut-skin axis, investigating the impact of gut-derived metabolites, particularly short-chain fatty acids, postbiotics, synbiotics, and psychobiotics, on the function of skin barriers and the aging process. Dietary supplements, including prebiotics along with probiotics, have demonstrated significant potential in altering gut microbiota composition and, in turn, improving skin health. Future studies must focus on investigating the connection between gut microbiota and cellular senescence, the effectiveness of microbiota-targeted therapeutics, and the incorporation of targeted therapy to delay the aging process. Comprehending these processes may facilitate the development of novel ways to enhance healthy aging and alleviate age-related diseases through the gut-skin axis via microbiome regulation.}, } @article {pmid41863933, year = {2026}, author = {Dong, X and Zhu, L and He, Y and Li, C and Wu, R and Li, D}, title = {Microbial degradation of plastics in the environment: Mechanisms, enzymatic pathways, and constraints from laboratory studies to environmental reality.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129422}, doi = {10.1016/j.jenvman.2026.129422}, pmid = {41863933}, issn = {1095-8630}, mesh = {*Biodegradation, Environmental ; *Plastics/metabolism ; Bacteria/metabolism ; Animals ; *Microplastics/metabolism ; }, abstract = {Microplastic (MP) pollution has become a persistent environmental challenge, raising increasing concern due to its global distribution and potential risks to human health. Biological degradation, including microbial and insect mediated processes, represents a promising and environmentally sustainable strategy for mitigating plastic and MP pollution; however, its effectiveness remains highly variable and strongly context dependent. This review systematically summarizes recent advances in microbial degradation of plastic, as well as emerging research on insect mediated plastic biodegradation, focusing on degrading microorganisms, key enzymes, metagenomic discovery, and enzyme engineering strategies. A wide range of bacterial and fungal taxa capable of degrading major plastic polymers, including polyethylene (PE), polypropylene (PP), polyethylene terephthalate (PET), polystyrene (PS), polyvinyl chloride (PVC), polyurethane (PU), and polylactic acid (PLA), has been reported. In addition, several insect species capable of ingesting and transforming plastics have been identified as model systems for studying plastic degradation, where mechanical fragmentation, host digestive processes, and gut microbial metabolism jointly contribute to polymer transformation. Among these, PET degrading enzymes, particularly PETase, are the most extensively characterized, benefiting from detailed structural insights and intensive protein engineering efforts that have markedly enhanced catalytic efficiency and thermostability. In contrast, enzymatic mechanisms involved in the biodegradation of polyolefins such as PE and PP remain poorly understood, representing a major knowledge gap. Recent metagenomic approaches have substantially expanded the repertoire of candidate plastic degrading enzymes by accessing uncultured MP associated microbial communities and insect gut microbiomes. Nevertheless, functional validation and evaluation under environmentally relevant conditions remain critical bottlenecks. Moreover, most reported degradation efficiencies are derived from optimized laboratory settings and may substantially overestimate microbial performance under natural environmental constraints, including low temperature, high salinity, nutrient limitation, and mixed polymer substrates. Overall, this review highlights the gap between laboratory based biodegradation studies and real world applications and emphasizes the need for integrated strategies to advance scalable plastic and MP remediation solutions.}, } @article {pmid41863937, year = {2026}, author = {Liu, X and Liu, X and Zhu, D and Wang, J and Wang, Z and Liu, W and Zhou, X and Zhou, H and Wu, L}, title = {Harvesting reshapes greenhouse gas exchange in reservoir drawdown soils via soil state control and context-dependent microbial functions.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129375}, doi = {10.1016/j.jenvman.2026.129375}, pmid = {41863937}, issn = {1095-8630}, mesh = {*Greenhouse Gases/analysis ; *Soil/chemistry ; Carbon Dioxide/analysis ; *Soil Microbiology ; Methane/analysis ; China ; Nitrous Oxide/analysis ; }, abstract = {Reservoir drawdown zones, the seasonally exposed and re-flooded margins of reservoirs, are extensive pulsed wetlands that can act as hotspots of greenhouse gas (GHG) exchange. Vegetation harvesting is common in these zones, yet its net climate effect across CO2, CH4, and N2O, and the controls behind it, remain unclear. We compared harvested and unharvested plots across longitudinal river reaches and elevation bands in the drawdown zone of the Three Gorges Reservoir (China). We measured soil-atmosphere fluxes of CO2, CH4, and N2O, together with soil physicochemical properties and metagenome-derived functional markers. Harvesting increased CO2 flux and decreased CH4 flux, while N2O showed no detectable net treatment effect. Across analyses, soil hydrothermal and nutrient conditions were the dominant predictors of flux variation; microbial functional signals added information mainly through soil-dependent interactions. In CO2-equivalent terms, lower CH4 emissions only partly compensated for higher CO2, leaving a net positive effect under both 20- and 100-year horizons. These results underscore that harvest impacts in drawdown soils should be assessed as multi-gas trade-offs and interpreted through soil moisture-redox dynamics.}, } @article {pmid41863981, year = {2026}, author = {Fu, Z and Fu, J and Wang, Y and Zhan, K and Liang, Y and Ao, N and Shen, Q and Liu, C}, title = {Effects of tea polyphenols on intestinal barrier, antioxidant capacity, and cecal microbiota in lion-head geese.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106706}, pmid = {41863981}, issn = {1525-3171}, mesh = {Animals ; *Polyphenols/metabolism/administration & dosage ; *Antioxidants/metabolism ; Male ; Diet/veterinary ; Dietary Supplements/analysis ; Animal Feed/analysis ; *Tea/chemistry ; *Geese/microbiology/physiology/metabolism ; Cecum/microbiology/drug effects ; *Gastrointestinal Microbiome/drug effects ; Intestinal Barrier Function/drug effects ; Random Allocation ; *Intestines/drug effects/physiology/anatomy & histology ; *Camellia sinensis/chemistry ; }, abstract = {Tea polyphenols are natural bioactive compounds associated with enhanced antioxidant capacity and improved gut health in poultry. This study evaluated the effects of dietary supplementation with tea polyphenols on intestinal morphology, barrier integrity, antioxidant status, and cecal microbiota in lion-head geese. A total of 240 one-day-old male lion-head geese were randomly allocated to 2 treatments: a basal diet (control) or the same diet supplemented with 1,000 mg/kg tea polyphenols (catechin purity, 50.4%) for 18 wk (6 replicates/treatment; 20 birds/replicate). Compared with the control, dietary supplementation with tea polyphenols significantly increased villus height and villus-to-crypt ratio (V/C) in the jejunum and ileum (P < 0.05) and reduced serum lipopolysaccharide (LPS) concentration (P < 0.05), whereas serum diamine oxidase (DAO) activity did not differ (P > 0.05). In the jejunum, mRNA expression of ZO-1, Claudin-5, and Occludin was significantly upregulated (P < 0.05); in the ileum, mRNA expression of ZO-1, Claudin-5, Occludin, and E-cadherin was significantly upregulated (P < 0.05). Tea polyphenols increased jejunal total antioxidant capacity (T-AOC) and upregulated GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). In the ileum, tea polyphenols significantly increased glutathione peroxidase (GSH-Px) and total superoxide dismutase (T-SOD) activities, decreased malondialdehyde (MDA) content, and upregulated SOD1, GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). Metagenomic sequencing showed lower relative abundances of Firmicutes and Verrucomicrobia at the phylum level (P < 0.05). At the genus level, tea polyphenols increased Prevotella and Subdoligranulum and decreased Oscillibacter and Desulfovibrio (P < 0.05). Functional annotation (KEGG, eggNOG, and CAZy) indicated enrichment of carbohydrate transport and metabolism, glycosyltransferases (GT), and polysaccharide lyases (PL) in the tea polyphenol group. Spearman correlation analysis indicated positive associations of Prevotella with KEGG thermogenesis and the two-component system, and of Desulfovibrio with biotin metabolism (P < 0.05). Overall, tea polyphenols promoted intestinal development, enhanced barrier- and antioxidant-related responses, and altered the composition and functional potential of the cecal microbiota, supporting improved gut health in lion-head geese.}, } @article {pmid41864025, year = {2026}, author = {Yu, H and Zhang, X and Liang, Y and Mu, Q and Shi, X and Deng, Z and Chen, J and Cao, J and Deng, Y and Han, Z and Chen, H and Zhang, C}, title = {Deciphering the environmental fate of halogenated organic compounds in cold seep sediments: Insights from non-targeted analysis and metagenomics across vertical redox gradients.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141804}, doi = {10.1016/j.jhazmat.2026.141804}, pmid = {41864025}, issn = {1873-3336}, mesh = {*Geologic Sediments/chemistry/microbiology ; Metagenomics ; Oxidation-Reduction ; *Water Pollutants, Chemical/analysis ; *Hydrocarbons, Halogenated/analysis ; Bacteria/genetics/metabolism ; }, abstract = {Halogenated organic compounds (HOCs) are pervasive in marine environments, yet their molecular diversity, vertical distribution, and fate in deep-sea ecosystems remain largely uncharted. Here, we integrated non-targeted analysis, geochemical profiling, and metagenomics to systematically analyze a 500-cm sediment core from the Haima deep-sea cold seep, deciphering these key aspects and their controlling factors. Non-targeted analysis identified 669 HOCs (at molecular formula level), predominantly of marine origin with saturated structures. The highest HOC diversity was found in the oxic/suboxic (OS) zone, where 73.4% of the frequently detected HOCs reached their peak abundance. Concurrently, a marked decrease in organochlorines was observed at the OS-suboxic/anoxic (SA) interface, followed by level stabilization below this transition, suggesting regulation by abrupt redox shifts. Correlation analyses revealed co-regulation of HOC distribution by geochemical (e.g., depth, pH, and SO4[2-]) and microbial (e.g., reductive and hydrolytic dehalogenases) factors. Metagenomics combined with redundancy analysis further demonstrated significant interactions between HOCs and dehalogenating microbial community along the vertical profile. In summary, this study provided an integrated perspective on the biogeochemical cycling of HOCs in the deep-sea cold seep, linking their removal at redox boundaries, long-term burial, and spatial organization to underlying microbial and geochemical drivers.}, } @article {pmid41864063, year = {2026}, author = {Jian, X and Yu, P and Zhang, Y and Pan, H and Wu, K and Zhang, H and Zhang, H and Huang, Y and Zhao, Y and Wang, Y and Wang, Y and Zhou, Q and Zhang, X and Zhao, G and Li, B and Guo, J and Xia, K and Tang, B and Li, J}, title = {Large-scale profiling of blood microbial signatures in patients with Parkinson's disease and its association with disease progression: a cross-sectional study.}, journal = {EBioMedicine}, volume = {126}, number = {}, pages = {106224}, pmid = {41864063}, issn = {2352-3964}, mesh = {Humans ; *Parkinson Disease/blood/microbiology/diagnosis ; Disease Progression ; Cross-Sectional Studies ; Female ; Aged ; Male ; Whole Genome Sequencing ; Biomarkers ; *Microbiota ; Middle Aged ; Bacteria/genetics/classification ; Metagenomics/methods ; }, abstract = {BACKGROUND: Emerging evidence supports the presence of microbial signatures in the blood, yet their clinical relevance remains poorly understood. In this study, we profiled blood microbial signatures in patients with Parkinson's disease (PD) and investigated their associations with disease progression.

METHODS: We analysed 4018 whole-genome sequencing (WGS) data of blood samples from two independent cohorts. The high-quality non-human reads were extracted for microbial annotation using Kraken 2 and Bracken software with the PlusPF database. To identify PD-associated signatures, we implemented a population-based, cross-cohort filtration process with resequencing validation to minimise noise and putative contaminants.

FINDINGS: Microbial DNA signals, predominantly bacterial, were extensively detected in the sequencing data and were more abundant in individuals with PD than in controls. Across the two cohorts, 126 bacterial species were identified as key signatures, nearly two-thirds of which are known to colonise human body sites. Among these, 19 species exhibited increased abundance and higher prevalence in PD, and could serve as features to discriminate effectively patients from controls. Furthermore, several microbial signatures were correlated with more severe clinical manifestations, such as motor dysfunction and cognitive impairment.

INTERPRETATION: Our findings supported blood microbial signatures as promising biomarkers in PD, although their origin and functional relevance remain to be validated. The analytical framework may facilitate future investigations into the potential clinical implications of blood microbial signatures in disease contexts.

FUNDING: This work was supported by Hunan Innovative Province Construction Project, National Natural Science Foundation of China, and Natural Science Foundation of Hunan Province.}, } @article {pmid41864266, year = {2026}, author = {Wang, X and Wang, Y and Yan, G and Chu, N and Huang, H and Nie, W}, title = {The clinical diagnostic value of metagenomic next-generation sequencing for patients with suspected nontuberculous mycobacterial osteoarticular infection: A national multicenter clinical cohort.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {167}, number = {}, pages = {108578}, doi = {10.1016/j.ijid.2026.108578}, pmid = {41864266}, issn = {1878-3511}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Female ; *Nontuberculous Mycobacteria/genetics/isolation & purification ; Sensitivity and Specificity ; Male ; *Metagenomics/methods ; Aged ; Middle Aged ; Predictive Value of Tests ; Aged, 80 and over ; }, abstract = {OBJECTIVES: This study aimed to determine the accuracy of metagenomic next-generation sequencing (mNGS) in diagnosing nontuberculous mycobacteria (NTM) osteoarticular infection (OAI) and compare it with mycobacteria growth indicator tube (MGIT) culture.

METHODS: This study was conducted on 193 patients with suspected NTM OAI treated from January 2019 to July 2022 at the Beijing Chest Hospital, Capital Medical University, Yantai Qishan Hospital, or The Fourth People's Hospital of Nanning who had mNGS assay and MGIT culture results. Clinical comprehensive diagnosis was taken as the "gold standard." We investigated the diagnostic sensitivity, specificity, predictive value, and likelihood ratio of these tests.

RESULTS: Of the 193 patients, 26 (13.47%) were diagnosed with NTM OAI, and 167 (86.53%) had non-NTM OAI. Compared to the MGIT culture results, mNGS showed higher sensitivity (100.0% vs 7.7%), specificity (99.4% vs 80.2%), positive predictive value (96.3% vs 5.7%), negative predictive value (100.0% vs 84.8%), positive likelihood ratio (167.000 vs 0.389), and negative likelihood ratio (0.000 vs 1.150). The area under the curve of the mNGS assay was 0.997 (95% confidence interval, 0.990-1.000).

CONCLUSION: The mNGS assay had greater diagnostic accuracy than the MGIT culture in patients with suspected NTM OAI.}, } @article {pmid41864408, year = {2026}, author = {Wang, Z and Chen, Z and Zhu, L and Liu, Y and Wen, Q}, title = {Substrate type determines the interplay between metabolic efficiency and microbial stress response in mixed culture PHA production under high salinity.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124330}, doi = {10.1016/j.envres.2026.124330}, pmid = {41864408}, issn = {1096-0953}, mesh = {*Polyhydroxyalkanoates/biosynthesis/metabolism ; *Salinity ; *Fatty Acids, Volatile/metabolism ; Energy Metabolism ; Stress, Physiological ; }, abstract = {Polyhydroxyalkanoates (PHAs) from mixed cultures offer a sustainable alternative to plastics, and high salinity presents a promising selective pressure for PHA producers. However, the osmotic stress imposed by high salinity perturbs carbon and energy metabolism, yet how different volatile fatty acid (VFA) substrates influence PHA synthesis efficiency under sustained saline conditions remains poorly understood, particularly regarding carbon flux partitioning and energy trade-offs. This study investigated the effects of single VFA (acetate, propionate, butyrate, and valerate) on the enrichment, PHA accumulation, and metabolic flux of PHA-producing mixed cultures under 1.8% salinity. Butyrate and valerate-fed systems achieved superior PHA accumulation (0.636 ± 0.015 and 0.698 ± 0.005 g PHA/g VSS, respectively) compared to acetate (0.541 ± 0.006 g PHA/g VSS) and propionate (0.382 ± 0.021 g PHA/g VSS). This was due to more direct precursor supply and lower energy demands. Carbon flux analysis confirmed butyrate and valerate directed over 85% of utilized carbon to PHA, whereas propionate diverted more to cell maintenance. Metagenomics revealed that Paracoccus was a versatile salt-tolerant PHA producer across all substrates. Cultures fed with butyrate and valerate also exhibited enhanced respiratory chain activity and higher ATP/NAD(P)H, enabling better salt stress while maximizing PHA synthesis. These findings highlight the critical interplay between VFA type, salt stress, and metabolic trade-offs, providing crucial insights for optimizing high-salinity waste to PHA bioprocesses.}, } @article {pmid41864933, year = {2026}, author = {Dai, QB and Lai, LM and Zhu, Q and Yuan, L}, title = {Clinical efficacy of plasma cell-free DNA metagenomic next-generation sequencing in diagnosing bloodstream infections.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41864933}, issn = {1471-2334}, support = {20242BAB20430//the Natural Science Foundation of Jiangxi Province/ ; 202510284//the Science and Technology Plan of Jiangxi Provincial Health Commissio/ ; }, abstract = {BACKGROUND: Our initial goal was to assess the clinical efficacy of using plasma cell-free DNA (cfDNA) to perform metagenomic next-generation sequencing (mNGS) to detect suspected infections. METHODS: We retrospectively analyzed 425 patients who underwent plasma cfDNA mNGS. Of them, 84 patients had various systemic infections, 69 were ruled out of infectious diseases, and 272 had bloodstream infections. Conventional microbiological tests (CMTs) and plasma cfDNA mNGS were conducted concurrently in clinical practice. The sensitivity and specificity of the two techniques were examined based on the final diagnosis. RESULTS: The total positive rate (276/425) for the cfDNA mNGS test indicated the presence of microorganisms. The mean length of stay in the hospital for mNGS-positive patients was longer than for mNGS-negative patients (P = 0.0079). Compared with patients with negative mNGS tests, those with positive mNGS tests have significantly lower white blood cell counts in peripheral blood (P = 0.0085). Among all the disorders in our patients, bloodstream infection (272/425, 64.0%) accounted for the most significant percentage. The diagnostic sensitivity of mNGS is also higher than that of CMTs (72.8% vs. 32.9%). However, its diagnostic specificity is lower than CMT’s (75.4% vs. 85.5%). Bacteria were the most frequently identified potential pathogens by mNGS. Klebsiella pneumoniae (n = 46) was the most common pathogen. Candida albicans is the most common fungal infection (n = 18). Human cytomegalovirus (n = 45) is the most common viral infection. The detection rate of mNGS in empirically treated groups was significantly higher than in non-empirically treated groups(71.9% vs. 51.4%, p < 0.0001), which is contrary to conventional microbiological tests(21.7% vs. 41.0%, p < 0.0001). Of the 276 patients with positive mNGS results, clinical management was positively affected in 122 (44.2%) cases. Negative mNGS results led to a modified clinical management regimen in 121 patients. The average hospitalized days for the day 1–3 sampling time were significantly shorter than for the other two groups(sampling time 4–7 days and sampling time ≥ 8 days). CONCLUSIONS: Our research found that mNGS has higher positive predictive values (PPVs) than CMTs. Plasma cfDNA mNGS can be used in addition to CMTs to help doctors provide effective anti-infection treatment and reduce hospital stays.}, } @article {pmid41865546, year = {2026}, author = {Fan, X and Wang, Y and Liang, W and Ma, X and Zhang, W and Yu, C}, title = {Organic fertilizers reduce N2O and NH3 emissions by regulation soil nitrogen pool and microbiome.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129432}, doi = {10.1016/j.jenvman.2026.129432}, pmid = {41865546}, issn = {1095-8630}, mesh = {*Fertilizers ; Nitrogen ; Soil/chemistry ; *Microbiota ; *Ammonia ; *Soil Microbiology ; *Nitrous Oxide ; Animals ; }, abstract = {Organic fertilizers are generally considered beneficial towards maintaining long term soil health, yet they could elevate N2O and NH3 emissions which raise concerns regarding air pollution and climate change. In this study, four types of organic fertilizers (raw sheep manure, RSM; composted sheep-manure organic fertilizer, OF; biochar-amended organic fertilizer, CharOF; sterilized OF, SOF) were applied onto three kinds of soils in microcosm cultivation to explore their effects on N2O and NH3 emissions and the underlining mechanisms. The results showed that traditional organic fertilizers (RSM and OF) significantly increased N2O and NH3 emissions from the soils, whereas CharOF reduced by as much as 23.0% in N2O and 18.4% in NH3 from that of RSM/OF peaks. Both OF and SOF significantly increased soil total nitrogen (TN) and organic nitrogen (Org-N), while CharOF significantly improved soil NO3[-]-N, NH4[+]-N and microbial biomass nitrogen (MBN). Metagenomic sequencing showed that RSM and OF significantly increased denitrification genes norB and narI, dissimilatory nitrate reduction genes nasA, napA and nirB, and mineralization gene ureC, while CharOF slightly suppressed denitrification genes nirS and narI, dissimilatory nitrate reduction genes nasA/B, napA, nirB and NR, and mineralization gene ureC. RDA analysis revealed that NO3[-]-N, NH4[+]-N, MBN and pH were the environmental factors affecting NC relevant genes and gas emissions. PLS-PM model revealed that soil nitrogen pool correlated stronger to the NH3 and N2O emissions than that of nitrogen cycle (NC) relevant genes. This study provides a theoretical foundation for the promotion of low-pollution fertilization practices in green agriculture, and contributes to the advancement of agricultural sustainability. Additionally, it offers fresh perspectives on organic fertilizer production and its role in enhancing socio-economic systems for public benefits.}, } @article {pmid41865575, year = {2026}, author = {Xie, H and Zhou, J and Shi, Y}, title = {Bioaugmentation of weathered petroleum-contaminated soil with a yeast-based consortium: Degradation performance and mechanism insights.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141830}, doi = {10.1016/j.jhazmat.2026.141830}, pmid = {41865575}, issn = {1873-3336}, mesh = {*Petroleum/metabolism ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Saccharomyces cerevisiae/metabolism/genetics ; *Soil Microbiology ; *Hydrocarbons/metabolism ; Microbial Consortia ; }, abstract = {Bioremediation of total petroleum hydrocarbons (TPHs) in weathered soil is often constrained by the inefficiency of indigenous microbial synergistic networks. The mechanisms governing these network responses remain poorly understood, frequently overlooking the system-level functional dynamics. This 7-week study contrasted biostimulation (NZ) with yeast-based bioaugmentation (NS), linking microbial succession and functional network reconstruction to TPHs degradation. The NS group showed a clear advantage in TPHs removal (83.1%) and, crucially, in degrading the heavy C22-C40 fraction (76.3%). The NZ community, despite possessing degradation genes, was trapped in a "functional lock", lacking a cohesive synergistic network. The TPHs and heavy C22-C40 fraction removal efficiencies of the NZ community are only 75.3% and 39.3%, respectively. In contrast, the introduced Saccharomyces cerevisiae in the NS group acted as a pioneer species. It initiated a system-wide reconstruction by (1) altering the soil microenvironment through intense metabolic stress responses (e.g., upregulation of protein quality control systems and high-affinity MFS transporters) and (2) activating a novel, synergistic indigenous consortium, including Altererythrobacter and Cellulosimicrobium. It is indicated that effective bioaugmentation is not the mere addition of strains but a deliberate ecological network reconstruction. The pioneer species alleviates the functional stagnation of the native community, driving the emergence of a novel, highly effective synergistic degradation system. This provides a key theoretical basis for developing bioremediation technologies centered on ecological network regulation.}, } @article {pmid41865593, year = {2026}, author = {Asokan, S and Banerjee, N and Saleem, M and Atiyah, HM and Pandey, RK and Abbas, RK and Yousif, SIA and Radhamanalan, G and Parashar, A and Gowtham, B and Balaji, VK and Jacob, T and Vijayan, S and Rajeswary, D and Atiyah, MM}, title = {Healthcare associated infections (HAI): Insights into epidemiology, microbiology, and diagnostics.}, journal = {Diagnostic microbiology and infectious disease}, volume = {115}, number = {3}, pages = {117376}, doi = {10.1016/j.diagmicrobio.2026.117376}, pmid = {41865593}, issn = {1879-0070}, mesh = {Humans ; *Cross Infection/epidemiology/diagnosis/microbiology/prevention & control ; Biofilms ; Infection Control/methods ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Healthcare associated infections remain a major global health concern because they increase illness, mortality, hospital stay, and healthcare costs. This review provides an updated synthesis of recent evidence on the epidemiology, microbiology, diagnostics, and prevention of healthcare associated infections. These infections arise from patient susceptibility, invasive procedures, antibiotic overuse, contaminated equipment, and poor infection control practices. Device associated infections such as catheter associated urinary tract infection, central line associated bloodstream infection, ventilator associated pneumonia, and surgical site infection are common and often involve multidrug resistant pathogens. Biofilm formation on devices and hospital surfaces creates persistent reservoirs that promote resistance spread. Advances in automated culture systems, rapid molecular assays, metagenomics, and whole genome sequencing improve detection and surveillance. This article integrates evidence from 2020 to 2025 to provide a multidisciplinary framework for understanding and controlling HAIs.}, } @article {pmid41865818, year = {2026}, author = {Wang, J and Sun, Y and Zhang, Y and Guo, Y and Liu, J and Wang, X and Yang, Y and Shi, L}, title = {Mechanisms underlying differences in nitrogen removal characteristics of anammox granular sludge immobilization filler with varying particle sizes: Performance, structure, and nitrogen removal pathways.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134471}, doi = {10.1016/j.biortech.2026.134471}, pmid = {41865818}, issn = {1873-2976}, mesh = {*Nitrogen/isolation & purification ; Particle Size ; *Sewage/microbiology/chemistry ; Bacteria/metabolism ; Oxidation-Reduction ; Anaerobic Ammonia Oxidation ; }, abstract = {The anaerobic ammonium oxidation (anammox) process serves as a green, low-carbon, and sustainable wastewater nitrogen removal technology. However, anammox processes based on granular sludge systems face structural instability issues, resulting in the loss of anammox bacteria (AnAOB). In this study, an immobilized filler system for AnAOB based on hydrogel encapsulation was constructed using anammox granular sludge (AnGS) of varying particle sizes (G1: < 0.10 cm, G2: 0.10-0.20 cm, G3: 0.20-0.32 cm, and G4: > 0.32 cm). The differences in nitrogen removal characteristics, microstructures, and pathways of these AnGS immobilized fillers were thoroughly investigated. The large particles (G3 and G4) immobilized fillers showed the best nitrogen removal performance, with total nitrogen removal rates reaching 0.591 kgN·m[-3]·d[-1] and 0.615 kgN·m[-3]·d[-1], respectively. The G2 immobilized filler was more conducive to the self-growth and enrichment of AnAOB, and the absolute abundance and relative abundance of Candidatus Brocadia increased by 23-fold and 9.20-fold, respectively. Conversely, the G1 immobilized filler displayed the poorest nitrogen removal rate due to insufficient microbial growth. The G1-G3 immobilized fillers possessed uniform and dense small pores, whereas the G4 filler featured uniform large pores. Metagenomic analysis confirmed that the abundance of denitrification-related genes in G3 and G4 immobilized fillers was highest, indicating that anammox and denitrification synergistically achieve nitrogen removal, whereas G2 immobilized fillers mainly relied on anammox. This study provides a crucial theoretical basis and technical guidance for optimizing the application of anammox immobilized filler systems.}, } @article {pmid41865820, year = {2026}, author = {Luo, Z and Li, W and Zhang, N and Lei, M and Chen, B and Li, Y and Liu, Q and Zhang, M and Lv, S and Cheng, F and Li, J}, title = {A novel continuous-flow three-stage tandem system based on partial nitrification/Anammox granular sludge and partial denitrification-Anammox biofilm (PN/A-PD-A) for advanced nitrogen removal from mature landfill leachate.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134474}, doi = {10.1016/j.biortech.2026.134474}, pmid = {41865820}, issn = {1873-2976}, mesh = {*Biofilms ; *Nitrogen/isolation & purification ; *Denitrification ; *Nitrification ; *Sewage/microbiology ; *Water Pollutants, Chemical/isolation & purification ; Bioreactors/microbiology ; Continuous Flow Chemistry ; Anaerobic Ammonia Oxidation ; Water Purification/methods ; }, abstract = {A novel continuous-flow system coupling partial nitrification/Anammox (PN/A), partial denitrification (PD), and Anammox (Amx) biofilm reactors was developed (PN/A-PD-A) to treat mature landfill leachate (MLL). To maximize synergy, the NH4[+]-N removal in the PN/A reactor was regulated based on the NO2[-]-N accumulation ratio (NAR) in the PD stage, ensuring optimal substrate stoichiometry for the final Amx polishing step. Over 174 days of operation, the system achieved a superior total nitrogen removal efficiency (TNRE) of 98.30 ± 0.14% (effluent TN: 21.80 ± 1.71 mg/L). The PN/A granular sludge, enriched with Candidatus_Kuenenia (5.87%) and Nitrosomonas (9.73%), demonstrated high adaptability to MLL characteristics and contributed to 83.51% of the TN removal. In the PD stage, the dominant genus Thauera (43.91%) facilitated efficient NAR (82.86 ± 1.61%) at a limited COD/NO3[-]-N ratio of 2.32 ± 0.02. The Anammox biofilm (Candidatus_Kuenenia, 27.80%) in the Amx reactor contributed to 13.10% of TN removal, ensuring to meet the MLL discharge standard. Kinetic and metagenomic analyses confirmed that distinct shifts from complete to partial nitrification (and denitrification) in enzymes activity and gene abundance under chronic MLL stress underpinned the robust NO2[-]-N accumulation in both PN/A and PD reactors. Notably, compared to conventional nitrification-denitrification process, the PN/A-PD-A system significantly reduced oxygen demand (60.18%), exogenous organic carbon consumption (91.61%), sludge yield (83.72%), and CO2 emission (94.66%), demonstrating a sustainable pathway for low-carbon nitrogen removal from high-strength wastewater.}, } @article {pmid41865821, year = {2026}, author = {Wang, X and Liang, BJ and Wu, DN and Zhang, XM and Zhao, HP and Lai, CY}, title = {Efficient anaerobic metformin biodegradation driven by a Cross-Feeding Consortium: Novel Pathways, Enzymes, and toxicity dynamics.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134473}, doi = {10.1016/j.biortech.2026.134473}, pmid = {41865821}, issn = {1873-2976}, mesh = {*Metformin/metabolism/toxicity ; Bioreactors/microbiology ; Biodegradation, Environmental ; Anaerobiosis ; Water Pollutants, Chemical/metabolism ; }, abstract = {Metformin is one of the most widely prescribed antidiabetic drugs worldwide and is now ubiquitously detected in aquatic environments, yet its anaerobic biodegradation remains largely unexplored and mechanistically unresolved. Here, an anaerobic membrane bioreactor (AnMBR) was operated and near-complete metformin removal (∼98%) at influent concentrations up to 5.3 mg/L was achieved, corresponding to a maximum degradation rate of 7.2 mg/L/d, approximately sixfold higher than previously reported anaerobic systems degrading metformin. High-resolution mass spectrometry identified three concurrent anaerobic metformin transformation pathways. Notably, a previously unreported biological -C-N bond cleavage route yielding dimethylguanidine was discovered, expanding the known anaerobic metabolic repertoire of metformin. In silico toxicity prediction revealed a non-monotonic toxicity trajectory during metformin transformation, with transiently elevated toxicity at intermediates (particularly 2,4-AMT) followed by an overall attenuation at the terminal product guanidine. Metagenomic and metatranscriptomic analyses uncovered a cooperative, cross-feeding microbial network dominated by Ignavibacterium album and Denitrolinea symbiosum, and identified HypAB (metformin-to-guanylurea), YafV and AmiA/B/C/E (guanylurea-to-guanidine), and, critically, SpeB as the key enzyme initiating the newly proposed -C-N bond cleavage pathway. Molecular dynamics simulations further suggested stable binding of metformin to SpeB with strong affinity, providing mechanistic support for SpeB-mediated initiation of the novel pathway. Overall, this study establishes the first mechanistic framework for anaerobic metformin biodegradation, reveals an unprecedented -C-N scission pathway, and demonstrates that high-rate, low-carbon pharmaceutical removal can be achieved through intrinsic microbial metabolism, offering new conceptual and practical foundations for energy-efficient treatment of emerging pharmaceutical contaminants.}, } @article {pmid41865866, year = {2026}, author = {Wang, Y and Wang, D and Wang, H}, title = {Comparative analysis of the gut microbiome and bile acid profiles in sympatric Rana chensinensis and Fejervarya multistriata tadpoles.}, journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology}, volume = {316}, number = {}, pages = {111996}, doi = {10.1016/j.cbpa.2026.111996}, pmid = {41865866}, issn = {1531-4332}, mesh = {Animals ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; Larva/microbiology/metabolism ; *Ranidae/microbiology/metabolism/growth & development ; Metagenomics ; Sympatry ; }, abstract = {Environmental temperature is an essential exogenous factor influencing the gut microbiota of amphibians, which exerts profound physiological impacts on the host by modifying bile acids (BAs). Even sympatric amphibians often have considerably different optimal breeding temperatures. However, the effect of different developmental temperatures on gut microbiota and BA profiles in sympatric amphibians remains unclear. To address this deficiency, morphological, histological, metagenomics and metabolomics information were compared between Rana chensinensis (R. chensinensis) and Fejervarya multistriata (F. multistriata) tadpoles. Morphological and histological results showed that body mass index (BMI), intestinal mass to body mass ratio (IM/BM), and enterocyte height (EH) were higher in F. multistriata, whereas body mass (BM), total length (TL), and intestine mass (IM) were higher in R. chensinensis. Metagenomics analysis revealed the relative abundance of microorganisms (Bacteroides, Clostridium, and Enterococcus) producing bile salt hydrolase (BSH) is higher in F. multistriata, whereas the relative abundance of microorganisms (Dorea spp, Extibacter muris, Clostridium leptum, and Proteocatella sphenisci) possessing the BAI operon is higher in R. chensinensis. Comparative metabolomic analysis identified that F. multistriata has a higher ratio of unconjugated to conjugated BAs (CA/TCA, CDCA/TCDCA, and DCA/TDCA), which may suppress the abundance of pathogen (e.g., Clostridioides difficile). Additionally, the lower TDCA content in F. multistriata may be potentially linked to its stronger absorptive capacity. In contrast, R. chensinensis exhibits a higher ratio of DCA to CA, which probabaly enhance their cold tolerance. Overall, this study elucidated the potential impacts of developmental temperature-driven differences in gut microbiota and BAs on sympatric amphibians' physiological metabolism.}, } @article {pmid41865966, year = {2026}, author = {Zhou, L and Zhu, S and Wu, J and Wang, W and Zhao, Z and Hao, X and Wang, J and Yu, W and Li, Y and Liang, J}, title = {Co-inoculation of arbuscular mycorrhizal fungi and rhizobia reshapes microbial ecology and nutrient metabolism to rehabilitate iron ore tailings.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124325}, doi = {10.1016/j.envres.2026.124325}, pmid = {41865966}, issn = {1096-0953}, mesh = {*Mycorrhizae/metabolism/physiology ; *Soil Microbiology ; *Rhizobium/metabolism/physiology ; *Iron/metabolism ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; Mining ; Medicago sativa/metabolism ; Nutrients/metabolism ; Nitrogen/metabolism ; Cadmium/metabolism ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) and rhizobia play crucial roles in soil-plant systems for ecological restoration. However, their specific remediation characteristics and synergistic effects on tailings remain poorly understood. In this study, we investigated the remediation characteristics of tailings inoculated with AMF and rhizobia, focusing specifically on synergy mechanism for iron tailings improvement under the co-inoculation. The results demonstrated that microbial inoculation significantly enhanced overall remediation performance. The co-inoculation led to a 6.25-fold increase in alfalfa biomass, substantial improvements in nutrient availability (N/C/P), and enhanced soil structure through aggregate formation. Concurrently, the cadmium bioavailability was effectively reduced by 35.56%. Functional metabolic analysis revealed that the upregulation of phosphate-related genes (phoB, phoR) enhanced microbial phosphate solubilization and plant phosphate uptake efficiency. Furthermore, the primary pathways for nitrogen uptake shifted from reliance on biological nitrogen fixation to prioritizing internal nitrogen cycling, while activation of the GABA shunt reduced dependence on the TCA cycle. Notably, the restructured microbial community preferentially stimulated organic carbon-nitrogen (C/N) metabolism, and these metabolic shifts were key to enhanced plant nutrients acquisition efficiency. These findings indicate that AMF and rhizobia could stimulate microbial community restructuring and drive the remodeling of nutrient metabolism in tailings, representing a pivotal process in promoting soil formation from tailings.}, } @article {pmid41866358, year = {2026}, author = {Deepthi, M and Vadakkadath Meethal, K}, title = {Bacterially expressed recombinant TMOF induces mortality and gut microbial alterations in Aedes albopictus larvae.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41866358}, issn = {2045-2322}, abstract = {UNLABELLED: Mosquitoes, as vectors of numerous diseases, pose significant threat to human health. Aedes mosquitoes transmit diseases such as dengue, yellow fever and chikungunya, with dengue fever alone responsible for approximately 40,000 deaths and more than 96 million symptomatic cases annually. Current mosquito control methods are inadequate and results in environmental health hazards and development of resistance. Therefore, targeted control strategies are essential. In this context, we cloned and expressed the Trypsin Modulating Oostatic Factor (TMOF), a decapeptide that inhibits trypsin biosynthesis in mosquitoes by binding to a receptor. The codon-optimized gene for the TMOF peptide was synthesised and cloned in to pFN29AHis6Halo vector and expressed in Escherichia coli. The supernatant from the bacterial lysate containing recombinant TMOF peptide exhibited larvicidal activity against Aedes albopictus mosquito larvae, with an LC50 (48 h) of 242.1 ± 6.04 µg/mL. However, lysate from BL21 cells alone or recombinant peptide expressed with a single base shift in reading frame did not cause any mortality. The recombinant TMOF peptide was purified using nickel affinity chromatography and showed an LC50 of 2.13 ± 0.02 µg/mL, exhibiting 113.6 times more efficacy than the bacterial lysate supernatant. The LC90 (48 h) for bacterial lysate and affinity purified TMOF was 340.41 ± 6.04 µg/mL and 4.39 ± 0.20 µg/mL, respectively. TMOF peptide released from the recombinant protein by trypsin digestion also showed larvicidal activity. Exposure of larvae to TMOF fusion protein resulted in inhibition of trypsin biosynthesis in-vivo. Metagenomic analysis of the gut microbiota from TMOF-treated larvae resulted in reduction in abundance of bacteria belonging to Pseudomonadota and Bacillota compared to that of untreated larvae. Recombinant TMOF is also effective against Culex mosquito larvae, but shows no effects on non-target organisms such as Drosophila melanogaster, Luprops tristis, and Aplocheilus lineatus. Thus, the use of TMOF expressed in E. coli offers a promising eco-friendly method of mosquito control. (Patent number: 554267).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41440-3.}, } @article {pmid41866421, year = {2026}, author = {Mathur, S and Prasad, M and Kumar, S and Chaurasia, A and Ranjan, R}, title = {A metagenomic survey of the rhizosphere bacterial community of P. longum from the herbal garden, Dayalbagh Educational Institute (D.E.I), Agra, India.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41866421}, issn = {1573-0972}, abstract = {The rhizosphere of medicinal plants harbors complex microbial communities that plays a key role in nutrient cycling, plant growth, and environmental adaptation. Piper longum L., an important medicinal plant, remains poorly explored with respect to its rhizospheric microbiome. In this study, rhizospheric soil samples of P. longum were collected at the spike stage from the Herbal Garden of Dayalbagh Educational Institute, Agra, India, and analyzed using metagenomic approach. Soil physicochemical analysis revealed a neutral to slightly alkaline pH with moderate nutrient availability, indicating favorable conditions for microbial activity. High-throughput Illumina sequencing generated ~ 19.94 million paired-end reads (~ 5.92 Gb), which were assembled into 97,432 scaffolds (52.26 Mb total length), and 45,876 protein-coding genes were predicted. Taxonomic profiling revealed dominance of Proteobacteria (42%), followed by Actinobacteria (13.9%), Thaumarchaeota (13.16%), Chloroflexi (8.21%), and Acidobacteria (7.28%). At the genus level, Nitrososphaera was the most abundant (23.58%), with Candidatus Nitrososphaera gargensis as the predominant species (11.21%), indicating an active microbial community of ammonia-oxidizing archaea involved in nitrogen fixation. Functional annotation using COG, KEGG, Pfam, GO, and FIGfams databases revealed enrichment of genes associated with amino acid transport and metabolism, carbohydrate metabolism, energy production, and environmental adaptation. Overall, this study provides the first metagenomic baseline of the P. longum rhizosphere microbiome and highlights its potential role in nutrient cycling and sustainable cultivation.}, } @article {pmid41866581, year = {2026}, author = {Halo, BA and Aljabri, YAS and Glick, BR and Yaish, MW}, title = {Metagenomic and functional insights into root endophytic bacteria associated with drought stress in cowpea.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41866581}, issn = {2045-2322}, support = {IG/SCI/BIOL/24/03//Sultan Qaboos University, College of Science, Oman/ ; }, abstract = {UNLABELLED: Endophytic bacterial communities enhance plant drought resilience, yet their dynamics in cowpeas (Vigna unguiculata) remain poorly understood. To explore this, we analyzed the root endophytic bacteriome under drought stress using 16 S rRNA gene metagenomics and evaluated isolated bacteria for plant growth-promoting traits. Drought significantly reduced both alpha and beta diversity, indicating a loss of microbial richness and evenness and community homogenization. Taxonomic shifts revealed enrichment of Cyanobacteriota, Cyanophyceae, and Marileptolyngbya sina in drought conditions. Forty-seven endophytic isolates were identified and characterized, including Enterobacter spp., Bacillus spp., Leclercia adecarboxylata, and Stenotrophomonas spp. The isolated strains exhibited plant growth-promoting traits in vitro and, in a pot assay, some enhanced wheat biomass under both control and drought conditions. The reduction in diversity due to drought indicates a loss of microbial richness and evenness, along with homogenization of microbial composition, suggesting that drought selectively enriches specific taxa, which may enhance plant stress resilience through specialized metabolic functions. By combining metagenomic profiling with functional assays, this study highlights the role of drought-induced bacterial shifts in supporting plant growth and development. These insights could lead to the development of microbial inoculants to improve crop drought tolerance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-45459-4.}, } @article {pmid41866595, year = {2026}, author = {Taha, MME and Abdelwahab, SI and Binjomah, AZ and Memish, Z and Sahli, KA and Qadri, M and Alarifi, A and Khardali, A and Farasani, A and Madkhali, F and Moshi, JM and Alsaadi, KH and Alshahrani, S}, title = {Mapping the genomic frontier: a comprehensive bibliometric analysis and thematic evolution of whole-genome sequencing for Mycobacterium tuberculosis (1994-2025).}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41866595}, issn = {1573-0972}, abstract = {Whole-genome sequencing of Mycobacterium tuberculosis (WGS-TB) has revolutionized tuberculosis research by providing high-resolution insights into drug resistance, transmission dynamics, and evolutionary pathways. However, the global research landscape, collaboration networks, and thematic evolution of WGS-TB remain underexplored. A comprehensive dataset of WGS-TB publications was retrieved from Scopus. Analyses were conducted using Bibliometrix for productivity trends, Lotka’s and Bradford’s Laws, normalized word cloud, and thematic mapping; VOSviewer for co-authorship, co-occurrence, bibliographic coupling, and unsupervised term clustering; and CiteSpace for reference co-citation analysis (RCCA) and thematic evolution. Between 1994 and 2025, WGS-TB publications exhibited exponential growth, particularly after 2015. The United States, China, and the United Kingdom were leading contributors, supported by globally connected institutions. Collaboration networks revealed strong North–South partnerships, with South Africa acting as a critical bridge. Keyword and thematic analyses identified dominant themes such as drug resistance, genomics, and epidemiology, with emerging areas including metagenomic sequencing and mutation dynamics. Bradford’s Law identified 12 core journals, while RCCA delineated clusters in drug resistance surveillance and molecular epidemiology. This study offers the first integrative mapping of WGS-TB research, illuminating its thematic evolution, global collaboration structure, and emerging directions in genomic surveillance and precision medicine.}, } @article {pmid41867450, year = {2026}, author = {Jia, C and Liu, X and Liu, W and Yao, X and Chen, X and Zhao, J and Wang, P and Ge, W and Han, Y}, title = {Multi-Omics Reveal the Potential Associations of Streptococcus, 13'-Hydroxy-Alpha-Tocopherol and Glutathione Metabolism in Children with Chronic Rhinosinusitis with Nasal Polyps.}, journal = {Journal of inflammation research}, volume = {19}, number = {}, pages = {567582}, pmid = {41867450}, issn = {1178-7031}, abstract = {BACKGROUND: Chronic rhinosinusitis with nasal polyps (CRSwNP) in children is a clinically significant inflammatory disorder characterized by persistent symptoms and complex underlying mechanisms. This study used multi-omics approaches to investigate potential microbial and metabolic associations in pediatric CRSwNP.

METHODS: Nasal secretions from 20 children with CRSwNP and 19 healthy controls were analyzed using metagenomics, untargeted metabolomics, and proteomics.

RESULTS: CRSwNP patients showed higher microbial diversity and altered microbial communities, with increased Streptococcus abundance. Metabolomic sequencing revealed that 13'-Hydroxy-alpha-tocopherol was significantly upregulated in the CRSwNP group and exhibited a positive correlation with the abundance of Streptococcus. Proteomic sequencing revealed that proteins involved in glutathione metabolism were significantly downregulated in the CRSwNP group, with GCLM and GGCT showing a significant negative correlation with 13'-Hydroxy-alpha-tocopherol.

CONCLUSION: These associative findings suggest potential links among Streptococcus, 13'-Hydroxy-α-tocopherol, and glutathione metabolism, indicating that oxidative stress-related imbalance may contribute to pediatric CRSwNP. These results provide preliminary evidence that 13'-Hydroxy-α-tocopherol may serve as a potential biomarker for pediatric CRSwNP.}, } @article {pmid41867493, year = {2025}, author = {Alali, M and Imani, M}, title = {Bayesian Topology Inference of Regulatory Networks under Partial Observability.}, journal = {Results in control and optimization}, volume = {19}, number = {}, pages = {}, pmid = {41867493}, issn = {2666-7207}, support = {R21 EB032480/EB/NIBIB NIH HHS/United States ; }, abstract = {Biological systems, such as microbial communities in metagenomics and gene regulatory networks (GRNs) in genomics, are composed of a vast number of interacting components observed through inherently noisy data. These systems play a critical role in understanding fundamental biological processes, including gene regulation, microbial interactions, and cellular dynamics. For example, microbial communities involve complex interactions between microbes, bacteria, genes, and small molecules observed through omics data, while GRNs consist of numerous interacting genes observed via various gene-expression technologies. However, reconstructing the topology of such networks poses significant challenges due to their large scale, high dimensionality, and the presence of noise. Existing inference techniques often struggle with scalability, interpretability, and overfitting, making them unsuitable for analyzing large and complex biological systems. To overcome these challenges, this paper proposes a Bayesian topology optimization framework for efficient and scalable inference of regulatory networks modeled as partially-observed Boolean dynamical systems (POBDS). The method combines the Boolean Kalman Filter (BKF) as an optimal estimator for POBDS, with Bayesian optimization, which employs Gaussian Process regression and a topology-inspired kernel function to model the log-likelihood function. Numerical experiments demonstrate the superior performance of our framework. In the p53-MDM2 network, our method accurately infers topology with 8 and 16 unknown regulations, achieving higher log-likelihood with 100 and 200 evaluations, respectively. For the mammalian cell cycle network with 10 unknown regulations, proposed method identifies the correct topology among 59,049 possibilities with lower error and faster convergence.}, } @article {pmid41867523, year = {2026}, author = {Kanno, N and Ohtani, T and Oda, N and Kato, S and Ohkuma, M and Shigeto, S}, title = {Domain-Level Classification of Archaea and Bacteria Using AI-Assisted Single-Cell Raman Spectroscopy.}, journal = {ACS omega}, volume = {11}, number = {10}, pages = {16913-16921}, pmid = {41867523}, issn = {2470-1343}, abstract = {Archaea and Bacteria are two fundamentally distinct domains of life that share prokaryotic traits, yet differ markedly in molecular and cellular architecture. While many archaeal species identified thus far have been found in extreme environments, recent metagenomic studies have revealed their widespread presence in moderate habitats, including soils, oceans, and even the human microbiome. However, archaea remain less well characterized than bacteria, largely due to the technical challenges associated with culturing and identifying these microorganisms. In this study, we present a culture-independent method for discriminating archaea from bacteria at the single-cell level using Raman spectroscopy combined with machine learning. We constructed a Raman spectral data set comprising 22 prokaryotic species (11 archaea and 11 bacteria) and developed a domain-level Archaea-Bacteria (AB) classifier using the LightGBM tree-based machine learning algorithm. Our AB classification model achieved an average classification accuracy of 89.1% and a sensitivity of 98.1% on eight representative species (including two independent held-out test species) with minimal data size and preprocessing. We also compared its performance to convolutional neural networks with transfer learning, a widely used deep learning approach. Our method provides a robust analytical framework for archaeal detection and represents a valuable addition to the microbiological toolkit, particularly for studying unculturable or low-abundance archaeal populations in complex microbial communities.}, } @article {pmid41867691, year = {2026}, author = {Jiang, D and Wang, Y and Ling, Y and Eremin, SA and Mukhametova, LI and Du, J and Hu, H}, title = {Impacts of high-temperature and humidity transportation on rice quality: an integrated analysis of microbial community succession and flavor compound alterations.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1792369}, pmid = {41867691}, issn = {2296-861X}, abstract = {This study investigated the dynamic changes in rice quality, microbial communities, and volatile compound profiles during simulated summer transportation (35 °C, 70% RH, 15 days). Indica rice samples were systematically collected every 3 days and analyzed using HS-SPME-GC-MS/MS, HS-GC-IMS, and metagenomic sequencing. Prolonged transportation significantly altered the physicochemical properties of the rice. Moisture content plateaued on day 12, while germination rates declined significantly starting from day 6. Furthermore, fatty acid values increased continuously due to accelerated lipid hydrolysis and oxidation. Visible mold growth became evident on day 12, marking a critical tipping point for quality deterioration. The odor activity value (OAV) and relative odor activity value (ROAV) analyses revealed that the decline in unsaturated fatty aldehydes such as (E)-2-nonenal and the significant accumulation of alcohols, ketones, and short-chain esters, including 1-octen-3-ol and ethyl acetate, drove the transition from a "fresh and fatty" aroma to one characterized by moldy, fermented, and pungent notes. Metagenomic analysis demonstrated a profound ecosystem shift from bacterial dominance (Proteobacteria, Actinobacteria) to fungal dominance. Notably, Lichtheimia surged from <0.01% to 23.95%, becoming the dominant genus, while Aspergillus increased from 0.03% to 4.57%. Correlation analysis indicated that while Pseudomonas was associated with elevated fatty acid levels, the flavor shift was primarily linked to microbial succession. These findings provide insights into the synergistic mechanisms of rice spoilage and suggest that specific volatile markers could serve as early warning indicators for quality control in real-world grain logistics.}, } @article {pmid41867766, year = {2026}, author = {Schmitt, MS and Lee, KK and Bunbury, F and Landsittel, JA and Vitelli, V and Kuehn, S}, title = {Learning functional groups in complex microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41867766}, issn = {2692-8205}, abstract = {From soil to the gut, communities composed of thousands of microbes perform functions such as carbon sequestration and immune system regulation. Here, we introduce a data-driven approach that explains how community function can be traced to just a few groups of microbes or genes. In gut communities, our neural-network based clustering algorithm correctly recovers known functional groups. In the ocean metagenome, it distills ~500 gene modules down to three sparse groups highlighting survival strategies at different depths. In soils, it distills ~4400 bacterial species into two groups that enter a mathematical model of nitrate metabolism. By combining interpretable ML with strain isolation and sequencing experiments, we connect the metabolic specialization of each group to community-wide responses to perturbations. This integrated approach yields simple structure-function maps of microbiomes, allowing the discovery of molecular mechanisms underlying human and environmental health. More broadly, we illustrate how to do function-informed dimensionality reduction in biology.}, } @article {pmid41867767, year = {2026}, author = {Nguyen, MH and Schatz, MC}, title = {Perseus: Lineage-Aware Refinement of Kraken2 Taxonomic Classification for Long Read Metagenomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41867767}, issn = {2692-8205}, abstract = {MOTIVATION: Long-read metagenomic sequencing improves assembly contiguity and enables genome-resolved analysis of complex microbial communities, but accurate taxonomic classification of long reads and assembled contigs remains challenging. Highly scalable k-mer-based classifiers such as Kraken2 frequently over-assign fine-rank taxonomic labels when applied to long-read data, producing high false positive classification rates driven by sparse or localized k-mer matches, particularly in microbiomes with extensive taxonomic novelty.

RESULTS: We present Perseus, a lineage-aware confidence estimation framework for taxonomic classification that models the spatial distribution and hierarchical consistency of k-mer evidence along sequences. This formulation reframes taxonomic classification as a hierarchical confidence estimation problem rather than a single-rank prediction task. Perseus refines k-mer-level taxonomic signals from Kraken2 using a multi-headed convolutional neural network that estimates calibrated confidence scores for taxonomic correctness at each canonical rank. Using these estimates, Perseus confirms assignments, backs off to higher taxonomic ranks, or abstains when evidence is insufficient, prioritizing correctness and lineage consistency over overly specific assignments. Across simulations of taxonomic novelty and real-world metagenomic datasets, Perseus consistently and substantially reduces the false assignment rate while improving precision and lineage-consistent accuracy. These improvements are most pronounced for long reads and assembled contigs, where spatial context enables reliable discrimination between consistent taxonomic signal and spurious matches.

Perseus integrates with existing Kraken2 workflows and is available at https://github.com/matnguyen/perseus.}, } @article {pmid41868021, year = {2026}, author = {Zhan, M and Tu, S and Yang, S and Yin, Y and Wang, Z and Zhang, F and Zhang, Y and Wang, Q and Zhao, C and Wang, X and Wang, H and Chen, H}, title = {Clinical Utility of Metagenomic Next-Generation Sequencing in Diagnosing Central Nervous System Infections in Hematopoietic Stem Cell Transplant Recipients: A Retrospective and Prospective Cohort Study.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {554425}, pmid = {41868021}, issn = {1178-6973}, abstract = {BACKGROUND: Diagnosing central nervous system infections (CNSI) in hematopoietic stem cell transplant (HSCT) recipients remains challenging due to nonspecific presentations and low sensitivity of conventional microbiological methods.

METHODS: This study evaluated the clinical utility of cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) in 127 HSCT recipients (87 retrospective, 40 prospective) from Peking University People's Hospital. Pathogens detected by mNGS and conventional methods were validated via Sanger sequencing.

RESULTS: mNGS identified 20 pathogen-positive samples (19 confirmed by sequencing), while conventional methods detected none. mNGS demonstrated 82.6% sensitivity and 99.0% specificity for CNSI diagnosis, with sensitivity rising to 100.0% when combined with conventional approaches. Notably, mNGS excelled in detecting viral pathogens, particularly in allogeneic HSCT recipients.

CONCLUSION: Our findings advocate for the integration of mNGS into the diagnostic algorithm for CNSI, especially in immunocompromised hosts. This approach enables earlier and more precise pathogen identification, which has the potential to streamline antimicrobial therapy and improve clinical management. To maximize its benefit and ensure reliable interpretation, mNGS results should be correlated with comprehensive clinical and paraclinical data. Further prospective studies are warranted to validate its impact on therapeutic decision-making and patient prognosis.}, } @article {pmid41868024, year = {2026}, author = {Wang, QL and Teng, SN and Zhang, XJ and Guo, YX and Kong, Y and Tian, XH and Zhang, Y}, title = {Fatal Primary Amoebic Meningoencephalitis in Coastal Areas of North China in an Immunocompetent Patient: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {559408}, pmid = {41868024}, issn = {1178-6973}, abstract = {PURPOSE: Primary amoebic meningoencephalitis (PAM) is a rapidly fatal infection caused by Naegleria fowleri (N. fowleri) with a mortality rate exceeding 95%. This study presented the clinical course, diagnosis, treatment, and outcome of a confirmed PAM case in an adult female. Additionally, we analyzed the epidemiology of PAM in China and review the therapeutic regimens of surviving cases worldwide, aiming to enhance disease awareness and improve clinical outcomes.

CASE PRESENTATION: The patient was a 50-year-old immunocompetent woman with a history of hot spring bathing before symptom onset, which was not initially disclosed. Moreover, her early infectious symptoms, particularly fever following a tick bite in an orchard, directed clinical suspicion toward tick-borne disease. Four days later, she was hospitalized with generalized convulsions and coma. Clinical examination suggested a bacterial intracranial infection, and treatment with meropenem and vancomycin was initiated. However, her condition deteriorated rapidly. The presence of N. fowleri was identified by cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) and smear. The etiology was clarified only after retrospective confirmation of hot spring contact, which was later confirmed by blood mNGS. Despite intensive therapy with amphotericin B (AmB), the patient unfortunately died. To provide insights into PAM management in China, we also conducted a systematic analysis of 15 domestic cases and 18 global survivors.

CONCLUSION: PAM is characterized by rapid progression, underscoring the importance of early diagnosis. In cases of rapidly advancing meningoencephalitis, clinicians should maintain a high index of suspicion for rare pathogens such as N. fowleri, with thorough and repeated assessment of recent environmental exposures such as hot spring immersion or freshwater swimming. Early application of mNGS is essential for timely pathogen identification. While AmB remains the first-line therapy, its dosing and duration should be tailored to individual patient factors, and combination therapy should be considered to enhance efficacy. Overall, improved clinical vigilance, advanced pathogen diagnostics, and standardized anti-amoebic therapy form the cornerstone of enhancing outcomes in PAM. As the first documented PAM case in Shandong Province, China, this report highlights the need for heightened awareness in coastal regions while contributing valuable epidemiological insights into this devastating disease.}, } @article {pmid41868028, year = {2026}, author = {Wang, Z and Ma, R and Ding, Z and Ma, L and Liu, X and Wang, Y}, title = {Brucellosis Complicated by Thyroid Abscess and Life-Threatening Hemophagocytic Syndrome: A Case Report.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {583365}, pmid = {41868028}, issn = {1178-6973}, abstract = {INTRODUCTION: Brucella infections can affect various systems in the body, such as the osteoarticular and genitourinary systems; however, cases involving the thyroid gland are rare. This case report describes the clinical management of a thyroid abscess associated with brucellosis in a farmer.

CASE PRESENTATION: A 67-year-old male farmer presented to Shanxi Bethune Hospital on 17 March 2024 with a chief complaint of "intermittent fever with fatigue for over 3 months and neck swelling and pain for 2 months". Upon admission, his serum Brucella tube agglutination test titre was 1:200, Rose Bengal plate agglutination test was positive, and blood culture was negative for Brucella. Neck computed tomography revealed a low-density nodular shadow in the right thyroid lobe measuring approximately 4.79×4.45 cm. Coffee-coloured pus was aspirated during thyroid puncture. Pathogenic metagenomic next-generation sequencing and pus culture confirmed Brucella infection as the cause of the thyroid abscess. During treatment, the patient developed hemophagocytic syndrome. The patient's condition was controlled with aggressive anti-infective therapy and glucocorticoid treatment. However, because of symptom recurrence, the patient ultimately underwent surgical intervention, comprising partial thyroidectomy, abscess incision and drainage, and thyroid injection, following which he recovered fully.

CONCLUSION: This article reports an extremely rare case of brucellosis leading to a thyroid abscess. Physicians should consider the possibility of brucellosis when encountering patients with thyroid abscesses and be vigilant of other potential complications.}, } @article {pmid41868358, year = {2026}, author = {Ribeiro-Junior, MR and Cardwell, KF and Nascimento, D and Espindola, AS and Ramachandran, A and Gupta, SK and Tyungu, D}, title = {Rapid detection of human and animal respiratory viruses using Microbe Finder (MiFi[®]).}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1743643}, pmid = {41868358}, issn = {1664-302X}, abstract = {Rapid and accurate detection of respiratory pathogens is essential for timely diagnosis, effective treatment, and outbreak monitoring in both human and veterinary medicine. We evaluated the Microbe Finder (MiFi[®]) software for detection of nine RNA viruses of human and veterinary clinical importance. Species specific signature sequences in the different pathogen genomes were identified, and specific electronic probe sets were curated using the MiFi[®] software. Analytical specificity and sensitivity were evaluated through simulated metagenomes and public sequence databases, respectively. Host-specific internal control probes were designed to ensure diagnostic reliability and quality control. Diagnostic performance was assessed using Oxford Nanopore sequence data from clinical nasal swab samples. In silico validation showed 100% specificity across 83 datasets and limits of detection as low as 0.0010% of total reads (10 reads per 10[6]) for some targets. Internal controls generated stable background signals without interfering with pathogen detection. In vivo testing of 44 clinical samples matched PCR performance for Human respiratory syncytial virus (HRSV), Influenza B virus (IBV), Influenza A virus (IAV), Bovine respiratory syncytial virus (BRSV), and Canine distemper virus (CDV). These findings demonstrate that the MiFi[®] software enables rapid, multiplex, and strain-specific detection of respiratory viruses in metagenomic sequence data without the need for advanced bioinformatics expertise. The approach supports scalable use in clinical laboratories, veterinary diagnostics for surveillance and triage, offering a valuable tool for improving respiratory pathogen detection across diverse settings.}, } @article {pmid41869352, year = {2026}, author = {Zhou, YM and Cui, XQ and Zhao, P and Peng, ZG and Guo, N and Sun, HB and Liu, SL}, title = {The species, distribution, resistance of donor-derived pathogens and their impact on solid organ transplant recipients.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1777244}, pmid = {41869352}, issn = {1664-3224}, mesh = {Humans ; Female ; Retrospective Studies ; Male ; *Tissue Donors ; *Liver Transplantation/adverse effects ; *Kidney Transplantation/adverse effects ; Middle Aged ; Adult ; Transplant Recipients ; *Bacteria/drug effects/isolation & purification ; Drug Resistance, Multiple, Bacterial ; *Organ Transplantation/adverse effects ; Incidence ; *Bacterial Infections ; }, abstract = {BACKGROUND: Donor-derived infections (DDIs) have become a significant cause of infection in organ transplant recipients. Elaborating on the species, distribution, and resistance of donor-derived pathogens (DDPs) holds important implications.

METHODS: A retrospective cohort study included 302 deceased donors and their corresponding 464 kidney transplant recipients and 175 liver transplant recipients. We detected DDPs in preservation fluid (PF) using both conventional culture and mNGS, and subsequently analyzed the incidence of DDIs after transplantation.

RESULTS: 89.4% (270/302) of donors had positive cultures. Predominant multidrug-resistant organism included HLAR-Enterococcus, CRAB, CRKP, CRPA, MRS and ESBL-Escherichia coli. Compared with conventional culture, mNGS exhibited superior sensitivity for detecting bacteria and fungus in PF, with shorter turnaround time (p < 0.001). The incidences of DDIs in kidney and liver transplant recipients were 16.6% (77/464) and 19.4% (34/175) respectively. The recipients with DDIs were associated with elevated serum creatinine or total bilirubin levels, increased infection events, higher risks of graft loss, elevated mortality, and longer length of hospital stay (p < 0.05).

CONCLUSIONS: Multidrug-resistant organism are prevalent in deceased donors, with PF contamination primarily originating from donors. Integration of mNGS into donor screening protocols enables timely antimicrobial intervention, potentially improving transplant outcomes.}, } @article {pmid41869502, year = {2026}, author = {Wang, D and Xu, X and Liu, L and Wang, C and Deng, Y and Polz, MF and Zhang, T}, title = {Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.}, journal = {Environmental science and ecotechnology}, volume = {30}, number = {}, pages = {100683}, pmid = {41869502}, issn = {2666-4984}, abstract = {Mobile genetic elements (MGEs) such as bacteriophages and plasmids profoundly shape microbial community structure and drive horizontal gene transfer across ecosystems. Wastewater treatment systems, with their high cell densities, steep physicochemical gradients and close cell-to-cell contact, act as hotspots for MGE proliferation and exchange, yet the in situ assembly dynamics and host interaction networks of these elements have remained largely unresolved because conventional methods fail to establish direct MGE-host linkages in complex matrices. Here we show that an integrated framework combining metagenomics, metatranscriptomics, metaviromics, and Hi-C proximity ligation sequencing enables the efficient elucidation of DNA phage and plasmid assembly dynamics alongside their host interaction networks in biofilms. We reconstructed 17,672 viral operational taxonomic units and 11,454 high-confidence non-redundant plasmids, and established 529 phage-host and 5739 plasmid-host associations that link up to 52 % of phages to 56 % of prokaryotes and 70 % of plasmids to 91 % of prokaryotes, respectively. Hi-C substantially expanded and refined these networks, revealing taxon-specific and multi-host patterns. Host community composition and biofilm architecture emerge as primary drivers of MGE occurrence and abundance along the reactor flow path. Expression of auxiliary metabolic genes, antibiotic resistance genes and virulence factors carried by these MGEs demonstrates their active roles in modulating biogeochemical cycles and maintaining ecosystem stability. These findings establish a scalable, cultivation-independent framework for deciphering MGE-host networks in complex microbial ecosystems, and underscore the power of Hi-C sequencing to transform our mechanistic understanding of gene flow, resistome dissemination, and ecological resilience in engineered and natural microbiomes.}, } @article {pmid41869518, year = {2026}, author = {Liu, J and Wu, R}, title = {Intraoperative sampling for postoperative metagenomic next-generation sequencing to guide biofilm-targeted therapy for Cutibacterium acnes infective endocarditis complicated by ruptured sinus of Valsalva aneurysm: a case report.}, journal = {Frontiers in cardiovascular medicine}, volume = {13}, number = {}, pages = {1707117}, pmid = {41869518}, issn = {2297-055X}, abstract = {BACKGROUND: Cutibacterium acnes is an easily overlooked pathogen in infective endocarditis (IE) due to its slow growth, propensity for biofilm formation, and high rate of culture-negative results. When complicated by structural heart disease such as a ruptured sinus of Valsalva aneurysm (RSVA), its indolent course can lead to severe hemodynamic compromise.

CASE SUMMARY: A 35-year-old male with a known ventricular septal defect (VSD) and unruptured aortic sinus aneurysm presented with persistent fever and progressive heart failure (NYHA class IV). Echocardiography revealed a ruptured right coronary sinus of Valsalva aneurysm (RCSVA) into the right ventricular outflow tract (RVOT) with a large vegetation. Blood cultures were negative. After 6 days of ineffective empirical antibiotic therapy, emergency surgery was performed to resect the aneurysm and vegetation and repair the cardiac structures. Intraoperatively, a vegetation sample was collected for metagenomic next-generation sequencing (mNGS). Postoperatively, mNGS identified Cutibacterium acnes with high sequence reads (1,284) and coverage (47.62%), enabling a definitive diagnosis. Pathology confirmed microcolonies and necrotic inflammation. The antibiotic regimen was switched to a regimen with potential activity against biofilms with oral doxycycline and intravenous clindamycin for 6 weeks. The patient's inflammatory markers normalized, and cardiac function recovered to NYHA class I, with no recurrence at 12-month follow-up.

CONCLUSION: This case highlights the diagnostic synergy of intraoperative histopathology and mNGS for pathogen identification, underscores the rationale for biofilm-conscious adjuvant therapy, and reaffirms the crucial role of early surgical debridement and repair in achieving cure.}, } @article {pmid41869816, year = {2026}, author = {Tumeo, A and Miliotis, G and O'Connor, A and Vijayakumar, V and Sengupta, P and McDonagh, F and Kovarova, A and Clarke, C and Hooban, B and Kumar Singh, N and Rosado, AS and Raman, K and Venkateswaran, K}, title = {Plasmidome, resistome, and virulence-associated gene characterization of Acinetobacter johnsonii in NASA cleanrooms and a clinical setting.}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0250325}, pmid = {41869816}, issn = {2165-0497}, abstract = {Evidence suggests the persistence of non-spore-forming Acinetobacter johnsonii in high-stakes controlled and nutrient-limited environments. Here, we investigated the mechanisms underlying this adaptability through a comprehensive genomic analysis of 22 isolates of A. johnsonii from NASA's Payload Hazardous Servicing Facility (PHSF) and one carbapenem-resistant strain (E154408A) from patient colonization in Ireland. Core-genome phylogeny revealed clustering of PHSF-originating isolates in a monophyletic clade divergent from the main species lineage. Species-wide virulence-associated genes and metabolic reconstruction indicated the exclusive presence in PHSF-originating isolates of two complete efflux pumps and a conserved allantoin racemase, suggesting adaptability for multiple environmental stresses. The ubiquity of blaOXA in genomes analyzed (n = 112) and the phenotypically validated multidrug-resistant profile of the E154408A strain highlight A. johnsonii's potential as an antimicrobial resistance (AMR) reservoir. Plasmidome analysis suggested gain/loss events across the monophyletic population and potential AMR acquisition pathways. Genome-to-metagenome mapping identified genomic signatures of A. johnsonii in PHSF >10 years post-initial isolation.IMPORTANCEAcinetobacter johnsonii is increasingly recognized as an emerging human pathogen, with growing evidence of its ability to persist in controlled, high-stakes environments, posing risks as both a persistent environmental contaminant and an antimicrobial resistance (AMR) reservoir. Yet, gaps remain in our understanding of its AMR profile and the mechanisms that enable its enhanced environmental adaptability. This knowledge is necessary in contexts where biological cleanliness is a priority, such as clinical settings and spacecraft assembly facilities' cleanrooms, where contamination of hardware with terrestrial microorganisms is concerning. In this study, we aim to address some of the key knowledge gaps by providing genomic insights into a rare multidrug-resistant clinical isolate and 22 NASA cleanroom isolates that persisted for over a decade in extremely clean conditions. Our findings will help assess the contamination risk of A. johnsonii in high-stakes environments and ultimately strengthen our ability to manage this microbial contaminant across terrestrial and extraterrestrial settings.Cleanroom-derived A. johnsonii genomes show traits consistent with increased adaptability.Genomic signatures of A. johnsonii persisted in the cleanrooms for over 10 years.blaOXA is ubiquitously found in all 112 A. johnsonii genomes analyzed.Isolate E154408A is the first reported patient colonization case by carbapenem-resistant A. johnsonii in Europe.}, } @article {pmid41869825, year = {2026}, author = {Mehta, A and Stebliankin, V and Mathee, K and Narasimhan, G}, title = {MEditome: Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {33}, number = {5-6}, pages = {643-659}, doi = {10.1177/15578666261428562}, pmid = {41869825}, issn = {1557-8666}, mesh = {*RNA Editing/genetics ; Humans ; *Computational Biology/methods ; *Microbiota/genetics ; Escherichia coli/genetics ; Genome, Bacterial ; *RNA, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; }, abstract = {RNA editing is a post-transcriptional modification that alters single-nucleotide sites within RNA strands, thus diversifying transcriptomes and proteomes and modulating gene expression. While better characterized in eukaryotes and in a few microbes, the study of RNA editing in entire microbiomes remains unexplored. Recent studies have demonstrated that A-to-I RNA editing contributes to bacterial adaptation and pathogenicity. Previously, we developed MetaEdit, a reference-based computational pipeline to detect RNA edit sites in microbiomes. While MetaEdit successfully identified RNA edit sites in Escherichia coli within the context of the human gut microbiome, including previously reported loci, it relied primarily on aligning reads to reference genomes of target bacteria. This dependence on reference genomes introduced potential biases, as editing can only be identified in reference genomes, while editing in novel microbial strains missing from the reference databases could be overlooked. Even for reference genomes, the search for edit sites is inefficient since it would have to be conducted one reference genome at a time.Here, we introduce MEditome, employing de novo assembly to overcome these limitations. This crucial change enables the detection of RNA edit sites across all microbial organisms in the microbiome, including novel bacterial strains for which comprehensive reference genomes are unavailable. Using sequencing data from the Integrative Human Microbiome Project, MEditome identified 2,295 unique RNA editing sites across diverse bacterial taxa. Several of these overlaps with previously identified edits in E. coli detected by MetaEdit in hok/gef gene family and arginine-associated genes, providing in silico validation of accuracy. We observed taxon-specific editing patterns and gene-level differential editing associated with inflammatory bowel disease, highlighting RNA editing as a potential regulatory mechanism influencing microbial adaptation and host-microbe interactions.}, } @article {pmid41869887, year = {2026}, author = {Wang, Z and Guo, S and Li, J and Huang, Q and Ning, J and Xia, B and Lv, X and Liu, X and Gao, Z and Li, J and Liu, L and Song, M and Wang, J}, title = {Identifying Cytokine Motif-Containing, Immunomodulatory Bacterial Proteins in Human Gut Microbiome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {29}, pages = {e20332}, pmid = {41869887}, issn = {2198-3844}, support = {2025YFA1309200//National Key Research and Development Program of China/ ; 2023KF-05//Open funding project of State Key Laboratory of Pharmaceutical preparation/ ; }, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/immunology/genetics ; Mice ; *Colorectal Neoplasms/immunology/microbiology ; *Bacterial Proteins/immunology/genetics/metabolism ; *Cytokines/immunology/genetics/metabolism ; *Immunologic Factors/immunology ; Escherichia coli/genetics ; }, abstract = {Accumulating evidence emphasizes the importance of microbiota-immune interactions in health and disease development, and identified bacteria-derived small-molecule metabolites as well as macromolecules such as peptides and proteins as promising therapeutic approaches. Here, we identify cytokine motif-containing, immunomodulatory bacterial proteins (CMCPs) as a special category of bacterial proteins in both bacterial genomes and gut metagenomes using Hidden Markov Models (HMMs). We further find eight colorectal cancer‑associated CMCPs differentially enriched in patients or healthy controls. Engineered E. coli Nissle 1917 (EcN) expressing selected CMCPs administered to Apc[min/+] mice selectively colonize intestinal tumors, deliver functional CMCPs in situ, and elicit significant antitumor immune responses while reducing tumor burden. In vitro, purified CMCPs modulate mouse splenic T cells, bone marrow‑derived macrophages and dendritic cells. Our findings indicate that bacterially encoded CMCPs can directly modulate tumor immunity and serve as microbiota‑derived proteins as candidate immunomodulators, which can further be applied in microbiome-mediated immune therapies for CRC.}, } @article {pmid41870053, year = {2026}, author = {Pasaribu, B and Vincent Mishael Dilens, C and Wahyudin Lewaru, M and Ayuningrum, D and Patria, MP and Juliandri Prihadi, D and Purba, NP and Untung Kurnia Agung, M and Maqbul, I and Sulistiowati, S}, title = {Shotgun metagenomic dataset of seawater bacterial communities from Pari Islands, Indonesia.}, journal = {Microbiology resource announcements}, volume = {15}, number = {4}, pages = {e0147625}, pmid = {41870053}, issn = {2576-098X}, abstract = {Pari Island is located in Seribu Islands, Indonesia, and is well-known for its marine biodiversity. Shotgun metagenomic sequencing was performed using the DNaseq-G400 platform, and bioinformatics approaches were applied to analyze the sequence data.}, } @article {pmid41870088, year = {2026}, author = {Park, J-Y and Yoon, CK and Lee, J-J and Shin, YJ and Kim, B-S}, title = {Potential role of the ocular surface microbiome in dry eye: microbial interactions and symptom alleviation.}, journal = {mSystems}, volume = {11}, number = {4}, pages = {e0010426}, pmid = {41870088}, issn = {2379-5077}, support = {NRF-2019R1G1A1002215//Ministry of Science and ICT, South Korea/ ; NRF-2019R1G1A1002215, NRF-2023R1A2C2002674//Ministry of Science and ICT, South Korea/ ; 2023-ER2105-02//Korea National Institute of Health/ ; }, mesh = {Humans ; *Dry Eye Syndromes/microbiology/drug therapy ; *Microbiota/drug effects ; Female ; Male ; Middle Aged ; Cyclosporine/therapeutic use/administration & dosage ; *Microbial Interactions ; Meibomian Gland Dysfunction/microbiology/drug therapy ; Aged ; Tears/microbiology ; *Eye/microbiology ; Bacteria/classification ; Meibomian Glands/microbiology ; }, abstract = {Dry eye is a prevalent ocular disorder characterized by tear film instability, inflammation, and ocular discomfort. Although the ocular surface (OS) microbiome contributes to immune regulation and pathogen defense, its role in dry eye pathophysiology remains unclear. Therefore, the present study aimed to characterize alterations in the OS microbiome of patients with dry eye undergoing cyclosporin A or NewHyalUni treatment and to identify their potential roles related to clinical improvement. Patients with dry eye were treated with either cyclosporin A and NewHyalUni drop combination or NewHyalUni alone. OS samples were collected before and after treatment, and the microbiome was analyzed by whole metagenome sequencing. Potential contaminants were removed before downstream analysis to account for the low-biomass nature of OS samples. Clinical evaluations included symptom scores and the assessment of meibomian gland dysfunction (MGD). No significant differences in the overall microbial composition were observed between the treatment groups. Nevertheless, both groups demonstrated symptomatic improvement. OS microbiome alterations were strongly correlated with improvements in MGD scores. Moreover, microbial interactions were found to shift following treatment. Key species (Staphylococcus epidermidis, Staphylococcus pseudintermedius, Streptomyces lividans, and Edwardsiella tarda) were identified as potential mediators of MGD score improvement by modulating microbiome functions and suppressing inflammation-associated species. Although distinct treatment regimens did not lead to divergent microbiome profiles, symptomatic improvement was associated with alterations in a specific microbiome. These findings highlight the OS microbiome's potential role in dry eye and support the development of microbiome-based therapeutic strategies.IMPORTANCEDry eye is a common ocular disorder with complex pathophysiology that extends beyond tear deficiency and inflammation. Despite growing evidence of host-microbiome interactions at mucosal surfaces, the contribution of the ocular surface (OS) microbiome to dry eye remains poorly understood. Our findings in this study reveal that shifts in specific taxa and ecological interactions correlate with improvements in meibomian gland function and dry eye symptoms, even in the absence of major changes in overall microbiota. By identifying microbial signatures potentially linked to clinical improvement, we provide systems-level insight into the role of low-biomass microbiomes in ocular health. This work expands the current understanding of microbiome-host dynamics in non-gut environments and supports future development of microbiome-informed therapeutic strategies.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT06936462.}, } @article {pmid41870133, year = {2026}, author = {Ni, B and Chen, XP and Lin, D and Yao, Z and Xia, J and Zhang, TL and Zheng, J and Cai, TG and Wang, X and Vollertsen, J and Zhu, D and Zhu, DZ}, title = {Potential Viral Regulation of Sulfur Cycling in Urban Sewer Sediments.}, journal = {Environmental science & technology}, volume = {60}, number = {13}, pages = {10067-10080}, doi = {10.1021/acs.est.5c15040}, pmid = {41870133}, issn = {1520-5851}, mesh = {*Sewage ; *Sulfur ; Geologic Sediments ; }, abstract = {Sewer sediments are microbial hotspots for sulfur cycling and sulfide generation, which is the leading cause of sewer corrosion and poses significant economic losses and public safety concerns. However, viruses in sewer sediments remain inadequately explored regarding their characteristics, interactions with their hosts, and ecological regulatory potential for sulfur cycling. In this study, we explored viral characteristics and virus-host interactions in sewer sediments from three distinct types of urban functional areas through metagenomics and viromics. Compared with single-function (commercial and residential) areas, sewer sediments in multifunctional areas contain higher nutrients and nutrient-induced acidification, which can promote host density and drive a shift from lytic to lysogenic infection. This shift may potentially enhance sulfide formation through the insertion of more auxiliary metabolic genes related to sulfate reduction into host genomes. Conversely, a higher viral lytic tendency in single-function area can lyse sulfate-reducing microorganisms, thereby mitigating sulfide formation. Phage transplantation experiments and the high prevalence of key viral hosts across global sewers (76 cities across six countries) demonstrated the high potential of viruses in alleviating sewer corrosion. Our findings reveal the dual role of viruses as metabolic "tuners" in sewer sulfur dynamics, suggesting that comprehensive urban sewer management requires consideration of exploiting viral lysis.}, } @article {pmid41870192, year = {2026}, author = {Ranga, A and Malhotra, AG and Singh, J and Pandey, KM}, title = {Genomic Sequencing from Sanger to Next-Generation Sequencing: Historical Context, Comparative Advances, and Prospects for Next-Generation Phenomics.}, journal = {Omics : a journal of integrative biology}, volume = {}, number = {}, pages = {15578100261433762}, doi = {10.1177/15578100261433762}, pmid = {41870192}, issn = {1557-8100}, abstract = {DNA sequencing has revolutionized biological and biomedical research, offering profound insights into genome organization, function, and variability. From the pioneering Sanger capillary electrophoresis method to the advent of next-generation sequencing, the field has evolved toward unprecedented speed, scalability, and cost decreases over the years. These advancements have enabled diverse applications across genomics, transcriptomics, metagenomics, epigenomics, and precision medicine, powering global initiatives such as the Human Genome Project, the Human Microbiome Project, and the 1000 Genomes Project. Bioinformatics has also advanced in data processing, variant detection, and functional annotation, helping transform raw sequencing data into biologically meaningful insights and knowledge. Although highly advanced, sequencing technologies still encounter challenges, including accuracy trade-offs and the need for efficient management of rapidly increasing volumes of data. Leveraging the genomic revolution, this review explores the shifts toward next-generation phenomics (NGP), an archetype that uses artificial intelligence that integrates multi-omics data with digital phenotyping, the Internet of Things, and real-time analytics. The goal of NGP is to integrate genotypic and phenotypic data to support predictive modeling of health, disease, and environmental interactions. By tracing history, advances in sequencing technologies, and future perspectives on NGP, this article offers a comprehensive overview for researchers and clinicians, highlighting how the integration of omics and digital data will drive the generation of personalized and systems-level biology.}, } @article {pmid41870201, year = {2026}, author = {Li, N-P and Gupta, S and Kollipara, SK and Hung, T-H and Rao, GP and Kuo, C-H}, title = {Draft genome sequence of "Candidatus Phytoplasma australasiaticum" strain TBB-AP associated with tomato big bud disease in India.}, journal = {Microbiology resource announcements}, volume = {15}, number = {4}, pages = {e0003326}, pmid = {41870201}, issn = {2576-098X}, support = {//Academia Sinica/ ; //Indian Council of Agricultural Research/ ; }, abstract = {We report the draft metagenome-assembled genome (MAG) of "Candidatus Phytoplasma australasiaticum" strain TBB-AP, obtained from a symptomatic tomato plant collected in Andhra Pradesh, India. This assembly provides a genomic resource for functional and evolutionary studies of phytoplasmas associated with tomato big bud disease.}, } @article {pmid41870280, year = {2026}, author = {Werbowy, O and Håkansson, M and Dorawa, S and Stefańska-Kaźmierczak, A and Svensson, LA and Al-Karadaghi, S and Jurczak-Kurek, A and Kwiatkowska-Semrau, K and Plotka, M and Fridjonsson, OH and Hreggvidsson, GO and Aevarsson, A and Dąbrowski, S and Kaczorowska, AK and Kaczorowski, T}, title = {Structural and functional characterization of a hyperthermostable single-stranded DNA-binding protein from a hot spring metagenome.}, journal = {Protein science : a publication of the Protein Society}, volume = {35}, number = {4}, pages = {e70538}, pmid = {41870280}, issn = {1469-896X}, support = {UMO-2019/34/H/NZ2/00584//National Science Centre (Poland)/ ; 685778//European Union Horizon 2020/ ; }, mesh = {*DNA-Binding Proteins/chemistry/genetics/metabolism ; *Hot Springs/microbiology ; Crystallography, X-Ray ; Models, Molecular ; *Metagenome ; *DNA, Single-Stranded/metabolism/chemistry ; Escherichia coli/genetics/metabolism ; Amino Acid Sequence ; *Bacterial Proteins/chemistry/genetics/metabolism ; Protein Multimerization ; }, abstract = {We present the structural and functional characterization of a single-stranded DNA-binding protein (SSB-M5) identified from a hot spring metagenome in Vatnajökull National Park, Iceland. This small protein (136 aa; 15,695 Da) shares 100% amino acid sequence identity with two previously uncharacterized SSBs from hyperthermophilic Fervidobacterium species. Functional complementation assay demonstrated that SSB-M5 can substitute for Escherichia coli SSB in an ssb[-] mutant strain, confirming its biological activity. A recombinant C-terminally His-tagged SSB-M5 was overproduced, purified to homogeneity, and subjected to structural, biochemical, and biophysical analysis. The crystal structure revealed that SSB-M5 forms a dimer through a crystallographic twofold axis, with each monomer contributing to a large antiparallel β-sheet. The flat surfaces of the β-sheets from the two dimers are packed together via a second crystallographic twofold axis, forming a tetramer that serves as the functional unit of the SSB-M5. Electrophoretic mobility shift assays showed that SSB-M5, after heat treatment up to 100°C, forms stable DNA-protein complexes with the (dT)40 oligo. Quantitative analyses revealed that SSB-M5 binds (dT)70 oligonucleotide with very high affinity (KD = 72 ± 6 pM). Hill analysis indicated cooperative binding, yielding an EC50 of 141 pM and a Hill coefficient of 2. Moreover, inclusion of SSB-M5 in PCR reactions significantly enhanced amplification by eliminating non-specific products. Together, these findings identify SSB-M5 as a hyperthermostable, high-affinity single-stranded DNA-binding protein with potential applications in molecular biology and biotechnology.}, } @article {pmid41871361, year = {2026}, author = {Lipovac, J and Šikić, M and Vicedomini, R and Križanović, K}, title = {MADRe: Strain-level metagenomic classification through assembly-driven database reduction.}, journal = {GigaScience}, volume = {15}, number = {}, pages = {}, pmid = {41871361}, issn = {2047-217X}, support = {IP-2018-01-5886//Croatian Science Foundation/ ; MOH-000649-01//National Medical Research Council/ ; }, mesh = {*Metagenomics/methods ; *Metagenome ; *Software ; *Databases, Genetic ; *Computational Biology/methods ; Algorithms ; }, abstract = {Strain-level metagenomic classification is essential for understanding microbial diversity and functional potential, yet remains challenging, particularly when sample composition is unknown and reference databases are large and redundant. Here, we present MADRe, a modular and scalable pipeline for long-read strain-level metagenomic classification based on Metagenome Assembly-Driven Database Reduction. Beyond system-level integration, MADRe introduces statistical strategies that leverage assembly-derived genomic context to guide database reduction and probabilistic read reassignment. Specifically, it combines long-read metagenome assembly, contig-to-reference reassignment using an expectation-maximization framework for reference reduction, and probabilistic read mapping reassignment on a reduced database to achieve sensitive and precise strain-level classification. We extensively evaluated MADRe on simulated datasets, mock communities, and a real anaerobic digester sludge metagenome. Across diverse similarity and coverage conditions, MADRe consistently improves precision by reducing false-positive strain detections. MADRe's design allows users to apply either the database reduction or read classification step individually. Using only the read classification step shows results on par with other tested tools. MADRe is open source and publicly available at https://github.com/lbcb-sci/MADRe.}, } @article {pmid41871943, year = {2026}, author = {Awoniyi, M and El Hag, M and Hernandez, J and Yang, Q and Evans, N and Nemet, I and Ngo, B and Coskuner, D and Zhou, J and Farmer, M and Su, L and Zhou, H and Roach, J and Stappenbeck, T and Sartor, RB}, title = {Dysbiotic microbiota trigger colitis-associated colorectal cancer and imprint a distinctive bile acid profile in a PSC-IBD model.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-336675}, pmid = {41871943}, issn = {1468-3288}, abstract = {BACKGROUND: Primary sclerosing cholangitis-associated UC (PSC-UC) carries excess colorectal neoplasia despite often mild-appearing endoscopy, implicating persistent microscopic inflammation and microbiota-bile acid (BA) dysfunction.

OBJECTIVE: To test whether PSC-UC neoplasia is driven by transferable microbiota-mediated inflammation linked to secondary BA loss.

DESIGN: Surveillance colonoscopies (2012-2022) from PSC-UC (n=251) and UC-only (n=8839) were compared for segmental endoscopic/histological activity and dysplasia. We generated multidrug resistance protein 2 (MDR2)[-/-] × interleukin (IL)-10[-/-] double-knockout (DKO) mice and used germ-free (GF) derivation, faecal microbiota transplantation (FMT), antibiotic conditioning and cohousing with shotgun metagenomics and liquid chromatography-tandem mass spectrometry BA profiling.

RESULTS: PSC-UC showed greater inflammatory activity and a right-shifted dysplasia burden versus UC-only. Under specific-pathogen-free conditions, DKO mice developed early right-predominant colitis and multifocal dysplasia progressing with age. DKO communities were depleted of 7α-dehydroxylation capacity with near absence of deoxycholic and lithocholic acids and no enrichment of canonical bacterial genotoxins. GF DKO mice were protected, whereas live DKO donor FMT reinstated severe colitis and dysplasia; sterile-filtered stool supernatant was inactive. IL-10[-/-] donor FMT or cohousing attenuated colitis and increased recipient secondary BA, whereas wild-type/MDR2[-/-] donor transfers were non-colitogenic. In GF DKO mice, direct deoxycholic acid repletion caused hepatotoxicity.

CONCLUSION: PSC-UC neoplasia associates with transmissible microbiota-dependent inflammation and secondary BA deficiency. Controlled restoration of BA-transforming microbial functions, rather than indiscriminate secondary BA replacement, is a rational translational direction.}, } @article {pmid41871945, year = {2026}, author = {Vázquez-Castellanos, JF and Yoon, SJ and Won, SM and Raes, J and Kwon, HC and Si, J and Suk, KT}, title = {Stage-dependent gut microbiome and functional signatures across the liver disease spectrum: an integrative multicohort study.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337436}, pmid = {41871945}, issn = {1468-3288}, abstract = {BACKGROUND: The gut-liver axis plays a critical role in liver disease progression; however, how gut microbial ecology and function vary across disease stages remains unclear.

OBJECTIVE: To define stage-specific microbial and functional signatures and evaluate their diagnostic potential.

DESIGN: We analysed faecal samples from 1168 individuals spanning healthy controls, fatty liver, hepatitis, cirrhosis and hepatocellular carcinoma by 16S rRNA sequencing, with a subset (n=141) profiled by shotgun metagenomics. To increase statistical power and enable external validation, 2376 publicly available metagenomic datasets, including 734 liver-related, were integrated. Machine learning-based multicohort analysis was used to identify microbial biomarkers, assess risk factors and classify disease stages.

RESULTS: Microbial diversity declined and a low-richness enterotype expanded with disease severity. Machine learning revealed a discordance in hepatitis, which lacked taxonomic markers but was defined by a conserved functional signature of biosynthetic upregulation. In contrast, advanced stages featured consistent markers like Ligilactobacillus and Veillonella, with strain-level evidence confirming oral-gut transmission. Functional profiling delineated a metabolic continuum from anabolic precursor synthesis in hepatitis to virulence factor production in cirrhosis and putrefactive metabolism in carcinoma. Comparative analysis confirmed that these signatures were distinct from those in non-liver metabolic and oncologic disorders. Importantly, the expansion of oral-derived Veillonella spp and the low-richness enterotype were significantly associated with increased mortality.

CONCLUSION: This large-scale study delineates stage-dependent ecological and functional remodelling of the gut microbiome across liver diseases. These findings highlight the potential of microbiome-based markers for non-invasive diagnosis and prognostic risk stratification in liver diseases.}, } @article {pmid41872229, year = {2026}, author = {Ji, M and Li, Y and Wang, M and Liu, X and Gong, X and Tu, Q}, title = {Unveiling the biodiversity of large DNA viruses in intertidal mudflats via metagenomics.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41872229}, issn = {2041-1723}, mesh = {*Metagenomics/methods ; *Biodiversity ; *DNA Viruses/genetics/classification ; Phylogeny ; Genome, Viral/genetics ; Seashore ; Metagenome ; Bacteriophages/genetics/classification ; Giant Viruses/genetics/classification ; Genetic Variation ; }, abstract = {Large DNA viruses (LDVs) are unique members of the Earth's virosphere, remarkable for their extra-large genome sizes and broad metabolic potential. However, our knowledge of this viral group remains very limited, particularly in complex dynamic habitats. In this study, 237 metagenome-assembled LDV genomes are comprehensively recovered from intertidal mudflats using multiple sampling and sequencing strategies totaling 5.3 TB data. A phylogenetically distinct subgroup within Imitervirales is identified, showing broad associations with multiple eukaryotic lineages. Certain LDV populations can persist locally and exhibit significant genomic variations potentially driven by dynamic intertides. Ecological patterns are observed at both community and genetic levels, with giant viruses showing steeper community turnover but weaker nucleotide diversity variations than large phages. Moreover, LDVs exhibit similar macroecological patterns to their potential hosts, which substantially shape LDV community assembly. The intertidal LDVs encode diverse functional genes, most of which remain uncharacterized, with a 27.32% improvement for unknown phage genes using a protein language model. Although giant viruses and large phages share comparable functional gene composition, they exhibit distinct preferences for specific metabolic pathways, especially those associated with carbon and nitrogen cycling. This study broadens our understanding of the biodiversity and ecology of LDVs in the understudied intertidal ecosystems.}, } @article {pmid41872577, year = {2026}, author = {Shan, X and Cao, K and Jeckel, H and Alcalde, RE and Trindade, IB and Kwiecinski, JV and Newman, DK}, title = {Drought drives elevated antibiotic resistance across soils.}, journal = {Nature microbiology}, volume = {11}, number = {4}, pages = {867-876}, pmid = {41872577}, issn = {2058-5276}, support = {2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2209379//National Science Foundation (NSF)/ ; ALTF 191-2023//European Molecular Biology Organization (EMBO)/ ; }, mesh = {*Soil Microbiology ; *Droughts ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/isolation & purification/classification ; *Drug Resistance, Bacterial ; Soil/chemistry ; Humans ; Metagenomics ; }, abstract = {Antibiotic resistance is a growing threat to human health and is often attributed to excessive clinical usage that selects for resistance. Although many antibiotics are derived from soil microorganisms, how environmental changes to soil ecosystems might promote resistance is poorly understood. Here we establish drought as a driving force of antibiotic resistance in the soil, with potentially far-reaching public health consequences. Across various geographic regions and soil types, we consistently observe metagenomic signatures of enrichment for antibiotic producers under drought conditions. Experimentally, we demonstrate that drought-induced lowering of water content concentrates natural antibiotics, thereby intensifying selection against sensitive strains and favouring antibiotic-resistant bacteria. Using clinical surveillance data from 116 countries, we show that the average frequency of hospital antibiotic resistance is strongly correlated with the local aridity index, even after controlling for regional income differences. Together, our findings reveal an underrecognized link between climate factors and antibiotic resistance.}, } @article {pmid41872600, year = {2026}, author = {Segev, T and Barak, D and Zahavi, L and Godneva, A and Rein, M and Krongauz, D and Samocha-Bonet, D and Rossman, H and Weinberger, A and Segal, E}, title = {Diet-microbiome associations in 10,068 individuals from the Human Phenotype Project to guide personalized nutrition.}, journal = {Nature medicine}, volume = {32}, number = {5}, pages = {1884-1894}, pmid = {41872600}, issn = {1546-170X}, mesh = {Humans ; *Diet ; Phenotype ; *Gastrointestinal Microbiome/genetics/physiology ; Female ; Metagenomics ; Male ; Streptococcus thermophilus ; Yogurt/microbiology ; *Precision Medicine ; Adult ; Coffee/microbiology ; Milk/microbiology ; Bifidobacterium/genetics ; }, abstract = {Diet is a major environmental factor influencing the human gut microbiome. However, the effects of specific foods and dietary patterns on microbial composition, diversity and function is not fully understood, limiting progress toward personalized dietary strategies. Here, leveraging 10,068 participants from the Human Phenotype Project with app-based diet logs and shotgun metagenomics, we predicted diet-microbiome associations at species-level resolution. Diet significantly predicted microbial diversity (richness r = 0.26, Shannon Index r = 0.24), the relative abundance of 669 of 724 species tested (92.4%, false discovery rate <0.05), and 313 of 320 pathways (97.8%, false discovery rate <0.05). Feature attribution identified distinct food-microbe links, including coffee with Lawsonibacter asaccharolyticus (r = 0.43), yogurt with Streptococcus thermophilus (r = 0.42) and milk with Bifidobacterium species (r = 0.31-0.36). In parallel, broader dietary patterns, especially the degree of food processing, emerged as predictors of microbial diversity and composition. We also show that diet-microbiome associations persist over four years, with 82.5% of species exhibiting significant longitudinal tracking between predicted and observed abundances. Finally, we developed an exploratory analysis for simulating personalized dietary interventions with predicted microbiome shift effects that are associated with improvements in cardiometabolic health. Our findings demonstrate that diet is strongly associated with microbiome composition, diversity and function, and highlight its potential for guiding personalized interventions.}, } @article {pmid41872905, year = {2026}, author = {Zhao, H and Hua, J and Lu, W and Lv, X and Chen, C and Liang, Y}, title = {Rubber seed cake supplementation alters meat quality, intestinal health, and gut microbiota in Hu sheep.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41872905}, issn = {2524-4671}, support = {880698//Key Technology Integration and Application of Standardized Rearing Management for Meat Sheep in Agricultural Areas/ ; }, abstract = {This study aimed to investigate the effects of rubber seed cake (RSC) supplementation on slaughter performance, intestinal health, and gut microbiota in Hu sheep. Forty-eight Hu sheep (17.01 ± 0.57 kg; 3 months old) were randomly allocated to four dietary treatments: 0% (CON), 6% (R6), 12% (R12), and 18% (R18) RSC. Following an 80-day feeding trial, six sheep per group were randomly selected for slaughter. Samples of the longissimus dorsi, small intestine, and intestinal mucosa were collected for meat quality, morphological, and intestinal health analyses. Additionally, ileal contents were harvested and frozen for metagenomic sequencing. Dietary supplementation with RSC reduced the shear force of the longissimus dorsi muscle (P = 0.043) and lowered meat color L* (P = 0.044) and b* (P = 0.035) values in the R6 group compared to the CON group. Quadratic effects were observed for the villus height to crypt depth (VH/CD) ratio in the duodenum (P = 0.006), jejunum (P = 0.006), and ileum (P = 0.001) with increasing RSC supplementation, and the VH/CD ratio was significantly increased in the R6 and R12 groups (P < 0.05). Ileal pro-inflammatory cytokine concentrations, including tumor necrosis factor-alpha (TNF-α), interleukin-1 beta (IL-1β), and interleukin-6 (IL-6), decreased both linearly and quadratically with increasing RSC supplementation (P < 0.05). Quadratic effects (P < 0.05) were observed for the concentrations of mucin 2 (MUC2) and tight junction proteins such as zonula occludens-1 (ZO-1), occludin, and claudin in the jejunal and ileal mucosa with increasing RSC supplementation. Specifically, the concentrations of MUC2 and tight junction proteins in the jejunum, as well as MUC2 and ZO-1 in the ileum, were significantly higher in the R6 group (P < 0.05). RSC supplementation significantly altered the relative abundance of specific taxa, including Stenotrophomonas, Piromyces, Lichinomycetes, and Syntrophobacteria, as well as CAZyme gene sequences such as GH119, GT39, and GH13-8 (P < 0.05). In conclusion, these findings indicate that a 6% dietary supplementation of RSC is optimal in Hu sheep, as it improves meat quality and intestinal health by modulating the ileal microbiota composition and CAZyme abundance, thereby strengthening mucosal barrier function and alleviating inflammation.}, } @article {pmid41872963, year = {2026}, author = {Kim, B and Kim, HN and Cheong, HS and Jeong, S and Kim, J and Park, DI and Joo, EJ}, title = {Fecal microbiota from hepatitis B-infected individuals alters triglyceride metabolism and microbial pathways in mice.}, journal = {Gut pathogens}, volume = {18}, number = {1}, pages = {}, pmid = {41872963}, issn = {1757-4749}, support = {RS-2023-KH135855//Korea Health Industry Development Institute/Republic of Korea ; NRF-2021R1A2C4002454//National Research Foundation of Korea/ ; }, abstract = {BACKGROUND: This study investigates the impact of chronic hepatitis B virus infection on triglyceride metabolism through alterations in the gut microbiome, using a faecal microbiota transplantation (FMT) mouse model. METHODS: This shotgun metagenomic analysis was conducted using stored samples from a previously published FMT experiment. Nineteen mice with sufficient faecal DNA for sequencing were included, comprising ten mice transplanted with microbiota from two hepatitis B virus (HBV)-infected donors and nine mice transplanted with microbiota from two non-infected donors. Shotgun metagenomic sequencing was performed on stool collected two weeks post-FMT, and metabolic parameters were compared between two and five weeks post-transplantation. RESULTS: Mice receiving microbiota from HBV-infected individuals exhibited lower triglyceride levels (100.05 ± 10.82 vs. 111.69 ± 12.27 mg/dL, p = 0.04) at five weeks post-FMT compared with those receiving microbiota from non-infected individuals. HBV-positive mice also showed higher microbial diversity and an increased abundance of short-chain fatty acid–producing bacterial species, including Anaerofustis stercorihominis, Bacteroides cellulosilyticus, and Butyricimonas virosa. Shotgun analysis revealed reduced activity in the pentose phosphate pathway and galactitol degradation pathways, both involved in carbohydrate and fatty acid metabolism, alongside unique bile acid dihydroxylation pathways. CONCLUSIONS: These findings indicate that gut microbiota with chronic HBV infection modulate host lipid metabolism, particularly triglyceride levels, through distinct microbial species and metabolic pathways.}, } @article {pmid41874180, year = {2026}, author = {Garzon, A and Miramontes, C and Weimer, BC and Profeta, R and Hoyos-Jaramillo, A and Fritz, HM and Pereira, RV}, title = {Characterizing the nasopharyngeal microbiome and resistome of dairy cattle with and without bovine respiratory disease.}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0264825}, pmid = {41874180}, issn = {2165-0497}, abstract = {Bovine respiratory disease (BRD) remains a significant economic challenge in dairy cattle despite extensive vaccination programs that have been developed and implemented during the last few decades. This study investigated the nasopharyngeal microbiome and resistome of dairy cattle across various life stages to understand the roles of microbial communities associated with BRD. A case-control study was conducted on three commercial dairy farms in Northern California, collecting nasopharyngeal swabs from 69 animals, including preweaned calves, weaned heifers, and lactating cows with and without BRD. Shotgun metagenomic sequencing was used to characterize both microbiome and resistome profiles observed at the time of BRD diagnosis. Results revealed that BRD is associated with distinct microbial community patterns, rather than the increased abundance of a specific pathogen. Age was a critical factor influencing microbial diversity, with adult cows showing the highest diversity and weaned heifers with BRD showing the lowest. A total of 1,164 bacterial species were identified, with BRD cases harboring 14 unique species compared to control animals. BRD cases were characterized by the co-occurrence of multiple respiratory pathogens, including Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mesomycoplasma species, which showed positive correlation with BRD cases but negative correlations in BRD controls, while BRD control animals showed significantly higher abundance of commensal Staphylococcus species. Resistome analysis identified 65 antimicrobial resistance genes, with BRD cases harboring more unique resistance genes than BRD controls. These findings challenge traditional single-pathogen models and demonstrate that BRD is likely the result of complex microbial community interactions and changes in community abundance, providing new potential targets to explore when considering prevention strategies toward promoting microbial communities that prevent or reduce the risk of BRD.IMPORTANCEBovine respiratory disease (BRD) represents one of the most economically challenging conditions in cattle production, with an estimated direct cost that exceeds $165 million annually in the United States alone. Despite decades of vaccination efforts targeting known pathogens, BRD prevalence remains unchanged, indicating an incomplete understanding of disease pathogenesis. This study provides critical insights by shifting focus from individual pathogens to entire microbial communities, revealing that BRD involves complex bacterial interactions, as well as the role of the understudied nasal commensal microbiome in healthy animals. The identification of distinct "pathobiomes" associated with disease and protective commensal communities in healthy animals fundamentally changes approaches to BRD prevention and treatment. The discovery that age significantly influences microbiome stability highlights critical intervention periods. Furthermore, the association between BRD and increased antimicrobial resistance genes raises concerns about current treatment and overall management practices, selecting for drug-resistant communities. This research provides a foundation for developing microbiome-based diagnostic tools and interventions supporting healthy microbial ecosystem development.}, } @article {pmid41874256, year = {2026}, author = {Lam, WKJ and Chan, KKP and Wang, G and Lai, CKC and Kang, G and Chan, C and Leung, ACY and Wong, NHL and Tso, CSN and Chow, KM and Ramakrishnan, S and Wong, KT and Lau, CHY and Ng, JKC and Lo, RLP and Yip, WH and Ngai, JCL and To, KW and Tse, IOL and Cheng, SH and Shang, H and Chan, KW and Lai, A and Chan, CML and Lee, VCT and Malki, Y and Choy, LYL and Ma, ML and Zhou, Q and Yu, SCY and Jiang, P and Ko, FWS and Chan, KCA and Hui, DSC and Lee, YCG and Lo, YMD}, title = {Sequencing of Pleural Fluid and Plasma for Tuberculous Pleuritis.}, journal = {NEJM evidence}, volume = {5}, number = {4}, pages = {EVIDoa2500237}, doi = {10.1056/EVIDoa2500237}, pmid = {41874256}, issn = {2766-5526}, mesh = {Humans ; *Tuberculosis, Pleural/diagnosis/blood/microbiology ; Female ; *Mycobacterium tuberculosis/genetics/isolation & purification ; Male ; *DNA, Bacterial/analysis/blood ; Middle Aged ; *Pleural Effusion/microbiology ; Sensitivity and Specificity ; Prospective Studies ; Adult ; Aged ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The laboratory diagnosis of tuberculous pleuritis (TBP) is hindered by the paucibacillary nature of Mycobacterium tuberculosis in the pleural space, resulting in low sensitivity of microbiological culture and polymerase chain reaction-based analyses on pleural fluid. The use of metagenomic next-generation sequencing for diagnosing TBP may be limited by the background noise of DNA from nontuberculous mycobacteria.

METHODS: We performed targeted sequencing to analyze M. tuberculosis DNA in paired pleural fluid and plasma from prospectively enrolled consecutive patients with new-onset pleural effusion. We used a bioinformatics alignment algorithm to the M. tuberculosis genome that was masked for regions with high sequence similarity to nontuberculous mycobacteria. Our primary outcome was a comparison of diagnostic sensitivity between M. tuberculosis sequencing as described above and culture using McNemar's test.

RESULTS: Among the included 329 patients with pleural effusion, 34 patients with TBP were identified. Targeted sequencing detected M. tuberculosis DNA fragments in the pleural fluid of all TBP cases (median, 267.6 reads per 10 million [RP10M]; interquartile range [IQR], 30.8-2644.3) but absent in 288 out of 295 (97.6%) non-TBP samples (median, 0 RP10M; IQR, 0-0). Targeted sequencing of pleural fluid achieved a sensitivity of 97.1% for TBP detection at a cutoff of 2 RP10M, in contrast to 47.1% by M. tuberculosis culture (P<0.001, McNemar's test). Sequencing yielded an area-under-the-curve value of 0.9996 (95% confidence interval, 0.9988-1.0000) for differentiating TBP and non-TBP. Plasma analysis by targeted sequencing with the same alignment algorithm reported an area-under-the-curve value of 0.9475 (95% confidence interval, 0.8929-1.0000).

CONCLUSIONS: Targeted sequencing of pleural fluid with selectively masked M. tuberculosis genomic alignment accurately diagnosed TBP and outperformed conventional diagnostic tests. (Supported by InnoHK and the Hong Kong Tuberculosis, Chest and Heart Diseases Association; ClinicalTrials.gov number, NCT05397730.).}, } @article {pmid41874416, year = {2026}, author = {Koseli, E and Tyc, KM and Buzzi, B and Akbarali, HI and Damaj, MI}, title = {The Role of the Gut Microbiome in Nicotine Withdrawal and Dependence.}, journal = {Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco}, volume = {}, number = {}, pages = {}, doi = {10.1093/ntr/ntag057}, pmid = {41874416}, issn = {1469-994X}, abstract = {INTRODUCTION: Smoking is considered a global pandemic with more than 1.3 billion people being active smokers. Increasing evidence suggests that nicotine exposure can lead to changes in the gut microbiome, increases in permeability, and impaired mucosal immune responses in the gastrointestinal tract. However, the literature on behavioral aspects of nicotine-microbiome interaction, such as dependence and withdrawal, is limited. In this study, we used homologous fecal material transplants (FMT) to modify the gut microbiome and its impact on the intensity of nicotine withdrawal in mice.

METHODS: We used osmotic minipumps as an application of chronic nicotine for 15 days and orally gavaged FMT 2x a day to the mice. We assessed the nicotine withdrawal by measuring the number of somatic signs and anxiety-like behaviors at 24 h and 1 week after the mini pump removal. Fecal samples were also collected points to identify the gut microbiome changes.

RESULTS: Fecal transplants reduced the number of somatic signs and anxiety-like behaviors in nicotine-treated mice up to a week after the removal of minipumps. The shotgun metagenomic results of the fecal samples from 24 h after minipumps removal time point show altered gut microbiome with a significant shift in the species composition between the nicotine treated and its homologous FMT treatment.

CONCLUSIONS: Our results indicate that under our experimental conditions fecal transplant can reduce the severity of nicotine withdrawal. This suggests that interactions along the gut-brain axis are important for the development of nicotine dependence and might help lower the risk of cancer and other serious health problems in humans.}, } @article {pmid41874421, year = {2026}, author = {Wang, J and Lu, L and Sun, Y and Messer, LF and Wu, M and Duan, Z and Shi, J and Yang, Y and Li, C and Mao, Y and Zhu, D and Rillig, MC and Wang, X}, title = {AHL-mediated quorum sensing drives plastisphere formation and elevates pathogenic potential.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41874421}, issn = {1751-7370}, support = {2024YFD1700702//National Key Research and Development Program of China/ ; U24A20634//National Natural Science Foundation of China/ ; 42377381//National Natural Science Foundation of China/ ; U21A2038//National Natural Science Foundation of China/ ; //2115 Talent Development Program of China Agricultural University/ ; //Alexander von Humboldt Foundation/ ; }, mesh = {*Quorum Sensing/genetics ; *Acyl-Butyrolactones/metabolism/pharmacology ; *Biofilms/growth & development ; Gene Expression Regulation, Bacterial ; *Plastics ; Multiomics ; Virulence ; }, abstract = {The biofilm colonizing plastic debris, termed "the plastisphere," is of growing global concern due to escalating plastic pollution. However, the biological mechanisms underpinning plastisphere formation remain poorly understood. Here, we analyzed public global metagenomes, revealing a significant enrichment of genes associated with quorum sensing (QS) and biofilm formation, with a pronounced signal for acyl-homoserine lactone (AHL) QS. Using controlled microfluidic and tubular column experiments, we further demonstrate that exogenous AHL actively promotes plastisphere formation, biomass accumulation, and extracellular polymeric substance production on microplastics, whereas a quorum-quenching agent (AHL acylase) effectively inhibits these processes. Multi-omics analyses revealed that AHLs can transcriptionally activate genes involved in adhesion, motility, chemotaxis, and matrix production, fundamentally reshaping community structure, restructuring inferred microbial interaction networks, and driving community assembly toward stronger deterministic selection. AHL stimulation also increased the relative abundance and expression of pathogen-associated and virulence-related functions, suggesting an elevated virulence potential within the plastisphere under QS-promoting conditions. Together, our findings establish AHL-mediated QS as a central driver of plastisphere assembly and a key determinant of risk profile, highlighting its critical role in understanding and potentially mitigating the growing environmental and health hazards associated with microplastic pollution.}, } @article {pmid41874457, year = {2026}, author = {Mohr, AE and Berryman, CE and Harris, MN and Lawrence, AB and Chakraborty, N and Campbell, R and Dimitrov, GI and Gautam, A and Hammamieh, R and Lieberman, HR and Rood, JC and Pasiakos, SM and Karl, JP}, title = {Testosterone administration partially modulates gut microbiota responses to severe energy deficit.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {330}, number = {5}, pages = {E606-E626}, pmid = {41874457}, issn = {1522-1555}, support = {W81XWH-17-2-0026//DOD | OSD | Defense Technical Information Center (ADD)/ ; T32 DK137525/DK/NIDDK NIH HHS/United States ; T32DK137525//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; //DOE | Oak Ridge Institute for Science and Education (ORISE)/ ; Joint Program Committee-5//Military Operational Medicine Research Program (MOMRP)/ ; W81XWH-14-1-0335//DOD | OSD | Defense Technical Information Center (ADD)/ ; }, mesh = {Humans ; Male ; *Testosterone/analogs & derivatives/pharmacology/administration & dosage ; *Energy Metabolism/drug effects ; *Gastrointestinal Microbiome/drug effects ; Adult ; Feces/chemistry/microbiology ; Fatty Acids, Volatile/metabolism ; *Energy Intake/drug effects ; *Androgens/pharmacology/administration & dosage ; Young Adult ; }, abstract = {Severe diet- and exercise-induced energy deficit (SED) suppresses androgen production in healthy men, altering metabolism and driving muscle loss. The gut microbiota modulates host metabolism, yet the community's response to SED and any role of androgen hormones are unclear. Herein, healthy, physically active men were randomized to receive 200 mg/wk testosterone enanthate (n = 24) or placebo (n = 26) during a 28-day residential intervention that restricted energy intake and increased energy expenditure inducing a ∼2,000 kcal/day SED. Multiomic analyses revealed altered gut microbiota composition, reduced fecal short-chain fatty acids (SCFA), and shifts in bacterial metabolic pathways toward lipid utilization and mucin degradation during SED, suggesting adverse effects of SED on gut microbiota metabolic functions. Testosterone administration preserved certain SCFA-producing taxa and bioenergetic pathways without fully counteracting the effects of SED indicating a limited but potentially important interplay between androgen status and the gut microbiota under conditions of SED.NEW & NOTEWORTHY This study is the first to demonstrate that testosterone administration partially preserves gut microbiota composition and metabolic function during severe energy deficit in healthy men. Using a multiomic approach, we show that testosterone modulates short-chain fatty acid-producing taxa and microbial pathways linked to host energy metabolism. These findings reveal a novel role for androgens in shaping host-microbiome interactions during catabolic stress and may inform strategies to maintain metabolic resilience.}, } @article {pmid41874663, year = {2026}, author = {Hu, C and Lin, M and Hu, T and Zeng, Y and Zeng, R and Wang, C}, title = {Linking Bacterial r/k Ecological Shifts to Spatiotemporal Nitrogen Removal Dynamics in Recirculating Aquaculture Systems.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41874663}, issn = {1432-184X}, support = {NO.2024SJRC4//the Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.LTO2326//State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences/ ; NO.2023A04J0897//Guangzhou Science and Technology Program Project/ ; NO.SL2023E04J00185//Demonstration and Promotion of Key Technologies for Land-based Factory Farming of Hybrid Eleotris oxycephala/ ; }, abstract = {The composition and function of bacterial communities in recirculating aquaculture systems (RAS) vary significantly across operational phases and treatment units. Yet the causal links between these bacterial dynamics and nitrogen removal mechanisms remain obscure. In this study, we demonstrated dynamic shifts in bacterial community composition and nitrogen removal function within RAS throughout cultivation and in each unit, by water quality monitoring, 16 S rRNA gene sequencing, metagenomics, 15N isotope tracing and kinetic modeling. Bacterial community composition shifted temporally, marked by a decline in r-strategists and increases in both α- and β-diversity from the start-up to the culture phase, a succession primarily driven by salinity, total dissolved solids, and conductivity. Ecologically, this transition is indicative of a shift in dominant life-history strategies, from an r-selected pioneer community to a K-selected, more stable and resilient community. Denitrification, anammox, and nitrification dominated nitrogen removal pathways, collectively representing 45.2% of the nitrogen-cycling functional genes. In addition, there was significant spatiotemporal heterogeneity in bacterial nitrogen removal. Spatially, aquatic bacteria exhibited higher denitrification activity, while biofilm-attached anammox bacteria of K-strategist demonstrated disproportionately high metabolic activity relative to their low abundance; this was probably regulated by biofilm-associated quorum sensing. Temporally, the ammonia-oxidizing bacteria (AOB) enabled an initial rapid ammonia degradation, whereas nitrite-oxidizing bacteria (NOB) and denitrifiers dominated later-stage decreases in nitrite and nitrate, indicating that the bacterial nitrogen removal function responded to nutrient dynamics. This study demonstrated the coupling mechanisms between ecological adaptation strategies of bacterial communities and nitrogen removal function in RAS, thereby establishing a basis for precision management technologies targeting functional bacteria.}, } @article {pmid41874734, year = {2026}, author = {de Medeiros Azevedo, T and Aburjaile, FF and Pandolfi, V and Ferreira-Neto, JRC and Fracetto, GGM and de Oliveira Silva, RL and Gonçalves-Oliveira, RC and de Carvalho Azevedo, VA and Brenig, B and Benko-Iseppon, AM}, title = {Unlocking the microbiome of an extremophile plant: metagenomic insights into Calotropis procera's endo-rhizosphere communities.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41874734}, issn = {1573-0972}, abstract = {This study explores the root-associated microbiome of Calotropis procera, a drought-adapted, invasive plant thriving in Brazil. We analyzed microbial communities from the root endosphere, rhizosphere, and adjacent soil in two contrasting ecosystems: Caatinga (semi-arid) and Restinga (coastal). Using 16S rDNA sequencing and shotgun metagenomics, we tested three hypotheses: (I) environmental specificity of the rhizospheric bacterial microbiome, (II) continuity of bacterial composition between bulk soil and rhizosphere, and (III) host-driven filtering of the endophytic microbiome. Despite differing soil conditions – more sodium in Restinga and higher organic carbon in Caatinga – microbial profiles in root compartments remained consistent. The root endosphere was enriched with stress-tolerant bacteria and novel archaea, while fungal genera included Fusarium and Puccinia. Results partially supported environmental specificity and showed moderate soil-rhizosphere continuity, with evidence of plant-mediated selection. Host filtering was evident for bacteria and fungi but not archaea. These data indicate a C. procera-mediated regulation of its root microbiome composition, whereby the plant may either selectively recruit specific taxa from prevalent soil microbial communities (e.g., through root exudates) or vertically transmit a conserved subset of its microbiome via seeds. Our study enhances understanding of the C. procera microbiome and its microbial interactions, identifying potential candidates for future biotechnological applications.}, } @article {pmid41874898, year = {2026}, author = {Son, JS and Lee, SY and Sang, MK and Spinelli, F and Ryu, CM}, title = {Protective holobiome promotes strawberry tolerance of biotic stresses.}, journal = {Stress biology}, volume = {6}, number = {1}, pages = {}, pmid = {41874898}, issn = {2731-0450}, support = {. RS-2022-RD010288//RDA/ ; CN00000022//Italian Academy for Advanced Studies in America, Columbia University/ ; KRIBB202434//Korea Research Institute of Bioscience and Biotechnology/ ; }, abstract = {The commercial cultivation of strawberry (Fragaria × ananassa) is increasingly challenged by biotic stresses such as plant pathogens and insect pests, while climate change exacerbates abiotic stresses. Reliance on chemical fumigants and broad-spectrum pesticides presents risks to human health, environmental quality, and microbial diversity. The strawberry holobiome, defined as the integrated community of plant-associated microorganisms that inhabit the rhizosphere, phyllosphere, endosphere, and fruit surface, is emerging as a key determinant of plant health and productivity. Recent metagenomic and metabolomic studies have identified cultivar-specific microbial consortia that suppress plant disease, enhance stress tolerance via induced systemic resistance, and modulate fruit quality. The engineering of synthetic microbial communities (SynComs) offers a targeted approach to microbiome augmentation, but the lack of high-resolution functional data hinders the development of effective SynComs, especially in hydroponic and substrate culture systems. This review synthesizes recent advances in holobiome profiling, evaluates microbial biocontrol strategies against major pathogens, and outlines future directions, including AI (artificial intelligence)-driven community design, integrated multi-omics analysis, and microbiome-assisted breeding. Addressing these gaps will enable precision management of the strawberry microbiome to sustain yield, quality, and resilience under dynamic environmental conditions.}, } @article {pmid41874931, year = {2026}, author = {Gong, K and Xie, Z and Zhang, P and Xu, J and Huang, J and Li, X and Huang, L}, title = {Limosilactobacillus reuteri LR-99 Modulates Gut Microbiota and Core Symptoms in Children with Autism Spectrum Disorder: A Single-arm Pilot Study.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41874931}, issn = {1867-1314}, support = {3502Z202372073//Xiamen Natural Science Foundation of China/ ; }, abstract = {Gut microbiota dysbiosis has been implicated in the pathophysiology of autism spectrum disorder (ASD). This study aimed to evaluate the effects of Limosilactobacillus reuteri LR-99 on gut microbiota composition and core symptoms in children with ASD. In this single-arm pilot study, 17 children with ASD received L. reuteri LR-99 (5.0 × 10[10] CFU, three times daily) for four weeks. Gut microbiota profiles were characterized using metagenomic sequencing and compared with those of neurotypical family members. Behavioral symptoms were assessed using the Childhood Autism Rating Scale (CARS) and Social Responsiveness Scale (SRS). Gastrointestinal symptoms were evaluated using the Gastrointestinal Symptom Rating Scale (GSRS) and Bristol Stool Form Scale (BSFS). The intervention significantly modulated the gut microbiota, characterized by an increased relative abundance of Bifidobacterium and a decreased relative abundance of Proteobacteria. Clinically, the intervention was associated with significant improvements in gastrointestinal symptoms (lower GSRS scores and more normal stool consistency on the BSFS) and in core autistic behaviors (lower CARS and SRS scores). The gut microbiota profile of children with ASD also shifted toward that of neurotypical controls. A four-week L. reuteri LR-99 intervention was associated with beneficial modulation of the gut microbiota, alleviation of gastrointestinal symptoms, and improvement in behavioral symptoms in children with ASD. These preliminary findings suggest that L. reuteri LR-99 may be a promising adjunctive therapy; however, given the limitations of the single-arm design and age differences between groups, larger randomized, placebo-controlled trials are needed to confirm efficacy.}, } @article {pmid41875072, year = {2026}, author = {van der Heyde, M and Curran, M and Floeckner, S and Nevill, P and White, NE and Austin, AD and Guzik, MT}, title = {Validating COI eDNA Metabarcoding Primers for Detection of Subterranean Fauna.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70127}, pmid = {41875072}, issn = {1755-0998}, support = {LP190100555//Australia Research Council Linkage Project/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA Primers/genetics ; *Electron Transport Complex IV/genetics ; Animals ; *DNA, Environmental/genetics ; Biodiversity ; Extrachromosomal DNA/genetics ; *Metagenomics/methods ; Ecosystem ; }, abstract = {Subterranean ecosystems host a diverse range of ancient fauna, but studying these ecosystems is challenging due to significant sampling difficulties. Environmental DNA (eDNA) metabarcoding offers a promising approach for monitoring subterranean biodiversity, yet issues such as primer bias and non-target amplification can complicate its effectiveness. Thus, thorough validation of metabarcoding primers is crucial for accurate and comprehensive assessments of subterranean faunal diversity. This study aimed to address the need for robust primer validation through in silico, in vitro and in situ analyses, shedding light on primer performance across various subterranean taxa. The primary objective was to evaluate the effectiveness of COI metabarcoding primers for assessing subterranean faunal diversity. In silico analyses involved curating COI sequences from the Barcode of Life Database (BOLD) and selecting 14 primer combinations for in vitro testing using mock communities. Results revealed varying primer performance in terms of PCR efficiency and detection limits across different taxa. One primer combination (BF1/jgHCO2198) detected 82% of taxa in the mock community, but only at high DNA concentrations of the target taxa. The highest proportion of subterranean taxa detected in a diluted mock community was 68% using the fwhF2/fwhR2n primer combination. For in situ field validation, this same primer set detected 13 out of 16 subterranean taxa identified in haul net samples, along with an additional four taxa not identified by haul net. These findings highlight the potential of COI metabarcoding and the critical importance of primer selection for eDNA studies aimed at conserving subterranean biodiversity.}, } @article {pmid41875156, year = {2026}, author = {Shen, LQ and Wang, L and Yao, Z and Lin, D and Ye, YQ and Zhang, WR and Ye, M and Sun, MM and Du, S and Wu, D and O'Connor, P and Zhu, D}, title = {Phages drive the dissemination of antibiotic resistance genes by facilitating host adaptation to heavy metal stress.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {13}, pages = {e2535653123}, pmid = {41875156}, issn = {1091-6490}, support = {22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 2024YFE0106300//MOST | National Key Research and Development Program of China (NKPs)/ ; 2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; }, mesh = {*Metals, Heavy/toxicity/metabolism ; *Bacteriophages/genetics/physiology ; Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/virology/drug effects ; Adaptation, Physiological/genetics ; *Drug Resistance, Bacterial/genetics ; Stress, Physiological ; }, abstract = {Heavy metals are increasingly recognized as major drivers of antibiotic resistance gene (ARG) dissemination in soil ecosystems. However, the role of phages in heavy metal-driven ARG dissemination and the underlying mechanisms remain poorly understood. Here, through integrative metagenomic, viromics, and metabolomic analyses of paddy soils across China, we reveal that soil phages promote ARG dissemination under heavy metal stress, likely through two potential mechanisms. First, phage-encoded auxiliary metabolic genes (AMGs) reprogram host metabolism to enhance bacterial survival and adaptation, thereby facilitating the cotransfer of adjacent ARGs and indirectly promoting horizontal dissemination. Second, phage-encoded heavy metal detoxification genes (HDGs) directly mediate metal detoxification, driving the cotransfer of neighboring ARG fragments and inducing lipid peroxidation-associated increases in membrane permeability, which collectively enhance ARG mobilization. We further identify a significant enrichment of lysogenic phages coharboring ARGs with AMGs or HDGs (AMG-ARG and HDG-ARG fragments), underscoring their contribution to ARG dissemination. Phage transplantation experiments confirm that elevated heavy metal stress triggers lysogenic phage-mediated ARG transduction to bacterial hosts. Cumulatively, our experiments highlight the pivotal role of phages in mediating ARG transfer under heavy metal pressure and underscore the necessity of incorporating phage dynamics into ARG risk assessments.}, } @article {pmid41875508, year = {2026}, author = {Estrada, CSD and de Oliveira, OA and Lopes, TAC and Maria, CRC and Avelino-Alves, D and Lima, M and Vidal, LM and de Siqueira Campos, L and Dias, GM and Thompson, C and Tschoeke, D and Thompson, F}, title = {Rhodolith metagenome diversity shifts across the Great Amazon System.}, journal = {The Science of the total environment}, volume = {1027}, number = {}, pages = {181652}, doi = {10.1016/j.scitotenv.2026.181652}, pmid = {41875508}, issn = {1879-1026}, mesh = {*Metagenome ; *Rhodophyta/genetics ; *Coral Reefs ; Brazil ; Bacteria/genetics/classification ; Archaea/genetics ; Biodiversity ; Metagenomics ; }, abstract = {Rhodolith-forming coralline algae in the Great Amazon Reef System (GARS) occur under strong light and redox gradients imposed by the Amazon River plume. We tested whether a conserved microbial and metabolic core persists across sectors while functions reorganize with local conditions. We conducted shotgun metagenomics on rhodolith holobionts collected in the South, Central, and North sectors and profiled taxonomic composition and pathway markers (KEGG/SEED; METABOLIC). Bacteria dominated the holobiont, with Proteobacteria, Chloroflexi, and Bacteroidetes prevailing, and Thaumarchaeota as the main archaeal lineage. Functional profiles showed structured not random variation among sectors. In the South, high water transparency supported oxygenic phototrophy (psa/psb, rbcL/S; phycobiliproteins) and stronger coupling between carbon fixation and respiration. The Central sector displayed a transitional configuration combining oxygenic and anoxygenic phototrophy (pufL/M; bch genes) with co-occurring nitrification-denitrification (amoA, nxrAB, nirK, nosZ), indicating tight NS cycling. The North was enriched in sulfur redox pathways linked to suboxic microzones, with sulfate-reducing and sulfur-oxidizing lineages and contributions from methanogenic archaea. Across sectors, high diversity and functional redundancy likely underpin holobiont persistence in mesophotic settings. Our results indicate a resilient, sector-specific reorganization of rhodolith-associated microbiomes along plume-driven gradients, with implications for biogenic calcification and biogeochemical stability under climate change and ocean acidification scenarios.}, } @article {pmid41875555, year = {2026}, author = {Lu, L and Li, M and Kang, G and Wu, P and Wang, N and Tan, Y and Su, G and Ruan, J and Zhang, S}, title = {Fate of per- and polyfluoroalkyl substances (PFAS) and microbial communities in wastewater treatment: Disinfection-driven changes in microbial dynamics and PFAS profiles.}, journal = {Ecotoxicology and environmental safety}, volume = {314}, number = {}, pages = {120059}, doi = {10.1016/j.ecoenv.2026.120059}, pmid = {41875555}, issn = {1090-2414}, mesh = {*Wastewater/microbiology/chemistry ; *Fluorocarbons/analysis ; *Water Pollutants, Chemical/analysis ; *Disinfection ; Bacteria/genetics ; *Waste Disposal, Fluid/methods ; *Microbiota/drug effects ; Water Purification/methods ; China ; Environmental Monitoring ; Caprylates/analysis ; }, abstract = {Municipal wastewater treatment plants (MWWTPs) are both sinks and sources of per- and polyfluoroalkyl substances (PFAS) due to limited removal efficiency in current treatment systems. However, the role of treatment processes, especially disinfection, in altering PFAS and microbial communities remains underexplored. In this study, we investigated the occurrence of 17 PFAS in two MWWTPs in Northwest China and characterized microbial communities through metagenomic sequencing. Results showed that total PFAS concentrations increased from 56.8 to 60.3 ng/L in MWWTPA and from 5.1 to 19.1 ng/L in MWWTPB, indicating ineffective removal. Perfluoropentanoic acid (PFPeA) and perfluorononanoic acid (PFNA) dominated the influent, accounting for 86.6% and 33.3% in MWWTPA and MWWTPB, respectively. In contrast, perfluorooctanesulfonic acid (PFOS, 46.8-52.4%) and perfluorooctanoic acid (PFOA, 5.1-8.9%) concentrations increased markedly in the effluent, becoming the predominant PFAS. Meanwhile, disinfection also altered microbial diversity and homogenized community structures between the two MWWTPs. Further analysis revealed strong associations (p < 0.01) between elevated PFAS levels and specific microbial taxa, including Actinomycetia and Thermoprotei, alongside increased relative abundance of genes annotated as haloacid dehalogenases, monooxygenases, and cytochrome P450. These associations may reflect potential influences on PFAS precursor dynamics. Overall, these findings highlight the importance of considering both chemical and microbial shifts when evaluating PFAS behavior during wastewater treatment.}, } @article {pmid41875615, year = {2026}, author = {Kesavan, D and Meenatchi, R and Mohanakrishna, R and Tripathi, A and B S, Y and Narayanane, S and Gupta, S and Yadav, P and Pasupuleti, M and Mani, G and Balachandran, KRS and Rangamaran, VR and Verma, P and Kumar, AG and Vinithkumar, NV and Gopal, D and Pazhani, GP and Arockiaraj, J}, title = {Metagenomic mining of microbial communication genes from Indian deep-sea sediments using a quorum sensing- and quenching-related protein database.}, journal = {Marine genomics}, volume = {86}, number = {}, pages = {101245}, doi = {10.1016/j.margen.2026.101245}, pmid = {41875615}, issn = {1876-7478}, mesh = {*Quorum Sensing/genetics ; *Geologic Sediments/microbiology ; *Metagenome ; Indian Ocean ; Metagenomics ; Databases, Protein ; }, abstract = {Cell-to-cell communication among microbes plays a key role in environmental adaptation and highly contributes to global biogeochemical cycling. However, microbial communication systems in deep-sea sediments, where diverse microbial communities employ quorum sensing (QS) and quorum quenching (QQ) mechanisms to regulate ecological interactions, remain largely understudied. Their distribution patterns and functional dynamics in deep-sea ecosystems are poorly understood. This study investigated QS and QQ communication systems alongside microbial community distribution in Arabian Sea sediments collected from depths of 334, 492, 550, and 992 m across the northern and southern Arabian Sea. Shotgun metagenomic sequencing was performed in conjunction with a curated QS- and QQ-related protein (QSP) database. Both individual assemblies and metagenome-assembled genomes (MAGs) were analyzed to comprehensively identify communication-associated proteins. In total, around 359 QSPs were detected across four sediment samples. Shallow sediments (334 and 492 m) exhibited greater abundance and diversity of QS and QQ elements, particularly acyl-homoserine lactone (AHL)-driven QS systems and acylase/lactonase-based QQ systems, indicating active microbial interactions. In contrast, deeper sediments (550 and 992 m) displayed reduced diversity of canonical QS elements with enrichment of autoinducer-2 (AI-2), diffusible signal factor (DSF), and cyclic-di-GMP signalling pathways, suggesting adaptive mechanisms conducive to oligotrophic and high-pressure conditions of deep-sea. Correlation analyses revealed potential intra- and inter-system associations among QS regulators and QQ enzymes, indicating complex regulatory networks. MAG-derived protein analyses detected conserved catalytic motifs, and molecular docking supported functional interactions with signal molecules. Overall, these findings provide a preliminary overview of QS and QQ related genes in deep sea sediments of the Arabian Sea and suggest potential variability in microbial communication systems within these environments.}, } @article {pmid41875710, year = {2026}, author = {Gadoin, E and Massot, M and Callens, M and Arnout, P and Bedhomme, S and Rajkovic, A}, title = {Shotgun metagenomic profiling reveals a high diversity of taxa and genes within biofilms formed on microplastics incubated in urbanised aquatic ecosystems.}, journal = {Marine pollution bulletin}, volume = {228}, number = {}, pages = {119569}, doi = {10.1016/j.marpolbul.2026.119569}, pmid = {41875710}, issn = {1879-3363}, mesh = {*Biofilms ; *Microplastics ; Bacteria/genetics ; Ecosystem ; Metagenomics ; Environmental Monitoring ; *Water Pollutants, Chemical ; }, abstract = {Microplastics (MPs) are ubiquitous in aquatic ecosystems, where they are colonized by microbial communities, called the plastisphere. Of great concern is the detection of potential pathogens and antimicrobial resistance genes (ARG) in the plastisphere, which might be transported across ecosystems through MPs drifting. We used shotgun metagenomic profiling to assess taxa diversity, ARG and virulence genes (VG), within biofilm formed on polypropylene (PP) particles incubated in situ in five locations, following an anthropic gradient around Ostend (Belgium). Our results demonstrated significant variability of the plastisphere across incubation sites, but not between PP and control glass beads. Potential pathogenic bacteria (PPB) represented about 7% of bacterial reads within biofilms and VG were mainly involved in nutrition and adherence. Using dqPCR results to normalize metagenomic reads, we demonstrated a selective enrichment of ARG and VG in biofilms, while these were less abundant but more diverse in surrounding water. These findings highlight the presence of PPB, ARG and VG across all sites, likely driven by anthropogenic pressures. Although no substrate-specific effect was detected, the ability of PP particles to act as microbial reservoirs, coupled with their high mobility, reinforces concerns about their potential role in the transport and dissemination of microbial hazards.}, } @article {pmid41875745, year = {2026}, author = {Zhang, H and Li, B and Ni, R and Ye, L and Bai, G and Zhao, J}, title = {Stable functional consortium assembly via uncoupled SAD/anammox inoculation drives synergistic nitrogen‑sulfur removal in sediment.}, journal = {Water research}, volume = {297}, number = {}, pages = {125768}, doi = {10.1016/j.watres.2026.125768}, pmid = {41875745}, issn = {1879-2448}, mesh = {*Nitrogen/metabolism ; *Sulfur/metabolism ; *Geologic Sediments/chemistry/microbiology ; Denitrification ; Oxidation-Reduction ; Anaerobic Ammonia Oxidation ; *Microbial Consortia ; }, abstract = {The remediation of black‑odorous sediments remains challenging due to the intricate sediment matrix, the co-occurrence of multiple pollutants, and the difficulty in maintaining stable functional microbial consortia under fluctuating redox conditions. Although calcium nitrate (CN) is a used chemical oxidant, its sole application often results in incomplete nitrogen removal and risks of secondary pollution. While the integration of CN with sulfur-autotrophic denitrification (SAD) and anaerobic ammonia oxidation (anammox) presents a promising alternative, the microbial, especially concerning the assembly and efficacy of different microbial inoculation strategies, are poorly understood. This study systematically compared two distinct bioaugmentation approaches: the pre-coupled addition of a SAD and anammox consortium versus an uncoupled strategy involving separate additions of SAD and anammox consortium, both in combination with CN. Results demonstrated that the CN+S+A (uncoupled) treatment achieved optimal performance, enhancing the removal of NH4[+], NO3[-], and total nitrogen by 42%, 40%, and 35%, respectively, compared to CN alone, while also effective oxidizing acid‑volatile sulfide. Mechanistic analysis revealed that CN first optimized the sediment microenvironment. The uncoupled inoculation uniquely fostered a stable, dual-core microbial consortium dominated by Thiobacillus (3.00%) and Candidatus Brocadia (0.83%), which established a sustainable "sulfur-driven nitrogen removal" cycle. Metagenomic and isotopic tracing confirmed the enrichment of key functional genes and elevated process rates underpinning this synergy. These findings highlight that CN combined with uncoupled bioaugmentation is a novel and effective strategy for rebuilding stable nitrogen-sulfur cycles in black-odorous sediments.}, } @article {pmid41875962, year = {2026}, author = {Rector, A and Karataş, M and Bloemen, M and De Coninck, L and Swinnen, J and Close, L and Thijssen, M and Pourkarim, MR and Matthijnssens, J and Desmet, S and Van Ranst, M and Johnson, MC and Wollants, E}, title = {Airplane wastewater as a gateway for pathogen surveillance.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {140}, number = {}, pages = {105930}, doi = {10.1016/j.meegid.2026.105930}, pmid = {41875962}, issn = {1567-7257}, mesh = {*Wastewater/virology/microbiology ; Humans ; *SARS-CoV-2/genetics/isolation & purification/classification ; *Aircraft ; *COVID-19/virology/epidemiology ; Metagenomics/methods ; Animals ; Wastewater-Based Epidemiological Monitoring ; }, abstract = {BACKGROUND: Air travel plays a key role in the global spread of many diseases, including COVID-19. Surveillance of international travelers is useful for the detection of emerging viruses and variants of concern, especially in a context of global relaxations in testing policy. We aimed to assess the feasibility of using wastewater surveillance from airplanes as a method for monitoring SARS-CoV-2 variants and other pathogens entering Belgium.

METHODS: From January to March 2023, in the wake of the COVID pandemic, 32 wastewater samples were collected at Brussels Airport from direct flights originating in Beijing, China. We applied various qPCR panels and sequencing methods, including hybrid-capture metagenomic sequencing (Twist Bioscience) targeting more than fifteen thousand strains of known human and animal viruses.

RESULTS: Nineteen out of 32 samples tested positive for SARS-CoV-2. Various other pathogens, including enterovirus/rhinovirus, adenovirus, norovirus, adenovirus 40/41, and multiple clinically relevant bacteria, were identified using respiratory and gastrointestinal qPCR panels. In 7 samples, SARS-CoV-2 variants could be determined, belonging to known lineages BA4/BA5, BA4.6/BF7, and XBB. Moreover, hybrid-capture approach allowed us to recover complete genomes of viruses from families Polyomaviridae, Papillomaviridae, Herpesviridae as well as Aichivirus A and Hepatitis B virus.

CONCLUSION: This pilot project demonstrates the feasibility of detecting SARS-CoV-2 and its variants in wastewater of commercial airplanes. This method offers a valuable means of obtaining information from regions with limited SARS-CoV-2 genomic surveillance data. Moreover, using a hybrid-capture approach, a broad range of viruses of concern can be detected. The implementation of this novel screening approach is promising for enhancing traveler-based surveillance.}, } @article {pmid41876072, year = {2026}, author = {Shen, Q and Xiong, JQ and Wang, Q and Yang, L and Shen, Z and Lei, Z and Ru, S}, title = {Cyanobacteria-driven morphology and adaptive microbial succession: Resilience mechanisms in algal-bacterial granular sludge under tripartite stress.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134481}, doi = {10.1016/j.biortech.2026.134481}, pmid = {41876072}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Stress, Physiological ; *Cyanobacteria/physiology/metabolism ; *Adaptation, Physiological ; Sulfamethoxazole/pharmacology ; Carbon ; *Bacteria ; }, abstract = {Algal-bacterial granular sludge (ABGS) is a promising wastewater treatment technology, yet its practical application is constrained by its unknown stability under realistic multi-stressor conditions. This work demonstrated that ABGS could withstand combined low temperature (< 15°C), carbon scarcity, and sulfamethoxazole (SMX) exposure (0-100-1000 μg/L) through the defense strategy that integrated morphological, microbial and metabolic adaptations. Metagenomics revealed a metabolic trade-off, characterized by the downregulation of energy-intensive pathways (e.g., oxidative phosphorylation and TCA cycle), and the upregulation of biosynthetic and stress-responsive pathways (e.g., glyoxylate shunt and amino sugar metabolism), redirecting carbon towards extracellular polymeric substances (EPS) production. This was synergized by the protective cyanobacterial surface barrier and reconfigured protein-rich EPS for SMX sequestration. Microbial community restructuring enhanced functional resilience, as exemplified by the shift from Nitrospira to Candidatus Nitrotoga, which sustained stable nitrification. This coordinated adaptation not only enabled the robust removal of COD (> 90%) and NH4[+]-N (> 97%), but also suppressed the proliferation of antibiotic resistance genes (ARGs) under 100 μg/L SMX stress. These findings position ABGS as self-engineering ecosystems that actively modulate microbial community assembly and metabolic networks to remove nutrients and mitigate the dissemination of ARGs.}, } @article {pmid41876074, year = {2026}, author = {Zhang, Y and Wu, J and Yue, C and Wang, X and Qu, Y and Zhang, X and Sun, Y and Liu, Z and Qu, J and Xu, X}, title = {Enhancing anaerobic digestion of agricultural waste via a stable Fe-Emodin-Biochar composite: Kinetic performance, energy recovery, and metabolic insights.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134463}, doi = {10.1016/j.biortech.2026.134463}, pmid = {41876074}, issn = {1873-2976}, mesh = {Anaerobiosis ; Kinetics ; Methane/biosynthesis ; *Iron/chemistry ; *Agriculture ; *Refuse Disposal/methods ; }, abstract = {Anaerobic digestion (AD) efficiency is often constrained by energy transfer in interspecies electron transfer. To address this, a cost-effective electron mediator was engineered by immobilizing industrial-grade Emodin onto an Fe-biochar matrix via one-step hydrothermal synthesis. The optimal composite (Fe/Emodin molar ratio 1.5:1) achieved a 43.3 % increase in cumulative methane yield and shortened the lag phase by 38.1 %. According to biochemical tests, the composite reduced energy barriers on the breakdown of volatile fatty acids, as shown by a 2.2-fold rise in ATP levels and increased expression of Coenzyme F420. A community shift marked by the co-enrichment of Methanothrix and syntrophic bacteria was revealed by metagenomic analysis. A change from energetically constrained hydrogen transfer to pathways mediated by the composite was suggested by the abundance of Type IV pili genes and Cytochrome c genes, which suggested the possible activation of direct interspecies electron transfer (DIET). By utilizing low-cost precursors and overcoming the instability of free mediators, this study offers a scalable biotechnological method for agricultural residue valorization. Furthermore, this approach demonstrates economic viability and potential life-cycle sustainability.}, } @article {pmid41876075, year = {2026}, author = {Wu, H and Wang, H and Man, S and Yan, Q}, title = {Biogenic FeS Reshapes microbial interactions to regulate acetogenesis in CO2-Fed microbial electrosynthesis.}, journal = {Bioresource technology}, volume = {450}, number = {}, pages = {134480}, doi = {10.1016/j.biortech.2026.134480}, pmid = {41876075}, issn = {1873-2976}, mesh = {*Carbon Dioxide/metabolism ; *Acetates/metabolism ; *Shewanella/metabolism ; *Microbial Interactions ; Electrodes ; *Bioelectric Energy Sources/microbiology ; *Iron/metabolism ; }, abstract = {Inefficient electron transfer and poorly coordinated microbial communities often limit stable CO2-to-acetate conversion in microbial electrosynthesis (MES). Herein, Shewanella oneidensis MR-1 was introduced to induce in situ biogenic FeS formation at the cathode to regulate microbial interactions and enhance acetogenesis. Under the acetogenesis dominant condition (RAT: sludge to MR-1 ratio of 2:1, Fe/S = 5/10 mM, initial MR-1 inoculation), acetate production reached 1330.6 mg L[-1] with the carbon recovery efficiency of 62.9%. Community and metagenomic analyses showed that FeS selectively enriched acetogens and Fe/S transforming microorganisms while restructuring functional pathways related to redox metabolism and energy conservation. Co-occurrence network analysis further revealed that FeS promoted coordinated, function oriented microbial interactions rather than competitive associations. This study highlights the role of biogenic FeS in linking electron transfer with microbial cooperation, providing a mechanistic basis for improving MES performance through community level regulation.}, } @article {pmid41876513, year = {2026}, author = {Jovicic, D and Anestis, K and Fiutowski, J and Jørgensen, BB and Kjeldsen, KU and Rotaru, AE}, title = {Genome-centric metagenomics reveals electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41876513}, issn = {2041-1723}, support = {1026-00159B//Natur og Univers, Det Frie Forskningsråd (Natural Sciences, Danish Council for Independent Research)/ ; 101045149//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Geologic Sediments/microbiology ; *Metagenomics/methods ; Acetates/metabolism ; Oxidation-Reduction ; Electron Transport ; Methane/metabolism ; Cytochromes/metabolism/genetics ; Phylogeny ; Methanosarcina/genetics/metabolism ; Genome, Bacterial ; *Microbial Consortia/genetics ; Electric Conductivity ; }, abstract = {Conductive particles are common in coastal sediments, yet their role in shaping methane-producing communities and pathways remains unclear. We applied genome-resolved metagenomics to a sediment-derived consortium serially transferred for a decade and obligately dependent on granular activated carbon (GAC). We discovered a particle-obligate food web composed of electrogenic syntrophic acetate oxidizers (SAO), an electrotrophic methanogen, and necromass recyclers. The primary SAO electrogen, Candidatus Geosyntrophus acetoxidans, represents a new genus and possesses a complete acetate oxidation pathway and extracellular electron-transfer (EET) machinery, including two porin-cytochrome conduits, 43 additional multiheme cytochromes and conductive pili. A secondary SAO, a Lentimicrobium sp. with a giant PCC-cluster, supplies an alternative EET-linked acetate-oxidation route. Electrons from electrogens transfer via GAC to a Methanosarcina equipped with the heptaheme cytochrome MmcA and flagellin for electron uptake. These results provide a genomic blueprint of this particle-obligate environmental consortium and suggest an overlooked acetate-to-methane electron-transfer route in geoconductor-rich anoxic sediments.}, } @article {pmid41876637, year = {2026}, author = {Wang, R and Ma, R and Cai, Y and Zhang, L and Lu, W and Zheng, W and Kong, J and Miao, Q and Li, X and Guan, L and Gao, Y and Chen, K and Kwan, ATH and McIntyre, RS and Xu, G and Yu, CK and Lam, BY and So, KF and Lin, K}, title = {Exploratory characterization of gut microbiota and cognitive profiles in adolescents with subthreshold depression: a shotgun metagenomics sequencing study.}, journal = {Npj mental health research}, volume = {5}, number = {1}, pages = {}, pmid = {41876637}, issn = {2731-4251}, support = {No. 2021A1515011361//Natural Science Foundation of Guangdong Province/ ; No. 202102020735//Science and Technology Program of Guangzhou/ ; No. 2024SRP208//Guangzhou Medical University Research Capacity Enhancement Program/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 82171531//National Natural Science Foundation of China/ ; No. PX-66221557//Guangzhou Medical University student innovation ability enhancement Program/ ; STG STG1/M-501/23-N//the Hong Kong RGC theme-based Strategic Target Grant Scheme/ ; }, abstract = {Subthreshold depression (SD) in adolescents is a prevalent condition associated with significant functional impairment and an increased risk of developing major depressive disorder. Currently, the lack of reliable objective markers complicates its accurate identification. Investigating the gut microbiome may offer novel insights into its underlying mechanisms. This study aimed to investigate the association between gut microbiome and cognitive function in adolescents with subthreshold Depression (SD). Thirty-eight adolescents with SD and 139 clinically-well (CW) adolescents were recruited. Gut microbiome and cognitive function were assessed by metagenomic sequencing and the MATRICS Consensus Cognitive Battery (MCCB), respectively. Compared with the CW adolescents, the SD group showed higher relative abundance of Spirochaetes, Synergistetes, Spirochaetia, Synergistia, Spirochaetales, Rhizobiales, Synergistales, Thermoanaerobacterales, Rhodospirillales, Synergistaceae, and Oxalobacteraceae at four levels. The Spatial Span scores were higher in the SD group compared to the CW group. Moreover, EggNOG analyses showed a significant negative correlation of the intracellular trafficking secretion, and vesicular transport with the Spatial Span scores. The KEGG pathway of the neurodegenerative diseases and translation was depleted in the microbiome of adolescents with SD. The higher abundance of Spirochaetes, Spirochaetia, and Spirochaetales was the best predictor of SD in adolescents. Our findings suggest that gut microbiome abnormalities, depressive symptoms, and cognitive influences co-occur in adolescents with SD, which may play a crucial role in the pathogenesis of SD and cognitive function in adolescent. Gut microbiome may serve as a potential biomarker for the identification and treatment of adolescents with SD.}, } @article {pmid41876857, year = {2026}, author = {Peñuelas, J and Zheng, B and Tariq, A and Sardans, J}, title = {Microbial phosphorus cycling in terrestrial ecosystems.}, journal = {Nature reviews. Microbiology}, volume = {24}, number = {7}, pages = {478-495}, pmid = {41876857}, issn = {1740-1534}, mesh = {*Phosphorus/metabolism ; *Ecosystem ; *Soil Microbiology ; *Archaea/metabolism ; *Bacteria/metabolism ; *Fungi/metabolism ; Soil/chemistry ; }, abstract = {Phosphorus is an essential yet often limiting macronutrient that shapes primary productivity and microbial activity in terrestrial ecosystems. Unlike carbon and nitrogen cycles, which have gaseous phases, the terrestrial phosphorus cycle is primarily governed by soil biogeochemistry, wherein microorganisms orchestrate key transformations. This Review synthesizes current knowledge of the microbial phosphorus cycle, emphasizing the diverse mechanisms used by bacteria, fungi and archaea to mobilize phosphorus (for example, via phosphatases such as PhoA and PhoD and organic acids such as citrate) and to directly enhance plant phosphorus uptake. We explore the ecological significance of these processes in maintaining soil health, supporting ecosystem productivity and influencing carbon sequestration. We propose the Microbial Phosphorus Adaptive Evolution Theory (MPAET): chronic phosphorus scarcity drives evolutionary and ecological shifts in microbial communities towards higher scavenging investment, polyphosphate handling and lipid remodelling. Furthermore, we examine how environmental factors, land use and climate modulate these shifts (for example, phoD expression increases under phosphorus stress), with cascading effects on ecosystem function and global phosphorus availability. New technologies such as metagenomics, [18]O-phosphate tracing and nanoscale secondary ion mass spectrometry are now revolutionizing our understanding of these dynamics. This Review underscores the critical need to integrate microbial phosphorus cycling into ecosystem models and to develop sustainable strategies for phosphorus smart management. Such approaches are essential for addressing global challenges related to soil degradation, food security and environmental change.}, } @article {pmid41877145, year = {2026}, author = {Zhang, QN and Zhang, XH and Shi, SS}, title = {Tacrolimus-induced interstitial lung injury in a pediatric cardiac transplant recipient: a case report and literature review.}, journal = {BMC pediatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41877145}, issn = {1471-2431}, abstract = {BACKGROUND: Tacrolimus-induced interstitial lung injury (TI-ILI) is a rare but potentially fatal adverse effect of calcineurin-inhibitor therapy. To our knowledge, TI-ILI has not previously been reported in a paediatric heart-transplant recipient.

CASE PRESENTATION: A 6-year-old boy with PLN-related dilated cardiomyopathy underwent orthotopic heart transplantation. Maintenance immunosuppression comprised tacrolimus, mycophenolate mofetil and prednisone. On post-operative day 13 he developed bilateral ground-glass opacities with interlobular septal thickening on chest CT. Broncho-alveolar lavage metagenomics showed only low-abundance Pseudomonas aeruginosa and Acinetobacter baumannii; extensive microbiological, cardiac work-up was negative. Infiltrates progressed despite targeted antibiotics, but resolved within 4 weeks after tacrolimus was replaced by cyclosporine and corticosteroids were doubled. No relapse occurred during 6 months of follow-up.

CONCLUSIONS: TI-ILI should be considered in any heart transplant recipient with unexplained progressive bilateral pulmonary infiltrates. Early tacrolimus withdrawal and prompt corticosteroid therapy are associated with complete recovery; re-exposure to tacrolimus is contraindicated.}, } @article {pmid41877267, year = {2026}, author = {Peirson, LE and McKenney, EA and Patterson, JR and Beasley, JC and Périquet-Pearce, S and Cloete, C and Melton, MH and PetersonWood, B and Portas, R and Aschenborn, O and Lafferty, DJR}, title = {African carnivore gut bacterial diversity and composition are associated with sample condition but not storage technique.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41877267}, issn = {2524-4671}, support = {Financial Assistance Award no. DE-EM0005228//U.S. Department of Energy/ ; Peter White Scholar Award//Northern Michigan University/ ; }, abstract = {Non-invasive fecal sampling is essential for molecular wildlife studies such as gut microbiome (GMB) research, yet field conditions often limit preservation options. To test the effects of preservation methods on the results of GMB community composition, we compared gut bacterial communities in paired fecal samples preserved in stabilization tubes and air-dried in paper bags collected from anesthetized African lions (Panthera leo) and spotted hyenas (Crocuta crocuta) in Etosha National Park, Namibia. Additional opportunistic samples from the ground around carnivore feeding sites that varied in moisture content were also analyzed. No differences in alpha or beta diversity were detected between preserved and dried samples, although bacterial beta diversity differed between preserved and opportunistic samples, supported by NMDS ordinations and PERMANOVA results. Core bacterial communities remained consistent across opportunistic sample conditions, indicating that host-associated taxa persist despite environmental exposure supporting the use of opportunistic samples for GMB studies in remote arid settings. However, consistent sampling protocols and future field-based desiccation studies remain critical for comparative analyses. These findings highlight that rapid air-drying offers a reliable, low-cost preservation option that maintains core microbiome patterns, expanding the feasibility of GMB research in remote or resource-limited field contexts where refrigeration and preservatives may be unavailable.}, } @article {pmid41877288, year = {2026}, author = {Wei, G and Liu, M and Huang, L and Chen, C}, title = {Metagenomic sequencing reveals the dynamic changes of pig gut fungal composition following the ages and identifies fungal species associated with diarrhea in piglets.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41877288}, issn = {2524-4671}, support = {32272831//National Natural Science Foundation of China/ ; }, abstract = {Fungi are crucial components of the pig gut microbiome, influencing host immunity and metabolism. However, the investigation about gut fungi via metagenomic sequencing remains challenging due to analytical complexity. Here, we characterized pig gut fungal profiles using 750 metagenomes collected from public repositories and our previous datasets based on a comprehensive collection of fungal reference genomes, and revealed dynamic compositional changes of pig gut fungi from birth to market (7d, 14d, 21d, 28d, 35d, 70d, and 140d). Weaning significantly shaped the gut fungal community, affecting key fungi like Lachancea kluyveri and Kazachstania slooffiae. Inter-kingdom interaction analysis revealed significant correlations between fungi and bacteria, such as between L. kluyveri and Lactobacillus amylovorus (r = -0.48) and between K. slooffiae and Lactobacillus johnsonii (r = 0.75). We identified 87 diarrhea-associated fungal species at the significance threshold of LDA > 2.0 in three experimental piglet cohorts. In antibiotic-free piglets, fungal species from Saccharomyces and Aspergillus, some of which have been considered as potential probiotics, were enriched in healthy individuals, whereas in antibiotic-treated groups, Saccharomyces spp. and K. slooffiae were higher in diarrheal piglets. Notably, K. slooffiae were negatively correlated with the pathogen M. circinelloides, suggesting a protective role during gut dysbiosis. This study provides a foundation for developing fungal-based interventions to improve pig health.}, } @article {pmid41877907, year = {2026}, author = {Xie, S and Zhang, H and Xie, Y and Liu, F and Ye, S and Liu, X and Lai, Z}, title = {Analysis of the Clinical Features of HSV-2 Encephalitis Confirmed by the mNGS Technique: Insights Derived from Seven Patient Studies.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {567731}, pmid = {41877907}, issn = {1178-6973}, abstract = {BACKGROUND: Herpes simplex virus type 2 (HSV-2) encephalitis is rare in immunocompetent adults. Diagnosis typically depends on cerebrospinal fluid (CSF) polymerase chain reaction (PCR), which has limited sensitivity and potential for false negatives. Metagenomic next-generation sequencing (mNGS) provides unbiased pathogen detection, facilitating rapid HSV-2 identification in CSF and minimizing misdiagnosis risks, especially in atypical cases or immunocompetent individuals. This study examines the diagnostic value of mNGS in a cohort of patients with HSV-2 encephalitis presenting atypically.

METHODS: A retrospective analysis was performed on patients diagnosed with HSV-2 encephalitis using mNGS at our institution between January 2022 and January 2025. Clinical characteristics, ancillary test results, and patient outcomes were analyzed to evaluate the diagnostic value of mNGS.

RESULTS: Seven patients (2 males, 28.57%; 5 females, 71.43%) with a mean age of 33.57 years were included; one had pre-existing immunodeficiency (14.28%). Most presented atypical symptoms; six treated within three days fully recovered, while one with delayed treatment died. Mean follow-up was 14.71 ± 5.82 months. Higher viral sequence counts correlated with worse outcomes. Initial CSF analysis showed normal cell counts in one patient; all exhibited lymphocytic pleocytosis and elevated protein levels.

CONCLUSION: This study contributes to the limited clinical data on adult HSV-2 encephalitis by summarizing clinical manifestations and treatment outcomes, thereby informing improved diagnostic and management strategies. It also highlights the prognostic importance of early diagnosis and immune status assessment through the application of mNGS.}, } @article {pmid41877920, year = {2026}, author = {Zeng, F and Zhu, T and Chen, X and Huang, K and Liu, L and Wang, G and Mai, J and Zhang, S}, title = {Gut microbiota and metabolic status during pregnancy in captive Asian elephants.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1749490}, pmid = {41877920}, issn = {2297-1769}, abstract = {BACKGROUND: The gut microbiota is regarded as one of the key factors regulating host health. The gut microbiota and its connection to fecal metabolites are crucial for supporting fetal development and ensuring maternal health during reproductive stages. Although studies have examined Asian elephants, the composition and function of the gut microbiota in pregnant and non-pregnant captive Asian elephants have not been reported.

METHODS: We compared the fecal microbiota and fecal metabolites of pregnant (G1), non-pregnant (never gotten pregnant after reaching sexual maturity, G2), and subadult (G3) captive Asian elephants using metagenomic sequencing and untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics.

RESULTS: We found significant differences in the gut microbiota among the G1, G2, and G3 groups. The phylum Bacteroidetes showed notable differences between G1 and G2. The analysis of fecal metabolomics revealed significant differences in 49 metabolites between G1 and G2, of which 25 were upregulated and 24 were downregulated. These results suggested significant differences in the composition of gut microbiota and fecal metabolites during reproductive stages, while gut microbial diversity remained stable. These findings inform our ongoing research on the potential health conditions of captive Asian elephants, with the aim of better understanding the role of the gut microbiota in reproductive regulation.}, } @article {pmid41877937, year = {2025}, author = {Zhang, M and Pak, H and King, SD and Zuniga, AA and Hassan, YA and King, MD}, title = {Mitigating airborne pathogen risks in a full-scale meat processing facility.}, journal = {Total environment microbiology}, volume = {1}, number = {3}, pages = {}, pmid = {41877937}, issn = {3050-6417}, support = {R21 AI169046/AI/NIAID NIH HHS/United States ; }, abstract = {Foodborne illnesses caused by Shiga toxin-producing Escherichia coli (STEC) and Salmonella represent a major public health concern, particularly in meat processing facilities where bioaerosols generated during processes like carcass spraying and dehiding can lead to contamination. In this study, we assessed airborne concentrations of STEC and Salmonella at multiple locations within a full-scale meat processing facility using quantitative polymerase chain reaction (qPCR) and Illumina MiSeq sequencing. Additionally, we utilized computational fluid dynamics (CFD) simulations to model airflow within the facility and evaluated the effectiveness of air curtains in mitigating the transfer of bioaerosols between high-risk (dehiding and tripe) and low-risk (chiller and fabrication) areas. qPCR results showed that pathogen concentrations in the dehiding rooms were 126 GCN/m[3] for STEC and 105 GCN/m[3] for Salmonella during spring, with levels rising significantly in summer (2198 GCN/m[3] for STEC and 1799 GCN/m[3] for Salmonella). Simulated airflow patterns revealed that entrained bioaerosols could be transported from unclean to clean areas, increasing the risk of cross-contamination. The use of air curtains effectively reduced this spread by creating barriers between high- and low-risk areas. Our findings suggest that bacterial survivability and aerosolization was enhanced in summer, highlighting the critical role of environmental factors and airflow management in controlling contamination risks. This study demonstrates the value of integrating experimental data with CFD simulations to assess pathogen spread and identify effective mitigation strategies in meat processing facilities.}, } @article {pmid41878086, year = {2026}, author = {Luo, D and Jia, S and He, W and Fan, Z and Yin, W}, title = {Periplaneta americana Powder Alleviates Neuropathic Pain and is Associated with Gut Microbiota Changes in Rats.}, journal = {Journal of pain research}, volume = {19}, number = {}, pages = {564911}, pmid = {41878086}, issn = {1178-7090}, abstract = {BACKGROUND: This study aims to evaluate the therapeutic potential of Periplaneta americana powder (PAP) in alleviating neuropathic pain in a rat model of sciatic nerve injury induced by chronic constriction injury (CCI), and to systematically analyze its effects on the composition and structure of the gut microbiota during the intervention process, with the goal of elucidating the mechanisms underlying the analgesic effects of PAP.

METHODS: A rat model of CCI was established (n = 12 per group), and PAP was administered for intervention. The analgesic effects were evaluated using mechanical withdrawal threshold (MWT) and thermal withdrawal latency (TWL). Pathological changes in the spinal cord and colon tissues were examined via hematoxylin-eosin (HE) staining, and the expression of the astrocyte marker glial fibrillary acidic protein (GFAP) in the spinal cord was detected by immunohistochemistry. The expression levels of pro-inflammatory cytokines TNF-α and IL-1β in spinal cord tissues were measured using enzyme-linked immunosorbent assay (ELISA). Fecal samples were collected at the endpoint of treatment for metagenomic sequencing and analysis.

RESULTS: After PAP treatment, behavioral tests in CCI rats showed a significant increase in MWT and TWL (P < 0.05). Histological analysis revealed marked alleviation of spinal cord and colon tissue damage as well as reduced inflammatory cell infiltration (P < 0.05). Immunohistochemistry further demonstrated a significant decrease in GFAP expression in the spinal cord (P < 0.05). ELISA results showed that the expression levels of TNF-α and IL-1β in spinal cord tissues were significantly decreased (P < 0.05).Metagenomic analysis indicated that PAP reshaped the gut microbiota structure, increased the abundance of SCFA-producing bacteria, and was associated with the butyrate metabolism pathway.

CONCLUSION: This study indicates that PAP can significantly alleviate neuropathic pain in a rat model of sciatic nerve chronic constriction injury (CCI) and suppress the central inflammatory response.Notably, this effect is accompanied by changes in the gut microbiota, particularly characterized by a significant alteration in the abundance of short-chain fatty acid-producing bacteria. These results suggest that PAP not only possesses substantial analgesic effects but may also mediate the intervention of CCI-induced neuropathic pain by regulating the structure of the gut microbiota.}, } @article {pmid41878266, year = {2026}, author = {Huang, J and Yan, X and Su, Q and Tu, H and Yu, Z and Liu, D and Wu, B}, title = {Temporal dynamics of gut microbiota and virome in preterm infants: insights from longitudinal metagenomic analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1598786}, pmid = {41878266}, issn = {2235-2988}, mesh = {Humans ; *Infant, Premature ; *Virome ; *Metagenomics/methods ; Infant, Newborn ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Bacteriophages/genetics/isolation & purification/classification ; Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Enterococcus faecalis ; Staphylococcus epidermidis ; Metagenome ; Gastrointestinal Tract/microbiology/virology ; Klebsiella pneumoniae/isolation & purification ; Feces/microbiology/virology ; }, abstract = {INTRODUCTION: Preterm infants exhibit heightened vulnerability to morbidity and mortality due to their underdeveloped immune systems and immature gastrointestinal tract. The gut microbiota plays a pivotal role in neonatal health, yet its establishment is influenced by multiple factors, including prematurity, antibiotic exposure, and feeding modalities. This study aimed to examine the interactions among gut bacteriophages, bacterial communities, and clinical variables in preterm infants to identify potential microbial biomarkers associated with health outcomes.

METHODS: We employed metagenomic shotgun sequencing and co-occurrence network analysis to characterize the virome and bacterial communities in 12 preterm neonates at 14 and 28 days post-birth. This approach enabled the identification of dynamic microbial colonization patterns and key bacterial species and bacteriophages associated with clinical parameters.

RESULTS: Staphylococcus epidermidis exhibited a significant decline over time, whereas Enterococcus faecalis and its associated bacteriophages showed progressive enrichment, becoming predominant by day 28. In contrast, the relative abundances of Clostridioides difficile and Klebsiella pneumoniae remained statistically stable between the two time points (14 vs. 28 days).

DISCUSSION: These findings suggest that microbial changes during the first month of life may reflect a combination of host developmental processes and external influences, such as antibiotic exposure or delivery mode. The observed microbial signatures provide preliminary insights into early gut microbiota and virome development in preterm infants. However, their functional relevance and long-term stability require confirmation in larger, well-powered longitudinal studies with denser temporal sampling. The enrichment of Enterococcus faecalis may indicate its opportunistic colonization potential in the preterm gut and warrants further investigation regarding its role in gut homeostasis and immune system maturation.}, } @article {pmid41878461, year = {2026}, author = {Li, Z and Zhang, Y and Xu, D and Huang, B}, title = {Diagnostic and therapeutic journey of infantile endobronchial tuberculosis: a case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1778717}, pmid = {41878461}, issn = {2296-2360}, abstract = {BACKGROUND: Endobronchial tuberculosis (EBTB) in infants is rare and is often overlooked because of nonspecific clinical manifestations. Coexisting primary immunodeficiency and opportunistic infections further increased diagnostic and therapeutic complexity.

CASE PRESENTATION: We reported a male infant aged 40 days who presented with fever and mild cough. Chest imaging showed progressive bilateral nodular and granulomatous lesions despite broad-spectrum antibacterial therapy. Microbiological evaluation revealed positive T-SPOT.TB and GeneXpert MTB/RIF results from bronchoalveolar lavage fluid (BALF), while metagenomic next-generation sequencing identified Pneumocystis jirovecii. Genetic testing demonstrated a heterozygous IKZF1 mutation, consistent with underlying immunodeficiency. Serial bronchoscopies confirmed necrotizing endobronchial tuberculosis with airway stenosis. The patient received standard anti-tuberculosis therapy, systemic corticosteroids, trimethoprim-sulfamethoxazole, intravenous immunoglobulin, and repeated bronchoscopic intraluminal drug delivery. Clinical and radiological remission was achieved, with no airway sequelae during 18-month follow-up.

CONCLUSIONS: This case highlighted the unique coexistence of infantile EBTB, IKZF1-related immunodeficiency, and P. jirovecii coinfection. Early bronchoscopy played a pivotal diagnostic and therapeutic role. Repeated intraluminal bronchoscopic therapy combined with systemic treatment might prevent irreversible airway damage in severe pediatric EBTB.}, } @article {pmid41878469, year = {2026}, author = {de Azevedo, PS and Vedovatto, MM and de Freitas, PCG and Luz, RBS and Streit, RSA and Persinoti, GF}, title = {parsomics: a data-driven framework for metagenomics data integration powered by a local relational database.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag049}, pmid = {41878469}, issn = {2635-0041}, abstract = {MOTIVATION: Metagenomics enables the analysis of complex microbial communities directly from environmental samples, resulting in massive datasets that are processed using multiple tools and workflows. Data integration is key for metagenomics research, however, challenges in data organization and management locally remain open in existing workflows.

RESULTS: We present parsomics, a lightweight and extensible data management tool designed for efficient local storage, organization, and integration of metagenomic analysis results. Built upon PostgreSQL and implemented in Python, parsomics leverages a user-defined configuration file to automatically construct a relational database tailored to metagenomics-based data. It is user-friendly, easy to deploy, and implements modular plugin-based extensions to support diverse data types and outputs. parsomics can be installed in every major GNU/Linux environment and currently focuses on prokaryotic metagenomics analysis.

parsomics is an open-source project and its source code is available at https://gitlab.com/parsomics under the GPLv3 license. Comprehensive documentation can be found at https://parsomics.org and https://api.parsomics.org.}, } @article {pmid41878742, year = {2026}, author = {Armijo-Godoy, G and Cottet, L and Rupayan, A and Carrasco, M and Levicoy, D and Salvo-Garrido, H}, title = {Functional and ecological characterization of Labrys methylaminiphilus subsp. lupini subsp. nov., associated with Lupinus luteus nodules in acidic soils of southern Chile.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1759558}, pmid = {41878742}, issn = {1664-302X}, abstract = {BACKGROUND: Members of the genus Labrys are widely distributed in soil and plant-associated environments, yet their ecological roles and functional contributions within plant-associated microbiomes remain poorly understood. Labrys methylaminiphilus strain La1 was isolated from nodules of Lupinus luteus growing in acidic soils of southern Chile, providing an opportunity to investigate strain-level traits relevant to plant-microbe interactions under environmental stress.

METHODS: Strain La1 was characterized using physiological and biochemical, chemotaxonomic, and genomic approaches, including whole-genome sequencing and comparative genomics. Functional traits related to plant interaction were assessed through in vitro assays for indole-3-acetic acid (IAA) production, antifungal activity against lupine pathogens, and in planta experiments evaluating plant growth under salinity and osmotic stress. The ecological distribution of closely related taxa was inferred from screening of publicly available environmental microbiomes using protologger pipeline.

RESULTS: Although strain La1 showed high genomic similarity to L. methylaminiphilus JLW10[T], it exhibited distinct phenotypic, metabolic, and ecological features. These included tolerance to acidic and moderately saline conditions, utilization of rhizosphere-associated carbon sources, and a fatty acid profile consistent with adaptation to terrestrial environments. Genomic analyses revealed genes related to stress tolerance, exopolysaccharide biosynthesis, carbohydrate-active enzymes, siderophore production, IAA synthesis, and non-ribosomal peptide synthetases. Consistent with these traits, La1 inhibited the growth of Colletotrichum lupini and Pleiochaeta setosa and significantly enhanced L. luteus biomass under osmotic and salinity stress. Metagenomic screening indicated that sequences closely related to La1 are predominantly associated with soil, rhizosphere, and plant-associated habitats.

CONCLUSION: This study demonstrates that strain La1 represents a functionally versatile and ecologically specialized lineage within L. methylaminiphilus, contributing traits relevant to plant-associated microbiomes in acidic soils. This integrated functional and ecological evidence supports the designation of Labrys methylaminiphilus subsp. lupini subsp. nov. and highlights the relevance of strain-level analyses for understanding plant-microbe interactions.}, } @article {pmid41878750, year = {2026}, author = {Du, Z and Li, L and Liu, J and Wang, H and Li, J and Xu, Y and Cui, L and Yin, J}, title = {Wheat-Dependent Exercise-Induced Anaphylaxis Patients on a Wheat-Free Diet Exhibit a Gut Microbiota Composition More Similar to Healthy Individuals.}, journal = {Journal of asthma and allergy}, volume = {19}, number = {}, pages = {464532}, pmid = {41878750}, issn = {1178-6965}, abstract = {PURPOSE: There are limited studies on the intestinal microbiome in patients with wheat-dependent exercise-induced anaphylaxis (WDEIA), and changes in the gut microbiome in WDEIA patients after wheat-free diet have not been studied.

METHODS: This is a cross-sectional analysis. Fecal samples and clinical data were collected from 26 non-wheat-free patients with WDEIA, 11 wheat-free patients with WDEIA, and 24 healthy controls (HCs). The gut microbiota was evaluated through metagenomic sequencing.

RESULTS: The sequencing revealed differences in the gut microbiome between patients with WDEIA on a non-wheat-free diet and HCs; more specifically, the non-wheat-free group exhibited a downregulation of two families (Rikenellaceae and Odoribacteraceae), three genera (Alistipes, Odoribacter, and Catenibacterium), and four species (Bacteroides_stercoris, Alistipes_putredinis, Bacteroides_intestinalis, and Bacteroides_cellulosilyticus). A wheat-free diet is associated with intestinal flora more similar to the structure of healthy individuals. The species Bacteroides_stercoris was negatively correlated with T-IgE, and the genus Catenibacterium was negatively correlated with T-IgE, as well as wheat, gluten, or gliadin-specific IgE. The genus Catenibacterium was positively correlated with the healthy control-enriched "Apoptosis (ko04210)" pathway and negatively correlated with the non-wheat-free WDEIA group-enriched "Thyroid hormone signaling pathway (ko04919)" pathway.

CONCLUSION: Patients with WDEIA exhibit a specific gut microbiota signature and function, which demonstrated the potential association between the gut microbiome and WDEIA development. WDEIA patients on a wheat-free diet exhibit a gut microbiome composition more similar to healthy individuals.}, } @article {pmid41878990, year = {2026}, author = {Sun, Y and Li, Y and Temur, B and Lin, Y and Liu, Y and Yi, L and Sun, Z and Zhang, G and Li, J and Guo, Y and Li, L and Cai, J and Tian, W and Meng, G and Jiang, L and Fang, M and Ding, F and Zhou, X and Tu, C and He, B}, title = {Diversity Patterns of Domestic Herbivore Viruses in China Reveal Transmission Dynamics with Disease Management Implications.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {32}, pages = {e17444}, pmid = {41878990}, issn = {2198-3844}, support = {32130104//National Natural Science Foundation of China/ ; 2025-NK-112//Qinghai Science and Technology Achievement Transformation Special Project/ ; }, mesh = {Animals ; China/epidemiology ; *Herbivory ; Humans ; *Animals, Domestic/virology ; *Virome/genetics ; *Viruses/genetics/classification ; }, abstract = {Domestic herbivores have complex interactions with humans and wildlife, playing important roles in zoonotic and epizootic disease emergence and transmission. Yet their viral diversity and cross-species transmission dynamics remain understudied. Through pan-viromic profiling of 10,225 swabs and 4,304 serum samples from 5,710 adult individuals across China's five major herbivore-rearing provinces, we prepare the domestic herbivore viromic catalog of China (DhCN-Virome) comprising 1,085,360 viral metagenomes, nearly capturing their family-level viral diversity while expanding by 2.3-fold global subgenus-level viral diversity. Distinct viromic signatures emerge across herbivore species and sample types. Viral communities generally follow a "higher openness, greater stability" pattern, with animals raised in confined settings being more susceptible to external influences. Viral circulations, particularly involving viruses of health concern, occur primarily within herbivore species but also extensively between herbivores and other species, including potential human-herbivore and avian-horse viral transmission. Bacteriophages constitute the most abundant viral entities, characterized by lytic replication strategies with some targeting pathogenic bacterial hosts. These findings expand our knowledge of herbivore viral diversity patterns and ecological transmission dynamics, underscoring the need for unified disease management strategies across all herbivore species. Particularly, the risk viruses represent potential triggers for future outbreaks, necessitating urgent epidemiological surveillance and vaccination programs.}, } @article {pmid41879294, year = {2026}, author = {Liu, Y and Zhao, X and Gao, J and Xu, K}, title = {Therapeutic evolution and outcomes in EGPA complicated by diffuse alveolar haemorrhage: Case-based review.}, journal = {Modern rheumatology case reports}, volume = {10}, number = {1}, pages = {}, doi = {10.1093/mrcr/rxag028}, pmid = {41879294}, issn = {2472-5625}, mesh = {Humans ; Female ; Middle Aged ; *Hemorrhage/etiology/drug therapy/diagnosis ; *Pulmonary Alveoli/pathology ; Treatment Outcome ; *Lung Diseases/etiology/drug therapy ; *Churg-Strauss Syndrome/complications/drug therapy/diagnosis ; Rituximab/therapeutic use ; }, abstract = {Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare, systemic vasculitis characterised by asthma, eosinophilia, and multi-organ involvement. Diffuse alveolar haemorrhage (DAH) is an uncommon, but life-threatening pulmonary complication in EGPA. We report on a 49-year-old, previously healthy woman who presented initially with asthma-like symptoms and later developed a fever, haemoptysis, cutaneous purpura, and periorbital oedema. Laboratory evaluation revealed marked eosinophilia, anaemia, elevated inflammatory markers, and a strongly positive MPO-ANCA. Bronchoalveolar lavage fluid was haemorrhagic and contained hemosiderin-laden macrophages, indicating DAH. Broad-spectrum antibiotics were empirically initiated but discontinued after metagenomic next-generation sequencing (mNGS) of the bronchoalveolar lavage fluid excluded infection. A bone marrow biopsy showed eosinophilic hyperplasia without clonal mutations. A diagnosis of MPO-ANCA positive EGPA with DAH was established. The patient received pulse methylprednisolone, prednisone, intravenous immunoglobulin, mepolizumab, and rituximab. Clinical symptoms improved rapidly, and radiological signs of alveolar haemorrhage had nearly resolved within days. Our case illustrates that the integration of rituximab and mepolizumab with corticosteroids can achieve rapid remission and steroid sparing in EGPA-DAH. While evidence remains limited to case reports and small series, targeted biologics may fundamentally improve outcomes in this high-risk subset. Prospective studies are warranted to define optimal treatment strategies.}, } @article {pmid41879323, year = {2026}, author = {Mortensen, GA and Schmidt, H and Radivojac, P and Ye, Y and Haas, DM}, title = {Metagenomic profiling and predictive modeling of the gut microbiome reveal signatures of gestational disease.}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0315525}, pmid = {41879323}, issn = {2165-0497}, abstract = {The gut microbiome plays a vital role in maternal health and pregnancy outcomes, yet its impact on conditions like gestational hypertension (GH) and gestational diabetes mellitus (GDM) remains poorly understood. This study explores how the gut microbiome differs between pregnant women with these conditions and healthy controls, using metagenomic sequencing to analyze microbial composition and function. Our findings reveal that women with GH and GDM exhibit greater microbiome variability and distinct shifts in bacterial communities compared to healthy pregnancies. Key beneficial bacteria, such as Bacteroides fragilis and Roseburia intestinalis, were reduced in cases, suggesting potential disruptions in gut-related metabolic and immune functions. In addition to multiple differentially abundant species of Sphingobacterium in cases versus controls, functional analysis indicated changes in carbohydrate and lipid metabolism, reinforcing the microbiome's connection to metabolic health. Furthermore, machine learning models demonstrated promising results in predicting disease status based on microbiome data, underscoring the potential for gut bacteria as potential predictive biomarkers for pregnancy-related conditions. These insights highlight the gut microbiome's role in pregnancy health and suggest it may be a promising target for future interventions aimed at reducing complications and improving maternal-fetal outcomes.IMPORTANCEGut microbial dysbiosis has been implicated in pregnancy complications, yet most studies rely on 16S rRNA sequencing, which limits resolution and functional insight. Here, using shotgun metagenomic sequencing and machine learning, we identified robust microbial taxonomic and functional signatures that distinguish gestational hypertension and gestational diabetes from healthy pregnancies. A combined feature set enabled accurate classification of disease status, with overlapping features between statistical and predictive frameworks underscoring biological relevance. Altogether, our study defines high-resolution microbiome signatures with translational potential as predictive biomarkers for maternal health, while also providing an open, reproducible analysis pipeline to support future investigations.}, } @article {pmid41879886, year = {2026}, author = {Chen, W and Li, X and Zhao, X and Zuo, Z and Wang, D and Zhao, F}, title = {GMW: a hybrid graph-based approach for post-assembly metagenome analysis and decontamination.}, journal = {Science China. Life sciences}, volume = {69}, number = {6}, pages = {1910-1917}, pmid = {41879886}, issn = {1869-1889}, mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Algorithms ; Genome, Viral/genetics ; Influenza A virus/genetics ; *Computational Biology/methods ; *Software ; Decontamination/methods ; }, abstract = {Accurate genome assembly from metagenomic sequencing data remains challenging, particularly in mixed infections involving multiple pathogens, due to data complexity and contaminant sequences. Here, we present GMW (Genomic Microbe-Wise), a novel computational tool that improves pathogen genome assembly accuracy and enhances contaminant removal capabilities by simplifying the post-assembly graph. GMW leverages community detection algorithms, sequence similarity analysis, and coverage patterns to resolve strain mixtures and improve assembly accuracy. Using datasets of influenza A virus subtypes, we demonstrate GMW's ability to disentangle mixed infections and reconstruct complete viral genomes with high precision. Additionally, GMW outperforms traditional sequence similarity methods in classifying target contigs from contaminants. This tool also provides interactive visualization modules to streamline the inspection of assembly outputs, including simplified representations of complex assembly graphs. By enhancing assembly quality and contamination filtering, GMW emerges as a versatile solution for applications in clinical diagnostics, microbial ecology, and pathogen surveillance.}, } @article {pmid41880538, year = {2026}, author = {Consuegra-Asprilla, JM and Cuesta-Astroz, Y and González, Á}, title = {Characterization of the vaginal microbiome and its metabolic potential in Colombian patients with recurrent vulvovaginal candidiasis.}, journal = {Medical mycology}, volume = {64}, number = {4}, pages = {}, pmid = {41880538}, issn = {1460-2709}, support = {2019-2020//Programmatic Health Sciences Call/ ; //Universidad de Antioquia/ ; }, mesh = {Humans ; Female ; *Candidiasis, Vulvovaginal/microbiology ; *Vagina/microbiology ; Adult ; *Microbiota ; Middle Aged ; Colombia ; Young Adult ; Recurrence ; Lactobacillus/isolation & purification ; Dysbiosis/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Prevotella ; }, abstract = {Recurrent vulvovaginal candidiasis (RVVC) is a multifactorial condition in which vaginal microbiota dysbiosis plays a key role. This study aimed to characterize the vaginal microbiome of patients with RVVC using metagenomic sequencing. Vaginal scraping samples were collected from 34 women aged 20-47 years and classified into three groups: (1) 14 women with RVVC who had experienced 3-7 episodes of VVC in the previous year; (2) 9 women with severe RVVC, defined as ≥8 episodes in the last year; and (3) 11 healthy women as controls. The results revealed an increased relative abundance of bacteria associated with bacterial vaginosis-including Gardnerella vaginalis, G. swidsinskii, and Prevotella bivia-as well as higher levels of Lactobacillus iners in both RVVC groups. In contrast, healthy women showed a greater abundance of L. crispatus and L. gasseri. Diversity analyses indicated lower α-diversity in the healthy group compared to RVVC patients. Metabolic potential profiling showed a differential increase in sequences related to the phosphotransferase system, fructose/mannose metabolism, pentose phosphate pathway, and cysteine/methionine and purine metabolism in RVVC groups relative to controls; no significant differences were observed between RVVC groups, indicating that microbial profiles alone do not correlate with the degree of disease severity. These findings provide relevant insights into the taxonomic and functional characteristics of the vaginal microbiome in women with RVVC and may support the development of targeted therapeutic strategies.}, } @article {pmid41880703, year = {2026}, author = {Liang, H and Liu, J and Huang, Y and Wang, Z and Wang, J and Liu, H and Zhang, L and Peng, Y}, title = {Engineering the anammox pathway in a full-scale AOA process for industrial wastewater treatment.}, journal = {Water research}, volume = {298}, number = {}, pages = {125793}, doi = {10.1016/j.watres.2026.125793}, pmid = {41880703}, issn = {1879-2448}, mesh = {*Waste Disposal, Fluid/methods ; *Wastewater/microbiology/chemistry ; Nitrogen/metabolism ; Bioreactors/microbiology ; Bacteria/metabolism/genetics ; Ammonia/metabolism ; *Industrial Waste/analysis ; Aerobiosis ; Anaerobiosis ; Oxygen ; Denitrification ; Oxidation-Reduction ; Biofilms ; *Water Purification/methods ; }, abstract = {The anammox process holds significant potential for municipal wastewater treatment, yet its full-scale application in industrial wastewater treatment plants (IWTP), particularly within endogenous denitrification-based processes, remains challenging. This study demonstrates the successful establishment of the anammox pathway in a full-scale (16,000 m[3]/d) anaerobic-aerobic-anoxic (AOA) process IWTP by implementing a synergistic control strategy that integrates low dissolved oxygen (DO: 0.5 - 1.4 mg/L) with residual ammonia (1.6 - 2.9 mg/L) at the aerobic outlet. During 450 days of operation, the system achieved stable and advanced nitrogen removal, with effluent NH4[+]-N and total nitrogen (TN) averaging only 0.2 mg/L and 5.7 mg/L, respectively. Metagenomic and isotope tracing analyses identified that the anoxic zone biofilm as a functional hotspot for anammox, where the relative abundance of anammox bacteria (AnAOB), predominantly Candidatus Brocadia, was significantly enriched to 0.074%. This community contributed to 36.7% of the TN removal via dual pathways coupling anammox with endogenous and exogenous partial denitrification. Economically, the incorporation of anammox reduced aerobic zone aeration energy consumption by 18.2% and decreased external carbon dosage by 44.4%. This work provides a pioneering demonstration of anammox under complex water quality conditions and offers a viable technological route toward low-carbon wastewater treatment.}, } @article {pmid41881056, year = {2026}, author = {Chetruengchai, W and Sriwattanapong, K and Manaspon, C and Fakhruddin, KS and Samaranayake, L and Shotelersuk, V and Porntaveetus, T}, title = {Metagenome and Metabolic Pathways in Plaque Biofilms of Thai ELANE-Associated Neutropenic Patients: An Original Study and Scoping Review.}, journal = {European journal of dentistry}, volume = {}, number = {}, pages = {}, doi = {10.1055/s-0046-1818559}, pmid = {41881056}, issn = {1305-7456}, abstract = {OBJECTIVE: Congenital neutropenia, particularly ELANE-associated forms, is associated with recurrent oral infections and aggressive periodontitis. While ELANE deficiency compromises oral health, its relationship to plaque biofilm ecology and metabolic function remains unclear. The oral microbiome-metabolome interplay in this condition remains largely uncharacterized globally. Here, we address this gap by characterizing the dental plaque metagenome and inferred metabolic pathways in a defined cohort of Thai neutropenia patients.

MATERIALS AND METHODS: In this exploratory study, we sequenced dental plaque samples from a defined cohort of nine individuals: three patients with severe congenital neutropenia or cyclic neutropenia (CyN) with confirmed ELANE variants, and six from age- and gender-matched healthy controls. Shotgun metagenomics was used for genomic analysis, followed by comprehensive microbiota examination. Subsequently, MetaCyc, a curated database, was used for in silico analysis and comparisons of the predicted functional pathways between the test and control plaque biofilms.

RESULTS: The principal coordinate analysis plot and heat map revealed distinct segregation of microbial profiles between the patients and control groups. A significant variation in the proportions of the five core phyla was noted in patients and controls. Two commensal species, Aggregatibacter sp oral taxon 458 and Leptotrichia sp oral taxon 212, were enriched in the controls. Conversely, four species were significantly enriched in the patients, Selenomonas flueggei, Streptococcus milleri, Kingella oralis, and Actinobaculum sp oral taxon 183; the latter being notably elevated across all patients. The MetaCyc in silico analyses suggested predicted enrichment of functional pathways associated with inflammation and oxidative stress in patients, including L-methionine biosynthesis IV, formaldehyde assimilation III, L-rhamnose degradation, and the superpathway of (R,R)-butanediol biosynthesis pathways.

CONCLUSION: Our study advances the understanding of ELANE-associated periodontitis by moving beyond descriptive microbiota analysis to suggest potential associations between host immune deficiency, microbial dysbiosis, and the microbiota-associated metabolic pathway alterations. These findings provide preliminary insights into targeted periodontal care in neutropenic patients, though further validation in larger cohorts is required.}, } @article {pmid41881128, year = {2026}, author = {Song, Z and Yang, J and Zhang, L and Peng, Y}, title = {Photocatalytic Fe3O4@CDs Drives Nitrite-Independent extracellular respiration of anammox via efficient bidirectional electron transfer.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134489}, doi = {10.1016/j.biortech.2026.134489}, pmid = {41881128}, issn = {1873-2976}, mesh = {Electron Transport ; *Nitrites/metabolism ; *Sulfides/chemistry ; *Cadmium Compounds/chemistry ; Catalysis ; Oxidation-Reduction ; Bacteria/metabolism ; Nitrogen/isolation & purification/metabolism ; *Ammonium Compounds/metabolism ; *Anaerobic Ammonia Oxidation ; *Extracellular Space/metabolism/drug effects ; Photochemical Processes ; }, abstract = {Anaerobic ammonium oxidation (Anammox) process relying on extracellular electron transfer (EET) overcomes nitrite scarcity in practical wastewater, but inefficient EET rate constrains nitrogen removal. Herein, Fe3O4 with carbon dot shell (Fe3O4@CDs) was self-assembled with anammox bacterial as a photocatalytic hybrid. Building on bacteria inward uptake of photogenerated electrons from CDs and outward transfer of respiratory electrons to Fe3O4, a bidirectional electron pathway was established firstly. This novel route achieved efficient nitrite-independent Anammox, enabling direct and rapid removal of 80 mg/L NH4[+]-N. To elucidate efficient nitrogen removal essence, metagenomics was employed to reveal photogenerated electrons fate and their mediated nitrogen metabolism mechanism. Results showed that, following assembly via -PO bonds, bacteria internalized CDs photogenerated electrons (0.82 µA/cm) into menaquinone (MQ) pool. This influx activated energy-generation route constructed by bc1 and Rnf enzymes, increasing intracellular ATP level by 3.36---6.51-fold. Consequently, energy drove electrons pumping from MQ pool to cytochrome c, followed by transport outward via CDs, pili and flavin, amplifying electrons eflux by 1.77-fold. Such efflux generated MQ pool electron vacancies, which were efficiently replenished by electrons from hydrazine synthase- and hydrazine dehydrogenase-catalyzed NH4[+]-N oxidation to N2 without nitrite. Underpinned by the photogenerated electron-driven EET process, Anammox bacteria was enriched from 25.26% to 48.02%, thus sustaining a total nitrogen removal efficiency of > 97% for over 80 days-far exceeding the performance of existing system. This technology provides an efficient and sustainable theoretical framework for the application of anammox in practical wastewater treatment.}, } @article {pmid41881328, year = {2026}, author = {Zhang, N and Wang, J and Yang, S and Liu, F}, title = {Biogeochemical and genomic drivers of groundwater DNRA: predictability of ammonium accumulation risk.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {397}, number = {}, pages = {128006}, doi = {10.1016/j.envpol.2026.128006}, pmid = {41881328}, issn = {1873-6424}, mesh = {*Groundwater/chemistry/microbiology ; *Water Pollutants, Chemical/analysis ; *Ammonium Compounds/analysis/metabolism ; Nitrates/metabolism ; Denitrification ; Nitrogen ; }, abstract = {Widespread ammonium (NH4[+]-N) contamination in groundwater, with local concentrations exceeding 20 mg/L, challenges traditional nitrogen removal, which is dominated by denitrification. Dissimilatory nitrate reduction to ammonium (DNRA), a nitrogen-retaining pathway, competes with denitrification. However, the environmental conditions that promote DNRA in aquifers and its quantitative contribution to NH4[+]-N loading remain critical knowledge gaps in groundwater nitrogen cycling research. We investigated how C/N ratios, Fe[2+] concentrations, initial NO3[-]-N, hydrochemical types, total dissolved solids (TDS), and pH influenced DNRA efficiency and its competition with denitrification. We found that DNRA efficiency peaked in organic-rich aquifers (15.70-26.69%) and was minimum in industrially and agriculturally contaminated groundwater (0.71%). High Fe[2][+], high initial NO3[-]-N, and HCO3[-]-type environments markedly promoted DNRA, whereas Cl[-]-type water inhibited it. Competition analysis revealed that elevated C/N ratios, Fe[2+], and TDS increased the relative contribution of DNRA to nitrate reduction. Metagenomic analysis further demonstrated that high C/N ratios and Fe[2+]-rich conditions promoted DNRA dominance via selective enrichment of Enterobacteriaceae carrying the abundant nrfA gene. Conversely, high mineralization and Na-Cl water types drastically reduced DNRA efficiency by suppressing the expression of key functional genes. Furthermore, under intermittent nitrate input, NH4[+]-N accumulated even with low DNRA efficiency, posing long-term water quality risks. We developed a DNRA efficiency prediction model using the Extreme Gradient Boosting algorithm (R[2] = 0.92), thereby enabling accurate assessment across diverse groundwater conditions. This work advances mechanistic understanding and provides an innovative predictive methodology for assessing DNRA-driven NH4[+]-N enrichment risks in groundwater.}, } @article {pmid41881444, year = {2026}, author = {Kringeland, GD and Tangedal, S and Julian, D and Paytuví-Gallart, A and Sanseverino, W and Bertelsen, RJ and Husebø, GR and Knudsen, KS and Lehmann, S and Nielsen, R and Eagan, TML}, title = {Antimicrobial resistance genes and antibiotic use in chronic lung disease: a bronchoscopy study of the lower airways microbiome.}, journal = {BMJ open respiratory research}, volume = {13}, number = {1}, pages = {}, pmid = {41881444}, issn = {2052-4439}, mesh = {Humans ; Female ; Male ; *Microbiota/genetics ; Cross-Sectional Studies ; Bronchoscopy ; *Anti-Bacterial Agents/therapeutic use ; Aged ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy ; Case-Control Studies ; *Drug Resistance, Microbial/genetics ; *Lung Diseases/microbiology/drug therapy ; Idiopathic Pulmonary Fibrosis/microbiology ; Asthma/microbiology ; }, abstract = {BACKGROUND: Antimicrobial resistance genes (ARGs) in the respiratory microbiome are poorly characterised. We compared the presence of ARGs in healthy controls with patients with chronic lung disease in a cross-sectional study, adjusted for time since antibiotic use.

METHODS: Bronchoalveolar lavage was collected from 100 controls, and 93 patients with chronic obstructive pulmonary disease (COPD), 13 with asthma, 34 with sarcoidosis, 12 with idiopathic pulmonary fibrosis (IPF) and 11 patients with unclassifiable interstitial lung disease (uILD). Participants had not used antibiotics 14 days prior to sampling. Shotgun metagenomic sequencing was performed with Illumina NovaSeq. ARGs were identified using the National Database of Antibiotic-Resistant Organisms. Sample reads were normalised to counts per million.

RESULTS: In total, 38% of controls had at least one ARG, compared with 51%, 39%, 65% and 83% of patients with COPD, asthma, sarcoidosis and IPF, respectively (p=0.01). ARGs against tetracycline (33%) were the most common ARG class, followed by beta-lactam and macrolide resistance (both 26%). In a logistic regression analysis adjusted for sex, age, body composition, smoking and antibiotic use, the OR (95% CI) for having ARGs in the lower airways was 1.30 (0.70 to 2.41) in COPD, 1.00 (0.29 to 3.52) in asthma, 3.52 (1.40 to 8.83) in sarcoidosis, 6.40 (1.25 to 32.73) in IPF and 3.27 (0.76 to 14.16) in uILD compared with controls. Overall mean (SD) ARG counts per million were 403.8 (537.7) in the 35 subjects who had used antibiotics ≤3 months before bronchoscopy, compared with 197.6 (355.9) in the 228 subjects without (p=0.02).

CONCLUSION: The presence of ARGs in the lower airways microbiome was significantly higher in patients with sarcoidosis and IPF than in controls. The counts per million for ARGs were significantly associated with recent antibiotic use.}, } @article {pmid41881804, year = {2026}, author = {Gutiérrez, J and Vergara-Amado, J and Martorell, C and Navedo, JG and Wille, M and Guajardo-Leiva, S and Castro-Nallar, E and Verdugo, C}, title = {Functional Shifts in the Gut DNA Virome in a Long-Distance Migratory Shorebird During the Pre-Migratory Fattening.}, journal = {Molecular ecology}, volume = {35}, number = {6}, pages = {e70315}, doi = {10.1111/mec.70315}, pmid = {41881804}, issn = {1365-294X}, support = {FONDECYT N°1191769//Agencia Nacional de Investigación y Desarrollo/ ; ANILLO ATE220062//Agencia Nacional de Investigación y Desarrollo/ ; Doctoral scholarship N°21201700//Agencia Nacional de Investigación y Desarrollo/ ; //The Pathogen Watchtower Program (Biotia Inc. & The Rockefeller Foundation)/ ; //Universidad Austral de Chile/ ; }, mesh = {Animals ; *Virome/genetics ; Feces/virology ; *Animal Migration ; *Charadriiformes/virology ; *Gastrointestinal Microbiome/genetics ; Sequence Analysis, DNA ; Bacteriophages/genetics ; DNA, Viral/genetics ; Metagenomics ; }, abstract = {Migration represents one of the most energetically demanding phases in the life cycle of long-distance migratory birds. Pre-migratory fattening is a critical preparatory stage characterized by hyperphagia, rapid fat accumulation, organ remodelling, and immune modulation. Although the gut microbiome has been recognized as a key contributor to these physiological adaptations, the role of the gut virome remains poorly understood. In this study, the diversity, functional potential, and temporal dynamics of the gut DNA virome in a trans-hemispheric migratory shorebird, the Hudsonian godwit (Limosa haemastica), were assessed during pre-migratory fattening. Adult individuals were maintained under controlled aviary conditions for 15 weeks during the preparation for northbound migration, and faecal samples were collected at two distinct physiological time points: at the beginning and the end of pre-migratory fattening. Shotgun metagenomic sequencing revealed 798 high-quality viral operational taxonomic units (vOTUs), the majority of which were bacteriophages (92%). Potential functional annotation identified auxiliary metabolic genes (AMGs) associated with nucleotide metabolism, redox balance, and host adaptation. Although overall gut virome diversity did not differ between stages, significant changes in potential functional profiles of phages were observed, especially during the final stage of fattening when energy demands are at their highest. In addition to bacteriophages, we report two divergent adenoviruses potentially associated with the Siadenovirus and Aviadenovirus genera. These findings suggest that dynamic viral communities may play underrecognized roles in supporting host physiology during energetically costly life stages.}, } @article {pmid41881873, year = {2026}, author = {Zhao, C and Yao, R and Xiong, M and Liu, X and Yu, J and Jumpponen, A and Romantschuk, M and Ur Rahman, S and Hui, N}, title = {Microbial exposure and antibiotic resistance gene dynamics shift between indoor and outdoor school activities.}, journal = {Ecotoxicology and environmental safety}, volume = {314}, number = {}, pages = {120044}, doi = {10.1016/j.ecoenv.2026.120044}, pmid = {41881873}, issn = {1090-2414}, mesh = {Humans ; *Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; *Schools ; China ; *Genes, Bacterial ; Nasal Cavity/microbiology ; Hand/microbiology ; Bacteria/genetics ; }, abstract = {School curricular and extracurricular activities, including indoor study and sports like basketball, significantly impact adolescent physical and mental health. However, their effects on hand and nasal microbiomes, particularly regarding antibiotic resistance genes (ARGs), are underexplored. Here, we recruited 42 junior middle school students in Shanghai to investigate microbial composition and ARGs, collecting 336 hand and nasal samples after handwashing, indoor study, indoor basketball, and outdoor basketball. Our results showed that playing basketball either indoors or outdoors increased microbial diversity in nasal cavities and on hands, compared to post-handwashing. Notably, nasal microbiomes were predominantly derived from hand microbiomes, regardless of the activity performed. Among ARGs, macB genes were more abundant after outdoor basketball than indoor basketball, with this difference more pronounced in nasal cavities than on hands. Metagenomic sequencing identified Aureimonas phyllosphaerae as the primary macB gene host. Although this bacterium harbors ARGs, it is non-pathogenic and lacks mobile genetic elements, indicating a low potential for horizontal gene transfer or interspecies ARG transmission. Collectively, even though students may be exposed to more ARGs during outdoor activities, the health risks are likely minimal because the observed ARG bacteria are non-pathogenic and the likelihood of interspecies ARG transmission is low.}, } @article {pmid41881888, year = {2026}, author = {Tuveng, TR and Hagen, LH and Rese, M and Eijsink, VGH and Arntzen, MØ}, title = {Meta-omics profiling of denitrifying bacterial communities with lignin as carbon source.}, journal = {Microbiological research}, volume = {308}, number = {}, pages = {128503}, doi = {10.1016/j.micres.2026.128503}, pmid = {41881888}, issn = {1618-0623}, mesh = {*Lignin/metabolism ; *Denitrification ; *Bacteria/metabolism/genetics/classification/enzymology ; *Carbon/metabolism ; Metagenomics ; Oxidoreductases/metabolism/genetics ; Proteomics ; Metagenome ; Anaerobiosis ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Lignin is the most abundant renewable source of aromatic carbon and its microbial depolymerization and metabolism under aerobic conditions is well studied. However, lignin breakdown in the absence of oxygen remains poorly understood. In this study, we established long-term bacterial enrichment cultures supplied with diverse lignin preparations as the sole carbon source under denitrifying conditions. Denitrification dynamics were followed by monitoring nitrogenous gases. Metagenomics analysis of eight enrichments involving five lignins recovered 62 metagenome-assembled genomes (MAGs), several of which encoded enzymes for both denitrification and anaerobic metabolism of aromatic compounds. Quantitative metaproteomics confirmed expression of such enzymes and additionally showed that several MAGs expressed multiple oxidoreductases and uncharacterised proteins that are potential candidates for involvement in lignin modification. The detection of several oxygen-dependent oxidoreductases despite anaerobic conditions prompts intriguing discussion of potential mechanistic explanations. This systems-level study expands our understanding of bacterial processing of lignin-associated carbon in anaerobic environments and suggests enzymatic targets for further exploration of lignin depolymerization under oxygen-limited conditions.}, } @article {pmid41882035, year = {2026}, author = {Kumar, M and Ansari, WA and Singh, A and Kumar, SC and Zeyad, MT and Chakdar, H and Farooqi, MS and Sharma, A and Srivastava, S and Jha, GK and Srivastava, AK}, title = {Impact of genotype and soil fertility on wheat rhizosphere microbiota under the trans-gangetic plain.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41882035}, issn = {2045-2322}, support = {2020//Centre for Agricultural Bioinformatics/ ; }, mesh = {*Triticum/microbiology/genetics/growth & development ; *Rhizosphere ; *Soil Microbiology ; *Genotype ; *Microbiota/genetics ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; India ; Bacteria/genetics/classification ; Metagenomics ; Phylogeny ; }, abstract = {The effects of genotypes (HD3086 and PBW343) and soil physicochemical properties on the wheat rhizospheric bacterial communities along the trans Indo-Gangetic plains were studied. The trans-Indo-Gangetic Plains of India are one of the areas in the country where wheat is grown the most. Despite the agricultural significance of this region, extensive studies on the rhizosphere microbial abundance and community structure related to wheat cultivation in this area are still lacking. To address this knowledge gap, the present study was undertaken to characterize the rhizosphere microbiome using full-length 16 S rRNA-based metagenomic profiling, implementing universal primers, tailed with PacBio Sequel II barcode sequences, providing new insights into microbial dynamics across this major wheat-producing landscape. Statistical analysis revealed significant differences in both abundance and diversity among the different soil samples and wheat genotypes. Four phyla exhibited significant differences in relative abundance between the genotypes (p < 0.05): Proteobacteria (p = 0.002), Planctomycetes (p = 0.000), Verrucomicrobia (p = 0.000), and Firmicutes (p = 0.030). The number of genera identified in genotype HD3086 across all locations was 421, while it was 322 for genotype PBW343. There were 251 genera found common, with 170 genera exclusively present in HD3086 and 71 in PBW343. Significant differences were observed in the relative abundance of eighteen genera (p < 0.05) between the genotypes; some of them include Luteolibacter, Gemmata, Pseudomonas, Stenotrophobacter, Pseudarthrobacter, Devosia, Lacibacter, Gaiella, Luteimonas, and Nitrosospira. Correlation analysis indicated significant associations between microbial diversity and soil parameters like pH, total and available nitrogen, potassium, phosphorus, iron, and organic carbon for both varieties. Core taxa analysis revealed 27 core taxa across both genotypes. The study highlights significant genotype effects on rhizosphere microbiomes, with implications for soil health and crop management strategies.}, } @article {pmid41882344, year = {2026}, author = {Muammar, A and Retnaningrum, E and Daryono, BS and Prijambada, ID and Yashima, Y and Peterbauer, C}, title = {A fast workflow to explore active enzymes from environmental samples through functional metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {110}, number = {1}, pages = {}, pmid = {41882344}, issn = {1432-0614}, mesh = {*Metagenomics/methods ; Animals ; *Cellulases/genetics/metabolism ; Multiplex Polymerase Chain Reaction ; Feces/microbiology ; Workflow ; Indonesia ; Metagenome ; Gene Library ; Cloning, Molecular ; }, abstract = {Functional metagenomics has emerged as an effective tool for discovering novel enzymes directly from environmental samples, overcoming the limitations of traditional culture-based methods. In this study, we used a functional metagenomic approach on stool samples from Axis kuhlii, an endemic deer species from Indonesia, to identify active cellulases. We created an efficient workflow for expression of metagenomic sequences directly in Komagatella phaffii by combining metagenomic sequencing to investigate enzyme diversity, multiplex PCR to build a genes library, and rolling circle amplification (RCA) to streamline the cloning process, eliminating the need for intermediate Escherichia coli transformation and propagation steps. Furthermore, a semi-high-throughput screening method was used to evaluate multiple samples at once, allowing for the rapid identification of active enzymes. Using this approach, we discovered five endoglucanases and three β-glucosidases with confirmed enzyme activity. This study shows that functional metagenomics can bridge the gap between computational predictions and experimental validation, providing a reliable platform for enzyme discovery and characterization from complex environmental microbiomes. KEY POINTS: • We established K. phaffii expression of metagenomic sequences via multiplex PCR and RCA. • This approach links metagenomic and activity screening to enable enzyme discovery. • Eight active cellulases were obtained from environmental samples through this approach.}, } @article {pmid41882399, year = {2026}, author = {Çilkiz, M}, title = {Microbial Biotechnology in Agriculture.}, journal = {Progress in molecular and subcellular biology}, volume = {62}, number = {}, pages = {251-306}, pmid = {41882399}, issn = {0079-6484}, mesh = {*Agriculture/methods ; *Biotechnology/methods ; Soil Microbiology ; Crops, Agricultural ; }, abstract = {Global food security has become one of the greatest challenges of the twenty-first century due to the rapidly growing world population's food demands and environmental threats such as climate change, soil erosion, and the depletion of freshwater resources. The extensive use of chemical fertilizers and pesticides throughout conventional agriculture has increased productivity significantly, but it has additionally resulted in major ecological and socioeconomic problems, such as soil acidity, groundwater resource pollution, and decreased biodiversity. In this regard, microbial biotechnology is a particularly noteworthy technique that improves agricultural production while promoting environmental sustainability, maintaining ecological balance, and making effective use of resources. This application makes use of microorganisms to enhance soil health and structure, promote plant growth, and minimize both abiotic and biotic stresses. Microbial applications include nitrogen fixation, as well as biofertilizers that reduce the dependency on synthetic materials and biopesticides. Microbial consortia and biostimulants that improve plant physiology by producing phytohormones produce more dependable and durable consequences in the field. Metagenomics and metabolomics are the two types of omic technologies used in these areas of study that provide a thorough description of the variety and roles of microorganisms. Furthermore, the intentional production of microbes targeted at specific organisms has been made practical via synthetic biology and gene editing techniques. In-depth case studies performed in several countries reveal that microbial technologies significantly reduced expenses and improved soil production, advancing the sustainable development goals. Nevertheless, there are several barriers to the widespread use of microbial biotechnology in agriculture. These include unpredictable conditions in the fields, strict regulations, especially related to genetically modified organisms' problems with product quality, and farmers' insufficient understanding. Microbial biotechnology aims to accomplish its full potential as an advancement in technology and as an essential aspect of resource-efficient and environmentally friendly agricultural systems via responsible innovation, adaptable regulations, and worldwide cooperation.}, } @article {pmid41882401, year = {2026}, author = {Erözden, AA and Tavşanlı, N and Çalışkan, M and Arıkan, M}, title = {Microbial Omics.}, journal = {Progress in molecular and subcellular biology}, volume = {62}, number = {}, pages = {333-366}, pmid = {41882401}, issn = {0079-6484}, mesh = {*Metabolomics/methods ; Multiomics ; *Proteomics/methods ; *Genomics/methods ; *Metagenomics/methods ; *Microbiota/genetics ; Computational Biology/methods ; Transcriptome ; }, abstract = {Omics technologies have revolutionized research across diverse fields, and their increasing use in microbiology has provided new opportunities for understanding microbial life. These methods enable detailed investigation of the molecular biology of individual organisms as well as the complex interactions within microbial communities. In this chapter, we describe key single-organism omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, as well as meta-omics techniques such as metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics. We also discuss integrative multi-omics strategies for studying microbial ecosystems. For each omics method, we outline its main features, experimental and bioinformatic workflows, major applications, and commonly used computational tools, thereby providing a practical guide for researchers aiming to explore microbial structure, function and interactions at multiple molecular levels.}, } @article {pmid41882608, year = {2026}, author = {Chen, M and Wu, Z and Du, Y and Jiang, J and Feng, J}, title = {Construction of caries risk assessment scale and oral microecology analysis of adolescents with fixed orthodontic treatment.}, journal = {BMC oral health}, volume = {26}, number = {1}, pages = {}, pmid = {41882608}, issn = {1472-6831}, abstract = {OBJECTIVE: This study aimed to develop and initially validate a caries risk assessment scale for adolescents undergoing fixed orthodontic treatment, and to exploratorily analyze the potential association between oral microbiota and caries risk levels. METHODS: Clinical examinations and questionnaires were conducted on 210 adolescent orthodontic patients before orthodontic treatment and at 1st, 3rd, and 6th month, and the caries risk assessment scale was constructed according to the correlation statistics. Six patients in low-risk group and middle-risk group were randomly selected. Dental plaque samples were collected before orthodontic treatment and 1st month, respectively. Bioinformatics analyses were performed to explore differences in microbial community composition and function. RESULTS: The caries risk assessment scale involves 7 factors, such as simplified debris index (DI-S), brushing time, and frequency of sugar intake. Differences in scale scores before and during orthodontic treatment at the 1st, 3rd, and 6th months correlated with the presence of caries at the corresponding orthodontic stages (P < 0.001). Differences in scores at 1st month correlated with the presence or absence of caries at 3rd and 6th month (P < 0.05). The differences in scores at 3rd month correlated with the caries status at 6th month (P < 0.001). The caries risk related Glycan biosynthesis and metabolism pathways were positively correlated with Prevotella_jejuni, Prevotella_scopos and Candidatus_Nanosynbacter_sp._HMT-352 (P < 0.01). The Carbohydrate Metabolism pathways were positively correlated with Prevotella_melaninogenica, Prevotella_jejuni, Prevotella_scopos and Candidatus_Nanosynbacter_sp._HMT-352 (P < 0.01). CONCLUSIONS: A practical caries risk assessment scale for orthodontic adolescents was established and shows promise for cross-sectional risk stratificationthroughout the orthodontic treatment cycle. Its longitudinal predictive efficacy requires further validation with appropriate statistical models. The microbial findings, particularly the involvement of Candidatus_Nanosynbacter_sp._HMT-352 in relevant metabolic pathways, are preliminary and hypothesis-generating. These results are constrained by the study's limited sample size and the lack of a high-risk comparator group, necessitating confirmation in larger, more comprehensive future studies.}, } @article {pmid41882673, year = {2026}, author = {Deng, J and Qiu, Q and Ye, S and Yu, J and Yao, D and Deng, H and Wang, C and Han, L and Deng, Y and Chen, Y and Liu, Y and Liu, C and Shang, X and Fang, X and Lu, C}, title = {Disentangling environmental and disease-specific signatures in the gut microbiome of psoriasis: discovery of Fimenecus sp. as a novel biomarker and characterization of the gut virome.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41882673}, issn = {1479-5876}, mesh = {Humans ; *Psoriasis/microbiology/virology ; Biomarkers/metabolism ; Case-Control Studies ; *Gastrointestinal Microbiome ; Female ; *Virome ; Male ; *Environment ; Feces/microbiology ; Middle Aged ; Adult ; Bacteria ; }, abstract = {BACKGROUND: The contribution of the gut microbiome to the pathogenesis of psoriasis remains a subject of debate, with inconsistent findings across studies likely confounded by environmental factors. This study aimed to statistically disentangle the effects of a shared household environment from disease-specific microbial signatures in psoriasis. Our objective was to identify novel, multi-kingdom biomarkers, encompassing bacteria and viruses, that hold significant diagnostic and therapeutic potential.

METHODS: We conducted a nested case-control study, performing shotgun metagenomic sequencing on stool samples from 143 participants. The cohort comprised 98 psoriasis patients, 28 healthy cohabiting relatives, and 17 unrelated healthy controls. A comprehensive multi-kingdom analysis of bacteria, viruses, and their associated metabolic pathways was implemented. To ensure the robustness of our findings, a two-stage discovery-validation strategy was employed to identify distinct microbial features associated with psoriasis.

RESULTS: Our analysis revealed that the shared household environment was the predominant factor shaping the overall gut microbiome structure. Despite this strong confounding effect, we successfully identified a novel bacterial species, Fimenecus sp000432435, as a robust biomarker for psoriasis, achieving an area under the curve (AUC) of 0.84. Genomic functional prediction indicated that this species encodes pathways with the potential for B-vitamin and secondary bile acid biosynthesis. Furthermore, characterization of the gut virome identified five disease-associated bacteriophages. Among these, vBin_422 exhibited a significant negative correlation with the abundance of Fimenecus sp000432435, suggesting a potential ecological interaction. Notably, the biotin biosynthesis pathway was negatively correlated with disease severity, whereas specific viral taxa showed a positive correlation with systemic inflammatory markers within the patient cohort.

CONCLUSIONS: Controlling for environmental confounders reveals that psoriasis is associated with sparse but distinctmicrobial signatures rather than broad dysbiosis. Fimenecus sp000432435 is a promising candidate for non-invasive diagnostics, while the characterized virome opens new therapeutic avenues targeting bacteriophage-bacteria interactions in psoriasis management.

TRIAL REGISTRATION: ChiCTR-IOR-17011075. Registered 6 April 2017, http://www.chictr.org.cn/showproj.aspx?proj=17334.}, } @article {pmid41882801, year = {2026}, author = {Langlois, A and Duplessis, M and Ronholm, J and Vincent, AT and Poulin-Laprade, D and Petri, RM}, title = {Impact of differential dietary concentrations of cobalt, manganese and zinc on gastrointestinal microbiome and resistome of lactating dairy cattle.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41882801}, issn = {2524-4671}, abstract = {BACKGROUND: Dietary trace mineral (TM) concentrations for lactating cows often exceed national recommendations under commercial feeding practices. Excess TM supplementation may exert selection pressure on the gut microbiota, promoting metal resistance and potentially co-selecting for important antimicrobial resistance genes (ARGs). This study used a cross-over design to investigate the impact of overfeeding a commericially representative TM premix on the gut microbiome and resistome of lactating dairy cattle. Cows were fed either recommended or surplus TM levels for 31 days followed by sample collection from rumen papillae, whole rumen content, and feces. Targeted amplicon, shotgun metagenomic sequencing, and droplet digital PCR (ddPCR) were used to assess microbial community compositions and the associated resistome. RESULTS: While a surplus TM did not significantly affect the overall microbial diversity, specific taxa differed between the matrices and to a lesser extent by diet. Spirochaetota were more abundant in papillae of cows fed the recommended TM diet, whereas Bacillota were more prevalent in the rumen and feces from cows fed the surplus TM. Phosphorus had the greatest impact on prokaryotic taxa in rumen content. Cows fed surplus levels of TM showed increased abundances of Ruminococcus in their rumen, but decreased Campylobacter, Desulfovibrio, and Treponema adhered to their rumen papillae, Methanosphaera in their rumen and feces, as well as Treponema in their feces. Despite these changes, no significant differences in the presence of key ARGs or metal resistance genes were detected by metagenomics, and ddPCR showed no significant impact of TM supplementation on blaCTX−M, pcoA and zntA gene levels. CONCLUSIONS: Overfeeding TM in a commercial premix resulted in modest matrix specific shifts I the microbial composition without detectable enrichment of selected ARGs or metal resistance genes. These findings suggest short-term resilience of the rumen ecosystem to surplus TM supplementation. Additionally this work provides foundational knowledge to further guide mechanistic and long-term investigations.}, } @article {pmid41883029, year = {2026}, author = {Dip, SA and Mallick, D and Acharjee Shuvo, U and Barua Soumma, S and Rafsani, F and Kumar Paul, B and Ahmed Moumi, N and Ahmed, S and Zhang, L}, title = {Large language model agents for biological intelligence across genomics, proteomics, spatial biology, and biomedicine.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {2}, pages = {}, pmid = {41883029}, issn = {1477-4054}, support = {2125798//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; 2344169//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; 2319522//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; }, mesh = {*Large Language Models ; *Genomics ; *Proteomics ; Humans ; *Computational Biology/methods ; }, abstract = {Large language models (LLMs) are evolving from passive predictors into agentic systems capable of planning, tool-use, and multimodal reasoning. This shift is especially consequential for biology, where complex, noisy, and multi-scale data require adaptive and integrative computational strategies. In this review, we provide the first systematic synthesis of LLM-based agents across genomics, molecular biology, imaging, biomedical analysis, and automated bioinformatics workflows. We analyze >60 emerging systems and organize them within a unifying framework that characterizes agentic traits, such as autonomous decision-making, external tool invocation, memory, and self-correction. Across domains, agentic LLMs show early promise in enabling multi-step analysis, linking heterogeneous evidence, and supporting exploratory scientific tasks. At the same time, our comparative assessment highlights consistent challenges, including unstable reasoning, limited biological grounding, retrieval misalignment, and barriers to reproducibility and biosafety. We conclude by outlining opportunities for trustworthy and collaborative biological agents, including multimodal integration, closed-loop experimental design, and robust evaluation practices. This survey aims to clarify the emerging landscape and chart a path toward reliable agentic systems for biological discovery.}, } @article {pmid41883089, year = {2026}, author = {Duchêne, C and Jaubert, M and Falciatore, A}, title = {Beyond red/far-red sensing: phytochrome perception of the marine light field by microalgae.}, journal = {The New phytologist}, volume = {250}, number = {5}, pages = {2837-2844}, pmid = {41883089}, issn = {1469-8137}, support = {ANR-25-CE20-4776//Agence Nationale de la Recherche/ ; ANR-20-CE20-0024//Agence Nationale de la Recherche/ ; ANR-25-CE20-1717//Agence Nationale de la Recherche/ ; ANR-11-LABX-0011-01//Agence Nationale de la Recherche/ ; 101082304//Fourth Framework Programme/ ; }, mesh = {*Phytochrome/metabolism ; *Microalgae/radiation effects/physiology/metabolism ; *Light ; Red Light ; *Seawater ; }, abstract = {Phytochromes (PHYs) are a major group of photoreceptors, described as red and far-red light sensors in land plants. Recent genomic and metagenomic explorations have revealed the presence of PHYs also in various eukaryotic microalgae originating from distinct endosymbiotic events. Growing evidence indicates that these PHYs are spectrally and functionally tuned to shorter wavelengths, which are prevalent in the aquatic environments as depth increases. Investigations using emerging phytoplankton model species, along with environmental surveys, are uncovering new PHY-mediated responses that likely influence their growth and distribution in marine environments. This Tansley Insight explores the implications of these discoveries for understanding the evolution and functional significance of this major photoreceptor class in the upper ocean, where light drives both energy and information flow.}, } @article {pmid41883376, year = {2026}, author = {Mao, C and Wang, Y and Li, X and Kong, Q and Al-Farraj, SA and Xu, EG and Grossart, HP and Huang, J and Song, W}, title = {Resistance Gene Dynamics, Biogeochemical Coupling, and Ecological Risks in Sediments of Anthropogenically Impacted Lake Wetlands in China.}, journal = {Environment & health (Washington, D.C.)}, volume = {4}, number = {3}, pages = {420-433}, pmid = {41883376}, issn = {2833-8278}, abstract = {Antibiotic resistance is a growing global threat to both public health and ecosystem stability. While the "One Health" framework emphasizes the need to monitor antibiotic resistance genes (ARGs) across diverse environments worldwide, the risks posed by ARGs in lakes affected by human activities, particularly in lake sediments that serve as natural reservoirs of ARGs, remain poorly understood. Metagenomics enables culture-independent analysis of microbial communities and resistance genes, providing essential insights into ARG dynamics. This study investigates microbial communities, ARGs, metal resistance genes (MRGs), and mobile genetic elements (MGEs) in sediments from Lake Donghu and Lake Weishan in China, two contrasting lake ecosystems subject to urbanization and agricultural activities for over four decades, using high-throughput metagenomic sequencing and assembly. ARGs and MRGs were more strongly influenced by deterministic environmental factors, particularly heavy metals (Cd, Pb, Cu), whereas microbial community structures were predominantly shaped by stochastic processes. Metagenomic binning yielded 293 metagenome-assembled genomes (MAGs), 125 of which were identified as potential ARG hosts, with Proteobacteria and Desulfobacterota being the most common. These hosts frequently cocarried MGEs, virulence factor genes (VFGs), and MRGs and exhibited metabolic pathways linked to carbon, nitrogen, and greenhouse gas (CO2 and N2O) cycling. Dissolved organic carbon (DOC) was determined as a key factor influencing microbial metabolism and promoting resistance gene dissemination. Our findings highlight a tight coupling between ARG dissemination, microbial ecological functions, and biogeochemical processes, underscoring ecosystem-level risks associated with resistance proliferation in human-impacted wetlands of China and elsewhere.}, } @article {pmid41883694, year = {2026}, author = {Feigl, V and Röhberg, MZ and Masa, K and Hegedűs, H and Janek, Z and Deák, V and Fehér, C and Buda, K and Medgyes-Horváth, A}, title = {Extremophilic microbial isolates and metagenomic analysis of Greek and Hungarian bauxite residues.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {50}, number = {}, pages = {e00956}, pmid = {41883694}, issn = {2215-017X}, abstract = {Bauxite residue (BR) is an extreme environment for microorganisms. The aim of the work was to isolate extremophilic microorganisms for further biotechnological applications, such as bioleaching or waste rehabilitation. At the same time, metagenomic analysis was performed to monitor short-term changes in deposited BR. We isolated and identified alkaliphilic and extreme halotolerant strains of Nesterenkonia massiliensis, N. natronophila, Micrococcus luteus, Aspergillus iizukae, Gibellulopsis serrae, and G. nigrescens from Greek and Hungarian BRs. Most strains were siderophore producers, cellulose degraders and produced oxalic and acetic acids. Metagenomic analysis revealed a shift in the most abundant bacterial classes from the freshly produced BR during 1 month and 3 months of storage: from Gammaproteobacteria (29% relative abundance), to Actinomycetes (31%) and Gammaproteobacteria (39%), respectively. Metagenomic analysis showed the presence of Nesterenkonia species. These results highlight the diverse microbiome of BR and underscore its potential as a valuable reservoir of extremophilic microorganisms.}, } @article {pmid41883790, year = {2026}, author = {Way, J and Sherman, T and Leleika, S and Crippen, K and Wilson, R and Fida, TT}, title = {Enrichment and comparative metagenomics of microbes involved in biocorrosion of gas transport or storage steel infrastructure.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1771929}, pmid = {41883790}, issn = {1664-302X}, abstract = {Biocorrosion, also known as microbiologically influenced corrosion (MIC), is the deterioration of metals caused by microbial activities that compromise the structural integrity, reliability, and safety of steel infrastructure. To identify the genetic determinants that MIC-causing microorganisms may use to attack steel infrastructure, field samples from natural gas infrastructure with a potential history of MIC were collected, enriched for different MIC categories, and subjected to whole-genome shotgun sequencing for metagenomic analysis. Biofilms were grown on carbon steel coupons or glass slides as attachment substrates to assess differences in microbial community composition and metabolic activities. The highest corrosion activities were observed in enrichments dominated by acid-producing bacteria (APB) and hydrogen-utilizing bacteria. APB enrichments resulted in the highest accumulation of organic acids and a severe decrease in culture fluid pH. A total of 57 metagenome-assembled genomes were recovered from the biofilms, some of which differed between carbon steel coupons and glass slide substrates. The metagenomes contained most of the known genes implicated in MIC and sulfide production, with substantial variation in estimated gene copy numbers among metagenomes and attachment substrates. Overall, comparative analysis of these biofilm metagenomes enriched from natural gas production and processing infrastructure highlights similarities to microbial communities commonly observed in oil production and processing systems and provides an overview of candidate genes that may be used as molecular probes for MIC.}, } @article {pmid41883806, year = {2026}, author = {Peng, L and Zhang, Y and Li, X and Hu, Z}, title = {Integrated multi-omics analysis reveals gut microbiota and metabolic characteristics in coronary heart disease.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1743914}, pmid = {41883806}, issn = {1664-302X}, abstract = {BACKGROUND: Coronary heart disease (CHD) is a leading cause of morbidity and mortality worldwide. Increasing evidence indicates that gut microbiota dysbiosis contributes to CHD pathogenesis through metabolic, inflammatory, and coagulation-related mechanisms. However, comprehensive multi-omics investigations of individuals with CHD remain limited. In this study, we aimed to characterize the multi-omics features of CHD and to identify potential diagnostic biomarkers.

METHODS: The study included 10 patients with clinically diagnosed CHD and 10 healthy controls. Blood and fecal samples were collected for further analysis. The gut microbiota composition was assessed using 16S ribosomal RNA high-throughput sequencing, and shotgun metagenomic sequencing was further performed to evaluate microbial functional potential through the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation and differential pathway analysis. Non-targeted metabolomic profiling was performed using ultra-high-performance liquid chromatography coupled with Orbitrap mass spectrometry, and quantitative proteomic analysis was conducted using liquid chromatography-tandem mass spectrometry. Functional interaction networks between differentially expressed metabolites and proteins were constructed using Spearman correlation analysis, and the diagnostic potential of candidate biomarkers was evaluated using receiver operating characteristic (ROC) curve analysis.

RESULTS: At the phylum level, the CHD group exhibited an increased abundance of Pseudomonadota and a decreased abundance of Bacillota and Actinomycetota. At the genus level, Escherichia-Shigella, Bacteroides, and Klebsiella were significantly enriched, whereas Bifidobacterium and Faecalibacterium were decreased in abundance. Shotgun metagenomic analysis revealed functional remodeling of gut microbiota in CHD, with upregulation of KEGG pathways related to energy metabolism, inflammatory signaling, and host-microbe interactions. Serum metabolomics and proteomic analyses identified 32 differentially expressed metabolites and 38 differentially expressed proteins, respectively. Correlation analysis revealed significant associations between phospholipid metabolites and apolipoproteins, inflammatory mediators and the complement system, asymmetric dimethylarginine and endothelial function-related proteins, and oxidative stress metabolites and antioxidant proteins. ROC analysis identified several potential biomarkers with high diagnostic value.

CONCLUSION: We demonstrate that individuals with CHD exhibit significant gut microbiota dysbiosis, distinct metabolic pathway alterations, and aberrant expression of coagulation- and inflammatory-related proteins. These findings provide novel insights into potential targets for CHD prevention and treatment strategies.}, } @article {pmid41884347, year = {2026}, author = {Liu, H and Li, J and Yang, K and Li, H and Cao, S and Bao, Y and Feng, L and Zhang, L and Niu, J and Tian, T}, title = {Oral microbiome alterations and their association with long-term heavy metal exposure and early health effects.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2647511}, pmid = {41884347}, issn = {2000-2297}, abstract = {BACKGROUND: Long-term heavy metal exposure poses health risks, and non-invasive biomarkers for early detection are needed.

OBJECTIVE: This study investigated whether oral microbiome alterations can serve as a non-invasive indicator of long-term HMs exposure and associated early biological effects.

DESIGN: Soil, buccal mucosa, blood, and urine samples were collected from contaminated (CA) and uncontaminated (UA) areas. Soil contamination was assessed, and internal biomarkers were measured. Oral bacterial diversity was analyzed using metagenomic sequencing.

RESULTS: Severe Cd and Pb contamination was found in CA soil. Participants in CA had elevated internal Cd levels, renal impairment, and immune alterations. Oral microbiome analysis revealed decreased alpha diversity, reduced network complexity, and a shift from beneficial to pathogenic keystone taxa in CA. Functional analysis showed enrichment of stress-response pathways, suppression of metabolic pathways, and increased pathways linked to human diseases. Specific bacterial taxa correlated with internal biomarker levels.

CONCLUSIONS: There is a close association between long-term HMs exposure and reproducible, multi-faceted shifts in the oral microbiome. The oral microbiome may represent a promising, non-invasive biomarker for assessing environmental exposure and its early biological impacts.}, } @article {pmid41885442, year = {2026}, author = {Rysava, M and Stredanska, K and Schwarzerova, J and Jakubickova, M and Cejkova, D and Aytan-Aktug, D and Otani, S and Dolejska, M and Palkovicova, J}, title = {Dynamic changes in the plasmidome and resistome in the gastrointestinal tract of chickens.}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0407425}, pmid = {41885442}, issn = {2165-0497}, abstract = {The expansion of intensive poultry farming has led to a substantial increase in antibiotic use, which, in turn, has promoted the accumulation of antibiotic resistance genes (ARGs). The chicken gut serves as a reservoir for these genes and provides favorable conditions for their horizontal transfer via mobile genetic elements, such as plasmids. Through this process, commensal bacteria can transfer ARGs to pathogens, facilitating their spread and increasing the risk of transmission to humans. In this study, long-read sequencing was used to characterize the plasmidome and resistome in 12 fecal samples from 3 houses of a commercial broiler chicken farm. All chickens received enrofloxacin in the first days of life, with one house additionally treated with sulfamethoxazole/trimethoprim combination. For comparison, metagenomic analysis using short-read sequencing was performed on the same samples. This study revealed the presence of various ARGs associated with resistance to 25 antibiotic classes. A strong genetic association between MOBP-type plasmids and fluoroquinolone resistance was observed within broiler chicken farms. Temporal trends indicated progressive mobilization of these ARGs, suggesting an increasing potential for horizontal gene transfer. While fluoroquinolone resistance expanded over time, diaminopyrimidine resistance remained stable despite the antibiotic treatment. Most ARGs were carried on small plasmids, and complete plasmid reconstructions ranged from 2.6 to 47.6 kb. Our findings demonstrate that plasmidome sequencing enables high-resolution detection of resistance-associated plasmids that may be overlooked by conventional metagenomic approaches. The observed patterns are consistent with an association between fluoroquinolone use in poultry farms and the presence of plasmid-mediated resistance genes with potential for horizontal dissemination.IMPORTANCEDespite the crucial role of plasmids in antimicrobial resistance (AMR) dissemination, studies focusing on plasmidomes, defined as the complete set of plasmids, remain limited. This study is the evidence that chicken farms, where fluoroquinolone treatment is a standard practice, act as an important reservoir of plasmid-mediated antibiotic resistance which may not be revealed by commonly used approaches. Combining a metagenomic approach with a focus on plasmids enhances our ability to understand the genetic context and mechanisms underlying AMR transmission. The findings emphasize the importance of targeted plasmid analysis to improve surveillance and risk assessment of AMR transmission in microbial ecosystems.}, } @article {pmid41885716, year = {2026}, author = {Xu, H and Yang, H and Shi, Y and Hu, X and Zhang, L and Li, P and Ma, Y and Yang, T and Xu, Y and Dong, C and Shen, Q}, title = {Genotype-Dependent Rhizosphere Microbiome Assembly Improves Potassium Use Efficiency in Pear Rootstocks Under Low Potassium Stress.}, journal = {Plant, cell & environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70499}, pmid = {41885716}, issn = {1365-3040}, support = {32272802//National Science Foundation of China/ ; CARS-28-10//China Agriculture Research System/ ; }, abstract = {Potassium (K) is a vital nutrient for fruit quality in pears (Pyrus spp.), and rhizosphere microbes play a critical role in enhancing plant K uptake and utilization. To investigate the genotype-dependent influences of the rhizosphere microbiome on potassium use efficiency (KUE) in pears, we compared two rootstocks with contrasting KUE (Pyrus betulaefolia and Pyrus ussuriensis) using integrated pot and long-term field experiments, 16S rRNA amplicon sequencing, and metagenomic analyses. Synthetic community (SynCom) inoculation and transcriptome profiling were employed to elucidate the mechanisms underlying enhanced K acquisition. Under low-K conditions, P. betulaefolia recruited distinct microbial communities, which significantly improved K accumulation by upregulating genes (e.g., ATP1A, kdPB, and COG3158) associated with K transport and homoeostasis. Field trials further confirmed that P. betulaefolia-grafted trees sustained higher Bacillaceae abundance, superior fruit quality, and elevated K content than P. ussuriensis under K-deficient conditions. SynComs constructed from five Bacillaceae strains enhanced low-K tolerance by promoting root metabolic activity, stimulating root hair development, modulating K[+] transporter (e.g., NRT2.4) expression, and activating calcium-dependent signalling pathways. Inoculation with SynComs led to substantial improvements under K limitation, including a 105.86% increase in plant biomass, a 164.99% increase in K accumulation, and a 125.91% enhancement in the aboveground K utilisation index. These findings reveal that genotype-driven enrichment of Bacillaceae-dominated microbiomes significantly enhances pear KUE, offering mechanistic insights to guide the development of microbiome-based bioinoculants and breeding of "microbiome-responsive" rootstocks for sustainable fruit production under K-limiting conditions.}, } @article {pmid41885787, year = {2026}, author = {Ayed, M and Cadavez, V and Gonzales-Barron, U}, title = {Current research trends towards the control of protozoans in foods.}, journal = {Italian journal of food safety}, volume = {}, number = {}, pages = {}, doi = {10.4081/ijfs.2026.15114}, pmid = {41885787}, issn = {2239-7132}, abstract = {Protozoan parasites such as Cryptosporidium spp., Giardia duodenalis, Toxoplasma gondii and Cyclospora cayetanensis remain difficult-to-control hazards in food due to environmental persistence, low infectious doses, and the interpretability gap between nucleic acid detection and infectivity. This review synthesizes 4-year research trends shaping protozoan control in food systems, focusing on three critical pillars: matrix-adapted front-end processing (concentration, lysis, inhibitor management); inhibitor-resilient quantification; and sequencing-based attribution for outbreak investigation and source tracking. Recent benchmarking across wastewater, the water-soil-produce nexus, and food-relevant matrices repeatedly indicates - depending on matrix and study design - that upstream workflow steps often dominate analytical sensitivity and reproducibility. Accordingly, tiered analytical strategies are emerging in which the quantitative polymerase chain reaction (PCR) technique supports scalable screening, droplet digital PCR is used for decision-grade confirmation/quantification under inhibition and low-template conditions, and targeted sequencing or metagenomics is deployed selectively for traceback and contextual investigation. We integrate these developments into an actionable control framework that links prevention at the water-soil-plant interface with tiered analytics and viability-aware interpretation of post-intervention results. Research priorities ahead include harmonized performance reporting (recovery, inhibition controls, limit of detection/quantification), transparent endpoint hierarchy for intervention claims (detectability versus viability/infectivity), and interoperable sequence databases to enable cross-laboratory attribution and program-level learning. The field is moving from "can we detect?" towards "can we decide? - requiring reproducible front-end processing, inhibitor-resilient quantification, interoperable attribution resources, and endpoint discipline for intervention efficacy claims.}, } @article {pmid41886617, year = {2026}, author = {Qiao, Z and Chen, Z and Gong, H and Guo, X and Yu, H and Chen, L}, title = {Exogenous Elemental Sulfur Promoting Methane Production and Simultaneous Ammonia Nitrogen Removal in Anaerobic Digestion of Food Waste: Experimental Verification and Mechanism Analysis.}, journal = {Environmental science & technology}, volume = {60}, number = {13}, pages = {10029-10041}, doi = {10.1021/acs.est.5c18148}, pmid = {41886617}, issn = {1520-5851}, mesh = {*Methane ; *Sulfur ; Ammonia ; Food Loss and Waste ; Anaerobiosis ; Nitrogen ; Bioreactors ; }, abstract = {The treatment of food waste (FW) via anaerobic digestion (AD) is frequently plagued by a low methane yield and ammonia (NH4[+]) inhibition. This study demonstrates that the addition of elemental sulfur (S[0]) effectively mitigates both of these issues. Through batch and continuous experiments, it was found that the specific methane yield was enhanced by up to 48.1% and the NH4[+] concentration decreased by 26.9% at the optimal S[0] dosages of 20 mg/L. Metagenomic analysis revealed a dual mechanism underlying this enhancement: at low dosages, S[0] provides a sulfur-containing functional group for the biosynthesis of methyl-coenzyme M, thereby accelerating the rate-limiting "methyl-transfer" step in methanogenesis; at high dosages, it promotes the biosynthesis of coenzyme A, which markedly enhances acidogenesis. Furthermore, S[0] alleviates NH4[+] inhibition by fostering a synergistic interaction between sulfate-reducing bacteria and anammox bacteria, which convert NH4[+] to N2. Continuous operation over 140 days confirmed the long-term stability and effectiveness of this S[0] addition strategy. This study provides mechanistic insights into S[0]-driven methanogenesis in complex organic waste (FW) and offers a cost-effective, sustainable approach to enhancing AD efficiency and stability.}, } @article {pmid41886785, year = {2026}, author = {Tian, M and Li, J and Dai, S and Ma, L}, title = {Clinical Characteristics and Management of Four Cases of Visceral Leishmaniasis-Associated Hemophagocytic Lymphohistiocytosis.}, journal = {The American journal of tropical medicine and hygiene}, volume = {114}, number = {5}, pages = {882-888}, pmid = {41886785}, issn = {1476-1645}, mesh = {Humans ; *Leishmaniasis, Visceral/complications/drug therapy/diagnosis ; *Lymphohistiocytosis, Hemophagocytic/drug therapy/diagnosis/etiology/parasitology ; Male ; Female ; Leishmania donovani/isolation & purification ; Antiprotozoal Agents/therapeutic use ; Child, Preschool ; Child ; Bone Marrow/pathology/parasitology ; Antimony Sodium Gluconate/therapeutic use ; }, abstract = {The aim for the present study was to analyze clinical features, diagnostic approaches, and therapeutic strategies for visceral leishmaniasis (VL)-associated hemophagocytic lymphohistiocytosis (HLH) in pediatric patients. The clinical characteristics and test results of the children were summarized. Among the four patients, three resided in VL-endemic regions, and one had traveled to a VL-endemic region. All patients presented with recurrent fever (>38.5°C), hepatosplenomegaly, and decreased hemoglobin (HGB) levels ([78.75 ± 8.50] g/L) and platelet (PLT) counts ([59.50 ± 17.48] × 109/L). Before a definitive diagnosis could be made, patients exhibited progressive declines in white blood cell counts, HGB levels, and PLT counts, along with elevated triglyceride, serum cytokine (interleukin [IL]-6, IL-10, IL-2R, and tumor necrosis factor α) levels. Bone marrow aspirate smears revealed hemophagocytosis and Leishmania donovani (LD) bodies in all cases: two were diagnosed via direct identification of LD bodies, one was diagnosed through re-examination of bone marrow smears after confirming a travel history, and one was diagnosed via re-examination prompted by metagenomic next-generation sequencing, which revealed leishmaniasis. All the patients were initially diagnosed with HLH and received HLH-directed immunochemotherapy before VL diagnosis, with suboptimal response. After confirmation of VL, sodium stibogluconate therapy was initiated, resulting in a partial response in all cases. Etiological investigation is critical for HLH diagnosis. For VL-associated HLH, sodium stibogluconate as targeted therapy rapidly controls HLH, facilitates immunosuppression withdrawal, and significantly improves patient outcomes. White blood cell count, HGB level, PLT count, and lactate dehydrogenase level may serve as critical prognostic biomarkers for VL-associated HLH.}, } @article {pmid41886955, year = {2026}, author = {Ling, GC and Chen, SJ and Li, ZL and Yang, S and Xiao, YY and Xiao, M and Zhang, YY and Zhong, HJ and Zhang, JY and Li, Y and Xie, JJ}, title = {A microbiota-tryptophol-AhR axis mediates the gut-kidney protective effects of Hushen Tongfengtai Granules in hyperuricemic nephropathy.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158089}, doi = {10.1016/j.phymed.2026.158089}, pmid = {41886955}, issn = {1618-095X}, mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology ; *Hyperuricemia/drug therapy/complications ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; *Receptors, Aryl Hydrocarbon/metabolism ; *Indoles/metabolism/pharmacology ; *Kidney Diseases/drug therapy ; Kidney/drug effects ; Mice, Inbred C57BL ; Dysbiosis/drug therapy ; Feces/microbiology ; }, abstract = {BACKGROUND: Hyperuricemia (HUA) may result in hyperuricemic nephropathy (HN), and gut dysbiosis with barrier dysfunction can worsen disease progression. Hushen Tongfengtai granules (HSTFT), a traditional Chinese herbal prescription, have been used clinically to mitigate HUA and related renal injury. However, the mechanisms behind their effects remain to be explored.

OBJECTIVE: To find HSTFT to mitigate HN through mechanisms dependent on gut microbiota.

METHODS: Fecal metagenomics and UPLC-ESI-MS/MS metabolomics were employed to identify key microbial taxa and metabolites modulated by HSTFT. Antibiotic-treated mice were used to investigate the gut microbiota-dependent mechanisms of HSTFT. In vivo and in vitro experiments were further conducted to validate the ameliorative effects of HSTFT on gut dysbiosis and barrier dysfunction in HUA mice.

RESULTS: HSTFT could improve renal injury and intestinal barrier dysfunction in HUA. Fecal metagenomic analysis revealed enrichment of Bifidobacterium breve. Antibiotic depletion could abolish the therapeutic efficacy of HSTFT, while Bifidobacterium breve (B.breve) recolonization could restore intestinal and renal protection. Metabolomic analysis identified tryptophol as a key HSTFT-associated metabolite. Exogenous tryptophol (TOL) recapitulated the protective effects and may activate the aryl hydrocarbon receptor (AhR) pathway. The AhR antagonist CH223191 could inhibit the TOL/HSTFT-mediated protective effects on intestinal barrier integrity and renal function.

CONCLUSION: HSTFT could ameliorate HN by enhancing intestinal barrier integrity and renal protection, with the underlying mechanism involving upregulation of intestinal B.breve and its metabolite TOL via AhR pathway activation.}, } @article {pmid41887041, year = {2026}, author = {Huang, J and Fu, Z and Zhou, S and Hu, J and Yu, G and Qin, C and Ma, Z}, title = {Metagenomic insights into sex-specific taxonomic and functional differentiation of epidermal mucus microbiota in the humphead wrasse (Cheilinus undulatus).}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {59}, number = {}, pages = {101810}, doi = {10.1016/j.cbd.2026.101810}, pmid = {41887041}, issn = {1878-0407}, mesh = {Animals ; Female ; Male ; *Mucus/microbiology ; *Microbiota ; *Fishes/microbiology/genetics ; *Metagenomics ; *Epidermis/microbiology ; *Metagenome ; *Bacteria/genetics/classification ; }, abstract = {The humphead wrasse (Cheilinus undulatus) is a large coral reef fish of high ecological and economic importance, whose epidermal mucus microbiota plays a critical role in host defense, immune regulation, and environmental adaptation. However, the influence of host sex on the structure and functional potential of epidermal mucus microbiota remains poorly understood. In this study, epidermal mucus samples were collected from sexually mature female and male humphead wrasse, and shotgun metagenomic sequencing was performed to systematically compare microbial community composition, diversity, and functional gene profiles between sexes. The results showed no significant differences in alpha diversity (ACE and Shannon indices) between female (FM) and male (M) groups. In contrast, beta diversity analyses and hierarchical clustering revealed clear sex-related separation of microbial community structures at both phylum and genus levels. Although both groups were dominated by Pseudomonadota, Bacillota, Bacteroidota, and Verrucomicrobiota, their relative abundances and sex-specific taxa differed markedly. Functional annotation based on KEGG indicated that female-specific taxa harbored a greater number and broader range of functional genes, mainly associated with carbohydrate, amino acid, energy, and cofactor metabolism, as well as disease-related pathways. Furthermore, Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) analyses revealed that female-specific taxa exhibited higher diversity of antibiotic resistance genes and virulence factors, whereas male-specific taxa showed a more limited functional repertoire, primarily related to basic metabolism and biofilm formation. Overall, this study demonstrates pronounced sex-associated differences in both the taxonomic composition and functional potential of epidermal mucus microbiota in humphead wrasse, highlighting the importance of host sex in shaping host-microbiome interactions and providing new insights for health management and conservation of coral reef fishes.}, } @article {pmid41887065, year = {2026}, author = {Song, J and Hou, YN and Li, R and Feng, Z and Wang, AJ and Ren, N and Wei, W and Ni, BJ and Huang, C}, title = {Ectoine modulates mixotrophic denitrification pathway partitioning to sustain stable nitrogen and phenol removal under hypersaline stress.}, journal = {Water research}, volume = {298}, number = {}, pages = {125764}, doi = {10.1016/j.watres.2026.125764}, pmid = {41887065}, issn = {1879-2448}, mesh = {*Denitrification ; *Nitrogen/metabolism ; *Amino Acids, Diamino ; Salinity ; *Phenol ; Bioreactors ; }, abstract = {Hypersaline wastewater containing phenolic compounds imposes coupled osmotic and cytotoxic stresses that severely disrupts biological treatment processes. While compatible solutes are known to enhance cellular osmoprotection, their capacity to regulate microbial metabolic, particularly the balance between autotrophic and heterotrophic denitrification pathways under combined salinity stress remain poorly understood. This study reveals that the compatible solute ectoine modulates pathway partitioning in mixotrophic denitrification systems, enabling efficient nitrogen and phenol removal under 4% salinity. The ectoine amended reactor maintained nitrogen removal above 95% and phenol degradation above 80%, whereas the unprotected control collapsed to 34% and 33% respectively. Multi-scale mechanistic investigations revealed a coordinated protection cascade. First, ectoine enhanced cellular resilience by suppressing reactive oxygen species (ROS) by 88.2%, maintaining ATP level and electron transport activity, thereby preserving bioenergetic integrity. Second, structural fortification was achieved through intensified extracellular polymeric substance (EPS) production. The protein-to-polysaccharide ratio increased from 0.70 to 1.51 creating a protective matrix that stabilized membrane permeability and preserved catalytic enzymes, with nitrate reductase and nitrite reductase activities increasing 2.16- and 2.93-fold. Third, metagenomic profiling revealed community reconfiguration, with selective enrichment of halotolerant heterotrophs (Halomonas, Marinobacter) to 49% relative abundance. Aromatic‑degradation genes (catA, benB) rose by 7‑ and 48‑fold, while nitrogen‑metabolism genes (nasA, norC) remained high representation. This restructuring reversed pathway contributions from 81% sulfur-autotrophic dominance to 82% heterotrophic dominance. Ectoine thus functions as a metabolic modulator that links cellular stress alleviation and community-level functional potential to pathway repartitioning, offering a feasible strategy for the biotreatment of saline phenolic wastewater.}, } @article {pmid41887066, year = {2026}, author = {Wang, H and Wu, Y and Weng, H and Zhang, L and Peng, Y}, title = {Denitrification mode management selects resource-conserving consortia for low-carbon municipal wastewater treatment.}, journal = {Water research}, volume = {298}, number = {}, pages = {125775}, doi = {10.1016/j.watres.2026.125775}, pmid = {41887066}, issn = {1879-2448}, mesh = {*Denitrification ; *Carbon/metabolism ; *Wastewater/microbiology/chemistry ; *Waste Disposal, Fluid/methods ; Bioreactors/microbiology ; Nitrogen/metabolism ; Bacteria/metabolism/genetics ; Anaerobiosis ; }, abstract = {Low-carbon municipal wastewater treatment increasingly relies on carbon-limited denitrification, yet how carbon limitation reorganizes denitrifying communities and their greenhouse-gas footprint remains poorly resolved. We implemented denitrification mode management in a municipal wastewater sequencing batch reactor by switching from anaerobic-aerobic (AO) to anaerobic-aerobic-anoxic (AOA) operation. This shift moved denitrification from an pre-anaerobic stage with higher carbon availability to a post-anoxic stage where readily available carbon was limited. We combined metagenomics and metatranscriptomics to link process performance with microbial traits and gene expression. The mode switch improved nitrogen removal from 67.1 ± 1.8% to 88.5 ± 3.9% and reduced carbon requirement from 4.9 ± 0.5 to 3.3 ± 0.4 mg COD per mg N removed, while decreasing the N2O emission factor from 0.024 to 0.005 mg N2O-N per mg NO3[-]-N and lowering CO2 and CH4 emissions by 20-30%. Carbon-limited post-denitrification selected taxa with smaller genomes, reduced metabolic redundancy and a pronounced shift from broad extracellular carbon catabolism and complete denitrification towards intracellular carbon storage and truncated denitrification. Intracellular carbon pools insulated organics at the single-cell level and buffered electron delivery across denitrification steps, enabling a division-of-labour network that prevents electron imbalance and suppresses N2O build-up. Together, these findings link denitrification mode management to trait-based community restructuring and offer a process-level framework for understanding low-carbon, low-emission nitrogen removal under carbon-limited conditions.}, } @article {pmid41887069, year = {2026}, author = {Qiang, H and Xu, X and Liu, Z and Heo, S and Yue, X and Zhou, A and Makinia, J}, title = {New insights into the interplay between chain elongation and homoacetogenesis in microbial electrosynthesis: Chloroform-enhanced medium-chain carboxylate production.}, journal = {Water research}, volume = {298}, number = {}, pages = {125790}, doi = {10.1016/j.watres.2026.125790}, pmid = {41887069}, issn = {1879-2448}, mesh = {*Chloroform ; *Carboxylic Acids/metabolism ; }, abstract = {Microbial electrosynthesis (MES)-assisted chain elongation (CE) is a promising strategy for sustainable medium-chain carboxylic acid (MCCA) production from waste streams. However, MES induces inevitable H2 evolution, and the understudied interaction between H2-driven homoacetogenesis and CE creates a critical knowledge gap. To resolve this metabolic conflict, chloroform (CHCl3) at 0.0075%-0.045% was used to inhibit homoacetogenesis, with systematic investigations on carbon flux distribution, functional microbial communities, and key metabolic pathways. Results showed 0.03% CHCl3 optimized MCCA production to 2902.8 ± 116.1 mg COD/L (103.0% increase), with electron efficiency (40.8%) and acetate utilization efficiency (94.3%) significantly higher than the Control (21.8% and 43.5%, respectively). Homoacetogenesis inhibition conserved reducing power (moderated H2, lowered NAD[+]/NADH) and redirected acetyl-CoA to drive CE. Microbial community analysis revealed enriched chain-elongating bacteria with more modular, cooperative interaction networks. Metagenomic analysis confirmed elevated abundances of reverse β-oxidation genes (e.g., ACAT, crt) and reduced homoacetogenesis genes (e.g., cooF, cooS) after treatment. Taxon-function contribution analysis identified Clostridium_kluyveri as the dominant functional agent for CE-related key genes. Economic and life-cycle assessments demonstrated a net economic gain of $1.61-4.22/m[3] and mitigated key environmental impacts due to improved product yield. This study elucidates how regulating the competition between homo-acetogens and chain-elongating bacteria directionally enhances CE, providing a novel ecological perspective and strategy for optimizing electricity-driven biomanufacturing processes.}, } @article {pmid41887245, year = {2026}, author = {Reddy, K and Sinha, P and Antcliffe, DB and McDowell, C and Bradley, PA and Black, L and Murphy, L and Barbaras, J and Conlon, J and Camporota, L and Ostermann, M and Hopkins, P and Szakmany, T and Cherian, S and Welters, I and Brealey, D and Parekh, D and Rostron, AJ and Bos, LDJ and Nichol, A and Shankar-Hari, M and Gordon, AC and Delucchi, K and O'Kane, CM and Matthay, MA and Calfee, CS and McAuley, DF and , }, title = {Bedside identification of subphenotypes in acute respiratory failure (PHIND): a multicentre, observational cohort study.}, journal = {The Lancet. Respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2213-2600(26)00040-8}, pmid = {41887245}, issn = {2213-2619}, abstract = {BACKGROUND: Acute respiratory distress syndrome (ARDS) is a clinically defined, biologically heterogeneous condition with no proven disease-modifying therapies. Retrospective analyses have identified two biologically distinct subphenotypes (hyperinflammatory and hypoinflammatory) of ARDS, with differing outcomes and responses to therapy. Rapid identification of these subphenotypes in an actionable timeframe has previously not been possible. The PHIND study aimed to prospectively identify these subphenotypes and to demonstrate differing 60-day mortality.

METHODS: The PHIND study was a prospective, multicentre, observational cohort study conducted in intensive care units (ICUs) within the National Health Service in the UK and the Health Service Executive in Ireland. Adult patients aged 18 years and older with ARDS or acute hypoxaemic respiratory failure (AHRF) were enrolled within 72 h of onset of the syndrome. Eligible patients were required to be receiving invasive mechanical ventilation, non-invasive ventilation, or high-flow nasal oxygen. Plasma interleukin (IL-6) and soluble TNF receptor-1 (TNFR1) were quantified at enrolment using a near-patient benchtop immunoanalyser (Randox multiSTAT) with a run time of approximately 1 h. Together with plasma bicarbonate measured from an arterial blood sample, these values were used to prospectively determine subphenotypes on an individual patient basis using a validated parsimonious logistic regression model. The primary outcome was 60-day mortality. The study was registered on ClinicalTrials.gov, NCT04009330.

FINDINGS: Between Nov 22, 2019, and Sept 28, 2023, 1853 patients from 30 centres were screened for eligibility. Of these, 1328 were excluded and 525 were recruited into the study, with 512 individuals included. 308 (60%) patients were male, 204 (40%) were female, and mean age was 57·0 years (SD 15·1). 443 (87%) patients were white, 18 (4%) were Black, and 16 (3%) were Asian. 490 were subphenotyped using the near-patient assay: 89 (18%) were classified as hyperinflammatory and 401 (82%) as hypoinflammatory. The primary outcome of 60-day mortality was measured in 486 patients after four patients withdrew consent for confirmation of vital status. 60-day mortality was significantly higher in the hyperinflammatory group (45 [51%] of 88) than in the hypoinflammatory group (111 [28%] of 398; risk ratio 1·8 [95% CI 1·4-2·4], p<0·0001). After adjustment, hyperinflammatory patients had increased odds of 60-day mortality (adjusted odds ratio 2·7 [95% CI 1·6-4·4], p=0·0002).

INTERPRETATION: Rapid identification of ARDS inflammatory subphenotypes using a near-patient assay was feasible and associated with many clinical characteristics and outcomes consistent with those described in earlier retrospective studies, including mortality, prevalence of sepsis, and incidence of metabolic acidosis. These findings support the implementation of precision medicine approaches in ARDS and the urgent need for prospective, subphenotype-stratified interventional trials.

FUNDING: Innovate UK, Randox Laboratories, and Belfast Health & Social Care Trust.}, } @article {pmid41887297, year = {2026}, author = {Lin, X and Yang, J and Kong, H and Pu, L and Ma, P and Mu, W and Sheng, H and He, J and Zou, Y and Wang, Y and Guo, X and Zhang, S and Wang, S}, title = {Metagenomic analysis of the gut microbiota in Cryptosporidium-infected Tibetan sheep.}, journal = {Microbial pathogenesis}, volume = {215}, number = {}, pages = {108461}, doi = {10.1016/j.micpath.2026.108461}, pmid = {41887297}, issn = {1096-1208}, mesh = {Animals ; *Cryptosporidiosis/parasitology/microbiology ; Sheep ; *Cryptosporidium/genetics/isolation & purification ; Feces/parasitology/microbiology ; *Metagenomics ; *Sheep Diseases/parasitology/microbiology ; Tibet ; *Gastrointestinal Microbiome/genetics ; Polymerase Chain Reaction ; Bacteria/classification/genetics ; }, abstract = {Cryptosporidium are important causative parasitic protozoa that cause gastrointestinal discomfort and diarrhea in humans and animals, posing a huge threat to public health. Ruminants serve as the main source of Cryptosporidium infection. However, the relationship between this intestinal parasite and host gut microbiota in Tibetan sheep remains almost unknown. In the present study, using nested PCR targeting the SSU rRNA gene, we detected Cryptosporidium in 9% (38/420) of fecal samples. The positive rate was significantly higher in 4-7 month-old lambs than in adult sheep. Infection of Cryptosporidium spp. was associated with limited overall structural and functional alterations of the host gut microbiota, characterized by increased the relative abundance of Escherichia and reduced functional pathways related to amino acid biosynthesis and nucleotide/nucleoside biosynthesis. Additionally, the data indicates that age served as a primary determinant of the gut microbiota, whereas Cryptosporidium load showed no significant association with microbial variation. Machine learning model analysis revealed that these differential microbial features could effectively discriminate between infected and uninfected animals. These findings elucidate that Cryptosporidium infection is associated with specific and limited gut microbiota alterations in sheep.}, } @article {pmid41887416, year = {2026}, author = {Zhang, L and Xie, J and Lu, Y and Kong, L and Zhou, L and Wu, S and Wang, W and Huang, J and Li, J and Cheng, S}, title = {Enhanced nitrogen removal and mitigated greenhouse gas emissions in bioelectrochemical system-modular moving bed wetland at low temperature: Functional zonation and multi-pathway electron transfer.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134493}, doi = {10.1016/j.biortech.2026.134493}, pmid = {41887416}, issn = {1873-2976}, mesh = {*Nitrogen/isolation & purification ; Electron Transport ; *Wetlands ; *Bioelectric Energy Sources/microbiology ; *Greenhouse Gases ; *Cold Temperature ; Electrodes ; Biofilms ; }, abstract = {This study integrated bioelectrochemical systems (BESs) into modular moving bed constructed wetlands (MMBCWs) to mitigate low temperature constraints on nitrogen removal and greenhouse gas emissions. Conventional MMBCW, microbial fuel cell-MMBCW (MFC-MMBCW), and microbial electrolysis cell-MMBCW (MEC-MMBCW) were constructed to assess feasibility. Results showed that MEC-MMBCW achieved superior nitrogen removal and the lowest global warming potential under cold conditions. Biofilm characteristics and metagenomic analyses revealed that MEC-MMBCW established spatially stratified functional zones. Specifically, the anode promoted organic matter and ammonia oxidation, while enhanced denitrification outcompeted compensatory anammox in the cathode. Furthermore, a multi-pathway extracellular electron transfer (EET) network mediated by extracellular polymeric substances (EPS), cytochrome c, and conductive pili accelerated electron transfer rates. These mechanisms synergistically boosted metabolic potential and activated latent degradation pathways, enhancing treatment resilience. Consequently, MEC-MMBCW represents a viable strategy for sustainable wastewater treatment in cold regions.}, } @article {pmid41887490, year = {2026}, author = {Li, Z and Fu, J and Hu, J and Li, T and Xu, Y}, title = {Sediment-water interface reoxygenation by NO3-LDH promotes tetracycline degradation in sediments and modulates antibiotic resistance gene dynamics.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124357}, doi = {10.1016/j.envres.2026.124357}, pmid = {41887490}, issn = {1096-0953}, mesh = {*Geologic Sediments/chemistry/microbiology ; *Tetracycline/metabolism ; Oxygen/chemistry ; *Anti-Bacterial Agents/metabolism ; *Nitrates/chemistry ; *Water Pollutants, Chemical/metabolism ; *Tetracycline Resistance/genetics ; Genes, Bacterial ; }, abstract = {The widespread presence of antibiotics in aquatic sediments, together with hypoxic conditions, constrains oxygen-driven natural degradation, thereby prolonging their environmental persistence. In this work, nitrate-intercalated layered double hydroxide (NO3-LDH) was employed as a controlled-release nitrate amendment to alleviate interfacial oxygen limitation while minimizing the secondary environmental risks associated with the high release peaks of conventional nitrate reagents. As a result, NO3-LDH increased dissolved oxygen (DO) from 1.05 to 3.39 mg/L, enhanced TC removal from 64.5% to 89.8% within 15 d, and reduced the combined abundance of tetracycline resistance genes (tetA, tetQ, and tetS) by 53.0%. Mechanistically, DO enrichment increased •OH generation 1.94-fold and upregulated cytochrome P450-related genes, supporting coupled enhancement of abiotic oxidation and oxygen-dependent microbial transformation. The improved oxidative microenvironment also favored the enrichment of aerobic aromatic-degrading taxa, further promoting TC attenuation. Although overall antibiotic resistance genes (ARGs) levels declined, fluoroquinolone- and macrolide-associated ARGs exhibited a transient early increase, likely triggered by an abrupt redox perturbation upon oxygen recovery that imposed oxidative stress on anaerobic microorganisms, intensified ATP-demanding stress responses, and increased membrane permeability. As interfacial redox conditions stabilized and TC concentrations decreased, these stress responses subsided and ARGs abundances declined at later stages. Overall, restoring interfacial DO strengthens oxygen-driven natural antibiotic degradation and inhibits the long-term accumulation of ARGs, providing a mechanistically grounded strategy for in situ remediation of antibiotic-contaminated sediments.}, } @article {pmid41887505, year = {2026}, author = {Wang, Q and Zhang, J and Xia, Y and Zha, M and Li, J and Jambal, T and Dorjgotov, D and Tseveen, S and Chen, Y}, title = {Traditional fermented goat milk products in Mongolia: Analysis from the perspective of metagenomics to metabolomics.}, journal = {Journal of dairy science}, volume = {109}, number = {5}, pages = {4811-4825}, doi = {10.3168/jds.2025-27796}, pmid = {41887505}, issn = {1525-3198}, mesh = {Animals ; Goats ; Mongolia ; Metagenomics ; *Cultured Milk Products/microbiology/analysis ; Fermentation ; *Milk/microbiology/chemistry ; Metabolomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; Microbiota ; Food Microbiology ; }, abstract = {Mongolia is known for its rich dairy traditions, with goat milk representing a distinctive and valuable dairy resource. Fermentation improves the quality and nutritional value of goat milk, which is closely associated with microbial activity. As traditional Mongolian fermented dairy products primarily depend on natural fermentation, investigating the microbial and metabolic changes during this process is essential for understanding product quality. In this observational study, raw goat milk (RGM) and fermented goat milk (FGM) samples were collected from Mongolia, and a total of 102 microbial species were identified using shotgun metagenomic sequencing. The RGM contained a higher proportion of viruses and nonlactic acid bacteria (non-LAB), including Macrococcus caseolyticus. Following fermentation, the microbial community composition shifted, becoming dominated by LAB species such as Lactobacillus helveticus and Lactobacillus delbrueckii, with beneficial microorganisms attaining predominant abundance. A total of 22 differential metabolites were identified between RGM and FGM. Approximately half of these metabolites were related to AA metabolism, while the remainder were involved in energy metabolism, antioxidant processes, and lipid metabolism. Spearman correlation analysis suggested that LAB, primarily Lactobacillus species, were positively associated with the abundance of metabolites such as organic acids and AA in the fermented products. In contrast, the presence of pathogenic microorganisms such as viruses showed a negative correlation with fermentation efficiency markers. It was hypothesized as a potential factor affecting product quality, possibly through disrupting host microbial metabolism. Overall, this observational study identifies understanding of the factors governing FGM quality and provides a scientific foundation for improving the goat milk industry and harnessing microbial resources in traditional fermented dairy products.}, } @article {pmid41887507, year = {2026}, author = {Scott, J and Brouard, JS and Drouin, G and Ouellet, DR and Ster, C and Petri, RM}, title = {Microbiota changes in rumen and milk corresponding to dietary protein intake in transition dairy cows.}, journal = {Journal of dairy science}, volume = {109}, number = {6}, pages = {6287-6300}, doi = {10.3168/jds.2025-27576}, pmid = {41887507}, issn = {1525-3198}, mesh = {Animals ; *Rumen/microbiology ; Female ; Cattle/microbiology/physiology ; *Milk/microbiology/chemistry ; Lactation ; *Dietary Proteins/metabolism/administration & dosage ; Diet/veterinary ; Animal Feed/analysis ; *Microbiota ; Postpartum Period ; }, abstract = {During the transition period in dairy cows, the incidence of disease increases due to a negative energy balance affecting both the metabolic and immune health status. Limiting milk production at the beginning of lactation improves the metabolic status of cows. However, past strategies tested to achieve this reduction either negatively affected milk yield for the rest of the lactation or were difficult to implement on large-scale dairy farms. This study evaluated the impact of a temporary reduction in MP supply during the transition period on the rumen and milk microbiota and their metabolic composition. Treatment cows (n = 5) were fed 80% of their MP needs (MP80) from 14 d before calving to 14 d after calving, before being switched to a 100% MP diet (MP100) for an additional 14 d. Control cows (n = 6) were fed MP100 for the entire experiment. Samples of rumen content and milk were taken in the immediate postpartum phase (PP) on d 2 and 7, as well as after dietary change in the experimental recovery phase on d 21 and 28 postpartum. All samples were extracted for DNA and analyzed using shotgun metagenomic sequencing (Illumina NovaSeq). Milk samples were additionally analyzed for composition, and rumen fluid was analyzed for short-chain fatty acids and ammonia-N. Significant changes to the microbial composition were almost exclusively associated with the effect of day of sampling, with the exception being the family Micrococcaceae, which was found to be differentially abundant in the MP100 compared with the 80% group in PP milk samples. This study used a metagenomics approach to understanding the impact of altered protein supply on rumen and milk microbiota, to better understand impacts on these separate ecosystems.}, } @article {pmid41887601, year = {2026}, author = {Wei, Y and Liu, Q and Gong, Z and Han, GZ}, title = {Unveiling the cryptic diversity and distribution of elements related to virophage mavirus through deep mining of pPolB proteins.}, journal = {Virologica Sinica}, volume = {41}, number = {2}, pages = {371-381}, pmid = {41887601}, issn = {1995-820X}, mesh = {*Virophages/genetics/classification/enzymology ; Phylogeny ; *Viral Proteins/genetics ; *Genetic Variation ; Genome, Viral ; Metagenome ; Metagenomics ; *DNA-Directed DNA Polymerase/genetics ; }, abstract = {Virophages are unique double-stranded DNA (dsDNA) viruses that parasitize viruses of Nucleocytoviricota (NCVs). While conventionally viewed as a viral group, growing evidence suggests that "virophage" is better understood as a parasitic lifestyle, rather than a natural group. Despite this conceptual shift, their diversity and evolution remain largely obscure and contentious. Through deep mining of protein-primed type B DNA polymerase (pPolB) in 7041 eukaryotic genomes and 12,053 metagenomes sampled globally, we expand the diversity of pPolB-carrying mavirus virophage-related elements (pMVREs), which include virophages, transpovirons, and Polinton-like viruses (PLVs). Our phylogenomic and metagenomic mining reveals the widespread distribution of pMVREs in eukaryotic genomes (97/7041, 1.38%) and global environments (2450/12053, 20.33%). pMVREs possess genome architectures of high plasticity and promiscuity. The presence of pMVREs and NCVs is statistically correlated in both eukaryotic genomes and global metagenomes, supporting a specific co-occurrence association between pMVREs and NCVs. Moreover, pMVRE diversity and composition exhibit strong heterogeneity across global ecosystems. Together, this study unveils a vast diversity of virophage-related elements and provides insights into the intricate relationship among virophages, transpovirons, PLVs, pMVREs, and NCVs.}, } @article {pmid41887858, year = {2026}, author = {Zheng, D and Li, D and Wang, J}, title = {Beyond ammonia-oxidizing bacteria-centric paradigms: Geobacter-assisted anodic anaerobic ammonia oxidation.}, journal = {Journal of environmental sciences (China)}, volume = {163}, number = {}, pages = {399-408}, doi = {10.1016/j.jes.2025.07.035}, pmid = {41887858}, issn = {1001-0742}, mesh = {*Geobacter/metabolism/physiology ; *Ammonia/metabolism ; Oxidation-Reduction ; Electrodes ; Biofilms ; Anaerobic Ammonia Oxidation ; Anaerobiosis ; }, abstract = {Anodic anaerobic ammonium oxidation (anodic anammox) presents a sustainable approach for nitrogen removal, yet its bioelectrochemical mechanisms remain unclear due to biofilm complexity and undefined roles of electroactive microorganisms (EAMs). This study reveals that nitrite (NO2[-]) is the direct product of ammonia-oxidizing bacteria (AOB)-driven anodic anammox, with extracellular electron transfer (EET) mediated by indirect mechanisms via redox shuttles. Metagenomic analysis identified two ammonia oxidation pathways: (1) a novel short-range nitrification pathway (NH4[+] → NO2[-]) governed by ncd2 genes, and (2) a traditional ammonia oxidation pathway (NH4[+] → NH2OH) facilitated by amoABC. Intriguingly, Geobacter exhibited potential NH2OH oxidation capability, bridging AOB activity and electrode respiration. Functional inhibition experiments demonstrated that EAMs-derived electron shuttles and reactive oxygen species (ROS) are critical for enhancing EET efficiency, with ROS serving as a key electron acceptor for AOB under anaerobic conditions. Spatial and metabolic synergy between EAMs and AOB-via substrate cross-feeding, cofactor provision, and electron transfer-was essential for maintaining biofilm stability. These findings challenge the conventional view of AOB-driven anodic anaerobic anammox mechanisms and provide new insights into sustainable nitrogen removal in engineered bioelectrochemical systems.}, } @article {pmid41887859, year = {2026}, author = {Chen, J and Li, G and Liu, J and Yuan, X and Zhao, G and Yang, X and Huang, S and Zheng, Z}, title = {Comparative assessment of novel nematicide trifluenfuronate and fosthiazate on soil ecosystem: From microbial community structure to KEGG functional pathways.}, journal = {Journal of environmental sciences (China)}, volume = {163}, number = {}, pages = {409-419}, doi = {10.1016/j.jes.2025.05.033}, pmid = {41887859}, issn = {1001-0742}, mesh = {*Soil Microbiology ; *Thiazolidines/toxicity ; Soil/chemistry ; *Soil Pollutants/toxicity ; Ecosystem ; *Microbiota/drug effects ; Pesticides/toxicity ; RNA, Ribosomal, 16S ; Bacteria/drug effects ; Organophosphorus Compounds ; }, abstract = {In recent years, the increasing demand for environmentally friendly pesticides in agricultural production has driven the development of novel pesticides characterized by high efficiency, low toxicity, and improved environmental compatibility. Simultaneously, greater emphasis is being placed on evaluating their impact on the soil ecosystem to ensure sustainable pesticide use and the stability of agroecosystems. In this study, we employed 16S rRNA gene high-throughput sequencing and metagenomic analysis to compare the effects of the novel nematicide trifluenfuronate and the commonly used nematicide fosthiazate on soil physicochemical properties, bacterial community structure, and metabolic functions in cucumber cultivation soils. Results showed that soil enzyme activity, microbial community structure and diversity exhibited the most significant differences on day 7 following nematicide application but stabilized by day 100. Both nematicide type and concentration were key factors influencing bacterial community structure. Compared to fosthiazate, trifluenfuronate more significantly enhanced soil bacterial community abundance while exerting fewer negative impacts on related enzyme activities and KEGG pathways. In addition, fosthiazate preferentially regulated membrane-associated efflux genes, whereas trifluenfuronate primarily interfered with the transcriptional regulation of target genes to mitigate antibiotic stress. These alterations in microbial community structure and function led to changes in soil nutrient bioavailability. This made the trifluenfuronate treatment group have higher available nitrogen and phosphorus content to supply to cucumber. This research contributes to understanding their ecological effects and paves the way for future sustainable pesticide research.}, } @article {pmid41887904, year = {2026}, author = {Jin, R and Chen, C and Zhang, J and Li, Y and Wu, Y and Wang, F and Chen, Z and Huang, T and Cheng, Q and Yu, X and Jia, P}, title = {Solid waste dumping differentially impacts soil prokaryotic, fungal, and viral communities: Insights from metagenomics.}, journal = {Journal of environmental sciences (China)}, volume = {163}, number = {}, pages = {867-879}, doi = {10.1016/j.jes.2025.10.021}, pmid = {41887904}, issn = {1001-0742}, mesh = {*Soil Microbiology ; Metagenomics ; Fungi ; *Environmental Monitoring ; *Solid Waste ; Microbiota ; *Refuse Disposal ; Soil Pollutants/analysis ; Soil/chemistry ; Viruses ; }, abstract = {Rapid urbanization and industrialization have dramatically increased global solid waste generation, placing immense pressure on waste management systems. In many developing countries, illegal and uncontrolled dumping remains widespread, yet its ecological impacts, particularly on soil microbial communities, are still poorly understood. To address this knowledge gap, we applied high-throughput amplicon sequencing and metagenomic profiling to analyze soil microbiomes across three categories of solid waste dumping. Our results show that solid waste dumping significantly altered both biotic and abiotic components of soil ecosystems. Soil properties shifted abruptly, with elevated pH and increased concentrations of pollutants such as petroleum hydrocarbons and fluorides. Microbial communities were extensively restructured, exhibiting both taxonomic turnover and functional adaptations. Viral communities displayed greater sensitivity to dumping-induced disturbances than prokaryotic or fungal communities. These findings provide new insights into soil microbiome responses to anthropogenic pollution and highlight taxon-specific adaptation strategies. To our knowledge, this is among the first comparative studies integrating prokaryotic, fungal, and viral responses to solid waste dumping using high-throughput molecular approaches. Our findings present a novel perspective that may guide future monitoring efforts and enhance approaches to environmental damage identification and assessment.}, } @article {pmid41888119, year = {2026}, author = {Rodríguez-Varela, R and Pochon, Z and Mas-Sandoval, A and Yaka, R and Fortes-Lima, CA and García Rubio, A and Márquez-Grant, N and Marí, J and Graziani, G and Ferrer Abárzuza, A and Vicente, M and Lorca-Francisco, L and Linderholm, A and Lagerholm, VK and Arauna, LR and Pérez-Ramallo, P and Krzewińska, M and Schlebusch, CM and Götherström, A}, title = {Analysis of medieval burials from Ibiza reveals genetic and pathogenic diversity during the Islamic period.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41888119}, issn = {2041-1723}, support = {2019-00849_VR//Vetenskapsrådet (Swedish Research Council)/ ; }, mesh = {Humans ; Spain ; *Islam ; *Genetic Variation ; History, Medieval ; *Mycobacterium leprae/genetics/isolation & purification/pathogenicity ; *Burial/history ; Gene Flow ; Metagenomics ; North African People ; DNA, Ancient ; }, abstract = {Ibiza, an island in present-day Spain, was conquered in 902 CE by the Umayyad Emirate of Córdoba. The island remained under Islamic rule until 1235. Here, we analyse the genetic and metagenomic profiles of 13 individuals from an Islamic cemetery in Ibiza, dated to 950-1150 CE. Genome-wide analyses reveal heterogeneity, with ancestry components from Europe, North Africa, and Sub-Saharan Africa. Our analyses estimate that North African gene flow occurred two to seven generations before these individuals lived, suggesting admixture following the Islamic conquest of Iberia and potentially on Ibiza itself. Notably, two individuals trace their Sub-Saharan origins to distinct regions, Senegambia and present-day southern Chad, providing direct evidence of trans-Saharan connections via military and slave networks documented in contemporary Arabic sources. Metagenomic analyses detect several pathogens in this community, with one individual carrying Mycobacterium leprae, offering insight into the presence of leprosy in Ibiza. Our findings align with the historically documented two-pulse demographic model, indicating an initial settlement following the early tenth-century conquest and a second influx associated with Almoravid movements in the twelfth century. These securely dated genomes offer insights into medieval population dynamics and health in the Balearics.}, } @article {pmid41888125, year = {2026}, author = {Fu, J and Zhang, J and He, R and Dong, Q and Mao, H and Shen, W and Wu, W and Chen, X and Ma, W and Zhai, Q and Chen, L and Zhou, H and Hu, S and He, Y and Qi, C}, title = {A global metagenomic atlas of aging identifies a microbiota phase transition associated with disease risk.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41888125}, issn = {2055-5008}, support = {2023A1515012538//Basic and Applied Basic Research Foundation of Guangdong Province/ ; NSFC82300623//National Natural Science Foundation of China/ ; NSFC82272391//National Natural Science Foundation of China/ ; NSFC82302610//National Natural Science Foundation of China/ ; 2019YFA0802300//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Aging ; *Metagenomics/methods ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Metagenome ; }, abstract = {Biological aging has been associated with altered risk of aging-related diseases, but the contribution of the gut microbiota to this process remains poorly understood. Here, we constructed an interpretable gut microbiota age clock using metagenomic data from 8115 fecal samples across five continents. We discovered a key microbial perturbation occurring at 56-60 years of chronological age, which was validated in an independent cohort of 2263 metagenomes. This perturbation was associated with a decline in ecological stability and substantial changes in the abundance of core species. Notably, the association between gut microbiota age and diseases was identified to be significantly altered before and after this inflection time. Moreover, within-species analyses uncovered phylogenetic divergence for seven age-related species, such as Escherichia coli, alongside functional alterations in older individuals, including enhanced cell motility, carbohydrate metabolism and horizontal gene transfer. Overall, our global gut microbiome atlas uncovers a critical age transition phase, highlighting opportunities for microbiota-based therapies and offering novel insights into evolutionary dynamics during aging.}, } @article {pmid41888178, year = {2026}, author = {Ariaeenejad, S and Abedanzadeh, S}, title = {Enhanced stability and reusability of metagenomic laccase via immobilization on functionalized mesoporous silica for antibiotic contaminant removal.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41888178}, issn = {2045-2322}, mesh = {*Laccase/chemistry/metabolism ; *Silicon Dioxide/chemistry ; *Enzymes, Immobilized/chemistry/metabolism ; *Anti-Bacterial Agents/chemistry/isolation & purification/metabolism ; Enzyme Stability ; Tetracycline/chemistry/isolation & purification ; Doxycycline/chemistry/isolation & purification ; Porosity ; Imidazoles/chemistry ; Metagenome ; *Water Pollutants, Chemical/isolation & purification/chemistry ; }, abstract = {The extensive application of tetracycline antibiotics in agriculture and medicine has led to persistent contamination of aquatic and terrestrial ecosystems, disrupting microbial communities and contributing to the spread of antibiotic resistance. Conventional treatment methods often suffer from poor efficiency, limited stability, and high environmental costs, underscoring the need for robust and sustainable alternatives. Here, we present a biocatalytic platform in which a metagenome-derived laccase (PersiLac1) is covalently immobilized onto imidazole-functionalized SBA-15 mesoporous silica to overcome the limitations of free laccase, including low stability and high leaching. Immobilization markedly enhanced thermal stability, reusability, and catalytic efficiency toward the degradation of doxycycline (DC) and tetracycline (TC). The optimized system exhibited minimal enzyme leaching (9.6% at 25 °C; 22.0% at 80 °C) and achieved removal efficiencies of 76.7 ± 2.8% for DC and 53.7 ± 2.1% for TC within 24 h. High removal performance was maintained even at elevated antibiotic concentrations (200 mg L[-1]), with 43.9% and 42.8% removal for DC and TC, respectively. The immobilized laccase retained over 83% (DC) and 73% (TC) of its initial activity after 10 consecutive reuse cycles. To the best of our knowledge, this is the first report of integrating a metagenomic laccase with an imidazole-functionalized SBA-15 support for antibiotic degradation, offering a unique combination of enhanced stability, high reusability, and environmentally relevant performance. These findings highlight the potential of this immobilization strategy as a sustainable and high-performance solution for the remediation of antibiotic contaminants in water systems.}, } @article {pmid41888223, year = {2026}, author = {Afshar Jahanshahi, D and Ariaeenejad, A and Hasannejad, A and Zabihi, MR and Ghaffari, MR and Ariaeenejad, S and Kavousi, K}, title = {MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41888223}, issn = {2045-2322}, support = {4020052//Center for International Scientific Studies & Collaborations (CISSC)/ ; }, mesh = {*Metagenome ; Metagenomics/methods ; Microbiota/genetics ; }, abstract = {Antimicrobial agents play a vital role in human and environmental health, with applications spanning medicine, food preservation, agriculture, and biotechnology. Among them, enzybiotics enzyme-based antimicrobials have emerged as powerful alternatives to conventional antibiotics due to their targeted mechanisms and lower propensity for resistance. Beyond their medical relevance, enzybiotics have emerging applications in food preservation, animal health, and agriculture, thereby broadening their industrial and environmental value. To support the discovery and characterization of these versatile biomolecules, we present the first genome-resolved metagenomic gene and protein targeted enzybiotic catalog focused on enzybiotics, derived from diverse environmental microbiomes. The Microbial Enzybiotic Gene and Protein Catalog (MiGPC), integrates 15 whole-metagenome datasets from oceans, soils, fecal samples, vegetation, and plastic-contaminated environments, capturing a wide ecological spectrum. Enzybiotic sequences were compiled through a hybrid strategy combining public database mining and manual literature curation, yielding over 136,000 enzybiotic sequences, 7654 metagenome-assembled genomes (MAGs), and ~ 100 million unique genes and proteins. MiGPC integrates taxonomic and enzybiotic gene profiles, offering a robust platform for the discovery, annotation, and ecological mapping of antimicrobial enzymes. Functional analyses using KEGG and eggNOG revealed that approximately 62% of the genes remained uncharacterized, highlighting a rich source of potentially novel functions. Glycoside hydrolases and glycosyl transferases were the most prevalent CAZyme families, while the dominant enzybiotic-producing taxa belonged primarily to the Pseudomonadota and Bacillota phyla. Statistical modeling uncovered two major ecological clusters that distinguished polluted from relatively pristine environments. MiGPC enables high-throughput screening of previously unexplored metagenomes, facilitating the identification of novel antimicrobial agents from under characterized ecosystems. Overall, MiGPC represents a landmark resource that will support multi-omics research, microbial ecology, and the development of next-generation biotechnological solutions based on enzybiotics.}, } @article {pmid41888360, year = {2026}, author = {Belay, G and Suarez, C and Simachew, A and Paul, CJ}, title = {Microorganisms and functional genes in an aerobic-anoxic integrated gold mine wastewater treatment system.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41888360}, issn = {1573-0972}, abstract = {Biological treatment of cyanide-contaminated wastewater is mediated by microbial consortia in which different organisms perform distinct, functionally specialized roles. This study investigated microbial communities involved in gold mine wastewater treatment with integrated aerobic-anoxic reactors seeded with consortia from an alkaline soda lake, Lake Chitu. Whole-genome sequencing of isolates (WGS) and metagenomic sequencing of the bioreactor were performed to characterize the consortia, resulting in the identification of 23 non-redundant genomes, comprising 14 whole-genome sequencing isolates and 19 metagenome-assembled genomes (MAGs). Most isolated genomes were similar to the recovered metagenomes of MAGs. Except for Alkalibacterium, all isolates possessed one or more genes potentially involved in cyanide or cyanate transformation, along with at least one type of terminal oxygenase; however, the gene encoding cynD, which is required for the direct hydrolysis of free cyanide (CN[-]), was not detected. Three representative Halomonas isolates harboured the nitrate reductase narGHI, nitrite reductase nirS, nitric oxide reductase norB/norC, and nitrous-oxide reductase nosZ genes for full denitrification. All of the isolates possessed several gene clusters associated with different heavy metal resistances. This study suggests that the microbial inoculum sourced from Lake Chitu harbors diverse microorganisms possessing genes potentially involved in cyanide-related metabolic pathways. The findings of this study add to our understanding of the alkaliphilic microbial population that degrades cyanide and cyanide intermediates and provide insight into how these organisms break down cyanide and resist cyanide and heavy metal inhibitory effects.}, } @article {pmid41888867, year = {2026}, author = {Tao, M and Fan, Y and Qian, L and Liu, H and Ming, Y and Yu, X and Wu, K and Niu, M and Yan, Q and Huang, X and He, Z}, title = {Microbially driven methane and sulfur cycling processes and coupling mechanisms in mangrove sediments.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41888867}, issn = {2524-6372}, support = {2021M703751//China Postdoctoral Science Foundation/ ; SML2023SP205, SML2024SP002, SML2024SP022//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42430707, 52070196, 32370113 and 92251306//National Natural Science Foundation of China/ ; 2024A1515010931//Guangdong Basic and Applied Basic Research Foundation/ ; }, abstract = {BACKGROUND: Methane (CH4) as a powerful greenhouse gas is the second largest contributor to global climate warming. Mangrove sediments are an important natural source of biogenic CH4 with rich organic carbon (C) and diverse sulfur (S) compounds, ideally for studying CH4 and S cycling processes and coupling mechanisms. Here we sampled mangrove sediment cores and analyzed their key microbial groups, key environmental factors and possible coupling mechanisms for CH4 and S cycling by metagenome sequencing approaches.

RESULTS: Our results showed that Methanomicrobiales and Methanophagales were predominant methanogens, Methanospirareceae was a representative of anaerobic methanotrophic archaea (ANME), and Desulfobacteraceae and Desulfobulbaceae were abundant sulfate-reducing bacteria (SRB), while Ectothiorhodospiraceae, Chromatiaceae and Comamonadaceae were dominant S-oxidizers. Correlation network analysis revealed positive interactions among methanogens, ANME and SRB. Also, metagenome-assembled genome (MAG) analysis indicated interspecies hydrogen transfer and extracellular electron exchange via conductive pili, flagella, and cytochromes were potential coupling mechanisms between methanogens and SRB. ANME could form consortia with SRB by intermediate metabolites (e.g., acetate) and/or direct interspecies electron transfer (e.g., flagella, pili, cytochromes). Furthermore, methanogen MAGs encoded thiosulfate oxidation and partial sulfate reduction pathways, while the ANME MAGs possessed potentials for S disproportionation and incomplete sulfate reduction. Additionally, SO4[2-], total sulfur, moisture content and salinity were important environmental factors affecting the microbial community structure and gene families involved in CH4 and S cycling.

CONCLUSION: This study provides novel insights into coupling mechanisms of CH4 and S cycling processes in mangrove sediments, having important implications for mitigating global warming.}, } @article {pmid41888912, year = {2026}, author = {Krull, J and Sidhu, C and Solanki, V and Bligh, M and Rößler, L and Singh, RK and Huang, G and Robb, CS and Teeling, H and Seeberger, PH and Schweder, T and Crawford, CJ and Hehemann, JH}, title = {Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41888912}, issn = {2049-2618}, support = {101029842//MSCA/ ; Project number 570219261//Deutsche Forschungsgemeinschaft/ ; HE 7217/5-1//DFG/ ; 101044738//ERC/ ; }, mesh = {*Diatoms/metabolism/chemistry ; *Mannans/metabolism/chemistry ; *Microbiota ; Oceans and Seas ; *Seawater/microbiology ; Sulfates/metabolism/chemistry ; Metagenome ; Metagenomics ; Bacteria/genetics/classification/metabolism ; }, abstract = {BACKGROUND: Diatoms, a keystone phylum in Earth's ecosystems, are responsible for substantial oxygen production and the fixation of carbon dioxide in the form of carbohydrates that fuel global food webs. They host diverse prokaryotes, yet how diatoms preferentially recruit those with complementary metabolic traits remains unknown.

RESULTS: We discovered that diatoms exude a C6-sulfated α-1,3-mannan that serves as a selective carbon source for adapted Polaribacter. Its structure was resolved using NMR spectroscopy, chromatography, chemical synthesis, and enzymatic dissection. Biochemical, physiological, and structural analyses demonstrated, that specialized Bacteroidota employ a four-enzyme pathway to metabolize this glycan. Metagenomic and transcriptomic data revealed that sulfated mannan utilization loci are globally abundant and actively expressed in surface ocean bacterioplankton. Because this mannan provides only carbon, oxygen, sulfur, and hydrogen, bacteria must obtain other essential elements elsewhere, reinforcing metabolic interdependence.

CONCLUSIONS: Together, these results define a chemically specific interaction between diatoms and specialized bacteria that is mediated by a single sulfated polysaccharide and a dedicated four-enzyme degradation pathway. Presence of this pathway in marine metagenomes and transcriptomes indicates that a sulfated mannan from diatoms exerts selection pressure in the sunlit ocean microbiome. Video Abstract.}, } @article {pmid41889037, year = {2026}, author = {Muddiman, KJ and Doble, A and Stephen, AS and Bescos, R and Illsley, CS and Nicholas, TL and Hanks, S and Toit, LD and Brookes, ZLS}, title = {A Pilot Study Assessing the Oral Microbiome in Women of Menopausal Age: Do Oral Nitrate-Reducing Bacteria Play a Role?.}, journal = {International dental journal}, volume = {76}, number = {3}, pages = {109518}, pmid = {41889037}, issn = {1875-595X}, mesh = {Humans ; Female ; Pilot Projects ; Middle Aged ; *Microbiota/physiology ; Aged ; Adult ; *Menopause ; Saliva/microbiology/chemistry ; *Mouth/microbiology ; Aged, 80 and over ; *Nitrates/metabolism ; Cross-Sectional Studies ; Retrospective Studies ; Young Adult ; Adolescent ; *Bacteria/metabolism ; Estradiol/analysis/metabolism ; Nitrites/metabolism ; }, abstract = {INTRODUCTION: The links between oral health and female ageing are poorly understood, but many changes occur in the oral cavity of menopausal women that affect quality of life, and few current oral health interventions consider gender as part of their approach. The aim of this pilot study was to test the hypothesis that the oral microbiome and microenvironment change during female ageing and are thus worthy of further consideration both experimentally and clinically.

METHODS: This observational pilot study retrospectively assessed women aged 18 to 89 years (n = 60) attending a UK primary care dental school facility for blood pressure screening, further analysing the salivary oral microbiome using metagenomics and the biochemical microenvironment using high-performance liquid chromatography. Periodontal health screening (Basic Periodontal Examination [BPE]) was then conducted as part of routine clinical care.

RESULTS: The cross-sectional design classified women into <32 years (n = 18), 40 to 49 years (n = 10), 50 to 59 years (n = 20), and 60+ years (n = 12), but the differences in salivary oestradiol levels between groups were inconclusive. Small numbers were not enough to detect differences in oral microbiome abundance, but nitrate-reducing species (P < .05), nitrate-nitrite-reducing activity (P < .05), and buffering capacity all increased as women aged 60+ years (P < .01), warranting increased numbers. Ageing women also had higher blood pressure (P > .05), were more likely to have periodontal pockets >5.5 mm (BPE4), and had an increased abundance of Porphyromonas (P < .05), but a full periodontal assessment is needed.

CONCLUSIONS: These observations suggest that the composition of the oral microbiome changes as women age, and thus, prospective and longitudinal oral microbiome studies with larger numbers are needed, including concurrent full periodontal assessment, plasma hormonal levels, and salivary flow. However, this study suggests that the oral microbiome in older women may require special consideration, with an increased focus on tailored oral hygiene interventions for this group.}, } @article {pmid41889316, year = {2026}, author = {Niyazi, HA and Niyazi, HA and AbdulMajed, H and Juma, N and Helmi, N and Alqarni, M and Saleh, BH and Zubair, M and Alfadil, A and Alhazmi, W and Alharbi, OS and Halabi, WS and Altalhi, R and Moglad, E and Alharbi, MT and Gazzaz, M and Alharthi, TM and Altayb, HN and Ibrahem, K}, title = {Pan-genome analysis and phylogenetic characterization of Klebsiella pneumoniae from global isolates.}, journal = {Future microbiology}, volume = {21}, number = {8}, pages = {701-712}, doi = {10.1080/17460913.2026.2617118}, pmid = {41889316}, issn = {1746-0921}, mesh = {*Klebsiella pneumoniae/genetics/classification/isolation & purification/drug effects ; *Phylogeny ; *Genome, Bacterial ; Genetic Variation ; *Klebsiella Infections/microbiology/epidemiology ; Anti-Bacterial Agents/pharmacology ; Humans ; Evolution, Molecular ; Genomics ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {AIMS: This study aimed to investigate the global genetic diversity, evolutionary relationships, and antimicrobial resistance (AMR) profiles of Klebsiella pneumoniae by performing a comprehensive pan-genome and phylogenetic analysis across worldwide isolates.

MATERIALS AND METHODS: A total of 72,057 K. pneumoniae genomes were retrieved from the NCBI database, from which 91 high-quality representative genomes each from a unique country were selected based on completeness, metadata availability, and sequence quality. Genomic assemblies were assessed using QUAST, annotated with PROKKA, and analyzed for pan-genomic composition and phylogenetic relatedness using standard bioinformatics pipelines.

RESULTS: The pan-genome revealed a large accessory component, reflecting extensive genomic plasticity and adaptability. QUAST analysis indicated significant variability in genome size and contig number, while PROKKA annotation identified diverse coding sequences, tRNA, rRNA, and AMR genes. Phylogenetic clustering demonstrated both geographically localized and globally disseminated lineages, suggesting regional adaptation and intercontinental transmission.

CONCLUSIONS: This study provides a global perspective on the genomic diversity and evolutionary patterns of K. pneumoniae. The widespread presence of AMR determinants underscores the urgent need for continuous genomic surveillance and integration of metagenomic approaches to improve monitoring, infection control, and therapeutic strategies against multidrug-resistant strains.}, } @article {pmid41889516, year = {2026}, author = {Mao, J and Jin, Q and Ye, D and Yang, Y}, title = {Case Report: A rare presentation of pulmonary tuberculosis with extensive ground-glass opacities in an immunocompetent patient: lessons from metagenomic next-generation sequencing.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1696371}, pmid = {41889516}, issn = {2296-858X}, abstract = {Pulmonary tuberculosis (PTB) is typically diagnosed through sputum smear microscopy and culture. However, diagnosis is challenging in patients with atypical radiological features and negative conventional tests. Ground-glass opacities (GGOs) are common but non-specific computed tomography (CT) findings and are rarely observed in immunocompetent PTB patients. We report the first case of an immunocompetent 53-year-old female presenting with extensive bilateral GGOs without classic clinical symptoms. Conventional microbiological cultures, acid-fast staining, and serological assays were all negative. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified Mycobacterium tuberculosis, further supported by a positive T-spot TB assay. Standard anti-tuberculosis therapy led to complete resolution of GGOs over nine months, confirmed by follow-up CT imaging. This case underscores the diagnostic challenge of atypical PTB presenting with non-classical CT manifestations in an immunocompetent host. It highlights the decisive role of mNGS as a complementary tool in cases where conventional methods fail, enabling timely diagnosis, precise treatment, and improved patient outcomes.}, } @article {pmid41889550, year = {2026}, author = {Xiu, Q and He, H and Liu, Z and Ou, X and Meng, Y and Zhao, K and Yang, Q and Zhang, X and Hou, Y and Yao, S and Gao, P and Xia, W}, title = {Biosurfactant-driven desorption and remediation of heavy oil contaminated soils underpinned by molecular simulations and microbial dynamics.}, journal = {RSC advances}, volume = {16}, number = {18}, pages = {16316-16328}, pmid = {41889550}, issn = {2046-2069}, abstract = {This study integrates molecular dynamics simulations and bench-scale experiments to investigate the adsorption and desorption behaviors of heavy oil on five mineral substrates: SiO2, kaolinite, muscovite, and Ca[2+]-/Na[+]-montmorillonite. Adsorption followed Langmuir isotherms, with montmorillonite exhibiting the highest capacities (0.061-0.062 molecules per Å[2] for aromatics in simulations; 0.086-0.091 g g[-1] in bench-scale tests) and SiO2 the lowest (0.027 pcs per Å[2]; 0.013 g g[-1]). Among four biosurfactants evaluated-rhamnolipid, sophorolipid, trehalose lipid, and mannosylerythritol lipid-sophorolipid consistently achieved the greatest desorption efficiency, removing up to 99.63% of adsorbed oil from Na[+]-montmorillonite and 96.04% from field-contaminated soil. 16S rRNA and metagenomic sequencing revealed an increased abundance of hydrocarbon-degrading bacteria within the soil microbial community, highlighting a synergistic effect between biosurfactant-induced desorption and biodegradation. These findings underscore the critical roles of mineralogical properties, oil fraction characteristics, and biosurfactant selection in soil washing treatment. This work presents a viable and eco-friendly strategy for remediating crude oil-contaminated soils, with important implications for optimizing large-scale environmental restoration efforts.}, } @article {pmid41889698, year = {2026}, author = {Almatrafi, R and Alasiri, A and Almuneef, G and Al-Hazzani, AA and Alghoribi, MF and Hakami, M and Arafah, AM and Alotibi, RS and Alrabiah, S and Alqurainy, N and Ajina, R and Aldriwesh, MG}, title = {First metagenomic analysis of age-associated changes in the gut microbiome among healthy Saudi adults: SAMS pilot study.}, journal = {Frontiers in aging}, volume = {7}, number = {}, pages = {1733638}, pmid = {41889698}, issn = {2673-6217}, abstract = {INTRODUCTION: The gut microbiome undergoes dynamic changes with aging across diverse healthy populations. However, data from Saudi Arabia remain limited. This pilot study investigated age-related variations in the gut microbiome among healthy Saudi adults to characterize region-specific microbial signatures and identify taxa potentially associated with aging in a healthy population.

METHODS: We established the Saudi Aging and Microbiome Study (SAMS) to investigate age-related changes in fecal microbiome of Saudi adults. In this pilot phase, 145 healthy participants aged 19-69 years were enrolled. Shotgun metagenomic sequencing was performed to profile fecal microbiome at the species level. Microbial diversity and taxonomic composition were compared across five age groups. Spearman and confounder-adjusted partial Spearman correlation were applied to identify taxa significantly associated with chronological age.

RESULTS: We analyzed fecal microbiome of 145 healthy adults distributed among five age groups: G1 (19-29 years, n = 33; 22.7%), G2 (30-39 years, n = 30; 20.7%), G3 (40-49 years, n = 27; 18.6%), G4 (50-59 years, n = 31; 21.4%), and G5 (60-69 years, n = 24; 16.6%). Of these, 75 (51.7%) were male, and 70 (48.3%) were female. Alpha diversity increased from young to older adulthood for observed richness and Shannon indexes (all q < 0.05). Beta diversity also varied significantly with age (PERMANOVA R [2] = 0.13, q = 0.023), indicating distinct microbial community structures in healthy older adults. At the phylum level, Firmicutes significantly increased with age (FC = 1.35; q = 0.026), whereas Bacteroidota decreased (FC = 0.59; q = 0.01). Consistent with these trends, Blautia obeum showed positive correlations, while Bacteroides thetaiotaomicron and Phocaeicola vulgatus showed negative correlations with chronological age.

CONCLUSION: In healthy Saudi adults, increasing age was associated with higher microbial diversity and compositional shifts at phylum and species levels. These age-associated microbial taxa might represent biomarkers of healthy aging and suggest an enhanced community capacity for short-chain fatty acids (SCFAs) production, a hypothesis warranting validation through future functional analyses.}, } @article {pmid41889817, year = {2026}, author = {Lu, T and Dietz, ZK and Ericsson, AC and Picking, WD and Picking, WL}, title = {Eco-tank Housing Maintains Wild-Type Microbiota and Rewilds the Laboratory Mouse Gut Microbiome to Restore Natural Immune Tone.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41889817}, issn = {2692-8205}, abstract = {Laboratory mice housed under individually ventilated cage (IVC) conditions harbor simplified gut microbiota and immune phenotypes that diverge substantially from those shaped by environmental exposure, limiting translational relevance. To reintroduce controlled ecological complexity while maintaining biosafety and reproducibility, we developed the Eco-tank, a pathogen-monitored semi-natural housing system incorporating environmental substrates and dietary diversity. Longitudinal 16S rRNA sequencing revealed that even wild-caught Mus musculus rapidly lose microbial richness and predicted metabolic breadth under IVC housing. Eco-tank conditions stabilized diversity and preserved elements of wild-associated community structure during extended captivity. In parallel, standardized C57BL/6 mice housed in Eco-tanks underwent rewilding-like restructuring, with increased richness and community shifts toward a wild-associated configuration. Functional inference analyses indicated expansion of predicted pathways linked to short-chain fatty acid production, amino acid metabolism, and environmental substrate utilization. Eco-tank housing enhanced baseline resistance to pulmonary Pseudomonas aeruginosa (Pa) infection without compromising vaccine-induced protection, indicating that restoration of environmental microbial signals does not impair adaptive immunity. Together, these findings identify housing ecology as a dominant determinant of microbiome structure and functional potential. The Eco-tank provides a scalable and tractable framework for integrating environmental microbial complexity into laboratory models to better align preclinical immunology with ecologically conditioned immune systems.}, } @article {pmid41889866, year = {2026}, author = {Van Camp, AG and Park, J and Ozcelik, E and Eskiocak, O and Ozler, KA and Papciak, K and Subhash, S and Alwaseem, H and Ergin, I and Chung, C and Shah, V and Yueh, B and Alici, A and Fein, MR and Durmaz, C and Mozsary, C and Kilic, E and Damle, N and Najjar, D and Nelson, TM and Ryon, KA and Butler, DJ and Patel, CJ and Thaiss, CA and Birsoy, K and Mason, CE and Meydan, C and Tierney, BT and Beyaz, S}, title = {Diverse high-fat diets drive multi-omic reprogramming that persists after dietary reversal.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41889866}, issn = {2692-8205}, abstract = {Dietary fat composition modulates host physiology and the gut microbiome, but the long-term effects of specific fat sources and the extent to which these changes resolve after dietary reversal remain incompletely defined. Here, we present a longitudinal multi-omic resource of mice maintained for one year on a purified control diet, seven high-fat diets differing in predominant fat source, or reversal regimens in which animals were switched from high-fat to control diet after 4 or 9 months. We further incorporated two cohorts with distinct pre-existing microbiome configurations to determine how baseline community structure shapes diet-induced remodeling of the gut microbiome ecosystem. By integrating longitudinal phenotyping, fecal metagenomics, fecal metabolomics, plasma metabolomics and lipidomics, and intestinal single-cell RNA sequencing, we defined the shared and dietary fat-specific responses across host and microbiome compartments. Baseline microbiome composition strongly influenced microbial responses to diet, indicating that pre-existing community structure is a major determinant of dietary ecosystem remodeling. Although many altered features shifted toward baseline after dietary reversal, only approximately half of diet-associated microbial changes recovered within the study window. A subset of taxa exhibited persistent alterations, including sustained depletion of Lactobacillus johnsonii and Bifidobacterium pseudolongum and sustained enrichment of Alistipes finegoldii, consistent with a "microbiome memory" of prior high-fat diet exposure. This memory effect is mirrored in the host, by sustained suppression of major histocompatibility complex class II (MHC-II) gene expression in intestinal epithelial cells after dietary reversal. These findings indicate that dietary fats leave a lasting imprint on the host-microbiome interactome that survives dietary intervention. Together, these data establish a resource for defining how dietary fat source, baseline microbiome composition, and dietary history shape host-microbiome states. The entire resource is available online as an RShiny app.}, } @article {pmid41890171, year = {2026}, author = {Zhao, S and Sai, Y and Jia, M and Qiao, Y and Guo, W and Ding, W and Shao, X and Zheng, Y}, title = {Comprehensive insights into the mechanism of flavor formation in Cheonggukjang: Integration of metagenomics, volatomics, and metabolomics.}, journal = {Food chemistry: X}, volume = {35}, number = {}, pages = {103756}, pmid = {41890171}, issn = {2590-1575}, abstract = {Microbial metabolism shapes the unique flavor profile of Cheonggukjang; however, the formation pathways of characteristic flavor compounds mediated by microbiota remain unclear, hindering precise quality control. To fill this gap, this study innovatively integrated metagenoics, volatilomics, and metabolomics to systematically decode the flavor formation mechanism during Cheonggukjang fermentation. Volatile compound analysis defined three fermentation stages for Cheonggukjang (0-18, 18-60, and 60-72 h), identifying the 60-72 h period as the most critical for flavor formation. A total of 15 key flavor compounds were identified, with 10 designated stage-specific flavor markers. LefSe analysis revealed that Bacillus subtilis, Bacillus velezensis, Caldibacillus thermoamylovorans, and Bacillus licheniformis were the key biomarkers across different fermentation stages, while redundancy analysis (RDA) indicated that total sugar as the key driver of microbial succession. Additionally, this study reconstructed the metabolic network responsible for characteristic flavor formation and identified C. thermoamylovorans, B. licheniformis, B. velezensis, B. subtilis, Bacillus paralicheniformis, and Caldibacillus hisashii as core functional microbiota modulating amino acid metabolic to drive flavor development. This study lays a theoretical framework for standardizing Cheonggukjang production and targeted regulating its flavor quality.}, } @article {pmid41890980, year = {2026}, author = {Shi, Y and Sanderson, H and Chuan, J and Khan, IUH and Sunohara, M and Craiovan, E and Lapen, DR and Diarra, M and Chen, W}, title = {Dual-platform metagenomic surveillance distinguishes pathogen and resistome hotspots across agricultural and mixed-use watersheds.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101384}, pmid = {41890980}, issn = {2352-7714}, abstract = {Freshwater systems embedded in agricultural landscapes serve as dynamic reservoirs and conduits for fecal-associated microbes, zoonotic pathogens, and antimicrobial resistance (ARG) and virulence factor (VF) genes. Yet factors that govern their densities and diversity remain a research challenge. From 2016 to 2021, we conducted a longitudinal water surveillance in an agriculturally dominated river basin in eastern Ontario, Canada; characterizing fecal-associated bacterial communities using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Agricultural drainage ditches consistently harbored higher fecal-associated bacterial diversity with pronounced seasonal shifts; i.e., higher levels during larger flow periods in spring and fall. Elevated discharge was associated with enrichment of genera containing zoonotic or opportunistic pathogens, such as those in Pseudomonas, Sphingomonas, and Massilia. Conditionally rare taxa (CRTs), although typically low in abundance, accounted for ∼12.6% of all pathogen-associated genera and disproportionately contributed to community turnover, highlighting their role as transient reservoirs of microbial risk. Shotgun metagenomics detected 27 ARGs, primarily at mixed-use sites, and 14 VFs, mainly in agricultural ditches. Clinically relevant β-lactamase genes (e.g., oxa, imp, sme) co-occurred with metal-resistance operons, a pattern suggestive of possible co-selection, although selective agents were not directly measured. Although the prevalence of ARG and VF was low (<5% of samples), their ecological context indicates potential transmission pathways. Limited overlap in ARGs between short-read and metagenome-assembled genome (MAG)-based profiling reflects their complementary strength: gene-level sensitivity versus host-resolved analysis. Together, these findings demonstrate the utility of integrated amplicon and shotgun metagenomic surveillance for proactive One Health risk assessment in agricultural watersheds.}, } @article {pmid41891006, year = {2026}, author = {Mills, EG and Evans, KM and Dorazio, AJ and Squires, KM and Sundermann, AJ and Stellfox, ME and Culyba, MJ and Shields, RK and Van Tyne, D}, title = {Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant Enterococcus faecium.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41891006}, abstract = {Colonization of the gastrointestinal (GI) tract by vancomycin-resistant Enterococcus faecium (VREfm) often precedes bloodstream infection and serves as a reservoir for onward patient transmission in healthcare settings. Routine clonal isolate-based sequencing often underestimates within-patient diversity, and can miss transmission involving low-abundance and co-colonizing strains. Here we applied culture-enriched metagenomic sequencing to matched GI tract and blood VREfm populations collected ≤14 days apart from 35 patients with positive VREfm blood cultures collected between 2020 and 2025 at a single hospital. GI populations exhibited greater within-patient diversity than bloodstream populations, including multi-strain colonization in five patients. Among single-strain populations, variant analysis suggested distinct environment-specific pressures between the GI tract and bloodstream environments. To assess transmission using culture-enriched metagenomic sequencing, we compared all 70 VREfm populations against 470 contemporary clinical VREfm isolate genomes collected from the same hospital and identified 19 putative transmission clusters, including six clusters involving multi-strain populations. Together, these results demonstrate how culture-enriched metagenomic sequencing improves resolution for assessing within-patient VREfm diversity and enhances the detection of transmission events that could be missed by clonal isolate-based surveillance.}, } @article {pmid41891018, year = {2026}, author = {Basso, M and Hildebrand, F and Winder, C and Baker, DJ and Manders, R and Barberis, M and Gibbons, SM and Cohen Kadosh, K}, title = {Anxiety associated with dietary intake and gut microbiome features in a cross-sectional cohort of sub-clinically anxious young women.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41891018}, abstract = {BACKGROUND: Emerging evidence highlights the gut-brain axis as a key pathway linking diet and anxiety, yet the key determinants remain unclear. Most studies have focused on single components of diet and rarely integrate long- and short-term intake. Furthermore, prior gut-brain work has focused on microbiome composition, while functional features remain underexplored. In this study, we investigated associations between long- and short-term dietary intake, gut microbiome composition and functions, and anxiety in a subclinical cohort of 46 females (18-24 years) from the United Kingdom.

RESULTS: Long-term diet quality was assessed using the Healthy Eating Index (HEI-2020) derived from a food frequency questionnaire, stratifying participants into lower and higher diet quality clusters. Short-term dietary intake was assessed via 24-hour recalls. Shotgun metagenomics of stool samples was used to assess differences in α and β diversity indices, species abundances, and bacterial pathways putatively metabolizing gut-brain-axis relevant molecules. Anxiety was measured using the State-Trait Anxiety Inventory (state subscale - STAI-s). Regression models identified diet quality (HEI cluster) as the primary dietary feature of anxiety variation. The presence of Ruminococcus B gnavus and Flavonifractor plautii, and the abundances of Bilophila wadsworthia and Bacteroides thetaiotaomicron were positively associated with anxiety. The presence of Feacalibacterium prausnitzii and greater abundances of butyrate, propionate, and GABA synthesis pathways were inversely associated with anxiety. Non-linear models revealed a U-shaped relationship between inositol synthesis and STAI-s. Finally, we found that habitual diet quality may modulate anxiety-related responses to short-term dietary variation.

CONCLUSIONS: These findings reveal widespread links between long-term diet quality, microbiota composition and function, and anxiety symptoms. These results point towards several promising targets for prebiotic, probiotic, postbiotic, and dietary interventions targets aimed at reducing anxiety.}, } @article {pmid41891399, year = {2026}, author = {Elsheikh, M and Ibrahim, MA and Fares, S and Bhongade, M and Adhem, K and Ramirez-Morales, XI and Kaseb, AO and Petrosino, J and Hassan, MM and Jalal, PK}, title = {Influence of Gut Microbiota on Response to Immune Check Point Inhibitors in MASLD Patients With HCC: Unraveling the Connection.}, journal = {Cancer medicine}, volume = {15}, number = {4}, pages = {e71738}, pmid = {41891399}, issn = {2045-7634}, support = {R21CA293626/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Carcinoma, Hepatocellular/drug therapy/immunology/microbiology/complications ; *Liver Neoplasms/drug therapy/microbiology/immunology/complications ; *Gastrointestinal Microbiome/immunology/drug effects ; Fecal Microbiota Transplantation ; Dysbiosis/immunology/microbiology ; *Liver Diseases/microbiology ; }, abstract = {Immune checkpoint inhibitors (ICIs) have emerged as a promising treatment for various cancers, including advanced hepatocellular carcinoma (HCC). However, a significant proportion of patients with HCC, particularly those with metabolic dysfunction-associated liver disease (MASLD), exhibit resistance to ICI therapy. Studies have revealed that the presence of specific gut bacteria, such as Akkermansia, Bifidobacterium, and Lachnoclostridium, is associated with improved outcomes with ICI-treated HCC patients. Conversely, the overgrowth of bacteria like Enterobacteriaceae is linked to resistance to therapy. This review investigates the role of gut microbiota in shaping immune checkpoint inhibitor responses in MASLD-related hepatocellular carcinoma, focusing on how dysbiosis may contribute to ICI resistance and exploring microbiome modulation strategies, such as fecal microbiota transplantation and probiotics, aiming to optimize therapeutic outcomes.}, } @article {pmid41891696, year = {2026}, author = {Toth, CRA and Molenda, O and Nesbø, CL and Luo, F and Devine, CE and Chen, X and Wu, K and Xiao, JZ and Puri, R and Guo, S and Bawa, N and Wang, P-H and Wei, Y and Flick, R and Edwards, EA}, title = {Identification of a highly expressed gene cluster likely coding for benzene activation enzymes in a methanogenic enrichment culture.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {4}, pages = {e0208325}, pmid = {41891696}, issn = {1098-5336}, support = {OGI-102 and OGI-173//Genome Canada/ ; OGI-102 and OGI-173//Ontario Genomics/ ; OGI-102 and OGI-173//Ministry of Colleges and Universities/ ; Post Doctoral to CT//Mitacs/ ; OGI-102 and OGI-173//Federated Cooperatives Limited/ ; OGI-102 and OGI-173//Imperial Oil Resources (Imperial Oil Resources Ltd.)/ ; }, mesh = {*Benzene/metabolism ; *Multigene Family ; *Deltaproteobacteria/genetics/metabolism/enzymology ; *Bacterial Proteins/genetics/metabolism ; *Methane/metabolism ; Biodegradation, Environmental ; Metagenome ; Phylogeny ; }, abstract = {UNLABELLED: The oil refinery (OR) consortium is a model methanogenic enrichment culture used to study anaerobic benzene degradation. Over half of the culture's bacterial community consists of two closely related Desulfobacterota strains, designated ORM2a and ORM2b, whose mechanisms of benzene activation are unknown. Three proteomics data sets were integrated and analyzed using high-quality OR metagenomes and metagenome-assembled genomes (MAGs), including a complete circularized ORM2a MAG, to identify active metabolic pathways and proteins expressed during methanogenic benzene degradation. Among the proteins identified were Bam-like subunits of an ATP-independent benzoyl-CoA degradation pathway, as well as downstream β-oxidation proteins yielding acetate. The most abundant proteins identified mapped to two ORM2a gene clusters of unknown function. Homologous and syntenic gene clusters were identified in the MAGs of ORM2b and a sulfate-reducing Pelotomaculum that also degrades benzene, as well as in nine contigs assembled from hydrothermal vent metagenomes. Extensive homology and structural predictions suggest that the first cluster-termed the "Magic" gene cluster-encodes for enzymes catalyzing the chemically challenging activation of benzene and subsequent transformation steps yielding benzoyl-CoA. The second ("Nanopod") gene cluster encodes a transmembrane complex that may facilitate benzene transport across the cell membrane. Phylogenomic analyses place ORM2a and ORM2b within a novel genus of strict anaerobes specialized for benzene degradation, which we propose naming "Candidatus Anaerobenzenivorax."

IMPORTANCE: Benzene is a widespread, persistent, and toxic pollutant that can accumulate in anoxic environments such as groundwater and sediments. Benzene can be metabolized in the absence of oxygen; however, despite decades of research, the biochemical mechanisms for benzene activation under anaerobic conditions remain unproven. This study provides strong genetic and proteomic evidence for a new suite of enzymes that initiate anaerobic benzene activation. These findings lay a foundation for future biochemical studies and expand our understanding of how microbes carry out difficult chemical reactions in the absence of oxygen.}, } @article {pmid41891698, year = {2026}, author = {Li, Y and Ji, M and Tu, Q}, title = {Patterns and drivers of macro- and micro-diversity of mudflat intertidal archaeomes along the Chinese coasts.}, journal = {mSystems}, volume = {11}, number = {4}, pages = {e0143425}, pmid = {41891698}, issn = {2379-5077}, support = {32371598, 31971446, 92051110//National Natural Science Foundation of China/ ; 2020YFA0607600//National Key Research and Development Program of China/ ; }, mesh = {*Biodiversity ; Seashore ; *Archaea/genetics/classification ; Phylogeny ; China ; Ecosystem ; Genetic Variation ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Archaea are widespread in Earth's ecosystems, contributing to ecosystem multifunctioning and stability. Compared to bacteria, our understanding of the biodiversity and underlying drivers of archaeal communities in representative ecosystems remains much less tapped. In this study, the macro- and micro-diversity of mudflat intertidal archaeomes were comprehensively analyzed at a large geographic scale, aiming to resolve the ecological drivers determining the variations in archaeal biodiversity. The compositions of mudflat intertidal archaeal taxa highly varied, especially the dominant Thaumarcheota and Euryarchaeota, but maintained relatively stable functional potential across space, demonstrating that functional traits were selected by the ecosystem in priority. While archaeal communities carried important functional traits mediating various biogeochemical cycling processes, horizontal gene transfer played critical roles in endowing functional genes for many archaeal lineages, such as the citric acid cycle in Methanosarcinia and various amino acid metabolism genes in Thermoplasmata. Spatial scaling, including latitudinal diversity gradient and distance-decay patterns (DDR), was clearly observed for archaeal taxonomic groups, but only DDR was weakly observed for functional traits. Intra-population genetic variations were significantly and positively associated with community macro-diversity, demonstrating covariations between nucleotide-level micro- and community-level macro-diversity. The compositions of intertidal archaeomes were mainly structured by homogeneous selection, with different phylogenetic bins being shaped by distinct ecological processes and remarkable variations across different sites. The study contributes to a comprehensive insight into the mechanisms shaping archaeal diversity and ecological characteristics within a fluctuating ecosystem.IMPORTANCEThe dynamic intertidal mudflat ecosystems host intense biogeochemical activities mediated by microbial communities, among which archaea contribute as an essential component but remain much less understood compared to bacteria. To gain better insights into the diversity, functional potential, and ecological drivers of archaeal communities in intertidal mudflats, archaeal phylogenetic signatures and genomic sequences were recovered via amplicon sequencing of 16S rRNA genes and shotgun metagenomes, targeting both macro- and micro-diversity. The results showed that archaeal taxonomic composition highly varied across space, whereas the functional potential remained relatively stable. Horizontal gene transfer served as an important source of archaeal metabolic diversity, obtaining additional genes linked to key biochemical pathways. The dominance of environmental selection further demonstrated the ecological forces governing archaeal communities in highly variable coastal habitats. This study established a large-scale framework for understanding the microbial ecology of intertidal archaeomes in dynamic coastal ecosystems.}, } @article {pmid41892210, year = {2026}, author = {Liang, X and Li, X and Mi, N and Wu, Y and Wu, J and Chen, H and Liu, D}, title = {Early-Life Diarrhea Disrupts Antioxidant-Immune Homeostasis and Gut Microbiota in Suckling Calves.}, journal = {Biology}, volume = {15}, number = {6}, pages = {}, pmid = {41892210}, issn = {2079-7737}, support = {YLXKZX-NND-012//First-class Disciplines of Inner Mongolia Scientific Research Special Program/ ; 2023-JSGG-5//National Center of Technology Innovation for Dairy/ ; BR22-11-17//Basic Scientific Research Business Project of Universities directly under the Inner Mongolia Au-tonomous Region/ ; 2024LHMS03054//nner Mongolia Natural Science Foundation Project/ ; }, abstract = {Calf diarrhea is a common early-life disorder that adversely affects growth, oxidative balance, immune function, and intestinal microbiota, thereby compromising health and production performance. This study systematically investigates the effects of naturally occurring diarrhea in 7-day-old suckling calves on oxidative stress, immune responses, intestinal barrier integrity, and gut microbiota structure and function. Fecal scores, serum antioxidant and immune indices, and intestinal permeability markers were measured, and fecal samples were subjected to metagenomic sequencing. Diarrhea-affected calves exhibited higher fecal scores, increased oxidative stress indicated by reduced total antioxidant capacity, elevated lipid peroxidation, and altered antioxidant enzyme activities. Humoral immunity was impaired, inflammatory responses were dysregulated, and intestinal barrier function was disrupted. Gut microbial diversity declined, showing a depletion in health-associated taxa and the enrichment of opportunistic pathogens. Correlation analyses revealed that pathogenic bacteria abundance positively associated with diarrhea severity, oxidative stress, inflammation, and barrier disruption, while beneficial genera correlated with antioxidant and immune function. Functional profiling indicated a microbial shift from amino acid metabolism and antioxidant homeostasis toward carbohydrate and energy metabolism under diarrheic conditions. These findings highlight the pivotal role of gut microbiota dysbiosis in diarrhea pathogenesis and provide a foundation for developing microbiome-targeted interventions to improve calf health.}, } @article {pmid41892424, year = {2026}, author = {Gomes, E and Mesquita, TG and Serra, P and Araújo, D and Almeida, C and Machado, A and Oliveira, R and Castro, J}, title = {Antimicrobial Resistance in the Food Chain: Bridging Knowledge Gaps for Effective Detection and Control.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41892424}, issn = {2079-6382}, support = {https://doi.org/10.54499/2024.13640.PEX//Fundação para a Ciência e Tecnologia/ ; https://doi.org/10.54499/2022.07654.PTDC//Fundação para a Ciência e Tecnologia/ ; APTA4shiga (number 14840)//Fundação para a Ciência e Tecnologia/ ; }, abstract = {Antimicrobial resistance (AMR) poses a critical global public health threat, with the food chain serving as a significant transmission route connecting animals, environment, and humans. This review adopts a One Health perspective to analyze the key drivers of AMR dissemination across animal agriculture, aquaculture and food processing. We evaluate detection methodologies, contrasting the regulatory gold standard of culture-based phenotypic testing with rapid molecular advancements, including Whole Genome Sequencing (WGS), metagenomics, and emerging CRISPR-Cas diagnostics. While molecular tools offer unprecedented speed and resolution, challenges such as matrix interference, the viable but non-culturable (VBNC) state, and the genotype-phenotype disconnect remain. Finally, integrated mitigation strategies are also described, ranging from on-farm antimicrobial stewardship and innovative biofilm control to consumer hygiene practices. It is essential to bridge the technical and regulatory gaps in AMR surveillance in order to develop effective interventions and ensure a safer food system.}, } @article {pmid41892439, year = {2026}, author = {Gomes-Gonçalves, S and Bento, JT and Moreira, G and Mourão, J and Cruz, R and Esteves, F and Baptista, AL and Pereira, MA and Caseiro, P and Carreira, P and Figueira, L and Mesquita, JR}, title = {Comprehensive Shotgun Metagenomic Profiling of Antibiotic Resistance Genes in Sheep and Goat Farming Environments.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41892439}, issn = {2079-6382}, support = {PRR-C05-i03-I-000190//RumiRes project-"Vigilância epidemiológica de resistências antimicrobianas e resíduos medicamentosos em Pequenos ruminantes da Região Centro"/ ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a growing global health concern, driven in part by antibiotic use in animal production systems. Despite its relevance, the microbiome and resistome of small ruminant farm environments remain largely underexplored.

METHODS: In this study, shotgun metagenomics was applied to environmental samples from 46 sheep, goat and mixed-species farms across 14 municipalities in central Portugal.

RESULTS: Microbial profiling revealed a well-preserved microbiome with Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota (syn. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes respectively) as the most dominant phylum across different farm types. Regarding AMR, a total of 706 unique antimicrobial resistance genes (ARGs), covering 15 antibiotic classes, were detected. Tetracycline, aminoglycoside and macrolide resistance genes dominated across all samples, forming a conserved core resistome. While overall resistome profiles were broadly similar among farm types, significant differences were observed in specific ARG classes, such as pleuromutilin and fosfomycin.

CONCLUSIONS: These findings highlight small ruminant farm environments as potential reservoirs of clinically relevant ARGs, including WHO highest priority critically important antimicrobial (HPCIA) resistance genes for macrolides (mph(c), erm(f), erm(b)) and fluoroquinolones (qnrD1), as well as critically important antimicrobial (CIA) resistance genes for glycopeptides (vanR-SC, vanR-O) and aminoglycosides (str, aadA), supporting the need to incorporate these environments into surveillance strategies.}, } @article {pmid41892455, year = {2026}, author = {Dashti, AA and Vali, L and Walsh, F}, title = {Metagenomic Profiling of Soil Microbiomes and Resistomes in Arid Ecosystems of Kuwait.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41892455}, issn = {2079-6382}, support = {(RN01/15))//Kuwait University/ ; (code EASREF).//University of Gloucestershire/ ; }, abstract = {Background/Objective: This study addresses a significant knowledge gap in the literature concerning antibiotic resistance genes (ARGs) in arid soils by employing metagenomic approaches to characterise their diversity, using Kuwait as a model environment. Methods: Soil samples were collected from two agriculturally managed sites (K1 and K3) and one coastal unmanaged site (K2), representing distinct ecological conditions. Results: Taxonomic profiling revealed notable variation in microbial communities at both the phylum and genus levels. Alpha diversity analyses based on the Chao1 and Shannon indices indicated that agricultural soils exhibited greater microbial richness and diversity than the coastal soil. Beta diversity analysis further demonstrated substantial differences in microbial community composition among the sites. Consistent with previous soil microbiome studies, ARGs such as tetA, aac(3)-Ib, sul1, qep, muxB, mexW, mexB, and macB were detected across the sites. However, the identification of distinct clinically relevant resistance genes, including ugd, blaOXA-18, blaCMY-19, blaMOX-7, blaFOX-7, blaLRA-12, and novA, suggests the influence of site-specific or extreme selective pressures. Conclusions: Several of the detected ARGs appear to be rare or previously unreported in soil environments. Although the sample size is too small to support broad generalisations, the detection of ugd in soil is particularly noteworthy, suggesting that soils may serve as reservoirs of polymyxin resistance, potentially undermining the effectiveness of polymyxin antibiotics.}, } @article {pmid41892478, year = {2026}, author = {Scarlata, GGM and Belančić, A and Štimac, D and Fajkić, A and Meštrović, T and Abenavoli, L}, title = {Bacteriophage Therapy Against Shigella spp.: A Precision Antimicrobial Strategy.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41892478}, issn = {2079-6382}, abstract = {Shigellosis remains a significant global cause of infectious colitis, increasingly complicated by multidrug-resistant strains and the microbiota-disrupting effects of broad-spectrum antibiotics. Although conventional antimicrobial therapy can reduce symptom duration and bacterial shedding, it also contributes to gut dysbiosis, loss of colonization resistance, and further selection for antimicrobial resistance. These challenges have renewed interest in precision antimicrobial strategies, particularly bacteriophage therapy, which provides strain-level specificity and preserves the gut microbiota. This narrative review evaluates the biological rationale, preclinical and early clinical evidence, safety considerations, and translational challenges associated with bacteriophage therapy targeting Shigella spp. The historical development and mechanistic basis of phage therapy are summarized, with emphasis on the advantages of obligately lytic phages, receptor-specific targeting, self-amplification at infection sites, and activity against both planktonic and biofilm-associated bacteria. Recent microbiota research indicates that shigellosis is closely associated with early and persistent disruption of gut ecology, including depletion of short-chain fatty acids-producing taxa and reduced microbial resilience. Phage-based approaches may reduce pathogen burden while preserving beneficial microbial communities. Evidence from in vitro systems, animal models, human intestinal organoids, and a Phase 1 clinical trial demonstrates targeted efficacy and favorable safety profiles for Shigella-specific phages and phage cocktails. Major barriers to clinical adoption include immune interactions, phage resistance dynamics, genomic safety screening, regulatory classification, and the need for standardized susceptibility testing. Future directions emphasize the development of personalized phage therapy platforms that integrate rapid diagnostics, phage libraries, metagenomics, and artificial intelligence-assisted matching to enable scalable, precision treatment.}, } @article {pmid41892488, year = {2026}, author = {Mise, K and Wasai-Hara, S and Itoh, H}, title = {Global terrestrial distribution of N2O-reducing Acidobacteriota members.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41892488}, issn = {1751-7370}, support = {JP24K21255//JSPS/ ; }, mesh = {*Nitrous Oxide/metabolism ; *Soil Microbiology ; *Oxidoreductases/genetics/metabolism ; Phylogeny ; Metagenome ; *Bacteria/genetics/classification/metabolism ; Oxidation-Reduction ; Metagenomics ; Genome, Bacterial ; }, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas, and soil is its largest terrestrial source. Microbial N2O reductase (NosZ) is the only known enzyme capable of reducing N2O to N2, making nosZ-harboring prokaryotes important sinks in terrestrial ecosystems. Despite being among the most abundant and ubiquitous bacterial phyla in soil, the potential role of Acidobacteriota in N2O reduction remains largely unexplored. In this study, we addressed this gap using genomic, metagenomic, and physiological analyses. We first analyzed 199,602 prokaryotic genomes, including genomes from both isolated strains and metagenome-assembled genomes (MAGs). We found that 491 Acidobacteriota genomes harbored nosZ, predominantly the Sec-dependent NosZ gene (nosZII). Global metagenomic analysis of 321 soil samples revealed that Acidobacteriota nosZII is one of the most abundant groups of nosZ and distributed across different continents. Among Acidobacteriota, nosZII from the class Vicinamibacteria was the most prevalent in the soils. Finally, we provide the physiological evidence of N2O-reducing activity in Acidobacteriota by demonstrating that the Vicinamibacteria type strain, Luteitalea pratensis KCTC52215T, can reduce N2O. Taken together, these findings highlight the previously overlooked potential role of Acidobacteriota as a global N2O sink and underscore the need to include them in future studies on soil N2O dynamics.}, } @article {pmid41892593, year = {2026}, author = {Krasenbrink, J and Chen, SC and Tanabe, TS and Sarikeçe, H and Meurs, P and Borusak, S and Samrat, R and Guan, G and Priemer, C and Osvatic, J and Séneca, J and Hausmann, B and Speth, DR and Selberherr, E and Wanek, W and Schleheck, D and Mussmann, M and Loy, A}, title = {Sulfoquinovose degradation by cow rumen microbiota.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41892593}, issn = {1751-7370}, mesh = {Animals ; *Rumen/microbiology ; Cattle ; *Bacteria/classification/metabolism/genetics ; Sulfides/metabolism ; Sequence Analysis, DNA ; *Microbiota ; Methylglucosides ; }, abstract = {Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release sulfoquinovose from sulfoquinovosyl (diacyl)glycerol. Despite its ecological importance, the diversity and functional roles of sulfoquinovose-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments. We revealed high richness of yihQ-containing microorganisms in the analyzed cow rumen samples, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of sulfoquinovose metabolism in ruminant digestion. Anoxic microcosm experiments with sulfoquinovose-amended rumen fluid revealed cooperative microbial degradation of sulfoquinovose to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics and metatranscriptomics identified yet undescribed and uncultured sulfoquinovose-degrading taxa. Members of Caproiciproducens (Acutalibacteraceae), Candidatus Limivicinus (Oscillospiraceae), and Sphaerochaetaceae transcribed the isethionate-producing sulfo-transketolase pathway, whereas isethionate was likely respired by a Candidatus Mailhella bacterium (Desulfovibrionaceae). This study presents a functional gene-based assay for tracking environmental yihQ richness, highlights sulfoquinovose degradation as a central metabolic process in the cow rumen, describes previously unknown sulfoquinovose-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.}, } @article {pmid41892682, year = {2026}, author = {Murgina, O and Stafeeva, K and Karaulova, S and Vostrikova, A and Kononova, S and Chursina, D and Pozdeeva, S and Makogonova, A and Burakova, I and Pogorelova, S and Morozova, P and Smirnova, Y and Syromyatnikov, M and Shutikov, V and Mikhailov, E and Gureev, A}, title = {Probiotic Bacillus subtilis, but Not a Lactobacillus spp., Ameliorates Cognitive Impairment in a Mouse Model of LPS and Zidovudine-Induced Neuroinflammation.}, journal = {Brain sciences}, volume = {16}, number = {3}, pages = {}, pmid = {41892682}, issn = {2076-3425}, support = {FZGW-2024-0003//Mikhail Syromyatnikov/ ; }, abstract = {Background/Objectives: The gut-brain axis is increasingly recognized as a critical modulator of cognitive function. This study investigated the neurotoxic effects of combined exposure to bacterial lipopolysaccharide (LPS) and the antiretroviral drug zidovudine (ZDV) in a mouse model, and evaluated the protective potential of two probiotic interventions: Bacillus subtilis and a mixture of lactobacilli. Methods: Cognitive function was assessed using the Morris water maze (MWM). Gut microbiota composition was analyzed by 16S rRNA sequencing, and intestinal morphology was examined histologically. Gene expression of neuroinflammatory markers and mitophagy-related genes in brain tissue was quantified by RT-PCR. Plasma levels of cell-free mitochondrial DNA (cf-mtDNA) were measured as a marker of mitochondrial damage. Results: Combined LPS + ZDV exposure induced systemic inflammation, impaired spatial memory, damaged the intestinal mucosa, and caused dysbiosis characterized by an increase in pro-inflammatory Muribaculaceae. In the brain, LPS + ZDV significantly upregulated Tnfa expression, confirming neuroinflammation. Bacillus subtilis administration prevented cognitive deficits, maintained Tnfa at control levels, and significantly reduced Il1b and Il6 expression compared to the LPS + ZDV group. This was accompanied by activation of the PINK1/PTEN-dependent mitophagy pathway, prevention of cf-mtDNA release, and restoration of gut microbial diversity. In contrast, the Lactobacilli mixture not only failed to improve outcomes but was associated with exacerbated intestinal damage, more pronounced cognitive dysfunction, and no reduction in neuroinflammatory markers. Conclusions: Combined exposure to LPS and ZDV induces gut-brain axis dysfunction characterized by neuroinflammation, cognitive impairment, intestinal damage, and dysbiosis. Bacillus subtilis effectively preserves cognitive function through activation of PINK1/PTEN-dependent mitophagy and suppression of neuroinflammation, highlighting its potential as a therapeutic candidate for cognitive impairments associated with gut-brain axis dysfunction. The contrasting effects of the lactobacilli mixture underscore the critical importance of strain-specificity in probiotic interventions.}, } @article {pmid41893096, year = {2026}, author = {Fan, J and Liu, S and Zhang, H and Jin, C and Wu, N}, title = {Dysbiosis of the Gut-Lung Axis and Its Immune Correlates During Pulmonary Cryptococcus neoformans Infection.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {41893096}, issn = {2309-608X}, support = {Grant No. 2023YFC2506004//National Key Research and Development Program of China/ ; }, abstract = {Cryptococcus neoformans is a major fungal pathogen responsible for life-threatening meningitis, especially in immunocompromised individuals. Although the gut-lung axis is known to regulate immune responses in respiratory infections, its role in cryptococcosis remains unclear. This study aimed to define the dynamic changes in the gut and lung microbiota and their relationship with host immunity during C. neoformans infection. Using a mouse model, we found that pulmonary infection induced significant dysbiosis in both the lung and gut microbiota, marked by decreased beneficial commensals and increased opportunistic pathogens. Integrated analysis showed these microbial shifts were closely associated with distinct immune responses: lung dysbiosis correlated with a strong IL-17-mediated pulmonary inflammatory response, while gut dysbiosis was linked to systemic immune activation in the spleen. Functional metagenomic prediction further revealed widespread disruption in microbial metabolic pathways, including energy metabolism and biosynthesis, in both sites. Importantly, a positive correlation was observed between lung and gut dysbiosis, indicating an interconnected gut-lung axis during cryptococcosis. These findings demonstrate that C. neoformans infection causes coordinated disruptions in microbiota and immunity across the gut-lung axis, underscoring the microbiome as a critical modulator of host response and suggesting potential avenues for microbiome-targeted therapies.}, } @article {pmid41893137, year = {2026}, author = {Francis, DV and Kishorkumar, M and Ahmed, ZFR and Neumann, EG and Kurup, SS}, title = {Molecular Advances and Sustainable Strategies in Mushroom Production for Food Security: A Review.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {41893137}, issn = {2309-608X}, support = {21R097//ARIFSID/ ; }, abstract = {Mushrooms offer a promising solution for sustainable food production due to their nutritional value, low resource requirements, and ability to grow in diverse environments. As interest in mushrooms grows, it is important to understand where current research is focused and where key gaps remain. A bibliometric analysis of 776 research articles indexed in Web of Science revealed a strong emphasis on yield, substrate reuse, and enzymatic degradation, but limited attention to molecular approaches, climate adaptation, and studies from arid regions such as the Middle East. Building on these findings, this review explores the ecological diversity of mushrooms and their adaptations across tropical, temperate, boreal, and arid ecosystems. It discusses the role of mycorrhizal and microbial interactions in nutrient cycling and environmental resilience, including desert truffle symbioses. Key pathways and genetic regulation involved in lignin degradation are outlined, along with recent advancements in transcriptomics, proteomics, genomics, metabolomics, and metagenomics that support improved cultivation and bioactive compound production. The review also addresses sustainable practices, such as microbiome integration and resource recycling, to enhance mushroom farming. The aim is to bring together ecological insights and molecular strategies to support sustainable mushroom production, particularly in regions facing resource and climate challenges.}, } @article {pmid41893308, year = {2026}, author = {Yeerjiang, B and Manaer, T and Liu, X and Bieerdimulati, R and Nabi, X}, title = {Mechanistic Insights into Lactobacillus harbinensis and Other Probiotics Regulating Lipid Metabolism in T2DM Mice via the PPARγ-LXRα-NPC1L1 Signaling Pathway Based on Multi-Omics Analysis.}, journal = {Metabolites}, volume = {16}, number = {3}, pages = {}, pmid = {41893308}, issn = {2218-1989}, support = {No. 82260640//National Natural Science Foundation of China/ ; }, abstract = {Background/Objectives: Intestinal dysbiosis is a pivotal trigger of type 2 diabetes mellitus (T2DM). Our previous studies confirmed that composite probiotics derived from fermented camel milk (CPCM), containing Lactobacillus harbinensis and 13 other strains, can ameliorate glucose and lipid metabolism in T2DM mice by reshaping bile acid profiles, and its effect may be associated with the PPARγ-LXRα-NPC1L1 signaling pathway. Methods: Metagenomic analysis characterized alterations in intestinal microbiota structure and functional genes post-CPCM intervention, proteomic analysis detected changes in protein expression profiles related to glucose and lipid metabolism in mice, and Caco-2 cells were used for in vitro validation to clarify the regulatory effect of exopolysaccharides (EPS) (the active component of CPCM) on the PPARγ-LXRα-NPC1L1 signaling pathway. Results: The results showed that CPCM significantly improved glucose and lipid metabolism and remodeled the intestinal flora structure in mice, markedly enriching beneficial bacteria such as Lactobacillus and Akkermansia and enhancing the expression of functional genes related to the peroxisome proliferator-activated receptor (PPAR) signaling pathway and short-chain fatty acid synthesis in the microbiota. Proteomic analysis revealed that CPCM reversed the expression of key proteins involved in fatty acid oxidation and transport, thereby restoring the function of the PPAR signaling pathway. In vitro experiments validated that extracellular polysaccharides, the active component of CPCM, significantly upregulated the expression of PPARγ and liver X receptor α (LXRα) and inhibited the expression of Niemann-Pick C1-Like 1 (NPC1L1), a cholesterol absorption transporter, in Caco-2 cells. Conclusions: In conclusion, CPCM ameliorates glucose and lipid metabolic disorders in T2DM through multiple mechanisms: reshaping the intestinal probiotic community, enhancing its beneficial metabolic functions, restoring the activity of the PPARγ-LXRα signaling pathway, and subsequently downregulating NPC1L1.}, } @article {pmid41893658, year = {2026}, author = {Lisjak, A and Correa Lopes, B and Pilla, R and Nemec, A and Lampreht Tratar, U and Suchodolski, JS and Tozon, N}, title = {Assessment of Fecal Microbiota in Healthy Dogs and Dogs with Cutaneous Mast Cell Tumors Treated with Electrochemotherapy Combined with Gene Electrotransfer of IL-12.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, pmid = {41893658}, issn = {2306-7381}, support = {P3-0428, P4-0053, P3-0003, and J4-2546//The Slovenian Research and Innovation Agency/ ; The microbiome research at the Gastrointestinal Laboratory at Texas A&M University is in part funded through Purina PetCare Research Excellence Fund//Purina PetCare Research Excellence Fund/ ; }, abstract = {Cancer is a major health concern, with its incidence rate continuing to increase. There is growing interest in the microbiota and its role in carcinogenesis, as it significantly influences physiological and pathological processes. Various aspects of the microbiome have been shown to have both anti-tumor and pro-tumor effects. Advances in techniques such as high-throughput DNA sequencing have greatly improved our understanding of microbial populations in the human and canine gut. We aimed to (1) characterize the intestinal microbiota of healthy dogs and dogs with cutaneous mast cell tumors (MCTs), (2) assess changes in the intestinal microbiota of dogs undergoing electrochemotherapy (ECT) combined with gene electrotransfer (GET) of the IL-12 plasmid (IL-12), and (3) explore possible associations with the expression of immune markers Programmed cell death protein 1 (PD-1), Programmed death-ligand 1 (PD-L1), and Granzyme B (GZMB) in MCT tissue. Stool samples were collected from healthy dogs (n = 24) and dogs with MCTs (n = 24) before and after ECT and IL-12 GET. DNA was extracted from the samples, and shallow shotgun sequencing was performed. Immunohistochemistry was performed on the tumors to assess the expression of PD-1, PD-L1, and GZMB. The dysbiosis index, alpha diversity, and beta diversity did not differ between groups. Regarding microbial composition, Bifidobacterium animalis, Corynebacterium variabile, Lactobacillus johnsonii, Pediococcus pentosaceus, Streptococcus anginosus, Streptococcus equinus, Streptococcus intermedius, Clostridium thermobutyricum, Megasphaera elsdenii, and Anaerobiospirillum sp. were found in lower relative abundance in feces of dogs with MCTs, while Bacteroides togonis, Lactobacillus amylolyticus, Prevotella sp. CAG:279, and Megamonas hypermegale were more abundant compared to healthy dogs. Our study provides further insight into the composition of the gut microbiota in dogs with MCTs, where ECT and IL-12 GET did not lead to major shifts. We were unable to establish any association between the expression of immune markers and the microbiota.}, } @article {pmid41893667, year = {2026}, author = {Karakaya, E and Satıcıoğlu, İB and Yarım, D and Güran, Ö and Güran, C and Alpman, U and Atalan, G and Abay, S and Aydın, F}, title = {Culture and Metagenomic Insights into the Ear Microbiota in Dogs with Healthy Ears and Otitis Externa.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, pmid = {41893667}, issn = {2306-7381}, support = {TSA-2022-12342 and THD-2024-13751//Erciyes University/ ; }, abstract = {The canine ear microbiota plays an important role in ear health, and dysbiosis is associated with otitis externa (OE) and antimicrobial resistance (AMR). This study aims to investigate the ear microbiota of dogs with healthy ears and OE using bacterial culture-based methods and shotgun metagenomic sequencing, and to screen for AMR and virulence-associated genetic signatures. Ear swab specimens from 100 healthy and 100 OE-affected dogs were analyzed. The isolates obtained via bacterial culture were identified by MALDI-TOF MS and 16S rRNA sequencing. Metagenomic analysis was performed via Illumina shotgun sequencing. The most commonly defined species in healthy dogs in culture were Staphylococcus pseudintermedius (24.5%) and Staphylococcus epidermidis (5.7%); in dogs with OE, the most commonly defined species were S. pseudintermedius (30.5%), and Clostridium perfringens (4.5%). In healthy samples, metagenomic analysis revealed higher relative abundances of Bacteroides fragilis (15.8%) and Ezakiella coagulans (8.2%), while S. pseudintermedius (38.7%) dominated in OE. AMR profiling demonstrated diverse resistance determinants, including efflux pump systems and methicillin resistance-associated genes. In conclusion, the present study shows that S. pseudintermedius is a predominant member of canine ear microbiota, with higher presence in OE highlighting microbial shifts, and demonstrates that combining culture and metagenomic analyses provides a concise view of microbial communities and clinical relevance.}, } @article {pmid41893692, year = {2026}, author = {Shehla, S and Obaid, MK and Niaz, S and Khan, MA and Ahmad, AA and Abdel-Maksoud, MA and Alamri, A and Alrokayan, S and Shoaib, M and Shams, S and Ren, Q}, title = {Shotgun Metagenomics Reveals Microbial Diversity, Resistome, and Plasmidome in Dairy Cattle Feces.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, pmid = {41893692}, issn = {2306-7381}, support = {ORF-RC-2026-2600//King Saud University/ ; }, abstract = {Fecal microbiota are shaped by upstream digestive processes and reflect the outcome of host-microbe interactions, including the resistant microbial fraction that survives to be excreted. This is particularly crucial for assessing zoonotic risks and environmental contamination, as feces are the primary source of dissemination, which is considered an emerging One Health threat. Therefore, we conducted a pilot study to obtain the exploratory findings regarding the cattle GIT microbial composition, potential resistome, and their transmission drivers, such as plasmids, using metagenomic analysis from different districts in Khyber Pakhtunkhwa (KP) province, Pakistan. For this purpose, a total of 150 fecal samples (50 from each district) of healthy cattle were collected from various farms in Mardan (FC1), Peshawar (FC2), and Dera Ismail Khan (FC3) districts. Total DNA from each sample was extracted, pooled (FC1, FC2, and FC3), and sequenced via the Illumina platform. Bacteria were the highly abundant kingdom, while Pseudomonadota and Bacillota were dominant phyla in all samples. Caryophanon latum and Escherichia coli were highly abundant at the species level. A large resistome (40-49 genes), including critical genes, such as tet(X), blaOXA-427, and plasmidomes (16-22), such as IncF, was detected in the samples. The prominence of certain commensal or opportunistic pathogens in the fecal microbiota may indicate the presence of sub-clinical gastrointestinal disruptions or disease that may affect cattle herds. The fecal resistome is extensive, identifying dairy cattle in these regions as important reservoirs for AMR genes capable of spreading via HGT. This pilot study establishes that the fecal microbiota of dairy cattle in this region are not merely a waste product but a complex ecosystem, rich in microbiota of One Health significance.}, } @article {pmid41893724, year = {2026}, author = {Qiu, Q and Gong, T and Du, L and Li, W and Hu, Y and Li, D and Zhou, C and Liu, W}, title = {Comparative Analysis of Microbial Community Structure and Function in the Gut of South China Tigers Under Different Dietary Treatments.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, pmid = {41893724}, issn = {2306-7381}, support = {2110499//Diagnosis and Treatment of Genetic Diseases and Training for Stereotypic Behaviors in South China Tigers at Changsha Ecological Zoo/ ; 2110499//Artificial breeding of Reeves's pheasant (Syrmaticus reevesii) at Changsha Ecological Zoo/ ; }, abstract = {The gut microbiota is a crucial component of a tiger's health and plays a significant role in adapting to changes in food and the environment. Although extensive studies have been carried out on the gut microbiota of tigers, investigating the responses of gut microbial composition and function to preadaptation to wild predation patterns under captive conditions is particularly significant for South China tigers, given that it is the only tiger subspecies existing solely in captive settings at present. Here, we performed shotgun metagenomic sequencing for a comprehensive analysis of the gut microbiota of South China tigers assigned to two dietary groups (live prey group, LP group; frozen meat group, FM group), thereby generating abundant valuable data for this endangered subspecies. The results indicated that the core intestinal microbial composition was similar between the two dietary groups. Differential analysis revealed associations between dietary treatments and microbial abundance in the intestines of South China tigers. Functional gene analysis revealed that the LP group exhibited upregulation of genes and pathways related to antimicrobial resistance, bacterial infection-related disease, cell motility and proliferation, while the FM group displayed efficient energy metabolism. A total of 1251 antibiotic resistance genes (ARGs) were identified in the gut microbiome of South China tigers. The core resistome mainly included resistance to peptides, glycopeptides, tetracyclines, fluoroquinolones, and macrolides. In addition, the differences in ARGs between the LP group and FM group may be related to a broader range of animal tissues of live prey and the processing conditions of frozen meat. In summary, although feeding live prey did not change the core framework of the gut microbiota in South China tigers, it was associated with differences in microbial abundance, metabolic pathways, and antibiotic resistance gene profiles.}, } @article {pmid41893914, year = {2026}, author = {Pistone, D and Bevivino, G and Dipaola, MG and Bandi, C and Lombardo, F}, title = {Current and emerging molecular diagnostic approaches in the detection of human parasites.}, journal = {Parasitology research}, volume = {125}, number = {1}, pages = {}, pmid = {41893914}, issn = {1432-1955}, abstract = {Microscopy and morphological identification remain the gold standard for diagnosing most parasitic infections, yet their limited sensitivity in asymptomatic or low-burden cases, along with technical constraints, has accelerated the adoption of molecular diagnostics. Over the past three decades, advances in nucleic acid amplification and sequencing technologies have transformed parasite detection by improving sensitivity, specificity, and reproducibility, enabling earlier intervention and stronger surveillance. PCR remains the foundation of molecular diagnostics, with real-time PCR and digital PCR improving analytical performance and quantification. Multiplex qPCR supports simultaneous detection of multiple pathogens, while dPCR enables absolute quantification and rare variant detection, although broader implementation is limited by instrument cost. Isothermal amplification methods such as tHDA, NASBA, LAMP, and RPA offer rapid, low-cost amplification at constant temperature and are well suited for field diagnostics in resource-limited settings. Next-Generation Sequencing has advanced genotyping and epidemiological surveillance by resolving cryptic species, resistance mutations, and mixed infections through targeted panels, whole-genome sequencing, and metagenomics. CRISPR/Cas-based assays provide rapid and sensitive nucleic acid detection with strong potential for point-of-care deployment due to their simplicity and adaptability. Emerging biomarkers, including circulating cell-free DNA, non-coding RNAs, and microRNAs in extracellular vesicles, offer promising non-invasive diagnostic strategies, though further validation is required. This review offers a concise overview of these molecular approaches, emphasizing recent innovations such as dPCR, NGS, CRISPR/Cas systems, and biomarker-based detection. For each method, core technical principles, representative applications, and comparative strengths and limitations are presented to illustrate their diagnostic potential.}, } @article {pmid41894043, year = {2026}, author = {Tian, X and Feng, Y and Wang, C and Zhao, W and Xue, L and Zhu, L and Ji, X and Wang, H and Gu, Y and Jiang, Q and Zhang, J}, title = {Analysis of the characteristics of rumen microorganisms and their metabolites and plasma metabolites in crossbred beef cattle at different stages.}, journal = {Veterinary research communications}, volume = {50}, number = {3}, pages = {}, pmid = {41894043}, issn = {1573-7446}, support = {2021BEF01002//Major Project of Science and Technology ofNingxia Autonomous Region/ ; 2023AAC03050//Natural Science Foundation of Ningxia Hui Autonomous Region/ ; }, abstract = {The rumen microbial community is influenced by various factors such as diet, age, genetics, and breed. This study employs metagenomics and untargeted metabolomics to investigate the characteristics of rumen microbiota and plasma metabolite changes in crossbred beef cattle (Simmental♀× Belgian Blue♂) as they age, as well as their regulatory effects on growth performance. The LEfse analysis results indicated that the dominant microorganisms in the 12-month-old crossbred beef cattle group were Stomatobaculum sp., Succiniclasticum ruminis, and uncultured Succiniclasticum sp., etc., while the dominant microorganisms in the 18-month-old crossbred beef cattle group were Succinivibrio sp., Oceanobacillus sp., and uncultured Holdemanella sp., etc. The differentially expressed metabolites in the rumen and plasma were significantly enriched in the Pyrimidine metabolism pathway and the Valine, leucine and isoleucine biosynthesis pathway. Through GSEA analysis, it was found that the rumen metabolites Thymidine, 4,5-Dihydroorotic acid, Uracil, and Uridine were more abundant at 12 months of age (P < 0.05), while the plasma metabolite 2s-Amino-3s-methylpentanoic acid was more abundant at 18 months of age (P < 0.05). As the age increases, the rumen microbiota of crossbred beef cattle tends to mature and stabilize, and the ability of rumen metabolites and plasma metabolites to provide protein for the host gradually enhances. In summary, our research results aim to provide basic information on the regulatory role of microorganisms and metabolites in the growth performance of crossbred beef cattle, and also offer targets for precise nutritional regulation of beef cattle.}, } @article {pmid41894133, year = {2026}, author = {Zhang, X and Chen, L and Wang, F and Xu, X and Wu, Y and Xu, J and Xu, Y and He, X}, title = {Torque teno virus in the lower respiratory tract: association with immunosuppression but not mortality in severe pneumonia-a multicenter retrospective cohort study.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41894133}, issn = {1435-4373}, support = {2024C3186//Key Research and Development Program of Zhejiang Province/ ; GZY-ZJ-KJ-24030//Major Project of National-Zhejiang Provincial Administration of Traditional Chinese Medicine/ ; }, } @article {pmid41894264, year = {2026}, author = {Yu, Y and Hong, S and Wang, Z and Li, S and Zhang, S}, title = {Leptospirosis-induced diffuse alveolar hemorrhage: A rare case report from a non-epidemic area and literature review.}, journal = {Medicine}, volume = {105}, number = {13}, pages = {e48131}, pmid = {41894264}, issn = {1536-5964}, support = {No. LY21H100002//Zhejiang Natural Science Foundation Project/ ; No.2024C31025//Science and Technology Plan Project of zhoushan/ ; }, mesh = {Humans ; Female ; *Leptospirosis/complications/diagnosis/drug therapy ; *Hemorrhage/etiology/diagnosis/microbiology ; Aged ; *Pulmonary Alveoli/pathology ; Community-Acquired Pneumonia ; Shock, Septic/etiology ; Anti-Bacterial Agents/therapeutic use ; *Lung Diseases/etiology ; Respiratory Distress Syndrome/etiology ; Multiple Organ Failure/etiology ; }, abstract = {RATIONALE: Leptospirosis is an uncommon cause of severe pneumonia and diffuse alveolar hemorrhage (DAH), particularly in non-endemic areas, posing a significant diagnostic challenge. This case highlights the critical role of advanced molecular diagnostics in identifying this rare and life-threatening presentation.

PATIENT CONCERNS: A 65-year-old woman presented with an acute onset of high fever, chest tightness, and rapidly progressive shortness of breath.

DIAGNOSES: The patient was initially misdiagnosed with severe community-acquired pneumonia. She subsequently developed septic shock and multiple organ dysfunction syndrome. A definitive diagnosis of leptospirosis-induced DAH was confirmed through metagenomic next-generation sequencing, reverse transcription quantitative PCR, and subsequent seroconversion shown by immunoglobulin M enzyme-linked immunosorbent assay.

INTERVENTIONS: Upon diagnosis, targeted antimicrobial therapy with intravenous penicillin was initiated. Supportive care included management of septic shock and lung-protective ventilation for concomitant acute respiratory distress syndrome.

OUTCOMES: Following the confirmation of leptospirosis and initiation of targeted treatment, the patient's condition gradually stabilized. After a course of intensive care, she made a full recovery and was successfully discharged.

LESSONS: This case underscores that leptospirosis can present as fulminant DAH even in non-endemic regions. A high index of suspicion, aided by epidemiological clues and the rapid application of metagenomic next-generation sequencing/reverse transcription quantitative PCR, is crucial for timely diagnosis. Prompt targeted antimicrobial therapy combined with intensive organ support is essential for a favorable outcome in severe cases.}, } @article {pmid41894564, year = {2026}, author = {McCartin, LJ and Vohsen, SA and Wood, AL and Horowitz, J and Orozco-Juarbe, JJ and Pittoors, N and Morrissey, D and Vaga, CF and Hansel, CM and Collins, AG and Quattrini, AM and Herrera, S}, title = {Accounting for Intra- and Intergenomic Sequence Variation in Reference Barcodes Improves eDNA Metabarcoding Biodiversity Assessment.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70130}, pmid = {41894564}, issn = {1755-0998}, support = {NA18OAR0110289//NOAA Ocean Exploration/ ; NA21OAR0110202//NOAA Ocean Exploration/ ; NA18NOS4780166//National Centers for Coastal Ocean Science/ ; //Smithsonian Institution/ ; //Smithsonian Women's Committee/ ; //Bureau of Ocean Energy Management/ ; 2000013668//National Academies of Sciences, Engineering, and Medicine/ ; //NOAA Fisheries Office of Science and Technology/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods/standards ; Animals ; *Biodiversity ; *DNA, Environmental/genetics ; *Genetic Variation ; *Metagenomics/methods ; Puerto Rico ; *Anthozoa/genetics/classification ; Extrachromosomal DNA ; }, abstract = {Environmental DNA (eDNA) metabarcoding can rapidly characterise biodiversity, yet its accuracy and effectiveness are limited by incomplete DNA barcode reference databases. We evaluated how comprehensive reference databases that include sequence variation within genomes (intragenomic) and across individuals and species (intergenomic) improve eDNA-based biodiversity assessments. We collected coral tissue and water samples at deep sites offshore Puerto Rico for reference barcoding and eDNA metabarcoding. Genome skimming coral specimens yielded 28S barcodes for 314 of 346 samples (90.8%) and revealed divergent intragenomic 28S lineages in multiple octocoral families. Incorporating local reference barcodes substantially changed ASV taxonomic classifications: 22 ASVs (8.9%) gained genus-level resolution, 19 ASVs (7.7%) were reassigned to different genera, and 14 ASVs (5.7%) lost incorrect genus-level classifications. Thus, incomplete reference databases produce not only unclassified ASVs but also false positive detections and ecologically meaningful misclassifications. When intragenomic 28S lineages were excluded from the reference database, 18 ASVs (7.4%) could not be classified to family or genus, demonstrating that unrecognised intragenomic variation can be mistaken for unsampled taxa. Integrating reference genome skimming and eDNA metabarcoding expanded known coral family richness by 36% at depths shallower than 1000 m and by 181% at depths greater than 1000 m. eDNA also detected two coral families previously unknown off Puerto Rico and nearby islands, underscoring its potential for biodiversity discovery.}, } @article {pmid41894872, year = {2026}, author = {Chen, H and Chai, Z and Chen, J and Song, C and Zheng, M}, title = {Anthraquinone-2-sulfonate enhances endogenous denitrification and phosphorus removal: Electron shuttle-mediated syntrophic partnerships.}, journal = {Water research}, volume = {298}, number = {}, pages = {125783}, doi = {10.1016/j.watres.2026.125783}, pmid = {41894872}, issn = {1879-2448}, mesh = {*Denitrification ; *Phosphorus ; *Anthraquinones ; Electrons ; Electron Transport ; }, abstract = {Endogenous denitrification (EnD) and denitrifying phosphorus removal (DPR) offer distinct advantages for low-carbon wastewater treatment, yet the nutrient removal performance is often constrained by inefficient electron transfer and nitrite/free nitrous acid (FNA) inhibition. Here, we demonstrate that anthraquinone-2-sulfonate (AQS) acts as an effective redox mediator to overcome these bottlenecks. With nitrate (NO3[-]-N) as the electron acceptor, the addition of 0.05 mmol/L AQS significantly amplified the electron transfer system activity (ETSA) by 3.66-fold. Consequently, this enhancement promoted the NO3[-]-N removal rate to 25.90 mg/(g VSS·h) (12.65-fold increase) and increased the phosphorus uptake rate to 3.69 mg/(g VSS·h) (1.95-fold improvement), achieving removal efficiencies of 96.22±1.00 % and 96.03±2.98 % for phosphorus and nitrogen, respectively. Moreover, when nitrite (NO2[-]-N) served as the electron acceptor, AQS enhanced the phosphorus uptake rate and nitrogen removal rate by 1.69-fold and 1.54-fold, respectively. Microbial analysis revealed a robust syntrophic partnership wherein Thauera, Candidatus Competibacter and Defluviicoccus (functioning as denitrifying glycogen-accumulating organisms) efficiently reduced NO3[-]-N to NO2[-]-N, which was subsequently scavenged by Dechloromonas and Candidatus Accumulibacter clade Ⅱ (functioning as denitrifying polyphosphate-accumulating organisms) for coupled phosphorus uptake. Metagenomic analysis further indicated that AQS facilitated electron transfer from Complexes I/Ⅱ to nitrate reductase and Complex Ⅲ, accelerating NO2[-]-N generation while alleviating FNA toxicity via coupled electron transfer from Cyt c to nitrite reductase. Crucially, this accelerated electron flux potentially intensified the proton motive force, suggesting an enhanced capacity for ATP generation to fuel the upregulation of phosphate transport (pit/pst) and polyphosphate synthesis (ppk) genes. These findings highlight AQS as a promising strategy to regulate electron transfer kinetics and metabolic coupling for advanced nutrient removal.}, } @article {pmid41894881, year = {2026}, author = {Zhao, Y and Li, Y and Zheng, Y and Yan, P and Lai, Y and Wang, X and Zhuang, LL and Zhang, J}, title = {Enhanced co-removal of nutrients and glyphosate from rural sewage in siphon-driven constructed wetlands: Optimization and mechanisms.}, journal = {Water research}, volume = {298}, number = {}, pages = {125812}, doi = {10.1016/j.watres.2026.125812}, pmid = {41894881}, issn = {1879-2448}, mesh = {*Wetlands ; Glyphosate ; *Glycine/analogs & derivatives ; *Sewage/chemistry ; Phosphorus ; Nitrogen ; Waste Disposal, Fluid ; Water Pollutants, Chemical ; Wastewater ; }, abstract = {Constructed wetlands (CWs) often suffer from limited carbon/oxygen availability and poorly controlled redox conditions, constraining pollutant removal from rural sewage. Hence, siphon-driven CWs (S-CWs) were optimized for the co-removal of the typical rural pollutant glyphosate (N-(phosphonomethyl)glycine, PMG) and typical wastewater pollutants (carbon (C), nitrogen (N), phosphorus (P)). S-CWs exhibited strong PMG resilience, tolerating up to 8 mg/L, and achieved 50.91-92.14%, 50.93-56.82% and 96.19-97.18% for PMG, N and P removal, respectively. These results indicated superior performance compared with unaerated and aerated CWs. Mechanistic analysis showed that PMG removal was dominated by biodegradation in the aerobic, carbon-enriched inlet area of S-CWs. This process was driven by genera such as Alcaligenes and Geobacillus, and enzymes like PhnI, PhnJ via aminomethylphosphonic acid (AMPA) and C-P lyase pathways, as confirmed by metagenomics and AlphaFold 3 predictions. PMG transiently inhibited N removal by suppressing denitrification but not nitrification. However, microbial adaptation over 135 days restored N removal along the first 50% pathway, even under high PMG stress (10 mg/L). In contrast, P removal was more persistently inhibited throughout the system, as the additional PMG-derived P increased total P load and accelerated substrate adsorption saturation. Long-term operation confirmed the robustness of S-CWs, including reduced effluent toxicity, healthier plant growth, lower oxidative stress, and minimal clogging (only 1.40-13.53% porosity decline). These observations highlight the hydraulic stability and long-term suitability of S-CWs for treating PMG-laden rural wastewater.}, } @article {pmid41895431, year = {2026}, author = {Ceruti, A and Bisia, M and Balatsos, G and Kobialka, RM and Zamil, MF and Hasan, A and Truyen, U and Lucati, F and Sanpera-Calbet, I and Palmer, JRB and Alam, MS and Michaelakis, A and Wahed, AAE}, title = {MosquitoID: Rapid metagenomic sequencing for offline mosquito surveillance.}, journal = {Acta tropica}, volume = {278}, number = {}, pages = {108071}, doi = {10.1016/j.actatropica.2026.108071}, pmid = {41895431}, issn = {1873-6254}, mesh = {Animals ; *Metagenomics/methods ; *Culicidae/genetics/classification/virology ; High-Throughput Nucleotide Sequencing/methods ; *Mosquito Vectors/genetics/virology ; Spain ; Aedes/genetics/virology ; Computational Biology ; }, abstract = {Mosquitoes transmit numerous infectious diseases, with climate change expanding their global distribution through warmer environments. Next-generation sequencing offers significant advantages for mosquito genomic surveillance and potential early warning systems. In this study, a portable metagenomic sequencing approach using Oxford Nanopore Technologies (ONT) for field-based mosquito analysis (MosquitoID protocol) was developed, enabling species and host feeding patterns identification, and pathogen detection, all coming from a single amplification-free workflow. DNA was extracted from 62 mosquito samples (Aedes albopictus, Aedes cretinus, Culex pipiens, Culiseta longiareolata) from Greece and Spain, either single-species pools (1-10 specimens) or mixed-species pools, with reverse purification method or archived samples. Additionally, 30 pooled Aedes aegypti samples from Bangladesh underwent cDNA reverse purification. All samples were sequenced using ONT rapid barcoding kits. Offline bioinformatics analysis via Geneious screened custom BLAST databases for species, host, and virus identification. MosquitoID accurately identified mosquito species in 89% of samples overall, with main discrepancies in Aedes cretinus. Virus screening detected Phasi Charoen-like virus in cDNA samples. Host DNA sequences identified multiple species including horses, cattle, and ducks. This study demonstrates metagenomic ONT sequencing's effectiveness for rapid host, species, and virus identification. After further benchmarking, the approach shows potential for real-time disease monitoring and enhanced surveillance systems. Integrating portable next-generation sequencing with offline bioinformatics tools could significantly strengthen mosquito-borne disease prevention strategies, particularly for non-bioinformaticians and in resource-limited settings.}, } @article {pmid41895455, year = {2026}, author = {Yin, W and Li, Y and Pan, A and Wu, J and Su, X and Xiao, X and Dong, F and Xu, L and Chen, C and Fu, H and Sun, F}, title = {Synergistic inhibition and microbial adaptation in anammox systems under long-term salinity and fulvic acid stress.}, journal = {Bioresource technology}, volume = {451}, number = {}, pages = {134498}, doi = {10.1016/j.biortech.2026.134498}, pmid = {41895455}, issn = {1873-2976}, mesh = {*Salinity ; *Benzopyrans/pharmacology ; *Adaptation, Physiological/drug effects ; Bioreactors/microbiology ; *Stress, Physiological/drug effects ; *Anaerobic Ammonia Oxidation/drug effects ; Wastewater/chemistry ; Oxidation-Reduction ; *Bacteria/metabolism/genetics/drug effects ; Nitrogen ; *Ammonium Compounds/metabolism ; }, abstract = {Salinity and fulvic acid frequently coexist in high-strength wastewater, yet their combined effects on anaerobic ammonium oxidation (anammox) remain unclear. This study evaluated their impacts on reactor performance, microbial community structure, and functional genes. Moderate salinity (5-10 g L[-1] NaCl) slightly enhanced anammox activity, whereas higher salinity (15 g L[-1]) and fulvic acid (> 60 mg L[-1]) significantly inhibited nitrogen removal. Under such combined stress, specific anammox activity decreased by about 40%, indicating a synergistic inhibition. Extracellular polymeric substances increased by 198%, suggesting a microbial stress-response strategy. Microbial community analysis showed a decline in Planctomycetes by 11%, and enrichment of Proteobacteria by 7% and Chloroflexi by 4%. Metagenomic results revealed suppression of key anammox genes and enrichment of denitrification genes, with quorum sensing and polysaccharide biosynthesis genes increased, suggesting EPS-mediated adaptation under combined stress. These findings provide insights for improving anammox stability in saline and humic-rich wastewater treatment systems.}, } @article {pmid41895928, year = {2026}, author = {Movsesijan, T and Alcañiz, AJ and Roch, FF and Chaughtai, MS and Dzieciol, M and Stessl, B and Thalguter, S and Strachan, CR and Raindl, M and Wagner, M and Selberherr, E and Quijada, NM}, title = {Biofilm capacity of the psychrophilic bacteria triggers their persistence in the equipment and their spread to beef products throughout processing.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118808}, doi = {10.1016/j.foodres.2026.118808}, pmid = {41895928}, issn = {1873-7145}, mesh = {*Biofilms/growth & development ; Animals ; Cattle ; *Food Microbiology ; *Red Meat/microbiology ; *Food Handling/instrumentation ; *Pseudomonas/genetics/isolation & purification/physiology ; *Psychrobacter/genetics/isolation & purification/physiology ; *Equipment Contamination ; Abattoirs ; Food Contamination/analysis ; }, abstract = {Microbial contamination in food processing remains a persistent and complex challenge. Understanding the sources, contributing factors, and control measures is essential for effective mitigation. In this study we employed a combination of metagenomic sequencing, targeted culturomics, and whole-genome sequencing of key isolates to gain a comprehensive view of bacterial dynamics and functional capabilities throughout a working shift in a beef slaughter and cutting facility. This allowed us to identify which bacteria are i) most prevalent in the clean facility before the start of the work, ii) able to establish themselves over time, and iii) detectable in the final product. We further generated a functional profile of the microbial community within the facility, with a particular focus on antimicrobial resistance and biofilm formation genes, and the presence of specific pathogens and spoilage organisms. Both culture-based and sequencing data showed that Psychrobacter and Pseudomonas strains present in the final product were also detected on the membrane skinner, a machine used to remove all the excess tissues from meat, and in the drains even after cleaning. We found a high number of genes involved in biofilm formation in Psychrobacter immobilis, a characteristic that may explain their biofilm capacity and the survival of this species during the cleaning process and persistence throughout the facility. Taken together, our findings suggest potential sources of contamination and highlight the advantages of integrating culture-dependent methods with high-throughput sequencing technologies to enhance microbial monitoring and control strategies in food production environments.}, } @article {pmid41895935, year = {2026}, author = {Li, H and Hu, H and Lu, W and Liu, J and Peng, Q and Wang, S and Dan, T}, title = {Metagenomic analysis of lactic acid bacteria communities in inner Mongolian fermented dairy products: influence of milk source and geography.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118849}, doi = {10.1016/j.foodres.2026.118849}, pmid = {41895935}, issn = {1873-7145}, mesh = {*Cultured Milk Products/microbiology ; Animals ; *Lactobacillales/genetics/classification/isolation & purification ; China ; *Milk/microbiology ; *Metagenomics/methods ; *Food Microbiology ; Fermentation ; Geography ; Cattle ; }, abstract = {Inner Mongolia, a key grassland region in China, has a long-standing tradition of fermented dairy products. This study aimed to elucidate the influence of milk source and geographical origin on the community structure and functional characteristics of lactic acid bacteria (LAB) in fermented milk. Twenty-four fermented milk samples from four regions were subjected to metagenomic sequencing analysis including α/β-diversity assessment, taxonomic classification, and functional annotation. The milk source and geographical region jointly shaped the diversity of LAB. The LAB community structure in fermented mare milk displayed more pronounced geographical differentiation than that in fermented cow milk. The core dominant LAB species included Lactobacillus kefiranofaciens, Lactobacillus helveticus, and Lactococcus lactis, with L. helveticus being more abundant in fermented mare milk. The functional profiles of LAB varied depending on the milk source used. The data indicated that milk source was a primary factor associated with the core LAB composition, while geographical origin was associated with the modulation of community diversity and functional attributes. These findings provide region-specific insights into the microbial ecology of traditional Inner Mongolian fermented dairy products.}, } @article {pmid41895941, year = {2026}, author = {Zhang, J and Li, Y and Zhao, X and Wang, Q and Li, J and Xia, Y and Jambal, T and Dorjgotov, D and Zha, M and Chen, Y}, title = {The cheese of Xilingol: A comparative study on microbial diversity and metabolic profiles across typical and meadow steppes.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118860}, doi = {10.1016/j.foodres.2026.118860}, pmid = {41895941}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Animals ; Milk/microbiology ; *Food Microbiology ; *Microbiota ; *Metabolome ; China ; Amino Acids ; }, abstract = {Xilingol cheese (hurood), a traditional product of Inner Mongolia, acquires its superior flavor and quality from region-specific microbial communities. Understanding the microorganisms and metabolites of hurood across different grassland ecosystems is crucial. This study collected milk and hurood samples from typical and meadow steppes. A total of 179 species were identified, with Moraxella osloensis being more abundant in milk and Lactococcus lactis dominant in hurood. Additionally, 26 differential metabolites were screened from different grasslands, with 19 metabolites found in higher concentrations in hurood, such as N-lactoyl-phenylalanine and N-Acetyl-L-Histidine. These differential metabolites are mainly involved in lipid, carbohydrate, amino acid, and energy metabolism. Spearman correlation analysis revealed that L. lactis was significantly and positively correlated with differential metabolites such as O-phospho-l-serine and gluconic acid, which may affect hurood quality through carbohydrate and protein metabolism, especially amino acid metabolism. M. osloensis was positively correlated with metabolites such as 2-Methylhippuric acid and γ-Glu-Cys. Samples from typical steppe showed a richer microbial diversity, while samples from meadow steppe exhibited a higher enrichment of beneficial microorganisms and metabolites. Superior milk quality and the environmental conditions for lactic acid bacteria colonization may both promote the formation of superior flavor characteristics and functional components. This observational study offers valuable insights into the microbial and metabolic characteristics of hurood, thereby supporting efforts to improve hurood quality.}, } @article {pmid41895971, year = {2026}, author = {Silva, FA and Cabral, L and de Assis, BBT and Ferreira, DP and Egea, MB and Pimentel, TC and Magnani, M}, title = {Microbiota of foods: a comprehensive review of diversity and potential implications.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118899}, doi = {10.1016/j.foodres.2026.118899}, pmid = {41895971}, issn = {1873-7145}, mesh = {*Food Microbiology/methods ; *Microbiota/genetics ; *Fermented Foods/microbiology ; Fermentation ; Metagenomics ; *Bacteria/classification/genetics ; Multiomics ; Humans ; }, abstract = {Microbial communities play a central role in food ecosystems. Fermented foods, in particular, host complex and dynamic microbiomes that are shaped by raw materials, fermentation substrates, processing environments, and regional production practices. This review provides an in-depth analysis of microbial diversity in various spontaneously fermented food products, including beverages, dairy products, and ethnic and other traditional food products. It highlights how microbial composition evolves throughout fermentation and how specific microorganisms contribute to the safety and sensory profiles of the final products. The field has undergone a methodological transformation, moving from classical culture-based methods to advanced omics technologies. Culture-independent approaches such as metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metabolomics enable a more comprehensive characterization of microbial communities, providing insights not only into their taxonomic composition but also into their functional roles. Despite increasing interest in metagenomics and metatranscriptomics, metataxonomic high-throughput sequencing, particularly 16S rRNA and ITS gene analyses, remains the most widely used technique due to its lower cost and accessibility. However, it provides limited resolution at the species level and cannot distinguish between live and dead cells. Microbiome characterization using omics has practical implications for the food industry, including the identification of microbial signatures in artisanal foods and the improvement of understanding fermentation processes. Our manuscript emphasizes a broad comparative overview of microbial diversity across multiple categories of fermented foods and integrates this with a methodological perspective on omics approaches used to characterize these communities. Findings outline the main methodological approaches, sequencing platforms, primer sets, and bioinformatic tools used in studies, as well as the current limitations and future directions in the field. Integrative multi-omics strategies are expected to significantly enhance food safety, quality, traceability, and functionality across diverse food systems.}, } @article {pmid41896456, year = {2026}, author = {Habot-Wilner, Z and Ostrovsky, M and Zur, D and Schwartz, S and Hagin, D and Gadoth, A and Ben-Ami, R and Paran, Y and Goldshmidt, H and Slutzkin, M and Adler, A and Levytskyi, K}, title = {Response to: 'Comment on 'Metagenomic next-generation sequencing: a game changer in the diagnosis of unique intraocular infections''.}, journal = {Eye (London, England)}, volume = {40}, number = {9}, pages = {1420}, pmid = {41896456}, issn = {1476-5454}, } @article {pmid41896477, year = {2026}, author = {Shaw, J and Marin, MG and Li, H}, title = {High-resolution metagenome assembly for modern long reads with myloasm.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41896477}, issn = {1546-1696}, support = {R01 HG010040/HG/NHGRI NIH HHS/United States ; PDF-587396//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; R01HG010040//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; }, abstract = {Long-read metagenome assembly promises complete genomic recovery from microbiomes. However, the complexity of metagenomes poses challenges. Here we present myloasm, a metagenome assembler for modern long reads such as PacBio HiFi and Oxford Nanopore Technologies (ONT) R10.4 long reads. Myloasm uses polymorphic k-mers to construct a high-resolution string graph and then leverages differential abundance for graph simplification. On real-world ONT metagenomes, myloasm assembled three times more complete circular contigs than the next-best assembler. Myloasm can make ONT and HiFi assemblies comparable. For example, on a jointly sequenced gut metagenome, myloasm with ONT assembled more complete circular genomes than any assembler with HiFi. Myloasm also recovers previously inaccessible within-species diversity. Here, we recovered six complete Prevotella copri single-contig genomes from a gut metagenome and eight complete TM7 (Saccharibacteria) contigs with >93% similarity from an oral metagenome. Overall, we show that myloasm outperforms existing long-read metagenome assemblers across a range of environments and modern sequencing technologies.}, } @article {pmid41896490, year = {2026}, author = {Zheng, M and Yang, X and Tian, R and Xia, X and Xu, Q and Hui, Y and Chen, S and Liu, Y and Wang, A}, title = {A Segatella Copri-centered Gut Microbiota-mediated Metabolic Dysregulation Associated with Transition from Asymptomatic to Symptomatic Intracranial Atherosclerosis.}, journal = {Translational stroke research}, volume = {17}, number = {2}, pages = {}, pmid = {41896490}, issn = {1868-601X}, support = {82504498//National Natural Science Foundation of China/ ; 82473699//National Natural Science Foundation of China/ ; 2022YFC3600600//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Intracranial Arteriosclerosis/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Case-Control Studies ; Biomarkers ; Middle Aged ; Aged ; Metabolomics ; *Ischemic Stroke/metabolism/microbiology ; *Eubacteriales ; }, abstract = {The mechanisms underlying the continuum from asymptomatic intracranial atherosclerotic stenosis (aICAS) to symptomatic intracranial large-artery atherosclerotic ischemic stroke (iLAA-IS) remain unclear. We investigated the gut microbiota-metabolite axis in this transition to identify predictive biomarkers and clarify key functional pathways. In a case-control study (63 iLAA-IS cases; 56 aICAS controls), fecal shotgun metagenomics and untargeted plasma metabolomics were profiled. Using machine learning with 10-fold nested cross-validation, we identified five robust biomarkers associated with the transition: Alistipes putredinis (risk-associated) and four protective features (Segatella copri, Gln-Gly, Methionine Sulfoxide, and N6-Acetyl-L-Lysine). Integrated models incorporating these markers significantly improved predictive performance relative to conventional risk factors (e.g., mean AUC of Gln-Gly: 0.9104 vs. 0.7188). Mechanistic analyses revealed a Segatella copri-centered metabolic dysregulation: its depletion coincided with a broad loss of anabolic pathways (BCAA biosynthesis, folate-SAM-methionine metabolism, and tRNA charging), which were positively linked to amino acid-related metabolites. In contrast, the pathways of Alistipes putredinis showed no such coupling. These findings suggest that the aICAS-to-iLAA-IS transition is characterized by chronic metabolic dysregulation, involving a Segatella copri-centered microbiota-metabolite axis. This multi-omic signature offers novel insights into stroke pathogenesis and potential targets for prevention.}, } @article {pmid41896556, year = {2026}, author = {Walsh, LH and Soni, V and Ancla, J and Somerville, V and Segata, N and Joyce, S and Sinderen, DV and Mahony, J and Shkoporov, AN and Kenny, JG and Cotter, PD and O'Sullivan, O}, title = {Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41896556}, issn = {2055-5008}, support = {DOMINO-101060218//European Union's Horizon Europe programme/ ; }, mesh = {*Bacteriophages/genetics/classification/isolation & purification ; *Metagenome ; Metagenomics/methods ; *Bacteria/virology/genetics/classification ; *Food Microbiology ; Genome, Viral ; Phylogeny ; Biodiversity ; }, abstract = {Bacteriophages are key drivers of microbial ecology, co-existing and co-evolving with bacteria across diverse environments. Limitations in culturing, alongside advances in sequencing and bioinformatics, have driven the use of metagenomics to explore viral diversity. Viral-specific analysis of >3000 food metagenomes from cFMD produced the FVGC, comprising ~3400 metagenome-assembled viruses, most of which belong to novel Caudoviricetes lineages (n = 91), with only ~15% represented in IMG/VR v4. Together, these findings reveal extensive uncharacterized viral diversity in food systems. Beyond serving as a reference, the FVGC facilitates detailed investigation of virus-host interactions. Viral sequences were pervasive across microbial genomes, with several bacterial families exhibiting near-universal associations with viral elements. Bacterial antiviral defence systems were abundant and taxonomically diverse, dominated by restriction-modification systems, while CRISPR-Cas systems showed pronounced lineage-specific distributions; in contrast, viral anti-defence genes were detected at low frequency (<10% of MAVs). Host prediction linked MAVs to clinically relevant taxa, including expanded ESKAPE pathogens such as Klebsiella pneumoniae, Acinetobacter baumannii, Staphylococcus aureus, and Enterobacter spp., highlighting the ecological connectivity between food-associated viruses and clinically important bacteria. Antimicrobial resistance signals were scarce, suggesting minimal phage-mediated AMR dissemination in food environments. This new publicly available viral database represents a valuable resource for further exploration of viral diversity.}, } @article {pmid41896639, year = {2026}, author = {Puetz, LC and O Delmont, T and Mitchell, AL and Finn, RD and Zhang, G and Shepeleva, DV and Kharlamova, AV and Kukekova, AV and Trut, LN and Gilbert, MTP}, title = {Gut microbiome community structure correlates with different behavioral phenotypes in the Belyaev Farm-Fox Experiment.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41896639}, issn = {2399-3642}, support = {NIH R35 GM144276//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; RSF-21-44-04405//Russian Science Foundation (RSF)/ ; DNRF143 Center for Evolutionary Hologenomics//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; }, mesh = {Animals ; *Foxes/microbiology/physiology ; *Behavior, Animal ; Phenotype ; *Gastrointestinal Microbiome ; Domestication ; *Bacteria/classification/genetics ; }, abstract = {Domestication represents one of the largest biological shifts of life on Earth, and for many animal species, behavioral selection is thought to facilitate early stages of the process. The gut microbiome of animals can respond to environmental changes and have diverse and powerful effects on host behavior. As such, we hypothesize that selection for tame behavior during early domestication, may have indirectly selected on certain gut microbiota that contribute to the behavioral plasticity necessary to adapt to the new social environment. Here, we explore the gut microbiome of foxes from the tame and aggressive strains of the "Russian-Farm-Fox-Experiment". Microbiota profiles reveal a significant depletion of bacteria in the tame fox population that have been associated with aggressive and fear-related behaviors in other mammals. Our metagenomic survey allows for the reconstruction of microbial pathways enriched in the gut of tame foxes, such as glutamate degradation, which converge with host genetic and physiological signals, revealing a potential role of functional host-microbiota interactions that could influence behaviors associated with domestication. Overall, by characterizing how compositional and functional potential of the gut microbiota and host behaviors co-vary during early animal domestication, we provide further insight into our mechanistic understanding of this adaptive, eco-evolutionary process.}, } @article {pmid41896653, year = {2026}, author = {Zhao, Z and Yang, Y and Zhang, L and He, X and Ding, K and Chen, Y and Huo, Y and Li, P and Li, R and Ali, T and Zhao, D and Choe, H and Ma, J and Shang, D and Zhang, L}, title = {Multi-omics and network pharmacology reveal the mechanisms of Scutellaria barbata D.Don and Scleromitrion diffusum (Willd.) R.J.Wang against pancreatic cancer.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41896653}, issn = {2045-2322}, support = {2022-BS-244//Liaoning Provincial Doctoral Research Startup Fund Project/ ; XLYC1907113//Liaoning Revitalization Talents Program/ ; 2022RJ19//Distinguished Young Scholars in Dalian/ ; }, mesh = {Animals ; *Pancreatic Neoplasms/drug therapy/metabolism/pathology ; Humans ; *Scutellaria/chemistry ; Mice ; Cell Line, Tumor ; Network Pharmacology/methods ; Apoptosis/drug effects ; *Plant Extracts/pharmacology ; Xenograft Model Antitumor Assays ; Multiomics ; Mice, Nude ; Cell Proliferation/drug effects ; Cell Survival/drug effects ; *Antineoplastic Agents, Phytogenic/pharmacology ; Proteomics ; Cell Movement/drug effects ; Gastrointestinal Microbiome/drug effects ; Male ; }, abstract = {Pancreatic cancer (PC) is a common gastrointestinal malignancy whose initiation and progression may be closely linked to the gut microbiota. Previous research indicates that Scutellaria barbata D. Don and Scleromitrion diffusum (Willd.) R.J. Wang (SB-SD) exhibit diverse biological activities, such as anti-inflammatory, antioxidant, and antitumor effects, though their precise regulatory mechanisms are not fully elucidated. Here, we treated PC cells with SB-SD to assess its impact on cell viability, apoptosis, migration, and cell cycle progression, while Western blotting analyzed the expression of HSP90AA1, MAPK3, p53, CDK1, and p21. We also established a pancreatic cancer xenograft model in nude mice to evaluate the in vivo inhibitory effect of SB-SD on tumor growth. Furthermore, we employed metagenomic sequencing, untargeted metabolomics, and quantitative proteomics to comprehensively profile changes in the gut microbiota, serum metabolites, and differentially expressed proteins, with Western blotting subsequently validating BCKDK, GATM and p53 expression. The results show that SB-SD significantly inhibited PC cell proliferation, promoted apoptosis, and induced S/G2 phase cell cycle arrest, potentially via modulation of the HSP90AA1/MAPK3 signaling pathway. Measurements of tumor volume and weight, complemented by histopathological analysis, confirmed that SB-SD effectively suppressed the growth of PANC-1 xenograft tumors. Integrated multi-omics analyses suggest that the antitumor effects of SB-SD may involve the modulation of key gut microbes like Bacteroides caccae and Lactobacillus, the promotion of choline metabolism, and the regulation of BCKDK and GATM. Together, these findings not only corroborate the direct antitumor activity of SB-SD against pancreatic cancer but also offer novel mechanistic insights by constructing a microbiota-metabolite-protein interaction network.}, } @article {pmid41896698, year = {2026}, author = {Jung, S and Militsi, E and Huck, O}, title = {Oral Microbiome in Systemic Autoimmune Diseases: A Systematic Review.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.70215}, pmid = {41896698}, issn = {1601-0825}, abstract = {OBJECTIVE: The oral cavity represents a key but underexplored interface between host immunity and microbial communities. The aim of this systematic review was to synthesize current literature on oral microbiota alterations in systemic autoimmune diseases.

METHODS: PubMed and Web of Science databases were searched for human studies published between January 2000 and April 2025. Eligible observational studies compared adults with diagnoses of systemic autoimmune diseases to controls and characterized oral microbiota diversity and/or composition using sequencing-based methods. Different oral habitats were analyzed (saliva, dental plaque, oral mucosa, gingival crevicular fluid).

RESULTS: 42 studies met inclusion criteria: 19 on rheumatoid arthritis, 18 on primary Sjögren's syndrome, 5 on systemic lupus erythematosus, and 1 on anti-neutrophil cytoplasmic autoantibody-associated vasculitis. 16S rRNA gene sequencing predominated and only 3 studies used shotgun metagenomics, among which one also profiled the oral virome. Across systemic autoimmune diseases, dysbiosis was characterized by enrichment of anaerobic genera (Prevotella, Veillonella) and depletion of commensals (Neisseria, Haemophilus), with distinct β-diversity separation from controls. Periodontal disease and reduced salivary secretion significantly modulated microbial communities but did not fully explain disease-associated alterations.

CONCLUSION: The oral microbiome exhibited shared dysbiotic signatures. However, methodological and clinical heterogeneity limited direct comparison between studies.}, } @article {pmid41897379, year = {2026}, author = {Zhang, Y and Zhao, B and Li, J and Yuan, T and Liu, Y and Sun, Z}, title = {Effects and Adaptive Responses of Sulfate-Reducing Biochemical System to Acid Stress.}, journal = {Biomolecules}, volume = {16}, number = {3}, pages = {}, pmid = {41897379}, issn = {2218-273X}, support = {41772266//State Key Laboratory of Nuclear Resources and Environment, the National Natural Science Foundation of China/ ; }, mesh = {*Sulfates/metabolism ; *Desulfovibrio/metabolism/genetics ; Oxidation-Reduction ; Hydrogen-Ion Concentration ; *Stress, Physiological ; Adaptation, Physiological ; *Acids ; }, abstract = {A decrease in pH can affect the biochemical properties of a sulfate reduction system, but the stress responses to such pH fluctuations and acid-adaptive mechanisms of the microorganisms remain incompletely understood. Here, we compared the sulfate (SO4[2-]) reduction performance of a sulfate-reducing consortium (SRB system) and a pure Desulfovibrio sp. system (Des. system, control) under pH 7.0, 5.5, and 5.0 via batch experiments. A key novelty is the integration of microbial physiology and metagenomics to reveal adaptive mechanisms: the Des. system showed significant inhibition of growth and sulfate reduction with decreasing pH, while the SRB system maintained superior SO4[2-] removal efficiency through three synergistic adjustments: (1) physiological regulation (enhanced H[+]-ATPase activity, stress protein production, and cell membrane cyclopropane fatty acid content); (2) microbial community restructuring (enrichment of acid-resistant Bacillus and Clostridium); and (3) functional gene upregulation (sulfate import, dissimilar sulfate reduction, sulfide oxidation, and SOx system-related genes, p < 0.05). This study links physiological responses to metagenomic functional shifts under acid stress, providing critical theoretical support for applying sulfate-reducing consortia in acidic sulfate-containing wastewater remediation.}, } @article {pmid41897502, year = {2026}, author = {Khan, A and Xiong, Z and Khan, IA and Cheng, X and Luo, Q and Jia, L and Liu, W and Huang, C and Chen, Z}, title = {Dimercaprol Reprograms Intestinal Redox Homeostasis and Organelle Crosstalk to Combat Iron-Induced Gut Dysbiosis Through NRF2/HO-1 Signaling.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41897502}, issn = {2076-3921}, support = {2024YFHZ0325//Zhengli Chen/ ; 32071161//Chao Huang/ ; 2023NSFC1929//Chao Huang/ ; }, abstract = {Gut disorders are largely caused by iron-induced microbial dysbiosis. Excess iron disrupts barrier integrity by inducing oxidative stress, leading to impaired cellular processes. The determination of therapeutic compounds that can reduce iron-induced damage and maintain gut cellular integrity is still a top objective. Dimercaprol (DP) represents a novel iron-chelating strategy for the treatment of iron-induced gut disorders. A chronic iron-overload model was established in mice via intragastric gavage of ferric citrate (FC) (286 mg/kg BW) for 16 weeks. Similarly, IPEC-J2 cells were exposed to FC (50 µmol/L) for 24 h. DP was used as a mechanistic probe to elucidate the pathways involved in iron-induced toxicity. Cells were transfected with or without NRF2 siRNA and exposed to DP post-FC. Colonic contents were assessed via metagenomics and metabolomics. Both in vivo and in vitro experiments were analyzed through a multifaceted analysis, Western blot, RT-qPCR, ELISA, transmission electron microscopy and immunofluorescence assays. Thiols in DP protect gut cells from damage by boosting their natural antioxidant defenses via the NRF2/HO-1 pathway. The DP mechanism of action is multifaceted, including enhancement of barrier integrity, protecting mitochondrial structure and function, suppression of inflammation and endoplasmic reticulum (ER) stress and restoration of gut microbial and metabolic homeostasis. These protective effects are mainly caused by the activation of the NRF2/HO-1 pathway, which makes DP a potential therapeutic agent for disorders caused by chronic gut injury induced by FC. DP provides strong protection against iron-induced gut damage by restoring organelle crosstalk, redox homeostasis and microbial-metabolic balance through NRF2/HO-1 signaling.}, } @article {pmid41897791, year = {2026}, author = {Xie, M and Xue, F and Sun, M and Zhuang, Q and Tang, S and Huang, Y and Zhang, Y and Hu, J and Zhou, Y}, title = {Determination of the Modulatory Effects of Selenium-Enriched Egg Powder on the Physiological Immune Response and Cecal Microbiota of Kunming Mice.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, pmid = {41897791}, issn = {2304-8158}, support = {20252BAC240155//Natural Science Foundation Project of Jiangxi Province/ ; JX-202401//the Open research projects of key laboratories of the Jiangxi Province "Mechanism Research of the Regulation on Immune System by Selenium-enriched Eggs"/ ; }, abstract = {Se-enriched functional eggs are prevalent nowadays, which may help improve body health and anti-oxidant capacities. However, the modulatory effects on cecal microbiota are still limited. This study aims to investigate the underlying mechanism of Se-enriched egg powder in modulating the cecal microbiota of Kunming mice. A total of 72 mice were randomly assigned to a control treatment (CON), a conventional egg powder treatment (EP), and four gradient Se-enriched egg powder treatments (EPS1-EPS4, with the Se content ranging from 0.01 to 0.04% of total dietary content) for a 35-day feeding procedure. Parameters included growth performance, tissue Se content distribution, serum anti-oxidant capacities (GSH-Px, SOD, MDA), and immune cytokines (IgG, TNF-α), and cecal microbiota composition was further measured. Results showed dietary 0.02% (EPS2) significantly improved growth performance, physiological anti-oxidant defenses, and cytokine TNF-α (p < 0.05), while significantly reducing feed conversion ratio and malondialdehyde (MDA) compared with CON (p < 0.05). Metagenomic results revealed that Se-enriched egg powder significantly increased bacterial α-diversity and the abundance of Akkermansia, Bacteroides, and Bifidobacterium (p < 0.05), while significantly decreasing Desulfovibrio and Escherichia-Shigella (p < 0.05). In conclusion, dietary supplementation with Se-enriched egg powder effectively enhances growth performance, anti-oxidant capacity, and immunity, mainly through the promotion of beneficial bacteria diversity and suppression of pathogens.}, } @article {pmid41897857, year = {2026}, author = {Yang, Y and Wang, J and Wang, Z and Li, C and Hu, X and Liao, S and Wang, L}, title = {Airborne Microbiome of Tropical Ostrich Farms: Diversity, Antibiotic Resistance, and Biogeochemical Cycling Potential.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, pmid = {41897857}, issn = {2076-2615}, support = {42367014//The National Natural Science Foundation of China/ ; }, abstract = {The expansion of tropical specialty livestock farming raises urgent concerns about airborne pathogen and antibiotic resistance dissemination. Ostrich farming, characterized by high-density stocking and feed exposure, yet their microbial ecology remain poorly characterized. This study analyzed 48 bioaerosols samples from an ostrich farm in Hainan, China, across dry and rainy seasons using 16S rRNA sequencing and metagenomics. The bacterial community were dominated by Firmicutes, Proteobacteria, and Actinobacteria, followed by Staphylococcus, Bacillus, and Acinetobacter as predominant genera, with particle size significantly shaping their structure. Large particles (>7.0 μm) carried higher species richness, while medium particles (2.1-3.3 μm) exhibited the highest diversity and evenness. Notably, small particles (0.65-1.1 μm), which can penetrate deep into the lungs, were enriched with Brevibacillus and Corynebacterium. Metagenomic analysis identified 638 antibiotic resistance genes (ARGs), dominated by efflux pump-associated determinants. The detection of clinically relevant ARGs (e.g., mcr-1 and blaTEM) reflects the genetic potential of the airborne resistome, rather than confirmed resistance phenotypes or active horizontal gene transfer. Functional analysis revealed a strong potential for organic matter degradation, driven by abundant carbohydrate-active enzymes (CAZymes) and their corresponding CAZyme genes, as well as a nitrogen cycle dominated by assimilation and reduction pathways, while genes for nitrogen fixation and nitrification were absent. Our findings demonstrate that ostrich farming enhanced airborne microbial diversity and functional potential, facilitating the ARG dissemination and nitrogen transformation. This study provides critical insights into the ecological and health risks of bioaerosols in tropical livestock farms, informing environmental monitoring and risk management strategies.}, } @article {pmid41897913, year = {2026}, author = {An, Q and Chen, S and Ma, S and Bai, R and Lu, Z and Liu, Y and Wang, F and Wang, Q and Song, Y and Zhang, G and Lyu, Y and Wang, L and Wang, Y and Xia, Z}, title = {Shotgun Metagenomics Reveals Gut Microbiome Remodeling with Altered Taxonomic Composition and Functional Potential in Diabetic Dogs.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, pmid = {41897913}, issn = {2076-2615}, support = {1051-2225006//General Program of the 2025 Talent Fund, Veterinary Teaching Hospital, China Agricultural University/ ; }, abstract = {Gut microbiota dysbiosis is implicated in metabolic disorders, yet taxonomic and functional alterations in canine diabetes remain incompletely defined. Here, we performed shotgun metagenomic sequencing of fecal samples from 38 diabetic dogs and 37 healthy controls under controlled conditions (no recent antibiotic/probiotic exposure and stable commercial diets). Alpha-diversity indices did not differ between groups, whereas beta-diversity revealed significant separation of community structure at both genus and species levels (p < 0.05). Linear discriminant analysis effect size (LEfSe) identified enrichment of opportunistic-associated taxa in diabetic dogs, including Enterobacterales/Enterobacteriaceae (e.g., Escherichia coli, Klebsiella pneumoniae, Salmonella enterica) and Enterococcus faecalis. In contrast, healthy dogs were enriched for putatively beneficial taxa linked to bile acid and short-chain fatty acid (SCFA) metabolism, including Turicibacter spp. and Romboutsia spp. Functional profiling showed higher abundances of pathways related to carbohydrate/energy metabolism, membrane transport, and virulence/colonization in diabetic dogs; 17 KEGG level-3 pathways and 320 KOs differed at FDR < 0.05, with enriched modules including bacterial secretion systems, lipopolysaccharide biosynthesis, chemotaxis/flagellar assembly, and biofilm formation. Collectively, canine diabetes is associated with a remodeled gut microbiome characterized by expansion of opportunistic pathogens and elevated virulence and metabolic potential, supporting exploration of microbiota-targeted strategies as a complement to conventional management.}, } @article {pmid41897927, year = {2026}, author = {Fukuda, EP and Lu, Y and Fowler, E and Jessup, RW and Drewery, ML}, title = {Metagenomic Insights into the Effects of Dietary Thymol on the Structure and Function of the Rumen Microbial Community in Beef Steers Consuming Forage.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, pmid = {41897927}, issn = {2076-2615}, support = {2021-77040-34881//National Institute of Food and Agriculture/ ; 2020-38422-32250//National Institute of Food and Agriculture/ ; N/a//Translational Health Research Center/ ; }, abstract = {While essential oils are gaining momentum as a strategy to modulate rumen function and potentially reduce enteric methane in cattle, little is known about how their bioactive components, terpenes, affect rumen microbes. Our objective was to evaluate how in vivo doses of thymol affect the structure and function of the rumen microbial community via whole genome shotgun sequencing (WGS). Four beef steers were used in a 4 × 4 Latin square with four 28 d periods. Steers consumed ad libitum forage and received one of four thymol doses (0 [CON], 120 [120-T], 240 [240-T], and 480 [480-T] mg/kg forage intake). Rumen contents were separated into liquid and solid fractions, DNA was extracted, analyzed via WGS, and assessed with orthogonal contrasts. After FDR correction, no taxa were affected by thymol; however, raw p-values demonstrated responses to thymol supplementation for solid-associated uncultured Lachnospiraceae bacterium (p = 0.04), uncultured Methanobrevibacter (p = 0.05), and uncultured Coriobacteriaceae bacterium (p = 0.02). Liquid-associated uncultured Prevotellaceae bacterium (p = 0.03), Prevotella sp. (p = 0.04), and Bacteroides sp. (p = 0.02) also responded to thymol, with the highest abundances observed at various thymol doses. Genes involved in energy production and amino acid metabolism transport were observed at the highest abundances at 240-T, while genes associated with cell cycle control, cell division, and chromosome partitioning were present in the highest abundances at 120-T. The findings suggest that thymol exerts dose-dependent effects on rumen microbial abundances and functional pathways, with 240 mg/kg forage intake appearing to be the most effective dose to downregulate methanogenic enzymes while also enhancing the enzymes associated with metabolism without negatively impacting microbial diversity.}, } @article {pmid41898277, year = {2026}, author = {Qiu, D and Suo, L and Wei, T and Lu, Z and Weng, Q and Xiao, J and Wang, X and Xu, Q and Wu, J}, title = {Mediation Role of Gut Microbiota in the Causal Relationship Between m6A Regulatory Genes and Metabolic Dysfunction-Associated Steatotic Liver Disease: A Mendelian Randomization Study.}, journal = {Biomedicines}, volume = {14}, number = {3}, pages = {}, pmid = {41898277}, issn = {2227-9059}, support = {3502Z20227102//Qinyu Xu/ ; }, abstract = {Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a globally prevalent condition with a complex pathogenesis. While both m6A RNA methylation regulators and gut microbiota have been independently implicated in MASLD, their potential causal interplay remains unexplored. This study aimed to investigate the causal relationships among m6A regulatory genes, gut microbiota, and MASLD, and to assess the mediating role of gut microbiota. Methods: We performed a two-sample Mendelian randomization (MR) analysis using publicly available genome-wide association study (GWAS) data. Genetic instruments for m6A regulators were derived from blood expression quantitative trait loci (eQTL) data. Gut microbiota and MASLD data were obtained from large-scale metagenomic and disease GWAS, respectively. The inverse-variance weighted method was the primary analysis, supplemented by sensitivity and mediation analyses to evaluate potential mediating pathways. Results: Genetically predicted levels of four m6A regulators showed significant causal associations with MASLD risk: ALKBH3 increased risk (OR = 1.17), whereas ALKBH5 (OR = 0.89), CBLL1 (OR = 0.76), and RBM15B (OR = 0.83) were protective. Nineteen gut microbial taxa were causally linked to MASLD. Among these, seven taxa were influenced by the four identified m6A genes. Although no mediation effects reached strict statistical significance, the pathway from ALKBH5 to MASLD via Parabacteroides abundance showed a suggestive indirect effect accounting for 21.9% of the total effect (p = 0.068). Given the limited statistical power of mediation analyses in MR settings, this observation should be interpreted with caution and requires validation in larger, well-powered studies. Conclusions: This MR study provides genetic evidence supporting causal roles of specific m6A regulators in MASLD and suggests that gut microbiota may partially mediate these relationships. The findings highlight a potential "m6A-gut microbiota-liver" axis in MASLD pathogenesis.}, } @article {pmid41898335, year = {2026}, author = {Schultheiss, HP and Escher, F and Aleshcheva, G and Wiegleb, G and Baumeier, C}, title = {Diagnostic and Therapeutic Options in Myocarditis and Inflammatory Cardiomyopathy.}, journal = {Biomedicines}, volume = {14}, number = {3}, pages = {}, pmid = {41898335}, issn = {2227-9059}, support = {KK5175802AP2, KK5463501AP2, KK5463901AP2//Federal Ministry of Economic Affairs, Germany/ ; 10169096, 10169098, 10169028//ProFIT grant of the Investitionsbank Berlin/co-funded by EFRE/ ; }, abstract = {Myocarditis and inflammatory cardiomyopathy are inflammatory diseases of the heart muscle that can have both infectious and non-infectious causes. They can be caused by an unresolved viral infection or other infection, or they can be autoimmune, toxic, or allergic in nature. The specific identification of the pathogen and/or confirmation of inflammation can only be achieved through direct tissue analysis using endomyocardial biopsy (EMB), as neither detection of the virus nor assessment of the quality and intensity of the inflammation is possible using non-invasive methods. Accordingly, the removal and analysis of an EMB is considered the diagnostic gold standard in international guidelines and statements. The sudden onset of atypical angina pectoris and initially exertion-dependent dyspnea, as well as arrhythmias, pericardial effusion, and progressive symptoms of heart failure, indicate an acute inflammatory process of the myocardium. In addition, nonspecific symptoms such as fatigue and reduced physical performance may also occur. Diagnostic evaluation includes an electrocardiogram (ECG), cardiac imaging, and laboratory tests. The analysis of the EMB is crucial for a definitive diagnosis and thus for the initiation of an etiology-based, specific and personalized therapy. This includes histological and immunohistochemical inflammation diagnostics as well as molecular virological diagnostics. These enable both the detection of viruses and the assessment of transcriptional virus activity. New analyses using metagenomic next generation sequencing (NGS) techniques provide insights of enormous diagnostic and therapeutic relevance. This applies both to the spectrum of detectable pathogens and to the possibility of confirming transcriptional viral activity. In addition, gene expression profiling enables the differentiation of specific forms of myocardial inflammation (e.g., giant cell myocarditis, cardiac sarcoidosis, and eosinophilic myocarditis) and reduces the influence of "sampling errors" in focal inflammatory processes. The treatment of heart failure or ventricular arrhythmias is always symptomatic according to general evidence-based guidelines. In severe cases, mechanical circulatory support or even a heart transplant may be necessary. Patients with histologically confirmed myocardial inflammation or intramyocardial viral infection can be offered specific, causal, and personalized therapy. These patients can be successfully treated with immunosuppressive or antiviral therapy, which significantly improves the prognosis of the disease.}, } @article {pmid41898386, year = {2026}, author = {Tahtouh Zaatar, M and Othman, R and Abushawish, M and Akl, M and Alachkar, MT and Almatboona, G and Alriyami, F and Alshaibani, A and Ashkanani, D and Basharova, M and Imam, M and Khassay, N and Mikhael, MS and Naderi Far, R and Shaqra, S and Verwey, K and Suleimanova, A and Yousafzada, M and Burmagina, Y}, title = {The Women's Microbiome: Molecular Insights, Clinical Gaps, and Future Frontiers in Precision Health with Implications for Gulf Cooperation Council Populations.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, pmid = {41898386}, issn = {1422-0067}, mesh = {Humans ; Female ; *Microbiota ; *Precision Medicine/methods ; Probiotics ; *Women's Health ; Pregnancy ; }, abstract = {The human microbiome has emerged as a central regulator of health and disease; however, women-specific microbiome research has only recently gained focused scientific attention. Accumulating evidence demonstrates that microbial ecosystems across the gut, vagina, skin, breast tissue, and reproductive tract are dynamically shaped by female hormones, life-stage transitions, and environmental exposures. These interactions influence immune regulation, metabolic homeostasis, reproductive outcomes, mental health, and cancer risk, in part through microbiome-mediated endocrine pathways such as the estrobolome. Advances in high-resolution molecular technologies-including metagenomics, metabolomics, spatial and single-cell profiling, and artificial intelligence-driven modeling-have shifted microbiome research from descriptive taxonomy toward functional, mechanistic, and predictive science. These approaches highlight microbial function and metabolite production as stronger determinants of health outcomes than taxonomic composition alone. Nonetheless, major gaps persist, including limited causal evidence, methodological heterogeneity, underrepresentation of non-Western populations, and barriers to clinical translation. Microbiome-targeted interventions, including probiotics, prebiotics, postbiotics, and emerging microbiota-based therapies, have garnered increasing interest in women's health. Select Lactobacillus and Bifidobacterium strains show potential in modulating vaginal and gastrointestinal health, pregnancy outcomes, and immune function; however, clinical effects remain highly strain-specific and context-dependent. Discrepancies between experimental findings, commercial claims, and validated clinical use underscore the need for rigorous, women-centered trials and standardized outcome measures. This narrative review synthesizes current molecular insights into the women's microbiome across endocrine interactions, pregnancy, reproductive and metabolic health, lifestyle influences, and microbiome-based therapeutic strategies. We integrate clinical perspectives to identify diagnostic and translational challenges and propose future directions emphasizing precision microbiome medicine, validated biomarkers, careful evaluation of microbiome-targeted interventions, and inclusive research frameworks, including populations from the Gulf Cooperation Council (GCC). Collectively, this review positions the microbiome as a critical yet underutilized axis in women's health and outlines a roadmap toward personalized, evidence-based care across the female lifespan.}, } @article {pmid41898595, year = {2026}, author = {Makiel, K}, title = {Anti-Inflammatory Diets in Metabolic Syndrome and Obesity: Multi-Omics Perspectives on the Interplay Between Gut Microbiota, DNA Methylation, and Adipokine Regulation-A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, pmid = {41898595}, issn = {1422-0067}, support = {//University of Physical Education, 31-571 Cracow, Poland/ ; }, mesh = {Humans ; *Metabolic Syndrome/diet therapy/metabolism/microbiology/genetics ; *Obesity/diet therapy/metabolism/microbiology/genetics ; *Adipokines/metabolism/genetics ; *DNA Methylation ; Multiomics ; *Gastrointestinal Microbiome ; Animals ; *Diet ; *Anti-Inflammatory Agents ; Inflammation/diet therapy ; Nutrigenomics ; }, abstract = {An anti-inflammatory dietary pattern represents a key component of non-pharmacological management in obesity and metabolic syndrome (MetS), as it targets chronic low-grade inflammation, adipose tissue dysfunction, insulin resistance, and disturbances of the gut-metabolic axis. In the present work, we outline a framework for an "omics-based" approach that integrates data on gut microbiota composition and function (metagenomics), adipokine profiles, nutrigenomics, epigenetics, and related transcriptomic and metabolomic layers in order to enable more precise characterization of the metabolic phenotype and to support precision nutrition strategies. The proposed dietary model emphasizes the quality rather than merely the quantity of macronutrients, with particular focus on lipid profile optimization. Specifically, total fat intake is recommended to remain below 30% of total energy through the reduction in saturated fatty acids (SFA), trans fats, and excessive omega-6 fatty acids, alongside increased consumption of omega-3 PUFA (EPA/DHA) and plant-based sources of α-linolenic acid (ALA). Concurrently, greater intake of lean protein sources and low-glycemic-index carbohydrates rich in dietary fibre-particularly fermentable fractions-is recommended. The model also highlights the importance of polyphenols with antioxidant and immunomodulatory properties. To enhance feasibility and long-term adherence, recommendations are structured as flexible food substitutions rather than rigid prescriptions. Further well-designed interventional studies are required to confirm the impact of a multi-omics-based anti-inflammatory diet on both molecular and clinical endpoints.}, } @article {pmid41898625, year = {2026}, author = {Chaplin, AV and Podoprigora, IV and Shcherbakova, VA and Zakharzhevskaya, NB and Evseev, PV and Vasilyeva, AA and Koshkin, FA and Kardonsky, DA and Vorobyeva, EA and Kashatnikova, DA and Kazakova, VD and Efimov, BA}, title = {Parabacteroides vesiculifaciens sp. nov., a Novel Immunomodulatory, Vesicle-Producing Gut Commensal Isolated from the Human Gut.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, pmid = {41898625}, issn = {1422-0067}, support = {24-75-10100//Russian Science Foundation/ ; }, mesh = {Humans ; Phylogeny ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Bacteroidetes/genetics/classification/isolation & purification/metabolism ; Animals ; Genome, Bacterial ; Mice ; Fatty Acids/metabolism ; *Extracellular Vesicles/metabolism ; }, abstract = {The genus Parabacteroides comprises widespread gastrointestinal commensals, known to produce immunomodulatory molecules and extracellular vesicles, yet its full diversity is incompletely cataloged. This study describes strain ASD2025[T], isolated from healthy child feces, using a polyphasic taxonomic approach including phenotypic profiling, chemotaxonomy, and comparative genomics. Cells were non-motile, polymorphic rods that produced extracellular vesicles. Phylogenomic analysis placed ASD2025[T] within the genus Parabacteroides within a species complex consisting of P. acidifaciens, P. hominis, "P. massiliensis", P. merdae, and P. johnsonii, with average nucleotide identities to the type strains of 85.5-89.9%. The large genome (5.16 Mbp, 46.2% GC content) contained integrative conjugative elements harboring antibiotic resistance genes and hankyphage-related prophage. The strain produced succinate as the major metabolic end product, and its major fatty acids were anteiso-C15:0, iso-C17:0 3-OH, and C15:0. Conditioned medium from ASD2025[T] antagonized the interleukin-8 response caused by E. coli lipopolysaccharide in HT29 cells. The majority of related metagenome-assembled genomes originate from mouse microbiomes. Based on these distinct characteristics, strain ASD2025[T] (=VKM B-3926[T] = JCM 37967[T]) represents a novel species of the genus Parabacteroides, for which the name Parabacteroides vesiculifaciens sp. nov. is proposed.}, } @article {pmid41898646, year = {2026}, author = {Dang, X and Hanson, BA and Lopez, M and Miller, J and Jimenez, M and Koralnik, IJ}, title = {Predictive Utility of ViroFind Detection of Blood and CSF Virome for Viral Presence in Human Brain Tissue.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, pmid = {41898646}, issn = {1422-0067}, support = {DA048493/DA/NIDA NIH HHS/United States ; }, mesh = {Humans ; *Brain/virology ; *Virome ; HIV Infections/virology/blood/cerebrospinal fluid ; Herpesvirus 4, Human/isolation & purification/genetics ; Female ; Torque teno virus/isolation & purification/genetics ; Viral Load ; Parvovirus/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Male ; }, abstract = {Viral presence in the brain may contribute to chronic neurologic diseases. However, investigating these associations is limited by the difficulty of directly sampling brain tissue in living individuals. Here, we evaluated whether peripheral viral detection using unbiased target-enrichment next-generation sequencing could inform viral presence in the brain across a diverse set of viral taxa. We applied ViroFind to matched brain, blood (peripheral blood mononuclear cells, spleen, and/or lymph node), and cerebrospinal fluid (CSF) to assess the predictive utility of viral detection in blood and CSF for identifying viral presence in brain samples obtained from the National NeuroAIDS Tissue Consortium, including both HIV-infected (HIV[+]) and HIV-uninfected (HIV[-]) individuals without known active viral infection of the brain. Blood negativity was generally more informative for predicting the absence of viruses in the brain than blood positivity for predicting viral presence. CSF viral detection demonstrated limited predictive utility for brain presence across most viral taxa examined. Among blood[+] individuals, viral burden differed significantly between brain[+] and brain[-] cases for Epstein-Barr virus (EBV), parvovirus, and torque teno virus (TTV). Blood viral burden showed moderate ability to distinguish brain[+] from brain[-] cases for EBV and parvovirus, and strong discriminatory ability for TTV, with similar decision thresholds across HIV[+] and HIV[-] individuals.}, } @article {pmid41898837, year = {2026}, author = {Li, S and Chiodi, C and Maucieri, C and Della Lucia, MC and Zardinoni, G and Ravi, S and Squartini, A and Concheri, G and Geng, G and Wang, Y and Stevanato, P}, title = {Profiling Soil-Plant-Microbial Communities: DNA and Multi-Omics Techniques.}, journal = {Genes}, volume = {17}, number = {3}, pages = {}, pmid = {41898837}, issn = {2073-4425}, mesh = {Multiomics ; *Soil Microbiology ; Rhizosphere ; *Plants/microbiology/genetics ; Metagenomics/methods ; *Microbiota/genetics ; Genomics/methods ; Soil ; }, abstract = {Interactions among plant roots, soil, and microorganisms in the rhizosphere regulate nutrient cycling, plant health, and ecosystem resilience. Recent advances in DNA sequencing and multi-omics are contributing to a shift from primarily descriptive surveys toward more mechanistic and predictive frameworks. This review synthesizes methodological developments and conceptual insights spanning microbial ecology, functional genomics, and agricultural applications. We first summarize DNA-based approaches-marker-gene sequencing, shotgun metagenomics, and quantitative nucleic acid assays-and then complementary omics layers, including metatranscriptomics, metaproteomics, metabolomics, epigenomics, ionomics, and phenomics. We next outline computational advances in data integration, network modeling, and visualization that help represent complex multi-layered datasets as biologically interpretable systems. Applications relevant to climate resilience and sustainable agriculture are discussed, including the design of synthetic microbial communities, the identification of biomarkers for soil health and stress tolerance, and case studies in which rhizosphere multi-omics informs crop breeding and soil management strategies. Overall, these developments underscore the potential of treating microbes as functional and, to some extent, manageable components of the plant holobiont. Looking ahead, we identify key research gaps involving standardized workflows, cross-scale causal inference, and real-time monitoring pipelines that integrate molecular diagnostics with remote sensing and edge-cloud analytics. By linking ecological mechanisms with translational practice, multi-omics frameworks may support the development of more sustainable, data-driven agriculture that better aligns productivity with environmental stewardship.}, } @article {pmid41898993, year = {2026}, author = {Tanachaiwiwat, P and Sanscrainte, ND and Okech, BA and Estep, AS}, title = {Insecticide Resistance Mutations, Enzymatic Activity, and Pathogen Infection in Culex quinquefasciatus from Haiti.}, journal = {Insects}, volume = {17}, number = {3}, pages = {}, pmid = {41898993}, issn = {2075-4450}, support = {P0138_22_HS//Armed Forces Health Surveillance Directorate, Global Emerging Infection Surveillance Program/ ; 6036-10400-002-000-D//United States Department of Agriculture/ ; }, abstract = {Haiti is a Caribbean country of about 11 million people with a high burden of mosquito-transmitted disease and limited vector control, thereby making effective operational mosquito control of high importance. Previous studies have examined vector-borne disease burden and insecticide resistance markers in Haitian Aedes and Anopheles mosquitoes, but not Culex species. In this study, we examined collections of Culex quinquefasciatus from 12 locations in northern and southern Haiti for the presence of markers of insecticide resistance (using a variety of target-site mutations and biochemical assays) and pathogens (using a deep-sequencing microbiome workflow). The metagenomic analysis identified Wolbachia, Rhabdoviridae, and Plasmodium infections in all sample pools at relatively high levels, along with less frequent detections of other potential pathogens. Insecticide resistance marker examination identified variable frequencies of knockdown resistance and acetylcholinesterase resistance mutations, as well as variation in resistance-associated enzymatic activities in these populations. These findings indicate that insecticide resistance to pyrethroid and organophosphate insecticides is likely. Although there was variation among Culex mosquito populations and no clear activity pattern, enzymatic activity was significantly higher at the southern sites than at the northern sites. Similar findings in Cx. quinquefasciatus populations in other locations in the Americas strongly suggest that vector control with pyrethroid and organophosphate adulticides may be of limited efficacy.}, } @article {pmid41900279, year = {2026}, author = {De Luca, L and Menna, F and Lupo, S and Vingolo, EM and Carlà, MM and Mancini, M and Oliverio, GW and Minutoli, L and Baldascino, A and Mazzotta, C and Aragona, P and Meduri, A}, title = {The Ocular Surface Bacterial Microbiome and the Impact of Contact Lens Use: A Literature Review.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900279}, issn = {2076-2607}, abstract = {The ocular surface microbiome plays a critical role in maintaining ocular health, preventing infections, and regulating immune responses. Contact lens (CL) wear has been linked to alterations in microbial composition, potentially leading to dysbiosis and increased susceptibility to ocular infections. This review aims to summarize current evidence on the effects of CL use on the ocular microbiome and to discuss strategies to preserve microbial homeostasis. A literature search was conducted in PubMed, Scopus, Web of Science, and Google Scholar for English-language human studies published between January 2005 and January 2025. We included original studies and systematic reviews evaluating the ocular surface bacterial community in contact lens (CL) wearers using either sequencing-based approaches (microbiome; e.g., 16S rRNA gene sequencing/metagenomics) or culture-based methods (microbiota). Two authors screened titles/abstracts and full texts. Overall, 12 studies met the inclusion criteria and were qualitatively synthesized. Across included studies, CL wear was associated with reproducible changes in the ocular surface bacterial community, most commonly a shift toward a skin-like profile and increased detection/relative abundance of opportunistic taxa (e.g., Pseudomonas, Acinetobacter, and Staphylococcus aureus) together with reduced representation of typical ocular commensals in several sequencing-based datasets. Culture-based studies reported increased recovery of opportunistic bacteria from lenses and storage cases, supporting contamination/biofilm-related mechanisms. Lens care solutions and preservatives were reported to modulate bacterial profiles and may contribute to dysbiosis, although evidence remains heterogeneous across study designs and analytic pipelines. CL use is associated with significant alterations in the ocular microbiome, increasing the risk of microbial keratitis and corneal inflammatory events. Strategies to maintain microbial balance, including careful selection of lens care products and development of antimicrobial lenses, may improve ocular surface health in CL wearers. Future longitudinal studies with standardized sampling and analytic workflows are needed to clarify causal links between CL-associated microbial changes and clinical outcomes.}, } @article {pmid41900284, year = {2026}, author = {Kwon, H and Seo, JW and Jeong, M and Kim, Y and Chang, CL and Kim, JH and Choi, GE}, title = {Dietary Administration of a Soybean Fermented Preparation Reshapes Gut Microbial Community Structure and Colonic Mucosal Features in BALB/c Mice.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900284}, issn = {2076-2607}, support = {NRF-2022R1F1A1074419//National Research Foundation of Korea/ ; NRF-2022S1A5C2A04093562//National Research Foundation of Korea/ ; //Busan Metropolitan City and Busan Techno Park/ ; //RESEARCH FUND offered from Catholic University of Pusan in 2024./ ; }, abstract = {BACKGROUND/AIM: Fermented soybean-based products are known to influence gut microbial composition; however, the long-term effects of multicomponent soybean fermented preparations on gut microbiota and colonic mucosal features remain insufficiently characterized. This study examined the effects of a commercially available soybean fermented preparation (SFP), containing additional fermented plant and marine derived components, on gut microbial community structure and colonic histological features in BALB/c mice.

METHODS: BALB/c mice received oral SFP (1000 mg/kg) for 30 and 60 days. Gut microbial communities were analyzed using full-length rRNA operon sequencing. Colonic mucosal architecture and goblet cell density were evaluated via histological analysis (H&E).

RESULTS: SFP supplementation induced significant β-diversity separation at both 30 and 60 days (p < 0.05), indicating consistent restructuring of the gut microbial community. While alpha diversity (Observed OTUs) remained stable at 30 days, Shannon and Simpson indices were significantly reduced at 60 days (p = 0.001), indicating reduced community evenness driven by increased dominance of specific taxa, including Duncaniella. At the genus level, SFP administration was associated with increased relative abundances of Akkermansia, Lactobacillus, and Duncaniella, accompanied by reductions in several genera previously linked to dysbiosis. Histological analysis demonstrated a significant increase in goblet cell density (p < 0.01) in SFP-treated mice.

CONCLUSIONS: Long-term SFP supplementation was associated with sustained alterations in gut microbial composition and measurable histological changes in the colonic mucosa. While these findings indicate that SFP intake influences microbial structure and goblet cell abundance, further studies are required to determine the functional and physiological implications of these changes, particularly in relation to epithelial barrier function and host health.}, } @article {pmid41900290, year = {2026}, author = {Singh, K and Mitra, S}, title = {Operationalising Genomic Surveillance for Antimicrobial Resistance in Low- and Middle-Income Countries: A One Health Perspective from Bangladesh.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900290}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) represents a critical global health challenge, with low- and middle-income countries (LMICs) disproportionately affected due to limited surveillance capacity. Advances in microbial genomics offer powerful tools for AMR detection and monitoring; however, translating these technologies into sustainable, policy-relevant surveillance systems in resource-constrained settings remains challenging. This review synthesises current approaches to genomic surveillance of AMR in LMICs and presents Bangladesh as a case study to illustrate how genomic, environmental, and clinical data can be integrated within a One Health framework. We examine key barriers to implementation, including laboratory infrastructure, bioinformatics capacity, data governance, and cross-sector coordination, alongside emerging opportunities for capacity building and regional collaboration. Using Bangladesh as a case study, we highlight practical pathways for embedding genomic surveillance into national AMR strategies, integrating human, animal, and environmental reservoirs of antibiotic resistance. We argue that genomic surveillance can move beyond data generation to inform infection prevention, antibiotic stewardship, and public health decision making when supported by context-appropriate infrastructure and interdisciplinary engagement. By focusing on operational and translational considerations rather than technology alone, this review provides actionable insights for microbiologists, public health practitioners, and policymakers seeking to strengthen AMR surveillance systems in LMICs through a One Health approach.}, } @article {pmid41900318, year = {2026}, author = {Liu, X and Xiao, N and Yu, J and Geng, X and Zhang, M and Zhang, Y and Xu, H and Nie, C and Wang, M and Li, L}, title = {Divergent Microbial Community and Pathogenicity at a University-Urban Interface: A Comparative Analysis.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900318}, issn = {2076-2607}, support = {grant number 2022YFE0199800//National Key Research and Development Program of China/ ; grant number 24-1-8-smjk-13-nsh//Qingdao Science and Technology Wellness Promotion Demonstration Program/ ; grant number 82271658//the National Natural Science Foundation of China/ ; grant number SKLMTFCP-2023-01//SKLMT Frontiers and Challenges Project/ ; grant numbers ZR2024QD228 and ZR2024QC311//Shandong Provincial Natural Science Foundation/ ; grant number 24-4-4-zrjj-40-jch//Qingdao Natural Science Foundation/ ; grant number FDLAP24008//Opening Project of Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP)/ ; }, abstract = {Environmental metagenomics and microbial taxonomy provide essential frameworks to evaluate how population structures shape the evolution of antimicrobial resistance and microbial community dynamics within densely populated environments. To evaluate microbial community composition and pathogenic potential, high-touch surfaces at high-traffic sites on and off campus were analyzed using metagenomics and characterization of 188 bacterial isolates, including antibiotic susceptibility testing, hemolytic assays, and whole-genome sequencing. Off-campus sites showed significantly higher bacterial richness and more complex communities enriched with diverse potential pathogens. Notably, high-risk carbapenemase genes were predominantly identified in these off-campus urban environments. In contrast, on-campus environments harbored less diverse communities dominated by opportunistic, antibiotic-resistant Staphylococcus species, with metagenomic analysis confirming a concentrated enrichment of β-lactam resistance determinants associated with methicillin-resistant staphylococci. Phenotypic profiling revealed extensive antimicrobial resistance, with 84.7% of isolates exhibiting resistance to at least one antibiotic and 35.1% of Staphylococcus showing hemolytic activity. Whole-genome sequencing further revealed that these resistance and pathogenic traits are predominantly localized on mobile plasmids, highlighting a high potential for horizontal gene transfer. These findings indicate that population activities shape distinct microbial communities in closely adjacent environments and highlight the importance of monitoring high-risk resistance determinants in densely populated university settings.}, } @article {pmid41900320, year = {2026}, author = {Cheng, H and Han, J and Liu, K and Wang, L and Meng, Q and Liu, C and Liu, X and Wang, M and Yang, F and Li, X}, title = {Integrated Metagenomic and Metabolomic Profiling of Boar Semen During Ambient-Temperature Storage.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900320}, issn = {2076-2607}, support = {2022020101//Agricultural Breeds Research Project of Henan Province/ ; HAAS2023RCQD01//the Key Technology Research and Development Program for Precision and Efficient Breeding of Local Pigs in Hainan Province/ ; }, abstract = {The reproductive efficiency of breeding boars substantially influences swine industry productivity. Sperm viability during ambient-temperature storage is critically affected by environmental factors, including microbial activity. This study aimed to elucidate the dynamics and interactions between the seminal microbiome and metabolome during boar semen storage at 17 °C. Using integrated 16S rRNA sequencing and untargeted metabolomics, we analyzed semen samples from six healthy boars (31-33 months old) collected at day 0 (control), 2, 4, and 6 of storage. Our results demonstrate that storage leads to a marked decline in microbial diversity, progressive enrichment of the opportunistic genus Proteus, depletion of key antioxidant and cofactor metabolites such as vitamin B6, and extensive metabolic reprogramming-including alterations in short-chain fatty acid, purine, and lipid oxidation pathways. Multi-omics correlation analysis further revealed strong associations between microbial succession and metabolic shifts, highlighting their combined role in driving sperm functional decline. These findings provide a mechanistic basis for improving semen preservation strategies through microbiome and metabolite-targeted interventions.}, } @article {pmid41900339, year = {2026}, author = {Malik, PK and Mohapatra, A and Trivedi, S and Kolte, AP and Sahoo, A and Bhatta, R}, title = {In Vitro Degradation of Chlorpyrifos by the Ruminal Microbes: Insights from the Rumen Metagenome.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900339}, issn = {2076-2607}, abstract = {In vitro studies were conducted in a series to investigate if the ruminal microbes are capable of degrading chlorpyrifos. This in vitro study presents the results from three experiments: Exp. I was conducted without feed, while Exp II and III were conducted with feed, either with or without methanol for dissolving chlorpyrifos, respectively. A basal diet comprising finger millet straw and concentrate was prepared. Incubation medium with feed but without chlorpyrifos served as the control. A total of six replicates each of control and chlorpyrifos spiked were used for the incubation. The pesticide concentration in the incubation medium before and after 24 h of incubation was analyzed using GC-MS/MS. The genomic DNA was isolated from the incubation fluid of the individual samples, and the shotgun metagenomic sequencing was performed. The clean reads were taxonomically classified using the Kraken2 database, and microbial classification at different taxonomic ranks was separated using Pavian v1.0. The microbial genes in the metagenome data were predicted and assigned functional roles using the MetaErg v1.2.3 pipeline. The assigned KEGG Orthology (KO), EC numbers (Enzyme Commission number), Gene Ontology (GO), and corresponding NCBI taxonomy information relevant to chlorpyrifos metabolism/degradation were retrieved. Results from the study revealed that the chlorpyrifos concentration was decreased from 5.78 to 1.64 ppm over 24 h of in vitro incubation with feed. Similar alpha and beta diversity indices between control and chlorpyrifos treatments revealed that the richness and the evenness of the microbial population were not affected by the presence of chlorpyrifos in the rumen fluid. There was no difference in the microbiota affiliated to the major phyla such as Bacteroidota, Fibrobacterota, Bacillota, and Pseudomonadota. The EC 3.1.8.1, EC 3.1.3.1, EC 1.14.13.-, and EC 1.1.1.- reported for chlorpyrifos degradation were not detected in the metagenome, and only EC 3.1.1.1 was identified, which demonstrated that degradation of chlorpyrifos was carried out by the affiliated enzyme carboxylesterase. The presence of GO:0004035, GO:0004364, GO:0019637, GO:0016791, and GO:0042178 in the metagenome strengthens that the chlorpyrifos degradation in the present study was primarily assigned to the rumen microbiota. This in vitro study provided insights into the rumen microbiota involved in the chlorpyrifos degradation and the initial clue that the rumen microbes are capable of degrading chlorpyrifos. Further, the animal studies in different species with the variable levels of chlorpyrifos are also warranted to confirm the efficacy of rumen microbes in mixed syntrophy and determine the threshold capabilities of the ruminal microbes.}, } @article {pmid41900342, year = {2026}, author = {Ntzouvaras, A and Koletti, A and Zografaki, ME and Marka, S and Skliros, D and Vasilakis, G and Karavidas, I and Koukouvinis, AK and Efrose, RC and Kalloniati, C and Tzovenis, I and Flemetakis, E}, title = {Isolation and Characterization of Microalgae Isolates from Hydroponic Effluent Water: Metagenomics and Biotechnological Insights.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900342}, issn = {2076-2607}, support = {PRIMA2019-04//European Union research and innovation Horizon 2020/ ; }, abstract = {Hydroponic systems are gaining prominence in sustainable agriculture, yet their nutrient-rich effluents remain an underexplored source of microbial biodiversity with potential biotechnological interest. In this study, shotgun metagenomic sequencing was employed to profile, with a high taxonomic resolution, the photosynthetic microbial community in hydroponic effluent before and after a natural algal bloom, revealing pronounced shifts in microbial composition. Notably, relative abundance increased sixfold for Chlamydomonas reinhardtii and tenfold for Bigelowiella natans. Four dominant microalgal strains (PR1-PR4) were subsequently isolated and characterized through integrative morphological and molecular taxonomy, with phylogenetic analyses based on four genetic markers (18S rRNA, ITS, rbcL and tufA) confirming that each isolate represents a distinct lineage within Chlorophyceae families, including Chlorella sp., Chlamydomonas sp., and Scenedesmus sp. Growth kinetics under three temperature regimes, typical of Greek environmental conditions from spring to autumn (15 °C, 23 °C, 32 °C), demonstrated broad ecological plasticity and rapid biomass production, highlighting strains with strong adaptive resilience. Biochemical profiling of the isolates revealed significant inter-strain differences in primary and secondary metabolite content, including proteins (up to 43% DW), lipids (up to 31% DW), carbohydrates (up to 44% DW), photosynthetic pigments, phenolics, flavonoids, and antioxidant activity. The observed metabolic diversity of autochthonous microalgal strains from hydroponic environments, combined with their high growth rates, underscores their potential for applications in bioremediation, bioenergy, and the development of value-added products within a circular bioeconomy framework.}, } @article {pmid41900399, year = {2026}, author = {Yi, X and Lin, Y and Peng, Y and Liu, Y and Ning, C and Lei, J and Wang, L and Chen, C and Wu, L and Liao, J}, title = {Urbanization-Induced Shifts in Microbial Functional Genes of Wetland Nitrogen Cycling Promote Nitrous Oxide (N2O) Emissions.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900399}, issn = {2076-2607}, support = {32401392//National Natural Science Foundation of China/ ; OT-S-KTA4//Hunan Forest Quality Improvement and Efficiency Enhancement Demonstration Project Funded by the European Investment Bank Loan/ ; XLKY202216//Forestry Science and Technology Innovation Project of Hunan Province/ ; XLKY202319//Forestry Science and Technology Innovation Project of Hunan Province/ ; 2024JJ5235//Hunan Provincial Natural Science Foundation of China/ ; }, abstract = {Urban wetlands are assumed to contribute to nitrous oxide (N2O) emissions; however, the microbial mechanisms underlying enhanced N2O fluxes in urban wetlands and differences in microbial responses between aquatic and soil compartments have not been clearly identified. Here, we characterized the nitrogen (N) cycling microbial communities and their functional metabolic pathways in urban and rural wetlands using metagenomics and N2O flux measurements. Results showed that urbanization drove a 6~8-fold increase in N2O fluxes from urban wetlands compared to rural wetlands. Structural equation modeling (SEM) confirmed that urbanization intensity was a primary driver (standardized coefficients: 0.72 for soil and 0.92 for water). In wetland water, N2O emissions were negatively correlated with inorganic nutrient concentrations (coefficient = -0.62). Aquatic microbial communities exhibited substantial taxonomic shifts but preserved network connectivity, indicating adaptive strategies for surviving urban perturbations at the cost of reduced functional redundancy. In wetland soil, microbial communities maintained stability under urbanization, which was attributed to environmental buffering from heterogeneous microenvironments. Soil N2O emissions were positively linked to microbial alpha diversity (coefficient = 0.79). Furthermore, urban wetlands enriched genes mediating nitrification and denitrification while depleting genes associated with N fixation and organic N metabolism. This functional shift reflects microbial specialization in processing elevated reactive N (Nr) inputs from urban sources, trapping urban wetlands in an "N loss loop" that reinforces high N2O fluxes. This study elucidates the microbial mechanisms governing wetland N2O emissions under urbanization, thereby enhancing understanding of microbially mediated N cycling in the urban wetland ecosystem.}, } @article {pmid41900403, year = {2026}, author = {Zhang, W and Fan, C and Yang, L and Sun, Y and Tang, L}, title = {Integrated Metagenomic and Metabolomic Analyses Reveal Rhizosphere Soil Microecological Changes in Thlaspi arvense L. Lines with Different Alkaloid Contents.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900403}, issn = {2076-2607}, support = {CARS-16-S3//The China Agriculture Research System of MOF and MARA/ ; }, abstract = {Pennycress (Thlaspi arvense L.), a representative and economically valuable cover crop, supports and enhances key ecological processes throughout its life cycle via its root system. It is hypothesized that pennycress selectively modulates its rhizosphere microbial community through root-derived metabolites, which may influence both the crop's growth and the subsequent crops in rotation. However, systematic investigations comparing the rhizosphere microbiomes and metabolomes among different pennycress lines remain limited. This study employed metagenomic and metabolomic approaches to examine the dynamic changes in the rhizosphere microbial community and metabolite profiles of three pennycress lines with significantly different total alkaloid contents. The goal was to elucidate the interactions between microbes and metabolites. Results indicated significant differences in microbial community structure across the cultivars. JiL67 maintained stable community diversity, while LiN54 (with the lowest alkaloid content) showed reduced diversity. HeL43 (with the highest alkaloid content) exhibited increased diversity but also potential community homogenization, accompanied by the significant enrichment of microbial taxa capable of alkaloid tolerance. Metabolomic analysis identified metabolites such as Portulacaxanthin II, Oleanolic acid, and Soraphen A as significantly enriched in the rhizosphere soil of pennycress. This study reveals the shifts in rhizosphere microbial communities and metabolites linked to different pennycress lines and uncovers their interactive mechanisms, providing a scientific foundation for developing more economically efficient pennycress cultivation strategies.}, } @article {pmid41900432, year = {2026}, author = {Guerrero-Torres, LE and García-Galindo, JJ and Gómez-Galindo, MF and Delgado, DIR and Retolaza Carlos, CE and Suárez-Rico, DO and Beltrán-Ramírez, A and Balleza Alejandri, LR}, title = {The Gut Microbiota in Parkinson's Disease: Mechanistic Insights into Microbial-Host Interactions.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900432}, issn = {2076-2607}, abstract = {Parkinson's disease (PD) is a multifactorial neurodegenerative disorder characterized by progressive motor and non-motor manifestations, including early gastrointestinal dysfunction. Growing evidence implicates the gut microbiota as an active modulator of host immune tone and neurodegenerative vulnerability, extending beyond descriptive taxonomic associations toward functional and metabolic mechanisms. PD-associated dysbiosis is consistently characterized by altered microbial functional capacity, including reduced short-chain fatty acid (SCFA) production, enrichment of pro-inflammatory metabolic traits, and sustained immune stimulation at the intestinal interface. These shifts promote chronic low-grade inflammation and intestinal barrier perturbations, creating conditions that may facilitate abnormal α-synuclein aggregation within the enteric nervous system. Current management predominantly relies on dopaminergic replacement and related symptomatic strategies, such as levodopa combinations, dopamine agonists, monoamine oxidase-B and catechol-O-methyltransferase (COMT) inhibitors, and device-aided therapies, which alleviate symptoms but do not halt underlying neurodegeneration or modify long-term disease course. These therapeutic limitations have intensified interest in upstream mechanisms that might be amenable to disease-modifying interventions, particularly those arising at the level of the gut microbiota and gut-immune-brain axis. This narrative review integrates clinical, metagenomic, metabolomic, and mechanistic evidence to propose a unified model in which microbiota-driven immune and metabolic perturbations may act as upstream drivers converging on α-synuclein pathology, neuroinflammation, and neurovascular dysfunction.}, } @article {pmid41900479, year = {2026}, author = {Park, H and Kim, JS and Kim, DJ and Suk, KT}, title = {Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900479}, issn = {2076-2607}, support = {NRF-2020R1I1A3073530//National Research Foundation of Korea/ ; NRF-2020R1A6A1A03043026//National Research Foundation of Korea/ ; }, abstract = {Advances in sequencing technologies have transformed human microbiome research, yet most analyses still rely on species-level profiles. However, strains rather than species represent the true ecological and functional units of the microbiome. Individual strains can vary substantially in gene content, metabolic capacity, virulence factors, antimicrobial resistance, and host-interaction properties. These differences critically influence immune responses, epithelial barrier integrity, disease susceptibility, and therapeutic outcomes. Here, we synthesize recent human microbiome studies that provide robust strain-resolved evidence, focusing on three major themes: (i) the emergence and long-term persistence of personalized strain repertoires, (ii) strain-specific pathobiont traits that drive host pathology, and (iii) the implications of strain-level ecology for the development of next-generation microbiome therapeutics. We also highlight key methodological innovations including high-resolution amplicon profiling, advanced metagenomic and single-cell genomics, and culture-based functional approaches that collectively enable strain-level resolution and are reshaping the field.}, } @article {pmid41901034, year = {2026}, author = {Lee, YK and Kim, HY and Shim, D}, title = {A Triple-Hit Multi-Omics Framework for Psoriasis: Microbial Metabolic Remodeling and Immune Cell Methylome Signature Associated with an AMP-Dominant Lesional Program.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {3}, pages = {}, pmid = {41901034}, issn = {2075-1729}, support = {RS-2023-00263429//Ministry of Science and ICT (MSIT), South Korea/ ; }, abstract = {The gut-skin axis is increasingly implicated in psoriasis pathogenesis, yet the cross-compartment convergence of molecular programs remains incompletely defined. We constructed a conceptual "Triple-Hit" multi-omics framework by integrating five independent public datasets spanning gut microbial functional remodeling (shotgun metagenomics), systemic immune cell methylomes (PBMC and CD8+ T-cell EPIC 850K), and lesional skin regulatory layers (miRNA and bulk RNA-seq). In the gut compartment, functional profiles exhibited a selective reduction in microbial lipid catabolic potential, including decreased fatty acid degradation and a lowered composite lipid degradation score, alongside heterogeneous shifts across SCFA-associated metabolic pathways. Systemically, PBMC methylomes revealed widespread regional remodeling (45,396 DMRs) enriched for membrane-proximal signaling and cytoskeletal programs, while CD8+ T cells showed specific epigenetic alterations in lipid- and glycosphingolipid-associated loci, suggesting a systemic metabolic-epigenetic alignment. In the skin, we identified a compact miRNA signature (168 DE-miRNAs) and a mechanistically interpretable, directionality-constrained miRNA-mRNA bridge that aligns with an AMP-dominant inflammatory transcriptome, consistent with reduced post-transcriptional restraint. Collectively, these findings support a convergent multi-omics framework linking putative microbial metabolic remodeling, systemic immune priming, and cutaneous effector programs. This study provides a systems-level perspective on psoriasis pathogenesis, highlighting the metabolic-epigenetic-transcriptional convergence as a potential avenue for therapeutic intervention.}, } @article {pmid41901100, year = {2026}, author = {Kim, HJ and Park, J and Oh, S and Kim, D and Kim, HJ and Jo, C and Kim, EB and Jang, A}, title = {Effect of Alpha-Lipoic Acid, Betaine, and L-Carnitine Supplementation on Gut Microbiota and Obesity Biomarkers in Mice.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901100}, issn = {2072-6643}, support = {2022R1A2C1005235//National Research Foundation of Korea/ ; }, mesh = {Animals ; *Thioctic Acid/pharmacology/administration & dosage ; *Carnitine/pharmacology/administration & dosage ; Male ; *Obesity/microbiology/metabolism/blood ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Biomarkers/blood ; Mice ; *Betaine/pharmacology/administration & dosage ; Disease Models, Animal ; Bacteria/classification ; }, abstract = {Background/Objectives: This exploratory study (n = 6 per group) investigated the associations between supplementation with α-lipoic acid (AL), betaine (BT), and L-carnitine (LC) and gut microbiota composition in a high-fat diet (HFD)-induced obesity mouse model. Methods: Four-week-old male C57BL/6J mice were fed a control diet (10% fat), HFD (60% fat), or HFD supplemented with AL, BT, or LC (300 mg/kg BW/day) for nine weeks. Results: All three compounds were associated with shifts in microbial composition compared to the HFD-only group. While AL and BT supplementation moderately modulated specific Firmicutes and Bacteroidetes taxa, LC supplementation was linked to a more pronounced reduction in the Firmicutes/Bacteroidetes ratio and a decreased abundance of genera such as Christensenellaceae, Lachnospiraceae, and Coprococcus 3. These microbial changes were correlated with obesity-related metabolic and adiposity markers, including leptin and lipid parameters. Furthermore, functional profiling via PICRUSt suggested potential alterations in amino acid metabolism; however, these findings represent inferred metabolic potential rather than direct metagenomic measurements. Conclusions: Collectively, these results indicate differential associations between dietary supplementation and gut microbiota composition in HFD-fed mice. Although this study was conducted within an exploratory framework and utilized a modest sample size, the observed microbial shifts consistently paralleled metabolic alterations, supporting biologically plausible associations that warrant further mechanistic investigation.}, } @article {pmid41901112, year = {2026}, author = {Solano-Aguilar, G and Lakshman, S and Chen, C and Beshah, E and Molokin, A and Vinyard, B and Dawson, HD and Santin-Duran, M and Bruna, G and Smith, A and Urban, JF}, title = {Fruit and Vegetable Supplemented-Diet Ameliorates Dextran Sodium Sulfate (DSS)-Induced Colitis by Modulating Host Transcriptome and Gut Metagenome Response.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901112}, issn = {2072-6643}, support = {Cris 8040-51000-058-00D//United States Department of Agriculture/ ; }, mesh = {Animals ; Dextran Sulfate ; *Fruit ; *Metagenome ; *Transcriptome ; *Colitis/chemically induced/prevention & control/microbiology ; *Gastrointestinal Microbiome/genetics ; *Vegetables ; *Dietary Supplements ; Swine ; *Diet ; Colon/pathology ; Disease Models, Animal ; }, abstract = {Background/Objectives: Dietary intake of fruits and vegetables (FVs) has been inversely associated with a lower risk of ulcerative colitis. Using a pig model, we evaluated the effect of FV supplementation on dextran sulfate sodium (DSS)-induced colitis. Methods: Six-week-old pigs were fed a grower diet (negative control), grower diet + 4% DSS (positive control), half-FV diet + DSS, or full-FV diet + DSS. FV levels matched half or full daily recommendations from the Dietary Guidelines for Americans (DGA). Clinical signs were monitored; proximal colon contents (PCs) and mucosa (PCM) were analyzed for metagenome, transcriptome and histopathology. Results: Full-FV pigs showed no diarrhea, less fecal occult blood (FOB), crypt hyperplasia, but no changes in gene expression or microbiome diversity (p < 0.05). Half-FV pigs had increased FOB, differentially expressed genes (DEGs) linked to tissue remodeling, crypt/goblet cell hyperplasia and two cases of diarrhea (p < 0.05). DSS controls showed reduced immune-related DEGs, altered microbiome, PCM erosion, FOB, and persistent diarrhea in one pig (p < 0.05). Conclusions: A three-week full-FV diet conferred protection against DSS-induced colitis, with a dose-dependent protection of intestinal tissue and gut metagenome under inflammatory challenge.}, } @article {pmid41901564, year = {2026}, author = {Gonzalez, A and Argotsinger, J and Oram, RJ and Miller, JL}, title = {Impact of Metagenomic Next-Generation Sequencing on Antibiotic Management in Pediatric Patients.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {62}, number = {3}, pages = {}, pmid = {41901564}, issn = {1648-9144}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods/statistics & numerical data ; Retrospective Studies ; *Anti-Bacterial Agents/therapeutic use ; Child ; *Metagenomics/methods ; Female ; Child, Preschool ; Male ; Infant ; Adolescent ; Pediatrics/methods ; }, abstract = {Background and Objectives: Metagenomic next-generation sequencing (mNGS) is an emerging diagnostic tool used to guide the management of infectious diseases. However, clinical criteria in which there is a clear benefit have not been identified, and more real-world clinical experience is needed to identify patient populations in which mNGS testing may have the most benefit. The aim of this article is to evaluate the utilization of mNGS to determine the impact on clinical practice for pediatric patients. Materials and Methods: This retrospective analysis included pediatric patients that had a mNGS test performed between January 2020 and September 2024. The primary outcome was the clinical impact of the mNGS test on patient management defined as either a positive impact or no impact. Secondary outcomes included test turnaround time, agreement or discordance between conventional testing and mNGS, and hospital length of stay. Results: Forty-six mNGS tests in 42 patients were evaluated. Of 60 organisms identified from the 46 tests, 27 organisms (45%) were considered clinically significant. mNGS had a positive clinical impact in 18 (39.1%) patients, primarily due to antimicrobial modifications (16, 34.8%) and new diagnoses (6, 13.0%). The majority of patients with a positive clinical impact were immunosuppressed (15/18, 83.3%). Conclusions: mNGS demonstrated utility in a subset of pediatric patients, particularly those considered immunosuppressed. Its ability to confirm or exclude infections, particularly fungal infections in this patient population, contributed to its impact. However, its limited benefit in immunocompetent patients underscores the importance of careful patient selection to optimize diagnostic and antimicrobial stewardship.}, } @article {pmid41901695, year = {2026}, author = {Philips, CA and Oommen, TT and Theruvath, AH and Sreemohan, A and Baby, A and Alex, AA and Thomas, S and John, SM and Ahamed, R and Tharakan, A and Augustine, P}, title = {Novel Insights on Clinical Outcomes Using Integrated Shotgun Metagenomic Profiling of the Gut Microbiome, Resistome, and Host Immune-Inflammatory Response in Hospitalized Patients with Decompensated Cirrhosis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901695}, issn = {2076-0817}, mesh = {Humans ; *Liver Cirrhosis/microbiology/immunology/mortality ; Male ; *Metagenomics/methods ; Female ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; India ; Sepsis ; Cytokines/metabolism ; Feces/microbiology ; Hospitalization ; Aged ; Metagenome ; }, abstract = {Background and Aims: Sepsis drives mortality in cirrhosis, yet the gut antimicrobial resistance (AMR) landscape remains unmapped in high-burden settings like India. This study aimed to integrate shotgun metagenomics with deep immunophenotyping to define the gut-immune-resistome axis and correlate specific microbial and genetic signatures with clinical outcomes in decompensated cirrhosis. Methods: We analysed 78 hospitalized patients with cirrhosis using stool shotgun metagenomics, multiplex cytokine arrays, and flow cytometry. The microbiome and resistome (AMR genes) were mapped and correlated with disease severity, immune function (monocyte HLA-DR, neutrophil CD64), and clinical endpoints including mortality. Results: Disease severity was characterized by a "Gram-negative bloom" (Klebsiella) alongside pathogenic Enterococcus expansion and novel markers: Clostridium sp. C5-48 (severe decompensation) and Sutterella (ascites). A specific, dense resistome predicted adverse outcomes; the quinolone-resistance gene QnrB4 correlated with mortality and immune paralysis, while the carbapenemase OXA-833 gene was linked to gastrointestinal bleeding. Notably, the commensal Ligilactobacillus salivarius was associated with systemic inflammatory cytokines. Conclusions: This study reveals a "pathogenic ecosystem" in Indian decompensated cirrhosis where the resistome is intrinsically linked to host immune failure. The identification of specific prognostic markers (QnrB4, OXA-833) and inflammatory associations with L. salivarius challenges generic probiotic use and underscores the urgent need for precision, resistome-targeted therapies.}, } @article {pmid41901767, year = {2026}, author = {He, P and Wang, H and Li, P and Yan, Y and Gao, L and Chen, L}, title = {Pyogenic Spondylitis with Epidural Abscess Caused by Streptococcus suis Serotype 2 ST7: Tissue mNGS Confirmation and Whole-Genome Characterization of a Human Isolate.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901767}, issn = {2076-0817}, support = {2026JKP-07//Disease Prevention and Control Innovation Team of Zhejiang Province/ ; }, mesh = {Humans ; *Epidural Abscess/microbiology/diagnosis ; Aged ; *Streptococcus suis/genetics/isolation & purification/classification/drug effects ; *Spondylitis/microbiology/diagnosis ; *Streptococcal Infections/microbiology/diagnosis/drug therapy ; Male ; Whole Genome Sequencing ; Genome, Bacterial ; Animals ; Anti-Bacterial Agents/therapeutic use/pharmacology ; High-Throughput Nucleotide Sequencing ; Serogroup ; Magnetic Resonance Imaging ; }, abstract = {Streptococcus suis is an emerging zoonotic pathogen that typically causes bacteremia or meningitis in humans, whereas vertebral osteomyelitis with epidural abscess is exceedingly rare and may be missed. We describe a 65-year-old farmer with fever and severe low back pain after long-term bare-handed handling of raw pig lungs. Pre-treatment blood cultures yielded S. suis identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). After transient improvement on empirical therapy, fever recurred with worsening lumbar pain. Contrast-enhanced magnetic resonance imaging (MRI) demonstrated multilevel thoracolumbar pyogenic spondylitis with an epidural abscess and a sub-ligamentous abscess beneath the posterior longitudinal ligament (PLL) extending from L2 to L5. Computed tomography-guided lumbar biopsy followed by tissue metagenomic next-generation sequencing (mNGS) detected S. suis, providing concordant evidence supporting pathogen involvement at the vertebral focus. The bloodstream isolate (SS-JX2025-01) was serotype 2, sequence type 7 (ST7). It remained susceptible to β-lactams and glycopeptides but was resistant to macrolide-lincosamide and tetracycline classes, consistent with erm(B), tet(O), tet(40), and ant(6)-Ia detected by whole-genome sequencing (WGS). Virulence profiling revealed an epf[+]/sly[+]/mrp[-] pattern with multiple adhesins and immune-evasion factors, whereas canonical 89K pathogenicity island markers were absent. Core-genome phylogeny placed SS-JX2025-01 within the Chinese ST7 lineage associated with previous outbreaks. This biopsy-supported case expands the clinical spectrum of invasive S. suis infection, highlights the value of tissue mNGS as an adjunct for supporting deep-seated foci in zoonotic infections, and underscores the importance of occupational prevention in small-scale farming households.}, } @article {pmid41901791, year = {2026}, author = {Alessandri, G and Beligni, G and Gori Savellini, G and Mistral De Pascali, A and Gobbo, F and Montarsi, F and Mileto, D and Rizzo, L and Cusi, MG}, title = {Molecular Epidemiology of Toscana Virus in Northern and Central Italy Using Metagenomic Next-Generation Sequencing.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901791}, issn = {2076-0817}, support = {PE00000007//NextGeneration EU-MUR PNRR Extended Partnership Initiative on Emerging Infectious Diseases INF-ACT/ ; P2022WYNAH//Ministero dell'Università e della Ricerca, Progetti di Rilevante Interesse Nazionale PRIN2022 PNRR/ ; }, mesh = {Italy/epidemiology ; Humans ; *Sandfly fever Naples virus/genetics/classification/isolation & purification ; Animals ; Phylogeny ; Molecular Epidemiology ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Psychodidae/virology ; Genome, Viral ; Genotype ; Genetic Variation ; Phylogeography ; *Bunyaviridae Infections/epidemiology/virology ; }, abstract = {Toscana virus (TOSV) is an arthropod-borne virus, transmitted by sandflies, which represents a major cause of aseptic meningitis in Mediterranean countries during summer months. Despite its epidemiological importance, recent genomic data on circulating Italian strains remain limited. We performed comprehensive phylogenetic and genotypic characterization of 34 TOSV isolates (32 obtained from human biological samples and 2 from sandfly homogenates) collected between 2022 and 2025 from Northern/Central Italy. All the sequenced isolates clustered within Lineage A, with strains circulating in Tuscany showing significantly lower intra group genetic divergence (p < 0.05), indicative of compartmentalized local circulation. Both S and M segments exhibited negative selection and identified non-synonymous mutations deserving functional investigation. This study documents stable Lineage A predominance across Italian regions, with Tuscany showing distinct phylogeographic structuring. mNGS proves effective for TOSV genomic surveillance, supporting refined public health strategies, including targeted sandfly control in endemic foci.}, } @article {pmid41902210, year = {2026}, author = {Zhang, Y and Ding, X and Tao, X and Tuohuti, N and Wang, X and Maimaiti, A and Su, Z and Ma, X}, title = {Viral Metagenomic Analysis Reveals High Prevalence of Dromedary Camel Bocavirus and Porcine Astrovirus in Bactrian Camel Intestinal Tissue.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902210}, issn = {1999-4915}, support = {2022KY025//Autonomous Region Science and Technology Commissioner Project of Xinjiang Uygur Autonomous Region, China/ ; }, mesh = {Animals ; *Camelus/virology ; Phylogeny ; Metagenomics ; *Bocavirus/genetics/isolation & purification/classification ; Prevalence ; *Astroviridae Infections/veterinary/epidemiology/virology ; Swine ; *Parvoviridae Infections/veterinary/epidemiology/virology ; *Intestines/virology ; China/epidemiology ; *Mamastrovirus/genetics/isolation & purification/classification ; Swine Diseases/virology ; Virome ; }, abstract = {Bactrian camels (Camelus bactrianus) are economically vital livestock in arid regions; however, their intestinal virome is poorly understood. We employed viral metagenomics to analyze intestinal tissue samples from deceased camels at a breeding facility in Urumqi, Xinjiang, China, and uncovered a diverse viral population dominated by dromedary camel bocavirus (DBoV1) and porcine astrovirus (PoAstV5). A molecular epidemiological survey of 261 anal swab samples collected across Xinjiang revealed prevalence rates of 36.40% (95/261) for DBoV1 and 26.44% (69/261) for PoAstV5, indicating their widespread circulation. Phylogenetic analyses of the DBoV1 NS1 and PoAstV5 ORF1a genes showed close relationships with known strains, with no evidence of recombination. This study expands the known viral spectrum of Bactrian camels, marking the first report of PoAstV5 in this species, a finding suggestive of cross-species transmission. These results enhance our understanding of camel viral diversity and provide critical data for managing enteric diseases in camel populations, with potential implications for livestock health and surveillance of zoonotic risks.}, } @article {pmid41902228, year = {2026}, author = {Shankar, A and Zheng, H and Cowan, D and Jia, H and Osis, G and Burgin, A and Sheth, M and Hoff, NA and Halbrook, M and Rimoin, AW and Goldberg, TL and Chapman, CA and Ting, N and Switzer, WM}, title = {Molecular Characterization of Complete Simian Foamy Virus Genomes from Three Colobine Monkeys Reveals Highly Divergent Evolutionary Trajectories and Identifies Transmission to Humans.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902228}, issn = {1999-4915}, support = {TW009237//Canada Research Chairs Program ; NIH/ ; R01 AI084787/GF/NIH HHS/United States ; R01 AI077376-04A1/GF/NIH HHS/United States ; }, mesh = {Animals ; *Genome, Viral ; *Simian foamy virus/genetics/classification/isolation & purification ; Phylogeny ; *Retroviridae Infections/transmission/virology/veterinary ; Humans ; *Evolution, Molecular ; *Colobinae/virology ; *Monkey Diseases/virology/transmission ; Colobus/virology ; }, abstract = {Simian foamy viruses (SFVs) are ancient retroviruses that co-evolve with nonhuman primates (NHPs), although genomic data from Asian and African monkeys are limited. We report the characterization of three new SFV colobine genomes from two Asian species (Trachypithecus francoisi (Tfr) and Pygathrix nemaeus (Pne)) and one African monkey (Colobus guereza, Cgu), obtained via metagenomics analysis of peripheral blood leukocyte tissue culture isolates. Genomic analyses found conserved structural, enzymatic, and auxiliary genes flanked by long terminal repeats, with all major transcriptional and structural motifs highly preserved. An in-frame Δtas mutation in tissue culture and ex vivo specimens was identified in the SFVpne genome, which may promote viral latency. Phylogenetic analyses revealed that these colobine SFVs have distinct evolutionary trajectories without clustering together, contradicting a strict virus-host co-evolution. We developed a new generic SFV PCR assay using these genomes with increased detection sensitivity for Colobinae SFVs and identified four new human infections with Cgu-derived SFV in the Democratic Republic of Congo. Our findings indicate that SFV evolution in colobine monkeys is shaped by host switching, cross-species transmission, and high viral diversity. Our study underscores the importance of broadening SFV genomic sampling to better understand viral evolution, zoonotic risk, and improved diagnostic capabilities.}, } @article {pmid41902303, year = {2026}, author = {Munguti, FM and LaTourrette, K and Silva, G and Maina, S and Kilalo, DC and Macharia, I and Mwango'mbe, AW and Nyaboga, EN and Garcia-Ruiz, H}, title = {Metagenomics Analysis of Viruses Associated with Cassava Brown Streak Disease in Kenya.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902303}, issn = {1999-4915}, support = {Grant ID: RU/2018/CARP+/04//MasterCard Foundation/ ; }, mesh = {Kenya ; *Potyviridae/genetics/classification/isolation & purification ; *Plant Diseases/virology ; *Manihot/virology ; Phylogeny ; Genome, Viral ; *Metagenomics ; Polymorphism, Single Nucleotide ; Genetic Variation ; }, abstract = {Cassava brown streak disease (CBSD), caused by cassava brown streak virus (CBSV; Ipomovirus brunusmanihotis) and Ugandan cassava brown streak virus (UCBSV; Ipomovirus manihotis) (family Potyviridae, genus Ipomovirus), is increasingly becoming a threat to cassava production in several parts of Africa, especially in Eastern, Central and Southern Africa. In Kenya, the disease continues to wreak havoc on cassava production leading to a significant reduction in crop yields and economic losses of up to USD 1 billion. Variation in virus populations make the control of CBSD challenging as virus genomic variation can affect the accuracy of diagnostic tests, lead to resistance breaking isolates and jeopardize strategies of breeding for resistance. CBSV and UCBSV populations obtained from cassava fields in Kenya were characterized. In total, 44 new complete sequences of CBSV and UCBSV were assembled and 40 sequences successfully submitted to GenBank. Single Nucleotide Polymorphism (SNP) analysis revealed that the cylindrical inclusion protein (CI) is the most stable region across the genome of CBSV and UCBSV. In contrast, protein 1 (PI) and the coat protein (CP) were the most hypervariable regions. Phylogenetic analysis showed three major geographical groupings for both UCBSV and CBSV isolates, suggesting a continued spread of the viruses through human-mediated movement of infected planting materials. The data obtained in this study can support the development of disease management strategies through improved molecular diagnostic tests and targets for breeding for resistance against CBSD.}, } @article {pmid41902972, year = {2026}, author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Sierra, JL and Pagaza-Straffon, EC and Hurtado-Ramírez, JM and Quispe-Ricalde, MA and Castelán-Sánchez, HG and Dávila-Ramos, S}, title = {Unveiling a Microbial Treasure Trove: Phylogenetic Diversity and Bioremediation Potential in a High-Altitude Andean Saline System.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41902972}, issn = {1432-184X}, support = {227-2015-FONDECYT//Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica/ ; Contract No. 23 2018 UNSAAC//UNSAAC/ ; grant No. 103.5/15/10446//Programa de Mejoramiento del Profesorado, Universidad Autónoma del Estado de Morelos, Secretaría de Educación Pública/ ; }, abstract = {The reconstruction of metagenome-assembled genomes (MAGs) has improved our knowledge of how microbiomes perform biological and chemical processes in diverse ecosystems, including extreme environments. However, in Latin America, these ecosystems have received insufficient attention. In this study, we used shotgun metagenomics to reconstruct MAGs in Acos a high-altitude intermediate saline system in Cusco, Peru. Most of the MAGs detected were classified only at the phylum level, indicating significant phylogenetic novelty. Of particular note is the presence of two poorly characterized archaeal MAGs from the genus Methanonatronarchaeum, belonging to the phylum Halobacteriota. All reconstructed MAGs displayed a broad spectrum of metabolic pathways associated with the nitrogen and sulfur cycles, indicating metabolic versatility that allows them to cope with the harsh conditions of the saline environment. Both bacterial and archaeal MAGs are enriched in various metabolic processes related to the metabolism of amino acid and nitrogenous compounds; this could indicate a mechanism for adapting to osmotic stress. Among the genes detected, those involved in the degradation of the common herbicide atrazine were identified; this provides information on potential microbial mediation processes for the bioremediation of contaminated soils. Furthermore, and equally important, these habitats harbor a great diversity of viruses, many of which have unknown in current databases. Taxonomic classification revealed bacteriophages belonging to the class Caudoviricetes, specifically the families Myoviridae, Siphoviridae, and Podoviridae. Overall, our work provides high-quality MAGs that expand current knowledge of the diversity, function, and ecological dynamics of Bacteria, Archaea, and viruses in high-altitude intermediate saline environments.}, } @article {pmid41903008, year = {2026}, author = {Heyse, J and Props, R and Defoirdt, T and Boon, N}, title = {Life strategies of bacterial taxa in rearing water microbiomes of whiteleg shrimp (Litopenaeus vannamei) larviculture.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41903008}, issn = {1573-0972}, support = {1S80618N//Fonds Wetenschappelijk Onderzoek/ ; 1221020N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {Enhancing our understanding of the role of microbial life strategies and their trade-offs in the functioning of microbial communities is essential for improving the management of microbial communities. In aquaculture microbiomes, management aimed at increasing the dominance of K-strategists has experimentally been shown to influence cultivation performance. To understand the mechanisms behind such observations, we need to improve our understanding of the typical properties and behaviour of r- and K-strategists. Several studies have advanced our understanding of theoretical trade-offs that may shape these life strategies, but our understanding of which trade-offs are relevant under natural conditions is still limited. In this study, we investigated the in situ growth strategies of bacterial taxa in rearing water microbiomes of whiteleg shrimp (Litopenaeus vannamei) larviculture by reconstructing 67 high quality metagenome assembled genomes (MAGs), which covered between 31 and 85% of the sampled communities. We found evidence for niche separation between r- and K-biased strategists residing in these communities, with r-biased strategists typically encoding more and more versatile transport and metabolism pathways, and having a higher fitness for exploitation of spatially structured nutrient hotspots. We further increased the knowledge regarding the influence of r- and K-biased strategistson aquaculture cultivation performance by showing that the in situ growth activity of r-biased strategists could be linked better with cultivation performance than the relative abundance of r- and K-biased strategists.}, } @article {pmid41903015, year = {2026}, author = {Ma, N and Zhang, H and Yuan, L and Lian, P and Yang, W and Huang, Y}, title = {Bioremediation of enrofloxacin and modulation of nitrogen cycling in a simulated aquaculture system by the fungus Cladosporium cladosporioides 11.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41903015}, issn = {1573-0972}, support = {NO. 2025A005//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; }, abstract = {While microbial bioremediation is a promising strategy for antibiotic removal, the potential of fungi in mitigating antibiotic contamination and its associated ecological impacts in aquaculture systems remains largely unexplored. This study evaluated the bioremediation efficacy of the fungus Cladosporium cladosporioides 11 (CC11) in a simulated aquaculture ecosystem. The introduction of CC11 significantly accelerated enrofloxacin (ENR) removal in the aquaculture system and mitigated ENR bioaccumulation in crucian carp. Meanwhile, CC11 application notably lowered the accumulation of total nitrogen and ammonium nitrogen in the water column. Metagenomic analysis revealed that CC11 helped maintain a more active nitrogen-cycling microbial community, sustaining higher abundances of key genes involved in nitrogen fixation (nifB/K/T/Z) and assimilatory nitrate reduction (nasA/C/E/B/D) under ENR stress. Furthermore, CC11 restored specific bacterial taxa correlated with these functional genes, including methylotrophs associated with nif genes and Comamonadaceae members linked to nas genes, thereby reinforcing the functional network for nitrogen transformation. These findings demonstrate that CC11 acts as a multifunctional bioremediation agent, capable of simultaneously enhancing antibiotic removal and regulating nitrogen dynamics, offering a sustainable strategy for managing ENR pollution in aquaculture environments.}, } @article {pmid41903026, year = {2026}, author = {Wolthuis, JC and Schultheiss, JPD and Magnúsdóttir, S and Stigter, E and Tang, YF and Jans, J and Oldenburg, B and de Ridder, J and van Mil, S}, title = {Univariate- and machine learning-based plasma metabolite signature differentiates PSC-IBD from IBD and is predicted to be driven by gut microbial changes.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {22}, number = {2}, pages = {}, pmid = {41903026}, issn = {1573-3890}, mesh = {Humans ; *Machine Learning ; *Inflammatory Bowel Diseases/blood/diagnosis/metabolism/microbiology ; *Cholangitis, Sclerosing/diagnosis/blood/metabolism/microbiology ; *Metabolomics/methods ; Biomarkers/blood ; *Gastrointestinal Microbiome/physiology ; Metabolome ; Mass Spectrometry/methods ; Crohn Disease ; }, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is a group of chronic inflammatory conditions of the gastrointestinal tract comprising two major phenotypes, Crohn's disease (CD) and ulcerative colitis (UC). Up to 8% of patients with IBD also develop primary sclerosing cholangitis (PSC), characterised by cholestasis and progressive destruction of the biliary tree, resulting in cirrhosis, end-stage liver disease and cholangiocarcinoma. Clinical outcome can currently not be improved through medication, denoting the importance of diagnosis prior to irreversible damage, which requires biomarkers of (early) disease.

OBJECTIVES: We employed direct infusion mass spectrometry (DI-MS)-based metabolomics on plasma to build predictive, potentially diagnostic models for PSC-IBC and other phenotypes including IBD subtype, stricture and fistula presence and more. We used this dataset to simultaneously investigate aetiology of these phenotypes.

METHODS: Samples of 348 IBD patients were included for analysis. The data was analysed using our previously reported tool, MetaboShiny. We built predictive models using Random Forest (RF), and subsequently combined with univariate statistics to rank m/z features connected to PSC-IBD. This ranking was used to perform mummichog enrichment analysis connected to metabolic and metagenomic changes.

RESULTS: The highest performing predictive model differentiated PSC-IBD from PSC. The metabolic signature was enriched in changes to amino acid and vitamin metabolism, alongside changes to the metagenome suggesting decreases in anti-inflammatory microbial species and increases in pro-inflammatory species.

CONCLUSION: These results demonstrate the potential of DI-MS-based metabolomics with machine learning to create diagnostic models and generate hypotheses on the metabolomic-metagenomic level. Sharing our dataset of patients will enrich future human IBD metabolomics research possibilities.}, } @article {pmid41903099, year = {2026}, author = {Sumona, AA and Hossen, MB and Hadi, SB and Haque, MA and Haider, MN and Hossain, MT and Alam, MS}, title = {Host-derived Probiotics Enhance Immune Response and Gut Microbiome in the Freshwater Prawn Macrobrachium rosenbergii.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41903099}, issn = {1867-1314}, abstract = {Probiotics, including beneficial bacteria and yeasts, are vital for maintaining a healthy gut and overall well-being of animals. Host-derived probiotics may provide a viable alternative to commercial probiotics, positively affecting the growth performance, immune response, and gut microbiome of the Giant Freshwater prawn, Macrobrachium rosenbergii. To explore this, the study was designed with four treatments: two for commercial probiotics (T1 and T2), one for host-derived probiotics (T3), and one control (without probiotics). A total of 264 post-larval prawns (PLs), each with an initial weight of (0.25 ± 0.05) g, were randomly distributed among 12 tanks and fed a commercial diet supplemented with probiotics at a target dosage of 1 × 108 CFU/g for 127 days. Immune-related biochemical parameters and enzyme activities were significantly enhanced in the host-derived probiotic treatment (T3) compared with the control (p < 0.05), whereas commercial probiotics showed only moderate improvements. Microbial community profiling was conducted using an amplicon sequence variant (ASV)-based approach. Alpha-diversity indices tended to be higher in probiotic-fed groups, particularly in T3. Ordination analyses revealed visually distinct but statistically nonsignificant differences in gut microbial community structure among treatments, likely due to limited replication. Differential abundance analysis identified members of the phylum Actinobacteriota as characteristic taxa associated with the host-derived probiotic treatment. Overall, the findings suggest that host-derived probiotics can enhance immune response and influence gut microbial composition in M. rosenbergii. While microbiome-level changes should be interpreted cautiously, the results highlight the potential of host-derived probiotics as a functional dietary strategy for improving prawn health and gut ecosystem stability in aquaculture.}, } @article {pmid41903138, year = {2026}, author = {Zheng, W and Wu, C and Wang, Y and Yan, X and Han, W and Liu, X and He, C and Chen, X and Zhou, X and Zhang, L and Liu, C and Xu, J and Wang, J and Yuan, X and Song, W and Wang, X and Liang, S and Huang, J and Zhang, Y and Yang, R and Zhang, L and Qin, N and Ma, X and Xu, Q and Li, G}, title = {Mutation elevation and functional alterations in Escherichia coli are pertinent to the onset of gestational diabetes mellitus.}, journal = {Cell reports}, volume = {45}, number = {4}, pages = {117143}, doi = {10.1016/j.celrep.2026.117143}, pmid = {41903138}, issn = {2211-1247}, abstract = {In the gut microbiome, purifying selection clears deleterious mutations. However, it is unknown whether this selection pressure is modifiable or what its health implications are. Here, we studied metagenomic and metabolic changes linked to gestational diabetes mellitus (GDM), and observed an increase in Escherichia coli (E. coli) mutations during host pregnancy, linking these genetic changes to host physiology. Severe depletion of bacterial genes before GDM onset was mostly traced to E. coli despite its stable abundance-indicating that functional genetic signals outweigh taxonomic shifts. E. coli and related microbes displayed pregnancy-linked single nucleotide polymorphism elevation, enriched at GDM onset in loci encoding membrane and biofilm components. These pangenomic alterations correlated with handicapped intermicrobial interactions of E. coli and with host serum metabolic abnormalities. We propose that pregnancy relaxes purifying selection, permitting mutation elevation in certain gut bacteria. Resulting functional deficits, potentially through altered ecology and metabolism, may subsequently impact host glucose regulation.}, } @article {pmid41903180, year = {2026}, author = {Xu, Y and Akinbi, H and Shen, Z and Zhu, J and Shi, L and Du, L and Haslam, DB}, title = {Clinical Care Practices Shape Microbiome-Associated Bloodstream Infection Risk in Geographically Distinct NICUs.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciag213}, pmid = {41903180}, issn = {1537-6591}, abstract = {BACKGROUND: Bloodstream infections (BSI) remain a major cause of morbidity and mortality in preterm infants. Although BSI pathogens vary geographically, the role of local microbial colonization patterns and clinical practices in driving these differences is not well understood.

METHODS: We conducted a prospective cohort study on 127 preterm infants from two geographically distinct NICUs: University of Cincinnati Medical Center (UCMC, USA) and Children's Hospital, Zhejiang University School of Medicine (ZCH, China). Six hundred and sixty-nine longitudinal stool and skin samples collected during the first three weeks of life underwent metagenomic sequencing. Associations between microbiome composition, clinical factors, and BSI epidemiology were evaluated using Generalized Linear Mixed Models and Random Forest.

RESULTS: Distinct gut and skin microbiome profiles were observed between NICUs and corresponded closely with local BSI patterns. Staphylococcus aureus predominated at UCMC, while Klebsiella pneumoniae and Enterococcus species were more common at ZCH. Skin microbiota showed strong association with BSI isolates, implicating the skin as an underrecognized potential reservoir for pathogen translocation. Linear mixed models and Random Forest machine learning approaches revealed that clinical practices, including intravenous catheter placement and antibiotic exposure had greater influence on microbiome composition than geographic location alone.

CONCLUSIONS: Our findings demonstrate that modifiable clinical care practices shape the developing microbiome of preterm infants and contribute to geographic differences in BSI epidemiology. The skin microbiome represents a potentially significant risk factor for invasive infection. Further work to clarify how specific clinical practices influence pathogen colonization may inform strategies to reduce BSI incidence in preterm infants.}, } @article {pmid41903463, year = {2026}, author = {Rathnayake, M and Shaik, NA and Palkumbura, A and Ranaraja, A and Basnayake, Y and Basyouni, R and Taylor, A and Ambrose, N and Popowich, S and Ayalew, LE and Tikoo, S and Gomis, S}, title = {Effects of conventional and raised without antibiotic feeding systems and exposure to infectious bursal disease virus on microbial diversity of the jejunal microbiota in broiler chickens.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106823}, pmid = {41903463}, issn = {1525-3171}, mesh = {Animals ; *Chickens/microbiology ; *Infectious bursal disease virus/physiology ; *Jejunum/microbiology ; *Poultry Diseases/virology/microbiology ; *Birnaviridae Infections/veterinary/virology ; *Animal Husbandry/methods ; *Anti-Bacterial Agents/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; Diet/veterinary ; RNA, Ribosomal, 16S/analysis ; RNA, Bacterial/analysis ; }, abstract = {Preventative use of antimicrobials in the feed in broiler chicken production is decreasing due to consumer demand. Hence broiler chickens raised without antibiotics (RWA) receive increased attention. The objective of this study was to compare jejunal microbiota in RWA and conventional feeding systems in commercial broiler chickens. A total of 6 broiler chicken farms were selected for this study, in each farm raising both conventional and RWA chicken flocks. Jejunal contents were collected from Ross 308 (n=8/flock) at 25 d of age for metagenomics analysis for 16SrRNA amplicon sequencing. Serum samples from each flock were tested for infectious bursal disease virus (IBDV) and chicken anemia virus (CAV). The 16SrRNA microbial analysis revealed that there was no substantial impact of feeding systems on the diversity of the microbial community between RWA and conventional feeding systems. The condemnation rate was significantly higher in RWA flocks compared to conventional flocks (p = 0.037). Significantly high antibody titer against IBDV was detected in 9 (75%) of 12 flocks. The microbiota significantly differed in flocks exposed to IBDV compared to flocks not exposed to IBDV irrespective of the feeding system. Alpha diversity indices revealed that richness (p = 0.025), Chao1 (p = 0.031), and Shannon index (p = 0.04) were significantly lower in flocks exposed to IBDV indicating reduced species diversity. Flocks exposed to IBDV had increased Escherichia, Anaerotignum, Clostridium, Weissella andLiquorilactobacillus genera while Furfurilactobacillus, Helicobacter, Campylobacter, Fructilactobacillus and Terrisporobacter were decreased compared to flocks not exposed to IBDV. These results suggest that broiler chickens exposed to IBDV infection irrespective of the feeding system lead reduction in microbial diversity. This study highlights the importance of control strategies of IBDV in broiler flocks since IBDV infection not only causes immunosuppression but also affects intestinal microbiota.}, } @article {pmid41903724, year = {2026}, author = {Ouyang, E and Liu, J and Zhou, Z and Yang, H and Wang, W and Qian, K and Zhu, M and Wei, Z and Sun, X and Chen, Z}, title = {Metagenomic surveillance of temperature-drived bacterial threats to drinking water safety.}, journal = {Environmental research}, volume = {300}, number = {}, pages = {124364}, doi = {10.1016/j.envres.2026.124364}, pmid = {41903724}, issn = {1096-0953}, mesh = {*Drinking Water/microbiology ; *Temperature ; *Bacteria/genetics/isolation & purification ; *Water Microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {Climate warming may exacerbate the risk of pathogenic bacteria and antibiotic resistance genes (ARGs) in aquatic environments. However, research on the impact of climate warming on bacterial pathogenic risks and virulence factors (VFs) communities in drinking water sources remains scarce. This study combined field multi-season monitoring with controlled laboratory temperature simulation experiments. Using 16S rRNA and metagenomic sequencing, we investigated the effects of gradually increasing temperature on pathogenic bacteria and VF community in the Gan River source area. A significant positive correlation with temperature was observed in the seasonal shifts of Legionella, Mycobacterium, and Pseudomonas during field multi-season monitoring. Our laboratory temperature simulation experiments further illustrated the differential modulation of temperature on opportunistic pathogens and their VFs. The abundance of 9 specific VFs was significantly associated with temperature. Within the high-temperature range (35-40 °C), Legionella showed a synergistic increase in both its population and the abundance of its VF (Hsp60); Mycobacterium's VF (NuoG) abundance increased significantly with increasing temperature, while the population size remained stable. Furthermore, 3 key bacterial infectious disease pathways- Bacterial invasion of epithelial cells, Staphylococcus aureus infection, and Vibrio cholerae infection were significantly enriched with elevated temperature. Furthermore, high temperatures may also weaken the microbial inactivation efficiency of the conventional chlorine disinfection process, thereby posing a potential threat to drinking water safety. This study elucidates how elevated temperature is linked to the enhanced pathogenic potential of opportunistic pathogens, mediated through the differential regulation of VFs. This provides a scientific basis for assessing aquatic microbial risks under climate warming.}, } @article {pmid41903868, year = {2026}, author = {Manfredonia, I and Chioso, L and Mateescu, I and Konu, M and Brons, JK and Deelman-Driessen, C and Viljakainen, L and Wertheim, B and Lequime, S}, title = {Prevalence and distribution of two polycipiviruses in wild black garden ants (Lasius niger L.) in the Netherlands.}, journal = {Journal of invertebrate pathology}, volume = {217}, number = {}, pages = {108611}, doi = {10.1016/j.jip.2026.108611}, pmid = {41903868}, issn = {1096-0805}, mesh = {Animals ; Netherlands ; *Ants/virology ; Genetic Variation ; *Insect Viruses/genetics ; Phylogeny ; Prevalence ; Genome, Viral ; }, abstract = {Metagenomic studies have revealed diverse viruses in insects. Yet, our understanding of the ecology of insect viruses, especially in ants, remains limited, despite the insects' ecological importance. Viruses of the family Polycipiviridae are increasingly recognized as widespread yet poorly characterized components of ant viromes. In this study, we investigated the prevalence and genetic diversity of Lasius niger virus 1 (LniV-1) and Myrmica scabrinodis virus 1 (MsaV-1) in wild colonies of the black garden ant (Lasius niger L.) across the Netherlands. We surveyed 40 wild L. niger colonies, sampled at geographically distinct locations, using RT-PCR to assess viral prevalence and genetic diversity. Viral prevalence was estimated at both colony and individual levels. Amplicons were sequenced to explore potential correlations between geographic distribution and genetic diversity for both viruses. In addition, complete or almost complete viral genome sequences were obtained and assembled for one MsaV-1 genome from Groningen, The Netherlands, and one MsaV-1 and one LniV-1 from Vienna, Austria. In the Netherlands, LniV-1 was detected in 17.5% of colonies, whereas MsaV-1 was detected in 27.5%, including evidence of co-infection at the colony level. Neither the geographical distribution of infected colonies nor the inferred phylogenies for both viruses showed strong geographic structuring. The prevalence in workers within colonies was variable, ranging from 10 to 60%. These findings suggest that polycipiviruses are common in natural L. niger populations and may transmit via both horizontal and vertical routes. This study provides baseline data on ant-virus interactions in natural environments, advancing understanding of viral ecology in social insects and informing future research on virus transmission dynamics in natural ecosystems.}, } @article {pmid41904207, year = {2026}, author = {Yan, Y and Zhen, W and Hongxia, S and Zhenhong, S and Xianghui, M and Na, W and Li, S and Defeng, W}, title = {Impact of Lactobacillus johnsonii on glycemic control and lipid metabolism in type 2 diabetes with circadian disruption.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41904207}, issn = {2045-2322}, support = {(BJK2024152)//Funded by Science and Technology Project of Hebei Education Department/ ; (20241988)//Hebei Province Medical Science Research Project Plan for 2024/ ; (No. [2020] No.23).//Project Fund of Clinical Medicine Excellent Talents funded by Hebei Provincial Department of Finance/ ; }, abstract = {UNLABELLED: Although most patients with type 2 diabetes mellitus (T2DM) and circadian rhythm disruption have poor blood glucose control, a fraction of patients with T2DM and circadian rhythm disruption who still have good blood glucose control. Previous studies have shown that individuals with circadian rhythm disruption are more prone to developing T2DM, and the occurrence of T2DM is associated with the gut microbiota. However, the role of gut microbiota in patients with T2DM and circadian rhythm disruption remains unclear. Stool samples were collected from 6 patients with poorly controlled type 2 diabetes mellitus (T2DM) and circadian rhythm disruption, as well as from 6 patients with well-controlled T2DM and circadian rhythm disruption. Metagenomic sequencing was performed on the stool samples. Compared to the well-controlled group, the abundance of Lactobacillus johnsonii(L. johnsonii) was significantly decreased in the poorly controlled group. To investigate the effects of L. johnsonii supplementation on glucose and lipid metabolism, diabetic mice with circadian rhythm disruption were administered L. johnsonii and their metabolic indicators were measured. Metagenomic sequencing of the gut microbiota revealed a higher microbial diversity in the well blood glucose controlled type 2 diabetes combined with disrupted circadian rhythm group (W-T2D-RD). Additionally, a significant decrease in the abundance of L. johnsonii was observed in patients with poor blood glucose controlled type 2 diabetes combined with disrupted circadian rhythm group (P-T2D-RD) when compared to those with W-T2D-RD. Following supplementation of L. johnsonii to the mice in the type 2 diabetes mellitus rhythm disruption Lactobacillus johnsonii group (T2DM-RD-L), the fasting blood glucose levels and postprandial blood glucose levels were significantly reduced. Additionally, total cholesterol and low-density lipoprotein levels decreased, high-density lipoprotein levels increased in the T2DM-RD-L group. Lactobacillus johnsonii has a positive impact on both glucose and lipid metabolism in patients with type 2 diabetes mellitus and circadian rhythm disruption.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-94359-6.}, } @article {pmid41904356, year = {2026}, author = {Vojtkuf, I and Čačković, A and Soares, AR and Probst, AJ and Orlić, S}, title = {Seasonal Dynamics of Freshwater Bacterial Communities in Continental and Mediterranean Lakes.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41904356}, issn = {1432-184X}, support = {426547801//Deutsche Forschungsgemeinschaft/ ; IP-2020-02-9021//Hrvatska Zaklada za Znanost/ ; }, abstract = {Lakes are highly dynamic freshwater ecosystems where complex interactions between environmental factors and microbial communities regulate biogeochemical cycling and ecosystem stability. Seasonal dynamics of rare and dominant bacterial taxa, as well as the links between dominant taxa and environmental drivers in freshwater ecosystems across Croatia’s contrasting climatic regions, remain insufficiently explored. To address this gap, this study investigated six deep karstic lakes across both regions. Amplicon-based 16 S rRNA gene sequencing coupled with FAPROTAX-based functional predictions revealed that microbial community structure and inferred functional potential were strongly influenced by environmental variability. Dissolved organic carbon (DOC) was identified as the primary driver of community composition. Typical freshwater bacterial genera, including hgcl, Cyanobium PCC-6307, and Luteolibacter, dominated across all lakes. Mediterranean lakes exhibited greater heterogeneity in inferred functional potential across seasons, with variable enrichment in predicted pathways associated with carbon, nitrogen, and sulfur cycling. By contrast, continental lakes showed more stable inferred functional potential with less pronounced seasonal fluctuations. Overall, this study highlights how environmental and climatic variability shape the taxonomic composition and inferred functional potential of microbial communities in freshwater systems, emphasizing the ecological dynamics of dominant bacterial taxa, while also revealing seasonal and regional differences between dominant and rare bacterial taxa across contrasting climatic regions.}, } @article {pmid41904418, year = {2026}, author = {Kousar, R and Latif, S and Zahoor, M and Tabassum, S}, title = {A pilot study revealed the gut microbiota based on 16S rRNA metagenomics in gestational diabetes.}, journal = {BMC genomic data}, volume = {27}, number = {1}, pages = {}, pmid = {41904418}, issn = {2730-6844}, abstract = {OBJECTIVE: Microbiome being a potential biomarker holds the future hope for insight into GD pathogenesis, diagnosis and cure. Many factors such as diet, lifestyle, environment, host genetics shape the diversity and composition of human microbiome. Although recent studies have indicated that gut microbiome dysbiosis was significantly associated with the onset of gestational diabetes mellitus (GDM). Information on the alteration of gut microbiota composition in Pakistani women is limited. Therefore, present study was designed to elucidate gut microbiota taxonomic composition and relative abundance of taxa in local GD women. DATA DESCRIPTION: 16S Metagenomics data revealed variation in bacterial community structure in gestational diabetic (GD), pregnant non-diabetic (PND), non-pregnant diabetic (NPD) and non-pregnant non-diabetic (NPND) women. Predominant bacterial phyla residing faecal sample of GD, NPD, PND included Firmicutes, Bacteriodota, Proteobacteria accounting for 95.07%, 97.1% and 97.04%, of relative abundance respectively. While Predominant phyla inhabiting faecal sample of NPND included firmicutes, Bacteriodota, and Actinobacteriodota accounting for 98.4%. Simpson’s Reciprocal Index showed great variability, the value ranged between 11.655 and 16.17. The distance matrix depicted dissimilarity between samples with dissimilarity coefficient values ranging between 0.381 and 0.588. These findings would pave the way for future studies, which will aid in early diagnosis, management and treatment. CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid41904571, year = {2026}, author = {Kolenda, R and Hassan, MM and Arrieta-Gisasola, A and Kamara, A and Ansorge, R and Sidorczuk, K and Acton, L and Thilliez, G and Baker, DJ and Burdukiewicz, M and Stares, MD and Browne, HP and Le Gall, G and Torres, RC and Chavez-Arroyo, A and Garrett, J and Stevens, MP and Lawley, TD and Bäumler, AJ and La Ragione, R and Hildebrand, F and Kingsley, RA}, title = {Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41904571}, issn = {2049-2618}, support = {BB/W003155/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Salmonella typhimurium/drug effects/genetics/physiology ; Swine ; *Copper/pharmacology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Metagenomics/methods ; Genomic Islands ; Salmonella Infections, Animal/microbiology ; Whole Genome Sequencing ; Intestines/microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Foodborne pathogens, including Salmonella enterica serovar Typhimurium (S. Typhimurium), pose a significant threat to both human health and livestock productivity. The pandemic S. Typhimurium ST34 clone acquired a genomic island (SGI-4) conferring high copper resistance, an adaptation relevant in the context of the widespread use of copper sulphate at therapeutic levels in pig farming. We investigated how high dietary copper influences the piglet gut microbiota and Salmonella-microbiota interactions that may explain the global spread of S. Typhimurium ST34.

RESULTS: An on-farm study combined with faecal shotgun metagenomics revealed that several potential Salmonella competitor species, including Bifidobacterium, Escherichia, and Lactobacillus, were less abundant in piglets on high-copper diets. Anaerobic and aerobic culturing alongside whole genome sequencing of 131 species and copper sulphate susceptibility testing identified copper resistance gene acquisition in selected microbes, particularly within Escherichia. Niche competition assays demonstrated that copper resistance is critical for inter-species competition under high-copper conditions, with Salmonella's Type VI Secretion System providing a distinct advantage over Escherichia in the copper-modified niche.

CONCLUSIONS: Our findings suggest that copper supplementation alters the piglet gut environment, impacting competitive dynamics between pathogenic and commensal bacteria, likely to influence the zoonotic transmission of pathogens. Video Abstract.}, } @article {pmid41904606, year = {2026}, author = {Birkeland, S and Rohde Mæhlum, I and Senneset, M and Wik Taxerås, I and Snipen, L and Markov Arnesen, H and Boysen, P and Carlsen, H}, title = {A naturalized gut microbiome interacts with dietary fibers to protect against colonic inflammation.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2649435}, pmid = {41904606}, issn = {1949-0984}, mesh = {Animals ; *Dietary Fiber/metabolism/administration & dosage ; *Colitis/prevention & control/microbiology/chemically induced ; *Gastrointestinal Microbiome ; Mice ; Feces/microbiology ; Dextran Sulfate/adverse effects ; Colon/pathology/microbiology ; Mice, Inbred C57BL ; Male ; Bacteria/classification/genetics/isolation & purification/metabolism ; Intestinal Mucosa/metabolism ; Intestinal Barrier Function ; Diet ; Disease Models, Animal ; }, abstract = {"Feralized" mice, housed in farmyard-type environments, show a matured immunophenotype, altered intestinal barrier, and a shifted gut microbiome compared to conventionally housed laboratory mice. Since dietary fibers support gut health in part by microbial fermentation into immunomodulatory short-chain fatty acids, we hypothesized that feralization influences the intestinal barrier by enhancing the fiber-degrading properties of the microbiome. We explored whether susceptibility to low-grade dextran sulfate sodium-induced colitis differed between feralized and clean laboratory mice fed diets high or low in fermentable fibers. Feralized mice were protected against colitis, displaying low disease scores and biomarkers of inflammation in feces, plasma, and liver; and altered colonic mucosal gene expression, compared to clean mice. This protection was strongest with a fiber-rich diet, which, in contrast, worsened colitis in clean mice. Transfer of fecal microbiota from feralized mice to clean recipients conferred colitis protection. Fecal metagenome-assembled genomes revealed that the fiber-rich diet enriched the microbiome with predicted genes encoding fiber-degrading enzymes, while the low-fiber diet promoted mucin-degrading enzyme genes. However, the dominant microbial species contributing to these functions differed between feralized and laboratory mice. Differential abundance of bacterial taxa in feralized and laboratory mice further identified potential microbial modulators of colitis that merit targeted investigation in future studies. Overall, these findings suggest that fibers affect intestinal inflammation in a microbiota-dependent manner, underscoring the complex interplay between diet and microbiota in disease development.}, } @article {pmid41904875, year = {2026}, author = {Mu, H and Hu, Y and Zhang, S and Zhang, X and Wei, Q}, title = {Anaerobic digestion model reconstruction of red mud-Pretreated food waste based on the Metagenomics: Improvement of the high-solid ADM1 incorporating SAO and DIET metabolic pathways.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129357}, doi = {10.1016/j.jenvman.2026.129357}, pmid = {41904875}, issn = {1095-8630}, mesh = {Anaerobiosis ; Food Loss and Waste ; Metagenomics ; Wastewater ; Waste Disposal, Fluid ; }, abstract = {Anaerobic Digestion Model No. 1 (ADM1) can accurately describe the biochemical processes in anaerobic digestion (AD) of wastewater, but it fails in the simulation of organic waste's AD due to the different biochemical reaction pathways. To address this limitation, this study proposed an ADM1 improved method based on metagenomics information. For the red mud pretreated food waste anaerobic digestion system, an anaerobic digestion model (RF-ADM1) was developed, focusing on integrating two functional pathways: syntrophic acetate oxidation (SAO) and direct interspecies electron transfer (DIET). Feature kinetic parameters for DIET (Y_pro_ac and Y_bu_ac) were extracted to enhance the model's ability to characterize metabolic processes within this system. The coefficient of determination (R[2]) of the batch experiment reaches 0.996, while Theil's inequality coefficient (TIC) of continuous testing reaches 0.05.}, } @article {pmid41904906, year = {2026}, author = {Zheng, Y and Wu, Q and Xia, Y and Deng, H and Zhao, Y and Luo, J and Feng, D and Ge, C}, title = {Dark side of biodegradable microplastics in mangrove ecosystem: Plastisphere as an overlooked hotspot of sulfate-reducing metabolism.}, journal = {Water research}, volume = {298}, number = {}, pages = {125802}, doi = {10.1016/j.watres.2026.125802}, pmid = {41904906}, issn = {1879-2448}, mesh = {*Sulfates/metabolism ; *Microplastics/metabolism ; Biodegradation, Environmental ; Geologic Sediments ; Ecosystem ; *Wetlands ; Oxidation-Reduction ; }, abstract = {Microplastics (MPs) have increasingly accumulated in the sulfate-rich and anoxic mangrove sediment. However, it remains unclear whether MPs serve as hotspots for sulfate-reducing microbes (SRM) and what potential risks this activity poses to this ecosystem. To address this issue, polyethylene MPs (PE-MPs) and polylactic acid MPs (PLA-MPs) were in-situ exposed to bare mudflat, invasive S. apetala and native B. gymnorhiza sediment, respectively. After 150 days of exposure, microbially-driven sulfur metabolism patterns on plastisphere in three distinct habitats were compared using metagenomic sequencing. Results showed that PLA-MPs enriched more SRM than PE-MPs and non-MPs particles. Dissimilatory sulfate reduction was one of the most abundant sulfur-metabolic pathways on plastisphere, and the abundance of genes driving this process on MPs followed an order of mudflat (9.37 % ± 0.72 %) < S. apetala (22.31 % ± 5.29 %) < B. gymnorhiza (28.69 % ± 1.10 %), indicating that MPs in B. gymnorhiza sediment fostered more active sulfate reduction, primarily driven by sat/met3, apr and dsr gene clusters. Furthermore, CO2 release from plastisphere was greater on PLA-MPs than on PE-MPs in sediments. Given the tight coupling between sulfate reduction and organic carbon degradation, these findings highlighted the potential of biodegradable MPs to affect carbon-sulfur biogeochemical processes in mangrove ecosystems.}, } @article {pmid41905022, year = {2026}, author = {Benschop, KSM and Zwagemaker, F and Andersson-Li, L and Andrés, C and Antón, A and Berengua, C and Berginc, N and Bessaud, M and Bisseux, M and Bujaki, E and Canning, B and Christiansen, CB and Couderé, K and Broberg, EK and Cassidy, H and Castilletti, C and Celma, C and Cinek, O and Deézsi-Magyar, N and Eis-Hübinger, AM and Flipse, J and Jiřincová, H and Gatej, R and Georgieva, I and Giardina, F and González-Sánchez, A and Hack, B and Helfferich, J and Hutchings, S and Hietanen, E and Hönemann, M and Virant, MJ and Kalogera, E and Johannesen, CK and Kenicer, J and Kleines, M and Lagarejos, E and Landaas, ET and Kandulu, CC and Xavier López Labrador, F and Lunar, MM and Maier, M and Majumdar, M and Martin, J and McClure, CP and Muñoz-Almagro, C and Ošep, A and Øverbø, J and Palminha, P and Papa, A and Pariani, E and Pellegrinelli, L and Pietsch, C and Piralla, A and Poljak, M and Pomari, E and Prats-Méndez, I and Rector, A and Reuter, G and Riess, M and Ruta, S and Schibler, M and Nilsen, HS and Simmonds, P and Sourvinos, G and Szomor, K and Susi, P and Tabain, I and Vallely, P and von Eije, KJ and Weil, M and Wieczorek, M and Wollants, E and Wolthers, KC and Zuckerman, NS and Fischer, TK and Harvala, H}, title = {Next generation sequencing approaches for the detection and characterization of enteroviruses in clinical, public health, and research settings: Expert view of the European non-polio enterovirus network (ENPEN).}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {184}, number = {}, pages = {105940}, doi = {10.1016/j.jcv.2026.105940}, pmid = {41905022}, issn = {1873-5967}, mesh = {Humans ; *Enterovirus Infections/diagnosis/virology/epidemiology ; *High-Throughput Nucleotide Sequencing/methods ; *Enterovirus/genetics/isolation & purification/classification ; Public Health ; Europe ; Computational Biology/methods ; Genome, Viral ; }, abstract = {Enteroviruses (EVs) are a common cause of a wide spectrum of infectious diseases, ranging from mild respiratory illnesses to severe neurological conditions, particularly affecting children. Current molecular methods, such as 5'UTR-based PCR for detection and (partial) VP1 gene sequencing for typing, are widely utilized. However, Next-Generation Sequencing (NGS), and bioinformatics offer a comprehensive alternative, enabling full-genome analyses for improved virus characterization, genomic epidemiological surveillance, and outbreak investigation. Despite its advantages, implementation of NGS poses challenges, particularly in standardizing and optimizing laboratory workflows (wet-lab) and bioinformatics analyses (dry-lab), methods that are not often readily accessible in many laboratories. Here, we discuss the potential of NGS as a tool for EV detection/characterization in clinical virology, public health, and research settings. We provide practical options for actions for implementing NGS to advance the understanding and management of enterovirus infections. These recommendations are based on expert discussions during the recent European non-polio enterovirus network (ENPEN) workshop held in Corfu, Greece, on 23-24 May 2024, aiming to guide harmonization of NGS practices across clinical, public health, and research settings.}, } @article {pmid41905052, year = {2026}, author = {Liu, Z and Zhao, C and Chen, N and Zhu, K and Chen, Y and Feng, C}, title = {Synergistic and competitive interactions between solid carbon sources and current-driven sulfate reduction in a single-chamber microbial electrolysis cell.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141881}, doi = {10.1016/j.jhazmat.2026.141881}, pmid = {41905052}, issn = {1873-3336}, mesh = {*Sulfates/chemistry/metabolism ; Electrolysis ; *Carbon/chemistry ; Oxidation-Reduction ; Triticum ; *Bioelectric Energy Sources ; Iron/chemistry ; Sulfur/metabolism/chemistry ; Electrodes ; }, abstract = {Conventional microbial sulfate reduction technologies for sulfate pollution control often suffer from low efficiency, insufficient sulfur immobilization, and poor stability under extreme carbon-to-sulfur (C/S) ratios, leading to secondary pollution. To overcome these limitations, this study combined electrical stimulation with a solid-phase carbon source (wheat straw) to construct a single-chamber microbial electrolysis cell for long-term operation. Under optimal conditions (hydraulic retention time = 2.0 d, C/S = 1.5, current density = 100 mA/m[2]), the sulfate removal efficiency and the accumulation rate of dissolved sulfide reached 92.45% and 26.30%, respectively. The system maintained stable performance over 293 days and during five shock events, demonstrating a pronounced synergistic effect between electrical input and the carbon source. The iron anode facilitated the directional conversion of sulfide into FeS and S[0], enabling efficient sulfur immobilization and significantly suppressing secondary pollution. During operation, microbial activity was sustained at a high level (electron transport system activity = 0.357 μL O2·g[-1]·min[-1], ATP = 0.024 μmol). Metagenomic analysis revealed that electrical stimulation markedly enhanced the abundance of sulfur metabolism-related genes and promoted direct extracellular electron transfer process, whereas the wheat straw facilitated mediated extracellular electron transfer through the slow release of exogenous electron shuttles. The synergistic interaction between these processes optimized the electron transfer network within the system. This study elucidates the mechanisms underlying directional sulfur transformation and electron transfer during long-term operation, providing critical insights for optimizing microbial ecosystems involved in sulfate reduction and supporting the practical application of this technology in water in situ remediation.}, } @article {pmid41905084, year = {2026}, author = {Xiang, H and Deng, Y and Xu, Y and Zhang, X and Zhang, C and Guo, B and Xu, Z and Wang, Y}, title = {Fe-S interactions and geological background shape phosphorus bioavailability in mangrove sediments.}, journal = {Marine pollution bulletin}, volume = {228}, number = {}, pages = {119655}, doi = {10.1016/j.marpolbul.2026.119655}, pmid = {41905084}, issn = {1879-3363}, mesh = {*Geologic Sediments/chemistry ; *Iron/chemistry ; *Phosphorus/analysis ; *Wetlands ; Environmental Monitoring ; *Sulfur/chemistry ; Water Pollutants, Chemical/analysis ; }, abstract = {Mangrove sediments act as critical phosphorus (P) sinks and potential sources in coastal ecosystems, with P release risk dominated by bioavailable phosphorus (BAP), including exchangeable P, iron-bound P (Fe-P), and organic P (OP). While Fe-S cycles tightly regulate P speciation, how the geological background mediates Fe-S-P coupling across heterogeneous mangroves remains unclear. We integrated Fe-S-P fractionation, water-soluble organic matter (WSOM) fluorescence spectroscopy, and metagenomics to compare volcanic weathering (V) and Quaternary coastal (Q) sediments in Dongzhai Harbor. Key findings are as follows: Total P in shallow V sediments (8.89-30.90 μmol/g) is higher than in Q (6.95-17.09 μmol/g). OP dominates V's BAP (48.87%) linked to OP mineralization genes (e.g., appA), whereas Fe-P dominates Q's BAP (57.31%) and is stabilized by amorphous Fe oxides. In deep V sediments, Fe-P is positively correlated with acid-volatile sulfide (AVS; R[2] = 0.57) and Fe/S reduction genes (fsr, omcF), indicating Fe-S-coupled P mobilization and release. In deep Q sediments, Fe-P remains stabilized by Feox1, and P mobilization is driven by microbial iron reduction, with iron-reduction genes (e.g., mtrA) being significantly enriched. Two distinct P release pathways are identified: in volcanic weathering zone sediments, P release shifts from OP dominance to Fe-S-coupled regulation, while in Quaternary coastal zone sediments, Fe-P mobilization relies on microbial iron reduction. These findings clarify the geological controls on Fe-S-P interactions in mangrove sediments, providing a scientific basis for site-specific P risk assessment and the formulation of targeted strategies for mangrove ecosystem restoration and coastal eutrophication control.}, } @article {pmid41905194, year = {2026}, author = {Li, J and Silvester, R and Williams, RC and Chan-Herur, V and Goldman, M and Fidler, D and Jones, DL}, title = {Metagenomics-based source attribution of antimicrobial resistance in wastewater for improved epidemiological risk assessment.}, journal = {Water research}, volume = {298}, number = {}, pages = {125810}, doi = {10.1016/j.watres.2026.125810}, pmid = {41905194}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; *Metagenomics ; Humans ; Risk Assessment ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; }, abstract = {Wastewater-based epidemiology (WBE) offers a powerful approach for monitoring antimicrobial resistance (AMR) at the population level. However, distinguishing between human gut-derived and sewer-derived AMR-carrying organisms remains a key challenge for accurate surveillance and risk assessment. In this study, we used genome-resolved metagenomics to distinguish human gut-derived organisms, and their associated antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs) and virulence-associated determinants (VFs), from taxa endemic to the sewer network. We applied this approach to wastewater samples collected from three hospital outflows (near-source healthcare sites), as well as from untreated influent and final treated effluent at the corresponding municipal wastewater treatment plants serving the surrounding communities. Along the wastewater pathway, microbial communities progressively shifted from human gut-associated to sewer adapted taxa; consequently, the final treated effluent was dominated by sewer-adapted taxa. Human gut-derived taxa were further examined in detail: 84% carried ARGs and VFs, predominantly within Bacillota and Bacteroidota; all gut-associated Pseudomonadota also harboured multiple ARGs, VFs and MGEs. Opportunistic-pathogen taxa of gut origin (Escherichia coli, Klebsiella spp., E. faecium) accounted for a substantial fraction of ARGs in hospital wastewater. Combined sewer overflow (CSO) events may allow these carriers to bypass wastewater treatment and reach receiving waters, posing public health risks. This genome-resolved framework strengthens WBE by resolving human-derived contributions for surveillance and risk assessment.}, } @article {pmid41905375, year = {2026}, author = {Wrønding, T and Vomstein, K and Lundgaard, AT and DeLong, K and Mollerup, S and Mortensen, B and Bosma, EF and Hellerung, AM and Engel, EV and Wiil, KD and Heintz, JE and Halkjær, SI and Hugerth, LW and Hartwig, TS and Petersen, AM and Thomsen, AB and Westergaard, D and la Cour Freiesleben, N and Westh, H and van Hylckama Vlieg, JET and Ensign, LM and Nielsen, HS}, title = {Vaginal microbiota transplantation for treatment of vaginal dysbiosis without the use of antibiotics: a double-blind, randomised controlled trial in women with vaginal dysbiosis.}, journal = {The Lancet. Microbe}, volume = {7}, number = {4}, pages = {101294}, doi = {10.1016/j.lanmic.2025.101294}, pmid = {41905375}, issn = {2666-5247}, mesh = {Humans ; Female ; Double-Blind Method ; Adult ; *Dysbiosis/therapy/microbiology ; *Vagina/microbiology ; *Microbiota ; Young Adult ; Adolescent ; Anti-Bacterial Agents ; Lactobacillus ; Treatment Outcome ; }, abstract = {BACKGROUND: A vaginal microbiota dominated by Lactobacillus species is associated with reduced risk of infection and adverse reproductive outcomes. Effective interventions to restore healthy microbiota remain scarce. In this study, we aimed to assess the efficacy of vaginal microbiota transplants (VMTs) without antibiotic pretreatment in achieving conversion to a Lactobacillus-dominated vaginal microbiome.

METHODS: This single-centre, double-blind, randomised controlled trial was done at Copenhagen University Hospital (Hvidovre, Denmark) between June 1, 2021, and March 1, 2023. We enrolled women aged 18-40 years with asymptomatic or symptomatic molecular vaginal dysbiosis (<10% total relative abundance of Lactobacillus spp and >20% relative abundance of Gardnerella spp, Fannyhessea vaginae, and Prevotella spp) who were otherwise healthy premenopausal women and not pregnant as recipients; donors were healthy women aged 18-40 years with a Lactobacillus-dominated vaginal microbiota (>80%) and a low (<5%) abundance of Gardnerella spp, F vaginae, and Prevotella spp, and negative screening for sexually transmitted infections. Participants were randomly assigned (3:1) to the intervention or placebo through a computer-generated schedule with block randomisation and stratification by hormonal contraception. Participants and investigators were masked to the group. Up to three administrations of VMT or placebo were given across three menstrual cycles, with follow-up for six cycles. The primary endpoint was resolution of dysbiosis at any timepoint during follow-up, defined as at least 70% relative abundance of Lactobacillus spp and less than 10% combined abundance of Gardnerella spp, F vaginae, and Prevotella spp, as assessed by shotgun metagenomic sequencing of vaginal samples. This analysis was done in the intention-to-treat population, excluding any participants who withdrew consent. An extension study assessed the effect of antiseptic pretreatment before additional VMT in refractory participants. This study was registered with ClinicalTrials.gov (NCT04855006) and is completed.

FINDINGS: A total of 302 women were screened, of whom 49 were enrolled. 37 women were randomly assigned to the VMT group (mean age 26·1 years [SD 3·8]) and 12 to the placebo group (27·3 years [4·8]). The primary outcome showed no significant difference in dysbiosis resolution between active and placebo groups (HR 0·65; 95% CI 0·20-2·16, p=0·49). In an extension study of refractory participants, five (50%) of the ten women who received antiseptic pretreatment followed by VMT had a microbiome conversion. Adverse events occurred in 15 (42%) VMT participants and five (42%) placebo participants; none were serious or led to withdrawal. A single pregnancy and one new human papillomavirus infection occurred, both unrelated to treatment.

INTERPRETATION: VMT without antibiotics did not significantly improve microbiome conversion in this trial. However, findings from the extension study suggest that antiseptic pretreatment might enhance efficacy. Future trials should explore optimised dosing and use donor engraftment as a primary outcome.

FUNDING: Freya Biosciences.}, } @article {pmid41905742, year = {2026}, author = {Wu, Z and Duan, A and Liu, Y and Chen, R and Md Din, MF and Sanjaya, EH and Ali, EAE and Saad, A and Liu, Z and Chen, H}, title = {Mechanistic insights into sulfate-driven performance adaptation and membrane fouling in a UASB-SBR-AXMBR system: metabolic network reconstruction and microbial community succession.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124374}, doi = {10.1016/j.envres.2026.124374}, pmid = {41905742}, issn = {1096-0953}, mesh = {*Bioreactors/microbiology ; *Sulfates/metabolism ; *Waste Disposal, Fluid/methods ; Membranes, Artificial ; Wastewater ; Metabolic Networks and Pathways ; *Microbiota ; Bacteria/metabolism ; }, abstract = {Sulfate-rich wastewater poses considerable challenges to the operational stability of biological treatment systems. This study investigated the long-term (294 days) response of a combined UASB-SBR-AXMBR process to stepwise increases in sulfate concentration from 100 to 2000 mg/L. The system maintained stable carbon and nitrogen removal performance under sulfate stress, with COD removal exceeding 90.3% and total nitrogen removal stabilizing at 85.5% via a partial nitritation-anammox (PN/A) pathway. However, high sulfate loading significantly intensified membrane fouling, with the primary driving factor likely being the co-deposition of elemental sulfur (S[0]) and soluble extracellular polymeric substances (S-EPS). Microbial analysis revealed persistent enrichment of Bacteroidota and Proteobacteria in the SBR, alongside a marked increase in Anammoxoglobus (from 17.1% to 51.2%) in the Anaerobic Ammonia Oxidation Membrane Bioreactor (AXMBR), underpinning system resilience. Metagenomic profiling further indicated adaptive shifts in key nitrogen-cycling genes (hao, amoA) and sulfur metabolism pathways. Notably, sulfate-reducing bacteria (SRB) outcompeted methanogens, redirecting carbon flow from methanogenesis to sulfur reduction, while niche diversification in the AXMBR expanded nitrogen removal pathways. These findings provide new mechanistic insights into the adaptive responses of integrated bioprocesses under sulfate stress and provide practical guidance for the treatment of high-sulfate industrial wastewaters such as monosodium glutamate effluent.}, } @article {pmid41905975, year = {2026}, author = {Barbe, V and de Toro-Martín, J and Garneau, V and Couture, P and Roy, D and Couillard, C and Marette, A and Vohl, MC}, title = {Functional gut microbiome signatures underlying interindividual variability in metabolic responses to red raspberry consumption.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41905975}, issn = {2045-2322}, abstract = {UNLABELLED: Red raspberries have been shown to exert beneficial effects on immunometabolic health in numerous studies; however, these effects are subject to interindividual variability. Building on a previous transcriptomic-based clustering analysis from an 8-week randomized controlled trial in which 24 individuals consumed 280 g of red raspberries daily, we investigated whether functional metagenomic profiling may enhance our understanding of the observed interindividual variability in metabolic responses. Participants were classified as responders (n = 13) or non-responders (n = 11) based on prior clustering approaches, which identified significant reductions in plasma levels of C-reactive protein (CRP), triglycerides, and total cholesterol in responders. Microbial DNA extracted from fecal samples collected before and after the intervention was sequenced, and carbohydrate-active enzyme (CAZyme) counts were generated using a bioinformatics pipeline. Differential analysis revealed distinct functional metagenomic profiles between responders and non-responders. Multiple linear regressions identified potential associations between baseline CAZyme levels and changes in CRP, with contrasting trends observed between responders and non-responders. CBM8 and CBM49 were among the highlighted CAZymes. GH5 and several GH5 subfamilies were also identified as candidate CAZymes associated with interindividual variability observed in metabolic responses. These findings support the integration of microbiome-derived functional data alongside other omics to improve precision nutrition strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-45955-7.}, } @article {pmid41906088, year = {2026}, author = {Bai, D and Wang, Z}, title = {Neurosyphilis with simultaneous brain and spinal cord involvement mimicking intracranial tumors: a case report.}, journal = {BMC neurology}, volume = {26}, number = {1}, pages = {}, pmid = {41906088}, issn = {1471-2377}, abstract = {BACKGROUND: Neurosyphilis is a heterogeneous manifestation of Treponema pallidum infection with diverse clinical and radiological presentations. Concurrent involvement of the brain and spinal cord is rare and may mimic intracranial neoplasms, leading to diagnostic uncertainty. CASE PRESENTATION: A 48-year-old woman presented with acute-onset limb numbness and diplopia. Brain and cervical spine magnetic resonance imaging (MRI) revealed multiple nodular and ring-enhancing lesions involving the brain parenchyma and cervical spinal cord, initially raising suspicion of lymphoma or metastatic tumors. Diffusion-weighted imaging (DWI) showed atypical hypointensity without diffusion restriction. Histopathological examination demonstrated perivascular inflammatory infiltration without evidence of malignancy. Serological testing confirmed a reactive serum rapid plasma reagin (RPR) titer with treponemal confirmation, and metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) detected Treponema pallidum deoxyribonucleic acid (DNA), supporting the diagnosis of neurosyphilis. HIV serology was negative. Due to a documented penicillin allergy (positive penicillin skin test), the patient received alternative antimicrobial therapy with fosfomycin (8 g/day intravenously) and minocycline (100 mg orally twice daily), resulting in marked clinical improvement and regression of lesions on follow-up imaging. CONCLUSION: This report describes a patient in whom neurosyphilis presented with concurrent brain and spinal cord lesions that radiologically resembled malignant central nervous system (CNS) tumors. Multifocal nodular and ring-enhancing lesions without diffusion restriction, combined with clinical improvement following antimicrobial therapy, were features observed in this case that contributed to the diagnostic re-evaluation. This case highlights the importance of including neurosyphilis in the differential diagnosis of tumor-like CNS lesions when imaging findings are atypical, while acknowledging that definitive diagnostic conclusions are limited by the single-case nature of this report.}, } @article {pmid41906342, year = {2026}, author = {Wu, J and Tian, J and Zhang, X and Kong, Z}, title = {Metagenomic Analysis of Soybean Rhizosphere Microbiome in Black Soil: Community Composition and Functional Insights.}, journal = {Plant, cell & environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70505}, pmid = {41906342}, issn = {1365-3040}, support = {XDA28030201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 32241045//National Natural Science Foundation of China/ ; }, } @article {pmid41907005, year = {2026}, author = {Jeunen, GJ and Mills, S and Bailie, M and Mauvisseau, Q and Lamare, M and Mariani, S and Pearman, W and Zavodna, M and Treece, J and Ferreira, S and Gemmell, NJ}, title = {Recovering Historical eDNA From Museum-Preserved Filter Feeders via Non-Destructive Metabarcoding.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70132}, pmid = {41907005}, issn = {1755-0998}, support = {MFP-UOO2116//Royal Society of New Zealand Marsden Fast-Start Fund/ ; ANTA1801//Ministry of Business, Innovation, and Employment/ ; //University of Otago Research Grant (UORG)/ ; }, mesh = {Animals ; Museums ; *DNA Barcoding, Taxonomic/methods ; *Metagenomics/methods ; *Specimen Handling/methods ; *DNA/isolation & purification/genetics ; Preservation, Biological/methods ; Filtration ; RNA, Ribosomal, 16S/genetics ; *DNA, Environmental/isolation & purification/genetics ; }, abstract = {Recent technical advances have significantly enhanced the value of museum specimens for molecular research, with metagenomic and metabarcoding approaches expanding further the utility of museum collections. However, given the finite number of specimens, there is a critical need to move past destructive DNA extraction approaches and to explore non-destructive techniques. In this proof-of-concept study, we evaluated the feasibility of extracting historical eDNA from the ethanol preservative used to store museum specimens. We compared a variety of extraction methods (centrifugation, evaporation, filtration, and precipitation) using ten replicate samples per treatment for statistical analyses. To assess potential differences in preservative-derived eDNA recovery across different filter-feeding taxonomic groups, we included a bryozoan, a demosponge, and a glass sponge. Comparative analyses with tissue biopsies revealed that 10 mL ethanol filtration performed equal to or, in some instances, outperformed tissue biopsies for all three specimens when examining the historical eDNA of Antarctic fish using a 16S rRNA metabarcoding approach, both for the number of species detected (α-diversity) and community characterisation (β-diversity). This initial study demonstrates the potential of ethanol preservative as a valuable, non-destructive source of historical eDNA from museum-stored filter-feeding specimens. These findings highlight the viability of non-destructive sampling for molecular research on museum collections, preserving specimen integrity while enabling biodiversity assessments. Further refinement of non-destructive eDNA extraction could expand its applicability across taxa, collection types, and preservation methods, ensuring the long-term sustainability of museum-based genomic, metagenomic, and metabarcoding research.}, } @article {pmid41907295, year = {2026}, author = {Liu, J and Zhou, Y and Xu, F and Liu, W and Chen, H and Yan, Q and Guo, J and Lai, L}, title = {Case Report: Cavitary Legionella pneumophila pneumonia in a kidney transplant recipient: mNGS-guided diagnosis and prolonged combination therapy.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1697062}, pmid = {41907295}, issn = {2296-858X}, abstract = {Legionella pneumophila is an uncommon but potentially life-threatening cause of pneumonia in solid organ transplant (SOT) recipients. Diagnosis is challenging due to nonspecific features and the limited sensitivity of conventional assays. Metagenomic next-generation sequencing (mNGS) offers unbiased detection and may be particularly valuable in immunocompromised hosts with refractory pneumonia. We report the first documented case in Asia of cavitary Legionella pneumonia in a kidney transplant recipient. A 60-year-old man presented with fever and bilateral pulmonary nodules 5 months post-transplant. Despite empirical antifungal and antibacterial therapy, his condition progressed radiologically to cavitary disease. Bronchoalveolar lavage fluid mNGS identified abundant L. pneumophila reads, confirming the diagnosis. Initial azithromycin monotherapy achieved transient improvement but failed to prevent radiological progression. Escalation to prolonged dual therapy with azithromycin and levofloxacin resulted in rapid symptomatic relief, progressive cavity regression on serial computed tomography, and preserved allograft function. Sequential blood-based mNGS demonstrated declining pathogen reads paralleling recovery. This brief research report emphasizes three practice points for SOT recipients with refractory pneumonia: (1) early mNGS can shorten time-to-diagnosis when routine tests are inconclusive; (2) Legionella infection may manifest with atypical cavitary lesions in immunocompromised hosts, warranting scheduled imaging even when symptoms improve; and (3) prolonged macrolide-fluoroquinolone combination therapy may be required for severe or non-resolving cases. Together with our literature review, this case expands understanding of the radiological spectrum, diagnostic strategies, and therapeutic considerations of Legionella pneumonia in transplant populations.}, } @article {pmid41907709, year = {2024}, author = {Nirmalkar, K and Patel, J and Kang, DW and Bellinghiere, A and Bowes, DA and Qureshi, F and Adams, JB and Krajmalnik-Brown, R}, title = {Bimodal distribution of intestinal Candida in children with autism and its potential link with worse ASD symptoms.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2358324}, pmid = {41907709}, issn = {2993-3935}, abstract = {The gastrointestinal (GI) tract harbors a complex and remarkably diverse microbial ecosystem that profoundly impacts various aspects of health and pathophysiology. While bacteria overwhelmingly represent most of the GI microbiota, it is imperative to consider the presence and function of fungal constituents (i.e. mycobiota) within the GI ecosystem. The substantial incidence of GI disorders and associated manifestations in children diagnosed with autism spectrum disorder (ASD) suggests a plausible contributory role of the gut mycobiota. This work aimed to elucidate the gut mycobiota in a cohort of 38 typically developing children (TD) and 40 children with ASD. Fecal samples were collected from all participants, autism severity and GI symptoms were assessed to unravel the potential implications of mycobiota alterations in the gut. We performed fungal internal transcribed spacer (ITS) gene amplicon sequencing to analyze the fungal composition and investigate their relationship with GI and autism symptoms. Among gut mycobiota, Saccharomyces cerevisiae was significantly lower (relative abundance) in the ASD fecal samples compared to TD children. Candida and C. albicans demonstrated a bimodal distribution among children with ASD. The small subset of children with elevated C. albicans or decreased S. cerevisiae had increased Autism Treatment Evaluation Checklist (ATEC) scores. Our findings suggest that a deficit of S. cerevisiae, and an overgrowth of C. albicans in a subset of children is associated with worse autism severity. Future work employing shotgun metagenomics with a larger cohort is encouraged to advance understanding of the functional role of fungi, and their possible interplay with GI symptoms and autism severity in children with ASD.}, } @article {pmid41907719, year = {2024}, author = {Dixit, K and Ahmed, A and Singh, A and Inamdar, M and Chavan, S and Bodkhe, R and Mehtab, W and Chauhan, A and Saroj, SD and Ahuja, V and Shouche, Y and Dhotre, D and Makharia, G}, title = {Site-Specific Gut Microbial Signatures in Non-Celiac Gluten Sensitivity.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2438621}, pmid = {41907719}, issn = {2993-3935}, abstract = {Gut microbiota in non-celiac gluten sensitivity (NCGS) has been poorly studied for its involvement in the disorder and site specificity. We investigated small intestinal, large intestinal and stool microbiota profiles in patients with NCGS and highly overlapping disorder irritable bowel syndrome (IBS) as well as effect of gluten-free diet (GFD) on microbiota in patients with NCGS. True NCGS patients were recruited based on serological response for anti-gliadin antibodies, 6-week gluten free diet (GFD) and symptom recurrence with gluten-rechallenge. Analyses using 16S rRNA gene amplicon and shotgun sequencing revealed community differences in core microbiome and diversity measures across sample types indicating dysbiosis mainly in mucosa-associated small intestinal microbiome of NCGS patients. Genera Elusimicrobiaum, Succinivibrio, Bacillus and Alcaligenes appeared as signatures in small intestine and stool in NCGS patients. Presence of differential taxa co-occurring at sampling sites, enabled recognition of site-specific microbial signatures. GFD led to a shift in mucosa-associated small intestinal core microbiome. Metagenome analysis revealed subtle differences in pathways for amino acid biosynthesis including L-ornithine. Mucosa-associated small intestine microbial structure was quite distinct in patients with NCGS in comparison to that with IBS.}, } @article {pmid41908157, year = {2024}, author = {Pfavayi, LT and Sibanda, EN and Baker, S and Woolhouse, M and Mduluza, T and Mutapi, F}, title = {Diversity and composition of gut protist in young rural Zimbabwean children.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1399160}, pmid = {41908157}, issn = {2813-4338}, abstract = {BACKGROUND: The human gut microbiome harbours diverse species of archaea, bacteria, fungi, protists and viruses. To date, most gut microbiome studies have focused on bacteria, neglecting other microbial communities. Consequently, less is known about the diversity and abundance of the latter. Here, we aimed to characterise the diversity and composition of protists in the gut of preschool-aged children (PSAC) in rural Zimbabwe relative to host age, sex, and schistosome infection status.

METHODS: The gut protist of 113 PSAC (1-5 years) was examined via shotgun metagenomic sequencing and analysed for diversity. Variation in protist abundance with host and environmental factors was analysed by permutational multivariate analysis of variance (PERMANOVA). To investigate how the composition of specific taxa varies across age, sex, nutritional measures and Schistosoma hematobium infection status, analysis of the composition of microbiomes (ANCOM) was used.

RESULTS: Eighty protist genera were identified, and the most abundant genera detected was Blastocystis. The prevalence of pathogenic protists was comparatively low, with 12.4% and 3.4% of the participants' gut colonised by E. histolytica and Cryptosporidium, respectively. Of all the independent variables only S. haematobium infection showed significant relationship with the structure of the gut protist, being associated with increases in Peronospora, Pseudoperonospora, Plasmopara and Blastocystis (FDR= 0.009).

SUMMARY: This study provides data on the prevalence and diversity of the gut protists in young Zimbabwean children with an emphasis on the host factors; age, sex and schistosome infection status. Our results showed no association between the host factors investigated, including anthropometric measures adjusted for age and the intestinal protist composition and structure, but S. haematobium infection status was associated with composition of specific taxa. There is a need for more studies determining how pathogenic protist interact with non-pathogenic protist in people exhibiting clinical symptoms to inform therapy and nutraceuticals.}, } @article {pmid41908294, year = {2026}, author = {Schulz, S and Börner, S and Bitter, K and Gheit, H and Partsakhashvili, J and Ukkat, J and Misiak, D and Reichert, S}, title = {Possible association between the microbiota in subgingival and atherosclerotic plaque in a cohort of patients with carotid stenosis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2648325}, pmid = {41908294}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontal pathogens have been implicated in systemic diseases, including atherosclerosis. This study investigates the relationship between subgingival and microbial colonization of carotid plaque in patients undergoing carotid endarterectomy (DRKS00021598).

METHODS: Microbial samples from both subgingival and carotid plaques were collected from 25 hospitalized patients. Preoperative all patients underwent periodontal examination. The microbial composition was assessed using metagenomics sequencing of 16S rRNA gene (V3/V4 regions).

RESULTS: Bacterial DNA was detected in both subgingival and carotid plaque samples. The microbial composition differed between both communities. Alpha diversity was significantly higher in subgingival samples than in carotid plaques (p = 0.039). Beta diversity analysis, (including unweighted UniFrac (p < 0.001), linear discriminant analysis, principal component analysis) confirmed significant differences between subgingival and carotid plaque microbiota. The study revealed overlaps in a few individual cases.

CONCLUSIONS: These findings show that carotid plaque microbiota differ from subgingival communities and are not exclusively of oral origin, suggesting additional systemic sources.}, } @article {pmid41908297, year = {2026}, author = {Shantha, JG and Chen, C and Hinterwirth, A and Gonzales, JA and Acharya, NR and Lietman, TM and Doan, T}, title = {Integrated metagenomic sequencing and phage display-based immunoprecipitation sequencing for presumptive viral infection: a case report.}, journal = {American journal of ophthalmology case reports}, volume = {42}, number = {}, pages = {102561}, pmid = {41908297}, issn = {2451-9936}, abstract = {PURPOSE: To report a case of uveitis in which unbiased metagenomic sequencing (MDS) and phage immunoprecipitation sequencing (PhIP-Seq) were performed on intraocular fluid.

OBSERVATIONS: A female patient with a past medical history of human immunodeficiency virus (HIV-1) who presented with chronic active anterior and intermediate uveitis with cystoid macular edema in the left eye. She had a previous ocular history of viral retinitis presumed to be secondary to cytomegalovirus (CMV). An anterior chamber tap was performed for viral polymerase chain reactions (PCRs), MDS, and pathogen PhIP-Seq. PCR testing and MDS were negative for pathogen genetic materials. PhIP-Seq detected antibody enrichment of CMV, as well as HIV-1 andSARS-CoV-2.

CONCLUSIONS: The combination of MDS and PhIP-Seq has the potential to provide additional insights into the pathogenesis and the ocular microenvironment of uveitis patients.}, } @article {pmid41908958, year = {2026}, author = {Song, Y and Pu, X and Liu, Q and Hou, S and Zou, D and Xiang, Y and Gu, S and Chu, M}, title = {Dietary energy alters jejunal microbial function without changing its structure in small-tailed Han sheep.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1730873}, pmid = {41908958}, issn = {2297-1769}, abstract = {Dietary energy levels typically influence the structure and functional profile of the gastrointestinal microbial community. In this study, thirty 6-month-old Small-tailed Han (STH) sheep were randomly divided into three groups and fed corn-based diets with different energy levels for 150 days. Jejunal contents were then collected and analyzed using metagenomic sequencing to assess microbial alpha diversity and taxonomic composition. Functional annotation and enrichment analysis were performed using the KEGG database. Principal coordinate analysis (PCoA) and alpha diversity indices (Chao1, Shannon, Simpson and good coverage) revealed no significant changes in the overall structure or macro-ecological characteristics of the jejunal microbial community in response to dietary energy levels. At the phylum level, Bacillota was the absolutely dominant phylum, while at the genus level, Methanobrevibacter was the most abundant genus. The abundances of these core microbial taxa did not differ significantly among groups. However, KEGG functional enrichment analysis revealed significant differences in microbial functions between groups. The low-energy group exhibited enrichment in pathways related to energy deficiency and stress adaptation, whereas the high-energy group showed significant enrichment in pathways associated with active growth and anabolic metabolism. In conclusion, although dietary energy levels did not significantly alter the microbial community structure in the jejunum of STH sheep, they profoundly influenced its functional potential. These findings suggest that dietary energy may modulate host nutrient acquisition and health status by regulating the functional characteristics of the jejunal microbiota.}, } @article {pmid41909054, year = {2025}, author = {Hanna, M and Huang, S and Ross, M and Reyes, A and Perera, D and Surathu, A and Cregeen, SJ and Hagan, J and Pammi, M}, title = {Microbiome Signatures and Inflammatory Biomarkers in Culture-Negative Neonatal Sepsis.}, journal = {Applied microbiology (Basel, Switzerland)}, volume = {5}, number = {3}, pages = {}, pmid = {41909054}, issn = {2673-8007}, support = {R03 HD098482/HD/NICHD NIH HHS/United States ; }, abstract = {Overuse of antibiotics is a concern in 'culture-negative sepsis' but it is unclear whether this is due to infection with viruses, fungi or other microbes that are not easily cultured, or whether it results from inflammatory processes. In a prospective study, we enrolled 50 preterm neonates with culture-positive sepsis (CP), culture-negative sepsis (CN), and asymptomatic preterm controls (CO). The microbiome of stool, skin, and blood, including bacterial, viral and fungal components and serum cytokine profiles were evaluated. The microbiome alpha or beta diversity did not differ between CN and CO groups. A MaAsLin analysis revealed increased relative abundances of specific bacterial and fungal genera in stool and skin samples in the CN group compared to CO. The virome analysis identified 24 viruses from skin samples, but they were not statistically different among the three groups. The cytokine and chemokine biomarker profiles were elevated in the CP group but were not statistically different between the CN and CO groups. Although the CN group had a longer hospital stay and higher BPD rates than the controls in unadjusted analyses, these differences were not significant after adjusting for gestational age and birth weight. The CN infants demonstrated microbial shifts without systemic immune activation or significantly worse clinical outcomes, supporting the rationale for discontinuing antibiotics in the absence of positive cultures.}, } @article {pmid41909251, year = {2026}, author = {Sun, F and Yuan, M and Liao, C and Sun, Y and Yu, L and Zhuo, Y and Peng, Y and Tang, X and Zeng, Q and Song, J and Tao, X and Li, Q and Chen, M and Zhang, Y}, title = {Optimizing flue-cured tobacco planting patterns: enhanced rhizosphere nutrient availability and microbial community dynamics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1735540}, pmid = {41909251}, issn = {1664-302X}, abstract = {INTRODUCTION: Continuous monoculture of flue-cured tobacco causes soil degradation and microbial dysbiosis. While crop rotation can alleviate these obstacles, how different cropping patterns regulate soil carbon (C) and nitrogen (N) metabolic functions remains unclear.

METHODS: A four-year field experiment compared tobacco monoculture (CK), tobacco-maize rotation (TM), tobacco-rice rotation (TR), and tobacco-sweet potato intercropping (TP). Soil physicochemical properties, enzyme activities, metagenomic sequencing, and microbial network analysis were integrated.

RESULTS: TR significantly improved soil health: pH (+6.6%), organic matter (+22.1%), and urease activity (+12.5%). It enriched beneficial microbes (Pseudomonadota +16.4%, Mucoromycota +327%) and upregulated C-cycle (korA +42.3%) and N-assimilation genes (amoC +460%), while suppressing denitrification (nirK). TM increased available P/K but enriched oligotrophic taxa and reduced sucrase activity. TP triggered pathogenic fungi (Olpidium +160%), depleted beneficial microbes, and broadly suppressed C/N metabolic genes (cbbL -94.5%, nirS -21.8%).

DISCUSSION: Cropping patterns differentially reshape microbial communities and metabolic functions, determining their efficacy against continuous cropping obstacles. TR establishes efficient C/N cycling with "high assimilation, low denitrification," whereas TP induces pathogenic proliferation and metabolic suppression. This provides a functional framework for designing cropping systems to enhance soil health and tobacco productivity.}, } @article {pmid41909254, year = {2026}, author = {Pan, K and Zhang, Z and Feng, L and Wu, X and Yang, X and He, X and Xiao, Y and Yang, D and Duan, C and Wang, Q}, title = {Biochar regulates putative keystone microbial taxa to drive phosphorus cycling and increase availability in urban greenspace soils.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786258}, pmid = {41909254}, issn = {1664-302X}, abstract = {The quality of soil in urban green spaces often deteriorates due to poor design practices, insufficient maintenance, and environmental pressures associated with urbanization. Although biochar, as an effective soil additive, can significantly improve the soil quality in greenspace, it significantly influences the phosphorus (P) cycling processes through functional regulation of microbial community; however, further analysis is essential to validate this mechanism. Therefore, this study reported pot experiments using Euonymus kiautschovicus, a typical urban greenspace plant, followed by metagenomic analysis for investigating microbial-driven P cycle mechanisms. Four treatment groups were established according to the dosage of biochar, including 0% (CK), 4% (BC4), 8% (BC8), and 12% (BC12). Biochar application significantly increased soil available P (AP) and total P (TP) content, with BC12 demonstrating maximum AP and TP content of 21.79 mg kg[-1] and 0.62 g kg[-1], respectively. On the one hand, biochar serves as a direct source of P. On the other hand, it enhances AP by regulating P-cycling functional microorganisms. Random forest model identified phnP, phoA, relA, ppnK, pstA, phnD, and pstS as the putative keystone genes regulating soil P cycling. Microbial co-occurrence network analysis and partial least squares path modeling (PLS-PM) demonstrated that the biochar application improved soil AP by regulating putative keystone microbial taxa (Modules 1 and 2) involved in P cycling. This study elucidates the microbial mechanisms underlying biochar-mediated P cycling in greenspace soils, providing a scientific basis for biochar application for improved soil quality in urban greenspace.}, } @article {pmid41909264, year = {2026}, author = {Li, L and Zhao, D and Du, R and Tang, K and Zhang, Y}, title = {Niche adaptation of particle-associated ammonia-oxidizing archaea sustains nitrification under marine deoxygenation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1773718}, pmid = {41909264}, issn = {1664-302X}, abstract = {Marine deoxygenation is restructuring coastal microbial niches and metabolic networks, with cascading effects on biogeochemical cycles, a key component of which is the nitrogen cycle. Particles constitute a critical ecological interface that mediates microbial niche partitioning and oxygen-sensitive balance between nitrogen loss and retention in deoxygenating coastal waters. However, the niche-dependent metabolic partitioning of microbial communities and its influence on the nitrogen cycle under deoxygenation remains poorly constrained. We conducted a 22-day field investigation of the deoxygenated water column off the Zhoushan coast, China, combining temporal [15]N-tracer-based nitrification rate measurements with size-fractionated metagenomic sequencing during the day of the most severe bottom-water oxygen depletion. Our data revealed a nitrification hotspot in the low-oxygen waters below the pycnocline, with persistently elevated rates and an enriched abundance of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria. Notably, particle-associated AOA exhibited significantly enriched genomic potential for coupled nitrogen cycling and carbon fixation, while the dominant groups adapted to low-oxygen particles via distinct metabolic strategies. Nitrosomarinus-like AOA exhibited higher gene counts (amoA-normalized) for ammonia (amt) and high-affinity phosphate (pst) transporters, whereas their Water column group A-like counterparts were enriched in low-affinity phosphate transporters (pit). Urease gene enrichment in both major AOA clades implicates urea as an ecologically relevant alternative nitrogen source for ammonia acquisition in coastal waters. Furthermore, particle-associated AOA may couple nitrite production and consumption via co-enriched ammonium monooxygenase (amoA) and nitrite reductase (nirK), potentially increasing nitrogen loss through local nitrite utilization. Collectively, our findings demonstrate that differential adaptation across clades underpins the pivotal role of AOA in nitrogen cycling under deoxygenation.}, } @article {pmid41909265, year = {2026}, author = {Nagy, Á and Tóth, GE and Sály, P and Pereszlényi, CI and Babinszky, GC and Makrai, L and Somogyi, BA and Gyuranecz, M}, title = {Development of Nanopore amplicon sequencing method for culture-free genotyping of Bacillus anthracis strains directly from environmental samples.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1771578}, pmid = {41909265}, issn = {1664-302X}, abstract = {Fast and accurate genetic subtyping of pathogens is required to respond appropriately to biological events caused by natural outbreaks or bioattacks involving anthrax. In this study, we developed and validated a culture-free genotyping method that combines a multiplex PCR-based amplicon sequencing method on the Nanopore platform with in silico multiple-locus variable-number tandem repeat analysis (MLVA) of 31 loci to identify an unknown Bacillus anthracis strain directly from environmental samples. The novel method accurately identified repeat numbers for all loci in 12 different MLVA genotype Bacillus anthracis strains analyzed in the study, matching 100% with the reference capillary electrophoresis and Sanger sequencing results. The detection limit of the method, at which all 31 variable-number tandem repeat loci were successfully identified, was found to be 10[4] CFU spores/sample for pure spore samples and at 10[6] CFU spores/sample for spiked environmental samples from three matrices (soil, swab, and muddy water). Specificity tests yielded negative results for samples containing only non-Bacillus anthracis members of the Bacillus cereus group, which produced sequencing reads for 15 loci but were non-specific to Bacillus anthracis. To validate the method, we genotyped 11 Bacillus anthracis strains originating from a historical collection of Hungarian isolates. The MLVA31 typing scheme classified the strains into five groups, four of which fell into the A.Br.008/009 Trans-Eurasian (TEA) group within the clade A, and one into the B.Br.CNEVA group within the clade B. The largest group within clade A comprises six strains that are assumed to be members of the dominant Bacillus anthracis population in Hungary. Our results demonstrate that PCR-based amplicon sequencing using the portable MinION device is highly effective for on-site genotyping of pathogens directly from environmental samples. This establishes the NGS-based MLVA genotyping as a valuable tool for biodefense laboratories in preliminary forensic investigations of bioterrorism-related anthrax outbreaks. Furthermore, our results provide new insights into the genetic diversity of Bacillus anthracis in a region (Hungary, Central Europe) that is underrepresented in research and has limited scientific data.}, } @article {pmid41909643, year = {2026}, author = {Yao, Y and Hu, X and Li, R and Tan, Z and Yu, H and Lin, Z and Zhang, T and Habimana, O}, title = {Probiotic yeast engineers a protective biofilm environment to enhance bioremediation and seahorse health in aquaculture.}, journal = {Biofilm}, volume = {11}, number = {}, pages = {100357}, pmid = {41909643}, issn = {2590-2075}, abstract = {Sustainable animal farming via intensive aquaculture relies on a balanced microbial ecosystem that promotes animal well-being. This research explored the use of the probiotic yeast Saccharomyces boulardii to influence tank biofilm microbiomes for improving the health of lined seahorses, Hippocampus erectus. Following a severe mortality event at week 6 that affected both groups, the control group demonstrated partial recovery to 71.4% survival, whereas the probiotic group achieved a higher survival, with a final rate of 88.9% after a disease challenge. This recovery led to a notable reduction in enteritis occurrences with a significant increase in average body weight and a 3.9-fold increase in activity compared to control conditions. Shotgun metagenomic analysis indicated that the enhancements were significantly supported by a marked reorganization of the tank's biofilm community. Probiotic supplementation significantly reduced microbial diversity and selected for a beneficial consortium enriched in taxa with recognized roles in nutrient cycling, including Rhodobacterales (involved in sulfur cycling and pathogen antagonism) and Pirellulaceae (key in polysaccharide breakdown). This engineered biofilm has greater genetic potential for energy generation, glucose degradation, and inorganic ion transfer. Crucially, virulence factor genes and pathogen-associated sequences were substantially suppressed in probiotic-treated biofilms. Our research shows that S. boulardii acts as a crucial modulator, creating a protective biofilm that boosts bioremediation while decreasing pathogenic threats. This ecological approach to the application of probiotics (targeting the environmental rather than host-associated microbiome) may offer a sustainable means to promote health and resilience within aquaculture systems.}, } @article {pmid41909838, year = {2026}, author = {Zhang, B and Wang, L and Wang, J and Qi, D and Zhang, N}, title = {Comparative diagnostic performance of metagenomic next-generation sequencing and conventional microbial culture in spinal infections: a systematic review and meta-analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1689254}, pmid = {41909838}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Sensitivity and Specificity ; *Spinal Diseases/diagnosis/microbiology ; }, abstract = {BACKGROUND: Spinal infections are relatively uncommon but clinically serious conditions that require timely and accurate diagnosis to prevent severe complications. Traditional microbial culture methods remain the gold standard but suffer from low sensitivity and prolonged turnaround times. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool offering broad-spectrum pathogen detection. However, its diagnostic performance in spinal infections remains unclear.

OBJECTIVE: To systematically evaluate and compare the diagnostic accuracy of mNGS and conventional microbial culture in detecting pathogens in spinal infections.

METHODS: This systematic review and meta-analysis adhered to the 2020 PRISMA guidelines and was registered in PROSPERO. A comprehensive literature search of PubMed, Cochrane Library, Web of Science, and Scopus was performed up to July 2025. Studies involving suspected spinal infection patients tested by both conventional microbiological methods and metagenomic next-generation sequencing (mNGS) were included. Data extraction and quality assessment were independently conducted by two reviewers using standardized tools. Meta-analyses were performed to pool diagnostic accuracy metrics, and publication bias was assessed.

RESULTS: A total of 14 studies involving 1,353 patients were included after screening 4,132 records. All studies originated from China, with sample sizes ranging from 17 to 301. Quality assessment showed generally high methodological rigor with low risk of bias. Conventional meta-analysis demonstrated that mNGS had significantly better positive agreement (OR = 0.46, p < 0.00001), higher sensitivity (OR = 0.45, p < 0.00001), and superior negative predictive value (OR = 0.36, p < 0.00001) compared to traditional methods, while specificity and positive predictive value were comparable. Diagnostic meta-analysis revealed pooled sensitivity and specificity of 0.86 and 0.90, respectively, with an AUC of 0.90, indicating high diagnostic accuracy. Fagan nomogram analysis showed that with a 50% pre-test probability, positive and negative mNGS results corresponded to post-test probabilities of 89% and 13%, respectively. No significant publication bias was detected.

CONCLUSIONS: mNGS exhibits superior sensitivity and overall diagnostic accuracy compared to traditional microbial culture in spinal infections, supporting its use as a valuable complementary diagnostic tool. Further prospective, multicenter studies are warranted to validate these findings and promote standardized clinical implementation.

PROSPERO, identifier CRD420251114975.}, } @article {pmid41909845, year = {2026}, author = {Wang, C and Min, M and Dai, Z and Wang, G and Wang, Y and Hu, T and Ma, Y and Zhang, S and Wu, C and Zhou, R}, title = {Diagnostic value of metagenomic next-generation sequencing in patients with febrile lung cancer with negative conventional microbiological tests and without neutropenia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1715563}, pmid = {41909845}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; *Lung Neoplasms/complications/microbiology/diagnosis ; Male ; *Fever/microbiology/etiology/diagnosis ; Aged ; Middle Aged ; Neutropenia ; }, abstract = {INTRODUCTION: Fever in nonneutropenic lung cancer often remains microbiologically unresolved because of the limitations of conventional microbiological tests (CMT). We assessed whether plasma metagenomic next-generation sequencing (mNGS) improves diagnostic yield and accelerates defervescence in these patients.

METHODS: We retrospectively analyzed 53 CMT-negative febrile lung cancer patients (August 2023-October 2024). Patients were classified into high-suspicion infectious fever (HSIF) or high-suspicion tumor fever (HSTF) groups based on mNGS results, and clinical management was adjusted accordingly.

RESULTS: mNGS identified pathogens in 69.8% (37/53) of patients, commonly including Epstein-Barr virus, Mycobacterium tuberculosis, and Candida albicans. Patients in the HSIF group showed significantly higher baseline inflammatory markers than those in the HSTF group. Importantly, following mNGS-guided antimicrobial therapy, the HSIF group achieved significantly higher defervescence rates at 48 h (73.0% vs. 37.5%; p = 0.029) and 96 h (89.2% vs. 68.8%; p = 0.027) compared to the HSTF group.

DISCUSSION: In conclusion, in CMT-negative, nonneutropenic febrile lung cancer, plasma mNGS significantly increases pathogen detection and informs antimicrobial decisions associated with earlier defervescence, although interpretation is limited by the retrospective design and lack of an independent gold standard.}, } @article {pmid41909847, year = {2026}, author = {Huang, Y and Cai, Q and Chen, Y and Amutijiang, D and Lu, Y and Huang, W and Li, L}, title = {Phage characterization analysis in respiratory samples from infected patients based on metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779296}, pmid = {41909847}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/virology/microbiology ; *Metagenomics/methods ; *Sputum/virology/microbiology ; *Bronchoalveolar Lavage Fluid/virology/microbiology ; *Bacteriophages/genetics/classification/isolation & purification ; Female ; Bacteria/virology ; Computational Biology ; Male ; Metagenome ; Middle Aged ; Microbiota ; Aged ; }, abstract = {BACKGROUND: Respiratory tract infections are common infectious diseases, with microbial dysbiosis closely linked to clinical outcomes in the host. As key regulators of bacteria, phages can influence the structure and stability of microbial communities by infecting host bacteria. Metagenomic next-generation sequencing (mNGS) enables comprehensive analysis of phage community characteristics in clinical samples.

METHODS: This study included 6,404 clinical samples, comprising 4,837 bronchoalveolar lavage fluids (BALF) and 1,567 sputum samples, for metagenomic next-generation sequencing (mNGS), while collecting patient demographics, sample types, mNGS results, and clinical outcomes. Host-derived sequences were removed post-sequencing and aligned against viral reference databases. Phage community structures across sample types were assessed using alpha and beta diversity metrics. Spearman correlation analysis explored associations between phages and bacteria. Further bioinformatics analysis was performed on 194 samples, including viral sequence assembly and identification using SPAdes, VirSorter2, and PhaMer; CD-HIT clustering and redundancy removal; CheckV quality assessment; PhaTYP lifestyle prediction; Prodigal protein gene annotation; and BLASTP alignment against the CARD database to screen for phage resistance genes.

RESULTS: The sputum and BALF groups exhibited comparable richness, diversity, and evenness, yet their community structures differed significantly. Intensive Care Unit (ICU) admission status was closely associated with reduced phage community diversity and significant alterations in community structure, and the abundance distribution of several phage families (Peduoviridae, Autoscriptoviridae, Casjensviridae, Demerecviridae) also changed significantly. Additionally, the phage community structure in sputum samples was significantly associated with patient clinical outcomes. Correlation analysis demonstrated that the Aliceevansviridae family in sputum samples had extensive positive associations with various bacteria. After assembly, 69.5% of pOTUs were predicted to be temperate phages, and 28.9% were predicted to be virulent phages; moreover, the vast majority (99.2%) of phage sequences showed low similarity to antibiotic resistance genes.

CONCLUSION: This study identifies distinct phage community characteristics across respiratory sample types and reveals that ICU patients exhibit reduced phage diversity and markedly altered community structures. Furthermore, the phage composition in upper respiratory tract samples shows a clear relationship with patient prognosis, providing new insights into respiratory infection microecology.}, } @article {pmid41909891, year = {2025}, author = {Manzoor, H and Kayani, MUR}, title = {Insights into the gut microbiome-metabolite dynamics in breast cancer.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2483446}, pmid = {41909891}, issn = {2993-3935}, abstract = {In recent years, understanding the intricate connection between gut microbiome and cancer development has gained significant attention. The gut microbiome has a key role in maintaining overall human health and modulating the body's defense mechanism against various diseases. This review examines the multifaceted association between the gut microbiome and breast cancer, providing a comprehensive overview of studies from the last two decades that investigate both anti-cancer and pro-cancer properties of gut metabolites. Compounds such as nisin, inosine, acetate, propionate, and conjugated linoleic acids have demonstrated potential as therapeutic agents against breast cancer, while others, including butyrate, lactate, certain bile acids, and secondary metabolites, exhibit dual roles, showing both anti-cancer and pro-cancer properties under different conditions, with some implicated in tumor progression. Moreover, emerging research highlights the dual roles of these metabolites in influencing the efficacy of conventional breast cancer therapies. Despite promising evidence, the molecular mechanisms underlying these opposing actions remain unclear and require further investigation. To advance our understanding, future research should prioritize elucidating these mechanisms, establishing dose-response relationships, and conducting animal and clinical studies to validate in vitro findings. This review also identifies key gaps and highlights potential directions for future research in this field.}, } @article {pmid41909892, year = {2025}, author = {Montenegro-Borbolla, E and Wakim El-Khoury, J and Bertelli, C and Schoepfer, A and Guery, B and Galperine, T}, title = {Resolution of long-term severe irritable bowel syndrome following fecal microbiota transplantation: A case report and microbiota analysis.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2487905}, pmid = {41909892}, issn = {2993-3935}, abstract = {The diagnosis and management of irritable bowel syndrome (IBS) is challenging due to its complex symptoms and inconsistent treatment responses. Given the important role of gut microbiota in gastrointestinal health, fecal microbiota transplantation (FMT) is a promising intervention. We describe the case of a 55-y-old woman without prior gastrointestinal issues who, following severe depression, developed multiple gastrointestinal symptoms, including abdominal pain, fluctuating bowel habits, and a persistent burning sensation in her mouth and upper gastrointestinal tract. At Lausanne University Hospital, she was diagnosed with IBS resistant to multiple lines of treatment and a multidisciplinary team proposed multiple oral FMTs. One-month post-FMT, her gastrointestinal symptoms significantly improved and remained better after a year, with only the burning sensation persisting. Analysis of pre- and post-FMT samples and donor material, using 16S rRNA amplicon metagenomics, revealed a 90% genus-level taxonomic overlap between the patient and the donor. The observed changes in the relative abundance of these genera, including the enrichment of beneficial gut commensals, as well as the elimination of IBS-associated genera likely supported her recovery. Overall, FMT led to substantial improvement in her long-standing gastrointestinal symptoms.}, } @article {pmid41909896, year = {2025}, author = {Yasuda, T and Takagi, T and Naito, Y and Inoue, R and Mizushima, K and Asaeda, K and Hashimoto, H and Kitae, H and Uchiyama, K and Ouchi, N and Adachi, A and Kamitani, T and Matoba, S and Itoh, Y}, title = {Sarcopenia-related gut microbiota in the elderly: Insights from the longevity region of Kyotango and its nutritional associations.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2591561}, pmid = {41909896}, issn = {2993-3935}, abstract = {Sarcopenia is influenced by the gut microbiota and dietary habits; however, the underlying mechanisms remain elusive. This study investigated the gut microbiota composition of elderly individuals in a healthy longevity region and examined its association with sarcopenia and dietary habits. Fecal metagenomic analysis was used to identify gut microbiota taxonomy. Sarcopenia was diagnosed on the basis of grip strength, gait speed, and muscle volume. Japanese dietary habits were assessed using a brief-type self-administered diet history questionnaire. A total of 318 elderly individuals from Kyotango were recruited, 5.7% of whom were diagnosed with sarcopenia. Individuals with sarcopenia exhibited a lower abundance of a genus belonging to the family Lachnospiraceae, and a higher abundance of Megasphera. Several butyrate-producing bacteria, including Lachnospira and Coprococcus showed a positive correlation with sarcopenia related factors, whereas Dorea and Streptococcus were negatively correlated. Hierarchical cluster analysis revealed that these beneficial genera were also positively associated with the frequent intake of traditional Japanese dietary components. These findings suggest that the observed microbial and dietary associations may provide a mechanistic basis for potential protective effects against sarcopenia. Our findings suggest that butyrate-producing bacteria associated with Japanese dietary patterns play a protective role against sarcopenia.}, } @article {pmid41909897, year = {2025}, author = {Gitton-Quent, O and Sola, M and Maziers, N and Hiol, A and Dechamp, N and Le Chatelier, E and Touvier, M and Galan, P and David, A and Morabito, C and Famechon, A and Quinquis, B and Mariadassou, M and Veiga, P and Dore, J and Berland, M and Deschasaux-Tanguy, M}, title = {Alterations in gut microbiota characteristics along a type 2 diabetes risk gradient linked with family history.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2527766}, pmid = {41909897}, issn = {2993-3935}, abstract = {Type 2 diabetes (T2D) is a major global health issue, with growing evidence linking it to gut microbiome changes. However, whether these alterations precede T2D onset and act as predictors, risk factors, or contributors remains unclear. This study analyzed the gut microbiota of 192 individuals from the French NutriNet-Santé cohort, divided into four groups: non-T2D adults with no (n = 47), one (n = 48), or two (n = 51) T2D-affected parents, and T2D-affected adults (n = 46). A progressive microbiota shift was observed in non-T2D groups based on parental history, converging toward the T2D profile. Changes included altered enterotype distribution, increased oral-associated species, disrupted ecological networks, and a shift in Gram-positive-to-negative ratios. Notably, Prevotella copri abundance increased, alongside bacteria potentially enhancing branched-chain amino acid (BCAA), lipopolysaccharide (LPS), and acetate production. Diet also influenced microbiota patterns, with sweet product intake, vitamin levels, and copper/zinc ratios playing roles. A gradual microbiome transition from non-diabetic to T2D participants underscores its association with family history-based risk. While these shifts may reflect or drive T2D progression, further studies are needed to confirm these findings and explore their potential for preventive strategies.}, } @article {pmid41909909, year = {2025}, author = {Wang, H and Yu, S and Zhao, K and Hu, T and Wu, Z and Liang, H and Lin, X and Cui, L and Yao, J and Liu, X and Tong, X and He, N and Xiao, L and Kristiansen, K and Li, S and Zou, Y}, title = {Faecalibacterium longum alleviates high-fat diet-induced obesity and protects the intestinal epithelial barrier in mice.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2459599}, pmid = {41909909}, issn = {2993-3935}, abstract = {Numerous studies have indicated that depletion of Faecalibacterium is related to obesity. Here we show that Faecalibacterium longum CM04-06 out of 29 strains of the Faecalibacterium genus annotated in CGR2 exhibited the strongest inverse correlation with body mass index (BMI) in a cohort of 1120 han Chinese individuals. Administration of F. longum CM04-06 to mice prevented high-fat diet (HFD)-induced obesity, improved glucose tolerance, reduced adipose tissues mass, and liver steatosis. Supplementation with F. longum CM04-06 reduced the level of pro-inflammatory cytokines in liver, colon, and circulation. F. longum CM04-06 protected the intestinal epithelial barrier increasing the expression of tight junction proteins. Metagenomic sequencing indicated that F. longum supplementation did not change the overall composition of the gut microbiota in mice, but selectively increased the relative abundance of Staphylococcus xylosus and Staphylococcus nepalensis. In conclusion, our results point to a potential therapeutic potential of F. longum CM04-06.}, } @article {pmid41909910, year = {2025}, author = {Batool, M and McMahon, S and Franklin, S and Ramont, C and Sahasrabhojane, P and Chang, CC and Hayase, T and Hayase, E and Blazier, JC and Jenq, R and Shelburne, S and Galloway-Peña, J}, title = {Gut microbiome features and resistome elements associated with colonization and infection with antibiotic-resistance threats.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2570502}, pmid = {41909910}, issn = {2993-3935}, support = {K01 AI143881/AI/NIAID NIH HHS/United States ; }, abstract = {Infection with antimicrobial-resistant (AR) pathogens is a leading cause of morbidity and mortality among patients with hematological malignancies; however, little is known about the gut microbiome dynamics in acute myeloid leukemia patients and its impact on AR infections (ARI) and/or colonization with AR pathogens (ARC). Longitudinal stool samples collected from 154 patients undergoing induction chemotherapy were analyzed using 16S rRNA sequencing, selective and differential media culturing, MALDI-TOF, and VITEK2 to identify patients with ARC or ARI and to isolate AR infectious and colonizing bacterial strains. Shotgun metagenomic sequencing of baseline stool samples revealed taxa abundances, resistome features, and KEGG pathways associated with AR-events. Baseline observed species were lower in patients with AR-events (p = 0.01). Although several baseline taxa were more abundant in AR-event patients, they were not statistically significant when they were corrected for false discovery. Functional analysis revealed that penicillin and cephalosporin biosynthesis pathways were significantly enriched in patients with ARC. In summary, identifying the baseline microbiome, resistome, and functional pathway biomarkers may forecast an increased risk of ARI and/or ARC, thereby informing antimicrobial treatment strategies in AML patients.}, } @article {pmid41909911, year = {2025}, author = {Shi, J and Nguyen, SM and Yu, D and Wang, L and Liu, L and Cai, H and Wu, J and Long, J and Cai, Q and Shrubsole, MJ and Zheng, W and Shu, XO}, title = {Association of physical activity with gut microbiome among low-income black American adults in the Southern Community Cohort Study.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2589861}, pmid = {41909911}, issn = {2993-3935}, abstract = {Physical activity (PA) has been suggested to influence the gut microbiome. We evaluated this association among low-income Black American adults. This study included 489 self-identified Black American participants from the Southern Community Cohort Study. PA data, including exercise/sport- and work/home-related moderate-vigorous PA (MVPA), was collected at cohort enrollment (2002-2009). Stool samples were collected between 2018 and 2021, and microbial composition was profiled using shotgun metagenomic sequencing. General linear regression models were employed to evaluate associations between PA and gut microbial α-diversity, abundance of individual species and metabolic pathways. Among all participants, MVPA measures were not associated with Shannon α-diversity (p > 0.05) and explained approximately 0.2-0.3% variation of Bray-Curtis dissimilarity. A total of 32 bacterial species, including seven Bacteroides species, two Streptococcus species, two Prevotella species, and nine microbial metabolic pathways, including D-fucofuranose biosynthesis, xyloglucan degradation, biosynthesis of L-citrulline, L-aspartate and L-asparagine biosynthesis, and urea cycle, were significantly associated with work/home-related and/or total MVPA (all false discovery rates < 0.10). In conclusion, MVPA, particularly from work and home activities, may modulate the composition and functionality of the gut microbiome among Black American adults.}, } @article {pmid41910132, year = {2026}, author = {Sáenz, JS and Yergaliyev, T and Rios-Galicia, B and Seifert, J and Camarinha-Silva, A}, title = {The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.}, journal = {mSystems}, volume = {11}, number = {4}, pages = {e0019126}, pmid = {41910132}, issn = {2379-5077}, mesh = {Animals ; *Chickens/virology ; *Virome/genetics ; *Gastrointestinal Tract/virology ; Genome, Viral ; Metagenome ; Bacteriophages/genetics/classification ; *Gastrointestinal Microbiome ; Metagenomics ; Phylogeny ; }, abstract = {UNLABELLED: Viral communities, especially phages, affect prokaryotic diversity and thus influence the host's metabolic processes. However, the makeup and role of the chicken gut virome remain poorly understood. To address this gap, we mined 1,458 chicken gut metagenomes and 56 viral-enriched samples to recover viral sequences and assemble a comprehensive collection of draft viral genomes. We identified 19,778 viral operational taxonomic units (vOTUs), of which 97% were dsDNA phages from the Caudoviricetes class, primarily targeting gut bacteria such as Lactobacillus, Limosilactobacillus, and Escherichia. Most protein-coding genes in these genomes were uncharacterized and lacked known biological functions. Additionally, the distribution of vOTUs across samples showed that the chicken virome is highly individual-specific. Yet, the viral community also exhibited strong spatial stratification along the gastrointestinal tract, with notable differences between proximal and distal regions, primarily driven by phages linked to the Lactobacillaceae family. Moreover, this study shows that the geographical region, breed, and diet drive the chicken gut viral diversity and composition. This underscores the significant novelty of the chicken gut virome and its largely unexplored functional potential, much of which would be missed if analyses were restricted to fecal samples.

IMPORTANCE: The chicken gut harbors a vast community of viruses that remain largely unexplored despite their potential to influence poultry health and productivity. By analyzing 1,514 samples from different gut regions across 15 countries, we discovered nearly 20,000 distinct viruses, most of which were previously unknown phages. The chicken virome showed strong spatial differences along the gastrointestinal tract, meaning each gut section harbors a unique viral community, underscoring that fecal samples alone miss much of the virome's diversity. We also uncovered that the geographical region, breed, and diet could drive the chicken gut viral diversity and composition. Overall, our findings greatly expand our understanding of gut virus diversity and microbiome ecology, offering a valuable foundation for developing strategies to monitor or manipulate the microbiome to improve poultry health.}, } @article {pmid41910137, year = {2026}, author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L}, title = {Temperature modulates gut microbiome disruption and resistome enrichment in oxytetracycline-treated channel catfish (Ictalurus punctatus).}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0418725}, pmid = {41910137}, issn = {2165-0497}, abstract = {UNLABELLED: Oxytetracycline (OTC) is one of the few antibiotics approved by the U.S. Food and Drug Administration for catfish aquaculture. Unfortunately, OTC resistance has been frequently detected in production environments, with the fish gut identified as a potential hotspot for resistance selection. In aquaculture systems, water temperature is a critical factor influencing fish physiology, antibiotic pharmacokinetics, and water resistome development. However, its role in modulating OTC effects on the fish gut microbiome remains underexplored. This study examined temperature-dependent microbiome and resistome responses in channel catfish (Ictalurus punctatus) when treated with OTC at 20°C, 25°C, and 30°C. Gut contents collected at treatment completion and after withdrawal were analyzed via metagenomic sequencing. In untreated fish, temperature alone shaped microbial structure and function, with the Shannon diversity increasing with temperatures and the β-diversity differing significantly across temperature groups. After OTC exposure, microbial responses were markedly temperature dependent with few taxa affected at 20°C, whereas substantial shifts occurred at 25°C and 30°C, indicating reduced microbial resilience at higher temperatures. OTC elevated total antimicrobial resistance gene (ARG) abundance, enriching tetracycline and β-lactam resistant genes consistent with co-selection. ARG-host linkages were diffuse at 20°C but consolidated within Klebsiella, Enterococcus, Enterobacter, and Paraclostridium at 25°C and 30°C. Notably, OTC-induced dysbiosis persisted through the withdrawal period. These findings demonstrate that temperature modulates both the magnitude and persistence of OTC-driven microbiome disruption and resistome enrichment, underscoring the importance of temperature-aware antibiotic management to mitigate antimicrobial resistance risks and safeguard fish health and food safety in aquaculture.

IMPORTANCE: This study reveals that water temperature critically shapes how antibiotics affect the gut microbiome and antimicrobial resistance in channel catfish. Metagenomic sequencing results showed that oxytetracycline (OTC) treatment caused minimal disruption of the microbiome at 20°C, but induced significant community shifts and enrichment of antimicrobial resistance genes (ARGs) at 25°C and 30°C. Higher temperatures reduced microbial resilience, consolidating ARGs within key bacterial genera such as Klebsiella and Enterococcus. Importantly, OTC-induced microbiome changes and resistance persisted through the withdrawal period. These findings highlight temperature as a major driver of antibiotic impact in aquaculture, emphasizing the prudent use of antibiotics at different disease breakout temperatures.}, } @article {pmid41910214, year = {2026}, author = {Zhang, F and Xu, W and Zeng, R and Chen, J and Huang, J}, title = {Limosilactobacillus reuteri normalizes gut microbiota dysfunction and social deficits of rat offspring associated with prenatal exposure to stress.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2649440}, pmid = {41910214}, issn = {1949-0984}, mesh = {Animals ; Female ; Pregnancy ; *Limosilactobacillus reuteri/physiology ; *Prenatal Exposure Delayed Effects/microbiology/psychology ; Rats ; Oxytocin/metabolism ; *Gastrointestinal Microbiome ; *Social Behavior ; Fecal Microbiota Transplantation ; Male ; Paraventricular Hypothalamic Nucleus/metabolism ; *Stress, Psychological ; Rats, Sprague-Dawley ; }, abstract = {Prenatal stress (PS) is a potential risk factor for social behavior impairment in offspring. Here, we demonstrate that PS induces gut microbiota alterations that are associated with impaired sociability and social novelty preference in rat offspring. In addition, we found that these behavioral deficits could be partially rescued through either cohousing with normal offspring or fecal microbiota transplantation from control donors. Metagenomic analysis identified Limosilactobacillus reuteri (L. reuteri) as a key species based on the considerable difference in its abundance between the PS and control offspring. Subsequent investigations revealed that supplementing L. reuteri during critical neurodevelopmental windows restored oxytocin levels in the paraventricular nucleus (PVN) and rescued dopamine reward pathway function, thereby ameliorating PS-induced social deficits. Notably, these beneficial effects were completely abolished by either treatment with an oxytocin receptor antagonist or subdiaphragmatic vagotomy. Thus, both oxytocin signaling and vagal afferent pathways play essential roles in the observed benefits of L. reuteri. Our findings indicate that social behavior impairments in offspring exposed to prenatal maternal stress can be explained by a novel mechanism involving the gut microbiota-brain axis: whereby PS-induced depletion of specific commensal bacteria (particularly L. reuteri) disrupts vagus nerve-mediated oxytocinergic modulation of PVN-to-VTA dopaminergic circuits, ultimately leading to social behavior impairments in offspring.}, } @article {pmid41910252, year = {2026}, author = {Yang, H and Liu, W and Niu, J and Geng, B and Qiu, P and Li, H and Bao, J and Pu, X and Li, Y and Jia, X and Sun, Y and Han, Y}, title = {Integrated metagenomic-metabolomic insights into plant-microbe interactions mediated by Bacillus volatile compounds.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {4}, pages = {e0252325}, pmid = {41910252}, issn = {1098-5336}, support = {2024CXPT056//Key R&D Plan of Shandong Province (Competitive Innovation Platform) Project: Green, Ecological and Efficient Modern Agricultural Biological Product Development/ ; 32170093//National Natural Science Foundation of China/ ; }, mesh = {*Volatile Organic Compounds/metabolism ; Acetoin/metabolism ; Rhizosphere ; *Bacillus/metabolism/genetics ; Butylene Glycols/metabolism ; *Bacillus subtilis/metabolism/genetics ; Metagenomics ; Metabolomics ; *Solanum lycopersicum/microbiology/growth & development/metabolism ; Microbiota ; Soil Microbiology ; *Host Microbial Interactions ; }, abstract = {Modulation of plant-microbe interactions with signaling molecules offers a promising strategy to promote plant growth and stress adaptation. However, identifying effective signaling molecules and elucidating the mechanisms for regulating the rhizosphere microbiome remain major challenges. In this study, the roles and mechanisms of Bacillus volatile compounds as potential signaling molecules in plant-microbe interactions were investigated. First, the genome and metabolism of a novel Bacillus subtilis strain capable of producing acetoin and 2,3-butanediol were studied, and the titers of the two compounds were increased to 86.76 g/L by sequential metabolic engineering. Subsequently, the effects of volatile compounds on the growth of vegetables (Brassica rapa and Solanum lycopersicum var.) were studied. Plant growth, nutrient (nitrogen, phosphorus, and potassium) utilization efficiency, and salt stress resistance were improved significantly. Compared with water as a control, significant changes in the abundance of 109 microbial genera of B. rapa's rhizosphere microbiome were identified with volatile compound application. Notably increased microbes included nitrogen-fixing, phosphate- and potassium-solubilizing, stress-resistant, plant growth-promoting, and auxin-secreting microbes. Additionally, genes involved in nitrogen, phosphorus, and potassium utilization in the rhizosphere microbiome were significantly increased, and corresponding metabolism was found. Finally, metabolomic analyses of S. lycopersicum var.'s roots and leaves revealed 67 significantly upregulated compounds with the application of volatile compounds. These compounds were primarily involved in stress resistance, oxidative stress alleviation, free radical scavenging, and auxin-related plant growth promotion. This work demonstrates that Bacillus volatile compounds regulate rhizosphere microbiome and plant-microbe interactions and enhance plant nutrient utilization efficiency, stress tolerance, and growth.IMPORTANCEPlant productivity and stress resilience are strongly influenced by interactions between plants and the rhizosphere microbiome, yet practical strategies to rationally modulate native soil microbial communities remain limited. This study demonstrates that Bacillus volatile compounds, specifically acetoin and 2,3-butanediol, function as effective signaling molecules that coordinate plant-microbe interactions in the rhizosphere. By integrating plant physiology, metagenomics, and metabolomics, we show that these volatile compounds not only enhance plant growth and nutrient use efficiency but also reprogram rhizosphere microbial communities toward functions that benefit nitrogen, phosphorus, and potassium acquisition and stress adaptation. Notably, volatile application improved plant salt tolerance, highlighting their strong ecological and physiological impact. This work provides mechanistic evidence that Bacillus-derived volatiles act as signaling molecules to activate the rhizosphere microbiome and plant metabolic responses. The findings offer a scalable and environmentally friendly strategy for improving crop performance and soil health, with broad implications for sustainable agriculture.}, } @article {pmid41910273, year = {2026}, author = {Tobias-Hünefeldt, SP and Woodhouse, JN and Ruscheweyh, H-J and Sunagawa, S and Russnak, V and Streit, WR and Grossart, H-P}, title = {Osmotolerance is a driver of microbial carbon processes in the Elbe estuary.}, journal = {mSystems}, volume = {11}, number = {4}, pages = {e0179025}, pmid = {41910273}, issn = {2379-5077}, support = {407270017/RTG2530//Deutsche Forschungsgemeinschaft/ ; GR1540/37-1//Deutsche Forschungsgemeinschaft/ ; 03F0864C//Bundesministerium für Bildung und Forschung/ ; Core Funding//ETH Zürich Foundation/ ; }, mesh = {*Estuaries ; *Carbon/metabolism ; Salinity ; *Microbiota ; Metagenome ; Bacteria/metabolism/genetics/classification ; Water Microbiology ; }, abstract = {UNLABELLED: Estuaries are blue carbon loci, storing and exchanging carbon between aquatic, atmospheric, and terrestrial environments. Estuarine particles facilitate the transformation and transport of organic matter. The fate of particulate organic matter in estuaries is driven by structural changes in polymers that modify buoyancy, determining the proportions of sinking and suspended particles. In the open ocean and coastal ecosystems, the microbial composition and function of sinking and suspended particles differ, impacting carbon remineralization and sedimentation rates. We leverage 190 metagenomes and 73 metatranscriptomes to assess free-living, sinking, and suspended particle-associated microbial composition and function across the Elbe estuary. The salinity gradient in the Elbe estuary is the primary driver of microbiome composition and function. Transparent exopolymer particles (TEP) production was localized to freshwater, with seemingly no TEP-associated organisms detected above 20 practical salinity units (PSU). We observed differences in the function of free-living and particle-associated microbial communities, with diazotrophs enriched on particles. We observed that sinking particles may better support methanogenesis, and suspended particles showed signs of continued primary and secondary production. From this, we conclude that activities such as dredging, which resuspend sediment, will exacerbate carbon turnover and greenhouse gas emissions, and reduced dredging may lower greenhouse gas (GHG) emissions in the Elbe estuary. Many of these GHG linking processes are inhibited by salinity due to the osmosensitivity of methanogens and methanotrophs along the estuary. Changes in sea level and precipitation rates will likely directly interact with activities such as dredging, with as yet uncertain impacts on microbial carbon processing and storage.

IMPORTANCE: Estuaries, lower river areas that merge into oceans, play a large role in Earth's carbon cycle. Estuaries store carbon and manage greenhouse gases, exchanging carbon between land, water, and the air. As carbon travels down estuaries, it is processed by free-living and particle-associated microbes. We explore the relationship between environmental conditions and present and expressed genes. Based on gene profiles, methane concentrations in the water column may be related to the abundance of sinking particles, while suspended particles are linked to growth and energy acquisition. Therefore, the balance of suspended vs. sinking particles is important in highly turbid estuaries, like the Elbe estuary, where urban activities affect greenhouse gas emissions and salinity intrusions. Dredging often tips the balance toward sinking particles and therefore increased greenhouse gas emissions. Our study thereby informs future policy decisions and the impact these decisions will have on our future climate.}, } @article {pmid41910342, year = {2026}, author = {Dixit, K and Busi, SB and Ahmed, A and Kshirsagar, A and Jäger, C and Singh, A and Shah, V and Saroj, SD and Ahuja, V and Wilmes, P and Shouche, Y and Makharia, G and Dhotre, D}, title = {Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.}, journal = {mSphere}, volume = {11}, number = {4}, pages = {e0085625}, pmid = {41910342}, issn = {2379-5042}, mesh = {Humans ; Multiomics ; Metagenomics ; *Glutens/metabolism/adverse effects ; Irritable Bowel Syndrome/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Metabolomics ; Metabolome ; Archaea/classification/genetics ; Bacteria/classification/genetics ; }, abstract = {UNLABELLED: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis, and its symptoms overlap with irritable bowel syndrome (IBS). The gut microbiome is likely to play a role in the pathogenesis of NCGS. We analyzed the gut microbiome in patients with NCGS and in patients with IBS, using shotgun metagenomics and metabolomics of fecal samples. Analyses of taxonomic and functional microbial diversity revealed a higher abundance of methanogenic archaea, such as Methanobrevibacter filiformis, Methanobrevibacter boviskoreani, Methanosphaera stadtmanae, and a higher fold change in urea, uridine 5-monophosphate, and adenosine monophosphate in patients with NCGS compared to patients with IBS, who showed higher fold changes in metabolites gamma-aminobutyric acid and lactic acid. Furthermore, pangenome and metabolome analyses revealed disease-specific gene clusters, as well as genomic and metabolic features differentiating NCGS from IBS. While patients with NCGS did not show lower potential for gluten degradation, a lower synthetic potential for fructan beta-fructosidase was found in them. The present study provides an extensive analysis of taxonomic, genomic, and metabolic features that may play a role in the pathogenesis and symptom development in patients with NCGS.

IMPORTANCE: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis with symptoms that overlap with irritable bowel syndrome (IBS). Using shotgun metagenomics and metabolomics, we report deeper insights into the microbiome profile, including viral and archaeal diversity, lower fructan degradation potential, the differential abundance of metabolites, and genomic features of gut bacteria in patients with NCGS. Understanding the microbiome associated with this disorder may shed light on the possible role of the microbiome in the pathophysiology of NCGS.}, } @article {pmid41910375, year = {2026}, author = {Sprenger, GA and Gee, JE and Elrod, MG and Weiner, ZP and Gulvik, CA}, title = {Shotgun metagenome sequencing and informatics can accurately form a metagenome-assembled genome (MAG) of the bacterial tier 1 select agent Burkholderia pseudomallei for rapid public health response events.}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0292625}, pmid = {41910375}, issn = {2165-0497}, abstract = {Shotgun metagenomics, when sufficient read depth exists for each taxon, enables capturing metagenome-assembled genomes (MAGs) directly from a microbial community. In 2021, an aromatherapy spray contaminated with Burkholderia pseudomallei caused an outbreak of melioidosis in the United States. Metagenome-assembled genome binning depends in part on different nucleotide compositions, and the contaminated aromatherapy spray contained other bacteria, including related species (e.g., Burkholderia cepacia, Burkholderia cenocepacia, Burkholderia multivorans, Burkholderia pseudomultivorans, Cupriavidus pauculus, and Pseudomonas aeruginosa with average nucleotide identity (ANI) to B. pseudomallei being 84.2%, 84.4%, 84.7%, 84.8%, 75.7%, and 72.3%, respectively, and AAI being 79.5%, 79.8%, 80.5%, 80.4%, 62.5%, and 52.9%, respectively). We performed metagenomic sequencing on the contaminated aromatherapy spray to determine if a public metagenomic pipeline (https://github.com/nf-core/mag) can form a MAG of B. pseudomallei. Upon completion of the pipeline, inter- and intracontig comparisons revealed few potential contaminants of related taxa. Conservative removal of those contigs was especially valuable, ultimately obtaining an ANI of 99.9% between the B. pseudomallei MAG and the genome of an isolate from the aromatherapy spray. This underscores the importance of quality checking recovered MAGs (e.g., for congeneric chimerism) for high-resolution objectives such as outbreak pathogenomics. Importantly, our analysis revealed that the identical conclusion was made possible with the B. pseudomallei MAG (as with its corresponding isolate genome), which was that the aromatherapy B. pseudomallei originated from South Asia (specifically India). Because rapid read-based (k-mer) taxonomic classification methods often report false positives, this operational framework could be valuable for rapid biothreat radar detection systems in public health surveillance.IMPORTANCEIn 2021, an imported aromatherapy spray caused a U.S. outbreak of melioidosis after contamination with Burkholderia pseudomallei. Using shotgun metagenomics, we reconstructed a near-complete genome of the pathogen directly from the product, despite the presence of other related microbes. The assembled genome showed 99.9% similarity to a cultured isolate. This work demonstrates that metagenomics can recover high-quality pathogen genomes from complex samples, supporting outbreak investigations and enhancing public health surveillance.}, } @article {pmid41910449, year = {2026}, author = {Santos, JCE and Go, DJL and Unciano, RD and Yu, PK and Lao, AR and Enriquez, MLD and Espiritu, LM and Shrestha, AMS}, title = {Investigating the resistome, taxonomic composition, and mobilome of bacterial communities in hospital wastewaters of Metro Manila using a shotgun metagenomics approach.}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0396325}, pmid = {41910449}, issn = {2165-0497}, abstract = {We profiled antibiotic resistance genes, bacterial communities, and mobile genetic elements in untreated hospital wastewater from three tertiary hospitals in Metro Manila using shotgun metagenomic sequencing. The resistome analysis revealed high abundances of genes known to confer resistance against sulfonamides (sul1, sul2), aminoglycosides (aadS), and macrolides/streptogramins (msrE, mphE). High-risk resistance genes were also detected, including those known to confer resistance to β-lactams (blaOXA, blaTEM, blaGES, blaNDM, blaKPC), colistins (mcr-5), and tetracyclines [tet(C), tet(A), tet(L), tet(M)]. Comparisons with hospital wastewater resistome profiles from regional neighbors and other lower-and-middle-income countries indicated broadly similar relative abundances of dominant resistance genes, with differences largely driven by low-abundance resistance genes. The bacterial community was dominated by the phylum Pseudomonadota, with high relative abundances of the genera Stenotrophomonas, Rhodococcus, and Pseudomonas, while ESKAPEE pathogens were detected at lower levels. A diverse array of mobile genetic elements-many known to be associated with resistance to multiple drug classes and disinfectants-was also observed. Overall, this study provides a valuable preliminary evidence base for future antimicrobial resistance and epidemiological surveillance efforts in the Philippines, particularly those employing wastewater-based approaches.IMPORTANCEAntimicrobial resistance (AMR) is a growing public health threat caused by pathogenic bacteria that are no longer controlled by commonly used treatments. Infections caused by these resistant bacteria may lead to prolonged illness, more severe symptoms, or even death. Hospitals are critical hotspots for the emergence and spread of AMR. Their wastewater, which contains antibiotics, medical and human waste, and diverse microbial communities, can support the persistence and dissemination of resistant bacteria. The significance of this research lies in identifying and characterizing these bacterial communities and the resistance genes they carry. Such information can provide an indication of the resistance burden faced by patients and serve as an early warning system to strengthen infection prevention and control measures, support national surveillance efforts, and inform the development of more effective treatment and management strategies in healthcare settings.}, } @article {pmid41910593, year = {2026}, author = {Bartelli, TF and Baydogan, S and Sahin, I and Hoffman, KL and Petrosino, J and Blackburn, KW and Zhao, J and Wood, A and Ayvaz, T and Surathu, A and Cagigas, MN and Barcenas, EC and Mata, T and Nguyen, VK and Zulbaran-Rojas, A and Li, L and Faraoni, EY and White, JR and Ajami, N and Li, L and Yadav, D and Conwell, DL and Serrano, J and Pandol, SJ and Fogel, EL and Van Den Eden, SK and Vege, SS and Topazian, MD and Park, WG and Hart, PA and Forsmark, C and Bellin, MD and Maitra, A and Bhutani, MS and Kim, M and Van Buren, G and Fisher, WE and McAllister, F and , }, title = {Whole Metagenomic Profiling Identifies a Gut Microbial Signature for Chronic Pancreatitis via Machine Learning.}, journal = {Pancreas}, volume = {55}, number = {5}, pages = {e458-e468}, pmid = {41910593}, issn = {1536-4828}, support = {U01 DK108327/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Pancreatitis, Chronic/microbiology/diagnosis ; Feces/microbiology ; Female ; *Metagenomics/methods ; *Machine Learning ; Male ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Adult ; Prospective Studies ; Saliva/microbiology ; Predictive Learning Models ; Case-Control Studies ; Random Forest ; }, abstract = {BACKGROUND: Pancreatitis significantly alters the microbial composition of the oral and intestinal compartments, causing dysbiosis that may contribute to disease mechanisms and potentially serve as a basis for diagnosis or treatment.

OBJECTIVE: To determine whether the oral or gut microbial signature can classify chronic pancreatitis (CP).

METHODS: Stool samples (n=707) were collected from participants in the Prospective Evaluation of Chronic Pancreatitis for Epidemiologic and Translational Studies (PROCEED). Samples were distributed among 200 healthy (HC), 310 CP, 49 acute pancreatitis (AP), and 148 recurrent acute pancreatitis (RAP). In addition, saliva samples were collected for a subset of participants (n=156). Whole genome sequencing was performed to assess microbiome composition. Machine learning algorithms were utilized to identify a signature with microbial features predictive of CP.

RESULTS: Gut alpha diversity was significantly decreased in AP, RAP, and CP compared with HC, with CP exhibiting the lowest diversity. In contrast, oral microbial diversity showed no significant variation across groups. Beta diversity analysis revealed distinct gut microbiome compositions between HC and pancreatitis subtypes, with CP showing the most pronounced differences. Random forest models using gut microbial species demonstrated robust predictive performance for CP using a minimum of 10 species (Area under the curve-AUC: 0.834; accuracy: 0.774). Despite similarities in gut microbiome composition across pancreatitis subtypes, a unique gut microbial signature for CP was identified highlighting the microbiome's potential in CP diagnosis.

CONCLUSION: Our study reveals a gut microbial signature predictive of CP using machine learning models in a large US multi-institutional cohort.}, } @article {pmid41910796, year = {2026}, author = {Zahran, E and Elbahnaswy, S and Bruce, TJ and Hegab, YE and Palic, D}, title = {Preliminary microbiome characterization of shrimp gut and pond water in Egyptian aquaculture farms: Implications for pathogen dynamics and management practices.}, journal = {Veterinary research communications}, volume = {50}, number = {3}, pages = {}, pmid = {41910796}, issn = {1573-7446}, abstract = {Shrimp aquaculture is a rapidly expanding food sector; however, its sustainability is challenged by disease outbreaks often linked to imbalances in the microbiome. Here, we characterized the microbial communities in the intestines of shrimp and pond water from three Egyptian farms (A, B, and C) using Oxford Nanopore long-read sequencing. Descriptive comparisons of relative abundance and diversity trends revealed that pond water harbored significantly higher alpha diversity than shrimp guts. In contrast, beta diversity confirmed a strong separation between host-associated and environmental microbiomes. For the observed phyla, taxonomic profiling revealed that shrimp guts were dominated by Proteobacteria, Actinomycota, and Bacillota, whereas pond water contained additional constituents, including Cyanobacteria and Bacteroidota. Pathogen-associated genera, particularly Vibrio spp. and Pseudomonas spp., were more abundant in water samples, with farm-specific variations linked to management practices such as salinity and feed protein content. Venn analysis highlighted that pond water harbored the largest pool of unique taxa, reinforcing its role as a putative reservoir for pathogens. These findings provide the first integrative microbiome baseline for Egyptian shrimp farms, underscoring the need for microbiome-informed management to mitigate the risk of pathogens.}, } @article {pmid41910822, year = {2026}, author = {Kumar, V and Nautiyal, CS}, title = {From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41910822}, issn = {1573-0972}, abstract = {Plants, together with their resident endophytes, constitute a functional holobiont whose integrated traits enable plant growth, stress resilience, disease resistance, and ecosystem remediation. This review discusses advances across ten converging domains that are reshaping research and applications of endophytes, including the following: genomics and metagenomics that identify core genes for colonization, nitrogen fixation, hormone modulation, and stress adaptation; functional genomics and systems biology deciphering host-microbe signaling networks; synthetic biology and CRISPR-based tools for the rational improvement of beneficial traits; microbiome engineering aimed at designing and stabilizing endophytic consortia; multi-omics integration connecting genomic, transcriptomic, proteomic, and metabolomic layers during colonization and under stress; environmental and climatic factors shaping endosphere diversity; bioinformatic platforms predicting biosynthetic gene clusters, secretomes, and metabolic potential; and agricultural and environmental applications in biocontrol and bioremediation. Remaining challenges are the uncultured majority of endophytes, context-dependent transitions between mutualism and pathogenicity, limited field validation, and evolving biosafety frameworks. Thus, the forward framework developed here emphasizes the importance of standard strain benchmarking, causal multi-omics workflows, synthetic community design, and multisite agronomic trials. For their part, endophytes form a scalable, climate-resilient platform for the dual purposes of sustainable agriculture and environmental restoration. In the process, endophytes are emerging as a tractable and scalable foundation for climate-resilient biotechnology, wherein molecular innovation connects with field-level sustainability.}, } @article {pmid41910951, year = {2026}, author = {Dasgupta, S}, title = {Metagenomics in Obstructive Lung Diseases: Insights into Microbial Dysbiosis, Host-Microbe Interactions, and the Gut-Lung Axis.}, journal = {Omics : a journal of integrative biology}, volume = {30}, number = {4}, pages = {191-202}, doi = {10.1177/15578100261419483}, pmid = {41910951}, issn = {1557-8100}, mesh = {Humans ; *Metagenomics/methods ; *Dysbiosis/microbiology ; *Host Microbial Interactions/genetics ; *Lung/microbiology ; *Gastrointestinal Microbiome ; Animals ; *Lung Diseases, Obstructive/microbiology ; }, abstract = {Obstructive lung diseases (OLDs), including asthma and chronic obstructive pulmonary disease (COPD), arise from complex interactions among microbial ecosystems, host immunity, metabolic regulation, and environmental exposures. Metagenomic approaches have substantially advanced understanding of these interactions by enabling comprehensive profiling of respiratory and gut-associated microbiomes and their functional potential. Evidence indicates that asthma is frequently associated with early-life microbial perturbations, reduced community diversity, enrichment of Streptococcus, Moraxella, and allergen-associated fungi, and gut dysbiosis that influences immune maturation and tolerance. In contrast, COPD is characterized by adult-onset dysbiosis with Proteobacteria dominance, depletion of commensal anaerobes such as Prevotella and Veillonella, and functional signatures linked to chronic inflammation, xenobiotic metabolism, and exacerbation risk. Across both diseases, alterations in gut microbial composition and metabolite profiles, including short-chain fatty acids, highlight the gut-lung axis as a key regulatory interface shaping airway immune responses. Despite these advances, critical knowledge gaps remain, including limited longitudinal data, incomplete multi-kingdom analyses, and insufficient mechanistic and translational validation of disease-associated microbiome signatures. This review integrates current metagenomic evidence to delineate disease-specific and shared microbial patterns, examines host-microbe interaction pathways within molecular and clinical contexts, and critically evaluates the implications and limitations of microbiome-based interventions. By framing microbiome research within a systems biology and public health perspective, this article underscores the importance of context-dependent interpretation and identifies priorities for future longitudinal, mechanistic, and translational studies in OLDs.}, } @article {pmid41911008, year = {2026}, author = {Hosen, ME and Horwood, PF and Sarker, S}, title = {Integrating metagenomics and metatranscriptomics into Orthoflavivirus diagnosis: a transformative approach for clinical virology.}, journal = {The Journal of general virology}, volume = {107}, number = {3}, pages = {}, pmid = {41911008}, issn = {1465-2099}, mesh = {*Metagenomics/methods ; Humans ; *RNA Viruses/genetics/isolation & purification ; Virology/methods ; *Gene Expression Profiling/methods ; *RNA Virus Infections/diagnosis/virology ; Transcriptome ; }, abstract = {Diagnostic inaccuracies are a major yet often overlooked threat to global health, leading to delayed treatment, preventable harm and systemic gaps in disease control. Among the most affected domains are Orthoflavivirus infections, which pose ongoing diagnostic challenges due to antigenic cross-reactivity, overlapping clinical symptoms and the narrow temporal sensitivity of standard tools such as serology and reverse transcription polymerase chain reaction. These constraints have led to widespread misdiagnoses and underreporting, ultimately hampering both effective clinical management and public health response. Recent advances in metagenomic and metatranscriptomic sequencing offer a transformative solution by enabling unbiased, simultaneous pathogen detection and real-time profiling of viral and host transcriptomics. In this review, we assess the diagnostic performance and translational value of these approaches in resolving Orthoflavivirus infections, with case examples from clinical settings in countries like the USA, UK, China and Germany which have already implemented these approaches into routine diagnosis in some settings. We examine key methodological considerations, including optimal sample timing, sample types and processing, sequencing strategy selection and the diagnostic performance of various platforms. We highlight the growing use of metatranscriptomics for detecting active infections, profiling viral and host responses, identifying coinfections and supporting real-time surveillance. We also discuss the key challenges such as technical expertise, lack of standardization, cost, turnaround time and regulatory approval that currently limit global implementation. Finally, we highlight emerging international efforts to integrate sequencing-based diagnostics into routine hospital workflows. Together, these innovations mark a critical shift toward precision diagnostics for Orthoflavivirus infections, with broad implications for clinical settings.}, } @article {pmid41911519, year = {2026}, author = {Zhang, H and Cao, Z and Zha, X and Wang, W and Jashenko, R and Hu, H and Ji, R}, title = {Host intestinal microbiota adaptive changes following Paranosema locustae infection and mechanism of chronic pathogenesis.}, journal = {Journal of insect science (Online)}, volume = {26}, number = {2}, pages = {}, pmid = {41911519}, issn = {1536-2442}, support = {2023D01D08//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; TSYCLJ0016//Tianshan Talent Training Program/ ; 32260254//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Male ; *Grasshoppers/microbiology ; Female ; Bacteria ; }, abstract = {Paranosema locustae infection reduces the abundance and diversity of the intestinal bacteria in locusts, although the microbial adaptive changes and the underlying mechanism of chronic pathogenesis remain unclear. In this study, the intestinal microbial changes in Calliptamus italicus (Linnaeus, 1758) (Orthoptera: Acrididae) were analyzed with metagenomic sequencing after P. locustae infection. Results showed that the diversity of intestinal microbial communities in C. italicus declined after P. locustae infection, while the abundance of infection-specific taxa in C. italicus in the experimental groups was significantly higher than those in the control groups, irrespective of sex (P<0.05). The populations of opportunistic pathogenic bacteria such as Klebsiella aerogenes and Enterococcus faecalis increased significantly (P < 0.05). Meanwhile, the abundances of probiotics such as Pediococcus acidilactici and Enterobacter hormaechei increased significantly (P <0.05), which could inhibit the pathogenicity of P. locustae. The results suggested that the interplay of changes in the species and quantities of probiotics and pathogenic bacteria in the intestine of C. italicus after P. locustae infection was an important factor contributing to the difficulty of P. locustae in quickly breaching the host defense system and to its chronic pathogenicity.}, } @article {pmid41912071, year = {2026}, author = {Zhang, PP and Cui, MY and Shen, Y and Han, B and Yu, W and Wei, TT and Zeng, KW and Tu, PF}, title = {Ophiopogon japonicus polysaccharide ameliorates pulmonary fibrosis via gut microbiota-metabolite crosstalk.}, journal = {Microbial pathogenesis}, volume = {215}, number = {}, pages = {108464}, doi = {10.1016/j.micpath.2026.108464}, pmid = {41912071}, issn = {1096-1208}, mesh = {Animals ; *Ophiopogon/chemistry ; *Polysaccharides/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Metabolomics ; Metagenomics ; Lung/pathology/drug effects ; *Plant Extracts/pharmacology ; Saponins/pharmacology ; Flavonoids/pharmacology ; Mice, Inbred C57BL ; *Idiopathic Pulmonary Fibrosis/drug therapy/chemically induced ; Male ; }, abstract = {Despite the clinical application of Ophiopogon japonicus in idiopathic pulmonary fibrosis (PF), its key anti-fibrotic components and underlying mechanisms remain poorly defined. Using a bleomycin-induced murine PF model, we systematically compared the efficacy of the total extract (OJTE), polysaccharides (OJTP), saponins (OJTS), and flavonoids (OJTF). The active component was further investigated via integrated metagenomics and metabolomics (serum/feces) to decipher the gut-lung axis mechanism. All O. japonicus components attenuated lung injury and collagen deposition, with OJTP demonstrating the most potent efficacy (reducing lung hydroxyproline content by 42.12% (p < 0.01) compared to the model group). Multi-omics analysis revealed that OJTP remodeled the gut microbiota, notably enriching probiotic strains such as Muribaculaceae bacterium (log2FC = 2.17) and Duncaniella muricolitica (log2FC = 2.06), as well as the polysaccharide-utilizing species Prevotella sp. MGM2 (log2FC = 2.79). Concomitantly, OJTP significantly altered host metabolism, upregulating key metabolites including urobilinogen (p < 0.0001) and 5-amino valeric acid betaine (5-AVAB, p < 0.002). These metabolites are implicated in porphyrin and amino acid metabolism, respectively. Correlation networks further established strong associations between these OJTP-modulated microbes and metabolites. Our study first identifies OJTP as the primary bioactive component of O. japonicus against PF. We propose a novel trans-organ mechanism wherein OJTP ameliorates PF via orchestrating a "gut microbiota-metabolite" axis, highlighting the therapeutic potential of targeting polysaccharide-probiotic synergy.}, } @article {pmid41912361, year = {2026}, author = {Rathwell, C and Fuchsman, CA and Rocap, G}, title = {Hi-C Links Reveal Viral Activity and Infection Within the Free-Living Microbial Community of a Secondary Chlorophyll Maximum in the Eastern Tropical North Pacific.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70274}, pmid = {41912361}, issn = {1462-2920}, support = {DGE-2140004//National Science Foundation/ ; DEB-1542240//National Science Foundation/ ; OCE-2022911//National Science Foundation/ ; }, mesh = {Phylogeny ; *Bacteria/virology/genetics/classification/metabolism ; Pacific Ocean ; *Chlorophyll/analysis/metabolism ; *Seawater/microbiology/virology/chemistry ; *Bacteriophages/genetics/classification/physiology ; Metagenomics ; *Microbiota ; *Viruses/genetics/classification/isolation & purification ; Metagenome ; }, abstract = {Oxygen-deficient zones (ODZs) influence global nitrogen cycling as key sites for the removal of bioavailable nitrogen through denitrification and anammox. Despite their importance, many microbes and viruses in ODZs remain uncultivated, limiting our understanding of their ecological roles. This study employed Hi-C proximity linkages, combined with long and short read metagenomic sequencing to characterise active viral interactions in the prokaryotic community at a secondary chlorophyll maximum in the Eastern Tropical North Pacific ODZ. Among the identified 861 assembled viral contigs over 10 kb, 75 showed significant links to microbial genomes. Virus-host linkages indicated 19 novel virus-microbe pairs that were likely infectious, and which conventional in silico host prediction methods largely missed. The virus-host relationships involved nine distinct microbial phyla, with previously unrecorded viral infections of Planctomycetes, Chloroflexota, Alphaproteobacteria, Gammaproteobactera, Myxococcota and Verrucomicrobia. Most hosts carried the genomic potential for denitrification. Phylogenetic analysis of the terminase large subunit (terL) genes from linked viruses suggested that many active phages resemble known temperate phages, indicating that lysogeny may be an ecological strategy in ODZs. Our comprehensive metagenomic approach offers new insights into viral-host interactions in this ecosystem, highlighting the importance of including proximity methods in viral ecology studies of uncultivated microbial populations.}, } @article {pmid41912389, year = {2026}, author = {Wang, YY and Zhang, Q and Zhao, ZF and Zhao, YX and He, Y and Liu, PL and Li, YH}, title = {[Coexistence of lung cancer, brucellosis, and tuberculosis in a single patient: a case report].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {49}, number = {4}, pages = {421-424}, doi = {10.3760/cma.j.cn112147-20260105-00006}, pmid = {41912389}, issn = {1001-0939}, support = {H2024206551//Hebei Natural Science Foundation/ ; 20260411//Hebei Medical Research Project/ ; }, mesh = {Humans ; Male ; Middle Aged ; *Lung Neoplasms/complications/diagnosis ; *Tuberculosis, Pulmonary/complications/diagnosis ; *Brucellosis/complications/diagnosis ; *Carcinoma, Squamous Cell/complications/diagnosis ; Mycobacterium tuberculosis/isolation & purification ; Fatal Outcome ; Coinfection ; }, abstract = {Lung cancer, pulmonary tuberculosis, and brucellosis are common clinical diseases. They share overlapping clinical manifestations and pulmonary imaging findings, and all may involve multiple organ systems, making differential diagnosis challenging. We reported a rare case of lung cancer, and co-infection with pulmonary tuberculosis and brucellosis. A 57-year-old male was admitted to our hospital, presenting with intermittent fever for 7 months and cough accompanied by shortness of breath for 1 month. He had previously sought medical care at multiple hospitals, where he was diagnosed with brucellosis and suspected of having pulmonary tuberculosis. Despite receiving anti-tuberculosis and anti-brucellosis treatments, his pulmonary imaging abnormalities and dyspnea progressively worsened. Pathological examination of mucosal biopsies obtained via bronchoscopy and cervical lymph node biopsy at our hospital confirmed squamous cell lung carcinoma. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid detected Mycobacterium tuberculosis. Although his pulmonary condition temporarily improved following standardized anti-tuberculosis treatment and chemotherapy for lung cancer, the lung cancer subsequently progressed, and the patient ultimately died.}, } @article {pmid41912482, year = {2026}, author = {Shao, Y and Wang, J and Liu, Y and Ni, Y and Liu, Z and Li, Y and Jia, Q and Li, Q and Wang, X and Li, T and Liu, M and Zhang, S and Guo, Y and Guo, X and Wang, D and Liu, Y and Liu, C and Cai, H and Ning, Y and Zhang, J and Xu, G and Le, W}, title = {Distinct metabolomic and proteomic signatures in Parkinson's disease patients with REM sleep behavior disorder.}, journal = {Signal transduction and targeted therapy}, volume = {11}, number = {1}, pages = {}, pmid = {41912482}, issn = {2059-3635}, support = {82271524//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82401742//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024RY003//Dalian Science and Technology Bureau/ ; No. 2023-MS-262//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; }, mesh = {Humans ; *Parkinson Disease/genetics/metabolism/pathology/complications ; *REM Sleep Behavior Disorder/genetics/metabolism/pathology/complications ; *Proteomics ; *Metabolomics ; Female ; Male ; Middle Aged ; Aged ; Metabolic Reprogramming ; }, abstract = {Rapid eye movement sleep behavior disorder (RBD) is the most specific prodromal marker of Parkinson's disease (PD), affecting 40-50% of PD patients. PD with RBD (RBD-PD) represents a clinically aggressive subtype characterized by more severe motor and nonmotor symptoms, prominent autonomic dysfunction, and accelerated disease progression; however, its underlying pathogenesis remains poorly understood. Here, we integrated multiplatform metabolomics and proteomics with precise clinical phenotyping to delineate molecular signatures in plasma across different PD subtypes. Our analyses demonstrated that PD patients exhibit significant metabolic reprogramming, characterized by a shift in energy metabolism from the tricarboxylic acid cycle toward glycolysis, a dysregulated urea cycle, and lipid remodeling, as well as extensive activation of inflammatory and immune responses involving the PI3K-Akt, IL-17, NF-kappaB, MAPK and TNF signaling pathways. Notably, the RBD-PD subgroup exhibited distinctive metabolic disturbances characterized by the accumulation of gut microbiota-derived toxic aromatic amino acid catabolites. Importantly, these alterations were also observed in idiopathic RBD (iRBD) patients, representing the prodromal stage of PD. By integrating metagenomic profiles, we further revealed that gut microbial dysbiosis in RBD-PD and iRBD drives a functional shift away from dietary fiber fermentation and toward enhanced degradation of protein, aromatic amino acids, glycine, and intestinal mucin glycans. This metabolic reprogramming is associated with exacerbated oxidative stress, neuroinflammation, and accelerated pathological progression. These findings provide multiomic evidence that clarifies the molecular heterogeneity in PD and highlights gut microbiota-driven dysfunction as a key contributor to both the iRBD and RBD-PD subtypes.}, } @article {pmid41912529, year = {2026}, author = {Achudhan, AB and Narayanan, R and Madhavan, T}, title = {Metagenome Sequencing and Recovery of 52 Microbial Genomes from Plastic-Polluted Coastal Sediment.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41912529}, issn = {2052-4463}, mesh = {*Geologic Sediments/microbiology ; *Plastics ; *Metagenome ; India ; *Genome, Microbial ; }, abstract = {Plastic pollution is an escalating environmental concern, particularly in coastal regions where sediments serve as long-term sinks for plastic debris. Despite this, the microbial communities inhabiting plastic-contaminated sediments remain poorly characterized in highly polluted hotspots. In this study, we conducted a genome-resolved metagenomic investigation of sediment sample from plastic pollution hotspot in India. Using Illumina short-read sequencing and three high-performing binning tools we reconstructed 52 non-redundant metagenome-assembled genomes (MAGs) from 2,374 initial bins. All MAGs met the MIMAG criteria with 15% reaching near-complete genomes. Taxonomic classification revealed diverse representation of 18 different phyla. Interestingly, 90% of the MAGs could only be classified at intermediate taxonomic levels in the Genome Taxonomy Database (GTDB), suggesting the presence of novel microbial lineages. Taxonomic novelty was further confirmed using the Type Strain Genome Server (TYGS), which identified 3 novel orders, 16 families, and 28 genera. This study provides the first comprehensive genomic insight into microbial communities from plastic-polluted coastal sediments in India and lays the groundwork for exploring their ecological functions.}, } @article {pmid41913056, year = {2026}, author = {Marques, LL and Pinho, AJ and Pratas, D}, title = {FALCON2: compression-based metagenomic classification of ancient viruses.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {5}, pages = {}, pmid = {41913056}, issn = {1367-4811}, support = {//Helsinki University Library/ ; }, mesh = {*Metagenomics/methods ; *Viruses/genetics/classification ; *Software ; *DNA, Ancient/analysis ; }, abstract = {MOTIVATION: Ancient DNA (aDNA) sequences present unique challenges for taxonomic classification due to extreme fragmentation (reads 20-100 bp), end-biased cytosine deamination, and high contamination rates. Conventional metagenomic classifiers based on exact k-mer matching or alignment lose discriminative power on such short and damaged reads, limiting the analysis of paleogenomic samples.

RESULTS: We present FALCON2, a compression-based metagenomic classifier that leverages position-aware finite-context models to maintain high accuracy on degraded viral ancient viruses. FALCON2 consolidates the capabilities of its predecessor, FALCON-meta, into a unified executable with enhanced features including model persistence, direct processing of compressed inputs, multiple file handling, and optional pre-filtering methodologies for contaminated samples. Under controlled benchmarking with database, taxonomy, and thread parity on simulated viral datasets, FALCON2 achieved an Area Under the Curve of Receiver Operating Characteristic (AUC-ROC) of 0.999, an Area Under Precision-Recall Curve (AUPRC) of 0.968, and an F1-score of 0.918, substantially outperforming Centrifuge (AUPRC = 0.625), Kraken2 (AUPRC = 0.184), and CLARK-S (AUPRC = 0.013) on pooled micro-averaged metrics. FALCON2's advantage is most pronounced on ultra-short reads (20-40 bp), where exact k-mers become sparse. FALCON2 pre-filtering at threshold 0.7 improved precision by 10 percentage points with negligible recall loss. FALCON2 runs on systems with 4-8 GB RAM for typical analyses.

FALCON2 is freely available at https://github.com/cobilab/FALCON2 under GPL v3 license. Benchmarking data and scripts are archived at DOI: https://doi.org/10.5281/zenodo.17291214.}, } @article {pmid41913289, year = {2026}, author = {Kieri, O and Narayanan, A and Jütte, BB and Svensson, P and Aleman, S and Sönnerborg, A and Ray, S and Nowak, P}, title = {Linking gut microbiome to HIV-1 reservoir size in people living with HIV.}, journal = {Gut pathogens}, volume = {18}, number = {1}, pages = {}, pmid = {41913289}, issn = {1757-4749}, abstract = {The gut microbiome is altered during HIV-1 infection and contributes to immune dysfunction and inflammation in people living with HIV (PLWH), these changes may persist despite effective antiretroviral therapy (ART). We explored the associations between the fecal gut microbiome and blood HIV-1 reservoir size in PLWH (n = 30) on long-term ART. The intact proviral DNA assay (IPDA) and shotgun metagenomic sequencing were performed to identify microbial species and metabolic pathways associated with the size of the HIV-1 reservoir. PLWH with a smaller intact reservoir exhibited lower evenness compared to individuals with a larger intact reservoir. We found that Phocaeicola plebeius and Lachnospira sp000437735 were significantly enriched in individuals with a smaller intact reservoir and lower intact-to-total proviral ratio, respectively. We observed a negative association between Faecalibacterium prausnitzii and a positive association of Prevotella copri, with the intact proviral reservoir size. Additionally, the metabolic pathways of glycolysis and branched-chain amino acid biosynthesis were enriched in individuals with larger reservoir. HIV reservoir size in blood is associated with gut microbiome evenness, specific metabolic pathways and microbial signatures, including Lachnospira, Prevotella, and Faecalibacterium. Our findings underscore the potential role of the gut microbiome in viral persistence, raising the possibility that modulating microbial composition could influence the HIV reservoir.}, } @article {pmid41913691, year = {2026}, author = {Erens, J and Heine, C and Lötters, S and Krehenwinkel, H and Crawford, AJ and Rueda-Solano, LA and Plewnia, A}, title = {A Field-Deployable eDNA Metabarcoding Workflow Including De Novo Reference Assembly for Characterising Understudied Biodiversity Hotspots.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70122}, pmid = {41913691}, issn = {1755-0998}, support = {//Ministerium für Wirtschaft, Verkehr, Landwirtschaft und Weinbau Rheinland-Pfalz/ ; //Deutsche Gesellschaft für Herpetologie und Terrarienkunde/ ; //Forschungsfonds of Trier University/ ; //Forschungsinitiative Rheinland-Pfalz through Trier University/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Biodiversity ; Amphibians/classification/genetics ; *Metagenomics/methods ; *DNA, Environmental/genetics ; Workflow ; Extrachromosomal DNA ; }, abstract = {Field-deployable DNA metabarcoding offers a transformative approach to biodiversity research and monitoring, yet its application remains limited due to technical constraints and a lack of reference data in poorly studied ecosystems. Combining isothermal Recombinase Polymerase Amplification (RPA) and Oxford Nanopore sequencing, we introduce a two-step approach that uses non-invasive species barcoding to directly generate reference sequences for use in environmental DNA (eDNA) metabarcoding, and enables real-time, PCR-free and cost-effective molecular assessment of ecological communities in the field. Using an endemic and understudied tropical amphibian assemblage as a model, we demonstrate the functionality of this novel workflow. De novo generation of a reference sequence library from amphibian skin swab samples significantly improved the accuracy and taxonomic resolution of sequence assignments from eDNA samples, particularly on the species level, in turn allowing a characterisation of fine-scale patterns in community composition. Beyond generating new RPA-compatible amphibian metabarcoding primers, our results show that combining field-based eDNA metabarcoding with the offline assembly of a local reference database can directly bridge existing data gaps in molecular biodiversity monitoring, providing a scalable solution to accelerate biodiversity assessments in data-deficient ecosystems. This workflow paves the way for broader deployment of molecular tools in global biodiversity hotspots-particularly in remote and resource-limited tropical regions-to directly contribute critical baseline data, and support conservation efforts in regions where they are most urgently needed.}, } @article {pmid41913730, year = {2026}, author = {Kwoji, ID and Edwards, W and Ruffell, A and Shaw, D and Denoyelle, C and Figuiredo, A and Guadano-Procesi, I and Makkimane, J and Pantzi, K and Godfrey, A and Gentekaki, E and Stensvold, CR and Kolisko, M and Tsaousis, A}, title = {BlastoDB: first release of a community-driven multi-omics and epidemiological resource for Blastocystis biology and subtyping.}, journal = {Open research Europe}, volume = {6}, number = {}, pages = {65}, pmid = {41913730}, issn = {2732-5121}, abstract = {BlastoDB (https://www.blastodb.com/) is developed as an open-access, community-driven resource dedicated to Blastocystis, one of the most common yet understudied intestinal protists. BlastoDB will offer the scientific community up-to-date, curated information on Blastocystis by integrating epidemiological data, microbiome profiles, multi-omics datasets (genomics, transcriptomics, proteomics, and metabolomics), reference sequences for subtypes, protocols, microscopy images, and related metadata. In this initial release, we describe the data model, database architecture, curation pipelines, and web interface, which together facilitate subtype classification, comparative and integrative analyses, and cross-study synthesis of epidemiological and experimental data. We outline submission and governance workflows designed to support community contributions, training activities, and sustainable curation under the " Blastocystis under One Health" COST Action (CA21105). Finally, we highlight planned extensions, including expanded metagenomic and metatranscriptomic content, automated genome quality assessments, metagenome-assembled genomes, and geospatial and analytical dashboards. BlastoDB provides a central, FAIR-aligned hub for Blastocystis data, images, and protocols, reducing technical barriers and fostering a collaborative ecosystem for studying this globally prevalent protist.}, } @article {pmid41913758, year = {2026}, author = {Chin, D and Campbell, B and Petersen, J and Lim, SJ and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the buttercup lucine, Anodontia alba Link, 1807 (Lucinida: Lucinidae) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {131}, pmid = {41913758}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Anodontia alba (buttercup lucine; Mollusca; Bivalvia; Lucinida; Lucinidae). The genome sequence has a total length of 1 862.85 megabases. Most of the assembly (99.28%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 18.48 kilobases. Gene annotation of this assembly by Ensembl identified 12 083 protein-coding genes. From the metagenome data, we recovered four bins, of which three were high-quality MAGs.}, } @article {pmid41913906, year = {2026}, author = {Lu, P and Liu, M and Zhang, L and Fan, JJ and Han, G and Hou, B and Meng, Y and Wang, L and Sun, Y}, title = {Gut-Brain Axis Dysregulation in Inflammatory Bowel Disease: Implications for Coagulation Abnormalities and Extraintestinal Manifestations.}, journal = {International journal of general medicine}, volume = {19}, number = {}, pages = {590621}, pmid = {41913906}, issn = {1178-7074}, abstract = {Inflammatory bowel disease (IBD) involves chronic intestinal inflammation driven by gut-brain axis imbalance, fostering complications through an "inflammation-neuro-coagulation" triad. Current staging systems inadequately capture the dynamics of this multidimensional network. Therefore, integrated multi-omics analyses-including metagenomics, metabolomics, and single-cell transcriptomics-are essential to construct dynamic models that monitor coagulation, microbiome, and metabolism for precise assessment of disease activity and thrombotic or bleeding risks. Interventions targeting gut-brain axis nodes, such as eliminating tissue factor-positive (TF[+]) T cells or modulating vagal activity, show potential to disrupt the inflammation-coagulation cycle, although rigorous randomized trials are still needed. Artificial intelligence (AI)-assisted systems that integrate real-time biomarker monitoring with multi-omics predictions represent a novel paradigm for managing IBD-related coagulation dysfunction. Key challenges include elucidating gut-brain-liver axis regulation of coagulation and characterizing platelet functional heterogeneity. Future efforts must prioritize ethically compliant multi-omics platforms and racially stratified risk models to advance personalized coagulation management in IBD.}, } @article {pmid41914171, year = {2026}, author = {Yildirim, EA and Laptev, GY and Tiurina, DG and Filippova, VA and Ilina, LA and Novikova, NI and Sokolova, KA and Ponomareva, ES and Brazhnik, EA and Zaikin, VA and Klyuchnikova, IA and Bolshakov, VN and Korochkina, EA and Vorobyov, NI and Griffin, DK and Romanov, MN}, title = {Compositional and Functional Metabolic Shifts in the Endometrial Microbiota of Cows (Bos taurus) During the Transition Period: A Metagenomic Next-Generation Sequencing Approach.}, journal = {Frontiers in bioscience (Elite edition)}, volume = {18}, number = {1}, pages = {39439}, doi = {10.31083/FBE39439}, pmid = {41914171}, issn = {1945-0508}, support = {24-16-00131//Russian Science Foundation/ ; }, mesh = {Animals ; Female ; Cattle ; High-Throughput Nucleotide Sequencing ; *Endometrium/microbiology/metabolism ; *Microbiota ; Metagenomics ; }, abstract = {BACKGROUND: Significant alterations in feeding, housing, and physiology are observed in dairy cows during the transition period (3 weeks pre- and post-calving), in addition to changes in the composition and abundance of the endometrial microbiota. Thus, this study aimed to evaluate any changes in the composition and predicted metabolic pathways in the cow uterine microbiome during this transition period.

METHODS: Scrapings were sampled from the endometrial surface of clinically healthy cows (n = 3) in dynamics as follows: in the 10 Days period before, and on Days 3, 5, and 20 after calving. Total DNA was isolated from the samples, and the composition of the microbial community was assessed using targeted next-generation sequencing (NGS) technology. Based on the subsequent NGS data, the dynamics of the predicted metabolic pathways of the microbiota were evaluated.

RESULTS: Seven superphyla and phyla of microorganisms were found in the endometrial microbiota of cows during the transition period. Among these, the phylum Firmicutes (with a dominant class of Clostridia) and the superphylum Fusobacteriota (represented by a single class of Fusobacteriia) can be considered the dominant bacteria in the endometrium, with representation noted from 25.2 to 68.2% and from 12.3 to 51.1%, respectively. The microbiome composition underwent significant changes (p < 0.05) during the transition period. In particular, the high abundance of the Fusobacteriaceae family (up to 68.2%) in the uterus of clinically healthy cows was unexpected, given the potential association of Fusobacteriaceae with the occurrence of metritis in cows. The numbers of microorganisms in two dominant classes, Fusobacteriia and Clostridia, showed generally opposite changes in their relative abundance during the transition period. The predicted functional potential level for 32 pathways in the endometrium changed (p < 0.05) in cows during the transition period. Indeed, the activity of the predicted pathways, such as pyridoxal 5'-phosphate biosynthesis I and teichoic acid (poly-glycerol) biosynthesis, was lowered on day 3 postpartum (p < 0.05).

CONCLUSIONS: Microbiota composition and the activity of the predicted metabolic pathways in the cow endometrium underwent significant changes at different critical stages in the transition period. Moreover, even clinically healthy cows exhibited signs of dysbiotic disorders.}, } @article {pmid41914631, year = {2026}, author = {Arogundade, AA and Dumaguit, CDC and Melton, A and Buerki, S and Bittleston, LS}, title = {Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.}, journal = {Microbiology spectrum}, volume = {14}, number = {5}, pages = {e0219825}, pmid = {41914631}, issn = {2165-0497}, abstract = {Advanced sequencing technologies and improvements in bioinformatics have provided a new way to study plant-associated microbial communities, including the use of host genomic sequencing. Our study focuses on the leaf microbiome of basin big sagebrush (Artemisia tridentata subsp. tridentata), a foundational shrub of western North America. We analyzed Illumina shotgun sequences from sagebrush leaves to investigate the metagenomes of leaf-associated microbes that were sequenced alongside their plant hosts. We aimed to profile the leaf microbiome across different sample sources (magenta box, greenhouse, and field/wild), reconstruct metagenome-assembled genomes (MAGs) where possible, and investigate functional gene annotations of the resulting MAGs, specifically with regard to the potential metabolism of sagebrush chemicals. To achieve this, Illumina shotgun sequence reads (containing both host and associated microbial reads) were mapped to the reference genomes of Artemisia tridentata, Artemisia annua, and the human reference genome to remove plant host and human-associated sequences. Host-cleaned reads were then analyzed using microbial metagenomics techniques. Taxonomic profiling revealed that Phyllobacterium and Sphingomonas were the most abundant microbial genera in greenhouse-grown plants, with very little variation among the samples. Wild, field-collected samples were much more variable and were dominated by Klebsiella and Aureobasidium species. From the co-assembly of greenhouse samples, we reconstructed two high-quality MAGs (a Phyllobacterium species and a Sphingomonas species) with >98% completion and <1% contamination. Functional annotation of these MAGs uncovered genes associated with the degradation and metabolism of camphor and other essential oils such as pinene, geraniol, and limonene, which are part of sagebrush leaf chemistry.IMPORTANCEBig sagebrush (Artemisia tridentata), the foundation species of the sagebrush steppe, has broad ecological importance because its evergreen leaves offer nutrients and shade that facilitate the establishment of diverse understory plants in arid environments. Sagebrush leaves contain various secondary metabolites, including terpenoids, flavonoids, and phenolic compounds. These chemicals contribute to the plant's defense mechanisms against herbivores and pathogens. Despite this, sagebrush hosts diverse bacterial and fungal communities. We found that the microbial metagenome-assembled genomes (MAGs) we recovered contained genes that have the potential to degrade some of the chemical compounds in sagebrush leaves that could inhibit the growth of other microbes. This is the first study to mine plant genome data using host-derived sequences to generate microbial MAGs. Our results showed that MAGs can be recovered from plant host-derived sequence data, providing a new way to explore the identity and functional capabilities of difficult-to-culture microbes.}, } @article {pmid41914733, year = {2026}, author = {Nandi, S and Stephens, TG and Garcia, R and Sánchez-García, M and Roberson, LM and Avalos, JL and Chundawat, SPS and Bhattacharya, D}, title = {Rafts of change: microbial and functional dynamics in simulated Sargassum strandings.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {4}, pages = {e0235725}, pmid = {41914733}, issn = {1098-5336}, support = {NJ01180//USDA | USDA Rural Development (RD)/ ; 2128073//National Science Foundation/ ; //Schmidt Sciences and FFAR/ ; }, mesh = {*Sargassum/microbiology/metabolism ; *Microbiota ; *Bacteria/metabolism/genetics/classification ; Polysaccharides/metabolism ; Arsenic/metabolism ; Biodegradation, Environmental ; }, abstract = {Massive influxes of pelagic Sargassum spp. across the tropical Atlantic and Caribbean regions have created urgent ecological and economic challenges that need to be addressed to stabilize local ecosystems. Use of this abundant biomass feedstock resource for biorefining and bioproducts manufacturing is a promising avenue, but this goal requires elucidating the microbial processes that regulate Sargassum degradation, which are still poorly understood. Here, we investigated the microbial degradation of the benthic Sargassum filipendula by native microbiota using multi-omics approaches. Metagenomic and meta-transcriptomic analyses identified diverse carbohydrate-active enzymes (CAZymes), including alginate lyases, fucoidanases, and cellulases, that were differentially expressed over the course of the in vitro degradation timeline. Furthermore, we identified the need for arsenic detoxification pathways in microbes utilizing Sargassum-derived substrates. We observed a suite of factors influencing microbial dynamics, including prokaryotic competition, arsenic detoxification, viruses, and substrate availability. Lineages potentially capable of degrading recalcitrant polysaccharides such as fucoidan appeared to be rapidly outcompeted by other bacteria that utilized simpler substrates like mannitol. These results highlight the metabolic potential of native marine microbial communities to degrade complex Sargassum polysaccharides and the importance of the in vitro degradation experiment time scale to capture the activities of non-dominant specialists. Our findings elucidate microbial ecosystem dynamics during Sargassum degradation and provide novel insights that can be used to advance the development of biotechnological approaches that leverage renewable Sargassum biomass as a biorefinery feedstock of the future.IMPORTANCEThis work addresses a crisis in the tropical Atlantic and Caribbean regions, the massive population growth and stranding of the floating brown seaweed Sargassum, which is wreaking havoc on ecosystems and fouling beaches vital to local tourism. One solution to this problem is to utilize the seaweed as feedstock to generate useful bioproducts. This approach requires characterizing the microbiome of Sargassum that drives its degradation in nature. To this end, we devised an in-lab degradation assay using Sargassum and identified a variety of carbohydrate-active enzymes, including alginate lyases, fucoidanases, and cellulases which break down seaweed cell wall polysaccharides. We also find that microbes compete in the closed reactors, with diversity being reduced over time. These results highlight the metabolic potential of native marine microbial communities to degrade Sargassum and elucidate microbial ecosystem dynamics during this process. These insights allow the use of renewable Sargassum as a biorefinery feedstock of the future.}, } @article {pmid41914849, year = {2026}, author = {Deng, T and Wang, H and Zhang, S-F and Wu, X-Y and Yang, Z-S and Wang, D-Z and Zheng, Y}, title = {Functional determinism amid taxonomic stochasticity: insights into rules governing the assembly of algal-microbial symbioses.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {4}, pages = {e0035926}, pmid = {41914849}, issn = {1098-5336}, support = {2024J010010//Natural Science Foundation of Fujian Province/ ; 20720240092//Headmaster' Faculty Fund/The Fundamental Research Funds for the Central Universities/ ; 423B2603//National Natural Science Foundation of China/ ; 42522607//National Natural Science Foundation of China/ ; 2023YFC3108600//National Key Research and Development Program of China/ ; }, mesh = {*Symbiosis ; *Diatoms/physiology/classification/microbiology ; *Microbiota ; Seawater/microbiology ; Stochastic Processes ; }, abstract = {Marine algal-microbial symbioses constitute essential functional units that drive ocean biogeochemical cycles and trigger harmful algal blooms. Yet, a long-standing controversy persists regarding the mechanisms of algal-microbial symbiose assembly, specifically whether phycosphere microbiota are predominantly shaped by deterministic algal-driven selection or by stochastic environmental processes, with no definitive resolution to date. Here, we examined phycosphere communities associated with a series of Skeletonema strains, tracking their taxonomic and functional dynamics across successive growth stages. Despite pronounced taxonomic diversity, reflected in distinct community compositions, successional trajectories, and microbial networks, shotgun metagenomic analyses revealed highly conserved functional repertoires across samples, with consistently abundant core pathways, including amino acid biosynthesis, secondary metabolite and antibiotic production, and ABC transport systems. Statistical analyses further revealed a marked decoupling of taxonomy and function, with functional redundancy enabling taxonomically distinct lineages to perform equivalent metabolic roles. Based on these findings, we propose a dual assembly model in which deterministic algal host-driven selection constrains functional composition, while stochastic processes govern species-level membership. This "function-first, taxonomy-stochastic" paradigm reconciles opposing assembly theories, underscores functional resilience in the face of taxonomic turnover, and provides a conceptual foundation for the rational design of synthetic algal-microbial consortia in marine biotechnological applications.IMPORTANCEMarine algae live in close association with diverse microorganisms that influence nutrient cycling and ecosystem stability. Yet, how these algal-microbial partnerships assemble and maintain functional integrity remains unresolved. Using Skeletonema as a model, this study demonstrates that while the microbial species surrounding different algal strains vary greatly, their metabolic functions remain remarkably consistent. This finding reveals that algal hosts deterministically shape the functional needs of their microbiome, whereas the specific bacterial members fulfilling those roles are interchangeable. Such a "function-first" organization explains how algal-microbial symbioses persist despite environmental fluctuations. Understanding these assembly rules not only advances our knowledge of marine microbial ecology but also provides a conceptual foundation for engineering stable and resilient algal-microbial consortia for sustainable ocean biotechnologies.}, } @article {pmid41915015, year = {2026}, author = {Sun, Y and Wu, X and Zanina, OG and Rivkina, EM and Lloyd, KG and Löffler, FE and Vishnivetskaya, TA}, title = {Incomplete denitrifying bacteria drive N2O fluxes in ancient Siberian permafrost microcosms.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {5}, pages = {}, pmid = {41915015}, issn = {1574-6941}, support = {DEB-1442262//NSF/ ; DEB-1831599//NSF/ ; DE-SC0020369//U.S. Department of Energy/ ; AAAA-A18-118013190181-6//The Russian Government/ ; }, mesh = {*Permafrost/microbiology ; *Nitrous Oxide/metabolism ; *Denitrification ; Siberia ; *Bacteria/metabolism/genetics/classification ; Metagenome ; Nitrogen/metabolism ; Nitrates/metabolism ; }, abstract = {Nitrous oxide (N2O) contributes to stratospheric ozone depletion and global warming. Knowledge about microbial formation and consumption of N2O in old permafrost remains limited. Permafrost samples collected on the East Siberian Sea coast of Russia from a single borehole at depths of 5.4 and 16.9 m, which showed presence of nitrogen substances and nitrogen cycling genes, were used to establish microcosms supplemented with NO3- and N2O to assess denitrification and N2O consumption at 4°C and 20°C. Rapid N2O formation was observed in NO3--supplemented microcosms, but N2O consumption was slow and incomplete over a 1-year incubation in all microcosms. Twenty-three qualified metagenome-assembled genomes (MAGs) harboring genes involved in NO3- and/or N2O reduction were recovered from both NO3-- and N2O-supplemented microcosms. Twenty MAGs represent novel taxa. Four MAGs, two of each from NO3-- and N2O-supplemented microcosms, contained nosZ genes indicating N2O consumption potential, however the complete denitrification (i.e. NO3-→N2) gene sets were not detected in these MAGs. Though, N2O production exceeded N2O consumption in NO3--supplemented microcosms at 4°C. Our microcosm experiments suggest N2O formation surpasses its consumption in newly thawed ∼120 kyr old permafrost, emphasizing the importance of using integrated approaches to assess and predict N turnover in response to permafrost degradation.}, } @article {pmid41915167, year = {2026}, author = {Venetsianou, NK and Paragkamian, S and Kalaentzis, K and Loukas, A and Damianou, C and Lagani, V and Jensen, LJ and Pafilis, E}, title = {LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41915167}, issn = {1432-184X}, abstract = {Microbiome studies reveal the taxonomic and functional composition of microbial communities inhabiting many diverse environments. Comprehensive microbiome repositories, such as MGnify, organize data into studies, each consisting of multiple sequencing runs or assemblies and accompanying metadata. This structure enables integrative, large-scale, cross-study analyses, leading to broader insights across ecosystems, hosts, and experimental contexts. Despite extensive microbiome research, methods for defining similarity between studies and validating those similarity metrics, remain insufficiently established, especially for large-scale analyses. To address this, we evaluate whether taxonomic and functional similarities from MGnify can serve as reliable indicators of study relatedness between study pairs, testing multiple metrics against conceptual relatedness (e.g., shared environments, goals, or methods). To scale validation, we introduce a framework that applies a Large Language Model (LLM) to study descriptions, categorizing study pairs by relatedness. Our results show that functional similarity correlates more strongly with LLM-inferred study relatedness than taxonomic similarity, highlighting both the promise and limitations of current metrics. Via the above, we demonstrate the value of combining microbial profiles with LLM-driven semantic reasoning to navigate the expanding landscape of metagenomic research.}, } @article {pmid41915265, year = {2026}, author = {Volk, A and Mills, M and Chae, S and Lee, J}, title = {Investigation of cyanobacteria-hosted antibiotic resistance genes in cyanoHAB-impacted drinking water sources.}, journal = {Environmental science and pollution research international}, volume = {33}, number = {13}, pages = {6140-6164}, pmid = {41915265}, issn = {1614-7499}, mesh = {*Cyanobacteria/genetics ; *Drinking Water/microbiology ; Lakes ; *Drug Resistance, Microbial/genetics ; Eutrophication ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents ; }, abstract = {Freshwater cyanobacterial blooms (cyanoHABs) are expanding across the world, and their frequency and severity are becoming more intense due to prevalent eutrophication and a changing climate. Traditionally, the concerns about cyanoHABs have mainly focused on cyanotoxins in water. CyanoHABs are also hypothesized to play a role in the antibiotic resistome, but whether cyanobacteria host clinically relevant antibiotic resistant genes (ARGs) in the environment is largely unknown. To investigate this emerging issue, we examined whether cyanobacteria host ARGs within the broader microbiome context. We looked for the presence of cyanobacteria-hosted ARGs using shotgun metagenomic sequencing of drinking water source samples collected during the bloom season (summer and fall) from Lake Erie and Grand Lake St. Marys (GLSM). ARGs were annotated using DeepARG and Resistance Gene Identifier (RGI). Cyanobacteria were annotated to host genes conferring putative antibiotic resistance, including efflux pumps qac/EmrE, vatB, van genes, and an OXA homolog. A maximum likelihood tree with cyanobacteria and OXA reference sequences showed OXA-like homology across multiple families of cyanobacteria. Most cyanobacteria sequences clustered in a large clade with ybxI, suggesting very limited or negligible class-D beta-lactamase activity, but a small subset formed a clade with OXA-2 and OXA-46. While those hits suggest potential resistance to clinical antibiotics, overall cyanobacteria were not found to host ARGs conferring resistance to drugs of last resort in these samples. Additionally, BLAST searches of the cyanobacteria ARG contigs and coding sequences resulted in top hits for cyanobacteria, further supporting that annotated genes are likely intrinsic rather than acquired. rpoB2 and arlR ARG annotations appear to be spurious hits on housekeeping genes, which demonstrates the need to verify automated ARG annotation tool results. Selected cyanotoxins, cyanobacteria, and ARGs were also chosen for quantification. We found high levels of Microcystis in Lake Erie as well as Planktothrix and microcystin concentrations in GLSM, supporting previous trends in these water bodies. This study takes a novel approach, pairing the issues of cyanoHABs and ARGs together in two drinking water sources. In a changing climate, drinking water treatment strategies should consider the treatment and public health implications of multiple contaminants.}, } @article {pmid41915324, year = {2026}, author = {Varshney, A and Sarethy, IP}, title = {Metagenome-based insights into bacteriophage diversity of an urban river ecosystem.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {41915324}, issn = {1573-4978}, abstract = {BACKGROUND: The Yamuna River, one of India’s major freshwater systems, has experienced severe ecological deterioration due to the continuous discharge of untreated domestic and industrial effluents, resulting in high microbial and chemical pollution loads. This degradation has promoted the proliferation of pathogenic and antimicrobial-resistant bacteria, underscoring the urgent need for sustainable microbial control strategies. METHODS: This study comprehensively characterized the bacteriophage diversity of the Yamuna River through an integrative approach combining conventional phage isolation, transmission electron microscopy (TEM), and high-throughput metagenomic analysis. RESULTS: Phages infecting Escherichia coli and Pseudomonas fluorescens exhibited distinct plaque morphologies and strong lytic activity, confirming the presence of active viral populations. TEM analysis revealed diverse tailed morphotypes characteristic of the class Caudoviricetes. Metagenomic profiling identified 28,993 viral contigs across 21 viral classes, predominantly Caudoviricetes (49%). Of these, 57% were classified phages, while 43% remained unclassified, indicating substantial unexplored viral diversity within this ecosystem. Notably, 19% of the detected phages were associated with pathogenic bacterial hosts, including multidrug-resistant (MDR) ESKAPE pathogens of 544 abundance (4%), highlighting their clinical and ecological significance. Functional annotation further revealed auxiliary metabolic genes (AMGs) involved in nutrient cycling, host metabolism modulation, and viral replication, reflecting the adaptive versatility of these phages. CONCLUSION: This study presents an integrated, phage-centric investigation from the polluted water column of the Yamuna River in Delhi. By combining wet-lab isolation, transmission electron microscopy, and metagenomic analysis of bacteriophages, we identify a diverse reservoir of largely uncultivated waterborne phages with relevance to microbial regulation, environmental monitoring, and antimicrobial resistance mitigation. These findings provide a genomic basis for exploring environmental phages in sustainable water quality management and the development of phage-based therapeutic interventions.}, } @article {pmid41915473, year = {2026}, author = {Zhao, Y and Li, J and Han, K and Chen, L and Zhuang, Q and Li, S and Hua, M and Li, N and Yue, J and Gu, C and Rong, C and Yang, D and Deng, Z and Huang, J and He, L and Zeng, H and Yu, Z and Chen, C}, title = {Phage-related symbiosis and antagonism shape gut ecosystem dynamics in Lachnospiraceae and Bacteroidaceae.}, journal = {Cell reports}, volume = {45}, number = {4}, pages = {117166}, doi = {10.1016/j.celrep.2026.117166}, pmid = {41915473}, issn = {2211-1247}, abstract = {The human gut microbiota is shaped by intricate, yet poorly resolved interactions among bacteria, as well as their relationship to bacteriophages. However, resolving this complex interaction and dynamics has been limited by the challenges in genome recovery and functional characterization. We develop culture-enriched metagenomic co-barcoding sequencing (cMECOS), obtain 5,006 high- or medium-quality (HMQ) metagenome-assembled genomes (MAGs) and reconstruct bacteria-phage interaction networks via CRISPR spacer mapping. This framework uncovers two ecologically distinct, inter-specific bacterial networks: a Lachnospiraceae-dominated community associates with temperate phages and is characterized by metabolic cross-feeding and a Bacteroidaceae-dominated community linked to virulent phages and marked by resource competition. Both network architectures are disrupted in both inflammatory bowel disease (IBD) and obesity (OB), underscoring their role in ecosystem stability. Our work establishes cMECOS as a powerful platform for deciphering complex microbiome interactions and identifies phage-related bacterial networks as critical regulators of gut homeostasis, providing a foundation for phage-informed therapeutic development.}, } @article {pmid41915526, year = {2026}, author = {Xiao, Z and Wei, A and Jia, Y and Zhao, W and Jiang, X}, title = {Semantic fusion of dual perspectives on genomic sequences and quorum sensing for bacteriophage lifestyle prediction.}, journal = {IEEE journal of biomedical and health informatics}, volume = {PP}, number = {}, pages = {}, doi = {10.1109/JBHI.2026.3679001}, pmid = {41915526}, issn = {2168-2208}, abstract = {As the most ubiquitous and abundant viral community, bacteriophages (phages for short) play a vital role in regulating the ecological balance by infecting bacteria and archaea. Phages can be classified into two types based on their lifestyles: virulent phages and temperate phages, which are closely related to their functional characteristics and influence their interaction patterns with hosts. Therefore, identifying phage lifestyle is critical for understanding the mechanisms by which phages infect bacteria and represents a key step in mastering their functions and potential applications. In this paper, we propose a novel method for phage lifestyle identification by considering two perspectives. One perspective is based on the genomic sequences of phages, in which both local and global semantic features are integrated. The other perspective focuses on the host quorum sensing phenomena that influence phage lysogen-lysis decisions. Specifically, we first capture local sequence variation patterns by extracting the relative positional information of nucleotide fragments at different intervals, which enables robust representation of local genomic semantics. Secondly, the pretrained nucleotide language model DNABERT is applied to capture the semantics of genome sequences by considering the global contextual information. Finally, combined with quorum sensing signals from the bacterial host, a final fusion representation is obtained, which is fed into a predictive model to identify the phage's lifestyle. Experimental results show that our method has excellent and stable performance in both phage complete genome and short contigs from metagenomic data. We also investigate early-life viral colonization in the human gut metagenome, further validating the model's generalizability and real-world applicability.}, } @article {pmid41915541, year = {2026}, author = {Yue, Y and Kang, YJ and Wang, H and Jiang, H and Zhou, H and Jiang, W and Li, K}, title = {Diagnosis of Cat-Scratch Disease by Metagenomic Next-Generation Sequencing.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {}, number = {}, pages = {15303667261435870}, doi = {10.1177/15303667261435870}, pmid = {41915541}, issn = {1557-7759}, abstract = {Cat-scratch disease caused by Bartonella henselae is a worldwide distributed zoonotic disease. Cats are the major reservoirs of B. henselae, and human infection cases are usually resulted from contact with pet cats. In this study, a 49-year-old woman presented to the hospital after 10 days of fever. She also complaint lymph node enlargement and pain. Laboratory tests indicated liver dysfunction and inflammation. Pathological examination of the lymph node suggested the possibility of cat-scratch disease, and then doxycycline was used. Metagenomic next-generation sequencing showed that 59496 sequences of B. henselae were identified, confirming the diagnosis of cat-scratch disease. Meanwhile, Acinetobacter towneri and Epstein-Barr virus were also identified. Doxycycline therapy was continued, and the enlargement of lymph node was apparently alleviated. Epidemiological investigation showed that she had a pet cat, and she was possibly infected through direct contact with the cat. Cat-scratch disease in China may be an underestimated disease. Although multiple methods for detecting B. henselae have been established, low bacteremia is still a key challenge to molecular diagnosis. mNGS is a preferable choice for the diagnosis of cat-scratch disease due to its feasibility, sensitivity, and timeliness.}, } @article {pmid41916285, year = {2026}, author = {Makumbi, JP and Leareng, SK and Bezuidt, OK and Coelho, LP and Makhalanyane, TP}, title = {Persistence of high-risk antimicrobial resistance genes in extracellular DNA along an urban wastewater-river continuum.}, journal = {Cell reports}, volume = {}, number = {}, pages = {117128}, doi = {10.1016/j.celrep.2026.117128}, pmid = {41916285}, issn = {2211-1247}, abstract = {Inadequate wastewater treatment can drive the spread of antimicrobial resistance (AMR), threatening ecosystems and human health. Extracellular DNA (exDNA) stabilizes antimicrobial resistance genes (ARGs) in the environment and facilitates horizontal gene transfer, yet its taxonomic structure and influence on AMR ecology remain poorly understood, especially in African aquatic systems. We profile exDNA-associated resistomes across nine South African wastewater treatment plants and receiving rivers, comparing single-stage activated sludge process (ASP-only) and combined ASP-biofilter systems. exDNA harbors high-risk mobile ARGs conferring resistance to last-resort antibiotics, with enrichment in effluents and downstream rivers. Surprisingly, upstream river samples also carry abundant ARGs, indicating cumulative inputs from multiple environmental reservoirs. ARGs are mainly associated with Pseudomonadota and Bacteroidota, suggesting that exDNA constitutes an ecologically distinct AMR reservoir dominated by key taxa. These findings underscore the need to integrate exDNA into AMR surveillance and highlight its broader role in microbial adaptation within freshwater environments.}, } @article {pmid41917109, year = {2026}, author = {Foresto, L and Radaelli, E and Leuzzi, D and Palladino, G and Scicchitano, D and Bejaoui, S and Turroni, S and Rampelli, S and Santolini, C and Pari, A and Marcellini, F and Danovaro, R and Corinaldesi, C and Candela, M}, title = {Metagenomic profiling reveals distinct signatures of pathogens, antibiotic-resistance genes and human viruses in urban river mouths of the north-western Adriatic coast.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41917109}, issn = {2045-2322}, abstract = {UNLABELLED: Coastal ecosystems are increasingly threatened by microbiological risk due to urban wastewater discharges, which might affect public health and have important economic consequences on the blue tourism. Here, we examine the changes in water and sediment microbiomes at the mouths of three urban-draining rivers (Marecchia, Marano, Rio Melo) and at the Santa Giustina wastewater treatment plant, situated in one of the most densely urbanized and touristic areas of the Adriatic Sea. During the peak summer season, water and sediment samples were analysed through 16 S rRNA metabarcoding and shotgun metagenomics to identify the presence of pathogenic bacteria, human viruses, and antibiotic resistance genes (ARGs). Results revealed that impacted river mouths hosted distinct microbial fingerprints, with seawater showing higher levels of pathogenic bacteria (including Vibrio, Enterococcus, Escherichia-Shigella, and Streptococcus) than sediments. Several human viruses of risk groups 2 and 4, such as Adenoviridae, Herpesviridae, Papillomaviridae, Poxviridae, were detected, along with 99 ARGs, 82 of which were classified by the World Health Organization (WHO) as critically important. Our data suggest the persistence of pathogens in treated effluents and reveal a specific combination of bacterial taxa, viruses, and ARGs, with site-specific profiles. Overall, our findings underscore the need for systematic genomic-based monitoring to safeguard bathing water quality and mitigate risks to human and environmental health, in line with One Health principles.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-45229-2.}, } @article {pmid41917256, year = {2026}, author = {Shen, Z and Liu, Y and Liu, Y and Zhang, P and Li, Y and Li, Z and Qi, H}, title = {Clinical characteristics and mixed infection patterns of ocular surface infection with Epstein-Barr virus.}, journal = {Journal of ophthalmic inflammation and infection}, volume = {16}, number = {1}, pages = {}, pmid = {41917256}, issn = {1869-5760}, abstract = {PURPOSE: To analyze the clinical features of ocular surface diseases caused by Epstein-Barr virus (EBV) infection. METHODS: A retrospective case series study was conducted. Data from 48 patients (54 eyes) with EBV infection who visited Peking University Third Hospital between January 2023 and October 2025 were collected. Patient demographics and baseline information were recorded. Ophthalmic slit-lamp examination, ocular surface (conjunctiva/cornea) scrapings, bacterial culture of ocular secretions, real-time fluorescence quantitative PCR detection, EBV-specific antibody testing, and metagenomic next-generation sequencing (mNGS) were performed. RESULTS: Among patients infected with EBV on the ocular surface, the majority were middle-aged individuals in the 31–40 age group. The primary risk factors for onset were keeping pets (10/48), followed by colds (6/48); among those keeping pets, parrots were the most common (5/9). The main clinical manifestations were foreign body sensation (37/54) and yellow discharge (34/54). Common signs included mixed conjunctival hyperemia (31/54), follicles on the lower eyelid conjunctiva (17/54), papillae on the upper eyelid conjunctiva (8/54), and punctate epithelial defects on the cornea (17/54). In most ocular surface scrapings, small round lymphocytes were observed alongside a small number of reactive lymphocytes (44/54), which could simultaneously present with a large number of neutrophils (36/54). There was a significant difference between the presence of yellow discharge and the type of conjunctival hyperemia [Formula: see text]. However, no statistically significant correlation was found between the presence of yellow discharge and the presence of neutrophils in the scraping results [Formula: see text]. Significant differences were found in EBV viral loads among different groups of combined symptoms [Formula: see text] and among different follicle groups [Formula: see text]. No statistically significant correlation was found between the lymphocyte count in the scraping and the EBV viral load in the affected eye [Formula: see text]. CONCLUSION: EBV infection of the ocular surface is prone to concurrent infections; therefore, a detailed medical history inquiry is crucial. Ocular surface tissue scraping examination can rapidly identify viral infection-related inflammatory characteristics and rule out bacterial/fungal infections, providing effective supportive auxiliary diagnostic evidence for viral ocular surface infection, and precise diagnosis of EBV infection needs to be achieved in combination with molecular biological and serological tests.}, } @article {pmid41917329, year = {2026}, author = {Sun, Y and Hu, X and Han, J and Wang, Y and Luo, J and Yu, J and Duan, Y and Wang, X and Liu, J}, title = {Rapid and noninvasive artificial intelligence-assisted diagnostic method for oral squamous cell carcinoma.}, journal = {NPJ digital medicine}, volume = {9}, number = {1}, pages = {}, pmid = {41917329}, issn = {2398-6352}, support = {Grant No. 82272815//The National Natural Science Foundation of China/ ; Grant No. 62322114//The National Natural Science Foundation of China Outstanding Youth Fund/ ; Grant No. YG2023LC06//The Medical Engineering Cross Foundation of Shanghai Jiao Tong University/ ; }, abstract = {Oral squamous cell carcinoma (OSCC) remains the most common head and neck malignancy, for which early detection is critical yet challenging with current invasive methods. This study aimed to establish a comprehensive diagnostic framework for OSCC by integrating proton transfer reaction-time-of-flight mass spectrometry (PTR-TOF-MS) breath analysis and metagenomic sequencing with artificial intelligence (AI). Exhaled breath and saliva samples were collected from participants in a discovery cohort (n = 222) and an external validation cohort (n = 83). Samples were analyzed using PTR-TOF-MS and metagenomic sequencing, and multimodal diagnostic models were constructed and trained on the discovery cohort data. We identified OSCC-specific biomarkers, including methanethiol and Fusobacterium nucleatum, and developed an interactive online platform (https://bio.futurecnn.com/) enabling real-time predictions and biomarker interpretability. The AI-driven diagnostic model achieved excellent accuracy (ROC-AUC: 0.92) in distinguishing OSCC patients from healthy controls in the external set. This approach offers a practical, noninvasive solution for OSCC screening and establishes an adaptable framework for other breath-based diagnostics.}, } @article {pmid41917792, year = {2026}, author = {Karnachuk, OV and Lukina, AP and Avakyan, MR and Panova, IA and Kadnikov, VV and Beletsky, AV and Mardanov, AV and Novikov, AA and Scherbakova, VA and Ravin, NV}, title = {A Novel Slowly Evolving Lineage of the Desulforudis Clade From the Deep Subsurface.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70293}, doi = {10.1111/1462-2920.70293}, pmid = {41917792}, issn = {1462-2920}, support = {24-14-00396//Russian Science Foundation/ ; 22-14-00178-Р//Russian Science Foundation/ ; }, mesh = {Phylogeny ; *Deltaproteobacteria/genetics/classification/isolation & purification ; Genome, Bacterial ; RNA, Ribosomal, 16S/genetics ; *Evolution, Molecular ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; }, abstract = {Endemic to the deep subsurface biosphere sulphate-reducing 'Desulforudis audaxviator' has been called a living microbial fossil due to the high nucleotide sequence identity of its genomes across continents. Evolutionary stasis of this bacterium was established based on the analysis of metagenome assembled genomes, single cell genomes and a single axenic culture. The lack of high-quality reference genomes necessitates efforts to cultivate and isolate pure cultures that could shed light on the hypothetical slow evolution of Desulforudis-clade bacteria deep underground. Molecular signatures demonstrated the presence of Desulforudis-like phylotypes in subsurface environments worldwide. Here we report the isolation of four novel strains of the Desulforudis-clade, all belonging to Desulfosceptrum tomskiensis gen. nov. sp. nov. Four strains of the new species were isolated from deep boreholes in Western Siberia, separated by hundreds of kilometres. Genome comparisons revealed minimal differences between these strains, with average nucleotide sequence identity (ANI) values above 99.9%, low number of SNPs, and near-identical CRISPRs. The bacterium, together with Desulforudis audaxviator BYF[T] gen. nov. sp. nov., deposited in international culture collections, provides a bases for understanding the slow evolution of Bacillota endemic to the deep biosphere.}, } @article {pmid41917812, year = {2026}, author = {Shi, K and Zhang, H and Ji, L and Li, W and Zhang, Q and Liu, N and Liu, J and Guo, S and Huang, S and Chen, Y and Zhang, X and Wang, W and Lei, W and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ma, X and Yang, H and Zhang, W}, title = {Systemic remodeling of the multi-organ virome following Echinococcus infection in mice.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41917812}, issn = {1471-2180}, support = {No. 2023YFD1801300//the National Key Research and Development Programs of China/ ; No. 82341106//the National Natural Science Foundation of China/ ; No. 202208170046//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents-Leading Talents/ ; }, abstract = {UNLABELLED: The interaction between parasitic infection and the host virome represents a frontier issue in microbial ecology, yet how Echinococcus infection affects the multi-organ virome and whether these alterations hold diagnostic or interventional potential remains poorly understood. In this study, we performed viral metagenomic sequencing on gut, liver, and lung samples from both infected and uninfected mice, integrating community structure clustering, diversity indices, and differential analyses, including STAMP and LEfSe. Our results reveal that Echinococcus infection induced significant tissue-specific virome remodeling. Compared to healthy controls, gut virome diversity increased, characterized by marked expansion of the class Caudoviricetes, particularly the family Siphoviridae (LDA > 4), alongside Picornaviridae enrichment (LDA > 4). In contrast, virome diversity decreased in both the liver and lung, with significant enrichment of Reoviridae (LDA > 4) in the liver and Retroviridae (LDA > 4) in the lung, respectively. Conversely, Picobirnaviridae (LDA > 4) was significantly reduced in the infected liver and lung. Based on phylogenetic analysis, Echinococcus infection significantly altered the murine gut viral community, with eukaryotic viruses (e.g., norovirus, picobirnavirus, and picornavirus) detected exclusively in infected animals, while bacteriophage populations remained stable across groups. Phage host prediction further revealed that phages enriched in infected samples targeted opportunistic pathogens (Clostridium septicum, Trueperella pyogenes), whereas control phages predominantly targeted commensals (Bacteroides thetaiotaomicron). Together, these findings demonstrate that Echinococcus infection drives both eukaryotic virus enrichment and a shift in phage predation toward pathogens, suggesting that infection-induced immune modulation creates a permissive environment for viral replication and associated bacterial dysbiosis.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04923-x.}, } @article {pmid41918091, year = {2026}, author = {Luo, S and Chen, X and Guo, S and Hu, S and Dong, Z and Geng, J}, title = {Temperature-driven metabolic adaptation in thermophilic microbial communities of Western Sichuan hot springs.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41918091}, issn = {1471-2180}, support = {2022YFC26023002//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Understanding microbial adaptation to extreme environments remains a key challenge in microbial ecology. Geothermal hot springs, characterized by temperature gradients and varying geochemical conditions, represent valuable natural laboratories for studying microbial diversity, adaptive strategies, and evolutionary mechanisms. However, despite many studies of hot spring communities, how temperature gradients shape key microbial adaptation strategies remains insufficiently understood, limiting our ability to explain survival and function in extreme environments.

RESULTS: Our study investigated microbial community composition and functional profiles across a natural thermal gradient (50–93 °C) in six hot springs on the Western Sichuan Plateau using optimized contig- and MAG-based metagenomic strategies. Enhanced annotation approaches significantly improved taxonomic resolution in these extreme environments. Metagenomic analyses revealed distinct shifts in microbial communities along the thermal gradient: moderate-temperature springs (50–70 °C) were dominated by Pseudomonadota and Bacteroidota, exhibiting heterotrophic flexibility and utilizing the Calvin–Benson–Bassham cycle and diverse nitrogen reduction pathways; high-temperature springs (70–90 °C) were enriched in Chloroflexota, which primarily employed the Wood–Ljungdahl pathway coupled with enhanced sulfur metabolism; and extreme-temperature springs (≥ 90 °C) were characterized by Aquificota and Thermoproteota, relying on specialized autotrophic pathways (rTCA, DH/HH cycles), streamlined nitrogen assimilation, and sulfur oxidation pathways. These thermophilic lineages showed genome streamlining, reduced regulatory complexity, and specialized metabolic strategies, reflecting narrower ecological niches and deeper phylogenetic branches.

CONCLUSIONS: This metagenomic investigation across a temperature gradient in western Sichuan hot springs highlights temperature as an essential driver of microbial community structure, genome evolution, and adaptive specialization. Thermophilic lineages in extreme-temperature environments exhibited streamlined genomes, specialized metabolic functions, and narrower ecological niches, consistent with adaptation to persistent thermal stress. The findings enhance understanding of microbial evolutionary strategies and underscore the ecological significance of temperature-driven adaptation in extreme environments.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04921-z.}, } @article {pmid41918132, year = {2026}, author = {Gao, L and Fang, BZ and Yang, J and Lian, ZH and Chen, Y and Mohamad, OAA and Xu, QY and Liu, YH and Wu, D and Yuan, Y and Abdugheni, R and Li, MM and Wang, P and Ortúzar, M and Li, XY and Huang, JR and Liu, L and Jiang, HC and Shu, W and Hedlund, BP and Li, WJ and Jiao, JY}, title = {Microbial decomposer diversity and metabolic function during the decomposition of brine shrimp carcasses in a saline lake.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41918132}, issn = {2049-2618}, support = {2022B0202110001//Guangdong S&T Program/ ; }, mesh = {Animals ; *Lakes/microbiology/chemistry ; *Archaea/classification/genetics/metabolism/isolation & purification ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Artemia/microbiology/metabolism ; Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; China ; Phylogeny ; Carbon Cycle ; }, abstract = {BACKGROUND: Decomposition of brine shrimp carcasses has a crucial role in carbon cycling of saline lakes, yet the microbial dynamics remain poorly understood.

RESULTS: Here we integrated metagenomics, metatranscriptomics, culturomics, metabolomics, and microcosm experiments to investigate microbial community succession and function during brine shrimp (Artemia sp.) carcass decomposition in Barkol Lake, a hypersaline lake in China. A total of 149 metagenome-assembled genomes (MAGs) and 77 pure culture genomes were recovered across 33 phyla, with 72.12% genomes representing species-level novel lineages. Our results reveal diverse bacterial and archaeal taxa, including novel lineages from CG03, T1Sed10-126 and rare archaeal taxa (Asgardarchaeota, Thermoplasmatota, Nanoarchaeota, and Halobacteriota), involved in degradation of biomacromolecules-proteins, carbohydrates, lipids, and nucleic acids-via extracellular hydrolysis, nutrient transport, and intracellular catabolism. These taxa exhibit substrate preferences, rapidly responding to the breakdown of polysaccharides and proteins, followed by lipids and nucleic acids. Hydrolyzed oligomers are further oxidized by various microbes through fermentation, sulfate reduction, and methanogenesis via metabolic handoffs. Additionally, viral auxiliary metabolic genes (AMGs) further enhance microbial host functions, contributing to key ecological processes such as carbon cycling and stress response. A temporally structured microbial decomposer network (MDN) was observed, driving mineralization cascades from fermentation to sulfate reduction and methanogenesis.

CONCLUSIONS: This study reveals microbial metabolic handoffs and virus-mediated modulation as critical mechanisms for organic matter turnover, expanding the known diversity and function of decomposers in saline ecosystems. Our findings offer new insights into biogeochemical processes in saline lakes and highlight a synergistic microbial decomposer network involving bacteria, archaea, and viruses that collectively drive nutrient cycling during brine shrimp carcass decomposition. Video Abstract.}, } @article {pmid41918376, year = {2026}, author = {Yuan, H and Guan, T and Yuan, Q and Zeng, Q and Yu, J and Cai, Y and Liu, E and Li, Q and Wang, Y}, title = {Molecular-Microbial Cascades Regulate Organic Phosphorus Mineralization in Lake Sediments.}, journal = {Environmental science & technology}, volume = {60}, number = {14}, pages = {10828-10839}, doi = {10.1021/acs.est.5c15353}, pmid = {41918376}, issn = {1520-5851}, mesh = {*Lakes ; *Phosphorus ; *Geologic Sediments/chemistry ; }, abstract = {Organic phosphorus (Po) mineralization is a major internal source of soluble reactive phosphorus (SRP) in lakes, yet the molecular and microbial mechanisms governing this transformation remain poorly understood. Here, we aim to elucidate these mechanisms by integrating excitation-emission fluorescence spectroscopy, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), and metagenomics across two contrasting ecological niches in Taihu Lake, namely the Cyanophyta-dominated and macrophyte-dominated regions. We also supplement our results with the findings from a global meta-analysis. We found that fulvic-associated Po (Fu-Po) dominated sedimentary Po inventories, whereas Po extracted with NaHCO3 (NaHCO3-Po) and microbial biomass Po (biomass-Po) exhibited higher decomposition potential. Fluorescence indices indicated increasing lability with depth, and humic-like materials exhibited a higher tendency to be decomposed under anoxia, accompanied by the accumulation of fulvic-like fractions. FT-ICR-MS revealed proteins and lignins as key constituents of humic-associated Po and Fu-Po, supporting their bioavailability, while NaHCO3-Po was enriched in compounds with lipid-like CHOSP formulas, suggesting greater lability. Metagenomics identified phoD as the most abundant phosphatase-encoding gene, with rare but highly connected phoD-harboring taxa emerging as potential keystone regulators alongside abundant functional groups. Across global lake sediments, alkaline phosphatase activity, Po content, and phoD abundance were found to covary positively, and structural equation modeling highlighted Fu-Po as a disproportionate indirect driver of SRP replenishment via phoD-mediated phosphatase activity. These findings reveal a mechanistic cascade linking molecular composition to phoD-mediated enzymatic potential in Po mineralization, identifying Po bioavailability, rather than inorganic phosphorus pools alone, as a critical driver for reducing internal loading. Targeting this pathway could modulate Po mineralization mechanisms in sediments worldwide, offering valuable insights into the management of lake eutrophication under accelerating nutrient pressures.}, } @article {pmid41918527, year = {2026}, author = {Yang, K and Huang, Y and Gu, L and Li, J and Ma, Y and Gao, P and Qiu, W and Liu, K and Zhang, Y and Liu, H and Xu, J and Xu, J and Liu, T}, title = {Er-Chen Decoction ameliorates metabolic dysfunction-associated steatotic liver disease via gut microbiota-barrier axis-driven hepatic metabolic reprogramming.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1768664}, pmid = {41918527}, issn = {1664-302X}, abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) constitutes a critical global health challenge, with gut-liver axis dysfunction and metabolic endotoxemia serving as key drivers. The traditional Chinese medicinal formula Er-Chen Decoction (ECD) has proven effective in treating metabolic disorders, yet the specific mechanisms by which it modulates gut-liver crosstalk have not been fully elucidated.

METHODS: A mouse model of MASLD was established via a high-fat diet (HFD). The therapeutic effects of ECD were evaluated using the glucagon-like peptide-1 (GLP-1) receptor agonist semaglutide (SE) as a positive control. A comprehensive analysis of the underlying mechanisms of ECD treatment was conducted by integrating fecal metagenomic sequencing, untargeted serum metabolomic profiling, hepatic transcriptomic analysis, and molecular biology assays.

RESULTS: Treatment with ECD markedly ameliorated hepatic steatosis, insulin resistance, and hyperlipidemia, demonstrating a therapeutic efficacy comparable to that of SE. Fecal metagenomic analysis indicated that whereas SE predominantly enriched the genus Akkermansia, the relative abundance of Bifidobacterium and Lactobacillus was markedly and specifically elevated following ECD treatment. Serum metabolomic profiling revealed that ECD specifically activated the tryptophan-indole metabolic pathway, as evidenced by elevated concentrations of indoleacrylic acid and indole-3-acetic acid. Correlation analyses established a strong positive correlation between these indole derivatives and the bacterial genera enriched by ECD. Mechanistically, our findings suggest that elevated indoles activate the aryl hydrocarbon receptor (AHR) in the colon, upregulating tight junction proteins ZO-1 and Occludin and restoring intestinal barrier integrity, thereby significantly reducing serum lipopolysaccharide (LPS) levels. In hepatic tissue, the diminished LPS influx alleviated the suppression of DNA methyltransferase 3B (DNMT3B), thereby promoting the epigenetic silencing of the lipid droplet fusion protein CIDEA and inhibiting pathological hepatic lipogenesis.

CONCLUSION: Our findings elucidate a novel mechanism through which ECD may ameliorate MASLD via the distinctive "gut microbiota-indole-barrier" axis. In contrast to SE, ECD modulates gut microbiota composition to boost indole production and subsequently activate AHR signaling. This activation inhibits endotoxin translocation and induces hepatic DNMT3B-mediated epigenetic reprogramming to reverse hepatic steatosis. These results offer scientific evidence supporting the potential of ECD as an effective therapeutic strategy for MASLD.}, } @article {pmid41918743, year = {2026}, author = {Schröder Alvarez, L and Conejeros, I and Espinosa, G and Salinas-Varas, C and Ott, B and Weigel, M and Imirzalioglu, C and Fritzenwanker, M and Windhorst, AC and Hain, T and Taubert, A and Hermosilla, C and Wagenlehner, F}, title = {Presence of neutrophil extracellular traps (NETs) in different types of human urinary tract infections (UTI). A pilot study.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1745166}, pmid = {41918743}, issn = {1664-3224}, mesh = {Humans ; *Extracellular Traps/immunology/metabolism ; Female ; Pilot Projects ; Male ; *Urinary Tract Infections/immunology/urine/microbiology ; *Neutrophils/immunology/metabolism ; Adult ; Middle Aged ; Aged ; Leukocyte Elastase ; Bacteriuria/immunology/urine ; Biomarkers ; Pyelonephritis/immunology/urine ; RNA, Ribosomal, 16S/genetics ; }, abstract = {INTRODUCTION: Activated polymorphonuclear neutrophils (PMN) release neutrophil extracellular traps (NETs) composed of a web-like DNA core, concomitant with nuclear histones, granular peptides and enzymes. NETs in human urine and their potential role in human urinary tract infections (UTI) pathogenesis is still understudied. This pilot study aimed to analyze presence of NETs in urine samples of patients with different types of UTI.

METHODS: Urine and blood samples were collected from three cohorts: group (A) included females (n = 24) with cystitis (n = 10), pyelonephritis (n = 6), and asymptomatic bacteriuria (n = 8); group (B) composed of males with catheter-associated UTI (n = 20) and a control group (C) consisting of healthy patients of mixed gender (n = 20). NETs in urine samples were confirmed by immunofluorescence-based detection of neutrophil elastase and citrullinated histone. The presence of granular enzymes (myeloperoxidase, cathelicidin), calprotectin (subunits S100A8, S100A9) and CD15[+] PMN were detected by ELISA, western blot and flow cytometry, respectively. To study potential associations of NETs with the respective UTI microbiome, bacterial spectrum of each urine sample was estimated by 16S rRNA gene analysis.

RESULTS AND DISCUSSION: On average, 23.29% ± 16.89% of PMN forming NETs were detected in group A [subgroups cystitis (27.72% ± 17.88%), pyelonephritis (22.75% ± 12.91%), asymptomatic bacteriuria (18.17% ± 17.14%)] and 30.63% ± 17.88% in group B, with no differences observed between UTI groups, including patients with asymptomatic bacteriuria. For the control group (group C), a low incidence of NET-releasing cells was observed (0.32% ± 1.42%), resulting in a significant difference (p < 0.05) when compared to all UTI groups studied. Furthermore, different NET-phenotypes [i. e. spread NETs (sprNETs), diffuse NETs (diffNETs) and aggregated NETs (aggNETs)] were detected in both UTI groups. The presence of NET-associated proteins was confirmed in all UTI groups, but absent in the control samples. Microbiome analyses revealed a reduced microbial variability within UTI samples with the predominance of the bacterial family Enterobacteriaceae. Overall, PMN-derived NETs were consistently found in all UTI samples, suggesting a role of NETs in diverse UTI pathologies. Future studies should investigate its utility as an inflammatory biomarker in clinical human UTI.}, } @article {pmid41918857, year = {2026}, author = {Erözden, AA and Tavşanlı, N and Demirel, G and Sanli, NO and Çalışkan, M and Arıkan, M}, title = {MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20990}, pmid = {41918857}, issn = {2167-8359}, mesh = {*Antineoplastic Agents/pharmacology ; *Peptides/genetics/pharmacology ; Prediction Algorithms ; *Metagenome ; Humans ; *Genome, Microbial ; Computational Biology/methods ; Algorithms ; Software ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Anticancer peptides (ACPs) are increasingly recognized as promising therapeutic candidates due to their ability to selectively target cancer cells. However, the systematic discovery of novel ACPs, particularly from high-throughput sequencing datasets, remains hindered by technical and methodological limitations. Current prediction frameworks require pre-extracted peptide sequences, involve manual preprocessing, and yield variable results, which restricts their applicability for large-scale, data-driven discovery.

METHODS: To address these limitations, we developed MetaPepticon, a modular, end-to-end pipeline for the discovery of ACP candidates from diverse sequencing inputs, including raw genomic, metagenomic, transcriptomic, and metatranscriptomic reads, as well as assembled contigs and peptide sequences. MetaPepticon automates quality control, filtering, assembly, small open reading frame prediction, ACP classification using multiple predictive algorithms, and in silico toxicity filtering.

RESULTS: MetaPepticon enables scalable and reproducible ACP prediction from raw sequences through integration of multiple predictors within a configurable agreement framework. Applied to 41,171 microbial genomes and 4,072,884 peptides, MetaPepticon identified 10,725 moderate-agreement ACP candidates, including 4,590 novel, non-toxic peptides. MetaPepticon expands the practical applicability of existing ACP prediction methods to high-throughput sequencing data and is freely available at: https://github.com/arikanlab/MetaPepticon.}, } @article {pmid41918874, year = {2026}, author = {Su, X and Yang, J and Le, Z and Xiao, J and Zhao, D}, title = {Integrative multi-omics analysis reveals probiotic-induced microbiota shifts in women with gestational diabetes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1782744}, pmid = {41918874}, issn = {2235-2988}, mesh = {Humans ; Female ; *Diabetes, Gestational/microbiology ; *Probiotics/administration & dosage ; Pregnancy ; Multiomics ; *Gastrointestinal Microbiome/drug effects ; Metabolomics ; Adult ; Metagenomics ; }, abstract = {INTRODUCTION: Gestational diabetes mellitus (GDM) is a common pregnancy disorder. It is associated with impaired glucose tolerance and insulin resistance, increasing the potential risks for both maternal and fetal complications. GDM is associated with an increased risk of type 2 diabetes later in life. Management is a big issue in maternal health. New work has underscored the role of the gut microbiota in metabolism and immune function. This indicates that probiotics might exert their mode of action through modulating the microbiota and controlling metabolism.

METHODS: This study employs a multi-omics strategy to assess the impact of probiotic administration on gut microbiota composition, metabolomic profiles, and host gene expression in GDM women. Women with GDM received probiotics for 8 weeks. Metagenomic sequencing quantified alterations of gut microbiota composition and LC-MS provided untargeted metabolomics in serum and urine. Gene expression was analyzed by qRT-PCR in reference to other physiological factors such as insulin signaling, inflammation, oxidative stress, and gut barrier. Data integration was performed using Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and network analysis, then pathway enrichment analysis was conducted with KEGG and MetaboAnalyst.

RESULTS: The supplementation of probiotics resulted in a significant change of gut microbiota (Lactobacillus 7.6-fold; Bifidobacterium 6.4-fold). Escherichia/Shigella was reduced. The amounts of short-chain fatty acids (SCFAs), especially butyrate and acetate, were increased 3.1 fold and 2.5 fold, respectively. In a gene expression assessment, the insulin receptor and AKT increased 2.5- and 1.9-fold higher, respectively, indicating greater insulin sensitivity. Levels of TNF-α and IL-6 decreased; however, genes related to gut barrier function (ZO-1, CLDN1) increased.

DISCUSSION: The administration of probiotic has a great impact on gut microbiome, metabolic activity, and host gene expression in women with GDM. Our data indicate that probiotics may represent a non-invasive and safe treatment for gestational diabetes through enhancing insulin sensitivity, anti-inflammatory environment, and gut health status. Larger confirmatory studies are needed to corroborate these findings and augment future clinical application of probiotics in GDM patients.}, } @article {pmid41918946, year = {2026}, author = {Hsiao, CC and Chen, CH and Liu, CS and Wang, JY and Lin, CY and Yang, KD and Lee, CH and Lin, TT and Lin, CJ and Tsai, YG}, title = {Airway microbial dysbiosis and oxidative mitochondrial DNA damage in the development of bronchopulmonary dysplasia.}, journal = {ERJ open research}, volume = {12}, number = {2}, pages = {}, pmid = {41918946}, issn = {2312-0541}, abstract = {BACKGROUND: This study investigated the association between airway microbiome composition, oxidative mitochondrial DNA (mtDNA) damage and the development of bronchopulmonary dysplasia (BPD) in preterm infants.

METHODS: A prospective cohort study enrolled 82 very low birth weight preterm infants (<32 weeks' gestation). Tracheal aspirates (TA) were collected at birth and on postnatal day 28. Airway microbial diversity and composition were assessed using 16S rRNA sequencing. Oxidative mtDNA damage was measured using 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels in TA samples. We used PICRUSt2-based metagenome predictions from 16S rRNA gene sequencing of TA samples, with functional pathway annotations based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

RESULTS: Infants who developed BPD (n=25) had lower gestational age, birth weight and prolonged ventilatory support (p<0.05). Oxidative mtDNA damage was significantly higher in infants with BPD, particularly in moderate-to-severe cases (p<0.05). BPD was associated with reduced microbial alpha diversity and distinct beta diversity clustering. Infants with BPD exhibited higher relative abundance of Proteobacteria and lower relative abundance of Firmicutes, with enrichment of Stenotrophomonas, Acinetobacter and Serratia (p<0.05). By day 28, KEGG-based functional predictions revealed enrichment in microbial pathways related to bacterial motility proteins, circadian rhythm signalling pathway, MAPK signalling pathway and α-linolenic acid metabolism. Proteobacteria abundance correlated positively with oxidative mtDNA damage (r=0.49, p<0.01).

CONCLUSIONS: Airway microbial dysbiosis and oxidative mtDNA damage are strongly associated with BPD severity. Targeting oxidative stress and microbiome modulation may offer potential strategies for BPD prevention and management.}, } @article {pmid41919078, year = {2026}, author = {Fan, Y and Qin, H and Liu, J and Abbas, M and Yang, C and Cheng, H and Dong, X}, title = {Lactobacillus acidophilus alleviates slow transit constipation by modulating 5-HT pathway and gut microbial composition.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1775405}, pmid = {41919078}, issn = {2296-861X}, abstract = {INTRODUCTION: Slow transit constipation (STC) is a chronic disease characterized by delayed intestinal transit and weakened spontaneous contractions of colonic smooth muscle. Current pharmacological treatments are often associated with adverse effects, highlighting the need for safe and more effective therapeutic strategies. This study investigated the potential role of Lactobacillus acidophilus (L. acidophilus) in regulating intestinal motility and alleviating STC, as well as the underlying mechanism.

METHODS: A humanized mouse model was established by intragastric administration of fecal bacterial suspension from STC patients on alternate days, in order to evaluate the effect of L. acidophilus on constipation. The regulatory effect of L. acidophilus on intestinal motility was evaluated using defecation parameters. Colon histopathology was assessed by hematoxylin-eosin (H&E) staining. Immunohistochemistry (IHC), RT-qPCR, ELISA, and in vitro cell experiments were performed to examine the inflammatory cytokine levels and changes in the 5-hydroxytryptamine (5-HT) signaling pathway. In addition, metagenomic sequencing was used to analyze changes in the intestinal microbial community.

RESULTS: The results showed L. acidophilus treatment significantly enhanced intestinal peristalsis and maintained the intestinal barrier by up-regulating Occludin expression and down-regulating inflammatory cytokines, including TNF-α and IL-1β, thereby suppressing inflammatory responses. Both in vivo and in vitro experiments showed that L. acidophilus affected the synthesis and release of 5-HT by regulating the expression of TPH1 and the mechanosensitive ion channel Piezo1. Additionally, L. acidophilus reshaped the intestinal microbial community structure and altered the inter-bacterial interaction network, which was closely associated with improved intestinal motility.

CONCLUSION: Our current research reveals that constipation symptoms by L. acidophilus through the gut microbiota composition, intestinal barrier, and the 5-HT signaling pathway. These findings provide a strong theoretical basis for the development of L. acidophilus as a potential therapeutic strategy for the treatment of STC.}, } @article {pmid41919237, year = {2026}, author = {Zheng, D and Li, L and Qi, H and Jiao, XF and Wang, K}, title = {Successful azithromycin treatment of Chlamydia psittaci pneumonia in second-trimester pregnancy resulting in term delivery: a case report.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1780706}, pmid = {41919237}, issn = {1663-9812}, abstract = {Psittacosis pneumonia is a zoonotic infection caused by Chlamydia psittaci (C. psittaci), primarily transmitted via contact with infected avian species. Diagnostic challenges arise from the inherent difficulties of pathogen culture and serological testing, frequently resulting in misdiagnosis or underdiagnosis. Gestational psittacosis, in particular, is a rare but life-threatening condition, with delayed diagnosis conferring risk of severe maternal and fetal complications. We present a case of C. psittaci pneumonia in a 24-week pregnant woman, with the diagnosis confirmed by metagenomic next-generation sequencing (mNGS). Empirical intravenous azithromycin (0.5 g daily) was promptly initiated for 3 days, leading to rapid symptomatic resolution. After a 2-day interruption, targeted oral azithromycin (0.5 g daily) was restarted for an additional 3 days following pathogen confirmation via mNGS. The patient was successfully discharged after a 10-day hospital stay under multidisciplinary management. She finally gave birth to a healthy baby girl at 40 weeks and 3 days of gestation, with favorable maternal and neonatal outcomes. To our knowledge, this represents one of the few reported cases of full-term delivery following azithromycin monotherapy for gestational psittacosis. It provides valuable insights into the diagnosis and management of gestational psittacosis, emphasising the importance of multidisciplinary involvement in preserving maternal and fetal safety.}, } @article {pmid41919563, year = {2026}, author = {Afridi, R and Ibrahim, M and Yaqoob, M and Ahmad, W}, title = {Synergistic Effect of Glyphosate and Polyethylene Microplastics on Culturable Gut Microbiota Alterations in Zebrafish.}, journal = {Environmental toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1002/tox.70091}, pmid = {41919563}, issn = {1522-7278}, abstract = {The coexistence of emerging pollutants, that is, microplastics (MPs) and pesticides poses significant threat to aquatic organisms. This study investigated the combined effects of polyethylene microplastics (PE-MPs) and glyphosate on the gut microbiome of zebrafish. Following a 21-day exposure, 16S rRNA sequencing revealed that co-exposure caused the most significant disruption, surpassing the individual effects of each stressor. Co-exposure resulted in the lowest alpha diversity and a distinct microbial community structure, characterized by the depletion of A. veronii and a marked enrichment of opportunistic pathogens like A. hydrophila. Clear separation of all exposed groups from controls, with the co-exposure group forming the most distinct cluster was observed in non-metric multi-dimensional scale analysis. Specifically, a higher number of ASVs were differentially abundant in the co-exposure group compared to the individual exposures. In the MPs group, Aeromonas species were markedly replaced by Enterobacter species. Glyphosate significantly enriched A. hydrophila species in the gut. Treatment-specific clustering, with Enterobacter species associated with MPs, and A. hydrophila with glyphosate and co-exposure groups were observed in Heatmap analysis. The findings indicate that microplastics not only act as direct stressors but also as glyphosate carriers, leading to amplified, non-additive shifts in the gut microbiome and posing a heightened ecological risk.}, } @article {pmid41919955, year = {2026}, author = {Pan, W and Tang, S and Wanek, W and Liu, X and Zhou, J and Gregory, AS and Marsden, KA and Chadwick, DR and Liang, Y and Wu, L and Jones, DL and Ma, Q}, title = {Organic Fertilization Promotes the Microbial Formation of Moderately Active Soil Phosphorus Pools to Sustain Phosphorus Availability: Insights from 180 years of Fertilization.}, journal = {Environmental science & technology}, volume = {60}, number = {17}, pages = {12918-12929}, doi = {10.1021/acs.est.5c12810}, pmid = {41919955}, issn = {1520-5851}, mesh = {*Phosphorus ; *Fertilizers ; *Soil/chemistry ; *Soil Microbiology ; }, abstract = {Phosphorus (P) fertilization is essential for crop production, but most applied P is rapidly fixed into mineral-associated forms. Although fertilization regulates P distribution in soils, its effects on microbe-mediated processes that regulate P availability and stabilization remain unclear. Here, we investigated P transformations under organic fertilization (FYM), inorganic fertilization (NPK), and no fertilization (NIL) using the 180 year Broadbalk experiment. Through [33]P isotopic tracing, metagenomics, and enzymatic profiling, we found that FYM and NPK stimulate distinct P transformation pathways. FYM, through sustained organic carbon inputs, enhanced microbial immobilization and phosphatase activity, causing a 41% reduction in stable P formation and 47% increase in moderately active P levels and shifting P dynamics toward more bioavailable forms. NPK fertilization reduced pH and limited microbial carbon availability; 33% of [33]P was recovered in the stable P fraction, indicating abiotic immobilization into inorganic P pools. The microbial community under NPK adapted to P fixation by enriching P-cycling-related genes and acid-tolerant taxa, enhancing P turnover relative to NIL but preventing long-term immobilization less effectively than FYM. Thus, organic fertilization maintains P in more biologically available forms and mitigates abiotic P fixation; our research provides a mechanistic foundation for more efficient and resilient P management in agroecosystems.}, } @article {pmid41919968, year = {2026}, author = {Zhou, C and Wang, S and Zhao, H and Wang, S and Jiang, L and Yu, C}, title = {Metagenomic mining reveals extensive novelty, enhanced biodegradation potential, and untapped biosynthetic capacity in Chinese oilfield microbiomes.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {4}, pages = {e0039226}, pmid = {41919968}, issn = {1098-5336}, support = {52374051//National Natural Science Foundation of China/ ; U24B2037//National Natural Science Foundation of China/ ; }, mesh = {Biodegradation, Environmental ; China ; *Oil and Gas Fields/microbiology ; *Microbiota/genetics ; *Metagenome ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; Phylogeny ; Petroleum ; Genome, Bacterial ; }, abstract = {Oil reservoir microorganisms represent a vast and largely unexplored reservoir of biological diversity and functional potential, yet comprehensive studies on their genomic and metabolic characteristics remain limited. To address this gap, we collected 101 metagenomic sequencing samples from 13 distinct oilfields across China. Through extensive de novo assembly and binning processes, we successfully reconstructed 3,057 medium and high-quality metagenome-assembled genomes (MAGs), providing an unprecedented genomic resource for reservoir microbiome research. Strikingly, 73.77% of these MAGs correspond to novel taxa at the species level, highlighting the significant unexplored microbial diversity in these environments. Detailed genomic analysis revealed that MAGs classified under the class Planctomycetia exhibited notably larger genome sizes, primarily driven by the expansion of specific gene families, suggesting adaptive evolutionary strategies in hydrocarbon-rich environments. Furthermore, we identified 68 genes implicated in anaerobic alkane biodegradation pathways, with samples from the Shengli oilfield demonstrating particularly enhanced biodegradation potential, indicating site-specific functional adaptations. Beyond biodegradation, our study uncovered three MAGs assigned to the genus Tistrella, which harbored a remarkable abundance of biosynthetic gene clusters (BGCs) for secondary metabolites. Additionally, 14 candidate antimicrobial peptides (cAMPs) were detected, signifying the potential for novel bioactive compound discovery. Critically, both the Tistrella MAGs and cAMPs were identified for the first time within petroleum reservoir ecosystems, underscoring the unique biotechnological value of these environments. This research not only expands our understanding of oil reservoir microbial communities but also emphasizes their substantial implications for industrial applications, including bioremediation, antimicrobial development, and sustainable resource management.IMPORTANCEThis study provides a groundbreaking genomic exploration of oil reservoir microbiomes across 13 Chinese oilfields, reconstructing 3,057 medium and high-quality metagenome-assembled genomes (MAGs). Remarkably, 73.77% of these MAGs represent novel species, revealing vast unexplored microbial diversity. We observed genome expansion in Planctomycetia lineages and identified 68 genes involved in anaerobic alkane degradation, with heightened biodegradation potential in Shengli oilfield samples. Crucially, we discovered three Tistrella MAGs rich in biosynthetic gene clusters (BGCs) for secondary metabolites and 14 candidate antimicrobial peptides (cAMPs), both reported for the first time in petroleum reservoirs. These findings highlight the immense biotechnological potential of reservoir microbiomes, offering new pathways for bioremediation strategies in oil-contaminated environments and novel sources for antimicrobial discovery. This work underscores the critical need for continued investigation into these unique ecosystems to harness their functional capabilities for energy sustainability and pharmaceutical innovation.}, } @article {pmid41920399, year = {2026}, author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Rahman, R and Hassan, J and Rahman, MS and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT}, title = {Rooftop and surface garden soils in Bangladesh harbor diverse resistome profiles.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {4}, pages = {}, pmid = {41920399}, issn = {1573-2959}, support = {Grant ID: Proc-451-05//This work was conducted as part of the CGIAR Research Initiative on Resilient Cities Through Sustainable Urban and Peri-urban Agri-food Systems and is supported by contributors to the CGIAR Trust Fund (https://www.cgiar.org/funders)./ ; }, mesh = {*Soil Microbiology ; Bangladesh ; *Soil/chemistry ; *Drug Resistance, Microbial/genetics ; *Environmental Monitoring ; *Gardens ; Bacteria/genetics ; Agriculture ; Metagenome ; Drug Resistance, Bacterial/genetics ; }, abstract = {Despite the growing expansion of urban agriculture, the diversity, composition, and antimicrobial resistance (AMR) profiles (i.e., resistome) of microbial communities in rooftop and surface garden soils in Bangladesh remain insufficiently characterized, limiting our understanding of their potential role as reservoirs and disseminators of AMR. In this study, shotgun metagenome sequencing was applied to 27 soil samples, including 7 from Dhaka rooftop gardens (DRG), 6 from Dhaka surface gardens (DSG), 8 from Gazipur rooftop gardens (GRG), and 6 from Gazipur surface gardens (GSG) to comprehensively characterize their resistome profiles. We identified 88 antibiotic resistance genes (ARGs), of which 19 (21.6%) were shared across all sites, and found significant differences in resistome composition by garden type (p = 0.04). Rooftop soils harbored more ARGs (DRG, 50; GRG, 48) than surface soils (DSG, 40; GSG, 41) and were dominated by glycopeptide resistance genes, collectively representing 62.43-74.07% of ARGs. Rooftop garden soils were also enriched in efflux pumps (adeF, 45.21% of rooftop ARGs) and ribosomal-protection-related oxazolidinone resistance gene O23S (62.13% in GRG). Conversely, surface soils featured a higher abundance of genes mediating antibiotic inactivation, such as CATA (11.64% in DSG) and fosBx1 (5.94% of surface ARGs), as well as those conferring co-resistance to biocides (qacG) and metals. The efflux pump gene adeF also remained a significant component of the surface resistome (24.33% of surface ARGs). Geographic location also modulated resistome composition. Garden soils from Gazipur emerged as notable hotspots, characterized by extremely high abundances of tetracycline efflux pumps (TET45) and multiple copper resistance genes and regulators (e.g., COPA, YCNJ, CSOR). Key ARG carriers included Bacillus licheniformis, B. paralicheniformis, Pseudomonas sabulinigri, and Paenibacillus spp. Spearman correlation analyses revealed strong positive associations (r = 1.0) between specific taxa and resistance mechanisms, as well as co-occurrence patterns among antibiotic, biocide, and metal resistance genes. Collectively, these results indicate that garden soils represent important reservoirs of ARGs, with resistome architecture influenced by both garden type and location, highlighting the necessity for sustainable management practices and a One Health approach to environmental resistome surveillance.}, } @article {pmid41921236, year = {2026}, author = {Lu, D and Ping, C and Jia, D and Liu, J and Wang, H and Song, Y and Cai, X}, title = {Mechanism of Legionella pneumophila-induced liver injury via gut microbiota translocation under immunosuppression.}, journal = {Pathology, research and practice}, volume = {282}, number = {}, pages = {156456}, doi = {10.1016/j.prp.2026.156456}, pmid = {41921236}, issn = {1618-0631}, mesh = {Animals ; *Legionnaires' Disease/immunology/microbiology/pathology ; *Legionella pneumophila/pathogenicity/immunology ; *Gastrointestinal Microbiome/immunology ; Guinea Pigs ; *Bacterial Translocation ; *Immunocompromised Host ; *Liver/pathology/microbiology/immunology ; Apoptosis ; Disease Models, Animal ; Dysbiosis/microbiology ; }, abstract = {Legionnaires' disease presents substantial clinical challenges in immunocompromised patients, with the pathogenesis of multi-organ dysfunction remaining poorly understood. Through an immunosuppressed guinea pig model, we demonstrate that Legionella pneumophila (Lp) infection triggers a systemic pathological cascade that extends beyond pulmonary damage. Our results show that Lp infection not only induces severe pulmonary inflammation and endothelial barrier disruption but also initiates gut-liver axis injury mediated by intestinal microbiota dysbiosis. Metagenomic sequencing revealed specific enrichment of Anoxybacillus kestanbolensis and Geobacillus vulcani in both intestinal and hepatic tissues post-infection, indicating microbial translocation. This bacterial dissemination was associated with enhanced hepatocyte apoptosis and exacerbated liver injury. Mechanistically, we demonstrate that Lp infection compromises intestinal epithelial integrity, promotes translocation of enteric pathogens, and subsequently activates hepatic apoptotic pathways, thereby aggravating systemic inflammation and multi-organ failure. These findings elucidate the gut microbiota-gut-liver axis as a pivotal mechanism in Lp-induced systemic damage and suggest potential therapeutic targets for severe Legionnaires' disease in immunocompromised hosts.}, } @article {pmid41921318, year = {2026}, author = {Wang, F and Shi, C and Zhang, W and Chen, Y and Chen, Z and Yang, S and Zhang, J and Liu, W and Cao, W}, title = {Fresh-seawater interface shapes nitrogen fate in a subtropical estuary: Insights from multi-isotopic and metagenomic analyses.}, journal = {Water research}, volume = {298}, number = {}, pages = {125836}, doi = {10.1016/j.watres.2026.125836}, pmid = {41921318}, issn = {1879-2448}, mesh = {*Estuaries ; *Nitrogen ; *Seawater/chemistry ; Metagenomics ; Fresh Water ; Nitrates ; Rivers ; Nitrogen Cycle ; }, abstract = {Estuaries, the key transitional interface between freshwater rivers and saline seas, are hotspots of nitrogen (N) cycling processes. In this study, we integrated multi-isotope and metagenomic sequencing techniques to characterize nitrate (NO3[-]) sources, mixing and transformation processes, and the regulatory roles of microbial functional genes in different seasons and subzones in the Jiulong River estuary, a typical subtropical estuary. NO3[-]-N was the dominant form of dissolved inorganic N (70.31-91.70 %), with significantly lower concentrations in the seaward subzone than those in other subzones. Hydrochemical parameters, dual-isotope (δ[15]N-NO3[-] and δ[18]O-NO3[-]) signatures, and MixSIAR model indicated that soil N was the largest contributor to NO3[-] (44.7 %), followed by M&S and groundwater in the riverward subzone. The upstream inflow from the riverward subzone accounted for 64.6 % of NO3[-] sources in the mixing subzone. Extensive aquaculture activities in the estuary were the dominant NO3[-] source (44.8 %), followed by M&S and the upstream inflow from the mixing subzone in the seaward subzone. Nitrate reduction genes dominated the N-cycling functional genes and mediated the primary NO3[-] transformation pathways. The PLS-PM model indicated dissimilatory nitrate reduction to nitrite (DNRN) genes had a significant positive effect (0.892) on NO3[-] concentrations and influenced competition between dissimilatory nitrate reduction to ammonium (DNRA) and denitrification for substrates through the C/N ratios. The lower nosZ/narG ratios and higher nitrous oxide concentrations in the riverward and mixing subzones led to more susceptibility to incomplete denitrification, whereas the higher DNRA/DNRN ratios and the significant positive correlation between DNRA and the C/N ratios favored DNRA in the seaward subzone. The lower temperatures and river flows in winter were significantly lower than those in other seasons, which constrained N transforming capacity and resulted in the lowest dissolved nitrous oxide concentration. Therefore, salinity and temperature regulated the primary N-cycling processes by reshaping the composition of functional genes. Overall, this study clarifies the N sources and transformation pathways and provides a systematic theoretical foundation for the development of subzone-based management strategies for estuarine ecosystems.}, } @article {pmid41921321, year = {2026}, author = {Sudarshan, AS and Konstantinidis, KT and Pinto, AJ}, title = {Gene-centric analysis of Raskinella chloraquaticus reveals a functionally conserved taxonomic group in global drinking water distribution systems.}, journal = {Water research}, volume = {298}, number = {}, pages = {125784}, doi = {10.1016/j.watres.2026.125784}, pmid = {41921321}, issn = {1879-2448}, mesh = {*Drinking Water/microbiology ; Phylogeny ; }, abstract = {A recent metagenomic survey of drinking water systems revealed that a highly prevalent and dominant uncultured bacterial genus (Raskinella) was represented globally by a single species (Raskinella chloraquaticus). R. chloraquaticus comprises of two sub-species groups, Lineages 1 and 2, the former representing a globally prevalent genomovar. The objective of this study was to perform comparative analysis of the gene content of R. chloraquaticus to characterize the gene-level diversity and determine factors shaping the diversity of this species. Pangenome analysis revealed that R. chloraquaticus possesses a core set of genes that constitute a major portion (87.74%) of the known gene content of the genome. Furthermore, most of the gene diversity of R. chloraquaticus is associated with Lineage 2 organisms, which consists of at least four distinct genomovars. Lineage 1 organisms consist of a higher proportion of identical genes than would have been expected if changes primarily occurred through random mutations and thus is potentially indicative of recombination. In contrast, Lineage 2 organisms appear to have emerged through random mutations and display stronger geographic preference. These results indicate that homologous recombination and geographic isolation likely shape the genetic repertoire of R. chloraquaticus. Further, the high level of gene conservation in R. chloraquaticus may be reflective of highly selective environment in drinking water systems. Thus, R. chloraquaticus may represent a model organism to probe selective pressures shaping the drinking water microbiome.}, } @article {pmid41921326, year = {2026}, author = {Liu, X and Li, C and Zhao, Y and Li, X and Zhang, Q and Zhang, L and Peng, Y}, title = {A novel approach for achieving high enrichment of anammox and nitrogen removal rate in municipal wastewater treatment: A pure biofilm process.}, journal = {Water research}, volume = {298}, number = {}, pages = {125838}, doi = {10.1016/j.watres.2026.125838}, pmid = {41921326}, issn = {1879-2448}, mesh = {*Biofilms ; *Nitrogen/metabolism/isolation & purification ; *Wastewater/microbiology ; *Waste Disposal, Fluid/methods ; Bioreactors/microbiology ; Sewage/microbiology ; }, abstract = {Against the backdrop of global carbon neutrality goals and increasingly stringent pollutant discharge standards, the anammox nitrogen removal process has gained significant attention due to its high efficiency, energy-saving, and environmentally friendly characteristics. The current mainstream wastewater treatment technologies still encounter challenges in enriching anaerobic ammonium-oxidizing bacteria (AnAOB) and managing the disposal of substantial amounts of residual sludge. The pure biofilm process has garnered significant attention as the primary focus for autotrophic nitrogen removal transformation in wastewater treatment plants (WWTPs), owing to its ability to efficiently enrich AnAOB and produce low amounts of sludge. This study innovatively proposed a novel pure biofilm process and explored the self-enrichment mechanism of AnAOB in this system. Over 200 days of municipal wastewater treatment under a low C/N ratio (average of 3), the effluent ammonia nitrogen removal efficiency (ARE) and total nitrogen removal efficiency (NRE) achieved 97.72 ± 1.50 % and 94.27 ± 2.92 %, respectively. Long-term operation and batch experiments revealed that carbon source regulation is crucial for the performance of pure biofilm systems. Furthermore, the pure biofilm system demonstrates greater resilience to organic loading shocks compared to floc sludge and hybrid systems. QPCR and 16S rRNA sequencing confirmed the successful enrichment of AnAOB (pre-anoxic:8.94 %, post-anoxic:8.61 %), with anammox contributing to an impressive 81.10 % of nitrogen removal. Additionally, fluorescence in situ hybridization combined with confocal laser scanning microscopy (FISH-CLAM) technology demonstrated a spatially uniform distribution of AnAOB within the system, in contrast to hybrid systems. Metagenomic sequencing revealed the carbon and nitrogen metabolic pathways of functional bacteria in the pure biofilm system, showing that AnAOB's metabolic diversity and ecological niche adaptation within the biofilm structure drove their self-enrichment. Finally, microelectrode measurements of N2O production in the pure biofilm system confirmed its substantial potential for emission reduction. This work offers a practical solution for WWTPs aiming to reduce energy consumption and transition from heterotrophic to autotrophic nitrogen removal processes.}, } @article {pmid41921531, year = {2026}, author = {Li, W and Lv, M and Cheng, M and Han, Y and Yu, H and Huang, Y and Meng, D and Xu, X and Sun, L and Lu, Z and Liu, Q}, title = {Feasibility of low-biomass exhaled breath microbiome sequencing using a PDC-sampler in febrile and healthy individuals.}, journal = {Journal of breath research}, volume = {20}, number = {2}, pages = {}, doi = {10.1088/1752-7163/ae5a51}, pmid = {41921531}, issn = {1752-7163}, mesh = {Humans ; Breath Tests/methods/instrumentation ; *Microbiota/genetics ; *Exhalation ; Feasibility Studies ; Female ; Male ; Adult ; *Fever/microbiology ; Middle Aged ; Healthy Volunteers ; }, abstract = {Exhaled breath is a noninvasive and repeatable biological matrix offering new opportunities for respiratory microbiome analysis, yet its extremely low microbial biomass limits current high-throughput applications. Building on our previously developed phase-change drywall cyclone sampler (PDC-sampler), which integrates condensational growth with dry-wall cyclone separation, we established a validated workflow for efficient aerosol collection and multi-Omics sequencing of exhaled breath. Using this platform, exhaled breath from 15 febrile patients and 6 healthy volunteers was analyzed via shotgun metagenomic and 16 S rRNA sequencing to assess microbial composition, diversity, and functional features. The PDC-sampler significantly increased microbial DNA yield, enabling stable detection of bacterial taxa dominated byPseudomonadota, Bacillota, Bacteroidota, andActinomycetota. Functional annotations and diversity metrics revealed distinct microbial and metabolic patterns between individuals, confirming the platform's analytical sensitivity and biological representativeness. This work experimentally validates the feasibility of exhaled breath microbiome sequencing using the PDC-sampler, providing a practical and generalizable framework for noninvasive respiratory microecology studies and future diagnostic applications.}, } @article {pmid41921761, year = {2026}, author = {Nee, GW and Agrawal, K and Dalan, R and Kasahara, K and Xiang Darren, LY and Ali, Y and Wong, S}, title = {The oral-gut microbiome axis in diabetes mellitus: a systematic review and emerging clinical perspectives.}, journal = {Diabetes research and clinical practice}, volume = {235}, number = {}, pages = {113232}, doi = {10.1016/j.diabres.2026.113232}, pmid = {41921761}, issn = {1872-8227}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mouth/microbiology ; *Diabetes Mellitus/microbiology/metabolism ; Dysbiosis/microbiology ; }, abstract = {Emerging evidence suggests that diabetes mellitus (DM) is not only a metabolic disorder but also a mucosal disease shaped by microbial interactions across body niches. This review synthesizes current evidence on the oral-gut microbiome axis in DM, focusing on microbial transmission, functional overlap, and clinical relevance. A systematic search of six databases identified studies profiling paired oral and gut microbiomes in individuals with diabetes. Across included studies, consistent findings demonstrate concurrent dysbiosis in both niches. Notably, oral-associated taxa such as Streptococcus, Prevotella, Fusobacterium, and Porphyromonas were detected in the gut, suggesting ectopic colonization and inter-niche microbial transmission. Functional analyses revealed shared disruptions in key metabolic pathways, including short-chain fatty acid production and glycine betaine metabolism, with downstream effects on inflammation and insulin resistance. These microbial alterations correlated with established clinical markers such as HbA1c, fasting glucose, and inflammatory indices. Emerging machine-learning models integrating oral and gut microbiota demonstrated promising diagnostic performance (AUC > 0.83). Collectively, these findings support a potential bidirectional oral-gut axis associated with metabolic dysregulation in DM. Despite limitations including cross-sectional design and heterogeneity, this axis represents a novel target for biomarker development and therapeutic intervention. Future longitudinal and interventional studies are required to determine causal relationships and clinical utility.}, } @article {pmid41921901, year = {2026}, author = {Möller, TM and Kreft, A and Dennebaum, M and Hess, G and Michel, C and Kriege, O}, title = {Disseminated Strongyloides stercoralis infection diagnosed by metagenomic next-generation sequencing of a cell-free DNA blood sample in a patient with hematologic malignancy in Germany: A case report.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {167}, number = {}, pages = {108668}, doi = {10.1016/j.ijid.2026.108668}, pmid = {41921901}, issn = {1878-3511}, mesh = {Humans ; *Strongyloidiasis/diagnosis/drug therapy/parasitology/blood ; Animals ; *Strongyloides stercoralis/genetics/isolation & purification ; Male ; High-Throughput Nucleotide Sequencing ; Immunocompromised Host ; *Cell-Free Nucleic Acids/blood/genetics ; Germany ; Ivermectin/therapeutic use ; Metagenomics/methods ; *Hematologic Neoplasms/complications ; Albendazole/therapeutic use ; Anthelmintics/therapeutic use ; Middle Aged ; DNA, Helminth/blood ; }, abstract = {BACKGROUND: Rare infections that are atypical for Central Europe are increasingly relevant due to global migration, climate change, and the widespread use of immunosuppressive therapies. Diagnosing such infections is often delayed or missed entirely because conventional testing relies on prior clinical suspicion and region-specific test panels. Hypothesis-free metagenomic next-generation sequencing (mNGS) offers a promising diagnostic strategy in these cases.

CASE PRESENTATION: We report a case of disseminated Strongyloides stercoralis (S. stercoralis) infection with hyperinfection syndrome in a man undergoing B-cell-depleting lymphoma therapy. The patient presented with gastrointestinal and pulmonary symptoms, weight loss, and eosinophilia. Conventional microbiological and serological testing failed to identify a cause. Diagnosis and relevant bacterial and fungal coinfection were established using mNGS (DISQVER) from blood-derived cell-free DNA. Treatment with ivermectin and albendazole led to rapid clinical improvement, and the patient recovered completely.

CONCLUSION: This case illustrates the diagnostic challenges posed by rare infections in immunocompromised patients in nonendemic regions. It highlights the growing need for broad, rapid, and hypothesis-independent diagnostic tools such as mNGS, which can play a key role in identifying unexpected pathogens and guiding early targeted therapy in high-risk populations.}, } @article {pmid41921920, year = {2026}, author = {Yang, MT and Qin, Y and Xu, C and Leng, X and Li, XM and Hou, QY and Sun, YZ and Zhao, Q and Liu, S and Tang, LY and Ma, H and Chen, BN and Zhang, XX and Li, ZY and Ni, HB}, title = {Virulence and antimicrobial resistance profiling of Klebsiella pneumoniae isolated from foxes in northern China.}, journal = {Microbial pathogenesis}, volume = {215}, number = {}, pages = {108476}, doi = {10.1016/j.micpath.2026.108476}, pmid = {41921920}, issn = {1096-1208}, mesh = {Animals ; *Klebsiella pneumoniae/drug effects/genetics/isolation & purification/pathogenicity/classification ; China ; *Anti-Bacterial Agents/pharmacology ; *Foxes/microbiology ; *Klebsiella Infections/veterinary/microbiology/epidemiology ; *Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Feces/microbiology ; Whole Genome Sequencing ; Virulence/genetics ; Genetic Variation ; Plasmids/genetics ; Genes, Bacterial/genetics ; Virulence Factors/genetics ; }, abstract = {Klebsiella pneumoniae is a significant opportunistic pathogen in animal farming. To investigate the occurrence of K. pneumoniae and associated antimicrobial resistance risk in foxes, this study collected 350 fecal samples from foxes across five northern Chinese provinces. A total of 163 K. pneumoniae isolates were recovered (isolation rate: 46.57%), and all isolates were classified as multidrug-resistant (MDR). All isolates were resistant to azithromycin and sulfisoxazole, with high resistance to enrofloxacin (98.16%), ciprofloxacin (87.12%), and tetracycline (70.55%). Resistance to tigecycline and polymyxin B was lower. Notably, all isolates were susceptible to meropenem. Antimicrobial resistance gene (ARG) analysis revealed high carriage rates of tet(E), aac(3)-IIa, and qnrS, alongside the colistin resistance genes mcr-1 and mcr-8. Whole-genome sequencing of 66 isolates revealed substantial genetic diversity: 45 sequence types (STs) were identified among 64 typeable isolates, with ST35 and ST603 being the most common (5/64, 7.81% each), and lineages previously reported in human clinical settings (e.g., ST307 and ST15) were also detected; however, no direct cross-host transmission was evaluated in this study. Capsular types KL22 (10/64, 15.63%) was the most common. Metagenomic analysis further showed that the fox gut microbiome harbored diverse ARGs, with 29 ARGs detected in both K. pneumoniae isolates and fox gut resistome datasets (descriptive overlap). Among these, 20 genes (e.g., blaCTX-M-55 and aac(3)-IIa) were located on predicted plasmids or transposons, suggesting potential mobility rather than confirmed transfer. Conjugation assays provided limited proof-of-concept evidence for plasmid-mediated transfer of tet(A) and tet(E). Collectively, these findings suggest that farmed foxes may serve as potential reservoirs of MDR K. pneumoniae and transferable resistance determinants, supporting the need for continued surveillance and prudent antibiotic use within a One Health framework.}, } @article {pmid41922261, year = {2026}, author = {Adebayo, AA and Babalola, OO}, title = {Rhizosphere Microbiome as an Underexplored Resource for Agroecosystem Sustainability: Insights From the Carrot Root Zone.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70325}, pmid = {41922261}, issn = {1758-2229}, support = {CRP/ZAF22-93//International Centre for Genetic Engineering and Biotechnology/ ; }, mesh = {*Daucus carota/microbiology/growth & development ; *Rhizosphere ; *Microbiota ; Agroecology ; *Plant Roots/microbiology ; *Soil Microbiology ; Agriculture ; Bacteria/classification/isolation & purification/genetics ; }, abstract = {Rhizosphere microbiome is critical for nutrient turnover, pathogen suppression, and stress modulation, forming the basis of microbial products relevant to agriculture. However, microbial communities associated with carrot root zone remain relatively underexplored, with limited studies focused beyond descriptive surveys. Here, we synthesise existing information on the structural, functional, and ecological dynamics of the carrot rhizomicrobiome, highlighting its emerging yet underdeveloped mechanistic profiling. Existing literature indicates that carrot-associated microbes may play a role in nutrient mobilisation, growth promotion, and antagonism. The early proof-of-concept works demonstrate that the microbes may gain potential applications in biofertilizers, biostimulants, and biocontrol agents. While these functions are strongly influenced by soil properties, genotype, and management, only a few carrot-specific isolates/consortia have been multi-environmentally validated. The limited progress partly reflects the overall underrepresentation of vegetables in microbiome-based studies, compared to other major crops. We explored the key characteristics, economic, and agricultural significance of the carrot rhizosphere, highlighting its richness with beneficial microorganisms. Among the gaps identified are inadequate functional-level and field trial, and insufficient multi-omics integration, which currently limit biotechnological translation. Addressing these gaps through targeted isolation, mechanistic functional and field validation could position carrot rhizosphere microbiome as a valuable yet underexplored resource for enhancing agroecosystem sustainability.}, } @article {pmid41922337, year = {2026}, author = {Doni, L and Trinanes, J and Bosi, E and Vezzulli, L and Martinez-Urtaza, J}, title = {Deciphering the Hidden Ecology and Connectivity of Vibrio in the Oceans.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41922337}, issn = {2041-1723}, mesh = {*Vibrio/genetics/isolation & purification/physiology/classification ; Oceans and Seas ; Animals ; *Seawater/microbiology ; Humans ; Metagenomics ; Water Microbiology ; }, abstract = {Long-range dispersals of marine bacteria in the oceans have remained largely indecipherable, which is particularly relevant for Vibrio, responsible for global epidemics in humans and animals. Here, we combine the analysis of 40 terabases of metagenomic data and satellite-tracked surface drifter data, from across the globe revealing that Vibrio are abundant members of the ocean surface and show a strong association with microplankton, which appears to govern their distribution and connectivity at a global scale. We identify long-distance biological corridors connecting Vibrio communities, including potentially pathogenic Vibrio. These corridors allow movement over thousands of kilometres in a fairly short time, with estimates of less than 1.5 years to cross an ocean basin. These findings have deep implications for the demography and community dynamics of Vibrio species and the epidemiology of associated diseases.}, } @article {pmid41922358, year = {2026}, author = {Korchagina, MV and Mullin, CE and Soufi, HH and Lambert, S and Moran, IG and Porch, R and Albright, SE and Doran, AS and Jones, LM and Malamud, N and Jin, Q and Wood, AM and Louca, S}, title = {Genome-resolved metagenomic survey of 500 samples from 56 hot springs across the Western US.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41922358}, issn = {2052-4463}, mesh = {*Hot Springs/microbiology ; *Metagenome ; Metagenomics ; Archaea/genetics ; United States ; *Genome, Archaeal ; Bacteria/genetics/classification ; Genome, Bacterial ; }, abstract = {Hot springs are natural laboratories for studying microbial diversity, evolution, and adaptation to extreme environments. Despite their abundance across the Western US, information about the functional and genomic structure of inhabiting microbial communities is restricted to a handful of locations. Here we present a dataset of 500 deep metagenomes, totaling 3.38 terabasepairs and collected from 56 remote hot springs across the US Great Basin and Yellowstone, with 25 of the hot springs surveyed annually over 4 consecutive years. Additionally, we present 780 bacterial and archaeal metagenome-assembled genomes (MAGs) binned from these metagenomes, with completeness ≥80% and contamination ≤5%, of which 149 are considered "high quality". Many of the MAGs likely represent entirely novel genera and even families, relative to the Genome Taxonomy Database. Our spatiotemporally extensive dataset yields insight into the microbial functional structure at dozens of previously unstudied locations, substantially expands our repertoire of extremophile microbial genomes, provides a new resource for high-temperature biotechnology, and enables future phylogenomic studies of these communities through space and time.}, } @article {pmid41923365, year = {2026}, author = {Merritt, B and Ratcliff, JD and Ta, S and Osis, G and Mauldin, MR and Thielen, PM}, title = {TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {4}, pages = {}, pmid = {41923365}, issn = {1367-4811}, support = {NU60OE000104//Cooperative Agreement/ ; //Centers for Disease Control and Prevention through the Association of Public Health Laboratories/ ; //TaxTriage/ ; //NIH Fogarty International Center/ ; N00024-22-D-6404//NAVSEA IDIQ/ ; /HH/HHS/United States ; //Association of Public Health Laboratories/ ; }, mesh = {*Software ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Animals ; Humans ; Sequence Analysis, DNA/methods ; }, abstract = {MOTIVATION: TaxTriage is a comprehensive pathogen identification workflow designed for both short- and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative pathogens are identified through comparisons to curated pathogens and abundance expectations from healthy cohort data. Flexible installation options are enabled using Nextflow™ (NF), including cloud deployment via NF Tower (Seqera Platform) and local installation on a variety of systems, including standalone installations without external internet access. Final analysis summaries are compiled into an Organism Discovery Report, which lists likely pathogens and supporting data, including a custom confidence score.

RESULTS: Evaluation of published in silico, clinical, and outbreak datasets identified performance comparable to alternative cloud-based processing pipelines for expected pathogen and co-infection detection with similar sensitivity and increased specificity. To support both public health and veterinary diagnostics communities, customization options have been incorporated to enable improved performance for host species of interest.

Source code for TaxTriage is freely available at https://github.com/jhuapl-bio/taxtriage. TaxTriage v2.1.1 has been archived on Zenodo at https://zenodo.org/records/17081354 to permit reproducible analysis as described in this manuscript.}, } @article {pmid41923466, year = {2026}, author = {King, Z and Buckley, HL and Lear, G and Seale, B and Lee, KC and Schwendenmann, L and Lacap-Bugler, DC}, title = {Comparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70324}, pmid = {41923466}, issn = {1758-2229}, support = {C09X1817//New Zealand's Biological Heritage/ ; //Ministry of Business, Innovation and Employment/ ; }, mesh = {*Soil Microbiology ; *Phytophthora/genetics/physiology/isolation & purification ; *Metagenome ; Forests ; *Microbiota/genetics ; Shotgun Sequencing ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; New Zealand ; Plant Diseases/microbiology/parasitology ; Bacteria/genetics/classification/isolation & purification ; Nucleic Acid Amplification Techniques ; }, abstract = {Soil-borne pathogens can influence microbial communities and ecosystem function, making it important to understand their broader ecological impacts. We investigated interactions between Phytophthora agathidicida (the causal agent of kauri tree dieback) and soil microbial communities, while also comparing detection and community-profiling methods. Soils from 60 kauri trees across three sites in the Waitākere Ranges, New Zealand, were analysed using loop-mediated isothermal amplification (LAMP) for pathogen detection, and 16S rRNA gene/ITS gene amplicon sequencing alongside shotgun metagenomics for community characterisation. LAMP detected P. agathidicida in 39/60 samples, while shotgun sequencing detected Phytophthora-associated DNA at low abundance across all samples. Microbial community structure and functional potential showed weak association with pathogen presence, though differential abundance testing identified several genera enriched in pathogen-detected soils, including taxa previously linked to disease suppression. Amplicon and shotgun profiles indicated broadly comparable patterns at higher taxonomic and functional levels, while differences between approaches emerged primarily at finer taxonomic resolution. Importantly, functional predictions from PICRUSt2 closely matched shotgun-derived profiles at broader scales, indicating its suitability as a cost-effective tool for broad-scale monitoring. These findings suggest limited direct pathogen effects on microbial communities and highlight how integrating molecular approaches provides complementary insights into soil microbiome-pathogen interactions.}, } @article {pmid41923582, year = {2026}, author = {Menezes, GA and Sekar, P and Akhter, A and Tayade, KD and Fathima, S and Hussain, ZFZ and Nigam, A}, title = {Gut Microbiota and Dyslipidemia in Type 2 Diabetes: A Pilot Study of 16S rRNA Profiles and Predicted Functional Shifts.}, journal = {Journal of diabetes research}, volume = {2026}, number = {1}, pages = {e9317962}, pmid = {41923582}, issn = {2314-6753}, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/blood/complications ; *Dyslipidemias/microbiology/blood ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Pilot Projects ; Female ; Male ; Middle Aged ; *Bacteria/genetics/classification ; Aged ; }, abstract = {Hyperlipidemia is a major, modifiable driver of global cardiovascular risk. The intestinal microbiota, comprising bacteria, archaea, fungi, and viruses, modulates lipid metabolism through bile acid transformation, energy harvest, and inflammatory signaling. This study profiled the gut microbiota of 15 adults with type 2 diabetes mellitus (T2DM) and explored associations with fasting lipid measures using 16S rRNA gene sequencing (V3-V4 region) on the Illumina MiSeq platform and PICRUSt2 functional prediction. Overall α-diversity was reduced, and community composition was dominated by Firmicutes and Actinobacteria with relative depletion of Bacteroidetes. At lower taxonomic ranks, enrichment of Prevotella copri, Collinsella spp., Ruminococcus spp., and selected Bifidobacterium spp. was observed, alongside depletion of short-chain fatty acid (SCFA)-linked taxa, including Akkermansia muciniphila, Lactobacillus plantarum, and members of the Bacteroides and Parabacteroides lineages. Exploratory within-cohort trends indicated that higher triglycerides (TGs) and lower HDL-C tended to co-occur with increased Collinsella and clostridial signals and reduced SCFA-associated taxa. Predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog functions suggested shifts in lipid, carbohydrate, and secondary bile acid metabolism, consistent with a metabolically activated and proinflammatory intestinal milieu. In this single-arm cohort of adults with T2DM, a low-diversity, Firmicutes/Actinobacteria-weighted microbiome with depletion of SCFA-linked taxa paralleled an atherogenic lipid profile, supporting an association between gut microbial dysbiosis and lipid abnormalities in adults with T2DM. These findings suggest the potential of microbiota-informed adjuncts, including dietary fermentable fiber, targeted probiotics and next-generation biotherapeutics, and bile-acid-modulating strategies as supportive approaches to lipid management in T2DM. This was a pilot, single-arm, exploratory study without a nondiabetic control group, and findings should be interpreted as hypothesis-generating. Nevertheless, the cross-sectional design, small sample size, and 16S-based taxonomic resolution limit causal interpretation. Larger, longitudinal studies integrating shotgun metagenomics and metabolomics are needed to confirm these associations, validate biomarkers, and elucidate mechanistic pathways that could guide precision interventions for diabetic dyslipidemia.}, } @article {pmid41923636, year = {2026}, author = {Xiong, C and Delgado-Baquerizo, M and Liang, J and Wang, J and Yan, Z and Jensen, SO and Gao, M and Sáez-Sandino, T and Guirado, E and Muñoz-Rojas, M and Román, R and Maestre, FT and Singh, BK}, title = {Soil microbial diversity associates with lower prevalence of human bacterial pathogens across global soils.}, journal = {Cell host & microbe}, volume = {34}, number = {5}, pages = {830-843.e6}, doi = {10.1016/j.chom.2026.03.011}, pmid = {41923636}, issn = {1934-6069}, mesh = {*Soil Microbiology ; Humans ; *Biodiversity ; *Bacteria/classification/pathogenicity/genetics/isolation & purification ; *Microbiota ; Prevalence ; Ecosystem ; Metagenome ; }, abstract = {Soil-inhabiting pathogens threaten human health, but their biogeography and associations with soil biodiversity remain poorly understood. Here, we present global patterns of dominant human bacterial pathogens by integrating 1,602 soil metagenomes from 59 countries across continents. We show that dominant human pathogens are more prevalent (i.e., relative abundance) in wet (tropical and temperate) ecosystems and are particularly abundant in cropland soils. We find a global negative association between soil microbiome diversity and pathogen prevalence. We further reveal a significant and positive correlation between the abundance of dominant human pathogens and both disease virulence and global patterns of mortality associated with infectious diseases. Many dominant pathogens are likely to increase their proportion under global change scenarios. Our work provides a global atlas of dominant soil-inhabiting human pathogens and reveals their biogeography and ecology. These findings can guide the development of effective surveillance and risk management strategies to reduce outbreaks and pandemics.}, } @article {pmid41923798, year = {2026}, author = {Ibisanmi, TA and Jiang, X and Willcox, M and Kumar, N}, title = {Recent advances in computational antimicrobial peptide discovery through big data, modeling, and artificial intelligence and their interplay in ushering the next golden era of drug development.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1749404}, pmid = {41923798}, issn = {2673-7647}, abstract = {The accelerating antimicrobial resistance (AMR) crisis continues to render more and more conventional antibiotics ineffective. Antimicrobial peptides (AMPs) are promising alternatives to traditional antibiotics due to their broad-spectrum activity, diverse mechanisms of action, and lower propensity for resistance. Traditional discovery approaches face limitations arising from the vast sequence space and the challenge of balancing efficacy with low toxicity. Addressing these challenges is critical for developing next-generation antimicrobial agents, and computational methods are increasingly driving progress. Public repositories, and techniques such as molecular docking enable in silico evaluation of peptide target interactions, identifying candidates with strong binding potential. Molecular dynamics (MD) simulations offer deeper insights into how AMPs disrupt membranes, form pores, or act synergistically, while Steered MD extends this to probing membrane penetration. Artificial intelligence (AI) methods, including machine learning and deep learning, capture complex sequence activity relationships, predict novel AMPs from genomic and metagenomic data, and design new peptides de novo using generative models. Despite rapid advances, most existing reviews treat these approaches in isolation, leaving a fragmented understanding of their interplay. This paper addresses that gap by unifying computational strategies, highlighting synergies, and critiquing limitations. Ultimately, integrating these methodologies offers a path toward more efficient AMP discovery to fight AMR.}, } @article {pmid41923934, year = {2026}, author = {Dhawi, F and Alsanie, SI}, title = {Contrasting leaf transcriptomic responses to drought and heat stress in the desert CAM species Mesembryanthemum forsskalii.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1805066}, pmid = {41923934}, issn = {1664-462X}, abstract = {INTRODUCTION: Dryland ecosystems are increasingly exposed to extreme heat and prolonged water limitation. Facultative crassulacean acid metabolism (CAM) enables certain desert plants to enhance water-use efficiency and adjust carbon assimilation under stress conditions. Mesembryanthemum forsskalii Hochst. ex Boiss. (Aizoaceae; locally known as Samh) is a hyper-arid adapted species native to Saudi Arabia, yet genomic and transcriptomic resources for this plant remain scarce. This study aimed to generate foundational genomic resources and characterize transcriptional responses to drought and heat stress.

METHODS: We integrated rhizosphere metagenomics and leaf transcriptomics. A genome-resolved rhizosphere metagenome was generated from mature field-grown plants. In parallel, micropropagated plants were exposed under controlled conditions to progressive drought (17 days without irrigation) or acute heat shock (55 °C for 120 min), each compared with well-watered controls. RNA sequencing generated 123.77 Gb raw data and 121.96 Gb clean reads after quality filtering. Differential gene expression was identified using thresholds of |log2FC| ≥ 2 and FDR ≤ 0.05, followed by transcription factor profiling and KEGG pathway annotation.

RESULTS: Heat stress induced substantially broader transcriptional reprogramming than drought. A total of 1,348 genes were differentially expressed under heat stress, compared with 84 genes under drought. Heat exposure strongly increased the expression of transcription factor families including B3 (20.00-fold relative to drought), bHLH (22.65-fold), and bZIP (8.94-fold). KEGG pathway analysis revealed expanded representation of metabolic pathways under heat, including secondary metabolite biosynthesis, ribosome function, carbon metabolism, and endoplasmic reticulum protein processing. Rhizosphere binning recovered archaeal and bacterial genomes affiliated with stress-tolerant lineages, providing the first microbial genomic framework associated with M. forsskalii.

DISCUSSION: These results demonstrate a heat-dominant transcriptional response in M. forsskalii and provide the first integrated transcriptomic and rhizosphere metagenomic resources for this desert facultative CAM species. Heat-inducible transcription factors, particularly B3 and NAC families, emerge as promising targets for improving thermotolerance and water-use efficiency in crops.}, } @article {pmid41924127, year = {2026}, author = {Booker, AE and Fei, C and Amin, SA and Custer, J and Watkins, K and Yaeger, W and Ahn, SH and Vidyarathna, NK and Burns, A and Klass, S and Glibert, PM and Heil, CA and Schulz, F and Martínez Martínez, J}, title = {Complex viral interactions revealed for the harmful bloom-forming dinoflagellate Karenia brevis.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag051}, pmid = {41924127}, issn = {2730-6151}, abstract = {Karenia brevis regularly forms harmful blooms along the West Florida Shelf that negatively affect marine and terrestrial organisms through toxin production. These blooms impose economic and environmental hardship, driving the need for research to understand the factors influencing their dynamics and to mitigate their impacts. A mostly unresolved issue is the potential role of viruses in bloom termination. We conducted an experiment incubating K. brevis cultures with size-fractionated bloom water samples. Flow cytometry revealed giant virus-like populations (VLPs) in replicate cultures with <1 μm-filtered and <0.2 μm-filtered bloom water. The VLPs' abundance was paralleled by declines in photoefficiency and culture lysis. Metagenomic analyses of the lysates revealed 11 giant virus genomes (35%-100% complete) representing 7 viral operational taxonomic units (vOTUs) within the order Imitervirales (Nucleocytoviricota). Ten of these vOTUs were more abundant in the incubations with <0.2 μm-filtered bloom water, coinciding with the absence or low abundance of algicidal bacteria. The vOTUs and K. brevis cell abundances showed a positive correlation at a coastal site during bloom and nonbloom periods. The most apparent association was to vOTU6, which may owe its competitive advantage to the presence of the auxiliary metabolic genes bacteriorhodopsin, carbonic anhydrase, and dinoflagellate viral nucleoprotein. The metagenomes also contained polinton-like virus (PLV) genomes. Since many PLVs are hypothesized to depend on co-infection with Nucleocytoviricota viruses for their propagation, our results suggest complex viral interactions within K. brevis blooms. Future research to elucidate virus-bacteria-K. brevis interaction mechanisms may be key to understanding bloom dynamics and developing management tools.}, } @article {pmid41924306, year = {2026}, author = {Batacan, R and Rao, A and Bajagai, YS and Stanley, D and Briskey, D}, title = {Oleoylethanolamide supplementation enriches Akkermansia muciniphila and modulates intestinal barrier function in adults with obesity: A randomized, double-blind, placebo-controlled trial.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2622259}, pmid = {41924306}, issn = {2993-3935}, abstract = {Targeted modulation of the gut microbiome represents a promising nutritional strategy to support metabolic and intestinal health in overweight and obese adults. Oleoylethanolamide (OEA) is an endogenous lipid mediator that regulates satiety, lipid metabolism, and inflammation, but its effects on the human microbiome are not well defined. In this randomized, double-blind, placebo-controlled trial, 57 adults with obesity (BMI 30-40 kg/m[2]) received either 300 mg of TRPTI, providing 250 mg/day of OEA (n = 28), or placebo (n = 29) for 12 weeks. Outcomes included shotgun metagenomics, microbiome profiling, intestinal barrier and inflammatory biomarkers, and safety measures. OEA was safe and well-tolerated with no adverse changes in clinical biomarkers. Although overall microbial diversity remained stable, OEA induced selective, health-relevant compositional shifts. Notably, Faecalibacterium prausnitzii and Akkermansia muciniphila were enriched. These changes coincided with functional host benefits, including increased occludin at Week 12 and interleukin-2 at Week 6, while reducing interleukin-1β, consistent with improved epithelial barrier dynamics and reduced inflammation. Functional pathway analysis suggested enhanced microbial metabolic and redox capacity. These findings indicate OEA supplementation selectively enriches beneficial gut bacteria - particularly A. muciniphila, while improving gut barrier biomarkers and immune function without disrupting microbiome stability. These findings position OEA as a safe, targeted microbiome-modulating ingredient with potential applications for supporting gut and metabolic health.}, } @article {pmid41924310, year = {2026}, author = {Chen, X and Wang, N and Jiang, C and Luo, S and Cheng, M and Chu, D and Hu, C and Zhang, P and Chen, K and Yang, F and Xiong, J and Ning, K and Miao, W}, title = {Data Mining of Sediment Microbiomes of the Tibetan Plateau Revealed a Genomic Repository of Ancient Lineages and Adaptive Evolution of Asgardarchaeota.}, journal = {Research (Washington, D.C.)}, volume = {9}, number = {}, pages = {1213}, pmid = {41924310}, issn = {2639-5274}, abstract = {The extreme climatic conditions of the Tibetan Plateau foster unique microbial communities, especially in the sediment ecosystem. A thorough understanding of these communities could facilitate revealing their microbial diversity, biological resources, and response to climate change. Here, we have constructed the Tibetan Plateau Microbial Catalog of Sediment (TPMC-S) based on 248 metagenomic sediment samples from the Tibetan Plateau. We identified 511,056,752 nonredundant genes and recovered 13,696 metagenome-assembled genomes with enormous phylogenetic novelty (over 90% novel species), far exceeding other contemporary Tibetan microbial catalogs and expanding the microbial functional diversity. We also revealed that similarities of sediment microbial communities followed the distance-decay relationship. Furthermore, sediments contained a high proportion of evolutionarily "possible ancient species (PAS)" compared with paired aquatic samples, especially ancient archaeal lineages, suggesting a microbial "sedimentary archive" in sediment. Finally and most importantly, Asgardarchaeota, including 2 potentially novel genera, were identified from the sediments, and their latest divergence predated the uplift of the Tibetan Plateau, while they still gained functions to adapt to extreme environments. Our findings positioned the Tibetan Plateau as both a genomic repository of microbial antiquity, especially Asgardarchaeota, and an active arena for modern extremophile innovation, providing insights for deciphering microbial resilience strategies in climate-sensitive ecosystems and informing novel bioprospecting efforts.}, } @article {pmid41924424, year = {2026}, author = {Wangprapa, P and Nagy-Szakal, D and Wells, HL and Fidler, G and Sangtian, M and Panmontha, W and Bunlungsup, S and Techasathit, W and Couto-Rodriguez, M and Danko, DC and Mason, CE and O'Hara, NB and Sriswasdi, S and Viangteeravat, T}, title = {Correction: Analytical validation of a metagenomic next-generation diagnostic platform for urinary tract infection in a Thai tertiary hospital setting: a BI-Biotia UTI cohort study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1817909}, doi = {10.3389/fcimb.2026.1817909}, pmid = {41924424}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2026.1751074.].}, } @article {pmid41924426, year = {2026}, author = {Pan, Y and Du, N and Liu, Y and Wu, M and Hao, S and He, Y and Jiang, Y}, title = {Clinical features of Tropheryma Whipplei in pediatric pneumonia: an mNGS and tNGS-based case-control study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1753963}, pmid = {41924426}, issn = {2235-2988}, mesh = {Humans ; Case-Control Studies ; *Tropheryma/genetics/isolation & purification/pathogenicity ; Bronchoalveolar Lavage Fluid/microbiology ; Child, Preschool ; Female ; Male ; Child ; Infant ; High-Throughput Nucleotide Sequencing ; *Whipple Disease/microbiology ; Metagenomics ; *Pneumonia/microbiology ; Adolescent ; *Pneumonia, Bacterial/microbiology ; }, abstract = {INTRODUCTION: Tropheryma whipplei (TW), which causes Whipple disease, has recently been associated with respiratory diseases, particularly pneumonia. To understand its role in pediatric pneumonia, this study analyzed the clinical and pathogenetic characteristics of TW in pediatric pneumonia patients.

METHODS: We utilized metagenomic and targeted next-generation sequencing (mNGS/tNGS) data from 3,759 pediatric bronchoalveolar lavage fluid (BALF) samples (2023-2024). This case-control study included 103 TW-positive pediatric pneumonia patients (59 with severe pneumonia, SPTW+; 44 with mild pneumonia, MPTW+), along with 206 TW-negative pneumonia patients as controls (118 with severe pneumonia, SPTW-; 88 with mild pneumonia, MPTW-).

RESULTS: Through inter-group comparisons, the results showed that TW-positive patients were younger and had lower BMIs than controls, with shorter hospital stays and milder inflammation. Severe TW-positive cases showed more localized right-lung lesions, less pleural effusion, and more bronchial involvement. Mycoplasma pneumoniae co-detection was frequent (86.4%), along with Moraxella catarrhalis, human bocavirus type 1, and rhinovirus A.

DISCUSSION: TW-positive pediatric pneumonia presents with milder symptoms, suggesting that TW may act as a colonizer rather than a primary pathogen. Consequently, antimicrobial treatment specifically targeting TW may not be immediately warranted at detection. These results provide important insight for the individualized treatment of pediatric pneumonia with TW positive.}, } @article {pmid41925105, year = {2026}, author = {Zu, S and Yu, X and Song, J and Xiao, Y and Yi, H and Li, H}, title = {The Role of Gut Microbiota and Their Derived Metabolites in Chemotherapy-Induced Nausea and Vomiting in Ovarian Cancer.}, journal = {Cancer medicine}, volume = {15}, number = {4}, pages = {e71752}, pmid = {41925105}, issn = {2045-7634}, support = {2023QH1193//Startup Fund for Scientific Research, Fujian Medical University/ ; YCXH 22-10//Nursing Research Special Fund of Fujian Maternal and Child Health Hospital/ ; }, mesh = {Female ; Animals ; Humans ; *Gastrointestinal Microbiome ; *Ovarian Neoplasms/drug therapy/microbiology ; Rats ; *Vomiting/chemically induced/microbiology/metabolism ; *Nausea/chemically induced/microbiology/metabolism ; Dysbiosis/microbiology ; Cisplatin/adverse effects/administration & dosage ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Rats, Sprague-Dawley ; Fecal Microbiota Transplantation ; Carboplatin/adverse effects/administration & dosage ; Paclitaxel/adverse effects/administration & dosage ; Metabolomics/methods ; Aged ; Feces/microbiology ; }, abstract = {OBJECTIVE: This study aimed to investigate the relationship between gut microbiota and chemotherapy-induced nausea and vomiting (CINV) in patients with ovarian cancer undergoing platinum-based chemotherapy (carboplatin or cisplatin combined with paclitaxel).

METHODS: Clinical data and fecal samples were collected from patients with ovarian cancer after admission but prior to the initiation of their first chemotherapy cycle. Patients were divided into the CINV (n = 25) and non-CINV (n = 25) groups on the basis of symptoms occurring after chemotherapy. No additional samples were collected during chemotherapy. Integrated metagenomic sequencing and untargeted metabolomic profiling identified CINV-associated microbial taxa and metabolites. Additionally, fecal microbiota transplantation (FMT) in SD rats validated causal links between gut dysbiosis and CINV pathogenesis.

RESULTS: Bacteroides caccae, Corynebacteriales, and Corynebacterium were significantly enriched in the CINV group. KEGG enrichment revealed upregulated pathways in CINV, including focal adhesion, lysosome function, and eukaryotic cellular communities. Metabolomic analysis identified 19 significantly increased metabolites in the fecal samples of CINV patients versus 10 in non-CINV controls. KEGG enrichment revealed that the pentose phosphate pathway, glutathione metabolism, and lipoic acid metabolism were significantly implicated in CINV pathogenesis. Multi-omics integration revealed Bacteroides sp. A1C1 strongly correlated with hesperetin, arbutin, orciprenaline, and myristolic acid. In rats, cisplatin-induced CINV models showed higher kaolin consumption versus controls (p < 0.05). FMT from non-CINV donors reduced kaolin consumption in cisplatin-treated rats (p < 0.05). The expression of 5-HT3R, NK1R, and NK2R in the medulla oblongata and colon was significantly increased in the cisplatin model group (p < 0.05) and partially reversed by non-CINV FMT (p < 0.05).

CONCLUSIONS: Gut microbiota dysbiosis directly contributes to CINV pathogenesis. Bacteroides sp. A1C1 and its putatively identified metabolites (hesperetin, arbutin, orciprenaline, and myristolic acid) represent potential diagnostic biomarkers for CINV.}, } @article {pmid41925202, year = {2026}, author = {Leibovitzh, H and Krongauz, D and Schlesinger, Y and Aviv Cohen, N and Hirsch, A and Ron, Y and Thurm, T and Godneva, A and Weinberger, A and Segal, E and Maharshak, N}, title = {Phage-Display Immunoprecipitation Sequencing Reveals Distinct Antibody Signatures Against Bacterial Flagellins Associated With Treatment Response in Crohn's Disease.}, journal = {Clinical and translational gastroenterology}, volume = {}, number = {}, pages = {}, pmid = {41925202}, issn = {2155-384X}, support = {R01HL160862//Kenneth Rainin Foundation, National Heart, Lung, and Blood Institute, Louis H. Sackin Research Fellow Chair/ ; }, abstract = {INTRODUCTION: Enhanced immune response against bacterial flagellins among patients with Crohn's disease (CD) is associated with aggressive disease course. However, its association with response to biologic treatment is unknown. We aimed to assess whether treatment response among patients with CD is associated with antibody reaction to bacterial flagellins and related microbial alterations.

METHODS: Thirty-nine patients with active CD (Harvey-Bradshaw Index > 4 or fecal calprotectin > 150 μg/g) commencing biologic treatment were included. Serum and stool samples were collected at baseline and during treatment at weeks 14, 22, and 52. Serum samples were analyzed using high-throughput phage-display immunoprecipitation sequencing (PhIP-Seq) and fecal samples by DNA shotgun metagenomic sequencing.

RESULTS: Using PhIP-Seq analysis, only the antiflagellin antibodies' library showed consistently attenuated antibody responses against bacterial flagellins in patients achieving remission (Harvey-Bradshaw Index ≤ 4 and fecal calprotectin ≤ 150) vs nonremission at all time points (P < 0.05). Of the 55 antiflagellin antibodies analyzed, 15 showed consistent >1.5-fold overrepresentation in nonremission samples, with high conservation of amino-acid sequences and targeting of Clostridiales , Lachnospiraceae , or Roseburia species. Remission was associated with increased abundance of flagellin-target taxa including Roseburia intestinalis and decreased Ruminococcus_B gnavus and pathways involved in cellular oxidative stress, while nonremission showed increased Bacteroides species and pathways involved in 5-aminoimidazole ribonucleotide and semiessential amino acids biosynthesis (q < 0.05).

DISCUSSION: PhIP-Seq revealed that biologic treatment response in patients with CD associates with consistently decreased antibody responses against specific bacterial flagellins with conserved sequences. These findings identify potential biomarkers and therapeutic targets for improving treatment outcomes.}, } @article {pmid41925227, year = {2026}, author = {Deng, F and Han, Y and Peng, Y and Xu, Z and Yang, J and He, J and Li, D and Dong, G and Zhang, P and Jiang, H and Chai, J and Wang, C and Zhao, J and Li, Y}, title = {Microoxic conditions promote Escherichia-associated cellulase expression in the giant panda gut.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41925227}, issn = {1751-7370}, support = {32170430//National Natural Science Foundation of China/ ; 32400412//National Natural Science Foundation of China/ ; 2023B10564001//Specific University Discipline Construction Project/ ; }, mesh = {Animals ; *Ursidae/microbiology ; *Cellulase/genetics/metabolism ; *Escherichia coli/enzymology/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; }, abstract = {Giant pandas possess a carnivore-like gastrointestinal tract yet subsist on bamboo, and their gut communities contain few canonical cellulolytic taxa. We investigated how fiber processing proceeds in this setting by building a species-resolved reference and linking community features to cellular transcriptional profiles and isolate phenotypes. Using culturomics and PacBio HiFi metagenomics, we assembled a species-resolved reference catalog for the panda gut microbiome (Pbac v2; 466 species-level genomes). Community profiling across 142 samples resolved three enterotypes dominated by Escherichia coli (ET-Ecoli), Clostridium SGBP116 (ET-Clos), and Streptococcus alactolyticus (ET-StreA), with ET-Ecoli enriched for tricarboxylic-acid and respiratory-chain modules and showing higher abundance of an endo-β-1,4-glucanase marker. Droplet-based microbial single-cell RNA-seq from four samples (16 659 cells) assigned a substantial share of cellulase-associated transcripts (GH1/GH3/GH5/GH9) in situ to Escherichia and revealed within-species heterogeneity: E. coli subpopulations segregated into respiration-enriched versus three-carbon/anaerobic-like programs, with cellulase/lytic polysaccharide monooxygenase-linked transcripts concentrated in the former. Guided by these associations, panda-derived E. coli isolates assayed under defined atmospheres showed oxygen-dependent cellulolytic readouts in vitro. Although in vivo oxygen levels were not measured, the convergence of species-resolved community signatures, single-cell attribution, and isolate phenotypes indicates that E. coli can contribute to cellulose processing under microoxic conditions in this cohort. The Pbac v2 resource and the integrated workflow (culturomics + HiFi metagenomes, multi-omics, microbial scRNA-seq) provide a template for species-level assignment of microbiome functions in hosts with unconventional diet-physiology combinations.}, } @article {pmid41926886, year = {2026}, author = {Hoang, HG and Chacha, WE and Binh, QA and Mukherjee, S and Jiang, Y and Zhang, T and Van Tung, T and Tran, HT and Naidu, R}, title = {Biotechnologies for removal of per- and polyfluoroalkyl substances (PFAS) in biosolids: Current status and challenges.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129237}, doi = {10.1016/j.jenvman.2026.129237}, pmid = {41926886}, issn = {1095-8630}, mesh = {Biodegradation, Environmental ; *Biosolids ; *Fluorocarbons ; *Biotechnology ; }, abstract = {Per- and polyfluoroalkyl substances (PFAS), widely recognized as "forever chemicals," pose significant environmental management challenges due to their persistence, mobility, and bioaccumulative behavior. Biosolids derived from wastewater treatment plants represent an important pathway for PFAS redistribution into terrestrial environments, particularly through land application. This review provides a comprehensive assessment of the global distribution, environmental behavior, toxicity, and biodegradation potential of PFAS in biosolids. A bibliometric analysis was conducted using the Web of Science database, and keyword co-occurrence mapping with VOSviewer was applied to evaluate research trends from 2018 to 2024. The findings indicate that research activity is concentrated in China (31%), Europe (30%), and North America (16%), with limited data available from South America, Oceania, and Africa, highlighting regional knowledge gaps. The environmental fate of PFAS in biosolids is governed by pH, temperature, redox conditions, and organic matter content, which influence sorption-desorption processes, mobility, and long-term persistence in soils. Biodegradation pathways include anaerobic reductive defluorination and aerobic oxidative transformation. Certain bacterial genera, such as Dehalobacter spp. and Gordonia spp., have demonstrated degradation efficiencies approaching 80-90% under optimized laboratory conditions. Fungal-mediated oxidative processes may further promote partial mineralization through enzymatic defluorination. In phytoremediation systems, long-chain PFAS preferentially accumulate in plant roots, whereas short-chain compounds exhibit greater mobility and translocation potential. Emerging remediation strategies integrating metagenomics, functional gene characterization, and enzyme-based treatments show promise for enhancing PFAS attenuation. However, substantial uncertainties remain regarding long-term bioaccumulation, biomagnification, and regulatory risk thresholds. Addressing these gaps is essential for developing science-based management strategies for PFAS-contaminated biosolids and protecting environmental and human health.}, } @article {pmid41926891, year = {2026}, author = {Duan, P and Guan, Y and Zhang, J and Han, Z and Li, H and Wang, S and Kong, F and Cui, Y}, title = {Enhanced performance and mechanism of nano-iron-nickel modified substrate in the treatment of compound antibiotic wastewater in constructed wetland.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129455}, doi = {10.1016/j.jenvman.2026.129455}, pmid = {41926891}, issn = {1095-8630}, mesh = {*Wetlands ; *Wastewater ; *Anti-Bacterial Agents ; Nickel/chemistry ; Iron/chemistry ; Adsorption ; Water Pollutants, Chemical ; Waste Disposal, Fluid/methods ; Animals ; Sulfamethoxazole ; }, abstract = {Nano zero-valent iron nickel (nZVI/Ni) was loaded on the walnut shell activated carbon (AC) and its spheres (ACS) to prepare nZVI/Ni-ACS and nZVI/Ni/AC-SAS composites. These were applied in constructed wetlands (CWs) to construct a "substrate-microorganism" synergistic system for treating tetracycline (TC) and sulfamethoxazole (SMX) in livestock and poultry wastewater. Adsorption experiments determined the optimal mass ratios were ACS:Fe:Ni = 2:1:0.05; AC:Fe:Ni = 1:1:0.05; nZVI/Ni/AC:SA = 6:1. At 500 μg/L influent concentrations, TC and SMX removal efficiencies in CWs with modified substrates (CW-LA: 86.96%/87.79%; CW-LB: 89.88%/86.94%) significantly exceeded gravel (CW-G: 26.07%/55.28%) and ACS (CW-Z: 39.90%/67.56%) systems. Mechanistically, the modified substrates strongly adsorbed TC and SMX, while Fe and Ni acted as electron donors and catalysts to drive their chemical reduction and stimulate biological co-metabolism. Metagenomic analysis revealed that the TC/SMX removal mechanisms were associated with an increased abundance of antibiotic-resistant microorganisms (Methanothrix, Desulfobacter, Thauera, Geobacter, Pseudomonas), which benefited efficient antibiotic degradation, while their immobilization within the tightly bound EPS (TB-EPS) matrix effectively minimized ecological risks. This study provided critical data for the enhanced CW treatment of TC and SMX in livestock and poultry wastewater by modified substrates.}, } @article {pmid41927118, year = {2026}, author = {Huang, H and Liu, Z and Liu, X and Li, Q and Yang, X and Chen, L and Ye, W}, title = {Coinfection of Human Cytomegalovirus and Pneumocystis jirovecii Caused Severe Pneumonia in a Non-HIV Elderly Patient: A Case Report.}, journal = {Annals of clinical and laboratory science}, volume = {56}, number = {1}, pages = {122-129}, pmid = {41927118}, issn = {1550-8080}, mesh = {Humans ; *Pneumonia, Pneumocystis/complications/microbiology/drug therapy/virology ; *Pneumocystis carinii/pathogenicity ; *Cytomegalovirus Infections/complications/virology/drug therapy ; *Coinfection/virology ; *Cytomegalovirus/pathogenicity/isolation & purification ; Male ; Aged ; }, abstract = {OBJECTIVE: To present a case of a non-human immunodeficiency virus (HIV)-infected patient with human cytomegalovirus (HCMV) viremia and severe Pneumocystis jirovecii (PJ) pneumonia.

CASE REPORT: The patient was admitted in June 2024 for chronic dry cough and dyspnea. Sputum-targeted next-generation sequencing (tNGS) and blood pathogen metagenomic detection were used to identify concurrent infections of sputum HCMV and PJ, along with blood HCMV. The extensive treatment included intravenous ganciclovir, in conjunction with caspofungin and oral sulfamethoxazole, augmented by glucocorticoids and breathing assistance. After three weeks, the patient's oxygenation index markedly improved, accompanied by the significant resolution of imaging lesions, leading to patient discharge in June 2024.

CONCLUSION: This case underscores the diagnostic efficacy of tNGS on several opportunistic infections for older people with several comorbidities.}, } @article {pmid41927536, year = {2026}, author = {Dong, Y and Wang, M and Zhou, X and Wang, P and Yan, K and Wang, S and Zhong, JC and Li, H and Zhao, L and Li, B and Li, J}, title = {Multi-cohort analysis of metagenome for type 2 diabetes identified universal gut microbiota signatures across populations.}, journal = {Nutrition & diabetes}, volume = {16}, number = {1}, pages = {}, pmid = {41927536}, issn = {2044-4052}, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Cohort Studies ; Middle Aged ; Europe ; Feces/microbiology ; Asia ; Dysbiosis/microbiology ; Adult ; Bacteria/classification/genetics ; Aged ; }, abstract = {BACKGROUND: Several studies have investigated the association between the gut microbiota and type 2 diabetes mellitus (T2D) in various populations. Nonetheless, noises specific to individual cohorts might distort the microbial dysbiosis characteristics and result in inconsistent findings across studies. Thus, we aimed to identify the universal features of perturbed gut microbiota across diverse populations.

METHODS: A total of 433 fecal shotgun metagenomic sequences were analyzed to profile and compare the gut microbiome shifts between patients with T2D and healthy controls from cohorts in Europe and Asia.

RESULTS: Based on cross-cohort integrative analysis, patients with T2D showed significantly higher microbial alpha diversity, and distinctive microbial structures compared to healthy individuals. By excluding bacteria exhibiting divergent directional changes, consistent characteristics with ten T2D-enriched bacteria, such as Clostridium bolteae and Clostridium citroniae and eight T2D-depleted bacteria, including Streptococcus thermophiles and Haemophilus parainfluenzae were revealed across populations. Particularly, these reliable bacterial markers, which were robust against demographic variation, distinguished patients with T2D from healthy controls with high accuracy (AUCs > 0.8) in both European and Asian cohorts. Correlation analysis demonstrated that T2D-enriched and T2D-depleted bacteria, respectively, formed their own mutualistic networks that were negatively linked to each other. Moreover, T2D-enriched bacteria were dramatically positively associated with fasting blood glucose and glycated hemoglobin. Functionally, 10 KEGG pathways with consistent directional changes across European, Asian, and combined cohorts were identified. Specifically, the Nucleotide excision repair pathway was markedly downregulated in patients with T2D, while the AGE-RAGE signaling pathway in diabetic complications was consistently enriched in patients with T2D across cohorts.

CONCLUSIONS: Our results elucidated reproducible profiles of gut commensal bacteria in patients with T2D, which are robust across populations. Identifying the universal gut microbiome signatures of T2D in heterogeneous cohorts offers valuable insights for understanding disease development and is crucial for prevention and diagnosis across diverse populations.}, } @article {pmid41927550, year = {2026}, author = {Oki, H and Takebe, K and Bonsu, A and Fujii, K and Masuda, R and Henderson, N and Mima, T and Koide, T and Moradi, M and Matsushita, O and Sakon, J and Kawahara, K}, title = {Bacterial collagenase harnesses collagen geometry for processive cleavage.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41927550}, issn = {2041-1723}, support = {24K10218//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23K14519//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23K06545//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 2218054//Armenian National Science and Education Fund (Armenian National Science & Education Fund)/ ; GM103429 and GM151696//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; }, mesh = {*Collagen/metabolism/chemistry ; *Hathewaya histolytica/enzymology ; Cryoelectron Microscopy ; *Collagenases/metabolism/chemistry ; Proteolysis ; Catalytic Domain ; Models, Molecular ; Protein Conformation ; }, abstract = {Collagen, the major structural protein in the animal extracellular matrix, forms a triple helix that resists proteolysis and requires specialised enzymes for degradation. Flesh-eating bacteria secrete collagenases that unwind the collagen triple helix and processively trim Gly-X-Y triplet repeats, yet the molecular basis of this process has remained obscure. Here, cryo-electron microscopy reveals how Hathewaya histolytica collagenase ColH engages its substrate and exploits the helix's architecture for catalysis. ColH encircles a single collagen triple helix in a closed-ring conformation and, through dynamic domain motions, dehydrates and destabilises it. The enzyme undergoes substrate-assisted twisting to adopt a rigid ratcheted conformation, in which one chain is bent into a tripeptide-long 'bight' and threaded into the active site for cleavage, while two uncut strands are partitioned to non-catalytic sites. Release of the bight appears to reset the enzyme, with the uncut strands serving as guiding tracks. Repeated cycling between dynamic and rigid states likely enables triplet-by-triplet translocation, allowing ColH to harness collagen's geometry for processive degradation. These findings reveal a bacterial strategy for collagen unwinding and cleavage distinct from that of mammalian collagenases, highlighting divergent evolutionary solutions for degrading one of nature's most intractable substrates.}, } @article {pmid41927589, year = {2026}, author = {Jiang, P and Liang, Z and Kovacevic, V and Shi, J and Milicevic, N and Wang, F and Liu, L and Liu, Y and Jiang, Y and Han, M and Lin, X and Petronić, Č and Stanojevic, N and Wang, L and Wang, S and Cheng, H and Li, J and Chen, R and Zhang, Y and Li, Y and Li, J and Fang, X and Yue, Z and Xue, C and Yin, P and Chen, H}, title = {The Extreme Environment Microbiome Catalog (EEMC): a global resource for microbial diversity and antimicrobial discovery.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41927589}, issn = {2041-1723}, mesh = {*Microbiota/genetics ; *Antimicrobial Peptides/pharmacology/genetics ; Phylogeny ; *Bacteria/genetics/classification/drug effects ; Multigene Family ; Archaea/genetics/classification ; Genome, Bacterial ; Metagenome ; Genome, Archaeal ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Microorganisms in extreme environments represent a promising source of novel metabolites, yet their global diversity and biosynthetic potential remain underexplored. Here, we reconstruct 78,213 bacterial and archaeal genomes from 2293 publicly available metagenomes and 3214 microbial isolates to establish a unified database, the Extreme Environment Microbiome Catalog (EEMC). The EEMC expands known global phylogenetic diversity, encompassing 32,715 representative species and nearly 4 billion non-redundant genes, 63.00% and 19.21% of which are previously unannotated, respectively. It also comprises 163,693 biosynthetic gene clusters, grouped into 64,733 gene cluster families, 58.68% of which are classified as novel, underscoring the functional diversity of microbial communities across various extreme habitats. We further develop protein large language models to predict genome-encoded candidate antimicrobial peptides (cAMPs) from the EEMC, identifying 3032 non-toxic candidates. Of 100 synthesized peptides, 84% demonstrate antibacterial activity, and all 50 tested cAMPs exhibit low cytotoxicity. Notably, six of the most potent cAMPs show significant efficacy against multidrug-resistant, Gram-negative pathogens in vitro, indicating their biomedical potential. Together, our study establishes the EEMC as a foundational resource for uncovering novel microbial lineages and biosynthetic capabilities, highlighting its substantial potential for drug discovery and laying the foundation for future advances in biotechnology and biomedicine.}, } @article {pmid41927746, year = {2026}, author = {Akanmu, AM and Hassen, A and van Marle-Köster, E and Adejoro, FA}, title = {Dietary plant extracts reduce methane emission and modulate rumen microbial functionality in Merino lambs.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41927746}, issn = {2045-2322}, support = {SRUG2204254606//National Research Foundation/ ; }, mesh = {Animals ; *Methane/metabolism ; *Rumen/microbiology/drug effects ; *Plant Extracts/pharmacology/administration & dosage ; Animal Feed/analysis ; Sheep ; Dietary Supplements ; Jatropha/chemistry ; Fermentation/drug effects ; *Gastrointestinal Microbiome/drug effects ; Aloe/chemistry ; }, abstract = {The formation of enteric methane from ruminants represents a significant loss of dietary energy that adversely affects growth and production while also contributing to the environmental footprint of livestock production through greenhouse gas accumulation. Phytogenic feed additives rich in bioactive compounds have been proposed as sustainable alternatives to synthetic additives for improving nutrient utilisation and reducing methane. This study evaluated the effects of Moringa oleifera, Jatropha curcas, and Aloe vera extracts on growth performance, nutrient digestibility, methane production, rumen fermentation in South African Mutton Merino lambs using an in vivo feeding trial while the microbial diversity and functionality was evaluated using shotgun metagenomic sequencing. Supplementation with Moringa and Jatropha improved dry matter and crude protein digestibility (P < 0.05). Methane emission decreased in all plant extract groups, with reductions of 17% (Jatropha), 9% (Moringa), and 12% (Aloe) relative to control (P < 0.05). Ammonia nitrogen concentrations were lower in supplemented groups, particularly Moringa and Aloe (P < 0.01), while volatile fatty acids and growth performance were unaffected. Metagenomic profiling revealed Bacteroidetes as the dominant phylum and showed enrichment of genes which may be associated with protein biosynthesis and carbohydrate metabolism in Moringa and Jatropha lambs, aligning with improved digestibility and reduced methane emissions. Dietary inclusion of M. oleifera, J. curcas, and A. vera extracts reduced methane emissions and improved dry matter and crude protein digestibility without compromising growth. These results suggest that these phytogenic extracts can serve as sustainable feed additives to improve efficiency and mitigate environmental impacts in ruminant production systems.}, } @article {pmid41525926, year = {2026}, author = {Sbampato, V and De Marco, G and Tsoupras, A and Khan, A and Beaugé, A and Dayer, R and Tabard-Fougère, A and Ceroni, D}, title = {Next-generation sequencing for diagnosing primary osteoarticular infections compared to conventional culture: A systematic review and meta-analysis.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {164}, number = {}, pages = {108380}, doi = {10.1016/j.ijid.2026.108380}, pmid = {41525926}, issn = {1878-3511}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Osteoarthritis/diagnosis/microbiology ; Sensitivity and Specificity ; Child ; Metagenomics/methods ; }, abstract = {BACKGROUND: Osteoarticular infections (OAIs) in children is a significant diagnostic challenge for healthcare professionals. Traditional culture techniques are often time-consuming and demonstrated low sensitivity. This systematic review aims to evaluate the diagnostic yield of metagenomic next-generation sequencing (mNGS) compared to standard culture for detecting pathogens in OAIs.

METHODS: A systematic review (PROSPERO CRD420251131272) of three databases (2000-2025) was performed. Study quality was assessed using the QUADAS-2 tool. A meta-analysis was performed using a random-effects model to calculate pooled positive detection rate with 95% confidence intervals (95% CI). Heterogeneity was quantified (I[2]), and sensitivity analysis with leave-one-out and subgroups were performed.

FINDINGS: From 35 included studies (>3000 patients), mNGS demonstrated a significantly higher pooled positive detection rate (81%; 95% CI: 75%-85%) than traditional culture (35%; 95% CI: 29%-41%) with high heterogeneity (>80%). mNGS performed consistently in pediatric (79%) and adult (81%) subgroups and was particularly effective for spinal infections (82%).

INTERPRETATION: The mNGS demonstrates a significantly higher diagnostic yield than standard culture for pathogen detection in OAIs. Its simplicity of execution, its fast-processing methods, and high sensitivity are promising factors that could lead to a more reliable detection of the causative microorganism responsible for an OAI.

LEVEL OF EVIDENCE: level I.}, } @article {pmid41525981, year = {2026}, author = {Yan, Y and Gao, Y and Gao, M and Chen, J and Cui, L and Ma, Y}, title = {Decipherment of dissolved organic matter compositions on waste activated sludge under in situ multi-enzyme pretreatment: novel bioavailability-oriented evaluation framework.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {133995}, doi = {10.1016/j.biortech.2026.133995}, pmid = {41525981}, issn = {1873-2976}, mesh = {*Sewage/chemistry/microbiology ; *Organic Chemicals/analysis/metabolism ; Methane/biosynthesis ; Biological Availability ; Hydrolysis ; Anaerobiosis ; Biodegradation, Environmental ; Bacteria/metabolism ; *Enzymes/metabolism ; Solubility ; }, abstract = {This study systematically elucidated the dissolved organic matters (DOM) molecular conversion and biological response mechanisms during anaerobic digestion (AD) of waste activated sludge (WAS) under different multi-enzyme pretreatment durations. Fourier transform ion cyclotron resonance mass spectrometry analysis revealed that the biodegradable protein-like and amino sugar-like substances were converted into recalcitrant aromatic nitrogen-containing compounds via hydrolysis, condensation, and cyclization processes as extended pretreatment duration, significantly reducing DOM bioavailability. Metagenomic sequencing further indicated that the DOM deterioration inhibited the enrichment of hydrolytic and acidogenic bacteria, thereby suppressed the acetotrophic methanogenesis and methane production. Based on these insights, a novel DOM bioavailability-oriented evaluation framework was proposed for WAS pretreatment optimization, focusing on three key metrics, including the relative abundance of biodegradable substrates, key microorganisms and functions, and methanogenic pathways. Expectantly this study may provide theoretical and data support for future precise design of enzymatic pretreatment process and high-efficiency AD of WAS.}, } @article {pmid41526357, year = {2026}, author = {Cronin, P and Siegers, JY and Heang, V and Tok, S and Sin, S and Sievers, B and Omondi, V and Nuon, S and Chhel, K and Nouhin, J and Chim, V and Seng, B and Hak, M and San, S and Tum, S and Claes, FF and Firth, C and Su, YCF and Smith, GJD and Karlsson, EA}, title = {Environmental metagenomics enhances detection of circulating viruses from live poultry markets in Cambodia.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {1525}, pmid = {41526357}, issn = {2041-1723}, support = {75N93021C00016/AI/NIAID NIH HHS/United States ; U01 AI151378/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Metagenomics/methods ; Cambodia/epidemiology ; Chickens/virology ; Ducks/virology ; *Environmental Monitoring/methods ; Influenza A Virus, H5N1 Subtype/genetics/isolation & purification ; Influenza in Birds/virology ; *Viruses/genetics/isolation & purification/classification ; Humans ; *Poultry/virology ; }, abstract = {Environmental surveillance has emerged as a pivotal strategy for early detection of pathogens that pose a threat to humans. In Asia, live-bird markets (LBMs) are key human-animal interfaces for zoonotic virus transmission. Traditional sampling strategies are time-consuming, expensive and carry significant biosafety risks. Here, we assess the performance of metagenomics on environmental samples (ES) versus traditional poultry swabs for detecting viral pathogens in two Cambodian LBMs between January 2022 and April 2023. ES, including air (n = 35), cage swabs (n = 17), carcass wash water (n = 17) and drinking water (n = 9) are collected alongside oropharyngeal and cloacal swabs from chickens (n = 30) and ducks (n = 29). ES is sensitive in detecting 40 viruses from pathogen families including Orthomyxoviridae and Coronaviridae. Air samples capture the greatest diversity of poultry viruses. Viral contigs from ES show high sequence identity to poultry swab contigs when aligned to the same gene. We show ES outperforms poultry samples in detecting the highly pathogenic influenza A/H5N1, including clades 2.3.4.4b and 2.3.2.1c, which are found in the environment but are missed by poultry swabs. Our findings show metagenomics on ES replicates traditional surveillance, offering broader coverage and improved pathogen detection. This approach could be pivotal for mitigating zoonotic spillover and enhancing pandemic preparedness.}, } @article {pmid41526362, year = {2026}, author = {Ascandari, A and Aminu, S and Benhida, R and Daoud, R}, title = {Cross-cohort resistome and virulome gradients structure the colorectal cancer microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {40}, pmid = {41526362}, issn = {2055-5008}, mesh = {*Colorectal Neoplasms/microbiology ; Humans ; Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Virulence Factors/genetics ; Cohort Studies ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Metagenome ; Drug Resistance, Bacterial ; }, abstract = {The gut microbiome is increasingly implicated in colorectal cancer (CRC), yet the functional signatures associated with disease progression remain poorly resolved across populations. We performed an assembly-based metagenomic analysis of more than 500 samples from three geographically distinct cohorts to characterize resistome and virulome patterns associated with CRC. Using a cross-validated modeling framework based on Partial Least Squares (PLS) regression, we identified two reproducible latent functional gradients that structured variation in antimicrobial-resistance and virulence-factor profiles. One gradient was enriched for adhesion, efflux, and biofilm-associated functions, while the second reflected immunomodulatory and barrier-related pathways. These components were statistically robust, directionally stable across cohorts, and consistent with functional themes frequently reported in CRC microbiome studies. To summarize variation along these gradients, we derived an exploratory Dual-Axis Index (DAI) based on the two stable PLS components. Although its discriminative performance was moderate, the DAI provided an interpretable low-dimensional representation of how resistome-virulome patterns differed across healthy, adenoma, and carcinoma states. These results suggest that functional gene profiles in CRC are organized along reproducible statistical axes, and highlight functional modules, such as adhesion-, iron-associated, and immune-interaction pathways that may complement taxonomic or metabolic biomarkers in future multimodal approaches. Our work provides a reproducible, assembly-based framework for examining the functional organization of CRC-associated microbiomes across diverse populations.}, } @article {pmid41526579, year = {2026}, author = {Fang, H and Pu, M and Jiang, A and Haiti, F and Liu, Y and Ailijiang, N and Mamat, A and Tu, X}, title = {Prevalence of antibiotic resistance gene in different wastewater treatment systems and effluent-irrigated soils through metagenomic analysis.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {5167}, pmid = {41526579}, issn = {2045-2322}, support = {XJJT2KX-FWCG-202411-0736//Research and Demonstration Application of Technology for the Construction of Near Zero Carbon Smart Service Areas with Self Consistent Water Resources and Energy in Desert Areas/ ; 51968067//National Natural Science Foundation of China/ ; 2024TSYCCX0014//the "Tianshan Yingcai" Cultivation Program/ ; }, mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Water Purification/methods ; Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Agricultural Irrigation ; Bacteria/genetics ; }, abstract = {Wastewater treatment systems (WWTS) are considered to be the main source of antibiotic resistance genes (ARGs) spreading into the environment. In this study, samples were collected from WWTS influent, biological treatment tank effluent, and recycled water treatment plant (RTP) effluent during summer and winter, followed by metagenomic sequencing. The study investigated the differences in antibiotic resistance gene transfer between two typical wastewater treatment plants (WWTPs) processes and the impact of recycled water irrigation on ARG dissemination in soil. The WWTS (HD and MD) adopting two combined processes of "Adsorption-Biodegradation Process(AB)+ Anaerobic-Anoxic-Oxic Process(AAO)" and "AAO + Membrane Bioreactor(MBR)" as the research objects for the first time.The primary ARGs types identified were multidrug resistance, tetracycline, macrolide, and aminoglycoside resistance genes. The top three ARGs subtypes by relative abundance in the influent, biological treatment tank effluent, and total effluent were msrE, mphE, and ANT(6)-Ia, respectively. Seasonal variations did not significantly influence the distribution of ARGs in the two WWTSs. The AAO and AB processes increase the relative abundance and diversity of ARGs, while ARGs relative abundance decreases after RTP treatment but may proliferate new ARGs subtypes. Additionally, the efficiency of reducing the relative abundance of ARGs in summer is higher than that in winter. The two WWTSs were able to efficiently remove msrE and mphE. The abundance and diversity of ARGs and microorganisms were maximum in soil samples from the RTP. The microbial genera significantly related to ARGs may become its potential host, such as Rhodanobacter had significant correlations with ropB2, carA, and oleB. These results provide new insights into the control of ARGs contamination and focus on the risks associated with irrigated wastewater.}, } @article {pmid41526915, year = {2026}, author = {Shao, D and Li, Y and Chen, S and Ma, S and Liu, Y and Huang, W and Liu, D and Lyu, Y and Xia, Z and Wang, Y}, title = {Improved RNA-based metagenomic sequencing for rapid pathogen detection in pets.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {41526915}, issn = {1746-6148}, support = {2022YFD18000400//National Key Research and Development Program of China/ ; PC2023A01002//Pinduoduo-China Agricultural University Research Fund/ ; }, abstract = {UNLABELLED: In veterinary medicine, particularly in pet clinics, the accurate and rapid detection of pathogens is crucial for effective disease diagnosis and treatment. Traditional diagnostic methods are often time-consuming and fall short in identifying a broad spectrum of pathogens. The newly developed metagenomic transcriptomics next-generation sequencing (mtNGS) technology is a promising tool for the rapid detecting RNA- and DNA-based pathogens. However, its application in pet clinics has been limited due to high costs, complex operational procedures, and the absence of unified protocols. Here we established a standardized mtNGS workflow for pathogen detection tailored to various clinical sample types from pets. This workflow involves the extraction of total RNA without rRNA depletion and sequencing using Illumina platforms. It also incorporates Bowtie2 to eliminate host genome sequences and MetaPhlAn3 to identify microbial compositions. Our mtNGS technology was evaluated in 16 diverse clinical cases involving body fluids, fecal samples, nasopharyngeal swabs, and tissue samples from dogs, cats, and parrots. Notably, it detected pathogens in all cases, including an identification of Mycobacterium intracellulare in a cat, highlighting its utility in diagnosing zoonotic diseases. These results, corroborated by traditional techniques, demonstrate that the mtNGS-based diagnostic approach is particularly advantageous in cases where conventional diagnostics are insufficient or when multiple co-infections are suspected. This method exhibits potential in diagnosing complex clinical diseases that are challenging to identify using traditional techniques, thus representing a promising tool and can be widely applied in veterinary diagnostics.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12917-025-05174-0.}, } @article {pmid41526953, year = {2026}, author = {Quijia-Pillajo, J and Naik, S and Chapin, LJ and Owen, JS and Jones, ML}, title = {Calcium phosphate-solubilizing bacteria promote growth and alleviate phosphorus deficiency in French marigold with minimal impact on the rhizosphere microbiome.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {24}, pmid = {41526953}, issn = {2524-6372}, support = {2021-09976//NIFA Agriculture and Food Research Initiative - Foundational Knowledge of Agricultural Production Systems/ ; }, abstract = {BACKGROUND: Plant roots are surrounded by communities of microbes that influence plant growth, development, and disease resistance. In soilless culture, microbial diversity in root-associated communities primarily originates from the substrate, irrigation water, and applied microbial inoculants. Phosphate solubilizing bacteria (PSB) capable of mobilizing phosphate from insoluble Ca3(PO4)2 were identified from a greenhouse rhizobacteria collection. Plant growth promoting efficacy was investigated at different substrate pH. The influence of the inoculum composition on plant growth responses to the bacteria was also evaluated. Finally, we analyzed the impact of PSB inoculation on microbiome composition and function.

RESULTS: From 1044 isolates in the rhizobacteria collection, 14 solubilized more than 25% of the phosphorus provided in vitro. Only eight bacterial strains resulted in growth promotion benefits in planta when inoculated as a substrate drench onto marigolds grown in a peat-based substrate (pH 7.0) and fertilized with insoluble Ca3(PO4)2. In a follow up experiment, two newly identified (Pantoea sp. C2G6 and Enterobacter soli C4A1) and three previously identified PSB (Pantoea trifolii C2B11, Pantoea formicae C8D10, and Bacillus velezensis) that have demonstrated superior phosphate-mineral solubilization were evaluated. The PSB were tested at a substrate pH of 6.0 and 6.5 using water, 1% glucose, 2% Micromate, or 0.1X Luria-Bertani (LB) broth as inoculant supplements. All five bacteria promoted growth and improved plant health at both pH levels. A greater benefit to marigold growth and health was observed in plants growing at pH 6.5. C2B11, C8D10, C2G6, and B. velezensis treatment resulted in a significant increase in shoot P content. Microbiome diversity and community structure exhibited no significant alterations in response to PSB treatment. Genes enriched in PSB treated rhizospheres were mostly related to colonization, competition, and biofertilization traits.

CONCLUSIONS: PSB isolated from the rhizosphere of floriculture crops grown in soilless substrates promoted growth and enhanced health of marigolds grown under P limitation. They also enhanced growth under optimal or slightly basic pH, but their efficacy was not improved by the inoculant supplements evaluated in this experiment. The native microbial community in peat-based soilless substrate was resilient to PSB inoculation.}, } @article {pmid41527012, year = {2026}, author = {Weber, C and Wind, D and Petzsch, P and Supprian, T and Dilthey, A and Christl, J and Finzer, P}, title = {Dysbiotic shift in the oral microbiota of patients with Alzheimer's disease compared to their healthy life partners-a combinatorial approach and a paired study design.}, journal = {Alzheimer's research & therapy}, volume = {18}, number = {1}, pages = {23}, pmid = {41527012}, issn = {1758-9193}, mesh = {Humans ; *Alzheimer Disease/microbiology ; Female ; Male ; *Microbiota ; *Dysbiosis/microbiology ; *Mouth/microbiology ; Aged ; Aged, 80 and over ; Saliva/microbiology ; Metagenomics ; }, abstract = {BACKGROUND: The oral microbiota has been associated with Alzheimer's disease (AD). However, earlier studies provided conflicting results using varying sampling methods, sequencing techniques, and statistics, as well as independent subjects.

METHODS: To robustly identify disease-associated microbial features, we recruited patients and their healthy life partners from the same households sharing a more similar microbiota compared to independent individuals increasing statistical power via paired design and combined three different sequencing methods - including metagenomics-and several bioinformatic pipelines. We recruited 26 AD-patients and their life partners. Salivary and supragingival samples were collected and a clinical examination of the mouth was performed.

RESULTS: Both groups showed comparable oral health. By focusing primarily on recurrently identified species across the different datasets we were able to identify a Core dysbiosis. This Core dysbiosis surprisingly spares the most central of oral diseases pathogens, namely Porphyromonas gingivalis. However, it includes numerous other species commonly associated with oral pathologies such as Prevotella nigrescens, Streptococcus anginosus, Dialister invisus, Anaeroglobus geminatus, Olsenella uli and Mogibacterium timidum. In contrast, more host-compatible species such as Prevotella melaninogenica or Streptococcus parasanguinis are identified in controls.

CONCLUSIONS: This is the first study using a combined sequencing approach and a paired study design to identify robust features of the oral microbiota of AD-patients. Although promising, the results should nevertheless be interpreted with caution, as the cross-sectional study design limits the possibilities of interpretation, and larger, longitudinal data are necessary for causal conclusions. However, this combined approach on multiple processing levels to identify intra-partnership differences still offers the possibility to better identify disease-associated microbial features potentially involved in AD-pathogenesis.

TRIAL REGISTRATION: This study was prospectively registered at the German Clinical Trials Register (DRKS00023456) at the 30th of November 2020.}, } @article {pmid41527052, year = {2026}, author = {Zhou, L and Xu, Y and Wang, L and Li, X}, title = {Trichoderma harzianum fungemia following COVID-19-related immune dysregulation in an immunocompetent patient: a case diagnosed by mNGS.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {298}, pmid = {41527052}, issn = {1471-2334}, support = {No.2020SCZT062//Jilin Provincial Department of Finance,China/ ; }, abstract = {BACKGROUND: Trichoderma harzianum is a filamentous saprophytic fungus rarely implicated in human infections. Invasive Trichoderma infections are uncommon and are typically observed in immunocompromised hosts. CASE PRESENTATION: We report a 68-year-old immunocompetent male farmer who developed persistent fever and dizziness after COVID-19 infection. Initial empirical antibacterial and antiviral therapy failed to relieve symptoms. Repeated blood cultures and serological fungal tests were negative, whereas metagenomic next-generation sequencing (mNGS) of whole blood identified T. harzianum sequences (794 reads), confirming fungemia. The patient experienced severe infusion reactions to amphotericin B and visual disturbances with voriconazole, but responded well to posaconazole therapy. Fever subsided within seven days, mNGS sequence reads declined markedly, and no recurrence occurred during 12 weeks of follow-up. CONCLUSIONS: This case represents the first documented instance of T. harzianum fungemia in an immunocompetent individual following transient immune dysregulation associated with COVID-19. The report underscores the diagnostic value of mNGS in detecting rare opportunistic fungi when conventional cultures are negative and highlights posaconazole as a potential therapeutic option.}, } @article {pmid41527141, year = {2026}, author = {Liu, YY and Xia, F and Yimuran, R and Nuermamaiti, A and Yang, Y and Zhou, JT}, title = {Assessing whether rectal swabs reflect appendiceal microbiota profiles in acute appendicitis: a 16S rRNA-based comparative study.}, journal = {Gut pathogens}, volume = {18}, number = {1}, pages = {10}, pmid = {41527141}, issn = {1757-4749}, support = {2023D01A93//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; }, abstract = {BACKGROUND: Acute appendicitis is associated with characteristic changes in the intestinal microbiota, but direct sampling of appendiceal contents is invasive and cannot be performed in healthy controls. We therefore evaluated whether rectal swabs could partially capture appendiceal microbiome signatures in adults with acute appendicitis.

METHODS: In a prospective cross-sectional study, we enrolled adults with acute appendicitis and healthy volunteers between October 2023 and December 2024. Four types of samples were collected: feces from healthy controls (HC), appendiceal luminal contents from patients with acute appendicitis (AC), intraoperative rectal swabs from patients with acute appendicitis (RS), and initial postoperative feces from patients with acute appendicitis (IF; first stool within 24 h after surgery). 16 S rRNA gene (V3-V4) sequencing was performed, and reads were processed with QIIME2. Alpha and beta diversity, differential taxonomic composition, and PICRUSt2-based functional predictions were compared across matrices. Genus-level and functional concordance between paired AC-RS samples was assessed.

RESULTS: After quality control, 64 AC, 34 RS, 24 IF, and 29 HC samples were included. Phylogenetic diversity (PD whole-tree) was higher in AC and RS than HC, with AC also higher than RS; IF showed lower PD than AC. Bray-Curtis principal coordinate analysis showed AC forming a distinct cluster separated from HC and RS along PC1, whereas IF overlapped with HC and RS. AC, RS, and IF were enriched for Escherichia/Shigella and Fusobacterium and depleted in butyrate-producing genera such as Faecalibacterium compared with HC. In the 21 paired AC-RS cases, genus-level relative abundances and several predicted functional pathways showed concordance, indicating that RS captured many but not all appendiceal dysbiosis features.

CONCLUSIONS: Our findings suggest that intraoperative rectal swabs may partially reflect appendiceal microbiome alterations at the genus and pathway levels and may serve as a minimally invasive adjunct for microbiome profiling in acute appendicitis. However, these associations are inferred from 16 S amplicon data in a modestly sized, antibiotic-exposed cohort and should be validated using shotgun metagenomics in larger, clinically stratified populations.}, } @article {pmid41527156, year = {2026}, author = {Buffoni, M and Kerkvliet, JJ and Enting, H and Kers, JG and Rogers, M and Visser, JAGM and Paganelli, FL and Willems, RJL and Schürch, AC}, title = {Coccidiosis prevention strategies shape the microbiome, resistome and mobilome composition in the broiler gut.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {3}, pmid = {41527156}, issn = {2524-4671}, abstract = {BACKGROUND: Coccidiosis is a parasitic infection in the gut of livestock that poses a significant health challenge in poultry farming, underscoring the important role of intervention and prevention strategies in the poultry industry. The use of anticoccidial drugs raises concerns about antimicrobial resistance (AMR) due to their antimicrobial properties and the ability of bacteria to evolve resistance to these drugs. Whether anticoccidial drug resistance could extend beyond coccidiostats, leading to cross-resistance and co-selection against other antimicrobial resistance genes (ARGs), is currently under discussion. Also, it is not well understood to what extent coccidiosis reduction strategies may enable the emergence of ARGs in farm environments and transmission of ARGs to other environments through bacterial clonal transfer or horizontal transmission via mobile genetic elements (MGEs) like plasmids or transposons. RESULTS: In this study, we used metagenomic sequencing of caecal and faecal dropping samples from broiler chickens to investigate how two anticoccidial prevention strategies (vaccination and coccidiostat drugs) influence bacterial taxonomic composition and ARG profiles. We also explored the mobile resistome, ARGs located on mobile genetic elements (MGEs) such as plasmids, which are capable of disseminating, investigating ARGs identifying with the potential to disseminate within and beyond farm settings. Our exploratory findings in bacterial composition, as well as resistome composition with 21 differentially abundant ARGs, illustrating the potential impact of anticoccidial strategies on the chicken gut microbiome and resistome. We also identified 14 plasmid fragments containing ARGs in faecal dropping samples, highlighting mobile ARGs potentially able to disseminate to other environments, including humans. CONCLUSIONS: Our findings demonstrate the impact of anticoccidial strategies on the chicken gut microbiome and resistome with potential consequences for the dissemination of ARGs.}, } @article {pmid41527291, year = {2026}, author = {Chen, W and Guo, R and Zhang, W and Yan, Q and Wang, X and Chen, R and Hu, X and Liang, J and Xing, G and Xu, D and Ma, X and Chen, Q and Sha, S and Tao, E and Cheng, L and Fan, S and Liu, H and Lu, T and Yu, H and Su, J and Xu, J and Qin, Y and Liu, J and Zhong, X and Hu, X and Hu, X and Zheng, W and Hu, Z and Kang, J and Yang, J}, title = {Alterations of the gut virome in patients with Parkinson's disease.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {81}, number = {3}, pages = {}, doi = {10.1093/gerona/glag001}, pmid = {41527291}, issn = {1758-535X}, support = {82370563//National Natural Science Foundation of China/ ; 2024JJ7423//Natural Science Foundation of Hunan Province/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; }, mesh = {Humans ; *Parkinson Disease/virology/diagnosis ; *Gastrointestinal Microbiome ; *Virome ; Female ; Male ; Aged ; Metagenomics ; Case-Control Studies ; }, abstract = {Gut microbiota plays a pivotal role in Parkinson's disease (PD) pathogenesis. However, the role of enteric viruses remains underexplored. Here, we reanalyzed publicly available metagenomic datasets from two independent cohorts, including 79 PD patients and 79 controls, to characterize gut virome profiles and explore the potential role of enteric viruses in PD pathogenesis and early diagnosis. Our findings indicate increased richness and diversity of the gut virome in PD, with 640 vOTUs differing in abundance between groups. Notably, Siphoviridae and Myoviridae were more abundant in PD patients. A variety of viruses enriched in PD or healthy subjects (HS) preferentially infect bacterial hosts that produce short-chain fatty acids. Furthermore, specific viral functional orthologs, such as thymidylate synthase (K00560) and integrases (K14059), displayed notable differences in prevalence between PD-enriched and HS-enriched vOTUs. Finally, we constructed a random forest model using the top 22 most significant vOTUs, which achieved an AUC of 0.822, demonstrating strong performance in distinguishing PD patients from healthy controls. This is the first study to characterize the gut virome profile in PD, laying a robust foundation for future investigations into the underlying mechanisms and early diagnosis strategies for PD as well as other neurodegenerative disorders.}, } @article {pmid41527828, year = {2026}, author = {Kaur, I and Shaw, B and Multani, A and Malhotra, S and Dong, HV and Lukose, C and Prabaker, K and Saleh, T and Sim, YB and Tymchuk, CN and Uslan, DZ and Zhou, H and Brewer, TF and Yang, S}, title = {Clinical utility of serial plasma cell-free DNA metagenomic next-generation sequencing assays.}, journal = {Infection control and hospital epidemiology}, volume = {47}, number = {3}, pages = {325-327}, pmid = {41527828}, issn = {1559-6834}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; *Cell-Free Nucleic Acids/blood ; Female ; Male ; }, abstract = {This single center retrospective observational study of serial plasma metagenomic next-generation sequencing testing shows that >95% of serial testing was without meaningful clinical impact. Only 5/173 cases were adjudicated as having significant clinical impact.}, } @article {pmid41528122, year = {2026}, author = {McMurray-Jones, A and Spann, K and Yarlagadda, PKDV and Fernando, J and Roberts, LW}, title = {Environmental surveillance of bacteria in a new intensive care unit using plate sweeps.}, journal = {Microbial genomics}, volume = {12}, number = {1}, pages = {}, pmid = {41528122}, issn = {2057-5858}, mesh = {*Intensive Care Units ; Humans ; *Bacteria/genetics/isolation & purification/classification ; Metagenomics/methods ; Queensland ; Drug Resistance, Bacterial/genetics ; *Environmental Monitoring/methods ; Microbiota ; High-Throughput Nucleotide Sequencing ; }, abstract = {The hospital environment plays a critical role in the transmission of infectious diseases. Surveillance methods often rely on selective enrichment or deep metagenomic sequencing, which both have significant drawbacks in terms of community resolution and cost. Plate sweeps provide a practical moderate approach to cultivate a wide range of bacteria, capturing more diversity than a single colony pick without high sequencing costs. Here, we use this approach to characterize a newly built hospital intensive care unit (ICU) in Queensland, Australia. Between November 2023 and February 2024, we sampled 78 sites within an 8-bed private hospital ICU pre- and post-patient introduction to the environment. Samples were enriched on non-selective media before DNA was extracted from whole plate sweeps and sequenced using Illumina. We assessed species, antimicrobial resistance (AMR) genes, virulence genes and transmission across all samples and between the pre- and post-patient samples using Kraken2, AbritAMR and Tracs. While the rate of positive microbial growth within the ICU environment did not change significantly pre- and post-patient introduction, the post-patient microbiome consisted of largely different bacterial species; of 22 genera identified, only 3 genera were represented at both timepoints. Post-patient samples were enriched in AMR genes, including resistance to fosfomycin, quinolones and beta-lactams. Common genera identified post-patient were Pseudomonas, Delftia and Stenotrophomonas, often associated with areas of plumbing. Cluster analysis identified 17 possible transmission links from a single timepoint, highlighting several areas in the ICU (e.g. communal bathrooms) as key areas for transmission. We demonstrate the utility of plate sweeps as a means of economical non-selective environmental surveillance and highlight their ability to identify hotspots of transmission within a hospital ward that could be targeted by infection control prior to an outbreak of a more serious pathogen.}, } @article {pmid41528142, year = {2026}, author = {Boey, JS and Tee, HS and Waite, DW and Handley, KM}, title = {Genetic mechanisms for estuarine carbohydrate degradation and linked transcriptional activity.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {2}, pages = {e0185225}, pmid = {41528142}, issn = {1098-5336}, support = {1806//Genomics Aotearoa/ ; 2101//Genomics Aotearoa/ ; }, mesh = {*Estuaries ; *Carbohydrate Metabolism ; Geologic Sediments/microbiology ; *Bacteria/genetics/metabolism ; Metagenome ; Polysaccharides/metabolism ; Transcription, Genetic ; }, abstract = {The current understanding of carbohydrate substrate degradation is largely derived from incubation experiments involving specific substrates. In estuaries, carbohydrates are often grouped together with other sources of carbon, for analytical purposes, and measured as total and fractional organic matter. Here, we describe putative carbohydrate degradation at the polysaccharide level by the prokaryotic community in an estuary. Samples were collected along a freshwater-to-marine salinity gradient from both the water column and underlying benthic sediments. Metagenomic and metatranscriptomic data were used to determine carbohydrate-active enzyme (CAZyme)-encoding metagenome-assembled genomes and associated transcriptional activity across the gradient. Previous work demonstrated assimilation of xylan (a component of hemicellulose) in estuaries. We show the genetic mechanisms associated with the degradation of xylan, as well as arabinogalactan (also from hemicellulose), and various other glycans were widespread among estuarine taxa and actively expressed. In addition, results show different carbohydrate degradation strategies between planktonic and benthic organisms. For example, results indicate that sediment communities harbored a greater variety and density of CAZyme-encoding genes and capacity to degrade complex plant biomass (cellulose and hemicellulose) and dedicated more gene transcription overall to CAZymes than planktonic communities. In contrast, planktonic prokaryotes tended to express a greater fraction of their CAZyme-encoding gene repertoires. The transcription of gene clusters associated with degrading beta-1,3-glucans such as laminarin was prevalent in the water column. Microbial activity to degrade alpha-glucans such as glycogen was predicted to be ubiquitous but was greatest in planktonic communities. Taken together, results highlight differences in the capacity of planktonic and benthic communities to degrade carbohydrates, which reflect differences in substrate availability and complexity.IMPORTANCEEstuaries are productive ecosystems that combine various forms of organic carbon from autochthonous (e.g., algal primary producers and mangroves) and allochthonous (e.g., terrestrial plant) sources. The degradation and recycling of this organic carbon is driven by heterotrophic bacteria that are expected to harbor diverse genetic mechanisms for carbohydrate degradation to match the diversity and complexity of organic carbon encountered in the environment. Results here illustrate the diversity of carbohydrate-active enzymes (notably glycosyl hydrolases) encoded by estuarine communities and the different substrate prioritizations of planktonic and benthic communities.}, } @article {pmid41528333, year = {2026}, author = {Velioglu, EM and Arslan, U and Kayis, SA and Maçin, S and Kamada, N and Hakki, SS}, title = {Corrigendum: Correlation in the change of gut microbiota with clinical periodontal parameters in grade C periodontitis patients after non-surgical periodontal therapy.}, journal = {Journal of medical microbiology}, volume = {75}, number = {1}, pages = {}, doi = {10.1099/jmm.0.002120}, pmid = {41528333}, issn = {1473-5644}, } @article {pmid41528680, year = {2026}, author = {Wu, C and Zeng, B and Ning, Z and Wang, W and Wang, Y and Zhang, Q and Lu, D}, title = {Cloning and Characterization of a PL6 Alginate Lyase Aly94 from the Marine Bacteria.}, journal = {Molecular biotechnology}, volume = {68}, number = {7}, pages = {3158-3170}, pmid = {41528680}, issn = {1559-0305}, support = {32201039//National Natural Science Foundation of China/ ; ZR2022QC247//Natural Science Foundation of Shandong Province/ ; 2023YX040//Weifang Science and Technology Development Plan Project (Medical Category)/ ; }, mesh = {*Polysaccharide-Lyases/genetics/metabolism/chemistry ; Cloning, Molecular ; Substrate Specificity ; Alginates/metabolism/chemistry ; *Bacteria/enzymology/genetics ; Oligosaccharides/metabolism ; Hydrogen-Ion Concentration ; *Bacterial Proteins/genetics/metabolism/chemistry ; Amino Acid Sequence ; Aquatic Organisms ; }, abstract = {Microbial alginate lyases are essential biocatalysts for analyzing alginate structure and sustainably producing bioactive alginate oligosaccharides (AOS). In this study, we characterized Aly94, a novel alginate lyase from the polysaccharide lyase family 6 (PL6) family, identified from a marine sediment metagenomic library. Biochemical analyses showed Aly94 exhibits optimal activity at 40 ℃ in 50 mM NaH2PO4-Na2HPO4 buffer (pH 7.0). Adding 20 mM NaCl significantly increases its catalytic efficiency. The enzyme exhibits a strong preference for polyguluronate (polyG) over polymannuronate (polyM), with specific activities of 4.19 U/mg (polyG), 0.25 U/mg (polyM), and 2.45 U/mg (alginate). When degrading substrates-particularly polyG-Aly94 primarily generates trisaccharides. Although Aly94 acts as an endolytic alginate lyase, it also could digest the monosaccharides from small oligosaccharide chains (∆G3, ∆G4). These catalytic properties, combined with its polyG-specific depolymerization, made Aly94 a promising candidate for biotechnological applications requiring controlled alginate saccharification and high-value AOS production.}, } @article {pmid41529347, year = {2026}, author = {Singh, S and Bajaj, A and Manickam, N}, title = {Microbiome of soil waste dumpsite and adjacent river habitat harbors dynamic plastic degrading bacterial diversity and abundant functional enzymes.}, journal = {The Science of the total environment}, volume = {1014}, number = {}, pages = {181331}, doi = {10.1016/j.scitotenv.2025.181331}, pmid = {41529347}, issn = {1879-1026}, mesh = {*Rivers/microbiology ; *Plastics/metabolism/analysis ; India ; *Microbiota ; *Bacteria/classification/metabolism ; Biodegradation, Environmental ; *Soil Microbiology ; *Waste Disposal Facilities ; *Soil Pollutants/metabolism/analysis ; Metagenome ; }, abstract = {Landfill leachates and adjacent riverine ecosystems are usually the reservoirs of plastic-derived contaminants and other xenobiotics. Yet these sites are still less explored for their degradation potential. This study employed a whole metagenome analysis to characterize microbial communities and functional genes from the Ghaila municipal dumpsite and the Gomti river, Lucknow, India. Physicochemical analyses revealed neutral to slightly alkaline pH and elevated BOD and COD in downstream river sites, indicating high organic and plastic-associated pollutant loads. Taxonomic profiling identified 57 phyla, dominated by Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, with occurrence of key genera such as Pseudomonas, Acinetobacter, Flavobacterium, and Sphingomonas in abundance. Functional annotation of the metagenomic sequences detected 31 enzymes targeting 24 polymeric substances, including PETase, MHETase, urethanases, laccases, and nylon hydrolases in both dumpsite leachate and sludge (p < 0.05) samples. Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were widely distributed, particularly in leachate and sludge, underscoring their role as resistance reservoirs. These findings demonstrate that municipal dumpsite ecosystems are hotspots for plastic and xenobiotic degradation, highlighting their potential as genetic resources for bioremediation and advancing understanding of contaminant-driven microbial adaptation at landfill-river interfaces. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The complete metagenome sequence has been deposited at NCBI GenBank having accession no: SAMN42678420 to SAMN42678429 (BioProject).}, } @article {pmid41529381, year = {2026}, author = {Haars, J and Cumlin, T and Ladenvall, C and Lennerstrand, J and Kaden, R}, title = {Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel.}, journal = {Virology}, volume = {616}, number = {}, pages = {110789}, doi = {10.1016/j.virol.2026.110789}, pmid = {41529381}, issn = {1096-0341}, mesh = {Humans ; *Nanopore Sequencing/methods ; *Viruses/genetics/classification/isolation & purification ; Genome, Viral ; *Metagenomics/methods ; *Virus Diseases/virology ; High-Throughput Nucleotide Sequencing/methods ; Virome ; }, abstract = {The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, designed to target all known pathogenic viruses. Unlike shotgun metagenomics, where human DNA dominates, this method enriches for viral sequences within samples. This study presents a novel protocol called Twist-ONT, integrating Twist CVRP with Oxford Nanopore Technologies (ONT) long-read sequencing. Using clinical nasopharyngeal/throat swab and plasma samples PCR-positive for a variety of different viruses, the protocol's capability for viral species classification was demonstrated. It is also shown how high-quality whole-genome assemblies and consensus sequences can be generated from the sequencing reads of this protocol. This protocol facilitates further studies into the viromes of clinical samples and viral genomics in general using ONT sequencing.}, } @article {pmid41529435, year = {2026}, author = {Xiao, Y and Sheng, ZM and Taubenberger, JK}, title = {Precursors to the 1918 pandemic: Finding Rickettsia felis and Mucor co-infection associated with a death in 1912.}, journal = {International journal of paleopathology}, volume = {52}, number = {}, pages = {69-75}, pmid = {41529435}, issn = {1879-9825}, support = {Z01 AI000986/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; Female ; *Coinfection/history/microbiology ; *Mucormycosis/history/complications ; Infant ; *Pandemics/history ; Pneumonia/history/microbiology ; Lung/microbiology/pathology ; }, abstract = {OBJECTIVE: To investigate potential molecular evidence of the presence of infuenza A in a patient who died in 1912.

MATERIALS: Two to three paraffin curls from a formalin-fixed paraffin-embedded (FFPE) lung sample from an autopsy case of a one-and-a-half-year-old girl who reportedly died of acute pneumonia at the Royal London Hospital on February 1, 1912.

METHODS: RNA was extracted from the sample. Real-time reverse transcription PCR (RT-PCR) was performed to screen for influenza A virus, followed by total RNA library preparation and high-throughput sequencing on the Illumina NextSeq platform. Bioinformatic analysis was conducted on the obtained reads, which included metagenomic classification and sequence alignment to reference genomes.

RESULTS: Real-time RT-PCR and next-generation sequencing both revealed no evidence of influenza A virus infection. However, metagenomic analysis identified a significant number of reads matching Rickettsia felis, with 233 unique reads specifically aligning to its OmpB gene, and over 4 million fungal reads classified within the Mucor genus, although the exact species could not be determined. These findings provide suggestive molecular evidence of co-infection with R. felis and a Mucor species.

CONCLUSIONS: This study demonstrates the utility of modern molecular techniques in evaluating early diagnoses. Despite records attributing the cause of death to acute pneumonia, no influenza A virus RNA was detected. The identification of R. felis and Mucor sequences suggests that this rare co-infection may have contributed to the infant's death.

SIGNIFICANCE: Retrospective diagnosis is enhanced by the use of modern molecular and bioinformatic techniques. This case study provides important paleopathological insight into the etiology of recorded "acute pneumonia", indicating the presence of pathogens other than influenza A leading up to the 1918 pandemic.

LIMITATIONS: Contamination during autopsy, tissue processing, or storage cannot be ruled out. Due to the lack of remaining material, histopathological confirmation of Mucor or Rickettsia infection was not possible.

Molecular and bioinformatic research into other cases of suspected influenza A.}, } @article {pmid41529629, year = {2026}, author = {Chen, Z and Zhao, Y and Jin, L and Ma, R and Zhao, H and Ren, H and Huang, H}, title = {Insights into the molecular mechanism driving transformation and detoxification of erythromycin in anoxic biofilters.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141116}, doi = {10.1016/j.jhazmat.2026.141116}, pmid = {41529629}, issn = {1873-3336}, mesh = {*Erythromycin/chemistry/toxicity/metabolism ; *Water Pollutants, Chemical/chemistry/toxicity/metabolism ; Filtration ; *Anti-Bacterial Agents/chemistry/toxicity/metabolism ; Molecular Docking Simulation ; Anaerobiosis ; Water Purification/methods ; Waste Disposal, Fluid/methods ; }, abstract = {Erythromycin (ERY), the most prevalent macrolide antibiotic detected in aquatic environments worldwide, has attracted considerable scientific interest. This concern stems from its persistent environmental presence, largely due to the limited removal efficiency of conventional wastewater treatment processes. Anoxic biofilters were established with two nutritional modes (heterotrophic/autotrophic) and two filter media (bio-ceramic/poly-urethane particle) to reveal the migration and transformation patterns of ERY. Through non-targeted and targeted analysis, 18 transformation products (TPs) were identified, including 11 previously unreported TPs. By integrating metagenomic analysis with molecular docking, key genes, enzymes, and pathways were identified. Linking the molecular mechanism of ERY transformation with toxicity prediction can categorize the toxicity of TPs from high to low into four levels. It is worth noting that the hydrolysis, phosphorylation, and oxidation of hydroxy process is most conducive to reducing the environmental toxicity of ERY. This study elucidated the fate characteristics of ERY in anoxic biofilter at the molecular level. This work provides a theoretical basis for optimizing biofilter operation to mitigate ERY. It also offers insights for developing green, advanced wastewater treatment technologies aimed at ensuring water quality health.}, } @article {pmid41529631, year = {2026}, author = {Wang, Y and Qian, Y and Shi, C and Bi, J and Dong, P and Zou, Y and Yang, Y and Tao, Y and Li, H}, title = {Seasonal dynamics and stability of gut antibiotic resistance genes in plateau pika (Ochotona curzoniae) and plateau zokor (Eospalax baileyi).}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141112}, doi = {10.1016/j.jhazmat.2026.141112}, pmid = {41529631}, issn = {1873-3336}, mesh = {Animals ; Seasons ; *Lagomorpha/microbiology/genetics ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The extreme ecosystems of the Tibetan Plateau harbor an alarming reservoir of antibiotic resistance genes (ARGs) within wildlife gut microbiomes-an emerging contaminant with significant implications for One Health. However, seasonal dynamics and pathogenic risks of these ARGs remain poorly understood. Through a 2.5-year study comparing the subterranean plateau zokor (Eospalax baileyi) and the surface-dwelling plateau pika (Ochotona curzoniae), we demonstrate how species-specific ecological strategies shape distinct ARG transmission patterns. Our results demonstrated striking eco-evolutionary trade-offs: surface pikas showed 1.3 times higher ARG diversity with strong seasonal variation, influenced by temperature-modulated bacterial community turnover and mobile genetic elements (MGEs). Conversely, subterranean zokors maintained stable, were enriched with high-risk ARGs dominated by mepA and tetO, reflecting their isolated niche. Both species consistently carried pathogenic-ARG complexes (Clostridium-bacA, Staphylococcus-Ermb) across seasons, genders, and ages, indicating established resistance reservoirs in plateau food webs. Metagenomic binning revealed co-transfer potential between ARGs and MGEs. This pioneering longitudinal study exposes a dual pattern: seasonal changes cause temporary turnover of ARGs, which harbor lower resistance risk in surface-dwelling animals, while subterranean hosts retain stable, higher-risk resistance. These findings establish critical baselines for monitoring antimicrobial resistance in vulnerable ecosystems and underscore the need for integrated One Health strategies.}, } @article {pmid41529636, year = {2026}, author = {Díaz-Moreno, N and Lebrero, R and Cantera, S}, title = {Toluene bioconversion into ectoines by halophile mixed microbial cultures.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141045}, doi = {10.1016/j.jhazmat.2026.141045}, pmid = {41529636}, issn = {1873-3336}, mesh = {*Toluene/metabolism ; *Amino Acids, Diamino/metabolism/biosynthesis ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; }, abstract = {Toluene, which has been listed in the Pollutant Release and Transfer Register (PRTR) of many countries, is one of the most emitted pollutants to the atmosphere. This study demonstrates for the first time a new perspective in toluene treatment based on its continuous bioconversion into high-value chemicals, specifically ectoine and hydroxyectoine, which hold considerable commercial relevance in the cosmetic industry with market prices reaching 1000 € kg[-1]. Specific ectoine and hydroxyectoine contents of 27.3 mg gTSS[-1] were achieved together with toluene elimination capacities of 7.2 ± 1.9 g m[-3] h[-1] and a maximum biomass concentration of 1.8 g L[-1]. Ectoine synthesis predominated initially, later shifting toward hydroxyectoine, reaching a combined amount of 71.2 mg L[-1] (ectoine:hydroxyectoine 32:68) by the end of the assay. Metagenomic analysis revealed key pathways and taxa involved in toluene degradation and ectoine and hydroxyectoine synthesis. Members of Paenibacillus, Rhodococcus and Microbacterium were identified as possessing the enzymes required for toluene degradation via the TOL pathway, while Gordonia, the most abundant genus, was primarily associated with the degradation of intermediates such as benzoate, muconate, or oxoadipate derivatives and their bioconversion into ectoine. These findings revealed a potential metabolically diverse consortium with functional complementarities, where metabolic synergies overcome species-specific limitations and promote the elimination and subsequent valorization of toluene into high-value products fostering sustainable industrial innovation.}, } @article {pmid41529797, year = {2026}, author = {Cao, X and Zhang, L and Tu, H and Li, T and Wang, G and Xiao, L and Zhang, Y and Liu, P and Li, Y and Li, J and Li, X and Hu, B and Zhang, S and Li, B}, title = {Membrane aerated biofilm reactor for largely enhanced nitrogen removal in low carbon/nitrogen ratio municipal wastewater: integrating nitrification, partial denitrification, and anammox.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {133994}, doi = {10.1016/j.biortech.2026.133994}, pmid = {41529797}, issn = {1873-2976}, mesh = {*Nitrogen/isolation & purification ; *Bioreactors/microbiology ; *Carbon ; *Biofilms ; *Denitrification ; *Wastewater/chemistry/microbiology ; *Nitrification ; *Membranes, Artificial ; Bacteria/metabolism/genetics ; *Water Purification/methods/instrumentation ; Anaerobic Ammonia Oxidation ; Aerobiosis ; }, abstract = {This study first established an integrated nitrification-partial denitrification-anammox (INPDA) process in a single-stage membrane aerated biofilm reactor (MABR) under low dissolved oxygen concentrations (0.12-0.27 mg/L) and low carbon/nitrogen ratios (1.0-3.0), without the need for anaerobic ammonia-oxidizing bacteria (AnAOB) inoculation. The optimal effluent total nitrogen (TN) concentration reached below 5 mg/L, achieving a 92.7% TN removal efficiency. Nitrifiers (including Ellin6067 and Nitrospira) oxidized a portion of ammonium to nitrate, which was subsequently reduced to nitrite by partial denitrifier Thauera utilizing influent organic carbon. Subsequently, AnAOB Candidatus Brocadia converted remaining ammonium and available nitrite into nitrogen. Metagenomics further confirmed a 32.96-fold increase in anammox-associated gene (hdh) abundance during INPDA establishment. Notably, this elevated hdh abundance remained stable even as carbon/nitrogen ratio increased, demonstrating process robustness. This study established a promising single-stage MABR strategy to advance mainstream anammox application.}, } @article {pmid41530018, year = {2026}, author = {FitzGerald, JA and Lester, KL and O' Sullivan, N and Crispie, F and Lawton, EM and Cotter, PD and McNally, P and Cox, DW}, title = {Parallel metagenomic- and culture-based approaches show nasal swabs are a good proxy for broncho-alveolar lavage in children with cystic fibrosis.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {25}, number = {2}, pages = {232-239}, doi = {10.1016/j.jcf.2025.12.011}, pmid = {41530018}, issn = {1873-5010}, mesh = {Humans ; *Cystic Fibrosis/microbiology/diagnosis ; *Metagenomics/methods ; Child, Preschool ; Female ; Male ; *Bronchoalveolar Lavage Fluid/microbiology ; *Bronchoalveolar Lavage/methods ; *Specimen Handling/methods ; Microbiota ; Oropharynx/microbiology ; }, abstract = {BACKGROUND: Broncho-Alveolar Lavage (BAL) is the reference standard for airway surveillance in clinical management of cystic fibrosis (CF), but is invasive and requires general anaesthesia in children. Non-invasive alternatives can lack specificity (Oropharyngeal swabs; OPS), or evaluation in paediatric CF (Middle meatus sampling; MMS). We sought to determine if MMS via nasal-swabs performed better than OPS at representing the microbiological attributes of BAL.

METHODS: In a stable preschool CF cohort attending a single specialist centre, we evaluated the microbiological yield of BAL, MMS, and OPS sampling using both standard clinical culturing, and shotgun metagenomic sequencing (Illumina NextSeq 500).

RESULTS: Matched BAL, MMS, and OPS from 30 preschool children provided 88 samples. While both culture and metagenomic surveillance performed well at detecting S. pneumoniae in BAL, MMS performed better at detecting S. aureus, M. catarrhalis and Escherichia coli, while OPS performed better at detecting H. Influenzae. Metagenomics revealed a significantly more diverse microbiome in OPS than BAL or MMS. While agreement on pathogen profiles varied widely between metagenomics and culture methods, MMS more accurately represented BAL, particularly for Streptococcus, M. catarrhalis, and Escherichia.

CONCLUSIONS: MMS and OPS cultures performed well as proxies for BAL in relation to certain pathogens. Metagenomics detected pathogens in many samples that were unobserved in culture, and showed the oropharynx microbiome to be much more diverse. Lung and nares microbiomes were more similar in composition and diversity. Our data suggest that nasal sampling of the middle meatus may be a more accurate surrogate for lower airway samples.}, } @article {pmid41530166, year = {2026}, author = {Zhang, Q and Chen, B and Zhang, Z and Yu, Y and Jin, M and Lu, T and Zhang, Z and Pang, Q and Xu, N and Sun, J and Chen, J and Wang, J and Zhu, D and Qian, H and Penuelas, J and Zhu, YG}, title = {Cobamide-producing microbes as a model for understanding general nutritional interdependencies in soil food webs.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {1533}, pmid = {41530166}, issn = {2041-1723}, support = {2022C02029//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Soil Microbiology ; *Food Chain ; *Cobamides/metabolism/biosynthesis ; *Bacteria/metabolism/genetics/classification ; Animals ; Phylogeny ; Soil/chemistry ; Microbiota ; }, abstract = {Nutrient crossfeeding critically governs microbiome-host interactions and ecosystem stability. Cobamides, synthesized only by prokaryotes, offer a powerful and tractable model for studying nutrient-mediated interdependencies in soil food webs; however, their ecological role in sustaining soil health remains unclear. Here, we construct the Soil Cobamide Producer database (SCP v.1.0) by integrating over 48,000 metagenomic and genomic datasets from 1,123 sampling sites. This database catalogs phylogenetically diverse prokaryotes (19 phyla, 302 genera) with cobamide biosynthetic potential. Using this resource, we identify host-specific colonization patterns of cobamide-producing microbes in fauna. These microbes also carry diverse functional traits that may contribute to trophic cascades and microbial community stability. In an Enchytraeid model, these colonizers support host development, modulate gene expression, and promote gut stability through transkingdom interactions, with cobamide biosynthesis serving as one representative trait among multiple microbial functions. At macroecological scales, cobamide-producing microbes occur across relatively high trophic levels, reflecting a broader principle of nutrient transfer that may also apply to other essential metabolites. This framework provides a general basis for studying nutritional microbes in soil food webs and advances One Health research.}, } @article {pmid41530170, year = {2026}, author = {Maeke, MD and Hassenrück, C and Aguilar-Muñoz, P and Aravena, C and Burmeister, C and Crispi, O and Diallo, POD and Fernández, C and Gouriou, M and Jamont, A and Laymand, E and Marie, B and Molina, V and Ortega-Retuerta, E and Rabouille, S and Sajeeb, MI and Sierks, M and Stevens, M and Turon, R and Valdés-Castro, V and Beier, S}, title = {Metabarcoding and metagenomic data across aquatic environmental gradients along the coasts of France and Chile.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {29}, pmid = {41530170}, issn = {2052-4463}, support = {Laboratoire international associé program//Centre National de la Recherche Scientifique (National Center for Scientific Research)/ ; 1211977//Fondo Nacional de Desarrollo Científico y Tecnológico (National Fund for Scientific and Technological Development)/ ; BE 5937/2-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Chile ; France ; Metagenomics ; Ecosystem ; *DNA Barcoding, Taxonomic ; *Metagenome ; Seawater/microbiology ; Salinity ; Microbiota ; }, abstract = {Coastal marine environments, such as lagoons, fjords or estuaries, experience pronounced environmental variability, with fluctuations in salinity, temperature and nutrient levels shaping microbial community structure and function. These gradients result in diverse habitats, which may harbour taxonomic and genetic novelty with biogeochemical and biotechnological relevance. To explore microbial diversity and functional potential across these dynamic ecosystems, we sampled 26 sites along the coasts of France and Chile, including lagoons, estuaries, fjords, harbours, as well as coastal and offshore marine sites. Surface waters were collected from all sites, with deeper layers included at three sites. Monthly sampling at six sites in France enabled the assessment of seasonal dynamics. In total, 116 samples were processed for both metabarcoding and metagenomic sequencing yielding over 53,000 amplicon sequence variants (ASVs) and 1,372 metagenome-assembled genomes (MAGs). This dataset further includes a comprehensive gene catalogue and environmental variables such as salinity, temperature, nutrient concentrations, productivity, as well as oxygen consumption metrics collected across the different ecosystems.}, } @article {pmid41530663, year = {2026}, author = {Yu, HL and Elsheikha, HM and Liang, HR and Qin, SY and Peng, P and Liu, J and Tang, Y and Guo, L and Ni, HB and Xie, LH and Lei, CC and Su, JW and Yu, MY and Qin, Y and Jiang, J and Liu, J and Xu, Y and Zhang, XX}, title = {Blastocystis infection enhances vitamins B and K2 biosynthesis in the Tibetan antelope (Pantholops hodgsonii) gut microbiota.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {40}, pmid = {41530663}, issn = {1471-2164}, support = {2023YFF1305403//the National Key Research and Development Program of China/ ; 2022KJ169//the Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; }, abstract = {The gut microbiota of the Tibetan antelope (Pantholops hodgsonii) plays a vital role in host nutrition, particularly by contributing to the biosynthesis of essential micronutrients such as vitamins B and K2. In this study, we integrated existing P. hodgsonii gut metagenome-assembled genomes with healthy and Blastocystis-infected gut metagenomic samples to investigate microbial strategies for vitamins B and K2 production, as well as the potential modulation of these biosynthetic pathways in the gut of P. hodgsonii. From a total of 33,925 metagenome-assembled genomes, we identified 14,549 non-redundant genomes encoding 182 KEGG orthologs linked to vitamin biosynthesis. Among these, 2,115 high-quality genomes were predicted to synthesize at least one vitamin de novo, yet only 2.9% could produce four or more vitamins. Comparative analyses across multiple host species, including humans, chickens, cats, and mice, revealed that members of the phyla Bacillota_A and Bacteroidetes consistently serve as primary contributors to microbial vitamin biosynthesis. Blastocystis infection was associated with a significant increase in the abundance and diversity of vitamin biosynthesis genes, reflecting adaptive shifts in microbial metabolism. Detailed genomic analyses of the thiamine biosynthesis pathway highlighted the core contributions of Bacillota_A, Bacteroidota, Verrucomicrobiota, and Methanobacteriota, underscoring complex taxonomic cooperation. These results provide novel insights into the functional specialization and taxonomic composition of the P. hodgsonii gut microbiota, offering novel insights into microbial adaptation and metabolic cooperation that support host nutritional homeostasis and resilience in extreme environments.}, } @article {pmid41530817, year = {2026}, author = {Li, R and Liao, X and Fu, X and Li, X and Liao, X and Cen, S and Zeng, J and Huang, L and Chi, H and Zou, Y}, title = {Microbiota-driven tryptophan metabolism and AhR triggered intestinal stem cell differentiation: mechanisms of huangqin decoction in ulcerative colitis repair.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {33}, pmid = {41530817}, issn = {1749-8546}, support = {2022A1515140011//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023A1515010012//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 20231800936162//Dongguan Science and Technology of Social Development Program/ ; 20221800905632//Dongguan Science and Technology of Social Development Program/ ; }, abstract = {BACKGROUND: Promoting intestinal barrier repair and epithelial regeneration is a core therapeutic objective in managing ulcerative colitis (UC). Intestinal stem cell (ISC) differentiation is pivotal in sustaining epithelial renewal and mucosal homeostasis. Huangqin decoction (HQD), a classical herbal formulation comprising Scutellaria baicalensis, Ziziphus jujuba, Paeonia lactiflora, and Glycyrrhiza uralensis, is clinically used for inflammatory bowel disease. Nevertheless, how HQD precisely regulates ISC differentiation to promote UC repair remains unclear.

PURPOSE: This research sought to assess whether HQD ameliorates UC by concurrently modulating the gut microbiome, tryptophan metabolism, aryl hydrocarbon receptor (AhR) activation, and ISC differentiation.

METHODS: Mice developed colitis after drinking water with a 3.5% (w/v) concentration of dextran sulfate sodium. We evaluated HQD effects on colon length, weight trajectory, disease activity index score, histological damage, and colonic inflammatory mediator abundance. Metagenomic sequencing resolved microbiota restructuring, while UPLC-MS/MS quantified fecal tryptophan metabolites such as indole derivatives. AhR pathway activity (AhR, CYP1A1), its downstream cytokine IL-22, and ISC fate were mapped by combining immunofluorescence, ELISA, Western blot, and RT-qPCR, probing Lgr5 for stem-cell identity and MUC2, LYZ, and ChgA for lineage-specific differentiation. The involvement of AhR and gut microbiota was investigated using AhR inhibitors and broad-spectrum antibiotics.

RESULTS: High-dose HQD significantly alleviated colitis symptoms, reduced colon damage, and corrected gut dysbiosis. HQD increased the abundance of related bacteria that elevated colonic levels of indole-3-propionic acid, indole-3-acetamide, and tryptamine, acting as AhR ligands that upregulate AhR and its downstream targets CYP1A1 and IL-22. Crucially, HQD promoted a shift in expression from the ISC marker Lgr5 toward differentiation markers MUC2, LYZ, and ChgA, indicating enhanced ISC differentiation and improved barrier function. These effects were effectively blocked by AhR inhibition or antibiotic treatment.

CONCLUSION: HQD restores intestinal mucosal integrity and attenuates colonic inflammation by modulating gut microbiota composition, increasing microbial tryptophan metabolites with AhR-agonist activity, activating the AhR signaling pathway, and promoting ISC differentiation into functional epithelial cells. This work reveals a novel "microbiota-tryptophan metabolism-AhR-ISC differentiation" axis underlying HQD's therapeutic efficacy in UC.}, } @article {pmid41530889, year = {2026}, author = {Bonacolta, AM and Keeling, PJ}, title = {Modern microbialites harbor an undescribed diversity of chromerid algae.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {25}, pmid = {41530889}, issn = {2524-6372}, support = {GBMF9201//Gordon and Betty Moore Foundation/ ; }, abstract = {BACKGROUND: Chromerid algae are the closest photosynthetic relatives of apicomplexan parasites. While chromerids have been central to understanding the evolutionary transition from free-living algae to parasitism within Apicomplexa, their ecology remains poorly understood. Although often considered coral-associated symbionts, emerging evidence suggests this link is incidental and that chromerids may be more broadly associated with calcium carbonate environments, including microbialites. These microbial structures represent modern analogues of ancient reef-like ecosystems but are difficult to study due to their rarity and protected status as world heritage sites. Prokaryotic members of the microbialite microbiome have been studied at length, while the microeukaryotes associated with these environments have gone mostly ignored. To further investigate the link between microbialites and chromerid algae, we re-analyzed previously published microbialite sequencing data with the aim of investigating chromerid diversity and distribution.

RESULTS: Through a novel plastid-focused metagenomic binning workflow combined with re-analysis of rRNA metabarcoding data, we reveal that chromerid algae are consistent associates of microbialites across diverse marine and freshwater environments worldwide. Most notably, we report the first recovery of plastid genomes from microbialite-associated chromerids: a complete Vitrella brassicaformis plastid genome and a second, partial plastid genome from a previously undescribed Chromera-related lineage in Highborne Cay thrombolites. This partial plastid genome contained photosystem genes, confirming this novel Chromera-related lineage as a photosynthetic chromerid. These findings not only expand the known ecological and biogeographic range of chromerids but also provide evidence for their overlooked diversity.

CONCLUSIONS: Our analyses prove that this overlooked algal lineage is not found exclusively associated with corals, but instead occurs across a wide range of microbialite habitats, including those found in freshwater. By extending their known distribution beyond coral hosts and the marine environment, our results not only highlight the diversity and ecological range of the most recently discovered algal lineage but also broaden our understanding of the ancestral lifestyles that may have preceded apicomplexan evolution. This research underscores the value of targeted mining of public sequencing datasets to address specific ecological questions, particularly in rare or hard-to-access environments such as microbialites.}, } @article {pmid41530917, year = {2026}, author = {Lee, HG and Song, JY and Yoon, J and Chung, Y and Kwon, SK and Kim, JF}, title = {metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2611544}, pmid = {41530917}, issn = {1949-0984}, mesh = {*Metagenomics/methods ; *Software ; *Big Data ; Humans ; *Metagenome ; Reproducibility of Results ; Microbiota/genetics ; Computational Biology/methods ; Colorectal Neoplasms/microbiology ; }, abstract = {Metagenomic approaches offer unprecedented opportunities to characterize microbial community structure and function, yet several challenges remain unresolved. Inconsistent genome quality impairs reliability of metagenome-assembled genomes, lack of unified taxonomic criteria limits cross-study comparability, and multi-step workflows involving numerous programs and parameters hinder reproducibility and accessibility. We benchmarked existing programs and parameters using simulated metagenomic data to identify optimal configurations. metaFun is an open-source, end-to-end pipeline that integrates quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomic analysis, pangenome annotation, network analysis, and strain-level microdiversity analysis into a unified framework. Interactive modules support standardized data interpretation and exploratory visualization. The pipeline is implemented with Nextflow and containerized with Apptainer, ensuring environment reproducibility and scalability. Comprehensive documentation is available at https://metafun-doc.readthedocs.io/en/main. The pipeline was validated using a colorectal cancer cohort dataset. By addressing key methodological gaps, metaFun facilitates accessible and reproducible metagenomic analysis for the broader research community.}, } @article {pmid41531057, year = {2026}, author = {Fan, YT and Chang, S and Wang, ER and Zhu, YY and Wang, SJ and Yin, XY}, title = {[Distribution， Diffusion Regularity， and Influencing Factors of Antibiotic Resistance Genes in the Water Transfer Chain from Luanhe River to Tianjin Based on Metagenomics].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {47}, number = {1}, pages = {256-268}, doi = {10.13227/j.hjkx.202410104}, pmid = {41531057}, issn = {0250-3301}, mesh = {Rivers ; *Drug Resistance, Microbial/genetics ; Metagenomics ; China ; *Water Microbiology ; *Genes, Bacterial ; Environmental Monitoring ; }, abstract = {Yuqiao Reservoir is an important drinking water source for Tianjin. As the source of the "Water Diversion Project from Luanhe River to Tianjin"， there are more than one hundred types of contamination of antibiotic resistance genes （ARGs） in the Panjiakou and Daheiting Reservoirs. However， the level of ARGs in the upstream water transfer chain of Yuqiao Reservoir （Linhe River， Shahe River， and Lihe River） has not yet been studied. It is necessary to characterize the dynamic mechanism of ARGs in this basin to gain a deeper understanding of water ecosystem security. In this study， metagenomic methods were used to investigate the distribution characteristics of ARGs and mobile genetic elements （MGEs） in the surface water of the water transfer chain from Luanhe River to Tianjin during different periods， combined with the correlation mechanisms among microbial community structure and environmental factors. The results showed that the water transfer chain of the Luan River to Tianjin contained 21 types of ARGs with 1 161 subtypes. The main types of ARGs were multidrug， macrolide-lincosamide-streptogramin b （MLSB）， and tetracycline， with macB and tetA58 being the dominant ARGs. The predominant types of MGEs were integration/excision （IE） and replication/recombination/repair （RRR）. Compared to that during the flood period， there was a significant positive correlation between ARGs and MGEs during the dry period. Correlation analysis indicated that temperature， dissolved oxygen， and nitrate showed significant correlation with various ARGs （P < 0.05）. The abundance of ARGs was more easily affected by multiple environmental factors， but the composition of ARGs showed correlations only with total phosphorus and dissolved total phosphorus. Proteobacteria was the most dominant phylum， and several dominant microbial genera， such as Acidovorax and Rhodoferax， also showed significant correlation with ARGs， especially during the dry period. The co-occurrence network analysis revealed the most significant co-occurrence relationship between ARGs and MGEs， and some microbial genera related to nutrient elements and photosynthesis also showed co-occurrence relationships with major ARGs. This project aims to profoundly understand the biogeochemical cycle mechanisms of ARGs in the upstream water transfer chain of the reservoir， and it can provide a scientific basis for decision-making to control the transmission of resistance genes within the regional basin.}, } @article {pmid41531093, year = {2026}, author = {Liu, SE and Dong, ZF and Zhang, AH and Min, W}, title = {[Effect of Biodegradable Mulching Film on Soil Microbial Community in Cotton Field was Revealed Based on Metagenomics].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {47}, number = {1}, pages = {650-662}, doi = {10.13227/j.hjkx.202411219}, pmid = {41531093}, issn = {0250-3301}, mesh = {*Soil Microbiology ; *Metagenomics ; *Gossypium/growth & development ; Biodegradation, Environmental ; *Agriculture/methods ; Soil/chemistry ; Bacteria/classification ; }, abstract = {Biodegradable mulching films （BMPs） have been widely used as an alternative to conventional plastic mulching films （CMPs）. However， the long-term effects of BMPs on soil microbial community structure remain unclear. Therefore， in this study， we set up two treatments， CMPs and BMPs， and conducted a field experiment with 26 a of CMPs and 11 a of BMPs coverage. Using metagenomics technology， the effects of BMPs on soil microbial community structure in cotton fields in arid areas were investigated. The results showed that compared with those under the CMPs treatment， the BMPs treatment significantly reduced soil water content （SWC）， bulk density （BD）， and available phosphorus （AP） by 25.00%， 12.50%， and 12.09%， respectively， but significantly increased soil porosity （SP） by 10.07%. The BMPs treatment （124） significantly reduced the number of unique species compared with that in the CMPs treatment （182）. At the phylum level， the BMPs treatment significantly increased the relative abundance of Proteobacteria and significantly decreased the relative abundance of Actinobacteria. At the genus level， the BMPs treatment significantly increased the relative abundances of Nocardioides， Solirubrobacter， and Nitrospira and significantly decreased the relative abundance of Sphingomonas. Meanwhile， the proportion of positive correlations and the average degree between microbial communities in the BMPs treatment were increased significantly by 16.32% and 8.71% compared with those in the CMPs treatment， respectively， reducing the modularization degree of the microbial community by 1.89% and promoting the symbiotic relationship and stability of the microbial community. The BMPs treatment significantly increased the relative abundance of genes such as xylA， narG/nxrA， and nasA and significantly decreased the relative abundance of genes such as accA， frdA， nirB， nrtA， gcd， and phoR， promoting carbon degradation， denitrification， and assimilative nitrate reduction processes and inhibiting dissimilatory nitrate reduction and inorganic phosphorus solubilization processes. Soil SWC and AP were the key environmental factors affecting microbial community composition. Biodegradable mulching film increased the complexity and stability of soil microbial communities compared with traditional mulching film， and soil SWC and AP were the key environmental factors affecting the composition of microbial communities.}, } @article {pmid41531535, year = {2025}, author = {Walia, A and Selvarajan, R and Ogola, HJO and Chauhan, R and Bala, J and Verma, SK and Kumar, R}, title = {Genome-resolved analysis of traditional fermented biofertilizers as scalable solutions for soil restoration.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1725475}, pmid = {41531535}, issn = {1664-302X}, abstract = {Soil degradation threatens global food security by eroding nutrient reserves and biological resilience. Microbial solutions that regenerate soil fertility through ecological processes offer a sustainable alternative to chemical intensification, yet lack mechanistic validation linking genomic potential to field performance. Fermented microbial consortia, naturally assembled through traditional practices worldwide, represent promising but underexplored technologies for biological soil restoration. Here, we integrate shotgun metagenomics, metagenome-assembled genome (MAG) reconstruction, and two-season field trials to evaluate Jeevamrit, a cattle-derived fermented biofertilizer widely used across South Asia, as a model system for understanding microbial-mediated soil restoration. Metagenomic profiling revealed that Jeevamrit fermentation of cattle dung and urine produces a functionally rich microbial consortium dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. Thirty high-quality MAGs encoded genes for nitrogen fixation (nifHDK), phosphate solubilization (phoA, pstS), potassium transport (trkA, phoR), siderophore biosynthesis, and phytohormone production (trpA, miaB), alongside enriched CAZymes (GH13, PL1) and biosynthetic clusters (NRPS, PKS, terpenes) supporting nutrient turnover and rhizosphere signaling. Field application in severely degraded Himalayan rice soils substantially improved soil health relative to controls: soil organic carbon increased from 0.53%-0.68% to 0.76%-1.04% (up to 96% increase), microbial biomass carbon rose from ~72 mg C kg[-1] to 186-282 mg C kg[-1] (159% increase), available phosphorus increased 39.5%, and grain yield improved 74%, while pH and electrical conductivity remained stable. Principal component analysis confirmed that SOC, microbial biomass, and nutrient availability drove treatment differentiation, corroborating genomic predictions. This genome-to-field framework establishes fermented microbial consortia as multifunctional solutions that restore soil fertility through ecological intensification rather than chemical supplementation. By demonstrating that traditional farmer innovations can be genomically validated and mechanistically understood, this work provides a replicable model for scaling nature-based, low-cost soil restoration technologies to address global agricultural sustainability challenges.}, } @article {pmid41532487, year = {2026}, author = {Goh, KM and Nurhazli, NAA and Tan, JH and Liew, KJ and Chan, KG and Pointing, SB and Sani, RK}, title = {Thermophiles in the genomic Era (2015-2025): a review on biodiversity, metagenome-assembled genomes, and future directions.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-18}, doi = {10.1080/1040841X.2026.2614431}, pmid = {41532487}, issn = {1549-7828}, abstract = {Thermophile research has been transformed over the past decade by advances in genome sequencing. Once centered on culture collections and physiological studies of terrestrial hot springs and deep-sea hydrothermal vents, the field now employs amplicon sequencing, shotgun metagenomics, and long-read platforms to reveal the diversity, ecology, and genomic potential of thermophiles. Metagenome-assembled genomes (MAGs), metatranscriptomes, and metaproteomes have become crucial for linking taxonomy with function, uncovering previously hidden microbial dark matter in heated ecosystems. Bioinformatics, increasingly integrated with machine learning, has expanded insights into microbial biology, biomolecules, and ecological interactions. These advances highlight the broader environmental significance of thermophiles, spanning fundamental roles in ecosystem processes to practical applications. In 2015, we published Thermophiles in the Genomic Era: Biodiversity, Science, and Application to capture early next-generation sequencing milestones. A decade later, with tremendous progress achieved, this review revisits the field by synthesizing recent advances across viruses, planktonic thermophiles, and biofilm communities, emphasizing the power of genome-resolved approaches. We also highlight overlooked areas, opportunities for ecological integration and predictive modeling, and the importance of translating discoveries into biotechnological innovation. Our aim is to provide young researchers with a roadmap of emerging questions and strategies likely to shape the next decade of thermophile research.}, } @article {pmid41533582, year = {2026}, author = {Ahrendt, SR and Haridas, S and Stong, S and Salamov, A and Steindorff, A and LaButti, K and Riley, R and Shabalov, I and Lukashin, I and Dusheyko, S and Schulz, F and Romero, MF and Villada, JC and Grigoriev, IV and Mondo, SJ}, title = {Comparative mitogenomics of kingdom Fungi - evolutionary insights and metagenomic applications.}, journal = {Nucleic acids research}, volume = {54}, number = {2}, pages = {}, pmid = {41533582}, issn = {1362-4962}, support = {//U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; }, mesh = {*Genome, Mitochondrial ; *Evolution, Molecular ; *Metagenomics/methods ; *Fungi/genetics/classification ; Phylogeny ; Ascomycota/genetics ; Genome, Fungal ; RNA, Transfer/genetics ; Oxidative Phosphorylation ; Molecular Sequence Annotation ; Mitochondria/genetics ; Cell Nucleus/genetics ; }, abstract = {Mitochondria are essential components of eukaryotic cells, responsible for ATP production through oxidative phosphorylation. Despite their biological importance, unique challenges have hindered the adoption of automated mitochondrial genome (mitogenome) annotation methods, obstructing mitochondrial comparative genomics in a broad evolutionary context. Using Fungi as a study system and a Joint Genome Institute (JGI) annotated high-quality reference set, we observed broad patterns of mitochondrial evolution across the kingdom. We found that the median fungal mitogenome size is 58 kb and identified exceptionally large examples over 1 Mb in Pezizomycetes. All 14 expected oxidative phosphorylation protein-coding genes, plus rps3, were generally conserved. We found evidence of major evolutionary transitions within the Ascomycota, including the transfer of mitochondrially encoded atp8 and atp9 to the nuclear genomes across the Pezizomycotina and shifts in mitogenome tRNA patterns across the kingdom. We found substantial concordance between mitochondrial and nuclear evolution, enabling us to document 3131 total fungal mitogenomes from JGI-derived metagenomic datasets. We also identified 6467 total undeclared mitogenomes embedded in Genbank fungal nuclear assemblies. We provide interactive tools for mitogenome analysis through the JGI MycoCosm platform. Collectively, this work generated nearly 10 000 new fungal mitogenome annotations, providing a foundation and resources for future exploration of comparative fungal mitogenomics.}, } @article {pmid41533915, year = {2026}, author = {Pang, J and Wei, Z and Zhang, Z and Xu, X and Peng, Y and Chen, Q and Wei, Y and Liu, J and Zhang, Y and Shi, Q and Wang, Z and Zhang, Y and Chen, K and Zhou, M and Lu, X and Liang, Q}, title = {Genomic Landscape Reveals Correlation of Endosymbiont Ralstonia With Acanthamoeba Keratitis Severity.}, journal = {Investigative ophthalmology & visual science}, volume = {67}, number = {1}, pages = {17}, pmid = {41533915}, issn = {1552-5783}, mesh = {Animals ; *Acanthamoeba Keratitis/microbiology/parasitology/diagnosis/genetics ; Mice ; *Acanthamoeba/genetics/microbiology ; *Ralstonia/genetics/isolation & purification ; *Symbiosis ; Disease Models, Animal ; In Situ Hybridization, Fluorescence ; Humans ; Microscopy, Electron, Transmission ; Female ; Genome, Bacterial ; Whole Genome Sequencing ; Male ; }, abstract = {PURPOSE: To identify the basic genomic profile of Acanthamoeba, obtain information on Acanthamoeba endosymbionts, and analyze the correlation between these endosymbionts and the prognosis of Acanthamoeba keratitis (AK) patients.

METHODS: Whole-genome sequencing was conducted on 30 cornea-derived Acanthamoeba strains. Pan-genome analysis was performed, and endosymbionts were identified by metagenomic analysis. Gimenez staining, fluorescence in situ hybridization, and transmission electron microscopy were used to prove the existence of endosymbionts. Linear discriminant analysis effect size was used to associate endosymbiont species with AK clinical prognosis. The correlation between the endosymbiont Ralstonia and pathogenicity was experimentally validated by assessing the biological characteristics of Acanthamoeba and by performing clinical and histopathological evaluations in AK mouse models.

RESULTS: Whole genome sequencing revealed that the Acanthamoeba genome size was 37.1-105.0 Mb and GC content was 53.9%-60.5%. Pan-genomic analysis indicated an open state of the Acanthamoeba genome. Metagenomic analysis identified the presence of endosymbionts within Acanthamoeba, notably the endosymbiont Ralstonia, which was associated with poor prognosis at the genus level (P = 0.047). Acanthamoeba harboring the endosymbiont Ralstonia exhibited an increased migration area, enhanced adhesion, and had a more pronounced cytopathic effect. The size of clinical scores and corneal ulcers showed a significant increase in mouse models induced by Acanthamoeba with endosymbiont Ralstonia.

CONCLUSIONS: Whole-genome sequencing highlighted the symbiotic relationship between Acanthamoeba and associated microorganisms. The presence of the endosymbiont Ralstonia influenced the biological characteristics of Acanthamoeba and was correlated with clinical poor prognosis in AK, suggesting its potential as a target for clinical intervention.}, } @article {pmid41534271, year = {2026}, author = {Zhou, W and Duan, C and Xue, M and Li, S and Fan, X and Wu, H}, title = {Diversity and potential environmental risks of DNA viruses on international ships' ballast water at Shanghai port, China.}, journal = {Marine pollution bulletin}, volume = {225}, number = {}, pages = {119198}, doi = {10.1016/j.marpolbul.2025.119198}, pmid = {41534271}, issn = {1879-3363}, mesh = {China ; *Ships ; *DNA Viruses ; *Water Microbiology ; *Environmental Monitoring ; }, abstract = {Over 10 billion tons of ballast water is transferred annually globally, transporting many microorganisms such as bacteria and viruses into new environments and harming local ecology, economy and human health. Numerous studies on bacteria in ballast water have shown its remarkable bacterial diversity and potential risks in recent years. However, the diversity of viruses present in ballast water and their potential environmental implications remain extremely limited in our understanding. In this investigation, we utilized viral metagenomic sequencing to evaluate the viral diversity and distribution in ballast water sourced from five distinct shipping routes that docked at Shanghai Port. Additionally, we compared the distribution of antibiotic resistance genes (ARGs) and virulence factors (VFs) harbored by viruses in ballast water from different routes. The viral diversity and community composition exhibited significant differences in the ballast water samples collected along distinct shipping routes. The virus diversity index varies across different routes, and notably, for the Shannon and Pielou indices, the DJ and GG routes were significantly lower than other routes. Although Caudoviricetes was the dominant viral group, the abundances of Megaviricetes and Faserviricetes were also relatively high, albeit showing variations among different routes. 224 ARGs were identified, including 143 single resistance genes (SARGs) and 81 multiple resistance genes (MARGs), and their distribution varied across different shipping routes. Similarly, certain types of VFs also exhibit differences across various routes, including nutritional/metabolic processes, biofilm formation, and exotoxins. Moreover, the comparison of viral environmental risks showed that ballast water from routes through the Indian Ocean and the South China Sea posed a greater environmental risk. In summary, the results of our research have uncovered the virus diversity and potential risks associated with different routes. This underscores the imperative of implementing targeted management strategies for each individual route.}, } @article {pmid41534337, year = {2026}, author = {Huang, X and Ni, Y and Ma, Z and Xie, Z and Ding, Z and Xu, H and Wei, H and Jin, Q and Zhou, R}, title = {Polymer type and aging drive the selective enrichment of antibiotic resistance genes and pathogens in microplastics biofilms.}, journal = {Water research}, volume = {292}, number = {}, pages = {125364}, doi = {10.1016/j.watres.2026.125364}, pmid = {41534337}, issn = {1879-2448}, mesh = {*Biofilms ; *Microplastics ; *Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Polymers ; Polyesters ; }, abstract = {Microplastics (MPs) biofilms are critical vectors for antibiotic resistance in aquatic environments. In this study, in situ incubation coupled with metagenomic sequencing was employed to investigate microbial colonization patterns, antibiotic resistance gene (ARG) profiles, and mobile genetic element (MGE) dissemination characteristics of biofilms on MPs surfaces of different polymer types and aging states within a unique wetland ecosystem. Results demonstrated that microorganisms preferentially colonized the hydrophobic surface of conventional polypropylene (PP) over biodegradable polylactic acid (PLA). Aging treatments further enhanced MP-microbe interactions. Microbial community analysis revealed selective enrichment of microbial communities in MPs biofilms, including clinically relevant pathogens such as Acinetobacter baumannii. Notably, despite showing lower microbial colonization, PLA enriched a higher abundance of priority antibiotic-resistant pathogens and high-risk ARGs, which further amplified following environmental aging. Co-occurrence network analysis identified seven key MGEs strongly correlated with multiple ARGs and exhibited the highest abundance on PLA-derived biofilms, indicating a high potential for horizontal gene transfer mediating the propagation of antibiotic resistance. Furthermore, Enterobacteriaceae were identified as critical co-hosts of ARGs and MGEs within the plastisphere, potentially playing a central role in maintaining antibiotic resistance. Our findings highlight a significant ecological threat from biodegradable and aged MPs in amplifying antibiotic resistance.}, } @article {pmid41534338, year = {2026}, author = {Potgieter, S and Oosthuizen-Vosloo, S and Langenfeld, K and Dowdell, KS and Vedrin, M and Lahr, R and Pinto, AJ and Raskin, L}, title = {Biofiltration, seasonality, and distribution system factors influence nitrifier communities in a full-scale chloraminated drinking water system.}, journal = {Water research}, volume = {292}, number = {}, pages = {125288}, doi = {10.1016/j.watres.2025.125288}, pmid = {41534338}, issn = {1879-2448}, mesh = {*Drinking Water/microbiology ; *Chloramines ; Filtration ; Nitrification ; Seasons ; Water Purification ; Bacteria ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Nitrification in chloraminated drinking water systems has been widely studied, although limited information is available on the role of biofiltration in shaping the nitrifier communities within drinking water distribution systems (DWDS). Additionally, the co-occurrence of comammox and canonical nitrifiers in drinking water systems remains unclear. This study investigates how biofiltration shapes nitrifier communities in a full-scale drinking water system where chloramine is a secondary disinfectant, and biofilters are backwashed with chloraminated water. Samples were collected monthly for one year from biofilter effluent, finished water, and three DWDS sites with varying water ages, water quality, and nitrite concentrations. Nitrifier abundances were quantified using droplet digital PCR, which showed contrasting temporal trends between the ammonia-oxidizing bacteria amoA gene and both nitrite-oxidizing bacteria 16S rRNA gene and comammox amoB gene abundances. Genome-resolved quantitative metagenomics revealed Nitrosomonas cluster 6a species, canonical Nitrospira species, and Nitrospira-like comammox species as the dominant nitrifiers. The same populations were detected in biofilter effluent and across DWDS sites, indicating that biofilter operation contributed to the persistence of nitrifiers in the DWDS. Further, DWDS site-specific factors, such as water age and disinfectant degradation, influenced the presence and abundance of individual nitrifier populations. These findings advance our understanding of how upstream treatment processes influence microbial community structure and nitrifier persistence in full-scale chloraminated DWDSs, and highlight the importance of considering biofilter operation, alongside disinfection practices, within integrated nitrification control strategies.}, } @article {pmid41534355, year = {2026}, author = {He, S and Wang, Z and Zhong, Z and Shi, C and Li, D and Yin, F}, title = {Soil salinization alters biogeochemical cycles in agricultural ecosystems by reducing carbon-cycling microorganisms.}, journal = {Ecotoxicology and environmental safety}, volume = {309}, number = {}, pages = {119706}, doi = {10.1016/j.ecoenv.2026.119706}, pmid = {41534355}, issn = {1090-2414}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Salinity ; Agriculture ; *Carbon Cycle ; Ecosystem ; Metagenomics ; Bacteria/genetics/metabolism ; Alphaproteobacteria/genetics ; }, abstract = {Salinity stress can decline crop yield in agricultural systems. Beyond the environmental conditions that drive agricultural plant growth, the diverse roles of microbes represent a critical, often overlooked factor in shaping crop health and productivity. Salinization exerts a profound effect on soil microbial communities, with consequences for biogeochemical cycles. However, the salinity adaptation mechanisms of microorganisms participating in biogeochemical cycles remain incompletely understood, which hold considerable promise for microbial solutions in saline agriculture. In this study, metagenomics-based technology was employed to analyze agricultural soils within a region-scale irrigation area characterized by varying degrees of salinization. According to the results of generalized linear models, bell-shaped trends were observed for the diversity and abundance of biogeochemical cycling genes along the soil salinity gradient, all of which peaked at a salinity of approximately 7.5 ‰. Further comparisons indicated reduced total abundance of all biogeochemical cycling genes in high salinity soils (>7.5 ‰) compared to those in low salinity soils (<7.5 ‰). Furthermore, correlation analysis indicated the coupling of different biogeochemical cycling genes, which were observed to be possessed by similar functional microorganisms, with a predominance of Gammaproteobacteria and Alphaproteobacteria. The presence of elevated salt levels resulted in a decline in the abundance of various microorganisms that play roles in biogeochemical cycling, including members of the Alphaproteobacteria, Actinomycetia, Limnocylindira, and Gemmatimonadetes phyla. Concurrently, there was an enrichment of a limited number of salt-tolerant bacteria, predominantly classified under the Bacteroidia and Bacilli taxonomic groups. The coupling of different biogeochemical cycling genes in some metagenome-assembled genomes (MAGs) was confirmed through metagenomics binning. Three MAGs (strains of Methylophaga, Salinimicrobium, and Sediminibacterium, respectively) with diverse biogeochemical cycling functions were recognized as potential plant-growth-promoting bacteria under salinity stress. These findings contribute to the existing body of knowledge on the salinity adaptability of soil microbial communities and offer guidance for the management of saline agriculture.}, } @article {pmid41534561, year = {2026}, author = {Chai, X and Zhang, X and Chen, D and Rong, D}, title = {Whole blood metagenomic next-generation sequencing in the diagnosis of bloodstream infection in patients with hematologic diseases.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {164}, number = {}, pages = {108375}, doi = {10.1016/j.ijid.2026.108375}, pmid = {41534561}, issn = {1878-3511}, mesh = {Humans ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Metagenomics/methods ; Middle Aged ; *Hematologic Diseases/complications/microbiology/blood ; Aged ; Adult ; Cell-Free Nucleic Acids/blood ; *Sepsis/diagnosis/microbiology/blood ; Prognosis ; }, abstract = {OBJECTIVES: This study aimed to evaluate the value of cell-free DNA (cfDNA) in plasma and genomic DNA (gDNA) in nucleated cell layer of whole blood samples detected by metagenomic next-generation sequencing (mNGS) in the diagnosis of bloodstream infection in patients with hematologic diseases.

METHODS: Whole blood samples collected from hematologic patients with suspected bloodstream infections were divided into the plasma and nucleated cell layers. The DNA of plasma and nucleated cell layers was extracted for mNGS. The pathogenic results were compared between whole blood (plasma plus nucleated cell layers) and plasma layer. In addition, the factors influencing the prognosis at discharge were analyzed.

RESULTS: In total, 92 patients were included. The positive rate of mNGS in whole blood was higher than those of the single plasma layer (58.70% vs 53.26%) and the culture layer (58.70% vs 17.39%). The consistency of plasma and nucleated cell layers was 57.6%. The proportion of fungi detected in nucleated cell layer was higher than that in plasma layer (30.2% vs 17.0%). A total of 10 patients had extra pathogens detected in whole blood compared with the single plasma layer, and the positive rate of mNGS increased by 10.87%. gDNA microbe reads and non-host ratios in the extra-detection group were significantly higher than those in the non-extra-detection group. cfDNA microbe reads, non-host ratios, and microbe percentage showed no significant differences between the two groups. The maximum Sequential Organ Failure Assessment (SOFA) score and age in the death group were significantly higher, whereas cfDNA/gDNA species richness was significantly lower compared with the survival group. The maximum SOFA score and cfDNA Shannon diversity index were found as risk factors for improved prognosis. The maximum SOFA score and cfDNA concentration were combined for the diagnosis of poor prognosis at discharge, with the highest area under the curve at 0.95.

CONCLUSIONS: Simultaneous metagenomic sequencing of plasma layer and nucleated cell layer contributes to the detection of pathogens in patients with bloodstream infections. cfDNA detection has a certain significance in predicting the prognosis of patients with bloodstream infections.}, } @article {pmid41534666, year = {2026}, author = {Chang, Y and Qiu, S and Collins, G and Hu, Y and Lee, PH and Zhan, X}, title = {Iron modulation of sulfur-mediated autotrophic denitrification: denitrification efficiency, microbial succession, and metabolic pathways.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {133997}, doi = {10.1016/j.biortech.2026.133997}, pmid = {41534666}, issn = {1873-2976}, mesh = {*Denitrification/drug effects ; *Sulfur/metabolism/pharmacology ; *Autotrophic Processes/drug effects ; *Iron/pharmacology/metabolism ; *Metabolic Networks and Pathways/drug effects ; Nitrates/metabolism ; *Bacteria/metabolism/genetics/drug effects ; }, abstract = {The application of iron sulfide-mediated autotrophic denitrification is promising for nitrate reduction in carbon-deficient wastewater and polluted groundwater. Previous studies have shown distinct functional microbial communities in different iron sulfide-mediated autotrophic denitrification systems, obscuring how iron modulates their composition and activity. In this study, iron-modulated sulfur autotrophic denitrification efficiency, microbial succession, and key pathways were investigated at different iron levels. Results showed that 1 mM Fe[2+] enhanced denitrification efficiency (91.1 %) and prevented cell encrustation. Metagenomic analysis indicated that phylum Campylobacterota (16.0 %) and genus Sulfurimonas (14.4 %) were enriched under iron-modulated conditions. Iron modulated nitrate reduction by improving the relative abundance of complete denitrification genes (napA, napB, and nosZ) and stimulating sulfur metabolism through the SOX complex pathway (soxZ and soxY). These findings reveal the role of iron in modulating sulfur-mediated autotrophic denitrification and provide new insights into the microbial mechanisms involved in iron-sulfur coupling systems.}, } @article {pmid41534755, year = {2026}, author = {Liu, K and Peng, W and Yang, X and Zeng, Y and Liu, Y and Yu, K and Zhu, Y and Gou, H and Li, L and Zhang, C}, title = {Efficacy and multi-omics regulatory effects of Guilou Tongluo formula in patients with chronic obstructive pulmonary disease combined with pulmonary hypertension: A prospective, multicenter, randomized controlled trial.}, journal = {Journal of ethnopharmacology}, volume = {361}, number = {}, pages = {121204}, doi = {10.1016/j.jep.2026.121204}, pmid = {41534755}, issn = {1872-7573}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/drug therapy/complications/physiopathology ; *Drugs, Chinese Herbal/therapeutic use/adverse effects ; Male ; Female ; *Hypertension, Pulmonary/drug therapy/physiopathology ; Prospective Studies ; Aged ; Middle Aged ; Treatment Outcome ; Gastrointestinal Microbiome/drug effects ; Medicine, Chinese Traditional ; }, abstract = {Pulmonary hypertension (PH) is a serious and common complication in patients with chronic obstructive pulmonary disease (COPD), and this clinical gap has been newly emphasized in the GOLD 2025 guidelines. Guilou Tongluo Formula (GLTLF) is a traditional Chinese herbal prescription widely used in clinical practice for the treatment of COPD combined with PH (COPD-PH). However, there is a lack of high-quality clinical trials to support its efficacy, and the underlying mechanisms of action remain unclear.

AIM OF THE STUDY: This study aims to evaluate the efficacy and safety of GLTLF in the treatment of COPD-PH, and to explore the potential mechanisms underlying its therapeutic effects.

MATERIALS AND METHOD: A total of 104 patients with COPD-PH were randomized to receive either conventional therapy alone (Control group) or in combination with GLTLF (GLTLF group). Clinical efficacy was assessed by changes in traditional Chinese medicine (TCM) syndrome scores, pulmonary artery systolic pressure (PASP), pulmonary function, arterial blood gases, COPD Assessment Test (CAT), modified Medical Research Council (mMRC) grade, WHO functional class (WHO-FC), 6-min walk distance (6MWD), and laboratory parameters. Potential mechanisms were explored via gut metagenomic and metabolomic analyses.

RESULTS: Clinical efficacy evaluation indicated that the TCM syndrome scores were significantly reduced in both groups post-treatment (P < 0.001). PASP, FEV1, and FEV1/FVC improved significantly in the GLTLF group (P < 0.05), and were superior to the control group post-treatment (P < 0.05). PaO2, PaCO2, BNP, and D-dimer improved after GLTLF intervention (P < 0.05). Both groups had increased 6MWD (P < 0.001), with the GLTLF group performing better (P = 0.006). CAT score, mMRC grade, and WHO-FC improved in both groups (P < 0.05), with superior outcomes in the GLTLF group (P < 0.05). Metagenomic sequencing revealed that GLTLF altered the structure and function of the gut microbiota in patients with COPD-PH. Metabolomic analysis identified a total of 87 differential metabolites following GLTLF intervention, which were significantly enriched in 18 metabolic pathways.

CONCLUSION: GLTLF can effectively treat patients with COPD-PH, enhance clinical efficacy, and modulate both metabolic status and gut microbiota composition.}, } @article {pmid41534886, year = {2026}, author = {Idrees, S and Chen, H and Sadaf, T and Rehman, SF and Johansen, MD and Paudel, KR and Liu, G and Wang, Y and Luecken, MD and Hortle, E and Philp, AS and Budden, KF and O'Rourke, M and Kaiko, GE and Lucas, SEM and Dickinson, JL and Allen, PC and Powell, JE and Zhang, LY and Chambers, DC and Corte, T and Caramori, G and Sauler, M and Wark, PA and Gote-Schniering, J and Lehmann, M and Conlon, TM and Kapellos, TS and Yildirim, AÖ and Faner, R and Dharmage, SC and Wheelock, CE and van den Berge, M and Nawijn, MC and Polverino, F and Belz, GT and Chotirmall, SH and Segal, LN and Faiz, A and Hansbro, PM}, title = {Multi-omics to study chronic respiratory diseases and viral infections.}, journal = {European respiratory review : an official journal of the European Respiratory Society}, volume = {35}, number = {179}, pages = {}, pmid = {41534886}, issn = {1600-0617}, mesh = {Humans ; *Multiomics ; *Metabolomics/methods ; Chronic Disease ; *Proteomics/methods ; *Virus Diseases/genetics/metabolism/diagnosis/virology ; *Genomics/methods ; *Respiratory Tract Infections/metabolism/genetics/virology/diagnosis ; Biomarkers/metabolism ; Animals ; Host-Pathogen Interactions ; Prognosis ; Predictive Value of Tests ; Epigenomics ; *Respiratory Tract Diseases/genetics/metabolism/diagnosis ; Genetic Predisposition to Disease ; Phenotype ; }, abstract = {Despite recent advances, the underlying mechanisms of the development and progression of many chronic respiratory diseases remain to be elucidated. Factors such as heterogeneity and complexity of human diseases and difficulty interpreting large datasets hinder research into chronic respiratory diseases. Omics assesses the changes in specific biological entities, such as mRNA expression, epigenetics/epigenomics, genomics, proteomics, metagenomics and metabolomics, and provides valuable insights into the roles of these processes in chronic respiratory diseases. High-throughput omics at bulk, single-cell and spatial levels empower the exploration of disease-related changes through untargeted data-driven statistical methods. Multi-omics is the exploration and integration of multiple biological processes, which compared to a single-omics, can provide a substantially greater and more holistic overview of the pathogenic mechanisms that underpin complex diseases. Multi-omics analysis can comprehensively characterise the mechanisms that drive chronic respiratory diseases, capturing unique biological signatures and cellular interactions at different omics levels. Use of these methods has begun to identify key factors and biomarkers in chronic respiratory diseases. Here, we review current omics approaches and highlight recent advances in respiratory research achieved using multi-omics and integrative methods. Our review provides a valuable resource for researchers and clinicians in this area.}, } @article {pmid41535070, year = {2026}, author = {Zhang, W and Liu, Y and Li, G and Xu, J and Chen, E and Schönhuth, A and Luo, X}, title = {Strain-level metagenomic profiling using pangenome graphs with PanTax.}, journal = {Genome research}, volume = {36}, number = {2}, pages = {405-420}, pmid = {41535070}, issn = {1549-5469}, mesh = {*Metagenomics/methods ; *Metagenome ; *Software ; *Bacteria/genetics/classification ; Phylogeny ; Genome, Bacterial ; }, abstract = {Microbes are omnipresent, thriving in a range of habitats, from oceans to soils, and even within our gastrointestinal tracts. They play a vital role in maintaining ecological equilibrium and promoting the health of their hosts. Consequently, understanding the diversity in terms of strains in microbial communities is crucial, as variations between strains can lead to different phenotypic expressions or diverse biological functions. However, current methods for taxonomic classification from metagenomic sequencing data have several limitations, including their reliance solely on species resolution, support for either short or long reads, or their confinement to a given single species. Most notably, most existing strain-level taxonomic classifiers rely on the sequence representation of multiple linear reference genomes, which fails to capture the sequence correlations among these genomes, potentially introducing ambiguity and biases in metagenomic profiling. Here, we present PanTax, a pangenome graph-based taxonomic profiler that overcomes the shortcomings of sequence-based approaches, because pangenome graphs possess the capability to depict the full range of genetic variability present across multiple evolutionarily or environmentally related genomes. PanTax provides a comprehensive solution to taxonomic classification for strain resolution, compatibility with both short and long reads, and compatibility with single or multiple species. Extensive benchmarking results demonstrate that PanTax drastically outperforms state-of-the-art approaches, primarily evidenced by its significantly higher F1 score at the strain level, while maintaining comparable or better performance in other aspects across various data sets.}, } @article {pmid41535300, year = {2026}, author = {Wong, OWH and Xu, Z and Chan, SSM and Mo, FYM and Shea, CKS and Su, Q and Wan, MYT and Cheung, CP and Ching, JYL and Tang, W and Tun, HM and Chan, FKL and Ng, SC}, title = {A novel synbiotic (SCM06) for anxiety and sensory hyperresponsiveness in children with autism spectrum disorder: an open-label pilot study.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {36}, pmid = {41535300}, issn = {2055-5008}, support = {NCI202346//New Cornerstone Science Foundation/ ; }, mesh = {Humans ; Pilot Projects ; *Autism Spectrum Disorder/microbiology/complications/psychology ; Male ; Child ; *Synbiotics/administration & dosage ; *Anxiety/therapy ; Female ; Feces/microbiology ; Metagenomics ; Gastrointestinal Microbiome ; Child, Preschool ; Pentanoic Acids ; Treatment Outcome ; }, abstract = {Anxiety and sensory hyperresponsiveness are common in children with autism spectrum disorder (ASD), but effective treatments are lacking. Targeting the microbiota-gut-brain axis is a promising strategy. This open-label pilot study evaluated SCM06, a novel synbiotic designed to target anxiety and sensory hyperresponsiveness, in 30 children with ASD (mean age 8.2 years, 22 males). We assessed symptom improvement, compliance, and safety, and collected stool samples for metagenomics and metabolomic analysis over 12 weeks. SCM06 was safe and well-tolerated, and significant improvements were observed in anxiety, sensory hyperresponsiveness, and abdominal pain. Following SCM06 treatment, increase in Bifidobacterium pseudocatenulatum was associated with improved functional abdominal pain (p = 0.0011, p_adj = 0.054), while the abundances of valeric acid and butyric acid increased (p_adj = 0.004 and p_adj = 0.072). Key microbial species, Coprococcus comes and Veillonella dispar, were candidate mediators of symptom improvements. Further randomised controlled trials are warranted to confirm its clinical efficacy.}, } @article {pmid41535304, year = {2026}, author = {Courtine, D and Lepère, C and Wawrzyniak, I and Moné, A and Billard, H and Colombet, J and Monjot, A and Cruaud, C and Da Silva, C and Aury, JM and Debroas, D and Bronner, G}, title = {A multi-Omic resource for exploring microbial eukaryotes in the meromictic freshwater Lake Pavin.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {252}, pmid = {41535304}, issn = {2052-4463}, support = {ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; }, mesh = {*Lakes/microbiology ; *Eukaryota/genetics ; Multiomics ; *Metagenome ; France ; Metagenomics ; }, abstract = {Although recent advances in high-throughput sequencing have greatly expanded our understanding of microbial diversity and function in aquatic ecosystems, progress in studying freshwater microbial eukaryotes has been more limited, mainly due to their large genomes, immense diversity, and largely uncharacterised physiologies. In this work, we present a comprehensive multi-omic dataset, eukaryote-centred, including targeted-metagenomic (18S rDNA V4 and V9), metagenomic, metatranscriptomic and single amplified genomes (SAGs). Both the oxic and anoxic layers of Lake Pavin (France), a permanently stratified freshwater lake, were sampled at four distinct times throughout 2018, by day and night, targeting microbial eukaryotes of two size classes (0.65-10 µm and 10-50 µm). This dataset comprises 106 eukaryotic metagenome-assembled genomes (MAGs), over 9 million unigenes and 11 SAGs, encompassing several under-represented taxa in public databases (e.g. Perkinsea, Chytridiomycota, Cryptista). Altogether, this dataset represents a resource for exploring the functional diversity and spatio-temporal dynamics of microbial eukaryotes.}, } @article {pmid41535683, year = {2026}, author = {Chen, S and Yuan, Y and Wang, Y and Peng, Y and Tun, HM and Jiang, Z and Miao, Y and Lee, S and Yin, X and Shen, X and DeLeon, O and Chang, EB and Chan, FKL and Sun, Y and Ng, SC and Su, Q}, title = {Identification of antimicrobial peptides from ancient gut microbiomes.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {1788}, pmid = {41535683}, issn = {2041-1723}, support = {2025 Youth Science and Technology Talent Development Program//China Association for Science and Technology (China Association for Science & Technology)/ ; }, mesh = {Humans ; *Antimicrobial Peptides/pharmacology/isolation & purification/chemistry ; Animals ; Feces/microbiology ; Metagenome ; *Gastrointestinal Microbiome ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Fecal coprolites preserve ancient microbiomes and are a potential source of extinct but highly efficacious antimicrobial peptides (AMPs). Here, we develop AMPLiT (AMP Lightweight Identification Tool), an efficient tool deployable to portable hardware for AMP screening in metagenomic datasets. AMPLiT demonstrates AUPRC performances of 0.9486 ± 0.0003 and reasonable overall training time of 3200 ± 53 s. By computationally utilizing AMPLiT, we analyze seven ancient human coprolite metagenomes, identifying 160 AMP candidates. Of 40 representative peptides synthesized, 36 (90%) peptides demonstrate measurable antimicrobial activity at 100 μM or less in vitro. Strikingly, approximately two-thirds of these peptides are sourced from Segatella copri, a dominant ancient gut commensal that is conspicuously underrepresented in modern populations, particularly those with Westernized lifestyles. Representative S. copri-derived AMPs exhibit disruptions against membranes of pathogenic bacteria, coupled with low cytotoxicity and hemolytic risk. In vivo, lead peptides demonstrate potent antibacterial and wound-healing efficacy comparable to traditional antibiotics, especially in combating gram-positive pathogens. Our findings highlight the ancient gut microbiomes as sources of novel AMPs, offering valuable insights into the historical role of S. copri in human health and its decline in contemporary populations.}, } @article {pmid41535719, year = {2026}, author = {Almonte, AA and Thomas, S and Iebba, V and Kroemer, G and Derosa, L and Zitvogel, L}, title = {Gut dysbiosis in oncology: a risk factor for immunoresistance.}, journal = {Cell research}, volume = {36}, number = {2}, pages = {103-120}, pmid = {41535719}, issn = {1748-7838}, support = {INCA_16698//CNIB (INCA)/ ; 955575//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Neoplasms/immunology/microbiology/therapy ; *Gastrointestinal Microbiome/immunology ; Risk Factors ; Animals ; }, abstract = {The gut microbiome is recognized as a determinant of response to immune checkpoint inhibitor (ICI) therapies in cancer. However, the clinical translation of microbiome science has been hampered by inconsistent definitions of dysbiosis, inadequate biomarker frameworks, and limited mechanistic understanding. In this review, we synthesize the current state of knowledge on how gut microbial composition and function influence ICI efficacy, highlighting both correlative and causal evidence. We discuss computational approaches based on α-diversity or taxonomic abundance and argue for more functionally and clinically informative models, such as the topological score (TOPOSCORE) and other dysbiosis indices derived from machine learning. Using retrospective analyses of metagenomic datasets from thousands of patients and healthy controls, we examine microbial patterns that distinguish responders from non-responders. We also explore how dysbiosis perturbs immunoregulatory pathways, including bile acid metabolism, gut permeability, and mucosal immunomodulation. Finally, we assess emerging therapeutic strategies aimed at correcting microbiome dysfunction - including dietary modification, bacterial consortia, and fecal microbiota transplantation - and describe how they are being deployed in multiple clinical trials. We conclude with a brief discussion of the ONCOBIOME initiative, which works with international partners to incorporate microbiome science into oncology workflows. By refining our understanding of gut-immune interactions and translating it into action, microbiome-informed oncology may unlock new therapeutic potential for patients previously resistant to immunotherapy.}, } @article {pmid41535941, year = {2026}, author = {Parida, S and Nandi, D and Verma, D and Yi, M and Yende, A and Queen, J and Gabrielson, KL and Sears, CL and Sharma, D}, title = {A pro-carcinogenic oral microbe internalized by breast cancer cells promotes mammary tumorigenesis.}, journal = {Cell communication and signaling : CCS}, volume = {24}, number = {1}, pages = {}, pmid = {41535941}, issn = {1478-811X}, support = {90047965//Breast Cancer Research Foundation/ ; BC191572//Congressionally Directed Medical Research Programs/ ; }, mesh = {Animals ; Female ; Humans ; *Breast Neoplasms/pathology/microbiology/genetics ; *Carcinogenesis/pathology ; *Fusobacterium nucleatum/physiology ; Mice ; Cell Line, Tumor ; BRCA1 Protein/genetics ; DNA Damage ; Cell Proliferation ; *Mouth/microbiology ; }, abstract = {The intricate relationship between microbiota and breast cancer presents an additional risk factor that can have a profound impact on disease progression. Focusing on dysbiosis, our metagenomic analysis shows overabundance of an oral pathogenic microbe F. nucleatum and co-habitation of associated biofilm forming oral microbes in cancerous breast. Mammary gland colonization with F. nucleatum results in the development of metaplastic lesions accompanied with inflammation, DNA damage and hyper-proliferation in healthy mice. Exhibiting the impact of circulating F. nucleatum introduced via hematogenous route, breast tumor bearing mice show accelerated tumor growth and metastatic progression. Increased proliferation, migration, self-renewal and chemoresistance in breast cancer cells as well as non-tumorigenic breast epithelial cells bearing pathogenic BRCA1 mutation is observed upon F. nucleatum exposure which is internalized by the cells in a Gal-GalNAc dependent manner. Of interest, cells harboring BRCA1 mutations exhibit greater cell surface accumulation of Gal-GalNAc sugar residue. This work sheds light on the oncogenic impact of a pro-carcinogenic oral bacterium, F. nucleatum, on normal mammary epithelium and breast cancer, implicates the impairment of DNA damage and repair pathways as its functional mediators, and proposes the concept of increased vulnerability of BRCA1 mutant breast cancer cells owing to their preferential internalization of F. nucleatum.}, } @article {pmid41536169, year = {2026}, author = {Abdulkareem, AA and Gul, SS and Abdulbaqi, HR and Sha, AM and Preshaw, PM}, title = {Assessing Evidence to Include Filifactor alocis as a Novel Candidate in Socransky's Complexes.}, journal = {Molecular oral microbiology}, volume = {41}, number = {3}, pages = {117-130}, doi = {10.1111/omi.70018}, pmid = {41536169}, issn = {2041-1014}, mesh = {Humans ; Animals ; *Periodontal Diseases/microbiology ; Microbiota ; *Periodontitis/microbiology ; Eubacteriales ; }, abstract = {Socransky's complexes have identified a range of bacteria as key contributors to the onset and progression of periodontal disease. However, advancements in microbiological detection methods have allowed for exploration of the microbiome in periodontal health/disease in greater detail. In recent years, Filifactor alocis has emerged as a potential periodontal pathogen. Therefore, the aim of this review was to investigate whether this bacterium could be included in Socransky's model by summarizing the available evidence. A comprehensive literature search performed using PubMed, ScienceDirect, and Scopus databases was undertaken. The retrieved articles were filtered according to defined eligibility criteria, which yielded 24 studies. Data were extracted from these observational and clinical studies to synthesize findings. Findings regarding the host immune response were derived from in vitro and experimental animal models and narratively summarized. Observational studies and clinical trials showed heterogeneity and a lack of standardized outcomes. However, the general trend indicated a higher prevalence of F. alocis at diseased sites than at healthy sites. In addition, periodontal treatment was found to significantly reduce F. alocis levels and was associated with improvements in clinical periodontal parameters. Experimental models and in vitro studies showed that F. alocis exhibits a range of virulence attributes and pathogenic behavior similar to that of putative pathogenic periodontal bacteria. The evidence is not sufficient to include F. alocis as a new member of Socransky's model. However, this review suggests that this bacterium has the potential to be included in Socransky's complexes in the future after further research which would require to be highly standardized to enhance comparability and generalizability of findings.}, } @article {pmid41536238, year = {2026}, author = {Corona-Cervantes, K and Urrutia-Baca, VH and Gámez-Valdez, JS and Jiménez-López, B and Rodríguez-Gutierrez, NA and Chávez-Caraza, K and Espiricueta-Candelaria, F and Villalobos, UAS and Ramos-Parra, PA and Uribe, JAG and Brunck, M and Chuck-Hernández, C and Licona-Cassani, C}, title = {Maternal obesity alters human milk oligosaccharides content and correlates with early acquisition of late colonizers in the neonatal gut microbiome.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2607043}, pmid = {41536238}, issn = {1949-0984}, mesh = {Humans ; *Milk, Human/chemistry/metabolism ; Female ; *Oligosaccharides/metabolism/analysis ; Infant, Newborn ; Feces/microbiology ; Adult ; *Gastrointestinal Microbiome ; Pregnancy ; Longitudinal Studies ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Obesity/metabolism/microbiology ; Infant ; Mexico ; Body Mass Index ; Metagenomics ; Young Adult ; *Pregnancy in Obesity/metabolism/microbiology ; Mothers ; }, abstract = {Metabolic and immune development in neonates are shaped by the succession of the gut microbiome. Maternal obesity can perturb this process by altering interactions of human milk bioactive elements, including oligosaccharides (HMOs), microbial populations, and metabolites. We conducted a longitudinal study of Mexican mother-infant dyads to examine maternal BMI-associated variations in HMOs and infant fecal microbiota. Breastmilk samples from 97 mothers were collected at 48 h, one month, and three months postpartum. We used targeted and untargeted metabolomics to profile breastmilk samples, while shotgun metagenomics was used to analyze infant fecal microbiome composition in a subset of samples. Mothers with obesity showed decreased concentration of key HMOs shortly after birth, correlating with an altered succession of their infant's gut microbiota. This included reduced early colonizers (Enterobacteriaceae) and increased abundance of intermediate and late colonizers (Bifidobacterium and members of the Lachnospiraceae family), over subsequent months. These taxa negatively correlated with HMOs such as 6'SL, LNnT, and LNT. Additionally, functional profiling revealed alterations in metabolic pathways related to polyamine biosynthesis, suggesting changes in microbial metabolism linked to maternal BMI. Despite the cohort's size, our study offers unique insights into the relationship between maternal obesity, HMO composition, and early infant microbial colonization in Latin-American mothers. This exploratory research serves as proof of concept, underscoring the need for larger-scale studies to validate these findings and better understand their implications for infant health. More importantly, our results highlight the interplay between maternal BMI and human milk bioactives, underscoring the importance of correlating microbial succession with maternal metabolic health to better understand early immune development in neonates.}, } @article {pmid41537457, year = {2026}, author = {Chari, NR and DeAngelis, KM and Aguilar, AA and Chan, ALH and Burgin, GA and Frey, SD and Taylor, BN}, title = {Warming mitigates root exudate-induced priming effects via changes to microbial biomass, community structure, and gene abundance.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41537457}, issn = {1751-7370}, support = {DEB-1456610//Long-Term Research in Environmental Biology/ ; DEB-1832110//U.S. National Science Foundation (NSF) Long-Term Ecological Research Program/ ; }, mesh = {*Plant Roots/metabolism/microbiology/chemistry ; *Soil Microbiology ; Biomass ; RNA, Ribosomal, 16S/genetics ; Carbon/metabolism ; *Bacteria/genetics/classification ; Soil/chemistry ; Climate Change ; *Plant Exudates/metabolism ; DNA, Bacterial/genetics ; Metagenomics ; }, abstract = {Root exudation, the export of soluble carbon compounds from living plant roots into soil, is an important pathway for soil carbon formation, but high rates of exudation can also induce rapid soil organic matter decomposition - a phenomenon known as the priming effect. Long-term soil warming associated with climate change could alter exudation rates and impact soil microbes by changing soil carbon chemistry. We hypothesized that warming-induced changes to exudation rate combined with direct effects of long-term warming on soil microbial communities would regulate the microbial priming effect. We tested this hypothesis with an artificial root exudate experiment using intact soil cores from a long-term soil warming experiment in a temperate forest. We found that chronic soil warming did not alter soil carbon formation from exudates, but did reduce the exudate-induced priming effect; exudation caused greater soil carbon loss in unwarmed than warmed soils. We used DNA stable isotope probing with 16S ribosomal RNA gene and shotgun metagenomic sequencing to determine whether long-term warming affected which microbes consume 13carbon-labeled artificial exudates. We found significant differences in bacterial community composition and relative gene abundances of 13carbon-enriched compared to natural abundance DNA. Both soil bacterial community composition and specific enzyme-coding gene families were strongly correlated with soil carbon priming in unwarmed treatments, but these effects were absent in warmed treatments. Our results suggest that the root exudate-induced priming effect is mediated by microbial biomass, community structure, and gene abundance, and that chronic warming reduces the priming effect by altering these microbial variables.}, } @article {pmid41537461, year = {2026}, author = {Choi, KY and Kang, S and Cook, S and Li, D and Choi, YY and Seo, EH and Han, X and Park, JE and Lee, S and Lee, S and Chung, JY and Chong, A and Choi, SM and Ha, JM and Song, MK and Lee, JS and Choo, IH and Kim, JH and Song, HC and Kim, BC and Kim, H and Farrer, LA and Gim, J and Jun, GR and Lee, KH}, title = {The Gwangju Alzheimer's & Related Dementias (GARD) cohort: Over a decade of Asia's largest longitudinal multimodal study.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {22}, number = {1}, pages = {e70981}, pmid = {41537461}, issn = {1552-5279}, support = {25-BR-03-05//the KBRI Basic Research Program through the Korea Brain Research Institute, funded by the Ministry of Science and ICT/ ; NRF-2014M3C7A1046041//the Original Technology Research Program for Brain Science of the National Research Foundation funded by the Korean government, MSIT/ ; RS-2024-00407198//Brain Pool program funded by the Ministry of Science and ICT through the National Research Foundation of Korea/ ; 2023-ER1007-01//Korea National Institute of Health research project/ ; //by the Technology Innovation Program (20022810, Development and Demonstration of a Digital System for the evaluation of geriatric Cognitive impairment) funded By the Ministry of Trade, Industry & Energy (MOTIE, Korea)/ ; RS-2024-00433283//the Technology Innovation Program funded by the Ministry of Trade, Industry & Energy, Republic of Korea/ ; HR22C141105//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; }, mesh = {Humans ; Longitudinal Studies ; *Alzheimer Disease/epidemiology/diagnostic imaging/diagnosis/genetics ; Female ; *Cognitive Dysfunction/epidemiology/diagnosis ; Aged ; Male ; Republic of Korea/epidemiology ; Disease Progression ; Multiomics ; Biomarkers ; Middle Aged ; Magnetic Resonance Imaging ; Neuroimaging ; Cohort Studies ; Proteomics ; Aged, 80 and over ; }, abstract = {INTRODUCTION: Alzheimer's disease (AD) is a major public health concern in Korea, with a high prevalence among older adults. A community-based longitudinal study is essential for tracking disease progression, identifying biomarkers, and developing targeted prevention and treatment strategies. The Gwangju Alzheimer's & Related Dementias (GARD) cohort was established to address these needs through a multimodal approach.

METHODS: Participants aged ≥60 years undergo comprehensive clinical evaluations, neuroimaging, and biospecimen collection for multi-omics analyses (genomics, transcriptomics, proteomics, and metagenomics) at baseline and systematic follow-up visits.

RESULTS: From over 17,000 screened individuals, 12,877 were enrolled. Baseline diagnoses include 5,123 cognitively unimpaired (CU), 3,250 mild cognitive impairment (MCI), and 2,125 AD dementia. The resource includes magnetic resonance imaging scans (n = 10,843) and extensive multi-omics data: genomic (n = 10,775), proteomic (n = 116), and microbiome (n = 595).

DISCUSSION: The integrated GARD dataset provides a powerful and scalable resource for identifying novel biomarkers, understanding disease heterogeneity, and advancing precision medicine for AD.

HIGHLIGHTS: Gwangju Alzheimer's & Related Dementias (GARD) is a large-scale, longitudinal, community-based cohort study in South Korea. The study focuses on early detection and monitoring of dementia progression. GARD includes cognitive testing, imaging, biospecimens, and multi-omics data. We aim to identify Korean-specific biomarkers predictive of cognitive decline. Supports East Asian insights and fills gaps in global Alzheimer's research.}, } @article {pmid41537582, year = {2026}, author = {Robertson, S and Mosca, A and Ashraf, S and Corral, A and Alegria Terrazas, R and Arnton, C and Thorpe, P and Morris, J and Hedley, PE and Babbi, G and Savojardo, C and Martelli, PL and Møller, FD and Nielsen, HN and Leekitcharoenphon, P and Aarestrup, FM and Halder, R and Laczny, CC and Wilmes, P and Pietrantonio, L and Di Cillo, P and Catara, V and Abbott, J and Bulgarelli, D}, title = {Acinetobacter enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants.}, journal = {mSphere}, volume = {11}, number = {2}, pages = {e0084225}, pmid = {41537582}, issn = {2379-5042}, support = {818290//Horizon 2020 Framework Programme/ ; 2734186/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Solanum lycopersicum/microbiology/growth & development ; *Microbiota ; Soil Microbiology ; *Acinetobacter/genetics/classification/physiology ; Rhizosphere ; Metagenomics ; Plant Roots/microbiology ; Metagenome ; High-Throughput Nucleotide Sequencing ; }, abstract = {Tomato is a staple crop and an excellent model to study host-microbiota interactions in the plant food chain. In this study, we describe a "lab-in-the-field" approach to investigate the microbiota of field-grown tomato plants. High-throughput amplicon sequencing revealed a three-microhabitat partition, phyllosphere, rhizosphere, and root interior, differentiating host-associated communities from the environmental microbiota. An individual bacterium, classified as Acinetobacter sp., emerged as a dominant member of the microbiota at the plant-soil continuum. To gain insights into the functional significance of this enrichment, we subjected rhizosphere specimens to shotgun metagenomics. Similar to the amplicon sequencing survey, a "microhabitat effect," defined by a set of rhizosphere-enriched functions, was identified. Mobilization of mineral nutrients, as well as adaptation to salinity and polymicrobial communities, including antimicrobial resistance genes (ARGs), emerged as a functional requirement sustaining metagenomic diversification. A metagenome-assembled genome representative of Acinetobacter calcoaceticus was retrieved, and metagenomic reads associated with this species identified a functional specialization for plant-growth promotion traits, such as phosphate solubilization, siderophore production, and reactive oxygen species detoxification, which were similarly represented in a tomato genotype-independent fashion. Our results revealed that the enrichment of a beneficial bacterium capable of alleviating plant abiotic stresses appears decoupled from ARGs facilitating microbiota persistence at the root-soil interface.IMPORTANCETomatoes are at center stage in global food security due to their high nutritional value, widespread cultivation, and versatility. Tomatoes provide essential vitamins and minerals, contribute to diverse diets, and support farmer livelihoods, making them a cornerstone of sustainable food systems. Beyond direct dietary benefits, the intricate relationship between tomatoes, their associated microbiota, and antimicrobial resistance gene (ARG) is increasingly recognized. Tomato plants host diverse microbial communities in association with their organs, which influence plant health and productivity. Crop management impacts the composition and function of these communities, contributing to the prevalence of ARGs in the soil and on the plants themselves. These genes can potentially transfer to human pathogens, posing a food safety and public health risk. Understanding these complex interactions is critical for developing sustainable agricultural practices capable of mitigating the impact of climatic modifications and the global threat of antimicrobial resistance.}, } @article {pmid41537586, year = {2026}, author = {Belay, KH and Abdelrazek, S and Kaur, S and Mazloom, R and Bily, D and Gyatso, T and Avin, FA and Bonkowski, J and Liyanapathiranage, P and Rodriguez Salamanca, L and Heath, LS and Baysal-Gurel, F and Vinatzer, BA}, title = {Genomic insights into Ceratobasidium sp. associated with vascular streak dieback of woody ornamentals in the United States using a metagenomic sequencing approach.}, journal = {Microbiology spectrum}, volume = {14}, number = {3}, pages = {e0252325}, pmid = {41537586}, issn = {2165-0497}, support = {2023-67013-39920//U.S. Department of Agriculture/ ; 838//Virginia's Agricultural Council/ ; }, mesh = {United States ; *Plant Diseases/microbiology ; Phylogeny ; Metagenomics ; Genome, Fungal ; Wood/microbiology ; *Basidiomycota/genetics/classification/isolation & purification ; }, abstract = {UNLABELLED: Woody ornamentals are integral to urban landscapes and play important roles in habitat restoration and ecological conservation, yet their national and international trade facilitates the spread of plant diseases with significant ecological and economic consequences. Vascular streak dieback (VSD) recently emerged on woody ornamentals in the United States and was found to be associated with the fungal pathogen Ceratobasidium sp. (Csp), but little is known about its genomic diversity and associated microbial communities. We thus applied metagenomic sequencing to 106 symptomatic samples that had tested positive for Csp and had been collected from 34 woody ornamental species in seven states. Taxonomic profiling identified Csp as the only putative pathogen of which we recovered 17 high-quality draft genomes. Phylogenomic and pangenome analyses revealed that U.S. Csp isolates form a tight genetic cluster, distinct in gene content from C. theobromae, a pathogen of cacao, avocado, and cassava in Southeast Asia. Comparative analyses highlighted gene content differences, including candidate effectors and secondary metabolite clusters, which may underlie host interactions and offer diagnostic targets. These findings provide the first genomic insights into the U.S. Csp population, suggest the recent introduction of a single genetic lineage with a broad host range, and establish a framework for improved detection, monitoring, and management of VSD in woody ornamentals.

IMPORTANCE: Identification of the pathogen that causes an emerging disease, be it of humans, animals, or plants, is a prerequisite to develop effective treatment and/or management practices and to try to control the disease outbreak to prevent further pathogen spread. Vascular streak dieback (VSD) is an emerging disease of ornamental bushes and trees in the United States. Identification of the pathogen has been hindered by the difficulty in growing the fungal pathogen found to be associated with diseased plants in pure culture. Here, we succeeded in sequencing the DNA of the likely pathogen directly from plant tissue or from the fungal mass growing out of collected plant tissue. The sequences were assembled into genomes, which allowed us to precisely identify the pathogen, compare it to related pathogens of other plants, and predict how it causes disease. These results can now be used to inform management and control of VSD.}, } @article {pmid41537603, year = {2026}, author = {Zou, Y and Zhou, J and Zeng, Y and Chen, B and Liu, L and Xu, G}, title = {Mining and engineering of ene-reductases from marine sediment metagenome for prochiral ACE inhibitor synthesis.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {2}, pages = {e0233325}, pmid = {41537603}, issn = {1098-5336}, support = {42376097//National Natural Science Foundation of China/ ; }, mesh = {*Geologic Sediments/microbiology ; *Metagenome ; *Angiotensin-Converting Enzyme Inhibitors/metabolism ; Substrate Specificity ; *Oxidoreductases/genetics/metabolism/chemistry ; China ; Escherichia coli/genetics/metabolism ; Seawater/microbiology ; }, abstract = {The development of sustainable biocatalytic processes for pharmaceutical synthesis represents a major goal in green chemistry. Ene-reductases (ERs) are attractive biocatalysts for asymmetric hydrogenation of activated alkenes, yet their industrial application is often constrained by limited substrate scope and stability. In this study, we explored the deep-sea sediment metagenome of the South China Sea and identified 41 putative ER genes, with 22 successfully solubly expressed in Escherichia coli. Biochemical characterization revealed broad substrate specificity, achieving up to 90% conversion for diverse α,β-unsaturated compounds. Notably, three enzymes (S2gene2614772, S2gene1139, and S2gene22028) exhibited exceptional adaptability, maintaining high activity over a wide pH range (5.5-8.5) and at low temperatures (15°C). However, none of the wild-type ERs showed significant activity toward the prochiral substrate 2-oxo-4-phenyl-3-butenoic acid, a key intermediate for angiotensin-converting enzyme inhibitors (ACEIs). Through directed evolution, we obtained a mutant (S2gene22028-G102S) with 30-fold enhanced activity, reaching 90% conversion at 10 mM substrate. Scale-up synthesis (5 mmol substrate) afforded 2-oxo-4-phenylbutyric acid (OPBA) at 11 mg/mL, demonstrating industrial potential. This study highlights marine metagenomes as valuable sources of novel ERs and provides an efficient biocatalytic route to ACEI precursors.IMPORTANCEThe development of sustainable biocatalysts for pharmaceutical synthesis is a pivotal goal in green chemistry. This study leverages the untapped enzymatic diversity of the South China Sea deep-sea sediment metagenome to discover novel ene-reductases (ERs). We not only identified robust ERs with broad substrate promiscuity and exceptional adaptability to low temperature and pH fluctuations but also successfully engineered a variant to overcome the key biocatalytic challenge in the synthesis of 2-oxo-4-phenylbutyric acid (OPBA), a critical precursor to angiotensin-converting enzyme inhibitors. Our work underscores marine metagenomes as a valuable reservoir for discovering industrially relevant biocatalysts and demonstrates the power of combining metagenomic mining with protein engineering to enable greener manufacturing routes for high-value pharmaceuticals.}, } @article {pmid41538320, year = {2026}, author = {}, title = {Correction to 'MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis'.}, journal = {Nucleic acids research}, volume = {54}, number = {2}, pages = {}, doi = {10.1093/nar/gkag015}, pmid = {41538320}, issn = {1362-4962}, } @article {pmid41538522, year = {2026}, author = {Hoyos-López, R and Echeverri-De la Hoz, D and Martínez-Bravo, C and Gastelbondo-Pastrana, B and Alemán-Santos, M and Garay, E and López, Y and Contreras, H and Galeano, K and Arrieta, G and Mattar, S}, title = {Viral metagenomics in mosquitoes as potential vectors of arboviruses in the Colombian Caribbean: characterisation of a "core" regional RNA virome.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {120}, number = {}, pages = {e250131}, pmid = {41538522}, issn = {1678-8060}, mesh = {Animals ; *Arboviruses/genetics/isolation & purification/classification ; Colombia ; *Mosquito Vectors/virology/classification ; Metagenomics ; *Culicidae/virology/classification ; Seasons ; Caribbean Region ; *Virome/genetics ; *RNA, Viral/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; }, abstract = {BACKGROUND: Mosquitoes are critical vectors in tropical regions where arboviruses like dengue and Zika are prevalent. This study focuses on characterising the RNA virome of mosquitoes in the Colombian Caribbean, emphasising the core regional virome and its role in the dynamics of arboviruses.

OBJECTIVES: The objective was to identify and analyse the core RNA virome of mosquitoes across different genera and seasons in the Colombian Caribbean to understand its composition and potential influence on arbovirus transmission dynamics.

METHODS: In 2023, 4,074 mosquitoes from the genera Mansonia, Coquillettidia, and Anopheles were collected across Córdoba, Sucre, Bolívar, and Magdalena during rainy and dry seasons. Specimens were pooled in groups of 50, subjected to RNA extraction, and sequenced on the MGI-G50™ platform. Bioinformatic analyses utilised the DIAMOND-MEGANizer pipeline and R packages (phyloseq, vegan, ggplot2) to identify viral communities.

FINDINGS: The analysis identified 22 viral families and 24 unclassified RNA viruses. The core regional virome, consistently present across species and seasons, was dominated by insect-specific viruses (ISVs) such as Aedes aegypti to virus 1 and 2, Astopletus, and Cumbaru, alongside Picornaviridae (30% of reads), Rhabdoviridae (20%), Orthomyxoviridae, and Bunyavirales. Mansonia titillans (38 species) and Coquillettidia nigricans (21 species) exhibited the highest viral richness. No significant arboviruses were detected, highlighting ISV dominance. Virome composition varied seasonally, with greater diversity in the rainy season due to increased breeding site availability and temperature.

MAIN CONCLUSIONS: The stability of the core virome suggests it modulates vector competence, potentially reducing arbovirus transmission. These findings advocate the use of metagenomics for enhanced vector surveillance and biological control strategies in neotropical ecosystems.}, } @article {pmid41538947, year = {2026}, author = {Zhang, X and Feng, Y and Jiang, X and Sun, W and Zhang, C and Han, J and Hou, Y and You, X and Zhang, H and Wang, X and Wu, X and Wang, J}, title = {Unveiling hidden risks of chiral fungicide benzovindiflupyr: Stereoselectivity in soil antibiotic resistance gene transmission.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141088}, doi = {10.1016/j.jhazmat.2026.141088}, pmid = {41538947}, issn = {1873-3336}, mesh = {Stereoisomerism ; *Fungicides, Industrial/chemistry/toxicity ; *Soil Microbiology ; *Soil Pollutants/toxicity/chemistry ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance gene (ARG) dissemination is closely associated with modern agricultural practices. However, the stereoselective effects of widely applied chiral pesticides on resistance evolution remain insufficiently investigated. This study systematically explored the differential effects of benzovindiflupyr enantiomers on transmission of ARGs through long-term soil incubation experiments combined with metagenomic and in vitro studies. Results demonstrated that 1S,4R-enantiomer exhibited significantly longer half-life than 1 R,4S-enantiomer. 1 R,4S-enantiomer induced extreme enrichment of a few ARGs. 1S,4R-enantiomer persistently increased abundance of multiple ARGs. Compared with 1 R,4S-enantiomer, 1S,4R-enantiomer more consistently enhanced abundance of mobile genetic elements (MGEs) related to conjugative transfer. Moreover, 1 R,4S-enantiomer primarily enriched specific genera within Pseudomonadota. 1S,4R-enantiomer simultaneously promoted abundance of multiple genera across both Pseudomonadota and Bacteroidota, driving cross-phylum genera to correlate with shared ARGs. Genomic analysis confirmed that Pseudomonadota under 1S,4R-enantiomer treatment carried more ARGs and MGEs. In vitro transformation experiments ultimately validated that 1S,4R-enantiomer significantly enhanced transformation efficiency across multiple ARGs consistently, substantially exceeding 1 R,4S-enantiomer effects. Overall, 1S,4R-enantiomer poses more significant risks for horizontal transfer of ARGs. This study elucidates enantioselective effects of chiral pesticides on transmission of ARGs, providing a foundation for improving chiral agrochemical risk assessment.}, } @article {pmid41539094, year = {2026}, author = {Wang, L and Xiong, Z and Chen, J and Liu, J and Liu, M and Yan, X and Fang, Z}, title = {Synergistic gut microbiome-host lipid axis underlies the antihypertensive effect of Qianyang Yuyin formula.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {151}, number = {}, pages = {157804}, doi = {10.1016/j.phymed.2026.157804}, pmid = {41539094}, issn = {1618-095X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology ; *Antihypertensive Agents/pharmacology ; Male ; Rats ; *Lipid Metabolism/drug effects ; Rats, Inbred SHR ; Blood Pressure/drug effects ; *Prehypertension/drug therapy/microbiology ; Fecal Microbiota Transplantation ; Dysbiosis ; Hypertension/drug therapy ; Disease Models, Animal ; }, abstract = {BACKGROUND: Prehypertension (Pre-HTN) is highly prevalent and substantially increases the risk of developing hypertension and cardiovascular disease. Gut microbiota (GM) dysbiosis and altered lipid metabolism are increasingly recognized as critical regulators of blood pressure (BP). Traditional Chinese Medicine (TCM) formulas, such as Qianyang Yuyin Granules (QYYY), offer multi-target interventions, yet their preventive mechanisms in Pre-HTN remain unclear.

PURPOSE: This study aimed to investigate the antihypertensive effects of QYYY and elucidate its underlying mechanisms in a prehypertensive rat model.

METHODS: Prehypertensive spontaneously hypertensive rats (SHRs) were treated with QYYY for four weeks. Multi-omics analyses, including metagenomics, plasma metabolomics, and transcriptomics, were conducted. Causal involvement of GM was tested using antibiotic-induced pseudo-germ-free SHRs with fecal microbiota transplantation (FMT) from QYYY-treated donors, administered alone or in combination with QYYY. Gut barrier integrity, systemic inflammation, and vascular function were evaluated by histology, immunofluorescence, transmission electron microscopy, and ELISA.

RESULTS: QYYY significantly lowered SBP and DBP, reversed GM dysbiosis, normalized the Firmicutes/Bacteroidetes ratio, and modulated differential bacteria including Frisingicoccus and Blautia. These microbial shifts correlated with restoration of lysophosphatidylethanolamines (LPEs), inversely associated with BP, revealing a GM-lipid-BP axis. FMT alone was insufficient, whereas the combination of FMT+QYYY produced the strongest antihypertensive effect, restoring intestinal barrier integrity, enhancing ZO-1 expression, and normalizing Ang-II and NO levels. Transcriptomic analyses suggested PPAR and ROS signaling pathways as potential mechanisms mediating the antihypertensive effect of QYYY.

CONCLUSION: QYYY prevents BP elevation in Pre-HTN via synergistic microbiota-dependent and independent mechanisms, offering a comprehensive strategy for early hypertension prevention.}, } @article {pmid41539238, year = {2026}, author = {Sitthipunya, A and Uthaipaisanwong, P and Sinwat, N and Kanjanavaikoon, K and Cheevadhanarak, S and Kusonmano, K}, title = {Metagenomic insights into the effects of Clostridium butyricum and Bacillus subtilis probiotics on the gut microbiome and metabolic pathways of industrial broilers in Thailand.}, journal = {Poultry science}, volume = {105}, number = {3}, pages = {106371}, pmid = {41539238}, issn = {1525-3171}, mesh = {Animals ; *Bacillus subtilis/chemistry ; *Probiotics/pharmacology/administration & dosage ; *Clostridium butyricum/chemistry ; *Chickens/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Thailand ; Diet/veterinary ; Metabolic Networks and Pathways/drug effects ; Animal Feed/analysis ; Male ; Cecum/microbiology ; *Metagenome ; Metagenomics ; }, abstract = {Probiotic supplementation has become increasingly important in broiler production due to its safety and well-documented health benefits. The gut microbiome of broilers plays a vital role in feed digestion and maintaining intestinal homeostasis, which directly influences the efficacy of probiotics under specific farm conditions. This study aims to investigate the effects of single Bacillus subtilis probiotics and double-strain probiotics of Clostridium butyricum and B. subtilis supplementation on the gut microbiome of broilers in industrial farms. We evaluated sequencing data obtained from broilers supplemented with these probiotics through amplicon sequencing and metagenomic analysis. Our study revealed that probiotics significantly influence the cecal microbiome and its functionality in broilers. The use of double-strain probiotics increased butanoate metabolism, as well as the metabolism of glycine, serine, and threonine. This suggests their contribution from microbial gut species, including Alistipes onderdonkii, Alistipes finegoldii, Bacteroides uniformis, and Phocaeicola dorei. Supporting this finding, network analysis shows more connections between probiotics and commensal cecal microbiota, highlighting a cascade-linked association with butanoate-producing microbiota. Furthermore, single-strain B. subtilis probiotic supplementation uniquely enhanced arginine and proline metabolism, likely due to the presence of species such as Bacteroides sp. zj-18, Bacteroides cellulosilyticus, and Parabacteroides distasonis. Overall, our findings indicate that double-strain probiotics increased richness in the cecal microbial community, reshaped the microbial network, and enriched short-chain fatty acid and amino acid metabolism, contributing to improved gut health and performance in broiler production.}, } @article {pmid41539415, year = {2026}, author = {Liu, P and He, G and Guo, Z and Tang, Y and Tan, Z and Song, Y and He, T and Lee, SL}, title = {Characteristics of microbial community succession and functional metabolite accumulation during microaerobic fermentation of high-sugar-load fruit and vegetable residues: Potential implications for guiding home production of environmental-friendly bioactive fertilizer.}, journal = {Genomics}, volume = {118}, number = {2}, pages = {111204}, doi = {10.1016/j.ygeno.2026.111204}, pmid = {41539415}, issn = {1089-8646}, mesh = {*Fermentation ; *Vegetables/metabolism/microbiology ; *Fruit/metabolism/microbiology ; *Microbiota ; *Fertilizers ; Germination ; Lactuca/growth & development/microbiology ; }, abstract = {Household fermentation tanks offer simple, low-cost solutions for fruit and vegetable waste utilization, yet staged metabolite formation during sugar-mediated fermentation remains understudied. Using metagenomic and metabolomic approaches, we characterized microbial succession and metabolite dynamics over 28 days. Three phases emerged: substrate activation (1-7d) with Enterobacter/Escherichia dominance producing organic acids; metabolic transition (8-21d) with Lactiplantibacillus proliferation (312.5% increase) accumulating phytohormones 3-hydroxycinnamic acid (2.84-fold) and adenine (1.38-fold); functional stability (21-28d) establishing Lactiplantibacillus-Acetobacter synergy enriching antioxidants and antimicrobial peptides. Multi-omics analysis revealed strong correlations between amino acid metabolism and functional metabolites (r = 0.78, p < 0.01). Fermentation broth (1:500 dilution) enhanced lettuce germination to 92.22% (p < 0.05).Although the potential of household agriculture is demonstrated through staged microbial community development and the formation of bioactive products, functional characteristics still need to be verified in the soil-plant system beyond seed germination assays.}, } @article {pmid41539526, year = {2026}, author = {Uddin, G and Song, J and Lu, Z and Chaofie, Z and Sajjad, W and Li, P and Fan, Q}, title = {Microbial taxonomic and functional responses to heavy metal gradients in mining-impacted stream sediments.}, journal = {Environmental research}, volume = {293}, number = {}, pages = {123778}, doi = {10.1016/j.envres.2026.123778}, pmid = {41539526}, issn = {1096-0953}, mesh = {*Metals, Heavy/analysis/toxicity ; *Geologic Sediments/microbiology/chemistry ; *Bacteria/drug effects/classification/genetics ; Archaea/drug effects/classification ; *Water Pollutants, Chemical/analysis/toxicity ; *Mining ; Fungi/drug effects/classification ; *Rivers/microbiology/chemistry ; China ; Environmental Monitoring ; }, abstract = {Legacy heavy metal pollution from historical mining restructures sediment microbial composition and function directly impacting contaminant fate and ecosystem health. The Dongdagou stream (Baiyin, China) possesses a pronounced geochemical gradient caused by long-term discharge of potentially toxic metals including Cd, Cu, Pb, and Zn. We employed this natural gradient to characterize microbial taxonomic and functional responses to metal stress. Sediment samples from four zones along the contamination gradient were analyzed for geochemistry, metal concentrations, and microbial composition (bacteria, archaea, and fungi) via high-throughput amplicon sequencing, with functional potential inferred using PICRUSt2. We found that microbial community structure and function were primarily shaped by metal concentration, with db-RDA explaining 18.1 %, 12.4 %, and 12.9 % of the variance for bacteria, archaea, and fungi, respectively. Cadmium was identified as the strongest individual predictor for both bacterial (r[2] = 0.50, p = 0.001) and fungal (r[2] = 0.38, p = 0.001) communities. Bacterial diversity increased significantly downstream as contamination declined, with Shannon diversity increasing from 5.17 in the Source Zone to 6.28 in the Distal Zone (Tukey's multiple comparison test, p < 0.05). Upstream sediments were dominated by metal-tolerant taxa such as Sulfurifustis (17.4 %) and Acidithiobacillus (5.0 %), while downstream taxa shifted to heterotrophic genera like Gallionella (4.8 %) with diverse metabolic capabilities. Despite cadmium being a key predictor, archaeal and fungal communities demonstrated greater compositional stability than bacteria, as shown by their lower beta-dispersion (ANOSIM R = 0.3152 and 0.5762, respectively, compared to 0.7222 for bacteria), indicating potential functional redundancy. Metagenomic predictions revealed a significant enrichment of genes for metal detoxification, anaerobic respiration, and oxidative stress response in polluted zones. These findings establish that microbial communities are both sensitive bioindicators and key mediators of contaminant dynamics, providing a framework for using microbial signatures to assess sediment health and monitor remediation efficacy.}, } @article {pmid41539568, year = {2026}, author = {Farhat, I and Kaminski, H and Woerther, PL and Rodriguez, C and Pierre, C and Cheval, J and Korbi, S and Couzi, L and Merville, P and Jambon, F and Moreau, K}, title = {Spiroplasma infection complicated by macrophage activation syndrome and fulminant hepatitis in a kidney transplant recipient.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {26}, number = {6}, pages = {1495-1499}, doi = {10.1016/j.ajt.2026.01.008}, pmid = {41539568}, issn = {1600-6143}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; Aged ; *Macrophage Activation Syndrome/etiology/microbiology/complications ; *Gram-Negative Bacterial Infections/microbiology/complications ; Male ; Fatal Outcome ; *Hepatitis/etiology/microbiology ; Prognosis ; *Kidney Failure, Chronic/surgery ; }, abstract = {A 65-year-old kidney transplant recipient was admitted with isolated fever. Initial tests revealed pancytopenia and elevated C-reactive protein levels but failed to detect any pathogen. A bone marrow aspirate was performed because of signs suggestive of hemophagocytic lymphohistiocytosis, but the results were negative. The patient subsequently developed fulminant hepatitis. Liver biopsy showed severe acute cytolytic hepatitis with a neutrophil-rich infiltrate, suppurative hepatocytic necrosis, and hemophagocytosis. Etoposide, N-acetylcysteine, and piperacillin-tazobactam were initiated. However, the patient died from hemorrhagic complications of the biopsy. Posthumous shotgun metagenomics on liver samples identified Spiroplasma ixodetis.}, } @article {pmid41539598, year = {2026}, author = {Wei, S and Li, W and Ran, S and Zhang, J and Zhang, Z and Yang, Z and Tian, F and Chen, L and Hu, P and Yuan, J and Lin, H}, title = {Multi-organ metabolic dysregulation and cecal microbiota alterations following black carbon exposure.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.01.027}, pmid = {41539598}, issn = {2090-1224}, abstract = {BACKGROUND: Black carbon (BC) has been linked to adverse health outcomes, yet underlying mechanisms remain unclear. Integrating metabolomic and metagenomic data across tissues may clarify BC-induced biological pathways.

METHODS: We performed human epidemiology and mice experimental approaches. We included 248,288 participants with annual BC exposure estimates and plasma metabolomic profiles. Elastic net regression identified BC-associated metabolites. Male C57BL/6J mice were exposed to filtered air or BC (1 mg/m[3], 1 h/day, 5 days/week, 12 weeks). Multi-tissue metabolomics and cecal contents microbiota sequencing were conducted, with histology and gene expression measurements.

RESULTS: In humans, long-term BC exposure significantly altered plasma metabolites, notably increasing saturated fatty acids (β = 0.048), while decreasing docosahexaenoic acid (β = -0.002). Amino acid metabolism was broadly disrupted, involving elevated valine (β = 0.011) and reduced glutamine (β = -0.006). In mice, metabolomic profiling showed organ-specific shifts, including increased glutathione and cortisol in the liver (2.88-fold and 2.06-fold), increased PC(16:0/18:1(9Z)) in the heart (3.22-fold), elevated anandamide and arachidonic acid in the kidney (2.35-fold and 1.48-fold), and decreased multiple fatty acids and lysophospholipids across organs. Cecal microbiota exhibited reduced alpha-diversity (Shannon: 3.67 vs. 4.50, P < 0.05) and taxonomic shifts, including an increased abundance of g_Akkermansia and decrease in g_Bacteroides. Multi-omics integration revealed significant microbiota-metabolome correlations in the cecum and plasma (Mantel r = 0.276, P = 0.012). Histological examination confirmed organ injuries, notably lung inflammation, cardiac edema, and neuronal condensation. Gene expression analysis showed increased Il-6 in the lung (5.35-fold, P = 0.047), increased Mb in the heart (5.18-fold, P = 0.010), and increased Igfbp7 in the kidney (3.03-fold, P = 0.001), while Tjp1 expression in cecum was reduced (0.42-fold, P = 0.004).

CONCLUSIONS: Our findings suggest that BC exposure may alter systemic metabolism and gut microbiota, potentially contributing to tissue injury and inflammation. The gut-organ axis could be a target for mitigating BC-related health effects.}, } @article {pmid41539600, year = {2026}, author = {Li, W and Guo, H and Wang, Q and Peng, D and Wang, Y and Lu, Z}, title = {Phocaeicola vulgatus promote growth rate via tryptophan metabolism pathway mediated gut sIgA production in Taihe Silky fowl.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.01.022}, pmid = {41539600}, issn = {2090-1224}, abstract = {INTRODUCTION: Taihe Silky Fowl (TSF) has a long growth cycle and slow growth rate, how to effectively improve the growth rate of TSF has become the primary concern for breeders. Currently, extensive research has established the gut microbiota's role in modulating growth rate of commercial chicken breeds, while the specific microbial mechanisms influencing TSF growth rate remain poorly understood.

OBJECTIVES: Therefore, this study aimed to identify growth rate-associated key microbial species in TSF through multi-omics approaches, experimentally validate their growth-promoting roles via controlled interventions, and elucidate the species-metabolite-host interaction mechanisms.

METHODS: Cecal metagenome and metabolome was used to search for differential key microbiota and metabolites of TSF with different growth rate, the whole genome of key microbiota was used to identify the relationship between microbiota and metabolites, and gavage key microbiota to TSF was used to demonstrate the effectiveness of probiotics and preliminarily explore their mechanisms of action.

RESULTS: Cecal metagenome analysis demonstrated a significant enrichment of Phocaeicola vulgatus (P. vulgatus) in high-growth-rate fowls, Erysipelotrichaceae bacterium was significantly enriched in low-growth-rate fowls. The differential metabolites between the two groups were significantly enriched in tryptophan metabolism pathway. Subsequently, gene analysis revealed that P. vulgatus encoded tryptophan biosynthesis genes. In feeding experiment, oral gavage P. vulgatus improved the TSF final body weight, average growth rate and average daily gain, increased cecal P. vulgatus abundance, enriched the metabolites in tryptophan metabolism pathway both in the cecum and serum, and upregulated cecal tissue gene expression in the 'intestinal immune network for IgA production' pathway resulting in the higher secretory IgA (sIgA) concentrations in cecal tissue and luminal content than the control group.

CONCLUSION: P. vulgatus promoted the growth rate of TSF by optimizing the cecal microbiota, elevating cecal tryptophan metabolites and stimulating sIgA production via sIgA gene upregulation in cecal tissues, thereby enhancing host immune modulation. These findings elucidated the microbiota-metabolite-host axis governing TSF growth regulation, providing both mechanistic insights and practical applications for probiotic-based strategies to enhance growth performance and gut health in this valuable poultry breed.}, } @article {pmid41539626, year = {2026}, author = {Vijande, C and Balboa, S and Lazzari, M and Lema, JM and Pabst, M}, title = {Multi-omics reveals wastewater sludge bacteria with genomic potential to degrade poly(ethylene terephthalate).}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {134003}, doi = {10.1016/j.biortech.2026.134003}, pmid = {41539626}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Polyethylene Terephthalates/metabolism ; *Wastewater/microbiology ; *Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Multiomics ; Biofilms ; Spectroscopy, Fourier Transform Infrared ; *Genome, Bacterial/genetics ; Proteomics ; Metagenomics ; }, abstract = {Plastic pollution is a growing concern, especially poly(ethylene terephthalate) (PET), one of the most produced plastic polymers. Although several microorganisms capable of degrading PET have been identified, little is known about those present in wastewater treatment plants (WWTPs). This study explores their ability to degrade PET and the enzymes involved. Activated sludge from two facilities-one urban WWTP and one industrial WWTP-was cultivated with PET of different crystallinities. The inoculum source primarily determined differences in microbial community composition. Metagenomics revealed more than 300 genes homologous to PET-degrading enzymes in all biofilms; however, metaproteomics confirmed expression of only a few of these enzymes in industrial WWTP-derived biofilms. This inoculum demonstrated the ability to degrade PET breakdown products within 24 h. In addition, FTIR analysis revealed initial signs of surface alteration. In conclusion, this study reveals the presence of microorganisms in industrial wastewater treatment sludge that possess the genetic potential to degrade PET.}, } @article {pmid41539627, year = {2026}, author = {Wang, Z and Yang, Y and Qiu, B}, title = {Synergistic improvement of methane production and phosphorus recovery from anaerobic digestion of waste activated sludge by Fe2O3-assisted electroactive microorganisms.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {134004}, doi = {10.1016/j.biortech.2026.134004}, pmid = {41539627}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Methane/biosynthesis ; *Ferric Compounds/pharmacology ; Anaerobiosis/drug effects ; *Phosphorus/isolation & purification/metabolism ; *Bacteria/metabolism/genetics/drug effects ; Electron Transport ; Oxidation-Reduction ; }, abstract = {Conductive materials and electroactive microorganisms (EAM) are key factors on enhancing methane production in anaerobic digestion of waste actived sludge via the direct interspecies electron transfer (DIET). However, their combined impact on simultaneous methane production and phosphorus recovery remains unclear. The Fe2O3 and EAM were added together to synergistically improve anaerobic processes, resulting in a 1.53-fold increase in methane production and a remarkable 12.03-fold enhancement in phosphorus removal. The co-additon of Fe2O3 and EAM promoted Fe(III/II) redox cycling, increased enzyme activity, and enhanced electron transport system (ETS) functionality while enriching DIET-associated bacteria (e.g., Brooklawnia, Anaerolineae) and methanogens (Methanosarcina). Metagenomic analysis revealed the upregulated genes related to phosphorus and iron metabolism, ETS, and DIET-coupled electron bifurcation. Notably, Fe2O3 may act as an alternative to cytochromes and pili in mediating DIET in electron transfer processes.}, } @article {pmid41539628, year = {2026}, author = {Peng, Y and Liu, H and Xing, T and Zhen, F and Wu, D and Sun, Y}, title = {Instability mechanisms of overloaded anaerobic digestion: Insights from volatile fatty acid metabolism.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {134006}, doi = {10.1016/j.biortech.2026.134006}, pmid = {41539628}, issn = {1873-2976}, mesh = {*Fatty Acids, Volatile/metabolism ; Anaerobiosis ; Bioreactors/microbiology ; Methane/metabolism/biosynthesis ; }, abstract = {To clarify the mechanisms driving process instability under overload stress, a long-term semi-continuous overload instability simulation experiment was conducted. High-throughput sequencing and metagenomics were used to determine the response of the process parameters, community composition, and volatile fatty acid (VFA)-related metabolic functional genes to the organic loading rate (OLR). When the OLR increased to 12.5 kg VS/m[3]/d, the methane yield remained low at 226.40 ± 10.78 mL CH4/g VS. Further increasing the OLR to 20 kg VS/m[3]/d completely destabilized the reactor, resulting in a final methane yield as low as 0.29 mL CH4/g VS, a hydrogen partial pressure as high as 357.37 Pa, and concentrations of butyrate, propionate, and acetate of 4328.49 ± 538.18, 1036.13 ± 75.48, and 9939.67 ± 427.68 mg/L, respectively. Organic overload stress caused reactor instability mainly by blocking VFA metabolism. When the OLR was ≥ 11 kg VS/m[3]/d, the relative abundances of key genes (aceE, buk, ptb, atoD) in the butyrate and propionate metabolic pathways decreased, resulting in the accumulation of butyrate and propionate. Despite a shift in syntrophic acetate oxidation metabolism from the methyl to the carbonyl branch under overload, the latter's recovery was insufficient to compensate for the severe impairment of the methyl branch, ultimately leading to acetate accumulation. VFA accumulation caused severe inhibition of acetogens and some methanogens, while hydrolytic and acidogenic bacteria dominated the microbiome (relative abundance: 94.18 %). As a result, the microbial metabolic balance was broken. Our results provide new insights into the mechanisms driving process instability under overload stress.}, } @article {pmid41539810, year = {2026}, author = {Liu, Y and Guo, Y and Mu, H and Aaqil, M and Zhang, F and Zheng, J and Sheng, J and Tian, Y and Zhao, C}, title = {Microbial succession-potential influence mechanism on flavor modulation in spontaneously fermented Moringa oleifera leaves: An integrative multi-omics approach.}, journal = {Food research international (Ottawa, Ont.)}, volume = {226}, number = {}, pages = {118184}, doi = {10.1016/j.foodres.2025.118184}, pmid = {41539810}, issn = {1873-7145}, mesh = {*Moringa oleifera/microbiology/chemistry ; *Fermentation ; Gas Chromatography-Mass Spectrometry ; *Plant Leaves/microbiology/chemistry ; *Taste ; Odorants/analysis ; Multiomics ; Amino Acids/analysis ; Volatile Organic Compounds/analysis ; *Food Microbiology ; *Microbiota ; *Bacteria/metabolism/classification ; *Fermented Foods/microbiology ; Food, Processed ; }, abstract = {In this study, the relationship between flavor composition and microbial succession in Moringa oleifera pickles (MOPs) at different stages of spontaneous fermentation was systematically investigated. The results demonstrated a significant increase in the content of organic acids and amino acids during fermentation including malonic acid, citric acid, valine (Val), and asparagine (Asn). These compounds not only enhanced the overall flavor profile but also provided favorable nutritional conditions that supported microbial succession. Furthermore, an integrated aroma network was established through the combined application of gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS). GC-MS identified key aroma-active compounds such as ethyl caproate (fruity note), 3-hexenal (green, grassy note), and 2-phenylethanol (floral, rosy note). Complementarily, GC-IMS confirmed that esters, alcohols, and terpenes were the major contributors to fruit-like, mushroom-like, and fresh herbal aromas, indicating their critical role as flavor-modulating compounds throughout fermentation. Metagenomic analysis revealed Corynebacterium, Escherichia, Pseudomonas, Xanthomonas, and Pantoea as the dominant microbial genera involved in fermentation. These microbes primarily participated in amino acid, carbohydrate, and nucleotide metabolism and exhibited a close association with the formation of key flavor compounds. The strong influence of microbial succession on flavor evolution is likely driven by the observed correlations between microbial taxa and volatile organic compounds (VOCs). These correlations may stem from a series of complex ecological and metabolic interactions, including substrate competition, niche adaptation, and upstream-downstream dependencies within microbial metabolic networks. This study provides a theoretical foundation for the quality control of MOPs and the mitigation of potential pathogenic microorganisms, thereby supporting its application in enhancing product quality and consumer sensory satisfaction in the pickle industry.}, } @article {pmid41539847, year = {2026}, author = {Kong, M and Zhou, W}, title = {Clinical characteristics and outcomes of Rickettsia japonica infection: A retrospective case series of five patients.}, journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)}, volume = {44}, number = {1}, pages = {503047}, doi = {10.1016/j.eimce.2025.503047}, pmid = {41539847}, issn = {2529-993X}, mesh = {Humans ; Retrospective Studies ; Middle Aged ; Male ; Aged ; Female ; *Rickettsia Infections/diagnosis/drug therapy/microbiology ; *Rickettsia/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; Treatment Outcome ; }, abstract = {OBJECTIVE: To characterize the clinical manifestations of Rickettsia japonica (R. japonica) infection and to generate evidence facilitating early diagnosis and targeted treatment.

METHODS: We retrospectively reviewed the clinical data of five patients with R. japonica infection who were treated in the Emergency Department, Xiling Campus, Yichang Central People's Hospital, between January 2023 and December 2024.

RESULTS: All patients were residents of Yichang City, Hubei Province, aged 58-70 years, and 80% (4/5) were farmers. The onset of illness occurred exclusively between May and September, and all patients reported a definite history of outdoor exposure. The predominant clinical manifestations were fever, rash, and eschar. Laboratory findings revealed thrombocytopenia, elevated aspartate aminotransferase (AST) and creatine kinase (CK), as well as increased inflammatory markers including C-reactive protein (CRP), procalcitonin (PCT), and interleukin-6 (IL-6). R. japonica nucleic acid was detected in all patients by metagenomic next-generation sequencing (mNGS) of blood samples. Three patients initially received empirical doxycycline therapy, which was subsequently adjusted to a standard regimen after diagnostic confirmation. Defervescence occurred at a median of two days (range, 1-7 days), followed by gradual resolution of rash and alleviation of systemic symptoms. All patients achieved complete clinical recovery and were discharged without complications.

CONCLUSION: This study highlights the importance of heightened clinical awareness of R. japonica infection, emphasizing the integration of epidemiological context with hallmark clinical features - particularly fever, rash, and eschar - during peak transmission seasons in endemic areas. Early recognition allows the timely initiation of doxycycline therapy, which is essential for achieving favorable outcomes. Moreover, metagenomic next-generation sequencing (mNGS) provides the definitive identification of pathogens and guides targeted antimicrobial therapy.}, } @article {pmid41539854, year = {2026}, author = {Choi, S and Kwon, H and Kim, WK and Ko, G}, title = {Attenuation of Clostridioides difficile Infection by Clostridium hylemonae.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2510017}, pmid = {41539854}, issn = {1738-8872}, mesh = {Animals ; *Clostridium Infections/microbiology/therapy/prevention & control ; *Clostridioides difficile ; *Clostridium/physiology/genetics ; Gastrointestinal Microbiome ; Mice ; Disease Models, Animal ; Feces/microbiology ; Bile Acids and Salts/metabolism ; }, abstract = {Clostridioides difficile infection (CDI) is a bacterial infection of the colon that can cause diarrhea and colitis. The use of antimicrobials disrupts the intestinal microbiota, weakening colonization resistance and creating an environment in which C. difficile can establish infection. It is, therefore, necessary to identify specific bacteria that are helpful for the recovery of the intestinal microbiota in individuals with CDI. Previous studies have identified several strains that showed a negative correlation with C. difficile. Among these strains, C. hylemonae DSM 15053, which possesses the bai operon similar to Clostridium scindens, was selected. To test this hypothesis, we utilized a CDI mouse model and evaluated the inhibitory effect of C. hylemonae DSM 15053. Furthermore, to gain insights into the underlying mechanisms, we performed gut microbiota analysis. Contrary to our expectations, C. hylemonae DSM 15053 did not significantly produce SBAs. Interestingly, however, microbial diversity and richness were significantly higher in the C. hylemonae DSM 15053-treated group compared with the PBS control group. In addition, we observed a higher abundance of the genera Phocaeicola, Akkermansia, and Parabacteroides in the C. hylemonae DSM 15053 group. Moreover, metagenomic and metabolomic analyses revealed that C. hylemonae DSM 15053 mitigates CDI through a mechanism distinct from that of C. scindens KCTC 5591, which primarily functions as a regulator of bile acid metabolism.}, } @article {pmid41539958, year = {2026}, author = {Chen, D and Luo, LL and Yang, M and Wang, Y and Zhang, HY and Liu, ZQ and Qiao, LN}, title = {[Clinical characteristics of Pneumocystis jirovecii pneumonia in non-human immunodeficiency virus infected children].}, journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics}, volume = {64}, number = {2}, pages = {204-209}, doi = {10.3760/cma.j.cn112140-20250811-00740}, pmid = {41539958}, issn = {0578-1310}, support = {2021YFC2701704//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/drug therapy ; Female ; Male ; Retrospective Studies ; *Pneumocystis carinii/isolation & purification ; Child, Preschool ; Infant ; Prognosis ; Child ; China ; C-Reactive Protein ; }, abstract = {Objective: To analyze the clinical characteristics of Pneumocystis jirovecii pneumonia (PJP) in non-human immunodeficiency virus (HIV) infected children, aiming to provide a basis for early diagnosis, timely treatment, and improved prognosis. Methods: A single-center retrospective case series study was conducted to analyze the general information, laboratory indicators, imaging features, treatment, and outcomes of 59 pediatric patients with non-HIV-infected PJP admitted to the Department of Pediatrics, West China Second Hospital, Sichuan University, from February 2022 to June 2025.These patients were categorized into two groups based on the presence or absence of underlying diseases.Comparative analysis was performed to assess differences in hospitalization duration, intensive care unit (ICU) admission rate, mechanical ventilation rate, mortality, and other relevant aspects between the 2 groups.The rank sum test, χ[2] test or Fisher exact test was employed for intergroup comparisons. Results: The age at presentation of 59 patients: 0.5 (0.3, 2.5) years, including 40 males and 19 females. Among the underlying diseases, there were 12 cases (20%) of primary immunodeficiency, 4 cases (11%) each of autoimmune diseases, hematologic malignancies, and organ transplantation 30 cases (51%) had received treatment with glucocorticoids and immunosuppressants before diagnosis. The main clinical symptoms were cough in 57 cases (97%), dyspnea in 51 cases (86%) and, fever in 35 cases (59%). The peripheral white blood cell count was 9.2 (6.3, 13.9)×10[9]/L, with neutrophils 4.4 (1.8, 7.4)×10[9]/L and lymphocytes 3.4 (2.0, 6.1)×10[9]/L. C-reactive protein (CRP) 1.4 (0.5, 11.6) mg/L, procalcitonin 0.2 (0.1, 0.6) μg/L, the lactate dehydrogenase was (582±49) U/L. Fifty-three percent (16/30) of fungal G-test results were positive, 27% (11/41) of the children had CD4[+] T-cell counts <0.5×10[9]/L, and 32% (13/41) had CD4[+]/CD8[+] ratios <1.0.The main imaging findings included consolidation or patchy opacities in 48 cases (81%), diffuse ground-glass opacities in 29 cases (49%), and decreased transparency in 20 cases (34%). Pneumocystis was detected via metagenomic next-generation sequencing (mNGS) in all cases. Co-infections were present in 57 cases (97%). Among the 59 pediatric patients, 34 cases (58%) were treated with trimethoprim-sulfamethoxazole monotherapy, 19 cases (32%) received combination therapy with micafungin, and 7 cases (12%) received combination therapy with clindamycin. Fifty-three cases (90%) required varying degrees of respiratory support. Concurrent glucocorticoid therapy was administered in 70% (41/59) of cases at anti-PJP treatment initiation. Fifty-five cases (93%) improved, and 4 cases (7%) died.There were 36 cases in the group with underlying diseases and 23 cases in the group without underlying diseases. No statistically significant differences were observed between the two groups in terms of length of hospital stay, ICU admission rate and length of ICU stay, mechanical ventilation rate, or mortality rate (all P>0.05). Conclusions: Non-HIV-infected children with PJP tend to occur in infants under 3 years old. It is often complicated by underlying diseases such as immunodeficiency, with most patients having a history of glucocorticoid or immunosuppressant use. Clinical manifestations and imaging findings lack specificity, and mNGS facilitates early diagnosis. The core treatment is trimethoprim-sulfamethoxazole, most children require respiratory support, and combination with low-dose glucocorticoids may improve prognosis.}, } @article {pmid41540059, year = {2026}, author = {St John, E and Reysenbach, AL}, title = {Global deep-sea hydrothermal deposit metagenomes and metagenome-assembled genomes over time and space.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {283}, pmid = {41540059}, issn = {2052-4463}, support = {DEB-2409507//National Science Foundation/ ; }, mesh = {*Hydrothermal Vents/microbiology ; *Metagenome ; *Archaea/genetics ; Bacteria/genetics ; Genome, Archaeal ; }, abstract = {Actively venting high temperature deep-sea hydrothermal vent deposits along tectonic spreading centers and in backarc basins harbor a rich diversity of thermophilic Bacteria and Archaea, many of which have no representatives in cultivation nor any genomic representation in databases. Here, in order to produce a global-scale time series metagenomic resource for studying the microbial functional and genomic diversity in these high temperature ecosystems, we obtained 70 metagenomes from collections across spatial and temporal gradients from 21 different vent fields spanning 16 years (1993-2009). The dataset (Deep-Sea Hydrothermal Vent dataset (DSV70)) includes 3.56 Tbp of raw DNA sequence reads, that have been assembled to produce 7,422 medium- to high-quality (based on CheckM2) metagenome-assembled genomes (MAGs) of Bacteria (6,063 MAGs) and Archaea (1,359 MAGs). Collectively, this DSV70 dataset and the published 40 metagenomes from more recent deep-sea collections (2004 to 2018), represent a valuable resource for exploring the functional and phylogenomic diversity of the deep-sea hydrothermal microbiomes, and provide many reference genomes for studies in the taxonomy and systematics of poorly studied microbial lineages. Further, with the interest in mining the mineral resources at deep-sea vents, the DSV70 provides a genomic legacy for monitoring impacts on the microbial communities in these systems.}, } @article {pmid41540332, year = {2026}, author = {Wang, Y and Wu, C and Zhu, Q and Fan, C and Zhu, Y and Chen, Y and Wei, X and Feng, L}, title = {Comparative metagenomic characterization of gut microbiota and antibiotic resistome in multi-facility SPF mice.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41540332}, issn = {1471-2180}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics/drug effects ; Mice ; *Metagenomics/methods ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Mice, Inbred C57BL ; Anti-Bacterial Agents/pharmacology ; Mice, Inbred BALB C ; Specific Pathogen-Free Organisms ; Cecum/microbiology ; *Drug Resistance, Microbial/genetics ; Female ; Metagenome ; China ; Sequence Analysis, DNA ; }, abstract = {Specific pathogen-free (SPF) mice are pivotal preclinical models linking basic microbiology to clinical translation, yet comprehensive high-resolution profiling of their gut microbiome, especially antibiotic resistance genes (ARGs), remains limited. To address this gap, metagenomic sequencing was conducted on cecal contents from C57BL/6 and BALB/c SPF mice from five Shanghai laboratory animal facilities, generating 141 Gbp high-quality sequencing data. From 1,761,909 predicted genes, 1,048,575 non-redundant genes were identified for analysis. Taxonomic annotation identified Bacillota (73.0%), Bacteroidota (16.6%), and Actinomycetota (2.9%) as dominant phyla. At the genus level, microbial communities varied markedly across facilities, with Muribaculaceae prevailing in SHA/SHD and Blautia or Enterococcus enriched in SHB/SHE. Beta diversity analysis showed communities clustered by facility, indicating breeding environment had a stronger impact on gut microbiota diversity than host strain. KEGG, COG, and GO functional annotation revealed broad metabolic and molecular diversity. Antibiotic resistome profiling identified 11 ARG categories, predominantly associated with glycopeptides (18.1%) and tetracycline (11.3%) resistance. The most enriched ARG carriers were Pseudomonadota (acrD, emrB, mdtB etc.), Bacillota (tet(44), tet(M), tet(O) etc.), Bacteroidota (tet(Q), mel, tet(X) etc.), and Actinomycetota (rpoB, ileS). Furthermore, ARGs resistance mechanisms varied between facilities with distinct beta-diversity clustering: SHB and SHE mice mainly employed antibiotic target alteration against glycopeptides, whereas SHA, SHD, and SHC-C57BL/6 primarily utilized antibiotic target protection against tetracyclines. This study presents a high-resolution comparison of gut microbiota and ARGs in SPF mice from multiple facilities, highlighting facility-dependent microbial and resistome variation and providing valuable references for preclinical microbiological standardization and risk assessment.}, } @article {pmid41540749, year = {2026}, author = {Kong, L and Xu, H and Wang, Y and Tao, Y and Xiao, P and Wang, Z and Zhang, M and Zheng, X and Zhang, C and Cui, S and Xu, T and Pang, Z and Wang, A and Ren, N and Zheng, C}, title = {Single-Cell Profiling Reveals Hidden Drivers of Sediment Phosphorus Release.}, journal = {Environmental science & technology}, volume = {60}, number = {6}, pages = {4830-4839}, doi = {10.1021/acs.est.5c15684}, pmid = {41540749}, issn = {1520-5851}, mesh = {*Geologic Sediments/chemistry ; *Phosphorus ; Spectrum Analysis, Raman ; Single-Cell Analysis ; Bacteria/metabolism ; Eutrophication ; }, abstract = {As external phosphorus inputs are progressively brought under control, microbe-mediated release of legacy phosphorus from sediments to the overlying waters has become a primary contributor to persistent eutrophication and recurrent algal blooms in global freshwater ecosystems. However, inherent challenges exist in capturing the in situ metabolic activity of phosphorus-solubilizing bacteria (PSB) due to intrinsic cultivation biases and the disconnect between bulk metagenomic profiles and the functions of viable cells. Furthermore, a lack of research into the coupling the phenotypic activity and adaptive genetic strategies of PSB in heterogeneous sedimentary environments has led to limited understanding of the mechanisms underlying endogenous phosphorus release. Here, using single-cell Raman spectroscopy coupled with deuterium oxide labeling (Raman-D2O), distinct in situ phosphorus-solubilizing activities of PSB inhabiting eutrophic, mesotrophic, and oligotrophic sediments were quantified. Inorganic PSB dominated in all sediment types but exhibited the highest activity in nutrient-rich eutrophic sites. Their activities correlated strongly with phosphorus speciation and release fluxes at the sediment-water interface of their habits. In contrast, organic PSB prevailed in oligotrophic sediments. Raman-activated cell sorting conbined with metagenomic sequencing uncovered that low-abundance taxa (e.g., Bacillus and Acinetobacter) acted as disproportionate drivers of phosphorus mobilization. PSB from eutrophic sediments were enriched in genes encoding phosphatases and organic acid hydrolysis pathways, whereas their oligotrophic counterparts favored genes related to high-affinity transporters and polyphosphate storage. These findings elucidate how nutrient regimes shape PSB metabolic traits, advancing mechanistic insights into microbial phosphorus dynamics in aquatic ecosystems and providing a theoretical basis for optimizing lake management strategies to mitigate endogenous pollutant-driven eutrophication risks.}, } @article {pmid41541065, year = {2025}, author = {Zhang, X and Liu, C and Han, Y and She, J and Wu, W and Wang, L and Song, J and Gao, GF and Xu, Z and Liang, H and Liu, J}, title = {Sustained circulation of Aedes albopictus-derived novel almendraviruses in the urban parks.}, journal = {Biosafety and health}, volume = {7}, number = {6}, pages = {369-376}, pmid = {41541065}, issn = {2590-0536}, abstract = {The Rhabdoviridae family comprises a diverse range of negative-sense single-stranded ribonucleic acid (RNA) viruses, including significant human and mammalian viruses transmitted by various arthropod species. Herein, using Aedes albopictus (Ae. albopictus) samples collected in two urban parks during 2023 and 2024, through metagenomics sequencing, 16 sequences were identified as putative novel viruses, showing closest homology to insect-specific viruses, mycoviruses, or plant-associated viruses. Notably, two novel viruses, Aedes albopictus almendravirus GCCDC15 (Aealb-AlmV GCCDC15) and Aedes albopictus almendravirus GCCDC16 (Aealb-AlmV GCCDC16) were identified and successfully isolated. Both of these viruses belong to the genus Almendravirus within the Rhabdoviridae family. Phylogenetic analysis revealed that Aealb-AlmV GCCDC15 and GCCDC16 are distantly related to Coot Bay virus (the United States of America, 2013) and Menghai rhabdovirus (Yunnan Province, China, 2017). The genetic distances between these two viruses and their most similar viruses are marked by 59.85 % and 87.20 % of amino acid identity in the L protein, respectively, supporting their classification as two new species in the Rhabdoviridae family. Cytopathic effects and rod-like virions were observed in mosquito cells (C6/36) after inoculating with supernatants from the Ae. albopictus samples. To investigate the natural distribution and persistence of the novel almendraviruses, we conducted a specific reverse transcription-polymerase chain reaction (RT-PCR) screening of Ae. albopictus mosquitoes collected from two urban parks across different time points. The assays confirmed the presence of both Aealb-AlmV GCCDC15 and GCCDC16 in mosquito populations. Critically, these viruses were detected repeatedly over successive sampling periods and in mosquitoes from geographically distinct sites within the urban environment. In summary, our study delineates the virome characteristics of Aedes mosquitoes in the urban ecosystem and successfully isolated two novel rhabdoviruses. The recurrent detection provides clear evidence for the sustained circulation of Ae. albopictus-derived almendraviruses in urban parks, highlighting their ongoing transmission and establishment in these habitats.}, } @article {pmid41541500, year = {2025}, author = {Broedlow, CA and Swanson, E and Cherenack, EM and Basting, C and Nogueira, NF and France, M and Yue, P and Chakrawarti, A and Salazar, A and Acosta, L and Raccamarich, P and Gale, M and Ravel, J and Fein, LA and Holm, J and Alcaide, ML and Klatt, NR}, title = {Common cervicovaginal sequencing methods result in discordant molecular diagnoses of bacterial vaginosis and reveal strain level effects of Gardnerella vaginalis.}, journal = {npj women's health}, volume = {3}, number = {}, pages = {}, pmid = {41541500}, issn = {2948-1716}, support = {P30 AI073961/AI/NIAID NIH HHS/United States ; R01 AI138718/AI/NIAID NIH HHS/United States ; }, abstract = {Bacterial vaginosis (BV) is associated with HIV transmission and pre-term birth, yet the etiology of BV remains unknown. Our analysis addressed that knowledge gap by comparing diagnostic techniques and using Bayesian inference to find species-specific associations with clinical indicators. We also assessed the effect of sequencing methodology on the results of molecular BV profiling. We observed significant differences in microbial diversity within BV-associated CSTs based on clinical diagnosis. CST assignments were substantially influenced by sequencing methodology, with concordance between methods as low as 59% for metatranscriptomic and metataxonomic-based CST assignment. We also found that Gardnerella has a strain-dependent association with individual Amsel's criteria, and that Dialister micraerophilus and Parvimonas micra are positively associated with Amsel's criteria while Lactobacillus is negatively associated. These results highlight the challenge of characterizing a condition without a single etiological agent, reinforcing the need for more granular diagnoses and treatments that are sensitive to BV variability.}, } @article {pmid41542073, year = {2025}, author = {Kapoor, S and Mehta, P and Patial, V and Pandey, R and Padwad, YS}, title = {Phloretin-induced modulation in gut microbiome, mitigates colonic inflammation and alleviates colitis-associated colorectal cancer in mice.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {2730-2746}, pmid = {41542073}, issn = {2001-0370}, abstract = {Colitis associated colorectal cancer (CAC) is the fourth common cancer known to cause significant mortalities worldwide. Phloretin is a dihydrochalcone naturally found in apple, pear and strawberry. It exhibited different biological activities, namely anti-inflammatory, anticancer and anti-microbial. In the present study, the role of phloretin towards alleviating colonic inflammation and regulating gut microbiota was explored. The treatment of phloretin led to the reduction in the intestinal inflammation and maintained colon length-weight ratio by decreasing the total number of tumor nodules. We registered reduction in the colonic inflammatory cytokines levels namely TNFα, IL1β, IFNγ, and IL6 as well as expression of HSP90, Cox2, and Src found decreased. Results highlighted the restoration in the levels of tight junction proteins and the expression of Muc2 and Muc3. Further, role of phloretin in inducing apoptosis of tumor cells and the deregulation β-catenin pathway was studied. The histopathological analysis revealed normal colonic structure by decreasing leukocyte infiltration, as well as, circumvention in the reduction of the numbers of goblet cell, crypt abscess and ulceration in phloretin and 5-ASA (5-aminosalicylic acid) treated animals, compared to the diseased group. Metagenomic analysis of the gut microbiome in CAC mice revealed that phloretin significantly increased the abundance of Lactobacillus species, which exert probiotic effects and inhibit synchronous colon tumor growth by modulating β-catenin signaling. The increased abundance of L. reuteri and L. murinus was associated with regulated cellular proliferation, reduced TNF-α production, and decreased expression of COX-2, cyclin D1, and Bcl-2. In conclusion, the results obtained signify the nutraceutical potential of phloretin in restoring the intestinal barrier, maintaining the beneficial gut microbial population, and amelioration of CAC in mice.}, } @article {pmid41542089, year = {2025}, author = {Zhang, D and Hu, J and Gu, B and Cao, B and Lu, J and Chen, Q and Wang, L and Pei, G and Liu, ZX and Cheng, MG and Gao, S and Li, X}, title = {BodyMeta: A comprehensive database for microbes under various pathological and physiological conditions.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {3685-3692}, pmid = {41542089}, issn = {2001-0370}, abstract = {Microorganisms residing in the gut and other anatomical sites exhibit substantial alterations under both physiological and pathological conditions, which are intricately linked to human health. Consequently, the establishment of a comprehensive metagenomic database encompassing diverse body sites under both pathological and physiological conditions is highly important. In this study, we developed BodyMeta (Body Metagenome Database), an upgraded version of the gutMEGA (gut Metagenome Atlas database), and we expanded the included studies considerably from 182 to 1261. These studies were classified into two categories: 600 literature-based studies without raw data (comprising 107 whole-genome sequencing and 493 16S amplicon sequencing studies) and 661 studies containing 663 raw datasets. We systematically categorized 1842 conditions derived from the 1261 studies into 966 pathological and 879 physiological conditions spanning 31 body sites, with the pathological conditions organized according to MeSH (Medical Subject Headings) terms. We comprehensively annotated the microbial contents, diversities, biomarkers and functional differences of the curated raw 16S amplicon sequencing data. In total, 59010 microbial taxa from literature sources and 40657 from raw datasets were mapped to the NCBI Taxonomy database. Additionally, related information about literature and experiments were compiled within BodyMeta. Collectively, the BodyMeta database provides a comprehensive resource for metagenomic investigations related to both physiological and pathological conditions, which can be freely accessed at https://bodymeta.omicsbio.info/.}, } @article {pmid41542367, year = {2026}, author = {Sladký, O and Veselý, P and Břinda, K}, title = {FroM Superstring to Indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT).}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbaf290}, pmid = {41542367}, issn = {2635-0041}, abstract = {MOTIVATION: The growing volumes and heterogeneity of genomic data call for scalable and versatile k-mer-set indexes. However, state-of-the-art indexes such as SBWT and SSHash depend on long non-branching paths in de Bruijn graphs, which limits their efficiency for small k, sampled data, or high-diversity settings.

RESULTS: We introduce FMSI, a superstring-based index for arbitrary k-mer sets that supports efficient membership and compressed dictionary queries with strong theoretical guarantees. FMSI builds on recent advances in k-mer superstrings and uses the Masked Burrows-Wheeler Transform, a novel extension of the classical Burrows-Wheeler Transform that incorporates position masking. Across a range of k values and dataset types-including genomic, pangenomic, and metagenomic-FMSI consistently achieves superior query space efficiency, using up to 2-3× less memory than state-of-the-art methods, while maintaining competitive query times. Only a space-optimized version of SBWT can match the FMSI's footprint in some cases, but then FMSI is 2-3× faster. Our results establish superstring-based indexing as a robust, scalable, and versatile framework for arbitrary k-mer sets across diverse bioinformatics applications.

FMSI is developed in C++ and released under the MIT license, with source code provided at https://github.com/OndrejSladky/fmsi and an installable package available through Bioconda. The datasets used in the experiments are deposited at Zenodo (https://doi.org/10.5281/zenodo.14722244).}, } @article {pmid41542635, year = {2026}, author = {Robertson, CM and Mercado-Evans, V and Larson, AB and Branthoover, H and Ottinger, S and Mejia, ME and Hameed, ZA and Gonzalez, LA and Serchejian, C and Ogilvie, L and Zulk, JJ and Patras, KA}, title = {Type 2 diabetes mellitus exacerbates vaginal group B Streptococcus colonization via impaired mucosal cytokine response.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41542635}, issn = {2692-8205}, support = {F31 DK138748/DK/NIDDK NIH HHS/United States ; R21 AI173448/AI/NIAID NIH HHS/United States ; F31 HD117458/HD/NICHD NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; T32 AI055449/AI/NIAID NIH HHS/United States ; F31 DK136201/DK/NIDDK NIH HHS/United States ; R25 GM069234/GM/NIGMS NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; F31 AI167547/AI/NIAID NIH HHS/United States ; F31 HD111236/HD/NICHD NIH HHS/United States ; F31 AI167538/AI/NIAID NIH HHS/United States ; }, abstract = {Type 2 diabetes mellitus (T2D) is a metabolic disorder that confers increased risk of microbial infections, including those caused by the opportunistic pathogen group B Streptococcus (GBS). Asymptomatic GBS carriage in the vaginal tract is a notable reservoir for infection, but the impact of T2D on the vaginal mucosa and GBS colonization is not fully understood. We employed a diet-induced mouse model of T2D paired with vaginal GBS colonization to investigate the impact of diabetes on glucose availability, vaginal microbiome composition, and vaginal cytokine profiles at baseline and in response to GBS. We observed enhanced susceptibility of diabetic mice to GBS vaginal colonization and reproductive tract dissemination. Despite experiencing hyperglycemia, diabetic mice did not exhibit elevated glucose in the reproductive tract. Regarding the vaginal microbiota, diabetic mice had minimal compositional differences with decreased Mammaliicoccus being the only significant taxonomic variance. Vaginal cytokine profiling revealed consistently depressed cytokines in diabetic mice, beginning with KC at baseline and expanding to an array of eight pro-inflammatory cytokines post-GBS infection. Pairing cytokine observations with GBS colonization outcomes revealed a correlation between delayed vaginal IL-1α induction and persistent vaginal GBS, suggesting that vaginal cytokine deficiency may contribute to diabetic GBS vaginal colonization. Supplementation with intravaginal rIL-1α was sufficient to resolve GBS burden differences between diabetic mice and non-diabetic controls, confirming that deficient vaginal cytokine responses contribute to diabetic GBS vaginal persistence. These findings advance our understanding of diabetic vaginal mucosal susceptibility to pathogens and support the potential for immunological intervention in the susceptible diabetic population.}, } @article {pmid41543189, year = {2026}, author = {Hasan, GM and Mohammad, T and Zaidi, S and Shamsi, A and Sohal, SS and Hassan, MI}, title = {<p>Klebsiella pneumoniae and pyogenic liver abscess: Emerging clinical threats, virulence mechanisms and therapeutic strategies (Review)</p>.}, journal = {Molecular medicine reports}, volume = {33}, number = {3}, pages = {}, pmid = {41543189}, issn = {1791-3004}, mesh = {*Klebsiella pneumoniae/genetics/immunology/isolation & purification/pathogenicity ; *Liver Abscess, Pyogenic/diagnosis/drug therapy/epidemiology/microbiology ; Virulence/genetics ; Drug Resistance, Multiple, Bacterial/genetics/immunology ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Metagenomics ; Point-of-Care Testing ; Global Health ; Polysaccharides, Bacterial/genetics/immunology ; Immune Evasion/genetics ; Humans ; Animals ; Global Burden of Disease ; }, abstract = {

Klebsiella pneumoniae has emerged as a leading cause of pyogenic liver abscess (PLA), driven by hypervirulent and multidrug‑resistant (MDR) strains that pose major diagnostic and therapeutic challenges. This organism exhibits extensive capsular diversity (K1‑K80), with serotypes K1, K2, K5, K20, K54 and K57 being the most associated with invasive infections and severe clinical outcomes. Increasing convergence between hypervirulence and MDR determinants threatens effective management worldwide. Pharmacological and safety limitations of current antibiotics, including nephrotoxicity of colistin, hepatotoxicity of tigecycline and poor drug penetration into abscess cavities, further complicate treatment and encourage exploration of non‑traditional strategies such as anti‑virulence or immunomodulatory approaches. Recent advancements in rapid diagnostic tools such as metagenomic sequencing, MALDI‑TOF and point‑of‑care PCR assays offer promising prospects for early detection and antimicrobial optimization. Pharmacokinetic challenges at the abscess site and the emergence of hybrid hvKp‑MDR strains emphasize the urgency of precision‑guided therapy and robust global surveillance. K. pneumoniae‑associated PLA thus represents an evolving global health threat and understanding serotype diversity, antibiotic limitations and diagnostic innovations is essential for developing more effective preventive and therapeutic strategies. The present review provides current insights into the epidemiology, pathogenesis and therapeutic challenges of K. pneumoniae‑associated PLA, while highlighting translational opportunities and research priorities to counter the escalating dual threat of hypervirulence and resistance.

.}, } @article {pmid41543249, year = {2026}, author = {Beals, DG and Carper, DL and Hochanadel, LH and Jawdy, SS and Klingeman, DM and Piatkowski, BT and Weston, DJ and Doktycz, MJ and Pelletier, DA}, title = {Genomic signatures in Variovorax enabling colonization of the Populus endosphere.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0160525}, pmid = {41543249}, issn = {2379-5077}, mesh = {*Populus/microbiology ; Plant Roots/microbiology ; Rhizosphere ; *Comamonadaceae/genetics/classification/isolation & purification ; *Genome, Bacterial ; Soil Microbiology ; Metagenomics ; }, abstract = {Microbial colonization of plant roots involves strong selective pressures that shape the structure and function of root-associated communities. In particular, the endosphere represents a highly selective environment requiring host entry and in planta persistence. However, strain-specific microbial traits that enable endosphere colonization remain poorly understood. Here, we use a defined, genome-resolved community of 28 Variovorax strains isolated from the roots of Populus deltoides and Populus trichocarpa (poplar trees) to determine which strains partition between rhizosphere and endosphere compartments and to identify the genomic traits associated with endosphere specialization. By combining strain-resolved metagenomic profiling, comparative genomics, and functional assays, we demonstrate that dominant endosphere colonizers are enriched in genes related to nutrient metabolism, redox balance, transcriptional regulation, and a conserved L-fucose utilization pathway experimentally shown to enhance root colonization. Not all strains succeed through the same strategy. Community-wide functional profiling revealed a distinct and reduced set of traits in the endosphere, including orthogroups associated with low-abundance strains that were overlooked in strain-level analyses. These findings reveal that multiple ecological strategies, such as metabolic competition, regulatory adaptation, and niche specialization, can support endosphere colonization. Our results advance the understanding of how bacterial colonization traits are distributed and deployed within a plant microbiome and suggest that host filtering selects for distinct, and sometimes complementary, microbial strategies. This work supports a shift toward mechanistic, genome-resolved models of microbiome assembly and offers a framework for linking microbial function to host colonization success.IMPORTANCEPlants often depend on diverse microbial partners to support their growth, resilience, and adaptation to changing environments. Among these microbes, some bacteria inhabit the rhizosphere (the narrow zone around roots where microbes interact with the plant) while others are able to enter and persist within root tissues. The traits that distinguish these two lifestyles remain poorly understood. In this study, we examined a group of related Variovorax strains from poplar tree root microbiomes to ask why some rhizosphere-associated strains also become successful endosphere colonizers. We found that strains appear to succeed through different strategies: some may benefit from rapid growth on plant-derived carbon sources, while others may rely on stress tolerance or fine-tuned regulation. These results suggest that there is no single path from the rhizosphere into the root interior, but rather multiple strategies shaped by the host environment. Understanding this diversity can inform efforts to design resilient plant-microbe communities.}, } @article {pmid41543271, year = {2026}, author = {Yamazaki, K and Yamaguchi, T and Yokoyama, Y and Tonosaki, Y and Kursanbaeva, K and Motooka, D and Akeda, Y and Kashimoto, T}, title = {Nutrient acquisition drives Edwardsiella tarda pathogenesis in necrotizing soft tissue infection.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0165725}, pmid = {41543271}, issn = {2379-5077}, support = {19K15979//Japan Society for the Promotion of Science/ ; 22K14998//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Edwardsiella tarda/pathogenicity/genetics/metabolism ; *Soft Tissue Infections/microbiology/metabolism ; *Enterobacteriaceae Infections/microbiology/metabolism ; Mice ; Virulence Factors/genetics/metabolism ; Virulence ; DNA Transposable Elements ; *Nutrients/metabolism ; Bacterial Proteins/genetics/metabolism ; Female ; Humans ; Necrosis ; }, abstract = {Necrotizing soft tissue infections (NSTIs) are rapidly progressive and life-threatening diseases caused by diverse bacterial pathogens. While classical virulence factors, such as toxins and secretion systems, have been extensively characterized, the role of metabolic fitness in supporting bacterial survival within the nutrient-restricted host environment remains underexplored. Edwardsiella tarda, a human-pathogenic bacterium implicated in NSTIs, represents an emerging model for studying non-canonical pathogenic strategies. Here, we employed transposon-directed insertion site sequencing (TraDIS) to identify genes critical for E. tarda survival in a murine soft tissue infection model. A genome-wide screen revealed 41 genes significantly depleted during the infection, including those involved in iron and zinc acquisition (fetB, zupT), vitamin biosynthesis (pdxK, cobA), and polyamine metabolism (speB). Functional assays using defined minimal media demonstrated that supplementation with vitamin B6 or putrescine enhanced bacterial growth, validating their contribution to fitness under nutrient-limited conditions. Our findings indicate that E. tarda pathogenesis is driven not solely by classical virulence factors but also by its ability to acquire essential nutrients and adapt metabolically to host-imposed nutritional stress. This study provides the first genome-wide fitness map for E. tarda during soft tissue infection and reveals new targets for therapeutic intervention that disrupt nutrient acquisition systems. These results also emphasize the broader relevance of metabolic adaptation as a determinant of virulence in invasive bacterial infections.IMPORTANCENecrotizing soft tissue infections (NSTIs) are severe, rapidly progressing bacterial infections with high morbidity and mortality. Although classical virulence factors such as toxins have been widely studied, much less is known about how pathogens adapt metabolically to survive within the nutrient-restricted environment in host tissues. This study uses Edwardsiella tarda, an emerging NSTI pathogen, as a model to identify genes required for in vivo fitness using transposon insertion sequencing. By revealing the critical roles of nutrient acquisition and metabolic adaptation, rather than toxin production alone, this work challenges conventional paradigms of bacterial virulence. Our findings suggest that targeting bacterial nutrient acquisition pathways may offer a novel therapeutic approach to control invasive infections. Furthermore, this study provides the first genome-wide fitness map of E. tarda during soft tissue infection, offering a valuable resource for future research into polymicrobial wound infections and host-pathogen nutrient competition.}, } @article {pmid41543328, year = {2026}, author = {Ji, Q and Wang, Y and Huo, L and Qiao, C and Li, F and Yang, F and Pan, L}, title = {Therapeutic Mechanisms of Lactiplantibacillus plantarum NXU0014 Against Chronic Alcohol-Induced Liver Injury Mediated by Gut-Liver Axis Modulation.}, journal = {Molecular nutrition & food research}, volume = {70}, number = {1}, pages = {e70375}, doi = {10.1002/mnfr.70375}, pmid = {41543328}, issn = {1613-4133}, support = {2023BCF01028//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2023BCF01029//Key R & D Program of Ningxia Hui Autonomous Region/ ; 2024AAC05047//Ningxia Hui Autonomous Region Excellent Young Scientists Fund/ ; NYG2024042//Higher Education Scientific Research Grant, Department of Education of Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; Male ; Mice, Inbred C57BL ; *Probiotics/pharmacology ; *Lactiplantibacillus plantarum/physiology ; Liver/metabolism/drug effects ; *Liver Diseases, Alcoholic/therapy/microbiology ; Mice ; *Gastrointestinal Microbiome/drug effects/physiology ; Oxidative Stress ; Dysbiosis ; Intestinal Barrier Function ; }, abstract = {This study investigated the protective effects of Lactobacillus plantarum NXU0014 against chronic alcoholic liver injury (CALI) and its underlying mechanisms in a mouse model. Forty-eight male C57BL/6J mice were divided into four groups: blank control, model, silymarin, and L. plantarum NXU0014. The CALI model was induced by administering 56% Hongxing Erguotou liquor. Multi-omics analyses revealed that alcohol intake induced gut microbiota dysbiosis, characterized by an increased Firmicutes/Bacteroidetes ratio and decreased abundance of probiotics (e.g., Lactobacillus and Bifidobacterium). These changes were associated with hepatic pro-inflammatory upregulation, downregulation of antioxidant genes (Nrf2, HO-1), and impaired intestinal barrier function (ZO-1). Metabolomic disturbances featured elevated fecal bile acids, reduced amino acids, and enriched pathways for ABC transporters and bile secretion. Intervention with NXU0014 restored probiotic levels (including Bifidobacterium pseudodanubicum and Lactobacillus reuteri), alleviated hepatic inflammation and oxidative stress by activating the Nrf2/HO-1 pathway, and repaired the intestinal barrier. Integrated microbiome-metabolome analysis revealed a negative correlation between Lactobacillus and toxic bile acids, and a positive correlation between Bifidobacterium and anti-inflammatory metabolites. These findings demonstrate that NXU0014 mitigates liver injury by modulating gut-liver axis metabolic interactions, highlighting its potential as a novel probiotic-based therapy for alcoholic liver disease.}, } @article {pmid41544440, year = {2026}, author = {Yang, L and Ru, J and Guo, S and Yang, X and Li, P and Deng, L and Wang, X}, title = {Research note: The chicken gut virome: Spatiotemporal dynamics and divergent responses to antibiotic versus phytogenic supplementation.}, journal = {Poultry science}, volume = {105}, number = {3}, pages = {106373}, pmid = {41544440}, issn = {1525-3171}, mesh = {Animals ; *Chickens/virology ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Bacteriophages/drug effects/physiology ; Animal Feed/analysis ; *Chlortetracycline/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Virome/drug effects ; Dietary Supplements/analysis ; *Plant Extracts/administration & dosage/pharmacology ; Gastrointestinal Tract/virology ; Diet/veterinary ; }, abstract = {This study employed metagenomic sequencing data to comprehensively investigate the gut virome, with a focus on the bacteriophage communities (the phageome), across intestinal regions and developmental stages in 360 chickens. We characterized the spatiotemporal dynamics of phage communities and assessed the impact of chlortetracycline (CTC), an antibiotic, and Macleaya cordata extract (MCE), a phytogenic supplement. Our analysis revealed that phage community assembly was highly structured, exhibiting distinct successional patterns across age and between foregut and hindgut segments. A key finding was the identification of a potential antibiotic-phage synergy, mediated by phage-encoded auxiliary metabolic genes (AMGs) involved in bacterial immune evasion, suggesting a novel mechanism for enhanced infectivity under antibiotic pressure. In contrast, phytogenic supplementation promoted gut ecosystem homeostasis by fostering significantly richer and more diverse phage communities. Our results delineate the fundamental ecology of the chicken gut virome and provide mechanistic insights into how different growth promoters exert contrasting effects on viral populations, supporting the use of phytogenics as sustainable alternatives for animal husbandry.}, } @article {pmid41544536, year = {2026}, author = {Chen, R and Li, Z and Li, D and Mao, X and Xu, Z}, title = {Clinical utility of bronchoalveolar lavage fluid metagenomic next-generation sequencing in the etiological diagnosis of community-acquired pneumonia in children.}, journal = {International journal of medical microbiology : IJMM}, volume = {322}, number = {}, pages = {151701}, doi = {10.1016/j.ijmm.2026.151701}, pmid = {41544536}, issn = {1618-0607}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; *Community-Acquired Pneumonia/diagnosis/microbiology ; Child ; *Molecular Diagnostic Techniques/methods ; *Community-Acquired Infections/diagnosis ; }, abstract = {CAP is a major cause of pediatric hospitalization on a global scale, particularly in developing countries where the morbidity and mortality rates remain high. The etiological diagnosis of CAP in children is challenging, particularly for children with severe and high-risk conditions, such as immunodeficiency. This is primarily due to the nonspecific distribution of the causative agent and the limitations of traditional detection methods. As an emerging molecular diagnostic technology, BALF mNGS has been shown to detect the nucleic acid sequences of bacterial, viral, fungal, and atypical pathogens directly from clinical samples. This is attributed to the technology's unbiased, high throughput, and high sensitivity, which significantly improves the detection rate of pathogens. Furthermore, BALF mNGS also improves the detection of mixed infections. This capacity for precise analysis is of significant value, as it facilitates the identification of drug-resistant genes and rare pathogens. Consequently, this enhanced diagnostic capability provides a reliable foundation for the precise treatment of childhood CAP. Nevertheless, its clinical application continues to encounter challenges, including high cost, invasive sampling methods, complex data analysis processes, and insufficient standardization of pre-analytical sample processing. The technical principles, clinical value and optimization strategies of BALF mNGS are systematically reviewed in this paper, with the aim of providing a reference for improving the pathogenetic diagnosis of CAP in children.}, } @article {pmid41544592, year = {2026}, author = {Zheng, Z and Lyu, H and Li, Z and Tang, J and He, J}, title = {Unraveling water depth dependent microplastic aging driven by functional microbial community interaction in a real urban river.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141133}, doi = {10.1016/j.jhazmat.2026.141133}, pmid = {41544592}, issn = {1873-3336}, mesh = {*Biofilms ; *Rivers/microbiology/chemistry ; *Microplastics/metabolism/chemistry ; *Water Pollutants, Chemical/metabolism/analysis ; Polyvinyl Chloride/chemistry ; Polyesters ; Bacteria/metabolism/genetics ; }, abstract = {Microplastic (MPs) biofilms are dynamic microhabitats that regulate substance transformation processes. However, the influence of natural urban water depth gradients on the biofilm functions and subsequent aging of MPs remains poorly understood. Herein, we characterized the aging process of MPs in different depths of a real urban river, and the biofilm driven aging mechanism was illustrated. Surface characterization of the MPs showed an increase in oxygen-containing functional groups (CO, C-O) and O/C in polylactic acid (PLA) during aging, which indicated oxidation and hydrolysis reactions, especially at 2.0 m deep water depth. In polyvinyl chloride (PVC) MPs, carbonyl index (CI) was 2 times higher at 2.0 m as compared to 0.1 m water depth and lower chlorine content was found, indicating higher oxidative degradation and dechlorination processes in deeper water. Moreover, biofilms may regulate the synergism between oxygenase and hydrolases in PLA biofilms and oxygenase and dehalogenase in PVC biofilms. Microorganisms with both denitrification and MPs degradation functions, such as Acidovorax, Comamonas, Dechloromonas, were enriched in MPs biofilm. In addition, a positive correlation was found between MPs degradation genes (TGL2, katG, ncd2) and denitrification genes (napA, nirS, norB) in PLA biofilms at deeper water depth, suggesting a potential effect of denitrification functions on MPs aging (45 d incubation). This research challenges the conventional thoughts of higher MPs aging in shallow water, emphasizing the significant role of moderate depth gradients water in regulating the ecological function of microplastic biofilm, which is essential for evaluating the fate of MPs in real urban rivers.}, } @article {pmid41544844, year = {2026}, author = {Wei, Y and Hu, Y and Shi, Q and Su, N and Chen, X and Chong, L and Cui, X}, title = {Successful treatment of probable disseminated mucormycosis using liposomal amphotericin B and isavuconazole in myelodysplastic syndrome: A case report and literature review.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {164}, number = {}, pages = {108394}, doi = {10.1016/j.ijid.2026.108394}, pmid = {41544844}, issn = {1878-3511}, mesh = {Humans ; *Nitriles/therapeutic use ; *Triazoles/therapeutic use ; *Mucormycosis/drug therapy/diagnosis/complications ; *Myelodysplastic Syndromes/complications ; *Pyridines/therapeutic use ; *Amphotericin B/therapeutic use ; Female ; *Antifungal Agents/therapeutic use ; Aged ; Drug Therapy, Combination ; Immunocompromised Host ; Fatal Outcome ; }, abstract = {BACKGROUND: Mucormycosis is a rare, aggressive, and life-threatening fungal infection that predominantly affects immunocompromised individuals and is associated with a high mortality rate.

CASE PRESENTATION: We treated a 72-year-old woman with myelodysplastic syndrome (MDS) who developed disseminated mucormycosis involving the lungs, skin, and central nervous system (CNS). Diagnosis was supported by metagenomic next-generation sequencing (mNGS), and she received combination antifungal therapy with liposomal amphotericin B and isavuconazole. Her clinical status stabilized after 4 weeks of treatment. She later died approximately 2 weeks after discharge because of carbapenem-resistant Pseudomonas aeruginosa bacteremia.

CONCLUSIONS: Our case highlights the importance of prompt diagnosis and timely initiation of therapy for mucormycosis and indicates that combination antifungal therapy may be an effective approach to managing severe disseminated mucormycosis in immunocompromised patients.}, } @article {pmid41544986, year = {2026}, author = {Liu, X and Zhang, J and Niu, Y and Bai, Y and Jia, X and Cai, S and Wang, Y and Zhang, X and Shi, B and Hu, J and Zhang, C and Zhao, Z}, title = {Dynamic changes in rumen fermentation, microbial communities, and metabolite profiles of non-pregnant and gestational Ashidan yaks.}, journal = {Genomics}, volume = {118}, number = {2}, pages = {111205}, doi = {10.1016/j.ygeno.2026.111205}, pmid = {41544986}, issn = {1089-8646}, mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle/microbiology/metabolism ; Fermentation ; Female ; *Metabolome ; Metagenome ; Pregnancy ; *Gastrointestinal Microbiome ; *Microbiota ; }, abstract = {Rumen microbiota and their metabolites in ruminants across reproductive stages benefit the animals' growth, health and offspring's development. However, the impact of rumen fermentation profiles, microbial composition, and metabolite dynamics between non-pregnant and gestating Ashidan yaks remains poorly understood. This study analyzed the rumen fermentation, metagenome and metabolome of five 2-3-year-old Ashidan yaks during the non-pregnant period (NP; 11-30 days pre-mating) and the gestational period (GP; 112-148 days post-conception). Research has found that gestation had higher acetic acid and ammonia nitrogen (NH3-N) (P < 0.05), increased Ascomycota, Apicomplexa, Rhodococcus, Acinetobacter, Methanosphaera (P < 0.05); differential metabolites enriched in valine, leucine, isoleucine biosynthesis and histidine metabolism (P < 0.05), with L-threonine and urocanic acid as major ones. Additionally, microorganisms, metabolites and fermentation parameters correlated. The study shows Ashidan yaks adapt to reproductive stages via regulating rumen microbiota and metabolism, providing a basis for feeding management.}, } @article {pmid41545429, year = {2026}, author = {Maharaj, SD and Nkuna, R and Matambo, TS}, title = {Shotgun metagenomic and physicochemical profiling of municipal wastewater treatment plants using activated sludge and trickling filters.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {5486}, pmid = {41545429}, issn = {2045-2322}, mesh = {*Metagenomics/methods ; *Sewage/microbiology/chemistry ; *Wastewater/microbiology/chemistry ; Bacteria/genetics/classification/isolation & purification ; *Water Purification/methods ; *Metagenome ; South Africa ; Shotgun Sequencing ; High-Throughput Nucleotide Sequencing ; *Waste Disposal, Fluid/methods ; Filtration ; Biological Oxygen Demand Analysis ; }, abstract = {In this study, which aimed to evaluate wastewater treatment and provide data to support improved wastewater treatment plant (WWTP) design, operation and ongoing monitoring strategies, mixed liquor, return activated sludge, primary effluent and secondary effluents of two WWTPs (n = 15) and five of the industries they service (n = 15) in Emfuleni municipality, Gauteng Province, South Africa, were characterised following a 5-month monitoring study. Following physical and chemical analysis, the parameters, including the Chemical Oxygen Demand (COD), were higher than local limits (75 mg/L) for both WWTPs and extremely high for the abattoir industry (13400 mg/L). In particular, high ammonia levels were recorded in both WWTPs. Following Illumina high-throughput sequencing and analysis using the Whole Metagenome Sequencing Assembly-based (WGSA2) pipeline on the Nephele platform, Bacteria was the dominant domain in the WWTPs. The dominant phyla were Proteobacteria (87.7%), followed by Firmicutes (8.25%), Actinobacteria (2.71%) and Bacteroidetes (0.68%). Aeromonas (39.86%) was the most dominant genus, with Acinetobacter (9.29%), Pseudomonas (6.78%), Bacillus (5.99%), and Thauera following (4.78%). Total Suspended Solids (TSS), pH, Total Dissolved Solids (TDS), and DO have influenced the diversity and distribution of the microbiome. Krona charts elucidated the xenobiotics degradation and metabolism distribution potential of the microbiome of each sampled site. This study reiterates the need for constant monitoring of WWTPs due to the high pollution parameters recorded from the WWTP effluent. The metagenomic data generated in this study provides insight into the diversity and functionality of the microbiome present in WWTPs of different process configurations which can inform existing WWTP configurations and future designs.}, } @article {pmid41545588, year = {2026}, author = {Buddle, S and Brown, LK and Morfopoulou, S and Torres Montaguth, OE and Scoto, M and Herder, V and Dhawan, A and Brown, JR and Atkinson, L and Kopec, A and Davis, D and Storey, N and Campos, L and Sebire, N and Macpherson, H and Lee, J and Orton, R and Baranello, G and Asamaphan, P and Ilia, G and Karda, R and Belfield, H and , and Counsell, J and Waddington, SN and Thomson, EC and Muntoni, F and Breuer, J}, title = {Contaminating plasmid sequences and disrupted vector genomes in the liver following adeno-associated virus gene therapy.}, journal = {Nature medicine}, volume = {32}, number = {2}, pages = {472-480}, pmid = {41545588}, issn = {1546-170X}, mesh = {Humans ; *Dependovirus/genetics ; *Genetic Therapy/adverse effects ; *Genetic Vectors/genetics/adverse effects ; *Liver/virology/pathology ; *Plasmids/genetics ; *Genome, Viral/genetics ; *Muscular Atrophy, Spinal/therapy/genetics ; Gene Therapy Agents ; Recombinant Fusion Proteins ; }, abstract = {Adeno-associated viruses (AAVs) are common vectors in gene therapy but can frequently cause liver complications in patients. The mechanisms underlying AAV-related liver toxicity remain poorly understood, posing challenges for effective prevention and intervention. Here we conducted a case study of a child with spinal muscular atrophy type 1 experiencing substantial hepatitis after receiving onasemnogene abeparvovec, undertaking long- and short-read metagenomic sequencing of liver tissue. We identified manufacturing plasmid sequences with complex structures and recombination. Vector genomes had extensive disruption and concatemerization as well as numerous vector-human fusion junctions. We also identified human betaherpesvirus 6B in the liver. Further work and investigation of more patients is needed to establish whether the presence of manufacturing plasmid sequences or helper viruses contribute to the formation of these complex concatemeric DNA structures in the liver, and whether these are a factor in the development of liver toxicity after AAV gene therapy.}, } @article {pmid41545847, year = {2026}, author = {Xu, Z and Gao, L and Chen, Z and Tang, L and Wang, Y}, title = {Metagenomic next-generation sequencing for the diagnosis and evaluation of pediatric pleural effusion: a case series.}, journal = {BMC pulmonary medicine}, volume = {26}, number = {1}, pages = {69}, pmid = {41545847}, issn = {1471-2466}, support = {2023C03009//the "Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; }, abstract = {BACKGROUND: Pleural effusion is a common symptom in children with respiratory diseases, with infections being the leading cause. Currently, the use of metagenomic next-generation sequencing (mNGS) for pleural effusion has not been fully evaluated in pediatric lung disease patients. METHODS: Patients who had undergone mNGS for pleural effusion were included in the study. Patients were categorized into a clinically useful group and a not clinically useful group on the basis of their clinical data, laboratory results, and mNGS results. RESULTS: A total of 48 children were included in this study. The number of positive mNGS results was 32/48 (66.7%), which was greater than that of conventional tests (22/48 [45.8%]). The diagnostic concordance of mNGS for detecting bacterial infections was 62.5% (20/32) higher than that of conventional detection methods, which was 15.6% (5/32). However, the diagnostic concordance of mNGS in detecting mycoplasma infections (4/9 vs. 7/9) and tuberculosis infections (0/5 vs. 5/5) was lower than that of conventional detection methods. Compared with the not clinically useful group, the clinically useful group had a lower mean age (50.50 [IQR, 32.25, 102.50] vs. 98.00 [IQR, 60.00, 118.50] months, P = 0.019), a greater incidence of wheezing (n = 5/23 vs. n = 0/23, P = 0.018), a greater incidence of pulmonary consolidation (n = 15/23 vs. n = 8/23, P = 0.039), and a greater incidence of loculated pleural effusion (n = 5/23 vs. n = 0/23, P = 0.018). Additionally, the clinically useful group had a longer hospital stay (17.0 [IQR, 10.75, 25.0] vs. 12.0 [IQR, 6.75, 15.00] days, P = 0.011). Nevertheless, the rate of improvement after treatment was greater in the clinically useful group than in the not clinically useful group (100% vs. 73.9%, P = 0.009). CONCLUSION: mNGS has distinct diagnostic advantages, with more accurate bacterial identification in pediatric pleural effusion. Negative results may prompt exploration of non-infectious causes. However, pathogen-specific limitations should be considered.}, } @article {pmid41546385, year = {2026}, author = {Chang, H and Qin, X}, title = {Red Complex Bacteria as a Hidden Cause of Chronic Lung Abscess: A Case Report.}, journal = {The American journal of case reports}, volume = {27}, number = {}, pages = {e949102}, pmid = {41546385}, issn = {1941-5923}, mesh = {Humans ; *Lung Abscess/microbiology/diagnostic imaging/diagnosis/drug therapy ; Chronic Disease ; Male ; *Chronic Periodontitis/complications/microbiology ; Tomography, X-Ray Computed ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; Hemoptysis/etiology ; }, abstract = {BACKGROUND Common oral pathogens such as Treponema denticola, Porphyromonas gingivalis, and Tannerella forsythia, which form biofilms in the periodontal pockets, are classified together as Red Complex bacteria in Socransky's subgingival cluster model and are key pathogenic bacteria in periodontitis. Oral pathogens play a critical role in pulmonary infections, particularly in the pathogenesis of lung abscesses. Lung abscesses caused by Red Complex bacteria have rarely been described; to our knowledge, few cases have been reported to date. CASE REPORT We present the first documented case of chronic lung abscess caused by Red Complex bacteria, with recurrent hemoptysis as the main symptom. The patient had chronic periodontitis and uncontrolled diabetes, and exhibited an indolent clinical course with consistently negative bacterial cultures. Chest computed tomography (CT) demonstrated a thick-walled cavity with minimal liquefactive changes in the right upper lobe. Red Complex bacteria in the bronchoalveolar lavage fluid and the lung tissue were identified by metagenomics next-generation sequencing (mNGS). The patient underwent intravenous penicillin therapy. The hemoptysis resolved completely coupled with improvement in clinical status and inflammatory markers. The chest CT demonstrated near-complete resolution of the lung abscess during follow-up. CONCLUSIONS Red Complex bacteria are rare pathogens in patients with periodontitis who develop culture-negative chronic lung abscesses accompanied by recurrent hemoptysis. This case report highlights this rare etiology and reveals a critical diagnostic limitation, as routine cultures frequently fail to detect these fastidious organisms. The incorporation of mNGS into the diagnostic algorithm for such cases can facilitate a definitive diagnosis and guide precise antimicrobial therapy.}, } @article {pmid41546513, year = {2026}, author = {Yang, YY and Bueno de Mesquita, CP and Lawrence, CR and Weyman, PD and Dores, D and Timmermann, T and Fierer, N and Fuenzalida-Meriz, GA}, title = {Synergistic Effects of a Microbial Amendment and Crushed Basalt: Soil Geochemical and Microbial Responses.}, journal = {Global change biology}, volume = {32}, number = {1}, pages = {e70705}, pmid = {41546513}, issn = {1365-2486}, support = {//Andes Ag, Inc./ ; }, mesh = {*Soil Microbiology ; *Bacillus subtilis/physiology ; *Soil/chemistry ; Carbon Dioxide/metabolism ; *Silicates/chemistry ; Glycine max/growth & development ; }, abstract = {Over geologic timescales, the natural weathering of silicate minerals in soils and regolith regulates atmospheric CO2. Although this process is slow relative to anthropogenic emissions, several strategies have been proposed to accelerate this process for climate mitigation. These include the application of finely-ground silicate rock to increase mineral surface area (enhanced weathering, EW) and the use of microbes that catalyze mineral dissolution and CO2 biomineralization (microbial carbon dioxide mineralization, MCM). While both approaches show promise, their combined application has rarely been tested. Here, we examined how soil chemistry and bacterial communities respond to a basalt feedstock rich in silicate minerals, a Bacillus subtilis strain (MP1) previously shown to enhance weathering, and their combination. In a 91-day soybean mesocosm experiment with slightly acidic soil (pH 6.6), MP1 persisted where applied, indicating successful inoculation via seed treatment. Basalt amendments had the strongest effect on soil bacterial community composition, whereas inoculation with MP1 exerted a smaller but detectable influence. Biogeochemical indices of weathering indicated that co-application of basalt and MP1 enhanced carbonate alkalinity beyond basalt alone. Soil carbonate alkalinity increased with MP1 treatment both with and without basalt, while soil pH and cation exchange capacity (CEC) increased with basalt in both MP1 and non-MP1 treatments. Total carbon was highest in the combined MP1 + basalt treatment, suggesting that MP1 may mitigate short-term organic carbon losses associated with basalt-driven priming. Overall, these results provide new insights into interactions between biological and mineral-based carbon dioxide removal (CDR) strategies, suggesting that co-application of MP1 with basalt in slightly acidic soil may enhance carbonate alkalinity while reducing organic carbon losses relative to basalt alone. Thus, pairing B. subtilis MP1 with enhanced weathering deployments emerges as a promising strategy to improve CDR efficiency.}, } @article {pmid41546695, year = {2026}, author = {Zhang, T and Liu, H and Huang, Z and Fan, Y and Liu, F and Su, E and Ming, Y and Zhu, W and Wang, C and Yu, X and Niu, M and Wu, K and Sun, X and Yang, Y and He, Z and Yan, Q}, title = {Microbially Driven Organic Carbon Degradation and Nutrient Cycling during Macroalgal Decomposition.}, journal = {Environmental science & technology}, volume = {60}, number = {4}, pages = {3216-3229}, doi = {10.1021/acs.est.5c09758}, pmid = {41546695}, issn = {1520-5851}, mesh = {*Carbon/metabolism ; *Seaweed/metabolism ; Geologic Sediments ; Nutrients ; }, abstract = {The release of labile organic carbon (OC) and nutrients during seasonal macroalgal blooms can undermine blue carbon sequestration in coastal ecosystems. Although marine microorganisms mediate OC degradation during macroalgal decay, the underlying mechanisms remain poorly defined. This study employed an integrated multiomics approach (amplicon sequencing, metagenomics, and metatranscriptomics) to investigate microbial regulation of OC degradation and coupled nutrient cycling in coastal sediments with and without decomposing Sargassaceae. Total carbon in sediments increased by over 33% in the Sargassaceae area. Microbial α-diversity in the Sargassaceae area decreased significantly (p < 0.05), while processes linked to OC degradation, carbohydrate metabolism, nitrate (NO3[-]) reduction, inorganic phosphorus utilization, and sulfur metabolism were significantly upregulated (p < 0.05). Accordingly, gene expression and extracellular hydrolase activities targeting key biopolymers (i.e., cellulose, hemicellulose, starch, and chitin) were significantly upregulated (p < 0.05) in the area with Sargassaceae. Metabolism reconstruction of metagenome-assembled genomes identified Vibrio, Pseudoalteromonas, Alteromonas, and Exiguobacterium_A as primary OC degraders, with genomic capacities enriched in NO3[-] reduction and assimilatory sulfate reduction. Key environmental drivers─including the C/N ratio, dissolved organic carbon, total dissolved nitrogen (DON), and NO3[-]─shaped microbial metabolic activities during macroalgal decomposition. Our finding demonstrates that microbially driven OC degradation is a pivotal process coupled with nutrients cycling, advancing the mechanistic understanding of microbial carbon processing and its biogeochemical linkages during macroalgal decomposition in coastal ecosystems.}, } @article {pmid41546704, year = {2026}, author = {Ramadoss, R and Siddique, A and Rashid, N and Liberski, AR and Vincent, AS and Mackey, HR}, title = {Effects of nitrogen and phosphorous concentrations on PHA synthesis by PNSB enriched phototrophic mixed microbial culture.}, journal = {Bioprocess and biosystems engineering}, volume = {49}, number = {3}, pages = {621-636}, pmid = {41546704}, issn = {1615-7605}, support = {NPRP11-S-0110-180245//Qatar National Research Fund/ ; }, mesh = {*Nitrogen/pharmacology/metabolism ; *Phosphorus/pharmacology/metabolism ; *Polyhydroxyalkanoates/biosynthesis ; *Phototrophic Processes ; Wastewater/microbiology ; }, abstract = {Global economic burden due to plastic pollution is estimated to be over $3 trillion annually. Bioplastics derived from bacteria-synthesized biopolymers like polyhydroxyalkanoates (PHAs), are a remarkably versatile sustainable alternative. Research on optimal growth-conditions for microbial PHA-synthesis fed-on sustainable substrates, particularly by phototrophic-mixed-cultures (PMC) enriched with purple non-sulphur bacteria (PNSB) is essential. This study intends to understand the effect of nitrogen and phosphorus concentrations on PHA-production by PMC grown using fuel synthesis wastewater (FSW) (organic by-product of Fischer-Tropsch process) as substrate. Stoichiometric quantification and 16 S metagenomic sequencing followed by statistical and bioinformatic analysis were done. High PHA-production (65-82% of biomass) is observed to be induced by Low-Nitrogen conditions enriching Rhodopseudomonas, Paludibacter and Pleomorphomonas and a Low-Phosphorus condition enriching Rhodopseudomonas, Rhodoplanes and Lentimicrobium. Analysis of metabolic-potential revealed 16 enzymes (of 8 different PHA-synthesis-pathways) inherent within the genomes of bacteria enriched by these culture conditions. This study identifies optimal nitrogen and phosphorus concentrations and the corresponding microbial-composition of FSW substrate-grown PMC-system to maximize PHA-production in a laboratory-scale bioprocess.}, } @article {pmid41547150, year = {2026}, author = {Liu, J and Huang, X and Wang, Y and Wang, Y and Luo, R and Lu, X and Cao, K and Xing, J and Tu, Y and Zheng, W}, title = {Metagenomics insights into the effects of lactic acid bacteria inoculation on the microbial communities and antibiotic resistance genes in mare milk.}, journal = {International journal of food microbiology}, volume = {450}, number = {}, pages = {111622}, doi = {10.1016/j.ijfoodmicro.2026.111622}, pmid = {41547150}, issn = {1879-3460}, mesh = {Animals ; *Milk/microbiology ; Horses ; *Lactobacillales/genetics/physiology ; Metagenomics ; Fermentation ; Female ; *Microbiota ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/isolation & purification/classification ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging contaminants threatening public health, yet their transmission risk via mare milk products remains understudied. Using metagenomics, we analyzed lactic acid bacteria (LAB)-inoculated fermented, naturally fermented, raw, and pasteurized mare milk to investigate the effect of LAB inoculation on the distribution and transmission pathways of ARGs in mare milk. The results showed that naturally fermented, raw, and pasteurized mare milk had the highest number of pathogens, relative abundance of ARGs, and relative abundance of mobile genetic elements (MGEs), while LAB inoculation significantly reduced these (p < 0.05). Bacillota was the dominant microbial group in different samples. Compared to naturally fermented and raw mare milk, LAB-inoculated fermentation significantly altered microbial community structure (p < 0.05). This not only reduced or eliminated certain harmful bacteria but also decreased the abundance of total ARGs and multiple ARG subtypes by reducing host bacteria and MGEs. Microbes and MGEs jointly drove ARG transmission, with microbes being key. Transposon, Bacteroidota, and Pseudomonadota are the major MGEs and microbial taxa for ARG transmission. LAB inoculation can effectively inhibit the spread of 11 ARG types, including β-lactam and multidrug resistance, by weakening the co-occurrence network among microbes, ARGs, and MGEs. This study enhances understanding of resistance genes in diverse equine dairy products, elucidates the impact of LAB fermentation on ARG distribution and transmission pathways in mare milk, and provides valuable data references and theoretical guidance for safer equine dairy processing.}, } @article {pmid41547203, year = {2026}, author = {Zhi, C and Wang, D and He, B and Hou, G and Gao, M and Mu, H and Wei, R and Wu, X and Bai, J and Jiao, Y and Hu, X}, title = {Metabolic coupling of arsenic, carbon, nitrogen, sulfur and iron in high-salinity groundwater in the Yellow River Delta: Insights from metagenomic analyses.}, journal = {Water research}, volume = {292}, number = {}, pages = {125368}, doi = {10.1016/j.watres.2026.125368}, pmid = {41547203}, issn = {1879-2448}, mesh = {*Groundwater/chemistry ; Arsenic/metabolism ; Sulfur/metabolism ; Salinity ; Iron/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Metagenomics ; Rivers ; }, abstract = {Arsenic (As) mobilization in deltaic aquifers is regulated by tightly linked C-N-S-Fe-As biogeochemical processes, yet the influence of salinity on these interactions remains poorly resolved. Here, we investigated high-salinity groundwater from the Yellow River Delta, where total dissolved solids range from 1 to 35 g/L and As concentrations reach 303 μg/L. By integrating metagenomic sequencing, metagenome-assembled genomes (MAGs), and nitrogen and sulfur isotopic measurements, we characterized how salinity and redox gradients restructure microbial functional potential and regulate As cycling. Functional-gene profiles show a transition from nitrate- and Fe(III)-coupled metabolisms in low-salinity groundwater to sulfate- and sulfite-driven anaerobic pathways under high-salinity conditions, consistent with δ[15]N-NH4[+], δ[15]N-NO3[-], and δ[34]S-SO4[2-] signatures. Genome-resolved analyses further reveal that Pseudomonadota and Desulfobacterota dominate carbon oxidation, nitrogen and iron reduction, and sulfur-intermediate reduction, while Muiribacteriota and Planctomycetota specialize in sulfite reduction and anammox/Feammox, respectively. Together, these results show that microbial communities reorganize along the salinity gradient, with arsenic mobilization associated with nitrogen- and iron-coupled reductive processes in low-salinity groundwater and with sulfur-driven reduction under high-salinity conditions. By linking microbial metabolic interactions to salinity-related redox environments, this study provides a process-based basis for anticipating how arsenic mobility may change as coastal aquifers undergo salinization.}, } @article {pmid41547254, year = {2026}, author = {Li, C and Liu, Z and Zhao, N and Pan, H and Wang, H and Zhang, Y}, title = {Hidden oral-joint-lung axis: Porphyromonas gingivalis Infection promotes the EMyT of RA-ILD by inhibiting the JUN-regulated palmitoylation balance.}, journal = {International immunopharmacology}, volume = {172}, number = {}, pages = {116210}, doi = {10.1016/j.intimp.2026.116210}, pmid = {41547254}, issn = {1878-1705}, mesh = {Animals ; Humans ; *Porphyromonas gingivalis ; Lipoylation ; Mice ; *Bacteroidaceae Infections/complications/immunology/metabolism ; *Arthritis, Rheumatoid/complications/immunology/metabolism/microbiology/pathology ; Male ; Lung/pathology ; *Proto-Oncogene Proteins c-jun/metabolism ; Disease Models, Animal ; Mice, Inbred C57BL ; Epithelial-Mesenchymal Transition ; }, abstract = {BACKGROUND: Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a major cause of mortality among patients with rheumatoid arthritis (RA), yet the pathological mechanism linking joint and lung involvement remains poorly understood. The pathogenic role of Porphyromonas gingivalis (P.g) in RA has been established. This study investigated how P.g infection drives RA-ILD through palmitoylation-mediated epithelial-myofibroblast transition (EMyT), thereby uncovering a mechanistic basis for the oral-joint-lung connection.

METHODS: Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and 16S rRNA sequencing of fecal samples from patients with RA-ILD were analyzed to assess the association between P.g and RA-ILD. A collagen-induced arthritis (CIA) mouse model and human lung epithelial cell lines (A549 and BEAS-2B) infected with P.g were established. Palmitoylation dynamics, EMyT marker expression, and the function of the hub gene JUN were evaluated using immunopathology, qPCR, western blotting (WB), single-cell sequencing, and molecular docking. Mechanistic studies employed the JUN activator c2-ceramide, the JUN inhibitor pterostilbene, and the palmitoylation inhibitor 2-BP to determine how P.g regulates palmitoylation in promoting RA-ILD.

RESULTS: Both mNGS and 16S rRNA analyses revealed a strong association between Porphyromonas spp. infection and RA/RA-ILD. P.g infection significantly increased EMyT marker expression (collagen I, fibronectin, and vimentin) in vitro and induced pulmonary fibrosis in CIA-ILD mice, with palmitoylation playing a central role. Mechanistically, JUN was identified as a key regulator of palmitoylation. P.g suppressed JUN level, activated ZDHHC3, and inhibited PPT1, leading to palmitoylation imbalance. Activation of JUN by c2-ceramide, combined with inhibition of palmitoylation by 2-BP, effectively suppressed EMyT progression in RA-ILD.

CONCLUSION: This study identifies a novel "oral-joint-lung axis" in which P.g infection promotes EMyT and fibrosis in RA-ILD by disrupting JUN-regulated palmitoylation homeostasis. Modulation of this axis provides a promising therapeutic strategy for RA-ILD.}, } @article {pmid41547817, year = {2026}, author = {Xiao, Y and Tang, Y and Yan, Y and Cheng, Q and Chen, X and Wang, L and Li, X}, title = {Targeted next-generation sequencing has comparable clinical value to metagenomic NGS for pulmonary infections in hematological malignancy patients: a real-world propensity score-matched study.}, journal = {European journal of medical research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40001-026-03893-0}, pmid = {41547817}, issn = {2047-783X}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is widely recognized in immunocompromised populations due to its unbiased ability to identify pathogens, while targeted next-generation sequencing (tNGS) combines PCR amplification with high-throughput sequencing technology, with advantages of lower costs and shorter turnaround times. However, it remains unclear whether tNGS can be applied in the same way as mNGS for immunodeficient patients with hematologic malignances (HM).

METHODS: This retrospective study analyzed clinical data from 245 HM patients suspected of pneumonia between April 2019 and April 2024. Bronchoalveolar lavage fluid (BALF) samples were tested using either tNGS or mNGS. Propensity score matching (PSM) (1:1) balanced the groups.

RESULTS: tNGS and mNGS showed comparable sensitivity, specificity, and accuracy for pathogen detection (97.3% vs 94.2%, 26.3% vs 26.1%, 82.6% vs 77.2%; all P > 0.05), with similar accuracy across immunodeficiency states (severe immunodeficiency: 80.0% vs 81.8%; non-severe immunodeficiency: 64.7% vs 86.7%; both P > 0.05). For non-severe pneumonia, tNGS was comparable to mNGS (accuracy: 77.9% vs 86.3%, P > 0.05), but mNGS was significantly superior in severe cases (accuracy: 50.0% vs 100.0%, P = 0.002). Both groups improved rate of correct antibiotic use (tNGS: 50.9% to 84.3%; mNGS: 57.1% to 77.8%, P < 0.01) and reduced overuse rates (tNGS: 25.9% to 2.8%; mNGS: 4.8% to 25.4%; P < 0.01), with no difference in chemotherapy intervals (37.5 ± 22.9 days vs 41.0 ± 38.4 days; P = 0.89).

CONCLUSION: In HM patients suspected of pulmonary infection, BALF-tNGS showed comparable diagnostic efficacy as BALF-mNGS, with similar clinical value across varying immunodeficiency states. tNGS is a viable alternative for non-severe pneumonia, while mNGS is superior in severe cases. Collectively, the findings of this study highlight tNGS as an alternative diagnostic approach for HM patients.}, } @article {pmid41547860, year = {2026}, author = {Castillo-Fernandez, J and Gilroy, R and Jones, RB and Honaker, RW and Whittle, MJ and Watson, P and Amos, GCA}, title = {Waltham catalogue for the canine gut microbiome: a complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {25}, pmid = {41547860}, issn = {2049-2618}, mesh = {Animals ; Dogs/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; Sequence Analysis, DNA/methods ; Metagenome ; Phylogeny ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The canine microbiome is a vastly understudied area relative to the importance of dogs in society, particularly given the potential importance of the microbiome in veterinary medicine. This has led to a large knowledge gap in the basic taxonomy and functions of the canine gut microbiome and an overreliance on human databases for canine-specific research. Using a broad sample set, long read sequencing, short read sequencing, and metagenomic assembly approaches, we have produced the most comprehensive microbiome resource in all companion animal research.

RESULTS: Here, we describe the recovery of 240 core species that account for > 80% of the canine gut microbiome when tested on an independent validation dataset. We uncovered > 900 new canine-specific strains, 89 novel species, and 10 novel genera, providing a dramatic increase in previous knowledge of the canine microbiome and allowing for mapping rates of up to 95%, a 70% increase on historic mapping rates of ~ 25% using publicly available resources. Through detailed annotation of function, we demonstrate the potential importance of the novel species and genera to health and nutrition and provide evidence of new canine-adapted strains of existing genera and species previously unknown to inhabit canines that provide important metabolic function to the canine host. We discovered the canine microbiome has an expansive ability to metabolize carbohydrates, providing insight into how canines process diverse carbohydrates given their known limited host genomic potential. We uncovered a range of species with abilities to produce butyrate, propionate, and vitamins, highlighting the importance of the canine microbiome to host nutrition. We describe two novel Peptacetobacter species that could regulate host bile acid metabolism, an important finding in the context of chronic GI disease in pets. We demonstrated all new species and genera had no known virulence, suggesting they are commensal and, finally, provided a baseline for antimicrobial resistance in the microbiota species of healthy pets.

CONCLUSIONS: This work gives entirely new perspectives on the functional capabilities of the canine gut microbiome, suggesting the canine microbiome is distinct, presumably having evolved to its host, diet, and environment over several millennia. Video Abstract.}, } @article {pmid41547908, year = {2026}, author = {Kim, YC and Won, SY and Jeong, BH}, title = {Identification of an altered gut microbiome and the protective effect of microbiome changer in prion diseases.}, journal = {Veterinary research}, volume = {57}, number = {1}, pages = {31}, pmid = {41547908}, issn = {1297-9716}, support = {2022R1C1C2004792//National Research Foundation of Korea/ ; RS-2023-00273199//National Research Foundation of Korea/ ; 2017R1A6A1A03015876//National Research Foundation of Korea/ ; B0080529001944//Gyeongbuk RISE CENTER/ ; 2021R1A6C101C369//Korea Basic Science Institute/ ; }, mesh = {Animals ; *Prion Diseases/microbiology/drug therapy/prevention & control ; *Catechin/analogs & derivatives/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; }, abstract = {Prion diseases are fatal and contagious brain disorders caused by a pathogenic prion protein (PrP[Sc]) derived from the benign prion protein (PrP[C]). To date, there are no therapeutic substances to completely block prion diseases. Thus, the development of a therapeutic substance is necessary, and the identification of a novel biomarker of prion disease is the first essential step to develop new drugs. In the present study, we carried out a metagenomic analysis to identify microbiome biomarkers for prion disease using next-generation sequencing and bioinformatics tools in intraperitoneally prion-infected mice. In addition, we evaluated the protective effects of epigallocatechin-3-gallate (EGCG), a potent microbiome changer, in prion-infected mice by western blotting and survival analysis. We found a total of 14 differentially abundant taxa between prion-infected and control mice. In addition, we found that prion diseases caused altered microbiome networks and upregulation of DNA repair-related pathways. Furthermore, we observed the protective effect of the microbiome changer EGCG against prion disease in prion-infected mice. Given previous reports of microbiome alterations in prion diseases, we further validated these associations and demonstrated the protective effects of a microbiome-modulating compound.}, } @article {pmid41548304, year = {2026}, author = {Mao, C and Zhao, A and Chen, Z and Ge, F and Tang, T and Qiao, Z and Wu, Z and Zhang, Y and Liu, G and Wang, H and Li, Q and Li, T}, title = {Spatiotemporal transmission mechanisms of resistance genes in the Chishui River: Perspectives from environmental drivers and microbial interactions.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141134}, doi = {10.1016/j.jhazmat.2026.141134}, pmid = {41548304}, issn = {1873-3336}, mesh = {*Rivers/microbiology ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; *Water Microbiology ; Microbiota/genetics ; Bacteria/genetics ; }, abstract = {The accelerating spread of antimicrobial resistance in natural ecosystems, driven principally by the dissemination of antibiotic resistance genes (ARGs), represents an escalating challenge for both environmental integrity and public health security. Aquatic systems contaminated with ARGs alongside associated virulence factors (VFs) and metal resistance elements (MRGs) have emerged as critical reservoirs of resistance propagation. This study employed metagenomic approaches to analyze microbial communities and functional diversity in the Chishui River, which spans three distinct regions under significant anthropogenic influence. The results revealed that microbial communities exhibit distinct spatiotemporal variations predominantly governed by temperature, DO, TP, and TN. In addition, variations in land use types across different regions also directly shaped microbial diversity patterns, subsequently exerting direct and indirect effects on mobile genetic elements (MGEs), ARGs, and VFs, ultimately leading to the enrichment and dissemination of high-risk resistance genes. Both microbial communities and ARGs exhibited short-distance migration patterns. Notably, a synergistic covariation pattern was observed between antibiotic resistance genes (ARGs) and dissimilatory nitrate reduction to ammonium (DNRA) functional genes, indicating a potential ecological linkage between these two genetic traits. A total of 138 metagenome-assembled genomes have been identified as potential vectors for ARG dissemination. We further revealed a novel synergistic link between ARG abundance and the DNRA process, and the class Gammaproteobacteria was identified as the primary vector of resistance dissemination, functioning as dominant co-hosts for ARGs, MRGs, VFs, and DNRA genes in the Chishui River. These findings offer new insights into river ecosystems, underscoring the importance of monitoring the fate of ARGs to enhance our understanding of how river ecosystems respond to human activities.}, } @article {pmid41548597, year = {2026}, author = {Zhao, M and Yu, X and Zhao, M and Zhang, G}, title = {Structured framework for the application of metagenomic next-generation sequencing in the whole-process management of lower respiratory tract infections.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {32}, number = {2}, pages = {102910}, doi = {10.1016/j.jiac.2026.102910}, pmid = {41548597}, issn = {1437-7780}, mesh = {Humans ; Female ; *Respiratory Tract Infections/diagnosis/microbiology/drug therapy ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Male ; *Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use ; Middle Aged ; Adult ; Aged ; China ; }, abstract = {OBJECTIVES: This study aims to assess the impact of metagenomic next-generation sequencing (mNGS) on optimizing diagnostic-therapeutic pathways for lower respiratory tract infections (LRTIs).

METHODS: This retrospective observational study analyzed 42 consecutive LRTI patients at Jiading Branch of Shanghai General Hospital (June 2023-October 2024). Comprehensive clinical data were evaluated including demographic features, laboratory result, radiological findings, mNGS interpretation, treatment modifications, and outcomes.

RESULTS: The mNGS detected pathogens in 37/42 patients (88.1 %), despite the fact that 38 patients (90.5 %) had received ineffective empirical antibiotic therapy prior to mNGS testing. More than half the patients (22/42, 52.4 %) had comorbidities and about half the cases were within the normal range in the level of inflammatory biomarker. Pathognomonic CT features suggesting specific pathogens were observed in 33.3 % (14/42) of cases. With regard to the interpretation of mNGS reports combaining the clinical characteristics, the results were consistent with the final diagnosis in 30 (30/42, 71.4 %) patients. Crucially, 92.9 % (39/42) underwent treatment modifications: 66.7 % (28/42) transitioned to targeted/narrower-spectrum antibiotics and 26.2 % (11/42) discontinued antimicrobial therapy following infection exclusion. Patients receiving targeted regimens demonstrated universal clinical improvement with radiological resolution, particularly in complex infections.

CONCLUSION: While mNGS provides robust pathogen detection, its clinical application requires integration with multidimensional patient data. The standardized protocol proposed in this study has the potential to enhances diagnostic efficiency and resource utilization in LRTI management.}, } @article {pmid41548675, year = {2026}, author = {Li, D and Wang, Y and Qiang, H and Liu, Z and He, Z and Liu, W and Yue, X and Zhou, A}, title = {Tailoring microbial communities for medium chain fatty acid production from waste activated sludge: Comparative performance of endogenous vs. exogenous consortia.}, journal = {Bioresource technology}, volume = {444}, number = {}, pages = {134038}, doi = {10.1016/j.biortech.2026.134038}, pmid = {41548675}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Fatty Acids/biosynthesis ; Bacteria/metabolism ; *Microbial Consortia/physiology ; Bioreactors/microbiology ; Caproates/metabolism ; Carbon Dioxide/metabolism ; }, abstract = {Optimizing medium chain fatty acid (MCFA) production from waste activated sludge (WAS) requires tailoring microbial communities, yet it remains unclear whether combining substrate sterilization with exogenous caproate-synthesizing bacteria (CSB) can enhance chain elongation. Here, we compared the MCFA production achieved using this strategy with that driven by the endogenous microbiomes in both the solid residue and the supernatant. Among all experimental groups, this strategy achieved the highest MCFA production in the supernatants (3935 ± 21 mg COD/L). This strategy increased CSB abundance in both the solid residue and the supernatant relative to the abundance in the endogenous microbiome systems. Notably, in supernatant systems, this strategy not only enriched acidogens but also led to the highest soluble protein utilization rate, maximal CO2 release/uptake, and an increased gene abundance related to pyruvate generation. Life cycle assessment confirmed economic and environmental benefits. This work provides new insights into optimizing MCFA recovery from WAS.}, } @article {pmid41549250, year = {2026}, author = {Ye, L and Cao, L and Du, Q and Xu, R and Han, Y and Liu, J}, title = {Fecal metagenome and plasma metabolome analyses reveal changes in gut microbiota composition and plasma metabolites in rats with abemaciclib-induced diarrhea.}, journal = {BMC gastroenterology}, volume = {26}, number = {1}, pages = {}, pmid = {41549250}, issn = {1471-230X}, support = {No:2023MW35//This work was supported by the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16) and Minhang District Health Commission of Shanghai Municipality(No:2023MW35)./ ; mwyjyx16//the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16)/ ; }, abstract = {Abemaciclib-induced diarrhea is a common side effect of HR+/ HER2 − breast cancer treatment. The aim of this study was to explore changes in gut microbiota composition and plasma metabolites in rats with abemaciclib-induced diarrhea. Female rats were randomly divided into abemaciclib (orally administered abemaciclib, n = 12) and control (orally administered 0.9% saline, n = 6) groups. When the rats reached grade 3 diarrhea, the jejunum, ileum, and colon tissues were collected for histological analysis to assess intestinal mucosal damage. Rat feces were obtained for metagenomic analysis to analyze changes in the gut microbial composition. Rat plasma was used for untargeted metabolomic analysis to analyze plasma metabolic alterations. Pearson’s correlation analysis was conducted to examine the association between differential gut microbiota and differential plasma metabolites, and a microbiota-metabolite-pathway network was constructed. Rats in the abemaciclib group developed noticeable diarrhea and exhibited histopathological changes in the ileal epithelium and jejunum. In the abemaciclib group, α-diversity indices (Shannon, Simpson, and Invsimpsom) were significantly lower than in the control group, with reductions of 0.5, 0.01, and 52.77, respectively. Firmicutes, Bacteroidetes, and Proteobacteria were the most abundant phyla in all groups. Compared with the control group, the abundance of Firmicutes remarkably decreased in the abemaciclib group, whereas that of Proteobacteria and Verrucomicrobia dramatically increased. Differentially abundant species in the abemaciclib group included Escherichia coli, Butyricimonas virosa, Desulfovibrionaceae bacterium, and Helicobacter ganmani. Functional analysis showed that pathways related to carbohydrate metabolism were significantly altered. Additionally, 319 metabolites were differentially expressed between the two groups, including trimethylamine N-oxide, sarsasapogenin, tyrosol, brinzolamide, and cis-3-hexenyl acetate. Multiple pathways, including mTOR signaling pathway, were significantly enriched by differential metabolites. Furthermore, close associations between differential microbiota and metabolites were observed, and numerousmicrobiota-metabolite-pathway axes were identified, such as Pseudodesulfovibrio mercurii/Desulfovibrionaceae bacterium-cis-3-hexenyl acetate-alpha-linolenic acid metabolism. Our findings revealed that abemaciclib alters the gut microbiota composition, plasma metabolite profiles, and their related metabolic pathways in SD rats, and these changes are closely associated with the occurrence of diarrhea. However, this association does not establish a causal relationship, and further in-depth mechanistic studies are required for validation.}, } @article {pmid41549294, year = {2026}, author = {Noronha, JM and Hudson, SB and Sharma, G and Ghadi, SC}, title = {Metagenomic Insights into Viral Diversity from an Underexplored Khazan Creek and a Tropical Freshwater Lake.}, journal = {Current microbiology}, volume = {83}, number = {2}, pages = {139}, pmid = {41549294}, issn = {1432-0991}, mesh = {*Lakes/virology ; *Viruses/classification/genetics/isolation & purification ; Genome, Viral ; *Virome ; Metagenomics ; India ; *Biodiversity ; Ecosystem ; Phylogeny ; Fresh Water/virology ; }, abstract = {The virus communities of inland aquatic ecosystems have typically received less attention from the research perspective than those of marine ecosystems. In this study, we compared the viromes of an estuarine creek (Santana Creek) belonging to the khazan ecosystem and an agriculturally relevant freshwater lake (Verna Lake), both located in Goa, India. Taxonomically, the viral realm Duplodnaviria predominated in both the lake and creek communities, Varidnaviria had a minor presence in both, and Monodnaviria was exclusively present in the lake community. Sequences identified in the creek virome bore a greater resemblance to those of marine ecosystems than those in the lake virome. Functional annotation confirmed the taxonomic findings, indicating most proteins were involved in the infective and replicative functions of bacteriophages. Predicted complete viral genomes included those of Synechococcus and Proteus phages in the creek dataset, and of Gokushovirinae phages in the lake dataset. Viral communities of the khazan ecosystem and similar ecosystems worldwide are understudied, and hence the present virome analysis offers a valuable reference for further studies on these ecosystems.}, } @article {pmid41549319, year = {2026}, author = {Sun, Y and Guo, K and Tang, J and Zhao, J and Zhang, X and Yan, Y and Yuan, L and Zhang, Y and Qiu, C and Luo, J and Chen, J and Fang, H}, title = {The impact of the timing of mNGS-guided antibiotic adjustment on clinical outcomes in ICU patients with severe community-acquired pneumonia: a retrospective study.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {25}, number = {1}, pages = {12}, pmid = {41549319}, issn = {1476-0711}, support = {No. 2023KY1296//Zhejiang Provincial Department of Health/ ; No. 2022K71//the Quzhou Bureau of Science and Technology/ ; }, mesh = {Humans ; Retrospective Studies ; *Community-Acquired Pneumonia/drug therapy/microbiology/mortality ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; Intensive Care Units ; Female ; Male ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Treatment Outcome ; *Metagenomics/methods ; *Community-Acquired Infections/drug therapy/microbiology ; }, abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) remains a major cause of intensive care unit (ICU) admission and mortality. Prompt pathogen identification and timely administration of appropriate antimicrobial therapy are essential for improving patient outcomes. Although metagenomic next-generation sequencing (mNGS) enables rapid pathogen detection, the prognostic impact of the timing of mNGS-guided antibiotic adjustment remains unclear.

METHODS: We conducted a multicenter retrospective study of ICU patients diagnosed with SCAP who underwent both bronchoalveolar lavage fluid (BALF) mNGS and conventional microbiological tests (CMTs). Patients were categorized into early (≤ 72 h) and late (> 72 h) antibiotic adjustment groups based on the interval from ICU admission to the time of antibiotic adjustment guided by mNGS results. Subgroup analyses were performed according to immune status.

RESULTS: In our study, mNGS significantly outperformed conventional microbiological tests (CMTs) in pathogen detection (92.70% vs. 57.18%, P < 0.001), with a particularly higher yield for mixed infections (51.63% vs. 19.14%, P < 0.001). Early mNGS-guided antibiotic adjustment was associated with a significantly reduced 28-day mortality compared to late adjustment (41.98% vs. 53.76%, P = 0.037). Furthermore, multivariate logistic regression analysis confirmed early adjustment as an independent protective factor for 28-day mortality (adjusted OR = 0.44, 95% CI: 0.23-0.83, P = 0.011). In the immunocompromised subgroup, early mNGS-guided adjustment was associated with significantly lower 28-day mortality than late adjustment (39.29% vs. 60.00%, P = 0.029), with a significant interaction observed between timing and immune status (P = 0.042).

CONCLUSION: Early mNGS-guided antibiotic adjustment is associated with improved survival among ICU patients with SCAP. This benefit is more pronounced in immunocompromised patients, underscoring the importance of early mNGS application to guide antimicrobial decision-making in this vulnerable population.}, } @article {pmid41550372, year = {2025}, author = {Tenea, GN and Jarrin-V, P and Lin, L}, title = {Editorial: Trigger the microbiome changes in foods via metagenomic technologies: from diagnostic to potential changes in product safety or quality risk profiles.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {13}, number = {}, pages = {1766291}, doi = {10.3389/fbioe.2025.1766291}, pmid = {41550372}, issn = {2296-4185}, } @article {pmid41550607, year = {2025}, author = {Zhang, W and Zhang, L and Liu, H}, title = {Correction: Necrotizing enterocolitis in a neonate with severe congenital pulmonary valve stenosis complicated by a postoperative right atrial thrombus: a case report.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1760028}, doi = {10.3389/fped.2025.1760028}, pmid = {41550607}, issn = {2296-2360}, abstract = {[This corrects the article DOI: 10.3389/fped.2025.1594899.].}, } @article {pmid41551013, year = {2025}, author = {Wang, C and Chang, K and Chen, M and Zou, X and Ni, Y and Zhang, Q and Zhao, L and Xing, B and Guo, L and Chen, W and Cao, B}, title = {Enrichment of the commensal microbiome in the lower respiratory tract is associated with improved outcomes following lung transplantation.}, journal = {Chinese medical journal pulmonary and critical care medicine}, volume = {3}, number = {4}, pages = {308-318}, pmid = {41551013}, issn = {2772-5588}, abstract = {BACKGROUND: Alterations in the respiratory microbiome are common following lung transplantation; however, the complex relationship between microbial composition and posttransplant clinical outcomes remains insufficiently characterized. This study aimed to delineate microbial signatures within the lower respiratory tract and to elucidate their associations with posttransplant outcomes in lung transplant recipients (LTRs).

METHODS: Metagenomic sequencing was performed on 138 bronchoalveolar lavage fluid (BALF) samples collected in 2023 from patients who had undergone lung transplantation between 2017 and 2023 at the China-Japan Friendship Hospital. Lung function indices, hematologic parameters, and serum cytokine levels were assessed, and patients were prospectively followed to record adverse clinical events.

RESULTS: The lung microbiome of stable LTRs formed four distinct clusters, exhibiting marked heterogeneity in both α- and β-diversity. The most prevalent cluster, enriched with oral-origin commensals, such as Neisseria subflava (N. subflava), Prevotella melaninogenica, and Streptococcus mitis (S. mitis), demonstrated the highest microbial diversity, and was associated with the lowest C-reactive protein levels, fewest adverse events, and the longest complication-free postoperative duration. In contrast, a virus-enriched cluster characterized by reduced diversity and high abundance of Torque teno virus and Cytomegalovirus human betaherpesvirus 5 was associated with poorer outcomes. BALF samples from infected LTRs exhibited more severe dysbiosis than those from immunocompetent individuals, with reduced diversity and pathogen dominance. Concurrent infections aggravated antibody-mediated rejection-related lung function decline, indicating complex microbiome-immune interactions. Integrative modeling of microbiome, hematologic, and pulmonary function data yielded superior diagnostic performance for infection detection (area under the receiver operating characteristic curve = 0.93).

CONCLUSION: The composition of the lung microbiome may serve as a prognostic biomarker for clinical outcomes after lung transplantation. The presence of diverse, commensal-dominated communities was associated with improved outcomes, whereas viral enrichment correlated with adverse events. These findings underscore the clinical importance of microbiome monitoring in posttransplant management and suggest that targeted modulation of microbial communities could improve long-term graft stability and patient prognosis.}, } @article {pmid41551170, year = {2026}, author = {Chang, CC and Pak, J and Bae, S and Kim, GD and Son, HS}, title = {Impact of low aging temperature on the microbial and metabolic dynamics of rice wine during long-term storage.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101294}, pmid = {41551170}, issn = {2665-9271}, abstract = {This study investigated the effects of aging temperature and microbial inoculation on the physicochemical, microbiological, and metabolic properties of Korean rice wine (makgeolli) during long-term storage. Samples were aged at three different temperatures (4 °C, -1 °C, and -5 °C) for 180 days and were inoculated with Lactiplantibacillus plantarum or Saccharomyces cerevisiae to examine their respective influences on metabolite shifts during cold storage. Microbial communities were analyzed using amplicon (16S rRNA) and shotgun metagenomic sequencing, and metabolite profiles were determined by GC-MS to provide an integrative understanding of microbial and metabolic stability during long-term cold storage. Lower aging temperatures reduced fluctuations in metabolic and microbial activities, particularly among LAB, thereby contributing to a more stable physicochemical profile and extended shelf life. During rice wine aging, LAB exerted a more pronounced effect on metabolite dynamics than yeast, particularly for pyruvate, γ-aminobutyric acid, and lactic acid, underscoring their role in the aging process. Additionally, sub-zero aging temperatures preserved the initial microbial composition, limited enzymatic degradation, and stabilized organic acid profiles, reflecting enhanced chemical stability of the product during aging. While such chemical stability may have implications for sensory outcomes, this remains a hypothesis that requires direct sensory evaluation in future studies. Overall, the findings suggest that controlled storage temperatures and targeted microbial inoculation can improve the chemical and microbiological stability of rice wine during long-term storage.}, } @article {pmid41551178, year = {2026}, author = {Esposito, A and Valentino, V and Tagliamonte, S and Sequino, G and Vitaglione, P and Ercolini, D and De Filippis, F}, title = {Development of a synbiotic dietary supplement containing potential Next Generation Probiotics for modulation of the gut microbiome and metabolome.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101289}, pmid = {41551178}, issn = {2665-9271}, abstract = {The term Next Generation Probiotics (NGPs) refers to microbial strains positively impacting on human health, but do not belong to common probiotic species (e.g., lactic acid bacteria, LAB). We characterized genomically and phenotypically 14 strains isolated from the gut microbiome of healthy individuals, to evaluate their ability to produce urolithins, equol and short-chain fatty acids (SCFA). The 4 most promising strains (namely Bacteroides uniformis A4, Bacteroides thetaiotaomicron A14, unclassified Bacteroidaceae A26 and unclassified Lachnospiraceae A49) were used for the production of a synbiotic formulation, containing the strains and the precursors of health-promoting molecules. This dietary supplement was administered for 2 weeks to a continuous mucosal-Simulator of the Human Intestinal Microbial Ecosystem (mSHIME) model inoculated with a faecal sample from a low fiber-consuming donor. We performed Shotgun Metagenome Sequencing on a total of 204 samples collected from lumen and mucosa compartments, and determined the concentration of SCFA, equol and urolithin. Our results highlighted that the potential NGP strains contained in the supplement persisted in the gut ecosystem during 2 weeks of washout (Wilcoxon's rank sum test, p-value <0.05). In addition, the treatment led to an enrichment in beneficial taxa and to an increase in the production of SCFAs (p-value <0.05). This study demonstrated that feeding the gut microbiota with NGPs and dietary prebiotics can modulate both the gut microbiome and metabolome, suggesting a potential beneficial impact on human health. However, further in vivo studies are needed to confirm these results.}, } @article {pmid41551289, year = {2025}, author = {Zhang, J and Thomas Backet, RV and Sekela, JJ and Zeller, MJ and Sellers, RS and Redinbo, MR and Gulati, AS and Bhatt, AP}, title = {Commercially Purchased and In-House Bred C57BL/6 Mice with Different Gut Microbiota Exhibit Distinct Indomethacin-Induced Toxicities.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {}, pmid = {41551289}, issn = {2993-3935}, support = {R01 GM135218/GM/NIGMS NIH HHS/United States ; R35 GM155168/GM/NIGMS NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R01 DK122042/DK/NIDDK NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; R35 GM152079/GM/NIGMS NIH HHS/United States ; }, abstract = {Non-steroidal anti-inflammatory drug (NSAID)-induced toxicities are a significant clinical problem, yet the factors influencing these outcomes remain incompletely understood. Here, we investigated the impact of mouse vendor on indomethacin-induced injury using C57BL/6 mice from different breeding facilities (in-house "Tar Heel" and commercial Charles River). We found that Tar Heel mice exhibited significantly enhanced susceptibility to indomethacin toxicity, characterized by greater body weight loss, increased ileal ulceration, elevated fecal lipocalin-2 levels, and higher goblet cell numbers in ileum compared to Charles River mice. Importantly, whole genome metagenomic analysis revealed distinct baseline gut microbiomes between the two types of mice. Notably, Tar Heel mice showed higher abundances of β-glucuronidase (GUS)-producing bacteria, particularly those expressing Loop-1 GUS enzymes, and elevated levels of mucolytic enzyme-encoding bacteria. These differences suggest that enhanced indomethacin toxicity observed in Tar Heel mice may be related to functional changes in their gut microbiome, which may predispose to an exaggerated response to NSAID exposure. Together, our findings demonstrate that vendor-specific differences significantly influence NSAID-induced intestinal toxicity and highlight the importance of considering mouse sources and gut microbial compositions in experimental design. Moreover, we highlight potential functional roles that gut microbes play in host-indomethacin interactions.}, } @article {pmid41551358, year = {2026}, author = {Wu, X and Yin, Y and Guo, Y and Sun, L and Shi, Q and Ji, T and Wang, H}, title = {A case of atypical cat scratch disease with bone and joint infection diagnosed through clinical metagenomics.}, journal = {IDCases}, volume = {43}, number = {}, pages = {e02482}, pmid = {41551358}, issn = {2214-2509}, abstract = {Cat scratch disease (CSD) is a common zoonotic infection caused by Bartonella henselae (B. henselae) and typically presents with fever and regional lymphadenopathy. However, skeletal involvement, including osteomyelitis and arthritis, is rare. We report a 28-year-old immunocompetent female who presented with a five‑month history of persistent right knee swelling without fever or lymphadenopathy. She had previously undergone distal femoral tumor resection with prosthetic joint replacement, and this episode of chronic knee swelling together with the imaging findings was highly suggestive of prosthetic joint infection. Approximately one month before the onset of knee swelling, she had sustained a scratch from a cat. Conventional microbiological tests, including joint effusion and drainage fluid cultures, were negative. Metagenomic next‑generation sequencing (mNGS) of joint effusion identified B. henselae with 27 specific sequence reads, 0.1 % genome coverage and an RPM ratio of 1.9. This result was subsequently confirmed by a quantitative PCR assay targeting the nuoG gene. The patient underwent surgical debridement followed by oral minocycline and rifampin for 8 weeks, resulting in marked clinical improvement. This case underscores that B. henselae infection should be considered in culture‑negative bone and joint, particularly prosthetic joint, infections with a history of cat exposure, and that mNGS can provide valuable etiological evidence in atypical CSD.}, } @article {pmid41551460, year = {2026}, author = {Cornman, RS and Hepner, MJ and Otto, CRV}, title = {The Appalbees menu: a multiyear, multilocus metagenetic assessment of pollen foraging by Appalachian Bombus affinis workers.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20284}, pmid = {41551460}, issn = {2167-8359}, mesh = {Animals ; Bees/physiology ; *Pollen/genetics/classification ; Virginia ; West Virginia ; DNA Barcoding, Taxonomic ; Appalachian Region ; *Feeding Behavior ; Metagenomics ; Pollination ; }, abstract = {BACKGROUND: Detailed studies of foraging behavior are needed for scientific management of the endangered rusty-patched bumblebee (Bombus affinis) in the disjunct and ecologically differentiated habitats it presently occupies. Current knowledge gaps hinder recovery planning but are challenging to redress through direct observation of rare interactions in the field.

METHODS: We used genetic metabarcoding to characterize the taxonomic composition of pollen collected by B. affinis workers in the Appalachian mountains of Virginia and West Virginia from 2021-2023. We developed a custom sequence database of the regional flora and compared results for two independent genetic loci, internal transcribed spacer 1 and internal transcribed spacer 2 (ITS1 and ITS2).

RESULTS: While ITS2 consistently detected more plant diversity, results from the two loci were broadly concordant with a few notable exceptions. The plant genera Hydrangea, Actaea, Rhododendron, Tilia, and (unexpectedly) Laportea were prominent in midsummer samples, with Rubus a consistent contributor in late spring and early summer. Pea flowers (family Fabaceae) were relatively infrequent but the genera Securigera and Trifolium were detected before the Hydrangea bloom and again in late summer afterwards. The diversity of forage plants was highest in late summer, driven primarily by various genera of Asteraceae. Comparing the current data with previous work indicates regional differentiation in forage plants between Appalachia and the upper Midwest, but also allows 'consensus' forage sources that are supported by multiple lines of evidence and shared between regions to be tabulated. These results should help managers focus survey efforts for this endangered species and plan habitat enhancements.}, } @article {pmid41551517, year = {2025}, author = {Wang, Y and Zhang, X}, title = {Rapid diagnosis of Lemierre's syndrome by metagenomic next-generation sequencing: a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1730031}, pmid = {41551517}, issn = {2296-858X}, abstract = {Lemierre's syndrome, also known as postopharyngeal septicaemia or necrobacillosis, is a rare, fatal opportunistic infection, often caused by Fusobacterium necrophorum invading the throat. Bacterial culture is a conventional method to establish a diagnosis, but is time-consuming and insensitive in some cases. Metagenomic next-generation sequencing (mNGS), as an emerging technique, has become an important supplementary detection method for infectious diseases. It greatly favors the rapid, precise diagnosis and treatment of Lemierre's syndrome through accurately obtaining etiological information. We reported a case of Lemierre's syndrome that was rapidly and accurately diagnosed by mNGS.}, } @article {pmid41551583, year = {2026}, author = {Chen, T and Huang, R and Huang, Y and Wang, J and Wang, Z and Zhang, X}, title = {Shared signatures of alcohol-associated dysbiosis in humans and non-human primates.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100534}, pmid = {41551583}, issn = {2666-5174}, abstract = {Alcohol use disorder (AUD) is a chronic brain disease with limited therapeutic options. Increasing evidence suggests that the gut microbiome contributes to AUD via the microbiome-gut-brain axis. Here, we conducted a cross-species investigation of gut microbiota alterations in patients with clinically diagnosed AUD and in non-human primates (NHPs) subjected to long-term alcohol (ethanol) self-administration, using metagenomic sequencing. Both cohorts showed reduced microbial diversity and conserved dysbiosis, with consistent depletion of Verrucomicrobia, Actinobacteria, Faecalibacterium, Akkermansia, Intestinibacter, Phascolarctobacterium, and Ruminococcus, alongside increased Blautia and Coprococcus. These microbial shifts correlated with liver function indices, notably positive associations between Ruminococcus and bilirubin levels in both species, suggesting a potential role in liver injury. Functional analyses revealed conserved microbial adaptations, including upregulated DNA repair pathways, fermentative energy metabolism, and downregulated glutamate/glutamine biosynthesis. Together, these results identify evolutionarily conserved microbial and metabolic alterations linking alcohol consumption, gut dysbiosis, and hepatic dysfunction. Our cross-species evidence highlights the gut microbiome as a potential biomarker and therapeutic target for AUD.}, } @article {pmid41551588, year = {2026}, author = {Arnold, CB and Kelder, A and Woltemate, S and Geffers, R and von Felde, A and Knudsen, KEB and Visscher, C and Vital, M}, title = {Uncovering differences in rye and wheat degradation by human gut microbiota applying a quantitative multi-metaOmics in vitro approach.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100532}, pmid = {41551588}, issn = {2666-5174}, abstract = {While wheat is the most common grain used in bread-making worldwide, rye is popular in many European countries too. Rye is associated with several health benefits, which is attributed to its comparatively higher dietary fiber content (primarily fructans and arabinoxylans) that promote production of short chain fatty acids (SCFA) by gut microbiota, in particular butyrate. Intervention studies revealed bacterial alterations upon rye administration, however, the detailed mechanisms involved in its degradation are not understood. We grew fecal communities (n = 20) on pre-digested rye and wheat, respectively, demonstrating that rye was yielding higher cell and SCFA concentrations in almost all samples along with distinct abundances of many taxa. A multi metaOmics (metagenomics/metatranscriptomics) approach (n = 5 donors) showed higher bacterial growth rates for most taxa on rye compared to wheat. The higher growth rate of rye was accompanied by increased expression of genes involved in growth and energy generation suggesting higher carbon substrate accessibility. The carbohydrate active enzyme repertoire was greatly distinct between communities growing on the two substrates with several specific glycoside hydrolases increasingly expressed in rye containing cultures. Agathobacter faecis was revealed as the key butyrogenic species for rye degradation and its expression pattern based on metagenome assembled genomes showed adaptation to growth on rye via expression of genes involved in arabinoxylan degradation and fructose (major monomer of fructans) uptake. Our study verifies higher SCFA production from rye over wheat and gives detailed insights into molecular mechanisms involved. It suggests that the observed health benefits of rye are mediated by gut microbiota.}, } @article {pmid41551788, year = {2026}, author = {Song, Q and Li, J and Liu, Y and Li, W and Li, M and Zhang, B and Guo, B}, title = {Metagenomics and volatile metabolomics reveal microbial succession and its correlations with fruity flavor volatile compounds during Mianhua industrial processing.}, journal = {Food chemistry: X}, volume = {33}, number = {}, pages = {103446}, pmid = {41551788}, issn = {2590-1575}, abstract = {Mianhua, a traditional fermentation-type staple food popular in northern China, undergoes dynamic microbial and volatile compound changes during industrial processing. 848 volatile compounds were identified using volatile metabolomics dominated by esters (18.51 %), notably hexanoic acid ethyl ester and octanoic acid ethyl ester, which confer fruity flavors. Metagenomics analysis revealed Proteus (25.93 %), Fructilactobacillus (16.63 %), Lactobacillus (10.16 %) and Companilactobacillus (7.14 %) as dominant genera. Mixing with traditional starters was critical for flavor development, driven by microbial succession and synergistic interactions between Lactobacillaceae (e.g., Fructilactobacillus sanfranciscensis and Lactobacillus helveticus) and Kazachstania during fermentation. Notably, F. sanfranciscensis and L. helveticus were significantly correlated with the formation of key esters with fruity characteristics, elucidating their roles in substrate conversion via carbohydrate metabolism and the esterification pathways. This study clarifies the microbial contributions to fruity flavor and provides insights into volatile-microbiota correlations, laying a foundation for future flavor-oriented research and industrial applications of microbiota regulation in Mianhua production.}, } @article {pmid41551812, year = {2026}, author = {Zhang, T and Xing, M and Zhang, H and Song, X and Song, Z and Yuan, C and Zhang, J and Zhang, Z and Xie, F and Ai, L}, title = {Docynia delavayi polyphenols enhance short-chain fatty acid synthesis via the chlorogenic acid-caffeic acid-protocatechuic acid pathway: insights from in vitro digestion-fermentation.}, journal = {Food chemistry: X}, volume = {33}, number = {}, pages = {103416}, pmid = {41551812}, issn = {2590-1575}, abstract = {Docynia delavayi fruit polyphenols (DDP) demonstrate potential for enhancing short-chain fatty acid (SCFA) synthesis; however, underlying mechanisms remain poorly understood. This study utilized an in vitro digestion-fermentation model combined with multi-omics analyses to explore these mechanisms. The in vitro model revealed notable alterations in both 1,1'-diphenyl-2-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical-scavenging capacities, as well as in total phenolic and flavonoid content, accompanied by increased production of acetic, propionic, and butyric acids. Metagenomic indicated that DDP stimulated Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Bifidobacterium longum, and Bifidobacterium bifidum growth. Metabolomics demonstrated enrichment of SCFA-associated metabolic pathways, including propanoate and butyrate metabolism, and identified caffeic acid and protocatechuic acid as primary bioactive metabolites produced from DDP. Multi-omics analysis suggested that DDP modulated gut microbiota by enriching the chlorogenic acid-caffeic acid-protocatechuic acid metabolic pathway (r > 0.95, p < 0.01), ultimately boosting SCFA biosynthesis. This study offers new insights into the mechanisms by which polyphenols regulate health.}, } @article {pmid41551931, year = {2026}, author = {Mak, L and Tierney, B and Wei, W and Ronkowski, C and Toscan, RB and Turhan, B and Toomey, M and Andrade-Martínez, JS and Fu, C and Lucaci, AG and Solano, AHB and Setubal, JC and Henriksen, JR and Zimmerman, S and Kopbayeva, M and Noyvert, A and Iwan, Z and Kar, S and Nakazawa, N and Meleshko, D and Horyslavets, D and Kantsypa, V and Frolova, A and Kahles, A and Danko, D and Elhaik, E and Labaj, P and Mangul, S and , and Mason, CE and Hajirasouliha, I}, title = {CAMP: a modular metagenomics analysis system for integrated multistep data exploration.}, journal = {NAR genomics and bioinformatics}, volume = {8}, number = {1}, pages = {lqaf172}, pmid = {41551931}, issn = {2631-9268}, support = {R01 AI151059/AI/NIAID NIH HHS/United States ; R35 GM138152/GM/NIGMS NIH HHS/United States ; T32 GM083937/GM/NIGMS NIH HHS/United States ; U54 AG089334/AG/NIA NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; *Software ; *Computational Biology/methods ; Workflow ; }, abstract = {Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click bioinformatics pipelines can help organize these tools into workflows, they face compatibility and maintainability challenges that can prevent replication. To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed the Core Analysis Modular Pipeline (CAMP), a module-based metagenomics analysis system written in Snakemake, with a standardized module and directory architecture. Each module can run independently or in sequence to produce target data formats (e.g. short-read preprocessing alone or followed by de novo assembly), and provides output summary statistics reports and Jupyter notebook-based visualizations. We applied CAMP to a set of 10 metagenomics samples, demonstrating how a modular analysis system with built-in data visualization facilitates rich seamless communication between outputs from different analytical purposes. The CAMP ecosystem (module template and analysis modules) can be found at https://github.com/Meta-CAMP.}, } @article {pmid41552431, year = {2026}, author = {Buonaccorsi, A and McMullen, BN and Builder, B and Drummond, K and Halteman, S and See, JC and Thomas, E and Viands, A and Worley, S and Wright, JR and Keeney, J and Lamendella, R}, title = {Metagenomic surveillance of tick-borne pathogens and microbiomes in Huntingdon County, Pennsylvania.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101305}, pmid = {41552431}, issn = {2352-7714}, abstract = {The rise in tick populations across the United States has contributed to a surge in tick-borne diseases, with Pennsylvania ranking among the highest in reported cases. To better understand local pathogen prevalence and microbial community structure, an integrative study of ticks collected from ten recreational trails in Huntingdon County, Pennsylvania during the summer of 2023 was conducted. A total of 96 ticks were sampled, with 33 PCR-positive specimens selected for shotgun metagenomic sequencing. Pathogen screening via qPCR detected Borreliella burgdorferi, Borrelia miyamotoi, Babesia spp., and Anaplasma phagocytophilum. Shotgun metagenomics revealed a broader diversity of tick-borne pathogens, including Rickettsia and Ehrlichia spp., and demonstrated increased sensitivity by detecting low-abundance pathogens in samples that were PCR-negative. Co-infections were common, and multivariate statistical analysis identified significant associations between environmental variables (e.g., humidity, time of day, land cover) and microbial diversity and predicted gene function. Notably, diversity was higher in ticks collected during early afternoon and from northern sites. Co-occurrence network analysis showed Rickettsia as a central taxon with multiple significant positive associations with other microbes while other pathogens were largely absent or peripheral. These findings underscore the enhanced resolution of metagenomic approaches for pathogen detection and the value of combining molecular surveillance with ecological metadata. Our study provides critical insights into local tick microbiomes and pathogen prevalence, which may inform public health interventions and vector management strategies in central Pennsylvania.}, } @article {pmid41552860, year = {2026}, author = {Wang, F and Xiong, W and Huang, X and Li, S and Zhan, A}, title = {Residual eDNA in eRNA Extracts Skews eRNA-Based Biodiversity Assessment: Call for Optimised DNase Treatment.}, journal = {Molecular ecology resources}, volume = {26}, number = {2}, pages = {e70102}, pmid = {41552860}, issn = {1755-0998}, support = {2025ZD1207600//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2025ZD1200800//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2024ZY0128//Guiding Funds of Central Government for Supporting the Development of Local Science and Technology/ ; 32471608//National Natural Science Foundation of China/ ; }, mesh = {*Biodiversity ; Deoxyribonucleases/metabolism ; Animals ; Extrachromosomal DNA ; *DNA, Environmental/isolation & purification/genetics ; *Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; Fishes/classification/genetics ; Rivers ; }, abstract = {Environmental RNA (eRNA) metabarcoding has rapidly emerged as a powerful tool for assessing contemporary biodiversity patterns across diverse ecosystems. However, the potential for false positive detections caused by co-extracted environmental DNA (eDNA) remains unquantified. Distinguishing true signals from false positives caused by residual eDNA is a technical challenge in eRNA-based metabarcoding. To address this issue, we employed a freshwater river receiving treated effluent from a wastewater treatment plant as a model system. In such settings, eDNA in the treated effluent can lead to the detection of non-local species (e.g., marine taxa). Treated effluent typically contains minimal or no eRNA, making it well-suited for evaluating the influence of eDNA carryover. By comparing DNase-treated and untreated eRNA samples, we assessed the impact of residual eDNA on fish species richness and community composition. Our results showed that omitting DNase treatment significantly inflated taxonomic richness, with untreated samples detecting a conservative estimate of over 25% more taxa per site. Fold-change analysis revealed that residual eDNA inflated taxon abundances in both high- and low-abundance taxa, with some showing over 10-fold increases. Community composition analyses revealed clear clustering between treated and untreated samples, highlighting substantial shifts driven by residual eDNA. These findings demonstrate that co-extracted eDNA can severely distort eRNA-based biodiversity estimates, leading to false positives and misrepresented contemporary community profiles. We recommend further evaluation of DNase treatment parameters, including enzyme concentration, incubation time and treatment times, and the adoption of optimised protocols to standardise and improve the accuracy of eRNA-based biodiversity monitoring.}, } @article {pmid41552936, year = {2026}, author = {Lu, Y and Chang, L and Liu, S and Wang, M and Zhao, Y}, title = {Rutin alleviates dietary advanced glycation end products (AGEs)-induced insulin resistance in mice by modulation of gut microbiota.}, journal = {Food & function}, volume = {17}, number = {3}, pages = {1451-1464}, doi = {10.1039/d5fo04604a}, pmid = {41552936}, issn = {2042-650X}, mesh = {Animals ; Male ; Mice ; *Insulin Resistance ; *Dietary Advanced Glycation End Products/adverse effects ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Rutin/pharmacology ; *Glycation End Products, Advanced/adverse effects ; Bacteria/classification/genetics/isolation & purification ; Fatty Acids, Volatile/metabolism ; }, abstract = {Dietary advanced glycation end products (AGEs), formed during thermal food processing, are associated with metabolic disorders. This study investigated the efficacy of rutin in alleviating AGEs-induced insulin resistance (IR) in a mouse model. Male C57BL/6 mice were fed a high-AGEs diet for 12 weeks to induce IR, followed by 8 weeks of rutin intervention (100 mg per kg body weight per day). Rutin supplementation markedly ameliorated IR, as indicated by reduced hyperglycemia and dyslipidemia, a reduced homeostasis model assessment of insulin resistance (HOMA-IR) index, an elevated insulin sensitivity (HOMA-IS) index, and upregulation of insulin receptor substrates IRS-1 and IRS-2. Metagenomic analysis demonstrated that rutin intervention restored gut microbial richness and diversity and induced structural shifts in the microbiota composition. Specifically, rutin enriched beneficial genera, including Akkermansia, Bifidobacterium, Faecalibacterium, Lactobacillus, and Coriobacteriales, while reducing populations of IR-associated taxa such as Erysipelotrichaceae, Coprobacillus, Enterococcus, Adlercreutzia, and Allobaculum. Concurrently, rutin increased fecal concentrations of short-chain fatty acids (SCFAs), notably acetic acid and propionic acid. Spearman's correlation analysis confirmed negative associations between rutin-modulated microbiota and IR indicators. These results demonstrate that rutin mitigates AGEs-induced IR by reshaping the gut microbiome and promoting beneficial microbial metabolites.}, } @article {pmid41552949, year = {2026}, author = {Dani, M and Beszteri, S and Castellanos, AB and Schimani, K and Skibbe, O and Zimmermann, J and Soares, AR and Griesdorn, L and Probst, AJ and Kahlert, M and Beszteri, B}, title = {Species delimitation within the Achnanthidium minutissimum complex (Bacillariophyta), based on morphological, molecular, and ecophysiological approaches.}, journal = {Journal of phycology}, volume = {62}, number = {1}, pages = {25-43}, pmid = {41552949}, issn = {1529-8817}, support = {CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; ZI 1628/2-1//Deutsche Forschungsgemeinschaft/ ; Dnr. 18/171//Swedish EPA, Swedish Agency for Marine and Water Management/ ; }, mesh = {*Diatoms/classification/genetics/physiology ; Phylogeny ; Germany ; Sweden ; Algal Proteins/genetics ; DNA, Algal/analysis/genetics ; Sequence Analysis, DNA ; Species Specificity ; Ribulose-Bisphosphate Carboxylase/genetics ; }, abstract = {The benthic diatom species Achnanthidium minutissimum belongs to a species complex with a challenging taxonomy. Achnanthidium minutissimum has been reported to be a widespread and abundant species occurring in a broad range of freshwater habitats. However, differentiating and delimiting it from other Achnanthidium species is challenging due to the small size and great similarity of the different species, often with overlaps in morphological features. Therefore, reports of the occurrence of these taxa probably come with a large uncertainty due to potential misidentification. To gain a better understanding of the boundaries between species within the A. minutissimum species complex, we applied an integrative taxonomic approach and investigated the congruence between morphological, molecular, and ecophysiological variability among 13 monoclonal strains isolated from Germany, Sweden, and Spitsbergen. In addition to the characterization of valve morphology, we assessed their growth under different temperatures and salt concentrations and compared sequences of the rbcL marker gene as well as of a broad set of homologous loci sampled by genome skimming. Molecular and ecophysiological variability was mostly congruent with scanning electron microscopy-based morphological identification; the main exception was that two pairs of strains identified as A. cf. microcephalum and A. jackii could be distinguished neither in their ecophysiological profiles nor in their DNA sequences. Extending this integrated taxonomic approach to more strains will be beneficial for a better understanding of the morphological, molecular, and niche differentiation among different Achnanthidium species. The added value of the combined morphological-molecular-ecophysiological approach is an improved delineation of morphological features applicable for species differentiation and a better understanding of ecological differentiation.}, } @article {pmid41554738, year = {2026}, author = {Zheng, J and Zhang, C and Xiang, S and Li, M and Wang, H and Shi, K and Tondrob, D and Han, Y}, title = {Integrated metabolomics and metagenomics uncover pathogenic mechanisms of Fusarium wilt and faba bean defense responses.}, journal = {NPJ science of food}, volume = {10}, number = {1}, pages = {25}, pmid = {41554738}, issn = {2396-8370}, support = {31901929//National Natural Science Foundation of China/ ; cstc2021jcyj-msxmX1021//Natural Science Foundation of Chongqing Municipality/ ; }, abstract = {Fusarium wilt diseases pose a huge threat to faba bean (Vicia faba L.) production globally, with significant outbreaks in Chongqing, China. Symptomatic plants showed wilting leaves and rotten roots, ultimately perishing in the advanced stage. Morphological features, multilocus phylogenetic analyses, and pathogenicity tests demonstrated that the primary causal agent was Fusarium oxysporum. Untargeted metabolomics of faba beans revealed substantial metabolic differences in the infected faba bean roots. Plants responded to fungal biotic stress by reprogramming key metabolic pathways, including alanine, aspartate, and glutamate metabolism, the citrate cycle, arginine biosynthesis, and jasmonic acid metabolism, which collectively underscore activated defense responses. Metagenome sequencing showed that Fusarium wilt significantly reshaped the structure of the rhizosphere microbiota and affected the abundance of genes encoding element cycling in soil. This work elucidates the pathogenic mechanisms of F. oxysporum by integrating pathogen identification, host metabolism, and microbiome ecology. Our findings offer biomarkers for disease diagnosis and targets for biocontrol, advancing sustainable management of Fusarium wilt diseases in legumes.}, } @article {pmid41554846, year = {2026}, author = {Sumithra, TG and Sharma, SRK and Gayathri, S and Gop, AP and Shravana, KS and Jagannivasan, A and Nair, AV and Sudarsan, KS and Santhosh, B and Ebeneezar, S and Gopalakrishnan, A}, title = {Egg disinfection improves larval survival and shapes the microbial community in snubnose pompano (Trachinotus blochii).}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {5761}, pmid = {41554846}, issn = {2045-2322}, support = {BT/AAQ/3/SP28267/2018//Department of Biotechnology, Government of India/ ; }, mesh = {Animals ; *Larva/microbiology/drug effects ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; *Ovum/microbiology/drug effects ; *Fishes/microbiology ; *Disinfection/methods ; Disinfectants/pharmacology ; Bacteria/genetics/drug effects/classification ; }, abstract = {Early microbial colonization is crucial for immunity and survival in aquatic animals. This study evaluated the impact of egg disinfection on microbial colonization and larval performance in Trachinotus blochii, a high-value mariculture fish. Optimal egg disinfection protocols were initially identified as 20 ppm iodophor for 10 min, 400 ppm H2O2 for 10 min, and 40 ppm glutaraldehyde for 5 min to improve hatchability. Sequential analyses included 16S rRNA amplicon sequencing of larval microbiota at 10-days post hatching (DPH) and assessment of survival and antioxidant status till 25 DPH. Disinfection significantly enhanced hatchability (up to 90.88 ± 2% with 40 ppm glutaraldehyde), larval survival (up to 34.80 ± 1.1% in glutaraldehyde and 31.18 ± 1.5% in H2O2), and catalase activity. Notably, egg disinfection reshaped the larval microbiota, enriching microbial diversity measures and beneficial bacterial taxa, such as Hyphomonadaceae, Halieaceae, Nannocystaceae, and Alteromonadaceae. Improved survival correlated with enhanced taxonomic and functional metagenomic diversity, lower Proteobacteria: Bacteroidota ratio and higher combined proportions of Fusobacteriota, Firmicutes, and Bacteroidota relative to Proteobacteria. The findings suggest that egg disinfection acts as a microbiota programming strategy to promote larval health, offering a practical approach to enhance sustainability in T. blochii aquaculture.}, } @article {pmid41555276, year = {2026}, author = {Zhang, J and Feng, S and Liu, Z and Xie, K and Gu, C and Shen, J and Zhang, Y and Zhou, Y}, title = {Surgical treatment of Emphysematous Osteomyelitis of the spine in malnutrition and anemia patient: a rare case report.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {82}, pmid = {41555276}, issn = {1471-2334}, abstract = {BACKGROUND: Emphysematous Osteomyelitis is a rare and potentially fatal form of severe osteomyelitis. It is characterized by gas produced by pathogenic bacteria accumulating in bone structures and surrounding soft tissues. Its rarity and severe nature pose significant challenges for diagnosis and treatment. This case report describes the diagnosis and treatment of Emphysematous Osteomyelitis of the spine in a patient with long-term malnutrition and anemia. CASE PRESENTATION: A 72-year-old agricultural worker presented with persistent low back pain accompanied by radiating pain in both lower limbs for one month. The patient reported continuous dull pain that worsened with postural changes and improved when lying flat. Based on clinical presentation, biochemical indicators, and imaging studies, spinal infection was initially suspected. Empirical antimicrobial therapy administered for two weeks after admission proved ineffective and was complicated by an epidural abscess, leading to the decision for surgical intervention in the third week. Intraoperative tissue samples were identified through culture identification and high-throughput culture and metagenomic pathogen detection, identifying Citrobacter koseri and Staphylococcus aureus as causative pathogens. Postoperatively, based on antimicrobial susceptibility testing results, treatment was switched to intravenous meropenem and levofloxacin. One month postoperatively, the patient showed good recovery with normalized infection markers, no fever, and significant pain relief. DISCUSSION AND CONCLUSION: In summary, this rare and severe form of Emphysematous Osteomyelitis requires prompt diagnosis and treatment in clinical practice. The diagnosis of Emphysematous Osteomyelitis of the spine relies on imaging studies. Failure to achieve accurate and timely diagnosis may lead to misdiagnosis or delayed treatment, which not only compromises therapeutic efficacy but may also result in catastrophic consequences. Timely antibiotic therapy, early detection, and aggressive surgical intervention when necessary are key to the successful management of Emphysematous Osteomyelitis of the spine.}, } @article {pmid41555453, year = {2026}, author = {Orr, RJS and Brynildsrud, O and Bøifot, KO and Gohli, J and Skogan, G and Kelly, FJ and Hernandez, MT and Udekwu, K and Lee, PKH and Mason, CE and Dybwad, M}, title = {Spatial and temporal patterns of public transit aerobiomes.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {64}, pmid = {41555453}, issn = {2049-2618}, mesh = {*Bacteria/classification/genetics/isolation & purification ; *Air Microbiology ; *Fungi/classification/genetics/isolation & purification ; *Microbiota ; Shotgun Sequencing ; Metagenomics/methods ; Cities ; Humans ; Aerosols/analysis ; Biodiversity ; Seasons ; Spatio-Temporal Analysis ; }, abstract = {BACKGROUND: Aerobiome diversity is extensive; however, species-level community structure remains poorly resolved. Likewise, microbiomes of public transit systems are of public interest due to their importance for health, though few studies have focused on these ecosystems whilst utilising shotgun metagenomics. Aerosol studies have focused predominantly on individual cities, with limited between-city comparisons suggesting specific community structures. Longitudinal studies show aerobiome diversity as dynamic, fluctuating during seasonal and daily cycles, though interannual cycles remains to be considered. Further, a bacterial bias has limited fungal aerobiome studies, with few considering both fractions collectively. As such, the objective of this study was to examine spatial and temporal patterns in the species diversity of public transit aerobiomes, with an emphasis on bacteria and fungi.

RESULTS: Air samples taken over a 3-year period (2017-2019) from six global cities were subjected to shotgun metagenomic sequencing. Improved classification databases, notably for fungi, applying stringent parameters for trimming, exogenous contamination removal and classification yielded high species-level resolution. Microbial diversity varied substantially among cities, while human and environmental factors, recorded in parallel, were of secondary significance. Bacteria dominated the public transit aerobiome with increased presence in cities with higher population densities. All aerobiomes had complex compositions, consisting of hundreds to thousands of species. Interannual variation had limited significance on the public transit aerobiome diversity and community structure.

CONCLUSIONS: Cities were the most important factor contributing to diversity and community structure, demonstrating specific bacterial and fungal signatures. Further, possible correlation between geographical distance and genetic signatures of aerobiomes is suggested. Bacteria are the most abundant constituent of public transit aerobiomes, though no single species is globally dominant, conversely indicating a large inter-city variation in community structure. The presence of a ubiquitous global species core is rejected, though an aerobiome sub-core is confirmed. For the first time, local public transit aerobiome cores are presented for each city and related to ecological niches. Further, the importance of a robust bioinformatics analysis pipeline to identify and remove exogenous contaminants for studying low-biomass samples is highlighted. Lastly, a core and sub-core definition of contaminant aerobiome species with taxon tables, to facilitate future environmental studies, is presented. Video Abstract.}, } @article {pmid41556085, year = {2026}, author = {Chen, J and Ling, D and Wang, F and Liu, L and Ren, Y and Chen, C and Su, N}, title = {Septic Shock Caused by Coinfection of Shewanella algae Bloodstream Infection and Epstein-Barr Virus: Clinical Characteristics and Genomic Analysis.}, journal = {MicrobiologyOpen}, volume = {15}, number = {1}, pages = {e70221}, pmid = {41556085}, issn = {2045-8827}, support = {2023170//Chengdu Medical Research Project/ ; Q22080//Youth Innovation Project of Sichuan Medical Association/ ; 2024001//Youth Innovation Medical Research Project of Chongzhou People's Hospital/ ; }, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; *Bacteremia/microbiology/complications ; China ; *Coinfection/diagnosis/microbiology/virology ; *Epstein-Barr Virus Infections/complications/virology/diagnosis ; Genome, Bacterial ; Genomics ; *Gram-Negative Bacterial Infections/microbiology/complications/diagnosis ; *Herpesvirus 4, Human/isolation & purification/genetics ; Microbial Sensitivity Tests ; Phylogeny ; *Shewanella/genetics/isolation & purification/classification/pathogenicity ; *Shock, Septic/microbiology/diagnosis/virology ; Virulence Factors/genetics ; }, abstract = {Shewanella algae, a marine-origin opportunistic pathogen, has shown a significant increase in non-coastal infections, yet its environmental adaptability and synergistic pathogenic mechanisms with Epstein-Barr virus (EBV) coinfection remain unclear. This study reports a clinical case of S. algae bloodstream infection complicated by EBV reactivation leading to septic shock in Sichuan Province, China, and elucidates the molecular mechanisms through genomic analysis. Pathogen identification was performed via blood culture, antibiotic susceptibility testing, and genomic annotation. The strain harbored resistance genes (acrB, tolC, tet(35), golS) and virulence factors (bplL/bplF, clpC/clpP, tonB). Phylogenetic analysis indicated the highest genetic affinity to freshwater-derived Shewanella chilikensis, while pan-genome analysis identified 1412 unique genes, including transmembrane transporters and carbohydrate-active enzyme genes, suggesting freshwater adaptive evolution. Metagenomic next-generation sequencing (mNGS) detected a high EBV load. The patient succumbed to multi-organ failure. This study reveals that S. algae may evolve freshwater adaptability to cause inland infections, and EBV coinfection accelerates septic shock through immunosuppression and inflammatory cascades. Genomic analysis provides critical insights for precision diagnosis and treatment of polymicrobial infections.}, } @article {pmid41556347, year = {2026}, author = {}, title = {Correction to: HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.}, journal = {Nucleic acids research}, volume = {54}, number = {2}, pages = {}, doi = {10.1093/nar/gkag014}, pmid = {41556347}, issn = {1362-4962}, } @article {pmid41556498, year = {2026}, author = {Becsei, Á and Munk, P and Fuschi, A and Otani, S and Stéger, J and Visontai, D and Papp, K and Brinch, C and Kant, R and Weinstein, I and Vapalahti, O and de Graaf, M and Schapendonk, CME and Roelfsema, J and van den Beld, M and Pijnacker, R and Franz, E and Alba, P and Battisti, A and De Cesare, A and Indio, V and Troja, F and Sironen, T and Oliveri, C and Pasquali, F and Liachko, I and Auch, B and O'Cathail, C and Bányai, K and Makó, M and Pollner, P and Koopmans, M and Csabai, I and Remondini, D and Aarestrup, FM}, title = {A comprehensive database for biological data derived from sewage in five European cities.}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, pmid = {41556498}, issn = {1758-0463}, support = {NNF16OC0021856//Novo Nordisk Foundation/ ; NNF24SA0094147//Novo Nordisk Foundation/ ; 874735//Horizon 2020/ ; INV-044643/GATES/Gates Foundation/United States ; NKKP-153428//National Research, Development and Innovation Office of Hungary/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office of Hungary/ ; }, mesh = {Cities ; *Databases, Genetic ; Europe ; *Metagenome ; *Metagenomics ; *Sewage/microbiology ; Datasets as Topic ; }, abstract = {Sewage metagenomics is a powerful tool for proactive pathogen surveillance and understanding microbial community dynamics. To support such efforts, we present a highly curated and accessible longitudinal dataset of 239 sewage samples collected from five European cities. The dataset, processed through metagenomic sequencing, includes rich analytical outputs such as taxonomic profiles, identified antimicrobial resistance genes, assembled contigs with annotated origins, metagenome-assembled genomes with functional gene annotations, and metadata. Given the computational intensity and time required to reproduce such analyses, we share this dataset to promote reuse and advance research. In addition to the metagenomic data, qPCR was used to identify specific pathogens, and Hi-C sequencing was performed on a subset of the samples to strengthen genomic linkage analysis. Central to this resource is a publicly available PostgreSQL database, designed to facilitate efficient exploration and reuse of the data. This comprehensive database allows users to perform targeted queries, subset data, and streamline access to this extensive resource.}, } @article {pmid41556507, year = {2026}, author = {Cheng, S and Tang, X and Huang, X and Li, Y and Huang, S and He, D and Moreno-Jiménez, E and Xu, J and Rillig, MC and Dai, Z and Delgado-Baquerizo, M}, title = {Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies.}, journal = {Global change biology}, volume = {32}, number = {1}, pages = {e70704}, doi = {10.1111/gcb.70704}, pmid = {41556507}, issn = {1365-2486}, support = {41721001//National Natural Science Foundation of China/ ; 2019YFC1803704//National Key Research and Development Program of China/ ; +226-2024-00029//The Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Soil Microbiology ; *Stress, Physiological ; *Microbiota ; *Metagenome ; Biodiversity ; Metagenomics ; Bacteria/genetics/classification ; }, abstract = {Soil microorganisms constitute the largest portion of Earth's biodiversity. However, soil microorganisms are also highly sensitive to on-going global change, and the influence of an increasing number of stressors on common, rare, and unknown taxa across large environmental gradients remains virtually unknown. Here, we combined a large-scale spatial field survey across multiple different ecosystems and found that the diversity and abundance of soil rare taxa were significantly reduced under high environmental stressor number (i.e., a high number of stressors passing a 75% stressor threshold). Strikingly, the abundance of unknown soil taxa and unknown genes increased with increasing environmental stress number. We further identified the metagenome-assembled genomes (MAGs) that were considered as relatively common taxa using metagenomics. Compared to 9% of negative responders, 32% of common MAGs were resistant or positively responsive to multiple stress, displaying a reduced potential for cellular processes and an enhanced potential for environmental, genetic, and metabolic processes. Our study suggests that as stress increases, we would have less rare, but more unknown microorganisms and unique genomes of resistant common taxa, suggesting major changes in the soil microbiome in a world subjected to multiple global change stressors.}, } @article {pmid41556662, year = {2026}, author = {Zhang, N and Atoni, E and Nyaruaba, R and Kibaba, P and Shadrack, K and Wang, F and Agwanda, B and Zheng, Z and Dai, J and Yuan, Z and Xia, H}, title = {Host and geography shape microbial communities in Kenyan mosquitoes: insights from metatranscriptomics.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0142725}, pmid = {41556662}, issn = {2379-5077}, support = {2022YFC2302700, 2023YFC2305900//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Kenya ; *Microbiota/genetics ; Virome ; Bacteria/genetics/classification/isolation & purification ; *Culex/microbiology/virology/genetics ; *Aedes/microbiology/virology/genetics ; Phylogeny ; Transcriptome ; Metagenomics ; Geography ; }, abstract = {Mosquitoes harbor diverse microbial communities that influence their potential to transmit pathogens. However, the ecological drivers shaping these microbiomes, particularly in under-sampled regions like Africa, remain poorly resolved. We conducted a large-scale metatranscriptomic survey of 3,940 Aedes and Culex mosquitoes from diverse ecological zones across Kenya. Our analyses revealed that viruses dominated the overall transcriptome, while bacteria exhibited the greatest taxonomic richness. Geographic location emerged as the primary driver of microbial community structure, whereas host genus identity shaped virome diversity at local or city-level scales. Culex mosquitoes harbored higher viral richness, particularly in coastal regions, while Aedes supported more diverse bacterial assemblages. Microbial co-occurrence networks exhibited distinct topologies across hosts: Culex networks featured cross-domain interactions and viral keystone taxa, whereas Aedes networks were more cohesive and robust, centered on bacterial hubs. We identified 102 distinct viruses from 24 families, including 31 putative novel RNA viruses. Segment-resolved phylogenies revealed cryptic clades within Bunyavirales, Picornavirales, and other lineages. Collectively, our findings highlight the scale-dependent influences of geography and host identity on mosquito microbiomes in East Africa and demonstrate the utility of metatranscriptomics in uncovering hidden microbial diversity and ecological interactions. These insights provide a foundation for ecologically informed arthropod vector surveillance and microbiome-based intervention strategies.IMPORTANCEMosquitoes are more than just flying syringes; they are complex ecosystems hosting a variety of microbes. Understanding what shapes this microbial world inside mosquitoes is key to developing new control strategies. Our study of nearly 4,000 mosquitoes from Kenya reveals that where a mosquito lives matters most for its overall microbial makeup, but its genus dictates which viruses it carries. We discovered that different mosquito types have distinct microbial social networks: one type has a fragile network centered on viruses, while the other has a resilient network built around bacteria. This means that strategies to disrupt disease transmission by targeting mosquito microbes may need to be tailored to a specific mosquito genus. Our work provides a map of these microbial ecosystems, highlighting potential new viruses and offering insights for future public health surveillance and interventions.}, } @article {pmid41556741, year = {2026}, author = {Cao, L and Wang, X and Zhou, Y and Qiu, J and Zeng, Q and Zhang, C and Pan, L}, title = {Diagnosis of Paralytic Rabies by Metagenomics Next-Generation Sequencing: A Case Report and Review of the Literature.}, journal = {Veterinary medicine and science}, volume = {12}, number = {1}, pages = {e70748}, pmid = {41556741}, issn = {2053-1095}, mesh = {Animals ; Dogs ; *Dog Diseases/diagnosis/virology ; High-Throughput Nucleotide Sequencing/veterinary ; Metagenomics ; *Rabies/diagnosis/veterinary/virology ; *Rabies virus/genetics/isolation & purification ; }, abstract = {Paralytic rabies is an atypical form of the disease that is notoriously difficult to diagnose early due to the absence of classic features like hydrophobia. The case being discussed presents a patient who has altered mental status, for whom the initial diagnosis was difficult due to an absent clear bite history and typical symptoms. The final diagnosis of the case was confirmed by metagenomic next-generation sequencing (mNGS) of directly from cerebrospinal fluid, which led to the detection of the rabies virus. This case underscores the critical diagnostic value of mNGS in identifying elusive neurotropic infections.}, } @article {pmid41557465, year = {2026}, author = {Ivanov, A and Popov, V and Morozov, M and Olekhnovich, E and Ulyantsev, V}, title = {MetaFX: feature extraction from whole-genome metagenomic sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {42}, number = {2}, pages = {}, pmid = {41557465}, issn = {1367-4811}, support = {23-75-10125//Russian Science Foundation/ ; }, mesh = {*Metagenomics/methods ; *Software ; Humans ; *Whole Genome Sequencing/methods ; *Metagenome ; Algorithms ; Machine Learning ; Inflammatory Bowel Diseases/microbiology/genetics ; }, abstract = {MOTIVATION: Microbial communities consist of thousands of microorganisms and viruses and have a tight connection with an environment, such as gut microbiota modulation of host body metabolism. However, the direct relationship between the presence of certain microorganism and the host state often remains unknown. Toolkits using reference-based approaches are limited to microbes present in databases. Reference-free methods often require enormous resources for metagenomic assembly or results in many poorly interpretable features based on k-mers.

RESULTS: Here we present MetaFX-an open-source library for feature extraction from whole-genome metagenomic sequencing data and classification of groups of samples. Using a large volume of metagenomic samples deposited in databases, MetaFX compares samples grouped by metadata criteria (e.g. disease, treatment, etc.) and constructs genomic features distinct for certain types of communities. Features constructed based on statistical k-mer analysis and de Bruijn graphs partition. Those features are used in machine learning models for classification of novel samples. Extracted features can be visualized on de Bruijn graphs and annotated for providing biological insights. We demonstrate the utility of MetaFX by building classification models for 590 human gut samples with inflammatory bowel disease. Our results outperform the previous research disease prediction accuracy up to 17%, and improves classification results compared to taxonomic analysis by 9±10% on average.

MetaFX is a feature extraction toolkit applicable for metagenomic datasets analysis and samples classification. The source code, test data, and relevant information for MetaFX are freely accessible at https://github.com/ctlab/metafx under the MIT License. Alternatively, MetaFX can be obtained via http://doi.org/10.5281/zenodo.16949369.}, } @article {pmid41557799, year = {2026}, author = {Liao, T and Chen, S and Wang, S and Huang, Y and Tsui, SKW and Stüeken, EE and Cao, Q and Luo, H}, title = {Noncanonical genetic markers resolve the pre-GOE emergence of aerobic bacteria in Earth's history.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {4}, pages = {e2515709123}, pmid = {41557799}, issn = {1091-6490}, mesh = {Earth, Planet ; *Bacteria, Aerobic/genetics/metabolism/classification ; Genome, Bacterial/genetics ; Genetic Markers ; Oxygen/metabolism ; Evolution, Molecular ; Phylogeny ; Aerobiosis ; Biological Evolution ; Machine Learning ; }, abstract = {The transition from anaerobic to aerobic life was a pivotal adaptation in Earth's history, yet the timing and genomic drivers remain poorly resolved. Traditional approaches relying on oxygen-utilizing genes need improvement for obligate anaerobes and fragmentary environmental genomes, where gene absence may reflect poor assembly rather than phenotype. We developed a machine learning model (GBDT40-LR) to predict microbial oxygen requirements using 40 broadly conserved genes, 35 without direct oxygen roles. This approach overcomes incompleteness biases in environmental genomes. Applied to 80,787 bacterial genomes [including metagenome-derived assemblies (MAGs)], the model classified 42,014 aerobes and 38,775 anaerobes, enabling large-scale ancestral reconstruction. Molecular clock dating indicates an emergence of aerobic bacterium prior to the Great Oxidation Event (GOE, 2.5 to 2.3 Ga), likely around ~2.7 Ga. Aerobic lineages subsequently diversified during the GOE and Neoproterozoic Oxygenation Event (NOE, 0.8 to 0.55 Ga), with persistent anaerobe diversity across Earth's oxygenation. This establishes that aerobic bacteria originated planetary oxygenation, potentially by 200 to 400 My, providing insights into phenotypic evolution and prolonged anaerobe-aerobe coexistence.}, } @article {pmid41558030, year = {2026}, author = {Fan, C and Hayase, T and Chang, CC and Glover, IK and Flores, II and McDaniel, LK and Ortega, MR and Sanchez, CA and El-Himri, RK and Brown, AN and Karmouch, JL and Jamal, MA and Ahmed, SS and Halsey, TM and Jin, Y and Tsai, WB and Prasad, R and Enkhbayar, A and Mohammed, A and Schmiester, M and Damania, A and Ajami, NJ and Wargo, JA and Peterson, CB and Rondon, G and Al-Juhaishi, T and Alousi, AM and Molldrem, JJ and Champlin, RE and Shpall, EJ and Martens, E and Arias, CA and Jenq, RR and Hayase, E}, title = {Fecal carbohydrate-degrading bacteria are associated with reduced incidence of lower gastrointestinal GVHD.}, journal = {Blood advances}, volume = {10}, number = {6}, pages = {1979-1991}, pmid = {41558030}, issn = {2473-9537}, mesh = {Humans ; *Feces/microbiology ; *Graft vs Host Disease/etiology/epidemiology/microbiology ; *Carbohydrate Metabolism ; *Bacteria/metabolism ; Hematopoietic Stem Cell Transplantation/adverse effects ; Incidence ; *Gastrointestinal Diseases/etiology/microbiology/epidemiology ; *Gastrointestinal Microbiome ; }, abstract = {Lower gastrointestinal graft-versus-host disease (LGI-GVHD) carries morbidity and mortality for patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), with critical contributions from the intestinal microbiome. In a retrospective cohort of metagenomic sequencing of stool from patients with allo-HSCT (N = 90), we found that a reduction in specific Parabacteroides and Bacteroides species around the time of engraftment contributes to LGI-GVHD risk. Given the known diverse carbohydrate-degrading functionality of these bacteria, we investigated gene abundances for carbohydrate-active enzymes (CAZymes) and found that Parabacteroides merdae, P distasonis, and Bacteroides ovatus abundances were significantly correlated with CAZymes in patients who did not develop LGI-GVHD compared with those who did. The specific gene abundances of xylosidase, which contribute to the degradation of xylose-containing polysaccharides, were significantly associated with a reduced risk of LGI-GVHD. All these findings show the importance of the carbohydrate-degrading functionality of putative beneficial bacteria in mediating risk of LGI-GVHD.}, } @article {pmid41558076, year = {2026}, author = {Zhao, M and Wu, F and Feng, S and Li, C and Liu, S and Chen, S and Liu, Y and Chen, B and Zhang, G and Han, S}, title = {Ursolic acid modulates gut microbiota and metabolites to enhance Treg/Th17 balance and intestinal health in broilers.}, journal = {Poultry science}, volume = {105}, number = {3}, pages = {106427}, pmid = {41558076}, issn = {1525-3171}, mesh = {Animals ; *Chickens/immunology/microbiology ; *Triterpenes/administration & dosage/metabolism/pharmacology ; Ursolic Acid ; *T-Lymphocytes, Regulatory/immunology/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Th17 Cells/immunology/drug effects ; *Intestines/drug effects/physiology ; Diet/veterinary ; Dietary Supplements/analysis ; Animal Feed/analysis ; Random Allocation ; Intestinal Barrier Function ; Dose-Response Relationship, Drug ; Male ; }, abstract = {Ursolic acid (UA), a naturally occurring pentacyclic triterpenoid abundant in various plants, possesses potent biological activities. However, its effects and mechanisms on immune competence in broilers remain unclear. In this study, 320 one-day-old Cobb broilers were randomly allocated to four groups (8 replicates of 10 birds each) for a 42-day trial: a control group (CON) and three treatment groups supplemented with 50, 200, or 400 mg/kg UA (UA 50, UA 200, or UA 400). We employed enzyme-linked immunosorbent assay (ELISA), alcian blue-periodic acid schiff (AB-PAS) staining, immunofluorescence (IF), immunohistochemistry (IHC), qRT-PCR, metagenomics, and untargeted metabolomics to analyze the effects of UA on immune factors, inflammatory cytokines, intestinal barrier function, regulatory T (Treg) cell / T helper 17 (Th17) cell balance, as well as intestinal microbial composition and metabolism in broilers. The results indicated that UA significantly increased immune factor levels while reducing pro-inflammatory cytokine concentrations in broilers. Regarding intestinal barrier function, UA supplementation effectively reduced lipopolysaccharide (LPS) and D-lactic acid levels, promoted goblet cell proliferation, and enhanced the expression of tight junction proteins (Claudin-1, ZO-1). Notably, UA also significantly modulated Treg/Th17 balance. Furthermore, UA supplementation modulated the gut microbial composition, which was marked by an increase in the beneficial Lactobacillus johnsonii and a concurrent suppression of the pathobiont Escherichia coli. Furthermore, UA reduced the enrichment of microbial pathways associated with pathogenic Escherichia coli and Salmonella infection. Further analysis indicated that UA modulated propionate and tryptophan metabolism, thereby increasing the concentrations of propionic acid and the tryptophan metabolites (5-Hydroxyindole-3-Acetic Acid (5HIAA) and Indole-3-Acetic Acid (IAA)). In summary, our findings demonstrate that UA enhances broiler immunity and intestinal barrier function. These benefits appear to be mediated by the UA-driven enrichment of Lactobacillus johnsonii, which promotes the production of propionate and tryptophan-derived metabolites (5-HIAA and IAA), thereby rebalancing the Treg/Th17 balance and ultimately reinforcing intestinal integrity. These findings underscore the potential of UA as a natural supplement for sustainable poultry production.}, } @article {pmid41558305, year = {2026}, author = {Gu, X and Yu, P and Duan, X and Chen, J and Zhou, Y and Jian, Q and Huang, M and Xue, G and Li, X}, title = {Metatranscriptomics reveals system-specific viral adaptive strategies and prokaryotic defense trade-offs across anaerobic digestion systems.}, journal = {Water research}, volume = {292}, number = {}, pages = {125401}, doi = {10.1016/j.watres.2026.125401}, pmid = {41558305}, issn = {1879-2448}, mesh = {Anaerobiosis ; Transcriptome ; Metagenomics ; Metagenome ; }, abstract = {Viruses are increasingly recognized as critical modulators of microbial community dynamics in anaerobic digestion (AD) systems, yet their ecological roles across distinct AD process types remain poorly understood. Here, we investigated viral ecology in three full-scale food waste treatment systems representing three predominant process types-dry AD (Dry-AD), wet AD (Wet-AD), and two-stage wet AD (2St-wet-AD)-through integrated metatranscriptomics and metagenomics. We recovered 4404 viral operational taxonomic units (vOTUs) and 206 metagenome-assembled genomes (MAGs). Dry-AD exhibited unique viral-prokaryotic diversity decoupling, elevated lysogeny (48.7% vs. 22.1%-26.5% in wet systems), and reduced transcriptionally active communities (viruses: 65.5% vs. 89.4% and 80.7% in wet systems; prokaryotes: 76.9% vs. 94.5% and 86.3% in wet systems). Comparative analyses revealed stronger viral endemism (55.4% system-specific vOTUs) than prokaryotes (30.6% MAGs). Virus-host networks demonstrated highly centralized infection patterns in Dry-AD with uneven transcript-based virus-host ratios (VHR) (Clostridia: 18.28 vs. Methanomicrobia: 0.15) compared to more uniform ratios (≈1.0) in wet systems. Transcriptomic profiling provided the first quantitative evidence of system-specific antiviral defense strategies: Wet-AD exhibited the highest defense gene transcriptional activity (3833 TPM), Dry-AD reduced defenses transcription (2614 TPM), while 2St-wet-AD displayed the lowest defense transcriptional activity (2455 TPM). Functional annotation revealed viral auxiliary metabolic genes exhibited distinct transcriptional patterns: enhancing host stress resilience in Dry-AD, promoting nutrient acquisition in Wet-AD, and improving metabolic efficiency in 2St-wet-AD. These findings reveal that viruses adopt distinct ecological roles across different AD process types, providing mechanistic insights for developing system-specific strategies to optimize stability and efficiency.}, } @article {pmid41558352, year = {2026}, author = {Xia, J and Li, C and Zhen, Y and Liu, M and Guo, J and Jiang, F}, title = {Bell-shaped response of mercury methylation to sulfate loading in urban sewer systems: Implications for source-level control.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141191}, doi = {10.1016/j.jhazmat.2026.141191}, pmid = {41558352}, issn = {1873-3336}, mesh = {*Sulfates/chemistry ; *Sewage/microbiology/chemistry ; *Mercury/metabolism/chemistry ; Bioreactors ; Methylation ; *Water Pollutants, Chemical/metabolism/analysis ; *Methylmercury Compounds/metabolism ; }, abstract = {Urban sewer systems act as incubators for mercury-methylating (hgcA) microorganisms, yet how sulfate-an abundant and variable sewage constituent-drives this process remains unclear. Here, we combined controlled bioreactor experiments, batch incubations, and genome-resolved metagenomics to demonstrate that Hg methylation potential follows a nonlinear, bell-shaped response to sulfate loading. The MeHg production rate peaked at moderate sulfate concentrations (75-150 mg/L), reaching levels 1.2-5.4 times higher than those observed under low sulfate conditions (6-30 mg/L). This enhancement arose from distinct community responses: at 75 mg/L, a phylogenetically diverse hgcA consortium emerged, with methanogens and fermenters complementing SRB, whereas at 150 mg/L, SRB-methylators such as Desulfobulbus dominated, indicating functional specialization. Outside this range, low sulfate (<30 mg/L) suppressed most hgcA populations due to electron acceptor scarcity, while high sulfate (>300 mg/L) favored non-methylating SRB like Desulfobacter postgatei, thereby reducing overall methylation potential. Importantly, by integrating our findings with reported sewage data, we show that sulfate concentrations in most domestic sewage fall within the optimal range for hgcA proliferation, explaining their consistently high abundances worldwide. Our results also highlight the potential basis for source-level interventions, such as substituting sulfate-free coagulants or restricting sulfate-rich industrial discharges, to reduce hgcA proliferation and mitigate downstream MeHg risks in urban water systems.}, } @article {pmid41558437, year = {2026}, author = {Wang, S and Zhang, T and Shi, Y and Zhang, Y and Fan, J and Shen, Z}, title = {Immobilized exogenous proteinase K enhances mesophilic anaerobic co-digestion of polylactic acid and food waste.}, journal = {Journal of environmental management}, volume = {399}, number = {}, pages = {128634}, doi = {10.1016/j.jenvman.2026.128634}, pmid = {41558437}, issn = {1095-8630}, mesh = {*Polyesters ; Food Loss and Waste ; Anaerobiosis ; *Endopeptidase K/metabolism ; Biodegradation, Environmental ; Methane ; Hydrolysis ; }, abstract = {Hydrolysis efficiency constraints impede anaerobic biodegradation of plastics, inducing kinetic imbalance during co-digestion with organic substrates. To address this limitation in food waste (FW) and commercial polylactic acid (PLA) biodegradable plastics (BPs), protease K (Pro K) was embedded onto BPs to leverage PLA-specific depolymerization activity. Regulatory mechanisms of enzymatic action on anaerobic microbial degradation were investigated through integration of classical model equations with metagenomic analysis. Results demonstrate that during hydrolysis, enzymatic reinforcement augmented hydrolysis rates, elevating BPs degradation from 7.3 % to 19.3 %. Throughout hydrogen/acidogenesis, microbial cascade responses were activated, enabling directional enhancement of the 'lactate-propionate-acetate' metabolic pathway. During methanogenesis, methyl oxidation was inhibited while concurrent reinforcement of hydrogenotrophic methanogenesis occurred, yielding 23.32 % (311.37 mL/g·VSadded[-1]) methane elevation. Metagenomic analysis revealed Pro K-mediated regulation of anaerobic metabolic gene pathways, establishing a novel strategy for accelerated BPs degradation and methane yield.}, } @article {pmid41558447, year = {2026}, author = {Han, Y and Wang, A and Zhang, Z and Liu, L and Chen, Q and Fan, W and Tan, E and Tang, K}, title = {Multi-omics reveal the prevalence of Thaumarchaeota and their biogeochemical roles in coastal low oxygen zones.}, journal = {Marine pollution bulletin}, volume = {225}, number = {}, pages = {119293}, doi = {10.1016/j.marpolbul.2026.119293}, pmid = {41558447}, issn = {1879-3363}, mesh = {*Oxygen ; Multiomics ; *Archaea ; Seawater ; China ; Nitrogen ; }, abstract = {The intensification of coastal hypoxia under anthropogenic eutrophication and climate change necessitates understanding microbial adaptive mechanisms. However, the composition of microbial communities and their biogeochemical roles in response to oxygen gradients remain poorly understood. Here, we employed ‌integrated multi-omics‌ approaches to analyze microbial communities and their biogeochemical functions across oxic to low oxygen gradients off the Yangtze River Estuary in East China Sea. Results revealed that surface oxic waters hosted phytoplankton (Synechococcus) and opportunistic bacteria (Flavobacteriia, Pelagibacterales), while bottom layers enriched chemolithoautotrophs (Thaumarchaeota, Nitrospina) and facultative anaerobes (Planctomycetes, Marine Group II), with sediment resuspension further amplified particle-attached taxa. Meanwhile, a remarkable shift in microbial nitrogen metabolism was observed between oxic and low oxygen waters, with dissolved nitrogen assimilation dominated in oxic waters. Despite genomic potential for complete nitrogen reduction in low oxygen waters, our metaproteomics revealed only a significant expression of nitrate reductases. This decoupling between genomic potential and proteomic expression implies that ambient oxygen levels remain above thresholds for full pathway activation, showcasing microbial metabolic plasticity. Both metagenomic and metaproteomic have confirmed that Thaumarchaeota, particularly the genus Nitrosopumilus, emerged as keystone taxa, contributing to nitrification and dark carbon fixation, thereby coupling nitrogen‑carbon biogeochemical cycling in coastal hypoxic zones. These findings highlight redox-driven microbial niche differentiation and metabolic adaptation, providing predictive insights into biogeochemical feedbacks under expanding coastal deoxygenation.}, } @article {pmid41558481, year = {2026}, author = {Keller, V and Calchera, A and Otte, J and Tuovinen Nogerius, V and Schmitt, I}, title = {Ubiquitous occurrence of the black fungus Melanina gundecimermaniae in the lichen Umbilicaria pustulata.}, journal = {Current biology : CB}, volume = {36}, number = {3}, pages = {748-759.e5}, doi = {10.1016/j.cub.2025.12.046}, pmid = {41558481}, issn = {1879-0445}, mesh = {*Symbiosis ; *Lichens/microbiology ; *Ascomycota/physiology/genetics ; Europe ; *Metagenome ; North America ; }, abstract = {Lichen symbioses frequently include additional fungal associates beyond the canonical mycobiont (fungus) and photobiont (alga/cyanobacterium). Despite the prevalence and diversity of these lichen cohabitants, their geographic distribution and role within the lichen consortium remain poorly understood. Combining genomics, metagenomics, and advanced microscopy, we identified the black fungus Melanina gundecimermaniae as a constant cohabitant in the lichen Umbilicaria pustulata. We analyzed metagenomes from 149 individuals across 15 populations, spanning the Europe-wide range of U. pustulata. Additionally, we screened pooled metagenomes of U. pustulata and Umbilicaria phaea along five elevation gradients (Europe and North America). Genome mapping, using a near-complete reference genome of M. gundecimermaniae, revealed that the black fungus was present in 100% of the screened lichen metagenomes, with 0.85%-3.78% of reads mapping against the reference. Among all lichen-associated fungi, it was one of the most common. These findings indicate that the black fungus is widely distributed and associated with different lichen species, underscoring its potential ecological significance. Using fluorescence in situ hybridization coupled with confocal laser scanning microscopy, we confirmed the presence of M. gundecimermaniae within various structures of U. pustulata, including vegetative symbiotic propagules involved in dispersal. Elucidating its widespread occurrence across continents, consistent presence in U. pustulata, and ability to be dispersed together with the lichens' canonical partners, our findings suggest a potential interaction of M. gundecimermaniae that extends beyond incidental colonization. Our study contributes to the growing body of evidence that organismal complexity within lichens is a prevalent and largely unexplored dimension of the lichen symbiosis.}, } @article {pmid41558536, year = {2026}, author = {Kasuma, N and Fitri, H and Wulandari, RW and Ernesto, G and Juwita, DR and Effendi, MDS and Wirza, TR}, title = {Salivary Microbiome Differences in Stunted and Healthy Children: A Metagenomic Analysis.}, journal = {European journal of dentistry}, volume = {}, number = {}, pages = {}, doi = {10.1055/s-0045-1814094}, pmid = {41558536}, issn = {1305-7456}, abstract = {This study aimed to compare the composition and diversity of the salivary microbiome in stunted and nonstunted children using 16S rRNA gene sequencing to explore the relationship between nutritional status and oral microbiota.A total of 20 saliva samples were collected from children aged 6 to 10 years, comprising two groups: stunted (n = 10) and healthy controls (n = 10). Deoxyribonucleic acid was extracted, and the V3-V4 region of the 16S rRNA gene was amplified and sequenced. Bioinformatics analysis included taxonomic assignment, calculation of relative abundance, α diversity (using Shannon and Simpson indices), β diversity (UniFrac-based principal coordinate analysis and permutational multivariate analysis of variance [PERMANOVA]), and differential abundance testing using the Mann-Whitney U test.The dominant phyla in both groups were Proteobacteria, Firmicutes, and Bacteroidota, with Proteobacteria being more prevalent in the stunted group. At the genus level, Neisseria and Veillonella were more abundant in stunted children. Notably, Veillonella was significantly elevated in the stunted group (28.6%) compared with controls (14.9%, p = 0.0376). Alpha diversity indices revealed a higher diversity trend in the stunted group, although this difference was not statistically significant (Shannon, p = 0.130; Simpson, p = 0.762). Beta diversity analysis revealed no considerable clustering between groups (PERMANOVA p > 0.05), indicating moderate interindividual variability but no clear group separation.Children with stunted growth demonstrated distinct microbial signatures in their salivary microbiota, particularly in the increased abundance of Proteobacteria and Veillonella, suggesting a potential link between chronic undernutrition and oral microbial dysbiosis. These findings underscore the need for additional studies to investigate the impact of nutritional status on oral and systemic health through the microbiome axis.}, } @article {pmid41559018, year = {2026}, author = {Liu, J and Li, D and Wang, S and Gao, S and Xu, B and Zhao, J and Liu, Q and Chen, M and Zhou, X and Cai, Y and He, L}, title = {Congenital babesiosis in China: first molecularly confirmed case of vertical transmission of Babesia microti.}, journal = {Emerging microbes & infections}, volume = {15}, number = {1}, pages = {2608389}, pmid = {41559018}, issn = {2222-1751}, mesh = {Female ; Humans ; Infant ; Male ; Antiprotozoal Agents/therapeutic use ; *Atovaquone/therapeutic use ; Azithromycin/therapeutic use ; *Babesia microti/genetics/isolation & purification/classification ; *Babesiosis/transmission/drug therapy/diagnosis/parasitology ; China ; *Infectious Disease Transmission, Vertical ; *Proguanil/therapeutic use ; Drug Combinations ; }, abstract = {Congenital babesiosis is rarely reported globally. We report a 74-day-old male infant presented with fever, pallor, and severe, life-threatening haemolytic anaemia (haemoglobin: 45 g/L). The infant had 16% parasitemia with ring forms evident on peripheral blood smear. Babesia microti infection was confirmed in both the mother and infant by PCR and metagenomic next- generation sequencing. Genetic analysis revealed an identical strain in bot. Treatment with intravenous azithromycin and oral atovaquone/proguanil resulted in rapid clearance of parasitemia and resolution of anaemia. This first molecularly confirmed case of congenital B. microti transmission in China demonstrates vertical transmission from an asymptomatic mother. It underscores the need for heightened clinical suspicion in neonates with unexplained haemolytic anaemia in endemic regions and highlights critical gaps in access to essential anti-babesia therapies.}, } @article {pmid41559060, year = {2026}, author = {Ding, Z and Wen, T and Teng, X and Yang, W and Yuan, X and Liu, X and Xie, P and Zhao, X and Shen, Q and Yuan, J}, title = {Enhancing soil citrulline degrading function to mitigate soil-borne Fusarium wilt.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41559060}, issn = {2041-1723}, support = {42322708//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Fusarium/metabolism/pathogenicity ; *Citrulline/metabolism ; Soil Microbiology ; Rhizosphere ; *Plant Diseases/microbiology/prevention & control ; *Soil/chemistry ; Pseudomonas putida/genetics/metabolism ; Fusaric Acid/metabolism ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Continuous cropping often exacerbates soil-borne diseases, particularly Fusarium wilt, yet the intricate rhizosphere relationships among phyto-derived metabolites, pathogens, and particular microbial functions remain poorly understood. Here, we observe that citrulline accumulation during continuous cropping is positively correlated with Fusarium wilt severity by enhancing fusaric acid production in Fusarium oxysporum. Metagenomic analyses reveal that citrulline turnover-related functions, represented by functional modules including M00978, are significantly enriched in healthy rhizosphere soils but are notably reduced in Fusarium-conducive soils. The functional genes, arcB and argH, are identified in Pseudomonas putida YDTA3, with arcB being essential for citrulline-degradation via knockout experiments. The inoculation of an arcB-expressing indigenous Escherichia consortium (EO-arcB) in three independent continuous cropping systems of cucurbit crops demonstrates that enhancing and maintaining the soil citrulline-degrading function mitigates soil-borne Fusarium wilt. In summary, this study advances our understanding of rhizosphere interactions underlying Fusarium wilt disease occurrence and offers a promising biocontrol strategy.}, } @article {pmid41559596, year = {2026}, author = {Liu, Y and Zhang, Q and Li, J and Wu, X and Zang, Q and Wang, Q and Huang, P and Wang, Y and Zhang, S and Liu, S and Zhu, C and Zhao, Y and Yan, T and He, Y}, title = {mNGS improves the efficiency of infection diagnosis and treatment in acute-on-chronic liver failure.}, journal = {BMC gastroenterology}, volume = {26}, number = {1}, pages = {129}, pmid = {41559596}, issn = {1471-230X}, mesh = {Humans ; *Acute-On-Chronic Liver Failure/complications/microbiology ; Female ; Male ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Adult ; Propensity Score ; Early Diagnosis ; *Mycoses/diagnosis/complications ; }, abstract = {INTRODUCTION: The early diagnosis of infections in acute-on-chronic liver failure (ACLF) is still difficult. mNGS(metagenomic next-generation sequencing) is a no-bias, sensitive pathogen diagnosis method, and further research on mNGS in ACLF is needed.

METHODS: A total of 275 ACLF patients with suspected or confirmed infections were recruited and divided into the mNGS group and the non-mNGS group. Differences between the two groups were assessed.

RESULTS: The 1:1 Propensity score matching (PSM) for balancing the baseline variables produced 86 patients in each group. From these 86 patients in the mNGS group, 134 samples were collected and analyzed. The overall microbiological positive rate (103/134, 76.9%) detected by mNGS was higher than that detected by culture (24/134, 17.9%), particularly for fungi (14.9% vs. 2.2%). The etiological diagnosis rates for pulmonary and thoracoabdominal infections detected by the mNGS method were higher than those of the culture method (47.9% vs. 11.4%; 52.0% vs. 18.4%, respectively). The etiological diagnosis can be confirmed 22.83 ± 26.27 h ahead of time. mNGS testing did not significantly improve 90-day transplant-free survival in the overall cohort (sHR 0.96, 95% CI 0.72-1.27; P = 0.76). In the subgroup where mNGS guided therapy, numerically higher resolution rates were observed for pulmonary (53.8% vs 37.1%), abdominal (63.2% vs 52.6%), and bloodstream infections (66.7% vs 50.0%), though these differences were not statistically significant.

CONCLUSIONS: mNGS is a valuable diagnostic tool for ACLF with infections, especially for viruses and fungi. mNGS allows for precise and earlier pathogen diagnosis, enabling timely and targeted anti-infective therapy. mNGS may be associated with improved clinical outcomes in ACLF patients with co-infections, though this potential association requires further validation.

TRIAL REGISTRATION: The study was registered on Clinicaltrials.gov (registration number: NCT05740696, release date: February22,2023). Accessible at: https://classic.

CLINICALTRIALS: gov/ct2/show/NCT05740696.}, } @article {pmid41559772, year = {2026}, author = {Gómez-Martínez, S and Pérez-Pérez, L and Ucero-Carrretón, A and López-García, Á and Galisteo, C and Carvajal, A and Argüello, H}, title = {Exploring the potential for competitive exclusion of commensal probiotic candidates against the insidious swine pathogen Brachyspira hyodysenteriae.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {19}, pmid = {41559772}, issn = {2524-4671}, support = {EDU/1868/2022//Junta de Castilla y León/ ; EDU 1009/2024//Junta de Castilla y León/ ; CNS2022-136066//Junta de Castilla y León/ ; PRE-2020-093762//Ministerio de Ciencia e Innovación/ ; Predoc grant 2025//Universidad de León/ ; }, abstract = {BACKGROUND: Research into animal microbiota reveals the intricate relationships between commensal bacteria and enteric pathogens. Metagenomics and culturomics offer novel opportunities in probiotic research, which is particularly interesting for diseases where treatment alternatives are limited, such as swine dysentery (SD), which is caused by Brachyspira hyodysenteriae (B. hyo). This study evaluates the potential ability of a collection of 28 isolates from species of interest to outcompete the anaerobic pathogen B. hyo by an array of in vitro assays designed to characterize their competitive exclusion capacity in co-cultures, alongside assessing the antimicrobial activity of the isolates cell-free supernatants (CFS) and the mechanisms by which they inhibit B. hyo growth. RESULTS: 20 of the 28 isolates tested were able to reduce the growth of B. hyo by more than one log10 bacteria/mL after 96 h of co-culture, with different inhibitory dynamics observed. Notably, Intestinibaculum porci (J1/23 CM6), Dorea longicatena (J1/23 YB16), Bifidobacterium thermoacidophilum (J1/23 YB69), Mobilitalea sibirica (J1/23 YB21), Clostridium butyricum (CECT 361), and Parabacteroides goldsteinii (DSMZ 29187) reduced B. hyo growth in more than 2 log10 units (bacteria/mL). The anti-B. hyo activity of the tested CFS demonstrated that the mechanisms involved went beyond nutrient competition, with a CFS concentration-dependent reduction. CFS from 11 isolates achieved a reduction of over 2 log10 bacteria/mL, with C. butyricum and Paraprevotella clara (DSMZ 19731) CFS standing out with values of 2–3 log10 bacteria/mL. A pH-dependent effect was disclosed for part of the isolates tested, while C. butyricum, Limosilactobacillus mucosae, B. thermoacidophilum and Lactiplantibacillus plantarum maintained part of their anti-B. hyo activity at fixed pH (7.0). A combined analysis of the short chain fatty acid profile and pH on B. hyo growth inhibition revealed differences between isolates, with similar effect for CFS of isolates with similar production of lactic and acetic acids and no clear effect of the pH. CONCLUSIONS: This study demonstrates the potential of pig gut commensals to outcompete B. hyo and discloses part of the mechanisms involved in the growth inhibition, providing a foundation into future research in competitive exclusion as strategy to control SD.}, } @article {pmid41559841, year = {2026}, author = {Galgano, S and Faruk, MU and Eising, I and Houdijk, JGM and Khattak, F}, title = {Dietary muramidase leads to the downregulation of peptidoglycan biosynthesis and to caecal microbial modulation in laying hens.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {7}, pmid = {41559841}, issn = {2524-4671}, abstract = {BACKGROUND: In-feed muramidase enzyme has been linked to numerous advantages in several animal species. In the past years, muramidase has been shown to be effective in hydrolyzing peptidoglycan fragments, especially at small-intestine level in broilers, and to improve digestibility and performance. Moreover, previous studies also showed a possible anti-inflammatory effect of some secondary metabolites derived from the hydrolysis of peptidoglycan. Although a major effort has been carried out to unravel the in vivo mechanism of action of muramidase, there is currently little information on its metabolic interactions in laying hens, especially considering the fundamental differences with broilers in terms of microbiota and host genetics. Therefore, we conducted a 20-week study, testing five different levels of inclusion of muramidase, from 0 mg/kg to 600 mg/kg. We analyzed dry matter and nitrogen digestibility, apparent metabolizable energy, body weight gain, caecal microbiota and microbiome. RESULTS: The intervention with muramidase (Balancius®, DSM Nutritional Products Ltd., Basel, Switzerland) led to a drop in α-diversity (Shannon index; P < 0.05) and to microbial composition changes, with a decrease in Lactobacillus and an increase in Collinsella, amongst others (Q < 0.05), at all the muramidase concentrations compared to 0 mg/kg. In parallel, we found that muramidase led to an increased protein digestibility as revealed by the increased nitrogen retention, together with a dose-dependent amelioration of body weight, dry matter digestibility and metabolizable energy (P < 0.05). At functional gene level, we observed a net decrease in the microbial potential to metabolize amino acids, likely as a direct consequence of the lower amino acid availability at caecal level, as linked to the increased nitrogen retention. Moreover, muramidase also led to a decreased microbial functional potential to synthesize peptidoglycan. CONCLUSION: This study is the first to investigate the effects of dietary muramidase supplementation on nutrient digestibility and metagenomics in laying hens. Our findings align perfectly with the previous studies in broilers, especially in terms of increased protein digestibility. Moreover, for the first time, a direct correlation between the observed phenotype and both microbiota and microbiome has allowed us to gain further insights into the mechanism of action of muramidase in laying hens.}, } @article {pmid41559953, year = {2026}, author = {Wu, J and Sun, D and Pan, Y and Liu, DF and Zhang, H and Zhou, JH and Gao, T and Wu, J and He, RL and Chen, YG and Li, WW}, title = {Overlooked Roles of Pharmaceutical Metabolic Products in Stimulating Microbial Metabolism and Antibiotic Resistance Gene Dissemination of Anaerobic Sludge.}, journal = {Environmental microbiology}, volume = {28}, number = {1}, pages = {e70247}, doi = {10.1111/1462-2920.70247}, pmid = {41559953}, issn = {1462-2920}, support = {51878638//National Natural Science Foundation of China/ ; 52192681//National Natural Science Foundation of China/ ; 22106160//National Natural Science Foundation of China/ ; U21A20160//National Natural Science Foundation of China/ ; 202423110050028//Key R&D Project of Anhui Province, China/ ; SYG2024111//Science and Technology Program of Suzhou/ ; WK2060000099//Fundamental Research Funds for the Central Universities/ ; //Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education/ ; JYB2025XDXM909//State Key Laboratory of Advanced Environmental Technology/ ; SKLAET2025-LH01//State Key Laboratory of Advanced Environmental Technology/ ; }, mesh = {*Sewage/microbiology ; Anaerobiosis ; *Bacteria/genetics/metabolism/drug effects ; *Drug Resistance, Microbial/genetics ; *Metformin/metabolism/pharmacology ; *Genes, Bacterial ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Biotransformation ; Wastewater/microbiology ; }, abstract = {The roles of non-antibiotic pharmaceuticals in shaping the dissemination behaviours of antibiotic resistance genes (ARGs) in wastewater treatment systems remain poorly understood, and the influences of their transformation products have been overlooked. Here, we unveil more profound impacts of the metformin (MET) biotransformation product than the parent pollutant on the microbial community structure and ARG propagation of wastewater anaerobic sludge. The exposure to MET and its metabolic products guanylurea (GUA) at environmentally relevant concentrations both raised the methane production and resulted in up to 52.5% higher sludge ARGs abundance relative to the unexposed control. Especially, the GUA group showed up to 188-fold upregulation in several ARGs including bcrA, PmrF, acrB and mexF, enabled 3218-fold enrichment of plasmids from several bacteria. The underlying mechanisms were elucidated by integrated metagenomics, molecular dynamics simulations, and metabolic profiling analyses. MET and GUA were found to trigger coordinated cellular responses including disrupted glycerophospholipid metabolism, increased membrane permeability and broad metabolic reprogramming, which collectively boosted the ARGs dissemination. Overall, this work establishes a mechanistic link between micropollutant-induced microbial stress and ARGs propagation in anaerobic sludge, and advocates for re-evaluating the environmental risks of non-antibiotic pharmaceuticals and integrating resistance control into wastewater management framework.}, } @article {pmid41560107, year = {2026}, author = {Duan, JX and Jian, H and Chang, L and Teng, J and Lai, SY and Yang, QX and Che, GL and Luo, LL and Liu, F}, title = {mNGS facilitates the diagnosis of pediatric murine typhus: A case report.}, journal = {Medicine}, volume = {105}, number = {3}, pages = {e47253}, pmid = {41560107}, issn = {1536-5964}, mesh = {Child ; Humans ; Anti-Bacterial Agents/therapeutic use ; Dexamethasone/therapeutic use ; Doxycycline/therapeutic use ; *High-Throughput Nucleotide Sequencing/methods ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/drug therapy/microbiology ; *Rickettsia typhi/genetics/isolation & purification ; *Typhus, Endemic Flea-Borne/complications/diagnosis/drug therapy/microbiology ; }, abstract = {RATIONALE: Murine typhus, caused by Rickettsia typhi, is a globally distributed flea-borne rickettsiosis. Although rarely recognized, it can trigger hemophagocytic lymphohistiocytosis (HLH), a life-threatening hyperinflammatory syndrome. Nonspecific febrile illness and atypical petechial eruptions frequently lead to delayed or missed diagnoses. This report aims to illustrate the diagnostic process and clinical implications of murine typhus-associated HLH in a pediatric patient, and to evaluate the utility of metagenomic next-generation sequencing (mNGS) as an unbiased detection tool for occult pathogens.

PATIENT CONCERNS: A 10-year-old child was admitted with unexplained recurrent fever and generalized petechiae, refractory to treatment at outside hospitals.

DIAGNOSES: The patient was ultimately diagnosed with murine typhus-associated HLH caused by R typhi, based on a comprehensive diagnostic work-up.

INTERVENTIONS: Empirical dexamethasone was initiated promptly to control hyperinflammation. After mNGS confirmation, oral doxycycline was added for targeted anti-rickettsial therapy.

OUTCOMES: The patient's clinical status continued to improve, culminating in discharge.

LESSONS: Murine typhus-associated HLH should be considered in febrile children with unexplained cytopenias and petechiae. Early empiric HLH-directed immunosuppression followed by pathogen-specific therapy improves prognosis. mNGS provides a rapid, unbiased method to detect rare, overlooked pathogens and guide definitive treatment when conventional tests are negative.}, } @article {pmid41560354, year = {2026}, author = {He, N and Wang, H and Yang, Z and Li, H and Liu, B and Chen, K and Wu, Z and Zhao, X and Liang, H and Wang, M and Li, X and Zhong, Y and Zhang, H and Xiao, L and Kristiansen, K and Peng, J and Zou, Y and Li, S}, title = {The Gut Commensal Butyricimonas Virosa Modulates Gut Microbiota-Dependent Thiamine Metabolism and Attenuates Mouse Steatotic Liver Disease.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {17}, pages = {e17596}, pmid = {41560354}, issn = {2198-3844}, support = {82470615//National Natural Science Foundation of China/ ; 2024KJJ042//Shandong Provincial Youth Entrepreneurship Program for Colleges and Universities/ ; ZR2022MH217//Shandong Provincial Natural Science Foundation/ ; 2023TD52//Central Public-interest Scientific Institution Basal Research Fund/ ; 2023TD76//Central Public-interest Scientific Institution Basal Research Fund/ ; KCXFZ20240903094006009//Shenzhen Municipal Government of China/ ; JCYJ20241202124801003//Shenzhen Municipal Government of China/ ; No.25-1-5-smjk-13-nsh//Qingdao Municipal Demonstration Project for Science & Technology to Benefit the People/ ; 2025YFA1310200//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Mice ; *Thiamine/metabolism ; *Gastrointestinal Microbiome/physiology ; *Fatty Liver/metabolism/microbiology ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Liver/metabolism ; Prebiotics/administration & dosage ; Diet, High-Fat ; *Eubacteriales/metabolism ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common chronic liver disease. This study investigates the anti-MASLD effects of dietary prebiotic stachyose (STA) on disease progression identifying Butyricimonas virosa as a key bacterium boosted by STA supplementation. Oral gavage of B. virosa to high fat diet (HFD)-fed mice significantly suppresses the progression of MASLD and modulates gut microbiota composition. Integration of metagenomic and metabolomic data demonstrates that B. virosa treatment significantly enhances the production of thiamine monophosphate (TMP), as well as its conversion to thiamine and subsequent accumulation in the liver. The accumulation of hepatic thiamine further leads to elevated thiamine pyrophosphate (TPP) concentrations enhancing the activity of branched-chain α-keto acid dehydrogenase E1 subunit α (BCKDHA) associated with augmented degradation of branched chain amino acids (BCAAs). Administration of B. virosa compensates via production of gut bacterial-derived TMP for hepatic TPP deficiency in mice fed a thiamine-deficient HFD. A population-based analysis reveals an inverse correlation between plasma thiamine levels, abundances of bacterial genes involved in thiamine synthesis and metabolism, and phenotypes associated with MASLD, suggesting that key genes involved in fecal thiamine metabolism, as well as serum thiamine determination, may potentially serve as biomarkers for the diagnosis of MASLD.}, } @article {pmid41560360, year = {2026}, author = {Zhang, J and Wang, Z and Li, S and Luo, C and Li, H and Ma, S and Wang, P and Liu, H and Sun, L and Yin, Y and Zhang, W and Wang, Q}, title = {Phocaeicola coprophilus-Derived 6-Methyluracil Attenuates Radiation-Induced Intestinal Fibrosis by Suppressing the IDO1-Kynurenine-AHR Axis.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {18}, pages = {e18502}, pmid = {41560360}, issn = {2198-3844}, support = {JDYY15202429//Youth Development Fund of the First Hospital of Jilin University/ ; JDYY-DEP-2022006//Doctor of Excellence Program (DEP), The First Hospital of Jilin University/ ; YDZJ202402012CXJD//Department of Science and Technology of Jilin Province/ ; 82330017//National Natural Science Foundation of China/ ; 82270610//National Natural Science Foundation of China/ ; 20240484505//Beijing Nova Program/ ; 2024ZD0530100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; }, mesh = {Animals ; *Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism/genetics ; *Kynurenine/metabolism ; *Fibrosis/metabolism ; Mice ; *Receptors, Aryl Hydrocarbon/metabolism ; *Uracil/analogs & derivatives/metabolism/pharmacology ; *Intestines/pathology/drug effects ; Gastrointestinal Microbiome ; Humans ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; }, abstract = {Therapeutic options for radiation-induced intestinal fibrosis (RIF) remain limited. This study reveals that intestinal kynurenine (Kyn) is persistently elevated after radiation and correlates with fibrosis severity in both murine models and human rectal cancer samples. Exogenous Kyn exacerbated RIF, whereas inhibition of indoleamine 2,3-dioxygenase 1 (IDO1) attenuated fibrotic progression. Mechanistically, Kyn activates the aryl hydrocarbon receptor (AHR) to promote fibroblast activation and fibrosis. Antibiotic depletion of gut microbiota abrogates radiation-induced IDO1-Kyn upregulation and protects against RIF. Conversely, fecal microbiota transplantation from irradiated mice recapitulates the elevated IDO1-Kyn phenotype. Metagenomic analysis identify radiation-induced depletion of Phocaeicola coprophilus (P. coprophilus), whose abundance inversely correlates with Kyn levels. Supplementation with live P. coprophilus suppresses IDO1-Kyn signaling and ameliorates RIF. Untargeted metabolomics further show that radiation reduces 6-methyluracil, a metabolite derived from P. coprophilus. Exogenous 6-methyluracil replenishment inhibits repression of the IDO1-Kyn axis and mitigates fibrosis. Together, these findings define a microbiota-metabolite-host pathway in which radiation depletes P. coprophilus, leading to loss of 6-methyluracil and derepression of the IDO1-Kyn-AHR axis, thereby driving fibrogenesis. Restoration of either P. coprophilus or its metabolite 6-methyluracil represents a promising therapeutic strategy against RIF.}, } @article {pmid41560914, year = {2025}, author = {Chevokina, E and Sibiryakina, D and Sobolev, A and Slonova, D and Demkina, A and Yurikova, D and Galivondzhyan, A and Konovalova, O and Sutormin, D and Isaev, A}, title = {Efficient recovery and DNA extraction for algae-associated microbial communities.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1693747}, pmid = {41560914}, issn = {1664-462X}, abstract = {The extraction of high-quality microbial DNA from environmental samples is critical for many downstream applications, including short- and long-read metagenomic sequencing. However, environmental DNA is prone to low recovery, degradation, and contamination by enzymatic inhibitors, with the extent of these issues largely dependent on the DNA purification method. The embedding of bacterial cells in a mucoid matrix within biofilms further complicates the process, making the study of algal symbionts particularly challenging. This study benchmarked five methods to recover microbial cells from biofilms associated with three major groups of marine macroalgae, namely: red (Palmaria stenogona), brown (Saccharina japonica), and green (Ulva lactuca). This was followed by a systematic evaluation of six widely used commercial DNA purification kits for their ability to extract high-quality DNA suitable for 16S rRNA gene and shotgun sequencing. A universal trade-off was observed between the quantity and quality of the extracted DNA. While whole-sample homogenization and manual collection of biofilms resulted in high levels of chloroplast contamination, washing microbial cells with a buffer led to low DNA recovery; however, the use of a detergent improved DNA yields. A comparison of the DNA extraction kits revealed that their efficiency varied significantly among algal species, with the GeneJET Genomic DNA Purification Kit (Thermo Scientific) identified as the most versatile. The present findings provide a comparative benchmark of methods to recover algae-associated microbial communities and extract their DNA, offering guidance in selecting procedures suited for metagenomic sequencing.}, } @article {pmid41561024, year = {2025}, author = {Chen, YX and Xuan, YS and Wang, MH and Li, Y and Shi, SM and Zhao, HY and Niu, YH and Chen, M and Li, SY}, title = {Research on the regulation of gut microbiota homeostasis and immune function in asthmatic mice by Huanglong Zhixiao Formula.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1726388}, pmid = {41561024}, issn = {1664-302X}, abstract = {BACKGROUND: Asthma affects approximately 334 million people worldwide. Accumulating evidence indicates that gut dysbiosis exacerbates airway inflammation through the gut-lung axis. In the present study, using an OVA-induced murine model of asthma, we investigated whether Huanglong Zhixiao Formula (HLZXF) restores gut lung homeostasis by reshaping the gut microbiota and enhancing intestinal barrier function, thereby attenuating pulmonary pathological changes.

METHODS: Female BALB/c mice were randomly assigned to three groups (n = 15 per group): Control (C), Asthma Model (MX), and HLZXF-treated (ZG) groups. Asthma was induced by OVA sensitization and challenge over a 6-week period. The ZG group received daily oral gavage of HLZXF, 1 h prior to each OVA challenge. Fecal samples were collected for metagenomic sequencing. Lung and intestinal tissues were excised for HE and IHC staining of tight junction proteins, including Claudin, Occludin, and ZO-1. Alpha and beta diversity analyses were conducted to evaluate the composition and structure of the gut microbiota.

RESULTS: We analyzed the structure of the gut microbiota, detected the expression levels of intestinal barrier-related proteins, and assessed inflammatory injury in the lungs and intestines. Results demonstrated that HLZXF significantly ameliorated gut microbiota dysbiosis in asthmatic mice, as evidenced by the significant enrichment of Heminiphilus faecis and Paramuribaculum intestinale. Additionally, certain fungal taxa, such as Piromyces finnis and Rhizopus arrhizus, were significantly enriched in the ZG group. HLZXF also significantly upregulated the expression levels of the tight junction proteins Claudin, Occludin, and ZO-1 in intestinal tissues, thereby promoting the repair of the intestinal mucosal barrier. Furthermore, HLZXF significantly attenuated inflammatory cell infiltration and tissue injury in the lungs and intestines, alleviated alveolar septal thickening, and enhanced the integrity of the intestinal mucosal barrier.

CONCLUSION: This study elucidates the potential therapeutic mechanisms of HLZXF in the treatment of asthma from the perspective of gut microbiota and intestinal barrier function. It highlights that HLZXF can attenuate pulmonary inflammation by regulating the balance of gut microbiota and enhancing intestinal barrier function.}, } @article {pmid41561026, year = {2025}, author = {Li, F and Qiu, Z and Pei, Z and Zhu, Q and Shen, S and Fan, L and Xu, L and Huang, C and Wang, J and Huang, B and Huang, L and Liu, X and Han, Q}, title = {Effects of pesticides on soil microbial community structure and nitrogen transformation in tobacco fields affected by root rot.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1733977}, pmid = {41561026}, issn = {1664-302X}, abstract = {INTRODUCTION: In tobacco planting soil infected with root rot disease, the potential impacts of prothioconazole (T1), pyrisoxazole (T2), kasugamycin combined with Paenibacillus polymyxa (T3), and cyclobutrifluram (T4) on soil microecology remain unclear. This study examined their effects on soil microbial communities and nitrogen transformation processes.

METHODS: By measuring soil nitrogen forms and enzyme activities, combined with metagenomic sequencing, we conducted a comprehensive assessment of the soil microecology, focusing on shifts in microbial community composition, xenobiotic degradation potential, and nitrogen cycling processes.

RESULTS AND DISCUSSION: The results revealed that pesticide application significantly changed the content of nitrogen forms and their transformation rate. T1 and T2 treatments significantly increased the accumulation of ammonium nitrogen (NH4 [+]-N), while T2 and T4 markedly promoted the accumulation of nitrate nitrogen (NO3 [-]-N). Microbial community analysis indicated that the T2 and T4 treatments significantly affected the microbial structure. Analysis of xenobiotic degradation pathways showed that multiple pathways were suppressed by the four pesticide treatments, with the T2 treatment exhibiting the broadest suppressive effect. Metagenomic analysis further revealed that the T2 treatment promoted the accumulation of both NH4 [+]-N and NO3 [-]-N by up-regulating the mineralization gene (gdh) and nitrification genes (hao and nxrAB), while the T4 treatment facilitated NO3 [-]-N accumulation by up-regulating nitrification genes (hao and nxrAB). Correlation network analysis uncovered relationships between key nitrogen cycle genes and microbial genera, showing that nitrification genes (hao and nxrAB) in the T2 and T4 treatment groups exhibited positive correlations with Nitrobacter and Nitrosovibrio. This research clarifies the pathways through which these four pesticides influence the soil nitrogen cycle, providing an important theoretical basis for their ecological risk assessment and rational application.}, } @article {pmid41561037, year = {2025}, author = {Zhang, S and Mo, Y and Yang, J and Chen, X and Gao, M and Su, Y and Qiu, Q and He, Q}, title = {Vertical stratification of P pools in subtropical plantation soils under fertilization and dry-season irrigation: multiomics regulatory strategies.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1714023}, pmid = {41561037}, issn = {1664-302X}, abstract = {The rapid expansion of fast-growing plantations in subtropical regions is closely linked to silvicultural practices, however, improper practices often lead to soil acidification and reduced nutrient bioavailability. Phosphorus (P), one of the most critical elements for plantation tree growth, shows complex spatial distribution patterns in soil that are influenced by multiple factors, directly affecting plantation productivity. This study investigated the effects of long-term fertilization and dry-season irrigation on the vertical distribution of phosphorus in an 8-year-old subtropical Eucalyptus plantation. This study employed stratified sampling (0-30 cm topsoil, 30-60 cm subsoil, 60-90 cm substratum) during dry seasons, coupled with metagenomics, metabolomics, and environmental factor analysis, to reveal vertical phosphorus cycling patterns and multiomics regulatory networks. Key findings: (1) Fertilization and dry-season irrigation had a limited influence on labile phosphorus and the diversity of P-cycling microorganisms. The topsoil presented significantly greater P availability than did the subsoil, manifested as elevated acid phosphatase activity (ACP), significant enrichment of the tryptophan metabolic pathway, and greater microbial diversity. (2) pH and the C:P ratio represent critical factors of vertical stratification in soil P cycling. Under acidic conditions, topsoil microorganisms facilitate P release via diverse metabolic pathways, whereas oligotrophic constraints in the substratum limit enzymatic activities. (3) Potential cross-stratum microbial functional coordination exists in acidic soil P cycling, with linkages to tryptophan metabolism and polyphosphate, synthesis/degradation. Our study provides theoretical multiomics insights for optimizing the management of soil P pools in subtropical plantations under fertilization and dry-season irrigation.}, } @article {pmid41561086, year = {2025}, author = {Zhang, MY and Chen, SY and Lin, YH and Yuan, XX}, title = {Gut microbiota modulation in gastrointestinal disorders: current evidence and therapeutic perspectives.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1740322}, pmid = {41561086}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Diseases/therapy/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Gastrointestinal Tract/microbiology ; Dysbiosis/therapy ; }, abstract = {Gut microbiome medicine is a promising field in functional medicine, offering personalized treatment strategies for gastrointestinal disorders. Advanced metagenomic and metabolomic technologies have revealed the gut microbiome's systemic influence, extending to distant organs like the brain and lungs. While small molecules and genes facilitate these effects, the gut microbiota's greatest abundance and activity are concentrated in the gastrointestinal tract, particularly in the distal regions. The balance of microbial communities in the small and large intestines is crucial for gastrointestinal health. However, the dominance of pathogenic bacteria can disrupt this balance, leading to tissue damage and contributing to gastrointestinal disorders. Emerging interventions, such as probiotics, fecal microbiota transplantation, and dietary enrichment with short-chain fatty acids, show potential in restoring microbial balance, enhancing immune function, and potentially protecting against carcinogenesis. Current evidence from clinical trials and animal models supports the therapeutic role of gut microbiome modulation in reversing gastrointestinal disorders. However, variability in study outcomes highlights the need for further research to standardize these approaches for clinical practice. This review underscores the gut microbiome's pivotal role in gastrointestinal health and the therapeutic promise of functional medicine in addressing these disorders. This review also explores emerging interventions, such as phage therapy and engineered microbes, and provides comparative analyses of microbiota signatures and therapeutic approaches across different gastrointestinal disorders.}, } @article {pmid41561096, year = {2025}, author = {Wan, L and Huang, C and Kong, W and Li, M and Lu, C}, title = {The analysis of gut microbiota characteristics in children with global developmental delay.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1606453}, pmid = {41561096}, issn = {2235-2988}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Prospective Studies ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Developmental Disabilities/microbiology ; High-Throughput Nucleotide Sequencing ; Female ; Child, Preschool ; Male ; DNA, Bacterial/genetics ; Child ; China ; Biodiversity ; Infant ; }, abstract = {OBJECTIVE: To explore the composition and functional changes of gut microbiota in children with Global Developmental Delay(GDD),and to explore the role of gut microbiota in the pathogenesis of GDD using high-throughput sequencing.

METHODS: A prospective study was conducted to select 26 children diagnosed with GDD at Longgang District Maternal and Child HealthCare Hospital of Shenzhen City from January 2024 to December 2024 as the disease group(GDD), and 59 healthy children of the same age were selected as the healthy group(HC).General information of the children was collected through a questionnaire survey, and fecal samples from all participants were collected. Total DNA was extracted and amplified, and high-throughput sequencing of the 16S rRNA gene was performed for biological analysis of the sequencing results.

RESULTS: The alpha diversity analysis revealed a significant reduction in microbial diversity in the GDD group (Chao1 index, P = 0.007), while the beta diversity showed significant segregation between groups (R² = 0.067, P = 0.001);At the phylum level, the relative abundance of Actinobacteria was significantly increased (P < 0.01), while the abundance of Bacteroidetes was significantly decreased (P < 0.05) in the GDD group;At the genus level, the abundance of Bifidobacterium, Fusicatenibacter, and Erysipelatoclostridium were significantly increased in the GDD group (all P < 0.001), while the abundance of Faecalibacterium, Phascolarctobacterium, and Alistipes were significantly reduced (all P < 0.001);Functional prediction based on 16S rRNA data suggested potential differences in microbial metabolic pathways, including mRNA surveillance, proteasome, and atrazine degradation, in the GDD group. These findings hypothesize a functional shift in the gut microbiome associated with GDD, which requires validation by direct metagenomic or metabolomic methods.

CONCLUSION: Children with GDD have significant differences in gut microbiota composition and diversity compared to HC,and the abundance and abnormal metabolic pathway may be closely related to the neuroinflammatory process, suggesting that intestinal microecological regulation may become a new intervention target for GDD.}, } @article {pmid41561308, year = {2026}, author = {Mei, Z and He, C and Balcazar, JL and Fu, Y and Dou, Q and Liu, Y and Dercon, G and Jiang, X and Elsner, M and Wang, F}, title = {Antibiotic-degrading bacteria shape resistome dynamics and horizontal gene transfer potential in soils with contrasting properties.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycaf246}, pmid = {41561308}, issn = {2730-6151}, abstract = {Soils act as both reservoirs and filters of antimicrobial resistance genes (ARGs); however, the ecological and genetic traits of antibiotic-degrading bacteria (ADB) and their interactions with nondegrading bacteria (NADB) across soil types remain poorly understood. In particular, the role of ADB in ARG dynamics and their potential contribution to horizontal gene transfer (HGT) are still underexplored. Here, we applied [13]C-DNA stable isotope probing (DNA-SIP) combined with metagenomic sequencing to resolve active ADB from NADB in two contrasting soils: Ultisol and Mollisol. ADB harbored significantly more abundant and diverse chromosomal ARGs - especially multidrug and tetracycline resistance genes - often co-localized with mobile genetic elements (MGEs) and degradation genes, suggesting robust and regulated resistance strategies. In contrast, NADB relied more on plasmid-borne ARGs, reflecting flexible but potentially transient adaptation. Soil properties shaped both resistome composition and host taxa. Mollisol enriched enzymatic degraders such as Lysobacter and Nocardioides, while Ultisol favored stress-tolerant Burkholderia, which carried up to 34 ARGs and exhibited membrane-associated resistance. Notably, 89 ARGs or MGEs were found co-localized with degradation genes on assembled contigs, highlighting a strong potential for HGT. In addition, 24 high-potential ARG hosts were identified, including Ralstonia pickettii and Saccharomonospora viridis. These findings reveal that antibiotic degradation is embedded within complex, soil-specific resistome networks. This work enhances our understanding of ARG ecology and supports targeted mitigation strategies based on soil microbiome characteristics.}, } @article {pmid41561899, year = {2026}, author = {Labbancz, J and Birnbaum, A and Dhingra, A}, title = {Long-read metagenomic dataset from domestic rabbit manure and domestic rabbit manure-derived vermicompost.}, journal = {Data in brief}, volume = {64}, number = {}, pages = {112425}, pmid = {41561899}, issn = {2352-3409}, abstract = {This dataset describes samples collected from two Domestic Rabbit manure sources and three Domestic Rabbit manure-derived vermicompost bins. Three samples were taken from each and total DNA was isolated. Nanopore sequencing was used to collect data from all isolated DNA samples. After length and quality filtering, 181.5 gigabases (Gb) of sequencing data was collected across 15 samples. Streptomyces, Bradyrhizobium, Mesorhizobium, and Microbacterium were in the top 5 genera for all vermicompost samples, but two vermicompost samples had very high proportions of Escherichia and Mycobacterium. Vermicomposting can enable the development of beneficial microbial communities, but often lacking a thermophilic phase, may also allow for the growth of potentially pathogenic microbes. The vermicomposts described by this dataset contains both beneficial and potentially harmful microbial communities and may be used to support comparisons between composts and vermicomposts of different backgrounds for safety and utility.}, } @article {pmid41562034, year = {2026}, author = {Sanchez-Cid, C and Vrchovecká, S and Dehon, E and Wacławek, S and Vogel, TM}, title = {Environmental Consequences of Anthropogenic Pollution: Non-antibiotic-Drug-Driven Antibiotic Resistance Selection in a Model Aquatic Ecosystem.}, journal = {Environment & health (Washington, D.C.)}, volume = {4}, number = {1}, pages = {132-143}, pmid = {41562034}, issn = {2833-8278}, abstract = {Non-antibiotic drugs (NADs) used in human therapy may induce antibiotic resistance selection and dissemination in vitro. However, the potential risks of antibiotic resistance emergence associated with environmental NAD pollution have not been addressed. Here, we conducted a multidisciplinary study on river water microcosms using growth kinetics, qPCR, metagenomics, 16S rRNA sequencing, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to determine whether NADs alter river bacterial ecology and select for antibiotic resistance genes (ARGs). Four NADs with different mechanisms of action were included at a high (mg/L) and low (μg/L) dose to establish dose-response relationships: chlorpromazine (antipsychotic), diclofenac (anti-inflammatory), diphenhydramine (antihistamine), and fluoxetine (antidepressant). Although the community response to NAD pollution was compound-specific and dose-dependent, all NADs and doses were stable in the environment, altered the composition and activity of bacterial communities, and selected for several ARGs, mostly β-lactamases and aminoglycoside resistance genes, some of which were associated with horizontal gene transfer genes. Pseudomonas (including some ARG-harboring subpopulations) was identified as a key player in the response to NAD pollution. Here, we demonstrate NAD-driven antibiotic resistance selection in complex aquatic communities, raising concerns about the collateral effects on human and environmental health due to the extensive anthropocentric use of NADs.}, } @article {pmid41562094, year = {2025}, author = {Tang, K and Zhang, Y and Meneses, C and Rogerio, LA and Willen, L and Iniguez, E and Kamhawi, S and Valenzuela, JG and Oliveira, F and Cecilio, P}, title = {Phlebotomus duboscqi gut microbiota dynamics in the context of Leishmania infection.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1717935}, pmid = {41562094}, issn = {1664-3224}, mesh = {Animals ; *Phlebotomus/microbiology/parasitology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics ; Female ; Insect Vectors/microbiology ; Metagenomics/methods ; *Leishmaniasis ; *Leishmania major ; }, abstract = {INTRODUCTION: The manipulation of the gut microbiota of disease vectors has emerged as a new approach to use in the integrated control of vector-borne diseases. For this purpose, a deep knowledge of their gut microbial communities is essential. To our knowledge, to date, no study has documented the gut microbiome dynamics of Phlebotomus duboscqi sand flies over the entire time-period required for the maturation of a Leishmania infection. Here, we address this limitation.

METHODS: P. duboscqi midguts were dissected both before and at different days after L. major infection and subjected to genomic DNA extraction followed by amplification of the V3-V4 hypervariable regions of the 16S rRNA, sequencing, and metagenomics analysis.

RESULTS: We observed a decrease in the number of Amplicon Sequence Variants (ASVs) early after infection, at D2, and late after infection, at D12. More so Sphingomonas, Ochrobactrum, and Serratia emerged as the most prevalent genera in relative terms, before, early after, and late after infection, respectively. These results translated into a separation between the 3 groups in the context of a beta diversity analysis, with statistical relevance. Importantly, we were able to establish Corynebacterium spp. and Enterococcus spp. as potential markers of non-infected and infected sand flies, respectively, as well as Streptococcus spp., Sphingomonas spp., Ralstonia spp., and Abiotrophia spp. as potential specific markers of late infections (ANCOM-BC analysis).

DISCUSSION: Overall, we show that the composition of the gut microbiota of P. duboscqi sand flies changes significantly over the course of an infection with L. major parasites.}, } @article {pmid41562140, year = {2026}, author = {Assenmacher, CA and Mou, K and Li, G and Hsu, K and Sahin, O and Cole, SD}, title = {Actinomyces sp. detected by next-generation sequencing in paraffin-embedded, formalin-fixed tissues of a dog with severe panophthalmitis and periocular cellulitis.}, journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc}, volume = {38}, number = {2}, pages = {288-292}, pmid = {41562140}, issn = {1943-4936}, support = {S10 OD023465/OD/NIH HHS/United States ; }, mesh = {Animals ; Dogs ; Male ; *Dog Diseases/microbiology/pathology/diagnosis ; *Actinomyces/isolation & purification/genetics ; *Panophthalmitis/veterinary/microbiology/pathology/diagnosis ; High-Throughput Nucleotide Sequencing/veterinary ; *Cellulitis/veterinary/microbiology/pathology ; Paraffin Embedding/veterinary ; *Actinomycosis/veterinary/microbiology/pathology/diagnosis ; }, abstract = {A 9-mo-old, castrated male Saint Bernard dog was presented for evaluation of periorbital swelling, severe uveitis, and secondary glaucoma. Concurrently, chest radiographs had evidence of pneumonia. Enucleation was performed after failure of aggressive medical management. Histopathology of the globe confirmed severe necrosuppurative panophthalmitis and periocular cellulitis with myriad intra- and extracellular bacteria forming long filamentous chains. The bacteria were gram-positive and GMS-positive but acid-fast-negative. Next-generation sequencing (NGS) was performed on formalin-fixed, paraffin-embedded (FFPE) tissue from the eye. We identified a bacterium in the Actinomycetaceae family with a 100% BLAST match, suggestive of the previously described Actinomyces catuli strain (CCUG 41709). Clinical improvement followed enucleation and continued medical management, leading to reduction of the periocular swelling and resolution of the lung disease. Uveitis is common in dogs and is the most common cause of glaucoma. In many cases of bacterial uveitis, the exact bacterial organisms remain unknown if culture is not performed before fixation. Actinomyces sp. should be considered in patients with severe endophthalmitis or panophthalmitis, especially with evidence of systemic disease. NGS on FFPE samples may be a useful tool for identifying infectious organisms, especially in cases in which culture is not an option.}, } @article {pmid41562342, year = {2026}, author = {Winkler, M and Seel, W and Kornblum, C and Simon, MC and Reimann, J}, title = {The MicroIBioM study: the gut microbiome in inclusion body myositis.}, journal = {Clinical and experimental rheumatology}, volume = {44}, number = {2}, pages = {186-193}, doi = {10.55563/clinexprheumatol/1b8sv1}, pmid = {41562342}, issn = {0392-856X}, mesh = {Humans ; *Myositis, Inclusion Body/microbiology/diagnosis ; Female ; Aged ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; *Bacteria/genetics/classification ; Feces/microbiology ; Case-Control Studies ; Ribotyping ; Severity of Illness Index ; Metagenomics ; }, abstract = {OBJECTIVES: Inclusion body myositis (IBM) is a disorder with features of both inflammation and degeneration yet without effective treatment. Influences of the gut microbiome on degenerative as well as inflammatory disorders and immune treatments are known. We sought to investigate whether the gut microbiome might influence the development or recalcitrance of IBM.

METHODS: We appealed to IBM patients and their unaffected spouses/cohabitants for stool samples and data on clinical symptoms, gathering questionnaire data (modified Gastrointestinal Symptom Rating Scale (mGSRS), IBM Functional Rating Scale (IBMFRS) and Bristol Stool Scale) and stool samples for 16S rRNA V3V4 metagenomic analysis from 21 IBM and 20 control probands. Bioinformatic analyses used QIIME2 and MicrobiomeAnalyst software packages. LEfSe and Random Forest analysis aimed to identify group specific biomarkers. PICRUSt was used to perform pathway analysis.

RESULTS: No overall differences of alpha and beta diversity were found between IBM and control group. No impact of immune treatments was found, but a reduction in alpha diversity was identified comparing older (≥ 72 years) IBM and control probands. Increased abundances of some genera, in particular Bacteroides, were detected in the IBM group. Bacteroides, Clostridium CAG 352, and Eggerthella were identified as IBM biomarkers at genus level. Gastrointestinal symptoms (mGSRS) correlated with disease severity (IBMFRS).

CONCLUSIONS: General differences of gut microbiome seem unlikely to play a role in the genesis of IBM. Whether the late occurring or the more specific differences detected are part of the disease course needs to be addressed by investigations of further biosamples.}, } @article {pmid41562434, year = {2026}, author = {Jasilionis, A and Sivakumar, P and Dobruchowska, JM and Fjermedal, S and Guðmundsson, H and Adalsteinsson, BT and Hreggviðsson, GÓ and Meyer, AS and Nordberg Karlsson, E}, title = {Characterisation of a phylogenetically distinct PL25 family ulvan lyase from a seaweed biomass enriched metagenome.}, journal = {The FEBS journal}, volume = {293}, number = {10}, pages = {2885-2907}, pmid = {41562434}, issn = {1742-4658}, support = {//European Commision/ ; }, mesh = {*Polysaccharide-Lyases/genetics/chemistry/metabolism/classification ; *Metagenome ; Substrate Specificity ; Phylogeny ; *Seaweed/genetics/enzymology ; Biomass ; Recombinant Proteins/genetics/metabolism/chemistry ; Amino Acid Sequence ; Polysaccharides/metabolism/chemistry ; Hydrogen-Ion Concentration ; Kinetics ; Escherichia coli/genetics ; }, abstract = {Ulvan is a polysaccharide most abundant in green macroalgae biomass. Investigation of ulvan confirmed the potential of the polysaccharide for food, pharmaceutical and chemistry applications, emphasising the beneficial properties of ulvan oligosaccharides. Efficient production of oligosaccharides requires action of ulvan lyases capable of ensuring polysaccharide enzymatic depolymerisation. The armoury of available ulvan lyases was expanded by characterisation of SH2L_Ulv3 ulvan lyase, which was found to be phylogenetically distinct from previously characterised lyases attributed to PL25 family. A gene encoding a novel ulvan lyase was identified among sequences from a seaweed biomass metagenome enriched in an intertidal coastal hot spring. Identified ulvan lyase was most similar to a hypothetical protein from a Bacteroidales bacterium. Recombinant SH2L_Ulv3 was heterologously (over)produced in Escherichia coli at a high yield, remaining soluble in the expression host as well as after affinity purification. Ulvan lyase active as a 48.6 kDa monomer with evaluated activity optimum pH 7.5 and 200 mm NaCl at 25 °C demonstrated broad substrate specificity. SH2L_Ulv3 degraded ulvan from blade-thallus as well as tubular-thallus morphology algae species, efficiently producing three different DP4 and DP2 unsaturated oligosaccharides. The kinetic parameters of SH2L_Ulv3 were KM 3.63 ± 0.12 mg·mL[-1], Vmax 1.78 ± 0.04 μmol·min[-1]·mL[-1] and kcat 1.46 ± 0.04 s[-1]. Magnesium ion stimulated SH2L_Ulv3 activity. The characterised enzyme was not thermostable, displaying Tm 42 °C. The computationally modelled structure of SH2L_Ulv3 revealed structural organisation and active site architecture as well as ligand substrate binding and zinc ion coordinating residues typical for PL25 lyases; however, with a larger central active site cleft facilitating ulvan polysaccharide degradation.}, } @article {pmid41562608, year = {2026}, author = {Kos, D and Warr, B and Suchan, DM and Wadt, D and Russell, JN and Norfield, M and Liang, J and Jelinski, M and Cameron, ADS and Ruzzini, A}, title = {Survey of bacteria associated with septic arthritis in beef feedlot cattle.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {2}, pages = {e0167525}, pmid = {41562608}, issn = {1098-5336}, support = {20210572//Saskatchewan Agriculture Development Fund/ ; 2021-088//Saskatchewan Cattle Association/ ; //Natural Sciences and Engineering Research Council of Canada/ ; POC.35.23//Beef Cattle Research Council of Canada/ ; }, mesh = {Animals ; *Arthritis, Infectious/microbiology/veterinary ; Cattle ; *Cattle Diseases/microbiology ; *Bacteria/isolation & purification/genetics/classification/drug effects ; Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Canada ; }, abstract = {Septic arthritis (SA) is a cause of lameness in cattle attributed to bacterial infections. Mycoplasmopsis bovis is the best known and characterized etiological agent of SA; however, cases caused by diverse bacteria have been reported. Accordingly, we surveyed bacteria associated with septic and healthy joints from animals in western Canadian feedlots. Microbial community profiling showed that M. bovis was the most frequently detected pathogen in septic joints, followed by Metamycoplasma alkalescens and Trueperella pyogenes. In most cases, disease was ostensibly caused by a single pathogen, though polymicrobial infections and complex communities were also observed in DNA isolated from septic joints. The application of enhanced metagenomics by target DNA hybridization capture sequencing (CapSeq) provided more robust pathogen detection and characterization. CapSeq revealed resistance determinants that escaped detection using a conventional shotgun metagenomic approach. Notably, a series of nucleotide polymorphisms to M. bovis rrs, rrl, gyrA, and parC gene sequences were observed that confer resistance to macrolides and oxytetracycline-resistant T. pyogenes were also apparent in the CapSeq data. Complementary pathogen isolation, whole-genome sequencing, and phenotyping efforts were focused on the two most prominent pathogens, M. bovis and M. alkalescens, and corroborated metagenomic data sets.IMPORTANCEInformed antimicrobial use for the treatment of septic arthritis (SA) has been limited by overlooking the potential diversity of causative agents and our knowledge of their antimicrobial resistance (AMR) profiles. This survey begins to provide epidemiological insights, offering renewed appreciation of Metamycoplasma alkalescens as an etiological agent of SA and highlighting the prominence of important AMR determinants. Finally, the survey suggests that our knowledge of even the identities of the causative agents of SA is incomplete.}, } @article {pmid41563008, year = {2026}, author = {Karatzas, E and Beracochea, M and Baltoumas, FA and Aplakidou, E and Richardson, L and Fellows Yates, JA and Lundin, D and , and Buluç, A and Kyrpides, NC and Georgakopoulos-Soares, I and Pavlopoulos, GA and Finn, RD}, title = {nf-core/proteinfamilies: a scalable pipeline for the generation of protein families.}, journal = {GigaScience}, volume = {15}, number = {}, pages = {}, pmid = {41563008}, issn = {2047-217X}, support = {//European Union/ ; DE-AC02-05CH11231//Hellenic Foundation for Research and Innovation/ ; }, mesh = {*Proteins/chemistry/genetics ; *Software ; Metagenomics/methods ; *Computational Biology/methods ; Databases, Protein ; Sequence Alignment ; Algorithms ; Amino Acid Sequence ; }, abstract = {The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterized sequences with the few experimentally characterized ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein families closely resemble manually curated families in widely used databases.}, } @article {pmid41563943, year = {2026}, author = {Xiong, HF and Zhang, WT and Liu, Y and Hou, F and Liu, B and Cui, TT and He, ZY and Zhang, X and Zhao, R and Sun, LY}, title = {Successful Use of Sulbactam-Durlobactam in Treating Carbapenem-Resistant Acinetobacter baumannii Pneumonia and Sepsis After Liver Transplantation: A Case Report.}, journal = {The American journal of case reports}, volume = {27}, number = {}, pages = {e949738}, pmid = {41563943}, issn = {1941-5923}, mesh = {Humans ; Female ; *Sulbactam/therapeutic use ; *Liver Transplantation/adverse effects ; *Acinetobacter baumannii/drug effects ; *Acinetobacter Infections/drug therapy ; *Sepsis/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use ; Young Adult ; *Pneumonia, Bacterial/drug therapy/microbiology ; *Postoperative Complications/drug therapy ; Carbapenems/pharmacology ; }, abstract = {BACKGROUND Orthotopic liver transplantation is the primary treatment for end-stage liver disease; however, postoperative infections, especially those caused by carbapenem-resistant Acinetobacter baumannii (CRAB), remain a major cause of mortality due to limited therapeutic options. Sulbactam-durlobactam (SUL-DUR), a novel b-lactam/b-lactamase inhibitor combination, has shown potent activity against CRAB. This report describes the first reported use of SUL-DUR in a liver transplant recipient with CRAB pneumonia and sepsis. CASE REPORT A 22-year-old woman with acute liver failure underwent auxiliary liver transplantation. Postoperatively, she developed CRAB pneumonia and septicemia confirmed by imaging, bronchoscopy, and metagenomic next-generation sequencing. She received combination therapy with SUL-DUR (1 g/1 g every 8 h), meropenem, eravacycline, and neutralized polymyxin B. Blood and sputum cultures confirmed CRAB susceptibility to SUL-DUR. Following treatment, inflammatory markers (CRP, IL-6, PCT) and pathogen loads markedly decreased, leading to complete clinical resolution without significant adverse effects. The patient was successfully discharged after rehabilitation. CONCLUSIONS SUL-DUR demonstrated excellent efficacy and safety in treating CRAB pneumonia and sepsis after liver transplantation. This case supports Phase III trial data and suggests the potential for use in high-risk, immunocompromised populations. Further studies are warranted to validate its clinical role and inform future guidelines for multidrug-resistant infections.}, } @article {pmid41564488, year = {2026}, author = {Huang, Z and Shen, J and Wang, J and Wang, C and Liu, H and Tian, C and Feng, J and Wang, X}, title = {Seasonal dynamics of sedimentary dissolved organic matter in plateau lakes: Driving effects on microbial community and functional genes in elements cycling.}, journal = {Journal of environmental management}, volume = {399}, number = {}, pages = {128688}, doi = {10.1016/j.jenvman.2026.128688}, pmid = {41564488}, issn = {1095-8630}, mesh = {*Lakes/chemistry/microbiology ; Seasons ; *Dissolved Organic Matter/analysis ; *Geologic Sediments/chemistry ; Carbon ; *Microbiota ; }, abstract = {Plateau lakes, as sensitive zones to global climate change and critical hubs for land-water carbon exchange, remain understudied in terms of the seasonal dynamics of their sedimentary dissolved organic matter (DOM) and its interactions with microbial ecological function. This study employed Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic techniques to unravel the seasonal variations of DOM and their regulatory roles in microbial community and elements cycling. During the dry season, low water temperature (WT), dissolved oxygen (DO), and high electrical conductivity (EC) promoted accumulation of lignin-like and carboxyl-rich aliphatic molecules (CRAMs), with Fuxian Lake exhibiting the strongest sequestration. The subsequent wet period raised microbial biomass carbon (MBC) and easily oxidizable organic carbon (EOC), lowered average mass-to-charge ratios and increased both nominal hydrogen-to-carbon ratios (H/C) and the molecular lability index (MLB%). Labile sugars and peptides enhanced microbial α-diversity, whereas refractory compounds selected for specialist taxa and intensified community differentiation. Random forest identified sugars, peptides, O3S + O5S, biological index (BIX), and WT as core drivers of element cycling genes expression. Functional gene modules diverged along trophic status. The oligotrophic deep lake underwent seasonal turnover, whereas the eutrophic shallow lake preserved stable supermodules integrating multiple metabolic pathways to buffer perturbations. Anthropogenic disturbances elevated sulfur/nitrogen-containing heteroatomic compounds and threatened sediment carbon sinks and element cycling balance. This study advances the understanding of DOM-driven biogeochemical cycles and provides a scientific framework for managing multi-element interactions in climatically sensitive plateau lakes.}, } @article {pmid41564537, year = {2026}, author = {Asokan, S and Damilare, II and Kumar, S and Pandey, RK and Verma, G and Banerjee, N and Radhamanalan, G and Vijayan, S and Jacob, T and Rajeswary, D}, title = {From pandemic influenza to novel coronaviruses: emerging infectious diseases of the 21st century.}, journal = {Diagnostic microbiology and infectious disease}, volume = {114}, number = {4}, pages = {117277}, doi = {10.1016/j.diagmicrobio.2026.117277}, pmid = {41564537}, issn = {1879-0070}, mesh = {Humans ; *Communicable Diseases, Emerging/epidemiology/virology ; Animals ; *Pandemics ; *Influenza, Human/epidemiology ; *Coronavirus Infections/epidemiology ; Zoonoses/epidemiology ; SARS-CoV-2 ; COVID-19 ; }, abstract = {Emerging infectious diseases have risen significantly in the twenty-first century as ecological disruption, climate change, expanding human-animal interfaces, and global mobility intensify opportunities for pathogen transmission. This review synthesizes historical and contemporary evidence across viral, bacterial, fungal, and parasitic threats to characterize how diverse pathogens emerge and spread. Foundational events such as the 1918 influenza pandemic, mid-century influenza pandemics, the emergence of HIV/AIDS, and the eradication of smallpox provide context for understanding modern disease dynamics. In recent decades, coronaviruses including SARS, MERS, and SARS-CoV-2, pandemic H1N1, avian influenza subtypes, and major arboviruses such as dengue, chikungunya, Zika, West Nile virus, and yellow fever have demonstrated the rapidity with which zoonotic pathogens can disseminate globally. Viral hemorrhagic fevers including Ebola, Marburg, Lassa, and Crimean-Congo hemorrhagic fever remain critical threats, especially in regions with limited health-care capacity. Concurrently, antimicrobial resistance, the emergence of Candida auris, and the climate-driven expansion of endemic mycoses involving Histoplasma, Coccidioides, and Blastomyces highlight the increasing importance of fungal pathogens. Parasitic diseases such as artemisinin-resistant malaria, zoonotic trypanosomiasis, and expanding Leishmania transmission reflect shifting ecological conditions. These patterns are shaped by intersecting drivers including deforestation, wildlife trade, agricultural intensification, urban crowding, conflict, and rapid microbial evolution that enable spillover and sustained transmission. Although advances in genomic surveillance, metagenomic diagnostics, mRNA vaccines, monoclonal antibodies, and broad-spectrum antivirals have strengthened global response capacity, substantial gaps persist in equity, surveillance, and access to countermeasures. Strengthening One Health systems and resilient public health infrastructures is essential to anticipate and mitigate emerging infectious threats.}, } @article {pmid41564676, year = {2026}, author = {Liu, J and Zhang, W and Wang, R and Wu, S and Bai, X and Wang, X and Zhu, W and Ding, C}, title = {Functional decoupling between plant remediation efficacy and microbial metal resistance in iron tailings: A Robinia pseudoacacia-driven paradox.}, journal = {Ecotoxicology and environmental safety}, volume = {310}, number = {}, pages = {119760}, doi = {10.1016/j.ecoenv.2026.119760}, pmid = {41564676}, issn = {1090-2414}, mesh = {*Robinia/metabolism ; Biodegradation, Environmental ; *Soil Pollutants/metabolism/toxicity/analysis ; Mining ; *Iron/metabolism ; *Metals, Heavy/metabolism/toxicity/analysis ; Soil Microbiology ; Soil/chemistry ; Rhizosphere ; Hydrogen-Ion Concentration ; China ; *Environmental Restoration and Remediation/methods ; }, abstract = {Mining-derived iron tailings pose severe ecotoxicological risks through soil degradation and persistent heavy metal contamination. This study evaluates the ecorestoration potential of three tree species-Populus davidiana, Robinia pseudoacacia, and Rhus typhina-in iron tailings from China's Huluyu Iron Mine. Using an integrated assessment combining soil quality index (SQI), enzymatic activities, metagenomics, and partial least squares path modeling (PLS-PM), we demonstrate that Robinia pseudoacacia achieved the highest SQI (0.68) by significantly mitigating metal stress, which was associated with a marked reduction in soil pH (to 6.29). This acidification is consistent with the well-documented role of root exudates in legumes, alongside enhancing nutrient accumulation (total carbon: 24.8 g/kg; total nitrogen: 1.5 g/kg), and stimulating sucrase and phosphatase activities. Paradoxically, Robinia pseudoacacia soils exhibited minimal enrichment of microbial metal resistance genes, challenging the prevailing "Rhizosphere Synergy Hypothesis." Instead, Robinia pseudoacacia's efficacy relied on functional decoupling from microbial metal detoxification pathways, favoring metabolic optimization of carbon/nitrogen cycling and organic acid-driven pH regulation. PLS-PM confirmed soil chemical properties (pH, total carbon, nitrogen) and enzymatic activities as direct positive drivers of SQI (p < 0.05), while heavy metal content exerted significant negative effects (r = -0.55, p < 0.001). These findings establish RP as an optimal species for iron tailings restoration, reconciling soil fertility enhancement with a potential reduction in metal bioavailability mediated by soil acidification. We propose a predictive SQI framework for selecting remediation species in metalliferous environments, offering critical insights into sustainable management of mining-associated ecotoxicological risks.}, } @article {pmid41564978, year = {2026}, author = {Yuan, C and Jin, P and He, Z and Guo, J and Xiong, M and Sun, J and Wang, L and Wang, Z and Han, N and Feng, W and Hou, Y and Qi, H and Jia, Z}, title = {Maxing Shigan decoction serves as a key component of Lianhua Qingwen in alleviating lung and gut injury by restoring gut microbiota homeostasis and inhibiting inflammation via TLR4/NF-κB and JAK2/STAT3 dual regulation.}, journal = {Microbial pathogenesis}, volume = {212}, number = {}, pages = {108285}, doi = {10.1016/j.micpath.2026.108285}, pmid = {41564978}, issn = {1096-1208}, mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology ; Toll-Like Receptor 4/metabolism ; Janus Kinase 2/metabolism ; STAT3 Transcription Factor/metabolism ; NF-kappa B/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Acute Lung Injury/drug therapy ; Male ; Homeostasis/drug effects ; Signal Transduction/drug effects ; Mice ; Lung/pathology/drug effects ; *Inflammation/drug therapy ; Colitis, Ulcerative/drug therapy/chemically induced ; Cytokines/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Intestinal Barrier Function ; Lipopolysaccharides ; }, abstract = {Lianhua Qingwen (LHQW), a clinically validated herbal medicine containing Maxing Shigan Decoction (MXSGT) and others, shows broad efficacy in various respiratory disease. However, its regulatory role on the gut-lung axis, particularly the contribution of its MXSGT components, remains unexplored. This study employed a formula-disassembled approach to decipher this mechanism. Three preparations, including the complete LHQW prescription, LHQW excluding MXSGT components (LHQW-MXSGT), and MXSGT along, were administered to LPS-induced acute lung injury and DSS-induced ulcerative colitis to evaluate their therapeutic effects via the gut-lung axis. Pathological changes, mucosal barrier integrity, inflammatory cell infiltration and pro-inflammatory cytokine levels were evaluated by H&E staining, histochemical staining, immunofluorescence, ELISA, RT-qPCR and Western blot. Metagenomic analysis (16S rDNA sequencing) was conducted to examine their regulatory role of gut microbiota. Network pharmacology analysis and cellular validation was employed to explore their underlying mechanisms. Our analyses demonstrated that LHQW and MXSGT, but not LHQW-MXSGT, significantly attenuated lung/intestinal pathology damage, reduced pro-inflammatory cytokines (TNF-α, IL-1β, IL-6), and restored gut barrier proteins (ZO-1, Occludin, MUC2). LHQW/MXSGT suppressed pathogenic bacteria (Escherichia coli, Salmonella, Klebsiella pneumoniae) while enriching Akkermansia muciniphila, correlating with decreased systemic LPS. Network pharmacology and subsequent validation identified dual inhibition of TLR4/NF-κB and JAK2/STAT3 pathways as key mechanism of MXSGT. In conclusion, MXSGT serves a pivotal pharmacologically active component of LHQW for its gut-lung axis regulation, acting through gut microbiota homeostasis restoration, intestinal barrier integrity maintenance, and anti-inflammatory signaling pathways, providing compelling scientific evidence supporting LHQW's potential therapeutic application in managing diseases characterized by comorbid gut and lung inflammation.}, } @article {pmid41565402, year = {2026}, author = {Zhou, Y and Wang, H and Guo, L and Liu, X and Wang, X and Liu, Y and Shang, M and Zheng, B and Li, K and Liu, L and Li, J and Ding, G}, title = {Human umbilical cord MSC-derived exosomes attenuate radiation-induced pulmonary fibrosis via remodeling the gut-lung axis in mice.}, journal = {Life sciences in space research}, volume = {48}, number = {}, pages = {204-215}, doi = {10.1016/j.lssr.2025.11.011}, pmid = {41565402}, issn = {2214-5532}, mesh = {Animals ; *Exosomes/transplantation/metabolism ; Humans ; Mice ; *Mesenchymal Stem Cells/cytology/metabolism ; *Lung/pathology/metabolism ; *Umbilical Cord/cytology ; Male ; *Pulmonary Fibrosis/etiology/therapy ; Gastrointestinal Microbiome ; Mice, Inbred C57BL ; *Radiation Pneumonitis/therapy ; Intestinal Barrier Function ; }, abstract = {OBJECTIVE: To investigate whether human umbilical cord mesenchymal stem cell-derived exosomes (hUC-MSC-Exos) attenuate radiation-induced pulmonary fibrosis (RIPF) through modulation of the gut-lung axis.

METHODS: The therapeutic efficacy of hUC-MSC-Exos was evaluated in a mouse model of RIPF through histopathology and western blot analysis of fibrosis markers (α-SMA, Vimentin, and E-cadherin). Gut barrier integrity (ZO-1, Occludin) and intestinal inflammation (IL-6, IL-1β) were examined using immunohistochemistry, RT-qPCR, and ELISA. Gut microbial composition and metabolic profiles were characterized via metagenomics and untargeted metabolomics, followed by integrated bioinformatics analyses to identify key pathways and metabolites.

RESULTS: hUC-MSC-Exos significantly reduced pulmonary collagen deposition and restored fibrosis markers expression, concomitant with enhanced gut barrier function and attenuated intestinal inflammation. Multi-omics analysis revealed restoration of gut microbiota homeostasis and metabolic reprogramming, with the alanine, aspartate, and glutamate pathway being notably co-regulated. L-Glutamic acid was the most significantly altered metabolite and correlated significantly positively with the severity of pulmonary fibrosis and gut dysfunction. Gut microbiota associated with L-Glutamic acid (e.g., Duncaniella, Ruminococcus) were also significantly restructured.

CONCLUSIONS: hUC-MSC-Exos attenuate RIPF through a comprehensive remodeling of the gut-lung axis, in which L-Glutamic acid and its associated microbiota serve as potential mediators. These findings highlight the gut-lung axis as a promising therapeutic target for RIPF.}, } @article {pmid41565669, year = {2026}, author = {Schneeberger, PHH and Dommann, J and Rahman, N and Hürlimann, E and Sayasone, S and Ali, S and Coulibaly, JT and Keiser, J}, title = {Profound taxonomic and functional gut microbiota alterations associated with trichuriasis: cross-country and country-specific patterns.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {45}, pmid = {41565669}, issn = {2055-5008}, support = {101019223/ERC_/European Research Council/International ; }, mesh = {*Trichuriasis/parasitology/microbiology/epidemiology ; Humans ; Animals ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Fatty Acids, Volatile/metabolism ; *Bacteria/classification/genetics/isolation & purification ; Cote d'Ivoire ; Tanzania ; Trichuris ; Feces/microbiology/parasitology ; Mucins/metabolism ; }, abstract = {The human gut microbiota is vital for immune function, metabolism, and resistance to pathogens. Soil-transmitted helminths like Trichuris trichiura can disrupt this microbial community, but the extent and functional significance of these disruptions across diverse regions remain unclear. We investigated the impact of T. trichiura infection on gut microbiota composition and function in three endemic regions-Côte d'Ivoire, Laos, and Tanzania-using standardized, high-resolution metagenomic profiling. Our findings reveal consistent depletion of key short-chain fatty acid (SCFA) producers, including Blautia sp. MSJ 9 and Holdemanella biformis, and enrichment of mucin-degrading genera such as Ruminococcus and Bacteroides. These changes coincided with increased microbial utilization of host-derived carbohydrates and destabilization of microbial networks, notably with the emergence of Segatella copri in infected individuals. Although taxa-level responses varied by region, similar trends in SCFA depletion and mucin degradation were observed across sites, pointing to a potentially shared metabolic response to infection. These alterations suggest compromised gut barrier function and immune modulation, potentially promoting parasite persistence. Our results underscore the potential of microbiome-based strategies, such as targeted probiotics or dietary interventions, to support helminth control by restoring microbial balance and improving host resilience.}, } @article {pmid41565819, year = {2026}, author = {Ricci, L and Heidrich, V and Punčochář, M and Armanini, F and Ciciani, M and Nabinejad, A and Fazaeli, F and Piperni, E and Servais, C and Pinto, F and Valles-Colomer, M and Asnicar, F and Segata, N}, title = {Baby-to-baby strain transmission shapes the developing gut microbiome.}, journal = {Nature}, volume = {651}, number = {8104}, pages = {191-200}, pmid = {41565819}, issn = {1476-4687}, support = {/ERC_/European Research Council/International ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Infant ; Female ; Feces/microbiology ; Male ; Infant, Newborn ; Longitudinal Studies ; Anti-Bacterial Agents/pharmacology ; Siblings ; Adult ; Bacteria/classification/genetics/isolation & purification/drug effects ; Metagenomics ; }, abstract = {The early infant microbiome is largely primed by microbial transmission from the mother between birth and the first few weeks of life[1-3], but how interpersonal transmission further shapes the developing microbiome in the first year remains unexplored. Here we report a metagenomic survey to model microbiome transmission in the nursery setting among babies attending the first year, their educators and their families (n = 134 individuals). We performed dense longitudinal microbiome sampling (n = 1,013 faecal samples) during the first year of nursery and tracked microbial strain transmission within and between nursery groups across 3 different facilities. We detected extensive baby-to-baby microbiome transmission within nursery groups even after only 1 month of nursery attendance, with nursery-acquired strains accounting for a proportion of the infant gut microbiome comparable to that from family by the end of the first term. Baby-to-baby transmission continued to grow over the nursery year, in an increasingly intricate transmission network with single strains spreading in some classes, and with multiple baby-acquisition and species-transmissibility patterns. Having siblings was associated with higher microbiome diversity and reduced strain acquisition from nursery peers, while antibiotic treatment was the condition that most accounted for the increased influx of strains. This study shows that microbiome transmission between babies is extensive during the first year of nursery, and points to social interactions in infancy as crucial drivers of infant microbiome development.}, } @article {pmid41566339, year = {2026}, author = {Fernández-Trapote, E and Cobo-Díaz, JF and Oliveira, M and Puente, A and Berdejo, D and Puente, H and Cordero-García, R and López, M and Prieto, M and Argüello, H and Alvarez-Ordóñez, A}, title = {Microbiome and resistome successions in pig carcasses and fresh pork meat throughout slaughtering, processing and shelf-life.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {67}, pmid = {41566339}, issn = {2049-2618}, support = {FPU21/03421//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; PRE2021-098910//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; CNS2022-136066//Ministerio de Ciencia, Innovación y Universidades, Spain/ ; No 818368//European Commission under the European Union´s Horizon 2020/ ; PID2020-118813GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; }, mesh = {Animals ; Swine/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Acinetobacter/isolation & purification/genetics ; Abattoirs ; *Pork Meat/microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Metagenomics ; Food Storage ; Metagenome ; Food Handling ; Food, Processed ; Pseudomonas/isolation & purification/genetics ; Brochothrix/isolation & purification/genetics ; Food Microbiology ; }, abstract = {BACKGROUND: Slaughterhouses and meat cutting plants represent potential hotspots for the spread and transfer of spoilage and pathogenic, including antimicrobial resistant, bacteria to meat and meat products. Here, we characterise the progression of the microbiome and resistome of two pork cuts (loin and sirloin) at different stages of processing, from the slaughter line to the end of shelf-life. To this end, we analysed samples from facility surfaces, carcasses, and meat cuts using whole metagenome sequencing.

RESULTS: The taxonomic and antimicrobial resistance gene (ARG) profiles of carcasses and meat cuts were significantly influenced by the point of sampling and the processing room. The facility surfaces were found to be the main source of some abundant genera, such as Anoxybacillus, Acinetobacter, Pseudomonas, and Brochothrix, in carcasses and meat cuts. A total of 1,291 metagenome-assembled genomes were reconstructed, corresponding to the most prevalent species identified in the taxonomic analysis at the read level. A reduction in bacterial and ARGs richness and diversity was observed for carcasses and meat cuts along the production chain, which suggests that processing procedures are effective in reducing bacterial and ARGs loads. Nonetheless, an increase in the ARGs load was observed at two sampling points: the carcass after evisceration and the sirloin at the end of its shelf-life (in this case linked to the increase of a single gene, tet(L)). The ARGs most frequently detected were those associated with resistance to tetracyclines, aminoglycosides, and lincosamides. Acinetobacter (in processing environments and carcass/meat samples) and Staphylococcus (in carcasses and meat) were identified as the main genera associated with the ARGs found.

CONCLUSIONS: Overall, our results provide the most detailed metagenomics-based perspective on the microbial successions of pig carcasses and fresh meat cuts during slaughtering, processing, and commercialisation. The observations made suggest that selection pressures imposed by processing steps and contact with facility surfaces contribute to shaping the microbiome and resistome of the two pork products throughout their production line and shelf-life. Video Abstract.}, } @article {pmid41567008, year = {2026}, author = {Zhao, S and Rogers, MJ and Ding, C and He, J}, title = {Stable Function, Dynamic Phylotypes: Microdiversity as a Reservoir for Resilience in Dehalococcoides.}, journal = {Environmental science & technology}, volume = {60}, number = {4}, pages = {3364-3373}, doi = {10.1021/acs.est.5c14525}, pmid = {41567008}, issn = {1520-5851}, mesh = {*Dehalococcoides/metabolism/genetics ; Phylogeny ; Biodiversity ; }, abstract = {Organohalide-respiring bacteria (OHRB) are key contributors to global halogen cycling and mitigation of anthropogenic halogenated pollutants, yet their persistence is challenged by slow growth and restricted metabolic capacity. The mechanisms supporting long-term functional stability remain unclear. As a key OHRB, Dehalococcoides faces similar constraints, including declining abundance and loss or divergence of functional genes in bioaugmentation. Here we demonstrate that strain-level microdiversity within Dehalococcoides supports the resilience of community-scale dehalogenation. In AEDhc, a reconstructed consortium derived from eight Dehalococcoides-containing enrichment cultures, sequencing of a Dehalococcoides-specific marker gene revealed 30 distinct Dehalococcoides phylotypes coexisting within the community. Despite fluctuations in phylotype abundance over successive transfers, AEDhc consistently debrominated tetra- and pentabrominated diphenyl ethers (0.39 ± 0.06 - 0.45 ± 0.05 μM Br[-]/d), producing no detectable accumulation of intermediates. Proteomics analyses revealed that among 71 putative reductive dehalogenase (RDase) genes identified in metagenomic analysis, expression was consistently dominated by PcbA1-like and TceA-like RDases across transfers. These findings demonstrated that Dehalococcoides phylotypes can coexist and fluctuate dynamically even under constant cultivation conditions, with genetic variation serving as a reservoir of metabolic potential. Such microdiversity enhances functional stability and ecological resilience, highlighting the need to consider strain-level heterogeneity in bioremediation strategies.}, } @article {pmid41567631, year = {2025}, author = {Wang, S and Hu, Y and Li, X and Ou, Y and Chen, J and Chen, Y and Chen, J and Bai, K and Xu, F and Wang, X and Du, H and Yuan, D and Yang, Z and Yuan, J and Niu, H}, title = {Gut microbiota-dependent anti-inflammatory mechanisms of berberine in ameliorating hypertension: role of SCFAs, LPS reduction, and STAT3 signaling.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1696934}, pmid = {41567631}, issn = {1663-9812}, abstract = {BACKGROUND: Hypertension is a chronic disease closely related to vascular remodeling, inflammatory response and intestinal flora disorders. Traditional Chinese medicines, especially Rhizoma Coptidis, are becoming increasingly popular as a possible cardioprotective drug. Berberine, the main active ingredient of Rhizoma Coptidis, has various pharmacological activities, but its specific mechanism of regulating blood pressure through intestinal flora is not clear.

METHODS: In this study, the potential targets of berberine were predicted using network pharmacology, and its antihypertensive mechanism was validated in spontaneously hypertensive rats (SHR). A comprehensive evaluation integrating non-invasive blood pressure measurement, echocardiography, histological analyses (H&E and Masson staining), immunohistochemistry, qPCR, metagenomic sequencing, and untargeted metabolomics was performed to investigate the effects of berberine on cardiovascular remodeling, intestinal barrier integrity, gut microbial composition, and metabolic profiles.

RESULTS: Network pharmacology screened 160 common targets of berberine and hypertension, among which STAT3 may play a key role. Animal experiments confirmed that berberine significantly reduced SHR blood pressure and improved aortic fibrosis and cardiac function. In addition, berberine repaired intestinal barrier damage, upregulated ZO-1 and Occludin expression, and significantly altered the structure of the intestinal flora, increasing the abundance of Short-chain fatty acids (SCFAs) - producing bacteria (e.g., Marvinbryantia, Bacteroides), while decreasing pro-inflammatory bacteria (e.g., Mycoplasma, Treponema). Metabolomics analysis showed that berberine increased fecal SCFAs levels and decreased serum Lipopolysaccharide (LPS). Molecular docking and experimental validation showed that berberine attenuated the inflammatory response by inhibiting STAT3 activation and decreasing colonic IL-6 expression.

CONCLUSION: Berberine exerts antihypertensive effects by regulating the gut flora-SCFAs-LPS-IL6-STAT3 axis, improving intestinal barrier function, and reducing systemic inflammation. This study provides a new mechanistic basis for berberine treatment of hypertension.}, } @article {pmid41568034, year = {2025}, author = {Yu, F and Song, J and Qi, L and Liu, J and Yang, Y and Li, W and Li, L and Ma, ZS}, title = {Gene and function diversity-area relationships in the inflammatory bowel disease fecal and mucosal microbiome.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1660973}, pmid = {41568034}, issn = {1664-302X}, abstract = {The diversity-area relationship (DAR), an extension of the classic species-area relationship (SAR), provides a powerful framework for understanding how biodiversity scales across space. In this study, we applied DAR and its metagenomic counterpart (m-DAR) to investigate the spatial scaling of metagenomic genes (MGs) and metagenomic functional gene clusters (MFGCs) of seven functional databases in the gut microbiomes of individuals with inflammatory bowel disease (IBD) and healthy cohorts. Using shotgun sequencing data from 42 mucosal and 22 fecal samples from both healthy and IBD cohorts, we modeled how this MGs and MFGCs accrues with area (samples), estimating diversity scaling parameters (z), pair-wise diversity overlap (PDO), and maximal accrual diversity (MAD), which reflects the total potential diversity. We found that mucosal communities exhibited greater dissimilarity (less pair-wise diversity overlap) between individuals than fecal cowmmunities at the levels of gene richness and evenness (q = 1, 2), whereas fecal communities showed a stronger influence from dominant, abundant genes (q = 2, 3). Furthermore, healthy gut microbiomes showed greater similarity than those of IBD at the level of gene richness (q = 0), but showed greater dissimilarity at the level of abundant genes and dominant genes. Healthy gut microbiomes generally demonstrated a higher potential total diversity compared to those from IBD patients. Notably, fecal samples captured a broader range of microbial diversity than mucosal samples. Additionally, mucosal communities showed greater dissimilarity than fecal communities in almost all the MFGCs of the seven databases except ARDB, which showed the same trend as MGs. We also identified that specific functional clusters related to antibiotic resistance, such as genes for chloramphenicol and vancomycin resistance, displayed distinct scaling behaviors, suggesting their potential role in IBD pathogenesis. These findings demonstrate that the gut microbiome in IBD is not merely less diverse but is fundamentally restructured in its spatial architecture. The application of DAR provides a novel, quantitative insight to diagnose and understand this dysbiosis, moving beyond simple diversity metrics to capture the spatial diversity scaling of microbial genes and functions.}, } @article {pmid41568044, year = {2025}, author = {Kan, Y and Ma, XY and Wang, YL and Sun, B and Wang, S}, title = {A comprehensive comparison of web-based tools for amplicon-metagenomic analysis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1711000}, pmid = {41568044}, issn = {1664-302X}, abstract = {Amplicon sequencing provides a suitable approach for microbiome profiling, supported by a variety of R-based and web-based tools. In this review, we systematically evaluated eight freely accessible web-based tools suitable for users without scripting experience, comparing their performance across modules including alpha and beta diversity, taxonomic composition, differential comparison, network and correlation analysis, functional profiling, machine learning, tree-plot and user experience. While all tools exhibit limited data filtering and normalization options, performance varied considerably across modules. Mian and MicrobiomeAnalyst 2.0 excelled in alpha diversity analysis and taxonomic composition analysis, METAGENassist outperformed others in beta diversity, and MicrobiomeAnalyst 2.0 achieved the highest score in differential comparison and functional analysis. Namco and Mian outperform in network analysis and correlation analysis, respectively. Machine-learning functions were comparable across animalcules, MicrobiomeAnalyst 2.0 and METAGENassist, with the best treeplot visualization in animalcules and MicrobiomeAnalyst 2.0. And, user experience was highest for animalcules and Mian. Overall, MicrobiomeAnalyst 2.0 achieving the highest overall performance, followed by Mian and Namco. Several limitations among evaluated tools include inconsistent accessibility, diverse input data formats, restricted feature sets, and incomplete retention of key information in exported figures. Future development should integrate preprocessing, interactive visualization and figure export, alongside advanced statistical methods, multi-omics integration and meta-analytical capabilities, to enhance flexibility, reproducibility and interpretability. This comprehensive assessment provides a practical reference for researchers in selecting the most suitable web-based tools for specific microbiome analysis tasks, highlighting the importance of both module-specific performance and overall tool capabilities.}, } @article {pmid41568321, year = {2026}, author = {Yahyapour, A and Najafi, A and Ahmadi, A and Salarizadeh, N}, title = {Immunoprotective and neuroprotective properties of gut microbiome in psoriasis.}, journal = {Journal of translational autoimmunity}, volume = {12}, number = {}, pages = {100348}, pmid = {41568321}, issn = {2589-9090}, abstract = {Psoriasis impacts nearly 100 million people globally and is associated with neuropsychiatric comorbidities such as depression and anxiety. With gut microbiome dysbiosis serving as a primary pathophysiological factor, the gut-brain-skin axis provides a crucial framework for understanding this relationship. This review evaluates the mechanisms of the gut-brain-skin axis in psoriasis pathophysiology and assesses the therapeutic potential of microbiome-based treatments, combining preclinical, clinical, and multi-omics data. Patients with psoriasis show specific gut dysbiosis patterns, including reduced microbial diversity, lower SCFA-producing bacteria (especially Faecalibacterium and Akkermansia), and increased pro-inflammatory bacteria. This microbial imbalance damages intestinal barrier integrity, triggers systemic inflammation, activates cutaneous Th17 pathways, and induces neuroinflammation through blood-brain barrier disruption. Axis communication occurs through immune-inflammatory mechanisms mediated by SCFAs and neuroendocrine pathways involving microbially-derived neurotransmitters (GABA, serotonin, dopamine). Metagenomic research indicates functional deficiencies in neurotransmitter and SCFA synthesis pathways are more significant than taxonomic alterations. Machine learning models can utilize these functional features to identify patients at risk for neuropsychiatric comorbidities and predict treatment response. Recent randomized controlled trials demonstrate that targeted interventions (probiotics, prebiotics, postbiotics, fecal microbiota transplantation) significantly improve Psoriasis Area and Severity Index scores, inflammatory markers, and microbiota composition. The evidence supports a shift toward integrated microbiome strategies, emphasizing functional approaches including mitochondrial therapies, psychobiotics, precision nutrition, and multi-omics-guided therapies.}, } @article {pmid41568738, year = {2026}, author = {Warren, A and Wynia, Z and Corr, PG and Devin, MF and Celikkol, Z and Gordon, L and Farah, M and Karam, M and Villarreal, D and Jackson, SA and Frame, LA}, title = {The microbiota-gut-brain axis in mild cognitive impairment and Alzheimer's disease: a scoping review of human studies.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {22}, number = {1}, pages = {e71023}, pmid = {41568738}, issn = {1552-5279}, support = {//TMCity/ ; }, mesh = {Humans ; *Cognitive Dysfunction/microbiology ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Probiotics/therapeutic use ; *Brain ; }, abstract = {Alzheimer's disease (AD) is projected to become the highest-burden neurological disorder globally. Mounting evidence implicates the gut microbiome in AD pathogenesis. This scoping review of gut microbiomes in mild cognitive impairment (MCI) and AD included dietary and probiotic interventions. We included original research and systematic reviews/meta-analyses. Animal and non-English studies were excluded. We searched PubMed, Scopus, and Cochrane Library through February 2023. Using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA)-Extension for Scoping Reviews (ScR) checklist, we screened 4751 articles, with 58 meeting predefined inclusion criteria. Our results demonstrated that gut dysbiosis was frequently reported in MCI and AD, including increased Pseudomonadota and Actinomycetota in AD and reduced diversity in some cases. Probiotic and dietary interventions showed promise in modulating cognition and microbiota, inconsistently. Emerging evidence links dysbiosis to cognitive decline; however, methodological heterogeneity and limited follow-up impede causal inference. Research should prioritize standardized protocols, functional microbiome analysis, and longitudinal human studies to clarify therapeutic potential. HIGHLIGHTS: Gut dysbiosis is a common feature of MCI and AD, with phylum-level microbial shifts frequently observed. Pseudomonadota and Actinomycetota are enriched in AD across multiple human studies. Beneficial genera like Faecalibacterium and Roseburia are consistently reduced in MCI and AD in a small number of studies. Probiotic and dietary interventions are promising to modulate the microbiota-cognition axis. More longitudinal human studies are needed to assess causal microbiome relationships.}, } @article {pmid41569097, year = {2026}, author = {Ayala-Montaño, S and Afolayan, AO and Kociurzynski, R and Loeber, U and Reuter, S}, title = {Mitigation and detection of putative microbial contaminant reads from long-read metagenomic datasets.}, journal = {Microbial genomics}, volume = {12}, number = {1}, pages = {}, pmid = {41569097}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *DNA Contamination ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; *Bacteria/genetics/classification/isolation & purification ; }, abstract = {Metagenomic sequencing of clinical samples has significantly enhanced our understanding of microbial communities. However, microbial contamination and host-derived DNA remain a major obstacle to accurate data interpretation. Here, we present a methodology called 'Stop-Check-Go' for detecting and mitigating contaminants in metagenomic datasets obtained from neonatal patient samples (nasal and rectal swabs). This method incorporates laboratory and bioinformatics work combining a prevalence method, coverage estimation and microbiological reports. We compared the 'Stop-Check-Go' decontamination system with other published decontamination tools and commonly found poor performance in decontaminating microbiologically negative patients (false positives). We emphasize that host DNA decreased by an average of 76% per sample using a lysis method and was further reduced during post-sequencing analysis. Microbial species were classified as putative contaminants and assigned to 'Stop' in nearly 60% of the dataset. The 'Stop-Check-Go' system was developed to address the specific need of decontaminating low-biomass samples, where existing tools primarily designed for short-read metagenomic data showed limited performance.}, } @article {pmid41569365, year = {2026}, author = {Duarte, M and Mansilha, C and Melo, A and Sobral, D and Ferreira, R and Gomes, JP and Rebelo, H and Veber, A and Puskar, L and Schade, U and Jordao, L}, title = {Detection of polycyclic aromatic hydrocarbons, microplastic presence and characterization of microbial communities in the soil of touristic zones at Alqueva's edges (Alentejo, Portugal).}, journal = {Environmental science and pollution research international}, volume = {33}, number = {4}, pages = {1447-1458}, pmid = {41569365}, issn = {1614-7499}, mesh = {Portugal ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Soil Pollutants/analysis ; *Microplastics/analysis ; Environmental Monitoring ; *Soil Microbiology ; Bacteria ; Soil/chemistry ; Microbiota ; }, abstract = {Environmental pollution is a growing concern. Here, we assessed the occurrence of two groups of persistent organic pollutants (POPs-polycyclic aromatic hydrocarbons (PAHs) and microplastics (MPs)) and bacterial populations in the topsoil of three tourist spots located at the Alqueva's edges during 1 year, once per season. Soil chemical analysis revealed low content of total organic carbon, pH close to neutrality, and nitrogen and phosphorus levels consistent with acquisition of these nutrients only by atmospheric deposition. PAH's concentrations were in the range of ng/kg, being significantly below the "reference values" for contaminated soils. Nevertheless, potentially carcinogenic PAHs, detected at all locations, raise ecotoxicological concerns. Polyamide, polyester, polystyrene, and styrene acrylonitrile resin MPs were found. Six bacterial phyla constitute the core microbiome in the three locations and include genera of bacteria reported as plastic degraders, such as Bacillus, Exiguobacterium, Paenibacillus, and Pseudomonas. The presence of POPs, even at low levels, in the soil at the edges of a water reservoir should be monitored. The identification of bacteria reported as plastic degraders in the soil, and previously in the water, is promising, and their ability to spontaneously ensure the detoxification of the ecosystem should be further investigated.}, } @article {pmid41570020, year = {2026}, author = {Beuker, C and Schulte-Mecklenbeck, A and Wirth, T and Kleffner, I and Thomas, C and Strunk, D and Schmidt-Pogoda, A and Gross, CC and Klotz, L and Minnerup, J}, title = {Spontaneous cervical artery dissection is associated with a distinct peripheral immune cell signature.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0340592}, pmid = {41570020}, issn = {1932-6203}, mesh = {Humans ; Male ; Female ; Middle Aged ; Adult ; Case-Control Studies ; *Leukocytes, Mononuclear/immunology ; Aged ; Killer Cells, Natural/immunology ; CD4-Positive T-Lymphocytes/immunology ; Dissection, Blood Vessel ; Flow Cytometry ; *Vertebral Artery Dissection/immunology ; }, abstract = {OBJECTIVES: Despite being a major cause of ischemic stroke in young adults, the biological underpinnings of cervical artery dissection (CeAD) remain poorly defined. Recent data implicate immune activation as a potential contributor. We aimed to determine whether patients with CeAD display a distinct peripheral immune signature, which may provide insights into pathogenic inflammatory processes.

METHODS: Peripheral blood mononuclear cells (PBMCs) from patients with spontaneous CeAD (n = 7 without and n = 11 with ischemic stroke) and ten age-matched healthy controls were analyzed via multi-color flow cytometry. Immune cell composition and activation markers were assessed, and sparse partial least squares discriminant analysis (sPLS-DA) was employed to identify CeAD-associated immune features. A secondary comparison with ischemic stroke controls was included to assess the specificity of identified immune alterations.

RESULTS: Compared to healthy controls, CeAD patients displayed increased frequencies of CD4 ⁺ T cells and decreased natural killer T (NKT) cells. sPLS-DA demonstrated clear separation of CeAD and control immune profiles, driven by increased CD28 expression on naïve CD8 ⁺ T cells, NKp46 on NK cells, and IL-2Rα (CD25) on myeloid dendritic cells (mDC2). Elevated granzyme K in naïve CD8 ⁺ T cells indicated enhanced cytotoxic potential, while regulatory T cells were diminished. These alterations were largely preserved when compared to ischemic stroke controls, suggesting CeAD-specific immune activation. No microbial pathogens were detected by untargeted metagenomic sequencing.

DISCUSSION: CeAD is associated with a distinct peripheral immune signature characterized by enhanced cytotoxic activity and reduced regulatory features. These alterations may reflect a post-infectious autoimmune mechanism triggering CeAD or a secondary immune-inflammatory response to vascular injury. Larger, longitudinal studies are needed to clarify causality and assess whether immune modulation could serve as a therapeutic target in CeAD.}, } @article {pmid41570402, year = {2026}, author = {Nitert, MD and Sternes, PR and Altemani, F and Callaway, LK and McIntyre, H and Tyson, GW and Barrett, HL}, title = {Gut microbiota is different before the development of preeclampsia.}, journal = {Pregnancy hypertension}, volume = {43}, number = {}, pages = {101415}, doi = {10.1016/j.preghy.2026.101415}, pmid = {41570402}, issn = {2210-7797}, mesh = {Humans ; Female ; Pregnancy ; *Pre-Eclampsia/microbiology/physiopathology ; *Gastrointestinal Microbiome ; Adult ; Feces/microbiology ; Blood Pressure ; Case-Control Studies ; }, abstract = {OBJECTIVES: The gut microbiota contributes to the regulation of blood pressure during and outside pregnancy. Preeclampsia (PE) is characterised by the development of hypertension along with renal, liver or other systemic complications. In women with PE, alterations in the gut microbiota composition have been reported.

STUDY DESIGN: We investigated whether changes in the gut microbiota composition were present before the onset of symptoms in a group of 10 women who developed late-onset PE and 24 women who remained normotensive throughout pregnancy. Faecal samples were obtained at 28 weeks' gestation from a subset of participants of the Study of PRobiotics IN Gestational diabetes (SPRING) and sequenced by metagenomic sequencing.

MAIN OUTCOME MEASURES: Taxonomic and functional characteristics were compared between the groups.

RESULTS: There were no taxonomic or functional differences in alpha diversity; however, for beta diversity, women who developed PE demonstrated a different taxonomic composition compared to women who remained normotensive. Women who developed PE had lower abundance of numerous taxa and functions. Both systolic and diastolic blood pressure were correlated with the abundances of specific species, though members of the same genus did not show consistency in the direction of correlation.

CONCLUSION: Despite a limited sample size, this study demonstrates numerous taxonomic and functional alterations in the gut microbiota composition. However, a clear signature to identify women at high risk of developing late-onset PE remains to be uncovered. The species-level data indicate that the regulation of blood pressure by the gut microbiota in pregnancy is complex and needs further investigation.}, } @article {pmid41570486, year = {2026}, author = {Lahariya, R and Anand, G and Kumari, B and Priyadarshi, K}, title = {Postbiotics and the gut-brain axis: A mechanistic review on modulating neuroinflammation and cognitive aging.}, journal = {Journal of neuroimmunology}, volume = {413}, number = {}, pages = {578870}, doi = {10.1016/j.jneuroim.2026.578870}, pmid = {41570486}, issn = {1872-8421}, mesh = {Humans ; Animals ; *Neuroinflammatory Diseases/metabolism/microbiology ; *Brain-Gut Axis/physiology/drug effects ; *Gastrointestinal Microbiome/physiology/drug effects ; *Cognitive Aging/physiology ; *Probiotics/administration & dosage ; *Brain/metabolism ; *Dysbiosis/metabolism ; *Aging ; }, abstract = {Aging triggers gut microbiota dysbiosis that disrupts the gut-brain axis (GBA), promoting neuroinflammation and neurodegeneration. Elderly exhibit reduced microbial diversity, depleted beneficial bacteria, and expanded pathobionts, elevating neurotoxic metabolites-lipopolysaccharides (LPS), trimethylamine-N-oxide, kynurenine derivatives, and secondary bile acids. These drive "inflammaging," blood-brain barrier breakdown, microglial activation, mitochondrial impairment, and proteinopathies in Alzheimer's and Parkinson's disease. Conversely, neuroprotective metabolites from commensals-short-chain fatty acids, indole-3-propionic acid, and urolithins-preserve gut integrity, suppress inflammation, upregulate BDNF for synaptic plasticity, and enhance mitophagy. Postbiotics, stable probiotic-derived bioactives (butyrate, polyphenol metabolites, and lactate derivatives), surpass live probiotics in safety and precision. They modulate GBA via histone deacetylase inhibition, GPR41/43 signaling, NF-κB blockade, and microglial M2 shift, blocking LPS translocation and bolstering neuronal resilience. Preclinical rodent studies demonstrate robust neuroprotection, but human translation reveals challenges: inter-individual microbiota variability (diet/genetics/comorbidities), inconsistent metabolite absorption/brain penetration between species, methodological limitations (16S rRNA vs. functional metagenomics), postbiotic standardization barriers, and sparse Phase I/II trials showing biomarker benefits without cognitive endpoints. This review synthesizes gut dysbiosis-metabolite-brain aging mechanisms, positioning postbiotics as precision therapeutics. Multi-omics stratified controlled trials are essential to validate long-term efficacy for delaying neurodegeneration and extending cognitive health.}, } @article {pmid41570514, year = {2026}, author = {Yan, S and Ahmad, HA and Xie, Y and Liu, S and Wu, J and Cui, J and Yang, B and Su, L and Ding, T and Liu, T}, title = {Metagenomic insights into the trophic gradient influence on nitrogen cycling microbiomes in plateau lakes.}, journal = {Marine pollution bulletin}, volume = {225}, number = {}, pages = {119288}, doi = {10.1016/j.marpolbul.2026.119288}, pmid = {41570514}, issn = {1879-3363}, mesh = {*Lakes/microbiology ; *Nitrogen Cycle ; *Microbiota ; Nitrogen ; Metagenomics ; Metagenome ; Proteobacteria ; Denitrification ; Bacteria ; }, abstract = {The increasing prevalence of nitrogen (Nr) pollution in lake ecosystems is a growing global concern. Understanding the dynamics of Nr-cycling microbial communities in these environments is crucial for assessing how ecosystem processes and functions respond to trophic gradients. This study investigates the microbial Nr-metabolism in plateau lakes with varying trophic states across a broad geographical range. A detailed metagenomic study revealed that increasing trophic status index (TSI) reduced the α-diversity of Nr-cycling microbial communities, while TSI and altitude jointly shaped the β-diversity patterns. The Nr-cycling microorganisms predominantly belonged to the phylum Proteobacteria, with the most abundant functional genes associated with organic Nr degradation and synthesis, dissimilatory/assimilatory nitrate reduction to ammonium (DNRA and ANRA), and denitrification processes (DNiF). Key Nr functional genes exhibited differential enrichment across lakes, indicating changes in Nr-metabolism strategies along the trophic gradient. A total of 126 metagenome-assembled genomes (MAGs) contributed to Nr-cycling, with the majority assigned to Proteobacteria (36) and Planctomycetes (25). Among these, MAG110 was enriched in eutrophic lakes and possessed near-complete DNiF and ANRA pathways, while MAG115, predominant in oligotrophic lakes, relied solely on ANRA. This functional divergence reflects trophic-specific ecological adaptations, that denitrification is favored in nutrient-rich, low-oxygen conditions and Nr- retention is prioritized under Nr-limited environments. Moreover, enzymes like nitronate monooxygenase (encoded by both genomes) and nitroalkane oxidase highlight a novel metabolic interaction between Nr-transformations and organic C1 compound oxidation in freshwater ecosystems. Overall, this study highlights the complex relationship among trophic status, microbial diversity, and Nr-metabolism in lake ecosystems.}, } @article {pmid41570646, year = {2026}, author = {Sidikjan, N and Li, Y and Chen, Y and Guo, XP and Liu, M and Huang, Y}, title = {Multimedia profiling of metal resistance genes in the Yangtze Estuary: Biofilm dominance and community-driven regulatory pathways.}, journal = {Ecotoxicology and environmental safety}, volume = {310}, number = {}, pages = {119769}, doi = {10.1016/j.ecoenv.2026.119769}, pmid = {41570646}, issn = {1090-2414}, mesh = {*Biofilms/drug effects ; *Metals, Heavy/analysis/toxicity ; *Estuaries ; *Water Pollutants, Chemical/analysis/toxicity ; Environmental Monitoring/methods ; China ; Geologic Sediments/microbiology/chemistry ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; *Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {Biofilms are critical microbial assemblages that function as sinks and potential reservoirs of metal resistance genes (MRGs) in contaminated aquatic systems. In this study, metagenomic sequencing and environmental profiling were employed to characterize MRGs distribution, heavy metal contamination, and microbial community structure across water, sediment, and biofilm samples in the Yangtze Estuary. Biofilms exhibited significantly higher concentrations of heavy metals and MRGs than other matrices, particularly for key genes such as corS (Cu-resistance), nrsS (Ni-resistance), and pbrA (Pb-resistance). Ecological risk assessment identified cadmium as the primary risk contributor, especially in biofilms. Partial redundancy analysis revealed that microbial community composition was the dominant factor shaping MRGs distribution, rather than metal concentrations alone. Network and canonical correspondence analyses further demonstrated strong co-occurrence patterns between MRGs and antibiotic resistance genes (ARGs), regulated by eutrophication (TN, Chl-a) and heavy metals (Pb, Cd, Cu). Notably, Pb-resistance genes in biofilm communities were significantly enriched and closely associated with Cyanobacteria and Proteobacteria, reflecting a multi-stage co-occurrence pattern potentially involving pbrT, pbrA, cadD, and czcD. These findings highlight the ecological significance of biofilms in MRGs enrichment, dissemination, and risk propagation in estuarine ecosystems under combined pollution stress.}, } @article {pmid41570777, year = {2026}, author = {Wang, Z and Lu, J and Wang, X and An, W and Zhao, Y and Han, B and Tao, H and Liu, J and Guo, J and Wang, J}, title = {Long-term pet ownership promotes resistome similarity between cats and their owners.}, journal = {Environment international}, volume = {208}, number = {}, pages = {110074}, doi = {10.1016/j.envint.2026.110074}, pmid = {41570777}, issn = {1873-6750}, mesh = {Animals ; Cats/microbiology ; *Pets/microbiology ; Humans ; *Ownership ; *Drug Resistance, Microbial/genetics ; Feces/microbiology ; Interspersed Repetitive Sequences ; *Gastrointestinal Microbiome ; Drug Resistance, Bacterial/genetics ; }, abstract = {Pet ownership offers physical and mental health benefits, but the risks of antibiotic resistance genes (ARGs) transmission between pets and humans remain underexplored. In this study, we used metagenomics analysis of fecal samples to compare resistome profiles among four groups: owned cats and their owners, and caged cats and non-cat owners. Our findings show significant similarities in gut microbial composition, ARGs, and mobile genetic elements (MGEs) between owned cats and their owners, identifying 73 shared core ARGs and 80 shared MGEs. In contrast, caged cats and non-cat owners shared only 30 ARGs and 73 MGEs. Long-term contact was positively correlated with a higher number of shared ARGs (from 20 + to 60 +) and MGEs (from 10 + to 40 +), as well as increased resistome risk (2.47- to 4.92-fold) between pet cats and owners. The gut microbiota played a key role in shaping the ARGs and MGEs profiles, with Escherichia coli and Klebsiella pneumoniae identified as primary carriers, each genome harboring 20 to 62 ARGs and 6 to 29 MGEs. ARGs transfer events were more frequent between pet cats and their owners than in other groups. These findings underscore a potential risk of shared antimicrobial resistance between companion animals and humans within the studied population in China.}, } @article {pmid41572158, year = {2026}, author = {Wijaya, SC and Richi, M and Waturangi, DE and Yulandi, A}, title = {Linking metagenomic insight to cultivable microbes: isolation of a vitamin B12-producing Sphingomonad from Indonesian tempeh.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {127}, pmid = {41572158}, issn = {1471-2180}, abstract = {BACKGROUND: Tempeh, a famous traditional Indonesian fermented soybean product, reportedly contains vitamin B12. Although Enterobacteriaceae have been previously implicated in vitamin B12 production in tempeh, the function of Sphingomonadaceae, which is abundant in some tempeh samples, remains unknown. This study aimed to identify and characterize vitamin B12-producing bacteria from Empang (EMP) tempeh, with a focus on the understudied Sphingomonad.

RESULTS: Metagenomic analysis focusing on vitamin B12 biosynthesis genes revealed that Sphingomonad genes had a complete set gene that required for producing the vitamin. A total of 44 yellow-pigmented isolates, characteristic of Sphingomonas, were screened via a vitamin B12 assay, three of which demonstrated potential for de novo biosynthesis. On the basis of 16S rRNA gene analysis, all three isolates were identified as Sphingomonas paucimobilis. Whole-genome sequencing and annotation of the EMP5-4 isolate revealed a complete gene set for the aerobic vitamin B12 biosynthesis pathway, including hem genes, cob genes and cobalamin riboswitches. Vitamin B12 production was confirmed through fermentation in a TSB medium with cobalt and DMBI supplementation and quantified at 0.949 µg/mL via HPLC. A genome-based safety assessment identified only low confidence antibiotic resistance and virulence genes, and a hemolysis assay revealed no red blood cell lysis, suggesting minimal pathogenicity.

CONCLUSION: These findings demonstrate that S. paucimobilis from tempeh may serve as a novel microbial source of vitamin B12, supporting its potential application in functional foods for individuals who avoid animal-derived products.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04681-2.}, } @article {pmid41572308, year = {2026}, author = {Zakharevich, N and Strokach, A and Shitikov, E and Klimina, K}, title = {Bacteriophages in gut metagenomes: from analysis to application.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {40}, pmid = {41572308}, issn = {1743-422X}, support = {23-75-10125//Russian Science Foundation/ ; }, mesh = {Humans ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; *Metagenome ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Computational Biology/methods ; Virome ; Genome, Viral ; }, abstract = {Bacteriophages constitute a major component of the human gut virome, playing very important roles in shaping of the structure and function of the gut microbiota. Moreover, bacteriophages interact with the human immune system, thereby influencing various disease processes. Recent advancements in metagenomic sequencing and computational analysis have substantially expanded our understanding of gut phage diversity and the scale of the so-called 'viral dark matter'. In this review, we summarize current bioinformatic approaches for identifying and annotating bacteriophage sequences in metagenomic data, discuss key challenges in taxonomic classification and host prediction of phages, as well as the limitations associated with the assembly and analysis of viral metagenome-assembled genomes (vMAGs). We also analyze the therapeutic potential of bacteriophages, including their application in cancer immunotherapy, inflammatory diseases, and liver diseases, and their promise as diagnostic and prognostic biomarkers.}, } @article {pmid41572348, year = {2026}, author = {He, W and Yu, Z and Wu, Z and Olesen, AK and Madsen, JS and Dechesne, A and Smets, BF and Nesme, J and Sørensen, SJ}, title = {Beyond borders: plasmids drive a shared antibiotic resistome in European urban water systems.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {39}, pmid = {41572348}, issn = {2049-2618}, support = {NNF 200C0062223//Novo Nordisk Foundation Data Science Collaborative Research Programme 2020/ ; DARWIN project #7044-00004B//Joint Programming Initiative-Antimicrobial Resistance grant/ ; }, mesh = {*Plasmids/genetics ; *Wastewater/microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenomics/methods ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Spain ; Denmark ; Bacteroides/genetics/isolation & purification ; Europe ; United Kingdom ; }, abstract = {BACKGROUND: Urban wastewater systems (UWSs) act as reservoirs and conduits for the dissemination of antibiotic resistance genes (ARGs), with plasmids playing a central role in their spread. Despite their significance, the diversity and persistence of plasmids in UWSs remain underexplored.

RESULTS: This study applies a multi-omics approach, including metagenomic and direct plasmidome sequencing, high-throughput qPCR array, and whole genome sequencing of plasmid isolates, to comprehensively profile the microbial plasmidome and resistome on 78 samples across UWSs in Denmark, Spain, and the UK. We successfully uncovered an extensive plasmid and ARG diversity that could not be fully captured by a single method, especially identified 78,574 plasmids, including 20,925 plasmids previously unreported. We also observed that plasmids carried a disproportionate share of clinically relevant ARGs, particularly beta-lactamase resistance genes; most importantly, they were preferentially located on transmissible plasmids. Furtherly, plasmids harbor ARG can enhance their persistence in wastewater ecosystems, especially harboring multiple types of ARGs. Moreover, Bacteroides emerged as a unique persistent ARG reservoir not only for harboring and disseminating diverse resistance genes especially in residential-relevant areas, but also emerged as a major driver of antimicrobial resistance dynamics across different wastewater treatment processes.

CONCLUSIONS: Overall, this work provides the first attempt at a holistic description of the UWSs' resistome, its structure, dynamics, and mobility and significantly expands the current knowledge. Video Abstract.}, } @article {pmid41572438, year = {2026}, author = {Maes, M and Almulla, AF and Vasupanrajit, A and Jirakran, K and Tunvirachaisakul, C and Maes, A and Chanchaem, P and Klomkliew, P and Payungporn, S and Zhang, Y}, title = {Functional shotgun metagenomic insights into gut microbial pathway and enzyme disruptions linking metabolism, affect, cognition, and suicidal ideation in major depressive disorder.}, journal = {Acta neuropsychiatrica}, volume = {38}, number = {}, pages = {e16}, pmid = {41572438}, issn = {1601-5215}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; *Major Depressive Disorder/microbiology/metabolism/psychology/genetics ; Metagenomics/methods ; Female ; Dysbiosis/microbiology ; Male ; Adult ; *Cognition/physiology ; Oxidative Stress ; Middle Aged ; }, abstract = {BACKGROUND: Major depression (MDD) is linked to neuro-immune, metabolic, and oxidative stress (NIMETOX) pathways. The gut microbiome may contribute to these pathways via leaky gut and immune–metabolic processes.

AIMS: To identify gut microbial alterations in MDD and to quantify functional pathways and enzyme gene families and integrate these with the clinical phenome and immune–metabolic biomarkers of MDD.

METHODS: Shotgun metagenomics with taxonomic profiling was performed in MDD versus controls using MetaPhlAn v4.0.6, and functional profiling was conducted using HUMAnN v3.9, aligning microbial reads to species-specific pangenomes (Bowtie2 v2.5.4) followed by alignment to the UniRef90 v201901 protein database (DIAMOND v2.1.9).

RESULTS: Gut microbiome diversity, both species richness and evenness, is quite similar between MDD and controls. The top enriched taxa in the multivariate discriminant profile of MDD reflect gut dysbiosis associated with leaky gut and NIMETOX mechanisms, that is, Ruminococcus gnavus, Veillonella rogosaem, and Anaerobutyricum hallii. The top four protective taxa enriched in controls indicate an anti-inflammatory ecosystem and microbiome resilience, that is, Vescimonas coprocola, Coprococcus, Faecalibacterium prausnitzii, and Faecalibacterium parasitized. Pathway analysis indicates loss of barrier protection, antioxidants, and short-chain fatty acids, and activation of NIMETOX pathways. The differential abundance of gene families suggests that there are metabolic distinctions between both groups, indicating aberrations in purine, sugar, and protein metabolism. The gene and pathway scores explain a larger part of the variance in suicidal ideation, recurrence of illness, neurocognitive impairments, immune functions, and atherogenicity.

CONCLUSION: The gut microbiome changes might contribute to activated peripheral NIMETOX pathways in MDD.}, } @article {pmid41572814, year = {2026}, author = {Fathima, N and Mascarenhas, R and Umar, D and Rekha, PD and Shetty, S and Amin, V}, title = {Impact of removing fixed orthodontic appliances on oral microbial dysbiosis: A longitudinal study and metagenomic sequencing analysis.}, journal = {Journal of orthodontics}, volume = {53}, number = {1}, pages = {34-44}, doi = {10.1177/14653125251408048}, pmid = {41572814}, issn = {1465-3133}, mesh = {Humans ; Longitudinal Studies ; *Orthodontic Appliances, Fixed/adverse effects ; *Microbiota/genetics ; *Dysbiosis/microbiology/etiology ; Metagenomics ; Female ; RNA, Ribosomal, 16S/genetics ; Male ; Saliva/microbiology ; *Mouth/microbiology ; Adolescent ; *Dental Debonding ; }, abstract = {OBJECTIVE: To investigate the impact of appliance removal on oral microbial diversity, composition, and abundance using metagenomic sequencing. It aims to identify the core microbiome and assess changes between mid-treatment and 2 weeks after debonding to understand the relationship between orthodontic therapy and oral health better.

METHODS: This longitudinal cohort study recruited 26 patients undergoing fixed orthodontic treatment between January 2022 and June 2023. Saliva samples were collected at two predefined time points: mid-treatment (T0, defined as before appliance removal) and 2 weeks after debonding (T1). Microbial DNA was extracted and the V1-V3 hypervariable regions of the 16S rRNA gene were sequenced using Illumina NovaSeq. Bioinformatics analysis was performed using QIIME and the SILVA database to evaluate microbial diversity and composition at T0 and T1. Beta diversity metrics and statistical tests, including PERMANOVA and Wilcoxon signed-rank tests, were applied to identify significant differences (P < 0.05). Effect sizes with 95% confidence intervals (CIs) were reported.

RESULTS: The analysis revealed significant shifts in microbial diversity and composition between T0 and T1. A total of 189 species across 63 genera were identified, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria as dominant phyla. Genera such as Fusobacterium periodonticum (↑ 12.4%, 95% CI = 10.1-14.7) and Veillonella parvula (↑ 9.8%, 95% CI = 7.6-11.3) increased after debonding, while Prevotella melaninogenica (↓ 10.2%, 95% CI = 8.1-12.0) and Rothia dentocariosa (↓ 7.9%, 95% CI = 6.3-9.2) decreased. Beta diversity analysis confirmed a statistically significant microbial community shift (P < 0.05).

CONCLUSION: This study demonstrated significant microbial shifts between mid-treatment and 2 weeks after debonding, including increases in potentially pathogenic genera and alterations in the core microbiome. These findings indicate microbial changes persist for at least 2 weeks after appliance removal. Further research with pre-treatment baselines and extended follow-up is required to better define the long-term trajectory of these changes.}, } @article {pmid41572827, year = {2025}, author = {Xu, B and Liu, P and Yan, N and Wang, T and Liu, L and Cheng, Y}, title = {Multi-omics insights into gut microbial dysbiosis and metabolic alterations in immune checkpoint inhibitor-induced thrombocytopenia.}, journal = {Immunotherapy}, volume = {17}, number = {17-18}, pages = {1231-1239}, pmid = {41572827}, issn = {1750-7448}, mesh = {Humans ; Multiomics ; *Dysbiosis/metabolism ; *Thrombocytopenia/chemically induced/metabolism ; *Gastrointestinal Microbiome ; *Immune Checkpoint Inhibitors/adverse effects ; Proteomics ; Metabolomics ; Female ; Male ; Middle Aged ; Aged ; *Neoplasms/drug therapy ; }, abstract = {BACKGROUND: Immune checkpoint inhibitors-induced thrombocytopenia (ICIs-TCP) is a rare immune-related adverse events (irAEs). The physiological changes underlying ICIs-TCP remain incompletely elucidated.

METHODS: We performed multi-omics analysis (gut microbiome, plasma metabolomics/proteomics) comparing microbial/metabolic alterations in cancer patients with (n = 8) and without ICIs-TCP (n = 8). Fecal metagenomic shotgun sequencing was performed to assess microbial composition and function, while plasma metabolomics and proteomics analyses identified systemic metabolic and protein expression changes associated with ICIs-TCP.

RESULTS: Patients with ICIs-TCP exhibited distinct gut microbiota profiles, with an increased abundance of Segatella, Prevotella, and Clostridium, alongside a depletion of Bacteroides and Roseburia. Functional analysis revealed significant downregulation of metabolic pathways, including arginine biosynthesis, alanine, aspartate, and glutamate metabolism. Plasma metabolomics identified reduced arginine levels and disruptions in key amino acid and energy metabolism pathways, suggesting systemic arginine depletion. Proteomic analysis further demonstrated down-regulation of folate hydrolase 1 (FOLH1), a key enzyme in glutamate metabolism, implicating metabolic dysregulation in TCP pathogenesis.

CONCLUSION: The depletion of arginine and associated metabolic disruptions are associated with ICIs-TCP and may represent a potential therapeutic target for mitigating TCP risk in patients receiving ICIs.}, } @article {pmid41572901, year = {2026}, author = {Hock, L and Luiken, R and Valério, E and Vargha, M and Vierheilig, J and Börjesson, S and Pitkänen, T and Schmitt, H}, title = {Integrating AMR surveillance into wastewater monitoring systems in 2025: a position on the implementation of Article 17 of the Urban Wastewater Treatment Directive (UWWTD).}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {31}, number = {3}, pages = {}, pmid = {41572901}, issn = {1560-7917}, mesh = {*Wastewater/microbiology ; Humans ; *Environmental Monitoring/methods ; European Union ; *Water Purification ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; Public Health ; Europe ; *Bacteria/drug effects/genetics ; }, abstract = {The recast Urban Wastewater Treatment Directive (UWWTD) calls for monitoring antimicrobial resistance (AMR) in wastewater of large European agglomerations (≥ 100,000 person equivalents). Guidance on scope and methods is currently in development. Two European Joint Actions share a goal to harmonise procedures and indicators: the European Union (EU)-Wastewater Integrated Surveillance for Public Health (EU-WISH), aiming to strengthen wastewater-based surveillance (WBS) for public health and the EU-Joint Action Antimicrobial Resistance and Healthcare Associated Infections (EU-JAMRAI) 2, providing among others, approaches for environmental surveillance of AMR. An EU-WISH survey in 2024, mapping WBS AMR-related activities across Europe, revealed that of 27 countries surveyed, 11 had an operative AMR WBS system and mainly employed WBS to determine AMR trends, primarily through culture-based analyses, in-depth characterisation of specific bacteria, and quantitative PCR for specific resistance genes. Occasionally metagenomics was used. We argue that prioritising AMR WBS targets should consider the intended objectives of surveillance, which could include uncovering AMR trends and emerging AMR determinants in humans, the assessment of antimicrobial/AMR environmental release, and wastewater treatment efficiency. Targets should be assessed for their public health relevance and the usefulness of complementary information they provide, while integrating measurability, resource efficiency, and expertise from different One Health domains.}, } @article {pmid41574048, year = {2026}, author = {Ru, SS and Li, W and Hao, J and Cao, CY and Ma, L and Zhang, X}, title = {Evaluation of the diagnostic value of metagenomic next-generation sequencing for zoonotic cestode Spirometra mansoni infection.}, journal = {Food and waterborne parasitology}, volume = {42}, number = {}, pages = {e00316}, pmid = {41574048}, issn = {2405-6766}, abstract = {Metagenomic next-generation sequencing (mNGS) technology offers substantial advantages in parasite detection; however, we still know very little about its diagnostic value for Spirometra mansoni infection. In this study, mNGS technology was used to analyse faecal samples and blood samples from cats infected with S. mansoni, as well as tissue samples and blood samples from mice infected with the plerocercoid larvae of S. mansoni. Moreover, polymerase chain reaction (PCR) was employed to validate the mNGS results. The diagnostic value of mNGS for S. mansoni infection was systematically evaluated. The mNGS results revealed that the read counts of S. mansoni in the cat faeces (CF) samples were 301,497 (CF1), 1,330,549 (CF2), 1,181,162 (CF3), and 0 (CF0), with relative abundances of 3.17%, 16.64%, 13.14%, and 0%, respectively. In the mouse tissue (MT) samples, the read counts of S. mansoni were 10,791 (MT1), 438 (MT2), 3697 (MT3), and 10 (MT0), with relative abundances of 67.21%, 3.65%, 21.12%, and 0.16%, respectively. No sequences of S. mansoni were detected in the cat blood samples or mouse blood samples. The PCR results were consistent with the mNGS results, confirming the accuracy of the mNGS analysis. In addition, during the detection process, the assembly-based analysis did not detect sequences of S. mansoni in all samples. In contrast, the read-based analysis successfully detected the target sequences without fail. Finally, the analysis of microbiota diversity in the definitive host faecal samples revealed that compared with those in the control group, the elevated microbial taxa in the infected group mainly were probiotics, such as Prevotella copri and Bifidobacterium adolescentis. Conversely, the decreased microbial populations were primarily associated with certain diseases, such as Collinsella stercoris and Catenibacterium sp. In this study, the diagnostic value of mNGS for S. mansoni infection was systematically evaluated. These findings establish a foundation for the more precise application of mNGS technology in the detection of S. mansoni and related cestode infections.}, } @article {pmid41574217, year = {2026}, author = {Rulhania, A and Panigrahi, S and Swami, S and Singh, Y and Balyan, P and Singh, KP and Mir, RR and Kumar, U}, title = {Identification and expression analysis of putative genomic regions disseminating biotic stress tolerance in chickpea (Cicer arietinum).}, journal = {3 Biotech}, volume = {16}, number = {2}, pages = {81}, pmid = {41574217}, issn = {2190-572X}, abstract = {UNLABELLED: Chickpea (Cicer arietinum L.) productivity is heavily constrained by major biotic stresses, particularly Fusarium wilt, Ascochyta blight and Botrytis gray mold, which collectively cause significant annual yield losses worldwide. To develop a refined understanding of the genetic architecture underlying resistance to these pathogens, a comprehensive meta-analysis was conducted using 113 QTLs taken from 24 independent studies, including diverse mapping populations. This analysis led to the identification of 27 MQTLs, which represent both novel genomic regions and, crucially, refined positions of previously known QTLs with reduced confidence intervals. Four robust Breeders' MQTLs were identified on the basis of high phenotypic variance (PVE ≥ 10%), a low confidence interval (CI ≤ 2 cM) and the involvement of multiple initial QTLs. Among these breeder MQTLs, 229 candidate genes, including key players in plant defense, such as receptor-like kinases (RLKs), resistance gene analogues (RGAs) and genes for RML1A, HSPRO2 and endochitinase A, were identified. These genes were validated through qRT‒PCR expression profiling in contrasting genotypes (WR-315 and JG-62). These refined genomic regions and their associated markers provide a direct pathway for pyramiding multiple resistance QTLs through marker-assisted selection and provide a direct pathway to breed chickpea varieties with durable, broad-spectrum resistance to key fungal diseases. The integrated meta-genomic framework significantly enhances precision and utility and paves the way for the functional characterization of the underlying resistance mechanisms.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04698-y.}, } @article {pmid41574290, year = {2025}, author = {Chen, J and Gong, G and Su, X and Song, X and Zhang, J and Wu, P and Wang, H and Shan, T and Zhang, W}, title = {Viral metagenomic analysis of fecal samples from Bos grunniens on the Qinghai-Tibet Plateau reveals novel picornaviruses and diverse CRESS-DNA viruses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1719300}, pmid = {41574290}, issn = {2235-2988}, mesh = {Animals ; Phylogeny ; *Metagenomics ; Tibet ; *Feces/virology ; *DNA Viruses/genetics/classification/isolation & purification ; Cattle/virology ; *Virome/genetics ; Genome, Viral ; *Picornaviridae/genetics/classification/isolation & purification ; }, abstract = {INTRODUCTION: The Qinghai-Tibet Plateau (QTP), one of the most extreme environments on Earth, provides a unique natural setting for exploring viral diversity and evolution under conditions of high altitude, hypoxia, and intense ultraviolet radiation. The yak (Bos grunniens), a key endemic ruminant species of the QTP, plays an essential ecological and economic role, yet its fecal virome remains poorly characterized.

METHODS: In this study, we analyzed 43 yak fecal samples collected from Yushu, Qinghai Province, and constructed nine metagenomic libraries to investigate the composition, diversity, and phylogenetic characteristics of the yak fecal virome.

RESULTS: Metagenomic sequencing generated approximately 463 million raw reads, of which 2.87 million were classified as viral. The viral reads in the sequenced libraries were primarily composed of single-stranded DNA viruses (92.46%), particularly members of Smacoviridae, Circoviridae, and Genomoviridae, whereas RNA viruses such as Picornaviridae accounted for a minor fraction (0.71%). Phylogenetic analyses revealed that several circular single-stranded DNA (CRESS-DNA) virus and picornavirus genomes share high similarity with known ruminant-associated viruses, while forming independent evolutionary clades, suggesting potential cross-species transmission among plateau animals. The large-scale divergence within Smacoviridae further reflects extensive lineage expansion under the plateau's extreme environmental pressures.

DISCUSSION: Compared with our previous yak virome study, this work provides independent and complementary insights into the genomic and evolutionary characteristics of key viral taxa. Overall, our findings expand the genomic landscape of the yak fecal virome and highlight the Qinghai-Tibet Plateau as an important reservoir for exploring viral diversity, evolution, and host-environment interactions in extreme ecosystems.}, } @article {pmid41574306, year = {2025}, author = {Guo, S and Wang, L and Sai, X and Tang, S and Wang, J and Wang, A and Qiu, D and Han, S and Wu, Y and Chen, C}, title = {Effect of BALF-based mNGS on clinical outcomes of immunocompromised subjects with opportunistic pulmonary infections: a multicenter propensity score-matched study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1724935}, pmid = {41574306}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Immunocompromised Host ; Aged ; Propensity Score ; *Opportunistic Infections/diagnosis/microbiology/drug therapy/mortality ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Adult ; Treatment Outcome ; Aged, 80 and over ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a promising tool for pathogen detection. However, its clinical utility in detecting opportunistic pulmonary infections of immunocompromised patients remains controversial.

METHODS: This multicenter retrospective study involving 162 immunocompromised patients with opportunistic pulmonary infections was conducted across four respiratory centers. The enrolled patients were divided into the conventional microbiological tests (CMT) group and the mNGS group based on whether mNGS of BALF was performed after admission. Propensity score-matching (PSM) was adopted to minimize selection bias, and sensitivity analysis confirmed the robustness. The primary outcomes were >30% improvement in oxygenation index (OI) at 7 days post-admission and clinical improvement by day 14 as assessed with the WHO 7-category ordinal scale. Secondary outcomes included 21-day mortality, incidence of septic shock during hospitalization, and pathogen detection rate.

RESULTS: Among the 110 patients who underwent mNGS, the results prompted modifications to the antibiotic therapy in 89 patients (80.9%), encompassing both escalation and de-escalation of therapy. The remaining 52 patients received only CMT. After the PSM, 41 matched pairs were further analyzed. Compared to the CMT group, OI improvement >30% on day 7 was more frequent in the mNGS group (41.5% vs. 9.8%, P = 0.001). Clinical improvement on day 14 in the mNGS group was higher than in the CMT group (36.6% vs. 9.8%, P = 0.004). Additionally, BALF mNGS was associated with decreased 21-day mortality (7.3% vs. 34.1%; P = 0.003) in patients with opportunistic pulmonary infections, while showing no significant association with reduced incidence of septic shock during hospitalization. Moreover, the causative pathogen detection rate was significantly higher in the mNGS group compared to the CMT group (97.6% vs. 22.0%, P<0.001), demonstrating the superior diagnostic yield of mNGS.

CONCLUSION: Our study indicated that early BALF mNGS testing upon admission was associated with improved OI up to day 7, clinical improvement on day 14, and decreased 21-day mortality. These benefits are likely facilitated by the higher diagnostic yield of mNGS and its direct impact on guiding targeted antibiotic therapy.}, } @article {pmid41574341, year = {2025}, author = {Destras, G and Sabatier, M and Bal, A and Simon, B and Semanas, Q and Regue, H and Boyer, T and Ploin, D and Gillet, Y and Lina, B and Anani, H and Josset, L}, title = {Comparison between metatranscriptomics and viral metagenomics, 16S, and host transcriptomics for comprehensive profiling of the respiratory microbiome and host response.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1685035}, pmid = {41574341}, issn = {1664-302X}, abstract = {INTRODUCTION: Omics-based studies focusing on a single kingdom, such as bacterial 16S gene sequencing, viral metagenomics, and human mRNA sequencing, are commonly used to explore the microbiome and its association with host responses. But combining these approaches is often expensive and time-consuming. Metatranscriptomics provides a snapshot of the entire active microbiome through bulk RNA sequencing in a single test, yet its performance relative to kingdom-specific methods has not been systematically assessed.

METHODS: We compared metatranscriptomics with three kingdom-specific sequencing approaches in 20 nasopharyngeal aspirates from infants 7 months of age hospitalized for bronchiolitis at the Hospices Civils de Lyon.

RESULTS: Applying specific sequencing depth thresholds (≥1,000 bacterial reads, ≥100,000 human reads, and detection of an internal RNA control), metatranscriptomics showed high detection concordance and correlated abundance for RNA viruses and human coding genes. Metatranscriptomics also detected RNA from both eukaryotic and prokaryotic DNA viruses, suggesting potential for identifying transcriptional activity. For the bacteriome, 82% of genera exceeding 0.5% relative abundance were captured, revealing distinct transcriptional profiles at the species level. Metatranscriptomics reproduced multi-omics-derived host-microbiome endotypes and revealed stronger key microbial associations, particularly for transcriptionally active microorganisms.

DISCUSSION: These findings indicate that a single metatranscriptomics run can complement or replace kingdom-specific approaches for profiling RNA viruses and the host transcriptome, while also identifying transcriptionally active bacteria and DNA viruses. Low-abundance or latent microorganisms may still require targeted assays. Metatranscriptomics thus provides a cost- and time-efficient strategy for integrated microbiome research and holds promise for clinical applications in acute infections and cases of diagnostic uncertainty.}, } @article {pmid41574342, year = {2025}, author = {Feng, Q and Liu, B and Liu, H and Fan, Y and Gao, S and Zhang, J and Kuang, Y and Wang, W and Liang, H and Qiu, Y and Wen, H and Feng, Z and Huang, Y and Zuo, W and Zhang, X and Zeng, J and Wu, J and Liang, Y and Gu, J}, title = {The application value and limitations of metagenomic detection technology based on cerebrospinal fluid samples in suspected central nervous system infection: a retrospective study.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1689253}, pmid = {41574342}, issn = {1664-302X}, abstract = {BACKGROUND: Accurately diagnosing central nervous system (CNS) infections remains challenging. This study aimed to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) in diagnosing suspected CNS infections and its role in facilitating rapid and accurate pathogen identification.

METHODS: This retrospective study enrolled cerebrospinal fluid specimens from 246 patients with suspected CNS infections and 20 controls with definitively ruled-out infections. Using clinical diagnoses established by an expert panel based on comprehensive criteria as the reference standard, we evaluated the diagnostic performance of mNGS relative to culture and conventional tests. Additionally, we analyzed the therapeutic guidance value of positive mNGS results and risk factors for false negatives.

RESULTS: mNGS showed 73.2% (180/246) agreement with clinical diagnosis, superior to culture (54.1%, 133/246) and conventional methods (61.4%, 151/246). For general bacteria and fungi, mNGS showed 61.9% (26/42) concordance with culture. False negatives in mNGS predominantly involved viral missed detection. Age, presence of systemic infection, headache, and cerebrospinal fluid glucose levels were likely key determinants of mNGS performance. mNGS detection of Epstein-Barr virus, Streptococcus spp., Mycobacterium tuberculosis complex, herpes simplex virus type 1, and Staphylococcus spp. suggested high pathogenic potential, whereas Torque teno virus detection more likely indicated carriage or experimental contamination.

CONCLUSION: mNGS holds significant value for the diagnosis, therapeutic management, and prognostic assessment of suspected CNS infections.}, } @article {pmid41574343, year = {2025}, author = {Saba Villarroel, PM and Piorkowski, G and Laojun, S and Liégeois, F and Gumpangset, N and Missé, D and Chaiphongpachara, T and Wichit, S}, title = {Metagenomic exploration of the virome of Rhipicephalus sanguineus ticks from Chachoengsao, Thailand.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1736178}, pmid = {41574343}, issn = {1664-302X}, abstract = {Ticks are obligate blood-feeding ectoparasites that harbor a wide diversity of microorganisms. Rhipicephalus sanguineus, the brown dog tick, is globally distributed and poses significant veterinary and public health concerns due to its close association with companion animals and its occasional infestation of humans. However, the virome of this species in Thailand remains poorly characterized. In this study, we employed DNA Nanoball sequencing to investigate the virome of 80 R. sanguineus ticks, grouped into five pools, collected from dogs in Chachoengsao Province, Thailand, in 2023. Three viruses were identified: Brown dog tick phlebovirus 2 (BDTPV2), Changping tick virus 2 (CpTV-2), and Bole tick virus 4 (BLTV4), all detected in male ticks. These results highlight the need for further investigation into the ecological roles and biological significance of these viruses. Overall, our findings provide an updated perspective on the R. sanguineus virome in Thailand and underscore the importance of continued surveillance of tick-associated viruses within the One Health framework.}, } @article {pmid41574363, year = {2025}, author = {Xiao, J and Pu, C and Zhou, X and Zhang, X and Zhang, S and Yang, P and Zhang, Y and Xiong, L}, title = {Solving the diagnostic dilemma in bone infections: metagenomic next generation sequencing enhances pathogen identification accuracy.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1699607}, pmid = {41574363}, issn = {2296-858X}, abstract = {OBJECTIVE: Metagenomic Next Generation Sequencing (mNGS) offers a rapid, unbiased, and culture-independent approach to pathogen identification by analyzing all nucleic acids present in clinical samples. Despite its growing use, the diagnostic utility of mNGS in bone infections remains inadequately characterized. This study aimed to assess the diagnostic accuracy of mNGS compared to conventional microbial cultures and to explore its associations with clinical severity and patient outcomes.

METHODS: We retrospectively enrolled 135 adult patients treated for suspected bone infections between October 2023 to January 2025 at Union Hospital, Tongji Medical College. Among these, 101 patients were classified as the infection group (IG) based on clinical and laboratory criteria, encompassing osteomyelitis, post-traumatic limb infections, and diabetic foot infections. mNGS results were compared to traditional cultures in terms of sensitivity, specificity, predictive values, and discordant cases. The IG was further stratified into mNGS-positive (n = 95) and mNGS-negative (n = 6) subgroups. Clinical parameters-including leukocyte differentials, C-reactive protein (CRP), procalcitonin (PCT), albumin, length of hospital stay, and mortality-were analyzed in relation to mNGS findings.

RESULTS: Among all patients, 74.81% were confirmed to have infections. mNGS demonstrated a markedly higher sensitivity than culture (94.06% vs. 47.52%, p = 0.000) while maintaining comparable specificity (85.29% vs. 76.47%, p = 0.549). Age showed a potential trend in influencing mNGS positivity (p = 0.092). Although not statistically significant, mNGS-positive patients tended to have longer hospitalizations (p = 0.098), suggesting possible associations with infection complexity or pathogen load.

CONCLUSION: mNGS substantially enhances the diagnostic yield for bone infections, particularly in polymicrobial, low-abundance, or culture-negative scenarios. mNGS-negative patients had significantly shorter hospital stays and a lower rehospitalization rate. Its rapid and comprehensive pathogen detection may enable more timely and targeted antimicrobial therapy, potentially improving patient outcomes and reducing healthcare burden. These findings support the integration of mNGS as a valuable adjunct to conventional diagnostic workflows in orthopedic infectious diseases.}, } @article {pmid41574538, year = {2026}, author = {Thakur, M and Dolker, S and Ghosh, A and Wangmo, LK and Singh, VK and Hasan, M and Acharya, AP and Biswas, A and Sarkar, S and Sharma, LK and Banerjee, D}, title = {Metagenomic Surveillance of Blood-Fed Mosquitoes for Assessing Zoonotic Risk in Managed Animal Settings.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {26}, number = {4}, pages = {201-210}, doi = {10.1177/15303667261417424}, pmid = {41574538}, issn = {1557-7759}, mesh = {Animals ; *Zoonoses ; *Culicidae/microbiology ; Female ; *Metagenomics ; Humans ; India ; *Mosquito Vectors/microbiology ; }, abstract = {BACKGROUND: Vector-borne zoonotic diseases remain a major global public health concern, particularly at interfaces where humans, domestic animals, and wildlife interact closely. Conventional surveillance approaches often fail to detect early zoonotic spillover events, especially in farm and zoological settings. Blood-fed mosquitoes, which feed on diverse vertebrate hosts, offer a unique opportunity for non-invasive environmental surveillance through xenosurveillance. This study evaluates the feasibility of using blood-fed mosquitoes as biological samplers to assess zoonotic risk in managed animal settings in eastern India.

METHODS: A total of 185 blood-fed female mosquitoes were collected from livestock farms and zoological enclosures in West Bengal, India, and grouped based on host association (cattle, buffalo, goat, poultry, zebra, and deer). Mosquito species were identified using mitochondrial cytochrome c oxidase I (COI) gene sequencing. Host-group-wise pooled DNA from mosquito heads and abdomens was subjected to shotgun metagenomic sequencing using Oxford Nanopore MinION technology. Taxonomic classification was performed using Kraken 2, and microbial diversity was analyzed through alpha and beta diversity metrics using phyloseq.

RESULTS: Six mosquito species were identified, including Culex tritaeniorhynchus, Culex vishnui, and Mansonia uniformis, known vectors of zoonotic pathogens. Metagenomic analysis revealed diverse microbial communities dominated by Actinobacteria, Proteobacteria, and Firmicutes, with significant host-associated variation in microbial composition. Buffalo- and zebra-associated mosquitoes exhibited the highest microbial richness, while cattle-associated mosquitoes showed comparatively lower diversity. Genomic fragments corresponding to potential zoonotic and veterinary pathogens-including Plasmodium relictum, Babesia bigemina, and Clostridium botulinum-were detected across multiple host groups. Beta diversity analysis demonstrated clear host-driven clustering of mosquito-associated microbiomes.

CONCLUSION: This pilot study demonstrates that blood-fed mosquitoes can serve as effective non-invasive biological samplers for detecting environmental DNA signatures of potential zoonotic pathogens in managed animal settings. While the detection of pathogen-associated genomic fragments does not confirm active infection or transmission, the findings highlight the utility of mosquito-based metagenomic surveillance as an early warning and risk-detection tool within a One Health framework. Integrating such approaches with targeted diagnostics and epidemiological surveillance may strengthen preparedness for emerging vector-borne zoonotic threats.}, } @article {pmid41575223, year = {2026}, author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W}, title = {Hidden reservoir of highly adaptable multi-host plasmids that propagate antibiotic genes in healthy human populations.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41575223}, issn = {1751-7370}, support = {//The National Key Research and Development Program of China/ ; Project32098//National Science and Technology Major Project/ ; }, mesh = {Humans ; *Plasmids/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Extrachromosomal DNA ; }, abstract = {Plasmids are key vectors for disseminating antibiotic resistance genes, yet their diversity and dynamics in the healthy human gut microbiome remain largely unexplored. Using fecal metagenomes from two cohorts (n = 498 samples), we constructed a comprehensive atlas of the healthy human gut plasmidome. We observed a polarization: while 97.4% of 19 151 plasmid clusters exhibited low prevalence (<5%), we identified 17 plasmid clusters that were detected in >30% of individuals. Among these, the plasmid pGut1 emerged as a paradigm of a stealth vector. Prevalent globally (>50% in independent cohorts), pGut1 possesses a minimal 4-kb conserved backbone ensuring stability and a hypervariable region acting as a "plug-and-play" module. We documented 40 distinct cargo inserts, including multiple antibiotic resistance genes such as cfr(C), erm(B), and aphA, across individuals, within individuals over time, and even within single fecal samples- validated by single-cell and long-read Nanopore sequencing. Screening of 2.3 million bacterial genomes revealed pGut1 in 93 strains across 49 genera and 2 phyla, including pathogenic Clostridioides difficile and three distinct Salmonella enterica strains. This pattern suggests potential repeated cross-species transmission events, equipping diverse pathogens with new antibiotic resistance genes. Our study exposes a hidden reservoir of highly adaptable, multi-host plasmids like pGut1 silently propagating antibiotic resistance genes in healthy populations. These plasmids, pre-adapted for cross-boundary dissemination, may pose a threat by fueling the emergence of multidrug-resistant pathogens.}, } @article {pmid41575959, year = {2026}, author = {Duan, Z and Lian, D and Wang, K and Hu, Y and Fu, H and Wen, R and Zhao, Y and Hu, X and Pan, P and Xu, J and Chen, J and Xiao, L and Wang, L and Yu, X and Han, X and Xie, W and Xie, F and Xie, L and Han, Z}, title = {Multi-modal data to identify key factors influencing lung injury in ARDS patients undergoing invasive mechanical ventilation: A prospective multi-center observational study protocol.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0332985}, pmid = {41575959}, issn = {1932-6203}, mesh = {Humans ; *Respiratory Distress Syndrome/therapy ; *Respiration, Artificial/adverse effects ; Prospective Studies ; Biomarkers ; *Lung Injury/etiology ; Multicenter Studies as Topic ; Female ; Male ; }, abstract = {BACKGROUND: Patients with moderate to severe acute respiratory distress syndrome (ARDS) exhibit extremely poor prognoses following mechanical ventilation, with mortality rates as high as 40% to 55%. Despite extensive research into ARDS classification and prognostic assessment, the disease's pathogenesis remains incompletely understood, and there remains a critical lack of specific biomarkers and effective therapeutic targets for its prevention and management. The core challenges lie in two key areas. First, ARDS demonstrates marked heterogeneity in etiology, pathophysiology, and pathogenesis. Existing research, predominantly reliant on population-level average data, fails to capture inter-individual variability, hindering the precise identification of patient subgroups responsive to specific therapeutic regimens. Second, current definitions of ARDS phenotypes are often confined to clinical symptoms and routine diagnostic indices, lacking integrated analysis of deeper mechanistic indicators, such as key biomarkers and respiratory mechanics parameters, thereby limiting the stability and clinical utility of existing classification systems.

METHODS/DESIGN: We designed a prospective multicenter cohort study incorporating multi-omics analyses. This research aims to investigate the mechanisms underlying the development and progression of ARDS during mechanical ventilation, providing a theoretical foundation and practical guidance for future ARDS therapies. The study plans to enroll over 165 patients with moderate to severe ARDS receiving mechanical ventilation across 10 medical centers. Peripheral blood and bronchoalveolar lavage fluid (BALF) samples will be collected on the first 24 hours after enrollment and at extubation for metagenomic/meta-transcriptomic sequencing, bulk RNA sequencing, single-cell RNA sequencing, proteomics detection, and metabolomics analyses. Concurrently, comprehensive monitoring of physiological indices, electrical impedance tomography, transpulmonary pressure, pulmonary ultrasound findings, and other relevant parameters will be conducted during the enrollment. Study participants will be stratified by survival and mortality outcomes to analyze the dynamic trends of all measured indices and their underlying molecular mechanisms. Biomarkers derived from multi-omics data and clinical baseline characteristics will be evaluated and integrated, followed by multidimensional dimensionality reduction. Predictive models will be subsequently constructed via early or late fusion to identify core prognostic markers, with performance validated using standardized metrics.

DISCUSSION: Through comparative analysis of multi-omics data, we aim to identify specific markers and risk factors associated with distinct clinical trajectories of ARDS, further clarifying the key determinants of lung injury. Ultimately, this research will reveal critical immune cell subtypes that govern ARDS onset and prognosis, offering novel insights and therapeutic targets to advance precision medicine for ARDS.

STUDY PROTOCOL REGISTRATION: ClinicalTrials.gov NCT05922826.}, } @article {pmid41576448, year = {2026}, author = {Ding, Y and Liu, BW and Wu, D and Li, HZ and Du, S and Zhu, D}, title = {Effects of earthworms on soil virus-associated ARGs and resistance phenotypes in long-term field cropping systems.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141205}, doi = {10.1016/j.jhazmat.2026.141205}, pmid = {41576448}, issn = {1873-3336}, mesh = {Animals ; *Oligochaeta ; *Soil Microbiology ; Phenotype ; Zea mays/growth & development ; Rhizosphere ; Triticum/growth & development ; Agriculture ; }, abstract = {Long-term effects of earthworms on soil resistomes under realistic field conditions remain poorly understood. Here, we conducted a two-year corn-wheat rotation study within a long-term field experiment established in 2018 to systematically investigate how a one-time earthworm addition durably modulates resistomes. Integrated metagenomics and viromics analyses revealed that diverse ARGs and virulence factor genes (VFGs) were consistently higher in rhizosphere than bulk soils, identifying the rhizosphere as a hotspot for resistance dissemination. Despite limited metagenomic shifts, long-term earthworm activity suppressed virus-associated ARGs and VFGs, as well as high-risk ARGs, especially in bulk soils. Notably, early phenotypic resistance in the rhizosphere increased markedly in Year 1 (ciprofloxacin + 38.9 %, meropenem + 31.3 %) without concurrent genotypic changes, whereas significant genotypic shifts emerged only in Year 2, indicating that phenotypic resistance preceded genotypic changes. Long-term earthworm addition reshaped microbial life-history strategies from R- to K-strategist traits, enhanced lysogeny proportions that dominated 72.73-85.05 % of the viromes throughout the 2-year crop rotation, and stabilized virus-host networks. Caudovirales infecting Streptomyces and Pseudomonas acted as hubs linking ARGs to nutrient-cycling taxa, with earthworms reinforcing cooperative cross-kingdom interactions. These findings highlight earthworms' long-term regulatory role in microbial adaptation and resistome dynamics, informing resistance risk management under the One Health framework.}, } @article {pmid41576514, year = {2026}, author = {Hao, Y and Li, Y and Liu, F and Long, J and Yang, H}, title = {Metagenomic insights into the influence of goose farming on the gut microbiome and antibiotic resistome of workers.}, journal = {Poultry science}, volume = {105}, number = {4}, pages = {106487}, pmid = {41576514}, issn = {1525-3171}, mesh = {Animals ; *Geese/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Drug Resistance, Microbial/genetics ; *Bacteria/drug effects/genetics ; *Metagenome ; *Animal Husbandry ; Metagenomics ; Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Farmers ; }, abstract = {Antimicrobial resistance (AMR) seriously threatens the health of humans and animals. Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) were enriched in the goose farms. However, the influence of goose farming exposure on the gut microbiota and ARGs of workers was unclear. In this study, metagenomic analysis was used to characterize gut microbiome structures, annotate bacterial taxa, and quantify the abundances of ARGs and MGEs in geese and human samples. Results showed that goose feces harbored more abundant ARGs and ARB than human feces. Significantly higher abundances of special ARGs (such as vanY, lsaE, AAC3-IId and ampC) were identified in workers compared to villagers. Compositions of gut bacteria were significantly different between workers and villagers, and some certain gut pathogens were abundant in the feces of workers, including Bacillus anthracis, Clostridium perfringens, and Escherichia coli O45:K1:H7. A total of 51 ARGs were pinpointed in the metagenome-assembled genomes (MAGs). Based on ARG-MGE associations and co-occurrence signals in MAGs, the potential for horizontal gene transfer (HGT) was inferred. With this transfer capacity and ubiquitous gut colonization, E. coli carrying 38 ARGs is proposed as a putative AMR indicator for the goose farm. This study demonstrates that goose farming had non-ignorable influences on the gut microbiome and antibiotic resistome of workers. More efforts should be made to control the ARGs and ARB in the goose farm.}, } @article {pmid41576635, year = {2026}, author = {Quan, M and Zhang, X and Chen, C and Feng, Y and Lv, X and Wang, X and Ye, H}, title = {Perinephritic and psoas abscess by an unusual coinfection with Trichomonas vaginalis and Lactobacillus johnsonii.}, journal = {Diagnostic microbiology and infectious disease}, volume = {114}, number = {4}, pages = {117276}, doi = {10.1016/j.diagmicrobio.2026.117276}, pmid = {41576635}, issn = {1879-0070}, mesh = {Humans ; Female ; Middle Aged ; *Trichomonas vaginalis/isolation & purification/genetics ; *Coinfection/diagnosis/parasitology/microbiology ; *Psoas Abscess/diagnosis/parasitology/microbiology/therapy ; *Lacticaseibacillus/isolation & purification/genetics ; *Trichomonas Infections/diagnosis ; Anti-Bacterial Agents/therapeutic use ; Metronidazole/therapeutic use ; }, abstract = {Trichomoniasis, caused by Trichomonas vaginalis, is a common nonviral sexually transmitted infection that presents with vaginitis, urethritis, cystitis, prostatitis, and rarely perinephric abscess. Here we presented a 49-year-old female with fever and lumbago diagnosed with a coinfection of perinephric and psoas abscess caused by Lactobacillus johnsonii and T. vaginalis, with the etiological diagnosis established using pus culture and metagenomic next-generation sequencing (mNGS). The patient achieved complete recovery following abscess drainage, incision, and combined therapy with metronidazole and piperacillin/tazobactam. Rare manifestations of trichomoniasis are easily misdiagnosed, and mNGS can help identify T. vaginalis quickly and accurately without prediction.}, } @article {pmid41576748, year = {2026}, author = {Maza-Márquez, P and González-López, J and Rodelas, B}, title = {Metagenomic profiling of bacterial resistomes in full-scale wastewater treatment plants in Spain.}, journal = {Journal of environmental management}, volume = {400}, number = {}, pages = {128695}, doi = {10.1016/j.jenvman.2026.128695}, pmid = {41576748}, issn = {1095-8630}, mesh = {*Wastewater/microbiology ; Spain ; Bioreactors/microbiology ; *Bacteria/genetics ; Waste Disposal, Fluid ; Metagenomics ; Anti-Bacterial Agents ; Sewage/microbiology ; }, abstract = {Investigating the resistome of activated sludge communities is critical to understand the spread of antimicrobial resistances. Here, the resistomes of five full-scale wastewater treatment plants (WWTPs) in Spain were analyzed using a metagenomic approach. 888, 1361 and 1062 unique antibiotic resistance genes (ARGs) were identified in the aerated bioreactors, the anoxic/anaerobic bioreactors, and the treated effluents, respectively. The core resistome comprised 25 ARGs conferring resistance to betalactams (penP, blaI), fosmidomycin (fsr), tetracycline (tetA), thiopeptides (tipA), and vancomycin (vanJ, vanR, vanW, vanX, vanY). The cumulative coverages of ARGs for betalactams, cationic antimicrobial peptides (CAMPs), mercury, lincomycin, quaternary ammonia, and multidrug resistance mechanisms decreased in the effluents. In contrast, the ARGs for ethionamide, methylenomycin, thiopeptides, and vancomycin increased their relative abundances in the effluents of some WWTPs. Proteobacteria were the major putative hosts of ARGs in all samples, followed by Bacteroidetes in the bioreactors and Actinobacteria in the effluents. The genera making bigger contributions to the cumulative coverage of ARGs shifted across the different WWTPs and sample types, showing that different groups of bacteria hosting the resistome were enriched in each case. Many genera identified as putative hosts of ARGs are key players of biological wastewater treatment, including filamentous bacteria, nitrifiers, denitrifiers, and polyphosphate-accumulating organisms. These findings point to the optimization of the tertiary treatment of effluents and management of sludge as the most suitable approaches to mitigate the dissemination of ARGs from WWTPs globally.}, } @article {pmid41576933, year = {2026}, author = {Hernandez-Leyva, AJ and Berna, AZ and Bui, MH and Liu, Y and Rosen, AL and Lint, MA and Whiteside, SA and Jaeger, N and McDonough, RT and Joardar, N and Santiago-Borges, J and Tomera, CP and Luo, W and Odom John, AR and Kau, AL}, title = {The gut microbiota shapes the human and murine breath volatilome.}, journal = {Cell metabolism}, volume = {38}, number = {4}, pages = {779-793.e8}, pmid = {41576933}, issn = {1932-7420}, support = {T32 GM007200/GM/NIGMS NIH HHS/United States ; R01 HD109963/HD/NICHD NIH HHS/United States ; R21 AI154370/AI/NIAID NIH HHS/United States ; R33 HD105594/HD/NICHD NIH HHS/United States ; F30 DK127584/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Volatile Organic Compounds/metabolism/analysis ; Breath Tests ; Mice ; *Gastrointestinal Microbiome ; Child ; Female ; Male ; Asthma/microbiology/metabolism ; Gas Chromatography-Mass Spectrometry ; Germ-Free Life ; Child, Preschool ; Mice, Inbred C57BL ; }, abstract = {The gut microbiota is crucial to health, yet implementation of microbiota-based therapeutics is limited by the lack of rapid diagnostics. We hypothesize that breath contains gut microbe-derived volatile organic compounds (VOCs) reflecting microbiota composition and metabolism. In healthy children, we found that breath VOC composition (or volatilome), assessed by gas chromatography-mass spectrometry, correlates with gut microbiome composition and function. By capturing exhaled breath from human-stool-colonized and monocolonized gnotobiotic mice, we profiled breath VOCs and discovered that murine breath is also significantly influenced by the gut microbiome. VOCs from cultured gut microbes were identified in vivo in monocolonized gnotobiotic colonized mice. As a proof of principle, we demonstrated that exhaled breath predicts the abundance of a disease-associated bacterium, Eubacterium siraeum, in children with asthma. Altogether, our studies identify microbe-derived VOCs in breath, show that gut bacterial metabolism directly contributes to mammalian breath VOC profiles, and inform the development of non-invasive microbiome diagnostics.}, } @article {pmid41576939, year = {2026}, author = {Nalapareddy, K and Haslam, DB and Kissmann, AK and Alenghat, T and Stahl, S and Rosenau, F and Zheng, Y and Geiger, H}, title = {Microbiota from young mice restore the function of aged ISCs.}, journal = {Stem cell reports}, volume = {21}, number = {2}, pages = {102788}, pmid = {41576939}, issn = {2213-6711}, support = {R01 DK137771/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Stem Cells/metabolism/cytology ; Wnt Signaling Pathway ; *Aging ; Mice ; *Intestinal Mucosa/cytology/metabolism/microbiology ; Regeneration ; *Gastrointestinal Microbiome ; *Microbiota ; Basic Helix-Loop-Helix Proteins/metabolism ; Homeostasis ; Akkermansia ; }, abstract = {Homeostasis in the intestinal epithelium depends on intestinal stem cells (ISCs). A reduction in the function of ISCs, caused by a decline of canonical Wnt signaling in ISCs, contributes to a reduced regenerative potential of the aged intestine. The composition of the intestinal microbiota changes upon aging. We report here that aging-associated changes in the composition of the microbiota result in reduced canonical Wnt signaling through Ascl2 in ISCs, which causes a decline in the regenerative potential of aged ISCs in vivo. We demonstrate, using microbiota transfer experiments, that interestingly, elevated levels of Akkermansia muciniphila in the intestine cause a reduction of Ascl2-mediated canonical Wnt signaling in ISCs and thus reduced regeneration of the aged epithelium. The composition of the intestinal microbiota thus plays a critical role in regulating the function of ISCs. Our data imply potential therapeutic approaches via modulation of the composition of microbiota for aging-associated changes in the function of ISCs.}, } @article {pmid41576942, year = {2026}, author = {Masi, D and Watanabe, M and Clément, K}, title = {Gut microbiome and obesity care: Bridging dietary, surgical, and pharmacological interventions.}, journal = {Cell reports. Medicine}, volume = {7}, number = {2}, pages = {102573}, pmid = {41576942}, issn = {2666-3791}, mesh = {*Obesity/microbiology/therapy/metabolism/drug therapy ; Humans ; Animals ; *Gastrointestinal Microbiome/physiology/drug effects ; Multiomics ; *Diet ; }, abstract = {In the mid-2000s, mouse studies suggested that the gut microbiome might influence energy harvest, fat storage, appetite, insulin sensitivity, and inflammation. Since then, our understanding of the gut microbiome's role in obesity has advanced significantly. Mechanistic studies identified microbial metabolites, such as short-chain fatty acids, bile acids, branched-chain amino acids, tryptophan catabolites, and imidazole propionate, as key modulators of metabolism, inflammation, and gut-brain communication. Metagenomic and multi-omics technologies now provide deeper insights into the intricate interactions between microbes, metabolites, and host factors, reshaping obesity research and reinforcing the need for phenotype stratification by recognizing microbiome-driven metabolic profiles. Integrating gut microbiome data into clinical strategies may enable targeted interventions for specific obesity subtypes, advancing prevention and personalized care. However, as new anti-obesity medications emerge, it is imperative to determine how microbiome-based therapies can complement them, considering efficacy, cost, and patient-specific variability.}, } @article {pmid41576946, year = {2026}, author = {Lan, X and Liang, Q and He, J and Wu, J and Zhang, X and Li, F and Li, L and Zhao, G and Guo, R and Jia, H}, title = {Microbial single-cell omics in situ.}, journal = {Cell genomics}, volume = {6}, number = {4}, pages = {101128}, pmid = {41576946}, issn = {2666-979X}, mesh = {Humans ; *Single-Cell Analysis/methods ; Animals ; Mice ; Single-Cell Gene Expression Analysis ; Transcriptome/genetics ; Colorectal Neoplasms/microbiology ; Multiomics ; Bacillus/genetics ; Saliva/microbiology ; Bacteroides/genetics ; }, abstract = {Metagenomics has enabled the understanding of the microbial composition and functional potential in various environments. Using laser-induced forward transfer (LIFT) technology, we report high-quality microbial single-cell genomes or transcriptomes in complex samples such as mouse gut, human saliva, and tumor sections. Bacterial cells in close proximity to each other or to host cells could be directly analyzed using this single-cell approach. Bacterial cells in mice or human samples could be fluorescently labeled for single-cell visualization before collection. The high-quality single-cell transcriptome results allow us to delineate cell-fate commitment in Bacillus sporulation and preliminarily characterize gene expression from Bacteroides in a colorectal cancer sample. The method is scalable and precise and empowers insights about microbial populations and single-cell interactions with the host.}, } @article {pmid41577053, year = {2026}, author = {Wang, Z and Luo, Z and You, J and Zhu, X and Sui, X and Ji, G}, title = {Synergistic application of biochar with organic fertilizer enhances soil carbon sequestration by optimizing mineral-associated organic matter formation pathway contributions.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134063}, doi = {10.1016/j.biortech.2026.134063}, pmid = {41577053}, issn = {1873-2976}, mesh = {*Charcoal/chemistry ; *Fertilizers ; *Soil/chemistry ; *Carbon Sequestration ; *Minerals/chemistry ; Carbon ; *Organic Chemicals ; Soil Microbiology ; }, abstract = {Mineral-associated organic matter (MAOM) constitutes the dominant long-term carbon pool for soil organic carbon (SOC) sequestration, yet how MAOM formation pathways respond to soil management strategies remains unclear. We conducted a field experiment with four treatments: no addition (Control), biochar (BC) applied alone, or combined with low-dose (BC + LF) and high-dose (BC + HF) organic fertilizer (OF). Enzyme activity and metagenomic analyses revealed that different amendments enhanced MAOM formation by facilitating microbial carbon pump (MCP)-mediated turnover pathway. BC + LF appropriately improved MCP by elevating multiple enzyme activities (57.7%-198.8%), enriching r-strategists (e.g., Pseudomonadota), and shifting microbial communities toward resource acquisition, while simultaneously preserving microbial community structure to maximize MAOM formation (37.3%). In contrast, BC alone marginally promoted recalcitrant carbon turnover, whereas BC + HF overstimulated labile carbon turnover. Both treatments limited MAOM accumulation, resulting in only 18.6% and 22.2% increases, respectively. Given the dual role of dissolved organic matter (DOM) as microbial substrate and MAOM precursor, we analyzed DOM characteristics and DOM-microbial interactions to reveal two pathways for MAOM formation: direct sorption of aromatic compounds and microbial transformation of DOM molecules to highly unsaturated compounds (HUCs). A DOM "abundance-transformation" indicator-based approach was applied to estimate the proportional contributions of these two pathways. The amendments increased microbial contributions from 24.3% to 77.1%, with peak MAOM accumulation occurring when microbial contributions reached a critical threshold of 56.2%. Overall, our findings advance mechanistic understanding of how organic amendments regulate microbial turnover to enhance stable carbon pools and highlight that optimizing the balance of MAOM formation pathways can maximize SOC sequestration.}, } @article {pmid41577432, year = {2026}, author = {Shen, J and Tigabu, A and Mishra, SK and Urmi, U and Ozkan, J and Stapleton, F and Yasir, M and Willcox, M}, title = {Antimicrobial resistance surveillance: lessons learnt from large databases of antimicrobial resistance genes.}, journal = {The British journal of ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1136/bjo-2025-328620}, pmid = {41577432}, issn = {1468-2079}, abstract = {Ocular infections, caused by a variety of microbes, are likely to become more difficult to treat due to the global increase in antimicrobial resistance (AMR). Traditional assays for resistance only analyse a small proportion of the possible resistance capability of microbes. This review discusses the use of genomic datasets for predicting AMR and their current applications in investigating ocular infections. The use of whole genome sequencing coupled with several large databases on antimicrobial resistance genes (ARGs) can predict phenotypic resistance and multidrug resistance in bacteria. Use of this technology for viral and fungal infections is less advanced and would be a useful area for future research. Metagenomic analysis of the ocular surface microbiome for ARGs could be a sensitive and rapid method for tracking resistance in ocular infections, and monitoring commensal reservoirs of transferable ARGs. Applications of these newer technologies to ocular infections also have the potential to assess the long-term impact of topical antibiotics, disinfectants and preservative use on the ocular microbiome, as well as being used in epidemiological studies to study acquisition and transmission of ARGs.}, } @article {pmid41577947, year = {2026}, author = {Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Henry, AR and Davis, RL and Laboune, F and Longtine, ER and Godbole, S and Horigan, S and Ruhs, EC and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Heraud, JM and Dussart, P and Douek, DC and Brook, CE}, title = {Co-speciation and host-switching drives diversity of picornaviruses and sapoviruses in Malagasy fruit bats.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6583}, pmid = {41577947}, issn = {2045-2322}, support = {P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; OPP1211841//Bill and Melinda Gates Foundation/ ; D18AC00031//Defense Sciences Office, DARPA/ ; P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; }, abstract = {UNLABELLED: Bats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied. Picornavirales are an order of enteric viruses that cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification of Picornavirales worldwide. Picornaviridae and Caliciviridae (families within Picornavirales) have been described in bats across mainland Africa, but surveillance for these viruses has been rare in the Southwest Indian Ocean Islands. Prior work in Madagascar has described numerous bat viruses, some with zoonotic potential, that demonstrate both high identity to and extreme divergence from viruses found in sister bat species in Africa. Using metagenomic Next Generation Sequencing of urine and fecal samples obtained from three species of endemic Malagasy fruit bats (Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis), we identify and describe 13 full-length and 38 partial-length genomic sequences within the Picornaviridae and Caliciviridae families (36 picornavirus and 15 Sapovirus sequences). We find evidence that host-switching between Madagascar and mainland African bat picornaviruses and sapoviruses, followed by host-parasite co-speciation, likely shaped the diversification pattens of these novel sequences, with little evidence for cross-species transmission among Malagasy bat species in close contact.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-34969-2.}, } @article {pmid41578124, year = {2026}, author = {Candeliere, F and Sola, L and Busi, E and Pedroni, S and Raimondi, S and Amaretti, A and Greco, S and Dominici, M and Rossi, M}, title = {Altered abundance in cancer patients gut of diadenylate cyclase-encoding bacteria.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6070}, pmid = {41578124}, issn = {2045-2322}, support = {Progetto identificato con codice PE00000019, Titolo "HEAL ITALIA" - Spoke 5 - CUP E93C22001860006//PIANO NAZIONALE DI RIPRESA E RESILIENZA(PNRR) - MISSIONE 4 COMPONENTE 2/ ; }, mesh = {Humans ; *Bacteria/enzymology/genetics ; *Gastrointestinal Microbiome/genetics ; *Neoplasms/microbiology/immunology/therapy ; *Phosphorus-Oxygen Lyases/genetics/metabolism ; Dinucleoside Phosphates/metabolism ; }, abstract = {c-di-AMP is a bacterial second messenger recognized by host immune sensors such as the STING pathway, linking gut microbiota activity to tumor immunity. This interaction holds significant therapeutic potential particularly for oncologic patients, given the increasingly recognized relationship between gut microbiota and tumor immunity. Recent evidence shows that microbial c-di-AMP can enhance anti-tumor responses and improve the efficacy of PD-1/PD-L1 blockade and radiotherapy. This study identified gut microbial species capable of synthesizing c-di-AMP by mining the Unified Human Gastrointestinal Protein catalogue for diadenylate cyclases (DACs), generating a database of 4,228 DACs across 3,901 species out of 4,744 presents in the Unified Human Gastrointestinal Genome catalogue. Analysis of metagenomic data from 190 healthy subjects and 569 cancer patients (melanoma, NSCLC, renal carcinoma) revealed a significantly higher abundance of DAC-encoding species in healthy microbiota, with no differences between responders and non-responders to immunotherapy. These findings indicate that c-di-AMP-producing bacteria are depleted in cancer-associated microbiota, supporting further studies on their role in modulating anti-tumor immunity.}, } @article {pmid41578762, year = {2025}, author = {Shen, F and Xu, C and Wang, C}, title = {Gut Microbiome Diagnostic Biomarkers for Colorectal Cancer.}, journal = {The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology}, volume = {37}, number = {1}, pages = {62-74}, pmid = {41578762}, issn = {2148-5607}, mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; Feces/microbiology ; Female ; Male ; *Biomarkers, Tumor/analysis ; *Adenoma/microbiology/diagnosis ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Fusobacterium nucleatum/isolation & purification/genetics ; Aged ; Peptostreptococcus/isolation & purification/genetics ; Disease Progression ; Adult ; Prognosis ; Early Detection of Cancer/methods ; Sensitivity and Specificity ; }, abstract = {BACKGROUND/AIMS: Gold standard diagnostic methods, such as invasive procedures and serum biomarkers, have limited sensitivity and specificity for the detection of colorectal cancer (CRC). Thus, the development of more accurate and noninvasive detection approaches is imperative. Emerging research elucidating the intricate role of the gut microbiota in CRC pathogenesis underscores the need for precision screening tailored to high-risk cohorts to improve early detection and intervention strategies and comprehensively address this challenging clinical problem.

MATERIALS AND METHODS: Fecal metagenomic sequencing datasets were employed to identify potential bacterial biomarkers for CRC diagnosis and selected relevant microbial taxa for subsequent validation. A total of 180 participants were enrolled: 65 healthy controls (HC), 65 colorectal adenoma patients, and 50 CRC patients, and fecal samples were analyzed using fluorescence quantitative polymerase chain reaction to confirm biomarker relative abundance, culminating in the establishment of an evolutionary model for CRC progression; furthermore, a treatment efficacy and prognostication model supported by comprehensive statistical methodologies was established.

RESULTS: This study analyzed fecal microbial biomarkers associated with CRC progression and identified differentially abundant bacterial species across HCs, adenoma, and CRC patient groups. Notably, Fusobacterium nucleatum (Fn) and Peptostreptococcus anaerobius (P. anaerobius) showed significant correlations with CRC stage and metastasis, highlighting their potential as diagnostic biomarkers. Among individual microbes, P. anaerobius exhibited the highest diagnostic value when combined with Fn.

CONCLUSION: The results underscore the potential application of fecal microbial markers, particularly Fn and P. anaerobius, for diagnosing CRC and monitoring its progression.   Cite this article as: Shen F, Xu C, Wang C. Gut microbiome diagnostic biomarkers for colorectal cancer. Turk J Gastroenterol. 2026;37(1):62-74.}, } @article {pmid41578951, year = {2026}, author = {Yang, Q and Wei, X and Wang, DP and Lai, Y and Luo, H and Liu, AF}, title = {Unraveling the taxonomic novelty and functional significance of viruses in anammox granular sludges.}, journal = {FEMS microbiology letters}, volume = {373}, number = {}, pages = {}, doi = {10.1093/femsle/fnag008}, pmid = {41578951}, issn = {1574-6968}, support = {2025A1515010753//Natural Science Foundation of Guangdong Province/ ; XBY-K1-2023-19//Key Science and Technology Project of PowerChina Northwest Engineering Corporation Limited/ ; 230225176275072//Science and Technology Planning Project of Shaoguan City/ ; }, mesh = {Metagenomics ; *Sewage/virology/microbiology ; *Viruses/classification/genetics/isolation & purification ; Bioreactors/microbiology/virology ; Phylogeny ; *Bacteria/virology/metabolism/genetics ; Genome, Viral ; Oxidation-Reduction ; Anaerobic Ammonia Oxidation ; }, abstract = {The microbial communities in anaerobic ammonium oxidation (anammox) bioreactors have been extensively studied to unveil their diversity and roles in nitrogen removal. Yet, the viruses infecting the key functional microorganisms in these systems remain unexplored. Here, we utilize genome-resolved metagenomics to systematically assess viral diversity, functions and interaction with microbial hosts in granular sludges of different sizes from three laboratory-scale (LS) and full-scale (FS) anammox reactors. Analysis of the 190 microbial genomes recovered through bulk metagenomics revealed the predominance (FS 29%-54% and LS 31%-45%) of anammox species exclusively from the Brocadiae in all sludges examined. Viral metagenomics identified 5210 candidate viral species, 61.1∼97.3% of which were novel. Members of six genera from the Caudovirales order constitute the majority of the taxonomically assigned viral species. Between-group variance analysis revealed that both environment (reactor type) and granule size had a significant influence on the metabolic potential of viruses. In silico predictions showed that many of the important functional microbes were frequent targets of previously unrecognized viruses, including six viral populations infecting the anammox bacteria. Our results suggest that viruses actively infect microbial hosts and thus may have a major impact on the microbial metabolic processes and biogeochemical cycling in the anammox reactors.}, } @article {pmid41579151, year = {2026}, author = {Gan, T and Zhang, N and Liu, L and Li, W and Ding, M and Chen, J and Zhou, T and Mao, A}, title = {Lactobacillus plantarum CCFM639 Alleviates Hypertension by Reshaping Gut Microbiota and Regulating Key Metabolites.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41579151}, issn = {1867-1314}, support = {82400481//National Natural Science Foundation of China/ ; }, abstract = {A strong association between the gut microbiome and hypertension has emerged. Our previous work demonstrated that supplementation with L. plantarum CCFM639 (CCFM639) reduced blood pressure (BP) in hypertensive mice involving inhibiting the growth of S. aureofaciens Tü117 and conducted an exploratory randomized trial in adults with prehypertension or stage 1 hypertension. Here, we evaluate the effects of CCFM639 supplementation (10[9] CFU/day for 8 weeks) on the gut microbiome and serum metabolome in a subset of these participants (n = 20). Untargeted metabolomic analysis was performed on serum samples, and stool microbiome composition was assessed via metagenomic sequencing. Mono-CCFM639 supplementation altered the metabolomic profile without affecting gut microbiota diversity but reshaped microbial composition. CCFM639 supplementation modulated both the gut microbiome and serum metabolome. Circulating gut-derived metabolites are likely to account for the improvements in BP, suggesting that CCFM639 supplementation could be a key component of nutritional interventions targeting the gut microbiota for hypertension management.}, } @article {pmid41579934, year = {2026}, author = {Yu, Y and Che, L and Sun, L and Wang, S and Du, N}, title = {A rare case of disseminated Mycoplasma pneumoniae infection spreading from a pelvic lesion to a psoas muscle abscess.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {167}, number = {}, pages = {108420}, doi = {10.1016/j.ijid.2026.108420}, pmid = {41579934}, issn = {1878-3511}, mesh = {Humans ; Female ; Adolescent ; *Mycoplasma pneumoniae/genetics/isolation & purification/drug effects ; Immunocompromised Host ; Anti-Bacterial Agents/therapeutic use ; *Psoas Abscess/microbiology/drug therapy/diagnosis ; *Pneumonia, Mycoplasma/drug therapy/microbiology/diagnosis ; RNA, Ribosomal, 23S/genetics ; Drug Resistance, Bacterial ; Anemia, Aplastic/complications ; Retrospective Studies ; }, abstract = {OBJECTIVES: Extrapulmonary infections caused by Mycoplasma pneumoniae are uncommon, and their manifestation as soft tissue abscesses is particularly rare. Diagnosing such culture-negative infections in immunocompromised hosts poses a significant clinical challenge. This study reports a case of M. pneumoniae-induced soft tissue abscesses in an immunocompromised patient, highlighting the diagnostic utility of advanced microbiological techniques.

METHODS: We retrospectively analyzed the clinical course of a 17-year-old female with aplastic anemia and a history of haploidentical hematopoietic stem cell transplantation, who presented with recurrent fever and pelvic/psoas abscesses. Metagenomic next-generation sequencing (mNGS) was performed on abscess drainage to identify the causative pathogen and its resistance profile.

RESULTS: mNGS of the abscess fluid identified M. pneumoniae as the dominant pathogen and revealed a macrolide-resistant 23S rRNA A2063G mutation. Consequently, targeted antimicrobial therapy with tigecycline and omadacycline was administered, which led to the resolution of clinical symptoms.

CONCLUSION: This case underscores the critical role of mNGS in the accurate diagnosis of culture-negative extrapulmonary infections. Furthermore, it demonstrates how mNGS-guided resistance profiling can inform effective antimicrobial therapy in immunocompromised patients.}, } @article {pmid41579937, year = {2026}, author = {Wu, Y and Yu, X and Qi, J and Chen, Y and Wang, R and Liu, J and Zhang, Y and Zhang, W}, title = {Metagenomic next-generation sequencing enables early detection and outcome improvement in perioperative mucormycosis after liver transplantation: A single-center experience.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {165}, number = {}, pages = {108419}, doi = {10.1016/j.ijid.2026.108419}, pmid = {41579937}, issn = {1878-3511}, mesh = {Humans ; Male ; *Liver Transplantation/adverse effects ; *Mucormycosis/diagnosis/drug therapy/microbiology ; Retrospective Studies ; Middle Aged ; Antifungal Agents/therapeutic use ; *High-Throughput Nucleotide Sequencing/methods ; Adult ; *Metagenomics/methods ; Early Diagnosis ; Aged ; Treatment Outcome ; }, abstract = {OBJECTIVES: Mucormycosis is a rapidly progressive and highly lethal fungal infection in liver transplant recipients, with early diagnosis remaining a major challenge. This study aimed to evaluate the clinical utility of metagenomic next-generation sequencing (mNGS) for early detection and management of perioperative mucormycosis in adult liver transplant patients.

METHODS: A retrospective analysis was conducted on 539 adult patients who underwent liver transplantation between June 2022 and August 2025 at a single tertiary center. Nine patients with clinically confirmed perioperative mucormycosis, in whom mNGS was the first positive diagnostic tool, were included. Clinical characteristics, diagnostic modalities, antifungal strategies, and outcomes were systematically reviewed.

RESULTS: Mucormycosis was identified in 1.67% (9/539) of liver transplant recipients. All patients were male with a median age of 51 years. Pulmonary mucormycosis was the most common presentation (n = 5), followed by disseminated (n = 3) and cutaneous infection (n = 1). In all cases, mNGS provided the earliest microbiological evidence, preceding culture and histopathology. Species detected included Cunninghamella spp., Rhizopus microsporus, and Rhizomucor pusillus. The mortality rate of disseminated disease was 100%, whereas localized pulmonary and cutaneous infections had a combined cure or improvement rate of 66.7%. Early targeted antifungal therapy guided by mNGS (amphotericin B formulations combined with posaconazole or isavuconazole) was associated with improved outcomes in nondisseminated cases.

CONCLUSION: mNGS enables earlier detection of perioperative mucormycosis compared to conventional diagnostic methods and supports timely initiation of targeted therapy. Rapid mNGS-guided intervention may prevent progression to disseminated disease and improve prognosis in liver transplant recipients. Integration of mNGS into the diagnostic workflow is recommended for high-risk patients with unexplained pulmonary or cutaneous lesions.}, } @article {pmid41579975, year = {2026}, author = {Ferrero, G and Mastrocola, R and Tarallo, S and Pardini, B and Scheijen, J and van de Waarenburg, M and Gallo, G and Chatziioannou, AC and Robinot, N and Keski-Rahkonen, P and Piccinno, G and Segata, N and Aglago, EK and Hughes, DJ and Jenab, M and Schalkwijk, CG and Naccarati, A}, title = {Integrative analyses of dicarbonyls and advanced glycation end-products with multiomic profiles across tissue, plasma and stool samples reveal methylglyoxal accumulation in colon cancer.}, journal = {Free radical biology & medicine}, volume = {246}, number = {}, pages = {518-530}, pmid = {41579975}, issn = {1873-4596}, support = {001/WHO_/World Health Organization/International ; }, mesh = {Humans ; *Colonic Neoplasms/metabolism/pathology/genetics ; *Pyruvaldehyde/metabolism ; *Glycation End Products, Advanced/metabolism ; Multiomics ; Feces/chemistry/microbiology ; Male ; Female ; Glyoxal/metabolism ; Deoxyglucose/analogs & derivatives/metabolism ; Aged ; Middle Aged ; Lactoylglutathione Lyase/genetics/metabolism ; Metabolomics ; Gastrointestinal Microbiome ; }, abstract = {Advanced Glycation Endproducts (AGEs) arise from the reaction of proteins with highly reactive dicarbonyl compounds such as methylglyoxal (MGO), glyoxal (GO) and 3-deoxyglucosone (3-DG), which have been implicated in inflammation and carcinogenesis. How dicarbonyls and AGEs are distributed across tumor tissue and surrogate specimens, and how they relate to systemic metabolism, AGE-related pathways, and alterations in gut microbiota in colon cancer, remains poorly understood. An integrative multi-specimen analysis of MGO, GO, 3-DG and major AGEs was performed using targeted tandem mass spectrometry in matched tumor tissue, adjacent normal mucosa, plasma, and stool from 26 sporadic colon cancer patients. These measurements were combined with tumor RNA-sequencing, untargeted plasma metabolomics, and stool shotgun metagenomics generated from the same individuals. A marked accumulation of MGO was observed in tumor tissue when compared with adjacent mucosa, accompanied by higher levels of the MGO-derived AGE Nδ-[5-hydro-5-methyl-4-imidazolon-2-yl]-ornithine (MG-H1). Tissue MG-H1 concentrations significantly correlated with corresponding plasma levels. Elevated tumor MGO levels were associated with up-regulation of GLO1 (encoding for the detoxifying enzyme glyoxalase-1), DDOST (coding for the AGE-clearance receptor AGE-R1), and the glycolytic flux marker triose phosphate isomerase (TPI), alongside down-regulation of the AGE-scavenger receptor CD36. These findings suggest a candidate remodeling of dicarbonyl-handling pathways. The MGO/GO ratio in tumors was positively associated with the relative abundances of Fusobacterium nucleatum and Parvimonas micra, two bacterial species related to colorectal carcinogenesis, and with metagenomic signatures of oral-derived taxa colonizing the gut. This pilot integrative analysis highlighted novel coherent associations among tissue, circulating, and stool levels of MGO-derived AGEs, the expression of AGE-related metabolic pathways, and microbial signatures in colon cancer. If confirmed in larger studies, these candidate molecular and microbial interactions may provide novel insights into the dicarbonyl stress involvement in tumor biology.}, } @article {pmid41581053, year = {2026}, author = {Li, X and Ma, R and Gan, L and Zhang, R and Qian, J}, title = {Metagenomic sequencing provides evidence of the nasal microbiota's influence on idiopathic orbital myositis: A case-control study.}, journal = {Indian journal of ophthalmology}, volume = {74}, number = {2}, pages = {307-309}, pmid = {41581053}, issn = {1998-3689}, } @article {pmid41581112, year = {2026}, author = {Lett, JM and Scussel, S and Chéhida, SB and Hoareau, M and Filloux, D and Fernandez, E and Roumagnac, P and Parvedy, E and Quirin, E and Clain, C and Minatchy, J and Roux, E and Teycheney, PY and Lefeuvre, P}, title = {Metagenomic screening of the virome of symptomatic tomato plants from La Réunion Island uncovers a complex of viruses including a newly identified whitefly-transmitted polerovirus.}, journal = {Archives of virology}, volume = {171}, number = {2}, pages = {62}, pmid = {41581112}, issn = {1432-8798}, mesh = {*Solanum lycopersicum/virology ; Animals ; *Hemiptera/virology ; Reunion ; Phylogeny ; *Plant Diseases/virology ; Metagenomics ; *Luteoviridae/genetics/classification/isolation & purification ; *Virome ; Genome, Viral ; Insect Vectors/virology ; }, abstract = {Using unbiased high-throughput sequencing for metagenomic screening of viruses in diseased tomato plants, we identified a viral complex that includes viruses previously reported in tomato crops on La Réunion Island as well as a novel polerovirus, tentatively named "tomato necrotic yellowing virus" (ToNYV, proposed species, "Polerovirus ToNYV"). Molecular characterization and phylogenetic analysis revealed that ToNYV is closely related to two recently described poleroviruses from Africa and the Middle East, one of which is transmitted by the whitefly Bemisia tabaci, a trait uncommon among poleroviruses. Our transmission experiments demonstrated that ToNYV is also transmitted by B. tabaci and is prevalent across major tomato-growing regions of La Réunion. These findings highlight the value of metagenomic virome analysis in diseased plants for identifying novel viruses potentially involved in emerging plant diseases, either individually or as components of viral complexes.}, } @article {pmid41581292, year = {2026}, author = {Diehl, C and Breyer, GM and Torres, MC and Wuaden, CR and Rebelatto, R and Pastore, J and da Silveira Nicoloso, R and Dorn, M and Kich, JD and Siqueira, FM}, title = {Shaping soil fungal communities: How swine waste treatment systems and geography drive fungal community shifts.}, journal = {The Science of the total environment}, volume = {1015}, number = {}, pages = {181376}, doi = {10.1016/j.scitotenv.2026.181376}, pmid = {41581292}, issn = {1879-1026}, mesh = {Animals ; *Soil Microbiology ; Swine ; *Fungi/classification ; Brazil ; Fertilizers ; Soil/chemistry ; Agriculture ; }, abstract = {The use of swine waste as an organic fertilizer is an important practice in sustainable agriculture. This study aims to evaluate the effects of two common swine waste treatment systems, Covered Lagoon Biodigesters (CLB) and Waste Stabilization Ponds (WSP), on fungal community structure in soil. Soil and waste samples were collected from swine farms across five Brazilian states, representing different geographical regions with distinct climate, soil types, and vegetation. A metagenomic approach was employed to analyze the fungal communities present in the samples. Our results revealed that fertilization with swine waste did not significantly affect the overall diversity of fungal communities, although distinct shifts in community composition were observed between fertilized and non-fertilized soils. Notably, reads assigned to Sugiyamaella lignohabitans were detected only in samples from waste stabilization ponds, suggesting that this environment may favor fungal taxa associated with lignocellulose degradation. Furthermore, the fungal genera Fusarium and Rhizophagus exhibited contrasting responses to fertilization, with Fusarium being more abundant in fertilized soils and Rhizophagus decreasing in abundance. Geographic variation in fungal community composition was also observed, correlating with the physicochemical properties of the soil. These findings indicate that, in our dataset, the waste treatment systems had little influence on the fungal diversity of waste samples, whereas soil fertilization with swine waste was associated with marked shifts in fungal community composition, particularly in terms of taxonomic structure.}, } @article {pmid41581397, year = {2026}, author = {Fan, Y and Wang, Y and Liu, D and Yao, Y and Liu, J and Zhao, J and Dong, L and Wang, C and Liu, W}, title = {Exposure evidence and transmission characteristics of biological aerosols in a high-rise building.}, journal = {Journal of hazardous materials}, volume = {503}, number = {}, pages = {141221}, doi = {10.1016/j.jhazmat.2026.141221}, pmid = {41581397}, issn = {1873-3336}, mesh = {Aerosols/analysis ; *Air Microbiology ; *Air Pollution, Indoor/analysis ; Environmental Monitoring ; Humans ; Sewage/microbiology ; Bacteria/genetics ; }, abstract = {Indoor bioaerosols originating from residential drainage systems have the potential to migrate into living spaces, possibly posing a respiratory concern. By coupling the technology of metagenomic shotgun sequencing with fluorescein tracers, the residents living on the same drainage riser of a 17-story residence and their associated sewage wells were studied to analyse the microbial spectrum of indoor bioaerosols and the spatiotemporal distribution characteristics of their lateral and longitudinal propagation. The air samples collected from these apartments and the sewage samples collected from corresponding sewage wells revealed that the relative abundances of P. aeruginosa and A. baumannii of the bacterial community in the air reached 30% and 10 % respectively. Moreover, the fecal indicator bacterium S. enterica could be detected, confirming the presence of the "fecal-water-air"" chain. Tracer experiments further revealed that a breach in water seals allowed aerosols of less than 0.5 µm cross-floor to diffuse over three layers within 19 min through the stack effect, with upwards deposition 2.5-3.1 times greater than downwards deposition. Even though the water seals remained intact, a single toilet flush could horizontally spread 0.3 µm biological aerosols into adjacent rooms within 6 min. In summary, the contribution of the drainage system to indoor bioaerosols was confirmed for the first time in both genetic sequencing and aerosol transport dimensions, providing a reference basis for the biosafety design of high-rise residential buildings.}, } @article {pmid41581442, year = {2026}, author = {Chen, Y and Huang, S and Zhang, S and Wang, H and Song, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Wang, X and Zhang, W}, title = {Viral metagenomics reveals the RNA viral composition of herbivorous wildlife on the Qinghai-Tibet Plateau.}, journal = {Virology}, volume = {617}, number = {}, pages = {110814}, doi = {10.1016/j.virol.2026.110814}, pmid = {41581442}, issn = {1096-0341}, mesh = {Animals ; *Metagenomics ; Phylogeny ; *RNA Viruses/genetics/classification/isolation & purification ; *Animals, Wild/virology ; Tibet ; Feces/virology ; *Virome ; RNA, Viral/genetics ; Genetic Variation ; Genome, Viral ; }, abstract = {RNA viruses, a widely distributed group of pathogens in nature, possess exceptionally high genetic diversity and rapid evolutionary potential. High-altitude ecosystems, represented by the Qinghai-Tibet Plateau, with their unique environmental conditions, may harbor distinct viral communities. However, there remains a lack of systematic understanding regarding the composition and distribution of RNA viruses in wildlife under such extreme environments. In this study, a total of 741 fecal samples were collected from three regions on the Qinghai-Tibet Plateau, and viral metagenomics technology was used to reveal the composition and diversity of RNA viruses in the fecal samples of six species of herbivorous wild animals on the plateau. We identified a substantial abundance of RNA viruses, classified into 18 distinct viral families. Furthermore, the structure of the viral communities varied among different host species. Through assembly, 28 viral sequences belonging to the families Astroviridae, Picornaviridae, Picobirnaviridae, Tobaniviridae, and Caliciviridae were identified. Phylogenetic analysis revealed that the newly identified viral strains share close relationships with viruses found in humans, marmots, and other mammals. The results indicate that wildlife in this region are reservoirs of unidentified RNA viruses, some of which may pose potential threats to public health and the animal husbandry. These findings provide crucial scientific evidence and data support for future virus surveillance, ecological risk assessment, and the prevention and control of emerging infectious diseases at their source.}, } @article {pmid41581464, year = {2026}, author = {Trinh, HP and Lee, SH and Park, HD}, title = {Nitrogen loading fluctuations impact microbial community assembly and functional redundancy in anammox reactors.}, journal = {Water research}, volume = {293}, number = {}, pages = {125434}, doi = {10.1016/j.watres.2026.125434}, pmid = {41581464}, issn = {1879-2448}, mesh = {*Bioreactors/microbiology ; *Nitrogen/metabolism ; Bacteria/metabolism ; }, abstract = {Nitrogen loading rate (NLR) fluctuations are common in full-scale anammox systems and can compromise process stability, yet the ecological mechanisms underlying system resilience under disturbed conditions remain insufficiently understood. This study investigated how different intensities of NLR disturbances influence microbial community assembly processes and functional redundancy, and how these ecological responses shape nitrogen removal performance. Two anammox sequencing batch reactors were operated for 180 days under either stable (R1) or fluctuating (R2) NLR conditions. Moderate NLR fluctuations (1.4-fold, Phase A) enhanced nitrogen removal efficiency (up to 99.7%) and increased the relative abundance of anammox bacteria to 26.4%, whereas severe fluctuations (2.0-fold, Phase B) caused deterioration in nitrogen removal efficiency (to 72.2%) and a decline in anammox bacteria abundance (7.1%). Metagenome-assembled genome analysis revealed pathway-level reorganization of nitrogen metabolism under fluctuating conditions, with increases in anammox-associated genes (hzsABC and hdh/hao-like) and the DNRA gene (nrfAH) during Phase A, followed by partial declines in Phase B. Neutral community modeling showed that stochastic processes dominated microbial assembly under moderate fluctuations (R[2] = 0.77), promoting coexistence and community adaptability, while deterministic selection prevailed under severe fluctuations (R[2] = 0.56). Functional redundancy exhibited a similar non-linear response, increasing under moderate disturbance (0.73) and declining sharply under severe disturbance (0.48), indicating reduced buffering capacity. These findings provide quantitative insight into the mechanistic link between loading disturbances and ecosystem resilience, offering a foundation for developing operational strategies that enhance the robustness of anammox-based nitrogen removal systems.}, } @article {pmid41581489, year = {2026}, author = {Liu, Z and Zhao, F and Li, Q and Shang, Q and Fang, D and Li, X and Li, H and He, Q and Zhang, D and Cheng, J and Zhu, Y and Li, Z and Silva, AS and Chen, J}, title = {Multi-omics chemical and biochemical profiling reveals ellagic acid enhances insulin sensitivity via gut microbiota-tryptophan-indole signaling mechanism.}, journal = {Food chemistry}, volume = {505}, number = {}, pages = {147984}, doi = {10.1016/j.foodchem.2026.147984}, pmid = {41581489}, issn = {1873-7072}, mesh = {*Indoles/metabolism ; Animals ; *Insulin Resistance ; *Gastrointestinal Microbiome/drug effects ; *Tryptophan/metabolism ; *Ellagic Acid/metabolism/chemistry ; Signal Transduction/drug effects ; Multiomics ; Bacteria/isolation & purification/classification/genetics/metabolism ; Male ; Humans ; Mice ; }, abstract = {Ellagic acid (EA) is a dietary polyphenol with limited systemic bioavailability, resulting in substantial intestinal exposure. However, the biochemical mechanisms by which EA modulates gut microbiota and metabolism remain unclear. Here, EA improved glucose tolerance and enhanced insulin sensitivity, with histology confirming reduced lipid accumulation and restored tissue architecture in liver, skeletal muscle, brown adipose tissue, and mesenteric fat. Consistently, metagenomic analysis showed that EA enriched Akkermansia muciniphila, Muribaculum intestinale, and Duncaniella dubosii, while reducing Lachnoclostridium phocaeense. These microbial shifts were accompanied by elevated levels of tryptophan-derived metabolites-indole-3-propionic acid, indole, and indole-3-acrylic acid-known to enhance insulin sensitivity. Lipidomics revealed EA decreased triacylglycerols and ceramides, along with restored phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine levels. Transcriptomics revealed EA suppressed hepatic lipogenesis, inhibited MAPK signaling in skeletal muscle, activated thermogenic and oxidative phosphorylation in adipose tissues. Our findings highlight EA, a food-derived polyphenol, might alleviate insulin resistance through a gut microbiota-indole metabolite-multi-tissue axis.}, } @article {pmid41581932, year = {2026}, author = {Selvaraj, C and Desai, D and Santos-Villalobos, SL and Jayaprakashvel, M and Muthezhilan, R and Singh, SK}, title = {Marine-derived antimicrobial peptides (AMPs): Blue biotechnological assets for sustainable healthcare and circular bioeconomy.}, journal = {Advances in protein chemistry and structural biology}, volume = {149}, number = {}, pages = {171-201}, doi = {10.1016/bs.apcsb.2025.08.002}, pmid = {41581932}, issn = {1876-1631}, mesh = {*Antimicrobial Peptides/chemistry/pharmacology/economics ; *Biotechnology/economics ; *Aquatic Organisms/chemistry ; Animals ; Humans ; }, abstract = {The global antimicrobial resistance (AMR) crisis drives the demand for novel therapeutics, positioning marine-derived antimicrobial peptides (AMPs) as sustainable alternatives with unique structural and functional advantages. These cationic, amphipathic molecules, from the source of diverse marine organisms, such as invertebrates, extremophiles, and cyanobacteria, exhibit broad-spectrum activity against drug-resistant pathogens through mechanisms like membrane disruption and immunomodulation. Their low resistance propensity and multifunctional bioactivity (eg., antioxidant, antimicrobial, anticancer) underscore therapeutic potential beyond the conventional antibiotics. Advances in genomic and metagenomic tools, machine learning, and synthetic biology are revolutionizing AMP discovery, enabling targeted mining of marine biodiversity and peptide optimization for enhanced stability and specificity. Biotechnological innovations support scalable production through heterologous expression and marine biomass valorization, which aligns with the principles of the circular economy. Marine-sourced AMPs demonstrate transformative applications across various healthcare, aquaculture, food safety, and environmental remediation, that majorly reduce the dependence on synthetic chemicals. Their integration into blue bioeconomy frameworks is promoting sustainable bio-prospects, marine ecosystem conservation, and progress towards the United Nations Sustainable Development Goals. This review narrates the collective research and also addresses the critical challenges, including production scalability and regulatory frameworks, to outline a clear pathway for the marine sourced AMP commercialization. By bridging the antimicrobial innovation with circular biotechnology, marine-sourced AMPs are exemplifying the ocean's role as a reservoir of sustainable solutions for global health and bioeconomic resilience.}, } @article {pmid41582156, year = {2026}, author = {Shi, LD and Ercoli, MF and Kim, J and de Araujo Junior, AT and Estera-Molina, K and Soni, S and Weitz, TS and Shigenaga, AM and Dukovski, I and Sachdeva, R and Turumtay, H and Louie, KB and Bowen, BP and Kosina, SM and Scheller, HV and Pett-Ridge, J and Segrè, D and Northen, TR and Ronald, PC and Banfield, JF}, title = {Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41582156}, issn = {2041-1723}, support = {INV-037174/GATES/Gates Foundation/United States ; //Chan Zuckerberg Initiative Foundation/ ; }, mesh = {*Methane/metabolism ; *Oryza/genetics/metabolism/microbiology ; *Rhizosphere ; *Hydrogen/metabolism ; Plants, Genetically Modified/metabolism/genetics ; Soil Microbiology ; Genotype ; Plant Roots/metabolism/microbiology ; Bacteria/metabolism/genetics ; Oxidation-Reduction ; Tyrosine/metabolism/analogs & derivatives ; }, abstract = {Rice paddies significantly contribute to atmospheric methane (CH4). Here, we show that two independent rice genotypes overexpressing genes for PLANT PEPTIDES CONTAINING SULFATED TYROSINE (PSY) reduce cumulative CH4 emissions by 38% (PSY1) and 58% (PSY2) over 70 days of growth compared with controls. Genome-resolved metatranscriptomic data from PSY rhizosphere soils reveal lower ratios of gene activities for (mostly hydrogenotrophic) CH4 production versus consumption, decreased activity of H2-producing genes, and increased activity of bacterial H2 oxidation pathways. Metabolic modeling using metagenomic and metabolomic data predicts elevated H2 oxidation and suppressed H2 production in the PSY rhizosphere. Assembled genomes of rhizosphere H2-oxidizing bacteria are enriched in genes utilizing gluconeogenic acids compared with H2-producing counterparts, and their activities are likely stimulated by elevated levels of gluconeogenic acids, primarily amino acids, in PSY root exudates. Overall, our study indicates that decreased CH4 emissions are due to a lower amount of H2 available for hydrogenotrophic methanogenesis and provides a powerful strategy to mitigate CH4 emissions from increasingly widespread rice cultivation.}, } @article {pmid41582242, year = {2026}, author = {Chethan, D and Kavya, BS and Arati, and Chandana, R and Gowtham, HP and Ashika, S and Chanchala, S and Nagaraju, N and Reddy, CNL and Kunjeti, SG and Ningaraju, TM}, title = {Endophyte profiling of tomato leaf curl virus (ToLCV) resistant and susceptible tomato genotypes: Insights into microbial diversity and growth promotion.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {5348}, pmid = {41582242}, issn = {2045-2322}, mesh = {*Solanum lycopersicum/virology/genetics/growth & development/microbiology ; *Endophytes/genetics/isolation & purification/classification ; *Begomovirus/pathogenicity ; *Disease Resistance/genetics ; *Plant Diseases/virology/genetics/microbiology ; Genotype ; Bacteria/isolation & purification/classification/genetics ; Fungi/isolation & purification/genetics/classification ; Biodiversity ; }, abstract = {Tomato (Solanum lycopersicum L.) is one of the most widely cultivated vegetable crops globally. Still, its productivity is significantly constrained by tomato leaf curl virus (ToLCV), a devastating begomovirus transmitted by whiteflies. This study examined the diversity and plant growth-promoting potential of culturable endophytes associated with tomato cultivars differing in resistance to tomato leaf curl virus (ToLCV). A total of 59 fungal and bacterial endophytes were isolated. Resistant cultivars (Nandi, Sankranthi, and Vybhav) harboured more diverse and compositionally distinct communities than the susceptible cultivar Arka Vikas, as indicated by Shannon, Simpson, and Chao-1 indices and multivariate analyses. Several isolates, particularly from the genera Xylaria, Fusarium, Arcopilus, Epicoccum, Bacillus, Pseudomonas, Stutzerimonas, and Paenibacillus, displayed strong nutrient-solubilizing traits in vitro, highlighting their potential as plant growth-promoting candidates. Eleven promising isolates were further evaluated on the susceptible cultivar Arka Vikas. At 30 days after sowing, Epicoccum nigrum and Bacillus subtilis significantly increased seedling height, biomass, and leaf number relative to the control. Overall, the study reveals that resistant cultivars are associated with greater culturable endophyte diversity and identifies several isolates with strong potential for promoting plant growth. Future research should assess the antiviral potential of these endophytes under ToLCV challenge and employ metagenomic studies to elucidate their functional roles in enhancing plant health.}, } @article {pmid41582543, year = {2026}, author = {Tang, ZH and Lin, ZN and Li, JX and Liu, FC and Cao, J and Chen, SF and Huang, KY and Li, HF and Hu, DS and Huang, JF and Gu, DF and Lu, XF}, title = {Plasma Metabolites Mediate the Associations of Gut Microbial Diversity with Ambulatory Blood Pressure and Its Variability.}, journal = {Biomedical and environmental sciences : BES}, volume = {39}, number = {1}, pages = {26-35}, doi = {10.3967/bes2025.089}, pmid = {41582543}, issn = {2214-0190}, mesh = {Humans ; *Blood Pressure ; *Hypertension/microbiology/blood ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Adult ; Blood Pressure Monitoring, Ambulatory ; China ; Prospective Studies ; *Metabolome ; }, abstract = {OBJECTIVE: Evidence suggests that depleted gut microbial α-diversity is associated with hypertension; however, whether metabolic markers affect this relationship remains unknown. We aimed to determine the potential metabolites mediating the associations of α-diversity with blood pressure (BP) and BP variability (BPV).

METHODS: Metagenomics and plasma targeted metabolomics were conducted on 523 Chinese participants from the MetaSalt study. The 24-hour, daytime, and nighttime BP and BPV were calculated based on ambulatory BP measurements. Linear mixed models were used to characterize the relationships between α-diversity (Shannon and Chao1 index) and BP indices. Mediation analyses were performed to assess the contribution of metabolites to the observed associations. The influence of key metabolites on hypertension was further evaluated in a prospective cohort of 2,169 participants.

RESULTS: Gut microbial richness (Chao1) was negatively associated with 24-hour systolic BP, daytime systolic BP, daytime diastolic BP, 24-hour systolic BPV, and nighttime systolic BPV (P < 0.05). Moreover, 26 metabolites were strongly associated with richness (Bonferroni P < 0.05). Among them, four key metabolites (imidazole propionate, 2-hydroxy-3-methylbutyric acid, homovanillic acid, and hydrocinnamic acid) mediated the associations between richness and BP indices (proportions of mediating effects: 14.1%-67.4%). These key metabolites were also associated with hypertension in the prospective cohort. For example, each 1-standard deviation unit increase in hydrocinnamic acid significantly reduced the risk of prevalent (OR [95% CI] = 0.90 [0.82, 0.99]; P = 0.03) and incident hypertension (HR [95% CI] = 0.83 [0.71, 0.96]; P = 0.01).

CONCLUSION: Our results suggest that gut microbial richness correlates with lower BP and BPV, and that certain metabolites mediate these associations. These findings provide novel insights into the pathogenesis and prevention of hypertension.}, } @article {pmid41582602, year = {2026}, author = {Hernani, R and Albert, E and Hernani-Morales, C and Zúñiga, S and Benzaquén, A and González-Castillo, L and Colomer, E and Morell, J and Català-Senent, JF and Piñana, JL and Giménez, E and Pérez, A and Hernández-Boluda, JC and Arroyo, I and Rivada, M and Barber, T and Alemany, T and Santacatalina, E and Rentero-Garrido, P and Terol, MJ and Díaz, R and Navarro, D and Solano, C}, title = {Microbiome-Based Modeling of CAR-T Therapy Response in Lymphoma: Insights From Shotgun Metagenomics Sequencing.}, journal = {European journal of haematology}, volume = {116}, number = {5}, pages = {646-662}, pmid = {41582602}, issn = {1600-0609}, support = {//Fundación FERO and the Fundación para la Promoción de Acciones Solidarias/ ; //European Union through the Operational Program of the European Regional Development Fund/ ; CA23/00007//bioinformatics technician/ ; //2023 Strategic Action in Health/ ; //Instituto de Salud Carlos III/ ; //European Union/ ; }, mesh = {Humans ; *Metagenomics/methods ; Shotgun Sequencing ; Female ; Treatment Outcome ; *Microbiota ; *Immunotherapy, Adoptive/adverse effects/methods ; Male ; Middle Aged ; Adult ; *Receptors, Chimeric Antigen/genetics/metabolism ; Aged ; *Lymphoma/therapy/diagnosis/mortality ; Machine Learning ; }, abstract = {The interplay between the commensal microbiota and the mammalian immune system may influence the outcomes of T cell-driven cancer immunotherapies. However, clinical studies supporting microbiota-based interventions in chimeric antigen receptor T-cell (CAR-T) therapy remain scarce. This study included 30 adult patients with B-cell lymphoma treated with axicabtagene ciloleucel (axi-cel) or 4-1BB investigational product. Shotgun metagenomics sequencing (SMS) of fecal samples, collected before lymphodepletion and 1 month post infusion, enabled species-level resolution. We also trained 25 microbiome-based machine-learning (ML) models for response prediction. Neither prior "high-risk" antibiotics exposure nor alpha diversity influenced toxicity, response, or survival. However, dysbiosis was observed between 11 healthy controls and patients, particularly in those treated with axi-cel. SMS identified species associated with clinical outcomes. Increased abundance of Alistipes senegalensis and Alistipes onderdonkii correlated with lower neurotoxicity and improved survival, respectively. Bifidobacterium longum was associated with reduced cytokine release syndrome, whereas Bifidobacterium adolescentis , Bifidobacterium bifidum , and Bifidobacterium breve correlated with poorer survival. ML models demonstrated strong predictive performance, with some identifying non-responders using only six species selected by the Boruta method (Bacteroides xylanisolvens , Bifidobacterium bifidum , Bifidobacterium breve , Eubacteriaceae bacterium Marseille-Q4139, Negativibacillus massiliensis, and Sellimonas intestinalis). These findings deepen current knowledge and support prospective microbiota-based strategies in CAR-T therapy.}, } @article {pmid41582618, year = {2026}, author = {Wu, X and Lim, KJ and Ma, Y and Gu, J and Jiang, Y and Zhu, L and Chen, Y and Sun, J}, title = {The Effects of Soy Protein-Rich Meals on Muscle Health of Older Adults Are Linked to Gut Microbiome Modifications.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {17}, number = {1}, pages = {e70212}, pmid = {41582618}, issn = {2190-6009}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Aged ; Female ; Male ; *Soybean Proteins/administration & dosage/pharmacology ; *Sarcopenia/diet therapy ; *Muscle, Skeletal/physiology ; Aged, 80 and over ; Fatty Acids, Volatile ; Feces/microbiology ; }, abstract = {BACKGROUND: Sarcopenia is characterized by accelerated muscle mass and function loss in older adults. The role of nutritional interventions in sarcopenia is uncertain. This study investigates whether a soy protein-rich diet can enhance muscle health in older adults via gut microbiota changes.

METHODS: A 12-week randomized controlled trial was conducted with 84 older adults from a long-term care facility. Participants in the intervention group consumed three daily meals containing 10 g of soy protein (totalling 30 g/day), while the control group maintained their usual diets. Faecal samples from 53 participants were collected at Weeks 0, 6 and 12. We assessed changes in muscle function, gut microbiota composition and faecal short-chain fatty acids (SCFA).

RESULTS: The intervention group showed preserved calf circumference, while the control group experienced a decrease (W12-W0: Intervention, 0.56 ± 0.22 cm; Control, -0.91 ± 0.26 cm, p(interaction) < 0.001). Metagenomic analysis revealed significant alterations in gut microbiota among intervention participants who showed improvement in muscle performance parameters. The intervention increased SCFA-producing bacteria (Roseburia faecis, Intervention: 0.42 ± 0.21%, Control: -0.06 ± 0.16, p(interaction) < 0.05; Agathobaculum butyriciproducens, Intervention: 0.02 ± 0.007%, p(time) < 0.01, Control: -0.04 ± 0.01) and decreased species associated with poorer muscle outcomes (Alistipes putredinis, Intervention: -0.88 ± 0.40%, Control: 0.62 ± 0.63, p(interaction) < 0.05; Eubacterium_sp_CAG_38, Intervention: -0.64 ± 0.28%, Control: 0.10 ± 0.22, p(interaction) < 0.05). Functional pathway analysis showed enrichment of anaerobic amino acid degradation pathways and vitamin biosynthesis, with depletion of inflammatory pathways, particularly lipopolysaccharide biosynthesis. Microbiome phenotype prediction revealed a decrease in aerobic bacteria abundance in the intervention group (W12-W0, Intervention: -0.004 ± 0.002; Control: 0.001 ± 0.001, p(interaction) < 0.05). Interaction (group × time) for SCFA was not statistically significant; within-group increases at Week 6 were observed in only the intervention group (butyric acid, Intervention: 0.74 ± 0.34 mg/g, p(time) < 0.05, Control: 0.12 ± 0.43 mg/g; isobutyric acid, Intervention: 0.14 ± 0.08 mg/g, p(time) < 0.05, Control: 0.08 ± 0.10 mg/g; isovaleric acid, Intervention: 0.27 ± 0.14 mg/g, p(time) < 0.05; Control: 0.16 ± 0.20 mg/g), with partial reversal by Week 12. These changes, positively correlated with improved muscle function parameters, suggest intervention benefits on gut health and muscle function.

CONCLUSION: A soy protein-rich intervention improved muscle health in older adults through beneficial gut microbiota. These findings support the gut-muscle axis hypothesis and suggest dietary soy protein may alleviate sarcopenia by promoting a healthier gut microbiome.}, } @article {pmid41582887, year = {2026}, author = {Zhang, C and Atashgahi, S and Bosma, TNP and Smidt, H}, title = {Organohalide respiration by a Desulforhopalus-dominated community.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41582887}, issn = {1751-7370}, support = {NRGWI.obrug.2018.005/NWO_/Dutch Research Council/Netherlands ; //Innovation Program Microbiology/ ; }, mesh = {*Deltaproteobacteria/metabolism/genetics/classification/isolation & purification ; *Geologic Sediments/microbiology ; Phylogeny ; Metagenomics ; Oxidoreductases/genetics/metabolism ; Phenols/metabolism ; }, abstract = {Marine sediments harbor diverse organohalide-respiring bacteria (OHRB), but their functional roles and metabolic interactions remains poorly understood. To investigate these interactions, we obtained and characterized a debrominating consortium from Aarhus Bay marine sediments. The consortium transformed 2,6-dibromophenol (2,6-DBP) to phenol under sulfate-reducing conditions, with bacterial growth demonstrating respiratory energy conservation. Metagenomic analysis and binning revealed five new species-level populations (>85% complete, <3% contaminated) dominated by Desulforhopalus (bin.5). Critically, bin.5 encodes a thiolytic tetrachloro-p-hydroquinone reductive dehalogenase (RDase), previously characterized only in aerobic bacteria, representing evidence of this enzyme functioning in a strictly anaerobic sulfate-reducing bacterium. Two additional populations (Desulfoplanes bin.3 and Marinifilaceae bin.4) encoded two and one putative respiratory corrinoid-dependent RDase, respectively. Transcription of all four RDase genes was rapidly induced upon 2,6-DBP addition, indicating multi-population response. Acetylene inhibited debromination post-transcriptionally without affecting RDase gene transcription, or sulfate metabolism, confirming RDase-mediated catalysis. Genome analysis indicated bin.5 encodes a near-complete vitamin B12 biosynthesis pathway (lacking only cbiJ, which can be bypassed through alternative reductases), consistent with debromination activity independent of exogenous B12 addition. Comparative genomics identified Marinifilum and Ancylomarina as candidate OHRB taxa, substantially expanding known phylogenetic diversity of marine organohalide respirers. This work reveals previously unrecognized biochemical versatility in anaerobic dehalogenation and demonstrates metabolic self-sufficiency enabling organohalide respiration in oligotrophic marine sediments.}, } @article {pmid41584315, year = {2026}, author = {Ibrahim, O and Aboushaala, R and Ahmed, N and Savoia, A and Ward, SO and Patel, SN and Lopez, G and Sansom, SE and Williams, B and Singh, K and Al-Harthi, L and Aboushaala, K}, title = {The diagnostic value of metagenomic next-generation sequencing versus traditional microbiological testing in native pyogenic spinal infections: A systematic review and meta-analysis.}, journal = {North American Spine Society journal}, volume = {25}, number = {}, pages = {100840}, pmid = {41584315}, issn = {2666-5484}, support = {KL2 TR002387/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Native pyogenic spinal infections (PSIs), including spondylodiscitis and vertebral osteomyelitis, are challenging to diagnose due to low culture sensitivity and delayed results. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool, but its comparative clinical utility remains uncertain. The purpose of this study is to systematically compare the diagnostic performance and clinical impact of mNGS versus conventional microbial culture in detecting pathogens responsible for native PSIs.

METHODS: The current systematic review and meta-analysis was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A comprehensive literature search was performed across 6 major databases. Eligible studies directly compared mNGS with standard culture for native PSIs and reported diagnostic performance metrics. Data were extracted and analyzed using a random-effects model to produce pooled estimates. Study quality was assessed using the Newcastle-Ottawa Scale. Primary outcomes included pooled sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Secondary outcomes assessed diagnostic yield, time to diagnosis, treatment modification, and false-positive or contamination events.

RESULTS: A total of 1,227 patients from 12 studies were included, encompassing those with suspected or confirmed native PSIs. Pooled sensitivity and specificity of mNGS were 89.7% (95% CI: 85.6-93.1%) and 86.2% (95% CI: 80.5-91.0%), respectively. mNGS demonstrated a significantly higher diagnostic yield (69-90%) compared to culture (27.2-44.7%) and enabled faster diagnosis (range, 17.7-48 hours). mNGS informed antimicrobial selection in up to 70.3% of cases and detected a broader pathogen spectrum. The incidence of false positives was low (range, 1-5) but non-negligible, emphasizing the need for careful interpretation.

CONCLUSIONS: mNGS outperforms conventional culture in sensitivity, speed, and breadth of pathogen detection in native PSIs and supports more tailored antimicrobial therapy. However, careful interpretation is necessary due to potential false positives. These findings support the integration of mNGS into clinical workflows, particularly in complex or culture-negative infections.}, } @article {pmid41585260, year = {2025}, author = {Gao, Y and Wang, X and Cheng, Y and Ye, S and Dong, X and Zhu, C}, title = {Case Report: NGS-guided rapid diagnosis of tuberculous otitis media-a rare case of dual-site Mycobacterium tuberculosis infection.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1734666}, pmid = {41585260}, issn = {2296-858X}, abstract = {BACKGROUND: Tuberculous otitis media (TOM) is an exceptionally rare form of extrapulmonary tuberculosis that was usually diagnosed only after long-standing ear discharge or profound hearing loss. This case reported a young man in whom deafness was the sentinel event leading to the discovery of pulmonary tuberculosis and molecular confirmation of concurrent TOM.

CASE PRESENTATION: A 23-year-old male presented with bilateral, progressive hearing loss that had been labeled "chronic suppurative otitis media" by local clinics. Persistent constitutional symptoms prompted chest imaging that revealed bilateral cavitary infiltrates. Broncho-alveolar lavage metagenomic next-generation sequencing identified Mycobacterium tuberculosis complex (MTBC). After transfer to our tuberculosis center, targeted NGS of serous middle-ear fluid detected MTBC; the isolate carried an rpsL K43R mutation conferring streptomycin resistance, identical to the pulmonary strain. Standard four-drug anti-tuberculosis therapy was initiated; within 4 weeks, cough and fever resolved, inflammatory markers normalized, and the pulmonary cavity showed reduction in size compared to baseline.

CONCLUSION: This case highlights that unexplained hearing loss may serve as an early indicator of disseminated tuberculosis. High-throughput sequencing of aural discharge enables rapid diagnosis of TOM, facilitates resistance-guided treatment, and helps trace the pathways of pathogen transmission.}, } @article {pmid41585377, year = {2026}, author = {Tollenaar, SL and Khorasaniha, R and Jovel, J and Ba, I and Voisin, A and Miller, R and Olof, H and Mahmood, R and Marrie, RA and Strachan, E and Soares, LP and Cheng, C and Janveaux, J and Zaidi, D and Bernstein, CN and Bonner, C and Bar-Or, A and Waubant, E and Yeh, EA and Graham, M and Arnold, DL and O'Mahony, J and Banwell, BL and Zhu, F and Mirza, AI and Karimi-Abdolrezaee, S and Tsai, S and Tremlett, H and McGregor, K and Willing, BP and Armstrong, H}, title = {Reduced fibre-fermenting capacity of gut microbes in multiple sclerosis may result in prebiotic dietary fibre β-fructan promoting inflammation and CNS damage.}, journal = {eGastroenterology}, volume = {4}, number = {1}, pages = {e100296}, pmid = {41585377}, issn = {2976-7296}, abstract = {BACKGROUND: Some people with multiple sclerosis display changes in their gut microbiota with separate evidence suggesting that symptoms may worsen following a high-fibre diet. We hypothesised that in people with multiple sclerosis whose gut microbiota are less able to efficiently ferment dietary fibres, unfermented β-fructans induce inflammation.

METHODS: Diet data (n=48 individuals with multiple sclerosis, n=78 unaffected controls) and stool microbiome data (n=31 individuals with multiple sclerosis, n=61 unaffected controls) were previously collected from participants. Daily fibre subtype intakes were calculated and compared with faecal shotgun metagenomic sequencing in paediatric onset multiple sclerosis and unaffected persons. Response to unfermented β-fructans was examined in a germ-free experimental autoimmune encephalomyelitis (EAE) mouse model (unable to ferment fibres). Mice were fed β-fructans or control fibre diet beginning at symptom onset (day 14). EAE scores and weights were recorded daily. Intestinal and central nervous system tissues were collected at two endpoints to examine inflammatory responses and demyelinating lesions.

RESULTS: Individuals with paediatric onset multiple sclerosis consumed less β-fructans (2.4 g/day±0.3 SD; p<0.05) than unaffected participants (3.6 g/day±0.4), which coincided with differences in the gut microbiota including lower fibre fermenting enzymes. Mice exposed to unfermented β-fructans sustained worsened EAE symptoms (day 20-28; p<0.05), immune activation in the gut and immune activation plus demyelinating lesions in the spinal cord compared with mice on control diet.

CONCLUSIONS: The gut microbiota of individuals with paediatric-onset multiple sclerosis showed reduced fibre fermenting properties, and our animal findings suggest that unfermented β-fructans can worsen demyelination and promote gut-brain axis immune activation. Lower β-fructan consumption was observed among participants with paediatric-onset multiple sclerosis. Future longitudinal studies are warranted to confirm the findings uncovered in this manuscript.}, } @article {pmid41585407, year = {2025}, author = {Marcatti, R and Franco, LAM and Rocha, EC and Nardi, MS and Summa, JL and da Silva, ETBC and da Rosa, AR and de Oliveira, DC and Graciolli, G and Sabino, EC}, title = {Metagenomics enables the first detection of Trypanosoma sp. in Streblidae (Diptera: Hippoboscoidea) parasitizing bats in São Paulo, Brazil.}, journal = {Frontiers in systems biology}, volume = {5}, number = {}, pages = {1721019}, pmid = {41585407}, issn = {2674-0702}, abstract = {INTRODUCTION: Bats play important ecological roles but can also harbor a wide diversity of pathogens, including trypanosomatids. Knowledge about the circulation of Trypanosoma spp. in bat ectoparasites remains limited, particularly in peri-urban environments.

METHODS: In this study, we used shotgun metagenomic sequencing to investigate the presence of Trypanosoma spp. in streblid flies parasitizing Carollia perspicillata bats collected in a peri-urban fragment of the Atlantic Forest in São Paulo, Brazil. A small, preliminary set of pooled samples was analyzed, followed by phylogenetic reconstruction.

RESULTS: Trypanosoma sequences were detected in flies from the family Streblidae. Phylogenetic analysis showed that these sequences cluster within the Neobat 4 clade, which has previously been reported in Carollia spp. bats. This represents the first detection of Trypanosoma sp. in streblid flies parasitizing bats in São Paulo.

DISCUSSION: Although the vector competence of streblid flies for Trypanosoma transmission is still unknown, their close ecological association with bats suggests that they may serve as a non-invasive tool for pathogen surveillance when direct bat sampling is limited. This study expands the known geographic distribution of the Neobat 4 clade and contributes to understanding parasite circulation among bats and their ectoparasites.}, } @article {pmid41585514, year = {2025}, author = {Wei, C and Chen, Z}, title = {Comprehensive genome analysis uncovers the diversity of jumbo phages in the pig gut microbiome.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1697229}, pmid = {41585514}, issn = {2297-1769}, abstract = {Gut microbiome research has historically focused on bacterial communities. In contrast, the roles of viruses, especially jumbo phages, remain poorly understood. Jumbo phages are of major interest because their large genomes encode unique functions that can influence host metabolism and ecosystem dynamics. This study bridges this gap by identifying 1,545 jumbo phage genomes from 450 pig gut metagenomes. Using CRISPR spacer analysis, we predicted archaeal or bacterial hosts and reconstructed competitive phage networks within this ecosystem. Phylogenetic divergence combined with orthologous protein comparisons supported establishing 14 novel jumbo phage families. Functionally, 10 of these novel families encode auxiliary metabolic genes (AMGs) that enhance host metabolism alongside anti-defense systems including DNA methyltransferases, HNH endonucleases, and glycosyltransferases. Ecological interactions were further elucidated through co-abundance networks (n = 857 pairs) and CRISPR spacer matching (n = 425 pairs), revealing relationships between novel jumbo phages and other jumbo phages. Collectively, this work expands genomic resources for pig gut viromes and delivers new insights into jumbo phages' functional capabilities, host associations, and global prevalence.}, } @article {pmid41585543, year = {2026}, author = {Li, T and Wang, Q and Lin, Y and Li, Y and Luo, Z and Zhang, W and Sun, N and Dong, H and Zhang, W and Meng, Y}, title = {Mycobacterium avium complex causing transverse pericardial sinus infection: A case report.}, journal = {IDCases}, volume = {43}, number = {}, pages = {e02479}, pmid = {41585543}, issn = {2214-2509}, abstract = {Nontuberculous mycobacteria (NTM) are increasingly recognized as significant opportunistic pathogens in humans, yet they remain rarely implicated in cardiac conditions. Here, we report a rare case of Mycobacterium avium complex (MAC) infection in the transverse pericardial sinus, an unusual site previously undocumented for NTM infection. The patient, a 68-year-old male with prior cardiac surgery, presented with recurrent fever lasting for over 10 days. Positron emission tomography/computed tomography demonstrated a hypermetabolic mass-like lesion within the transverse pericardial sinus, radiologically suggestive of an infectious process. Empirical broad-spectrum antimicrobial therapy failed to achieve clinical response. Following surgical intervention to remove lesion tissue from the transverse pericardial sinus, histopathological analysis revealed granulomatous inflammation and acid-fast bacilli, indicating NTM infection. Metagenomic next-generation sequencing (mNGS) identified MAC in the tissue sample. After starting antimycobacterial therapy, the patient's body temperature gradually returned to normal, and no recurrence was noted during a 7-month follow-up via serial surveillance imaging. This case suggests that, in patients with a history of cardiac surgery who present with unexplained pericardial or mediastinal lesions and non-diagnostic routine cultures and examinations, atypical pathogens such as NTM may warrant consideration within a broad differential diagnosis. It also illustrates the potential value of surgical intervention and mNGS in diagnosing and managing such rare infections.}, } @article {pmid41585813, year = {2025}, author = {Rong, F and Mingying, Z and Ying, B and Yiyun, H and Ying, Q and Zheng, X and Xiaolei, C}, title = {Pulmonary mucormycosis with bacterial coinfection in an adolescent with poorly controlled type 1 diabetes: a case report.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1724850}, pmid = {41585813}, issn = {1664-2392}, mesh = {Humans ; Female ; *Diabetes Mellitus, Type 1/complications/microbiology/drug therapy ; *Mucormycosis/complications/drug therapy/microbiology ; *Coinfection/microbiology/drug therapy ; Child ; *Lung Diseases, Fungal/drug therapy/complications/microbiology ; Antifungal Agents/therapeutic use ; *Bacterial Infections/complications/drug therapy ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: Pulmonary Mucormycosis (PM), a severe fungal infection affecting mainly immunocompromised individuals, is often caused by fungi like Rhizopus and Mucor. This report details a 12-year-old diabetic girl with pulmonary mucormycosis from an unusual Rhizopus species. Successful treatment involved stabilizing her blood glucose and managing multiple co-infections. This case provides important insights into diagnosing and treating rare fungal infections in diabetic children.

CASE SUMMARY: A 12-year-old girl with a two-year history of type 1 diabetes, inconsistently monitored, was hospitalized. She had a persistent cough for over ten days and a six-day high fever. Previous treatments with dexamethasone and antibiotics were ineffective. She showed symptoms of a productive cough, right-sided pleuritic chest pain, and a fever of 40°C. Examination revealed reduced breath sounds and moist rales in the right lung. Tests confirmed a severe infection, and imaging showed inflammatory consolidation, multiple cavitations, and pleural effusion in the right lung.

DIAGNOSIS: Metagenomic next-generation sequencing (mNGS) analyzes all nucleic acids from a patient's bronchoalveolar lavage fluid to identify various pathogens without traditional cultures. The analysis identified Rhizopus species and Streptococcus pneumoniae, confirming pulmonary mucormycosis with a bacterial infection. Additionally, the glycated hemoglobin (HbA1c) level was 14.3%, indicating poorly controlled diabetes.

TREATMENT: A comprehensive treatment regimen was employed. The bacterial co-infection was addressed with intravenous administration of meropenem and linezolid, while nebulized amphotericin B was utilized to treat the pulmonary mucormycosis. To mitigate the underlying risk factor, intensive glycemic control was achieved through the use of an insulin pump. Furthermore, bronchoscopy was conducted to clear respiratory secretions.

OUTCOME: After 11 days in the hospital, the patient stabilized and was discharged. At a follow-up 1.5 months later, infection markers and blood glucose levels were normal.

CONCLUSION: This case highlights the high risk of severe infections like pulmonary mucormycosis in adolescents with poorly managed type 1 diabetes. Metagenomic sequencing was crucial for quickly identifying co-infections. Successful treatment required a comprehensive approach, including targeted antimicrobial therapy, strict glycemic control, and bronchoscopic support, leading to a positive outcome.}, } @article {pmid41585896, year = {2025}, author = {Jiang, H and Hu, XW and Deng, X and Huang, XJ and Chen, YL and Yang, YF and Du, Y and Ji, S and Tang, DQ}, title = {Liuwei Dihuang pills ameliorate renal injury in experimental type 2 diabetes mellitus rat by regulating host-gut microbiota interaction.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1715600}, pmid = {41585896}, issn = {1663-9812}, abstract = {BACKGROUND: Liuwei Dihuang pills (LW) are widely used as the traditional tonic prescription for the treatment of diabetes and diabetic kidney disease (DKD). This study aimed to investigate the potential mechanism underlying LW-mediated prevention and treatment of DKD from the perspective of host-gut microbiome co-metabolism.

METHODS: A rat model of DKD was established using high-fat diet and streptozotocin. Levels of type IV collagen (Col IV), fibronectin (FN), laminin (Lam), transforming growth factor-β (TGF-β), SMAD family member 7 (SMAD7), and SMAD3 in the kidneys were determined by real time-polymerase chain reaction and Western blot. Fecal metabolites were profiled using ultra-high-performance liquid chromatography-tandem mass spectrometry. Metagenomic sequencing of the feces was performed using high-throughput sequencing.

RESULTS: When combined with metformin (MET)-based therapy, LW significantly improved serum creatinine and blood urea nitrogen levels, kidney index, 24-h urine volume, urine protein content and excretion rate, and urinary creatinine and cystatin C levels. It also attenuated morphological changes. Correspondingly, LW intervention reduced the renal expression of TGF-β, SMAD3, Col IV, LAM, FN, interleukin (IL)-6, and IL-1β, while increasing SMAD7 expression. Additionally, it normalized metabolic pathway abnormalities in galactose, butyric acid, fructose, mannose, amino sugar, and nucleotide sugar metabolism. Moreover, LW regulated bacterial imbalances, notably in specific species such as Allobaculum unclassified, Escherichia coli, Pseudoflavonifractor capillosus, Desulfovibrio porci, Oscillibacter sp. CU971, Parablautia muri, Phocaeicola dorei, Phocaeicola faecalis, Phocaeicola vulgatus, and Raoultella unclassified.

CONCLUSION: The combination of LW and MET ameliorated renal impairment in DKD rats by regulating the TGF-β/SMAD signaling pathway, metabolic disturbances in endogenous metabolites, and gut microbiota dysbiosis.}, } @article {pmid41586308, year = {2025}, author = {Wang, X and Ye, L and Liu, Y and Li, H and Shi, H and Zheng, L}, title = {Metagenomic analysis reveals severity-dependent microbial succession and correlation with host inflammatory response in oral and maxillofacial space infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1695928}, pmid = {41586308}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics ; Female ; Cross-Sectional Studies ; Retrospective Studies ; *Microbiota ; Male ; *Inflammation/microbiology ; *Abscess/microbiology ; Severity of Illness Index ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Aged ; }, abstract = {BACKGROUND: Oral and maxillofacial space infections (OMSI) vary widely in clinical severity, yet the relationships between microbial community patterns in the abscess niche and host inflammatory responses remain incompletely characterized.

METHODS: We conducted a retrospective, cross-sectional, severity-stratified study of 197 patients diagnosed with OMSI between January 2020 and November 2023. Patients were stratified into mild (n=90), moderate (n=41), and severe (n=66) groups based on established clinical criteria. We performed mNGS on abscess pus samples to characterize the microbial community composition and assessed associations between these features and systemic inflammatory markers.

RESULTS: Although α-diversity did not differ significantly among severity groups, β-diversity analysis revealed distinct microbial communities. Pairwise analyses indicated a threshold-like community shift, characterized by a significant divergence between mild and severe infections, while the moderate group exhibited an intermediate composition that overlapped with both. Severe infections were characterized by an enrichment of Prevotella. Furthermore, analysis of predominant taxa (>30% abundance) revealed considerable microbial heterogeneity, challenging a simple monoinfection model. Notably, a machine learning-identified microbial profile comprising Streptococcus, Corynebacterium, and Pseudomonas was significantly correlated with elevated systemic inflammatory markers.

CONCLUSION: This study characterizes associations between abscess-site microbial communities and host inflammatory profiles across OMSI severity strata. Given the cross-sectional design and the lack of an external validation cohort, the present findings should be interpreted as exploratory and non-causal. Future multicenter prospective studies including independent validation cohorts are warranted to test reproducibility and to evaluate whether any candidate features possess generalizable predictive value.}, } @article {pmid41586357, year = {2025}, author = {Wuyunsiqin, and Bai, T and Yang, D and Hashentuya, and Namila, and Jin, C and Tana, and Zhao, P and Wang, M and Menggenduxi, }, title = {Mongolian medicine Wulanwendusu-11 alleviates myocardial ischemia-reperfusion injury by modulating the intestinal microbiota and associated metabolic pathways.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1693472}, pmid = {41586357}, issn = {1664-302X}, abstract = {OBJECTIVE: Wulanwendusu-11 (WLWDS-11) is a commonly used Mongolian medicine for treating cardiovascular diseases. However, its regulating effect on intestinal flora-host metabolism in relieving chronic myocardial ischemia-reperfusion injury (MIRI) is still unclear. Therefore, this study aims to systematically explore the cardioprotective mechanism of WLWDS-11 from the perspective of metabolic interaction between intestinal microbiota and host.

METHODS: C57BL/6J mice were randomized into six experimental groups: MIRI model, sham surgery, and treatment groups for compound Danshen dripping pills (CDDP) plus three dosages of WLWDS-11 (denoted WLWDS-11-L, WLWDS-11-M, and WLWDS-11-H). General physiological indicators of mice in each group were observed, body weight, myocardial structure and pathological features were assessed by electrocardiogram, plasma cardiac enzyme levels. The cardiac function of mice was obtained by echocardiography. Immunohistochemical staining was used to detect the pathological changes in the heart. Immunofluorescence assay was used to detect the degree of apoptosis. Metabolomics and metagenomics were used to analyze treatment effects on intestinal microbiota and metabolites. Integrated analysis of the enriched oxidative phosphorylation and necrosis and apoptosis pathways. qRT-PCR and western blot were used to detect the expression of COX4I1, NDUFB8, SDHA, TFAM, RIPK1, RIPK3, MLKL and TNF-α.

RESULTS: WLWDS-11 (especially in high dose) can significantly improve the cardiac function, reduce the area of myocardial infarction and weaken apoptosis and fibrosis in MIRI mice. Metabolomic profiling revealed extensive metabolic alterations, pathway analysis implicated arginine/proline and unsaturated fatty acid metabolism, and hierarchical clustering identified specific correlations between differential flora (e.g., Kosakonia, Helicobacter spp.) and key metabolites. Integrated multi-omics analysis demonstrated that MIRI induces gut microbiota dysbiosis and systemic metabolic disturbances, characterized by the accumulation of oxidized lipids/lysophospholipids and disruption of critical metabolic pathways. The intervention of WLWDS-11 effectively reshaped the intestinal microbial community and made the metabolic spectrum return to normal. More importantly, correlation and network analysis confirmed the correlation between specific intestinal bacteria (such as Prevost, Kosakonia and Helicobacter) and host metabolites, and formed a flora-metabolite axis regulated by WLWDS-11. KEGG pathway analysis further confirmed the effects of the treatment on key pathways, including necrotizing apoptosis and oxidative phosphorylation. From the point of view of mechanism, WLWDS-11 reversed the mitochondrial dysfunction induced by MIRI by up-regulating the expressions of COX4I1, NDUFB8, SDHA and TFAM. By inhibiting the RIPK 1/RIPK 3/MLKL pathway and TNF-α, necrotizing apoptosis and inflammatory response are inhibited. These results suggest that WLWDS-11 may protect MIRI's heart by regulating the metabolic pathway of flora.

CONCLUSION: WLWDS-11 positively reshaped the gut microbial environment by suppressing pathogenic bacteria and promoting beneficial strains, thereby fostering eubiosis, attenuating cardiac pathology, and ultimately conferring cardio protection. These findings identify WLWDS-11 as a potential candidate drug and provide a molecular mechanistic basis for the clinical treatment of MIRI.}, } @article {pmid41586370, year = {2025}, author = {Zeng, B and Peng, X and Xiao, P and Nie, K and Zhang, G and Xia, L}, title = {Salt sensitivity potentiates high-salt diet-induced intestinal barrier disruption and gut microbiome dysbiosis in rats.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1718782}, pmid = {41586370}, issn = {1664-302X}, abstract = {INTRODUCTION: The high-salt diet is a prevalent eating habit associated with health risks. This study investigated the impact of high salt on intestinal barrier disruption and gut microbiome dysbiosis using Wistar and Dahl salt-sensitive rat models.

METHODS: Rats were fed a normal diet or a high-salt diet for eight weeks. Body weight and plasma inflammatory cytokines were monitored in the study. Colon tissue damage was assessed via histopathological examination, and metagenomic sequencing was utilized to analyze alterations in microbial composition, functional pathways, and biodiversity.

RESULTS: The results indicated that high salt significantly elevated pro-inflammatory cytokine levels and induced structural damage in the colon. Metagenomic analysis revealed that high salt concentrations resulted in approximately a 15% difference in microbial species composition. And led to a decrease in Alpha diversity, along with an increase in the Firmicutes/Bacteroidetes ratio. Taxon-specific alterations included reduced abundance of Lactobacillus and Clostridium, and increased abundance of Enterobacter and Bifidobacterium. Correlation analyses further revealed a positive correlation between Bifidobacterium abundance and tumor necrosis factor-α level in Dahl salt-sensitive rats.

DISCUSSION: This study illuminates the gut microbiota's role in salt-sensitivity and provides a foundational basis for developing microbiota-targeted interventions for at-risk individuals.}, } @article {pmid41586495, year = {2026}, author = {Carroll, AC and Mortimer, L and Ghosh, H and Reuter, S and Grundmann, H and Brinda, K and Hanage, WP and Li, A and Paterson, A and Purssell, A and Rooney, AM and Yee, NR and Coburn, B and Able-Thomas, S and Antonio, M and McGeer, A and MacFadden, DR}, title = {Prediction of genetic relatedness of Escherichia coli using neighbor typing: a tool for rapid outbreak detection.}, journal = {Antimicrobial agents and chemotherapy}, volume = {70}, number = {3}, pages = {e0107125}, pmid = {41586495}, issn = {1098-6596}, mesh = {*Escherichia coli/genetics/classification/drug effects ; Disease Outbreaks ; *Escherichia coli Infections/microbiology/epidemiology ; Humans ; Genome, Bacterial/genetics ; }, abstract = {Identifying the genetic relatedness of resistant bacterial pathogens in healthcare settings can help identify undetected transmission events and outbreaks. However, current methods are time- and resource-intensive. We evaluated a rapid neighbor typing method paired with long-read sequencing for assessment of genetic relatedness. Utilizing a data set of primary clinical samples and published isolate data from two outbreaks of Escherichia coli, we applied genomic neighbor typing of long-read sequence data to rapidly estimate genetic relatedness. We assessed the correlation between neighbor typing predicted genetic distance and pairwise genetic distance from short-read draft whole genomes for all sample pairs. Predicted genetic trees using neighbor typing were compared to reference genetic trees generated using mash distances and maximum-likelihood (ML) methods to assess the extent of agreement, along with metrics of cluster similarity (cluster comparability and Baker's gamma index [BGI]) and tree topology similarity (generalized Robinson-Foulds [GRF] metric). For all three data sets, we found strong correlations between the reference methods and predicted genetic distances (Spearman's rho = 0.75-0.95, P < 0.001), which improved when using a lineage score-informed approach (Spearman's rho = 0.93-0.94, P < 0.001). Predicted genetic trees and clusters from neighbor typing were comparable to those generated using either mashtree or an ML method, with a range of cluster comparability of 85.8-99.5%, BGIs of 0.8-0.95, and GRF values of 0.34-0.8. Pairing the neighbor typing method with long-read sequencing can enable accurate predictions of the relatedness of E. coli samples and isolates, and could potentially be used as a rapid outbreak surveillance tool.}, } @article {pmid41586524, year = {2026}, author = {Bloemen, B and Delvoye, M and Hoffman, S and Marchal, K and Vanneste, K and Fraiture, M-A and Roosens, NHC and De Keersmaecker, SCJ}, title = {Recovery and microbial host assignment of mobile genetic elements in complex microbiomes: insights from a spiked gut sample.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0128225}, pmid = {41586524}, issn = {2379-5077}, mesh = {*Interspersed Repetitive Sequences/genetics ; DNA Methylation ; *Gastrointestinal Microbiome/genetics ; Plasmids/genetics ; Humans ; *Bacillus/genetics ; Gene Transfer, Horizontal ; Bacteriophages/genetics ; Genome, Bacterial ; Bioreactors/microbiology ; }, abstract = {UNLABELLED: Mobile genetic elements (MGEs) are major drivers of horizontal gene transfer, including the spread of antimicrobial resistance (AMR) genes. However, determining the microbial host of an MGE in complex microbiomes remains challenging. Here, we spike a niche-aspecific Bacillus velezensis strain carrying a plasmid and linear phage-plasmid into a batch bioreactor simulating the human gut, and use it as a spike-in control to assess the performance of Hi-C sequencing and Oxford Nanopore Technologies (ONT)-enabled DNA methylation detection to identify MGE-host pairs. To improve recovery of low-abundance genomes, we used a novel ONT adaptive sampling (AS) strategy that depletes de novo assembled, sample-specific high-abundance contigs, rather than relying on reference genomes. This approach led to an approximately twofold enrichment of low-abundance replicons, including the spike-in strain. Methylation-based host assignment failed for the B. velezensis MGEs, likely due to the absence of DNA methylation. In contrast, Hi-C successfully linked the phage-plasmid to its host, but not the plasmid, likely due to non-intact cells, and only after removing artefactual signals through bioinformatic processing. For a native Escherichia coli strain, Hi-C and methylation data linked it to two plasmids. Selective isolation and whole-genome sequencing of both the native E. coli and spike-in B. velezensis then confirmed the metagenomic observations. Our results highlight that Hi-C and methylation data can provide powerful insights into MGE-host associations, but their interpretation requires careful computational analysis and biological validation. Moreover, our AS strategy offers a cost-efficient method to boost coverage of low-abundance genomes, improving metagenomic investigation of MGEs in complex microbiomes.

IMPORTANCE: Mobile genetic elements are important contributors to horizontal gene transfer, including of antimicrobial resistance genes. Understanding which microbes carry these mobile elements is vital to assess the spread of resistance. Here, we use a nanopore adaptive sampling approach to increase detection of low-abundance bacteria and mobile elements and use DNA methylation detection and Hi-C sequencing to determine mobile element hosts. By introducing a known bacterium and isolating a native strain, we could evaluate the performance of these methods, indicating that although powerful, they require careful experimental design, interpretation, and validation. However, when combined, these approaches enable a comprehensive investigation of mobile elements and gene transfer dynamics in complex environments.}, } @article {pmid41586525, year = {2026}, author = {Díaz-González, F and Rojas-Villalobos, C and Issotta, F and Reyes-Impellizzeri, S and Hedrich, S and Johnson, DB and Temporetti, P and Quatrini, R}, title = {Trait-based meta-analysis of microbial guilds in the iron redox cycle.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0148825}, pmid = {41586525}, issn = {2379-5077}, support = {ANID/BASAL FB210008//Agencia Nacional de Investigación y Desarrollo/ ; ANID/FONDECYT 1221035//Agencia Nacional de Investigación y Desarrollo/ ; ANID/FONDECYT 3230527//Agencia Nacional de Investigación y Desarrollo/ ; ANID/BECAS 21241467//Agencia Nacional de Investigación y Desarrollo/ ; ANID/Becas 21241350//Agencia Nacional de Investigación y Desarrollo/ ; Beca 10202955//Vicerrectoria de Investigacion y Doctorados Universidad San Sebastian/ ; }, mesh = {Oxidation-Reduction ; *Iron/metabolism ; *Bacteria/metabolism/genetics/classification ; Phylogeny ; }, abstract = {UNLABELLED: Microbial iron (Fe) redox cycling underpins key biogeochemical processes, yet the functional diversity, ecological roles, and trait architectures of iron-transforming microbes remain poorly synthesized across global environments. Here, we present a systematic review and trait-based meta-analysis of 387 microbial taxa spanning 314 studies and 76 years of research, integrating phenotypic, genomic, and environmental data to define ecologically coherent microbial iron redox cycle guilds. Rather than relying on taxonomy, our framework delineates first-order functional guilds-Fe(III) reducers, Fe(II) oxidizers, and dual-capacity Fe oxidizers/reducers-and resolves second-order guilds based on trait syndromes, such as acidophily, redox flexibility, or metabolic breadth. Trait profiling revealed that iron-cycling capacities frequently transcend phylogenetic boundaries, with multiple guilds converging in chemically stratified hotspots like hot springs, hydrothermal vents, and acid mine drainages. Dual-capacity Fe oxidizers/reducers (e.g., Acidithiobacillus ferrooxidans and Metallosphaera sedula) emerged as overlooked mediators of "cryptic" iron cycling, possessing genomic repertoires capable of toggling between oxidative and reductive modes in response to redox oscillations. Hierarchical clustering and kernel density analyses of ecophysiological traits highlighted niche partitioning along key environmental filters, including pH, iron availability, salinity, and temperature. Collectively, this work introduces the Guild Exploitation Pattern as a conceptual lens for understanding iron microbiome assembly, providing a data-driven foundation for predicting microbial contributions to iron cycling under changing environmental conditions.

IMPORTANCE: Iron redox reactions shape nutrient turnover, contaminant mobility, and primary productivity, yet the microbes driving these processes are often studied in isolation. By integrating decades of data into a trait-based guild framework, we reveal the ecophysiological diversity and niche differentiation of microbial iron redox cycling taxa across environments. Our synthesis exposes major gaps, such as limited trait data for >80% of dual-capacity Fe oxidizing/reducing species and highlights the need for functional trait surveys to complement metagenomics and cultivation efforts. The guild framework presented here advances predictive microbial ecology by linking metabolic traits with environmental gradients, offering a robust foundation for incorporating iron cycling into ecosystem models and biogeochemical forecasts.}, } @article {pmid41587207, year = {2026}, author = {Krzynowek, A and Snoeks, J and Faust, K}, title = {PlasticEnz: An integrated database and screening tool combining homology and machine learning to identify plastic-degrading enzymes in meta-omics datasets.}, journal = {PLoS computational biology}, volume = {22}, number = {1}, pages = {e1013892}, pmid = {41587207}, issn = {1553-7358}, mesh = {*Machine Learning ; *Metagenomics/methods ; *Plastics/metabolism/chemistry ; Metagenome/genetics ; Computational Biology/methods ; *Software ; Biodegradation, Environmental ; Hidden Markov Models ; }, abstract = {PlasticEnz is a new open-source tool for detecting plastic-degrading enzymes (plastizymes) in metagenomic data by combining sequence homology-based search with machine learning techniques. It integrates custom Hidden Markov Models, DIAMOND alignments, and polymer-specific classifiers trained on ProtBERT embeddings to identify candidate depolymerases from user-provided contigs, genomes, or protein sequences. PlasticEnz supports 11 plastic polymers with ML classifiers for PET and PHB, achieving F1 > 0.7 on an independent test set. Applied to plastic-exposed microcosms and field metagenomes, the tool recovered known PETases and PHBases, distinguished plastic-contaminated from pristine environments, and clustered predictions with validated reference enzymes. PlasticEnz is fast, scalable, and user-friendly, providing a robust framework for exploring microbial plastic degradation potential in complex communities.}, } @article {pmid41587575, year = {2026}, author = {Kongor, B and Chatterjee, R}, title = {Saliva Speaks: A Critical Analysis of Salivary Biomarkers as an Early Oral Cancer Diagnostic Tool.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {584}, number = {}, pages = {120853}, doi = {10.1016/j.cca.2026.120853}, pmid = {41587575}, issn = {1873-3492}, mesh = {Humans ; *Saliva/chemistry/metabolism ; *Biomarkers, Tumor/analysis/metabolism ; *Mouth Neoplasms/diagnosis/metabolism ; *Early Detection of Cancer/methods ; }, abstract = {Saliva is an easily accessible bio-fluid which consists of various diagnostic components that can reflect any tumor-related changes, offering a promising non-invasive approach for more accurate and early detection of oral cancer. The primary aim of this review is to provide an integrative evaluation of salivary biomarkers for oral cancer by combining qualitative synthesis with a semi-quantitative analysis of various diagnostic parameters. The work highlights biomarker trends by understanding their diagnostic potential across molecular categories through the visual representation of these quantitative data in bar graphs and heatmaps. Comprehensive literature evaluation was performed by using search engines like Pubmed, Science Direct, Google Scholar etc. on the topic of using salivary biomarkers as an oral cancer detection tool. Relevant data on study design, demographic information, sample type, analytical method, biomarker significance etc. were qualitatively summarized. Quantitative parameters including sensitivity, specificity, accuracy and p-values were either extracted or calculated from selected studies and visualized through bar graphs and heatmaps to facilitate comparative interpretation of diagnostic performance. Multiple salivary biomarkers were identified across genomic, transcriptomic, proteomic, metabolomic, and metagenomic levels, each showing significant involvement in molecular alterations and metabolic pathway dysregulation linked to oral malignancies. This review offers a novel semi-quantitative approach that bridges comprehensive literature summarization with diagnostic data interpretation. By integrating quantitative indices into bar graphs and heatmaps, it enables rapid visual comparison of salivary biomarker performance by revealing high-performing candidates of early oral cancer detection. Thus, saliva-based diagnostics hold great potential as a non-invasive, cost-effective reliable alternative to the conventional oral cancer detection methods.}, } @article {pmid41587576, year = {2026}, author = {Mburu, D and Kumar, S and Wang, Y and Namagerdi, AA and Bai, K and Ali, B and Minalla, A and Gonzales, KO and Abdelhalim, KA}, title = {The oxalobiome: unraveling the role of gut microbiota in oxalate metabolism and its implications for kidney health and disease management.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {584}, number = {}, pages = {120852}, doi = {10.1016/j.cca.2026.120852}, pmid = {41587576}, issn = {1873-3492}, mesh = {Humans ; *Oxalates/metabolism ; *Gastrointestinal Microbiome ; *Kidney/metabolism ; Disease Management ; Oxalobacter formigenes/metabolism ; Hyperoxaluria/metabolism/therapy ; Animals ; }, abstract = {The oxalobiome, comprising microbial communities involved in oxalate metabolism, plays a critical role in maintaining oxalate homeostasis and preventing associated health issues, particularly calcium oxalate nephrolithiasis. Key organisms, notably Oxalobacter formigenes, are essential for degrading oxalate, yet their abundance is influenced by factors such as diet, genetics, and antibiotic use. Recent advances in research have elucidated the complex interactions between the gut microbiome and oxalate metabolism, highlighting the potential for therapeutic interventions. Innovative strategies, including RNA interference therapies (e.g., lumasiran, nedosiran), engineered probiotics, and gene-editing technologies, show promise in managing conditions like primary hyperoxaluria. However, challenges remain, including limitations in oxalate measurement techniques and variability in microbial populations. Multi-omics approaches and metagenomic analyses have enhanced our understanding of the oxalobiome, revealing novel microbial taxa and metabolic pathways involved in oxalate degradation. Despite the potential of emerging therapies, clinical translation is still in its infancy, necessitating further research to establish efficacy and safety. Future studies should focus on mechanistic insights, standardized methodologies, and targeted microbiome-based therapies to optimize management strategies for hyperoxaluria and related systemic diseases. A comprehensive understanding of the oxalobiome is essential for developing precision medicine approaches that effectively address oxalate dysregulation and improve patient outcomes.}, } @article {pmid41587649, year = {2026}, author = {Shi, J and Li, LK and Lin, LH and Li, DK and Lu, J and Saleh, SM and Zhang, TY and He, H and Dong, ZY and Xiao, Q and Xu, B and Zeng, C}, title = {Magnetic properties driving nitrogen removal improvement in magnetite-enhanced activated sludge: Mechanistic insights and process validation.}, journal = {Environmental research}, volume = {294}, number = {}, pages = {123870}, doi = {10.1016/j.envres.2026.123870}, pmid = {41587649}, issn = {1096-0953}, mesh = {*Sewage/microbiology/chemistry ; *Ferrosoferric Oxide/chemistry ; *Nitrogen/metabolism ; *Waste Disposal, Fluid/methods ; Denitrification ; Bacteria/metabolism/genetics ; Bioreactors/microbiology ; *Water Pollutants, Chemical ; }, abstract = {The magnetite-enhanced activated sludge (MEAS) process offers a promising in situ strategy for upgrading wastewater treatment plants (WWTPs) to meet increasing treatment demands and stricter discharge regulations. Unlike conventional materials, magnetite possesses intrinsic magnetic properties, yet their influence on biological treatment efficiency and microbial ecology remains underexplored. This study systematically evaluated three types of magnetite particles with varying properties, focusing on their roles in denitrification, sludge settling, and microbial responses. Batch experiments under low carbon-to-nitrogen conditions (C/N = 4.4) demonstrated that magnetite with high saturation magnetization (65.9 emu/g) achieved 79.3 ± 10.2 % nitrate removal, 3.3 times higher than the control. It reduced the sludge volume index (SVI) from 84.7 to 28.4 mL/g by promoting compact floc formation through extracellular polymeric substance (EPS) protein conformational changes and enhanced microbe-particle interactions. It also increased bio-capacitance of the sludge and achieved a 77.0 % increase in electron transport system activity (ETSA). Surface analysis confirmed that magnetite served as a passive electron mediator rather than actively participating in redox cycling. Metagenomic sequencing further demonstrated the selective enrichment of denitrifying and magnetotactic bacteria and enrichment of key nitrogen metabolism genes (narG, nirK, narK, narH). Validation in an anaerobic-anoxic-aerobic (AAO) reactor treating real municipal wastewater achieved NH4[+]-N and total nitrogen removal efficiencies of 98.7 % and 73.6 %, respectively, meeting stringent discharge limits. These results identify saturation magnetization as a critical parameter for selecting or engineering magnetite materials and provide mechanistic insights and engineering guidance for deploying MEAS as an efficient, retrofit-friendly technology for WWTP upgrading.}, } @article {pmid41587907, year = {2026}, author = {Ma, H and Dai, Y and Xu, C and Geng, H and Li, R and Wang, S and Yang, M}, title = {Identification of Three Novel Umami Peptides from Metagenomics of Traditional Fermented Fish, Suanyu, and Receptor Binding Mechanism via the Graph Neural Network-Based Model and Molecular Dynamics Simulation.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {4}, pages = {3879-3891}, doi = {10.1021/acs.jafc.5c14362}, pmid = {41587907}, issn = {1520-5118}, mesh = {Graph Neural Networks ; Animals ; Molecular Dynamics Simulation ; *Peptides/chemistry/metabolism ; Metagenomics ; Fishes/metabolism ; *Fish Products/analysis/microbiology ; Molecular Docking Simulation ; Humans ; Receptors, G-Protein-Coupled/chemistry/metabolism ; *Fermented Foods/analysis ; *Flavoring Agents/chemistry/metabolism ; Amino Acid Sequence ; Taste ; Protein Binding ; *Fish Proteins/chemistry/metabolism/genetics ; Bioactive Peptides, Dietary ; }, abstract = {Fermented fish products are vital sources of umami peptides. In this study, a hierarchical graph attention network-based model was developed to identify candidate umami peptides. Via an integrated approach combining metagenomics, molecular docking, attention weight analysis, molecular dynamics simulations, and experimental validation, three novel umami peptides (GYSSYK, LYSDSK, and TRTKASY) were identified from the Suanyu system, a traditional fermented fish product. It was revealed that T1R1 and T1R3 could form stable complexes with these peptides involving critical residues: GLU301, ARG277, LYS328, SER384, ASP147, GLN278, and HIS71. In sensory evaluation, candidate peptides showed high umami properties with umami threshold values of 0.28 (±0.14) mg/mL. Overall, this study presents a hierarchical graph attention network-based screening methodology for the rapid screening and in-depth study of umami peptides.}, } @article {pmid41587946, year = {2026}, author = {Quraishi, MN and Moakes, CA and Yalchin, M and Blackwell, C and Segal, J and Ives, NJ and Magill, L and Manzoor, SE and Gerasimidis, K and McMullan, C and Mathers, J and Horniblow, R and Loi, S and Kaur, M and Loman, NJ and Sharma, N and Hawkey, P and McCune, V and Quick, J and Nicholls, S and McMurray, C and Nichols, B and Svolos, V and Raguideau, S and Kerbiriou, C and Oo, YH and Beggs, AD and Crees, N and Hansen, R and Hart, AL and Gaya, DR and Quince, C and Iqbal, TH}, title = {Mechanistic insights into fecal microbiota transplantation for the treatment of ulcerative colitis: analysis of the STOP-Colitis trial.}, journal = {Journal of Crohn's & colitis}, volume = {20}, number = {3}, pages = {}, pmid = {41587946}, issn = {1876-4479}, support = {13/179/01//National Institute for Health and Care Research/ ; }, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Colitis, Ulcerative/therapy/immunology/microbiology ; Adult ; Female ; Male ; Feces/microbiology/chemistry ; Middle Aged ; Prospective Studies ; Pilot Projects ; Treatment Outcome ; Colonoscopy ; Enema ; T-Lymphocytes, Regulatory ; Fatty Acids, Volatile/analysis ; RNA, Ribosomal, 16S ; Leukocyte L1 Antigen Complex/analysis ; }, abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation (FMT) is a promising therapy for ulcerative colitis, but variable responses and unclear mechanisms limit its efficacy. We aimed to compare nasogastric versus colonic FMT delivery and define the microbial and immunological changes associated with clinical response.

METHODS: In this prospective, open-label, randomized pilot trial (STOP-Colitis), 30 adults with active ulcerative colitis were randomized to receive multidose FMT via nasogastric tube or colonoscopy with subsequent enemas. Key endpoints were clinical outcomes at week 8 and longitudinal multi-omic analyses of stool and biopsies to define changes in microbial composition (16S rRNA and shotgun metagenomics), short-chain fatty acids (SCFAs), mucosal T-cells, and host gene expression.

RESULTS: Colonic FMT was superior to nasogastric delivery, with a higher clinical response rate at week 8 (75% [9/12] vs 25% [2/8]; risk ratio 2.94, 95% CI 0.84-10.30-per protocol analysis). Response was underpinned by successful microbial engraftment, leading to significantly increased fecal microbial diversity and enrichment of SCFA-producing taxa, including Oscillospiraceae and Christensenellaceae. This correlated with reduced fecal calprotectin. Responders showed a significant increase in mucosal regulatory T cells (P = .01), with a concurrent decrease in Th17 (P = 0.03) and CD8+ T cells. This anti-inflammatory shift was confirmed by mucosal transcriptomics, which revealed upregulation of metabolic pathways and downregulation of proinflammatory defense pathways in responders. (Trial registration: ISRCTN74072945).

CONCLUSION: Colonic FMT is a more effective delivery route than nasogastric administration. Clinical response is driven by the engraftment of immunomodulatory bacteria that restore a healthy host-microbe dialogue, providing rationale for developing targeted microbial therapeutics.}, } @article {pmid41588069, year = {2026}, author = {Muñoz-Hisado, V and Bartolomé, M and Osácar, MC and Giménez, R and Cazenave, G and Garcia-Lopez, E and Moreno, A and Cid, C}, title = {Microbial communities and biomineralization potential within mountain permafrost of the Devaux ice cave in the Central Pyrenees.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6232}, pmid = {41588069}, issn = {2045-2322}, support = {HORIZON-MSCA-2022-PF-01 (01107943)//European Union/ ; PTA2022-021737-I//the Spanish Ministry of Science and Innovation/State Agency of Research MCIN/ ; }, mesh = {*Permafrost/microbiology ; *Biomineralization ; *Caves/microbiology ; *Microbiota ; Bacteria/genetics/classification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Metagenomics ; }, abstract = {Ice caves constitute one of the last cryospheric environments studied in the meridional regions. They are undergoing a pronounced ice reduction, and are an important example of ecosystems that have not yet been thoroughly explored from a microbiological point of view. The Devaux cave, in the Central Pyrenees, still hosts perennial ice. To test whether this ice contained microbial communities, prokaryotic and eukaryotic microorganisms were searched by sequencing their 16S and 18S rRNA genes. From the taxonomic information, the potential functional pathways of these communities were predicted using bioinformatic techniques. In addition, the genome of the microorganisms housed in the perennial ice samples was investigated, and through metagenomic studies their metabolic capacity was elucidated. The cryogenic mineralization of the Devaux cave leads to the production of various Ca and Mg carbonates: calcite, aragonite, vaterite, Mg-rich calcite, and nesquehonite, whose formation may have been favored by the microorganisms in the cave. Among the genes encoding enzymes that enable reactions involved in biomineralization, those belonging to the nitrate and sulfate reduction dissimilatory pathways as well as ureases, ammonia lyases, and carbonic anhydrases were identified. This research takes a further step in the investigation of biomineralization, using the Devaux cave as a model.}, } @article {pmid41588163, year = {2026}, author = {Young, V and Dohai, B and Halder, H and Fernandez-Macgregor, J and van Heusden, NS and Hitch, TCA and Weller, B and Hyden, P and Saha, D and Pieren, DKJ and Rittchen, S and Lambourne, L and Maseko, SB and Lin, CW and Tun, YM and Bibus, J and Pletschacher, L and Boujeant, M and Choteau, SA and Bergogne, L and Perrin, J and Ober, F and Schwehn, P and Rothballer, ST and Altmann, M and Altmann, S and Strobel, A and Rothballer, M and Tofaute, M and Kotlarz, D and Heinig, M and Clavel, T and Calderwood, MA and Vidal, M and Twizere, JC and Vincentelli, R and Krappmann, D and Boes, M and Falter, C and Rattei, T and Brun, C and Zanzoni, A and Falter-Braun, P}, title = {Effector-host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation.}, journal = {Nature microbiology}, volume = {11}, number = {2}, pages = {442-460}, pmid = {41588163}, issn = {2058-5276}, support = {01EA1803//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 101003633//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 210592381//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 403224013//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 11819559//Österreichische Forschungsförderungsgesellschaft (Austrian Research Promotion Agency)/ ; ANR-16-CONV-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-HDIM-000//Agence Nationale de la Recherche (French National Research Agency)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Type III Secretion Systems/metabolism/genetics/immunology ; Bacterial Proteins/metabolism/genetics ; Crohn Disease/microbiology/immunology ; NF-kappa B/metabolism ; *Immunomodulation ; Host-Pathogen Interactions ; Colitis, Ulcerative/microbiology/immunology ; Host Microbial Interactions ; Protein Interaction Maps ; Metagenomics ; }, abstract = {Pseudomonadota (formerly Proteobacteria) are prevalent in the commensal human gut microbiota, but also include many pathogens that rely on secretion systems to support pathogenicity by injecting proteins into host cells. Here we show that 80% of Pseudomonadota from healthy gut microbiomes also have intact type III secretion systems (T3SS). Candidate effectors predicted by machine learning display sequence and structural features that are distinct from those of pathogen effectors. Towards a systems-level functional understanding, we experimentally constructed a protein-protein meta-interactome map between human proteins and commensal effectors. Network analyses uncovered that effector-targeted neighbourhoods are enriched for genetic variation linked to microbiome-associated conditions, including autoimmune and metabolic diseases. Metagenomic analysis revealed effector enrichment in Crohn's disease but depletion in ulcerative colitis. Functionally, commensal effectors can translocate into human cells and modulate NF-κB signalling and cytokine secretion in vitro. Our findings indicate that T3SS contribute to microorganism-host cohabitation and that effector-host protein interactions may represent an underappreciated route by which commensal gut microbiota influences health.}, } @article {pmid41588320, year = {2026}, author = {Guo, W and Yu, J and Wang, W and Wang, J and Ni, M and Zhou, M and Chen, X}, title = {Multi-kingdom fecal microbiome and virus-host interactions associated with growth performance of indigenous beef calves in Guizhou.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41588320}, issn = {1471-2180}, support = {32402705//the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The associations between the gut microbiome and growth performance in calves have been investigated; however, most existing studies have primarily focused on rumen microbiomes. Whether fecal microbiomes in terms of composition and function are altered among calves with different growth rates remains unclear. Therefore, the objective of this study was to investigate how fecal microbiomes influence calf growth rates. A total of 16 beef calves under the same management were recruited and classified into two groups based on their growth rates (average daily gain: ADG; 4-month-old, n = 8 per group x 2 growth rate groups). At 4 months of age, fecal samples were collected from the rectum for the quantification of volatile fatty acids (VFAs) and characterization of microbial communities via metagenomic sequencing.

RESULTS: The VFA profiles did not differ between the two groups. Calves with higher growth rates exhibited lower bacterial and archaeal Shannon diversity, and the overall microbial community structure showed a clear separation between the two groups. Moreover, fecal bacterial and archaeal species associated with improved growth performance were identified, characterized by the enrichment of Alistipes shahii, Alistipes onderdonkii, Bifidobacterium thermophilum, Akkermansia glycaniphila, and Methanobrevibacter sp. AbM4 in calves with higher growth rates. In addition, the metabolic pathways involved in lipid and amino acid metabolism and CAZyme genes linked to carbohydrate degradation were enriched in the calves with better growth performance. The viral community composition and diversity differed between the two groups, with lower diversity observed in calves exhibiting higher growth rates. Additionally, viruses predicted to infect bacterial hosts such as Prevotella and Succinivibrio, which are involved in carbohydrate degradation, were positively associated with ADG. Interestingly, a virus associated with Methanobrevibacter sp017652345 exhibited a positive correlation with ADG. The relationships between fecal microbes and host phenotypic traits were divergent between the two groups.

CONCLUSIONS: These findings suggest that fecal microbiomes are associated with calf growth rates through potential multi-kingdom interactions, particularly those between viruses and their prokaryotic hosts, indicating possible avenues to improve animal performance via microbiome modulation.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04631-y.}, } @article {pmid41588461, year = {2026}, author = {Zheng, H and Payne, L and He, W and Mestre, MR and Yang, L and Dechesne, A and Pinilla-Redondo, R and Nesme, J and Sørensen, SJ}, title = {Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {50}, pmid = {41588461}, issn = {2049-2618}, mesh = {*Plasmids/genetics ; *Wastewater/microbiology ; *Bacteria/genetics/classification/virology ; Bacteriophages/genetics ; Metagenomics/methods ; Interspersed Repetitive Sequences ; Metagenome ; Water Purification ; }, abstract = {BACKGROUND: Bacterial antiphage defense systems play essential roles in microbial ecology, yet their dynamics within urban wastewater systems (UWS) remain poorly characterized.

RESULTS: In this study, we performed comprehensive metagenomic and plasmidome analyses on 78 wastewater samples collected during two seasons and four sampling points across UWS from three European countries. We observed a significant reduction in the abundance, diversity, and mobility potential of defense systems during biological treatment. However, these reductions were not directly correlated with changes in microbial abundance. Defense systems were significantly enriched on plasmids, particularly conjugative plasmids, where their gene density was approximately twice as high as on chromosomes and remained relatively stable across compartments. In contrast to chromosomal defense systems, plasmid-borne systems exhibited more frequent co-localization with a wide range of mobile genetic elements (MGEs)-associated genes, thereby facilitating multilayered dissemination networks. Furthermore, we detected a strong correlation between phage abundance and host defense system profiles, indicating ongoing phage-host co-evolutionary dynamics in these environments.

CONCLUSIONS: In summary, our results demonstrate that UWS reduce the abundance and diversity of bacterial defense system genes. However, plasmid-associated defense systems can persist through shared mobile genetic reservoirs. These findings underscore the critical role of plasmids in bacterial immunity and provide new insights into defense system dynamics within urban wastewater environments.}, } @article {pmid41588512, year = {2026}, author = {Yu, S and Wu, Q and Ma, Y and Bano, S and Zhang, X}, title = {Keystone bacterial taxa drive denitrification and N2O emission via adaptive genomic and metabolic strategies in contrasting agricultural soils.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41588512}, issn = {2524-6372}, support = {42577128 and 31971526//National Natural Science Foundation of China/ ; (2017YFD0200102)//Key R&D project of the Ministry of Science and Technology/ ; }, abstract = {BACKGROUND: Soil denitrification mediated by microbial communities is a major source of nitrous oxide (N2O), a potent greenhouse gas. However, the regulatory roles of keystone taxa in this process remain poorly understood, particularly under distinct edaphic conditions. Black soil (BS) and fluvo-aquic soil (FS), two representative agricultural soils in China, exhibit contrasting N2O emission potentials, offering an ideal model for exploring microbial mechanisms driving soil-specific denitrification dynamics.

RESULTS: We integrated microbial co-occurrence networks, metagenomics, and functional phenotyping to identify and characterize keystone bacterial taxa involved in denitrification across the two soil types. Structural equation modeling (SEM) and correlation analyses revealed strong associations between keystone taxa and denitrification rates and N2O emission patterns. Ensifer ASV205 was identified as a conserved keystone taxon in both soils and exhibited strain-level niche specialization. Comparative genomic analysis revealed that variations in denitrification gene composition and carbon-nitrogen metabolic pathways enabled Ensifer strains to act either as N2O producers or reducers, depending on environmental conditions.

CONCLUSIONS: Our findings demonstrate that soil-specific denitrification processes and N2O emissions are governed by keystone taxa through adaptive genomic and metabolic strategies shaped by environmental filtering. This study provides new insights into the microbial mechanisms regulating N2O emissions and lays the groundwork for developing microbiome-informed strategies to mitigate greenhouse gas emissions in agricultural soils.}, } @article {pmid41589071, year = {2026}, author = {Caserta, MT and Mariani, TJ and Walsh, EE and Gill, SR and Gill, AL and Corbett, A and Harrington, D and Chu, C and Qiu, X}, title = {Nasal Biomarkers of Acute Illness Severity and Predictors of Recurrent Wheeze in Infants Infected With Respiratory Syncytial Virus.}, journal = {The Journal of infectious diseases}, volume = {233}, number = {6}, pages = {1027-1035}, doi = {10.1093/infdis/jiag049}, pmid = {41589071}, issn = {1537-6613}, support = {58711//Merck Investigator Studies Program/ ; //Merck and Co, Inc/ ; }, mesh = {Humans ; *Respiratory Syncytial Virus Infections/diagnosis/virology ; *Respiratory Sounds/etiology ; Infant ; Male ; Severity of Illness Index ; Female ; *Biomarkers/analysis ; Recurrence ; Microbiota ; Respiratory Syncytial Virus, Human ; Acute Disease ; }, abstract = {BACKGROUND: Respiratory syncytial virus (RSV) is a leading cause of hospitalization in infants, and those with RSV disease appear more likely to develop recurrent wheeze. We examined nasal airway gene expression and microbiome composition during primary RSV infection to test associations with illness severity and identify infants with recurrent wheeze.

METHODS: Previously healthy infants with RSV infection were enrolled (December 2019-December 2023). Clinical and demographic data were collected, as were 2 anterior nasal swabs and a nasal wash for metagenome and transcriptome sequencing. Disease severity was measured by the improved Global Respiratory Severity Score (iGRSS). Participants were followed for approximately 1 year to identify recurrent wheeze. Multivariate regression models were developed to identify correlates and predictors of disease severity and recurrent wheeze, respectively.

RESULTS: One hundred infants (90 hospitalized) were enrolled (mean ± SD age, 3.2 ± 2.3 months; 61% male). An overall 405 genes (false discovery rate, 0.10) were significantly and consistently associated with illness severity (iGRSS), implicating innate immune and interleukin signaling pathways. The abundance of nasal Dolosigranulum was inversely associated with iGRSS, while the abundance of Haemophilus was directly associated with iGRSS. Predictive models based on nasal gene expression during infection had the power to classify recurrent wheeze (in-sample area under the curve, 0.992; cross-validated area under the curve, 0.882), while metagenomic features did not improve predictive performance.

CONCLUSIONS: We prospectively followed infants with primary RSV infection and identified associations among nasal gene expression, microbiome composition/function, and acute disease severity and recurrent wheeze. Host transcriptional profiles during infection were predictive of recurrent wheeze within the following year.}, } @article {pmid41589125, year = {2026}, author = {Panyako, PM and Ogada, S and Kuria, SN and Musina, J and Lichoti, JK and Ommeh, SC}, title = {Metagenomic Profiling of Fecal and Cecal Microbiota and Their Antimicrobial Resistance Genes in Indigenous Backyard Poultry.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {7306065}, pmid = {41589125}, issn = {1687-918X}, abstract = {Indigenous backyard poultry is the predominant type of poultry in developing countries. Rural smallholder farmers in these regions usually adopt the free-range (backyard) production system, which exposes the poultry to diverse environments and a broad spectrum of microorganisms that influence their diet and gut microbiota. In this cross-sectional purposive study, we evaluated the microbial community profiles of indigenous backyard poultry and their antimicrobial resistance genes (ARGs) using both cecal samples, which provide a more accurate representation of the core gut microbiota, and fecal samples, which allow for noninvasive monitoring and pathogen screening. We analyzed 32 pooled fecal and cecal samples using shotgun metagenomics, followed by functional and antimicrobial resistance (AMR) analyses to identify genes and metabolic pathways associated with poultry gut health and production. We report the presence of many commensal microorganisms in indigenous backyard poultry, with the most abundant being Bacteroidetes, Firmicutes, and Proteobacteria. The most dominant genera in the feces were Bacteroides, Methanobrevibacter, and Phocaeicola, while Bacteroides, Methanobrevibacter, and Chlamydia dominated in the ceca. No marked differences in microbial diversity were observed between the fecal and cecal samples. KEGG and COG database analyses revealed significantly enriched pathways associated with metabolism, cellular processes, and information storage and processing. Genes that confer resistance to tetracycline were the most abundant, raising concerns about the risks associated with inappropriate and excessive use of this antibiotic in poultry treatment. These findings deepen our understanding of the poultry gut microbiome, particularly regarding indigenous backyard poultry. Furthermore, the information about ARGs is a valuable indicator of antimicrobial use by rural smallholder farmers who have adopted the free-range production system in Kenya and other developing countries. These insights are crucial for farmers and the national livestock sector to monitor AMR in poultry, thereby enabling improved poultry management practices and informed policy decisions.}, } @article {pmid41589836, year = {2026}, author = {Darlenski, R and Manuelyan, K and Dimova, I and Menzel, P and Schwarzer, R and Fluhr, JW and Bogdanov, I}, title = {Skin surface microbiome dynamics in the extremes: Learnings from Antarctica distinct community.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {}, number = {}, pages = {}, doi = {10.1111/jdv.70324}, pmid = {41589836}, issn = {1468-3083}, support = {80-25-69/3.8.2021//Bulgarian National Program for Polar Research 2017-2021/ ; }, } @article {pmid41589896, year = {2026}, author = {Conrad, RE and Tsementzi, D and Meziti, A and Hatt, JK and Montoya, J and Konstantinidis, KT}, title = {Metagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {2}, pages = {e0258925}, pmid = {41589896}, issn = {1098-5336}, support = {ECOGIG Consortium//Gulf of Mexico Research Initiative/ ; 1831582//National Science Foundation/ ; 2129823//National Science Foundation/ ; }, mesh = {Gulf of America ; *Metagenome ; *Fresh Water/microbiology ; *Seawater/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics ; Phylogeny ; }, abstract = {Genomic and metagenomic explorations of the oceans have identified well-structured microbial assemblages showing endemic genomic adaptations with increasing depth. However, deep water column surveys have been limited, especially of the Gulf of Mexico (GoM) basin, despite its importance for human activities. To fill this gap, we report on 19 deeply sequenced (~5 Gbp/sample) shotgun metagenomes collected along a vertical gradient, from the surface to about 2,000 m deep, at three GoM stations. Beta diversity analysis revealed strong clustering by depth, and not by station. However, a community-level pangenome style gene content analysis revealed ~54% of predicted gene sequences to be station-specific within our GoM samples. Of the 154 medium-to-high-quality MAGs recovered, 145 represent novel species compared with the NCBI genomes and Tara Oceans MAGs databases. Two of these MAGs were relatively abundant at both surface and deep samples, revealing remarkable versatility across the water column. A few MAGs of freshwater origin (~6% of total detected) were relatively abundant at 600 m deep and 270 miles from the coast at one station, revealing that the effects of freshwater input in the GoM can sometimes be far-reaching and long-lasting. Notably, 1,447/16,068 of the total COGs detected were positively (Pearson's r ≥ 0.5) or negatively (Pearson's r ≤ -0.5) correlated with depth, including beta-lactamases, dehydrogenases, and CoA-associated oxidoreductases. Taken together, our results reveal substantial novel genome and gene diversity across the GoM's water column, and testable hypotheses for some of the diversity patterns observed.IMPORTANCETo what extent microbial communities are similar between different ocean basins at similar depths, and what the impact of freshwater input by major rivers may be on these communities, remain poorly understood issues with potentially important implications for modeling and managing marine biodiversity. In this study, we performed metagenomic sequencing and recovered 154 medium-to-high-quality metagenome-assembled genomes (MAGs) from three stations in the Gulf of Mexico (GoM) and from various depths up to about 2,000 m. Comparison to MAGs recovered from other ocean basins highlighted the unique diversity harbored by the GoM, which could be driven by more substantial input from the Mississippi River and by human activities, including offshore oil drilling. The data and results provided by this study should be useful for future comparative analysis of marine biodiversity and contribute to its more complete characterization.}, } @article {pmid41589901, year = {2026}, author = {Engl, T and Jakubova, L and Skrob, Z and Campeggi, S and Skala, R and Folkmanova, M and Pajer, P and Chmel, M and Cajthaml, T and Strejcek, M and Suman, J and Uhlik, O}, title = {Catabolism of acetosyringone and co-metabolic transformation of 2,4,6-trichlorophenol by a novel FAD-dependent monooxygenase.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0124225}, pmid = {41589901}, issn = {2379-5077}, support = {22-00132S//Grantová Agentura České Republiky/ ; CZ.02.01.01/00/22_008/0004597//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; }, mesh = {*Mixed Function Oxygenases/metabolism/genetics ; *Chlorophenols/metabolism ; *Flavin-Adenine Dinucleotide/metabolism ; Pseudomonas/metabolism/genetics/enzymology ; Metabolic Networks and Pathways ; *Bacterial Proteins/metabolism/genetics ; Acetophenones ; }, abstract = {Acetosyringone (AS), a prototypical syringyl-type monomer of lignin, functions as a model compound for the study of microbial catabolism of S-lignin-derived aromatics. In this study, we present the discovery of a novel metabolic pathway for AS catabolism, initiated by a previously uncharacterized FAD-dependent oxidoreductase, designated AsdA. In contrast to the sole previously documented AS funneling route, which entails side chain modification and conversion to syringic acid, AsdA catalyzes direct hydroxylation of the aromatic core. This represents a mechanistically distinct entry into central metabolism. The identification of this enzyme was achieved through metagenomic and functional analyses of a bacterial consortium enriched on AS as the sole carbon source. The consortium, predominantly comprising Pseudomonas rhizophila, exhibited co-metabolic transformation of the chlorinated pollutants 2,4,6-trichlorophenol (2,4,6-TCP) and 2,6-dichlorophenol. Subsequent functional assays substantiated the hypothesis that AsdA facilitates the transformation of both AS and 2,4,6-TCP. Induction assays employing a biosensor strain derived from the bacterial isolate Pseudomonas rhizophila AS1 confirmed AS-specific upregulation of the asd gene cluster. A survey of publicly available metagenomes has revealed that asdA is narrowly distributed but enriched in rhizosphere environments, pointing to its ecological significance. In summary, the present study unveils a hitherto unrecognized route for AS transformation and identifies an enzyme that exhibits dual functions in lignin-derived aromatic catabolism and environmental pollutant transformation. While the mechanisms underlying TCP degradation are well-established, the specific enzyme responsible for the conversion to 2,6-dichloro-p-hydroquinone had remained elusive-a knowledge gap that has now been addressed by AsdA.IMPORTANCEThe microbial conversion of lignin monomers is central to the global carbon cycle, yet pathways for syringyl-derived aromatics remain poorly resolved. Here, we identify AsdA, an enzyme initiating a previously unrecognized route for acetosyringone catabolism, providing new insight into how this abundant plant-derived compound is integrated into microbial metabolism. Beyond expanding the mechanistic diversity of lignin degradation, AsdA also catalyzes a key step in the transformation of the chlorinated pollutant 2,4,6-trichlorophenol, linking natural and anthropogenic compounds within a shared metabolic framework. The restricted yet rhizosphere-enriched distribution of asdA underscores its specialized role in plant-microbe interactions. By integrating enzyme function, microbial community context, and metagenomic distribution, we demonstrate how a single catalytic activity connects metabolic pathways and ecosystem processes, illustrating a multi-scale systems biology perspective on aromatic compound turnover.}, } @article {pmid41590413, year = {2025}, author = {Ansari, RA and Egamberdievich, KE and Raximovna, MT and Sa'dinovna, YD and Enverovna, BL and Abbasovich, AS and Muqumovich, AD and Kurbonovich, TM}, title = {Phytomycobiomes and Ecosystem Services: Mechanisms, Evidence and Routes to Application.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {41590413}, issn = {2309-608X}, abstract = {Phytomycobiomes refer to the fungal consortia that inhabit plant tissues and the rhizosphere. Their documented functions include nutrient mobilization, carbon retention, stress mitigation and pathogen suppression, although measurable effects often depend on plant and soil conditions. In this review, we examine the current evidence for their ecological relevance and assess the molecular approaches most commonly used to characterize them. Arbuscular Mycorrhizal (AM) fungi, endophytes and saprotrophic taxa indicate measurable gains in nutrient acquisition, disease resistance and soil aggregation, although long-term consistency is rarely evaluated. Each function appears to have an explicit mechanistic attribution, with direct links between fungal groups, enzymatic pathways and measurable ecosystem outcomes. Several sequencing-based techniques are available, yet none offer complete accuracy. Internal Transcribed Spacer (ITS) amplicon surveys provide rapid taxonomic coverage but suffer from primer bias; shotgun metagenomics offers functional insight but at significant financial cost; and quantitative polymerase chain reaction (qPCR) assays remain useful for targeted quantification, whereas long-read technologies show promise but still lack widespread adoption. The field faces a number of unresolved constraints, including limited knowledge of host range, inconsistent performance under fluctuating environmental conditions and the absence of a standardized bioinformatic pipeline. Despite these limitations, we regard phytomycobiomes as viable candidates for replacing or reducing synthetic inputs, provided their application is guided by context-specific evidence rather than broad generalization.}, } @article {pmid41590723, year = {2026}, author = {Atak, E and Tavčar Verdev, P and Petek, M and Coll, A and Bosch, D and Dolinar, M and Komarysta, V and Glavaš, N and Rotter, A}, title = {Identification and Cultivation of Biotechnologically Relevant Microalgal and Cyanobacterial Species Isolated from Sečovlje Salt Pans, Slovenia.}, journal = {Marine drugs}, volume = {24}, number = {1}, pages = {}, pmid = {41590723}, issn = {1660-3397}, support = {L4-4564//The Slovenian Research and Innovation Agency/ ; Euro-MED 0200514//Interreg Euro-MED Program/ ; }, mesh = {*Cyanobacteria/isolation & purification/genetics/growth & development ; *Microalgae/isolation & purification/genetics/growth & development ; Slovenia ; Salinity ; Metagenomics ; Biotechnology ; Biodiversity ; Ecosystem ; }, abstract = {Studies of complex natural environments often focus on either biodiversity or on isolating organisms with specific properties. In this study, we sought to widen this perspective and achieve both. In particular, hypersaline ecosystems, such as the Sečovlje salt pans (Slovenia), are particularly promising sources of novel bioactive compounds, as their microorganisms have evolved adaptations to desiccation and high light intensity stress. We applied shotgun metagenomics to assess microbial biodiversity under low- and high-salinity conditions, complemented by isolation and cultivation of photosynthetic microorganisms. Metagenomic analyses revealed major shifts in community composition with increasing salinity: halophilic Archaea became dominant, while bacterial abundance decreased. Eukaryotic assemblages also changed, with greater representation of salt-tolerant genera such as Dunaliella sp. Numerous additional microorganisms with biotechnological potential were identified. Samples from both petola and brine led to the isolation and cultivation of Dunaliella sp., Tetradesmus obliquus, Tetraselmis sp. and cyanobacteria Phormidium sp./Sodalinema stali, Leptolyngbya sp., and Capilliphycus guerandensis. The newly established cultures are the first collection from this hypersaline environment and provide a foundation for future biodiscovery, production optimization, and sustainable bioprocess development. The methods developed in this study constitute a Toolbox Solution that can be easily replicated in other habitats.}, } @article {pmid41591393, year = {2026}, author = {Walden, N and Kiefer, C and Koch, MA}, title = {Unravelling complex hybrid and polyploid evolutionary relationships using phylogenetic placement of homologous gene copies from target enrichment data.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syag007}, pmid = {41591393}, issn = {1076-836X}, abstract = {Phylogenomic datasets comprising hundreds of genes have become the standard for plant systematics and phylogenetics. However, large-scale phylogenomic studies often exclude polyploids and hybrids due to the challenges in assessing the origin of duplicated loci and incorporating them into tree reconstruction methods. Using a newly generated target enrichment dataset of 1081 genes from 452 samples from the Brassicaceae tribe Arabideae, including many hybrid and high ploidy taxa, we developed a novel approach to disentangle the evolutionary history of this phylogenetically and taxonomically challenging clade. Our approach extends beyond commonly used gene tree-species tree reconciliation techniques by using phylogenetic placement, a method adopted from metagenomics, of gene copies into a diploid tree. We show how it allows for the simultaneous assessment of the origins of ancient and recent hybrids and autopolyploids, and the detection of nested polyploidization events. Additionally, we demonstrate how synonymous substitution rates provide further evidence for the mode of polyploidization, specifically to distinguish between allo- and autopolyploidization, and to identify hybridization events involving a ghost lineage. Our approach can serve as an exploratory tool for large and complex phylogenomic datasets and can aid in identifying polyploid and hybrid clades for further analysis with specialized methods.}, } @article {pmid41591576, year = {2026}, author = {Robayo, MIG and Armijo, JHC and Rosa, LH and Passarini, MRZ}, title = {Metagenomic analysis of the fungal community present in unimpacted and oil-impacted soil, South Shetland Islands, maritime Antarctica.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {2}, pages = {62}, pmid = {41591576}, issn = {1573-0972}, support = {440218/2023-3//CNPq PROANTAR/ ; PRPPG Nº 118/2024//Institutional Program to Support Research Groups/ ; CNPq 18/2024//National Council for Scientific and Technological Development/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Fungi/classification/genetics/isolation & purification/metabolism ; *Metagenomics ; Islands ; Soil/chemistry ; Biodiversity ; Phylogeny ; *Mycobiome/genetics ; Nitrogen/analysis ; Ascomycota/genetics/classification/isolation & purification ; }, abstract = {We assessed the fungal diversity and functional profile of two soils collected in contrasting environments: one unimpacted soil, Hennequin Point, King George Island, and the other impacted by whale oil, Whalers Bay, Deception Island, Maritime Antarctica, using metagenomic approaches. Taxonomic assignment revealed a predominance of Ascomycota in both soils. A total of 20 and 23 fungal genera were identified at King George and Deception islands, respectively. The rare genera Thermothielavioides, Pyricularia, Fulvia, and Coccidioides were detected in the Antarctic environment. The highest fungal diversity was observed in the soil of Deception Island. Canonical analysis of King George Island soil displayed higher values of total organic carbon, sulfur, and lead, which may have favored the presence of the genera Puccinia, Lachancea, and Akanthomyces. The soil of Deception Island presented correlations with higher levels of nitrogen, chromium, and iron, with a predominance of genera such as Aspergillus, Trichoderma, and Malassezia. Functional analysis revealed distinct adaptive strategies among the soils. Domains related to translation, gene regulation, and metabolic efficiency were observed for fungi in Hennequin Point soil, King George Island, suggesting resource optimization in a cold, moss-covered environment. In Deception Island soil, fungal redox metabolism, iron acquisition, and the degradation of nitrogen compounds were highlighted, reflecting adaptation to an anthropogenic soil rich in metal oxides. Both soils exhibited functional fungal networks involved in hydrolytic enzymatic pathways that may act in the decomposition of organic compounds. New sequencing must be performed due to the insufficient depth of the data. Our results indicated that the soil from Hennequin Point and Whalers Bay exhibited distinct fungal communities, which can be influenced by environmental and ecological factors such as moss, oil, and heavy metals encountered in pristine and oil-impacted soils resulting from anthropogenic activities over the years.}, } @article {pmid41591600, year = {2026}, author = {Bilecen Şen, D and Ertürkmen, P and Alp Baltakesmez, D}, title = {Microbiota and quality profiling of fermented goat meat sausages (sucuk) under nitrite-reduced and mixed-culture strategies.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {2}, pages = {64}, pmid = {41591600}, issn = {1573-0972}, abstract = {The bioprotective activity of lactic acid bacteria (LAB) to modulate the microbiota and quality of nitrite-reduced fermented goat meat sucuk was investigated. Antagonistic activity of LAB strains against foodborne pathogens was evaluated using agar well diffusion, spot-on lawn, and cross-streak assays. Three LAB isolates affiliated with the genera Weissella, Limosilactobacillus, and Lactiplantibacillus, exhibiting inhibition zones > 18 mm, were selected and applied as a mixed culture (MC; 2:1:1). Sucuk formulations with 150, 75, and 0 ppm sodium nitrite were produced in the presence or absence of a MC and analyzed during fermentation (days 0 and 7) and refrigerated storage (days 7 and 14). Among the treatments, 75 ppm nitrite combined with MC (75-MC) exhibited the highest LAB counts, enhanced acidification (pH 4.7 on fermentation day 7), inhibited pathogens and spoilage microorganisms, and improved moisture and color stability (> 90% of initial L* and a*), with a significant treatment × day interaction (P < 0.05). Metagenomic analysis of the 16 S rRNA (V3–V4) and ITS2 regions revealed a LAB-dominated sucuk microbiota, characterized by Levilactobacillus (69.5%), Lactiplantibacillus (12.1%), Psychrobacter (8.8%), and Lacticaseibacillus (3.0%) among bacteria, and Yarrowia (46%), Kurtzmaniella (11.8%), Geotrichum (6.7%), and Cladosporium (5.5%) among fungi. This microbial composition was associated with enhanced microbial stability and technological quality, while mixed-culture strategies under nitrite-reduced conditions promoted a Lactobacillaceae-enriched microbiota, highlighting their potential role in bioprotection and product quality.}, } @article {pmid41591867, year = {2026}, author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C}, title = {Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes.}, journal = {MicrobiologyOpen}, volume = {15}, number = {1}, pages = {e70215}, doi = {10.1002/mbo3.70215}, pmid = {41591867}, issn = {2045-8827}, support = {//European Union, NextGeneration EU, PNRR-M4C2- I1.1, PRIN 2022 - Project Code 20229LEB99 - CUP Code D53D23014150006/ ; T5-AN-11//Piano di Sviluppo e Coesione of the Italian Ministry of Health 2014-2020/ ; }, mesh = {*Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; *Databases, Genetic ; *Environmental Pollutants/metabolism ; Metagenomics ; Biocuration ; Microbiota/genetics ; Metagenome ; }, abstract = {Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.}, } @article {pmid41592401, year = {2026}, author = {Sandes, S and Figueiredo, N and Pires, S and Assis, D and Pedroso, S and Paiva, MJ and Neumann, E and Alvarenga, VO and Contreras-Castillo, CJ and Sant'Ana, AS}, title = {Lactic acid spraying on split carcasses reshapes microbial succession and reduces the occurrence of blown pack spoilage in vacuum-packaged beef stored at different temperatures over extended shelf life.}, journal = {International journal of food microbiology}, volume = {450}, number = {}, pages = {111659}, doi = {10.1016/j.ijfoodmicro.2026.111659}, pmid = {41592401}, issn = {1879-3460}, mesh = {Animals ; *Food Packaging/methods ; Vacuum ; Cattle ; *Lactic Acid/pharmacology ; *Bacteria/drug effects/genetics/classification/isolation & purification/growth & development ; Volatile Organic Compounds/analysis ; Temperature ; Food Microbiology ; *Red Meat/microbiology ; Food Storage ; Food Preservation/methods ; Hydrogen-Ion Concentration ; Colony Count, Microbial ; Food, Processed ; }, abstract = {Beef is a highly perishable product due to its high moisture content, neutral pH, and rich nutrient profile, which favor microbial growth and spoilage. While vacuum packaging extends shelf life by limiting aerobic bacteria, it may promote the proliferation of anaerobic and facultative anaerobic spoilage organisms, leading to blown pack spoilage. This study investigated the effects of lactic acid spraying on split carcasses categorized by two pH levels (high or ideal) on microbial succession and volatile organic compound (VOC) production in vacuum-packaged sirloins, stored at 0 °C, 4 °C, and 7 °C for up to 120 days. Using culture-based methods, 16S rRNA gene sequencing, and VOC profiling, it has been found that lactic acid treatment significantly reduced initial bacterial loads, especially in high-pH split carcasses (P < 0,05), and modulated microbial communities over time. Treated samples exhibited a lower incidence of blown pack spoilage (BPS) under specific storage time-temperature conditions. Nevertheless, bacterial changes under specific time-temperature storage conditions were characterized by a microbiota dominated by Lactococcus, Lactobacillus, Leuconostoc, Enterococcus, Carnobacterium, Hafnia-Obesumbacterium, and Serratia, regardless type of treatment. Overall microbial diversity was not significantly affected; however, the composition of dominant bacterial genera and VOC profiles differed between treated and non-treated groups, suggesting that specific bacterial taxa and compounds may serve as indicators of spoilage progression in vacuum-packed meat under defined storage conditions.}, } @article {pmid41592403, year = {2026}, author = {Zhang, B and Wang, M and Zheng, J and Yu, C and Wei, C and Ren, J and Sun, S and Wang, G and Wang, J and Lu, Y and Lin, L and Zhang, C}, title = {Strain-specific impacts of Pichia kudriavzevii on metabolite profiles and microbial community dynamics in Chinese Baijiu fermentation: Integrated metabolomics and metagenomics analysis.}, journal = {International journal of food microbiology}, volume = {450}, number = {}, pages = {111660}, doi = {10.1016/j.ijfoodmicro.2026.111660}, pmid = {41592403}, issn = {1879-3460}, mesh = {Fermentation ; *Pichia/metabolism/genetics/classification ; Metabolomics ; Metagenomics ; *Microbiota ; *Alcoholic Beverages/microbiology/analysis ; Metabolome ; Bacteria/genetics/classification/metabolism/isolation & purification ; Food Microbiology ; }, abstract = {Pichia kudriavzevii is a dominant yeast species in Chinese baijiu fermentation, yet its intraspecific diversity remains underexplored. This study used metabolomics and metagenomics analysis to investigate the impact of four distinct P. kudriavzevii strains (PK12, PK25, PK97, and PK360) on the metabolite profiles and microbial community structure in a controlled baijiu solid-state fermentation. Metabolomics analysis identified 49 key volatile compounds and 2792 non-volatile metabolites. Strain PK97 exhibited exceptional capacity for butanoic acid metabolism, inducing a 55.27-fold increase in butanoic acid and a 30.54-fold enhancement in ethyl butanoate production. Strain PK25 specialized in acetoin biosynthesis, while PK360 maximized 2-phenylethanol production. Metagenomic analysis uncovered that strains PK12, PK25, and PK360 promoted Lactobacillus acetotolerans population, increasing its relative abundance to 67.39%, 58.57%, and 71.79%, respectively. In contrast, strain PK97 orchestrated a dramatic ecological shift, elevating Enterobacter mori abundance from 0.56% to 17.60%, transforming the community from Lactobacillus-dominated to Enterobacteriaceae-enriched. Integration of metabolomic and metagenomic data revealed that strain PK97's promotion of Enterobacter mori correlated with significant upregulation of key enzymes including α-amylase (EC 3.2.1.1), enoyl-CoA hydratase (EC 4.2.1.17), and succinyl-CoA synthetase (EC 6.2.1.5), creating a metabolic environment favoring enhanced starch hydrolysis, altered TCA cycle flux, and butanoic acid accumulation. Strain PK25 specifically upregulated acetyl-CoA hydrolase (EC 3.1.2.1), facilitating acetic acid and acetoin formation. Strain PK360 enhanced glucose pyrophosphorylase (EC 2.7.7.9) and asparagine synthetase (EC 6.3.1.1) activities, accelerating galactose metabolism and amino acid transformations. These findings illustrate the impact of P. kudriavzevii intraspecific diversity on reshaping microbial ecology and flavor chemistry in Chinese baijiu, offering novel insights for targeted fermentation control and quality enhancement strategies in baijiu production.}, } @article {pmid41592660, year = {2026}, author = {Anburajan, P and Lee, SH and Maulana, DD and Park, HD}, title = {Functional genes and microbial interactions governing methanogenesis via direct interspecies electron transfer: Functions and emerging concepts.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134086}, doi = {10.1016/j.biortech.2026.134086}, pmid = {41592660}, issn = {1873-2976}, mesh = {*Methane/biosynthesis ; Electron Transport ; *Microbial Interactions/genetics ; Anaerobiosis ; Species Specificity ; *Genes, Bacterial ; }, abstract = {Direct interspecies electron transfer (DIET) has emerged as an electron-exchange mechanism that enhances methane production in anaerobic digestion (AD) systems. Although the concept of direct electron exchange in syntrophic microbial communities was proposed in the early 2010 s, experimental validation and systematic recognition of methanogenesis via DIET have advanced primarily in the past decade. Significant progress has been made in identifying DIET-active microbial consortia; however, the functional genes and metabolic pathways governing these processes remain unclear. Recent advances in multi-omics approaches, including metagenomics, metatranscriptomics, and proteomics, have provided deeper insights into microbial community organization and gene-level functions underlying electron transfer in AD systems. This review synthesizes current knowledge on functional genes directly mediating DIET (e.g., pilA, omcS), as well as genes that indirectly support DIET, including hydrogenases, extracellular polymeric substance (EPS)-related genes, and methanogenesis-associated enzymes. Understanding of these functional genes is essential for optimizing AD processes and advancing bioenergy production.}, } @article {pmid41592665, year = {2026}, author = {Yu, X and Lei, Z and Xu, L and Chen, S and Zeng, G and Wang, N and Lai, X and Liu, J}, title = {Disseminated Mycobacterium abscessus lymphadenopathy in an anti-interferon-γ autoantibody syndrome patient treated with anti-NTM therapy combined with hemoadsorption: A case report.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {164}, number = {}, pages = {108438}, doi = {10.1016/j.ijid.2026.108438}, pmid = {41592665}, issn = {1878-3511}, mesh = {Humans ; Female ; Aged ; *Mycobacterium Infections, Nontuberculous/drug therapy/immunology/therapy/microbiology ; *Lymphadenopathy/microbiology/immunology/therapy ; *Mycobacterium abscessus/isolation & purification ; *Interferon-gamma/immunology ; *Autoantibodies/immunology/blood ; Anti-Bacterial Agents/therapeutic use ; *Immunologic Deficiency Syndromes/immunology ; Positron Emission Tomography Computed Tomography ; *Hemoperfusion/methods ; }, abstract = {BACKGROUND: Anti-interferon-γ autoantibody syndrome (AIGAs) is a primary immunodeficiency disorder characterized by neutralizing autoantibodies blocking interferon-γ signaling, predisposing patients to severe opportunistic infections. No definitive treatment protocol exists, and conventional therapies carry infection risks. Hemoadsorption (HA) is effective for autoimmune diseases but has not been specifically investigated for AIGAs.

CASE PRESENTATION: A 65-year-old Chinese female was admitted with 10-month painless disseminated lymphadenopathy. 18F-fluorodeoxyglucose positron emission tomography/computed tomography showed multiple hypermetabolic lymph nodes, and ultrasound-guided biopsy revealed necrotizing granulomatous inflammation. Metagenomic next-generation sequencing identified Mycobacterium abscessus, and enzyme-linked immunosorbent assay confirmed high AIGA levels (88.05% at 1:3200 dilution). She received anti-nontuberculous mycobacteria therapy (clarithromycin, minocycline, contezolid) combined with one HA session using a cytokine adsorption column. Post-treatment, AIGA levels normalized to 0% at 24 weeks and remained stable. 72-week follow-up showed resolved lymphadenopathy and reduced lymph node size/metabolic activity on PET/CT.

CONCLUSION: This is the first report of single-session HA for AIGAs complicated by disseminated M. abscessus infection. HA effectively reduced AIGA levels, controlled infection, and avoided global immunosuppression, providing a promising adjunctive therapy for AIGA patients with severe disseminated infections.}, } @article {pmid41592677, year = {2026}, author = {Si, M and Xiong, X and Yun, C and Chen, Y and Niu, H and Qu, Y and Liu, M and Wang, Y and Huang, L and Long, X and Wang, W and Yang, R and Liu, R and Pang, Y and Zhen, X and Li, R and Tian, T and Qi, X and Qiao, J}, title = {Microplastics and nanoplastics in follicular fluid are associated with diminished ovarian reserve: clinical and molecular insights.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.01.074}, pmid = {41592677}, issn = {2090-1224}, abstract = {INTRODUCTION: Ovarian aging is a significant concern, yet the influencing factors remain unclear. Environmental factors are crucial determinants of diminished ovarian reserve (DOR). Microplastics and nanoplastics (MNPs) are widespread in the environment and pose health risks. The effect of MNPs on ovarian function remains uncertain.

OBJECTIVES: The study aims to investigate whether exposure to MNPs negatively affects ovarian function. In particular, the research focuses on elucidating the association between MNPs-especially polyamide 66-and DOR, and validating Parabacteroides goldsteinii (P. goldsteinii) as a potential intervention.

METHODS: We conducted a case-control study analyzing MNPs in follicular fluid from 110 DOR patients and 110 age-matched controls. A mouse MNPs-exposure model assessed ovarian function and intestinal barrier integrity. Gut microbiota alterations were analyzed by metagenomic sequencing of fecal samples from MNPs-exposed mice. P. goldsteinii was identified and selected for microbial intervention, administered via oral gavage. The human granulosa cell line was treated with MNPs for 48 h, followed by transcriptomic sequencing to examine PI3K/AKT/mTOR pathway alterations.

RESULTS: Human follicular fluid contained multiple MNPs, with polyamide 66 levels significantly linked to DOR. Polystyrene and polyvinyl chloride concentrations were also higher in the DOR group. MNPs induced DOR-like phenotypes in mice, causing hormonal imbalances, disrupted estrous cycles, and increased atretic follicles, alongside intestinal barrier damage and gut microbiota dysbiosis. Notably, the abundance of P. goldsteinii and its key metabolite 7-keto-lithocholic acid (LCA) was significantly reduced following MNPs exposure. Supplementation with P. goldsteinii effectively reversed MNPs-induced DOR-like phenotypes, restored hormonal homeostasis, normalized estrous cyclicity, reduced follicular atresia, and elevated 7-keto-LCA levels. Mechanistically, MNPs triggered the PI3K/AKT/mTOR pathway, impairing granulosa cell function and ovarian reserve.

CONCLUSION: These findings elucidate how exposure to MNPs may harm female ovarian function and provide potential new strategies for ameliorating reproductive disorders through the environment‒gut‒ovarian axis.}, } @article {pmid41592952, year = {2026}, author = {Iacucci, M and Zammarchi, I and Pugliano, CL and Santacroce, G and Capobianco, I and Majumder, S and Ruffa, A and Naranjo, V and Grisan, E and Nardone, OM and Ghosh, S}, title = {Shaping the future of postoperative recurrence in Crohn's disease: personalised approaches with AI-enabled imaging and multi-omics.}, journal = {Gut}, volume = {75}, number = {6}, pages = {1237-1247}, pmid = {41592952}, issn = {1468-3288}, mesh = {Humans ; *Crohn Disease/surgery/diagnostic imaging ; Multiomics ; *Artificial Intelligence ; Recurrence ; *Precision Medicine/methods ; *Postoperative Complications ; Intelligent Systems ; }, abstract = {Postoperative recurrence (POR) is a major challenge in the long-term management of Crohn's disease (CD), affecting up to 70% of patients within the first year after surgical resection. The multifactorial pathogenesis of POR complicates prevention, while evolving surgical techniques and different anastomotic configurations further hinder accurate prediction and monitoring.Current surveillance strategies, including standard ileocolonoscopy and faecal calprotectin, remain limited by suboptimal accuracy, the absence of validated scoring systems and the lack of standardised monitoring intervals. Recent advances in high-resolution endoscopic imaging, such as confocal laser endomicroscopy and endocytoscopy, enable real-time, in vivo microstructural assessment of the anastomosis, offering opportunities for earlier and more precise detection of recurrence. In parallel, developments in intestinal ultrasound and cross-sectional imaging are reshaping non-invasive monitoring by providing transmural evaluation. Beyond imaging, multiomics approaches, spanning genomics, transcriptomics, proteomics, metabolomics and metagenomics, are uncovering novel biological pathways linked to POR, providing new mechanistic insights.Artificial intelligence (AI) has the potential to integrate clinical, endoscopic, imaging and omics data into predictive multimodal models for POR, supporting individualised risk stratification, early detection and personalised treatment strategies. While promising, these innovations require prospective validation, methodological standardisation and integration into clinical workflows before translation into routine practice.This review summarises the current understanding of POR, highlights emerging diagnostic and monitoring technologies and explores how AI-enabled endoscopy and multi-omics approaches may transform future management, paving the way towards precision medicine for POR in CD.}, } @article {pmid41593136, year = {2026}, author = {Menke, S and Fackelmann, G and Vucetich, LM and Vucetich, JA and Forbey, JS and Sommer, S}, title = {Forage quality shapes physiological and gut microbial responses in moose (Alces alces) of Isle Royale National Park.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {3724}, pmid = {41593136}, issn = {2045-2322}, abstract = {UNLABELLED: Plant secondary compounds (PSCs) impose physiological and nutritional constraints on herbivores, yet many species continue to rely on PSC-rich forage during critical periods of the year. Moose (Alces alces) on Isle Royale National Park depend heavily on balsam fir (Abies balsamea) during winter, exposing them to a chemically defended and nutritionally limited diet. To investigate how this foraging strategy shapes both physiological responses and gut microbial communities, we integrated fecal diet composition, urinary markers of detoxification and nutritional status, 16S rRNA gene sequencing, and shotgun metagenomic profiling from free ranging moose of two separated populations from the western and eastern region of the island. Balsam fir consumption varied strongly by region and was positively associated with glucuronic acid to creatinine (GA:C) and urea nitrogen to creatinine (UN:C) ratios, indicating increased detoxification activity and reduced nutritional condition. Microbial alpha diversity declined with higher fir intake in nutritionally limited individuals, while beta diversity differed by region, balsam fir consumption, and UN:C. Several bacterial genera responded to PSC exposure, including increases in the butyrate-producing genus Roseburia and shifts in network prominence of Phascolarctobacterium. Metagenomic data revealed pathways involved in the degradation of aromatic and terpenoid PSCs, although pathway abundances did not differ significantly with balsam fir consumption after multiple testing correction. These results show that winter foraging on balsam fir produces coordinated dietary, physiological, and microbial patterns, with both host and gut microbial detoxification capacities interacting to accommodate the chemical and nutritional challenges of a PSC-rich winter diet.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-35555-w.}, } @article {pmid41593326, year = {2026}, author = {Kotay, SM and Parikh, HI and Gweon, HS and Barry, K and Stoesser, N and Sarah Walker, A and Crook, DW and Vegesana, K and Mathers, AJ}, title = {Biofilm removal in hospital sink drains drives unintended surges in antibiotic resistance.}, journal = {npj antimicrobials and resistance}, volume = {4}, number = {1}, pages = {5}, pmid = {41593326}, issn = {2731-8745}, support = {BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; HPRU-2012-10041//National Institute for Health and Care Research/ ; HPRU-2012-10041//National Institute for Health and Care Research/ ; HPRU-2012-10041//National Institute for Health and Care Research/ ; }, abstract = {The prevalence and proliferation of antimicrobial-resistant bacteria is considered one of the critical issues of our time. Wastewater is a habitat for complex microbial communities where bacteria share antimicrobial-resistance genes through horizontal gene transfer. Hospital wastewater plumbing systems are an ideal reservoir for environmental and pathogenic bacteria to interface and exchange antimicrobial-resistance genes. Replacement of contaminated plumbing may be the most intuitive and widely deployed response to the detection and colonization of highly-resistant potentially pathogenic bacteria in hospital sink drains. In this study, we analyzed sink-drain biofilms from six intensive-care patient rooms using shotgun metagenomic sequencing and microbial culture. We show an evident shift in biofilm community structure toward increased abundance of Enterobacteriaceae following plumbing replacement. Higher resistome load and abundance of clinically relevant resistance and typically encountered mobile genes in the newly replaced plumbing was also observed. Taken together, these finding suggest that exchanging contaminated plumbing for new plumbing may actually have the unexpected consequence of increased abundance of Enterobacterales and antimicrobial-resistance genes in the sink drains. Disruption of preexisting complex environmental biofilms may result in an unintended microbial population shifts and a potential subsequent increase in the amount of antimicrobial-resistant Enterobacterales which are targeted for elimination.}, } @article {pmid41593363, year = {2026}, author = {Sorensen, PO and Karaoz, U and Beller, HR and Bill, M and Bouskill, NJ and Banfied, JF and Chu, RK and Hoyt, DW and Eder, E and Eloe-Fadrosh, E and Sharrar, A and Tfaily, MM and Toyoda, J and Tolic, N and Wang, S and Wong, AR and Williams, KH and Zhong, Y and Brodie, EL}, title = {Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt.}, journal = {Nature microbiology}, volume = {11}, number = {2}, pages = {359-374}, pmid = {41593363}, issn = {2058-5276}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DBI-1315705//National Science Foundation (NSF)/ ; }, mesh = {*Bacteria/metabolism ; Biomass ; Bradyrhizobium/metabolism ; Climate Change ; Metagenome ; Microbiota ; Nitrogen/metabolism ; *Nitrogen Compounds/metabolism ; *Nitrogen Cycle ; *Seasons ; *Snow ; *Soil Microbiology ; Ecosystem ; Multiomics ; }, abstract = {Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.}, } @article {pmid41593438, year = {2026}, author = {Wang, X and Tian, D and Han, B and Zhao, K and Hao, W and Du, K and Li, X and Duan, Z}, title = {Exploring the impact of rumen microbiome on ovine flavor-related compounds and comparing flavor profiles between Tibetan sheep and Small-tail Han sheep.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41593438}, issn = {1471-2180}, support = {2024YFF0728800//National Key Research and Development Program of China/ ; 2024-ZJ-949//the Natural Science Foundation of Qinghai Province/ ; XDA26040305//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, mesh = {Animals ; *Rumen/microbiology ; *Microbiota ; Sheep/microbiology ; Fatty Acids, Volatile/analysis/metabolism ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Tibet ; Metagenomics ; Taste ; Meat/analysis ; Tandem Mass Spectrometry ; *Flavoring Agents/analysis ; Metagenome ; }, abstract = {The characteristic 'mutton flavor', primarily attributed to branched-chain fatty acids (BCFAs), is influenced by various factors including rumen microbes. This study aims to elucidate the disparities in meat flavor compounds and their underlying regulatory mechanisms mediated by rumen microbes between two important sheep breeds on the Qinghai-Tibetan Plateau. We used LC-MS/MS to analyze BCFAs and rumen short-chain fatty acids (SCFAs), along with metagenomic sequencing to characterize the rumen microbiome. Compared to Tibetan sheep, Small Tail Han sheep exhibited significantly higher concentrations of BCFAs, including 4-ethyloctanoic acid (EOA) and 4-methyloctanoic acid (MOA), as well as SCFAs such as pentanoate, glutarate, and propionate. In contrast, acetate levels were inversely correlated with these fatty acids. Metagenomics revealed a predominance of Bacteroidota (formerly Bacteroidetes) and Bacillota (formerly Firmicutes) in sheep. Furthermore, random forest and LEfSe analyses identified seven bacterial biomarkers, including Lactobacillus, Ligilactobacillus, Blautia, Anaerovibrio, Selenomonas, Phocaeicola, Sodaliphilus. Functional analysis indicated differences in carbohydrate degradation capabilities of two breeds. Likewise, strong positive correlations of propionate with MOA, and glutarate with EOA were observed, respectively. The findings are expected to provide critical insights into the potential for modulating meat flavor through nutritional strategies targeting rumen microbes.}, } @article {pmid41593440, year = {2026}, author = {Lv, J and Liu, R and Sun, Z and Zhang, J and Zhang, Y and Zhao, X and Liu, J and Zhou, X and Zhang, M and Liu, Q and Gao, F}, title = {Gut Microbiota as Neuroimmune Modulators in Myasthenia Gravis: Mechanistic Insights from the Gut-Brain Axis to Therapeutic Innovations.}, journal = {The American journal of Chinese medicine}, volume = {54}, number = {1}, pages = {65-85}, doi = {10.1142/S0192415X26500023}, pmid = {41593440}, issn = {1793-6853}, mesh = {Humans ; *Myasthenia Gravis/immunology/therapy/microbiology ; *Gastrointestinal Microbiome/immunology/physiology ; Animals ; *Brain/immunology ; Fecal Microbiota Transplantation ; *Neuroimmunomodulation ; Cytokines/metabolism ; Dysbiosis ; Probiotics ; }, abstract = {Myasthenia gravis (MG) is a chronic autoimmune disorder characterized by an immune-mediated attack on neuromuscular junction acetylcholine receptors (AChRs), and its pathogenesis is closely linked to immune dysregulation. Emerging evidence has highlighted the pivotal role of the gut microbiota in the pathophysiology of MG through immunomodulation, microbial metabolite signaling, and gut-brain axis interactions. This review combines 16S rRNA sequencing, metagenomic, and metabolomic data to reveal distinct gut microbial signatures in patients with MG. These signatures include reduced α-diversity, depletion of beneficial taxa like Bacteroides and Bifidobacterium, enrichment of pathobionts such as Escherichia and Enterococcus, and diminished levels of the short-chain fatty acids (SCFA), which were inversely correlated with disease severity. Experimental models have demonstrated that fecal microbiota transplantation (FMT) and probiotic supplementation with strains like Bifidobacterium ameliorate symptoms by restoring Th17/Treg equilibrium, suppressing the expression of pro-inflammatory cytokines including IL-6 and TNF-α, and enhancing intestinal barrier integrity. Mechanistically, gut dysbiosis exacerbates autoimmunity via NF-αB pathway activation, disrupts tryptophan metabolism and impairs gut-brain signaling. While existing studies have established microbiota-MG associations, further causal validation, personalized therapeutic strategies, and multi-omics integration remain critical priorities. Microbiota-targeted interventions, including precision FMT and metabolite delivery, hold translational potential, but their validation via large-scale randomized controlled trials and interdisciplinary approaches like AI-driven microbiota profiling is essential if they are to advance precision medicine for MG management.}, } @article {pmid41593479, year = {2026}, author = {Cheng, Z and Ye, Y and Gou, L and Chen, X and Zhang, L and Cao, W and Zhang, Q and Yin, H and Gao, F}, title = {Comprehensive analysis of microorganisms in severe septic patients in the intensive care unit by mNGS and microbial culture.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41593479}, issn = {1471-2180}, support = {21624318//Fundamental Research Funds for the Central Universities/ ; A2024458//the Guangdong Medical Research Foundation/ ; 2021TQ0126//the China Postdoctoral Science Foundation/ ; 2021ZT09Y552//the Program for Guangdong Introducing Innovative and Entrepreneurial Teams/ ; }, mesh = {Humans ; Intensive Care Units ; *Sepsis/microbiology ; *Bacteria/isolation & purification/genetics/classification/drug effects ; Female ; *Fungi/isolation & purification/genetics/classification/drug effects ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Aged ; *Metagenomics/methods ; Viruses/isolation & purification/genetics/classification ; Microbial Sensitivity Tests ; Sputum/microbiology ; Adult ; }, abstract = {BACKGROUND: Severe sepsis is a life-threatening condition involving dysregulated systemic inflammatory responses and acute organ dysfunctions. Timely and accurate pathogen identification is critical for the effective treatment of severe septic patients in the intensive care unit (ICU). Although metagenomic next-generation sequencing (mNGS) enables the sensitive and unbiased detection of pathogens, its clinical implications in identification of causative pathogens, the association with the outcomes and the development of treatment regimens in such patients remain underexplored.

METHODS: 184 clinical samples were collected from 81 severe septic patients and subjected to mNGS analysis. Blood and bronchoalveolar lavage fluid (BAL) samples were collected from the majority of patients, while sputum, cerebrospinal fluid (CSF), pleural effusion (PE), ascites, urine, hydropericardium (HPC) and blister effusion (BE) samples were also collected from select patients. Microorganisms were detected by DNA and RNA mNGS and the top 5 microorganisms detected by mNGS in each sample were used for analysis. Microbes were isolated from most patients and the isolates were tested for drug susceptibility.

RESULTS: mNGS identified 183 top 5 microorganisms, with bacteria (92.3%), viruses (3.3%) and fungi (2.7%) as the major detected microbes. Among them, 40, 98 and 45 were pathogenic (21.9%), opportunistic (53.6%) and non-pathogenic (24.6%), respectively. Significantly more pathogenic microbes were detected in the sputum (83.3%) and the bronchoalveolar lavage fluid (BAL; 75.0%) than the blood (36.1%) by RNA mNGS (87.4%) than DNA mNGS (58.2%). Patients having the top-1 pathogenic microorganism detected by DNA mNGS or 4-5 pathogenic microorganisms detected by RNA mNGS had a poor association with clinical outcomes. Moreover, detection of R. pickettii, C. difficile and S. enterica were significantly associated with high mortality. The majority of patients (89.5%) were positive for microbial cultures. Each of these patients had at least one drug-resistant organism and nearly half (45.1%) were infected with two or more drug-resistant strains.

CONCLUSIONS: Detection of predominant pathogenic microorganisms or particular bacteria in the sputum or BAL samples by mNGS are associated with poor clinical outcomes among severe septic patients in ICU in this cohort. The high prevalence of multidrug-resistant bacteria among these patients underscores the importance of integration of mNGS with antimicrobial susceptibility assessment in the clinical practice to develop the most effective treatment regimens.}, } @article {pmid41593721, year = {2026}, author = {Xi, J and Tao, H and Zhang, Z and Lian, B and Sun, W and Zhang, Y and Bu, S and Yang, X and Qian, X}, title = {Captive breeding of specialty animals represents an overlooked yet critical reservoir for spreading antibiotic resistance genes.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41593721}, issn = {1751-7370}, mesh = {Animals ; Feces/microbiology ; *Deer/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Breeding ; *Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/drug effects/isolation & purification ; Animals, Wild/microbiology ; *Genes, Bacterial ; }, abstract = {Driven by wildlife conservation and economic demands, captive breeding has expanded globally, intensifying wildlife-human interactions. In specialty animal breeding, particularly for species with short domestication histories and underdeveloped breeding protocols, clinically important antibiotics are commonly misused, posing potential ecological and health risks that remain largely unexplored. We collected fecal samples from three groups of musk deer (Moschus berezovskii): those exposed to clinically important antibiotics, those not exposed for six months, and wild musk deer, and analyzed their microbiomes and resistomes using metagenomic and culture-based methods. We found that captivity significantly expanded and reshaped the fecal resistome of musk deer. The antibiotic-exposed musk deer harbored a significantly higher diversity and abundance of antibiotic resistance genes (ARGs) compared to those non-exposed to antibiotics and wild deer. We observed a higher abundance of clinically important ARGs within Enterobacteriaceae in fecal samples of captive musk deer. This observation was further supported by the antibiotic susceptibility profiles of 124 Escherichia coli strains isolated from antibiotic-exposed musk deer. Seven identical mobile genetic element-associated ARGs were detected in distinct bacterial hosts across fecal samples from musk deer and farm workers, indicating potential conjugative transfer between the two groups. Our results suggest that captive breeding of specialty animals is an overlooked but significant reservoir for disseminating clinically important ARGs, and underscore the transmission risk at the animal-human interface.}, } @article {pmid41593747, year = {2026}, author = {Lin, L and Zheng, X and Tao, Y and Zhu, W and Guan, LL and Mao, S}, title = {Genome-resolved metagenomics uncovers diversity and functional landscapes of the gastrointestinal epithelium-associated microbiome in cattle.}, journal = {Genome biology}, volume = {27}, number = {1}, pages = {44}, pmid = {41593747}, issn = {1474-760X}, support = {U2202203//NSFC-Regional Innovation and Development Joint Fund/ ; 3236114378//NSFC-International (Regional) Cooperation Research and Exchange Programme/ ; }, mesh = {Animals ; *Metagenomics/methods ; Cattle/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Rumen/microbiology ; Biodiversity ; }, abstract = {BACKGROUND: The ruminant gastrointestinal epithelium harbors a diverse and functionally critical remains poorly characterized microbial community due to persistent host-derived DNA contamination in metagenomic studies.

RESULTS: We develop Dilute-MetaSeq (dilution-based metagenomic sequencing), a novel, metagenomic workflow integrating gradient dilution with multiple displacement amplification. Dilute-MetaSeq reduces host DNA interference by 52.4-fold and achieves > 90% microbial sequencing efficiency to assess gastrointestinal epithelium-associated microbiome. This enables the construction of the microbial genome atlas of gastrointestinal epithelium (MGA-GE). This comprehensive resource, comprising 1,907 nonredundant prokaryotic and 5,603 viral genomes, reveals extraordinary microbial diversity and novelty, with 41.4% of prokaryotic and 99.9% of viral genomes representing taxonomically unclassified lineages. Spatial profiling identifies the rumen and reticulum as a biodiversity hotspot dominated by epithelium-adapted Butyrivibrio and methylotrophic Methanomassiliicoccales, while functional annotation uncovers 1,200 biosynthetic gene clusters (primarily RiPPs and NRPSs) and 1,212 viral auxiliary metabolic genes linked to host metabolism modulation. Pangenome analysis of 987 strains, including a novel Butyrivibrio clade with reduced genome sizes, elevated GC content, and butyrate synthesis from amino acid-derived substrates (e.g., glutarate, lysine), highlights metabolic adaptations to the nutrient-scarce epithelial niche compared to digesta-associated microbes.

CONCLUSIONS: Collectively, the MGA-GE provides transformative insights into host-microbe-virus interactions and establishes a foundation for developing microbiome-based intervention strategies to enhance ruminant health, agricultural productivity, and bioactive discovery.}, } @article {pmid41593761, year = {2026}, author = {Tigabu, A and Leung, PHM}, title = {Broad-spectrum antibiotic treatment reshapes the gut microbiome, resistome, and colonization potential of opportunistic pathogens: a metagenomics study.}, journal = {Gut pathogens}, volume = {18}, number = {1}, pages = {}, pmid = {41593761}, issn = {1757-4749}, abstract = {BACKGROUND: The gut microbiota (GM) harbors diverse antibiotic resistance genes (ARGs), which are primarily disseminated through horizontal gene transfer (HGT), contributing to the emergence and spread of multidrug-resistant (MDR) pathogens. Broad-spectrum antibiotics are commonly used to treat a wide range of bacterial infections; however, they also exert collateral effects on non-target microbes. A comprehensive understanding of the impact of broad-spectrum antibiotic treatment on GM composition and the resistome is essential for the effective management of dysbiosis-related complications.

METHODS: Twenty-one fecal samples were collected from randomly selected study participants. Metagenomic sequencing was performed using the Illumina NovaSeq 6000 platform. FastQC v0.12.1, Trimmomatic v0.39, and Bowtie2 were used for quality control, removal of low-quality reads and adapter sequences, and host DNA removal, respectively. Metagenome assembly, gene prediction, and taxonomic annotation were conducted using MEGAHIT v1.2.9, MetaGeneMark-2, and the NCBI non-redundant protein database (nr), respectively. Resistome profiling was performed using the Comprehensive Antibiotic Resistance Database (CARD) v3.3.4. Functional annotation of protein-coding genes was carried out against the KEGG v112.0, eggNOG v5.0, and CAZy databases.

RESULTS: An enrichment of the phylum Bacillota and a depletion of Bacteroidota were observed in fecal samples from antibiotic-treated patients. Specifically, the genus Enterococcus and Streptococcus were the most prominent genera in antibiotic-treated patients, whereas Prevotella, Bacteroides, and Faecalibacterium were more abundant in healthy controls. Notably, the opportunistic pathogen E. faecium was elevated in antibiotic-treated patients. In longitudinal patients receiving augmentin treatment, the genera Escherichia and Enterococcus predominated, with E. coli and E. faecium showing increased prevalence compared with baseline in the first and second longitudinal patients, respectively. Antimicrobial resistance genes associated with antibiotic target alteration and protection were strongly linked to Bacillota, whereas efflux pump-mediated resistance mechanisms were positively associated with Bacteroidota and Pseudomonadota. The genes tetM, tet45, vanHM, vanYM, and vanRM were enriched in antibiotic-treated patients, whereas tetQ, tetW, cfxA6, adeF, vanTG, vanYB, and vanWI were more abundant in controls. Furthermore, pmrF, vanM, and cfxA were identified as principal biomarker genes in the first, second, and third augmentin-treated longitudinal patients, respectively.

CONCLUSIONS: Dysbiosis of the gut microbiota and alterations in the resistome were detected in antibiotic-treated patients. Notably, the opportunistic pathogens E. faecium and E. coli were enriched in antibiotic-treated individuals, suggesting that broad-spectrum antibiotic therapy may facilitate their proliferation and colonization, thereby contributing to dysbiosis-related complications. These findings warrant validation in larger cohorts to better elucidate the dynamics of antibiotic-induced dysbiosis and the dissemination of resistance genes.}, } @article {pmid41594066, year = {2025}, author = {Domingues, CPF and Rebelo, JS and Dionisio, F and Nogueira, T}, title = {Clinical and Environmental Plasmids: Antibiotic Resistance, Virulence, Mobility, and ESKAPEE Pathogens.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41594066}, issn = {2079-6382}, support = {UI/BD/153078/2022//Fundação para a Ciência e Tecnologia/ ; SFRH/BD/04631/2021//Fundação para a Ciência e Tecnologia/ ; UIDP/00329/2025//Fundação para a Ciência e Tecnologia/ ; }, abstract = {BACKGROUND/OBJECTIVES: Plasmids are autonomous DNA molecules that can replicate independently and transfer horizontally between bacterial cells. They play a key role in disseminating adaptive traits, such as antimicrobial resistance and virulence. Our study investigates the fundamental differences between plasmid populations originating from clinical/isolates and environmental/metagenomes.

METHODS: We compare three distinct plasmid genome datasets-the NCBI Reference Sequence Database (RefSeq), the Integrated Microbial Genomes & Microbiomes system (IMG/PR) from bacterial isolates (I) and microbiomes (M)-to assess how plasmid origin shapes their characteristics, including mobility types, antimicrobial resistance genes (ARGs), virulence genes (VGs) and host taxonomy.

RESULTS: We show that plasmids originating from bacterial isolates, more enriched in clinical samples, are fundamentally distinct from recovered from metagenomic data. Plasmids from isolates are larger, enriched in conjugative plasmids and display a higher frequency of ARGs and VGs than the ones assembled from metagenomes. Furthermore, ARGs are more frequently associated with highly mobile plasmids, particularly pCONJ.

CONCLUSIONS: These findings highlight the importance of plasmid origins in studies of plasmid epidemiology, functional potential and mobility.}, } @article {pmid41594081, year = {2026}, author = {Mohamed, FA and Al-Bulushi, M and Melegh, S and Timmer, B and Meszéna, R and Freytag, C and Laczkó, L and Miló, L and Urbán, P and Bőkényné-Tóth, R and Gyenesei, A and Kardos, G and Nyul, A and Urbán, E and Pál, T and Sonnevend, Á}, title = {Emergence of OXA-48-like Carbapenemase-Producing Escherichia coli in Baranya County, Hungary.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41594081}, issn = {2079-6382}, support = {300852//University of Pécs Medical School, Hungary/ ; }, abstract = {Background: Carbapenem-resistant Escherichia coli (CREC) producing OXA-48-like carbapenemase was first detected in Hungary in 2022. The aim of the present study was to characterize such strains isolated in 2022-2025 in Baranya County, Hungary. Methods: Antibiotic susceptibility and the whole-genome sequence (WGS) of E. coli isolates, identified as OXA-48-like carbapenemase producers using the CARBA-5 NG test, were established. The transferability of blaOXA-48-like plasmids was tested by conjugation. Results: Of the 6722 non-repeat E. coli isolates, 6 produced an OXA-48-like carbapenemase. They exhibited variable resistance to ertapenem and were susceptible to imipenem and meropenem. WGS revealed that all OXA-48-like producer E. coli belonged to high-risk clones: two clonally related OXA-181-producer E. coli ST405 were isolated in Hospital A, three OXA-244-producing E. coli ST38 (two identical via cgMLST from Hospital B), and an OXA-48-producing E. coli ST69. The blaOXA-48 and blaOXA-244 genes were chromosomally located, while blaOXA-181 was on a non-conjugative IncFIB-IncFIC plasmid. So far, the blaOXA-181-bearing plasmid of this incompatibility type has only been described in Ghana, but all blaOXA-48-like gene-carrying transposons in this study have already been identified in Europe and other continents. The E. coli ST38 isolates, showing close association based on core genome SNP distances to European and Qatari strains, belonged to Cluster A and harbored blaCTX-M-27. All but the E. coli ST69 isolate had cephalosporinase gene(s). Conclusions: This study describes small-scale intra-hospital transfers of OXA-48-like carbapenemase-producer E. coli. Interestingly, E. coli ST405 of Hungary carried blaOXA-181 on an IncFIB-IncFIC plasmid, which has only been reported from Africa so far.}, } @article {pmid41594088, year = {2026}, author = {Soto-López, JD and Velásquez-González, O and Barrios-Izás, MA and Belhassen-García, M and Muñoz-Bellido, JL and Fernández-Soto, P and Muro, A}, title = {Metagenomic Comparison of Bat Colony Resistomes Across Anthropogenic and Pristine Habitats.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41594088}, issn = {2079-6382}, abstract = {BACKGROUND/OBJECTIVES: The mammalian microbiota constitutes a reservoir of antimicrobial resistance genes (ARGs), which can be shaped by environmental and anthropogenic factors. Although bat-associated bacteria have been reported to harbor diverse ARGs globally, the ecological and evolutionary determinants driving this diversity remain unclear.

METHODS: To characterize ARG diversity in wildlife exposed to contrasting levels of human influence, we analyzed homologs of resistance mechanisms from the Comprehensive Antibiotic Resistance Database in shotgun metagenomes of bat guano. Samples were collected from a colony exposed to continuous anthropogenic activity in Spain (Salamanca) and from a wild, non-impacted bat community in China (Guangdong). Metagenomic analyses revealed marked differences in taxonomic and resistome composition between sites.

RESULTS: Salamanca samples contained numerous hospital-associated genera (e.g., Mycobacterium, Staphylococcus, Corynebacterium), while Guangdong was dominated by Lactococcus, Aeromonas, and Stenotrophomonas. β-lactamases and MurA transferase homologs were the most abundant ARGs in both datasets, yet Salamanca exhibited higher richness and functional diversity (median Shannon index = 1.5; Simpson = 0.8) than Guangdong (Shannon = 1.1; Simpson = 0.66). Salamanca also showed enrichment of clinically relevant ARGs, including qacG, emrR, bacA, and acrB, conferring resistance to antibiotics critical for human medicine. In contrast, Guangdong exhibited a more restricted resistome dominated by β-lactamase and MurA homologs. Beta diversity analysis confirmed significant compositional differences between resistomes (PERMANOVA, R[2] = 0.019, F = 1.33, p = 0.001), indicating ecological rather than stochastic structuring.

CONCLUSIONS: These findings suggest that anthropogenic exposure enhances the diversity and evenness of resistance mechanisms within bat-associated microbiomes, potentially increasing their role as reservoirs of antimicrobial resistance.}, } @article {pmid41594136, year = {2026}, author = {Kitano, T and Matsunaga, N and Akiyama, T and Azuma, T and Fujii, N and Tsukada, A and Hibino, H and Kuroda, M and Ohmagari, N}, title = {Environmental Dissemination of Antimicrobial Resistance: A Resistome-Based Comparison of Hospital and Community Wastewater Sources.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41594136}, issn = {2079-6382}, support = {JP22fk0108131//Japan Agency for Medical Research and Development/ ; JP25fk0108666//Japan Agency for Medical Research and Development/ ; }, abstract = {Background/Objectives: Comparative analysis of antimicrobial resistomes in hospital and community wastewater can provide valuable insights into the diversity and distribution of antimicrobial resistance genes (ARGs), contributing to the advancement of the One Health approach. This study aimed to characterize and compare the resistome profiles of wastewater sources from a hospital and community. Methods: Longitudinal metagenomic analysis was conducted on wastewater samples collected from the National Center for Global Health and Medicine (hospital) and a shopping mall (community) in Tokyo, Japan, between December 2019 and September 2023. ARG abundance was quantified using reads per kilobase per million mapped reads (RPKM) values, and comparative analyses were performed to identify the significantly enriched ARGs in the two sources. Results: A total of 46 monthly wastewater samples from the hospital yielded 825 unique ARGs, with a mean RPKM of 2.5 across all detected genes. In contrast, 333 ARGs were identified in the three shopping mall wastewater samples, with a mean RPKM of 2.1. Among the ARGs significantly enriched in the hospital samples, 23, including genes conferring resistance to aminoglycosides (nine groups) and β-lactam antibiotics (eight groups), exhibited significantly high RPKM values. No ARGs were found to be significantly enriched in the community wastewater samples. Conclusions: This study highlights the higher diversity and abundance of ARGs, particularly those conferring resistance to aminoglycosides and β-lactam antibiotics including carbapenems, in hospital wastewater than in community wastewater. These findings underscore the importance of continuous resistome monitoring of hospital wastewater as part of the integrated One Health surveillance strategy.}, } @article {pmid41594301, year = {2026}, author = {Camatti, J and Bonasoni, MP and Santunione, AL and Cecchi, R and Radheshi, E and Carretto, E}, title = {Postmortem Microbiology in Forensic Diagnostics: Interpretation of Infectious Causes of Death and Emerging Applications.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {2}, pages = {}, pmid = {41594301}, issn = {2075-4418}, abstract = {Background/Objectives: Postmortem microbiology has traditionally been regarded with caution in forensic practice due to concerns related to contamination, bacterial translocation, and postmortem microbial overgrowth. As a result, microbiological findings obtained after death have often been considered unreliable or of limited diagnostic value. However, growing evidence indicates that, when appropriately interpreted and integrated with autopsy findings, histopathology, and circumstantial information, postmortem microbiology can provide crucial support for cause-of-death determination. This narrative review critically examines the current role of postmortem microbiology in forensic diagnostics, with a focus on its diagnostic applications, interpretative challenges, and future perspectives. Methods/Results: The transition from conventional culture-based techniques to molecular approaches-including polymerase chain reaction, microbiome analysis, and metagenomic methods-is discussed, highlighting both their potential advantages and inherent limitations within the forensic setting. Particular attention is devoted to key interpretative issues such as postmortem interval, sampling strategies, contamination, and bacterial translocation. In addition to cause-of-death attribution, emerging applications-including postmortem interval estimation, trace evidence analysis, and artificial intelligence-based models-are reviewed. Although these approaches show promising research potential, their routine forensic applicability remains limited by methodological heterogeneity, lack of standardization, and interpretative complexity. Conclusions: In conclusion, postmortem microbiology represents a valuable diagnostic tool when applied within a multidisciplinary forensic framework. Its effective use requires cautious interpretation and integration with pathological and contextual evidence, avoiding standalone or automated conclusions. Future progress will depend on standardized methodologies, multidisciplinary collaboration, and a clear distinction between experimental research and routine forensic practice.}, } @article {pmid41594560, year = {2025}, author = {Dissanayaka, DMS and Jayasinghe, TN and Sohrabi, HR and Rainey-Smith, SR and Taddei, K and Masters, CL and Martins, RN and Fernando, WMADB}, title = {Gut Microbial Composition and Short-Chain Fatty Acid Metabolism in Cognitively Unimpaired Adults Stratified by Amyloid-β Status.}, journal = {Biomolecules}, volume = {16}, number = {1}, pages = {}, pmid = {41594560}, issn = {2218-273X}, mesh = {Humans ; *Fatty Acids, Volatile/metabolism ; *Amyloid beta-Peptides/metabolism ; *Gastrointestinal Microbiome ; Female ; Aged ; Male ; Feces/microbiology/chemistry ; Alzheimer Disease/metabolism/microbiology ; Middle Aged ; }, abstract = {Short-chain fatty acids (SCFAs) produced by gut microbial fermentation influence host metabolism and neuroinflammatory processes implicated in Alzheimer's disease (AD). However, the relationship between fecal SCFAs, microbial taxa, and cerebral amyloid-β (Aβ) burden in cognitively unimpaired individuals remains unclear. Fecal SCFAs were quantified using GC-MS, and microbial species were profiled by shotgun metagenomics in 87 participants. Associations between SCFAs, demographics, APOE ε4 status, and Aβ burden were tested using nonparametric statistics and multivariable regression. Microbial-SCFA links were evaluated using Spearman correlations and multivariate ordinations, with mediation analysis exploring potential indirect pathways. Acetate was the predominant SCFA and demonstrated the most robust microbial associations. Higher acetate concentrations were positively associated with Bacteroides ovatus and Faecalibacterium prausnitzii, whereas lower acetate levels were linked to species such as Bifidobacterium animalis and Lachnoclostridium scindens. Stratified analyses indicated that individuals with elevated Aβ burden exhibited more pronounced species-SCFA relationships, including a notable association between Bacteroides thetaiotaomicron and butyrate. Multivariate ordination further identified a significant overall coupling between SCFA profiles and microbial community structure. Mediation analysis suggested that an Oscillospiraceae species may represent a potential intermediary linking valerate concentrations with Aβ status. SCFA concentrations were not strongly influenced by demographic or genetic factors, but specific species demonstrated robust associations with acetate levels. Distinct SCFA-microbial interaction patterns in Aβ High individuals suggest subtle early gut microbial alterations linked to amyloid burden. These findings highlight the potential role of SCFA-related microbial pathways in preclinical AD.}, } @article {pmid41594852, year = {2026}, author = {Zhao, Q and Li, B and Ma, J and Wei, J and Qin, W}, title = {The Gut Microbiome of the Goitered Gazelle Enables Plasticity by Responding to Environmental Factors in the Qaidam Basin.}, journal = {Biology}, volume = {15}, number = {2}, pages = {}, pmid = {41594852}, issn = {2079-7737}, support = {32160316//National Natural Science Foundation of China/ ; }, abstract = {The Qaidam Basin on the Qinghai-Tibet Plateau is an extreme arid environment, posing severe survival challenges. The goitered gazelle (Gazella subgutturosa) is a keystone species in this fragile ecosystem, yet the ecological role of its gut microbiota and its associations with environmental drivers remain poorly understood. We collected fecal samples from gazelles across seven regions of the basin. Metagenomic sequencing was employed to characterize the gut microbiome. Statistical analyses (Mantel tests, multiple regression on matrices, co-occurrence networks) were used to link microbial composition and function with key environmental factors. The gut microbiota was dominated by fiber-degrading phyla (Firmicutes, Bacteroidota) and enriched in metabolic pathways, aligning with a high-fiber diet. Regarding environmental drivers of gut microbial composition variations, isothermality and soil organic carbon were significant predictors, likely via vegetation and environmental inoculation. Regarding environmental drivers of gut microbial function variations, winter solar radiation was uniquely associated with metabolic function without altering microbial composition, suggesting a functional plasticity-the capacity to shift metabolic profiles independently of taxonomic turnover-in response to environmental variation. The gut microbiota of the goitered gazelle exhibits a stable core composition alongside environmentally responsive functional modules. This suggests the microbiome may serve as a significant mediator of host resilience, highlighting adaptation as a dynamic interplay between host, microbiome, and environment. These insights are crucial for microbiome-assisted conservation.}, } @article {pmid41594879, year = {2026}, author = {Han, H and Yang, Y and Zhu, X and Wangdwei, M and Yang, L}, title = {Age-Specific Composition and Predicted Function of Gut Microbiota in Plateau Pikas (Ochotona curzoniae).}, journal = {Biology}, volume = {15}, number = {2}, pages = {}, pmid = {41594879}, issn = {2079-7737}, support = {202401ZR0101//Natural Science Foundation of the Xizang Autonomous Region/ ; 2021-GSP-B015//High-level Personnel Training Program of Xizang University/ ; }, abstract = {Gut microbes play a crucial role in regulating physiological processes such as host energy metabolism, nutrient absorption, and environmental adaptation. The predicted functions of gut microbes can be influenced by many factors, both extrinsic and intrinsic to the hosts. The plateau pika is a key species in the alpine ecosystem of the Qinghai-Tibet Plateau. Previous research on the plateau pika primarily examined how extrinsic factors affected its gut microbiota. However, studies on intrinsic factors are scarce. Here, we used live-trapping to capture plateau pikas and collect cecum contents. Using metagenomic sequencing of cecum content samples, we characterized and compared the gut microbial composition and predicted function of plateau pika in adult (n = 9) and juvenile (n = 9) populations. The results indicated that Bacillota and Bacteroidete were the major bacterial phyla. The core gut microbial genera were the same, but the relative abundance of Oscillospira in juveniles was significantly lower than that in adults. The changes in the proportion of cellulose-degradation-related bacterial communities in juveniles suggest that they tend to choose low-fiber diets. In this study, we found no significant differences in the gut microbial composition and diversity, KEGG level 1 metabolic pathways, or CAZy class level between adult and juvenile plateau pikas. In total, the composition and predicted functions of cecal microorganisms in juvenile and adult male plateau pikas were not different. Regarding KEGG level 2 metabolic pathways, the juvenile group had a higher relative abundance of metabolic pathways for cofactors and vitamins, terpenoids, and polyketides, whereas the adult group had a higher relative abundance of energy metabolism. However, the resulting differences remain unclear. Therefore, future research should validate the above findings on a broader spatio-temporal scale and conduct cross-species comparisons to construct a microbial ecological framework for the health management of plateau wild animals.}, } @article {pmid41595429, year = {2025}, author = {Wu, H and Li, J and Long, J and Liao, H and Zhan, K and Chen, H and Lei, F}, title = {Enhancing Ecological Functions in Chinese Yellow Earth: Metagenomic Evidence of Microbial and Nitrogen Cycle Reassembly by Organic Amendments.}, journal = {Genes}, volume = {17}, number = {1}, pages = {}, pmid = {41595429}, issn = {2073-4425}, support = {Grants 2022YFD1901500 and 2022YFD1901505//the National Key R&D Program of China/ ; Grant U2420626//the National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Soil Microbiology ; Metagenomics/methods ; *Nitrogen Cycle/genetics ; Nitrogen/metabolism ; Soil/chemistry ; China ; Zea mays/growth & development ; Fertilizers ; Agriculture/methods ; }, abstract = {BACKGROUND: Chinese Yellow Earth is a key subtropical agricultural resource in southwestern China; however, its productivity is limited by acidity and poor nutrient retention. This study examined how reduced nitrogen plus organic amendments affect its soil microbial structure and maize yield.

METHODS: A field experiment with four treatments evaluated reduced nitrogen fertilization amended with rice husk plus rapeseed cake (RS) or RS with biochar (BC). Soil properties (pH, nitrogen, organic matter) and maize yield were analyzed. Metagenomic analysis (NR database) characterized microbial communities, and correlation analysis with Mantel tests identified key relationships.

RESULTS: Combined organic amendments under reduced N significantly increased soil pH, nitrogen components, and organic matter, increasing maize yield by 4.41-8.97%. Metagenomics revealed enriched beneficial genera including Sphingomonas and Bradyrhizobium. Yield positively correlated with nitrate nitrogen and a beneficial microbial cluster containing Lysobacter and Reyranella, whereas Steroidobacter negatively correlated with key fertility indicators. Mantel tests revealed nitrate nitrogen as the primary correlate of functional gene community succession.

CONCLUSIONS: This study reveals that reduced nitrogen with organic amendments promotes soil improvement and microbial modulation, demonstrating potential as a sustainable practice to maintain crop productivity in Chinese Yellow Earth. The observed trend toward yield improvement underscores its promise and warrants further validation through additional trials. Overall, the findings highlight the beneficial effects of these amendments on soil health and their role in supporting sustainable subtropical agriculture under reduced nitrogen input.}, } @article {pmid41595438, year = {2025}, author = {Vougiouklaki, D and Letsiou, S and Ladias, K and Tsakni, A and Mavrokefalidou, I and Siateli, Z and Halvatsiotis, P and Houhoula, D}, title = {Lactobacillus-Dominated Cervical Microbiota Revealed by Long-Read 16S rRNA Sequencing: A Greek Pilot Study.}, journal = {Genes}, volume = {17}, number = {1}, pages = {}, pmid = {41595438}, issn = {2073-4425}, mesh = {Humans ; Female ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Cervix Uteri/microbiology ; Greece ; Pilot Projects ; *Lactobacillus/genetics/classification/isolation & purification ; Vagina/microbiology ; Human Papillomavirus Viruses/genetics ; }, abstract = {Background/Objectives: The vaginal microbiota constitutes a highly dynamic microbial ecosystem shaped by the distinct mucosal, hormonal, and immunological environment of the female genital tract. Accumulating evidence suggests that shifts in cervical microbial composition and function may influence host-microbe interactions and contribute to gynecological disease risk. Within this framework, the present study aimed to perform an in-depth genomic characterization of the cervical microbiota in a well-defined cohort of Greek women. The primary objective was to explore the functional microbial landscape by identifying dominant bacterial taxa, taxon-specific signatures, and potential microbial pathways implicated in cervical epithelial homeostasis, immune modulation, and disease susceptibility. Methods: Microbial genomic DNA was isolated from 60 cervical samples using the Magcore Bacterial Automated Kit and analyzed through full-length 16S rRNA gene sequencing using the Nanopore MinION™ platform, allowing high-resolution taxonomic assignment and enhanced functional inference. In parallel, cervical samples were screened for 14 HPV genotypes using a real-time PCR-based assay. Results: The cervical microbial communities were dominated by Lactobacillus iners, Lactobacillus crispatus, and Aerococcus christensenii, collectively representing over 75% of total microbial abundance and suggesting a functionally protective microbiota profile. A diverse set of low-abundance taxa-including Stenotrophomonas maltophilia, Stenotrophomonas pavanii, Acinetobacter septicus, Rhizobium spp. (Rhizobium rhizogenes, Rhizobium tropici, Rhizobium jaguaris), Prevotella amnii, Prevotella disiens, Brevibacterium casei, Fannyhessea vaginae, and Gemelliphila asaccharolytica-was also detected, potentially reflecting niche-specific metabolic functions or environmental microbial inputs. No HPV genotypes were detected in any of the cervical samples. Conclusions: This genomic profiling study underscores the functional dominance of Lactobacillus spp. within the cervical microbiota and highlights the contribution of low-abundance taxa that may participate in metabolic cross-feeding, immune signaling, or epithelial barrier modulation. Future large-scale, multi-omics studies integrating metagenomics and host transcriptomic data are warranted to validate microbial functional signatures as biomarkers or therapeutic targets for cervical health optimization.}, } @article {pmid41595535, year = {2026}, author = {Ma, Y and Wang, L and Hu, H and Shieh, AR and Li, E and He, D and He, L and Liu, Z and Paing, TM and Chen, X and Cao, Y}, title = {Composition and Function of Gut Microbiome: From Basic Omics to Precision Medicine.}, journal = {Genes}, volume = {17}, number = {1}, pages = {}, pmid = {41595535}, issn = {2073-4425}, mesh = {Humans ; *Precision Medicine/methods ; Multiomics ; Animals ; *Gastrointestinal Microbiome/genetics/physiology ; Genomics ; Host Microbial Interactions ; }, abstract = {The gut microbiome is defined as the collective assembly of microbial communities inhabiting the gut, along with their genes and metabolic products. The gut microbiome systematically regulates host metabolism, immunity, and neuroendocrine homeostasis via interspecies interaction networks and inter-organ axes. Given the importance of the gut microbiome to the host, this review integrates the composition, function, and genetic basis of the gut microbiome with host genomics to provide a systematic overview of recent advances in microbiome-host interactions. This encompasses a complete technological pipeline spanning from in vitro to in vivo models to translational medicine. This technological pipeline spans from single-bacterium CRISPR editing, organoid-microbiome co-culture, and sterile/humanized animal models to multi-omics integrated algorithms, machine learning causal inference, and individualized probiotic design. It aims to transform microbiome associations into precision intervention strategies that can be targeted and predicted for clinical application through interdisciplinary research, thereby providing the cornerstone of a new generation of precision treatment strategies for cancer, metabolic, and neurodegenerative diseases.}, } @article {pmid41596119, year = {2026}, author = {Patanè, GT and Moreira, RJ and Almeida-Santos, M and Putaggio, S and Barreca, D and Oliveira, PF and Alves, MG}, title = {Anthocyanins and Metabolic Disease: A New Frontier in Precision Nutrition.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41596119}, issn = {2076-3921}, support = {2024.03012.BD//Fundação para a Ciência e Tecnologia/ ; UIDB/50006/2020//Laboratório Associado para a Química Verde/ ; CEECINST/00026/2018//Fundação para a Ciência e Tecnologia/ ; CDL-CTTRI-267-SGRH/2022//Fundação para a Ciência e Tecnologia/ ; UIDB/04501/2020-DOI 10.54499/UIDB/04501/2020 and UIDP/04501/2020-DOI 10.54499/UIDP/04501/2020//iBiMED/ ; }, abstract = {Metabolic syndrome (MetS) represents a global health challenge mainly driven by chronic low-grade inflammation and persistent oxidative stress (OS). Current therapeutic and nutritional strategies often fail to resolve these interconnected core pathologies due to the multifactorial nature of MetS. Anthocyanins (ACNs), a class of potent dietary flavonoids, offer significant promise due to their established pleiotropic effects, including robust antioxidant activity through modulation of the Nrf2/ARE pathway, anti-inflammatory effects via NF-κB suppression, and overall support for glucose and lipid homeostasis. However, the therapeutic efficacy of ACNs is characterized by interindividual variability, which is intrinsically linked to their low systemic bioavailability. This heterogeneity in the response is due to the complex interplay between genetic polymorphisms affecting absorption, distribution, metabolism, and excretion (ADME), as well as the specific biotransformation capacity of the gut microbiome. This review proposes that achieving the full clinical potential of ACNs requires moving beyond conventional nutritional advice. We propose that precision nutrition, which integrates multi-omics data (e.g., genomics, metagenomics, and metabolomics), can determine the individual phenotype, predict functional metabolic response, and tailor safer and effective ACN-rich interventions. This integrated, multifactorial approach is essential for optimizing the antioxidant and metabolic benefits of ACNs for the prevention and management of MetS and its associated pathologies.}, } @article {pmid41596486, year = {2026}, author = {Sá, L and Machado, E and Ginani, V and Timbó, R and Romiti, R and Kurizky, P and Gomes, C}, title = {Species-Level Comparative Metagenomic Analysis of the Bacterial Abundance of the Gut Microbiome in Psoriasis, Hidradenitis Suppurativa, and Pemphigus Foliaceous Patients Using Shotgun Next-Generation Sequencing.}, journal = {International journal of molecular sciences}, volume = {27}, number = {2}, pages = {}, pmid = {41596486}, issn = {1422-0067}, support = {00193-00000279/2023-70//Fundação de Apoio à Pesquisa do Distrito Federal (FAP-DF)/ ; 445040/2023-8//National Council for Scientific and Technological Development/ ; 21/2023//Departamento de Ciência e Tecnologia, da Secretaria de Ciência, Tecnologia, Inovação e Com-plexo da Saúde, do Ministério da Saúde (Decit/SECTICS/MS)/ ; }, mesh = {Humans ; *Psoriasis/microbiology ; *Hidradenitis Suppurativa/microbiology ; Female ; Male ; Adult ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Pemphigus/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Middle Aged ; *Bacteria/genetics/classification ; Metagenome ; }, abstract = {Recent studies have revealed a specific relationship between gut bacteria and inflammatory skin profiles. We aimed to perform a species-level comparative metagenomic analysis of the gut microbiome in patients with psoriasis, hidradenitis suppurativa (HS), and pemphigus foliaceus (PF). We included omnivorous nonsmokers and nondrinkers with psoriasis (n = 24), HS (n = 10), and PF (n = 11), as well as healthy controls (n = 10). We collected faecal samples from all patients for classic parasitological analysis. Gut microbiome analysis was conducted using shotgun next-generation sequencing. We used the Deseq2, Limma_voom, LinDA, and MaAMaAsLin 2 bioinformatics tools to evaluate concordance and differential abundance between patients. Thirteen patients (23.64%) were diagnosed with active intestinal parasitosis. The presence of intestinal parasitosis was significantly related to immunosuppression (p = 0.009). The most abundant microorganism species found in the faeces of the patients evaluated was Escherichia coli. Psoriasis patients presented a greater abundance of bacteria from the Veillonellaceae family, whereas PF patients presented a greater abundance of Firmicutes bacteria. Patients with PF showed increased E. coli virulence and antibiotic resistance functional markers. Immunosuppression significantly influenced the presence of intestinal parasitosis as well as increased the virulence of functional markers in patients with PF receiving systemic corticosteroid therapy.}, } @article {pmid41596633, year = {2026}, author = {Tamayo-Ordóñez, YJ and Rosas-García, NM and Bello-López, JM and Tamayo-Ordóñez, MC and Tamayo-Ordóñez, FA and Calzada-Mendoza, CC and Ayil-Gutiérrez, BA}, title = {A Possible Recently Identified Evolutionary Strategy Using Membrane-Bound Vesicle Transfer of Genetic Material to Induce Bacterial Resistance, Virulence and Pathogenicity in Klebsiella oxytoca.}, journal = {International journal of molecular sciences}, volume = {27}, number = {2}, pages = {}, pmid = {41596633}, issn = {1422-0067}, mesh = {*Klebsiella oxytoca/genetics/pathogenicity ; Gene Transfer, Horizontal ; Virulence/genetics ; Phylogeny ; Virulence Factors/genetics ; Genome, Bacterial ; Evolution, Molecular ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences ; }, abstract = {Klebsiella oxytoca has emerged as an important opportunistic pathogen in nosocomial infections, particularly during the COVID-19 pandemic, due to its capacity to acquire and disseminate resistance and virulence genes through horizontal gene transfer (HGT). This study presents a genome-based comparative analysis of K. oxytoca within the genus Klebsiella, aimed at exploring the evolutionary plausibility of outer membrane vesicle (OMV) associated processes in bacterial adaptation. Using publicly available reference genomes, we analyzed pangenome structure, phylogenetic relationships, and the distribution of mobile genetic elements, resistance determinants, virulence factors, and genes related to OMV biogenesis. Our results reveal a conserved set of envelope associated and stress responsive genes involved in vesiculogenic pathways, together with an extensive mobilome and resistome characteristic of the genus. Although these genomic features are consistent with conditions that may favor OMV production, they do not constitute direct evidence of functional OMV mediated horizontal gene transfer. Instead, our findings support a hypothesis generating evolutionary framework in which OMVs may act as a complementary mechanism to established gene transfer routes, including conjugation, integrative mobile elements, and bacteriophages. Overall, this study provides a genomic framework for future experimental and metagenomic investigations into the role of OMV-associated processes in antimicrobial resistance dissemination and should be interpreted as a recently identified evolutionary strategy inferred from genomic data, rather than a novel or experimentally validated mechanism.}, } @article {pmid41596659, year = {2026}, author = {Sánchez-Recillas, E and Almanza-Aguilera, E and Bars-Cortina, D and Zamora-Ros, R and Godínez-Santillán, RI and Sánchez-Tusié, AA and Vergara-Castañeda, HA}, title = {Effect of Garambullo (Myrtillocactus geometrizans) Consumption on the Intestinal Microbiota Profile in an Early-Phase Rat Model of Colon Cancer.}, journal = {International journal of molecular sciences}, volume = {27}, number = {2}, pages = {}, pmid = {41596659}, issn = {1422-0067}, support = {1560335//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; FME202404//Autonomous University of Queretaro - FONFIVE/ ; }, mesh = {Animals ; *Colonic Neoplasms/microbiology/chemically induced ; Male ; *Gastrointestinal Microbiome/drug effects ; Rats ; Rats, Sprague-Dawley ; Azoxymethane ; Disease Models, Animal ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Dextran Sulfate ; *Plant Extracts/pharmacology ; Bacteria/genetics/classification ; }, abstract = {Bioactive compounds in food contribute to reducing the risk of developing colon cancer by modulating the gut microbiota. We have recently demonstrated that garambullo (Myrtillocactus geometrizans), an endemic fruit of Mexico rich in bioactive compounds, attenuates aberrant crypt foci in an animal model. However, its potential to modulate the gut microbiota is unknown. The main objective of this study was to evaluate whether its consumption modulates colon carcinogenesis by altering the microbiota in an in vivo model induced by azoxymethane and dextran sulfate sodium (AOM/DSS). Fecal samples were collected from twelve male Sprague-Dawley rats and analyzed for microbiota composition after 0, 8, and 16 weeks of treatment with saline (control), AOM/DSS, garambullo (G), or residue of garambullo (RG) with AOM/DSS (G+AOM/DSS and RG+AOM/DSS, respectively). Characterization of the microbiome was based on the conserved region of the 16S rRNA V3-V4 gene, and analyzed by the ZymoBIOMICS' Targeted Metagenomics Sequencing (Zymo Research) service. In an animal model induced with AOM/DSS for 8 weeks, consumption of G and its residue increased the bacterial genera Shuttleworthiia, Subdoligranulum, Lactobacillus, Faecalibacterium, and Alloprevotella (p < 0.05). Consumption of G and its residue allowed the proliferation of bacteria that produce short-chain fatty acids and are associated with protective mechanisms of the colon.}, } @article {pmid41596857, year = {2026}, author = {Tsouggou, N and Korozi, E and Pemaj, V and Drosinos, EH and Kapolos, J and Papadelli, M and Skandamis, PN and Papadimitriou, K}, title = {Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41596857}, issn = {2304-8158}, abstract = {The cheese microbiome is a complex ecosystem strongly influenced by both technological practices and the processing environment. Moving beyond traditional cultured-based methods, the integration of shotgun metagenomics into cheese microbiology has enabled in-depth resolution of microbial communities at the species and strain levels. The aim of the present study was to review recent applications of shotgun metagenomics in cheese research, underscoring its role in tracking microbial dynamics during production and in discovering genes of technological importance. In addition, the review highlights how shotgun metagenomics enables the identification of key metabolic pathways, including amino acid catabolism, lipid metabolism, and citrate degradation, among others, which are central to flavor formation and ripening. Results of the discussed literature demonstrate how microbial composition, functional traits, and overall quality of cheese are determined by factors such as raw materials, the cheesemaking environment, and artisanal practices. Moreover, it highlights the analytical potentials of shotgun metagenomics, including metagenome-assembled genomes (MAGs) reconstruction, characterization of various genes contributing to flavor-related biosynthetic pathways, bacteriocin production, antimicrobial resistance, and virulence, as well as the identification of phages and CRISPR-Cas systems. These insights obtained are crucial for ensuring product's authenticity, enabling traceability, and improving the assessment of safety and quality. Despite shotgun metagenomics' advantages, there are still analytical restrictions concerning data handling and interpretation, which need to be addressed by importing standardization steps and moving towards integrating multi-omics approaches. Such strategies will lead to more accurate and reproducible results across studies and improved resolution of active ecosystems. Ultimately, shotgun metagenomics has shifted the field from descriptive surveys to a more detailed understanding of the underlying mechanisms shaping the overall quality and safety of cheese, thus bringing innovation in modern dairy microbiology.}, } @article {pmid41596861, year = {2026}, author = {Iturritxa, E and Mesanza, N and Torija, MJ}, title = {Wild Yeasts as Reservoirs of Bacterial Diversity: Biotechnological Insights from 16S rRNA Metabarcoding.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41596861}, issn = {2304-8158}, abstract = {Recently acquired evidence indicates that bacteria can utilise yeasts as survival niches. This study investigated the presence of hidden, intracellular bacteria (endobacteria) within wild yeasts collected from natural ecosystems and evaluated whether biotechnological processes influenced these bacterial communities. We examined the microbiotas of 28 axenic cultures of wild yeasts; these were selected due to their potential brewing and biocontrol uses and were isolated from habitats associated with Quercus and Vitis. We also analysed the microbiotas present after these strains were used to ferment beer wort. Bacterial communities were characterised using 16S rRNA gene amplicon metagenomics. The results indicate that yeast strains and their endobacterial partners have coevolved, and their compositions are shaped by the environmental conditions. Substantial bacterial diversity was detected across strains in both axenic cultures and post-fermentation samples. The ecological origin of the yeast (oak- or grape-associated) did not significantly affect the endobacterial community structure. Across all samples, the dominant phyla were Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, with Proteobacteria representing over 90% of sequences. Most bacterial genera were shared between axenic and fermentation conditions. However, Escherichia and Comamonas predominated in axenic cultures, while Parvibaculum dominated after fermentation. These findings suggest that yeasts constitute stable microhabitats for bacterial communities, and their relative abundances can shift during fermentation processes.}, } @article {pmid41597216, year = {2026}, author = {Mamun, MAA and Rakib, A and Mandal, M and Li, W and Miller, DD and Chen, H and Nagarkatti, M and Nagarkatti, P and Singh, UP}, title = {VERU-111 Promotes an Anti-Tumor Response Through Restoration of Gut Microbial Homeostasis and Associated Metabolic Dysregulation.}, journal = {Cells}, volume = {15}, number = {2}, pages = {}, pmid = {41597216}, issn = {2073-4409}, support = {AI140405//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Homeostasis/drug effects ; Mice ; *Colorectal Neoplasms/drug therapy/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Antineoplastic Agents/pharmacology ; Dextran Sulfate ; Mice, Inbred C57BL ; Azoxymethane ; Male ; }, abstract = {The rising global burden of colorectal cancer (CRC) has now positioned it as the third most common cancer worldwide. Chemotherapy regimens are known to disrupt the composition of the gut microbiota and lead to long-term health consequences for cancer patients. However, the alteration of gut microbiota by specific chemotherapeutic agents has been insufficiently explored until now. The purpose of this study was to assess changes in the gut microbiota following treatment with VERU-111 as a chemotherapy agent for the treatment of CRC. We thus performed a metagenomic study using 16S rRNA gene amplicon sequencing of fecal samples from different experimental groups in the azoxymethane (AOM) and dextran sodium sulfate (DSS)-induced murine model of CRC. To predict the functional potential of microbial communities, we used the resulting 16S rRNA gene sequencing data to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. We found that the administration of VERU-111 led to a restructured microbial community that was characterized by increased alpha and beta diversity. Compared to the mice treated with DSS alone, VERU-111 treatment significantly increased the relative abundance of several bacterial species, including Verrucomicrobiota species, Muribaculum intestinale, Alistipes finegoldii, Turicibacter, and the well-known gut-protective bacterial species Akkermansia muciniphila. The relative abundance of Ruminococcus, which is negatively correlated with immune checkpoint blockade therapy, was diminished following VERU-111 administration. Overall, this metagenomic study suggests that the microbial shift after administration of VERU-111 is associated with suppression of several metabolic and cancer-related pathways that might, at least in part, facilitate the suppression of CRC. These favorable shifts in gut microbiota suggest a novel therapeutic dimension of using VERU-111 to treat CRC and emphasize the need for further mechanistic exploration.}, } @article {pmid41597231, year = {2026}, author = {Feng, Y and Geng, Y and Liu, S and Huang, X and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y}, title = {Overwinter Syndrome in Grass Carp (Ctenopharyngodon idellus) Links Enteric Viral Proliferation to Mucosal Disruption via Multiomics Investigation.}, journal = {Cells}, volume = {15}, number = {2}, pages = {}, pmid = {41597231}, issn = {2073-4409}, support = {2024YFD2401102//National Key R&D ProgramNational Key R&D Program/ ; 2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; }, mesh = {Animals ; *Carps/virology/microbiology/genetics ; Multiomics ; *Intestinal Mucosa/virology/pathology ; *Fish Diseases/virology/microbiology ; Gastrointestinal Microbiome ; *Virus Replication ; }, abstract = {Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the 'low-temperature-pathogen' model and shifts focus to mucosal barrier dysfunction and host-microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host-microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention.}, } @article {pmid41597535, year = {2025}, author = {Wang, Y and Liu, S and Zheng, Z and Ma, J and Xiang, Y and Wu, L and Ding, C and Shi, Y}, title = {Deciphering the Structure and Genetic Basis of Adaptive Mechanism of Soil Microbial Communities in a Manganese Electrolysis Plant.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597535}, issn = {2076-2607}, support = {QKHJCZK [2021] 224//Science and Technology Program of Guizhou Province/ ; QKHCG [2023] ZD008//Guizhou Provincial Science and Technology Projects/ ; No. [2023] 026//Guizhou Key Laboratory of Green Metallurgy and Process Strengthening/ ; No. [2023] 70//Science and Technology Major Project of Tongren/ ; }, abstract = {The development of China's manganese (Mn) industries has caused severe water and soil pollution, threatening ecological and human health. Microbes are usually regarded as an important indicator of environmental pollution assessment. However, the current understanding of microbial community characteristics and their formation mechanisms in Mn production areas remains limited. In order to address this, soil properties and microbial structural characteristics across different functional zones in a typical Mn electrolysis plant in China's "Manganese Triangle" were investigated via metagenomic sequencing. Results showed soil Mn levels significantly exceeded background values, indicating high environmental risk. Acidobacteria and Proteobacteria were dominant phyla. Microbial abundance was lowest in the adjacent natural reservoir, whereas diversity was highest in the sewage treatment plant. Correlation analyses identified Mn, nitrate nitrogen, ammonium nitrogen, pH, and moisture as key environmental drivers, with Mn being the primary one. Metagenomic analysis revealed abundant Mn resistance genes, enabling microbial survival under high Mn stress. This study demonstrated that excessive Mn exposure enriched Mn-resistant genes, thereby shaping unique microbial communities dominated by Mn-resistant bacteria. These findings clarified the structural characteristics and adaptive mechanisms of soil microbial communities in Mn-contaminated areas, providing a theoretical basis for ecological risk management and bioremediation.}, } @article {pmid41597576, year = {2025}, author = {Wang, L and Zhao, Y}, title = {The Response of Substrate Microbial Communities to the Addition of Mineral Nutrients During the Growth Period of Straw Mushroom Volvariella volvacea.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597576}, issn = {2076-2607}, support = {No. 2024YFD1200204//National Key R&D Program of China/ ; No. 21N51900500//Shanghai Committee of Science and Technology/ ; 2020-02-08-00-12-F01479//Shanghai Agricultural Commission Program/ ; KFKT2023-03//the Shanghai Key Laboratory of Agricultural Genetics and Breeding/ ; }, abstract = {Volvariella volvacea were grown on an abandoned cotton-based substrate, which was divided into two conditions: a group with added nutrients (N3P3) and a control group (CK). Using metagenomic sequencing technology, the study investigated the effect of nutrient addition during the growth process of V. volvacea on the microbial community and metabolic pathways of the substrate. The study found that the main bacteria in the N3P3 group were Proteus and Microsporidium, while in the CK group, Bacillus marinosus and Microsporidium globosa were more common. At all stages of V. volvacea growth, Proteobacteria and Firmicutes dominated. Metabolic function analysis showed that the N3P3 group significantly increased amino acid metabolism, nitrogen metabolism, genetic information processing, and cellular processes, while reducing the contents of pathogenic and saprophytic symbiotic fungi. Nitrogen metabolism, phosphorus metabolism, and carbon metabolism were closely related to the growth of V. volvacea, and nutrient addition significantly improved microbial community diversity and metabolic levels, which can be used as a substrate optimization formula. This is of great significance for the development of sustainable agriculture.}, } @article {pmid41597613, year = {2026}, author = {Jarrín-V, P and Carrión-Olmedo, JC and Loján, P and Reyes-Barriga, D and Lara, M and Oña, A and Quiroz-Moreno, C and Castillejo, P and Tenea, GN and Díaz, M and Monfort-Lanzas, P and Molina, CA}, title = {Predicted Bacterial Metabolic Landscapes of the Sumaco Volcano: A Picrust2 Analysis of 16S rRNA Data from Amazonian Ecuador.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597613}, issn = {2076-2607}, support = {NA//National Institute of Biological Resources (NIBR) and the Korea International Cooperation Agency (KOICA) of the Republic of Korea/ ; }, abstract = {The Sumaco volcano in Ecuador, which has a distinct geological origin from the Andes and is located in the Amazon basin, offers an opportunity to study untouched microbiomes. We explored comparative patterns of abundance from predicted functional profiling in soil samples collected along the elevation and sulfur gradients on its slopes. Using 16S rRNA gene metabarcoding, we inferred metagenome functional profiles, contrasting sample groups by altitude or soil sulfur concentration. We inferred that high-altitude communities may have higher predicted abundance for anaerobic metabolism (crotonate fermentation), coenzyme B12 synthesis, and degradation of diverse carbon sources (sugars and octane). High-sulfur soils were associated with an inferred enrichment of pathways for degrading complex organic compounds and nitrogen metabolism, reflecting adaptation to unique geochemical conditions. In contrast, low-sulfur soils are consistent with a higher predicted abundance of glycerol degradation. Within the limitation imposed by the potential weak associations of the applied predicted functional profiling to actual gene content, we propose that the inferred metabolic changes represent different ecological strategies for resource acquisition, energy generation, and stress tolerance, and they are optimized for varying conditions in this unique volcanic ecosystem. Our findings highlight how environmental gradients shape soil microbiome functional diversity and offer insights into microbial adaptation in Sumaco's exceptional geochemistry within the Amazon. Further efforts linking functional predictions back to specific taxa will offer a complete ecological perspective of the microbiome exploration in the Sumaco volcano.}, } @article {pmid41597664, year = {2026}, author = {Liepa, E and Ustinova, M and Gudra, D and Roga, A and Kalnina, I and Dejus, B and Dejus, S and Strods, M and Tomsone, LE and Kibilds, J and Bartkevics, V and Berzins, A and Dumpis, U and Juhna, T and Fridmanis, D}, title = {Urban Wastewater Metagenomics Reveals the Antibiotic Resistance Gene Distribution Across Latvian Municipalities.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597664}, issn = {2076-2607}, support = {VPP-COVID-2020/1-0008//Latvian Council of Science/ ; No.5.2.1.1.i.0/2/24/I/CFLA/001//CFLA/ ; }, abstract = {Antimicrobial resistance (AMR) poses a global health threat, with urban wastewater systems serving as key reservoirs for resistance dissemination. This study aimed to investigate the relationships among urban environments, bacterial communities, and AMR patterns, and evaluate the specific municipal-scale drivers of resistance gene distribution. Shotgun metagenomic analysis was conducted on 45 wastewater samples collected from 15 municipalities across Latvia to determine the composition of the resistome and its correlation with local factors. The analysis identified 417 distinct antibiotic resistance genes (ARGs) belonging to 108 families, with geographic location serving as the primary driver of ARG distribution, which explained 65.87% of community variation (p = 0.001). Local industrial factors demonstrated significant effects, with food industry wastewater significantly influencing both bacterial taxonomy and ARG profiles (p < 0.05). While the presence of a regional hospital did not shape the overall municipal resistome, hospital-associated wastewater showed 19 overlapping ARGs, including clinically critical carbapenemases. Municipal wastewater systems function as geographically structured reservoirs of AMR that are shaped by localized industrial and healthcare outputs. These findings support wastewater-based AMR surveillance as a valuable tool for tracking specific resistance sources.}, } @article {pmid41597665, year = {2026}, author = {Khachatryan, A and Vardanyan, A and Zhang, R and Zhang, Y and Shi, X and Willscher, S and Nguyen, NHA and Vardanyan, N}, title = {Metagenome Insights into Armenian Acid Mine Drainage: A Novel Thermoacidophilic Iron-Oxidizing Bacterium with Perspectives for Copper Bioleaching.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597665}, issn = {2076-2607}, support = {22rl-031//Higher Education Science Committee of Armenia/ ; 23-YSIP-012//Higher Education Science Committee of Armenia/ ; }, abstract = {The microbial ecology of acid mine drainage (AMD) systems in Armenia, with a long mining history, remains unexplored. This study aimed to characterize the microbial diversity and functional potential of AMD in the Syunik region and to isolate novel microorganisms with biotechnological value. A comprehensive analysis of the microbial communities' structure of Kavart abandoned, Kapan exploring mines effluent, and Artsvanik tailing was conducted. Metagenomics revealed bacterial-dominated communities, comprising Pseudomonadota (previously "Proteobacteria") (68-72%), with site-specific variations in genus abundance. A high abundance and diversity of metal resistance genes (MRGs), particularly for copper and arsenic, were identified. Carbohydrate-active enzyme (CAZy) analysis showed a dominance of GT2 and GT4 genes, suggesting a high potential for extracellular polymeric substances (EPS) production and biofilm formation. A novel strain of iron-oxidizing bacteria Arm-12 was isolated that shares only ~90% similarity with known Leptospirillum type species, indicating it may represent a new genus without culturable representatives. The strain exhibits enhanced copper extraction from concentrate. This study provides the first metagenomic insights into Armenian AMD systems and tailing, revealing a unique community rich in metal resistance and biofilm-forming genes. The isolation of a novel highly effective iron-oxidizer Arm-12 highlights the potential of AMD environments as a source of novel taxa with significant applications in biomining and bioremediation processes.}, } @article {pmid41597701, year = {2026}, author = {Mollova, D and Baev, V and Borisova, T and Rusinova, M and Iliev, I}, title = {A Metagenomic Comparison of the Colostrum Microbiome in Bulgarian Mothers by Delivery Mode: A Pilot Study.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597701}, issn = {2076-2607}, support = {KP-06-M81/6//Bulgarian Science Fund/ ; }, abstract = {Colostrum harbors a highly diverse microbial community, predominantly composed of genera such as Staphylococcus, Streptococcus, Lactobacillus, Bifidobacterium, and Enterococcus. The composition and diversity of this microbiota are influenced by maternal factors-including age, body mass index, lactation activity, stress levels, and gestational diabetes-as well as external factors such as mode of delivery, antibiotic exposure, diet, and geographic location. This microbial community plays a critical role in maternal and neonatal health by contributing to early gut colonization, supporting digestion, promoting immune system development, and protecting against pathogenic microorganisms through mechanisms such as antimicrobial peptide production by lactic acid bacteria. The primary aim of this study was to evaluate the impact of mode of delivery on colostrum microbiota by comparing mothers who delivered vaginally with those who underwent cesarean section. Colostrum samples from 15 mothers were subjected to DNA extraction, high-throughput sequencing, and bioinformatic analyses to characterize microbial composition and predicted functional profiles. Although substantial inter-individual variability was observed, no statistically significant differences were detected in overall microbial diversity or community structure between the two delivery groups. However, distinct bacterial taxa and functional characteristics were identified that were specific to each mode of delivery, suggesting subtle delivery-related influences on colostrum microbiota composition.}, } @article {pmid41597714, year = {2026}, author = {Isgandarov, I and Abilda, Z and Kanat, R and Daurov, D and Sapakhova, Z and Daurova, A and Zhambakin, K and Volkov, D and Begaly, A and Shamekova, M}, title = {Long-Read Metagenomics Profiling for Identification of Key Microorganisms Affected by Heavy Metals at Technogenic Zones.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597714}, issn = {2076-2607}, support = {BR24992837//Ministry of Agriculture of the Republic of Kazakhstan/ ; }, abstract = {Heavy metal pollution poses a serious threat to soil ecosystems worldwide, as long-term exposure can alter microbial community functioning and reduce overall ecosystem resilience. This study investigated the impact of heavy metal contamination in technogenic industrial areas of the East Kazakhstan Region on soil microbial communities. Soil samples were collected for chemical and metagenomic analyses. Concentrations of Zn, Pb, Cu, and Cd were quantified by flame atomic absorption spectrometry (FAAS). Using long-read whole-metagenome nanopore sequencing, we conducted strain-level profiling of soils with different levels of metal contamination. This approach provided high-resolution taxonomic data, enabling detailed characterization of microbial community structure. Heavy metal exposure did not significantly reduce microbial diversity or richness but influences the quality of community composition. Metal-resistant taxa dominated contaminated soils. Overall, the results highlight the value of long-read sequencing for resolving strain-level responses to environmental contamination.}, } @article {pmid41597726, year = {2026}, author = {Lee, HJ and Park, SH and Han, SY and Lee, JH and Kim, DU and Seo, HI}, title = {Differences in the Biliary Microbiome Between Biliary Tract Cancer and Benign Biliary Disease.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597726}, issn = {2076-2607}, support = {202100350001//Biomedical Research Institute, Pusan National University Hospital/ ; }, abstract = {Bile contains many bacteria that can contribute to various diseases. Therefore, identifying bile microbiome differences between benign and malignant conditions is essential. In this study, bile samples were collected aseptically from 141 patients with biliary tract cancer (BTC) or benign biliary diseases (BBDs) who underwent endoscopic retrograde cholangiopancreatography or biliary tract surgery. Quality control PCR was performed to amplify the V3-V4 region of the bacterial 16S rRNA gene. Metagenomic sequencing of bile was successfully performed in 35 of 56 samples collected from patients with BTC and 24 of 85 samples from patients with BBD. The mean alpha diversity values comprised 2.788 ± 2.833 and 2.319 ± 1.355 in the BBD and BTC groups, respectively (p = 0.399). The bacterial species (4.7%) were shared between groups, whereas 12.3% and 83% were indicated to patients with BTC and BBD, respectively. Bacteroides coprocola, Prevotella copri, and Bacteroides plebeius were more frequently identified in the bile of patients with BTC, whereas Bacteroides vulgatus and Bacteroides uniformis were more abundant in the bile of patients with BBD. Distinct patterns of microorganism abundance between the two groups of patients suggest association of bile microbiome with disease status, so its diagnostic potential should be validated in further studies.}, } @article {pmid41597735, year = {2026}, author = {Moser, K and Ballif, A and Pillonel, T and Concu, M and Montenegro-Borbolla, E and Nickel, B and Stampfli, C and Ruf, MT and Audry, M and Kapel, N and Gerber, S and Jacot, D and Bertelli, C and Galpérine, T}, title = {Fecal Microbiota Transplantation Donor Screening: Is Dientamoeba fragilis a Valid Criterion for Donor Exclusion? A Longitudinal Study of a Swiss Cohort.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597735}, issn = {2076-2607}, support = {//internal funding at the Lausanne University Hospital (CHUV)/ ; grant number 51NF40 180575//he salaries of K.M. and E.M.-B. were supported as a part of NCCR Microbiomes, a National Centre of Competence in Research, funded by the Swiss National Science Foundation/ ; }, abstract = {Dientamoeba fragilis is a protozoan of the human digestive tract, yet its transmission and pathogenic role remain poorly understood. This study aimed to evaluate its impact on the efficacy and safety of fecal microbiota transplantation (FMT) in treating recurrent Clostridioides difficile infection (rCDI). This longitudinal cohort study analyzed stool samples from FMT donors and recipients pre-treatment and at 2 and 8 weeks post-FMT. All samples were retrospectively tested using real-time PCR. Shotgun metagenomics was also performed on selected donor-recipient pairs to explore transmission. CDI cure rates, gastrointestinal adverse events (AEs), and serious adverse events (SAEs) were assessed prospectively. A total of 53 FMT were analyzed (179 samples), with 23 (43%) derived from D. fragilis-positive donor stool (4 of 10 donors, 40%). Four of 52 recipients (18.2%), initially negative and who received treatment from positive donors, tested positive post-FMT. Shotgun metagenomics could not definitely confirm transmission due to the lack of a good reference genome. No significant differences in efficacy, AE, or SAE were observed between FMT from D. fragilis-positive versus -negative donors, even in immunocompromised patients. No SAEs were attributed to FMT. D. fragilis may be transmitted via FMT without evidence of short-term clinical impact. Consequently, RT-PCR detection should be interpreted cautiously in the context of donor exclusion decisions.}, } @article {pmid41597738, year = {2026}, author = {Xi, D and Zhu, F and Zhang, Z and Zhou, S and Zhang, J}, title = {Forest Type Shapes Soil Microbial Carbon Metabolism: A Metagenomic Study of Subtropical Forests on Lushan Mountain.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597738}, issn = {2076-2607}, support = {20232BAB205020//Jiangxi Provincial Natural Science Foundation/ ; 22-315-6-18//the Science and Technology Program of Shenyang/ ; JJXC2023010//Jiujiang City's "Xuncheng Talent" Program/ ; 20242BCC32138//Jiangxi Provincial Key Laboratory of Carbon Neutrality and Ecosystem Carbon Sinks/ ; }, abstract = {Forest type strongly influences soil microbial community composition and associated carbon cycling, yet its influence on microbial functional traits remains poorly understood. In this study, metagenomics sequencing was used to investigate soil microbial communities and carbon metabolism genes across three forest types: deciduous broadleaf (DBF), mixed coniferous-broadleaf (CBMF), and coniferous forest (CF) at two soil depths (0-20 cm and 20-40 cm) on Lushan Mountain in subtropical China. The results showed that CF exhibited higher bacterial diversity and a distinct microbial composition, with an increase in Actinomycetota and Bacteroidota and a decrease in Acidobacteriota and Pseudomonadota. The Calvin cycle was the dominant carbon fixation pathway in all forests, while the relative abundance of secondary pathways (i.e., the 3-hydroxypropionate bi-cycle and reductive citrate cycle) varied significantly with forest type. Key carbon fixation genes (sucD, pckA) were more abundant in CF and CBMF, with higher levels of rpiA/B and ackA in DBF. Functional profiling further indicated that CF soils, especially in the surface layer, were enriched in glycoside hydrolases (GHs) and carbohydrate esterases (CEs), while CBMF showed a greater potential for starch and lignin degradation. Multivariate statistical analyses identified soil available phosphorus (AP) and pH as primary factors shaping microbial community variation, with AP emerging as being the dominant regulator of carbon-related functional gene abundance. Overall, the prevalence of these distinct genetic potentials across forest types underscores how vegetation composition may shape microbial functional traits, thereby influencing the stability and dynamics of the soil carbon pool in forest ecosystem.}, } @article {pmid41597740, year = {2026}, author = {Lowell, JL and Brown, L}, title = {Metals and Microbes: Microbial Community Diversity and Antibiotic Resistance in the Animas River Watershed, Colorado, USA.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597740}, issn = {2076-2607}, support = {RL5GM118990//NIH Building Infrastructure Leading to Diversity (BUILD) Initiative (U54)/ ; }, abstract = {Antimicrobial resistant (AMR) infections are a persistent public health issue causing excess death and economic impacts globally. Because AMR in clinical settings is often acquired from nonpathogenic bacteria that surround us, environmental surveillance must be better characterized. It has been well established that metals can co-select for bacterial AMR. Furthermore, recent studies have shown that compromised microbial community diversity may lead to community invasion by antibiotic resistance genes (ARGs). Widespread legacy mining has led to acid mine drainage and metal contamination of waterways and sediments throughout the western United States, potentially compromising microbial community diversity while simultaneously selecting for AMR bacteria. Our study objectives were to survey metal contaminated sediments from the Bonita Peak Mining District (BPMD) in southwestern Colorado, USA, compared to sites downstream in Durango, CO for bacterial and ARG diversity. Sediment bacteria were characterized using 16S rRNA Ilumina and metagenomic sequencing. We found that overall, bacterial diversity was lower in metal-contaminated, acidic sites (p = 0.04). Metagenomic sequencing revealed 31 different ARGs, with those encoding for efflux pumps (mex and spe gene families) substantially more prevalent in the BPMD sites, elucidating a specific AMR marker fingerprint from the high metal concentration sediments. Raising awareness and providing antimicrobial tracking techniques to resource limited communities could help provide information needed for better antibiotic use recommendations and environmental monitoring.}, } @article {pmid41597751, year = {2026}, author = {Liu, PY and Tang, HJ and Lee, SS and Liao, CH and Huang, CH and Kuo, HY and Sheng, WH and Taiwan Metagenomic Sequencing Microbiology Study Group, }, title = {Comparative Analysis of Microbial Detection in Traditional Culture Versus Metagenomic Next-Generation Sequencing in Patients with Periprosthetic Joint Infection: A Prospective Observational Study.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597751}, issn = {2076-2607}, support = {M09A7321 and MOHW113-TDU-B-211-114006//the Ministry of Health and Welfare of Taiwan/ ; NSTC 113-2321-B-002-016//the National Science and Technology Council of Taiwan/ ; }, abstract = {Identifying pathogens causing periprosthetic joint infection (PJI) is a challenge for clinicians. We aimed to evaluate the application of metagenomic next-generation sequencing (mNGS) to identify pathogens in PJI. A prospective analysis was conducted of patients diagnosed PJI between 2022 and 2024 at twelve hospitals in Taiwan. Both conventional bacterial culture (CMT) and mNGS of joint fluid and debrided tissue were performed. Demographic characteristics, laboratory results and clinical outcomes were collected. The diagnostic performance of these two methods was analyzed. A total of 42 patients with a mean age of 67.9 years were enrolled in analysis. The knee was the most common joint involved (69.1%). A high proportion of patients (78.6%) received prior antibiotics within the two weeks at sample collection. mNGS identified pathogens in 28 out of 42 patients (66.7%), whereas CMT yielded positive results in 12 out of 42 patients (28.6%) (McNemar's test, p = 0.01). Staphylococcus species was the most common genus detected (n = 11), followed by Cutibacterium (n = 4). Other detected genera included Escherichia, Mycobacterium, Enterobacter, Klebsiella (n = 2 each), Acinetobacter, and Corynebacterium (n = 1 each). Our results support the idea that mNGS could serve as a valuable diagnostic tool for PJI in addition to traditional culture methods.}, } @article {pmid41597762, year = {2026}, author = {Xiong, Y and Dai, Z and He, F and Liu, R and Wang, J and Zhan, Z and Jia, H and Chen, S and Cai, L}, title = {Effect of Hantavirus Infection on the Rodent Lung Microbiome: Specific Regulatory Roles of Host Species and Virus Types.}, journal = {Microorganisms}, volume = {14}, number = {1}, pages = {}, pmid = {41597762}, issn = {2076-2607}, support = {2024JJ9472//The natural science foundation of Hunan provincial/ ; }, abstract = {The lung-targeting characteristic of Hantavirus infection and the unclear mechanism underlying its interaction with the lung microbiome hampers the development of effective prevention and control strategies. In this study, lung tissues from Apodemus agrarius and Rattus norvegicus were collected at Hantavirus surveillance sites in Hunan Province. Metagenomic sequencing was subsequently applied to compare microbiome diversity, community structure, and function between infected and uninfected groups. Then the linear discriminant analysis effect size (LEfSe) was employed to identify key biomarkers. The results indicated that after infection with Hantaan virus (HTNV), Apodemus agrarius exhibited significantly increased evenness but markedly decreased richness of lung microbial communities, as reflected by consistent reductions in the number of observed species, Abundance-based Coverage Estimator (ACE) index, and Chao1 index. In contrast, Rattus norvegicus infected with Seoul virus (SEOV) showed no significant difference in microbial richness compared with uninfected controls, and even a slight increase was observed. These findings suggest that host species and virus type may play an important role in shaping microbial community responses. Furthermore, β-diversity analysis showed that the community structure was clearly separated by the host rodent species, as well as by their virus infection status. LEfSe analysis identified taxa with discriminatory power associated with infection status. Streptococcus agalactiae and Streptococcus were associated with SEOV-infected Rattus norvegicus, while Chlamydia and Chlamydia abortus were relatively enriched in uninfected Apodemus agrarius. This exploratory study reveals preliminary association between specific host-Hantavirus pairings (HTNV-Apodemus agrarius and SEOV-Rattus norvegicus) and the rodent lung microbiome, offering potential insights for future research into viral pathogenesis.}, } @article {pmid41598263, year = {2026}, author = {Liu, Y and Zhao, M and Zhong, S and Wu, G and Yang, F and Zhou, J}, title = {Review on Mining Robust Lactic Acid Bacteria for Next-Generation Silage Inoculants via Multi-Omics.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {1}, pages = {}, pmid = {41598263}, issn = {2075-1729}, support = {2023J06019//Fujian Provincial Outstanding Youth Fund Projects/ ; KFB25053A and KFB25010A//Science and Technology Innovation Specia Fund Project of Fujian Agriculture and Forestry University/ ; }, abstract = {Lactic acid bacteria (LAB), as the core microorganisms in silage fermentation, play a crucial role in improving silage quality and ensuring feed safety, making the screening, identification, and functional characterization of LAB strains a significant research focus. Researchers initially isolate and purify LAB from various samples, followed by identification through a combination of morphological, physiological, biochemical, and molecular biological methods. Systematic screening has been conducted to identify LAB strains tolerant to extreme environments (e.g., low temperature, high temperature, high salinity) and those possessing functional traits such as antimicrobial activity, antioxidant capacity, production of feruloyl esterase and bacteriocins, as well as cellulose degradation, yielding a series of notable findings. Furthermore, modern technologies, including microbiomics, metabolomics, metagenomics, and transcriptomics, have been employed to analyze the structure and functional potential of microbial communities, as well as metabolic dynamics during the ensiling process. The addition of superior LAB inoculants not only facilitates rapid acidification to reduce nutrient loss, inhibit harmful microorganisms, and improve fermentation quality and palatability but also demonstrates potential functions such as degrading mycotoxins, adsorbing heavy metals, and reducing methane emissions. However, its application efficacy is directly constrained by factors such as strain-crop specific interactions, high dependence on raw material conditions, limited functionality of bacterial strains, and relatively high application costs. In summary, the integration of multi-omics technologies with traditional methods, along with in-depth exploration of novel resources like phyllosphere endophytic LAB, will provide new directions for developing efficient and targeted LAB inoculants for silage.}, } @article {pmid41598312, year = {2026}, author = {Thant, EP and Klaysubun, C and Suwannasin, S and Dechathai, T and Singkhamanan, K and Yaikhan, T and Chaichana, N and Pomwised, R and Wonglapsuwan, M and Chusri, S and Surachat, K}, title = {Global Comparative Genomics of Stenotrophomonas maltophilia Reveals Cryptic Species Diversity, Resistome Variation, and Population Structure.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {1}, pages = {}, pmid = {41598312}, issn = {2075-1729}, abstract = {Background:Stenotrophomonas maltophilia is an increasingly important multidrug-resistant opportunistic pathogen frequently isolated from clinical, environmental, and plant-associated niches. Despite its medical relevance, the global population structure, species-complex boundaries, and genomic determinants of antimicrobial resistance (AMR) and ecological adaptation remain poorly resolved, partly due to inconsistent annotations and fragmented genomic datasets. Methods: Approximately 2400 genome assemblies annotated as Stenotrophomonas maltophilia were available in the NCBI Assembly database at the time of query. After pre-download filtering to exclude metagenome-assembled genomes and atypical lineages, 1750 isolate genomes were retrieved and subjected to stringent quality control (completeness ≥ 90%, contamination ≤ 5%, ≤500 contigs, N50 ≥ 10 kb, and ≤1% ambiguous bases), yielding a final curated dataset of 1518 high-quality genomes used for downstream analyses. Genomes were assessed using CheckM, annotated with Prokka, and compared using average nucleotide identity (ANI), pan-genome analysis, core-genome phylogenomics, and functional annotation. AMR genes, mobile genetic elements (MGEs), and metadata (source, host, and geographic origin) were integrated to assess lineage-specific genomic features and ecological distributions. Results: ANI-based clustering resolved the S. maltophilia complex into multiple distinct genomospecies and revealed extensive misidentification of publicly deposited genomes. The pan-genome was highly open, reflecting strong genomic plasticity driven by accessory gene acquisition. Core-genome phylogeny resolved well-supported clades associated with clinical, environmental, and plant-related niches. Resistome profiling showed widespread intrinsic MDR determinants, with certain lineages enriched for efflux pumps, β-lactamases, and trimethoprim-sulfamethoxazole resistance markers. MGE analysis identified lineage-specific integrative conjugative elements, prophages, and transposases that correlated with source and geographic distribution. Conclusions: This large-scale analysis provides the most comprehensive genomic overview of the S. maltophilia complex to date. Our findings clarify species boundaries, highlight substantial taxonomic misannotation in public databases, and reveal lineage-specific AMR and mobilome patterns linked to ecological and clinical origins. The curated dataset and evolutionary insights generated here establish a foundation for global genomic surveillance, epidemiological tracking, and future studies on the evolution of antimicrobial resistance in S. maltophilia.}, } @article {pmid41598908, year = {2026}, author = {González-Peña, R and Hidalgo-Martínez, DO and Laredo-Tiscareño, SV and Huerta, H and de Luna-Santillana, EJ and Adame-Gallegos, JR and Rodríguez-Alarcón, CA and Rubio-Tabares, E and García-Rejón, JE and Muñoz-Ramírez, ZY and Tangudu, C and Garza-Hernández, JA}, title = {Characterization of the Bacteriome of Culicoides reevesi from Chihuahua, Northern Mexico: Symbiotic and Pathogenic Associations.}, journal = {Insects}, volume = {17}, number = {1}, pages = {}, pmid = {41598908}, issn = {2075-4450}, support = {419- 395 24-23//Secretaría de Ciencia, Humanidades, Tecnología e Innovación (SECIHTI)/ ; SIP20250075//Secretaría de Investigación y Posgrado from Instituto Politécnico Nacional/ ; }, abstract = {Culicoides biting midges are vectors of veterinary and zoonotic pathogens, yet the bacteriome of several species remains unexplored. Culicoides reevesi, a poorly studied species in northern Mexico, represents an opportunity to investigate microbial associations that may influence vector biology. Adults of C. reevesi were analyzed using 16S rRNA amplicon sequencing, followed by functional prediction with PICRUSt2. Heatmaps and pathway summaries were generated to highlight dominant taxa and functions. The bacteriome was dominated by Pseudomonadota, followed by Actinomycetota, Bacillota, and Bacteroidota. Symbiotic taxa such as Asaia and Cardinium were identified alongside potentially pathogenic bacteria, including Escherichia coli, Mycobacterium avium, Vibrio parahaemolyticus, and Enterococcus faecalis. Functional predictions indicated metabolic versatility, with abundant pathways related to aerobic respiration, the TCA cycle, amino acid biosynthesis, and quorum sensing. Despite all samples being collected from the same site and date, apparent differences in bacterial composition were observed across pools, suggesting microhabitat or host-related variability. This study provides the first taxonomic and functional baseline of the C. reevesi bacteriome. The detection of both symbiotic and pathogenic bacteria highlights the dual ecological role of the microbiome in host fitness and pathogen transmission potential. In conclusion, we suggest that these microbial associations influence vector physiology and competence, providing a basis for future microbiome-based control strategies. These findings emphasize the importance of integrating microbiome analyses into entomological surveillance and vector control strategies in endemic regions.}, } @article {pmid41598945, year = {2026}, author = {Hirata, K and Suzuki, T and Yura, K and Asahi, T and Kataoka, K}, title = {Gut Microbiome Differences Across Mixed-Sex and Female-Only Social Rearing Regimes in Female Field Crickets Teleogryllus occipitalis (Orthoptera: Gryllidae).}, journal = {Insects}, volume = {17}, number = {1}, pages = {}, pmid = {41598945}, issn = {2075-4450}, support = {24KJ2101//Japan Society for the Promotion of Science/ ; JPJ009237//Cabinet Office/ ; }, abstract = {The insect gut microbiome contributes to various host physiological processes and behaviors, such as digestion, nutrient absorption, immunity, mate choice, and fecundity. The social environment can shape gut microbial communities. Mixed-sex vs. female-only rearing is an important social context because it differs in exposure to the opposite sex and mating opportunities, which may in turn affect female physiology that may influence their gut microbiome. Despite the growing recognition of these social-microbial interactions, most studies have relied on 16S rRNA amplicon sequencing or qPCR, which provide only coarse taxonomic resolution and limited functional insight. In this study, we used whole-genome shotgun metagenomics to examine changes in microbial diversity and functional gene composition in the female field cricket Teleogryllus occipitalis (Serville) (Orthoptera: Gryllidae) reared under two social conditions: mixed-sex rearing and female-only rearing. Species richness and diversity analyses revealed that community composition separated between females from mixed-sex and female-only rearing. Functional profiling indicated higher relative abundances of genes annotated to nutrient processing and inter-bacterial competition in females from mixed-sex rearing, whereas females from female-only rearing showed relative enrichment of genes annotated to stress resistance and nitrogen fixation. These findings provide a genome-resolved foundation for testing how social rearing conditions covary with gut microbiome composition and functional potential in female crickets.}, } @article {pmid41599039, year = {2026}, author = {Wang, Z and Chen, G and Yang, M and Wang, S and Fang, J and Shi, C and Gu, Y and Ning, Z}, title = {Host-Filtered Blood Nucleic Acids for Pathogen Detection: Shared Background, Sparse Signal, and Methodological Limits.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41599039}, issn = {2076-0817}, support = {2024-PWXZ-04//New Quality Clinical Specialty Program of High-end Medical Disciplinary Construction in Shanghai Pudong New Area/ ; 2024ZDXK0019//Shanghai Municipal Health Commission, Key Discipline of Shanghai Health System, Cardiology/ ; PW2025D-01//The Scientific Research Program of Shanghai Pudong New Area Health Commission (the Joint Research and Development Program)/ ; }, mesh = {Humans ; Microbiota ; *Cell-Free Nucleic Acids/blood/genetics ; *Metagenomics/methods ; Coronary Artery Disease/microbiology/blood/diagnosis ; *Tuberculosis/diagnosis/microbiology/blood ; }, abstract = {Plasma cell-free RNA (cfRNA) metagenomics is increasingly explored for blood-based pathogen detection, but the structure of the shared background "blood microbiome", the reproducibility of reported signals, and the practical limits of this approach remain unclear. We performed a critical re-analysis and benchmarking ("stress test") of host-filtered blood RNA sequencing data from two cohorts: a bacteriologically confirmed tuberculosis (TB) cohort (n = 51) previously used only to derive host cfRNA signatures, and a coronary artery disease (CAD) cohort (n = 16) previously reported to show a CAD-shifted "blood microbiome" enriched for periodontal taxa. Both datasets were processed with a unified pipeline combining stringent human read removal and taxonomic profiling using the latest versions of specialized tools Kraken2 and MetaPhlAn4. Across both cohorts, only a minority of non-host reads were classifiable; under strict host filtering, classified non-host reads comprised 7.3% (5.0-12.0%) in CAD and 21.8% (5.4-31.5%) in TB, still representing only a small fraction of total cfRNA. Classified non-host communities were dominated by recurrent, low-abundance taxa from skin, oral, and environmental lineages, forming a largely shared, low-complexity background in both TB and CAD. Background-derived bacterial signatures showed only modest separation between disease and control groups, with wide intra-group variability. Mycobacterium tuberculosis-assigned reads were detectable in many TB-positive samples but accounted for ≤0.001% of total cfRNA and occurred at similar orders of magnitude in a subset of TB-negative samples, precluding robust discrimination. Phylogeny-aware visualization confirmed that visually "enriched" taxa in TB-positive plasma arose mainly from background-associated clades rather than a distinct pathogen-specific cluster. Collectively, these findings provide a quantitative benchmark of the background-dominated regime and practical limits of plasma cfRNA metagenomics for pathogen detection, highlighting that practical performance is constrained more by a shared, low-complexity background and sparse pathogen-derived fragments than by large disease-specific shifts, underscoring the need for transparent host filtering, explicit background modeling, and integration with targeted or orthogonal assays.}, } @article {pmid41599943, year = {2026}, author = {Rocha, HR and Ribeiro, P and Rodrigues, PM and Gomes, AM and Pintado, M and Coelho, MC}, title = {Bioinformatic Insights into the Carotenoids' Role in Gut Microbiota Dynamics.}, journal = {Nutrients}, volume = {18}, number = {2}, pages = {}, pmid = {41599943}, issn = {2072-6643}, mesh = {*Carotenoids/pharmacology/chemistry ; *Computational Biology ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; Humans ; Antioxidants/pharmacology ; Lutein/pharmacology ; Lycopene/pharmacology ; *Bacteria/classification/drug effects/metabolism ; beta Carotene/pharmacology ; }, abstract = {Background/Objectives: Carotenoids are bioactive pigments with well-established antioxidant and immunomodulatory properties, yet their impact on gut microbiota remains poorly understood from a chemical standpoint. This study explores how carotenoid structure and gastrointestinal stability shape microbial responses combining in vitro fermentation with bioinformatic analyses. Methods: Individual carotenoids (beta (β)-carotene, lutein, lycopene) and combined carotenoids, as well as algal-derived extracts were subjected to 48 h in vitro fermentation, and microbial composition and activity were assessed through sequencing and computational analysis. Results: β-carotene and lycopene promoted acid-tolerant taxa such as Escherichia-Shigella, whereas lutein, due to its higher polarity, supported more transient fluctuations. Mixtures and algal carotenoids exhibited synergistic effects, sustaining beneficial genera including Bifidobacterium and Bacteroides and promoting structured ecological trajectories. Conclusions: These findings provide a chemistry-driven perspective on how carotenoids act as modulators of microbial ecosystems, with direct implications for the formulation of carotenoid-enriched functional foods and dietary interventions.}, } @article {pmid41600629, year = {2026}, author = {Wang, D and Sun, J and Zhang, Y and Yuan, L and Xu, X and Xue, Y and Sun, H}, title = {Integrated 13C-DNA Stable Isotope Probing and Metagenomics Approaches to Identify Bisphenol A Assimilating Microorganisms and Metabolic Pathways in Biofilms.}, journal = {Toxics}, volume = {14}, number = {1}, pages = {}, pmid = {41600629}, issn = {2305-6304}, support = {52100082//National Natural Science Foundation of China/ ; KYCX25_3358//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; SJCX25_1722//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; BK20240983//Natural Science Foundation of Jiangsu Province/ ; ZMF23020040//Changzhou University Research Start-up Fund Project/ ; }, abstract = {Bisphenol A (BPA) is a persistent environmental contaminant requiring effective removal strategies. Biofilms offer advantages over conventional activated sludge for refractory compound degradation, yet the specific microorganisms and mechanisms driving BPA removal in biofilms remain poorly understood. This study employed an integrated approach, combining [13]C-DNA stable isotope probing (SIP) and metagenomics to identify BPA-assimilating microorganisms and elucidate their metabolic pathways in biofilms. Two moving bed biofilm reactors (MBBRs) were operated at contrasting BPA concentrations (500 μg/L and 10 mg/L) to enrich distinct microbial communities. Using DNA-SIP, we revealed differences in assimilating bacteria across diverse concentrations of BPA-enriched biofilms. Simultaneously, we reconstructed the genomes of these assimilating bacteria, dissecting the functional genes essential to the degradation process and identifying significant gene variations among different assimilating bacteria. By integrating these gene functions, we constructed the BPA metabolic pathway, which surprisingly comprised genes from various assimilating bacteria. This research significantly advances our understanding of BPA-assimilating bacteria within biofilms and provides valuable insights for refining biofilm technologies aimed at BPA removal from wastewater.}, } @article {pmid41600842, year = {2026}, author = {Hake, N and von Holtum, C and Höper, D and Nijhof, AM and Dietze, K and Hoffmann, B}, title = {Identification and Long-Term Detection of Hepacivirus bovis Genotype 1 and 2 on a Cattle Farm in Germany.}, journal = {Viruses}, volume = {18}, number = {1}, pages = {}, pmid = {41600842}, issn = {1999-4915}, mesh = {Animals ; Cattle ; Germany/epidemiology ; *Genotype ; *Cattle Diseases/virology/epidemiology/diagnosis ; Phylogeny ; *Hepacivirus/genetics/classification/isolation & purification ; Farms ; Genome, Viral ; *Hepatitis C/veterinary/virology/epidemiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Female ; }, abstract = {In 2020, a dairy farm in northwest Germany reported several cows with severe respiratory disease, fever, and reduced milk production. Multiple direct and indirect diagnostic methods were used to identify the cause of the disease. However, the pathogens detected could not be correlated with the severity of the clinical symptoms, so further diagnostic steps were taken. Blood and nasal swab samples were examined using next-generation sequencing (NGS) as part of a metagenomic analysis. For the first time in Germany, Hepacivirus bovis genotype 2 was detected. Real-time RT-PCR assays confirmed the presence of BovHepV genotypes 1 and 2 in the herd between 2020 and 2023. Analyses of complete and partial genome sequences demonstrated the presence of different virus variants in the herd over several years. In addition, the sequence data indicated that cattle can be reinfected with viruses belonging either to different BovHepV subtypes or to the same subtype. Although no direct link could be established between the detection of bovine hepaciviruses and the observed clinical symptoms, the PCR and sequence data obtained provide valuable insights into the epidemiology and pathogenesis of BovHepV infections.}, } @article {pmid41600881, year = {2026}, author = {Li, J and Baumgartner, W and Wang, L}, title = {Histopathologic and Genomic Characterization of a Novel Caprine Astrovirus Identified in a Boer Goat Kid in Illinois, United States.}, journal = {Viruses}, volume = {18}, number = {1}, pages = {}, pmid = {41600881}, issn = {1999-4915}, mesh = {Animals ; Goats/virology ; *Goat Diseases/virology/pathology ; *Astroviridae Infections/veterinary/virology/pathology ; Phylogeny ; Genome, Viral ; *Astroviridae/genetics/classification/isolation & purification ; Genomics ; High-Throughput Nucleotide Sequencing ; }, abstract = {Astroviruses are non-enveloped, positive-sense single-stranded RNA viruses known to infect various mammals and birds, including humans, often causing gastrointestinal disorders. In recent years, astroviruses have also been linked to neurological and respiratory diseases across several species, including ruminants, mink, deer, and other mammals. Notably, astrovirus infections in goats have been documented in countries such as Switzerland and China, where novel genotypes have been identified in fecal samples. However, their role in the context of disease remains unclear, and reports focusing solely on goat astrovirus in the United States have not been published. A necropsy case of a Boer goat kid with a history of diarrhea was submitted for investigation following death in January 2025. Fresh tissues were received and used for histopathology and enteric pathogen testing, including parasitic, bacterial, and viral workups. Metagenomic-based next-generation sequencing (mNGS) was also applied for this case. Histological examination revealed severe necrotizing enterocolitis. The small intestine exhibited epithelial ulcerations, villus atrophy, hyperplastic and dilated crypts with necrotic debris, few intraenterocytic coccidian parasites, and increased inflammatory cells in the lamina propria. The large intestine showed similar findings with pleomorphic crypt enterocytes. Standard enteric pathogen tests were negative except for aerobic culture that identified Escherichia.coli and Enterococcus hirae. mNGS and bioinformatic analysis identified a novel astrovirus in the intestinal content that showed the highest nucleotide identity (86%) to the sheep strain Mamastrovirus 13 sheep/HA3 from China based on BLAST analysis. Phylogenetic analysis indicated that the newly identified caprine astrovirus IL90175 clustered with astrovirus strains from small ruminants in Asia and Europe. This research reports the discovery, histopathologic features, and genetic characteristics of a gastrointestinal disease-causing astrovirus in a goat kid, which had not been previously described in the United States.}, } @article {pmid41601042, year = {2026}, author = {Sun, Y and Tu, Q and Shao, Z and Li, H}, title = {The normalization of gene abundance affects the discovery: A case of metal resistance genes in coastal sediments.}, journal = {Ecotoxicology and environmental safety}, volume = {309}, number = {}, pages = {119608}, doi = {10.1016/j.ecoenv.2025.119608}, pmid = {41601042}, issn = {1090-2414}, mesh = {*Geologic Sediments/microbiology/chemistry ; China ; Metagenomics/methods ; *Metals/toxicity ; Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis/toxicity ; Bacteria/genetics ; Estuaries ; }, abstract = {The advent of metagenomic technologies has given rise to a plethora of gene abundance calculation methods, which have emerged in a successive manner. Nevertheless, the extent to which these approaches are appropriate for metagenomic data and the specific research objectives remain subjects of debate. In this study, metagenomics sequencing was utilised to analyse the sediments from two coastal regions of China: the Beibu Gulf (BBG) and the Liaohe Estuary (LHE). The abundance of metal resistance genes (MRGs), which are critical genetic elements that influence ecosystem functioning and health, in the regions under study was obtained by two different calculation methods: the cell-normalized abundance (copies per prokaryotic cell) and the ppm abundance (sequences per million sequences). The application of diverse abundance calculation methodologies yielded markedly divergent outcomes. The cell-normalized and ppm abundances indicated a substantial elevation of total MRG abundance in the BBG and LHE sediments, respectively. Furthermore, disparate comparison outcomes were identified based on the varied abundance calculation methodologies employed across distinct MRG types, including genes demonstrating resistance to Fe, Al, Cr, Se, and multi-metals. These disparities can be ascribed to the variations in the prokaryotic biomass among different sediments, signifying that it is imperative to select an appropriate abundance calculation method according to whether the research objective necessitates the consideration of biomass differences. Furthermore, the results of multiple correlation analyses indicated that petroleum content was the key factor, and the ruvB gene was identified as an indicator for the MRG level based on both two abundance calculation methods. These findings establish a methodological foundation for metagenomics-based research and offer insights into the MRGs present in coastal sediments.}, } @article {pmid41601044, year = {2026}, author = {Sun, X and Zheng, L and Qi, R and Li, H}, title = {Salinity and redox-driven niche differentiation of ammonia-oxidizing microbes in a saline-alkaline river system.}, journal = {Ecotoxicology and environmental safety}, volume = {309}, number = {}, pages = {119613}, doi = {10.1016/j.ecoenv.2025.119613}, pmid = {41601044}, issn = {1090-2414}, mesh = {*Ammonia/metabolism ; Oxidation-Reduction ; *Archaea/metabolism/genetics ; *Bacteria/metabolism/genetics ; *Rivers/microbiology/chemistry ; *Salinity ; Geologic Sediments/microbiology/chemistry ; Nitrification ; Ecosystem ; }, abstract = {The ammonia oxidation process constitutes a critical step in the nitrogen cycle within river ecosystems. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are the major contributors to this process; however, their relative contributions differ substantially across different environments, particularly in saline-alkaline regions. To investigate the differences in ammonia oxidation processes between soil and sediment across various riparian zones in the Yinbei Irrigation District in Ningxia, samples were collected from five representative riparian types along the Third Drainage Ditch: a gravel-reed mixed zones, a reed zones, a high-salt Kochia scoparia zones, an Iris lactea embankment zones, and a bare soil zone. The potential nitrification rate (PNR) and associated environmental factors were quantified, and the community structure of microorganisms was analyzed by metagenomic sequencing, while the abundances of AOA and AOB functional genes (amoA) were quantified by quantitative PCR (qPCR). Through a multi-dimensional investigation of the ammonia oxidation process in riparian zones and sediments of saline-alkali wetlands, this study provided critical evidence for the mechanisms underlying habitat-specific nitrogen transformations. Pronounced physical and chemical differences were observed between sediments and riparian zones. Whereas the sediments exhibited strong reducing conditions, the riparian zones were characterized by pronounced saline-alkali stress. PCoA analysis revealed a clear separation between AOA and AOB communities, with saline-alkali-tolerant AOA predominating in riparian zones and AOB predominating in sediments. The strong reducing condition impedes the activity of AOB in sediments, thereby resulting in the accumulation of NH4[+] -N. AOA contributed 67-68.9 % of the total PNR in riparian zones, thereby driving substantial NO3[-]-N production. Seasonal variations exhibited no significant influence on the partitioning of microbial functions, which were jointly regulated by the saline-alkali gradient and redox state. This study demonstrates that the ammonia oxidation process of saline-alkali wetlands exhibits a pronounced mechanism of habitat-specific functional differentiation: AOB in sediments are constrained by the anoxic conditions induced by elevated total organic carbon (TOC), whereas AOA in riparian zones overcome the inhibition of nitrification under high pH or electrical conductivity (EC) through evolved salt-tolerant adaptations This discovery provides a novel theoretical framework for elucidating the microbial mechanisms driving the nitrogen cycle in saline-alkaline environments.}, } @article {pmid41601218, year = {2025}, author = {Li, CT}, title = {[Applications and challenges of forensic microbiomics].}, journal = {Fa yi xue za zhi}, volume = {41}, number = {5}, pages = {441-442}, doi = {10.12116/j.issn.1004-5619.2025.551105}, pmid = {41601218}, issn = {1004-5619}, mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Forensic Medicine/methods ; *Gastrointestinal Microbiome ; China ; Genomics ; Human Genome Project ; *Forensic Sciences ; Metagenome ; }, } @article {pmid41601644, year = {2025}, author = {Song, DJ and Dong, R and Liu, YM and Wang, T and Ma, J}, title = {Autoimmune cerebellar ataxia with anti-Homer3 antibodies associated with herpesvirus infection: a case report and literature review.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1709326}, pmid = {41601644}, issn = {1664-3224}, mesh = {Humans ; Female ; Adolescent ; *Cerebellar Ataxia/cerebrospinal fluid/immunology/virology ; *Herpesviridae Infections/cerebrospinal fluid/complications/immunology ; Herpesvirus 7, Human ; Homer Scaffolding Proteins ; Autoantibodies ; }, abstract = {Autoimmune cerebellar ataxia (ACA) is a cerebellar syndrome mediated by autoimmune mechanisms. ACA is particularly rare, and cases of ACA with anti-Homer-3 antibodies associated with herpesvirus infection are even rarer. In this study, we report a case of a 15-year-old girl who was admitted with a one-month history of progressive vertigo and unsteady gait. Metagenomic next-generation sequencing (mNGS) of her cerebrospinal fluid (CSF) revealed eight sequences of human herpesvirus 7 (HHV-7). Anti-Homer-3 antibodies were detected in both serum and CSF samples. Following a series of immunotherapy, the patient showed improvements in dizziness and gait stability. However, her symptoms recurred during the tapering of corticosteroids. The patient developed three episodes of generalized seizures. Concurrently, gait instability significantly worsened. Repeat first-line immunotherapies including corticosteroid and IVIG were not effective. Rituximab was initiated and symptoms were partial improved. In this study, we present the clinical symptoms of this patient with anti-Homer-3 antibody-associated ACA, conduct long-term follow-up, and review relevant literature. Our aim is to enhance the understanding of this rare disease by summarizing key clinical features, thus providing valuable insights into the diagnosis and treatment of ACA.}, } @article {pmid41602101, year = {2025}, author = {Deng, Q and Liu, Y and Zhang, J and Zhang, H and Zhang, Y and Wang, M and Jia, M and Ding, D and Fang, Y and Wang, Y and Gu, H and Wang, H}, title = {Clinical validation and utility of targeted nanopore sequencing for rapid pathogen diagnosis and precision therapy in lung cancer patients with pulmonary infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1730098}, pmid = {41602101}, issn = {2235-2988}, mesh = {Humans ; *Lung Neoplasms/complications/microbiology ; Female ; *Nanopore Sequencing/methods ; Aged ; Male ; Sputum/microbiology ; Middle Aged ; *Respiratory Tract Infections/diagnosis/microbiology/drug therapy ; High-Throughput Nucleotide Sequencing ; Microbiota ; *Precision Medicine/methods ; Metagenomics ; Sensitivity and Specificity ; Bacteria/genetics/classification/isolation & purification ; Aged, 80 and over ; }, abstract = {BACKGROUND: Pulmonary infections are common in patients with lung cancer (LC), complicating diagnosis and treatment. This study explored the diagnostic performance and clinical utility of targeted nanopore sequencing (TNPseq) for detecting pathogens in LC-related pulmonary infections.

METHODS: A total of 143 patients with LC or benign pulmonary diseases complicated by pulmonary infections were included and stratified into diagnostic and therapeutic cohorts. Sputum samples underwent conventional culture, metagenomic next-generation sequencing (mNGS), and TNPseq analyses. Microbiota profiles were compared across disease groups and correlated with tumor therapy responses. In the therapeutic cohort, clinical outcomes were assessed between empirical therapy and TNPseq-guided therapy.

RESULTS: TNPseq identified a significantly higher proportion of clinically relevant pathogens compared to mNGS (48.76% vs. 16.80%, p < 0.001) and demonstrated superior sensitivity (81.25% vs. 68.75%), with a 40.7% reduction in turnaround time (16 hours vs. 27 hours). Both sequencing methods revealed an enrichment of Lactobacillus species in non-initial diagnosis lung cancer (NDLC) patients (p < 0.01). Patients exhibiting partial response or stable disease (PR/SD) showed increased abundance of Neisseria, Veillonella, and Prevotella species (p < 0.05). Clinical remission was achieved in all patients; however, 68.4% of those initially receiving empirical therapy subsequently required a switch to TNPseq-guided treatment due to its ineffectiveness. Compared to this empirical-to-TNPseq group, the median treatment duration was significantly shorter under direct TNPseq guidance (total: 6 days vs. 13 days, p < 0.01; LC subgroup: 5 days vs. 15.5 days, p < 0.05), thereby reducing unnecessary antibiotic exposure.

CONCLUSIONS: By enabling rapid pathogen detection and profiling of the pulmonary microbiome, TNPseq facilitates targeted therapy and reduces antibiotic overuse in LC patients. These findings highlight the potential of TNPseq as a promising, rapid, and non-invasive diagnostic candidate for first-line use, offering a comprehensive view of both infection and host-microbe interactions in immunocompromised patients.}, } @article {pmid41602753, year = {2025}, author = {Nissan, I and Peretz, A}, title = {Editorial: Innovation in tackling the global challenge of eradicating antibiotic-resistant microorganisms.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1774105}, doi = {10.3389/fmicb.2025.1774105}, pmid = {41602753}, issn = {1664-302X}, } @article {pmid41602756, year = {2025}, author = {Chisompola, D and Luwaya, E and Nzobokela, J and Mwansa, P and Chakulya, M}, title = {AI-powered analysis of viral metagenomic sequencing data for rapid outbreak investigation and novel pathogen discovery.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1717859}, pmid = {41602756}, issn = {1664-302X}, abstract = {Emerging viral outbreaks continue to pose a persistent global health threat, underscoring the urgent need for a shift from reactive to proactive health security strategies. Viral metagenomic next-generation sequencing (mNGS) offers an unbiased, powerful approach to pathogen detection and discovery, yet its utility has been constrained by the computational complexity and slow turnaround time of data analysis during outbreak crises. The integration of artificial intelligence (AI) and mNGS is dismantling these barriers, enabling faster, more scalable outbreak response. This review synthesizes how AI-driven analytics are transforming mNGS applications, from genome assembly to sequence classification, using advanced architectures such as convolutional neural networks, recurrent neural networks, and transformers. Beyond accelerating workflows, AI's capacity for pattern recognition outperforms traditional homology-based methods, facilitating the discovery of novel viral families and tracing hidden transmission chains through anomaly detection. Nonetheless, critical challenges remain, including limited training data, the interpretability of AI models, and resource-intensive computational demands that risk widening an "AI divide" in global health. We evaluate these obstacles and highlight forward-looking strategies, including federated learning for privacy-preserving data sharing and explainable AI for improving trust and biological insight. Looking ahead, we envision an "AI-first" paradigm for outbreak preparedness, anchored in integrated "Digital Immune Systems" for continuous, global-scale surveillance. By framing the synergy between mNGS and AI as a transformative leap, this review underscores its potential to strengthen resilience against future pandemics.}, } @article {pmid41602763, year = {2025}, author = {Xu, J and Li, J and Kong, X and Zhang, C and Qi, B and Zhu, X and Zhu, Y and Xu, Y}, title = {Dysbiosis and metabolic pathway shifts in the gut microbiome of children with sepsis: a comparative analysis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1715990}, pmid = {41602763}, issn = {1664-302X}, abstract = {BACKGROUND: The newly published Phoenix Sepsis Score in 2024 for assessing sepsis in children mainly focuses on respiratory, cardiological, coagulation and neurological indicators, whereas the gut microbiome also plays key roles in the occurrence and progression of sepsis. Additionally, emerging evidence suggests that specific biomarkers in gut microbiome are associated with disease progression. This study aimed to explore the differences in gut microbiome diversity, composition and function between septic and healthy children, and to establish correlations with clinical indicators and outcomes, providing new possibilities for the diagnosis and treatment of sepsis.

RESULTS: Analysis of gut microbiome was performed in 20 sepsis children and 9 healthy controls aged between 3 and 18 years old. The anal swab samples were analyzed by metagenomic next-generation sequencing. Significant differences were observed in α and β diversity of gut microbiome between sepsis group and healthy controls groups. Especially, Shannon diversity was significantly correlated with white blood cell count, serum lactate, length of pediatric intensive care unit stay and length of hospital stay (all R > 0, p < 0.05). Firmicutes and Bacteroidetes were both dominant in most of children in SG and HC groups, while three in SG showed extremely low combined abundances of Firmicutes and Bacteroidetes (<10%), which might be associated with chemistry therapy and death outcome. Bacteria associated with nosocomial infections, including genus taxa Acinetobacter, Prevotella, Escherichia, Klebsiella, Bacteroides, and Corynebacterium, can be dominant (relative abundance>70%) in sepsis group, which were absent in healthy control group. Enterococcus abundance not only predicted sepsis risk (AUC = 0.85) but also was correlated with 28-day mortality (R > 0, p = 0.004). Gene function prediction based on Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated significant differences profile in SG and sepsis-deaths groups. The enriched gut microbiome genes were related to cellular proliferation, energy metabolism, signal transduction, the oxidative stress response and arginine metabolism.

CONCLUSION: Significant differences in diversity, taxa composition and gene function in the gut microbiome existed between septic and healthy children. The associations between gut microbiome dysbiosis and clinical indicators were identified. Enterococcus could be a biomarker to predict sepsis risk.}, } @article {pmid41602774, year = {2025}, author = {Zhang, M and Zhu, Y and Sun, Z and Wang, B and Chen, J and Zhou, F and Zeng, J and Li, M and Zou, D and Jiang, Z}, title = {Correction: Chemoautotrophic Thermodesulfobacteriota as a key genomic potential group in the hypoxic diazotrophic community of the Changjiang (Yangtze River) estuary.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1766907}, doi = {10.3389/fmicb.2025.1766907}, pmid = {41602774}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1671267.].}, } @article {pmid41602901, year = {2025}, author = {Sun, Y and Yuan, L and Hu, T and Sun, C and Yang, D and Tian, M and Dong, S and Gu, H}, title = {Isavuconazole as initial antifungal therapy combined with surgical management of pediatric pulmonary mucormycosis: a case report and literature review.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1701905}, pmid = {41602901}, issn = {2296-2360}, abstract = {Invasive mucormycosis (IM) in pediatric patients is a rare but life-threatening fungal disease with limited treatment options. Isavuconazole is a new triazole that has shown efficacy and safety in adults for both primary and salvage treatment of mucormycosis. However, data regarding the initial use of isavuconazole in children are rare. In this study, we report a case of a 6-year-old girl with diabetes mellitus. Metagenomic next-generation sequencing detected Rhizopus oryzae in her bronchoalveolar lavage fluid , and a chest computed tomography revealed a reversed halo sign. Oral isavuconazole was given as primary monotherapy with continuous control of blood glucose. After the lesion partially shrank and became confined, the patient visited the thoracic surgery department to undergo lobectomy; she recovered well after the procedure. This report highlights the importance of quick diagnosis of mucormycosis and may provide a reference for providing the initial antifungal treatment in pediatric mucormycosis. All of the aforementioned interventions helped buy time for subsequent surgical treatment, leading to the curing of the child. Isavuconazole may represent an effective and safe therapeutic option as first-line monotherapy for pediatric mucormycosis.}, } @article {pmid41603333, year = {2026}, author = {Tiwari, P and Gupta, A and Kaushik, M and Dwivedi, R and Tripathi, M and Dada, R}, title = {Association of yoga with cognitive and gut microbiome changes in Alzheimer's disease: An exploratory case-control study.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {110}, number = {2}, pages = {562-575}, doi = {10.1177/13872877261415612}, pmid = {41603333}, issn = {1875-8908}, mesh = {Humans ; *Yoga/psychology ; *Alzheimer Disease/psychology/microbiology/therapy ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Case-Control Studies ; *Cognition/physiology ; Aged ; Depression/psychology ; Middle Aged ; }, abstract = {BackgroundAlzheimer's disease (AD) is marked by cognitive decline, depressive symptoms, and gut microbial dysbiosis. Yoga may support cognitive and emotional health while modulating gut microbiota, but integrative clinical evidence is limited.ObjectiveTo evaluate the effects of a 12-week yoga intervention on cognition, depressive symptoms, and gut microbial diversity, composition, and function in Indian patients with mild AD.MethodsIn this hospital-based case-control study, 16 AD patients and 17 cognitively healthy controls (HCs) were recruited at AIIMS, New Delhi. AD diagnosis followed NIA-AA criteria, supported by Montreal Cognitive Assessment (MoCA) and Patient Health Questionnaire-9 (PHQ-9) assessments. AD participants underwent 60-min supervised yoga sessions daily for 12 weeks. Cognitive performance, depressive symptoms, and stool microbiota were assessed pre- and post-intervention. Metagenomic sequencing enabled taxonomic and functional profiling, with alpha diversity, beta diversity (Bray-Curtis distance), and differential abundance analyses performed using standard bioinformatics tools.ResultsYoga was associated with improved cognition (MoCA: 22.33 ± 2.34 → 25.44 ± 2.01; p = 0.001) and reduced depressive symptoms (PHQ-9: 5.78 ± 3.11 → 2.22 ± 1.71; p = 0.007). Alpha diversity remained stable, while beta diversity shifted post-yoga AD samples toward the HC cluster. Beneficial taxa (Faecalibacterium prausnitzii, Roseburia intestinalis, Bifidobacterium, Akkermansia) increased, whereas pro-inflammatory taxa (Collinsella aerofaciens, Klebsiella spp.) decreased. Functional analysis showed partial recovery of metabolic and short-chain fatty acid pathways.ConclusionsA 12-week yoga intervention was associated with cognitive and mood improvements and partial normalization of gut microbial function in mild AD. Larger randomized trials with lifestyle monitoring and multi-omics integration are warranted to confirm causal mechanisms.}, } @article {pmid41603547, year = {2026}, author = {Gschwind, R and Bonnet, M and Abramova, A and Jarquín-Díaz, VH and Wenne, M and Löber, U and Godron, N and Kampouris, ID and Tskhay, F and Nahid, F and Debroucker, C and Bui-Hai, M and El Aiba, I and Klümper, U and Berendonk, TU and Forslund-Startceva, SK and Zahra, R and Bengtsson-Palme, J and Ruppé, E}, title = {Cefiderocol resistance genes identified in environmental samples using functional metagenomics.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41603547}, issn = {1751-7370}, support = {//Establishing a Monitoring Baseline for Antibiotic Resistance in Key Environments/ ; }, mesh = {Cefiderocol ; *Metagenomics/methods ; *Cephalosporins/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; }, abstract = {Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to pathogenic bacteria, as highlighted by the "One Health" framework. Cefiderocol is a siderophore cephalosporin recently introduced in clinical practice which displays a "Trojan Horse" mechanism, utilizing bacterial iron transportation systems for cell entry. Although it is only used as a last-line antibiotic, resistance has already been observed in clinical isolates. Yet, cefiderocol resistance genes are difficult to monitor as resistance mechanisms remain mostly undescribed in antibiotic resistance gene databases and therefore uncharacterized in the environment. To address this critical gap, we applied functional metagenomics to diverse environmental samples (wastewater, freshwater, and soil) from France, Germany, Sweden, and Pakistan. Four antibiotic resistant genes were identified as responsible for increased cefiderocol minimum inhibitory concentrations to clinically-relevant levels (ranging from 1 to 4 mg/l), including ꞵ-lactamases (VEB-3, OXA-372 homolog, and YbxI homolog) and a partial penicillin-binding protein homolog. None of these genes had been previously reported as a cefiderocol resistance gene. Three out of four had their closest homologs in pathogenic bacteria. The blaVEB-3 gene was associated with a mobile genetic element and distributed across all wastewater metagenomes analyzed in this study. We therefore highlight the critical need for functional metagenomics, to characterize previously uncharacterized last-line antibiotic resistance mechanisms which will be used to enrich antibiotic resistance gene databases and thereby improving antibiotic resistance surveillance in all One Health compartments.}, } @article {pmid41603859, year = {2026}, author = {Ahmed, N and Abdjan, MI and Aminah, NS and Helianti, I}, title = {Computational design of carbohydrate binding modules-fused PETase like enzyme for enhanced polycaprolactone (PCL) degradation: structural insights, molecular dynamics, and QM/MM simulations.}, journal = {Journal of biomolecular structure & dynamics}, volume = {44}, number = {8}, pages = {4148-4175}, doi = {10.1080/07391102.2026.2619892}, pmid = {41603859}, issn = {1538-0254}, mesh = {*Molecular Dynamics Simulation ; *Polyesters/chemistry/metabolism ; Molecular Docking Simulation ; Carbohydrate Binding Modules ; Protein Binding ; Thermodynamics ; Binding Sites ; *Hydrolases/chemistry/metabolism ; Protein Conformation ; Bacterial Proteins/chemistry ; Burkholderiales ; }, abstract = {A novel PET hydrolase-like enzyme identified from metagenomic databases using HMMR search was computationally fused with five different carbohydrate-binding modules (CBMs). AlphaFold3 predicted the 3D structures of the fused enzyme-CBM, which were validated using ERRAT, Verify3D, and PROCHECK. Molecular docking was performed with polycaprolactone triol using AutoDock Vina, followed by 100 ns molecular dynamics (MD) simulations using AMBER. Trajectory analyses and binding free energy calculations (QM/MM-GBSA) were conducted. The putative PET hydrolase-like enzyme shared 49.62% similarity with Ideonella sakaiensis PETase (5XJH). The fused models exhibited the best stability, with an instability index of <40 and a thermostability aliphatic index between 58.83 and 68.27. Structure validation confirmed high-quality 3D models, with >90% of the residues in the allowed Ramachandran regions. All the fused models showed favourable binding to PCL-triol, exhibiting strong interactions. In MD simulations, BlCBM5 and TrCBM complexes displayed a minimal fluctuation: all-atom RMSD ∼0.35 and ∼0.45 nm, backbone RMSD ∼0.48, ∼0.41 nm, atom contacts ∼4.2-5, ∼2-6, and H-bonds ∼2-5, ∼1-2, respectively. The BlCBM5 and TrCBM complexes showed the lowest binding energies, with MM-GBSA values of -36.66 ± 0.12 and -21.48 ± 0.11 kcal/mol, and QM/MM-GBSA values of -37.36 ± 0.13 and -21.70 ± 0.11 kcal/mol, respectively. Residue-level analysis identified key contributors (M133, W157, and F62) in both models. BlCBM5 and TrCBM complexes were the top candidates for enhancing PCL plastic degradation. The findings of this study were based on predictive insights, and experimental validation is required in the future.}, } @article {pmid41604101, year = {2026}, author = {Nihel, AB and Rania, AD and Hamadou, OH and Ghiles, G and Imen, B and Fatma, A and Ali, A and Basma, M and Hayet, S and Radhouan, G and Leila, AK and Mokdad-Gargouri, R}, title = {Nanopore sequencing of the Tunisian gut microbiome: effect of the DNA extraction methods.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {47}, pmid = {41604101}, issn = {1678-4405}, support = {952583//H2020 European Research Council/ ; }, abstract = {High-throughput sequencing technologies have revolutionized the field of microbiome research, offering unprecedented insights into microbial diversity, community structure, and evolution. In this study, we compared three DNA extraction methods including; enzymatic lysis (ELM), commercial kit (CKM) and Phenol/Chloroform (PCAI) for their efficacy in microbiome taxonomy using Nanopore Sequencing. Metagenomic analysis of DNA extracted from stool samples were analyzed to determine the variability in microbial compositions. Our results revealed significant differences in DNA yield, microbial diversity, and community structure among the extraction methods tested. Globally, Phocaeicola_vulgatus, Ruminococcus_bicirculans, Faecalibacterium_prausnitzii, Prevotella copri, and Bacteroides ovatus are the most abundant identified species in all the samples. Further, the results showed that Ruminococcus_bicirculans is the most abundant specie identified in ELM, whereas the richness of Bacteroides_fragilis is higher in PCAI than ELM and CKM-processed samples. Our findings underscore the importance of methods selection in microbiome research and provide insights into optimizing DNA extraction protocols for nanopore sequencing.}, } @article {pmid41604102, year = {2026}, author = {Rocha, LBA and Gonçalves, VN and de Oliveira, FS and Corrêa, GR and Senra, EO and Duarte, EB and Lopes, FAC and Silva, MC and Convey, P and Câmara, PEAS and Rosa, LH}, title = {Endolithic fungal diversity is present in the unique phosphatized rocks of an environmentally extreme equatorial archipelago revealed by DNA amplicon metagenomics.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {46}, pmid = {41604102}, issn = {1678-4405}, abstract = {We evaluated endolithic fungal diversity associated with rocks sampled at the polyextreme Brazilian São Pedro and São Paulo archipelago using a DNA amplicon metagenomics approach. We detected 808,547 fungal DNA reads grouped into 92 amplicon sequence variants (ASVs). The rocks sampled were geologically characterized as mylonitized peridotites, serpentinized peridotites, and carbonate-matrix sedimentary breccias. Ascomycota was the dominant phylum, followed by Basidiomycota, Mucoromycota, Mortierellomycota and Chytridiomycota. Hortaea werneckii, Cladosporium sp., Simplicillium sp., Blastobotrys serpentis, Penicillium sp., P. simplicissimum, Malassezia restricta, Ascomycota sp., Verrucariaceae sp., and Fungal sp. were the dominant assigned taxa. The endolithic assemblages displayed moderate to low diversity indices. Among the fungal community, only the dominant Fungal sp. occurred in all samples. The data obtained in our environmental DNA (eDNA) amplicon metagenomics approach suggest that the rocks of the isolated equatorial São Pedro and São Paulo archipelago host a complex fungal diversity, including taxa regarded to be cosmopolitan, extremophilic hypersaline and xerophilic, plant pathogens, and human/animal opportunistic pathogens. As eDNA studies do not confirm the presence of viable organisms or propagules, further research using culturing approaches is now required to develop strategies to recover these fungi for physiological, biogeochemical, genetic and potential biotechnological studies.}, } @article {pmid41604220, year = {2026}, author = {Yao, ML and Lin, P and Hua, K and Zhang, W}, title = {The biosynthetic gene cluster landscape of the oral microbiome across health and dental caries.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jimb/kuag005}, pmid = {41604220}, issn = {1476-5535}, abstract = {Specialized metabolites encoded by biosynthetic gene clusters (BGCs) in the oral microbiome remain largely unexplored in the context of oral health and disease. Previous genome-centric surveys have identified hundreds of uncharacterized BGCs in the oral cavity associated with health and disease, but these studies relied on reference genomes and did not capture strain-level variation or the native distribution of BGCs. Here, we assembled three independently sourced metagenomic datasets from healthy and dental caries samples, extracted BGCs, and quantified their metagenomic abundance and transcriptional activity. We found that aryl polyene, ribosomally synthesized and post-translationally modified peptide (RiPP), and nonribosomal peptide (NRP) encoding BGCs were the most prominent BGCs identified across the three metagenomic datasets. We grouped the identified BGCs into homology-based gene cluster families (GCFs) and found that specific GCFs were consistently associated with either health or caries across diverse taxa, suggesting that some specialized metabolites may perform conserved ecological functions. Conversely, other BGCs showed more restricted taxonomic distributions and were linked to disease-associated taxa, such as Propionibacterium acidifaciens, suggesting niche-specific biosynthetic capacities within the oral environment. Applying elastic-net regression to the metatranscriptomic dataset further identified a subset of 51 BGCs out > 3 000 that distinguished healthy from caries samples, reinforcing the discriminatory power of BGC expression patterns. Together, these results demonstrate that BGCs provide functional resolution beyond taxonomic profiling and that BGC expression, rather than genomic presence alone, differentiates oral microbial community states. This underscores the relevance of specialized metabolism to oral health and supports the use of BGC-centric analyses to interrogate microbial interactions underlying community stability and disease-associated shifts.}, } @article {pmid41604225, year = {2026}, author = {Bilhalva, LC and Yacoub, MN and Dos Santos, AP and Manley, SR and Guasch, PM and Krumbeck, JA and Brinker, EJ and Martinez-Romero, G and Conrado, FO and Knoll, JS and Sharkey, LC}, title = {First report of Castellaniella spp. infection in dogs and the genomic evidence of a novel species.}, journal = {Journal of applied microbiology}, volume = {137}, number = {2}, pages = {}, doi = {10.1093/jambio/lxag033}, pmid = {41604225}, issn = {1365-2672}, mesh = {Animals ; Dogs ; *Dog Diseases/microbiology/pathology ; *Alcaligenaceae/genetics/isolation & purification/classification ; *Gram-Negative Bacterial Infections/veterinary/microbiology/pathology ; Phylogeny ; Female ; RNA, Ribosomal, 16S/genetics ; Pleural Effusion/microbiology/veterinary ; Male ; High-Throughput Nucleotide Sequencing ; Fatal Outcome ; }, abstract = {AIMS: This study reports the first documented cases of Castellaniella spp. infection in dogs, describing associated clinical and pathological findings and characterizing a novel species within this genus.

METHODS AND RESULTS: Pleural effusions from two dogs presenting with acute respiratory distress and systemic illness were evaluated via cytology, bacterial culture, and next-generation sequencing. Both cases exhibited neutrophilic-macrophagic inflammation with intracellular Gram-negative rods, primarily within macrophages. Bacterial culture failed to identify the organisms. Metagenomic analysis identified organisms belonging to the genus Castellaniella in both cases. In case 2, an unclassified Castellaniella species was detected, suggesting the presence of a previously undescribed species within the genus. Both dogs died shortly after presentation, and necropsy and histopathology findings were described.

CONCLUSIONS: Castellaniella spp. warrant consideration as potential emerging pathogens in domestic animals, challenging their previous classification as non-pathogenic environmental bacteria. The identification of a novel species also underscores the genus's genetic diversity and adaptive potential.}, } @article {pmid41604303, year = {2026}, author = {Guo, Z and Cheng, H and Shi, H and Liu, D and Zhai, X and Li, X and Zhang, X and Liu, L and Zhang, XH and Zhang, Y}, title = {Potential for microbial methanethiol-dependent dimethylsulfide production in different marine sediments.}, journal = {Cell reports}, volume = {45}, number = {2}, pages = {116891}, doi = {10.1016/j.celrep.2025.116891}, pmid = {41604303}, issn = {2211-1247}, mesh = {*Geologic Sediments/microbiology ; *Sulfides/metabolism ; *Sulfhydryl Compounds/metabolism ; Hydrogen Sulfide/metabolism ; *Bacteria/metabolism/genetics ; Phylogeny ; }, abstract = {Dimethyl sulfide (DMS) plays a pivotal role in sulfur cycling and climate regulation. This study investigates microbial DMS production via the methylation of hydrogen sulfide (H2S) and methanethiol (MeSH) in nearshore, pelagic deep-sea, and cold-seep sediments using culture-dependent and -independent methods. DMS production is detected in all sediments with exogenous MeSH addition. High mdd abundance is found in pelagic deep-sea sediments (24.55%-26.73%) from the Kuroshio-Oyashio Extension region, as well as in the nearshore sediments (25.78%). Metagenomic analyses reveal previously unrecognized Mdd-encoding taxa, such as Polyangia, and eight Bacteroidota and Bacillota isolates may possess unknown Mdd enzymes. Importantly, a widespread alternative pathway that converts H2S to MeSH is identified, representing a significant source of MeSH. These findings reveal a prevalent and diverse microbial pathway for DMS production in marine sediments, underscoring the need for further investigation to discover Mdd[+] microbial contributors.}, } @article {pmid41604988, year = {2026}, author = {Zhou, Y and Wu, Y and Shu, B and Xu, F}, title = {Resourceful utilization of Bougainvillea horticultural waste for synchronous degradation and power generation in MFCs.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {170}, number = {}, pages = {109237}, doi = {10.1016/j.bioelechem.2026.109237}, pmid = {41604988}, issn = {1878-562X}, mesh = {*Bioelectric Energy Sources/microbiology ; *Nyctaginaceae/chemistry/metabolism ; Polysaccharides/metabolism ; Biodegradation, Environmental ; Lignin/metabolism ; Electricity ; }, abstract = {The disposal of horticultural waste derived from Bougainvillea species poses substantial environmental challenges in coastal cities of southeastern China. This study innovatively employs Bougainvillea horticultural waste (BHW) as the main substrate in microbial fuel cells (MFCs) for simultaneous organic degradation and bioenergy recovery, with an acid-pretreated BHW-fed MFC (MFC-ABG) included for comparison. Results indicated that the untreated BHW-fed MFC (MFC-BG) achieved a peak voltage of 0.401 V and sustained operation for 19 days, coupled with 78.7% polysaccharide removal. Metagenomics showed that MFC-BG significantly enriched electroactive Geobacter (29.39%) and hydrolytic Proteiniphilum (2.69%), driving lignocellulose decomposition through oxidative auxiliary enzymes (AA4/AA6). Comparatively, MFC-ABG achieved an enhanced voltage of 0.706 V and a high polysaccharide reduction efficiency of 85.6%, benefits attributable to acid-induced substrate solubilization and glycoside hydrolase (GH)-dominated enzymatic shifts. Although microbial community diversity declined in both MFC systems, MFC-BG retained a higher species richness (MFC-BG: Sobs = 28,209; MFC-ABG: Sobs = 25,746), reflecting the adaptive resilience of the associated microbial community. This study confirms BHW as a viable feedstock for MFCs and clarifies the microbial mechanisms underlying the synergistic coupling of substrate degradation and electron transfer.}, } @article {pmid41605063, year = {2026}, author = {Tang, B and Lin, L and Li, W and Li, Z and Zhao, J and Zhao, W and Zhao, C}, title = {Successful treatment with oseltamivir of an atypical influenza B-associated encephalitis identified by mNGS: A case report.}, journal = {Diagnostic microbiology and infectious disease}, volume = {115}, number = {1}, pages = {117286}, doi = {10.1016/j.diagmicrobio.2026.117286}, pmid = {41605063}, issn = {1879-0070}, mesh = {Humans ; Female ; *Oseltamivir/therapeutic use/administration & dosage ; Middle Aged ; *Influenza B virus/genetics/isolation & purification ; *Influenza, Human/drug therapy/diagnosis/virology/complications ; *Antiviral Agents/therapeutic use/administration & dosage ; *Encephalitis, Viral/drug therapy/diagnosis/virology ; High-Throughput Nucleotide Sequencing ; Treatment Outcome ; Metagenomics ; Cerebrospinal Fluid/virology ; }, abstract = {This case report describes a 51-year-old female with influenza B-associated encephalitis (IBAE) presenting primarily with insomnia, headache, and dizziness, but without fever, following an initial cough. Routine microbiological tests (cultures, staining, multiplex PCR) on cerebrospinal fluid (CSF) and initial brain/chest CT scans were negative. Diagnosis was confirmed by metagenomic next-generation sequencing (mNGS) detecting influenza B virus in the CSF. Treatment involved oral oseltamivir and fluid replacement for headache/intracranial pressure. Symptoms significantly improved after eight days of oseltamivir, leading to discharge. This case highlights sleep disturbances and headache as primary IBAE symptoms without fever. Routine CSF testing often fails to detect influenza B; early mNGS enables definitive diagnosis, allowing precise, timely treatment (like oseltamivir) and avoiding ineffective empiric therapy or disease worsening.}, } @article {pmid41605275, year = {2026}, author = {Wu, L and Li, H and Gu, Y and Zhou, Y and Shen, Z and Zuo, J}, title = {In situ ammonia recovery relieves ammonia stress in anaerobic digestion and multi-omics elucidate community-dominant and functionally dominant genera of methanogens.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134098}, doi = {10.1016/j.biortech.2026.134098}, pmid = {41605275}, issn = {1873-2976}, mesh = {*Ammonia/isolation & purification/metabolism ; *Methane/metabolism/biosynthesis ; Anaerobiosis ; Bioreactors/microbiology ; Multiomics ; Biofuels ; }, abstract = {The accumulation of endogenous ammonia nitrogen in anaerobic digestion (AD) is widely recognized as a critical factor inhibiting methanogenesis. Gas-permeable membranes (GPM), leveraging their selective permeation properties, provide a large gas-liquid mass transfer interface and demonstrate significant potential in preventing ammonia accumulation. In this study, integrating GPM into AD achieved in situ ammonia removal and recovery, fundamentally alleviating ammonia inhibition and enabling ammonia valorization. GPM reactors (with H2SO4 absorption/vacuum distillation) maintained ammonia at 1300-1500 mg/L (vs. >5000 mg/L in controls) and sustained biogas yield 0.67-0.72 L/g VS at 7 g VS/(L·d) OLR (controls inhibited at 5 g VS/(L·d)). Multi-omics revealed microbial mechanisms: community-dominant Methanobacterium contributed little to methanogenesis, while functionally dominant Methanothrix retained robust activity via dual methanogenic pathways and upregulated biosynthesis-related proteins. This study validates GPM-AD efficacy and provides theoretical support for optimization.}, } @article {pmid41605932, year = {2026}, author = {Raethong, N and Patumcharoenpol, P and Vongsangnak, W}, title = {Modeling diet-gut microbiome interactions and prebiotic responses in Thai adults.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41605932}, issn = {2055-5008}, support = {N42A660907//National Research Council of Thailand/ ; }, mesh = {Humans ; Thailand ; *Prebiotics/administration & dosage ; *Diet ; *Gastrointestinal Microbiome ; Adult ; Fatty Acids, Volatile/metabolism ; Metagenomics ; Systems Biology ; *Bacteria/classification/metabolism/genetics ; }, abstract = {The impact of diet on gut microbial metabolism is essential for advancing microbiome-based health interventions. This study introduces a novel systems biology pipeline that integrates genome-scale metabolic models (GSMMs) with Thai dietary intake data to simulate gut microbiome metabolism and assess prebiotic responses. Utilizing metagenomic data from healthy Thai adults and an average Thai diet derived from national surveys, community-scale metabolic models (CSMMs) were developed and simulated under both typical dietary and prebiotic-supplemented condition. Flux variability analysis was employed to assess metabolic capacities, short-chain fatty acids (SCFAs) production in relation to microbial taxonomy. The results promisingly revealed inter-individual variability in SCFA profiles, with Bacteroides and Phocaeicola notably linked to isobutyrate production and Bifidobacterium emerged as a key responder to prebiotic supplementation. This integrative framework offers biological insights into diet-gut microbiome interactions and provides a foundation for the development of precision nutrition strategies tailored to the Thai population.}, } @article {pmid41606121, year = {2026}, author = {Duttagupta, S and Messaoudene, M and Hunter, S and Desilets, A and Jamal, R and Mihalcioiu, C and Belkaid, W and Marcoux, N and Fidelle, M and Suissa, D and Ponce, M and Geiger, M and Malo, J and Piccinno, G and Punčochář, M and Filin, A and Heidrich, V and Rusu, D and Mbaye, B and Durand, S and Ben Aissa, I and Puller, V and de Lahondès, R and Blais, N and Tehfe, M and Owen, S and Bélanger, K and Parvathy, SN and Shieh, B and Raphael, J and Lenehan, J and Breadner, D and Rothenstein, J and Rozza, N and Maillou, J and Nili, S and Prifti, DK and Pinto, F and Armanini, F and Kim-Schulze, S and Marron, TU and Kroemer, G and Derosa, L and Zitvogel, L and Silverman, M and Segata, N and Maleki Vareki, S and Routy, B and Elkrief, A}, title = {Fecal microbiota transplantation plus immunotherapy in non-small cell lung cancer and melanoma: the phase 2 FMT-LUMINate trial.}, journal = {Nature medicine}, volume = {32}, number = {4}, pages = {1337-1350}, pmid = {41606121}, issn = {1546-170X}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/immunology ; *Fecal Microbiota Transplantation/methods/adverse effects ; Female ; *Melanoma/therapy/immunology ; Male ; *Lung Neoplasms/therapy/immunology ; Middle Aged ; *Immunotherapy/methods ; Aged ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology ; Combined Modality Therapy ; Immune Checkpoint Inhibitors/therapeutic use ; Adult ; CTLA-4 Antigen/antagonists & inhibitors/immunology ; Treatment Outcome ; Animals ; }, abstract = {Immune checkpoint inhibitors (ICI) have improved outcomes for patients with non-small cell lung cancer (NSCLC) and melanoma, yet over half of patients exhibit primary resistance. Fecal microbiota transplantation (FMT) may overcome resistance to anti-programmed cell death protein 1 (PD-1) therapy. The clinical activity and safety of FMT plus anti-PD-1 in NSCLC or anti-PD-1 plus anti-cytotoxic T-lymphocyte antigen 4 (CTLA-4) therapy in melanoma have not been evaluated. Here we report results from FMT-LUMINate, a multicenter, open-label, phase 2 trial assessing healthy donor FMT plus anti-PD-1 in NSCLC (n = 20) or anti-PD-1 plus anti-CTLA-4 (dual ICI) in melanoma (n = 20), in the first-line setting. Eligible patients received a single FMT via oral capsules prior to ICI initiation. The primary endpoint was objective response rate (ORR) in NSCLC. Secondary endpoints included ORR in melanoma, safety and donor-host microbiome similarity. In NSCLC, the ORR was 80% (16/20), meeting the study primary endpoint. In melanoma, the ORR was 75% (15/20). FMT was deemed safe in both cohorts by an independent data and safety monitoring committee, with no grade 3 or higher adverse events (AEs) in NSCLC and 13 (65%) patients experiencing grade 3 or higher AEs in melanoma. Shotgun metagenomic sequencing revealed that responders developed a distinct post-FMT gut microbiome composition, independent of acquired donor-recipient similarity or strain-level engraftment. Responders exhibited significantly greater loss of baseline bacterial species compared to non-responders, with frequent depletion of Enterocloster citroniae, E. lavalensis and Clostridium innocuum. This finding was reproduced across three published FMT oncology trials. We recolonized antibiotic-treated, tumor-bearing mice with post-FMT stool from two responder patients, and reintroduction of the specific bacterial species that were lost after FMT abrogated the antitumor effect of ICI. Taken together, these findings confirm the clinical activity of FMT in combination with ICI and suggest that the elimination of deleterious taxa is required for FMT-mediated therapeutic benefit. ClinicalTrials.gov identifier: NCT04951583 .}, } @article {pmid41606218, year = {2026}, author = {Abdelhameed, A and Hussein, RH and Hatem, ZA and Bağcı, C and Ziemert, N}, title = {From niche to niche: investigating microbial communities and their specialised metabolite gene clusters in human microbiomes.}, journal = {World journal of microbiology & biotechnology}, volume = {42}, number = {2}, pages = {65}, pmid = {41606218}, issn = {1573-0972}, mesh = {Humans ; *Microbiota/genetics ; *Multigene Family ; Metagenomics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Biosynthetic Pathways/genetics ; Metagenome ; Skin Microbiome ; Phylogeny ; }, abstract = {Diverse microbial communities within the human microbiome perform vital functions which influence both health and disease in hosts. Specialized metabolites produced by microbes via biosynthetic gene clusters (BGCs) drive ecological interactions and offer possibilities for therapeutic application. The biosynthetic capabilities of microorganisms present in human microbiomes are still mostly unexplored despite metagenomics advancements. The study examines the variety of microbial communities and BGC locations through metagenomic data from 1,191 samples across eight human microbiomes taken from the IMG/M database. Kraken2 executed taxonomic classification while antiSMASH v6.1.1 identified BGCs. The study used BiG-SCAPE to build a sequence similarity network while Bracken and Pavian tools analyzed microbial diversity. A total of 25,681 BGCs were identified, of which 97.5%, showed no significant match to existing clusters in MIBIG database, indicating substantial potential for novel biosynthetic discoveries . Showing no match to existing clusters in the MIBiG database which shows huge potential for new biosynthetic discoveries. New strains were discovered that produce unique RiPPs, NRPs, and siderophores primarily within the microbiomes of the large intestine, oral cavity, and skin. The large intestine showed maximum microbial and biosynthetic diversity compared to other areas while the biliary tract and nasal cavity displayed minimal diversity. New BGCs associated with antibiotic, cytotoxic, and immune-modulating functions present potential therapeutic uses. The investigation uncovers essential information about how microbial communities develop specific functions within various body regions. Uncharacterized BGC discoveries present new opportunities for drug development and treatments that target microbiomes.}, } @article {pmid41606550, year = {2026}, author = {Zhang, X and Xu, J and Chen, M and Wu, Y and Chen, D and Xu, X and He, X}, title = {Aspergillus fumigatus in mechanically ventilated pneumonia- independent mortality risk and synergistic microbiome signatures from a multicenter mNGS cohort.}, journal = {BMC pulmonary medicine}, volume = {26}, number = {1}, pages = {}, pmid = {41606550}, issn = {1471-2466}, support = {2022GYX28//Lishui Public Welfare Technology Application Research Program Project/ ; }, abstract = {AIM OF THE STUDY: Invasive aspergillosis is a life-threatening complication in mechanically ventilated patients with pneumonia, predominantly caused by Aspergillus fumigatus. However, its independent mortality risk and early-warning strategies in critically ill populations remain unclear. METHODS: In this multicenter retrospective cohort study, we enrolled 1567 mechanically ventilated patients with severe pneumonia who underwent bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) across 12 tertiary hospitals in China (January 2019–March 2023). Propensity score matching (1:1) balanced confounders, and Cox regression quantified the independent mortality risk of A. fumigatus infection. RESULTS: The A. fumigatus detection rate was 10.27% (161/1567). Post-matching, 28-day mortality was significantly higher in A. fumigatus-positive versus negative cohorts (66% vs 47%, p = 0.001). Multivariable analysis confirmed A. fumigatus as an independent mortality risk factor (HR = 1.79, 95%CI 1.49–2.17, p < 0.001), with significant associations to underlying renal disease (19% vs 12%, p = 0.005), connective tissue disease (7% vs 4%, p = 0.026), and multi-organ dysfunction (ep < 0.05). Microbial community analysis revealed co-colonization synergies with Enterococcus faecium, Enterococcus faecalis, Candida albicans, HSV-1, and EBV. CONCLUSIONS: A. fumigatus infection independently increases 28-day mortality risk in mechanically ventilated patients. Early intensified screening and intervention are warranted for individuals with ≥ 3 organ dysfunctions, underlying renal/connective tissue diseases, or respiratory co-colonization by synergistic microbes.}, } @article {pmid41606854, year = {2025}, author = {Okoye, CO and Abhadiomhen, SE and Ezenwanne, BC and Chen, X and Jiang, H and Wu, Y and Jiang, J}, title = {Machine learning-based predictive modeling of foodborne pathogens and antimicrobial resistance in food microbiomes using omics techniques: A systematic review.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 1}, pages = {117255}, doi = {10.1016/j.foodres.2025.117255}, pmid = {41606854}, issn = {1873-7145}, mesh = {*Machine Learning ; *Food Microbiology ; *Foodborne Diseases/microbiology ; *Microbiota ; *Drug Resistance, Bacterial/genetics ; Animals ; Genomics/methods ; Metagenomics ; Salmonella/pathogenicity/genetics ; Food Safety ; Humans ; }, abstract = {The globalization of food systems has heightened the risk of foodborne pathogens such as Salmonella, Listeria monocytogenes, and Campylobacter, exacerbated by rising antimicrobial resistance (AMR). Traditional pathogen identification and AMR risk surveillance methods are often labor-intensive and low-throughput, while single-omics approaches fail to capture microbial complexity. Moreover, reliance on individual machine learning (ML) models limits predictive robustness, posing challenges to food safety and public health. This systematic review evaluates ML-based predictive modeling integrated with omics techniques (genomics, metagenomics, and transcriptomics) for foodborne pathogen and AMR risk surveillance. Following PRISMA guidelines, 1245 articles from PubMed, Scopus, and other databases (2015-2025) were screened, selecting 13 relevant studies. These studies applied ML algorithms, including Random Forest (RF), Extreme Gradient Boosting (XGBoost), and Support Vector Machines (SVM), to enhance predictive accuracy. The selected studies demonstrated predictive accuracies up to 99 % and AUROC scores above 0.90. Key discoveries include genetic markers for Salmonella virulence, Listeria attribution to fruits and dairy, and 145 mobile antimicrobial resistance genes (ARGs) in poultry. Despite these advancements, limitations such as small sample sizes, inconsistent metadata, overfitting, and computational scalability hinder real-world implementation. This review underscores the potential of ML-driven omics frameworks to revolutionize foodborne pathogen and AMR risk monitoring, paving the way for smarter, more resilient food safety systems. However, methodological inconsistencies necessitate standardized protocols, larger datasets, and explainable AI (XAI) to improve reliability and applicability in global food safety monitoring.}, } @article {pmid41606855, year = {2025}, author = {Yang, J and He, Y and Huang, J and Li, M and Wu, X and Pei, X and Yang, X}, title = {Decoding resistome profiles and horizontal transfer of antibiotic resistance genes across the pork production chain under One Health sectors.}, journal = {Food research international (Ottawa, Ont.)}, volume = {221}, number = {Pt 1}, pages = {117259}, doi = {10.1016/j.foodres.2025.117259}, pmid = {41606855}, issn = {1873-7145}, mesh = {Animals ; *Gene Transfer, Horizontal ; Swine ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Pork Meat/microbiology ; *Drug Resistance, Microbial/genetics ; One Health ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Metagenomics ; Food Microbiology ; Abattoirs ; }, abstract = {The emergence of antimicrobial resistance has become a global threat to public health. Intensive antibiotic use in swine farming has accelerated the proliferation of antibiotic resistance genes (ARGs) in animal-derived foods, making the production chain a potential ARG transmission route to humans. However, shared resistome profiles and horizontal gene transfer (HGT) mechanisms along this chain remain unclear. Here, we systematically investigated the resistome profile, ARGs' host, and potential HGT of ARGs across interconnected swine farm, slaughterhouse, and retail market by metagenomic assembly and binning. From 42 metagenomes, 1354 ARG subtypes were identified, with 303 shared across all interfaces. Both microbiome and mobile genetic elements (MGEs) contributed to the variation in ARG profiles. Pseudomonadota were the dominant drivers that shape the resistome through plasmid-mediated HGT. Among the 133 reconstructed ARG-carrying genomes (ACGs), 38 of them carried multiple ARGs, indicating the potential mobility of ARGs. Notably, 3 ACGs taxonomically assigned to Pseudomonas_E alcaligenes, Serratia_J grimesii, and Escherichia coli carrying 9, 13, and 41 ARGs, respectively. Furthermore, MetaCHIP analysis uncovered 445 potential HGT events, and ARGs including CpxR, macB, fusA, and vanR were annotated as potentially transferred subtypes. This study decodes the resistome profiles and tracks horizontal ARG transfer at the community level across the entire pork supply chain - from swine farms to retail outlets. To our knowledge, few studies have explored ARG transmission subtypes and directional flows among humans, pigs, and environmental compartments in the pork production chain using metagenomic approaches. These findings highlight the important role of the pork production chain as a critical transmission vector for ARGs under One Health framework.}, } @article {pmid41607747, year = {2026}, author = {Luo, L and Huang, G and Yang, H and Chi, H}, title = {Revisiting multi-region 16S sequencing in gastric cancer.}, journal = {World journal of gastrointestinal oncology}, volume = {18}, number = {1}, pages = {114708}, pmid = {41607747}, issn = {1948-5204}, abstract = {Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome, demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches. While the study represents a valuable methodological step forward, it remains limited by single-center design, lack of quantitative calibration, and insufficient control for contamination and inter-laboratory variability. This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized, consensus-driven workflows to ensure reproducibility and clinical reliability. The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration, particularly for recurrence prediction, treatment-response monitoring, and perioperative complication risk assessment. By addressing these methodological, economic, and ethical challenges, the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.}, } @article {pmid41607902, year = {2025}, author = {Song, Z and Huang, Y and Gu, Y and Che, L and Zhang, K and Liu, Q and Guan, Q and Sui, L}, title = {Genetic characterization of the respiratory tract viruses in Jilin, Northeast China, 2023.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1756127}, pmid = {41607902}, issn = {2296-2565}, mesh = {Humans ; China/epidemiology ; *Respiratory Tract Infections/virology/epidemiology ; Phylogeny ; Adult ; Child ; High-Throughput Nucleotide Sequencing ; Female ; SARS-CoV-2/genetics ; Child, Preschool ; Male ; Metagenomics ; *Virus Diseases/virology/epidemiology ; }, abstract = {OBJECTIVE: Respiratory viral infections impose a significant global health burden, necessitating continuous regional surveillance to understand pathogen circulation. This study aimed to characterize the spectrum of respiratory pathogens and identify potential causative agents in Jilin Province, northeast China, during 2023.

METHODS: Using metagenomic next-generation sequencing, we analyzed 250 respiratory samples and 195 blood samples, sequencing of all samples yielded 399,256 viral reads. Bioinformatic and phylogenetic analyses were conducted to identify and characterize the detected viruses.

RESULTS: Severe acute respiratory syndrome coronavirus 2 (lineage BA.2), human respiratory syncytial virus B (lineage GB5.0.5a), and influenza B virus (lineage V1A.3a.2) were identified as common respiratory pathogens across both pediatric and adult populations. Influenza A virus (lineage 3C.2a1b.2a.2a.3a.1), rhinovirus (subtype C), human respiratory syncytial virus A (lineage GA2.3.5), human respiratory syncytial virus B (lineage GB5.0.5a), and human metapneumovirus (lineage A2c) were detected in pediatric or adult respiratory samples. Human Pegivirus (genotype 3) was detected exclusively in adult blood samples. Strikingly, a novel picobirnavirus was identified in adult sputum samples, sequence and structural analyses consistently indicate that this picobirnavirus is closely related to human-associated strains, exhibiting ≥70% amino acid identity and an RdRP structure nearly identical to that of picobirnaviruses previously identified in human upper respiratory swabs from Cambodia. This finding was validated by nested RT-PCR, representing the first documented detection of picobirnavirus in respiratory specimens from China. As most identified strains were first reported in northeast China, we also conducted comprehensive phylogenetic analyses of representative viruses, revealing high sequence similarity with epidemic strains from other regions of China.

CONCLUSION: These findings delineate the respiratory viruses of northeast China, providing data for region-specific surveillance to mitigate future public health risks.}, } @article {pmid41607944, year = {2025}, author = {Gao, YQ and Hou, QY and Hou, XW and Wei, YJ and Shang, KM and Ma, H and Geng, HL and Liu, R and Yang, LH and Elsheikha, HM and Ni, HB and Huang, YF}, title = {Metagenomics-based characterization of fecal microbiome and resistome of laying hens during the production cycle.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1740567}, pmid = {41607944}, issn = {2297-1769}, abstract = {The extensive use of antimicrobials in livestock has accelerated the emergence of antimicrobial resistance (AMR), raising serious global concerns. Poultry feces are recognized as important reservoirs of antibiotic resistance genes (ARGs) and their associated mobile genetic elements (MGEs); however, the microbial community characteristics and ARG profiles of laying hens across different laying stages remain poorly understood. In this study, 40 fecal samples were collected from laying hens at five sampling points, including the early laying stage (HE), three peak laying stages (HPI, HPII, and HPIII), and the late laying stage (HL), with eight randomly selected samples per stage. Shotgun metagenomic sequencing was conducted to characterize the taxonomic structure and functional profiles of the intestinal microbiota and to systematically analyze the diversity and distribution patterns of ARGs. The results showed that most ARGs were harbored by bacteria belonging to the phyla Pseudomonadota and Bacillota, with Escherichia coli serving as the primary carrier of antibiotic resistance genes. Moreover, significant correlations were observed between the co-abundance and co-occurrence of ARGs and MGEs, suggesting that MGEs play a key role in facilitating ARG dissemination. Overall, these findings provide novel insights into the prevalence of ARGs in laying hens across different laying stages and may inform strategies to mitigate the spread of antimicrobial resistance in poultry production systems.}, } @article {pmid41608298, year = {2026}, author = {Aldoori, J and Mitra, S and Davie, A and Toogood, GJ and Edwards, C and Hull, MA}, title = {The effect of omega-3 polyunsaturated fatty acids on short-chain fatty acid production and the gut microbiome in an in vitro colonic fermentation model.}, journal = {Gut microbiome (Cambridge, England)}, volume = {7}, number = {}, pages = {e1}, pmid = {41608298}, issn = {2632-2897}, abstract = {Oral administration of omega-3 polyunsaturated fatty acids (PUFAs) to rodents and humans is associated with an increase in gut bacteria that are predicted to synthesise short-chain fatty acids (SCFAs). We tested the hypothesis that physiological levels of omega-3 PUFAs in the distal intestinal lumen (1-50 μg/mL) are associated with increased SCFA synthesis in an in vitro fermentation model using faecal slurry from 10 healthy participants (mean age 30 years), with and without exogenous dietary fibres. SCFAs were measured by gas chromatography-flame ionisation detection (n = 10), and changes in bacterial composition were analysed by shotgun metagenomic sequencing (n = 6). In the presence of omega-3 PUFAs, there was a mean 9.3% (no inulin; P = 0.03) and 19.3% (+ 0.01 mg/mL inulin; P = 0.01) increase in total SCFA concentration at 24 h compared with paired control fermentations. Omega-3 PUFAs had a limited effect on the fermentation model microbiome in the absence of inulin. However, omega-3 PUFAs (50 μg/mL) were associated with increased abundance of Bifidobacteriaceae compared with paired control fermentations, if inulin (0.01 mg/mL) was present. Prebiotic activity of omega-3 PUFAs drives SCFA synthesis in an in vitro colonic fermentation model and is augmented by the soluble fibre inulin.}, } @article {pmid41609167, year = {2026}, author = {Koo, WLY and Thng, KX and Tiew, PY and Chotirmall, SH}, title = {The Airway Microbiome in Chronic Obstructive Pulmonary Disease (COPD): A Guide for Clinicians.}, journal = {British journal of hospital medicine (London, England : 2005)}, volume = {87}, number = {1}, pages = {50163}, doi = {10.31083/BJHM50163}, pmid = {41609167}, issn = {1759-7390}, support = {MOH-001636//National Research Foundation Singapore/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000710//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001275-00//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000955//Singapore Ministry of Health's National Medical Research Council/ ; RT1/22//Singapore Ministry of Education/ ; }, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology ; *Microbiota ; Dysbiosis ; Disease Progression ; }, abstract = {Chronic obstructive pulmonary disease (COPD) is a progressive and debilitating respiratory condition marked by chronic symptoms and frequent exacerbations, contributing to significant morbidity and mortality. The advent of molecular microbiology and next-generation sequencing (NGS) has expanded our understanding of the lung microbiome, and integration of microbiome datasets with other omics reveals important microbial-metabolic-immuno-inflammatory interactions that influence COPD pathogenesis. Recent studies have highlighted dysbiosis of the airway microbiome, with shifts in bacterial, viral, and fungal communities playing a crucial role in disease progression, exacerbations and clinical outcomes. Moreover, microbiome changes are observed in COPD associated overlap syndromes, complicating diagnosis and treatment. This review synthesizes current microbiome research in COPD, focusing on its clinical relevance, including its potential as a diagnostic and prognostic tool. We additionally discuss the challenges of integrating microbiome data into clinical practice, emphasizing the need for personalized, precision medicine approaches to optimize COPD management and improve patient outcomes.}, } @article {pmid41609355, year = {2026}, author = {Li, Y and Li, Q and Quan, K and Xie, Y and Yang, N and Ma, T and Zheng, L and Zhou, W and Li, Y and Jin, H and Sun, Z and Chen, Y and Kwok, L-Y and Lu, N and Zhu, W and Liu, W and Zhang, H}, title = {Adjunctive probiotic therapy sustains symptom relief in gastroesophageal reflux disease through gut microbiome-metabolome remodeling.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0156825}, pmid = {41609355}, issn = {2379-5077}, support = {No.2022LJRC0003//the Inner Mongolia Autonomous Region Science and Technology Leading Talent Team Project/ ; No. U22A20540//National Natural Science Foundation of China/ ; No. 2022YFD2100700//National Key Research and Development Program of China/ ; CARS-36//the Earmarked Fund for China Agriculture Research System/ ; BX20250337//the China National Postdoctoral Program for Innovative Talents/ ; }, mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Gastroesophageal Reflux/microbiology/metabolism/drug therapy/therapy ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; *Metabolome/drug effects ; Double-Blind Method ; Adult ; Middle Aged ; Rabeprazole/therapeutic use ; Proton Pump Inhibitors/therapeutic use ; Treatment Outcome ; Metabolomics ; }, abstract = {Proton pump inhibitors (PPIs) are standard therapy for gastroesophageal reflux disease (GERD), but long-term use causes dysbiosis, gastrointestinal side effects, and symptom relapse after discontinuation. Probiotics may offer adjunctive benefits by modulating the gut ecosystem. The study aimed to evaluate the efficacy of a multi-strain probiotic (Lihuo) with rabeprazole in GERD and its impact on gut microbiota and metabolome. A randomized, double-blind, placebo-controlled trial was conducted in 120 GERD patients assigned to receive rabeprazole with either Lihuo (n = 64) or placebo (n = 56) for 8 weeks, followed by 4 weeks of probiotic or placebo alone. The primary outcome was change in the Reflux Disease Questionnaire (RDQ) score. Secondary outcomes included Gastrointestinal Symptom Rating Scale, endoscopic healing, and multi-omics profiling (shotgun metagenomics, phageome, and untargeted/targeted metabolomics). Compared with the placebo group, the probiotic group exhibited a pronounced 36.51% reduction in RDQ scores after 12 weeks of intervention (P = 0.017), alongside a higher numerical endoscopic healing rate (36.84% vs 12.50%; P = 0.365). Metagenomics revealed enrichment of Bifidobacterium animalis, Lactiplantibacillus plantarum, and Clostridium sp900540255, with reductions in Bacteroides uniformis and Clostridium Q fessum. Metabolomics showed increased γ-aminobutyric acid, succinate, citrulline, and short-chain fatty acids levels, with interesting microbe-metabolite correlations such as Bifidobacterium animalis-γ-aminobutyric acid and Bacteroides fragilis-succinate (r ≥ 0.30, P < 0.01). Our findings support that adjunctive probiotic therapy sustains post-PPI symptom relief, associated with targeted modulation of gut microbiota and bioactive metabolites.IMPORTANCELong-term proton pump inhibitor use in gastroesophageal reflux disease (GERD) may disrupt gut microbiota and cause symptom relapse after discontinuation. We found that adjunctive probiotic therapy sustained reflux reduction post-proton pump inhibitor. Probiotic use enriched beneficial taxa (Bifidobacterium and Lactiplantibacillus plantarum) and increased γ-aminobutyric acid, succinate, citrulline, and short-chain fatty acids. Strong correlations linked microbial shifts to metabolic and clinical improvements. This study demonstrates that adjunctive probiotic therapy enhances symptom control and supports microbial-metabolic homeostasis in GERD.CLINICAL TRIALSThis study is registered with the Chinese Clinial Trial Registry as ChiCTR2000038409.}, } @article {pmid41609371, year = {2026}, author = {Panattoni, A and De Boeck, I and Wittouck, S and Deffner, P and Lillie-Jaschniski, K and Stadler, J and Lebeer, S and Theuns, S}, title = {Exploring the functional microbiome of pigs within the porcine respiratory disease complex: viral-bacterial co-infections and virulence factor profiling.}, journal = {Microbiology spectrum}, volume = {14}, number = {3}, pages = {e0191025}, pmid = {41609371}, issn = {2165-0497}, support = {HBC.2023.0154//Agentschap Innoveren en Ondernemen/ ; }, mesh = {Animals ; Swine ; *Virulence Factors/genetics ; *Microbiota/genetics ; *Coinfection/veterinary/microbiology/virology ; *Bacteria/genetics/classification/isolation & purification/pathogenicity ; RNA, Ribosomal, 16S/genetics ; *Swine Diseases/microbiology/virology ; *Respiratory Tract Infections/veterinary/microbiology/virology ; Porcine respiratory and reproductive syndrome virus/genetics/isolation & purification ; *Bacterial Infections/veterinary/microbiology ; Influenza A virus/genetics/isolation & purification ; Respiratory System/microbiology/virology ; Porcine Reproductive and Respiratory Syndrome/microbiology/virology ; }, abstract = {Respiratory infections are among the most impacting on pigs' health and economic productivity. Despite this, detailed insights into the microbial community of the lower respiratory tract (LRT) are currently lacking, mainly because of difficulties in the processing of respiratory samples. In this study, we characterized the microbiota of the LRT of finisher pigs aged 3-5 months with respiratory symptoms for both the viral and bacterial components, using a previously validated metagenomic diagnostic assay and a full-length 16S rRNA gene sequencing approach, respectively. Functional characterization was carried out using metagenomic shotgun sequencing, revealing the presence of specific virulence factors (VFs). Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and swine Influenza A Virus (swIAV) were the most prevalent viruses, being detected in 30% and 23% of the tested samples, respectively. Mesomycoplasma hyopneumoniae, Glaesserella parasuis, and Pasteurella multocida were the three most abundant bacterial taxa based on both sequencing approaches, while other detected bacterial taxa consisted mainly of Streptococcus, Clostridium, and Rothia species. Detected virulence factors belonged mainly to Mesomycoplasma and Pasteurella and consisted of adhesion factors such as p102, p97, p146, mhp108, mhp107 and the hemolysin-encoding gene hlyA for Mesomycoplasma, and adhesin-encoding ptfA and endoxtoxin-related gene lpxC for Pasteurella. Our data show how the microbial community of the lower respiratory tract in pigs with respiratory symptoms includes key viral (PRRSV, swIAV) and bacterial pathogens (M. hyopneumoniae, G. parasuis, and P. multocida), along with specific virulence factors likely contributing to disease.IMPORTANCEThe obtained results offer insights into the composition of the swine respiratory tract microflora, opening new perspectives on its correlation with viral infections, functional characteristics, and overall health conditions. Moreover, the present study provides technical advancement on the possibility of extracting and amplifying bacterial DNA from low-biomass respiratory samples, with the resulting possibility of identifying virulence factors and better understanding their contribution to the disease state. These discoveries pave the way for future studies aimed at improving diagnostic accuracy and treatment strategies for respiratory disease in both veterinary and human medicine.}, } @article {pmid41609375, year = {2026}, author = {Yepes-García, J and Falquet, L}, title = {2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.}, journal = {mSystems}, volume = {11}, number = {2}, pages = {e0084425}, pmid = {41609375}, issn = {2379-5077}, support = {//Federal Commission for Scholarships for Foreign Students/ ; }, mesh = {*Software ; *Metagenomics/methods ; *Metagenome ; Workflow ; *Computational Biology/methods ; *Whole Genome Sequencing/methods ; }, abstract = {Whole-genome sequencing has boosted our ability to explore microbial diversity by enabling the recovery of metagenome-assembled genomes (MAGs) directly from environmental DNA. As a result, the vast availability of sequencing data has prompted the development of numerous bioinformatics pipelines for MAG reconstruction, along with challenges to identify the most suitable pipeline to perform the analysis according to the user needs. This report briefly discusses the computational requirements of these pipelines; presents the variety of interfaces, workflow managers, and package managers they feature; and describes the typical modular structure. Also, it provides a compacted technical overview of 41 publicly available pipelines or platforms to build MAGs starting from short and/or long sequences. Moreover, recognizing the overwhelming number of factors to consider when selecting an appropriate pipeline, we introduce an interactive decision-support web application, 2Pipe, that helps users to identify a suitable workflow based on their input data characteristics, desired outcomes, and computational constraints. The tool presents a question-driven interface to customize the recommendation, a pipeline gallery to offer a summarized description, and a pipeline comparison based on key factors used for the questionnaire. Beyond this and foreseeing the release of novel pipelines in the near future, we include a quick form and detailed instructions for developers to append their workflow in the application. Altogether, this review and the application equip the researchers with a general outlook of the growing metagenomics pipeline landscape and guide the users toward deciding the workflow that best fits their expectations and infrastructure.}, } @article {pmid41609629, year = {2026}, author = {Huang, R and Wang, Y and Liu, D and Wang, S and Lv, H and Yan, Z}, title = {Retraction for Huang et al., "Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites.}, journal = {Microbiology spectrum}, volume = {14}, number = {3}, pages = {e0238124}, pmid = {41609629}, issn = {2165-0497}, } @article {pmid41609929, year = {2026}, author = {Mo, Y and Ahlgren, N and Fuhrman, JA and Sun, F and Hou, S}, title = {A Beginner's Guide to Using DeepVirFinder for Viral Sequence Identification From Metagenomic Datasets.}, journal = {Current protocols}, volume = {6}, number = {2}, pages = {e70310}, doi = {10.1002/cpz1.70310}, pmid = {41609929}, issn = {2691-1299}, support = {549943//Simons Foundation/ ; 42476109//National Natural Science Foundation of China/ ; 42276163//National Natural Science Foundation of China/ ; EF-2125142//National Science Foundation/ ; 3779//Gordon and Betty Moore Foundation/ ; }, mesh = {*Metagenomics/methods ; *Software ; *Deep Learning ; *Viruses/genetics ; Genome, Viral ; *Computational Biology/methods ; }, abstract = {Identifying viral sequences from metagenomic datasets is critical for investigating their origins, evolutionary patterns, and ecological functions. Previously, we developed a novel deep learning software, DeepVirFinder, to predict viral sequences from shotgun metagenomic assemblies. This method employs a twin convolutional neural network model to extract features from known viral and prokaryotic host genomic sequences for binary classification of input query sequences. With the rapid accumulation of environmental metagenomic data, this approach has accelerated the discovery of novel viruses from diverse environments through an alignment-free and reference-free deep learning strategy. To facilitate the rapid adoption of this software for beginning users, here we have further improved DeepVirFinder by optimizing its runtime performance, while maintaining the essential user interface of the original version. This comprehensive guide provides basic workflows for the most common use cases of DeepVirFinder. Additionally, to assist users in downstream analyses, supplementary scripts were provided in the software for extracting viral sequences and inspecting the results, thereby helping researchers more effectively mine viral information from metagenomic datasets. © 2026 Wiley Periodicals LLC. Basic Protocol 1: Predicting viral sequences in metagenomic assemblies Basic Protocol 2: An integrated pipeline for viral sequence analysis: Prediction, extraction, and visualization Basic Protocol 3: Retraining the DeepVirFinder model using a customized dataset.}, } @article {pmid41610081, year = {2026}, author = {Kiige, JK and Kavoo, AM and Mwajita, MR and Mogire, D and Ogada, S and Wekesa, TB and Kiirika, LM}, title = {Correction: Metagenomic characterization of bacterial abundance and diversity in potato cyst nematode suppressive and conducive potato rhizosphere.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0342019}, pmid = {41610081}, issn = {1932-6203}, abstract = {[This corrects the article DOI: 10.1371/journal.pone.0323382.].}, } @article {pmid41610462, year = {2026}, author = {Nagy, EZ and Szeredi, L and Földi, D and Belecz, N and Kovács, ÁB and Sulyok, KM and Grózner, D and Wehmann, E and Bányai, K and Marton, S and Tenk, M and Kreizinger, Z and Gyuranecz, M}, title = {Development and efficacy test of a live, attenuated Mycoplasma hyorhinis vaccine candidate strain.}, journal = {Vaccine}, volume = {75}, number = {}, pages = {128278}, doi = {10.1016/j.vaccine.2026.128278}, pmid = {41610462}, issn = {1873-2518}, mesh = {Animals ; Vaccines, Attenuated/immunology/administration & dosage ; *Bacterial Vaccines/immunology/administration & dosage ; *Mycoplasma Infections/prevention & control/veterinary ; Antibodies, Bacterial/blood ; *Mycoplasma hyorhinis/immunology/genetics ; Swine ; *Swine Diseases/prevention & control/microbiology/immunology ; Vaccination ; Methylnitronitrosoguanidine ; Vaccine Efficacy ; Adjuvants, Immunologic/administration & dosage ; Vaccine Development ; }, abstract = {BACKGROUND: Mycoplasma (M.) hyorhinis causes substantial economic losses in swine. Currently, prevention and treatment rely on minimizing risk factors and administering antibiotics, as no vaccines are commercially available in Europe. However, antibiotics often cannot fully eliminate the bacteria. The development of an effective vaccine could lead to a potentially long-term control method.

MATERIALS AND METHODS: A temperature-sensitive M. hyorhinis strain was developed using 1-methyl-3-nitro-1-nitrosoguanidine (NTG) mutagenesis. The immunogenicity and efficacy of this vaccine candidate clone were evaluated in combination with an adjuvant. Three-week-old piglets were immunized with the candidate vaccine strain, and the vaccination site was monitored daily. At six weeks of age, the pigs were challenged intravenously on two subsequent days. Daily clinical examinations were conducted, with blood and nasal swabs collected weekly throughout the study for M. hyorhinis enzyme-linked immunosorbent assay (ELISA), real-time PCR analysis, and isolation. Three weeks post-challenge, the animals were euthanized for gross and histopathological examinations. Body temperature was recorded daily, and body weight was measured upon arrival, and then at six and nine weeks of age.

RESULTS: Vaccination significantly reduced clinical signs (p = 0.03), as well as gross pathological (p = 0.01) and histopathological (p = 0.005) lesions compared with the positive control group. The vaccinated group exhibited an earlier and higher increase in M. hyorhinis-specific IgG antibody levels post-challenge than the positive control group. However, the vaccine candidate did not mitigate the impact of M. hyorhinis infection on the weight gain. After the challenge (days 21-42), both the vaccinated (p = 0.001) and the positive control (p = 0.003) groups exhibited reduced weight gain compared with the negative control group.

DISCUSSION: Overall, the attenuated M. hyorhinis strain, combined with the adjuvant, provided protection against M. hyorhinis infection. These results form a basis for the development of a novel vaccine candidate that offers effective prevention.}, } @article {pmid41610548, year = {2026}, author = {Zafar, S and Alimohammadi, M and Hatami Moghadam, P and Hadei, M}, title = {Investigating the types of bacterial species with antimicrobial resistance genes in Iran's wastewaters: a systematic review.}, journal = {The Science of the total environment}, volume = {1016}, number = {}, pages = {181385}, doi = {10.1016/j.scitotenv.2026.181385}, pmid = {41610548}, issn = {1879-1026}, mesh = {*Wastewater/microbiology ; Iran ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antimicrobial resistance (AMR) is a major global health threat, with wastewater systems performing as critical reservoirs and dissemination pathways for antimicrobial-resistant bacteria (ARB) and resistance genes (ARGs). Despite rising AMR rates in Iran, a comprehensive understanding of resistance patterns in wastewater remains limited. This systematic review aimed to investigate the prevalence, bacterial diversity, and resistance gene profiles in hospital, municipal, and industrial wastewater across Iran. A systematic search was conducted in Scopus, PubMed, Web of Science, and Iranian databases for studies published between 1990 and September 2024. Data extraction followed PRISMA guidelines, and study quality was assessed using the JBI checklist. A total of 43 studies from 13 provinces met the inclusion criteria, with nearly half originating from Tehran (21/43, 48.8%), indicating uneven national coverage. Hospital wastewater (18 studies, 41.9%) harbored the highest burden of clinically significant AMR, including MRSA (22%), VRE (17%), and ESBL-producing E. coli (17%). Municipal wastewater (31 studies, 72.1%) frequently contained VRE Enterococcus faecium (32%) and Enterococcus faecalis (23%), ESBL-producing E. coli (19%), and MRSA (10%). Industrial wastewater (10 studies, 23.3%), primarily from slaughterhouses, exhibited high ESBL rates in E. coli (80%), with some studies reporting up to 93% ESBL production among isolates. Across studies, the most recurrent ARGs were blaCTX (16.3%), vanA (20.9%), mecA (9.3%), tetracycline genes, and intI1. Detection methods were predominantly culture- and PCR-based, with limited use of qPCR, molecular typing, or metagenomics. The most frequently detected resistance genes included blaCTX-M, mecA, vanA, tetA, and intI1. Most studies used culture and PCR-based detection; molecular typing and metagenomic approaches were rarely applied. The persistent detection of MDR pathogens and high-priority ARGs highlights significant gaps in AMR surveillance. Strengthening national wastewater monitoring through standardized protocols, broader geographic coverage, and integration of advanced molecular tools is essential to support effective One Health based public-health strategies.}, } @article {pmid41610602, year = {2026}, author = {Phusathian, B and Pongmanee, K and Theapparat, Y and Saikhwan, N and Trairatapiwan, T and Chaosap, C and Seemacharoensri, A and Tactacan, GB and Wong, LY and Ruangpanit, Y}, title = {Bacterial xylanase supplementation improves nutrient utilization, gut integrity, and microbial metabolism in broilers fed energy-reduced diets.}, journal = {Poultry science}, volume = {105}, number = {4}, pages = {106515}, pmid = {41610602}, issn = {1525-3171}, mesh = {Animals ; *Chickens/physiology/microbiology/growth & development/metabolism ; Male ; Animal Feed/analysis ; Diet/veterinary ; Dietary Supplements/analysis ; *Endo-1,4-beta Xylanases/administration & dosage/metabolism ; Animal Nutritional Physiological Phenomena/drug effects ; Digestion/drug effects ; Random Allocation ; Nutrients/metabolism ; *Gastrointestinal Microbiome/drug effects ; Energy Metabolism ; Intestines/drug effects/physiology ; *Bacterial Proteins/administration & dosage/metabolism ; }, abstract = {This study evaluated the effects of bacterial xylanase supplementation on growth performance, nutrient digestibility, intestinal integrity, and microbial metabolic function in broilers fed energy-reduced diets. A total of 1,050 one-day-old male Ross 308 broiler chicks were randomly assigned to three dietary treatments, each comprising 14 replicates of 25 birds: a positive control (CON; standard corn-soybean meal diet), a negative control with reduced energy (NC; -85 kcal/kg), and an energy-reduced diet supplemented with bacterial xylanase (NCX; 100 g/ton Belfeed Xylanase™). During the starter phase, broilers fed the NC diet exhibited higher feed intake and FCR compared with those fed the CON and NCX diets (P < 0.05), with no significant difference between the CON and NCX diets. Apparent digestibility of dry matter, crude protein, and fat did not differ among dietary treatments (P > 0.05). However, broilers fed the NCX diet showed higher (P < 0.05) digestibility of crude fiber, NDF, and ADF than those fed the CON or NC diets. Apparent metabolizable energy was higher in broilers fed the CON and NCX diets compared with the NC diet. Furthermore, broilers receiving the CON and NCX diets exhibited significantly lower serum fluorescein isothiocyanate-dextran concentrations than those fed the NC diet, indicating improved intestinal barrier integrity. Bacterial xylanase supplementation increased microbial alpha diversity and altered beta diversity clustering, with enrichment of beneficial taxa such as Bifidobacteriaceae and Lactobacillaceae. Functional metagenomic prediction suggested greater representation of carbohydrate metabolism and energy production pathways in the NCX diet, whereas the NC diet was associated with enrichment of stress-related and xenobiotic degradation pathways. Overall, bacterial xylanase supplementation mitigated the adverse effects of dietary energy reduction by improving fiber utilization, maintaining gut integrity, and modulating the cecal microbiota toward a more favorable metabolic profile.}, } @article {pmid41611023, year = {2026}, author = {Li, W and Li, J and Wu, Y and Chen, M and Fu, Y and Li, W and Liu, S and Wang, J and Chen, Y}, title = {Artificial regulation of aerobic and anaerobic layers interface enhanced efficient nitrogen removal by weaving insulating grid and conductive carbon fiber in membrane aerated biofilm reactor.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134074}, doi = {10.1016/j.biortech.2026.134074}, pmid = {41611023}, issn = {1873-2976}, mesh = {*Biofilms ; *Bioreactors/microbiology ; *Nitrogen/isolation & purification ; *Membranes, Artificial ; *Carbon/chemistry ; Aerobiosis ; Carbon Fiber ; Anaerobiosis ; RNA, Ribosomal, 16S/genetics ; Electric Conductivity ; Electrodes ; }, abstract = {Artificial regulation of aerobic and anaerobic biofilm thickness is crucial for enhancing nitrogen removal efficiency of the membrane aerated biofilm reactor (MABR). In this study, conductive aeration membrane modules were fabricated by physical weaving technology to couple MABR with microbial electrochemistry for efficient nitrogen removal. Insulating grids of different thickness and conductive carbon fibers were woven onto the aeration membrane to form aerobic and anaerobic layers. When the total biofilm thickness reached 254 μm (150 μm aerobic layer and 104 μm anaerobic layer), the TN removal efficiency (89.49 ± 2.89 %) was optimal. 16S rRNA gene sequencing and metagenomics analysis confirmed that the aerobic and anaerobic layers in the biofilm were completely separated, but there was a synergistic effect in nitrogen removal. The composite cathode structure provides a mechanism for efficient spatial coupling between the aerobic and anaerobic layers, establishing a basis for regulating biofilm stratification.}, } @article {pmid41611051, year = {2026}, author = {Shi, J and Sun, C and Su, Y and Wu, Y and Zhan, M and Ji, C and Wang, R and Lv, B}, title = {Ecosystem-specific composition and drivers of plastisphere resistome in freshwater and marine environments.}, journal = {Environmental research}, volume = {294}, number = {}, pages = {123858}, doi = {10.1016/j.envres.2026.123858}, pmid = {41611051}, issn = {1096-0953}, mesh = {*Seawater/microbiology ; *Fresh Water/microbiology ; *Microplastics/analysis ; *Ecosystem ; *Bacteria/genetics/drug effects ; *Water Pollutants, Chemical/analysis/toxicity ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; }, abstract = {Microplastics in aquatic environments facilitate the formation of specific plastisphere microbiomes and serve as potential hotspots for antibiotic resistance genes (ARGs) propagation. However, the systematic comparisons of ARG profiles on microplastics from different aquatic ecosystems remain limited, particularly the prevalent ARGs and their bacterial hosts. This study performed a comparative meta-analysis of existing metagenomic datasets to investigate the resistome between freshwater and seawater microplastics (FMP and SMP) and their driving factors. Our results revealed that the ARG profiles on both FMP and SMP were significantly distinct from their surrounding waterbody. Moreover, FMP exhibited a higher diversity and abundance of ARGs rather than SMP. Ten core ARGs were shared on FMP and SMP, while 23 core ARGs were exclusively detected on FMP. The bacterial community on microplastics exhibited an ecosystem-specific composition, and was identified as the primary determinant shaping the ARG profiles. Notably, more complex bacteria-ARG co-occurrence pattern was identified on FMP, involving a broader spectrum of core genera and potential pathogenic hosts (e.g., Mycobacterium, Streptomyces). Furthermore, a significant and specific correlation between mobile genetic elements and ARGs was identified on FMP but not SMP, suggesting a markedly elevated horizontal gene transfer potential, with mechanistic support from the concurrent enrichment of oxidative stress and SOS response genes on FMP. These findings provide a comprehensive characterization of ARGs on aquatic microplastics, and especially highlight the role of FMP in the ARG dissemination.}, } @article {pmid41611053, year = {2026}, author = {Ma, WJ and Ma, ZS and An, ZJ and Zhang, HM and Tian, Y}, title = {Commercial powdered activated carbon achieves high-efficiency nitrogen removal in sulfur-driven autotrophic denitrification at low temperatures.}, journal = {Environmental research}, volume = {294}, number = {}, pages = {123882}, doi = {10.1016/j.envres.2026.123882}, pmid = {41611053}, issn = {1096-0953}, mesh = {*Denitrification ; Nitrogen/metabolism ; *Carbon ; Autotrophic Processes ; Sulfur/metabolism ; Waste Disposal, Fluid/methods ; }, abstract = {Sulfur-driven autotrophic denitrification (SAD), a nitrate removal process, is characterized by low carbon emissions and high sustainability. However, its efficiency is notably affected by low temperatures. This study confirmed that the addition of powdered activated carbon (PAC) could enhance denitrification capacity at low temperatures in the SAD process. At 15-10 °C, the nitrogen removal efficiency was 80.38 %, 1.38 times higher than that of the blank reactor. At low temperatures, PAC enhanced the activities of nitrate reductase and nitrite reductase. Meanwhile, PAC stimulated extracellular polymeric substances secretion and improved bio-electrochemical properties. Concurrently, both extracellular and intracellular electron transfer were enhanced by the addition of PAC. Microbial analysis indicated that the microbial network with PAC addition exhibited greater stability and robustness. Furthermore, PAC increased the relative abundances of denitrifying bacteria at low temperatures, particularly those of Ferruginibacter and Dokdonella. Metagenomic sequencing indicated that PAC enhanced pathways related to nucleotide sugar metabolism and synthesis, tRNA charging, and coenzyme A biosynthesis. At the genes level, the functional genes narIL, nirS, nasE, norCE, nosZ, soxA, soxZ, and dsrA were enriched with PAC addition. This study proposed and validated the feasibility of using PAC to enhance nitrogen removal efficiency in the wastewater treatment process at low temperatures, and further elucidated the underlying mechanisms.}, } @article {pmid41611279, year = {2026}, author = {Ma, XJ and Wang, F and Han, XT and Fang, F and Han, LY and Liu, HX}, title = {[Clinical characteristics and prognostic factors in patients with cerebrospinal fluid torque teno virus positivity after allogeneic hematopoietic stem cell transplantation].}, journal = {Zhonghua yi xue za zhi}, volume = {106}, number = {5}, pages = {455-460}, doi = {10.3760/cma.j.cn112137-20250711-01704}, pmid = {41611279}, issn = {0376-2491}, mesh = {Humans ; *Torque teno virus ; *Hematopoietic Stem Cell Transplantation ; Prognosis ; Retrospective Studies ; Female ; Male ; Transplantation, Homologous ; Adult ; *DNA Virus Infections ; }, abstract = {Objective: To investigate the clinical characteristics and prognostic factors for patients with cerebrospinal fluid positivity for torque teno virus (TTV) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Methods: A retrospective analysis was conducted on the patients who received allo-HSCT at Hebei Yanda Lu Daopei Hospital from 2022 to 2023 year and showed positive cerebrospinal fluid metagenomic next-generation sequencing (mNGS) results post-transplantation, with their clinical data collected accordingly. The patients were categorized into TTV-negative and TTV-positive groups based on the detection of TTV in cerebrospinal fluid. The TTV-positive group was further subdivided into low-RPM [TTV reads per million sequencing reads (TTV-RPM)<1] and high-RPM (TTV-RPM≥1) subgroups using the threshold of TTV-RPM. The patients were followed until December 9, 2025, to investigate the clinical features of cerebrospinal fluid TTV positive patients after allo-HSCT. The survival curve was drawn to compare the difference of survival rate between groups. The influencing factors of patient prognosis were analyzed using a multivariate Cox regression model. Results: A total of 134 patients were enrolled: sixty in the TTV-negative group, including 35 males and 25 females, aged [M (Q1, Q3)] 30 (14, 42) years, and 74 in the TTV-positive group, including 45 males and 29 females, aged 24 (15, 40) years. Within the TTV-positive group, 44 were classified as low-RPM subgroup and 30 as high-RPM subgroup. Baseline characteristics, including gender, age, primary disease, donor type, neutrophil engraftment time, platelet engraftment time, whether acute graft-versus-host disease (aGVHD) occurred, and other microbial infections in cerebrospinal fluid, showed no significant differences between the TTV-negative and TTV-positive groups, or between the low-RPM and high-RPM subgroups (all P>0.05). The median follow-up time was 30.0(18.0, 35.4) months, the median survival period was not reached in the low-RPM subgroup, while that in the high-RPM subgroup was 25.6 months (95%CI: 5.3-45.9), and the 3-year survival rate was lower than that in the low-RPM subgroup (41.1% vs 76.8%, P=0.014). Multivariate Cox regression analysis confirmed high TTV-RPM level (≥1) in cerebrospinal fluid as a risk factor for mortality in allo-HSCT patients (HR=2.57, 95%CI: 1.09-6.08). Conclusions: There is no difference in clinical characteristics among allo-HSCT patients with or without TTV infection or with different TTV viral loads. A high TTV-RPM value (≥1) in cerebrospinal fluid is a risk factor for mortality in allo-HSCT patients.}, } @article {pmid41611489, year = {2026}, author = {Li, W and Zhang, N and Li, Z and Cui, L and Wang, X and DU, Y}, title = {[Research progress on nanopore sequencing data alignment analysis methods and reference databases].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {42}, number = {1}, pages = {77-92}, doi = {10.13345/j.cjb.250554}, pmid = {41611489}, issn = {1872-2075}, mesh = {*Nanopore Sequencing/methods ; *Sequence Alignment/methods ; *Nanopores ; *Sequence Analysis, DNA/methods ; *Databases, Genetic ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Nanopore sequencing, as an emerging hotspot in sequencing technology, demonstrates tremendous potential in species identification, genome assembly, variant detection, and transcriptome analysis, owing to its distinctive advantages including extended read lengths, rapid detection capabilities, and compact instrumentation. However, nanopore sequencing data are characterized by high error rates and presence of insertions and deletions, which pose novel challenges for the application of conventional sequence alignment tools and the construction of reference databases. Focusing on the characteristics of nanopore data, this paper systematically sorts out sequence alignment tools suitable for nanopore sequencing, and elaborates on their advantages and limitations in processing sequence data for five different application scenarios: long-read sequencing, real-time sequencing, error rate compatibility, metagenomics, and structural variation detection. Meanwhile, from the perspective of data sources, this paper conducts multi-dimensional classification and organization of reference genome databases, and sorts out the key technologies for constructing high-quality nanopore databases. Through the collaborative analysis of alignment tools and databases, this paper provides references for the optimization and innovation of nanopore sequencing data analysis, and promotes the in-depth transformation of metagenomic sequencing from data generation to functional analysis.}, } @article {pmid41611691, year = {2026}, author = {Srivathsan, A and Arzika, AM and Maliki, R and Abdou, A and Lipsitch, M and Blumberg, S and O'Brien, KS and Porco, TC and Hinterwirth, A and Doan, T and Keenan, JD and Lietman, TM and Arnold, BF}, title = {Geographic spillover of antimicrobial resistance from mass distribution of azithromycin.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41611691}, issn = {2041-1723}, support = {R01 AI158884/AI/NIAID NIH HHS/United States ; R01 AI166671/AI/NIAID NIH HHS/United States ; /GATES/Gates Foundation/United States ; }, mesh = {*Azithromycin/administration & dosage/pharmacology/therapeutic use ; Humans ; *Anti-Bacterial Agents/administration & dosage/pharmacology/therapeutic use ; *Mass Drug Administration ; Infant ; *Drug Resistance, Bacterial/genetics ; Child, Preschool ; Niger/epidemiology ; Macrolides/pharmacology ; Geography ; Genotype ; }, abstract = {Large-scale, placebo-controlled, cluster-randomized trials in high-mortality settings in sub-Saharan Africa demonstrated a 14-18% reduction in childhood mortality following twice-annual mass drug administration (MDA) of azithromycin among children aged 1-59 months. Azithromycin MDA also selected for antimicrobial resistance (AMR), particularly macrolide resistance. It is unknown whether the AMR from azithromycin MDA could spill over to neighboring untreated populations. If present, such geographic spillover effects could lead trials to underestimate AMR risks. We assess between-village geographic spillover effects of genotypic macrolide resistance using metagenomic deep sequencing in rectal swabs collected from 300 children in 30 monitoring villages in Niger after two years of MDA in 594 surrounding villages. Conditional permutation tests assess associations between proximal azithromycin treatment intensity and resistance gene abundance. We find no evidence of geographic spillover of macrolide resistance in untreated villages, as the genetic load of AMR remains at baseline levels in placebo-treated villages regardless of surrounding azithromycin treatment intensity (Spearman ρ = -0.05, P = 0.83). Sensitivity analyses confirm robustness across metrics, and no spillover effects are detected for other antibiotic classes. Azithromycin MDA-induced macrolide resistance appears localized to treated villages, mitigating some concerns about geographic spillover of AMR to nearby untreated villages at 24 months.}, } @article {pmid41611767, year = {2026}, author = {Jain, AG and Agwan, D and Kumar, A and Pancha, I and Rathod, J and Mohapatra, B}, title = {Mixing regimes shape microbial community composition, nutrient regimes, and plant growth attributes in Jeevamrit: metagenomics and culturomics-based insights.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6603}, pmid = {41611767}, issn = {2045-2322}, support = {GSBTM/JD(R&D)/661/2022-23/00173054//GSBTM/ ; }, mesh = {*Metagenomics/methods ; *Soil Microbiology ; *Nutrients/metabolism ; *Plant Development ; *Microbiota ; *Bacteria/genetics/classification ; Soil/chemistry ; Nitrogen/metabolism ; }, abstract = {Jeevamrit, a microbial inoculant widely used in zero-budget natural farming (ZBNF) that relies on local farm-based resources to enhance overall biological health of soil, is reported for inconsistent crop yield enhancements. This is mainly due to variability in its preparation methods, e.g., mixing intensity, incubation regimes, and quality of ingredients used. Hence, the current study aimed to decipher the effect of mixing intensity (extent of oxygenation) on microbial community composition, nutrient transformation, and plant growth attributes of Jeevamrit, using a combined metagenomics-culturomics approach. Frequent mixing (Constant/Intermediate) enhanced nutrient solubilization (Fe, Zn, Cu, Mn) with higher total N and dissolved organic carbon, while less mixing (Anoxic/No-mix) led to accumulation of soluble Fe and NH4[+]-N with higher microbial diversity. Mixing-driven differential enrichment of taxa were noted, i.e., constant mixing (CM) dominated by Acinetobacter (~ 40%), Comamonas, Pseudomonas, and Lysinibacillus, linked to oxidative C/N cycling and metal dissolution. Whereas, anoxic (AO) favored Clostridium sensu stricto, Lactobacillales, Enterococcus, and Enterobacterales (> 60%), correlating to fermentative metabolism-driven reductive elemental cycling. Co-occurrence network analysis identified Acinetobacter, Pseudomonas, Comamonas, Trichococcus, and Stenotrophomonas as hubs, indicating keystone functions in structuring metabolic interactions. The metagenome-recovered MAGs belonged to Acinetobacter sp., Clostridium saccharobutylicum, Trichococcus flocculiformis, and Enterococcus gallinarum with potential to participate in multiple nutrient cycling. Cultivable members of Shigella, Rhodococcus, and Bacillus spp. showed high IAA production (135-145 µg mL[-][1]), NH3 release (~ 0.12 µg mL[-][1]), and K and P solubilization (~ 55.2 µg mL[-][1]). We hypothesize that oxygenation drives the Jeevamrit's microbial guild assembly, where mixing intensity modulates oxido-reductive metabolism and nutrient mobilization efficiency, indicating the requirement for standardization of formulation aligned to soil-specific conditions.}, } @article {pmid41611865, year = {2026}, author = {Ulloa, MA and Serrano, AV and Camelo, LC and Guyot, R and Vela, D and Muñoz, AR}, title = {Bacterial genome reconstruction and community profiling in Neotropical Drosophila.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6601}, pmid = {41611865}, issn = {2045-2322}, mesh = {Animals ; *Drosophila/microbiology ; *Genome, Bacterial ; *Microbiota/genetics ; Phylogeny ; Metagenomics/methods ; Metagenome ; *Bacteria/genetics/classification ; Ecuador ; }, abstract = {Drosophila species serve as key models for microbiota research due to their relatively simple microbial communities. However, microbial diversity and dynamics in Neotropical Andean Drosophila remain underexplored. Here we applied shotgun metagenomics to characterize the microbiota of 24 Neotropical Drosophila species from Ecuador, reconstructing 64 high-quality bacterial genomes predominantly from Acetobacteraceae and Enterobacterales. Microbial communities were consistently dominated by yeasts, lactic acid bacteria, acetic acid bacteria, and Wolbachia. Comparative analyses revealed no strong correlation between host phylogeny and microbial community composition, suggesting environmental factors and microbial interactions shape these communities. Notably, shifts in relative abundances indicate dynamic ecological succession and metabolic cooperation among microbes. These findings expand genomic resources for Drosophila-associated bacteria and highlight the complex ecological processes influencing host-microbiota relationships in natural populations.}, } @article {pmid41612181, year = {2026}, author = {Zhang, J and Deng, J and He, B and Wang, H and Lin, D and Li, J and Zhong, Q and Chen, Y and Liao, S and Wang, J and Wang, Y and Su, M and Guo, X}, title = {The study on the identification of cross-boundary microbiome enterotypes between high-altitude and coastal populations and their predictive value.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41612181}, issn = {1471-2180}, support = {2024B03J0562//the Science and Technology Program of Guangzhou/ ; }, abstract = {OBJECTIVE: To investigate the differences in gut microbiome composition among multi-center populations from coastal and high-altitude regions of China and their association with colorectal adenoma (CRA).

METHODS AND ANALYSIS: Metagenomic sequencing was performed on stool samples collected from 295 participants. Diversity, principal component, and linear discriminant analyses were conducted to assess microbial composition and functional differences related to geography and disease status.

RESULTS: In high-altitude populations, bacterial enterotypes were predominantly Prevotella, fungal enterotypes Saccharomyces, and archaeal enterotypes Methanobrevibacter, differing from those in coastal populations. Combining bacterial, fungal, and archaeal features improved classification accuracy between high-altitude and coastal populations (AUC = 0.84) and between high-altitude and coastal adenoma patients (AUC = 0.85). Specific enterotypes were observed to correlate significantly with metabolic pathways in high-altitude populations.

CONCLUSION: Significant differences in gut microbiome enterotypes exist across geographic populations, with specific enterotypes in high-altitude populations potentially associated with a lower prevalence of CRA. These findings provide new insights into the gut microbiome–geography relationship and support microbiome-based diagnostic and therapeutic strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04578-0.}, } @article {pmid41612194, year = {2026}, author = {Ballandras, V and McNamara, L and Carolan, JC and Pichon, A and Byrne, S}, title = {Whole genome sequencing of 18 economically important aphid pests with photographic vouchers for taxonomic validation.}, journal = {BMC genomic data}, volume = {27}, number = {1}, pages = {}, pmid = {41612194}, issn = {2730-6844}, abstract = {OBJECTIVES: Accurate molecular identification in insect monitoring programs relies on validated genomic references, yet many pest species remain underrepresented or incorrectly annotated in public databases. This Data Note provides a curated genomic resource for 18 economically important aphid pests. For each species, we generated whole-genome shotgun sequences and captured high-resolution photographic vouchers of the sequenced individuals to ensure taxonomic verification. Specimens were collected from field or suction trap networks to incorporate intraspecific variation. This dataset will support the development of reliable DNA barcoding, metabarcoding, and mitochondrial metagenomic assays, and contribute to improved reference libraries for aphid pest surveillance. DATA DESCRIPTION: This dataset includes whole-genome shotgun sequencing data for 18 agriculturally important aphid pest species selected from suction trap monitoring programs. Specimens were morphologically identified using standard aphid identification keys, and diagnostic traits were documented with high-resolution Leica Flexacam C3 images to provide taxonomic verification. For each species, pooled individuals (up to 15 per species) were used for DNA extraction using the Monarch® Genomic DNA Purification Kit. Illumina 150 bp paired-end sequencing (10.1–22.7 Gb per species) was performed by Novogene. These data enable extraction of Cytochrome Oxidase I (COI) barcodes, mitochondrial genomes, and associated endosymbiont sequences.}, } @article {pmid41612232, year = {2026}, author = {Chen, Q and Yin, Q and Chen, J and Jin, L and Guo, W and Huang, M}, title = {Comparison of the diagnostic value of targeted next-generation sequencing, metagenomic next-generation sequencing, and Xpert MTB/RIF in adult pulmonary tuberculosis.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41612232}, issn = {1471-2334}, abstract = {Tuberculosis (TB) has high morbidity and mortality rates, and drug-resistant strains pose an increasing challenge. Traditional methods for detecting the Mycobacterium tuberculosis complex (MTBC) are insufficient for rapid clinical diagnosis. This prospective study compared the diagnostic efficacy of targeted next-generation sequencing (tNGS), metagenomic next-generation sequencing (mNGS), and Xpert MTB/RIF using bronchoalveolar lavage fluid (BALF) samples from 121 patients with suspected pulmonary TB. Against the reference standard of mycobacterial culture, tNGS demonstrated the highest sensitivity (97.44%), followed by Xpert MTB/RIF (92.31%) and mNGS (84.62%), specificities were 69.51%, 69.51%, and 75.61%, respectively. To address the limitations of culture as an imperfect reference standard and the potential bias from clinical diagnosis, Bayesian Latent Class Analysis (BLCA) was employed. BLCA, which does not assume a perfect gold standard, estimated sensitivities of 98.7%, 99.8%, and 91.0% for tNGS, Xpert MTB/RIF, and mNGS, with corresponding specificities of 89.3%, 93.3%, and 97.8%, respectively. Both tNGS and Xpert MTB/RIF consistently detected rifampicin resistance mutations (rpoB) (p = 0.219, Kappa = 0.730). In conclusion, tNGS offers comparable specificity and sensitivity to Xpert MTB/RIF for TB diagnosis, with the advantage of distinguishing between MTBC, non-tuberculous Mycobacteria (NTM), and other microorganisms. Simultaneously, it provides insights into anti-TB drug resistance. Thus, tNGS is a valuable tool for diagnosing TB in various clinical settings. Clinical trial number, Not applicable.}, } @article {pmid41612472, year = {2026}, author = {Wang, Y and Shen, Y and Shen, J and Bi, J and Xu, J and Wei, T and Wang, R and Wu, X and Li, F and Bai, J and Jie, Z and Hou, D and Song, Y}, title = {Airway microbiome dysbiosis in severe pneumonia: metagenomic evidence of pathogen expansion and commensal depletion.}, journal = {European journal of medical research}, volume = {31}, number = {1}, pages = {}, pmid = {41612472}, issn = {2047-783X}, support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-18//Shanghai Three-year Action Plan to Strengthen the Construction of Public Health System/ ; 82130001//National Natural Science Foundation of China/ ; 2024YFC3044400//National Key Research and Development Program of China/ ; GZNL2024A02003//R&D Program of Guangzhou National Laboratory/ ; W2020-013//The Construction of Multi-Disciplinary Treatment System for Severe Pneumonia/ ; 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; }, abstract = {BACKGROUND: The pulmonary microbiome is increasingly recognized as a key determinant of pneumonia severity, yet its clinical implications remain incompletely understood. Disruption of microbial ecology, or dysbiosis, may impair host immune responses and exacerbate disease progression. This study aimed to characterize microbiome alterations associated with severe pneumonia and their correlation with host inflammatory and coagulative parameters.

METHODS: In this multicenter, prospective observational cohort study conducted across nine hospitals in Shanghai (2021-2025), bronchoalveolar lavage fluid (BALF) samples from 306 patients with clinically diagnosed pulmonary infections were analyzed using metagenomic next-generation sequencing (mNGS). Patients were stratified into severe (n = 196) and non-severe (n = 110) groups using WHO-derived severe pneumonia criteria at the time of bronchoalveolar lavage (BAL). Microbial taxonomic profiles, diversity indices, co-occurrence networks, and correlations with clinical markers were comprehensively assessed using standard bioinformatic and statistical approaches.

RESULTS: Severe pneumonia was associated with marked microbial dysbiosis, including reorganization of co-occurrence network topology with centrality shifting away from commensals toward opportunistic taxa in severe disease, characterized by reduced α-diversity, altered β-diversity, and enrichment of opportunistic Gram-negative pathogens including Acinetobacter and Klebsiella. In contrast, commensals such as Rothia and Prevotella were depleted. Co-occurrence network analysis revealed fragmentation of microbial interactions in severe cases, with centrality shifting from commensals to opportunists like Corynebacterium striatum. Shannon diversity negatively correlated with SOFA scores, and specific taxa positively associated with systemic inflammation (CRP, PCT) and coagulation abnormalities. Nearly all samples demonstrated polymicrobial infection, with distinct microbial patterns observed across monomicrobial and polymicrobial subgroups.

CONCLUSION: Our multicenter observational analysis suggests that severe pneumonia is associated with marked ecological disruption of the lower-airway microbiome, characterized by commensal loss, opportunist expansion, and fragmented interspecies networks, and with concurrent inflammatory and coagulative abnormalities. These hypothesis-generating findings warrant external validation in independent, multi-region cohorts and longitudinal sampling to test directionality and causality before informing clinical decision-making.}, } @article {pmid41612514, year = {2026}, author = {Enagbonma, BJ and Pierneef, RE and Modise, DM and Babalola, OO}, title = {Effects of legume-based rotation on subsequent sorghum rhizosphere microbial communities and their drought tolerance-related genes.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41612514}, issn = {2524-6372}, support = {CRP/ZAF22-03//ICGEB/ ; }, abstract = {INTRODUCTION: The impacts of incorporating legumes into cereal crops on soil microbial structure, composition, functional genes involved in nitrogen, carbon and phosphorus cycling, signaling pathways and hydraulic conductivity adaptations have been well studied. However, the same cannot be said for functional genes that increase drought tolerance.

OBJECTIVES: Here, we examined the changes in microbial community structure and functional genes involved in drought tolerance in response to legume‒cereal rotation and cereal‒cereal rotation. This study provides a preliminary, exploratory characterization of microbial community and functional gene shifts, without direct evidence of functional impact on plant physiology or productivity.

METHODS: DNA extracted from soil samples collected across cowpea-sorghum treatment (CS) or maize-sorghum treatment (MS) was sequenced via shotgun sequencing.

RESULTS: Nonmetric multidimensional scaling analysis revealed that the microbial communities in the CS treatment significantly differed from those in the MS treatment. Compared with the MS rotation, the CS rotation increased the relative abundances of Pseudomonadota, Acidobacteriota, Chloroflexota, Gemmatimonadota, Euryarchaeota, and Candidatus Bathyarchaeota and reduced the abundances of Actinomycetota, Ascomycota, and Nitrososphaerota at the phylum level. Furthermore, the CS rotation increased the abundance of microbial genera such as Solirubrobacter, Sphingomonas, Nitrosocosmicus, Nitrosotenuis Aspergillus, and Metschnikowia when related to the MS rotation. STAMP analysis revealed that in the CS rotation, genes involved in trehalose biosynthesis, biofilm formation, oxidative stress mitigation (e.g., sodA, katG), stress signaling (e.g., rpoS, ipdC), nutrient provisioning (e.g., nifH, pqqC), membrane fluidity (desA, desB), dormancy (spo0A, spoVF), and ion homeostasis (nhaB, kup) predominated. In the MS rotation, proline biosynthesis (proA, proB, and proC), glycine betaine synthesis (betA and betB), aquaporin (aqpZ), and structural integrity genes (murA and murC) were predominant. The RDA results revealed that crop rotation influenced the soil physicochemical parameters, which in turn impacted both the microbial communities and drought tolerance genes in both treatments, probably creating a favorable environment for resilience under drought.

CONCLUSION: These research findings provide insight into the relationships between cowpea cropping sequences and the soil microbiome and drought-tolerant functional genes fundamental for the productivity of successive crops and this understanding guides sustainable crop selection.}, } @article {pmid41612676, year = {2026}, author = {Asin, J and Carvallo, F and Gonzales-Viera, OA and Macías-Rioseco, M and Streitenberger, N and Abdelrazek, S and Crossley, B and Pesavento, PA and Uzal, FA}, title = {Interstitial pneumonias of undetermined etiology in foals in California, 1990-2020.}, journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc}, volume = {}, number = {}, pages = {10406387251410524}, pmid = {41612676}, issn = {1943-4936}, abstract = {Interstitial and bronchointerstitial pneumonias of undetermined etiology in young foals are relatively common in autopsy services with an equine focus. Unknown viruses, toxins, hyperthermia, surfactant or alveolar macrophage function deficiency, certain antibiotics, and aberrant responses to Rhodococcus equi or other bacteria have been proposed as causes. We performed a retrospective study of autopsies on foals with a diagnosis of interstitial or bronchointerstitial pneumonia with an unidentified etiology. Forty-one foals (median age: 3-mo-old) were included. Most were received in summer (n = 28) and spring (n = 10). The most frequently reported clinical signs were dyspnea and/or tachypnea (n = 28) and fever (n = 19). Antibiotic treatment was reported in 21 cases, and the most frequently used antibiotics were penicillin (n = 9) and gentamicin (n = 8). Grossly, most of the lungs were diffusely rubbery-to-firm (n = 35) and did not collapse (n = 22). Histologically, combinations of exudative (E; hyaline membranes), proliferative (P; type II pneumocyte hyperplasia), and fibrotic (F; fibroplasia) phases were common (E + P, n = 15; E + P + F, n = 13) in the interstitial component. Necrosis of the bronchiolar epithelium was rare (n = 4), concurrent suppurative bronchopneumonia was common (n = 22), and a few foals (n = 5) had pulmonary pyogranulomas. Pneumocystis spp. organisms were observed in 8 cases using Grocott-Gomori methenamine silver stain. Bacteria were recovered from the lungs in 22 cases, with R. equi (n = 7) and E. coli (n = 6) being the most common isolates. No unequivocal viral causes were identified during the regular diagnostic work-up and after using novel diagnostic approaches such as herpesvirus consensus PCR and viral metagenomics in a subset of the cases.}, } @article {pmid41613303, year = {2025}, author = {Huang, J and Lan, C and Liang, Y and Chen, H and Liang, H and He, H and Che, S and Chen, Y}, title = {Case Report: Metagenomic next-generation sequencing diagnosed a rare case of sternal tuberculosis mimicking a malignant tumour.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1708834}, pmid = {41613303}, issn = {2296-858X}, abstract = {This is a case report of a 17-year-old female patient who presented with a painless, palpable swelling on the anterior chest wall. Imaging studies revealed osteolytic lesions involving the manubrium and adjacent ribs, along with multiple enlarged lymph nodes, raising a high suspicion of malignant tumour with metastasis. An ultrasound-guided needle biopsy revealed the pathological finding of "granulomatous inflammation." Multidisciplinary consultation and clinical indicators, including a strongly positive purified protein derivative (PPD) test and markedly elevated erythrocyte sedimentation rate, were taken to indicate a potential diagnosis of tuberculosis. Consequently, subsequent metagenomic next-generation sequencing (mNGS) of the biopsy specimen identified nucleic acid sequences belonging to the Mycobacterium tuberculosis complex, thereby confirming the rare diagnosis of sternal tuberculosis. Following the administration of standardised anti-tuberculosis therapy, a substantial reduction in the size of the lesion was observed, thereby validating the accuracy of the diagnosis. This case underscores the importance of considering extrapulmonary tuberculosis in the differential diagnosis of bone-destructive lesions and demonstrates the critical value of mNGS technology in confirming challenging infectious diseases.}, } @article {pmid41613591, year = {2025}, author = {Xu, Y and Ma, Y and Huang, Q and Guo, X and Guo, L and Ren, Y and Lu, W and Wu, X and Li, D and Li, S}, title = {The role of bronchoalveolar lavage fluid metagenomic next-generation sequencing in detecting pathogens and optimising antibiotic therapy in paediatric severe community-acquired pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1688473}, pmid = {41613591}, issn = {2235-2988}, mesh = {Humans ; *Community-Acquired Pneumonia/drug therapy/microbiology/diagnosis ; Child, Preschool ; *Anti-Bacterial Agents/therapeutic use ; Male ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Infant ; *Bronchoalveolar Lavage Fluid/microbiology ; Child ; Female ; Adolescent ; *Bacteria/genetics/isolation & purification/classification ; *Community-Acquired Infections/drug therapy/microbiology ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) remains a major cause of mortality in the paediatric population, with current diagnostic and treatment approaches often proving insufficient and contributing to the growing challenge of antibiotic resistance. This study explored the potential of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid as a tool to enhance the precision of antibiotic management in children with SCAP.

METHODS: A retrospective cohort study of 202 paediatric patients with community-acquired pneumonia (aged 1 month-18 years) admitted to the First Affiliated Hospital of Xinxiang Medical University (November 2020-March 2023) was conducted. Patients were grouped by severity (intensive care unit [ICU]/non-ICU) and mNGS timing (early: ≤72 hours post-admission; late: >72 hours). The diagnostic efficacy of mNGS versus conventional microbiological techniques (CMT) was evaluated using sensitivity, specificity, positive/negative predictive values and area under the receiver operating characteristic curve (AUC) analysis. Antibiotic adjustments and clinical outcomes were analysed via survival statistics.

RESULTS: Metagenomic next-generation sequencing showed a higher positive detection rate (98.51%) than CMT (47.52%) (AUC = 0.82, 95%CI: 0.76-0.88). Of the 202 patients, 127 (62.87%) were male, with a median age of 1.88 years (interquartile range: 0.29-7 years). Early mNGS was associated with fewer extrapulmonary complications (69.63% vs 55.22% in the late group, p < 0.05), and shorter hospitalisation (median 13 vs 15 days, p <0.01). Antibiotic escalation occurred in 50 (24.75%) cases, de-escalation in 22 (10.89%) and same-level adjustment in 25 (12.38%).

CONCLUSION: Metagenomic next-generation sequencing outperforms CMT in pathogen detection. Early mNGS is associated with improved clinical outcomes, suggesting its potential utility in paediatric SCAP management.}, } @article {pmid41614121, year = {2025}, author = {Shi, M and Guo, A and Qin, S and Kang, Y and Zhang, W and Yang, X}, title = {Metagenomic insights into short-term legume rotation: modulating potato rhizosphere microbiota to enhance tuber yield and quality.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1680056}, pmid = {41614121}, issn = {1664-302X}, abstract = {OBJECTIVE: This study aims to investigate the effects of legume crop rotation on the rhizosphere microbiota and its potential to improve potato (Solanum tuberosum L.) productivity and tuber quality. We specifically focus on the microbial functional potential revealed through metagenomic sequencing under different legume rotation systems in the intensive agricultural region of the Chinese Loess Plateau.

METHODS: A five-year field experiment (2018-2022) was conducted to establish three cropping systems: (1) continuous potato monocropping for 5 years (CK), (2) continuous potato cropping for 3 years followed by one-year pea rotation and one-year potato cropping (T1), and (3) continuous potato cropping for 3 years followed by one-year faba bean rotation and one-year potato cropping (T2). The impacts of these rotation regimes on potato yield formation, tuber quality, and rhizosphere microbial communities were systematically evaluated, with a focus on microbial diversity and functional potential, using metagenomic sequencing and network analysis.

RESULTS: Metagenomic analysis demonstrated that legume rotation, particularly the T2 system, significantly enriched the relative abundances of Actinobacteria (38.31%) and Proteobacteria (28.40%) in the potato rhizosphere while reducing Acidobacteria (10.03%). Functional annotation further revealed that T2 promoted the expression of microbial genes involved in carbon fixation (K00626, K01895, etc.), nitrogen assimilation (narB, narA, etc.), and sulfur metabolism (cysNC, cysN, etc.), enhanced potential for nutrient cycling. Co-occurrence networks revealed Actinobacteria and Acidobacteria as keystone taxa forming robust interaction modules potentially linked to soil ecological stability. Compared to CK, T2 increased the commercial tuber rate by 85.82%, overall tuber yield by 28.38%, starch content by 34.85%, and vitamin C content by 30.79%, while reducing sugar levels decreased by 9.35%.

CONCLUSION: Faba bean-potato rotation (T2) effectively mitigated the adverse impacts caused by continuous potato cropping by altering the rhizosphere microbial structure and enhancing microbial functional pathways related to nutrient cycling. This study provides a detailed metagenomic perspective on the microbial mechanisms underlying the benefits of crop rotation and offers a theoretical basis for developing microbiome-informed ecological management strategies to mitigate continuous cropping obstacles in potato production on the Loess Plateau.}, } @article {pmid41614128, year = {2025}, author = {Wang, J and Bai, C and Tian, Y and Bao, J and Liu, J}, title = {Intercropping reshapes soil stress resistance and growth promotion capabilities through rhizosphere exudates in conjunction with the microbiome.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1708938}, pmid = {41614128}, issn = {1664-302X}, abstract = {Terrestrial plants can affect the growth and health of neighboring plants through interspecific interactions. Long-term monoculture in agricultural and pastoral production can lead to the occurrence of soil-borne diseases, depletion of nutrients, and a decline in soil microbial diversity, thereby affecting the sustainable development of cultivated ecosystems. In this study, we employed three cultivation patterns: monoculture of Melilotus officinalis (L.) Pall. (M. officinalis), monoculture of Avena sativa L. (A. sativa), and intercropping of M. officinalis and A. sativa. To introduce ecologically protective plants into cultivated ecosystems and investigate the effects of plant root exudates on the recruitment of rhizosphere microbiota of neighboring plants, as well as the disease resistance and growth promotion capabilities of intercropping, we conducted non-targeted metabolomics and metagenomics analyses on root exudates and soil microbiota. The sequencing data obtained provided strong evidence for the interaction mechanisms between root exudates and microorganisms in intercropping ecosystems. We observed that in intercropping ecosystems, the abundance and variety of root exudates were more similar to those of the crop plants. The differential metabolites between intercropping and A. sativa were inclined to be chemically defensive, while those between intercropping and M. officinalis were more inclined to promote material synthesis. Compared with A. sativa, intercropping enhances the alpha and beta diversity of soil microbial communities, particularly increasing the enrichment abundance in pathways such as the bacterial secretion system, sulfur metabolism, and phenylpropanoid biosynthesis, which is closely associated with the suppression of soil-borne pathogens. Compared with M. officinalis, intercropping further enhanced the synthesis of plant-available substances in the soil, driving microorganisms to optimize the levels of carbon, nitrogen, and trace elements in the soil. In comparison, intercropping had a significant impact on the aggregation of soil-specific microorganisms, which can optimize nitrogen utilization to promote plant growth and enhance plant defense and stress tolerance. The results of this study will provide a theoretical basis for cultivated ecosystems and sustainable land management.}, } @article {pmid41614136, year = {2025}, author = {Zhao, S and Wang, X and Zhu, H and Guo, G and Mustafa, GR and Mustafa, A and Chen, Y and Li, X and Wang, Y and Zhao, B}, title = {Metagenomic analysis revealed the distribution of antibiotic resistance genes of Awang sheep (Ovis aries) gut microbiota.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1740198}, pmid = {41614136}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) in livestock is a major contributor to the global AMR crisis, yet little is known about its dynamics in high-altitude pastoral systems. We performed deep metagenomic sequencing of 100 fecal samples from Tibetan Awang sheep reared under grazing (aw_fm) and captive (aw_qs) conditions. Microbiome profiling revealed striking community shifts: grazing sheep were enriched in Bacteroidetes and Firmicutes, whereas captive sheep showed expansion of Proteobacteria, particularly Acinetobacter, suggesting dysbiosis. The resistome comprised 302 unique ARGs, dominated by rpoB2 (43.3%), Bifidobacterium_adolescentis_rpoB (11.2%), and ugd (10.2%). Grazing sheep carried ARGs mainly against rifamycins and peptide antibiotics, reflecting natural selective pressures, while captive sheep exhibited significantly broader resistance, including tetracyclines, macrolides, and fluoroquinolones (p < 0.05). Enrichment of efflux pump genes (MexK, adeJ) in captive sheep highlighted a shift toward multidrug resistance. These findings demonstrate that rearing practices profoundly restructure the gut resistome, underscoring the need for targeted antibiotic stewardship in high-altitude livestock systems.}, } @article {pmid41614172, year = {2026}, author = {Li, Y and Wang, J and Zhang, Z and Zhang, Y and Müller, R and Huo, L}, title = {Deep-Sea Genome Mining Reveals Cooperative ATP-Grasp Ligase-Directed Biosynthesis of Pentacyclic Myxomiditides with Potent Protease Inhibition.}, journal = {JACS Au}, volume = {6}, number = {1}, pages = {607-620}, pmid = {41614172}, issn = {2691-3704}, abstract = {Microviridins are ribosomally synthesized and post-translationally modified peptides, typically featuring a conserved tricyclic structure formed by two ATP-grasp ligases. However, the diversity and evolution of these enzymes remain incompletely understood. Here, we identify a distinct ATP-grasp ligase subclade (MyxF) that specifically modifies the conserved (KxxE)n motif, defining a new subclass of microviridins with the (KxxE)nTxKxPSDx-(D/E)-(D/E) sequence signature. Guided by SSN analysis, we discovered a deep-sea myx biosynthetic gene cluster from 10,000 m sediments and heterologously expressed two pentacyclic microviridin-like peptides, Myxomiditide A and B. Using mass spectrometry and NMR, we fully elucidated their chemical structures, revealing not only the conserved tricyclic core but also two additional N-terminal lactam rings within the KxxEKxxE motif, distinguishing them from known microviridins. Combined in vivo coexpression and in vitro reconstitution uncovered a noncanonical division of labor among four ATP-grasp ligases involved in myxomiditide biosynthesis. MyxF and MyxD1 act as functional isozymes responsible for installation of the N-terminal lactam moieties, whereas MyxD2(?)catalytically inactive on its own(?)requires the synergistic presence of both MyxF and MyxD1 to enable formation of the C-terminal lactone rings. The pathway is finalized by MyxC, which catalyzes the terminal lactam macrocyclization, collectively revealing a highly cooperative enzymatic assembly mechanism governing myxomiditide maturation. Furthermore, MyxF exhibited remarkable catalytic plasticity, catalyzing multiple lactam macrocyclizations beyond its native substrate architecture. Notably, Myxomiditide A potently inhibited elastase with nanomolar IC50 values. Collectively, this study expands the enzymatic landscape of ATP-grasp ligases and highlights the deep sea as a rich source of evolutionary innovation in RiPP biosynthesis.}, } @article {pmid41614733, year = {2025}, author = {Kim, D and Kim, WJ and Woo, HM and Jeong, H}, title = {PixelCut: A Unified Solution for Zero-Configuration 16S rRNA Trimming via Computer Vision.}, journal = {Current issues in molecular biology}, volume = {47}, number = {12}, pages = {}, pmid = {41614733}, issn = {1467-3045}, support = {ncheon National University Research Grant in 2023. 284//Incheon National University/ ; }, abstract = {16S rRNA amplicon sequencing has been an effective method for profiling microbial taxonomy in microbiome research, as it offers lower per-sample costs and higher sample throughput than shotgun metagenomics. Although 16S rRNA sequencing offers clear advantages over shotgun sequencing, it depends on precise trimming of low-quality bases at the 3' ends of reads. Given the widespread use of 16S rRNA amplicon sequencing, there is an increasing demand for analysis tools that can identify errors in the 3' region of reads and remove erroneous bases. While various algorithms for predicting trim locations are widely employed, most are command-line standalone tools, which pose challenges for users with limited computational background or resources. Furthermore, in the absence of biological or experimental priors such as amplicon size, trim position predictions may be unreliable. Here, we introduce PixelCut, a fully automated trim-position prediction framework that requires no hyperparameters or prior biological information for accurate prediction. Unlike most available algorithms that operate on raw FASTQ data, PixelCut analyzes the per-base quality report generated by FastQC to infer trimming positions. Based on the recommended quality score threshold from the quality report, PixelCut inspects the quality scores across bases and automatically determines the recommended trim position using character recognition techniques based on computer vision. We have also developed a user-friendly web application to make the method accessible to those without programming expertise, while offering a command-line version for advanced users. Through comprehensive computer simulations, we show that PixelCut produces taxonomic profiling results that are consistent with those from popular trim-location prediction algorithms.}, } @article {pmid41615027, year = {2025}, author = {Jiménez, DJ and Marasco, R and Schultz, J and Díaz Rodríguez, CA and Nogales, J and Rodriguez-R, LM and Overmann, J and Rosado, AS}, title = {Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41615027}, issn = {1751-7370}, support = {MCIN/AEI/10.13039/501100011033//Spanish Ministry of Science and Innovation/ ; 101081782 (deCYPher)//European Union/ ; 101036768 (PROMISEANG)//European Union/ ; PID2022-139247OB-I00 (Rob3D)//European Union/ ; BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; }, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Bacteria/genetics/classification/isolation & purification/growth & development ; Microbiota ; }, abstract = {Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a persistent bottleneck in microbiology and microbial ecology. This perspective outlines a conceptual framework to improve the transition from genome-resolved metagenomics to the targeted isolation of yet-uncultured prokaryotic taxa. The proposed framework integrates the induced reshaping of microbiomes, genome-based inferences of physiological and phenotypic traits, culture media design, and targeted culturomics, enabling hypothesis-driven cultivation. In addition, this manuscript addresses the critical limitations in the field, including the sequence-to-function gap, and emphasizes the synergistic potential of experimental microbiology, microbial ecology, metagenomics, and artificial intelligence-based predictions to enhance rational and actionable roadmaps for discovering and cultivating novel prokaryotic lineages.}, } @article {pmid41615149, year = {2026}, author = {Mora-Martínez, C and Molina-Mendoza, G and Cenit, MC and Medina-Rodríguez, EM and Larroya-García, A and Sanchez-Carro, Y and Gonzalez-Blanco, L and Bobes, J and Lopez-Garcia, P and Zandio-Zorrilla, M and Lahortiga-Ramos, F and Gili, M and Garcia-Toro, M and Barcelo, B and Ibarra, O and Sanz, Y}, title = {Gut microbiome signatures associated with depression and obesity.}, journal = {mSystems}, volume = {11}, number = {3}, pages = {e0126325}, pmid = {41615149}, issn = {2379-5077}, support = {EarlyCause 848158//Horizon 2020 Framework Programme/ ; Centro de Excelencia Severo Ochoa CEX2021-001189-S/MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; FPI PRE2018-083895//Ministerio de Ciencia e Innovación/ ; Miguel Servet CP22/00031//Instituto de Salud Carlos III/ ; }, mesh = {Humans ; *Obesity/microbiology ; *Major Depressive Disorder/microbiology ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Female ; Male ; Middle Aged ; Adult ; Body Mass Index ; Metagenomics ; Metagenome ; Bacteria/classification/genetics ; }, abstract = {UNLABELLED: Depression and obesity are highly comorbid and likely involve common risk factors and pathophysiological mechanisms, which could crosslink to gut microbiome dysfunction. Here, we performed a case-control study with a total of 105 subjects, 43 with major depressive disorder (MDD) and 62 non-depressed controls free from psychiatric comorbidities, to identify gut microbiome signatures associated with MDD and dissect its relation to body mass index (BMI) and lifestyle (diet and exercise). We performed shotgun metagenomics, followed by taxonomic and functional annotations. Using different machine learning methods, we were able to classify subjects into depressed and non-depressed controls with a balanced accuracy of 0.90 and into depressed or non-depressed and normal weight or overweight with a balanced accuracy of 0.78 based solely on taxonomic profiles. We identify novel bacterial taxa associated with depression, including reductions in Butyrivibrio hungatei and Anaerocolumna sedimenticola, and also replicate previously reported associations, such as decreased Faecalibacterium prausnitzii in patients with MDD. Functional annotation of metagenomes shows differences in pathways linked to the synthesis of fundamental nutrients, which have been associated with diet, as well as inflammation. Strikingly, we found an increase in tryptophan degradation and a decrease in queuosine synthesis pathways, both of which are directly related to a decrease in monoaminergic neurotransmitter availability. Additionally, our functional analysis shows that most of the functions that are more abundant in controls than in depressed subjects are encoded by F. prausnitzii. These findings reveal distinct microbial and functional signatures associated with depression, including taxa and pathways linked to neurotransmitter metabolism and independent of other covariates. This suggests that gut microbiome profiling could support diagnosis and the development of gut-directed depression treatments.

IMPORTANCE: This study identifies gut microbiome signatures that are predictive of major depressive disorder (MDD) and explores their links to body mass index (BMI). We uncover bacterial species and metabolic pathways that are associated with MDD, some of them related to neurotransmitter metabolism and inflammation. Among the differences identified, depletion of Faecalibacterium prausnitzii stands out as an important feature in the MDD microbiome, which suggests the possible use of this species to improve depression symptoms. Importantly, we demonstrate shared microbiome features between MDD and BMI, suggesting common underlying mechanisms. This research not only provides a framework for developing microbiome-based diagnostics but also informs future stratified interventions targeting gut microbial functions to improve mental health outcomes.}, } @article {pmid41615376, year = {2026}, author = {Eichler, H and Butta, NV and Riddell, A and Augustsson, C and Kjalke, M and Jensen, K and Paramo-Florencio, A and Astermark, J and Chowdary, P and Jiménez-Yuste, V}, title = {Investigation of the Suitability of the ROTEM Assay to Measure Coagulation Potential in Blood From Patients on Concizumab Prophylaxis.}, journal = {Haemophilia : the official journal of the World Federation of Hemophilia}, volume = {32}, number = {2}, pages = {490-498}, pmid = {41615376}, issn = {1365-2516}, support = {//Novo Nordisk A/S/ ; }, mesh = {Humans ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Thrombelastography/methods ; *Blood Coagulation/drug effects ; *Hemophilia A/drug therapy/blood ; Blood Coagulation Tests/methods ; Male ; }, abstract = {BACKGROUND: Rotational thromboelastometry (ROTEM) aims to measure the coagulation potential in whole blood. Concizumab, an anti-tissue factor pathway inhibitor (TFPI) antibody for prophylaxis in haemophilia, enhances tissue factor (TF)-initiated coagulation by preventing inhibition of activated factor X (FXa), thus increasing thrombin generation.

OBJECTIVES: To evaluate a modified ROTEM assay for monitoring patients on concizumab prophylaxis.

METHODS: The TF reagent (r_exTEM) was diluted 50,000-fold to make the ROTEM assay sensitive to haemophilia and to concizumab. The effect of concizumab was evaluated in the modified ROTEM in haemophilia A (HA)-like blood (normal blood with added anti-FVIII antibody). ROTEM analysis was performed in blood from patients participating in the explorer7/8 trials during 24 weeks of concizumab prophylaxis. Rotrol N plasma was used as quality control.

RESULTS: In vitro experiments showed concizumab concentration-dependent reduction in clot time (CT) and increase in clot development (α-angle) in HA-like blood. At three of four clinical sites, CT and clot development were stable, variance of the control plasma was ≤12.4% and TF content of the diluted reagent (r_exTEM) was consistent. At these three sites, the correlation between CT versus concizumab exposure, free TFPI and thrombin generation assay parameters was weak (-0.508 to +0.359). Prothrombin time positively correlated with CT (0.523) and negatively correlated with α-angle (-0.659).

CONCLUSION: Due to the poor correlation between ROTEM parameters, concizumab exposure, free TFPI and thrombin generation parameters and the lack of consistent and reliable performance of the modified ROTEM assay, it cannot be recommended for general monitoring of patients on concizumab prophylaxis.}, } @article {pmid41615602, year = {2025}, author = {Fedonenko, YP and Grinev, VS and Velichko, NS and Lipatov, NN and Selivanov, NY and Kuzina, MS and Sigida, EN and Konnova, SA}, title = {Isolation and Characterization of Halophilic Bacteria of the Halomonadaceae Family, Promising Producers of Extracellular Polysaccharides.}, journal = {Doklady. Biochemistry and biophysics}, volume = {525}, number = {2}, pages = {653-658}, pmid = {41615602}, issn = {1608-3091}, mesh = {*Polysaccharides, Bacterial/chemistry/biosynthesis ; *Halomonadaceae/metabolism/isolation & purification/genetics ; Antioxidants/chemistry ; Viscosity ; }, abstract = {Exopolysaccharide (EPS) production is one of the key mechanisms of bacterial survival in hypermineralized environments. Representatives of the Halomonadaceae family are recognized as basic organisms for next-generation industrial biotechnology; however, the range of Halomonas used and information on the structural diversity of their EPSs are rather limited. The results of metagenomic analysis of salt, peloid, and soil samples from the coastal zone of salt lakes in the Volgograd region with subsequent seeding on selective mineral media made it possible to isolate bacteria of the Halomonadaceae family. For taxonomically identified strains, cultivation conditions were optimized and EPSs were obtained, the structure of which was characterized based on chemical analysis data and NMR spectroscopy. The study of the physicochemical properties of EPSs (viscosity, hygroscopicity, emulsifying activity, and antioxidant properties) showed that these polymers are promising for biotechnological applications.}, } @article {pmid41615921, year = {2026}, author = {Kiige, JK and Kavoo, AM and Mwajita, MR and Mogire, D and Ogada, S and Wekesa, TB and Kiirika, LM}, title = {Correction: Metagenomic characterization of bacterial abundance and diversity in potato cyst nematode suppressive and conducive potato rhizosphere.}, journal = {PloS one}, volume = {21}, number = {1}, pages = {e0342098}, pmid = {41615921}, issn = {1932-6203}, abstract = {[This corrects the article DOI: 10.1371/journal.pone.0323382.].}, } @article {pmid41616624, year = {2026}, author = {Sun, Y and Zhang, M and Teng, Y and Yin, Y and Ran, J and Su, H and Li, H and Huang, X and Long, Z and Sun, X and Pan, H and Wang, X and Li, M}, title = {Human activities and horizontal gene transfer shape the resistome landscapes of non-human primates.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141276}, doi = {10.1016/j.jhazmat.2026.141276}, pmid = {41616624}, issn = {1873-3336}, mesh = {Animals ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Primates/microbiology/genetics ; Humans ; *Human Activities ; Soil Microbiology ; Bacteria/genetics/drug effects ; China ; Metagenome ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance represents a growing threat to human, animal, and ecosystem health, yet its dynamics in wildlife remain poorly understood. We conducted a systematic analysis of the gut resistomes in non-human primates (NHPs) and environmental soils in Guizhou Province, China, a biodiversity hotspot. Metagenomic analyses reveal that human activities and horizontal gene transfer (HGT) influence primate resistome landscapes and enhance their dissemination potential. A total of 1927 antibiotic resistance ontologies (AROs) distributed across 1477 species-level genome bins (SGBs), providing a comprehensive genomic catalog of the NHPs resistome. Bacterial genera such as Pseudomonas, Stenotrophomonas, and Comamonas drive ARG mobilization, with a core subset of ARGs that reliably predict overall resistance burdens. Notably, widely distributed primate species, with large habitat ranges and frequent interspecies interactions exhibit the most potential for ARG dissemination. Ecological modeling identifies current and future hotspot regions requiring prioritized monitoring amid ongoing human disturbance and climate change. These findings provide a molecular-indicator-based framework for environmental antibiotic resistance (AR) monitoring and conservation strategies for endangered species. Despite limitations in temporal and spatial coverage, our study highlights the need to integrate wildlife, particularly NHPs, as sentinel species into "One Health" AR surveillance and policy. This approach will strengthen our understanding of ARG transmission dynamics and their long-term impacts on host adaptation, ecosystem stability, and public health.}, } @article {pmid41616686, year = {2026}, author = {Sattari Khavas, D and Schwartz, SK and Bird, P and Truong, A and Silberg, JJ}, title = {Microbial spies and bloggers: programming cells to convert environmental information into discernible signals.}, journal = {Current opinion in biotechnology}, volume = {98}, number = {}, pages = {103436}, doi = {10.1016/j.copbio.2026.103436}, pmid = {41616686}, issn = {1879-0429}, mesh = {*Biosensing Techniques/methods ; Synthetic Biology ; *Bacteria/metabolism/genetics ; *Microbiota ; }, abstract = {Microbes regulate their dynamic behaviors using the chemical and physical characteristics of their environment. The ability of microbes to continuously convert this physicochemical information into biochemical information and to use organic matter in the environment as a power source makes these organisms attractive as chassis for building sensors. However, most biosensors have severe limitations when considering applications in hard-to-image settings like soils, sediments, and wastewater. Emerging technologies at the interface of biomolecular design, microbiome engineering, and synthetic biology offer new tools to program cells and communities as biosensors for these settings. In this review, we describe innovations in biosensor outputs that are enabling new applications in complex environments, including reporters that are read out using electrochemical, gas chromatography, hyperspectral imaging, and next-generation sequencing methods. We also discuss computational advances that are accelerating the diversification of sensing components by mining metagenomics data for new transcriptional regulators and by designing allosteric protein switches that directly regulate reporter outputs using analytes. We highlight emerging opportunities for programming undomesticated microbes in communities to function as distributed sensors in the environment. Finally, we discuss the need for responsible biosensor development and to modernize regulatory frameworks to support evidence-based assessment of environmental biosensors.}, } @article {pmid41616716, year = {2026}, author = {Breyer, GM and Torres, MC and Rebelatto, R and Wuaden, CR and Pastore, J and Lazzarotti, M and Nicoloso, RDS and Dorn, M and Kich, JD and Siqueira, FM}, title = {From farm to environment: the microbiome and the silent spread of antimicrobial resistance genes in soil despite manure management in swine farms.}, journal = {Journal of environmental management}, volume = {400}, number = {}, pages = {128747}, doi = {10.1016/j.jenvman.2026.128747}, pmid = {41616716}, issn = {1095-8630}, mesh = {Animals ; *Manure/microbiology ; *Soil Microbiology ; *Microbiota ; Swine ; Farms ; Soil ; Bacteria/genetics ; }, abstract = {The swine industry generates large amounts of organic waste containing antimicrobial residues, requiring efficient manure management to reduce environmental risks. Covered lagoon biodigesters (CLBs) and waste stabilization ponds (WSPs) are commonly used digestion systems, with digestates subsequently applied as organic fertilizers. Although these systems successfully reduce pathogenic bacteria, their effectiveness in removing antimicrobial resistance genes (ARGs) remains unclear. In this study, we compared microbiome and resistome profiles from CLB- (n = 23) and WSP-farms (n = 20) using shotgun metagenomic sequencing of raw and digested manure, as well as fertilized and non-fertilized soils. Our findings indicate that digestate application slightly shifted soil microbial communities and significantly increased bacterial diversity, suggesting the introduction of diverse manure-derived bacteria. Reads from taxonomic markers associated with clinically important pathogens, including Enterobacterales, streptococci (groups A and B), Enterococcus faecium, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, and Salmonella enterica were still detected in digestates and fertilized soils, regardless of the digestion system. Moreover, DNA sequences associated with ARGs against critical antimicrobials, such as carbapenems, cephalosporins, and glycopeptides persisted. Notably, WSPs exhibited greater accumulation of some ARGs, including OXA-347 and vanG. Overall, although CLBs exerted a lower impact on soil microbial communities and resistomes compared to WSPs, neither system effectively eliminated ARGs. These findings highlight the potential for environmental dissemination of ARGs through manure fertilization and underscore the urgent transition toward more sustainable production practices, including eliminating non-therapeutic antimicrobial use in the swine industry, as well as the need for improved digestion technologies and continuous monitoring under the One Health framework.}, } @article {pmid41616776, year = {2026}, author = {Liu, C and Sun, S and Ren, X and Geisen, S and Wang, S and Jiang, G and Xu, Y and Shen, Q and Jousset, A and Wei, Z and Xiong, W}, title = {Predation by soil protists shifts bacterial metabolism from competitive to cooperative interactions.}, journal = {Cell host & microbe}, volume = {34}, number = {2}, pages = {201-211.e6}, doi = {10.1016/j.chom.2026.01.006}, pmid = {41616776}, issn = {1934-6069}, mesh = {*Soil Microbiology ; *Bacteria/metabolism/genetics ; Rhizosphere ; *Eukaryota/physiology ; *Microbial Interactions ; Microbiota ; Metagenomics ; Soil/parasitology ; }, abstract = {Many soil protists are bacterivores, yet how protist predation reshapes bacterial metabolic interactions and functions remains poorly understood. Here, we combine global soil samples with microbial metabolic simulations, along with soil microcosm-pot validations, to investigate the influence of protists on bacterial metabolic interactions. Across 3,785 metabolic simulations spanning 757 soils, increased protists predicted higher bacterial metabolic interaction potential and cross-feeding but lower metabolic resource overlap and competition. These patterns were confirmed using an independent rhizosphere dataset and metagenomic analysis. Protist predation selected bacterial communities containing GC-rich genomes, acid-carbon-preferring taxa, and enhanced metabolite exchange. Additionally, exposing a synthetic community (SynCom) to protist predation elevated the expression of bacterial genes associated with plant growth-promoting functions. Consistently, microcosm- and pot-based experiments showed that protist addition increased bacterial cross-feeding over time and improved plant performance. Together, we establish a scalable framework to evaluate protist-driven bacterial cooperation and function to guide rational rhizosphere microbiome engineering.}, } @article {pmid41617120, year = {2026}, author = {Hu, S and Wang, X and Xu, H and Xiong, J and Gu, Y and Cao, X and Zhou, L and Fan, Y and Wang, S and Bai, X and Shi, H and Zhu, Q and Chen, L and Shi, Z}, title = {Vaginal microbiota in late pregnancy associates with the outcomes of planned induced labor: a multicenter prospective cohort study.}, journal = {American journal of obstetrics and gynecology}, volume = {234}, number = {6}, pages = {1740-1758}, doi = {10.1016/j.ajog.2026.01.026}, pmid = {41617120}, issn = {1097-6868}, mesh = {Female ; Humans ; Pregnancy ; *Labor, Induced/methods ; *Vagina/microbiology ; *Microbiota ; Prospective Studies ; Adult ; Cervical Ripening ; Animals ; Lactobacillus crispatus ; Pregnancy Outcome ; Genome-Wide Association Study ; Lactobacillus ; Cesarean Section/statistics & numerical data ; Oxytocin/therapeutic use ; }, abstract = {BACKGROUND: Induction of labor is a commonly used obstetric method for terminating pregnancy in cases of delayed or expired pregnancy or complications, with cervical maturity being a key determinant of success. Balloon-induced labor is a safe, effective, and cost-effective induction of labor method. While clinical factors such as parity, cervical Bishop score, prepregnancy body mass index, are known to influence outcomes. Emerging evidence suggests that vaginal microbiota may also play a critical role through activation of local complement mediators and inflammatory signalling that accelerates cervical ripening. Additionally, genetic factors may influence both preterm birth risk and vaginal microbiota composition. However, the specific impact of vaginal microbiota and genetic factors on balloon-induced labor outcomes remains unclear and requires further investigation.

OBJECT: To explore the impact of the vaginal microbiota prior to delivery on the maternal and fetal outcomes of planned induced labor through metagenomic sequencing and genome-wide association studies.

STUDY DESIGN: A multicenter prospective cohort study was conducted from October 2022 to June 2024 across 5 hospitals, enrolling 635 pregnant women undergoing planned sequential induction of labor using cervical balloons combined with oxytocin. The clinical data throughout the entire pregnancy and labor period, as well as samples of vaginal and cervical secretions before the induction of labor, were collected. Firstly, the characteristics of the vaginal microbiota in all pregnant women were analyzed through metagenomic sequencing, and then the impact of vaginal microbiota differences on the maternal and fetal outcomes of planned induced labor was studied. Subsequently, a nested case-control study was performed, based on human whole genome sequencing combined with genome-wide association studies analysis on vaginal secretion samples, to investigate the role of genetic factors in planned induced labor. Finally, vaginal microbiota transplantation in pregnant rats was conducted to verify the effects of vaginal microbiota on the maternal and fetal outcomes of labor.

RESULTS: Among the participants, 167 delivered within 24 hours, 318 delivered within 24-72 hours, 50 failed induction, and 100 underwent cesarean section for miscellaneous indications. Vaginal microbiota analysis in parturients revealed that the probability of delivery within 24 hours is negatively correlated with Lactobacillus iners (L. iners) abundance, while failed induction is negatively correlated with Ralstonia mannitolilytica abundance. Cesarean section probability is positively correlated with Lactobacillus crispatus (P=0.03). Additionally, the time from balloon placement to delivery is positively correlated with L. iners (P=0.002) and negatively correlated with Lactobacillus crispatus (P=0.08, not fully significant). Genome-wide association studies analysis shows that single-nucleotide polymorphisms associated with adverse pregnancy outcomes are mainly concentrated on chromosomes 1, 4, 8, and 10. Vaginal microbiota transplantation experiments showed that pregnant rats transplanted with vaginal bacteria from women who delivered within 24 hours had the shortest delivery time, while those transplanted with vaginal bacteria from women who failed to induced labor had the longest delivery time and some experienced dystocia.

CONCLUSION: This study reveals that, in addition to genetic factors, the outcomes of planned labor induction, especially the total duration of labor and the success rate of induction, are closely related to the vaginal microbiota in women during the late stages of pregnancy. The study provides new evidence to explain the different outcomes of labor induction.}, } @article {pmid41617130, year = {2026}, author = {Wang, J and Ma, Y and Shi, X and Han, Y and Zhang, Y and Diao, Z and Li, Z and Lai, H and Meng, S and Zhang, C and Zhao, F and Qin, X and Li, J and Zhang, R}, title = {A multicentre evaluation of metagenomic sequencing for pathogen detection in central nervous system infections.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {32}, number = {5}, pages = {797-805}, doi = {10.1016/j.cmi.2026.01.015}, pmid = {41617130}, issn = {1469-0691}, mesh = {Humans ; *Metagenomics/methods ; *Central Nervous System Infections/diagnosis/microbiology/cerebrospinal fluid/virology ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Cerebrospinal Fluid/microbiology/virology ; Reproducibility of Results ; }, abstract = {OBJECTIVES: Metagenomic next-generation sequencing (mNGS) is a promising tool for diagnosing central nervous system infections. However, the low-biomass nature of cerebrospinal fluid (CSF) increases susceptibility to contamination and host-background interference, potentially compromising accuracy. This study aimed to evaluate CSF mNGS performance across multiple laboratories and to identify key factors influencing detection accuracy.

METHODS: A reference panel of 15 CSF samples was designed to evaluate CSF mNGS performance across laboratories, including 3 replicate samples, 5 serial concentration-gradient samples, 3 anti-interference samples with added human serum albumin or increased host nucleic acids, and 3 simulated clinical case samples, along with 1 negative sample. A total of 127 laboratories participated, which apply mNGS in clinical diagnostics or research. Each laboratory used independently developed mNGS workflow, which varied in experimental procedures, bioinformatic pipelines, and positive detection thresholds. Accuracy, repeatability, sensitivity, and anti-interference capability were systematically evaluated, and sources of erroneous results and methodological factors influencing accuracy were analysed.

RESULTS: Overall performance across 127 laboratories was favourable (average F1-score 0.98, reflecting overall accuracy by balancing sensitivity and specificity). Most false-positive results (83.43%) were due to experimental contamination, whereas false negatives were mainly attributed to RNA viruses (57.14%). Methodological factors significantly affected detection, with impact varying by microbial type. Generally, pelleting impaired the detection of all microbes. Notably, microbial enrichment through DNase treatment and Kraken2 improved detection accuracy for DNA viruses, bacteria, fungi and atypical pathogens, but had little effect on RNA viruses.

CONCLUSIONS: This large-scale study underscores the need for improved contamination controls, optimized RNA virus detection, and enhancement of key wet-lab procedures to strengthen CSF mNGS reliability. These findings provide actionable insights to refine mNGS workflows and advance its clinical utility for diagnosing central nervous system infections.}, } @article {pmid41617300, year = {2026}, author = {Shah, D and Balendra, S and Petrushkin, H and Patel, A}, title = {Paediatric ocular toxocariasis with relentless progression despite negative metagenomic testing.}, journal = {The Lancet. Infectious diseases}, volume = {26}, number = {2}, pages = {e130-e131}, doi = {10.1016/S1473-3099(25)00685-1}, pmid = {41617300}, issn = {1474-4457}, } @article {pmid41617710, year = {2026}, author = {Shrestha, B and Romero, MF and Villada, JC and , and Blaby-Haas, CE and Schulz, F}, title = {Global metagenomics reveals plastid diversity and unexplored algal lineages.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41617710}, issn = {2041-1723}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, mesh = {*Plastids/genetics ; *Metagenomics/methods ; Phylogeny ; Symbiosis ; Cyanobacteria/genetics ; Haptophyta/genetics/classification ; Cryptophyta/genetics/classification ; Alveolata/genetics/classification ; Genetic Variation ; Evolution, Molecular ; Stramenopiles/genetics ; Genome, Plastid ; }, abstract = {Photosynthetic organelles in eukaryotes originated through primary endosymbiosis with a cyanobacterium, an event that profoundly shaped the evolutionary landscape of the eukaryotic tree of life. Primary plastids in Archaeplastida, especially in cultivable plants and algae, contribute most to known plastid diversity. Secondary and higher-order endosymbiosis, involving eukaryotic hosts and algal endosymbionts, further spread photosynthesis among protists within the CASH lineages (Cryptophyta, Alveolata, Stramenopila, and Haptophyta). Despite various hypotheses explaining secondary plastid evolution and distribution, empirical support remains limited. Here, we employ cultivation-independent global metagenomics to expand plastid diversity and investigate plastid origins. We capture 1,027 plastid sequences, including 300 novel sequences belonging to previously unsequenced plastids and representing yet-to-be described microeukaryotes. This includes a new lineage that offers insights into plastid evolution in haptophytes and cryptophytes. Our results confirm that Archaeplastida plastids originate from an early branching cyanobacterial lineage closely related to Gloeomargaritales and identify the closest extant relative of Paulinella plastids. Additionally, our findings suggest two independent origins of secondary red-algal plastids, contributing to plastid diversity in CASH lineages and challenging the prevailing model of single secondary plastid origin. Our study highlights the importance of metagenomic data in uncovering biological diversity and advancing understanding of plastid relationships across photosynthetic eukaryotes.}, } @article {pmid41617723, year = {2026}, author = {Pratama, AA and Pérez-Carrascal, O and Sullivan, MB and Küsel, K}, title = {Diversity and ecological roles of hidden viral players in groundwater microbiomes.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41617723}, issn = {2041-1723}, support = {EXC 2051, Project-ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DE-SC0023307//U.S. Department of Energy (DOE)/ ; }, mesh = {*Groundwater/virology/microbiology ; *Microbiota/genetics ; Archaea/genetics/virology ; Bacteria/genetics/virology/classification ; *Virome/genetics ; *Viruses/genetics/classification/isolation & purification ; Metagenomics ; Metagenome ; Phylogeny ; }, abstract = {Groundwater ecosystems harbor diverse microbial communities adapted to energy-limited, light-deprived conditions, yet the role of viruses in these environments remains poorly understood. Here, we analyzed 1.24 terabases of metagenomic and metatranscriptomic data from seven wells in the Hainich Critical Zone Exploratory (CZE) to characterize groundwater viromes. We identified 257,252 viral operational taxonomic units (vOTUs) (≥ 5 kb), with 99% novel at order, family and genus levels against global ocean, freshwater and/or other publicly available datasets. In silico host predictions suggest that vOTUs primarily targeted Proteobacteria, Candidate Phyla Radiation (CPR) bacteria, and DPANN archaea, which reflects abundant and active groundwater microbial members. Patterns of virus-host abundance ratios, CRISPR-spacers, and prophage screening suggest the potential for multi-layer interactions involving CPR/DPANN lineages, their hosts, and viruses. Additionally, we identified 289 KEGG metabolic modules, 31.1% of which were targeted by 3378 vOTUs encoded auxiliary metabolic genes (AMGs) linked to carbon, nitrogen, and sulfur cycling. These findings provide a baseline for exploring how viruses influence microbial community dynamics, metabolic reprogramming and nutrient cycling in groundwater.}, } @article {pmid41617724, year = {2026}, author = {Dong, Z and Sun, MS and He, YD and Zhou, L and Xiang, W and Li, X and Huang, P and Zeng, JG}, title = {Fungal photobiont and microbiome genome composition in the Cladonia uncialis tripartite symbiosis.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41617724}, issn = {2052-4463}, mesh = {*Symbiosis ; *Lichens/microbiology/genetics ; *Microbiota ; *Ascomycota/genetics ; *Genome, Fungal ; Genome, Bacterial ; Metagenome ; }, abstract = {As symbiotic complexes formed through the association of bacteria or algae with fungi, lichens exhibit exceptional adaptability to extreme environments and function as pioneer species in rocky habitat ecological succession. The absence of high quality chromosome-level genome has constrained investigations into lichen adaptive evolution, while functional contributions of symbiotic bacterial communities remain inadequately explored. This study presents the chromosome-level genome assembly of the mycobiont Cladonia uncialis, comprising 28 chromosomes with a total size of 43.49 Mb, generated through integrated PacBio HiFi and Hi-C methodologies. We characterized the symbiotic microbiota using integrated short and long-read sequencing and constructed 31 metagenome-assembled genomes. The community was dominated by Ascomycota (41.16%), Proteobacteria (17.61%), and Bacteroidota (14.20%). Long-read sequencing significantly enhanced detection sensitivity for low-abundance taxa. This study provides essential genomic resources and comprehensive profiles of the symbiotic microbiota, enabling mechanistic exploration of adaptive evolution within lichen symbiotic systems under extreme environmental conditions.}, } @article {pmid41617733, year = {2026}, author = {Thangaraj, S and Sun, J}, title = {Depth Resolved Metagenomic Dataset from Surface and Deep Chlorophyll Maximum Layers in the Western Pacific Ocean.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41617733}, issn = {2052-4463}, mesh = {Pacific Ocean ; *Metagenomics ; *Chlorophyll/analysis ; *Metagenome ; Seawater/microbiology ; }, abstract = {Stratified microbial communities are central to ocean biogeochemical cycles, yet their vertical structure and functional potential remain under characterized in oligotrophic regions. We present a metagenomic dataset from surface ocean and the deep chlorophyll maximum (DCM) layers of the stratified Western Pacific Ocean, sampled at four stations spanning approximately 800 kilometres. Each of the eight samples generated over 22.9 Gb of high-quality Illumina HiSeq 2500 paired end reads (Q20 > 95%, Q30 > 90%). De novo assemblies yielded 1.3-1.9 million contigs per sample, with total assembly sizes of 948 Mb to 1.33 Gb and N50 values of 632-749 bp. Gene prediction identified ~5.26 million non-redundant genes across all samples, reflecting substantial microbial diversity and depth-specific variation. Assembly statistics, taxonomic profiles, and functional annotations of genes are included for technical validation of the dataset, demonstrating data completeness and analytical depth. This dataset offers annotated sequence data and environmental metadata suitable for benchmarking, method development, and comparative studies of marine metagenomes.}, } @article {pmid41618101, year = {2026}, author = {Park, SJ and Özdinç, BE and Coker, KG and Walsh, DM and Fox, DJ and Evans, S and Farahnik, J and Moffat, K and Boomgaarden, M and Mischley, LK}, title = {Metagenomics indicates an interplay of the microbiome and functional pathways in Parkinson's disease.}, journal = {NPJ Parkinson's disease}, volume = {12}, number = {1}, pages = {}, pmid = {41618101}, issn = {2373-8057}, abstract = {Previous studies suggest there are distinct gut microbial and functional variations in patients with Parkinson's disease (PwPD) that may reveal potential microbiome signatures or biomarkers to aid in early detection of the disease. In this case-control study, we used whole genome sequencing to compare the stool samples of 55 PwPD to 42 healthy controls (HC) from a public database (BioProject Accession PRJEB39223). For bacterial phyla, we observed a greater relative abundance in Firmicutes and Actinobacteria among PwPD, while that of Bacteroidetes was lower. For phages, PwPD had a greater relative abundance of Siphoviridae, Tectiviridae, and Podoviridae, while Microviridae was lower. Moreover, we described 10 functional pathways that most significantly differed between PwPD and HC (all P < 0.0001). In conclusion, significant differences were observed in gut bacteria, phages, and functional pathways between PwPD and HC that both support and conflict with previous case-control studies and warrant further validation.}, } @article {pmid41618136, year = {2026}, author = {Liu, J and Elsheikha, HM and Lei, CC and Qin, SY and Liu, Y and Ni, HB and Qin, Y and Yu, HL and Su, JW and Chen, BN and Jiang, J and Sun, HT and Zhang, XX}, title = {Genome-resolved analysis of bile acid-metabolizing microbiota in Tibetan antelope (Pantholops hodgsonii).}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41618136}, issn = {1471-2180}, support = {2025ZD01900110//National Science and Technology Major Project for Prevention and Control of Emerging and Re-emerging Infectious Diseases/ ; 2022KJ169//Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; }, abstract = {BACKGROUND: The Tibetan antelope (Pantholops hodgsonii), an iconic species endemic to the Qinghai-Tibet Plateau, thrives at altitudes of 4,500–5,000 m under conditions of extreme hypoxia, cold, and limited nutrition. As a critical mediator of host physiology, the gut microbiome may play a key role in supporting these adaptations.

RESULTS: This study presents the first genome-centric investigation of bile acid (BA) metabolism in the gut microbiome of the Tibetan antelope, unveiling unique microbial pathways that potentially facilitate survival in harsh environments. Comparative analysis of metagenome-assembled genomes revealed that the antelope’s BA-metabolizing microbiota is taxonomically distinct from that of other Caprinae species and humans, with only two of the top ten BA-producing genera shared across groups. Importantly, individuals infected with Blastocystis exhibited marked differences in BA-related KEGG ortholog (KO) profiles compared to uninfected counterparts. Our findings highlight that the proportion of bile salt hydrolase (K01442) genes in the gut microbiota of Tibetan antelopes is higher than that in other Caprinae species and humans. Among them, the genus Alistipes carries the highest proportion of K01442 in the Tibetan antelope’s gut microbiota. Additionally, infection-associated KO gene shifts were observed, suggesting a microbial contribution to the Tibetan antelope’s remarkable physiological resilience.

CONCLUSIONS: In Tibetan antelopes, Alistipes was the dominant genus associated with bile acid synthesis. While bile acid synthesis KO distributions were broadly similar across species, K01442 higher proportion than other in Tibetan antelope gut microbiomes. Furthermore, Blastocystis infection altered three key bile acid synthesis KOs and induced distinct shifts in gut microbiome composition.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04750-0.}, } @article {pmid41618383, year = {2026}, author = {Pérez-Pérez, L and Arguello, H and Cobo-Díaz, JF and Galisteo, C and Puente, H and Gómez-Martínez, S and Carvajal, A}, title = {From predisposition to recovery: field evidence of interactions between the gut microbiota and Brachyspira hyodysenteriae infection.}, journal = {Veterinary research}, volume = {57}, number = {1}, pages = {25}, pmid = {41618383}, issn = {1297-9716}, support = {PRE2020-093762//Ministerio de Ciencia, Innovación y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovación y Universidades/ ; EDU-1868-2022//Junta de Castilla y León/ ; }, mesh = {Animals ; Swine ; *Swine Diseases/microbiology ; *Brachyspira hyodysenteriae/physiology ; *Gram-Negative Bacterial Infections/veterinary/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Disease Susceptibility/veterinary/microbiology ; Sus scrofa ; }, abstract = {Restrictions on antibiotics use have increased interest in the gut microbiota relationship to host health, particularly in enteric infections. The present field study, performed on two farms with endemic swine dysentery (SD) infection, characterises the faecal microbiota in 102 faecal samples from 13 diseased and 13 non-diseased pigs by shotgun metagenomic sequencing. The samples were collected during four samplings, which allowed us to monitor the animals before, during and after the clinical disease to investigate the role of the gut microbiota in disease outcome, assess the impact of infection on microbial composition and evaluate the microbiota evolution following recovery. Samples collected before disease demonstrated that SD susceptible pigs had lower microbial diversity, with significantly lower abundance of Treponema rectale, Prevotella spp. or Ruminiclostridium E compared with SD resistant pigs, which remained healthy. Marked alterations in microbial species composition and their functional profiles were evident during clinical disease. Brachyspira hyodysenteriae, Dysosmobacter sp. BX15, Acetivibrio ethanolgignens and Mucispirillum sp. 910586745 were significantly increased in abundance, which was associated with an increase of functions such as Bacteroides capsular polysaccharide transcription antitermination proteins or pterin carbinolamine dehydratase. No changes in the microbiota were observed after the disease when compared with non-diseased pigs, thus evidencing a restoration of the microbiota composition after therapeutic treatment and recovery. The study demonstrates that the microbiota may play a relevant role in SD disease outcome and evidences the changes that occur during clinical disease do not persist over time after pig therapeutic treatment.}, } @article {pmid41618433, year = {2026}, author = {Wang, Y and Zuo, W and Huang, J and Sun, F and Du, Y}, title = {Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.}, journal = {Genome biology}, volume = {27}, number = {1}, pages = {}, pmid = {41618433}, issn = {1474-760X}, support = {EF-2125142//National Science Foundation/ ; }, mesh = {*Metagenomics/methods ; Benchmarking ; Software ; *Sequence Alignment/methods ; Algorithms ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: Metagenomics combined with High-throughput Chromosome Conformation Capture (Hi-C) provides a powerful approach to study microbial communities by linking genomic content with spatial interactions. Hi-C complements shotgun sequencing by revealing taxonomic composition, functional interactions, and genomic organization within a single sample. However, aligning Hi-C reads to metagenomic contigs is challenging due to variable insert sizes of Hi-C paired-end reads, multi-species complexity, and gaps in assemblies. Although several benchmark studies have evaluated general alignment tools and Hi-C data alignment, none have specifically focused on metagenomic Hi-C data.

RESULTS: We evaluated seven alignment strategies commonly used in Hi-C analyses: BWA MEM -5SP, BWA MEM default, BWA aln default, Bowtie2 default, Bowtie2 -very-sensitive-local, Minimap2 default, and Chromap Hi-C default. We benchmarked these tools on one synthetic dataset and seven real-world environments. Performance was assessed based on the number of inter-contig Hi-C read pairs and their impact on downstream tasks, such as binning quality.

CONCLUSIONS: We show that BWA MEM -5SP generally outperformed all other tools across most environments in terms of inter-contig read pairs and binning quality, followed by BWA MEM default. Chromap and Minimap2, while less effective in these metrics, demonstrated the highest computational efficiency.}, } @article {pmid41618437, year = {2026}, author = {Chong-Nguyen, C and Fuentes Artiles, R and Pilgrim, T and Yilmaz, B and Döring, Y}, title = {The gut-heart axis in coronary artery disease: a scoping and narrative review of sex-based microbial and metabolic disparities.}, journal = {Biology of sex differences}, volume = {17}, number = {1}, pages = {24}, pmid = {41618437}, issn = {2042-6410}, mesh = {Humans ; *Coronary Artery Disease/microbiology/metabolism ; *Sex Characteristics ; *Gastrointestinal Microbiome ; Female ; Male ; }, abstract = {BACKGROUND: The gut microbiota significantly influences cardiovascular health by regulating host metabolism and generating bioactive compounds like trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), both linked to coronary artery disease (CAD). Emerging research indicates sex-based differences in microbial composition and metabolite production, yet their impact on CAD pathophysiology remains unclear. This scoping review summarizes current findings on sex-specific microbial and metabolic differences in individuals with CAD.

METHODS: A systematic search of PubMed and EMBASE was conducted through March 2025 for peer-reviewed studies comparing gut microbiota or metabolite profiles between male and female patients with CAD. Eligible studies used 16S rRNA sequencing, shotgun metagenomics, or metabolite profiling to analyze microbial communities and atherosclerosis-associated metabolites. Mechanistic links from genetics, epigenetics, and hormone-microbiota interactions were integrated to provide a more comprehensive understanding of how gut microbiota may contribute to sex differences in CAD.

RESULTS: Eleven studies met the inclusion criteria for this review. Men with CAD exhibited increased relative abundances of taxa such as Prevotella, Clostridia_UCG_014, UCG_010, and other pro-inflammatory genera, whereas women microbiota was comparatively enriched in Barnesiella, Bifidobacteriales, and other potentially beneficial taxa. Parallel differences emerged in microbial metabolite profiles: men demonstrated elevated plasma levels of TMAO and IS, both associated with heightened cardiovascular risk and disease burden. Conversely, women with CAD had higher circulating levels of secondary bile acids and lower TMAO concentrations.

CONCLUSION: Preliminary studies suggest sex-related differences in gut microbiota composition and metabolite profiles in CAD patients. Integrating mechanistic links from microbial metabolism, genetics, epigenetics, and hormones supports a potential role of the microbiota in sex-dependent disease pathways. Current evidence is limited and mostly observational; well-designed studies are needed to clarify mechanisms, clinical relevance of sex-specific microbiome signatures and specifically assess whether these sex-specific microbial and metabolic differences influence CAD progression and outcomes.}, } @article {pmid41618766, year = {2026}, author = {Yan, Y and Li, F and Huang, T and Cheng, Y and Liao, Y and Liu, H}, title = {Intraocular infection of Moraxella nonliquefaciens accompanied by secondary angle-closure glaucoma: A case report.}, journal = {The Journal of international medical research}, volume = {54}, number = {1}, pages = {3000605251411736}, pmid = {41618766}, issn = {1473-2300}, mesh = {Humans ; Male ; Anti-Bacterial Agents/therapeutic use ; *Endophthalmitis/microbiology/complications ; *Eye Infections, Bacterial/microbiology/complications ; *Glaucoma, Angle-Closure/microbiology/etiology/diagnosis ; *Moraxella/isolation & purification ; *Moraxellaceae Infections/microbiology/complications/drug therapy/diagnosis ; Trabeculectomy/adverse effects ; Vancomycin/therapeutic use/administration & dosage ; Vitrectomy ; Middle Aged ; }, abstract = {Infectious endophthalmitis after ocular surgery is a rare complication that can result in severe vision loss. Moraxella nonliquefaciens is an opportunistic pathogen that rarely causes ocular infections. We report a rare case of Moraxella nonliquefaciens endophthalmitis complicated by secondary angle-closure glaucoma occurring years after trabeculectomy and cataract surgery. Cycloplegia resulted in deepening of the anterior chamber and opening of the angles. Metagenomic next-generation sequencing of the aqueous humor identified Moraxella nonliquefaciens. Following multiple intravitreal vancomycin injections and vitrectomy with posterior capsulectomy, direct communication between the anterior chamber and the vitreous cavity was established, leading to resolution of the condition. The patient's visual acuity was fully restored. We hypothesize that persistent infection with Moraxella nonliquefaciens may damage the lens zonules, resulting in zonular laxity and weakness; however, this represents only one possible mechanistic explanation and may play a secondary role in the development of secondary angle-closure glaucoma. Ophthalmologists should be aware that patients with Moraxella nonliquefaciens endophthalmitis may be at risk of zonular laxity and secondary angle-closure glaucoma, particularly years after trabeculectomy and cataract surgery. Prompt recognition and intervention may be vision-saving.}, } @article {pmid41618858, year = {2026}, author = {Yang, T and Gao, Z and Huang, H and Zhang, C and Tang, Y and Qu, Q and Li, H and Ke, J and Chen, Z and Feng, M and Zhou, H and Shu, Y and Yuan, W}, title = {Gut-Metabolome-Proteome Interactions in Age-Related Hearing Loss: Insights from Fecal Microbiota Transplantation and Multi-Omics Analyses.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {18}, pages = {e14269}, pmid = {41618858}, issn = {2198-3844}, support = {81873702//National Natural Science Foundation of China/ ; 81470694//National Natural Science Foundation of China/ ; 82225014//National Natural Science Foundation of China/ ; 82171114//National Natural Science Foundation of China/ ; 2024NF008//National Clinical Research Center for Otolaryngologic Diseases/ ; CSTB2023TIAD-KPX0059//Chongqing Technology Innovation and Application Development Special Project/ ; 2022DBXM006//Major Programs of Chongqing Science and Health Union/ ; cstc2022ycjh-bgzxm0126//Chongqing Talent Project/ ; CSTB2022NSCQ-MSX0553//Chongqing Natural Science Foundation/ ; }, mesh = {Animals ; Mice ; Multiomics ; *Gastrointestinal Microbiome/physiology ; *Fecal Microbiota Transplantation/methods ; *Metabolome/physiology/genetics ; *Proteome/metabolism ; *Aging ; Disease Models, Animal ; Proteomics/methods ; Male ; *Hearing Loss/metabolism ; Metabolomics ; *Presbycusis/metabolism ; }, abstract = {Age-related hearing loss (ARHL) is a prevalent sensory disorder lacking disease-modifying interventions. The biological drivers, particularly the contribution of the gut microbiota and gut-inner ear crosstalk, remain poorly defined. Here, we utilize germ-free (GF) mice and fecal microbiota transplantation (FMT) to isolate microbiota-dependent effects on ARHL progression. Through integrated metagenomic, metabolomic, and proteomic profiling, we map molecular signatures of auditory aging and uncover functional gut-inner ear network, prioritizing 5-hydroxytryptophan (5-HTP) as a key intermediate metabolite within this network. Furthermore, in an aging-like House Ear Institute-Organ of Corti 1 (HEI-OC1) model, 5-HTP exhibits protective effects, potentially mediated through the PI3K/Akt-antioxidant signaling axis. Collectively, this study provides a valuable multi-omics resource and highlights microbiota-derived metabolic regulation as a promising avenue for biomarker discovery and therapeutic development in ARHL.}, } @article {pmid41619209, year = {2026}, author = {Tang, R and Wang, J and Wang, X and Zeng, M and Gao, W and Yang, K and Xu, L and Li, Y and Zhou, C and Yue, B and Fan, Z and Song, Z}, title = {Large-scale metagenomic analysis reveals host genetics shapes microbiomes in wild freshwater fish gut and skin.}, journal = {Cell reports}, volume = {45}, number = {2}, pages = {116930}, doi = {10.1016/j.celrep.2026.116930}, pmid = {41619209}, issn = {2211-1247}, mesh = {*Metagenomics ; *Microbiota/genetics ; *Fishes/classification/microbiology ; Fresh Water ; *Gastrointestinal Tract/microbiology ; *Skin/microbiology ; Gastrointestinal Microbiome/genetics ; Phylogeny ; Animals ; *Host Microbial Interactions ; Cyprinidae/classification/microbiology ; Symbiosis ; Aquaculture/methods ; Probiotics ; }, abstract = {Wild freshwater fish microbiomes remain underexplored despite their ecological and economic importance. Through metagenomic sequencing of 903 gut/skin samples from 121 species in southwest China, we constructed the Wild Freshwater Fish Microbiome Catalog, comprising 705 metagenome-assembled genomes and 3,271 viral operational taxonomic units. Host phylogeny dominates microbial community variation, explaining 48.2% (skin) and 22.28% (gut) of the variation. Significant phylosymbiosis occurs in wild freshwater fish, particularly Cyprinidae, with a stronger skin than gut signal. Deterministic selection underpins phylosymbiosis via host-specific ecological filtering. Lifestyle factors (diet, living water layer) and geographical location also impact microbial communities. Notably, wild freshwater fish microbiota harbor a complete set of vitamin B12de novo biosynthesis genes, with Cetobacterium as a keystone genus with probiotic potential. Our work expands gut and skin microbial genome resources, reveals host-microbe coevolution in freshwater fishes, and provides probiotic resources for aquaculture.}, } @article {pmid41619244, year = {2025}, author = {Zahanuddin, A and Rahim, FF and Lau, YL and Mokhtar, AS}, title = {Genetic diversity, microbiome composition and socio-sanitary predictors of head lice (Pediculus humanus capitis) among disadvantaged children in Klang Valley, Malaysia.}, journal = {Tropical biomedicine}, volume = {42}, number = {4}, pages = {435-445}, doi = {10.47665/tb.42.4.010}, pmid = {41619244}, issn = {2521-9855}, mesh = {Humans ; Malaysia/epidemiology ; *Pediculus/genetics/microbiology ; Animals ; *Genetic Variation ; *Lice Infestations/epidemiology/parasitology ; Female ; Male ; Child ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Child, Preschool ; *Bacteria/classification/genetics/isolation & purification ; Vulnerable Populations ; }, abstract = {Pediculosis capitis remains a neglected public health issue in Malaysia, particularly among disadvantaged children. While the genetic diversity of head lice is well studied, their associated microbiome and links to socio-sanitary conditions remain unclear. This study examined 266 children from ten children's establishments in Klang Valley and Greater Kuala Lumpur, of whom 89 (33.46%) were positive for pediculosis capitis. Cytochrome c oxidase subunit I (COI) barcoding identified two clades: A (36%) and C (64%). 16S rRNA metagenomic profiling of pooled samples revealed higher microbial diversity in Clade C compared to Clade A, with opportunistic bacteria, including Propionibacterium acnes, Streptococcus spp., Bacteroides fragilis, and Staphylococcus aureus being detected. Logistic regression identified age, head lice awareness, and eating with hands as significant predictors of infection. These findings demonstrate that head lice not only cluster genetically but also may harbour clade-dependent microbiomes, with potential health implications. The integration of genetic diversity, microbial variation, and socio-sanitary data highlights the multifactorial risks of pediculosis capitis in vulnerable populations, underscoring the importance of combined ectoparasite control and hygiene interventions.}, } @article {pmid41619271, year = {2026}, author = {Dissanayaka, DMS and Jayasinghe, TN and Sohrabi, HR and Rainey-Smith, SR and Taddei, K and Masters, CL and Martins, RN and Fernando, WMADB}, title = {Functional Pathways of the Gut Microbiome Associated with SCFA Profiles in Preclinical Alzheimer's Disease.}, journal = {Aging and disease}, volume = {}, number = {}, pages = {}, doi = {10.14336/AD.2025.1539}, pmid = {41619271}, issn = {2152-5250}, abstract = {Functional activities of the gut microbiome, particularly those contributing to short-chain fatty acid (SCFA) metabolism, play a central role in host-microbe interactions and are linked to neuroinflammatory mechanisms underlying Alzheimer's disease (AD). How microbial metabolic functions relate to SCFA concentrations and cerebral amyloid-β (Aβ) burden during the preclinical stage of AD remains poorly understood. In this study, faecal metagenomes from 87 cognitively unimpaired adults were profiled using HUMAnN3 to generate MetaCyc pathway abundance data, normalised and filtered to retain pathways present in at least 30% of participants. A keyword-based search identified 362 SCFA-related pathways spanning acetate, propionate, butyrate, isobutyrate, valerate and isovalerate metabolism. Associations between microbial functions, SCFA concentrations and Aβ status were evaluated using Spearman correlations, Kruskal-Wallis tests across SCFA quartiles, and multivariable linear regression with false discovery rate correction, supported by canonical correspondence analysis and network modelling. A total of 38 significant SCFA pathway correlations were identified. Acetate, butyrate and total SCFA levels showed positive associations with biosynthetic pathways, including L-arginine biosynthesis II, peptidoglycan biosynthesis and flavin biosynthesis, whereas fermentative pathways such as pyruvate fermentation to acetone and lysine fermentation to butanoate were negatively correlated. Butyrate quartiles demonstrated dose-dependent increases in biosynthetic functions and declines in fermentative routes. Canonical Correspondence Analysis (CCA) confirmed a significant multivariate association, and network analysis revealed enhanced fermentative and methanogenic connectivity among Aβ High participants. These findings indicate that amyloid burden is associated with a shift from anabolic to fermentative microbial metabolism and may inform future studies examining potential mechanistic links in preclinical AD.}, } @article {pmid41619464, year = {2026}, author = {Umunnawuike, C and Abutu, D and Nwaichi, PI and Nyah, F and Agi, A}, title = {Thermophilic biohydrogen production from reservoir residual hydrocarbons using palm oil mill effluent-derived microbial consortia.}, journal = {The Science of the total environment}, volume = {1016}, number = {}, pages = {181482}, doi = {10.1016/j.scitotenv.2026.181482}, pmid = {41619464}, issn = {1879-1026}, mesh = {Palm Oil ; *Hydrogen/metabolism ; *Microbial Consortia ; Oil and Gas Fields ; *Hydrocarbons/metabolism ; Bioreactors ; *Petroleum/metabolism ; *Waste Disposal, Fluid/methods ; *Biofuels ; Biodegradation, Environmental ; Plant Oils ; }, abstract = {Residual crude oil remaining in depleted reservoirs represents a largely untapped carbon source for biological hydrogen generation. Previous studies have relied on indigenous bacteria present in oil reservoirs but reported low hydrogen yields, as not all reservoir microorganisms are hydrogen-producing. Therefore, in this study, external mixed culture bacterial consortia obtained from palm oil mill effluent (POME) were used to degrade crude oil for hydrogen production. Morphological changes in microbial communities were assessed using field emission scanning electron microscopy. Metagenomic profiling was conducted to identify the dominant microbial taxa capable of producing biohydrogen. Thereafter, a high-temperature and high-pressure (800 °C/30 MPa) stainless-steel bioreactor containing crude oil was inoculated with mixed culture consortia to simulate an oilfield reservoir for hydrogen production. Box-Behnken design was applied to systematically examine the effects of exposure time (6-90 h), crude oil volume (10-40 mL), and temperature (35-70 °C) on continuous hydrogen production. Statistical analysis of variance was used to evaluate model parameters. Heat pretreatment selectively enriched hydrogenogenic spore-formers (Clostridium and Bacillus), resulting in a ~ 4-fold increase (97.40 ± 0.02 mL/L) in hydrogen yield compared to 25.68 ± 0.04 mL/L POME for untreated sludge. In the presence of crude oil, the optimum hydrogen production was 152.50 ± 0.01 mL/L at 50 °C, compared to 125.45 ± 0.03 mL/L and 29.95 ± 0.01 mL/L crude oil at 35 °C and 70 °C, respectively. Predicted hydrogen production, with R[2] value of 97.4% close to unity, indicates that the model was highly consistent with the experimental results, with high precision and reliability. Thermodynamic analysis shows negative Gibbs free energy changes of -122 to -236 kJ/mol, demonstrating that hydrocarbon-to‑hydrogen conversion was energetically favorable and feasible across all tested temperatures. Overall, the experimental, statistical, and thermodynamic analyses establish the technical and energetic feasibility of microbial enhanced hydrogen recovery in depleted oil reservoirs.}, } @article {pmid41619482, year = {2026}, author = {Wang, M and Ye, X and Hsu, CY and Fugate, H and Zhang, X and Adhikari, PA and Fan, P and Elliott, K and Macklin, K and Zhang, L}, title = {Application of culturomics to explore the cultivable microbiota and enable targeted bacterial isolation from the ceca of broiler chickens.}, journal = {Poultry science}, volume = {105}, number = {4}, pages = {106527}, pmid = {41619482}, issn = {1525-3171}, mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Bacteria/isolation & purification/classification/genetics ; RNA, Ribosomal, 16S/analysis ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; RNA, Bacterial/analysis ; }, abstract = {Metagenomic analyses have significantly advanced our understanding of microbial composition in the poultry gut. However, many microbes identified through metagenomic studies remain uncultured, largely due to the lack of understanding of their cultivation conditions, which hinders efforts to explore their functional roles in gut health and metabolism. In this study, we performed culturomics, a culture-dependent approach that combines diverse culture conditions with high-throughput 16S rRNA gene sequencing, to comprehensively assess the cultivability of chicken cecal microbiota and provide guidance for isolating target species of interest. Microbial profiling was performed using both culture-dependent (CD) and culture-independent (CI) approaches. For CI, genomic DNA (gDNA) was directly extracted from six broiler chicken cecal samples and subjected to full-length 16S rRNA gene sequencing. For CD, the same samples were cultured under 28 conditions, yielding 161 colony mixtures for sequencing. Based on diversity profiles of the colony mixtures, 10 conditions were selected for single-colony isolation and analysis. Results showed that CD and CI approaches identified 350 and 502 bacterial species, respectively, with 160 species detected by both methods. The dominant species recovered by the CD approach,including Escherichia coli, Proteus mirabilis, Limosilactobacillus reuteri, Enterococcus faecalis, and Ligilactobacillus salivarius, were detected at much lower abundances in the CI analysis, highlighting the capacity of culturomics to enrich and recover minority taxa that are often poorly detected by CI apparoach. Cultivation profiling showed that MRS selectively enriched Limosilactobacillus and Ligilactobacillus as well as Lactobacillus, whereas CNAB and MSA enriched Enterococcus and Bacillus, respectively. Community diversity and structure were significantly influenced by culture conditions (P < 0.01), with medium as the primary factor and air condition as a secondary factor. Subsequent single-colony analysis from 10 selected culture conditions identified 150 single-species isolates belonging to 14 distinct bacterial species. This study provides foundational insight into the cultivability of chicken cecal microbiota, facilitating future research to isolate specific strains and characterize their roles in poultry health and nutrition.}, } @article {pmid41619490, year = {2026}, author = {Deng, S and Zheng, X and Chu, H and Hong, L and Zhang, J and Yang, H and Gu, L and Pu, L}, title = {Antibiotic-free Wenchang chickens may promote blood levels of B vitamins by modulating the gut microbiota: An integrated analysis of cecal content metagenomics and serum metabolomics.}, journal = {Poultry science}, volume = {105}, number = {4}, pages = {106506}, pmid = {41619490}, issn = {1525-3171}, mesh = {Animals ; *Chickens/microbiology/blood/genetics ; Cecum/microbiology ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Metabolome ; Metabolomics ; Diet/veterinary ; Male ; Anti-Bacterial Agents ; }, abstract = {Through the selective breeding of superior strains, livestock and poultry can achieve enhanced disease resistance and production performance, thereby improving farming efficiency and increasing chicken meat yield. This study analyzed the expression of gut health-related genes, cecal microbiota, and untargeted serum metabolomics in Wenchang chickens from the NS strain (Normal strain) and the AFS strain (Antibiotic-free strain), and explored the relationships between their cecal microbiota and serum metabolites. Our results show that in the ileum, antioxidant-related indicators T-AOC (P < 0.05), T-SOD (P < 0.05), and GSH-PX (P < 0.05) were significantly higher in the AFS strain than in the NS strain, while MDA (P < 0.05) was significantly lower in the AFS strain than in the NS strain. The mRNA expression level of RORγt/FoxP3, which is related to immune regulation, was significantly lower in the AFS strain than in the NS strain (P < 0.05). The differential microorganisms in the cecum primarily included Muribaculum, Cryptobacteroides, Blautia, Enterocloster, Lachnoclostridium, Hydrogenoanaerobacterium, Ruminococcus, Subdoligranulum, Clostridioides, and Evtepia. The main differential metabolites in serum included folinic acid, biotin, lysophosphatidic acid (LPA), 3-hydroxy-3-methylbutanoic acid, 3-hydroxybutyric acid, and others. The differential metabolites are primarily enriched in the following metabolic pathways: gap junction, glycolipid metabolism, and fatty acid biosynthesis. In addition, the Pearson correlation analysis between the gut microbiota and serum metabolites showed that Blautia was positively correlated with folinic acid (P < 0.05) and biotin (P < 0.05); Lachnoclostridium was positively correlated with biotin (P < 0.01); and Ruminococcus was positively correlated with 3-hydroxybutyric acid (P < 0.05). This study mainly elucidates the metabolic characteristics of the antibiotic-free Wenchang chicken strain by analyzing gut microbiota and serum metabolites.}, } @article {pmid41619541, year = {2026}, author = {Shayo, MJ and Kuchaka, D and Beti, M and Kimu, P and Wadugu, B and Jensen, EEB and Kumburu, H and Kazyoba, P and Ali, M and , and Clausen, PTLC and Muro, F and Mmbaga, BT and Alifrangis, M and Aarestrup, FM and Sonda, T}, title = {Genomic diversity of human adenoviruses in Tanzanian children under five: Insights into F40, F41, B, and rare A18 genotypes.}, journal = {Virology}, volume = {617}, number = {}, pages = {110813}, doi = {10.1016/j.virol.2026.110813}, pmid = {41619541}, issn = {1096-0341}, mesh = {Humans ; Tanzania/epidemiology ; *Adenoviruses, Human/genetics/classification/isolation & purification ; *Genetic Variation ; *Genome, Viral ; *Adenovirus Infections, Human/virology/epidemiology ; *Genotype ; Phylogeny ; Infant ; Child, Preschool ; Diarrhea/virology/epidemiology ; Female ; }, abstract = {Human adenoviruses (HAdVs) are important pathogens that are associated with a wide array of clinical diseases, particularly in the pediatric population. Despite numerous reports of HAdV infections in Tanzania, there are currently no whole genome sequences from this region available in global public databases. This gap presents challenges to our efforts to understand their dissemination and evolution over time. This study employed nanopore-based metagenomic sequencing to detect and sequence the whole genomes of HAdV strains in Tanzanian infants with diarrhea. We present the first whole genome of HAdV-A18 from Africa, representing only the third worldwide. Additionally, it includes the first complete genomes of HAdV-F40, HAdV-F41, and HAdV-B3 obtained from Tanzania. In addition, this study provides information on the enteric adenovirus lineages circulating in Tanzania. These findings provide crucial genomic insights into the diversity of viruses in sub-Saharan Africa and underscore the importance of genomic surveillance to deepen our understanding of adenovirus transmission and evolution.}, } @article {pmid41619556, year = {2026}, author = {Xiao, Y and Ke, C and Wang, D and Chen, N and Chen, G and Qu, L and Liu, Y}, title = {Atractyloside-A ameliorates spleen deficiency diarrhea in mice via modulating Lactobacillus johnsonii-butyric acid-GPR43 axis and NF-κB -NLRP3 signaling pathway.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {152}, number = {}, pages = {157875}, doi = {10.1016/j.phymed.2026.157875}, pmid = {41619556}, issn = {1618-095X}, mesh = {Animals ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; *Receptors, G-Protein-Coupled/metabolism ; Signal Transduction/drug effects ; NF-kappa B/metabolism ; *Diarrhea/drug therapy/microbiology/metabolism ; Mice ; *Lactobacillus johnsonii/drug effects ; Male ; Butyric Acid/metabolism ; Gastrointestinal Microbiome/drug effects ; Spleen ; *Sesquiterpenes/pharmacology ; Disease Models, Animal ; Fatty Acids, Volatile/metabolism ; Mice, Inbred C57BL ; *Lactones/pharmacology ; Intestinal Barrier Function ; }, abstract = {BACKGROUND: Spleen deficiency diarrhea (SDD) is regarded as a common gastrointestinal dysfunction in Traditional Chinese Medicine (TCM), which may lead to intestinal barrier damage and trigger intestinal inflammation. Previous studies have shown that Atractylenolide-A (AA) can effectively treat SDD by regulating intestinal flora. However, it remains uncertain whether AA can increase the levels of short-chain fatty acids (SCFAs) by restoring intestinal microbiota, thereby activating specific signaling pathways to regulate target protein and subsequently alleviate issues related to intestinal barrier function and inflammation.

PURPOSE: This study focused on examining the function of the signaling pathway involving microbiota, SCFAs, and G protein-coupled receptors (GPRs) in the anti-SDD effects of AA.

METHODS: The effects of AA on the Senna (SE) - induced SDD mouse model were assessed through various methods, including diarrhea scoring, H&E staining, qRT-PCR, and ELISA analysis. Subsequently, targeted metabolomics was employed to pinpoint essential metabolites that influence the intestinal microenvironment, while western blotting was utilized to measure the expression of GPRs and the NLRP3 inflammasome. Additionally, experiments involving dietary supplementation with SCFAs and AAV-shGPR43 were performed to determine whether the pharmacological effects of AA operate through SCFAs and rely on GPR43. Key bacterial species that play a role in AA's modulation of SCFAs' pharmacological effects were identified through metagenomic sequencing and single-strain experiments.

RESULTS: The findings of this research revealed that AA is capable of significantly reducing the intestinal inflammatory response, reversing damage to mucin synthesis, and alleviating the pathological symptoms linked to SDD. Furthermore, the use of Lactobacillus johnsonii, sodium butyrate (NaB), and SCFAs individually can lead to notable enhancements in various phenotypes related to SDD. In terms of mechanism, AA achieves its anti-SDD effects by elevating the levels of Lactobacillus johnsonii, facilitating the concentration of butyric acid, boosting GPR43 expression, and modulating the TLR4/NF-κB signaling pathway, which in turn inhibits the assembly of the NLRP3 inflammasome. Nonetheless, following the injection of AAV-shGPR43, the advantageous effects of both AA and NaB were negated, underscoring the significance of this target.

CONCLUSIONS: Gut microbiota-SCFAs-GPRs axis and NF-κB-NLRP3 pathway involve in the alleviation of diarrhea and inflammation in SDD mice intervened with AA, AA promotes the production of butyrate by influencing Lactobacillus johnsonii, stimulates GPR43, and suppresses the formation of the NLRP3 inflammasome via the regulation of the TLR4/NF-κB signaling pathway, which subsequently improves SDD in mice.}, } @article {pmid41619830, year = {2026}, author = {Zheng, C and Zhang, Y and Wang, Y and Sun, Y and Wei, F and Zhang, Y and Ma, Y and Cai, M}, title = {Two-case cluster of rapidly progressive influenza B and Staphylococcus aureus pneumonia with one death.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {165}, number = {}, pages = {108442}, doi = {10.1016/j.ijid.2026.108442}, pmid = {41619830}, issn = {1878-3511}, mesh = {Humans ; *Influenza B virus/genetics/isolation & purification ; *Influenza, Human/complications/virology/drug therapy/diagnosis ; *Coinfection/microbiology/virology ; *Staphylococcus aureus/genetics/isolation & purification ; Leukocidins/genetics ; Exotoxins/genetics ; *Pneumonia, Staphylococcal/microbiology/drug therapy/complications/diagnosis ; Male ; Bacterial Toxins/genetics ; Fatal Outcome ; *Pneumonia, Necrotizing/microbiology ; Occupational Exposure ; Middle Aged ; Retrospective Studies ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {OBJECTIVES: To report a cluster of two epidemiologically linked construction workers with fulminant necrotizing pneumonia associated with co-infection by Panton-Valentine leukocidin (PVL)-positive methicillin-susceptible Staphylococcus aureus (MSSA) and influenza B virus.

METHODS: Clinical characteristics, imaging findings, and microbiological results were retrospectively reviewed. Metagenomic next-generation sequencing (mNGS) was performed on sputum and bronchoalveolar lavage fluid after conventional diagnostic tests failed to identify the causative pathogens.

RESULTS: Following shared occupational exposure, both patients developed severe pneumonia. One patient experienced rapid progression and died. For the second patient, mNGS successfully identified co-infection with PVL-positive sequence type 22 MSSA and influenza B virus, prompting a timely shift to targeted antimicrobial therapy that led to survival after prolonged intensive care.

CONCLUSION: This report demonstrates the extreme virulence of PVL-positive MSSA-influenza co-infection, highlights the diagnostic value of mNGS in severe treatment-refractory pneumonia, and emphasizes the need for effective respiratory protection in high-risk occupational environments.}, } @article {pmid41619833, year = {2026}, author = {Tran, LNB and Zhuo, R and Singha, M and Sekhon, H and Yang, S and Fishbein, GA and Tymchuk, C and Allyn, PR}, title = {First reported case of Capnocytophaga cynodegmi infective endocarditis: A diagnostic odyssey.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {164}, number = {}, pages = {108446}, doi = {10.1016/j.ijid.2026.108446}, pmid = {41619833}, issn = {1878-3511}, mesh = {Humans ; Male ; *Capnocytophaga/isolation & purification/genetics ; Adult ; *Gram-Negative Bacterial Infections/diagnosis/microbiology/drug therapy ; *Endocarditis, Bacterial/diagnosis/microbiology/drug therapy ; Aortic Valve/abnormalities/microbiology/surgery ; Animals ; High-Throughput Nucleotide Sequencing ; Bicuspid Aortic Valve Disease ; Anti-Bacterial Agents/therapeutic use ; *Endocarditis/microbiology/diagnosis ; }, abstract = {Capnocytophaga cynodegmi, a commensal of canine and feline oral flora, is rarely implicated in human infections, with most cases limited to localized soft tissue infections. We present the first case of C. cynodegmi-associated infective endocarditis (IE) in a 39-year-old man with bicuspid aortic valve and alcohol use disorder. The patient presented with sepsis, aortic valve vegetations, and systemic complications, including heart failure and shock liver. Despite negative blood and valve cultures, metagenomic sequencing of plasma (Karius test) initially detected Capnocytophaga canimorsus, while targeted Next-Generation Sequencing (NGS) of explanted valve tissue confirmed C. cynodegmi (100% match). The patient underwent valve replacement and completed a 6-week course of ampicillin-sulbactam with clinical recovery. This case underscores the diagnostic challenges of fastidious pathogens and demonstrates the potential of C. cynodegmi to cause life-threatening IE. It highlights the necessity of advanced molecular diagnostics, such as NGS, in atypical cases of IE. Clinicians should consider zoonotic Capnocytophaga spp. in culture-negative IE, particularly in high-risk patients with animal exposure or valvular abnormalities.}, } @article {pmid41619990, year = {2026}, author = {Ni, H and Hou, QY and Xu, C and Leng, X and Li, XM and Qin, Y and Liu, S and Yang, MT and Tang, LY and Sun, YZ and Zhao, Q and Ni, HB and Zhang, XX and Jiang, J and Yang, LH and Ma, H}, title = {Antimicrobial resistance and genomic characterization of Escherichia coli isolated from mink in northern China.}, journal = {Microbial pathogenesis}, volume = {213}, number = {}, pages = {108328}, doi = {10.1016/j.micpath.2026.108328}, pmid = {41619990}, issn = {1096-1208}, mesh = {Animals ; *Escherichia coli/genetics/drug effects/isolation & purification ; China ; *Anti-Bacterial Agents/pharmacology ; *Mink/microbiology ; Feces/microbiology ; Microbial Sensitivity Tests ; *Drug Resistance, Multiple, Bacterial/genetics ; Virulence Factors/genetics ; *Escherichia coli Infections/veterinary/microbiology ; Genome, Bacterial ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Escherichia coli (E. coli) is one of the most common commensal bacteria in the intestinal tract of humans and animals. It serves as a major reservoir of antimicrobial resistance genes and may facilitate their horizontal transfer among different hosts. In this study, 212 fecal samples were collected from mink across four northern provinces of China, a total of 110 E. coli isolates were recovered (isolation rate, 51.89 %). Preliminary antimicrobial screening was conducted using four clinically critical antibiotics, including ceftazidime (CAZ), polymyxin B (PMB), meropenem (MEM), and tigecycline (TGC), with CAZ resistance being the most prevalent, followed by PMB, MEM, and TGC. Further antimicrobial susceptibility testing against ten commonly used antibiotics in 49 representative isolates revealed universal multidrug resistance (MDR), including 100 % resistance to imipenem, tetracycline, enrofloxacin, florfenicol, and sulfamethoxazole. Genetic screening identified multiple resistance genes such as aac(3')-IIa, blaCTX-M, tet(A), and mcr-1. Conjugation assays demonstrated that CAZ resistance was the most transferable. Virulence profiling revealed a low prevalence of classical pathogenic virulence factors, with only six virulence gene types detected, consistent with the results of Galleria mellonella infection assays. Whole-genome sequencing of 41 representative isolates revealed 87 unique antibiotic resistance genes (ARGs) types spanning 14 antibiotic classes including alinically important determinants such as blaCTX-M, tet, and mcr, and 71 unique virulence genes assigned to 65 functions. Metagenomic analysis further identified diverse ARGs within the mink gut microbiota, with 21 shared between whole-genome and metagenomic sequencing. Correlation analysis suggested co-occurrence patterns among ARGs, virulence factor genes (VFGs), and mobile genetic elements (MGEs), particularly between ARGs and MGEs. Overall, mink-derived E. coli exhibited extensive MDR but limited classical pathogenic virulence, and the mink gut microbiota may represent an important reservoir and transmission hub for resistance genes in intensive farming ecosystems.}, } @article {pmid41620043, year = {2026}, author = {Chang, XL and Xing, BS and Qin, Y and Xie, J and Li, ZB and Wang, XC and Chen, R and Li, YY}, title = {Sustained performance and microbial succession in novel artificial rumen system coupling dynamic membrane with methanogenic granules for acid absorption.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134119}, doi = {10.1016/j.biortech.2026.134119}, pmid = {41620043}, issn = {1873-2976}, mesh = {*Rumen/microbiology ; Animals ; *Methane/metabolism/biosynthesis ; Fatty Acids, Volatile/metabolism ; *Membranes, Artificial ; *Bioreactors/microbiology ; Fermentation ; Lignin/metabolism ; Biomass ; *Acids/metabolism ; Bacteria/metabolism ; Cellulose ; }, abstract = {Artificial rumen systems promise for converting lignocellulosic biomass into renewable products but face challenges in long-term operation. This study developed a novel artificial rumen system combined fermentation with acid absorption using methanogenic granules and a dynamic membrane. Over 480 days, volatile fatty acids (VFAs) were effectively separated by the dynamic membrane and immediately absorbed by granules, simulating natural ruminant acid absorption. Despite increasing the organic loading rate from 3.27 to 8.18 g-VS/L/day, stable VFA yields of 0.21-0.24 g-COD/g-VS were maintained. After 440 days, removal efficiencies for cellulose, hemicellulose, and lignin reached 62.7 %, 52.1 %, and 40.7 %, respectively. The acid absorption unit efficiently converted VFAs into biomethane (302-304 mL/g COD), showing high bioenergy potential. Metagenomic analysis confirmed key rumen microbes (Firmicutes, Bacteroidetes) were dominant, with enrichment of low-abundance species like Prevotella and Solobacterium that secreted lignocellulose-degrading enzymes. The system enables long-term biomass conversion and supports future high-load artificial rumen engineering.}, } @article {pmid41620049, year = {2026}, author = {Xia, Q and Li, J and Li, Q and Hu, Z and Wu, H and Xie, H and Lu, J and Liu, H and Zhang, J}, title = {Immobile iron-rich particles enhance simultaneous nitrogen removal and phosphorus retention in treatment wetlands.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134129}, doi = {10.1016/j.biortech.2026.134129}, pmid = {41620049}, issn = {1873-2976}, mesh = {*Wetlands ; *Nitrogen/analysis/isolation & purification ; *Phosphorus/analysis ; *Eutrophication ; Iron/chemistry ; Bacteria/classification/genetics/metabolism ; Environmental Microbiology ; Phylogeny ; *Conservation of Natural Resources/methods ; }, abstract = {Eutrophication control requires cost-effective and sustainable technologies capable of simultaneously removing nitrogen and phosphorus from wastewater treatment plant (WWTP) effluents. Widely used post-treatment systems, treatment wetlands (TWs) typically exhibit limited nutrient removal because of imbalances in electron supply and demand, and rapid saturation of substrate adsorption capacity. In this study, immobile iron-rich particles (IIRPs) were introduced into TWs via a drainage-injection strategy to enhance nutrient removal from municipal WWTP effluent. Following the start-up phase, the IIRP-amended TWs consistently achieved effluent concentrations that met the target quasi-Class IV surface water quality standards (TN ≤ 10 mg L[-1]; TP ≤ 0.3 mg L[-1]) for 300 days of continuous operation. The enhanced NH4[+]-N and TN removal with iron-rich particles amendment could not be attributed to nitrification or anammox, as evidenced using qPCR, metagenomic binning, and removal profiles. Instead, Fe-N redox-coupling processes, including Fe(III) reduction-driven and Fe(II) oxidation-driven nitrogen-removal pathways, contributed to enhanced nitrogen removal. The IIRPs amendment increased the equilibrium phosphorus adsorption capacity of wetland substrate by threefold, and the improved phosphorus retention was attributed to Fe-P interactions. These findings reveal a coupled Fe-N-P mechanism that enables efficient and stable nutrient removal and provide a mechanistic foundation for developing low-carbon, sustainable strategies to upgrade existing TWs for advanced wastewater polishing.}, } @article {pmid41620544, year = {2026}, author = {Kirsche, L and Leary, P and Blaser, MJ and Scharl, M and Negussie, A and Müller, A}, title = {Gut microbial signatures expose the westernized lifestyle of urban Ethiopian children.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41620544}, issn = {2399-3642}, support = {310030_192490//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {Humans ; Child, Preschool ; Ethiopia ; *Urban Population ; *Gastrointestinal Microbiome/genetics ; Female ; Feces/microbiology ; *Life Style ; Male ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics ; Metagenomics ; }, abstract = {Gut microbiota composition has been extensively studied in European and North American pediatric cohorts, as well as in rural African children. Much less attention has been paid to urban African children, whose families have transitioned to a "Western" lifestyle characterized by smaller family sizes, access to perinatal care including C-section delivery, non-traditional food sources and widespread availability of antibiotics. We analyzed fecal samples from ~200 Ethiopian children aged 2-5 years from Adama, Ethiopia, using 16S rRNA gene sequencing and shotgun metagenomics. We found that well-studied factors such as delivery mode, breastfeeding and family size have only minor effects on α-diversity, whereas household crowding (single vs. multiple rooms) and consumption of the traditional fermented cereal Eragrostis tef predict higher α-diversity. Stunted growth and absence of Helicobacter pylori infection were additional factors associated with increased fecal microbial diversity. Metagenomic profiling revealed that rural African signature genera such as Segatella and Prevotella were largely absent; instead, urban Ethiopian children displayed a high Firmicutes/Bacteroidota ratio and enrichment of metabolic pathways linked to a westernized diet, resembling European rather than rural Ethiopian children. These results indicate that an urban westernized lifestyle alters gut microbiota composition, which may be partially offset by a traditional fermented diet.}, } @article {pmid41620643, year = {2026}, author = {Ratcliff, JS and Kumari, M and Varga-Weisz, P and O'Gorman, R}, title = {Socioeconomic position and the gut microbiota: a narrative synthesis of the association and recommendations.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2623356}, pmid = {41620643}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Socioeconomic Disparities in Health ; *Socioeconomic Factors ; Bacteria/classification/isolation & purification/genetics ; }, abstract = {Evidence suggests that socioeconomic position (SEP) may shape the gut microbiota (GM), representing a mechanism through which social and environmental factors may drive health inequalities, yet no systematic review has examined this association. In this narrative systematic review, we searched PubMed, Web of Science, and Scopus up to 30 November 2024 for observational studies examining associations between measures of SEP and GM diversity, composition, or function in participants of any age, ethnicity, or location. We identified 1,479 unique studies, of which 26 met the inclusion criteria for this review. Associations were observed between SEP indicators and GM features, including alpha (α) and beta (β) diversity, taxonomic composition, and functional pathways. Notably, socioeconomic patterns in α-diversity differed by context, with greater diversity observed in advantaged groups in high-income countries (HICs) but in disadvantaged groups in low- and middle-income countries (LMICs). Differences in β-diversity suggest that advantaged and disadvantaged groups have distinct GM profiles. Furthermore, considerable heterogeneity was evident across studies, particularly in sampling, sequencing, and analytical methods. Overall, socioeconomic-related differences in the GM are evident globally, highlighting the microbiota as a potential target for interventions aimed at reducing health disparities. Further research employing larger and more diverse cohorts, longitudinal designs, metagenomic sequencing approaches, and comprehensive measurement and adjustment of key covariates is needed to deepen understanding of this relationship.}, } @article {pmid41620752, year = {2026}, author = {Sharma, A and Küsel, K and Wegner, CE and Pérez-Carrascal, OM and Taubert, M}, title = {Two worlds beneath: Distinct microbial strategies of the rock-attached and planktonic subsurface biosphere.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41620752}, issn = {2049-2618}, support = {218627073//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Thüringer Ministerium für Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; }, mesh = {*Plankton/classification/genetics ; *Groundwater/microbiology ; Biofilms/growth & development ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Ecosystem ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Oxidation-Reduction ; Phylogeny ; Proteobacteria/genetics/classification/isolation & purification ; Carbonates ; }, abstract = {BACKGROUND: Microorganisms in groundwater ecosystems exist either as planktonic cells or as attached communities on aquifer rock surfaces. Attached cells outnumber planktonic ones by at least three orders of magnitude, suggesting a critical role in aquifer ecosystem function. However, particularly in consolidated carbonate aquifers, where research has predominantly focused on planktonic microbes, the metabolic potential and ecological roles of attached communities remain poorly understood.

RESULTS: To investigate the differences between attached and planktonic communities, we sampled the attached microbiome from passive samplers filled with crushed carbonate rock exposed to oxic and anoxic groundwater in the Hainich Critical Zone Exploratory and compared it to a previously published, extensive dataset of planktonic communities from the same aquifer ecosystem. Microbial lifestyle (attached vs. planktonic) explained more variance in community composition than redox conditions, prompting us to further investigate its role in shaping functional and activity profiles. Metagenomic analysis revealed a striking taxonomic and functional segregation: the 605 metagenome-assembled genomes (MAGs) from attached communities were dominated by Proteobacteria (358 MAGs) and were enriched in genes for biofilm formation, chemolithoautotrophy, and redox cycling (e.g., iron and sulfur metabolism). In contrast, the 891 MAGs from planktonic communities were dominated by Cand. Patescibacteria (464 MAGs) and Nitrospirota (60 MAGs) and showed lower functional versatility. Only a few genera were shared, and even closely related MAGs (> 90% average nucleotide identity) differed in assembly size and metabolic traits, demonstrating lifestyle-specific functional adaptation. Analysis of active replication indicated that the active fraction of the attached community was primarily represented by the most abundant MAGs. Planktonic communities featured a higher fraction of active MAGs compared to attached communities, but overall with lower relative abundances.

CONCLUSIONS: The high abundance, metabolic specialization, and carbon fixation potential of attached microbes suggest that they are key drivers of subsurface biogeochemical processes. Carbonate aquifers may act as much larger inorganic carbon sinks than previously estimated based on CO2 fixation rates of the planktonic communities alone. Our findings underscore the need to incorporate attached microbial communities into models of subsurface ecosystem function. Video Abstract.}, } @article {pmid41620987, year = {2026}, author = {Tian, H and Liu, J and Li, L and Ge, J}, title = {From Interface to Cell: The Complex Interaction and Transfer Process Coupling Mechanism between Microplastics and Antibiotic Resistance Genes.}, journal = {Environmental science & technology}, volume = {60}, number = {6}, pages = {5039-5052}, doi = {10.1021/acs.est.5c11841}, pmid = {41620987}, issn = {1520-5851}, mesh = {*Microplastics ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Microplastic-phase interfaces (MPPIs) were established as critical vectors for accelerating antibiotic resistance gene (ARG) dissemination. Through integrated anaerobic/aerobic wastewater treatment system experiments combined with physicochemical characterization, metagenomic sequencing, and molecular dynamics simulations (MD), we elucidated MP-ARG interaction mechanisms from the interfacial to the cellular scale. Polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) MPPIs underwent significant aging during 60 days of exposure, resulting in elemental enrichment (C/O/P), the formation of C═C/C-H/C-O/C-OH functional groups, and elevated oxidation. These transformations enhanced extracellular polymeric substance production (184.81 mg/g MLSS) and selectively enriched antibiotic-resistant bacteria, ARGs, and mobile genetic elements (MGEs), promoting horizontal gene transfer. XDLVO theory revealed spontaneous microbial adhesion (ΔGadh = -23.63 mJ/m[2]) driven by Lifshitz-van der Waals (LW) and acid-base interactions. MD demonstrated direct MP penetration into the membrane via dominant LW forces (-1200 kJ/mol) and increased permeability. Concurrently, compared with sewage water (SW), MPPIs induced a 2.06-fold overproduction of reactive oxygen species, which upregulated genes encoding efflux pumps (acrF, 3.2-fold), outer membrane porins (OmpF, 4.1-fold), and conjugative transfer genes (traF, 3.8-fold). Material-specific (PET > PE > PP) and oxygen-driven redox mechanisms governed ARG dissemination: aerobic conditions favored radical-driven oxidation and MGE entrapment, whereas anaerobic systems enhanced hydrophobic adhesion.}, } @article {pmid41621269, year = {2026}, author = {Li, J and Dong, W and Kong, A and Wang, G and Yang, J and Zhou, Y and Song, K and Kong, L and Tong, L}, title = {Floating macrophyte growth and decomposition greatly affects the exogenous antimony mobility and microbial community functions in water-sediment system.}, journal = {Water research}, volume = {293}, number = {}, pages = {125448}, doi = {10.1016/j.watres.2026.125448}, pmid = {41621269}, issn = {1879-2448}, mesh = {*Antimony ; *Geologic Sediments/chemistry/microbiology ; Water Pollutants, Chemical ; *Amaranthaceae/metabolism/growth & development ; Biodegradation, Environmental ; }, abstract = {Anthropogenic antimony (Sb) contamination in aquatic systems poses persistent ecological risks, yet the role of floating macrophyte life-cycle processes in regulating Sb migration and speciation remains poorly understood. In this study, a mesocosm experiment was conducted to investigate how the growth and decomposition of Alternanthera philoxeroides (AP) influence Sb mobility and transformation following exogenous Sb(V) input. Results show that Sb was ultimately sequestered in sediments, which acted as a dynamic regulator rather than a passive sink, controlling Sb retention and long-term reactivity. Rapid surface adsorption was followed by progressive downward migration driven by redox-sensitive remobilization and re-adsorption onto deeper mineral phases, with Sb predominantly associated with amorphous and poorly crystalline Fe/Al (hydr)oxides (67.3-84.1%). Growth of AP accelerated Sb removal from the water column mainly through indirect, DOM-mediated sequestration rather than direct plant uptake, while simultaneously enhancing the vertical redistribution of bioavailable Sb within sediments. In contrast, AP removal followed by decomposition caused pronounced physical and biogeochemical disturbances. These disturbances induced transient reducing conditions, organic matter release, and a marked increase in pH (up to 9.14), collectively promoting Sb remobilization and Sb(III) release into the overlying water. As a result, Sb(III) concentrations were up to 67-fold higher than those in the unvegetated control. Exogenous Sb strongly reshaped sediment microbial communities, selectively enriching metal-tolerant taxa such as Actinomycetota (genus Streptomyces) and favoring functional traits related to Sb detoxification and elemental cycling. Metagenomic evidence indicates that Sb resistance, coupled with coordinated C, N, P, and S cycling functions, enables the indigenous microbiome to actively regulate Sb speciation and mobility, particularly under organic matter inputs derived from macrophyte growth and decomposition. These findings demonstrate that floating macrophytes exert process-level control over Sb cycling, with life-cycle-mediated biogeochemical feedbacks governing its mobility, speciation, and persistence in water-sediment systems.}, } @article {pmid41621514, year = {2026}, author = {Ren, X and Zhang, W and Liu, M and Ge, J and Yang, H and Chi, G}, title = {Colon-targeted probiotic delivery system based on oxidized konjac glucomannan/thiolated chitosan/bacterial cellulose: Enhanced survival, mucoadhesion, and gut microbiota modulation.}, journal = {International journal of biological macromolecules}, volume = {346}, number = {}, pages = {150646}, doi = {10.1016/j.ijbiomac.2026.150646}, pmid = {41621514}, issn = {1879-0003}, mesh = {*Probiotics/administration & dosage/chemistry/pharmacology ; *Mannans/chemistry ; *Chitosan/chemistry ; *Colon/microbiology/metabolism/drug effects ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Cellulose/chemistry ; Humans ; Microspheres ; Oxidation-Reduction ; *Drug Delivery Systems ; Sulfhydryl Compounds/chemistry ; }, abstract = {Probiotics play a critical role in maintaining human health homeostasis, yet their oral delivery faces challenges due to poor gastrointestinal survival, uncontrolled release, and inefficient targeted colonization. To address these limitations, we developed colon-targeted mucoadhesive (sCS-BC)/OKGM-SA microspheres using a W1/O/W2 double emulsion technique combined with ionic crosslinking, employing oxidized konjac glucomannan (OKGM), thiolated chitosan (sCS), and bacterial cellulose (BC). In vitro digestion assays revealed that the microspheres effectively shielded probiotics under simulated gastric and bile salt, while enabling pH- and enzyme-responsive release in the intestinal, achieving a viable probiotic count of 1.5 × 10[8] CFU/mL. Rheological characterization and in vivo gastrointestinal transit studies demonstrated that the microspheres enhanced colonic colonization through interactions with the intestinal mucus layer. Histological analysis further indicated that the microspheres stimulated colonic goblet cell proliferation and mucus layer formation. Metagenomic and metabolomic profiling confirmed that oral administration of the probiotic-loaded microspheres markedly enriched gut microbial diversity and helped preserve intestinal barrier integrity, showing potential in modulating gut immune function. The (sCS-BC)/OKGM-SA system integrates upper gastrointestinal protection, colon-targeted delivery, mucus adhesion, and probiotic proliferation, offering a novel strategy for targeted probiotic delivery. This work establishes a foundational framework for designing next-generation colon-targeted probiotic carriers and underscores their therapeutic promise in modulating intestinal ecosystems.}, } @article {pmid41621540, year = {2026}, author = {Sun, H and Han, Y and Ren, S and Zhang, X and Li, X and Bi, P and Chen, L and Zhu, L and Yang, G and Ma, J and He, Q}, title = {Convergent enrichment of core functional guilds involved in Fe-N metabolism in anammox and activated sludge: Insights into genome-resolved metagenomics.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134125}, doi = {10.1016/j.biortech.2026.134125}, pmid = {41621540}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Metagenomics/methods ; *Nitrogen/metabolism ; *Iron/metabolism ; Oxidation-Reduction ; Bacteria/metabolism/genetics ; *Genome, Bacterial ; }, abstract = {The coupled process of ferric ammonium oxidation (Feammox) and nitrate-dependent ferrous oxidation (NDFO) is a cost-effective nitrogen removal strategy, yet insufficient molecular evidence supports its microbial mechanisms. This study successfully established anaerobic Fe-N coupling systems using anammox sludge and activated sludge as inoculum. Batch experiments and microbial community analysis revealed that two systems achieved similar nitrogen removal, dominated by anammox and Feammox performed by anammox bacteria (AnAOB), with a minor NDFO contribution, and convergently enriched core functional guilds under identical environmental pressures. Genome-resolved metagenomics further indicated that the porin-cytochrome protein complex associated with extracellular electron transfer co-occurred with anammox genes in Brocadia sapporoensis, suggesting its potential Feammox capability. Meanwhile, the iron oxidation gene Cyc2 co-occurred with mtr pathway homologs and complete denitrification genes in IGN3 sp900696555, suggesting its role in NDFO. This genomic evidence supports their dual metabolic capabilities, providing new insights into nitrogen removal in the coupled Feammox-NDFO process.}, } @article {pmid41622108, year = {2026}, author = {Deng, Z and Sanchis-López, C and Hernández-Plaza, A and Davín, AA and Huerta-Cepas, J}, title = {TreeProfiler: large-scale metadata profiling along gene and species trees.}, journal = {Molecular biology and evolution}, volume = {43}, number = {2}, pages = {}, pmid = {41622108}, issn = {1537-1719}, support = {SEV-2016-0672-18-2:PRE2018-084075//FPI-Severo Ochoa predoctoral fellowship/ ; CPP2021-008717//FPI-Severo Ochoa predoctoral fellowship/ ; MICIU/AEI/10.13039/501100011033//Proyecto de investigación financiado por/ ; FPU19/06635//Unión Europea NextGeneration/ ; PTA2019-017593-I/AEI/10.13039/501100011033//Research Technical Support Staff Aid/ ; /SNSF_/Swiss National Science Foundation/Switzerland ; 51NF40_225148//NCCR Microbiomes/ ; DAF2020-218584//CZI/ ; PID2021-127210NB-I00//Silicon Valley Community Foundation/ ; //National Programme for Fostering Excellence in Scientific and Technical Research/ ; }, mesh = {*Phylogeny ; *Software ; *Metadata ; Genomics/methods ; Archaea/genetics ; Evolution, Molecular ; }, abstract = {Profiling biological traits along gene or species tree topologies is a well-established approach in comparative genomics, widely employed to infer gene function from co-evolutionary patterns (phylogenetic profiling), reconstruct ancestral states, and uncover ecological associations. However, existing profiling tools are typically tailored to specific use cases, have limited scalability for large datasets, and lack robust methods to aggregate or summarize traits at internal tree nodes. Here, we present TreeProfiler, a tool for automated annotation and interactive exploration of hundreds of features along large gene and species trees, with seamless summarization of mapped traits at internal nodes. TreeProfiler supports the profiling of custom continuous and discrete traits, as well as ancestral character reconstruction and phylogenetic signal tests. It also integrates commonly used genomic features, including multiple sequence alignments, protein domain architectures, and functional annotations. We demonstrate TreeProfiler's utility beyond traditional phylogenetic profiling, as well as its ability to efficiently handle massive datasets, by analyzing the functional diversification of the methyl-accepting chemotaxis protein family comprising over 400,000 genomic and metagenomic sequences and by profiling the relative abundance of 124,295 bacterial and archaeal species across 51 biomes. TreeProfiler is open-source and freely available at https://github.com/compgenomicslab/TreeProfiler.}, } @article {pmid41622302, year = {2026}, author = {Li, S and Zhang, J and Han, L and Yu, Y and Mousa, AA and Zhu, W and Leng, J and Xie, F and Mao, S}, title = {Comparative metagenomic and metatranscriptomic analyses reveal the role of the gayal rumen and hindgut microbiome in high-efficiency lignocellulose degradation.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {18}, pmid = {41622302}, issn = {1674-9782}, support = {U2202203//Joint Funds of the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The gayal (Bos frontalis), a semi-domesticated bovine species, demonstrates exceptional adaptability to lignocellulose-rich diets dominated by bamboo, suggesting the presence of a specialized gastrointestinal microbiome. However, the functional mechanisms underlying this host-microbiome interaction remain poorly understood. Here, we conducted integrated metagenomic and metatranscriptomic analyses of rumen, cecum, and colon digesta from yellow cattle and gayal raised on the same bamboo-based high-fiber diet.

RESULTS: The results showed that gayal exhibited superior fiber-degrading capacity relative to yellow cattle, evidenced by significantly higher (P < 0.05) fiber digestibility, cellulase and xylanase activities, and increased volatile fatty acids production despite identical feed intake. Microbial community analysis revealed distinct composition in both the rumen and hindgut of gayal compared to yellow cattle, with notable enrichment of taxa specialized in lignocellulose degradation. Metatranscriptomic profiling further identified upregulation of key lignin-modification enzymes, particularly AA6, AA2, and AA3, primarily encoded by Prevotella, Cryptobacteroides, Limimorpha, and Ventricola. These enzymes are known to modify lignin structure to increase polysaccharide accessibility. These results demonstrate that gayal hosts a unique and metabolically active gastrointestinal microbiome capable of efficient lignocellulose deconstruction through a coordinated enzymatic cascade, especially effective in dismantling lignin barriers.

CONCLUSIONS: This study provides novel insights into host-microbiome co-adaptation to fibrous feeds and highlights the potential of gayal-derived microbial consortia and enzymes for improving roughage utilization in ruminant agriculture.}, } @article {pmid41622335, year = {2026}, author = {Ota, C and Bamba, M and Sato, S and Tsuchimatsu, T}, title = {Soil microbial composition and abundance influence the growth of Lotus japonicus.}, journal = {Journal of plant research}, volume = {139}, number = {2}, pages = {195-205}, pmid = {41622335}, issn = {1618-0860}, mesh = {*Lotus/growth & development/microbiology ; Symbiosis ; *Soil Microbiology ; *Mesorhizobium/physiology/genetics ; Root Nodules, Plant/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rhizobium/physiology ; }, abstract = {In mutualistic symbiosis between plants and bacteria, the abundance and composition of symbiotic bacterial groups in the soil microbiota can be important for plant growth. Here, we focused on the nitrogen-fixing mutualism between Lotus japonicus and nodule bacteria to investigate whether and how much the abundance of symbiotic rhizobia in the soil microbiota of natural environments contributes to variations in host plant growth. An inoculation experiment of soil microbiota revealed extensive variations in plant growth phenotypes, even between microhabitats. We found that the local presence of L. japonicus and the relative abundance of Mesorhizobium bacteria showed positive correlations with plant growth supported by both 16S amplicon sequencing and shotgun metagenome analyses. Among bacteria investigated, the abundance of Mesorhizobium was most strongly associated with plant growth phenotypes, supporting its role as the primary symbiotic rhizobia in natural environments. Given the specificity and the selectivity of plants for favorable rhizobia, legume-rhizobia interactions could trigger a positive plant-soil feedback that enriches favorable rhizobia into the soil surrounding legume plant habitats.}, } @article {pmid41623309, year = {2026}, author = {Luo, Y and Ding, H and Pan, J and Xu, G}, title = {Use of metagenomic next-generation sequencing to diagnose Tropheryma whipplei infection-related pneumonia: A case report.}, journal = {Experimental and therapeutic medicine}, volume = {31}, number = {3}, pages = {75}, pmid = {41623309}, issn = {1792-1015}, abstract = {Whipple's disease is caused by Tropheryma whipplei (T. whipplei), an uncommon pathogen that is often related to gastrointestinal symptoms. Extraintestinal involvement, particularly pulmonary manifestations, is rare and poses notable diagnostic challenges. An objective technique for identifying undiscovered infections is the application of metagenomic next-generation sequencing (mNGS). The present case report described a 55-year-old female presenting with community-acquired pneumonia (CAP), who received empirical treatment with moxifloxacin, ultimately diagnosed through mNGS performed on bronchoalveolar lavage fluid. The results indicated that the patient was infected with T. whipplei and that the patient exhibited notable clinical improvement within 2 weeks following intravenous moxifloxacin during hospitalization and continuation of oral moxifloxacin following discharge. The present case report highlighted the utility of mNGS in diagnosing atypical infections and identified T. whipplei as a potential etiological agent of CAP in immunocompetent hosts.}, } @article {pmid41623458, year = {2026}, author = {Li, QM and He, LS and Wang, Y}, title = {Small proteins from prokaryotes in the marine water column at full ocean depth.}, journal = {iScience}, volume = {29}, number = {2}, pages = {114585}, pmid = {41623458}, issn = {2589-0042}, abstract = {Small proteins (SPs, ≤50 aa) are often overlooked in genomics. We conducted the first systematic analysis of prokaryotic SPs across the full ocean-depth gradient. From 433,311 short open reading frames (sORFs) predicted from 71 western Pacific metagenomes, we identified 193,281 SP clusters. Filtration yielded 75,581 prevalent SPs, including 4,307 high-confidence clusters (RfSPs). Notably, 87.09% of RfSPs lacked non-marine homologs, and ∼70% contained unknown domains. While most (65.57%) were phylum-specific, twelve were distributed across ≥5 phyla, and some were prophage-associated. Geographically, twenty-three core RfSPs were universally present. Co-occurrence analysis revealed that interacting RfSPs typically originated from the same or adjacent zones. Finally, we confirmed the transcription of 8.20% RfSP clusters in deep-sea metatranscriptomes. The zone-specific transcription of certain RfSPs suggests adaptive functions, such as stress response and molecular chaperoning, in distinct marine environments. Our study reveals SPs as a critical strategy for prokaryotic adaptation to deep-sea stressors.}, } @article {pmid41623619, year = {2025}, author = {Wei, T and Qian, N and Wang, H and Song, Y and Wang, W and Li, Y and Zhao, Z and Xu, F and Yang, W}, title = {Wilson's disease-associated gut dysbiosis: novel insights into microbial functional alterations, virulence changes, and resistance markers.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1714276}, pmid = {41623619}, issn = {1664-302X}, abstract = {BACKGROUND: Although the gut microbiota is associated with a variety of metabolic, inflammatory, and neurological disorders through microbial dysbiosis, current studies on the gut microbiota in Wilson's disease (WD) remain limited. Critical gaps exist in understanding the roles of key functional microbial factors in WD pathogenesis, which hinders the acquisition of mechanistic insights into this disease.

OBJECTIVE: This study aims to characterize alterations in the gut microbiome associated with WD, with a particular emphasis on virulence factors (VFs) and antibiotic resistance genes (ARGs), as well as functional mobile genetic elements (MGEs), in order to elucidate their potential roles in disease progression and clinical manifestations.

METHODS: We analyzed fecal samples from 37 patients with WD and 33 healthy controls (HCs) using metagenomic sequencing, with a specific focus on examining virulence gene profiles and antibiotic resistance patterns and MGE composition in relation to liver function markers.

RESULTS: Beta diversity analysis revealed significant differences in the gut microbial community structure between patients with WD and HCs, and a distinct set of microbial taxa was identified that showed significant associations with clinical indicators. A gut microbial co-occurrence network identified key species playing central roles in the microbial community structure, including Prevotella stercorea, Firmicutes bacterium CAG 110, Bacteroides salyersiae, Lactococcus petauri, Streptococcus cristatus, Actinomyces sp. HMSC035G02, and Streptococcus viridans. Widespread functional dysbiosis was detected across multiple biological levels in patients with WD, with significant correlations identified between these microbial alterations and clinical indicators. Significant disruptions were identified in key metabolic pathways, including the Pentose Phosphate Pathway, Pyruvate Metabolism, and Starch and Sucrose Metabolism, which were associated with the dysregulation of carbohydrate-active enzymes (CAZymes). These alterations showed significant correlations with clinical markers of liver dysfunction (e.g., procollagen III N-terminal peptide PIIINP, aspartate transaminase/alanine transaminase AST/ALT). A total of 54 virulence factor (VF) genes exhibited differential abundance in WD, with 36 genes depleted and 18 enriched. Notably, these included colibactin genes (clbB, clbH) from Escherichia coli and type IV secretion system genes (aec19, pilB). These VFs were significantly associated with indicators of liver function (e.g., bilirubin levels) and coagulation abnormalities. Among the detected antibiotic resistance genes (ARGs), 21 exhibited disease-specific patterns in WD, notably tetQ (encoding tetracycline resistance), ErmB (conferring macrolide resistance), and cfxA6 (mediating cephamycin resistance). Furthermore, ARG profiles were associated with Bifidobacterium enrichment and showed significant correlations with lipid metabolism markers [e.g., triglycerides (TG), high-density lipoprotein cholesterol (HDL-C)]. Critically, we identified significant enrichment of 60 functional mobile genetic elements (MGEs) in WD, spanning categories involved in DNA replication/repair, phage activity, and conjugative transfer, indicating heightened genomic plasticity and horizontal gene transfer potential. Strikingly, correlation network analysis revealed strong and specific co-occurrence between key ARGs (e.g., ErmX) and defined suites of MGEs, suggesting MGE-facilitated dissemination of resistance determinants.

CONCLUSION: Wilson's disease (WD) patients exhibit significant alterations in gut microbial community structure and functional dysbiosis, wherein the enrichment of virulence genes (such as colibactin genes clbB/clbH) and the specific antibiotic resistance genes (such as tetQ and ErmB), and the activation of mobile genetic elements are closely associated with clinical indicators including liver function impairment, coagulation abnormalities, and lipid metabolism disorders.}, } @article {pmid41623622, year = {2025}, author = {Li, Y and Cheng, Y and Liu, W and Li, J and Li, S and Suriguga, and Ma, T and Kwok, LY and Cai, Z and Sun, Z}, title = {Gut microbial and functional signatures in breast cancer: an integrated metagenomic and machine learning approach to non-invasive detection.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1722632}, pmid = {41623622}, issn = {1664-302X}, abstract = {INTRODUCTION: Breast cancer is associated with significant restructuring of the gut ecosystem. Gut microbial composition and function may influence cancer development and progression through immune modulation, metabolic regulation, and inflammation-related pathways.

METHODS: Using shotgun metagenomic sequencing of fecal samples from 38 stage I-III breast cancer patients and 36 age- and body mass index-matched healthy controls. Machine learning models were constructed to evaluate the diagnostic potential of integrated microbial and metabolic features.

RESULTS: Significant alterations were observed in gut microbiota composition, including depletion of beneficial taxa (Limosilactobacillus fermentum, Blautia sp.) and enrichment of Prevotella copri. Pathways involved in short-chain fatty acid and purine metabolism were reduced. The gut phageome exhibited structural changes and altered correlations with bacterial hosts. Predictive analysis revealed depletion of short-chain fatty acids (butyrate, propionate), purine intermediates (hypoxanthine, xanthine), and nicotinate in patients. A machine learning model integrating microbial and predicted metabolic features achieved an area under the curve values of 0.78 in the discovery cohort and 0.73 (recall = 0.74) in an independent validation cohort.

DISCUSSION: Coordinated gut microbiome, phageome, and metabolome alterations characterize breast cancer, offering potential non-invasive biomarkers and mechanistic insights for disease detection and intervention.}, } @article {pmid41623634, year = {2025}, author = {Zeng, J and Gong, L and Qin, S and Fang, P and Shu, F and Zhang, W and Zhou, Y and Li, X and He, Q and Sun, P and Deng, H}, title = {Multi-omics reveals glutinous rice varieties shape Baijiu flavor via microbial and metabolic modulation.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1721127}, pmid = {41623634}, issn = {1664-302X}, abstract = {INTRODUCTION: Glutinous rice significantly influences Baijiu flavor, yet standardized brewing-specific indicators are lacking.

METHODS: In this study, metagenomic, metaproteomic, and non-targeted GC-MS analyses of Zaopei, along with HS-SPME-GC-MS analysis of Baijiu, were used to compare the effects of three glutinous rice varieties with distinct nutritional profiles on microbial diversity and flavor formation.

RESULTS: The Wuliangye-specific variety Dajiugu, with high sucrose, high amino acids, and low fatty acids, promoted early growth and metabolic activity of Saccharomycopsis, Enterobacter, and Klebsiella. Functional genera such as Saccharopolyspora, Pediococcus, and Clostridium enhanced fatty acid and amino acid accumulation in Zaopei and increased ethyl acetate, 4-vinylphenol, and dimethyl trisulfide in Baijiu.

DISCUSSION: These findings highlight the pivotal role of glutinous rice variety in shaping Baijiu flavor and offer a scientific basis for breeding brewing-specific glutinous rice.}, } @article {pmid41623638, year = {2025}, author = {Kane, Y and Ma, Y and Yan, B and Zhao, X and Ge, T and Li, Y and Cao, L and Zhang, M and Wan, Z and Zhang, T and Zhang, C}, title = {The human plasma anellome exhibits age- and sex-dependent patterns with links to cardiometabolic health in older adults.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1716110}, pmid = {41623638}, issn = {1664-302X}, abstract = {The human plasma virome is dominated by anelloviruses which are increasingly associated with several clinical conditions including among others HIV-1, COVID-19, autoimmune diseases, and cardiovascular and metabolic diseases. Due to their high genetic divergence, most studies investigated human anellome at broad family or genus level. These approaches obscure the contributions of specific anellovirus species to clinical conditions. We conducted plasma metagenomics in 218 individuals from young (0-16 years) and old (63-100 years) cohorts to resolve the anellome at the species level and examine its patterns across age, sex, and associations with cytokines and cardiometabolic outcomes. Older adults exhibited near-universal anellovirus detection and significantly higher abundance compared with youth. Species-specific analysis revealed that Alphatorquevirus_homin1 and Alphatorquevirus_homin13 were markedly enriched in diseased older adults. Predictive modeling based on machine learning algorithms distinguished disease status in the young cohort with high accuracy (AUC = 0.86), but performance was limited in the elderly (AUC = 0.58), suggesting a lack of diagnostic value in advanced age. Specific species abundances and diversity were associated with stroke and coronary heart disease, while cytokine correlations revealed module-specific immune signatures: Gammatorquevirus-dominated modules associated positively with pro-inflammatory cytokines and growth factors (e.g., IL-1β, IL-15, VEGF), whereas Beta- and some Alphatorquevirus-dominated modules showed predominantly negative correlations with several inflammatory and regulatory mediators (e.g., IL-6, TNF-α, IL-10). These findings demonstrate that the anellome is influenced by age and immune status and shows associations with cardiometabolic health, although these relationships do not guarentee diagnostic or causal significance. Additonally, we found no significant differences of Human endogenous retrovirus K Env expression between disease and healthy controls. This work underscores the importance of resolving human anollome to species level in future longitudinal studies to strengthen their clinical significance and biomarker potential.}, } @article {pmid41623642, year = {2025}, author = {Kuang, HF and Jiang, XY and Tie, SY and Lian, K and Hao, MY and Xu, H and Huang, X and Yang, Y and Guo, Q and Li, J and Chen, LL}, title = {Global research trends in bacteriophage and gut microbiota: a bibliometric and visual analysis from 2012 to 2025.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1738456}, pmid = {41623642}, issn = {1664-302X}, abstract = {BACKGROUND: The gut microbiota constitutes a complex microbial ecosystem that plays a fundamental role in host metabolism and immune homeostasis. As the most abundant viral entities in the gut, bacteriophages are increasingly recognized as key modulators of microbial community structure and function. Nevertheless, the global research landscape and thematic evolution of bacteriophage-gut microbiota studies have not been systematically evaluated.

METHODS: Publications related to bacteriophages and the gut microbiota published between 2012 and 2025 were retrieved from the Web of Science Core Collection and Scopus databases. Bibliometric and visual analyses were conducted using CiteSpace, VOSviewer, and Scimago to examine publication trends, countries/regions, institutions, authors, journals, references, and research hotspots.

RESULTS: A total of 687 articles and reviews were included. The annual number of publications increased steadily, with accelerated growth after 2018 and a peak in 2023. China ranked first in publication output, while the United States demonstrated strong centrality in global collaboration networks. The University of California, San Diego and the University of Copenhagen were identified as leading institutions. Highly productive authors included Colin Hill, Bernd Schnabl, Zhang Yue, Li Shenghui, and Ross R. Pau. Frontiers in Microbiology and Nature are the most influential journals in this field. Keyword analyses revealed major research hotspots, including viral metagenomics, antimicrobial resistance, phage-microbiota-immune interactions, and the transition from phage therapy toward microecological and immunomodulatory interventions.

CONCLUSION: Research on bacteriophage-gut microbiota interactions has shifted from descriptive profiling to mechanistic and translational studies, driven by advances in viral metagenomics and phage culturomics. Increasing attention has been directed toward disease-associated phage-microbiota interactions, particularly in inflammatory bowel disease, as well as the development of precision interventions such as phage therapy and engineered phages. This bibliometric analysis provides a comprehensive overview of global research trends and highlights emerging directions for future microbiome research.}, } @article {pmid41623646, year = {2025}, author = {Thagulisi, F and Baatjies, L and Sharma, A and Ngom, JT and Nyambo, K and Jooste, T and Tapfuma, KI and Mavumengwana, V}, title = {Antimycobacterial activity of intertidal sediment-derived bacteria from False Bay, South Africa.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1745248}, pmid = {41623646}, issn = {1664-302X}, abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a global health burden due to the pathogen's ability to develop resistance to current treatment options. Consequently, drug discovery studies are essential for identifying new antimycobacterial agents with novel mechanisms of action. This study investigated the antimycobacterial activity of crude extracts derived from mixed culturable bacteria isolated from intertidal marine sediments. The bacterial diversity of the bioactive mixed cultures was characterized using 16S rRNA gene-based metagenomic analysis. Their pathogen-targeted effects were evaluated against Mycobacterium smegmatis mc[2]155 and M. tuberculosis H37Rv, and THP-1-derived macrophages infected with M. smegmatis mc[2]155. Of the 48 mixed bacterial crude extracts derived from 17 intertidal marine sediments, five-PPB1, GCR1, BB1, PPB2, and CR1-demonstrated strong antimycobacterial activity against M. smegmatis mc[2]155 and M. tuberculosis H37Rv with minimum inhibitory concentrations ranging from 31.25 to 62.50 μg/mL and 7.8125 to 15.625 μg/mL, respectively. At 62.50 μg/mL, CR1 significantly reduced the intracellular M. smegmatis mc[2]155 burden in THP-1-derived macrophages, resulting in 28.08 ± 4.25% mean decrease in bacterial survival (p < 0.0001) and 94.4% ± 1.14 mean growth inhibition. From the CR1 mixed cultures, nine axenic bacterial isolates were cultivated, and their resulting crude extracts were evaluated for bioactivity. The identified isolates included Marinobacter maritimus, Psychrobacter celer, Pseudomonas benzenivor, Bacillus altitudinis, Bacillus aerius, Bacillus stratosphericus, and Paenibacillus glucanolyticus. Metabolite profiling of axenic crude extracts identified several compounds, including tenacibactin B, maremycin D1, and tubercidine. These findings suggest that South African intertidal marine sediments host diverse microbial communities capable of producing novel antimycobacterial agents.}, } @article {pmid41624426, year = {2026}, author = {Santi, I and Pavloudi, C and Abagnale, M and Azua, I and Baña, Z and Bastianini, M and Belser, C and Berg, K and Bilbao, J and Bird, K and Broudin, C and Camusat, M and Cancio, I and Caray-Counil, L and Casotti, R and Castel, J and Comtet, T and Cox, CJ and Cunliffe, M and Daguin, C and Deneudt, K and Díaz de Cerio, O and Exter, K and Fauvelot, C and Fontana, Y and Frada, MJ and Galand, PE and Gallia, R and Garczarek, L and González Fernández, J and Guillou, L and Heynderickx, H and Koplovitz, G and Labrune, C and Lagaisse, R and Laroquette, A and Lescure, L and Lopes, E and Loulakaki, M and Louro, B and Magalhães, C and Margiotta, F and Moal, H and Moussy, A and Not, F and Percopo, I and Paredes Rosendo, E and Péru, E and Poulain, J and Praebel, K and Rigaut-Jalabert, F and Romac, S and Rzeznik-Orignac, J and Sarno, D and Souza Troncoso, J and Thiébaut, E and Thomas, W and Tkacz, A and Tramontano, F and Trano, AC and Wincker, P and Pade, N}, title = {Next release of the European Marine Omics Biodiversity Observation Network (EMO BON) shotgun metagenomic data from water and sediment samples (Release 2).}, journal = {Biodiversity data journal}, volume = {14}, number = {}, pages = {e178484}, pmid = {41624426}, issn = {1314-2828}, abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is a long-term genomic observatory run by the European Research Infrastructure European Marine Biological Resource Centre (EMBRC). It was established in 2021 to support the challenges of biodiversity observation and unsystematic management of biodiversity data in the European seas. EMO BON introduced and coordinated the systematic and harmonised observation of biodiversity amongst more than fourteen marine stations in the European coastline. Here, we report the next release (Release 2) of shotgun metagenomic data from seawater and sediment microbial communities.}, } @article {pmid41624871, year = {2025}, author = {Zhu, H and Hu, L and Feng, Z and Zhang, Z and Zhu, H and Li, H}, title = {Case Report: Murine typhus complicated by symmetrical peripheral gangrene: first report and diagnostic insights from metagenomic next-generation sequencing.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1746919}, pmid = {41624871}, issn = {1664-3224}, mesh = {Female ; Humans ; High-Throughput Nucleotide Sequencing ; *Typhus, Endemic Flea-Borne/diagnosis/complications/drug therapy/microbiology ; *Gangrene/diagnosis/etiology/microbiology ; Aged ; *Rickettsia typhi/genetics ; Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use ; Animals ; Doxycycline/therapeutic use ; }, abstract = {BACKGROUND: Murine typhus, a flea-borne infection caused by Rickettsia typhi, often presents with nonspecific symptoms that delay diagnosis. While usually self-limiting, it can rarely progress to multiple organ dysfunction syndrome (MODS). We report the first case of murine typhus complicated by symmetrical peripheral gangrene (SPG), in which metagenomic next-generation sequencing (mNGS) enabled rapid diagnosis and guided timely doxycycline therapy.

CASE PRESENTATION: A 69-year-old female from South China was hospitalized with persistent abdominal pain and low-grade fever. She was a farmer and had suspected animal exposure. Laboratory investigations revealed hypoxia, abnormal coagulation profile, hepatorenal impairment, and thrombocytopenia. Despite empirical antibiotic therapy, her condition deteriorated progressively, manifested as hemodynamic instability, respiratory failure, and the emergence of purpuric-petechial cutaneous eruptions. Immediate interventions were initiated, including administration of vasoactive agents and mechanical ventilation. Based on mNGS, R. typhi was confirmed, she received targeted antibiotic treatment with intravenous doxycycline (100 mg twice daily). On the hospital day 16, gangrene of all four extremities became evident. The patient underwent amputation of all four extremities and survived, with systemic symptoms gradually resolving during 6-months follow-up.

CONCLUSION: This first reported case of murine typhus complicated by symmetrical peripheral gangrene (SPG) establishes its potential to cause life-threatening multiorgan failure. Metagenomic next-generation sequencing (mNGS) resolved the diagnostic challenge by rapidly identifying Rickettsia typhi, guiding life-saving doxycycline therapy and underscoring its value in severe zoonotic infections.}, } @article {pmid41625489, year = {2026}, author = {Zhou, L and Liu, J and Li, S and Xiong, Y and Qin, F and Luo, Z and Huang, D and Chen, H and Wang, X}, title = {Association between anxiety symptoms on risky e-biking riding behavior among adolescents: based on gut-brain axis.}, journal = {Comprehensive psychoneuroendocrinology}, volume = {25}, number = {}, pages = {100337}, pmid = {41625489}, issn = {2666-4976}, abstract = {OBJECTIVE: This study aimed to investigate the association between anxiety symptoms and risky e-bike riding behavior (RERB) among adolescents and to explore whether gut microbiota mediates this relationship.

METHODS: Adolescents using e-bikes were recruited through a combined online and offline recruitment approach. Data collection involved supervised electronic questionnaire completion in face-to-face settings, with biological samples collected independently by participants. Anxiety symptoms were assessed using the Generalized Anxiety Disorder-7 scale. RERB were evaluated via a structured questionnaire, yielding separate scores for aggressive behaviors (ABS), violation behaviors (VBS), and negligent behaviors (NES), along with total behavior scores (TBS). Fecal samples were obtained for metagenomic sequencing to characterize gut microbiota composition. Multiple linear regression was employed to elucidate the associations between anxiety symptoms and RERB. Partial Least Squares Path Modeling (PLS-PM) was applied to evaluate the potential mediating role of gut microbiota in these associations.

RESULTS: A total of 71 adolescents were included in this cross-sectional study. Anxiety symptoms were significantly associated with RERB, including TBS and VBS (both P < 0.05). Among the 15 microbial genera identified from fecal samples, 17 species showed significant association with both anxiety symptoms and RERB. PLS-PM modeling revealed a significant mediating effect of specific gut microbiota in the anxiety→behavior pathway, particularly for TBS and VBS. In contrast, for ABS, a reverse pathway-microbiota→anxiety→behavior-was found significant.

CONCLUSIONS: Anxiety symptoms were significantly associated with RERB among adolescents. Specific gut microbiota may mediate these associations, suggesting a potential microbiota-brain-behavior pathway.}, } @article {pmid41625740, year = {2025}, author = {Su, J and Liu, K and Wu, X and Lin, B and Ying, F and Zhu, Y and Li, M and Guo, P}, title = {Case Report: Confocal microscopy in the early diagnosis of microsporidial keratitis.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1745070}, pmid = {41625740}, issn = {2296-858X}, abstract = {This report describes a rare case of microsporidial stromal keratitis (MSK) complicated by corneal perforation in a 69-year-old male farmer with a 5-month history of ocular redness, pain, photophobia, and epiphora. In vivo confocal microscopy (IVCM) revealed pathognomonic findings-hyperreflective double-walled spore casings and vesicular clusters, providing the earliest diagnostic clues for microsporidia infection. Subsequent metagenomic next-generation sequencing (mNGS) and histopathology confirmed Microsporidia species. The patient underwent therapeutic penetrating keratoplasty followed by targeted anti-microsporidial therapy, achieving globe preservation and visual improvement. This case underscores IVCM's pivotal role in diagnosing MSK, particularly in atypical presentations. Because MSK remains a rare corneal disorder, its insidious progression necessitates high clinical vigilance. In summary, IVCM's ability to detect microsporidial structures in real-time significantly enhances early diagnosis, complementing molecular methods like mNGS. We conclude that IVCM, as a non-invasive and rapid diagnostic tool, provides a convenient and efficient means for the early differentiation of challenging corneal infections.}, } @article {pmid41625836, year = {2025}, author = {Matsukawa, M and Sakai, Y and Aoki, K and Ishii, Y}, title = {Urinary Microbiome Profiling by Shotgun Metagenomic Sequencing in Women Having Acute Cystitis-Like Symptoms With Negative Urine Cultures.}, journal = {Cureus}, volume = {17}, number = {12}, pages = {e100451}, pmid = {41625836}, issn = {2168-8184}, abstract = {BACKGROUND: Women presenting with typical symptoms of acute cystitis but with negative urine cultures, termed acute cystitis-like symptoms with negative urine cultures (ACNCs) in this study, are not uncommon. Despite previous attempts to detect bacterial DNA in urine, the etiology remains unclear. Although alterations in the urinary microbiome have been linked to other urological disorders, its involvement in ACNC has not been thoroughly investigated.

METHODS: Between September 2016 and December 2017, midstream urine samples were collected from women aged ≥16 years who had at least one typical symptom of acute cystitis and a negative urine culture. Samples were obtained at the initial (V1) and follow-up (V2) visits. Shotgun metagenomic sequencing (SMG) was performed via an Illumina MiSeq system. Taxonomic analysis at the genus level included taxa with ≥10 assigned reads in samples with ≥10,000 human-subtracted reads (HSRs).

RESULTS: Of 206 eligible women, 15 (7.3%; median age, 65 years) met the ACNC criteria and were enrolled. SMG was conducted for 15 samples at V1 and nine samples at V2. At V1, the HSR varied widely, and only five samples met the criteria for reliable interpretation. Seven samples, particularly those with high-grade pyuria, contained fewer than 1,000 HSRs, indicating potentially very low microbial loads or technical limitations. ACNC microbiomes demonstrated marked interindividual variation in taxonomic composition. The predominant taxa most frequently observed were Lactobacillus spp., Gardnerella spp., and JC polyomavirus. Conventional uropathogens, such as Escherichia spp., were not identified at interpretable levels. At V2, microbial diversity remained heterogeneous, but eight samples yielded sufficient read counts for interpretation.

CONCLUSIONS: While conventional uropathogens below interpretable criteria are unlikely to be responsible for most ACNCs, it is not necessarily recommended to regard the leading taxon in each case as the cause or to exclude microbiological involvement simply due to a low HSR because no validated metagenomic signature distinguishes pathogens from commensals. However, the observed diversity in ACNC microbiome profiles may reflect a heterogenous group of microbial conditions, including potentially viral, and nonmicrobial etiologies.}, } @article {pmid41625959, year = {2026}, author = {de Melo Pereira, GV and da Silva Vale, A and Ribeiro-Barros, AI and Rodrigues, LRS and de França Bettencourt Mirção, GM and Camilo, B and da Piedade Ernesto Tapaça, I and de Mello Sampaio, V and Brar, SK and Soccol, CR}, title = {Integrated microbial-metabolomic analysis reveals how fermentation contributes to the unique flavor of African Arabica coffee.}, journal = {Food chemistry. Molecular sciences}, volume = {12}, number = {}, pages = {100344}, pmid = {41625959}, issn = {2666-5662}, abstract = {Post-harvest fermentation is a decisive stage in shaping the flavor complexity of Arabica coffee. In this study, we mapped for the first time the microbial-driven flavor metabolic network underlying the fermentation of high-quality African coffee, using a combined metabolomic, meta-barcoding, and metagenomic approach applied to samples from Chimanimani National Park, Mozambique. Over 72 h of spontaneous fermentation, chemical analyses revealed rapid sucrose hydrolysis, lactic acid accumulation, and the formation of 74 volatile compounds. These transformations were driven by a previously unreported core microbiome (Leuconostoc-Hanseniaspora-Galactomyces axis), whose functional repertoire (1791 genes) highlighted the Ehrlich pathway and ester biosynthesis as central flavor routes. Among the volatiles formed, linalool, phenylethyl alcohol, and ethyl acetate were most abundant, emerging as predictive drivers of the floral and fruity notes identified in the resulting high-quality coffee beverage (score 87.25 ± 0.25). This study underscores microbial terroir as a key factor adding value to emerging African origins.}, } @article {pmid41625985, year = {2026}, author = {Taboada, S and Riesgo, A and Busch, K and Erpenbeck, D and Hentschel, U and Galià, C and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {15}, pmid = {41625985}, issn = {2398-502X}, abstract = {We present a genome assembly from a specimen of Phakellia ventilabrum (Porifera; Demospongiae; Bubarida; Bubaridae). The genome sequence has a total length of 211.92 megabases. Most of the assembly (99.97%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.36 kilobases in length. Gene annotation of this assembly by Ensembl identified 21 622 protein-coding genes. Thirty-three binned genomes were generated from the metagenome assembly, of which eight were classified as high-quality metagenome assembled genomes (MAGs) and of which four of the MAGs are fully circular. The MAGs were taxonomically assigned to Pseudomonadota (i.e. Candidatus Poriferihabitaceae), Nitrospirota, Nitrospinota, and the archaeal Nitrosopumilus clade.}, } @article {pmid41626090, year = {2026}, author = {Chen, L and Tang, M and Wang, Q and Jiang, H}, title = {Why a Mycobacterium Avium Infected Patient Showed a Positive Xpert MTB/RIF Result?.}, journal = {Clinical case reports}, volume = {14}, number = {2}, pages = {e71965}, pmid = {41626090}, issn = {2050-0904}, abstract = {This article discusses whether a MAC infected patient with a positive Xpert MTB/RIF test has a co-infection with Mycobacterium tuberculosis (MTB). The patient presented with chronic, indolent pulmonary patchy shadows on imaging but lacked typical symptoms. The MTB antigen-specific interferon-gamma enzyme-linked immunospot assay (T-SPOT.TB) was negative. Bronchoalveolar lavage fluid (BALF) testing yielded conflicting results: Xpert MTB/RIF assay detected trace levels of MTB DNA, whereas reverse dot blot hybridization confirmed the presence of Mycobacterium avium complex (MAC); in contrast, metagenomic next-generation sequencing (mNGS) returned a negative result for all pathogens. Mycobacterial culture ultimately returned positive; however, the MPB64 assay-employed for species identification-yielded a negative result, indicating a probable nontuberculous mycobacterial (NTM) infection. Despite contradictory lab results, the patient's symptoms and culture findings favored MAC infection. However, MTB infection could not be definitively ruled out in this patient, so a treatment regimen combining anti-tuberculosis and anti-MAC medications (isoniazid, rifampicin, ethambutol, and azithromycin) was initiated, leading to significant radiographic improvement. The discordance between the positive Xpert MTB/RIF result and other diagnostic evidence highlights important diagnostic challenges, underscoring the need for integrated clinical interpretation and providing actionable insights for clinicians.}, } @article {pmid41626263, year = {2026}, author = {Liu, Y and Fu, H}, title = {Pulmonary Tropheryma whipplei Infection Presenting With Multiple Thick-Walled Cavities on Chest CT: A Case Report and Literature Review.}, journal = {Respirology case reports}, volume = {14}, number = {2}, pages = {e70487}, pmid = {41626263}, issn = {2051-3380}, abstract = {Whipple's disease (WD) is a rare chronic multisystem infectious disease caused by the actinomycete Tropheryma whipplei. Pulmonary involvement is uncommon, and its clinical manifestations lack specificity, with diverse imaging findings, making it prone to misdiagnosis. We report a rare case of a 50-year-old woman who presented with a 2-week history of cough. Chest CT showed multiple thick-walled cavities in both lungs, a highly unusual presentation for WD pneumonia. Routine microbiological tests, including acid-fast staining and culture of bronchoalveolar lavage fluid (BALF), were negative, which made the diagnosis challenging. Metagenomic next-generation sequencing (mNGS) of BALF detected T. whipplei, confirming the diagnosis of WD pneumonia. After oral doxycycline treatment, follow-up chest CT showed complete resolution of the pulmonary cavities. This case demonstrates that multiple thick-walled cavities may be a characteristic imaging manifestation of WD pneumonia, highlights the diagnostic value of mNGS for this rare infection, and supports oral doxycycline monotherapy as an effective treatment option for isolated pulmonary TW infection.}, } @article {pmid41626594, year = {2026}, author = {Sapino, R and Fernández-González, Á and Castresana, J}, title = {Development of Metagenomic Methods for Health Monitoring of Endangered Species Using Fecal Samples.}, journal = {Evolutionary applications}, volume = {19}, number = {2}, pages = {e70199}, pmid = {41626594}, issn = {1752-4571}, abstract = {Metagenomic analysis of fecal samples is emerging as a powerful tool for monitoring endangered species, particularly in assessing the burden of pathogens and parasites that can threaten population viability. However, accurate identification in non-model species remains challenging due to the frequent absence of host-specific pathogen reference genomes. In this study, we developed a robust computational framework for detecting potentially pathogenic bacteria from metagenomic sequences by mapping them to available reference genomes in databases. Several key parameters affecting the analysis, including mapping algorithm, database configuration, and identification parameters, were analyzed to optimize detection sensitivity and specificity. Applying this approach to fresh fecal samples of the Iberian desman (Galemys pyrenaicus), a critically endangered semi-aquatic mammal, we identified 26 potentially pathogenic bacterial species, with prevalences ranging from isolated cases to nearly half of the individuals examined. Furthermore, our analysis revealed that some desmans had atypical compositions of potential pathogens, suggesting variations in environmental exposure or host genetic factors. This work demonstrates a novel application of fecal metagenomics for species-level detection of microorganisms implicated in disease, providing a powerful approach to gain essential insights into the health and epidemiology of endangered species and to support the development of more effective conservation strategies.}, } @article {pmid41627236, year = {2026}, author = {Yu, M and Wang, Y and Huangfu, K and Wu, S and Huang, H and Ma, Z and Wang, Y and Qiu, Y and Liu, S}, title = {Oxygen Vacancy-Engineered High-Entropy Oxide Nanozymes for Spatiotemporal Cascading Antifouling in Marine Environments.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {22}, number = {19}, pages = {e13363}, doi = {10.1002/smll.202513363}, pmid = {41627236}, issn = {1613-6829}, support = {52272271//National Natural Science Foundation of China/ ; }, mesh = {*Oxygen/chemistry ; *Biofouling/prevention & control ; *Oxides/chemistry ; *Entropy ; Quorum Sensing/drug effects ; *Aquatic Organisms ; }, abstract = {The catalytic versatility and compositional tunability of oxidative attack-based nanozymes offer a promising strategy for marine antifouling, yet their performance is often constrained by insufficient active-site accessibility, transient catalytic intermediates and restricted diffusion. Inspired by haloperoxidases (HPOs) in marine organisms, this study reports oxygen vacancy (Vo)-enriched high-entropy oxides (Vo-HEO) as multifunctional nanozymes to address these challenges. The entropy-stabilized multicomponent lattice, synergistically coupled with abundant Vo sites, reconfigures electronic structures and diversifies catalytic pathways, enabling efficient HPO-mimetic generation of hypobromous acid (HOBr), which is a selective and long-lived biocide (half-life > 36 days) capable of disrupting bacterial quorum sensing (QS) signals and oxidizing key biomolecules. By further integrating persistent HOBr with highly reactive hydroxyl radicals, Vo-HEO establishes a spatiotemporally cascading protective regime at the substrate interface, combining long-range QS suppression in the bulk phase with rapid oxidative eradication at the nano-biological interface, ultimately reducing bacterial adhesion by 90%. Microbiological characterization and metagenomic sequencing analyses further verify that Vo-HEO systematically collapses the coordination of microbial communication and energy metabolism across temporal and spatial scales. Collectively, this work demonstrates intelligent regulation of marine microecology and establishes a paradigm for adaptive antifouling design.}, } @article {pmid41627458, year = {2026}, author = {Jiang, F and Gu, H and Song, P and Zhang, J and Cai, Z and Liang, C and Gao, H and Zhang, R and Zhang, T}, title = {Post-defecation exposure alters gut microbiota of forest musk deer with implications for conservation metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {110}, number = {1}, pages = {53}, pmid = {41627458}, issn = {1432-0614}, support = {32200408//National Natural Science Foundation of China/ ; 2023-ZJ-952Q//Natural Science Foundation of Qinghai Province/ ; 2023M743743//China Postdoctoral Science Foundation/ ; }, mesh = {Animals ; *Deer/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Endangered Species ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Time Factors ; Biodiversity ; }, abstract = {In endangered species conservation, fecal samples are a vital non-invasive tool for gut microbiota analysis. Yet, the influence of external exposure time on microbial composition and function remains unclear, constraining data accuracy and reliability. To address this, we investigated the time-gradient effect in the globally endangered forest musk deer (Moschus berezovskii). Using non-invasive sampling under standardized captive conditions, fecal samples were collected at six storage times: (0, 1, 2, 4, 6, 8 days). Gut microbiota composition, diversity, enterotypes, and functional differences were assessed through 16S rRNA gene sequencing on the Illumina MiSeq platform. In total, 147,013 valid ASVs (amplicon sequence variants) were obtained showing significant shifts in microbial composition with storage time. Dominant phyla included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Increasing storage time led to declining α-diversity, reduced community stability, and more unique genera. PCoA (principal coordinates analysis) and NMDS (non-metric multidimensional scaling) indicated progressive separation of experimental groups from control groups, with Anosim and Adonis confirming progressive separation with storage time. Structurally, Firmicutes decreased while Proteobacteria, specifically the Acinetobacter genus, increased with storage time. Community assembly shifted from deterministic to stochastic processes, reflecting stronger environmental disturbance effects. These results demonstrate that the gut microbiota composition, diversity, and ecological functions in forest musk deer feces are highly sensitive to storage time. Thus, preservation duration must be strictly controlled as a critical variable in microbiome studies. This work establishes methodological standards for non-invasive fecal metagenomics in endangered species, providing theoretical insights and practical guidance for improving scientific rigor in conservation-related microbiome research. KEY POINTS: Fecal microbiota diversity and stability decline significantly with longer storage. Firmicutes decrease while Proteobacteria, especially Acinetobacter, increase over time. Storage duration strongly impacts microbiome data, requiring strict sampling control.}, } @article {pmid41627460, year = {2026}, author = {Do, TH and Dao, TK and Pham, TTN and Nguyen, MH and Nguyen, TQ and To, LA and Nguyen, TVH and Phung, TBT}, title = {Understanding the bacteriome, phageome and phage-associated bacteriome in healthy Vietnamese children under two years of age.}, journal = {Archives of microbiology}, volume = {208}, number = {4}, pages = {167}, pmid = {41627460}, issn = {1432-072X}, support = {DTDLCN.63/22//Ministry of Science and Technology/ ; }, mesh = {Humans ; Infant ; Vietnam ; *Bacteriophages/genetics/classification/isolation & purification ; *Bacteria/classification/genetics/isolation & purification/virology ; Feces/microbiology/virology ; *Gastrointestinal Microbiome ; Child, Preschool ; Metagenome ; Virome ; Male ; }, abstract = {The establishment of the intestinal microbiota during early life plays an important role in physical and mental development and in shaping disease susceptibility in adult. However, knowledge of the gut microbiota in healthy Vietnamese children remains limited. In this study, real-time PCR was used to detect 24 diarrheal pathogens in stool samples, revealing that 41% of healthy infants aged 6-24 months living in Hanoi, Hung Yen were asymptomatic carriers of Escherichia coli (29.1%), Clostridioides difficile (10.3%) and Sapovirus. Pooled metagenomes of gut bacteria (HMG1, HMG2) and viruses (HV1, HV2) from two groups of pathogen-negative infants aged 6-11 months (n = 17) and 12-24 months (n = 13) were subsequently sequenced. As expected, from the classified reads, HMGs comprised of 99.99% bacterial reads, while HVs comprised of bacteria (78.5% in HV1, 42.3% in HV2), phages (8.3% in HV1, 41.0% in HV2) and viruses. The gut microbiota was formed by core bacteria: Actinobacteria (82.6-84.5%), Firmicutes, Proteobacteria and Bacteroidetes, with abundance of Bifidobacterium (> 80%), phages: Podoviridae (65.5-70.2%), Siphoviridae, Myoviridae with dominant crAssphage. The HMGs and HVs shared core bacterial composition but differed in relative abundance. The gut microbiota of older children was characterized by an increase of probiotic bacteria, Escherichia phage, Lactococcus phage and decrease of bacterial pathogens and phages targeting Lactobacillus, Klebsiella, Acinetobacter. Bacterial genes in the gut phage fraction may reflect bacterial community in recent past. Overall, this study provides a scientific basis for understanding the gut microbiome in relation to health and diseases in children particularly within the Vietnamese population.}, } @article {pmid41627733, year = {2026}, author = {Hałakuc, P and Maciszewski, K and Karnkowska, A}, title = {Euglenid Extrachromosomal DNA: Assembly and Annotation.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3013}, number = {}, pages = {109-120}, pmid = {41627733}, issn = {1940-6029}, mesh = {*Extrachromosomal DNA/genetics ; *Molecular Sequence Annotation/methods ; *Computational Biology/methods ; Sequence Analysis, DNA/methods ; Genomics/methods ; *Euglenozoa/genetics ; Phylogeny ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing ; Genome, Mitochondrial ; }, abstract = {Euglenids (Euglenozoa) contain several forms of extrachromosomal DNA (ecDNA) in their cells, including the ribosomal DNA operon (rDNA), the mitochondrial genome (mtDNA), and, in photosynthetic species, the plastid genome (ptDNA). These ecDNA elements can be easily and accurately assembled and annotated even from limited sequencing data, such as single-cell genomic or metagenomic datasets. They are an important source of information for phylogenomic analyses, metabarcoding and evolutionary studies. In this chapter, we present a robust and adaptable bioinformatics pipeline for the identification, assembly, and annotation of extrachromosomal DNA from whole-genome datasets. The pipeline was developed with euglenids in mind and takes into account their unique genomic features, but can also be adapted for other Euglenozoa (and protists). This approach enables the recovery of organellar and rDNA sequences with high confidence and supports both targeted studies and large-scale environmental analyses.}, } @article {pmid41628276, year = {2026}, author = {Habib, I and Hernandez-Valencia, JC and Martinu, J and Novakova, E}, title = {Viral metagenome characterization reveals species-specific virome profiles in Triatominae populations from the southern United States.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {2}, pages = {e0013576}, pmid = {41628276}, issn = {1935-2735}, mesh = {Animals ; *Virome ; *Triatominae/virology ; *Viruses/classification/genetics/isolation & purification ; Arizona ; Texas ; New Mexico ; Phylogeny ; Female ; Sequence Analysis, DNA ; Male ; Species Specificity ; }, abstract = {Kissing bugs (Triatominae) are hematophagous insects and the principal vectors of Trypanosoma cruzi, the causative agent of Chagas disease. While their bacterial microbiomes have received considerable attention, the diversity of viruses associated with these insects remains poorly understood. To address this gap, we investigated the metavirome of five Triatominae species from the southern United States (Triatoma rubida, T. sanguisuga, T. gerstaeckeri, T. indictiva, and Hospesneotomae protracta), sampled in Texas, New Mexico, and Arizona. We sequenced 23 samples, including abdomen, gut and reproductive tissues from 13 field-collected individuals and assembled 41 viral operational taxonomic units (vOTUs), 40 of which are novel and together constitute 13 viral families, including Chuviridae, Arenaviridae, Orthomyxoviridae, Partitiviridae, Solemoviridae, Circoviridae, Rhabdoviridae, Microviridae, Xinmoviridae, Astroviridae, Narnaviridae, Tombusviridae, and the order Elliovirales. The vOTUs composition and abundance analysis examined variables including species, sex, tissue type, blood meal, and T. cruzi infection status, showing that metavirome diversity varied significantly among Triatominae species. Our findings demonstrate a species-specific metavirome and the presence of virus taxa linked to insects, plants, and vertebrates, highlighting the complex ecological interactions between viruses and triatomines. This study uncovers a diverse and largely novel set of metaviromes within North American Triatominae, providing a foundation for future research on virus-vector interactions.}, } @article {pmid41628665, year = {2026}, author = {Hartog, M and Korsten, SGPJ and Popa, CD and Pelle, T and Gavriilidou, A and van den Bemt, BJF and Willemsen, LEM and Koenders, MI and Vermeiden, JPW and Smidt, H and van den Ende, CHM}, title = {Effectiveness of Sustained Release Calcium Butyrate on the microbiome and clinical burden in osteoarthritis of the hand: A proof-of-concept placebo-controlled randomized trial.}, journal = {Osteoarthritis and cartilage}, volume = {34}, number = {6}, pages = {869-881}, doi = {10.1016/j.joca.2026.01.630}, pmid = {41628665}, issn = {1522-9653}, mesh = {Humans ; Female ; Middle Aged ; *Osteoarthritis/drug therapy/physiopathology/microbiology ; Delayed-Action Preparations ; Male ; *Gastrointestinal Microbiome/drug effects ; *Butyric Acid/therapeutic use/administration & dosage/pharmacology ; Aged ; Hand ; Proof of Concept Study ; Double-Blind Method ; Intestinal Barrier Function ; Feces/microbiology ; Treatment Outcome ; }, abstract = {OBJECTIVE: This study primarily assessed effects of Sustained Release Calcium Butyrate (SRCaBu) on gut microbiome composition and function in hand OA patients. Secondary objectives included its impact on hand pain and function, markers of intestinal permeability, systemic inflammation, and safety.

METHOD: A participants, researchers, and pharmacy assistants blinded, randomized, placebo-controlled proof-of-concept trial compared 600 mg daily dose SRCaBu with placebo over 4-5 weeks. The primary domain was microbiome composition and function, assessed via fecal 16S rRNA gene- and metagenome sequencing, and short-chain fatty acid analysis. Secondary outcomes included parameters for intestinal barrier function, clinical outcomes and adverse events. Primary analyses followed the per-protocol principle.

RESULTS: 35 participants (mean age 62.5±6.9 years, 82% female) were randomized to SRCaBu (n=18) or placebo (n=17). Two SRCaBu participants discontinued treatment for pre-existing liver impairment and need for pain medication. SRCaBu tended to reduce the relative abundance of Streptococcus (regression coefficient:-0.67, 95%CI:-1.46,0.13) and Faecalibacterium -0.38(-0.83,0.07), increase fecal acetate (median between-group difference: 9.5, [IQR]: [-3.5,22.5]), and was inversely associated with microbial LPS biosynthesis- and virulence genes. SRCaBu increased toxin-related genes, primarily from beneficial Blautia species, without association to pathogenicity. SRCaBu did not significantly affect biomarkers of intestinal permeability, inflammation, or clinical outcomes. Adverse events were mild and comparable between groups.

CONCLUSION: Our study yielded indicative findings that SRCaBu supports microbiome health in patient with hand OA by improving compositional and functional characteristics of the microbiome. Although the treatment was well tolerated, effects on serum markers for intestinal barrier function and systemic inflammation, and clinical symptoms remained unclear.

TRIAL REGISTER: 2020-001071-33 / NL73382.091.21.}, } @article {pmid41628768, year = {2026}, author = {Frizzera, A and Vázquez, N and Sacristán, H and Tapella, F and Lovrich, G and Khalaf, A and Bojko, J and Cremonte, F}, title = {Patagonian king crabs (Lithodes santolla and Paralomis granulosa) and their diseases: Pathogen survey and taxonomic clarification of Areospora rohanae (Microsporidia).}, journal = {Journal of invertebrate pathology}, volume = {216}, number = {}, pages = {108560}, doi = {10.1016/j.jip.2026.108560}, pmid = {41628768}, issn = {1096-0805}, mesh = {Animals ; *Anomura/parasitology/microbiology ; *Microsporidia/classification/genetics/physiology ; Symbiosis ; }, abstract = {Lithodid crabs constitute a valuable natural resource with commercial interest; however, their health status in South America is scarcely studied. The presence of pathogens may have a negative impact on affected populations, endangering the fishery. This study surveys the symbionts present in populations of the king crab, Lithodes santolla, and the stone/false king crab, Paralomis granulosa, using histology, transmission electronic microscopy, and molecular analyses to characterise various symbionts. The histological and molecular data revealed a wide range of infections in L. santolla, including prokaryotic microorganisms, Areospora rohanae (Microsporidia), apicomplexan gregarines, ciliated protozoans, ectoparasitic crustaceans, and various epibiotic associations. In the case of P. granulosa, apicomplexan gregarines, ciliated protozoans, and various ectoparasites were observed. Molecular analyses confirmed the presence of the microsporidian A. rohanae, occurring at high prevalences (30%) in L. santolla, and some bacterial associations. We use metagenomic tools to extract a partial genome of this parasite to aid in its identification and taxonomic position, which leads us to erect the taxonomic orders Astathelohaniida and Areosporida and further clarify the previously assigned: "Glugeida+". The results of this study represent the first broad survey for symbionts in both king crab species and take us another step forward to a more accurate microsporidian taxonomy.}, } @article {pmid41628857, year = {2026}, author = {Theodosiou, AA and Bogaert, D and Cleary, DW and Fady, PE and Feehily, C and Gilbert, JA and Greenhough, B and Guardabassi, L and Hall, LJ and Harman, T and Kuijper, EJ and Lebeer, S and Lorimer, J and Spector, TD and Jones, CE}, title = {Microbiome research in practice: priorities for clinical translation and impact.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {32}, number = {6}, pages = {927-935}, doi = {10.1016/j.cmi.2026.01.021}, pmid = {41628857}, issn = {1469-0691}, mesh = {Humans ; *Microbiota ; *Translational Research, Biomedical ; *Translational Science, Biomedical ; }, abstract = {BACKGROUND: Rapid advances in microbiome science have sparked clinical and commercial enthusiasm for interventions, yet translation into practice risks outpacing both mechanistic understanding and the infrastructure required for safe adoption.

OBJECTIVES: To outline a coordinated research, clinical, social, and policy agenda for advancing safe, effective, and equitable microbiome-based interventions.

SOURCES: We convened an interdisciplinary Royal Society-funded expert workshop (Leeds, UK, October 2024) with international leaders in microbiome science, clinical trials, regulation, and social science. Thematic analysis of workshop discussions and written contributions identified priority domains for translation.

CONTENT: Three intersecting priorities emerged: scientific credibility, practical viability, and stakeholder engagement. Scientific credibility demands investment in multiomic and strain-level characterization of host-microbiome interactions on a large scale, benchmarking of clinical and microbiological endpoints, and harmonization of trial conduct and reporting. Clinical adoption requires fit-for-purpose regulation, diversified investment to address funding bottlenecks, and coordinated capacity building. Meaningful stakeholder engagement with clinicians, patients, policymakers, and the public is essential to foster confidence, develop clinically relevant research questions, and ensure equitable implementation of any new technology.

IMPLICATIONS: To realize the clinical impact of microbiome interventions, sustained collaboration across disciplines is essential. This review offers a translational roadmap and actionable priorities to accelerate safe, effective, and equitable microbiome-based interventions-ensuring the field fulfils its clinical potential and delivers real-world impact.}, } @article {pmid41628881, year = {2026}, author = {Sun, G and Guo, S and Yao, Y and Lin, Z and Gao, H and Stauber, RH and Li, BC and Ding, GB}, title = {Facile immobilization of an unstable recombinant α-L-rhamnosidase on magnetite nanoparticles for efficient naringin biotransformation.}, journal = {International journal of biological macromolecules}, volume = {347}, number = {}, pages = {150652}, doi = {10.1016/j.ijbiomac.2026.150652}, pmid = {41628881}, issn = {1879-0003}, mesh = {*Flavanones/metabolism/chemistry ; *Enzymes, Immobilized/chemistry/metabolism ; *Magnetite Nanoparticles/chemistry ; Biotransformation ; *Glycoside Hydrolases/chemistry/metabolism/genetics ; Hydrogen-Ion Concentration ; Recombinant Proteins/chemistry/metabolism ; Temperature ; Enzyme Stability ; Humans ; Biocatalysis ; }, abstract = {α-L-Rhamnosidase is a significant biocatalyst that specifically cleaves terminal α-L-rhamnose group from natural flavonoid diglycosides, enabling the biocatalytic production of high-value flavonoid glucosides like prunin from naringin. Compared to its precursor naringin, prunin exhibits superior solubility and bioavailability, making this enzymatic conversion commercially valuable for the food and pharmaceutical industry. However, the industrial application of free α-L-rhamnosidases faces significant challenges, including enzyme instability, difficulty in recovery, and unsatisfactory reusability. To address these issues, this study developed an innovative magnetically recoverable biocatalyst (Fe3O4-Rha) through covalent immobilization of recombinant α-L-rhamnosidase from human fecal metagenome onto Fe3O4 nanoparticles using EDC/NHS chemistry, and the immobilization parameters were systematically optimized. The successful preparation of Fe3O4-Rha was verified by TEM, FTIR, TGA, and SQUID analysis. Fe3O4-Rha retained the catalytic property of free Rha in terms of optimal pH and temperature but exhibited superior tolerance on organic solvent especially ethanol and isopropanol. Moreover, Fe3O4-Rha could effectively biotransform naringin to prunin and maintained 61.34% of initial activity after 5 cycles. In a scaled-up reaction system, Fe3O4-Rha also efficiently converted naringin into prunin and the complete conversion was achieved within 10 h. This work successfully developed a magnetically recoverable immobilized α-L-rhamnosidase system for the efficient and reusable biotransformation of naringin, offering a promising approach for the enzymatic modification of bioactive small molecules using biological macromolecular catalysts.}, } @article {pmid41629097, year = {2026}, author = {Lyu, WT and Jia, QQ and Tong, X and Fan, H}, title = {[STAT1 gain-of-function mutation leading to disseminated Talaromyces marneffei infection combined with hemophagocytic syndrome: a case report].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {49}, number = {2}, pages = {184-187}, doi = {10.3760/cma.j.cn112147-20250730-00456}, pmid = {41629097}, issn = {1001-0939}, mesh = {Humans ; Male ; *Talaromyces ; *STAT1 Transcription Factor/genetics ; *Lymphohistiocytosis, Hemophagocytic/genetics/complications ; Adult ; *Gain of Function Mutation ; *Mycoses/genetics/complications/drug therapy ; Antifungal Agents/therapeutic use ; Amphotericin B/therapeutic use/administration & dosage ; }, abstract = {This study reports a 28-year-old HIV-negative male with a STAT1 gain-of-function mutation who presented with a systemically disseminated Talaromyces marneffei (TM) infection, which was complicated by hemophagocytic lymphohistiocytosis (HLH). The patient presented with recurrent fever, weight loss, oral mucosal ulcers, as well as lymphopenia and markedly elevated inflammatory markers during the acute phase of the illness. Imaging revealed scattered ground-glass opacities and nodular shadows in both lungs, as well as localized bronchiectasis, and splenomegaly. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and bone marrow aspirate specimens revealed TM-specific sequences. Whole-exome sequencing was performed to elucidate the underlying mechanism of recurrent fungal infections. This revealed a de novo heterozygous dominant mutation in the STAT1 gene (c.1151G>A, p.Gly384Asp), localized to the DNA-binding domain at amino acid position 384. This confirmed a STAT1 gain-of-function (STAT1-GOF) variant, which is consistent with the clinical phenotype of impaired antifungal immunity. Over the clinical course, the patient developed HLH. Following a two-week course of intravenous amphotericin B liposome (5 mg/kg per day), followed by oral voriconazole maintenance therapy (200 mg, twice daily), the patient exhibited significant improvements in clinical symptoms and laboratory parameters. Notably, the marked resolution of HLH was closely linked to the successful eradication of the fungal infection. This case highlights three critical clinical implications: (1) Patients with a predisposition to primary immunodeficiency disorders (e.g., STAT1-GOF mutations) should be evaluated for disseminated TM infections, even if they are HIV-negative; (2) mNGS is instrumental in etiological diagnosis and facilitates early intervention for fungal infections; (3) early identification of genetic defects establishes a theoretical basis for precision medicine and guides targeted therapeutic strategies.}, } @article {pmid41629364, year = {2026}, author = {Spörri, L and Studer, JM and Kreuzer, M and Rotzetter, J and Schärer, D and Largiadèr, CR and Jaggi, D and Zinkernagel, MS and Zysset-Burri, DC}, title = {Linking the microbiome to the complement system in geographic atrophy.}, journal = {NPJ genomic medicine}, volume = {11}, number = {1}, pages = {}, pmid = {41629364}, issn = {2056-7944}, support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; }, abstract = {Age-related macular degeneration (AMD) is the leading cause of vision loss in the aged population with the late stage geographic atrophy (GA). Risk factors for AMD include age, genetic variants in the complement system, nutritional factors, and alterations in the gut microbiome (GM). To identify taxonomic and functional differences in the microbiome associated to disease pathophysiology and genetic risk factors, this study investigated the GM and the ocular surface microbiome (OSM) of GA patients compared to healthy controls by whole-metagenome shotgun sequencing. 16 AMD-associated SNPs were genotyped from blood samples using TaqMan assays and Sanger sequencing. While GA patients showed differences in the GM, and altered metabolic pathways including inosine 5'-phosphate degradation, NAD salvage, and ketogenesis, no alterations in the OSM were found. Genetic analysis associated SNP rs1061170 in the complement factor H gene with GA. These findings suggest that microbial alterations may contribute to GA through inflammation and oxidative stress.Registry: ClinicalTrials.gov, NCT02438111, Registration date: 28 April 2015, and NCT04658238, Registration date: 01 December 2020.}, } @article {pmid41629500, year = {2026}, author = {Levhar, N and Hadar, R and Braun, T and Shacham, H and Algavi, Y and Naamneh, R and Efroni, G and Agranovich, B and Abramovich, I and Talan Asher, A and Picard, O and Yavzori, M and Lahat, A and Yablecovitch, D and Kopylov, U and Denson, L and Borenstein, E and Eliakim, R and Ben-Horin, S and Amir, A and Haberman, Y}, title = {Fecal metabolic signals are associated with changes in microbiota and systemic metabolic pathways in Crohn's disease.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6991}, pmid = {41629500}, issn = {2045-2322}, support = {758313//ERC/ ; 785/22//Israel Science Foundation/ ; 4361//Israel Science, Culture, and Sport/ ; 1165359//LITWIN IBD PIONEERS AWARDS/ ; 41/11//I-CORE program/ ; }, abstract = {UNLABELLED: Metabolites play a crucial role in the interactions between the host and its microbiome, influencing disease pathogenesis. To explore metabolic signals linked to Crohn’s Disease (CD), we analyzed paired fecal and serum metabolomics, combined with microbial characterization. Metabolites were identified using liquid chromatography-mass spectrometry, and microbial data were obtained through V4-16 S sequencing and shotgun metagenomics. 202 serum and 294 fecal samples from 80 CD patients and 43 healthy controls were included. Longitudinal analysis highlighted individual variations in metabolic signals and microbial composition. 6602 significant correlations were identified between fecal metabolites and microbes, implying their involvement in microbial-driven disease pathways. Notably, five CD-enriched fecal carbohydrates positively correlated with oral bacteria (e.g., Veillonella parvula, Veillonella dispar, Streptococcus). Additionally, arachidonic acid and three of its derivatives were associated with R. gnavus and Fusobacteria, often implicated in CD pathogenesis. Active CD, defined clinically or by elevated biomarkers (CRP, fecal-calprotectin), exhibited heterogeneous metabolic signatures, with consistent associations between fecal metabolites and established microbial-based indices (CD-related dysbiosis index and alpha diversity). This suggests that specific fecal metabolites potentially sustain microbial imbalances and that targeting metabolic and microbial shifts may offer novel strategies to promote healthier states in CD.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-38558-9.}, } @article {pmid41629563, year = {2026}, author = {Suksa, W and Li, WJ and Luo, ZH and Jiao, JY and Ponce, V and Nuñez-Montero, K and Arce-Johnson, P and Sharma, NR and Thamchaipenet, A and Narsing Rao, MP}, title = {Metagenomic analysis revealed the presence of novel Actinomycetota "Candidatus Solincola uaceae" sp. nov., obtained from a hot spring.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6922}, pmid = {41629563}, issn = {2045-2322}, support = {PHD/0136/2561//The Royal Golden Jubilee Ph.D. Program (RGJ Ph.D.), Thailand Research Fund, National Research Council of Thailand (NRCT)/ ; }, mesh = {*Hot Springs/microbiology ; Phylogeny ; *Metagenomics/methods ; Genome, Bacterial ; *Actinobacteria/genetics/classification/isolation & purification ; *Metagenome ; Base Composition ; }, abstract = {Metagenomic analysis of the hot spring led to the recovery of a high-quality metagenome-assembled genome (MAG), MPNR_HS_01, affiliated with the phylum Actinomycetota. Taxonomy analysis assigned the MAG to "Candidatus Solincola", clustering closely with "Candidatus Solincola tengchongensis". MPNR_HS_01 was 2.82 Mb in size, assembled into 27 contigs, with a G+C content of 63.4%, 49 tRNAs, 4 rRNAs, 98.7% completeness, and no detectable contamination. Functional annotation revealed the presence of complete glycolysis and nonoxidative pentose phosphate pathways, while the tricarboxylic acid cycle was incomplete. Notably, MPNR_HS_01 encoded Wood-Ljungdahl pathway, suggesting carbon assimilation. Energy conservation was supported by hydrogenases, heterodisulfide reductase, Rnf complex, and V-type ATPase. Stress adaptation traits included genes for heat shock proteins, proline biosynthesis, and ion transporters involved in osmotic homeostasis. Although lacking flagellar machinery, MPNR_HS_01 possessed type IV pili and genes associated with twitching motility. Secondary metabolite analysis identified a betalactone biosynthetic gene cluster. Genome-relatedness analyses showed that MPNR_HS_01 was distinct from "Candidatus Solincola" species, with both average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values falling below the established species threshold (95-96% ANI and 70% for dDDH), supporting its designation as a novel species, for which we propose the name "Candidatus Solincola uaceae" sp. nov.}, } @article {pmid41629580, year = {2026}, author = {Khurajog, B and Saenkankam, I and Apiwatsiri, P and Supimon, N and Kamwa, R and Niyomtham, W and Yindee, J and Phupolphan, C and Hampson, DJ and Prapasarakul, N}, title = {Effectiveness of probiotic supplementation on growth performance, gut microbiota, and Salmonella reduction in broiler chicks challenged with Salmonella Typhimurium.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {6983}, pmid = {41629580}, issn = {2045-2322}, support = {FOOD66310012//the 2022-Fundamental Fund, Thailand Science Research and Innovation (TSRI), Chulalongkorn University/ ; }, mesh = {Animals ; *Probiotics/administration & dosage/pharmacology ; *Chickens/microbiology/growth & development ; *Salmonella typhimurium ; *Salmonella Infections, Animal/microbiology/prevention & control ; *Gastrointestinal Microbiome/drug effects ; *Poultry Diseases/microbiology/prevention & control ; Dietary Supplements ; Pediococcus acidilactici ; Animal Feed ; Ligilactobacillus salivarius ; }, abstract = {Salmonella infection poses a major threat to poultry production, affecting both animal health and food safety. With rising concerns over antimicrobial resistance, probiotics have gained attention as effective non-antibiotic interventions to control enteric pathogens while supporting gut health. This study evaluated the efficacy of a locally isolated probiotic blend comprising Ligilactobacillus salivarius BF12, and Pediococcus acidilactici strains BF9 and BYF20 (ProCU) in comparison with a commercial Clostridium butyricum-based probiotic (TOP GUT) in broiler chicks challenged with Salmonella Typhimurium (ST). A total of 196 chicks were assigned to seven groups receiving different treatments with or without Salmonella challenge. Parameters assessed included growth performance, intestinal histomorphometry, cecal Salmonella load, and microbiota composition and function. Before challenge, ProCU increased fecal lactic acid bacteria (LAB) and enriched amino acid and carbohydrate metabolism pathways. Post-challenge, TOP GUT significantly reduced Salmonella load and maintained growth, while ProCU showed a limited effect on pathogen reduction. Both probiotics improved intestinal morphology, increased Lactobacillus and Akkermansia abundance, and upregulated oxidative stress defense genes. Notably, TOP GUT also enriched Parabacteroides and other Bacteroidetes members and prolonged microbial metabolic activity. These findings emphasize strain-specific probiotic effects and suggest that continuous supplementation, particularly with spore-forming strains, may enhance gut health and reduce the Salmonella burden in poultry.}, } @article {pmid41629813, year = {2026}, author = {Astudillo-Guerrero, C and Garrido, Á and Masferrer, D and Sepúlveda, C and Olavarría, L and Del Campo, R and Bravo-Sagua, R and Cubero, FJ and Salech, F and Thumala-Dockendorff, D and Urrutia, PJ and Quera, R and Bunout, D and Espinoza, R and Jorquera, G}, title = {Randomized, double-blind, placebo-controlled trial of fecal microbiota transplantation from young physically active donors to promote resilient aging: clinical trial protocol (ARMOR study).}, journal = {BMC geriatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41629813}, issn = {1471-2318}, abstract = {BACKGROUND: Sarcopenia, characterized by the progressive loss of skeletal muscle mass and strength in older adults, is a key determinant of frailty and functional decline. Affecting up to 15% of individuals aged 65–80 years and more than 50% of those over 80, sarcopenia not only compromises physical autonomy but also increases the risk of metabolic dysfunction and cognitive decline. Emerging evidence suggests that age-related gut microbiota dysbiosis contributes to these impairments by reducing microbial diversity and altering host metabolic signaling, leading to chronic inflammation and mitochondrial dysfunction. The present study aims to evaluate the safety, tolerability, and preliminary efficacy of oral fecal microbiota transplantation derived from young, physically active donors administered to older adults, focusing on outcomes related to functional autonomy, muscle performance, metabolism and cognition. METHODS: This is a double-blind, randomized, placebo-controlled clinical trial involving community-dwelling adults aged 65–84 years. Participants will be randomized 1:1 to receive either FMT capsules or placebo following a short course of oral rifaximin (or placebo). Assessments will be performed at baseline and at 4, 8, and 20 weeks post-intervention. The primary outcomes are safety and tolerability, as well as changes in the Global Index of Functional Autonomy (GDLAM battery) and muscle strength. Secondary outcomes include gait speed, body composition (DXA), metabolic biomarkers, gut microbiota composition (shotgun metagenomics), cognitive performance, and psychological well-being. EXPECTED IMPACT: By restoring microbial diversity and function, FMT from young, active donors may enhance muscle quality, cognitive resilience, and metabolic health in older adults. This study introduces a novel, non-invasive therapeutic approach based on lyophilized and encapsulated microbiota, offering a feasible and scalable strategy to promote healthy aging. TRIAL REGISTRATION: ClinicalTrials.gov NCT06649981. Date of registration October 21, 2024.}, } @article {pmid41629849, year = {2026}, author = {Li, L and Wang, J and Li, Z and Xing, D}, title = {High fever with rash: a case report of spotted fever group rickettsial infection at a construction site.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41629849}, issn = {1471-2334}, abstract = {BACKGROUND: Spotted Fever Group Rickettsiae (SFGR) infection is one of the global public health threats. With the improvement of current hygiene conditions, the incidence of rickettsial infections has significantly decreased compared with previous years; however, in clinical practice, rickettsial infections should still be considered in the differential diagnosis of febrile cases of unknown etiology. CASE PRESENTATION: A construction worker, residing in crowded and poor sanitary conditions, presented with high fever and diffuse cutaneous rash, without reporting other associated discomfort. Empirical treatment with cephalosporin antibiotics failed to alleviate the symptoms. Given the unknown etiology of the patient’s high fever and rash, routine etiological tests yielded negative results, with concurrent abnormalities in the white blood cell differential count of the complete blood count. A strong suspicion of infection by an unusual microorganism prompted the performance of metagenomic next-generation sequencing (mNGS) on venous blood. This test identified infection with Rickettsia rickettsii belonging to the spotted fever group, confirming a rickettsial infection. Following the establishment of the etiology, the antimicrobial treatment regimen was adjusted, and the patient was administered doxycycline for antimicrobial therapy. After treatment, the patient’s body temperature returned to normal, the rash resolved, and the patient was discharged in a state of full recovery. For patients working at construction sites with poor living conditions who present with high fever and rash but lack evidence of conventional microbial infection, clinicians should enhance their differential diagnostic capabilities and maintain vigilance for the occurrence of rickettsial infection.}, } @article {pmid41629888, year = {2026}, author = {Luo, M and Xiao, X and Wu, Y}, title = {Impact of phototherapy on gut microbiota composition and function in neonates with hyperbilirubinemia: a metagenomic analysis.}, journal = {BMC pediatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41629888}, issn = {1471-2431}, support = {No. YTWS20210102//Science and Technology Funding Program of Yantian District Bureau of Science and Technology/ ; }, abstract = {BACKGROUND: Phototherapy serves as the primary treatment for neonatal hyperbilirubinemia (NH). This research aims to investigate the impact of phototherapy on the gut microbiota of NH, and to provide reliable theoretical evidence for the clinical application of phototherapy in such cases.

METHODS: In this self-controlled longitudinal study, 26 newborns diagnosed with NH were enrolled. Fecal samples were collected before (pre-treatment) and 48 h after (post-treatment) initiating phototherapy. The gut microbiota was profiled using high-throughput 16 S ribosomal RNA (rRNA) gene sequencing. Gut microbiota composition and diversity were analyzed using standard bioinformatics pipelines. Data were processed with standard bioinformatics tools for taxonomic annotation, diversity analysis, and functional prediction based on the COG, KEGG, and MetaCyc databases. Statistical significance was assessed using the Wilcoxon signed-rank test (P < 0.05).

RESULTS: While no significant differences were observed at the species level, analysis at the genus level revealed significant alterations in the gut microbiota. The genera Clostridium and Megamonas were identified as significantly increased post-phototherapy. Linear discriminant analysis effect size (LEfSe) analysis further confirmed distinct microbial signatures between the two groups: pre-treatment samples were enriched with families such as Porphyromonadaceae, Lachnospiraceae, Alcaligenaceae, Ruminococcaceae, Moraxellaceae, and the order Pseudomonadales. In contrast, post-treatment samples were predominantly characterized by the class Erysipelotrichi and its associated taxa (Erysipelotrichales and Erysipelotrichaceae). α-diversity indices (Sobs, Chao, Shannon, Simpson) showed no significant differences between the two groups, whereas β-diversity analysis indicated significant microbial community separation (P < 0.05). Predicted functional profiles (based on 16 S rRNA gene data using PICRUSt2) suggested predominant roles in metabolism, genetic information processing, and biosynthesis. However, no significant differences were observed between the pre- and post-treatment groups.

CONCLUSIONS: Phototherapy significantly modulated the gut microbial composition of neonates with NH, notably increasing the abundance of Clostridium and Megamonas, and shifting the community towards Erysipelotrichi, while overall microbial functional capacity remained stable. These findings highlight the dynamic yet resilient nature of the neonatal gut microbiota under phototherapy and provide a foundation for microbiome-informed management strategies in neonatal hyperbilirubinemia.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12887-026-06531-0.}, } @article {pmid41630069, year = {2026}, author = {Jia, X and Zhang, Y and Tian, B and Zhang, G and Mao, S and Qian, W and Sun, D and Liu, J}, title = {Integrative analysis of rumen microbiota and host multi-organ interactions underlying feed conversion efficiency in Hu sheep.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {19}, pmid = {41630069}, issn = {1674-9782}, support = {2021YFF1000703//National Key Research and Development Program of China/ ; KJJQ2025020//Fundamental Research Funds for the Central Universities/ ; HS202302//Research Fund of Tarim University/ ; }, abstract = {BACKGROUND: Rumen microbiota drive fermentation and contribute to variation in feed efficiency among ruminants, yet the underlying host-microbe mechanisms remain poorly understood. This study explores how rumen microbes shape feed conversion efficiency (FCR) through integrated interactions with multiple host organs.

RESULTS: We applied a multi-omics strategy-combining rumen metagenomics and host multi-organ transcriptomics-in Hu sheep with divergent FCR. From a uniform cohort of 150 weaned male Hu lambs, 13 low-FCR (LFCR) and 13 high-FCR (HFCR) individuals were selected for integrated analyses. LFCR sheep exhibited greater growth performance and higher ruminal propionate concentrations compared with HFCR animals. The ruminal microbiomes were enriched in Saccharofermentans and Succinivibrionaceae_UBA2804, and showed functional convergence on amino acid biosynthesis, central carbon metabolism, and propionate-oriented fermentation in LFCR sheep. Carbohydrate-active enzyme profiles indicated that LFCR animals favored fiber- and starch-associated modules (GH126, CBM27, EPS-GT), whereas HFCR animals were enriched in host-glycan and uronic acid-degrading families (CE14, GH89, PL15). Hydrogen metabolism highlighted a clear dichotomy: LFCR animals redirected H₂ toward propionate and sulfate reduction, while HFCR animals retained greater butyrate-producing and methanogenic capacity. Transcriptomic profiling across rumen epithelium, liver, and muscle identified tissue-specific regulatory modules. Only the liver showed strong enrichment of carbohydrate metabolism, with a complete glycogen turnover and glucose export system (GYS2, PYGL, PGM2, G6PC1) and pathways linking microbial short-chain fatty acids to gluconeogenesis. In contrast, muscle efficiency modules were dominated by contractile and cytoskeletal genes (e.g., MYL2, TNNC1, TPM3), reflecting optimized energy expenditure rather than substrate metabolism. No efficiency-associated modules were detected in the rumen epithelium, consistent with its role in propionate absorption rather than metabolism.

CONCLUSIONS: The rumen microbiota of LFCR sheep possess highly efficient capacities for volatile fatty acid and amino acid synthesis, thereby enhancing energy utilization at its source. The resulting propionate further promotes hepatic gluconeogenesis, directly supplying energy for muscle cell growth and ultimately improving FCR. Thus, co-metabolism between rumen microbiota and the liver provides energy for muscle cell growth and is a key determinant of improved feed efficiency.}, } @article {pmid41630101, year = {2026}, author = {Zheng, A and Wang, F and Li, Y and Li, W and Wu, W and Gan, J and Jin, Y}, title = {Concurrent pulmonary candidiasis and tuberculosis in type 2 diabetes mellitus: immune pathogenesis and multidisciplinary management challenges: a case report.}, journal = {Journal of medical case reports}, volume = {20}, number = {1}, pages = {}, pmid = {41630101}, issn = {1752-1947}, mesh = {Humans ; *Diabetes Mellitus, Type 2/complications/drug therapy/immunology ; Aged ; Male ; *Tuberculosis, Pulmonary/drug therapy/diagnosis/complications/immunology ; Tomography, X-Ray Computed ; Antifungal Agents/therapeutic use ; Antitubercular Agents/therapeutic use ; Mycobacterium tuberculosis/isolation & purification ; Treatment Outcome ; Fluconazole/therapeutic use ; Opportunistic Infections/drug therapy ; *Candidiasis, Invasive/drug therapy/diagnosis ; Bacilloscopy ; }, abstract = {BACKGROUND: Type 2 diabetes mellitus predisposes to opportunistic pulmonary infections. We report sequential invasive pulmonary candidiasis followed by tuberculoma in a patient with newly diagnosed type 2 diabetes mellitus and summarize diagnostic pitfalls and management lessons.

CASE PRESENTATION: A 67-year-old Han Chinese man with no previously known diabetes presented with cough and severe hyperglycemia (random glucose 36.3 mmol/L; HbA1c 12.7%). Initial chest computed tomography showed right‑upper‑lobe consolidation. Bronchoalveolar lavage metagenomic next‑generation sequencing detected abundant Candida albicans and sputum Gram stain showed Gram‑negative bacteria predominance; sputum culture yielded no definite pathogen, blood cultures were negative, and human immunodeficiency virus test was negative. After intravenous then oral fluconazole plus intensive insulin therapy, the consolidation regressed. Suspected secondary organizing pneumonia was treated with tapering methylprednisolone. One month later, a new 1.5 cm × 1.3 cm solid nodule appeared in the prior lesion bed. computed tomography‑guided biopsy revealed necrosis, and tissue metagenomic next-generation sequencing confirmed Mycobacterium tuberculosis; standard anti‑tuberculosis therapy was initiated.

CONCLUSION: In patients with diabetes and pulmonary lesions, concomitant or sequential fungal and tuberculous infections should be actively sought with stepwise microbiology (including bronchoalveolar lavage and tissue‑based methods) and early molecular testing (metagenomic next-generation sequencing/Xpert). Steroid exposure for organizing pneumonia may worsen or unmask tuberculosis and must be weighed against infectious risk. Multidisciplinary care (endocrinology-pulmonology-infectious diseases) and rigorous glucose control are essential.}, } @article {pmid41630175, year = {2026}, author = {Lim, SJ and Breitbart, M}, title = {Genetic Features of the Scuticociliate Pathogen Philaster sp. Isolate FWC2 That Causes Sea Urchin Mass Mortality.}, journal = {The Journal of eukaryotic microbiology}, volume = {73}, number = {2}, pages = {e70065}, pmid = {41630175}, issn = {1550-7408}, support = {//University of South Florida/ ; OCE- 2527605//National Science Foundation/ ; }, mesh = {Animals ; *Sea Urchins/parasitology ; *Ciliophora/genetics/isolation & purification/pathogenicity/classification ; Phylogeny ; Genome, Mitochondrial ; Base Composition ; Sequence Analysis, DNA ; }, abstract = {A scuticociliate most closely related to Philaster apodigitiformis caused mass mortalities of diadematoid sea urchins and was cultured as Philaster sp. isolate FWC2. We sequenced the metagenomic content of this isolate, which was predicted to represent ≤ 56% of the complete genome. Based on k-mer counts, the haploid genome size was predicted to be 122-136 Mbp. We assembled and annotated a 4,088 bp nuclear ribosomal operon, a 41,396 bp mitochondrial genome with 19.22% G + C content, 24 protein-coding genes, 6 tRNA genes, and 2 rRNA genes, and a protein sequence homologous to β-PKA in Philaster apodigitiformis potentially involved in host infection.}, } @article {pmid41630294, year = {2026}, author = {Li, R and Liu, X and Song, G and Zhang, CQ and Shen, LJ and Li, WX and Bai, ZP}, title = {Misdiagnosis of pulmonary paragonimiasis as tuberculosis: A case report.}, journal = {Medicine}, volume = {105}, number = {5}, pages = {e47555}, pmid = {41630294}, issn = {1536-5964}, mesh = {Humans ; Female ; *Paragonimiasis/diagnosis/drug therapy ; *Diagnostic Errors ; Adolescent ; Praziquantel/therapeutic use ; *Tuberculosis, Pulmonary/diagnosis ; Animals ; Paragonimus/isolation & purification/genetics ; Antitubercular Agents/therapeutic use ; Anthelmintics/therapeutic use ; Tomography, X-Ray Computed ; *Lung Diseases, Parasitic/diagnosis/drug therapy ; High-Throughput Nucleotide Sequencing ; Hemoptysis/etiology ; }, abstract = {RATIONALE: Pulmonary paragonimiasis and pulmonary tuberculosis exhibit overlapping clinical and imaging manifestations, resulting in frequent misdiagnosis in endemic areas. This case underscores the value of metagenomic next-generation sequencing (mNGS) in correcting such misdiagnoses and emphasizes the importance of managing drug-drug interactions between antituberculosis agents and praziquantel.

PATIENT CONCERNS: An 18-year-old female from Yunnan, a paragonimiasis-endemic region, presented with recurrent cough, expectoration, and hemoptysis for 4 years. She was initially diagnosed with pulmonary tuberculosis based on a positive tuberculin pure protein derivative test and chest computed tomography findings but failed to respond to antituberculosis therapy.

DIAGNOSES: Pulmonary paragonimiasis (initially misdiagnosed as pulmonary tuberculosis).

INTERVENTIONS: In-hospital tuberculosis-related tests (GeneXpert MTB/RIF, sputum/bronchoalveolar lavage fluid culture, bronchoscopic biopsy) were negative. Bronchoalveolar lavage fluid mNGS identified 87 Paragonimus sequences, and Paragonimus antibody enzyme-linked immunosorbent assay was positive. A history of raw crab ingestion was confirmed. Antituberculosis treatment was discontinued for 4 weeks (due to drug interaction), followed by oral praziquantel (1.2 g, 3 times daily for 3 consecutive days).

OUTCOMES: Hemoptysis resolved within 15 days of treatment initiation, and peripheral blood parameters returned to normal ranges. Chest computed tomography at 2 months posttreatment showed marked reduction in lesion size, and complete resolution of pulmonary cavities was observed at the 6-month follow-up, with no recurrence of symptoms.

LESSONS: For chronic respiratory symptoms unresponsive to antituberculosis treatment in endemic regions, proactive inquiry of raw freshwater crustacean consumption history and combined use of serology/mNGS can improve diagnostic accuracy. A 4-week washout period after rifampicin discontinuation is critical before praziquantel administration.}, } @article {pmid41630746, year = {2025}, author = {Yang, B and Zhang, Y and Su, S and He, J and Hu, J and Wang, K}, title = {Metagenomic next-generation sequencing identifies tick-carried pathogens on Tarim Red Deer in Southern Xinjiang.}, journal = {Open veterinary journal}, volume = {15}, number = {11}, pages = {6109-6117}, pmid = {41630746}, issn = {2218-6050}, mesh = {Animals ; *Deer/parasitology ; High-Throughput Nucleotide Sequencing/veterinary ; China/epidemiology ; *Tick Infestations/veterinary/parasitology/epidemiology/virology ; Metagenomics ; *Ticks/virology/microbiology ; Enzyme-Linked Immunosorbent Assay/veterinary ; Bacteria/isolation & purification/genetics ; }, abstract = {BACKGROUND: Ticks are important vectors for a wide range of pathogens, including viruses, bacteria, and protozoa, that impact both humans and animals. Recent advances in metagenomic sequencing have established it as a powerful tool for uncovering the microbial diversity within ticks, enabling the discovery of previously unrecognized pathogens.

AIM: This study aimed to enrich the pathogen database for Tarim red deer in southern Xinjiang and provide experimental data to aid in the diagnosis, prevention, control, and treatment of viral diseases in Tarim red deer.

METHODS: Metagenomic sequencing was employed to analyze the viral species carried by ticks parasitizing the red tarim deer. Additionally, enzyme-linked immunosorbent assay based antibody testing was conducted on 195 red deer samples from four farms M01, M02, M03, and M04 to detect antibodies against the Orf virus.

RESULTS: Next-generation sequencing was used to obtain partial sequences of viruses and bacteria, with further analysis focusing on viruses with higher abundance, such as mule deer pox virus and Orf virus. Serological testing for Orf virus antibodies in 195 red deer samples identified 7 positive cases, resulting in a positivity rate of 3.59% (7/195). Positivity rates were 5.26% (4/76) and 6.12% (3/49) for farms M02 and M04, respectively, whereas no seropositive individuals were identified at farms M01 and M03.

CONCLUSION: This study expands the current knowledge of tick-borne pathogens in southern Xinjiang by identifying diverse viral species associated with tick-infested Tarim red deer. The findings confirm the presence of Orf virus in red deer populations, particularly on farms M02 and M04. These results underscore the importance of ongoing surveillance efforts and offer valuable insights into the diversity and geographical distribution of tick-associated viruses within the arid and semi-arid ecosystems of southern Xinjiang.}, } @article {pmid41630783, year = {2026}, author = {Sachdeva, C and Prasad, SS and Shenoy, KR and Kudva, A and Badareesh, L and Veerabhadrappa, BS and Krishna, SM and Murali, TS}, title = {A longitudinal profiling of microbiome of diabetic foot ulcers shows functional role of microbial communities in wound worsening and chronicity.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100544}, pmid = {41630783}, issn = {2666-5174}, abstract = {Microbial communities in infected diabetic foot ulcers (DFUs) play a critical role in wound morbidity and healing outcomes. While cross-sectional studies that profile the microbial communities using culture-independent approaches are available, we conducted a longitudinal microbiome analysis of 30 diabetic individuals to elucidate the relationship between microbial composition, host factors, and wound healing trajectories. Using a 16S rRNA-based metagenomic approach, we characterized the core microbial communities associated with DFU. Alpha diversity analysis revealed significant differences between DFU microbiome from same individuals across visits, and between DFU and non-DFU cohorts, while no significant differences in beta diversity was observed. Core microbiome analysis identified Pseudomonas to be consistently present across all cohorts, higher abundance of Escherichia and Prevotella in DFU samples across visits while Acinetobacter and Morganella were predominant in non-DFU wounds. Healed DFUs were enriched in Alcaligenes and Corynebacterium while worsened DFUs showed increased abundance of Enterococcus and Serratia. In amputated individuals, Escherichia was found in high abundance, while Staphylococcus was reduced. DFU subjects with high HbA1c levels (7.3-14.9%) had higher abundance of Pseudomonas and Acinetobacter, while Prevotella and Escherichia were abundant in individuals with lower HbA1c (<7.2%). Functional predictive profiling of microbiome communities using MicrobiomeAnalyst showed significant differences between healed and worsened DFUs, especially related to genes with roles in wound healing, drug resistance, biofilm formation, tissue invasion and pathogenicity. Our findings provide insights into the microbial ecology of DFUs, while the longitudinal screening of microbes associated with DFU revealed microbial dynamics and their probable role on wound outcome.}, } @article {pmid41630880, year = {2026}, author = {Liu, MK and Liu, CY and Tang, YM and Liu, Y and Su, Y and Tian, XH and Feng, J and Ni, XL}, title = {Innovative use of unhulled rice in Baijiu brewing: impact on flavor and microbial composition.}, journal = {Food chemistry: X}, volume = {34}, number = {}, pages = {103569}, pmid = {41630880}, issn = {2590-1575}, abstract = {The quality of light-flavor Baijiu (LFB), a traditional Chinese liquor, is strongly influenced by fermentation raw materials. Traditional Baijiu brewing uses rice husk as an excipient, requiring energy-intensive steaming to remove off-flavors-a process that increases production time and costs. This study introduces an innovative co-fermentation technique using unhulled rice (Jingkangyou/Pinxiangyou varieties) with sorghum, improving LFB quality while reducing expenses. Metagenomic and flavoromic analyses compared three groups: a rice husk control and two experimental groups with varying proportions of unhulled rice. Results showed significant flavor differences, with D-lactic acid, leucinic acid, and putrescine levels correlating significantly positively to unhulled rice content. Experimental groups exhibited altered microbial diversity, flavor profiles, and physicochemical properties compared to the control. Key metabolic pathways, including galactose, phenylalanine, and lysine metabolism, were significantly modified, indicating unhulled rice reshaped biochemical reactions. These findings advance understanding of LFB fermentation dynamics and offer strategies for raw material optimization.}, } @article {pmid41631112, year = {2026}, author = {Ji, X and Wang, M and Jin, P and Kong, L and Xu, Y and Chen, W and Liu, B and Wang, Q}, title = {Intracranial hepatitis B virus (HBV) infection following intracerebral hemorrhage in a patient with seronegative occult HBV infection.}, journal = {IDCases}, volume = {43}, number = {}, pages = {e02502}, pmid = {41631112}, issn = {2214-2509}, abstract = {Hepatitis B virus (HBV) infection is primarily associated with liver diseases but can also manifest with various extrahepatic complications. While numerous extrahepatic manifestations have been reported in acute or chronic hepatitis B patients, intracranial HBV infection remains clinically rare. A 43-year-old male had a pre-existing diagnosis of serologically negative occult HBV infection (OBI), which was initially diagnosed by detecting HBV DNA in serum while HBsAg, anti-HBs, anti-HBe, and anti-HBc were all negative. Following intracerebral hemorrhage, the patient's consciousness gradually restored through a course of rehabilitation therapy. Subsequently, the patient developed persistent fever and his level of consciousness progressively deteriorated. Serological testing confirmed the presence of HBsAg and HBeAg, the HBV loads in the serum was high, subsequent metagenomic next-generation sequencing (mNGS) of the cerebrospinal fluid (CSF) revealed positivity for HBV. After 8 weeks of treatment with entecavir, the HBV loads in the serum and CSF decreased significantly, the patient's consciousness improved, and the patient's temperature returned to normal. This study first reported a seronegative OBI patient developing intracranial HBV infection following intracerebral hemorrhage and clarified the diagnostic value of mNGS in rare intracranial infections.}, } @article {pmid41632094, year = {2026}, author = {Gómez-Martínez, D and Ngou, JS and Ugolini, V and Lai, FY and Nilsson, RH and Kristiansson, E and Corcoll, N}, title = {Antibiotic resistance gradient along a large Scandinavian river influenced by wastewater treatment plants.}, journal = {FEMS microbiology ecology}, volume = {102}, number = {3}, pages = {}, pmid = {41632094}, issn = {1574-6941}, support = {AF2022-0079//Adlerbertska forkningsstifelsen/ ; 2019-01161//Formas/ ; }, mesh = {*Rivers/microbiology ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/isolation & purification ; Geologic Sediments/microbiology ; Genes, Bacterial ; Sweden ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Sewage/microbiology ; Metagenomics ; }, abstract = {Recent studies have identified the environment as a key reservoir from which antibiotic resistance genes (ARGs) can be acquired and transmitted to pathogens. However, our knowledge about the presence of ARGs in high-flow river sediments is still limited. We analyzed the resistome of sediment bacterial communities along the Swedish river Göta Älv and investigated the potential dissemination of ARGs and antimicrobials from effluents of wastewater treatment plants (WWTPs). While we detected nine different antimicrobials in the effluent water from the WWTPs through HPLC-MS, their presence was not observed in the river surface water. Analysis by qPCR revealed that the genes sul1 and ermB were the most dominant ARGs among sediment, sludge, and effluent samples. Shotgun metagenomics revealed unique differences between the sludge resistomes of the WWTPs. Moreover, our findings show that ARGs increase downstream of the Göta Älv and their diversity differs from that of the upstream sites. Efflux pump resistance-related genes were most abundant in sediment samples, and beta-lactams and tetracyclines were the most common antibiotic classes targeted by ARGs. Our study emphasizes the importance of urban river sediments as a reservoir of ARGs, as tracking ARGs in WWTPs and their receiving environments improves our understanding of their spread and characteristics.}, } @article {pmid41632347, year = {2026}, author = {Yang, H and Hensley, MK and Nguyen, VD and Al-Yousif, NS and Britton, N and Haidar, G and Yang, L and Shah, F and Bain, W and Wang, X and Qin, S and Ahmed, AA and Blauwkamp, T and Bercovici, S and Kaufman, BA and Redding, KM and Fitch, A and Methé, B and Benos, PV and McVerry, BJ and Morris, A and Kitsios, GD}, title = {Microbial lung-to-blood translocation associates with systemic inflammation in severe pneumonia: evidence from paired plasma and lower respiratory tract metagenomics.}, journal = {Intensive care medicine experimental}, volume = {14}, number = {1}, pages = {10}, pmid = {41632347}, issn = {2197-425X}, support = {P01 HL114453/HL/NHLBI NIH HHS/United States ; R01 HL176668/HL/NHLBI NIH HHS/United States ; R01HL176668/HL/NHLBI NIH HHS/United States ; P01 HL 114453/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: Biological heterogeneity in host inflammatory responses to severe pneumonia predicts clinical outcomes and may influence the effectiveness of immunomodulatory therapy. The upstream drivers of this heterogeneity remain poorly defined. We hypothesized that microbial translocation from the lungs to the bloodstream, detectable via multi-compartment metagenomic analysis, contributes to divergent host responses in pneumonia.

METHODS: In this nested case-control study of mechanically ventilated patients with severe pneumonia, we collected paired plasma and endotracheal aspirate samples at baseline. Plasma samples underwent microbial cell-free DNA (mcfDNA) sequencing, and endotracheal aspirates were analyzed by Nanopore metagenomic sequencing. Host-response biomarkers were measured in both plasma and endotracheal aspirate samples. Microbial translocation of pulmonary origin was defined by the genus-level concordance of detectable taxa between matched endotracheal aspirate and plasma samples.

RESULTS: Among 98 patients (76 pneumonia, 22 controls), plasma mcfDNA was markedly higher in microbiologically confirmed pneumonia compared with culture-negative pneumonia (median 4015 vs. 210 molecules/μL, p = 0.0006). Pulmonary microbial translocation was identified in 31 (41%) pneumonia patients and correlated significantly with plasma soluble ST2 levels, independent of clinical severity. Patients classified into the prognostically adverse hyperinflammatory subphenotype exhibited greater translocating microbial DNA levels compared to hypoinflammatory patients (p = 0.04), further linking translocation to host-response heterogeneity.

CONCLUSIONS: Microbial lung-to-blood translocation is a measurable biological process associated with systemic inflammatory heterogeneity in severe pneumonia. This pathway may represent a novel mechanistic target for precision therapeutic strategies aimed at mitigating immune dysregulation.}, } @article {pmid41633028, year = {2026}, author = {Xue, L and Zhao, W and Wang, C and Ma, Y and Tian, J and Yang, L and Ma, L and Jiang, Q and Chen, Y and Tian, X and Ji, X and Zhang, J and Gu, Y}, title = {Integrating multi-omics to characterize the dynamics of rumen microorganisms and metabolites in Angus cattle at different growth stages.}, journal = {Research in veterinary science}, volume = {203}, number = {}, pages = {106092}, doi = {10.1016/j.rvsc.2026.106092}, pmid = {41633028}, issn = {1532-2661}, mesh = {Animals ; *Rumen/microbiology ; Cattle/microbiology/growth & development/metabolism ; Multiomics ; Male ; Metabolome ; Metabolomics ; Metagenomics ; *Microbiota ; }, abstract = {The development of the bovine rumen microbiome is crucial for growth, yet the dynamic interactions between the microbiome and metabolome during key growth stages remain poorly understood. This study aims to integrate metagenomics and metabolomics approaches to decipher the stage-specific patterns of rumen microbial community and metabolite changes in castrated Angus cattle at three critical growth stages (6, 12, and 18 months of age), and to elucidate their associations with host growth performance. We collected rumen fluid samples from 24 Angus steers (8 per age group) reared under standardized conditions and performed metagenomic and non-targeted metabolomic analyses. Integrated analysis revealed distinct rumen ecosystem succession patterns: multiple species represented by Prevotella_sp._ne3005 dominated at 6 months, Fibrobacter_succinogenes showed significantly increased abundance at 12 months, and Methanobrevibacter_millerae exhibited the most pronounced enrichment at 18 months. Concurrently, key metabolites 12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol exhibited a significant positive correlation with age. Further Pearson correlation analysis revealed strong correlations between the 18-month-enriched characteristic microorganism Methanobrevibacter_millerae and key metabolites (12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol) as well as higher body weight. This study delineates a dynamic map of synergistic interactions between the rumen microbiome and metabolome, confirming their close association with host growth performance. This work provides a systematic multi-omics framework for understanding rumen development in ruminants and identifies potential targets for optimizing beef cattle production performance through microbial or metabolic interventions.}, } @article {pmid41633112, year = {2026}, author = {Tang, X and Bao, Y and Li, J and Liu, B and Huang, Y and Hou, L and Lee, PKH and Han, P}, title = {Microplastics promote N2O emissions by enhancing nitrification via ammonia-oxidizing bacteria in estuarine and coastal sediments.}, journal = {Water research}, volume = {293}, number = {}, pages = {125458}, doi = {10.1016/j.watres.2026.125458}, pmid = {41633112}, issn = {1879-2448}, mesh = {*Nitrification ; Ammonia/metabolism ; *Geologic Sediments/microbiology ; *Nitrous Oxide ; Bacteria/metabolism ; *Microplastics ; Oxidation-Reduction ; Archaea/metabolism ; Estuaries ; }, abstract = {Estuarine and coastal ecosystems are critical interfaces between land and ocean, serving as sinks for anthropogenic pollutants such as ammonium and microplastics. However, the impact of microplastic pollution on nitrification processes in these environments remains largely unexplored. This study investigates the coastal region of the Yangtze River to examine how different microplastic types (polyethylene terephthalate, polypropylene, and polyethylene) affect nitrous oxide (N2O) emissions and the dynamics of nitrifiers, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) Nitrospira, and nitrite-oxidizing Nitrospira. Results from incubation experiments show that all microplastic types significantly increase N2O emissions across sediment samples. The reconstructed representative metagenome-assembled genomes revealed that AOA belong to group I.1a, while AOB are classified within the Nitrosomonas genus. Microplastics were found to have a stronger stimulatory effect on AOB, which are linked to higher N2O production, than on AOA, which are associated with low N2O production, thereby enhancing N2O emissions during nitrification. Furthermore, AOB genomes encode a range of putative plastic-degrading enzymes, which may partially explain their enrichment in microplastic-contaminated environments, although other factors such as differential tolerance to ammonium or oxidative stress cannot be ruled out.}, } @article {pmid41633137, year = {2026}, author = {Zhang, FY and Shu-Kui, D and Wang, LL and Ma, YT and Wu, MZ and Yuan, HM and Yang, JN and Zhang, Y and Zhang, GA and Zhao, J and Liu, C and Guan, DW and Zhao, R}, title = {Metagenomic profiling reveals lung multi-kingdom microbes as forensic markers for aquatic corpses investigation.}, journal = {Forensic science international. Genetics}, volume = {83}, number = {}, pages = {103435}, doi = {10.1016/j.fsigen.2026.103435}, pmid = {41633137}, issn = {1878-0326}, mesh = {Animals ; Humans ; *Drowning/diagnosis ; *Lung/microbiology ; *Microbiota/genetics ; Mice ; *Metagenomics ; Postmortem Changes ; Immersion ; Biomarkers ; Real-Time Polymerase Chain Reaction ; Male ; }, abstract = {The forensic investigation of corpses recovered from aquatic environments presents a major practical challenge. Recent studies have demonstrated that the bacterial community in the lung serves as a valuable indicator for diagnosing drowning, determining the drowning medium and estimating postmortem submersion interval (PMSI). However, the application and significance of lung multi-kingdom microbiome (archaea, eukaryota, and viruses) remains inadequately characterized. Meanwhile, the insufficient sequencing depth of commonly employed techniques, such as amplicon sequencing, restricts our understanding of microbial communities. In this study, we characterized the postmortem lung microbiome of mice submerged in water for up to 10 days using metagenomic sequencing, and subsequently validated the potential microbial biomarkers in both murine and human forensic specimens via qPCR. Integrated analyses were conducted followed by the confirmation of significant lung bacterial communities for drowning diagnosis, inference of drowning site, and estimation of the PMSI. Our findings revealed that bacteria constituted the predominant component of the lung microbiome in submerged murine carcasses, with eukaryota serving as the secondary dominant taxa. Seventeen bacterial and nine eukaryotic features at the species level were identified as potential biomarkers for drowning diagnosis. By detecting the specific molecular markers for Aeromonas species in both murine and human samples, the positive detection of Aeromonas species, particularly Aeromonas hydrophila, provides solid evidence for drowning diagnosis. Additionally, 14 and 17 bacterial species were identified as biomarkers for the inference of drowning site and estimation of PMSI, respectively. Based on the identified potential biomarkers, robust forensic models were constructed using the random forest (RF) algorithm. The accuracy of the bacterial model for drowning diagnosis was 89.29 %, while the accuracy of the eukaryotic model was 87.5 %. For the inference of the drowning site, the bacterial model achieved an accuracy of 100 %. Furthermore, the estimation of the PMSI yielded a mean absolute error of 0.66 ± 0.097 days. Collectively, our findings revealed that the selected 17 bacterial and 9 eukaryotic features in the lungs, particularly Aeromonas hydrophila, are beneficial for drowning diagnosis. Additionally, the other selected bacterial species contribute to the estimation of the drowning site and PMSI, thereby providing more comprehensive and refined information for accurate forensic investigations of corpses recovered from aquatic environments.}, } @article {pmid41633147, year = {2026}, author = {Klaes, S and Gerundt, K and Deobald, D and Henneberger, L and Escher, B and Adrian, L and Cooper, M}, title = {Sequential exposure to anoxic/oxic conditions leads to biotransformation and reduced sitagliptin toxicity in urban hyporheic zones.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141299}, doi = {10.1016/j.jhazmat.2026.141299}, pmid = {41633147}, issn = {1873-3336}, mesh = {*Sitagliptin Phosphate/toxicity/metabolism/chemistry/analysis ; Biotransformation ; *Water Pollutants, Chemical/toxicity/metabolism/analysis/chemistry ; Animals ; Oxidation-Reduction ; Anaerobiosis ; Geologic Sediments/chemistry/microbiology ; Aliivibrio fischeri/drug effects ; Pseudomonas/metabolism/genetics ; Daphnia/drug effects ; *Hypoglycemic Agents/toxicity/metabolism ; Groundwater/chemistry ; }, abstract = {Pharmaceuticals are increasingly recognized as contaminants of concern in aquatic environments. Sitagliptin, an antidiabetic drug that carries a C-CF3 group, which is a precursor of the persistent trifluoroacetic acid, is excreted largely unmetabolized and inefficiently removed in wastewater treatment plants, leading to its widespread detection in surface waters. The hyporheic zone, a region between surface water and groundwater, serves as a natural bioreactor with high microbial activity and diverse redox conditions, offering the potential for sitagliptin attenuation. This study explored the biotransformation of sitagliptin in hyporheic sediments under varying redox conditions through batch experiments and field observations. We showed that batch experiments can complement field observations to capture both mechanistic insights and their environmental relevance. Batch experiments revealed amide hydrolysis and N-acetylation of sitagliptin under anoxic conditions, with subsequent deamination and oxidation of transformation products under oxic conditions. Metagenome-resolved metaproteomics suggested Pseudomonas asiatica as a key player in the oxic transformation. Field analysis of pore water samples identified up to 6.47 µg L[-1] sitagliptin and ten transformation products with concentrations of up to 4.82 µg L[-1] . Amide hydrolysis products were the most abundant transformation products and preferentially formed under anoxic conditions. All investigated transformation products exhibited lower cytotoxicity and oxidative stress responses than sitagliptin in in vitro bioassays, highlighting the toxicity reducing potential of the hyporheic zone. By identifying conditions that promote sitagliptin transformation and characterizing its transformation products toxicologically, our work provides parameters for enhanced sitagliptin removal in aquatic environments and improved risk assessment of fluorinated trace organic contaminants.}, } @article {pmid41633490, year = {2026}, author = {Kelly, MS and Huang, CY and Kim, M and Haghnazari, D and Baig, A and Sun, Y and Lenneman, BR and Tisza, MJ and Cunningham, A and Gold, D and Phipatanakul, W and Lai, PS}, title = {Nasal microbiome and phageome profiles are associated with prospective respiratory viral infection risk in school-age children.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, pmid = {41633490}, issn = {1097-6825}, support = {R01 AI144119/AI/NIAID NIH HHS/United States ; R21 AI175965/AI/NIAID NIH HHS/United States ; R21 AI178155/AI/NIAID NIH HHS/United States ; U01 AI110397/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Respiratory viral infections are common and can trigger asthma exacerbations in children. The roles of the nasal microbiome and phageome (viruses that infect microbes) are not well understood.

OBJECTIVE: We sought to characterize the epidemiology of respiratory viral infections and the interplay between the nasal microbiome, phageome, and viral infections in school-age children with asthma.

METHODS: We performed metagenomic sequencing and quantitative RT-PCR detection of respiratory viruses on 375 nasal samples from 227 school-age children with asthma collected routinely 3 times over a year. Surveys on parent-reported cold and asthma symptoms were administered routinely every 2 months. We evaluated multikingdom changes to the nasal microbiome during infection. A sparse partial least-squares discriminant analysis model identified microbial signatures associated with prospective viral infection risk.

RESULTS: Respiratory viruses were identified in 124 (33%) samples, with rhinovirus being the most prevalent. Cold and asthma symptoms within the previous 14 days had a sensitivity of 79% and 59%, respectively, for quantitative RT-PCR-confirmed infection. Respiratory viral infection increased asthma symptoms and was accompanied by loss of nasal bacterial diversity and a reproducible bloom of pathobionts with no change in the mycobiome or phageome. A baseline bacteriome-dominated profile was protective (adjusted odds ratio, 0.41 [95% CI, 0.25-0.67]; P < .001), whereas phageome profiles increased risk (adjusted odds ratio, 3.74 [95% CI, 1.85-7.55]; P < .001) of viral infection. Specific phages inversely correlated with Staphylococcus epidermidis abundance, the most protective commensal against infection risk.

CONCLUSIONS: The nasal microbiome and phageome exert opposing influences on respiratory viral infection risk, highlighting their potential roles in modulating susceptibility to viral infections.}, } @article {pmid41634308, year = {2026}, author = {Campos-Madueno, EI and Aldeia, C and Endimiani, A}, title = {Gut microbiota and resistome profiles of Swiss expatriates in Africa revealed by Nanopore metagenomics.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {7016}, pmid = {41634308}, issn = {2045-2322}, support = {192514//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Switzerland ; *Bacteria/genetics/classification/drug effects ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Feces/microbiology ; Africa ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The gut microbiota and resistome may change upon exposure to environments with high prevalence of multidrug-resistant pathogens, potentially impacting health and contributing to the spread of antimicrobial resistance genes (ARGs). In this context, expatriates may acquire endemic microbial communities and ARGs while living abroad. In this work, we investigated the microbiota and resistome of Swiss expatriates living in African countries using Nanopore shotgun metagenomics (SMS).Stool samples from expatriates residing in African and European countries (n = 33 and n = 39, respectively) were sequenced using Nanopore V14 chemistry. Taxonomic and resistome profiling was performed with Kraken2 and ResFinder, respectively. Diversity metrics (e.g., Shannon, Simpson) assessed microbial composition. ARG and bacteria associations were determined using GTDB-Tk on metagenome-assembled genomes (MAGs). Plasmid-borne ARGs were characterized with PlasmidFinder.Our results indicated that microbiota composition did not differ between expatriates in African and European countries. However, resistome analysis revealed a higher prevalence of tetracycline (tet) and folate pathway antagonist (dfr, sul) ARGs in those residing in Africa, suggesting adaptation to the local microbial environment or antibiotic policy. Unique plasmid families were also identified in Gram-negative (IncF) and -positive (repUS43) bacteria across African and European cohorts, indicating the potential for ARG dissemination via mobile genetic elements. Overall, Nanopore-based SMS may provide an alternative approach to monitor microbiota and resistome dynamics, and thus assisting early epidemiological surveys.}, } @article {pmid41634410, year = {2026}, author = {Chen, YJ and Ho, HJ and Tseng, CH and Chen, YF and Shieh, JJ and Wu, CY}, title = {Akkermansia Muciniphila Ameliorates Imiquimod-Induced Skin Thickening, Colitis, and Gut Microbiota Alterations: A Metagenome Association Study.}, journal = {Inflammation}, volume = {49}, number = {1}, pages = {78}, pmid = {41634410}, issn = {1573-2576}, support = {NSTC 108-2314-B-075A-008//National Science Technology Council/ ; 110-2314-B-075A-008//National Science Technology Council, Taiwan/ ; TCVGH- 1136801B//Taichung Veterans General Hospital/ ; }, abstract = {UNLABELLED: A decreased abundance of fecal Akkermansia muciniphila (Akk) has been observed in patients with psoriasis and psoriatic arthritis. The potential beneficial effects of Akk in managing psoriasis have been proposed, yet results remain inconsistent and mechanisms unclear. Using imiquimod (IMQ)-treated C57BL/6 mice, we conducted a metagenomic association study of pasteurized Akk (pAkk) in the IMQ mice through whole-genome shotgun sequencing. We also performed a dextran sodium sulfate (DSS)-induced colitis experiment and an intestinal permeability test. The association among pAkk supplements, skin thickness, inflammatory profiles, fecal microbiota alterations, functional genetic predictions, intestinal epithelium inflammation, and barrier integrity was investigated. The study demonstrated that pAkk supplementation ameliorated IMQ-induced skin thickening, weight loss, spleen weight gain, serum IL-17A, TNF-α levels, and DSS-induced colitis. pAkk supplementation was linked to greater fecal microbial diversity and alterations in fecal microbiota composition, with increased prevalence of Muribaculaceae, Bifidobacterium pseudolongum, Desulfovirionaceae, Erysipelotrichaceae, and Alistipes ihumi, which have been implicated in the Gamma-Aminobutyric Acid (GABA) shunt, cholinergic synapse, cell cycle, and Mitogen-Activated Protein Kinase (MAPK) pathways. In conclusion, pAkk may mitigate IMQ-induced skin thickening and DSS-induced colitis, associated with reduced levels of TNF-α and IL-17A. pAkk supplementation alters fecal microbiota and metabolic pathways in IMQ-treated mice.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10753-025-02436-9.}, } @article {pmid41634542, year = {2026}, author = {Sun, M and Wei, J and Wang, M and Xu, H and Ma, W and Wang, Y}, title = {Research on the process of synergistic degradation of corn straw by probiotics-enzymes based on microbiome and metabolomics.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41634542}, issn = {1471-2180}, support = {CARS-39-27//National Wool Sheep Industry Technology System/ ; jytms20231736//Liaoning Provincial Department of Education General Project/ ; 2024010768-JH3/107, 2024012131-JH4/4800//Liaoning Provincial Natural Science Foundation Project/ ; S202410160014//College Student Innovation Project/ ; }, abstract = {BACKGROUND: Probiotics enzyme co-fermentation significantly improves the use efficiency and nutritional value of crop straw, although the underlying synergies are not clear.

METHODS: The experiment used corn straw as the raw material. It was treated with a 0.2% composite enzyme preparation containing cellulase, xylanase, lignin peroxidase, manganese peroxidase, and laccase. A composite microbial inoculant was also added at a total inoculum level of 1 × 10⁸ CFU/g, using a ratio of Lactobacillus, yeast, and Bacillus subtilis of 3:2:1. After thorough mixing, the solution was sprayed evenly onto the straw surface. Fermentation proceeded under room temperature conditions. Multipoint random sampling was carried out on days 7, 14, 21, and 28. By integrating metagenomic, metabolomic, and conventional analytical approaches, this study systematically investigated microbial community structure, dynamic metabolic pathways, and fermentation quality during the process.

RESULTS: The application of a probiotics-enzyme composite led to a clear improvement in fermentation quality. It also reduced the cellulose content of corn stover compared to the untreated control. The results showed that major microbial taxa, such as Proteobacteria and Firmicutes, are influenced by environmental factors like pH and lactic acid. These microbes significantly degraded fibre components (p < 0.05) by secreting extracellular enzymes and organic acids. This process encouraged the accumulation of raw proteins and dipeptides. Key metabolic pathways, such as pyrimidine metabolism and the TCA cycle, were significantly enhanced. This led to the synthesis of valuable metabolites, including mevalonate and biopterin, which have increased antioxidant and metabolic properties.

CONCLUSION: The research results demonstrate that the “microbiota structure—metabolic function—fermentation quality” relationship constitutes a complex and mutually influential system, providing important theoretical support for targeted microbial community regulation and optimization of fermentation processes in straw.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04776-4.}, } @article {pmid41634815, year = {2026}, author = {Hao, X and Wang, X and Wang, X and Wang, C and Li, C and Lu, Y and Cheng, Q and Chen, Z and Zhu, L and Li, C and Shen, X}, title = {Synthetic community derived from the root core microbes of a desert shrub Caragana korshinskii enhances wheat drought tolerance.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41634815}, issn = {2049-2618}, mesh = {*Caragana/microbiology ; Drought Resistance ; *Plant Roots/microbiology ; *Triticum/microbiology/growth & development/physiology ; Desert Climate ; *Microbiota ; Droughts ; Biofilms/growth & development ; Quorum Sensing ; Pseudomonas/genetics/physiology ; Metagenomics ; }, abstract = {BACKGROUND: Drought, intensified by climate change, poses a mounting threat to global food security by severely constraining crop productivity. While microbial inoculants offer promise for drought tolerance, their poor adaptability remains insufficient for extremely water-deficient environments. Desert plants host unique drought-adapted microbiomes that remain largely unexplored for agricultural applications.

RESULTS: Here, we investigated the microbial community of the desert shrub Caragana korshinskii and identified a core set of drought-responsive strains. A synthetic microbial community (SynCom) derived from these strains significantly improved wheat growth under drought stress. Metagenomic analyses revealed that microbial functions related to biofilm formation, quorum sensing, and carbon metabolism were enriched, with Pseudomonas identified as a key functional taxon. Guided by inter-strain interactions in biofilm assembly, we streamlined the consortium into a five-member synthetic community, where quorum-sensing signals promoted community-wide biofilm formation. Community biofilm production improved strain colonization and conferred greater drought tolerance compared to monocultures. In plants, mechanistic investigations indicated that the simplified SynCom inoculation universally upregulated MAPK and jasmonic acid signaling pathways. Furthermore, carbohydrate metabolic pathways such as starch and sucrose metabolism were specifically activated, suggesting a multi-level mechanism underlying SynCom-mediated drought tolerance.

CONCLUSIONS: These findings demonstrate that SynCom constructed on the endophytic flora of desert plants can significantly enhance crop drought tolerance. Our work highlights the pivotal role of community biofilm synthesis in facilitating root colonization and activating a multidimensional drought tolerance network in plants. This study not only gives an ecological perspective on desert microbiome adaptations but also offers a strategic framework for developing effective microbial inoculants for arid-region agriculture. Video Abstract.}, } @article {pmid41634818, year = {2026}, author = {Schuster, L and Greening, C and Malerba, ME and Trevathan-Tackett, S and Athukorala, N and Ricci, F}, title = {Cattle manure suppresses methane consumption and enhances denitrification-associated nitrous oxide production in farm dams.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {59}, pmid = {41634818}, issn = {2049-2618}, support = {APP1178715//National Health and Medical Research Council/ ; FT240100502//Australian Research Council/ ; DE220100752//Australian Research Council/ ; DE210101029//Australian Research Council/ ; ECPF24-4273843556//Faculty of Medicine, Nursing and Health Sciences, Monash University/ ; }, mesh = {Animals ; *Nitrous Oxide/metabolism/analysis ; *Methane/metabolism/analysis ; Cattle ; *Manure/microbiology/analysis ; *Denitrification ; Farms ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Greenhouse Gases/metabolism ; Australia ; Fresh Water/microbiology ; }, abstract = {BACKGROUND: Farm dams (or agricultural ponds) are often heavily polluted freshwater systems because of nutrient-rich manure entering the water through direct deposition and runoff. Accordingly, these systems have among the highest greenhouse gas emissions per area, accounting for 41% of global freshwater methane emissions. Sustainable management actions, such as limiting livestock access through fencing, can significantly reduce nutrient concentrations and greenhouse gas emissions. However, the microbes, processes, and factors controlling greenhouse gas cycling in these systems have not been described. Here, we systematically compared the composition, functions, and activities of the microbes in paired fenced and unfenced cattle farm dams in southeastern Australia.

RESULTS: We found that in situ methane (CH4) and nitrous oxide (N2O) emissions were strongly reduced in fenced dams. Even though methanogen abundance was higher in fenced dams, fencing increased levels of aerobic methanotrophs, including two previously uncharacterised, metabolically flexible species profiled via metagenome-assembled genomes (MAGs). In contrast, we provide gene- and genome-centric evidence that N2O emissions are likely higher in unfenced dams due to increased production (via denitrification) rather than decreased consumption. Manure likely increases CH4 and N2O emissions primarily by driving nutrient-induced eutrophication and hypoxia that, respectively, stimulate denitrifiers and inhibit methanotrophs. However, we also provide evidence that manure-associated methanogens and bacteria occur in farm dams, where they potentially enhance emissions.

CONCLUSIONS: Our findings highlight how anthropogenic activities such as livestock farming can impact microbial communities and biogeochemical cycling, thereby increasing greenhouse gas emissions from freshwater systems, and how simple management actions like fencing can mitigate such emissions. Video Abstract.}, } @article {pmid41634852, year = {2026}, author = {Yan, A and Li, X and Cheng, J and Cheng, Y and Gebeyew, K and Tan, Z and Kang, J and He, Z}, title = {The developmental trajectory and maturation of the Hulunbuir sheep (Ovis aries) microbiome.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {10}, pmid = {41634852}, issn = {2524-4671}, support = {32350410422//National Natural Science Foundation of China/ ; 2022JJ10054//Natural Science Foundation of Hunan Province of China/ ; 32350410422//the National Natural Science Foundation of China/ ; 32302783//Natural Science Foundation of China/ ; }, abstract = {The rumen microbiota plays a pivotal role in the growth performance of host animals, primarily due to its ability to ferment ingested feed. Hulunbuir sheep exhibited a slow growth rate compared to other local breeds. A deeper comprehension of the development of the rumen bacteria community in Hulunbuir sheep can offer insights into the factors contributing to their slow growth rate. This study utilized metagenomic analysis of rumen content samples from Hulunbuir sheep to investigate the patterns of microbial growth and their relationship with the ADG. The results of the PCoA and enterotype analyses demonstrated that the ruminal bacterial community developed distinct characteristics following weaning. The dominant bacterial phyla in the rumen of Hulunbuir sheep, Bacteroidetes and Firmicutes, exhibited a significant age-related change. At the genus level, while the abundance of dominant bacterial genera changed with the growth of Hulunbuir sheep, Prevotella consistently maintained a high abundance across all age time points. We then examined the effects of age on microbial function by analyzing carbohydrate-metabolizing enzymes and protein-metabolizing peptidases. The abundance of carbohydrate-metabolizing enzymes decreased with growth, while peptidases showed opposite dynamics. Under the current feeding conditions correlation analysis showed that the abundances of Firm-04, CAG-83, and GCA-900,199,385 were negatively correlated with ADG (R<-0.4, p < 0.05), while the abundance of Ga6A1 was positively correlated with ADG (R > 0.5, p < 0.05). In addition, we found 67 MAGs related to ADG, which are capable of secreting carbohydrates-metabolizing enzymes and peptidase. This study uncovers the temporal dynamics of rumen microbiota development during the early to late fattening phase and identifies microbes associated with ADG, which could inform strategies to improve growth and production efficiency.}, } @article {pmid41635301, year = {2025}, author = {Jin, X and Ren, L and Ren, X and Wang, J}, title = {Integrative single-cell and metagenomic analysis dissects SARS-CoV-2 shedding modes in human respiratory tract.}, journal = {Biosafety and health}, volume = {7}, number = {1}, pages = {5-16}, pmid = {41635301}, issn = {2590-0536}, abstract = {It is crucial to understand how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sheds in human respiratory tract, but this question remains elusive due to technical limitations. In this study, we integrated published human metagenomic data of SARS-CoV-2 and developed a novel algorithm named RedeCoronaVS to systematically dissect SARS-CoV-2 shedding modes with single-cell data as reference. Our study demonstrated that SARS-CoV-2 particles were the dominant mode of viral shedding in the very early infection phase (≤24 h after hospitalization). Within the first week after hospitalization, SARS-CoV-2 replicas within host cells dominated viral shedding alongside viral particles. One week later, viral fragments became the dominant mode in patients with mild or moderate symptoms, while viral replicas still dominated in some patients with severe symptoms. In addition to epithelial cells, SARS-CoV-2 replicas in neutrophils, macrophages, and plasma cells also played significant roles and were associated with sampling time and disease severity.}, } @article {pmid41635321, year = {2026}, author = {Ozturk, SZ and Aydin, B and Cifcibasi, E}, title = {Antibiotic Resistance Genes in the Subgingival Microbiome in Periodontitis: A Scoping Review of Prevalence, Mobility, and Future Directions.}, journal = {Cureus}, volume = {18}, number = {1}, pages = {e100685}, pmid = {41635321}, issn = {2168-8184}, abstract = {The objective of the study is to evaluate the prevalence, diversity, and mobility of antibiotic-resistant species and resistance genes within the subgingival microbiome of patients with periodontitis. A systematic scoping review was conducted in accordance with PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews) guidelines. Five electronic databases were searched for studies published between January 2020 and December 2025 that used molecular techniques (shotgun metagenomics, PCR/qPCR, 16S + PCR) to detect antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the subgingival plaque of patients with clinically diagnosed periodontitis. Only peer-reviewed articles presenting original data were included; reviews, animal studies, and investigations lacking clear methodological details were excluded. Data extraction included study design, sample size, identified ARGs, associated MGEs, and clinical context. Nine eligible studies involving over 900 subgingival samples were identified. A core resistome was consistently identified across all cohorts, predominantly comprising tetracycline genes (tetM, tetQ, tet32) and macrolide-lincosamide determinants (ermB, ermF, msrD), as well as β-lactamase genes such as cfxA. Sites affected by periodontitis showed higher abundance of these ARGs than healthy controls. Mobile elements, especially Tn916-family conjugative transposons, were often associated with macrolide resistance genes, suggesting potential for horizontal transfer. Methodological differences prevented meta-analysis, and no study compared results based on the 2017 stage/grade classification of periodontitis. The subgingival resistome in periodontitis features a consistent set of tetracycline, macrolide, and β-lactam resistance genes that are increased in disease and frequently associated with mobile transposons. Currently, the evidence remains primarily descriptive; future research should include standardized antibiotic washout periods, longitudinal follow-up, stage/grade stratification, and integrated multi-omics approaches to evaluate functional activity and guide personalized antimicrobial therapies.}, } @article {pmid41635749, year = {2025}, author = {de Oliveira Guimarães, L and de Almeida, AR and Ramos, EDSF and Telles-de-Deus, J and Helfstein, VC and Morais, VDS and Dos Santos, JM and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, É}, title = {Evolutionary features of new picorna-like viruses in Culex (Melanoconion) mosquitoes.}, journal = {Current research in parasitology & vector-borne diseases}, volume = {8}, number = {}, pages = {100333}, pmid = {41635749}, issn = {2667-114X}, abstract = {In this study, we investigated unclassified picorna-like viruses in Culex (Melanoconion) mosquitoes from São Paulo, Brazil, an area of high mosquito biodiversity and arbovirus activity. Two mosquito pools were processed using next-generation sequencing (NGS), and datasets were analyzed via de novo assembly to reconstruct viral genomes and assess evolutionary relationships. We identified two highly similar viral genomes, named Culex (Melanoconion) picorna-like virus, CmV_B38 and CmV_B39, exhibiting 99.93% nucleotide identity, both of which encode a three-domain replication block characteristic of viruses within the order Picornavirales. Phylogenetic reconstruction based on the RNA-dependent RNA polymerase (RdRp) gene revealed that these viruses form a distinct, previously undescribed clade, most closely related to Yongsan picorna-like virus 4 and several other unclassified viruses that have been reported predominantly in Asian regions. These findings may indicate possible geographical connectivity or convergence in viral evolution across distinct ecosystems. Notably, the results highlight the underexplored diversity of insect-specific viruses, particularly those associated with mosquito vectors. Furthermore, the data are consistent with the hypothesis that ecological factors and host specificity could influence the evolutionary dynamics of these viral lineages. The study not only enhances our understanding of the mosquito-associated virome but also emphasizes the critical need for ongoing viral surveillance, especially in biodiverse regions. Such efforts are essential for elucidating the evolutionary dynamics of RNA viruses and for anticipating the emergence of novel viral pathogens that may pose future risks to public health or agriculture.}, } @article {pmid41636304, year = {2026}, author = {Brown, LP and Marizzi, A and Borrego, CM and Gionchetta, G and Zhengzheng, Z and Carneiro, RB and Gago-Ferrero, P and Matamoros, V and Subirats, J}, title = {Metagenomic Assessment of Full-Scale Wastewater Treatment Plants Identifies Sentinel Antibiotic Resistance Gene Families for Monitoring Reclaimed Wastewater and Treated Sludge.}, journal = {Environmental science & technology}, volume = {60}, number = {6}, pages = {4632-4647}, pmid = {41636304}, issn = {1520-5851}, mesh = {*Wastewater ; Sewage ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Anti-Bacterial Agents ; }, abstract = {The new European (EU) regulation on water reuse explicitly incorporates antimicrobial resistance (AMR) into routine monitoring and risk management, creating an urgent need to define target antibiotic resistance genes (ARGs) for reclaimed irrigation water and agricultural sludge. However, existing global data largely focus on secondary effluents, providing little actionable evidence for reuse-oriented systems. Here, we present the first integrated framework combining targeted antibiotic residue analysis with shotgun metagenomics of the resistome, mobilome, and microbiome across full-scale reuse-oriented wastewater treatment plants (WWTPs) in Southern Europe to identify sentinel antibiotic resistance families for monitoring. Reclaimed effluents exhibited lower AMR exposure levels than those typically reported for secondary effluents (<0.5 ARGs/cell), while mobile genetic element (MGE) abundances were comparable to secondary effluents (1-2 MGEs/cell). Effluent communities differed by WWTP configuration: membrane bioreactor combined with ultrafiltration favored nutrient-removal/oxidative-stress taxa and reduced transferable MGEs, whereas plants relying on physical separation (sand filtration or reverse osmosis) retained fecal-associated taxa and MGEs. Specific clinically relevant ARGs persisted after treatments, including aadA and aph(3'')-Ibs (resistance to aminoglycosides), ermB and mphA (resistance to macrolides), and blaOXA-129 (resistance to beta-lactams), which we identify as sentinel markers for monitoring reclaimed water and sludge. We advance a generalizable two-step framework, metagenomic discovery to identify sentinel markers, followed by targeted assays for streamlined surveillance, that provides the first operational blueprint for integrating AMR into water reuse management under the EU regulation.}, } @article {pmid41636495, year = {2026}, author = {Kopp, OS and Morandi, SC and Kreuzer, M and Uldry, A-C and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC}, title = {Impact of contact lenses on the ocular surface microbiome, tear proteome, and dry eye disease.}, journal = {Microbiology spectrum}, volume = {14}, number = {3}, pages = {e0226425}, pmid = {41636495}, issn = {2165-0497}, support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; }, mesh = {Humans ; *Dry Eye Syndromes/microbiology/metabolism/etiology ; Female ; *Tears/chemistry/metabolism/microbiology ; *Microbiota ; Male ; *Proteome/metabolism ; *Contact Lenses/adverse effects/microbiology ; Adult ; *Bacteria/classification/genetics/isolation & purification ; *Eye Proteins/metabolism ; *Eye/microbiology ; Young Adult ; }, abstract = {Although contact lens wear is widespread and known to affect the ocular surface, its impact on the ocular surface microbiome (OSM) remains poorly understood, with existing studies reporting conflicting findings. Additionally, the relationship between contact lens wear, tear proteome, and dry eye disease (DED) is unclear. In this study, we aimed to characterize the OSM (via whole-metagenome shotgun sequencing) and the tear proteome of 25 contact lens wearers and 23 age- and sex-matched controls. The dominant phyla were Actinobacteria, Proteobacteria, and Firmicutes, with Cutibacterium acnes being the most abundant species. No significant differences in microbial composition, diversity, or tear proteome were observed between contact lens wearers and controls. DED parameters (tear breakup time, Schirmer's test, tear osmolarity, and Ocular Surface Disease Index [OSDI]) also showed no significant differences, although contact lens wearers reported a trend toward higher subjective symptoms (OSDI). Sex-stratified analysis revealed a marginal difference in microbial beta diversity between male contact lens wearers and male controls, along with increased tear production in male contact lens wearers. Female contact lens wearers reported a higher OSDI compared to female controls. These findings suggest that contact lens wear does not significantly alter the OSM or tear proteome in healthy individuals, although sex-specific responses may warrant further investigation.IMPORTANCEContact lenses are worn by millions of people, yet the scientific literature contains conflicting reports about their impact on the microbial communities that are naturally present on the eye surface. This study addresses these knowledge gaps by examining both the eye microbiome and tear proteins using advanced sequencing and linking them to dry eye symptoms. Understanding the relationship between contact lens wear, natural eye bacteria, and tear composition is essential for resolving contradictory findings in the field. Additionally, identifying potential sex-specific differences in how individuals respond to contact lens wear could lead to more personalized approaches to contact lens management.}, } @article {pmid41636510, year = {2026}, author = {Anne Hallowell, H and Malogan, J and Suez, J}, title = {Tools and approaches to study the human gut virome: from the bench to bioinformatics.}, journal = {mSystems}, volume = {11}, number = {3}, pages = {e0100225}, pmid = {41636510}, issn = {2379-5077}, mesh = {Humans ; *Virome/genetics ; *Computational Biology/methods ; *Gastrointestinal Microbiome/genetics ; *Viruses/genetics/isolation & purification ; Bacteriophages/genetics ; Metagenomics/methods ; Metagenome ; }, abstract = {The human gastrointestinal tract is home to a diverse community of microorganisms from all domains of life, collectively referred to as the gut microbiome. While gut bacteria have been studied extensively in relation to human host health and physiology, other constituents remain underexplored. This includes the gut virome, the collection of bacteriophages, eukaryotic viruses, and other mobile genetic elements present in the intestine. Like gut bacteria, the gut virome has been causatively linked to human health and disease. However, the gut virome is substantially more difficult to characterize, given its high diversity and complexity, as well as multiple challenges related to in vitro cultivation and in silico detection and annotation. In this mini-review, we describe various methodologies for examining the gut virome using both culture-dependent and culture-independent tools. We highlight in vitro and in vivo approaches to cultivate viruses and characterize viral-bacterial host dynamics, as well as high-throughput screens to interrogate these relationships. We also outline a general workflow for identifying and characterizing uncultivated viral genomes from fecal metagenomes, along with several key considerations throughout the process. More broadly, we aim to highlight the opportunities to synergize and streamline wet- and dry-lab techniques to robustly and comprehensively interrogate the human gut virome.}, } @article {pmid41636536, year = {2026}, author = {Della-Negra, O and Servien, R and Milferstedt, K and Hamelin, J and Klopp, C and Hoede, C}, title = {Metagenome-assembled genomes from oxygenic photogranules obtained from photobioreactors treating synthetic wastewater.}, journal = {Microbiology resource announcements}, volume = {15}, number = {3}, pages = {e0131025}, pmid = {41636536}, issn = {2576-098X}, support = {ANR-21-CE45-0036-0//Agence Nationale de la Recherche/ ; }, abstract = {Twenty-five high-quality metagenome-assembled genomes (MAGs) were recovered from photogranules to treat synthetic wastewater. They were dominated by Leptolyngbya boryana. Cyanobacterial MAGs encoded photosynthesis and nitrogen fixation pathways, supporting internal oxygen and nitrogen cycling. Most heterotrophic MAGs contributed to nitrogen removal, highlighting the metabolic complementarity within photogranules studied for wastewater treatment.}, } @article {pmid41637142, year = {2026}, author = {Dos Santos, SJ and Gloor, GB}, title = {Incorporating Scale Uncertainty into Differential Expression Analyses Using ALDEx2.}, journal = {Current protocols}, volume = {6}, number = {2}, pages = {e70307}, pmid = {41637142}, issn = {2691-1299}, mesh = {*Gene Expression Profiling/methods ; Uncertainty ; Transcriptome ; *Software ; *Metagenomics/methods ; Sequence Analysis, RNA/methods ; }, abstract = {Differential abundance or expression analyses are routinely performed on metagenomic, metatranscriptomic, and amplicon sequencing data. In such datasets, analysts usually have no information regarding the true scale (i.e., size) of the microbial community or sample under study, with inter-sample differences in sequencing depth instead being driven by technical variation rather than biological factors. Recent work has demonstrated that normalizations used in all analysis tools make incorrect assumptions about the biological scale of the system in question, leading to unacceptably high false-discovery rates in the output. To mitigate this, analysts can acknowledge and account for the uncertainty of the overall system scale during normalization by building scale models of the data-a feature that has been integrated into the ALDEx2 R package. Here, we provide reproducible examples that demonstrate how to incorporate scale models into differential expression analyses of RNA-seq data using bulk transcriptome and metatranscriptomic datasets, as well as the consequences of not doing so. We also show how to use the output of ALDEx2 to create high-level exploratory visualizations of their data through principal component analysis. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Using a simple scale model for differential expression analysis to avoid dual-cutoff P value/significance thresholds Basic Protocol 2: Implementing a full informed scale model to correct scale-related data asymmetry in differential expression analyses Basic Protocol 3: Visualizing ALDEx2 outputs using a compositional approach: Principal component analysis.}, } @article {pmid41637508, year = {2026}, author = {Kaur, G and Crawford, SE and Javornik Cregeen, S and Surathu, A and Ayyar, BV and Apostol, CV and Phuc, HN and Ettayebi, K and Boussattach, A and Zeng, XL and Blutt, SE and Doddapaneni, H and Muzny, DM and Coarfa, C and Anish, R and Prasad, BVV and Atmar, RL and Ramani, S and Estes, MK}, title = {Overcoming host restrictions to enable continuous passaging of GII.3 human norovirus in human intestinal enteroids.}, journal = {Science advances}, volume = {12}, number = {6}, pages = {eaeb0455}, pmid = {41637508}, issn = {2375-2548}, support = {U19 AI144297/AI/NIAID NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; S10 OD030414/OD/NIH HHS/United States ; P01 AI057788/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Norovirus/physiology/genetics ; Virus Replication/drug effects ; *Intestines/virology ; Chemokines/metabolism ; *Caliciviridae Infections/virology ; *Organoids/virology ; *Host-Pathogen Interactions ; }, abstract = {The establishment of human intestinal enteroids (HIEs) as a model for human norovirus (HuNoV) replication has been transformative for studying this leading cause of gastroenteritis. However, indefinite passaging of HuNoVs in HIEs remained a challenge, necessitating the use of patient stool samples as viral inocula. Using RNA-seq, we identified CXCL10, CXCL11, and CCL5 as up-regulated chemokines, suggesting their potential as host restriction factors. TAK-779, a CXCR3/CCR5/CCR2 antagonist, enhanced GII.3 HuNoV replication and viral spread in a dose- and time-dependent manner, enabling successful passaging of GII.3 HuNoV in two different HIE lines and generation of viral stocks. Sequencing passaged virus revealed one consensus change in the major capsid protein and several dynamic adaptations, suggesting emergence of variants. TAK-779 also enhanced replication of GI.1 and GII.17 strains, but not GII.4, suggesting strain-specific host interactions. This breakthrough in passaging provides insight into HuNoV-host interactions, establishes a scalable in vitro system for virus propagation, and opens avenues for structural, biochemical, and therapeutic studies.}, } @article {pmid41637515, year = {2026}, author = {Liu, X and Cheng, X and Zhang, Y and Zhao, R and Wang, W and Li, Y and Chen, ZQ and Qiu, X and Tuovinen, OH and Bull, ID and Evershed, RP and Wang, H}, title = {High-efficiency methane consumption by atmospheric methanotrophs in subsurface karst caves: The irrefutable methane sink.}, journal = {Science advances}, volume = {12}, number = {6}, pages = {eady5942}, pmid = {41637515}, issn = {2375-2548}, mesh = {*Methane/metabolism ; Oxidation-Reduction ; *Caves/microbiology ; *Atmosphere ; Soil Microbiology ; }, abstract = {Subsurface karst systems represent substantial but underexplored methane sinks, yet the identities and activities of cave-dwelling methanotrophs remain poorly characterized. We detected increased methane oxidation rates from 2.9 ± 0.1 to 90.7 ± 4.5 ng·g[-1]·hour[-1] while supplied with 2 to 500 parts per million (ppm) CH4 to cave sediments. Atmospheric methanotroph Upland Soil Clusters γ (USCγ), responsible for this oxidation, was further assigned to three genera within the family Candidatus (Ca.) Methyloligotrophaceae, including two previously unrecognized genera. Nano-scale secondary ion mass spectrometry (NanoSIMS) imaging and the produced [13]C-PLFAs (phospholipid fatty acids) and [13]CO2 in [13]CH4-fed microcosm confirmed methane as both carbon and energy sources. These methanotrophs exhibited low half-saturation constant (Km; 138.8 ± 15.8 ppm), high carbon assimilation efficiency (>50%), and metabolic versatility, as revealed by metagenomics and metatranscriptomics analyses. By extrapolating global distribution of Ca. Methyloligotrophaceae and comparing methane oxidation rates between caves and soil ecosystems, we conservatively estimate that subsurface karst in southwest China sequester ~0.56 Tg CH4 annually. These findings highlight the ecological importance of karst ecosystems as a previously overlooked methane sink.}, } @article {pmid41638014, year = {2026}, author = {Song, Y and Song, X and Liu, X and Jiang, L and Chai, L}, title = {Metagenomics and targeted metabolomics uncover concomitant gut microbiota dysbiosis and bile acid metabolism alteration in norfloxacin-exposed Bufo gargarizans tadpoles.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {292}, number = {}, pages = {107742}, doi = {10.1016/j.aquatox.2026.107742}, pmid = {41638014}, issn = {1879-1514}, mesh = {Animals ; *Norfloxacin/toxicity ; *Bile Acids and Salts/metabolism ; Larva/drug effects/microbiology ; *Water Pollutants, Chemical/toxicity ; Metagenomics ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/toxicity ; Metabolomics ; }, abstract = {Norfloxacin (NOR) is a fluoroquinolone antibiotic widely detected in aquatic environments, yet little is known about its toxic effects on amphibians. Bile acids (BAs) are crucial metabolites derived from gut microbiota-host co-metabolism and play vital roles in maintaining host health. BA composition is regulated by the gut microbiota through specific enzymes: bile salt hydrolases (BSHs) deconjugate primary BAs; bile acid-inducible enzymes (BAIs) and hydroxysteroid dehydrogenases (HSDHs) then convert them into secondary BAs. This study investigated the effects of NOR on Bufo gargarizans tadpoles using a combination of intestinal-targeted BA metabolomics, metagenomics, and histopathological analysis. Tadpoles were exposed to 10 and 100 μg/L NOR from Gs26 to Gs36, with 4 independent biological replicates per group. Our results showed that NOR exposure significantly increased the relative abundance of gut microbiota encoding BAIs, HSDHs, and/or BSHs, which was accompanied by a decrease in the ratios of primary/secondary BAs and conjugated/deconjugated BAs. Meanwhile, NOR treatment elevated antibiotic resistance gene abundance and induced intestinal histopathological alterations in tadpoles, characterized by reduced epithelial cell height and hypertrophy of smooth muscle cells (SMCs). In summary, environmentally relevant concentrations (10 and 100 μg/L) of NOR affected the intestinal microbiota, thereby disrupting BAs biotrasformation, ultimately potentially compromising intestinal health in tadpoles. This highlighted the potential ecological risks posed by NOR pollution in aquatic ecosystems.}, } @article {pmid41638332, year = {2026}, author = {Wu, B and Zhang, N and Yang, G and Yu, N and Xie, Z and Xia, J and Luo, W and Liu, X and Wang, D and Zhang, Y and Tang, L}, title = {Unraveling the microbial and functional mechanisms driving rapid algal-bacterial granular sludge formation in mariculture wastewater.}, journal = {Environmental research}, volume = {295}, number = {}, pages = {123941}, doi = {10.1016/j.envres.2026.123941}, pmid = {41638332}, issn = {1096-0953}, mesh = {*Sewage/microbiology ; *Wastewater/microbiology ; *Waste Disposal, Fluid/methods ; *Bacteria/metabolism/genetics ; Salinity ; }, abstract = {Algal-bacterial granular sludge (ABGS) has unique advantages and broad application prospects in the treatment of mariculture wastewater. However, the rapid granulation process and performance evolution of ABGS under high salt stress have not been clearly defined. Compared with AGS, the influence of algal intervention on the structural integrity and metabolic activity of particles under the same salinity gradient is also unknown. Therefore, in this study, a parallel ABGS and AGS system was established. The results showed that intertwined algal filaments provided a structural skeleton for particle formation and led to complete granulation of ABGS within 20 days. Compared with conventional AGS, ABGS formed under high-salinity conditions exhibited a larger average particle size (1.07 mm), higher biomass (7.59 g/L) and higher extracellular polymeric substance (EPS) secretion (258.56 mg/g VSS). Additionally, chemical oxygen demand (COD) and total inorganic nitrogen (TIN) removal efficiencies exceeded 99% and 66%, respectively. Metagenomic analysis revealed that Thauera, Fragilaria and Nitzschia were dominant taxa associated with granule formation and stabilization. ABGS also showed an elevated abundance of functional genes associated with nitrogen metabolism (nxrA, nasA, and nasD) and polysaccharide metabolism (glmM, glmU, and pmm-pgm), which were in accordance with the enhanced nitrogen removal and granulation capability. Increased abundance of tricarboxylic acid cycle genes further indicated the superior granulation performance of ABGS. Overall, this study clarifies the morphological evolution and microbial functional mechanisms underlying rapid ABGS formation in mariculture wastewater, offering valuable insights for engineering optimisation and application of this technology in saline wastewater treatment.}, } @article {pmid41638346, year = {2026}, author = {Behrens, LMP and Fernandes, GDS and Gonçalves, GF and Nunes, FVM and Weimer, RD and Moreira, JCF and Dorn, M}, title = {Limitations and opportunities in multi-omics integration for neurodevelopmental, neurodegenerative and psychiatric disorders: A systematic review.}, journal = {Neuroscience}, volume = {599}, number = {}, pages = {76-93}, doi = {10.1016/j.neuroscience.2026.01.019}, pmid = {41638346}, issn = {1873-7544}, mesh = {*Multiomics ; Humans ; *Neurodegenerative Diseases/metabolism/genetics ; *Mental Disorders/metabolism/genetics ; *Neurodevelopmental Disorders/genetics/metabolism ; Animals ; Genomics ; Proteomics ; Metabolomics ; }, abstract = {Recent advances in high-throughput technologies have led to an increased generation of biological data across genomics, transcriptomics, proteomics, epigenomics, and metabolomics. However, a major challenge remains: effectively integrating these multi-omics datasets to allow a more holistic understanding of the complex, interconnected mechanisms underlying human diseases. Neurodevelopmental, neurodegenerative, and psychiatric disorders are particularly multifactorial and heterogeneous, making them candidates for multi-omics approaches. In this context, this systematic review assesses the current state of multi-omics integration in neurological research. Records retrieved from five major databases were processed, and 156 studies were included for further analysis. The most frequently studied conditions were Alzheimer's Disease, Depressive Disorder and Parkinson's Disease, with epigenomics-transcriptomics and metagenomics-metabolomics emerging as the most common omics pairings. The field remains dominated by studies integrating pairs of omics layers. Only a limited number of computational tools are currently being applied to the integration of more than two omics layers, highlighting a gap in comprehensive multi-omics modeling. Despite progress, key challenges persist, including data accessibility and the need for standardized frameworks to allow cross-study comparisons. Moreover, most computational findings lack experimental validation in wet-laboratory settings. Future research should address these challenges, develop scalable algorithms for integrating multi-omics data, and leverage large, open-access datasets. Integrating computational predictions with experimental validation could help researchers prioritize high-confidence biomarkers relevant to clinical applications. Collaborative efforts among bioinformaticians, clinicians, and experimentalists will be essential to translating these advances into clinically actionable solutions.}, } @article {pmid41638592, year = {2026}, author = {Xiao, Y and Cheng, Z and Cai, J and Guo, Z and Chen, J and Su, Y and Cao, F and Chen, D}, title = {Metagenomic and metatranscriptomic analysis of sulfur-driven autotrophic denitrification coupled with carbon assimilation: roles of sulfur-to-nitrogen ratio and hydraulic retention time.}, journal = {Bioresource technology}, volume = {445}, number = {}, pages = {134153}, doi = {10.1016/j.biortech.2026.134153}, pmid = {41638592}, issn = {1873-2976}, mesh = {*Denitrification/genetics ; *Sulfur/metabolism ; *Nitrogen/metabolism ; *Carbon/metabolism ; *Autotrophic Processes ; Bioreactors/microbiology ; *Metagenomics/methods ; Nitrates/metabolism ; Biomass ; *Gene Expression Profiling ; *Transcriptome ; }, abstract = {The sulfur autotrophic denitrification (SAD) process is a promising technology for nitrogen-containing wastewater treatment, with research predominantly focused on nitrate and sulfide transformations, while the potential for inorganic carbon assimilation remains underexplored. In this study, a long-term stable SAD system was maintained in an airlift bioreactor by adding an inorganic carbon source to evaluate the effects of sulfur-to-nitrogen (S/N) ratio and hydraulic retention time (HRT) on operational performance. Under optimal operating conditions (S/N = 3:2; HRT = 8 h), the system sustained high performance, achieving 99.56 ± 1.47% nitrate removal, 60.28 ± 4.19% elemental sulfur yield, and 46.48 ± 4.07% inorganic carbon assimilation efficiency. Biomass sulfur acted as a sink for extracellular free organic carbon (EFOC), thereby alleviating its accumulation-induced negative feedback on carbon assimilation. Microbial community analysis revealed a substantial enrichment of the autotrophic sulfur-oxidizing bacterium Sulfurovum, showing a marked 9.46-fold increase in relative abundance compared with the original sludge. At S/N = 3:2, metagenomic and metatranscriptomic analyses detected a 6.39-fold increase in the transcription of CBB cycle genes (rbcL/rbcS), driving a clear shift in metabolic flux toward carbon assimilation. Shortening the HRT (4 h) preferentially activated the denitrification pathway, which was evidenced by an 84.65% rise in nosZ expression (from 2,623.29 to 4,844.01 TPM), thereby bolstering N2O reduction. Our findings offered critical insights for designing engineering solutions that enable concurrent efficient denitrification, sulfur recovery, and reduced carbon emissions.}, } @article {pmid41639055, year = {2026}, author = {Lai, D and Mosier, D and Palmer, M and Mayali, X and Johnston, J and Saldivar, W and Covington, JK and Jiao, JY and Murali, R and Seymour, CO and Liu, L and Hua, ZS and Li, WJ and Weber, PK and Pett-Ridge, J and Colman, DR and Boyd, ES and Nunoura, T and Dodsworth, JA and Hedlund, BP}, title = {Branched-chain amino acid specialization drove diversification within Calditenuaceae (Caldarchaeia) and enables their cultivation.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41639055}, issn = {2041-1723}, support = {1557042//National Science Foundation (NSF)/ ; 2038420//National Science Foundation (NSF)/ ; 80NNSC17KO548//National Aeronautics and Space Administration (NASA)/ ; 80NSSC25M0046//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 92251302//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32370011//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Amino Acids, Branched-Chain/metabolism ; Phylogeny ; Metagenome ; In Situ Hybridization, Fluorescence ; *Archaea/metabolism/genetics ; }, abstract = {Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching members of the archaeal phylum Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Metagenome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×10[6] cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through the TCA cycle coupled with aerobic respiration and through production of branched-chain organic acids by overflow metabolism. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities.}, } @article {pmid41639269, year = {2026}, author = {Piera Líndez, P and Danielsen, LS and Kovačić, I and Pielies Avellí, M and Nesme, J and Jensen, LJ and Andersen, JN and Sørensen, SJ and Rasmussen, S}, title = {Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41639269}, issn = {1546-1696}, support = {NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; }, abstract = {Plasmids are extrachromosomal DNA molecules that enable horizontal gene transfer in bacteria, often conferring advantages such as antibiotic resistance. Despite their importance, plasmids are underrepresented in genomic databases because of challenges in assembling them, caused by mosaicism and microdiversity. Current plasmid assemblers rely on detecting circular paths in single-sample assembly graphs but face limitations because of graph fragmentation, entanglement and low coverage. We introduce PlasMAAG (plasmid and organism metagenomic binning using assembly-alignment graphs), a method to recover plasmids and cellular genomes from metagenomic samples. PlasMAAG complements assembly graph signals across samples by generating an 'assembly-alignment graph', which is used alongside common binning features for improved plasmid reconstruction. On synthetic benchmark datasets, PlasMAAG reconstructed 50-121% more near-complete plasmids than competing methods and improved the Matthews correlation coefficient of geNomad contig classification by 28-106%. On hospital sewage samples, PlasMAAG outperformed competing methods, reconstructing 33% more plasmid sequences. PlasMAAG enables the study of organism-plasmid associations and intraplasmid diversity across samples.}, } @article {pmid41639568, year = {2026}, author = {Zeng, Y and Qi, H and Guo, W and Tan, X and Huang, B and Hu, R and Ouyang, X}, title = {Multi-omics insights into Shenling Baizhu Powder's amelioration of murine asthma through gut microbiota and Glutamine-GLS1 pathway.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41639568}, issn = {2045-2322}, support = {2023BSQD002//Doctoral Scientific Initiate Project of Shunde Women and Children's Hospital of Guangdong Medical University (Maternity & Child Healthcare Hospital of Shunde Foshan)/ ; 20241090//The Project of Administration of Traditional Chinese Medicine of Guangdong Province/ ; 2023A04J0550//Guangzhou Municipal Science and Technology Project/ ; 20250403//Medical Research Project of Foshan Municipal Health Bureau/ ; }, mesh = {Animals ; *Asthma/drug therapy/metabolism/microbiology ; Mice ; *Glutamine/metabolism ; *Gastrointestinal Microbiome/drug effects ; Multiomics ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Cytokines/metabolism ; Th17 Cells/immunology/drug effects ; Metabolomics ; Mice, Inbred BALB C ; Disease Models, Animal ; Th2 Cells/immunology/drug effects ; Ovalbumin ; Female ; Lung/drug effects/pathology ; }, abstract = {Shenling Baizhu Powder (SLBZP) is a prominent formulation widely used in the treatment of pulmonary diseases. However, studies examining the mechanisms of SLBZP for treating asthma are limited. This study aimed to clarify the efficacy and possible mechanisms of SLBZP in the context of asthma from the perspective of gut microbiota-metabolism-immune crosstalk. Key parameters including airway hyperresponsiveness, lung pathological features and the expression of inflammatory mediators from Th2 and Th17 cells were employed to validate the anti-inflammatory properties of SLBZP. The anti-asthma mechanism of SLBZP was investigated using metagenomic sequencing, metabolomics, flow cytometry, RT-qPCR, immunohistochemistry (IHC) and immunofluorescence (IF). SLBZP demonstrated significant capacity to mitigate histopathological alterations associated with ovalbumin-induced asthma and suppress the secretion of inflammatory mediators (IL-4, IL-5, IL-13 and IL-17A) in BALF. Metagenomic results demonstrated that the protective effects of SLBZP were primarily associated with Ligilactobacillus, Eubacterium and Clostridium. Additionally, metabolomics results identified that three vital metabolic pathways were substantially regulated by SLBZP in asthmatic mice, especially D-glutamine and -glutamate metabolism. Furthermore, IHC and IF results showed that SLBZP significantly inhibited the expression of GLS1 and GOT1, which inhibited the conversion of L-glutamine to α-ketoglutarate and regulated the imbalance of Th1/Th2 and Treg/Th17. RT-qPCR results showed that SLBZP promoted the expressions of T-bet, IFN-γ, IL-10 and Foxp3 mRNA, and inhibited the expression of GATA3, IL-4, IL-5, IL-13, IL-17A and RORγt mRNA. The findings from flow cytometry provided additional evidence. Thus, this modulated the imbalance of Th1/Th2 and Treg/Th17 and exerted the immunomodulatory properties of SLBZP. SLBZP exerted protective effects against OVA-induced asthma and modified the structure and functional characteristics of the gut microbiota, and serum metabolite profiles in asthmatic mice. The anti-asthma mechanism of SLBZP may be associated with the modulation of the gut microbiota and Glutamine-GLS1 pathway.}, } @article {pmid41639832, year = {2026}, author = {Ma, R and Sun, J and Zhu, J and Wu, Y and Shi, Y and Yang, Y and Wang, S and Han, X and Li, S and Gao, L and Zhao, X and Hua, R and Wang, Y}, title = {Metagenomic next-generation sequencing for efficient detection of human parvovirus B19 in amniotic fluid: a case study of diagnosis and prenatal management of fetal infection.}, journal = {BMC pregnancy and childbirth}, volume = {26}, number = {1}, pages = {}, pmid = {41639832}, issn = {1471-2393}, support = {HHJH2412//Medical Science and Technology Talent Promotion Project of The International Peace Maternity and Child Health Hospital/ ; 2023YFC2705901//National Science and Technology Major Project/ ; 22Y11902300//Science and Technology Commission of Shanghai Municipality/ ; 202440131//Shanghai Municipal Health Commission/ ; YG2023ZD26//Shanghai Jiao Tong University/ ; }, abstract = {OBJECTIVE: Human parvovirus B19 (B19V) infection during pregnancy can lead to a range of adverse outcomes such as miscarriage, premature delivery, fetal hydrops, severe anemia, myocarditis, heart failure, and even fetal demise, posing significant risks to maternal and fetal health. The aim of this study was to establish a more efficient method for detecting B19V in amniotic fluid and to explore and optimize early diagnosis and treatment strategies for fetal B19V infection. METHODS: Intrauterine transfusion (IUT) was performed due to the occurrence of severe fetal anemia and hydrops. Amniotic fluid was obtained for genetic detection. Metagenomic next-generation sequencing (mNGS) and bioinformatic analysis were performed on the amniotic cells to identify the viral genome. RESULTS: In this study, the B19V genome was identified in the amniotic cells of the suspected case, with three viral coding sequences mapped. The coverage density reached 99.9% of the viral sequences. No other pathogen sequences, including bacteria, fungi, parasites, chlamydia, mycoplasma, rickettsia and other viruses, were identified. CONCLUSION: Our study confirmed the diagnosis of fetal B19V infection in a suspected case via amniotic fluid virus genome detection. It is the first time to exhibit the clinical application of mNGS to systematically detect the B19V genome in amniotic fluid in prenatal practice, and to achieve good results in combination with clinical management. The study highlighted the importance of comprehensive management of B19V fetal infection and demonstrated the advantages and wide application prospects of mNGS in intrauterine infection diagnosis.}, } @article {pmid41640388, year = {2026}, author = {Li, S and Li, W and Zhang, X and Zhou, H and Zhan, J}, title = {Harnessing Population Genomics, Gut Microbiota, and Environmental DNA Surveillance for the Conservation of Chinese Spotted Seals in a Changing World.}, journal = {Ecology and evolution}, volume = {16}, number = {2}, pages = {e72952}, pmid = {41640388}, issn = {2045-7758}, abstract = {The triple planetary crisis-encompassing climate change, biodiversity loss, and pollution-poses escalating threats to Earth's systems, particularly impacting marine mammals. The spotted seal (Phoca largha Pallas 1811), currently recognized as the only pinniped species known to breed in China, holds the status of a National Grade I protected species in China. To elucidate the genetic diversity of Chinese spotted seal populations and provide scientific foundations for their conservation and management, this review systematically summarized the fundamental biological characteristics and documented migration routes of spotted seal populations in China, with particular emphasis on reviewing molecular-level research advancements regarding population genetic structure. Early studies primarily employed molecular markers such as microsatellite DNA and mitochondrial DNA (mtDNA), revealing relatively low genetic diversity levels within Chinese spotted seal populations. In recent years, rapid developments in omics technologies have enabled comprehensive investigations into both genomic compositions, as well as gut microbial community diversity and functional profiles of this species. Furthermore, this review critically examined current research limitations and challenges while proposing the potential advantages and developmental trends of environmental DNA (eDNA) technology in future population studies. These technological and strategic advancements are anticipated to significantly enhance survey efficiency and conservation effectiveness for Chinese spotted seal populations.}, } @article {pmid41640402, year = {2025}, author = {Williams, AD and Hooton, SPT and King, E and Avery, LM and Hough, RL and Hobman, JL and Stekel, DJ and Neal, AL and West, HM}, title = {Temporal signals in dairy cattle slurry and fertilized field soil resistomes and bacterial communities.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1666851}, pmid = {41640402}, issn = {1664-302X}, abstract = {INTRODUCTION: Dairy cattle waste is a globally significant source of organic fertilizer which contains a cocktail of microbes and antibiotic resistance genes (ARGs). These ARGs may present a risk to human and animal health, yet there is still limited farm-system-level understanding of how long-term and multiple slurry applications alter field soil resistomes and total microbial communities.

METHODS: Using metagenomics, we assessed both immediate and longer-term changes in grassland field soil resistomes and bacterial communities over a year of routine cattle slurry application.

RESULTS: Our findings suggest that soil microbial communities are resilient to bacteria and ARGs introduced via slurry, even after repeated applications. Most slurry-borne ARGs were not enriched in field soil, however, those common in soil, such as rifamycin resistance genes, were consistently elevated relative to field soil with no history of slurry application. We observed transient increases in slurry-associated macrolide-lincosamide-streptogramin ARGs, however, their persistence appeared to be influenced by timing of slurry application. Similar transient effects were shown by the recovery of a high quality, slurry-associated Proteiniphilum spp. metagenome assembled genome (MAG).

DISCUSSION: We show that MAGs represent a powerful tool for examining the transfer of slurry-borne microorganisms, as they can be more characteristic of these environments than typical sentinel organisms which are easily cultivated. Our findings indicate that while the soil bacterial community shows considerable resilience to slurry-borne bacteria and ARGs, this may be diminished by temporal factors that remain largely unexplored and poorly understood. This is important because resilience inferred from short-term observations may not fully capture delayed or transient responses, potentially leading to underestimation of the persistence of slurry-borne bacteria and ARGs.}, } @article {pmid41640408, year = {2025}, author = {Sun, G and Zou, Q and Wang, B}, title = {The interplay of carbon and nitrogen cycling driven by watershed microorganisms.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1696238}, pmid = {41640408}, issn = {1664-302X}, abstract = {Microorganisms play central roles in regulating carbon and nitrogen cycling across watersheds, driving processes such as organic matter decomposition, primary production, nitrification, and denitrification. Rapid advances in high-throughput sequencing and environmental monitoring have enabled unprecedented insights into the taxonomic diversity and functional capacities of microbial communities under global change. In this review, we synthesize findings from studies published in recent years to evaluate how hydrological connectivity, redox gradients, temperature shifts, and nutrient loading shape microbial metabolism across rivers, lakes, wetlands, and coastal interfaces. We further summarize emerging evidence on how antibiotic resistance genes (ARGs) propagate through these ecosystems and influence microbial functions. The integration of multi-omics technologies including metagenomics, metatranscriptomics, combined with ecological and biogeochemical modeling provides new opportunities to quantify microbe-mediated carbon sequestration and nitrogen transformation. Finally, we discuss current knowledge gaps, including the limited understanding of ARG-driven community restructuring and the insufficient mechanistic resolution of microbe-environment interactions under future climate scenarios. This review highlights the need for cross-scale, data-integrated frameworks to better predict how microbial processes regulate watershed-level biogeochemical cycles in a rapidly changing world.}, } @article {pmid41640705, year = {2026}, author = {Wang, HJ and Zhang, YN and An, L}, title = {Clinical and radiographic feature of pulmonary nocardiosis: A study of 102 cases.}, journal = {World journal of radiology}, volume = {18}, number = {1}, pages = {114552}, pmid = {41640705}, issn = {1949-8470}, abstract = {BACKGROUND: Nocardia pneumonia is an infection that occurs in patients with underlying diseases. Previously, due to limited detection methods, its detection rate and typing posed significant challenges. However, with advancements in detection techniques, the detection rate has significantly increased, and different Nocardia species exhibit distinct imaging characteristics.

AIM: To retrospectively analyze the etiological and imaging features of pulmonary Nocardia pneumonia and to examine the differences in chest imaging manifestations among different Nocardia species.

METHODS: The medical records of 102 patients with pulmonary nocardiosis who were admitted to Beijing Chaoyang Hospital from January 2017 to December 2024 were collected. Data including name, gender, underlying comorbidities, etiological characteristics, diagnostic methods, chest computed tomography features, and therapeutic agents were recorded.

RESULTS: Among the 102 patients, 55 were male and 47 were female, with a median age of 61 years. Bronchiectasis was the most common comorbidity, observed in 54 patients (52.9%). Sixty percent were diagnosed using metagenomic next-generation sequencing. Nocardia gelsenkin was the most prevalent Nocardia specie, while Aspergillus and Pseudomonas aeruginosa were identified as the predominant co-pathogens in these pulmonary nocardiosis cases. Pneumonia caused by Nocardia wallacei primarily presented with bronchopneumonia as the main imaging feature, while other Nocardia species more commonly manifested as consolidation, often accompanied by nodules, cavities, and pleural effusion. The imaging features in immunosuppressed patients were more diverse, with frequent coexistence of multiple patterns.

CONCLUSION: Nocardia pneumonia commonly coexists with bronchiectasis. While metagenomic next-generation sequencing has greatly enhanced its detection rate, Nocardia wallacei pneumonia is distinguished on chest computed tomography by its primary presentation of bronchopneumonia, unlike other types.}, } @article {pmid41640872, year = {2026}, author = {Chen, YX and Sun, NQ and Mo, SJ}, title = {Rhapontin activating nuclear factor erythroid 2-related factor 2 to ameliorate Parkinson's disease-associated gastrointestinal dysfunction.}, journal = {World journal of gastroenterology}, volume = {32}, number = {4}, pages = {114468}, pmid = {41640872}, issn = {2219-2840}, mesh = {*NF-E2-Related Factor 2/metabolism ; *Parkinson Disease/complications/microbiology ; Animals ; Humans ; *Gastrointestinal Diseases/etiology/therapy/microbiology/drug therapy ; Gastrointestinal Microbiome/drug effects ; Mice ; Signal Transduction/drug effects ; Disease Models, Animal ; Fecal Microbiota Transplantation ; }, abstract = {This commentary provides a critical evaluation of the study by Wang et al, which focuses on rhapontin activating colonic nuclear factor erythroid 2-related factor 2 (NRF2) to explore its therapeutic potential for Parkinson's disease (PD)-associated gastrointestinal dysfunction. The commentary acknowledges the academic value of the study: It has not only validated intestinal NRF2 as a therapeutic target for PD but also provided experimental support for the "enteric pathology hypothesis". However, several key gaps remain unresolved in the study. At the gut microbiota level, the exploration of the causal relationship of the microbiota is insufficient, with no validation conducted via methods such as fecal microbiota transplantation; additionally, it fails to systematically integrate the gut-brain axis with PD and does not assess the impact of rhapontin on the composition or function of the gut microbiota. At the pathway mechanism level, it lacks an analysis of the crosstalk between NRF2 and other rhapontin-targeted pathways, including nuclear factor kappa-B, mitogen-activated protein kinase, adenosine monophosphate-activated protein kinase, and sirtuin 1. At the experimental method level, the behavioral testing methods for PD mouse models and the limitations of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse models need attention. Additionally, certain flaws exist in some experimental result figures. Furthermore, this commentary puts forward improvement suggestions for the study. Future research should prioritize multi-omics analysis, encompassing combined metabolomics and metagenomics detection, while conducting mechanistic validation of NRF2-interacting molecules (KEAP1 and p62). In addition, it is necessary to improve refined behavioral tests, focusing on incorporating cognitive function and anxiety-related assessment items.}, } @article {pmid41640977, year = {2026}, author = {Xia, L and Xu, J and Chen, Z and Shen, Y and Zou, Y}, title = {Disseminated tuberculosis secondary to polymicrobial co-infection following long-term immunotherapy for sarcomatoid mesothelioma: A case report.}, journal = {Respiratory medicine case reports}, volume = {59}, number = {}, pages = {102367}, pmid = {41640977}, issn = {2213-0071}, abstract = {Malignant pleural mesothelioma (MPM), particularly its sarcomatoid subtype, is a highly aggressive sarcoma of the pleural lining with a dismal prognosis. Prolonged use of immune checkpoint inhibitors (ICIs), while improving survival in selected patients, can induce profound immunosuppression, increasing susceptibility to life-threatening opportunistic infections. This report describes a 77-year-old male with sarcomatoid MPM who developed fatal disseminated tuberculosis (TB), accompanied by concurrent Aspergillus and herpesvirus infections during extended immunotherapy. The case underscores the critical role of metagenomic next-generation sequencing (mNGS) in enabling rapid diagnosis of atypical TB reactivation in an immunocompromised host, even when conventional cultures are negative. mNGS identified co-infections with Aspergillus flavus and herpesviruses (HHV-5, HHV-4, HHV-1), demonstrating its superiority in polymicrobial infection detection.}, } @article {pmid41641055, year = {2025}, author = {Lai, SY and Chang, L and Duan, JX and Che, GL and Yang, QX and Teng, J and Jian, H and Liu, XJ and Liu, F}, title = {Clinical and epidemiological characteristics of cat scratch disease in children from southwestern China: a retrospective analysis of mNGS-confirmed cases.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1743423}, pmid = {41641055}, issn = {2296-2565}, mesh = {Humans ; *Cat-Scratch Disease/epidemiology/diagnosis/drug therapy ; Male ; Retrospective Studies ; Female ; China/epidemiology ; Child ; Bartonella henselae/isolation & purification ; Adolescent ; Animals ; Anti-Bacterial Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; Cats ; }, abstract = {BACKGROUND AND AIM: Cat scratch disease (CSD) is a zoonotic infection predominantly caused by Bartonella henselae, typically featured by regional lymphadenopathy and febrile illness. Although these classic features characterize most cases, the clinical spectrum extends to severe systemic manifestations including meningitis and neuroretinitis, leading to poor prognosis. Given this potential for diverse clinical presentations, prompt microbiological confirmation becomes essential for accurate diagnosis and appropriate management of CSD. The present study aimed to provide a comprehensive analysis of epidemiological patterns, clinical characteristics, diagnostic findings, and therapeutic outcomes in pediatric CSD cases, with the ultimate goal of optimizing early detection and enhancing the clinical understanding of this disease.

METHODS: This single-center retrospective study analyzed 20 pediatric cases diagnosed with CSD at West China Second University Hospital in southwestern China between September 2021 and July 2025. All diagnoses were established based on comprehensive clinical evaluation including medical history, characteristic symptoms, and imaging findings. Definitive B. henselae identification was achieved through metagenomic next-generation sequencing (mNGS). These diagnostic characteristics were systematically evaluated and discussed in detail.

RESULTS: Among the 20 patients with CSD included in the study, 18 (90.00%) reported a history of cat contact. Ten patients were male (50.00%). School-aged children (6-14 years) accounted for the majority of patients. Eleven cases (55.00%) occurred in autumn. Fever and lymphadenopathy were the primary reasons for hospitalization. B. henselae was detected in all cases using mNGS. Nine patients were diagnosed with atypical CSD, seven of whom were female. Atypical CSD was associated with higher body temperature and longer hospitalization stay. Antimicrobial agents, including azithromycin, doxycycline, and rifampin, achieved satisfactory therapeutic outcomes.

CONCLUSION: This study elucidates the epidemiological, clinical, and laboratory characteristics of CSD in children. mNGS may serve as a powerful tool to facilitate the diagnosis of CSD, including its atypical manifestations.}, } @article {pmid41641352, year = {2025}, author = {Cao, XG and Zhu, XF and Ni, JX and Meng, HD and Huang, CJ}, title = {Optimizing metagenomic next-generation sequencing in CNS infections: a diagnostic model based on CSF parameters.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1681643}, pmid = {41641352}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology ; Female ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Male ; ROC Curve ; Middle Aged ; *Cerebrospinal Fluid/cytology/chemistry ; Adult ; Aged ; Nomograms ; Logistic Models ; }, abstract = {OBJECTIVE: This study aimed to assess the association between routine cerebrospinal fluid (CSF) biochemical parameters and metagenomic next-generation sequencing (mNGS) results, and to develop a predictive model to optimize mNGS testing strategies in patients with suspected central nervous system (CNS) infections.

METHODS: We retrospectively enrolled 110 patients with suspected CNS infections between December 2019 and January 2024. All underwent both CSF analysis and mNGS testing. Patients were divided into mNGS-positive (n = 62) and negative (n = 48) groups. Logistic regression identified independent predictors, and a nomogram was constructed based on CSF cell count and protein concentration. Model performance was assessed via receiver operating characteristic (ROC) curves, calibration plots, and decision curve analysis (DCA). Internal validation included 10-fold cross-validation and 1000-sample bootstrap. An external validation was performed using a cohort of 40 patients enrolled from another hospital campus (May-October 2024). The derivation cohort was retrospectively collected, whereas the external validation cohort was prospectively enrolled.

RESULTS: mNGS positivity rate was 56.36%, significantly higher than CSF culture (6.36%), with an overall diagnostic concordance of 79.09%. Compared to the mNGS-negative group, positive patients had significantly higher CSF cell counts, protein levels, turbidity, ICU admission (ICUA), antimicrobial regimen adjustment (AAR), and mortality, while glucose was significantly lower (P < 0.05). Logistic regression confirmed CSF cell count binary variables (BV) and protein-BV as independent predictors (P < 0.05). The areas under curve (AUCs) for the cell-count, protein-only, and combined models were 0.827, 0.813, and 0.782, respectively. Internal validation showed stable results: 10-fold CV AUC = 0.773 ± 0.184 (95% CI: 0.641-0.904), bootstrap AUC = 0.770 ± 0.064 (95% CI: 0.766-0.774). External validation yielded an AUC of 0.763 (95% CI: 0.554-0.918), with sensitivity and specificity of 77.8% and 67.7%. Calibration and DCA demonstrated good agreement and clinical utility.

CONCLUSION: CSF cell count and protein are reliable predictors of mNGS positivity. The model for practice showed consistent diagnostic performance and may aid in guiding precision mNGS testing, particularly in resource-constrained settings.}, } @article {pmid41642002, year = {2026}, author = {Williams, A and Maros, A and France, MT and Ravel, J and Holm, JB}, title = {Not all vaginal microbiomes are equal: functional context shapes immune landscapes.}, journal = {mBio}, volume = {17}, number = {3}, pages = {e0364525}, pmid = {41642002}, issn = {2150-7511}, support = {UH2AI083264//National Institute of Allergy and Infectious Diseases/ ; K01AI163413//National Institute of Allergy and Infectious Diseases/ ; T32 AI162579/AI/NIAID NIH HHS/United States ; R01NR015495/NR/NINR NIH HHS/United States ; OPP1189217//Bill and Melinda Gates Foundation/ ; T32AI162579//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Female ; *Vagina/microbiology/immunology ; *Microbiota/immunology/genetics ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Gardnerella/genetics/classification/immunology ; Metagenome ; Algorithms ; }, abstract = {Taxonomic classification alone fails to capture the ecological and functional diversity of vaginal microbiomes, particularly those dominated by Gardnerella species. Using the expanded VIRGO2 gene catalog, we developed the vaginal inference of subspecies and typing algorithm (VISTA), a novel ortholog-based framework that defined metagenomic subspecies and 25 metagenomic community state types (mgCSTs), including six distinct Gardnerella-dominated profiles. The mgCSTs exhibit marked differences in species composition, functional gene content, transcriptional activity, and host immune responses. These findings reveal that Gardnerella predominance does not uniformly equate to dysbiosis and underscore the importance of functional context in shaping host-microbiome interactions. VISTA provides scalable classifiers and an interactive application to support mechanistic studies of vaginal microbiome function and its implications for reproductive health.IMPORTANCEThe vaginal microbiome plays a central role in reproductive and gynecologic health, yet its functional diversity and ecological organization remain poorly understood. Traditional 16S rRNA approaches provide only a partial view of this complexity, overlooking the strain-level variation that often determines microbial behavior and host outcomes. By applying metagenomic sequencing and scalable computational modeling, we developed the vaginal inference of subspecies and typing algorithm, a framework that defines gene-based subspecies and community state types across diverse populations. These classifications reveal new insights into the genomic and ecological foundations of vaginal community structure and offer a standardized resource for comparative and translational microbiome research. This work establishes the foundation for functionally informed diagnostics and precision interventions targeting women's reproductive health.}, } @article {pmid41642221, year = {2026}, author = {Pavan, RR and Sullivan, MB and Tisza, MJ}, title = {CRESSENT: a bioinformatics toolkit to explore and improve ssDNA virus annotation.}, journal = {Microbial genomics}, volume = {12}, number = {2}, pages = {}, pmid = {41642221}, issn = {2057-5858}, mesh = {*Computational Biology/methods ; *DNA, Single-Stranded/genetics ; *DNA Viruses/genetics/classification ; Genome, Viral ; Phylogeny ; *Molecular Sequence Annotation/methods ; Software ; Metagenomics/methods ; DNA, Viral/genetics ; }, abstract = {ssDNA viruses are important components of diverse ecosystems; however, it remains challenging to systematically identify and classify them. This is partly due to their broad host range and resulting genomic diversity, structure and rapid evolutionary rates. In addition, distinguishing genuine ssDNA genomes from contaminating sequences in metagenomic datasets (e.g. from commercial kits) has been an unresolved issue for years. Here, we present CRESSENT (CRESS-DNA Extended aNnotation Toolkit), a comprehensive and modular bioinformatic pipeline focused on ssDNA virus 'genome-to-analysis' and annotation. The pipeline integrates multiple functionalities organized into several modules: sequence dereplication, decontamination, phylogenetic analysis, motif discovery, stem-loop structure prediction and recombination detection. Each module can be used independently or in combination with others, allowing researchers to customize their analysis workflow. With this tool, researchers can comprehensively and systematically include ssDNA viruses in their viromics workflows and facilitate comparative genomic studies, which are often limited to dsDNA viruses, therefore leaving behind a crucial component of the microbiome community under study. Benchmarking analyses demonstrated that CRESSENT efficiently processes ssDNA virus datasets of varying scales, completing small family-level analyses within minutes and moderate comparative genomics studies within hours using standard computing resources. Its modular, parallelized design ensures scalability and low memory usage, making it accessible to research groups with diverse computational capacities.}, } @article {pmid41644119, year = {2026}, author = {Hung, JY and Cooke, I and Sato, Y and Miller, DJ and Bourne, DG}, title = {Microbial Metabolism and Disease Virulence Changes Across Day and Night in Coral Black Band Disease Lesions.}, journal = {Environmental microbiology}, volume = {28}, number = {2}, pages = {e70219}, pmid = {41644119}, issn = {1462-2920}, support = {//Earthwatch Institute/ ; //James Cook University/ ; //Mitsubishi Corporation/ ; //JCU CTBMB grant/ ; //JCU OIRS Morris Family Trust grant/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; Virulence ; *Bacteria/metabolism/genetics/pathogenicity ; *Cyanobacteria/genetics/metabolism/pathogenicity ; Metagenome ; Photosynthesis ; Light ; }, abstract = {Coral black band disease (BBD) is characterised as a cyanobacteria-dominated microbial mat that rapidly kills underlying coral tissue. Solar radiation promotes lesion progression by fuelling the cyanobacterial photosynthesis, while sulphate-reducing bacteria and sulphide-oxidising bacteria are implicated in sulphide dynamics within the mat. How the metabolism of the key microbial communities in the mat varies under light and dark conditions and impacts lesion virulence is poorly characterised, however. To compare microbial gene expression under different light regimes, we recovered 28 near-complete BBD-derived metagenome-assembled genomes (MAGs) using Oxford Nanopore Technologies long-read sequencing and profiled Illumina metatranscriptomic reads from BBD lesions collected at day and night by mapping to these MAGs. Genes from the cyanobacterium Roseofilum reptotaenium dominated the differentially expressed genes, with photosynthesis highly represented during the daytime. Relative expression of sulphur and nitrogen metabolism, cofactor biosynthesis, chemotaxis and motility increased among the non-cyanobacterial members at night. Enhanced sulphur reduction by Campylobacteriales and Desulfovibrionaceae at night likely supports a sulphide-rich and low oxygen micro-environment in the lesion, while increased chemotaxis and motility by Campylobacteriales and other heterotrophic bacteria drive lesion progression towards healthy coral tissue. This study provides insights into how diurnal light dynamics drive microbial metabolic pathways changes, thereby promoting BBD virulence.}, } @article {pmid41644290, year = {2026}, author = {Yang, F and Xiang, B and Xia, D and Wu, Y and Chang, X and Sun, P and Zhang, M and Zhang, Y}, title = {Lipidomic and Metagenomic Profiling of Chinese Female Emerging Adults With Oily Scalp.}, journal = {Journal of cosmetic dermatology}, volume = {25}, number = {2}, pages = {e70714}, pmid = {41644290}, issn = {1473-2165}, support = {//Proya Cosmetics Co. Ltd/ ; }, mesh = {Humans ; Female ; *Sebum/metabolism/microbiology ; *Scalp/microbiology/metabolism ; *Lipidomics/methods ; Adult ; *Dermatitis, Seborrheic/microbiology/metabolism ; Skin Microbiome ; Young Adult ; *Scalp Dermatoses/microbiology/metabolism ; Dandruff/microbiology/metabolism ; China ; Metagenomics/methods ; *Lipids/analysis ; Lipid Metabolism ; Malassezia/isolation & purification ; East Asian People ; }, abstract = {BACKGROUND: Excessive sebum secretion leads to oily scalps, which can disturb microbial homeostasis and cause various scalp issues, such as sensitive scalp, dandruff, and seborrheic dermatitis.

AIMS: This study aimed to investigate the characteristics of scalp lipids and microbiota in a group of females with excessive sebum secretion using omics technology, and to identify important relationships between feature lipids and dominant functional microbes on oily scalp.

METHODS: Through comparison of three lipidomic sampling methods, we first selected absorbent paper (AP) as a cost-effective and practical method for untargeted lipidomic profiling. Using this method, we then collected scalp surface lipids from 85 Chinese female emerging adults with varying degrees of excessive sebum and performed internal standard quantified lipidomic profiling using UPLC-QE Plus-MS equipped with LipidSearch software version 5.1. Simultaneously, we collected and analyzed scalp microorganisms using PE150 pair-end metagenomic sequencing on the Illumina NovaSeq platform followed by taxonomic and functional annotation with bioinformatic tools and databases. Afterwards, multivariate statistical analysis and bioinformatics were used to identify feature lipids related to high sebum levels, discern the roles of dominant microbes involved in lipid metabolism, and explore potential correlations between feature lipids and dominant functional microbes of oily scalp.

RESULTS: After comparison of three lipidomic sampling materials, absorbent paper (AP) was selected to collect scalp surface lipids from 85 volunteers. A total of 13 lipid classes were annotated and the most abundant in ESI (+) mode was triacylglycerol (TG, 99.18%) whereas in ESI (-) mode were fatty acid (FA, 56.94%) and O-acyl-(gamma-hydroxy) FA (OAHFA, 34.15%). We identified 27 TGs and 3 FAs as the major lipid molecules contributing to high sebum levels. Seventy percent of these TGs were unsaturated (33% monounsaturated, 26% diunsaturated, 11% triunsaturated), and 30% were saturated. Meanwhile, we found that although the dominant microorganisms, Cutibacterium, Lawsonella, Malassezia, and Staphylococcus were all involved in lipid metabolism on the scalp, only some of them were related to the degree of sebum level and also displayed species-specific preferences for lipids. Among them, Lawsonella clevelandensis and Malassezia globosa were weakly negatively associated with both unsaturated and saturated TGs, while Malassezia restricta and Cutibacterium granulosum were only weakly negatively correlated with saturated TGs, and Cutibacterium namnetense was weakly positively correlated with FA (26:0).

CONCLUSIONS: This study describes relevant lipid molecules contributing to higher sebum production, and reveals that L. clevelandensis, M. restricta, M. globosa, C. namnetense, and C. granulosum on the scalp are closely correlated with these lipids, showing species-specific preference. These findings provide new insights into the interaction between key surface lipids and dominant functional microorganisms on oily scalps.}, } @article {pmid41644450, year = {2026}, author = {Yan, D and Huang, W and Li, KS}, title = {[Advances in clinical diagnosis and treatment of pythium keratitis].}, journal = {[Zhonghua yan ke za zhi] Chinese journal of ophthalmology}, volume = {62}, number = {2}, pages = {156-160}, doi = {10.3760/cma.j.cn112142-20250820-00351}, pmid = {41644450}, issn = {0412-4081}, support = {2025JJ90271//Enterprise Joint Fund Project/ ; }, mesh = {Humans ; *Pythiosis/diagnosis/therapy/epidemiology/drug therapy ; Pythium ; *Keratitis/diagnosis/therapy ; Antifungal Agents ; }, abstract = {Pythium insidiosum is an aquatic algal oomycete that can induce Pythium insidiosum keratitis (PIK). PIK typically presents as acute, highly invasive corneal ulcers, rapidly progressing to corneal dissolution and perforation, and in severe cases, may lead to blindness. Due to its clinical presentation resembling fungal infections, it is often misdiagnosed as fungal keratitis. Epidemiological studies indicate that PIK is predominantly found in tropical and subtropical regions, with a higher incidence during the monsoon season. It is often associated with exposure to contaminated water sources or minor trauma caused by plants. Diagnostic methods include staining of corneal scrapings, PCR, metagenomic next-generation sequencing, and confocal microscopy. Since PIK shows a poor response to conventional antifungal treatments, antibiotics are the preferred treatments, with a combination of linezolid and azithromycin often used as the first-line therapy. Severe cases may require penetrating keratoplasty. In China, reports of PIK cases are relatively rare. This review summarizes the epidemiology, etiology, clinical manifestations, diagnosis, and treatment of PIK, aiming to provide a reference for its clinical management.}, } @article {pmid41644553, year = {2026}, author = {Wen, R and Xin, Y and Bao, S and Zhang, X and Wang, Q and Dang, Z and Zhou, Z and Wu, J and Song, D and Fu, L and Li, W and Niu, J and Wen, Y and Zhou, X and Han, M and Zhao, J}, title = {The gut microbiota mediates depression-like behaviors in mice with chronic Echinococcus multilocularis infection.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41644553}, issn = {2055-5008}, support = {NO. 32160181//National Natural Science Foundation of China/ ; 2022AAC02076//Ningxia Natural Science Found Project/ ; 2024BEG02028//Key research and development projects of the Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; *Echinococcus multilocularis/physiology ; *Depression/etiology/microbiology ; Mice ; Mice, Inbred BALB C ; *Echinococcosis/psychology/microbiology/complications ; Disease Models, Animal ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Fecal Microbiota Transplantation ; Behavior, Animal ; Chronic Disease ; Metabolomics ; Metagenomics/methods ; Multiomics ; Chemokine CCL2 ; Interleukin-6 ; Male ; Hippocampus/pathology ; }, abstract = {Alveolar echinococcosis (AE), a chronic parasitic disease caused by Echinococcus multilocularis (E. multilocularis), remains poorly characterized with respect to central nervous system (CNS) involvement, and its long-term effects on mental health have not been systematically investigated. In this study, we established a BALB/c mouse model of chronic E. multilocularis infection and applied an integrative framework combining behavioral assessments, histomorphological analyses (hematoxylin-eosin staining, Nissl staining, and transmission electron microscopy), cytometric bead array (CBA), and multi-omics approaches (16S rRNA sequencing, metagenomics, and untargeted metabolomics) to investigate infection-induced neuroimmune-gut microbiota interactions. Chronically infected mice exhibited pronounced depression-like behavioral phenotypes, accompanied by hippocampal neuronal nuclear membrane atrophy and disrupted microglial homeostasis. Both peripheral and central inflammatory profiling revealed elevated levels of pro-inflammatory mediators, particularly IL-6 and MCP-1, suggesting coordinated systemic immune activation and neuroimmune alterations. Notably, fecal microbiota transplantation (FMT) from infected donors was sufficient to induce depression-like behaviors in recipient mice, supporting a contributory role of infection-associated gut microbiota alterations in behavioral abnormalities. Integrated multi-omics analyses further revealed a marked reduction in Lactobacillus abundance in infected mice, which was positively correlated with decreased levels of key metabolites within the tryptophan/5-hydroxytryptamine (5-HT) metabolic pathway. Collectively, these findings suggest that chronic E. multilocularis infection may be associated with depression-like behaviors through gut microbiota dysbiosis and related metabolic perturbations. This study provides initial insights into the potential mechanisms underlying neuropsychiatric complications in AE and proposes a conceptual framework for future investigations into early intervention and microbiota-targeted therapeutic strategies.}, } @article {pmid41644585, year = {2026}, author = {Zhou, Y and Liu, K and Gong, P and Wu, J and Ren, Z and Jin, E}, title = {Integrated metagenomic and 16S rRNA analysis reveals temporal associations between resistance genes and microbial communities during dairy manure composting.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41644585}, issn = {2045-2322}, mesh = {*Composting/methods ; *Manure/microbiology ; *RNA, Ribosomal, 16S/genetics ; Animals ; *Metagenomics/methods ; *Microbiota/genetics ; Cattle ; Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Dairying ; Metagenome ; }, abstract = {Dairy manure composting is widely applied to stabilize organic waste and reduce environmental pollution, yet the behavior of resistance determinants during this process remains insufficiently resolved. In this study, shotgun metagenomic sequencing was used to characterize temporal changes in antibiotic resistance genes (ARGs), metal resistance genes (MRGs), biocide resistance genes (BRGs), mobile genetic elements (MGEs), and microbial community composition during dairy manure composting. Rather than inferring direct mechanistic causation, our analyses focused on identifying statistically supported trends, associations, and co-occurrence patterns across composting stages. We observed a rapid decline in the relative abundance of ARGs compared with MRGs and BRGs during the thermophilic phase, coinciding with increasing temperature, while specific genes such as sul2 persisted throughout the process. Shifts in microbial community composition, particularly changes in the relative dominance of Actinobacteria and Proteobacteria, were significantly associated with variations in resistome profiles. Correlation and network analyses further revealed strong associations among ARGs, MRGs, BRGs, and MGEs, suggesting potential co-selection and horizontal gene transfer linkages without implying direct causal mechanisms. In addition, several opportunistic bacterial genera showed positive associations with aminoglycoside- and macrolide-lincosamide-streptogramin-type ARGs, indicating possible dissemination risks following compost application. Overall, this study provides an integrated, association-based overview of resistome and microbial community dynamics during dairy manure composting and highlights the importance of considering multiple resistance determinants when evaluating composting as a manure management strategy.}, } @article {pmid41644796, year = {2026}, author = {Krukowski, H and Valkenburg, S and Vich Vila, A and Maciel, LF and Vázquez-Castellanos, JF and Gryp, T and Joossens, M and Van Biesen, W and Verbeke, F and Derrien, M and Huys, GRB and Glorieux, G and Raes, J}, title = {Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function.}, journal = {Nature microbiology}, volume = {11}, number = {3}, pages = {664-677}, pmid = {41644796}, issn = {2058-5276}, support = {860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101149152//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, mesh = {*Renal Insufficiency, Chronic/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; Glomerular Filtration Rate ; Humans ; Feces/microbiology ; Dysbiosis/microbiology ; *Kidney/physiopathology ; Biomarkers ; Disease Progression ; Male ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Female ; }, abstract = {Despite recent progress, microbial associations reported in chronic kidney disease (CKD) remain inconsistent. Here we combined quantitative faecal metagenomics (n = 130) and cross-study biomarker comparisons (ntotal = 4,420) to study microbiome associations with estimated glomerular filtration rate (eGFR; kidney function) and 4-year CKD progression. Intestinal transit time (ITT) and medications significantly explained microbiome variation, surpassing eGFR-related effects. Lower eGFR was associated with increased p-cresol and indole biosynthetic potential and reduced plant-to-animal CAZyme ratios. This was consistent with community-wide saccharolytic-to-proteolytic microbiome transitions linked to dietary guidelines and slowed-down ITT. Peritoneal dialysis patients showed distinct microbiome dysbiosis accompanied by increased intestinal inflammation. Only Escherichia coli, an unnamed Alistipes species and Bifidobacterium adolescentis were covariate-independent markers for eGFR, but neither these nor previous microbial markers convincingly replicated across 11 studies. No predictors for CKD progression were found. Nevertheless, our study adds insight into plausible ITT and nutrition-related effects, highlighting their potential in CKD interventions.}, } @article {pmid41645054, year = {2026}, author = {Zhang, XX and Zhang, H and Zhao, JX and Yu, HL and Wang, CR and Shang, KM and Wei, YJ and Qin, Y and Li, JM and Zhao, ZY and Xia, CY and Chen, BN and Elsheikha, HM and Ma, H}, title = {Gut microbiota response to Enterocytozoon bieneusi infection in wild rodents: enhanced vitamin B and K2 biosynthesis pathways.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41645054}, issn = {1471-2164}, support = {Grant No. 32170538//the National Natural Science Foundation of China/ ; 2022YFF0710503//the National Key R&D Program of China/ ; 32500449//the National Natural Science Foundation of China-Youth Science Fund/ ; ZD2022C006//the Natural Science Foundation of Heilongjiang Province/ ; Grant No. 667/2424025//the Horizontal Project of Qingdao Agricultural University/ ; }, mesh = {Animals ; *Enterocytozoon/physiology ; *Gastrointestinal Microbiome ; *Rodentia/microbiology ; *Microsporidiosis/microbiology/veterinary/metabolism ; *Vitamin B Complex/biosynthesis ; Metagenome ; *Biosynthetic Pathways ; Animals, Wild/microbiology ; }, abstract = {Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that affects immunocompromised individuals, including those with HIV, and represents a major cause of diarrhea. It can severely impact human health, causing gastrointestinal disease, nutritional deficits, and life-threatening complications. However, the microbial mechanisms by which E. bieneusi affects host nutrition are not well understood. Wild rodents have long been considered valuable models for studying human diseases due to similarities in gut microbiota dynamics and immune responses, making them particularly relevant for investigating parasitic infections. Here, we assembled a comprehensive catalog of 9,929 non-redundant microbial genomes from wild rodent gut metagenomes and evaluated their potential for B vitamins and vitamin K2 biosynthesis using comparative functional genomics. We identified 2,307 genomes encoding complete pathways for de novo biosynthesis of at least one essential vitamin, though no single genome encoded all pathways, indicating a distributed metabolic capacity within the microbial community. Infection with E. bieneusi significantly altered the microbial composition and the potential for vitamin biosynthesis, with a notable expansion of Methanobacteriota and reprogramming of pyridoxine (vitamin B6) biosynthesis pathways. These changes reveal a functional shift in microbial metabolism in response to parasitic pressure. By elucidating the microbial basis of vitamin biosynthesis in wild rodents and the impact of E. bieneusi infection on microbial functions, this study provides new insights into the role of gut microbiota in maintaining host health and supporting nutrient provision under parasitic stress. Moreover, the findings will provide valuable insights into the prevention and control of E. bieneusi infection in a variety of host, including humans.}, } @article {pmid41645073, year = {2026}, author = {Xu, C and Zhang, L and Liu, T and Zhu, G and Wei, H and Zheng, Y and Shi, J and Qiu, L and Xiao, Z and Zhu, X and Wang, J and Guo, J and Fan, Y and Song, Y and Jiang, E and Feng, S}, title = {Respiratory and blood samples metagenomic sequencing in diagnosing pulmonary infections in hematologic patients.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41645073}, issn = {1471-2334}, support = {2021-I2M-1-039//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 2021-I2M-1-017//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 2023ZD0510400//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 3332024210//Fundamental Research Funds for the Central Universities, Peking Union Medical College/ ; 82470208//National Natural Sciences Foundation of China/ ; }, abstract = {BACKGROUND: Bacterial and fungal pulmonary infections (BFPI) are common in hematological patients and pose significant diagnostic challenges. Metagenomic next-generation sequencing (mNGS) is valuable for diagnosing BFPI. However, for hematological patients with limited access to lower respiratory tract samples (LRTS), the clinical value of blood-mNGS compared to LRTS-mNGS requires further investigation. METHODS: A retrospective analysis was conducted on 160 cases with suspected pneumonia who underwent both blood-mNGS and LRTS-mNGS within one week. Diagnostic performance and impacts on antimicrobial adjustments were evaluated using clinical composite diagnosis (CCD) as the reference. RESULTS: Compared to CCD, LRTS-mNGS showed significantly higher positive percent agreement (PPA) than blood-mNGS [93.7% (119/127) vs. 34.6% (44/127), P < 0.001], with negative percent agreements (NPA) of 87.5% (21/24) and 91.7% (22/24), respectively. Blood-mNGS showed higher PPA in neutropenic than non-neutropenic patients [56.8% (21/37) vs. 25.6% (23/90), P = 0.001], with unique fungal detection advantages, identifying additional fungi in 7 cases: Mucorales (3), Aspergillus spp. (2), both Mucorales and Aspergillus spp. (1), and Pneumocystis spp. (1). Resistance genes were detected only by LRTS-mNGS. mNGS positively influenced antimicrobial adjustments in 54.3% (69/127) of cases, particularly for pathogens with low empirical coverage, such as Legionella spp. (0.0%, 0/7), Pneumocystis spp. (52.4%, 11/21), and Mucorales (55.6%, 5/9). Blood-mNGS detected these pathogens at rates of 71.4% (5/7), 23.8% (5/21), and 77.8% (7/9), respectively. CONCLUSION: LRTS-mNGS outperformed blood-mNGS in diagnostic performance and resistance detection. Blood-mNGS identified pathogens in one-third of BFPI cases, with value for certain fungal infections, especially in hematologic patients with limited LRTS access. TRIAL REGISTRATION: Not applicable. This study is a retrospective analysis and does not require clinical trial registration.}, } @article {pmid41645099, year = {2026}, author = {Qiu, Y and Mo, F and Chen, Y and Lai, Y and Zhang, K and Huang, Z}, title = {Intersite differences in gut microbiome are associated with habitat quality in a limestone forest-dwelling langur.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41645099}, issn = {1471-2180}, support = {2023GXNSFBA026045//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; no.32170488//National Natural Science Foundation of China/ ; }, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; Forests ; *Presbytini/microbiology ; Calcium Carbonate ; Feces/microbiology ; Metagenomics/methods ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Studying the compositional structure and function of the gut microbiome is essential for evaluating adaptability of wildlife to their environment. Given the high plasticity of the gut microbiome in primates, studying conspecific populations under different habitat quality can provide valuable insights for the conservation and management. To investigate intersite differences in composition and function of the gut microbiome of endangered François' langurs (Trachypithecus francoisi), we employed 16S rRNA and metagenomic sequencing.

RESULTS: The results showed that higher gut microbiota diversity of François' langurs was associated with higher habitat quality, possibly driven by the dietary diversity. In contrast, François' langurs inhabiting lower-quality habitats had a higher relative abundance of Bacillota and more enriched functional genes related to amino acid metabolism and metabolic pathways than those in higher-quality habitats, which support enhanced fiber degradation to meet energy demands. Additionally, the proportion of tetracycline-related ARGs (tetA(58)) was more abundant in lower-quality habitats, likely due to villagers applying livestock and poultry manure.

CONCLUSION: Our study concludes that intersite differences in gut microbiome are associated with habitat quality in the François' langurs, underscoring its role in habitat adaptation and necessity for physiological indicators to elucidate the mechanisms by which wildlife responds to human disturbance and ecological variability. In addition, we recommend prioritizing the restoration of native vegetation diversity in the langurs' habitats, which leverages their gut microbiota's adaptive potential to provide a suitable fundamental environment for the langurs' long-term survival.}, } @article {pmid41645132, year = {2026}, author = {Ma, D and Xu, S and Yu, D and Peng, A and Yang, L and Yang, H and Yuan, Q and Li, Y}, title = {Cytomegalovirus-induced severe enterocolitis associated with ANCA-associated vasculitis and diffuse alveolar haemorrhage in a child: a diagnostic and therapeutic dilemma.}, journal = {BMC pediatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41645132}, issn = {1471-2431}, abstract = {BACKGROUND: ANCA-associated vasculitis (AAV) is rare in children and may be triggered by infections. Cytomegalovirus (CMV), a common pathogen, can rarely cause severe gastrointestinal complications like stricture, obstruction, and perforation. While adult cases suggest a potential association between CMV and AAV, reports of severe intestinal complications leading to AAV in immunocompetent children are scarce.

CASE PRESENTATION: A previously healthy 12-year-old boy presented with fever, abdominal pain, and vomiting. Abdominal CT revealed intestinal obstruction and perforation. Emergency surgery confirmed acute hemorrhagic necrotizing enterocolitis, and metagenomic next-generation sequencing (mNGS) diagnosed CMV viremia. His condition deteriorated rapidly, culminating in acute respiratory failure and acute kidney injury requiring continuous renal replacement therapy. Serological testing using indirect immunofluorescence was positive for cytoplasmic-ANCA (C-ANCA). Confirmatory ELISA testing confirmed positivity for anti-proteinase 3 (PR3) antibodies at a titer of 1:51; anti-myeloperoxidase (MPO) antibodies were negative. Chest CT and bronchoscopy confirmed diffuse alveolar haemorrhage. AAV was diagnosed per the 2022 ACR/EULAR criteria. The central management challenge was the co-occurrence of active CMV infection and fulminant vasculitis. Immunosuppressive therapy was withheld until sepsis parameters normalized. A life-threatening bleeding event on day 13 prompted initiation of high-dose methylprednisolone and cyclophosphamide, leading to rapid clinical improvement. A subsequent renal biopsy showed subacute tubulointerstitial injury without crescents.

CONCLUSION: Severe CMV enterocolitis may be temporally associated with fulminant AAV in children. In pediatric cases of severe CMV infection with multi-organ dysfunction, a high index of suspicion for AAV and ANCA serology testing is warranted. Furthermore, multidisciplinary team input is crucial for guiding optimal timing of immunosuppression in the context of concurrent active infection, which is pivotal for improving patient outcomes.}, } @article {pmid41645540, year = {2026}, author = {Cuong, TM and Dan, NH and Hang, TTT and Le Luu, T and Scheynen, J and Dries, J}, title = {Enhanced the Treatment of Seafood Processing Wastewater Using the Anaerobic-Anoxic-Oxic (AAO) Process With Granular Sludge.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {98}, number = {2}, pages = {e70293}, doi = {10.1002/wer.70293}, pmid = {41645540}, issn = {1554-7531}, support = {FWO.105-2022.03//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; }, mesh = {*Sewage/microbiology ; Anaerobiosis ; Bioreactors/microbiology ; *Seafood ; *Waste Disposal, Fluid/methods ; *Wastewater/chemistry ; RNA, Ribosomal, 16S/genetics ; Biological Oxygen Demand Analysis ; Aerobiosis ; Nitrogen ; Bacteria/genetics/classification ; }, abstract = {Seafood processing wastewater contains high concentrations of organics and nutrients that need to have an effective solution. This study aims to explore the use of granular sludge in seafood wastewater treatment using anaerobic-anoxic-aerobic (AAO) process. The results showed that the granular sludges were successfully cultivated from the traditional activated sludge sources. The bioreactor demonstrated robust treatment performance, achieving a high chemical oxygen demand (COD) removal efficiency exceeding 93%, total nitrogen (TN) removal ranging from 56.6% to 68.6%, and ammonium removal (NH4 [+]-N) of 80% to 88.57%. However, total phosphorus (TP) removal efficiency was relatively moderate at 47.36% ± 10.33%. Metagenomic analysis (16S rRNA) revealed a diverse and evenly distributed microbial community within the granular sludge. In anaerobic granular sludge, the dominant phylum was Bacillota (45.3%), followed by Thermodesulfobacteriota (18.2%) and Synergistota (11.24%), with minor contributions from Campylobacterota (7.58%), Chloroflexota (3.98%), and Bacteroidota (3.6%), alongside other less abundant phyla (10.1%). Anoxic granular sludge exhibited a shift, with Pseudomonadota (32.87%) and Thermodesulfobacteriota (25.08%) dominating, while Bacillota (11.95%), Bacteroidota (7.9%), and Chloroflexota (4.1%) contributed less, and other phyla comprised 18.21%. For aerobic granular sludge, Pseudomonadota represented the most prevalent phylum (42.21%), followed by Thermodesulfobacteriota (14.94%) and Bacillota (14.87%), with lower abundances of Bacteroidota (7.74%) and Chloroflexota (4.91%), while other phyla accounted for 15.42%.}, } @article {pmid41646408, year = {2026}, author = {Bosquet, JG and Osazuwa-Peters, O and Wagner, VM and Polio, A and Hoyd, R and Tarhini, AA and Cosgrove, CM and Huang, MS and Corr, BR and Leiser, AL and Salhia, B and Darcy, K and Dood, RL and Dockery, LE and Cavnar, MJ and Landrum, L and Chambers, L and Tan, AC and Jin, N and Rounbehler, RJ and Churchman, ML and Spakowicz, D}, title = {Intrinsic tumor factors and extrinsic environmental and social exposures contribute to endometrial cancer recurrence patterns.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41646408}, issn = {2693-5015}, support = {P30 CA086862/CA/NCI NIH HHS/United States ; R01 CA099908/CA/NCI NIH HHS/United States ; }, abstract = {PURPOSE: In a previous study, we trained, validated and tested models of endometrial cancer (EC) recurrence integrating clinical, genomic and pathological data from the Oncology Research Information Exchange Network (ORIEN). Preliminary studies also have demonstrated that bacterial communities may influence the risk of EC recurrence by altering the local environment within the upper female genital tract. The objective of this study was to evaluate whether extrinsic and environmental factors, including tumor-associated bacterial communities, tumor immune contexture and air pollution alongside clinical, pathologic and genomic features are associated with EC recurrence across clinically relevant risk groups.

PATIENTS AND METHODS: We performed a retrospective, multi-institution, case-control study with data from the ORIEN network EC dataset. Data was stratified into low-risk, FIGO grade 1 and 2, stage I (N = 329), high-risk, or FIGO grade 3 or stages II-IV (N = 324), and non-endometrioid histology (N = 239) groups. RNA and DNA were extracted from tumor specimens and processed to obtain the necessary genomic/metagenomic data. Genus level microbiome data were extracted and curated) from RNA sequencing using Kraken2, Bracken and exotic software packages. Risk of EC recurrence was evaluated by integrating microbiome and environmental data alongside existing clinical, pathological and genomic data using topic modelling with latent dirichlet allocation (LDA). Prediction models of EC recurrence were created using machine and deep learning analytics (ML and DL) with MATLAB apps and TensorFlow. Finally, performance of both topic and prediction models were externally validated in an independent EC dataset from TCGA.

RESULTS: The resulting models, analyzed with topic modelling, demonstrated the complexity of factors involved in recurrence of disease for EC. The components of the resulting topic models, and specifically the microbiome, changed when environmental factors, like air pollutants, were introduced in the model. In the low-risk EC group, microbes that were quite abundant in models before introducing environmental factors, were scarcely seen afterwards, like genera Thermothielavioides, Theileria, Rhizoctonia. Bacillus was the genus with higher per-topic probability within all risk groups, especially for low-risk EC (28%). Ozone (O3) was a resulting component of all risk groups' models. BMI was the sole informative clinical variable after data integration, and only present in the low-risk group. Resulting models from the high-risk and non-endometrioid groups included differential gene expressions: MMP13, S100A7, SMOC1, ACACA and ADD2, DLX5, SLCO2B1, NWD1 respectively. CNVs also were present in both low-risk and non-endometrioid groups, but their per-topic probabilities were low. The same was true for the immune contexture data. The components of the resulting topic models were used to train, validate and test prediction models of EC recurrence by risk groups. Performances of these models were excellent (@ 0.9). Despite some missing microbiome data in TCGA from resulting topic models, prediction models trained in the ORIEN set, had similar performances in TCGA testing set, with overlapping AUC 95% CIs.

CONCLUSION: Both extrinsic factors (tumor-associated bacterial communities, tumor immune contexture and air pollution) and intrinsic factors predict EC recurrence. The complexity of tumor and host factors influencing cancer relapses underscore the need for more individualized prediction models of disease outcomes.}, } @article {pmid41647522, year = {2026}, author = {Liu, J and Chen, Y and Sheng, X and Gao, Y}, title = {Case Report: Nocardia farcinica infectious arthritis and myositis in an immunocompromised host: diagnostic and management challenges.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1762442}, pmid = {41647522}, issn = {2296-858X}, abstract = {BACKGROUND: Nocardia farcinica is a rare opportunistic pathogen predominantly affecting immunocompromised hosts. Infectious arthritis, cutaneous and deep soft tissue infections caused by this organism often present with nonspecific clinical manifestations. Additionally, due to its slow-growing and oligotrophic nature, both cultivation and identification pose considerable challenges, thereby complicating clinical diagnosis and management.

CASE PRESENTATION: This case report described an elderly female patient presenting with right shoulder redness, swelling, and pain. Her history included diabetes, local corticosteroid injections, and newly identified humoral immunodeficiency (hypogammaglobulinemia with low B-cell count). Imaging revealed infectious arthritis of the right shoulder, accompanied by infectious myositis and an intermuscular abscess in the right upper arm. Nocardia farcinica was confirmed by metagenomic next-generation sequencing (mNGS) and culture of aspirated fluid. Initial therapy with trimethoprim-sulfamethoxazole (TMP-SMX) and ceftriaxone was limited by renal impairment and gastrointestinal intolerance, and susceptibility testing indicated TMP-SMX resistance. Treatment was switched to linezolid. Due to inadequate clinical response, multiple surgical debridements were performed. Subsequently, therapy was changed to oral minocycline because of linezolid-induced bone marrow suppression and intolerance. At discharge, the maintenance regimen consisted of moxifloxacin combined with minocycline.

CONCLUSION: This case highlights the importance of considering low-virulence pathogens such as Nocardia in immunocompromised patients with atypical infections that respond poorly to initial empiric therapy. Pathogen identification, aided by tools like mNGS for rapid detection, is essential. When classic regimens are limited by adverse effects, susceptibility-guided alternative therapies can be effective. For localized infections refractory to medical management, multidisciplinary surgical intervention remains a critical component of care.}, } @article {pmid41647993, year = {2025}, author = {Jayakrishnan, T and Sangwan, N and Nair, KG and Kamath, SD and Patel, MH and Joyce, D and Walsh, M and Simon, R and Vadehra, D and Iyer, RV and Fountzilas, C and Khorana, AA}, title = {Tumor microbiome differences in early-onset versus average-onset pancreatic adenocarcinoma.}, journal = {ESMO gastrointestinal oncology}, volume = {9}, number = {}, pages = {100194}, pmid = {41647993}, issn = {2949-8198}, abstract = {BACKGROUND: Compelling evidence supports the biomarker potential of microbiome in pancreatic adenocarcinoma. Given the knowledge gap on the characteristics and significance of microbiome in early-onset pancreatic ductal adenocarcinoma (eoPDAC, age <50 years), we aimed to evaluate microbiome profiles in resected specimens from individuals with eoPDAC and average-onset PDAC (aoPDAC, age >50 years).

MATERIALS AND METHODS: We carried out shotgun metagenomic sequencing in resected specimens from individuals with eoPDAC (n = 24) and aoPDAC (n = 20). Statistical tests included Wilcoxon test, permutational analysis of variance, multiomic classifier modeling, differential abundance analysis, and linear regression. All P values were adjusted for multiple testing and P < 0.05 was considered statistically significant.

RESULTS: We successfully sequenced several bacteria and fungi in the tumor specimens from 44 individuals with resected PDAC (24 eoPDAC and 20 aoPDAC). The alpha diversity of the bacterial microbiome was higher in eoPDAC tumor tissue compared with aoPDAC (P = 0.04). In contrast, the fungal mycobiome's alpha diversity was higher for aoPDAC tumor tissue (P = 0.02). Key organisms with differential abundance between tumor tissue from individuals with eoPDAC and aoPDAC included Bacillus, Candida, Collimonas, Cupriavidus, Enterobacter, Escherichia, Klebsiella, Malasseiza, Mucilaginibacter, Neisseria, and Sphingomonas. Higher bacterial diversity in tumor tissue was associated with better overall survival for individuals with eoPDAC (R = 0.26, P = 0.02).

CONCLUSIONS: Shotgun metagenomic sequencing identified bacterial microbiome and fungal mycobiome in tumors from individuals with eoPDAC and aoPDAC. We observed significant differences in alpha and beta diversity and relative abundances of organisms suggesting distinct microbiome signatures. Microbiome associations with survival were observed in eoPDAC indicating unique potential as prognostic biomarker.}, } @article {pmid41648002, year = {2025}, author = {Zhang, H and Chen, K and Chen, R and Jia, E}, title = {Feeding patterns reprogram a gut microbial virulence-iron-quorum sensing functional axis linked to atherosclerotic risk.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1751844}, pmid = {41648002}, issn = {1664-302X}, abstract = {The feeding rhythm is a major temporal regulator of metabolic physiology, yet its impact on microbiome-derived functional traits relevant to cardiometabolic disease remains insufficiently understood. Our previous work demonstrated that ad libitum, daytime-restricted, and nighttime-restricted feeding produce markedly different atherosclerotic outcomes in Apoe[-]/[-] mice, indicating that the feeding rhythm acts as a modifiable determinant of atherogenic susceptibility. Here, we used shotgun metagenomics to profile risk-associated microbial functional modules-including Type III and Type VI secretion systems (T3SS/T6SS), siderophore-based iron acquisition pathways, quorum-sensing (QS) regulators, and antimicrobial resistance determinants-across feeding regimens. The feeding rhythm induced pronounced functional segregation independent of α-diversity, which was consistent with selective functional reprogramming rather than taxonomic restructuring. Daytime feeding, which is misaligned with the murine active phase, is associated with coordinated enrichment of the T3SS/T6SS, iron uptake, and QS pathways, forming a tightly interconnected "virulence-iron-QS-ARG" functional consortium. In contrast, circadian-aligned nighttime feeding resulted in attenuated virulence orientation and enhanced metabolic-cooperative signatures. Network inference further revealed strong coactivation of virulence secretion, iron mobilization, and QS modules under circadian misalignment. These findings show that the feeding rhythm modulates atherogenic susceptibility not only through host metabolism but also by remodeling gut microbial functional capacities, highlighting microbial functional ecology as an integral component of diet-host interactions.}, } @article {pmid41648004, year = {2025}, author = {Goncalves, AR and Ranganathan, H and Valdes, C and Zhu, H and Zhang, B and Kok, CR and Martí, JM and Mulakken, NJ and Thissen, JB and Jaing, C and Be, NA}, title = {Beyond microbial abundance: metadata integration enhances disease prediction in human microbiome studies.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1695501}, pmid = {41648004}, issn = {1664-302X}, abstract = {Multiple studies have highlighted the interaction of the human microbiome with physiological systems such as the gut, immune, liver, and skin, via key axes. Advances in sequencing technologies and high-performance computing have enabled the analysis of large-scale metagenomic data, facilitating the use of machine learning to predict disease likelihood from microbiome profiles. However, challenges such as compositionality, high dimensionality, sparsity, and limited sample sizes have hindered the development of actionable models. One strategy to improve these models is by incorporating key metadata from both the human host and sample collection/processing protocols. This remains challenging due to sparsity and inconsistency in metadata annotation and availability. In this paper, we introduce a machine learning-based pipeline for predicting human disease states by integrating host and protocol metadata with microbiome abundance profiles from 68 different studies, processed through a consistent pipeline. Our findings indicate that metadata can enhance machine learning predictions, particularly at higher taxonomic ranks like Kingdom and Phylum, though this effect diminishes at lower ranks. Our study leverages a large collection of microbiome datasets comprising 11,208 samples, therefore enhancing the robustness and statistical confidence of our findings. This work is a critical step toward utilizing microbiome and metadata for predicting diseases such as gastrointestinal infections, diabetes, cancer, and neurological disorders.}, } @article {pmid41648005, year = {2025}, author = {Liu, JJ and Yang, H and Xiao, ZY and Xie, JH and Su, L and Li, YT and Zheng, XY and Hu, WH and Fu, SJ and Li, CL and Huang, L and Yu, SY and Yu, Z and Yang, S and Yang, J}, title = {Gut microbiota and metabolic dysregulation in polycystic ovary syndrome: effects of acupuncture as an adjunct to in vitro fertilization on gut dysbiosis, metabolism, and oocyte quality.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1730714}, pmid = {41648005}, issn = {1664-302X}, abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is marked by disruptions in metabolic and reproductive endocrine functions. This study synthesizes systemic metabolic profiles, alterations in gut microbiota, and follicular fluid metabolism to elucidate the reproductive and endocrine metabolic changes associated with PCOS. Furthermore, it aims to elucidate the potential mechanisms through which acupuncture may exert therapeutic effects.

METHODS: In this open-label randomized controlled trial conducted in China (November 2021-January 2023), 60 women with PCOS scheduled for In Vitro Fertilization (IVF) were randomized to receive acupuncture combined with IVF treatment or IVF treatment alone, with 30 healthy women serving as controls. Gut microbiota was sequenced and analyzed by 16S rRNA and metagenomics; follicular fluid metabolites were determined by untargeted metabolomics.

RESULTS: Compared with healthy controls, PCOS exhibited gut microbiota dysbiosis and metabolic disorders. The specific gut microbiota in PCOS dominated by s_Lachnospiraceae, s_Blautia_sp. and g_Escherichia-Shigella, which correlated with body mass index (BMI), waist circumference, waist-to-hip ratio, and hormone levels. Acupuncture combined with IVF significantly regulated glucose and lipid metabolism, reduced g_Escherichia-Shigell abundance, and showed potential advantages in enhancing oocyte quality and embryonic developmental potential (p = 0.011). Analysis of the correlation between differential metabolites and oocyte and embryo quality demonstrated that methionine sulfoxide and boldione may be key metabolites to affect follicle quality.

CONCLUSION: PCOS is associated with systemic multi-pathway metabolic dysregulation and gut microbiota dysbiosis. It described the potential therapeutic benefits of acupuncture combined with IVF for PCOS, laying a foundation for further understanding the disease and the mechanisms of acupuncture for PCOS metabolic disorders, and providing directions for future research.}, } @article {pmid41648007, year = {2025}, author = {Schnabel, E and Vuillemin, A and Esser, S and Griesdorn, L and Soares, AR and Mørkved, PT and Jørgensen, SL and Probst, AJ and Kallmeyer, J and , }, title = {Geochemical variability and microbial metabolic functions in oligotrophic sediments exposed to minor seepage.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1720187}, pmid = {41648007}, issn = {1664-302X}, abstract = {Low primary productivity in Barents Sea surface waters and limited nutrient flux to the seafloor favor nitrification and nitrogen fixation in deep waters, resulting in a dearth of organic substrates in local sediments. The addition of labile hydrocarbons naturally occurring through seepage from subsurface reservoirs could promote microbial activity in organic-lean sediments, notably by denitrifying and sulfate-reducing microbes. Using gravity cores from an area with numerous hydrocarbon reservoirs, we document pore water geochemistry, dissolved gas concentrations, and total cell counts supplemented with taxonomic and functional marker gene analyses from metagenomes and metagenome-assembled genomes. We assess the contribution of the subsurface biosphere in producing geochemical gradients in oligotrophic sediments facing different exposure to minor seepage. In pristine seabed, i.e., not affected by hydrocarbon seepage, nitrate and ammonium profiles were consistent with denitrification down to 1 m below seafloor. By contrast, minor hydrocarbon seepage caused very different pore water profiles, which were indicative of more reducing geochemical conditions in the sediment and more advanced consumption of electron acceptors in pore water. Delivery of favorable organic substrates to anaerobic microbes through seepage was reflected in slightly higher cell densities, CH4 and CO2 concentrations, but appeared to have little impact on community diversity. This could be explained by metabolic versatility across functional guilds, with limited differentiation of sedimentary niches, favoring polyvalent fermenters at the expense of canonical denitrifiers and sulfate reducers. These versatile fermenters exhibited diverse predicted capabilities for nitrate and sulfate reduction combined with hydrocarbon degradation, (homo)acetogenesis, and nitrogen fixation. Our results further indicate that specific clades of homoacetogens (Lokiarchaeia, Bathyarchaeia, and Dehalococcoidia) could support cross-feeding interactions when fueled by simple hydrocarbons through seepage, particularly those associated with dissimilatory sulfur metabolism and fermentation of intermediate metabolites. In the absence of hydrocarbon-derived electron donors, the same clades appear capable of energy-conserving (homo)acetogenic fermentation on organic residues. Thus, we conclude that slow-growing (homo)acetogens that are ubiquitous in the marine subseafloor actively contribute to balancing biogeochemical cycles in oligotrophic sediments impacted by minor hydrocarbon seepage.}, } @article {pmid41648008, year = {2025}, author = {Pasquali, F and Crippa, C and Lucchi, A and Manfreda, G}, title = {Artisanal food of animal origin as reservoir of putative pathogenic Escherichia coli: a combined genomic and in vivo approach.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1718380}, pmid = {41648008}, issn = {1664-302X}, abstract = {The lack of a full automation and control of environmental parameters might result in potential risk of microbial contamination in small-scale production plants such as artisanal cheese and salami Italian productions. In a previous study, genomes of 33 E. coli isolates were sequenced. In the present study, the pathogenicity potential of E. coli strains was investigated by: (1) phylogenomic comparison with 202 public genomes of human, animal and environmental Italian origin; (2) pathogenicity assessment of strains with virulence patterns predicting specific E. coli pathotypes by using larvae of Galleria mellonella as in vivo infection model. Phylogenetic reconstruction revealed raw material and not the processing environment as source of salami contamination. Moreover, close proximity of some strains isolated from salami production with wild boar and extraintestinal human public strains was observed suggesting pigs and wild boar as potential reservoirs of pathogenic E. coli. The virulome of salami strains revealed the presence of genes already described as gene markers of atypical enteropathogenic E. coli (aEPEC; bfp-, eae+). Interestingly the analysis of virulence genes pointed toward additional genomes which showed genetic markers previously described as strongly associated to and/or extraintestinal pathogenic E. coli (ExPEC). In vivo experiments, confirmed the higher pathogenicity of strain 5STM5 with genetic pattern corresponding to hybrid aEPEC/ExPEC and two strains 3CP1522 and 6MB5 of cheese and salami production, respectively, with virulence genes previously associated to ExPEC pathotype. The combined approach pointed toward two genes espC for aEPEC, as well as malX for ExPEC which were significantly enriched in clinical genomes in comparison to genomes of other origins. These genes are worth of future investigations which could help to assess the risk for consumers after the consumption of contaminated artisanal food.}, } @article {pmid41648108, year = {2026}, author = {Martinez, NAP and Arnaldi, MR and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA}, title = {Microbiota-Based Interventions Differentially Rescue Gut and Social Behavior Phenotypes in a Drosophila Autism-like Model.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41648108}, issn = {2692-8205}, support = {P20 GM103642/GM/NIGMS NIH HHS/United States ; P30 GM149367/GM/NIGMS NIH HHS/United States ; }, abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a lifelong neurological and developmental disorder that has no cure and is often accompanied by gastrointestinal (GI) issues. The bidirectional communication system known as the gut microbiota-brain axis may help explain how GI dysfunction contributes to neurological symptoms. Loss-of-function mutations in the histone demethylases KDM5A, KDM5B or KDM5C are found in patients with intellectual disability and ASD. Previous studies using a Drosophila Kdm5 loss-of-function (Kdm5 [LOF]) ASD-like model revealed gut microbial dysbiosis, reduced abundance of Lactiplantibacillus plantarum, and impaired social behavior. While L. plantarum supplementation rescued intestinal abnormalities, it did not restore social behavior.

METHODS: Here, we evaluated multiple microbiota-based interventions, including probiotic supplementation with Lactiplantibacillus plantarum, Lactobacillus helveticus, their combination, and fecal microbiota transplantation (FMT), to determine their capacity to modulate gut microbial composition and behavior in Kdm5 [LOF] flies. Gut bacterial abundance was quantified using colony-forming unit (CFU) assays and full-length 16S rRNA gene sequencing. Social behavior was assessed using the social distance assay, while anxiety-like behavior and locomotion were evaluated using the open field test. Gut-specific Kdm5 knockdown was used to assess tissue-specific contributions to microbiota and behavioral phenotypes.

RESULTS: Kdm5 deficiency resulted in reduced abundance of culturable Lactobacillus, Acetobacter, and Enterobacter species, accompanied by impaired social behavior. L. plantarum supplementation restored gut microbial abundance in both whole-body Kdm5 [LOF] and gut-specific Kdm5 knockdown models but did not significantly rescue social behavior. In contrast, L. helveticus significantly improved social interaction in Kdm5 [LOF] flies despite minimal effects on gut bacterial abundance, revealing a dissociation between microbial restoration and behavioral outcomes. Gut-specific Kdm5 knockdown phenocopied both microbial and social defects observed in Kdm5 [LOF] mutants. Notably, FMT from healthy donors partially restored Lactobacillus abundance, reshaped gut microbial community structure, and partially improved social behavior in Kdm5 [LOF] recipient flies.

CONCLUSIONS: Together, these findings identify Kdm5 as a key regulator of gut microbial viability and social behavior and demonstrate that microbiota-based interventions exert strain- and phenotype-specific effects. Our results reveal that restoration of microbial abundance alone is insufficient to rescue social behavior and highlight the importance of functional host-microbe interactions in gut-brain communication. This work establishes Drosophila as a tractable platform for dissecting epigenetic regulation of microbiota-behavior relationships relevant to ASD and for evaluating targeted probiotic and microbiota-transfer strategies.}, } @article {pmid41648142, year = {2026}, author = {Mastrorilli, E and Herd, P and Rey, FE and Goodman, AL and Zimmermann, M}, title = {Linking interpersonal differences in gut microbiota composition and drug biotransformation activity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41648142}, issn = {2692-8205}, support = {P30 AG017266/AG/NIA NIH HHS/United States ; R01 AG060737/AG/NIA NIH HHS/United States ; R01 AT010014/AT/NCCIH NIH HHS/United States ; R35 GM118159/GM/NIGMS NIH HHS/United States ; }, abstract = {Individuals vary widely in their responses to drugs, and growing evidence implicates the gut microbiome as a contributor to this variability. While prior studies show that gut bacteria can metabolize drugs, how differences in microbial community composition influence drug metabolism remains poorly understood. Here, we characterize the biotransformation of 271 drugs by 89 gut microbial communities derived from human donors and preclinical animal models. Over 90% of tested drugs were metabolized by at least one microbiome. We identified 66 drugs exhibiting highly variable metabolism across human-derived microbiomes and several drugs whose biotransformation differed markedly between human and animal microbiomes. To enable prediction of microbiota-mediated drug metabolism, we developed and compared multiple modeling approaches based on metagenomic data. These results, together with the provided data and analytical resources contribute to a better understanding of microbiome-drug interactions and support their future integration into drug discovery, personalized prescription, and therapeutic drug monitoring.}, } @article {pmid41648310, year = {2026}, author = {Szenei, J and Burke, A and Liong, A and Korenskaia, A and Lukowski, AL and Ziemert, N and Nikel, PI and Leão, PN and Moore, BS and Weber, T and Blin, K}, title = {Computational pipeline reveals nature's untapped reservoir of halogenating enzymes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41648310}, issn = {2692-8205}, support = {R01 GM085770/GM/NIGMS NIH HHS/United States ; R35 GM159745/GM/NIGMS NIH HHS/United States ; }, abstract = {Microbial halogenated natural products (hNPs) hold ecological, agricultural, and biomedical relevance. The hNP-producing potential of the organism can be assessed by the precise prediction of biosynthetic enzymes, yet the detailed annotations of halogenases are often missing from genomic and metagenomic data. We created a manually curated database (https://halogenases.secondarymetabolites.org/) containing information on the halide-specificity, role, and position of verified catalytic residues and results of the mutagenesis studies of more than 120 experimentally validated or in silico inferred halogenases. The collection of experimental data supports a computational pipeline that allows the family-, substrate-, and halide-scope-level annotation of halogenating enzymes by relying on catalytic residues, conserved motifs, and profile Hidden Markov Models (pHMMs). Our analysis with sequence similarity networks (SSNs) highlighted several underexplored clusters in the UniRef50 database. Such finding was a halogenase from Rhodopirellula baltica (RhobaVHPO) previously labelled as a hypothetical chloroperoxidase, which clustered apart from the known chloroperoxidases and bromoperoxidases, but accepted chloride and preferred bromide. Our database and workflow provide extensive and scalable solutions for the systematic and precise annotation of halogenating enzymes in genomic and metagenomic data. The in-depth categorization of halogenases will improve the chemical structure prediction of microbial hNPs, supporting ecological assessments and natural product discovery.}, } @article {pmid41648334, year = {2026}, author = {Romo Bechara, N and Bardeskar, N and Hopkins, HA and Raymann, K}, title = {Genomic and phenotypic diversification of Pseudomonas aeruginosa during sustained exposure to a ciliate predator.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.13.699197}, pmid = {41648334}, issn = {2692-8205}, abstract = {UNLABELLED: Opportunistic bacterial pathogens often encounter strong selective pressures outside their hosts, yet the evolutionary consequences of long-term predator exposure remain poorly understood. Here, we used experimental evolution to examine how sustained interaction with a eukaryotic predator shapes genomic adaptation, phenotypic diversification, and virulence-associated traits in Pseudomonas aeruginosa . Replicate populations of P. aeruginosa were evolved for 60 days in the presence or absence of the ciliate predator Tetrahymena thermophila , followed by whole-population metagenomic sequencing, isolate-level genome sequencing, and quantitative phenotypic assays. We observed extensive genetic diversification across all populations, with strong signatures of both positive and purifying selection and pervasive parallel evolution at gene and nucleotide levels. Predator-exposed populations accumulated mutations enriched in regulatory, metabolic, and virulence-associated pathways, revealing predictable genomic targets of selection. However, many parallel mutations were shared between predator-exposed and predator-free populations, indicating that adaptation to the abiotic environment represented a dominant selective force. Genotype-phenotype analyses revealed pleiotropic effects and trade-offs linking motility, growth, and virulence-associated traits. Despite pronounced genomic adaptation and coordinated phenotypic shifts, changes in virulence in an in vivo host model were modest and context dependent. Taken together, our results indicate that predator exposure can influence evolutionary trajectories in P. aeruginosa and highlight the value of extending such approaches across multiple ecological and host contexts.

SIGNIFICANCE: Many bacterial pathogens spend much of their evolutionary history outside hosts, where they face intense ecological pressures such as predation. How these pressures shape pathogen evolution and disease potential remains unclear. Using experimental evolution, genomics, and phenotypic analyses, we show that prolonged exposure to a eukaryotic predator drives predictable genetic and phenotypic changes in the opportunistic pathogen Pseudomonas aeruginosa . Predator exposure altered regulatory, metabolic, and virulence-associated pathways, yet much adaptation was shared with predator-free populations, highlighting the dominant role of abiotic environments. Although predator-driven evolution reshaped traits linked to motility and growth, its effects on virulence were modest and context dependent. These findings clarify how environmental interactions influence pathogen evolution and underscore the importance of studying pathogens across diverse ecological settings.}, } @article {pmid41648417, year = {2026}, author = {Arasti, S and Şapcı, AOB and Rachtman, E and El-Kebir, M and Mirarab, S}, title = {Deconvolving Phylogenetic Distance Mixtures.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41648417}, issn = {2692-8205}, support = {R35 GM142725/GM/NIGMS NIH HHS/United States ; }, abstract = {Mixtures of multiple constituent organisms are sequenced in several widely used applications, including metagenomics and metabarcoding. Characterizing the elements of the sequence mixture and their abundance with respect to a reference set of known organisms has been the subject of intense research across several domains, including microbiome analyses, and methods must overcome two key challenges. First, the mixture constituents are related to each other through an evolutionary history, and hence, should not be considered independent entities. Second, sequence data is noisy, with each short read providing a limited signal. While existing approaches attempt to address these challenges, addressing both challenges simultaneously has proved challenging. For evolutionary dependencies, methods either define hierarchical clusters (e.g., taxonomies or operational taxonomic/genomic units) or use phylogenetic trees. For the second challenge, they either assemble reads into contigs, use statistical priors to summarize read placements, or attempt to analyze all reads jointly using k-mers. Despite this rich literature, a natural approach to simultaneously address both challenges has been underexplored: compute a distance from the mixture to all references, deconvolve those distances, and place the sample on multiple branches of a reference phylogeny with associated abundances. This multi-placement approach is a natural extension of the single-read phylogenetic placement used in practice. We argue that by placing the entire sample on multiple branches instead of placing reads individually, we can obtain a less noisy profile of the mixture. We formalize this approach as the phylogenetic distance deconvolution (PDD) problem, show some limits on the identifiability of PDDs, propose a slow exact algorithm, and an efficient heuristic greedy algorithm with local refinements. Benchmarking shows that these heuristics are effective and that our implementation of the PDD approach (called DecoDiPhy) can accurately deconvolve phylogenetic mixture distances while scaling quadratically. Applied to metagenomics, DecoDiPhy consolidates reads mapped to a large number of branches on a reference tree to a much smaller number of placements. The consolidated placements improve the accuracy of downstream tasks, such as sample differentiation and detection of differentially abundant taxa.}, } @article {pmid41648756, year = {2025}, author = {Grønbæk, IMB and Halkjær, SI and Hansen, EH and Mollerup, S and Paulsen, SJ and Konrad, CV and Engel, S and Bulinska-Balas, M and Wellejus, A and Haaber, AB and Christensen, AH and Engsbro, AL and Petersen, AM}, title = {Eight weeks of treatment with probiotic Bifidobacterium breve, Bif195 lowers fatigue scores in patients with diarrhoea-predominant irritable bowel syndrome: results from a randomised, clinical trial.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1701341}, pmid = {41648756}, issn = {2296-861X}, abstract = {UNLABELLED: Patients with irritable bowel syndrome experience abdominal pain and stool habit disturbances, and often also extraintestinal symptoms, such as fatigue. The disorder is linked to gut dysbiosis, and manipulation of the microbiota is considered a possible treatment strategy. This randomised, double-blinded, placebo-controlled study aimed to investigate the effects of the probiotic strain Bifidobacterium breve, Bif195™ (DSM 33360) (Bif195), on symptoms and gut microbiome composition in patients with diarrhoea-predominant irritable bowel syndrome. Sixty-one patients with moderate-severe disease activity were allocated to 8 weeks of treatment with either Bif195 or placebo (1:1), followed by 8 weeks of follow-up. The primary outcome was a change in symptom scores measured by the validated questionnaire, IBS-symptom severity scale. Secondary and explorative outcomes were the effects of Bif195 on intestinal symptoms, quality of life, fatigue, and the gut microbiota. Modulation of the transepithelial electrical resistance (TEER) of Caco-2 cells by Bif195 was investigated in vitro as a model of barrier integrity. The results showed no effect of Bif195 on primary or secondary outcomes; however, Bif195 lowered fatigue scores compared to placebo. Significantly increased TEER readings in vitro indicated enhanced barrier integrity, suggesting GI permeability as a mechanism for further clinical exploration.

CLINICAL TRIAL REGISTRATION: clinicaltrials.gov, identifier NCT04808271.}, } @article {pmid41649276, year = {2026}, author = {Castillo-Ramírez, S and López-Sánchez, R and Peralta, H}, title = {Acinetobacter-the bad, the ugly, but also the good!.}, journal = {mSphere}, volume = {11}, number = {3}, pages = {e0001026}, pmid = {41649276}, issn = {2379-5042}, mesh = {*Acinetobacter calcoaceticus/genetics/pathogenicity ; *Acinetobacter/genetics ; *Genome, Bacterial ; Metagenomics ; Solanum lycopersicum/microbiology ; Metagenome ; }, abstract = {The genus Acinetobacter is vast and diverse regarding its hosts. However, it is best known as an opportunistic pathogen that causes hard-to-treat nosocomial infections. Yet, some species of the genus can be beneficial for some hosts. Such is the case of Acinetobacter calcoaceticus, which can have a significant impact on tomato plants, as was recently shown in a paper by Robertson et al. (S. Robertson, A. Mosca, S. Ashraf, A. Corral, et al., mSphere 11:e00842-25, 2026, https://doi.org/10.1128/msphere.00842-25). Importantly, that study also exemplifies how metagenomics in general, but metagenome-assembled genomes in particular, can be employed to understand the functional specialization and identity of the bacterial species dwelling in particular environments.}, } @article {pmid41649278, year = {2026}, author = {Selleri, E and Tarracchini, C and Petraro, S and Mancabelli, L and Milani, C and Turroni, F and Shao, Y and Browne, HP and Lawley, TD and van Sinderen, D and Ventura, M and Lugli, GA}, title = {Assessment of genome evolution in Bifidobacterium adolescentis indicates genetic adaptation to the human gut.}, journal = {mSystems}, volume = {11}, number = {3}, pages = {e0117325}, pmid = {41649278}, issn = {2379-5077}, support = {PRIN 2022 Project Code 20229LEB99//European Union NextGeneration EU/ ; 12/RC/2273-P1, 12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Humans ; *Genome, Bacterial ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; *Bifidobacterium adolescentis/genetics/classification ; *Evolution, Molecular ; Metagenome ; Metagenomics ; *Adaptation, Physiological/genetics ; Genetic Variation ; }, abstract = {UNLABELLED: Bifidobacterium adolescentis is one of the most frequently encountered bifidobacterial species present in the adult human gut microbiota, with a prevalence of approximately 60%. Despite its high prevalence, B. adolescentis has not been extensively studied and characterized, and our understanding of its physiological traits, genetic diversity, and potential interactions with other members of the human gut microbiota or with its host is therefore fragmentary. In the current study, a data set comprising 1,682 B. adolescentis genomes was compiled by combining publicly available data and metagenome assemblies from 131 projects to uncover the unique genetic characteristics of this species. A pangenome analysis of B. adolescentis identified 203 clusters of orthologous genes absent from the other five human-associated Bifidobacterium species, six of which were in silico predicted to encode functions unique to this taxon. Furthermore, 2,597 genes were predicted to have been acquired by horizontal gene transfer, including genes encoding extracellular structures involved in interaction with the host and other microorganisms, and phage defense mechanisms against bacteriophages. Detailed phylogenetic analysis revealed seven clusters within the B. adolescentis species, each partially associated with the origin of strain isolation, suggesting phylogenetic differentiation shaped by geographical strain origin. Moreover, a large-scale metagenomic analysis of over 10,000 human gut metagenomes from healthy adults revealed that B. adolescentis co-occurs with 36 putative beneficial commensals and butyrate-producing taxa, highlighting its role as a key bifidobacterial species involved in microbial networking within the adult human gut microbiota.

IMPORTANCE: To comprehensively explore the biodiversity within a microbial species, the reconstruction of a substantial number of genomes is essential. In this study, we successfully uncovered the genetic diversity of Bifidobacterium adolescentis by retrieving a large number of genomes from human gut metagenomic samples. The complete overview of the B. adolescentis pangenome enabled us to investigate the genetic features that distinguish this gut commensal from other bifidobacterial species residing in the human intestinal microbiota.}, } @article {pmid41649661, year = {2025}, author = {Romão, IR and do Carmo Gomes, J and Silva, D and Vilchez, JI}, title = {The seed microbiota from an application perspective: an underexplored frontier in plant-microbe interactions.}, journal = {Crop health}, volume = {3}, number = {1}, pages = {12}, pmid = {41649661}, issn = {2948-1945}, support = {UIDB/04551/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/04551/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0087/2020//Fundação para a Ciência e a Tecnologia/ ; }, abstract = {Seed-associated microbiota represent a critical yet underexplored frontier in plant-microbe interactions, offering unique insights into plant health, resilience, and development. Unlike the soil or rhizosphere microbiome, the seed microbiota is closely tied to plant reproduction, facilitating both vertical and horizontal transmission of microbes. These microbial communities influence key plant processes, including germination, stress tolerance, nutrient acquisition, and pathogen resistance, providing plants with a pre-assembled microbial consortium tailored to their needs. Despite recent advances, significant gaps remain in understanding how seed-associated microbes are acquired, their ecological dynamics, and their functional roles. High-throughput sequencing, metagenomics, and spatial imaging techniques have revealed the diversity and complexity of the seed microbiota, emphasizing their potential for agricultural innovation. This research highlights the importance of these communities in shaping plant resilience and productivity, yet questions about their ecological and evolutionary significance persist. The present review synthesizes current knowledge on the composition, inheritance mechanisms, and functional roles of the seed microbiota. It also explores strategies to harness these microbes for sustainable agriculture, including microbiome engineering and breeding for microbial compatibility. By addressing these gaps, seed microbiota research could revolutionize sustainable agriculture, enhancing crop resilience and reducing reliance on chemical inputs.}, } @article {pmid41650192, year = {2026}, author = {Wang, H and Shan, X and Xing, D and Wang, Y and Jin, C and Zhao, Y and Guo, L}, title = {Rhamnolipid Modulates Microbial Interspecies Electron Transfer for Synchronous Sulfidogenesis and Acidogenesis from Mariculture Solid Wastes.}, journal = {Environmental science & technology}, volume = {60}, number = {6}, pages = {4900-4913}, doi = {10.1021/acs.est.5c16493}, pmid = {41650192}, issn = {1520-5851}, mesh = {Electron Transport ; *Glycolipids ; }, abstract = {Synchronous sulfidogenesis and acidogenesis (SSA) are critical for pollutant removal and resource recovery. However, inefficient electron transfer and metabolic imbalance between acidogenic bacteria and sulfidogens limit SSA performance, especially from mariculture solid wastes (MSW) containing high-strength sulfate. This work unveiled the neglected role and mechanism of rhamnolipid (RL) in modulating microbial interspecies electron transfer for SSA during MSW anaerobic fermentation. RL, at environmentally relevant levels of 20-200 mg/g suspended solids, simultaneously improved sulfide (40.1-87.9%) and short-chain fatty acids (8.0-19.3-fold) yield. Extracellular polymeric substances (EPSs) exhibited higher capacitance and electroactivity to store or transfer electrons in the presence of RL. Proper RL facilitated pili-like filament formation and redox mediator secretion. The flavins and cytochrome c combination was promoted by RL to mediate one-electron transfer with a higher transfer rate via the flavin semiquinone intermediate. RL increased the dipole moment of the α-helix peptide and spontaneously interacted with the C═O of amide groups, enabling efficient electron hopping in EPSs. RL also activated key components in the intracellular electron transfer system, delivering more electron flow to sulfate reductase. Metagenomic and metatranscriptomic analyses verified the differential enrichment of microorganisms and key gene upregulation related to SSA, EPS secretion, quorum sensing, ATP, type IV pili, and electron shuttle synthesis. These findings provide new insight into the roles and interactive mechanisms of biosurfactants in modulating microbial electron transfer.}, } @article {pmid41650276, year = {2026}, author = {Chen, L and Camargo, AP and Qin, Y and Koonin, EV and Wang, H and Zou, Y and Duan, Y and Li, H}, title = {Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism.}, journal = {Science advances}, volume = {12}, number = {6}, pages = {eaeb6265}, pmid = {41650276}, issn = {2375-2548}, mesh = {Animals ; *Bacteriophages/genetics/physiology/classification ; Humans ; *Gastrointestinal Microbiome ; Metagenome ; Genome, Viral ; Phylogeny ; Bacteroides/virology ; }, abstract = {Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (jumbo gut) phages with genomes of 360 to 402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38 to 57% identity, suggesting horizontal acquisition from other phages. Over 1500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug phages as potential major players in gut microbiome ecology.}, } @article {pmid41650846, year = {2026}, author = {Hosen, ME and Dunsdon, S and Sarker, S}, title = {Mosquito-borne viruses in Australia: An emerging trend of increasing prevalence in Northern Queensland.}, journal = {Virology}, volume = {617}, number = {}, pages = {110825}, doi = {10.1016/j.virol.2026.110825}, pmid = {41650846}, issn = {1096-0341}, mesh = {Queensland/epidemiology ; Animals ; Mosquito-Borne Diseases/epidemiology/virology ; Humans ; Mosquito Vectors/virology ; Aedes/virology ; Prevalence ; Wolbachia/physiology ; Mosquito Control ; *Arboviruses/genetics/classification/isolation & purification ; Ross River virus ; }, abstract = {Mosquito-borne viruses (MBVs) remain a significant public health concern in Northern Queensland, Australia, with dengue virus (DENV), Ross River virus (RRV), and Barmah Forest virus (BFV) representing the most common pathogens. Wolbachia-based biological control programs have made notable contributions to reducing dengue transmission by suppressing Aedes aegypti vector competence. Recent surveillance data indicates increased MBV activity, with national case numbers nearly doubling between 2023 and 2024 and early 2025 data suggesting sustained transmission during seasonal peak. Traditional surveillance approaches, while highly valuable for disease monitoring, have limitations in detecting novel or divergent viral strains in real time. Over the past decades, more than 919 unclassified flaviviruses have been reported nationwide, including 117 in Queensland. The advent of metagenomic and metatranscriptomic approaches now enable enhanced, field-based detection of both known and emerging arboviruses. Strengthening mosquito control programs through continued Wolbachia releases, alongside integrated genomic surveillance, predictive modelling, and community engagement will enhance early detection, guide targeted interventions, and reduce the MBV burden in Northern Queensland. This integrated framework provides a strategic pathway to sustains and expand vector control effectiveness while safeguarding public health in high-risk regions.}, } @article {pmid41650859, year = {2026}, author = {Wei, W and Zhang, Z and Li, J and Du, H and Wu, Q and Cui, R and Wang, X and Ren, L and Zhang, M and Wang, Y}, title = {Effects of microbial inoculation on mitigating odor release, curtailing nitrogen and sulfur losses, and accelerating the maturation during food-waste composting.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128800}, doi = {10.1016/j.jenvman.2026.128800}, pmid = {41650859}, issn = {1095-8630}, mesh = {*Composting ; *Odorants ; Nitrogen/metabolism ; Food Loss and Waste ; *Sulfur/metabolism ; RNA, Ribosomal, 16S ; Volatile Organic Compounds ; }, abstract = {A thermotolerant, odor-suppressing microbial agent was inoculated into food-waste (FW) composting to systematically evaluate its influence on odorants, volatile organic compounds (VOCs), microbial community structure, extracellular enzyme activities, and the transcriptional profile of nitrogen- and sulfur-cycle genes. Compared with the uninoculated control, cumulative emissions of NH3, H2S, ethanol, and acetaldehyde declined by 73.45%, 65.30%, 40.22%, and 37.20%, respectively, in the bio-augmented reactor. NH3 High-throughput 16S rRNA sequencing revealed that the inoculation enhanced the microbial richness and diversity, while increasing the abundance of thermophilic strains that promote compost maturation and reduce nitrogen loss. Concomitantly, the relative abundances of acid-producing and skatole-generating populations were suppressed. Quantitative PCR showed that the expression of narG, norB, nif, nrfA, nirB, aprA, and sat genes was down-regulated. This consequently reduced the production of NH4[+]-N and inhibited the sulfate reduction process, thereby coordinating nitrogen and sulfur metabolic transformations and significantly lowering NH3 and H2S emissions. Overall, this study demonstrates the feasibility of microbial inoculation for mitigating odor emissions, retaining nutrients, and accelerating compost maturation, while providing mechanistic insights into how microbial formulations regulate enzyme activities and the expression of functional genes during composting.}, } @article {pmid41650863, year = {2026}, author = {Wang, X and Zhao, HP and Lai, CY}, title = {Anaerobic biodegradation of ceftriaxone: Transformation pathways, toxicity assessment, and microbial mechanisms.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128859}, doi = {10.1016/j.jenvman.2026.128859}, pmid = {41650863}, issn = {1095-8630}, mesh = {Bioreactors ; *Ceftriaxone/metabolism/toxicity ; Anaerobiosis ; Biodegradation, Environmental ; Water Pollutants, Chemical/metabolism ; }, abstract = {The overuse of ceftriaxone has resulted in its widespread occurrence in aquatic environments, posing ecological and health risks. An anaerobic membrane bioreactor (AnMBR) was operated for 128 days to systematically investigate the anaerobic microbial transformation of CTX. The AnMBR exhibited stable and efficient performance, maintaining chemical oxygen demand removal above 90% and achieving an average CTX removal efficiency of 65.0 ± 15.2%. Several potential degradation pathways are proposed, involving β-lactam ring hydrolysis, C-S bond cleavage, and decarboxylation reactions. Toxicity assessments using ADMETlab 3.0 platform reveal that although most TPs showed reduced ecotoxicity and dermal toxicity compared to the parent compound, several intermediates exhibited elevated risks of nephrotoxicity and genotoxicity. Metagenomic analysis indicates that long-term CTX exposure reshaped the microbial community, enriching methanogens such as Methanothrix soehngenii and Methanosarcina mazei, though these taxa might not directly participate in CTX degradation. Several archaeal and bacterial MAGs carrying functional genes, including lactam hydrolase, thioesterase, and decarboxylase, were identified, suggesting a collaborative and functionally diverse microbial network involved in CTX transformation. This study offers mechanistic insights and technical foundations for advancing anaerobic biotechnologies in the treatment of antibiotic-contaminated wastewater, while highlighting the need for ongoing monitoring of potential long-term risks associated with TPs.}, } @article {pmid41651079, year = {2026}, author = {Xin, Y and Ma, H and Li, X and Sun, R and Fang, L and Pan, L}, title = {Multi-omics reveal the key role of gut microbiota metabolism in adenine-induced chronic kidney disease.}, journal = {Toxicology and applied pharmacology}, volume = {509}, number = {}, pages = {117754}, doi = {10.1016/j.taap.2026.117754}, pmid = {41651079}, issn = {1096-0333}, mesh = {Animals ; *Adenine/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Renal Insufficiency, Chronic/chemically induced/metabolism/microbiology ; Multiomics ; Male ; Metabolomics ; Mice, Inbred C57BL ; Mice ; Disease Models, Animal ; Kidney/metabolism/pathology ; Metagenomics ; }, abstract = {The gut microbiota plays a crucial role in the progression of chronic kidney disease (CKD). The adenine-induced CKD mouse model is widely employed in preclinical research, yet the effects of adenine on the composition and metabolic function of the gut microbiota remain to be elucidated. This study aimed to test the hypothesis that adenine-induced alterations in the structure and function of the gut microbiota are significantly associated with the onset and progression of CKD. To this end, a mouse CKD model was established by alternating feeding with 0.15% and 0.20% adenine for 7 weeks. Multi-omics analysis (untargeted metabolomics, metagenomics, and spatial metabolomics) was performed to compare the adenine-induced CKD group with a standard diet-fed normal control group. Integrated analysis of plasma metabolomics and intestinal content metabolomics identified 94 differentially co-regulated metabolites: among these, indolelactic acid was significantly upregulated, while indole-3-propionic acid was significantly downregulated. The bile acid metabolic pathway also underwent marked perturbations: taurochenodeoxycholic acid and tauro-β-muricholic acid (two taurine-conjugated bile acids) were significantly elevated, whereas nordeoxycholic acid and norcholic acid were notably reduced. Integrated metabolomics-metagenomics analysis further demonstrated that Lactobacillus exhibited a significant positive correlation with a subset of upregulated metabolites (including indolelactic acid), while Taurinivorans muris showed a strong negative correlation with the taurine-conjugated bile acids. Additionally, renal spatial metabolomics revealed that phospholipid metabolic disorders in the adenine-induced CKD group directly contributed to the aggravation of renal inflammatory responses. Collectively, these findings reveal a gut microbiota-metabolite-kidney axis perturbed by adenine, providing novel insights into the pathogenesis of CKD and potential targets for metabolic intervention.}, } @article {pmid41651131, year = {2026}, author = {Hantsoo, L and Ford, E and Friedman, ES and Hao, F and Patterson, AD and Bittinger, K and Wu, GD and Zemel, BS and Tanes, C}, title = {The impact of adverse childhood experiences on gut microbiota and markers of inflammation is mediated by obesity and depression.}, journal = {Brain, behavior, and immunity}, volume = {134}, number = {}, pages = {106479}, pmid = {41651131}, issn = {1090-2139}, support = {R03 HD101336/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Female ; Pregnancy ; *Depression/microbiology/metabolism ; *Obesity/microbiology/metabolism ; *Inflammation/metabolism/microbiology ; Adult ; *Adverse Childhood Experiences ; *Gastrointestinal Microbiome/physiology ; Biomarkers/blood ; Body Mass Index ; Feces/microbiology ; Surveys and Questionnaires ; Pregnancy Trimester, Third ; }, abstract = {BACKGROUND: Adverse childhood experiences (ACEs) are associated with poor health outcomes in adulthood including obesity, psychiatric symptoms, and elevated levels of inflammatory markers. Our previous work found ACEs are associated with altered gut microbiota composition. In the present work, we examined ACE associations with gut microbiota and peripheral measures of inflammation in pregnant women with or without obesity, and explored potential modifying factors including diet and depressive symptoms.

METHODS: Female participants were recruited in the third trimester of pregnancy as part of a larger growth study of African-American infants. Participants were categorized as healthy weight (BMI < 25) or obese (BMI ≥ 30) based on their early pregnancy BMI. They completed the Adverse Childhood Experiences Questionnaire (ACE-Q) and Center for Epidemiologic Studies Depression Scale (CES-D). Stool samples, blood, and dietary data were collected in the third trimester. Shotgun metagenomic sequencing was performed on DNA isolated from stool. Statistical models assessed relationships between gut microbiota and ACE. A false discovery rate (fdr) adjusted p-value q < 0.1 was considered statistically significant.

RESULTS: 107 women completed questionnaires and provided stool in the third trimester. ACEs were positively associated with BMI and depressive symptom severity but not with gut microbiota composition. Depressive symptoms were significantly negatively associated with abundance of gut Bifidobacterium longum (q = 0.02) and positively associated with Bacteroides thetaiotaomicron (q = 0.02). Path analysis revealed that ACEs predicted pre-pregnancy BMI which predicted elevated inflammatory markers. ACEs also predicted more severe depressive symptoms in pregnancy, which was associated with gut microbiome composition. Finally, ACEs interacted with dietary intake of sugar and whole grains to impact markers of inflammation, the gut microbiome, and enzymes produced by gut microbiota.

DISCUSSION: ACEs led to two risk pathways in pregnancy: one in which high pre-pregnancy BMI was linked with high levels of serum inflammatory markers during pregnancy, and the other in which greater depressive symptom severity was associated with alterations to the gut microbiome. Further, data suggested ACEs may influence the metabolic potential of the gut microbiome.}, } @article {pmid41651145, year = {2026}, author = {Wang, Y and Sun, T and Li, L and Wang, M and Hu, B and Chen, Z and Hu, S}, title = {Synergistic effects of carbon dots and arbuscular mycorrhizal fungi on mitigating PFAS stress and reinforcing the purification performance of constructed wetlands.}, journal = {Environmental research}, volume = {295}, number = {}, pages = {123952}, doi = {10.1016/j.envres.2026.123952}, pmid = {41651145}, issn = {1096-0953}, mesh = {*Wetlands ; *Carbon Quantum Dots ; *Mycorrhizae/physiology ; *Water Pollutants, Chemical/toxicity/metabolism ; *Fluorocarbons/toxicity/metabolism ; Biodegradation, Environmental ; }, abstract = {Per- and polyfluoroalkyl substances (PFASs) are highly persistent pollutants that disrupt plant-microbe interactions and compromise the performance of constructed wetlands (CWs). Here, we demonstrate a synergistic strategy combining carbon dots (CDs) and arbuscular mycorrhizal fungi (AMF) to alleviate PFAS-induced stress and enhance CW remediation efficiency. CD amendment markedly improved plant physiological performance under PFAS exposure, increasing photosynthetic efficiency and antioxidant enzyme activities, while simultaneously facilitating AMF colonization. Under high PFAS concentrations, the AMF-CDs treatment increased AMF colonization density by 33.3-100% relative to AMF alone, indicating substantial protection of symbiotic functionality. Metagenomic and community analyses revealed that the AMF- CDs combination reshaped the rhizosphere microbiome, enriching taxa such as Chloroflexi, Planctomycetes, and Campylobacterota that are functionally linked to nitrogen cycling, PFAS transformation, and metabolic resilience. These microbial shifts enhanced nutrient turnover and strengthened redox coupling processes critical for pollutant degradation. Consequently, the AMF-CDs system achieved pronounced improvements in water quality, with total phosphorus (TP), chemical oxygen demand (COD), total nitrogen (TN), and NH4[+]-N removal efficiencies elevated by 34.3-158.3% compared with untreated controls. This study provides the first evidence that CDs function as nano-bridging agents that stabilize the root-microbe interface, reinforce AMF-plant symbiosis, and drive microbial community specialization toward pollutant degradation. The AMF-CDs synergistic mechanism offers a sustainable and scalable nano-bio strategy for restoring PFAS-contaminated ecosystems and advancing next generation constructed wetland technologies.}, } @article {pmid41651377, year = {2026}, author = {Scholand, KK and Schaefer, L and Shao, J and Yu, Z and Pflugfelder, SC and Britton, RA and de Paiva, CS}, title = {Investigating conjunctival immune pathways in Sjögren and non-Sjögren disease associated dry eye.}, journal = {The ocular surface}, volume = {40}, number = {}, pages = {52-62}, doi = {10.1016/j.jtos.2026.02.001}, pmid = {41651377}, issn = {1937-5913}, support = {U24 EY035067/EY/NEI NIH HHS/United States ; }, mesh = {Humans ; *Conjunctiva/immunology/pathology/metabolism ; Female ; *Sjogren's Syndrome/immunology/complications/genetics/metabolism ; Male ; *Dry Eye Syndromes/immunology/genetics/metabolism/etiology ; Middle Aged ; *Keratoconjunctivitis Sicca/immunology ; Aged ; Adult ; Tears/metabolism ; }, abstract = {PURPOSE: Dry eye disease (DED) is classified based on its predominant etiology into aqueous tear-deficient (ATD), evaporative, or mixed. Sjӧgren disease keratoconjunctivitis sicca (SjD-KCS) is a very severe autoimmune form of ATD DED. The purpose of this work was to compare transcriptomic changes in the conjunctiva sampled from patients with ATD, SjD-KCS, and healthy controls (HC) to evaluate distinctions in the immune response on the ocular surface based on diagnosis.

METHODS: Impression cytology of the temporal bulbar conjunctiva was collected using the EyePrim device. RNA was extracted and submitted with the Nanostring nCounter Human Immunology V2 panel for gene expression analysis. Results were uploaded to ROSALIND and Metascape to identify DEGs by comparison (all DED vs HC; SjD vs HC; ATD vs HC) and associated predicted pathways. A subset of samples (n = 4 per group) were used for immunofluorescent staining of LAMP3 and HLA-DR.

RESULTS: 49 patients were enrolled in the study (25 HC; 12 SjD; 12 ATD). 100 DEGs were found in the comparison of all DED vs HC. 69 DEGs were found in the SjD vs HC. 11 DEGs were found in the ATD vs HC. There were no DEGs identified in the SjD vs ATD comparison. DEGs were involved in immune pathways related to viral response, adaptive immunity, and cell to cell communication. DED conjunctiva had increased expression of LAMP3 and HLA-DR compared to HC.

CONCLUSIONS: Our findings demonstrate that DED, regardless of the diagnosis, have similar immune-related DEGs and associated pathways on the ocular surface.}, } @article {pmid41651389, year = {2026}, author = {Shi, B and Zhang, L and Jia, X and Tao, Y and Wang, M}, title = {Profiles of gut microbiome in Litopenaeus vannamei artificially infected with Vibrio parahaemolyticus causing translucent post-larva disease.}, journal = {Developmental and comparative immunology}, volume = {176}, number = {}, pages = {105565}, doi = {10.1016/j.dci.2026.105565}, pmid = {41651389}, issn = {1879-0089}, mesh = {Animals ; *Penaeidae/microbiology/immunology ; *Vibrio parahaemolyticus/physiology ; *Vibrio Infections/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Virulence/genetics ; Host-Pathogen Interactions ; }, abstract = {As the primary defense against pathogen invasion, the dynamic equilibrium of the shrimp gut microbiome is recognized as a critical factor influencing pathogen colonization. In recent years, translucent post-larva disease (TPD) outbreaks during the early stages of shrimp farming have become a serious threat to the sustainable development of the shrimp industry. Compared with other vibriosis, TPD caused by certain Vibrio strains possessing drug resistance and high-virulence genes exhibits greater virulence in shrimp tissues, with mortality rates reaching up to 90%. However, no studies have yet explored the association between this pathogen and the gut microbiome. This study employed metagenomic sequencing technology to analyze differences in the axial distribution of the gut microbiome in shrimp at varying degrees of TPD infection. Histopathological sections revealed that multiple tissue lesions induced by TPD infection in shrimp were primarily concentrated in the midgut. Alpha diversity analysis indicated that the alpha diversity index of the shrimp gut microbiome showed an upward trend as pathogen load increased. Beta diversity analysis revealed the intestinal segment with the most significant microbial community changes during pathogen colonization. Within this region, the abundance of probiotics decreased, while that of pathogenic bacteria increased. Functional prediction results indicate that under TPD stress, the gut microbiome activates a multi-layered, synergistic defense adaptation program through nutritional metabolism shifts, biofilm reinforcement, and toxin efflux. This study elucidates the pathogenic mechanism of TPD from the perspective of pathogen-gut microbiome interactions, suggesting that controlling pathogen load and restoring targeted probiotics may serve as effective strategies for preventing and controlling TPD.}, } @article {pmid41651877, year = {2026}, author = {Zhang, E and Claesson, MJ and Cotter, PD}, title = {Adopting omics-based approaches to facilitate the establishment of microbial consortia to generate reproducible fermented foods with desirable properties.}, journal = {NPJ science of food}, volume = {10}, number = {1}, pages = {}, pmid = {41651877}, issn = {2396-8370}, support = {23/FFP-A/11857//Research Ireland/ ; 101060218//European Commission/ ; }, abstract = {The quality of fermented foods is governed by the composition, function, and interactions of their microbial communities. However, fermentations carried out using traditional approaches are often variable with respect to their composition and are difficult to control, thereby limiting industrial reproducibility. Recent advances in omics technologies-including metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics-have greatly enhanced our ability to analyze and reconstruct the microbial ecosystems in fermented foods. This review first highlights the importance of omics analyses for characterizing microbial composition, metabolic potential, and functional interactions. It then discusses the bipartite structure of defined microbial consortia (DMCs), distinguishing between the core microbiome, comprising taxa consistently associated with fermentation performance, and the supplementary microbiome, consisting of variable species that influence flavor diversity and system stability. Finally, we describe a multi-omics-guided strategy for the design and refinement of DMCs, framed within the Assembly-Assessment-Redesign (A-A-R) workflow, which enables iterative optimization of microbial consortia for reproducible and desirable fermentation outcomes. Integrating omics insights with DMC engineering provides a systematic approach for precision fermentation, paving the way for next-generation fermented food production.}, } @article {pmid41651883, year = {2026}, author = {Pantiukh, K and Org, E}, title = {Human gut archaea collection from Estonian population.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41651883}, issn = {2052-4463}, support = {PRG1414//Eesti Teadusagentuur (Estonian Research Council)/ ; 3573//European Molecular Biology Organization (EMBO)/ ; }, mesh = {Estonia ; *Archaea/genetics/classification ; Humans ; *Metagenome ; *Microbiota ; *Genome, Archaeal ; Feces/microbiology ; }, abstract = {While microbiota plays a crucial role in maintaining overall health, archaea, a component of microbiota, remain relatively unexplored. Here, we present a newly assembled set of archaeal metagenome-assembled genomes (MAGs) from 1,878 fecal microbiome samples. These MAGs were reconstructed from metagenomic reads of the Estonian Microbiome Deep (EstMB-deep) cohort, which were reused here specifically for archaeal MAG reconstruction. We identified 273 archaeal MAGs, representing 21 species and 144 strains which we curated into the "EstMB MAGdb Archaea-273" MAGs collection.}, } @article {pmid41651909, year = {2026}, author = {Kanyerezi, S and Ayitewala, A and Kabahita, JM and Oundo, HR and Sseruyange, J and Tenywa, W and Tusabe, G and Were, S and Murungi, M and Nabukyu, M and Nakintu, V and Makoha, C and Sserwadda, I and Onywera, H and Tanui, C and Mugerwa, I and Kagirita, A and Lubwama, B and Michael, ER and Kateete, DP and Otita, M and Giduddu, S and Jjingo, D and Nsawotebba, A and Mboowa, G and Ssemaganda, A and Nabadda, S and Tessema, SK and Ssewanyana, I}, title = {Targeted metagenomics reveals hidden chickenpox epidemic amid Mpox surveillance in Uganda.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41651909}, issn = {2045-2322}, abstract = {In regions where both monkeypox virus (MPXV) and varicella zoster virus (VZV) are co-circulating, overlapping clinical manifestations can complicate clinical diagnosis. During the MPXV outbreak declared in Uganda in July, 2024, symptomatic suspected cases tested PCR negative for Mpox. To determine the cause of symptoms, we employed metagenomic sequencing with a targeted Viral Surveillance panel in 284 MPXV negative samples. VZV was identified as the predominant pathogen in 86% of MPXV-negative cases, suggesting a concurrent chickenpox surge. Using the VaricellaGen pipeline for variant calling, clade typing, and phylogeny, 118 (49%) samples that achieved ≥ 70% genome coverage were of clade 5 based on the single-nucleotide polymorphism (SNP) dataset. This data confirms co-circulation of VZV during the MPXV outbreak in Uganda. Our results underscore the need for laboratory confirmation of MPXV and the inclusion of VZV in the testing algorithm during the Mpox outbreak.}, } @article {pmid41652580, year = {2026}, author = {He, L and Cheng, Y and Huang, L and Zhang, Z and Zhang, Q and Gong, L and Li, T and Lu, X and Cai, X and Yan, G}, title = {Metagenomic next-generation sequencing to detect Pneumocystis jirovecii pneumonia in critically ill, HIV-negative children: a retrospective multicenter study.}, journal = {BMC pulmonary medicine}, volume = {26}, number = {1}, pages = {}, pmid = {41652580}, issn = {1471-2466}, support = {2021YFC2701800//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/microbiology ; Retrospective Studies ; *Pneumocystis carinii/genetics/isolation & purification ; Child, Preschool ; Child ; Infant ; Male ; Female ; Bronchoalveolar Lavage Fluid/microbiology ; Adolescent ; Critical Illness ; *Metagenomics ; *High-Throughput Nucleotide Sequencing ; ROC Curve ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) plays a critical role in the rapid detection of infectious pathogens. We aimed to analyze the clinical characteristics of Pneumocystis jirovecii infection in children without HIV infection and to evaluate the performance of mNGS in distinguishing P. jirovecii colonization from true infection.

METHODS: A multicenter, retrospective analysis was conducted on critically ill, non-HIV-infected pediatric patients who tested positive for P. jirovecii via mNGS analysis of bronchoalveolar lavage fluid (BALF). Group differences were assessed using Mann-Whitney U-tests (for continuous data) and chi-square tests (for categorical data). Discriminatory performance was evaluated by calculating the area under the receiver operating characteristic curve.

RESULTS: A total of 59 HIV-negative children (age range: 2 months to 14 years) from four children's hospitals were included and classified into two groups based on P. jirovecii status: P. jirovecii pneumonia (PCP; n = 51) and P. jirovecii colonization (PCC; n = 8). Compared with the PCC group, the PCP group had significantly higher serum C-reactive protein levels and median P. jirovecii read counts in mNGS (both P < 0.05). The optimal threshold value for discriminating P. jirovecii infection from colonization appeared to be 556 reads (sensitivity, 77.6%; specificity, 100.0%). Eighteen patients (35.3%) in the PCP group died. Compared with survivors, these patients were significantly younger, had lower T-cell subset counts (CD3[+], CD4[+], and CD8[+]), and a higher prevalence of primary immunodeficiency (all P < 0.05).

CONCLUSIONS: BALF mNGS analysis may have utility for differentiating between colonization and infection by P. jirovecii, warranting further investigation.}, } @article {pmid41652998, year = {2026}, author = {Desorcy-Scherer, K and McNamara, K and Luellwitz, R and Stanton, E and Zuniga-Chaves, I}, title = {Early Insights Into Maternal Antidepressant Use and the Human Infant Gut Microbiome.}, journal = {Biological research for nursing}, volume = {28}, number = {3}, pages = {406-417}, doi = {10.1177/10998004261423546}, pmid = {41652998}, issn = {1552-4175}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/drug effects ; Pilot Projects ; Infant ; *Selective Serotonin Reuptake Inhibitors/adverse effects/therapeutic use ; Pregnancy ; *Antidepressive Agents/adverse effects/therapeutic use ; Adult ; Infant, Newborn ; Feces/microbiology ; }, abstract = {Maternal selective serotonin reuptake inhibitor (SSRI) use is common during pregnancy and lactation. Changes in serotonin signaling may affect diversity and composition of microbes in the gut. Although research suggests SSRI drives microbial change, the extent to which the infant gut microbiome is affected is unknown. The infant gut microbiome is critical in early life for support of developmental health including early training of the immune system and metabolic programming. A total of N = 20 (10 SSRI, 10 control) maternal/infant dyads were enrolled in a pilot study. Thirty-six infant stool samples were collected at 1-2 and 4-6 weeks of life and sequenced using 16S rRNA sequencing. Investigative models included SSRI exposure as the primary variable of interest with infant feeding pattern and mode of delivery included as covariates. Maternal antidepressant use was not associated with infant alpha (within-sample) diversity. The SSRI use may shape beta (between-sample) diversity, particularly at weeks 4-6 of life (p = .072). Increases in the genera Gemella, Staphylococcus and Corynebacterium were observed with SSRI exposure. Additionally, results reveal a SSRI-associated decrease in Lactobacillus. While this pilot study is not intended to provide conclusive evidence, it is an important step in informing future research directions. Results suggest a modest influence of maternal SSRI exposure on the infant gut microbiome. Future studies should seek to use techniques like metagenomics, providing functional information to assess for local or systemic health impact and ultimately, clinical relevance.}, } @article {pmid41653012, year = {2026}, author = {Asis, A and Rodríguez, A and Reyes, LF and Díaz, E and Nseir, S and Martín-Loeches, I}, title = {The double threat: bacterial and fungal co-/superinfection in viral pneumonia.}, journal = {Expert review of respiratory medicine}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/17476348.2026.2629003}, pmid = {41653012}, issn = {1747-6356}, abstract = {INTRODUCTION: Respiratory viral pneumonias are a leading cause of severe respiratory failure and intensive care unit (ICU) admission worldwide. Although viral infection itself drives significant morbidity and mortality, secondary bacterial and fungal superinfections represent a critical 'double threat' in critically ill adults, exacerbating lung injury, prolonging organ dysfunction, and complicating antimicrobial management. Experience from the Influenza A (H1N1) pdm09 and SARS-CoV-2 pandemics highlights a persistent mismatch between low documented bacterial co-infection rates and widespread empiric antibiotic exposure, underscoring diagnostic uncertainty and antimicrobial stewardship challenges in the ICU.

AREAS COVERED: This review examines the epidemiology, immunopathogenesis, and diagnostic approaches to bacterial and fungal superinfection in adult ICU patients with severe viral pneumonia. Evidence is synthesized from large ICU cohorts, pandemic data, and established consensus definitions for influenza- and COVID-19-associated pulmonary aspergillosis (IAPA, CAPA). The review discusses advances in molecular diagnostics, lower respiratory tract sampling, bronchoalveolar lavage - based mycology, and biomarker-guided strategies, with a focused literature search of ICU-specific studies.

EXPERT OPINION: Bacterial and fungal superinfections, while infrequent, carry substantial clinical impact in severe viral pneumonia. A multimodal, ICU-adapted diagnostic strategy integrating pathogen detection with host-response assessment is essential to support timely therapy, enable antimicrobial de-escalation, and align superinfection management with stewardship principles.}, } @article {pmid41653157, year = {2026}, author = {Qian, J and Fang, J}, title = {Letter to the editor regarding: 'Diagnostic value of plasma cell-free DNA metagenomic next-generation sequencing in patients with suspected infections and exploration of clinical scenarios - a retrospective study from a single center'.}, journal = {Annals of medicine}, volume = {58}, number = {1}, pages = {2624190}, pmid = {41653157}, issn = {1365-2060}, } @article {pmid41653605, year = {2026}, author = {Cho, DY and Haque, MA and Lee, HY and Jang, MY and Jeong, JB and Lee, GY and Son, KH and Lee, JH and Cho, KM}, title = {Amending metagenomic bacterial community in soybean-cultivated soils to enhance phytoestrogen in soybean roots by communicating with mixture of culturable rhizospheric bacteria.}, journal = {Plant physiology and biochemistry : PPB}, volume = {232}, number = {}, pages = {111093}, doi = {10.1016/j.plaphy.2026.111093}, pmid = {41653605}, issn = {1873-2690}, mesh = {*Glycine max/microbiology/metabolism ; *Soil Microbiology ; *Plant Roots/microbiology/metabolism ; *Rhizosphere ; *Phytoestrogens/metabolism ; *Bacteria/genetics/metabolism ; }, abstract = {The amendment of metagenomic bacterial community in soybean-cultivated soils to enhance phytoestrogen levels in soybean roots through communicating with mixture of culturable rhizospheric bacteria (RB) were rarely studied. RB from soybean roots and soybean-cultivated soils were isolated and applied to soybean plants. Treated soybean plants were divided into three groups: control (CTL), soybean root RB (SRR), and soybean-cultivated soil RB (SSR). Each group had a distinct influence on the metagenomic bacterial community of the soybean rhizosphere. The α-proteobacteria were the dominant class in all three groups, although SRR was enriched with Actinomycetes, Fimbriimonadia, and γ-proteobacteria, while SSR was enriched with Bacilli, Chitinophagia, and Gemmatimonadia classes. Additionally, at the significantly species level, SRR was enriched with Arthrobacter sp. and Azospirillum lipoferum, while SSR was enriched with Bradyrhizobium sp. and Rhizobium sp. Moreover, the RB treatment significantly affected the root metabolite composition. In the SSR-treated group, phenylalanine (18.80-47.81 mg/100 g) and tyrosine (8.03-21.98 mg/100 g) tended to be significantly enhanced. Additionally, secondary metabolites, such as isoflavones, total phenolics, and total flavonoids, were also significantly affected by the RB treatment; secondary metabolites were the highest in the SSR-treated group. These changes in metabolites also affected radical scavenging activities, with the SSR-treated group displaying significantly increased activities compared to the other groups. As a result, DPPH increased from 32.44 % to 47.21 % and ABTS from 53.41 % to 74.23 %. Therefore, RB treatment can influence the bacteria and root metabolite compositions within the soybean rhizosphere, revealing its potential applications in soybean productivity.}, } @article {pmid41653958, year = {2026}, author = {Gamez, I and Fouladi, F and Gonzalez, A and Ward, J and Wang, Z and Beane Freeman, LE and Motsinger-Reif, A and Peddada, SD and Knight, R and Lee, M and London, SJ}, title = {Household environmental characteristics influence the house dust metagenome.}, journal = {Environmental research}, volume = {295}, number = {}, pages = {123889}, pmid = {41653958}, issn = {1096-0953}, support = {Z01 CP010119/ImNIH/Intramural NIH HHS/United States ; ZIA ES049030/ImNIH/Intramural NIH HHS/United States ; ZIA ES102385/ImNIH/Intramural NIH HHS/United States ; ZIA ES103390/ImNIH/Intramural NIH HHS/United States ; }, mesh = {*Dust/analysis ; *Metagenome ; Housing ; *Air Pollution, Indoor/analysis ; *Microbiota ; Family Characteristics ; Bacteria/genetics/classification ; *Environmental Exposure ; Humans ; }, abstract = {Environmental exposures can shape microbial community compositions inside homes. Metagenomic sequencing methods can further elucidate the role of household exposures like indoor moisture and the surrounding landscape. To identify household environmental exposures associated with the house dust metagenome. Microbial communities in vacuumed dust from 771 homes in the Agricultural Lung Health Study were characterized using whole metagenome shotgun sequencing (5821 taxa across 45 phyla). Household characteristics (i.e. presence of leaks, de-humidifier, humidifier use) were assessed by questionnaires or field technicians. We evaluated associations between exposures and both overall microbial diversity and differentially abundant taxa (ANCOM-BC2). Additionally, we explored microbial networks based on Spearman correlations (SECOM). Microbial diversity was higher in homes with mold/mildew (p-value<0.05), leaks, humidifier use, or occupants removing shoes before entering (p-value<0.1). Examining individual species, <10 taxa were significantly differentially abundant (p-value<0.05 after Holm-Bonferroni correction) in relation to both mold/mildew and leaks. Greater than 10 species were significantly differentially abundant in relation to removing shoes and humidifier use. Additionally, the genera Clostridium, Prevotella, and Cryptobacteroides were positively associated with removing shoes. In this farming population, the house dust microbiome differed by moisture-related exposures, and removing shoes before entering the home. Many novel associations were identified between individual taxa and these exposures. Our findings further knowledge of the impact of environmental conditions inside the home on the indoor microbiome.}, } @article {pmid41654194, year = {2026}, author = {Wei, P and Zhang, L and Hu, Q and Zhu, A and Zhuang, Z and Zhang, Z and Zhang, S and Chen, J and Xiong, X and Qu, B and Zhang, Y and Chen, L and Xu, Z and Chen, Z and Zhong, Q and Xing, X and Li, X and Gao, J and He, Y and Xie, G and Shang, J and Guo, X and Jiang, J and Shi, Y and Zhao, J and Wang, Y and Zhao, J and Jin, Y}, title = {Integrated multiplex PCR and metatranscriptomics reveal upper-lower airway microbial landscapes in pediatric respiratory infections.}, journal = {Virologica Sinica}, volume = {41}, number = {1}, pages = {58-69}, pmid = {41654194}, issn = {1995-820X}, mesh = {Humans ; *Respiratory Tract Infections/microbiology/virology ; *Multiplex Polymerase Chain Reaction/methods ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Female ; Male ; Child, Preschool ; Infant ; *Microbiota/genetics ; Child ; *Bacteria/genetics/classification/isolation & purification ; Nasopharynx/microbiology/virology ; Gene Expression Profiling ; Viruses/genetics/isolation & purification/classification ; Metagenomics ; }, abstract = {Despite widespread use of multiple PCR, a substantial proportion of pediatric acute respiratory tract infections (ARTIs) lack identifiable pathogens and are classified as unknown etiology. The microbial characteristics and clinical relevance of these cases remain unclear. In this study, we compared the airway microbiomes of PCR-positive and PCR-negative ARTIs and examined their relationships with sampling site and disease severity. A total of 514 hospitalized children with ARTIs were enrolled. Nasopharyngeal swabs (NS) and bronchoalveolar lavage fluid (BALF) samples were tested using a 22-target multiplex PCR panel and subsequently stratified by pathogen status for pooled metatranscriptomic sequencing to profile active microbial communities, viral genotypes, and antibiotic resistance genes. PCR identified common respiratory pathogens in 77.0% of NS and 54.1% of BALF samples. Metatranscriptomic analysis showed that PCR-negative pools displayed markedly lower viral activity and comparatively higher bacterial transcript abundance, with notable enrichment of Pseudomonas. Microbial signatures differed between upper and lower airway samples and across clinical severity, with severe cases demonstrating increased bacterial burden and Pseudomonas enrichment, whereas mild infections exhibited relatively stronger viral signals. Under current thresholds, antibiotic resistance genes were detected in patient pools but not in healthy controls. Overall, PCR-negative pediatric ARTIs exhibited distinct, bacteria-enriched microbial profiles. Integrating metatranscriptomics with PCR enhances pathogen characterization and reveals site- and severity-related microbial patterns that may support diagnostic evaluation and clinical management.}, } @article {pmid41654251, year = {2026}, author = {Sun, L and Wang, Y and Fang, J and Li, Z and Yin, Y and Guo, Y and Wang, Q and Chen, H and Cao, B and Wang, H}, title = {Clinical experience with metagenomic next-generation sequencing (mNGS) for the detection of Tropheryma whipplei in respiratory specimens: A multicenter retrospective observational study.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {165}, number = {}, pages = {108457}, doi = {10.1016/j.ijid.2026.108457}, pmid = {41654251}, issn = {1878-3511}, mesh = {Humans ; *Tropheryma/genetics/isolation & purification ; Retrospective Studies ; *Whipple Disease/diagnosis/microbiology ; Male ; Aged ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Adult ; Aged, 80 and over ; }, abstract = {OBJECTIVES: Tropheryma whipplei (T. whipplei) is the causative bacterium of Whipple's disease (WD), a chronic and systemic infectious condition that predominantly affects the gastrointestinal tract. Sporadic cases of T. whipplei pneumonia have been documented recently.

METHODS: This multicenter retrospective observational study was conducted on patients with T. whipplei positive respiratory specimens admitted to Peking University People's Hospital and China-Japan Friendship Hospital, from Apr 2021 to Jul 2024. Metagenomic next-Generation sequencing (mNGS) was performed using the patient's bronchoalveolar lavage fluid (BALF), and the quantitative polymerase chain reaction (qPCR) of T. whipplei was also adopted. The clinical data of patients were systematically evaluated.

RESULTS: Among 91 patients (aged 25-82, mean 57; 48% male), common symptoms included cough (60%), expectoration (48%), dyspnea (42%), and fever (30%). Notably, 22% were asymptomatic. Besides, 20 patients (22%) had a pre-existing condition of interstitial lung disease. Among all 91 patients, 14 were diagnosed with pneumonia, while the remaining 77 had bacterial colonization. Pneumonia cases showed higher T. whipplei mNGS reads than colonization (P = 0.0298). Samples testing positive for T. whipplei by qPCR exhibited significantly higher mNGS sequence reads compared to qPCR-negative samples (P < 0.0001). All pneumonia patients received antibiotics therapy tailored to their condition. One died from respiratory failure, while the remaining 13 recovered.

CONCLUSION: The application of mNGS on respiratory specimens stands as an exceptional diagnostic modality, proficient in identifying rare microbial infections, exemplified by those induced by T. whipplei. Future research should launch prospective trials to optimize regimens, assess outcomes, and track long-term survival precisely.}, } @article {pmid41654659, year = {2026}, author = {Damgaard, F and Jespersen, MG and Møller, JK and Coia, JE and Dessau, RB and Sydenham, TV and Strube, ML and Møller-Jensen, J and Justesen, US}, title = {Distinct prophage infections in colorectal cancer-associated Bacteroides fragilis.}, journal = {Communications medicine}, volume = {6}, number = {1}, pages = {}, pmid = {41654659}, issn = {2730-664X}, abstract = {BACKGROUND: Colorectal cancer (CRC) patients exhibit distinct gut microbiota disruption, known as dysbiosis, which is believed to play a causative role in CRC. One of the key bacterial species implicated in CRC dysbiosis is Bacteroides fragilis, which presents a paradox as it is also present in most healthy individuals. This discrepancy underscores the need for analysis beyond species-level associations and to investigate intraspecies variation within B. fragilis.

METHODS: From a highly specific collection of B. fragilis isolates from CRC patients and controls, a pangenome-wide association study was conducted, identifying intraspecies genetic variations associated with CRC. The CRC association of these genetic variations were then validated in a metagenome sequencing cohort of faecal samples from 877 individuals, with and without CRC. To test group differences a mixed effects logistic regression with cohort as a random effect was performed for each genetic variation.

RESULTS: Here we show that CRC-associated B. fragilis isolates are infected with specific Caudoviricetes prophages, significantly more often than negative controls. The initial discovery was made in our highly specific isolate collection and then validated in an independent metagenome sequencing cohort, finding that CRC patients were twice as likely to have detectable levels of these phages (OR = 2.05, p = 2.522E-7, SE = 0.139).

CONCLUSIONS: To our knowledge, these findings mark the first link between one of the most implicated driver bacteria and phages in CRC and suggest a more complex role of phages in CRC dysbiosis than current models suggest and highlights the potential of phages as CRC biomarkers.}, } @article {pmid41654729, year = {2026}, author = {Wang, P and Yao, Y and Yan, K and Wang, S and Wang, M and Liu, X and Hu, C and Dong, Y and Li, J}, title = {A validation for sex differences in gut microbiome of essential hypertension based on cohort analysis.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41654729}, issn = {1471-2180}, mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Essential Hypertension/microbiology ; Sex Factors ; Middle Aged ; Cohort Studies ; China ; Fatty Acids, Volatile/metabolism ; Sex Characteristics ; Hypertension/microbiology ; Metagenomics ; Aged ; Eubacteriales ; }, abstract = {BACKGROUND: Prior research has demonstrated sex-specific differences in hypertension (HTN). The gut microbiota (GM) and its metabolic functions have emerged as key players in the development of HTN. To explore potential sex-based heterogeneity in gut bacteria among hypertensive patients, we conducted this study with the aim of validating sex differences in the gut flora associated with HTN.

METHODS: Here, we leveraged a metagenomic dataset comprising 106 fecal samples from a Chinese cohort of individuals with essential HTN to systematically analyze and compare alterations in the gut microbiome between male and female patients, as well as relative to a healthy control group.

RESULTS: Our study confirmed a statistically significant difference in the β-diversity of GM between hypertensive patients and healthy controls. When the subjects were further stratified by sex, significant differences in the distribution of gut flora were observed exclusively in females, whereas none was noted between groups in males. It was observed that certain genera of GM exhibit negative correlations with blood pressure. Notably, the relative abundance of these bacterial genera, including Lachnospira, Faecalibacterium, and Roseburia, was significantly diminished in female hypertensive patients. These organisms are primarily involved in the biosynthesis of short-chain fatty acids (SCFAs), with a notable emphasis on butyrate production. Ruminococcus gnavus was specifically enriched in hypertensive males, whereas certain bacteria, such as Lactobacillus, were notably depleted. The abnormality of the SCFAs-producing flora in female hypertensive patients may be related to that women are more likely to develop hypertensive organ damage.

CONCLUSIONS: The findings of our study indicate that GM dysbiosis is more significantly associated with HTN in females. Consequently, sex constitutes a critical factor in evaluating the role of intestinal flora in the pathogenesis of HTN.}, } @article {pmid41654875, year = {2026}, author = {Chen, Y and Ding, C and Ren, M and Li, Z and Liu, S and Sun, H and Yu, S and Niu, Q and Li, X and Li, B and Li, L and Yang, X and Sun, Q}, title = {Liver-muscle metabolic crosstalk: xanthosine as a key effector of broiler myogenesis.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {24}, pmid = {41654875}, issn = {1674-9782}, support = {No.2022YFF1001000//National Key Research and Development Program of China/ ; NSFC, No.82370639//the National Natural Science Foundation of China/ ; 2023-YBSF-138//Shaanxi Provincial Key R&D Program General Project-Social Development Field/ ; No. 2022JC-11//Science Fund for Distinguished Young Scholars of Shaanxi Province/ ; }, abstract = {BACKGROUND: Nutritional strategies aimed at augmenting growth performance remain a central focus in poultry science. The liver, as a pivotal metabolic organ, exerts profound influence on skeletal muscle development. Nevertheless, the mechanistic interplay between hepatic metabolism and myogenesis has not been fully delineated. Here, by integrating multi-omics analyses with functional validation, we identified xanthosine, a metabolic derivative of hepatic caffeine catabolism, as a previously unrecognized regulator of broiler muscle growth. We further elucidated its mechanistic role in promoting myoblast proliferation.

RESULTS: Comparative phenotypic assessment of high- and low-body-weight broilers revealed substantial differences in breast muscle mass. Metagenomic profiling of cecal microbiota demonstrated only a limited association between microbial composition and body weight. In contrast, untargeted plasma metabolomics uncovered a systemic upregulation of amino acid metabolism in high-body-weight broilers, concomitant with a pronounced activation of caffeine metabolism. Consistently, hepatic transcriptomic profiling revealed marked induction of cytochrome P450 family 1 subfamily A member 2 (CYP1A2), encoding a key enzyme catalyzing caffeine catabolism. Integrated KEGG pathway enrichment across metabolomic and transcriptomic datasets highlighted caffeine metabolism as a significantly perturbed pathway. Among its downstream metabolites, plasma xanthosine was robustly elevated in high-body-weight broilers. Functional validation via in ovo injection demonstrated that xanthosine administration significantly augmented post-hatch growth performance by increasing skeletal muscle mass. Mechanistic investigations further established that xanthosine drives myoblast proliferation through activation of the ERK/GSK3β/β-catenin signaling cascade.

CONCLUSIONS: Together, these findings delineate a liver-muscle metabolic axis in which hepatic CYP1A2-driven caffeine metabolism elevates circulating xanthosine, which in turn acts as a pivotal molecular effector of myogenic growth. This study uncovers a previously unappreciated metabolic mechanism by which hepatic activity orchestrates skeletal muscle development. It also highlights targeted modulation of xanthosine metabolism as a promising strategy to enhance broiler growth performance and production efficiency.}, } @article {pmid41655211, year = {2026}, author = {Su, XJ and Ma, L and Xiong, X and Meng, JH and Wu, Q and Zhang, Y and Dong, SG and Wang, YF and Wu, JH and Zeng, QY and Zhang, HF and Li, LL and Meng, L and Peng, M and Huang, XD and Wu, LQ and Wang, X}, title = {DRD2 Deficiency Underlies Pituitary Adenoma Dependent on Escherichia coli Translocation from the Gut.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {24}, pages = {e04247}, pmid = {41655211}, issn = {2198-3844}, support = {2020]74//Hubei Provincial Engineering Research Center for Inflammation Repair/ ; 2020ZYYD026//Special Funds for Local Science and Technology Development guided by the Central Government/ ; 2023AFA079//Hubei Science Foundation for Distinguished Young Scholars/ ; WX23Z27//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; WZ22A01//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; WZ24B86//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; }, mesh = {Animals ; Mice ; *Pituitary Neoplasms/microbiology/genetics/metabolism ; *Receptors, Dopamine D2/deficiency/genetics/metabolism ; *Escherichia coli ; Humans ; *Bacterial Translocation ; *Adenoma/microbiology/metabolism/genetics ; Disease Models, Animal ; Female ; *Gastrointestinal Microbiome ; Prolactinoma/genetics ; Male ; }, abstract = {Pituitary adenoma (PA) are common intracranial tumor types that have harmful effects on human health. However, the pathogenesis of PA remains unclear yet. The intratumoral microbiome has been reported playing an important impact on the occurrence, metastasis, immune monitoring, and drug resistance of various tumors. While normal dopamine receptor D2 (DRD2) expression is enriched in the apical junction of pituitary epithelium and colonic enterocytes, various factors-induced drd2 loss dampened its expression at both sites. DRD2 deficiencies are characterized by chronic hyperprolactinemia, pituitary lactotroph hyperplasia, and prolactinomas in mice, but the role of intratumoral microbiome in prolactinomas is not known. We employed specific pathogen-free (SPF) and germ-free (GF) mice models and patient samples of pituitary adenoma. In the mice pituitary tumor model, we used mice that developed prolactinomas following estradiol treatment or DRD2 deficiencies. Pituitary tumor samples from patients with nonfunctional pituitary adenoma or prolactinomas were obtained after surgical excision. Various molecular, cellular, and sequencing techniques were used to determine the role of intratumoral microbiome in pituitary adenoma. We demonstrate that human patients or murine bearing estradiol-induction or DRD2 loss are all characterized by the presence of live intratumor bacteria in the pituitary adenoma. Using metagenomic next-generation sequencing and mass spectrometry techniques, we confirm that the bacterial species of pituitary tumor tissues is Escherichia coli. In vitro tracing and immunofluorescence assay results showed that the pathobiont Escherichia coli translocates from the gut into the pituitary gland along with DRD2 loss while the blood pituitary barrier were both destroyed in mice. The Escherichia coli are phagocytosed by the microglial cells in the pituitary gland, then activate GSDMD protein releasing HMGB1, and promote the tumorigenesis of pituitary adenoma by activating the MAPK pathway. The depletion of bacteria systemically, microglial depletion or HMGB1 inhibitor ethyl pyruvate rescued prolactinomas. Our findings suggest that DRD2 deficiency underlies pituitary adenoma dependent on Escherichia coli translocation from the gut and activating microglia GSDMD/ HMGB1/MAPK pathway, and provide a novel preclinical rationale for antimicrobial agents, microglial depletion, or HMGB1 inhibitor ethyl pyruvate for the treatment of pituitary adenoma.}, } @article {pmid41655253, year = {2026}, author = {Shi, Y and He, S and Li, C and Chan, H and Liu, Z and Yang, B and Li, Q}, title = {Bifidobacterium Breve Yang08 Alleviates Atopic Dermatitis By Enriching Akkermansia Muciniphila and Inhibiting Neutrophil Extracellular Traps Formation In Mice.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {20}, pages = {e18588}, pmid = {41655253}, issn = {2198-3844}, support = {32470958//National Natural Science Foundation of China/ ; 82403246//National Natural Science Foundation of China/ ; 82574001//National Natural Science Foundation of China/ ; 2025A04J4030//Guangdong Provincial Science and Technology Plan Project/ ; }, mesh = {Animals ; *Extracellular Traps/metabolism/immunology ; *Dermatitis, Atopic/microbiology/immunology/therapy ; Mice ; *Bifidobacterium breve/physiology ; Humans ; Disease Models, Animal ; *Neutrophils ; *Gastrointestinal Microbiome ; *Akkermansia ; *Probiotics ; *Verrucomicrobia ; Male ; }, abstract = {Atopic dermatitis (AD) is linked to gut microbiota dysbiosis, yet the mechanisms connecting specific commensals to cutaneous immunoregulation remain elusive. We observed reduced Bifidobacterium breve (B. breve) abundance in AD patients. A new B. breve strain was isolated from human stools and nomenclated as Yang08. In MC903-induced AD-like mouse models, Yang08 outperformed a standard strain, ameliorating disease severity, including reduced ear thickening, epidermal hyperplasia, and mast cell infiltration in a manner dependent on viable bacteria and an intact gut microbiota. Antibiotic-mediated microbiota depletion abrogated its efficacy, while fecal microbiota transfer from Yang08-treated mice conferred protection, confirming microbial remodeling as essential. Metagenomics revealed Yang08 specifically enriched Akkermansia muciniphila, which was required for therapeutic effects in germ-free mice. Mechanistically, Yang08 abolished both neutrophil influx and NET deposition in lesions, with ex vivo experiments showing blunted NETosis capacity. Its therapeutic benefits were reversed by neutrophil depletion, NET degradation, or PAD4 inhibition. Overall, Yang08 alleviates AD by enriching A. muciniphila and inhibiting skin NETosis, emerging as a promising prophylactic candidate prevention for AD prevention.}, } @article {pmid41655310, year = {2026}, author = {Cheng, L and Li, H and Luo, C and Zhang, Y and Cheng, K and Wang, S and Hu, Z}, title = {In situ reactivation of aerobic granular sludge after extended idle conditions: Effect of different N-acyl-homoserine lactones (AHLs).}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128866}, doi = {10.1016/j.jenvman.2026.128866}, pmid = {41655310}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; *Acyl-Butyrolactones ; Bioreactors ; Waste Disposal, Fluid/methods ; Quorum Sensing ; Aerobiosis ; Phosphorus/metabolism ; }, abstract = {Prolonged idle conditions pose a major challenge to aerobic granular sludge (AGS) systems by compromising granule integrity and pollutant removal performance. This study investigates the in situ reactivation of AGS after three months of static storage using two quorum sensing molecules, N-hexanoyl-L-homoserine lactone (C6-HSL) and N-octanoyl-homoserine lactone (C8-HSL). All reactors rapidly restored COD and NH4[+]-N removal efficiencies to >92% and >98%, respectively. C6-HSL significantly accelerated phosphorus recovery, reaching removal efficiencies above 90% by day 26, compared to day 34 in the control and C8-HSL groups. C8-HSL enhanced EPS secretion and granule growth, yielding the largest granule size (1210 μm), which was 1.26-fold and 1.71-fold larger than those in the control and C6-HSL groups, respectively. Metagenomic analysis revealed comparable microbial structures at the phylum level, but distinct functional responses. C6-HSL increased the abundances of phosphorus metabolism genes (ppk, ppx, ppa), while C8-HSL notably upregulated genes related to the biosynthesis of tyrosine, tryptophan, and structural polysaccharides (e.g., alginate and Psl), supporting enhanced EPS production and granule stability. These results demonstrate molecule-specific regulatory roles of individual N-acyl-homoserine lactones during AGS reactivation, linking functional recovery and structural regeneration to distinct quorum sensing pathways. This study provides mechanistic and engineering insights into an energy-efficient strategy for restoring AGS performance after prolonged ambient idle conditions, with direct relevance to the stable operation and management of full-scale wastewater treatment systems.}, } @article {pmid41655382, year = {2026}, author = {Gupta, N and Biswas, R and Koley, A and Mukherjee, R and Das, N and Balachandran, S and Hoque, RR}, title = {Degradation of chrysene by Rhodococcus pyridinivorans C7 isolated from earthworm gut - Deciphering microbial community dynamics of the earthworm gut.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141328}, doi = {10.1016/j.jhazmat.2026.141328}, pmid = {41655382}, issn = {1873-3336}, mesh = {Animals ; *Rhodococcus/metabolism/genetics/isolation & purification ; *Chrysenes/metabolism/toxicity ; *Oligochaeta/microbiology ; Biodegradation, Environmental ; *Soil Pollutants/metabolism/toxicity ; }, abstract = {This study investigates the degradation of chrysene (a priority polycyclic aromatic hydrocarbon) by Rhodococcus pyridinivorans C7, isolated from the gut of Perionyx excavatus after 60 days acclimatization in petroleum-contaminated soil. After six days of incubation, strain C7 exhibited notable enzymatic activities, with catechol 1,2-dioxygenase (1.72 ± 0.14 U/mL) and catechol 2,3-dioxygenase (2.26 ± 0.19 U/mL). The strain achieved up to 75 % degradation of chrysene (40 mg/L) within this period. Gas chromatography-mass spectrometry analysis identified dibutyl phthalate as an intermediate product on day 2 and phenol 2,6-di-tert-butyl on days 4 and 6. Cytotoxicity assays revealed that the initial byproduct was highly toxic (IC50 = 0.19 µg/mL), whereas the final metabolite exhibited markedly reduced toxicity (IC50 = 19 µg/mL), indicating detoxification. Comparative genomics using Mauve software revealed strong genomic synteny between strain C7 and other PAH-degrading Rhodococcus species. Metagenomic analysis of earthworm gut microbiomes under different treatment - control (EG-C), petroleum contaminated (EG-P) and fly ash (EG-F) identified Proteobacteria as the predominant phylum with relative abundance of 21.17 %, 33.3 %, and 34.53 % respectively. Notably, the Rhodococcus genus exhibited a 1.46-fold and 1.42-fold increase in EG-P and EG-F, respectively compared to EG-C. R. pyridinivorans was detected in both EG-P and EG-F gut samples confirming its isolation through the earthworm gut. These results demonstrate that environmental perturbations can drive distinct shifts in gut microbial composition, enriching for hydrocarbon-degrading taxa. Understanding such adaptive microbial communities provides valuable insights for developing sustainable bioremediation strategies and identifying novel microbes for environmental cleanup.}, } @article {pmid41655417, year = {2026}, author = {Chen, Z and Tang, X and Su, Y and Liu, T and Klümper, U and Ju, F and Liu, M and Han, P}, title = {Impact of human activities on groundwater biogeochemical cycles and microbial communities: Insights from metagenomic analysis.}, journal = {Water research}, volume = {294}, number = {}, pages = {125493}, doi = {10.1016/j.watres.2026.125493}, pmid = {41655417}, issn = {1879-2448}, mesh = {*Groundwater/microbiology/chemistry ; Metagenomics ; Bacteria/genetics ; *Microbiota ; Nitrogen ; China ; }, abstract = {Anthropogenic nitrogen pollution poses a systemic threat to microbial interaction networks and biogeochemical cycling in groundwater ecosystems, yet the underlying mechanisms remain poorly understood. Employing an endpoint gradient comparison, we conducted metagenomic analyses of urban groundwater under severe nitrogen stress (Shanghai, China; with NH4[+] and NO3[-] concentrations ∼28× and ∼10× background levels, respectively) versus a near-pristine mountain aquifer (Calistoga, USA). This revealed a multi-level collapse and adaptive restructuring of microbial communities under nitrogen stress. Pollution triggered a fundamental restructuring of bacterial communities, with system type (urban vs. mountain) explaining 74 % of the compositional variation, accompanied by a significant reduction in bacterial alpha-diversity (Shannon index decreased by 34 %) and a taxonomic shift from Actinomycetota-dominated mutualistic networks in the mountain system to Pseudomonadota-dominated communities (> 0.86 relative abundance) in urban groundwater. Functionally, urban systems exhibited multi-pathway suppression of energy-intensive processes, including nitrification (e.g., hao, nxrB genes), methanogenesis, and inorganic sulfur oxidation, aligning with the theory of "pollution-induced metabolic decoupling." To survive, the microbial community pivoted to low-energy strategies, significantly enriching genes for organic sulfur metabolism (e.g., dddT, tsdB), which may exacerbate nitrogen retention by inhibiting denitrifiers via metabolites like H2S. Co-occurrence network topology analysis indicated a catastrophic loss of complexity in urban groundwater, with a ∼90 % reduction in connectivity and a collapse in modularity (from 19.94 to 3.33), alongside an abnormally high proportion of positive correlations (94.4 %), signaling a major loss of ecosystem stability and functional redundancy. Random Forest and redundancy analyses jointly identified ammonium (NH4[+]) as the core environmental driver of this cascading failure, explaining 86 % of the variance in functional gene profiles and likely disrupting the nitrification pathway through specific suppression of the rate-limiting hao gene (which explained 76 % of the variance in nitrification rates). Based on these insights, we propose a dual-track restoration framework that couples external NH4[+] source control with internal microbial network rewiring (e.g., restoring keystone taxa, regulating sulfur feedback loops) to break the nitrogen-sulfur inhibition cycle and restore ecological function. Our findings underscore the critical importance of integrating microbial network resilience into strategies for managing and rehabilitating contaminated groundwater ecosystems.}, } @article {pmid41655422, year = {2026}, author = {Wang, L and Liang, Z and Lu, D and Lv, S and Li, Z and Tan, R and Guo, Z and Wu, H and Wang, Y and Xu, X and Yu, J and Li, Z and Zhang, W and Zheng, W and Jiang, F and Yao, M and Zhou, P and Jiang, Z}, title = {Artificial reefs promote coastal carbon stabilization potential through hydrological condition and microbial pathways.}, journal = {Water research}, volume = {294}, number = {}, pages = {125502}, doi = {10.1016/j.watres.2026.125502}, pmid = {41655422}, issn = {1879-2448}, mesh = {*Carbon ; Hydrodynamics ; *Coral Reefs ; Geologic Sediments/chemistry ; Archaea ; Humic Substances ; }, abstract = {Artificial reefs (ARs) reshape near-bed hydrodynamics and benthic microbial functions, yet links to coastal carbon stabilization remain insufficiently resolved. Here, we combined hydrodynamic modeling with sediment geochemistry, fluorescence spectroscopy, and metagenomics across contrasting AR habitats in the northern Yellow Sea. Structurally complex ARs enhanced upwelling and wake turbulence and were associated with finer sediments and higher sediment total organic carbon (TOC). Path modeling showed that hydrodynamic indices, hydrographic state variables, and microbial functional gene profiles jointly explained spatial variations in sediment TOC and humic-like fluorescent. During a 42-day dark incubation, protein-like fluorescent dissolved organic matter (FDOM) fractions declined while the humic-like component (C2) increased, indicating net enrichment of humic-like byproducts during microbial reworking of labile DOC. Microbial succession included increased relative abundance of ammonia oxidizing archaea (e.g., Crenarchaeota, Nitrososphaeria), and the SAR202 clade, accompanied by higher functional potentials related to aromatic-compound transformation and nitrogen redox pathways. Collectively, these results support a framework in which AR-induced hydrodynamic modulation couples with nitrogen-redox linked microbial functions, promoting carbon stabilization potential reflected by humic-like DOM enrichment and benthic carbon storage proxies.}, } @article {pmid41655600, year = {2026}, author = {Susiyanti, M and Febrina, F and Putera, I and Jelita, A and Rokim, FS and Edwar, L and Aziza, Y and Sitompul, R and Nora, RD}, title = {Metagenomic sequencing in various ocular infections: A systematic review of diagnostic utility.}, journal = {Survey of ophthalmology}, volume = {71}, number = {4}, pages = {1213-1224}, doi = {10.1016/j.survophthal.2026.01.006}, pmid = {41655600}, issn = {1879-3304}, mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Eye Infections/diagnosis/microbiology ; Eye Infections, Bacterial/diagnosis ; Bacteria/genetics ; }, abstract = {Ocular infections are a common cause of visual morbidity worldwide and continue to pose significant diagnostic and therapeutic challenges. Metagenomic next-generation sequencing (mNGS) enables unbiased detection of wide range of pathogens; however, its diagnostic utility in ocular infections warrant further evaluation. We evaluate the diagnostic performance of mNGS, highlighting its advantages, limitations, and future directions for clinical application. Twenty-one studies involving 1219 eyes were included. mNGS positivity rates ranged from 10 % to 94 %. Sensitivity ranged from 15 % to 100 % and specificity from 12 % to 100 %. Viral pathogens were the most frequently detected (15 out of 21 studies), followed by bacteria (14 out of 21), fungi (10 out of 21), and parasites (6 out of 21). A broad spectrum of pathogens at both the genus and species levels was identified. mNGS also helps in assessing AMR-associated genes and mutations linked to therapy susceptibility. mNGS appears to be a valuable tool for pathogen indentification in ocular infections, particularly for organisms undetectable by conventional diagnostic methods, although careful interpretation is required. Overall, mNGS demonstrated promising diagnostic performance across different types of ocular infections. Larger, well-designed studies employing standardized protocols are needed to address current limitations and to enhance the clinical applicability of mNGS in routine clinical practice.}, } @article {pmid41655688, year = {2026}, author = {Jin, M and Xu, F and Liu, Y and Jiang, Z}, title = {Limosilactobacillus fermentum LF61: A multidimensional study on safety and functionality from genomics to clinical application.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {211}, number = {}, pages = {116002}, doi = {10.1016/j.fct.2026.116002}, pmid = {41655688}, issn = {1873-6351}, mesh = {Humans ; Animals ; Mice ; *Limosilactobacillus fermentum/genetics/physiology ; Genomics ; Caco-2 Cells ; *Probiotics ; Mice, Inbred ICR ; Female ; Double-Blind Method ; }, abstract = {This study presents a comprehensive multidimensional assessment of the safety and functional efficacy of Limosilactobacillus fermentum LF61, a strain isolated from human milk. Genomic analysis revealed no virulence factors (VFDB), drug resistance genes (CARD), or toxin synthesis gene cluster (antiSMASH) within its chromosome (2.04 Mb) and plasmid (15.5 kb), meeting EFSA's QPS safety criteria. In vitro studies demonstrated that LF61 exhibited a 2-h survival rate of >98% in gastric acid (pH 2.0) and a survival rate of 99.66% in intestinal fluid (pH 8.0). LF61 was also nontoxic to Caco-2 cells (metabolic activity at 20% concentration: 100.3 ± 2.1%). An acute oral toxicity test (in ICR mice) demonstrated an LD50 > 2 × 10[10] CFU/kg. In a randomized, double-blind clinical trial (n = 49), daily intake of 3 × 10[10] CFU of LF61 for 8 weeks increased serum levels of the antimicrobial peptide LL-37 by 12.3% (p < 0.05), and IgA, IgG, and IgM by 18.7%, 15.2%, and 9.8%, respectively (p < 0.05). Metagenomic analysis revealed that LF61 promoted colonization by short-chain fatty acid-producing bacteria, such as Mitsuokella and Turicibacter (LDA >3), activated the carbohydrate metabolism pathway (p = 0.002), and maintained stable α-diversity in the microbiome (Shannon index p > 0.05). Collectively, our findings indicate that LF61 exerts beneficial effects via a gut-immune axis bidirectional regulatory mechanism, offering a theoretical basis and clinical evidence for the development of novel immunomodulatory probiotics targeting the gut-immune axis.}, } @article {pmid41655773, year = {2026}, author = {Lala Bouali, M and Kezai, AM and Beaulieu, MJ and Roy, J and Badiane, PY and Lévesque, V and Filion, L and Vallières, L and Blanchet, MR and Hébert, SS}, title = {Indoor rewilding of laboratory mice recalibrates pulmonary mucosal immunity and mechanics.}, journal = {Mucosal immunology}, volume = {19}, number = {3}, pages = {100322}, doi = {10.1016/j.mucimm.2026.02.003}, pmid = {41655773}, issn = {1935-3456}, mesh = {Animals ; Female ; Mice ; *Lung/immunology/physiology ; *Immunity, Mucosal ; Mice, Inbred C57BL ; Cytokines/metabolism ; Humans ; Dendritic Cells/immunology ; *Respiratory Mucosa/immunology ; Respiratory Mechanics ; }, abstract = {Laboratory mice raised under specific-pathogen-free (SPF) conditions experience restricted microbial and antigenic exposure, which favours an immature immune system and limits their translational value for respiratory research. While microbial enrichment in "dirty" mouse models restores immune maturation, its impact on integrated respiratory function and model transferability to human disease remains understudied. Here, we tested whether ecological exposure through indoor rewilding of SPF-reared mice could reshape immune complexity and recalibrate pulmonary physiology. Two-month-old female C57BL/6J mice were housed for three months under SPF or indoor-rewilding conditions and assessed for immune, mechanical, and systemic parameters. Rewilded mice exhibited expanded pulmonary immune subsets, increased dendritic-cell immune checkpoint, with TNF/IFN-γ activation coupled to regulatory IL-10 signaling. Despite sustained exposure, the alveolar-capillary barrier integrity was preserved. Functionally, respiratory oscillometry revealed improved pulmonary mechanics, including lower airway resistance, higher compliance, and reduced airway responsiveness to methacholine. Systemic cytokine analyses indicated compartmentalized pulmonary immune activation, maintaining an overall anti-inflammatory balance. Importantly, PRIA screening detected no reportable pathogens introduced during rewilding, while cecal shotgun metagenomics confirmed microbial enrichment. Together, these findings demonstrate that indoor rewilding reestablishes coordinated lung immune and mechanical homeostasis in SPF-reared mice, providing a safe and scalable model for studying human-like mucosal immunity and respiratory physiology with broad implications for preclinical respiratory research and therapeutic testing.}, } @article {pmid41655932, year = {2026}, author = {Kannan, EP and Venkatachalam, P and Gopal, J and Sarkaraisamy, P and Muthu, M}, title = {Antimicrobial resistance status of small marine fishes off the coastal cities of east and west coast of India: an adaptive nanopore sequencing based metagenomics raises concerns.}, journal = {International journal of biological macromolecules}, volume = {347}, number = {}, pages = {150754}, doi = {10.1016/j.ijbiomac.2026.150754}, pmid = {41655932}, issn = {1879-0003}, mesh = {Animals ; *Fishes/microbiology/genetics ; India ; *Nanopore Sequencing/methods ; *Metagenomics/methods ; Cities ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; Humans ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Transmission of Antimicrobial resistance (AMR) through edible fishes has recently upsurged as a global health hazard owing to its potential impact on human and one health. India, as the second largest consumer of edible fish faces a high risk of AMR transmission, given the nutritional value, accessibility and affordability of fishes to people from all economic classes. The present study investigated the presence of Antimicrobial resistance genes (ARGs) in edible muscle, gills and intestines of five commercially important fishes, Nemipterus japonicus, Sardinella longiceps, Selaroides leptolepis, Stolephorus indicus, and Sardinella gibbosa sourced from two major densely populated cities of the East coast (Chennai) and the West coast (Mangalore) using adaptive nanopore sequencing technique. A total of 54 distinct ARGs associated with 12 classes of AMR were detected across both coasts with enhanced resistance observed towards aminoglycosides, macrolides, beta lactam, tetracycline and chloramphenicol. Cumulatively, the most abundant ARGs across both coasts includes cxpE, aac(3')-IIa, aac(6)-IB-cr, oqxA and oqxB. However, significant variation in the distribution of ARGs among the two coasts were studied with varying abundance patterns. Furthermore, this study predicted human pathogens such as Klebsiella sp., Escherichia sp., Staphylococcus sp. and Pseudomonas sp. as putative reservoirs of ARGs indicating potential zoonotic and foodborne transmission to humans. This study offers a novel, and in-depth characterization of edible fish associated AMR contamination in east and West coast of India, providing essential data for assessing the public health hazards posed by ARGs and the pathogenic taxa.}, } @article {pmid41656299, year = {2026}, author = {Fang, T and Bogensperger, L and Feer, L and Allam, A and Bezshapkin, V and Balázs, Z and von Mering, C and Sunagawa, S and Krauthammer, M and Schwank, G}, title = {Uncovering Cas9 PAM diversity through metagenomic mining and machine learning.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41656299}, issn = {2041-1723}, support = {//SNSF/ ; //Swiss National Science Foundation (SNSF)/ ; /ERC_/European Research Council/International ; }, mesh = {*Machine Learning ; *CRISPR-Cas Systems/genetics ; *Metagenomics/methods ; Data Mining ; Genome, Bacterial ; Databases, Genetic ; *Nucleotide Motifs/genetics ; Archaea/genetics ; Bacteriophages/genetics ; Genome, Archaeal ; }, abstract = {Recognition of protospacer adjacent motifs (PAMs) is crucial for target site recognition by CRISPR-Cas systems. In genome editing applications, the requirement for specific PAM sequences at the target locus imposes substantial constraints, driving efforts to search for novel Cas9 orthologs with extended or alternative PAM compatibilities. Here, we present CRISPR-PAMdb, a comprehensive and publicly accessible database compiling Cas9 protein sequences from 3.8 million bacterial and archaeal genomes and PAM profiles from 7.4 million phage and plasmid sequences. Through spacer-protospacer alignment, we infer consensus PAM preferences for 8003 unique Cas9 clusters. To extend PAM discovery beyond traditional alignment-based approaches, we develop CICERO, a machine learning model predicting PAM preferences directly from Cas9 protein sequences. Built on the ESM2 protein language model and trained on the CRISPR-PAMdb database, CICERO achieves an average cosine similarity of 0.69 on test data and 0.75 on experimentally validated Cas9 orthologs. For Cas9 clusters where alignment-based predictions are infeasible, CICERO generates PAM profiles for an additional 50,308 Cas9 proteins, including 17,453 high-confidence predictions with CICERO confidence scores above 0.8. Together, CRISPR-PAMdb and CICERO enable large-scale exploration of PAM diversity across Cas9 proteins, accelerating design of next-generation CRISPR-Cas9 tools for precise genome engineering.}, } @article {pmid41656341, year = {2026}, author = {Cai, J and Wu, W and Wang, L and Meng, D and Yang, H and Liu, S and Hou, S and Cao, Y}, title = {Dietary β-hydroxy-β-methyl butyrate supplementation improves intestinal health and growth performance in Tibetan sheep lambs via modulating small intestinal microbiota.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {25}, pmid = {41656341}, issn = {1674-9782}, support = {2022-NK-169//Construction of Standardized Production System for Improving quality and efficiency of Tibetan sheep industry/ ; 2025-YYKF-03//Key Laboratory of Qinghai-Tibet Plateau Grazing Yak and Tibetan Sheep Animal Nutrition and Feed-Forage, Ministry of Agriculture and Rural Affairs, P. R. China/ ; }, abstract = {BACKGROUND: Tibetan sheep grazing on the Qinghai-Tibet Plateau require dietary protein supplementation; however, they face economic constraints due to the high cost of feed transportation in this region. Given that the leucine metabolite β-hydroxy-β-methyl butyrate (HMB) enhances both protein synthesis and intestinal nutrient absorption, this study employed metagenomics and untargeted metabolomics to systematically evaluate HMB's effects on antioxidant capacity, immune response, microbiota, metabolites, and the health of the small intestine in Tibetan sheep. A total of 120 healthy weaned 60-day-old male Tibetan lambs were assigned to diets containing 0 mg/kg (control group, CON), 430 mg/kg (low HMB, L-HMB), 715 mg/kg (medium HMB, M-HMB), or 1,000 mg/kg (high HMB, H-HMB) for 90 d. At the end of the experiment, 6 lambs from each group were slaughtered for intestinal tissue and content sampling.

RESULTS: The M-HMB treatment significantly increased average daily gain of the lambs without affecting feed intake, thereby improving feed utilization efficiency. M-HMB promoted the development of small intestinal morphological and elevated villus height, while also enhancing the activities of digestive enzyme and disaccharidase activities. Furthermore, M-HMB enhanced the antioxidant capacity, immune response, and barrier function of the small intestine. Metagenomic analysis revealed that M-HMB supplementation improved the composition of the small intestinal microbiota in Tibetan sheep, specifically increasing the relative abundance of Ruminococcus bacterium P7 and R. bromii, and enhanced microbial carbohydrate degradation capacity. Metabolomic analysis demonstrated that M-HMB supplementation significantly altered the small intestinal metabolite profile, enhancing carbohydrate metabolic pathways and increased the production of short-chain fatty acids (SCFAs). M-HMB upregulated PLCβ1 and ERK1/2 protein expression levels in small intestinal tissue and elevated the proportion of Ki67-positive cells at the basal crypt region of small intestinal crypts, suggesting enhanced proliferative activity of intestinal epithelial cells.

CONCLUSIONS: In summary, dietary supplementation with M-HMB (715 mg/kg) promoted small intestinal growth and development, enhanced digestive and absorptive functions, optimized the microbial composition, improved carbohydrate degradation, and increased the production of SCFAs, ultimately improving the growth performance of Tibetan sheep lambs.}, } @article {pmid41656480, year = {2026}, author = {da Silva, EC and Beserra, MMN and Leitão, MGS and Vieira Camelo Maia, IF and de Souza Alves, BE and Gonçalves, PG and de Assis Leite, DC and Neves, BG and Pereira, KMA and Rodrigues, LKA and Gondim, DV}, title = {Fermentation time Determines Anti-inflammatory and Osteoprotective Activity of Green Tea Kombucha in a Rat Model of Experimental Periodontitis.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41656480}, issn = {1867-1314}, abstract = {This study aimed to characterize the microbial composition of green tea-fermented kombucha at different fermentation times and to evaluate its effects on inflammation and alveolar bone loss in rats with periodontitis. Microbial diversity was first assessed by metagenomic sequencing targeting bacterial 16 S rRNA and fungal 18 S rRNA regions. Sixty male rats were divided into six groups: control, periodontitis without treatment, green tea treatment, and kombucha fermented for 4, 8, or 12 days. Kombucha or green tea was administered daily by oral gavage for 39 days. Periodontitis was induced by ligation of the maxillary second molar on day 28. After euthanasia, hemimaxillae, liver, kidney, and blood samples were collected for analysis. Kombucha fermented for 4 days showed the highest abundance of bacteria from the Acetobacteraceae family and yeasts from the Saccharomycetaceae family. This fermentation time also produced the most pronounced reduction in periodontal inflammation and alveolar bone loss, with lower expression of tumor necrosis factor-alpha (42,9%) and receptor activator of nuclear factor kappa-B (43,6%), as well as higher expression of osteoprotegerin (approximately 55,4%) in periodontal tissues compared to animals with periodontitis without treatment. Notably, kombucha did not induce renal or hepatic toxicity regardless of fermentation time. These findings suggest that kombucha, particularly after 4 days of fermentation, reduces inflammation and alveolar bone loss without systemic toxicity, supporting its potential as an adjunctive therapy for periodontitis.}, } @article {pmid41656820, year = {2025}, author = {Zhang, W and Han, K and Zhao, K and Yang, C and Jin, M and Wang, Y and Jiang, Z}, title = {[Application of flavonoid in disease treatment based on multi-omics technologies].}, journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences}, volume = {50}, number = {10}, pages = {1915-1929}, pmid = {41656820}, issn = {1672-7347}, support = {XZ202201ZR0061G//the Natural Science Foundation of Xizang Autonomous Region/ ; 24MDQ05//Nationalities Youth Fund Project of Xizang Minzu University/ ; }, mesh = {*Flavonoids/pharmacology/therapeutic use ; Multiomics ; Humans ; Metabolomics/methods ; Genomics/methods ; Proteomics ; Medicine, Chinese Traditional ; *Drugs, Chinese Herbal/pharmacology ; Anti-Inflammatory Agents/pharmacology ; }, abstract = {Flavonoids are naturally occurring polyphenolic compounds widely distributed in nature, exhibiting pharmacological activities including anti-inflammatory effects and inhibition of cell proliferation. Their broader application has been constrained by unclear therapeutic targets. Recent advances in high-throughput sequencing and high-resolution mass spectrometry have elevated the importance of multi-omics analysis for elucidating flavonoid pharmacological effects, therapeutic targets, and regulatory networks. Integration of genomics, transcriptomics, proteomics, metabolomics, and metagenomics enables systematic characterization of flavonoid targets and modulation networks. Clarifying the application of multi-omics technologies in this field may support the clinical translation of flavonoids and provide new strategies for precision research in traditional Chinese medicine.}, } @article {pmid41657444, year = {2026}, author = {Zhong, S and Shan, W and Xiang, L and Wang, Y and Zhang, L}, title = {Human bocavirus 1 viremia-associated pediatric sepsis with a triphasic urinary course: a case report.}, journal = {Translational pediatrics}, volume = {15}, number = {1}, pages = {22}, pmid = {41657444}, issn = {2224-4344}, abstract = {BACKGROUND: Human bocavirus 1 (HBoV1) is a common pediatric respiratory virus, yet, its potential to cause severe systemic illness as a sole pathogen and its specific effects on the urinary system are not fully recognized. This report describes the first case of pediatric sepsis, meeting the 2024 Phoenix sepsis criteria, caused by high-load HBoV1 viremia, which was characterized by a novel triphasic urinary course.

CASE DESCRIPTION: A previously healthy 4-year-old girl presented with fever and cough and developed asymptomatic sterile pyuria on illness day 4. On day 7, her condition deteriorated to sepsis (Phoenix Sepsis Score of 2), with acute respiratory distress and a depressed level of consciousness. Blood metagenomic next-generation sequencing (mNGS) identified high-load HBoV1 viremia (7,513 reads) as the sole pathogen, with negative blood and urine cultures. During the septic peak, urinary tract ultrasonography was normal; however, follow-up imaging on day 13 revealed delayed-onset, non-obstructive pyelectasis and increased post-void residual (PVR) volume. These functional abnormalities were resolved completely within 2.5 months.

CONCLUSIONS: HBoV1 can act as a sole pathogen to cause pediatric sepsis. The observed triphasic urinary course-early sterile pyuria, imaging quiescence at the sepsis peak, and delayed functional impairment-supports an inflammation-mediated pathogenesis rather than direct viral invasion. This case highlights the critical role of advanced molecular diagnostics in identifying viral etiologies in culture-negative sepsis and underscores the necessity of longitudinal functional surveillance, as clinically significant organ dysfunction may manifest after the acute inflammatory phase has resolved.}, } @article {pmid41657896, year = {2026}, author = {Wicaksono, WA and Thorsen, J and Stokholm, J and Berg, G}, title = {Metagenomic analysis of the nasopharyngeal microbiomes and resistomes in asthma, COVID-19 infected, and healthy individuals.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1729707}, pmid = {41657896}, issn = {1664-302X}, abstract = {INTRODUCTION: The nasopharyngeal microbiome presents an important environmental human interface and a window in the fight against chronic diseases like asthma, respiratory infections, and antimicrobial resistance. To identify the microbial structure and function, we designed a pilot study with individuals with asthma, COVID-19 infection, and healthy controls.

METHODS: We compare the microbial and resistome profiles of healthy individuals, patients with asthma, and patients with PCR-confirmed COVID-19 using shotgun metagenome sequencing. Additionally, metagenome-assembled genomes were generated to assess the virulence potential of the bacteria identified in the nasopharynx.

RESULTS: We found different patterns in microbial diversity, richness, and structure between individuals with asthma and those who are healthy, but not for those with COVID-19. Our results revealed unexpected insights into the quite diverse nasopharynx resistome encompassing 23 distinct drug classes, mainly based on antibiotic efflux (63.9%) and antibiotic inactivation (24.6%), regardless of the disease state. The majority of the antimicrobial resistance genes (ARGs) confer resistance to multidrug (45%), followed by those genes that confer resistance to aminoglycosides, tetracyclines, polymyxin, beta-lactam, and macrolide-lincosamide-streptogramin. A high proportion of ARGs was associated with various Pseudomonas species, which was confirmed by analysing metagenome-assembled genomes. Pseudomonas brenneri exhibited the highest number of ARGs and virulence factors, indicating notable pathogenic potential.

CONCLUSION: The study reveals distinct bacterial community compositions in healthy individuals and individuals with asthma. Pseudomonadales, particularly Pseudomonas species, contribute to the nasopharyngeal resistome. No association was found between nasopharyngeal resistome profiles and asthma development. Future research may explore airway microbial functions' influence on asthma development.}, } @article {pmid41657901, year = {2026}, author = {Farinas, LMF and Dela Peña, LBRO and Rivera, WL}, title = {Shotgun metagenomics reveals the prevalence and mobility of antibiotic resistance genes in the West Bay of the human-impacted Laguna Lake.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1742578}, pmid = {41657901}, issn = {1664-302X}, abstract = {Laguna Lake, the largest freshwater lake in the Philippines, has been reported to harbor antibiotic-resistant bacteria, posing health risks to the millions who depend on it. However, limited knowledge of antibiotic resistance genes (ARGs) in the lake highlights the need for a comprehensive assessment of its resistome. In line with this, we characterized ARGs in the West Bay of Laguna Lake using shotgun metagenomic sequencing based on six metagenomes collected from three stations across two sampling months at a single depth. ARGs were quantified from short reads, and assembled contigs containing these genes-antibiotic-resistant contigs (ARCs)-were analyzed to assess mobility through associations with plasmids and mobile genetic elements (MGEs). β-lactam resistance genes (0.023-0.048 copies per cell) were the most prevalent, corroborating previous reports. Meanwhile, the detection of bacitracin (0.013-0.028 cpc) and polymyxin (0.009-0.011 cpc) resistance genes raises new concerns, as resistance to these antibiotic classes has not been previously reported in the lake. Furthermore, 44.8 and 30.4% of ARCs were associated with plasmids and MGEs, respectively. ARCs carrying genes for resistance to β-lactams, chloramphenicol, and tetracyclines were frequently identified as mobile, indicating a high potential for horizontal gene transfer and suggesting possible antibiotic contamination in the lake. Overall, this study provides the first metagenomic insight into the resistome of Laguna Lake using short-read sequencing and highlights its role as an environmental reservoir of mobile ARGs. The findings underscore the need for expanded ARG surveillance to improve antimicrobial resistance risk prediction.}, } @article {pmid41657906, year = {2026}, author = {Wu, H and Qin, J and Li, B and Huang, Z and Liao, G and Tang, X and Li, Z and Xiong, J and Gao, Z and Jiang, J and Zhong, R and Han, Z and He, L and Tang, R}, title = {The combined application of chemical and microbial fertilizers enhanced microbial diversity and improved soil fertility in the peanut rhizosphere within a sugarcane-peanut intercropping system.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1751211}, pmid = {41657906}, issn = {1664-302X}, abstract = {The decline in soil microecological balance and fertility caused by continuous cropping obstacles and excessive application of chemical fertilizers has become a critical bottleneck restricting the sustainable development of the peanut industry. However, intercropping can enhance resource utilization efficiency, and microbial fertilizers can improve soil properties and increase nutrient usability. Therefore, we evaluated the effects of six fertilization treatments [no fertilization (CK), 100% chemical fertilizer (T1), microbial fertilizer (T2), 100%chemical fertilizer+microbial fertilizer (T3), 80% chemical fertilizer+microbial fertilizer (T4) and 60% chemical fertilizer+microbial fertilizer (T5)] on chemical properties and microbial communities of the rhizosphere soil of intercropped peanuts. The results showed that compared with T1, the combined application of chemical and microbial fertilizers significantly increased soil organic matter content and alleviated soil acidification. Microbial analysis indicated that the T4 treatment had the highest Shannon diversity, which was significantly higher than T1, demonstrating its effectiveness in reversing the suppressive effect of chemical fertilizer alone on microbial diversity. Principal coordinate analysis and redundancy analysis further confirmed that fertilization significantly altered microbial community structure, with a clear separation between the combined application and chemical-fertilizer-alone treatments, forming a distinct microbial community. Specifically, the T4 treatment significantly increased the abundance of rhizobia. Under T4 treatment, the abundance of assimilatory nitrate reductase genes (such as nasB and NR) decreased, while that of narB, and nirA increased; simultaneously, the abundance of dissimilatory nitrate reductase and denitrification-specific genes significantly increased. Mantel test analysis revealed significant positive correlations between soil total nitrogen, available nitrogen content, microbial communities, and crop yield. In summary, the combined application of chemical and microbial fertilizers optimizes the soil microenvironment by synergistically enhancing soil fertility (increasing organic matter, regulating pH) and reshaping microbial community structure (increasing diversity, enriching beneficial bacteria). These findings can provide theoretical basis for the optimization of fertilization strategy in peanut intercropping system.}, } @article {pmid41657910, year = {2026}, author = {Pilgrim, J and Widlake, E and Wilson, R and Vaux, AGC and Medlock, JM and Darby, AC and Baylis, M and Blagrove, MSC}, title = {Mosquito viromes across England and Wales reveal hidden arbovirus signals and limited ecological structuring.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1749228}, pmid = {41657910}, issn = {1664-302X}, abstract = {Outbreaks of mosquito-borne viruses are increasing in temperate regions, with West Nile and Usutu viruses now established in wide regions across Europe, and both detected in the UK. Current surveillance strategies focus on targeted approaches which are well suited for monitoring established threats but limited in their ability to detect recently described or neglected viruses. High throughput sequencing (HTS) provides an unbiased alternative, allowing simultaneous identification of well-recognised and overlooked arboviruses, alongside insect-specific viruses (ISVs) that may modulate vector competence of the insects transmitting these pathogens. This study presents the first comprehensive virome survey of Culex mosquitoes in the UK, analysing populations collected from 93 sites across England and Wales through HTS and a systematic virus discovery pipeline. Across these sites, 41 distinct viral taxa were identified, including 11 novel species. Most viruses were rare or confined to a few sites, with only three detected in more than one third of sites, suggesting the absence of a broad conserved virome across populations. Within this diversity, three arbovirus-related lineages were detected: Hedwig virus (Peribunyaviridae), Umatilla virus (Sedoreoviridae), and Atherstone virus (Peribunyaviridae), the former two representing the first detections in the UK. These putative arboviruses were embedded in viral communities that showed minimal structuring by coarse land type but a modest decline in richness with latitude across rural sites, consistent with diversity gradients observed in other microbial systems. Together, these findings provide the first national-scale baseline of Culex mosquito-associated viral diversity in the UK, and demonstrate the value of metagenomic approaches in arbovirus preparedness.}, } @article {pmid41657984, year = {2025}, author = {Li, JL and Hu, W and Chen, XQ and Li, LH and Phurbu, D and Zheng, YY and Zhang, YW and Sun, J and Yang, ZF and Xie, KQ and Yang, LQ and Yin, YR}, title = {Characterization of thermophilic xylanases from Tengchong Qiaoquan hot spring for lignocellulose bioprocessing and prebiotic production.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1731615}, pmid = {41657984}, issn = {1664-302X}, abstract = {INTRODUCTION: Xylanases are key catalysts for valorizing lignocellulosic biomass, yet many available enzymes lack sufficient thermal stability and exhibit suboptimal activity on complex substrates. To address these limitations, we combined enrichment culturing with metagenomic analysis to discover and characterize two novel GH10 family xylanases, Tc15-Xyn6 and Tc15-Xyn10, from the Qiaoquan geothermal area in Tengchong, Yunnan Province.

METHODS: Following molecular cloning, heterologous expression, and purification by Ni[2+]-chelating affinity chromatography, both enzymes were comprehensively profiled.

RESULTS: Tc15-Xyn6 displayed optimal activity at 65 °C and pH 6.6 with a half-life of 2 h at 65 °C, while Tc15-Xyn10 exhibited optimal activity at 60 °C and pH 6.0 with a half-life of 1 h at 60 °C. Both enzymes showed broad pH stability at low temperature: after incubation at 4 °C for 12-24 h across pH 4.0-10.0, Tc15-Xyn6 and Tc15-Xyn10 retained more than 60 and 40% of their initial activity, respectively. Both efficiently hydrolyzed xylan in alkali-treated wheat straw, rice straw, and corn stover, as well as xylan from hot water-treated wheat bran, but yielded distinct product profiles: Tc15-Xyn6 primarily produced xylobiose and xylotetraose, whereas Tc15-Xyn10 generated xylotriose as the main product. The resulting xylooligosaccharides significantly promoted the growth of Lactococcus lactis. Kinetic analyses showed K m and V max values of 4.675 mg/mL and 125 μmol/min/mg for Tc15-Xyn6, and 9.36 mg/mL and 59.52 μmol/min/mg for Tc15-Xyn10.

DISCUSSION: Collectively, Tc15-Xyn6 and Tc15-Xyn10 combine thermophilicity, thermostability, near-neutral pH preference, and strong performance on complex lignocellulosic substrates, supporting their application in feed processing and targeted production of prebiotic xylooligosaccharides from biomass.}, } @article {pmid41657996, year = {2025}, author = {Kong, M and Pan, Z and Wang, X and Huang, J and Tulafu, H and Xu, Y and Sulaiman, Y and Wu, W}, title = {Integrated multi-omics analysis reveals rumen and rectal microbiota-metabolite interaction features in polytocous fine-wool sheep with divergent residual feed intake.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1712307}, pmid = {41657996}, issn = {1664-302X}, abstract = {Residual feed intake (RFI) is a key indicator of feed efficiency in ruminants. To elucidate the potential regulatory roles of microorganisms and metabolites under different RFI levels, we investigated 24 polytocous fine-wool sheep (12 high-RFI and 12 low-RFI) using metagenomic sequencing and non-targeted metabolomics of rumen and rectal contents. Significant differences in average daily feed intake, residual feed intake, and feed conversion ratio were observed between groups (p < 0.001). LEfSe analysis identified four and seventeen RFI-associated microbial biomarkers in the rumen and rectum, respectively, with s_Ruminococcus_albus and s_Ruminococcus_bicirculans as common core taxa. Functional annotation revealed that high-RFI sheep were enriched in amino acid metabolism and xenobiotic degradation pathways in the rumen, whereas low-RFI sheep were enriched in pathways related to development and regeneration. In the rectum, high-RFI sheep showed enrichment in protein folding and degradation, carbohydrate metabolism, and energy metabolism, while low-RFI sheep were enriched in transcriptional regulation and signal transduction pathways. Metabolomic analysis detected 297 and 1,130 differential metabolites in the rumen and rectum, respectively, mainly lipids, organic acids, and derivatives. KEGG enrichment indicated that rumen metabolites were primarily involved in bile acid biosynthesis and riboflavin metabolism, while rectal metabolites were enriched in energy metabolism and multiple amino acid pathways, including arachidonic acid, tryptophan, tyrosine, lysine, and methionine metabolism. Integrated analysis revealed significant associations between key bacterial taxa and metabolites, and network construction identified core nodes potentially engaged in synergistic regulation, providing insights into their roles in RFI phenotype formation. Collectively, these findings highlight the distinct contributions of the rumen and rectum to feed efficiency in sheep and offer theoretical support for nutritional regulation strategies to improve ruminant production performance.}, } @article {pmid41658006, year = {2025}, author = {Tada, Y and Nakajima, R and Kitamura, M and Marumoto, K}, title = {Distribution and function of prokaryotes involved in mercury methylation, demethylation, and reduction in the western North Pacific Subtropical Gyre.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1642479}, pmid = {41658006}, issn = {1664-302X}, abstract = {Methylmercury (MeHg), a bioaccumulative neurotoxic heavy metal, substantially threatens environmental and human health. In natural environments, MeHg formation and degradation are primarily mediated by microorganisms containing hgcAB, merA, or merB genes. However, these genes have not been simultaneously analyzed in open-ocean samples. This study aimed to investigate the distribution and phylogeny of functional genes associated with mercury (Hg) methylation (hgcA and hgcB), demethylation (merB), and reduction (merA), as well as dissolved total Hg (THg) and MeHg concentrations in the western North Pacific Subtropical Gyre (WNPSG) using metagenomic analysis. Although THg levels varied across sampling sites, MeHg concentrations consistently increased with depth. A strong correlation between dissolved MeHg and apparent oxygen utilization indicated a link between Hg methylation and microbial respiration. hgcA, merB, and merA were predominantly detected at depths of 500-1,500 m, where MeHg concentrations peaked, indicating active microbial Hg speciation within mesopelagic layers. A higher abundance of hgcA than merB suggests that microbial Hg methylation may surpass demethylation in this region. Phylogenetic analyses of hgcAB identified the Nitrospina lineage as dominant Hg methylators. Metabolic pathway analyses of metagenome-assembled genomes (MAGs) showed that Nitrospina harboring hgcAB possesses the nitrite reductase pathway, suggesting a linkage between Hg methylation and nitrogen cycling. MAGs with hgcA affiliated with Myxococcota (Deltaproteobacteria) exhibited a strong association with sulfur cycling. Diverse lineages harboring merB and merA genes were identified, suggesting that MeHg demethylation and Hg(II) reduction likely co-occur. Methanogenesis pathways in some Alphaproteobacteria with merB or merA suggest a potential connection between methane production and MeHg degradation and Hg(II) reduction. These findings provide novel insights into the intricate interactions between microbial communities, functional gene distributions, and Hg biogeochemical cycling in the WNPSG.}, } @article {pmid41658007, year = {2025}, author = {Alfonsi, S and Racciatti, F and Guzman, F and Fabbretti, A and Milon, P and Vitali, LA and Spurio, R and Petrelli, D}, title = {The plastisphere and river systems as reservoirs for antibiotic resistant bacteria.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1721325}, pmid = {41658007}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) is a critical global health threat. This phenomenon involves the diffusion of bacteria and genes among humans, animals and the environment. In particular, the presence of third generation cephalosporin (3GC)-resistant Enterobacteriaceae in natural environments is of high concern as they are classified as critical-priority pathogens of public health importance. In this work we studied the relation among plastic pollution in freshwater ecosystems, the spread of multidrug-resistant (MDR) bacteria and diffusion of antibiotic resistance genes (ARGs). Caged plastic fragments were deliberately introduced in a river of central Italy. Plastic samples were collected and analyzed in parallel with river water samples. Out of 267 cefotaxime (CTX) resistant isolates obtained, 65 CTX-resistant Enterobacteriaceae were selected for further analysis. Most of the isolates (75% of plastic-derived and 84% of water-derived isolates) were MDR with seven being carbapenem-resistant enterobacteria (CRE). Five of them synthesize KPC (Klebsiella pneumoniae carbapenemases) enzymes, and two strains were positive for metallo-β-lactamases (NDM). Among the KPC producers, three isolates were identified as K. pneumoniae sequence type ST1519. Their isolation in a natural ecosystem is alarming because they can potentially re-enter human populations through environmental pathways. Shotgun metagenomic analysis provided a comprehensive snapshot of the microbial communities associated to the plastisphere, revealing dominance of families such as Comamonadaceae, Sphaerotilaceae, and Flavobacteriaceae, which play key roles in environmental biofilm formation and stability. The resistome analysis highlighted the presence of ARGs conferring resistance to clinically important antibiotics, such as beta-lactams, vancomycin, and tetracyclines, alongside mobile genetic elements (MGEs) such as integrons, which facilitate the horizontal transfer of resistance genes. This study provides crucial experimental evidence that riverine plastic debris acts as a genetic reservoir and could act as an efficient vehicle for the accumulation and transfer of clinically relevant resistance determinants.}, } @article {pmid41658353, year = {2026}, author = {Liu, X and Li, Y and Xiao, J and Zhang, X and Liu, Y and Li, Z and Wang, L and Zhang, L and Liu, Y and Liang, P and Xu, Z and Liu, Y and Song, C}, title = {Emergence of a Novel CRESS-DNA Virus Associated with Swine Reproductive Failure in China.}, journal = {Transboundary and emerging diseases}, volume = {2026}, number = {}, pages = {4053892}, pmid = {41658353}, issn = {1865-1682}, mesh = {Animals ; Swine ; China/epidemiology ; *Swine Diseases/virology/epidemiology ; *DNA Viruses/genetics/isolation & purification/classification ; *Circoviridae Infections/veterinary/virology/epidemiology ; *Circovirus/genetics/isolation & purification/classification ; Phylogeny ; Genome, Viral ; Stillbirth/veterinary ; }, abstract = {The continuous emergence of circular Rep-encoding single-stranded (CRESS) DNA viruses across diverse hosts has been closely associated with the occurrence of severe diseases. Four circoviruses within the genus Circovirus have been identified in pigs, including porcine circovirus Type 1 (PCV1), PCV2, PCV3, PCV4, and PCV5. In late 2021, a large pig farm experienced an outbreak of reproductive disorders that were undiagnosed by standard tests. Subsequent viral metagenomic analysis of stillborn piglets identified a novel single-stranded circular DNA virus, designated porcine megalocircovirus (PMCV). PMCV has a large genome of 9426 nt and encodes nine open reading frames. Biochemical analyses of Rep confirm PMCV as a CRESS DNA virus. However, PMCV Rep showed low amino acid sequence identities to the four PCV species and several human CRESS DNA viruses, with the highest identity of 23.6% to PCV4 Rep. The genetic evolutionary tree indicates that PMCV belongs to an unknown family of the CRESS DNA viruses. The positive detection rate for PMCV in tested samples was 24% (30/125), while the positive rate regarding pig farms was 41.18% (14/34) in China. The emergence of PMCV warrants further investigation.}, } @article {pmid41658610, year = {2026}, author = {Bautista, J and Bedón-Galarza, R and Martínez-Hidalgo, F and Masache-Cruz, M and Benítez-Núñez, M and Valencia-Arroyo, C and López-Cortés, A}, title = {Decoding the microbial blueprint of pancreatic cancer.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1737582}, pmid = {41658610}, issn = {2296-858X}, abstract = {Pancreatic cancer (PC) represents one of the most formidable challenges in oncology, characterized by its asymptomatic onset, delayed clinical detection, and dismal prognosis. Among pancreatic neoplasms, pancreatic ductal adenocarcinoma (PDAC) accounts for over 90% of cases and remains the most aggressive form, driven by late diagnosis, intrinsic chemoresistance, and a profoundly immunosuppressive tumor microenvironment. Recent advances have reframed the human microbiome not as a passive bystander but as an active architect of pancreatic tumor biology. This review delineates the mechanistic axes through which microbial ecosystems orchestrate PDAC progression across four key anatomical niches-gastrointestinal, oral, urogenital, and intrapancreatic. We elucidate how microbial dysbiosis fosters oncogenesis through immune evasion, metabolic reprogramming, and chronic inflammation, implicating specific taxa such as Fusobacterium nucleatum, Malassezia spp., and Porphyromonas gingivalis in immune suppression and chemoresistance. Microbial enzymatic inactivation of gemcitabine and modulation of cytokine networks further underscore the microbiome's pivotal role in therapeutic failure. Conversely, commensal and probiotic species may potentiate immunosurveillance and enhance treatment efficacy. This review also explores microbiota-derived biomarkers for early detection and the translational promise of microbiome-targeted interventions, including fecal microbiota transplantation, probiotics, and selective antibiotics. By decoding the microbial blueprint of PC, we propose a paradigm in which the microbiome emerges as both a biomarker and a therapeutic axis, offering novel avenues for precision oncology. Furthermore, this integrative synthesis emphasizes the multi-omic, immunometabolic, and therapeutic dimensions of the pancreatic cancer-microbiome interface, where metagenomic, transcriptomic, metabolomic, and immunomic layers converge to shape tumor evolution and therapeutic response, advancing the vision of microbiome-informed precision oncology.}, } @article {pmid41658619, year = {2026}, author = {Pan, T and Zhuang, X and Xiang, L}, title = {Case Report: From trivial trauma to fulminant septic shock: multidisciplinary rescue of Vibrio vulnificus necrotizing fasciitis via a seven-stage surgical protocol with limb salvage.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1714153}, pmid = {41658619}, issn = {2296-858X}, abstract = {OBJECTIVE: To report a successful case of an inland seafood vendor who developed Vibrio vulnificus necrotizing fasciitis complicated by septic shock following a minor calf abrasion, and to explore its special epidemiological implications and key points for standardized management.

CASE SUMMARY: A 46-year-old male seafood vendor (hospitalized from July 3 to 10 August 2025) presented on post-injury day 7 with fulminant necrotizing fasciitis, septic shock, and multiple organ dysfunction syndrome. Vibrio vulnificus was identified by wound culture and metagenomic sequencing. Management included early combination antibiotics, ICU organ support, and seven sequential surgical interventions. The patient was successfully weaned from mechanical ventilation and extubated after 25 days of ICU care, and discharged on hospital day 30 with satisfactory wound healing.

CONCLUSION: This case alerts that high inoculum exposure due to cold-chain disruption can prolong the incubation period of V. vulnificus infection to 7 days, transcending traditional epidemiological boundaries. Successful management depended on early fasciotomy and strict adherence to standardized treatment protocols. Mandatory wound monitoring for high-risk occupational populations should become a new priority in public health prevention and control.}, } @article {pmid41658717, year = {2026}, author = {Al-Najjar, AS and Shata, FN and Ba Mhel, O and Gutob, Y and Alhazmi, M and Alharbi, Z and Choghari, RA and Qashar, AA and Basudan, B and Aljohani, N and Al-Juhani, A}, title = {Diatom Analysis in Drowning: A Critical Review of Reliability, Contamination, and Medico-Legal Interpretation.}, journal = {Cureus}, volume = {18}, number = {1}, pages = {e100870}, pmid = {41658717}, issn = {2168-8184}, abstract = {The diagnosis of fatal drowning remains one of the most challenging tasks in forensic pathology, as no single autopsy finding is pathognomonic, and interpretation relies on the integration of scene information, circumstances, and ancillary investigations. Among supportive tests, diatom analysis has been used for decades, yet its medico-legal value continues to be debated due to methodological heterogeneity, contamination risks, and inconsistent interpretive frameworks. This review critically examines diatom evidence in drowning from a comparative and fit-for-purpose perspective, focusing on mechanistic plausibility, alternative non-drowning explanations, and methodological blind spots that undermine evidentiary reliability. Conventional microscopy-based diatom testing and emerging DNA-based and metagenomic approaches are compared with respect to what they detect, how contamination may arise, and how results are currently interpreted in forensic casework. Particular emphasis is placed on low-count diatom findings in closed organs, where recent evidence demonstrates substantial vulnerability to laboratory, consumable, and postmortem contamination. Drawing on recent systematic syntheses, controlled postmortem studies, and newly identified contamination sources, this review argues that mechanistic plausibility does not equate to forensic reliability. Diatom findings are best interpreted as supportive evidence whose weight depends on explicit contamination control, transparent reporting, and alignment with a clearly defined medico-legal proposition. To address persistent comparability and interpretation gaps, a minimum reporting dataset, minimum contamination-control principles, and a decision-oriented interpretive framework are proposed. In conclusion, diatom testing should neither be regarded as definitive proof nor dismissed outright. When applied selectively and interpreted within a contamination-aware, proposition-driven framework, diatom evidence may contribute meaningfully to drowning diagnosis and drowning-site inference, while avoiding overstatement of its probative value.}, } @article {pmid41659075, year = {2026}, author = {Duggar, M and Sun, Y and Leardini, D and Jia, Q and Muratore, E and Dallas, RH and Ferrolino, J and Cherian, A and Cesaro, S and Faraci, M and Fraczkiewicz, J and Ussowicz, M and Englund, JA and Hakim, H and Hayden, RT and Klein, EJ and Wolf, J and Maron, G and Tang, L and Masetti, R and Margolis, EB}, title = {Pre-HCT Resistome Disruption Predicts ESBL Gene Expansion in Pediatric Transplant Recipients: A Prospective Multi-Center Study.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.20.26344466}, pmid = {41659075}, abstract = {BACKGROUND: Infections are the leading cause of non-relapse mortality in pediatric hematopoietic cell transplant (HCT) recipients. Up to 90% of bacteremias in these patients originate from gut microbiome organisms. However, selection for resistance genes, such as Extended-spectrum β-lactamase (ESBL), in these patient's gut microbiomes remains poorly understood.

METHODS: Stools were prospectively collected from pediatric HCT recipients at multiple centers (n=133 patients, five centers) on the day of HCT, the day of neutrophil engraftment, and 30 days post-HCT. Bacterial DNA was isolated and sent for shotgun metagenomic sequencing. Antibiotic resistance genes were identified using the MEGARes database. Associations between ESBL gene abundance changes and antibiotic exposure were examined using univariate and Inverse Probability of Treatment Weighting linear regression models with covariate balancing propensity scores.

RESULTS: Pre-existing gut resistome disruption at the time of HCT showed a stronger correlation with ESBL gene expansion than post-transplant antibiotic exposure. Specifically, patients with greater baseline resistome distance from healthy children showed increased ESBL genes during the neutropenic period. Post-transplant β-lactam exposure (total or ESBL-cleavable) did not correlate with increases in ESBL genes in already-colonized patients. However, aminoglycosides and anaerobic active antibiotics were associated with acquisition of new ESBL organisms during the neutropenic period, while pre-existing microbiome disruption primarily drove selection of resistant bacteria already present.

CONCLUSIONS: These findings indicate that antibiotic stewardship before HCT, in addition to reducing the use of anaerobic active antibiotics during early transplant, may be necessary to prevent ESBL-related infections in pediatric transplant recipients.

LAY SUMMARY: Infections are the leading cause of death after HCT, and recently the role of the gut microbiome in harboring dangerous bacteria has been highlighted. This study aims to understand multidrug resistant bacteria changes in the gut microbiome early after HCT.}, } @article {pmid41659429, year = {2026}, author = {Vallecillo-Zuniga, ML and Akeefe, A and Brown, DG and Wahlig, TA and Marchetti, M and Heiner, T and Davis, KL and Nieznanski, C and Flynn, A and Leung, DT}, title = {Longitudinal Changes in Nasal and Oral Microbiome and Antimicrobial Resistance Gene Profiles in Response to Human Fecal Microbiota Transplantation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41659429}, issn = {2692-8205}, support = {UM1 TR004409/TR/NCATS NIH HHS/United States ; UL1 TR002538/TR/NCATS NIH HHS/United States ; S10 OD034321/OD/NIH HHS/United States ; T32 HG008962/HG/NHGRI NIH HHS/United States ; S10 OD021644/OD/NIH HHS/United States ; T32 HL105321/HL/NHLBI NIH HHS/United States ; P30 CA042014/CA/NCI NIH HHS/United States ; }, abstract = {The gut-lung axis describes interactions between intestinal and respiratory mucosal systems through microbial, metabolic, and immune pathways, but the systemic impact of gut-targeted therapies on upper respiratory tract (URT) communities remains underexplored. We conducted a longitudinal study in adult patients undergoing fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infection (CDI) alongside healthy controls. Fecal, nasal, and oral samples were collected at baseline (Day 0) and on Days 14 and 56 following FMT. Shotgun metagenomic sequencing was performed to quantify microbial diversity, taxonomic composition, and the abundance of antimicrobial resistance genes (ARGs). FMT was associated with increased gut diversity and decreased levels of key intestinal taxa commonly considered pathobionts, including Klebsiella spp., Escherichia spp., Shigella spp., and Klebsiella pneumoniae. At the phylum level, fecal Bacteroidota increased, while Mucoromycota decreased following treatment. Post-FMT nasal microbiome changes included reduced richness and diversity, expansion of Moraxella, and decreases in taxa linked with respiratory colonization, including Staphylococcus aureus and Streptococcus pneumoniae. By Day 56, nasal communities partially recovered toward healthy profiles. Baseline nasal ARG abundance decreased following FMT, particularly among β-lactam, aminoglycoside, and fluoroquinolone resistance genes, and remained comparable to healthy controls by Day 56. In contrast, the oral microbiome and oral resistome remained largely stable, with only minor fluctuations, and no consistent increases in respiratory pathobiont-associated taxa. In summary, FMT was associated with broader effects beyond the gut, including changes in the URT microbial ecology and antimicrobial resistance profiles. Together, these findings are consistent evidence of gut-lung microbial interactions, linking intestinal dynamics with respiratory microbial composition and antimicrobial resistance patterns.}, } @article {pmid41659626, year = {2026}, author = {Priyadarshini, M and Jorgensen, J and Stauffer, SRC and Issa, L and Pandya, N and Nnyamah, C and Xu, K and Boyett, JE and Kular, P and Mhatre, A and Brahambhatt, VH and Gilbert, JA and Khan, MW and Wicksteed, B and Dai, Y and Layden, BT}, title = {A high fermentable fiber Western diet reduces indole levels.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.27.702025}, pmid = {41659626}, issn = {2692-8205}, abstract = {Changes in gut microbiota composition due to diet impact health. Fiber-rich diets promote beneficial microbiota and reduce the risk of metabolic diseases, while low-fiber, calorie-dense diets are linked to dysbiosis and increased disease risk. This study examines the effects of a Western diet (WD) and explores dietary fiber supplements as potential modifiers of those effects. 10-week-old C57Bl/6J male mice were fed control (low-fat) or WD (high-fat, high-sucrose) containing 0% fermentable fiber (FF) or WD supplemented with 20% FF (fructooligosaccharides, FOS; guar gum, GG, or pectin, Pec). After 19 weeks, analysis of the cecal metagenome using whole-genome shotgun sequencing, metabolome by untargeted and targeted LC-MS/MS, and tissue RNA and protein expression by RT-PCR and immunoblotting was undertaken. WD-FF reduced metabolic derangements from WD while also improving GM diversity and altering cecal metabolites, particularly tryptophan metabolism. A profound increase in cecal indole levels (targeted metabolomics) was noted in WD vs WD-FF groups. As the primary indole-oxidizing enzyme, CYP2E1 generates indoxyl sulfate, which contributes to oxidative stress and a leaky gut. Mice on WD displayed higher expression of Cyp2e1 mRNA in the gut. In the liver, the levels of both CYP2E1 protein and mRNA were higher in the WD group compared to the WD-FOS group, with protein levels also higher than in the WD-Pec group and mRNA levels higher than in the WD-GG group. mRNA expression of markers of oxidative stress, inflammation, and leaky barrier was significantly higher in the liver and intestine of the WD vs the WD-FF groups. FFs reduced high plasma indoxyl sulfate levels (except in WD-GG), and boosted short-chain fatty acids and indole acetic acid. Our data suggest that WD disrupts GM tryptophan metabolism, possibly by altering the balance between indole-producing and utilizing gut bacteria. Dietary fiber supplementation exerts protective effects, in part, by mitigating this imbalance.}, } @article {pmid41659795, year = {2026}, author = {Yang, F and Yang, C and Li, H and Zhang, X and Ding, X and Zhang, S}, title = {Metagenomic next-generation sequencing in diagnosing rhino-orbital-cerebral mucormycosis presenting as cerebral Infarction: a case series and diagnostic analysis of seven patients.}, journal = {Frontiers in fungal biology}, volume = {7}, number = {}, pages = {1751546}, pmid = {41659795}, issn = {2673-6128}, abstract = {INTRODUCTION: Rhino-orbital-cerebral mucormycosis (ROCM) is a rare, rapidly progressive, and fatal invasive fungal infection. This case series is the first to systematically characterize ROCM presenting primarily as cerebral infarction on imaging and highlights the value of metagenomic next-generation sequencing (mNGS) in the early diagnosis of such critical and atypical cases.

All seven patients had diabetes mellitus, with six concurrently presenting with ketoacidosis. Universal clinical features included fever and a fixed, dilated pupil. Most patients exhibited facial swelling (6/7, 85.7%) and visual impairment (5/7, 71.4%). Cerebral infarction was confirmed by head magnetic resonance imaging (MRI) in all individuals.

The diagnosis was confirmed in all cases by the detection of Rhizopus species sequences via mNGS of cerebrospinal fluid (CSF). Six patients received treatment with amphotericin B cholesteryl sulfate complex, and two of these also underwent surgical debridement. Ultimately, only one patient survived, yielding a mortality rate of 85.7% (6/7).

CONCLUSION: ROCM should be highly suspected in diabetic patients presenting with acute cerebral infarction accompanied by fever and facial or ocular symptoms. mNGS enables rapid and early etiological diagnosis of ROCM, which is crucial for improving outcomes. Earlier diagnosis, combined antifungal therapy, and surgical intervention may be associated with better prognosis.}, } @article {pmid41659841, year = {2026}, author = {Tao, Y and Liu, X and Liu, Y and Ma, Y and Liu, Y and Ding, M}, title = {The diagnostic efficacy of bronchoscopy guided by hand-drawn mapping in the diagnosis of initial treatment for sputum-smear negative peripheral pulmonary tuberculosis.}, journal = {Journal of clinical tuberculosis and other mycobacterial diseases}, volume = {43}, number = {}, pages = {100578}, pmid = {41659841}, issn = {2405-5794}, abstract = {BACKGROUND: This study aims to evaluate the clinical value and safety of hand-drawn mapping for bronchoscopic navigation combined with radial probe endobronchial ultrasound (RP-EBUS) in the diagnosis of primary peripheral sputum smear-negative pulmonary tuberculosis (SNPTB).

METHODS: Patients suspected of having peripheral-type primary SNPTB, who were admitted to Southeast University Zhongda Hospital from 2021 to 2024, were retrospectively analyzed. Patients were divided into two groups. The sensitivity, specificity, diagnostic accuracy rate, and area under the receiver-operating characteristic (ROC) curve were evaluated with different diagnostic methods.

RESULTS: A total of 212 patients were enrolled, including 149 in the SNPTB group and 63 in the non-SNPTB group. The success rate of ultrasound bronchoscopy exploration is 90.6 %. The sensitivity, specificity, diagnostic accuracy, and AUC value of bronchoscopy guided by hand-drawn mapping were 92.6 %, 95.2 %, 93.4 %, and 0.939, respectively, which were superior to those of T-SPOT detection (P < 0.05). Among the various sampling methods, EBUS-guided bronchoalveolar lavage fluid metagenomic next-generation sequencing (EBUS-BALF mNGS) demonstrated the highest sensitivity (86.6 %), positive predictive value (89.6 %), and AUC (0.917).

CONCLUSIONS: For peripheral SNPTB, the combination of hand-drawn navigation and RP-EBUS is both safe and effective. EBUS-BALF mNGS demonstrated the highest diagnostic efficiency. When radial ultrasound detects hypoechoic areas of the lesion, it is recommended to perform BALF mNGS. Conversely, in solid lesions, the negative rate of BALF mNGS is relatively high, and combining mNGS with biopsy is recommended to further improve diagnostic efficiency.}, } @article {pmid41659959, year = {2025}, author = {Abdelmegeid, M and Zeineldin, M and Seboussi, R and Mohamadin, M and Alharthi, AS and Mansour, N and Okasha, LA and Elolimy, AA and Saliu, EM}, title = {Metagenomic analysis of the camel rumen archaeome and its functional potential.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1738018}, pmid = {41659959}, issn = {2297-1769}, abstract = {The camel rumen harbors a unique and underexplored archaeal community that plays a critical role in methanogenesis and ruminal fermentation. This study aimed to characterize the taxonomic composition and functional potential of the camel rumen archaeome using whole-genome shotgun metagenomic sequencing. Across the seven healthy racing camel rumen samples, the archaeal community was dominated by Euryarchaeota (50.1 ± 0.02%) and the Methanomada group (49.7 ± 0.03%), with Methanobacteriaceae and Methanobrevibacter representing the predominant family and genus, respectively. Species-level analysis revealed Methanobrevibacter sp. YE315 and Methanobrevibacter millerae as the most abundant archaeal species across all samples. Alpha-diversity analyses indicated a diverse and evenly distributed archaeal population in the camel rumen. Beta-diversity based on Bray-Curtis and Jaccard dissimilarities demonstrated strong similarity among samples, highlighting a conserved archaeal community structure across individuals. Core microbiome assessment (≥ 80% occurrence) identified seven dominant Methanobrevibacter species as the stable core archaeome. Functional profiling revealed a consistent metabolic repertoire dominated by methanogenesis (PWY-5209), amino acid biosynthesis, and nucleotide metabolism pathways. Functional alpha-diversity metrics and beta-diversity clustering highlighted low inter-sample variability and a stable functional architecture. Overall, the camel rumen archaeome exhibited a stable and conserved community composition and functional architecture, underscoring its central role in hydrogen utilization and methane production within the rumen ecosystem. Although based on a small number of animals from a single location and therefore descriptive in nature, this study provides a comprehensive metagenomic overview of the taxonomic and functional profiles of the camel rumen archaeal community.}, } @article {pmid41660005, year = {2026}, author = {Wicaksono, WA and Zukancic, E and Zlatnar, M and Suwanto, A and Berg, G}, title = {Traditional fermented foods of Indonesia harbour functionally redundant but phylogenetically diverse taxa.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag005}, pmid = {41660005}, issn = {2633-6685}, abstract = {Fermented foods represent complex microbial ecosystems that contribute to food quality, functionality, and potential health benefits, yet many traditional fermented foods remain poorly characterized. The aim of this study was to study microbial diversity, and functional potential of underexplored traditional Indonesian fermented food. The fermented products displayed substantial variation in bacterial richness, ranging from 65 to 614 bacterial amplicon sequence variants across samples. The microbial communities were dominated by bacterial taxa affiliated with the orders Bacillales and Lactobacillales, alongside fungal taxa from the order Mucorales. The plant-based products i.e. tape ketan and tape singkong had a higher bacterial abundance but lower diversity than animal-based terasi. We found significant correlations between bacterial and fungal communities dominated by positive cooccurrence patterns and highly complex networks especially in terasi. Each food product was characterized by a unique functional profile of genes linked to beneficial metabolic functions (biosynthesis of bacteriocins, short-chain fatty acids, and vitamins) but tape ketan samples demonstrated the highest diversity and abundance of them. Metagenome assembled genomes reflect a high diversity of health beneficial properties as well as substrate-specific degradation capabilities. Traditional Indonesian fermented foods harbour functionally redundant but phylogenetically diverse taxa offering a potential source for probiotic traits and functional food development.}, } @article {pmid41660022, year = {2026}, author = {Shaji, A and Ramachandran, AK and Chandrasekaran, N and Savarimalai, KC and Adhira, R}, title = {A cross-sectional metagenomic analysis of the microbial ecology in symptomatic apical periodontitis - An in vivo study.}, journal = {Journal of conservative dentistry and endodontics}, volume = {29}, number = {1}, pages = {60-64}, pmid = {41660022}, issn = {2950-4708}, abstract = {BACKGROUND: Symptomatic apical periodontitis (SAP) is a painful inflammatory disease driven by root canal infection. A detailed understanding of its microbial ecology, compared to a noninfectious baseline, is needed.

AIMS: This study aimed to characterize the microbial ecology of SAP using 16S ribosomal (RNA) 16S rRNA metagenomic sequencing and compare it to control teeth undergoing root canal treatment after trauma.

MATERIALS AND METHODS: This cross-sectional study included 10 patients with SAP and 10 control patients. Pulpal samples were collected aseptically. Microbial DNA was extracted, and the full-length 16S rRNA gene was sequenced through Oxford Nanopore Technology. Analysis was performed using QIIME2.

STATISTICAL ANALYSIS USED: Microbial abundances and diversity indices were compared using an independent samples t-test or Mann-Whitney U-test (P < 0.05 significant).

RESULTS: The SAP microbiome was dysbiotic and enriched in anaerobes. Veillonella parvula was highly abundant in SAP (mean 13.1%) but absent in controls. Species like Dialister pneumosintes and Prevotella melaninogenica were found almost exclusively in SAP. Commensals including Faecalibacterium prausnitzii were significantly reduced.

CONCLUSION: SAP is associated with a distinct microbial signature defined by the enrichment of anaerobic pathobionts and a loss of commensals, revealing a polymicrobial, dysbiotic community.}, } @article {pmid41660100, year = {2026}, author = {Jaito, N and Kaewsawat, N and Sangawthong, K and Uengwetwanit, T}, title = {Identification of novel metagenomic lipases through integrated structural and sequence-based analysis.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20462}, pmid = {41660100}, issn = {2167-8359}, mesh = {*Lipase/chemistry/genetics/metabolism ; *Metagenomics/methods ; Hydrogen-Ion Concentration ; Enzyme Stability ; Temperature ; Databases, Protein ; }, abstract = {Enzymes, as key biocatalysts, are essential for advancing sustainable green technologies across diverse industrial sectors. The discovery of novel enzymes is essential for expanding their applications. In this study, we identified new lipases using an integrated screening strategy. This approach combines both structural and sequence-based methods on a large-scale metagenomic database. This strategy enabled the identification of new lipases with low sequence identity to known reference proteins. Our approach, therefore, circumvents the limitations of traditional sequence-only methods, which often fail to identify functionally similar enzymes with low sequence similarity. We first used Foldseek, a state-of-the-art structural homology search tool, to rapidly screen the database for proteins with structures similar to widely used lipases. This was followed by a rigorous sequence similarity filtering against public protein databases, yielding 711 putative novel lipases. We selected and experimentally validated three candidates, confirming their lipase activity. Further biochemical characterization revealed their notable properties including thermostability with optimal activity at 50-55 °C, and distinct alkaline activity profiles, maximal at pH of 8.0-9.0. Their unique properties, including high activity at elevated temperatures and alkaline pH, suggest potential for applications in detergent formulations, bioremediation, and industrial biocatalysis. Beyond identifying these promising enzymes, this study demonstrates the power of a combined structural and sequence-based approach for finding novel biocatalysts. This methodological innovation has broad implications for future enzyme discovery from metagenomic resources.}, } @article {pmid41660425, year = {2026}, author = {Ni, H and Zhu, J and Chen, Y and Zheng, Y and Chen, B and Dong, C and Zhang, S and Xu, Y and Jiang, Y}, title = {Clinical characteristics and prognostic impact of streptococcal colonization in critically ill patients with severe pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1647511}, pmid = {41660425}, issn = {2235-2988}, mesh = {Humans ; Critical Illness ; Male ; Female ; Prognosis ; Retrospective Studies ; *Streptococcal Infections/microbiology/mortality/diagnosis ; *Streptococcus/genetics/isolation & purification ; Aged ; Middle Aged ; Intensive Care Units ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {BACKGROUND: Streptococcus species are predominant commensal residents of the respiratory tract in healthy individuals and contribute to immune and metabolic regulation. However, the association between streptococcal colonization and clinical outcomes in patients with severe pneumonia remains undercharacterized. This study aimed to explore the clinical characteristics and the impact of streptococcal colonization on the prognosis of critically ill patients with pneumonia.

METHOD: We conducted a multicenter, retrospective, observational cohort study of critically ill pneumonia patients admitted to 12 intensive care units (ICUs) between January 2019 and December 2023 who underwent metagenomic next-generation sequencing (mNGS). Patients were stratified into Streptococcus-colonized and non-colonized groups based on bronchoalveolar lavage fluid (BALF) mNGS results, conventional microbiological testing (CMT), and clinical assessments. Propensity score matching (PSM) was utilized to minimize baseline confounding variables. Using nearest-neighbor matching at a 1:2 ratio, baseline characteristics were balanced between groups post-matching. The primary endpoint was 28-day all-cause mortality.

RESULTS: A total of 1,897 patients were enrolled in this study. Among them, 21 patients under 18 years of age, 139 patients lost to follow-up within 28 days, and 4 patients with confirmed streptococcal infection were excluded. Finally, 1,733 patients met the inclusion criteria. The cohort had a mean age of 65 years, with the majority being males (1,213/1,733, 70%). Among these, 148 (8.5%) were classified as Streptococcus-colonized, and 1,585 (91.5%) were Streptococcus-colonization-negative. No significant difference in 28-day all-cause mortality was observed between the colonized and non-colonized groups (35.81% vs. 38.51%, p=0.578). Patients with Streptococcus colonization had a significantly shorter median length of stay (LOS) (17 days, interquartile range [IQR] 11-30) than those without colonization (22 days, IQR 12-33; P = 0.044). Similarly, their median intensive care unit (ICU) LOS (11 days, IQR 7-16) was also significantly shorter than that of non-colonized patients (14 days, IQR 8-25; P = 0.003). Multivariable Cox regression analysis further demonstrated that Streptococcus colonization was not an independent risk factor for 28-day mortality (HR = 1.10, 95% CI: 0.79-1.51, p=0.579).

CONCLUSION: Our findings suggest a potential role for Streptococcus colonization in improving clinical outcomes in severe pneumonia. The presence or absence of Streptococcus colonization may influence short-term prognostic benefits in critically ill pneumonia patients. Further research is needed to clarify the clinical significance and potential mechanisms of Streptococcus colonization.}, } @article {pmid41660426, year = {2026}, author = {Wang, S and Yang, Y and Lei, L and Wan, R and Su, Z and Liu, Y and Tang, H and Hu, G and Li, C and Li, C and Meng, J and Yang, K}, title = {SSTDhunter: a curated gene database for investigating androgen producing potential in microbiota species.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1754671}, pmid = {41660426}, issn = {2235-2988}, mesh = {*Androgens/biosynthesis/metabolism ; Humans ; *Databases, Genetic ; *Microbiota/genetics ; Biocuration ; Computational Biology/methods ; }, abstract = {Androgens are critical for the growth of prostate cells, as well as prostate tumor cells. For prostate cancer patients under Androgen Deprivation Therapy (ADT) such as castration treatment, investigating the potential for androgen production by gut microbes is crucial. In microbe species, the side chain cleavage activity of steroid-17, 20-desmolase (SSTD) is responsible for 11-oxy-androgens production by biotransformation from cortisol, as well as from other endogenous steroids and pharmaceutical glucocorticoids. The side-chain cleavage product of prednisone could significantly promote the proliferation of prostate cancer cells. The SSTD is a complex formed by N-terminal and C-terminal transketolases encoded by desA and desB genes, whose activity has been well-characterized in Clostridium scindens ATCC 35704. While a void still existed in evaluating the androgen producing potential by gut microbiota owing to relatively low abundance of SSTD-carrying species and the lack of professional gene database. Meanwhile, mining SSTD encoding genes in explosion sequencing data has become computationally expensive and time-consuming using comprehensive database. Here, a professional database consisted of SSTD-coding genes, named SSTDhunter, was constructed using a large-scale genomic analysis along with homologous genes as background. These SSTD-coding genes were reconstruction through comprehensive characteristics consisted of operon structures, sequence identities, phylogenetic topologies and comparative analysis. To reduce false positives, protein sequences of homologous genes tktA, which encode component of sugar transketolase, were also included in SSTDhunter database as background noise. SSTDhunter is for rapid investigation of SSTD-coding genes in massive metagenomic data, which is freely available at http://www.orgene.net/SSTDhunter/.}, } @article {pmid41660499, year = {2025}, author = {Hensley, MK and Sayed, K and Haidar, G and Wang, X and Benos, PV and Ito, S and Im, A and Geramita, E and Shlomchik, W and Methé, B and Cruz, CD and Morris, A and Kitsios, GD}, title = {Rapid Metagenomic Sequencing of Bronchoalveolar Lavage Fluid for Diagnosis of Infection in Patients With Hematologic Malignancies and Pulmonary Complications.}, journal = {CHEST pulmonary}, volume = {3}, number = {4}, pages = {}, pmid = {41660499}, issn = {2949-7892}, support = {K23 AI154546/AI/NIAID NIH HHS/United States ; R01 HL159805/HL/NHLBI NIH HHS/United States ; R01 HL176668/HL/NHLBI NIH HHS/United States ; R03 HL162655/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: Diagnosing pulmonary complications (PCs) in hematologic malignancies remains challenging due to insensitive conventional microbiologic testing (CMT) and overlapping clinical manifestations of infectious and noninfectious pulmonary complications. For these reasons, empirical antimicrobials and immunosuppression (eg, corticosteroids) are used for prolonged periods.

RESEARCH QUESTION: How does metagenomic sequencing of the lower respiratory tract compare with conventional microbiologic testing among patients with hematologic malignancy?

STUDY DESIGN AND METHODS: Prospective proof-of-concept cohort study of 30 adult in-patients with hematologic malignancies and PCs who underwent bronchoscopy for suspected lower respiratory tract infection.

RESULTS: CMT identified a pathogen via culture- or polymerase chain reaction-based testing in 53% of patients. 16S sequencing demonstrated 66.7% positive and 42.9% negative concordance with CMT, while also identifying additional plausible respiratory pathogens in 59.3% of patients. Nanopore demonstrated 6.7% positive and 87.5% negative concordance with CMT and identified additional plausible respiratory pathogens in 42.3% of patients.

INTERPRETATION: Culture-independent sequencing approaches had modest agreement with CMT when considering bacterial PCs and showed poor detection of fungal pathogens. Sequencing frequently identified additional plausible respiratory pathogens, and further validation is needed to determine if such detection represents clinically missed infections or nonpathogenic colonization.}, } @article {pmid41660616, year = {2025}, author = {Liu, H and Liang, L and Wang, C and Luo, R and Luo, Q and Huang, C}, title = {Gut mycobiota dysbiosis and an emergent state of "co-dysbiosis" are associated with IgE sensitization in children with comorbid allergic rhinitis and constipation.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1745580}, pmid = {41660616}, issn = {1664-3224}, mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Immunoglobulin E/immunology/blood ; *Rhinitis, Allergic/immunology/microbiology/epidemiology ; Child, Preschool ; *Constipation/immunology/microbiology/epidemiology ; *Gastrointestinal Microbiome/immunology ; Child ; Female ; Male ; *Fungi/immunology/genetics ; Case-Control Studies ; Comorbidity ; Pilot Projects ; *Mycobiome/immunology ; }, abstract = {BACKGROUND: The comorbidity of allergic rhinitis (AR) and functional constipation (FC), termed ARFC, implies shared gut-immune pathways. Although bacterial dysbiosis has been implicated, the role of the gut mycobiota (fungal community) in this specific comorbidity remains unexplored.

METHODS: This pilot case-control study characterized the gut mycobiota in 19 ARFC and 17 healthy control (HC) children aged 3-6 years using metagenomic sequencing. Fungal community structure, taxonomic composition, and correlations with IgE levels were analyzed. Cross-kingdom bacterial-fungal interaction networks were constructed, and functional potential was predicted.

RESULTS: Alpha diversity was comparable, whereas beta diversity revealed significant structural shifts in the ARFC gut mycobiota. Key immunomodulatory fungi, including Cenococcum, Dentiscutata, Ambispora, and Saccharomyces, were markedly depleted in ARFC. These taxa served as top discriminators in random forest models and exhibited significant inverse correlations with total and allergen-specific IgE levels. Cross-kingdom network analysis identified dramatic ecological restructuring: the HC network was characterized by prevalent competitive interactions, whereas the ARFC network shifted exclusively to positive correlations, a state termed "co-dysbiosis." No significant differences were observed in predicted KEGG functional pathways.

CONCLUSION: This study provides the first evidence that gut mycobiota dysbiosis-marked by depletion of immunoregulatory fungi and an ecological shift toward cooperative interkingdom interactions ("co-dysbiosis")-is associated with IgE sensitization in ARFC children. These findings position the gut mycobiota as a novel element of the gut-nose axis in allergic disease, warranting further investigation.}, } @article {pmid41660808, year = {2026}, author = {Gangloff, V and Aldeguer-Riquelme, B and Yañez, MA and Potocki-Veronese, G and Severac, E and Antón, J and Soria, E and Santos, F}, title = {Microbial Biofilms Dynamics and Functionality in an Urban Mycobacterium-Dominated Drinking Water Distribution System.}, journal = {Environmental science & technology}, volume = {60}, number = {7}, pages = {5242-5258}, pmid = {41660808}, issn = {1520-5851}, mesh = {*Biofilms ; *Drinking Water/microbiology ; *Mycobacterium ; RNA, Ribosomal, 16S/genetics ; Water Supply ; }, abstract = {Microbial communities in drinking water distribution systems (DWDS) develop primarily as biofilms on pipe surfaces. Despite their impact on water quality, infrastructure maintenance, and biosafety, biofilms are not routinely controlled. In this study, we investigated the bacterial community dynamics and functionality in an urban chlorinated DWDS, dominated by Mycobacterium, through a multiphasic approach which included 16S rRNA gene metabarcoding, metagenomics and microscopy. Our results showed that biofilm communities were more functionally diverse compared to those from water and that the biofilm maturity was positively correlated with the prevalence of potential Mycobacterium emerging pathogens and a broader distribution of antibiotic resistance genes (ARGs) within the microbial community. The reconstruction of metagenome-assembled genomes (MAGs) and the corresponding genomospecies allowed the identification of key microbial taxa involved in the biofilm matrix remodeling, with 22% of them strongly responsible for biofilm formation. A diverse and novel viral community was detected across the system, including new putative Mycobacterium phages that might act against mycolic acids and thus contribute to biofilm destabilization. Our findings enhance our understanding of DWDS microbial composition and biofilm formation dynamics, focusing on "who does what" and then providing a foundation for developing effective biofilm control strategies in water distribution systems.}, } @article {pmid41660847, year = {2026}, author = {Lu, X and Kong, N and Wang, C and Lu, J and Li, W and Yang, H and Lu, X and Zhang, Z and Chen, Y and Huang, S and Zhou, C and Zhang, Y and Zhang, W and Shan, T}, title = {A novel parvovirus circulating in canine populations and sporadically detected in human oropharyngeal samples.}, journal = {Microbiology spectrum}, volume = {14}, number = {3}, pages = {e0332725}, pmid = {41660847}, issn = {2165-0497}, mesh = {Animals ; Dogs ; Humans ; Phylogeny ; *Parvoviridae Infections/veterinary/virology ; Genome, Viral ; *Oropharynx/virology ; *Dog Diseases/virology ; *Parvovirus, Canine/genetics/isolation & purification/classification ; Capsid Proteins/genetics ; Metagenomics ; *Parvovirus/genetics/classification/isolation & purification ; Recombination, Genetic ; High-Throughput Nucleotide Sequencing ; }, abstract = {Most human pathogens, while originating from animals, have crossed species barriers to infect humans, often leading to outbreaks of new infectious diseases. Despite significant efforts, the mechanisms, timing, and locations of these emerging diseases remain largely uncertain. Here, using a viral metagenomic approach, we discovered a novel canine-associated parvovirus in human oropharyngeal secretions. Molecular screening revealed the presence of this parvovirus in different canine tissues, including 24 of 108 pharyngeal lymph node samples. Further molecular investigation showed that the virus was detected in the oropharyngeal secretions of pet dogs and in human samples that were not linked to these animals. This parvovirus was therefore named human-canine associated parvovirus 1 (HCAPV-1). Nine complete genomes of HCAPV-1 were acquired through next-generation sequencing, combining Sanger sequencing. Genomic and phylogenetic analyses indicate that these nine strains of HCAPV-1 belong to the genus Protoparvovirus and form a distinct clade, with their closest relatives being newlaviruses from foxes. Amino acid substitutions have been characterized in the capsid proteins of the variants of HCAPV-1, which potentially alter their infection patterns. Potential genomic recombination was also observed in HCAPV-1. Taken together, our findings reveal the presence of a novel parvovirus in both canine and human samples, highlighting the need to investigate its host range and transmission dynamics.IMPORTANCEThis study identified a novel parvovirus, human-canine associated parvovirus 1 (HCAPV-1), which was detected in human oropharyngeal secretions and various canine tissues, suggesting that its host range may extend beyond a single species. Phylogenetic analysis revealed that HCAPV-1 forms a distinct clade within the genus Protoparvovirus, closely related to newlaviruses from foxes. Amino acid substitutions observed in the capsid proteins of HCAPV-1 variants indicate genetic divergence, warranting further investigation into their potential implications for host interactions. Recombination events may have contributed to its emergence. This finding highlights the importance of continued surveillance in settings where humans and companion animals coexist and underscores the need for further research to clarify the ecological and host-range characteristics of such viruses.}, } @article {pmid41661278, year = {2026}, author = {Zhang, H and Zhai, C and Hu, H and Qian, G and Mao, M}, title = {A metagenomic study of the gut microbiome in patients with type 2 diabetes mellitus and myocardial infarction.}, journal = {Acta diabetologica}, volume = {63}, number = {5}, pages = {789-799}, pmid = {41661278}, issn = {1432-5233}, support = {XFCX-DMYH//Jiaxing Institute of Arteriosclerotic Disease/ ; }, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/complications/metabolism ; *Myocardial Infarction/microbiology/metabolism/complications ; *Gastrointestinal Microbiome/genetics ; Female ; Metagenomics ; Middle Aged ; Male ; Aged ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {OBJECTIVE: This study aimed to investigate gut microbiota composition and metabolic functions in patients with type 2 diabetes mellitus (DM) complicated by myocardial infarction (MI) and to explore potential mechanisms linking the gut microbiome to MI development.

METHODS: Sixty patients with DM complicated by MI and 52 patients with DM alone were initially recruited. After quality control, 29 DM + MI patients and 33 DM patients were included in the final analysis. Gut microbial profiles were characterized using shotgun metagenomic sequencing and bioinformatics analyses. Microbial diversity, composition, and gene functions were compared between groups based on KEGG, COG, and CAZy annotations.

RESULTS: Overall microbial diversity and metabolic profiles were comparable between the two groups; however, significant differences were observed in specific taxa and functional genes. Taxa enriched in the DM + MI group included Bacteroidales, Prevotellaceae, and Lachnospiraceae. In total, 510 KEGG orthology (KO) units and 21 pathways-including ABC transporters, quorum sensing, and general metabolic pathways-differed significantly between groups. Carbohydrate transport and metabolism, as well as glycoside hydrolase activity, represented the most enriched functional categories. Random forest models based on selected microbial species, KO units, and KEGG pathways achieved areas under the curve (AUCs) of 0.868, 0.885, and 0.820, respectively.

CONCLUSION: Patients with DM complicated by MI exhibit distinct gut microbial compositions and functional gene signatures compared with patients with DM alone. These microbiome-based markers may contribute to early risk stratification and provide potential targets for microbiota-focused interventions to mitigate MI risk in patients with diabetes.}, } @article {pmid41661326, year = {2026}, author = {Umemura, A and Sasaki, A and Sasaki, D and Iizuka, A and Chiba, M and Aihara, K and Ubukata, N and Kumagai, H and Tanahashi, Y and Iwasaki, T and Ando, T and Nitta, H}, title = {Impact of laparoscopic sleeve gastrectomy on gut and oral microbiota diversity, weight loss, and the metabolic outcomes.}, journal = {Surgery today}, volume = {}, number = {}, pages = {}, pmid = {41661326}, issn = {1436-2813}, abstract = {PURPOSE: Metabolic and bariatric surgery (MBS) alters the gut microbiota (GM). Changes in oral microbiota (OM) after MBS have not yet been thoroughly investigated. In this study, we evaluated the changes in GM and OM before and after laparoscopic sleeve gastrectomy (LSG) in patients with severe obesity and investigated the relationship between improvements in GM/OM, weight loss, and the metabolic effects. METHODS: Thirty-seven severely obese patients who underwent LSG were enrolled in this study. We retrieved samples from the feces and oral mucosa from baseline to 1-year after LSG. These samples were subjected to a 16 S rRNA metagenomic analysis using a next-generation sequencer. We evaluated the significant changes in GM/OM and compared the results with clinical outcomes. RESULTS: Regarding OM diversity, g_Actinomyces (p = 0.003), o_Rothia (p = 0.020), and g_Streptococcus (p = 0.004) increased. With regard to GM, g_Slackia (p = 0.039), g_Bacillus (p = 0.030), g_Roseburia (p = 0.027), and g_Faecalibacterium (P = 0.003) increased, the proportion of p_ Firmicutes increased, and p_Bacteroidetes decreased in both groups. Changes in g_Akkermansia did not contribute to GM/OM diversity. The weight loss and remission rates of type 2 diabetes were higher in patients with increased normal oral flora and a recovery of g_Faecalibacterium in GM. CONCLUSIONS: We clarified that the LSG reconstructs GM/OM as weight loss and the metabolic effects are enhanced.}, } @article {pmid41661439, year = {2026}, author = {Moon, SH and Lee, TG and Ko, YS and Yoo, DS and Oh, Y and Cho, HS}, title = {First detection and genomic characterization of ungulate tetraparvovirus 1 in water buffalo (Bubalus bubalis) from vietnam.}, journal = {Virus genes}, volume = {62}, number = {2}, pages = {212-220}, pmid = {41661439}, issn = {1572-994X}, support = {RS-2024-00400152//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET)/ ; }, mesh = {Animals ; *Buffaloes/virology ; Vietnam ; Phylogeny ; *Genome, Viral ; Metagenomics ; Genomics ; *Parvoviridae Infections/veterinary/virology ; Cattle ; }, abstract = {Ungulate tetraparvovirus 1 (UTPV1), or bovine hokovirus, has been described in cattle but remains poorly characterized in Southeast Asia. In this study, we report the first detection and genomic characterization of UTPV1 in water buffalo (Bubalus bubalis) from Vietnam. Skin swab samples were collected from a buffalo with nodular lesions in northern Vietnam in 2024, and total nucleic acids were subjected to metagenomic sequencing. Analysis of Illumina MiSeq reads revealed the presence of both lumpy skin disease virus (LSDV) and UTPV1. The near-complete UTPV1 genome (NIVR-B12-2024) shared 90.7-93.3% nucleotide identity with reference strains but did not cluster with genotypes I or II, instead forming a distinct lineage. Phylogenetic analyses supported its independent position, and recombination detection indicated potential genetic exchange between Asian and South American strains. Several amino acid substitutions were identified in the NS1 protein, suggesting ongoing viral diversification. This study provides the first molecular evidence of UTPV1 in water buffalo and in Vietnam, expanding the recognized host range and geographic distribution of this virus. The findings highlight the value of non-invasive sampling and metagenomic sequencing for livestock surveillance and underscore the need for continued monitoring to evaluate the epidemiological significance and potential health risks of UTPV1 in Southeast Asia.}, } @article {pmid41662353, year = {2026}, author = {Wang, Y and Liang, V and Yin, N and Liu, S and Segal, E}, title = {SGAC: a graph neural network framework for imbalanced and structure-aware AMP classification.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {41662353}, issn = {1477-4054}, mesh = {*Graph Neural Networks ; *Antimicrobial Peptides/chemistry/classification ; Algorithms ; Classification Algorithms ; *Software ; }, abstract = {Classifying antimicrobial peptides (AMPs) from the vast collection of peptides derived from metagenomic sequencing offers a promising avenue for combating antibiotic resistance. However, most existing AMP classification methods rely primarily on sequence-based representations and fail to capture the spatial structural information critical for accurate identification. Although recent graph-based approaches attempt to incorporate structural information, they typically construct residue- or atom-level graphs that introduce redundant atomic details and increase structural complexity. Furthermore, the class imbalance between the small number of known AMPs and the abundant non-AMPs significantly hinders predictive performance. To address these challenges, we employ lightweight OmegaFold to predict the 3D structures of peptides and construct peptide graphs using C$_\alpha $ atoms to capture their backbone geometry and spatial topology. Building on this representation, we propose the spatial graph neural network (GNN)-based AMP classifier (SGAC), a novel framework that leverages GNNs to extract structural features and generate discriminative graph representations. To handle class imbalance, SGAC incorporates weight-enhanced contrastive learning to cluster structurally similar peptides and separate dissimilar ones through adaptive weighting, and applies weight-enhanced pseudo-label distillation to generate high-confidence pseudo labels for unlabeled samples, achieving balanced and consistent representation learning. Experiments on publicly available AMP and non-AMP datasets demonstrate that SGAC significantly achieves state-of-the-art performance compared to baselines. The complete code and dataset are available at: https://github.com/wyxwyx46941930/SGAC.}, } @article {pmid41662415, year = {2026}, author = {Zhang, J and Fan, J and Li, D and Yang, C and Cheng, Z and Cheng, Z and Qu, H and Li, G and Yuan, N and Song, T and Zhou, K and Zhao, Y and Wang, X}, title = {Antibiotic resistance in East Asia: current status, risks, and response strategies.}, journal = {Journal of infection in developing countries}, volume = {20}, number = {1}, pages = {43-51}, doi = {10.3855/jidc.21637}, pmid = {41662415}, issn = {1972-2680}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Asia, Eastern/epidemiology ; Metagenomics ; Japan ; China/epidemiology ; }, abstract = {INTRODUCTION: This study investigates the current status and regional disparities of resistance to novel antibiotics in East Asia, exploring links to socioeconomic factors and identifying high-risk resistance determinants.

METHODOLOGY: Metagenomic sequencing was performed on 1024 human fecal samples (25 local, 999 public) from 12 regions across China and Japan. Antibiotic resistance genes (ARGs) were identified by aligning sequences against a comprehensive antibiotic resistance database, focusing on 8 novel antibiotic classes. The relationship between regional per capita GDP and resistance rates for clinically relevant novel antibiotics was statistically analyzed.

RESULTS: Significant regional variation in resistance rates was observed for clinically used novel antibiotics (aminocoumarins, glycylcyclines, oxacephems, oxazolidinones, pleuromutilins). A significant inverse correlation was found between per capita GDP and resistance rates for aminocoumarins, glycylcyclines, and oxacephems, particularly pronounced within inland regions. Oxacephem resistance was alarmingly high (> 55% in all regions, > 90% in some). Oxazolidinone resistance remained low (< 28%). Pleuromutilin resistance showed a strong negative GDP correlation only inland. Analysis revealed 24 high-frequency ARGs (5 exceeding 45% coverage: CfxA, IsaB, MexB, abeS, IsaE). Minimal shared resistance determinants existed among novel antibiotic classes, except between oxazolidinones and pleuromutilins.

CONCLUSIONS: Resistance to novel antibiotics in East Asia exhibits significant regional heterogeneity, strongly influenced by local economic development levels. Resistance rates for specific agents (e.g., oxacephems) critically limit their clinical utility, necessitating mandatory susceptibility testing. High-frequency ARGs linked to traditional antibiotic misuse pose cross-resistance risks. Surveillance and stewardship strategies must be regionally tailored, prioritizing vulnerable areas and tracking critical resistance loci for novel agents.}, } @article {pmid41663920, year = {2026}, author = {Qian, Y and Shi, C and Wang, Y and Han, Q and Yu, Q and Li, M and Li, H}, title = {Metagenomic sequencing and binning reveal carbon cycling microorganisms and gene functions in park environments.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41663920}, issn = {1471-2180}, support = {32471575//National Natural Science Foundation of China/ ; 24JRRA458//Gansu Province Science and Technology Plan for Youth Science Fund/ ; lzuyxcx-2022-172//Medical Innovation and Development Project of Lanzhou University/ ; }, mesh = {*Metagenomics/methods ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Carbon Cycle/genetics ; *Parks, Recreational ; Carbon/metabolism ; Water Microbiology ; Metagenome ; Sequence Analysis, DNA ; Phylogeny ; Soil/chemistry ; Microbiota/genetics ; }, abstract = {In the midst of increasing global warming and accelerated urbanization, urban parks, serving as significant carbon sinks, are increasingly recognized for their role in mitigating the urban heat island effect. However, limited research investigating the urban park carbon cycle hinders our full understanding and effective use of their carbon sink potential. This study employed metagenomics sequencing and 16S rRNA gene sequencing to characterize the carbon cycle and its influencing factors within soil and water from collected from nine city parks. Notably, the abundance and alpha diversity of carbon cycle microbes and genes were higher in soil compared to water. Specifically, soil samples exhibited enrichment of carbon cycling genes involved primarily in polysaccharide metabolism, particularly those associated with starch and cellulose metabolism. Conversely, water samples, revealed a greater prevalence of genes associated with chitin metabolism. The most important factor affecting soil carbon cycling genes was bacterial community, followed by non-nutritional factors and nutrient factors, while heavy metals demonstrated no effect on soil carbon cycling genes. The most important factor affecting water carbon cycling genes was only bacterial community. The analysis yielded 381 high-quality metagenomic assembled genomes (MAGs) containing carbon cycling genes, with significant covariation observed between the pta and carbon cycling genes ackA and acyP, which encode cellulose degradation functions. These findings contribute to a better understanding of microbial carbon metabolism within urban parks and offer a foundation for effective carbon emission management strategies.}, } @article {pmid41663924, year = {2026}, author = {Li, B and Shi, X and Yao, X and Yan, Y and Wu, K and Zhang, C and Ren, Y}, title = {Association of the residual feed intake (RFI) with the rumen microbiota composition and metabolism in Dorper-Hu crossbred lambs.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41663924}, issn = {1471-2180}, support = {2020BQ53//The Science and Technology Innovation Program of Shanxi Agricultural University/ ; SXBYKY2021037//Shanxi Province Outstanding Doctor Award Fund/ ; J202011313//"1331 Project" Key Disciplines of Animal Sciences, Shanxi Province/ ; Modern Agro-industry Technology Research System in Shanxi Province//Modern Agro-industry Technology Research System in Shanxi Province/ ; }, abstract = {BACKGROUND: Improving feed efficiency in livestock is crucial for sustainable animal production. Residual feed intake (RFI) is a superior metric that accurately assesses feed efficiency. Animals with a low RFI (LRFI) usually consume less feed than animals with a high RFI (HRFI). Ruminal microbiota plays an important role in feed digestion in sheep. It is essential to elucidate the associations between rumen microbial composition, metabolic profiles, and growth performance of lambs with differing RFI by metagenomic sequencing and metabolomic profiling.

RESULTS: Although no significant differences were observed in growth performance, LRFI lambs exhibited significantly lower dry matter intake (P < 0.05) and improved feed efficiency. Integrative metagenomic and metabolomics analysis revealed that the LRFI group showed enrichment of bacteria (Prevotella, Roseburia, and Pseudoscardovia) (P < 0.05) and metabolites (N-Acetylneuraminic acid 9-phosphate, N-Succinyl-L-glutamate, 5-hydroxyindolepyruvate, pelargonidin, sinapic acid, and spermidine) associated with efficient nitrogen metabolism, enhanced microbial protein synthesis, and antioxidant activity. By contrast, the HRFI group was characterized by increased abundance of microorganisms (Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) (P < 0.05), coupled with elevated levels of metabolites (histidinal, tetrahydrocorticosterone, and sakuranetin). Correlation networks identified positive correlations among Prevotella, unclassified f_Prevotellaceae, several amino acid intermediates and specific flavonoids, and the host traits of reduced DMI and RFI. Conversely, the genera Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina were positively correlated with the increased DMI and RFI.

CONCLUSIONS: Efficient (low-RFI) animals exhibited a Prevotella-driven microbiome and a distinct metabolome characterized by enrichment of several amino acid intermediates and specific flavonoids, while a more diverse but methanogen-related microbial community (such as Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) is present in inefficient (HRFI) sheep. The identified microbial and metabolic profiles provide potential biomarkers for breeding feed-efficient animals and developing targeted nutritional interventions to improve ruminant production sustainability.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04788-0.}, } @article {pmid41663943, year = {2026}, author = {Li, M and Yang, R and Bai, Q and Yang, Z and Huang, T and Qiao, Y and Yang, B and Chen, J and Lin, W}, title = {Manipulating root-associated microbiomes to boost drought resistance in dryland winter wheat with Streptomyces pactum Act12.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41663943}, issn = {1471-2180}, support = {32401443//National Natural Science Foundation of China/ ; 2025CYJSTX02-16//the earmarked fund for Modern Agro-industry Technology Research System of Shanxi Province/ ; }, abstract = {BACKGROUND: Drought critically compromises agricultural productivity and threatens sustainable wheat production. Streptomyces pactum Act12 confers benefits to plant growth under drought stress, but its possible effects on root-associated microbiomes remain understudied. Here, shotgun metagenome sequencing and culture-dependent approaches were integrated to investigate the responses of rhizosphere and rhizoplane microbiomes in dryland winter wheat to exogenous S. pactum Act12 and their potential linkage to plant drought resistance.

RESULTS: Seed biopriming with S. pactum Act12 increased plant aboveground dry weight at flowering (by 63.2%) and maturation (by 41.9%) stages, leading to improved grain yield (by 8.7%). Microbial inoculation reduced malondialdehyde contents in wheat leaves and roots at the flowering stage alongside compartment-specific alterations in soil microbiomes. Metagenomic analysis revealed inoculation-induced enrichment of distinct taxa in rhizosphere soils (flowering: Fibrobacterota, Altererythrobacter; maturation: Mucoromycota, Rhodospirillum) and rhizoplane soils (flowering: Pseudomonadota, Serratia; maturation: Candidatus_Pacebacteria, Variovorax). Functional profiling showed up-regulation of key pathways related to oxidative phosphorylation in inoculated rhizosphere soils at the flowering stage. In rhizoplane soils, ABC transporters and pyrimidine metabolism were up-regulated across stages upon inoculation. Two key strains isolated from rhizoplane soils, designated Glycomyces lechevalierae A4 and Microbacterium algeriense B3, demonstrated the ability to enhance drought resistance in wheat seedlings.

CONCLUSIONS: Inoculation of S. pactum Act12 heightens drought resistance in dryland winter wheat through compartment-specific phylogenetic restructuring and functional reprogramming of root-associated microbiomes.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04812-3.}, } @article {pmid41664657, year = {2026}, author = {Chuckran, PF and Blazewicz, SJ and Ceja-Navarro, JA and Pett-Ridge, J and Schwartz, E and Dijkstra, P}, title = {The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20641}, pmid = {41664657}, issn = {2167-8359}, mesh = {*Soil Microbiology ; *Transcription, Genetic ; Codon Usage ; *Microbiota/genetics ; Glucose/metabolism ; Environment ; Codon ; }, abstract = {Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa-highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for functions associated with stress-such as genes associated with sporulation or heat shock. These results demonstrate that gene traits, such as codon usage, nucleotide selection, and amino acid selection, relate to the transcriptional expression of genes in soil microbial communities and suggests that these relationships may be dependent on both gene function and the specific type of environmental stimuli.}, } @article {pmid41664846, year = {2026}, author = {Stolf, CS and Paz, HES and Paraluppi, MC and Miguel, MMV and Santamaria, MP and Monteiro, MF and Amgarten, DE and Franco, RRA and Branco-de-Almeida, LS and Shaddox, LM and Casarin, RCV}, title = {Molar-Incisor and Generalized Grade C Periodontitis: Distinct Microbiome-Immune Interactions Suggest Divergent Pathogenesis.}, journal = {Journal of periodontal research}, volume = {61}, number = {4}, pages = {382-395}, doi = {10.1111/jre.70077}, pmid = {41664846}, issn = {1600-0765}, support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2021/14430-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; R01DE019456/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/immunology ; Biofilms ; Cross-Sectional Studies ; Female ; Gingival Crevicular Fluid/microbiology/immunology ; *Periodontitis/microbiology/immunology ; Male ; Adult ; Middle Aged ; Treponema denticola/isolation & purification ; Cytokines ; Tannerella forsythia/isolation & purification ; Eubacteriales ; }, abstract = {AIM: Molar-Incisor (PerioC-MIP) and Generalized (PerioC-G) Grade C Periodontitis could have distinctive etiopathogenesis behind their unique clinical patterns. Thus, this study aimed to distinguish these two phenotypes by analyzing the subgingival metagenomic profile and the inflammatory markers levels.

METHODS: In this cross-sectional comparative study, Gingival Crevicular Fluid (GCF) and Subgingival Biofilm (SB) were collected from 18 PerioC-MIP North Americans and 14 periodontally healthy controls (HC) from the same location (HC-MIP) and 20 PerioC-G Brazilians and 20 controls (HC-G). From GCF, immunoenzymatic analysis was performed. SB functional and taxonomic bacterial content was determined using shotgun metagenomics sequencing.

RESULTS: Taxonomic results showed significantly different alpha- and beta-diversity profiles between disease groups (p < 0.05). Aggregatibacter actinomycetemcomitans and Streptococcus sanguinis were associated with PerioC-MIP; levels of Tannerella forsythia, Filifactor alocis, Porphyromonas gingivalis, Fretibacterium fastidiosum, and Treponema denticola were significantly enriched at PerioC-G (p < 0.05). PerioC-G had the function for flagellar assembly enriched, while PerioC-MIP SB was associated with biofilm formation of Escherichia coli. Different GCF inflammatory marker levels for each pattern resulted in PerioC-G presenting higher levels of IL-1β, IL-6, and IL-10 than PerioC-MIP (p < 0.05).

CONCLUSION: PerioC-G and PerioC-MIP presented different taxonomical profiles and GCF cytokine levels, raising the hypothesis that they may represent two different stages/susceptibility patterns of Periodontitis Grade C.}, } @article {pmid41664936, year = {2026}, author = {Shaikh-Ibrahim, A and De Lise, F and Curci, N and Gargano, M and Sacco, O and Di Fenza, M and Moracci, M and Cobucci-Ponzano, B}, title = {A Hyperthermostable Archaeal GH78 Rhamnosidase Efficiently Hydrolyzes Flavonoid Glycosides for Juice Debittering.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {6}, pages = {5562-5574}, pmid = {41664936}, issn = {1520-5118}, mesh = {*Glycoside Hydrolases/chemistry/metabolism/genetics ; *Archaea/enzymology/genetics/chemistry ; Enzyme Stability ; *Fruit and Vegetable Juices/analysis ; *Flavonoids/chemistry/metabolism ; Hydrolysis ; *Glycosides/chemistry/metabolism ; *Archaeal Proteins/chemistry/genetics/metabolism ; Substrate Specificity ; Flavanones/chemistry/metabolism ; Hot Temperature ; Hydrogen-Ion Concentration ; Biocatalysis ; }, abstract = {α-L-Rhamnosidases are a class of glycosyl hydrolases (GHs) that catalyze the hydrolysis of terminal α-L-rhamnose residues from diverse glycoconjugates. While extensively characterized in bacterial and fungal sources, no archaeal α-L-rhamnosidases have been characterized to date. Herein, we report the identification and characterization of the first thermostable archaeal α-L-rhamnosidase (ArRha), derived from the metagenomic data set of Pisciarelli solfatara hot spring. ArRha, classified in glycoside hydrolase family GH78, efficiently hydrolyzes α-1,2 and α-1,6 rhamnosyl linkages in flavonoid glycosides with notable biological activities. The novel enzyme showed remarkable temperature stability, wide-range pH activity, organic solvent tolerance, and no metal dependence. Combined with a thermostable β-glucosidase, ArRha converts naringin to prunin and naringenin in sweet and blood orange juices, achieving >95% conversion within 2 h at 65 °C. This represents the first report of a hyperthermostable archaeal GH78 α-L-rhamnosidase with promising applications in industrial enzymatic juice debittering and sustainable flavonoid biotransformation.}, } @article {pmid41665259, year = {2025}, author = {Gaisin, VA and Hadjicharalambous, C and Mujakić, I and Villena-Alemany, C and Li, J and Koblížek, M and Pilhofer, M}, title = {Thermophilic bacteria employ a contractile injection system in hot spring microbial mats.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41665259}, issn = {1751-7370}, support = {CZ.02.01.01/00/22_008/0004624//OP JAK project Photomachines/ ; CoG 101000232/ERC_/European Research Council/International ; }, mesh = {*Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; Cryoelectron Microscopy ; Phylogeny ; Sequence Analysis, DNA ; Electron Microscope Tomography ; Metagenomics ; Bacteria/genetics/metabolism ; DNA, Bacterial/genetics/chemistry ; *Bacterial Proteins/metabolism/genetics ; }, abstract = {Bacterial contractile injection systems (CISs) are multiprotein complexes that facilitate the bacterial response to environmental factors or interactions with other organisms. Multiple novel CISs have been characterised in laboratory bacterial cultures recently; however, studying CISs in the context of the native microbial community remains challenging. Here, we present an approach to characterise a bioinformatically predicted CIS by directly analysing bacterial cells from their natural environment. Using cryo-focused ion beam milling and cryo-electron tomography (cryoET) imaging, guided by 16S rRNA gene amplicon sequencing, we discovered that thermophilic Chloroflexota bacteria produce intracellular CIS particles in a natural hot spring microbial mat. We then found a niche-specific production of CIS in the structured microbial community using an approach combining metagenomics, proteomics, and immunogold staining. Bioinformatic analysis and imaging revealed CISs in other extremophilic Chloroflexota and Deinococcota. This Chloroflexota/Deinococcota CIS lineage shows phylogenetic and structural similarity to previously described cytoplasmic CIS from Streptomyces and probably shares the same cytoplasmic mode of action. Our integrated environmental cryoET approach is suitable for discovering and characterising novel macromolecular complexes in environmental samples.}, } @article {pmid41665263, year = {2025}, author = {Hutchinson, TF and Holland, SR and Clarke, DA and Ricci, F and Jirapanjawat, T and Leung, PM and Lappan, R and Liu, WPA and Bay, SK and Bliss, A and McGeoch, MA and Chown, SL and Greening, C}, title = {Resilient Antarctic soil bacteria consume trace gases across wide temperature ranges.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41665263}, issn = {1751-7370}, support = {DE230100542//Australian Research Council Discovery Early Career Awards/ ; DE250101210//Australian Research Council Discovery Early Career Awards/ ; FT240100502//Australian Research Council Future Fellowship/ ; SR200100005//ARC SRIEAS Grant Securing Antarctica's Environmental Future/ ; }, mesh = {*Soil Microbiology ; *Bacteria/metabolism/genetics/classification ; Antarctic Regions ; *Hydrogen/metabolism ; *Carbon Monoxide/metabolism ; Temperature ; Oxidation-Reduction ; Methane/metabolism ; Metagenomics ; }, abstract = {Polar desert soils host diverse microbial communities despite limited nutrients and frequent temperature and light fluctuations. Adapting to these extremes, most bacteria possess high-affinity hydrogenases and carbon monoxide dehydrogenases, enabling them to use atmospheric trace gases such as hydrogen (H2) and carbon monoxide (CO) to generate energy and fix carbon (aerotrophy). Despite the foundational importance of this process in polar desert ecosystems, little is known about the thermal sensitivity of trace gas oxidation or how this process will respond to climate warming. Here, we show through in situ and ex situ incubations that H2 consumption is an exceptionally thermally resilient process that can occur from -20 to 75°C, at rates comparable to temperate ecosystems (peaking at 8.56 nmol H2 h-1 g dry soil-1 at 25°C). Temperature ranges of CO (-20 to 42°C) and methane (CH4; -20 to 30°C) oxidation are also wider than expected, though thermal sensitivity patterns conform with general theory. Metagenomic analyses, including generation of 554 medium- to high-quality metagenome-assembled genomes, support these data, revealing that aerotrophs are widespread, diverse, and abundant, and suggesting most Antarctic bacteria function below their temperature optima for these processes. Modelling of seasonal temperatures across ice-free Antarctica under current and future emissions scenarios indicates that H2 and CO oxidation can occur year-round, increasing by up to 35% or 44%, respectively, by 2100. Our results indicate constitutive aerotrophic activity contributing to Antarctic ecosystem functioning and biodiversity across spatial and temporal scales, with further studies required to understand how it interacts with photosynthesis in a changing climate.}, } @article {pmid41665524, year = {2026}, author = {Gao, W and Li, X and Wang, G and Ning, Z and Wang, W and Wang, Y and Wang, H and Lu, D and Zhang, Q}, title = {A Broad-Spectrum Polysaccharide Lyase CHa2 from Marine Metagenome Exhibits Dual Activities toward Glycosaminoglycans and Alginate.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {7}, pages = {6386-6397}, doi = {10.1021/acs.jafc.5c15335}, pmid = {41665524}, issn = {1520-5118}, mesh = {*Polysaccharide-Lyases/chemistry/metabolism/genetics ; *Glycosaminoglycans/metabolism/chemistry ; *Alginates/metabolism/chemistry ; Substrate Specificity ; Metagenome ; Glucuronic Acid/metabolism/chemistry ; *Bacterial Proteins/chemistry/genetics/metabolism ; Hydrogen-Ion Concentration ; Hexuronic Acids/metabolism/chemistry ; Enzyme Stability ; Kinetics ; *Aquatic Organisms/genetics/enzymology ; }, abstract = {Polysaccharide lyase family 8 (PL8), which comprises glycosaminoglycans (GAGs) lyases, xanthan lyases, and alginate lyases, is an important family of Carbohydrate-Active Enzymes database. In this study, a PL8 family enzyme, CHa2, which can degrade GAGs and alginate, was identified. CHa2 exhibits the highest activity at 40/50 °C and pH 8.0, and the enzyme activities toward HA, CSA, CSC, CSD, CSE, alginate, polyM, and polyG are 54.6, 161.1, 204.0, 163.6, 66.1, 4.0, 4.1, and 0.3 U/mg, respectively. CHa2 degrades CS and HA to generate disaccharides and tetrasaccharides as the final products in the endolytic mode. And when degrading alginate, CHa2 prefers to catalyze the M-rich regions. Though they showed higher activity toward CS, the tetrasaccharides like ΔC-A, ΔA-A, and ΔD-A would resist the degradation of CHa2. The study of CHa2 provides a tool enzyme capable of selectively preparing specific structural functional oligosaccharides, which has potential application value in functional food, biomedical, and other fields.}, } @article {pmid41666027, year = {2026}, author = {Lim, FS and González-Cabrera, J and Jehle, JA and Lefebvre, T and Wennmann, JT}, title = {No longer uncertain: the validation of tenebrionid insects as hosts of Blattambidensovirus incertum1 isolates by phylogeny and infection studies.}, journal = {The Journal of general virology}, volume = {107}, number = {2}, pages = {}, pmid = {41666027}, issn = {1465-2099}, mesh = {Animals ; Phylogeny ; *Tenebrio/virology ; Larva/virology ; *Densovirus/genetics/isolation & purification/classification ; Metagenomics ; Genome, Viral ; Pupa/virology ; }, abstract = {The mealworm (Tenebrio molitor) is one of the most commonly mass-reared insects for food and feed. Monitoring the health status of commercially reared mealworm populations is of great importance for the early detection of entomopathogens and for preventing pathogen outbreaks. Metagenomic screening is a suitable and commonly used method for detecting entomopathogens. The approach used here previously enabled the discovery of the Tenebrio molitor densovirus (TmDV) (family Parvoviridae, subfamily Densovirinae) in symptomatic larvae. In the present study, the search for TmDV was extended to larvae, pupae and adults of T. molitor, including 19 symptomatic and asymptomatic samples obtained from a commercial mealworm mass-rearing facility. The presence of TmDV in all life stages of T. molitor was demonstrated, and its relative abundance was quantified using Nanopore sequencing. The infectivity of TmDV to T. molitor was demonstrated by isolating viral particles from sample LD2 and feeding them to mealworms. The experiment confirmed T. molitor as a susceptible host but showed a rather asymptomatic course of the infection with little effect on larval growth during 56 days of observation. It is hypothesized that this largely covert infection may explain the lack of reports of TmDV in mealworms or other insects, despite its detection in metagenomics surveillance studies of various insectivorous vertebrates. The complete genomes of 15 different TmDV genotypes present in various ratios in the different life stages of T. molitor could be reconstructed. Including these genotype sequences in phylogenetic analyses allowed us to re-evaluate the relationship and diversity of previously reported TmDV and related isolates, all belonging to the species Blattambidensovirus incertum1. Our findings suggest that T. molitor and possibly other insects are susceptible hosts of viruses of Blattambidensovirus incertum1, while its occasional detection in metagenomic datasets of insectivorous vertebrates may not represent true densovirus host associations.}, } @article {pmid41666437, year = {2026}, author = {Kohsar, M and Haar, M and Schmidt-Chanasit, J and Ramharter, M and Buchholz, BM and Krasemann, S and Bernreuther, C and Cadar, D and Omansen, TF and Wichmann, D and Ko, LM and Jordan, S}, title = {Fatal Dengue Fever in a Traveler Returning from Togo to Germany.}, journal = {The American journal of tropical medicine and hygiene}, volume = {114}, number = {4}, pages = {720-723}, pmid = {41666437}, issn = {1476-1645}, mesh = {Humans ; *Dengue/complications/diagnosis ; Germany ; *Travel ; Fatal Outcome ; Togo ; Male ; Adult ; }, abstract = {A previously healthy traveler of Togolese origin visiting friends and relatives presented with severe dengue complicated by acute liver failure. Despite intensive care management and listing for high-urgency liver transplantation, the patient succumbed to the disease. This case highlights the risk for life-threatening travel-related complications of dengue.}, } @article {pmid41666549, year = {2026}, author = {Kang, X and Zhao, Z and Zhu, X and Ju, F}, title = {Uncovering plasticizer-degrading potential in landfill microbiomes with curated PzDE-HMM database and multi-scale validation from isolates to synthetic consortia.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141398}, doi = {10.1016/j.jhazmat.2026.141398}, pmid = {41666549}, issn = {1873-3336}, mesh = {*Plasticizers/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Waste Disposal Facilities ; *Bacteria/metabolism/genetics/isolation & purification ; Phthalic Acids/metabolism ; Microbial Consortia ; }, abstract = {Plasticizers are widely used additives that leach from plastic products and accumulate in landfills, yet the microbial functions supporting their degradation remain poorly resolved. Here, we combined curated functional annotation, substrate-driven enrichment, and isolate-level validation to dissect plasticizer degradation in landfill microbiomes. A plasticizer-degrading enzyme (PzDE) hidden Markov model database (PzDE-HMM) was assembled from 49 experimentally validated enzyme families. It was applied to metagenomes from five landfill niches, identifying 2219 candidate plasticizer-degrading genes, which is 3.6- and 19-fold more than those identified by KofamScan- and BLASTp-based annotation methods, respectively. Enrichment with three legacy phthalates (DEHP, DIDP, DBP) and three non-phthalate plasticizers (DOTP, DOA, ATBC) drove pronounced shifts in landfill microbial communities and functional gene repertoires, revealing coexisting broad-spectrum and substrate-specific degraders. Culture-based isolation from enriched media yielded 51 strains, and three representative isolates showed concordance between PzDE-HMM-predicted gene repertoires, substrate breadth, and degradation ability. Synthetic consortia assembled from these strains exhibited complementary degradation capacities and achieved higher removal of several plasticizers than the best single strains, illustrating how complementary gene sets can be combined to enhance multi-substrate degradation. Together, PzDE-HMM annotation workflow and this multilevel prediction-enrichment-isolate-consortium framework uncover the plasticizer-degrading and bioremediation potential of landfill microbiomes and provide a reusable resource and workflow for future plasticizer-focused microbiome studies.}, } @article {pmid41666551, year = {2026}, author = {Cai, Y and Zhai, JY and Zhang, GH and Lin, MQ and Luo, YH}, title = {Biodegradation of three xanthates with different carbon chains in flotation wastewater.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141392}, doi = {10.1016/j.jhazmat.2026.141392}, pmid = {41666551}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; *Wastewater/chemistry ; *Water Pollutants, Chemical/metabolism ; *Carbon/chemistry ; Bioreactors ; Biofilms ; Bacteria/metabolism/genetics ; }, abstract = {Xanthates are widely used collectors in sulfide ore flotation, but pose ecological risks due to their toxicity and the releasing of carbon disulfide (CS2). This study systematically investigated the biodegradation of three representative xanthates-potassium amyl xanthate (PAX), potassium butyl xanthate (PBX), and potassium isopropyl xanthate (PIX)-in an oxygen-based membrane biofilm reactor (O2-MBfR). The O2-MBfR achieved over 98 % removal of all xanthates across surface loadings up to 6000 mg-COD/m[2]·d, with corresponding COD removals of 62-90 %. While PIX exhibited slightly lower COD removal due to the slower oxidation of its branched isopropyl group, functional gene analyses revealed the co-enrichment of alcohol and sulfur oxidation genes (adh, ALDH, soxABC/XYZ, fccAB) and C-S bond cleavage genes (cynT, ssuD). Metagenomic and metatranscriptomic results showed that Pseudomonas and Rhodanobacter predominated in PIX degradation, whereas Thiobacillus, Zoogloea, and Ottowia were mainly involved in PAX and PBX oxidation. Monod kinetics indicated that PIX had the highest maximum specific degradation rate (33.85 mg/gVSS/h) and lowest sCOD decay rate constant (0.29 h[-1]), reflecting strong microbial affinity but limited mineralization. Continuous-flow treatment of real flotation wastewater achieved > 98 % xanthate and ∼85 % COD removal, confirming system robustness. These findings provide mechanistic insight into the structure-dependent biodegradability of xanthates and demonstrate the feasibility of O2-MBfR technology for sustainable treatment of flotation wastewater.}, } @article {pmid41666717, year = {2026}, author = {Zhang, B and Qian, G and Xie, C and Qiao, S}, title = {Microbial quorum quenching mitigates biofouling from polyvinyl chloride pipes in industrial circulating water systems.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128870}, doi = {10.1016/j.jenvman.2026.128870}, pmid = {41666717}, issn = {1095-8630}, mesh = {*Biofouling/prevention & control ; *Quorum Sensing ; Extracellular Polymeric Substance Matrix ; }, abstract = {To destabilize biofouling resulting from extracellular polymeric substances (EPS) in industrial circulating water systems, this study introduces a quorum sensing (QS)-based inhibition strategy using methyl anthranilate (MA) to disrupt biofouling structure. Strategical application of a low dose of MA at 1 mM reduced EPS content by 48.0 ± 5.2% and decreased biofouling thickness by 25.7 ± 5.0% (from 68.6 ± 2.8 to 51.0 ± 4.0 μm) compared to the control group. Further analysis indicated that MA altered secondary structure of EPS proteins, resulting in hydrogen bonds breakage and structural unfolding, thereby compromising biofouling stability and integrity. Metagenomic profiling revealed a significant downregulation of EPS-biosynthesis pathways (amino acid and carbohydrate metabolism) and QS-and EPS-related genes (trpE and nagB) following MA exposure. Microbial diversity analysis showed a substantial reduction in the abundance of key genera (e.g., Candidatus Kuenenia, Mycobacterium, Ideonella) harboring EPS- and QS-associated genes in response to MA treatment. Moreover, co-occurrence network analysis demonstrated that MA exposure triggered the loss of keystone taxa, leading to systematic destabilization of the biofouling layer. These findings underscore the potential and utility of MA-based QS inhibition as an effective and targeted approach for biofouling control in circulating water pipelines, which could inform important clues for anti-biofouling development in engineered water systems.}, } @article {pmid41666722, year = {2026}, author = {Mo, J and Guo, Z and Shao, M and Hu, Z and Liu, F and Guan, X}, title = {Nitrogen pollution alters bacterial carbonate mineralization potential in karst river.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128942}, doi = {10.1016/j.jenvman.2026.128942}, pmid = {41666722}, issn = {1095-8630}, mesh = {*Nitrogen ; *Rivers/microbiology/chemistry ; *Carbonates ; *Bacteria/metabolism ; Carbonic Anhydrases/metabolism ; }, abstract = {Karst systems represent critical carbon sinks where microbial-mediated carbonate precipitation is influenced by anthropogenic nitrogen pollution. This study investigated nitrogen pollution impacts on microbial mineralization in karst rivers using physicochemical and metagenomic analyses. Proteobacteria and Actinobacteria dominated carbonic anhydrase-producing bacterial communities, with β-carbonic anhydrases being most abundant (84.51%). Nitrogen pollution significantly reduced the diversity and relative abundance of these bacteria and drove variations in their community structure. This further triggered a cascade of changes in carbonic anhydrase activity, bicarbonate concentration, and total alkalinity. Co-occurrence network analysis showed that increased nitrogen pollution weakened interactions between carbonic anhydrase-producing and other non-producing bacteria. Functional analysis revealed that nitrogen pollution significantly impaired the potentials of alkalinity engine metabolism (particularly the Calvin-Benson-Bassham cycle and fatty acid catabolism), extracellular polysaccharides biosynthesis, and Mycobacterium cell wall formation. Furthermore, carbonate mineralization degenerates markedly beyond a critical threshold of ∼22 mg/L total inorganic nitrogen. These findings provide guidance for water resource management and establish a foundation for future carbon budget assessments in karst systems under anthropogenic influence.}, } @article {pmid41666743, year = {2026}, author = {Tong, J and Zhang, W and Yu, F and Liu, R and Yan, Y and Li, Y}, title = {Flow regime specific regulation shapes microbial-mediated nitrogen cycling of plain tidal river network.}, journal = {Water research}, volume = {294}, number = {}, pages = {125510}, doi = {10.1016/j.watres.2026.125510}, pmid = {41666743}, issn = {1879-2448}, mesh = {*Rivers/microbiology ; *Nitrogen Cycle ; Water Movements ; Ecosystem ; Hydrodynamics ; Nitrogen ; }, abstract = {Inter-basin water diversion projects are critical for mitigating regional water scarcity yet impose complex ecological pressures on recipient river networks. Understanding their microbial impacts is essential to optimize sluice operations and minimize ecosystem disruption. As pivotal regulators of biogeochemical cycles and ecological health, microbial communities in plain tidal networks remain poorly characterized under diversion-induced hydrodynamic shifts. This study integrated intensive field sampling across water and sediment sites in the lower tidal plain river network with a calibrated one-dimensional MIKE 11 hydrodynamic model, stratifying sampling points into low, medium, and high flow-velocity regimes. Results indicate a positive correlation between hydrological regime stability and microbial community stability. While community composition reorganizes along the flow gradient, microbial diversity and core taxa abundance remain resilient. Co-occurrence network analysis reveals that intermediate flow variability maximizes network connectivity and modular cohesion, whereas extreme hydrological conditions fragment network structures. Landscape modeling further identifies high-discharge variability zones as distinct "hotspots" for denitrification and organic matter processing, while hydrologically stable reaches act as "functional shadows" (coldspots). Structural equation modeling confirms that hydrological regulation operates not merely through direct physical forcing but via a "resource-diversity-function" cascade, indirectly driving biogeochemical cycles by modulating nutrient fluxes and reshaping microbial diversity. Consequently, this study recommends shifting management strategies toward maintaining intermediate flow variability to reinforce the robustness and self-purification capacity of riverine ecological networks.}, } @article {pmid41666744, year = {2026}, author = {Kelly, LT and Beach, DG and Blaszczak, JR and Bouma-Gregson, K and Brown, SM and Cheng, H and Davidson, JL and Fastner, J and Francis, M and Jimenez, AG and Genzoli, L and Goel, R and Gonzalez, D and Handley, KM and Hilt, S and Humbert, JF and Jamieson, R and Johnston, L and Junier, P and Lawrence, J and McCarron, P and Meissner, S and Mormando, J and Puddick, J and Quiblier, C and Rajpirathap, N and Schampera, C and Selwood, A and Shearer, K and Sohrab, A and Stancheva, R and Valadez-Cano, C and Zabrecky, JM and Wood, SA}, title = {The global proliferation of aquatic, benthic Microcoleus: Taxonomy, distribution, toxin production, ecology, and future directions.}, journal = {Water research}, volume = {294}, number = {}, pages = {125441}, doi = {10.1016/j.watres.2026.125441}, pmid = {41666744}, issn = {1879-2448}, mesh = {Ecosystem ; Animals ; Tropanes ; Fresh Water ; Ecology ; }, abstract = {There have been sporadic reports of aquatic, benthic Microcoleus proliferations in freshwater rivers, lakes, and reservoirs for four decades, with reports increasing in frequency over the last twenty years, suggesting a possible rise in their global distribution, frequency, and intensity. Microcoleus can produce anatoxins which are neurotoxic, and ingestion of toxic mats has caused hundreds of dog fatalities and raised serious human and ecological health concerns. This review synthesizes and evaluates current knowledge on Microcoleus distribution, taxonomy, toxin production, toxicity, ecology, environmental drivers, and biotic interactions. Toxin-producing Microcoleus have been reported in at least 18 countries, though many regions have not conducted toxin testing, suggesting a broader but under-reported distribution. Proliferations occur across diverse habitats, including cobble-bedded streams, large sandy rivers, reservoirs, and lakes. Microcoleus proliferations also occur on macrophytes, both in lakes and rivers. Genomic analyses currently classify anatoxin-producing Microcoleus into distinct species, with all known anatoxin-producers isolated from freshwater ecosystems. Anatoxin concentrations vary widely over space and time, within and among waterbodies. While studies on environmental drivers remain limited, research in cobble-bedded rivers suggests that moderate enrichment of dissolved inorganic nitrogen and low dissolved reactive phosphorus concentrations in the water column promote proliferation. Metagenomic approaches have revealed unique nutrient acquisition and storage strategies used by Microcoleus. Key knowledge gaps remain around the environmental and ecological triggers of proliferation, toxin production, genomic diversity and microbial interactions. Addressing these gaps through coordinated, global studies using robust datasets and consistent methods is critical to improve prediction, monitoring, and mitigation of this increasingly widespread public and ecological health threat.}, } @article {pmid41666834, year = {2026}, author = {S, H and A, P}, title = {Insights into microbial carbon sequestration mechanisms in the Eastern Arabian Sea using metagenomic analysis.}, journal = {Marine environmental research}, volume = {216}, number = {}, pages = {107903}, doi = {10.1016/j.marenvres.2026.107903}, pmid = {41666834}, issn = {1879-0291}, mesh = {*Carbon Sequestration ; Seasons ; *Seawater/microbiology ; Metagenomics ; *Microbiota ; Bacteria/classification/genetics/metabolism ; *Environmental Monitoring ; Oceans and Seas ; *Water Microbiology ; }, abstract = {This investigation elucidated how depth- and season-dependent environmental gradients shape microbial community composition, metabolic potential, and carbon sequestration pathways in the Eastern Arabian Sea (EAS). The study encompassed six stations (L1-L6) spanning coastal to offshore regimes, three depth zones (surface, 200 m, and 1000 m), and three monsoonal phases: Spring Inter-Monsoon (SIM), Summer Monsoon (SM), and Winter Monsoon (WM). A total of 10,500 taxa were identified across all samples. Alpha-diversity indices showed peak diversity during the SM and SIM periods. Across all depths, Pseudomonadota (53.2 ± 16.2%) remained the dominant phylum, underscoring its broad ecological adaptability. Cyanobacteria (31.3 ± 19%) were abundant in surface waters during SIM and WM, but declined sharply with depth (<2%), where Actinomycetota dominated (25 ± 16%), highlighting strong vertical niche portioning. Distinct seasonal restructuring was evident, particularly during the SM, when upwelling-driven nutrient enrichment resulted in a marked decline in Cyanobacteria and a concomitant increase in copiotrophic taxa such as Rhodobacterales, Flavobacteriales, Pseudomonadales, and Oceanospirillales, indicative of intensified heterotrophic processing of organic matter. In contrast, oligotrophic taxa (Pelagibacterales, Prochlorococcus, Synechococcus) prevailed during SIM and WM, suggesting nutrient-limited and microbially driven carbon cycling. Remarkably, even deep-water communities (200-1000 m) exhibited significant seasonal restructuring (p < 0.05), with Alteromonadales and Oceanospirillales enriched during SM and Sphingomonadales and Rhodobacterales dominating during WM, indicating active coupling between surface productivity and deep microbial assemblages. Functional analyses revealed pronounced depth-dependent stratification of metabolic potential (p < 0.05) reflecting shifts from growth-oriented processes in surface waters to adaptive and recycling strategies at depth. Collectively, these findings reveal robust monsoon-driven and depth-stratified microbial dynamics in the EAS and provide novel evidence inferred based on microbial community structure and functional potential that both the Biological Carbon Pump and the Microbial Carbon Pump operate concurrently across this climatically sensitive and highly productive region.}, } @article {pmid41666847, year = {2026}, author = {Matijašević, D and Kljajević, N and Malešević, M and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K}, title = {Heating-season dynamics of the airborne microbiome, resistome and mobilome in Belgrade, Serbia.}, journal = {Environment international}, volume = {208}, number = {}, pages = {110114}, doi = {10.1016/j.envint.2026.110114}, pmid = {41666847}, issn = {1873-6750}, mesh = {Seasons ; *Microbiota ; Serbia ; *Air Microbiology ; *Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Air Pollution/statistics & numerical data/analysis ; Air Pollutants/analysis ; Bacteria/genetics ; }, abstract = {Antimicrobial resistance (AMR) and air pollution are critical global health challenges, but their interplay remains poorly understood, particularly in Europe. Serbia, characterized by extensive antibiotic use, high prevalence of multidrug-resistant isolates and severe air pollution, provides a relevant model to study airborne AMR dissemination. During the heating season, air samples were collected at eight locations in Belgrade, representing industrial, traffic loaded and background environments. Shotgun metagenomics, co-occurrence networks and NMDS ordinations were applied to investigate the relationships between atmospheric pollutants, antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and mobile genetic elements (MGEs). Autumn microbiomes were dominated by Lactococcus spp., whereas winter lacked such dominance. ARGs associated with antibiotic inactivation accounted for > 50% in autumn and > 75% in winter, with β-lactam resistance (blaTEM) predominating in both seasons. Winter resistomes also showed more consistent patterns of BRGs and MRGs, with multibiocide/acid and multimetal resistance prevailing. Integron analysis revealed predominance of class 1 integrons (intI1) commonly associated with Escherichia coli. Plasmid-related contigs were most similar to sequences reported in Acinetobacter baumannii and E. coli, while plasmid signatures related to Lactococcus lactis were also detected in autumn. Crucially, the network analysis revealed a seasonal restructuring of the airborne resistome. Autumn networks displayed fragmented structure, showing antagonism between Lactococcus and Escherichia, whereas winter networks coalesced into a densely interconnected superhub that could facilitate horizontal gene transfer and co-selection of resistance determinants. These findings suggest that prolonged air pollution and seasonality jointly shape airborne resistomes, reinforcing the need for integrated environmental and AMR surveillance in highly polluted urban areas.}, } @article {pmid41666920, year = {2026}, author = {da Silva, AC and Lapkin, J and Yin, Q and Muller, E and Almeida, A}, title = {Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health.}, journal = {Cell host & microbe}, volume = {34}, number = {3}, pages = {379-392.e5}, doi = {10.1016/j.chom.2026.01.013}, pmid = {41666920}, issn = {1934-6069}, mesh = {Humans ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Health ; Vitamin B 12/biosynthesis ; }, abstract = {The human gut microbiome is important for host health, yet over 60% of gut species remain uncultured and inaccessible to experimental manipulation. Here, we analyze 11,115 human gut metagenomes from 39 countries, 13 noncommunicable diseases, and healthy individuals to understand the clinical relevance of the uncultured microbiome worldwide. We identify 317 species linked to distinct clinical states, noting an overrepresentation of uncultured bacteria in healthy subjects. The genus CAG-170 emerged as the strongest health-associated lineage across multiple diseases and geographies, standing as the most central taxon based on ecological networks of healthy populations. We find that CAG-170 is temporally stable, with its abundance and subspecies diversity negatively correlated with gut imbalance over time. Functional predictions show CAG-170 species have greater vitamin B12 biosynthesis capacity and cross-feeding potential, providing important biological insights into this elusive genus. Our findings shed light on the underexplored role of uncultured gut species in health and disease.}, } @article {pmid41666926, year = {2026}, author = {Kim, CY and Podlesny, D and Schiller, J and Khedkar, S and Fullam, A and Orakov, A and Schudoma, C and Robbani, SM and Grekova, A and Kuhn, M and Bork, P}, title = {Planetary microbiome structure and generalist-driven gene flow across disparate habitats.}, journal = {Cell}, volume = {189}, number = {7}, pages = {2073-2091.e21}, doi = {10.1016/j.cell.2025.12.051}, pmid = {41666926}, issn = {1097-4172}, mesh = {*Microbiota/genetics ; *Ecosystem ; Humans ; *Gene Flow/genetics ; Metagenome/genetics ; Gene Transfer, Horizontal ; Metagenomics ; Bacteria/genetics/classification ; }, abstract = {Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersal, driven by natural processes and human activities, interconnects microbiomes across habitats, yet most comparative studies focus on specific ecosystems. To study planetary microbiome structure, function, and inter-habitat interactions, we systematically integrated 85,604 public metagenomes spanning diverse habitats worldwide. Using species-based unsupervised clustering and parameter modeling, we delineated 40 habitat clusters and quantified their ecological similarity. Our framework identified key drivers shaping microbiome structure, such as ocean temperature and host lifestyle. Regardless of biogeography, microbiomes were structured primarily by host-associated or environmental conditions, also reflected in genomic and functional traits inferred from 2,065,975 genomes. Generalists emerged as vehicles thriving and facilitating gene flow across ecologically disparate habitat types, illustrated by generalist-mediated horizontal transfer of an antibiotic resistance island across human gut and wastewater, further dispersing to environmental habitats, exemplifying human impact on the planetary microbiome.}, } @article {pmid41667020, year = {2026}, author = {Lawal, MS and Hayashida, K and Sugi, T and Omoare, AA and Bile, N and Maikudi, HI and James, POI and Villeng, F and Babatunde, O and Idris, J and Yamagishi, J}, title = {Detection of novel Pegivirus C genome in an unexplained febrile outbreak, Gombe State, Nigeria, 2024 by enhanced mNGS approach.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {165}, number = {}, pages = {108470}, doi = {10.1016/j.ijid.2026.108470}, pmid = {41667020}, issn = {1878-3511}, mesh = {Humans ; Nigeria/epidemiology ; *Disease Outbreaks ; *Genome, Viral ; Phylogeny ; *Flaviviridae Infections/epidemiology/virology/diagnosis ; *Pegivirus/genetics/isolation & purification/classification ; Female ; High-Throughput Nucleotide Sequencing/methods ; Male ; Child ; Metagenomics/methods ; Child, Preschool ; Adult ; *Fever/virology/epidemiology ; }, abstract = {OBJECTIVES: In July 2024, an outbreak of acute febrile illness occurred in Chassi village, Gombe State, Nigeria, affecting over 30 individuals, primarily children, with symptoms including fever, jaundice, abdominal pain, and mucosal bleeding. The cause remained unidentified after conventional diagnostics excluded known viral hemorrhagic fevers, malaria, and bacterial infections. This study aimed to investigate the potential etiologic agent behind the outbreak using unbiased genomic techniques.

METHODS: We employed a metagenomic next-generation sequencing (mNGS) strategy with viral enrichment to analyze serum samples from 22 symptomatic patients. A novel complete 9.3 kb genome of Pegivirus C (GOMBE-017-2025) was reconstructed and phylogenetically compared to global sequences. Detection was validated using targeted PCR and Sanger sequencing. Environmental and microbial testing were conducted on local water sources.

RESULTS: Pegivirus C was consistently detected in all 22 samples. The reconstructed genome showed 92.7% identity to a 2018 Nigerian strain and clustered with West African isolates. PCR and sequencing confirmed its presence. Environmental and bacterial sources were ruled out as causative agents.

CONCLUSION: The uniform detection of Pegivirus C in this localized outbreak raises concern over its potential pathogenic or co-pathogenic role. These findings support the need for further investigation into its transmission dynamics, tropism, and clinical relevance.}, } @article {pmid41667040, year = {2026}, author = {Liu, J and Guan, H and Hu, S and Lu, H and Tang, X and Tang, CJ}, title = {Dialysis-controlled sulfur substrate delivery enhances Sulfur-Autotrophic denitrification under oxygen stress.}, journal = {Bioresource technology}, volume = {446}, number = {}, pages = {134158}, doi = {10.1016/j.biortech.2026.134158}, pmid = {41667040}, issn = {1873-2976}, mesh = {*Denitrification/drug effects ; *Sulfur/metabolism ; *Oxygen/metabolism ; Bioreactors/microbiology ; *Dialysis/methods ; Nitrogen/isolation & purification ; *Autotrophic Processes/drug effects ; Nitrates ; Thiobacillus/metabolism ; *Stress, Physiological/drug effects ; }, abstract = {Sulfur autotrophic denitrification (SAD) is a low-carbon nitrogen removal process using reduced sulfur compounds as electron donors. However, dissolved oxygen (DO) disrupts SAD by promoting unproductive sulfur oxidation and electron loss. Here, dialysis membranes (1000 and 100 Da) were applied to regulate thiosulfate release and establish controlled substrate gradients under engineering-relevant inhibitory DO conditions (0.5-3.5 mg L[-1]). Compared with direct dosing (Rck), the 100 Da reactor (R100) achieved 19% higher nitrate removal efficiency and greater fraction of electrons allocated to denitrification (EDUden ≈ 76%), accompanied by pronounced zero-valent sulfur accumulation, indicating pathway-level reallocation. Microbial analyzes revealed enrichment of Thiobacillus-like sulfur-oxidizing denitrifiers and increased prevalence of oxygen tolerant nitrate reductase (napA), confirmed by metagenomic and qPCR. These results demonstrate that controlled sulfur release creates an electron-buffered microenvironment that enhances SAD resilience to DO, offering a donor-efficient strategy for nitrogen removal in oxygen-fluctuating wastewater systems.}, } @article {pmid41667136, year = {2026}, author = {Tarrant, E and Cormack, IG and Hunter, CE and Werbowy, O and Dorawa, S and Wang, L and Steen, IH and Sandaa, RA and Guðmundsdóttir, EE and Ketelsen-Striberny, B and Kaczorowska, AK and Kaczorowski, T and Pohl, E and Freitag-Pohl, S}, title = {Structure, function, and applications of two novel phage recombinases from extreme environments.}, journal = {Nucleic acids research}, volume = {54}, number = {4}, pages = {}, pmid = {41667136}, issn = {1362-4962}, support = {//European Union's Horizon 2020 Research/ ; 685778//Innovation Programme Virus-X project: Viral Metagenomics for Innovation Value/ ; EP/S022791/1//Engineering and Physical Sciences Research Council/ ; UMO-2019/34/H/NZ2/00584//Norway Financial Mechanism through the National Science Center/ ; A/SP/453344/202//Ministry of Education and Science/ ; }, mesh = {Models, Molecular ; Rec A Recombinases/chemistry/metabolism/genetics ; *Viral Proteins/chemistry/metabolism/genetics ; DNA, Single-Stranded/metabolism ; *Bacteriophages/enzymology ; *Recombinases/chemistry/metabolism/genetics ; Amino Acid Sequence ; Molecular Sequence Data ; Crystallography, X-Ray ; DNA-Binding Proteins ; Escherichia coli Proteins ; }, abstract = {This study describes the identification and characterization of two new extremophilic phage recombinases, UvsXt and UvsXp, discovered through metagenomic analysis within the Virus-X project, and explores their potential applications in biotechnology. DNA recombinases are essential for maintaining genome integrity across all kingdoms of life by facilitating homologous recombination and repairing double-stranded DNA breaks. Their capacity to bind and stabilize single-stranded DNA (ssDNA) has led to wide-ranging applications in molecular biology. UvsXt and UvsXp show homology with known bacterial RecA and viral UvsX recombinases, including conservation of key catalytic residues and DNA-binding motifs. Biochemical assays reveal that both enzymes exhibit superior DNA strand-exchange activity compared to Escherichia coli RecA. High-resolution crystal structures of UvsXt (2.0 Å) and UvsXp (2.6 Å) confirm a conserved RecA-like core fold, with distinct structural variation at the N-terminus responsible for oligomerization. However, in spite of their similarities, we show that neither enzyme is capable to functionally replace RecA in E. coli. Their remarkable thermostability and functionality across diverse chemical environments highlights their robustness for biotechnological use. Notably, UvsXt enhances loop-mediated isothermal amplification of viral RNA by stabilizing ssDNA intermediates. These findings expand the repertoire of thermostable recombinases with potential utility in diagnostic applications.}, } @article {pmid41667306, year = {2026}, author = {Tong, Y and Chen, Y and Dong, Y and Chen, K and Yang, J and Dong, X and Wan, X and Luo, Z and Fang, J and Liu, Y and Li, W and Wang, Z and Gu, X}, title = {Characterization of the oral microbiota of Kawasaki disease patients by metagenomic analysis: A pilot study.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmii.2026.01.007}, pmid = {41667306}, issn = {1995-9133}, abstract = {BACKGROUND: Kawasaki disease (KD) is an acute febrile systemic vasculitis characterized by vascular inflammation. Its pathogenesis has been linked to the infiltration of IgA[+] plasma cells within the respiratory tract, suggesting the upper airway may act as a potential portal of entry. However, evidence connecting respiratory infections to KD remains limited. This study aimed to explore the relationship between oral microbiota and KD development.

METHODS: Oral swab samples were collected from 25 KD patients before and after intravenous immunoglobulin (IVIG) treatment, as well as from 25 healthy controls. Metagenomic sequencing was performed to characterize overall microbial composition and identify potential microbial markers associated with KD.

RESULTS: Significant alterations in oral microbiota composition were observed between KD patients and healthy controls. The diversity of oral microbiota in KD patients was markedly lower than that in healthy controls, and exhibited an upward trend following IVIG treatment. Elevated levels of Streptococcus, Prevotella, and Veillonella, along with reduced levels of Haemophilus, Neisseria, and Rothia, were closely associated with KD development. Putative novel pathogen Abiotrophia defectiva was significantly enriched in patients with KD. Correlation analysis revealed that the relative abundances of several Haemophilus species were positively correlated with albumin levels in KD patients before IVIG treatment. Additionally, the anti-inflammatory bacterium Rothia mucilaginosa may play a protective role against the development of coronary artery lesions in KD.

CONCLUSION: These findings provide new evidence that distinct alterations in the oral microbiome are associated with KD development. Oral microbiota-based biomarkers may represent a potential strategy for KD therapy.}, } @article {pmid41667397, year = {2026}, author = {Le Bastard, Q and Gschwind, R and Lao, J and Vibet, MA and Batard, E and Corvec, S and Montassier, E and Ruppé, E}, title = {Pre-existing β-lactamase gene diversity is associated with lower risk of ESBL-producing Enterobacterales colonization in patients exposed to ceftriaxone.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2627692}, pmid = {41667397}, issn = {1949-0984}, mesh = {Humans ; *beta-Lactamases/genetics/metabolism ; *Ceftriaxone/therapeutic use/administration & dosage ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Prospective Studies ; *Enterobacteriaceae Infections/microbiology/drug therapy ; *Enterobacteriaceae/genetics/enzymology/drug effects/isolation & purification ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Third Generation Cephalosporins ; Middle Aged ; Aged ; Genetic Variation ; Second Generation Cephalosporins ; }, abstract = {Exposure to broad-spectrum antibiotics, particularly to third-generation cephalosporins (3GC), increases the risk of colonization by extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E). While clinical risk factors for ESBL-E acquisition are well established, the role of the gut microbiome and resistome remains unclear. We conducted a prospective study of patients with suspected bacterial infections receiving ceftriaxone to identify microbiome and resistome features associated with ESBL-E acquisition. Rectal samples collected before antibiotic administration, during treatment, and 30 d after initiation were analyzed by shotgun metagenomic sequencing. Among 80 patients, 12 (15%) acquired ESBL-E colonization by day 30. Ceftriaxone exposure induced a profound and sustained reduction in microbial richness and diversity across all patients. However, no specific taxonomic signature predicted subsequent ESBL-E colonization. In contrast, patients who did not acquire ESBL-E displayed a significantly richer and more diverse repertoire of β-lactamase-encoding genes at baseline, which was independently associated with protection against colonization. Moreover, patients exposed to multiple antibiotics experienced greater and more sustained microbiome disruption compared with those receiving ceftriaxone alone. These findings provide the first real-world evidence that pre-existing β-lactamasome diversity may confer ecological protection against antibiotic-driven colonization by ESBL-E in infected patients, highlighting the importance of functional resistome diversity over taxonomic composition in colonization resistance.}, } @article {pmid41667950, year = {2026}, author = {Rodrigues, GVP and Ferreira, LYM and Aguiar, ERGR}, title = {ViralQuest: a user-friendly interactive pipeline for viral-sequences analysis and curation.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {41667950}, issn = {1471-2105}, support = {Financial Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {BACKGROUND: High-throughput sequencing (HTS) has become an essential, unbiased tool in virology for identifying known and novel viruses. However, analyzing the large and complex datasets generated by HTS presents significant bioinformatics challenges. The process of accurately identifying and characterizing viral sequences from assembled contigs remains a bottleneck, often requiring specialized expertise and involving non-standardized parameters. There is a pressing need for robust, user-friendly, and reproducible pipelines to streamline this post-assembly analysis. RESULTS: To address these challenges, we developed ViralQuest, a bioinformatics tool that automates the in-depth characterization of viral sequences from pre-assembled contigs. The pipeline integrates multiple lines of evidence for robust identification, using Diamond BLASTx against the Viral RefSeq database and pyHMMER searches against the RVDB, Vfam, and eggNOG profile HMM databases. For detailed characterization, ViralQuest performs taxonomic classification based on the ICTV nomenclature and functional annotation via Pfam domain analysis. Novel features of ViralQuest include an AI-powered summarization module that uses a Large Language Model (LLM) to generate contextual narratives for key viral findings and a comprehensive confidence score to rank putative viral contigs. All results are consolidated into a single, interactive HTML report that includes dynamic visualizations of contigs, ORFs, and protein domains, alongside detailed data tables that are exportable in TSV and SVG formats. CONCLUSION: ViralQuest provides an accessible and comprehensive solution for the post-assembly analysis of viral metagenomic data. By combining rigorous bioinformatics methods with novel AI-driven features and an intuitive reporting interface, it streamlines the complex process of viral identification and characterization. The tool enhances the interpretability and reliability of results, making in-depth virome analysis more accessible to the broader research community. ViralQuest is available on GitHub at https://github.com/gabrielvpina/viralquest/ .}, } @article {pmid41668110, year = {2026}, author = {Fujii, H and Sato, M and Nguyen, HAT and Vu, HTT and Kakiuchi, S and Dhoubhadel, BG and Nakamura, S and Motooka, D and Ogura, Y and Nakano, S and Parry, CM and Morimoto, K and Yoshida, LM and Anh, DD and Hayashi, T and Iida, T and Ariyoshi, K}, title = {Genomic analysis of the genetic background underlying Streptococcus pneumoniae beta-lactam nonsusceptibility in central Vietnam: increased beta-lactam nonsusceptibility and dynamics of the pbp2x gene.}, journal = {Tropical medicine and health}, volume = {54}, number = {1}, pages = {}, pmid = {41668110}, issn = {1348-8945}, support = {2014-Ippan-10, 2015-Ippan-25//Institute of Tropical Medicine, Nagasaki University/ ; }, abstract = {BACKGROUND: We previously reported alarmingly high carriage rates of Streptococcus pneumoniae (SP) serotype 19F and serogroup 6 isolates, which were not susceptible to multiple beta-lactams among children under five years of age in Vietnam. Multilocus sequence typing analysis revealed the predominance of two major lineages, ST320 and ST13223, among serotype 19F and serogroup 6 isolates, respectively. Investigating the association between nonsusceptible genotypes and clinical outcomes could help optimize patient care or lead to the development of new diagnostic tests.

METHODS: We performed WGS on SP isolates randomly selected from the two major lineages and their related strains. FASTQ quality control and de novo assembly were performed using CLC Genomics Workbench ver. 7.5.1. Draft genome sequences were annotated using DFAST (DDBJ Fast Annotation and Submission Tool), which revealed the serogroups/serotypes and the sequences of the three major penicillin-binding protein genes and the sequence types. Draft sequences were aligned using MUMmer ver. 3.23, and putative recombination events and phylogenetic relationships excluding recombination regions were identified using Gubbins ver. 2.4.1. Finally, the association between a detected nonsusceptible genotype and the duration of hospital stay was evaluated in patients with acute respiratory infection.

RESULTS: WGS analysis (serotype 19F/ST320, n = 22; serogroup 6/ST13223, n = 13; and isolates closely related to ST13223, n = 4) revealed substantial differences in genomic diversity and antimicrobial susceptibility between serogroup 6/ST13223 and serotype 19F/ST320 isolates, particularly the recombination-prone nature of serogroup 6/ST13223. Among the 23 recombination events observed in serogroup 6/ST13223, only those spanning the pbp2x region (15.5 kb and 6.4 kb) were associated with high MICs for multiple beta-lactams. A subset of ST13223 isolates and all ST320 isolates carried the identical pbp2x allele 16, which was significantly associated with a lack of susceptibility to the combination of penicillin, cefotaxime, and meropenem (p < 0.0001; odds ratio 11.5; 95% confidence interval [CI] 3.35-39.3). No significant association was demonstrated between the presence of this pbp2x allele and prolonged hospitalization (p = 0.6123).

CONCLUSIONS: We revealed that the widespread nonsusceptibility to multiple beta-lactams among SP isolates circulating in central Vietnam was primarily driven by the dynamics of the pbp2x gene. However, the nonsusceptible pbp2x allele had little effect on clinical outcome.}, } @article {pmid41668124, year = {2026}, author = {Zhang, R and Debeljak, P and Gadegaonkar, SS and Baudet, C and Ringard, A and Blain, S and Obernosterer, I}, title = {Microbial membrane transporters reveal trace metal niche adaptation in distinct water masses of the Southern Ocean.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41668124}, issn = {2049-2618}, support = {202006220057//China Scholarship Council/ ; ANR19-CE01-0012//Agence Nationale de la Recherche/ ; }, mesh = {*Membrane Transport Proteins/genetics/metabolism ; *Seawater/microbiology/chemistry ; *Trace Elements/metabolism ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Indian Ocean ; *Metals/metabolism ; Iron/metabolism ; Copper/metabolism ; Homeostasis ; Adaptation, Physiological ; Nickel/metabolism ; Manganese/metabolism ; Bacterial Proteins/genetics/metabolism ; }, abstract = {BACKGROUND: Trace metals are co-factors for enzymes that are essential for microbial metabolism and the cycling of major elements. Membrane transporters allow microbes to sense and react to trace elements in the environment and to balance their uptake and export for the regulation of intracellular metal homeostasis. The acquisition and efflux of trace metals could lead to reciprocal feedbacks between microbes and the surrounding environment. Whether these processes vary among trace metals and across habitats is presently not known. We used membrane transporters into and out of the cell as indicators for the uptake and efflux of trace metals and provide a detailed picture of the distribution of the respective genes in distinct provinces in surface waters and in subsurface water masses across a transect in the Southern Indian Ocean.

RESULTS: We observed marked spatial and vertical patterns in normalized gene abundances of transporters of iron (Fe), manganese (Mn), nickel (Ni) and copper (Cu). Changes in gene abundances were specific to the type of transporter and trace metal, and pronounced differences between surface and specific water masses emerged. We found an enrichment in genes related to efflux and homeostasis of Fe, Ni and Cu in two water masses of the deep ocean that are North Atlantic Deep Water (NADW) and Lower Circumpolar Deep Water (LCDW). This pattern was observed on the community level and for metagenome-assembled genomes (MAGs) affiliated with Alteromonadaceae and Burkholderiaceae that were abundant in these two water masses.

CONCLUSIONS: The enrichment in trace metal efflux and resistance genes points to microbially mediated processes, exerted by homeostasis, with potential influence on the trace metal speciation and distribution in specific water masses in the deep ocean. The gene repertoire and distinct distribution pattern of the taxa identified as potential key players could reflect an adaptation to these old water masses with trace metals acting as selective driver. Video Abstract.}, } @article {pmid41668418, year = {2026}, author = {Moguel, B and Carrillo Olivas, L and Guerrero-Osornio, MG and Herrera Paredes, S}, title = {Recent Microbial Evolutionary Insights From Metagenomics.}, journal = {Genome biology and evolution}, volume = {18}, number = {3}, pages = {}, pmid = {41668418}, issn = {1759-6653}, support = {2022-000002-01NACF-03333//DGAPA-PAPIIT/ ; 2023-000002-01NACF-03323//SECIHTI/ ; IN212524//SECIHTI/ ; //DGAPA-PAPIIT/ ; }, mesh = {*Metagenomics/methods ; *Evolution, Molecular ; *Microbiota/genetics ; *Biological Evolution ; Phylogeny ; Humans ; DNA, Ancient ; Genome, Microbial ; }, abstract = {Microorganisms have profoundly shaped Earth's biological and geological history, from the origins of oxygenic photosynthesis to present-day global biogeochemical cycles. Metagenomics-through its ability to recover genomic information directly from environmental samples-has revolutionized our understanding of microbial evolution by uncovering unbeknownst lineages, revealing functional adaptations, and reshaping our view of the Tree of Life. By bypassing the need for cultivation, shotgun metagenomics and metabarcoding approaches have enabled researchers to investigate microbial diversity, ecology, and evolutionary processes across aquatic, terrestrial, extreme, and host-associated environments. This review highlights recent advances in evolutionary biology driven by metagenomics, including studies on deep evolutionary branching events, microbial adaptation to extreme environments, the evolution of host-associated microbiomes, and the emergence and spread of pathogens and antimicrobial resistance. The integration of ancient DNA has expanded our ability to reconstruct past ecosystems and disease dynamics, offering insights into long-term microbial evolution. In parallel, studies of microbial domestication and urban settings reveal how human practices have shaped microbial genomes over millennia. Despite significant progress, key challenges remain-including improving bioinformatic tools for degraded ancient DNA, resolving deep phylogenetic relationships, identifying adaptive variants, and linking genomic shifts to ecosystem-level processes. The future of microbial evolutionary research will depend on combining longitudinal metagenomic data, experimental evolution, functional assays, and predictive modeling to better understand microbial responses to climate change and anthropogenic pressures. Together, these approaches will deepen our understanding of microbial evolution and its consequences for life on Earth-past, present, and future.}, } @article {pmid41668536, year = {2026}, author = {Wei, H and Guo, S and Ding, W and Yang, Y and Hu, X and Aili, A and Chen, X and Xue, X and Pan, L}, title = {Altered gut microbial dynamics and the antivascular remodeling effect of carnosine in hypobaric hypoxic pulmonary hypertension rats.}, journal = {Acta biochimica et biophysica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.3724/abbs.2025237}, pmid = {41668536}, issn = {1745-7270}, abstract = {Exposure to chronic hypobaric hypoxia provokes marked alterations in the gut microbiota and its metabolome, yet the functional significance of histidine-derived metabolites in hypobaric hypoxic pulmonary hypertension (PH) remains underexplored. Here, we employ 16S rDNA, metagenomic, and untargeted metabolomic sequencing to characterize longitudinal shifts in the fecal microbiota and metabolites during hypobaric hypoxic PH development in Sprague-Dawley rats. Fecal carnosine levels and the abundance of its producer, Ruminococcus bromii, both decrease significantly over 28 days of hypobaric hypoxia (P < 0.05). Spearman correlation shows that carnosine is inversely correlated with the percentage of pulmonary arteriole media thickness (MT%; r = -0.8741, P < 0.001). Therapeutic supplementation with carnosine restores systemic and pulmonary antioxidant defenses and attenuates vascular remodeling without altering right ventricular pressures. In vitro, carnosine inhibits hypoxia-induced pulmonary artery smooth muscle cell (PASMC) proliferation and migration and suppresses nuclear factor erythroid 2-related factor 2 (Nrf2) accumulation. These findings reveal dynamic gut-lung crosstalk in hypobaric hypoxic PH and nominate carnosine as a metabolite-based intervention to mitigate hypoxia-driven pulmonary vascular remodeling.}, } @article {pmid41668731, year = {2025}, author = {Gao, H and Li, J and Liu, L and Gu, Z and Yu, H and Xing, D and Zhao, T and Li, C}, title = {Multi-omics profiling reveals associations between gut microbiota and olfactory gene expression in mosquitoes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1745848}, pmid = {41668731}, issn = {2235-2988}, mesh = {Animals ; Female ; *Culex/microbiology/genetics/physiology ; Male ; Multiomics ; *Gastrointestinal Microbiome/genetics ; Gene Expression Profiling ; *Smell/genetics ; Arthropod Antennae/physiology/metabolism ; Metagenomics ; Transcriptome ; Computational Biology ; }, abstract = {INTRODUCTION: The interplay between gut microbiota and host physiological processes has been extensively studied in vertebrates, where it plays a crucial role in regulating appetite, emotion, immunity, and other physiological functions. However, whether a similar regulatory mechanism exists in insects remains unclear, especially regarding the long-distance regulation of olfactory function. This study focused on three Culex subspecies (Culex quinquefasciatus, Culex pipiens pallens, and Culex pipiens molestus) that are closely related but exhibit significant differences in olfaction-dependent ecological habits. By integrating antennal transcriptomic and gut metagenomic data, we systematically analyzed the expression characteristics of olfactory-related genes, the structure of gut microbial communities, and their intrinsic associations.

METHODS: We integrated antennal transcriptomic and gut metagenomic sequencing to analyze olfactory-related gene expression, gut microbial community structure, and their intrinsic associations in male and female individuals of the three Culex subspecies. Bioinformatics analyses included differential gene screening, functional enrichment, microbial taxonomic annotation, and Spearman correlation analysis.

RESULT: The results showed that a large number of sex-specific and species-specific differentially expressed genes (DEGs) were identified in the antennae of the three Culex subspecies. Among these, 345 DEGs were shared sex-specific genes across species, which were significantly enriched in pathways such as odor binding, signal transduction, and xenobiotic metabolism. At the phylum level, the gut microbial composition was dominated by Proteobacteria, Bacteroidetes, and Firmicutes, showing a conserved structure; at the genus level, 11 dominant genera (including Wolbachia, Elizabethkingia, and Asaia) exhibited distinct species-specific distribution patterns. Diversity analysis revealed that the gut microbial richness of male individuals was significantly higher than that of females, and the β-diversity showed an obvious "sex clustering" pattern.Correlation analysis further indicated that 152 DEGs were significantly correlated with 107 microbial genera. Among them, olfactory-related genes were closely associated with several core genera (e.g., Wolbachia, Asaia, Serratia). Gut microbes may remotely regulate the expression and function of olfactory genes in antennae through metabolites or signaling molecules, thereby influencing mosquito behaviors such as host localization, mating, and oviposition.

DISCUSSION: This study reveal the intrinsic association between gut microbes and olfactory function in Culex mosquitoes, providing a new perspective for understanding the "microbe-host" cross-organ regulatory mechanism and laying a theoretical foundation for the development of novel mosquito vector control strategies based on microbial or olfactory interference.}, } @article {pmid41668733, year = {2025}, author = {Sui, Q and Yu, J and Cui, S}, title = {An oral microbiome model for predicting atherosclerotic cardiovascular disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1707599}, pmid = {41668733}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; *Atherosclerosis/microbiology/diagnosis ; Aged ; Middle Aged ; Retrospective Studies ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Female ; Male ; ROC Curve ; Risk Factors ; Random Forest ; Bacteria/classification/genetics/isolation & purification ; *Cardiovascular Diseases/diagnosis/microbiology ; Predictive Learning Models ; Metagenomics ; Prediction Algorithms ; }, abstract = {OBJECTIVE: This study aimed to construct a predictive model for the early onset of atherosclerotic cardiovascular disease (ASCVD) by integrating oral microbiome data with traditional clinical risk factors.

METHODS: A retrospective study was conducted involving participants aged 50-70 years without pre-existing ASCVD. The patients were divided into a training set and a validation set at a ratio of 7:3 by the complete randomization method. The characteristics of the oral microbiome were characterized by 16S rRNA/metagenomic sequencing. In the training set, univariate analysis and multivariate Logistic regression analysis were applied to screen predictive variables, and Random Forest (RF), Gradient Boosting (GB), and K-nearest Neighbor (KNN) were constructed. The receiver operating characteristic (ROC) curve was validated. The model performance was evaluated by net reclassification improvement (NRI) and integrated discrimination improvement (IDI).

RESULTS: A total of 331 patients were enrolled and randomly divided into a training set (n=231) and a validation set (n=100). 40 out of 331 participants experienced major adverse cardiovascular events (MACE). Multivariate Logistic regression analysis confirmed that age, relative abundance of Fusobacterium nucleatum, Prevotella, Porphyromonas, Leptotrichia, Streptococcus and Actinomyces were significantly associated with ASCVD event risk (all P < 0.05). Three machine learning models (RF, GB, and KNN) were constructed, with the RF model achieving the highest predictive performance. The AUC values of the RF, GB, and KNN models in the training set were 0.888 (95% CI: 0.818-0.958), 0.823 (95% CI: 0.745-0.901), and 0.812 (95% CI: 0.727-0.898) respectively, and in the validation set were 0.845 (95% CI: 0.740-0.951), 0.746 (95% CI: 0.621-0.871), and 0.767 (95% CI: 0.647-0.887) respectively. Additionally, the integrated model showed significant improvements in net reclassification improvement (NRI = 0.315, P < 0.05) and integrated discrimination improvement (IDI = 0.227, P < 0.05) compared to traditional clinical models.

CONCLUSION: The integration of the oral microbiome and clinical data can improve the accuracy of the ASCVD risk prediction model, providing a novel biomarker strategy for primary cardiovascular prevention.}, } @article {pmid41668735, year = {2025}, author = {Cao, Y and Wang, C and Yin, H and Xu, D and Li, W and Yuan, Z and Xu, W and Song, Z and Pang, F and Wang, D}, title = {Establishing hospital-specific background microbial libraries to reduce false positives in mNGS diagnosis of periprosthetic joint infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1668697}, pmid = {41668735}, issn = {2235-2988}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Prosthesis-Related Infections/diagnosis/microbiology ; Humans ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Hospitals ; False Positive Reactions ; Computational Biology ; Fungi/genetics/classification/isolation & purification ; }, abstract = {BACKGROUND: Due to the high sensitivity of metagenomic next-generation sequencing (mNGS), trace amounts of nucleic acid contamination can lead to false positives, posing challenges for result interpretation. This study is the first to experimentally identify and establish background microbial libraries (BML) related to periprosthetic joint infection (PJI) across different medical institutions, aiming to demonstrate the necessity of institution-specific BMLs to improve mNGS diagnostic accuracy.

METHODS: Samples were taken from 3 different acetabular reamer for hip arthroplasty in 7 different hospitals. The whole process was strictly aseptic, mNGS was performed according to standard operating procedures. The sterility of instruments was confirmed by culture method. The sequencing results of specimens from different hospitals were compared to analyze the difference of background bacteria. Bioinformatics analysis and visualization were presented through R language.

RESULTS: A total of 26 samples (24 instrument swabs and 2 negative controls) generated 254 million reads, of which 1.13% matched microbial genomes. The proportion of microbial reads (1.13%) falls within ranges typically observed for contamination in low-biomass metagenomic sequencing studies. Among these, bacteria accounted for 87.48%, fungi 11.18%, parasites 1.26%, and viruses 0.06%. The most abundant bacterial genera included Cutibacterium, Staphylococcus, and Acinetobacter. Principal component analysis revealed distinct bacterial compositions among the seven hospitals, and clustering analysis showed significant inter-hospital variation (p < 0.05). Liaocheng People's Hospital exhibited the highest species richness (340 species), followed by Guanxian County People's Hospital (169 species).

CONCLUSIONS: The composition and abundance of residual bacterial DNA vary markedly among institutions, underscoring the necessity of establishing hospital-specific BMLs. Incorporating such libraries into clinical mNGS interpretation can effectively reduce false positives and enhance the diagnostic accuracy of PJI. arthroplasty, bacterial culture, next-generation sequencing, joint replacement, periprosthetic joint infection, background microbial libraries.}, } @article {pmid41668736, year = {2025}, author = {Wang, Q and Ding, H and Hao, Z and Liao, G}, title = {Metagenomic next-generation sequencing enhances diagnosis of fungal infections in kidney transplant recipients: a retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1667475}, pmid = {41668736}, issn = {2235-2988}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Retrospective Studies ; *Fungi/genetics/classification/isolation & purification ; *Mycoses/diagnosis/microbiology ; Female ; Male ; Middle Aged ; *Transplant Recipients ; Adult ; }, abstract = {BACKGROUND: Although fungal infections are relatively rare, they have low detection rates and high mortality rates. The value of metagenomic next-generation sequencing (mNGS) in kidney transplant patients with fungal infections remains insufficiently explored, especially regarding diagnosis and antimicrobial stewardship.

METHODS: From September 2021 to August 2023, 234 kidney transplant patients were enrolled, with detailed data collected on 66 patients suspected of fungal infections. The pathogen detection performance of mNGS and conventional microbiological tests (CMTs) was compared. The impacts of mNGS and CMTs on treatment adjustment were also assessed. Finally, the value of mNGS in detecting donor-derived infections was investigated.

RESULTS: Among 66 patients, 21 fungal species were identified: 18 species detected by mNGS and 10 by CMTs. The overall positive rate of mNGS was significantly higher than culture (90.67% vs. 26.67%), especially for multiple fungal infections (9vs0). mNGS identified more Candida (26vs12), Pneumocystis jirovecii (14vs0), Aspergillus (10vs4), Mucor (6vs2) organisms compared with CMTs. Donor-derived fungi were identified in 11 (6.7%) patients, including 10 cases of Candida spp. and 1 case of Mucor spp. Anti-infection therapies were adjusted in 28 (24.4%) cases based on mNGS.

CONCLUSION: The mNGS technique showed distinct advantages in detecting fungal infections in kidney transplant patients, facilitating informed anti-infection strategies and enhanced graft protection. Moreover, it provides effective identification of fungal infections originating from donor sources.}, } @article {pmid41669395, year = {2025}, author = {Criollo Delgado, L and Zewude, D and Karzhaev, DS and Polev, DE and Potokina, EК}, title = {Identification of CtE1 gene nucleotide polymorphisms and development of SNP-based KASP markers in guar (Cyamopsis tetragonoloba (L.) Taub.).}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {25}, number = {8}, pages = {1246-1254}, doi = {10.18699/vjgb-25-134}, pmid = {41669395}, issn = {2500-0462}, abstract = {Guar (Cyamopsis tetragonoloba (L.) Taub), is an important short-day legume crop, whose cultivation is limited at high latitudes due its photoperiod sensitivity, that negatively impacts flowering and maturation of this industrial-oriented crop. In its close relative, soybean, the E1 gene has been highly associated with the regulation of flowering time under long-day conditions. In this study we investigated the natural diversity of the E1 homologue gene (CtE1) in a panel of 144 guar accessions. For this purpose, the CtE1 gene was amplified and sequenced using Illumina. As a result, five novel SNPs were identified in the 5'-untranslated region, coding region, and 3'-untranslated region of the CtE1 gene. One non-synonymous SNP was located in the coding region causing a conservative Arg→Lys substitution. Based on the identified SNP, five KASP markers linked to polymorphism in the target gene were developed and tested in the guar collection. No significant associations were detected between discovered SNPs and available data on variability in flowering time or vegetation period length in the cohort of 144 accessions. These findings suggest that natural variation of the CtE1 gene in the studied germplasm collection has minimal effect on flowering or maturation. The limited functional allelic diversity observed in the CtE1 gene of guar compared to the E1 gene in soybean likely reflects differences in their evolutionary histories, domestication bottlenecks, and selection pressures.}, } @article {pmid41669550, year = {2026}, author = {Bunyoo, C and Phonmakham, J and Morikawa, M and Thamchaipenet, A}, title = {Species-level profiling of Landoltia punctata (duckweed) microbiome under nutrient stress using full-length 16S rRNA sequencing.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20648}, pmid = {41669550}, issn = {2167-8359}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Araceae/microbiology ; *Bacteria/genetics/classification ; *Stress, Physiological ; Phylogeny ; Nutrients/metabolism ; }, abstract = {Duckweed is a rapidly-growing aquatic plant utilized as food/feed and for wastewater remediation. It coexists with complex microbial communities that play crucial roles in its growth and capability for phytoremediation. In a previous study, microbiomes associated with four duckweed species (Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, and Wolffia globosa) grown under natural and nutrient-deficient conditions, were investigated using V3V4 16S rRNA sequencing. However, species-level classification was not achieved due to the partial 16S rRNA sequences obtained, restricting the selection of potential microbial species for further application. In this study, L. punctata samples from the previous work were investigated further by employing full-length 16S rRNA sequencing. A total of 31 predominant microbial species were identified. Under stress, the proportion of Proteobacteria increased significantly, along with potentially beneficial bacteria such as Roseateles depolymerans, Pelomonas saccharophila, Acidovorax temperans, Ensifer adhaerens and Rhizobium straminoryzae. Functional metagenomic predictions suggest that associated microbes adapt to stressors and may confer benefits to duckweed, including pathways related to host adhesion, biofilm formation, microbial growth modulation, and co-factors and vitamin biosynthesis. Furthermore, the study demonstrates both the advantages and limitations of full-length 16S rRNA amplicon sequencing. The findings provide more insight into L. punctata microbiomes at species-level, facilitating establishment of stable, beneficial microbial communities for duckweed applications. Ongoing investigations aim to isolate key microbial species from L. punctata and validate their roles through co-cultivation, along with establishing potential synthetic microbial communities based on the metagenomic findings.}, } @article {pmid41669552, year = {2026}, author = {Hearne, G and S Refahi, M and Duan, HN and Brown, JR and Rosen, GL}, title = {Normalized compression distance for DNA classification.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20677}, pmid = {41669552}, issn = {2167-8359}, mesh = {Humans ; Compression Algorithms ; *Data Compression/methods ; *Genomics/methods ; Open Reading Frames ; Algorithms ; *DNA/genetics/classification ; *Sequence Analysis, DNA/methods ; }, abstract = {Analyzing the origin and diversity of numerous genomic sequences, such as those sampled from the human microbiome, is an important first step in genomic analysis. The use of normalized compression distance (NCD) has demonstrated capabilities in the field of text classification as a low-resource alternative to deep neural networks (DNNs) by leveraging compression algorithms to approximate Kolmogorov information distance. In an effort to apply this technique toward genomics tasks akin to tools such as Many-against-Many sequence searching (MMseqs) and Kraken2, we have explored the use of a gzip-based NCD combination in both gene labeling of open reading frames (ORFs) and taxonomic classification of short reads. Our implementation achieved 0.89 accuracy and 0.88 macro-F1 on human gene classification, surpassing similar NCD-based approaches. In prokaryotic gene labeling tasks, NCD shows superior classification accuracy to traditional alignment or exact-match tools in out-of-distribution settings, while also outperforming comparable sequence-embedding methods in in-distribution classification. However, the computational complexity of O(MN) (in standard big-O notation, where M and N denote the sizes of the training and test databases, respectively) constrains scalability to very large datasets, though these findings nonetheless demonstrate that compression-based approaches provide an effective alternative for genomic sequence classification, particularly in low-data environments.}, } @article {pmid41669888, year = {2026}, author = {Yeo, LF and Palmu, J and Havulinna, AS and Pärnänen, K and Salomaa, V and Lahti, L and Knight, R and Niiranen, T}, title = {Prospective association between the gut microbiome and incident hypertension: a 20-year cohort study.}, journal = {Journal of hypertension}, volume = {44}, number = {4}, pages = {673-681}, pmid = {41669888}, issn = {1473-5598}, mesh = {Humans ; Female ; *Hypertension/epidemiology/microbiology ; Middle Aged ; Adult ; *Gastrointestinal Microbiome ; Male ; Aged ; Prospective Studies ; Finland/epidemiology ; Incidence ; Risk Factors ; }, abstract = {INTRODUCTION: Hypertension remains the leading modifiable risk factor attributable to 10.8 million premature deaths. Hence the study of hypertension and gut microbiome as a therapeutic target is very important. Yet the links between the gut microbiome and long-term incidence of hypertension are unknown.

AIM: This study assessed the association between gut microbiome and incident hypertension.

METHOD: The study sample consisted of 3311 nonhypertensive individuals (60.7% women) aged 25-74  years who were drawn from the general population in Finland. In the baseline examination performed in the year 2002, the participants underwent a health examination and provided a stool sample. The gut microbiome was assessed using shallow shotgun metagenomic sequencing. Microbiome analyses were performed with Cox proportional hazards model.

RESULTS: In total, 675 participants developed hypertension over a follow-up period of nearly 20 years. In multivariable-adjusted models, overall gut microbiome composition was not related to risk of future hypertension. Eight genera, including Agathobaculum, Blautia_A_141780, Blautia_A_141781, Mediterraneibacter_A_155590, Enterocloster , Bariatricus , CAG-317-146760 , and CAG-628 were significantly associated with incident hypertension in the age-adjusted and sex-adjusted models, but none remained significant in the multivariable-adjusted models. No functional pathways were associated with hypertension risk.

CONCLUSION: Our results do not provide strong evidence for an association between the gut microbiome and risk of future hypertension, especially after adjusting for covariates that are known to influence the gut microbiome.}, } @article {pmid41670185, year = {2026}, author = {Sampara, P and Tomatsu, A and Malmstrom, RR and Ziels, RM}, title = {Quantitative DNA Stable Isotope Probing Identifies Active Microorganisms Assimilating Volatile Fatty Acids in Full-Scale Enhanced Biological Phosphorus Removal Processes.}, journal = {Environmental science & technology}, volume = {60}, number = {7}, pages = {5570-5583}, doi = {10.1021/acs.est.5c14266}, pmid = {41670185}, issn = {1520-5851}, mesh = {*Phosphorus ; *Fatty Acids, Volatile/metabolism ; }, abstract = {Enhanced biological phosphorus removal (EBPR) systems often rely on exogenous carbon sources, such as volatile fatty acids (VFAs), to achieve higher P removal. Here, we employed DNA quantitative stable isotope probing (qSIP) using two VFAs, acetate and propionate, in cyclic anaerobic/aerobic incubations to assess their effects on P cycling and microbial activity with biomass from two full-scale EBPR water resource-recovery facilities that utilize VFA addition. We found that anaerobic VFA uptake preferences differed within known groups of PAOs, such as Candidatus Accumulibacter and Tetrasphaera-affiliated members (e.g., Ca. Phosphoribacter), between the two biomasses. The combination of qSIP with metagenomics identified isotopically labeled phages that were linked to active PAOs, highlighting their potential roles in modulating EBPR community composition and activity. The highest levels of anaerobic labeling from acetate were in genomes belonging to Saccharimonadales and Rickettsiales, which are generally host-associated with bacteria and eukaryotes, respectively. This finding highlights the possibility of cross-feeding between PAO hosts and their parasites or predators, as well as the role of so-far uncharacterized organisms participating in carbon cycling under EBPR conditions. Collectively, these results expand our understanding of the ecological interactions involved in communities anaerobically uptaking VFAs and cycling P that are central to EBPR.}, } @article {pmid41670373, year = {2026}, author = {Pham, S and Sharma, N and Sankaran, B and Nguyen, J and Estes, MK and Hyser, JM and Prasad, BVV}, title = {Tulane virus protease as a structural surrogate for inhibitor screening of human norovirus proteases.}, journal = {Journal of virology}, volume = {100}, number = {3}, pages = {e0217625}, pmid = {41670373}, issn = {1098-5514}, support = {P01 AI057788/AI/NIAID NIH HHS/United States ; P30 GM124169/GM/NIGMS NIH HHS/United States ; R01 DK115507/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Peptide Hydrolases/chemistry/metabolism ; *Norovirus/enzymology/drug effects ; *Protease Inhibitors/pharmacology/chemistry ; Animals ; Pyrrolidinones/pharmacology/chemistry ; Picornavirales ; *Antiviral Agents/pharmacology/chemistry ; Leucine/analogs & derivatives ; *Caliciviridae/enzymology/drug effects ; Models, Molecular ; Protein Conformation ; *Viral Proteins/chemistry/metabolism/antagonists & inhibitors ; Drug Evaluation, Preclinical/methods ; Crystallography, X-Ray ; Cell Line ; Isoxazoles ; Phenylalanine/analogs & derivatives ; Valine/analogs & derivatives ; }, abstract = {Human norovirus (HuNoV) is a significant cause of gastroenteritis worldwide, affecting people of all age groups. There are currently no vaccines or drugs available, leaving susceptible populations vulnerable to severe or protracted illness. A HuNoV cultivation system is pivotal for screening norovirus antivirals. While the human intestinal enteroid cultivation system allows robust replication of multiple HuNoV strains, it presents technical and cost barriers. Tulane virus (TV), a surrogate for HuNoV, replicates well in monkey kidney cell lines and is closely related to norovirus in cellular biology. Here, we determined the structures of TV protease (TV-Pro) alone and in complex with rupintrivir, a picornavirus inhibitor that also inhibits HuNoV proteases (HuNoV-Pro). Our data validate TV as an efficient surrogate system for rapid screening of HuNoV protease inhibitors. The TV protease structure exhibits significant backbone similarity to the GI.1 HuNoV protease in the substrate-binding domain, with the BII-CII loop in an open conformation stabilized by hydrogen bonds as present in the GI.1 protease. Structural differences in the S2 pocket and two amino acid changes in the S4 pocket result in slightly altered P2 and P4 substrate and inhibitor conformations. Despite these differences, we confirm previous findings that the TV protease can cleave the GI.1 and GII HuNoV polyprotein substrates with high and moderate efficiency, respectively. We found that rupintrivir efficiently inhibits TV protease in vitro and inhibits TV replication in cell culture with similar efficacy in combination with P-glycoprotein efflux pump inhibitors. We conclude that TV is a valuable surrogate for HuNoV protease inhibitor screening and outline strategies to improve its compatibility as such.IMPORTANCEHuman noroviruses (HuNoVs) are a significant cause of sporadic and epidemic gastroenteritis worldwide. There are no vaccines or antiviral drugs currently available to treat infections. Our work here demonstrates the potential of the Tulane virus cell culture system as a surrogate for screening small-molecule inhibitors of the human norovirus proteases.}, } @article {pmid41670415, year = {2026}, author = {Hasegawa, T and Iwai, S and Ikeda, HO and Miyaoka, D and Sato, N and Fujimoto, K and Wei, X and Kusaka, M and Miyata, M and Numa, S and Otsuka, Y and Imoto, S and Uematsu, S and Tsujikawa, A}, title = {Increased Gut Microbiota Diversity in Patients With Retinitis Pigmentosa and Implications for Disease Phenotypes and Progression.}, journal = {Investigative ophthalmology & visual science}, volume = {67}, number = {2}, pages = {27}, pmid = {41670415}, issn = {1552-5783}, mesh = {Animals ; Humans ; *Retinitis Pigmentosa/microbiology/diagnosis/drug therapy ; Mice ; Female ; Disease Progression ; Male ; *Gastrointestinal Microbiome/physiology/genetics ; Phenotype ; Disease Models, Animal ; RNA, Ribosomal, 16S/genetics ; Adult ; Middle Aged ; Mice, Inbred C57BL ; Anti-Bacterial Agents ; Feces/microbiology ; *Bacteria/genetics ; Young Adult ; }, abstract = {PURPOSE: Inflammation is often present in retinitis pigmentosa (RP) and is reported to affect visual outcome. Gut microbiota plays a crucial role in inflammatory diseases. This study aimed to elucidate the relationship between the gut microbiota and RP.

METHODS: The 16S rRNA gene sequencing analysis was performed on stool samples collected from 103 patients with RP and 64 healthy individuals. The α and β diversities of gut microbiota, along with relative abundances, were compared between patients and healthy individuals, as well as between patients with or without cystoid macular edema (CME). The RP model rd10 mice were treated with or without antibiotics starting at 7 days of age. Retinal structure and function were evaluated.

RESULTS: Gut microbiota diversity was higher in patients with RP than in healthy individuals (P < 0.001). Moreover, patients with CME had greater diversity than did those without CME and showed a higher abundance of Romboutsia and Ruminococcus (P < 0.05). Antibiotics-treated rd10 mice showed suppressed apoptosis, attenuated decrease of photoreceptors, and a significantly lower incidence of retinal detachment. Retinal function was significantly preserved in mice treated with antibiotics. In antibiotics-treated mice, the expression of Il-1β, Nlrp3, Caspase-1, pNFkb, pJNK, and pCREB1 was downregulated, suggesting suppression of the NLRP3 inflammasome.

CONCLUSIONS: Patients with RP exhibited distinct gut microbiota characteristics compared to that of healthy individuals. Treatment with antibiotics attenuated disease progression in the RP model mouse. Modifying the gut microbiota may be a potential therapeutic strategy for modifying disease progression in RP in future investigations.}, } @article {pmid41670507, year = {2026}, author = {Xing, Y and Chen, M and Shen, M and Zhong, Q}, title = {A Case of Rare Facial Infection Caused by Mycobacterium scrofulaceum.}, journal = {Clinical laboratory}, volume = {72}, number = {2}, pages = {}, doi = {10.7754/Clin.Lab.2025.250549}, pmid = {41670507}, issn = {1433-6510}, mesh = {Humans ; Male ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Facial Injuries ; Tomography, X-Ray Computed ; }, abstract = {BACKGROUND: In July 2024, our hospital confirmed a rare case of facial infection with Mycobacterium scrofulaceum. The patient visited our hospital due to pain and pus discharge from the right orbital incision for one month. The patient suffered multiple facial fractures due to trauma three months ago. He underwent systemic anti infection treatment and open reduction and internal fixation surgery at an external hospital. After the surgery, there was repeated swelling around the orbit, and the patient did not fully recover. One month ago, the infraorbital area was swollen again, locally ruptured, and purulent discharge was visible. After self-flushing and dressing change, the condition improved. Recently, there has been swelling around the eye socket again. In order to seek further treatment, he came to our hospital for treatment. Outpatient diagnosis: 1. Multiple space infections in the right orbit, temporal region, and skull base; 2. Postoperative open facial bone fracture.

METHODS: CT (skull and neck), facial wound pus: bacterial culture and identification, acid fast staining, Gram staining, T-SPOT tuberculosis infection detection, identification of Mycobacterium species (DNA microarray chip method), Metagenomic Next-generation Sequencing (mNGS). Other related auxiliary examinations included blood routine, urine routine, liver function, kidney function, electrocardiogram, etc. Results: CT (skull and neck) results: 1. After multiple fractures of the maxillofacial bone and anterior skull base, there is abnormal enhancement density shadow in the right maxillofacial region, indicating infection. Clinical laboratory tests: blood routine + high-sensitivity CRP (whole blood): white blood cell count 9.66 x 109/L, total neutrophil count 6.87 x 109/L, whole blood high-sensitivity C-reactive protein 46.21 mg/L, coagulation function: fibrinogen detection 6.61 g/L, D-dimer determination 1,231.52 FEU/L, inflammatory markers: interleukin-6 15.48 pg/mL, procalcitonin 0.037 ng/ml; Liver function test: total protein 85.2 g/L, globulin 44.4 g/L, aspartate aminotransferase 12.8 U/L. Facial wound pus examination: T-SPOT tuberculosis infection test: positive, with 40 antigen stimulated pore spots. Bacterial Gram staining: A small amount of Gram positive bacilli were found. Acid fast staining: acid fast bacilli detected ++: bacterial culture + identification: growth of mycobacteria ++, identification of mycobacterial species (DNA microarray method): Mycobacterium scrofulaceum, identification of Metagenomic Next-generation Sequencing (mNGS): Mycobacterium scrofulaceum. Clinical treatment plan: Chlorpheniramine 200 mg/d, Clarithromycin 0.5 g/d; Moxifloxacin 0.4 g/d, locally applied with 3% boric acid solution wet compress to enhance local wound dressing change. After 2 months of hospitalization, the patient's orbital swelling significantly improved, no obvious purulent discharge was observed locally, and the infection indicators significantly decreased. The patient improved and was discharged from the hospital.

CONCLUSIONS: This article reports a rare case of facial infection caused by Mycobacterium scrofulaceum. Mycobacterium scrofulaceum was quickly and accurately identified through mycobacterial strain identification (DNA microarray chip method) and mNGS. Reasonable treatment measures were adopted clinically, and the patient improved and was discharged. We hope that in the future, this study can provide assistance for the clinical diagnosis and treatment of Mycobacterium scrofulaceum infection.}, } @article {pmid41671148, year = {2026}, author = {Buczek, DJ and Kabir, W and Lindstedt, K and Mäklin, T and Thorpe, HA and Suzuki, Y and Corander, J and Samuelsen, Ø and Sundsfjord, A}, title = {Sequence type and strain-level detection of Klebsiella pneumoniae in culture-enriched bacterial metagenomes: comparative performance of mSWEEP and StrainGE bioinformatic tools.}, journal = {Microbial genomics}, volume = {12}, number = {2}, pages = {}, pmid = {41671148}, issn = {2057-5858}, mesh = {*Klebsiella pneumoniae/genetics/classification/isolation & purification ; *Computational Biology/methods ; *Metagenome ; Phylogeny ; Whole Genome Sequencing ; Humans ; Genome, Bacterial ; Metagenomics/methods ; Klebsiella Infections/microbiology ; }, abstract = {Klebsiella pneumoniae is a major cause of human infections and is frequently associated with antimicrobial resistance (AMR). Carriage of K. pneumoniae in the gut is a major risk factor for infection and a reservoir for the spread of high-risk clonal lineages and associated AMR determinants. Accurate detection of K. pneumoniae at the subspecies level is therefore essential to better understand K. pneumoniae gut colonization ecology and clonal dissemination. We analysed two recently developed bioinformatic tools, mSWEEP and StrainGE, for sequence type (ST) detection of K. pneumoniae in culture-enriched sweep metagenomes compared to single-colony whole-genome sequencing (WGS). We show that both mSWEEP and StrainGE perform highly accurate ST detection, concordant with culture in 46/49 and 44/49 samples with WGS-detected single STs, respectively, as well as in 2/3 samples with two WGS-detected STs. Within-sample ST diversity was detected in 19 and 15 samples by mSWEEP and StrainGE, respectively, highlighting a major advantage of these tools over conventional single-colony WGS. StrainGE could also reconstruct accurate phylogenetic relationships between strains of the same ST for 2/3 different STs tested. Additionally, assembly of the genomes provides better resolution of ST detection by mSWEEP. Together, our results show that both mSWEEP and StrainGE are accurate tools for the detection and analysis of K. pneumoniae STs from mixed bacterial samples.}, } @article {pmid41671170, year = {2026}, author = {Chettleburgh, C and Chiappe, C and Davidson, H and Taggar, G and Zhao, A and Habash, M and Landgraff, C and Parreira, VR and Lévesque, RC and Goodridge, L}, title = {Coffee cartridge filtration: a rapid, inexpensive, and easy method to concentrate nucleic acids from pathogens and fecal biomarkers in wastewater.}, journal = {Journal of applied microbiology}, volume = {137}, number = {2}, pages = {}, doi = {10.1093/jambio/lxag037}, pmid = {41671170}, issn = {1365-2672}, support = {//INSPIRE/ ; CBRF2-2023-00008//Canada Biomedical Research Fund Stage 2/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Canopy Canadian One Health Training Program on Emerging Zoonoses/ ; }, mesh = {*Wastewater/virology/parasitology/microbiology ; *Filtration/methods/instrumentation ; *Feces/virology/parasitology/microbiology ; Ontario ; Norovirus/genetics/isolation & purification ; Humans ; *Coffee ; *Nucleic Acids/isolation & purification ; Giardia/genetics/isolation & purification ; Biomarkers/analysis ; }, abstract = {AIMS: We propose coffee cartridge filtration as an alternative method for the concentration of nucleic acids from microorganisms in wastewater.

METHODS AND RESULTS: In this study, coffee cartridge filtration was directly compared with PEG precipitation through mass balance analysis. The utility of coffee cartridge filtration was further demonstrated through a 10-month longitudinal analysis of Giardia, human norovirus genogroup I and II, and hepatitis A virus in 45 wastewater samples from Guelph, Ontario, Canada. Fourteen of these wastewater samples were enriched with the Illumina Viral Surveillance Panel v2 and sequenced with the Illumina NextSeq 1000. PEG precipitation was more efficient at concentrating nucleic acids from all microorganisms and viruses, but all endogenous targets were detected following coffee cartridge filtration. Hepatitis A was detected in four wastewater samples and best correlated with four clinical cases when a 1-week wastewater lead time was applied. HuNoV-GI and HuNoV-GII were detected within the RT-qPCR linear dynamic range in 44/45 samples. Nucleic acids from the Polyomaviridae, Astroviridae, and Caliciviridae families were most identified in coffee cartridge-filtered wastewater samples.

CONCLUSIONS: Coffee cartridge filtration is an effective method to concentrate nucleic acids from microorganisms in wastewater in resource-limited settings.}, } @article {pmid41671795, year = {2026}, author = {Ji, J and Wang, Q and Hu, F and Yang, H and Li, Y and Wu, G and Dong, Y and Du, J and Li, H and Shen, B and Wang, B}, title = {Advantages of partial denitrification-anaerobic ammonium oxidation system under sulfamethoxazole stress: Adaptive mechanisms and synergistic metabolism.}, journal = {Bioresource technology}, volume = {446}, number = {}, pages = {134181}, doi = {10.1016/j.biortech.2026.134181}, pmid = {41671795}, issn = {1873-2976}, mesh = {*Sulfamethoxazole/pharmacology ; *Denitrification/drug effects ; Oxidation-Reduction ; *Ammonium Compounds/metabolism ; Anaerobiosis/drug effects ; *Stress, Physiological/drug effects ; *Adaptation, Physiological/drug effects ; Nitrogen/metabolism ; Bioreactors/microbiology ; }, abstract = {The widespread use of antibiotics has led to their persistence in aquatic environments, posing serious challenges to biological treatment systems. This study systematically compared the performance and adaptive mechanisms of partial denitrification (PD)/anaerobic ammonium oxidation (anammox) and single anammox systems under long-term sulfamethoxazole (SMX) stress over 193 days. At an influent SMX concentration of 3 mg/L, the PD/anammox system retained 75% of its initial total inorganic nitrogen (TIN) removal efficiency, significantly higher than that of the single anammox system (49%). The PD/anammox achieved an SMX degradation efficiency of 80%, substantially exceeding that of the single system (39%). Metagenomic analyses revealed higher abundances of key nitrogen metabolism genes (hzs, hdh, narG/H/I, napA/B, nirK/S) and SMX degradation genes (sadA, sadC, tmoABCDEF, dmpB/D) in the PD/anammox system. The enhanced performance was closely associated with the enrichment of the denitrifying microbiome (e.g., Thauera, Zoogloea, unclassified_f_Rhodocyclaceae), which provided a stable nitrite supply and carried SMX degradation genes. Both systems relied on extracellular polymeric substances (EPS) as a protective barrier under low SMX stress (1 mg/L). Under higher SMX concentrations (>1 mg/L), the PD/anammox system exhibited dynamic enrichment of sulfonamide resistance genes (sul1). These results demonstrated the superiority of the PD/anammox system over the single anammox system. The combined effects of a diverse microbiome, multi-level stress-response mechanisms involving EPS and antibiotic resistance genes, and efficient functional gene expression make PD/anammox a robust and promising technology for the treatment of antibiotic-containing wastewater.}, } @article {pmid41671813, year = {2026}, author = {Wang, N and Jin, M and Zhu, Z and Wang, Y and Li, X and Xu, J and Cheng, S and Zhu, Y and Wang, R and Xu, T and Yin, F and Li, X and Ke, Y and Yue, H}, title = {Ecological distribution and functional characterization of polyethylene-degrading enzymes from diverse metagenomes.}, journal = {The Science of the total environment}, volume = {1018}, number = {}, pages = {181486}, doi = {10.1016/j.scitotenv.2026.181486}, pmid = {41671813}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; *Polyethylene/metabolism ; *Metagenome ; Soil Microbiology ; }, abstract = {Polyethylene (PE), the most widely produced synthetic polymer, is highly resistant to degradation and poses long-term ecological risks due to its accumulation in terrestrial and aquatic ecosystems. Although biological degradation pathways have been investigated, research has primarily concentrated on heavily polluted environments, leaving the ecological distribution of PE-degrading enzymes largely unknown. In this study, we systematically screened more than 4.57 billion metagenomic sequences from diverse ecological sources-including farmland soils, Przewalski's horse gut microbiota, insect symbionts, and human oral microbiomes-for homologs of known PE-degrading enzymes. A total of 701 candidate sequences were identified using an integrated pipeline combining sequence homology, structural modeling, and molecular docking. Thirty-two representative enzymes were heterologously expressed and tested on pristine PE films and microspheres, among which 25 exhibited measurable activity, inducing surface erosion, up to ∼1.5% mass loss (w/w) of PE films over 30 days, and oxidative modifications. These degradative effects were validated by scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), gel permeation chromatography (GPC), and stable carbon isotope (δ[13]C) analysis, collectively supporting molecular-level oxidation and early-stage carbon turnover associated with enzymatic PE degradation. Notably, PE-degrading activity was observed in microbiomes from relatively minimally disturbed environments, suggesting that microbial communities may adaptively evolve plastic-degrading capabilities in response to chronic, low-level exposure. These findings expand our understanding of plastic pollution's ecological footprint and highlight naturally occurring enzymes as promising candidates for sustainable bioremediation.}, } @article {pmid41671864, year = {2026}, author = {Cui, W and Cui, Y and Hao, Y and Li, Y and Wang, Y and Liu, F and Long, J and Jin, Y and Chen, S and Duan, G and Yang, H}, title = {The effect of pet dog exposure on gut antibiotic resistome and microbiome of their owners.}, journal = {Journal of hazardous materials}, volume = {504}, number = {}, pages = {141429}, doi = {10.1016/j.jhazmat.2026.141429}, pmid = {41671864}, issn = {1873-3336}, mesh = {Animals ; Dogs ; Humans ; *Pets/microbiology ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Feces/microbiology ; Microbiota ; }, abstract = {Pet dogs provide well-documented physical and mental health benefits to humans through close interactions. However, the potential role of pet dogs as reservoirs of antibiotic resistance genes (ARGs) and the impact on shaping the gut microbiomes of their owners remains poorly characterized. The growing dual challenges of global antimicrobial resistance and widespread pet ownership underscore the importance of understanding human-animal resistome interactions crucial for One Health solutions. Consequently, this study conducted a metagenomic analysis of pet dogs, dog owners, and non-dog owners to investigate the effects of dogs on the microbiota composition, ARGs profiles, and mobile genetic elements (MGEs) of the human gut. The results indicated that pet dogs exhibited significantly higher gut abundance of both ARGs and ESKAPE pathogens (Enterococcus faecium and Acinetobacter baumannii) compared to humans. Moreover, the abundance of aminoglycoside resistance genes aac(6')-Im and aac(6')-Ie-aph(2'')-Ia, tetracycline resistance genes tetO and tet40 were was significantly higher in dog owners than in non-dog owners. Enterobacteriaceae were identified as shared core ARG hosts in both dog and human guts. Collectively, our results indicate that cohabitation with pet dogs is associated with a shared gut resistome, reflecting correlated patterns of ARGs and resistant microbes. These findings emphasize the necessity of monitoring antibiotic resistance in companion animals, while maintaining the benefits of human-dog relationships.}, } @article {pmid41671957, year = {2026}, author = {Wu, J and He, C and Wu, K and Feng, W and Yang, Y and Zhou, Q and Mao, P and Xiao, X}, title = {Silver sulfide nanoparticles amplify earthworm gut denitrification and elevate N2O emissions in subtropical forest soils under nitrogen deposition.}, journal = {Ecotoxicology and environmental safety}, volume = {311}, number = {}, pages = {119853}, doi = {10.1016/j.ecoenv.2026.119853}, pmid = {41671957}, issn = {1090-2414}, mesh = {Animals ; *Oligochaeta/drug effects/metabolism ; *Silver Compounds/toxicity ; *Denitrification/drug effects ; Forests ; *Metal Nanoparticles/toxicity/chemistry ; *Nitrogen/metabolism/analysis ; Soil/chemistry ; *Soil Pollutants/toxicity ; Nitrogen Cycle/drug effects ; Nitrification/drug effects ; *Nitrous Oxide/metabolism/analysis ; }, abstract = {Silver sulfide nanoparticles (Ag2S-NPs), commonly introduced into forest soils via sewage sludge, may disrupt nitrogen (N) cycling under elevated N deposition. This study examined how Ag2S-NPs and earthworms (Eisenia fetida) interact to influence N2O emissions in subtropical forest soils subjected to long-term simulated N deposition. A 60-day incubation was conducted using soils treated with low (1 mg Ag kg[-1]) and high (30 mg Ag kg[-1]) Ag2S-NP doses. Nitrogen deposition alone suppressed N2O emissions by acidifying soil and inhibiting nitrification. In contrast, earthworm activity enhanced emissions by stimulating organic matter turnover and N-cycling gene expression. Under N deposition, Ag2S-NPs significantly increased N2O emissions in a dose-dependent manner, with the high dose raising emissions by 68 % compared to earthworm-only treatments. Metagenomic analysis revealed that this effect was driven by increased gut-associated denitrification, with notable enrichment of narG/H/I and nirK/S genes, and denitrifiers such as Microbacterium and Bacillus. Conversely, soil nitrification declined, as reflected by reduced NO3[-] levels and amoA gene abundance. Multivariate models identified gut denitrification genes as key predictors of N2O flux. These findings highlight the synergistic impact of Ag2S-NPs and earthworms on greenhouse gas emissions in N-deposited soils and underscore the importance of considering nanomaterial-fauna-microbe interactions in forest ecosystems.}, } @article {pmid41671964, year = {2026}, author = {Zhao, G and Chen, W and Zhang, W and Zhang, R and Huang, X}, title = {Unveiling the environmental fate and risks of non-heterocyclic sulfacetamide: From a novel degradation mechanism to microecological effects.}, journal = {Water research}, volume = {294}, number = {}, pages = {125520}, doi = {10.1016/j.watres.2026.125520}, pmid = {41671964}, issn = {1879-2448}, mesh = {Biodegradation, Environmental ; Amidohydrolases/metabolism ; Sulfonamides ; }, abstract = {The presence of sulfonamides (SAs) in the environment has been demonstrated to be a significant factor in pollution. Despite extensive research on heterocyclic SAs, the degradation mechanisms and ecological effects of non-heterocyclic sulfacetamide (SA) remain poorly understood. Our previous study isolated a challenging-to-culture strain, Leucobacter sp. HA-1, known for its SAs-degrading capacity, contains the conserved gene sadA. However, SA was not detected within the degradation spectrum linked to monooxygenase SadA activity. This indicates that other genes may be involved in SA degradation in strain HA-1. In this study, two adjacent and functionally similar amidohydrolases, SamA1 and SamA2, were identified from strain HA-1 as initiators of SA degradation to sulfanilamide (SN). The amino acid sequence similarities of SamA1 and SamA2 with reported enzymes were 39.44% and 34.54%, respectively. The combined expression of SamA1 and SmaA2 had a synergistic effect in enhancing the degradation and resistance of SA. The molecular mechanism behind strain HA-1's SA degradation was elucidated through microscopic analysis combining enzyme characterization with toxicological assessments and comparative genomics. An artificial bioremediation microecosystem targeting SA was established, notably, adding HA-1 enhanced bioaugmentation efficacy for SA elimination significantly. Metagenomic analyses revealed dynamic changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and potential functional enzymes related to SA biodegradation within these microecosystems. Under our experimental conditions, bioaugmentation with HA-1 showed potential as a strategy for SA removal and reduced the accumulation or spread risk of ARGs and MGEs. This study revealed the fate mechanisms and microecological effects of non-heterocyclic sulfacetamide SA, which are different from typical SAs, and contributes to the further promotion of the elimination of the negative environmental and ecological impacts of antibiotics.}, } @article {pmid41671965, year = {2026}, author = {Niu, L and Pan, Y and Li, Y and Chen, X and Liu, X and Chen, Y and Wang, L and Zhang, W}, title = {WWTP effluents influence prokaryotic viral diversity and interaction with hosts: Regulating the virus-mediated nitrogen-cycling processes in river sediments.}, journal = {Water research}, volume = {294}, number = {}, pages = {125519}, doi = {10.1016/j.watres.2026.125519}, pmid = {41671965}, issn = {1879-2448}, mesh = {*Rivers ; *Nitrogen Cycle ; Viruses ; Geologic Sediments ; Nitrogen ; Wastewater ; Waste Disposal, Fluid ; }, abstract = {As an important water replenishment measure for urban rivers, the input of wastewater treatment plant (WWTP) effluents can change both the nutrient loading and the microbial community diversity of receiving rivers. However, our knowledge of the characteristics of viral communities and virus-mediated nitrogen-cycling processes in WWTP effluents-receiving rivers remains very limited. In this study, the prokaryotic virus, host and non-host communities in sediments were detected via metagenome and virome methods, to explore the variation characteristics of viral communities, interactions with hosts and virus-mediated nitrogen-cycling processes along the upper reference reach (UR), middle receiving reach (MR) and lower recovery reach (LR) of a typical WWTP effluents-receiving river. The results showed that compared to the non-hosts, viruses and hosts were much more sensitive to the influence of WWTP effluents. Among the three reaches, viruses and hosts showed more obvious spatial variability in community diversity and structures than those of non-hosts. Compared to UR, viruses in MR displayed the highest community diversity and virus-to-host abundance ratio, while viruses in LR maintained the high abundance ratio. Co-occurrence network analysis indicated the more important central roles of viruses than those of prokaryotes in bridging species or groups within the virus-host-prokaryote communities, especially in MR and LR. Functional gene analyses revealed that viral communities might potentially regulate nitrogen cycles in MR and LR via two pathways: directly carrying more abundant nitrogen-related auxiliary metabolic genes (N-vAMGs) and indirectly regulating hosts involved in nitrogen transformations (N-hosts) via enriched viruses, which showed strong responses to nitrogen loadings (TN and NO3[-]-N) in rivers. Both N-vAMGs and virus-enrichment N-hosts, dominantly involved in denitrification, dissimilatory nitrate reduction to ammonium, and organic degradation and synthesis processes, significantly increased in MR and LR, which highlighted a long-term regulation potential of viral communities to WWTP effluents-receiving rivers. Together, these findings provided a new insight into the nonnegligible ecological role of viruses in influencing biogeochemical cycles in WWTP effluents-receiving urban rivers.}, } @article {pmid41671969, year = {2026}, author = {Fan, B and Peng, H and Ran, J and Yao, H and Luo, W and Hong, B}, title = {Environmental and microbial regulation of multi-temporal scale methane flux dynamics in a shallow karst lake.}, journal = {Water research}, volume = {294}, number = {}, pages = {125511}, doi = {10.1016/j.watres.2026.125511}, pmid = {41671969}, issn = {1879-2448}, mesh = {*Methane/metabolism/analysis ; *Lakes/microbiology/chemistry ; Seasons ; Temperature ; Carbon Isotopes/analysis ; }, abstract = {Lakes are increasingly recognized as hotspots for methane (CH4) emissions, yet high-frequency (hourly-scale) measurements of CH4 fluxes throughout all seasons and a clear understanding of their underlying environmental control mechanisms are still lacking. Here, we explore the dynamics of CH4 flux and its hydrological and biogeochemical mechanisms in a karst shallow lake ecosystem, based on eddy covariance (EC), stable carbon isotope, and metagenomic sequencing techniques. Our 13-month EC monitoring shows that the lake was a CH4 source to the atmosphere, with average emission rate being 2.07 ± 1.20 mmol CH4 m[-2] d[-1], with the highest emissions in autumn (3.63 ± 0.5 mmol m[-2] d[-1]), accounting for more than twice those of winter. Seasonal CH4 flux variations were primarily driven by water temperature, water level, and electrical conductivity. Elevated temperature stimulated methanogenesis, water level changes altered redox gradients shaping methanogen activity, and electrical conductivity regulated substrate availability favoring acetoclastic methanogens. At the diurnal scale, CH4 emissions were higher at night than during the day, with diel flux variations were mainly controlled by water temperature, which enhanced methanogenesis while suppressing oxidation. These environmental controls on CH4 flux are consistent with the structure of the methanogenic community and support the dominance of acetoclastic methanogenesis. Methanothrix was found to be the dominant (∼65%) methanogenic microbe in this carbonate-rich alkaline karst lake. Additionally, the dominant pathway of CH4 production in the lake was acetoclastic methanogenesis, with the apparent fractionation factor of δ[13]C-CH4 being 1.041 ± 0.002. We emphasize the importance of integrating physicochemical variability with microbial functional potential to advance understanding of biogeochemical feedbacks in carbonate-rich karst systems and improve the accuracy of CH4 emission estimates across scales.}, } @article {pmid41672081, year = {2026}, author = {Miller, KJ and Wolff, IM and Montes de Oca Valeriano, LA and Soto-Giron, MJ and Jangi, S and Schott, EM and Charbonneau, MR and Ballok, AE and Toledo, GV}, title = {Targeted detection of microbes in synbiotic medical foods SBD111 and SBD121 to evaluate gut persistence: a randomised, open label trial.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-13}, doi = {10.1163/18762891-bja00109}, pmid = {41672081}, issn = {1876-2891}, abstract = {The viability and persistence of orally administered microbes in the human gut are essential to their biological function. We previously described the development of two synbiotic medical foods, SBD111 and SBD121, each comprising four food-derived microbial strains and prebiotic fibres for the dietary management of postmenopausal bone loss and rheumatoid arthritis, respectively. Here, we report a randomised, open-label clinical study examining gut persistence of SBD111 and SBD121 microbes by testing faecal samples from healthy adults following administration for seven days. Thirty-eight participants, aged 18-64 years with a body mass index (BMI) of 18.5-35 kg/m2, were randomised to receive one of the two synbiotic medical foods daily for one week, followed by a four-week monitoring period. Employing quantitative PCR (qPCR), shotgun metagenomics, and culture-based assays, we evaluated the presence and viability of the microbial strains comprising each synbiotic medical food during and after administration. SBD111 and SBD121 were well-tolerated with minimal adverse events reported. Strains were detected in over 80% of participants during the administration period, with strain abundance peaking in the first week. Persistence in the follow-up period varied by strain and detection method. The microbial strains were detected by qPCR and metagenomic sequencing for a median of seven days and three days during the follow-up period, respectively. However, Bacillus amyloliquefaciens was consistently detected for seven days by both methods. Culture-based assays confirmed the presence of viable strains from both synbiotic medical foods in stool samples up to one-week post-consumption. Faecal metagenome diversity and metabolic functional potential remained stable throughout the administration and follow-up periods. Collectively, these results establish that SBD111 and SBD121 deliver viable microbes that transiently persist in the gut, reinforcing their promise for safe and targeted dietary interventions and highlighting the value of multi-platform detection strategies for comprehensive microbial persistence assessment. This trial, funded by Sōlarea biō, is registered at ClinicalTrials.gov (NCT06614166).}, } @article {pmid41672314, year = {2026}, author = {Gao, C and Sui, Q and Tang, Q and Zhang, J and Yan, B and Yu, D and Zuo, F and Gui, S and Liu, Z and Hu, X and Wei, Y}, title = {Integration of real-time NH4[+]-N control and spatial microbial engineering achieves high removals of nitrogen and carbon in a sequence anoxic-oxic-anoxic (SAOA) system.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134189}, doi = {10.1016/j.biortech.2026.134189}, pmid = {41672314}, issn = {1873-2976}, mesh = {*Carbon/isolation & purification/metabolism ; *Nitrogen/isolation & purification/metabolism ; *Bioreactors/microbiology ; Animals ; Wastewater/chemistry ; Ammonia/metabolism ; Nitrification ; Anaerobiosis ; Biomass ; Bacteria/metabolism ; *Ammonium Compounds/metabolism ; Swine ; Water Purification/methods ; }, abstract = {The imbalance among nitrite supply, nitrate accumulation and aeration demand poses significant challenges in single-stage partial nitrification-anammox (PN/A) systems for stably treating high-strength anaerobically digested swine wastewater (ADSW) at low C/N ratio. Here, we propose a novel process that integrates real-time NH4[+]-N control with a floc-granule partitioned biomass architecture in a sequence anoxic-oxic-anoxic (SAOA) system to dynamically modulate free ammonia (FA) concentration while preventing free nitrous acid (FNA) inhibition. By maintaining an NH4[+]-N endpoint of 50 mg/L, FA was stabilized at 5.2 mg N/L, and FNA was effectively suppressed. Thus, the SAOA system achieved 94.14% TN removal at a loading rate of 0.24 kg N/(m[3]·d) and 92.71% COD at low influent COD/TN ratio of 1.71, respectively. Metagenomic and enzymatic profiling revealed a distinct ecological stratification: floccular biomass was enriched with Candidatus Kuenenia, whereas granular microenvironments favored ammonia-oxidizing bacteria (AOB), accompanied by the upregulation of key nitrification and anammox genes. Kinetic analysis of COD and NH4[+]-N removals revealed a stage-specific metabolic transition from carbon-driven to autotrophic nitrogen-dominated removal. This study provides mechanistically robust and scalable control paradigm for advancing simultaneous, high-efficiency nitrogen and carbon removal from nitrogen-rich and carbon-limited wastewater.}, } @article {pmid41672322, year = {2026}, author = {Gu, JJ and Mao, BD and Dou, XX and Zhang, BX and Xu, JW and Fu, CW and Lan, BJ and Zhang, XJ and Xu, Z and Gao, F}, title = {Unveiling the mechanisms of mechanical stirring for enhanced performance and stability of algal-bacterial flocs treating low C/N synthetic wastewater.}, journal = {Bioresource technology}, volume = {446}, number = {}, pages = {134175}, doi = {10.1016/j.biortech.2026.134175}, pmid = {41672322}, issn = {1873-2976}, mesh = {*Wastewater/chemistry/microbiology ; *Microalgae/metabolism ; *Nitrogen ; *Bacteria/metabolism ; *Carbon ; *Water Purification/methods ; Flocculation ; Extracellular Polymeric Substance Matrix/metabolism ; Biomass ; Sewage ; Biological Oxygen Demand Analysis ; }, abstract = {Algal-bacterial symbiotic systems (ABS) represent an environmentally sustainable wastewater treatment technology with significant application potential, though achieving stable and efficient operation remains a critical research challenge. This 180-day comparative study systematically investigated the performance differences and underlying mechanisms between mechanically stirred and aerated algal-bacterial symbiotic flocs (ABF) cultured in low C/N ratio wastewater. The results demonstrate that mechanical stirring enhances symbiotic interactions between microalgae and bacteria, leading to significantly improved performance metrics including higher biomass concentration (3.5 g/L), elevated dissolved oxygen levels (10.3 mg/L), increased lipid content (58.4%) and lipid productivity (9.3 mg/L/d), along with superior settling characteristics as evidenced by the reduced sludge volume index (80.7 mL/g). During Phase Ⅳ, the stirred ABFs exhibited exceptional contaminant removal efficiencies, achieving 98.2% ammonium nitrogen, 83.2% total nitrogen, and 89.7% chemical oxygen demand removal. Extracellular polymeric substance (EPS) analysis revealed stimulated secretion under stirring conditions (222.3 mg/g), with tight-bound EPS (TB-EPS) predominating, significantly enhancing floc structural stability. Metagenomic analysis demonstrated that stirring enriched functional genera like Thauera and Rubrivivax, strengthening denitrification and organic degradation capacities, while activating key pathways such as the TCA cycle and nitrogen metabolism, upregulating the abundance of EPS synthesis-related genes (e.g., galU), elucidating the molecular mechanisms underlying efficient nutrient removal and floc stability. This study presents an optimized strategy for establishing high-performance ABS in low C/N ratio wastewater treatment, offering both environmental sustainability and economic viability.}, } @article {pmid41672331, year = {2026}, author = {Yu, J and Allela, OQB and Alkhazali, WH and Bishoyi, AK and Oweis, R and Varma, P and Kashyap, A and Panigrahi, R and Chauhan, AS and Sameer, HN and Yaseen, A and Athab, ZH and Adil, M}, title = {The gut microbiome as a modulator of antibiotic resistance: Mechanisms, dynamics, and therapeutic interventions.}, journal = {Microbial pathogenesis}, volume = {215}, number = {}, pages = {108357}, doi = {10.1016/j.micpath.2026.108357}, pmid = {41672331}, issn = {1096-1208}, mesh = {Humans ; Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/drug effects/physiology/genetics ; Probiotics ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Prebiotics ; Animals ; Bacteriophages ; }, abstract = {The gut microbiome is increasingly recognized as a critical factor in the dynamics of antibiotic resistance, influencing the acquisition, persistence, and dissemination of antibiotic resistance genes (ARGs) among both commensal and pathogenic bacteria. This research focuses on elucidating the mechanisms by which the gut microbiome modulates the horizontal gene transfer (HGT) of ARGs, a key driver of the global antibiotic resistance crisis. By employing advanced metagenomic sequencing and functional assays, this study aims to identify specific microbial species, genetic elements, and metabolic pathways that either facilitate or inhibit the transfer of ARGs within the gut environment. Particular attention is given to the role of microbial metabolites, interspecies interactions, and environmental factors that shape the resistome the collection of all resistance genes within the microbiome. Additionally, this research explores innovative microbiome-based interventions, such as the use of probiotics, prebiotics, and bacteriophage therapy, to disrupt the transmission of ARGs and restore microbial balance. These interventions are designed to target the gut microbiome as a reservoir of resistance genes, offering a novel approach to curbing the spread of antibiotic resistance. The significance of this work lies in its potential to provide actionable insights into microbiome-mediated resistance mechanisms and to develop targeted strategies that complement traditional antibiotic therapies. By addressing the gut microbiome as a modifiable factor in the resistance landscape, this research could contribute to mitigating the global burden of antibiotic resistance, preserving the efficacy of existing treatments, and improving public health outcomes in the face of this pressing challenge.}, } @article {pmid41672407, year = {2026}, author = {Furst, AJ and Johnson, KE and Nagel, EM and Yerabandi, N and Kats, AM and Gallagher, TT and Gale, CA and Palmsten, K and Pierce, S and Hoffman, S and Jacobs, K and Fields, DA and Isganaitis, EM and Bode, L and Demerath, EW}, title = {Gestational diabetes, human milk oligosaccharide concentrations, and their links to infant weight gain and the gut microbiome in a United States observational cohort.}, journal = {The American journal of clinical nutrition}, volume = {123}, number = {4}, pages = {101235}, pmid = {41672407}, issn = {1938-3207}, support = {R00 HD113834/HD/NICHD NIH HHS/United States ; R01 HD080444/HD/NICHD NIH HHS/United States ; R01 HD109830/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Female ; *Milk, Human/chemistry ; *Oligosaccharides/metabolism/chemistry ; *Diabetes, Gestational/metabolism/microbiology ; Infant ; Adult ; Pregnancy ; *Gastrointestinal Microbiome ; *Weight Gain ; United States ; Feces/microbiology ; Cohort Studies ; Infant, Newborn ; Child Development ; Male ; }, abstract = {BACKGROUND: Gestational diabetes mellitus (GDM) increases offspring obesity risk, but whether this occurs via changes in human milk composition, including alterations in human milk oligosaccharides (HMOs), is unknown.

OBJECTIVES: This study aimed to identify differences in HMO concentrations in mothers with and without GDM and test whether GDM-associated HMOs are associated with infant growth, body composition, and fecal microbiome characteristics over the first 6-mo of life.

METHODS: Human milk was collected at 1-mo postpartum from 337 females (49 with GDM) who fed their infants breastmilk exclusively. HMOs were quantified by high-performance liquid chromatography and multivariate regression models were used to test differences in HMO concentrations by GDM status (false discovery rate adjustment for multiple testing set at q < 0.05). HMOs associated with GDM were then tested for associations with infant growth, body composition, and 1 and 6-mo infant fecal microbial abundances measured by metagenomic whole-genome sequencing.

RESULTS: Participants with GDM had ∼1 SD higher milk 6'sialyllactose (6'SL) {[β (95% confidence interval): 0.58 (0.20, 0.96)] and lacto-N-fucopentaose III (LNFP III) III [95% CI: 0.55 (0.16, 0.94)]} compared with those without GDM and 6'SL concentration was also positively associated with weight and length gain. Although infants of mothers with GDM had lower 1-mo fecal α-diversity and altered abundances of 6 of 56 microbial species detected compared with those without GDM, microbial features were not associated with the concentration of either 6'SL or LNFP III and evidence for mediation of GDM-growth and GDM-microbiome by HMOs was not found.

CONCLUSIONS: Mothers with a GDM diagnosis had higher milk concentrations of LNFP III and 6'SL, and 6'SL was in turn associated with increased infant growth rate, but neither HMO was associated with differential infant gut microbial abundances. The results suggest that the link between 6'SL and faster infant growth, if causal, occurs via mechanisms independent of the infant gut microbiome. This study was registered at clinicaltrials.gov as NCT03301753.}, } @article {pmid41672513, year = {2026}, author = {Nishijima, S and Hattori, M and Nagata, N}, title = {The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease.}, journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences}, volume = {102}, number = {2}, pages = {82-103}, pmid = {41672513}, issn = {1349-2896}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Health ; Japan ; Metagenomics ; Metagenome ; *Disease ; East Asian People ; }, abstract = {Metagenomics has become a powerful approach for deciphering the structure and function of the human gut microbiome, a complex microbial ecosystem in the gut. The human gut microbiome plays a crucial role in health and disease through multifaceted interactions with various factors, including age, diet, lifestyle, and medications. This review summarizes key advances in gut microbiome research over the past two decades and presents several topics from a recent large-scale, data-driven study, specifically a cohort-based initiative, the Japanese 4D microbiome project. These include a population-level characterization of the Japanese gut microbiome in a global context through comparison with 31,695 gut metagenomes from 37 countries, as well as an extensive analysis of the effects of medications. This review provides new insights into the ecology and uniqueness of the Japanese gut microbiome and highlights the importance of large-scale, well-phenotyped cohorts in advancing microbiome science.}, } @article {pmid41673004, year = {2026}, author = {Niu, M and Fu, L and Yan, Q and He, Z and Li, D and Zhen, Y and Wang, M and Li, C}, title = {35 metagenomic datasets from the northern and southern parts of the Yap trench sediments.}, journal = {Scientific data}, volume = {13}, number = {1}, pages = {}, pmid = {41673004}, issn = {2052-4463}, mesh = {*Metagenome ; *Geologic Sediments/microbiology ; Metagenomics ; *Microbiota ; Bacteria/classification/genetics ; }, abstract = {The hadal trench is the deepest part of the global ocean and harbors highly abundant microbial cells. However, the diversity and function of the majority of microbial communities in this part of the ocean are still unclear. Here, we collected 35 metagenomes from three push cores across different sites in both the northern and southern Yap trench to construct a comprehensive gene and genome dataset. A total of 32 million non-redundant genes were predicted from the whole metagenome datasets, with 63% assigned to known functional groups based on currently available databases. A total of 404 metagenome-assembled genomes (MAGs) with completeness >50% and contamination <10% were retrieved, and their taxonomy was highly diverse across 26 phyla. Alpha- and Gammaproteobacteria, Phycisphaerae, Nitrospiria, and Dehalococcoidia were dominant classes across all samples. The nonredundant gene and MAG datasets are valuable resources for advancing our understanding of the diversity, composition, and functions of microbiota in the sediment of the hadal trench.}, } @article {pmid41673107, year = {2026}, author = {Shepard, DM and Hahn, S and Chitre, M and Neff, H and Ward, DV and Jadhav, N and Richmond, JM and Ramirez-Ortiz, ZG}, title = {SCARF1 deficiency exacerbates gut inflammation and autoimmune pathology.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41673107}, issn = {2045-2322}, mesh = {Animals ; Mice ; *Lupus Erythematosus, Systemic/pathology/immunology/microbiology/genetics ; *Gastrointestinal Microbiome ; *Inflammation/pathology ; Mice, Knockout ; Dysbiosis ; Disease Models, Animal ; Female ; Autoimmunity ; Efferocytosis ; Autoimmune Diseases ; }, abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease known for its heterogeneity in both manifestation and presentation. Recent evidence has increasingly implicated the gut microbiome within immunomodulation and autoimmunity. This study aims to characterize the intestinal inflammation and microbial profile associated with autoimmune diseases, particularly SLE, and to identify unique biomarkers and shared microbial signatures for potential therapeutic measures. Our lab identified scavenger receptor class F, member 1 (SCARF1, SREC-1) as an efferocytosis receptor essential for the clearance of apoptotic debris, and its deficiency results in the development of lupus-like disease. SCARF1 is crucial in immune homeostasis, and defects in efferocytosis lead to inflammation. However, the role of SCARF1 in gut homeostasis remains to be elucidated. To answer our question, we analyzed and compared the metagenomic datasets generated through whole genome shotgun sequencing between our Scarf1[-/-] lupus-prone mouse model and healthy counterparts. We found that Scarf1[-/-] mice had significantly lengthened intestines, elevated immune cell infiltration, and structural changes in the colon. Microbiome analysis revealed gut dysbiosis, including reduced alpha diversity and increased Firmicute/Bacteroidetes ratio. Notably, beneficial taxa such as Akkermansia muciniphila was absent in Scarf1[-/-] mice. Linear regression analysis identified positive associations between lupus disease severity and increased abundances of Alistipes, Lachnospiraceae, and Clostridium. Function analysis of the gut microbiome in Scarf1[-/-] mice indicated downregulation of multiple pathways related to cell proliferation. These findings highlight the role of SCARF1 involvement in the gut microbiome and immune regulation in the context of inflammation and SLE.}, } @article {pmid41673333, year = {2026}, author = {Lu, L and Wang, X and Qin, Y and Xiao, Y and Zhang, Y and Ma, H and Wang, D and Li, Z}, title = {Hydrological Fragmentation Driving Microbial Carbon Necromass Reduction in Columnar Sediments: Evidence from CAZyme Genomic Signatures in Cascade Reservoirs.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41673333}, issn = {1432-184X}, support = {52470202//National Natural Science Foundation of China/ ; U2340222//National Natural Science Foundation of China/ ; NBWL202200489 and 202403005//China Three Gorges Corporation/ ; 309GJHZ2024110GC//Chinese Academy of Sciences/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Bacteria/genetics/enzymology/metabolism/classification/isolation & purification ; *Carbon/metabolism/analysis ; *Fungi/genetics/enzymology/metabolism/isolation & purification ; Carbon Cycle ; Rivers/microbiology/chemistry ; Metagenomics ; Carbon Sequestration ; }, abstract = {Microbial necromass carbon (MNC), a key component of soil organic carbon, plays a vital role in aquatic carbon sequestration. Its accumulation and transformation are highly sensitive to environmental changes, particularly in reservoir sediments-critical zones for organic matter storage and biogeochemical cycling. This study investigated the vertical distribution and regulatory mechanisms of MNC in cascade reservoir systems through sediment analysis and metagenomic sequencing. Our findings reveal that MNC constitutes 15 ~ 35% of total sediment organic carbon (SeOC) , with fungal-derived necromass consistently dominating over bacterial contributions. Metagenomic data highlight distinct functional potentials in carbon cycling, showing that bacterial necromass exhibits higher lability than fungal necromass, as evidenced by shifts in carbohydrate-active enzyme (CAZyme) gene abundances-particularly those involved in glucan and peptidoglycan degradation. Notably, cascade damming introduced spatial heterogeneity in MNC distribution , with downstream reservoirs experiencing reduced MNC accumulation due to altered hydrological connectivity and nutrient regimes. These results underscore the pivotal role of MNC in aquatic carbon storage while highlighting the complex interplay between environmental factors, microbial metabolic traits, and anthropogenic disturbances in regulated river systems. Therefore, our findings demonstrate that fungal necromass is a dominant and relatively stable component of sediment carbon, and its dynamics must be integrated to accurately assess and predict carbon sequestration in dammed rivers.}, } @article {pmid41673414, year = {2026}, author = {Salokas, J and Sofieva-Rios, S and Paatero, J and Asmi, E and Karppinen, A and Sofiev, M}, title = {Evaluation of commercial kits and purification approaches for DNA extraction from atmospheric samples for 3rd generation sequencing without amplification.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41673414}, issn = {2045-2322}, support = {101086109//HORIZON EUROPE Research Infrastructures/ ; 479507//Research Council of Finland/ ; 337552//Research Council of Finland/ ; 318194//Research Council of Finland/ ; }, mesh = {*DNA/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; *Environmental Monitoring/methods ; *Atmosphere/chemistry ; Aerosols/analysis ; Sequence Analysis, DNA/methods ; }, abstract = {We present a DNA extraction protocol for atmospheric bioaerosol samples collected on glass-fiber filters widely used in air quality monitoring. The protocol produces high-quality molecules suitable for third-generation sequencing and other applications. The initial protocol was developed and applied in a Bioaerosol campaign performed in Finland and Lithuania in 2021 using low-volume air samplers, which posed stringent requirements to the method sensitivity. The protocol included a phenol-chloroform step for DNA purification, thus involving aggressive reagents; it was also quite time consuming and laborious. The present study advances this protocol to exclude the use of hazardous chemicals by using the SPRI paramagnetic bead technology for DNA purification and compares it to several commercial extraction methods. Despite trailing in efficiency to the initial method, the new development proved to be more efficient than several column-based commercial kits. The updated protocol was effective for a relatively high mass ratio of biological material to filter material: 70 nanograms of potential DNA on the filter to one milligram of filter fiber, as detected with the initial phenol-chloroform-based method. However, the new approach was not effective for a mass ratio lower than 15 nanograms of potential DNA per milligram of the filter material. The applicability of the new protocol for preparation of samples for the 3rd generation sequencing was confirmed by subsequent processing of the samples with the Oxford Nanopore (ONT) GridION sequencer.}, } @article {pmid41673713, year = {2026}, author = {Touchette, D and Michoud, G and Boutroux, M and Gonzalez Mateu, M and Baier, F and Altshuler, I and Peter, H and Battin, TJ}, title = {Experimental insights in taxon-specific functional responses to droughts in glacier-fed stream biofilms.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {65}, pmid = {41673713}, issn = {2049-2618}, support = {197325/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Biofilms/growth & development ; *Ice Cover/microbiology ; *Droughts ; *Rivers/microbiology ; Diatoms/genetics/physiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; Metagenomics/methods ; Metagenome ; Multiomics ; Switzerland ; Cyanobacteria/genetics/classification ; }, abstract = {BACKGROUND: Glacier-fed streams are predicted to face increasingly frequent and intense droughts. However, the impacts of drought events on benthic biofilm, including bacteria, eukaryotes, and viruses, the dominating life form in glacier-fed streams, remain poorly understood.

RESULTS: Using streamside flume mesocosms in the Swiss Alps, we grew glacier-fed stream biofilms over 103 days and exposed them to three droughts. Using a multi-omics approach (metagenomics, metatranscriptomics, and metaproteomics), we assessed the effects of a series of droughts on the taxonomy and metabolic activity of bacterial, eukaryotic, and viral metagenome-assembled genomes (MAGs). We found that the first drought (6 h) caused only minor changes, including mild upregulation of heterotrophic metabolism and signs of stress in diatoms. In contrast, the second drought (24 h) significantly altered both the composition and functionality of the microbiome, shifting phototrophic dominance from diatoms to Cyanobacteriota, while maintaining overall phototropic biomass and further upregulating the heterotrophic metabolism. Interestingly, a third 24 h drought had no detectable transcriptomic effect between pre- and post-drought conditions, suggesting a certain level of adaptive responses to droughts, but with the low diatom abundance being maintained.

CONCLUSIONS: These findings indicate that glacier-fed biofilm microorganisms initially resisted short-term drought, but a second longer drought caused important shifts in their community structure, activity, and function. Climate-induced increases in drought frequency or duration may therefore have a lasting impact on microbial ecosystem functioning in glacier-fed streams. Video Abstract.}, } @article {pmid41673851, year = {2026}, author = {Zhu, Z and Kang, J and Song, M and Liu, Y and Dong, H and Wang, L and Fu, M and Ma, C and Guo, Q and Liu, Q}, title = {Early diagnosis of extranodal NK/T lymphoma presenting with oral ulcer and lip swelling by metagenomics next-generation sequencing: a case report.}, journal = {BMC oral health}, volume = {26}, number = {1}, pages = {}, pmid = {41673851}, issn = {1472-6831}, mesh = {Humans ; Male ; *Lymphoma, Extranodal NK-T-Cell/diagnosis/virology ; Adult ; *Oral Ulcer/virology/diagnosis ; *High-Throughput Nucleotide Sequencing ; *Metagenomics ; Herpesvirus 4, Human/genetics/isolation & purification ; }, abstract = {BACKGROUND: Extranodal natural killer/T-cell lymphoma, is a rare, aggressive lymphoma strongly associated with Epstein-Barr virus infection. Its clinical manifestations are often non-specific, and atypical presentations outside the nasal cavity, such as lip swelling or oral ulcers, can mimic benign oral conditions, leading to delayed diagnosis. Histological variability and tissue necrosis further hinder early diagnosis. Metagenomic next-generation sequencing (mNGS) has emerged as a useful adjunct for detecting pathogen-specific nucleic acids when conventional pathology is inconclusive.

CASE PRESENTATION: A 39-year-old man presented with a one-month history of recurrent upper lip swelling and a persistent labial and hard palate ulcer. Examination revealed firm swelling of the upper lip, a U-shaped ulcer on the upper labial mucosa, and an ulcer on the right hard palate. Laboratory tests were normal. Considering the patient's recollection of a prior fish bone injury to the oral mucosa, we performed mNGS on biopsy tissue in addition to routine histopathology. mNGS revealed a high load of Epstein-Barr virus DNA, prompting targeted immunohistochemistry and in situ hybridization, which confirmed the presence of Epstein-Barr virus-encoded RNA in atypical lymphocytes, establishing the diagnosis of extranodal NK/T-cell lymphoma. PET/CT showed a hypermetabolic upper-lip mass without systemic spread. The patient was classified as Ann Arbor stage IE, group A. Treatment with two cycles of pegaspargase, gemcitabine, and oxaliplatin resulted in complete healing of oral lesions, followed by localized radiotherapy. No recurrence was observed at the eight-month follow-up.

CONCLUSIONS: This case illustrates that extranodal NK/T-cell lymphoma can present with isolated oral lesions, posing significant diagnostic challenges. Incorporating mNGS into the evaluation of suspicious or infection-like oral lesions expedite Epstein-Barr virus detection, guide targeted pathological workup, and reduce diagnostic delays, ultimately improving patient outcomes.}, } @article {pmid41673994, year = {2026}, author = {Lin, C and Wang, J and Chai, S and Yan, Y and Cao, D and Guo, Y and Xu, M and Zhang, Y and Yuan, Z and Shi, Y and Liu, GR and Luo, LJ and Deng, S and Zhao, Y and Zhang, XH and Kang, X and Wei, J and Zhang, Z and Yang, J and Liu, SL and Liu, H}, title = {Enterolactone and THBS1-3TSR synergistically inhibit ovarian cancer and suppress angiogenesis in the tumour microenvironment.}, journal = {British journal of pharmacology}, volume = {183}, number = {11}, pages = {2837-2856}, doi = {10.1111/bph.70327}, pmid = {41673994}, issn = {1476-5381}, support = {CYCX24017//Heilongjiang CHUNYAN Innovation Team Program/ ; 82104217//National Natural Science Foundation of China/ ; 82020108022//National Natural Science Foundation of China/ ; LH2024H028//Heilongjiang Provincial Natural Science Foundation/ ; YJSCX2025-18HYD//Postgraduate Research & Practice Innovation Program of Harbin Medical University/ ; 2018M630380//China Postdoctoral Science Foundation/ ; LBH-Q21139//Heilongjiang Postdoctoral Financial Assistance/ ; LBH-Z18198//Heilongjiang Postdoctoral Financial Assistance/ ; 2019QD0026//Merit-based Funding for Returned Oversea Students in Heilongjiang Province/ ; 2019-YQ-08//Harbin Medical University Excellent Young Talents Funding/ ; 6101020101//Special Fund of Harbin Medical University/ ; XSTS2025164//Academic Enhancement Support Program of Hainan Medical University/ ; }, mesh = {Female ; *Ovarian Neoplasms/drug therapy/pathology/metabolism ; Humans ; Animals ; *Thrombospondin 1/metabolism ; *Tumor Microenvironment/drug effects ; *Neovascularization, Pathologic/drug therapy ; *4-Butyrolactone/analogs & derivatives/pharmacology ; *Lignans/pharmacology ; Zebrafish ; Cell Line, Tumor ; Mice, Nude ; Mice ; *Antineoplastic Agents/pharmacology ; *Angiogenesis Inhibitors/pharmacology ; Cell Proliferation/drug effects ; Molecular Docking Simulation ; }, abstract = {BACKGROUND AND PURPOSE: Ovarian cancer is a highly malignant disease with poor prognosis due to its insidious occurrence, early metastasis and high rate of recurrence after treatment. Enterolactone (ENL) has previously been reported to inhibit ovarian cancer in positive correlation with THBS1 expression, but the involved molecular events remain unknown. In this study, we looked into interactions between ENL and THBS1 to elucidate the mechanisms underlining their joint inhibitory effects on ovarian cancer.

EXPERIMENTAL APPROACH: We observed the suppressive effect of ENL on ovarian cancer cells by cell counting kit-8, wound healing, transwell, western blot and immunohistochemistry assays. The binding of ENL to THSB1 was assessed by molecular docking and microscale thermophoresis assays. Inhibition of malignant angiogenesis by ENL was inspected by tube formation assay and zebrafish experiment. The in vivo anticancer abilities of ENL were investigated by xenograft and allograft ovarian cancer animal models, and the fecal microbiota was analysed by metagenomics.

KEY RESULTS: This study demonstrated potent inhibitory effects of ENL on ovarian cancer by both in vitro and in vivo experiments. Analysis of 61 clinical samples showed a correlation between poor prognosis and low THBS1 expression. ENL affected the expression of THBS1 and other proteins such as CD36. ENL through binding with the 3TSR domain of THBS1 inhibited malignant angiogenesis and suppressed cancer progression. ENL administration could also ameliorate gut dysbacteriosis.

CONCLUSIONS AND IMPLICATIONS: ENL has potent inhibitory effects on ovarian cancer and suppresses malignant angiogenesis by binding to THBS1-3TSR. ENL ameliorates gut dysbacteriosis.}, } @article {pmid41674065, year = {2026}, author = {Jo, S and Seo, H and Lee, KA and Kim, S and Rahim, MA and Barman, TI and Kim, HS and Song, HY}, title = {Skin Microbiome Profiling in Patients with Primary Sjögren Disease Compared to Healthy Individuals.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2510010}, pmid = {41674065}, issn = {1738-8872}, mesh = {Humans ; *Sjogren's Syndrome/microbiology ; *Skin Microbiome ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Female ; Middle Aged ; Male ; Adult ; *Skin/microbiology ; Biodiversity ; Biomarkers ; Metagenomics ; *Microbiota ; DNA, Bacterial/genetics ; }, abstract = {Primary Sjögren disease (SjD) is a systemic autoimmune disease characterized by inflammation of exocrine glands, most commonly leading to dry mouth and dry eyes. Although the etiology of SjD remains unclear, emerging evidence suggests that the microbiome modulates immune homeostasis. This study aimed to compare the skin microbiomes of SjD patients with those of healthy controls (HCs) using 16S rRNA gene sequencing. Taxonomic composition, alpha and beta diversity, and predicted functional profiles were evaluated. We observed a significant depletion of Cutibacterium and a marked reduction in microbial diversity in SjD patients. Beta diversity analyses revealed distinct clustering among groups. Functional prediction suggested the downregulation of metabolic pathways associated with microbial homeostasis. Our findings propose that alterations in the skin microbiota may contribute to SjD pathogenesis and serve as potential biomarkers or therapeutic targets.}, } @article {pmid41674105, year = {2026}, author = {Song, B and Zeb, J}, title = {The midgut of Aedes albopictus shapes its bacteriome but not its mycobiome.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70505}, pmid = {41674105}, issn = {1526-4998}, support = {//City University of Hong Kong/ ; }, abstract = {BACKGROUND: Midgut microbiota consists mainly of bacteria and fungi and can interact directly or indirectly with ingested pathogens. However, both the specific microbes that stably colonize the mosquito midgut and how the midgut shapes their microbiome remain poorly understood. In this study, we analyzed the midgut microbiome of the insect vector Aedes albopictus at three different developmental stages collected from the field. Additionally, we reared field-collected larvae under laboratory conditions, using either field water from the breeding habitat or sterilized water, to track the linear evolution of the microbiome from larvae to adulthood.

RESULTS: Our metagenomic analysis revealed that the mosquito host selected specific bacterial species, while the mycobiome remained virtually identical to that of the surrounding water. We identified 42 core bacterial species that form a highly interactive network, as well as two core fungal species, both of which were consistently more abundant in the mosquito gut than in the surrounding water across all life stages in both laboratory and field conditions. Furthermore, we successfully assembled 271 bacterial genomes de novo, 14 of which belonged to core species. These 14 bacterial genomes were enriched in genes associated with antioxidant function and cAMP metabolism.

CONCLUSION: This study uncovers fluctuating bacterial dynamics alongside conserved fungal communities in the mosquito gut, suggesting distinct mechanisms that shape the bacteriome and mycobiome. This study highlights the antioxidant function in stabilizing bacteria in Aedes albopictus. © 2026 Society of Chemical Industry.}, } @article {pmid41674268, year = {2026}, author = {Zaccaria, T and Beblo-Vranesevic, K and de Jonge, MI and Netea, MG and Rettberg, P}, title = {Survival limits of psychrotolerant microorganisms with relevance for planetary protection of the icy moons.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {384}, number = {2314}, pages = {}, doi = {10.1098/rsta.2024.0435}, pmid = {41674268}, issn = {1471-2962}, support = {//Deutsches Zentrum für Luft- und Raumfahrt/ ; //Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; /ERC_/European Research Council/International ; }, mesh = {*Extraterrestrial Environment ; *Moon ; Spacecraft ; Planets ; *Microbial Viability ; Arctic Regions ; *Extremophiles/physiology ; Solar System ; }, abstract = {Investigating the survival limits of extremophilic microorganisms exposed to simulated space conditions can shed light on the ability of terrestrial microorganisms to survive and propagate on other planetary bodies. Although microbes can be found in all environmental niches on Earth, this study focuses on psychrophilic and psychrotolerant microorganisms (prokaryotes and eukaryotes) which have been isolated from locations of interest such as icy moon analogue environments (e.g. Canadian high arctic, Antarctica) and cleanrooms, which might be relevant for forward planetary protection. Our research aimed to reproduce conditions for microorganisms on spacecraft travelling to the outer solar system which could contaminate the icy moon's subsurface oceans. The microorganisms were grown under oligotrophic conditions in minimal media supplemented with only a single carbon source and exposing them to extreme conditions, in terms of temperature fluctuations, in terms of freeze and thaw cycles, and radiation, as they occur during the space travel to the outer solar system. Our results in combination with future metagenome data and phenotype prediction tools will allow the identification of planetary protection relevant microorganisms in spacecraft assembly cleanrooms and on spacecraft and support the development of a target-oriented planetary protection constraints for missions to the icy moons. This article is part of the theme issue 'Planetary Protection for sustainable space exploration'.}, } @article {pmid41674272, year = {2026}, author = {Macey, MC and Mahnert, A and Stephens, BP and Kucukkilic-Stephens, E and Olsson-Francis, K}, title = {An ensemble binning approach to identify functional diversity in cleanroom environments.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {384}, number = {2314}, pages = {}, doi = {10.1098/rsta.2024.0438}, pmid = {41674272}, issn = {1471-2962}, support = {//UK Space Agency/ ; }, mesh = {*Environment, Controlled ; *Microbiota/genetics ; Bacteria/genetics/classification ; Metagenome ; Metagenomics/methods ; *Ecological Systems, Closed ; Spacecraft ; }, abstract = {Cleanroom environments, crucial for spacecraft assembly, are subject to stringent sterilization protocols to minimize microbial contamination. However, tolerant microbes can persist and pose a potential risk for planetary protection. This study employs an ensemble binning approach, integrating multiple metagenome binning programs, to analyse published metagenomic datasets generated from NASA cleanrooms to investigate functional diversity within cleanrooms. Twenty-six medium and high-quality, non-redundant metagenome-assembled genomes (MAGs) spanning six bacterial phyla were generated. Functional analysis of these MAGs identified potential metabolic pathways for the degradation of commonly used cleaning agents, suggesting that these compounds could serve as carbon sources. Furthermore, genomic analyses identified diverse physiological tolerances, with many MAGs possessing polyextremophilic traits, including resistance to high salinity, temperature and alkalinity. Growth rate index (GRiD) analysis also suggested some MAGs were actively replicating within the cleanroom environments. This study demonstrates the power of ensemble binning in revealing the functional diversity and adaptive strategies of cleanroom microbiomes and provides critical insights for refining planetary protection protocols. This article is part of the theme issue 'Planetary Protection for sustainable space exploration'.}, } @article {pmid41674474, year = {2026}, author = {Sun, Y and Shuai, X and Sheng, Q and Lu, Y and Wu, Z and Sun, Y and Wu, D and Guo, X}, title = {Torque Teno Virus or Herpesviruses Detection By Metagenomic Next-Generation Sequencing Predicts In-Hospital Major Adverse Events in Critically Ill Patients With Severe Infections.}, journal = {Journal of medical virology}, volume = {98}, number = {2}, pages = {e70840}, pmid = {41674474}, issn = {1096-9071}, support = {//Zhongguancun Precision Medicine Foundation/ ; }, mesh = {Humans ; *Torque teno virus/genetics/isolation & purification ; *Critical Illness ; Female ; High-Throughput Nucleotide Sequencing ; Middle Aged ; *DNA Virus Infections/diagnosis/virology/epidemiology ; Male ; *Herpesviridae/genetics/isolation & purification ; Aged ; Metagenomics ; *Cross Infection/virology/epidemiology/diagnosis ; China/epidemiology ; Intensive Care Units ; Risk Factors ; *Herpesviridae Infections/diagnosis ; Incidence ; Adult ; }, abstract = {Viral detection occurs frequently in critically ill patients. Patients with multiple viremic events had a higher ICU mortality. The highly sensitive mNGS technology has significantly enhanced viral pathogen detection rates. We enrolled 134 critically ill patients with severe infections who underwent mNGS testing during January 2019 to December 2021, at Qilu Hospital (Qingdao) of Shandong University. Viral pathogens were identified in 78 cases (58.2%). Torque teno virus (TTV) or herpesviruses (HVs) showed the highest detection rates (23.1% and 29.9%, respectively). The incidence of major adverse events (MAEs) in the hospital was 53.0%. Patients with TTV or HVs detection had more secondary nosocomial infections and stress ulcers, and the incidence of MAEs showed an increasing trend. Multivariate Logistic regression analysis showed that APACHE II score (OR: 1.10, 95%CI: 1.02-1.19, p = 0.018) and TTV or HVs detection by mNGS (OR: 2.40, 95% CI: 1.05-5.50, p = 0.038) were independent risk factors for MAEs. This study advocates the use of mNGS for detecting viruses in critically ill patients with severe infections, as it serves as a predictor for heightened risk of in-hospital MAE.}, } @article {pmid41674563, year = {2025}, author = {Lyu, W and Chen, L and Li, DF and Li, SY and Dai, Q and Zhou, HL and Liu, YY and Zhou, JY and Liang, XJ and Wang, L}, title = {Lactobacillus johnsonii-FM1 modulates gut microbiota and secretes anticancer metabolite vanillic acid to inhibit colorectal tumorigenesis.}, journal = {iMetaOmics}, volume = {2}, number = {3}, pages = {e70050}, pmid = {41674563}, issn = {2996-9514}, abstract = {During colorectal cancer (CRC) progression, probiotics support gut microbial balance, enhance intestinal barrier integrity, and exert antioxidant and anti-inflammatory effects. Such supplementation may slow tumor growth and serve as an adjunctive therapy for CRC. In this study, we evaluated the impact of Lactobacillus johnsonii-FM1 in Apc [Min/+] and azoxymethane/dextran sulfate sodium-induced CRC mouse models. Our results demonstrate that L. johnsonii-FM1 markedly reduces tumor number, size, and volume in both models. Shotgun metagenomic sequencing showed that L. johnsonii-FM1 increases the abundance of potentially beneficial taxa while decreasing opportunistic pathogens, thereby preserving gut barrier function. Moreover, untargeted metabolomics paired with liquid chromatography-tandem mass spectrometry identified vanillic acid (VCA) as a key bioactive metabolite produced by L. johnsonii-FM1. In vitro, VCA inhibits CRC cell line proliferation, diminishes colony formation, induces cell-cycle arrest, and promotes apoptosis. Mechanistically, VCA attenuates CRC progression by suppressing Wnt/β-catenin signaling. Our findings suggest a promising probiotic-based adjunctive strategy for CRC prevention and treatment.}, } @article {pmid41674575, year = {2025}, author = {Zhang, Z and Xu, Y and Pang, K and Wu, C and Zhao, C and Lei, T and Zhang, J and Hai, T and Zhao, F and Zhao, Y}, title = {Microbiota humanization drives human-like metabolic and immune transcriptomic shifts in pigs.}, journal = {iMetaOmics}, volume = {2}, number = {3}, pages = {e70034}, pmid = {41674575}, issn = {2996-9514}, abstract = {Pigs are increasingly recognized as promising candidates for clinical xenotransplantation and as large-animal models for biomedical research; however, interspecies differences in gut microbiota, immune function, and metabolism remain major barriers. To address this, we established gut microbiota-humanized (GMH) pigs by transplanting human fecal microbiota into antibiotic-treated pigs. We systemically evaluated alterations in microbiota composition, serum metabolites, and immune cell profiles using integrated metagenomic, quasi-targeted metabolomic and single-cell transcriptomic (scRNA-seq) analyses. Metagenomic profiling revealed a shift in the intestinal microbiota of GMH pigs toward a human-like composition, characterized by enrichment of Bacteroidia and depletion of Bacilli. Metabolomic analysis showed that GMH pigs exhibited serum metabolite profiles more closely resembling those of humans. Among 423 detected serum metabolites, 136 that were lower in control pigs than in humans were upregulated in GMH pigs, whereas 79 that were elevated in control pigs decreased post-transplantation. Notably, pathways related to tryptophan metabolism, bile acid biosynthesis, and fatty acid metabolism were enhanced in GMT pigs, while carbon-related and glycolytic pathways were attenuated, indicating partial convergence toward human metabolic phenotype. Integration of microbial and metabolite data identified 20 and 33 metabolites associated with Bacteroidia and Bacilli, respectively. scRNA-seq profiling of peripheral blood mononuclear cells demonstrated transcriptional and compositional remodeling of T cells, monocytes, and B cell subsets in GMH pigs. These findings demonstrated that human fecal microbiota can reshape both systemic metabolic and immune artitecture in pigs, offering a robust large-animal platform for studying host-microbiota interactions and advancing translational application in xenotransplantation and microbiome-based therapeutics.}, } @article {pmid41674603, year = {2026}, author = {Agudelo, C and Nsereko, M and Ainebyona, A and Andama, A and Castro, R and Leung, SRM and Nakafeero, J and Nannyonga, G and Nolan, K and Teran, L and Wambi, P and Young, MG and Kato-Maeda, M and Cattamanchi, A and Jaganath, D and Wobudeya, E and Wolf, AR}, title = {Evaluating metagenomic sequencing as a stool-based diagnostic in children with presumptive TB in Uganda.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.29.26345155}, pmid = {41674603}, support = {R35 GM147512/GM/NIGMS NIH HHS/United States ; K23 HL153581/HL/NHLBI NIH HHS/United States ; R21 AI176295/AI/NIAID NIH HHS/United States ; U01 AI152087/AI/NIAID NIH HHS/United States ; R01 HL139717/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: Stool-based molecular tests are a noninvasive option for pediatric tuberculosis (TB) diagnosis, but have lower sensitivity compared to sputum-based tests. Untargeted metagenomic sequencing (mNGS) on stool could improve sensitivity and identify new gene targets for molecular testing.

METHODS: We performed shotgun mNGS on DNA isolated from stool samples of children undergoing assessment for pulmonary TB in Uganda. We defined the performance of mNGS to identify Mycobacterium tuberculosis (Mtb) against a microbiological reference standard (MRS, TB if sputum Xpert Ultra or culture positive) and a composite reference standard (TB if confirmed or unconfirmed TB). We also compared accuracy of mNGS against the stool-based Xpert Ultra test. Finally, we identified enriched genomic loci among Mtb classified reads.

RESULTS: We analyzed 176 stool samples of children with a median age of 3.6 years (IQR, 1-6 years). !"#$%&'(')*(+,-. (')*(&*%&$'$/$'$*&(01(234-(5$')(60&$'$/*(78(9*1$%*9(as ≥ 1, 2, or 5 sequence fragments were 35.5% (95% CI 19%:;;<=.(>;?@<(AB>< : 45%), and 19.4% (13%-25%) respectively, and specificities 92.64% (87%-96%), 97% (93%-99%), and 99.3% (96%-100%). Stool Xpert Ultra had similar sensitivity (22.6%) to stool mNGS considering all samples tested. In a head-to-head comparison, stool mNGS had lower sensitivity than stool Xpert Ultra (38.5% vs. 53.8%, difference -15.3%, 95% CI 14-68 to 25-81). mNGS utilized rRNA, virulence proteins and membrane proteins not targeted in current PCR-based platforms.

CONCLUSIONS: Metagenomic sequencing of stool DNA did not increase sensitivity of TB detection, but identified novel targets for molecular testing that may support development of more sensitive tests.}, } @article {pmid41674628, year = {2026}, author = {Ueland, K and Elahi, T and Rasmussen, M and Wolfe, AE and Purcell, H and Chakka, SR and Mirimo-Martinez, M and Persinger, H and Johnson, K and Boynton, A and McMillen, K and Byelykh, M and Biernacki, MA and Yeh, AC and Ali, N and Manjappa, S and Wuliji, N and Fredricks, DN and Bleakley, M and Holmberg, LA and Schenk, JM and Raftery, D and Ma, J and Hill, GR and Neuhouser, ML and Lee, SJ and Markey, KA}, title = {Plant-based whole-food diets are feasible during autologous stem cell transplantation and are associated with dose-dependent microbiome modulation: Results from a pilot clinical trial.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.02.26345403}, pmid = {41674628}, support = {P30 DK035816/DK/NIDDK NIH HHS/United States ; }, abstract = {Plant-based dietary strategies may offer a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing autologous hematopoietic cell transplantation (auto-HCT) for multiple myeloma, a population in whom intestinal dysbiosis has been linked to infectious complications and inferior survival. We conducted a single-arm study to test the feasibility and biological activity of a high-fiber, plant-based, whole-food meal delivery intervention during the peri-transplant period. Adults with multiple myeloma (n = 22) received fully prepared, plant-based meals for 5 weeks spanning conditioning, neutropenia, and early recovery, with the goal of supporting consumption of nutrient-dense, high-fiber foods despite transplant-related symptoms that often limit oral intake. The primary endpoints were feasibility and tolerability, defined by successful enrollment, adherence to study procedures, and patient-reported intake of study meals; diet was quantified using prospective food diaries and 24-hour dietary recall surveys. Secondary endpoints included changes in gut microbiome composition and function assessed by shotgun metagenomic sequencing and stool short-chain fatty acid (SCFA) measurements. The intervention was feasible and generally well tolerated, with all participants consuming at least some proportion of delivered meals and with adherence sufficient to support planned dietary and correlative analyses. Greater intake of study meals was associated with more pronounced shifts in gut microbial communities, including enrichment of SCFA-producing taxa and compositional changes consistent with a fiber-responsive microbiome. Stool SCFA concentrations increased from baseline to the end of the intervention, suggesting a functional impact of the dietary strategy on microbial metabolite production during the peri-transplant period. These findings demonstrate that a plant-based meal delivery intervention is implementable during auto-HCT and suggest dose-dependent modulation of the gut microbiome and its metabolic output. Larger randomized trials are warranted to determine whether microbiome-targeted nutrition can reduce transplant-related toxicities, enhance immune recovery, and improve disease control in multiple myeloma. The trial is registered at ClinicalTrials.gov (NCT06559709).}, } @article {pmid41674736, year = {2026}, author = {Mukenschnabl, K and Humpel, O and Abdalla, TE and Wood, E}, title = {An Unusual Case of Unexplained Infertility: Co-colonization of the Uterus and Seminal Fluid.}, journal = {Cureus}, volume = {18}, number = {1}, pages = {e101251}, pmid = {41674736}, issn = {2168-8184}, abstract = {Chronic endometritis (CE) is defined as a persistent, mild inflammation of the endometrium induced by intrauterine bacterial infection. CE has been associated with infertility in patients with recurrent in vitro fertilization (IVF) failure. We report an unusual case of bacterial co-colonization of the endometrium and seminal fluid in a couple with unexplained infertility. A 35-year-old woman presented to the office for infertility evaluation after 16 months of inability to conceive naturally using ovulation kits. Initial workup revealed adequate ovarian reserve with an anti-Müllerian hormone (AMH) level of 4.8 ng/mL, tubal patency on hysterosalpingogram, and normal semen analysis. The patient and her partner failed to conceive following three cycles of ovulation induction with intrauterine insemination (IUI). In preparation for IVF, an endometrial biopsy (EMB) was performed, and five CD138+ plasma cells per 10 high-power fields suggested CE. The patient underwent antibiotic therapy, yet EMB remained positive. At this time, the partner's semen culture was positive for Enterococcus faecalis and Escherichia coli. Endometrial microbiome metagenomic analysis (EMMA) and analysis of infectious chronic endometritis (ALICE) demonstrated co-colonization with the same bacteria seen on her partner's semen culture. Both the patient and her partner required multiple rounds of antibiotic therapy before successful conception via IVF. This case demonstrates an unusual occurrence of bacterial co-colonization of the endometrium and seminal fluid in a couple with unexplained infertility, suggesting a potential pathway for CE development from bacteriospermia. The patient's EMMA/ALICE tests and the partner's semen cultures revealed the presence of the same bacteria. While current literature does not identify the development of CE from the bacteria in a partner's semen, there is an association between bacteria in semen and infertility. In couples with unexplained infertility, thorough evaluation for CE with EMB and EMMA/ALICE can be performed in conjunction with a semen culture on the partner to explore potential co-colonization and guide dual-partner treatment.}, } @article {pmid41674838, year = {2026}, author = {Berta, J and Rowe, L and Garry, B}, title = {Catching the Mardi Gras fever: Quantifying the impact of mass gathering tourism on local bacterial prevalence and community diversity in municipal wastewater.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {41674838}, issn = {2693-5015}, support = {U01 AI151812/AI/NIAID NIH HHS/United States ; }, abstract = {We employed 16S metagenomic analysis to measure the impact of Mardi Gras tourism on the bacterial ecology found in New Orleans' municipal wastewater. Throughout the peak of the 2023 Carnivale season, species turnover was significantly higher in New Orleans than it was in our control site. Alpha diversity metrics peaked 2-to-3 weeks after Mardi Gras Day, increasing between 65% and 1967% over Carnivale. We also found that human pathogens and microbiota had significantly stronger, more positive correlations with the rise in Mardi Gras tourism than did environmental control species. These changes in wastewater abundance for two species - S. enterica and E. coli - mirrored the concurrent clinical isolate data from the same region for Salmonella spp. and STEC. We also found that multiple alpha and beta diversity measures correlated strongly with increases in tourism during the peak of Carnivale season.}, } @article {pmid41674903, year = {2025}, author = {Ding, Z and Ren, K and Xu, Y and Feng, T and Cui, K and Liu, Q and Liao, C}, title = {Disease-driven restructuring of the gut microbiome underlies inflammatory bowel disease dysbiosis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1744574}, pmid = {41674903}, issn = {1664-302X}, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic and recurrent intestinal disorder with rising global incidence, yet its complex pathogenesis remains poorly understood, underscoring the need to clarify the microbial mechanisms underlying intestinal inflammation. IBD is associated with a profound imbalance of the gut microbial ecosystem. However, the ecological and functional remodeling of the gut microbiota during IBD progression remains unclear. This study used metagenomic sequencing to investigate microbial composition, functional capacity, and ecological interactions in the gut microbiota of IBD patients compared with healthy individuals.

RESULTS: The IBD group exhibited significantly reduced microbial diversity and a distinct community structure compared with healthy controls. Pro-inflammatory genera such as g_Fusobacterium (p < 0.001) and g_Morganella (p < 0.001) were enriched, whereas short-chain fatty acid producing bacteria, including g_Ruminococcus (p < 0.0001) and g_Agathobacter (p < 0.0001), were markedly depleted. Functional annotation revealed decreased abundance of carbohydrate-active enzymes (GH3, GH44, GH53, and GH77; all p < 0.05) associated with polysaccharide degradation, together with enrichment of pathways related to immune activation and inflammation, such as the JAK-STAT and chemokine signaling pathways (p < 0.05). Co-occurrence network analysis further showed that IBD-associated microbes formed positively correlated clusters dominated by inflammatory taxa, whereas healthy microbiota were organized around SCFA-producing commensals.

CONCLUSION: Compared with healthy individuals, the gut microbiota of IBD patients undergoes functional reprogramming characterized by loss of metabolic versatility and enrichment of inflammation-related pathways. These findings provide new insights into the ecological and metabolic mechanisms through which the gut microbiota contribute to intestinal inflammation and disease progression.}, } @article {pmid41674905, year = {2025}, author = {Díaz-Santiago, E and Sadio, TD and Diéme, JS and Hurtado-Martínez, M and Kindler, C and Manrique, E and Pugnaire, FI}, title = {Soil microbial communities in contrasting environments show a common core of species linked to Maytenus senegalensis shrubs.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1699694}, pmid = {41674905}, issn = {1664-302X}, abstract = {INTRODUCTION: The existence of a core microbiota specific to a plant species, or the set of microorganisms shared by all plant individuals of the species, is of utmost importance because of its many conceptual and practical consequences. The core microbiota is assumed to gather the most ecologically and functionally relevant microorganisms associated to a plant in a given environment, presumably establishing positive feedbacks that support its persistence and performance in a plant community.

METHODS: We tested the existence of a potential core microbiota in Maytenus senegalensis shrubs in two contrasted, distant ecosystems; a dry environment (Almeria, Spain) and a relatively wetter ecosystem (Dakar, Senegal).

RESULTS: Soil microbial community structure widely differed between sites influenced by soil and climate. However, a subset of microbial phylotypes appeared consistently associated to all M. senegalensis plants across our two disparate ecosystems while they were absent in the surrounding soil, suggesting the presence of a core microbiota in M. senegalensis.

DISCUSSION: Microbiota had an effect on germination that differed between sites, perhaps due to climatic constrains. We show that the assembly of understory microbial communities depends on the plant's sorting effect on the surrounding soil microbiota, plus some other taxa likely transferred by seeds; this assembly mechanism is relevant for the coevolution of plants and microorganisms, and critical for potential community responses to environmental changes.}, } @article {pmid41675149, year = {2025}, author = {Shen, H and Du, C and Jiang, S and Dong, W and Li, J and Hu, Y and Peng, N and Zhao, S}, title = {Native synthetic microbial communities enhance zha-chili by boosting the fermentation capacity of indigenous microorganisms.}, journal = {iMetaOmics}, volume = {2}, number = {2}, pages = {e70009}, pmid = {41675149}, issn = {2996-9514}, abstract = {Fermented foods are a crucial part of the global diet, accounting for one-third of global food intake. Traditional fermented foods often rely on natural fermentation, leading to safety risks. The construction of synthetic microbial communities (SynComs) tailored for fermented foods is a key strategy to solve these issues. Here, we designed and constructed SynComs consisting of two bacterial and three fungal species, utilizing the study model of zha-chili. Using various high-throughput sequencing technologies, the dynamic alternations of microorganisms during the fermentation process were investigated, and the impact of SynComs on the fermentation process was evaluated. SynComs reduced fermentation time by approximately 15 d, increased flavor yields (8% for ethyl lactate and ethyl acetate), and greatly improved the quality of the zha-chili. Meanwhile, SynComs altered the succession of the fungal community so that Pichia became the dominant microorganism throughout the fermentation process, and the pattern of fungal community succession was brought closer to the null model. Metagenomic annotation results showed notable changes in functional genes, especially in glycoside hydrolases family. SynComs enhanced the positive correlations between indigenous microorganisms and flavor compounds while increasing other community microorganisms' contribution to flavor production. These findings provide a new approach to improve the quality of zha-chili and other traditional fermented foods through natural fermentations. We proposed that SynComs enhanced fermented foods by boosting the fermentation capacity of indigenous microorganisms.}, } @article {pmid41675151, year = {2025}, author = {Skoog, EJ and Kebabonye, K and Klempay, B and Gondwe, M and Makati, K and Babayani, N and Jongman, M and Bowman, J and Aluwihare, L}, title = {Viral metagenomics of Okavango Delta water pans reveal novel insights into wildlife disease potential.}, journal = {iMetaOmics}, volume = {2}, number = {2}, pages = {e70018}, pmid = {41675151}, issn = {2996-9514}, abstract = {Botswana's Seronga region saw a mass elephant die-off potentially linked to water sources. This study analyzes Okavango Delta metagenomes, uncovering a diversity of viruses and harmful pathogens. Findings highlight the importance of understanding viral ecology in these waters and support One Health's objective in protecting human, animal, and ecosystem health.}, } @article {pmid41675153, year = {2025}, author = {Ye, L and Hu, Q and Zang, T and Wang, Y and Heng, H and Chan, EWC and Chen, S}, title = {Deciphering comprehensive profiles of pathogenies and resistome of pork using integrating metagenomic and isolation strategies.}, journal = {iMetaOmics}, volume = {2}, number = {2}, pages = {e70004}, pmid = {41675153}, issn = {2996-9514}, abstract = {The pork microbiome was investigated using an integrated approach combining isolation and metagenomic sequencing methods to comprehensively analyze the pathogens and resistome on pork surfaces. The study revealed a large number and diversity of pathogens and resistance genes, potentially originating from air, transportation, water, or cross-contamination. These findings underscore the importance of implementing multifaceted food surveillance strategies to monitor and mitigate these risks effectively.}, } @article {pmid41675165, year = {2025}, author = {Liu, S and Ye, Y and Guo, B and Hu, Y and Jiang, K and Liang, C and Xia, S and Wang, H}, title = {ViOTUcluster: A high-speed, All-in-one pipeline for viromic analysis of metagenomic data.}, journal = {iMetaOmics}, volume = {2}, number = {2}, pages = {e70023}, pmid = {41675165}, issn = {2996-9514}, abstract = {ViOTUcluster is a user-friendly, high-speed, accurate, All-in-one solution that streamlines the entire viromic analysis workflow-from raw reads to the generation of viral operational taxonomic units tables, as well as other key viromic analysis tasks.}, } @article {pmid41675545, year = {2024}, author = {Huang, L and Luo, S and Liu, S and Jin, M and Wang, Y and Zong, X}, title = {Comparative multiomics analyses reveal the breed effect on the colonic host-microbe interactions in pig.}, journal = {iMetaOmics}, volume = {1}, number = {1}, pages = {e8}, pmid = {41675545}, issn = {2996-9514}, abstract = {Dysregulation of the gut microbiota often leads to immune-related disorders, indigestion, or diarrhea. Here, Jiaxing Black (JXB) pig, a local Chinese pig breed known for its great tolerance and digestibility of nutrients, was employed for a metagenomic and transcriptomic integrative analysis to reveal the gut microbiota-genes and gut microbiota-pathway interactions. A total of 452 differentially expressed genes, and 174 phyla were found between the JXB and the Duroc × Landrace × Yorkshire (DLY) pigs. Detailed analysis revealed that the differences in colon gene expression signatures between the JXB and DLY are mainly enriched in metabolic and inflammatory responses, with Lactobacillus and Lachnospiraceae enriched in DLY and JXB, respectively. Notably, Pacebacteria, Streptophyta, and Aerophobetes were found to participate in the PI3K-Akt mediated immune response in both pig breeds; however, they only accelerated the metabolism in the intestines of JXB pigs. Moreover, the host could regulate microbe metabolism and immune response by Ig-like domain-containing protein and ITIH2, PAEP, and TDRD9, respectively. Taken together, our results revealed both common and breed-specific regulations of host genes by gut microbiota in two pig breeds.}, } @article {pmid41675707, year = {2025}, author = {Wu, J and Yang, X and Zhao, L and Li, Z and Zhao, G and Zhang, L}, title = {Systematic characterization of horizontally transferred biosynthetic gene clusters in the human gut microbiota using HTBGC-Finder.}, journal = {iMetaOmics}, volume = {2}, number = {1}, pages = {e62}, pmid = {41675707}, issn = {2996-9514}, abstract = {The human gut microbiota contains biosynthetic gene clusters (BGCs) that encode bioactive secondary metabolites, which play pivotal roles in microbe-microbe and host-microbe interactions and serve as a rich source of pharmaceutical lead compounds. Understanding the horizontal transfer of BGCs can reveal insights into microbial adaptation, resource utilization, and evolutionary mechanisms, thereby advancing biotechnological applications. Despite its importance, horizontal transfer of BGCs within the gut microbiota remains poorly understood. In this study, we introduce a novel tool, the Horizontally Transferred Biosynthetic Gene Clusters Finder (HTBGC-Finder), designed to systematically identify potential horizontally transferred BGCs (HTBGCs) within the extensive human gut microbiota. Using HTBGC-Finder, we identified 81 potential HTBGCs, underscoring the prevalence and significance of horizontal gene transfer in shaping the genetic landscape of the gut microbiome. Remarkably, ribosomally synthesized and post-translationally modified peptides (RiPPs) constituted the majority of these HTBGCs (76 out of 81, 93.83%), exhibiting a significantly higher transfer rate compared to non-RiPPs (Chi-squared test, p < 0.001). Upon detailed examination of BGCs, cyclic-lactone-autoinducer (CLA) and RiPP recognition element (RRE)-containing BGCs were predominant, representing nearly three-quarters of the total (45, or 55.56%, and 14, or 17.28%, respectively). Notably, CLA BGCs also demonstrated a higher transfer rate than non-CLA BGCs (Chi-squared test, p < 0.001). Taxonomy profiling revealed that horizontal BGC transfer occurred exclusively in the phyla Bacteroidota (synonym Bacteroidetes) and Bacillota (synonym Firmicutes), with 50 and 31 instances, respectively. Furthermore, cross-phylum transfer events were observed, highlighting the complex interactions between the gut microbiota and host health. These findings offer valuable insights into the horizontal transfer dynamics of BGCs within the gut microbiome and their potential implications for host-microbiota interactions.}, } @article {pmid41675709, year = {2025}, author = {Lin, W and Niu, M and Mu, C and Wang, C and Ye, Y}, title = {Key species drive community and functional stability of segment-specific gut microbiomes after the swimming crab molting.}, journal = {iMetaOmics}, volume = {2}, number = {1}, pages = {e51}, pmid = {41675709}, issn = {2996-9514}, abstract = {Molting is a crucial process for crab growth and development. However, the impacts of molting on the structure and function of the gut bacterial community in swimming crab Portunus trituberculatus are poorly understood. Then, dynamic changes in the microbiotas of gut segments (foregut, midgut, and hindgut) after molting were investigated using 16S rRNA gene amplicon and shotgun metagenomic sequencing. We highlight the segment-specific responses in bacterial community compositions, alpha-diversity, and co-occurrence patterns, emphasizing the significant impact of hindgut bacteria on the analysis of the whole gut. The identification of enriched and emerged species and their source, coupled with insights into functional stability and multifunctionality, adds granularity to our understanding of postmolt microbial ecology. We offer potential keys to driving microbial community succession. These findings provide essential insights into the stability and dynamics of gut microbiota, which are crucial for both ecological understanding and sustainable management of crab probiotic regulation.}, } @article {pmid41676059, year = {2026}, author = {Li, X and Yi, H and Wu, G and He, A and Li, R and Long, Y and Lin, C and Jiang, Z}, title = {Neutrophil CD64 index for rapid diagnosis of Pneumocystis jirovecii pneumonia in malignancy patients requiring mechanical ventilation: a retrospective analysis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1706786}, pmid = {41676059}, issn = {1664-302X}, abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) incidence and associated mortality have risen significantly in non-HIV immunocompromised patients, highlighting the urgent need for rapid, non-invasive diagnostics. Current methods face limitations including invasiveness, prolonged processing, or inadequate specificity. The neutrophil CD64 (nCD64) index emerges as a promising novel biomarker. Here, we conducted this study to evaluate the diagnostic performance of nCD64 index for PJP and further assess the predictive value of its longitudinal changes for 28-day mortality.

METHODS: This retrospective cohort study (July 2022-March 2025) analyzed mechanically ventilated malignancy patients with unexplained diffuse pulmonary infiltrates at a tertiary intensive care unit (ICU). PJP diagnosis required predefined clinical, radiological, and bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF mNGS) criteria. The nCD64 index was measured via flow cytometry at ICU admission and serially after ≥3 days of anti-PJP therapy. Diagnostic performance for PJP and prognostic value for 28-day mortality were assessed.

RESULTS: Among 28 PJP and 38 non-PJP patients, nCD64 index was significantly higher in PJP (13.33 vs. 2.84, p < 0.001). Receiver operating characteristic (ROC) curve analysis showed an area under the curve (AUC) of 0.846 (95% CI: 0.736-0.932) for PJP diagnosis, with sensitivity 89.3% and specificity 71.1% at cutoff ≥7. Multivariate analysis confirmed nCD64 index as an independent PJP predictor (OR = 1.097, 95% CI: 1.026-1.173; p = 0.007). Post-therapy nCD64 index elevation predicted 28-day mortality with high sensitivity (81.8%) and specificity (86.7%).

CONCLUSION: The nCD64 index functions as a dual-purpose biomarker for malignancy patients with respiratory failure requiring mechanical ventilation: it provides a rapid, non-invasive diagnostic tool for PJP and dynamically stratifies mortality risk. Moreover, dynamic tracking offers a real-time window into treatment response, guiding therapeutic decisions.}, } @article {pmid41676099, year = {2026}, author = {Zheng, H and QuBie, X and Wang, J and Liu, P and Zhang, W}, title = {Clinical features and chest CT findings of Chlamydia pneumoniae pneumonia.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1717744}, pmid = {41676099}, issn = {2296-858X}, abstract = {OBJECTIVE: This study aimed to investigate the clinical features and chest computed tomography (CT) findings in 42 patients with Chlamydia pneumoniae pneumonia, as confirmed by metagenomic next-generation sequencing (mNGS).

METHODS: We conducted a retrospective analysis of clinical data and chest CT findings (both at disease onset and within 1 month thereafter) in 42 patients diagnosed with Chlamydia pneumoniae pneumonia by mNGS at our hospital between August 2022 and August 2025.

RESULTS: Of the 42 patients, 25 (59.5%) presented with fever, 26 (61.9%) with sore throat, 30 (71.4%) with cough, 27 (64.3%) with expectoration, 11 (26.2%) with myalgia, 10 (23.8%) with general fatigue, and 10 (23.8%) with neurological symptoms such as headache and dizziness. Laboratory tests revealed that 12 patients (28.6%) showed a mild increase in white blood cell count, 10 (23.8%) had elevated neutrophil counts, 21 (50.0%) exhibited elevated C-reactive protein (CRP) levels, and 6 (14.3%) had CRP levels exceeding 100 mg/L. In the early stage, chest CT demonstrated a lobular pneumonia pattern in 16 patients (55.2%), involvement of a single lung lobe in 20 (69.0%), predominant lower-lung distribution in 19 (65.5%), and a nodular-patchy pattern in 8 patients (27.6%) with a nodular-patchy pattern. The main accompanying features included a halo sign in 25 patients (86.2%), centrilobular nodules in 23 (79.3%), and bronchial wall thickening in 20 (69.0%). In the mid-to-late stage, chest CT revealed a lobular pneumonia pattern in 23 patients (76.7%), single-lobe involvement in 23 (76.7%), and predominant lower-lung distribution in 20 (66.7%). The major concomitant features were a halo sign in 21 patients (70.0%), centrilobular nodules in 20 (66.7%), and bronchial wall thickening in 24 (80.0%).

CONCLUSION: Chest CT findings of Chlamydia pneumoniae pneumonia are predominantly characterized by a lobular pneumonia pattern, lower-lobe distribution, and associated features such as bronchial wall thickening, centrilobular nodules, and a peripheral halo sign. Certain imaging differences exist between early and middle-to-late stages, with the nodular-patchy pattern potentially representing an ultra-early imaging marker, which may provide clues for early clinical intervention.}, } @article {pmid41676115, year = {2024}, author = {Zhou, Y and Zheng, J and Song, W and Yan, X and Du, L and Ma, Z and Fu, Y and Ouyang, Z and Xiao, Y and Liu, Z and Tian, F and Wong, JWH and Shih, JHD and Liang, S and Tian, H and Liu, L and Wei, K and Zhang, C and Li, J and Wang, X}, title = {OUTPOST: A comprehensive analysis software for whole-metagenome shotgun sequencing incorporating group stratification.}, journal = {iMetaOmics}, volume = {1}, number = {2}, pages = {e29}, pmid = {41676115}, issn = {2996-9514}, abstract = {The whole metagenOme shotgun seqUencing sTream Pipeline that is cOmprehensive and uSeful for mulTi groups experiments (OUTPOST) is a comprehensive analysis software for whole-metagenome shotgun sequencing incorporating group stratification, which encompasses 14 modules and boasts over 50 functions, distinguishing itself for its comprehensiveness when compared with 17 existing whole-metagenome shotgun sequencing (WMGS) tools. OUTPOST introduces innovative methods for multi-group experimental designs and meta-analysis-based biomarker identification.}, } @article {pmid41676117, year = {2024}, author = {Shi, P and Xu, S and Yang, Z and Wang, L and Wu, Y and Li, Y and Zhu, Z}, title = {Harnessing gut microbiota for longevity: Insights into mechanisms and genetic manipulation.}, journal = {iMetaOmics}, volume = {1}, number = {2}, pages = {e36}, pmid = {41676117}, issn = {2996-9514}, abstract = {The gut microbiota is pivotal in maintaining health, with most microorganisms being beneficial, except for a few pathogens. Emerging evidence suggests a link between the gut microbiome and aging, hinting at its potential role in longevity. However, understanding the relationship is challenging due to the microbiota's complexity. This perspective summarizes the mechanisms by which gut microbes regulate host lifespan and explores genetic manipulation strategies to promote healthy aging in the elderly.}, } @article {pmid41676120, year = {2024}, author = {Ling, Y and Liu, Z and Han, S and Wu, H and Mu, C and Zhu, W}, title = {Integrated omics revealed the altered colonic microenvironment after inhibition of peripheral serotonin synthesis by LP533401.}, journal = {iMetaOmics}, volume = {1}, number = {2}, pages = {e34}, pmid = {41676120}, issn = {2996-9514}, abstract = {Gut-derived 5-hydroxytryptamine (5-HT), known as serotonin, plays a crucial role in regulating gastrointestinal functions. However, the impact of disruptions in gut-derived 5-HT synthesis on the early gut microbiome and intestinal microenvironment remains unclear. In this study, LP533401, an inhibitor targeting peripheral 5-HT synthesis, was administered orally to neonatal rats starting at 4 days post-birth. By day 11, inhibition of gut-derived 5-HT resulted in altered colonic morphology, characterized by increased crypt depth and reduced myenteric thickness. To investigate the mechanisms underlying these alterations, we employed a combination of metagenomics, mucosal transcriptome, and untargeted metabolomics on colonic samples. Metagenome profiling revealed an upregulation in the microbial two-component system (ko02020) and tyrosine metabolism (ko00350), with minimal effects on taxa abundances. Transcriptome profiling analysis indicated the discriminant expression of genes enriched in pathogen infection-responsive signaling (e.g., Salmonella and Yersinia infection) and the Wnt signaling pathway that affected stem cell proliferation. Consistent with increased crypt depth, marker genes related to cell proliferation were excessively activated. Metabolomics analysis indicated lower ascorbate level and higher succinic acid level, correlating with 5-HT concentrations and increased crypt depth. Additionally, altered metabolic pathways (e.g., nucleotide metabolism, signal transduction, metabolism of cofactors and vitamins) suggested an impact on the colonic function. In summary, early inhibition of gut-derived 5-HT may unfavorably reshape the colonic microenvironment, affecting gut morphology, microbial function, stem cell proliferation, and mucosal metabolism.}, } @article {pmid41676124, year = {2024}, author = {Xie, Y and Xu, S and Xi, Y and Li, Z and Zuo, E and Xing, K and Bai, L and Li, K}, title = {Global meta-analysis reveals the drivers of gut microbiome variation across vertebrates.}, journal = {iMetaOmics}, volume = {1}, number = {2}, pages = {e35}, pmid = {41676124}, issn = {2996-9514}, abstract = {Shifts in gut microbial diversity and structure are one route by which vertebrate hosts adapt to local environmental conditions. However, recent studies have mostly been limited to a single species, small sample sizes, or restricted geographic ranges. Therefore, drawing a global picture of vertebrate gut microbiome diversity, community structure, and determinants for their adaptive shifts remains to be elucidated. We here collected 6508 samples from 113 vertebrate species covering diverse classes, feeding behaviors, and host habitats based on 16S rRNA gene sequencing. The results showed that host diet pattern had a significant impact on gut microbiome variation, which might drive taxonomic and functional contents of gut microbiome across vertebrates. Of note, the phylum Fusobacteria were enriched in carnivorous vertebrate gut while herbivorous vertebrate gut selectively increased the abundance of Verrucomicrobia. Also, climate factors were strongly associated with gut microbiome variation across vertebrates. Interestingly, we found that the abundance of microbiota belonging to Bacteroidetes increased gradually while the members from Proteobacteria showed a decreasing trend from high- to low-latitude zones, potentially contributing to vertebrate adaptation to local climate condition. Additionally, we comprehensively deciphered the common antibiotic resistomes and their potential mobility between terrestrial vertebrate gut microbiome (n = 487) and their sympatric soil biological environment samples (n = 203) by integrating metagenomic sequencing datasets. Particularly, potential horizontal antibiotic resistance genes (e.g., bacA) transfers were detected between vertebrates gut microbiome and their sympatric soil biological environment. Together, our findings provide new evidence of how external environmental factors affect vertebrate gut microbiome variation.}, } @article {pmid41676125, year = {2024}, author = {Xia, JJ and Zhong, Q and Li, ZM and Wei, QZ and Jiang, LY and Duan, C and Jia, HJ and Tan, YM and Han, LY and Krutmann, J and Wang, J and Liu, X}, title = {Culture dependent and independent approaches reveal the role of specific bacteria in human skin aging.}, journal = {iMetaOmics}, volume = {1}, number = {2}, pages = {e26}, pmid = {41676125}, issn = {2996-9514}, abstract = {Skin aging is a dynamic process involving a spectrum of phenotypic changes, making it an attractive model for studying microbiome-phenotype interactions. Therefore, 822 facial microbial samples and 14 skin phenotypes from corresponding areas were assessed in a Chinese cohort. Porphyrins and the chronological age exhibited the most significant microbial variability. We further profiled the dynamics of the skin microbiome associated with age and aging phenotypes. Using a multiple linear regression model, we predicted premature/delayed aging-related microbial species, mainly Moraxella osloensis and Cutibacterium acnes. We also validated the biological functions of the host-microbe interactions in vitro. Moraxella osloensis isolated from healthy skin regulates collagen metabolism and extracellular matrix assembly, and promotes cell senescence in human keratinocytes and fibroblasts, making it potentially applicable in the development of antiaging interventions.}, } @article {pmid41676130, year = {2024}, author = {Yousuf, S and Luo, H and Zeng, M and Chen, L and Ma, T and Li, X and Zheng, M and Zhou, X and Chen, L and Xi, J and Lu, H and Cao, H and Ma, X and Bian, B and Zhang, P and Wu, J and Gan, R and Jia, B and Sun, L and Ju, Z and Gao, Y and Malik, WA and Ma, C and Lyu, H and Li, Y and Hou, H and Zhou, Y and Bai, D and Wang, Y and Yang, H and Xun, J and Du, S and Zhang, T and Wan, X and Peng, K and Xu, S and Wen, T and Chen, T and Liu, YX}, title = {Unveiling microbial communities with EasyAmplicon: A user-centric guide to perform amplicon sequencing data analysis.}, journal = {iMetaOmics}, volume = {1}, number = {2}, pages = {e42}, pmid = {41676130}, issn = {2996-9514}, abstract = {The advent of next-generation sequencing has revolutionized microbiome research, enabling in-depth exploration of microbial communities through amplicon sequencing. The widespread adoption of sequencing across diverse fields, coupled with decreasing costs, underscores the critical need for validated, fully automated, reproducible, and adaptable analysis pipelines. However, analyzing these high-throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility for many researchers. To address this challenge, in 2023 we developed EasyAmplicon, a comprehensive, user-friendly pipeline that integrates popular tools such as USEARCH and VSEARCH, offering a streamlined workflow from raw data to results. Remarkably, EasyAmplicon has garnered significant recognition within a year, as evidenced by 127 citations to date. To further facilitate the researchers and enhance usability, we present a detailed protocol with a video recording that guides users through each step of the pipeline, including data preprocessing (quality filtering, chimera removal), amplicon sequence variant analysis, diversity analysis, and data visualization. The protocol is designed for ease of use, with each step documented, allowing researchers to execute the workflow without requiring complex scripting skills. The EasyAmplicon pipeline is freely available on GitHub (https://github.com/YongxinLiu/EasyAmplicon).}, } @article {pmid41676189, year = {2026}, author = {Zhang, G and Fang, X and Yang, H and Zhu, Y}, title = {Severe empyema caused by mixed oral anaerobic bacterial infection: a case report.}, journal = {AME case reports}, volume = {10}, number = {}, pages = {28}, pmid = {41676189}, issn = {2523-1995}, abstract = {BACKGROUND: Empyema is a life-threatening pleural infection that can result from various bacterial sources. While oral anaerobic bacteria are recognized as potential pathogens, severe empyema caused by mixed oral anaerobic bacterial infection remains clinically rare. Recent advances in metagenomic next-generation sequencing (NGS) have improved the etiological diagnosis of complex infections. This case demonstrates the clinical significance of NGS technology and oral health in preventing systemic infections.

CASE DESCRIPTION: An 80-year-old male with poor oral hygiene and multiple dental caries presented with acute onset of left-sided chest pain, chills, and fever. Physical examination revealed diminished breath sounds over the left lung. Imaging studies confirmed left-sided empyema. Pleural fluid NGS identified mixed oral anaerobic bacteria including Porphyromonas gingivalis, Prevotella intermedia, Fusobacterium nucleatum, and Finegoldia magna. The patient underwent thoracoscopic empyema debridement, with postoperative tissue pathology showing suppurative inflammation with fibrinous necrosis. Surgically excised tissue NGS additionally detected Finegoldia magna along with Epstein-Barr virus and human herpesvirus 6. Following targeted anti-infective therapy with meropenem and metronidazole, the patient recovered successfully.

CONCLUSIONS: This case highlights the critical role of NGS technology in identifying mixed oral anaerobic pathogens and guiding precision-targeted treatment of empyema. The atypical presentation of empyema caused by oral anaerobic bacteria warrants early surgical intervention combined with appropriate antimicrobial therapy. Our findings emphasize the importance of oral health maintenance in preventing life-threatening systemic infections and broaden our understanding of oral-systemic disease relationships.}, } @article {pmid41676216, year = {2026}, author = {Dang, Y and Deng, Z and Wang, K and Luo, J and Wang, C and Long, F and Kong, J}, title = {Cystic fibrosis complicated by allergic bronchopulmonary aspergillosis in a Chinese adolescent: a case report and literature review.}, journal = {AME case reports}, volume = {10}, number = {}, pages = {43}, pmid = {41676216}, issn = {2523-1995}, abstract = {BACKGROUND: Cystic fibrosis (CF) predisposes patients to allergic bronchopulmonary aspergillosis (ABPA). The objective of this study is to enhance the recognition of CF-related ABPA (CF-ABPA) in adolescents through a detailed case study. A multidisciplinary management approach is essential. Early diagnosis and intervention could substantially improve outcomes, warranting further longitudinal research on optimized treatment protocols.

CASE DESCRIPTION: A 15-year-old patient presenting with persistent respiratory symptoms underwent a series of diagnostic tests, including serum immunoglobulin E (IgE) testing, chest computed tomography (CT), bronchoscopy, bronchoalveolar lavage metagenomic next-generation sequencing (mNGS), and whole-exome sequencing to identify CFTR mutations. The diagnostic findings revealed markedly elevated serum IgE levels (2,359.0 IU/mL), the presence of bronchiectasis with mucus plugging on CT imaging, and mNGS detection of Aspergillus fumigatus with an abundance of 97.28%. The diagnosis of CF-ABPA was confirmed by identification of a pathogenic CFTR mutation. Later antifungal therapy and corticosteroids produced notable clinical improvement.

CONCLUSIONS: CF was under-recognized historically, but this case shows that it is a clinically important cause of bronchiectasis and ABPA in Chinese adolescents. The identification of Aspergillus was accurate with the mNGS. Genetic test confirmed that the subject is a CF patient with compound heterozygous mutations in CFTR gene. The finding urges the clinician to have a high index of suspicion for the CF-ABPA in those with asthma-like refractory symptoms with structural lung disease. When diagnosed early and accurately, antifungal therapy and inhaled corticosteroids can be administered timely. The patient experienced a notable improvement both clinically and radiologically, as well as functionally. The future work should promote awareness of this clinical entity and systematic screening of similar patients in China. Further multicenter studies are necessary to formulate diagnostic and therapeutic guides for CF-ABPA in Asia.}, } @article {pmid41676438, year = {2025}, author = {Liu, Y and Ise, Y and Takami, H and Urakawa, R and Tateno, R and Toyoda, A and Ohte, N and Shi, W and Jiang, L and Isobe, K}, title = {Soil pH modulates microbial nitrogen allocation in soil via compositional and metabolic shifts across forests in Japan.}, journal = {iMetaOmics}, volume = {2}, number = {4}, pages = {e70054}, pmid = {41676438}, issn = {2996-9514}, abstract = {Ammonium release (ammonification) and uptake (immobilization) by soil microbial communities are fundamental processes of forest nitrogen (N) cycling, representing major N fluxes that influence plant productivity and ecosystem N retention. However, because these processes involve diverse metabolic pathways distributed across many taxa, they are difficult to evaluate using gene- or taxon-specific approaches, and it remains unclear how microbial community structure governs the patterns of these processes. In this study, we examined how the abundance, taxonomic composition, richness, and metabolic capabilities of microbial communities regulate ammonium-related N cycling processes across a wide range of forests in Japan, using rRNA gene sequencing and quantification, shotgun metagenomics, and [[15]]N tracer assays. Across the full gradients of soil pH and N content, microbial abundance was primarily correlated with the absolute rates of N cycling processes, while taxonomic composition and richness were more strongly correlated with N allocation-that is, the balance among ammonium release, ammonium uptake, and subsequent nitrification. Soils with higher pH supported taxonomic compositions linked to enhanced ammonium release and nitrification, whereas lower-pH soils hosted compositions associated with greater ammonium uptake and retention. Notably, the regulatory influence of taxonomic composition on N allocation was pronounced within the higher-pH range but diminished within the lower-pH range. Despite this environmental dependency, N allocation by soil microbial communities was ultimately constrained by their overall metabolic capabilities. In higher-pH soils, microbial communities were enriched in metabolic functions related to nutrient acquisition and respiratory N transformations, supporting increased ammonium release and N mobility. By contrast, microbial communities in lower-pH soils were enriched in stress-adaptive functions, which promoted ammonium retention and limited N transformations-thereby diminishing the regulatory influence in N cycling. Together, our findings provide a mechanistic understanding of how microbial community structure and metabolic capabilities regulate ammonium-related N cycling processes across forests under varying environmental conditions.}, } @article {pmid41676442, year = {2025}, author = {Chaboy-Cansado, R and Talavera-Marcos, S and Gallego-Simón, R and Cobeta, P and Roscales, G and Rastrojo, A and de Cárcer, DA}, title = {Modular automated high-throughput isolation and phylogenetic identification of bacteria from complex microbiomes.}, journal = {iMetaOmics}, volume = {2}, number = {4}, pages = {e70037}, pmid = {41676442}, issn = {2996-9514}, abstract = {Metagenomic analysis can generate hypotheses about microbiome interactions and function, yet mechanistic understanding is only possible through precise experimentation manipulating its microbiota composition. The high-throughput isolation of microbiome members thus represents a core resource in this field of research.}, } @article {pmid41676447, year = {2025}, author = {Deng, F and Han, Y and Li, M and Peng, Y and Chai, J and Yang, G and Li, Y and Zhao, J}, title = {HiFi based metagenomic assembly strategy provides accuracy near isolated genome resolution in MAG assembly.}, journal = {iMetaOmics}, volume = {2}, number = {4}, pages = {e70041}, pmid = {41676447}, issn = {2996-9514}, abstract = {Recovering high-contiguity, circular bacterial genomes from complex microbiomes (e.g., gut) is challenged by limitations of short-read and error-prone long-read sequencing. This study comprehensively compares PacBio High-Fidelity (HiFi) sequencing-based metagenome-assembled genomes (MAGs) against Illumina MAGs, Oxford Nanopore Technologies (ONT) MAGs, and isolate whole-genome sequencing genomes from the same sample. HiFi sequencing yielded 31 high-quality MAGs, including 10 complete circular genomes. HiFi MAGs demonstrated significantly higher completeness, continuity, and lower contamination than Illumina or ONT MAGs (p-adj < 0.05). Crucially, HiFi MAGs exhibited closer genomic proximity to corresponding isolates at both single-nucleotide polymorphism and gene presence/absence levels. This benchmarking establishes HiFi as a robust approach for generating MAGs rivaling isolated genome quality, providing critical insights for accurate microbial genomic studies.}, } @article {pmid41676450, year = {2025}, author = {Zhang, L and Liu, Y and Wang, S and Ching, JY and Tam, WH and Leung, TF and Leung, TY and Chan, PKS and Mak, JWY and Cheung, CP and Tun, HM and Chang, EB and DeLeon, O and Huang, Q and Chen, X and Huo, H and Miao, Y and Cheong, PK and Ip, KL and Yeung, YL and Chang, MK and Lyu, C and Yang, H and Li, B and Fan, Y and Sun, Y and Jiang, S and Ng, SC and Chan, FKL}, title = {MOMMY study profile: An integrative early-life multi-omics cohort in China.}, journal = {iMetaOmics}, volume = {2}, number = {4}, pages = {e70068}, pmid = {41676450}, issn = {2996-9514}, abstract = {Large-scale, prospective birth cohorts capturing the complex interplay between the gut microbiome, host biology, and environmental exposures are crucial to understanding early-life health but remain scarce, particularly within Asian populations. To address this gap, we established the MOMMY cohort (The MOther-infant Microbiota transmission and its link to long terM health of babY), a large, prospective birth cohort uniquely designed to investigate maternal-paternal-infant microbiota transmission and its impact on child health within the understudied Chinese population. MOMMY aims to recruit 20,000 families from three geographically and economically diverse regions across China. This cohort prospectively follows pregnant mothers, fathers, and their infants, with children up to 7 years of age. Since September 2019, we have systematically collected a comprehensive repository of longitudinal biospecimens-including maternal and infant stool, breast milk, cord blood, and parental blood-stored in an accredited biobank. This is complemented by extensive data on environmental exposures, diet, and health outcomes gathered through validated questionnaires and physician assessments. The MOMMY cohort's unique value lies in its unprecedented scale, geographic diversity, and its integrative multi-omics design, which will combine metagenomic, metabolomic, immunologic, and epigenetic data. By creating this unique resource, MOMMY will elucidate how early-life microbial and molecular trajectories, shaped by genetic and environmental factors, influence child development and disease risk, thereby filling a critical gap in global microbiome research.}, } @article {pmid41676497, year = {2026}, author = {Lindstedt, K and Wheelock, A and Samutela, M and Kabir, W and Chasaya, M and Namuziya, N and Marsden, EJ and Kapasa, M and Mumba, C and Mulenga, B and Nkole, L and Pieciak, R and Mudenda, V and Chikoti, C and Ngoma, B and Chimoga, C and Chirwa, S and Pemba, L and Nzara, D and Lungu, J and Forman, L and Simulundu, E and MacLeod, W and Moyo, C and Somwe, SW and Holt, KE and Sundsfjord, A and Gill, CJ}, title = {Genomic analysis of Klebsiella pneumoniae causing community-acquired respiratory deaths among Zambian infants and children using targeted RNA-probe hybridization-capture metagenomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41676497}, issn = {2692-8205}, support = {T32 HL125232/HL/NHLBI NIH HHS/United States ; }, abstract = {Klebsiella pneumoniae (Kp) is a leading cause of neonatal and infant deaths in sub-Saharan Africa and frequently associated with antimicrobial resistance. Previously, we identified Kp as a major cause of fatal community-associated lower respiratory infections among infants and children under five years in Lusaka, Zambia, using postmortem tissue sampling and pathogen specific multiplex qPCR. In this follow-up study, we employed a novel culture-independent RNA-probe hybridization-capture metagenomic sequencing approach, targeting Kp pan-genome core and accessory genes, to perform in-depth genomic analysis of Kp from eleven post-mortem lung biopsy samples from seven of these children. Analysis detected Kp in all cases except one, which identified Klebsiella quasipneumoniae subspecies similipneumoniae. Core-genome multi-locus sequence typing (cgMLST) revealed six clonal groups (CG607, CG1123, CG10072, CG280, CG3648, and CG10344) belonging to five sublineages (SL607, SL17, SL280, SL37, and SL10072), with perfect concordance between paired samples from the same case. Two infants sampled the same month harbored SL607 lineages sharing 621 out of 629 cgMLST alleles, suggesting clonal spread. Kp capsule (K) loci were detected in all but one case and included potential vaccine targets KL25, KL23, and KL122. Antimicrobial resistance genes were widespread among samples, particularly encoding resistance toward aminoglycosides, β-lactams, sulphonamides, tetracyclines, and trimethoprim. Extended spectrum β-lactamases were identified in four cases, three of which were bla CTX-M-15. The acquired Kp sideophore yersiniabactin (lineage ybt14) was identified in both cases associated with SL607, and the acquired siderophore aerobactin (lineage iuc5) was identified in one of these, suggesting possible convergence of antimicrobial resistance and hypervirulence. The detection of Kp with extensive antimicrobial resistance causing fatal community acquired pneumonia signals a deeply concerning epidemiologic shift from a largely nosocomial pathogen. This calls for urgent epidemiological investigations to better understand the burden, transmission dynamics, antimicrobial resistances, and potential vaccine targets for Kp in other community settings across sub-Saharan Africa.}, } @article {pmid41676723, year = {2026}, author = {Kafer, LA and Escapa, IF and Boyd, AI and Tostado, AR and Kambal, A and Blutt, SE and Avadhanula, V and Piedra, PA and Lemon, KP}, title = {Streptococcus pneumoniae colonization modulates human nasal epithelial responses to respiratory syncytial virus infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41676723}, issn = {2692-8205}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; U19 AI144297/AI/NIAID NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; }, abstract = {Respiratory syncytial virus (RSV) is a major cause of morbidity and mortality in infants globally. Specific nasal bacterial genera are differentially associated with RSV severity in infants: Haemophilus and Streptococcus with more severe disease and Dolosigranulum with healthy controls or milder outcomes. We hypothesized these differential bacterial effects begin at the epithelial level. Therefore, we established human nasal epithelial organoids differentiated at air-liquid interface (HNO-ALI) as a model system to assess effects of individual nasal microbionts on the epithelial response to subsequent RSV infection and of RSV on those microbionts. Infant-derived HNO-ALI were monocolonized with either Streptococcus pneumoniae, nontypeable Haemophilus influenzae, or Dolosigranulum pigrum one day before viral infection. RSV reduced colonizing S. pneumoniae and D. pigrum levels without affecting H. influenzae. S. pneumoniae precolonization uniquely reduced RSV levels during infection. S. pneumoniae precolonization also modulated the epithelial transcriptional response to RSV infection more so than H. influenzae or D. pigrum, with a pronounced effect on genes involved in immune response, cell cycle, stress, and growth signaling. Gene set enrichment analysis showed S. pneumoniae precolonization blunted RSV-induced increase in inflammatory and immune responses, consistent with S. pneumoniae also modulating RSV-induced cytokine production. Furthermore, S. pneumoniae precolonization blocked RSV-mediated dysregulation of cell-cycle genes, consistent with preventing arrest. Bacterial rescue of cell-cycle progression is a potential mechanism for reduced infectious virion production, since cell-cycle arrest enhances RSV replication. HNO-ALI facilitated elucidation of bacterial-viral-epithelial interplay at a frequent site of viral infection, directly linking nasal bacterial colonization to RSV infection dynamics.}, } @article {pmid41677194, year = {2026}, author = {Simm, NM and Williams, GM and Fowler, S and Barlow, K and Carter, B and Talley, NJ and Keely, S and Duncanson, K and Hoedt, EC}, title = {A Scoping Review of Methods Used to Investigate Relationships between Dietary Intake and the Gastrointestinal Microbiome.}, journal = {Nutrition reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/nutrit/nuaf306}, pmid = {41677194}, issn = {1753-4887}, support = {//Australian Government Research Training Program Scholarship/ ; //Australian NSW Health Round 5 Early-Mid Career Grant/ ; }, abstract = {The gastrointestinal (GI) microbiome is intrinsically linked to human health and disease, with dietary intake being a major modifiable variable contributing to microbial colonization and fermentation. Diet-microbiome studies are heterogeneous in the methods used to assess and record dietary intake, to sequence the microbiome data, and to analyze associations. To capture the extent of these inconsistencies, we performed a systematic scoping review to synthesize the information on methods used to assess and compare relationships between diet and the GI microbiome in human studies. Our search identified papers with metrics of both dietary intake and the GI microbiome (using either 16S rRNA or metagenomic shotgun sequencing) and specific diet-microbiome associative analysis. The databases searched were MEDLINE, EMBASE, CINAHL, Cochrane, and Google Scholar, and the search produced 22, 228 unique records after de-duplication. After full-text screening, 1,262 articles were selected for full extraction. A subset of 295 studies captured whole dietary intake and investigated associations with the GI microbiome. This subset assessed diet using 84 different food frequency questionnaires, 12 alternative surveys, and 4 types of diet recalls or diaries ranging from 1 to 14 days. Fifty-five percent (n = 163) of studies investigated habitual dietary intake, 35% (n = 101) investigated recent dietary intake, and 10% (n = 30) used methods to assess both. Eighty-one percent of studies employed 16S rRNA sequencing, with wide variation in extraction, sequencing, pre-processing, and annotation methods. Gaps in the reporting of the methods for each step of the sequencing and analysis process were evident, limiting future comparison of study outcomes. Microbiome-specific statistical methods were used in 11% of the subset-predominantly correlational methods that are not recommended for microbiome data. In conclusion, this review revealed extensive inconsistencies within the exploratory diet-microbiome studies, despite the existence of recommendations to assist researchers. Collaborative efforts to develop consensus in methods and reporting are needed to substantially progress the obtaining of high-quality evidence and meta-analysis in the diet-microbiome research field.}, } @article {pmid41677732, year = {2026}, author = {Dos Santos, LCRM and de Almeida, JDR and de Sousa, NSO and Fernandes, FDS and Ennes, JFV and Frickmann, H and de Souza, JVB and de Souza, ÉS}, title = {Amazonian Fungal Diversity and the Potential of Basidiomycetes as Sources of Novel Antimicrobials.}, journal = {Biology}, volume = {15}, number = {3}, pages = {}, pmid = {41677732}, issn = {2079-7737}, support = {EDITAL N. 020/2024 - PRODUTIVIDADE EM CT&I//Fundação de Amparo à Pesquisa do Estado do Amazonas/ ; CNPq/MCTI Universal Call No. 10/2023//National Council for Scientific and Technological Development/ ; }, abstract = {The Amazon Forest harbors one of the largest fungal diversities on the planet, occupying a wide variety of ecological niches comprising terra firme (non-flooded forest), várzea (white-water floodplains), and igapó (black-water floodplains). In this review article, we examine Amazonian fungal diversity based on three complementary approaches-culture-based surveys, in situ inventories of macrofungi, and environmental DNA/metagenomic analyses-discussing advances, limitations, and contributions to regional mycological knowledge. Subsequently, we present a critical synthesis of the potential of Amazonian basidiomycetes regarding the production of metabolites with antimicrobial activity, highlighting the main genera reported in the literature, the chemical classes involved (e.g., terpenes, steroids, quinones, and bioactive peptides), and the metabolic pathways responsible for their biosynthesis. The integration between biodiversity and bioprospecting underscores the importance of Amazonian fungi both for understanding ecological processes and for the development of new solutions to the antimicrobial resistance challenge. This work seeks to fill current gaps in the academic literature and to contribute to future strategies for the conservation and sustainable use of regional mycobiota.}, } @article {pmid41678125, year = {2026}, author = {Hou, Y and Sun, H and Meng, S and Xu, W and Yu, Y and Wang, W and Liu, D and Jia, H and Wang, Y and Chu, H and Sun, Z}, title = {Deciphering the different Mycobacterium avium complex infections of HIV and non-HIV patients by bacterial GWAS and immune cells flow cytometry.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {45}, number = {5}, pages = {1419-1429}, pmid = {41678125}, issn = {1435-4373}, support = {82272347//National Natural Science Foundation of China/ ; 2022-1G-2161//Capital Health Research and Development of Special Fund/ ; }, mesh = {Humans ; *Mycobacterium avium Complex/genetics/isolation & purification/immunology/classification ; *Mycobacterium avium-intracellulare Infection/microbiology/immunology ; Animals ; Mice ; *HIV Infections/complications/microbiology/immunology ; Male ; Flow Cytometry ; Female ; Genome-Wide Association Study ; Natural Killer T-Cells/immunology ; Middle Aged ; Adult ; Immunophenotyping ; Disease Models, Animal ; }, abstract = {PURPOSE: Pulmonary diseases caused by Mycobacterium avium complex (MAC) show species-specific epidemiology: M. avium predominates in HIV-positive patients, while M. intracellulare mainly affects immunocompetent hosts. This study aimed to elucidate the bacterial and host mechanisms underlying these differences.

METHODS: We integrated clinical metagenomic next-generation sequencing (mNGS), k-mer-based bacterial genome-wide association study (GWAS) of clinical isolates, peripheral blood immunophenotyping of 175 patients, and mouse infection models with or without CD4 depletion.

RESULTS: K-mer GWAS identified lipid metabolism and transport genes (notably mce) enriched in isolates from hosts with different HIV statuses. Immunophenotyping showed that in HIV-negative patients, M. intracellulare infection elicited higher NKT cell frequencies than M. avium, a difference absent in HIV-positive hosts. In mice, anti-CD4[-]/M. intracellulare infection showed steadily increasing bacterial burden with time (ρ = 0.824), whereas M. avium exhibited no such trend. Early after infection (weeks 1-2), anti-CD4[-]/M. avium group had higher bacterial burden and NKT levels than anti-CD4[-]/M. intracellulare, but by week 4 the pattern reversed (all p < 0.05). CD4 depletion eliminated species-specific differences in NKT activation, and at both weeks 2 (p < 0.05) and 4 post-infection (p > 0.05), the anti-CD4[+]/M. avium groups carried a higher bacterial burden than the anti-CD4[+]/M. intracellulare groups.

CONCLUSION: MAC species exhibit fundamentally divergent infection dynamics driven by differential NKT cell activation, likely shaped by species-specific lipid antigens. This lipid-NKT axis explains contrasting clinical patterns of M. avium and M. intracellulare and highlights a potential target for host-directed interventions.}, } @article {pmid41678126, year = {2026}, author = {Yao, Y and Lai, Y and Wu, Q and Xu, W}, title = {Targeted next-generation sequencing improves diagnosis and antimicrobial stewardship in Chlamydia psittaci pneumonia.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {45}, number = {5}, pages = {1431-1439}, pmid = {41678126}, issn = {1435-4373}, support = {20231001//Changning District Medical Key Specialty/ ; }, mesh = {Humans ; Female ; *Chlamydophila psittaci/genetics/drug effects/isolation & purification ; *Antimicrobial Stewardship ; Retrospective Studies ; Male ; *Anti-Bacterial Agents/therapeutic use ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Psittacosis/diagnosis/drug therapy/microbiology ; *Chlamydial Pneumonia/diagnosis/drug therapy/microbiology ; Adult ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; }, abstract = {UNLABELLED: PURPOSE : Chlamydia psittaci pneumonia (CPP) remains underdiagnosed due to nonspecific clinical manifestations. This study assessed the clinical utility of targeted next-generation sequencing (tNGS) in optimizing CPP diagnosis and antimicrobial stewardship, with a focus on empirical quinolone efficacy.

METHODS: We conducted a retrospective cohort study of 35 CPP patients (November 2022-October 2023) diagnosed by tNGS of respiratory specimens (8 sputum/27 bronchoalveolar lavage fluid [BALF]). Data included epidemiological history, laboratory findings, imaging features, therapeutic interventions, and clinical outcomes. Statistical comparisons between severe and non-severe CPP were performed using Student's t-test and Mann-Whitney U tests.

RESULTS: Median diagnostic delay post-admission was 4 days (IQR:3-5). Fever predominated as initial presentation (97.1%), with 45.7% reporting avian contact. Leukocyte counts were normal/mildly elevated,, yet neutrophil ratio (83.86 ± 6.17%) and D-dimer (1.31 ± 0.86 mg/L) were notably increased. All patients showed elevated CRP (175.52 ± 87.62 mg/L) and ESR (70.00 ± 22.62 mm/h). Severe CPP cases (n = 8) exhibited higher CRP (p = 0.041) and procalcitonin (p = 0.013) than non-severe cases. Common comorbidities included hepatic dysfunction (68.6%) and pleural effusion (34.3%). Polymicrobial co-infections occurred more frequently in severe CPP cases than in non-severe cases (OR = 21.07, 95% CI:1.11-402.30). tNGS-guided diagnosis prompted antibiotic adjustment in 60.0% of patients (21/35) to targeted quinolone, tetracycline, or combination therapy. Clinical recovery was achieved in 97.1%, with 2.9% mortality.

CONCLUSIONS: tNGS enhances early CPP diagnosis and targeted antimicrobial adjustment. Quinolones demonstrate high efficacy as empirical treatment. The strong association between severe CPP and polymicrobial co-infections necessitates comprehensive pathogen screening. Study limitations include a single-center design and a small sample size, warranting validation through prospective multicenter studies.}, } @article {pmid41678593, year = {2026}, author = {Chen, HC and Tang, TWH and Pasaribu, SNN and Wu, DC and Rey, FE and Hsieh, PCH}, title = {Gut-Heart Axis in Myocardial Repair: Mechanisms, Cross-Organ Networks, and Therapeutic Opportunities.}, journal = {Circulation research}, volume = {138}, number = {4}, pages = {e326978}, pmid = {41678593}, issn = {1524-4571}, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/physiology ; *Myocardium/metabolism/pathology ; *Regeneration ; *Heart/physiology ; Multiomics ; *Heart Diseases/metabolism/therapy/microbiology ; }, abstract = {Cardiovascular diseases remain the leading global cause of morbidity and mortality, placing an escalating burden on health care systems and economies. While the gut microbiota is well recognized in atherosclerosis and cardiometabolic disorders, its influence on myocardial injury, repair, and regeneration is only beginning to emerge. Growing evidence reveals that gut microbes and their metabolites regulate myocardial health through intricate cross-organ networks, including the gut-brain-heart, gut-liver-heart, and gut-lung-heart axes. These findings suggest that the heart plays a key role in systemic host-microbe communication. Advances in metagenomics, metabolomics, and single-cell transcriptomics are now defining the molecular and cellular pathways by which microbial metabolites modulate immune tone, endothelial integrity, metabolic resilience, and cardiomyocyte survival. Studies in gnotobiotic models have established causal links between specific microbial taxa and myocardial outcomes while illuminating their roles in fibrosis resolution, angiogenesis, and regeneration. In this review, we synthesize current knowledge on the bidirectional gut-heart dialogue, emphasizing immunometabolic signaling, cross-organ integration, and regenerative mechanisms. We propose that coupling high-resolution multiomics with mechanistic modeling in controlled microbial systems will be pivotal for next-generation, microbiota-informed diagnostics, and therapeutics. We explore the emerging role of the gut-myocardium axis as both a driver of disease and as a promising modifiable therapeutic target and highlight a new frontier in precision cardiovascular medicine, with the potential to transform strategies for prevention, repair, and tissue regeneration.}, } @article {pmid41679088, year = {2026}, author = {Leducq, JB and St-Amand, LP and Ross, D and Kembel, SW}, title = {A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on hyphomicrobiales dark matter.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {2}, pages = {126697}, doi = {10.1016/j.syapm.2026.126697}, pmid = {41679088}, issn = {1618-0984}, mesh = {*Phylogeny ; Metagenomics ; *Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; *Biodiversity ; Sequence Analysis, DNA ; Methylobacterium/genetics/classification ; Lichens/microbiology ; *Alphaproteobacteria/classification/genetics/isolation & purification ; Bacteria/classification/genetics ; DNA Barcoding, Taxonomic ; }, abstract = {The phyllosphere, or above-ground part of plants, hosts diverse bacterial communities that play critical ecological roles and provide beneficial functions for the plant. The Hyphomicrobiales (Alphaproteobacteria) are a highly diverse and ecologically important clade known to be key members of the plant microbiome, in particular in association with plant roots, but their diversity remains largely uncharacterized in the phyllosphere. Using a meta-analysis combining metabarcoding, metagenomics and phylogenomics, we explored the diversity of leaf-associated Hyphomicrobiales. We confirmed Methylobacterium was ubiquitous in the phyllosphere and revealed the dominance of two under-characterized Hyphomicrobiales taxa: Lichenihabitantaceae, a lichen-associated family previously identified as "1174-901-12" in taxonomic databases, and RH-AL1, an undescribed lineage of bacteria related to Beijerinckiaceae. Despite their abundance in the phyllosphere, Lichenihabitantaceae and RH_AL1 could not be properly identified by 16S rRNA gene barcoding, due in part to limitations of short read sequencing leading to a lack of recognition of certain Hyphomicrobiales genera, and to incongruencies in the assignment of genera to families among existing taxonomic databases. A significant proportion of Lichenihabitantaceae were detected in association with lichens and in environments with harsh conditions like exposed surfaces, air and snow. Overall, our study stresses the need to agree on a common systematic framework to properly classify and identify key leaf-associated Hyphomicrobiales taxa, and to move toward metagenomics and culturomics to increase their representation in reference databases, to provide a better understanding of the evolutionary and functional mechanisms underpinning bacteria adaptations to living on plants.}, } @article {pmid41679417, year = {2026}, author = {Dash, S and Zhao, D and Schuppe-Koistinen, I and Du, J}, title = {Female reproductive microbiome in fertility care.}, journal = {Fertility and sterility}, volume = {125}, number = {4}, pages = {558-573}, doi = {10.1016/j.fertnstert.2026.02.015}, pmid = {41679417}, issn = {1556-5653}, mesh = {Humans ; Female ; *Microbiota/physiology ; *Fertility ; *Infertility, Female/microbiology/therapy/diagnosis/physiopathology ; *Genitalia, Female/microbiology ; *Bacteria/genetics/classification ; }, abstract = {The microbiome has emerged as a critical determinant of female reproductive health and fertility outcomes. Although conventional infertility evaluations, encompassing medical history, ovulation assessment, uterine and tubal evaluation, genetic screening, hormonal profiling, and reproductive tract imaging, provide essential diagnostic information, a substantial proportion of infertility cases remain unexplained, prompting increased attention to microbial factors. This review provides a comprehensive, critical evaluation of the methods for assessing the female reproductive microbiome, spanning traditional culture-based microbiology to contemporary molecular approaches. We systematically discuss the diagnostic performance, clinical utility, and established techniques, including microscopic examination, Nugent scoring, and Amsel criteria, alongside modern molecular methods such as quantitative PCR panels, 16S rRNA gene sequencing, shotgun metagenomics, and other multiomics. Critically, we evaluate the current microbiome testing platforms in clinical validity and utility. We identify significant gaps between research-grade methodologies and clinically actionable diagnostics, including a lack of standardized protocols, inconsistent reporting of absolute bacterial loads vs. relative abundances, and limited validation against reproductive outcomes. We propose evidence-based criteria for selecting appropriate diagnostic approaches on the basis of clinical context and discuss emerging technologies, including multiomics integration for implementing microbiome assessment in fertility care.}, } @article {pmid41679496, year = {2026}, author = {Jing, M and Zhang, X and Li, X and Tan, L and Niu, Z and Ma, Y}, title = {Direct Evidence of Microplastic-Mediated Microbial Migration Across the River-Sea Transition via a Novel Field-Laboratory Coupled Approach.}, journal = {Environmental research}, volume = {296}, number = {}, pages = {123973}, doi = {10.1016/j.envres.2026.123973}, pmid = {41679496}, issn = {1096-0953}, mesh = {*Microplastics/toxicity/analysis ; *Rivers/microbiology ; *Seawater/microbiology ; Bacteria/drug effects/genetics ; *Water Pollutants, Chemical/toxicity/analysis ; *Microbiota/drug effects ; Biofilms ; *Water Microbiology ; }, abstract = {Large amounts of microplastics (MPs) are transported annually from river into the ocean. Biofilm-covered MPs, termed as the "plastisphere", may mediate microbial transfer. Previous studies have mostly focused on the evolution of the plastisphere itself, covering field experiments and its transformation during migration. Direct evidence for their impact on marine communities is still limited. To address this, we combined field and laboratory experiments to directly evaluate the effects of MPs on marine microbial communities along the river-sea shift. MPs were incubated for 0, 28, and 140 days in freshwater. They were then transferred to a laboratory-simulated marine micro-ecosystem constructed with a fresh seawater microbiome to allow the microbial communities to acclimate, and then further incubated in the laboratory for 1, 3, and 7 days. Microbial community dynamics were examined using metagenomic analysis. Long-term incubated plastispheres (140 days) rapidly shifted marine community structure toward plastisphere-like composition as early as Day 1. However, this overall structural change faded by Day 7. Interestingly, the presence of 28-day and 140-day plastispheres led to a consistent increase in microbial species diversity and a higher number of antibiotic resistance genes (ARGs) and virulence factors (VFs), this effect persisted through Day 7. Additionally, salt-tolerant, potentially pathogenic bacteria were also detected, reflecting the as carrier roles of plastispheres. This study provides direct evidence that plastispheres mediate microbial transfer, thereby enhancing diversity and spreading ARGs and VFs, contributing to a better understanding of the potential ecological and environmental risks of microplastics.}, } @article {pmid41679688, year = {2026}, author = {Tibi, MF and Argote, YM and Walker, AC and Pandey, S and Puente, C and Ellward, GL and Safwat, A and Rincon-Limas, DE and Czyż, DM}, title = {Modulation of host proteostasis by Prevotella corporis via induction of the heat shock response.}, journal = {Cell stress & chaperones}, volume = {31}, number = {2}, pages = {100150}, pmid = {41679688}, issn = {1466-1268}, support = {R01 AG077534/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; *Proteostasis ; Caenorhabditis elegans/microbiology/metabolism ; *Prevotella/physiology/metabolism ; *Heat-Shock Response ; Humans ; Proteotoxic Stress ; HSP70 Heat-Shock Proteins/metabolism ; Peptides ; }, abstract = {Neurodegenerative protein conformational diseases (PCDs) are progressive, currently incurable disorders driven by toxic protein aggregation that leads to neuronal death. Emerging evidence supports a microbial role in PCDs, including the most prevalent: Alzheimer's and Parkinson's disease. While metagenomic studies consistently associate gut dysbiosis with these disorders, the mechanisms by which microbes influence host proteostasis remain poorly understood. In particular, considerable attention has been given to proteotoxic bacteria, whereas the mechanisms by which commensal microbes confer proteoprotection have received comparatively little attention. We previously employed Caenorhabditis elegans models to characterize the role of over 220 bacterial isolates from the Human Microbiome Project on host proteostasis. Strikingly, members of the Prevotella genus exhibited proteoprotective effects. Most notably, transient exposure to Prevotella corporis uniquely induced Hsp70, a critical molecular chaperone that maintains proteostasis, and significantly reduced aggregation of polyglutamine (polyQ), Aβ42, and α-synuclein. In the present study, we expand on these findings, demonstrating that among 13 Prevotella species tested, P. corporis robustly activates the heat shock response (HSR) and confers conserved aggregate-suppressing activity in Drosophila melanogaster. We further demonstrate that transient exposure to P. corporis results in the activation of protective stress pathways and promotes disaggregation of existing intestinal polyQ aggregates in C. elegans, leading to a general enhancement of global proteostasis. This is supported by significantly improved survival and enhanced thermotolerance. Together, our findings reveal a beneficial niche for P. corporis in activating the HSR to enhance organismal proteostasis and support a microbe-mediated gut-proteostasis axis. This work underscores the therapeutic potential of targeting the gut microbiota for the management of PCDs, highlights the importance of species-level resolution in microbiome studies, and supports the emerging view of the intestine as a proteostasis-modulating organ.}, } @article {pmid41679750, year = {2026}, author = {Lamont, RF and Jørgensen, JS}, title = {The Influence of the Vaginal Microbiome on the Prediction and Prevention of Preterm Birth.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {133}, number = {6}, pages = {1129-1146}, doi = {10.1111/1471-0528.70173}, pmid = {41679750}, issn = {1471-0528}, mesh = {Humans ; Female ; *Vagina/microbiology ; *Microbiota ; *Vaginosis, Bacterial/microbiology/complications ; Pregnancy ; *Premature Birth/prevention & control/microbiology ; *Dysbiosis/microbiology/complications ; Probiotics/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: Spontaneous preterm labour that leads to preterm birth is known to be associated with vaginal dysbiosis, particularly bacterial vaginosis, and this may explain why progress has been slow in the last few decades. Bacterial vaginosis was considered enigmatic with unknown aetiology, difficulty in diagnosis, different response to treatment, be that persistence or recurrence, and different phenotypic outcomes.

METHODOLOGY: A narrative review.

RESULTS: New information from the Human Microbiome Project using molecular-based, culture-independent technology has added important new knowledge to our understanding of vaginal eubiosis and dysbiosis. While this metagenomics are currently mainly research tools, we hope further studies will better elucidate the full profile of dysbiosis. This will hopefully aid the choice of antibiotic to suit each dysbiotic profile identified rather than for a single organism. By measuring abundance and diversity of the vaginal microbiome, we can develop molecular means of differentiating eubiosis and dysbiosis to predict preterm birth. We can also choose which antibiotic is appropriate for different dysbiotic subtypes, the local subtype of milieu created by that microbiota, the host response, and the phenotypical outcomes of which preterm birth is paramount. In addition, we can develop suitable probiotic species of lactic acid producing bacteria to aid in the prevention of preterm birth.}, } @article {pmid41679819, year = {2026}, author = {Ding, Y and Li, X and Hao, Y and Ding, P and Chen, N and Luo, L and Wan, C and Wu, M}, title = {Structural elucidation and effects on gut microbiota of soluble galactans from edible Boletus.}, journal = {Carbohydrate polymers}, volume = {378}, number = {}, pages = {124886}, doi = {10.1016/j.carbpol.2026.124886}, pmid = {41679819}, issn = {1879-1344}, mesh = {*Galactans/chemistry/pharmacology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; *Agaricales/chemistry ; Molecular Docking Simulation ; Fatty Acids, Volatile/metabolism ; Solubility ; Probiotics ; }, abstract = {Edible Boletus mushrooms hold considerable development potential due to their exceptional nutritional and biological profiles. This study characterized two novel galactans, NBP and BRP, extracted from Neoboletus brunneissimus and Butyriboletus roseoflavus, respectively. Structural analysis revealed that both NBP and BRP possess a backbone composed of α-1,6-linked galactopyranosyl residues substituted at O-2, with structural diversity arising from variations in the side-chain substituents. Although both polysaccharides exhibit low viscosities, BRP forms a shear-stable elastic gel network, contrasting with the predominantly linear structure of NBP. In vitro fermentation demonstrated that both galactans markedly promoted the proliferation of beneficial probiotics, optimized gut microbiota composition, and enriched butyrate-producing bacteria including Faecalibacterium prausnitzii. Furthermore, they stimulated the production of lactic acid and short-chain fatty acids (SCFAs), leading to a reduction in fermentation pH and thereby modulating microbial ecology and host energy metabolism. Metagenomic annotation revealed that galactan degradation was driven by glycoside hydrolases (GHs) from Bacteroidaceae, and molecular docking analyses indicated that these GHs exhibit distinct binding preferences for specific structural regions of the polysaccharides. These results explain the basis for the microbiota-dependent improvement of gut health by Boletus galactans, providing a theoretical foundation for their development as precision prebiotics.}, } @article {pmid41679837, year = {2026}, author = {Sacco, O and Johansen, EL and Tian, Y and Holck, J and Kirkensgaard, JJK and Blennow, A and De Lise, F and Shaikh-Ibrahim, A and Moracci, M and Curci, N and Svensson, B and Cobucci-Ponzano, B and Wang, Y}, title = {Biochemical characterisation of the 4-α-glucanotransferase from the hyperthermophilic archaeon Pyrobaculum arsenaticum and its formation of high-amylose resistant starch.}, journal = {Carbohydrate polymers}, volume = {378}, number = {}, pages = {124919}, doi = {10.1016/j.carbpol.2026.124919}, pmid = {41679837}, issn = {1879-1344}, mesh = {*Glycogen Debranching Enzyme System/metabolism/chemistry ; *Pyrobaculum/enzymology ; *Starch/chemistry/metabolism ; *Amylose/chemistry/metabolism ; Hot Temperature ; Hydrolysis ; }, abstract = {High-amylose starch (HAS) is gaining attention in biotechnology for its thermal stability, structural resilience and health benefits. Its dense crystalline structure hinders hydrolysis by human gut enzymes, making it a promising source of type 2 resistant starch for hydro-thermal and enzymatic upgrading. 4-α-Glucanotransferases (4αGTs) of glycoside hydrolase family 77 catalyse disproportionation of α-1,4-glucan chains in HAS, enhancing functionality and nutritional properties. Here, a 4αGT, ParGT from the hyperthermophilic archaeon Pyrobaculum arsenaticum, identified in a metagenomic dataset from Pisciarelli hot spring (85 °C, pH 5.5; Naples, Italy), showed highest activity at 100 °C and pH 5.5, and specific activity of maltotriose disproportionation at 75 °C of 1170 U/mg. ParGT effectively modified HAS granules under controlled heating (annealing) at 75 °C, altering crystallinity, surface order and chain length. Comparative analysis of native, heat-treated and ParGT-modified HAS granules from wheat, potato, maize, and barley revealed distinct effects of botanical source, enzymatic modification, and heating. Notably, ParGT increased the resistant starch (RS) contents in wheat and potato HASs subjected to in vitro digestion. Interfacial kinetics correlated the increased resistance to decreased density of glucoamylase attack sites. Overall, ParGT showed strong potential in enzyme- and hydro-thermal modifications developing starch-based ingredients for health and food applications.}, } @article {pmid41680314, year = {2026}, author = {Alrasheed, AS and Zawawi, AM and Alsulami, LM and Alghirash, FA and Alsalmi, SO and Alhalal, IA}, title = {Clinical utility of metagenomic next-generation sequencing in diagnosing spinal infections: a systematic review and meta-analysis.}, journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society}, volume = {}, number = {}, pages = {}, pmid = {41680314}, issn = {1432-0932}, abstract = {PURPOSE: Spinal infection (SI) presents a major diagnostic challenge due to nonspecific clinical features and the limitations of conventional culturing techniques. Metagenomic next-generation sequencing (mNGS) has recently emerged as a valuable tool that enables broad, unbiased pathogen detection. This meta-analysis evaluated the diagnostic performance of mNGS for SI diagnosis, comparing it with conventional culturing techniques, with a particular focus on its role in spinal tuberculosis (TB) diagnosis. METHODS: A thorough literature search was conducted in PubMed, Web of Science, the Cochrane Library, and Scopus databases to retrieve potentially relevant articles. Data on diagnostic performance, including pathogen detection rate (PDR), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), were extracted and analyzed. To assess the risk of bias of the included studies, the quality assessment of diagnostic accuracy studies 2 (QUADAS-2) tool was used. Subgroup analyses were used to evaluate the performance of mNGS in spinal TB. Meta-regression analysis was performed to account for covariate effects on diagnostic performance. RESULTS: A total of 17 Chinese studies with 1788 patients were included. In SI diagnosis, mNGS showed a significantly greater PDR than conventional culturing techniques (RR: 2.43; 95% CI: 1.73–3.43; p = 0.0001; I[2] = 88.6%). mNGS exhibited higher sensitivity (81% vs. 33%) and NPV (60% vs. 36%) indicating higher reliability in excluding infection, while conventional culturing techniques exhibited higher specificity (82% vs. 76%) and PPV (90% vs. 85%). In spinal TB, mNGS showed higher sensitivity (75% vs. 41%) and NPV (87% vs. 74%) while maintaining comparable specificity (99% vs. 100%) and PPV (94% vs. 100%). CONCLUSION: This meta-analysis confirms that mNGS provides superior sensitivity, broader pathogen coverage, and faster diagnostic capability than conventional culturing techniques, particularly in spinal TB, where early detection is critical. Nevertheless, these findings should be interpreted cautiously, as the included studies were limited by retrospective designs, geographic bias, and inconsistent diagnostic reference standards. While mNGS represents a valuable adjunct to standard diagnostics, further prospective multicenter studies, cost reduction, and standardized protocols are required to optimize its integration into clinical practice.}, } @article {pmid41680318, year = {2026}, author = {Choudhary, S and Kanaujia, R and Bahadur, R and Angrup, A}, title = {The role of metagenomic next-generation sequencing in spinal infections: a systematic review and meta-analysis.}, journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society}, volume = {}, number = {}, pages = {}, pmid = {41680318}, issn = {1432-0932}, abstract = {BACKGROUND: The diagnosis of spinal infections (SI) (vertebral osteomyelitis, epidural abscess, spondylodiscitis) remains a challenge in low-income countries due to limited access to advanced microbiological techniques, prolonged culture times, and low diagnostic yields, particularly for fastidious and antibiotic-exposed bacteria. Metagenomic next-generation sequencing (mNGS) offers a culture-independent approach with high sensitivity, but its clinical utility in resource-constrained settings is limited by cost and infrastructure challenges. METHODS: We conducted a systematic review and meta-analysis of studies assessing the diagnostic performance of shotgun or targeted mNGS for bacterial detection in SIs. A comprehensive literature search of Embase, Medline, and Web of Science was performed till January 15, 2025. Studies including tubercular or fungal infections were excluded. The reference standard comprised composite clinical criteria and culture-based methods. Risk of bias was evaluated using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. RESULTS: A total of 15 studies with 944 patients were included. In comparison to the culture mNGS demonstrated a pooled sensitivity and specificity of 91% (95% CI: 87.1%–94%) and 35.0% (95% CI: 31.1%–38.9%) respectively. In comparison with the combined reference standard, the pooled sensitivity and specificity of mNGS was 86.0% (95% CI: 81.6%–90%) and 71.4% (95% CI: 63.1%–78.8%) respectively. The area under the summary receiver operating characteristic curve was 0.90, indicating moderate-to-high diagnostic performance. CONCLUSIONS: mNGS improves pathogen detection in SI. To enhance accessibility, future strategies should include the development of targeted NGS panels for common spinal pathogens, the establishment of centralized sequencing hubs for cost-sharing, integration with affordable molecular diagnostics, and public-private partnerships to subsidize sequencing costs. A multi-tiered diagnostic approach combining conventional microbiology, rapid molecular tests, and selective mNGS may provide a feasible strategy to enhance SI diagnostics globally.}, } @article {pmid41680419, year = {2026}, author = {Pedrazzini, C and Funari, R and Cucini, C and Nardi, F and Grabenweger, G and Widmer, F and Enkerli, J}, title = {Population genomics identifies Italian and North American origins of Popillia japonica in Switzerland.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41680419}, issn = {2045-2322}, support = {No. 861852//European Union's Horizon 2020/ ; }, mesh = {Animals ; Switzerland ; *Coleoptera/genetics/classification ; Phylogeny ; North America ; Introduced Species ; Italy ; Genetics, Population ; *Metagenomics/methods ; Genomics ; }, abstract = {The Japanese beetle (Popillia japonica), native to Japan, is a major invasive species in North America and Europe. Its colonization of Europe began on the Azores (1970s), followed by Italy (2014) and southern Switzerland (2017). In 2023, the presence of the pest was reported in three areas of Switzerland: Kloten (Canton of Zürich, north-eastern Switzerland), Basel (Canton of Basel-Landschaft, northern Switzerland), and in eastern Canton of Valais (South Switzerland) near the Italian border. In 2024, P. japonica individuals were discovered in several other Swiss Cantons. To trace P. japonica spread and origins in Switzerland, we investigated 42 individuals from infested areas, comprising scattered findings across Switzerland. Phylogenetic and population structure analyses using whole-genome resequencing, including data of previously sequenced samples from Japan, North America, the Azores, Italy, and Southern Switzerland, revealed distinct P. japonica migration patterns. Populations in Basel, Valais, and central Switzerland likely originated from Ticino/Northern Italy via road or rail transport. Conversely, the population near Zürich Airport was identified as an independent introduction from North America, likely through unintentional air transport. These findings offer insights into P. japonica spread across Switzerland, highlighting the need for enhanced monitoring and identification of invasion pathways.}, } @article {pmid41680567, year = {2026}, author = {Chen, L and Hong, C and Xie, Y}, title = {Bridging the gap between microbiome function and clinical benefit in sarcopenia.}, journal = {Aging clinical and experimental research}, volume = {38}, number = {1}, pages = {76}, pmid = {41680567}, issn = {1720-8319}, mesh = {Aged ; Humans ; *Gastrointestinal Microbiome/physiology ; Muscle Strength ; Probiotics/therapeutic use ; *Sarcopenia/microbiology/therapy/physiopathology ; Systematic Reviews as Topic ; Meta-Analysis as Topic ; }, abstract = {We read the recent systematic review and meta-analysis on nutrition-based, gut microbiota-targeted interventions for sarcopenia in older adults with great interest. While the evidence suggests that probiotics and fiber-enriched diets may improve surrogate outcomes such as muscle strength and gait speed, we highlight two priorities to strengthen future mechanistic and clinical translation. First, microbiome measurements in existing trials are often limited to genus-level taxonomic shifts, which can be biologically misleading because a single genus may include members with divergent immunomodulatory properties. Even species-level profiling may be insufficient, as strains within the same species can differ markedly in genetic content and metabolic capacity. Moreover, taxonomic composition does not necessarily reflect functional output due to functional redundancy across microbial communities. We therefore recommend transitioning to whole-genome shotgun metagenomics to enable strain-level resolution and functional profiling, allowing investigators to quantify pathways and metabolites relevant to muscle preservation, including short-chain fatty acids and vitamin biosynthesis. Second, we argue that improvements in sarcopenia-defining parameters should be linked to patient-centered clinical benefit. Future randomized controlled trials should be adequately powered to assess hard endpoints, including falls, fractures, hospitalization rates, and functional independence, alongside muscle mass and performance measures, to establish whether microbiota modulation delivers meaningful reductions in healthcare burden.}, } @article {pmid41680579, year = {2026}, author = {López-Guzmán, SF and Sánchez-Jasso, DE and Hernández-Sánchez, J and Oviedo, N and Bermudez-Cruz, RM}, title = {Molecular Characterization of the Murine Catsper4 Promoter and its Regulation by CREMτ.}, journal = {Reproductive sciences (Thousand Oaks, Calif.)}, volume = {33}, number = {2}, pages = {411-423}, pmid = {41680579}, issn = {1933-7205}, support = {IMSS R-2023-785-056//Instituto Mexicano del Seguro Social/ ; }, mesh = {Animals ; *Promoter Regions, Genetic ; Male ; *Cyclic AMP Response Element Modulator/metabolism/genetics ; *Calcium Channels/genetics/metabolism ; Mice ; Sperm Proteins ; Gene Expression Regulation ; }, abstract = {Cation channel sperm-associated protein 4 (CATSPER4) is a subunit of the sperm-specific cation/calcium channel, CatSper, located in the principal piece of the sperm flagellum. It is expressed during the late stages of spermatogenesis, and disruption of the gene encoding this protein leads to male infertility. Mutations in Catsper4 are linked to asthenozoospermia. However, the molecular mechanisms regulating Catsper4 expression remain unclear. Here, we present a detailed molecular characterization of the Catsper4 promoter in mice, focusing on the role of the cAMP-responsive element modulator isoform τ (CREMτ) in its transcriptional regulation. Analysis of publicly available metagenomic chromatin immunoprecipitation-sequencing (ChIP-seq) data revealed the presence of activation histone marks-H3K4me3, H3K4me1, and H3K27ac-within a region corresponding to the 631 bp predicted promoter, suggesting an active promoter region. Although the predicted Catsper4 promoter showed minimal activity, a 65 bp deletion at the 3'-end of the promoter significantly enhanced the transcription. Moreover, removal of the 239 bp in the 5'-flanking region also increased the transcriptional activity, indicating that the core promoter region spans the region from - 99 to + 63 bp relative to the transcription start site (TSS). Notably, a cAMP-responsive element was predicted at + 91, a relevant site in the regulation of other Catsper family genes. To explore its function, we mutated this site and overexpressed CREMτ. Electrophoretic mobility shift assays (EMSA) and ChIP assays confirmed that CREMτ binds to the murine Catsper4 promoter both in vitro and in vivo. This study provides the first functional analysis of the Catsper4 promoter, shedding light on the mechanisms regulating its expression and highlighting the key role of CREMτ in this process.}, } @article {pmid41680629, year = {2026}, author = {Selhorst, P and Van Vyve, E and Falconi-Agapito, F and Mariën, J and Ariën, KK}, title = {Sensitive, flexible, and affordable serum RNA sequencing for pathogen detection on the Oxford Nanopore platform.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {188}, pmid = {41680629}, issn = {1471-2164}, support = {U01 AI151378/AI/NIAID NIH HHS/United States ; U01AI151378/NH/NIH HHS/United States ; }, abstract = {Metagenomic sequencing for pathogen detection has traditionally suffered from low sensitivity due to the overwhelming presence of host nucleic acids. Commercial host-depletion kits are often prohibitively expensive and limited to specific species, hindering adoption in resource-limited settings, where the burden of zoonotic diseases is highest. To address this, we optimized and combined Sequence-Independent Single Primer Amplification (SISPA) with Depletion of Abundant Sequences by Hybridization (DASH), establishing a low-cost metagenomic protocol on the Oxford Nanopore sequencing platform. Our approach can be adapted to any species to detect microbial RNAs in serum samples at PCR-range sensitivity, outperforming existing methods in the field.}, } @article {pmid41680679, year = {2026}, author = {Wang, P and Tian, B and Tian, C and Shan, C and Huang, R and Zhang, Q}, title = {Clinical characteristics and prognosis of patients with Chlamydia psittaci pneumonia identified by metagenomic next-generation sequencing.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41680679}, issn = {1471-2334}, support = {2024GSPKY23//Jiangsu Province High-Level Hospital Construction Funds of Zhongda Hospital, School of Medicine, Southeast University/ ; }, mesh = {Humans ; *Chlamydophila psittaci/genetics/isolation & purification ; Female ; Male ; Prognosis ; Retrospective Studies ; Middle Aged ; *Psittacosis/microbiology/diagnosis/mortality ; Aged ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing ; Adult ; Bronchoalveolar Lavage Fluid/microbiology ; DNA, Bacterial/genetics ; }, abstract = {BACKGROUND: Few studies comprehensively reported the clinical characteristics, prognosis, and factors associated with severe disease in patients with confirmed Chlamydia psittaci pneumonia identified by metagenomic next-generation sequencing (mNGS).

METHODS: This retrospective study included 63 patients with Chlamydia psittaci pneumonia diagnosed by mNGS. The clinical characteristics and prognosis were analyzed. Cox regression was used to identified factors associated with severe cases.

RESULTS: A total of 63 patients were confirmed with detected Chlamydia psittaci DNA by mNGS in the bronchoalveolar lavage fluid or blood. A total of 16 (25.4%) patients had severe disease. The overall in-hospital mortality was 4.7% (3/63), with a rate of 18.7% (3/16) in the severe group. 90.4% (57/63) of patients were older than 50 years. 21 (33.3%) patients had poultry/bird exposure. The most common symptoms included fever (100%), cough (63.5%) and fatigue (63.5%). All patients showed lung consolidation (100%) on chest CT, with air bronchograms (96.8%) and pleural effusion (41.3%). In the multivariable Cox regression, the levels of hs-CRP (P = 0.003), creatinine (P = 0.002), and presence of bilateral lung infection (P = 0.003) were independent factors associated with severe pneumonia.

CONCLUSION: Psittacosis pneumonia predominantly affects middle-aged and elderly adults. Elevated levels of hs-CRP and creatinine, the presence of bilateral lung involvement associated with progression to severe disease. Psittacosis-induced severe pneumonia is associated with high mortality.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid41680704, year = {2026}, author = {Huang, Y and Huang, X and Wei, X and Yang, X and Su, T and Duan, Q and Wan, J and Sun, Y and Xu, Y}, title = {Characterization of multiple herpes viremia via next-generation sequencing in patients with lower respiratory tract infections: a retrospective cohort study.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41680704}, issn = {1471-2334}, support = {H-2024060//the Yunnan health training project of high level talents/ ; XDYC-QNRC-2024-448//the Yunnan revitalization talent support program/ ; 202302AA310044-01//Key Projects of Yunnan Province Science and Technology Department/ ; }, abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) are a leading cause of the substantial morbidity and mortality associated with severe pneumonia. Herpesviruses (HHVs) frequently reactivate during critical illness, but their bronchoalveolar lavage fluid (BALF) coinfection patterns and clinical correlates remain incompletely defined. METHODS: A retrospective cohort study was conducted among hospitalized adults with suspected LRTIs who underwent BALF next-generation sequencing (NGS) at the Yunnan First People’s Hospital between November 2024 and May 2025. Two analytical workflows were evaluated, namely metagenomic DNA sequencing (mNGS-DNA) and a targeted NGS (tNGS) panel, including 289 and 675 patients, respectively. Participants were subsequently classified into a herpesvirus-detected (HD) group and a non-herpesvirus-detected group (non-HD). RESULTS: In mNGS-DNA, detection frequencies were EBV 17.30%, CMV 14.88%, HHV-7 9.00%, HSV-1 8.30%, HHV-6 4.15%, and VZV 0.34%, single- and multi-virus positivity were 22.84% and 11.76%. In tNGS, the corresponding values were 17.93%, 12.00%, 7.11%, 10.07%, 2.96%, and 0.30%, single- and multi-virus positivity were 24.44% and 15.11%. HD patients were older and more likely to have severe pneumonia in both cohorts (P < 0.0001). Bacteria were the predominant pathogens in the patients with suspected LRTIs, followed by viruses and fungi. In matched BALF subsets, sequencing outperformed culture for bacterial detection (mNGS-DNA 37.90% vs. 20.56%; tNGS 87.45% vs. 13.45%; all P < 0.001), underscoring the complementary yield over conventional culture methods. HHVs exhibited the highest co-infection rates with pathogens such as Stenotrophomonas maltophilia, Klebsiella pneumoniae, and Candida albicans. CONCLUSIONS: In BALF from hospitalized LRTI patients, EBV and CMV predominate among herpesviruses, with HHV-7 a frequent coinfection partner. These findings underscore the need for prospective studies to define the prognostic impact of HHV coinfections.}, } @article {pmid41681117, year = {2026}, author = {Maiakovska, O and Link, L and Zayas, M and Sano, Y and Koay, TW and Rapti, K and Liu, J and Bubeck, F and Xu, M and Baumgartl, C and Wiedtke, E and Krämer, C and Naber, L and Grimm, D}, title = {Metagenomic Reconstruction of Adeno-Associated Virus Genomes.}, journal = {Human gene therapy}, volume = {}, number = {}, pages = {10430342261419534}, doi = {10.1177/10430342261419534}, pmid = {41681117}, issn = {1557-7422}, abstract = {The exponential expansion of metagenomic data obtained through high-throughput sequencing technologies has surpassed the petabyte-scale threshold, resulting in an unprecedented abundance of data now enabling the in silico discovery of previously unknown viral and bacterial species. Here, we demonstrate the power and promise of mining sequencing data to uncover natural adeno-associated virus (AAV) cap(sid) genes, with the synergistic aims to expand our repertoire of templates for vector development and to enhance our understanding of the AAV space and of virus evolution across species. Specifically, we harnessed the Serratus Explorer to identify 29 AAV variant genomes from publicly accessible raw metagenomic data generated from birds, nonhuman primates, or human samples, of which 16 were classified as high-quality based on the high coverage of their cap region. To this end, we devised a comprehensive computational pipeline comprising (i) reference candidate selection, (ii) prealigned data acquisition, (iii) variant calling and frequency estimation, (iv) consensus calling, (v) variant resolution, (vi) phylogenetic analysis, and (vii) protein structure analysis steps. Eight representative cap genes from four different host organism species were synthesized and used to produce so-called metAAV vectors, which exhibited intriguing and biomedically relevant properties including partial escape from neutralizing anti-AAV antibodies and muscle tropism combined with robust liver detargeting in systemically injected mice. We concurrently pursued a conventional, reference-independent metagenome-based genome assembly, which also successfully reconstructed AAV cap genes but solely for abundant variants. Together with the fact that this traditional reference-independent method necessitates substantial computational resources and misses to accurately resolve multiple closely related variants, this highlights the assets and superiority of our original consensus-based reconstruction pipeline for fundamental virus research and for future gene therapy vector bioengineering.}, } @article {pmid41681414, year = {2026}, author = {Mohammed, EAH and Fehér, M and Bársony, P and Teye-Gaga, C and Czeglédi, L and Freytag, C and Váradi, A and Ahmed, AEM and Pál, K}, title = {Growth Performance, Gut Integrity and Intestinal Microbiome Responses of Juvenile Common Carp (Cyprinus carpio L.) to Probiotic and Prebiotic Supplementation.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {3}, pages = {}, pmid = {41681414}, issn = {2076-2615}, abstract = {The aim of this study was to examine the impact of the probiotics Saccharomyces cerevisiae (SC) and Pediococcus acidilactici (PA), as well as the prebiotic yeast cell wall extract (Cyberlindnera jadinii and S. cerevisiae) (YP), on the growth parameters, intestinal histomorphology, liver and gills normality, and gut microbiome of common carp (Cyprinus carpio L.). These feed supplements were subjected to a 60-day experimental period, during which 120 fish (26.4 ± 5.2 g) were distributed into four groups, with each group comprising 30 fish. The feed supplements were administered at a rate of 1 g/kg of body weight. Before the trial, the fish were acclimatized for two weeks, then injected with Passive Integrated Transponder (PIT) tags. The results showed that none of the feed supplements exhibited a significant effect (p > 0.05) on growth indices. In contrast, the villi length, villi width, muscular thickness, and crypt depth in the anterior, mid, and posterior intestine of the SC group exhibited significant (p < 0.05) improvements compared to the other groups. No alteration or abnormal growth were noticed in the gills and livers. The most dominant microbe genera in all groups, with abundances greater than 60% of the total, were Cetobacterium and Aeromonas. However, Polynucleobacter, Nordella, Mycoplasma, Romboutsia, and Staphylococcus species were present at lower abundances. The presence of Actinobacteria has been observed only in the intestine of fish that have been fed a diet supplemented with PA. It can be concluded that the tested probiotics and the yeast cell wall prebiotic have the potential to produce a remarkable improvement in intestinal morphology and a considerable change in the gut microbiome without notable effect on growth, livers, or gills of common carp.}, } @article {pmid41681750, year = {2026}, author = {Liepina, EE and Sivina, E and Jurkane, L and Daneberga, Z}, title = {Baseline Gut Microbiome and Metabolite Profiles Associate with Treatment Response in Breast Cancer Patients Undergoing Neoadjuvant Chemotherapy.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {3}, pages = {}, pmid = {41681750}, issn = {2075-4418}, abstract = {Background/Objectives: Response to neoadjuvant chemotherapy (NAC) varies substantially among breast cancer patients and is only partially explained by tumor-intrinsic factors. The gut microbiome has emerged as a potential modulator of chemotherapy efficacy, yet its role in breast cancer remains underexplored. This study aimed to characterize gut microbial composition, functional potential, and microbially derived metabolites in breast cancer patients undergoing NAC. Methods: baseline stool samples from 39 chemotherapy-naïve breast cancer patients undergoing NAC were analyzed using shotgun metagenomic sequencing and targeted metabolomics. Patients were stratified by pathological complete response (pCR, n = 17; no pCR, n = 22). Microbial taxonomic and functional profiles, short-chain fatty acids (SCFAs) and bile acids were assessed, with subgroup analysis performed in triple-negative breast cancer (TNBC). Results: Patients achieving pCR exhibited significantly higher baseline microbial richness compared to non-responders (p = 0.040). Differential abundance analysis revealed enrichment of Dialister, Kineothrix, and Jutongia in responders, whereas Rothia, Leuconostoc, Klebsiella, Jingyaoa, Cuneatibacter, Youxingia, and Bittarella were enriched in non-responders. SCFAs (acetate, propionate and butyrate) positively correlated with microbial glucose catabolic pathways, while caproate was negatively associated with multiple amino acid, lipid, vitamin, and cell wall biosynthesis pathways, including peptidoglycan maturation. Metabolomic analysis identified higher deoxycholic acid (DCA) levels in non-responders and increased C6 levels in responders, although these associations did not remain significant after multiple testing correction. Similar trends were observed in the TNBC subgroup (n = 15). Conclusions: Baseline gut microbiome diversity, taxonomic composition, and functional metabolic potential are associated with response to neoadjuvant chemotherapy in breast cancer, supporting the gut microbiome and its produced metabolites as a potential biomarker of treatment efficacy.}, } @article {pmid41683069, year = {2026}, author = {Betoret, E and Jiménez-Hernández, N and Duarte, S and Artacho, A and Bueno, A and Cruz, I and Betoret, N and Gosalbes, MJ}, title = {Persimmon Powder from Discarded Fruits as a Potential Prebiotic to Modulate Gut Microbiota in Postmenopausal Women.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41683069}, issn = {2304-8158}, support = {AGROALNEXT/2022/039//European Union Next Generation (PRTR-C17.I1)/ ; CIAICO/2022/27//Generalitat Valenciana/ ; }, abstract = {Faced with the challenge of reducing food waste, transforming discarded fruit into functional ingredients useful for the food industry is a valuable solution. Ingredients from fruit such as persimmons, which are rich in indigestible carbohydrates and bioactive compounds with antiradical capacity, could positively impact on the health of certain population groups due to their potential prebiotic effect. This study aimed to select the most suitable drying conditions and milling intensity for obtaining powdered persimmon ingredients with a prebiotic-like effects observed in vitro for postmenopausal women, and to evaluate this effect by considering the stimulation of health-promoting bacterial growth and short-chain fatty acids (SCFAs) production. First, the effect of the drying method (hot air drying at 60 and 70 °C, and freeze-drying) and grinding intensity on antiradical capacity, particle size, and the release of bioactive antiradical components into the intestinal lumen after an in vitro gastrointestinal digestion was determined. Next, the effect of these conditions on the microbiota composition of postmenopausal women was preliminary assessed in a batch colonic fermentation experiment for 24 h. The results showed that the ingredient dried with air at 70 °C had the highest phenol and flavonoid content, suffered the least degradation during in vitro gastrointestinal digestion and promoted the differential growth of fiber-degrader genera. Consequently, this was the ingredient selected as the most suitable. Lastly, the impact of this ingredient on the microbiota composition of 4 postmenopausal women has been evaluated in a long-term study using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]) coupled to high throughput sequencing. The growth stimulation of health-associated bacteria, such as Akkermansia muciniphila, Faecalibacterium prausnitzii or Phascolarctobacterium faecium, and the promotion of beneficial metabolic pathways, such as the sugar uptake-specific phosphotransferase system, sugar metabolism and propionate and isobutyrate production, were detected along 14 days of persimmon powder supplementation. A holistic framework for promoting human health while advancing environmental sustainability is represented by the combination of sustainable by-product valorization and microbiota-targeted functional food development.}, } @article {pmid41683205, year = {2026}, author = {Yu, W and Tang, K and An, R and Ma, S and Tan, H and Chen, M}, title = {Study on Association Between Gut Microbiota, Serum Metabolism and Gestational Diabetes Mellitus Based on Metagenomic and Metabolomics Analysis.}, journal = {Nutrients}, volume = {18}, number = {3}, pages = {}, pmid = {41683205}, issn = {2072-6643}, mesh = {Humans ; Female ; *Diabetes, Gestational/microbiology/blood/metabolism ; Pregnancy ; Case-Control Studies ; Adult ; *Metabolomics ; *Gastrointestinal Microbiome/physiology ; *Metagenomics ; Feces/microbiology ; Pregnancy Trimester, First ; }, abstract = {Background/Objectives: This study aimed to explore the association between maternal gut microbiota and metabolic profiles in the first trimester and the subsequent risk of gestational diabetes mellitus (GDM), as well as to characterize association patterns linking gut microbiota, serum metabolites, and metabolic traits. Methods: A nested case-control study was conducted among women with GDM (n = 47) and those without GDM (n = 94). Metagenomic sequencing was applied to analyze fecal microbiota, and liquid chromatography-mass spectrometry (LC-MS) was used for non-targeted plasma metabolomics. Differential microbiota and metabolites between groups were identified, and correlation analyses were conducted to assess their associations with clinical indicators. Results: Women who later developed GDM showed lower alpha diversity and higher beta diversity. Eleven differential species were identified, with Collinsella aerofaciens and Clostridium bartlettii enriched in GDM, while nine species such as Alistipes putredinis and Bacteroidales bacterium ph8 were enriched in controls. Sixty-four plasma metabolites differed between groups, including increased glycerol-3-phosphate, aromatic amino acids, and glycerophosphocholine, and decreased cysteine, tryptophan, niacinamide, and stearic acid. Correlation analyses revealed significant relationships between Alistipes putredinis, Eubacterium eligens, and Bacteroidales bacterium ph8 with metabolic and clinical indicators (e.g., TG, TC, LDL). Conclusions: In this nested case-control study, women who later developed GDM exhibited reduced gut microbial diversity and altered metabolic profiles during the first trimester of pregnancy. Several microbial taxa and microbiota-metabolite associations were observed in relation to subsequent GDM status, highlighting early-pregnancy microbial and metabolic features that may be relevant to GDM-related metabolic changes.}, } @article {pmid41683346, year = {2026}, author = {Fathima, S and Kilgore, PE and Sarkar, T and Sharma, N and Nguyen, HH}, title = {Muno-IgY Supplementation Improves Respiratory Health, Immune Response, and Exercise-Induced Physiological Stress in Healthy Adults: A Randomized Controlled Pilot Study.}, journal = {Nutrients}, volume = {18}, number = {3}, pages = {}, pmid = {41683346}, issn = {2072-6643}, mesh = {Humans ; Pilot Projects ; Adult ; Male ; Female ; Double-Blind Method ; *Dietary Supplements ; *Respiratory Tract Infections/prevention & control/immunology ; *Exercise/physiology ; *Stress, Physiological/drug effects ; Young Adult ; *Immunoglobulins/administration & dosage ; Gastrointestinal Microbiome/drug effects ; Biomarkers/blood ; }, abstract = {BACKGROUND/OBJECTIVES: Upper respiratory tract infections (URTIs) and exercise-induced immune perturbations are common in adults and may adversely affect quality of life, productivity, and physical performance. Immunoglobulin Y (IgY), a food-derived antibody with broad antimicrobial activity, has demonstrated immunomodulatory potential in preclinical and limited clinical studies. This study evaluated the effects of a multi-pathogen-specific IgY supplement (Muno-IgY) on respiratory health, immune and inflammatory markers, exercise-induced physiological stress, and gut microbiome composition in healthy adults.

METHODS: In this 12-week, double-blind, placebo-controlled trial, 28 healthy adults with a history of URTI were randomly allocated to receive Muno-IgY or placebo and URTI incidence, duration, and severity were recorded daily. Serum immune and inflammatory biomarkers were assessed longitudinally and in response to a standardized exercise challenge. Gut microbiome composition was analyzed using shotgun metagenomic sequencing at baseline and week 12. Safety and tolerability were assessed throughout the study.

RESULTS: URTI incidence was lower in the Muno-IgY group compared with placebo (14.3% vs. 35.7%), with shorter average duration and fewer missed workdays, though differences were not statistically significant (p > 0.05). Following an acute exercise challenge, Muno-IgY supplementation resulted in a significant increase in serum IgA at 24 h post-exercise (p = 0.022) and a significantly greater reduction in lactate dehydrogenase at 1 h post-exercise compared with placebo (p < 0.0001). Exploratory gut microbiome analyses suggested favorable directional shifts, though these changes were not statistically tested.

CONCLUSIONS: In this exploratory pilot study, Muno-IgY supplementation was safe and associated with significant improvements in selected markers of exercise-induced immune response and muscle damage. Numerical trends in URTI incidence and gut microbiome composition were observed but were not statistically significant. These findings are hypothesis-generating and support further evaluation of Muno-IgY in larger, adequately powered clinical trials.}, } @article {pmid41684123, year = {2026}, author = {Cheng, R and Deng, Z and Lin, F and Zhang, B and Liang, J and Lu, M}, title = {Clinical, laboratory, and radiological features of community-acquired pneumonia due to Chlamydia psittaci and Legionella pneumophila confirmed using next-generation sequencing.}, journal = {Annals of medicine}, volume = {58}, number = {1}, pages = {2627122}, pmid = {41684123}, issn = {1365-2060}, mesh = {Humans ; Male ; *Chlamydophila psittaci/isolation & purification/genetics ; *Community-Acquired Pneumonia/microbiology/diagnosis/drug therapy ; *Legionella pneumophila/isolation & purification/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Retrospective Studies ; Middle Aged ; *Legionnaires' Disease/diagnosis/drug therapy/microbiology ; Aged ; *Psittacosis/diagnosis/drug therapy/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; *Community-Acquired Infections/microbiology ; Anti-Bacterial Agents/therapeutic use ; Azithromycin/therapeutic use ; Adult ; }, abstract = {BACKGROUND AND OBJECTIVE: Chlamydia psittaci and Legionella pneumophila are common atypical pathogens that cause severe community-acquired pneumonia (CAP). This study aimed to compare the clinical features and outcomes of Chlamydia psittaci pneumonia (CPP) and Legionella pneumophila pneumonia (LPP) identified using next-generation sequencing (NGS) for accurate identification.

METHODS: This retrospective study included 68 patients with CPP and 42 patients with LPP. All cases were confirmed by metagenomic or targeted next-generation sequencing (mNGS/tNGS) of bronchoalveolar lavage fluid, serum, or sputum samples.

RESULTS: Patients with LPP had a higher prevalence of diabetes and were predominantly male. Poultry contact was common in CPP (64.7% vs. 14.3%), whereas recent travel was associated with LPP (47.6% vs. 2.9%). LPP presented with increased extrapulmonary symptoms. Inflammatory marker levels were higher in LPP, including leukocytosis, neutrophilia, C-reactive protein, and procalcitonin (all p < 0.05). Organ dysfunction was more frequent in LPP, with higher creatinine levels. Patients with LPP had more severe hypoxemia, required more respiratory support, and had higher intensive care admission rates. Targeted therapy guided by NGS was effective, with no significant differences in mortality or hospital stay between the two groups.

CONCLUSION: LPP demonstrated greater initial clinical and laboratory severity compared to CPP. Under NGS-guided targeted therapy, both groups achieved comparable outcomes. The observational finding that both pathogens respond to azithromycin and cause severe disease when left undetected underscore the value of guideline-recommended β-lactams/macrolide combination therapy in CAP settings, particularly where these intracellular pathogens remain undiagnosed without NGS.}, } @article {pmid41684459, year = {2026}, author = {Sgarabotto, E and Zadra, N and Tyrell, JA and Rossi, C and Hewson, I and Searle, JB and Hauffe, HC}, title = {Virome analysis reveals ORF7 sequences of type 2 porcine respiratory and reproductive syndrome virus (PRRSV) for the first time in a rodent host (Microtus pennsylvanicus).}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101345}, pmid = {41684459}, issn = {2352-7714}, abstract = {The lung virome of meadow vole (Microtus pennsylvanicus) from six neighbouring locations in New York State, USA was investigated using metagenomics to determine the circulation of potentially zoonotic viruses in a common wild rodent. This study provides the first evidence of the occurrence of Type 2 Porcine Respiratory and Reproductive Syndrome Virus (PRRSV2) in a rodent, or indeed in any species apart from wild and domestic pigs (Sus scrofa). PRRSV has the highest economic impact on the pig husbandry industry of any pathogen, but up to now, farm-to-farm transmission of this virus has been assumed to be associated with movement of and contact with infected pigs and fomites. Our results showing the natural occurrence of this virus in potential transmission hosts other than wild or domestic pigs challenge this scenario. Phylogenetic analysis of assembled partial genomes from four of our pooled samples and all other nucleocapsid protein (ORF7) sequences available in Genbank showed that the sequences recovered from meadow voles unambiguously clustered within the PRRSV2 clade together with sequences derived from wild and domestic pigs. Historical research suggests that spillover from voles to domestic pigs may be the most parsimonious explanation for these results; however, we cannot rule out the reverse: that the source of PRRSV2 in these wild voles derives from pigs. From a One Health perspective, our results reinforce the importance of characterizing wildlife viromes to survey possible sources of zoonotic pathogens, which is vital for making evidence-based decisions regarding potential threats to the health of humans, livestock and wild fauna.}, } @article {pmid41684676, year = {2026}, author = {Chukwujindu, C and Kolton, M and Fasakin, O and Pathak, A and Seaman, J and Chauhan, A}, title = {Microbial community structure and functional potential in a long-term uranium-nickel contaminated ecosystem.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1741152}, pmid = {41684676}, issn = {1664-302X}, abstract = {This study examined the microbial community structure, functional potential, and resistance determinants in uranium (U)- and nickel (Ni)-contaminated soils from the Savannah River Site (SRS), a former nuclear materials production and waste collection facility operated by the U. S. Department of Energy (DOE). Soil cores were collected from the Steed Pond area, where long-term discharge of acidic wastewater resulted in spatially variable contamination levels. Concentrations of U and Ni in the collected samples ranged from 0.22-10.44 g kg[-1] and 0.79-2.28 g kg[-1], respectively. Shotgun metagenomic and high-throughput quantitative PCR (HT-qPCR) analyses revealed bacterial communities dominated by Pseudomonadota, Actinomycetota, and Acidobacteriota, with enrichment of taxa affiliated with genera known to include diazotrophic members (e.g., Bradyrhizobium and Burkholderia), alongside increased abundance of nitrogen fixation-related functional genes. Carbon and nitrogen cycle genes were generally well represented across samples, with selective shifts observed in acetate assimilation genes (acsA/acsE) and comparatively low abundance of hydrazine oxidoreductase (hzo), indicating pathway-specific variation rather than broad metabolic suppression. A total of 117 resistance-associated genes were identified, comprising 93 antibiotic-resistance genes (ARGs), 3 metal-resistance genes (MRGs), and 21 mobile genetic elements (MGEs). Strong positive correlations among ARGs, MRGs, and MGEs indicate co-selection and horizontal gene transfer, forming a genetically mobile resistome. Collectively, these findings demonstrate that long-term U-Ni contamination selects for metabolically versatile, diazotroph-enriched, and genetically mobile microbiomes. Such communities exhibit both resistance proliferation and bioremediation potential, providing key insights into microbial adaptation and ecosystem recovery in legacy nuclear-contaminated soils.}, } @article {pmid41684743, year = {2025}, author = {Díaz-Velis, L and Salvador-Sagüez, F and Roach, F and Mancilla, E and Campos, MA and Ruiz-Gil, T and López-Moral, M and Garrido, G and Lázaro-Martínez, JL}, title = {Metagenomic and ribosomal transcript profiles of diabetic foot osteomyelitis in Hispanic patients: underestimated bacteria in biofilm persistence.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1729196}, pmid = {41684743}, issn = {2235-2988}, mesh = {Humans ; *Diabetic Foot/microbiology/complications ; *Osteomyelitis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics ; Chile ; *Biofilms/growth & development ; Female ; Microbiota ; DNA, Bacterial/genetics ; Male ; Middle Aged ; Sequence Analysis, DNA ; Aged ; Bone and Bones/microbiology ; }, abstract = {BACKGROUND: Diabetic foot osteomyelitis (DFO) is a serious complication of diabetes and a leading cause of lower-limb amputations. Conventional culture-based diagnostics often underestimate the microbial diversity of infected bone tissue. This study represents the first characterization of both total and ribosomally active bone microbiota in Hispanic patients with DFO using high-throughput 16S rRNA gene sequencing. The work aims to contribute to the inclusion of underrepresented populations in microbiome research and informing molecular-based antimicrobial strategies.

METHODS: Bone specimens (n = 13) were collected from seven Chilean patients with histologically confirmed DFO. Samples were analyzed using conventional aerobic culture and 16S rRNA gene sequencing from both genomic DNA (gDNA) and complementary DNA (cDNA) to characterize the total bacterial community and the ribosomally active fraction. In three patients, samples were stratified by bone depth (superficial/top, middle and bottom). Microbial diversity and relative abundance were assessed across patients and bone layers.

RESULTS: Acute osteomyelitis was the predominant histopathological pattern. Culture yielded 19 bacterial isolates, 95% of which were Gram-negative bacilli. Sequencing identified 3,412 operational taxonomic units (OTUs), with Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as dominant phyla. Enterobacteriaceae and Enterococcaceae were the most ribosomally active families. Microbial community composition varied substantially among patients and across bone depths. Staphylococcus aureus was infrequent (5% of culture isolates; ~1% of sequence reads), whereas low-abundance but ribosomally active taxa, such as Corynebacteriaceae, were consistently detected across all layers.

DISCUSSION: This combined metagenomic and ribosomal transcript analysis reveals a polymicrobial, patient-specific bone microbiota in Chilean patients with DFO, highlighting potentially active bacteria frequently overlooked by standard diagnostic methods. These findings underscore the value of integrating molecular approaches into clinical workflows to improve pathogen detection and support more personalized antimicrobial strategies, while also helping to address gaps in microbiome research among underrepresented populations.}, } @article {pmid41684896, year = {2025}, author = {Das, R and Malard, L and Pearce, DA and Convey, P and Rahlff, J}, title = {Diversity of DNA viruses in the atmosphere of sub-Antarctic South Georgia.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1726848}, pmid = {41684896}, issn = {1664-302X}, abstract = {Studying airborne viruses in remote environments like the sub-Antarctic island of South Georgia offers key insights into viral ecology, diversity, and their role in shaping ecosystems through microbial and nutrient interactions. We analyzed airborne viral community composition at two sites in South Georgia. Sampling took place using multiple methodologies, with the data produced subjected to viral metagenomics. The Coriolis μ device (wet collection) was the most effective, yielding 30 viral scaffolds. Two-thirds of the scaffolds were only obtained from the coastal location, indicating that location influences airborne viral diversity. Protein-based clustering of 39 viral operational taxonomic units (vOTUs) revealed similarities of 15 with known marine viruses, suggesting oceanic influence on the airborne viral community. Protein homologs related to UV damage protection and photosynthesis from two airborne vOTUs were widely distributed across major oceans, suggesting their potential role in supporting the resilience of marine microorganisms under changing climate conditions. Some vOTUs had protein similarities to viruses infecting extremophiles, indicating viral adaptations to harsh environments. This study provides a baseline for understanding the complexity and sustainability of airborne viral communities in remote ecosystems. It underscores the need for continued monitoring to assess how these communities respond to shifting atmospheric and ecological conditions.}, } @article {pmid41685410, year = {2026}, author = {Brandão-Dias, PFP and Guri, G and Shaffer, MR and Allan, EA and Kelly, RP}, title = {Estimating Organism Abundance Using Within-Sample Haplotype Frequencies of eDNA Data.}, journal = {Molecular ecology resources}, volume = {26}, number = {2}, pages = {e70104}, pmid = {41685410}, issn = {1755-0998}, support = {N00014-22-1-2719//Office of Naval Research/ ; }, mesh = {*Haplotypes ; *DNA, Environmental/genetics ; *Genetics, Population/methods ; Extrachromosomal DNA/genetics ; *Metagenomics/methods ; *Biostatistics/methods ; }, abstract = {Environmental DNA (eDNA) provides powerful insights into species presence and community composition but remains limited in its capacity to infer species abundance or population structure. Here, we show that the deviation between within-sample haplotype frequencies and the overall population-level haplotype frequencies can be used to estimate the number of individual contributors to a given sample. We first establish the theoretical framework for approximating population haplotype frequencies directly from eDNA data, enabling application even in the absence of tissue-derived references. Building on this foundation, we introduce a maximum likelihood estimator to infer the number of contributors and assess its performance through simulations spanning a range of haplotype frequency distributions and noise scenarios. These approaches assume that all samples are drawn from a single, panmictic population. We find that accurate estimates are attainable when haplotypes are sufficiently variable, population frequencies are well-characterised, and samples are large enough to capture frequency deviations. By bridging population genetic theory and eDNA, our method complements existing molecular approaches and offers a novel path towards quantifying abundance from eDNA metabarcoding data.}, } @article {pmid41685543, year = {2026}, author = {Mwakibete, L and Hoarau, AOG and Ahyong, V and Waltari, E and Bender, SJ and Davison, S and Niedringhaus, KD and Gibison, ML and Gagne, RB and Miller, EA and Murphy, LA and Kistler, AL and Tato, CM}, title = {Discovery of a novel bandavirus using metagenomic sequencing in a retrospective analysis of an unresolved 2020 mortality event involving wild black vultures in the northeastern United States.}, journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc}, volume = {38}, number = {3}, pages = {399-410}, pmid = {41685543}, issn = {1943-4936}, mesh = {Animals ; Retrospective Studies ; Phylogeny ; *Bird Diseases/virology/mortality ; Metagenomics ; Pennsylvania/epidemiology ; }, abstract = {Investigations of wildlife diseases and mortality events can sometimes lead to inconclusive results because of limitations in testing combined with an ever-increasing number of emerging viruses. The use of tools such as unbiased metagenomic next-generation sequencing (mNGS) can facilitate the identification of causative agents when conventional investigation methods fail. We performed a retrospective mNGS analysis on RNA isolated from postmortem samples collected during a mortality event in free-ranging, wild black vultures (Coragyps atratus) that occurred in eastern Pennsylvania and western New Jersey in 2020. We describe the discovery and identification of a novel species of bandavirus (family Phenuiviridae) in case specimens from this die-off, as well as some of the associated pathology findings. The Bandavirus genus comprises tickborne viral species that have been reported across 5 continents. These viruses have been implicated in outbreaks in a variety of mammalian hosts, including humans, and in avian species, making them important potential sources of zoonotic spillover events. Genomic and phylogenetic analyses of the bandavirus that we detected indicate that its closest relative is Hunter Island virus, a bandavirus previously implicated in albatross mortality events off the coast of Tasmania, Australia. Follow-up PCR testing of samples from 16 additional vultures from the same cohort indicate that this new bandavirus was the likely cause of death.}, } @article {pmid41685655, year = {2026}, author = {Zhai, Y and Wang, X and Deng, X and Li, X and Hu, B and van der Meer, W and van Loosdrecht, MCM and Liu, G and Pabst, M}, title = {Sequential Oxidizing-Reducing Degradation of Organic Micropollutants in Simulated Riverbank Filtration.}, journal = {Environmental science & technology}, volume = {60}, number = {7}, pages = {5804-5816}, doi = {10.1021/acs.est.5c18277}, pmid = {41685655}, issn = {1520-5851}, mesh = {Filtration ; Oxidation-Reduction ; *Rivers ; Water Pollutants, Chemical ; Biodegradation, Environmental ; }, abstract = {Riverbank filtration is a nature-based water treatment strategy known for its effective removal of organic micropollutants. Yet, the mechanisms governing their biodegradation, especially the role of redox transitions in mediating biotransformation, remain insufficiently understood. Here, we integrate metagenomic profiling with chemical analytics in a 10 m simulated riverbank filtration system to demonstrate how sequential oxidizing-reducing degradation enhances organic micropollutant transformation. Oxygen stratification structured distinct microbial and enzymatic pathways: oxidizing zones (>+200 mV redox potential) facilitated cytochrome P450-mediated oxidation (oxidizing condition, OXD), while subsequent redox shifts to reducing conditions (←400 mV, sequential oxidizing-reducing (SOR) conditions) activated reductive transformations (e.g., via nitronate monooxygenase and aldehyde dehydrogenase) and conjugation pathways. These SOR conditions significantly enhanced the removal of recalcitrant compounds, including irbesartan (+25.3%), benzotriazole (13.4%), and gabapentin (+9.7%). Metagenomic analysis revealed redox-driven microbial specialization, with Pseudomonadota and Nitrospirota dominating in oxidizing zones and reducing microzones enriched in pathways associated with nitrotoluene and ethylbenzene degradation, providing genomic evidence for sequential organic micropollutant breakdown. These findings establish a mechanistic framework for harnessing oxidizing-reducing microbial partnerships to amplify organic micropollutant removal in nature-based water treatment systems, which can be used for riverbank filtration site selection and well field construction and optimization.}, } @article {pmid41686173, year = {2026}, author = {Yang, Z and Zhang, F and Li, H and Liu, B and Liu, P and Wu, Z and Li, Y and Miao, J and Li, X and Liang, H and Zhong, Y and Xiao, L and Zou, Y and He, N and Li, S}, title = {Gut Commensal Phocaeicola vulgatus AF107-22 Alleviates Obesity-Induced Metabolic Syndrome via Promoting Gut Microbiota-Derived Spermidine Synthesis.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {7}, pages = {6218-6229}, doi = {10.1021/acs.jafc.5c14443}, pmid = {41686173}, issn = {1520-5118}, mesh = {*Spermidine/biosynthesis ; Animals ; *Metabolic Syndrome/microbiology/metabolism/etiology/therapy/drug therapy ; *Obesity/complications/microbiology/metabolism ; *Gastrointestinal Microbiome ; Humans ; Mice ; Male ; *Probiotics/administration & dosage ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; Spermine/metabolism ; }, abstract = {Obesity-induced metabolic syndrome (MetS) is a prevalent metabolic disorder, and therapeutic strategies targeting the gut microbiota hold considerable promise. Phocaeicola vulgatus (P. vulgatus) is a gut commensal bacterium that plays an important role in modulating the composition and metabolism of gut microbiota. This study demonstrated that the abundance of P. vulgatus is significantly negatively correlated to obesity-induced MetS and complications in human metagenomic data. Oral gavage of P. vulgatus significantly ameliorated high-fat-diet (HFD)-induced MetS symptoms in mice, reducing body weight, systemic inflammation, and hepatic steatosis. Furthermore, multiomics analyses indicated that P. vulgatus treatment significantly enhanced the production of gut microbiota-derived spermidine and spermine. Subsequently, population-based analysis confirmed a strong negative correlation between plasma spermidine levels and MetS progression, supporting that such parameters may serve as potential biomarkers for MetS. This study reveals a potential mechanism, bridging commensal probiotic and spermidine metabolism, with implications for treating obesity-induced MetS.}, } @article {pmid41686420, year = {2026}, author = {Senthilkumar, K and Muthiah, P}, title = {A Comprehensive Review of Kombucha Fermentation and Probiotic Functional Mechanisms: Microbial Dynamics, Bioactive Compounds and Health Effects.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41686420}, issn = {1867-1314}, abstract = {The rising demand for health-promoting beverages, kombucha presents significant opportunities for scientific innovation and commercial growth. Symbiotic culture of bacteria and yeast (SCOBY), which includes acetic acid bacteria (AAB), lactic acid bacteria (LAB), and several yeast species, plays a major role in kombucha fermentation. During fermentation, kombucha produces bioactive compounds mainly catechins, theaflavins, tannins, and organic acids that enhance health efficacy and probiotic properties, supporting gut health and non-communicable disease prevention. The present study emphasizes, nutritional qualities of kombucha through different Komagataeibacter starter cultures and alternative substrates such as herbal infusions and fruit extracts. This review also highlights the role of AAB, LAB, and Yeast in the production mechanism of the kombucha beverage by the different microbial strains of microbial species and the fibril network of bacterial cellulose. This study further explains the bioactivities in the human body, especially mechanisms of action in the intestine through fundamental signaling pathways such as PIK3-AKT, MAPK, NFκB, PPARγ, and JAK-STAT. Therapeutic efficacy of kombucha, including various substrate-based antioxidants, antimicrobials, synergistic impact, delivery mechanism of anticancer, anti-diabetic insulin, and glycaemic responses, regulations of inflammatory markers (ILs) in anti-obese properties, has also been reviewed. Further, it is necessary to develop the advanced kombucha beverage qualities through metagenomics, metabolomics. Future studies should address these research gaps to ensure controlled microbial and probiotic stability, validate metabolites availability, and explore innovative applications for improved functionality and shelf-life.}, } @article {pmid41686580, year = {2026}, author = {Zhang, H}, title = {Diagnostic value of mNGS in patients with suspected tumor: An observational study.}, journal = {Medicine}, volume = {105}, number = {7}, pages = {e47379}, pmid = {41686580}, issn = {1536-5964}, mesh = {Humans ; *DNA Copy Number Variations/genetics ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Male ; *Metagenomics/methods ; Middle Aged ; Chromosome Aberrations ; *Neoplasms/diagnosis/genetics ; Adult ; Aged ; }, abstract = {Some patients suspected of infection may have potential causes, such as tumors, but conventional examination methods are negative. Copy number variation (CNV) analysis based on metagenomics next generation sequencing (mNGS) can simultaneously detect pathogenic microorganisms and tumors signals. Patients with suspected infection in our department were retrospectively analyzed, and mNGS and chromosomal CNV analysis were performed simultaneously. A total of 9 patients with positive tumor signal were included in the study. This study was divided into 2 parts: in the first part, patients suspected of infection were finally diagnosed with a tumor by CNV assisted analysis; in the second part, the accuracy of this analysis was verified again by patients with a history of cancer. Three of five patients without a history of tumor were diagnosed with hematological malignancy. All patients with active tumor had obvious abnormal CNV signals. The chromosomal abnormalities mainly included multiple chromosome duplication and deletion, arm level duplication and deletion, and chromosome aneuploidy. mNGS-based CNV analysis had clinical value for patients with underlying tumor.}, } @article {pmid41686700, year = {2026}, author = {Ierardi, RA and Ericsson, AC and Lahmers, KK and Shen, Z and Raghavan, RK}, title = {Detection of Anaplasma marginale (Rickettsiales: Anaplasmataceae) in host-seeking adult Dermacentor variabilis (Acari: Ixodidae) on cattle pastures, Missouri, United States.}, journal = {Journal of medical entomology}, volume = {63}, number = {1}, pages = {}, doi = {10.1093/jme/tjag014}, pmid = {41686700}, issn = {1938-2928}, support = {00081722//Taylor Geospatial Institute/ ; 7003929 and 7006485//USDA National Institute of Food and Agriculture, Animal Health projects/ ; //University of Missouri College of Veterinary Medicine Veterinary Research Scholars Program/ ; 58-2090-2-020//USDA Agricultural Research Service/ ; }, mesh = {Animals ; *Dermacentor/microbiology/physiology ; *Anaplasma marginale/isolation & purification ; Cattle ; Male ; Missouri ; Anaplasmosis/epidemiology ; }, abstract = {Bovine anaplasmosis is an economically important and globally distributed disease of cattle caused by a rickettsia, Anaplasma marginale Theiler, which infects bovine red blood cells. In the United States, A. marginale is transmitted by adult male Dermacentor spp. ticks. Our objectives were to estimate the prevalence of A. marginale among host-seeking D. variabilis Say males and describe tick activity on beef cow-calf grazing operations in Missouri. Ticks were collected by dragging a total of 348 750-meter transects on 5 field sites from May 2022 to August 2024. In total, 29,132 ticks were collected: 27,502 Amblyomma americanum Linnaeus, 1,504 D. variabilis, 101 Haemaphysalis longicornis Neumann, and 25 individuals of uncommonly encountered species. A total of 692 adult male D. variabilis were divided into 154 pools of ≤5 ticks/pool for analysis. Anaplasma marginale was detected by quantitative polymerase chain reaction (qPCR) in 1 pool of 5 adult males (0.6%). Illumina sequencing detected an Anaplasma bovis (Donatien and Lestoquard 1936)-like sequence in 38 pools (24.7%). The endosymbionts Francisella spp. and Rickettsia spp. were detected in 100% and 32.5% of pools, respectively. To the best of our knowledge, this is the first study to detect A. marginale in host-seeking D. variabilis collected in the field. Our findings also represent the first reports of H. longicornis, an invasive species, in 4 Missouri counties.}, } @article {pmid41687083, year = {2026}, author = {Olaniyi, K and Moodley, J and Moodley, R and Mackraj, I}, title = {Assessment of human placental microbial signatures in pre-eclampsia using shotgun metagenomics.}, journal = {Canadian journal of physiology and pharmacology}, volume = {104}, number = {}, pages = {1-11}, doi = {10.1139/cjpp-2025-0274}, pmid = {41687083}, issn = {1205-7541}, mesh = {Humans ; Female ; Pregnancy ; *Pre-Eclampsia/microbiology ; *Placenta/microbiology ; *Metagenomics/methods ; Adult ; *Bacteria/genetics/isolation & purification/classification ; Shotgun Sequencing ; *Microbiota ; }, abstract = {This study evaluated the presence of bacterial species in the placenta of women with pre-eclampsia and compared with that of normotensive women. One hundred and twenty participants, comprising 60 pre-eclamptic (30 early- and late-onset, respectively) and 60 age-matched normotensive women (30 early and late-gestation normotensive, respectively) were recruited. After informed consent was obtained, the placenta were obtained through caesarean section with sterile and standardized clinical procedures. DNA was extracted from each tissue, and the samples were pooled into six libraries and sequenced on Illumina NextSeq500 using a shotgun metagenomic approach. Bioinformatics was used to analyse the reads with the implementation of Kraken2/MetaPhlAn classification methods and complemented by multi-layered contamination assessment strategy that included frequency-based decontam filtering. Most reads were classified as belonging to the phyla Cutibacterium acnes, Staphylococcus epidermidis, and various Bradyrhizobium species. PE samples showed notable Corynebacterium tuberculostearicum and Pseudomonas species, while Bradyrhizobium and Cutibacterium acnes dominated normotensive samples. Further analysis showed no significant difference between bacterial species of pre-eclamptic and normotensive placental samples. The results show very low levels of bacteria in the placental samples. In addition, a little difference was observed between the bacterial compositions of pre-eclamptic and age-matched normotensive placental tissues, but not statistically significant.}, } @article {pmid41687166, year = {2026}, author = {Wang, P and Wang, J and Zhang, P and Jiao, Z and Bai, X and Zhao, Z and Fan, J and Zhang, S and Zhao, B and Ren, X and Dou, H and Bai, W}, title = {Temperature-dependent effects of lanthanum-modified bentonite on sediment nitrogen removal processes and the underlying microbial mechanisms.}, journal = {Water research}, volume = {294}, number = {}, pages = {125514}, doi = {10.1016/j.watres.2026.125514}, pmid = {41687166}, issn = {1879-2448}, mesh = {*Bentonite/chemistry ; *Lanthanum/chemistry ; *Nitrogen ; Temperature ; Denitrification ; *Geologic Sediments/chemistry ; }, abstract = {Lanthanum-modified bentonite (LMB) is widely used for phosphorus control in eutrophic lakes, but its effects on sediment nitrogen removal remains unclear. This study investigated the effects of LMB on denitrification and anammox, and underlying microbial mechanisms, under different dissolved oxygen (DO) and temperature (T) conditions using isotope tracing and metagenomics. The results demonstrated that the influence of LMB on sediment nitrogen removal was highly temperature-dependent. At 15 °C, LMB significantly enhanced both processes: denitrification increased by an average of 67.75 % under aerobic conditions, while anammox increased by 163.52 % and 93.47 % under aerobic and anaerobic conditions, respectively. Conversely, at 30 °C, LMB inhibited both processes. The denitrification decreased by average reductions of 57.36 % and 79.46 %, and anammox decreased by 32.51 % and 54.46 % under aerobic and anaerobic conditions, respectively. Microbial results revealed that LMB regulated denitrification in a temperature-dependent manner by modulating the key functional gene nosZ. In contrast, LMB generally suppressed anammox genes (hzsA, hzsB, and hdh), particularly under anaerobic conditions. Redundancy analysis (RDA) and structural equation modeling (SEM) identified pH, moisture content (MC), electrical conductivity (EC), total carbon (TC), total nitrogen (TN), NO3[-]-N, and NH4[+]-N as the key environmental factors driving variations in functional gene abundances. Our findings reveal that the temperature-dependent effects are primarily driven by the regulation of the nosZ gene and synergistic interactions among key physicochemical factors. Therefore, for remediating of eutrophic lakes with severe nitrogen pollution, the addition of LMB should be strategically adjusted to low-temperature seasons to maximize its ecological benefits in promoting nitrogen removal.}, } @article {pmid41687314, year = {2026}, author = {He, J and Duan, Y and Yang, S and Toldrá, F and Zheng, J and Du, M and Wang, L and Ndraha, N and Wang, S and Chen, J}, title = {Insights into the mechanism of nutty aroma formation by Staphylococcus saprophyticus in fermented sausages.}, journal = {International journal of food microbiology}, volume = {451}, number = {}, pages = {111669}, doi = {10.1016/j.ijfoodmicro.2026.111669}, pmid = {41687314}, issn = {1879-3460}, mesh = {*Meat Products/microbiology/analysis ; Fermentation ; Animals ; *Odorants/analysis ; *Staphylococcus/metabolism/genetics ; Food Microbiology ; Swine ; Volatile Organic Compounds/metabolism/analysis ; Fermented Foods/microbiology ; }, abstract = {To achieve a starter culture with the ability of improving nutty aroma in the formulation of fermented sausage, this study evaluated sixteen staphylococci strains first, then demonstrated the function of the strain in sausage fermentation using volatolomics and metagenomics. Within sixteen tested strains, S. saprophyticus 108 presented superior safety and technological properties and produced the highest amounts of 3-methylbutanal. With spontaneously fermented sausage as control, S108 group distinctly enhanced the production of 3-methylbutanal, 3-methylbutanoic acid and its ethyl ester, and nutty note of S108 group was obviously perceivable. The relative abundance of S. saprophyticus in both control and S108 groups increased throughout the fermentation process and such increase was more dramatic in S108 group. Although the differences in the number of functional genes predicted by control and S108 group in CAZy, eggNOG, and KEGG databases were comparatively small, the contribution of S. saprophyticus to major nutrient metabolisms was the main difference. Both S. saprophyticus and L. mesenteroides were annotated with predominant abundances in main metabolic pathways, while S. saprophyticus abundance involved in the metabolic pathways was higher in S108 group than in control. Specifically, branched-chain amino acid degradation, phenylalanine metabolism, glycolysis, pyruvate metabolism, butanoate and propanoate metabolism, glycerolipid and glycerophospholipid metabolism were mainly driven by S. saprophyticus, linked to the higher generation of volatile compounds in S108 group compared to control. The results provided scientific support for developing a functional starter culture through clarifying the mechanism of nutty aroma formation by S. saprophyticus in the production of fermented sausages.}, } @article {pmid41687486, year = {2026}, author = {Wang, H and Tian, Z and Jiang, Q and Feng, L and Tian, Z and Cheng, J and Jiang, S and Li, B}, title = {Enhancing sulfide-based denitrification under dual high-salinity and sulfide stress: Metabolic adaptation via compatible solutes in functional microbes.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128858}, doi = {10.1016/j.jenvman.2026.128858}, pmid = {41687486}, issn = {1095-8630}, mesh = {*Denitrification ; *Sulfides ; Salinity ; }, abstract = {This study demonstrated enhanced sulfur autotrophic denitrification (SAD) under dual high-salinity (3% Na2SO4) and sulfide (142.5 mg L[-1] S[2-]) stress using biostimulants. Screening of ten biostimulants (1 mg L[-1]) revealed compatible solutes (glycine betaine, trehalose, and mannitol) as optimal enhancers. At a higher level of 100 mg L[-1], the addition of all compatible solutes significantly boosted TN removal rates >3-fold, with mannitol achieving the highest (9.38 mg L[-1] h[-1]) (p < 0.05). Short term of dosage tests further showed better TN removal at higher trehalose/mannitol concentrations (10-100 mg L[-1]), while glycine betaine peaked at 50 mg L[-1]. Furthermore, metagenomic analysis revealed potential mechanisms for resisting the dual stress of high salinity and sulfide. Those mechanisms act through osmotic protection (via specific transporter genes and elevated extracellular polymeric substances), carbon provision boosting TN removal via heterotrophic denitrification (nirS), and enzymatic antioxidant defense (SOD1/NQO1). The addition of exogenous compatible solutes critically mitigates dual stress from high salinity and sulfide toxicity, demonstrating significant potential for SAD system enhancement.}, } @article {pmid41687496, year = {2026}, author = {Shyam, S and Sarma, H}, title = {Microbial community shifts and nutrient alteration in rice rhizospheres induced by Fe functionalized magnetic nanocarbon derived from rice husk.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128840}, doi = {10.1016/j.jenvman.2026.128840}, pmid = {41687496}, issn = {1095-8630}, mesh = {*Oryza ; *Rhizosphere ; *Charcoal/chemistry ; *Soil Microbiology ; Iron/chemistry ; Soil/chemistry ; }, abstract = {Soil fertility degradation and low nutrient-use efficiency remain major constraints in sustainable rice cultivation, especially in acidic soils. Biochar-based nanocomposites have emerged as advanced tools to improve nutrient bioavailability and soil health. This study examines the influence of rice husk biochar (HB) and its Fe-functionalized nanoscale variant, magnetic nanocarbon husk biochar (MNHB), on soil physicochemical properties, early growth of Oryza sativa (rice), and rhizosphere microbial dynamics. MNHB exhibited a fixed carbon content of 49.6%, ash content of 17.4%, and strong thermal stability above 400 °C. Dynamic light scattering and zeta potential analyses confirmed nanoscale particle size (<100 nm) with a surface charge of -25 mV, indicating good colloidal stability. FE-SEM imaging verified nanoscale morphology (81.58 ± 17.22 nm). Application of MNHB (5%) significantly enhanced root length (15.7 ± 0.49 cm), shoot length (46.41 ± 1.89 cm), and biomass (48.9% above Control, 25.3% above HB; p < 0.05). Soil pH, electrical conductivity, organic carbon, and macronutrients (N, P, K) increased substantially, demonstrating improved nutrient cycling and bioavailability. Metagenomic sequencing revealed reduced microbial alpha diversity but a marked community shift favoring Pseudomonadota (∼20% increase) and enrichment of beneficial genera such as Streptomyces, Micromonospora, and Neurospora tetrasperma. This work lies in establishing that Fe-functionalization in biochar nanosystems not only enhances nutrient transformation and uptake efficiency but also selectively restructures the rhizosphere microbiome, thereby coupling nutrient enrichment with microbial modulation for sustainable soil fertility restoration and crop productivity improvement.}, } @article {pmid41687577, year = {2026}, author = {Feng, Y and Zhang, X and Lai, S and Chen, F and Hu, J and Li, M and Sun, W}, title = {Nontarget screening uncovers the overlooked impact of antibiotic transformation products on riverine resistomes.}, journal = {Journal of hazardous materials}, volume = {505}, number = {}, pages = {141425}, doi = {10.1016/j.jhazmat.2026.141425}, pmid = {41687577}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/analysis/chemistry ; *Rivers/microbiology/chemistry ; *Water Pollutants, Chemical/analysis ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Environmental Monitoring ; }, abstract = {Antibiotics, their transformation products (TPs), and antibiotic resistance genes (ARGs) pose a major environmental threat, yet the influence of TPs on ARGs remains poorly understood. This study combined target, suspect and nontarget analysis via high-resolution mass spectrometry with metagenomic analysis to systematically profile the occurrence of antibiotics, TPs, and ARGs in an urban river. A total of 32 parent antibiotics and 49 TPs were identified, with concentrations ranging from 0.002193 ng/L and not detected145 ng/L, respectively. TPs accounted for a substantial portion of total antibiotic loads (41.3 % in spring and 31.9 % in summer). Metagenomic sequencing revealed 1599 ARG subtypes conferring resistance to 28 classes of antibiotics. TPs can drive antimicrobial resistance directly by exerting selective pressure through their residual antibacterial activity, and indirectly through reverting to parent compounds, thereby reintroducing bioactive antibiotics into the environment. Therefore, the inclusion of TPs improved ARG-antibiotic correlations. Multivariate analyses revealed that TPs exerted comparable or greater influence on ARG profiles than parent antibiotics. Specific TPs, particularly β-lactams, macrolides, and quinolones, significantly affected the abundance of multiple ARGs, underscoring their substantial and non-negligible impact. This study highlights the previously underestimated role of antibiotic TPs in shaping ARG profiles and calls for an urgent update of risk assessment frameworks to incorporate TPs for comprehensive environmental and public health evaluation.}, } @article {pmid41687578, year = {2026}, author = {Zhou, Q and Liang, H and Huang, J and Klümper, U and Fang, P and Yu, Z and Wang, Y and Berendonk, TU and Lin, L and Li, X and Li, B}, title = {Impact of sulfonamides on microbial community and antibiotic resistome profiles in anaerobic digestion of swine wastewater.}, journal = {Journal of hazardous materials}, volume = {505}, number = {}, pages = {141426}, doi = {10.1016/j.jhazmat.2026.141426}, pmid = {41687578}, issn = {1873-3336}, mesh = {*Sulfonamides/pharmacology/toxicity ; Animals ; Swine ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; *Microbiota/drug effects ; *Water Pollutants, Chemical/toxicity ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; }, abstract = {Residual antibiotics in swine wastewater promote the proliferation of the antibiotic resistome, posing significant threats to environmental and human health. Although anaerobic digestion (AD) is widely applied for treating swine wastewater, the effects of antibiotics on the microbial community and resistome during AD remain unclear. This study employed amplicon and metagenomic sequencing, combined with long- and short-read hybrid assembly, to comprehensively investigate the impact of sulfonamides on the microbiome and resistome during AD. Enterococcus, a genus capable of utilizing exogenous folate, was identified as the dominant genus under sulfonamide stress. A total of 24 antibiotic resistance gene (ARG) types and 440 subtypes were identified. Sulfonamide stress selectively enriched sulfonamide resistance genes, with no notable co-selective effects on ARGs for other antibiotic classes. Short-term exposure significantly enriched sul2 (3.8-fold) and sul3 (4.0-fold), while long-term exposure enriched sul1 (1.6-fold). Sulfonamides especially promoted the proliferation of sulfonamide resistance genes on both mobilizable and non-mobilizable plasmids. The co-occurrence of multiple categories of mobile genetic elements and ARGs on contigs was inferred to play a critical role in driving ARG dissemination. Whereas a strain belonging to Enterococcus_I emerged as the dominant resistant bacterium in the AD system, a particular multidrug-resistance risk was identified for a strain belonging to the Filifactoraceae family. This work provides a new perspective on the impact of antibiotics on microbial community and antibiotic resistome composition and dynamics during the AD treatment process of swine wastewater.}, } @article {pmid41687586, year = {2026}, author = {Xu, L and Xu, W and Yang, Y and Wu, J and Su, X and Dong, F and Xiao, X and Chen, C and Zheng, X and Sun, F}, title = {Single-stage bioreactor integrating anammox and sulfur-driven autotrophic denitrification for nitrogen removal from landfill leachate.}, journal = {Journal of hazardous materials}, volume = {505}, number = {}, pages = {141444}, doi = {10.1016/j.jhazmat.2026.141444}, pmid = {41687586}, issn = {1873-3336}, mesh = {*Bioreactors/microbiology ; Denitrification ; *Water Pollutants, Chemical/metabolism ; *Nitrogen/metabolism ; *Sulfur/metabolism/chemistry ; Autotrophic Processes ; Oxidation-Reduction ; Anaerobiosis ; *Ammonium Compounds/metabolism ; }, abstract = {An integrated anaerobic ammonium oxidation-sulfur autotrophic denitrification (Anammox-SAD) bioreactor was developed for nitrogen removal from real landfill leachate without external organic carbon. The system was operated continuously for 105 days under stepwise-decreasing hydraulic retention time (HRT), with a stable influent NO2[-]-N/NH4[+]-N ratio of 1.2-1.5 provided by partial nitrification. The anammox zone maintained robust performance, yielding average effluent NH4[+]-N, NO2[-]-N and NO3[-]-N of 18 ± 5, 6 ± 9, and 110 ± 16 mg/L, respectively. At an HRT as low as 0.5 d, the maximum nitrogen removal rate reached 2.04 kg N/(m[3] d). Despite influent fluctuations (total nitrogen of 600-840 mg/L), the integrated reactor achieved a stable total nitrogen removal of 85-89 %. The downstream SAD zone effectively polished anammox-derived nitrate, reducing NO3[-]-N from 80-150 to 35-60 mg/L. Sulfur oxidation was confirmed by elevated sulfate concentrations, while anammox-associated alkalinity generation provided intrinsic pH buffering, sustaining favorable conditions for SAD. Metagenomic analyses revealed coordinated nitrogen-sulfur metabolic networks, showing that shortening HRT enhanced microbial diversity and functional redundancy but revealed kinetic limitations in substrate reduction. Overall, the integrated anammox-SAD system provides a robust and low-carbon strategy for treating high-strength landfill leachate.}, } @article {pmid41687589, year = {2026}, author = {Luo, S and Tang, C and Shan, Y and Wan, C and Mo, Y and Huang, Y and Wu, R and Yu, F and Li, Y}, title = {Phosphate-solubilizing bacteria enhance cadmium phytoremediation by Solanum nigrum L. through improved phosphorus availability and cycling in contaminated soil.}, journal = {Journal of hazardous materials}, volume = {505}, number = {}, pages = {141422}, doi = {10.1016/j.jhazmat.2026.141422}, pmid = {41687589}, issn = {1873-3336}, mesh = {*Solanum nigrum/metabolism/growth & development/microbiology ; *Cadmium/metabolism ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; *Phosphorus/metabolism ; *Enterobacter/metabolism ; *Phosphates/metabolism ; Solubility ; Soil/chemistry ; }, abstract = {Phosphate-solubilizing bacteria (PSB)-assisted phytoremediation has been recognized as an effective strategy for remediating cadmium (Cd)-contaminated soils, yet species-specific physiological and ecological traits among hyperaccumulators result in distinct Cd uptake mechanisms. Although the pivotal role of phosphorus (P) cycling in promoting Cd uptake is established, its mechanistic linkage with PSB-mediated phytoremediation remains poorly understood. This study employed Enterobacter sp. FM-1 and the Cd hyperaccumulator Solanum nigrum L. (S. nigrum L.) to elucidate how PSB regulate Cd accumulation through P cycling. Enterobacter inoculation significantly decreased soil pH and increased bioavailable Cd by 43.4 %-104.3 % relative to the control. The pH-driven mineralization of organic P was the primary process enhancing soil available P (AP), which rose by 12.1-32.2 %. Soil AP content was positively correlated with Cd concentrations in S. nigrum tissues, indicating a close association between enhanced phosphorus availability and plant Cd accumulation, accompanied by strengthened antioxidant defense related responses. Furthermore, PSB inoculation elevated phytochelatin levels via P-starvation response pathways, mitigating oxidative stress. Enhanced polyphosphate synthesis and phosphatase activity further promoted plant growth and P turnover. Metagenomic analysis revealed that Proteobacteria were the predominant carriers of P-cycling genes in the S. nigrum L. rhizosphere. Overall, Enterobacter sp. inoculation reshaped rhizosphere microbial communities, increased P bioavailability and improved Cd tolerance. These findings provide mechanistic insight into the coupling between microbial P activation and Cd uptake, offering a sustainable, microbially driven strategy for Cd-contaminated soil phytoremediation.}, } @article {pmid41687784, year = {2026}, author = {Thriene, K and Stanislas, V and Huang, KD and Strowig, T and Michels, KB}, title = {Impact of Yogurt and Rolled Oats Consumption on the Gut Microbiome: A Randomized Crossover Study Displaying Individual Responses and General Resilience.}, journal = {The Journal of nutrition}, volume = {156}, number = {4}, pages = {101408}, pmid = {41687784}, issn = {1541-6100}, mesh = {Humans ; *Yogurt ; *Avena ; Cross-Over Studies ; Female ; Male ; Feces/microbiology/chemistry ; Adult ; *Gastrointestinal Microbiome ; Young Adult ; *Diet ; }, abstract = {BACKGROUND: Yogurt and rolled oats are commonly linked to gut health through probiotic and prebiotic effects, but these potential benefits remain insufficiently studied, especially in healthy individuals.

OBJECTIVES: This study primarily aimed to investigate the effects of daily yogurt and rolled oats consumption on gut microbial composition. Secondary outcomes included stool metabolites and blood-based health markers.

METHODS: In this randomized, open-label, 2-period crossover trial, 119 healthy participants were randomly assigned to 1 of 2 sequences: 250 g of yogurt daily followed by 250 g of yogurt with 50 g of rolled oats, or the reverse with a washout period in between. Stool and blood samples were collected at baseline and post intervention. Metagenomic sequencing and metabolomic analyses were conducted on stool samples, whereas health markers related to metabolic control, inflammation, immune response, oxidative stress, and gut permeability were assessed in the participants' blood.

RESULTS: Of the 119 randomly divided participants, 110 completed the study (53 yogurt first, 57 yogurt and rolled oat first). Yogurt consumption transiently increased yogurt-associated bacteria, with Streptococcus thermophilus rising from absent to 0.97% [95% confidence interval (CI): 0.71, 1.26] in the yogurt intervention and 0.79% (95% CI: 0.58, 1.03) in the yogurt with oats intervention. In a small Prevotella-predominant subgroup (n = 8), adding rolled oats increased microbial evenness (q < 0.001) and reduced interindividual divergence (q < 0.05), suggesting a temporary slight homogenization. No additional effects on fecal short-chain fatty acids concentrations or human health markers were identified. Functional metagenomic changes were mainly driven by yogurt-derived bacterial enrichment.

CONCLUSIONS: A healthy gut microbiota is largely stable and resilient to short-term diet changes, yet individual differences highlight the importance of personalized dietary recommendations.

(German Trial Register): DRKS00023146 (https://drks.de/search/en/trial/DRKS00023146/details).}, } @article {pmid41687847, year = {2026}, author = {Wang, N and Kang, Z and Wang, X and Zhang, Y and Li, X and Sun, Y and Xi, J and Shen, L}, title = {Sewage-sludge-derived biostimulant enables fertilizer reduction while maintaining rice yield through microbiome-mediated nutrient cycling.}, journal = {Environmental research}, volume = {296}, number = {}, pages = {124020}, doi = {10.1016/j.envres.2026.124020}, pmid = {41687847}, issn = {1096-0953}, mesh = {*Fertilizers/analysis ; *Oryza/growth & development ; *Microbiota ; *Sewage/chemistry ; *Soil Microbiology ; *Agriculture/methods ; Nitrogen ; Phosphorus ; Soil/chemistry ; }, abstract = {Modern agriculture relies heavily on chemical fertilizers to sustain high yields, yet excessive inputs contribute to soil acidification, water eutrophication, greenhouse gas emissions, and biodiversity loss. Sewage-sludge-derived biostimulants (SS-BS) may help reduce fertilizer dependency while sustaining crop performance through plant-soil-microbiome interactions. Here, we evaluated SS-BS in a paddy rice field trial conducted during a single growing season (2024) under conventional management. Three fertilization regimes were compared: low-fertilizer control (CK), conventional fertilization (FP), and reduced mineral fertilization supplemented with SS-BS (BS). Across the 2024 season, rice yield and key yield components in BS were comparable to, or approached, those in FP with reduced mineral fertilizer input. Shotgun metagenomic profiling indicated that BS was associated with shifts in microbial functional pathways related to nitrogen, phosphorus, and potassium cycling, and with changes in the relative abundance of taxa linked to nutrient transformation processes. Partial least squares path modeling (PLS-PM) further suggested that microbial functional attributes were associated with the relationships among fertilization regime, soil properties, and yield outcomes. Collectively, these results from a single-season field experiment indicate that SS-BS has the potential to support fertilizer-reduction strategies in rice systems and motivate multi-season validation of its agronomic performance and microbiome-associated effects.}, } @article {pmid41687886, year = {2026}, author = {Jin, B and Yan, Y and Bai, Z and He, H and Du, J and Xu, Y and Ma, C and Wang, L and Ji, J}, title = {Metagenomics reveals the mechanisms of endogenous partial denitrification (EPD) driven by different valence iron states:Nitrite accumulation, microbial adaptation, functional gene and metabolic pathways.}, journal = {Bioresource technology}, volume = {446}, number = {}, pages = {134209}, doi = {10.1016/j.biortech.2026.134209}, pmid = {41687886}, issn = {1873-2976}, mesh = {*Denitrification/genetics/drug effects ; *Iron/chemistry/pharmacology/metabolism ; *Metagenomics/methods ; *Metabolic Networks and Pathways/genetics ; *Nitrites/metabolism ; *Bacteria/metabolism/genetics ; *Adaptation, Physiological/genetics/drug effects ; Nitrogen/metabolism ; Phosphorus/metabolism ; }, abstract = {To enhance the performance of endogenous partial denitrification (EPD) systems, different iron valence states (nano-zero-valent iron (nZVI), Fe(II), and Fe(III)) were introduced, and their effects on microbial communities and metabolic pathways were investigated using metagenomics. The results indicated that iron supplementation significantly improved the removal of COD, NO3[-]-N, and PO4[3-]-P, as well as NO2[-]-N accumulation. Notably, Fe(III) proved most effective, achieving a NO2[-]-N accumulation of 27.7 ± 3.7 mg/L and a PO4[3-]-P removal efficiency of 64.7 ± 7.5%, whereas excessive Fe(II) and Fe(III) (40 mg/L) inhibited NO2[-]-N accumulation. While the overall microbial community structure remained stable, iron addition enriched specific denitrifying and phosphorus-accumulating genera such as Candidatus Competibacteraceae (1.36%, 2.40%, 2.30%), Candidatus Competibacter (0.40%, 0.65%, 0.62%), and Thauera (3.02%, 1.76%, 3.00%). nZVI promoted carbon utilization and denitrification gene expression, enhanced the including endogenous carbon transformation and nitrogen metabolism. In contrast, Fe(II) and Fe(III) enhanced NO2[-]-N accumulation by suppressing key genes (nirS/nirK, norB, nosZ) and shifted phosphorus metabolism toward chemical removal as the dominant pathway. Exogenous iron optimizes the performance of the EPD system by downregulating iron metabolism genes (afuA, fbpA, and afu) to mitigate iron toxicity stress. These findings provide theoretical support for optimizing EPD systems and improving nutrient removal in wastewater treatment.}, } @article {pmid41688119, year = {2026}, author = {Akpulu, CP and Maikudi Sada, H and Ahmed, H and Idris, HB and Yakubu, R and Aminu, A and Iregbu, K and Oduwo, J and Owinoh, E and Lankapalli, AK and De Nies, L and Achi, CR and Thomson, K and Stracy, M and Walsh, TR and Sands, K}, title = {Cohort profile: Infant Gut Bacterial Study in Nigeria (INBUGS-NG).}, journal = {BMJ open}, volume = {16}, number = {2}, pages = {e111007}, pmid = {41688119}, issn = {2044-6055}, mesh = {Humans ; Nigeria ; Female ; *Gastrointestinal Microbiome/drug effects ; Infant ; Prospective Studies ; *Anti-Bacterial Agents/therapeutic use ; Feces/microbiology ; Longitudinal Studies ; Infant, Newborn ; Breast Feeding ; Male ; Adult ; Delivery, Obstetric ; Milk, Human/microbiology ; }, abstract = {PURPOSE: The Infant Gut Bacterial Study in Nigeria (INBUGS-NG) investigates how delivery mode, antibiotic exposure, feeding practices and environmental factors shape gut microbiome development and acquisition of antibiotic resistance genes (ARGs) during the first year of life in northern Nigeria.

PARTICIPANTS: Between February and July 2024, 90 mother-infant dyads were enrolled at a tertiary hospital in Kano city, Nigeria. This was a prospective longitudinal cohort with follow-ups at 10 scheduled time points: days 0, 1, 3, 5, 7, 14, 28, 90, 180 and 365. We also intensified stool sampling after infant antibiotic administration, enabling dense early-life sampling. To date, the cohort has contributed 480 infant stool samples, 232 maternal rectal swabs, 254 breast milk samples and 806 environmental samples (total 1772). In parallel, socio-demographic, clinical and cultural data were collected using Research Electronic Data Capture (REDCap) and household visit diaries.

FINDINGS TO DATE: Baseline data show that 84/90 mothers (93.3%) received postpartum antibiotics, and 26/90 infants (28.9%) received antibiotics within the first 3 months of life. Only 8% of infants were exclusively breastfed, with early water supplementation common. Caesarean deliveries accounted for 25% of births, and the mean gestational age was 38.5 weeks. Across the cohort, high retention was achieved, and the study has generated a unique long-read metagenomic resource from an African infant population, with analyses ongoing.

FUTURE PLANS: Shotgun long-read metagenomic sequencing (Oxford Nanopore) will enable strain-level and plasmid-level profiling of microbial communities and ARGs. Planned analyses include associations between early-life exposures and resistome dynamics, as well as cross-cohort comparisons with a parallel study in Pakistan. Follow-up will continue through 12 months.}, } @article {pmid41688638, year = {2026}, author = {Dekkers, KF and Pertiwi, K and Baldanzi, G and Lundmark, P and Hammar, U and Moksnes, MR and Coward, E and Nethander, M and Salih, GA and Miari, M and Nguyen, D and Sayols-Baixeras, S and Eklund, AC and Holm, JB and Nielsen, HB and Volpiano, CG and Méric, G and Thangam, M and Hakaste, L and Tuomi, T and Ahlqvist, E and Smith, CA and Allen, M and Reimann, F and Gribble, FM and Ohlsson, C and Hveem, K and Melander, O and Nilsson, PM and Engström, G and Smith, JG and Michaëlsson, K and Ärnlöv, J and Orho-Melander, M and Fall, T}, title = {Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation.}, journal = {Nature genetics}, volume = {58}, number = {3}, pages = {540-549}, pmid = {41688638}, issn = {1546-1718}, support = {2019-01471//Vetenskapsrådet (Swedish Research Council)/ ; 2020-02191//Vetenskapsrådet (Swedish Research Council)/ ; 2020-01392//Vetenskapsrådet (Swedish Research Council)/ ; 521-2013-2756//Vetenskapsrådet (Swedish Research Council)/ ; 2019-01236//Vetenskapsrådet (Swedish Research Council)/ ; 2021-02273//Vetenskapsrådet (Swedish Research Council)/ ; 2019-01291//Vetenskapsrådet (Swedish Research Council)/ ; 2019-01015, 2020-00243//Vetenskapsrådet (Swedish Research Council)/ ; 2018-02784, 2018-02837, EXODIAB 2009-1039//Vetenskapsrådet (Swedish Research Council)/ ; 2023-0687//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 20200173//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2022-0344//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2018-0343//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2020-0711//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; GNT2013468//Department of Health | National Health and Medical Research Council (NHMRC)/ ; MRC_MC_UU_12012/3//RCUK | Medical Research Council (MRC)/ ; 220271/Z/20/Z//Wellcome Trust (Wellcome)/ ; 190C0055250 and 22OC0078421//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; KAW 2015.0317//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; LU2021-0096//Lars Erik Lundbergs Stiftelse för Forskning och Utbildning (Lundberg Foundation for Research and Education)/ ; CKFUU-1025348, 987986, 976460, 963488, 936407, 695401, and 797891//Centrum fÖr Klinisk Forskning Dalarna (Center for Clinical Research Dalarna)/ ; }, mesh = {Genome-Wide Association Study ; *Gastrointestinal Microbiome ; *Metagenome ; Humans ; Male ; Female ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged ; Aged, 80 and over ; Metagenomics ; Single-Cell Gene Expression Analysis ; Cellular Microenvironment ; Phylogeny ; *Intestinal Mucosa/metabolism/microbiology ; Sodium-Glucose Transport Proteins/genetics ; *Receptors, G-Protein-Coupled/genetics ; Fatty Acids/metabolism ; Bile Acids and Salts/metabolism ; Scandinavians and Nordic People ; }, abstract = {Despite the importance of the gut microbiome to health, the role of human genetic variation in shaping its composition remains poorly understood. Here we report genome-wide association analyses of harmonized metagenomic data from 16,017 adults in four Swedish population-based studies, with replication in 12,652 people from the Norwegian HUNT study. We identified variants in the OR51E1-OR51E2 locus, encoding sensors for microbiome-derived fatty acids, associated with microbial richness. We further identified 15 study-wide significant genetic associations (P < 5.4 × 10[-11]) involving eight loci and 14 common bacterial species, of which 11 associations at six loci were replicated. The results confirm previously reported associations at LCT, ABO and FUT2, and provide evidence for new loci MUC12, CORO7-HMOX2, SLC5A11, FOXP1 and FUT3-FUT6, with supporting data from metabolomics and gene expression analyses. Our findings link gut microbial variation genetically to gastrointestinal functions, including enteroendocrine fatty acid sensing, bile composition and mucosal layer composition.}, } @article {pmid41689511, year = {2026}, author = {Xu, R and Mayer, MJ and Philo, M and Gall, GL and Mulaw, G and Ponsero, A and Narbad, A}, title = {Combining Lactiplantibacillus plantarum and Bifidobacterium adolescentis can improve GABA production in faecal fermentations.}, journal = {Journal of applied microbiology}, volume = {137}, number = {3}, pages = {}, doi = {10.1093/jambio/lxag047}, pmid = {41689511}, issn = {1365-2672}, support = {BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/QU/230001D/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //China Scholarship Council/ ; }, mesh = {*gamma-Aminobutyric Acid/biosynthesis/metabolism ; Fermentation ; *Feces/microbiology ; *Probiotics/metabolism ; *Bifidobacterium adolescentis/metabolism/growth & development ; *Lactiplantibacillus plantarum/metabolism/growth & development ; Humans ; Coculture Techniques ; Lactic Acid/metabolism ; }, abstract = {AIMS: This project aimed to investigate production of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) from potential probiotic strains. We studied production in co-cultures and faecal fermentations and examined the effect of selected strains on the faecal microbiome composition and metabolome in vitro.

METHODS AND RESULTS: Strains of intestinally derived Bifidobacterium adolescentis and Lactiplantibacillus plantarum from fermented cereals were grown singly, in co-culture and in faecal fermentations designed to simulate colonic conditions. Isolates synthesized varying amounts of GABA in vitro; GABA production could be increased by co-culture, lactic acid, or reduced pH but was decreased in the presence of high buffering. In faecal fermentations, selected strains inoculated singly or in combination persisted over 24 h and increased the GABA concentration without causing major disruptions in the microbiome or metabolome. Bifidobacterium adolescentis supplementation increased short-chain fatty acids acetate and propionate, and L. plantarum was associated with increased succinate levels, while all treatments exhibited a reduction in Escherichia compared to the controls.

CONCLUSIONS: GABA production from these lactic acid bacteria is strain-specific and the combination of these two species shows potential for future next-generation probiotic development.}, } @article {pmid41689625, year = {2026}, author = {Hayashi, T and Iida, N and Yasuda, K and Yoshio, T and Terashima, T and Takatori, H and Moriyama, H and Takeshita, Y and Takamura, T and Yamashita, T}, title = {Escherichia coli as a gut microbial marker of obesity and its reduction following bariatric treatment.}, journal = {Journal of gastroenterology}, volume = {61}, number = {6}, pages = {741-749}, pmid = {41689625}, issn = {1435-5922}, support = {19K17394//Japan Society for the Promotion of Science/ ; 23K15036//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; *Escherichia coli/isolation & purification/genetics ; Cross-Sectional Studies ; Female ; Feces/microbiology ; *Bariatric Surgery/methods ; *Gastrointestinal Microbiome/genetics ; Longitudinal Studies ; Middle Aged ; Male ; *Obesity, Morbid/microbiology/surgery ; Adult ; Biomarkers ; Dysbiosis/microbiology ; *Obesity/microbiology/surgery ; }, abstract = {BACKGROUND: Alterations in the gut microbiota have been implicated in obesity-related metabolic disorders; however, the disease-relevant microbial features that link gut dysbiosis to metabolic risk remain incompletely defined. In particular, whether quantitative expansion or strain-level divergence of specific taxa underlie metabolic dysfunction is unclear.

METHODS: We performed cross-sectional and longitudinal metagenomic analyses of fecal samples from 19 patients with severe obesity undergoing bariatric intervention and 30 healthy donors. Whole-genome shotgun sequencing was combined with quantitative PCR to assess both relative and absolute bacterial abundance. Cultured Escherichia coli isolates were further examined by whole-genome sequencing to evaluate strain-level diversity. Associations between microbial features and metabolic parameters were analyzed.

RESULTS: The gut microbiota of patients with severe obesity was taxonomically and functionally distinct from that of healthy donors. Among altered taxa, E. coli was significantly enriched in obesity and showed a consistent and marked reduction at 6 months post-intervention, irrespective of procedure type. Absolute E. coli abundance quantified by qPCR decreased significantly following intervention. In contrast, whole-genome analysis revealed no clear genotypic clustering of E. coli strains by host phenotype. Notably, E. coli abundance correlated positively with HbA1c and systolic blood pressure and negatively with serum albumin levels, whereas global microbial diversity and KEGG-based metabolic pathways showed limited longitudinal change.

CONCLUSIONS: Quantitative expansion of gut E. coli, rather than strain-specific genomic divergence, is associated with metabolic risk in severe obesity and is consistently reduced at 6 months after bariatric intervention. These findings suggest that microbial load-dependent effects of E. coli may be associated with obesity-related metabolic dysfunction and represent a potential biomarker. This exploratory, single-center study is hypothesis-generating and warrants further validation in larger, multi-center cohorts as well as interventional studies using preclinical animal models.}, } @article {pmid41690221, year = {2026}, author = {Jiang, Y and Shu, W and Wan, J and Yan, J and Liu, Q and Jiang, Y}, title = {Impacts of co-exposure to nanoplastics and ofloxacin on marine planktonic microbial communities and DMSP dynamics.}, journal = {Marine environmental research}, volume = {216}, number = {}, pages = {107908}, doi = {10.1016/j.marenvres.2026.107908}, pmid = {41690221}, issn = {1879-0291}, mesh = {*Sulfonium Compounds/metabolism ; *Water Pollutants, Chemical/toxicity ; Seawater/microbiology/chemistry ; *Ofloxacin/toxicity ; *Plankton/drug effects ; *Microbiota/drug effects ; *Anti-Bacterial Agents/toxicity ; }, abstract = {Dimethylsulfoniopropionate (DMSP) is a key organic sulfur compound in marine food webs and the main precursor of the climate-active gas dimethyl sulfide (DMS), yet its water-column cycling under the joint influence of emerging pollutants remains poorly constrained. A 19-day microcosm experiment was conducted to examine the long-term effects of single and combined exposure to nanoplastics (NPs) and the antibiotic ofloxacin on planktonic microbial communities and DMSP cycling in coastal seawater. Combined exposure induced much stronger inhibitory effects than either single pollutant, markedly weakening the late-phase biomass recovery observed under the antibiotic-only treatment. DMSP dynamics exhibited a biphasic disruption pattern: an initial transient accumulation was followed by persistently low concentrations later in the experiment, coinciding with pronounced declines in microeukaryotic and total biomass. Combined metagenomic and flow cytometric analyses revealed a "functional decoupling" scenario, in which the surviving community displayed elevated relative abundances of DMSP biosynthesis- and degradation-related genes, while the sharp reduction in microeukaryotic biomass and overall community size constrained the maintenance and renewal of the water-column DMSP pool. Co-occurrence network analysis further showed that co-exposure simplified the microbial network from a more distributed, complex structure to a highly centralized one, with fewer nodes and keystone taxa and decreased robustness indices along the pollution gradient. Together, these findings indicate that the co-occurrence of nanoplastics and antibiotics can disturb DMSP-related functions by eroding community structural stability and functional redundancy, providing experimental evidence for the vulnerability of coastal DMSP cycling to mixed-pollutant stress.}, } @article {pmid41690272, year = {2026}, author = {Bao, M and Liu, X and Chang, N and Wang, M and Zuo, S and Yin, G and Li, W and Zhang, S and Zhang, Y and Shen, W}, title = {Seasonal variation and co-occurrence of metal resistance and virulence genes in landfill leachate pathogens: Implications for environmental risk management.}, journal = {Journal of hazardous materials}, volume = {505}, number = {}, pages = {141460}, doi = {10.1016/j.jhazmat.2026.141460}, pmid = {41690272}, issn = {1873-3336}, mesh = {Seasons ; *Water Pollutants, Chemical/toxicity/analysis ; Groundwater/microbiology ; *Virulence Factors/genetics ; Genes, Bacterial ; China ; *Drug Resistance, Bacterial/genetics ; Waste Disposal Facilities ; *Metals, Heavy/toxicity ; Virulence/genetics ; Pseudomonas aeruginosa/genetics ; Escherichia coli/genetics ; }, abstract = {The co-dissemination of metal resistance genes (MRGs) and virulence factor genes (VFGs) in landfill leachate pathogens poses a significant yet underquantified public health risk. To address this gap, this study used metagenomic analysis to assess MRG/VFG occurrence and removal efficiency, and proposed a novel metal resistance index (MRI)-virulence risk index (RVI) framework to quantify microbial risks across raw, ultrafiltered, reverse-osmosis-treated leachate and adjacent groundwater in Hohhot, China. Metagenomic analyses identified 175 MRGs and 1024 VFGs, highlighting significant co-occurrence patterns (Spearman R > 0.6, P < 0.05) among dominant pathogens, including Pseudomonas aeruginosa and Escherichia coli. The results of PCoA analysis showed that the leachate treatment process could significantly change the spectrum of virulence gene and heavy metal resistance gene in the leachate. Linear regression analysis (all P < 0.001) revealed significant positive correlations between treated leachate and groundwater microbial VFGs/MRGs across seasons. Summer showed the strongest associations (R[2]: 0.733-0.892), followed by moderate correlations in spring (R[2]: 0.364-0.698) and autumn (R[2]: 0.349-0.642), with spatial heterogeneity in BG3 and marked seasonal impacts overall. MRI, RVI, and the MRI/RVI ratio increased sequentially after treated, indicating that high-risk microbial traits persist post-treatment. Importantly, this elevated MRI/RVI ratio is attributable to the relative proportional increase of high-risk genes rather than an absolute rise in their abundance. Our results demonstrate the leachate treatment partially mitigates heavy metal resistance/virulence loads but fails to eliminate all high-risk genes, revealing seasonal MRG-VFG co-enrichment and treatment efficacy. The MRI-RVI framework guides leachate management optimization for environmental and public health.}, } @article {pmid41690672, year = {2026}, author = {Zhang, Y and Bai, Y and Ni, J and Shi, J and Zhang, Y and Bell-Sakyi, L and Wu, X and He, C and Deng, F and Yin, F and Shen, S and Fang, Y}, title = {Evidence of human exposure to tick-borne viruses based on viromes of ticks and presence of specific antibodies among patients in Hainan Island, southern China.}, journal = {Virologica Sinica}, volume = {41}, number = {1}, pages = {70-83}, pmid = {41690672}, issn = {1995-820X}, mesh = {Animals ; China/epidemiology ; Humans ; *Antibodies, Viral/blood ; *Virome ; *Tick-Borne Diseases/virology/epidemiology/immunology ; *Viruses/genetics/classification/isolation & purification/immunology ; Female ; *Ticks/virology ; Phylogeny ; Islands ; *Rhipicephalus/virology ; Rhipicephalus sanguineus/virology ; }, abstract = {Hainan Island, located in the South China Sea, is known as an area with diseases related to Rickettsia spp. or spirochete infection; however, the potential threat there from infection with tick-borne viruses (TBVs) remains obscure. In the present study, the dominant tick species, including Rhipicephalus sanguineus and Rhipicephalus microplus, were collected in Hainan Island, and tick viromes were investigated by metagenomic sequencing. In total, 27 viral species were identified belonging to the families Orthomyxoviridae, Flaviviridae, Nairoviridae, Phenuiviridae, Totiviridae, Chuviridae, Rhabdoviridae, and Parvoviridae, amongst which one novel virus and 13 new strains were discovered. Subsequently, individual ticks were screened for seven TBVs, Huanggang Rhabd tick virus 1 (HRTV1), Lihan tick virus (LHTV), Mivirus (MIV), Guangdong tick quaranjavirus (GTQV), Wenchang Ephemerovirus (WEPMV), Jingmen tick virus (JMTV), and brown dog tick phlebovirus (BDPTV), resulting in high prevalence rates of 16.97%, 9.59%, 10.33%, 7.38%, 7.01%, 6.27%, and 3.69%, respectively. While co-infection with multiple viruses was more frequent in R. sanguineus, R. microplus ticks generally had higher viral loads. Four febrile patients showed antibody responses to three TBVs, one each to LHTV and JMTV, and two to GTQV; the patient with antibodies to JMTV also showed neutralizing activity against this virus. This study promoted our understanding of the diversity and complexity of the TBV community in Hainan Island. The results provide serological evidence that human exposure to TBVs like JMTV may have occurred in Hainan, raising concern about potential risks from TBVs and the need to perform further surveys of TBVs among ticks, animals and humans.}, } @article {pmid41691170, year = {2026}, author = {Zhou, W and Zou, X and Li, J and Alhaskawi, A and Abdalbary, SA and Lu, H}, title = {Chronic osteomyelitis of the right thumb caused by Actinomyces radingae and Finegoldia magna: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41691170}, issn = {1471-2334}, mesh = {Humans ; *Osteomyelitis/microbiology/diagnosis/surgery/diagnostic imaging ; Male ; *Actinomyces/isolation & purification/genetics ; Aged ; *Thumb/microbiology/diagnostic imaging/pathology ; *Actinomycosis/microbiology/diagnosis ; Anti-Bacterial Agents/therapeutic use ; *Bacillota/isolation & purification/genetics ; Chronic Disease ; Magnetic Resonance Imaging ; }, abstract = {BACKGROUND: Osteomyelitis of the hand is relatively uncommon and often results from penetrating trauma or postoperative infection. Rare pathogens such as Actinomyces radingae and Finegoldia magna pose diagnostic and therapeutic challenges due to their slow growth, frequent involvement in polymicrobial infections, and limited antibiotic susceptibility data.

CASE PRESENTATION: A 66-year-old male sustained a crush injury being caught in a door to his right thumb over two years prior, leading to repeated episodes of redness, swelling, pain, and restricted motion. Despite undergoing surgical intervention three months earlier at another hospital, his symptoms persisted. Radiography revealed cortical irregularity and surrounding soft tissue swelling of the distal phalanx. Magnetic resonance imaging revealed bone marrow edema of the distal phalanx and adjacent soft tissue inflammation, raising suspicion for underlying osteomyelitis in the appropriate clinical context. Laboratory markers of infection were within normal limits. The patient underwent surgery including necrotic bone removal, extensor tendon reconstruction with muscle transposition, and nail bed debridement. Intraoperative findings included purulent drainage, nail deformity, and tendon necrosis. Metagenomic next-generation sequencing (mNGS)of bone tissue identified Actinomyces radingae (8,019 reads) and Finegoldia magna (4,223 reads). Based on the chronic clinical course, imaging findings, intraoperative evidence of necrotic bone, and pathogen identification by metagenomic next-generation sequencing, a diagnosis of chronic osteomyelitis of the distal phalanx was established. Postoperatively, the patient received ertapenem (1 g QD) with good clinical response.

CONCLUSION: This case highlights the importance of considering uncommon pathogens in chronic post-traumatic hand infections and demonstrates the utility of mNGS in identifying atypical bacteria, enabling targeted therapy and improved outcomes.}, } @article {pmid41691172, year = {2026}, author = {Motta, H and Perin, APA and Rosin, GF and Reuwsaat, JCV and Mocelin, I and Lopes, FC and Mayer, FQ and de Medeiros, VP and Brum, IS and Baethgen, LF and Gregianini, TS and Staats, CC and Vainstein, MH and Kmetzsch, L}, title = {SARS-CoV-2 Infection disrupts lower respiratory tract microbiome function and interactions.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41691172}, issn = {1471-2180}, support = {405934/2022-0//Instituto Nacional de Ciência e Tecnologia (INCT FUNVIR)/ ; 408717/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 22/2551-0000396-6//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS)/ ; }, abstract = {BACKGROUND: The respiratory microbiome plays a critical role in host defense mechanisms and influences disease outcomes. However, the impact of SARS-CoV-2 infection on microbial community composition, function, and resistance potential across different respiratory tract compartments remains incompletely understood. To address this, we analyzed 127 retrospective respiratory samples from SARS-CoV-2-positive and negative patients from Southern Brazil. The dataset included nasopharyngeal swabs from the upper respiratory tract (URT) and samples from the lower respiratory tract (LRT) of patients with Severe Acute Respiratory Infection (SARI). Microbial taxonomic profiles, diversity, co-occurrence networks, functional pathways, and antibiotic resistance genes (ARGs) were assessed through shotgun metagenomic sequencing.

RESULTS: SARS-CoV-2 infection did not affect diversity in the URT, but was associated with altered bacterial beta diversity in the LRT. The LRT microbial composition was markedly altered in SARS-CoV-2-positive cases, with reduced abundance of pathogens such as Stenotrophomonas and Pseudomonas and an increased prevalence of Prevotella and Alloprevotella. Co-occurrence network analysis uncovered a loss of complexity in SARS-CoV-2-positive URT samples and the emergence of novel interactions associated with infection in the LRT. Functional profiling demonstrated that SARS-CoV-2-positive LRT samples were enriched in metabolic pathways, whereas SARS-CoV-2-negative LRT samples were enriched in virulence pathways. Resistome profiling indicated minimal differences in ARG diversity and mechanism distribution, although SARS-CoV-2-negative LRT samples exhibited higher ARG abundance.

CONCLUSION: SARS-CoV-2 infection reshapes the composition, interactions, and functional potential of the LRT microbiome, while the URT remains relatively stable. These findings underscore the compartment-specific impact of SARS-CoV-2 infection on the respiratory microbiome.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04828-9.}, } @article {pmid41691253, year = {2026}, author = {Daryani, NE and Jazayeri, SM and Izadi, N and Ahmadi, H and Baghi, HB and Shirmohammadi, M and Sabbaghian, M and Shekarchi, AA and Marvi, SS and Azadi, A and Poortahmasebi, V}, title = {Characterizing the gut virome in ulcerative colitis and crohn's disease: signatures of disease severity.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {46}, pmid = {41691253}, issn = {1743-422X}, support = {979157//National Institute for Medical Research Development/ ; }, mesh = {Humans ; *Virome ; *Colitis, Ulcerative/virology/pathology ; *Crohn Disease/virology/pathology ; Cross-Sectional Studies ; Male ; Female ; Metagenomics ; Severity of Illness Index ; Feces/virology ; Adult ; Iran ; Bacteriophages/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; *Viruses/classification/genetics/isolation & purification ; Middle Aged ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is a chronic disorder marked by intestinal inflammation and immune dysregulation. While bacterial dysbiosis has been widely investigated, the gut virome remains less explored. Altered viral communities, particularly bacteriophages, may destabilize microbial balance and amplify host inflammation.

METHODS: To characterize virome alterations, we conducted a cross-sectional observational study in Tabriz, Iran, involving fifty participants divided into five groups: mild UC, severe UC, mild CD, severe CD, and healthy controls. Stool samples were processed for viral nucleic acid extraction and analyzed using metagenomic next-generation sequencing. Bioinformatics pipelines included diversity assessment, taxonomic profiling, functional annotation, and discriminant analysis (LEfSe). Predictive modeling was performed with random forest classifiers.

RESULTS: Virome richness and diversity were reduced in severe UC and CD compared with controls, whereas mild cases showed values closer to healthy individuals. Taxonomic profiling revealed depletion of crAss-like phages and microviridae in IBD, along with enrichment of Caudovirales families such as siphoviridae and myoviridae. Among eukaryotic viruses, anelloviridae were prominent in severe IBD, and herpesviridae were enriched specifically in severe UC. Functional annotation highlighted enrichment of structural and lytic phage proteins in severe groups, whereas lysogeny-associated domains were more abundant in healthy controls. Random forest models based on viral features achieved appropriate accuracy, with an AUC of 0.89 for distinguishing IBD from controls and 0.83 for classifying mild versus severe disease.

CONCLUSION: Thus, IBD is associated with reduced virome diversity, loss of core protective phages, and selective enrichment of bacteriophages and eukaryotic viruses. These findings suggest that virome features may have potential as biomarkers for non-invasive diagnosis and severity stratification in IBD, requiring validation in larger and longitudinal cohorts.}, } @article {pmid41691450, year = {2026}, author = {Chen, S and Gu, Y and Bahadur, A and Liu, E and Wu, T and Zhu, X and Zou, Y and Liang, H and Wei, P and Wu, L and Wu, Q and Yang, P and Yu, H and Yang, Y}, title = {Divergent Responses of Bacterial Communities to Permafrost Degradation and Their Associations With Carbon Across Vertical Profiles.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {23}, pages = {e10516}, pmid = {41691450}, issn = {2198-3844}, support = {2022YFF0801903//National Key R&D Program of China/ ; xbzg-zdsys-202214//"Light of the West" Cross-team Project of the Chinese Academy of Sciences/ ; U23A2062//National Natural Science Foundation of China/ ; U24A20586//National Natural Science Foundation of China/ ; 23ZDFA017//Science and Technology Program of Gansu Province/ ; CSFSE-FX-2505//Freedom Project of the State Key Laboratory of Cryospheric Science and Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, CAS/ ; }, mesh = {*Permafrost/microbiology/chemistry ; *Carbon/metabolism/analysis ; *Bacteria/metabolism/genetics/classification ; *Microbiota/physiology/genetics ; *Soil Microbiology ; Tibet ; }, abstract = {Permafrost degradation poses a significant threat to the organic carbon (C) pool primarily through regulating microorganisms. However, microbial responses and their associations with C loss across vertical profiles remain unclear. Here, we use metagenomic sequencing to investigate bacterial communities in 125 samples from five 15 m-depth permafrost cores, spanning from the active layer to the permafrost layer along a degradation gradient on the Qinghai-Tibet Plateau. We find that α-diversity decreases, while stochastic processes and community stability increase from the active layer to the permafrost layer. Along permafrost degradation, these community attributes follow similar variations within the active layer but remain constant within the permafrost layer. The relative abundance and interaction of core taxa play important roles in maintaining community stability in the active and permafrost layers, respectively. As permafrost degrades, the negative relationships between community stability and C storage become more intense, especially in the active layer. These findings demonstrate that degradation induces microbial responses that potentially amplify C release, supporting a positive feedback loop to climate warming. Our work provides novel insights into the vertical heterogeneity of this mechanism and is crucial for modeling future permafrost C dynamics.}, } @article {pmid41691814, year = {2026}, author = {Guo, H and Liu, Q and Han, H and Xu, W and Shi, W and Zhao, M and Xiao, X and Liu, J and Li, T}, title = {Unveiling the adaptive evolution of halotolerant aceticlastic methanogenesis: Multi-scale responses and energy partition.}, journal = {Water research}, volume = {294}, number = {}, pages = {125552}, doi = {10.1016/j.watres.2026.125552}, pmid = {41691814}, issn = {1879-2448}, mesh = {*Methane/metabolism ; Acetates/metabolism ; }, abstract = {The high concentration of salt ions in saline organic wastewater poses significant challenges for wastewater treatment technologies, particularly impacting the stability of anaerobic digesters. Aceticlastic methanogenesis is a crucial pathway for converting acetate into methane through methanoarchaea whose metabolism is adversely impacted by salt stress. To address this, long-term adaptive laboratory evolution (ALE) was conducted to cultivate halotolerant aceticlastic methanoarchaea, incorporating metagenomics, metatranscriptomic sequencing, metabolomics, and metabolic modeling to delineate genetic and metabolic responses. The evolved microbiome achieved a substantial increase in methanogenic activity at 5 % sodium chloride, reaching 82.25 % theoretical conversion of acetate to methane, significantly outperforming the original microbiome. This ALE process overcame the natural scarcity of aceticlastic methanogens in hypersaline environments. Key adaptation mechanisms were confirmed at the transcriptional level, primarily involving the upregulation of genes for inorganic ion transport, compatible solute uptake, and de novo biosynthesis. Horizontal gene transfer also contributed significantly through the transfer of osmoregulation genes, particularly those for compatible solute transport, suggesting an energy-efficient adaptation strategy of accumulating rather than synthesizing solutes. Metabolic flux analysis revealed that adjustments in energy distribution under salt stress are driven by the energetic cost of synthesizing compatible solutes, which highlights the importance of solute transporters for energy conservation. This study elucidates the complex interplay between metabolic reprogramming and gene transfer in enhancing microbial resilience under salt stress, thereby deepening our understanding of microbial adaptations in extreme environments and advancing biotechnological approaches for saline wastewater treatment.}, } @article {pmid41691815, year = {2026}, author = {Xia, J and Han, J and Hong, L and Qiu, YY and Xie, Y and Xu, H and Zhang, L and Jiang, F}, title = {Resilient sulfur-driven treatment of real acid mine drainage enabled by reorganization of core sulfidogenic microorganisms.}, journal = {Water research}, volume = {294}, number = {}, pages = {125521}, doi = {10.1016/j.watres.2026.125521}, pmid = {41691815}, issn = {1879-2448}, mesh = {*Sulfur ; Bioreactors/microbiology ; *Mining ; Sulfides/metabolism ; Bacteria/metabolism ; }, abstract = {Elemental sulfur-driven sulfidogenic processes offer a promising alternative to conventional sulfate reduction for acid mine drainage (AMD) treatment, with advantages in lower operation cost induced by lower organic demand. However, their long-term performance and microbial stability under real AMD conditions, where high acidity and metal concentrations impose strong environmental stress, remain poorly understood. Here, we operated a laboratory-scale sulfur-driven bioreactor for 258 days to evaluate the long-term sulfide production, metal removal efficiency, and microbial succession when treating real AMD. The system maintained stable sulfide production (68.3 ± 12.1 mg S/L-h) under acidic conditions (pH 4.1 ± 0.2) with a carbon-to-sulfur ratio (∼0.23, mg TOC per mg sulfide) consistent with the theoretical value for sulfur reduction. Over 99.9% of Zn[2+], Cu[2+], Ni[2+], Cd[2+], and Co[2+] in AMD were effectively removed via in-situ precipitation with biogenic sulfide. Even exposed to high metal concentrations (e.g., ∼400 mg/L Zn[2+], ∼51 mg/L Cu[2+]), the sulfidogenic bacteria exhibited strong resilience and robustness. Microbial analyses revealed a substantial shift from diverse fermenters under synthetic wastewater to specialized, metal-tolerant sulfur reducers (e.g., Desulfurella, Athalassotoga) under AMD conditions. Metagenome-assembled genomes of these taxa revealed distinct metabolic strategies, including sulfur respiration, acid resistance, and metal detoxification, supporting their dominance under metal-rich and low-pH environments. Notably, the community exhibited strong structural resilience to both long-term metal exposure and acute metal shocks, maintaining sulfidogenic functionality through internal community reorganization rather than taxonomic turnover. These findings demonstrated the feasibility, robustness, and ecological adaptability of sulfur-driven sulfidogenic systems for cost-effective treatment of real-world AMD.}, } @article {pmid41691872, year = {2026}, author = {Zhang, XR and Hou, J and Rong, Z and Wu, YH and Cui, HL}, title = {Haladaptatus marinus sp. nov., Haladaptatus rarus sp. nov., Haladaptatus ordinarius sp. nov., and Halomicrococcus pelagicus sp. nov., halophilic archaea from diverse coastal tidal flats.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {2}, pages = {126698}, doi = {10.1016/j.syapm.2026.126698}, pmid = {41691872}, issn = {1618-0984}, mesh = {RNA, Ribosomal, 16S/genetics ; *Phylogeny ; China ; Sequence Analysis, DNA ; DNA, Archaeal/genetics ; Nucleic Acid Hybridization ; *Halobacteriaceae/classification/genetics/isolation & purification ; *Seawater/microbiology ; Seashore ; DNA-Directed RNA Polymerases/genetics ; Genome, Archaeal/genetics ; Metagenome ; Base Composition ; }, abstract = {Six novel halophilic archaeal strains, DFWS20[T], NG-SE-30[T], NG-WS-4[T], HHT-WS-8, NG-SE-24[T], and SG-WS-1, were isolated from different coastal regions of China. Metagenome and amplicon analyses showed that the abundance of archaea in the corresponding samples was very low. Strains DFWS20[T], NG-SE-30[T], NG-WS-4[T], and HHT-WS-8 were found to cluster with current Haladaptatus species, while strains NG-SE-24[T] and SG-WS-1 with those of Halomicrococcus based on 16S rRNA and rpoB' gene phylogenies. The overall-genome related indexes (OGRIs), average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values, between strains DFWS20[T], NG-SE-30[T], NG-WS-4[T], HHT-WS-8, and Haladaptatus species were 77.0-83.1%, 22.2-28.3%, and 74.7-84.8%, while those between strains NG-SE-24[T], SG-WS-1, and Halomicrococcus species were 79.6-94.9%, 26.0-63.9%, and 76.5-94.1%, respectively. These values were lower than the threshold of species classification. In contrast, the OGRIs between strains NG-WS-4[T] and HHT-WS-8, as well as those between strains NG-SE-24[T] and SG-WS-1, were above the threshold of species classification. Diverse differential phenotypic characteristics, such as nutrition, biochemical activities, and antibiotic sensitivity, were determined in these six strains and the existing species of the corresponding genera. The most abundant pathways in the genera Haladaptatus and Halomicrococcus were related to carbohydrate metabolism and amino acid metabolism. Based on the natural habitat analysis of the 16S rRNA genes of the strains, their target sequences were primarily found in habitats such as aquatic, soil, sediments, plant, and marine environments. The major polar lipids of strains DFWS20[T], NG-SE-30[T], NG-WS-4[T], and HHT-WS-8 were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS), and sulfated mannosyl glucosyl diether (S-DGD-1), while those of strains NG-SE-24[T] and SG-WS-1 were PG, PGP-Me, S-DGD-1, and galactosyl mannosyl glucosyl diether (TGD-2). Based on these polyphasic classification, strains DFWS20[T], NG-SE-30[T], NG-WS-4[T], and HHT-WS-8 represent three novel species of the genus Haladaptatus while NG-SE-24[T] and SG-WS-1 represent a novel species of the genus Halomicrococcus.}, } @article {pmid41691882, year = {2026}, author = {Xie, Y and Xu, Y and Ma, C and Chen, L and Cai, Y and Wu, S and Fan, Y and Zhang, C and Tian, Y and Tian, Y and Zhang, Y and Li, X and He, D}, title = {Cerebral sparganosis caused by spirometra sp.: A case report.}, journal = {Diagnostic microbiology and infectious disease}, volume = {115}, number = {1}, pages = {117311}, doi = {10.1016/j.diagmicrobio.2026.117311}, pmid = {41691882}, issn = {1879-0070}, mesh = {Humans ; Female ; *Sparganosis/diagnosis/parasitology/drug therapy/pathology ; *Spirometra/isolation & purification/genetics ; Aged ; Animals ; Albendazole/therapeutic use ; Praziquantel/therapeutic use ; Brain/parasitology/pathology/diagnostic imaging ; Anthelmintics/therapeutic use ; High-Throughput Nucleotide Sequencing ; *Brain Diseases/parasitology/drug therapy/diagnosis ; }, abstract = {Cerebral sparganosis is a rare parasitic infection caused by plerocercoid larvae of the genus Spirometra. Due to its nonspecific clinical manifestations, diagnosis remains challenging in clinical practice. Here, we report a case of a 72-year-old female who presented with intermittent fever and migratory intracranial mass lesions over a seven-year period, accompanied by progressive cognitive decline and right homonymous hemianopia. Metagenomic next-generation sequencing (mNGS) analysis of cerebrospinal fluid identified Spirometra sp. The diagnosis was further confirmed through brain lesion biopsy and tissue mNGS analysis. Following treatment with praziquantel and albendazole, the patient showed clinical improvement with no evidence of recurrence during 1-year follow-up. This case report highlights the diagnostic value of mNGS in identifying rare parasitic infections, particularly in cases of cerebral sparganosis where clinical presentation may be non-specific.}, } @article {pmid41691930, year = {2026}, author = {Liu, Q and Chen, S and Wang, Y and Wang, S and Zhou, R and Kou, G}, title = {Prunus persica (L.) Batsch root enriched Pseudomonas for enhanced saline-alkali tolerance by inducing fatty acid and flavonoid biosynthesis.}, journal = {Plant physiology and biochemistry : PPB}, volume = {232}, number = {}, pages = {111134}, doi = {10.1016/j.plaphy.2026.111134}, pmid = {41691930}, issn = {1873-2690}, mesh = {*Pseudomonas/physiology/metabolism/genetics ; *Plant Roots/microbiology/metabolism ; *Fatty Acids/biosynthesis ; *Flavonoids/biosynthesis ; *Prunus persica/microbiology/metabolism ; Rhizosphere ; Salt Tolerance ; Sodium Chloride ; *Alkalies ; }, abstract = {Peach (Prunus persica (L.) Batsch) is one of the most widely cultivated economic fruit crops worldwide. However, saline-alkali stress poses substantial challenges to its cultivation and production. This study investigated the synergistic response of peach roots and their rhizosphere microbiota to saline-alkali stress. We examined alterations in the rhizosphere bacterial community and its functional characteristics under such stress using 16S rRNA and metagenomic sequencing. The results indicated a significant enrichment of the genus Pseudomonas in the rhizosphere, accompanied by enhanced functional potential related to cell motility, biofilm formation, and signal transduction. Nine Pseudomonas strains were isolated from the stressed rhizosphere, all of which exhibited plant growth-promoting (PGP) traits in vitro, among which strains R8 showed the most comprehensive PGP profile and most significantly enhanced plant growth in pot experiments. Physiological and transcriptomic analyses demonstrated that R8 inoculation upregulates key genes involved in fatty acid (e.g., FAD, KCS, PAS) and flavonoid biosynthesis (e.g., CHS, CHI, F3H, FLS). This transcriptional reprogramming enhanced membrane stability (increased proline content) and antioxidant capacity (higher flavonoid levels), leading to systemic improvement in saline-alkali tolerance. This study reveals the adaptive strategy of peach to saline-alkali stress mediated by rhizobacteria and highlights the potential of R8 as a microbial inoculant for sustainable cultivation.}, } @article {pmid41691957, year = {2026}, author = {Jiang, W and Pu, J and Wang, F and Yan, J and Yang, Q and Yang, S and Bian, D}, title = {Study on the degradation performance and toxicity reduction mechanism of electroplating wash wastewater by a hydrolysis-acidification-MPR synergistic system.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128990}, doi = {10.1016/j.jenvman.2026.128990}, pmid = {41691957}, issn = {1095-8630}, mesh = {*Wastewater/chemistry ; Hydrolysis ; Biodegradation, Environmental ; Electroplating ; *Waste Disposal, Fluid/methods ; Water Pollutants, Chemical ; Aliivibrio fischeri ; }, abstract = {This study focuses on high-strength, low-biodegradability electroplating wash wastewater (COD ≥20,000 mg/L, BOD5/COD ≤0.1). A laboratory-scale hydrolysis-acidification (HA)-micro-pressure internal circulation multiphase reactor (MPR) combined treatment process was constructed. In the HA stage, wastewater biodegradability was significantly improved, with the BOD5/COD ratio being increased from 0.03 to 0.31. The MPR stage then further deepened degradation, enabling the system to maintain a COD removal rate above 97% during stable operation, linear alkylbenzene sulfonate (LAS) and TN removal rates were achieved at over 99% and 96.8%, respectively. Vibrio fischeri luminescence inhibition was reduced from >95% in the influent to approximately 65% in the HA effluent and <10% in the MPR effluent. GC-MS analysis revealed that the HA stage cleaved high-molecular-weight pollutants such as long-chain alkanes and esters into mid- and small-molecule products (e.g., 3-methylcyclohexanone and 2,5-dimethylnonane), while the MPR stage further converted these intermediates into low-toxicity small molecules (e.g., trimethylsilanol and hexamethylcyclotrisiloxane). Metagenomic analysis showed that facultative anaerobic fermenters (Aminivibrio, Alcaligenes) were enriched in the HA stage, whereas aerobic bacteria (Pseudomonas, Brevundimonas) predominated in the MPR stage. Key functional genes (alkB, cyp450, gpmB) were significantly enriched during the stable period, promoting carbon metabolism and stress resistance. This study elucidated that the HA-MPR synergistic system achieved efficient and stable degradation and toxicity mitigation of electroplating wash wastewater through a multi-stage cooperative mechanism of acidification cleavage and aerobic deep mineralization, providing theoretical and technical support for the engineering application of this process.}, } @article {pmid41691988, year = {2026}, author = {Pan, Y and Zong, G and Liu, M and Wang, Z and Zhu, H and Wei, Z and Shan, Y and Lu, Y}, title = {Restoring gut microbiota homeostasis to ameliorate colitis via Huangqin decoction.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {153}, number = {}, pages = {157929}, doi = {10.1016/j.phymed.2026.157929}, pmid = {41691988}, issn = {1618-095X}, mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Homeostasis/drug effects ; Mice ; *Colitis, Ulcerative/drug therapy/microbiology ; Mice, Inbred C57BL ; Disease Models, Animal ; Dextran Sulfate ; Male ; *Colitis/drug therapy/chemically induced ; Intestinal Mucosa/drug effects ; Wnt Signaling Pathway/drug effects ; }, abstract = {BACKGROUND: Ulcerative colitis (UC) is an inflammatory gut disorder involving dysregulated host-microbiota interactions. Huangqin decoction (HQD) is an herbal formula with known anti-inflammatory and microbiota-modulating effects, but its protective mechanism in ulcerative colitis remains unclear.

PURPOSE: To investigate whether HQD ameliorates colitis by rebalancing gut microbiota homeostasis and to elucidate the underlying immunological and regenerative mechanisms involved.

METHODS: A DSS-induced colitis mouse model was used to evaluate the effects of HQD. Colitis severity and inflammation were evaluated by the clinical disease index, histological analysis, and cytokine levels, and the gut microbiota profiles were analyzed via metagenomic sequencing. We used mechanistic assays to evaluate the effects of specific bacterial strains on intestinal organoids and neutrophil NETosis.

RESULTS: HQD significantly alleviated colitis symptoms and inflammation. It remodelled the gut microbiota, suppressing Desulfovibrionaceae while enriching Lachnospiraceae. This microbiota shift drove reduced NETosis and activated Wnt/β-catenin signaling to enhance intestinal stem cell (ISC) proliferation, thereby promoting mucosal repair. In organoid cultures, Lachnospiraceae promoted organoid growth, whereas Desulfovibrionaceae caused epithelial damage and, independently, triggered NETosis in immune contexts. Notably, administration of the Lachnospiraceae bacterium ameliorated colitis and increased colonic Wnt/β-catenin signaling, confirming its regenerative role.

CONCLUSION: HQD ameliorates colitis by rebalancing the gut microbiota, thereby suppressing harmful inflammation and promoting epithelial regeneration. These findings provide mechanistic support for HQD as a microbiota-mediated therapeutic strategy in colitis.}, } @article {pmid41692795, year = {2026}, author = {Vega, L and Birchenall-Jiménez, CI and Aponte, A and Durán, D and López, C and Moreno-Matson, MC and Perilla, C and Pinilla, D and Rodríguez-Leguizamón, G and Sánchez, E and Santana, A and Herrera, G and Ramírez, JD and Muñoz, M}, title = {Contrasting the gut microbiome in Colombian patients with diarrhea: a comparative metagenomic study in hospitalization and emergency room services.}, journal = {Gut pathogens}, volume = {18}, number = {1}, pages = {}, pmid = {41692795}, issn = {1757-4749}, abstract = {BACKGROUND: Diarrhea remains a major cause of morbidity worldwide, particularly in low- and middle-income countries. Hospital environments impose strong selective pressures on the gut microbiome through antimicrobial exposure, invasive procedures, and pathogen transmission, yet differences between hospital-onset and community-onset diarrhea remain poorly characterized at the microbiome level. This study aimed to compare the taxonomic and functional profiles of the gut microbiome in hospitalized (Hosp) and emergency room (ER) patients with diarrhea using shotgun metagenomics.

RESULTS: Fecal samples from 41 patients (Hosp = 24; ER = 17) attending the Hospital Universitario Mayor-Méderi (Bogotá, Colombia) were analyzed. The gut microbiomes were dominated by Enterobacteriaceae, particularly Klebsiella pneumoniae and Escherichia coli, together with abundant bacteriophages from the families Myoviridae, Siphoviridae, Podoviridae, and crAss-like phages. Phages predicted to infect Escherichia and Klebsiella were significantly depleted in Hosp patients (p < 0.05). Read-based functional profiling revealed the presence of virulence factors associated with K. pneumoniae capsule biosynthesis, secretion systems, and toxins from Clostridioides difficile and Clostridium perfringens. In parallel, Hosp patients showed a higher diversity of antimicrobial resistance markers, with a marked increase in glycopeptide resistance determinants. A total of 492 high-quality metagenome-assembled genomes were reconstructed, including multiple diarrhea-associated taxa. Hosp patients exclusively harbored genomes of K. pneumoniae, Enterococcus faecium, and most reconstructed Clostridium species (C. symbiosum, C. saccharolyticum_A, C. innocuum, C. scindens, C. leptum, and Clostridium sp000435835). In contrast, ER patients harbored genomes classified as Escherichia coli, Escherichia flexneri, and Enterococcus faecalis. Genomes associated with hospitalization carried higher loads of antimicrobial resistance markers (e.g., oqxA and aac(6')-Ii) and virulence factors (e.g., iutA and traT), whereas ER genomes, particularly E. coli and E. flexneri, encoded diverse aminoglycoside resistance and adhesion traits.

CONCLUSIONS: Hospital-onset diarrhea was associated with distinct microbiome features, including differences in phage-bacteria dynamics involving key diarrhea-associated taxa, as well as a higher abundance of virulence factors and antimicrobial resistance markers. These findings underscore the potential value of shotgun metagenomics as a complementary approach for infection surveillance and the development of precision diagnostic strategies in hospital settings.}, } @article {pmid41692940, year = {2026}, author = {Le, B and Jia, L and Pang, T and Han, S and Duan, Y and Zhao, XM}, title = {A review of computational approaches for metagenomics by long-read sequencing.}, journal = {Science China. Life sciences}, volume = {69}, number = {6}, pages = {1825-1839}, pmid = {41692940}, issn = {1869-1889}, mesh = {*Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Computational Biology/methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Humans ; }, abstract = {The metagenomic next-generation sequencing (mNGS), also known as short-read sequencing (SRS), is widely used to explore microbial composition and function. However, short reads, due to their difficulty in crossing repetitive regions, can lead to fragmented assemblies, hampering the comprehensive characterization of microbial genomes. In contrast, long-read sequencing (LRS) technologies, such as those from Pacific Biosciences (PacBio) and Oxford Nanopore, can span these complex repetitive regions and reconstruct continuous genomes, which enables high-resolution taxonomic classification and the precise recovery of essential genetic elements. This review provides a systematic overview of the computational approaches for long-read metagenomics, highlighting the progress in taxonomic profiling strategies, assembly and binning methods, and the detection of genetic elements. Furthermore, the review discusses the application of LRS in detecting structural variations (SVs), identifying methylation patterns, and characterizing strains. By combining advanced technologies and computational improvements, this review indicates the transformative potential of LRS in enhancing our understanding of microbial diversity, functions, and interactions within microbial communities.}, } @article {pmid41693232, year = {2026}, author = {Morsli, M and Magnan, C and Salipante, F and Dubois, A and Schuldiner, S and Cellier, N and Sotto, A and Lavigne, JP and Dunyach-Remy, C}, title = {Enhancing diabetic foot osteomyelitis diagnosis with metagenomics next-generation sequencing, proof of concept.}, journal = {Diabetic medicine : a journal of the British Diabetic Association}, volume = {43}, number = {4}, pages = {e70235}, pmid = {41693232}, issn = {1464-5491}, mesh = {Humans ; *Osteomyelitis/diagnosis/microbiology ; *Diabetic Foot/microbiology/diagnosis/complications ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; Retrospective Studies ; Pilot Projects ; Middle Aged ; Proof of Concept Study ; Aged ; Biopsy ; Bacteria/genetics/isolation & purification ; }, abstract = {Diabetic foot osteomyelitis (DFOM) is a serious medical condition that necessitates robust diagnostic tools for effective clinical management. Conventional diagnostic methods for DFOM rely heavily on bacterial culture, which is time-consuming and may fail to capture the full microbial diversity present in infections. This pilot study explored the utility of metagenomics next-generation sequencing (mNGS) as a complementary diagnostic tool for DFOM. We retrospectively analysed ten bone biopsies from nine diabetic persons using both routine microbiological culture and mNGS. Routine culture identified 11 bacterial species across seven biopsies, while mNGS detected 84 species, including all those found by culture. High microbial diversity (Shannon index = 1.10) was associated with severe osteomyelitis, leading to amputation in three of seven DFOM cases. Interestingly, one culture-negative biopsy revealed high bacterial diversity by mNGS and progressed to a severe infection within 7 days. mNGS also identified resistance genes, providing additional insights for targeted therapy. Integrating mNGS into routine clinical microbiology may serve as a complementary method to conventional diagnostics, particularly for distinguishing infection from colonization and predicting clinical outcomes. However, challenges such as human DNA contamination and limited sequencing depth must be addressed to optimize its clinical application. These findings support the integration of mNGS into diagnostic workflows for bone biopsies for improved management of DFOM.}, } @article {pmid41693402, year = {2026}, author = {Parveen, S and Shafi, Z and Shahid, M and Iqbal, MZ and Naznine, F and Ansari, MI}, title = {Omics-Driven Insights Into Soil Microbial Diversity and Phytopathogen Interactions for Sustainable Agriculture and Food Security.}, journal = {Journal of basic microbiology}, volume = {66}, number = {2}, pages = {e70155}, doi = {10.1002/jobm.70155}, pmid = {41693402}, issn = {1521-4028}, support = {//The authors are thankful for the support received from the Department of Science and Technology-Funds for Improvement of Science and Technology Infrastructure (DST-FIST), with grant acknowledgment and sanction number (SR/FST/LS-1/2017/13(C)). The authors express their deep gratitude to Integral University, Lucknow-226026, India, for their generous support of this work and for providing the manuscript communication number (IU/R&D/2025-MCN0003515)./ ; //Department of Science and Technology-Funds/ ; }, mesh = {*Soil Microbiology ; *Agriculture/methods ; *Food Security ; *Biodiversity ; Metabolomics ; Proteomics ; Crops, Agricultural/microbiology ; Multiomics ; Metagenomics ; *Plant Diseases/microbiology ; Plants/microbiology ; Soil/chemistry ; Ecosystem ; Microbiota ; Host-Pathogen Interactions ; }, abstract = {Soil microbial diversity plays a pivotal role in sustainable agriculture by regulating nutrient cycling, organic matter turnover, and natural suppression of phytopathogens, thereby supporting crop productivity and ecosystem resilience. However, intensive agricultural practices and environmental stressors have led to a decline in soil biodiversity, compromising soil functionality and food security. Recent advances in omics technologies-including metagenomics, transcriptomics, proteomics, and metabolomics offer powerful tools to unravel the complexity, of soil microbial communities and their interactions with plants and pathogens. These integrated approaches provide high-resolution insights into microbial structure, functional dynamics, metabolic pathways, and the mechanisms underpinning plant-microbe-pathogen interactions. Furthermore, omics-driven understanding supports the development of sustainable strategies such as organic farming, conservation practices, and microbial bioinoculants, which restore microbial diversity, enhance nutrient use efficiency, reduce chemical inputs, and mitigate disease pressure. By linking soil health to crop nutritional quality and broader food system sustainability, this review highlights the potential of omics-guided approaches to optimize soil microbial ecosystems for resilient agriculture and global food security.}, } @article {pmid41693862, year = {2025}, author = {Zhang, H and Zhang, L and Yang, B and Gao, C and Liu, H and Zhang, Y and Chen, X}, title = {Metagenomic and metatranscriptomic profiling of bronchoalveolar lavage fluid identifies microbial and host biomarkers of drug-resistant tuberculosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1726935}, pmid = {41693862}, issn = {2235-2988}, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Mycobacterium tuberculosis/genetics/drug effects ; *Metagenomics ; *Gene Expression Profiling ; *Tuberculosis, Multidrug-Resistant/microbiology/diagnosis/immunology ; Biomarkers/analysis ; Prospective Studies ; Microbiota ; Transcriptome ; Lung/microbiology ; Multiomics ; }, abstract = {BACKGROUND: Drug-resistant tuberculosis (DR-TB) undermines global TB control, yet how resistant Mycobacterium tuberculosis strains interact with the lung microbiome, phage communities, and local host immunity remains poorly defined.

METHODS: In a prospective cohort of 130 pulmonary TB patients (49 DR-TB, 81 drug-susceptible TB [DS-TB] patients), bronchoalveolar lavage fluid (BALF) was subjected to paired metagenomic and transcriptomic profiling. Microbial and bacteriophage community structures were assessed by diversity metrics and differential abundance testing, whereas host responses were characterized by gene expression, pathway enrichment, and immune cell deconvolution. A Random Forest model was trained to evaluate the diagnostic potential of host transcriptional signatures.

RESULTS: DR-TB airways presented distinct microbial beta diversity, with enrichment of Streptococcus spp. and streptococcal-targeting phages (e.g., Javan variants, phi-Ssu5SJ28rum). Transcriptomic analysis revealed 494 differentially expressed genes, which were associated with increased oxidative phosphorylation, suppressed ion channel and transporter activity, and enrichment of extracellular matrix remodeling pathways. Immune profiling demonstrated a significant reduction in γδ T cells in DR-TB patients (P = 0.0059). An 8-gene host-derived signature (ARHGEF5, PTGES3L, GAL3ST1, RANBP17, ACTA2_AS1, CBY3, MAMSTR, and LOC102031319) discriminated DR-TB from DS-TB with high accuracy (AUC = 0.837).

CONCLUSION: This dual-omics study defines the airway niche of DR-TB as a convergence of microbial dysbiosis, phage imbalance, and host immune-metabolic dysfunction. By uncovering DR-TB-specific microbial and transcriptional signatures, and deriving a predictive host-based classifier, our findings provide mechanistic insights and highlight novel opportunities for microbiome- and host-directed interventions in drug-resistant tuberculosis.}, } @article {pmid41693971, year = {2026}, author = {Xu, T and Hou, WX and Yang, ST and Shao, YP and Wang, J and Han, TT and Li, JN}, title = {Danggui-Baishao herb pair protects against dextran sulfate sodium-induced colitis by modulating the Wnt/β-catenin pathway.}, journal = {World journal of gastroenterology}, volume = {32}, number = {5}, pages = {113024}, pmid = {41693971}, issn = {2219-2840}, mesh = {Animals ; Dextran Sulfate/toxicity ; *Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry ; *Wnt Signaling Pathway/drug effects/immunology ; Disease Models, Animal ; Humans ; *Colitis/chemically induced/drug therapy/pathology ; Mice ; Male ; beta Catenin/metabolism ; Colon/pathology/drug effects/immunology/microbiology ; Molecular Docking Simulation ; HCT116 Cells ; Intestinal Barrier Function/drug effects ; Gastrointestinal Microbiome/drug effects ; Intestinal Mucosa/drug effects/pathology/immunology/microbiology ; }, abstract = {BACKGROUND: The Danggui-Baishao herb pair is the foundation of a traditional Chinese medicine formula known as Shaoyao decoction, which is widely used in the treatment of colitis.

AIM: To uncover the mechanisms underlying the anti-colitis effects of the Danggui-Baishao herb pair.

METHODS: The chemical composition of the herb pair was characterized by high performance liquid chromatography-quadrupole/time of flight mass spectrometry analysis. A mouse model of colitis was induced by administering 2.5% dextran sulfate sodium. The therapeutic effects of the herb pair were evaluated based on body weight changes, colon length, histopathological, intestinal inflammation, and barrier function. To investigate the underlying mechanisms, RNA sequencing, metabolomics, 16S rRNA sequencing, metagenomics, and the β-catenin inhibitor ICG-001 were utilized. Furthermore, molecular docking and dextran sulfate sodium-treated HCT 116 cells were conducted to explore the protective mechanisms of benzoylpaeoniflorin.

RESULTS: The herb pair improved body weight, colon length, intestinal inflammation, and barrier function. Additionally, the herb pair upregulated the expression of intestinal stem cells marker leucine-rich repeat-containing G-protein coupled receptor 5 and proliferation-related proteins. RNA sequencing analysis showed that the herb pair activated the Wnt/β-catenin signaling pathway. Metabolomic analysis revealed changes in bile acids composition. Through 16S rRNA and metagenomic sequencing, it was observed that the herb pair modulated the gut microbiota, with an enrichment of probiotics and a depletion of pathogenic bacteria. Following intraperitoneal injection of antagonist ICG-001, the therapeutic efficacy was diminished. Molecular docking showed that benzoylpaeoniflorin can bind to β-catenin. Furthermore, benzoylpaeoniflorin can activated the Wnt/β-catenin signaling pathway and the therapeutic efficacy was also diminished by the ICG-001 in vitro.

CONCLUSION: The herb pair effectively reduces colonic inflammation and maintains the integrity of the intestinal barrier. Moreover, the anti-colitis efficacy of the herb pair is closely associated with activation of the Wnt/β-catenin pathway.}, } @article {pmid41694087, year = {2026}, author = {Hu, Q and Sardi, MI and Naqvi, SA and Paton, ND and Hackenhaar, L and Pluk, P and de Laat, J and Chakrabarti, A and Khafipour, E}, title = {Effects of processed soybean meal on growth performance and gut microbiome composition in pigs in regular nursery and enterotoxigenic Escherichia coli challenged conditions.}, journal = {Translational animal science}, volume = {10}, number = {}, pages = {txag004}, pmid = {41694087}, issn = {2573-2102}, abstract = {Hydrothermal-mechanical (HTM) processing of soybean meal (SBM) has been shown to enhance intestinal health and growth in post-weaning pig compared to conventional SBM. It was hypothesized that HTM processing improves protein utilization, particularly under enterotoxigenic Escherichia coli (ETEC) challenge, resulting in better growth and a more resilient hindgut microbiome. A total of 268 weaned pigs (6.82 ± 0.85 kg body weight) were allotted to regular nursery (5 pigs/pen, 10-11 pens/treatment) or ETEC challenge (3 pigs/pen, 12 pens/treatment) and fed one of three isocaloric diets with equal standardized ileal digestible lysine: SBM, HTM SBM, or enzyme-treated (Enz Trt) SBM. Test soy products replaced SBM in a wheat-barley-SBM base diet for the first 3 wk, followed by a common diet for 3 wk. On d 14 post-weaning, ileal digesta and feces were collected for crude protein (CP) digestibility, short-chain fatty acid (SCFA), and microbiome analysis. Growth performance, digestibility, and SCFA data were analyzed using general linear models and microbiome data from Nanopore shotgun sequencing were center-log-ratio transformed for statistical analysis in R. No diet × challenge interaction was observed on ADG, ADFI or BW. Pigs in regular nursery conditions had higher ADG (P < 0.01) and ADFI (P < 0.05) than ETEC challenged pigs during d 0-7. HTM SBM and Enz Trt SBM improved ADG (P < 0.05) with similar ADFI compared to SBM across conditions. From d 7-12, pigs fed HTM SBM or Enz Trt SBM had greater ADG (P < 0.05) and ADFI (P < 0.01) than SBM-fed pigs. BW remained lower (P < 0.05) in SBM-fed pigs from d 12-21 and during the final 3 wk. Under regular nursery conditions, HTM SBM improved apparent total tract digestibility of CP (P < 0.01) compared SBM, but with no difference from Enz Trt SBM. Microbiome composition was affected by diet (P < 0.01) and ETEC challenge (P < 0.01). HTM SBM and Enz Trt SBM tended to increase α-diversity (P = 0.10) of the microbiome compared to SBM, with no difference between the two treatments. HTM SBM and Enz Trt SBM increased abundance of species positively correlated with growth and beneficial SCFA, such as caproate (P < 0.05) and valerate (P < 0.05). In conclusion, HTM SBM and Enz Trt improved ADFI, ADG resulting higher BW and promoted beneficial microbes linked to performance in nursery pigs under both regular nursery and ETEC-challenged conditions.}, } @article {pmid41694508, year = {2026}, author = {Scaglione, G and Mastroianni, N and Rizzo, A and Palomba, E and Carcione, D and Brigante, G and Principe, L and Colaneri, M and Gori, A and Borgonovo, F}, title = {Integrating artificial intelligence with genome sequencing against antimicrobial resistance: a narrative review.}, journal = {Frontiers in public health}, volume = {14}, number = {}, pages = {1757161}, pmid = {41694508}, issn = {2296-2565}, mesh = {*Artificial Intelligence ; Humans ; *Whole Genome Sequencing ; Machine Learning ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; }, abstract = {Antimicrobial resistance (AMR) represents an escalating global health threat, demanding diagnostic strategies capable of rapid, accurate, and comprehensive pathogen characterization. Genomic sequencing has transformed our ability to elucidate resistance mechanisms and track their evolution, yet its routine clinical adoption remains limited by cost, workflow constraints, and extended turnaround times. This narrative review examines how artificial intelligence (AI) and machine learning (ML) can enhance and operationalize sequencing-based diagnostics across the clinical microbiology continuum. We summarize current AI applications in whole-genome sequencing for AMR prediction, pan-genome feature extraction, and multicenter model generalizability, including emerging approaches such as federated learning. We then explore AI-driven metagenomic analytics for pathogen detection, resistome profiling, outbreak investigation, and prognostic modeling. Complementary non-genomic technologies, Raman spectroscopy and MALDI-TOF MS, are also evaluated for their potential to deliver rapid resistance profiling when integrated with ML. Finally, we discuss practical barriers, including cost, dataset standardization, interpretability, and regulatory challenges, while outlining future directions toward scalable, explainable, and equitable AI-guided diagnostics. Integrating AI with genomic and rapid phenotypic tools offers a pathway to real-time surveillance, optimized antimicrobial stewardship, and strengthened preparedness against emerging infectious threats.}, } @article {pmid41694517, year = {2026}, author = {Song, Z and Huang, Y and Gu, Y and Che, L and Zhang, K and Liu, Q and Guan, Q and Sui, L}, title = {Correction: Genetic characterization of the respiratory tract viruses in Jilin, Northeast China, 2023.}, journal = {Frontiers in public health}, volume = {14}, number = {}, pages = {1788645}, doi = {10.3389/fpubh.2026.1788645}, pmid = {41694517}, issn = {2296-2565}, abstract = {[This corrects the article DOI: 10.3389/fpubh.2025.1756127.].}, } @article {pmid41694529, year = {2026}, author = {Vivarelli, S and De Francesco, C and Paba, E and Giambò, F and Fenga, C}, title = {The resistome bridge between livestock and workers: novel frameworks for early detection and monitoring of antimicrobial resistance.}, journal = {Frontiers in public health}, volume = {14}, number = {}, pages = {1746385}, pmid = {41694529}, issn = {2296-2565}, mesh = {Animals ; Humans ; *Livestock/microbiology ; *Drug Resistance, Microbial/genetics ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; One Health ; *Drug Resistance, Bacterial/genetics ; *Occupational Exposure ; Animal Husbandry ; }, abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, driven by the extensive use of antibiotics in both human medicine and livestock production. In the context of the One Health framework, this review investigates the role of the gut microbiome and resistome, which represents the collection of antimicrobial resistance genes (ARGs), within livestock and among occupationally exposed workers. Intensive farming practices often involve routine, subtherapeutic antibiotic use, fostering antibiotic-resistant bacteria (ARB) in the gastrointestinal tract of animals. These ARB and ARGs are excreted into the environment, contributing to resistance spread through mobile genetic elements. From a Planetary Health perspective, this environmental dissemination reflects how human-driven livestock practices can perturb ecosystems, creating global health risks that link animal, human, and environmental well-being. Human exposure, particularly among farm workers and veterinarians, raises significant concerns about zoonotic transmission of pathogens and, potentially, ARB. Novel advances in metagenomic and metatranscriptomic technologies enhanced our understanding of gut microbial communities and their resistomes, revealing overlaps in ARG profiles between animals and livestock workers. These technologies also support the development of novel microbiome-targeted strategies, including prebiotics, probiotics, food supplementation and workplace-improvement strategies, aimed at reducing antimicrobial use and restoring healthy microbiome balance. The review also highlights the importance of integrated surveillance and cross-sectoral collaboration to monitor and control AMR transmission. Understanding the ecological dynamics of the gut resistome in livestock systems is essential for designing effective interventions that safeguard both animal and human health.}, } @article {pmid41695017, year = {2026}, author = {Galdamez, IA and Jimenez, K and Cira, M and Osborn, K and Ayad, M and Lee, CM and Patel, K and Galdamez, BA and Sloan, A and Shenkiryk, A and Cason, T and Gomez, NA and Phillips, M and Rosado, S and Rosado, A and Mishra, DR and Cherrington, EA and Griffin, R and Jay, JA}, title = {Evaluating Antibiotic Resistance in Urban Rivers and Coral Reefs of Belize: Evidence for Hotspots and a Potential Screening Tool.}, journal = {GeoHealth}, volume = {10}, number = {2}, pages = {e2025GH001427}, pmid = {41695017}, issn = {2471-1403}, abstract = {Antibiotic resistance is a significant threat to global public health and can disproportionately affect low- and middle- income countries (LMICs). There is a lack of studies focusing on antibiotic resistance in coral reef regions and environmental reservoirs in Central America. This study followed modified World Health Organization (WHO)'s Global Tricycle Surveillance protocols for the environmental sector to address these gaps. Water samples were collected from key areas in the lower Belize River, including above and below the Belize City, an open fish market, and sewage lagoon outfall, and coral reefs. Water samples underwent qPCR analysis for a suite of antibiotic resistance gene classes (sul1, sul2, ermF, tetA, and blaSHV), intI1, and 16S rRNA. Additionally, a subset of samples were tested for extended-spectrum β-lactamase (ESBL) E. coli and underwent shotgun sequencing. Results show that antibiotic resistance genes (ARGs) were highest and most diverse near Belize City, particularly near the treatment lagoons and open fish market. The coral reef regions had lower levels of antibiotic resistance though not void of their presence. This study is an application of a modified Global Tricycle Surveillance protocol integrated with qPCR- and metagenomics-based characterization of environmental antibiotic resistance in understudied areas. Notably, data from this study indicated that ESBL-E. coli could potentially be used as a screening tool for environmental antibiotic resistance, as it was only present at sites that had the highest levels of ARGs.}, } @article {pmid41695450, year = {2026}, author = {Rusiñol, M and Martínez-Puchol, S and Ribeiro, D and Verdaguer, J and Torrejón-Llorens, O and Itarte, M and Estarlich-Landajo, I and Mejías-Molina, C and Juliachs-Torroella, G and Girones, R and Ramírez, GA and Baliellas, J and Bofill-Mas, S and Fernández-Cassi, X}, title = {Livestock aggregated samples for monitoring viruses infecting animals and potentially zoonotic viral pathogens.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101340}, pmid = {41695450}, issn = {2352-7714}, abstract = {Active surveillance of livestock pathogens is essential to prevent animal health losses and zoonotic spillover. This study evaluted aggregated environmental sampling as a non-invasive approach for monitoring swine- and cattle-associated viruses across farms and slaughterhouses, bridging the gap between agricultural biosecurity and public health. Over eleven months, 105 samples, including swine slurry, cattle manure, farm air, and slaughterhouse wastewater, were collected and analyzed using pathogen-specific (RT) qPCR and targeted viral metagenomics. Seasonal and sample patterns were evident, with higher detection of rotavirus A (RoV-A) and bovine coronavirus (BCoV) in slurry and wastewater during winter, and porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus (TGEV) sporadicly in slaughterhouse wastewater. Farm slurry or manure were optimal for enteric viruses such as RoV-A or hepatitis E virus (HEV), and farm air proved valuable for respiratory viruses like BCoV. Targeted sequencing identified a broader viral community, revealing up to 80% of total detected viral species in slaughterhouse wastewater alone. Frequent detection of porcine bocavirus, circoviruses and astrovirus, alongside zoonotic viruses such as HEV and porcine bufavirus (PBuV), underscored the environmental transmission risk at the human-animal interface. Sequencing also uncovered viruses of unclear pathogenicity, including kobuvirus and copiparvovirus, underscoring the complexity of the livestock virome and the potential for emerging viral threats. Slaughterhouse wastewater consistently captured the highest viral richness, integrating inputs from multiple farms and regions, while farm air samples yielded lower diversity but detected respiratory (astrovirus, caliciviruses) and persistent viruses (papillomaviruses, polyomaviruses). Aggregated sampling proved particularly efficient in swine systems, while cattle surveillance may require adapted strategies due to lower stocking densities and greater ventilation. This work demonstrates the novelty and value of aggregated environmental samples, collected at different points in the production chain, as strategic One Health sentinels. This scalable, practical approach supports early warning and control of animal and zoonotic diseases, directly contributing to One Health surveillance.}, } @article {pmid41695690, year = {2026}, author = {Zhang, W and Zheng, Y and Han, G and He, X}, title = {A novel analysis workflow for simultaneous parsing prokaryotic and eukaryotic microbial genes from metagenomes.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20769}, pmid = {41695690}, issn = {2167-8359}, mesh = {*Metagenome ; Workflow ; *Metagenomics/methods ; *Prokaryotic Cells ; *Eukaryota/genetics ; *Genes, Microbial ; *Computational Biology/methods ; }, abstract = {Accurately predicting coding genes from metagenomic samples containing a high proportion of eukaryotic content remains a significant challenge. Novel and reliable methods for the simultaneous prediction of prokaryotic and eukaryotic microbial genes are crucial to address this. We evaluated gene prediction accuracy of MetaGeneMark and MetaEuk using representative genomes from diverse organisms. Based on these findings, we developed an innovative analytical workflow. This approach involves an initial prediction of eukaryotic genes using MetaEuk, followed by the masking of these predicted eukaryotic genes and any co-identified partial prokaryotic genes using a custom Perl script. Remaining prokaryotic genes are then predicted from the masked metagenome using MetaGeneMark or metaProdigal. This integrated strategy achieved similar quantities and average lengths of eukaryotic genes compared to using MetaEuk alone. Notably, the quantity of predicted prokaryotic genes and viral genes using the new workflow was 14-18% higher than that obtained with standalone prokaryotic predictors. Furthermore, validation on a mixed prokaryotic-eukaryotic metagenome demonstrated that our workflow yielded genes with significantly higher average lengths, indicating reduced fragmentation and improved gene integrity. This novel workflow effectively enables the rapid and comprehensive retrieval of high-quality prokaryotic and eukaryotic coding sequences from diverse metagenomes.}, } @article {pmid41695945, year = {2026}, author = {Kothe, CI and Mak, T and Julienne, A and Okazaki, K and Jahn, LJ and Evans, JD}, title = {Miso without kōji: nesashi miso ecology driven by spontaneous fermentation with Mucor plumbeus.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1759987}, pmid = {41695945}, issn = {1664-302X}, abstract = {Nesashi miso is a rare, traditionally fermented soybean paste from Japan, and unlike most misos is produced through spontaneous fermentation without the use of a kōji starter. Here we analyzed a nesashi miso alongside two other misos from the same producer (rice and black soybean) as well as a hatchō miso from another producer which, like the nesashi, is based only on soybeans. Shotgun metagenomics confirmed that while Aspergillus oryzae dominated the three kōji-based misos, nesashi miso lacked this starter culture, and revealed that it was instead dominated by other filamentous fungi, mainly Mucor spp. and Penicillium spp., and contained typical yeast and bacterial genera found in traditional misos such as Zygosaccharomyces and Tetragenococcus. Principal component analysis (PCA) of 65 publicly available metagenomes showed that the nesashi miso sample clustered with other spontaneous solid-state fermentations like Chinese qu rather than with traditional kōji-based misos. To further characterize this unique fermentation, we isolated the Mucor sp. from nesashi miso, and sequenced it using long-read genomic sequencing. Pangenomic analysis confirmed its identity as M. plumbeus, and revealed close relationships between food- and environment-derived strains, suggesting that some Mucor species may already be naturally equipped to grow, establish and function in food fermentation niches. The nesashi strain specifically shared a large core genome with M. racemosus C, a strain patented for use in food, suggesting the former's potential for use in and potentially even adaptation to food environments. Functional annotation highlighted unique genes in the food strain group associated with amino acid metabolism, which may contribute to flavor formation. Together, these findings bridge traditional fermentation practices with meta/genomic insights, highlighting the built fermentation environment as a reservoir of potential starter cultures and the genus Mucor as a worthy candidate for future food fermentation research and innovation.}, } @article {pmid41695957, year = {2026}, author = {Dobrzyński, J and Gradowski, M and Radkowski, A and Bujak, H}, title = {Chloroflexota in agricultural soils: current knowledge and future research directions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1705889}, pmid = {41695957}, issn = {1664-302X}, abstract = {The review organizes current knowledge on the biofunctions, life-history strategies, and environmental responses of Chloroflexota in agricultural soils. Members of this phylum play key roles in carbon, nitrogen, and phosphorus cycling through a high degree of metabolic versatility, including photosynthesis, redox reactions, and the degradation of complex organic compounds such as cellulose and lignin. Chloroflexota contribute to major soil processes, including nitrification, denitrification, and nitrogen fixation. In agricultural soils, the predominant classes are Anaerolineae and Ktedonobacteria, each exhibiting distinct ecological strategies. Anaerolineae members, such as Leptolinea, Bellilinea, and Anaerolinea, are often associated with nutrient-enriched conditions, suggesting copiotrophic or competitor- and ruderal-like traits. In contrast, Ktedonobacteria show negative responses to increased soil carbon and nitrogen, suggesting that its members are oligotrophic. Despite these trends, responses to soil organic carbon, nitrogen, phosphorus, and pH vary substantially across studies, likely due to functional heterogeneity within the phylum and insufficient taxonomic resolution in metataxonomic datasets. Emerging evidence from metagenome-assembled genomes (MAGs) reveals that Chloroflexota harbor genes involved in carbon fixation, nitrogen transformations, and phosphorus solubilization, highlighting their previously underestimated ecological significance. However, most Chloroflexota remain uncultured, and available genomic data are still limited. Future research integrating high-resolution taxonomic profiling, metagenomics, and cultivation-based approaches is needed to clarify the ecological roles and life-history strategies of Chloroflexota members. Such advances may ultimately establish this phylum as an important microbial indicator of soil fertility and environmental change in agricultural soils.}, } @article {pmid41696020, year = {2026}, author = {Kim, J and Murakami, T and Toyoda, A and Mori, H}, title = {Behavioural phase transitions in the migratory locust, Locusta migratoria, are related to changes in the gut bacterial composition.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag009}, pmid = {41696020}, issn = {2730-6151}, abstract = {Locusta migratoria is a grasshopper species that can change its behaviour from solitary to gregarious. Previous studies have implicated metabolites such as serotonin and dopamine in the regulation of behavioural transition in this species. While many studies using cultured microbes have demonstrated that some microbes harbor the neuroactive metabolic potential of these neurotransmitters, the association between microbial community composition and phase transition remains poorly understood. Here, we employed 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing analyses to compare the composition of gut microbial communities of L. migratoria in different behavioural phases. We found that Serratia ureilytica was enriched in the gut of gregarious individuals in contrast to the decreased presence of Klebsiella aerogenes, one of the most abundant taxa in wild individuals. The gut microbiome of gregarious individuals was functionally characterised by enriched kynurenine and tryptophan synthesis pathways, and by reduced representation of GABA, indole, and dopamine metabolism pathways compared with that of solitary individuals. These compositional changes were consistent with the enrichment of S. ureilytica and depletion of K. aerogenes, which possess the corresponding genes. In particular, the genes for kynurenine synthesis encoded by S. ureilytica specific to the gregarious phase, are known to be involved in the tryptophan production and are associated with reduced serotonin synthesis. These results highlight a distinct shift in both the taxonomic and functional composition of the gut microbiome across behavioural phases and suggest a potential microbial contribution to the behavioural changes of L. migratoria.}, } @article {pmid41696023, year = {2026}, author = {Chen, G and Jing, H and Liu, B and Zhang, J and Ou, Y and Liu, W and Tian, X and Wang, R and Yan, J and Mao, T and Yang, S and Zheng, Y and Hou, L and Dong, H}, title = {Unique phylogenies and metabolic adaptations of novel lineage III and comammox Nitrospira species from deep-sea sediments.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag003}, pmid = {41696023}, issn = {2730-6151}, abstract = {The genus Nitrospira, which includes canonical nitrite-oxidizing bacteria (NOB) and species capable of complete ammonia oxidation (comammox), plays an important role in the global biogeochemical nitrogen cycle. Typically, lineage IV Nitrospira predominate in marine environments, and other lineages are thought to be less abundant and remain poorly characterized in oceanic systems. Here, we recovered five novel metagenome-assembled genomes (MAGs) affiliated with Nitrospira lineage II-IV from deep-sea sediments. Notably, two of these MAGs represent members of lineage III and comammox Nitrospira, respectively, suggesting the presence of previously uncharacterized lineages in the deep sea. Phylogenetic and gene locus analyses indicated that deep-sea lineage III and comammox Nitrospira form distinct evolutionary clades that diverge from their terrestrial and coastal relatives, and we therefore designate these two marine-derived groups as "lineage III clade B" and "comammox clade A4", respectively. Comparative read recruitment analyses revealed that these lineages exhibit potential pan-oceanic distribution in deep-sea sediments and waters, albeit at very low abundances. Furthermore, the identification of genes encoding amtB-type ammonium transporters (amtB), the ABC-type glycerol-3-phosphate transport system (ugpABCE), a multi-subunit Na[+]/H[+] antiporter (mnh), and betaine transporters (BetT, opuABC) suggests that these newly discovered Nitrospira species possess adaptive capabilities to thrive in oligotrophic and saline marine environments. These findings provide novel insights into the occurrence, metabolic features, and adaptation strategies of lineage III and comammox Nitrospira, expand our understanding of Nitrospira diversity in the deep sea, and offer valuable perspectives on the evolutionary history of various Nitrospira lineages.}, } @article {pmid41696028, year = {2026}, author = {Tian, W and Petrová, E and Sakai, S and Nweze, JE and Daebeler, A and Angel, R}, title = {Cultivation and genomic characterization of novel methanogens from arid desert biocrust.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag013}, pmid = {41696028}, issn = {2730-6151}, abstract = {Methanogens are strictly anaerobic archaea capable of energy conservation by methane production, yet their presence in oxic and arid environments challenges existing paradigms. In this study, we enriched and genomically characterized seven methanogenic cultures from desert biocrusts, affiliated with the genera Methanobacterium, Methanosarcina, and Methanocella. Six of these new enrichment cultures represent new species. Nonetheless, phylogenomic analyses revealed close genetic relationships with organisms from anoxic environments, indicating the absence of an evolutionary distinction. Comparative genomics exposed diverse though non-unique repertories of antioxidant (e.g. catalase, superoxide dismutase and desulfoferrodoxin), and desiccation-resistance genes (including genes for maintaining osmotic pressure and repair of cell wall and membrane), with Methanobacterium spp possessing the lowest gene abundance and diversity for oxygen and desiccation tolerance. Nevertheless, the occurrence of a Class I methanogen such as Methanobacterium in arid soils challenges the notion that members of this class are less oxygen tolerant than Class II. Pangenome analysis further uncovered unique genes enriched in membrane-associated functions and potentially non-functional stress-related genes. Via a global metagenomic survey we find that methanogens are underdetected in dryland soils, likely due to sequencing depth limitations. Our findings highlight previously overlooked methanogen diversity and ecological plasticity in oxic and desiccated habitats, and emphasize the need for further studies to elucidate their survival strategies.}, } @article {pmid41696071, year = {2025}, author = {Forbrigger, Z and MacDonald, T and Kulkarni, K and Stadnyk, AW}, title = {Investigating diet to control asparagine uptake as an adjunct to asparaginase treatment.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1634113}, pmid = {41696071}, issn = {2234-943X}, abstract = {Ongoing refinements of multidrug regimens, and particularly the addition of L-asparaginase, resulted in an immediate gain in survival for pediatric acute lymphoblastic leukemia patients. Yet L-asparaginase has substantial side effects which may require dose reductions or delays in subsequent doses. There are at least 3 possible sources of L-asparagine to consider when balancing blood levels with asparaginase dosing, diet, cell synthesis and bacterial synthesis. To date, there is one precedent, in mice, in which blood L-asparagine levels are reduced as a consequence of reducing consumed levels. We build on that approach in experiments aimed at testing whether long-term dietary restriction of L-asparagine and possibly gut bacteria can impact blood levels. In our experiment, 2 groups of mice received food pellets with either 4% or 0% L-asparagine. Blood and fecal metabolites and fecal bacteria were sampled over 72 days. After this accommodation period, all mice continued their diet and received a single injection of pegylated E. coli recombinant L-asparaginase. Samples for bacteria and metabolites were collected 4 and 5 days later, respectively. Neither diet had adverse effects on the general health of the mice nor did diet alone change blood L-asparagine levels. Both diets led to changes in gut bacteria. L-asparaginase depleted blood L-asparagine in mice consuming either diet. Bacteria identified in fecal pellets revealed that the microbiomes of mice in the 2 cages were different (cage effect) and remained different although metagenomic analyses of day 72 feces indicated there were no diet-dependent differences in bacterial asparaginase or asparagine synthetase. These outcomes indicate that mice recover from any short-term down regulation of blood L-asparagine due to diet and consequently the metabolic controls become complex, and the gut microbes seem to not be a great influence. Further research should include approaches to determine the source of L-asparagine in the blood while ingesting diets with no/low or high amounts of L-asparagine.}, } @article {pmid41696361, year = {2026}, author = {Yin, L and Xu, L and Shan, YN and He, Z and Li, Y and Chen, W}, title = {Microbiota-driven therapeutic efficacy of Hyperoside in ulcerative colitis and associated anxiety.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1734356}, pmid = {41696361}, issn = {2235-2988}, mesh = {Animals ; *Quercetin/analogs & derivatives/pharmacology/therapeutic use ; *Anxiety/drug therapy ; *Colitis, Ulcerative/drug therapy/microbiology/chemically induced/complications ; Mice ; Disease Models, Animal ; Molecular Docking Simulation ; Male ; Signal Transduction/drug effects ; *Gastrointestinal Microbiome/drug effects ; Cytokines/metabolism ; Colon/pathology/drug effects ; Mice, Inbred C57BL ; Metabolomics ; Anti-Inflammatory Agents/pharmacology ; Dextran Sulfate ; Network Pharmacology ; NF-kappa B/metabolism ; }, abstract = {BACKGROUND: Ulcerative colitis (UC) is subtype of inflammatory bowel disease that is frequently comorbid with anxiety disorders. However, effective dual-targeting therapies are still lacking. Hyperoside (HYP), a natural flavonoid, exhibits anti-inflammatory and neuroprotective properties, yet its potential therapeutic effects on UC and associated anxiety, as well as the underlying mechanisms, remain largely unexplored.

METHODS: A murine model of DSS-induced colitis was established and treated with HYP. Disease activity was assessed through body weight, colon length, and histopathology. Anxiety-like behaviors were evaluated using open field and elevated plus maze tests. Neuroinflammation was examined through immunohistochemistry of BDNF expression and microglial activation. Gut microbiota composition was profiled by metagenomic sequencing, and metabolomic profiling was conducted using the Q300 Kit. Network pharmacology and molecular docking were employed to predict signaling pathways, which were further validated by Western blotting. Additionally, antibiotic depletion experiments were conducted to determine microbiota dependency.

RESULTS: HYP administration significantly ameliorated DSS-induced colitis, as evidenced by attenuated weight loss, restored colon length, and improved histopathology. It suppressed pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) and restored intestinal barrier integrity by upregulating Mucin-2 and ZO-1. Furthermore, HYP also alleviated anxiety-like behaviors and mitigated neuroinflammation by increasing BDNF levels and suppressing microglial activation. HYP treatment also restored gut microbial homeostasis, enriching beneficial bacteria such as Enterobacter ludwigii while reducing the abundance of Enterobacter hormaechei, Escherichia coli, and Acinetobacter baumannii. Metabolomic analysis revealed that HYP significantly promoted arginine biosynthesis. Network pharmacology and molecular docking identified the MAPK, PI3K-Akt, and NF-κB pathways as potential targets, with HYP showing strong binding affinity to MAPK3, AKT1, and NFκB1. Importantly, the therapeutic effects of HYP were abolished in microbiota-depleted mice.

CONCLUSION: Our findings demonstrate that HYP effectively alleviates DSS-induced colitis and comorbid anxiety-like behaviors. Its efficacy is dependent on the gut microbiota and is associated with the restoration of microbial homeostasis, enhancement of arginine metabolism, and modulation of the MAPK/PI3K-Akt/NF-κB signaling pathways. HYP represents a promising microbiota-targeting therapeutic candidate for UC and its neuropsychiatric comorbidities.}, } @article {pmid41696622, year = {2026}, author = {Zhu, Z and Miao, X}, title = {Research progress of metagenomic next-generation sequencing in infectious diseases of the spine: a systematic review.}, journal = {Therapeutic advances in infectious disease}, volume = {13}, number = {}, pages = {20499361251412789}, pmid = {41696622}, issn = {2049-9361}, abstract = {BACKGROUND: Infectious diseases of the spine (IDS) cause structural destruction and abscess formation, requiring precise early diagnosis. While conventional culture methods show limited sensitivity and slow turnaround, metagenomic next-generation sequencing (mNGS) offers a promising alternative with its broader pathogen spectrum, rapid turnaround time, high detection rate, and sensitivity, showing significant advantages in the diagnosis of IDS.

OBJECTIVES: This systematic review aims to synthesize the current evidence on the advantages and clinical utility of mNGS in diagnosing and managing IDS, focusing on pyogenic and granulomatous spinal infections.

DESIGN: The systematic review conducted in accordance with PRISMA guidelines.

DATA SOURCES AND METHODS: A comprehensive literature search was performed across nine electronic databases (including PubMed, Web of Science, and Embase) from 2010 to April 2025. Studies reporting on mNGS for pathogen detection in patients with suspected or confirmed spinal infections were included. The quality of included observational studies was assessed using the STROBE checklist. Data on detection spectrum, rate, sensitivity, turnaround time, and clinical impact were extracted and synthesized narratively due to high heterogeneity.

RESULTS: Twenty-nine studies (25 retrospective studies and 4 case reports) from China were included. mNGS demonstrated a significantly broader detection spectrum, identifying common pathogens (e.g., Staphylococcus aureus, Mycobacterium tuberculosis) as well as rare and fastidious organisms that were missed by conventional methods. The pooled detection rate of mNGS (36.8%-95.5%) was consistently and significantly higher than that of culture (5.9%-59.2%). mNGS also showed superior sensitivity (39%-94.7%) compared to culture. The average turnaround time for mNGS (29-53 h) was substantially faster than for culture (2-10 days). mNGS-guided therapy was associated with improved clinical outcomes, including significant reductions in inflammatory markers.

CONCLUSION: mNGS represents a powerful diagnostic tool for IDS, offering broader detection spectrum, higher detection rate, faster turnaround time, and greater sensitivity compared to conventional methods. This enables more targeted antimicrobial therapy and improves clinical management. Challenges including high costs and difficulty in distinguishing colonization from infection remain. Future efforts should focus on technical optimization, workflow automation, protocol standardization, and outcome validation in larger prospective studies.

TRIAL REGISTRATION: CRD420251170912.}, } @article {pmid41696869, year = {2026}, author = {Ju, Y and Lin, S and Hu, S and Jin, X and Xiao, L and Zhang, T and Zhang, Y and Zhang, L and Ma, X and Zhu, F and Guo, R}, title = {GutMIND: A multi-cohort machine learning framework for integrative characteristics of the microbiota-gut-brain axis in neuropsychiatric disorders.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2630563}, pmid = {41696869}, issn = {1949-0984}, mesh = {Humans ; *Mental Disorders/microbiology ; *Machine Learning ; *Gastrointestinal Microbiome ; *Brain/microbiology/metabolism ; Cohort Studies ; Metagenomics ; Bacteria/classification/isolation & purification/genetics ; Biomarkers ; }, abstract = {Emerging evidence underscores bidirectional communication along the microbiota-gut-brain axis in neuropsychiatric disorders. However, the field lacks dedicated metagenomic resources with standardized phenotyping for these conditions. Existing single-cohort studies face inherent limitations due to restricted sample sizes, confounding heterogeneity, and methodological fragmentation, compromising reproducibility and mechanistic insights. To overcome these challenges, we constructed the Gut Microbiome in Multinational Integrated Neuropsychiatric Disorders (GutMIND) database, a comprehensive resource integrating shotgun metagenomic data with harmonized metadata. Adhering to a standardized preprocessing protocol and rigorous quality control workflow, this dataset represents the largest gut-brain microbiome repository to date, encompassing 31 studies across 12 countries (n = 3,492) spanning 14 neuropsychiatric conditions. Utilizing this dataset, we characterized microbial community heterogeneity, which was significantly elevated in patients compared to healthy controls. Subsequently, we developed a computational framework, MetaClassifier, enabling the diagnosis of neuropsychiatric disorders and the identification of microbial biomarkers. Employing a comprehensive two-stage validation strategy, we first assessed the model utilizing taxonomic abundance profiles via nested cross-validation in the high-quality discovery cohort (n = 2,734), achieving a mean AUROC of 0.69 (range: 0.55-0.78) across 8 disorders. Its robustness was further confirmed in an independent platform-extended validation cohort (n = 400), yielding a mean AUROC of 0.71 (range: 0.60-0.76). We also developed the Microbial Gut-Brain Axis Health Index (MGBA-HI), which effectively distinguished neuropsychiatric status in both the high-quality cohort and the platform-extended cohort. Furthermore, integrative analysis of health-abundant species, index-derived biomarkers, and ecological prevalence, we identified 9 core neuropsychiatric-protective microbiota. These species predominantly exhibited metabolic capacities linked to glutamate synthesis and acetate production. Building upon this, the GutMIND framework ensures robust cross-cohort comparability while minimizing technical heterogeneity, thereby enhancing inferential rigor in gut microbiome-neuropsychiatry research. Notably, the MetaClassifier, MGBA-HI, and core microbiota hold translational potential for developing microbiome-based prognostic tools and personalized therapeutic strategies in neuropsychiatric disorders. The source code and usage instructions for MetaClassifier are accessible at https://github.com/juyanmei/MetaClassifier.}, } @article {pmid41697021, year = {2025}, author = {Han, B and Wen, H and Li, Y and Wang, Y and Lv, X and Kang, M and Huang, W and Lan, Y and Tong, S and Zhang, M and Chen, D and Zhu, C and Jiang, Y and Tang, D}, title = {Gut microbial production of lithocholic acid reprograms pro-resolutive macrophages to enhance vedolizumab responsiveness via the TGR5/FXR-NF-κB axis.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41697021}, issn = {1751-7370}, support = {LHGJ20250299//Henan Provincial Medical Science and Technology Research Joint Venture Project/ ; 2025M772035//China Postdoctoral Science Foundation/ ; 82460108//National Natural Science Foundation of China/ ; 2023GXNSFAA026135//Guangxi Natural Science Foundation/ ; 2025GXNSFDA069030//Key Project of Guangxi Natural Science Foundation/ ; }, mesh = {Animals ; *Lithocholic Acid/metabolism ; *Gastrointestinal Microbiome ; *Macrophages/metabolism/immunology/drug effects ; *NF-kappa B/metabolism ; Mice ; Humans ; Disease Models, Animal ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Receptors, Cytoplasmic and Nuclear/metabolism ; Receptor, Farnesoid X-Activated ; *Crohn Disease/drug therapy ; Colitis/chemically induced/drug therapy ; Signal Transduction ; Metabolomics ; *Gastrointestinal Agents/pharmacology ; Fecal Microbiota Transplantation ; Bile Acids and Salts/metabolism ; }, abstract = {Crohn's disease (CD) is a complex chronic transmural inflammatory bowel disease. Although vedolizumab (VDZ) markedly improves clinical outcomes in CD, treatment non-response remains a significant limitation, constraining its broader utility. Elucidating the mechanisms underlying VDZ responsiveness is thus critically needed. In this research, we employed a humanized mouse model of 2,4,6-trinitrobenzene sulfonic acid-induced colitis to investigate VDZ treatment response in CD. Our findings indicate that VDZ significantly alleviated disease phenotypes in a portion of CD mice. Integrated metagenomic and metabolomic profiling identified baseline gut microbiota-derived secondary bile acids as potential predictors of VDZ efficacy. Subsequent fecal microbiota transplantation from clinical donors into pseudo-germ-free mice confirmed that gut microbial composition critically influences VDZ responsiveness. Targeted metabolomics further pinpointed lithocholic acid (LCA) as a key microbially derived metabolite correlated with therapeutic remission. Single-cell RNA sequencing also revealed that intestinal macrophages serve as pivotal mediators of LCA-driven modulation of treatment outcomes. Furthermore, transcriptomic analyses demonstrated that LCA polarizes macrophages toward an M2-resolutive phenotype via concurrent engagement of the TGR5/FXR and their downstream nuclear factor kappa-B (NF-κB) pathways. Ultimately, using a conditioned medium co-culture system, we established that the regulatory effects of pro-resolutive macrophage niche on treatment response in a manner dependent on the TGR5/FXR-NF-κB axis. Taken together, our study elucidates a microbiota-immune circuit in which gut microbial metabolite LCA augments VDZ responsiveness in CD by reprogramming macrophages toward a pro-resolutive phenotype via the TGR5/FXR-NF-κB signaling network. These insights provide a mechanistic foundation for biomarker development and personalized therapeutic strategies in inflammatory bowel disease.}, } @article {pmid41697036, year = {2026}, author = {Reva, ON and Sifuna, A and Orata, F and Omolo, C and Iramiot, JS and Enright, MC and Mutshembele, A and Zhou, J and Shivoga, WA}, title = {From Lake Victoria to the Tap: Antibiotic Resistance and Pathogenic Contamination of Kisumu City Water Supply and Wastewater Network.}, journal = {Tropical medicine & international health : TM & IH}, volume = {31}, number = {4}, pages = {547-559}, pmid = {41697036}, issn = {1365-3156}, support = {GCRFNGR8\1143//UK Global Challenges Research Fund Networking/ ; NIHR163838//UK National Institute for Health and Care Research/ ; }, mesh = {*Lakes/microbiology ; *Drug Resistance, Microbial/genetics ; Kenya ; *Wastewater/microbiology ; *Water Supply ; *Water Microbiology ; Humans ; *Drinking Water/microbiology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/isolation & purification ; }, abstract = {Waterborne diseases and antimicrobial resistance (AMR) pose mounting public health threats across sub-Saharan Africa, particularly in rapidly urbanising regions dependent on untreated or poorly treated surface waters. This study applied shotgun metagenomic sequencing to characterise microbial communities, virulence factors and antibiotic resistance genes (ARGs) in water samples collected from Lake Victoria, River Wigwa, Dunga Water Treatment Plant, Nyalenda Wastewater Stabilisation Ponds and the tap water outlet in post-treatment supply pipe in Kisumu city (Kenya). Bacterial taxa dominated all metagenomes, with 121 classes represented. Cyanobacteria, particularly Planktothrix, were highly abundant in lake and tap water, whereas wastewater and river samples exhibited greater taxonomic diversity. Major human pathogens, including Pseudomonas aeruginosa , Klebsiella pneumoniae , Escherichia coli , Acinetobacter baumannii and Bacillus cereus/anthracis, were detected in nearly all samples, with unexpectedly high prevalence in tap water. Viral indicators of faecal contamination (adenoviruses, enteroviruses and torque teno viruses) corroborated widespread wastewater influence. Functional gene profiling revealed a rich resistome comprising aminoglycoside-modifying enzymes, β-lactamases, vancomycin-resistance operons and disinfectant-resistance determinants. The highest ARG and virulence gene frequencies occurred in tap and treatment-plant water, suggesting that incomplete disinfection and biofilm persistence promote the proliferation and exchange of ARGs between environmental and pathogenic taxa. In contrast, Lake Victoria water exhibited lower ARG abundance, reflecting natural self-purification processes. These findings underscore the inadequate water treatment and open wastewater systems create ecological 'hotspots' for ARG selection and horizontal gene transfer. Metagenomic surveillance integrated into One Health frameworks can enhance risk forecasting and guide interventions to mitigate AMR emergence and dissemination in freshwater systems serving over 35 million people across the Lake Victoria basin.}, } @article {pmid41697296, year = {2026}, author = {Chengcheng, L and Yanduo, Z and Zhebin, W and Jianzhang, L and Yangtao, Z and Jun, L and Yu, L and Felemban, HR and Alyahyawy, OY and Alhomodi, AF and Hadadi, F and Shaibah, A and Bingzhi, L and Xianwei, W}, title = {Metagenomic analysis of fecal microbial communities in dairy goats from different farms.}, journal = {Protoplasma}, volume = {263}, number = {3}, pages = {1031-1045}, pmid = {41697296}, issn = {1615-6102}, abstract = {This study aims to investigate the differences in the microbial community structure of goat manure under various breeding environments, providing scientific evidence and theoretical support for healthy breeding practices. Gut microbiota is a key determinant of feed conversion, disease resistance and overall productivity in ruminants. The gut microbiome is an integral part of the digestive system. Its composition and functional traits markedly influence digestive efficiency, immune development, gut homeostasis and reproductive performance. Using four goat dairy farms in the Yangling, Shaanxi Province as study subjects, fecal samples were collected and analyzed using 16S rRNA sequencing technology, combined with α-diversity indices and β-diversity analysis. The results revealed significant differences in the microbial community structure of goat feces across different farms, with each farm exhibiting unique microbial communities. Each farm harboured distinct microbial signatures and functional profiles, providing microbiota-based targets for precision management of Guanzhong dairy goats.}, } @article {pmid41697418, year = {2026}, author = {Hossain, A and Haque, I and Al Mamun, A and Al-Din, SMS and Ara, H and Das, TK and Rahman, MM}, title = {Physicochemical and metagenomic characterization of drinking water: Public health implications in Kushtia Municipality, Bangladesh.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {3}, pages = {224}, pmid = {41697418}, issn = {1573-2959}, mesh = {Bangladesh ; *Drinking Water/microbiology/chemistry ; *Environmental Monitoring ; Water Microbiology ; Metagenomics ; Public Health ; Water Quality ; Bacteria/classification/genetics ; RNA, Ribosomal, 16S ; }, abstract = {Physicochemical and bacterial contamination pose a significant threat to drinking water quality in Bangladesh, requiring comprehensive analysis. This study investigates the physicochemical and metagenomic quality of drinking water from one of four water treatment plants (WTPs) in Kushtia Municipality, Bangladesh. Water samples (n = 3) from untreated, treated, and supplied water were collected between March 1 and 7, 2025. Thirteen physicochemical parameters were analyzed using traditional methods, while bacterial load was assessed using Plate Count Agar. Microbial diversity was analyzed through metagenomic sequencing of DNA extracted using the DNeasy PowerWater Kit, targeting the 16S rRNA gene (V3-V4 region) on the Illumina MiSeq platform. Alpha and beta diversity were evaluated with Chao1, Shannon, and Simpson indices, and taxonomic and pathway analysis were performed on the Kaiju and Nephele platforms. Water quality was assessed using treatment efficiency metrics, the Water Quality Index (WQI), and the Nemerow Pollution Index (NPI). Results reveal that only three of the physicochemical parameters meet the water quality standards of Bangladesh. The WTP's cumulative efficiency metric was found to be 30.76%. The WQI indicated that all water samples were unfit for drinking. The NPI showed that eight out of thirteen physicochemical parameters significantly contribute to poor water quality. Microbial evaluations revealed high bacterial levels in untreated and supplied water samples. Alpha diversity analysis, using Shannon and Simpson indices, showed no significant differences in bacterial abundance across water types. Beta diversity analysis indicated minimal dissimilarity. Functional profiling suggested the presence of antibiotic resistance-associated pathways, with predicted beta-lactam resistance representing 24.1% in treated water and 25.0% in supplied water. The dominant phyla include Proteobacteria (38% in untreated, 39% in treated, and 42% in supplied). About 75%, 83%, and 67% of the identified bacterial species were found to be pathogenic, antibiotic-resistant, and biofilm-forming, respectively, while 58% were classified as opportunistic pathogens. These results underscore the need for improved water treatment practices and more robust monitoring systems to ensure the population can access safe drinking water.}, } @article {pmid41697419, year = {2026}, author = {Ni, W and Huang, H and Wang, X and Yu, A and Ren, J and Li, H}, title = {Metagenomic Analysis Reveals Alterations in the Gut Microbiome of Preterm Infants with Extrauterine Growth Restriction.}, journal = {Current microbiology}, volume = {83}, number = {4}, pages = {177}, pmid = {41697419}, issn = {1432-0991}, support = {No. 82101811//National Natural Science Foundation of China/ ; No. RCJC20231211085923029//Shenzhen Science and Technology Program/ ; No. SZSM202311027//Sanming Project of Medicine in Shenzhen/ ; Guangdong High-level Hospital Construction Fund//Guangdong High-level Hospital Construction Fund/ ; Clinical key specialty construction project of Guangdong Province//Clinical key specialty construction project of Guangdong Province/ ; No. 20232011//Project of Guangdong Provincial Administration of Traditional Chinese Medicine/ ; }, mesh = {Humans ; Metagenomics ; Female ; *Bacteria/classification/genetics/isolation & purification ; *Infant, Premature/growth & development ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; }, abstract = {Extrauterine growth restriction (EUGR) is a pervasive clinical issue in preterm infants, affecting neonatal development and their long-term health. This study aimed to characterize the gut microbiome and its derived genes in preterm neonates with EUGR using metagenomic sequencing. Sixty-two preterm infants hospitalized in the neonatal intensive care unit at Guangdong Women and Children Hospital were enrolled in this study. Participants were divided into two groups: the EUGR group (n = 34) and the normal growth group (AGA, n = 28). Fecal samples were collected at one month postnatally. Total bacterial DNA was extracted and sequenced using the Illumina HiSeq X Ten system. Significant differences in the gut microbial community between the EUGR and AGA groups were observed, as evidenced by the Bray-Curtis dissimilarity index. The EUGR group exhibited a notable increase in Klebsiella pneumoniae and Enterococcus faecalis, along with a significant decrease in Streptococcus raffinosi, Rothia mucilaginosa, Parabacteroides merdae and Eggerthella lenta compared to the AGA group. Functional annotation of metagenomic genes identified 415 genes with significantly different relative abundances between the groups. A classification model incorporating five discriminatory genes achieved effective separation of EUGR from AGA infants. Additionally, the EUGR group exhibited a higher relative abundance of antibiotic resistance genes. This study elucidates the alterations in the gut microbiome and its derived genes in preterm neonates with EUGR. These findings provide new insights into the potential microbial signatures associated with impaired growth, although further mechanistic studies are needed to clarify causal relationships.}, } @article {pmid41698031, year = {2026}, author = {Meng, Q and An, X and Hu, W and Ma, M and Chen, Z and Wei, G and Chen, C}, title = {Nanopriming with Silicon Quantum Dots Strengthens Wheat Drought Tolerance through Physiological Regulation and Microbial Functions.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {7}, pages = {5989-6001}, doi = {10.1021/acs.jafc.5c11900}, pmid = {41698031}, issn = {1520-5118}, mesh = {Drought Resistance ; *Triticum/microbiology/physiology/growth & development/drug effects/metabolism ; *Silicon/chemistry/pharmacology ; *Quantum Dots/chemistry ; Bacteria/classification/genetics/isolation & purification/metabolism ; Rhizosphere ; Seeds/growth & development/microbiology/physiology/drug effects ; Droughts ; Plant Roots/microbiology/growth & development/metabolism ; Water/metabolism ; Microbiota ; Germination ; }, abstract = {Seed priming offers a promising approach to strengthening drought resilience in wheat. In this study, seeds were primed with silicon quantum dots (SiQDs) at concentrations of 0, 250, 500, 750, and 1000 mg L[-1]. Under drought stress induced by 15% PEG-6000, 500 mg L[-1] SiQDs increased the level of germination by 18.2%. In a 30 day pot experiment conducted under drought conditions at 40% field capacity, 500 mg L[-1] SiQDs significantly enhanced shoot biomass (157.1%) and the relative water content (26.7%), reduced root malondialdehyde (24.7%), and increased root proline (76.7%) and soluble sugar (68.7%). 16S rRNA gene and metagenomic sequencing analyses revealed that SiQDs enriched Proteobacteria in the rhizosphere, including the genera Sphingomonas, Lysobacter, and Variovorax, and activated functional pathways associated with biofilm formation and bacterial colonization. These results demonstrate that SiQD priming enhances drought tolerance by improving plant physiological responses and modulating rhizosphere microbial communities.}, } @article {pmid41698498, year = {2026}, author = {Song, Y and Li, X and Li, C and Xu, J and Liu, F and Zhao, Z and Zhong, X}, title = {A case study of delayed-diagnosed leprosy: advancing diagnosis through MetaPath.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {166}, number = {}, pages = {108490}, doi = {10.1016/j.ijid.2026.108490}, pmid = {41698498}, issn = {1878-3511}, mesh = {Humans ; Male ; Aged ; *Mycobacterium leprae/genetics/isolation & purification ; Delayed Diagnosis ; Leprostatic Agents/therapeutic use ; *Leprosy, Paucibacillary/diagnosis/drug therapy/microbiology ; *Metagenomics/methods ; Dapsone/therapeutic use ; Rifampin/therapeutic use ; High-Throughput Nucleotide Sequencing/methods ; *Leprosy/diagnosis/drug therapy ; }, abstract = {BACKGROUND: Leprosy, a chronic infectious disease caused by Mycobacterium leprae, can lead to sensory deficits, motor impairment, disability, and social stigma, imposing a dual physical and psychological burden on patients. Early diagnosis and standardized treatment are therefore crucial. Metagenomic Capture Technology for Pathology (MetaPath) is a probe-capture-based high-throughput sequencing technology for pathogen nucleic acids, which holds promise for the early detection of Mycobacterium leprae in pathological specimens.

CASE SUMMARY: A 78-year-old male presented with erythematous, scaly and pruritic plaques on his trunk and extremities for over six months, worsening in the last two months. Initial differential diagnoses, including dermatomyositis, psoriasis, and mycosis fungoides, were not confirmed by laboratory or histopathological examinations. Subsequent, MetaPath revealed the presence of Mycobacterium leprae. Further history-taking revealed a prior contact with a leprosy patient and similar, undiagnosed symptoms dating back 5 years. The patient was finally diagnosed with paucibacillary leprosy (borderline tuberculoid type). Following isolation, referral, and initiation of standardized multidrug therapy (rifampicin and dapsone), the patient entered a long-term follow-up phase.

CONCLUSION: MetaPath successfully detected Mycobacterium leprae, providing a definitive molecular etiological evidence for this long-term undiagnosed case. This demonstrates the key advantage of MetaPath in the early diagnosis of challenging infectious diseases.}, } @article {pmid41698537, year = {2026}, author = {Wang, D and Ren, Z and Fu, W}, title = {Research on performance differences and mechanisms of sulfur-iron composite packing materials prepared from different iron sources in nitrogen and phosphorus removal from wastewater.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134220}, doi = {10.1016/j.biortech.2026.134220}, pmid = {41698537}, issn = {1873-2976}, mesh = {*Nitrogen/isolation & purification ; *Phosphorus/isolation & purification ; *Sulfur/chemistry ; *Iron/chemistry ; *Wastewater/chemistry ; Denitrification ; *Water Purification/methods ; Thiobacillus/metabolism ; Calcium Carbonate/chemistry ; }, abstract = {To address the structural instability and limited nutrient removal of traditional fillers, this study fabricated four novel composite fillers-incorporating zero-valent iron (Fe[0]), siderite (FeCO3), pyrite (FeS2), and calcium carbonate-via a melt-encapsulation method. Batch and continuous experiments systematically revealed distinct nitrogen and phosphorus removal mechanisms and microbial architectures among these fillers. While all exhibited denitrification potential, S-FeCO3 demonstrated superior shock resistance, maintaining 78.36-94.71 % nitrogen removal and reducing sulfate accumulation by 30.92 %. Conversely, S-Fe[0] caused significant nitrite accumulation (2.83 mg/L). For phosphorus, S-FeCO3 (80.53-84.49 %) significantly outperformed S-FeS2 (70.84-78.57 %) and S-Fe[0]. Microbial analysis showed a transition from Thiobacillus dominance in S-CaCO3 to Thiobacillus-Ferritrophicum co-dominance in iron-coupled systems. At the molecular level, sulfur-iron coupling up-regulated key denitrification genes (narG, nirS, nirK, nosZ) by accelerating electron transfer and relieving Fur-mediated repression, providing a systematic strategy for filler optimization in simultaneous nutrient removal processes.}, } @article {pmid41698575, year = {2026}, author = {Du, Y and Zhao, S and Hu, Y and Wang, X and Zhang, L and Lin, B and Wang, M and Xu, Q}, title = {Dietary selection of starters drives changes in growth performance, fermentation, hindgut microbiome, and metabolism in preweaning calves.}, journal = {Journal of dairy science}, volume = {109}, number = {4}, pages = {3970-3990}, doi = {10.3168/jds.2025-27473}, pmid = {41698575}, issn = {1525-3198}, mesh = {Animals ; Fermentation ; Cattle/growth & development/microbiology/metabolism/physiology ; *Animal Feed/analysis ; Starch/metabolism ; *Diet/veterinary ; Dietary Fiber/metabolism/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Animal Nutritional Physiological Phenomena ; Male ; }, abstract = {Early feeding of starter is an effective strategy for modulating gastrointestinal microbiota in newborn calves. However, the effects of starter nutrient composition on calf gut microbiota vary significantly. Although both fiber and starch are essential for early calf nutrition, each has distinct advantages and disadvantages. This study investigated how high-starch and high-fiber diets influence growth performance, hindgut health, and microbiota in calves. Two groups of calves were fed experimental starters with distinct nutrient compositions: a high-starch (HS, n = 8) diet containing 40.4% starch and 13.3% NDF, and a high-fiber (HF, n = 7) diet containing 18.8% starch and 30.5% NDF (DM basis). The experiment spanned calf ages 14 to 63 d, with weekly BW and body size measurements using calibrated scales and measuring tape. Serum was collected via jugular venipuncture for metabolic marker analysis. At trial end, animals were slaughtered to collect hindgut tissues and contents for immunoblotting, metagenomic sequencing, and metabolite analysis. We identified a fundamental trade-off that HS feeding shaped a Bifidobacterium-dominated enterotype, correlating with superior growth performance. In contrast, HF feeding selected for a Bacteroides-dominated, more mature microbiota and significantly enhanced gut barrier integrity by upregulating key tight junction proteins (ZO-1, claudin-1, and E-cadherin). Multiomics integration revealed that this trade-off was underpinned by different microbial metabolic pathways. The HS hindgut was enriched in enzymes and metabolites for carbohydrate and AA fermentation, driving growth. Conversely, the HF hindgut exhibited enhanced enzymatic capacity for fiber degradation (e.g., starch phosphorylase) and a metabolic profile favoring arginine biosynthesis and acetate production, which supported barrier function. This functional divergence was further evidenced in distinct short-chain fatty acid (SCFA) profiles. The HF group exhibited significantly elevated acetate and a trend for higher total SCFA concentration, whereas the HS group showed increased branched-chain fatty acids (isovalerate) and a trend toward higher butyrate and valerate proportions. Our findings provide a mechanistic model linking dietary carbohydrate source to a fundamental choice between growth optimization and gastrointestinal health in preweaning calves, offering novel insights for targeted nutritional strategies.}, } @article {pmid41698961, year = {2026}, author = {Mascarenhas, AC and Kantor, RS and Thissen, J and Kok, CR and Borucki, M and Morales, C and Messenger, S and Jaing, C and Wadford, DA}, title = {Metagenomic sequencing identifies potential respiratory pathogens in PCR-negative subset of surveillance samples.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41698961}, issn = {2045-2322}, support = {grant 6 Nu50CK000539//Centers for Disease Control and Prevention Epidemiology and Laboratory Capacity for Community Surveillance/ ; }, mesh = {Humans ; *Metagenomics/methods ; SARS-CoV-2/genetics/isolation & purification ; *COVID-19/virology/diagnosis/epidemiology ; *Respiratory Tract Infections/virology/diagnosis ; Viruses/genetics/isolation & purification ; Metagenome ; }, abstract = {Respiratory pathogens are a significant source of global morbidity, mortality, and economic burden, with the COVID-19 pandemic driving increased interest in and funding for respiratory disease surveillance. Syndromic panel multiplex nucleic acid amplification tests (NAATs) such as the BioFire Respiratory Panel (RP) are designed to identify the most common etiologic agents of respiratory illness. Untargeted metagenomic sequencing is a powerful tool for pathogen-agnostic detection, enabling the recovery of complete genomes for genomic epidemiology and variant tracking. In this study, we performed untargeted metagenomic sequencing of 305 samples previously negative by BioFire RP and SARS-CoV-2 testing and 26 samples that were previously positive by either of the diagnostic tests. A subset of 78 samples underwent probe-capture enrichment sequencing targeting human viruses. Using these methods, we identified human respiratory viruses in 16 of the 305 previously negative samples (5%). The most common viruses identified were Influenza C virus, Human Bocavirus, Rhinovirus A and C, and SARS-CoV-2. Consensus genomes were recovered for 14 viruses with > 90% coverage breadth, revealing closely related Bocavirus strains from neighboring counties and distinct Rhinovirus strains across samples. We also identified 21 samples with a single predominant bacterial or fungal species in the previous negative cohort. These findings underscore the challenges of identifying causal agents from multiplex NAAT-negative cases and highlight the utility of metagenomics for expanding the scope of pathogen surveillance.}, } @article {pmid41699049, year = {2026}, author = {Wu, LL and Liao, YJ and Peng, WH and Chen, LK and Huang, YC and Chen, CY and Juan, CC}, title = {FK506-binding protein-5 in high-fat diet-induced metabolic dysfunction-associated steatotic liver disease.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41699049}, issn = {2045-2322}, support = {108-2320-B-010-045-MY3, 110-2320-B-002-080-MY3, MOST 111-2314-B-A49-072, NSTC 112-2314-B-A49-028-MY3, NSTC 112-2740-B-A49-002, NSTC 113-2740-B-A49-003, NSTC 113-2321-B-A49-014-, NSTC 114-2321-B-A49-004 -, NSTC 114-2740-B-A49-003//Ministry of Science and Technology, Taiwan/ ; MOST 106-2320-B-010-009-MY3//Ministry of Science and Technology, Taiwan/ ; CI-110-22 and CI-111-24//Yen Tjing Ling Medical Foundation/ ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; Mice ; Mice, Knockout ; Male ; Tacrolimus Binding Protein 5 ; Gastrointestinal Microbiome ; *Fatty Liver/metabolism/etiology ; Liver/metabolism/pathology ; Obesity/metabolism ; *Non-alcoholic Fatty Liver Disease/metabolism/etiology ; Mice, Inbred C57BL ; *Metabolic Diseases/metabolism ; }, abstract = {A high-fat diet (HFD) alters the gut microbiota (GM), impairs metabolic efficiency, and increases gut permeability and inflammation. Obesity and insulin resistance are associated with GM dysbiosis. The GM is strongly associated with metabolic disorders and fatty liver disease. The co-chaperone protein FK506-binding protein-5 (FKBP5) regulates several vital cellular processes. Although FKBP5 has been implicated in stress-related disorders, it has not been directly linked to HFD-induced metabolic fatty liver disease. This study aimed to elucidate how FK506 binding protein 5 impairment affects the GM in HFD-induced metabolic dysfunction-associated fatty liver disease and metabolic dysfunction-associated steatotic liver disease (MASLD). Wild-type and FKBP5-knockout (FKKO) mice were fed a normal chow diet or a high-fat diet for 16 weeks. Mouse GM was examined using 16 S rRNA metagenomic analysis. The number of gut-liver immune cells was measured using flow cytometry. HFD-induced hepatic steatosis and inflammation were prevented in FKBP5-deficient mice. FKKO animals showed higher butyric acid levels and GM resistance to diet-induced obesity alterations according to 16 S ribosomal rRNA gene analysis and displayed an HFD-specific gut-liver immunological response that maintained gut barrier failure and mucosal immunity, which are important for GM homeostasis. FKBP5 helps the GM address inadequate immunological responses, including lower gut and liver CD11b[+]Ly6C[+] monocytes and neutrophils, and protects against obesity by improving the GM response to HFD-induced MASLD. FKBP5 protects against HFD-induced MASLD through metabolic coordination between the gut barrier and intrahepatic immunity.}, } @article {pmid41699270, year = {2026}, author = {Bashiardes, S and Heinemann, M and Adlung, L and Valdés-Mas, R and Mahdi, JA and Nobs, SP and Tuganbaev, T and Yamada, T and Horn, M and Mor, U and Cohen, Y and Israel, S and Korem, M and Oster, Y and Olshtain-Pops, K and Orenbuch-Harroch, E and Arslan, MD and Molina, S and Zur, M and Eliyahu-Miller, S and Bukimer, A and Federici, S and Dori-Bachash, M and Amar, N and Elbirt, D and Cohen-Poradosu, R and Turner, D and Hershcovici, T and Vainer, E and Stettner, N and Harmelin, A and Gebremeskel, H and Kebede, Y and Schmidt, S and Zmora, N and Dhamodaran, A and Puschhof, J and Bentwich, Z and Shapiro, H and Amit, I and Elinav, H and Elinav, E}, title = {Human immunodeficiency virus-associated gut microbiome impacts systemic immunodeficiency and susceptibility to opportunistic gut infection.}, journal = {Nature microbiology}, volume = {11}, number = {3}, pages = {690-703}, pmid = {41699270}, issn = {2058-5276}, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/immunology ; Dysbiosis/immunology/microbiology ; Mice ; Fecal Microbiota Transplantation ; *HIV Infections/immunology/microbiology/complications/virology ; Feces/microbiology ; *Opportunistic Infections/immunology/microbiology ; Ethiopia ; Female ; CD4-Positive T-Lymphocytes/immunology ; Male ; Disease Susceptibility ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Cryptosporidiosis/immunology ; CD4 Lymphocyte Count ; Cohort Studies ; }, abstract = {The gut microbiome of people living with human immunodeficiency virus (PLWH) has been characterized, but its role in influencing host immunity and associated clinical features are unclear. Here we used shotgun metagenomics to characterize the faecal microbiome of two geographically distinct cohorts of PLWH and healthy controls in Israel and Ethiopia. We uncovered disease-specific, geographically divergent microbial patterns including a shift from Bacteroides to Prevotella species in an Israeli cohort and multiple Enterobacteriaceae species including Escherichia coli and Klebsiella quasivariicola in an Ethiopian cohort. We identified correlations between human immunodeficiency virus-related dysbiosis and the extent of systemic immunodeficiency, as proxied by peripheral CD4[+] T cell counts. Faecal microbiome transplantation from PLWH with high peripheral CD4[+] T cell counts induced colonic epithelium-associated CD4[+] T cells in germ-free or antibiotic-treated recipient mice. Impaired epithelium-associated lymphocyte induction in recipients of faecal microbiome transplantation from severely immunodeficient PLWH donors was associated with altered protection from Cryptosporidium parvum infection. Collectively, our results suggest a link between systemic immunodeficiency and associated intestinal dysbiosis in PLWH, resulting in impaired gut mucosal immunity.}, } @article {pmid41699578, year = {2026}, author = {Wu, H and Li, N and Yang, S and Qiu, J and Zhang, M and Wang, L and Gao, R and Wu, L and Yu, Q and Cheng, X}, title = {Prevotella denticola promotes caries by inducing oral microbial dysbiosis.}, journal = {BMC oral health}, volume = {26}, number = {1}, pages = {}, pmid = {41699578}, issn = {1472-6831}, support = {82170937//the National Nature Science Foundation of China/ ; 81800955//the National Nature Science Foundation of China/ ; (No. 2025GH-YBXM-033)//External Cooperation Areas of the Key Research and Development (R&D) Program of Shaanxi Province/ ; LCB202408//the Special Project of the National Clinical Research Center for Oral Diseases/ ; }, abstract = {BACKGROUND: While the role of oral microbial dysbiosis in cariogenicity is widely appreciated, it remains unclear whether some resident microorganisms are active contributors in this process. Recently, increasing evidence showed that Prevotella spp. are associated with caries whereas the identified roles at species level remain undefined. This study aimed to analyze the effects of Prevotella denticola on microbial ecosystems and pathogenic mechanisms associated with caries. METHODS: Here, we applied metagenomics to supragingival microbiota (dental plaque) samples from 62 adults to identify disease-relevant species. P. denticola was highly enriched in caries-affected individuals (P < 0.001). The dynamic biofilm formation, spatial arrangement, and cariogenic activity of oral biofilms with or without P. denticola were examined via multiscale/computational imaging and virulence assays. RESULTS: P. denticola, exerting a previously unidentified mechanism in supragingival biofilms, promoted oral biofilm cariogenicity through altering the microbial ecosystem and biofilm structure. In vivo studies demonstrated that P. denticola induced the formation of a more cariogenic biofilm on supragingival tooth surfaces. CONCLUSIONS: Collectively, P. denticola has an ecological impact on the mixed oral microbiota and disrupts microbial equilibrium. These findings indicated that P. denticola infection plays a critical role in caries occurrence.}, } @article {pmid41699596, year = {2026}, author = {Hu, S and Chen, T and Liu, X and Wu, Z and Wang, X}, title = {Effects of aerobic exercise on inflammation and gut microbiota in obese mice: a metagenomic and metabolomic analysis.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41699596}, issn = {1479-5876}, support = {2025AFB925//Natural Science Foundation of Hubei Province/ ; XZ202501ZR0140//Key project of Natural Science Foundation of Tibet Autonomous Region/ ; SNSBJKJJHXM2024023//Shannan Science and Technology Plan Project/ ; Yz2024179//National Resource Center for the First-Year Experience and Students in Transition, University of South Carolina/ ; JY2024066//the University-level teaching and research project of Yangtze University/ ; (25Y117)//Philosophical and Social Science Research Project of the Education Department of Hubei Province/ ; 2025csz005//Key Project of Social Sciences Fund of Yangtze University/ ; }, abstract = {BACKGROUND: Aerobic exercise can ameliorate insulin resistance (IR). However, the mechanism by which aerobic exercise regulates the gut microbiome to ameliorate IR and obesity remains unexplored.

METHODS: Obese models were established by feeding C57BL/6 male mice a high-fat diet. A total of 26 mice were randomly divided into control group (group A, N = 8) and high-fat diet group (HFD group, N = 18). Successfully modeled mice were further assigned to model group (group B, N = 8) and exercise group (group C, N = 8). Group C underwent a 6-week treadmill exercise program (12 m/min, 60 min per day, 5 days per week). After intervention, colon tissue morphology was observed through hematoxylin-eosin staining, serum lipids and inflammatory indicators levels were detected by ELISA. The changes in the intestinal microbiota of the mice were also examined using metagenomic sequencing and UPLC-MS non-targeted metabolomics.

RESULTS: Compared with the group A, the body weight, TC, TG, LDL-C, blood glucose, insulin, and IR in the group B significantly increased (P < 0.01), while the levels of pro-inflammatory cytokines TXNIP, TNF-α, NLRP3, IL-1β, and IL-18 significantly increased (P < 0.05 or P < 0.01). Compared with the group B, aerobic exercise reduced the body weight, TC, blood glucose, insulin, IR, TXNIP, TNF-α and other indicators in obese mice (P < 0.05 or P < 0.01). Moreover, aerobic exercise can regulate the imbalance of the intestinal flora in obese mice and ameliorate the disorder of metabolites. The metabolic pathways including arachidonic acid metabolism and histidine metabolism showed the most significant differences after the intervention of aerobic exercise.

CONCLUSIONS: In conclusion, aerobic exercise can ameliorate glucose and lipid metabolism, IR, inflammatory response, and regulate the intestinal microecology and metabolic disorders in obese mice. The mechanism may be closely related to enhancing the diversity of intestinal flora, regulating the metabolism of arachidonic acid and histidine.}, } @article {pmid41700136, year = {2026}, author = {Hubot, N and Giering, SLC and Orel, N and Klun, K and Herndl, GJ and Hohaus, F and Lucas, CH and Tinta, T}, title = {Jellyfish mucus-derived organic matter as a source of labile nutrients for the ambient microbial community.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20784}, pmid = {41700136}, issn = {2167-8359}, mesh = {Animals ; *Scyphozoa/metabolism/chemistry ; Seawater/microbiology/chemistry ; *Mucus/chemistry/metabolism ; Nitrogen/metabolism/analysis ; *Nutrients/metabolism ; *Microbiota ; Amino Acids/metabolism ; *Dissolved Organic Matter/metabolism ; Carbon/metabolism/analysis ; }, abstract = {Jellyfish are increasingly recognized as a significant contributor to marine organic matter (OM) on a global scale, with implications for ecosystem dynamics. While the role of jellyfish detritus in microbial nutrient cycling has been explored, the contribution of OM released by live jellyfish-primarily as mucus (hereinafter referred to as mucus-associated OM, or MAOM)-remains understudied. This study investigates the release of organic and inorganic nutrients through MAOM from live jellyfish and their effects on ambient microbial communities in the northern Adriatic Sea using a series of leaching and short-term microcosm experiments. Our results show that per gram of MAOM dry weight from the jellyfish Aurelia spp, approximatively 2 µmol of phosphate, 4 µmol of dissolved inorganic nitrogen, 18 µmol dissolved organic nitrogen, 134 µmol of dissolved organic carbon and 15 µmol of dissolved free amino acids can be released in the ambient seawater in 24 h. Almost half of the OM is released as dissolved OM (DOM), of which a substantial part is low molecular weight (<1 kDa) molecules. During the first 20 h, the DOM fraction of MAOM was rapidly consumed by the ambient microbial community without a corresponding increase in biomass, likely due to nitrogen limitation. In the subsequent 22 h, microbial growth accelerated to 0.19 ± 0.03 h[-1] until phosphate became limiting, leading to a sharp decline in microbial production. Our metagenomics analysis revealed that the MAOM-degrading microbial community, dominated by Gammaproteobacteria opportunistic copiotrophs, exhibited increased functional capacity for nutrient assimilation and OM degradation, particularly in the transport and metabolism of amino acids (particularly glycine and taurine) and phosphorus. These traits mirror those found in detritus-degrading microbial communities, suggesting that jellyfish blooms promote the emergence of specialized microbial consortia with shared metabolic capabilities. Taken together, our findings highlight that live jellyfish, through the release of OM, play an active and previously underappreciated role in shaping ambient microbial community dynamics and nutrient fluxes in marine systems affected by jellyfish blooms.}, } @article {pmid41700755, year = {2026}, author = {You, C and Ren, P and Guan, Y and Gong, K and Hua, Z and Zhou, W and Mei, X and Wang, Y and Wang, X and Xu, Y and Shen, Q and Wei, Z}, title = {Forecasting Root Rot Disease through Predictive Microbial Functional Profiling.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {23}, pages = {e22628}, pmid = {41700755}, issn = {2198-3844}, support = {2022YFC3501501//National Key Research and Development Program of China/ ; GuiKe AA24010003//Guangxi Science and Technology Program/ ; KJYQ2025034//Fundamental Research Funds for the Central Universities/ ; BK20240194//Natural Science Foundation of Jiangsu Province/ ; 42377118//National Natural Science Foundation of China/ ; 42277113//National Natural Science Foundation of China/ ; BE2022423//Jiangsu Carbon Peak & Carbon Neutrality Science and Technology Innovation Special Fund/ ; 2024M760612//China Postdoctoral Science Foundation/ ; }, mesh = {*Soil Microbiology ; *Plant Roots/microbiology ; *Plant Diseases/microbiology/genetics ; Rhizosphere ; Machine Learning ; Metagenome/genetics ; *Microbiota/genetics ; Forecasting ; }, abstract = {Early diagnosis of soil-borne diseases like root rot is a long-standing challenge in agriculture. While microbial functional genes are recognized as potent indicators of soil healthy, their application has been primarily limited to current or past soil conditions. Here, we demonstrate that microbial functional genes can transition from descriptive indicators to reliable predictive biomarkers. By analyzing 199 paired metagenomes from healthy and diseased medicinal plants rhizosphere soil samples, we identified a conserved core set of functional genes, specifically those governing biofilm formation, stress response, and plant-microbe mutualism that are robustly associated with root rot disease. To bridge the gap between discovery and field application, we developed a framework that integrates cost-effective qPCR assay for these key genes and fused their abundance data with machine learning. This model achieved over 80% accuracy in predicting disease onset from independent, pre-symptomatic soil samples, identifying risks long before visible symptoms of infection appeared. Our findings suggest a practical path for moving beyond simple microbial correlations toward an active forecasting tool. By positioning microbial functional genes at the core of disease management, this framework provides a targeted approach for mitigating soil-borne risks and supporting sustainable agricultural practices.}, } @article {pmid41700856, year = {2026}, author = {Zhang, R and Poulain, AJ and Pu, Q and Liu, J and Abdelhafiz, MA and Feng, X and Meng, B and Grégoire, DS}, title = {Methane cycling microbes are important predictors of methylmercury accumulation in rice paddies.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {3}, pages = {e0202825}, pmid = {41700856}, issn = {1098-5336}, support = {[2024]013//Guizhou Provincial Major Scientific and Technological Program/ ; RGPIN-2022-04891//Natural Sciences and Engineering Research Council of Canada/ ; 42394092//National Natural Science Foundation of China/ ; }, mesh = {*Methylmercury Compounds/metabolism/analysis ; *Oryza/growth & development/microbiology ; *Methane/metabolism ; *Soil Pollutants/metabolism/analysis ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Mercury/metabolism ; Rhizosphere ; }, abstract = {Microbial production of methylmercury from inorganic mercury in rice paddies poses health risks to consumers of this essential dietary staple. Although mercury-methylating communities are well characterized, the microbial guilds contributing to methylmercury accumulation in rice paddies remain unclear. Here, we collected paddy soils across a mercury concentration gradient throughout the rice-growing season to identify microbial and environmental factors influencing methylmercury dynamics. We show that hgcA gene abundance, the key gene required for methylation, was not a significant predictor of methylmercury concentration in paddy soils. We also show that the merB gene abundance correlated with methylmercury in mercury-polluted rhizosphere samples. Methane cycling genes were actively expressed, and their beta-diversity was significantly associated with methylmercury levels. Methanogen abundance correlated with higher methylmercury under elevated total mercury concentrations. Analysis of the methanotroph-associated mbnT gene, implicated in demethylation, revealed an unexpected positive correlation with methylmercury. Multiple regression and machine learning models converged on mercury bioavailability and methanogen/methanotroph abundances as key predictors of methylmercury, with methanogen-associated hgcA gene abundance and methanogen-methanotroph interactions highlighted under flooded, low-redox conditions. These findings suggest that methane-cycling microbes play key roles in methylmercury cycling dynamics and point to management strategies that could simultaneously mitigate mercury pollution and greenhouse gas emissions.IMPORTANCEMethylmercury is a microbially derived neurotoxin that accumulates in the food staple rice (Oryza sativa). Mitigating the health effects of methylmercury exposure requires predicting mercury cycling dynamics in rice paddies. This task is challenging because of the complex interplay of microbial and environmental factors. Our study coupled genomic and geochemical measurements with machine learning models to identify the key biological indicators of methylmercury accumulation. We demonstrated that the abundance of methanogens and methanotrophs is a major microbial predictor of methylmercury variability. This predictive framework, which considers the interactions between these coupled microbial guilds, offers greater power than methods relying only on mercury methylation genes. These findings inform better management and remediation strategies for rice paddies, offering a path to reduce methylmercury exposure and mitigate greenhouse gas emissions.}, } @article {pmid41702408, year = {2026}, author = {Hernández-Vázquez, A and Garcia-Arellano, H and González-Cervantes, RM and López-Pérez, M and Soto, LMH and Meza, JAC and Aguirre-Garrido, JF}, title = {Study of Microbial Communities in the Soda Lake of Isabel Island: Identification of Polyhydroxybutyrate (PHB) Degrading Enzymes.}, journal = {Environmental microbiology reports}, volume = {18}, number = {1}, pages = {e70279}, pmid = {41702408}, issn = {1758-2229}, mesh = {*Lakes/microbiology ; Phylogeny ; *Hydroxybutyrates/metabolism ; *Bacteria/classification/genetics/enzymology/isolation & purification ; Polyhydroxybutyrates ; Metagenome ; Geologic Sediments/microbiology ; *Carboxylic Ester Hydrolases/genetics/metabolism ; *Polyesters/metabolism ; *Microbiota/genetics ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Crater Lake (Isabel Island, Mexico) is a meromictic, stratified, haloalkaline system. To identify and characterise PHB depolymerases across the vertical physicochemical gradients of the lake, we analysed seven metagenomes from the water column (0-23 m), one sediment metagenome, and the genomes of two organisms (HB105m and VN105m) isolated from 5 m. Taxonomic profiles revealed vertical stratification: Actinobacteriota and Cyanobacteriota dominated surface waters, while Pseudomonadota, Bacillota, and Bacteroidota prevailed in deeper layers and sediments. Alpha-diversity indices peaked at 5 and 20 m and declined at 23 m. We identified 16 putative PHB depolymerases spanning a broader phylogenetic range than previously documented for haloalkaline ecosystems. These included homologues affiliated with Vreelandella, Thiomicrorhabdus, Chloroflexota, Candidatus Cloacimonadota, and Desulfobacterales. The structural variation observed in lipase-box motifs and signal peptides suggests functional differentiation linked to redox and oxygen gradients across depths. Phylogenetic analysis of predicted and reference enzymes showed depth-specific clustering, with extracellular depolymerases predominant in oxic layers and intracellular forms more common in microoxic-anoxic zones. Overall, our results expand the known diversity of PHB-degrading lineages in extreme environments and highlight several candidate enzymes with potential biotechnological relevance for future experimental characterisation.}, } @article {pmid41702430, year = {2026}, author = {Nozaki, T and Kobayashi, Y and Ikeda, M and Shigenobu, S}, title = {Symbiont replacement and subsequent genome erosion reshape a dual obligate aphid symbiosis.}, journal = {Proceedings. Biological sciences}, volume = {293}, number = {2065}, pages = {}, doi = {10.1098/rspb.2025.2484}, pmid = {41702430}, issn = {1471-2954}, support = {//Japan Society for the Promotion of Science/ ; }, mesh = {*Aphids/microbiology/physiology ; *Symbiosis ; Animals ; *Buchnera/genetics/physiology ; *Serratia/genetics/physiology ; *Genome, Bacterial ; Phylogeny ; }, abstract = {Many insects rely on obligate microbial symbioses, often involving multiple partners. Although symbiont replacement is well-documented, how newly acquired and resident obligate symbionts adapt after such events remains unclear. Here, we investigate the dual obligate symbiosis of the aphid Lachnus tropicalis, where an ancestral Serratia lineage was replaced by a newly acquired Serratia lineage while the primary symbiont Buchnera remained. Our metagenomic sequencing yielded complete genomes of Buchnera (0.42 Mb) and Serratia (2.8 Mb), revealing developing metabolic complementarity. Although the Serratia genome retained abundant gene sets for amino acid synthesis, it also contained pseudogenes in leucine and methionine pathways, which would be compensated for by Buchnera or the host. Comparison with Lachnus roboris, which harbours the ancestral Serratia lineage, showed that the newly acquired Serratia in L. tropicalis exhibits identical tissue localization and vertical transmission pattern, suggesting the smooth succession of the prior microniche. Notably, Buchnera in L. tropicalis exhibited a slightly more degenerated genome than its counterpart in L. roboris, indicating that symbiont replacement can accelerate gene loss even in ancient symbionts. Overall, our findings provide new insights into the dynamics of novel mutualism establishment and highlight symbiont replacement as a driver of host-symbiont co-evolution.}, } @article {pmid41702469, year = {2026}, author = {Qin, L and Wu, D and Yang, J and Song, Y and Shen, C}, title = {Macro-scale resuspension governs gene-scale mechanisms of phosphorus cycling in a shallow lake.}, journal = {Environmental research}, volume = {296}, number = {}, pages = {124040}, doi = {10.1016/j.envres.2026.124040}, pmid = {41702469}, issn = {1096-0953}, mesh = {*Phosphorus/metabolism/analysis ; *Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; Bacteria/genetics/metabolism ; Alkaline Phosphatase/metabolism ; China ; }, abstract = {Internal phosphorus loading from sediments is becoming a major barrier to lake restoration, yet the mechanisms governing phosphorus dynamics under sediment resuspension remain poorly understood. Using controlled laboratory experiments with sediments collected from Lake Yangcheng, we examined how disturbance intensity, frequency, and duration regulate phosphorus fractions, alkaline phosphatase activity (APA), microbial community composition, and functional gene expression. Our results revealed that low-intensity disturbance, especially under high-frequency intermittent disturbance, enhanced organic phosphorus mineralization, characterized by elevated phosphate, increased APA and strong upregulation of phoB and phoX genes. Metagenomic sequencing results further showed that these conditions supported high richness of phosphorus-solubilizing bacteria (PSB), sustaining biologically mediated conversion of organic phosphorus to bioavailable phosphate. In contrast, high-intensity disturbance shifted phosphorus dynamics toward particulate dominance, rapidly satisfying microbial phosphate demand and suppressing phosphatase expression and enzymatic mineralization. Across all disturbance treatments, Pseudomonadota remained the dominant PSB phylum, and phoB consistently exhibited the highest abundance among functional genes, underscoring their central roles in phosphorus cycling. In all, our experiments demonstrate that disturbance intensity determines whether internal phosphorus loading is governed primarily by microbial or physical processes. This study highlights that optimizing resuspension patterns, rather than simply minimizing total disturbance, may provide a more effective strategy for controlling internal loading and reducing algal bloom risk in shallow urban lakes.}, } @article {pmid41702480, year = {2026}, author = {Wang, B and Jiang, Y and Li, D and Wang, C}, title = {Enhancing the diagnosis accuracy of Chlamydia psittaci infection via metagenomic next-generation sequencing.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {139}, number = {}, pages = {105895}, doi = {10.1016/j.meegid.2026.105895}, pmid = {41702480}, issn = {1567-7257}, mesh = {*Chlamydophila psittaci/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Psittacosis/diagnosis/microbiology ; *Metagenomics/methods ; }, abstract = {Metagenomic next-generation sequencing (mNGS) is an innovative diagnostic technique that integrates high-throughput sequencing with bioinformatics analysis. Recently, its unbiased approach, broad pathogen coverage, and rapid turnaround have led to its expanded use in diagnosing infectious diseases. This is particularly true for atypical bacterial pathogens such as Chlamydia psittaci, Chlamydia pneumoniae, Mycoplasma pneumoniae, and Legionella spp., for which mNGS has demonstrated significant diagnostic utility. C. psittaci, a highly pathogenic obligate intracellular bacterium, can cause severe community-acquired pneumonia (CAP). Its virulence is attributed to unique genomic pathogenicity islands, which encode both a specialized secretion system (such as the Type III Secretion System) and effector proteins like the Chlamydial Protease-like Activity Factor (CPAF), coupled with its capacity for rapid intracellular replication. Furthermore, its close genetic similarity to C. pneumoniae complicates differentiation by standard Polymerase Chain Reaction (PCR) assays. This review examines the advancements in using mNGS to diagnose C. psittaci infections in clinical settings and discusses the remaining challenges. The excessive use of antibiotics in clinical practice is still a common problem. Through its unbiased detection, mNGS can accurately identify mixed infections, thereby providing a microbiological basis for targeted antibiotic therapy. Our compilation of case reports and studies from the last five years indicates that mNGS effectively assists clinicians in promptly adjusting antibiotic regimens and holds great potential for the clinical identification of chlamydial co-infections.}, } @article {pmid41702518, year = {2026}, author = {Wang, X and Huo, X and Hu, H and Wang, Y and Cheng, W and Wang, Y and Sun, C and Wu, X and Chen, Y}, title = {Metagenomic mining and functional reconstitution of hexanoic acid biosynthetic enzymes from Baijiu pit bottom.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134231}, doi = {10.1016/j.biortech.2026.134231}, pmid = {41702518}, issn = {1873-2976}, mesh = {*Caproates/metabolism ; Saccharomyces cerevisiae/metabolism/genetics ; *Metagenomics/methods ; *Data Mining ; 3-Hydroxyacyl CoA Dehydrogenases/metabolism ; }, abstract = {Hexanoic acid is a key flavor compound in Baijiu and a valuable platform chemical, yet its efficient biosynthesis remains challenging. To overcome the carbon chain elongation bottleneck in the reverse β-oxidation (RBO) pathway in Saccharomyces cerevisiae, this study explored the metagenomic resource of a hexanoic acid-producing microbial community from the bottom of Jiang-flavor Baijiu pit. Three enriched hexanoic acid-producing consortia were obtained, all co-producing butanoic, hexanoic, and octanoic acids. Metagenomic analysis showed that while microbial compositions differed, the consortia shared similar core functional enzymes. Further correlation analysis identified 3-hydroxyacyl-CoA dehydrogenase (HBD) and acetate CoA-transferase (CAT) as key enzymes positively correlated with hexanoic acid synthesis. These enzymes were then expressed in an engineered RBO-pathway yeast strain. Expression of CAT-1 increased butanoic and hexanoic acid production by 25% and 34%, respectively, marking the first application of CAT in enhancing chain elongation in yeast. In summary, this study innovatively identified the key enzyme CAT from the microbiota of Jiang-flavor Baijiu pit bottom and achieved efficient hexanoic acid synthesis through heterologous expression. This work not only offers a strategy for mining high-performance enzymes but also provides theoretical support and technical references for the efficient biosynthesis of hexanoic acid.}, } @article {pmid41702524, year = {2026}, author = {Lips, S and Schmitt-Jansen, M and Borchert, E}, title = {Metagenomic analyses of the plastisphere reveals a common functional potential across oceans.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {395}, number = {}, pages = {127830}, doi = {10.1016/j.envpol.2026.127830}, pmid = {41702524}, issn = {1873-6424}, mesh = {Biofilms ; *Plastics/analysis ; Metagenomics ; *Metagenome ; *Bacteria/genetics ; Oceans and Seas ; *Seawater/microbiology ; Plankton ; }, abstract = {Trillions of plastic particles have accumulated in the oceans, covered by microbial biofilms (termed 'plastisphere') whose functional potential remains underexplored. We evaluated as one of the first of its kind genome-resolved bacterial metagenomes of the plastisphere from the North Atlantic and North Pacific garbage patches and compared their structure and functional potential to ambient plankton. Our data revealed a characteristic genetic potential of the plastisphere with functionally equivalent traits across both oceans. We found more coding genes, bigger genomes and higher GC-content in the plastisphere in comparison to the surrounding plankton community, despite residing in the same environment, reflecting an increased metabolic capacity in the plastisphere. An analysis of 340 functional genes confirmed that the plastisphere consists of microorganisms with a higher potential for nutrient metabolism, metabolize a wider range of carbon sources, attenuate radicals, fix their own nitrogen and use alternative energy sources like anoxygenic photosynthesis. Our results suggest that the overriding factor for the high functional similarity of the plastisphere in both oceans is the habitat for biofilm formation with the potential to support mutualism and nutrient sharing making genomic streamlining as found in plankton, unnecessary. Consequently, increasing plastic pollution promotes the expansion of a new functional unit at the surface of the oligotrophic oceans with various roles in biogeochemical cycles.}, } @article {pmid41702865, year = {2026}, author = {Zhang, Z and Li, Z and Chen, X and Zu, Y and Li, S and Liang, B and Ho, SH and Wang, A}, title = {Simultaneous Trichloroacetate Dechlorination Metabolism and Nitrogen Fixation in Nitrogen-Limited Aquifers.}, journal = {Environmental science & technology}, volume = {60}, number = {8}, pages = {6341-6352}, doi = {10.1021/acs.est.5c16767}, pmid = {41702865}, issn = {1520-5851}, mesh = {Nitrogen/metabolism ; *Nitrogen Fixation ; *Groundwater ; *Trichloroacetic Acid/metabolism ; Halogenation ; }, abstract = {Haloacetates, particularly trichloroacetate (TCAA), are pervasive contaminants, yet their biotransformation in anoxic, nutrient-limited environments remains poorly understood. Here, we elucidate a geographically widespread attenuation of haloacetates in nutrient-limited aquifers by field surveys across six Chinese provinces. Enrichment cultures metabolized TCAA as the sole carbon and energy source. Major metabolites (oxalate, acetate, CO2) indicated complete hydrolytic dechlorination accompanied by fermentation and mineralization. Isotope labeling and chemical probe studies confirmed the simultaneous occurrence of TCAA dechlorination and nitrogen fixation under fixed nitrogen-limited conditions. Integrated metagenomic, metabolomic, and transcriptional analyses demonstrated nitrogen-regulated metabolic reconfiguration. Acetyl-CoA potentially associated with TCAA metabolism may enter the TCA cycle under nitrogen-limited conditions. Dehalogenase gene (had) homologues extensively co-occurred with homologues of nitrogenase genes (nifHDK) in oligotrophic environments. Potential cross-feeding interactions among unclassified Azospira sp., Ralstonia pickettii, and Azospira inquinata mediated carbon-nitrogen intermediate exchange. This study identifies a previously unrecognized process that enables simultaneous TCAA detoxification and nitrogen acquisition in oligotrophic aquifers, thereby proposing an energy-conserving and ecologically adaptive strategy for haloacetate bioremediation.}, } @article {pmid41702980, year = {2026}, author = {Paoli, JE and Aung, O and Lilak, AA and Maw, MT and Cleary, NG and Watto, E and Hassell, J and Win, YT and Thein, WZ and Evans, TS and Valitutto, M and Goldstein, T and Johnson, CK and Mazet, JA and Fleischer, R and VanTassel, N and Subramaniam, K and Anderson, BD and von Fricken, ME and Mavian, CN and Murray, S}, title = {Detection of Wencheng shrew virus and cardiovirus from small mammals in Myanmar.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41702980}, issn = {2045-2322}, support = {AID-OAA-A-14-00102 , GHN-A-OO-09-0001000//United States Agency for International Development/ ; }, abstract = {UNLABELLED: Myanmar is one of the most biodiverse countries from a species perspective in Southeast Asia, yet there is minimal published data on zoonotic viruses in small mammals. From July 2017 to August 2018, wildlife sampling was conducted at human-animal interfaces at sites in the Yangon Region and Kayin State. To investigate virus diversity of commensal rodents and shrew, rectal swabs were collected from mice (Mus sp., N = 3), rats (Rattus norvegicus, N = 80; Rattus rattus, N = 6), and Southeast Asian shrews (Crocidura fuliginosa, N = 8). RNA was extracted from rectal swabs, made into cDNA, and subjected to metagenomic next-generation sequencing followed by phylogenetic analysis for virus identification and taxonomic placement. The study provides the first detection of Wencheng shrew virus (WESV) in Myanmar and the first report in C. fuliginosa. A novel member of the genus Cardiovirus was also detected in R. norvegicus and clustered with Cardiovirus theileri sequences previously identified in wild rats from China. Further characterization of viruses circulating in small mammals will help inform public health officials of potential zoonotic risks in a region with virus surveillance gaps and ongoing land use change which may be increasing the risk of zoonotic disease emergence.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-38406-w.}, } @article {pmid41703237, year = {2026}, author = {Ariyo, S and Sanusi, IO and Veerabhadrappa, K and Tenywa, MG and Olutona, GO and Onohuean, H}, title = {Deterministic and probabilistic health risk assessment of heavy metals in liquid herbal cough formulations from Western Uganda.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41703237}, issn = {2045-2322}, mesh = {*Metals, Heavy/analysis ; Uganda ; Risk Assessment ; Humans ; Spectrophotometry, Atomic ; *Cough/drug therapy ; Drug Contamination ; Monte Carlo Method ; }, abstract = {This study investigated the concentrations and human health risks (carcinogenic and non-carcinogenic) associated with heavy metals in liquid herbal cough formulations obtained from the Western Region of Uganda. Twelve brands of registered (government authority) herbal cough formulations from reputable pharmacies were obtained and analysed. The mixtures were acid digested prior to Atomic Absorption Spectroscopy (AAS) analysis to quantify cadmium (Cd), copper (Cu), iron (Fe), lead (Pb), nickel (Ni), and zinc (Zn) in the herbal formulations, followed by human health risk assessment, using two different approaches: deterministic and probabilistic (Monte Carlo simulation). The results showed significant variations in heavy metal concentrations, with Cu, Fe, Ni, Cd, Pb, and Zn ranging from 0.020 to 1.272, not detected (ND) to 6.734, ND to 0.129, 0.002 to 0.051, ND to 0.190, and 0.043 to 0.527 mg/L, respectively, within the World Health Organization limit (WHO). Multivariate statistical analysis revealed that anthropogenic activities were the major source of heavy metal contamination. The hazard index (HI) values obtained ranged from 7.0 × 10[-4] to 2.59 × 10[-2] in children and 6.0 × 10[-4] to 2.49 × 10[-2] in adults, indicating extremely low non-carcinogenic risk (HI < 1) of exposure to heavy metals. Similarly, the incremental lifetime carcinogenic risks (ILCRs) of Ni, Pb, and Cd for both the children and adults were below the acceptable limit of 1.0 × 10[-4], indicating no carcinogenic health risk. Moreover, the probabilistic risk assessment revealed that Pb and Cd had less than a 0.01% chance of exceeding the WHO limit (negligible risk). Findings from this study indicate that heavy metal concentrations in the brands of herbal cough formulations from Western Uganda are below the safety thresholds and are safe for consumption under realistic exposure conditions.}, } @article {pmid41703795, year = {2026}, author = {Pais, ACS and Ribeiro, TB and Coscueta, ER and Salsinha, AS and Pintado, MM and Silvestre, AJD and Santos, SAO}, title = {Phenolic compounds' impact on gut microbiota: Insights from in vitro batch fecal fermentation for composition modulation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {228}, number = {}, pages = {118167}, doi = {10.1016/j.foodres.2025.118167}, pmid = {41703795}, issn = {1873-7145}, mesh = {*Feces/microbiology ; Humans ; *Fermentation ; *Gastrointestinal Microbiome/drug effects ; *Phenols/pharmacology/metabolism ; Ellagic Acid/pharmacology/metabolism ; Flavanones/pharmacology/metabolism ; Fatty Acids, Volatile/metabolism/analysis ; Bacteria/drug effects/metabolism/growth & development/classification ; Phloroglucinol/pharmacology/metabolism ; Prebiotics ; }, abstract = {The relationship between phenolic compounds and gut microbiota (has been widely studied to explore the health benefits of these bioactive dietary compounds. Phenolic compounds are metabolized by gut microbiota, while also modulating its composition. However, the individual effects of these compounds on human gut microbiota remain underexplored. To address this, three phenolic compouds-ellagic acid, naringenin, and phloroglucinol-underwent in vitro batch fermentation with fecal samples from healthy donors. Samples were analyzed through 16S metagenomics sequencing, and short-chain fatty acids (SCFAs) were measured using gas chromatography. Results showed that ellagic acid and phloroglucinol had prebiotic properties, producing SCFAs like acetic, propanoic, and butyric acids and promoting the growth of beneficial bacteria such as Lactobacillus and Bifidobacterium. In contrast, naringenin was linked to the growth of pathogenic genera like Escherichia and Salmonella. This study provides valuable insights into how specific phenolic compounds influence gut microbiota composition, contributing to potential pharmaceutical or nutraceutical developments.}, } @article {pmid41703832, year = {2026}, author = {Yao, X and Chen, X and Niu, J and Li, J and Li, W and Zhu, H and Li, X and Sun, B}, title = {Storage time drives divergent microbial functions and flavor metabolism in high-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {228}, number = {}, pages = {118363}, doi = {10.1016/j.foodres.2026.118363}, pmid = {41703832}, issn = {1873-7145}, mesh = {*Hot Temperature ; *Alcoholic Beverages/microbiology/analysis ; *Food Storage/methods ; *Microbiota/physiology ; *Food Microbiology ; Gas Chromatography-Mass Spectrometry ; *Taste ; Time Factors ; Metagenomics ; Metabolomics ; Bacteria/metabolism ; }, abstract = {Baijiu is a traditional Chinese distilled liquor, whose unique flavor highly relies on the synergistic metabolism of diverse microbial communities during the brewing process. The high-temperature Daqu (HTD) used in sauce-flavor Baijiu plays a crucial role in flavor synthesis due to its enrichment of heat-resistant functional microbiota. However, traditional techniques have limited understanding of microbial community succession and functional dynamics during Daqu storage, hindering precise quality and flavor regulation. This study systematically investigated the dynamic evolution of physicochemical indexes, microbial community structure, metabolic functions, and flavor compounds in HTD during different storage periods (1st, 3rd, and 6th months) through integrated metagenomics and GC-MS metabolomics. Results showed continuous decreases in moisture, starch, and pH during storage, while aminopeptide nitrogen and acidity peaked at the 3rd month. Esters reached their highest levels at the 1st month (YQ), alcohols peaked at the 3rd month (EQ), and aldehydes dominated at the 6th month (SQ). LEfSe analysis identified Kroppenstedtia eburnea and Paecilomyces variotii as biomarkers for YQ, Saccharopolyspora rectivirgula and Aspergillus chevalieri for EQ, and Rasamsonia emersonii for SQ. Metagenomic analysis revealed differential carbohydrate and amino acid metabolism pathways: YQ showed highest enzyme abundance for phenethyl alcohol metabolism, EQ exhibited peak enzymes for pyrazine synthesis and ethanol metabolism, while SQ demonstrated superior glucoamylase activity. In addition, maximum tetramethylpyrazine at the 3rd month and highest microbial diversity in later storage (6th month).}, } @article {pmid41704276, year = {2026}, author = {Zhang, Y and Chen, W and Yu, X and Feng, J and Sammad, A and Wang, Z and Yin, K}, title = {Leonurine ameliorates experimental type 2 diabetes through gut microbiota remodeling, enhanced butyrate production, and MPC2 activation to restore GLP-1 secretion.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1747267}, pmid = {41704276}, issn = {1663-9812}, abstract = {The core pathophysiological mechanism of type 2 diabetes mellitus (T2DM) is closely associated with gut microbiota dysbiosis and its consequential impairment of enteroendocrine glucagon-like peptide-1 (GLP-1) secretion. T2DM mouse model was established using high-fat diet (HFD) feeding combined with streptozotocin (STZ) administration. Diabetic mice received 30 or 60 mg/kg of leonurine (LEO) via daily gavage for 12 weeks. Gut microbiota composition was profiled by metagenomic sequencing, fecal short chain fatty acids (SCFAs) concentrations were quantified via enzyme-linked immunosorbent assay (ELISA), and GLP-1 expression was assessed using oral glucose tolerance tests (OGTT), ELISA, and immunofluorescence. In vitro, high-glucose (25 mM)-challenged GLUTag enteroendocrine cells were employed to delineate the butyrate-mitochondrial pyruvate carrier 2 (MPC2) regulatory network using qPCR and Western blotting. LEO intervention significantly ameliorated glucose intolerance in diabetic mice and elevated GLP-1 levels in serum and colonic tissues. Metagenomic analysis revealed that LEO (60 mg/kg) remodeled gut microbiota structure, markedly enhancing α-diversity and specifically enriching butyrate-producing Alistipes. Mechanistically, butyrate activated MPC2 expression, effectively restoring cristae architecture defects observed by transmission electron microscopy, thereby promoting GLP-1 secretion. Crucially, MPC2 knockdown abrogated the secretagogue effect of butyrate on GLP-1 in GLUTag cells. LEO alleviates T2DM by remodeling the gut microbiota ecosystem, enhancing butyrate biosynthesis, and activating an MPC2-dependent mitochondrial energy metabolism pathway to reverse GLP-1 secretory dysfunction in intestinal L cells. This study establishes MPC2-mediated mitochondrial functional repair as a core mechanism through which microbial metabolites regulate enteroendocrine hormone secretion, identifying a novel therapeutic target within the "gut-islet axis" for diabetes intervention. Future studies should identify its active constituents, elucidate downstream effectors, and validate this mechanism in germ-free models.}, } @article {pmid41704313, year = {2026}, author = {Ramzan, F and Vassiliou, L and Tsaltas, D}, title = {Unveiling the diversity and mechanisms of plant growth-promoting bacteria in orchids: a comprehensive review.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1697953}, pmid = {41704313}, issn = {1664-302X}, abstract = {Orchids, one of the most diverse and ecologically important plant families, form complex associations with endophytic microorganisms that are vital for their survival, growth, and adaptation. These endophytes, including both fungi and bacteria, inhabit orchid tissues without causing harm and contribute to key physiological processes such as nutrient acquisition, stress tolerance, and disease resistance. This review explores the diversity and ecological roles of orchid-associated endophytes, emphasizing their significance in promoting germination, biomass production, and resilience to environmental stressors. Plant Growth-Promoting Bacteria (PGPB) such as Pseudomonas, Bacillus, and Burkholderia enhance nutrient uptake and plant defense, offering eco-friendly alternatives to chemical fertilizers and pesticides. Beyond ecological functions, endophytes show potential in biotechnology for sustainable agriculture, conservation, and novel bioactive compound discovery. Despite advances in molecular tools like metagenomics and next-generation sequencing, challenges persist in fully understanding and utilizing these microbes. This review highlights the need for multidisciplinary collaboration to optimize microbial inoculants, elucidate symbiotic mechanisms, and develop practical applications for conservation and sustainable horticulture. By integrating fundamental research with applied strategies, this work aims to unlock the full potential of orchid-associated endophytes in ecological and commercial domains.}, } @article {pmid41704314, year = {2026}, author = {Liu, Y and Xu, H and Cao, J and He, Q and Wang, N and Du, M and Zhao, Y and Dugarjaviin, M and Zhang, X}, title = {Effect of equine-derived Lactobacillus M11 on the reproductive performance of KM pregnant female mice.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1741988}, pmid = {41704314}, issn = {1664-302X}, abstract = {INTRODUCTION: This study aimed to evaluate the effects of equine-derived Lactobacillus M11 on reproductive performance and metabolic profiles in pregnant Kunming (KM) mice. The objective was to explore the potential of M11 as a safe and effective alternative to antibiotics in antibiotic-free farming systems.

METHODS: Specific pathogen-free (SPF) female KM mice were randomly assigned to a blank control group (BC) and three intervention groups (M11-L, M11-M, M11-H). The intervention groups received daily gavage of M11 at low (1.0 × 10[7] CFU/mL), medium (1.0 × 10[8] CFU/mL), and high (1.0 × 10[9] CFU/mL) concentrations for 21 days. Host physiological parameters, metagenomic profiles, and metabolomic signatures were analyzed to assess the impact of M11 supplementation.

RESULTS: (1) Host Physiology and Biochemistry: The M11-H group exhibited a significant elevation in albumin (ALB; 40.30 ± 1.75 g/L), suggesting enhanced nutritional status or hepatic protein synthesis. The M11-L group showed transient increases in alanine aminotransferase (ALT; 59.57 ± 10.34 U/L) and total cholesterol (TC; 2.90 ± 0.24 mmol/L), indicative of adaptive hepatic lipid metabolism. (2) Microbial Community Reconfiguration: Metagenomic analysis revealed significant structural shifts in the gut microbiota between the BC and M11-H groups. Notably, the M11-H group showed enrichment of Bacillota, which correlated with "O-antigen nucleotide sugar biosynthesis," while differences in Pseudomonadota were associated with immune regulation. (3) Metabolomic Profiling: Partial Least Squares Discriminant Analysis (PLS-DA) demonstrated clear separation in the cecal metabolome space. KEGG pathway enrichment analysis highlighted significant alterations in "glycine/serine/threonine metabolism" and "arginine/proline metabolism" pathways. (4) Integrated Multi-Omics Analysis: Correlation analysis identified a significant positive association between s_Clostridiaceae_bacterium (Bacillota) and specific metabolites (3-hydroxy-4-aminopyridine sulfate), suggesting the formation of a regulatory "gut-reproductive axis."

DISCUSSION: The results demonstrate that Lactobacillus M11 improves metabolic support during pregnancy through three primary mechanisms: modulation of the gut microbiota, activation of key metabolic pathways, and enhancement of antioxidant capacity. These findings provide a theoretical basis for the application of probiotic-mediated reproductive support in antibiotic-free farming, highlighting M11 as a promising candidate for improving livestock health and productivity.}, } @article {pmid41704501, year = {2026}, author = {Yoshioka, Y and Ando, C and Yamashita, H and Kawamitsu, M and Kawachi, M and Tsunematsu, Y and Shoguchi, E}, title = {A dataset for forty complete bacterial genome sequences in cultures of the toxic dinoflagellate Ostreopsis cf. ovata.}, journal = {Data in brief}, volume = {65}, number = {}, pages = {112499}, pmid = {41704501}, issn = {2352-3409}, abstract = {Increasing occurrences of toxic dinoflagellate blooms are a growing concern under climate change. The benthic dinoflagellate Ostreopsis blooms through mechanisms that remain poorly understood and is assumed to produce palytoxin-like compounds such as ovatoxins. Recent studies have highlighted the diversity of bacterial communities associated with Ostreopsis and suggested a possible role for these bacteria in toxin biosynthesis. However, genome information on potential bacterial toxin producers remains limited. Here, we report a dataset of bacterial metagenome-assembled genomes (MAGs) obtained from the culture of the toxic dinoflagellate Ostreopsis cf. ovata strain (NIES-3351). HiFi long reads from PacBio Revio system were assembled with hifiasm-meta. We identified forty complete bacterial MAGs, each with an estimated completeness of 93-100%. These MAGs span a wide range of genome sizes (1.5 Mb to 6.7 Mb) and GC contents (36% to 67%). The dataset is available at DDBJ/ENA/GenBank under accession number PRJDB37958.}, } @article {pmid41704508, year = {2026}, author = {Sidiq, Y and Rahayu, T and Indrayudha, P and Tyastuti, EM and Althaf, AZW and Sari, BK}, title = {Metabarcoding data: Full-length 16S rRNA sequence of endophytic bacteria in the root of asymptomatic and blast-symptomatic rice plants (Oryza sativa, L.).}, journal = {Data in brief}, volume = {65}, number = {}, pages = {112522}, pmid = {41704508}, issn = {2352-3409}, abstract = {There is a sustained demand for biofertilizers to enhance crop productivity. Endophytic bacteria associated with disease-tolerant rice varieties offer significant potential as biofertilizers; however, the bacteriome diversity within these plants remains underexplored. This dataset presents full-length 16S metagenomic sequences of endophytic bacteria isolated from the roots of blast-infected and uninfected rice plants. Root samples were processed and subjected to surface sterilisation. Following total genomic DNA extraction, sequencing was performed using 16S ribosomal RNA primers via the high-throughput Oxford Nanopore Technologies platform. The raw sequence data were filtered for quality control using NanoFilt. Subsequently, the sequences were aligned against the National Center for Biotechnology Information (NCBI) 16S RefSeq database to identify the species of the endophytic root bacteria. The data associated with this project have been registered in the NCBI BioProject database under accession number PRJNA992961. The dataset comprises two distinct sample groups, each analysed in duplicate, with sequencing yields ranging from 17.7 to 20.3 Mb. Consequently, this dataset provides valuable insights regarding the comparative composition of endophytic bacteria inhabiting healthy roots versus those found in blast-infected rice. Characterizing this diversity, particularly within healthy rice plants, is essential for foundational research underpinning the future development of biofertilizers.}, } @article {pmid41704740, year = {2026}, author = {Shi, X and Fan, C and Hui, M and Tian, Q and Zhang, F and Pan, C}, title = {Integrated metagenomic and metabolomic analysis reveals regional style differences in Maotai-flavour Baijiu.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100558}, pmid = {41704740}, issn = {2666-5174}, abstract = {This research focused on Maotai-flavour Baijiu from three representative production regions in the Chishui River Basin, namely Maotai Town (MT), Jinsha (JS), and Renhuai (RH). By integrating metabolomics and macrogenomics techniques, the study analyzed the differences in volatile flavor compounds and microbial community structures in the fourth-round fermented grains and base liquor. Additionally, it explored the associative mechanism between microorganisms and flavor metabolism. The findings indicate that the microbial community compositions of fermented grains vary significantly across different production areas. The production area of Maotai Town mainly consists of Saccharomyces and Lactobacillus, with the highest content of ester substances. The fungal community in Jinsha is extremely stochastic, abundant in Mucoromycota, and has elevated contents of aldehydes and phenols. The distribution of microorganisms and flavor substances in the Renhuai production area lies between the two. The sensory evaluation of the base liquor indicates that the Jinsha production area features prominent floral and fruity aromas, the Maotai Town exhibits significant sour and sauce aromas, and the Renhuai production area has a well-balanced flavor. The correlation analysis shows that yeasts such as Saccharomyces and Pichia are positively correlated with esters such as ethyl acetate, while bacteria such as Limosilactobacillus are closely associated with short-chain fatty acid metabolism. This research reveals the microbiological basis for the differences in the Maotai style among different production regions and provides a theoretical foundation for regional characteristic production and process optimization.}, } @article {pmid41704794, year = {2025}, author = {Basu, U and Ahanger, SA and Gai, X and Hu, X}, title = {Longitudinal metagenomics reveals continuous restructuring of soil pathobiome under persistent Phytophthora pressure.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1749879}, pmid = {41704794}, issn = {1664-462X}, abstract = {Soil borne pathogen, Phytophthora nicotianae causes black shank disease in tobacco, present a pervasive threat to global agriculture, with conventional control strategies often proving inadequate. A critical gap exists in our understanding of the long-term, dynamic interplay between the pathogen and the soil microbiome. To address this, we conducted a six-year longitudinal metagenomic study in a monocultured tobacco field, revealing a pathobiome in constant, non-equilibrium adaptation. Our analysis uncovered profound microbial restructuring, beginning with cumulative transcriptional reprogramming of highly significant genes. Functional profiling showed a critical metabolic shift toward anabolic capacity, with a 66.7% increase in KEGG orthologs and enrichment of amino acid biosynthesis (+8.9%), ribosomes (+13.0%), and quorum sensing (+11.0%). The soil resistome underwent dramatic succession, featuring an initial coordinated defense (R[2]=0.825), a comprehensive collapse in Year 3-4 (917 downregulated genes), and a resilient recovery that drove a net increase in antibiotic resistance, indicating a lasting ecosystem alteration. Virulence factor evolution revealed strategic trade-offs, with flagella systems dominating (2,583 occurrences) while more costly energy consuming secretion systems declined, and 87 core virulence factors persisted across time. Crucially, we observed a widespread decoupling between genetic potential and functional expression; key categories for defense and signal transduction declined in abundance (slopes of -150.4 and -264.9, respectively) despite stable gene counts, suggesting a systemic, energy conserving survival strategy. Concurrently, the community experienced progressive diversity loss (Shannon index slope = -0.0464/yr at genus level) despite maintained species richness (717 species), indicating restructuring was driven by shifting evenness rather than species loss. Our findings exhibit that persistent pathogen pressure drives the soil microbiome into a continuous state of adaptive restructuring, prioritizing coordinated defensiveness and metabolic efficiency over stability. This time resolved framework challenges static views of soil ecosystems and provides a foundational dataset for developing predictive, microbiome informed strategies to manage soil borne diseases sustainably.}, } @article {pmid41704809, year = {2026}, author = {Zhang, M and Jiao, T and Li, W}, title = {Allergic bronchopulmonary aspergillosis in a patient without history of asthma: a case report.}, journal = {Medical mycology case reports}, volume = {51}, number = {}, pages = {100770}, pmid = {41704809}, issn = {2211-7539}, abstract = {Allergic bronchopulmonary aspergillosis (ABPA) is a pulmonary hypersensitivity disease triggered by Aspergillus fumigatus. While the standard first-line therapy per International Society for Human and Animal Mycology (ISHAM) guidelines is glucocorticoids or itraconazole alone, combination therapy may be used briefly for rapid symptom control. We present a 39-year-old man without asthma who presented with cough and sputum. Chest computed tomography (CT) revealed diagnostic findings of central bronchiectasis and high-attenuation mucus, later confirmed as mucus plugs by bronchoscopy. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) detected a high load of A. fumigatus. Markedly elevated total IgE, A. fumigatus-specific IgE, and eosinophils confirmed ABPA. Although initial voriconazole monotherapy failed, adding oral glucocorticoids led to rapid clinical and radiographic improvement. No recurrence was observed on CT 7 months post-treatment, reinforcing that asthma is not a prerequisite for ABPA diagnosis.}, } @article {pmid41704848, year = {2025}, author = {Nayak, D and Behera, P and Singh, S and Tripathy, PS and Dash, SS and Dasgupta, M and Mohanty, S and Sahoo, MR and Satapathy, CR and Sasmal, A and Sahu, S}, title = {Sucrose supplementation influences gut microbial diversity and functional shifts in Apis cerana indica.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1733283}, pmid = {41704848}, issn = {1664-302X}, abstract = {Honeybee colonies are increasingly threatened by nutritional scarcity and biotic stressors, underscoring the need to understand the role of gut microbiota in mitigating these challenges. This study examined the gut microbial composition of Apis cerana indica under two dietary regimes: sucrose-fed and sucrose-unfed, to assess how nutrition influences microbial diversity and metabolic potential following metagenomics. Metagenomic sequencing of gut samples revealed 147,146 contigs, with the longest and shortest contigs measuring 615,154 kb and 200 kb, respectively. Comparative analysis indicated a higher relative abundance of Bacillus spp. in sucrose-fed bees, whereas Enterococcus was more dominant in unfed populations. Sucrose feeding significantly enhanced gut microbial diversity (Shannon index: 2.59; Simpson's index: 0.87) compared to unfed bees (Shannon: 1.91; Simpson: 0.68). Key genera, including Gilliamella, Bacillus, and Lactobacillus, were consistently present but showed varying relative abundances. Functional annotation via KEGG pathway analysis revealed elevated activity of glycolysis and the pentose phosphate pathway in sucrose-fed bees, with exclusive detection of key metabolic enzymes, hexokinase and enolase. Additionally, elevated sucrose metabolism and proteolytic enzyme activity were noted, reflecting enhanced metabolic versatility. Our findings highlight the importance of sucrose dietary supplementation in shaping gut microbial structure and function, their diversity, and metabolic capacity, suggesting its potential as a practical nutritional intervention to sustain honeybee health during a period of floral dearth. The outcome of the study encourages exploring the long-term ecological and physiological impacts of dietary strategies on colony resilience and productivity.}, } @article {pmid41704904, year = {2025}, author = {Av, EZ and Greenberg, A and Knaan, T and Melanson, EL and Youngster, I and Dubnov-Raz, G and Borenstein, E and Gepner, Y}, title = {The associations between physical activity, microbiome and metabolic adaptation in sedentary overweight adults.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1722274}, pmid = {41704904}, issn = {2296-861X}, support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; }, abstract = {Despite well-established benefits of exercise on metabolic regulation and the gut microbiome (GM), its impact on body composition is inconsistent and often attenuated by metabolic adaptation. This compensation mechanism adjusts energy expenditure including total daily energy expenditure (TDEE) and resting metabolic rate (RMR). Intra-individual variation in exercise response remains unclear, but might be explained by the GM. In this well-controlled study, we investigated the relationship between aerobic exercise, GM composition, and metabolic adaptation in a cohort of 16 sedentary overweight adults (ages 21-45, 50% female) over a 12-week moderate-intensity intervention (65-75% HRmax; 20 kcal/kg/week). Pre- and post-intervention RMR was measured via whole-room calorimetry, TDEE by doubly labeled water, and GM composition via shotgun metagenomics. While body composition did not change at the group-level, a subset of participants ("responders") showed improved body composition and aerobic capacity. Using machine learning, we identified bacterial species, including Faecalibacterium prausnitzii species, whose abundance pre-training is predictive of response. Additionally, we found that responder GM communities are more compositionally cohesive and post-training increases in GM diversity are associated with higher TDEE and RMR. These findings highlight the complex interaction between exercise, metabolism and the GM, and suggest that baseline GM characteristics may contribute to individual variability in metabolic adaptation. This insight may help guide microbiome-informed strategies to enhance exercise efficacy. Clinical trial registration: ClinicalTrials.gov, identifier NCT04460040.}, } @article {pmid41704957, year = {2026}, author = {Zhu, J and Xia, T and Wang, L and Yin, X and Ma, Y and Shen, J}, title = {Investigating the benefits of metagenomic next-generation sequencing for patients experiencing infections after total hip replacement surgery: a retrospective cohort study with a minimum of one year of follow-up.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1735867}, pmid = {41704957}, issn = {2235-2988}, mesh = {Humans ; *Arthroplasty, Replacement, Hip/adverse effects ; Female ; *High-Throughput Nucleotide Sequencing/methods ; *Prosthesis-Related Infections/microbiology/diagnosis/drug therapy ; Aged ; Middle Aged ; *Metagenomics/methods ; Retrospective Studies ; Male ; Aged, 80 and over ; Follow-Up Studies ; Adult ; *Bacteria/genetics/isolation & purification/classification ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {OBJECTIVE: To explore the clinical significance of metagenomic next-generation sequencing (mNGS) technology in diagnosing and treating periprosthetic joint infection (PJI) following total hip arthroplasty (THA).

METHODS: From September 2018 to September 2024, 15 patients with periprosthetic infection after total hip arthroplasty were admitted. There were 11 males and 4 females; ages ranged from 28 to 87 years old, with an average of 63 years old. Infection occurred 6 to 42 months after total hip arthroplasty, with an average of 22.7 months. The infection lasted between 15 and 115 days, averaging 37.6 days. After being admitted to the hospital, joint fluid was collected for bacterial culture and mNGS. Following admission, joint fluid was collected for bacterial culture and mNGS, and antibiotics were adjusted based on the results, with surgery used to control the infection if needed.

RESULTS: Bacterial culture method was positive in 10 cases (66.7%), with a total of 12 pathogenic bacteria types detected. MNGS was positive in 15 cases (100.0%), with a total of 19 pathogenic bacteria types detected. There was a statistically significant difference in the positive rate between the two methods (P < 0.05). Out of the 10 patients, 5 who tested positive using both the bacterial culture method and mNGS test showed identical pathogenic bacterial types, resulting in a 50.0% compliance rate. The testing time (from sample delivery to results) was (3.07 ± 0.96) days for bacterial culture method and (1.67 ± 0.49) days for mNGS test, and the difference was statistically significant (t=5.03, P<0.001). The patients were followed up for 13 to 82 months, with a mean of 40.7 months. In one patient, the infection returned three months after undergoing one-stage revision surgery, while the other 14 patients showed no signs of infection, resulting in an infection control rate of 93.3%.

CONCLUSION: MNGS can detect the pathogenic bacteria of postoperative PJI after THA more quickly and accurately than the bacterial culture method, which is crucial for guiding antibiotic and surgical treatment combinations for patients with postoperative PJI after THA.}, } @article {pmid41705163, year = {2026}, author = {}, title = {Correction to: Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag020}, doi = {10.1093/ismeco/ycag020}, pmid = {41705163}, issn = {2730-6151}, abstract = {[This corrects the article DOI: 10.1093/ismeco/ycaf183.].}, } @article {pmid41705261, year = {2026}, author = {Fentie, EG and Lim, K and Andargie, YE and Park, S and Shin, JH}, title = {Preserving fermented-foods microbial diversity through systematic culturomics for the discovery of multi-strain probiotic candidates.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101318}, pmid = {41705261}, issn = {2665-9271}, abstract = {Fermented foods (FFs) represent complex living ecosystems that deliver viable microbes and bioactive metabolites linked to human health benefits. However, many probiotic strains isolated from FFs fail to reproduce these effects in vivo, likely due to the disruption of their natural ecological synergy during isolation. Here, we employed a systematic, ecology-aware culturomics framework to transform the Kimchi microbiome into genome-vetted, multi-species probiotic candidates while preserving ecological fidelity. Specifically, 56 distinct enrichment culture conditions were established using six liquid media (In-situ, MRS, NB, TSB, BHI, BB) across varied redox states (aerobic, anaerobic, microaerophilic), incubation periods (12 h, 66 h), and selective suppressants (CHIR-090, nalidixic acid). Results indicated that In-situ and MRS media under microaerophilic conditions effectively preserved the lactobacilli core, whereas generalist media and aeration expanded taxonomic breadth to include rare taxa. Furthermore, extended incubation (66h) successfully unlocked 107 unique taxa compared to the limited diversity of short incubation (12h). Shotgun metagenomic mining further revealed promising functional properties, including acid tolerance, adhesion modules, and diverse bacteriocin-skewed biosynthetic gene clusters. Crucially, the collection exhibited a strong safety profile: only 1 % of identified risk factors were antibiotic resistance genes (ARGs) on mobile genetic elements (MGEs), and only 4 % represented colocalized ARGs, virulence factors, and MGEs. Systematic-culturomic isolation later yielded over 90 strains, including Weissella, Bacillus, and Lactococcus, significantly expanding beyond standard lactobacilli-centric portfolios. Overall, this study confirms that ecology-aware culturomics captures the functional diversity of the Kimchi microbiome, providing a scalable model for realizing the full therapeutic potential of FFs.}, } @article {pmid41705811, year = {2026}, author = {Paietta, EN and Kraberger, S and Gordon, M and Ehmke, E and Yoder, AD and Varsani, A}, title = {Metagenome-assembled genomes of anelloviruses in crowned lemur and aye-aye swabs.}, journal = {Microbiology resource announcements}, volume = {15}, number = {3}, pages = {e0147325}, pmid = {41705811}, issn = {2576-098X}, abstract = {Two circular, complete genomes of anelloviruses were identified from a crowned lemur anal swab and an aye-aye skin swab from individuals at the Duke Lemur Center (Durham, NC, USA). The anelloviruses represent two species in the Anelloviridae family and expand a developing lemur-associated anellovirus lineage.}, } @article {pmid41705822, year = {2026}, author = {Guo, Z and Xiao, Y and Zhao, J and Tang, Z and Lin, Y and Yang, K}, title = {MetaRanker: precise profiling of antibiotic resistome risk in metagenomes by integrating abundance and genetic co-occurrence.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {3}, pages = {e0242225}, pmid = {41705822}, issn = {1098-5336}, support = {22176133//National Natural Science Foundation of China/ ; }, mesh = {*Metagenome ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; *Computational Biology/methods ; Interspersed Repetitive Sequences ; Virulence Factors/genetics ; }, abstract = {The proliferation of antibiotic resistance genes (ARGs) in environmental microbiomes represents a major and growing threat to public health, creating a critical demand for precise and efficient tools to monitor resistance risk. Current approaches often depend on contig-based quantification or lack comprehensive risk indices, which compromises their accuracy and utility. To address this, we developed MetaRanker (https://github.com/SteamedFish6/MetaRanker), a computational pipeline that assesses resistome risk by integrating the abundance of ARGs, mobile genetic elements (MGEs), and virulence factors (VFs)-calculated directly from sequencing reads-with their genetic co-occurrence on contigs into a unified risk index (RI). This index reflects the potential for horizontal transfer and pathogen emergence. Evaluated using in silico and diverse real-world metagenomes (n = 353), MetaRanker demonstrated superior accuracy and stronger discriminatory power than existing methods. Its optimized compact database (29.6 MB) and alignment strategy reduced runtime by over 50% in comparison to MetaCompare 2.0 under identical hardware configurations (32 CPU cores, 128 GB RAM). Practical applications confirmed that MetaRanker effectively discriminates risk levels across environments (e.g., hospital wastewater versus natural soil) and quantifies risk mitigation through wastewater treatment. As a robust, lightweight, and sequencing-platform-agnostic tool, MetaRanker offers a powerful solution for comprehensive environmental resistome surveillance and evidence-based risk management.IMPORTANCEThe environmental reservoir of antibiotic resistance is a key contributor to the global health crisis of antimicrobial resistance. Effective surveillance and risk assessment of complex microbial communities are essential for prioritizing interventions and safeguarding public health. However, existing methods often provide fragmented or computationally demanding analyses, limiting their practical application for large-scale environmental monitoring. The significance of our work lies in developing MetaRanker, which overcomes these barriers by delivering a fast, accurate, and integrated metric of resistome risk. By simultaneously accounting for the abundance, mobility potential, and pathogenicity linkage of resistance determinants, MetaRanker enables a more realistic threat assessment. This tool empowers researchers and public health officials to track resistance hotspots, evaluate the impact of human activities such as waste disposal, and monitor the effectiveness of mitigation strategies, ultimately supporting data-driven decisions to curb the environmental spread of resistance.}, } @article {pmid41705858, year = {2026}, author = {Teixeira Martins, C and Gombert, AK and Venturini, AM}, title = {Lactobacillus and Limosilactobacillus MAGs from alcoholic fermentation in sugarcane biorefineries.}, journal = {Microbiology resource announcements}, volume = {15}, number = {3}, pages = {e0070525}, pmid = {41705858}, issn = {2576-098X}, support = {2022/15256-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2023/10728-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 306190/2022-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {We recovered and characterized four bacterial MAGs from two Brazilian sugarcane biorefineries, with the aim of investigating the microbial environment during fuel ethanol production. MAGs belonged to Lactobacillus amylovorus and Limosilactobacillus fermentum, both known lactic acid bacterial contaminants. Genomic analyses revealed key functional traits but no resistance or virulence genes.}, } @article {pmid41705859, year = {2026}, author = {Medeiros, WB and Centurion, VB and Silva, JB and Duarte, AW and Hidalgo-Martinez, KJ and Dos Santos, JA and Penna, DDPS and Bagci, C and Ziemert, N and Oliveira, VM}, title = {Antarctic soil prokaryotic diversity: a dataset of 319 metagenome-assembled genomes from Deception and Livingston Islands.}, journal = {Microbiology resource announcements}, volume = {15}, number = {3}, pages = {e0134625}, pmid = {41705859}, issn = {2576-098X}, support = {2020/11534-0, 2022/15112-8, and 2017/03172-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 88887.514375/2020-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {A total of 319 bacterial metagenome-assembled genomes (MAGs) were recovered from soil samples collected on the Antarctic Peninsula (Deception and Livingston Islands). These MAGs reveal microbial life's phylogenetic diversity and functional potential in extreme polar environments, providing resources for advancing microbial ecology, evolution, and Antarctic biotechnology.}, } @article {pmid41706260, year = {2026}, author = {Matsumoto, M and Shiotani, A and Osawa, M and Handa, O and Matsumoto, H and Umegaki, E and Yonezawa, H and Osaki, T}, title = {Metagenomic analysis of the intragastric and oral microbiome associated with gastric carcinogenesis after Helicobacter pylori eradication.}, journal = {Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association}, volume = {29}, number = {2}, pages = {338-346}, pmid = {41706260}, issn = {1436-3305}, support = {Research Project Grant//Kawasaki Medical School/ ; }, } @article {pmid41707175, year = {2026}, author = {Huang, X and Deng, K and Zhu, G and Huang, W and Gong, G and Liu, H and Yang, T and Gui, Y and Li, W}, title = {Dynamics of soil microbiome throughout the cultivation life cycle of Phallus rubrovolvatus.}, journal = {Canadian journal of microbiology}, volume = {72}, number = {}, pages = {1-14}, doi = {10.1139/cjm-2025-0279}, pmid = {41707175}, issn = {1480-3275}, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; China ; Metagenome ; Soil/chemistry ; *Basidiomycota/growth & development ; *Agaricales/growth & development ; Nitrogen/metabolism ; Metagenomics ; }, abstract = {Phallus rubrovolvatus is a valuable edible fungus extensively cultivated in Guizhou Province, China. However, the changes in the soil microbiome throughout its growth cycle remain poorly understood. In this study, we collected 35 casing soil samples across five growth stages covering the entire 120-day cultivation cycle of Phallus rubrovolvatus and conducted metagenomic sequencing to examine alterations in soil microbial composition, diversity, key biomarkers, and functional potential. Our analyses revealed significant stage-dependent shifts in microbial community structure, with alpha diversity reaching its lowest at the primordium stage (Shannon of 5.12) and network complexity peaking at harvest stage (1.8-fold increase in connectivity). Through LEfSe analysis, we identified 37 stage-specific microbial biomarkers primarily affiliated with Actinomycetota and Acidobacteriota. Notably, Acidobacteriota biomarkers dominated at the primordium stage, while Nitrospirota enrichment characterized the harvest stage. Functional analyses revealed that membrane transport and energy metabolism pathways were enriched during early mycelial colonization, whereas secondary metabolite biosynthesis and signaling pathways became prominent during fruiting body maturation. Correlation analyses identified available nitrogen as the primary soil variable associated with microbial community composition. These findings provide foundational knowledge of microbiome dynamics during Phallus rubrovolvatus cultivation and suggest that microbiome-based management strategies may benefit from stage-specific interventions synchronized with fungal developmental transitions.}, } @article {pmid41707285, year = {2026}, author = {Du, Z and Li, Z and Chen, X and Liu, M and Feng, L and Li, Q and Chen, Z and Chen, Q}, title = {Laboratory-scale simulation study on the bioremediation of marine oil pollution by phosphate-solubilizing bacteria Bacillus subtilis PSB-1.}, journal = {Marine pollution bulletin}, volume = {226}, number = {}, pages = {119422}, doi = {10.1016/j.marpolbul.2026.119422}, pmid = {41707285}, issn = {1879-3363}, mesh = {*Biodegradation, Environmental ; *Bacillus subtilis/metabolism ; Phosphates/metabolism ; *Petroleum/metabolism ; *Petroleum Pollution ; Seawater ; *Water Pollutants, Chemical/metabolism ; }, abstract = {Phosphate-solubilizing bacteria (PSB) are well-known for their ability to convert nonbioavailable phosphates into bioavailable forms, however, research on PSB that possess both phosphate solubilization and crude oil degradation capabilities in marine environments has not yet been explored, and the role of these bacteria in microbial remediation of petroleum contamination in seawater needs be investigated. In this study, laboratory simulated marine oil spill bioremediation experiment was carried out to explore the role of PSB with crude oil degradation capabilities (A strain of PSB-1 used in this study) in petroleum hydrocarbon degradation by indigenous microorganisms in marine environment. It was found that PSB-1 significantly enhanced crude oil removal, with a degradation efficiency of 60% achieved after 30 days at a crude oil concentration of 1 g/L, Concurrently, the concentration of soluble phosphate in seawater increased to 47.36 mg/L, reflecting a 170% increase compared to the control. Metagenomic analysis further indicated that the phosphate-solubilizing activity of PSB-1 not only augmented phosphate availability but also stimulated the growth and succession of indigenous hydrocarbon-degrading microorganisms, thereby altering the microbial community structure and improving overall degradation capacity. These findings highlight the ecological significance of PSB-1 in facilitating crude oil biodegradation in marine environments and offer novel insights into bioremediation strategies for crude oil-contaminated seawater.}, } @article {pmid41707316, year = {2026}, author = {Yang, J and Meng, X and Zhang, H and Sun, W and Yang, L and Li, S}, title = {Mobile genetic elements drive the assembly of high-risk resistance and virulence configurations at the riverine water-sediment interface.}, journal = {Environmental research}, volume = {296}, number = {}, pages = {124055}, doi = {10.1016/j.envres.2026.124055}, pmid = {41707316}, issn = {1096-0953}, mesh = {*Rivers/microbiology/chemistry ; *Geologic Sediments/microbiology ; *Drug Resistance, Microbial/genetics ; *Interspersed Repetitive Sequences ; Bacteria/genetics ; *Water Microbiology ; Water Pollutants, Chemical/analysis ; }, abstract = {Riverine ecosystems are major conduits and repositories for microplastics, heavy metals and antibiotics yet how these co-occurring stressors jointly shape resistance and virulence risks across water and sediments remains unclear. Here we combined shotgun metagenomics with pollutant profiling along a representative rural-to-urban gradient during the dry season to resolve the distribution, mobility and drivers of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), virulence factors (VFs) and mobile genetic elements (MGEs) in paired surface waters and surficial sediments. Bacterial communities were dominated by Pseudomonadota and Actinomycetota while fungal communities were dominated by Ascomycota and Uroviricota respectively with stronger land-use effects observed in water than in sediments. Across all samples we detected 36 ARG classes and 1589 subtypes where multidrug and efflux or target alteration mechanisms predominated. Furthermore ARG richness, abundance and diversity increased from rural to urban reaches in both media. MGEs were dominated by transposases where ARG-MGE co-localization on 1474 contigs revealed dense transposase-centered networks in urban sediments that linked multidrug, peptide, glycopeptide and tetracycline resistance. Crucially we identified contigs co-harboring ARGs, MRGs, and VFs as multi-trait risk gene carriers. Urban reaches hosted diverse carrier lineages whereas rural reaches were dominated by the high abundance of specific carriers. SourceTracker and partial least squares path modeling together indicated that rural sediments are the principal upstream sources of microbes and risk genes while MGEs in urban sediments translate multi-pollutant stress into enlarged and more mobile risk gene pools. These findings highlight the need to jointly manage agricultural inputs and urban sediments under multi-stressor conditions.}, } @article {pmid41707391, year = {2026}, author = {Werid, GM and Hemmatzadeh, F and Batterham, T and Miller, D and Edwards, R and Trott, DJ and Petrovski, K}, title = {Metagenomic and metatranscriptomic analyses reveal microbial dysbiosis and bacteria-virus interactions in the lungs of Australian feedlot cattle with bovine respiratory disease.}, journal = {Veterinary microbiology}, volume = {315}, number = {}, pages = {110926}, doi = {10.1016/j.vetmic.2026.110926}, pmid = {41707391}, issn = {1873-2542}, mesh = {Animals ; Cattle ; *Lung/microbiology/virology ; Metagenomics ; Microbiota ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/veterinary/microbiology/virology ; Australia ; *Bovine Respiratory Disease Complex/microbiology/virology ; Virome ; Bacteriophages/genetics ; *Cattle Diseases/microbiology/virology ; }, abstract = {Bovine respiratory disease (BRD) remains the leading cause of feedlot cattle morbidity and mortality. Despite its polymicrobial aetiology, microbial population structure and inter-pathogen dynamics within the lungs of cattle with BRD remain poorly understood. To characterise the lung microbiome and virome of feedlot cattle with (n = 23) and without BRD (n = 9), we applied RNA-sequencing and full-length 16S rRNA gene sequencing to bovine lung tissue samples collected at post-mortem. Host-depleted RNA-seq reads were assembled and profiled, bacterial communities were classified, and diversity, differential abundance, bacteria-virus correlations, co-occurrence networks, and phage-host links analysed. Lung samples from BRD- cattle revealed pathogen-dominated communities with reduced within-sample diversity. Metamycoplasmataceae/Mycoplasmataceae, and Pasteurellaceae accounted for approximately 65.3 % of the bacterial population in samples from cattle with BRD, compared to approximately 11.3 % in lung samples from non-BRD cattle. At the species level, a significantly increased abundance of Pasteurella multocida was observed in BRD cattle. The virome was bacteriophage-dominated in both groups (led by Peduoviridae) but revealed distinct BRD-associated changes. Strong correlation between bacterial genomic abundance and transcriptional activity was observed in cattle with BRD, particularly for Mycoplasmopsis bovis, P. multocida, and Trueperella pyogenes. Network analyses consistently identified M. bovis, P. multocida, and Histophilus somni as highly connected hubs, whereas phages predicted to infect BRD-associated bacteria and Pestivirus bovis were more prevalent and/or abundant in lung samples from BRD cattle. Overall, BRD is characterised by a shift to low-diversity, pathogen-centred bacterial communities within a phage-rich virome that includes enrichment of bacterial pathogen-associated phages. These findings provide a basis for microbiome-informed, multi-pathogen diagnostics and help prioritise surveillance and control strategies that can be included into feedlot BRD management programmes to reduce antimicrobial use, animal losses, and economic impacts.}, } @article {pmid41707423, year = {2026}, author = {Francés, Á and López, M and González-Raurich, M and Cobo-Díaz, JF and Prieto, M and Allende, A and Gil, MI and Truchado, P and Alvarez-Ordóñez, A and Oliveira, M}, title = {Characterization of microbial diversity, chemical hazards and antimicrobial resistant bacteria in wash water from a fresh-cut vegetable processing plant.}, journal = {International journal of food microbiology}, volume = {452}, number = {}, pages = {111667}, doi = {10.1016/j.ijfoodmicro.2026.111667}, pmid = {41707423}, issn = {1879-3460}, mesh = {*Bacteria/drug effects/isolation & purification/genetics/classification ; *Vegetables/microbiology ; *Water Microbiology ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Food Handling ; Microbial Sensitivity Tests ; Pesticides/analysis ; Food, Processed ; Food Microbiology ; }, abstract = {This study investigated the quality of process wash water (PWW) in an industrial fresh-cut produce facility. Traditional microbiological and physico-chemical parameters, such as aerobic mesophilic counts, coliforms, molds and yeasts, pH, free chlorine, oxidation-reduction potential, and organic matter indicators, were monitored to contextualize water quality dynamics across the workday. Additionally, untargeted analyses were performed to characterize the microbiome and resistome and identify chemical hazards in PWW, highlighting the occurrence of antimicrobial-resistant bacteria and the presence of some pesticides at low levels, including chlorantraniliprole, cyprodinil, fludioxonil, and propyzamide, in a real-world processing environment. Antimicrobial susceptibility tests and whole genome sequencing of twelve coliform isolates revealed multidrug-resistant strains, including Enterobacter mori, Enterobacter ludwigii, and Klebsiella oxytoca, carrying resistance genes such as oqxB, fosA, and blaACT-12, as well as the plasmid-borne blaOXY-2-2. Metagenome analyses revealed a microbial community dominated by the genus Pseudomonas, together with high abundance of Rheinheimera mangrovi and Pantoea agglomerans. Moreover, resistome analysis disclosed that 83% of detected antimicrobial resistance genes were associated with beta-lactam resistance. Additionally, the efficacy of chlorine against one K. oxytoca isolate obtained from PWW using a dynamic system simulating a produce washing operation confirmed that maintaining pH at 6.5 and stable free chlorine levels of 6 mg/L was sufficient for complete inactivation. These findings demonstrate the importance of implementing proper wash water management practices in fresh produce processing, including preventing excessive organic matter accumulation through adequate water replenishment and maintaining chemical parameters within the validated operational range, supported by systematic verification and monitoring.}, } @article {pmid41707490, year = {2026}, author = {Jian, Z and Zhao, R and Zi, X and He, S and He, X and Ye, Y and Wang, K and Ge, C and Jia, J and Hu, Y and Dou, T}, title = {Sustainable antibiotic reduction in poultry production with Pulsatilla saponins and herbal supplementation.}, journal = {Poultry science}, volume = {105}, number = {5}, pages = {106562}, pmid = {41707490}, issn = {1525-3171}, mesh = {Animals ; *Saponins/administration & dosage/metabolism ; *Chickens/immunology/growth & development/microbiology ; Dietary Supplements/analysis ; *Pulsatilla/chemistry ; Animal Feed/analysis ; Diet/veterinary ; *Anti-Bacterial Agents/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Male ; Random Allocation ; *Drug Resistance, Microbial/genetics ; Cecum/microbiology ; }, abstract = {The prolonged use of antibiotics in poultry production promotes the accumulation and spread of antibiotic resistance genes (ARG), raising concerns for animal health and public safety. Developing effective antibiotic alternatives that support performance while limiting resistance risk is therefore a priority. Using broiler chickens as a model, this study evaluated the effects of Pulsatilla saponins, alone or combined with a compound herbal formulation, on growth performance, immune responses, cecal microbiota, and the intestinal resistome, with an antibiotic-treated group as reference. Growth and immune parameters were integrated with shotgun metagenomic sequencing to characterize microbial and ARG responses to dietary interventions. Compared with antibiotic supplementation, the combination of 0.5% herbal medicine and 0.6% Pulsatilla saponins (ZBZ) combination significantly enhanced immune traits, including spleen index and serum IgA and IgM levels, while increasing cecal microbial diversity and reshaping community composition. Metagenomic analyses showed that antibiotic treatment enriched efflux pump and target modification associated ARG, indicative of a multidrug resistance profile. In contrast, ZBZ markedly reduced the abundance and diversity of multidrug resistance-related ARG. Notably, ZBZ supplementation enriched short-chain fatty acid-producing taxa that were negatively correlated with multiple ARG classes, suggesting that improvements in the intestinal metabolic environment and colonization resistance constrained the expansion of resistant bacteria. Overall, the combined use of Pulsatilla saponins and a compound herbal formulation improved growth and immune performance while reducing intestinal ARG burden through coordinated modulation of the cecal microbiota-resistome axis, providing a sustainable nutritional strategy for antibiotic-reduced poultry production.}, } @article {pmid41707528, year = {2026}, author = {Wang, Y and Ding, C and Zheng, Z and Liu, W and Shi, Y}, title = {The spatial distribution of heavy metal contamination, microbial communities, and resistance genes in agricultural soil near a manganese mine in China.}, journal = {Ecotoxicology and environmental safety}, volume = {311}, number = {}, pages = {119865}, doi = {10.1016/j.ecoenv.2026.119865}, pmid = {41707528}, issn = {1090-2414}, mesh = {*Metals, Heavy/analysis ; China ; *Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; *Mining ; *Bacteria/genetics/drug effects/classification ; Agriculture ; Environmental Monitoring ; *Manganese/analysis ; Soil/chemistry ; *Microbiota ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; }, abstract = {The large-scale manganese mining causes severe heavy metal contamination, posing a significant potential risk to human health. Songtao County is one of the most important manganese mining areas in China, where the disorderly mining and extensive production has inevitably caused serious pollution. However, it's still unclear how Mn production activities affect agricultural soils located relatively far from the mining sites. Therefore, we investigated the horizontal and vertical distribution of heavy metal contamination, microbial communities, and resistance genes in the agricultural soils located at Songtao County. Metagenomic sequencing revealed that Proteobacteria, Acidobacteria, Rokubacteria, Chloroflexi, and Actinobacteria were the most abundant phyla. The diversity and composition of the bacterial communities varied significantly between different sampling sites and depths. Redundancy and Spearman correlation analysis indicated that total nitrogen, total organic carbon, total K, and Mn were the primary environmental factors determining the distribution of bacterial communities. The bacterial communities in Wuluo were influenced by Hg, Zn, Cu, Ni, and As, whereas in Mushu, it was primarily affected by Mn levels. A large account of heavy metal resistance genes, manganese resistance genes, and antibiotics resistance genes were identified. The relative abundances and correlation analysis of these resistance genes exhibited observed correlations based on the potential co-selection mechanisms, suggesting that Mn and heavy metals, as well as antibiotics, might shape the microbiome and resistome in this agricultural soil. These findings provide an insight for the surveillance, maintenance, and remediation of the agricultural soil and offer theoretical evidence for improving the agricultural soil environment.}, } @article {pmid41707775, year = {2026}, author = {Yu, S and Jin, Y and Guo, T and Li, H and Liu, W and Chen, Z and Wang, X and Guo, J}, title = {Capacitive bimetallic redox cycles and ligand-to-metal charge transfer to Boost denitrification with Ni[II]/Fe[II]-Gallic acid phenolic networks.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134237}, doi = {10.1016/j.biortech.2026.134237}, pmid = {41707775}, issn = {1873-2976}, mesh = {*Denitrification ; Oxidation-Reduction ; *Gallic Acid/chemistry ; *Nickel/chemistry ; Ligands ; *Iron/chemistry ; Nitrates ; *Phenols/chemistry ; Pseudomonas/metabolism ; Electron Transport ; }, abstract = {Biological denitrification is limited by slow nitrate (NO3[-]) reduction due to low electron transfer efficiency, unsatisfactory community functional efficiency and insufficient metabolic activity of microbial communities. To overcome these challenges, Ni[2+] and Fe[2+] were incorporated with gallic acid (GA) to form bimetallic polyphenol networks (NiFeGA BPNs) with low-cost and high-biocompatibility. NiFeGA BPNs exhibited capacitive Ni(II)/Fe(II) redox cycles and excellent ligand-to-metal charge transfer capabilities to enable complete degradation of 200 mg/L NO3[-] within 8 h. All these improvements could be ascribed to that NiFeGA BPNs significantly improved electron transfer efficiency and stimulated microbial metabolic activity, which were proved by extracellular polymeric substances electrochemical analysis and electron transport chain inhibitors experiments. More importantly, metagenomic sequencing analysis confirmed that NiFeGA BPNs improved community structure by directionally enriching Pseudomonas. Consequently, NiFeGA BPNs significantly improving denitrification, which provides both theoretical guidance and technical frameworks for the continuous and efficient treatment of nitrate in wastewater.}, } @article {pmid41707923, year = {2026}, author = {do Nascimento, AC and de Albuquerque, TMR and de Oliveira, DG and de Oliveira, AP and da Costa, PCT and de Sales, LCS and da Silva, JYP and Lins, JDS and E Silva, AL and da Silva, EF and do Nascimento, YM and Tavares, JF and Lima, MDS and Bezerra, TKA and de Oliveira, MEG and El-Bacha, T and Alves, JLB and de Souza, EL}, title = {Integrated metagenomic and metabolomic profiling in an in vitro colonic fermentation study to assess the impacts of conventional, unconventional, and whole edible beet (Beta vulgaris L.) parts on the composition and metabolic responses of the intestinal microbiota of hypertensive individuals.}, journal = {The Journal of nutritional biochemistry}, volume = {153}, number = {}, pages = {110316}, doi = {10.1016/j.jnutbio.2026.110316}, pmid = {41707923}, issn = {1873-4847}, mesh = {*Beta vulgaris/chemistry ; *Gastrointestinal Microbiome ; *Hypertension/microbiology/metabolism/diet therapy ; Humans ; Fermentation ; *Colon/microbiology/metabolism ; Metabolomics ; Plant Leaves/chemistry ; Metagenomics ; Antioxidants ; Feces/microbiology ; Plant Roots/chemistry ; Dietary Fiber/analysis ; Bacteria/classification ; Nutritive Value ; Metabolome ; }, abstract = {Beet (Beta vulgaris L.) has been widely studied as a functional food, particularly for its bioactive compounds. This study evaluated the physicochemical characteristics, nutritional composition, antioxidant capacity, and the impacts of freeze-dried beet root (FDBR), freeze-dried beet stems and leaves (FDBSL), and freeze-dried whole beet (FDWB) on the composition and metabolic responses of the intestinal microbiota of hypertensive individuals. FDBR, FDBSL, and FDWB had high nutritional value. FDWB had the highest protein content (10.6/100 g), while FDBSL had the highest total dietary fiber content (46.6/100 g). Twenty-eight phenolic compounds were identified, and the antioxidant capacity reached up to 60.6 µmol Trolox/g in FDBR. 16S rRNA amplicon sequencing analysis demonstrated that colonic fermentation of FDBR, FDBSL, and FDWB with fecal inoculum from hypertensive individuals decreased the Firmicutes/Bacteroidetes ratio, decreased or maintained the bacterial diversity, increased the relative abundance of Bifidobacteriaceae, Lactobacillaceae, and Enterobacteriaceae, and decreased Lachnospiraceae, Oscillospiraceae, and Peptostreptococcaceae. Colonic fermentation of FDBR mainly increased the abundance of Bifidobacterium (1.18-7.63%), while FDBSL increased the abundance of Phocaeicola. FDBR, FDBSL, and FDWB decreased the pH values (6.74-5.09) and altered the metabolic profile during colonic fermentation by consuming sugar and producing several metabolites associated with health-promoting properties, while maintaining antioxidant capacity. FDBR, FDBSL, and FDWB may be circular resources with beneficial effects on the composition and metabolic responses of the intestinal microbiota in hypertensive individuals and could be exploited as dietary adjuvant strategies in the management of arterial hypertension.}, } @article {pmid41708005, year = {2026}, author = {Lin, CC and Uno, H and Yamada, C and Terada, T and Lu, TJ and Fushinobu, S}, title = {Structural insights into glycoside hydrolase family 1 β-glucosidase: Selective oligosaccharide hydrolysis, synthesis, and product profiling.}, journal = {The Journal of biological chemistry}, volume = {302}, number = {4}, pages = {111293}, pmid = {41708005}, issn = {1083-351X}, mesh = {*Oligosaccharides/chemistry/metabolism ; *beta-Glucosidase/chemistry/metabolism/genetics ; Hydrolysis ; Substrate Specificity ; Crystallography, X-Ray ; Molecular Dynamics Simulation ; Mutagenesis, Site-Directed ; Disaccharides ; Glucans ; }, abstract = {β-Glucosidases are essential enzymes in plant cell wall metabolism and have diverse biotechnological applications, including cellulose degradation and prebiotic oligosaccharide synthesis. Td2F2, a glycoside hydrolase family 1 (GH1) β-glucosidase derived from a compost metagenome, exhibits a unique preference for sophorose. However, the molecular basis of this specificity remains unclear. In this study, we determined high-resolution crystal structures of Td2F2 in complex with sophorose (1.64 Å) and laminaribiose (1.16 Å) using sodium malonate as a cryoprotectant. Structural analysis, complemented by molecular dynamics simulations, revealed a distinct subsite +1', where Asn223, Thr225, Glu296, and Arg325 form hydrogen bonds with the reducing-end glucose of sophorose, stabilizing an alternative, nonproductive binding mode adjacent to the catalytic subsites. Site-directed mutagenesis confirmed that residues in subsite +1' are critical for substrate specificity. Guided by structural insights, we designed T225N and E296D mutants, which exhibited enhanced hydrolytic activity toward sophorose. To further investigate the transglycosylation potential of Td2F2, we characterized its dynamic product profile, ranging from disaccharides to tetrasaccharides, using porous graphitic carbon liquid chromatography-orbitrap tandem mass spectrometry. When p-nitrophenyl β-D-glucopyranoside and glucose were used as substrates, Td2F2 preferentially formed β-1→2 and β-1→3 linkages. These findings provide structural evidence that the subsite +1' is a "waiting position" in the GH1 β-glucosidase, offering novel insights into its role in hydrolysis and transglycosylation selectivity. This structural and functional framework paves the way for future GH1 enzyme engineering and expanded biotechnological applications.}, } @article {pmid41708187, year = {2026}, author = {Fang, M and He, J and Zhou, S and Hong, P and Ke, L and Wu, H and Shu, Y}, title = {Pleurotus ostreatus polysaccharides improve microcystin-LR-induced intestinal damage in tadpoles by regulating the interaction between microbiota and intestine.}, journal = {Harmful algae}, volume = {153}, number = {}, pages = {103056}, doi = {10.1016/j.hal.2026.103056}, pmid = {41708187}, issn = {1878-1470}, mesh = {Animals ; *Microcystins/toxicity ; *Pleurotus/chemistry ; *Polysaccharides/pharmacology ; Marine Toxins ; *Intestines/drug effects ; Larva/drug effects ; *Ranidae ; *Gastrointestinal Microbiome/drug effects ; Oxidative Stress/drug effects ; }, abstract = {Exposure to microcystins (MCs) can cause severe intestinal damage. This study aimed to assess the efficacy of Pleurotus ostreatus polysaccharide in alleviating intestinal damage induced by microcystin-leucine-arginine (MC-LR) in tadpoles. Over a 30-day period, tadpoles (Pelophylax nigromaculatus) received daily exposures to MC-LR and were provided with diets either supplemented with or devoid of P. ostreatus polysaccharide. Results revealed that feeding P. ostreatus polysaccharide conferred protection against MC-LR-induced intestinal damage by mitigating barrier damage, lowering intestinal permeability, and reducing the tissue burden of MC-LR. The LPS/TLR4 pathway response was attenuated, reducing inflammation, and oxidative stress-mediated apoptosis response was also diminished. Gram-negative bacteria (e.g., Bacteroides) in the intestine show a positive correlation with LPS content and the transcription of key genes in the LPS/TLR4 pathway. Metagenomic and metabolite analysis of intestinal contents revealed increased abundance of the alanine-glyoxylate aminotransferase gene (agxt)-the key enzyme converting glyoxylic acid to glycine-and elevated glycine content in the MC-LR-exposed group fed polysaccharide. Results from the corresponding fecal microbiota transplantation experiment aligned with the trends observed in the exposure experiment. Therefore, polysaccharide alleviates MC-LR-induced intestinal damage by enhancing intestinal microbiota-mediated glycine synthesis, supplying raw materials for intestinal GSH production, reducing oxidative stress levels, and simultaneously dampening the LPS/TLR4 pathway response. Moreover, feeding polysaccharides might also regulate the intestine's defense against pathogens after MC-LR exposure by enhancing lysozyme activity. There is no evidence of intestinal damage in the P. ostreatus exopolysaccharide group. This study highlights for the first time the role of P. ostreatus polysaccharides in mitigating MC-LR-induced intestinal tissue damage, potentially offering novel insights for their application in aquaculture.}, } @article {pmid41708296, year = {2026}, author = {Huang, J and Zhang, J and Liang, H and Fang, P and Tang, A and Klümper, U and Guo, J and Berendonk, TU and Honda, R and Lin, L and Li, X and Li, B}, title = {Antibiotics or Heavy Metals in Livestock Wastewater: Which One Is the Main Driver for the Development and Spread of Antibiotic Resistance under Coexposure?.}, journal = {Environmental science & technology}, volume = {60}, number = {8}, pages = {6510-6524}, doi = {10.1021/acs.est.5c06042}, pmid = {41708296}, issn = {1520-5851}, mesh = {Metals, Heavy ; *Wastewater ; *Anti-Bacterial Agents ; Animals ; Livestock ; Drug Resistance, Microbial ; }, abstract = {Antibiotics and heavy metals are widely used in livestock farming to promote animal health and growth, leading to their frequent co-occurrence as contaminants in livestock wastewater. However, their relative contributions to shaping the antibiotic resistome in treatment systems remain unclear. In this study, we simulated an aerobic activated sludge process treating livestock wastewater containing enrofloxacin and heavy metals (Cu[2+] and Zn[2+]) to evaluate the development of antibiotic resistance using metagenomic and metatranscriptomic approaches. We observed a diverse and transcriptionally active resistome with over half of the detected antibiotic resistance genes (ARGs) showing expression. ARG profiles under coexposure to enrofloxacin and heavy metals more closely resembled those under heavy metal exposure alone than those under enrofloxacin exposure alone. Zn[2+] exposure resulted in the highest absolute ARG abundance, nearly double that of the control group. Both enrofloxacin and heavy metals significantly altered the abundance and phylogenetic composition of the antibiotic-resistant bacteria (ARB). The exposure to Zn[2+] enhanced the relative abundance and expression level of both metal resistance genes (MRGs)-carrying ARB and the ARGs-carrying plasmids. Phylogenetic analysis of ARG flanking sequences revealed high homology across various genetic contexts. Among mobile genetic elements, plasmids had a greater influence on ARG profiles than did phages or integrative and conjugative elements (ICEs). Transcriptional profiles of microbial physiological adaptations suggested that modulation of cell membrane permeability, promotion of conjugative transfer, and formation of biofilm might play roles in enhancing antibiotic resistance. These findings suggest at environmentally relevant concentrations, heavy metals such as Zn[2+] may present a stronger selective pressure than enrofloxacin for the propagation of antibiotic resistance in aerobic activated sludge process treating livestock wastewater.}, } @article {pmid41708335, year = {2026}, author = {Hkimi, C and Yaiche, H and Kamoun, S and Ben Aissa-Haj, J and Boujemaa, M and Abdelhak, S and Ghedira, K and Hamdi, Y}, title = {OMICs data from Tunisian population: challenges and opportunities in the era of precision medicine.}, journal = {Personalized medicine}, volume = {23}, number = {1}, pages = {23-33}, doi = {10.1080/17410541.2026.2632096}, pmid = {41708335}, issn = {1744-828X}, mesh = {Humans ; *Precision Medicine/methods/trends ; Tunisia ; *Genomics/methods ; Proteomics/methods ; Metabolomics/methods ; Multiomics ; Neoplasms/genetics ; }, abstract = {OBJECTIVE: The transition to precision medicine (PM) is revolutionizing healthcare by enabling diagnostics and treatments tailored to individual molecular and genetic profiles, with omics sciences at its core. In Tunisia, growing interest is seen through initiatives such as Personalized Medicine in North Africa (PerMediNA).

METHODS: This study assesses Tunisia's readiness for PM by mapping publicly available omics datasets and related publications using Tunisian human data. A structured search across PubMed and major repositories covered studies published between 2010 and 2023 involving high-throughput technologies.

RESULTS: A total of 11 omics datasets were found, mainly genomic, alongside 104 publications, of which 96 focused on genomics. Whole exome sequencing (n = 46) and targeted gene panels (n = 37) were the most used approaches. Only six proteomics, one transcriptomics, and one metagenomics studies were identified; no epigenomics or metabolomics datasets were found. Research centered mainly on cancers, including breast, colorectal, and leukemia. While Tunisia shows progress in genomics, major gaps exist in other omics domains.

CONCLUSIONS: Advancing PM in Tunisia requires establishing a national omics data repository with ethical governance, promoting North - South collaborations to build capacity in non-genomic omics fields, and fostering public - private partnerships to strengthen infrastructure, data sharing, and sustainable research development.}, } @article {pmid41708851, year = {2026}, author = {Appler, KE and Lingford, JP and Gong, X and Panagiotou, K and Leão, P and Langwig, MV and Greening, C and Ettema, TJG and De Anda, V and Baker, BJ}, title = {Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor.}, journal = {Nature}, volume = {652}, number = {8109}, pages = {405-415}, pmid = {41708851}, issn = {1476-4687}, support = {//National Natural Science Foundation of China/ ; /NWO_/Dutch Research Council/Netherlands ; }, mesh = {Aerobiosis ; *Archaea/metabolism/classification/genetics/enzymology ; *Eukaryota/metabolism/classification/genetics ; Genome, Archaeal/genetics ; Geologic Sediments/microbiology/chemistry ; Heme/biosynthesis ; Metagenome/genetics ; Origin of Life ; *Oxygen/metabolism ; Phylogeny ; Reactive Oxygen Species/metabolism ; }, abstract = {Asgard archaea were pivotal in the origin of complex cellular life[1]. Heimdallarchaeia (a class within the phylum Asgardarchaeota) are inferred to be the closest relatives of eukaryotes. Limited sampling of these archaea constrains our understanding of their ecology and evolution[2,3], including their role in eukaryogenesis. Here we use massive DNA sequencing of marine sediments to obtain 404 Asgardarchaeota metagenome-assembled genomes, including 136 new Heimdallarchaeia and several novel lineages. Analyses of their global distribution revealed they are widespread in marine environments, and many are enriched in variably oxygenated coastal sediments. Detailed metabolic reconstructions and structural predictions suggest that Heimdallarchaeia form metabolic guilds that are distinct from other Asgardarchaeota. These archaea encode hallmark proteins of an aerobic lifestyle, including electron transport chain complex (IV), haem biosynthesis and reactive oxygen species detoxification. Heimdallarchaeia also encode novel clades of respiratory membrane-bound hydrogenases with additional Complex I-like subunits, which potentially increase proton-motive force generation and ATP synthesis. Thus, we propose an updated Heimdallarchaeia-centric model of eukaryogenesis in which hydrogen production and aerobic respiration may have been present in the Asgard-eukaryotic ancestor. This expanded catalogue of Asgard archaeal genomic diversity suggests that bioenergetic factors influenced eukaryogenesis and constitutes a valuable resource for investigations into the origins and evolution of cellular complexity.}, } @article {pmid41708882, year = {2026}, author = {K-Jánosi, K and Sztojka, A and Kis, IE and Biksi, I and Bakos, Z and Kaszab, E and Mag, T and Albert, E}, title = {Characterisation of Salmonella Typhimurium from a fatal equine nosocomial outbreak and retrospective analysis of equine clinic salmonellosis cases (2010-2025).}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41708882}, issn = {2045-2322}, abstract = {UNLABELLED: In 2024, a highly fatal outbreak of equine salmonellosis occurred in a Hungarian equine referral hospital, resulting in the death or euthanasia of four out of five affected horses. Salmonella (S.) enterica subsp. enterica serovar Typhimurium was identified as the primary causative agent from equine faecal, reflux, and post-mortem intestinal content samples, while one case involved S. Coeln. Extensive environmental sampling during the outbreak also yielded multiple Salmonella serovars. Whole-genome sequencing revealed a high degree of genetic relatedness among the S. Typhimurium isolates, confirming nosocomial transmission. The source of the isolated S. Typhimurium was most likely a 3-year-old gelding imported immediately before the admission to the hospital. The isolates belonged to sequence type ST376 and exhibited multidrug resistance, including extended-spectrum β-lactamase and fluoroquinolone resistance genes. Retrospective analysis of microbiological records from 2010 to mid-2024 identified 23 Salmonella-positive equine cases involving eight serovars and three probable nosocomial clusters preceding the 2024 outbreak. Following the outbreak, enhanced passive surveillance was implemented between October 2024 and August 2025. During this period, 56 at-risk horses were examined using selective bacteriological testing of clinical and post-mortem samples, of which 11 (19.6%) were Salmonella-positive, representing eight different serovars. A distinct cluster of S. Martonos was detected, and six of the surveillance-associated cases resulted in fatal outcomes. These findings demonstrate that Salmonella is repeatedly introduced into the equine hospital environment and that serovars differ markedly in virulence and transmission dynamics. The exceptionally high case fatality observed during the 2024 outbreak underscores the importance of integrated genomic surveillance, rapid diagnostics, and sustained infection control measures to mitigate the risk of severe nosocomial salmonellosis in equine clinics.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-40617-0.}, } @article {pmid41708925, year = {2026}, author = {Wawina-Bokalanga, T and Makangara-Cigolo, JC and Ola-Mpumbe, R and Lokilo, E and Mwakisenda-Tshakotsho, F and Delphine, M and Kahindo, I and Tshonaka-Nkololo, A and Vakaniaki, EH and Loman, N and Houben, S and Lumembe-Numbi, R and Kinganda-Lusamaki, E and Ponga-Museme, A and Mukota-Nungu, Y and Kumar, A and Meris, M and Wilkinson, S and Colquhoun, R and Kenye, KM and Akil-Bandali, P and Amuri-Aziza, A and Martinez, GS and Kelvin, DJ and Dijkman, R and Hensley, LE and Kasita, C and Kafua-Wemba, F and Mwamba, D and Subissi, L and Hoff, NA and Peeters, M and Rimoin, AW and Mokili, JL and Lunguya-Metila, O and Nkwembe, E and Rambaut, A and Liesenborghs, L and Low, N and Kindrachuk, J and Vercauteren, K and Edwards, R and Kelly, JN and Mbala-Kingebeni, P and Ahuka-Mundeke, S and Mumba, D and Muyembe-Tamfum, JJ}, title = {Deciphering the etiology of the 2024 outbreak of undiagnosed febrile illness in Panzi, Democratic Republic of the Congo.}, journal = {Nature medicine}, volume = {32}, number = {4}, pages = {1374-1382}, pmid = {41708925}, issn = {1546-170X}, mesh = {Humans ; Female ; Democratic Republic of the Congo/epidemiology ; *Disease Outbreaks ; Child, Preschool ; Male ; *Fever/epidemiology/etiology/virology/diagnosis ; Infant ; Plasmodium falciparum/pathogenicity/isolation & purification ; Coinfection/epidemiology/virology ; Child ; Malaria, Falciparum/epidemiology ; Influenza A Virus, H1N1 Subtype/pathogenicity/isolation & purification ; SARS-CoV-2/isolation & purification/pathogenicity ; Influenza, Human/epidemiology/virology ; Adult ; Prospective Studies ; Adolescent ; }, abstract = {In late 2024, an outbreak of over 400 cases of undiagnosed febrile illness, predominantly presenting as fever and cough, was reported in Panzi Health Zone, southwestern Democratic Republic of the Congo. Here we conducted an epidemiological and laboratory investigation to determine the etiology of the outbreak. Clinical data and specimens were prospectively collected from 108 individuals, of whom 59/108 (54.6%) were female. Children aged <5 years were the most affected (47/108, 43.5%); 14/32 (43.7%) were malnourished. Oro/nasopharyngeal swabs from 96/108 individuals were PCR tested; 26 blood samples were sequenced. Plasmodium falciparum was detected in 56/108 (51.8%) individuals. Co-infections were also detected, with influenza A(H1N1)pdm09 virus in 16/56 (28.6%) and severe acute respiratory syndrome coronavirus 2 in 10/56 (17.9%) individuals. No novel pathogens were detected via metagenomics. Our findings suggest that the outbreak was primarily associated with a surge in malaria cases, with concurrent viral respiratory infections. Increasing decentralized laboratory capacity and strengthening broader health systems remain crucial for faster outbreak detection and investigation.}, } @article {pmid41709052, year = {2026}, author = {Idris, H and Hairi, HH and Ahmad, A and Danish-Daniel, M and Zin, NM and Sanderson, RA and Raja Yahya, MFZ and Majhool, AA and Hassan, MY and Azman, MAZ}, title = {Revealing actinobacterial diversity inhabiting Malaysian Beach Ridges Interspersed with Swales (BRIS) soil : insights from culture-dependent and metagenomic approaches.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {29}, number = {3}, pages = {301-313}, pmid = {41709052}, issn = {1618-1905}, abstract = {The discovery of novel antibiotics remains a pressing global challenge as many known microorganisms continue to yield compounds already present in existing drugs. To overcome this limitation, bioprospecting in underexplored and extreme environments using both culture-dependent and culture-independent strategies has become essential. In this study, we investigated the microbial diversity of Beach Ridges Interspersed with Swales (BRIS) soil from Setiu, Terengganu, Malaysia—an environment characterized by poor nutrient retention, low water-holding capacity, and acidic conditions with lack information available on their microbial community composition. Therefore, this study was conducted with the main objectives to investigate actinomycetes community composition in BRIS soil using metagenomics and culture-dependent approaches. To address these objectives, a dual approach was employed: (i) culture-dependent isolation of actinomycetes using selective media, followed by morphological and 16S rRNA gene-based phylogenetic analysis, and (ii) culture-independent high-throughput sequencing of the 16S rRNA gene (Illumina MiSeq) to characterize the broader microbial community. Results from the selective isolation yielded 180 actinomycete isolates grouped into 69 colour-based categories, with 15 representatives identified by 16S rRNA sequencing as belonging predominantly to Streptomyces, alongside the rare genus Dermacoccus. In contrast, metagenomic analysis revealed a far richer microbial landscape comprising 4719 OTUs, 32 bacterial phyla, and 380 genera, including a high proportion of uncultured taxa. Notably, actinobacterial diversity was dominated by Acidothermus, whereas Streptomyces predominated in culture-dependent isolation, highlighting the complementary nature of both approaches. These findings confirm that BRIS soil harbours unique microbial communities shaped by its physicochemical conditions, with potential as a reservoir for rare actinomycetes and novel bioactive compounds. The study provides the first combined culture-dependent and metagenomic insight into BRIS soil microbiota and underscores its promise for future pharmaceutical and biotechnological exploration.}, } @article {pmid41709267, year = {2026}, author = {Baquer, F and Grillon, A}, title = {Interaction between tick and host microbiotas: a four-step waltz.}, journal = {Parasites & vectors}, volume = {19}, number = {1}, pages = {}, pmid = {41709267}, issn = {1756-3305}, mesh = {Animals ; Humans ; *Ticks/microbiology ; Skin Microbiome ; *Tick-Borne Diseases/microbiology/transmission ; *Microbiota ; *Host Microbial Interactions ; Host-Pathogen Interactions ; Symbiosis ; *Arachnid Vectors/microbiology ; }, abstract = {Tick-borne diseases represent a growing public health concern worldwide, yet the microbial factors that govern pathogen transmission remain incompletely understood. Over the past decade, high-throughput metagenomics and functional studies have revealed that two distinct microbial communities-the vertebrate host's skin microbiota and the tick's own microbiome-act synergistically as key modulators of pathogen acquisition, persistence within the vector, and successful transmission to the vertebrate host. At the feeding site, the skin microbiota orchestrates local cutaneous immunity, influences inflammatory responses, and can either hinder or inadvertently facilitate dermal establishment of tick-borne pathogens such as Borrelia burgdorferi sensu lato (s.l.), Anaplasma phagocytophilum, Rickettsia species, Babesia spp., and tick-borne encephalitis virus. Tick feeding itself induces rapid and sometimes long-lasting dysbiosis of the skin microbial community, creating temporal windows of vulnerability for pathogen invasion. Concurrently, within the tick vector, a core set of endosymbiotic bacteria, including Rickettsia buchneri, Midichloria mitochondrii, Coxiella-like, and Francisella-like endosymbionts, engage in complex mutualistic, competitive, and facilitative interactions. These symbionts regulate vector competence through nutrient provisioning (especially B-vitamins), direct competition for niche space, and immune priming or suppression of the tick's innate immune system. Such interactions ultimately determine the maintenance, abundance, and transmissibility of tick-borne pathogens. By integrating these dual host-vector microbiome perspectives in a comprehensive review, we highlight emerging mechanistic insights into transmission ecology and biologically grounded targets for the prevention and control of tick-borne diseases, including anti-microbiota vaccines and paratransgenic and microbiome-based approaches.}, } @article {pmid41709323, year = {2026}, author = {Yin, S and Xiao, Z and Yu, Z and Zhou, C and Jian, J and Xiao, Y and Yang, H}, title = {Iterative enrichment cultivation and multiomic analysis reveal potential endophytic bacteria affecting the sinomenine synthesis in Sinomenium acutum.}, journal = {Microbial cell factories}, volume = {25}, number = {1}, pages = {}, pmid = {41709323}, issn = {1475-2859}, mesh = {*Endophytes/metabolism/genetics/isolation & purification ; *Morphinans/metabolism ; *Sinomenium/microbiology/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Multiomics ; }, abstract = {Endophytes play important roles in plant metabolite synthesis, and certain strains were capable of producing bioactive compounds identical to those of their hosts. However, it remains unknown whether culturable endophytes of S. acutum can synthesize intermediate metabolites for the plant principal bioactive compound-sinomenine (SIN) or the compound itself. In this study, we investigated the successions of the culturable bacterial community and the alkaloid profiles within S. acutum endophytes across ten iterative enrichment cultivations using Czapek-Dox and Gause's No. 1 chemically defined media. The results demonstrated significant alterations in the composition and structure of the endophytic consortium and metabolites of the endophytic consortium during iterative cultivation. Priestia aryabhattai dominated the community in the first generation, whereas Microbacterium paraoxydans and Bacillus velezensis became dominant by the tenth generation. SIN was detected at the first and the fifth generation, with declining concentrations, and was absent at the tenth generation. Correlation network analysis revealed a strong positive correlation between the relative abundance of P. aryabhattai and the SIN content. Furthermore, a specific strain, L15, identified as P. aryabhattai, was isolated from the iterative culture. UPLC-MS/MS analysis of P. aryabhattai L15 metabolites confirmed the presence of SIN, alongside other alkaloids including cyclanoline, N-methylhigenamine-7-O-glucopyranoside, and isoquinoline. Further metagenomic analysis also indicated that the relative abundance of P. aryabhattai was significantly (p < 0.05) positively correlated with the SIN content in plant tissues. This study systematically elucidated the role of endophytic bacteria and provides potential strains for the synthesis of bioactive compounds and pharmaceutical research.}, } @article {pmid41709890, year = {2026}, author = {Dai, L and Zhan, W and Huang, X and Lyu, L and Jiang, S and Zhou, P}, title = {Refractory multiple brain abscesses caused by Prevotella loescheii and Porphyromonas gingivalis: successful endoscopic lavage and drainage: a case report and review of the literature.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1736006}, pmid = {41709890}, issn = {2296-858X}, abstract = {BACKGROUND: Brain abscesses represent life-threatening conditions, with management complexities significantly heightened in cases involving multiple lesions that are refractory to standard empirical therapies. Prevotella loescheii and Porphyromonas gingivalis, anaerobic bacteria typically residing within the oral flora, are infrequent yet formidable pathogens responsible for intracranial abscess formation. The fastidious nature of these microorganisms often results in delayed diagnosis and initiation of targeted treatment.

CASE PRESENTATION: A 25-years-old male presented with a 1-month history of cough, sputum production, and persistent high-grade fever reaching 41 °C. Initially diagnosed with a brain abscess at a local hospital, he received empirical treatment with ceftriaxone, acyclovir, and mannitol, which failed to yield clinical improvement. His condition subsequently deteriorated, characterized by disturbances in consciousness and dysarthria. The antimicrobial regimen was escalated to include vancomycin and meropenem. Despite these efforts, the patient's neurological status continued to decline, with imaging studies revealing the development of multiple new intracranial abscesses and diffuse intracranial hypertension. Surgical intervention was undertaken, involving abscess excision and decompressive craniectomy. Postoperative imaging 1 week later showed further abscess expansion and the onset of right-sided hemiplegia. Upon admission to our institution, metagenomic next-generation sequencing (mNGS) of the cerebrospinal fluid identified the presence of Prevotella loescheii and Porphyromonas gingivalis. The antimicrobial regimen consisting of vancomycin and meropenem was maintained, and the patient underwent endoscopic intracranial abscess lavage with burr hole external drainage. This integrated approach led to significant radiographic resolution of the abscesses and a gradual improvement in the patient's level of consciousness. The refractory infection was traced back to an oropharyngeal source.

CONCLUSION: This case highlights the critical diagnostic value of mNGS in detecting fastidious oral anaerobic pathogens in culture-negative refractory brain abscesses. It illustrates that a combination of targeted antibiotic therapy and minimally invasive surgical intervention-specifically, endoscopic lavage and drainage-can be highly effective in managing complex, multi-loculated abscesses caused by Prevotella loescheii and Porphyromonas gingivalis. Maintaining a high index of suspicion for an odontogenic or oropharyngeal origin is crucial in the diagnostic evaluation of such infections.}, } @article {pmid41710035, year = {2026}, author = {John, J and Ortiz, M and Ramond, P and Campbell, BJ}, title = {Functional redundancy and metabolic flexibility of microbial communities in two Mid-Atlantic bays.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag021}, pmid = {41710035}, issn = {2730-6151}, abstract = {Functional redundancy (FRed) is expected to buffer ecosystems against change, yet it has rarely been characterized in natural systems. How changes in microbial metabolisms, activity, and FRed in ecosystems are influenced by temporal, spatial, and environmental patterns is especially unclear. Here, we analyzed paired metagenomic and metatranscriptomic datasets from surface water samples collected in the Chesapeake and Delaware Bays, USA. These adjacent estuaries experience similar climatic conditions but differ in nutrient availability, salinity, and other environmental factors. We reconstructed 345 high quality metagenome assembled genomes and assessed their metabolic flexibility, and the extent of gene encoded (potential) and expressed (realized) FRed as a function of environmental drivers, microbial lifestyle (free living vs. particle attached), and gene function. The microbiomes exhibited high metabolic flexibility, reflecting their potential, and in many cases, realized gene expression, to exploit diverse energy sources, ranging from organic carbon substrates to trace gases. Potential and expressed FRed varied across seasons, lifestyles, and gene functions, and was structured within each bay by environmental factors such as temperature, salinity, and concentrations of phosphate, silicate, and chlorophyll a. These findings highlight variability in community-level metabolism, and FRed across estuarine microbiomes, shaped by environmental conditions, seasonality, and lifestyle, and provide insights into how these communities may respond to future perturbations.}, } @article {pmid41710165, year = {2026}, author = {Stevenson, Z and Schultz, DL and Chamberlain, M and Rico, K and Anbar, A and Dekas, AE and Swanner, ED}, title = {Lowering the Mo limit for nitrogen fixation by Mo-nitrogenase.}, journal = {Communications earth & environment}, volume = {7}, number = {1}, pages = {169}, pmid = {41710165}, issn = {2662-4435}, abstract = {Archean ocean marine primary productivity may have been limited by biologically available nitrogen. Due to low molybdenum abundances, early biological nitrogen fixation is thought to have relied on alternative nitrogenases that incorporate vanadium or iron instead of molybdenum. Here, we examine nitrogen fixation in a Cyanobacteria-dominated, ferruginous, low-sulfate, low-molybdenum lake, which replicates biological and chemical conditions relevant to early marine primary productivity. Nitrogen fixation occurs even when molybdenum is <1 nM, 100x less than the abundance in modern oceans. Molybdenum additions did not increase nitrogen fixation rates, indicating that diazotrophs were not molybdenum limited. Only the molybdenum-iron nitrogenase was detected in metagenomes and metatranscriptomes, indicating that the alternative nitrogenases were not required. We suggest that low sulfate (<1 μM) and/or efficient uptake mitigated molybdenum limitation. These results indicate that molybdenum bioavailability may be strongly controlled by sulfate and that alternative nitrogenases are not essential for nitrogen fixation at low molybdenum.}, } @article {pmid41710374, year = {2026}, author = {He, L and Li, F}, title = {Clinicopathologic Features of Genitourinary Malakoplakia and Analytical Utility of the MetaPath Assay.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {582917}, pmid = {41710374}, issn = {1178-6973}, abstract = {PURPOSE: To describe the clinicopathological spectrum of genitourinary malakoplakia (MPL) and to evaluate the feasibility and clinical impact of metagenomic pathogen detection (MetaPath) performed on archival formalin-fixed paraffin-embedded (FFPE) tissue.

PATIENTS AND METHODS: Clinical imaging, histopathology, immunohistochemistry, special stains and MetaPath results were retrospectively analysed in five MPL cases diagnosed between January 2019 and August 2025.

RESULTS: The cohort comprised four men and one woman with a median age of 65.4 years. Four lesions arose in the prostate and one in the bladder. Histology showed chronic granulomatous inflammation with numerous eosinophilic histiocytes containing 5-10 µm targetoid Michaelis-Gutmann bodies. CD68 and CD163 were diffusely positive; PAS and iron stains highlighted the inclusions. MetaPath identified pathogens in 3/5 (60%) FFPE specimens (Escherichia coli in two, Pseudomonas aeruginosa in one). Antibiotic regimens were adjusted according to MetaPath results. After a median follow-up of 6 months (range 4-8) all patients remained symptom-free.

CONCLUSION: MPL is frequently misdiagnosed as malignancy. MetaPath can reliably detect pathogens in archival tissue and guide targeted antimicrobial therapy, representing a valuable adjunct to conventional culture.}, } @article {pmid41711070, year = {2026}, author = {Beauvais, M and Schatt, P and Soulié, T and Lambert, S and Montiel, L and Gaudin, M and Chaffron, S and Logares, R and Bouget, FY and Galand, PE}, title = {Functional complementarity between vitamin B1 and B12 metabolisms shapes seasonal marine microbial communities.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41711070}, issn = {1751-7370}, support = {ANR-24-CE02-7681//French Agence Nationale de la Recherche/ ; }, mesh = {*Vitamin B 12/metabolism ; Seasons ; *Seawater/microbiology ; *Thiamine/metabolism ; Mediterranean Sea ; Metagenomics ; *Bacteria/metabolism/genetics/classification ; Metagenome ; }, abstract = {Marine microbial communities are fundamental to nutrient and biogeochemical cycling, with intricate networks of metabolic interdependencies influencing their structure and dynamics. Among these, vitamins B1 (thiamin) and B12 (cobalamin) play crucial roles as enzymatic cofactors in central metabolic pathways. Despite their importance, the temporal dynamics of vitamin production, bioavailability, and associated microbial interactions remain poorly understood. Using a 7-year monthly metagenomic time series from the NW Mediterranean Sea (SOLA station), we found that vitamin B1/B12 auxotrophs (need for an exogenous vitamin source) were present throughout the year. Among B1 auxotrophs, those requiring the thiamin precursor pyrimidine were the most prevalent, with peak abundances in summer. Distinct metagenome-assembled genome co-abundance patterns between B1 and B12 producers/auxotrophs across seasons suggested mutualistic relationships. Double B1/B12 vitamin complementarities were more common in summer, and single vitamin complementarity was dominant in winter. As previously shown for vitamin B12, which is limiting during winter, bioassays revealed variable availability of vitamin B1 in winter seawater despite the abundance of its producers, suggesting potential transfer of vitamin B1 among microorganisms. Finally, microcosm experiments showed that B1 and B12 amendments significantly influenced the composition of microbial communities, with temporal variations in their impact. In some cases, B12 and B1 amendments favored both vitamin auxotrophs and producers, highlighting complex interdependencies between B1 and B12 producers and consumers. Our findings highlight the complexity of B vitamin-mediated metabolic interactions that shape microbial community dynamics and underscore the need for long-term, high-resolution studies to better understand vitamin-driven ecological processes in marine systems.}, } @article {pmid41711071, year = {2026}, author = {Boeckel, C and Lisovski, S and Stoof-Leichsenring, KR and Weiß, JF and Liu, S and Harms, L and Herzschuh, U}, title = {DNA virus-host patterns in lake and marine environments over the last glacial cycle.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41711071}, issn = {1751-7370}, support = {//International Science Program for Integrative Research/ ; 772852/ERC_/European Research Council/International ; }, mesh = {*Lakes/virology ; *DNA Viruses/genetics/classification/isolation & purification/physiology ; Ecosystem ; *Seawater/virology ; DNA, Ancient/analysis ; Bacteria/virology/genetics ; Archaea/virology/genetics ; Geologic Sediments/virology ; Siberia ; *Host Microbial Interactions ; }, abstract = {Viruses are integral to population dynamics, biogeochemical cycling, and host evolution, making them essential for ecosystem function. We explore long-term virus-host interactions mainly within microbial ecosystems in lake and marine environments across the late Pleistocene and Holocene. Sedimentary ancient DNA (sedaDNA) from five Siberian lakes and three Subarctic/Antarctic marine cores were analysed to infer past DNA virus taxa from metagenomic sequences. Viruses accounted for 357 161 reads (0.089% of total mapped reads), distributed across 2084 unique viral taxa. Virus communities differ between lakes and marine sites, with lakes dominated by Caudoviricetes and marine environments featuring Caudoviricetes and Algavirales. Each time series shows compositional changes from the Pleistocene to the Holocene, supporting sedaDNA as a tool to reconstruct time-resolved ancient viral assemblages. Among the most abundant viruses, we identified 83 virus-host pairs documented in published literature, spanning bacterial, archaeal, and eukaryotic hosts, and assessed their associations based on co-occurrence correlations. Over millennia, virus-host co-variations are particularly stable in marine systems, especially for phytoplankton-infecting viruses. However, in the Bering Sea, we find a lack of virus-host correlation, likely because an Arctic Pelagibacter strain expanded after the Bering Strait opened, potentially due to absent viral infection, although database limitations prevent clear interpretation. Antagonistic patterns also appear between bacteriophages and hosts, possibly linked to shifts between lytic and lysogenic cycles in response to environmental changes. This study demonstrates that sedaDNA time-series can reveal ancient viral community structures and long-term ecological patterns, highlighting the value of ancient viromes in understanding ecosystem-specific responses to environmental change.}, } @article {pmid41711085, year = {2026}, author = {Hart, LN and Errera, RM and Godwin, C and Loftin, KA and Laughrey, ZR and Katona, LR and Johnson, EC and Cory, RM and Kiledal, EA and Den Uyl, P and Kharbush, JJ and Sherman, DH and Dick, GJ}, title = {Diverse Cyanopeptides follow distinct temporal succession patterns in freshwater harmful algal blooms.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41711085}, issn = {1751-7370}, mesh = {*Harmful Algal Bloom ; *Cyanobacteria/genetics/metabolism/classification ; *Lakes/microbiology ; Seasons ; Multigene Family ; Microcystins ; Metagenomics ; Fresh Water/microbiology ; Metabolomics ; }, abstract = {Toxic cyanobacterial harmful algal blooms (cyanoHABs) threaten freshwater resources globally and are intensifying with increasing eutrophication. Bloom toxicity is strongly influenced by intraspecific variation in the biosynthetic repertoires of toxic cyanobacteria, yet few studies examine the diversity of cyanobacterial cyanopeptides beyond hepatotoxic microcystins. To understand the dynamics and drivers of cyanopeptide diversity in cyanoHABs, we analyzed temporal patterns of cyanobacteria, metabolites, and their biosynthetic gene clusters (BGCs) in western Lake Erie using a 7-year time series (2016-2022) of metagenomic and metabolomic data. Our findings demonstrate that shifts from Microcystis to Dolichospermum occur later in the bloom season, coinciding with lower temperatures. Modules of co-varying BGCs (biosynthesis modules) from these genera were identified with hierarchical clustering, with uncharacterized BGCs among the most abundant. Biosynthesis modules rich in nonribosomal peptide synthetases (NRPS) peaked in early August, coinciding with elevated levels of inorganic nitrogen, warmer temperatures, and high Microcystis abundance. In contrast, modules rich in polyketide synthases (PKS) and ribosomally synthesized and post-translationally modified peptides (RiPPs) peaked following the Microcystis maximum in mid-August. Metabolomic analyses confirmed that metabolites followed shared seasonal patterns with their associated biosynthesis modules, forming three phases characterized by (i) microcystins, (ii) anabaenopeptins and aeruginosins, and (iii) aerucyclamides. These phases co-varied with bottom-up and top-down pressures, with later phases coinciding with increased microbially processed organic nitrogen and reduced detection of grazers. This study demonstrates consistent seasonal patterns of cyanobacterial metabolite succession and co-occurrence beyond microcystins, suggesting tradeoffs between biosynthetic resource demands and ecological controls.}, } @article {pmid41711914, year = {2026}, author = {Demin, K and Onasenko, K and Beletskaya, A and Tsoy, A and Boyko, M and Kulikov, M and Kulikova, D and Prazdnova, E}, title = {Studying organosulfonate metabolism in southern Russia chernozem soil microbial community: ubiquity of the desulfonation pathways and possible mixotrophy in common soil heterotrophs.}, journal = {Archives of microbiology}, volume = {208}, number = {4}, pages = {201}, pmid = {41711914}, issn = {1432-072X}, support = {SP-12-23-04//Priority 2030/ ; }, abstract = {Microbial metabolism of organosulfonates (OS) have been researched for at least three decades. However, the studies conducted so far were heavily focused on marine ecosystems, while in terrestrial ecosystems microbial desulfonation pathways are poorly characterized. Here we describe culturable microbial community of chernozem soil from the perspective of OS-based metabolism. Using the metagenomic and culture-dependent approaches, we compare microbial isolates grown on OS to the isolates enriched using common media for soil bacteria and show that there is no substantial difference in terms of taxonomy and OS metabolism genes representation. Alkanesulfonates and taurine are the primary OS compounds metabolized by soil bacteria through ssuDE and tauD enzymatic systems, while other OS desulfonation pathways are rare or absent. Actinobacterial and alphaproteobacterial representatives were the dominant part of OS-utilization community. We show in vitro taurine desulfonation and subsequent re-utilization of produced sulfite by soil actinobacterial isolates of Streptomyces anulatus and Arthrobacter siccitolerans. We hypothesize that microbial desulfonation coupled to sulfite oxidation may be a strategy to generate energy from both organic and inorganic molecules oxidation in heterotrophs (that is, mixotrophy). Finally, it is that OS-metabolism represents a ubiquitous metabolic capability rather than a niche trait, interlinking key biogeochemical cycles, particularly sulfur, nitrogen, and carbon.}, } @article {pmid41711928, year = {2026}, author = {Farias, LABG and Viana Neto, OM and Lima Sobrinho, EP and de Melo, AGND and Pontes, IM and Gonçalves, BBS and Benevides, HP and Maia, SPO and Rodrigues, JLN and Perdigão Neto, LV}, title = {Streptococcus suis infection as an emerging zoonotic threat in Brazil: a One Health-based review.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {68}, number = {}, pages = {e19}, pmid = {41711928}, issn = {1678-9946}, mesh = {Animals ; *Streptococcus suis/genetics ; Humans ; Brazil/epidemiology ; *Streptococcal Infections/epidemiology/microbiology/veterinary/transmission/diagnosis ; *Zoonoses/microbiology/epidemiology ; Swine ; One Health ; *Bacterial Zoonoses/epidemiology/microbiology ; *Communicable Diseases, Emerging/epidemiology/microbiology ; Swine Diseases/microbiology/epidemiology ; }, abstract = {Streptococcus suis infection is an emerging zoonotic pathogen of growing concern in Brazil, particularly in the Northeast-a region lacking swine-focused surveillance. Although human contamination remains rare, they have been increasingly reported among individuals exposed to pigs or pork products, and most commonly present as central nervous system infections. Diagnostic challenges persist, especially related to culture-based methods, highlighting the need for advanced molecular tools like polymerase chain reaction and metagenomic Next-Generation Sequencing. Veterinary data reveal a high diversity of serotypes and concerning rates of antimicrobial resistance. These studies remain scarce in regions with reports of human infection. This review highlights the clinical, epidemiological, and microbiological aspects of S. suis in Brazil and underscores the importance of One Health approaches to enhance detection and prevention.}, } @article {pmid41712385, year = {2026}, author = {Hong, J and Xue, W and Wang, T}, title = {Universal gene-level bimodality in natural microbial communities.}, journal = {Cell reports}, volume = {45}, number = {3}, pages = {117013}, doi = {10.1016/j.celrep.2026.117013}, pmid = {41712385}, issn = {2211-1247}, mesh = {Humans ; *Microbiota/genetics ; Metagenome/genetics ; Machine Learning ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Bimodality-the coexistence of two peaks in trait distributions-is common in natural ecosystems. In microbiomes, bimodality of species abundances is known. However, whether this pattern applies to community functionality remains unclear. Here, we systematically investigate the abundance distributions of individual genes in different microbiomes, from human gut to ocean, revealing widespread gene-level bimodality. The bimodal genes are enriched in niche-specific pathways, suggesting their roles in ecological adaptation of the community. Based on their abundances, we develop a framework for microbiome functional typing, offering a gene-centric alternative to the taxonomy-based paradigm. Applied to the human gut, our approach identifies eleven genes exhibiting robust bimodality across western countries. These genes are associated with diseases such as liver cirrhosis. Machine learning models leveraging these genes are predictive of these diseases, underscoring their potential as clinically relevant biomarkers. Our work provides critical insights for microbiome functional architecture and has implications for microbiome-based diagnostics.}, } @article {pmid41712566, year = {2026}, author = {Bedoya-Urrego, K and Peñuela-Martínez, AE and Alzate, JF}, title = {Uncovering the hidden yeast diversity in fermented coffee: Insights from a shotgun metagenomic approach.}, journal = {PloS one}, volume = {21}, number = {2}, pages = {e0332370}, pmid = {41712566}, issn = {1932-6203}, mesh = {*Metagenomics/methods ; Fermentation ; Phylogeny ; *Coffee/microbiology ; *Yeasts/genetics/classification ; Metagenome ; Shotgun Sequencing ; Genome, Fungal ; }, abstract = {Yeasts play a pivotal role in coffee fermentation, shaping microbial succession and contributing to the development of final flavor profiles. Despite their importance, yeast taxonomy in this context remains poorly resolved. Traditional classification methods often result in misidentifications due to the limited resolution of classical microbiological techniques and the rapidly evolving taxonomic framework driven by advances in phylogenomic. Moreover, the diversity of budding yeasts in coffee fermentations remains underexplored using high-resolution approaches such as metagenomics. To address this gap, we applied a shotgun metagenomic strategy and reconstructed metagenome-assembled genomes (MAGs) from multiple coffee fermentation samples and, using a robust phylogenomic framework based on 832 conserved single-copy genes. We confidently classified 22 yeast MAGs within the subphylum Saccharomycotina. These included well-known taxa such as Pichia kluyveri, Hanseniaspora spp., Torulaspora delbrueckii, and members of the Kurtzmaniella clade. Most MAGs were placed in strongly supported monophyletic groups (ultrafast bootstrap = 100), with short intra-clade branch lengths indicative of intraspecific variation. Pichia kluyveri emerged as the most abundant and widespread species, detected in all analyzed metagenomes, followed by Hanseniaspora spp. Our results underscore the power of high-resolution phylogenomic for classifying yeast MAGs and highlight the ecological importance of Pichia, Hanseniaspora, Torulaspora, and Kurtzmaniella in spontaneous coffee fermentations.}, } @article {pmid41712638, year = {2026}, author = {Zhao, XD and Wang, YQ and Zhang, S and Li, JQ and Cai, YJ and Shu, X and Chen, Z and Zhang, SY}, title = {Spatially resolved denitrification coupled with methane and arsenite oxidation at the millimeter-scale straw-soil interface.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {8}, pages = {e2521285123}, pmid = {41712638}, issn = {1091-6490}, support = {52270198//National Natural Science Foundation of China/ ; 42477116//National Natural Science Foundation of China/ ; JYB2025XDXM904//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; }, mesh = {*Methane/metabolism ; *Arsenites/metabolism ; Oxidation-Reduction ; *Denitrification ; *Soil Microbiology ; *Soil/chemistry ; Nitrogen/metabolism ; Bacteria/metabolism/genetics ; }, abstract = {Straw return reshapes the biogeochemical processes in paddy soils by driving microbial transformation of key elements. Despite growing awareness of these individual processes, the integration of these processes under millimeter-scale spatiotemporal heterogeneity remains unclear. Combining high-resolution geochemical profiling with multiomics, we revealed that straw addition altered the depth-dependent dynamics of arsenic, carbon, and nitrogen, establishing a sophisticated three-layer microbial stratification. We identified 1) an 18 mm organic matter (OM)-rich layer extending from the straw layer, which serves as a methanogenic epicenter co-occurring with active nitrogen fixation microbes; 2) an overlying layer dominated by aerobic methane oxidation and denitrification microbes; and 3) a deeper substraw layer dominated by anaerobic arsenite oxidation and denitrification microbes. Significantly positively correlated abundances of transcribed mcrA with nifH genes and pmoA or aioA/arxA with denitrification genes were identified. Corroboratively, intensified co-occurrence patterns of mcrA with nifH, pmoA with denitrification, and aioA/arxA with denitrification genes were observed in the OM-rich, upper, and lower layers, respectively. Moreover, the co-occurred mcrA-nifH and aioA-nirS/arxA-narG genes in different metagenome-assembled genomes presented 80.6 to 260.8- and 1.55 to 6.85-fold greater transcriptional activity in the OM-rich and lower layers than in the other layers, respectively. Our results demonstrated that straw incorporation established a dynamic soil redox zone, restructuring millimeter-scale microbial networks and promoting potentially coupled denitrification with arsenite or methane oxidation, as well as methanogenesis with nitrogen fixation. These findings provide a mechanistic basis for optimizing subsurface straw placement and nitrate application to enhance nutrient cycling and mitigate environmental risks.}, } @article {pmid41713061, year = {2026}, author = {Cokro, A and Albert Ng, TC and Hill, ED and Lee, C and Chandra Segeran, US and Arumugam, K and Williams, RBH and Wuertz, S}, title = {Microbial community biomarkers can forecast methane production in full-scale anaerobic digesters.}, journal = {Journal of environmental management}, volume = {401}, number = {}, pages = {128828}, doi = {10.1016/j.jenvman.2026.128828}, pmid = {41713061}, issn = {1095-8630}, mesh = {*Methane/biosynthesis ; *Bioreactors/microbiology ; Anaerobiosis ; Sewage/microbiology ; *Microbiota ; Biomarkers ; Wastewater/microbiology ; Singapore ; Machine Learning ; }, abstract = {Methane production from wastewater sludge via anaerobic digestion is a complex process and a disturbance in any one of the microbial stages can lead to eventual failure. Hence, it is desirable to detect disturbances as soon as possible. Although machine learning has been used to predict methane production from a variety of different substrates, there are no studies using metagenomic or -transcriptomic microbial community data as predictor variables. We used random forest analysis on a combination of physicochemical and microbial predictors to forecast methane production from three full-scale sludge digesters representing replicates of one another in a wastewater treatment plant in Singapore. Digesters were sampled for 25 weeks, and 42 physicochemical variables were measured along with shotgun metagenome and total RNA transcriptome sequencing. Models built using samples from a single digester yielded reactor-specific predictors, largely due to the limited sample size per reactor and the influence of rarer taxa. When data from the three digesters were combined, the best predictors included both substrate-related physicochemical parameters, such as chemical oxygen demand, and microbial taxa. Simulation using learning curves indicated that 150 to 200 samples instead of the 75 used would have yielded the most accurate methane prediction. The selection of many unidentified operational taxonomic units as microbial predictors suggests the existence of important yet unknown microorganisms in anaerobic digestion. The prediction model supports onsite digester surveillance by identifying digester-specific predictors through sufficient sampling, after which only those predictors need to be measured for subsequent monitoring.}, } @article {pmid41713162, year = {2026}, author = {Liu, X and Cai, H and Zhao, L and Ke, D and Xu, X and Li, J and Yu, J and Shen, Y and Zhu, L and Jin, Y and Zhang, M and Liu, S and Du, J and Zheng, J and Dong, R}, title = {Microplastic-associated gut microbial profile and antibiotic resistance in preschool children: a multicentre cross-sectional study in China.}, journal = {EBioMedicine}, volume = {125}, number = {}, pages = {106177}, pmid = {41713162}, issn = {2352-3964}, mesh = {Humans ; Cross-Sectional Studies ; China/epidemiology ; *Gastrointestinal Microbiome/drug effects ; Child, Preschool ; Female ; Male ; *Microplastics/adverse effects ; RNA, Ribosomal, 16S/genetics ; *Drug Resistance, Microbial ; Feces/microbiology ; Metagenomics/methods ; }, abstract = {BACKGROUND: Microplastics (MPs) are ubiquitous in ecosystems and present in the human body, causing a worldwide environmental issue. However, the extent of human exposure to MPs remains largely unknown. Although mice exposed to MPs exhibit gut microbiota dysbiosis, the impact of MPs on the human intestinal microbiota remains unclear. Furthermore, MPs can carry and spread antibiotic resistance genes (ARGs). However, their potential influence on ARG abundance is underexplored.

METHODS: A multicentre cross-sectional study was conducted in Xiamen, Shanghai, and Nanjing in China from October 2022 to March 2023. A total of 335 couples of faecal samples were collected and analysed for MPs using Py-GC/MS and gut microbiota using 16S rRNA and metagenomic sequencing.

FINDINGS: Eight types of MPs were detected in 335 faecal samples, with a median concentration of 212.1 μg/g dw. MP exposure may be associated with the composition of the host gut microbiota. Microbial function analysis indicated the significant enrichment of 62 pathways primarily related to the metabolic pathways of macronutrients, vitamins, and bioactive substances. Total plastic concentration was significantly related to the relative abundance of species and ARGs, however this could not be attributed to specific plastic polymers after adjusting for covariates.

INTERPRETATION: This study provides baseline data on the gap in understanding of preschoolers' MP exposure, supporting the hypothesis that MP exposure might disrupt gut bacterial constitution and functions. This raises concerns regarding the potential adverse effects on the human gut when exposed to MPs, particularly drug resistance risks in younger populations.

FUNDING: Project of Shanghai Municipal Financial Professional foundation (Food Safety Risk Assessment) (grant number: RA-2023-10), National Natural Science Foundation of China (grant number: 2023YFF1104800), and Key Disciplines in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025) (grant number: GWVI-11.1-42).}, } @article {pmid41713270, year = {2026}, author = {Jiao, X and Ji, W and Zhang, X and Zhang, S and Dolfing, J and Yang, K and Xie, B and Zhang, Y and Feng, J and Wu, D}, title = {Microcystins 'steer' antibiotic resistome dynamics by synergetic metabolism and horizontal gene transfer in a megacity's water supply catchment microbiota.}, journal = {Journal of hazardous materials}, volume = {505}, number = {}, pages = {141525}, doi = {10.1016/j.jhazmat.2026.141525}, pmid = {41713270}, issn = {1873-3336}, mesh = {*Microcystins/metabolism ; *Gene Transfer, Horizontal ; *Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; *Microcystis/genetics/metabolism/growth & development ; Genes, Bacterial ; Water Supply ; China ; *Water Microbiology ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The proliferation of Microcystis has been linked to the widespread occurrence of antibiotic resistance genes (ARGs). Yet, the underlying mechanisms driven by the proliferation-induced microbial metabolic interactions and elevated microcystins (MCs) levels remain unclear. Here, through a year-long field study conducted in Shanghai's largest drinking water supply catchment, we demonstrated that Microcystis proliferation significantly increased ARG relative abundance (by 0.28 ± 0.05 log10(RPKM+1), corresponding to an approximately 60 % increase in abundance; P < 0.05, n = 63) and markedly reshaped the resistome structure (PERMANOVA, P < 0.01). During the whole Microcystis biomass cycle, the MCs were identified as the most predominant driver of the dynamics of waterborne ARGs (SNPs-RDA > 0.6, P < 0.01). Metagenomic binning and metabolic network reconstruction revealed that MC enhanced metabolic cooperation between ARG hosts and surrounding microorganisms (iNAP, Student's T-test, P < 0.001), suggesting MC-involved and nutrient co-metabolism that facilitated persistence of ARGs and the associated bacteria. Furthermore, plasmid conjugation experiments indicated that MCs significantly elevated plasmid-mediated ARG-transfer efficiency by twofold (Wilcoxon test, P < 0.05), promoting the spread of multidrug-resistant genes such as MexB, which may enable MCs to efflux. To quantify these effects, an MC index (MI) and a physiochemical index (PI) were developed, co-explaining > 80 % of ARG variation and identifying dissemination thresholds (TITAN, MI > 0.490 and PI > -0.032) for dominant resistance types. Our findings highlight MC as a natural promoter of ARG transmission, and the proposed indices offer viable tools for monitoring and mitigating antibiotic resistance in drinking water sources.}, } @article {pmid41713418, year = {2026}, author = {Shao, Y and Wang, S and Gichuki, BM and Stares, MD and Rozday, TJ and Kumar, N and Browne, HP and Dawson, NJR and Njunge, JM and Tigoi, C and Ngao, N and Chisti, MJ and Singa, BO and Kariuki, S and Diallo, AH and Saleem, AF and Ali, SA and Mupere, E and Mbale, E and Tickell, KD and Voskuijl, WP and Lancioni, CL and Bandsma, RHJ and Ahmed, T and Walson, JL and Berkley, JA and Lawley, TD}, title = {Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design.}, journal = {Cell}, volume = {189}, number = {6}, pages = {1854-1873.e17}, doi = {10.1016/j.cell.2026.01.007}, pmid = {41713418}, issn = {1097-4172}, mesh = {*Probiotics ; Humans ; *Genome, Bacterial ; *Bifidobacterium longum subspecies infantis/genetics/classification ; *Bifidobacterium longum/genetics/classification ; Phylogeny ; Genomics ; Infant ; }, abstract = {Bifidobacterium longum and B. infantis are pioneer colonizers of the neonatal gut and are widely used as probiotics to support infant growth, development, and disease resistance. However, commercial strains derived largely from high-income countries (HICs) may be suboptimal for infants in low- and middle-income countries (LMICs). We assembled a global genomic atlas of more than 4,000 genomes from 48 countries, increasing representation from LMICs by 12- to 17-fold. High-resolution phylogenomic and functional analyses support delineating B. longum and B. infantis as distinct species with divergent functions and epidemiological patterns. B. infantis dominates early-life microbiota in LMICs but is rarely detected in HICs. Natural B. infantis strains show extreme biogeographic stratification and predicted adaptations to local plant-glycan-rich diets and breast-milk-derived substrates, including urea and B vitamins. This genomic resource enables genome-guided selection of geographically matched strains to inform more effective probiotics and precision microbiome therapeutics for diverse infant populations.}, } @article {pmid41713744, year = {2026}, author = {Lemée, P and Le Roux, A and Feurer, C and Houée, P and Le Grandois, P and Hirchaud, E and Soumet, C and Bridier, A}, title = {Longitudinal Analysis of Surface-Associated Bacterial Ecology and Resistome Dynamics in a Pig Slaughterhouse.}, journal = {Journal of food protection}, volume = {89}, number = {4}, pages = {100724}, doi = {10.1016/j.jfp.2026.100724}, pmid = {41713744}, issn = {1944-9097}, mesh = {Animals ; *Abattoirs ; Swine ; Bacteria ; Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Food Microbiology ; Salmonella typhimurium ; }, abstract = {Slaughterhouses constitute key stages for the transmission of bacterial pathogens and antimicrobial resistance throughout the meat production chain, with significant implications for food safety. This study investigated the bacterial communities and resistome profiles of surface-associated microbes in a pig slaughterhouse sampled at two-year intervals in 2017 and 2019. Thirty-five strains of Salmonella enterica serovar Typhimurium and its monophasic variant, major pathogenic serovars of the sector, were collected through the slaughtering line in this time frame, and they displayed multidrug resistance profiles characteristic of the pig sector. Whole-genome analysis revealed no clear phylogenetic clustering by site or sampling date. Both 16S rRNA metabarcoding and shotgun metagenomics underlined site-specific bacterial communities dominated by the Moraxellaceae family and with a relatively stable composition across the sampling period. The upstream of the slaughtering line (dehairing stage) was characterized by aminoglycoside and tetracycline resistance genes, predominantly associated with Acinetobacter, Escherichia, and Clostridium, alongside oxidative stress genes carried by Streptococcus. At the downstream section of the slaughtering process, the red offal platform exhibited increased diversity and abundance of antibiotic and biocide resistance determinants. These included β-lactam and carbapenem resistance genes as well as efflux pump-associated elements (adeJ), mainly linked to Acinetobacter, which was consistently enriched, suggesting its potential role as a reservoir for resistance genes. Overall, these findings provide insights into the composition, stability, and functional potential of bacterial communities in slaughterhouse environments and their possible role in shaping pathogen and resistance gene dynamics along the food production chain.}, } @article {pmid41713817, year = {2026}, author = {Zhao, Q and Cao, Y and Zhang, Z and Yang, Y and Wang, L and Xu, M and Mao, Y and Zhang, X and Zeng, M and Yang, P and Chen, Q and Yan, H and Yang, G}, title = {Xiao-Chaihu-Tang preserves intestinal barrier and ameliorates irinotecan-evoked delayed diarrhea by anchoring endogenous tryptophol to modulate inflammation and oxidation dependent on AhR-UGT1A1-microbiota axis.}, journal = {Journal of ethnopharmacology}, volume = {363}, number = {}, pages = {121380}, doi = {10.1016/j.jep.2026.121380}, pmid = {41713817}, issn = {1872-7573}, mesh = {Animals ; *Irinotecan/toxicity ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Diarrhea/chemically induced/drug therapy/metabolism/prevention & control ; Male ; Rats, Sprague-Dawley ; UGT1A1 Enzyme ; Glucuronosyltransferase/metabolism ; *Gastrointestinal Microbiome/drug effects ; Receptors, Aryl Hydrocarbon/metabolism ; Rats ; Intestinal Barrier Function/drug effects ; Humans ; Inflammation/drug therapy/metabolism ; Oxidation-Reduction/drug effects ; *Indoles/metabolism ; }, abstract = {Xiao-Chaihu-Tang (XCHT), a well-known traditional formula, is commonly used to treat various types of diarrhea. It also exhibits promising efficacy against chemotherapy irinotecan (CPT-11)-induced delayed diarrhea (DD). However, its underlying mechanisms, specifically concerning endogenous metabolites, key pathways, and functional gut bacteria at the species level, remain unclear, severely restricting its clinical application.

AIM OF THE STUDY: This study aimed to elucidate the biomarkers, pathways, and functional bacteria involved in XCHT's alleviating CPT-11-evoked DD using multi-omics approaches, antagonists, and fecal microbiota transplantation (FMT).

MATERIALS AND METHODS: First, the ingredients of XCHT and absorbed compounds in rat plasma were identified using liquid chromatography-mass spectrometry (LC-MS). Next, the therapeutic effects of XCHT were assessed by monitoring perianal status, body weight, disease activity index, food and water intake, and histopathological changes in the colon (hematoxylin and eosin, alcian blue-periodic acid-schiff staining). The underlying mechanisms were studied using metabolomics and network pharmacology, which highlighted the role of endogenous biomarkers and associated pathways. Tryptophol was identified as a key correlate, and its efficacy was further validated in rat and Caco-2 models using antagonists of potential targets (AhR and UGT1A1). The levels of inflammatory cytokines, and oxidative stress markers, intestinal barrier proteins, and mucins were detected by enzyme-linked immunosorbent assay (ELISA), Western blotting, and immunofluorescence. Furthermore, functional gut bacteria were identified using metagenomic sequencing and validated using FMT, while gut leakage was detected using fluorescence in situ hybridization (FISH). Finally, the interactions between tryptophol with targets of AhR and UGT1A1 were examined using molecular docking, molecular dynamics, and surface plasmon resonance.

RESULTS: LC-MS analysis identified 43 phytochemicals in XCHT and 17 compounds absorbed in plasma. XCHT, similar to tryptophol, attenuated DD by improving perianal status, disease activity index, and colon pathology, while increasing body weight, food intake, and water intake. Metabolomics analysis revealed 33 potential endogenous biomarkers, including PGB3, LysoPA, and so on. Integrated with network pharmacology, the results indicated that the therapeutic effect of XCHT involved the regulation of tryptophan metabolism, arachidonic acid metabolism, inflammation, and oxidative stress. Tryptophol, which exhibited a strong correlation with efficacy indices, reduced inflammation and oxidation in vivo/vitro, and enhanced intestinal barrier protein and mucin expression in an AhR-UGT1A1-dependent manner. Furthermore, metagenomic sequencing and FISH demonstrated that both XCHT and tryptophol normalized the abundance of 10 gut bacterial species (for example, Lactobacillaceae bacterium, Massiliimalia timonensis, and Limosilactobacillus reuteri) and inhibited bacterial invasion. Molecular interaction studies confirmed the strong binding between tryptophol with AhR and UGT1A1.

CONCLUSION: This study demonstrates that XCHT preserves intestinal barrier integrity in rats and alleviates CPT-11-induced DD. This protective effect is mediated by modulating inflammation and oxidative stress via the tryptophol- AhR-UGT1A1-microbiota axis, providing a novel paradigm for mechanistic studies on toxicity reduction in clinical chemotherapy drugs.}, } @article {pmid41714186, year = {2026}, author = {Wang, B and Gao, P and Zhang, P and Zheng, Y and Liu, X and Ling, N and Shan, J and Yao, R and Zhao, S and Zhang, Z and Zhu, G and Jung, MY and Zou, J and Yan, X and Lee, S and Hazard, C and Nicol, GW and Zhou, J and Yang, Y and Zhu, Y and Stahl, DA and Wagner, M and Gao, Y and Jiang, J and Qin, W}, title = {Elevated temperature simulating heatwaves restructures active nitrifying communities and associated viruses in tidal flats and agricultural soils.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41714186}, issn = {1751-7370}, support = {//Cluster of Excellence "Microbiomes drive Planetary Health" of the Austrian Science Fund (FWF)/ ; RS-2025000518246//Korean government (Ministry of Science and ICT)/ ; DE-SC0025455//US Department of Energy Early Career Research Program/ ; 42477318//National Natural Science Foundation of China/ ; 42277304//National Natural Science Foundation of China/ ; U22A20590//National Natural Science Foundation of China/ ; }, mesh = {*Soil Microbiology ; *Nitrification ; *Archaea/metabolism/genetics ; *Hot Temperature ; *Bacteria/genetics/metabolism/classification/virology ; Ammonia/metabolism ; Seashore ; Nitrites/metabolism ; Metagenomics ; Climate Change ; }, abstract = {Global heatwave intensification under climate change will impact the nitrogen cycle; yet, its effect on active nitrifier groups or their interactions with viruses remains unclear. Using 13CO2-DNA-based stable-isotope probing coupled with metagenomics, we show that elevated temperatures under heatwave conditions fundamentally restructure active nitrifying communities and their associated viruses in Yangtze River estuary upper tidal flats and adjacent agricultural soils. In tidal flats, sustained high temperature constrained nitrification by reducing the abundance of active ammonia-oxidizing archaea and bacteria (AOA, AOB) and canonical nitrite-oxidizing bacteria (NOB). This was accompanied by a shift in the active community from marine to more thermotolerant but less salt-tolerant terrestrial ecotypes. Conversely, heatwave conditions in agricultural soils suppressed AOB but enhanced nitrification activity in thermotolerant terrestrial AOA ecotypes. Across both ecosystems, inferred virus-nitrifier interactions were temperature dependent. 13C-labeled nitrifier-infecting viruses exhibited coordinated shifts in virus-to-host abundance ratios and predicted lifestyles with their hosts, with sustained high temperatures reducing virus-to-host abundance ratios and favoring temperate infections, relative to higher abundance ratios and a greater proportion of predicted lytic cycles at lower temperatures. We identified AOA-infecting viruses that carry plastocyanin (pcy), encoding a key copper-dependent electron carrier in the AOA respiratory chain, with conserved active sites and a predicted protein fold that supports its capacity for electron transfer, potentially augmenting host energy metabolism. Together, our findings demonstrate that prolonged heatwaves drive coupled shifts in nitrifier community composition and virus-host interaction strategies in a land-use-dependent manner, with implications for nitrogen transformations and ecosystem feedbacks under climate extremes.}, } @article {pmid41714776, year = {2026}, author = {Balázs, B and Boros, Á and Pankovics, P and Mátics, R and Urbán, P and Herczeg, R and Knowles, NJ and Reuter, G}, title = {Genetic characterization of two novel picornaviruses from birds, white-tailed eagle (Haliaeetus albicilla) and pied avocet (Recurvirostra avosetta) in Hungary.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41714776}, issn = {2045-2322}, mesh = {Animals ; Hungary ; Phylogeny ; Genome, Viral ; *Picornaviridae/genetics/classification/isolation & purification ; *Picornaviridae Infections/veterinary/virology ; *Eagles/virology ; 3' Untranslated Regions ; Viral Proteins/genetics ; Amino Acid Sequence ; High-Throughput Nucleotide Sequencing ; }, abstract = {In this study, two novel picornaviruses (eagle/WE6/HUN/2014, PV454551-PV454552 and avocet/PA12/HUN/2018, PV454553) were detected in white-tailed eagle (Haliaeetus albicilla) and pied avocet (Recurvirostra avosetta) in Hungary, and characterized by next generation sequencing, RT-PCR and Sanger sequencing methods. The complete polyprotein coding genomes were 6,573 and 6,567 nt long and had the genome organization 5'UTR[IRES-III]-[VP4-VP2-VP3-VP1-2A-2B-2C[hel]-3A-3B[VPg]-3C[pro]-3D[pol]]-3'UTR-poly(A)n. The P1 and the 3C[pro] proteins of the eagle/WE6/HUN/2014 showed 47.9% and 62.4% aa sequence identities to the corresponding proteins of the picornavirus (MT138036) from a little egret metagenome, respectively. The 2C[hel]/3D[pol] had 44.1%/41% aa identity to the corresponding proteins of bat-origin picornaviruses (OR867633 and KX420952). The P1 protein of the avocet/PA12/HUN/2018 had 53% aa sequence identity to the P1 protein of crane70contig328 (OQ423840) from red-crowned crane metagenome; the 2C[hel], 3C[pro] proteins had 52.6%, 52.3% aa sequence identity to the corresponding proteins of picornavirus (MT138035) from bird metagenome and 3D[pol] had 43.2% aa identity to the 3D[pol] of the picornavirus (MT138036) from a little egret metagenome, respectively. The 3'UTR of avocet/PA12/HUN/2018 contained two repetitive nt sequence motifs (the 17-nt-long Motif-1 at five times forming a secondary RNA structure and the 9-nt-long Motif-2 at two times). The eagle/WE6/HUN/2014 and avocet/PA12/HUN/2019 represent the founding members of two potential novel bird-origin picornavirus species and even genera in the subfamily Heptrevirinae (family Picornaviridae).}, } @article {pmid41714781, year = {2026}, author = {Su, JW and Elsheikha, HM and Guo, L and Liu, R and Shang, KM and Yu, HL and Ma, H and Ni, HB and Chen, BN and Zhang, XX and Yang, X}, title = {Metagenomic analysis of antimicrobial resistance, virulence, and mobile genetic elements in the gut microbiota of Caprinae species.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41714781}, issn = {2399-3642}, support = {2022KJ169//Department of Education of Shandong Province (Department of Education, Shandong Province)/ ; }, mesh = {Animals ; *Interspersed Repetitive Sequences ; *Metagenomics ; Virulence/genetics ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Bacterial/genetics ; Virulence Factors/genetics ; *Metagenome ; *Bacteria/genetics/pathogenicity/drug effects ; }, abstract = {The livestock gut microbiota serves as a reservoir for antimicrobial resistance (AMR), yet Caprinae species remain understudied. Here, we present a large-scale metagenomic analysis of 779 gut samples from Caprinae animals, primarily originating from China (95.38%), including Capra hircus (79.85%) and Ovis aries (17.33%). We reconstruct 17,023 metagenome-assembled genomes (MAGs), and identify 2,440 antimicrobial resistance genes (ARGs) and 5,401 virulence factor genes (VFGs). Escherichia coli represents a major host for both. Correlation analyses between ARGs, VFGs, and mobile genetic elements (MGEs) suggest potential co-selection mechanisms. Although MGEs were detected in only 1.45% of MAGs, likely reflecting limitations in identifying MGEs within incomplete assemblies, 19 ARGs are physically co-located with MGEs, indicating mobility potential. Additionally, three ARGs are embedded within viral genomes, implicating bacteriophages in AMR dissemination. Comparative analyses reveal 184 distinct ARGs shared between Caprinae and humans, including 17 clinically critical genes such as tetX and van variants. These findings expand understanding of the Caprinae gut resistome and highlight its potential role in cross-host AMR transmission, and underscore the need for targeted AMR surveillance in this reservoir.}, } @article {pmid41714786, year = {2026}, author = {Paládi, P and Benmazouz, I and Tóth, M and Kövér, L and Lengyel, S}, title = {Spatial and temporal dynamics in the use of urban habitats by Hooded Crows.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41714786}, issn = {2045-2322}, abstract = {UNLABELLED: Understanding the habitat use of animals in cities is relevant for urban planning, human-wildlife conflict management and urban biodiversity conservation. We studied the habitat use of Hooded Crows, a nuisance bird in much of Europe, in 16 different neighborhoods (sections) of a recently crow-colonized city in E Hungary. In the breeding season, when crows defend territories, crow numbers increased with nesting site availability and the number of trashbins but were unaffected by habitat type or area of the section. However, colonization probability was negatively influenced by the number of trashbins and restaurants, was high in parks, sports complexes, and quieter residential areas, and was low in residential areas busy with traffic. Outside the breeding season, when crows move around in groups, crow numbers increased with time in the section with the highest number of trashbins, decreased in residential areas and was stable in parks and sports complexes. Our results suggest that while crows are attracted by the foraging opportunities offered by anthropogenic food sources, they avoid nesting in such areas, likely due to high human disturbance. This implies that residential areas with fewer food sources will attract fewer crows, potentially reducing human-crow conflicts. Our study also suggests that improved waste management, such as closed-top trashbins in public places or covered enclosures in zoos, may further reduce the availability of anthropogenic food sources to crows and that targeted crow control is best scheduled for the breeding season and in residential areas.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-40561-z.}, } @article {pmid41714980, year = {2026}, author = {Ceylani, T and Teker, HT and Önlü, H and Ünver, T and Allahverdi, H and Şahin, E and Atalan, E}, title = {Multi-omics insights into gut microbiota-metabolite interactions under probiotic intervention in a developmental cafeteria diet model.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41714980}, issn = {1471-2164}, support = {FOA-2024-3587//Inönü University Scientific Research Projects Coordination Unit (BAP)/ ; }, abstract = {BACKGROUND: The developmental phase is a pivotal biological period for the maturation of the gut microbiota and the establishment of lifelong metabolic health. During these period, dietary patterns that induce dysbiosis, such as the high-fat, low-fiber “cafeteria diet,” disrupt the production of key metabolites in the gut-metabolite axis, including short chain fatty acids (SCFAs) and indole-3-propionic acid (IPA). This study employs a multi-omics approach to examine the impact of cafeteria diet exposure during the developmental period (days 21–56) in 21-day-old male Wistar rats on microbiota composition, SCFA, and IPA levels, and to assess the extent to which concurrent probiotic administration can mitigate these disruptions.

RESULTS: The cafeteria diet led to a marked reduction in alpha diversity indices (Shannon p = 0.021; Simpson p = 0.034) and altered the Firmicutes/Bacteroidetes ratio (p = 0.015). Beta diversity analysis indicated a distinct separation between groups (PERMANOVA p = 0.002). Metabolite analysis revealed significant reductions in acetic acid (p = 0.004), isobutyric acid (p = 0.094), butyric acid (p = 0.0014), valeric acid (p = 0.0001), heptanoic acid (p = 0.0125), and IPA (p = 0.002), whereas probiotic administration largely restored these levels. At the species level, cafeteria diet markedly increased Segatella copri, while probiotic intervention partially restored beneficial taxa such as Faecalibacterium prausnitzii and butyrate-producing genera (Anaerostipes hadrus, Intestinimonas butyriciproducens, Blautia wexlerae, and Flintibacter sp. KGMB00164), as evidenced primarily by shotgun metagenomics. Correlation analysis further revealed strong positive associations between butyrate and F. prausnitzii (ρ = 0.65, p = 0.003) and between IPA and B. longum (ρ = 0.68, p = 0.002). Collectively, these results highlight the protective role of probiotic intervention against diet-induced dysbiosis by reinforcing microbiota metabolite interactions.

CONCLUSIONS: By integrating metagenomic and metabolomic analyses, this multi-omics study demonstrates that exposure to a high-fat cafeteria diet during the developmental period disrupts microbiota composition and metabolite production, whereas concurrent probiotic administration largely prevent these effects, serving a protective role in the gut-metabolite axis. The study underscores the potential of early-life probiotic intervention, supports SCFA and IPA production, as a critical strategy to optimize microbiota-metabolite interactions and promote long-term gut and systemic health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12650-w.}, } @article {pmid41715099, year = {2026}, author = {Fan, W and Tan, T and Yang, C and Cao, Y and Jin, C and Liu, X and Shang, K and Wang, J and Xu, J and Li, Y}, title = {Indole-acetaldehyde from Rothia mucilaginosa activates the PXR/NRF2 axis to enhance alveolar macrophage phagocytosis and protect against ARDS.}, journal = {Respiratory research}, volume = {27}, number = {1}, pages = {}, pmid = {41715099}, issn = {1465-993X}, support = {82102252//National Natural Science Foundation of China/ ; 82272245//National Natural Science Foundation of China/ ; 202440093, 2024ZZ1022//Shanghai Municipal Health Commission/ ; }, abstract = {BACKGROUND: Despite advances in therapeutic strategies, acute respiratory distress syndrome (ARDS) mortality remains high. Growing evidence links respiratory microbiome composition to ARDS outcomes. This investigation sought to elucidate how colonizing bacteria and their metabolites influence ARDS pathogenesis. METHODS: Bronchoalveolar lavage fluid (BALF) from patients with pulmonary infections was analyzed by metagenomic next-generation sequencing (mNGS) to identify characteristic bacteria. Bacterial culture supernatants were analyzed by untargeted metabolomics (LC-MS) to identify metabolites. A murine ARDS model was established through intratracheal LPS instillation. Single-cell sequencing datasets from the GEO database were analyzed to reveal differential cell populations and functional alterations in murine ARDS. Potential molecular mechanisms were explored through molecular docking, RNA-seq analysis, Western boltting, and targeted gene knockdown in murine and cellular model. RESULTS: R. mucilaginosa demonstrated enrichment in patients without ARDS (nARDS). The bacterial culture supernatant conferred substantial protection in murine models, whereas viable bacteria showed minimal efficacy. LC-MS analysis identified indole-3-acetaldehyde (IAAld) as the predominant metabolite in the supernatant. Single-cell sequencing suggested that resident alveolar macrophages (RAMs) were pivotal cells in murine ARDS model. IAAld enhanced RAMs phagocytosis, facilitating neutrophil and LPS clearance. Mechanistic studies revealed that IAAld likely activated PXR signaling, promoted NRF2 nuclear translocation, and upregulated the phagocytosis-related gene CD36. Targeted PXR knockdown eliminated these protective effects. CONCLUSION: The respiratory commensal R. mucilaginosa synthesizes IAAld, which—independent of bacterial colonization per se—ameliorates ARDS through PXR/NRF2/CD36 axis activation, thereby enhancing macrophage phagocytic function. These findings suggest that therapeutic targeting of microbial metabolites represents a novel ARDS treatment paradigm.}, } @article {pmid41715166, year = {2026}, author = {Zhang, J and Xu, L and Ge, X and Zi, X and Chen, S and Liu, C and Wang, K and Zhou, J and Dou, T and Wong, JWC and Lin, Q and Kang, X and Cao, Z}, title = {Cross-kingdom genomic variation in chicken gut microbiomes: insights from China's diverse local breeds.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41715166}, issn = {2049-2618}, support = {2024A1515140076//Guangdong Basic and Applied Basic Research Foundation/ ; 202401AU070079//Yunnan Fundamental Research Projects/ ; 221110133//Dongguan University of Technology Top Talent Professor Start Up Fund/ ; 202301BD070001-136//Key Project of Yunnan Province Agricultural Joint Special Project/ ; 202305AC160040//Yunnan Province Young and Middle-aged Academic and Technical Leader Reserve Talent Project/ ; }, mesh = {Animals ; China ; *Chickens/microbiology ; Metagenomics/methods ; Gene Transfer, Horizontal ; *Genetic Variation ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification ; Bacteriophages/genetics ; DNA Viruses/genetics/classification ; Polymorphism, Single Nucleotide ; Metagenome ; }, abstract = {BACKGROUND: The gut microbiome possesses substantial genetic diversity that supports microbial adaptation, but the genomic variation patterns across its prokaryotic and viral populations remain incompletely characterized.

RESULTS: Through integrated metagenomic and metatranscriptomic analysis of ten indigenous chicken breeds from China, we recovered 1527 representative prokaryotic MAGs, 37,555 representative DNA viral contigs, and 1867 representative RNA viral contigs (primarily comprising Bacillota/Bacteroidota, Uroviricota, and Lenarviricota/Pisuviricota, respectively). By integrating complementary short-read and long-read metagenomics with metatranscriptomics, we identified structural variants (SVs) and single-nucleotide variants (SNVs) in these cross-kingdom genomes. Positive SV-SNV density correlations occurred consistently across all microbial groups, indicating coordinated mutational processes. DNA viruses exhibited the highest variant prevalence (86.9% SNVs, 47.7% SVs), with temperate phages accumulating significantly more variants than virulent phages. Functionally, prokaryotic variants accumulated in carbohydrate metabolism and amino acid metabolism, while viral variants demonstrated broad metabolic hijacking. Horizontal gene transfer (HGT) was characterized by a strong virus-associated signature (69.40% of 536 events) and marked by an asymmetric pattern, with phage-to-bacteria (P-to-B) flow alone constituting 37.50% of all events. Random forest analysis revealed a strong bidirectional predictive relationship between SV and SNV densities across prokaryotic, DNA viral, and RNA viral populations, suggesting coupled genomic instability. Niche breadth emerged as a major driver of SNVs across kingdoms and was positively correlated with variant density. In prokaryotes, HGT events significantly shaped variant patterns. For viruses, genomic GC content was an important factor and consistently showed a negative correlation with SNV density in both DNA and RNA viruses.

CONCLUSIONS: These findings demonstrate that coordinated mutational processes and kingdom-specific intrinsic factors drive genomic variation, with viruses serving as key genetic exchange vectors in chicken gut ecosystems. Video Abstract.}, } @article {pmid41715225, year = {2026}, author = {Ding, L and Yang, S and Wu, F and Pilling, D and Zhang, J and Pool, K and Nishvanthi, M and Babington, S and Maloney, SK and Chen, L and Shi, J and Wang, Y and Blache, D and Wang, M}, title = {Association between the gut microbiome and plasma metabolites linked to vocalization-based temperament in Merino sheep.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41715225}, issn = {2049-2618}, mesh = {Animals ; Sheep/microbiology/blood ; *Gastrointestinal Microbiome/physiology ; *Temperament/physiology ; Rumen/microbiology ; Female ; Multiomics ; gamma-Aminobutyric Acid/metabolism ; *Vocalization, Animal/physiology ; Metabolome ; Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; }, abstract = {BACKGROUND: Temperament, as a determinant of behavioural and emotional responses, has a substantial adaptive value in different environments. This study aims to investigate the association between the gut microbiota and temperament plasticity, and clarify the potential metabolic mechanism that underpins that association by running a multi-omics study in sheep.

METHODS: The TrackSheep research cohort was generated using 200 healthy juvenile Merino ewes, and the rumen microbiota, plasma metabolome, and temperament phenotype was measured.

RESULTS: Rumen metagenomic analysis identified 25 microbial species and 16 MetaCyc pathways that explained 37.5% and 11.1%, respectively, of the variation in temperament as estimated using the vocal reactivity to stress. Among these, the γ-aminobutyric acid (GABA) shunt and allantoin degradation pathways showed the strongest associations with vocal behaviour. Multi-omic integration linked these microbial pathways to plasma metabolites that are involved in neurotransmission, antioxidant defense, and energy metabolism, including acetyl-L-carnitine (ALCAR) and urocortisone, which partially mediated the effects of microbial pathways on vocalisations. Notably, functional genomic and mediation analyses indicated that the abundance of Cryptobacteroides sp902761655 was associated with the activity of GABA shunt pathway, where GABA co-occurred with succinate production, in turn correlating with reduced inhibitory effects of ALCAR on stress-susceptible temperament. Although plasma metabolite shifts observed immediately after behavioural tests reflected stress exposure, their associations with rumen microbiota highlight microbiome-metabolite interplay that could underly behavioural variation.

CONCLUSIONS: Our study provides the first large-scale multi-omics evidence linking the rumen microbiome to a dimension of emotional reactivity in livestock, while underscoring the need for longitudinal and experimental validation to establish causal mechanisms. Video Abstract.}, } @article {pmid41715233, year = {2026}, author = {Choi, Y and Zhou, M and Oba, M and Romero-Pérez, A and Beauchemin, KA and Duval, S and Kindermann, M and Guan, LL}, title = {Comparative analysis of rumen metagenomes with dietary supplementation of 3-nitrooxypropanol revealed divergent modes of action in hydrogen metabolism and reductant pathways between beef and dairy cattle.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {72}, pmid = {41715233}, issn = {2049-2618}, support = {Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; FDE.18.21C//Beef Cattle Research Council Cluster/ ; FDE.18.21C//Beef Cattle Research Council Cluster/ ; ALLRP 588541-23//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and NSERC Alliance program/ ; ALLRP 588541-23//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and NSERC Alliance program/ ; }, mesh = {Metagenome ; *Rumen/enzymology/microbiology ; Animals ; *Cattle/microbiology ; Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Fatty Acids, Volatile/biosynthesis ; *Methane/biosynthesis ; Hydrogen/metabolism ; Metabolic Networks and Pathways/drug effects ; }, abstract = {BACKGROUND: The compound 3-nitrooxypropanol (3-NOP), an inhibitor of methyl-coenzyme M reductase (MCR), reduces enteric methane production in both beef and dairy cattle. Although the proposed mechanisms of 3-NOP involve on inhibiting the activity of MCR in vivo, it is unknown how this process could affect rumen microbiome as a whole and if it differs between beef and dairy cattle. This study conducted a comparative analysis of the rumen microbiome and its functional shifts in four different cattle studies (two beef and two dairy cattle studies) that evaluated 3-NOP supplementation using metataxonomics and metagenomics.

RESULTS: Comparative analysis of 281 rumen metataxonomic datasets (143 beef and 138 dairy cattle) revealed that dietary supplementation with 3-NOP affected rumen bacteria and methanogens. Further, comparative analysis of 54 metagenomic datasets (24 beef and 30 dairy cattle) revealed that 3-NOP inhibited mcrA, decreased the abundances of Methanobrevibacter gottschalkii and the protozoal species Isotricha prostoma, while increased the abundances of Methanobrevibacter ruminantium and Methanosphaera sp., Prevotella sp. was a significant bacterial taxon in both beef and dairy cattle, contributing to various pathways such as propionate and butyrate production. Its increased abundance after 3-NOP supplementation may also be linked to the decrease in Isotricha prostoma. Hydrogenotrophic methanogenesis decreased after 3-NOP supplementation with the abundance of genes involved in methylenetetrahydromethanopterin dehydrogenase decreased in beef cattle, while that of 4Fe-4S ferredoxin gene decreased in dairy cattle. The abundance of protozoal Polyplastron multivesiculatum increased after long-term 3-NOP supplementation in beef cattle, potentially due to changes in hydrogen (H2) partial pressure. During 3-NOP-mediated methanogenesis reduction, abundance of genes encoding methanogenic hydrogenase and H2 producing hydrogenase were decreased, while those encoding H2 sensory hydrogenase increased. Acyl-CoA dehydrogenase gene involved in propionate and butyrate production pathways increased in both beef and dairy cattle, while nitrite reductase increased specifically in beef cattle, indicating a rise in alternative H2 sinks. Video Abstract CONCLUSION: Our findings revealed broad effects of 3-NOP on rumen microbiome and functions in vivo, with varied effects in beef and dairy cattle, which provide mechanistic insights into the supplementation of 3-NOP in both beef and dairy cattle, supporting its more sustainable and effective use in the future.}, } @article {pmid41715245, year = {2026}, author = {Luna, N and Hernández, C and Ramírez, AL and Urbano, P and Barragán, K and Ariza, C and Muñoz, M and Patiño, LH and Ramírez, JD}, title = {Ecological insights into the cross-domain microbiome interactions in the hematophagous bat Desmodus rotundus.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {22}, pmid = {41715245}, issn = {2524-4671}, abstract = {BACKGROUND: Bats are recognised as reservoirs for a wide range of microorganisms, including viruses, bacteria, fungi, and parasites, some of which are of zoonotic concern. The common vampire bat (Desmodus rotundus) is particularly important due to its hematophagous feeding behaviour and ecological adaptability, both of which enhance its potential for cross-species pathogen transmission. Despite its well-established relevance to public health, the microbial communities associated with D. rotundus remain poorly characterised. This study aimed at investigating the composition, diversity, and interactions of prokaryotic, eukaryotic, and viral communities, alongside feeding sources, using high-throughput sequencing in 27 D. rotundus individuals from a rural area in Casanare, eastern Colombia. RESULTS: We analysed a total of 81 samples (blood, faeces, and oral swabs) using long-read amplicon sequencing of the 16S- and 18S-rRNA genes and viral metagenomics via Oxford Nanopore Technologies. The microbial profiles revealed highly diverse assemblages, encompassing a wide range of bacterial, fungal, eukaryotic parasites, and viral taxa, with significant variation in community structure and diversity metrics across the three sample types collected from each bat. Taxa of public health concern were detected, including Enterococcus faecalis, Mycoplasma spp. Acanthamoeba spp. and viruses from the families Coronaviridae, Retroviridae, and Circoviridae. Correlation analyses suggested potential intra- and inter-domain interactions and co-occurrence dynamics among these microbes. Additionally, feeding source profiling, based on vertebrate assignments from faeces and swab samples, indicated evidence of livestock consumption, suggesting possible transmission pathways between bats and domestic animals. CONCLUSIONS: The detection of multiple co-occurring pathogens across distinct sample types, coupled with their association with feeding sources, highlights the role of D. rotundus as a functionally specialised reservoir capable of harbouring and potentially disseminating zoonotic microbes. This study provides new insights into the cross-domain microbial ecology of hematophagous bats and underscores the need to integrate microbial community profiling with host behavioural data to enhance surveillance and mitigation strategies for zoonotic disease transmission.}, } @article {pmid41715924, year = {2026}, author = {Marín, MDC and Konno, M and Rozenberg, A and Béjà, O and Inoue, K}, title = {Novel light-driven schizorhodopsins from Antarctic Minisyncoccota (Patescibacteria) and cyanobacteria.}, journal = {Biophysical journal}, volume = {125}, number = {10}, pages = {2391-2404}, doi = {10.1016/j.bpj.2026.02.022}, pmid = {41715924}, issn = {1542-0086}, mesh = {*Light ; *Cyanobacteria/metabolism/radiation effects ; *Rhodopsins, Microbial/chemistry/metabolism/genetics ; Amino Acid Sequence ; Antarctic Regions ; Hydrogen-Ion Concentration ; Escherichia coli ; Models, Molecular ; Photolysis ; }, abstract = {Microbial rhodopsins represent a diverse superfamily of light-sensitive proteins composed of seven transmembrane helices with expanding phylogenetic diversity driven by advances in metagenomics. Among these, schizorhodopsins constitute a divergent family originally identified as inward proton pumps from Promethearchaeota (Asgard archaea). Here, we report that in addition to archaeal schizorhodopsins, many members of the family originate from bacteria and detail a comprehensive biophysical characterization of two schizorhodopsins from uncultured Antarctic bacteria: paSzR from Minisyncoccota (Patescibacteria) and psSzR from a Pseudanabaenacea cyanobacterium. Both proteins function as light-driven inward proton pumps, as confirmed through pH measurements in Escherichia coli cells. Laser-flash photolysis experiments identified multiple photointermediates (K, L, and M) characteristic of microbial rhodopsin photocycles, though with slower turnover rates compared with archaeal schizorhodopsins. Site-directed mutagenesis of conserved residues in the third and sixth transmembrane helices demonstrates differential structural requirements between paSzR and psSzR. Our phylogenetic reconstruction reveals that most bacterial schizorhodopsins cluster in a single lineage distinct from archaeal variants. These findings expand our understanding of microbial rhodopsin diversity and provide crucial insights into alternative molecular mechanisms for light-driven proton translocation, with implications for microbial ecology in extreme environments.}, } @article {pmid41716172, year = {2025}, author = {Nazerke, K and Ruslan, A and Saule, D and Aida, D and Svetlana, V}, title = {Advances and emerging technologies in the diagnosis of viral infections in pigs: Progress, challenges, and One Health perspectives.}, journal = {Veterinary world}, volume = {18}, number = {12}, pages = {3788-3805}, pmid = {41716172}, issn = {0972-8988}, abstract = {Viral infections continue to pose major challenges to pig health, farm productivity, and global food security. Early and accurate diagnosis is the cornerstone of disease prevention, surveillance, and control in swine populations. In recent years, remarkable progress has been achieved in molecular, serological, and digital diagnostic technologies, enabling more rapid, sensitive, and field-adaptable detection of important porcine viruses such as African swine fever virus, porcine reproductive and respiratory syndrome virus, and classical swine fever virus. This review summarizes current and emerging diagnostic approaches, highlighting polymerase chain reaction (PCR) and its advanced forms, quantitative PCR and digital PCR, as the gold standards for laboratory confirmation. The advent of next-generation sequencing and metagenomics has revolutionized pathogen discovery and genomic surveillance, providing comprehensive insights into viral evolution and transboundary transmission. Isothermal amplification techniques such as loop-mediated isothermal amplification and recombinase polymerase amplification have shown strong potential for on-farm diagnosis due to their simplicity, rapidity, and minimal equipment requirements. Innovations such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated-based assays, biosensors, lab-on-a-chip platforms, and point-of-care testing devices are bridging the gap between laboratory precision and field application, allowing rapid decision-making during outbreaks. The integration of artificial intelligence, machine learning, and geographic information systems has further enhanced diagnostic interpretation, real-time data sharing, and early outbreak prediction under the One Health framework. Despite these advances, challenges remain in ensuring assay standardization, affordability, and equitable access in resource-limited regions. Continued international collaboration, data sharing, and policy harmonization under the guidance of the Food and Agriculture Organization, the World Organization for Animal Health, and the World Health Organization are essential for the global control of swine viral diseases. Ultimately, combining molecular innovation with digital adaptability offers the most promising path toward resilient, cost-effective, and sustainable diagnostic systems for safeguarding animal and public health.}, } @article {pmid41716262, year = {2026}, author = {Qiao, YC and Jiang, XX and Zhan, JP and Cheng, XH and Liu, F and Zhang, WS and He, GP and Peng, JZ and Wu, YJ and Yang, SG}, title = {Effects of different mulching practices on soil microbial community structure, function, and interaction networks in a chieh-qua cultivation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1691984}, pmid = {41716262}, issn = {1664-302X}, abstract = {BACKGROUND AND AIMS: Mulching is a widely used agricultural management practice with profound effects on soil properties and crop productivity. However, its impact on soil microbial community structure and function remains insufficiently understood. This study aimed to investigate how different mulching treatments influence the composition, functional potential, and interaction networks of soil microbial communities in a chieh-qua-legume rotation system.

METHODS: Metagenomic sequencing was employed to analyze soil samples subjected to four mulching treatments (biodegradable mulch, non-degradable silver mulch, non-degradable black mulch, and straw mulch) as well as a no-mulch control (CK).

RESULTS: Mulching treatments significantly altered soil microbial diversity and community structure, with straw and biodegradable mulches supporting higher diversity than the control. Biodegradable mulch was strongly correlated with changes in soil pH and enriched denitrifying bacteria such as Thauera and Comamonadaceae, while reducing the abundance of genes related to energy metabolism and carbon fixation. These findings suggest that organic carbon from mulch degradation may enhance denitrification, potentially leading to nitrogen loss. Co-occurrence network analysis revealed that biodegradable mulch promoted more complex and connected microbial networks, whereas plastic mulches resulted in simpler structures. Additionally, all mulching treatments significantly reduced the abundance of the autotrophic ammonia-oxidizing archaeon Thaumarchaeota, likely due to reduced soil oxygen under mulch.

CONCLUSION: This study provides new insights into how different mulching practices modulate soil microbial communities and their ecological functions. The results underscore the importance of tailoring mulching strategies to maintain soil health and fertility. Specifically, nitrogen supplementation is recommended when using biodegradable mulch in chieh-qua cultivation systems.}, } @article {pmid41716274, year = {2026}, author = {Name, PE and Tibiri, EB and Tiendrébéogo, F and Sawadogo, S and Djigma, F and Traoré, L and Eni, AO and Pita, JS}, title = {Unraveling the intra-species genomic diversity of sweetpotato-infecting CRESS-DNA and RNA viruses in Burkina Faso using Oxford Nanopore sequencing.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1722370}, pmid = {41716274}, issn = {1664-302X}, abstract = {Sweetpotato is a key crop for global food security, particularly in Burkina Faso, where its productivity is increasingly threatened by viral diseases, especially those caused by CRESS-DNA viruses. However, the diversity of these viruses in Burkina Faso remains poorly characterized due to limitations of conventional diagnostic approaches. In this study, nanopore sequencing was used to investigate the diversity of CRESS-DNA viruses infecting sweetpotato in Burkina Faso. Ninety-eight symptomatic dried leaf samples from a previously established biobank were selected and analyzed. Total DNA was extracted, enriched using rolling circle amplification (RCA), and sequenced using the MinION Mk1C platform. In parallel, RNA viruses were also investigated using nanopore sequencing. RCA successfully amplified 53 of the 98 samples, from which 28 complete and 25 partial CRESS-DNA virus genomes were recovered. Sequence analyses revealed high genomic diversity, with sweet potato leaf curl virus (SPLCV) being the most prevalent. Sweet potato symptomless virus 1 (SPSMV-1) was detected for the first time in Burkina Faso in a co-infection with SPLCV. Additionally, 52 deltasatellite genomes (50 complete, 2 partial) were identified in association with SPLCV, displaying approximately 86% nucleotide identity with known sequences, suggesting the presence of genetically distinct putative deltasatellites. RNA virome analysis revealed frequent co-infections involving sweet potato feathery mottle virus (SPFMV) and sweet potato chlorotic stunt virus, with SPFMV commonly co-occurring with SPLCV. Four complete SPFMV genomes were recovered and clustered within phylogroup B, forming a distinct subclade. Overall, this study highlights the remarkable diversity of viruses infecting sweetpotato in Burkina Faso and reports, for the first time, the presence of SPSMV-1 and sweepovirus-associated deltasatellites in the country. These findings underscore the importance of ongoing molecular surveillance to support effective viral disease management strategies and food security.}, } @article {pmid41716833, year = {2026}, author = {Xie, F and Li, J and Liu, P and Xu, L and Wang, Y and Qiu, Q and Mao, S}, title = {Genome-resolved metagenomics reveals gastrointestinal microbiome adaptations in sheep responding to fiber- and starch-rich diets.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {24}, number = {}, pages = {233-245}, pmid = {41716833}, issn = {2405-6383}, abstract = {The gastrointestinal tract of ruminants hosts a specialized microbial ecosystem that has evolved to efficiently digest fiber. However, modern intensive farming practices, which often involve reduced dietary fiber and increased grain supplementation, are linked to metabolic disorders in ruminants. Despite this, the understanding of the taxonomic and functional adaptations of the gastrointestinal microbiome to dietary changes remains limited, largely due to the challenges in obtaining high-resolution characterization of microbial communities. This study employed genome-resolved metagenomics to examine how a starch-rich (SR) grain-based diet compares to a fiber-rich (FR) hay-based diet in shaping the composition and function of the gastrointestinal microbiome in the rumen, jejunum, and cecum of Hu sheep. A total of 10 sheep (approximately 180 d old, with a body weight of 25.6 ± 0.41 kg) were allocated to the 2 dietary groups (SR and FR groups) for a 28-d experimental period, and metagenomic sequencing was performed on digesta samples from different gastrointestinal regions. Using a representative microbial gene catalog (RGMGC) and 10,373 metagenome-assembled genomes from previous studies,microbial composition, strain-level diversity, and carbohydrate-active enzyme profiles at higher taxonomic and functional resolution were analyzed. The results showed that the transition from the FR diet to the SR diet significantly altered the fermentation patterns and the structure and function of the sheep gastrointestinal microbiota. Community analysis revealed microbial taxa such as Prevotella spp., Alistipes spp., RC9 spp., CAG-110 spp., and Akkermansia spp. with significantly altered abundances (P < 0.05), primarily associated with the reduced fiber content in the SR diet. Moreover, the gastrointestinal microbiome exhibited strain-level changes in carbohydrate degradation, leading to reduced metabolic functions necessary for fiber processing. Comparative genomics at the single-genome level pinpointed Prevotella as a core genus with strains showing significant functional differences, notably in the capacity to degrade plant polysaccharides. Overall, these findings provide new insights into microbial regulation of gastrointestinal health and offer valuable enzyme gene resources in ruminants.}, } @article {pmid41716871, year = {2026}, author = {Rosenqvist, T and Cleary, M}, title = {Detecting "invisible" Phytophthora lineages in publicly available sequencing data.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag019}, pmid = {41716871}, issn = {2730-6151}, abstract = {Our understanding of microbial eukaryotic diversity is limited by biases induced by cultivation and DNA-amplification. Microbial lineages which are challenging or impossible to culture and develop universal metabarcoding primers for can be considered "invisible." These "invisible" microbes can however be detected in genomic and metagenomic sequencing datasets. This study introduces a new pipeline for targeted assembly of internal transcribed spacer (ITS) sequences from genomes and metagenomes (https://github.com/tage-ro/denim), which provides advantages in sensitivity and precision over comparable marker-gene assembly software. It further shows how publicly sequencing datasets can be screened for the genus Phytophthora, which includes economically and ecologically devastating plant pathogens. Analysis of 104 sequencing datasets resulted in 733 full ITS sequences, 1626 ITS1 sequences and 2191 ITS2 sequences associated with a variety of eukaryotic lineages. Phytophthora ITS sequences associated with known species in clades 1, 2, 4, 6, 7 and 8 were assembled, along with sequences only distantly related to known taxa. In addition, it provided potential indications of new pathogen-host interactions, with potential impacts on agriculture and human health. This study presents a new approach towards discovering and detecting "invisible" microbes, thus expanding our understanding of microbial eukaryotic diversity. Moreover, it allows detection and monitoring of new host-microbe interactions, and characterizing the geographic distribution of cultured and uncultured microorganisms.}, } @article {pmid41716893, year = {2026}, author = {Cao, Y and Huang, J and Wu, W and Xu, Z and Wang, C and Wu, X and Zhan, C and Xing, J and Liu, J and Zhu, M and Ma, S}, title = {Clinical Utility and Therapeutic Strategy Value of Metagenomic Next-Generation Sequencing in Pulmonary Infection Among Cancer Patients.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {568562}, pmid = {41716893}, issn = {1178-6973}, abstract = {INTRODUCTION: Cancer patients, particularly those with lung cancer, are highly susceptible to pulmonary infections due to both the disease itself and the immunosuppressive effects of treatments such as chemotherapy and immunotherapy. The objective of this study was to analyze pathogenic distribution characteristics of pulmonary infections in cancer patients and evaluated the guidance of metagenomic next-generation sequencing (mNGS) on clinical administration.

METHODS: This retrospective study included 66 samples from cancer patients. Pathogens in patient specimens, encompassing peripheral blood, bronchoalveolar lavage fluid (BALF), sputum, and other samples, were identified using both mNGS and culture methods.

RESULTS: Compared to culture methods, mNGS demonstrated a sensitivity of 95.5% across all samples. In terms of overall detections, Human gammaherpesvirus 4 was identified as the most frequently detected pathogen in cancer patients, while Escherichia coli and Candida albicans were ranked as the most common bacterial and fungal pathogens, respectively. During the perioperative period, non-surgical short-term treatment, non-surgical long-term treatment, and long-term treatment groups, Escherichia coli and Achromobacter xylosoxidans were all identified. Moreover, the treatment strategies for patients were timely adjusted based on the mNGS results, resulting in a significant improvement in clinical symptoms for 59.3% (16 out of 27) of the cancer patients.

CONCLUSION: mNGS is an advanced approach for pathogen detection in cancer patients, with commendable diagnostic performance demonstrated. The results of mNGS contribute to the rapid modification of clinical medication, which may improve the survival rate of cancer patients.}, } @article {pmid41717089, year = {2025}, author = {Shi, S and Qi, J and Peng, W and Su, X and Chen, P and Xu, S and Li, S and Ma, L and Wang, W and Jiang, K and Liu, Z and Li, W and Xiong, H and Wang, Y}, title = {Convergent gut microbiome adaptation and pervasive antibiotic resistome in Qinghai-Tibet Plateau passerines.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1733974}, pmid = {41717089}, issn = {1664-302X}, abstract = {INTRODUCTION: The Qinghai-Tibet Plateau, an extreme high-altitude ecosystem, presents a unique model for studying host-microbe-environment coevolution under environmental stress. However, the role of resident wildlife, particularly non-migratory passerines, as reservoirs and vectors for cross-boundary antibiotic resistance gene (ARG) dissemination remains poorly understood.

METHODS: Here, through metagenomic analysis of two endemic passerines (Pseudopodoces humilis and Pyrgilauda ruficollis) and their habitats.

RESULTS: We reveal convergent adaptations in their gut microbiomes, dominated by Actinomycetota, Pseudomonadota and Bacillota. Functional enrichment in carbohydrate metabolism and genetic information processing underpins host energy optimization in extreme high-altitude environments. Critically, these birds constitute a major reservoir of ARGs, harboring 153 antibiotic resistance ontologies (AROs) with nearly universal resistance to clinical antibiotic classes. The core resistome-comprising glycopeptide (van clusters), fluoroquinolone, and tetracycline resistance genes-reflects anthropogenic contamination amplified by environmental persistence. Environmental transmission pathways were unequivocally demonstrated via 47 AROs shared between avian hosts and proximal matrices (soil/grass), coupled with livestock-derived antibiotic influx through excreta, establishing the plateau as a hotspot for resistance gene flux. Strikingly, "low-abundance-high-resistance" taxa (Pseudomonadota, Actinomycetota, and Bacillota; ≤30% abundance but >80% ARG contribution) drive resistome plasticity, potentially facilitated by horizontal gene transfer.

DISCUSSION: Our findings redefine resident passerines as sentinels of ecosystem health and bridges for cross-boundary antimicrobial resistance (AMR) spread. Mitigating global AMR thus necessitates interdisciplinary strategies targeting environmental reservoirs (e.g., regulating livestock antibiotic use) and monitoring avian-mediated gene flow.}, } @article {pmid41717629, year = {2026}, author = {Wang, X and Yang, Y and Li, Y and Zhu, Z and Khashaba, R and Yue, Q}, title = {Multi-omics reveals microbial community characteristics and flavonoid biotransformation mechanisms during mung bean sour fermentation.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101342}, pmid = {41717629}, issn = {2665-9271}, abstract = {Fermented foods are gaining popularity for their health benefits, and fermented mung bean products are recognized for their nutritional value. To investigate microbial community succession and abundance dynamics of bioactive compounds like flavonoids in fermented mung bean sour (MBS), parallel metagenomic and metabolomic analyses were performed. Metagenomic profiling identified Lactiplantibacillus, Lactococcus, Bifidobacterium, and Acetobacter as dominant genera. Functional gene analysis demonstrated a significant increase in the relative abundance of flavonoid degradation pathways, which exhibited strong positive correlations (r > 0.8, p < 0.05) with the dominant genera. Metabolomic analysis revealed a significant decrease in flavonoids, including vitexin and orientin. Moreover, increased activities of β-glucosidase and α-rhamnosidase were identified as key factors promoting the biotransformation of flavonoids into bioactive metabolites such as apigenin, naringenin, and quercetin. This study provides a foundation for further understanding the microbial conversion and utilization of flavonoid compounds in mung beans.}, } @article {pmid41718052, year = {2026}, author = {La Via, L and Ferlito, S and Di Modica, MS and Marino, A and Nunnari, G and Cacopardo, B and Lechien, JR and Lentini, M and Lavalle, S and Botto, GC and Buscema, P and Gruppuso, L and Maniaci, A}, title = {The Global Impact of Sepsis: Epidemiology, Recognition, Management, and Health System Challenges.}, journal = {Epidemiologia (Basel, Switzerland)}, volume = {7}, number = {1}, pages = {}, pmid = {41718052}, issn = {2673-3986}, abstract = {BACKGROUND: Sepsis constitutes a major healthcare burden worldwide, with an estimated 48.9 million incident cases and 11.0 million deaths in 2017, accounting for nearly one-fifth of all global deaths. Even with advances in definitions and guidelines, significant inequalities persist in awareness, early treatment, and health system readiness.

METHODS: We performed a structured narrative review of epidemiology studies, clinical case definitions, diagnostic approaches, stewardship interventions, and health system reports. Both electronic sources (PubMed, Web of Science, Embase, Scopus) and grey literature (World Health Organization [WHO], National Institute for Health and Care Excellence [NICE], Society Critical Care [SSC]) were explored. Evidence incorporated themes were organized across recognition, diagnostics, antimicrobial therapy, organ support, guidelines, and health system determinants.

RESULTS: Measurement tools, including quick Sequential Organ Failure Assessment (qSOFA) and Sequential Organ Failure Assessment (SOFA), exhibited suboptimal sensitivity and utility in varied clinical environments. Biomarkers (procalcitonin, presepsin, CD64) and rapid molecular diagnostics, including metagenomic next-generation sequencing (mNGS) and AI-based devices, enhance detection but are limited by cost and infrastructure constraints. Each hour of delay in antibiotic therapy is associated with a 6-10% increased risk of mortality, underscoring the importance of stewardship, including the incorporation of empiric regimens with rapid de-escalation. Health system bottlenecks-human resources, funding, infrastructure-continue to be a significant determinant of outcomes, especially in low- and middle-income countries.

CONCLUSIONS: Attaining the 2030 WHO targets for sepsis involves precision diagnostics, adaptable guidelines, stewardship frameworks, and resilient health systems. Fair application and resource allocation are crucial to lower the incidence and mortality worldwide.}, } @article {pmid41718326, year = {2026}, author = {Hernández-Cruz, E and Gómez-Godínez, LJ and Ruvalcaba-Gómez, JM and Arteaga-Garibay, RI}, title = {Optimized Method for Efficient DNA Extraction from Agricultural Soils.}, journal = {Methods and protocols}, volume = {9}, number = {1}, pages = {}, pmid = {41718326}, issn = {2409-9279}, abstract = {Soil harbors the highest concentration of microorganisms in ecosystems, and their molecular characterization through high-throughput sequencing is essential for metagenomic studies. However, obtaining high-quality, high-concentration DNA is limited by physicochemical properties (pH, heavy metals, humic acids) and adsorption to clay minerals. Although standardized commercial protocols exist, they present variable limitations depending on soil type. This study developed and validated the National Center for Genetic Resources-Microorganism Collection (CNRG-CM) method, which incorporates innovative pre-washing steps using phosphate-buffered saline (PBS) and sodium phosphate to effectively remove inhibitory humic acids and metal ions, combined with cetyltrimethylammonium bromide (CTAB)/chloroform extraction to achieve high-molecular-weight metagenomic DNA isolation. The CNRG-CM method was applied to three diverse soil types with variable physicochemical properties, recovering DNA concentrations ranging from 1000 to 1300 ng/μL ith a yield of 30 to 48 µg/g[-1], significantly exceeding those obtained with a standard commercial kit with maximum DNA concentrations of 360 ng/μL and a yield of 43 µg/g[-1]. The CNRG-CM protocol is established as an effective and adaptable alternative for metagenomic DNA extraction across diverse agricultural and ecological contexts. It enables subsequent metagenomic studies of soil microbial communities.}, } @article {pmid41718551, year = {2026}, author = {Gröger, L and Rishik, S and Ludwig, N and Beganovic, A and Koch, M and Rheinheimer, S and Hart, M and König, P and Trampert, T and Paul, P and Boese, A and Lehr, CM and Becker, SL and Fuhrmann, G and Keller, A and Meese, E}, title = {Extracellular vesicles and their RNA cargo facilitate bidirectional cross-kingdom communication between human and bacterial cells.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2630482}, pmid = {41718551}, issn = {1949-0984}, mesh = {Humans ; *Extracellular Vesicles/metabolism/genetics ; Caco-2 Cells ; MicroRNAs/metabolism/genetics ; *RNA, Bacterial/metabolism/genetics ; *Epithelial Cells/microbiology/metabolism ; Enterococcus faecalis/metabolism ; }, abstract = {While extracellular vesicles (EVs) are established mediators of intra-species signaling, their contribution to cross-kingdom communication remains incompletely understood. Here, we investigate the EV-mediated interactions between human colon epithelial cells and both Gram-positive and Gram-negative gut bacteria. We show that bacterial EVs (BEVs) derived from Lacticaseibacillus casei, Enterococcus faecalis, and Proteus mirabilis induce distinct transcriptomic changes in Caco-2 cells depending on the bacterial species, with up to ~6,000 differentially expressed genes, including CCL20, CXCL8, or CXCL10. Transfection of BEV-derived RNA independently induces a subset of similar effects, indicating that the EV-mediated communication is partially driven by the RNA cargo. Conversely, we demonstrate that bacteria interact with Caco-2-derived EVs and miR-192-5p, which is highly abundant (~36.4-fold higher) in EVs isolated from conditioned medium compared with EVs from unconditioned medium, with modest effects on bacterial growth. Furthermore, we show that lipid-based packaging of miR-192-5p modulates its association with the bacteria. Our findings support a conceptual model in which EVs and their RNA cargo contribute to species-dependent host-microbe interactions. This study introduces a framework for understanding EVs as cross-kingdom regulators and underscores the importance of tailored, context-specific analyses for understanding the scope of EV-mediated interactions in microbiome-host homeostasis and disease.}, } @article {pmid41719127, year = {2026}, author = {Wang, S and Su, LY and Lan, D and Pan, H and Xiong, M and Yao, M and Deng, Y and Fan, Z and Cao, Y and Zhou, H}, title = {Adenosine signaling driven by the gut microbiota underlies chronic alcohol-induced anesthetic resistance.}, journal = {Cell reports}, volume = {45}, number = {3}, pages = {117015}, doi = {10.1016/j.celrep.2026.117015}, pmid = {41719127}, issn = {2211-1247}, mesh = {Animals ; *Adenosine/metabolism ; *Signal Transduction/drug effects ; *Ethanol ; Humans ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; Mice, Inbred C57BL ; *Anesthetics/pharmacology ; Fecal Microbiota Transplantation ; Receptors, GABA/metabolism ; }, abstract = {Chronic alcohol consumption increases anesthetic tolerance, yet the underlying in vivo mechanisms remain unclear. Here, we demonstrate that long-term alcohol exposure reduces anesthetic efficacy in both humans and mice, prolonging induction and shortening maintenance. Fecal microbiota transplantation from alcohol-exposed donors recapitulated this phenotype in naive mice, indicating a causal role of gut microbiome alterations. Metagenomic and metabolomic analyses identified elevated adenosine as a key microbiota-derived metabolite. Adenosine supplementation decreased anesthetic sensitivity, likely via downregulation of gamma-aminobutyric acid (GABA) receptors. Our findings reveal a gut microbiota-adenosine pathway mediating alcohol-induced anesthetic resistance.}, } @article {pmid41719150, year = {2026}, author = {Ni, Y and Wang, Y}, title = {ICTV Virus Taxonomy Profile: Nipumfusiviridae 2026.}, journal = {The Journal of general virology}, volume = {107}, number = {2}, pages = {}, doi = {10.1099/jgv.0.002226}, pmid = {41719150}, issn = {1465-2099}, mesh = {Genome, Viral ; *DNA Viruses/classification/genetics/ultrastructure/isolation & purification ; Virion/ultrastructure ; *Archaeal Viruses/classification/genetics/ultrastructure/isolation & purification ; Phylogeny ; }, abstract = {The family Nipumfusiviridae includes DNA viruses with hosts deduced to be marine ammonia-oxidizing archaea, specifically those in the archaeal family Nitrosopumilaceae. Virus genomes have been discovered through metagenomics of samples from inlets, coastal areas, intertidal zones, epipelagic and oceanic waters, and soil. Viruses have neither been isolated nor enriched through experiments. The family Nipumfusiviridae includes several genera. The virions of nipumfusiviruses are predicted to have spindle-shaped morphology based on the analysis of the deduced structural models of the major capsid protein. Limited information can be provided about translation and replication from the genome. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Nipumfusiviridae, which is available at ictv.global/report/nipumfusiviridae.}, } @article {pmid41719263, year = {2026}, author = {Huang, G and Gallagher, TL and Tsongalis, GJ and Lefferts, JA}, title = {Development of a multiplex ddPCR assay for simultaneous absolute quantification of bacterial, fungal, and human DNA.}, journal = {PloS one}, volume = {21}, number = {2}, pages = {e0341560}, pmid = {41719263}, issn = {1932-6203}, mesh = {Humans ; *DNA, Bacterial/genetics/analysis ; *DNA, Fungal/genetics/analysis ; *Multiplex Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; RNA, Ribosomal, 16S/genetics ; DNA, Ribosomal/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Molecular methods in clinical and research applications frequently encounter complex mixtures of human and microbial DNA, sometimes alongside environmental or reagent contaminants. In metagenomic studies, the presence of host contamination poses a significant challenge, reducing the assay sensitivity of microbial detection and characterization. Different host-depletion and microbial enrichment platforms have been developed to reduce or eliminate host DNA in samples predominantly composed of human DNA. To establish an effective method to assess the efficacy of host DNA depletion or microbial enrichment platforms, this study aimed to develop a multiplex, broad-range 16S/18S ribosomal DNA droplet digital PCR (rDNA ddPCR) assay capable of simultaneously quantifying bacterial and fungal DNA, along with a human housekeeping gene, RPP30 (Ribonuclease P/MRP Subunit P30). Genomic DNA from key representatives of Gram-positive bacteria, Gram-negative bacteria, and fungi was tested in broad-range 16S/18S rDNA duplex (16S/RPP30 or 18S/RPP30) and triplex (16S/18S/RPP30) ddPCR assays to determine optimal assay conditions, specificity, and sensitivity. This assay demonstrated high sensitivity, specificity, and reproducibility, with detection limits of approximately 3 copies/µL for the 16S target (0.5 pg Staphylococcus aureus gDNA) and 1-2 copies/µL for the 18S target (16 fg of Candida albicans gDNA) in both duplex and triplex formats. Within a defined range, a linear relationship was observed between microbial DNA input and 16S/18S rDNA copy number by ddPCR. Furthermore, different commercial ddPCR master mixes had contrasting effects on the amplitudes of positive 16S/18S droplet clusters. As a proof of concept for the assay's utility in metagenomic studies, we demonstrated that one extraction kit achieved more efficient depletion of human DNA and better enrichment of microbial DNA. In summary, we developed a multiplex, broad-range 16S/18S ddPCR assay with high sensitivity and specificity, which holds promise as a QA/QC (Quality Assurance/Quality Control) platform in metagenomic studies and other research settings.}, } @article {pmid41719397, year = {2026}, author = {Cheng, G and Jiang, X and Zhu, L and Chen, X and Liu, R and Zhu, L and Hu, X and Zhang, S and Tan, W and Lin, D and Zhang, L and Wu, C and Li, M}, title = {Intratumoral Parvimonas micra promotes esophageal squamous cell carcinoma via p-cresol-induced Treg differentiation.}, journal = {Science advances}, volume = {12}, number = {8}, pages = {eady1644}, pmid = {41719397}, issn = {2375-2548}, mesh = {*T-Lymphocytes, Regulatory/immunology/metabolism ; *Esophageal Squamous Cell Carcinoma/microbiology/pathology/metabolism/immunology/etiology ; Humans ; Animals ; *Esophageal Neoplasms/microbiology/pathology/metabolism/immunology ; *Cresols/metabolism/pharmacology ; *Cell Differentiation/drug effects ; Tumor Microenvironment/immunology ; Mice ; Prognosis ; Cell Line, Tumor ; Reactive Oxygen Species/metabolism ; }, abstract = {Intratumoral microbiota has emerged as a notable factor influencing cancer initiation and progression. However, its composition and functional impact in esophageal squamous cell carcinoma (ESCC) remain largely unexplored. Here, we performed metagenomic sequencing on 119 paired tumor-normal tissues from patients with ESCC and single-cell RNA sequencing on 45 samples to investigate microbe-host interactions. We identified Parvimonas micra (P. micra), an anaerobic oral-derived bacterium, as significantly enriched in tumor tissues and associated with poor prognosis. Moreover, the abundance of P. micra correlated with increased regulatory T cell (Treg cell) infiltration in the ESCC tumor microenvironment. Through cellular and animal experiments, we demonstrate that P. micra promotes tumor growth by secreting p-cresol, a metabolite of amino acid fermentation, which elevates reactive oxygen species levels and induces FOXP3[+] Treg differentiation, thereby fostering immunosuppression and tumor growth. Our study establishes a mechanistic link between intratumoral microbiota and the immune microenvironment, highlighting the microbial contribution to ESCC progression and prognosis.}, } @article {pmid41719533, year = {2026}, author = {Ippolito, I and Hug, L}, title = {Antimicrobial resistance gene diversity, prevalence, and mobility within four landfills.}, journal = {Canadian journal of microbiology}, volume = {72}, number = {}, pages = {1-15}, doi = {10.1139/cjm-2025-0226}, pmid = {41719533}, issn = {1480-3275}, mesh = {*Waste Disposal Facilities ; *Genetic Variation ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; Soil Microbiology ; Plasmids/genetics ; }, abstract = {Antibiotics in landfills create selection pressures on the microorganisms present, selecting for antibiotic resistance genes (ARGs) and antibiotic resistant organisms (ARO). The aim of this study was to assess whether landfills are hot-spots of antimicrobial resistance and whether landfills may contribute to global ARO diversity through ARG lateral gene transfer. Genome resolved metagenomic sequencing combined with sequence-search-based and deep learning tools were used to determine ARG diversity and prevalence from four active municipal landfills and their adjacent ground or surface water systems. Comparison to pristine and anthropogenic environments highlighted that landfill microbial communities contain distinct ARG signatures, including a broader diversity of ARGs. Plasmids made up 4.1%-8.4% of assembled scaffolds and carried 5.4%-12.0% of the identified ARGs in assembled data, depending on the sample type. Enriched ARG resistance mechanisms on mobile elements included multidrug resistance and antibiotic inactivation. The results indicate that landfills house a high diversity of antimicrobial resistance mechanisms and drug classes, with a moderate fraction encoded on mobile elements. Landfills are thus likely mixing grounds for ARG transfer and evolution of novel or augmented ARO lineages.}, } @article {pmid41719987, year = {2026}, author = {Dang, X and Xu, S}, title = {Exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate is associated with aberrant barbering behavior in diabetic mice.}, journal = {Ecotoxicology and environmental safety}, volume = {311}, number = {}, pages = {119906}, doi = {10.1016/j.ecoenv.2026.119906}, pmid = {41719987}, issn = {1090-2414}, mesh = {Animals ; Male ; Mice ; Hippocampus/drug effects/microbiology ; Molecular Docking Simulation ; *Diabetes Mellitus, Experimental ; *Environmental Pollutants/toxicity ; *Behavior, Animal/drug effects ; Molecular Dynamics Simulation ; Colon/microbiology/drug effects ; Fluorobenzenes ; }, abstract = {This study originated from an incidental behavioral observation. We found that exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate (OBS; 3 μg/L), as reported in a previous field measurement study, was associated with aberrant barbering behavior in diabetic mice. To investigate the underlying mechanisms, sixteen 8-week-old male db/db mice were administered OBS at 3 μg/L for 91 days. Biochemical assays of endothelial- and barrier-related markers, hippocampal OBS quantification, stereotaxic hippocampal OBS administration, and metagenomic sequencing of the colonic contents and hippocampal tissues were performed. Based on the metagenomic results, computational biology analyses, including molecular docking, molecular dynamics simulations, and protein functional annotation, were conducted to assess potential OBS-bacterial protein interactions. The results showed that exposure to environmentally relevant concentration of OBS was associated with aberrant barbering behavior in the experimental mice (100 % prevalence). Circulating markers of endothelial activation and basal lamina injury were significantly elevated. Metagenomic analysis revealed that the abundance of Salmonella enterica subsp. diarizonae was significantly increased in both the colonic contents and hippocampal tissues, with hippocampal abundance positively correlated with colonic abundance. Molecular docking and molecular dynamics simulations indicated that OBS binds effectively to two bacterial proteins. Functional annotation suggested that these proteins are associated with central metabolic and biosynthetic processes relevant to bacterial proliferation. Together, these findings suggest that exposure to environmentally relevant concentration of OBS is associated with aberrant barbering behavior in diabetic mice and may be associated with increased colonic S. enterica subsp. diarizonae abundance and its presence in the hippocampus.}, } @article {pmid41720032, year = {2026}, author = {Kong, X and He, Y and Guo, J and Chen, Y and An, D}, title = {Chain-length-associated response patterns of chlorinated paraffins on activated sludge systems driven by microbial community response.}, journal = {Journal of hazardous materials}, volume = {505}, number = {}, pages = {141542}, doi = {10.1016/j.jhazmat.2026.141542}, pmid = {41720032}, issn = {1873-3336}, mesh = {*Sewage/microbiology/chemistry ; *Paraffin/toxicity/chemistry ; *Water Pollutants, Chemical/toxicity/chemistry ; Bioreactors/microbiology ; *Hydrocarbons, Chlorinated/toxicity/chemistry ; *Microbiota/drug effects ; Bacteria/genetics/metabolism/drug effects ; Phosphorus/metabolism ; Nitrogen/metabolism ; }, abstract = {Chlorinated paraffins (CPs) are emerging contaminants detected in wastewater treatment plants, yet their impacts on activated sludge systems remain poorly understood. In this study, parallel sequencing batch reactors were employed to comprehensively evaluate the effects of short-chain (SCCP), medium-chain (MCCP), and long-chain (LCCP) CPs on pollutant removal performance, sludge properties, and microbial ecological responses. Under the tested nominal loading, the C24-LCCP standard led to a clear reduction in nitrogen removal efficiency, whereas MCCP and SCCP maintained stable or even enhanced phosphorus removal performance. CP exposure generally increased oxidative stress and cytotoxicity, while SCCP and MCCP further stimulated extracellular polymeric substances secretion, consistent with an enhanced floc/cell-interface protective phenotype. Metagenomic analysis revealed that SCCP and MCCP enriched genera (Acinetobacter, Dechloromonas, Zoogloea) associated with phosphorus removal and increased the abundance of key nitrogen transformation genes, whereas the C24-LCCP standard exhibited comparatively weaker shifts in functional gene profiles. Metatranscriptomic profiling indicated treatment-associated differences in transcriptional responses under the tested nominal loading, with SCCP showing the largest DEG set (>30,000 genes) in this dataset. Integrated metagenomic and metatranscriptomic analyses revealed a coordinated stress‑response program under SCCP, characterized by activation of efflux pumps, DNA repair, redox regulation, environmental stress responses, and biofilm-associated functions, together with elevated energy metabolism and ABC transporter signals. These molecular and community-level patterns aligned with the observed variations in treatment performance and sludge properties, providing convergent evidence for a chain-length-associated response framework. These findings provide comparative molecular and phenotypic evidence that may inform future risk assessment and hypothesis-driven mitigation studies on CP impacts in biological wastewater treatment systems.}, } @article {pmid41720310, year = {2026}, author = {Zhao, W and Chen, P}, title = {Resilient biological nitrogen removal from surfactant-rich wastewater: construction of an indigenous community, quantitative tolerance assessment, and multi-level fault tolerance mechanisms.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134251}, doi = {10.1016/j.biortech.2026.134251}, pmid = {41720310}, issn = {1873-2976}, mesh = {*Nitrogen/isolation & purification ; *Wastewater/chemistry/microbiology ; *Surface-Active Agents/chemistry ; Denitrification/drug effects ; Biodegradation, Environmental/drug effects ; *Water Purification/methods ; Bacteria/metabolism/drug effects ; Alkanesulfonic Acids ; Kinetics ; Nitrification ; }, abstract = {Linear alkylbenzene sulfonates (LAS) severely inhibit biological nitrogen removal. In this study, an indigenous microbial community (ICM) with heterotrophic nitrification-aerobic denitrification (HN-AD) capability was developed through long-term directed acclimatization. The ICM exhibited markedly enhanced resistance to LAS over a concentration range of 0-300 mg/L, maintaining nitrogen transformation rates more than twofold higher than those of conventional activated sludge. By integrating Haldane kinetic modeling with species sensitivity distribution analysis, we demonstrated that the ICM increased the 5% hazardous concentration (HC5) by 78%, thereby substantially expanding its ecological tolerance. Metagenomics and qPCR linked ICM resilience to multi-level responses; quorum sensing regulation, EPS-mediated sequestration, and enhanced redox homeostasis reinforced HN-AD performance. Dominant genera Pseudomonas and Aeromonas coupled detoxification with nitrogen removal. These findings demonstrate the ICM's transition from passive survival to active nitrogen removal reinforcement, offering quantitative benchmarks for resilient surfactant-rich wastewater treatment.}, } @article {pmid41720311, year = {2026}, author = {Liu, C and Ji, M and Wu, W and Shi, Y and Treu, L and Wang, W and Campanaro, S}, title = {Self-sufficient fermentation paradigm for cassava stillage valorization into C6 carboxylic acids: regulatory mechanisms and novel microbe identification.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134236}, doi = {10.1016/j.biortech.2026.134236}, pmid = {41720311}, issn = {1873-2976}, mesh = {*Fermentation ; *Carboxylic Acids/metabolism ; *Manihot/metabolism/chemistry ; Hydrogen-Ion Concentration ; *Clostridium/metabolism/genetics ; Lactic Acid/metabolism ; Butyric Acid/metabolism ; }, abstract = {Cassava stillage (CS), a carbohydrate-rich byproduct of bioethanol production, holds significant untapped potential as a renewable resource. Upcycling this problematic wastewater offers great promise for addressing both environmental challenges and the demand for sustainable biochemicals. Here, this study proposed a self-sufficient biotechnological paradigm that directly valorizes CS into medium-chain carboxylic acids (MCCAs, e.g., caproic acid) by integrating lactic acid/butyric acid-type fermentation with microbial chain elongation (CE) by two phase fermentation regulatory. Lactic acid and butyric acid were regulated as dominant products with optimal ratio around 2 from CS degradation, and then chain elongated into caproic acid with optimal pH of 6. pH was found to play a crucial role in controlling product distribution in both phases of fermentation and shaping the microbiome. Meanwhile, chain elongation resilience was also found operational pH-dependent. Metagenomic analysis identified the bacterium Clostridium sp. BUCT163 as a putative lactic acid-driven chain elongating microbe. Whole-genome comparison between Clostridium sp. BUCT163 and Clostridium kluyveri species indicated that the genes encoding lactic acid conversion are not widespread among C. kluyveri populations. The combination of metagenomic-binning and comparative genomic analysis Clostridium sp. BUCT163 was distinguished as the novel potential lactic acid/ethanol-driven chain elongating microbe which successfully provided valuable data sets to link bacterial identities with chain elongating microbes. These findings provide foundation for the resource recovery process from CS in a self-sufficient anaerobic fermentation paradigm and the microbial management of chain elongating systems.}, } @article {pmid41720808, year = {2026}, author = {Jin, Y and An, HJ and Zheng, TT and Li, JJ and Gao, JM and Zhong, XL and Li, BH and Liu, YY and Zhuang, XJ and Chen, JH and Rao, JH}, title = {Adenosine from high-fat-diet-tolerant monkey-derived Limsolactobacillus reuteri MacFasB02 modulates cholesterol metabolism to alleviate hyperlipidemia and inflammation.}, journal = {NPJ science of food}, volume = {10}, number = {1}, pages = {}, pmid = {41720808}, issn = {2396-8370}, support = {82471097 and 82200966//National Natural Science Foundation of China/ ; 2020B121201006//Guangdong Key Laboratory of Nonhuman Primate Research/ ; 210183503006//Guangdong Provincial Science and Technology Leading Talent Project/ ; 2024GDASZH-2024010101//GDAS' Project of Science and Technology Development/ ; }, abstract = {Hyperlipidemia is a leading global health challenge, limited by the safety liabilities of current pharmacotherapies. Here, we isolated a novel Limosilactobacillus reuteri strain, MacFasB02, from fecal samples of cynomolgus monkeys tolerant to chronic high-fat diet (HFD). This study aimed to systematically evaluate its probiotic properties and therapeutic potential against hyperlipidemia. In vitro, MacFasB02 exhibited robust growth, acid production, and tolerance to acidic and bile environments. In HFD-fed mice, 13-week MacFasB02 administration reduced weight gain, serum triglycerides, low-density lipoprotein cholesterol and total cholesterol, while ameliorating hepatic steatosis and inflammation, as well as restoring intestinal barrier integrity by enhanced villus architecture, goblet cell function, and tight junction proteins expression. Metagenomic analysis revealed gut microbiota remodeling. Transcriptomic profiling coupled with in vivo validation demonstrated upregulation of Apoa1 and Pltp in cholesterol metabolism. Untargeted metabolomics integrated with whole-genome sequencing and supernatant metabolite profiling identified adenosine as a key MacFasB02-derived metabolite in purine metabolism. Consistently, In vitro experiments showed that adenosine reduced lipid accumulation and inflammation in hepatocytes by regulating Apoa1 and Pltp to modulate cholesterol metabolism. Collectively, MacFasB02 exerts dual lipid-lowering and anti-inflammatory effects probably via adenosine-mediated modulation of cholesterol metabolism, promising potential as a live biopharmaceutical agent for hyperlipidemia.}, } @article {pmid41720887, year = {2026}, author = {Clarenne, A and Suarez, LV and Muggeo, A and Meurice, J and Lecomte-Thenot, Q and Perotin, JM and Bessaci-Kabouya, K and Mulette, P and Abely, M and Gouriou, S and Dury, S and Deslée, G and Héry-Arnaud, G and Guillard, T}, title = {Assessing anaerobe detection in routine sputum analyses from cystic fibrosis patients.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41720887}, issn = {2045-2322}, support = {RINNOPARI//Université de Reims Champagne-Ardenne/ ; RINNOPARI//University Hospital of Reims/ ; }, mesh = {Humans ; *Cystic Fibrosis/microbiology ; *Sputum/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria, Anaerobic/isolation & purification/genetics/classification ; Female ; Male ; Adult ; }, abstract = {Pulmonary involvement in cystic fibrosis (CF) includes bronchiectasis and chronic airway infection, with nearly half of the airway bacteria being anaerobes. Some anaerobic species, such as Porphyromonas catoniae, have been identified as predictive biomarkers for Pseudomonas aeruginosa colonization, with P. catoniae decreasing as the disease progresses. Although 16S rRNA metagenomics offers a comprehensive view of airway anaerobes, it is not routinely performed in clinical microbiology laboratories. This study aimed to evaluate the ability of routine sputum culture to identify strict anaerobes in people with CF (pwCF) compared to 16S rRNA sequencing, and to assess the impact of sample transport conditions. Sputum from 48 pwCF was analyzed by anaerobic culture and 16S rRNA sequencing. Strict anaerobes were detected in 95.8% of patients by culture and 100% by 16S rRNA sequencing. Culture identified 23 strict anaerobic species (mean 2.6 per sample), while 16S rRNA sequencing revealed nearly 100 species (mean 43 per sample). Importantly, culture isolated key genera such as Veillonella and Prevotella, core members of the CF airway anaerobiome. Transport conditions (aerobic vs. anaerobic) did not affect anaerobe detection. These new findings support changes in the processing of CF sputum in the everyday practice of clinical microbiology laboratories and promote the characterization of the culturable anaerobic airway microbiota.}, } @article {pmid41721729, year = {2026}, author = {Wang, H and Zhao, Z and Lin, L and Dong, A and Deng, Y and Zhou, J and Ju, F}, title = {Candidatus Dermatophostum as a novel genus of polyphosphate-accumulating organisms for high-strength wastewater treatment.}, journal = {The ISME journal}, volume = {20}, number = {1}, pages = {}, pmid = {41721729}, issn = {1751-7370}, support = {WU2024MY003//Westlake University-Muyuan Joint Research Institute/ ; 42477517//National Natural Science Foundation of China/ ; 42207546//National Natural Science Foundation of China/ ; }, mesh = {*Wastewater/microbiology/chemistry ; *Polyphosphates/metabolism ; Phylogeny ; Phosphorus/metabolism ; *Water Purification/methods ; Metagenome ; }, abstract = {Dermatophilaceae polyphosphate-accumulating organisms (PAOs), formerly classified as Tetrasphaera PAOs, play pivotal roles in enhanced biological phosphorus removal (EBPR). However, their phylogenetic diversity, ecological preferences, and metabolic traits remain poorly characterized, and a robust marker gene for their classification is lacking. Here, we performed an extensive phylogenomic and metabolic analysis of Dermatophilaceae PAOs utilizing 46 newly recovered metagenome-assembled genomes from a laboratory-scale EBPR reactor treating high-strength wastewater and full-scale wastewater treatment plants. These analyses revealed a previously uncharacterized PAO genus, named here as Candidatus Dermatophostum, which shows specific preference for high-phosphorus environments. Its representative species, Ca. Dermatophostum ammonifactor, was enriched in the EBPR reactor and its PAO phenotype was confirmed by polyphosphate staining and fluorescence in situ hybridization. Integrative meta-omics combining genomic, transcriptomic, and protein structure analyses revealed its specialized metabolic capabilities for phosphate metabolism, glycogen synthesis, and dissimilatory nitrate reduction to ammonium. Moreover, Ca. Dermatophostum was found to be widely distributed across wastewater treatment plants worldwide, underscoring both its diverse metabolic capabilities and potential engineering implications for mitigating nitrous oxide (N2O) emissions for EBPR system. Finally, we propose a ppk1-based classification framework that resolves Dermatophilaceae PAOs into six distinct clades, consistent with whole-genome phylogeny, and demonstrates that ppk1 can serve as a reliable marker gene for tracking these populations. Together, these findings expand the ecological and functional understanding of Dermatophilaceae PAOs and highlight their promise for advancing sustainable wastewater treatment and resource recovery.}, } @article {pmid41721873, year = {2026}, author = {Sankar, SA and Girijan, SK and Shambhugowda, YB and Busala, SKK and Narayanane, S}, title = {Decoding the biotic networks and functional potential of seamount sediments in the Arabian sea.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {41721873}, issn = {1573-4978}, mesh = {*Geologic Sediments/microbiology/chemistry ; Metagenomics/methods ; Nitrogen/metabolism ; Oceans and Seas ; Metagenome/genetics ; Carbon ; }, abstract = {BACKGROUND: The Arabian Sea is ecologically and environmentally significant due to its high biotic diversity and its potential role as a reservoir of emerging resistance determinants. However, molecular-level insights into the taxonomic composition, functional potential, and resistome of sediment associated communities from deep-sea seamount sediments remain limited.

METHODS AND RESULTS: A metagenomic approach was employed to investigate the biotic composition, metabolic potential, resistome profiles, and physicochemical characteristics of two seamount sediment samples (SM1 and SM7) collected from the Arabian Sea. Distinct environmental conditions were observed, with SM1 enriched in inorganic nitrogen, whereas SM7 exhibited higher organic carbon content and pigment concentrations, indicating differences in substrate availability. These variations were consistent with differences in the community structure, with SM1 harbouring a less diverse assemblage dominated by Actinomycetota and fungi, while SM7 supported a broader community comprising Actinomycetota, diverse fungi, protists, metazoans, and a richer viral component. Functional annotation revealed enrichment of nitrogen metabolism pathways in SM1, whereas SM7 showed increased representation of carbohydrate metabolism and a higher proportion of novel gene content. Both sediment samples encoded antibiotic and heavy metal resistance genes; however, SM7 exhibited greater abundance and diversity of putative resistance-associated genes, including resistance to mupirocin, triclosan, and sulfonamides, along with broader metal resistance and stress response genes.

CONCLUSIONS: The results based on two samples demonstrate pronounced sample specific variation in community structure, metabolic potential, and resistome profiles across Arabian Sea seamount sediments. These findings highlight Arabian Sea deep-sea sediments as important molecular reservoirs of microbial diversity and adaptive potential shaped by local environmental conditions.}, } @article {pmid41722379, year = {2026}, author = {Steinberger, Y and Doniger, T and Marchi, E and Eshel, G and Bocchi, S and Zapperi, S and La Porta, CAM}, title = {Fungal community structure and network connectivity as indicators of soil health under long-term land use.}, journal = {The Science of the total environment}, volume = {1020}, number = {}, pages = {181545}, doi = {10.1016/j.scitotenv.2026.181545}, pmid = {41722379}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Fungi/classification ; *Agriculture ; *Environmental Monitoring/methods ; Soil/chemistry ; Israel ; Biodiversity ; Seasons ; }, abstract = {Agriculture practices induce profound changes in soil biological properties and soil functioning. However, we still lack an understanding of how soil fungal biodiversity responds to various practices. Metagenomic tools were used to investigate soil fungal communities and inferred ecological functions based on functional guild classification in response to the effect of climate region and land management. This study assessed how seasonal timing and long-term land management affect soil fungal communities, with the aim of exploring their potential as candidate indicators of soil biological status. We collected soil samples across two regions of Israel (Mediterranean north and semi-arid south), three land-use types-orchard (OR), field crops (FC), and non-cultivated control (CO)-and two seasons-autumn and spring. Abiotic parameters varied significantly by season, region, and depth, underscoring the importance of considering sampling time in soil assessment. Fungal community composition showed marked differences between land uses, suggesting sensitivity to long-term management. CO and OR soils consistently exhibited higher fungal diversity and network connectivity, while FC soils had lower richness and unique taxa. A stable core community of 10 genera was found across treatments. Functional guilds were dominated by saprotrophs, though specific taxa and guild contributions varied by management type and season. Overall, our results emphasize the importance of sampling timing and land-use history in shaping fungal communities and support the potential of fungal-based indicators for assessing soil status across agricultural systems.}, } @article {pmid41722567, year = {2026}, author = {Thurimella, K and Wu, E and Li, C and Graham, DB and Owens, RM and Plichta, DR and Sokol, CL and Xavier, RJ and Bacallado, S}, title = {Identifying microbial protease allergens through protein language model-guided homology.}, journal = {Cell systems}, volume = {17}, number = {3}, pages = {101510}, pmid = {41722567}, issn = {2405-4720}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AI151163/AI/NIAID NIH HHS/United States ; }, mesh = {*Allergens/immunology ; Humans ; Animals ; *Serine Proteases/immunology/metabolism ; Metagenomics/methods ; Hypersensitivity/immunology ; Microbiota ; }, abstract = {Emerging research links the gut, skin, and oral microbiomes to allergies, with serine proteases (SPs) identified as potential allergens. This study leverages deep learning and pre-trained protein language models (pLMs) to uncover allergenic SPs in metagenomic data. First, we develop a model to identify the catalytic serine residue in serine hydrolases, demonstrating how pLMs capture structural information. Next, we create a deep learning framework to detect candidate SP allergens across gene catalogs, using the conserved catalytic triad to identify homologs in gut and oral sites despite low sequence identity. Our model predicts a putative SP allergen resembling V8 protease, a known trigger for protease-activated receptor 1. It also identifies a cysteine protease similar to Der f 1 from dust mites. Immunization with these proteases induced allergic responses, validating their allergenic potential experimentally. This approach uncovers candidate allergens beyond traditional methods, offering new targets for allergy research. A record of this paper's transparent peer review process is included in the supplemental information.}, } @article {pmid41722709, year = {2026}, author = {Arhin, SG and Esposito, G and Cesaro, A}, title = {Single-stage microbial conversion of fish waste into linear and branched medium-chain fatty acids.}, journal = {Bioresource technology}, volume = {447}, number = {}, pages = {134253}, doi = {10.1016/j.biortech.2026.134253}, pmid = {41722709}, issn = {1873-2976}, mesh = {Animals ; *Fatty Acids/biosynthesis/chemistry/metabolism ; Fermentation ; *Fishes ; Food Loss and Waste ; }, abstract = {Anaerobic fermentation of biowaste into medium‑chain fatty acids (MCFAs) offers a scalable route for resource recovery within a circular bioeconomy framework, yet production from protein‑rich substrates such as fish waste remains underexplored. This study investigated the valorization of fish waste into MCFAs via mono- and co-fermentation in a single-stage chain elongation process. By leveraging endogenous electron donors and protein ammonification, the system maintained favorable pH conditions and sustained MCFA synthesis without external chemical inputs. Mono-fermentation favored isocaproate (4-methylvaleric acid) production, reaching a peak yield of 166.9 ± 11.6 mg COD/g VS (5.8 ± 0.4 g COD/L). Co-fermentation with carbohydrate-rich food waste in equal proportions shifted selectivity toward n-caproate (214.5 ± 18.8 mg COD/g VS) and n-heptanoate (145.8 ± 27.7 mg COD/g VS), achieving a maximum total MCFA yield of 366.3 ± 53.1 mg COD/g VS (12.8 ± 1.9 g COD/L). Bioaugmentation with Saccharomyces cerevisiae triggered solventogenesis and excessive ethanol oxidation (EEO) possibly due to elevated ammonium concentrations. Although sodium 2-bromoethanesulfonate (BES) addition transiently suppressed EEO, EEO resumed as H2 production declined, suggesting that promoting lactate-driven chain elongation via co‑fermentation is a more robust strategy under ammonia stress. Metagenomic analysis revealed that isocaproate formation during mono‑fermentation was associated with Stickland‑type amino‑acid fermentation, with Sporanaerobacter acetigenes as a potential key contributor. In contrast, co‑fermentation enriched genes associated with lactate metabolism, acetyl‑CoA generation, and linear MCFA synthesis, primarily linked to Clostridia and Betaproteobacteria. These results reveal tunable routes to straight‑ and branched‑chain MCFAs from protein‑rich waste, supporting green approaches to platform chemical generation.}, } @article {pmid41722974, year = {2026}, author = {Ji, M and Gong, J and Liu, Z and Liu, X and Wang, X and Ao, C and Tan, J}, title = {Multi-omics investigation of microbial community dynamics and metabolic regulation in mulberry wine fermentation under temperature and acid stress.}, journal = {Food microbiology}, volume = {137}, number = {}, pages = {105022}, doi = {10.1016/j.fm.2025.105022}, pmid = {41722974}, issn = {1095-9998}, mesh = {*Wine/microbiology/analysis ; Fermentation ; Multiomics ; Saccharomyces cerevisiae/metabolism/genetics ; Temperature ; *Morus/microbiology/metabolism/chemistry ; Ethanol/metabolism ; *Microbiota ; Hydrogen-Ion Concentration ; *Acids/metabolism ; Metabolomics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Stress, Physiological ; Lactobacillus/metabolism/genetics ; Metagenomics ; }, abstract = {This study employed an integrated approach of metagenomics and metabolomics to investigate microbial community dynamics during mulberry wine fermentation under varying temperatures (17-29 °C) and pH levels (3.0-4.5). Twenty treatment combinations, spanning 27 days, captured the temporal dynamics of microbial communities and metabolic activity. Environmental stress significantly shaped community assembly, with Saccharomyces cerevisiae acting as the dominant fermentation organism and Lactobacillus spp. associated with organic acids. Core population analysis revealed specialized functions in ethanol production, acid resistance, and flavor biosynthesis. An optimal fermentation efficiency of 82 % and an ethanol content of 9.1 % vol. were achieved with the response surface method, resulting in optimal fermentation conditions of 23 ± 1 °C with a pH of 3.5 ± 0.1. Multi-omics correlation network analysis revealed coordinated associations among gene expression, enzymatic activities, and metabolite profiles, including coordinated expression patterns of flavor compound biosynthesis pathways. This research provides evidence-based optimization strategies for industrial mulberry wine production, enhancing understanding of stress-responsive microbial adaptation mechanisms.}, } @article {pmid41723054, year = {2026}, author = {Prideaux, L and Goire, N and Crook, S and Dreyer, L and Sherry, N and Mahony, AA}, title = {A case of Helicobacter cinaedi meningitis confirmed via metagenomics sequencing.}, journal = {Pathology}, volume = {58}, number = {3}, pages = {377-379}, doi = {10.1016/j.pathol.2025.10.011}, pmid = {41723054}, issn = {1465-3931}, } @article {pmid41723172, year = {2026}, author = {Honda, T and Yu, S and Mai, D and Baumgart, L and Chan, EM and Babnigg, G and Yoshikuni, Y}, title = {CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41723172}, issn = {2041-1723}, support = {DE-AC02-06CH11357//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, mesh = {*Plant Roots/microbiology ; *Arabidopsis/microbiology/genetics/immunology ; *Pseudomonas/genetics ; Gene Expression Regulation, Bacterial ; Promoter Regions, Genetic ; Rhizosphere ; Gene Expression Profiling ; Transcription, Genetic ; }, abstract = {Plant roots release a wide array of metabolites into the rhizosphere, shaping microbial communities and their functions. While metagenomics has expanded our understanding of these communities, little is known about the physiology of their members in host environments. Transcriptome analysis via RNA sequencing is a common approach to learning more, but its use has been challenging because of low bacterial biomass and interference from plant RNA. To overcome this, we developed a randomly-barcoded promoter-library insertion sequencing (RB-PI-seq) combined with chassis-independent recombinase-assisted genome engineering (CRAGE). Using Pseudomonas simiae WCS417 as a model rhizobacterium, this method enabled targeted amplification of barcoded transcripts, bypassing plant RNA interference and allowing measurement of thousands of promoter activities during Arabidopsis root colonization. Our analysis revealed temporally resolved transcriptional regulation, including those associated with cell growth, chemotaxis, plant immune suppression, biofilm formation, and stress responses, reflecting the coordinated physiological adaptation to the root environment. Additionally, we discovered that transcriptional activation of xanthine dehydrogenase and a lysozyme inhibitor is crucial for evading plant immune systems. This framework is scalable to other bacterial species and provides new opportunities for understanding rhizobacterial gene regulation in native environments.}, } @article {pmid41723316, year = {2026}, author = {Moreno, IJ and Bogdanov, A and Palenik, B}, title = {Common capacity for far-red light photosynthesis in a canyon thermophilic freshwater system.}, journal = {Extremophiles : life under extreme conditions}, volume = {30}, number = {1}, pages = {}, pmid = {41723316}, issn = {1433-4909}, abstract = {UNLABELLED: Photosynthetic life is based on absorbing sunlight and turning it into biologically usable energy. In many cases however, canopy-like structures and cavern-like habitats in terrestrial environments can limit the intensity and alter the spectra of light. One acclimation to use filtered light in the near infrared range, typically between 700 and 800 nm is named far-red light photoacclimation or FaRLiP as in recent studies of cyanobacteria. Here we report the common capacity for FaRLiP in the dominant cyanobacterial genera in a canyon hot spring microbial mat ecosystem. We identified FaRLiP in the genomes of cyanobacterial isolates and the metagenomes of mat samples. We show using absorption spectroscopy and HPLC that under far red-light specific isolates show an increase in far red-light absorption and the presence of Chl f. Springs in narrow canyons are a microniche where FaRLiP seems highly ecologically advantageous.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00792-026-01422-9.}, } @article {pmid41723359, year = {2026}, author = {Wang, L and Xu, J and He, P and Hong, W and Jin, Y and Zeng, J and Liu, L and Liu, L}, title = {Refractory peritoneal dialysis-associated peritonitis caused by Mycobacterium tuberculosis identified by mNGS: a case report.}, journal = {BMC nephrology}, volume = {27}, number = {1}, pages = {}, pmid = {41723359}, issn = {1471-2369}, support = {0038481190612016//Zhuhai High-Level Talent Team Fund/ ; }, mesh = {Humans ; Female ; *Peritoneal Dialysis/adverse effects ; Adult ; *Kidney Failure, Chronic/therapy/complications ; *Mycobacterium tuberculosis/isolation & purification/genetics ; *Peritonitis/microbiology/etiology/diagnosis ; *Peritonitis, Tuberculous/diagnosis/etiology/microbiology/drug therapy ; Antitubercular Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; }, abstract = {BACKGROUND: Peritoneal dialysis-associated peritonitis (PDAP) is a common complication in patients undergoing peritoneal dialysis (PD) and may lead to technique failure or poor prognosis. Tuberculosis-related peritonitis in this setting is rare and difficult to diagnose because of nonspecific clinical manifestations and frequently negative conventional microbiological tests. Reporting such cases may help improve awareness and diagnostic strategies.

CASE PRESENTATION: We report the case of a 34-year-old woman with systemic lupus erythematosus and end-stage renal disease who was receiving maintenance peritoneal dialysis. She presented with fever, abdominal pain, and diarrhea. Repeated conventional bacterial and fungal cultures of peritoneal dialysis effluent and blood were negative, and empirical antibiotic therapy failed to achieve sustained clinical improvement. Metagenomic next-generation sequencing of the peritoneal dialysis effluent detected Mycobacterium tuberculosis, providing supportive diagnostic information. Based on the combined clinical presentation, molecular findings, and immunological testing, anti-tuberculosis therapy was initiated. The patient's symptoms gradually resolved, and peritoneal dialysis was temporarily suspended for 11 days before being successfully resumed. No recurrence of peritonitis was observed during a 6-month follow-up period.

CONCLUSIONS: This case highlights the diagnostic challenges of tuberculosis-related peritonitis in patients undergoing peritoneal dialysis. Metagenomic next-generation sequencing may serve as a useful adjunctive diagnostic tool in selected patients with persistent symptoms and repeatedly negative conventional cultures, facilitating earlier diagnosis and appropriate management.}, } @article {pmid41723514, year = {2026}, author = {Şapcı, AOB and Mirarab, S}, title = {krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement.}, journal = {Genome biology}, volume = {27}, number = {1}, pages = {}, pmid = {41723514}, issn = {1474-760X}, support = {R35 GM142725/GM/NIGMS NIH HHS/United States ; ASC150046//Advanced Cyberinfrastructure Coordination Ecosystem/ ; 1R35GM142725/NH/NIH HHS/United States ; #2138259//National Science Foundation/ ; }, mesh = {*Phylogeny ; *Metagenomics/methods ; Likelihood Functions ; Algorithms ; Sequence Analysis, DNA/methods ; *Software ; Sequence Alignment ; }, abstract = {Comparing each sequencing read in a sample to a reference database is a fundamental step in wide-ranging applications. Results of these comparisons can enable phylogenetic characterization. However, phylogenetic placement is currently only possible at scale for marker genes, a small fraction of the genome. We introduce krepp, an alignment-free k-mer-based method that enables placing reads from anywhere on the genome on an ultra-large reference phylogeny (e.g., 123,853 leaves). We show that krepp is scalable and computes accurate distances that approximate those using alignments, leading to accurate placements. These precise phylogenetic identifications improve our ability to compare and characterize metagenomic samples.}, } @article {pmid41723970, year = {2026}, author = {Wang, L and Wang, J and Zhu, Q and Zhang, Q and Qian, J}, title = {Rapid diagnosis of a mixed pulmonary infection with Rhizopus microsporus, Aspergillus fumigatus, Pneumocystis jirovecii, and Cytomegalovirus in a Lymphoma patient using metagenomic next-generation sequencing: A case report.}, journal = {Diagnostic microbiology and infectious disease}, volume = {115}, number = {2}, pages = {117320}, doi = {10.1016/j.diagmicrobio.2026.117320}, pmid = {41723970}, issn = {1879-0070}, mesh = {Humans ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; *Coinfection/diagnosis/microbiology/drug therapy ; Pneumocystis carinii/isolation & purification/genetics ; Immunocompromised Host ; Metagenomics/methods ; Rhizopus/genetics/isolation & purification ; *Cytomegalovirus Infections/diagnosis ; Bronchoalveolar Lavage Fluid/microbiology ; *Lymphoma/complications ; Aspergillus fumigatus/isolation & purification/genetics ; *Mucormycosis/diagnosis/microbiology ; Triazoles/therapeutic use ; Cytomegalovirus/genetics/isolation & purification ; Antifungal Agents/therapeutic use ; }, abstract = {Immunocompromised patients are at high risk for life-threatening polymicrobial infections, often challenging to diagnose conventionally. We report a 60-year-old male with relapsed angioimmunoblastic T-cell lymphoma, fever, and pancytopenia post-chemotherapy. Chest CT showed scattered inflammation. Bronchoalveolar lavage fluid (BALF) culture grew only Klebsiella aerogenes, but fluorescent staining revealed aseptate hyphae. Metagenomic next-generation sequencing (mNGS) of BALF identified concurrent infections with Rhizopus microsporus, Aspergillus fumigatus, Pneumocystis jirovecii, cytomegalovirus, and SARS-CoV-2 within 48 hours. Targeted therapy with isavuconazole, sulfamethoxazole-trimethoprim, and ganciclovir was promptly initiated. Despite therapy, the patient deteriorated due to profound immunodeficiency and was discharged palliatively. This case highlights mNGS as a rapid diagnostic tool for mixed infections, though clinical correlation remains essential.}, } @article {pmid41724049, year = {2026}, author = {Wang, D and Xin, J and Lai, C and Sun, N and Yang, Y and He, Y and Duan, L and Luo, J and He, Y and Zhang, Y and Zhang, Y and Wang, H and Zeng, D and Bai, Y and Ni, X}, title = {High fluoride exposure disrupts gut microbiota and induces intestinal barrier damage via RhoA/ROCK-mediated cytoskeletal remodeling.}, journal = {Ecotoxicology and environmental safety}, volume = {312}, number = {}, pages = {119898}, doi = {10.1016/j.ecoenv.2026.119898}, pmid = {41724049}, issn = {1090-2414}, mesh = {Animals ; Intestinal Barrier Function/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Cytoskeleton/drug effects/metabolism ; *rho-Associated Kinases/metabolism ; Mice ; *rhoA GTP-Binding Protein/metabolism ; *Fluorides/toxicity ; Male ; Signal Transduction/drug effects ; *Intestinal Mucosa/drug effects ; Mice, Inbred C57BL ; }, abstract = {Fluoride pollution-whether of geological or anthropogenic origin-disrupts gut microbiota-host homeostasis and compromises the intestinal barrier. We established an acute high-fluoride mouse model via intragastric NaF, integrating metagenomics, metabolomics, and molecular biological techniques to clarify the underlying mechanism of enhanced intestinal permeability caused by fluoride exposure in vivo. Mechanistically, high fluoride exposure activates the RhoA/ROCK signaling pathway, increases the level of phosphorylated myosin light chain (p-MLC), induces filamentous actin (F-actin) rearrangement, and disrupts the apical junctional complex (AJC)-characterized by downregulated expression or abnormal localization of AJC-related proteins (ZO-1, Claudin-1, β-catenin, Occludin). It also alters the morphology of intestinal epithelial cells, ultimately increasing ileal permeability. At the microbiota level, high fluoride disrupted the ileal microbiota; specifically, at the species level, Bifidobacterium sp. SO1 and Schaalia turicensis were identified as the key species with high specificity and high occupancy under fluoride exposure. Lactobacillus and Akkermansia were abnormally enriched in the intestines of mice exposed to fluoride. Metabolomic analysis revealed that high fluoride exposure enriched multiple pathways including linoleic acid metabolism and sphingolipid metabolism, altering the levels of 11 cytoskeleton-related metabolites. Correlation analysis confirmed that Bifidobacterium sp. SO1 and Schaalia turicensis were strongly correlated with damage phenotypes, pathway molecules, and metabolites, indicating that these two strains are closely associated with cytoskeleton changes and increased intestinal permeability under high fluoride exposure. Collectively, our findings reveal that gut microbiota drive fluoride-induced intestinal barrier dysfunction through the "microbiota-RhoA/ROCK-cytoskeleton" axis, highlighting a novel host-microbe interaction mechanism underlying environmental toxin-mediated gut injury.}, } @article {pmid41724250, year = {2026}, author = {Li, Y and Kang, L and Qin, X and Fei, R and Lu, A and Qishuang, H}, title = {Dual mechanism of electrochemical regulation to reduce soil Nitrous Oxide emissions-microbial recruitment and electron transfer pathway optimization.}, journal = {Bioresource technology}, volume = {448}, number = {}, pages = {134255}, doi = {10.1016/j.biortech.2026.134255}, pmid = {41724250}, issn = {1873-2976}, mesh = {*Nitrous Oxide/metabolism ; Electron Transport ; *Soil/chemistry ; *Soil Microbiology ; Fertilizers ; Nitrogen/metabolism ; Oxidation-Reduction ; Electrodes ; Urea ; *Electrochemical Techniques/methods ; Bacteria/metabolism ; }, abstract = {Greenhouse gas emissions from agricultural nitrogen cycling, primarily Nitrous Oxide (N2O), are intrinsically linked to fertilizer dynamics. Conventional mitigation strategies emphasize synthetic fertilizer reduction, yet suffer from inefficiency and lack of sustainability. This study introduces an electrochemical regulation approach and, through comparative analysis of two fertilizers (ammonium sulfate vs. urea), elucidates dual mechanisms (redox modulation and microbial community engineering). Key findings: (1) 500 mV electrostimulation enriched nitrate-reducing microbiota, reducing N2O by 11.9 ± 5.9% (sulfate) and 14.2 ± 4.4% (urea) via enhanced denitrification; (2) Electrode interventions accelerated N2O-to-N2 conversion (15.8 ± 1.4% and 14.9 ± 8.9%) by optimizing redox fluxes and boosting electroautotrophic Pseudomonas spp. activity; (3) Urea exhibited delayed electroresponsiveness (6-10 h lag) due to slower amide nitrogen hydrolysis kinetics compared to sulfate; (4) Metagenomics confirmed upregulation of nitrogen metabolic genes (norC: 2.9×, nirD: 2.7×, narI: 2.6 ×) and restructured microbial networks. This study elucidates a fundamental electro-microbial mechanism that reconfigures nitrogen-transforming networks, providing a novel paradigm for managing soil biogeochemical cycles.}, } @article {pmid41724273, year = {2026}, author = {Yang, X and Chen, H and Wu, T and Ji, ZY and Wang, ZW and Liu, ZL and Yang, JK and Zhao, Y and Zhou, M and Wang, XB}, title = {Neobavaisoflavone, a functional metabolite derived from valnemulin, ameliorates DSS-induced ulcerative colitis through activation of the AMPK signaling pathway.}, journal = {Biochemical pharmacology}, volume = {248}, number = {}, pages = {117841}, doi = {10.1016/j.bcp.2026.117841}, pmid = {41724273}, issn = {1873-2968}, mesh = {Animals ; *AMP-Activated Protein Kinases/metabolism ; *Colitis, Ulcerative/chemically induced/drug therapy/metabolism ; *Dextran Sulfate/toxicity ; Signal Transduction/drug effects/physiology ; Mice ; Mice, Inbred C57BL ; Humans ; Male ; *Diterpenes/metabolism ; }, abstract = {Ulcerative colitis (UC), a chronic inflammatory bowel disease (IBD), is characterized by sustained mucosal inflammation, disrupted epithelial barrier function, microbial dysbiosis, and impaired intestinal homeostasis. If chronic uncontrolled inflammation persists, it may lead to the development of colorectal cancer or other severe clinical complications. Emerging evidence suggests that cellular senescence promotes inflammatory cascades, aggravating UC symptoms and implicating a pathophysiological link to disease progression. Our previous studies have demonstrated that the anti-senescence compound Valnemulin (VAL) can mitigate colonic senescence and alleviate UC symptoms. In this study, subsequent integrative metagenomic and metabolomic analyses revealed that VAL's pharmacological mechanism involves restructuring the gut microbial community composition, enhancing the colonization abundance of beneficial bacteria, and thereby promoting the production of their key metabolites, which collectively contribute to UC remission. In vitro and in vivo studies demonstrated that VAL's anti-senescence effects are mediated by Neobavaisoflavone (NBIF), a functional metabolite produced by beneficial gut bacteria. NBIF effectively activates the AMP-activated protein kinase (AMPK) pathway, significantly reducing the expression levels of senescence marker proteins p16, p53, and p21. Consequently, this mechanism ameliorates the senescent phenotype in intestinal epithelial cells and contributes to the overall improvement of colonic tissue senescence in UC pathology. Concomitantly, NBIF also reduces levels of pro-inflammatory cytokines IL-1β, TNF-α, and IL-6, thereby attenuating DSS-induced pathological damage in UC. This study not only proposes a novel anti-senescence strategy for UC treatment but also elucidates the pivotal role of the gut microbiota-metabolite-AMPK axis in regulating intestinal inflammation.}, } @article {pmid41724378, year = {2026}, author = {Lin, YT and Graells, T and Sayols-Baixeras, S and Dekkers, KF and Schillemans, T and Baldanzi, G and Wuopio, J and Nielsen, N and Eklund, AC and Holm, JB and Nielsen, HB and Bergström, G and Smith, JG and Malinovschi, A and Engström, G and Orho-Melander, M and Fall, T and Ärnlöv, J}, title = {Association between the gut microbiota and estimated glomerular filtration rate in two Swedish population-based cohorts.}, journal = {Kidney international}, volume = {109}, number = {5}, pages = {1004-1013}, doi = {10.1016/j.kint.2026.01.021}, pmid = {41724378}, issn = {1523-1755}, mesh = {Humans ; *Glomerular Filtration Rate ; Female ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Sweden/epidemiology ; Male ; Feces/microbiology ; Metagenomics ; Adult ; Methylamines/metabolism/blood ; *Bacteria/metabolism/classification ; Carnitine/metabolism ; *Kidney/physiopathology ; Histidine/metabolism ; Aged ; Cohort Studies ; }, abstract = {INTRODUCTION: Evidence for gut-kidney interactions in early kidney disease is limited, particularly in community-dwelling adults with largely preserved kidney function. Here, we quantified links between gut microbiota and estimated glomerular filtration rate (eGFR) in two population-based Swedish cohorts.

METHODS: Deep shotgun metagenomics profiled fecal samples from 9788 adults in the Swedish CArdioPulmonary BioImage Study (SCAPIS) discovery cohort (mean age 58 ± 4 years; 52% women) and 2080 adults in the Malmö Offspring Study (MOS) replication cohort (mean age 40 ± 14 years; 52% women). Linear regression related the relative abundance of 494 metagenome-assembled species to the creatinine-based eGFR (by CKD-EPI equation), adjusting for demographics, albuminuria, cardiovascular risk factors and technical variables. Species passing false discovery rate under 0.05 in SCAPIS were tested in MOS for significant concordant direction. Functional enrichment linked eGFR-associated species to gut metabolic modules and plasma metabolites; partial Spearman correlations were used to assessed metabolite/species/eGFR relationships.

RESULTS: The alpha diversity showed a modest inverse association with eGFR across both cohorts. We identified 44 bacterial species consistently associated with eGFR in both cohorts, collectively explaining 7% of its variance. Enrichment analysis highlighted histidine and carnitine metabolism among the top three pathways involved. Their key products, trimethylamine N-oxide and imidazole propionate, were inversely related to eGFR, and a metabolite panel accounted for 51% of eGFR variation, underscoring metabolite-mediated microbial effects. Sensitivity analyses upheld these findings.

CONCLUSIONS: Gut microbial diversity and 44 reproducible species are independently linked to kidney function in community-dwelling adults. Enrichment of histidine and carnitine pathways and their circulating metabolites implicates microbial metabolism as a contributor to eGFR variability, suggesting tractable targets for early kidney protection.}, } @article {pmid41724403, year = {2026}, author = {Zhang, Y and Liu, Y and Zhang, S and Li, Y and Zhao, L and Wang, Z and Wang, Q and Zhang, N and Bachert, C and Bröker, BM and Wang, X and Zhang, L and Lan, F}, title = {Staphylococcal superantigen-specific IgE reveals functional superantigen production beyond Staphylococcus aureus in CRSwNP.}, journal = {The Journal of allergy and clinical immunology}, volume = {157}, number = {6}, pages = {1328-1338}, doi = {10.1016/j.jaci.2026.02.013}, pmid = {41724403}, issn = {1097-6825}, mesh = {Humans ; *Superantigens/immunology ; *Rhinosinusitis/immunology/microbiology ; *Staphylococcus aureus/immunology ; *Immunoglobulin E/immunology ; *Nasal Polyps/immunology/microbiology ; Female ; Chronic Disease ; Male ; *Staphylococcal Infections/immunology ; Antigens, Bacterial/immunology ; Adult ; Middle Aged ; }, abstract = {BACKGROUND: Staphylococcal superantigen-specific IgE (SAg-IgE) correlates with disease severity in patients with type 2 (T2) chronic rhinosinusitis with nasal polyps (CRSwNP). Although Staphylococcus aureus is recognized as a primary source of SAgs, SAg-IgE is detected even in patients with culture-negative S aureus.

OBJECTIVE: We sought to identify the source of SAgs in SAg-IgE-positive patients with T2 CRSwNP with culture-negative S aureus.

METHODS: Metagenomic sequencing was conducted in patients with T2 CRSwNP with repeatedly negative S aureus cultures, stratified by SAg-IgE status. We screened clinical isolates for SAg genes and evaluated SAg functionality by measuring SAg-specific T-cell receptor repertoire expansion and T2 inflammatory responses in an ex vivo infection model.

RESULTS: The SAg-IgE-positive group showed significantly higher abundances of S epidermidis, S aureus, Lysinibacillus xylanilyticus, and S capitis compared with the SAg-IgE-negative group. Interestingly, in all participants in whom S aureus was detected, S capitis was also present, albeit at low abundance. Redundancy analysis demonstrated clustering of the Staphylococcus genus, SAg-IgE, and IL-5, supporting a potential link between the Staphylococcus genus and SAg-driven immune responses. Notably, a clinical S capitis isolate carried SEA (staphylococcal enterotoxin A) and SEC genes and secreted functional SAgs, which triggered the clonal expansion of SEA/SEC-specific T-cell receptors and exacerbated the T2 inflammatory response via IL-33 induction.

CONCLUSIONS: Metagenomic sequencing reveals that S capitis, beyond S aureus, produces functional SAg to drive T2 response in SAg-IgE-positive patients with CRSwNP when conventional cultures fail to detect S aureus. Independent of culturable bacterial load, tissue SAg-IgE positivity reliably indicates bacterial colonization and SAg exposure in CRSwNP.}, } @article {pmid41724632, year = {2026}, author = {You, TY and Lee, NY and Tsai, WC and Lo, CL and Chen, PT and Chen, SY and Jan, HE and Ko, WC}, title = {Etiological identification of Orientia tsutsugamushi by metagenomic next-generation sequencing in an adult with septic shock in Taiwan.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmii.2026.02.002}, pmid = {41724632}, issn = {1995-9133}, } @article {pmid41724800, year = {2026}, author = {Bhuyan, B and Chutia, B and Singh, LS}, title = {Emerging strategies for heavy metal removal in soils: plant-microbe interactions and omics perspectives.}, journal = {Archives of microbiology}, volume = {208}, number = {5}, pages = {}, pmid = {41724800}, issn = {1432-072X}, mesh = {*Metals, Heavy/metabolism ; Biodegradation, Environmental ; *Plants/microbiology/metabolism ; *Soil Pollutants/metabolism ; Soil Microbiology ; Bacteria/metabolism/genetics ; Soil/chemistry ; Proteomics ; Multiomics ; Metabolomics ; }, abstract = {Rapid industrial expansion, intensive agricultural practices, and widespread petroleum extraction have led to the significant buildup of heavy metals (HMs) in soils and related ecosystems, posing serious environmental and public health risks. Hence, this review highlights the major sources, ecological impacts, and toxicity of HMs in the environment. However, physical and chemical remediation methods can reduce HMs concentrations, but issues such as high operational costs, prolonged treatment durations, and poor sustainability limit their suitability for large-scale application. Thus, bioremediation methods, especially those that utilize plants and microbes, have gained increasing attention as eco-friendly and cost-effective options. Plant-microbe-based interactions play an important role, as they act synergistically to facilitate metal uptake, stabilization, transformation, and detoxification of HMs in contaminated soils. Though, it is important to understand the plant-microbe interactions, especially since most current research is about how plants and microbes can work together to clean up contaminants in their natural environments. However, achieving higher remediation performance under stress conditions depends on the selection of plant and microbial species. Therefore, this review explores the mechanisms of plant-microbe interactions along with omics technologies employed to analyze samples for understanding this interaction in HMs-contaminated soils at the metagenomics, metatranscriptomics, proteomics, and metabolomics levels in enhancing the effectiveness of remediation. This review article also highlights key factors affecting remediation efficiency and discusses limitations, challenges, and future prospects of plant-microbe interactions in HMs-contaminated soils.}, } @article {pmid41724868, year = {2026}, author = {Aciole Barbosa, D and de Maria, YNLF and Menegidio, FB and de Oliveira, RC and Jabes, DL and Nunes, LR}, title = {Dysbiosis of the enteric DNA virome correlates with the development of cachexia in a murine Lewis lung carcinoma (LLC) model.}, journal = {Archives of virology}, volume = {171}, number = {3}, pages = {}, pmid = {41724868}, issn = {1432-8798}, mesh = {Animals ; *Cachexia/virology/etiology/microbiology ; *Dysbiosis/virology ; *Virome ; Mice ; *Carcinoma, Lewis Lung/complications/virology ; Disease Models, Animal ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; Male ; }, abstract = {Cachexia, a multifaceted wasting syndrome, profoundly impacts quality of life and survival rates in cancer patients. Gut inflammation is identified as a key player among the contributing factors for its development. Consequently, numerous studies have sought to characterize changes in gut microbiota of cachectic individuals, given the well-established roles of the gut microbiota in controlling and/or triggering both local and systemic inflammation in their hosts. Most of these investigations have applied mouse models of tumor-induced cachexia to show correlations between alterations in bacterial and fungal abundance in the digestive tract and the onset of cancer cachexia (CC). However, the role of viral dysbiosis in CC development remains unexplored. The present study aims to address this gap by characterizing the gut virome during the progression of murine cancer cachexia. Although our approach was limited to DNA viruses, our findings reveal that cachectic animals with Lewis lung carcinoma exhibited a subtle yet statistically significant modulation in composition (R[2] = 0.17622; p = 0.05). A linear discriminant analysis effect size (LEfSe) analysis revealed that the dysbiosis observed in the gut virome of CC animals was mostly characterized by a significant enrichment in giant viruses of the family Phycodnaviridae (LDA score, 4.2582; p-value, 0.004; pwrapp, 0.9984) and significantly decreased populations of bacteriophages of the families Microviridae (LDA score, 4.3458; p-value, 0.0127; pwrapp, 0.9065) and Inoviridae (LDA score, 3.3028; p-value, 0.0017; pwrapp, 0.9992). This cachexia-associated viral dysbiosis shares similarities with virome alterations documented in other conditions linked to gut inflammation, including, ulcerative colitis, Crohn's disease, and Clostridioides difficile infection. These new insights suggest the potential contributions of viral communities to the pathophysiology of CC and other inflammation-driven diseases.}, } @article {pmid41724983, year = {2026}, author = {Yang, K and Li, J and Li, L and Fu, L and Liu, W and Jia, Z and Wang, Z and Wei, Z and Zhang, F}, title = {Soil antibiotic resistome in farmland exhibits higher diversity and horizontal transfer potential than adjacent pastureland in agro-pastoral ecotone.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {}, pmid = {41724983}, issn = {2524-6372}, support = {CCPTZX2024QN03//National Center of Pratacultural Technology Innovation Special fund for innovation platform construction/ ; 42407171//National Natural Science Foundation of China/ ; 2025T180072, GZB20240311//China Postdoctoral Science Foundation/ ; }, abstract = {BACKGROUND: Soil antibiotic resistant genes (ARGs) and mobile genetic elements (MGEs) are associated with agricultural land-use differences. However, assessing the soil antibiotic resistome differences between farmland and pastureland is often limited due to geographically unbalanced sample collection. Leveraging a typical agro-pastoral ecotone in northern China as the study model, we compared the soil microbiome and resistome between 15 adjacent farmland and pastureland pairs using metagenomic sequencing.

RESULTS: Results showed that farmland soils harbored higher soil ARG diversity (+ 2.75%), MGE diversity (+ 1.62%) and multidrug resistance-related gene abundance (+ 19.5%) than pastureland. Among them, genes conferring multidrug resistances were dominant in farmland, mainly carried by Pseudomonadota. While, vancomycin-resistant ARGs were dominant in pastureland, mainly carried by Actinomycetota. Metagenome-assembled genomes revealed that sul2 conferring sulfonamide resistance was shared by both Pseudomonadota and Acidobacteriota in farmland together with insertion sequence ISVsa3. Structural equation model analysis integrating with soil geography, pedology and microbiome data showed microbial community and soil properties were identified as major driving factors shaping soil antibiotic resistome diversity in both land-use contexts. MGE diversity showed a clear positive effect on ARG diversity in farmland soils but a minor effect in pastureland.

CONCLUSIONS: Together, this study elucidates the shared and distinguished soil antibiotic resistome pattern between farmland and pastureland, extending our understanding of driving factors in agricultural soil ARG contamination.}, } @article {pmid41725012, year = {2026}, author = {Ramírez, AL and Páez, L and Vega, L and Aya, V and Hernández, C and Luna, N and Muñoz, M and Patiño, LH and Ramírez, JD}, title = {Metagenomic analysis of the human gut virome reveals functional signatures and viral stability across hospitalized and non-hospitalized diarrheal and non-diarrheal individuals.}, journal = {Gut pathogens}, volume = {18}, number = {1}, pages = {}, pmid = {41725012}, issn = {1757-4749}, abstract = {BACKGROUND: The human gut virome is a fundamental yet understudied component of the intestinal microbiome. However, its taxonomic composition and functional potential in Latin American populations remain poorly understood, particularly under clinical stressors such as hospitalization and diarrhea conditions often linked to microbial dysbiosis.

METHODS: We conducted a hybrid metagenomic analysis of the human gut virome from 37 fecal samples: 10 from patients admitted to intensive care units (ICU), 13 from hospitalized patients outside the ICU (Non-ICU), and 14 from non-diarrheic individuals, including taxonomic and functional profiling of viruses and detection of viral auxiliary metabolic genes (vAMGs).

RESULTS: We identified 494 high-quality viral vOTUs, from which 37,619 ORFs were predicted. Taxonomically, Caudoviricetes and Intestiviridae were consistently present across all groups, supporting their role as part of a conserved core virome. Functionally, we identified 309 putative vAMGs spanning 90 functional categories, primarily related to metabolism and environmental information processing. Non-diarrheic individuals harbored a higher number and diversity of vAMGs compared to hospitalized groups (Kruskal-Wallis, p < 0.01), whereas ICU and Non-ICU patients showed reduced and more variable functional profiles. Beta diversity analysis revealed that diarrhea status, rather than hospitalization per se, was associated with modest but significant shifts in functional composition (PERMANOVA, R² = 0.047, p = 0.025), driven by quantitative changes in shared AMGs rather than the presence of unique functions. Notably, resistance-related vAMGs, including bacitracin transporters and Zinc D-Ala-D-Ala carboxypeptidase, were detected across samples, highlighting the potential of phages as mobile reservoirs of antibiotic resistance.

CONCLUSION: Together, our findings indicate that hospitalization and diarrhea do not markedly alter the taxonomic structure of the gut virome but are associated with modest shifts in viral functional potential. The maintenance of a stable viral community alongside variable AMG repertoires suggests that phages may modulate host-microbiome interactions primarily through functional fine-tuning rather than large-scale community restructuring. Our study provides evidence for the ecological resilience of the human gut virome and underscores the need to integrate viral communities into resistome research.}, } @article {pmid41725015, year = {2026}, author = {Wang, R and Wang, Z and Liao, W and Wang, T and Su, Y}, title = {Mikania micrantha invasion restructures rhizosphere nitrogen cycling through enzyme activation, microbial recruitment, and allelopathic regulation.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41725015}, issn = {2049-2618}, support = {31872670//National Natural Science Foundation of China/ ; 2021A1515010911//Guangdong Basic and Applied Basic Research Foundation/ ; 202206010107//Science and Technology Projects in Guangzhou/ ; JCYJ20210324141000001//Project of Department of Science and Technology of Shenzhen City, Guangdong, China/ ; }, mesh = {*Rhizosphere ; *Mikania/microbiology/metabolism/growth & development ; *Soil Microbiology ; *Nitrogen Cycle ; Nitrogen/metabolism ; Metagenomics/methods ; Introduced Species ; Soil/chemistry ; Glutamate-Ammonia Ligase/metabolism/genetics ; *Bacteria/classification/genetics/metabolism ; Nitrogen Fixation ; Plant Roots/microbiology ; Metabolomics ; }, abstract = {BACKGROUND: Plant invasions profoundly influence terrestrial ecosystems by reshaping nutrient cycling processes. However, the mechanisms through which invasive plants such as Mikania micrantha modulate soil nitrogen (N) cycling and microbial communities remain insufficiently explored. Moreover, comparative studies with indigenous congener are scarce, limiting insights into whether such effects reflect species-specific strategies or genus-wide traits. This study investigates how M. micrantha modulates nitrogen metabolic pathways and rhizosphere microecology using combined metagenomic and metabolomic analyses.

RESULTS: Integrated analyses revealed that M. micrantha established a distinctive "high total nitrogen-low mineral nitrogen" profile in the rhizosphere soil. Metagenomic profiling showed consistent enrichment of key ammonium assimilation enzymes, including glutamine synthetase and glutamate dehydrogenase, promoting enhanced incorporation of NH₄⁺ into organic nitrogen pools. In contrast, genes encoding nitrate reductase and nitrate transporters were significantly lower in relative abundance, limiting nitrate assimilation. Mikania micrantha also selectively enriched nitrogen-fixing microbes (notably rhizobia genera) and plant growth-promoting rhizobacteria (PGPR), thereby enhancing biological nitrogen fixation capacity. Metabolomic analysis further identified several allelopathic compounds in invaded soils at higher relative abundance, particularly epicatechin, which exhibited inhibitory effects on nitrifying bacteria. Compared with the congener Mikania cordata, which exerted weaker impacts on soil nitrogen cycling and microbial assembly, M. micrantha deployed a more comprehensive strategy integrating biochemical, microbial, and metabolic regulation.

CONCLUSIONS: These findings demonstrate that under greenhouse-controlled conditions, M. micrantha reconfigures rhizosphere nitrogen cycling through a multi-dimensional strategy that couples biochemical regulation, microbial recruitment, and metabolite-mediated interference, thereby suggesting a potential mechanism that may contribute to its ecological advantage in natural settings. Video Abstract.}, } @article {pmid41725821, year = {2026}, author = {Wang, C and Zhang, C and Shah, AM and Wang, Z and Qiu, S and Xu, Z and Xue, B and Wang, L and Hu, R and Zou, H and Jiang, Y and Xiao, J and Peng, Q}, title = {The optimal dietary crude protein level improves goat production performance by enhancing the body's antioxidant function and energy metabolism.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1734810}, pmid = {41725821}, issn = {1664-302X}, abstract = {The current research was conducted to evaluate the impact of various crude protein (CP) concentrations in diets on growth performance, nutrient digestibility, nitrogen deposition, rumen fermentation, microbial community, and serum metabolomics in growing goats. Fifty healthy 4-month-old Chuannan black goats (Capra hircus) with similar body weight (13.75 ± 0.27 kg) were randomly distributed into 5 groups. Goats were fed diets with five different levels of CP: 8.12% (T8), 10.15% (T10), 12.17% (T12), 14.13% (T14), and 16.18% (T16), respectively. The total duration of the trial was 70 d, including a 14-day adaptation period. The average daily gain and feed conversion ratio displayed a quadratic upsurge and reduce respectively, with the rise of CP content in the diet. The group T14 exhibited the highest average daily gain and demonstrated the best feed conversion efficiency. A linearly (p < 0.05) increase of the digestibility of dry matter, neutral detergent fiber, and acid detergent fiber was observed, whereas a quadratic effect (p < 0.001) on nitrogen intake, fecal nitrogen, and urinary nitrogen was obtained with the increase of dietary CP. Moreover, dietary CP levels had a quadratic effect on the concentration of ruminal ammonia nitrogen (p = 0.021), rumen microbial protein (p = 0.042), total volatile fatty acid (p = 0.012), acetate (p = 0.040), isobutyrate (p = 0.024), and isovalerate (p < 0.001). Microbial metagenomics results showed that the relative abundance of Burkholderia and Bacillus increased (p < 0.05), while the relative abundance of Pseudomonas and Salmonella decreased (p < 0.05) when comparing group T14 to group T8. Metabolomic results showed that differently expressed metabolites were found to enrich the proline, glutathione and arginine metabolism, and citric acid cycle metabolic pathway. The concentration of serum genistein was positively correlated (p < 0.05, r = 0.665) with the abundance of Bacillus and negatively correlated (p < 0.05, r = -0.734) with the abundance of Pseudomonas. It is concluded that a dietary CP level of 14% enhances the antioxidant function and energy metabolism of the goats by altering the composition of rumen microorganisms, thereby improving production performance.}, } @article {pmid41726216, year = {2026}, author = {Gui, J and Long, C and Fu, Y and He, H and Li, J and Wang, F}, title = {Performance Evaluation of Targeted Nanopore Sequencing in Non-Tuberculous Mycobacteria Identification: A Comparative Study in Shenzhen, China.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {572430}, pmid = {41726216}, issn = {1178-6973}, abstract = {OBJECTIVE: This study aims to analyze the performance differences between targeted nanopore sequencing, Sanger sequencing, and metagenomic sequencing in comparatively identifying non-tuberculous mycobacteria (NTM) species. Additionally, it explores the clinical application potential of targeted nanopore sequencing for identifying NTM clinical isolates in the Shenzhen region.

METHODS: This retrospective study collected a total of 50 suspected NTM isolates from drug-resistant tuberculosis surveillance across 10 districts in Shenzhen, China, between December 2024 and June 2025. The species of the NTM isolates were initially identified using fluorescence PCR probe melting curve analysis. Genomic DNA was extracted from all 50 isolates, and species identification was performed using targeted nanopore sequencing (tNS), metagenomic sequencing (mNGS), and Sanger sequencing. The Jaccard similarity index, Kappa coefficient for classification consistency, and F1 score for model performance were calculated to evaluate the concordance among the three sequencing methods and assess the detection performance of targeted nanopore sequencing in NTM species identification.

RESULTS: The most frequently detected NTM species by tNS, mNGS, and Sanger sequencing were M.abscessus and M.fortuitum, while M. tuberculosis was predominantly identified through mNGS results. Among the 50 suspected NTM samples, 18 (36%) showed complete concordance between tNS, mNGS, and Sanger sequencing, with the highest agreement observed between mNGS and tNS (28 samples, 56%). The final species identification reference results for the 50 samples were confirmed through a comprehensive evaluation using the Jaccard similarity coefficient, precision, and recall. Based on reference results, the F1 scores for tNS, mNGS, and Sanger sequencing were 0.927, 0.896, and 0.543, respectively. The tNS exhibited the highest concordance with the reference results, outperforming the other two methods.

CONCLUSION: tNS represents a preferred auxiliary methodology for clinical identification of NTM isolates in Shenzhen, China, with identification results optimally validated through integration with mNGS findings. This study provides strong support for the application of tNS technology for NTM species identification.}, } @article {pmid41726388, year = {2025}, author = {Donbraye, E and McLeod, L and Carson, CN and Chai, Z and Lacoste, SR and Herman, EK and McCarthy, EL and Hill, JE and Erickson, NEN and Pollock, C and Links, MG and Otto, SJG and Gow, S and Stothard, P and Campbell, JR and Waldner, CL}, title = {Prevalences of respiratory viruses and bacteria in Western Canadian commercial feedlot calves detected using a single metagenomic sequencing protocol vary during the first two weeks of arrival and by age group.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1704412}, pmid = {41726388}, issn = {2297-1769}, abstract = {INTRODUCTION: Detection of pathogens associated with bovine respiratory disease (BRD) typically involves several laboratory tools, with results limited to a defined list of targets. This study adapted a previously reported method for metagenomic sequencing of nasal swabs to describe sequencing data from BRD associated viruses. Changes in virus composition were identified between arrival to a feedlot and 14 days on feed (DOF). These data were also assessed for the simultaneous characterization of bacteria and antimicrobial resistance genes (ARGs).

METHODS: Nasal swabs were obtained from fall-placed calves (FPC) and yearlings (YRL) from western Canadian commercial feedlots. Evidence of respiratory viruses were identified by sampling 380 animals during processing on arrival to the feedlot and again after 14 DOF using Nanopore metagenomic sequencing.

RESULTS: Twenty-one distinct viruses from 12 viral families were identified, with multiple viruses detected in most samples. In FPC arrival samples, the most common BRD associated viruses were bovine rhinitis B virus (BRBV; 46%), bovine coronavirus (BCoV; 32%), influenza D virus (IDV; 17%), bovine respiratory syncytial virus (BRSV; 8.5%), and bovine parainfluenza virus 3 (BPIV-3; 4.2%). The prevalences of bovine herpesvirus type 1 (BoHV-1; 2.7%), BPIV-3 (12%), BRSV (26%), and IDV (51%) were higher in 14 DOF samples compared to arrival samples (p < 0.05). Bovine viral diarrhea virus 1 (BVDV-1) and 2 (BVDV-2) were rarely detected at either time. The most prevalent viruses detected in YRL arrival samples were BRBV (42%), BRSV (39%), BPIV-3 (20%), IDV (16%), BCoV (12%), and BVDV-2 (7.5%). The prevalences of BRSV (60%), BPIV-3 (39%), and BVDV-2 (17%) were higher in 14 DOF samples than arrival samples (p < 0.05). BRSV (OR 7.0, 1.7-29) and BPIV-3 (OR 5.7, 1.5-21) were more likely to be detected in arrival samples from YRL than FPC (p = 0.01). In 14 DOF samples, BPIV-3 (OR 4.9, 1.3-19, p = 0.02) and BVDV-2 (OR 13, 2.0-83, p = 0.01) were identified more frequently in YRL than FPC. These data allowed the identification of respiratory bacteria and 33 ARGs in parallel with assessment of the viral components. The most prevalent bacteria detected in FPC at arrival were Mannheimia haemolytica (35%), Histophilus somni (35%) and Pasteurella multocida (23%). Detection of M. haemolytica increased at 14 DOF (p = 0.02), while P. multocida detection decreased (p = 0.03). At both arrival and 14 DOF in YRL, M. haemolytica was the most prevalent bacterium, followed by P. multocida and H. somni with no significant differences between arrival and 14 DOF samples. ARGs were detected more frequently in the 14 DOF samples than at arrival for both FPC (p = 0.03) and YRL (p = 0.01). The most commonly detected ARGs were associated with resistance to lincosamides and aminoglycosides; however, ARGs associated with other antimicrobials used in cattle including tetracyclines were also identified.

DISCUSSION: Changes in the prevalence of BRD associated viruses early in the feeding period reflect transmission and the potential risk of developing the disease. Frequent detection of BCoV, BRSV, and BPIV-3 in newly arrived feedlot cattle suggests the need for improved vaccination before shipping or limitations in existing commercial vaccine preparations.}, } @article {pmid41726584, year = {2026}, author = {Xie, G and Zhou, Q and Liao, J and Zheng, Y and Wang, W and Shen, K}, title = {The ketogenic diet alters microbiome-metabolome profiles to improve West syndrome therapy.}, journal = {Pediatric investigation}, volume = {10}, number = {1}, pages = {10-24}, pmid = {41726584}, issn = {2574-2272}, abstract = {IMPORTANCE: The ketogenic diet (KD) is effective in managing epilepsy, particularly West syndrome (WS); however, the role of gut microbiome (GM) and metabolome in its efficacy remains unclear. Understanding these mechanisms could optimize the KD for WS treatment.

OBJECTIVE: To identify microbiome-metabolome signatures associated with KD efficacy in WS by analyzing changes in GM composition and metabolic pathways.

METHODS: Fecal samples were collected from WS patients (n = 16) and healthy children (n = 24). Metagenome and metabolome analyses were performed to assess GM composition and metabolic profiles.

RESULTS: WS patients showed GM imbalances compared to healthy children. Disease status contributed sufficiently to the GM. The abundance of Bacteroides, Parabacteroides, and Faecalibacterium was lower in WS (3.30% vs. 39.86%, P-adj = 0.140; 0.14% vs. 0.73%, P-adj = 0.023; 0.04% vs. 1.35%, P-adj = 0.018), whereas Bifidobacterium and Escherichia were higher (6.08% vs. 2.23%, P-adj = 0.140; 7.57% vs. 0.15%, P-adj < 0.001). After KD, Parabacteroides (particularly P. distasonis) and Bacteroides (particularly B. fragilis) increased (0.14% vs. 0.35%, P-adj = 0.034; 3.30% vs. 21.18%, P-adj = 0.380); Bifidobacterium (particularly B. breve) and Escherichia (particularly E. coli) decreased from 6.08% and 7.57% to 1.24% and 2.52%, respectively. Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated that ATP-binding cassette (ABC) transporters, fatty acid biosynthesis, tyrosine metabolism, and other pathways were significantly altered in patients with WS, and these alterations were reversed following ketogenic diet (KD) consumption. The KD also altered intestinal metabolites. Integrative analysis of microbial features, gene functions, and metabolites revealed that Bacteroides species and P. distasonis were significantly associated with ABC transporters, alanine aspartate and glutamate metabolism, and negatively correlated with 3-sulfinoalanine, suggesting potential regulatory roles in metabolic pathways.

INTERPRETATION: KD induces significant shifts in GM composition and metabolic pathways, which may contribute to its therapeutic efficacy in WS. The restoration of Bacteroides and Parabacteroides dominance, alongside alterations in gene functions and neurotransmitter-related metabolites, suggests a potential mechanism for the antiepileptic effects of KD.}, } @article {pmid41726864, year = {2026}, author = {Vaziri, GJ and Pritchard, JC and Howard, JI and Stamm, GE and O'Connor, DH and Newman, CM and Aliota, MT and Dzikwi-Emennaa, A}, title = {Metagenomic surveillance of undiagnosed febrile illness in Nigeria does not reveal the etiological agent for most patients.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.07.704564}, pmid = {41726864}, issn = {2692-8205}, abstract = {Molecular and microscopy-based diagnostic capacity is often insufficient or unavailable in places where infectious disease burdens are highest, such as in West Africa. Rapid diagnostic testing (RDT) can provide quick and affordable diagnoses of common infections but is an imperfect solution due to limitations around detecting and dealing with false negative and false positive results. An alternative to RDT is unbiased metagenomic sequencing for pathogen surveillance. Here, we present data from unbiased metagenomic sequencing used to identify causes of undiagnosed febrile illness in Jos, Plateau State, Nigeria. Proof of concept for this approach has been demonstrated by several groups who have identified epidemic and endemic viral diseases like Lassa fever, yellow fever, and Chikungunya. Here, we show that unbiased deep sequencing and metagenomic analysis can be used to identify RNA viruses in clinical samples. We sequenced RNA from sera of patients (n = 343), many of whom were acutely febrile (76 %) in a survey of clinics in Jos. We detected five human-infecting viruses in 39 (11 %) specimens. Among these were hepatitis B virus, human pegivirus, and several anelloviruses. While most of the viruses identified are unlikely to cause clinical symptoms in the patients we sampled, their presence demonstrates the validity of our approach. Additionally, our sequencing data allowed us to identify genetic material from potentially pathogenic bacteria, another possible etiological agent of febrile illness.}, } @article {pmid41726920, year = {2026}, author = {Jensen, JSL and Maharjan, S and Münch, PC and Shen, J and Bowcutt, B and Sumner, JT and Morgan, XC and Thompson, KN and Nguyen, LH and Franzosa, EA and Huttenhower, C}, title = {Enhanced multi-omic viral profiling from microbial community sequencing with BAQLaVa.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41726920}, issn = {2692-8205}, abstract = {Viruses are crucial components of microbial communities, both phage that infect bacterial community members as well as pathogenic and other eukaryotic viruses. However, they remain unobserved by most current technologies, due to combinations of experimental and analytical factors. To address the latter, we developed the BAQLaVa algorithm for high-resolution profiling of >120,000 viral species (viral genome bins, VGBs) via reference-based metagenome (MGX) or metatranscriptome (MTX) alignment to complementary nucleotide markers and proteome sets. In comprehensive benchmarking, BAQLaVa substantially outperformed alternatives, achieving species-level recall and precision regularly over 90%. We applied BAQLaVa to MGX and MTX samples from the HMP2 IBDMDB cohort to identify previously undescribed viral perturbations in inflammatory bowel diseases. Most notably, virome diversity was reduced in tandem with bacterial diversity during inflammation, in contrast to previous findings based on a narrower range of viral detection. A subset of viruses were enriched during IBD, associated with carriage of abortive infection anti-defense systems such as AbiL and PD-λ-2, as well as genes involved in the regulation of lysogeny. Leveraging the corresponding viral profiles, we also inferred phage-host relationships using scalable co-occurrence and covariation signals, even in the absence of host references or genome annotations. By enabling high sensitivity and specificity viral profiling from metagenomes or metatranscriptomes, BAQLaVa provides a scalable framework for virome epidemiology and systematic analysis of virus-host interactions.}, } @article {pmid41726932, year = {2026}, author = {Montes, A and Klopmanbaerselman, D and Lee, B and Quiñones, B and Shim, H}, title = {Temporal dynamics of microbiome communities within urban compost piles undergoing the heat process.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41726932}, issn = {2692-8205}, abstract = {Urban composting supports soil health but also intersects with food safety, where compost is produced near farms and communities. Here, we profiled temporal microbiome dynamics across a 6-week heat compost cycle from the urban compost piles using paired physicochemical panels and long-read metagenomics. Nutrient composition and pH shifted with compost age, coinciding with stage-structured microbial succession, including temperature-linked turnover of compost communities from mesophilic to thermotolerant taxa. Bacterial profiles included the presence of antimicrobial resistance genes and foodborne-associated genera early in the cycle, with reduced representation during the thermophilic phase. Analysis of previously unclassified long reads reveals an extensive repertoire of putative bacteriophages, including several complete genomes and candidates linked to foodborne bacteria, and their abundance is coupled to the host abundance. Together, these results support thermophilic composting as a key mitigation step for microbiological hazards in urban-adjacent systems and identify compost piles as a promising reservoir for discovering candidate lytic phages for downstream isolation and host-range testing.}, } @article {pmid41726958, year = {2026}, author = {Khanal, S and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, C}, title = {Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41726958}, issn = {2692-8205}, support = {R35 GM140886/GM/NIGMS NIH HHS/United States ; }, abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Remarkably, time-lapse microscopy revealed that Archangium exhibited markedly reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate), while maintaining robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.}, } @article {pmid41727025, year = {2026}, author = {Chittimalli, K and Rozario, HE and Martinez, V and McAdams, ZL and Adkins, SA and Ericsson, AC and Jarajapu, YP}, title = {Alamandine/MrgD Pathway Modulates Gut-Bone Marrow Axis in Aging.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41727025}, issn = {2692-8205}, abstract = {Aging is associated with colon epithelial barrier integrity and upregulation of myelopoiesis in the bone marrow (BM). Alamandine (Ala) and MrgD are novel members of the renin angiotensin system (RAS). This study tested the hypothesis that Ala restores the colon epithelial barrier integrity in aging via modulating gut-BM axis. Mice of age 2-3 (Young) or 22-24 months (Old) were treated with saline or Ala by using Osmotic pumps. The intestinal permeability was evaluated by using FITC-dextran. Lgr5[+]Olfm4[+] intestinal stem cells (ISCs), Wnt3a and β-catenin were evaluated by immunohistochemistry or western blotting. Fecal microbiome was analyzed by 16S rRNA sequencing. Monocyte-macrophages were characterized by flow cytometry. Cecal or serum bacterial metabolites were analyzed. The pro-myelopoietic potential of cecal supernatants (CS) was tested in the Young-BM cells. MrgD was expressed in ISCs, which was decreased in the Old. Increased intestinal permeability in aging was reversed by Ala. In the colon organoids, Ala increased Wnt3a levels that were antagonized by the NF449, SQ22536 or 666-15. Ala restored phospho-CREB and active β-catenin levels that were decreased in the Old colon-organoids. Ala increased the richness and β-diversity of the aging microbiome and decreased Bacillota/Bacteroidota. Ala decreased the CD80[+] and increased CX3CR[+] cells in the Old colons. Old-CS induced myelopoiesis in vitro in BM cells with higher number of monocytes and pro-inflammatory macrophages which was not observed in the CS derived from Ala-treated Old mice. Ala is a promising pharmacological agent for reversing the leaky gut of aging by restoring homeostasis in the gut-BM axis.}, } @article {pmid41728114, year = {2026}, author = {Jiang, YL and Dong, SZ and Xu, YB and Fan, JL and Zhang, YM and Huang, SS}, title = {Metagenomic next-generation sequencing for diagnosis of immune checkpoint inhibitor-associated pneumonitis: a retrospective comparative clinical performance study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1730022}, pmid = {41728114}, issn = {2235-2988}, mesh = {Humans ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; Retrospective Studies ; *Pneumonia/diagnosis/etiology/chemically induced/microbiology ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Female ; Male ; Aged ; Middle Aged ; Neoplasms/drug therapy/complications ; Immunotherapy/adverse effects ; }, abstract = {OBJECTIVE: To evaluate the diagnostic performance and clinical utility of metagenomic next-generation sequencing (mNGS) in distinguishing immune checkpoint inhibitor-related pneumonitis (CIP) from infectious pneumonia in cancer patients undergoing immunotherapy.

METHODS: A retrospective tertiary hospital cohort included 34 cancer patients (Feb 2022-Jan 2024) with prior ICI exposure, new/worsening respiratory symptoms, imaging infiltrates, and both mNGS and conventional microbiological testing (CMT). Final diagnoses were adjudicated by a multidisciplinary panel. We compared pathogen detection rates, sensitivity, specificity, and turnaround times (TAT) between mNGS and CMT.

RESULTS: In the infectious pneumonia group, mNGS detected pathogens in 17/18 cases (94%), whereas CMT detected only 6/18 (33%). In the CIP group, mNGS was negative in 14/16 cases (88%), compared with 11/16 negatives by CMT (69%). Using the adjudicated diagnosis as the reference, mNGS showed sensitivity 88%, and specificity 94%. In contrast, CMT's sensitivity was 69%, and specificity 33%. The median TAT for mNGS was 24 hours (IQR 22-31 h), versus 121.5 hours (IQR 80.5-156 h) for CMT (P < 0.001).

CONCLUSION: mNGS outperforms CMT in both diagnostic accuracy and timeliness for distinguishing CIP from infectious pneumonia among immunotherapy recipients. Incorporation of mNGS into the diagnostic workflow for suspected CIP may improve etiological discrimination and enable timely, individualized treatment. Further large-scale prospective studies are required to confirm these findings.}, } @article {pmid41728322, year = {2026}, author = {Kim, DD and Worby, CJ and Wharton, H and Miklos, A and Chieng, B and Njenga, SM and Earl, AM and Pickering, AJ}, title = {Metagenomic strain tracking reveals patterns of bacterial spread and the impact of water chlorination.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {41728322}, abstract = {Bacterial infections are a major cause of morbidity and mortality among children under five in low- and middle-income countries (LMICs). Children in LMICs are exposed to and colonized by a range of pathogenic bacteria, yet patterns of bacterial exchange between humans are not well known, in part because culturing and sequencing single bacterial isolates is labor-intensive. Here, we apply a machine learning strain tracking approach to metagenomic data from 511 stool samples from children and mothers across urban and rural Kenyan communities to characterize bacterial dissemination and assess if community-wide water chlorination disrupts transmission. We identified distinct strain-sharing dynamics across species; potentially pathogenic taxa (e.g., Escherichia, Enterococcus, Campylobacter) exhibited distance-dependent dissemination driven by young children, while commensal taxa (e.g., Bifidobacterium, Bacteroides) showed patterns consistent with dietary exposure. Drinking water chlorination reduced community-level strain-sharing in rural communities. Our study provides the first strain-level insights into multi-species bacterial transmission dynamics in LMIC communities, identifying distinct dissemination pathways for facultative versus mostly anaerobic bacteria. Moreover, our findings highlight the utility of metagenomic strain tracking to uncover how community spread can be disrupted.}, } @article {pmid41728963, year = {2026}, author = {Enuh, BM and Myers, KS and Ackman, P and Weiland, T and Beach, N and Young, M and Donohue, TJ and Noguera, DR}, title = {Metagenomes and metagenome-assembled genomes from a nutrient removal plant at Los Angeles County Sanitation Districts (LACSD) that transitioned from high to low dissolved oxygen.}, journal = {Microbiology resource announcements}, volume = {15}, number = {3}, pages = {e0149425}, pmid = {41728963}, issn = {2576-098X}, abstract = {Operating biological nutrient removal (BNR) wastewater treatment plants with low dissolved oxygen (DO) conditions can reduce energy costs. We report on five metagenomes and 492 metagenome-assembled genomes (MAGs) obtained from samples collected at the Pomona water reclamation plant before and after a DO reduction from 3.5 to 0.7 mg/L.}, } @article {pmid41728976, year = {2026}, author = {La, N and Rattanapitoon, NK and Thanchonnang, C and Rattanapitoon, SK}, title = {Beyond a viral succession timeline: a phase-transition framework and re-analysis highlight hidden instability in the proposed "phage clock".}, journal = {Applied and environmental microbiology}, volume = {92}, number = {3}, pages = {e0230725}, pmid = {41728976}, issn = {1098-5336}, } @article {pmid41728996, year = {2026}, author = {Li, Z and Zhang, H and Wei, T and He, L and Wang, Y}, title = {Anoxia-adapted cyanobacteria in a marine blue hole.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {3}, pages = {e0257625}, pmid = {41728996}, issn = {1098-5336}, support = {42376149//National Natural Science Foundation of China/ ; KCXFZ20240903093905008//Science and Technology Major Project (Sustainable Development Special Project) of Shenzhen/ ; }, mesh = {*Cyanobacteria/genetics/physiology/classification/metabolism ; *Seawater/microbiology ; Phylogeny ; Anaerobiosis ; China ; *Oxygen/metabolism ; Genome, Bacterial ; Adaptation, Physiological ; Metagenome ; }, abstract = {Vertical transmission of marine particles brings ocean surface cyanobacteria into the deep ocean, where heterotrophic cyanobacterial lineages probably evolve to adapt to new environments even in oxygen-depleted zones. At present, active cyanobacteria have rarely been reported in dark and anoxic water columns in the deep sea. In this study, we recovered three metagenome-assembled genomes of cyanobacteria from the Yongle blue hole located in the South China Sea, two of which were actively transcribed in a dark, anoxic environment at 250 m depth, through integrated metagenomic and metatranscriptomic analyses of water samples from 21 stratified depths collected using in situ microbial fixation and filtration. These anoxia-adapted cyanobacteria were phylogenetically approximate to the sponge cyanobacterial symbionts, while the genomic features showed similarities with both free-living and sponge symbiotic counterparts. They exhibit genomic features shared with symbiotic lineages, including loss of substrate utilization, biosynthesis pathways, DNA repair, and circadian regulation. Conversely, they retain selected metabolic characteristics of free-living lineages, including phenylalanine biosynthesis and phosphoserine metabolism. Additionally, the discovery of taurine transport proteins in the genomes suggests the potential for organic sulfur uptake from the environment. Altogether, these findings reveal a distinct genomic configuration in cyanobacteria inhabiting a permanently dark and anoxic marine system, characterized by the retention of oxygen-dependent metabolic potential alongside sustained transcriptional suppression under in situ conditions. This study provides new insights into the ecological persistence and evolutionary adaptation of cyanobacteria under long-term oxygen limitation.IMPORTANCEWe report metabolically active cyanobacteria thriving in darkness and oxygen deprivation at 250 m depth in the ocean. Genomics results show these microbes share evolutionary roots with sponge cyanobacterial symbionts but developed unique adaptations for anoxic and sulfidic environments. Strikingly, they retain photosynthesis genes as genomic remnants (with no detected transcription) while losing genes critical for environmental stress responses, including DNA repair, osmotic regulation, and circadian control, suggesting a potential evolutionary connection to symbiotic relatives. Crucially, they maintain metabolic autonomy via phenylalanine biosynthesis and light-independent serine biosynthesis, exhibiting traits absent in most symbionts. This demonstrates how cyanobacteria adapt to anoxic environments through targeted genome reduction, revealing novel survival strategies in oxygen-depleted oceans and providing a research case for microbial resilience during marine deoxygenation.}, } @article {pmid41729067, year = {2026}, author = {Liu, Y and Zhang, T and Liu, J and Dong, X}, title = {Lactiplantibacillus plantarum Fermentation Enhances the Bioactivity of Polymeric Proanthocyanidins: Gut Microbiota Regulation via Caffeic Acid Production.}, journal = {Journal of agricultural and food chemistry}, volume = {74}, number = {8}, pages = {6824-6839}, doi = {10.1021/acs.jafc.5c14510}, pmid = {41729067}, issn = {1520-5118}, mesh = {Fermentation ; *Proanthocyanidins/metabolism/chemistry ; *Caffeic Acids/metabolism ; *Lactiplantibacillus plantarum/metabolism ; Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; Probiotics/metabolism ; Bacteria/isolation & purification/classification/genetics/metabolism ; Polymers/metabolism/chemistry ; }, abstract = {Polymeric proanthocyanidins (PPC) typically exhibit low bioavailability. While probiotic metabolism can enhance polyphenol bioactivity, the interaction between Lactiplantibacillus plantarum and PPC remains underexplored. In this study, L. plantarum SFFI23, a strain exhibiting excellent capacity to metabolize PPC, was selectively isolated. During in vitro digestion and fecal fermentation, SFFI23 reduced the degree of polymerization of PPC and enhanced overall antioxidant capacity. Metagenomic analysis revealed that SFFI23-PPC metabolism resulted in Firmicutes enrichment, accompanied by opportunistic pathogen reduction and an upregulation of health-associated pathways such as quorum sensing. Metabolomics analysis showed significant enrichment in 17 metabolic pathways. Multiomics analyses revealed that caffeic acid, derived from SFFI23-PPC metabolism, contributes to improved gut health by regulating gut microbiota and promoting metabolic reprogramming. This study outlines a triadic mechanism: "biotransformation by L. plantarum-metabolic activation of PPC-gut microbiota regulation", highlighting the potential of SFFI23 as an adjunct for enhancing PPC bioactivity.}, } @article {pmid41729089, year = {2026}, author = {Liu, J and Zheng, X and Jia, C and Sun, Z and Zhou, W and Zhang, J and Chen, Y and Zhou, Z and Tian, Y and Xiao, G and Du, L and Fan, C and Sun, L and Yue, M}, title = {Zoonotic Bordetella bronchiseptica infection at the swine-human interface: unveiling the evolutionary path from an animal to a human pathogen.}, journal = {Emerging microbes & infections}, volume = {15}, number = {1}, pages = {2637286}, pmid = {41729089}, issn = {2222-1751}, mesh = {Animals ; *Bordetella bronchiseptica/genetics/isolation & purification/pathogenicity/physiology/classification ; Humans ; Swine ; *Bordetella Infections/microbiology/veterinary/transmission/epidemiology ; *Swine Diseases/microbiology/transmission/epidemiology ; *Zoonoses/microbiology/transmission ; Plasmids/genetics ; *Bacterial Zoonoses/microbiology/transmission/epidemiology ; Evolution, Molecular ; Virulence ; Genome, Bacterial ; }, abstract = {Bordetella bronchiseptica, long regarded as a veterinary pathogen, is now emerging as a zoonotic threat to humans, particularly in immunocompromised individuals. We report a sentinel event involving a synchronized B. bronchiseptica outbreak in swine and their human caretaker, providing a unique opportunity to examine cross-species transmission and adaptation at the genomic level. Comparative genomics revealed that the human-adapted isolate (RL57) and its swine progenitor (XX35) share an identical chromosome, with XX35 harbouring an extra conjugative plasmid. Remarkably, RL57 did not simply lose this plasmid; instead, the entire plasmid was integrated into the chromosome via site-specific recombination. This integration allowed permanent retention of plasmid-encoded virulence and fitness genes, after which the plasmid was discarded to eliminate its replicative burden - a "capture-and-discard" mechanism of evolution. Following plasmid loss, the RL57 strain exhibited hypervirulence, faster growth, enhanced thermotolerance, and increased biofilm formation, indicating successful adaptation to the human host. Plasmid loss paradoxically rewired bacterial metabolism: sulfur assimilation and sulfonate utilization pathways were upregulated to fuel host adaptation. Strikingly, despite a collapse in transcription of specific metabolic modules, translational compensation maintained high protein levels, driving robust biofilm formation and thermal tolerance. These findings reveal a previously unrecognized evolutionary strategy in which plasmid integration followed by subsequent plasmid loss amplifies pathogenicity and host adaptability. Finally, we propose a One Health surveillance triad - metagenomic tracking of plasmid-chromosome dynamics, recombination hotspot screening, and metabolic shift monitoring - to proactively identify and mitigate such zoonotic events.}, } @article {pmid41729207, year = {2026}, author = {Gouda, MNR and Subramanian, S}, title = {Functional Genomics and Enzymatic Diversity of Gut Bacteria in Apis mellifera: A Multi-Approach Study from India.}, journal = {Current microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {41729207}, issn = {1432-0991}, mesh = {Animals ; Bees/microbiology ; India ; *Bacteria/genetics/classification/enzymology/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Phylogeny ; Genomics ; Biodiversity ; }, abstract = {The gut microbiota of the western honey bee Apis mellifera plays a vital role in host nutrition, digestion, immunity, and overall colony health. Although the functional and enzymatic capabilities of bee-associated microbes are increasingly recognized, studies integrating culture-dependent screening with metagenomic functional profiling remain scarce. This study characterizes the gut bacterial communities of forager and hive bees from the Indian subcontinent using cultivation, 16S rRNA gene sequencing, enzyme assays, and metagenomic analysis. A total of 165 isolates were obtained, yielding 85 unique strains deposited in GenBank. Metagenomic assembly generated 7.78 million non-redundant genes, including 11,050 KEGG-annotated and 2.43 million CAZy-annotated genes. Forager bees showed pronounced enrichment of carbohydrate-processing pathways such as glycolysis/gluconeogenesis (22.9%), galactose metabolism (4.42%), starch and sucrose metabolism, and ABC transporters (9.80%), consistent with their nectar- and pollen-rich diet. Culture-based biochemical assays revealed substantial enzymatic diversity among isolates belonging to Bacillus, Enterobacter, Serratia, Cedecea, Clostridium, Lysinibacillus, and Aneurinibacillus. High invertase activities were recorded in Xanthomonas sp. HAmf44 (2.509 U/mg), Clostridium argentinense HAmf20 (2.470 U/mg), Lysinibacillus fusiformis HAmh15 (2.509 U/mg), and Bacillus paralicheniformis HAmh05 (2.333 U/mg). Strong lipolytic activities were observed in Cedecea davisae HAmf19 (6.062 U/mg), Pseudomonas aeruginosa HAmh21 (5.927 U/mg), and Enterobacter cloacae HAmf26 (3.349 U/mg). Significant variation among isolates (p = 0.001) underscored the functional diversity of the gut microbiota. Integrating KEGG orthologs with species abundance revealed that dominant taxa-including Gilliamella, Snodgrassella, Lactobacillus, and Bifidobacterium-drive key metabolic pathways. Overall, this study provides the first combined enzymatic and metagenomic assessment of A. mellifera gut microbiota from India and identifies high-performing strains with probiotic potential to enhance honey bee nutrition and colony productivity.}, } @article {pmid41729287, year = {2026}, author = {Lima, NSM and Gomes-Pepe, ES and Kock, FVC and Colnago, LA and da Costa Aguiar Alves, PL and de Macedo Lemos, EG}, title = {Efficiency of Imazapic Degradation: an Assessment of LacMeta Treatments Utilizing Whole Cell.}, journal = {Current microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {41729287}, issn = {1432-0991}, abstract = {UNLABELLED: The extensive use of herbicides such as imazapic, from the imidazolinone class, raises environmental concerns due to its persistence and toxicity in ecosystems and subsequent crops. Enzymatic bioremediation emerges as a sustainable alternative for the mitigation of these contaminants. This study investigated the potential of the metagenomic laccase, LacMeta, expressed in Escherichia coli BL21 (DE3), to degrade imazapic using a whole-cell approach. LacMeta expression was optimized with CuSO4, which proved to be four times more effective than IPTG. The E. coli + LacMeta cells demonstrated high tolerance to the herbicide, maintaining cell viability even at high doses (350 g/ha). Notably, the enzymatic activity of LacMeta was not inhibited by imazapic; on the contrary, it was stimulated, reaching a specific activity nearly three times higher in the presence of the herbicide compared to the control. Degradation was confirmed by UV-Visible spectroscopy, which showed the disappearance of imazapic’s characteristic peaks (200–280 nm) over 15 days. [1]H-NMR and FTIR analyses corroborated the degradation, indicating structural changes in the herbicide molecule, particularly in the aromatic ring region (signals at 8.25 and 8.50 ppm). Phytotoxicity assays with lettuce seeds (Lactuca sativa) confirmed that treatment with the LacMeta-containing supernatant cell free significantly reduced the toxicity of imazapic in the soil. The results demonstrate that LacMeta has high potential for the bioremediation of imazapic, and the whole-cell approach represents a promising and cost-effective strategy for the decontamination of environments impacted by this herbicide.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00284-026-04760-1.}, } @article {pmid41730403, year = {2026}, author = {Liu, W and Zhang, Z and Wu, W and Yan, X and Huang, Y and Feng, H and Mou, Q and Wan, J and Yan, M and Tang, H and Liang, J and Zhang, Y and Peng, C and Pan, X}, title = {Ligilactobacillus murinus confers a dual benefit: Counteracting crotonis fructus-induced intestinal toxicity and synergizing with its processed form against ulcerative colitis.}, journal = {Journal of ethnopharmacology}, volume = {363}, number = {}, pages = {121420}, doi = {10.1016/j.jep.2026.121420}, pmid = {41730403}, issn = {1872-7573}, mesh = {Animals ; *Colitis, Ulcerative/chemically induced/microbiology/drug therapy ; Dextran Sulfate ; *Croton/chemistry ; Male ; Caenorhabditis elegans ; *Probiotics/pharmacology/therapeutic use ; Gastrointestinal Microbiome/drug effects ; Mice ; Fruit ; Disease Models, Animal ; Mice, Inbred C57BL ; Intestines/drug effects ; Intestinal Barrier Function ; }, abstract = {Ulcerative colitis (UC) poses a major clinical challenge. Classical Chinese medical texts record the use of Crotonis Fructus (CF), the seeds of Croton tiglium L., for treating conditions like "chronic dysentery" presenting symptoms similar to UC. However, the clinical application of both raw and processed CF is limited due to intestinal toxicity.

AIM OF THE STUDY: This study investigates the role of gut microbiota in mitigating the intestinal toxicity induced by CF and in enhancing the anti-UC efficacy of its processed form.

METHODS: Metagenomic analysis investigated CF-induced intestinal toxicity. The benefits of probiotics combined with CF or processed CF cream were evaluated in Caenorhabditis elegans (C. elegans) and a dextran sulfate sodium (DSS)-induced mouse model. Their combined effect was further assessed in DSS-exposed C. elegans, with qRT-PCR measuring intestinal barrier integrity.

RESULTS: Metagenomic analysis revealed that CF-induced intestinal toxicity was associated with gut microbiota dysbiosis characterized by a pronounced reduction in Ligilactobacillus murinus (L. murinus). Supplementation with L. murinus alleviated CF-induced damage in C. elegans. In DSS-induced UC mice, both L. murinus and processed CF cream ameliorated colitis and suppressed TNF-α, IL-6, and IL-1β. When co-administered in DSS-exposed C. elegans, two agents acted synergistically, leading to greater restoration of intestinal barrier integrity and more pronounced upregulation of barrier-function genes.

CONCLUSION: This study demonstrates that L. murinus plays a dual role: it mitigates CF-induced intestinal toxicity and acts synergistically with processed CF cream to enhance UC treatment, providing a microbiome-based strategy for safer clinical application.}, } @article {pmid41730992, year = {2026}, author = {Escalante, C and Reyes, AM and Zhao, C and Balkcom, KS and Jacobson, AL and Strayer-Scherer, A and Martin, KM and Koebernick, J and Huseth, A and Kozieł, E and Small, I and Greene, JK and Otulak-Kozieł, K and Mulvaney, MJ and Price, PP and Briseño, RIA and Bag, S and Conner, K}, title = {Metatranscriptomics analysis reveals the cotton virome in the southern United States.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41730992}, issn = {2045-2322}, mesh = {*Gossypium/virology ; *Virome/genetics ; *Plant Viruses/genetics/classification ; High-Throughput Nucleotide Sequencing ; Gene Expression Profiling ; Genome, Viral ; *Transcriptome ; Phylogeny ; RNA Viruses/genetics ; Metagenomics ; United States ; }, abstract = {High-throughput sequencing (HTS) has expanded our perspective on the distribution and diversity of plant viruses. Furthermore, improvements in HTS and decreasing sample costs have enabled the discovery of novel plant viruses in field-collected samples. This study examined the putative virome of cotton samples collected from fields across the southern United States. Leaf samples were collected, and total RNA was extracted. Library preparation was performed from pooled samples within locations before sequencing on an Illumina platform. Sequenced libraries were mapped to the cotton reference genome, and the resulting sequences were de novo assembled. A metatranscriptomics analysis revealed complete genome contigs of cotton leafroll dwarf virus in all tested samples. Additionally, 29 putative families of RNA and DNA plant viruses co-infecting cotton were found. Seven families of RNA viruses were more prevalent across all locations. These families included Botourmiaviridae, Hypoviridae, Mitoviridae, Narnaviridae, Partitiviridae, Solemoviridae, and Totiviridae. The information obtained in this investigation will help develop a broader perspective on cotton virus diversity and whether co-infections of viruses can influence (negatively or positively) plant physiology, product quality, and yield.}, } @article {pmid41731364, year = {2026}, author = {Liu, Y and Sun, H and Tan, X and Li, K and He, Z and Hu, S}, title = {Ultra-deep metagenomic sequencing enables reconstruction of diverse, high quality microbial genomes from human urine samples.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41731364}, issn = {1471-2180}, support = {2021YFF0703805//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Urinary tract infections (UTIs) represent a major global health challenge, necessitating the precise identification of causative pathogens for effective diagnosis and treatment. While metagenomic next-generation sequencing (mNGS) has emerged as a powerful diagnostic tool, its clinical application has been limited by the lack of high-quality microbial genomes from urine samples.

RESULTS: We reconstructed 223 reliable quality MAGs spanning bacterial, fungal, mycoplasmal, and viral, including the first demonstration of multiple Escherichia coli subpopulations within individual urine samples. The collection comprised six fungal genomes, ten mycoplasma genomes, and eight completed viral genomes. Comparative analysis showed 72% concordance with culture while detecting additional pathogens in 30% of cases, including fastidious organisms missed by conventional methods.

CONCLUSIONS: This study establishes an optimized mNGS framework that overcomes current diagnostic limitations in UTIs through high-depth sequencing and minimal host contamination, enabling unprecedented resolution of the urinary microbiota, including the first identification of intra-sample E. coli subpopulations. The comprehensive MAG collection provides a valuable resource for advancing UTI diagnostics, mechanistic research, and personalized treatment strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04826-x.}, } @article {pmid41731377, year = {2026}, author = {Diouf, AM and Mbaye, AL and Deh, M and Lahlali, R and Elhoumaizi, MA and Rchiad, Z and Barakate, M}, title = {Comparative metagenomic analysis of bacterial and fungal communities associated with bayoud-resistant and susceptible date palm cultivars in the Zagora oasis-Morocco.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41731377}, issn = {1471-2180}, abstract = {BACKGROUND: Fusarium oxysporum f. sp. albedinis (Foa) is a destructive soil-borne fungal pathogen responsible for bayoud disease, which threatens date palm cultivation in North Africa. This disease has caused significant agricultural losses, particularly in Morocco, where the Zagora oasis is a key region for date palm production. Within this oasis, two cultivars—Black Bousthammi and Jihel—are mainly cultivated and exhibit complete resistance and high susceptibility to Foa, respectively. Thus, this study aimed to identify and compare the bacterial and fungal communities associated with the two cultivars and understand their assemblage regarding the disease resistance or susceptibility. Moreover, we explored the influence of each cultivar on the composition and structure of its root-associated microbiome and examined its relationship with the microbial populations present in the surrounding bulk soil, to better understand the recruitment dynamics that shape the microbiome in the roots.

RESULTS: The results revealed significant differences in microbiome composition between the bulk soil and roots of the two date palm cultivars, and between the microbiome of the resistant and susceptible cultivars as well. Moreover, we observed that date palm cultivars had a greater effect on bacterial community composition than on fungal population. Interestingly, the susceptible cultivar exhibited a higher enrichment of several beneficial genera, such as Pseudomonas, Lysinibacillus, Actinomadura, Halomonas, Kocuria, Serratia, Phyllobacterium, Bacillus, Streptomyces, and Trichoderma.

CONCLUSION: The presence of these beneficial genera, known for their antagonistic activity against phytopathogens, may reflect a recruitment pattern associated with pathogen pressure in the susceptible cultivar. This study is the first to compare the microbial communities between a bayoud-resistant and susceptible cultivar and provides insights into the potential role of the root microbiome when plants are under pathogen pressure. This reinforces the need to further elucidate the genetic and biological mechanisms that trigger microbiome assembly, which could be a key step in developing effective methods to manage the bayoud disease.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04837-8.}, } @article {pmid41731555, year = {2026}, author = {Yasuda, S and Palomo, A and Smets, BF and Terada, A}, title = {Potential survival strategies of novel comammox and nitrite-oxidizing Nitrospira synthesizing osmoprotectants in a wastewater microbiome treating high-ammonia brackish landfill leachate.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41731555}, issn = {2049-2618}, mesh = {*Ammonia/metabolism ; *Nitrites/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Oxidation-Reduction ; *Wastewater/microbiology ; Metagenome ; Nitrification ; *Microbiota ; Phylogeny ; Archaea/genetics/classification/metabolism ; Waste Disposal Facilities ; Methanol/metabolism ; }, abstract = {BACKGROUND: In the late stages of landfill operation, leachate becomes brackish and contains high concentrations of ammonia with limited organic carbon. At leachate treatment facilities, it is typically subjected to nitrification followed by denitrification, with methanol supplied as an external electron donor. This unique environment may harbor novel microorganisms, including nitrifiers. Although a variety of microorganisms are involved in nitrification, their substrate specificity and salinity tolerance remain insufficiently understood. In this study, a genome-centric metagenome analysis was conducted on the microbiome from a leachate treatment facility at a closed landfill.

RESULTS: A total of 68 metagenome-assembled genomes (MAGs) were reconstructed, including 64 putative novel species. Among these, two Nitrospira MAGs were recovered: a novel complete ammonia-oxidizing bacterium (comammox), Nitrospira LAS72 (88.72% completeness, 2.10% contamination), and canonical nitrite-oxidizing Nitrospira LAS18 (99.98% completeness, 2.29% contamination). Comparative genomic analysis with 260 publicly available Nitrospira genomes revealed that LAS18 represents a new sub-lineage within lineage VII of the Nitrospira genus. Two ammonia-oxidizing archaea (AOA), Candidatus Nitrosocosmicus LAS21 and Nitrosarchaeum LAS73, were also identified, while canonical ammonia-oxidizing bacteria were not detected. Given the brackish conditions (1.23% salinity) and the methanol-fed operation of the treatment facility, the genomic potential for osmotic stress adaptation and methanol metabolism was investigated. Comammox Nitrospira LAS72 harbors biosynthetic pathways for several compatible solutes (osmoprotectants), including glycine betaine, proline, trehalose, and L-glutamate. Moreover, comammox Nitrospira LAS72 possesses genetic potential for oxidizing formaldehyde, suggesting that it may exploit these methanol-derived intermediates as energy sources. These features indicate that LAS72 may withstand osmotic fluctuations through the production of various osmoprotectants and thrive under the unique conditions of a methanol-fed environment.

CONCLUSIONS: The discovery of novel comammox Nitrospira and canonical Nitrospira forming a new sub-lineage within lineage VII of the Nitrospira genus in an ammonia-rich brackish environment provides the first genomic evidence for evolutionary adaptation among nitrifiers to saline, methanol-fed environments. These findings enhance our understanding of the ecological and evolutionary dynamics shaping nitrifier communities in complex treatment ecosystems. Video Abstract.}, } @article {pmid41731616, year = {2026}, author = {Fan, S and Lu, J and Cui, H and Ding, W and Li, S and Sun, J and Li, YX and Zhang, W}, title = {Unlocking the unexplored AMPSphere in marine rare species.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41731616}, issn = {2049-2618}, mesh = {Biofilms/growth & development ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Antimicrobial Peptides/pharmacology/chemistry/genetics ; *Seawater/microbiology ; Metagenome ; Metagenomics/methods ; *Aquatic Organisms/genetics ; Microbiota ; Anti-Bacterial Agents/pharmacology ; Genome, Bacterial ; }, abstract = {BACKGROUND: Antimicrobial peptides (AMPs) have advantages over traditional antibiotics in fighting against drug-resistant bacterial infections. Natural microbial communities are considered as the priority targets for next-generation AMP bioprospecting initiatives. While progress has been made in characterizing AMPs from the dominant microbial taxa in natural ecosystems, current research largely overlooks the biosynthetic potential of rare species. Given their distinct evolutionary pressures, rare species likely produce AMPs with novel structures and unconventional mechanisms of action.

RESULTS: In this study, enrichment cultivation of a marine biofilm was conducted in 138 carbon source- and oxygen level-based conditions, followed by metagenomic sequencing using both Illumina and Nanopore platforms. Analysis of 435 high-quality genomes derived from the metagenomes suggests that these bacterial strains are significantly underrepresented (< 0.01%) in global marine biofilm communities. Through multi-model prediction, we identified 3,054,472 candidate AMPs from the genomes, including 1048 high-confidence ones, thereby significantly expanding the previously known AMPSphere. Furthermore, AMPs derived from the rare bacterial species exhibit unique sequence characteristics, structural diversity, remarkable stability under diverse pH conditions and pepsin exposure, and strong therapeutic potential in animal models, reflecting their specialized adaptive and defensive strategies developed within ecological systems.

CONCLUSIONS: The features of the underexplored AMPs from low-abundance bacteria in marine biofilms provide valuable resources and theoretical foundations for the development of highly effective antimicrobial agents. Video Abstract.}, } @article {pmid41732151, year = {2026}, author = {Liu, X and Han, H and Zhang, X and Kong, F and Dai, D and Hao, Y and Wang, W and Li, S}, title = {Potassium carbonate improves milk quality by enhancing rumen metabolism in Holstein cows.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {24}, number = {}, pages = {534-548}, pmid = {41732151}, issn = {2405-6383}, abstract = {Mid-lactation is a key stage in dairy production characterized by high milk yields and metabolic stress in cows. Dietary potassium carbonate may enhance milk quality, but its response mechanisms, particularly the link between rumen microbiome changes and production performance, remain poorly understood. To address this knowledge gap, a total of 60 multiparous Holstein cows (parity = 2.47 ± 1.06, body weight = 601 ± 25 kg, and days in milk = 127.83 ± 31.91) were divided into four groups (n = 15 cows per group) using a randomized complete block design and fed the corresponding diets for 84 days. The feed treatments were as follows: a control group (CON, basal diet), a low dose group (LD, basal diet + 250 g/d K2CO3·1.5H2O per head), a medium dose group (MD, basal diet + 500 g/d K2CO3·1.5H2O per head), and a high dose group (HD, basal diet + 750 g/d K2CO3·1.5H2O per head). The results showed that potassium carbonate supplementation significantly influenced rumen fermentation patterns, particularly by increasing acetate (P = 0.008) and isovalerate concentrations (P < 0.001). Milk fat (P = 0.004) and protein percentage (P = 0.006) exhibited the most pronounced effects in the MD group. The rumen microbiota and metabolome revealed significant alterations in microbial community structure and function. Notably, the results indicated that in the MD group, there was an increase in the abundance of Kyoto Encyclopedia of Genes and Genomes (KEGG) genes associated with crucial metabolic pathways: amino acid biosynthesis, long-chain fatty acid biosynthesis and fatty acid elongation pathways. These findings suggest that dietary supplementation with 500 g/d of potassium carbonate optimizes milk composition by modulating the rumen microbiota and associated metabolic pathways, supporting the potential for targeted nutritional strategies in dairy management.}, } @article {pmid41732362, year = {2026}, author = {Tanja, Z and Maja, R}, title = {Gut microbiomes of wild and domesticated mammals and birds in Slovenia, Europe: 16S rRNA sequencing data.}, journal = {Data in brief}, volume = {65}, number = {}, pages = {112564}, pmid = {41732362}, issn = {2352-3409}, abstract = {From a One Health perspective, the gut microbiota of animals acts as a major driver of microbial exchange between animals and the environment. Animals continuously release gut microbes into their surroundings, shaping environmental and human microbial communities and potentially dispersing pathogens. Characterizing gut microbiota across diverse animal hosts is therefore critical for understanding the patterns of microbial spread through ecosystems and their impact on animal, human and environmental health. Here, we introduce a large, taxonomically diverse dataset of fecal microbiomes from 715 individual animals representing over 50 mammalian and avian species. We collected samples from both wild and domestic animals with an emphasis on capturing microbial diversity across a wide range of taxa and ecological contexts. The samples were subjected to 16S rRNA gene sequencing, targeting the V3-V4 hypervariable region. Bioinformatic analysis was performed using Usearch to generate zero-radius operational taxonomic units (ZOTUs). This dataset was generated primarily for the development of microbial source tracking (MST) assays used for identifying the sources of fecal pollution in contaminated water. However, it provides a valuable resource for broader microbiome research. It enables comparative studies across host species, trophic guilds, and environmental contexts such as domestication.}, } @article {pmid41732369, year = {2026}, author = {Fu, R and Li, J and Wang, M and Xiao, D and Li, F and Zhu, X}, title = {Microscopic-scale gut microbiota dataset of Kunming mice revealed by 16S rRNA gene high-throughput sequencing.}, journal = {Data in brief}, volume = {65}, number = {}, pages = {112572}, pmid = {41732369}, issn = {2352-3409}, abstract = {Gut microbiota profoundly influence host physiology, yet most studies rely on bulk-scale intestinal samples, overlooking microbial heterogeneity at the micro-scale. Here, we present a dataset generated from 378 colonic micro-scale grains (20-40 µm) and 20 bulk samples collected from four Kunming mice. Using Illumina NovaSeq 6000 sequencing of the 16S rRNA V4 region, we obtained over 8.0 million raw reads, processed into 1506 amplicon sequence variants (ASVs) spanning 19 phyla and 203 genera. Firmicutes and Bacteroidetes were the dominant phyla across scales, while marked differences were observed in ASV richness (p < 0.001, Wilcoxon test) and network complexity (number of edges, p = 0.03, Wilcoxon test) between bulk samples and micro-scale grains. The dataset, deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA1249752, provides a high-resolution view of gut microbial spatial organization at the sub-100 µm scale. These data advance current understanding of microbial assembly processes, interspecies interactions, and scale-dependent community structure, thereby serving as a valuable resource for microbiome ecology and future mechanistic studies.}, } @article {pmid41732520, year = {2026}, author = {Aguilar Ticona, JP and Amorim Santos, L and Meng, X and Nery, N and Fofana, MO and de Moraes, L and Morais Strobel, I and Vitoriano, R and Silveira Cucco, M and Andrade Belitardo, EMM and Thakku, G and Cruz, JS and Detweiler, AM and Neff, N and Tato, CM and Reis, MG and Costa, F and Cummings, DAT and Ko, AI and Khouri, R}, title = {Metagenomic surveillance reveals off-season circulation of respiratory viruses during the COVID-19 pandemic in Salvador, Brazil.}, journal = {New microbes and new infections}, volume = {70}, number = {}, pages = {101717}, pmid = {41732520}, issn = {2052-2975}, abstract = {BACKGROUND: Evidence from multiple countries suggests that the COVID-19 pandemic disrupted the transmission of other respiratory viruses. We characterized respiratory virus transmission during the pandemic in Salvador, Brazil, a tropical region in the Southern Hemisphere.

METHODS: From November 2021 to October 2022, we conducted biweekly household visits in an urban informal settlement to screen individuals with respiratory symptoms. Symptomatic individuals and their contacts were interviewed, and nasal swabs collected. Virus identification was performed using multiplex RT-qPCR, followed by metagenomic analysis in a subset of symptomatic participants with negative RT-qPCR results.

RESULTS: We screened 3174 residents from 1174 households, identifying 669 symptomatic episodes and detecting 219 respiratory viruses. including coinfections, SARS-CoV-2 was the most common with 118 cases (54%), followed by Influenza A with 39 (18%), Rhinovirus with 22 (10%), Human Parainfluenza Virus with 15 (7%), Respiratory Syncytial Virus with 13 (6%), and seasonal Human Coronaviruses with 12 (5%). Co-infections were observed, with combinations involving SARS-CoV-2, Influenza A, and Respiratory Syncytial Virus being the most common. Peaks of Influenza, HPIV, and RSV occurred in late 2021 during low Delta circulation, while Omicron BA.1 emerged in January 2022. Influenza and RSV showed low transmission during Brazil's winter months, and seasonal coronaviruses reappeared two years after the pandemic onset.

CONCLUSION: Multiplex RT-qPCR and metagenomic analysis allowed rapid detection and sequencing. An off-season influenza peak was identified, possibly due to relaxed hygiene measures or accumulated susceptibility after SARS-CoV-2 interventions. The household secondary attack rate for influenza was lower than for Omicron BA.1, possibly reflecting lower transmissibility or pre-existing immunity.}, } @article {pmid41732893, year = {2026}, author = {Zheng, Y and Li, Y and Song, C and Chai, Z and Fu, J and Dang, C and Ju, F and Wang, B and Niu, J and Zheng, M}, title = {Functional Dominance and Competitive Strategy of Comammox Bacteria among Ammonia Oxidizers in Urban Secondary Effluent-Constructed Wetlands.}, journal = {Environmental science & technology}, volume = {60}, number = {9}, pages = {7194-7207}, doi = {10.1021/acs.est.5c10262}, pmid = {41732893}, issn = {1520-5851}, mesh = {*Wetlands ; *Ammonia/metabolism ; *Bacteria/metabolism ; Oxidation-Reduction ; Nitrification ; Wastewater ; }, abstract = {Amid growing concerns over water pollution, the secondary effluent from wastewater treatment plants poses significant threats to aquatic ecosystems with limited self-purification capacity. Secondary effluent-constructed wetlands (SECWs) offer a sustainable solution for advanced nitrogen removal from this low-ammonia effluent, yet the functional role of comammox bacteria remains largely unexplored in such habitats. This study investigated the abundance, activity, kinetics, and ecological adaptations of comammox in typical SECWs. Quantitative PCR and amplicon sequencing revealed that comammox Nitrospira ubiquitously presented across all samples, even numerically dominated over ammonia-oxidizing bacteria/archaea (AOB/AOA). Consistent results from double-inhibition assays and DNA-stable isotope probing microcosm experiments indicated that comammox actively participated in nitrification, contributing 2.03-3.89 times those of canonical nitrifiers. Substrate kinetic and metagenomic analyses identified the Nitrospira nitrosa cluster as the sole active comammox population in SECWs, which exhibited relatively lower ammonia affinity (Km(app) = 0.055 ± 0.007 mg N/L) than other comammox species and distinct genomic adaptations to SECW-specific stressors, potentially explaining its dominance. Compared to AOB, comammox combines high substrate affinity with environmental resilience, aligning with K-strategist traits that enable it to outperform r-strategist AOB in SECWs. Overall, it is within this niche differentiation among comammox species and nitrifiers that the N. nitrosa cluster numerically and functionally dominated the nitrification process in SECWs, positioning comammox Nitrospira as pivotal biocatalysts for advanced nitrogen removal in engineered ecosystems.}, } @article {pmid41733350, year = {2026}, author = {Bian, K and Busch, A and Norton, J and Bott, C and Gonzalez, R and Curtis, K and Tolofari, D and Khunjar, W and Graham, KE and Pinto, AJ}, title = {Quantitative metagenomics using a portable protocol.}, journal = {Applied and environmental microbiology}, volume = {92}, number = {3}, pages = {e0217925}, pmid = {41733350}, issn = {1098-5336}, support = {5100//Water Research Foundation/ ; DE-EE0009270//U.S. Department of Energy/ ; }, mesh = {*Metagenomics/methods ; *Microbiota ; *Wastewater/microbiology ; Nanopore Sequencing/methods ; Bacteria/classification/genetics/isolation & purification ; Fungi/classification/genetics/isolation & purification ; DNA/analysis/genetics/isolation & purification ; RNA, Ribosomal, 16S/analysis/genetics ; RNA, Ribosomal, 18S/analysis/genetics ; DNA Barcoding, Taxonomic ; Workflow ; }, abstract = {A field-deployable DNA sequencing approach for quantitative microbial community profiling can enable rapid responses for a range of applications in the water sector-from process control to wastewater surveillance. Current quantitative approaches require complex instrumentation and have long turnaround times for DNA recovery and absolute quantitation. In this study, we report a field-deployable rapid detection and rapid absolute quantitation (rD+rQ) workflow that leverages real-time Nanopore sequencing for quantitative metagenomics. This workflow integrates a high-molecular-weight DNA recovery protocol for diverse environmental matrices of relevance to the water sector, and multiplexed Nanopore sequencing with barcoded spike-in-based calibration (BSINC). BSINC using multispecies genomic spike-in controls exhibits significantly higher calibration accuracy compared to conventional approaches that utilize either a single DNA fragment or single organism spike-in controls. Dynamic detection and quantitation limits were established based on the coverage fraction of sequenced genomes and the coefficient of variation of genome copy numbers across replicates to enhance the accuracy and precision of microbial quantitation. The rD+rQ workflow achieves species-level identification and absolute quantitative results comparable to digital PCR in environmental samples. This portable laboratory and easy-to-use rD+rQ workflow should facilitate rapid decision-making for the water industry.IMPORTANCERapid and real-time monitoring of microbial communities is critical for a vast array of applications in environmental microbiology and biotechnology. While recent developments in portable sequencing technologies and associated workflows make onsite analysis possible, these approaches do not provide quantitative data on microbial concentrations. In this study, we present a sample and data processing workflow that enables nontargeted and quantitative microbial community profiling and demonstrate its validity on complex environmental samples. This approach for acquiring quantitative data can drive rapid decision-making from bioprocess control to wastewater-based epidemiology.}, } @article {pmid41734043, year = {2026}, author = {Thakur, M and Dolker, S and Wangmo, LK and Sharma, LK and Acharya, S and Mohapatra, P}, title = {Illumina-Based Metagenomic Insights into the Gut Microbiome of Amblyomma helvolum (Koch, 1844) Parasitizing Xenochrophis trianguligerus from Great Nicobar Island, India.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {26}, number = {4}, pages = {233-240}, doi = {10.1177/15303667261423035}, pmid = {41734043}, issn = {1557-7759}, mesh = {Animals ; India/epidemiology ; *Amblyomma/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; *Snakes/parasitology ; *Gastrointestinal Microbiome ; *Ixodidae/microbiology ; *Tick Infestations/veterinary/parasitology/epidemiology ; Metagenome ; Phylogeny ; }, abstract = {During a faunal survey in Great Nicobar Island, we collected four Amblyomma helvolum ticks infesting the snake Xenochrophis trianguligerus and processed for gut-metagenomic analysis using Illumina paired-end sequencing. A total of 8.7 million high-quality reads were generated, revealing that the gut microbiome was dominated by Bacteria (∼99.9%), primarily represented by Proteobacteria (∼95.7%), followed by minor fractions of Firmicutes, Actinobacteria, and Bacteroidetes. The predominant bacterial families were Alcaligenaceae, Bradyrhizobiaceae, Boseaceae, and Rickettsiaceae, with Achromobacter xylosoxidans emerging as the most abundant species (∼30% of total reads). Species-level analyses revealed a complex microbial community dominated by Achromobacter, Brevibacillus, Stutzerimonas, and Aeromicrobium. Several putative opportunistic pathogens were detected, including Myroides sp., Sphingobacterium sp., Stutzerimonas stutzeri, Cutibacterium acnes, Mycobacterium abscessus, Staphylococcus hominis, Achromobacter xylosoxidans, and Pseudomonas otitidis. This study represents the first metagenomic characterization of A. helvolum from India and provides baseline data on reptile-tick-associated microbial diversity from Great Nicobar Island. The findings underscore the importance of molecular surveillance in remote ecosystems and highlight the potential of reptile ticks as reservoirs of opportunistic and zoonotic bacteria.}, } @article {pmid41734489, year = {2026}, author = {Sabatino, R and Gini, C and Borgomaneiro, G and Sbaffi, T and Corno, G and Sun, K and Zhang, XH and Di Cesare, A}, title = {Sinking particles as repository of antimicrobial resistome diversity in the Sansha Yongle Blue Hole.}, journal = {The Science of the total environment}, volume = {1021}, number = {}, pages = {181585}, doi = {10.1016/j.scitotenv.2026.181585}, pmid = {41734489}, issn = {1879-1026}, mesh = {China ; *Seawater/microbiology ; *Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; Metagenomics ; *Water Microbiology ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; *Environmental Monitoring ; }, abstract = {The aquatic environment plays a central role in the selection and spread of antimicrobial resistance genes (ARGs). Using metagenomic approaches, several studies have provided a comprehensive view of the antimicrobial resistome across different aquatic ecosystems. However, unique aquatic systems, such as oceanic blue holes, remain largely unexplored. Free-living and particle-associated samples from the Sansha Yongle Blue Hole (South China Sea) were analyzed by shotgun metagenomics to characterize the antimicrobial resistome and the potential mobility of detected ARGs. The diversity of the antimicrobial resistome significantly decreased with increasing water depth. This trend was driven by the free-living bacterial community, whereas it remained stable in particle-associated communities. Additionally, the latter showed a higher frequency of co-occurring ARGs and mobile genetic elements on the same contigs, with a frequent plasmid localization of these genes. Overall, particle-associated bacteria proved essential for sustaining antimicrobial resistome diversity. Furthermore, these findings suggest that horizontal transfer of ARG may be more frequent within particle-associated communities along the water column of the blue holes, potentially contributing to the persistence of resistances in deep marine waters.}, } @article {pmid41734506, year = {2026}, author = {Liu, X and Ding, J and Ji, B and Pastore, C and di Bitonto, L and Li, A}, title = {Synergistic effects of zero-valent iron-activated carbon on microalgal-bacterial granular sludge under antibiotic stress: Pollutant transformation and antibiotic resistance gene risk.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141581}, doi = {10.1016/j.jhazmat.2026.141581}, pmid = {41734506}, issn = {1873-3336}, mesh = {*Sewage/microbiology ; *Sulfamethoxazole/metabolism/toxicity/chemistry ; *Iron/chemistry ; *Anti-Bacterial Agents/metabolism/pharmacology/toxicity ; *Carbon/chemistry ; *Microalgae/metabolism ; *Drug Resistance, Microbial/genetics ; Molecular Docking Simulation ; *Water Pollutants, Chemical/metabolism ; Genes, Bacterial ; *Bacteria/genetics/metabolism/drug effects ; }, abstract = {Microalgal-bacterial granular sludge (MBGS) technology remains insufficiently understood regarding the strategies and mechanisms for mitigating antibiotics and antibiotic resistance genes (ARGs). In this study, a non-aerated MBGS system coupled with zero-valent iron-activated carbon (ZVI-AC) was established to evaluate sulfamethoxazole (SMX) removal, effluent toxicity, ARGs control and to elucidate the underlying multi-scale mechanisms using molecular docking and metagenomic analyses. The results showed that, under SMX stress, the introduction of ZVI-AC maintained average COD removal above 94.0 % and increased the SMX degradation rate constant by 69.2 %. The "micro-electrolysis-like" effect generated by ZVI-AC increased sludge electron transport activity by 55.0 %, promoted MBGS stability (average granule size of 872.7 μm) and reduced effluent suspended solids to ≤ 10.0 mg/L, thereby significantly enhancing the structural stability and operational robustness of the MBGS system. For the transformation and toxicity reduction of SMX, molecular docking showed that the enzyme CYP102 interacted with SMX with a binding energy of -8.6 kcal/mol, indicating its significant role in accelerating SMX degradation and removing highly toxic metabolites TP163 and TP246, effectively reducing overall biological toxicity. In addition, metagenomic sequencing and qPCR analyses showed that the potential ARGs-host bacteria (g_Leptolyngbya) was significantly reduced, and that key ARGs (intI1 and sul1) were also significantly reduced, indicating a decreased risk of horizontal ARGs transfer. Specifically, ZVI-AC enhances SMX removal through micro-electrolysis-like and CYP450 enrichment as well as reducing ARGs via host bacteria suppression. Overall, this study provides new insight into how ZVI-AC enhances MBGS systems.}, } @article {pmid41734642, year = {2026}, author = {Zhao, W and Liu, Y and Yu, G and Xia, S and Wang, S and Li, Y and Zhong, S and Zou, D}, title = {Microelectric field-enhanced air-lift A/O process: Mechanisms for advanced nutrient removal in low C/N rural domestic sewage.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129036}, doi = {10.1016/j.jenvman.2026.129036}, pmid = {41734642}, issn = {1095-8630}, mesh = {*Sewage/chemistry ; *Nitrogen ; Phosphorus ; *Waste Disposal, Fluid/methods ; Carbon ; Denitrification ; }, abstract = {The predominant challenge in treating rural domestic sewage (RDS) stems from its low carbon/nitrogen ratio (C/N), which fundamentally restricts the direct applicability of conventional municipal sewage treatment processes. To address this challenge, this study developed an innovative microelectric field-enhanced air-lift A/O process. The results demonstrated that this process achieved average removal efficiencies of 78.91% for total nitrogen (TN) and 93.80% for total phosphorus (TP), representing a significant improvement over conventional process. Mechanistic investigations revealed that the enhanced nitrogen removal primarily originated from the microelectric field-driven efficient reduction of NO3[-]-N in the anoxic zone, while phosphorus elimination resulted from synergistic interactions among chemical (sweep-flocculation by iron oxides/ions), physical, and biological processes. Microelectric field can stimulate microorganisms to produce more extracellular polymeric substances (EPS) and increase the ratio of protein (PN) and polysaccharide (PS). Metagenomic-based taxonomic comparison illustrated significant enrichment of nitrifying and denitrifying bacteria in the microelectric field-enhanced system, especially promoting the growth of autotrophic denitrifying bacteria, thereby providing an alternative electron source for nitrogen removal. Furthermore, the increased abundance of nitrogen/phosphorus metabolism-related functional genes and key enzymes provided molecular-level evidence for the enhanced metabolic pathways. Through parameter optimization, the optimal operating conditions were determined as follows: hydraulic retention time (HRT) of 12 h, internal recirculation ratio of 150-170%, and voltage of 1 V. This study demonstrated that microelectric field-enhanced technology offered an efficient and feasible strategy for addressing the challenges of nitrogen and phosphorus removal in RDS with low C/N.}, } @article {pmid41734917, year = {2026}, author = {van der Sande, MAB and Valia, D and Tigoi, C and Stoesser, N and Stamm, L and Marten, A and Riems, B and Musyimi, R and Sibidou, Y and Schurch, AC and Tiendrebeogo, EW and Mwaringa, S and Kohns Vasconcelos, M and Ingelbeen, B and Tinto, H and Bielicki, JA and Cooper, BS and Berkley, JA and van Kleef, E}, title = {ALARUM: Active One Health surveillance in LMICs to monitor and predict Antimicrobial Resistance Using Metagenomics - a cross-sectional study protocol.}, journal = {BMJ open}, volume = {16}, number = {2}, pages = {e107465}, pmid = {41734917}, issn = {2044-6055}, mesh = {Humans ; *Metagenomics/methods ; Cross-Sectional Studies ; *One Health ; Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; Animals ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; }, abstract = {BACKGROUND: In rural sub-Saharan Africa (sSA), the burden of antimicrobial resistance (AMR) remains high. As AMR continues to rise, there is a strong need for practical, implementable surveillance to monitor and mitigate risks, as well as inform timely, evidence-based clinical decision-making. Emerging evidence points to possible community-level drivers, such as transmission between human, animal and environmental reservoirs as contributing factors, yet microbiological surveillance or opportunities for wastewater-based surveillance are often limited and insufficient in these settings. Therefore, alternative sustainable and affordable approaches are needed. We intend to build on the demonstrated potential of metagenomic profiling of pooled faecal material, which accurately predicted population-level AMR prevalence in invasive Enterobacterales infections.

METHODS AND ANALYSIS: We aim to validate this metagenomic pooled approach on additional populations, and to evaluate whether AMR patterns could be similarly predicted from surveillance of community One Health reservoirs. We will assemble existing data from hospital-based microbiology diagnostic laboratories in rural Burkina Faso and Kenya, and determine to what extent community-level metagenomic data, and/or faecal material of patients on hospital admission, can predict AMR in clinical isolates. We will perform community-level surveys in eight clusters per country, randomly selecting 15 households per cluster. We will systematically sample suspected environmental AMR exposure sites in and around households (soil, drinking water, latrines, chicken faeces) and collect data on community-level antibiotic use, hygiene practices, contact with domestic animals and sanitary facilities. Samples and data will be collected twice: during the dry and during the rainy season.In addition to evaluating the accuracy of predicting resistance in clinical isolates, we will quantify community-level exposure risks. We will conduct metagenomic profiling on pooled DNA extracts from human stool samples (hospital and community-level) and from household environments. Bayesian statistical models will quantify relationships between AMR gene abundance in the environment and in human stool, and invasive bacteria identified among clinical patients, accounting for geography and seasonality. A cost-utility analysis will determine under what circumstances the use of pooled metagenomic data to inform empirical antibiotic policies would represent an efficient use of resources.

ETHICS AND DISSEMINATION: The proposed surveillance protocol is developed in partnership with local communities and local and international researchers and has received ethical approval in Kenya and Burkina Faso. It will assess whether intermittent, pooled-sample metagenomics provides a viable, low-cost and practical approach for population-level AMR surveillance in settings that-like many in rural sSA-lack systematic microbiological diagnostics and where sewage systems for wastewater-based surveillance are absent. By providing an alternative to routine microbiological-based surveillance where this proves challenging to implement, this approach may help improve treatment outcomes, contribute to equity and public health. Findings will be disseminated through peer-reviewed publications and academic conferences and will contribute to the recently proposed WHO AMR surveillance strategy, which combines survey-based approaches with routine AMR surveillance.}, } @article {pmid41735391, year = {2026}, author = {Kovács, ÁB and Wehmann, E and Bekő, K and Grózner, D and Bali, K and Kreizinger, Z and Sawicka, A and Bányai, K and Gyuranecz, M}, title = {Genome-wide association study of Mycoplasma anserisalpingitidis strains for antibiotic susceptibility.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41735391}, issn = {2045-2322}, mesh = {*Anti-Bacterial Agents/pharmacology ; Animals ; *Genome-Wide Association Study ; *Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Genome, Bacterial ; }, abstract = {Mycoplasma anserisalpingitidis is a facultative pathogenic bacterium affecting waterfowl, predominantly geese and sporadically ducks. Understanding the molecular basis of antimicrobial resistance mechanisms is crucial in the preservation of antibiotic efficiency. This study aimed to elucidate the genetic background of antibiotic susceptibility profiles of 110 M. anserisalpingitidis strains against nine antimicrobial agents. Significant associations between k-mers and five (tylvalosin, tilmicosin, enrofloxacin, lincomycin, spectinomycin) of the nine antimicrobial agents were identified by pyseer. Significant associations were found in multiple coding sequences that encode various members of efflux pumps, epigenetic regulation and topoisomerases among many other groups of functions. Certain k-mers associated with genes found putative prophage-like sequences suggest potential horizontal gene transfer events that could facilitate the acquisition of novel resistance mechanisms. Based on our findings, the genetic background of antimicrobial resistance of M. anserisalpingitidis is composed of multiple factors. Our results not only correlated with the majority of known antibiotic resistance mechanisms (e.g. drug target modification, efflux pumps, methyltransferases) but also showed potentially novel genes that could play a significant role in antimicrobial resistance. The results may serve to expedite the diagnosis of M. anserisalpingitidis antibiotic susceptibility profiles and support the fight against the spreading of resistance.}, } @article {pmid41735773, year = {2026}, author = {Liu, H and Zhang, Z and Xu, Y and Wen, J}, title = {Soybean roots recruit plant-beneficial Pseudomonas via secreting 3,4-dihydroxybenzaldehyde.}, journal = {Plant physiology}, volume = {200}, number = {3}, pages = {}, doi = {10.1093/plphys/kiag075}, pmid = {41735773}, issn = {1532-2548}, support = {32071637//National Natural Science Foundation of China/ ; }, mesh = {*Pseudomonas/metabolism/physiology ; *Plant Roots/microbiology/metabolism ; *Glycine max/microbiology/metabolism/genetics ; Rhizosphere ; Phytophthora/physiology ; *Benzaldehydes/metabolism ; Plant Diseases/microbiology ; Disease Resistance ; Soil Microbiology ; Biofilms ; }, abstract = {Rhizosphere microbiota mediate plant defense against soil-borne diseases, yet the mechanisms by which resistant soybean cultivars assemble protective microbiomes remain poorly understood. Using metagenomics, metabolomics, in vitro assays, and genetic approaches, we compared near-isogenic lines (Williams82, resistant; Williams, susceptible) to dissect plant-metabolite-microbe interactions mediating Phytophthora root rot resistance. Transplanting rhizosphere soil from the resistant cultivar to susceptible plants significantly reduced Phytophthora root rot severity, correlating with Pseudomonas enrichment and accumulation of the key rhizosphere metabolite 3,4-dihydroxybenzaldehyde. We isolated a core beneficial strain, Pseudomonas parafulva ZY6, from the resistant rhizosphere. In vitro, 3,4-dihydroxybenzaldehyde treatment promoted ZY6's biofilm formation, motility, and growth, while inhibiting Phytophthora sojae at higher concentrations. Knockout and overexpression of GmTL29 via hairy root transformation altered rhizosphere levels of 3,4-dihydroxybenzaldehyde, which in turn modulated the colonization of ZY6, the abundance of P. sojae, and the relative abundance of beneficial taxa such as Pseudomonas. Exogenous 3,4-dihydroxybenzaldehyde (0.1 μmol g-1 soil) significantly reduced Phytophthora root rot disease index, increased rhizosphere bacterial diversity, and enriched Bacillus and Pseudomonas. Our study demonstrates that resistant soybeans shape a disease-suppressive rhizosphere, in which 3,4-dihydroxybenzaldehyde contributes as a prebiotic by selectively enriching beneficial microbes. These findings offer a metabolite-based strategy to engineer rhizosphere communities for sustainable soil-borne disease management.}, } @article {pmid41735826, year = {2026}, author = {Qian, Q and Li, N and Cha, S and Zheng, S and Li, W and Yin, G and Sun, M and Ye, P and Hu, M and Shi, R and Zhang, Y and Shen, W}, title = {Identification and functional characterization of Pseudomonas fluorescens as a novel intratumoral bacterium in colorectal cancer.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41735826}, issn = {1471-2180}, support = {82303959//The National Natural Science Foundation of China/ ; 81302162//National Natural Science Foundation of China Youth Foundation/ ; SSPW2022-KF06//Open Project of Zhenjiang Traditional Chinese Medicine Spleen and Stomach Disease Clinical Medicine Research Center/ ; GSP-ZXY20//Zhongda Hospital Affiliated to Southeast University, Jiangsu Province High-Level Hospital Construction Funds/ ; }, abstract = {UNLABELLED: Colorectal cancer (CRC) remains a major global health burden as one of the leading causes of cancer-related mortality. Recent research has highlighted the crucial role of gut microbiota in CRC development. Through high-throughput full-length 16 S rDNA sequencing of tumor and adjacent non-tumor tissues from 14 CRC patients, significant microbial differences were identified. At the phylum level, Firmicutes (52.59%), Bacteroidetes (18.51%), and Proteobacteria (14.89%) dominated both tissue types, while at the genus level, Bacteroides (8.02%) and Escherichia (4.50%) showed the highest abundance. Notably, 17 bacterial species exhibited differential abundance between tumor and normal tissues, with Anaerotignum faecicola and Pseudomonas fluorescens being significantly enriched in tumor tissues. Functional prediction analysis revealed the microbiota’s predominant involvement in carbohydrate metabolism, amino acid metabolism, and energy metabolism pathways. Subsequent validation in 20 additional patient samples confirmed P. fluorescens enrichment in tumor tissues, and in vitro experiments demonstrated its ability to promote CRC cell viability and proliferation. These findings provide valuable insights into CRC-associated microbial signatures and suggest P. fluorescens as a potential contributor to tumor progression, offering new directions for developing diagnostic markers and therapeutic interventions in CRC management.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04827-w.}, } @article {pmid41735848, year = {2026}, author = {Van Uffelen, A and Gobbo, A and Fraiture, MA and Posadas, A and Roosens, NHC and Marchal, K and De Keersmaecker, SCJ and Vanneste, K}, title = {Filtering for truth: high-precision taxonomic classification in nanopore shotgun metagenomics data through a KMA-based bioinformatic pipeline (KAPTAIN).}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41735848}, issn = {1471-2164}, abstract = {BACKGROUND: Shotgun metagenomics enables to study microbial communities without biases from culturing and isolation, but taxonomic classification to the species level remains challenging due to high false positive rates. Oxford Nanopore Technologies offers new opportunities to address these challenges by producing longer reads. However, different pipelines and tools use different methods to reduce false positives, resulting in variable outcomes with limited exploration of what works best in practice. Relative abundance filtering is often used to improve precision by removing false positives but reduces also recall by removing true positives. In this study, we optimized a broadly applicable taxonomic classification pipeline for long-read nanopore sequencing data that improves precision. The pipeline uses the tool KMA as the underlying classifier, followed by specific post-processing and optimization of filtering thresholds. Based on ten defined mock communities, different filter thresholds were evaluated, alongside the effect of the sequencing yield and the limit of detection (LOD).

RESULTS: Our optimized pipeline substantially outperformed default classifier settings, and the conventionally used relative abundance filtering. Classification accuracy improved with higher sequencing yields, requiring at least a post-filtering yield of 500M bases, and ideally 1000M bases, for reliable results. At yields above 1000M bases, median precision could be improved up to 95% while maintaining median recall at 91.62%. Further increasing median precision to 99% reduced recall to 79.08%. Similarly, higher sequencing yields lowered LOD. For yields above 1000 M bases, the limit of detection remained stable at 0.1% up to a median precision of 95%, while yields below 1000M showed an LOD of 1%. Validation on ten probiotic-derived mock communities confirmed the pipeline’s performance and general applicability.

CONCLUSION: Our optimized classification pipeline for nanopore sequencing data provides substantially higher precision compared to default approaches and is suitable for diverse metagenomic applications. We provide specific guidance on expected recall and precision values for minimum sequencing yields and their associated LODs. Our optimized pipeline, called KAPTAIN (KMA-bAsed Pipeline for meTAgenomic specIes ideNtification), is publicly available on GitHub (https://github.com/BioinformaticsPlatformWIV-ISP/KAPTAIN) and also the Galaxy instance of our institute (https://galaxy.sciensano.be) to be used by other scientists.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12668-0.}, } @article {pmid41736108, year = {2026}, author = {Bruni, A and Garofalo, E and Russo, A and Pelaia, C and Longhini, F and Bona, E and Aquila, I and Navalesi, P and Boscolo, A and , }, title = {Characterization of lung microbiota in pneumonia: a pilot study in ICU and non-ICU patients.}, journal = {Journal of anesthesia, analgesia and critical care}, volume = {6}, number = {1}, pages = {}, pmid = {41736108}, issn = {2731-3786}, abstract = {OBJECTIVE: To identify potential differences in lung microbiota according to clinical severity, age, and gender in pneumonia patients compared to controls.

DESIGN: Pilot study.

SETTING: Single center (Azienda Ospedaliera Universitaria Dulbecco, Catanzaro, Italy).

PATIENTS: Thirty-three individuals-11 ICU patients requiring invasive mechanical ventilation, 11 non-ICU patients, and 11 cadaver controls without lung disease.

INTERVENTIONS: Bronchoalveolar lavage sample collection and analysis via microbiological cultures and metagenomic sequencing.

MEASUREMENTS AND MAIN RESULTS: Bacteroidota and Verrucomicrobiota phyla were more abundant in older (≥65 years) ICU and non-ICU patients versus controls. Massilia timonae showed a significantly lower relative abundance at the group level in cases compared to controls, potentially increasing infection susceptibility. Higher microbiota diversity was observed in older patients.

CONCLUSIONS: Alterations in lung microbiota composition were observed in pneumonia patients, with differences that appeared more evident in older patients. Microbiota phenotyping may offer novel insights into pneumonia pathophysiology and pulmonary dysbiosis.}, } @article {pmid41309644, year = {2025}, author = {Qiu, D and Wang, Y and Xu, N and Chen, B and Zhu, Y and Zhang, Z and Zhang, Q and Lu, T and Dong, H and Shou, J and Qian, H}, title = {Global variation in plant-beneficial bacteria in soil under pesticide stress.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10685}, pmid = {41309644}, issn = {2041-1723}, support = {42377107//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22376187//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Soil Microbiology ; *Pesticides/toxicity ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Soil/chemistry ; *Soil Pollutants/toxicity ; Agriculture ; Metagenomics ; Crops, Agricultural/microbiology/growth & development ; }, abstract = {The presence of plant-beneficial bacteria (PBB) in soil significantly affects crop production. Excessive agrochemical use in intensive agriculture causes substantial soil residue accumulation, compromising soil health, crop quality, and human health. Understanding changes in beneficial bacteria under pesticide pollution is crucial for guiding sustainable agricultural practices and promoting soil health. We analyze metagenomic data from 1919 soil samples to identify 364 PBBs. We find higher PBB diversity in agricultural soils than in non-agricultural soils; however, pesticide pollution negatively affects the abundance of PBB, particularly those with plant growth-promoting traits. Pesticides not only reduce PBB diversity as individual factors, but they also exert synergistic negative effects with other anthropogenic factors, as determined by Hedges'd effect size and 95% confidence intervals, further accelerating the decline in PBB diversity. Increased pesticide risk also leads to a loss of functional gene diversity in PBB about carbon and nitrogen cycling within essential nutrient cycles, and a reduction in specific amino acid and vitamin synthesis. Artificial application of specific amino acids and vitamins could be an effective strategy to restore PBB in high-pesticide-risk soils. This study provides guidance for regulating pesticide use to mitigate their negative effects on soil PBB and suggests potential remedial measures.}, } @article {pmid41309890, year = {2025}, author = {Kuzmichenko, P and Fedorov, D and Galeeva, J and Postoeva, A and Krieger, E and Kudryavtsev, A and Pavlenko, A and Vvedensky, A and Starikova, E and Govorun, V and Ilina, E}, title = {Comparing alignment and de-novo approaches for gut microbiota metagenomic data analysis reveals differences in taxonomic resolution and novel functional insights.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {42423}, pmid = {41309890}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; 075-15-2025-530//Ministry of Science and Higher Education of the Russian Federation/ ; 100217/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Metagenomics/methods ; Feces/microbiology ; Metagenome ; Male ; *Bacteria/genetics/classification ; Female ; Adult ; }, abstract = {Microbiome annotation based on metagenomic data is primarily conducted using two global approaches: alignment-based approach (AL) and de novo approach (DN). This study aimed to evaluate the limitations of each approach, explore correlations between their results, and assess the equivalence of findings derived from different methodologies when analyzing the same dataset. Shotgun metagenomic sequencing data from 346 fecal samples, collected longitudinally within individuals in Arkhangelsk, Northwestern Russia, were analyzed. Each of the 173 participants provided two samples, one during 2015-2017 and another in 2022. The alterations in the microbiota associated with BMI served as a critical variable for facilitating the comparisons between the AL and DN. Exploratory analyses, including PERMANOVA, alpha diversity and beta diversity, revealed no significant differences between the two approaches. However, differential abundance analysis based on the AL yielded more statistically significant results, with the DN producing only a subset of these findings. An analysis of the metagenome-assembled genomes (MAGs) of bacteria that were differentially abundant revealed that one group of MAGs of Alistipes onderdonkii encodes the enzyme 2,5-diketo-D-gluconate reductase A. Using AL and DN together offers complementary functional insights, as the methods produce partially overlapping results. The novel enzyme finding suggests a potential role in metabolic pathways and underscores the value of integrative metagenomic analysis.}, } @article {pmid41310063, year = {2025}, author = {Plomp, N and Gacesa, R and Slager, J and Samsom, JN and Faber, KN and Jonkers, IH and Withoff, S and Wijmenga, C and Weersma, RK and Harmsen, HJM}, title = {Synergy between culturomics and metagenomics of health status-associated gut bacteria originating from non-IBD and IBD populations.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {45469}, pmid = {41310063}, issn = {2045-2322}, support = {LSHM18057-SGF//Samenwerkende Gezondheidsfondsen/ ; NWO Gravitation project 024.003.001//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 016.136.308//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; MLDS D16-14//Maag Lever Darm Stichting/ ; 101095470//HORIZON EUROPE Framework Programme/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Inflammatory Bowel Diseases/microbiology ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/isolation & purification/classification ; Feces/microbiology ; Female ; Male ; Adult ; Middle Aged ; Health Status ; }, abstract = {The bacteria in the human intestinal tract are important for health and associate with diseases, such as inflammatory bowel disease (IBD). Although metagenomic studies can identify certain bacteria or even specific strains and associate their presence or specific phenotypes with health or diseases, actual isolates for experimental validation of metagenomic associations are often lacking. Therefore, this study sets out to culture health- and IBD-associated bacteria from 32 fecal samples from 2 cohorts, for which extensive metadata is available. The cultivation of those samples resulted in 4,347 isolates, of which 1,362 isolates were obtained from IBD patients. Irrespective of health or IBD, Actinomycetota, Bacillota and Bacteroidota were the most represented phyla and members of 5 other phyla were less frequently isolated (Campylobacterota, Fusobacteriota, Pseudomonadota, Thermodesulfobacteriota and Verrucomicrobiota). Comparison of the genus richness between the culturomics approach and available metagenomic sequencing data of the corresponding participants revealed that both methods largely capture the same genera. Although not all genera could be identified in both methods, our results show that combining both methods has a synergetic effect, providing a higher identification rate. Furthermore, genetic analysis of 2 isolates of Bifidobacterium adolescentis strains shows that these isolates closely resembled the metagenome-assembled genome that was identified within the same participant. This showcases that it is possible to isolate specific strains that are important in the experimental validation of specific associations within a species. The culture collection that is presented in this study contains bacterial isolates that are strongly associated with health or IBD. Our results show that we are able to generate a valuable culture collection that opens a promising avenue for functional validation experiments of associations that are identified with metagenomic data.}, } @article {pmid41310455, year = {2025}, author = {Feng, Y and Yang, F and Klopatek, SC and Oltjen, JW and Yang, X}, title = {The fecal resistome of beef cattle from conventional grain-fed and grass-fed systems in the Western United States.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {3}, pmid = {41310455}, issn = {1471-2180}, support = {20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; }, mesh = {Animals ; Cattle/microbiology ; *Feces/microbiology ; *Animal Feed/analysis ; *Bacteria/genetics/drug effects/isolation & purification/classification ; *Poaceae ; *Edible Grain ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; United States ; Gastrointestinal Microbiome ; Metagenomics ; }, abstract = {Bacteria in the gastrointestinal tract of cattle may develop antimicrobial resistance (AMR) due to the use of antibiotics in live animals and can be excreted in feces, posing a risk of contamination. However, it remains unclear whether different beef production systems influence the levels of AMR in cattle feces. The objective of this study was to characterize and compare the fecal resistome of cattle raised in grass and grain-feeding systems in the Western United States. Fecal samples were collected from individual cattle at 14 months of age and two days before their respective harvest date. Groups included: (1) Conventional grain-fed (CON, n = 10), (2) Grass-fed for 20 months (20GF, n = 10), (3) Grass-fed and then grain-finished for 45 days (GR45, n = 10), (4) Grass-fed for 25 months (25GF, n = 10). According to metagenomic analysis, grass-feeding systems, particularly the one with extended grass-feeding, are associated with a less diverse resistome. The 25GF group had smaller (P < 0.05) Chao1 value than the other groups at the harvest time. Antimicrobial resistance genes (ARGs) richness and evenness were higher in CON and GR45 than in 20GF and 25GF (P < 0.05). Additionally, the resistome of GR45 and CON differed from 25GF (P = 0.018). In grass-feeding systems where antibiotics were not administered, animals' feces exhibited greater (P < 0.05) diversity in transferable biocide and metal resistant genes (BMRGs) compared with the grass-fed but grain-finished system. Greater ARG diversity in grain-finished feeding systems may enhance the spread of antimicrobial-resistant bacteria (ARB) during production, posing additional risks to food safety. Similarly, higher BMRG diversity observed in grass-fed systems may promote ARB spreading through co-selection mechanisms, which could also contribute to potential food safety concerns.}, } @article {pmid41310458, year = {2025}, author = {Li, Q and Chen, T and Hu, B and Guo, L and Dou, Z and Feng, W and Ning, X and Xiao, H and Liu, G}, title = {Clinical characteristics and management of Listeria monocytogenes meningitis in children beyond the neonatal stage: a 10 years retrospective study.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1708}, pmid = {41310458}, issn = {1471-2334}, abstract = {INTRODUCTION: The data of Listeria monocytogenes (LM) meningitis in children beyond the neonatal stage has been limited. We aimed to summarize the clinical characteristics, management, and risk factors of neurological complications in LM meningitis children beyond the neonatal stage. METHODS: We retrospectively reviewed LM meningitis cases from January 2013 to December 2022 at Beijing Children’s Hospital. Clinical characteristics, pathogen detection results and management were analyzed. RESULTS: There were 41 LM meningitis patients at our center, with a median age of 2.3 years (ranging from 6 months to 9 years). Most patients (97.6%) were immunocompetent. Fourteen patients (34.1%) had a history of suspected food contamination. The most common symptom was fever (100%), and 29.2% of patients presented with diarrhea in the early stages of the disease. About 61% of patients showed monocyte predominance in their cerebrospinal fluid (CSF). Thirteen patients (31.7%) experienced neurological complications. Multivariate analysis indicated that a diagnosis delay of more than one week and a CRP level of 50 mg/L or higher were significant risk factors for these neurological complications (p < 0.05). CSF culture rates were much higher before hospital admission (85.7%) compared to after (31.7%, p < 0.05). Metagenomic next-generation sequencing (mNGS) identified pathogens in 3 culture-negative cases. In total, 97.5% of patients received meropenem, either alone or with other antibiotics, and all children recorded a Glasgow Outcome Scale (GOS) score of 5. CONCLUSION: LM meningitis can affect immunocompetent children. Strengthening food hygiene and safety education is crucial to prevent LM infection. Penicillin or ampicillin are the preferred treatments, while meropenem may be considered as an alternative treatment.}, } @article {pmid41310465, year = {2025}, author = {Bae, J and Han, JW and Song, JY and Nam, SH and Sung, JS and Ko, HC and Kim, SH and Lee, YJ}, title = {Targeted elimination of latent endophytes improves cryopreservation success in in vitro grapevine (Vitis vinifera) cultures.}, journal = {BMC plant biology}, volume = {26}, number = {1}, pages = {20}, pmid = {41310465}, issn = {1471-2229}, support = {PJ017462//the National Institute of Agricultural Sciences, RDA, ROK/ ; }, mesh = {*Vitis/microbiology/drug effects ; *Endophytes/drug effects/genetics/physiology ; *Cryopreservation/methods ; Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; }, abstract = {BACKGROUND: Latent endophytic bacteria are common in grapevine in vitro cultures and, while not always causing visible culture decline, can negatively affect downstream applications such as cryopreservation by reducing post-thaw recovery. While antibiotic treatments are widely used for microbial control, their efficacy varies with bacterial species, plant genotype, and application conditions. Few studies have directly linked targeted elimination of identified endophytes with improved post-cryopreservation recovery.

RESULTS: In this study, we identified Leifsonia poae in 'Ruby Seedless' and Curtobacterium oceanosedimentum in 'Merlot' using 16 S rRNA sequencing. Species-specific antibiotic susceptibility testing revealed rifampicin (minimum bactericidal concentration, MBC = 31 µg mL⁻¹) as effective against L. poae, and cefotaxime (MBC = 1000 µg mL⁻¹) as effective against C. oceanosedimentum. In vitro application of these antibiotics eliminated the respective endophytes without significant phytotoxic effects at optimal concentrations. Amplicon-based 16 S metagenomic profiling confirmed complete removal of the target bacteria and revealed substantial shifts in community composition, with reduced abundance of dominant taxa but maintenance of overall endophytic diversity. Cryopreservation experiments in 'Ruby Seedless' showed that removal of endophytes increased post-thaw survival from 31.8 to 70.9% and eliminated variability in regrowth across replicates.

CONCLUSIONS: This study demonstrates that targeted antibiotic elimination of dominant endophytes can restructure the in vitro microbial community and substantially improve cryopreservation outcomes in grapevine. The approach offers a reproducible sanitation strategy for clonal crops vulnerable to endophyte-related culture failures and can be readily adapted for germplasm conservation programs.}, } @article {pmid41310694, year = {2025}, author = {Liu, P and Deng, Z and Wang, Y and Wu, F and Peng, J and Huang, P and Wang, Y and Lao, J}, title = {Application of Probe-Capture metagenomics in rabies diagnosis.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {406}, pmid = {41310694}, issn = {1743-422X}, support = {82460480//National Natural Science Foundation of China/ ; 20223638//Qinzhou Scientific Research and Technology Development Program/ ; 2024GXNSFAA010067//Guangxi Natural Science Foundation/ ; }, mesh = {Animals ; Humans ; *Metagenomics/methods ; *Molecular Diagnostic Techniques/methods ; *Rabies/diagnosis/virology ; *Rabies virus/genetics/isolation & purification ; Retrospective Studies ; }, abstract = {BACKGROUND: Rabies, a lethal viral encephalitis caused by Rabies virus (RabV), is transmitted via bites, scratches, or mucosal contact with infected animals, as well as through inhalation of aerosolized particles, ingestion of contaminated raw animal products, or transplantation of infected organs. It's near-universal fatality, diverse transmission routes, and marked clinical variability significantly impede timely diagnosis, highlighting the demand for a rapid and precise diagnostic approach.

METHODS: Single-center retrospective case series.

RESULTS: This series reported three rabies cases admitted to the First People's Hospital of Qinzhou: one without identifiable exposure and two with confirmed exposure histories. Clinical presentations were highly variable and diagnostically misleading. Application of Probe-Capture Metagenomics (pc-mNGS) to cerebrospinal fluid and blood samples enabled direct identification of RabV and concurrent detection of coexisting pathogens.

CONCLUSION: pc-mNGS demonstrates potential as a rapid, economical diagnostic tool capable of detecting RabV in specimens with low viral loads-such as blood and cerebrospinal fluid-from both exposed and unexposed individuals. Simultaneous identification of additional pathogens further supports its diagnostic utility.}, } @article {pmid41310780, year = {2025}, author = {Liu, Y and Brinkhoff, T and Simon, M}, title = {Ecogenomics and functional biogeography of the Roseobacter group in the global oceans based on 653 MAGs and SAGs.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {247}, pmid = {41310780}, issn = {2049-2618}, support = {TRR51//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Oceans and Seas ; *Roseobacter/classification/genetics ; Seawater/microbiology ; Biodiversity ; *Phylogeography ; Genome, Bacterial ; }, abstract = {BACKGROUND: The Roseobacter group is a major component of prokaryotic communities in the global oceans. Information on this group is based predominantly on isolates and their genomic features and on the 16S rRNA gene. Assessments of prokaryotic communities in the pelagic of the global oceans indicated an unveiled diversity of this group but studies of the diversity and global biogeography of the entire group are still missing. Hence, we aimed at a comprehensive assessment of the Roseobacter group in the global oceans on the basis of MAGs and SAGs.

RESULTS: The obtained 610 MAGs and 43 SAGs of high quality were subjected to in-depth analyses of their phylogeny, genomic and functional features. The recruitment locations range from the tropics to polar regions, include all major ocean basins. The phylogenetic analysis delineated the known RCA cluster and five pelagic clusters, two of which were completely novel: TCR (Temperate and Cold Roseobacter), AAPR (Arctic-Atlantic-Pacific Roseobacter, novel), AAR (Arctic-Atlantic Roseobacter, novel), COR (Central Oceanic Roseobacter), LUX (Cand. Luxescamonaceae) cluster. These clusters account for ~ 70% of all Roseobacter MAGs and SAGs in the epipelagic. The TCR, AAPR, AAR, and LUX clusters are among the most deeply branching lineages of the Roseobacter group. These clusters and several sublineages of the RCA and COR clusters exhibit distinct features of genome streamlining, i.e. genome sizes of < 2.9 Mbp and G + C contents of < 40%. The clusters exhibit differences in their functional features and also compared to other lineages of the Roseobacter group. Proteorhodopsin is encoded in most species of the AAPR, AAR, TCR, and RCA clusters and in a few species of the COR cluster, whereas in most species of the latter, the LUX cluster and in a few species of the RCA cluster aerobic anoxygenic photosynthesis is encoded. Biogeographic assessments showed that the AAPR, AAR, TCR and RCA clusters constitute the Roseobacter group in the temperate to polar regions to great extent whereas the COR and LUX clusters in the tropics and subtropics.

CONCLUSIONS: Our comprehensive analyses shed new light on the diversification, genomic features, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. Video Abstract.}, } @article {pmid41310797, year = {2025}, author = {Du, H and Lin, B and Zhu, Y and Hao, X and Tang, M and Wu, W and Wang, D and Yang, Y and Liang, Y and Tang, W and Xu, H and Li, J and Gao, F and Du, X}, title = {Exploring the mechanisms of protective effect of high-energy X-ray FLASH radiotherapy on intestine through multi omics analysis.}, journal = {Radiation oncology (London, England)}, volume = {20}, number = {1}, pages = {179}, pmid = {41310797}, issn = {1748-717X}, support = {2025ZNSFSC0555//Sichuan Science and Technology Program/ ; U2330122//Projects of National Natural Science Foundation/ ; 2023ZYDF073//Minyang Science and Technology Program/ ; miancaijian2022-186//Mianyang Municipal Finance Bureau/ ; }, mesh = {Animals ; Mice ; Female ; Mice, Inbred C57BL ; *Colonic Neoplasms/radiotherapy/pathology ; *Intestines/radiation effects ; X-Rays ; Metabolomics/methods ; Gastrointestinal Microbiome/radiation effects ; Multiomics ; }, abstract = {BACKGROUND: The aim of this study is to investigate the potential mechanisms underlying the protective effects of high-energy X-ray FLASH radiotherapy (FLASH-RT) on intestine through multi-omics analysis.

METHODS: This study utilized syngeneic colon carcinoma mouse models of CT26 and MC38 to evaluate the therapeutic efficacy of FLASH-RT versus conventional dose rate radiotherapy (CONV-RT) by monitoring survival, tumor size, and body weight. Furthermore, healthy C57BL/6 female mice received whole-abdominal irradiation with either FLASH-RT, CONV-RT, or sham irradiation to compare differences in normal tissue protection. 72 h post-irradiation, intestinal contents from mice were collected for metagenomic analysis, and intestinal tissue was harvested for non-targeted metabolic and single-cell sequencing analyses.

RESULTS: In CT26 and MC38 models, both CONV-RT and FLASH-RT have demonstrated similar anti-tumor efficacy. Compared with CONV-RT, whole-abdominal FLASH-RT significantly alleviated acute intestinal injury in mice, as evidenced by better preservation of crypt numbers and villus architecture in the FLASH group. Metagenomic analysis revealed that the relative abundance of the gut-protective bacterium Ligilactobacillus ruminis was significantly higher in the FLASH group than in the CONVgroup. Non-targeted metabolomic profiling identified 34 differential metabolites, of which 29 were upregulated and 5 were downregulated in the FLASH group. Notably, the abundance of 2-hydroxyglutarate, a metabolite associated with the butyrate metabolism pathway, was significantly elevated in the FLASH group compared with the CONV group (p < 0.05). Single-cell sequencing data revealed notable differences in cell distribution and proportions between the groups, with a higher proportion of fibroblasts, proliferative cells, macrophages, and CD4 + T cells in the FLASH group compared to the CONV and control groups. Immunofluorescence analysis revealed a significantly greater number of Lgr5⁺ intestinal stem cells in the FLASH group compared to the CONV group. Conversely, immunohistochemical analysis demonstrated stronger p50/p65 staining intensity in the CONV group relative to the FLASH group.

CONCLUSIONS: This study confirms that FLASH-RT, compared to CONV-RT, maintains equivalent antitumor efficacy while mitigating damage to normal intestinal tissues. Moreover, it preliminarily reveals that the protective mechanism of FLASH-RT is multifaceted, involving remodeling of the microbiota-metabolite axis, attenuation of inflammatory responses, and enhanced preservation of stem cells.}, } @article {pmid41310806, year = {2025}, author = {Utkina, I and Fan, Y and Willing, BP and Parkinson, J}, title = {Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {248}, pmid = {41310806}, issn = {2049-2618}, support = {RGPIN-2019-06852//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Metagenome ; *Bacteroides/metabolism/genetics/classification ; *Bacteria/classification/metabolism/genetics ; Fatty Acids, Volatile/metabolism ; Escherichia coli/metabolism/genetics ; }, abstract = {BACKGROUND: Members of the Bacteroidales, particularly Bacteroides species, with their ability to degrade dietary fibers and liberate otherwise unavailable substrates, exert a substantial influence on the microbiome of the lower intestine. However, our understanding of how this influence translates to the metabolic interactions that support community structure remains limited. In this study, we apply constraint-based modeling to investigate metabolic interactions in chicken cecal communities categorized by the presence or absence of Bacteroides.

RESULTS: From metagenomic datasets previously generated from 33 chicken ceca, we constructed 237 metagenome-assembled genomes. Metabolic modeling of communities built from these genomes generated profiles of short-chain fatty acids largely consistent with experimental assays and confirmed the role of B. fragilis as a metabolic hub, central to the production of metabolites consumed by other taxa. In its absence, communities undergo significant functional reconfiguration, with metabolic roles typically fulfilled by B. fragilis assumed by multiple taxa. Beyond B. fragilis, we found Escherichia coli and Lactobacillus crispatus also mediate influential metabolic roles, which vary in the presence or absence of B. fragilis. Notably, the microbiome's compensatory adaptations in the absence of B. fragilis produced metabolic alterations resembling those previously associated with inflammatory bowel disease in humans, including energy deficiency, increased lactate production, and altered amino acid metabolism.

CONCLUSIONS: This work demonstrates the potential of using the chicken cecal microbiome as a model system for investigating the complex metabolic interactions and key contributions that drive community dynamics in the gut. Our model-based predictions offer insights into how keystone taxa like B. fragilis may shape the metabolic landscape and functional organization of microbial communities. The observed metabolic adaptations in the absence of B. fragilis share metabolic similarities with profiles seen in dysbiotic states in humans and underscore the translational relevance of these insights for understanding gut health across different host systems. Video Abstract.}, } @article {pmid41311042, year = {2025}, author = {Choi, JH and Oh, S and Yi, MH and Kang, D and Choi, DY and Chavarria, X and Shatta, A and Cho, YH and Choe, S and Lee, SH and Kim, JY}, title = {Detection of intestinal parasites in leopard cat fecal samples using shotgun metagenomics.}, journal = {Parasites, hosts and diseases}, volume = {63}, number = {4}, pages = {349-353}, pmid = {41311042}, issn = {2982-6799}, support = {RS-2024-00456300//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; //Korea Health Industry Development Institute/ ; RS-2024-00406488//Ministry of Health and Welfare/ ; RS-2023-KH139971//Ministry of Health and Welfare/ ; }, mesh = {Animals ; *Feces/parasitology ; *Metagenomics/methods ; *Intestinal Diseases, Parasitic/veterinary/parasitology/diagnosis ; RNA, Ribosomal, 18S/genetics ; *Panthera/parasitology ; *Parasites/isolation & purification/genetics/classification ; *Felidae/parasitology ; Cats ; }, abstract = {The leopard cat (Prionailurus bengalensis) is a wild felid species that serves as a reservoir of zoonotic parasites. In this study, we investigated intestinal parasite taxa by reanalyzing previously published shotgun metagenomic sequencing data from fecal samples of wild leopard cats using a custom 18S rRNA gene reference database constructed from the NCBI nucleotide database. Among 11 metagenomic samples, 5 parasite species were identified: Toxoplasma gondii, Clonorchis sinensis, Strongyloides planiceps, Cylicospirura petrowi, and Pharyngostomum cordatum. These findings demonstrate that shotgun metagenomic analysis of fecal samples can be a useful tool for monitoring zoonotic parasite infections in this species and for investigating parasite life cycles. However, this approach is limited by its dependence on existing reference databases and requires experimental validation of the findings.}, } @article {pmid41311478, year = {2025}, author = {Zhong, Y and Li, R and E, J and Chi, H and Cao, N and Bai, Z and Du, X and Wang, L}, title = {Effects of maize straw and corncob return on the soil quality and on the soil microbial structures and functions.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1675172}, pmid = {41311478}, issn = {1664-302X}, abstract = {Straw return is an effective agricultural strategy for incorporating organic carbon into soil organic matter pools through microbial decomposition. This process modifies soil physicochemical properties, thereby altering microbial habitats and resource availability, which can influence the structure and function of soil microbial communities. However, the changes of soil physicochemical properties and microbial communities under different straw incorporation forms remain poorly understood. And how these straw return materials alter soil physicochemical properties and microbial communities within a single cycle. In this study, we conducted straw returning experiments in a maize-producing region of Jilin Province, China, comparing the impact of two distinct maize-derived residues (crushed maize straw and crushed corncob) on soil quality and microbial communities. Our results demonstrated that corncob return more effectively improved key soil physicochemical properties compared to maize straw return. While neither residue significantly alters microbial alpha diversity, both induced shifts in beta diversity. We identified distinct correlations between dominant microbial taxa and key soil physicochemical parameters. Furthermore, KEGG and GO analyses revealed that both of the residues altered microbial functional hierarchies, with corncob return inducing more pronounced changes than maize straw return. These findings provide a mechanistic basis for optimizing straw management strategies to enhance microbial-mediated soil fertility.}, } @article {pmid41311484, year = {2025}, author = {Xu, J and Yao, Y and Pan, L and Zhang, N and Li, D and Chen, X}, title = {Pea-cucumber crop rotation suppresses Fusarium pathogens by reshaping soil microbial communities and enhancing nutrient availability.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1697343}, pmid = {41311484}, issn = {1664-302X}, abstract = {INTRODUCTION: Pea-cucumber rotation combined with straw return as green manure is an environmentally friendly management strategy to suppress cucumber (Cucumis sativus L.) Fusarium wilt (FW) and alleviate continuous cropping obstacles.

METHODS: We evaluated the variations in soil microbial compositions and nutrient levels between long-term cucumber monocropping and pea-cucumber rotation patterns via metagenomic sequencing and determination of soil properties.

RESULTS: The study found that the bacterial communities exhibited marked diversity, whereas the α-diversity of fungal communities was significantly reduced. Based on the relative abundance of differential fungi and bacteria at the genus level, the genus Bacillus showed the highest abundance, with a two-fold increase, whereas Fusarium species exhibited a 4.9-fold reduction following the pea-cucumber rotation. Additionally, the contents of available nitrogen, potassium, and phosphorus in the soil increased by more than 1.3-fold after the rotation. Correlation analysis revealed that the genus Bacillus and available potassium were significantly and negatively correlated with Fusarium pathogens. Notably, the isolated B. pumilus and B. safensis strains significantly suppressed the growth of cucumber FW pathogens.

DISCUSSION: These findings provide valuable insights for optimizing the combination of soil Bacillus populations and nutrient availability to maintain soil ecosystem health and improve cucumber growth and yield.}, } @article {pmid41311499, year = {2025}, author = {Wang, J and Su, W and Chen, Q and Zhou, J and Wang, X and Jiang, R and Li, J and Xing, P}, title = {Microbiome-metabolome dysbiosis of bronchoalveolar lavage fluid of lung cancer patients.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1669172}, pmid = {41311499}, issn = {1664-302X}, abstract = {BACKGROUND: Recent studies indicate that microorganisms significantly influence lung cancer pathogenesis. This research explores the variations in microbiota and metabolites in the lower respiratory tract between lung cancer patients and individuals with benign pulmonary lesions to identify potential diagnostic biomarkers.

METHODS: Two hundred eight patients undergoing bronchoscopy at Tianjin Cancer Institute & Hospital and Tianjin Chest Hospital from October 2022 to October 2023 were screened. Ninety-five bronchoalveolar lavage fluid (BALF) was collected for metagenomic sequencing and untargeted metabolomic analysis. Comparisons of microbial diversity, taxonomic composition, and metabolite profiles were conducted between groups with lung cancer and benign lung conditions.

RESULTS: The cohort comprised 70 patients with lung cancer and 25 with benign lung lesions. Patients with lung cancer showed significantly reduced β-diversity (p = 0.005). Predominant microbes in lung cancer cases included Streptococcus, Haemophilus influenzae, and Veillonella parvula. A microbial-based diagnostic model differentiated lung cancer from benign lesions with an AUC of 0.931 (95%CI: 0.916-0.946). Metabolites increased in lung cancer were Citric acid, N-Acetylneuraminic acid, Oxoglutaric acid, and Neopterin, whereas L-Tryptophan, Uridine, 3-Hydroxybutyric acid decreased. The KEGG pathways suggest a significant link between microbial presence and both tumorigenesis and progression.

CONCLUSION: Specific microbial patterns in the lower respiratory tract of lung cancer patients could assist in the auxiliary diagnosis of the disease. The notably altered microorganisms and metabolites in the BALF from lung cancer patients, as opposed to those with benign conditions, correlate with cancer initiation and advancement.}, } @article {pmid41311501, year = {2025}, author = {Wu, Q and Hu, S and Wang, Y and Wu, Y and Zhao, Y and Niu, L and Zhou, X and Shen, L and Liu, Y and Chen, Y and Gan, M and Zhu, L}, title = {Age-related gut microbiota succession in Neijiang pigs: insights for precision feeding and productivity.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1698169}, pmid = {41311501}, issn = {1664-302X}, abstract = {OBJECTIVE: To characterize age-related gut microbiota succession in Neijiang pigs and translate these dynamics into actionable insights for precision feeding and productivity improvement.

METHODS: Growth data from 0 to 180 days (n = 16, 780 weight records) were fitted with three non-linear models to determine the optimal growth curve and partition physiological stages. Fresh feces were collected at 25, 70, 110, and 150 days (n = 6/stage). 16S rRNA V3-V4 amplicon sequencing was used to profile microbiota composition and diversity; PICRUSt2 was employed to predict metagenome functions against the KEGG database.

RESULTS: The Gompertz model best described growth (R [2] = 0.996) with an inflection point at 84.2 days (25.9 kg). Microbial alpha-diversity (Shannon, Chao1) increased with age and plateaued after 110 days. Firmicutes and Bacteroidota dominated (>90% relative abundance), whereas Spirochaetota and Euryarchaeota expanded significantly in finishing pigs. LEfSe identified 45 stage-specific biomarkers: Prevotella_9, Collinsella and Blautia characterized suckling-weaning stages; Faecalibacterium and Clostridium_sensu_stricto_1 peaked at 70 days; Lactobacillus was dominant at 110 days; Treponema, Streptococcus and Bacteroides defined the 150-day microbiome. Functional prediction revealed a metabolic shift from basal biosynthesis and DNA repair in early life toward enhanced ABC transporters, bacterial motility proteins, oxidative phosphorylation and methane metabolism in finishing pigs.

CONCLUSION: Our data provide a temporal blueprint of gut microbiota maturation that mirrors host nutrient requirements across growth phases. These microbial indicators and functional signatures can guide stage-specific dietary formulations and microbiota-targeted interventions to improve feed efficiency, reduce environmental emissions and enhance the productivity of indigenous pig breeds.}, } @article {pmid41311850, year = {2025}, author = {Aditya, C and Bukke, SPN and Anitha, K and Meeraraje, P and Goruntla, N and Yadesa, TM and Onohuean, H}, title = {A comprehensive review on diabetic foot ulcer addressing vascular insufficiency, impaired immune response, and delayed wound healing mechanisms.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1622055}, pmid = {41311850}, issn = {1663-9812}, abstract = {Diabetic foot ulcers (DFUs) continue to represent one of the most significant and costly complications related to diabetes mellitus, posing serious challenges to healthcare systems and resulting in considerable morbidity rates. This narrative review explores the complex pathophysiology of DFUs, focusing on the interplay between peripheral neuropathy, vascular insufficiency, and a weakened immune response, all of which contribute to delayed wound healing. Neuropathy leads to a loss of protective sensation, causing unnoticed repetitive injuries, while both microvascular and macrovascular complications reduce tissue perfusion and hinder angiogenesis. Additionally, immune dysfunction and exaggerated inflammatory responses raise the occurrence of infection and negatively affect the healing process. The clinical manifestation, progression, and key risk factors of DFUs were discussed in this review, emphasizing the importance of early detection, careful foot care, and routine screening in individuals who are at risk. Numerous therapeutic approaches are reviewed, including wound debridement, sophisticated wound dressings, offloading techniques, glycemic control, and adjuvant therapies such as growth factor administration, hyperbaric oxygen therapy, and negative pressure wound therapy. For optimal results, a multidisciplinary team combining of vascular surgeons, podiatrists, endocrinologists, and wound care specialists was included. The analysis also points out that promising advancements in bioengineered skin substitutes, intelligent dressings, and regenerative medicine hold promise for the treatment of DFU in the future. Self-monitoring, appropriate footwear, and patient education are all important components of prevention, which remains a fundamental strategy. In the clinical management of DFUs, this narrative review incorporates the most recent research and highlights the value of proactive, customized, and multidisciplinary approaches.}, } @article {pmid41312164, year = {2025}, author = {Onohuean, H and Nnolum-Orji, NF and Naik Bukke, SP and Abass, KS and Alagbonsi, AI and Choonara, YE}, title = {Non-alcoholic fatty pancreas disease (NAFPD) as a pre-neoplastic niche: Metabolic and inflammatory Gateways to pancreatic ductal adenocarcinoma.}, journal = {Journal of clinical & translational endocrinology}, volume = {42}, number = {}, pages = {100424}, pmid = {41312164}, issn = {2214-6237}, abstract = {Non-alcoholic fatty pancreas disease (NAFPD), marked by ectopic triglyceride accumulation in the exocrine pancreas, is increasingly observed yet its recognition as a cancer-predisposing condition remains limited. We synthesize evidence supporting NAFPD as an early and modifiable niche for pancreatic ductal adenocarcinoma (PDAC), using a PRISMA-ScR-guided framework. The findings were synthesized into three domains: epidemiological risk, metabolic-inflammatory signaling, and immune-stromal remodeling. Mechanisms include palmitate-induced ER stress, ROS-driven NLRP3-IL-1β and STAT5 signaling, and KRAS^G12D-mediated lipotoxicity. Lipid-laden stellate cells promote fibrosis, immunosuppression, and epithelial-mesenchymal transition. NAFPD may represent an early, modifiable PDAC niche, warranting further imaging-omic studies and targeted prevention trials.}, } @article {pmid41312195, year = {2025}, author = {Chen, J and Gong, G and Huang, S and Chen, Y and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ji, L and Zhang, W}, title = {Gut Virome of Tibetan Pigs Reveals the Diversity, Composition, and Distribution of Potential Novel Viruses/Variants.}, journal = {Transboundary and emerging diseases}, volume = {2025}, number = {}, pages = {5191656}, pmid = {41312195}, issn = {1865-1682}, mesh = {Animals ; Swine ; Tibet/epidemiology ; *Virome ; Phylogeny ; *Swine Diseases/virology/epidemiology ; Feces/virology ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; Genetic Variation ; *Gastrointestinal Microbiome ; }, abstract = {As a local breed adapted to the extreme environment of the Tibetan Plateau, Tibetan pigs have not yet been systematically characterized in terms of their gut viral communities. In this study, we applied viral metagenomics to sequence fecal samples from 191 Tibetan pigs (including both healthy and diarrheal individuals) across four farms in Nyingchi, Tibet, aiming to reveal the diversity, composition, and distribution of gut viral communities in Tibetan pigs living at high altitudes. A total of nearly 120 million high-quality viral sequence reads were obtained, which were annotated into 16 viral families. The viral community was predominantly dominated by Microviridae, but its composition varied across different farms and health statuses. Phylogenetic analysis identified numerous virus sequences associated with pigs, including RNA viruses (such as Astroviridae (n = 7), Caliciviridae (n = 6), Picornaviridae (n = 15), etc.) and DNA viruses (such as Circoviridae (n = 3), Genomoviridae (n = 4), Smacoviridae (n = 41), Parvoviridae (n = 11), etc.). Notably, the study found multiple viral sequences exhibiting genetic differences from known strains, suggesting the potential presence of novel viruses or variants. For instance, a papain-like protease (PLP) insertion sequence, identified to have high sequence identity with Torovirus (ToV), was found in six Enterovirus G (EV-G) strains, indicating a cross-family genetic recombination event. This study systematically outlines the viral metagenomic profile of gut viral communities in Tibetan pigs at high altitudes, revealing their unique viral diversity and complex community structure. The results suggest that the gut viral community of Tibetan pigs consists of host-associated viruses, bacteriophages, and potentially viruses originating from the environment or diet, with its composition influenced by farming conditions and host health status. These findings provide an important data foundation for understanding the interactions between viruses, hosts, and the environment in unique ecological settings and offer new insights into the health management and virology research of Tibetan pigs.}, } @article {pmid41312302, year = {2025}, author = {Steindler, L and Maldonado, M and Pita, L and Riesgo, A and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The chromosomal genome sequence of the stone sponge Petrosia ficiformis (Poiret, 1789) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {450}, pmid = {41312302}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Petrosia ficiformis (stone sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence is 191.3 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.89 kilobases in length. Gene annotation of the host organism assembly identified 18,339 protein coding genes. The metagenome of the specimen was also assembled, and 112 binned bacterial genomes were identified, including 57 high-quality MAGs. Besides MAGs characteristic of HMA sponge symbionts (i.e., Chloroflexota, Acidobacteriota), the P. ficiformis specific symbiont Candidatus Synechococcus feldmanni (formerly Aphanocapsa feldmanni (Cyanobacteriota) was recovered, as well as notably MAGs of several candidate phyla (Candidatus Latescibacteria, Poribacteria, Tectomicrobia, Dadabacteria, Kapabacteria and Binatia).}, } @article {pmid41312456, year = {2025}, author = {Huang, W and Ran, X and Zhang, Z and Yang, L and Yin, J and Lv, S and Liu, G and Pei, Y}, title = {Multiple brain abscesses caused by Nocardia asiatica co-infection with Torque teno virus in an "immunocompetent" patient: a rare case report and literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1661345}, pmid = {41312456}, issn = {2296-858X}, abstract = {Brain abscess is a suppurative infection of brain tissue caused by one or more pathogens under specific susceptible conditions and is associated with a high clinical fatality rate. Beyond surgical intervention, the identification of pathogens is key to clinical antimicrobial therapy, yet this remains a challenge. Nocardia is a ubiquitous bacterium that typically manifests as an opportunistic infection, primarily affecting immunocompromised individuals. Pulmonary involvement, characterized by suppurative inflammation, commonly occurs following inhalation, with subsequent hematogenous dissemination potentially leading to widespread infection. To our knowledge, central nervous system (CNS) infection by Nocardia asiatica (N. asiatica) resulting in brain abscess has hitherto rarely been reported. We present a rare case of multiple brain abscesses caused by N. asiatica co-infection with Torque teno virus (TTV) in an immunocompetent patient with suspected multiple organ involvement. The patient was admitted to our hospital, presenting with a headache, and imaging revealed brain abscess-like lesions. A robot-assisted stereotactic puncture and drainage were used for abscess removal. N. asiatica and TTV were identified by metagenomic next-generation sequencing (mNGS) of the brain abscess aspirate, with N. asiatica subsequently confirmed by mass spectrometry of the cultured organism. A disseminated Nocardia infection was suspected based on the patient's skin trauma history, pulmonary inflammatory changes, and imaging findings (liver cysts, subcutaneous nodules). However, etiological confirmation was not obtained prior to his death. While this is not the first reported instance of Nocardia and TTV co-infection in brain abscesses, our case is notable for its occurrence in an immunocompetent patient. This report highlights the significance and value of TTV in the context of brain abscesses and warrants a re-evaluation of Nocardia and TTV co-infection. Given that the diagnosis of intracranial infection depends on the detection of pathogens, we advocate for the routine and early implementation of mNGS testing in patients with brain abscesses. Moreover, systemic nutritional support and immunomodulatory therapies should be considered in the early stage of treatment for complex cases. Earlier diagnosis and treatment in this case might have altered the patient's outcome.}, } @article {pmid41312645, year = {2026}, author = {Fiamenghi, MB and Camargo, AP and Chasapi, IN and Baltoumas, FA and Roux, S and Egorov, AA and Aplakidou, E and Ndela, EO and Vasquez, YM and Chen, IA and Palaniappan, K and Reddy, TBK and Mukherjee, S and Ivanova, NN and Schulz, F and Woyke, T and Eloe-Fadrosh, EA and Pavlopoulos, GA and Kyrpides, NC}, title = {Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D801-D812}, pmid = {41312645}, issn = {1362-4962}, support = {FWP 70880//BER's Genomic Sciences Program/ ; 1U01DE034196-01/GF/NIH HHS/United States ; //Royal Physiographic Society of Lund/ ; 45379//Natural Sciences, Medicine and Technology/ ; //Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//US DOE/ ; U01 DE034196/DE/NIDCR NIH HHS/United States ; }, mesh = {*Genome, Viral ; *Viruses/genetics/classification ; *Databases, Genetic ; Metagenomics/methods ; Phylogeny ; Biodiversity ; Genetic Variation ; Metagenome ; Software ; }, abstract = {Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.}, } @article {pmid41312680, year = {2026}, author = {Koike, Y and Morisaki, H and Motooka, D and Matsumoto, M and Takenaka, M and Murota, H}, title = {Postauricular Skin Mycobiome Profiles in Atopic Dermatitis Treated With Dupilumab or Cyclosporine A: A Descriptive Case Series.}, journal = {The Journal of dermatology}, volume = {53}, number = {3}, pages = {430-436}, pmid = {41312680}, issn = {1346-8138}, support = {//Leading Medical Research Core Unit, Life Science Innovation, Nagasaki University Graduate School of Biomedical Sciences/ ; 25K11567//Japan Society for the Promotion of Science/ ; JP256f0137009//Japan Agency for Medical Research and Development/ ; }, mesh = {Humans ; *Dermatitis, Atopic/drug therapy/microbiology/immunology ; *Cyclosporine/therapeutic use/pharmacology ; Male ; Female ; Adult ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Skin/microbiology/drug effects/immunology ; Middle Aged ; *Mycobiome/drug effects ; Malassezia/isolation & purification ; Young Adult ; Calcineurin Inhibitors/therapeutic use/pharmacology ; DNA, Fungal/isolation & purification ; Treatment Outcome ; }, abstract = {Atopic dermatitis (AD) essentially exhibits dysbiosis of skin fungal microbiome, mycobiome, characterized by depletion of Malassezia. The effects of recent systemic therapies for AD on skin mycobiome were not understood enough. We examined changes of skin mycobiome before and after systemic treatments with anti-IL-4Rα antibody (dupilumab: DUP) and calcineurin inhibitor (cyclosporine, CyA). Swab samples from postauricular areas in 19 AD patients treated with dupilumab (n = 13) and cyclosporine (n = 6) were collected before and 4-8 weeks after starting each treatment. Fungal DNA was amplified from the samples and sequenced with ITS1 metagenomic analysis, and taxonomic classification was performed. Fungi belonging to total 89 genera were detected. The share of the fungus was most occupied by Malassezia (81.3%), followed by Aspergillus (3.7%), and Trametes (1.1%) before DUP and CyA treatment, and occupied by Malassezia (87.3%), followed by Aspergillus (1.9%), and Candida (1.7%) after treatment. Three AD patients whose ratio of Malassezia in the skin mycobiome was under 50%, showed an exploratory increase of Malassezia after treatments (before 17.3%, after 67%). Analysis of the Malassezia species revealed an increase in M. restricta (before 70.5%, after 79.5%) and a decrease in M. globosa (before 23.9%, after 16.1%). No consistent patterns distinguishing DUP and CyA were observed. Systemic treatment with DUP and CyA was associated with shifts toward higher Malassezia abundance and modulation between M. restricta and M. globosa. These findings are exploratory and require validation in larger controlled studies.}, } @article {pmid41312992, year = {2026}, author = {D'Amico González, G and Rodríguez, MM and Penzotti, P and Brunetti, F and Ghiglione, B and Moe, LA and Centrón, D and Gutkind, G and Gao, L and Haider, S and Powers, RA and Klinke, S and Power, P}, title = {Proposal of metagenomic-origin LRA-5 as a precursor of active β-lactamases through Tyr69Gln and Val166Glu amino acid substitutions: a functional and structural analysis.}, journal = {Antimicrobial agents and chemotherapy}, volume = {70}, number = {1}, pages = {e0067525}, pmid = {41312992}, issn = {1098-6596}, support = {R01 AI160371/AI/NIAID NIH HHS/United States ; 2023//Universidad de Buenos Aires/ ; 11220200100191CO//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; R01AI160371/NH/NIH HHS/United States ; PICT-2021-I-A-0771//Agencia Nacional de Promoción Científica y Tecnológica/ ; }, mesh = {*beta-Lactamases/genetics/metabolism/chemistry ; Amino Acid Substitution ; Escherichia coli/genetics/drug effects ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Kinetics ; Crystallography, X-Ray ; Amino Acid Sequence ; Soil Microbiology ; beta-Lactams/pharmacology ; }, abstract = {Wild-type LRA-5, recovered from Alaskan soil samples, shares no more than 33% amino acid sequence identity with enzymes from pathogens like PER β-lactamases. Recombinant E. coli expressing wild-type LRA-5 and its engineered variants LRA-5[Y69Q] and LRA-5[V166E] showed MIC values equivalent to control strains. However, LRA-5[Y69Q/V166E] displayed MICs above the resistant breakpoint for some β-lactams. Kinetic parameters correlated with the MICs, showing that the catalytic efficiency of LRA-5[Y69Q/V166E] was comparable to those from class A β-lactamases, such as CTX-M-15, PER-2, and KPC-2. LRA-5[Y69Q/V166E] exhibited kcat/Km values up to 11,000-fold higher compared to wild-type LRA-5, which is associated with the presence of Glu166. The X-ray crystallographic structure of wild-type LRA-5 (1.80 Å; PDB 8EO5) shows that the lack of both Glu166 and a deacylation water molecule contributes to a biologically insignificant activity. Interactions observed between LRA-5 and ceftazidime (2.35 Å; PDB 8EO6) show structural conservation with other β-lactamases. In contrast, the crystallographic structure of LRA-5[Y69Q/V166E] (2.15 Å; PDB 8EO7) bears a deacylation water molecule that is associated with the increase in catalytic activity compared to the wild-type variant. Circular dichroism results confirm that amino acid substitutions in LRA-5 do not affect the overall content of the secondary/tertiary structures. Evidence suggests that alternative evolutionary paths could have occurred for β-lactamases like LRA-5, produced by environmental microorganisms: (i) proteins having similar structural features than active β-lactamases may accumulate a small number of mutations (e.g., Y69Q/V166E) to yield active enzymes and (ii) the β-lactamase fold may have lost key residues in the absence of antibiotics.}, } @article {pmid41313013, year = {2025}, author = {Babb, PL and Akhund-Zade, J and Spacek, D and Brick, K and Christians, FC and Portnoy, V and Tsai, M-S and Jarman, KH and Bercovici, S and Vilfan, ID and Blauwkamp, TA}, title = {In-matrix library preparation for metagenomic sequencing of microbial cell-free DNA.}, journal = {Journal of clinical microbiology}, volume = {63}, number = {12}, pages = {e0094425}, pmid = {41313013}, issn = {1098-660X}, mesh = {Humans ; *Metagenomics/methods ; *Cell-Free Nucleic Acids/genetics ; *Gene Library ; Sequence Analysis, DNA/methods ; *DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Metagenomic sequencing of microbial cell-free DNA (mcfDNA) enables comprehensive identification and quantification of diverse pathogens from blood and other biofluids. This approach enables minimally invasive diagnosis of deep-seated infectious disease, provides culture-free identification of antimicrobial resistance, and powers the discovery of novel microbial biomarkers for disease. However, widespread implementation of this approach is limited by lengthy and complex workflows, high host background cfDNA leading to high sequencing costs, and prevalent environmental DNA contamination risks. Addressing these barriers is critical for scalable deployment in both centralized and decentralized settings. To overcome these limitations, we developed Karius Helion-4 Chemistry (Helion-4), an in-matrix (DNA extraction-free) sample-to-DNA sequencing library workflow, to serve as a platform for mcfDNA sequencing applications in infectious disease, microbiome analyses, and disease biomarker discovery. We compared Helion-4 to two widely used metagenomic extraction-based sequencing workflows, as well as to the prior Karius chemistry platform (Digital Culture-3), using 36 clinical plasma specimens. Helion-4 enables end-to-end sequencing library construction for up to 96 samples in 5.25-6.1 h, including setup and final quality control evaluation, with 2.25 h of hands-on time when using automated liquid handling robots. Compared to the other methods, Helion-4 recovered 58-fold to 817-fold more endogenous mcfDNA per volume of plasma, while simultaneously demonstrating 1.8-fold to 6-fold lower exogenous background DNA contamination, likely due to the absence of DNA extraction. The fraction of mcfDNA reads among total reads was enriched by 60-fold to 164-fold for Helion-4 compared to current state-of-the-art methods, significantly lowering sequencing costs required for applications built on the Helion-4 platform vs other platforms. Collectively, these advances enable routine processing of small specimen volumes and provide a simple, efficient, and scalable approach for mcfDNA sequencing applications.IMPORTANCEMetagenomic sequencing of microbial cell-free DNA (mcfDNA) enables the identification and quantification of diverse pathogens from blood and other biofluids, providing minimally invasive and rapid diagnosis of deep-seated infectious disease. However, widespread implementation of this approach is limited by complex workflows, high sequencing costs, and prevalent contamination risks. Karius Helion-4 Chemistry, the first in-matrix (DNA extraction-free) sample-to-DNA sequencing library workflow, overcomes these limitations. Compared to the other methods, Helion-4 is faster, cleaner, and more sensitive. Helion-4 recovered up to 817-fold more endogenous mcfDNA per volume of plasma, while simultaneously demonstrating up to sixfold lower exogenous background DNA contamination. The fraction of mcfDNA reads among total reads was enriched by up to 164-fold for Helion-4, lowering sequencing costs. These advances by Helion-4 technology enable a simple, efficient, and scalable approach for mcfDNA sequencing applications and bring us closer to widespread, high-resolution, and real-time microbial profiling across diverse healthcare settings.}, } @article {pmid41313018, year = {2025}, author = {Wang, K and Wang, H and Zhao, Z and Shen, X and Zhao, J and Zhang, H}, title = {Bifidobacterium animalis subsp. lactis Probio-M8 enhances chondroitin efficacy for knee osteoarthritis in postmenopausal women via the gut-joint axis.}, journal = {mSystems}, volume = {10}, number = {12}, pages = {e0086225}, pmid = {41313018}, issn = {2379-5077}, support = {2022YFD2100700//National Key Research and Development Program of China/ ; U22A20540//National Natural Science Foundation of China/ ; BR221203//Fundamental Research Funds of Inner Mongolia Agricultural University/ ; }, mesh = {Humans ; Female ; *Osteoarthritis, Knee/drug therapy/microbiology/therapy ; *Probiotics/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Postmenopause ; Middle Aged ; *Bifidobacterium animalis ; Aged ; *Chondroitin Sulfates/therapeutic use ; Treatment Outcome ; *Chondroitin/therapeutic use ; }, abstract = {UNLABELLED: Knee osteoarthritis (KOA) is a chronic joint disease marked by cartilage degradation and inflammation. Probiotics exhibit anti-inflammatory properties and may influence the gut-joint axis. Thus, a 4-month human trial was conducted to assess the adjunctive effects of Bifidobacterium animalis subsp. lactis Probio-M8 on KOA in postmenopausal women. Sixty-five KOA patients were randomly allocated to the probiotic group (n = 37; Probio-M8 and chondroitin sulfate) or placebo group (n = 28; placebo and chondroitin sulfate). Following a 3-month intervention, participants from both groups entered a 1-month observation without probiotic supplementation. Our findings revealed that Probio-M8 co-administration significantly reduced Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scores at months 1, 3, and 4 compared to the placebo group (P < 0.001). The probiotic group showed a significant decrease in serum IFN-γ and increases in IL-4 and IL-10 (P < 0.05). Fecal metagenome analysis showed significant changes in the gut microbiota of the probiotic group, with increases in potentially beneficial species, including Agathobaculum butyriciproducens, Bacteroides stercoris, B. animalis, Roseburia hominis, and Ruminococcus bromii, while Dorea formicigenerans decreased (P < 0.05). Changes in B. animalis were strongly associated with WOMAC scores. The gut metabolic potential analysis showed elevated levels of N-oleoylethanolamine and decreased levels of cholesterol and hypoxanthine in probiotic receivers (P < 0.05). Metabolite analysis revealed post-interventional alternations in fecal prostaglandin E2, stearic acid, cholic acid, chenodeoxycholic acid, xanthine, testosterone, and serum bile acids (P < 0.05). Collectively, Probio-M8 enhances the effectiveness of chondroitin sulfate in KOA management through modulating the gut-joint axis, potentially via regulating multiple inflammatory pathways.

IMPORTANCE: The pathogenesis of knee osteoarthritis (KOA) and its phenotypic expression have been associated with the human gut microbiota. Our study demonstrated that the co-administration of Probio-M8 with chondroitin sulfate significantly alleviates KOA symptoms. This probiotic intervention enhances therapeutic efficacy through modulation of the gut microbiota and associated metabolic pathways, reducing inflammation and improving clinical outcomes. Our results underscore the potential of probiotic-driven therapies as an adjunctive treatment strategy and underscore the importance of the gut-joint axis in KOA management.}, } @article {pmid41313177, year = {2026}, author = {Hoque, MN and Rahman, MS}, title = {Bacteriome and resistome dysbiosis in subclinical mastitis and antibiotic-treated milk of dairy cows.}, journal = {Microbiology resource announcements}, volume = {15}, number = {1}, pages = {e0107025}, pmid = {41313177}, issn = {2576-098X}, abstract = {Shotgun metagenomics revealed distinct bacteriome profiles in subclinical mastitis, antibiotic-treated, and healthy cow milk, with enriched resistance repertoires in diseased and treated samples. Findings highlighted the need for better diagnostics, precision antimicrobial use, and antibiotic alternatives to ensure milk safety and address antimicrobial resistance in dairy farming.}, } @article {pmid41313246, year = {2025}, author = {Rigonato, J and Lozano, JC and Vergé, V and Jaillon, O and Bouget, FY}, title = {Latitudinal diversity in circadian and light-sensing genes in an ecologically vital group of marine picoeukaryote algae.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {41313246}, issn = {1751-7370}, mesh = {Photoperiod ; *Circadian Clocks/genetics ; *Chlorophyta/genetics/physiology ; *Circadian Rhythm/genetics ; Light ; Phylogeny ; *Phytoplankton/genetics/physiology ; Gene Expression Profiling ; }, abstract = {Organismal life cycles are influenced by Earth's rotation and orbit, generating daily and seasonal light cycles that vary with latitude, especially in temperate and polar zones. Photoperiodism relies on organisms' ability to measure time via the circadian clock and detect light through specific photoreceptors. Molecular basis of photoperiodism is well-characterized in plants, but photoperiod adaptation in phytoplankton remain largely unexplored. Here, we investigated circadian clock components, photoreceptors, and associated effectors in eukaryote picoalga species from Ostreococcus, Bathycoccus, and Micromonas. We showed that the investigated species shared a conserved set of homologous circadian clock-related genes that appeared in the early evolution of Mamielalles order. Furthermore, gene duplication events account for the specific occurrences and uneven gene copy numbers among these genera. Through metagenomic and metatranscriptomic analyses, we assessed the gene expression profiles of candidate photoperiod-related genes across the global ocean. Our findings reveal an unexpected diversity in photoreceptors, particularly within Micromonas, and highlight the CCT domain family, a key group of transcription factors governing circadian rhythms (TOC1 family) and photoperiodism (CONSTANS family) in plants. TOC1, a central component of the circadian clock in Ostreococcus tauri, is either absent or truncated in tropical species. Functional assays further indicate that the TOC1/CCA1 oscillator is nonfunctional in the tropical strain of Ostreococcus sp. RCC809. These results imply that certain circadian mechanisms may be dispensable at low latitudes, underscoring the diversity of photoperiod adaptations in marine phytoplankton. These results provide valuable insights into the molecular evolution of cosmopolitan plankton groups, particularly their mechanisms of local adaptation.}, } @article {pmid41313537, year = {2025}, author = {Vishwakarma, RK and Gautam, P and Sahu, M and Nath, G and Yadav, BS}, title = {Gut Microbiome in Obesity: A Narrative Review of Mechanisms, Interventions, and Future Directions.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41313537}, issn = {1867-1314}, abstract = {Obesity has reached pandemic levels worldwide and is increasingly recognized as a multifactorial condition beyond excess caloric intake and sedentary lifestyle. Accumulating evidence emphasizes that the gut microbiota (GM), primarily composed of Firmicutes and Bacteroidetes, plays a crucial role in regulating energy balance, immune response, and host metabolism. Gut dysbiosis, characterized by reduced microbial diversity and altered phylum-level composition and shifts toward commonly observed higher Firmicutes-to-Bacteroidetes ratios (although this finding is inconsistent across studies), contributes to enhanced energy harvest, systemic inflammation, and metabolic dysfunction. Key mechanisms involve GM production of short-chain fatty acids (SCFAs) and modulation of hormonal signals, including leptin, ghrelin, insulin, GLP-1, and PYY, alongside interactions via the gut-brain axis. These pathways link microbial composition to appetite regulation, fat storage, and energy balance. Emerging microbiome-targeted therapies, such as probiotics, prebiotics, dietary modulation (e.g., fiber-rich diets), fecal microbiota transplantation, and bacteriophage therapy, show promise in restoring GM balance, promoting weight loss, and improving metabolic health, though results vary and require further validation. Despite advances in metagenomics and metabolomics, gaps persist in establishing causality and long-term efficacy. The integration of GM data with host genetics, diet, and environmental factors through systems biology has the potential to facilitate personalized management of obesity. This review synthesizes the GM's role in obesity pathogenesis and hormonal regulation, highlighting therapeutic potential and research directions for microbiota-based prevention and treatment.}, } @article {pmid41313651, year = {2026}, author = {Zhang, Q and Jiang, X and Xi, Y and Ma, X and Zhang, W}, title = {Complete genome sequences of two Cressdnaviricota viruses identified in respiratory tract samples from forest musk deer in China.}, journal = {Microbiology resource announcements}, volume = {15}, number = {1}, pages = {e0063225}, pmid = {41313651}, issn = {2576-098X}, abstract = {We identified two circular single-stranded DNA viruses from forest musk deer in China through metagenomic analysis. Phylogenetic results suggest they represent unclassified Cressdnaviricota lineages. This study highlights the diversity of the deer's respiratory virome and underscores the importance of wildlife virus surveillance for conservation and public health.}, } @article {pmid41313659, year = {2025}, author = {Sun, W and Pan, J and Gao, X}, title = {Research on the influence mechanism of low-temperature storage on nitrifying bacteria.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {92}, number = {10}, pages = {1426-1440}, pmid = {41313659}, issn = {0273-1223}, support = {2022JH1/10800006//Science and Technology Program of Guizhou Province/ ; }, mesh = {*Nitrification ; *Bacteria/metabolism/genetics ; Sewage/microbiology ; *Cold Temperature ; Nitrites/metabolism ; Ammonia/metabolism ; Waste Disposal, Fluid/methods ; Oxidation-Reduction ; }, abstract = {To develop a more cost-effective nitrogen removal strategy, this study investigated the impact of low-temperature storage methods on nitrifying bacterial activity. Sludge was stored under laboratory-scale static batch conditions in three media: (1) distilled water, (2) nutrient solution, and (3) nutrient solution supplemented with hydroxylamine (NH2OH). Ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) activity, sludge properties, and microbial characteristics were examined. Results revealed that all storage methods inhibited both AOB and NOB activity. Notably, nutrient solution storage demonstrated the most significant effect: it suppressed NOB activity by 86.6% and reduced its relative abundance by 20%, while maintaining high extracellular polymeric substance content (43.5 mg/g VSS) and AOB relative abundance (0.18%). This method substantially shortened the required storage duration (from 8 months to 60 days) and better preserved AOB activity and sludge stability. Metagenomic analysis indicated strong inhibition of the NOB functional gene nitrite oxidoreductase across all methods, while nutrient solution storage specifically elevated the abundance of the AMO gene. Although NH2OH supplementation exhibited inhibitory effects on microorganisms, the concurrent addition of nutrient solution effectively mitigated this impact. Consequently, sludge properties and functional microbiota abundance showed no significant difference between the NH2OH-supplemented nutrient solution method and distilled water storage.}, } @article {pmid41313912, year = {2025}, author = {Li, Y and Tang, C and Qin, X and Qin, W and Fu, Y and Shi, D and Lan, W and Tang, Y and Wu, R and Yu, F}, title = {Rhizosphere nutrient dynamics and physiological responses of Oryza sativa L. under polyethylene terephthalate microplastic stress.}, journal = {Plant physiology and biochemistry : PPB}, volume = {229}, number = {Pt E}, pages = {110797}, doi = {10.1016/j.plaphy.2025.110797}, pmid = {41313912}, issn = {1873-2690}, mesh = {*Oryza/drug effects/metabolism/physiology ; *Rhizosphere ; *Polyethylene Terephthalates/toxicity ; *Microplastics/toxicity ; Nitrogen/metabolism ; Phosphorus/metabolism ; Plant Roots/metabolism/drug effects ; Soil Microbiology ; Soil/chemistry ; *Stress, Physiological/drug effects ; *Soil Pollutants/toxicity ; Carbon/metabolism ; }, abstract = {Polyethylene terephthalate microplastics (PET-MPs), as emerging environmental contaminants, pose growing threats to agricultural ecosystems. This study investigated the impacts of PET-MPs on key physiological traits of Oryza sativa L. and the abundance of functional genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycling within rhizosphere soils. Results demonstrated that PET-MPs were absorbed by rice roots and translocated to aerial tissues, significantly inhibiting chlorophyll biosynthesis (p < 0.05). Exposure to PET-MPs induced oxidative stress, with the 2.5 g kg[-1] treatment elevating root malondialdehyde levels by 175.3 %, and reducing plant height and biomass by 15.8 % and 44.6 %, respectively. Metagenomic analysis revealed a marked increase in the denitrification gene narI, while genes associated with C fixation (korB, korA), methanogenesis (mch), organic N metabolism (glnA), and P transport (ugpC) were significantly suppressed, indicating disruptions to soil nutrient cycling. Actinomycetota and Pseudomonadota were identified as predominant microbial hosts of these functional genes. Pearson correlation analysis showed significant positive associations (p < 0.05) between plant growth parameters and the abundance of korA, korB, IDH1, mch, glnA, and ugpC. These findings advance our understanding of the ecological risks posed by PET-MPs in terrestrial environments and underscore their potential to compromise soil fertility and sustainable rice production.}, } @article {pmid41313993, year = {2025}, author = {Zheng, Y and Crowther, TW and Qin, Y and Lei, J and Xu, M and Xu, Y and Chu, H and Wu, Q and Shi, Y}, title = {Liquor fermentation industry reshapes soil microbiomes and drives CO2 emissions via microbial dispersal.}, journal = {Journal of environmental management}, volume = {396}, number = {}, pages = {128135}, doi = {10.1016/j.jenvman.2025.128135}, pmid = {41313993}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Carbon Dioxide ; Fermentation ; *Microbiota ; Soil/chemistry ; }, abstract = {The rapid expansion of industrial fermentation has raised concerns about its environmental impacts, particularly regarding microbial dispersal from production facilities into adjacent terrestrial ecosystems; however, the ecological and functional consequences of microbial introductions originating from fermentation facilities remain poorly elucidated. We studied eight Chinese liquor fermentation facilities spanning 26°-47°N and 83°-124°E, covering the major geographical range of the industry. Using large-scale soil metagenomics, in situ CO2 flux measurements, and microcosm experiments, we demonstrate that industrial fermentation significantly alters local soil microbial communities and enhances carbon decomposition potential. The results showed that soil carbon decomposition genes increased 13.6 % around fermentation facilities. Biologically, the fermentation process at the facilities introduced microorganisms into soil, such as Actinobacteria, whose abundance increased by 2.8 %. These microorganisms directly increased the abundance of carbon decomposition genes in the soil, while Actinobacteria also enhance soil carbon decomposition capacity by reducing microbial α diversity. Abiotically, the soil total carbon increased by 3-89 % around facilities, thereby enriching carbon decomposition genes. These soil microbial activities changed by fermentation facilities lead to an increase in soil CO2 emissions. Our study provides the first evidence that industrial fermentation facilities inadvertently modify soil microbial community and function. These findings establish a critical link between fermented food production systems and terrestrial carbon emissions, with important implications for sustainable fermentation practices and climate-smart industrial planning.}, } @article {pmid41314069, year = {2025}, author = {Kumari, SP and Hooda, S and Diwan, P and Gupta, RK}, title = {Seasonal variations and functional insights into the urban air microbiome across public transit environments at railway stations in Delhi, India.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181062}, doi = {10.1016/j.scitotenv.2025.181062}, pmid = {41314069}, issn = {1879-1026}, mesh = {India ; Seasons ; *Microbiota ; *Railroads ; *Air Microbiology ; *Environmental Monitoring ; Cities ; Bacteria/classification ; }, abstract = {Airborne microbial communities play an underappreciated yet critical role in shaping urban environmental health, particularly in densely crowded public transit systems. This study aimed to explore the taxonomic and functional landscape of airborne bacteria, highlighting the seasonal disparities across summer and autumn seasons, in the public transit air (railway stations) of Delhi, a populated megacity characterized by extreme pollution levels and one of the world's busiest railway networks. Metagenomic analyses revealed distinct seasonal signatures in microbial community composition and diversity. Alpha diversity was higher during autumn, though not statistically significant, while beta diversity differed significantly between seasons. LEfSe analysis identified season-specific indicator taxa, including Moraxella, Barrientosiimonas, Methylobacterium, for autumn and Stutzerimonas, Caulobacter, Pseudomonas for summer, representing a mix of opportunistic pathogens and environmentally significant taxa. Correlation networks highlighted distinct seasonal clustering patterns. Resistome and virulome profiling revealed the presence of different resistance gene classes and virulence factor categories in abundance. Correlation networks uncovered significant associations between specific genes and bacterial genera, suggesting ecological partitioning in gene carriage. Temperature and air quality index explained a part of the variance observed in the taxonomic and functional dynamics. Metagenome-assembled genomes captured seasonally distinct taxa, and biosynthetic gene cluster screening identified 317 gene clusters, including terpene, RiPP-like, and hserlactone clusters. The findings underscore the ecological complexity and public health relevance of airborne bacteria and raise concerns about their potential role in microbial transmission and long-term respiratory health risks. These insights are crucial for public health surveillance, urban air quality management, and guiding future investigations into the microbial safety of urban environments.}, } @article {pmid41314145, year = {2026}, author = {Li, X and Lin, X and Dong, Z and Zhou, R and Niu, Q}, title = {Biomass ratio regulates methane conversion and carbon fixation in a methanotrophs-microalgae symbiotic system: Efficiency optimization and mechanisms driven by co-metabolism.}, journal = {Water research}, volume = {290}, number = {}, pages = {125016}, doi = {10.1016/j.watres.2025.125016}, pmid = {41314145}, issn = {1879-2448}, mesh = {*Methane/metabolism ; *Microalgae/metabolism ; Biomass ; *Carbon Cycle ; Symbiosis ; }, abstract = {The methanotrophs-microalgae symbiotic system for greenhouse gas treatment is a novel biological carbon fixation technology. However, practical applications are limited by low conversion efficiency, which arises from metabolic heterogeneity in growth rates and carbon-nitrogen resource utilization within the system. To improve metabolic stability of such symbiotic systems, this study systematically assessed CH4 metabolic fluxes by regulating the methanotrophs-microalgae biomass ratio, and further revealed synergistic mechanisms that enhance system stability. Experimental results indicated that at a methanotrophs to microalgae ratio of 1:5, the CH4 consumption rate peaked at 1.1 L CH4/d/g biomass. The extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory and the laser confocal revealed that the co-aggregation force of methanotrophs and microalgae was significantly enhanced at the optimal ratio. This enhancement was crucial for regulating the spatial mutualistic growth and metabolic interactions within the methanotrophs-microalgae symbiotic community. Structural equation modeling (SEM) indicated that poly-β-hydroxybutyrate (PHB) exerts a significant negative effect on methane consumption (-0.68***). Metagenomics results indicated that at the optimal methanotrophs-microalgae ratio, the relative abundance of genes associated with the methane oxidation center metabolic pathway increased by 1.38 times. This significantly enriched Type I methanotrophs (1.89 times) and Type II methanotrophs (1.51 times), while the relative abundance of genes involved in the PHB production pathway decreased by 16 %. This change accelerated the conversion and assimilation of methane carbon, ultimately improving the carbon fixation efficiency by 16 %. This study provided theoretical foundations and technical support for advancing the engineering application of methanotrophs and microalgae symbionts to achieve efficient, stable methane conversion and simultaneous carbon sequestration.}, } @article {pmid41314430, year = {2025}, author = {Gabbay, U and Carmi, D}, title = {The paradox of rapid and synchronized propagation of seasonal influenza 'A' outbreaks in contrast with COVID-19: a testable hypothesis.}, journal = {Virus research}, volume = {362}, number = {}, pages = {199670}, pmid = {41314430}, issn = {1872-7492}, mesh = {Animals ; Humans ; Seasons ; *COVID-19/epidemiology/transmission/virology ; *Influenza, Human/epidemiology/transmission/virology ; Birds/virology ; *Disease Outbreaks ; *Influenza in Birds/epidemiology/transmission/virology ; SARS-CoV-2 ; *Influenza A virus/genetics/physiology ; Basic Reproduction Number ; }, abstract = {Seasonal influenza A virus (SIAV) apparently exhibits a paradoxical pattern: despite a lower basic reproduction number (R0) than SARS-CoV-2, it propagates across the Northern Hemisphere with remarkable speed and synchronicity. We propose a testable hypothesis, developed in two conceptual steps to explain this phenomenon. First, we discuss what may explain the rapid, near-synchronous propagation of SIAV seasonal outbreak. We suggest that it may result from parallel seeding from multiple sources, rather than emerging from a singular origin, as observed with COVID-19. Second, we examined potential mechanisms for parallel seeding. We propose a hypothesis-generating framework that, despite its limitations, offers a structured approach for integrating avian ecology with human epidemiology. The hypothesis is testable through genomic and metagenomic methods. Sequencing viruses from humans and migratory birds across regions may be evaluated to reveal identical viral lineages. The hypothesis may highlight the potential role of ecological reservoirs in global influenza propagation dynamics. If validated, this framework would advance understanding of influenza seasonality and may guide integrated surveillance strategies linking avian ecology with human epidemiology.}, } @article {pmid41314968, year = {2026}, author = {Li, YX and Wang, RY}, title = {Autoimmune glial fibrillary acidic protein astrocytopathy following human herpesvirus-7 infection: a case report.}, journal = {Brain injury}, volume = {40}, number = {3}, pages = {207-210}, doi = {10.1080/02699052.2025.2596225}, pmid = {41314968}, issn = {1362-301X}, mesh = {Humans ; Male ; Adult ; *Herpesvirus 7, Human ; *Roseolovirus Infections/complications/diagnostic imaging ; *Glial Fibrillary Acidic Protein/immunology ; Magnetic Resonance Imaging ; *Astrocytes/pathology ; *Encephalitis, Viral/complications ; }, abstract = {OBJECTIVE: Human herpesvirus-7 encephalitis (HHV7E) is exceedingly rare in immunocompetent adults, and the subsequent development of autoimmune glial fibrillary acidic protein astrocytopathy (GFAP-A) following HHV7E is even rarer. We present the inaugural Chinese case of GFAP-A triggered by HHV7E, confirmed via metagenomic next-generation sequencing (mNGS).

RESULTS: A 37-year-old male initially presented with fever and significant memory impairment. Brain magnetic resonance imaging (MRI) revealed T2/fluid-attenuated inversion recovery (FLAIR) hyperintensity in the right temporal lobe. The diagnosis of HHV7E was confirmed by the detection of HHV7 in the cerebrospinal fluid (CSF) via mNGS. His symptoms improved significantly following acyclovir treatment. However, five weeks post-discharge, he experienced acute neurological deterioration, with symptoms including bifrontal headaches, vomiting, memory impairment, and visual hallucinations. Repeat brain MRI revealed new bilateral punctate and patchy T2/FLAIR hyperintensities in the periventricular white matter. Contrast-enhanced MRI demonstrated bilateral linear radial perivascular enhancements. A cell-based assay detected GFAP antibodies in CSF at a titer of 1:100, establishing a diagnosis of postinfectious GFAP-A. The patient responded well to combined intravenous steroid and immunoglobulin therapy.

CONCLUSIONS: This case highlights the importance of considering autoimmune encephalitis in patients with new or recurrent neurological symptoms after HHV7E recovery. Systematic mNGS and neuronal antibody testing are essential for timely diagnosis, and early aggressive immunotherapy may improve outcomes in post-HHV7E GFAP-A.}, } @article {pmid41315190, year = {2025}, author = {Worp, N and Nieuwenhuijse, DF and Izquierdo-Lara, RW and Schapendonk, CME and Brinch, C and Jensen, EEB and Munk, P and Hendriksen, RS and , and Aarestrup, F and Oude Munnink, BB and Koopmans, MPG and de Graaf, M}, title = {Unveiling the global urban virome through wastewater metagenomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10707}, pmid = {41315190}, issn = {2041-1723}, support = {874735//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)/ ; }, mesh = {*Wastewater/virology ; *Metagenomics/methods ; *Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation & purification ; Cities ; Animals ; Metagenome ; }, abstract = {Understanding global viral dynamics is critical for public health. Traditional surveillance focuses on individual pathogens and symptomatic cases, which may miss asymptomatic infections or newly emerging viruses, delaying detection and response. Wastewater-based epidemiology has been used to track pathogens through targeted molecular assays, but its reliance on predefined targets limits detection of the full viral spectrum. Here, we analyse longitudinal wastewater samples from 62 cities across six continents (2017-2019) using metagenomics and capture-based sequencing with probes targeting viruses associated with gastrointestinal disease. We detect over 2500 viral species spanning 122 families, many with human, animal, or plant health relevance. The bacteriophage family Microviridae and plant virus family Virgaviridae dominate the metagenomic dataset, while Astroviridae and Picornaviridae prevail in the capture-based sequence dataset. Virus distributions are broadly similar across continents at the family and genus levels, yet distinct city-level fingerprints reveal geographical and temporal variation, enabling spatiotemporal surveillance of viruses such as astroviruses and enteroviruses. Global wastewater-based epidemiology enables early detection of emerging viruses, including Echovirus 30 in Europe and Tomato brown rugose fruit virus. These findings highlight the potential of wastewater sequencing for the early detection of emerging viruses and population-wide virome monitoring across diverse hosts.}, } @article {pmid41315266, year = {2025}, author = {He, X and Gu, L and Wang, D and Baer, M and Schaaf, G and Apostolakis, A and Meijide, A and Chen, X and Hochholdinger, F and Yu, P}, title = {Rhizosheath inhabiting Massilia are linked to heterosis in roots of maize.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10777}, pmid = {41315266}, issn = {2041-1723}, support = {444755415//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Zea mays/microbiology/genetics/growth & development/metabolism ; *Hybrid Vigor/genetics ; *Plant Roots/microbiology/genetics ; Soil Microbiology ; Biomass ; Microbiota/genetics ; Flavonoids/metabolism ; Metabolomics ; Rhizosphere ; }, abstract = {Heterosis, or hybrid vigor, describes the superior performance of F1 hybrids compared to parental inbreds. While soil microbiomes are proposed to influence heterosis, it remains unclear how heterotic plants shape their microbiomes and how interactions relate to stress responses. Here, we investigate the role of rhizosheath formation-the soil tightly adhering to roots-in maize heterosis under nitrogen deprivation. Across sterilization, inoculation, and transplantation experiments, hybrids develop larger rhizosheaths than inbreds, and rhizosheath size associates with biomass heterosis. Rhizosheath-enriched genus Massilia correlates with lateral root density, rhizosheath size, and growth. Untargeted metabolomics and flavone-deficient mutants reveal links between Massilia and flavonoid pathways, while growth promotion by Massilia can also occur independently of host flavones. Metagenomic analysis shows that larger rhizosheaths recruit microbial functions related to nutrient cycling and stress adaptation. These findings identify rhizosheath formation as an integrative trait associated with heterosis and a promising target for breeding resilient crops.}, } @article {pmid41315331, year = {2025}, author = {Jiang, Y and Liu, J and Zhang, Y and Zhou, L and Kao, E and Hou, S and Niu, Q and Liu, Y and Xu, ZZ and Ding, T and Su, YX and Liu, Y and Zhang, G and Wang, X and Teng, F and Huang, S}, title = {High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {223}, pmid = {41315331}, issn = {2055-5008}, support = {10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; ZR2024MH23//Natural Science Foundation of Shandong Province/ ; tsqn201909126//Taishan Scholar Award For Young Expert/ ; }, mesh = {Humans ; *Microbiota/genetics ; Saliva/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Mouth Neoplasms/microbiology ; Dental Caries/microbiology ; *Host Microbial Interactions ; *Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Child ; Child, Preschool ; }, abstract = {Characterizing human microbiota in host-dominated samples is crucial for understanding host-microbe interactions, yet is challenged by the high host DNA context (HoC). Current depletion strategies are limited by DNA loss and require immediate processing. In this paper, we introduce 2bRAD-M, a reduced metagenomic sequencing method that enables efficient host-microbe analysis without prior host depletion. Validated on mock samples with >90% human DNA, 2bRAD-M achieved over 93% in AUPR and L2 similarity. In both saliva and oral cancer samples, 2bRAD-M closely matched WMS profiles; in the former, it captured diurnal and host-specific patterns with only 5-10% of the sequencing effort. In an early childhood caries (ECC) study, 2bRAD-M identified key bacterial indicators and distinguished ECC from healthy subjects (AUC = 0.92). By providing high-resolution microbial profiles without host depletion, 2bRAD-M offers a practical and efficient solution for HoC-challenged microbiome research.}, } @article {pmid41315421, year = {2025}, author = {Thystrup, C and Gobena, T and Salvador, EM and Fayemi, OE and Kumburu, H and Buys, EM and Gichure, J and Moiane, BT and Belina, D and Hugho, EA and Faife, S and Ogunbiyi, TS and Akanni, G and Ayolabi, CI and Mmbaga, B and Thomas, KM and Pires, SM and Njage, PMK and Hald, T}, title = {Using metagenomics and whole-genome sequencing to characterize enteric pathogens across various sources in Africa.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {11311}, pmid = {41315421}, issn = {2041-1723}, support = {OPP1195617//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; }, mesh = {*Whole Genome Sequencing/methods ; *Metagenomics/methods ; Humans ; *Foodborne Diseases/microbiology/epidemiology ; Phylogeny ; Genome, Bacterial/genetics ; Africa/epidemiology ; Shigella/genetics/isolation & purification ; Animals ; Campylobacter/genetics/isolation & purification ; Salmonella/genetics/isolation & purification ; Escherichia coli/genetics/isolation & purification ; }, abstract = {Foodborne diseases (FBDs) remain a major public health concern in low- and middle-income countries (LMICs), with the African region carrying the heaviest burden globally. Surveillance efforts in these settings often overlook rural and resource-limited communities, limiting our understanding of pathogens transmission dynamics in these settings. In this study, we use whole-genome sequencing (WGS) and metagenomic approaches to characterize enteric pathogens from human, animal, and environmental sources across four African LMICs between 2019 and 2023. We analyze 446 bacterial isolates of Salmonella, Shigella, Escherichia coli, and Campylobacter, of which 380 high-quality genomes were subjected to phylogenetic and genotypic analyses. Additionally, 139 of 168 metagenomic samples pass quality control and were assessed for pathogen abundance and diversity. Our results reveal a geographically stable distribution of foodborne pathogens over time, suggesting persistent ecological or infrastructural factors influencing their maintenance. Genomic comparisons also identify closely related isolates across distinct sources and regions, pointing to potential transmission routes. These findings highlight the value of incorporating targeted environmental and food-chain sampling into surveillance strategies and demonstrate that metagenomic sequencing can serve as a practical and informative addition to WGS-based surveillance in resource-limited settings.}, } @article {pmid41315430, year = {2025}, author = {Lynch, KF and Triplett, EW and Hyöty, H and Ahrens, AP and Laiho, JE and Petrosino, JF and Lloyd, RE and Agardh, D}, title = {Microbial associations and viruses on the risk of celiac disease (MAVRiC): a longitudinal post-hoc case-cohort study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {42704}, pmid = {41315430}, issn = {2045-2322}, support = {R01 DK124581/DK/NIDDK NIH HHS/United States ; R01 DK124581-01/NH/NIH HHS/United States ; 2022-00537//Swedish research Council, Sweden/ ; }, mesh = {Humans ; *Celiac Disease/virology/epidemiology/microbiology/immunology/etiology ; Female ; Male ; Longitudinal Studies ; Child, Preschool ; *Gastrointestinal Microbiome ; Autoantibodies/immunology ; Risk Factors ; Transglutaminases/immunology ; Child ; Autoimmunity ; Cohort Studies ; Glutens ; }, abstract = {Celiac disease etiopathogenesis requires genetic predisposition and exposure to gluten, yet these factors alone are not sufficient. Larger longitudinal studies are needed to determine the role of time-varying infections and gut microorganisms. The aim was to design a celiac disease case-cohort longitudinal study using The Environmental Determinants of Diabetes in the Young (TEDDY) study. By age 3-years, persistent tissue transglutaminase autoantibodies (tTGA), i.e., celiac disease autoimmunity (CDA), was confirmed in 704 of the 6132 genetically at-risk TEDDY children. Celiac disease onset (CD-onset) was defined as the age CDA developed when followed by a biopsy-proven diagnosis. A competing risk analysis on CD-onset and CDA children with no diagnosis (CDA-only) revealed female-sex, HLA and non-HLA genes and higher gluten-consumption correlate with an increased risk of both outcomes. However, reports of virus-related respiratory infections from August to October correlate consistently with an increased risk of CD-onset and not CDA-only. A sub-cohort of 561 children (9% sampling fraction) has been randomly selected to represent the TEDDY cohort. All incident CD-onset cases (N = 306) were included. The case-cohort will be utilized to analyze virus antibodies and bacteriome from longitudinal plasma and stool samples (the Microbial Associations and Viruses on the Risk of Celiac disease study, MAVRiC).}, } @article {pmid41315665, year = {2025}, author = {Goraj, W and Kagan, K and Kuźniar, A and Banach, A and Jurczyk, S and Podlewski, J and Wolińska, A}, title = {Spatial and functional differentiation of microbial biofilms in a traditional cheese ripening environment.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {45638}, pmid = {41315665}, issn = {2045-2322}, mesh = {*Biofilms/growth & development ; *Cheese/microbiology ; *Bacteria/genetics/classification ; *Fungi/genetics/classification ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Biodiversity ; Poland ; }, abstract = {Biofilms in historic buildings represent stable microbial ecosystems shaped by long-term environmental filtering. We investigated bacterial and fungal communities forming biofilms on walls and ceilings in a 19th-century cheese ripening cellar in Poland, characterized by low temperature, high humidity, and minimal light - conditions resembling natural subterranean habitats. Using high-throughput 16 S rRNA and ITS sequencing, we revealed distinct taxonomic and predicted functional profiles associated with surface type (wall vs. ceiling) and material (brick vs. stone). The wall biofilms exhibited greater taxonomic and functional diversity, with enrichment in heterotrophic, fermentative, and polymer-degrading taxa and pathways, whereas ceiling biofilms showed predicted enrichment in aerobic, stress-tolerant, and potentially methanogenic lineages. The co-occurrence network analysis revealed more complex and tightly connected associations in wall biofilms, dominated by Actinobacteriota (21-97%) and Ascomycota (60-97%), suggesting stable ecological organization despite the limited sample size. Environmental factors, such as pH, redox potential, and electrolytical conductivity, explained a substantial proportion of the variance in the microbial diversity and predicted functional traits. Overall, this study highlights traditional ripening cellars as semi-natural built ecosystems that sustain specialized, spatially structured microbiomes. The results provide new insights into microbial adaptation, functional potential, and ecological resilience in heritage food environments.}, } @article {pmid41315738, year = {2026}, author = {Medvedeva, S and Guyet, U and Pelletier, E and Ruscheweyh, HJ and Sunagawa, S and Ogata, H and Aylward, FO and Gaïa, M and Yutin, N and Koonin, EV and Krupovic, M and Delmont, TO}, title = {Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes.}, journal = {Nature microbiology}, volume = {11}, number = {1}, pages = {228-239}, pmid = {41315738}, issn = {2058-5276}, support = {R35 GM147290/GM/NIGMS NIH HHS/United States ; ANR-23-CE02-0025//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-23-CE02-0022//Agence Nationale de la Recherche (French National Research Agency)/ ; }, mesh = {*Introns/genetics ; *Cell Nucleus/virology ; *Eukaryota/virology ; Genome, Viral ; Phylogeny ; *Virus Replication ; *Giant Viruses/genetics ; Evolution, Molecular ; Metagenomics ; }, abstract = {Mirusviruses infect unicellular eukaryotes and are related to tailed bacteriophages and herpesviruses. Here we expand the known diversity of mirusviruses by screening diverse metagenomic assemblies and characterizing 1,202 non-redundant environmental genomes. Mirusviricota comprises a highly diversified phylum of large and giant eukaryotic viruses that rivals the evolutionary scope and functional complexity of nucleocytoviruses. Critically, major Mirusviricota lineages lack essential genes encoding components of the replication and transcription machineries and, concomitantly, encompass numerous spliceosomal introns that are enriched in virion morphogenesis genes. These features point to multiple transitions from cytoplasmic to nuclear reproduction during mirusvirus evolution. Many mirusvirus introns encode diverse homing endonucleases, suggestive of a previously undescribed mechanism promoting the horizontal mobility of spliceosomal introns. Available metatranscriptomes reveal long-range trans-splicing in a virion morphogenesis gene. Collectively, our data strongly suggest that nuclei of unicellular eukaryotes across marine and freshwater ecosystems worldwide are a major niche for replication of intron-rich mirusviruses.}, } @article {pmid41315849, year = {2025}, author = {Zhang, R and Wang, M and Liu, X and Yang, F and Xu, X and Zi, L and Liang, Z and Liu, X and Gao, H and Chen, X and Zhou, G}, title = {The bacterial spectrum of spinal infections based on blood culture, tissue culture, and molecular methods: a systematic review and meta-analysis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {45566}, pmid = {41315849}, issn = {2045-2322}, support = {CB23059C065A//Yunnan Fundamental Research Projects/ ; }, mesh = {Humans ; Blood Culture/methods ; *Bacteria/genetics/isolation & purification ; *Spinal Diseases/microbiology ; *Bacterial Infections/microbiology/diagnosis ; Staphylococcus aureus/isolation & purification/genetics ; High-Throughput Nucleotide Sequencing ; Mycobacterium tuberculosis/isolation & purification/genetics ; }, abstract = {Spinal infections (SI) are on the rise due to an aging population and the prevalence of more invasive procedures. This study aims to systematically review the microbiological spectrum of SI to enhance diagnostic accuracy and inform effective antibiotic treatment strategies. The last search was conducted on May 9th, 2024, from databases including EMBASE, PubMed, and Web of Science. The outcome variable is infection rate, and the detection method used should be blood culture, tissue culture, or molecular biology method. Two researchers independently extracted research data and evaluated its quality using the JBI Critical Appraisal Tools. Out of 14,639 identified records, 156 studies (encompassing 13,539 patients) were included. Staphylococcus aureus was identified as the most prevalent pathogen, with pooled infection rates of 17.6% (95%CI: 12.8-22.9%; I[2]=93%) in blood culture, 16.8% (95%CI: 14.0-19.8%; I[2]=96%) in tissue culture, and 12.0% (95%CI: 9.3-15.0%; I[2]=35%) in molecular methods. The bacterial spectrum also featured Staphylococcus epidermidis, Escherichia coli, and Mycobacterium tuberculosis (MTB). Molecular methods, particularly metagenomic next-generation sequencing (mNGS), demonstrated markedly superior sensitivity for MTB detection, with a pooled rate of 9.7% (95%CI: 4.6-16.3%; I[2]=90%) compared to 1.3% (95%CI: 0.6-2.1%; I[2]=86%) by tissue culture. The odds ratio for MTB detection with mNGS versus conventional culture was 4.24 (95%CI: 1.68-10.73). This review confirms that a core group of pathogens, including Staphylococcus aureus, Staphylococcus epidermidis, MTB, and Escherichia coli. Our findings underscore that tissue culture is fundamental for common pyogenic bacteria, while metagenomic next-generation sequencing is indispensable for detecting fastidious organisms like MTB. Trial registration: The protocol was registered with PROSPERO (No. CRD42023427429). Registered on May 28, 2023.}, } @article {pmid41315949, year = {2025}, author = {Chen, Y and Hu, Y and Liang, H and Xia, J and Tang, L and Zhang, S}, title = {Embolism of coronary, cerebral, and limb arteries resulting from infective endocarditis of a prosthetic aortic valve: a clinical case report.}, journal = {BMC cardiovascular disorders}, volume = {26}, number = {1}, pages = {2}, pmid = {41315949}, issn = {1471-2261}, mesh = {Humans ; Male ; Middle Aged ; *Heart Valve Prosthesis/adverse effects ; *Prosthesis-Related Infections/microbiology/therapy/diagnostic imaging/diagnosis ; *Endocarditis, Bacterial/microbiology/diagnosis/drug therapy/therapy/diagnostic imaging ; *Aortic Valve/surgery/microbiology/diagnostic imaging ; *Heart Valve Prosthesis Implantation/instrumentation/adverse effects ; Anti-Bacterial Agents/therapeutic use ; Treatment Outcome ; *Intracranial Embolism/diagnostic imaging/microbiology/therapy ; *Cardiobacterium/isolation & purification/genetics ; *Embolism/diagnostic imaging/therapy/microbiology/etiology ; Thrombectomy ; }, abstract = {BACKGROUND: Infective endocarditis (IE) involving prosthetic valves is a critical cardiac condition that can lead to complications such as structural heart damage, heart failure, and arterial embolism, with a high associated mortality rate. This report describes an uncommon instance of infective endocarditis of a prosthetic aortic valve leading to multiorgan embolism.

CASE PRESENTATION: A 52-year-old male with a history of Bentall surgery and prosthetic aortic valve replacement presented with chest pain and dyspnea. Coronary angiography demonstrated blockage of the distal left anterior descending artery, which was addressed with balloon angioplasty. A transesophageal echocardiogram (TEE) detected vegetation on the prosthetic valve, and metagenomic next-generation sequencing of blood confirmed infection with Cardiobacterium hominis. During treatment, he experienced acute ischaemia in the right lower limb necessitating thrombectomy, and MRI disclosed numerous tiny infarct foci in the brain. Following a period of six weeks of antibiotic treatment, the patient was discharged in a better condition. However, the valve dysfunction persisted and regular follow-up was required in order to determine whether to perform a further operation.

CONCLUSION: This case underscores the risk of multi-organ embolic consequences in prosthetic valve infective endocarditis, highlighting the necessity for prompt identification, antimicrobial treatment, and surgical intervention where warranted.}, } @article {pmid41316012, year = {2025}, author = {Ye, X and Li, JA and Wang, S and Luan, S and Zheng, J and Lv, S and Zheng, G and Jiang, W and Huang, X and Xu, J and Zhu, L and Niu, B}, title = {Submandibular infection in a healthy child caused by Legionella maceachernii.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1829}, pmid = {41316012}, issn = {1471-2334}, abstract = {Extra-pulmonary infections caused by Legionella maceachernii are exceptionally rare, particularly in immunocompetent children. This case report describes a young child with a submandibular infection caused by L. maceachernii, who achieved complete recovery following combination therapy with azithromycin and sulfamethoxazole-trimethoprim (SMZ-TMP). By detailing the diagnostic and therapeutic course in this case, we aim to raise clinical awareness of such soft tissue infections in pediatric patients caused by atypical pathogens, thereby reducing the risk of misdiagnosis and optimizing patient outcomes.}, } @article {pmid41316171, year = {2025}, author = {Meldrum, OW and Tiew, PY and Xu, H and Low, DY and Ivan, FX and Narayana, JK and Jaggi, TK and Ching, J and Chotirmall, SH}, title = {Integrated multi-omics profiling for risk stratification in Asians with COPD.}, journal = {Respiratory research}, volume = {27}, number = {1}, pages = {2}, pmid = {41316171}, issn = {1465-993X}, support = {(#020458-00001//LKCMedicine-ICL Fellowship/ ; MOH-001636//National Research Foundation Singapore under its Open Fund-Large Collaborative Grant and administered by the Singapore Ministry of Health's National Medical Research Council/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council under its Clinician-Scientist Individual Research Grant/ ; MOH-001855//Singapore Ministry of Health's National Medical Research Council under its Clinician-Scientist Award (CSA) Investigator (INV) category/ ; RT1/22//Singapore Ministry of Education under its AcRF Tier 1 Grant/ ; }, abstract = {BACKGROUND: Comorbidity-based risk stratification in Chronic Obstructive Pulmonary Disease (COPD) incompletely captures inherent biological heterogeneity, particularly in Asian populations that demonstrate high-risk clinical phenotypes including prior pulmonary tuberculosis. We investigated whether integrated sputum multi-omics could improve risk stratification in an Asian COPD cohort. METHODS: We conducted a prospective, multicenter assessment of N = 56 Asians with established COPD, classified as high- (N = 25; cardiovascular or ex-tuberculosis) or low-risk (N = 31; diabetic or low-comorbidity) based on established co-morbidity phenotyping. Sputum was subjected to mucus analysis (MUC5AC, MUC5B, mucus solids, rheology), metabo-lipidomics (LC-MS/MS) and microbiome assessment (shotgun metagenomics). Multivariate statistics was employed to integrate datasets. RESULTS: High-risk Asian COPD demonstrates abnormal mucus biochemistry characterized by elevated MUC5AC; extensive metabo-lipidomic alterations characterized by dysregulated tryptophan-kynurenine metabolism and lipid remodeling with enrichment of lysophosphatidylcholines and triacylglycerols. Microbial networks are disrupted in high-risk patients, typified by antagonistic interactions driven by K. pneumoniae, H. influenzae and Neisseria spp. Integrative assessment combining all datasets partitioned the cohort into two clusters: SNF 1 (N = 34) and SNF 2 (N = 22), the former representing an unfavorable group characterized by exacerbations, hospitalizations, mucus dysfunction, microbial pathogens and dysregulated metabo-lipidomic pathways. Remarkably, 42% (N = 13 of 31) of the originally classified low risk COPD exhibited the unfavorable SNF 1 endotype, distinguished by more severe exacerbations (hospitalizations), K. pneumoniae and elevated hypoxanthine, creatine, spermine and phosphatidylcholines. CONCLUSION: Integrative multi-omics profiling of Asian COPD significantly refines clinical risk stratification identifying a novel ‘high-risk’ biological endotype. Substantial proportions of clinically low-risk COPD exhibit this endotype, suggesting that clinical and co-morbidity profiling in Asians with COPD should be supplemented by molecular assessment to ensure accurate risk stratification.}, } @article {pmid41316248, year = {2025}, author = {Wang, L and Wang, L and Liu, M and Yuan, Q and Cheng, L and Chen, H and Mao, S and Li, S and Yan, Q and Xing, G and Zheng, N}, title = {Characterization of the gut virome in patients with nonalcoholic fatty liver disease.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {6}, pmid = {41316248}, issn = {1479-5876}, abstract = {BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a prevalent metabolic disorder with complex gut microbiome involvement. While bacterial dysbiosis in NAFLD has been widely studied, the role of the gut virome remains largely unexplored.

METHODS: We profiled gut viral communities from 90 NAFLD patients and 90 non-NAFLD controls using whole-metagenome shotgun sequencing. Viral taxonomic composition, host associations, and functional gene repertoires were analyzed. Serum metabolomic data were integrated to assess virus–metabolite interactions, and random forest models were constructed to evaluate the diagnostic potential of viral signatures.

RESULTS: Overall viral diversity showed no significant differences between NAFLD and controls, but subtle compositional shifts were detected at the vOTU level, with 105 viruses enriched in NAFLD and 185 in non-NAFLD individuals. NAFLD-enriched phages primarily targeted Bacteroides, whereas non-NAFLD-enriched phages were associated with beneficial genera such as Faecalibacterium, Oscillibacter, and Prevotella. Functional annotation revealed a reorganization of viral gene repertoires: genes involved in DNA recombination and horizontal transfer (e.g. int, recD) were depleted, while those related to host interaction and stress response (e.g. xerD, dnaK, hipB) were enriched in NAFLD, indicating enhanced viral persistence and host communication. Serum metabolomic profiling identified 8 differential metabolites, and correlation analysis linked specific vOTUs with altered metabolic pathways. A random forest model based on viral features achieved an AUC of 0.758, outperforming the bacterial model, while integration of viral and bacterial features further improved prediction (AUC = 0.837).

CONCLUSION: The gut virome in NAFLD undergoes compositional and functional remodeling characterized by a shift toward host-adaptive, metabolically interactive viral communities. These viral alterations are closely associated with host metabolic changes and demonstrate strong diagnostic potential. Our findings highlight the virome as an overlooked yet critical component of the gut ecosystem in NAFLD pathogenesis and as a promising source of noninvasive biomarkers for disease prediction and monitoring.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-07443-w.}, } @article {pmid41316344, year = {2025}, author = {Ren, Y and Liang, J and Xie, J and Hu, W and Lai, M and Li, X and Zhang, J and Zheng, Y and Wu, Q and Zhou, H and Yin, J}, title = {Sodium oligomannate modulates the gut-brain axis to alleviate post-stroke cognitive impairment by restoring butyrate metabolism.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {6}, pmid = {41316344}, issn = {2049-2618}, support = {82171317//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Female ; Male ; Mice ; Bacteria/metabolism ; *Brain-Gut Axis/drug effects ; *Butyrates/metabolism ; Cell Line ; *Cognitive Dysfunction/drug therapy/microbiology ; Gastrointestinal Microbiome ; Glucuronates/metabolism ; *Infarction, Middle Cerebral Artery/complications/microbiology ; *Mannose/analogs & derivatives/pharmacology/therapeutic use ; Mice, Inbred C57BL ; Neurogenesis/drug effects ; *Oligosaccharides/pharmacology/therapeutic use ; Disease Models, Animal ; }, abstract = {BACKGROUND: Post-stroke cognitive impairment (PSCI) affects up to half of stroke survivors, severely impacting their quality of life. Despite its prevalence, the pathogenesis of PSCI remains poorly understood, and no specific pharmacological treatments are currently available.

RESULTS: In PSCI patients, fecal butyrate levels were significantly reduced and correlated with cognitive scores. A machine learning model incorporating butyrate levels, butyrate-producing bacteria, and clinical factors (education, smoking, body mass index [BMI], hemoglobin) demonstrates strong predictive performance (area under the curve [AUC]: 0.793 internal, 0.795 external validation). In a transient middle cerebral artery occlusion (tMCAO) mouse model, both sexes displayed sustained gut microbiota dysbiosis featuring decreased butyrate-producing bacteria and fecal butyrate concentrations, concomitant with hippocampal neuronal loss and microglial activation. Sodium oligomannate (GV-971) treatment ameliorated cognitive impairment in a sex-independent manner and restored butyrate-producing gut bacteria. Metagenomic analysis revealed that GV-971 enhanced butyrate production by promoting D-glucuronate degradation and upregulating butyrate synthesis pathway abundance. The elevated butyrate promoted acetylation of histone H3 at lysines 9 and 14 (Ac-H3K9/K14) in colonic and hippocampal neurons, stimulating neurogenesis, while concurrently reducing gut-derived lipopolysaccharide (LPS) and microglial inflammation. Antibiotic treatment and fecal microbiota transplantation established the essential role of butyrate-producing microbiota in mediating GV-971's effects. In vitro, butyrate supplementation significantly inhibited HDAC3 enzymatic activity in HT22 cells and alleviated LPS-induced inflammatory responses in BV2 microglia.

CONCLUSIONS: Intestinal butyrate levels are significantly associated with PSCI. GV-971 mitigates post-stroke cognitive decline by modulating the gut microbiota to increase butyrate production, highlighting its potential as a therapeutic agent for PSCI.}, } @article {pmid41316726, year = {2026}, author = {Nishijima, S and Fullam, A and Schmidt, TSB and Kuhn, M and Bork, P}, title = {VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.}, journal = {Nucleic acids research}, volume = {54}, number = {D1}, pages = {D902-D911}, pmid = {41316726}, issn = {1362-4962}, support = {12/RC/2273-P2//Uehara Memorial Foundation/ ; //EMBL/ ; }, mesh = {*Genome, Viral ; *Virome/genetics ; *Metagenome ; *Viruses/genetics/classification ; *Databases, Genetic ; Metagenomics/methods ; Open Reading Frames ; Microbiota/genetics ; Humans ; Software ; Molecular Sequence Annotation ; }, abstract = {Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.}, } @article {pmid41316756, year = {2025}, author = {Huang, W and Zhu, C and Yang, YJ and Zhang, HZ and Hu, SG and Wu, K and Cui, KP and Chen, YH}, title = {[Distribution Characteristics and Driving Mechanism of Antibiotic Resistance Genes in a Water Source in Hefei, China].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {11}, pages = {6906-6916}, doi = {10.13227/j.hjkx.202409265}, pmid = {41316756}, issn = {0250-3301}, mesh = {China ; *Drug Resistance, Microbial/genetics ; *Water Microbiology ; Soil Microbiology ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Water Supply ; Bacteria/genetics ; *Drug Resistance, Bacterial/genetics ; Drinking Water/microbiology ; }, abstract = {One of the important water sources in Hefei serves as a crucial water supplier, playing a vital role in water provisioning. Its water quality is related to both drinking water safety and ecological water safety. To elucidate the distribution characteristics and influencing factors of antibiotic resistance genes (ARGs) within the water source, water, sediment, and soil samples were collected in July 2021 and December 2021. Metagenomic sequencing was employed to identify and characterize ARGs, mobile genetic elements (MGEs), and bacterial communities in the samples. The correlations between ARGs and physical-chemical properties, antibiotics, MGEs, and bacterial communities were also analyzed. Lastly, the factors were categorized into physical-chemical and biological factors, and their degrees of influence on ARGs were analyzed. The results showed that a total of 544 subtypes of ARGs were detected in the water source, which were classified into 26 major categories. Multidrug, bacitracin, β-lactam, and polymyxin resistance genes were the dominant types of ARGs in all three media, with the subtype bacA exhibiting the highest abundance across all. The numbers of certain classifications of ARGs tended to be higher in soil compared to those in sediment and water, and the abundance of ARGs in the soil was also significantly higher than that in the sediment. PCoA analysis showed significant differences in the structural composition of ARGs among the three media. Correlation analyses showed that TP, pH, LINs, and FQs in the water and SAs in the sediment were significantly correlated with ARGs. Additionally, strong correlations were observed between MGEs and bacterial communities and ARGs in the three media. The VPA results indicated that biological factors played a pivotal role in influencing ARGs in water, whereas physical-chemical factors exerted a stronger influence in soil. However, the synergistic effect of both physical-chemical and biological factors on ARGs in all three media was not negligible.}, } @article {pmid41316759, year = {2025}, author = {Li, RX and Qiu, CS and Li, F and Xu, F and Liu, NN and Chen, X and Qi, L and Wang, CC and Wang, D and Wang, SP}, title = {[Effects of Thermal-alkaline and Thermal Hydrolysis Treatments on Antibiotic Resistance Genes in Sludge].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {11}, pages = {6940-6947}, doi = {10.13227/j.hjkx.202410028}, pmid = {41316759}, issn = {0250-3301}, mesh = {*Sewage/microbiology/chemistry ; Hydrolysis ; *Waste Disposal, Fluid/methods ; *Drug Resistance, Microbial/genetics ; Hot Temperature ; Wastewater/microbiology ; Genes, Bacterial ; }, abstract = {Sewage sludge from urban wastewater treatment plants is an important source of antibiotic resistance gene (ARGs) dissemination into various environmental media. In this study, two treatment methods were employed to treat sewage sludge: thermal-alkaline lysis (60-100℃, pH 10-12) and thermal hydrolysis (140-200℃, 60-120 min). Through metagenomic sequencing and quantitative polymerase chain reaction technology (qPCR), the effects of different treatment conditions on the physicochemical properties of sludge and the removal of ARGs were systematically investigated. In addition, the correlation between ARGs, intI1, and the physicochemical properties of sludge was analyzed in detail. The results indicated that both thermal-alkaline lysis and thermal hydrolysis treatments could break sludge cells, with thermal hydrolysis showing a more significant effect. Moreover, both treatment methods could effectively reduce the abundance of ARGs in sludge under certain conditions. Under thermal hydrolysis conditions at 200℃ for 120 mins, the absolute abundance of ARGs in sludge reached its lowest level of 4.08×10[6] copies·g[-1], and the absolute abundance of intI1 also achieved its minimum value of 1.83×10[6] copies·g[-1] under these conditions. Correlation analysis revealed a significant positive correlation (P < 0.05) between soluble polysaccharides and intI1 under thermal-alkaline lysis conditions. However, under thermal hydrolysis conditions, multiple ARGs and intI1 exhibited significant negative correlations (P < 0.05) with physicochemical indicators such as soluble chemical oxygen demand (SCOD), soluble proteins, and soluble polysaccharides. The removal of ARGs by these different treatment methods was mainly influenced by the treatment conditions and the degree of microbial cell disruption in the sludge.}, } @article {pmid41316964, year = {2025}, author = {Puchol-Royo, R and Pascual, J and Ortega-Legarreta, A and Otto, P and Tideman, J and de Vries, SJ and Abendroth, C and Tanner, K and Porcar, M and Latorre-Perez, A}, title = {Metagenomic Insights Into the Ecology, Taxonomy and Metabolic Capabilities of 'Candidatus Darwinibacteriales' Ord. Nov. (Formerly MBA03), a Potential Key Player in Anaerobic Digestion.}, journal = {Microbial biotechnology}, volume = {18}, number = {12}, pages = {e70258}, pmid = {41316964}, issn = {1751-7915}, support = {101000470//European Union's Horizon 2020/ ; }, mesh = {Anaerobiosis ; Phylogeny ; Metagenomics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Metagenome ; Biofuels ; Sequence Analysis, DNA ; }, abstract = {Biogas, a mix of CO2, CH4 and small proportions of other gases, is a biofuel obtained by anaerobic digestion (AD). Biogas production is often considered a black box process, as the role and dynamics of some of the microorganisms involved remain undisclosed. Previous metataxonomic studies in the frame of the MICRO4BIOGAS project (www.micro4biogas.eu) revealed that MBA03, an uncharacterised and uncultured bacterial taxon belonging to phylum Bacillota, was very prevalent and abundant in industrial full-scale AD plants. Despite the efforts, this taxon has not yet been cultivated, which makes the analysis of its taxonomy, ecology and metabolism even more challenging. In the present work, 30 samples derived from anaerobic digesters were sequenced, allowing the reconstruction of 108 metagenome-assembled genomes (MAGs) potentially belonging to MBA03. According to phylogenetic analyses and genomic similarity indices, MBA03 was classified as a new bacterial order, proposed as 'Candidatus Darwinibacteriales' ord. nov., which includes 'Candidatus Darwinibacter acetoxidans' gen. nov., sp. nov. of 'Candidatus Darwinibacteriaceae' fam. nov., along with 'Candidatus Wallacebacter cryptica' gen. nov., sp. nov. of the 'Candidatus Wallacebacteriaceae' fam. nov. Ecotaxonomic studies determined that AD processes are the main ecological niche of 'Candidatus Darwinibacteriales'. Moreover, metabolic predictions identified Darwinibacteraceae members as putative syntrophic acetate-oxidising bacteria (SAOB), as they encode for the reversed Wood-Ljungdahl (W-L) pathway coupled to the glycine cleavage system. This suggests that Darwinibacteraceae members could work in collaboration with hydrogenotrophic methanogenic archaea to produce methane in industrial biogas plants. Overall, our findings present 'Candidatus Darwinibacteriales' as a potential key player in anaerobic digestion and pave the way towards the complete characterisation of this newly described bacterial taxon, which has not yet been cultured.}, } @article {pmid41317467, year = {2026}, author = {Huang, S and Yu, X and Tang, J and Peng, C and Wen, Q and Chen, S and Lei, L and Yang, C and Liu, Y and Xiang, W and Zhang, Q and Lin, H and Zhang, M}, title = {Unveiling the metabolic mechanism of pesticide in food fermentation through metagenomics and metabolomics: A case study of β-cypermethrin in Pixian broad-bean paste.}, journal = {Food chemistry}, volume = {498}, number = {Pt 2}, pages = {147299}, doi = {10.1016/j.foodchem.2025.147299}, pmid = {41317467}, issn = {1873-7072}, mesh = {Fermentation ; Metagenomics ; *Pyrethrins/metabolism/analysis/chemistry ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metabolomics ; *Fermented Foods/analysis/microbiology ; *Fabaceae/metabolism/microbiology/chemistry ; Food Contamination/analysis ; *Pesticides/metabolism ; *Pesticide Residues/metabolism ; }, abstract = {Fermented foods contain less chemical pollutants, such as pesticide residues, than raw materials. In this study, using Pixian broad-bean paste as a model system, the pesticide degradation during food fermentation was comprehensively elucidated through metagenomic and metabolomics analyses. As a result, β-cypermethrin (β-CY) at 5 mg/kg was almost completely degraded, with a half-life of 6.1 d. β-CY caused flavor changes in fermented products, reducing esters and increasing ketones. Metagenomic analysis revealed that β-CY promoted bacteria phyla Bacteroidota, Pseudomonadota, and enriched the genes of xenobiotic degradation pathways, which is beneficial to its degradation. Microbial-metabolite correlation analysis identified Cyclobacteriaceae, Sulfurovaceae, FEN-1099 and Rhodocyclaceae as key drivers in the synthesis and metabolism of aromatic compounds following β-CY degradation during PBP fermentation. This dual mechanism offers a crucial theoretical foundation for understanding microbial community adaptability and β-CY detoxification in the process.}, } @article {pmid41317490, year = {2026}, author = {Qin, Y and Xie, X and Li, D and Wu, Z and Liu, J and Li, W and Tang, D and Chen, S and Zhang, Y and Liu, N and Zhang, Q and Chen, Y}, title = {NADH-driven bioreductive degradation of azo dyes: Mechanisms of high NADH production, electron transfer, and microbial responses.}, journal = {Journal of hazardous materials}, volume = {502}, number = {}, pages = {140559}, doi = {10.1016/j.jhazmat.2025.140559}, pmid = {41317490}, issn = {1873-3336}, mesh = {*Azo Compounds/metabolism ; *NAD/metabolism ; *Coloring Agents/metabolism ; Electron Transport ; Biodegradation, Environmental ; Oxidation-Reduction ; Bacteria/metabolism ; *Water Pollutants, Chemical/metabolism ; Riboflavin/metabolism ; }, abstract = {Bioreductive co-metabolic degradation of azo dyes represents a promising green technology for addressing the environmental pollution caused by azo dyes. This study investigated the impact of co-metabolized substances on NADH production in microbial systems, focusing on the production of reducing power, electron transfer, and the synergistic effects of microbial communities and associated mechanisms during azo dye degradation. A culture system was developed to maximize NADH production at 3 g/L yeast extract, and it was observed that the system exhibited a significant increase in reducing power, with NADH concentration reaching 909.48 pg/mL (60 h). The electron transfer process in this system primarily depended on factors such as redox mediators, azoreductase, and formic acid. Azo dye reductive degradation and decolorization occurred through an indirect electron transfer pathway. Flavin-based redox mediators (riboflavin and flavin mononucleotide) played a key role in the system, with the application of riboflavin and flavin mononucleotide increasing the system's dye reduction ratio by 14.45 % and 14.40 %, respectively. They were endogenously expressed by the system and facilitated efficient electron transfer by synergizing with specific reductases, particularly when the electron transport chain was inhibited, and alternative pathways ensured the continuation of the reduction reaction. NADH production primarily occurred through glycolysis, the TCA cycle, and fatty acid β-oxidation, with glycolysis contributing the most. Microorganisms such as Enterococcus, Burkholderia, and Escherichia within the microbial community played a crucial role in NADH production while regulating community behavior through a quorum sensing system, thereby enhancing the stability and efficiency of dye degradation. This study investigated the bioreduction of azo dyes in terms of reducing power, offering a theoretical foundation and practical guidance for optimizing the microbial system and enhancing the biodegradation efficiency of azo dyes.}, } @article {pmid41317625, year = {2026}, author = {Kharaillah, A and Zhong, M and Soriano, JD and Gambardella, N and Sanz-Sáez, I and Yan, D and Bertilsson, S and Björn, E and Bravo, AG and Capo, E}, title = {Low-oxygen freshwaters as ecological niches for mercury methylators.}, journal = {Water research}, volume = {290}, number = {}, pages = {125014}, doi = {10.1016/j.watres.2025.125014}, pmid = {41317625}, issn = {1879-2448}, mesh = {*Methylmercury Compounds/metabolism ; *Oxygen ; *Mercury/metabolism ; *Fresh Water/microbiology/chemistry ; Ecosystem ; }, abstract = {Methylmercury (MeHg) is a hazardous neurotoxin, predominantly formed by microbial transformation of inorganic mercury in oxygen-depleted aquatic and terrestrial ecosystems. The ongoing deoxygenation of aquatic ecosystems due to global warming is likely to expand microbial niches for MeHg production. Although mercury methylators have also been reported to thrive in oxyge-deficients conditions in a few marine and freshwater ecosystems, there is a lack of comprehensive understanding of how they are distributed in freshwater systems. In this study, we retrieved hgcA genes, genomic marker for mercury methylation potential, from 586 metagenomes from the water column of 186 freshwater systems. Overall, hgcA genes were detected in the water column of 30 lakes, with the highest richness and abundance being detected in anoxic (0 mg O2l[-1]) and hypoxic (>0-2 mg O2l[-1]) compared to oxic conditions (>2 mg O2l[-1]). Although Desulfobacterota had the highest hgcA gene richness across most freshwater systems, certain systems were dominated by hgcA genes from Bacteroidales and Kiritimatiellales, implying metabolic and ecological versatility of mercury methylators as a group. Our findings suggest that projected expanding deoxygenation may lead to new niches for mercury methylators in inland waters.}, } @article {pmid41317922, year = {2026}, author = {Yang, G and Zhen, Z and Zhang, K and Yin, J and Zhong, X and Li, X and Li, Q and Nie, K and Miao, X and Lin, Z and Zhang, D}, title = {Biochar accelerated soil atrazine degradation by promoting dechlorination pathway: A novel mechanism revealed by DNA stable isotope probing (DNA-SIP).}, journal = {Bioresource technology}, volume = {442}, number = {}, pages = {133722}, doi = {10.1016/j.biortech.2025.133722}, pmid = {41317922}, issn = {1873-2976}, mesh = {*Atrazine/metabolism/isolation & purification ; *Charcoal/chemistry ; Biodegradation, Environmental/drug effects ; *Soil/chemistry ; *Soil Pollutants/metabolism/isolation & purification ; Halogenation ; Soil Microbiology ; Isotope Labeling/methods ; Bacteria/metabolism/genetics ; }, abstract = {Biochar can accelerate atrazine degradation in soils, with surface modification being a widely accepted method to improve the performance. Nevertheless, the underlying mechanisms remain unclear. This study explored the efficiency of modified biochar in facilitating soil atrazine biodegradation with the aid of DNA stable isotope probing (DNA-SIP) and metabolite profiling. DNA-SIP results confirmed the involvement of ten bacterial genera and six atrazine degradation-related genes in atrazine metabolism in situ. Among them, Candidatus Nitrososphaera, Pedosphaera and Conexibacter were reported to be associated with atrazine degradation for the first time. FeCl3-modified biochar significantly accelerated atrazine degradation (85%) by improving soil physicochemical properties (pH, soil organic matter and humus) and enriching the active atrazine degraders. Notably, atrazine dechlorination pathway was preferentially promoted by modified biochar. The findings suggested that DNA-SIP enabled the discovery of the active atrazine degraders and degradation-related genes in biochar-amended soils, providing novel insights into the mechanisms of biochar-facilitated atrazine removal.}, } @article {pmid41317994, year = {2026}, author = {Merrill, LC and Martínez, RL and Palacios, N and Dawson-Hughes, B and Noel, SE and Wang, Y and Tucker, KL and Mangano, KM}, title = {Gut microbes related to the Dietary Approaches to Stop Hypertension score are associated with bone quantity but not with bone quality in a cross-sectional study of older Puerto Rican adults.}, journal = {The American journal of clinical nutrition}, volume = {123}, number = {2}, pages = {101129}, pmid = {41317994}, issn = {1938-3207}, support = {R01 AG055948/AG/NIA NIH HHS/United States ; R01 AR072741/AR/NIAMS NIH HHS/United States ; RF1 AG075922/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Female ; Male ; Cross-Sectional Studies ; *Bone Density ; Aged ; *Gastrointestinal Microbiome/physiology ; *Dietary Approaches To Stop Hypertension ; Middle Aged ; Puerto Rico/ethnology ; Diet ; *Bone and Bones/physiology ; Absorptiometry, Photon ; Osteoporosis ; }, abstract = {BACKGROUND: Bone mineral density (BMD) explains fractures incompletely; studies relating lifestyle to bone quality are lacking.

OBJECTIVES: This study aims to examine associations of diet quality with bone measures [bone material strength index (BMSi), trabecular bone score (TBS), BMD], evaluate moderation by inflammation, identify gut microbiome features linked to diet quality, and quantify diet-microbiome-bone relationships.

METHODS: This cross-sectional study included participants from the Boston Puerto Rican Osteoporosis Study. Diet was assessed with a culturally tailored food frequency questionnairew, and diet quality with the Dietary Approaches to Stop Hypertension (DASH) score. BMSi was measured using microindentation; BMD by dual-energy X-ray absorptiometry (DXA); TBS derived from DXA. Inflammation was assessed with a biomarker score (BMS) and tested as a moderator of diet-bone associations via interaction terms in linear regression. Gut microbiome composition (shotgun metagenomics) was analyzed with microbiome multivariate association with linear models regression to assess diet associations. A machine learning algorithm determined dietary, microbial, and bone-related predictors of bone health; sample sizes varied by outcome: BMSi (n = 86); TBS (n = 204); BMD femoral neck (n = 220), total hip (n = 221), lumbar spine (n = 207).

RESULTS: DASH score was not associated with BMSi [β = -0.10; 95% confidence interval (CI): -0.46, 0.27; P = 0.60], TBS (β = 0.002; 95% CI: -0.002, 0.005, P = 0.36), BMD at the femoral neck (β = 0.002; 95% CI: -0.002, 0.005; P = 0.30), or lumbar spine (β = 0.002; 95% CI: -0.003, 0.006, P = 0.52) but was at total hip (β = 0.004; 95% CI: 0.003, 0.008; P = 0.03). The association was not moderated by inflammation (β = -0.0001, P = 0.89). Lachnospira eligens was 1 of 4 taxa positively associated with DASH score and BMD. No microbial pathways were associated with the DASH score.

CONCLUSIONS: DASH score was associated with hip BMD, but not with BMSi or TBS. Select diet-related gut microbes and an inflammation score were associated with BMD. Future studies should examine dietary inflammation in relation to bone quality.}, } @article {pmid41318438, year = {2025}, author = {Liu, J and Wu, J and Zhang, W and Huang, H and Liao, D}, title = {Disseminated Talaromyces marneffei infection mimicking tuberculosis in an HIV-negative adult with anti-IFN-γ autoantibodies: a case report.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {1}, pmid = {41318438}, issn = {1471-2334}, support = {2024J0112//the Nature Science Foundation of Fujian Province of China/ ; }, abstract = {BACKGROUND: Talaromyces marneffei (TM) is an opportunistic fungus causing life-threatening disseminated infections in immunocompromised individuals. While classically associated with HIV, TM is increasingly reported in HIV-negative patients, often misdiagnosed due to nonspecific manifestations. CASE PRESENTATION: A 38-year-old HIV-negative Chinese woman with a history of thyroid cancer presented with a three-month history of fever, cough, weight loss, and subcutaneous masses. Imaging revealed diffuse pulmonary nodules and osteolytic bone destruction. She was initially misdiagnosed with tuberculosis and received anti-TB therapy without improvement. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified TM, which was later confirmed by fungal culture. Anti–interferon-gamma autoantibodies (anti–IFN-γ auto-Abs) were markedly elevated (111.72 ng/mL). She was treated with liposomal amphotericin B(L-AmB) followed by itraconazole, achieving temporary remission. One month post-discharge, TM recurred with new Sweet syndrome–like skin lesions. Immunomodulatory therapy combined with antifungals led to disease control. CONCLUSION: This case highlights three key clinical insights: (1) TM can closely mimic tuberculosis, especially in HIV-negative individuals; (2) mNGS is a valuable diagnostic tool when conventional tests fail; and (3) Anti–IFN-γ auto-Abs may underlie recurrent or refractory TM infections. Clinicians in endemic regions should consider TM and evaluate immune status early in atypical or treatment-resistant cases.}, } @article {pmid41318497, year = {2025}, author = {Wang, Z and Xing, Y and Xu, M and Chen, C and Zhu, Q and Chen, H and Zhang, Y and Chen, W and Feng, J and Zhang, A and Ma, R and Liu, X and Li, S and Yan, Q and Xing, G and Yao, X and Kong, X}, title = {Altered gut mycobiome and cross-kingdom microbial interactions in systemic lupus erythematosus.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {24}, pmid = {41318497}, issn = {1479-5876}, support = {LJ212410161043//Basic Research Project of Liaoning Provincial Department of Education for Universities/ ; 2025-BS-0684//Doctoral Start-up Foundation of Liaoning Province/ ; }, abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) is a complex autoimmune disorder shaped by host genetics and environmental exposures, including the gut microbiota. While bacterial dysbiosis in SLE is well characterized, the role of the gut mycobiome and its cross-kingdom interactions remains largely unexplored.

METHODS: Using fecal metagenomic sequencing from 117 SLE patients and 115 healthy controls (HCs), we established a non-redundant fungal genome catalog and revealed significant alterations in fungal composition, function, and cross-kingdom ecology.

RESULTS: Fungal diversity was increased in SLE, with enrichment of potentially pathogenic taxa such as Candida, Malassezia, and Trichophyton, and depletion of commensal genera such as Pichia. Functional analysis showed expanded biosynthetic and redox capacities in SLE-associated fungi, including enrichment of RiPP- and terpene-related biosynthetic gene clusters and oxidative stress–related Pfam domains. Several predicted metabolites—such as kynurenine, phenylacetic acid, secondary bile acids, and acylcarnitines—were linked to immune activation and inflammation, suggesting that fungal metabolism may contribute to immune dysregulation. Network analysis revealed sparser and less centralized fungal–bacterial interactions in SLE, indicating disrupted ecological stability and the emergence of fungal taxa as key structural drivers. Integrating fungal and bacterial profiles markedly improved diagnostic performance (AUC = 0.934), underscoring the complementary predictive value of the gut mycobiome. In contrast, post-treatment samples showed reduced fungal richness but no major compositional shifts.

CONCLUSIONS: This study provides a comprehensive, multi-dimensional view of the gut mycobiome in SLE, demonstrating its taxonomic, functional, and ecological remodeling. Our findings highlight the potential contribution of fungal metabolic and redox activities to SLE pathogenesis and support the inclusion of fungi in multi-kingdom microbiome frameworks for disease diagnosis and therapeutic development.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-07423-0.}, } @article {pmid41318814, year = {2026}, author = {Li, J and Liu, L and Tao, M and Han, Z and Ma, M and Jiang, L and Liu, C and Liu, D and Zhang, P and Zhang, M and Xue, R and Gong, J and Zhang, X and Shen, L and Qi, C}, title = {Impact of concomitant medications on efficacy of CLDN18.2-specific CAR-T cell therapy in advanced gastric cancer.}, journal = {British journal of cancer}, volume = {134}, number = {3}, pages = {439-446}, pmid = {41318814}, issn = {1532-1827}, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Adrenal Cortex Hormones/administration & dosage/therapeutic use ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Antibodies, Monoclonal, Humanized/administration & dosage/therapeutic use ; *Claudins/immunology ; Gastrointestinal Microbiome/drug effects ; Granulocyte Colony-Stimulating Factor/administration & dosage/therapeutic use ; *Immunotherapy, Adoptive/methods ; Retrospective Studies ; *Stomach Neoplasms/therapy/immunology/pathology/drug therapy ; Treatment Outcome ; }, abstract = {BACKGROUND: Claudin18.2 (CLDN18.2)-specific CAR-T cell therapy has demonstrated promise in advanced gastric cancer (GC). However, the impact of concomitant medications on the efficacy outcomes remains unclear.

METHODS: We retrospectively analyzed advanced GC patients receiving CLDN18.2-specific CAR-T cell therapy from a phase I trial. Concomitant medications were defined as any drugs administered within 30 days before and after CAR-T cell infusion, including corticosteroids, antibiotics, tocilizumab, granulocyte colony-stimulating factor (G-CSF), thrombopoietin (TPO), and erythropoietin. Metagenomic sequencing was employed to elucidate the differences in gut microbiome signatures between responders and non-responders.

RESULTS: Of 72 patients included in the study, 6 (8.3%) received corticosteroids, 49 (68.1%) received tocilizumab, and 22 (30.6%) received antibiotics, 15 (20.8%) received G-CSF, 5 (6.9%) received thrombopoietin, and no patient received erythropoietin. The median progression-free survival (PFS) (2.6 vs. 5.8 months; P < 0.001) and overall survival (OS) (3.9 vs. 9.5 months; P < 0.001) were significantly shorter for patients who received antibiotics for infection compared to those who did not. No significant differences were observed in objective response rate (ORR), PFS, and OS between patients who received corticosteroids, tocilizumab, antibiotics for prophylaxis, G-CSF, or TPO and those who did not. A higher abundance of Fusobacterium nucleatum, Lactobacillus mucosae, Prevotella pallens, and Streptococcus pseudopneumoniae in gut microbiome was associated with a superior treatment response.

CONCLUSIONS: The study indicates that the use of antibiotics for infection reduces the efficacy outcomes of CLDN18.2-specific CAR-T cell therapy for advanced GC, while other concomitant medications do not affect the outcomes. Further research is needed to clarify the optimal administration of these medications and the underlying mechanisms of the gut microbiome in impacting CAR-T treatment response.

TRIAL REGISTRATION: NCT03874897.}, } @article {pmid41319383, year = {2026}, author = {Deng, H and Yang, J and Li, R and Li, K and Lu, H and Lin, B and Xu, X and Liao, J and Ye, C and Deng, J and Wu, B and Sun, L}, title = {ASSR-mediated sludge yield reduction couples deterministic enrichment of Nitrospira with metabolic resource partitioning.}, journal = {Water research}, volume = {290}, number = {}, pages = {125031}, doi = {10.1016/j.watres.2025.125031}, pmid = {41319383}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Bioreactors/microbiology ; Waste Disposal, Fluid ; Anaerobiosis ; Microbiota ; Wastewater ; }, abstract = {The anaerobic side-stream reactor (ASSR) process offers a microbiome-driven strategy for sustainable wastewater treatment, yet the ecological mechanisms governing its sludge yield reduction efficiency remain unresolved. Here, we demonstrate that a pilot-scale anaerobic-anoxic-oxic (AAO) system with integrated anaerobic side-stream reactor (ASSR) (designated AAO-ASSR/SR) reduced sludge production by 43.6 % compared to a conventional AAO system (designated AAO/CK), while maintaining effluent quality. Through integrated multi-omics and ecological modeling, we revealed the core microbiome-driven mechanism for ASSR-mediated sludge yield reduction. This mechanism is characterized by three key features: (1) enhanced microbial stability via cooperative networks, (2) deterministic assembly selecting slow-growing keystone taxa (e.g., Nitrospira, 18.6 % abundance in SR), and (3) metabolic resource partitioning from biomass synthesis to amino acid cross-feeding. Functional metagenomics revealed that Nitrospira (phylum Nitrospirota, comprising >99 % Nitrospira) and Novosphingobium (phylum Proteobacteria) mediated increased amino acid metabolism and reduced ATP biosynthesis in SR, contrasting with Bacteroidota-dominated biomass synthesis in CK through enhanced protein, nucleotide metabolism and ATP biosynthesis. By coupling deterministic microbial assembly with functional repartitioning, this work contributes to establish a design principle for targeted microbiome engineering in low-sludge systems, advancing sustainable wastewater management through ecological optimization of microbial resource allocation.}, } @article {pmid41319542, year = {2026}, author = {Chen, X and Tie, Y and Zhu, M and Wu, Z and Xu, W and Zhang, Z and Ju, F and Zhang, W}, title = {Unraveling microbial synergy in blended Daqu: A multi-omics approach to decoding the unique flavor profile of Jiuliangxiang baijiu.}, journal = {Food chemistry}, volume = {499}, number = {}, pages = {147314}, doi = {10.1016/j.foodchem.2025.147314}, pmid = {41319542}, issn = {1873-7072}, mesh = {*Flavoring Agents/metabolism/chemistry ; *Bacteria/genetics/metabolism/isolation & purification/classification ; Gas Chromatography-Mass Spectrometry ; Taste ; *Alcoholic Beverages/analysis/microbiology ; Volatile Organic Compounds/chemistry/metabolism ; *Wine/analysis/microbiology ; Microbial Consortia ; Metabolomics ; Multiomics ; }, abstract = {This study deciphers the microbial-ecological basis of Jiuliangxiang Baijiu's (JLX) unique flavor through blended Daqu multi-omics. GC-MS comparative analysis of five market-representative Baijiu types identified 25 aroma-active compounds (OAV ≥ 1) in JLX, with ethyl palmitate (OAV = 2) established as a potential characteristic marker. Subsequent investigation of its blended Daqu revealed how microbial consortia govern flavor formation. Physicochemical and microbial analyses demonstrated that Daqu blending elevated enzymatic capacities, including saccharification (+227.5 % vs single Daqu), esterification (+27.4 %), and liquefaction (+15.4 %), while enhancing microbial diversity. Metabolomic profiling identified glycerophospholipid Gpgro (14:0/16:0) as the ethyl palmitate precursor. Metagenomic tracking revealed that the core ester-producing taxa-primarily Bacillus licheniformis (from high-temperature Daqu) and Kroppenstedtia eburnea (from bacterial Daqu)-harbor complementary genetic potential for both esterase and acyltransferase pathways. The results provide a microbial-ecological framework for rational Daqu blending, offering actionable strategies to engineer microbial consortia for flavor-directed liquor innovation.}, } @article {pmid41319631, year = {2025}, author = {Wang, J and Tian, Y and Zhang, G and Li, Y and Chen, L}, title = {Metagenomic insights into nitrogen and phosphorus metabolisms of bacteria in lakes with distinct nutrient conditions.}, journal = {Journal of environmental management}, volume = {396}, number = {}, pages = {128121}, doi = {10.1016/j.jenvman.2025.128121}, pmid = {41319631}, issn = {1095-8630}, mesh = {*Phosphorus/metabolism ; *Lakes/microbiology ; *Nitrogen/metabolism ; *Bacteria/metabolism/genetics ; Ecosystem ; Nutrients ; }, abstract = {Nitrogen (N) and phosphorus (P) cycling are crucial for preserving ecosystem functioning in lakes, yet our comprehension of the dynamics of N/P cycling genes and microorganisms under diverse nutrient levels is still limited. Herein, we conducted a comprehensive investigation into the profiles of N/P cycling genes and bacteria across three lakes with distinct nutrient levels. We found that N and P cycling genes were most abundant in the high-nutrient lake, particularly those involved in ammonification, assimilatory nitrate reduction, P regulation, and P transportation. Bacteria responsible for mediating most N/P cycling processes (excluding nitrogen fixation and P regulation) were predominant in the high-nutrient lake and mainly affiliated with Cyanobacteria, Proteobacteria, Actinobacteriota, and Bacteroidota. Furthermore, a potential biogeochemical hotspot for the co-metabolism of N and P was identified in the high-nutrient lake, consolidated by the most intricate co-occurrence pattern between N and P cycling genes. More importantly, these versatile bacteria capable of N/P metabolisms, primarily influenced by total nitrogen, total phosphorus, Secchi depth, and total dissolved solids, played important roles in maintaining the stability of bacterial communities in lakes. These findings offer significant insights into microbial-mediated N and P biogeochemical cycling in lakes with varying nutrient conditions, improving our understanding of utilizing N/P co-metabolism microbes to regulate ecosystem function and service amid the challenges of global lake eutrophication.}, } @article {pmid41320324, year = {2026}, author = {Liu, C and Gong, J and Luo, Z and Lai, P and Guo, S and Liang, D and Chen, G and Xing, M and Yu, J and Xie, Y and Liu, D and Zeng, W and He, Z and Lan, P}, title = {Gut microbe alleviates stress-related cancer metastasis by oleic acid degradation.}, journal = {Gut}, volume = {75}, number = {5}, pages = {968-983}, pmid = {41320324}, issn = {1468-3288}, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Oleic Acid/metabolism ; Humans ; Mice ; *Colorectal Neoplasms/pathology/microbiology/metabolism ; *Stress, Psychological/complications/microbiology ; Neoplasm Metastasis ; *Dysbiosis/microbiology ; Male ; Female ; }, abstract = {BACKGROUND: Chronic stress is a known risk factor for cancer metastasis. However, the underlying mechanisms, particularly those involving the gut microbiota and their metabolites, remain unclear.

OBJECTIVE: To investigate whether gut microbiota dysbiosis and metabolic alterations mediate the sustained pro-metastatic effects of chronic stress, even after normalisation of stress hormone levels.

DESIGN: Multiple metastatic models were performed after stress cessation. Shotgun metagenomics and metabolomics were performed to assess changes in microbiota and metabolites. The effects of Bifidobacterium animalis and oleic acid (OA) on metastasis were evaluated in vivo and in vitro. Moreover, we explored how B. animalis degraded OA. Mechanistically, we discovered the interaction between corticosteroids and gut bacteria through guanine metabolism assays. Human samples were collected from patients with colorectal cancer (CRC) with varying perceived stress scores and metastatic status for validation.

RESULTS: Mice that underwent chronic stress exhibited increased metastasis even after hormone levels recovered. The gut microenvironment was altered, with a significant reduction in B. animalis and an increase in OA. B. animalis administration reduced OA levels and suppressed metastasis, while OA supplementation had the opposite effect. B. animalis expresses oleate hydratase, an enzyme that degrades OA. Stress hormones inhibited B. animalis by altering guanine metabolism in the intestinal epithelium. In patients, high stress was associated with more OA, lower B. animalis levels and increased metastasis.

CONCLUSIONS: Chronic stress promotes metastasis by altering microbiota and increasing OA. Targeting B. animalis and OA may help prevent stress-related tumour progression.}, } @article {pmid41320762, year = {2025}, author = {Peng, S and Liu, Z and Song, Z and Wang, C and Yu, Z and Zhao, N and Lu, W and Ning, Z and Lyu, A}, title = {Vinegar-processed frankincense extracts alleviate colorectal cancer by butyric acid mediating M1 tumor-associated macrophage pyroptosis.}, journal = {Chinese medicine}, volume = {20}, number = {1}, pages = {208}, pmid = {41320762}, issn = {1749-8546}, support = {CI2021A04201//the Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; 82003950//the National Natural Science Foundation Committee of China/ ; YZX-202334//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ14-YQ-035//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; }, abstract = {BACKGROUND: Olibanum (RF), a traditional Chinese medicinal resin, shows efficacy in colorectal cancer (CRC) treatment. Its vinegar-processed form (PF) is clinically recognized for enhanced therapeutic effects, with prior mechanistic studies focusing on lipophilic components like boswellic acids. Yet, the regulatory mechanisms of PF's aqueous extracts remain unclear.

METHODS: The aqueous extracts of RF and PF were characterized and compared through transmission electron microscopy (TEM), nanoparticle analysis, and protein profiling. The accumulation of these fractions in feces was confirmed using DiR dye labeling. A mouse CRC model was employed to evaluate and compare the therapeutic effects of RF and PF. The composition of butyric acid-producing microbiota was analyzed using 16S rRNA gene sequencing and metagenomics. Butyric acid levels were quantified using ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UHPLC-TQ-MS). Macrophage phenotypes were assessed via flow cytometry, while mRNA and protein expression levels were determined through RT-qPCR and western blot analysis.

RESULTS: PF aqueous extracts exhibited distinct morphology, particle size, and protein content and had a superior therapeutic effect in alleviating CRC compared to RF. Further analysis confirmed that both RF and PF accumulated in feces and modulated the butyric acid metabolism of gut microbiota. The increased levels of butyric acid contributed to CRC alleviation by promoting the polarization of M1 tumor-associated macrophages (TAMs) and suppressing the pyroptosis of M1 TAMs.

CONCLUSION: The study confirmed that vinegar-processed frankincense enhances its therapeutic effect on CRC by modulating M1 tumor-associated macrophages, which may provide efficient treatment of CRC from the perspective of host-gut metabolic interactions.}, } @article {pmid41321415, year = {2025}, author = {Horstmann, L and Lipus, D and Bartholomäus, A and Oses, R and Kitte, A and Friedl, T and Wagner, D}, title = {Microbial ecology of subsurface granitic bedrock: a humid-arid site comparison in Chile.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf199}, pmid = {41321415}, issn = {2730-6151}, abstract = {Subsurface microorganisms face extreme challenges such as anoxic, xeric, and oligotrophic conditions. In igneous systems, nutrient limitation is critical, as biomass input relies on surface-derived fluids via tectonic fractures. Despite growing interest in subsurface habitats, little is known about ecosystems beneath arid landscapes, where surface water input is limited by the low annual precipitation. This study compares granitic subsurface environments beneath arid and humid surface ecosystems, highlighting the link between surface climate and subsurface biodiversity. DNA was extracted from granitic subsurface rocks recovered from two endmember sites along a north-south climate gradient in Chile's Coastal Cordillera. Microbial communities inhabiting down to 55 m deep subsurface rocks were characterized using 16S rRNA amplicon and shotgun metagenomic sequencing. We identified an abundant and potentially active subsurface community below both climates dominated by heterotrophic bacteria, including Pseudarthrobacter, Janthinobacterium, and Pseudomonas. However, rare taxa affiliated with common chemolithoautrophs, e.g. Thiobacillus, Sulfuriferula, and Sulfuricurvum, were only observed in the arid subsurface, indicating increased oligotrophic conditions and reliance on inorganic electron donors in the deeper subsurface of the desert. Functional analysis revealed sulphur, hydrogen, and carbon monoxide as potential inorganic electron donors. These findings expand the current understanding of microbial life in the subsurface of granite rocks showing the influence of surface climate on nutrient conditions in the deeper subsurface, providing new insights into the extent and functional capacity of terrestrial subsurface habitats and their role in global biogeochemical processes.}, } @article {pmid41321463, year = {2025}, author = {Wang, W and Jiang, X and Wu, W and Zhang, L}, title = {Case Report: Primary segmental volvulus in an infant.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1707716}, pmid = {41321463}, issn = {2296-2360}, abstract = {Primary segmental volvulus (PSV) is a rare cause of acute abdomen in infants. It is characterized by a form of strangulated intestinal obstruction requiring prompt diagnosis and surgical intervention. This study aimed to report a case of PSV in an infant, which was managed successfully through early recognition, close clinical monitoring, and timely surgical treatment. Although both blood and ascitic fluid cultures were negative postoperatively, metagenomic next-generation sequencing (mNGS) identified the same pathogen in both specimens, enabling targeted antibiotic therapy. This case highlights the importance of including PSV in the differential diagnosis of infants presenting with unexplained abdominal distension and bilious vomiting, particularly when accompanied by anemia. Additionally, the elevated level of the coagulation system biomarker thrombin-antithrombin complex (TAT) may serve as a useful marker for monitoring coagulation status in the perioperative period. The integration of TAT assessment and mNGS-based pathogen identification provides a novel framework for individualized perioperative management in PSV.}, } @article {pmid41321514, year = {2025}, author = {Liu, Z and Jiang, A and Kong, Z and Lv, X and Zhang, J and Wu, J and Zhou, C and Tan, Z}, title = {Multi-omics analysis reveals the mechanism of rosemary extract supplementation in increasing milk production in Sanhe dairy cows via the "rumen-serum-milk" metabolic pathway.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {23}, number = {}, pages = {396-414}, pmid = {41321514}, issn = {2405-6383}, abstract = {Rosemary extract (RE) has shown potential as a plant-derived feed additive, but its effects on Sanhe dairy cows are still unknown. In this study, 30 multiparous Sanhe dairy cows (days in milk 171 ± 17 days) with similar body condition were randomly divided into two groups: the RE group (n = 15) was fed the basal diet plus 20 g RE/d, and the CON group (n = 15) was fed only the basal diet. The experiment lasted for 57 days, including a one-week adaptation period. Compared with the CON group, milk yield (P = 0.022) increased significantly with RE supplementation, while milk fat (P = 0.071) also tended to increase. Milk urea nitrogen (P = 0.003) and serum urea nitrogen (P = 0.013) contents were significantly reduced in the RE group compared with the CON group. In rumen fermentation, the content of butyric acid (P = 0.035) in RE group was significantly increased, while valeric acid (P = 0.080) content had an increasing trend. In addition, RE supplementation improved the antioxidant capacity of Sanhe dairy cows by significantly increasing the serum total antioxidant capacity (P < 0.001), superoxide dismutase activity (P = 0.001), immunoglobulin A content (P < 0.001), and immunoglobulin G content (P = 0.005), while decreasing serum malondialdehyde content (P < 0.001), to improve immunity and also affect the composition of serum free amino acids. Metabolomic results showed that a total of 13 co-differential metabolites were identified in rumen and serum, including ursolic acid, a major component of RE, which was higher in both rumen and serum. The milk metabolome analysis identified glycerides, glycerophospholipids, and sphingolipids as the three lipid types that exhibited higher identification intensity in RE. Rumen metagenomic results showed that RE supplementation affected the composition of rumen microorganisms, and differential microbial Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses revealed that the RE group was significantly enriched in the fatty acid biosynthesis pathway and the glycerophospholipid metabolism pathway; two pathways related to lipid synthesis. By associating the genus-level differential microorganisms in the rumen with the "rumen-serum-milk" metabolome and mapping the correlation network, it was found that g_Sharpea, g_Tistlia, and g_Acetobacter, which were more abundant in RE, correlated with more differential metabolites and clustered in the same module. Among the 10 microbial biomarkers screened in the rumen, g_Acetobacter and g_Prevotella were more abundant in the RE, and Mantel's analysis showed that they correlated with rumen fermentation parameters and oxidative and immunological indicators in serum. These results reveal the regulatory mechanism of RE supplementation feeding to enhance milk production and improve milk quality by improving oxidative stress capacity and immunity and reducing nitrogen loss in Sanhe dairy cows, suggesting that RE has the potential as a feed additive for dairy cows.}, } @article {pmid41322208, year = {2025}, author = {Duan, J and Li, X and Hu, Y and Pang, F and Cao, Y and You, Z}, title = {Case Report: Next-generation metagenomic sequencing in the diagnosis of Brucella-associated joint infections-a case series analysis and comprehensive literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1688037}, pmid = {41322208}, issn = {2296-858X}, abstract = {BACKGROUND: The application of next-generation metagenomic sequencing (mNGS) in the diagnosis of human brucellosis, particularly in cases of joint brucellosis infection, remains under-explored, with rarely no case reports available in the literature. We present the first case series focusing on the application of mNGS in the diagnosis of Brucella joint infections. The results indicate that mNGS plays a crucial role in diagnosing Brucella joint infections, serving as a valuable complement, particularly for culture-negative patients.

CASE PRESENTATION: This study presents a comprehensive analysis of four cases of human joint brucellosis diagnosed using mNGS on the BGI sequencing platform, involving three male and one female patients aged from 42 to 63 years, all of whom had documented epidemiological exposure histories. mNGS successfully identified Brucella sequences in all cases, with additional diagnostic findings including a positive Brucella agglutination test in Patient 1, positive joint fluid cultures in Patients 3 and 4, and no positive results in Patient 2. Following surgery and targeted antibiotic therapy, all patients exhibited clinical improvement and favorable follow-up outcomes.

CONCLUSION: These findings underscore the utility of mNGS as a critical diagnostic tool for joint brucellosis infections and highlight its potential as a complementary approach in cases of culture-negative joint infections. In cases where clinical suspicion of joint infection persists despite the absence of identifiable etiological evidence, the implementation of mNGS is strongly advised to facilitate timely and accurate clinical decision-making.}, } @article {pmid41322233, year = {2025}, author = {Chen, X and Yu, X and Deng, J and Yang, J and Chen, P}, title = {Case Report: Blood and cerebrospinal fluid mNGS-assisted diagnosis Toxoplasma gondii infection-associated with hemophagocytic syndrome and systemic lupus erythematosus.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1674391}, pmid = {41322233}, issn = {2296-858X}, abstract = {BACKGROUND: Reactivation of latent Toxoplasma gondii (T. gondii) infection is more prevalent than primary infection in patients with autoimmune diseases. We present a rare case of systemic lupus erythematosus (SLE) and hemophagocytic syndrome (HPS) associated with T. gondii infection.

CASE PRESENTATION: We describe the case of a young girl with SLE and HPS who presented with fever, dyspnea, and pancytopenia. The patient's T. gondii infection was diagnosed through the detection of double-positive IgM and IgG antibodies. Metagenomic next-generation sequencing (mNGS) analysis of both plasma and cerebrospinal fluid (CSF) samples revealed a high concentration of T. gondii DNA. The patient demonstrated a positive response to a combined treatment regimen consisting of anti-Toxoplasma medications and glucocorticoids.

CONCLUSIONS: Co-infection with uncommon pathogens is not uncommon in patients with autoimmune diseases. In individuals with immune disorders and positive T. gondii IgM antibodies, mNGS analysis of peripheral blood samples proves valuable in diagnosing disseminated T. gondii infection.}, } @article {pmid41322254, year = {2025}, author = {Al, MA and Wang, Y and Huang, J and Yu, Y and Juneau, P and He, Z and Yan, Q}, title = {Anammox and denitrifying bacteria and their nitrogen removal potential in lake sediments mediated by environmental changes.}, journal = {Marine life science & technology}, volume = {7}, number = {4}, pages = {670-681}, pmid = {41322254}, issn = {2662-1746}, abstract = {UNLABELLED: Anammox and denitrification are key processes for nitrogen removal in lake sediments. However, how environmental changes mediate the community structure and functional genes of nitrogen removal bacteria in lakes remain unclear. Using metagenome and amplicon sequencing, we investigated the anammox and denitrifying bacteria and their nitrogen removing potentials in lakes experiencing significant spatiotemporal and environmental variations. The community structure of anammox and denitrifying bacteria exhibited stronger lake-wide spatial variations than that of seasonality, while only the denitrification-related functional genes showed substantial variations in both lakes. Anammox genes (e.g., hzsA/B/C and hdh) showed no significant spatial variations. However, the abundances of anammox and denitrifying genes were significantly higher in winter than in summer. The mesotrophic Lake Weishan demonstrated a greater capacity for complete denitrification in winter, while the eutrophic Lake Donghu exhibited a higher potential of anammox in summer. Differences in functional gene abundances between lakes were more pronounced than variations in phylogenetic diversity, indicating clear functional adaptations to local environments. The coupled nitrogen removal potentials also reflected ecological interactions among anammox and denitrifying genes. Importantly, anammox and denitrifying bacterial communities and their functional genes were primarily driven by dissolved organic carbon, total phosphorous and zinc (Zn). The dissimilarities of anammox and denitrifying bacterial communities increased with geographic distance, indicating a clear distance-decay effect. This study highlights the anammox and denitrifying bacteria and their nitrogen removal potentials in lake sediments that are mediated by both spatial and seasonal environmental changes.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00310-z.}, } @article {pmid41322275, year = {2025}, author = {Dong, R and Liu, Y and Wang, N and Tan, KKY and Ji, M}, title = {The distribution of antibiotic resistance and virulence factor genes in the sediment of Inexpressible Island, East Antarctica.}, journal = {Marine life science & technology}, volume = {7}, number = {4}, pages = {978-988}, pmid = {41322275}, issn = {2662-1746}, abstract = {UNLABELLED: Inexpressible Island is a small rocky island in Terra Nova Bay, Victoria Land, Antarctica, which is an area with limited human activities. Understanding the distribution of antibiotic-resistance genes (ARGs) and virulence factor genes (VFGs) in this environment can provide key information on their potential risks to humans and their roles for microbial survival. In this study, we investigated the ARGs and VFGs in lake sediments from Inexpressible Island using metagenomic sequencing. We identified 11,502,071 open-reading frames (ORFs), with 1,749 classified as ARGs and 6,838 as VFGs. The dominant ARGs were associated with antibiotic target alteration and efflux pump mechanisms, while the VFGs were related to adherence and immune modulation functions. While associated within microbial genomes, these ARGs and VFGs were mobile genetic elements like viruses and insertion sequences, distinct from ecosystems with strong human influence. We identified 974 metagenome-assembled genomes (MAGs), with 465 being medium-to-high quality. Of these, 325 (69.9%) contained ARGs, primarily affiliated with Actinomycetota and Pseudomonadota. Additionally, 269 MAGs contained VFGs, with 174 MAGs carrying both ARGs and VFGs, highlighting significant microbial antibiotic resistance and pathogenic potential. Our findings highlight the need for ongoing monitoring of ARGs and VFGs in Antarctica, particularly in light of increasing human activity and climate change.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00323-8.}, } @article {pmid41323679, year = {2025}, author = {He, Y and Qiao, M and Zhang, H and Xiao, D and Guo, X}, title = {Microbial community, metabolic, and flavor differences among high-temperature Daqu with varying Douchi aroma intensities: a comprehensive metagenomic and metabolomic analysis.}, journal = {Food chemistry: X}, volume = {32}, number = {}, pages = {103265}, pmid = {41323679}, issn = {2590-1575}, abstract = {The Douchi aroma is widely regarded as a key quality marker of high-quality high-temperature Daqu, but the compounds related to Douchi aroma formation and the key aroma-producing microorganisms remain unclear, which this study seeks to clarify. Therefore, metagenomic and metabolomic approaches were employed to decode the characteristic compounds and core microbial contributors in high-temperature Daqu samples no (NF), light (LF), and strong (SF) Douchi aroma. Esters were the most abundant volatiles across all groups, while acids increased with aroma intensity. Lentibacillus daqui, enriched in SF, showed strong positive correlations with isocetic, phenylacetic, and nonanoic acids. In contrast, Lichtheimia ramosa and Monascus purpureus were dominant in NF and LF, respectively. Furthermore, functional prediction and KEGG analysis further revealed potential biosynthetic pathways for phenylacetic and acetic acid. These findings clarify the molecular and microbial basis of Douchi aroma formation and provide a scientific reference for targeted quality regulation in Daqu production.}, } @article {pmid41323686, year = {2025}, author = {Shi, X and Fan, C and Hui, M and Tian, Q and Zhang, F and Pan, C}, title = {Multiomics analysis of microbial succession and flavor formation mechanism during the fermentation process of Maotai-flavour Baijiu.}, journal = {Food chemistry: X}, volume = {32}, number = {}, pages = {103236}, pmid = {41323686}, issn = {2590-1575}, abstract = {This study employed metagenomics and metabolomics techniques to investigate the complex relationship between microbial succession and the formation of flavor compounds during the fermentation process of Maotai-flavour Baijiu. Results demonstrated that stacking fermentation, characterized by Weissella, Pichia, and Aspergillus, which secreted amylases and proteases to hydrolyze starch and proteins. Pitting fermentation facilitated the enrichment of anaerobic microbes such as Acetilactobacillus and Pichia, significantly promoting the synthesis of key flavor compounds, including esters, alcohols, and acids, through Glycosyltransferase and Esterification activities. Volatile compound analysis revealed distinct stage-specific profiles, with acids, alcohols, and esters accumulating predominantly in pitting fermentation. These findings elucidate the stage-specific microbial metabolic networks and synergistic mechanisms underlying flavor formation, providing a scientific basis for optimizing traditional Baijiu fermentation processes.}, } @article {pmid41323829, year = {2025}, author = {Luo, A and Liu, L and Shi, S and Liu, X and Hu, B}, title = {Analysis of Microbial Community Structure and Functional Genes for Volatile Flavor in Stinky Tofu.}, journal = {Food science & nutrition}, volume = {13}, number = {12}, pages = {e71257}, pmid = {41323829}, issn = {2048-7177}, abstract = {The distinctive flavor of stinky tofu arises from intricate microbial metabolic networks during traditional fermentation, yet the genetic mechanisms linking microbial community structure to flavor formation remain incompletely resolved. This study employed metagenomic sequencing (Illumina NovaSeq 6000, Q30 > 92%) to generate 7.32 Gb of high-quality data, integrated with functional annotations from KEGG, eggNOG, and CAZy databases, to systematically dissect core microbial taxa and metabolic genes driving flavor biosynthesis. Dominant genera included Pseudomonas (relative abundance: 74.3%), Acinetobacter (14.4%), and Enterobacter (5%), with Pseudomonas putida (12.5%) and Pseudomonas fluorescens (3.2%) orchestrating carbohydrate metabolism (68.22% KEGG pathways) and amino acid degradation via glycoside hydrolases (GHs, 73% of CAZy-annotated enzymes) and dehydrogenases (e.g., 125 lactate dehydrogenase genes). Key flavor compounds, such as diacetyl (379 α-acetolactate synthase genes) and 3-methylbutanoic acid, were synthesized through synergistic pathways. Additionally, Lactococcus and Kluyvera contributed to ester and short-chain fatty acid production via α-keto acid dehydrogenase complexes (55 genes). A total of 410,231 non-redundant genes were identified, annotated to 4690 microbial species, establishing a multi-layered microbial-gene-metabolite regulatory network. This work elucidates the molecular basis of stinky tofu flavor formation and provides a framework for optimizing traditional fermentation processes through targeted microbial engineering.}, } @article {pmid41323881, year = {2025}, author = {Aini, N and Wahyuningsih, SPA and Achhlam, DH and Fatimah, and Amin, MHF and Do, HDK}, title = {Modulation of Gut Microbiota, Intestinal Physiology, and Digestive Enzyme Levels by Duo-Strain Probiotics in African Catfish (Clarias gariepinus) Challenged With Aeromonas hydrophila.}, journal = {Aquaculture nutrition}, volume = {2025}, number = {}, pages = {6624613}, pmid = {41323881}, issn = {1365-2095}, abstract = {This study aimed to determine the effect of dual-strains probiotic (DSP) consisting of Lactobacillus casei and Bacillus subtilis on bacterial metagenomic profile, gut physiology, and digestive enzyme levels of African catfish (Clarias gariepinus) infected by Aeromonas hydrophila. The ratio between L. casei and B. subtilis was 1:1 each with a density of 10[8] CFU/mL. Catfish (n = 8 fish per tank, three replicates per treatment) were fed diets supplemented with 0%, 5%, 10%, or 15% DSP for 42 days. On the 35th day, selected groups were intraperitoneally challenged with A. hydrophila at a dose of 0.1 mL × 10[8] CFU/mL. The observed parameters included bacterial counts and microbial profile in the gastrointestinal tract (analyzed using next-generation sequencing [NGS]), gut physiology, and digestive enzyme levels (amylase, lipase, and protease). The results showed that DSP supplementation increased both the abundance and diversity of gastrointestinal microbes, elevated digestive enzyme levels, and enhanced the number of goblet cells in the intestinal lining. The dominant microbial phyla observed in the control group were Fusobacteria and Pseudomonadota.}, } @article {pmid41324077, year = {2025}, author = {Mah, JK and Hogan, JI and Kothadia, S and Keenan, JE and Berger, J and Carugati, M}, title = {Application of plasma cell-free metagenomic next-generation sequencing for the identification of Aspergillus fumigatus donor-derived infections among solid organ transplant recipients.}, journal = {Medical mycology case reports}, volume = {50}, number = {}, pages = {100751}, pmid = {41324077}, issn = {2211-7539}, abstract = {A cluster of Aspergillus fumigatus donor-derived infections (DDI) was rapidly diagnosed using plasma metagenomic next-generation sequencing (mNGS) among solid organ transplant recipients. The heart recipient, experiencing marginal hemodynamics, underwent an endomyocardial biopsy, which was concerning for a fungal infection on histopathology. Plasma mNGS was performed, identifying A. fumigatus two days prior to conventional diagnostics. This timely diagnosis enabled prompt nephrectomies in the kidney recipients, who survived. This report represents the first published use of mNGS in the diagnosis of Aspergillus fumigatus DDI, highlighting the utility of this novel, underutilized assay for early diagnosis of donor-derived infections.}, } @article {pmid41324436, year = {2025}, author = {Gu, H and Liu, Z and Liu, S and Hu, X and Yu, Z and Li, Y and Li, L and Sui, Y and Jin, J and Liu, X and Jia, Z and Sun, L and Adams, JM and van der Heijden, MGA and Liu, J and Wang, G}, title = {Land conversion to cropland homogenizes variation in soil biota, gene assemblages, and ecological strategies on local and regional scales.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {41324436}, issn = {1751-7370}, mesh = {*Soil Microbiology ; China ; *Bacteria/genetics/classification ; Archaea/genetics/classification ; *Agriculture ; Fungi/genetics/classification ; Soil/chemistry ; *Biota ; Metagenome ; Biodiversity ; Ecosystem ; }, abstract = {It is widely considered that conversion of natural landscapes to agriculture results in biotic homogenization. A recent study comparing soil biota of 27 paired natural steppe soil (NS) and agricultural soil (AS) sites across 900 km in north-eastern China found that conversion to agriculture had increased spatial gradients in soil functional genes. Using the same shotgun metagenome samples, and bacterial amplicon data, we instead analyzed total observed variation at the between-site and within-site level. We found that from the perspective of community taxonomic composition, archaeal and fungal community variation was decreased in AS compared to NS at both within- and between-site scales. In contrast, the bacterial and metazoal community was homogenized only at the local scale. Total functional KEGG gene assemblage was homogenized in AS at both the local and regional scale, whereas "Y-A-S" strategies in bacteria were homogenized at the local scale but not the between-site scale. Overall, these results show a clear homogenizing effect of agriculture with respect to multiple aspects of soil taxonomic and functional diversity, though varying by scale. Certain abiotic soil properties showed homogenization in AS at within-site and between-site scales may explain this homogenization, and uniformity of plant cover in croplands likely contribute to the effect. These findings confirm and extend global-scale studies showing homogenization of soil biota in agricultural environments, revealing that effects extend to functional genes and the broad taxonomic spectrum of life-with potential loss of soil ecosystem resilience to environmental change resulting from agriculture.}, } @article {pmid41324463, year = {2025}, author = {Furman, O and Sorek, G and Moraïs, S and Levin, L and Tovar-Herrera, OE and Winkler, S and Mizrahi, I}, title = {Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {41324463}, issn = {1751-7370}, support = {101000213//Horizon2020/ ; ERC 866530/ERC_/European Research Council/International ; ISF 979/25//Israel Science Foundation/ ; }, mesh = {Animals ; *Rumen/microbiology/growth & development ; Cattle ; Metagenomics ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; }, abstract = {The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of age, we reconstructed 2873 high-quality metagenome-assembled genomes, including 517 novel genomes primarily detected in early life. These novel genomes, spanning 274 genera and largely classified as non-core taxa, reveal a diverse and functionally distinct auxiliary microbiome. Unlike in other ecosystems, this early microbial community persists into adulthood, retaining ecological and functional relevance despite a decline in abundance. Temporal clustering revealed strong associations between auxiliary taxa and dietary transitions, with functional enrichments in environmental sensing, nutrient biosynthesis, and volatile fatty acid metabolism. Metabolic network analyses showed that auxiliary genomes complement non-auxiliary community members in key functions, with potential effects on the host. Our findings suggest that early colonizers act as ecosystem engineers, with the potential to shape the developmental trajectory of the rumen microbiome. This study thus positions the early microbiome not as a transient feature of colonization, but as a structured, functionally coherent auxiliary community that interacts with the mature rumen ecosystem.}, } @article {pmid41325946, year = {2026}, author = {Yin, Z and Ma, J and Bian, R and Wang, Y and Zhang, K and Ma, Y and Zhang, X and Ye, L}, title = {Xenobiotic degradation promotes enrichment but not dissemination of antibiotic resistance genes in activated sludge.}, journal = {Bioresource technology}, volume = {442}, number = {}, pages = {133748}, doi = {10.1016/j.biortech.2025.133748}, pmid = {41325946}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Xenobiotics/metabolism ; *Drug Resistance, Microbial/genetics ; Biodegradation, Environmental ; *Genes, Bacterial/genetics ; Bacteria/genetics ; }, abstract = {Activated sludge in wastewater treatment bioreactors plays a pivotal role in xenobiotic degradation but is also regarded as a hotspot for the dissemination of antibiotic resistance genes (ARGs). Yet, it remains unclear whether pollutant degradation itself also creates conditions that facilitate ARG spread. To address this, we developed a xenobiotic degradation gene (XDG) database covering 22 degradation pathways. Using this database, we analyzed over 30,000 complete bacterial genomes and identified widespread co-occurrence of ARGs and XDGs, particularly within Pseudomonadota and Campylobacterota. Metagenomic profiling of 119 activated sludge samples further revealed strong positive correlations (Pearson's r > 0.8) between XDG and intrinsic ARGs, especially, modules involved in aromatic ring cleavage showed the highest correlations with ARGs. However, only 30.9 % of ARG-HGT events were found in MAGs carrying XDGs, and genome-level proximity analysis indicated that such microorganisms did not exhibit higher horizontal transfer potential. Cultivation-based experiments revealed that Pseudomonas strains with high degradation capacity carried intrinsic but not mobile ARGs. Together, these results demonstrate that xenobiotic degradation promotes ARG enrichment primarily through shifts in community composition rather than by enhancing gene mobility.}, } @article {pmid41326129, year = {2026}, author = {Wu, M and Lu, P and Feng, Y and He, S and Han, G and Hu, S}, title = {Construction and functional characterization of a synthetic consortium for synergistic degradation of dimethachlon.}, journal = {Pesticide biochemistry and physiology}, volume = {216}, number = {Pt 1}, pages = {106807}, doi = {10.1016/j.pestbp.2025.106807}, pmid = {41326129}, issn = {1095-9939}, mesh = {Biodegradation, Environmental ; *Microbial Consortia ; Aniline Compounds/metabolism ; Animals ; Pseudomonas/metabolism/genetics ; *Soil Pollutants/metabolism/toxicity ; Zebrafish ; *Fungicides, Industrial/metabolism/toxicity ; Soil Microbiology ; }, abstract = {The residual dicarboximide fungicide dimethachlon and its primary metabolite 3,5-dichloroaniline entail significant health and ecological risks. Microbial degradation effectively mitigates associated environmental risks. The microbial degradation of organic contaminants is a complex process, typically facilitated by microbial consortia rather than individual species. However, research on the biodegradation of dimethachlon by synergistic microbial consortia is limited. In this study, an enriched bacterial consortium designated as JHJ-2 capable of degrading dimethachlon was obtained. A synthetic consortium was constructed, comprising Bosea sp. S6, which transforms dimethachlon to 3,5-dichloroaniline, and Pseudomonas sp. KH-1, which degrades 3,5-dichloroaniline; both strains were isolated from the enriched consortium JHJ-2 and synergistically degrade dimethachlon. Toxicity assays using the zebrafish showed that dimethachlon is converted into non-toxic products by the synthetic consortium (strains S6 and KH-1). Bioaugmentation with the synthetic consortium led to the complete removal of dimethachlon and its highly toxic metabolite 3,5-dichloroaniline from contaminated soil. In addition, 16 bins were successfully recovered by metagenomic binning, including bin 12 (Bosea sp.) and bin 15 (Pseudomonas sp.), and several potential degradation enzymes were hypothesized in the genomes of bins 12 and 15. Overall, the developed synthetic consortium exhibits significant potential for the enhanced bioremediation and detoxification of dimethachlon-contaminated sites.}, } @article {pmid41326588, year = {2025}, author = {Yadav, MK and Ranjan, R and Verma, P and Sharma, R}, title = {Discovery and characterization of an enantioselective family VIII esterase from effluent treatment plant sludge metagenome.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {252}, pmid = {41326588}, issn = {2045-2322}, support = {BSC0124//Council of Scientific and Industrial Research (CSIR), India/ ; }, abstract = {UNLABELLED: This study reports on the biochemical characterization of a novel esterase (EstN3) belonging to class C β-lactamases of family VIII esterases from the functional screening of an Effluent Treatment Plant (ETP) sludge metagenome library. The enzyme is 410 amino acids long and does not contain a signal peptide. It showed maximum amino acid sequence similarity with uncharacterized serine hydrolases from Phenylobacterium and Caulobacter species, suggesting that it is a member of family VIII esterase. EstN3’s primary structure contains SxxKs, YSx, KTG, PLGMxDTxF, LxxxPGxxW, and GGxG motifs observed in class C β-lactamases, peptidases, and carboxylesterases of family VIII. This supports its designation as a class C β-lactamase. EstN3 favored shorter-chain p-nitrophenyl esters (C2-C6) based on substrate specificity profiling with p-nitrophenyl esters (C2-18). EstN3 exhibited excellent stereoselectivity in the production of S-mandelic acid under aqueous hydrolytic conditions. We have discovered that EstN3, a family VIII esterase, shows enantioselectivity towards methyl mandelate. The novel esterase was identified from the ETP sludge, indicating that unexplored environments serve as rich reservoirs for the discovery of novel enzymes with unique properties, offering valuable opportunities for advancing biocatalysis and industrial biotechnology.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-29625-8.}, } @article {pmid41326768, year = {2025}, author = {Polizel, GHG and Cánovas, Á and Diniz, WJS and Ramírez-Zamudio, GD and Cesar, ASM and Fukumasu, H and Fernandes, AC and Furlan, É and de Almeida Santana, MH}, title = {Unveiling long-term prenatal nutrition biomarkers in beef cattle via multi-tissue and multi-OMICs analysis.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {22}, number = {1}, pages = {8}, pmid = {41326768}, issn = {1573-3890}, support = {23/09113-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 17/12105-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Animals ; Cattle ; Female ; Pregnancy ; *Biomarkers/metabolism/analysis ; *Metabolomics/methods ; Male ; Liver/metabolism ; Transcriptome ; *Maternal Nutritional Physiological Phenomena ; *Prenatal Nutritional Physiological Phenomena ; Multiomics ; }, abstract = {INTRODUCTION: Maternal nutrition during gestation plays a crucial role in shaping offspring development, metabolism, and long-term health, yet the underlying molecular mechanisms remain poorly understood.

OBJECTIVES: This study investigated potential biomarkers through multi-OMICs and multi-tissue analyses in offspring of beef cows subjected to different gestational nutrition regimes.

METHODS: A total of 126 cows were allocated to three groups: NP (control, mineral supplementation only), PP (protein-energy supplementation in the last trimester), and FP (protein-energy supplementation throughout gestation). Post-finishing phase, samples (blood, feces, ruminal fluid, fat, liver, and longissimus muscle/meat) were collected from 63 male offspring. RNA sequencing was performed on muscle and liver, metabolomics on plasma, fat, liver, and meat, and 16S rRNA sequencing on feces and ruminal fluid. Data were analyzed via DIABLO (mixOmics, R).

RESULTS: The muscle transcriptome showed strong cross-block correlations (|r| > 0.7), highlighting its sensitivity to maternal nutrition. Plasma glycerophospholipids (PC ae C30:0, PC ae C38:1, lysoPC a C28:0) were key biomarkers, particularly for FP. The PP group exhibited liver-associated markers (IL4I1 gene, butyrylcarnitine), reflecting late-gestation effects, while NP had reduced ruminal Clostridia (ASV151, ASV241), suggesting impaired microbial energy metabolism.

CONCLUSIONS: This integrative multi-OMICs approach provided deeper insights than single-layer analyses, distinguishing nutritional groups and revealing tissue- and OMIC-specific patterns. These findings demonstrate the value of combining transcriptomic, metabolomic, and microbiome data to identify biomarkers linked to maternal nutrition in beef cattle.}, } @article {pmid41327018, year = {2025}, author = {Gajjar, K and Patel, S and Chaudhary, M and Agrawal, D and Maniyar, R and Chaudhary, D and Patel, CK and Joshi, C and Joshi, M and Dharajiya, D}, title = {Metagenomic insights reveal the impact of natural farming on soil nutrients, enzyme activities, microbial communities, and yield in turmeric cultivation.}, journal = {BMC plant biology}, volume = {26}, number = {1}, pages = {28}, pmid = {41327018}, issn = {1471-2229}, support = {GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; }, abstract = {BACKGROUND: Turmeric (Curcuma longa L.) is a key spice, medicinal and industrially important crop that is increasingly being cultivated under sustainable practices such as natural farming system (NFS). This study compares NFS and conventional/chemical farming system (CFS) in terms of soil physicochemical properties, enzyme activities, microbial diversity, and yield parameters, providing a comprehensive understanding of their ecological and agronomic impacts.

RESULTS: Field experiments evaluated nine NFS treatments alongside CFS for high throughput amplicon (16S rRNA and ITS) metagenomics, soil physicochemical properties, enzyme activities, and yield parameters. NFS treatments with ≥ 5 t/ha mulching and 4 t/ha Ghanjeevamrit (i.e. NFS-T6 and NFS-T9) significantly enhanced soil organic carbon (~ 0.25%), nitrogen (~ 239.9 kg/ha), and phosphorus (~ 38.16 kg/ha), alongside elevated enzyme activities like alkaline phosphatase (ALP; ~112.11 µg PNP/g/hr) and protease (PR; ~16.22 µg Tyrosine/g/hr). These treatments also exhibited significantly higher microbial richness and evenness (Shannon index: ~5.09; Simpson index: ~0.981). NFS enriched beneficial bacterial (e.g., Priestia, unclassified Acidobacteria, etc.) and saprophytic fungal genera (e.g., Humicola, Mortierella, etc.), enhancing soil nutrient cycling and soil health. Conversely, CFS enriched chemical-resilient and pathogenic taxa (e.g., Alternaria, Curvularia, etc.). NFS-T5 (40.66 t/ha) and NFS-T9 (40.47 t/ha) yielded over twice the fresh rhizome compared to CFS. NFS treatments recorded higher net returns and Benefit-Cost Ratios (BCRs) of 7.51 to 10.57. Microbial profiling of natural farming (NF) inputs (Beejamrit, Jeevamrit, and Ghanjeevamrit) showed distinct bacterial and fungal communities influencing soil microbiome structure. Co-occurrence network analysis of NF soils revealed that microbial taxa introduced via NF inputs had limited integration into native soil communities, indicating selective incorporation governed by competitive ecological interactions.

CONCLUSIONS: Natural farming practices significantly enhanced soil fertility, microbial community structure, enzymatic activity (ALP and PR), and turmeric productivity with superior BCRs. These findings provide scientific evidence supporting natural farming as a viable and sustainable agricultural approach, contributing to improved soil health and crop performance in turmeric cultivation.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07781-3.}, } @article {pmid41327021, year = {2025}, author = {Chen, B and Shu, W and Le, J and Jin, D}, title = {Application of metagenomic next-generation sequencing technology in hematologic malignancy patients with sepsis following antibiotic use.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1678}, pmid = {41327021}, issn = {1471-2334}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has been widely applied in clinical pathogen detection; however, its utility in patients with hematologic malignancies complicated by sepsis after antibiotic therapy requires further investigation. METHODS: A total of 119 patients with hematologic malignancies complicated by sepsis, who had received antibiotic treatment for ≥ 3 days without clinical improvement, were enrolled in the study. All patients underwent simultaneous blood culture and mNGS analysis. The diagnostic value of mNGS and its impact on optimizing anti-infective therapy were evaluated. RESULTS: For the detection of bacterial and fungal pathogens, mNGS demonstrated a significantly higher positive rate compared to blood culture (89.36% vs. 25.53%). The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of mNGS were 58.33%, 0.00%, 16.67%, and 0.00%, respectively. The overall agreement rate between the two methods was 13.21% (kappa = -0.202). Based on mNGS results, anti-infective treatment regimens were modified in 47 patients (39.49%). Granulocytopenia related to antitumor therapy was identified as a high-risk factor for polymicrobial infections (P < 0.05) CONCLUSIONS: Patients with hematologic malignancies and sepsis, particularly those with antitumor therapy-induced granulocytopenia, are at increased risk for polymicrobial infections. Blood mNGS offers a rapid and comprehensive approach to pathogen identification, showing significant potential for guiding anti-infective therapy in this patient population. CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid41327286, year = {2025}, author = {Xu, W and Top, J and Viveen, MC and Slyzkyi, A and Hermans, N and van Erp, S and Eiloz, D and Anthony, R and Kremer, K and Schürch, AC}, title = {Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.}, journal = {BMC medical genomics}, volume = {19}, number = {1}, pages = {8}, pmid = {41327286}, issn = {1755-8794}, support = {LSHM22031//Health~Holland/ ; }, mesh = {*Sputum/microbiology ; Humans ; *Metagenomics/methods ; *Nanopores ; Workflow ; *Metagenome ; *Nanopore Sequencing/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Oxford Nanopore adaptive sampling (NAS) is a method by which the long-read sequencing flowcell accepts or rejects DNA molecules that are actively being sequenced based on their initial ~ 500 bp sequences, selectively increasing target data output. NAS promises up to 5-10 × enrichment of target sequencing yield without additional sample preparation, but this optimal performance is dependent on ideal sample parameters which may be difficult to achieve under many real-world use-cases. We evaluated the use of NAS for profiling clinical sputum metagenomes.

METHODS: We sequenced DNA extracted from clinical sputa and spike-in controls of a mock community of bacterial respiratory pathogens, using the current R10.4.1 MinION flowcell chemistry.

RESULTS: We achieved at best 3.1 × enrichment of bacterial sequence output with NAS due to the shorter read lengths (~ 2.5 kb) from the PCR amplification necessary to compensate for low DNA extraction yields. More critically, we encountered rapid pore loss during our runs that reduced total sequencing yield by an estimated 80%. We were unable to mitigate the pore loss despite extensive attempts to reduce contaminant carry-over, and we could not determine its cause but ruled out NAS and pore underloading as contributing factors.

CONCLUSIONS: We conclude that the utility of NAS is often limited by the characteristics of the metagenomic sample studied, and that the factors contributing to pore loss need to be resolved before ONT sequencing can be reliably applied to long-read metagenomics.}, } @article {pmid41327304, year = {2025}, author = {Zhang, X and Li, Y and Xiong, Z and Zheng, N and Wang, J and Zhao, S}, title = {Biochanin A improves nitrogen utilization efficiency by regulating ruminal microbial community in dairy goats.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {13}, pmid = {41327304}, issn = {2049-2618}, support = {32402768//National Natural Science Foundation of China/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; CARS-36//Earmarked Fund for CARS/ ; 2022YFD1301000//National Key R&D Program of China/ ; CAAS-ZDRW202304//Agricultural Science and Technology Innovation Program/ ; }, mesh = {Animals ; *Genistein/pharmacology/administration & dosage ; *Nitrogen/metabolism ; *Rumen/microbiology/metabolism ; *Goats/microbiology ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; Female ; Dietary Supplements ; Milk/chemistry ; Feces/microbiology ; Metabolomics ; Bacteria/classification/metabolism/genetics ; }, abstract = {BACKGROUND: Rumen microbial nitrogen metabolism is crucial for animal health, productivity, and environmental sustainability in ruminants. Natural products like biochanin A are garnering interest as potential feed additives due to their beneficial effects and safety profiles. Here, we collected total mixed diet, plasma, milk, urine, and feces samples of dairy goats to evaluate the impact of biochanin A on nitrogen metabolism and elucidated regulatory mechanisms of nitrogen metabolism using multi-omics approaches by analyzing plasma metabolites and ruminal microbial communities.

RESULTS: Supplementation with biochanin A significantly enhanced nitrogen utilization efficiency of dairy goats. Plasma metabolomics revealed that biochanin A altered pathways related to amino acid biosynthesis/metabolism and glycolysis/gluconeogenesis. In the rumen, biochanin A enriched microbial strains from the families Selenomonadaceae and Aminobacteriaceae. Up-regulated proteins predominantly associated with glycolysis were identified by metaproteomics. Integrated metagenomic and metaproteomic analyses demonstrated that biochanin A positively influenced carbohydrate metabolism, amino acid metabolism, and energy metabolism pathways.

CONCLUSION: Biochanin A enhances nitrogen metabolism by regulating rumen microbial community function, supporting its potential as a natural feed additive to improve nitrogen utilization of ruminants. Video Abstract.}, } @article {pmid41327409, year = {2025}, author = {Jin, J and Wang, X and Zhang, X and Mei, J and Zheng, W and Guo, L and Sun, H and Zhang, L and Liu, C and Ye, W and Guo, L}, title = {Grapevine phyllosphere pan-metagenomics reveals pan-microbiome structure, diversity, and functional roles in downy mildew resistance.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {10}, pmid = {41327409}, issn = {2049-2618}, support = {ZR2024QC241//Shandong Provincial Natural Science Foundation Youth Project/ ; 2024CXPT031//Key R&D Program of Shandong Province/ ; ZR2023JQ010//Natural Science Foundation for Distinguished Young Scholars of Shandong Province/ ; }, mesh = {*Vitis/microbiology ; *Plant Diseases/microbiology ; *Disease Resistance/genetics ; *Microbiota/genetics ; *Metagenomics/methods ; Plant Leaves/microbiology ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; }, abstract = {BACKGROUND: Grapevines are among the most economically important fruit crops, and the microbiome profoundly influences their health, yield, and quality. However, mechanistic insights into microbiome-orchestrated grapevine biology remain limited.

RESULTS: Here, we conduct large-scale pan-metagenomic and pan-metatranscriptomic analyses of the phyllosphere microbiome from 107 grapevine accessions spanning 34 Vitis species. We show that the grapevine core microbiome is dominated by phyla Bacillota and Pseudomonadota. Leveraging PacBio sequencing, we assembled 19 high-quality metagenome-assembled genomes (MAGs) from the grapevine pan-microbiome, representing the first MAG reconstruction in plant-associated microbial communities using PacBio reads. These MAGs encode genes associated with antibiotic resistance, secondary metabolism, and carbohydrate-active enzymes (CAZymes), which could potentially influence grapevine biology. During downy mildew (DM) infection, DM-resistant grapevines exhibit significantly higher microbial network complexity than susceptible counterparts. Among the key taxa contributing to this complexity, Bacillota emerged as the dominant phylum, displaying strong abundance correlations with phylum Euglenozoa and Cyanobacteriota, and an isolated Bacillota species from the grapevine leaves, Bacillus cereus, demonstrated potent biocontrol activity against DM infection. Pan-metatranscriptomic analysis further revealed significant upregulation of eukaryotic microbial genes involved in primary and secondary metabolism.

CONCLUSIONS: This pan-metagenomic study offers unprecedented insights into the complex structure, diversity, and functional roles of the grapevine phyllosphere microbiome and presents valuable genomic and microbial resources for microbiome research and engineering to enhance viticulture productivity and quality. Video Abstract.}, } @article {pmid41327428, year = {2025}, author = {Zorea, A and Moraïs, S and Pellow, D and Gershoni-Yahalom, O and Probst, M and Nadler, S and Shamir, R and Rosental, B and Elia, N and Mizrahi, I}, title = {ProFiT-SPEci-FISH: a novel approach for linking plasmids to hosts in complex microbial communities at the single-cell level.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {11}, pmid = {41327428}, issn = {2049-2618}, support = {ISF 1947/19//Israel Science Foundation/ ; 2476/2-1//German-Israeli Project Cooperation (DIP)/ ; ERC 866530//the European Research Council/ ; }, mesh = {*Plasmids/genetics ; *In Situ Hybridization, Fluorescence/methods ; *Single-Cell Analysis/methods ; *Bacteria/genetics/isolation & purification/classification ; *Microbiota/genetics ; Gene Transfer, Horizontal ; Humans ; }, abstract = {BACKGROUND: Plasmids are influential drivers of bacterial evolution, facilitating horizontal gene transfer and shaping microbial communities. Current knowledge on plasmid persistence and mobilization in natural environments is derived from community-level studies, neglecting the single-cell level, where these dynamic processes unfold. Pinpointing specific plasmids within their natural environments is essential to unravel the dynamics between plasmids and their bacterial hosts.

RESULTS: Here, we overcame the technical hurdle of natural plasmid detectability in single cells by developing SPEci-FISH (Short Probe EffiCIent Fluorescence In Situ Hybridization), a novel molecular method designed to detect and visualize plasmids, regardless of their copy number, directly within bacterial cells, enabling their precise identification at the single-cell level. To complement this method, we created ProFiT (PRObe FInding Tool), a program facilitating the design of sequence-based probes for targeting individual plasmids or plasmid families.

CONCLUSIONS: We have successfully applied these methods, combined with high-resolution microscopy, to investigate the dispersal and localization of natural plasmids within a clinical isolate, revealing various plasmid spatial patterns within the same bacterial population. Importantly, bridging the technological gap in linking plasmids to hosts in native complex microbial environments, we demonstrated that our method, when combined with fluorescence-activated cell sorting (FACS), can track plasmid-host dynamics in a human fecal sample. This approach identified multiple potential bacterial hosts for a conjugative plasmid that we assembled from this fecal sample's metagenome. Our integrated approach offers a significant advancement toward understanding plasmid ecology in complex microbiomes. Video Abstract.}, } @article {pmid41327449, year = {2025}, author = {Zhao, Y and Duanmu, X and Hu, Z and Fan, Y and Mao, R and Zhang, Y and Zhang, X}, title = {Temperature seasonality constrains soil T4-like bacteriophage abundance at large spatial scale.}, journal = {Environmental microbiome}, volume = {21}, number = {1}, pages = {2}, pmid = {41327449}, issn = {2524-6372}, support = {U21A20188//National Natural Science Foundation of China/ ; jxsq2023102216//Double Thousand Plan of Jiangxi Province/ ; }, abstract = {BACKGROUND: Viruses play key roles in regulating soil microbial dynamics and biogeochemical cycles. T4-like bacteriophages, one of the best-studied viral groups, are abundant in soils, but their biogeographical patterns and ecological drivers remain poorly understood. In this study, we performed the first large-scale assessment of soil T4-like bacteriophages based on metagenomic data using viral hallmark genes, revealing broad spatial structure, identifying dominant environmental factors, and projecting shifts under future climate scenarios.

RESULTS: We analyzed two viral hallmark genes, gene 20 (g20) and gene 23 (g23), retrieved from global soil metagenomes, and National Center for Biotechnology Information (NCBI) reference sequences, yielding 2,385 and 2,928 full-length sequences clustered into 1,211 and 1,269 operational taxonomic units (OTUs), respectively. Phylogenetic analysis revealed that only a small fraction of soil-derived sequences could be assigned to established viral families, with most remaining unclassified below the class Caudoviricetes. The relative abundances of g20 and g23 were assessed at 116 sites spanning 14 biomes across six continents. Consistent biogeographic patterns were observed for both genes, with higher relative abundance in tropical climates and lower levels in polar and dry regions, indicating strong climatic influence. Temperature seasonality (BIO4) was identified as the primary environmental driver, showing a significant negative correlation with the relative abundance of both genes. Using an extreme gradient boosting (XGBoost) model, we predicted global distribution patterns based on extrapolation, revealing concordant global trends, with lower relative abundances in regions with greater seasonal temperature variation. Future projections of BIO4 and viral gene abundance further supported this significant negative correlation.

CONCLUSIONS: Our findings reveal that temperature seasonality constrains the abundance of soil T4-like bacteriophages, which serve as sensitive indicators of climate-driven environmental shifts and play important ecological roles within soil microbial communities.}, } @article {pmid41327491, year = {2025}, author = {Wu, H and Sun, Z and Chen, B and Hu, X and Li, Y}, title = {Enhanced nitrogen load improved soil phosphorus availability by regulating P-cycling microbial genes in a typical subtropical estuary (Min River), Southeast China.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {151}, pmid = {41327491}, issn = {2524-6372}, support = {No. 42371105//the National Natural Science Foundation of China/ ; No. 2023J02012//the Key Program of Natural Science Foundation of Fujian Province/ ; }, abstract = {BACKGROUND: Enhanced nitrogen (N) load was considered a critical factor influencing phosphorus (P) availability and P-cycling in marsh soils. However, information on the links between soil P availability and microbial genes involved in P-cycling processes under N enrichment conditions remains scarce.

METHODS: A field N load experiment with four treatments (N0, Nlow, Nmedium, and Nhigh) was conducted in Cyperus malaccensis marsh of the Min River estuary, and soil P availability, the relative abundances of P-cycling functional genes and their regulatory roles on P availability were investigated.

RESULTS: The total phosphorus (TP) contents in soils were significantly positively correlated with N load levels (p < 0.05). Compared with the N0 treatment, the TP in the Nlow, Nmedium and Nhigh treatments increased by 8.97%, 17.34% and 15.21%, respectively. With increasing N load levels, the proportions of easily- and moderately-available P in TP contents noticeably increased, suggesting that N additions enhanced soil P availability. Metagenomic sequence analyses showed that N enrichment markedly altered the relative abundances of P-cycling functional genes. Briefly, the abundances of inorganic P solubilization genes (particularly ppa and ppx) increased substantially with increasing N load levels. The total abundances of organic P mineralization genes in the Nlow and Nmedium treatments decreased markedly, while those in the Nhigh treatment increased greatly. The abundances of genes coding for phytase (phy and appA) markedly increased with increasing N load levels, implying that phytase was more sensitive to N enrichment. Furthermore, enhanced N load noticeably reduced the abundances of genes participated in P transportation (particularly ugpABEC) and those involved in P-assimilating process (e.g., phoR, phoB, pstABCS and pit). As affected by enhanced N load, the contents of easily-available P showed strong correlations with the abundances of genes involved in inorganic P solubilization while those of moderately-available P (particularly Sonic-Pi, Sonic-Po and NaOH-Pi) were positively correlated with the abundances of genes involved in P regulation and transportation, indicating strong linkages between P-cycling functional genes and soil P availability.

CONCLUSIONS: This paper found that, under N enrichment conditions, the increased inorganic P solubilization potential and the weakened microbial P immobilization capacity were beneficial to increasing soil P availability.}, } @article {pmid41327872, year = {2026}, author = {Zhang, Y and Zhang, Z and Chen, Z and Yang, B and Cai, S and Chen, J and Guo, J and Zhang, W}, title = {2-line Ferrihydrite Enhance Microbial Synthesis of Plant Biostimulants in Composted Biosolid by Regulating Phyla Pseudomonadota and Actinomycetota.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {13}, number = {9}, pages = {e06502}, pmid = {41327872}, issn = {2198-3844}, support = {U24A20193,52270141//The National Natural Science Foundation of China/ ; 2024BCA006//Hubei Province Technological Innovation Plan Project/ ; 122-G1323522145//Fundamental Research Funds for the central Universities, China University of Geosciences/ ; }, mesh = {*Ferric Compounds/pharmacology/metabolism ; *Actinobacteria/metabolism/drug effects ; Sewage/microbiology ; Soil Microbiology ; Soil/chemistry ; }, abstract = {The discovery of plant biostimulants (PBs) in sewage sludge offers a promising avenue for biosolids valorization. Here, the study investigates how two mineral additives, including 2-line ferrihydrite (a disordered iron oxide) and disordered birnessite (a manganese oxide), modulate microbial activity and molecular pathways to enhance PB production during aerobic sludge composting. Application of 2-line ferrihydrite significantly promotes the synthesis of growth-promoting PBs, including arginine, valine, decanoic acid, and indoleacetic acid (IAA), while disordered birnessite primarily enhances resistance-related PBs, such as decanoic acid, L-pyroglutamate, and trans-aconitic acid. In pot trials, composted biosolids amended with 2-line ferrihydrite significantly improve plant biomass and leaf area compared to mineral-free and birnessite treatments. Metagenomic profiling reveals that PB biosynthesis is dominated by members of the phyla Pseudomonadota and Actinomycetota, with temporal niche partitioning across the thermophilic and maturation stages. 2-line ferrihydrite enhances the abundance of critical biosynthetic genes (e.g., trpA/C/D/E/F), particularly within taxa such as Xanthomonadaceae, Sphingomonadaceae, and Streptosporangiaceae. Additionally, genes involved in IAA and indole biosysnthesis (ALDH, DDC, and tnaA) are enriched, supporting enhanced tryptophan-to-IAA conversion. This study provides a mechanistic link between iron oxide-mediated microbial modulation and PB production in composted biosolids, offering a sustainable approach for upgrading waste into high-value agricultural inputs.}, } @article {pmid41328016, year = {2025}, author = {Fresno, C and Oropeza-Valdez, JJ and Alvarado-Luis, PI and Peña-González, P and Tovar, AR and Torres, N and Diener, C and Gibbons, S and Resendis-Antonio, O}, title = {MICOMWeb: a website for microbial community metabolic modeling of the human gut.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2587968}, pmid = {41328016}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Internet ; *Gastrointestinal Tract/microbiology/metabolism ; Models, Biological ; Software ; Computer Simulation ; Computational Biology/methods ; }, abstract = {MICOMWeb is a user-friendly website for modeling microbial community metabolism in the human gut. This website tackles three constraints when generating in silico metagenome-scale metabolic models: i) the prior Python user knowledge for metabolic modeling using flux balance analysis with the MICOM Python package, ii) predefined and user-defined diets to generate ad hoc metabolic models, and iii) the high-throughput computational infrastructure required to obtain the simulated growth and metabolic exchange fluxes, using real abundance from metagenomic shotgun or 16S amplicon sequencing; we present MICOMWeb's features to easily run in silico experiments as a functional hypothesis generator for experimental validation on three previously published databases. MICOMWeb has a constant run-time independent of the number of samples provided and database complexity. In practical terms, this behavior is upper-bounded by the sample with the greatest microbiota diversity, i.e., the sample with the largest metabolic reconstruction model size. The evidence suggests that the bigger the database, the better the MICOMWeb performs compared to MICOM in terms of consumed RAM (from 3.52 up to 7.13 folds) and total execution time (from 10.87 up to 205.05 folds).}, } @article {pmid41328030, year = {2025}, author = {Hickman, B and Korpela, K}, title = {Impact of data compositionality on the detection of microbiota responses.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2590841}, pmid = {41328030}, issn = {1949-0984}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Humans ; Computer Simulation ; *Gastrointestinal Microbiome ; Computational Biology/methods ; *Metagenomics/methods ; }, abstract = {Next-generation sequencing (NGS) data usage is widespread, but its compositional nature poses challenges. We evaluated four normalization methods (relative abundance, CLR, TMM, DESeq2) for identifying true signals in compositional microbiota data using simulations. Two experiments were conducted: one with only increases in specific taxa, and a 1:1 increase/decrease in specific taxa. Simulated sequencing produced compositional data, which were normalized using the four methods. The study compared absolute abundance data and the normalized compositional data using variance explained and false discovery rates. All normalization methods showed decreased variance explained and increased false positives and negatives compared to absolute abundance data. CLR, TMM, and DESeq2 did not improve over relative abundance data and sometimes worsened false discovery rates. The study highlights that false positives and negatives are common in compositional NGS datasets, and current normalization methods do not consistently address these issues. Compositionality artefacts should be considered when interpreting NGS results and obtaining absolute abundances of features/taxa is recommended to distinguish biological signals from artefacts.}, } @article {pmid41328248, year = {2025}, author = {Rossi, E and Pato, U and Ayu, DF and Melia, S and Sukma, A and Rahmayuni, R and Salman, AN}, title = {Bacterial biodiversity and metagenomic study of dadih, traditional fermented buffalo milk from Kampar district, Riau, Indonesia.}, journal = {Journal of advanced veterinary and animal research}, volume = {12}, number = {3}, pages = {717-727}, pmid = {41328248}, issn = {2311-7710}, abstract = {OBJECTIVE: This study aimed to investigate the metagenomic and microbial diversity of dadih in Kampar District, Riau, Indonesia.

MATERIALS AND METHODS: The dadih samples were collected from dadih producers in three villages, namely Limau Manis (LM), Rumbio (RB), and Muaro Jalai (MJ). DNA samples were extracted and sequenced through Oxford Nanopore Technology (ONT), operated by MinKNOW software version 23.04.5. Library preparations were conducted using kits from ONT.

RESULTS: The next-generation sequencing analysis on three dadih from Kampar identified two bacterial phyla, Bacillota and Pseudomonadota. Furthermore, there was a slight variation in dadih's microbiota composition between LM, RB, and MJ. The Bacillota phylum dominated the dadih microbiota in LM and RB villages, with a relative abundance of 60%-80%. The dadih from MJ was dominated by the phylum Pseudomonadota, which reached 55%. The dominant species found in all three dadih was Lactococcus lactis, with an abundance of 53.80, 80.80, and 40.31% for dadih LM, RB, and MJ, respectively.

CONCLUSION: Dadih MJ had the highest Simpson's value (~0.8), showing a relatively even abundance of species in the sample. Furthermore, dadih LM had a high Simpson's value (~0.75), indicating similar conditions to dadih MJ. Dadih RB had the lowest Simpson's value (~0.4), confirming that the microbiota in the sample tends to be dominated by certain species with a less even distribution.}, } @article {pmid41328415, year = {2025}, author = {Long, D and Zhao, W and Li, X and Sun, Q and Li, J and Lin, X}, title = {Rhizosphere Effect Enhances Belowground Competition of Coastal Invasive Spartina alterniflora With Mangroves.}, journal = {Ecology and evolution}, volume = {15}, number = {12}, pages = {e72565}, pmid = {41328415}, issn = {2045-7758}, abstract = {Spartina alterniflora has severely invaded mangroves in China. In order to explore the possible belowground interspecific interaction along with its invasion, the rhizosphere effect enhancing the competition of S. alterniflora neighboring mangroves was hypothesized. Here, both rhizosphere soil of S. alterniflora and bulk soil were collected from the center of S. alterniflora marsh and border sites where S. alterniflora was adjacent to Kandelia obovata and Aegiceras corniculatum, respectively, in both vigorous growth and senescent periods. Soil nutrient properties, rhizospheric low-molecular-weight organic acids (LMWOAs), soil microbiomes, and microbial functional genes were analyzed. Soil total carbon and total nitrogen contents of S. alterniflora neighboring mangroves were increased, and its LMWOAs were altered when adjacent to mangroves in both vigorous growth and senescent periods. These changes were significantly correlated with variation in the composition of S. alterniflora rhizosphere microbiome. Microbial interkingdom co-occurrence networks were simplified when S. alterniflora neighbored mangroves, while network modularity significantly increased. Metagenomics indicated that genes involved in methanogenesis (ackA, mvhD, etc.) and nitrogen fixation (nifH, nifK, etc.) were significantly enriched in those S. alterniflora neighboring K. obovata, and genes related to phosphate transporter (pstA, pstB, etc.) were significantly enriched in those S. alterniflora neighboring A. corniculatum. These results demonstrated that the rhizosphere effect intensified the belowground interspecific competition of S. alterniflora adjacent to mangroves by altering root exudates, changing the soil microbial composition, and modulating strategies for core nutrient metabolism.}, } @article {pmid41328416, year = {2025}, author = {Ueira-Vieira, C and Santos, ACC and Araújo, TN and Augusto, SC and de Avila, NB and Bonetti, AM and Dos Santos, AR}, title = {A Deep Metagenomic Snapshot as a Proof-of-Concept for Resource Generation: Simultaneous Assembly of Host, Food, and Microbiome Genomes From Stingless Bee Larval Food.}, journal = {Ecology and evolution}, volume = {15}, number = {12}, pages = {e72546}, pmid = {41328416}, issn = {2045-7758}, abstract = {Characterizing the complex web of ecological interactions is a central challenge in molecular ecology. Shotgun metagenomics of environmental samples offers a powerful, high-resolution approach, yet its potential for simultaneously generating multiple genomic resources from different trophic levels remains underexplored. This study serves as a proof-of-concept, using deep sequencing of a single, complex sample-the larval food of the stingless bee Tetragonisca angustula-to demonstrate the method's capacity to recover genomic information across varying template abundances. We successfully assembled three genomes of different completeness levels: a near-complete bacterial genome (Acetilactobacillus jinshanensis, 2,097,977 bp with 0.002% ambiguous bases), a draft mitochondrial genome (T. angustula, 15,498-15,549 bp), and a fragmented chloroplast genome (Lactuca sativa, 130,532 bp with 23.47% ambiguous bases). The assembly quality gradient, observed from complete to fragmented, directly reflects the relative abundance of each DNA template in the environmental sample, demonstrating the method's sensitivity and ecological informativeness. Beyond these genomic resources, the data provided a comprehensive biodiversity profile, revealing DNA from seven major taxonomic groups, including 209 bacterial genera, 123 plant families, and 55 insect taxa. Additionally, genomic comparisons using Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (dDDH) analyses suggest that the dominant bacterial strain represents a putative novel species within the genus Acetilactobacillus. This approach simultaneously provided insights into host genetics, food sources, and microbial communities, illustrating the potential of single metagenomic datasets to generate multiple valuable genomic resources for molecular ecology research.}, } @article {pmid41328492, year = {2025}, author = {Knoll, RL and Podlesny, D and Fortmann, I and Göpel, W and Zemlin, M and Lynch, S and Bork, P and Gehring, S and Härtel, C}, title = {Staphylococcus aureus colonization and bloodstream infection in very preterm infants.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2592423}, pmid = {41328492}, issn = {1949-0984}, mesh = {Humans ; *Staphylococcal Infections/epidemiology/microbiology ; Infant, Newborn ; Feces/microbiology ; *Staphylococcus aureus/isolation & purification/genetics/growth & development/classification ; Female ; Male ; Infant, Premature ; *Bacteremia/microbiology/epidemiology ; Gastrointestinal Microbiome ; Germany/epidemiology ; Infant ; Cohort Studies ; Infant, Very Low Birth Weight ; Metagenomics ; Incidence ; Gestational Age ; }, abstract = {BACKGROUND: Staphylococcus (S.) aureus remains a frequent pathogen for neonatal late-onset bloodstream infections (BSIs). The impact of colonization screening on BSI incidence is less understood.

METHODS: We assessed the epidemiology of late-onset S. aureus BSI in two independent multicenter cohorts of preterm infants born at < 33 weeks' gestation, the German Neonatal Network (GNN, very low birth weight infants) and PRIMAL (infants with a gestational age 28-32 weeks). In the PRIMAL cohort, we determined S. aureus colonization in fecal samples by culture and shotgun metagenomic sequencing (metaG) during the first year of life. In addition, we integrated publicly available metaG data from preterm infant cohorts born at 23-34 weeks' gestation.

RESULTS: Late-onset S. aureus BSI was noted in 1.5% (336/21491) in preterm infants in the GNN cohort and 0.5% (3/638) in the PRIMAL cohort, respectively. At day 30 of life, 7.6% (42/553) of fecal samples were positive for S. aureus, while available metaG data of corresponding samples revealed S. aureus positivity in 36.6% (159/434). Every 10-fold increase in S. aureus relative abundance (metaG) was associated with a 2.9-fold higher odds of S. aureus detection in blood culture. We also confirmed S. aureus detection in 22% (393/1782) of samples across several published cohorts of preterm infants by metaG, while 95 samples carried at least one Staphylococcus-specific virulence gene (SVG).

CONCLUSION: Our study demonstrates that metagenomic quantification of pathobionts such as S. aureus in intestinal samples provides a stronger predictor of colonization than culture. Future prevention strategies should focus on promoting S. aureus colonization resistance through microbiome-informed approaches.}, } @article {pmid41328758, year = {2026}, author = {Plewnia, A and Hoenig, BD and Lötters, S and Heine, C and Erens, J and Böning, P and Bending, GD and Krehenwinkel, H and Williams, MA}, title = {The Emergence of a CRISPR-Cas Revolution in Ecology: Applications, Challenges, and an Ecologist's Overview of the Toolbox.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70086}, pmid = {41328758}, issn = {1755-0998}, support = {//University of Warwick/ ; NE/S010270/1//Natural Environment Research Council/ ; }, mesh = {*CRISPR-Cas Systems ; *Ecology/methods ; *Gene Editing/methods ; }, abstract = {CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated nucleases) systems allow researchers to detect, capture, and even alter parts of an organism's genome. However, while the use of CRISPR-Cas has revolutionised many fields in the life sciences, its full potential remains underutilised in ecology and biodiversity research. Here we outline the emerging applications of CRISPR-Cas in ecological contexts, focusing on three main areas: nucleic acid detection, CRISPR-enhanced sequencing, and genome editing. CRISPR-based nucleic acid detection of environmental DNA samples is already reshaping species monitoring, providing highly sensitive and non-invasive tools for both scientists and the public alike, with reduced costs and minimal experience required. Further, CRISPR-enhanced sequencing, including Cas-mediated target enrichment, enables efficient recovery of ecologically relevant loci and supports diverse applications such as amplification-free metagenomics. Finally, while genome editing on wild species remains largely theoretical in ecology, these tools are already being used in controlled settings to study adaptation and resilience in the face of ongoing global stressors. Together, the applications of CRISPR-Cas are paving the way for more affordable, accessible, and impactful applications for species conservation, and promise to improve our ability to tackle the ongoing global biodiversity crisis.}, } @article {pmid41329990, year = {2025}, author = {Choi, HI and Cha, JM}, title = {Non-invasive colorectal cancer screening: emerging tools and clinical evidence.}, journal = {Clinical endoscopy}, volume = {}, number = {}, pages = {}, doi = {10.5946/ce.2025.246}, pmid = {41329990}, issn = {2234-2400}, abstract = {The fecal immunochemical test (FIT) is a widely used non-invasive screening method for colorectal cancer (CRC) in many countries, valued for its simplicity, affordability, and reasonable sensitivity. Typically recommended on an annual or biennial basis, the FIT is effective in reducing CRC incidence and mortality by facilitating early detection. Stool DNA tests, including multitarget DNA tests and DNA methylation assays, demonstrate higher sensitivity than FIT for CRC and advanced adenomas, although they have slightly lower specificity and higher cost. These tests are generally performed at longer intervals, such as every 3 years, and are useful alternatives for individuals who are unwilling or unable to undergo a colonoscopy. Emerging non-invasive CRC screening tools, such as liquid biopsy, microRNA, microbiome tests, and urine-based tests, are being developed to improve patient compliance and test convenience. In particular, liquid biopsy offers a minimally invasive option that may be more acceptable to populations hesitant to undergo stool-based tests. Furthermore, the integration of machine learning with metagenomic sequencing data has shown promise in distinguishing patients with CRC from healthy individuals. As CRC screening evolves, these novel approaches may enable the development of more personalized, accessible, and effective screening strategies, ultimately improving adherence and reducing CRC-related mortality.}, } @article {pmid41330099, year = {2025}, author = {Barman, P and Paul, A and Sinha, S and Saha, T and Mondal, N and Dutta, S and Chatterjee, S and Ghosh, W and Chakraborty, R}, title = {Microbial-viral synergy in Eisenia fetida gut supports earthworm survival, detoxification, and functional resilience.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181101}, doi = {10.1016/j.scitotenv.2025.181101}, pmid = {41330099}, issn = {1879-1026}, mesh = {Animals ; *Oligochaeta/physiology/virology/microbiology ; *Gastrointestinal Microbiome ; Soil Pollutants/metabolism ; Inactivation, Metabolic ; RNA, Ribosomal, 16S ; Biodegradation, Environmental ; Bacteria ; Metagenome ; }, abstract = {The ecological success of Eisenia fetida within decomposer food webs is closely linked to the functional diversity of its gut microbiome. This study integrates 16S rRNA gene profiling, whole-metagenome sequencing, and virome analysis to elucidate how microbial and viral communities within the earthworm gut contribute to nutrient biosynthesis, xenobiotic degradation, and environmental adaptation. Earthworms reared on compost feed enriched with Quisqualis indica plant matter showed selective enrichment of bacterial genera such as Ohtaekwangia, Nocardioides, and Steroidobacter, which are associated with hydrocarbon degradation and aromatic compound detoxification. Functional annotation of the gut metagenome revealed complete biosynthetic pathways for riboflavin, lysine, and methionine, and degradation routes for 3-nitropropionic acid (3-NPA) and aromatic pollutants. The gut virome, dominated by Siphoviridae and Myoviridae, carried auxiliary metabolic genes (AMGs) related to redox and xenobiotic metabolism, highlighting viral contributions to microbial adaptability. Reconstruction of metagenome-assembled genomes (MAGs), including a high-quality Flavobacterium MAG encoding both riboflavin biosynthesis and denitrification genes, underscored metabolic specialization within the gut. Collectively, these findings demonstrate that bacterial-viral metabolic synergy underpins E. fetida survival and ecological resilience, suggesting new microbiome-informed strategies for biowaste valorization and soil health restoration through vermicomposting.}, } @article {pmid41330199, year = {2026}, author = {Li, S and Wang, XR and Han, JR and Lian, WH and Ali, M and Liu, YH and Liu, J and Huang, J and He, HH and Govindan, R and Abdalla Abdelshafy Mohamad, O and Fang, BZ and Dong, L and Li, WJ}, title = {Genome-centric culture-enriched metagenomics reveals temperature-driven reassembly and functional stratification in culturable desert soil bacteria.}, journal = {Microbiological research}, volume = {304}, number = {}, pages = {128411}, doi = {10.1016/j.micres.2025.128411}, pmid = {41330199}, issn = {1618-0623}, mesh = {*Soil Microbiology ; *Metagenomics/methods ; Desert Climate ; *Bacteria/genetics/classification/isolation & purification/growth & development ; Temperature ; Rhizosphere ; Metagenome ; Microbiota/genetics ; Genome, Bacterial ; Soil/chemistry ; Phylogeny ; Ecosystem ; }, abstract = {Desert ecosystems cover nearly one-third of Earth's land surface and face rising temperatures and climatic variability. Soil microbiomes underpin biogeochemical cycling and ecosystem resilience in these arid landscapes, yet the genome-resolved temperature responses of their culturable fraction remain poorly understood. Here, we employed genome-centric culture-enriched metagenomics (CE-MGS) to rhizosphere and bulk desert soils from the Gurbantunggut Desert incubated at 15°C, 30°C, and 45°C. From 90 culture-enriched metagenomes, we reconstructed 1184 cultivated metagenome-assembled genomes (cMAGs), including 218 putative novel genomospecies across 73 bacterial genera, substantially expanding the genomic representation of desert bacteria. Temperature influenced both community composition and interactions, with Actinomycetota, Pseudomonadota, and Bacillota dominating at 15°C, 30°C, and 45°C, respectively. Co-occurrence networks showed that lower temperatures and rhizosphere soils supported more interconnected consortia of culturable bacteria and that key hub taxa shifted across thermal regimes, reflecting temperature-driven reorganization of interactions within the culturable microbial community. Functional profiling revealed that temperature selected for specialized taxa, with elevated temperatures favoring redox-efficient pathways and more energy-efficient resource use. While representing only the culturable fraction of desert soil microbiomes, CE-MGS enables genome reconstruction of experimentally tractable microbes, linking identity, function, and thermal adaptation. These results provide a genome-resolved view of temperature responses, extend understanding of desert microbial adaptation beyond previous culture-independent studies, and establish CE-MGS as a practical approach to access ecologically relevant microbes for conservation and biotechnological applications under a warming climate.}, } @article {pmid41330298, year = {2025}, author = {Huang, Y and Li, R and Dai, Y and Ren, Z and Wu, J}, title = {Migration characteristics of ARGs from pig manure in compost - soil - lettuce.}, journal = {Ecotoxicology and environmental safety}, volume = {308}, number = {}, pages = {119447}, doi = {10.1016/j.ecoenv.2025.119447}, pmid = {41330298}, issn = {1090-2414}, mesh = {*Manure/microbiology ; Animals ; *Composting ; *Lactuca/microbiology ; Swine ; *Soil Microbiology ; Soil/chemistry ; Anti-Bacterial Agents ; *Soil Pollutants/analysis ; }, abstract = {This study aims to reveal the contamination patterns, persistence characteristics, and fate dynamics of ARGs during aerobic composting of swine manure with different carbon-nitrogen ratios (C/N = 15:1, 25:1, 35:1) and their subsequent dissemination in soil-plant systems following fertilization. The absolute abundances of 101 ARGs of six categories ranged from 10[5] to 10[14] copies/g during the composting process. The tetracyclines, macrolides and β-lactams ARGs were effectively reduced by the maturation phase. Among them, the β-lactam ARGs had the highest abatement efficiency (73-89 %). Quinolones, aminoglycosides and sulfonamides ARGs had relatively high residues during the maturation phase. Composting treatments with higher C/N (25:1 and 35:1) exhibited superior performance in ARGs reduction. Metagenomic analysis revealed the compost microbial community succession from Firmicutes to Proteobacteria and Actinobacteria. Luteimonas may be potential hosts for high-residual ARGs in compost, while Acinetobacter exhibited strong associations with β-lactam and macrolide ARGs that can be easily reduced. The ARGs in the fertilized soil increased significantly. ARGs such as floR, tetG-01, sul1 and sul2 have the highest abundance in the soil where lettuce is grown. The ARGs reduction is better in C/N 25:1 group, and the ARGs abundance of the soil is lower after fertilization with compost products. The sulfonamide sul1 and sul2 genes have always maintained a high abundance in compost, soil and lettuce. This study provides a theoretical basis for controlling the residue and spread of ARGs by regulating the C/N of compost to drive changes in microbial community.}, } @article {pmid41330454, year = {2026}, author = {Zhao, D and Zou, B and Do, QL and Wu, SK and Shen, Y and Yang, Y and Kang, JX and Su, KP and Wang, B}, title = {Circadian rhythms and gut microbiota Dysbiosis: emerging gut-brain axis pathways in insomnia pathophysiology and Therapeutics.}, journal = {Brain, behavior, and immunity}, volume = {132}, number = {}, pages = {106203}, doi = {10.1016/j.bbi.2025.106203}, pmid = {41330454}, issn = {1090-2139}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Circadian Rhythm/physiology ; *Sleep Initiation and Maintenance Disorders/physiopathology/microbiology/therapy ; *Dysbiosis/physiopathology/microbiology ; Animals ; Brain/physiopathology ; Probiotics/therapeutic use ; Sleep/physiology ; *Brain-Gut Axis/physiology ; }, abstract = {Insomnia, a widespread sleep disorder, significantly impacts mental and physical health. Emerging research highlights the crucial role of gut microbiota (GM) in modulating circadian rhythms (CR), which regulate sleep-wake cycles. This review explores the interplay between GM dysbiosis, CR disruptions, and insomnia, synthesizing findings from human and animal studies. GM dysbiosis is linked to reduced microbial diversity and altered abundance of key taxa, such as short-chain fatty acid-producing bacteria, which influence clock gene expression and hormonal rhythms. CR disruption exacerbates GM imbalances, forming a feedback loop that impairs sleep regulation through both central and peripheral pathways. We also examine the therapeutic potential of probiotics in restoring GM balance and synchronizing CR. Clinical trials suggest that specific probiotic strains improve sleep quality by modulating microbial metabolites and their downstream effects on the circadian system. However, inconsistencies in outcomes underscore the need for precision interventions. The review concludes by identifying gaps in the current literature, emphasizing the necessity of integrative approaches combining metagenomics and personalized medicine to optimize GM-targeted therapies. These insights pave the way for novel, safer, and more effective strategies to manage insomnia by addressing its biological underpinnings.}, } @article {pmid41330588, year = {2025}, author = {Chen, HP and Zhu, B and Wang, XF and Zhou, XJ and Du, Y and Mu, ZL}, title = {[Nasal infection with Mycobacterium avium complex: a case report].}, journal = {Zhonghua er bi yan hou tou jing wai ke za zhi = Chinese journal of otorhinolaryngology head and neck surgery}, volume = {60}, number = {11}, pages = {1439-1440}, doi = {10.3760/cma.j.cn115330-20241219-00698}, pmid = {41330588}, issn = {1673-0860}, support = {82360504//National Natural Science Foundation of China/ ; }, mesh = {Female ; Humans ; Middle Aged ; Biopsy ; Endoscopy ; *Epistaxis/diagnosis/microbiology/therapy ; Metagenomics ; *Mycobacterium avium Complex/genetics/isolation & purification ; *Mycobacterium avium-intracellulare Infection/complications/diagnosis/microbiology/therapy ; Nasal Cavity/diagnostic imaging/microbiology/pathology ; Nasal Mucosa/diagnostic imaging/microbiology/pathology ; Nasal Septum/diagnostic imaging/microbiology/pathology ; *Rhinitis/complications/diagnosis/microbiology/therapy ; }, } @article {pmid41331251, year = {2025}, author = {Zhao, Y and Chen, H and Huang, J and Chistoserdova, L and Yu, Z}, title = {The gut methanotroph Methylocystis intestini modulates intestinal peristalsis and fat metabolism via reducing methane levels.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {2}, pmid = {41331251}, issn = {2041-1723}, support = {32300051//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Humans ; Male ; Mice ; Rats ; Constipation/microbiology ; Feces/microbiology ; Gastrointestinal Diseases/microbiology ; *Gastrointestinal Motility ; *Lipid Metabolism ; Metagenome ; *Methane/metabolism ; *Methylocystaceae/classification/genetics/isolation & purification/metabolism ; Mice, Inbred C57BL ; Obesity/microbiology ; Rats, Sprague-Dawley ; *Peristalsis ; Animals, Outbred Strains ; }, abstract = {Methane, a predominant component of human intestinal gas, has been reported to be associated with a reduction in intestinal transit speed, as well as correlations with elevated body mass index. While the gut methanogenic archaea that produce this gas have been studied, the countervailing role of methane-consuming bacteria (methanotrophs) within the human gut ecosystem remains a critical, under-explored area. The potential for these bacteria to act as a built-in sink for intestinal methane and thereby mitigate its negative physiological effects is unknown. Here, we isolate an unreported methanotroph from human fecal samples, classified as Methylocystis intestini. Using a mouse model, we observe that methane challenge is associated with gastrointestinal motility and fat metabolism. We then demonstrate that the administration of Methylocystis intestini effectively reverses these dysfunctional processes, restoring motility and metabolic parameters. Additional analysis of methane-oxidation genes abundance in 1207 public metagenomic sequences from individuals with varying health statuses, including obesity and constipation, provides consistent correlative support for our experimental conclusions. Expanding this view to a global scale, we conducted a metagenomic survey of 550 human fecal samples from populations across five continents. This broader analysis reveals that methane-oxidizing genes are not a rarity but a common feature of the human gut microbiome, being detectable in over 91% of samples. This ubiquity underscores their fundamental role in human biology. Collectively, our findings establish gut methanotrophs as key mediators of intestinal methane level. Their presence is widespread across global populations, and their functional capacity can balance the effects of methane on host physiology. This work elucidates a crucial component of gut homeostasis and opens a promising avenue for developing microbiome-based therapeutic strategies aimed at managing methane-related gastrointestinal disorders by harnessing the power of these native methane-consuming bacteria.}, } @article {pmid41331462, year = {2025}, author = {Xu, W and Wang, W and Liu, Q}, title = {Identification of a novel pegivirus in reindeer (Rangifer tarandus valentinae) in Northeastern China.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {9}, pmid = {41331462}, issn = {1746-6148}, support = {2024YFD1800103//This study was financially supported by the National Key Research and Development Program of China ./ ; }, mesh = {Animals ; *Reindeer/virology ; *Flaviviridae Infections/veterinary/virology/epidemiology ; Phylogeny ; China/epidemiology ; Genome, Viral ; *Pegivirus/genetics/isolation & purification/classification ; }, abstract = {BACKGROUND: Pegiviruses (family Flaviviridae), associated with persistent infections in diverse mammalian and avian hosts, are increasingly recognized for their evolutionary significance. Reindeer (Rangifer tarandus valentinae), semi-domesticated in northeastern China's Greater Khingan Mountains, are critical reservoirs for zoonotic pathogens and face growing human contact due to tourism. This study aims to investigate the viral diversity in reindeer, identify potential viruses of public health or veterinary significance, and highlight the need for viral surveillance at the human-animal interface.

RESULTS: The metagenomic sequencing analysis identified a novel pegivirus, Rangifer tarandus pegivirus (RPgV), in reindeer serum from Inner Mongolia. The near-complete genome (10,367 nucleotides; GenBank OQ164633) encodes a polyprotein (3,249 amino acids) processed into four structural (Y, E1, E2, X) and six non-structural (NS2-NS5B) proteins. RPgV shares 57.3% nucleotide and 60.6% amino acid identity with its closest relative, equine pegivirus (EPgV), but exceeds species demarcation thresholds for NS3 (p-distance: 0.340) and NS5B (p-distance: 0.408). Phylogenetic analyses placed RPgV within the equine pegivirus clade, while cophylogenetic models revealed strong host specificity and co-divergence over evolutionary timescales. With a 9.5% prevalence (2/21) in sampled reindeer, RPgV represents the first pegivirus detected in Cervidae, underscoring its potential role in wildlife virome dynamics.

CONCLUSION: This study identified a novel pegivirus, which expands its host range, geographic distribution, and genetic diversity. This discovery highlights the need for enhanced surveillance of understudied viral families in regions where human-wildlife interfaces amplify zoonotic risks.}, } @article {pmid41331561, year = {2025}, author = {Tian, J and Wang, X and Zhu, Y and Kong, F and Sun, J}, title = {Diagnosis of esophageal pleural fistula via metagenomic next-generation sequencing of pleural effusion: a case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {1689}, pmid = {41331561}, issn = {1471-2334}, abstract = {Esophageal injury is a rare and life-threatening event. Esophageal perforation can rapidly contaminate the neck, mediastinum, pleural cavity, or abdominal cavity, leading to sepsis or septic shock. Its high complication and mortality rates are often associated with adjacent organ damage and/or delays in diagnosis or definitive treatment. We present a case of a patient who developed esophago pleural fistula(EPF) due to traumatic fall.A 64-year-old man presented with respiratory sepsis after a traumatic fall. Imaging demonstrated a massive pleural effusion. The initial lung CT did not reveal any abnormal communication between the esophagus and the pleural cavity. Metagenomic next-generation sequencing (mNGS) of pleural fluid revealed a microbial profile overwhelmingly composed of typical oropharyngeal flora, which was highly suggestive of an aero-digestive fistula. Subsequent gastroscopy and contrast examination confirmed a fistula between the distal esophagus and the left pleural cavity through a ruptured diaphragm. The patient underwent conservative treatment. A persistent effusion with a history of blunt thoracoabdominal trauma may raise suspicion for EPF, which, if not diagnosed promptly, may result in significant morbidity. This case provides new insights for diagnosing EPF following blunt trauma. Interpreting key subtle clues in pleural fluid analysis and imaging can lead to a timely diagnosis and thus improves morbidity and mortality of EPF.}, } @article {pmid41331687, year = {2025}, author = {Abedi, Z and Sheikh Beig Goharrizi, MA and Abbasi, A and Sadat Soleimani Zakeri, N and Jangi, H}, title = {Metagenomic insights into microbial community alterations and co-occurrence networks in infective endocarditis.}, journal = {Genomics & informatics}, volume = {23}, number = {1}, pages = {25}, pmid = {41331687}, issn = {1598-866X}, abstract = {BACKGROUND: Infective endocarditis (IE) is a serious infection of the heart valves, and standard culture methods often miss the bacteria responsible, especially in culture-negative cases. To address this, we used 16S rRNA gene-based next-generation sequencing (NGS) on heart valve tissue. This approach allowed us to map out the bacterial communities present and evaluate their potential role in IE.

RESULT: We identified six key bacterial genera-Enterococcus, Streptococcus, Coxiella, Staphylococcus, Haemophilus, and Cutibacterium-plus three specific species: Streptococcus troglodytae, Haemophilus parainfluenzae, and Coxiella burnetii. Our co-occurrence analysis showed that these bacteria tend to exist independently within infected valve tissue, with no significant correlations between them.

CONCLUSION: We detected bacterial taxa, including Cutibacterium and Streptococcus troglodytae. Although S. troglodytae is rarely associated with IE, and Cutibacterium comprises low-abundance bacteria not typically linked to this condition. These findings demonstrate the value of NGS in identifying pathogens that standard culture methods may overlook. As these results are based on computational analyses, further laboratory validation is required. Incorporating NGS into diagnostic protocols may enhance pathogen detection in culture-negative IE and support more targeted treatment and prevention strategies.}, } @article {pmid41331807, year = {2025}, author = {Rouzban, T and Goudarzi, R and Motamedi, E and Ghollasi, M and Zeinalabedini, M and Ariaeenejad, S}, title = {Metagenomic laccase-catalyzed crosslinking of wheat proteins for enhanced soybean meal nutritional value: applications in poultry feed and food industry.}, journal = {BMC biotechnology}, volume = {26}, number = {1}, pages = {2}, pmid = {41331807}, issn = {1472-6750}, support = {0//Agricultural Biotechnology Research Institute of Iran (ABRII)/ ; }, abstract = {BACKGROUND: Soybean meal (SBM) is a major protein source for human and animal nutrition, particularly in broiler diets, due to its high amino acid content and digestibility. However, its use is limited by low solubility, poor emulsification, and weak foaming properties. Improving these characteristics is crucial for enhancing feed functionality and nutritional value. Laccase-mediated protein crosslinking using phenolic mediators offers an eco-friendly enzymatic strategy to modify protein structure and functionality. This study aimed to enhance the functional and nutritional quality of SBM by enzymatically crosslinking wheat albumin (WAP) and globulin (WGP) using a metagenomic laccase (PersiLac2) with phenolic mediators caffeic acid (CA) and vanillic acid (VA). RESULTS: Crosslinking increased the water-holding capacity (WHC) of SBM from 4.34 to 5.25 g/g and the oil-holding capacity (OHC) from 0.74 to 1.12 g/g, while solubility improved from 33.6% to 47.6%. The antioxidant activity of the crosslinked proteins also rose markedly, with ABTS and DPPH scavenging reaching 91% and 54%, respectively. SDS-PAGE confirmed higher molecular weight aggregates, indicating successful crosslinking. In WAP, foaming capacity increased from 30% to 120% and stability from 33% to 58%, while in WGP, VA raised foaming capacity to 44% and PersiLac2 improved stability to 33%. FTIR and SEM analyses showed enhanced secondary structure stability and smoother surface morphology in treated SBM. CONCLUSIONS: Metagenomic laccase-catalyzed crosslinking in the presence of natural phenolic mediators effectively improves SBM’s structural, antioxidant, and interfacial properties, providing a sustainable biocatalytic route for upgrading food and feed protein quality.}, } @article {pmid41331875, year = {2025}, author = {Kong, L and Mao, Y and Zheng, R and Feng, Y and Chen, B and Wu, X and Zhu, Q and Feng, J and Liu, S}, title = {Overlooked siderophore producers favor ammonium oxidation in global wastewater treatment plants.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {14}, pmid = {41331875}, issn = {2049-2618}, support = {523B2095//National Natural Science Foundation of China/ ; Nos. 52270016//National Natural Science Foundation of China/ ; 2022YFC3203003//National Key Research and Development Program of China/ ; }, mesh = {*Siderophores/metabolism/biosynthesis ; Oxidation-Reduction ; *Wastewater/microbiology ; Sewage/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Iron/metabolism ; *Ammonium Compounds/metabolism ; Metagenomics/methods ; Water Purification ; Metagenome ; }, abstract = {BACKGROUND: Iron is essential for biological nitrogen removal in wastewater treatment plants (WWTPs), as a significant portion of microbial nitrogen-transforming enzymes require iron. However, iron bioavailability is a global challenge for nitrogen removal microbes in WWTPs, where it often exists in insoluble forms due to its complexation with various wastewater constituents.

RESULTS: Combined laboratory experiment and metagenomic analysis of 52 global WWTPs, we found that siderophore-producing bacteria (SPB) were previously uncharacterized dominant members in activated sludge. SPB enhance the iron uptake of activated sludge microbial communities by facilitating the transport of iron ions from insoluble sources into the cells. Of the 1328 total recovered metagenome-assembled genomes (MAGs) from global WWTPs, 6.2% were identified as SPB, while 79.3% of MAGs could utilize siderophores, indicating widespread sharing of siderophores in WWTPs. Interestingly, nearly all ammonium-oxidizing bacteria (AOB) from WWTPs lacked siderophore-producing capacity, and exogenous siderophore (20 µM pyochelin) addition boosted ammonium oxidation rates by 28.2%. Moreover, strong indications were found for an association between AOB and the SPB in global WWTPs, suggesting their symbiotic interaction is a common and critical process to maintain ammonium oxidation performance. SPB in WWTPs were predominantly aerobic or facultative anaerobic heterotrophic bacteria, exhibiting low taxonomic diversity but high abundance.

CONCLUSIONS: This study reveals SPB as previously overlooked but crucial contributors to biological nitrogen removal in global WWTPs, providing foundational insights into iron-based microbial cooperation within engineered systems. Modulating SPB activity based on their metabolic characteristics is a promising strategy to cope with low iron bioavailability issue for biological processes in WWTPs. Video Abstract.}, } @article {pmid41332430, year = {2025}, author = {Li, L and Zhou, N and Wang, Z and Wang, T and Wang, Y and Qiao, F and Du, ZY and Zhang, ML}, title = {Intestinal microbiota contributes to the heterogeneity of fat deposition by promoting mitochondrial fatty acid β-oxidation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2593076}, pmid = {41332430}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Fatty Acids/metabolism ; Carnitine/biosynthesis/metabolism ; Oxidation-Reduction ; *Mitochondria/metabolism ; Zebrafish ; Lipid Metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Male ; Humans ; Feces/microbiology ; }, abstract = {The gut microbiota plays a crucial role in lipid metabolism in both humans and animals. However, the specific contributions of gut microbiota and their associated metabolites to fat deposition, as well as the underlying mechanisms, remain largely unexplored. In this study, we demonstrated that the intestinal microbiota mediated the heterogeneity of mesenteric fat index (MFI), as evidenced by fecal microbiota transplantation (FMT) experiments. Notably, analysis of the 16S rRNA gene amplicon sequencing of 44 samples revealed a significantly higher abundance of Cetobacterium somerae in the Low MFI group, with a positive correlation to reduced MFI. Serum metabolomics analysis confirmed that L-Carnitine emerged as the most differentially abundant metabolite in the Low MFI group and exhibited a strong positive correlation with C. somerae abundance. Metagenomic analysis showed that microbial genes related to L-Carnitine biosynthesis were significantly enriched in the Low MFI group. Further, C. somerae was isolated and cultured, and its subsequent monocolonization in germ-free zebrafish and tilapia demonstrated its lipid-lowering effects by enhancing mitochondrial fatty acid β-oxidation. Whole genome sequencing demonstrated C. somerae could encode the [EC:1.2.1.3] gene, which promotes the production of 4-trimethylammoniobutanoate, a precursor of L-Carnitine, thereby enhancing L-Carnitine biosynthesis by the host and gut microbiota, leading to the reduced fat deposition in Nile tilapia. In conclusion, C. somerae, a core gut microbe with high abundance in aquatic teleost intestines, plays an important role in host lipid metabolism. This study advances our understanding of how core gut microbes shape host phenotypes and provides novel insights into manipulating core gut colonizers to reduce fat deposition.}, } @article {pmid41332561, year = {2025}, author = {Ahmed, MA and John, J and Campbell, BJ}, title = {Ecological distribution, environmental roles and drivers of Actinobacteriota in two Mid-Atlantic estuaries.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.21.689735}, pmid = {41332561}, issn = {2692-8205}, abstract = {Actinobacteriota, a bacterial phylum renowned for members that produce bioactive compounds (e.g., antibiotics), has key roles in terrestrial and aquatic ecosystems. Although soil and marine/freshwater Actinobacteriota are well studied, functions and activities of their estuarine counterparts are poorly understood. We characterized 67 metagenome-assembled genomes (MAGs) belonging to 12 Actinobacteriota families from Chesapeake and Delaware Bay water samples across different seasons, salinities, and size fractions. MAGs from four dominant families, Ilumatobacteraceae, Nanopelagicaceae, Microbacteriaceae, and S36-B12, were examined in depth for their abundance, functional potential, estimated growth rates, and gene expression among samples. Actinobacteriota were most abundant in low- to medium-salinity samples during spring and summer. Their abundance patterns were strongly influenced by combinations of salinity, temperature, and phosphate, nitrate and silicate concentrations. Notably, many exhibited high estimated growth rates under low and medium salinities in summer. Members of the four major families showed a range of metabolic capacities from generalist to specialist, and all encoded biosynthetic gene clusters (BGCs) for secondary metabolites, particularly terpenes and betalactones, that were differentially expressed across conditions. Bay, salinity and size fraction were the primary drivers of gene expression differences. Distinct secondary metabolite genes were expressed between bays, with higher expression generally observed in medium compared to low salinities. These findings underscore the metabolic versatility and environmental responsiveness of Actinobacteriota, highlighting their active role in estuarine microbial communities and their contributions to biogeochemical cycling in dynamic coastal ecosystems.}, } @article {pmid41332906, year = {2025}, author = {Zhao, Z and Lu, L and Yi, Y and Gao, N and Hu, J and Han, G and Ma, X}, title = {Gut microbiota signature in a cohort of Chinese patients with rosacea.}, journal = {Biochemistry and biophysics reports}, volume = {44}, number = {}, pages = {102361}, pmid = {41332906}, issn = {2405-5808}, abstract = {BACKGROUND: Rosacea is a chronic inflammatory skin disease characterized by diverse symptoms and variable clinical progression, which can significantly impair patients' quality of life and mental health. The exact etiology of rosacea remains elusive. It has been hypothesized that specific microorganisms may trigger symptom onset and play crucial roles in the pathogenesis of the disease.

OBJECTIVE: We performed a case-control study to investigate the gut microbiome of rosacea patients compared to controls matched by age, sex in China.

METHODS: The study cohort comprised eight patients diagnosed with rosacea and eight age- and sex-matched healthy controls residing in Beijing. Metagenomic sequencing was performed using on a llumina Novaseq 6000 platform. Hospital Anxiety and Depression Scale was used to evaluate the severity of anxiety and depression of rosacea patients. Skindex-16 score was used to assess dermatology-specific health-related quality of life (HrQoL) in patients with rosacea. The clinical evaluation of acne was done using the ECLA score.

RESULTS: The rosacea patients showed higher HADS and Skindex-16 score (15.375 ± 1.302 and 46 ± 9.75 respectively) vs healthy controls (3.425 ± 1.308 and 0 respectively). A clear distinction was observed between the rosacea group and the control group, characterized by a significant increase in the abundance of Turicibacter_sp._TJ11, Turicibacter_sp._H121,Turicibacter_sp._TA25,Turicibacter_sp._T129,Ruminococcus_sp._AF18-22,Ruminococcus_sp._CAG:379,Ruminococcus_sp._AM2829LB,Ruminococcus_callidus, Ruminococcus_sp._AM36-18,Ruminococcus_sp._AF43-11,Ruminococcus_sp._AM28-41,Streptococcus sp. 23.2,Streptococcus infantarius, Streptococcus vestibularis, Streptococcus salivarius, Streptococcus gordonii, Clostridium_sp._CAG:798, Clostridium_tertium, Alistipes_sp._Z76 and Lachnospiraceae_bacterium_XBB2008in the rosacea group. In contrast, reduced levels were detected in the rosacea group for Clostridium_sp._AF12-41, Clostridium_sp._CAG:299, Clostridium_sp._OM05-5BH,Clostridium_sp._AF24-2LB, Clostridium_sp._AM18-55, Clostridium_sp._CAG:43, Clostridium_sp._OM047,Clostridium_sp._TF1113AC,Clostridium_sp._OF134,Clostridium_disporicum, Butyrivibrio_sp._CB08,Butyrivibrio_sp._INlla14, Roseburia_sp._CAG:50 (p < 0.05). Pearson correlation analysis revealed that Gemmiger_sp._An120 was positively correlated with Skindex-16 and negatively correlated with ECLA score (P < 0.05). Clostridium_sp._CAG:299 was negatively correlated with HADS scores and positive correlation with ECLA score (P < 0.05). KEGG pathway analysis found KO05034, KO04024 and KO00920 pathways exhibited increased activity in the Rosacea group (P < 0.05).

CONCLUSIONS: The gut microbiota in individuals with rosacea displayed changed from that of healthy control. These microbial alterations may contribute to the pathogenesis of rosacea through multiple mechanisms, including impairment of the intestinal barrier function, induction of pro-inflammatory cytokine release, and modulation of neurotransmitter synthesis. By integrating taxonomic shifts with functional alterations, this study provides deeper insights into the gut ecosystem changes associated with systemic inflammation in rosacea.}, } @article {pmid41333054, year = {2025}, author = {Kravchuk, OI and Finoshin, AD and Nikishina, YO and Melnikova, VI and Kublanov, IV and Sutormin, DA and Rusanova, AN and Ri, MT and Isaev, AB and Mikhailov, KV and Ziganshin, RH and Adameyko, KI and Anashkina, AA and Ignatyuk, VM and Gornostaev, NG and Voronezhskaya, EE and Sokolova, AM and Mikhailov, VS and Lyupina, YV}, title = {Evolutionary conservation of dopamine-mediated cellular plasticity in Arctic sponges (Porifera).}, journal = {Frontiers in molecular biosciences}, volume = {12}, number = {}, pages = {1671771}, pmid = {41333054}, issn = {2296-889X}, abstract = {Dopamine is an evolutionarily ancient signaling molecule implicated in stress responses across the tree of life. The role of dopamine is well-documented in the nervous system of animals, yet in the early-branching animal lineage of sponges its utility is poorly understood. Arctic marine sponges inhabiting the tidal zone of the White Sea, with fluctuating seasonal ice cover and solute concentrations, exhibit remarkable physiological plasticity, making them ideal models for studying conserved stress-response mechanisms. We investigated the dopamine signaling in two sponge species, Sycon ciliatum (class Calcarea) and Halisarca dujardini (class Demospongiae), using metagenomics, transcriptomics, high performance liquid chromatography, mass spectrometry, molecular docking, and immunofluorescence. S. ciliatum expresses an aromatic amino acid decarboxylase-like enzyme and efficiently converts L-DOPA to dopamine, whereas H. dujardini lacks this canonical biosynthetic enzyme, but accumulates dopamine, likely via its symbionts. During morphogenetic transitions in H. dujardini, genes involved in dopamine turnover, including tyrosinase, dopamine β-hydroxylase, and G protein-coupled receptors (GPCRs), showed dynamic expression. Molecular docking revealed that GPCR affinity for dopamine is modulated by cellular redox status. Notably, we report the first evidence of post-translational dopaminylation of cytoskeleton proteins in a non-bilaterian animal. Fluctuations in cellular dopamine levels and actin dopaminylation correlated with structural remodeling of the aquiferous system throughout the sponge life cycle. These findings demonstrate that dopamine regulates cellular plasticity through both transcriptional and post-translational mechanisms. The discovery of dopaminylation in sponges expands the evolutionary scope of catecholamine signaling and underscores the ancient role of dopamine in the regulatory interactions of animal cells.}, } @article {pmid41333773, year = {2025}, author = {Li, Q and Sun, X and Lei, W and Zhu, Y and Du, W and Jiang, X and Su, N}, title = {Psittacosis chlamydia pneumonia complicated with organizing pneumonia: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1670456}, pmid = {41333773}, issn = {2296-858X}, abstract = {BACKGROUND: Secondary organizing pneumonia (SOP) may develop following infections. Psittacosis, caused by Chlamydia psittaci (C. psittaci), is a zoonotic disease transmitted from birds to humans. It can present with a wide spectrum of symptoms, ranging from mild flu-like illness to life-threatening severe pneumonia. Cases of C. psittaci infection complicated by organizing pneumonia (OP) are rarely reported, and delayed treatment may pose a life-threatening risk.

METHODS: We report a case of C. psittaci pneumonia complicated by OP. To identify additional cases and clarify the clinical features of this condition, a literature search was conducted using the PubMed and Embase databases for the period from January 1995 to May 2025. The search included the following keywords: "psittacosis," "Chlamydia psittaci," "chlamydia," "organizing pneumonia," and "bronchiolitis obliterans with organizing pneumonia."

RESULTS: A 66-year-old male with a history of poultry farming presented with fever, cough, sputum production, and hemoptysis. Empirical antimicrobial therapy with ceftizoxime was ineffective. To identify the etiology of the pulmonary lesions, bronchoscopy was performed, and C. psittaci infection was confirmed by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). Although the lesions partially resolved after moxifloxacin therapy, the patient experienced recurrent episodes. Chest CT revealed migratory lesions, which are uncommon in C. psittaci pneumonia. Further pathological examination of the specimen confirmed the diagnosis of OP. The patient's condition improved following corticosteroid therapy. A review of the literature indicated that none of the three previously reported cases were definitively diagnosed at initial admission; all presented primarily with fever and cough. One case progressed to severe pneumonia and resulted in death.

CONCLUSION: OP caused by C. psittaci pneumonia presents with non-specific symptoms and signs, making early diagnosis challenging. During treatment of C. psittaci pneumonia, if empirical anti-infective therapy shows no response after three days, or if imaging reveals features such as consolidation, migratory lesions, or a reverse halo sign, the possibility of concurrent OP should be considered. Pathological examination is recommended in such cases to avoid missed diagnosis and to ensure timely intervention.}, } @article {pmid41333777, year = {2025}, author = {Zhang, Q and Gong, Q and Sun, X and Zhu, H}, title = {Massive hemoptysis as the sentinel symptom: a case report of pulmonary nocardiosis in an immunocompetent patient.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1677156}, pmid = {41333777}, issn = {2296-858X}, abstract = {Pulmonary nocardiosis is frequently missed or misdiagnosed due to its atypical clinical symptoms and non-specific imaging findings. Moreover, delayed diagnosis and treatment can lead to high mortality rates, underscoring the need to enhance etiological diagnosis. Here, we report a 55-year-old immunocompetent woman who developed pulmonary Nocardia cyriacigeorgica infection with massive hemoptysis as the initial symptom. The patient had no history of chronic respiratory diseases. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid collected via bronchoscopy was performed, which confirmed the diagnosis. After targeted therapy with oral sulfamethoxazole-trimethoprim and linezolid, the patient achieved significant symptomatic and radiological improvement, accompanied by normalization of white blood cell count and neutrophil count. No recurrence was observed during follow-up.}, } @article {pmid41333806, year = {2025}, author = {Al Bataineh, MT and Dash, NR and Mysara, M and Saeed, O and Alkhayyal, N and Talaat, IM and Bendardaf, R and Saber-Ayad, M}, title = {Metagenomic analysis of gut microbiota in colorectal adenocarcinoma in the MENA region.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1634631}, pmid = {41333806}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Male ; Female ; Middle Aged ; *Adenocarcinoma/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; DNA, Bacterial/genetics/chemistry ; Middle East ; Feces/microbiology ; Phylogeny ; DNA, Ribosomal/genetics/chemistry ; }, abstract = {BACKGROUND: Growing evidence suggests that gut microbiota plays a role in the development of colorectal cancer (CRC), and a few bacterial strains have been linked to carcinogenesis. Contrary to the Western population, the relationship between pro-cancer microorganisms and CRC among Middle Eastern individuals remains largely unexplored. Ninety-eight samples from Middle Eastern individuals with and without CRC were subjected to microbial profiling based on the 16S rRNA gene.

RESULTS: The CRC group exhibited a more complex gut microbiota with clusters that were significantly distinct from those of the control group. The taxonomic orders Caulobacterales, Rhizobiales, Sphingomonadales, and Burkholderiales, along with the genera Recibecterium and Sphingobium, were overrepresented in the CRC samples based on differential abundance testing between the CRC and control groups. Utilizing 16S-based functional prediction, we identified a significant enrichment of pathways vital for pentose and glucuronate interconversions, metabolism of terpenoids and polyketides, spliceosome, and dTMP kinase pathways within the CRC group. Moreover, we observed a link between Herbaspirillum huttiense and the pathways regulating the actin cytoskeleton; this intriguing connection may provide insights into the molecular mechanisms underlying cytoskeletal rearrangement and carcinogenesis triggered by H. huttiense.

CONCLUSIONS: The findings of this study support the connection between gut microbiota and the development of CRC and highlight region-specific microbial signatures that may serve as non-invasive diagnostic biomarkers or predictive tools for early screening in Middle Eastern populations, where CRC is increasingly diagnosed at advanced stages. These insights could inform the development of microbiome-based screening panels and personalized prevention strategies adapted to the MENA region's unique genetic, dietary, and environmental profiles.}, } @article {pmid41333904, year = {2024}, author = {Choi, CH and Lee, M and Lee, SE and Shin, H and Choi, MM and Kim, JW and Yi, H and Chung, YS}, title = {[Monkeypox Virus Genomic Analysis in the Republic of Korea: A Comparison of Metagenomic- and Probe Hybridization Capture Sequencing Methods].}, journal = {Jugan geon-gang gwa jilbyeong}, volume = {17}, number = {20}, pages = {859-873}, pmid = {41333904}, issn = {2586-0860}, abstract = {Monkeypox virus (MPXV) whole-genome from specimens of individuals diagnosed with mpox in the Republic of Korea (ROK) between May 2022 and November 2023 was analyzed comprehensively. An infectious disease originating in Africa, mpox gained global significance after the first case was confirmed in the UK in May 2022, subsequently spreading worldwide. In the ROK, 155 infection cases were recorded, predominantly transmitted through close contact with symptomatic individuals. MPXV, consisting of approximately 197,000 base pairs of double-stranded DNA, encompasses approximately 191 genes consisting of inverted terminal repeats at both ends and a central conserved region. The virus is categorized as Clade I (Central African type) and Clade II (West African type), with Clade I and II reporting fatality rates of 1–10% and less than 1%, respectively. Two sequencing methods, metagenomic and hybridization capture sequencing, were used to perform a thorough whole-genome analysis. Compared to metagenomic sequencing, hybridization capture sequencing demonstrated superior efficiency in generating MPXV read sequences. The proportion of virus reads varied based on specimen type, informing the selection of targets for whole-genome analysis. Genomic phylogenetic analysis revealed that the MPXV in the ROK belonged to lineage C.1, indicating sustained domestic transmission and providing crucial insights for national and international responses to MPXV variants. This information will contribute to understanding infection pathways and improving strategies for disease response and prevention.}, } @article {pmid41334206, year = {2025}, author = {Yang, L and Liu, Y and Guo, S and Li, T and Nie, Q and Zhang, Y and Zeng, S and Wang, F and Liu, L}, title = {Mechanism of tobacco-sweet potato intercropping in suppressing Ralstonia solanacearum in flue-cured tobacco.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1688379}, pmid = {41334206}, issn = {1664-462X}, abstract = {Tobacco bacterial wilt (Ralstonia solanacearum) is a fatal pathogen of tobacco, causing severe losses annually. Intercropping has been proposed as a sustainable strategy to mitigate soil-borne pathogens through rhizosphere interactions. However, the mechanisms by which tobacco-sweet potato intercropping specifically affects the microecological environment and suppresses R. solanacearum remain poorly understood. To investigate the effect of the TSP model on the soil-borne pathogen of bacterial wilt (Ralstonia solanacearum) in tobacco-growing soil, this study compared and analyzed the characteristics and differences in bacterial wilt incidence, Ralstonia solanacearum content, phenolic acid components, metabolome, and metagenome between (T) and (TSP) systems. The results showed that compared to the T treatment, the TSP treatment reduced the incidence of bacterial wilt in flue-cured tobacco and significantly decreased the abundance of R. solanacearum in the soil by 21.4%, while increasing the total phenolic acid content by 21.9%. The total phenolic content in the TSP soil was increased by 21.9% compared to T. Differentially abundant metabolites between TSP and T were primarily enriched in carbohydrate metabolic pathways, such as nucleotide sugar biosynthesis, fructose, and mannose metabolism. The content of substances such as rhamnose, D-allose, and mannitol in T-treated soil was 2.14-6.62 times higher than that in TSP-treated soil, with new tobacco alkaloids being up to 91.09 times higher. Compared to the T treatment, the TSP treatment significantly increased the relative abundances of Acidobacteriota, Chloroflexota, Bradyrhizobium, Pseudolabrys, and Sphingomonas by 64.08%, 18.86%, 23.55%, 21.80%, and 12.98%, respectively. The content of Ralstonia solanacearum in the soil was positively correlated with differential metabolites such as mannitol, rhamnose, and D-allose (r = 0.8), while negatively correlated with phenolic acids such as syringic acid, ferulic acid, caffeic acid, and gallic acid, as well as microorganisms such as Chloroflexota, Gemmatimonadota, Acidobacteriota, and Sphingomonas. In summary, TSP can regulate soil metabolites, phenolic acids, and beneficial microorganisms, forming a synergistic network to suppress the content of Ralstonia solanacearum and reduce the risk of tobacco bacterial wilt. This provides a theoretical basis for regulating soil microecology and enhancing crop disease resistance in intercropping systems.}, } @article {pmid41334589, year = {2025}, author = {Li, J and Xu, Y and Wang, M and Lin, J and Sun, J and Ma, J and Zhang, H}, title = {Dual-source DPP4 drives intestinal fibrosis in Crohn's disease: synergistic therapeutic targeting of host and microbiota pathways.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2593119}, pmid = {41334589}, issn = {1949-0984}, mesh = {Animals ; Humans ; *Dipeptidyl Peptidase 4/metabolism/genetics ; *Crohn Disease/pathology/drug therapy/microbiology/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Male ; Myofibroblasts/metabolism ; Dipeptidyl-Peptidase IV Inhibitors/pharmacology ; *Intestines/pathology ; Sitagliptin Phosphate/pharmacology ; Mice, Inbred C57BL ; Female ; Dextran Sulfate ; }, abstract = {Crohn's disease (CD), a chronic inflammatory bowel disorder, often progresses to intestinal fibrosis and stricture, yet no effective anti-fibrotic treatments exist. This study reveals dipeptidyl peptidase 4 (DPP4) as a pivotal driver of fibrosis through bioinformatics analysis, clinical samples, and experimental models. Elevated DPP4 expression was observed in stenotic intestinal tissues of CD patients and dextran sodium sulfate (DSS)-induced fibrotic mice. Mechanistically, both membrane-bound DPP4 and soluble DPP4 (sDPP4) activated human intestinal myofibroblasts (HIMFs) via the PI3K-AKT pathway, stimulating migration, proliferation, and extracellular matrix deposition. Importantly, metagenomic sequencing revealed enrichment of microbial Dpp4 genes in fecal samples from CD patients with stenosis, and in vivo colonization with engineered E. coli overexpressing microbial DPP4 exacerbated fibrotic remodeling, confirming microbiota-derived DPP4 (mDPP4) as a pathogenic driver. Furthermore, pharmacological inhibition of host DPP4 (sitagliptin) or selective blockade of mDPP4 (Dau-d4) attenuated fibrosis in murine models, with combined therapy showing enhanced efficacy. These findings underscore the roles of DPP4, originating from both host and microbiota, and existing in membrane-bound and soluble forms, in promoting CD-associated intestinal fibrosis. This study identifies DPP4 as a novel therapeutic target, proposing dual-source inhibition as a promising strategy to prevent stricture formation in CD patients, thereby addressing a critical unmet clinical need.}, } @article {pmid41334911, year = {2025}, author = {Kandathil, AJ and Clipman, SJ and Anantharam, R and Duchen, D and Cox, AL and Larman, HB and Thomas, DL}, title = {Antibody-mediated control of anellovirus infection: evidence from people who inject drugs.}, journal = {Journal of virology}, volume = {99}, number = {12}, pages = {e0161225}, pmid = {41334911}, issn = {1098-5514}, support = {R01 DA058567/DA/NIDA NIH HHS/United States ; U19 AI159822/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Antibodies, Viral/immunology/blood ; Viremia/immunology/virology ; Male ; Female ; Adult ; *Anelloviridae/immunology/genetics ; *Substance Abuse, Intravenous/immunology/virology/complications ; Capsid Proteins/immunology ; Middle Aged ; Capsid/immunology ; }, abstract = {Infections with viruses belonging to the family Anelloviridae are widespread among humans. Although generally considered a commensal, there is evidence to suggest that these infections may be controlled by host immune responses. However, the mechanism of immune control remains unclear. Previous research has also suggested a possible role of anellovirus capsid spikes in immune evasion. To investigate the role of antibodies in controlling infection, we used AnelloScan to profile plasma collected every 6 months over 2 years from 10 persons who inject drugs (PWID). Participants were selected based on viremia patterns: persistent (n = 6) versus intermittent (n = 4). Long-read metagenomic sequencing revealed a higher median number of alphatorquevirus (TTV) species in participants with persistent viremia compared to those with intermittent viremia (P < 0.0001). AnelloScan detected TTV-specific antibodies among all study participants. No significant differences were observed between the two groups when all antibody-reactive peptides located in the capsid were included. However, among participants with intermittent viremia, antibodies were more frequently reactive to peptides located in the amino acid variable region of the capsid spike domain (P = 0.0429). These findings suggest that among PWID, antibodies targeting the sequence variable region of the spike domain appear to be associated with control of anellovirus infection. Additionally, anelloviruses might be susceptible to pre-existing immunity, and the amino acid variable region of the spike protein may play a role in viral infectivity.IMPORTANCEAnelloviruses are highly diverse and are recognized as the major component of the blood virome in healthy humans. Despite this, little is known about their interactions with their hosts. In this study, we found that anelloviruses can elicit antibody responses. Notably, antibodies that targeted a sequence variable region on spikes present on viral capsids were associated with truncation of plasma viremia. These data suggest a possible mechanism of immune control of anellovirus infections while also indicating a role of the capsid spikes in viral infectivity.}, } @article {pmid41334926, year = {2026}, author = {Shulman, HB and Pyle, JAM and Classen, AT and Inouye, DW and Simberloff, R and Sorensen, PO and Thomas, W and Rudgers, JA and Kivlin, SN}, title = {Nutrient limitation shapes functional traits of mycorrhizal fungi and phosphorus-cycling bacteria across an elevation gradient.}, journal = {mSystems}, volume = {11}, number = {1}, pages = {e0052325}, pmid = {41334926}, issn = {2379-5077}, support = {DE-FOA-0002392//U.S. Department of Energy/ ; DEB2217353, DEB2106065, DEB1936195, DEB2338421//National Science Foundation/ ; 504086//Joint Genome Institute/ ; }, mesh = {*Mycorrhizae/metabolism/genetics ; *Phosphorus/metabolism ; Soil Microbiology ; *Bacteria/metabolism/genetics/classification ; Soil/chemistry ; Altitude ; *Nutrients/metabolism ; Phylogeny ; }, abstract = {In nutrient-limited high-elevation ecosystems, plants rely on arbuscular mycorrhizal (AM) fungi to provide mineral phosphorus (P) in the form of phosphate (PO4[3-]). AM fungi gather these nutrients from phosphorus-cycling bacteria (PCBs) that can mineralize PO4[3-] from organic matter and solubilize mineral-bound P. How climate, soil factors, and nutrient limitation influence AM fungi and PCB assembly remains unclear. We collected soil from montane meadows across a 1,000-m elevation gradient on three replicate mountainsides and analyzed AM fungal marker genes, P-cycling genes from shotgun metagenomes, and edaphic measurements. High-elevation soils had nearly 50-fold less soil PO4[3-] and 60% more AM fungal hyphae than low-elevation soils. AM fungal turnover was linked to changes in pH, organic carbon, and PO4[3][-]. The composition of 198 P-cycling genes was influenced by the AM fungal community structure. Drivers of individual PCB functional genes, including pH and organic carbon, varied with gene phylogeny. We found a trade-off in P-cycling strategies across elevation: P-rich, low-elevation soils supported root-colonizing AM fungi and organic P-mineralizing bacteria. P-poor, high-elevation soils were dominated by stress-tolerant AM fungi and mineral P-solubilizing bacteria. Our results suggest that AM fungi and PCB community turnover across elevation are both shaped by pH, organic carbon, and P availability. With continued climate warming, the structure and function of mountaintop ecosystems might shift to resemble lower elevations, disrupting long-established and specialized microbial assemblages, with consequences for P-cycling dynamics and the total P available to plant communities.IMPORTANCEPhosphorus (P) limits plant productivity in high-elevation ecosystems, yet the microbial networks that mobilize P, including arbuscular mycorrhizal (AM) fungi and phosphorus-cycling bacteria (PCBs), remain under-characterized in these nutrient-poor soils. We show that across a 10,00-m elevation gradient, AM fungi and P-cycling gene assemblages shift predictably with pH, organic carbon, and phosphate availability. Higher elevations, with less available P, select for stress-tolerant AM fungal taxa and PCB strategies geared toward mineral solubilization, while low-elevation sites favor root colonization by AM fungi and organic P mineralization. These results suggest that nutrient limitation can constrain microbial community assembly in consistent ways across landscapes. High mountain soils are low in P and rely on a network of underground AM fungi and PCB to deliver nutrients to plants. This study shows how those underground relationships reorganize with elevation and how climate change could collapse long-standing microbial strategies by pushing high-elevation ecosystems toward lowland conditions. As soils warm and dry, the microbial scaffolding that supports alpine plant life may become increasingly unstable.}, } @article {pmid41335362, year = {2025}, author = {Jia, Y and Shi, Y and Wang, J and Liu, H and Wang, H and Huang, Y and Liu, Y and Chen, P and Peng, J}, title = {Astragalin attenuates caerulein-induced acute pancreatitis by targeting the NLRP3 signaling pathway and gut microbiota.}, journal = {Bioresources and bioprocessing}, volume = {12}, number = {1}, pages = {139}, pmid = {41335362}, issn = {2197-4365}, support = {82170661//National Natural Science Foundation of China/ ; 2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; 2025JJ60669//Hunan Provincial Natural Science Foundation of China/ ; 2024M763719//China Postdoctoral Science Foundation/ ; GZC20242045//Postdoctoral Fellowship Program of CPSF/ ; }, abstract = {BACKGROUND: Acute pancreatitis (AP) has caused great concern worldwide due to its serious threat to human health. Astragalin is a bioactive natural flavonoid compound with several pharmacological activities, but it remains unclear about its effect on AP. The objective of this experiment was to explore the mitigating efficacy of astragalin on caerulein-induced AP model and examine the underlying mechanisms.

METHODS: Following the assessment of astragalin's direct effects on pancreatic acinar cells using an in vitro AP model, an in vivo mouse model was established to further validate its efficacy and elucidate the underlying mechanisms. Pancreatic histopathology, amylase, and lipase levels of mice were observed to determine the optimal therapeutic dose of astragalin. The network pharmacology and RNA sequencing technology were used to reveal the possible targets and pathways. Subsequent molecular docking and western blot were conducted to validate the association between astragalin and key target molecules, as well as the NLRP3 signaling pathway. Combined with metagenomics and metabolomics analysis, the astragalin effective gut microbiota-metabolite-gene network was constructed. Moreover, fecal microbiota transplantation experiments were performed to clarify the importance of gut microbiota in astragalin-mediated alleviation of AP.

RESULTS: The results showed that astragalin attenuated caerulein-induced injury in AR42J cells in vitro. Consistent with these findings, in vivo experiments revealed that astragalin treatment significantly improved pancreatic pathological injury, cell apoptosis, and systemic inflammatory response in AP mice, particularly at high doses. The integrated analysis of network pharmacology and transcriptomics revealed that the NLRP3 signaling pathway was a key molecular pathway, which was further validated using western blot. Docking analysis showed that 12 target genes had good docking activity with astragalin. More intriguingly, it was found that astragalin could reverse gut microbiota dysbiosis by restoring microbial diversity, altering bacterial community composition, and modulating key metabolic pathways. Specifically, astragalin-effective correlation networks were constructed with Lachnoclostridium sp. YL32, Roseburia intestinalis, Ruminococcus gnavus, Lachnospiraceae bacterium Choco86, Anaerobutyricum hallii, etc. as the core strains, 22 metabolites, including 5-Methoxytryptophan, D-Serine, L-Tryptophan, L-Methionine, etc. as core metabolites, and NLRP3 pathway-related genes as the main regulatory targets. Furthermore, fecal microbiota transplantation experiments confirmed the involvement of gut microbiota in AP remission.

CONCLUSION: Collectively, these findings identify astragalin as a promising therapeutic agent for AP, targeting both the NLRP3 signaling cascade and gut microbial homeostasis.}, } @article {pmid41335476, year = {2025}, author = {Docter, J and Mansfeldt, C}, title = {Environmental Census: Modeling Synthetic Biology Ecological Risk with Metagenomic Enzymatic Data and High-Performance Computing.}, journal = {ACS synthetic biology}, volume = {14}, number = {12}, pages = {4846-4856}, doi = {10.1021/acssynbio.5c00618}, pmid = {41335476}, issn = {2161-5063}, mesh = {*Synthetic Biology/methods ; *Metagenomics/methods ; Software ; Risk Assessment ; Metagenome ; *Enzymes/genetics/metabolism ; Bacteria/genetics ; }, abstract = {Engineered microorganisms in biotechnology present biosafety and environmental management challenges. As the synthetic biology market develops and deploys new technologies, these engineered organisms may escape into unintended environments. Improved predictive computational tools are necessary to assess the potential establishment risk and environmental location of these escaped engineered microorganisms, assisting their design and management. Here, we present EnCen, a risk assessment Python software package that predicts the environmental range of engineered microorganisms through annotated functional one-hot-encoded similarity between the engineered microorganism and resident microorganisms of a given environment. EnCen utilizes publicly available composite metagenomes as representatives of microbial environments that occur along an agriculture-water cycle and can be customized for any additional target environment. This tool was deployed against case studies reported in the literature and to reassess commercially available bacterial biopesticides, highlighting both the successful recapture of previously reported dynamics and the identification of select commercial products that pose a wider establishment risk in multiple environments. When further utilizing EnCen to investigate the receiving environments comprising the central database, key enzyme classes are mapped as characteristics to select environments, prioritizing certain modifications likely leading to a greater risk (or effectiveness) of establishment. The results demonstrate that EnCen meaningfully summarizes publicly available metagenomic data, prioritizes environments to monitor for adverse effects, and analyzes potential impacts on microbial community composition and functioning. Overall, this study demonstrates a computational approach to managing engineered microorganisms, aiding in the safe deployment and benefit of industrial synthetic biology.}, } @article {pmid41335477, year = {2025}, author = {Riskumäki, M and Ruuskanen, MO and Mäenpää, K and Ruokolainen, L and Mäkelä, MJ and Jousilahti, P and Vartiainen, E and Ottman, N and Laatikainen, T and Haahtela, T and Alenius, H and Fyhrquist, N and Sinkko, H}, title = {Shotgun metagenomics reveals distinct skin microbial species in allergen-sensitized individuals.}, journal = {Microbial genomics}, volume = {11}, number = {12}, pages = {}, doi = {10.1099/mgen.0.001527}, pmid = {41335477}, issn = {2057-5858}, mesh = {Humans ; *Metagenomics/methods ; *Allergens/immunology ; *Skin/microbiology/virology ; Finland ; Adolescent ; *Microbiota/genetics ; Male ; Russia ; Female ; *Hypersensitivity/microbiology/immunology ; Malassezia/genetics/isolation & purification ; Immunoglobulin E/immunology ; Bacteria/genetics/classification ; Child ; }, abstract = {The Karelian region, which spans the border between Finland and Russia, presents distinct environmental exposures and lifestyles on either side of the governmental border. In the more urbanized Finnish Karelia, allergic diseases are markedly more prevalent than in the more rural Russian Karelia. Prior studies, based on amplicon sequencing, have demonstrated major differences in skin microbiotas between the two populations. However, compositional differences in microbiota between sensitized and non-sensitized (NS) individuals have not been characterized. Here, in a selected population of 112 allergen-sensitized and NS adolescents, we used shotgun metagenomics to characterize the prokaryotic, eukaryotic and viral species in the skin potentially involved in allergic sensitization via distinct environmental exposures. In the more urban Finnish Karelia, the microbiome species composition was associated with IgE-mediated allergen sensitization status, while in the more rural Russian Karelia, the composition was associated with exposure to furry pets. Finnish participants showing high IgE-mediated sensitization to common allergens (allergen-specific IgE >7.5 kU/L) had less Cutibacterium acnes and Malassezia in their skin and displayed weaker interconnectedness of the microbial co-occurrence network compared with NS participants. Moreover, Malassezia restricta strain-level differences were related to allergen sensitization in both Finnish and Russian participants. In summary, we found distinct skin microbiomes between allergen-sensitized and NS participants and tracked the bacterial and fungal species associated with the degree of allergic sensitization in the more urbanized part of the Karelian region. These findings provide new insights into the factors that shape the human skin microbiome and influence allergic diseases.}, } @article {pmid41338072, year = {2025}, author = {Jose, S and Lohith Kumar, DH and Malla, MA and Featherston, J and Bux, F and Kumari, S}, title = {Insights into microbial community, nitrogen‑phosphorus metabolism from metagenomic and metabolomic analysis of microalgal-cyanobacterial consortium-based bioinoculants.}, journal = {The Science of the total environment}, volume = {1009}, number = {}, pages = {181092}, doi = {10.1016/j.scitotenv.2025.181092}, pmid = {41338072}, issn = {1879-1026}, mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism ; *Microalgae/physiology ; *Soil Microbiology ; Fertilizers ; *Cyanobacteria/physiology ; *Microbiota ; Metagenomics ; *Microbial Consortia ; Metabolomics ; Agriculture ; }, abstract = {The intensification of agriculture through chemical fertilizers has led to severe environmental consequences. This study provides a comprehensive investigation on chemical fertilizer, vermiculite and on microalgal-cyanobacterial consortia (bioinoculants) influencing soil microbial community. Chemical fertilizer application significantly altered the microbial community, suppressing the dominant phylum Proteobacteria to 48.3 % abundance from 60.9 % in the control soil. The bioinoculant treatments maintained a high Proteobacteria abundance (58.9 %-59.7 %) and fostered a growth-oriented, anabolic strategy. The 50:50 mix treatment uniquely promoted the fungal phylum Basidiomycota to 18.2 % abundance and showed the highest investment in the Glycolysis/Gluconeogenesis pathway (23.0 %). Chemical fertilizer treatment upregulated genes for rapid nitrogen assimilation (glnA, Log2FC = 0.60) and phosphorus starvation response (phoB, Log2FC = 0.65; pstS, Log2FC = 0.83). The enhanced energy production and conversion (11.83 %), amino acid transport and metabolism (11.20 %), and fatty acid biosynthesis (45.3 %) was observed in bioinoculant treatment. Unlike chemical fertilizer treatment, bioinoculant treatment led to the accumulation of the osmoprotectant trehalose and structural membrane lipids, while the 50:50 mix was uniquely characterized by a higher abundance of xylose. These findings demonstrate that the microalgal-cyanobacterial consortium can enhance nutrient recycling, and potentially boost soil health by reshaping the soil microbiome and metabolic functions, offering a promising strategy for sustainable agriculture.}, } @article {pmid41338123, year = {2026}, author = {Huang, S and Yang, P and Wang, X and Zhang, K and Li, L and Yao, S and Qian, L and Liu, C and Guo, J and Shi, L and Liu, F and Xie, W and Guo, Y}, title = {Integrated metagenome and metabolome analysis reveals a disease signature of gut microbiota and the key gut microbiota-associated metabolite proline in schizophrenia.}, journal = {Journal of psychiatric research}, volume = {193}, number = {}, pages = {223-235}, doi = {10.1016/j.jpsychires.2025.11.029}, pmid = {41338123}, issn = {1879-1379}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; *Schizophrenia/microbiology/metabolism ; Male ; Female ; Adult ; *Proline/metabolism ; *Metabolome/physiology ; *Metagenome ; Middle Aged ; }, abstract = {Schizophrenia (SCZ) is a multifaceted psychiatric condition with a complex set of etiological factors. Recent studies have revealed that gut microbiota play a significant role in the neurobiology associated with SCZ. Utilizing metagenomic sequencing and analysis techniques, we obtained composition and functional information of the gut microbiota from 68 SCZ patients and 61 healthy control (HC) subjects. We identified 72 inter-group differential species, 49 differential metabolic pathways, and 1987 differential functional genes. A. odontolyticus and F. prausnitzii were the core species enriched in the SCZ group and the HC group, respectively. Arginine and proline metabolism were the most significant differential metabolic pathways, with K00286 being the differential functional gene catalyzing the synthesis of L-proline in this pathway. Notably, a strong disease classification model was developed based on the gut microbiota data, achieving an outstanding AUC of 0.94, outperforming earlier models, the model achieved AUC values of 0.745 and 0.845 in two separate external datasets, respectively. Furthermore, insights into mechanisms were investigated by analyzing the relationships between microbial species and their associated metabolic pathways. Future research is essential to clarify causal connections, detail specific molecular pathways-particularly those involving functional proteins such as K00286-and to explore the communication processes between the gut microbiota and the brain. Our results underscore the potential for microbiota-based biomarkers and therapeutic targets in SCZ, emphasizing the essential role of gut microbiota in this intricate disorder.}, } @article {pmid41338426, year = {2026}, author = {Yan, L and Su, Y and Xie, X and Peng, K and Zhang, P and Deng, Y and Gan, Y and Li, Q and Zhang, Y}, title = {Decoding microbial-mediated sulfur transformation pathways in mangrove wetland: Metagenomic and hydrogeochemical insights.}, journal = {Environmental research}, volume = {290}, number = {}, pages = {123472}, doi = {10.1016/j.envres.2025.123472}, pmid = {41338426}, issn = {1096-0953}, mesh = {*Wetlands ; *Sulfur/metabolism ; China ; Metagenomics ; *Microbiota ; Geologic Sediments/microbiology ; Bacteria/metabolism/genetics ; Metagenome ; }, abstract = {Sulfur (S) cycling is essential to the ecological function of mangrove wetlands, but how microbial processes and gene-level patterns respond to environmental gradients remains poorly understood. Here, we integrated high-resolution hydrogeochemical profiling with metagenomic sequencing to characterize depth-resolved microbial communities and S-cycling genes in the mangrove wetlands of Dongzhai Harbor, Hainan, China. The results revealed pronounced differences in microbial community composition between zones, with Escherichia dominating mangrove sediments (4.22-20.07 %) and Salmonella prevailing in mudflat sediments (23.87-60.98 %). The abundance of S-cycling genes (e.g., tusA, soeA, aprA, dsrAB, sat) declined markedly with depth. Spatial variation in biogeochemical conditions shaped functional gene distributions: oxidative genes (aprA, soeA) were more abundant in mudflat profiles, whereas sat dominated reductive pathways in mangrove sediments. Environmental gradients structured microbial communities, with salinity, pH, total nitrogen (TN), and total organic carbon (TOC) showing negative correlations, and total sulfur (TS), total phosphorus (TP), SO4[2-] acting as positive drivers. Co-occurrence network analysis indicated tighter microbial associations in surface layers compared to deeper strata. The thiosulfate oxidation pathway was confined to the 5-10 cm interval in mudflat sediments and appeared at both 5-10 cm and 15-20 cm in mangrove sediments, while direct sulfite oxidation occurred in both zones. Moreover, methanogenesis, nitrification, and denitrification were more prominent in mudflat sediments, whereas methane oxidation prevailed in mangrove profiles. These findings advance our understanding of how microbial functional stratification and S metabolic pathways respond to environmental gradients, with implications for biogeochemical coupling in coastal wetland ecosystems.}, } @article {pmid41338553, year = {2025}, author = {, and , }, title = {[The Chinese guidelines for the diagnosis and treatment of invasive fungal disease in patients with hematological disorders and cancers (the seventh revision)].}, journal = {Zhonghua nei ke za zhi}, volume = {64}, number = {12}, pages = {1155-1168}, doi = {10.3760/cma.j.cn112138-20250808-00468}, pmid = {41338553}, issn = {0578-1426}, mesh = {Humans ; *Invasive Fungal Infections/diagnosis/therapy/drug therapy ; *Hematologic Diseases/complications ; Antifungal Agents/therapeutic use ; *Neoplasms/complications ; Hematologic Neoplasms/complications ; *Mycoses/diagnosis/therapy ; China ; }, abstract = {In 2005, the Chinese Invasive Fungal Infection Working Group published the first guidelines for the diagnosis and treatment of invasive fungal disease (IFD) in patients with hematological disorders and cancers, with the sixth revision released in 2020. Numerous advances in the fields of hematological oncology treatment and the diagnosis and management of IFD have significantly influenced the corresponding strategies. Therefore, the Chinese Invasive Fungal Infection Working Group has reviewed key research advances from 2020 to 2024 and released the seventh revision of the Chinese guidelines. Major revisions include: changes in the epidemiology of IFD; evaluation of novel diagnostic methods (especially PCR and metagenomic next-generation sequencing); updated recommendations on therapeutic drug monitoring and in vitro drug sensitivity test; management of breakthrough IFD; targeted therapy of Pneumocystis jiroveci pneumonia and cryptococcosis; and updated recommendation on the duration of antifungal therapy.}, } @article {pmid41339319, year = {2025}, author = {Harrison, LC and Allnutt, TR and Hanieh, S and Roth-Schulze, AJ and Ngui, KM and Stone, NL and Bandala-Sanchez, E and Backshell, L and Gurruwiwi, G and Gondarra, V and Couper, JJ and Craig, ME and Davis, EA and Huynh, T and Soldatos, G and Wentworth, JM and Vuillermin, P and Penno, MAS and Biggs, BA and , }, title = {Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9904}, pmid = {41339319}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Australia ; Female ; Male ; Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Infant, Newborn ; Indigenous Peoples ; Metagenome ; }, abstract = {Studies of traditional Indigenous compared to 'Western' gut microbiomes are underrepresented, and lacking in young children, limiting knowledge of early-life microbiomes in different cultural contexts. Here we analyze the gut metagenomes of 50 Indigenous Australian infants (median age